Mercurial > repos > dave > pipelign
changeset 0:9a3a2e04f47a draft default tip
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yaml Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,8 @@ +name: pipelign +owner: dave +description: A pipeline for automated multiple sequence alignment, particularly of viral sequences. +homepage_url: https://github.com/asmmhossain/pipelign/ +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign/ +type: unrestricted +categories: +- Metagenomics
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +categories: +- Metagenomics +description: A pipeline for automated multiple sequence alignment +homepage_url: https://github.com/asmmhossain/pipelign/ +long_description: Does multiple sequence alignment +name: pipelign +owner: dave +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pipelign.xml Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,70 @@ +<?xml version="1.0"?> +<tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0"> + <description>alignment with pipelign</description> + <macros> + <token name="@VERSION@">0.2</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">pipelign</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + pipelign -d files -c -i '$inFile' -o '$outFile' -t $lenThr -a $alphabet + -p $simPer -r $run -e $merge -q \${GALAXY_SLOTS:-1} + -s $mIterateLong -m $mIterateMerge -w $ambigPer + $keepOrphans $keepBadSeqs $excludeClusters + ]]></command> + <inputs> + <param argument="--inFile" type="data" format="fasta" label="Input sequence file" /> + <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" /> + <param argument="--alphabet" type="select" label="Alphabet for input sequences"> + <option value="dna">DNA</option> + <option value="rna">RNA</option> + <option value="aa">Amino Acids</option> + </param> + <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" /> + <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" /> + <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" help="Default: 0.8" /> + <param argument="--run" type="select" label="Parallelization version"> + <option value="J">Joblib</option> + <option value="G">GNU</option> + </param> + <param argument="--merge" type="select" label="Merge strategy"> + <option value="P">Parallel</option> + <option value="C">Consensus</option> + </param> + <param argument="--mIterateLong" type="integer" value="1" label="Number of iterations to refine long alignments" help="Default: 1" /> + <param argument="--mIterateMerge" type="integer" value="1" label="Number of iterations to refine merged alignment" help="Default: 1" /> + <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" help="Default: 0.1" /> + <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" /> + </inputs> + <outputs> + <data name="outFile" format="fasta" /> + </outputs> + <tests> + <test> + <param name="inFile" value="pipelign-in1.fasta" /> + <output name="outFile" file="pipelign-out1.fasta" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +------------------- + +A pipeline for automated multiple sequence alignment, particularly of viral sequences. + +]]> + </help> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{spond, + author = "A.S.Md.M. Hossain, S.D.W.Frost", + title = "Pipelign: an alignment pipeline for viral sequences.", + year = "2019", + note = "https://github.com/asmmhossain/pipelign/", + url = "https://github.com/asmmhossain/pipelign/"} + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_0.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG---------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT---------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT---------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT---------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG--------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA--------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------------ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------------ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------------ +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG--------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------------ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------------ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +-------------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT----- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +-------------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +-------------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +-------------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +-------------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +-------------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------------ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------------ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------------ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------------ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------------ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------------ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------------ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------------ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +-------------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +--------------------------------------------------TTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +ACACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +----------------------------------------GTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------------------------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAA----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +------------------------TGT-------------AACACCTCAGTCATTA---- +--CACAGG--------------CCTGTCCAAAGGTATCCTTTGAGCCAATTCC------- +----------------------------------------------------CATACATT +ATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +------------------------ATG-------------TATG---------------- +-----GGA--------------ATTGGCTGAAAGGATACCTTTGGACAGGCCT------- +----------------------------------------------------GAGTAATG +ACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +------------------------AA--------------GCTTGTGTAATTGTTAATTT +C---TCTG--------------TCCCACTCCATCCAGGTCGTGTGATTCCAAC------- +----------------------------------------------------TCTGTTCC +AG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +------------------------AA--------------AATTTCAAA----------- +-------------------------------AATTGGGCCTGAAAATCCATAC------- +----------------------------------------------------AATACTCC +AGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +------------------------GC--------------CTGCATGGAATGGATGACCC +GGAGAGAG--------------AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT------- +----------------------------------------------------AGCAATTC +A------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +------------------------GTA-------------CTTTCTATAGTGAATAGAGT +TAGGCAGG--------------TATATTCACCATTATCGTTTGAGACCCACCT------- +----------------------------------------------------CCCAACCC +-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------------------------------------------GGT----------- +-------------------------------GATATGGGCTGATGTACCATTT------- +----------------------------------------------------GCCCCTGG +ATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +------------------------ATAGAG----------CTTCCTTTAGTTGCCCCCCT +ATCTTTAT--------------TGTGACGAGGGGACGTTGCCAAAGAGTGACC------- +----------------------------------------------------TG------ +--------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +------------------------------------------------------------ +TTTTTCAG--------------TTCGCTTAGATGAAGACTTCAGGCAGTATAC------- +----------------------------------------------------TGCATTTA +CCATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +-----------------ATAACCACAGAA-----------------AGCATAGTAATATG +G------------------------------GGAAAGACTCCTAAATTTAAACT------ +---------------------------------------------------GCCCATACA +AAA---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +--------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAAAAGTAGT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +--------------------------GGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAACAGTAGTG----------------- +------------------------------------------------------------ +-------------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +-----------------------------------------TTTTATGGTTCATAATCCA +CTCCATGT--------------ACTGGTTCTTTTAGAATCTCTCATTTTTCT-------- +---------------------------------------------------GCCCGTTCT +AGCT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTCTAAAATA +ACCAGTAC--------------ATGGAGTGTATTATGACC-------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------CTCTAGTGTCCA +TTCATTGT--------------GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGG------ +---------------------------------------------------GCTTGTTCC +ATCTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +-----------------------------------------------------TGATTTG +TTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCTCTATTAG +TAACATAT--------------CCTGCTTTTCCTA------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +---------------------------GAA----------GTCTTGAGTTCTCTTATTAA +--------------------------GTTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------TTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +--------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACATAATAGCA +ACAGACAT--------------ACAAACTAAAGAATTACAA------------------- +------------------------------------------------------------ +-----------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAAGGTGTTTTACTAAACTTTTCCA------ +---------------------------------------------------TGTTGTAAT +CCTCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +-----------------------------------------CAGGATTAACTGCGAATCT +T---TCTAG------------CTCCCTTGTTGCCCATACTATATGTTTTAATT------- +----------------------------------------------------TATATTTT +TT--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_1.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,456 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG----------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT----------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT----------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT----------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT-------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG---------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------- +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------- +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------- +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------- +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------- +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG-------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG---------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA------------------------------ +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +--------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +--------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +--------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +--------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +--------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT------------------------------ +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +--------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +--------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_10.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,52 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +---------------------------------TTATCAGAAGG---------------- +AGCCACCCCACAAGATTTAAAC--ACCATGCTACACCC-------AGTGGGGGGACATCA +AGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +-----------------------GTTTTCAGCATTATCAGAAGG---------------- +AGCCACCCCACAAGATTTAAAC--ACCATGCTAAACAC-------AGTGGGGGGACAT-- +---------- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +-------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGG---------------- +AGCCACCCCACAAGATTTAAAC--ACCATGCTAAA------------------------- +---------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +-------TGT-------------AACACCTCAGTCATTA------CACAGGCCTGTCCAA +AGGTATCCTTTGAGCCAATTCC--CATACATTATTGTG---------------------- +---------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +-------ATG-------------TATG---------------------GGAATTGGCTGA +AAGGATACCTTTGGACAGGCCT--GAGTAATGACTGAGGTGTTACAA---------CTTG +TC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +-------AA--------------GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCC +ATCCAGGTCGTGTGATTCCAAC--TCTGTTCCAG-------------------------- +AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +-------AA--------------AATTTCAAA---------------------------- +AATTGGGCCTGAAAATCCATAC--AATACTCCAGTATT-TGCCATAAAGAAAAAAGACAG +TA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +-------GC--------------CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAG +AGTGGAGGTTTGAGAGCCACCT--AGCAATTCA--------------------------- +---------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +-------GTA-------------CTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCAC +CATTATCGTTTGAGACCCACCT--CCCAACCC---------------------------- +---------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +-----------------------------GGT---------------------------- +GATATGGGCTGATGTACCATTT--GCCCCTGGATGTTC-TGCACTATAGGGTAATTTTGG +CTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +-------ATAGAG----------CTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAG +GGGACGTTGCCAAAGAGTGACC--TG--------------------------AGG----- +---------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +-------------------------------------------TTTTTCAGTTCGCTTAG +ATGAAGACTTCAGGCAGTATAC--TGCATTTACCATACCTAGTATAAACAATGAG----- +---------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAA-----------------AGCATAGTAATATGG---------------- +GGAAAGACTCCTAAATTTAAACTGCCCATACAAAA---------------GGAAACAT-- +----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_11.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,40 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +---------------GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATAC +AAGATAATAGTGACATAAAAGTAGT----------------------------------- +---------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +---------------------------------GGAAAGGTGAAGGGGCAGTAGTAATAC +AAGATAATAGTGACATAACAGTAGTG---------------------------------- +-----CGAAGAAGAAAAGCAAA +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT---------- +---------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC------------------------------------- +---------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT----- +---------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------------ +---------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAAGTCTTGAGTTCTCTTATTAA--- +---------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC---- +---------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTT- +-ATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACA +GACATACAAACTAAAGAATTACAA------------------------------------ +---------------------A +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTC +CTTGCCACACAATCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_12.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,105 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +--------------------GATCCTGC-------------ATATAAGCAGCAGCTTTTT +GCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG----------------- +------ +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +-------------------CAGATACCT-------------AAATGATCAACAGCTCCTG +GGGATT-TGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT----------------- +------ +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG----------------------------GGCATCAAGCAGCTCCAGG------- +CAAGAATGCTGGCTGTGGAAAGATACCT-------------AAAGGATCAACAGCTCC-- +------------------------------------------------------------ +------ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-----------ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATC-- +-------TGGGTCCCCTCC-------------TGAGGATTGGT----------------- +------ +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-----------ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTC-- +-------TGGGTCCCCTCC-------------TGAGGATTGCT----------------- +------ +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG----------------------------------------ACTCCAA-------- +----------TACTGTAGGAGATTCCAC-----------------------CAATATT-- +-------TGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT-------------------- +------ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +--------------------------------------------ATCCTCAT-------- +-----GCATCTGTTCTACCATGTCATTTTT-----------CCACATGTTAAAATTTTCT +GT-----CACATTTAC---CAATACT---------------------------------- +------ +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +--------------------------------------------TT-------------- +-------GGTAAATGTGACAGAAAATTTTA-----------ACATGTGGAAAAATGACAT +GG-----TAGA---AC---AGATGCA----------------------TGAGGATATAA- +------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +-------GGTAAATGTGACAGAAAATTTTA-----------ACATGTGGAAAAATGACAT +GG-----TAGA---AC---AGATGCA----------------------TGAGGATATAAT +-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------TTAAAATTTTCT +GT-----CACATTTAC---CAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGG +CATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +------CACCCATCCAAAGGAATTGAGGTT-----------CTTT---CTGATGTTTTTT +GT-----CTGGTGTGG---TAAGTCCCCACCTCGACAG---------------------- +------ +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA----------------------------------TATTTTTTCTTAC-------- +-----CCCCTGGCCTTAACCGAATTTTTTC-----------CCATCGATCTAATTCTCC- +-------CCCGCTTAA-------------------------------------------- +------ +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC------------------------------------CTGTTCG-------------- +-------GGCGCCACTGCTAGAGATTTTCC-----------ACACTGACTAAAAGGGTCT +GA-----GGGA---TCTCTAGTTACC---------------------------------- +------ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------------------------AGTAAGTAGTACCTGTAAC--GCAAC +CTATACCAATAG-TAGCAATAGTAGCATTA-----------GTAGTAGCACTAATAAT-- +------------------------------------------------------------ +------ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------------------------------------------CAAC +CTATACCAATAG-TAGCAATAGTAGCATTA-----------GTAGTAGCAATAATAATAG +CAATAGTTGAGTGGTC-------------------------------------------- +CA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA----TTGGAG--------------AGCAATGGCTAGTGATTTTAACCTGCCAC +CTGTAGTAGCAA-AAGAAATAGTAGCCCG------------------------------- +------------------------------------------------------------ +------ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +-TATGGTACCAGTTAGAGAAAGAACCCCTA-----------GTAGGAGCAGAAACCTTCT +ATGTAGATGGGGCAGC-------------------------------------------- +TAACAG +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +-------------------------------------AGTTCATGTATCCAGT------- +---GGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT--- +------------------------------------------------------------ +------ +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGT------- +---GGATATATAGAAGCAGA---------------------------------------- +------------------------------------------------------------ +------ +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +------TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTT +CTTTT--CAAATTAG-----------------------------CAG------------- +------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +------TGCTAA-----------------------------TTTTAAAAGACAATATTCT +GTTTC--CTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT------------- +------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_13.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCA---CAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAG--GAGCTTAAG +AATGAAGCTGTTA--------------------------------GA +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CC--------------CCATAT----------TACTATGCTTTCTGTGGTTAATTTTTGC +ACTGCCTCTGTTAATTGTTTTACATCATTAG-------------TGT +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +--------CAGAGGAGGTCTCT-----------------------------CGACGCAGG +ACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +--GGAAACCAGAGGAGCTCTCT-----------------------------CGACGCAGG +ACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCG------ +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTT-----------------------------AAGTGTTTC +AATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG--------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_14.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,44 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +A------TTGCCTTAC-------------------------------------------- +--------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +-----------------------------------------------AGGATTTTACATA +A------TTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCA +----------------CTA-- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +--------------------------------------------ACTTTATATTTATATA +A------TTCACTTCTCCAATTGTCC----------------CTCATCTCTCCTCCTCCA +GGTCTGAAG---ATCTCGG-- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +A------TTCCCTTCT-------------------------------------------- +--------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------TCCAAG +-----CCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTA +CTTCAATAA------------ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +------------------------------ACCCATCTTATAGCA-AAATCCTTTCCAAG +-----CCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA-------------- +--------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +-----------------------------------------TCTACATAGTCTCTAAAGG +GTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCT---------AT------ +---ACATTC------------ +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +-----------------------------------------AATA-GCAATTTGTACAAG +-------CAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCT---------CTCGTCTA +-GGATCAAC------------ +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +-----------------------------------------TGTG-TTCAGCTGTACTAT +-------TATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT- +--------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +-----------CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTG +CTTTGATAGAGAAGCTTGATG +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +---------TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTA +A------TATTTGATT-------------------------------------------- +-----------AACATCTAA-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_15.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT-------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +----------TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGATTGTAAGACTA---------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +--------------------------------TGACAGAAACCTAGTTGGTCCAAAATGC +GAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_16.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,27 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +---------------------------CTACCTCTTCTTCTGCTAGACTGCC-------A +TTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +-------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA-------G +TCTAGCAGAAGAAGAGGTAGTAAT-------TAGATC------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAAC---AAGC +CCCAGAAGACGAAGGG---------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----- +-TTGGCACTTATCTGGGA-------------CGATCT------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--C +TCTGTCTCT-------------------------CTC------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA-----TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATC +CTAGGAAAATGTCTA----------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA-----TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATC +CTAGGAAAATGTCTAAC-----------------AGC------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC-----TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATATC +TTCCCTAAAAAATTAGC-----------------CTGTCT---- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA------------------GCAATCTGATTCACCCGATTTCTTCC-------A +ATTATGATGACAGGTGTAGGTCCTACTAATACAGT---------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_17.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,125 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +----------------------------GGTTTTATAGACATCACTATGAAAGCCCTCAT +CCAAGAAAAAGTTCAGAAGTACACA------------------TCCCACTAGG------- +-- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +-------------------------------TTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGG--------------TGCCCACACTAAT------- +-- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC---- +-----AGGAAGCAACCACCACTCTATT-----------------------TTGTGCATC- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT---- +-----AGCCAGTAGATCCTAGACTAT-------------------------AGCCCTGG- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +--------------------------------------GGAGCT----AGAACGAT---- +-----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGG +A----------------------------------------------------------- +-- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC +TTGTGGGGCTGTTGGCTCTGGTCTGCT--------------------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC +TGGTGGGGCAGTTGGCTCTGGTC------------------------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A-------------------------------------GGGATTATGGAAAACAGA---- +-----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG---- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC----------------------------ACT-------- +ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAG--TTAGC +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +-CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAG--TTAGC +CAGA----------------------------------------GAGCTCCCA------- +-- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------------------TGC +TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATT-------------------------------------------GACCAC------- +-- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC----------------------------ACCCTATCTTG +TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCCATCCAATCA------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGA +TAAA--------------------------------------CAGCAGTTGTT------- +-- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------------------TGCCAAGGATCCGTTCACTAA--TCGAA +TGGA---------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT------- +-- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +TTCTGGGAAGTTCAAT----------------TAGGAATACCACATCCCGCAGGGTTAAA +AAAG---------AAAAAATCAGT------------------AACAGTACTGG------- +-- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +CTATG------TTTAC----------------TTCTAATCCCGAATCCTGCAAAGCTAGA +TAAAT----TGCTTGTAACTCAGTC-----------------TTCTGATTTGT------- +-- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TCCCAAAGAAGACAAG----ATATCCTTGATC---------------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA---------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------------------GGCTAATTCAC +TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACCACCCACAAG------- +-------------------------------------------GCTACTTCCC------- +-- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------------------ACAACGGAATTGG---AGGAAATGAAC +CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACTATTTTT---------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------------------AATAGTACTTT---CCTGATTCCAG +CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCCTTTGTGTG-------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATCAG-------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA----------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------------------ACAGC---GACGAAGAGCT +CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGCAGTAAGTA-------- +--------------------------------------------TTACAT---------- +-- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +-------------------------------------AGCCATTGCTCTCCAA--TTACT +GTGA---------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTCCATCTAAAA +AT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_18.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,48 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +--------------------------TTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTACACCC-------AGTGGGGGGACATCAAGCAGCCA- +- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +----------------GTTTTCAGCATTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTAAACAC-------AGTGGGGGGACAT----------- +- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTAAA---------------------------------- +- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGT-------------AACACCTCAGTCATTA------CACAGGCCTGTCCAAAGGTATC +CTTTGAGCCAATTCCCATACATTATTGTG------------------------------- +- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATG-------------TATG---------------------GGAATTGGCTGAAAGGATA +CCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAA---------CTTGTC------- +- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA--------------GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGG +TCGTGTGATTCCAACTCTGTTCCAG--------------------------AG------- +- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA--------------AATTTCAAA----------------------------AATTGGG +CCTGAAAATCCATACAATACTCCAGTATT-TGCCATAAAGAAAAAAGACAGTA------- +- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC--------------CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAG +GTTTGAGAGCCACCTAGCAATTCA------------------------------------ +- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTA-------------CTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATC +GTTTGAGACCCACCTCCCAACCC------------------------------------- +- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +----------------------GGT----------------------------GATATGG +GCTGATGTACCATTTGCCCCTGGATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGA +T +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAG----------CTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGT +TGCCAAAGAGTGACCTG--------------------------AGG-------------- +- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------TTTTTCAGTTCGCTTAGATGAAGA +CTTCAGGCAGTATACTGCATTTACCATACCTAGTATAAACAATGAG-------------- +-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_19.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT------------------ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAACAGTAGTGCGAAGAAGAAAAGCAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_2.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,96 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +---------------------------------------------------------TTA +TCAGAAGG------------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAC +ACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +-----------------------------------------------GTTTTCAGCATTA +TCAGAAGG------------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAA +ACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +-------------------------------CAGAAGTGATACCCATGTTTTCAGCATTA +TCAGAAGG------------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAA +A----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +-------------------------------TGT-------------AACACCTCAGTCA +TTA------CACAGG--CCTGTCCAAAGGTATCCTTTGAGCCAATTCC--CATACATTAT +TGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +-------------------------------ATG-------------TATG--------- +------------GGA--ATTGGCTGAAAGGATACCTTTGGACAGGCCT--GAGTAATGAC +TGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +-------------------------------AA--------------GCTTGTGTAATTG +TTAATTTC---TCTG--TCCCACTCCATCCAGGTCGTGTGATTCCAAC--TCTGTTCCAG +--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +-------------------------------AA--------------AATTTCAAA---- +--------------------------AATTGGGCCTGAAAATCCATAC--AATACTCCAG +TATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +-------------------------------GC--------------CTGCATGGAATGG +ATGACCCGGAGAGAG--AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT--AGCAATTCA- +------------------------------------ +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +-------------------------------GTA-------------CTTTCTATAGTGA +ATAGAGTTAGGCAGG--TATATTCACCATTATCGTTTGAGACCCACCT--CCCAACCC-- +------------------------------------ +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +-----------------------------------------------------GGT---- +--------------------------GATATGGGCTGATGTACCATTT--GCCCCTGGAT +GTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +-------------------------------ATAGAG----------CTTCCTTTAGTTG +CCCCCCTATCTTTAT--TGTGACGAGGGGACGTTGCCAAAGAGTGACC--TG-------- +------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +-------TTTTTCAG--TTCGCTTAGATGAAGACTTCAGGCAGTATAC--TGCATTTACC +ATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------ATAACCACAGAA-----------------AGCATAG +TAATATGG------------------GGAAAGACTCCTAAATTTAAACTGCCCATACAAA +A---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +---------------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCA +GTAGTAATACAAGAT--AATAGTGACATAAAAGTAGT----------------------- +------------------------------------ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +---------------------------------GGAA----------AGGTGAAGGGGCA +GTAGTAATACAAGAT--AATAGTGACATAACAGTAGTG---------------------- +-----------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------TTTTATGGTTCA +TAATCCACTCCATGT--ACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAG +CT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTC +TAAAATAACCAGTAC--ATGGAGTGTATTATGACC------------------------- +------------------------------------ +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +-------------------------------------------------------CTCTA +GTGTCCATTCATTGT--GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCAT +CTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCT +CTATTAGTAACATAT--CCTGCTTTTCCTA------------------------------ +------------------------------------ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAA----------GTCTTGAGTTCTC +TTATTAA--------------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGT +CTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------------------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGT +CTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACAT +AATAGCAACAGACAT--ACAAACTAAAGAATTACAA------------------------ +---------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCC +TCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------CAGGATTAACTG +CGAATCTT---TCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATT--TATATTTTTT +--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_20.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,32 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT---------- +---------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC------------------------------------- +---------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT----- +---------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------------ +---------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAAGTCTTGAGTTCTCTTATTAA--- +---------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC---- +---------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTT- +-ATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACA +GACATACAAACTAAAGAATTACAA------------------------------------ +---------------------A +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTC +CTTGCCACACAATCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_21.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,68 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +--GATCCTGC-------------ATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTC +TGGTTAGACCAGATCTGAGCCTGGG----------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +-CAGATACCT-------------AAATGATCAACAGCTCCTGGGGATT-TGGGGTTGCTC +TGGAAAACTCATTTGCACCCCTGCT----------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG----------GGCATCAAGCAGCTCCAGG-------CAAGAATGCTGGCTGTGG +AAAGATACCT-------------AAAGGATCAACAGCTCC-------------------- +------------------------------------------------ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +-----------------------------------------------------ACAGTAG +AAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATC---------TGGGTCCCCTC +C-------------TGAGGATTGGT----------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +-----------------------------------------------------ACAGTAG +AAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTC---------TGGGTCCCCTC +C-------------TGAGGATTGCT----------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG----------------------ACTCCAA------------------TACTGTAG +GAGATTCCAC-----------------------CAATATT---------TGAGGGCTTCC +CACCCCCTGCGTCCCAGAAGTT-------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +--------------------------ATCCTCAT-------------GCATCTGTTCTAC +CATGTCATTTTT-----------CCACATGTTAAAATTTTCTGT-----CACATTTAC-- +-CAATACT---------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +--------------------------TT---------------------GGTAAATGTGA +CAGAAAATTTTA-----------ACATGTGGAAAAATGACATGG-----TAGA---AC-- +-AGATGCA----------------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +-------------------------------------------------GGTAAATGTGA +CAGAAAATTTTA-----------ACATGTGGAAAAATGACATGG-----TAGA---AC-- +-AGATGCA----------------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------TTAAAATTTTCTGT-----CACATTTAC-- +-CAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------CACCCATCCAAA +GGAATTGAGGTT-----------CTTT---CTGATGTTTTTTGT-----CTGGTGTGG-- +-TAAGTCCCCACCTCGACAG---------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA----------------TATTTTTTCTTAC-------------CCCCTGGCCTTAA +CCGAATTTTTTC-----------CCATCGATCTAATTCTCC--------CCCGCTTAA-- +------------------------------------------------ +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC------------------CTGTTCG---------------------GGCGCCACTGC +TAGAGATTTTCC-----------ACACTGACTAAAAGGGTCTGA-----GGGA---TCTC +TAGTTACC---------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------AGTAAGTAGTACCTGTAAC--GCAACCTATACCAATAG-TAGCA +ATAGTAGCATTA-----------GTAGTAGCACTAATAAT-------------------- +------------------------------------------------ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------------------------CAACCTATACCAATAG-TAGCA +ATAGTAGCATTA-----------GTAGTAGCAATAATAATAGCAATAGTTGAGTGGTC-- +------------------------------------------CA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAA-AAGAA +ATAGTAGCCCG------------------------------------------------- +------------------------------------------------ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +-------------------------------------------TATGGTACCAGTTAGAG +AAAGAACCCCTA-----------GTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGC-- +------------------------------------------TAACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_22.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +-------------------------------------AGTTCATGTATCCAGTGGATATA +TAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT------------- +----------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA-------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +--------------------------------------------------------TATA +AAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTCAAAT +TAG-----------------------------CAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +--------------------------------------------------------TGCT +AA-----------------------------TTTTAAAAGACAATATTCTGTTTCCTGCC +CTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_23.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAG--GAGCTTAAGAAT +GAAGCTGTTA-------------------GA +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CC-----------CCATAT----------TACTATGCTTTCTGTGGTTAATTTTTGCACT +GCCTCTGTTAATTGTTTTACATCATTAGTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_24.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +--------CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAG +AGGCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +--GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAG +AGGCGAGGGGCG------ +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG--------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_25.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,40 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +A------TTGCCTTAC-------------------------------------------- +--------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +-----------------------------------------------AGGATTTTACATA +A------TTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCA +----------------CTA-- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +--------------------------------------------ACTTTATATTTATATA +A------TTCACTTCTCCAATTGTCC----------------CTCATCTCTCCTCCTCCA +GGTCTGAAG---ATCTCGG-- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +A------TTCCCTTCT-------------------------------------------- +--------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------TCCAAG +-----CCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTA +CTTCAATAA------------ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +------------------------------ACCCATCTTATAGCA-AAATCCTTTCCAAG +-----CCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA-------------- +--------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +-----------------------------------------TCTACATAGTCTCTAAAGG +GTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCT---------AT------ +---ACATTC------------ +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +-----------------------------------------AATA-GCAATTTGTACAAG +-------CAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCT---------CTCGTCTA +-GGATCAAC------------ +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +-----------------------------------------TGTG-TTCAGCTGTACTAT +-------TATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT- +--------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +-----------CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTG +CTTTGATAGAGAAGCTTGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_26.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,24 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +---------------------------CTACCTCTTCTTCTGCTAGACTGCC-------A +TTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +-------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA-------G +TCTAGCAGAAGAAGAGGTAGTAAT-------TAGATC------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAAC---AAGC +CCCAGAAGACGAAGGG---------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----- +-TTGGCACTTATCTGGGA-------------CGATCT------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--C +TCTGTCTCT-------------------------CTC------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA-----TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATC +CTAGGAAAATGTCTA----------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA-----TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATC +CTAGGAAAATGTCTAAC-----------------AGC------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC-----TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATATC +TTCCCTAAAAAATTAGC-----------------CTGTCT----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_27.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,96 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +----------------------------GGTTTTATAGACATCACTATGAAAGCCCTCAT +CCAAGAAAAAGTTCAGAAGTACACA------------------TCCCACTAGG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +-------------------------------TTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGG--------------TGCCCACACTAAT +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC---- +-----AGGAAGCAACCACCACTCTATT-----------------------TTGTGCATC- +----------------------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT---- +-----AGCCAGTAGATCCTAGACTAT-------------------------AGCCCTGG- +----------------------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +--------------------------------------GGAGCT----AGAACGAT---- +-----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGG +A---------------------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC +TTGTGGGGCTGTTGGCTCTGGTCTGCT--------------------------------- +----------------------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC +TGGTGGGGCAGTTGGCTCTGGTC------------------------------------- +----------------------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A-------------------------------------GGGATTATGGAAAACAGA---- +-----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG---- +----------------------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC----------------------------ACT-------- +ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAG--TTAGC +----------------------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +-CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAG--TTAGC +CAGA----------------------------------------GAGCTCCCA +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------------------TGC +TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATT-------------------------------------------GACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC----------------------------ACCCTATCTTG +TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCCATCCAATCA------- +----------------------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGA +TAAA--------------------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------------------TGCCAAGGATCCGTTCACTAA--TCGAA +TGGA---------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +TTCTGGGAAGTTCAAT----------------TAGGAATACCACATCCCGCAGGGTTAAA +AAAG---------AAAAAATCAGT------------------AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +CTATG------TTTAC----------------TTCTAATCCCGAATCCTGCAAAGCTAGA +TAAAT----TGCTTGTAACTCAGTC-----------------TTCTGATTTGT +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TCCCAAAGAAGACAAG----ATATCCTTGATC---------------------------- +----------------------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA---------------------- +----------------------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------------------GGCTAATTCAC +TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACCACCCACAAG------- +-------------------------------------------GCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------------------ACAACGGAATTGG---AGGAAATGAAC +CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACTATTTTT---------- +----------------------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------------------AATAGTACTTT---CCTGATTCCAG +CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCCTTTGTGTG-------- +----------------------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATCAG-------------- +----------------------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA----------------------- +----------------------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------------------ACAGC---GACGAAGAGCT +CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGCAGTAAGTA-------- +--------------------------------------------TTACAT---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_28.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,40 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +--------------------------TTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTACACCC-------AGTGGGGGGACATCAAGCAGCCA- +- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +----------------GTTTTCAGCATTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTAAACAC-------AGTGGGGGGACAT----------- +- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTAAA---------------------------------- +- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGT-------------AACACCTCAGTCATTA------CACAGGCCTGTCCAAAGGTATC +CTTTGAGCCAATTCCCATACATTATTGTG------------------------------- +- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATG-------------TATG---------------------GGAATTGGCTGAAAGGATA +CCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAA---------CTTGTC------- +- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA--------------GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGG +TCGTGTGATTCCAACTCTGTTCCAG--------------------------AG------- +- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA--------------AATTTCAAA----------------------------AATTGGG +CCTGAAAATCCATACAATACTCCAGTATT-TGCCATAAAGAAAAAAGACAGTA------- +- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC--------------CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAG +GTTTGAGAGCCACCTAGCAATTCA------------------------------------ +- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTA-------------CTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATC +GTTTGAGACCCACCTCCCAACCC------------------------------------- +- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +----------------------GGT----------------------------GATATGG +GCTGATGTACCATTTGCCCCTGGATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGA +T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_29.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTG--------------------------AGG +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +--------------------------TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAG +TATACTGCATTTACCATACCTAGTATAAACAATGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_3.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,190 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +--------------------GA------TCCTGC-------------ATATAAGCAGCAG +CTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC--CAGATCTGAGCCT +GGG----------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +-------------------CAG------ATACCT-------------AAATGATCAACAG +CTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT--CATTTGCACCCCT +GCT----------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG----------------------------GGCATCAAGCAGCTCCAGG------- +CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGGATCAACAG +CTCC-------------------------------------------------------- +-------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-----------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGTGGTTACAA +TATC---------------------TGGGTCCCCTCC---------------TGAGGATT +GGT----------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-----------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGTGGTTACAA +TTTC---------------------TGGGTCCCCTCC---------------TGAGGATT +GCT----------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG----------------------------------------ACTCCAA-------- +----------TACTGTAGGAGA------TTCCAC-----------------------CAA +TATT---------------------TGAGGGCTTCCCACCCCCTG--CGTCCCAGAAGTT +-------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +--------------------------------------------ATCCTCAT-------- +-----GCATCTGTTCTACCATG------TCATTTTT-----------CCACATGTTAAAA +TTTTCTGT-----------------CACATTTAC---CAATACT---------------- +-------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +--------------------------------------------TT-------------- +-------GGTAAATGTGACAGA------AAATTTTA-----------ACATGTGGAAAAA +TGACATGG-----------------TAGA---AC---AGATGCA---------------- +--------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +-------GGTAAATGTGACAGA------AAATTTTA-----------ACATGTGGAAAAA +TGACATGG-----------------TAGA---AC---AGATGCA---------------- +--------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------TTAAAA +TTTTCTGT-----------------CACATTTAC---CAATACTA--CTTCTTGTGGGTT +GGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT---CTGATG +TTTTTTGT-----------------CTGGTGTGG---TAAGTCCC--CACCTCGACAG-- +-------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA----------------------------------TATTTTTTCTTAC-------- +-----CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATCGATCTAAT +TCTCC--------------------CCCGCTTAA-------------------------- +-------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC------------------------------------CTGTTCG-------------- +-------GGCGCCACTGCTAGA------GATTTTCC-----------ACACTGACTAAAA +GGGTCTGA-----------------GGGA---TCTCTAGTTACC---------------- +-------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------------------------AGTAAGTAGTACCTGTAAC--GCAAC +CTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGTAGCACTAA +TAAT-------------------------------------------------------- +-------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------------------------------------------CAAC +CTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGTAGCAATAA +TAATAGCAATAG------------TTGAGTGGTC-------------------------- +--------------------CA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA----TTGGAG--------------AGCAATGGCTAGTGATTTTAACCTGCCAC +CTGTAGTAGCAA-AAGAAATAG------TAGCCCG------------------------- +------------------------------------------------------------ +-------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +-TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGGAGCAGAAA +CCTTCTATGTAG------------ATGGGGCAGC-------------------------- +--------------------TAACAG +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +-------------------------------------AGTTCATGTATCCAGT------- +---GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTGAAACAGCA +TAT--------------------------------------------------------- +-------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGT------- +---GGATATATAGAAGCAGA---------------------------------------- +------------------------------------------------------------ +-------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGGAAACAGCA +TATTTTCTTTT--------------CAAATTAG--------------------------- +----CAG------------------- +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +------TGCTAA-----------------------------------TTTTAAAAGACAA +TATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA--TAACTTCTGCTTC +TATATAT------------------- +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +------GCCA---CAGAGGGAG------CCACACAA-----------TGAATGGACACTA +TAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA------------------------ +-----------GA------------- +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +------CC--------------------CCATAT---------------------TACTA +TGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA--CATCATTAG---- +----------TGT------------- +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +--------------CAGAGGAG------GTCTCT-------------------------- +--------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA--CGGCAAGAGGCGA +GGGGCGG-CGACT------------- +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +--------GGAAACCAGAGGAG------CTCTCT-------------------------- +--------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA--CGGCAAGAGGCGA +GGGGCG-------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +------TAGGAACCAAAGAAAG------ATAGTT-------------------------- +--------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA--CAGCCAGAAATTG +CAGG---------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC---------------------TGTTAGTGGTATTACTTCTGTTAGTGCTTTGG +TACCTCTAAGGAGTTTACATAA------TTGCCTTAC----------------------- +------------------------------------------------------------ +-------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +--------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTAAATCTGAC +TTGCCCAATT---------------CAATTTCCCCA----------------CTA----- +-------------------------- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-----ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC------------- +---CTCATCT---------------CTCCTCCTCCAGGTCTGAAG---ATCTCGG----- +-------------------------- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC---------------------CTTGGTTGGAGCAACTCCTAATGGTTGAATTT +TTACTACTTTATATTTATATAA------TTCCCTTCT----------------------- +------------------------------------------------------------ +-------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +---------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTGGCGCATAG +CTCTACAAGC---------------TCCTTGTACTACTTCAATAA--------------- +-------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +---------------------------------------------------ACCCATCTT +ATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTGGCGAATAG +CTCTACA----------------------------------------------------- +-------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +--TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAG +GGCT------------------------AT---------ACATTC--------------- +-------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +--AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGATGCTTCCAG +GGCT------------------------CTCGTCTA-GGATCAAC--------------- +-------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +--TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAAATTGACAG +ATCTAATTAC---------------TACCTCTTCT------------------------- +-------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +--------------------------------CTACTATTGCTACTAATGGTATAGGTTG +CGTTACATGT---------------ACTACTTACTGCTTTGATAGAGAAGCTTGAT---- +-------------------------G +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +------------------------------TCGGAGTCATTGTTGCTATTACCACCATCT +TTTGTTCATAGCAGCCCTGTAA------TATTTGATT----------------------- +-----------------------------------------------AACATCTAA---- +-------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +-------------------------------------------TTTGATTG--ACTAACT +CTGATTCACTTTGATCTTGTAG------TGCTTGAAT----------------------- +-----------------------------------------------GATTCCTAATGCA +TAT-----TGTGA----------GTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_30.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,28 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT---------- +-------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC------------------------------------- +-------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT----- +-------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------------ +-------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAAGTCTTGAGTTCTCTTATTAA--- +---------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC---- +-------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTA +TGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACA +GACATACAAACTAAAGAATTACAA------------------------------------ +-------------------A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_31.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,52 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +---------------------------------------------GATCCTGC------- +------ATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTG +AGCCTGGG----------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +--------------------------------------------CAGATACCT------- +------AAATGATCAACAGCTCCTGGGGATT-TGGGGTTGCTCTGGAAAACTCATTTGCA +CCCCTGCT----------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCT------- +------AAAGGATCAACAGCTCC------------------------------------- +------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------ACAGTAGAAAAATTCCCCTCCACC +ATTAAAACTGTGGTTACAATATC---------TGGGTCCCCTCC-------------TGA +GGATTGGT----------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------ACAGTAGAAAAATTCCCCTCCACA +ATTAAAACTGTGGTTACAATTTC---------TGGGTCCCCTCC-------------TGA +GGATTGCT----------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------ACTCCAA-----------TACTGTAGGAGATTCCAC------- +----------------CAATATT---------TGAGGGCTTCCCACCCCCTGCGTCCCAG +AAGTT-------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------ATCCTCAT------GCATCTGTTCTACCATGTCATTTTT----- +------CCACATGTTAAAATTTTCTGT-----CACATTTAC---CAATACT--------- +------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------TT--------------GGTAAATGTGACAGAAAATTTTA----- +------ACATGTGGAAAAATGACATGG-----TAGA---AC---AGATGCA--------- +-------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +--------------------------------GGTAAATGTGACAGAAAATTTTA----- +------ACATGTGGAAAAATGACATGG-----TAGA---AC---AGATGCA--------- +-------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +-------------TTAAAATTTTCTGT-----CACATTTAC---CAATACTACTTCTTGT +GGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +-------------------------------CACCCATCCAAAGGAATTGAGGTT----- +------CTTT---CTGATGTTTTTTGT-----CTGGTGTGG---TAAGTCCCCACCTCGA +CAG---------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------TATTTTTTCTTAC------CCCCTGGCCTTAACCGAATTTTTTC----- +------CCATCGATCTAATTCTCC--------CCCGCTTAA------------------- +------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------CTGTTCG--------------GGCGCCACTGCTAGAGATTTTCC----- +------ACACTGACTAAAAGGGTCTGA-----GGGA---TCTCTAGTTACC--------- +-------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_32.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------AGTAAGTAGTACCTGTAAC--GCAACCTATACCAATAG-TAGCA +ATAGTAGCATTAGTAGTAGCACTAATAAT------------------------ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------------------------CAACCTATACCAATAG-TAGCA +ATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTCCA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAA-AAGAA +ATAGTAGCCCG------------------------------------------ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +-------------------------------------------TATGGTACCAGTTAGAG +AAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_33.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +-------------------------------------AGTTCATGTATCCAGTGGATATA +TAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA-------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_34.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC-------------------------------------------------- +---------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +-----------------------------------------------AGGATTTTACATA +ATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCA------ +-------CTA +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +--------------------------------------------ACTTTATATTTATATA +ATTCACTTCTCCAATTGTCC----------------CTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT-------------------------------------------------- +----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_35.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGT +GGCGCATAGCTCTACAAGCTCCTTGTACTACTTCAATAA------------ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGT +GGCGAATAGCTCTACA----------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +-----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAA +TGCTGGTAGGGCT---------AT---------ACATTC------------ +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +-----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGA +TGCTTCCAGGGCT---------CTCGTCTA-GGATCAAC------------ +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +-----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGA +AATTGACAGATCTAATTACTACCTCTTCT---------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +-----------------------------------------CTACTATTGCTACTAATGG +TATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_36.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------CTACCTCTTCTTCTGCTAGACTGCC----ATTTAAC +AGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +----------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA----GTCTAGC +AGAAGAAGAGGTAGTAAT-------TAGATC------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG----------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_37.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----- +-TTGGCACTTATCTGGGACGATCT--- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--C +TCTGTCTCT------------CTC--- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA-----TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATC +CTAGGAAAATGTCTA------------ +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA-----TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATC +CTAGGAAAATGTCTAAC----AGC--- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC-----TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATATC +TTCCCTAAAAAATTAGC----CTGTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_38.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +----TCCCACTAGG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA----TTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGG +GTGCCCACACTAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_39.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,88 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC---- +-----AGGAAGCAACCACCACTCTATT-----------------------TTGTGCATC- +------------------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT---- +-----AGCCAGTAGATCCTAGACTAT-------------------------AGCCCTGG- +------------------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +--------------------------------------GGAGCT----AGAACGAT---- +-----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGG +A------------------------------------------------ +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC +TTGTGGGGCTGTTGGCTCTGGTCTGCT--------------------------------- +------------------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC +TGGTGGGGCAGTTGGCTCTGGTC------------------------------------- +------------------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A-------------------------------------GGGATTATGGAAAACAGA---- +-----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG---- +------------------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC----------------------------ACT-------- +ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAG--TTAGC +------------------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +-CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAG--TTAGC +CAGA------------------------------------GAGCTCCCA +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------------------TGC +TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATT---------------------------------------GACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC----------------------------ACCCTATCTTG +TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCCATCCAATCA------- +------------------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGA +TAAA----------------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------------------TGCCAAGGATCCGTTCACTAA--TCGAA +TGGA-----TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +TTCTGGGAAGTTCAAT----------------TAGGAATACCACATCCCGCAGGGTTAAA +AAAG-----AAAAAATCAGT------------------AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +CTATG------TTTAC----------------TTCTAATCCCGAATCCTGCAAAGCTAGA +TAAATTGCTTGTAACTCAGTC-----------------TTCTGATTTGT +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TCCCAAAGAAGACAAG----ATATCCTTGATC---------------------------- +------------------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA---------------------- +------------------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------------------GGCTAATTCAC +TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACCACCCACAAG------- +---------------------------------------GCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------------------ACAACGGAATTGG---AGGAAATGAAC +CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACTATTTTT---------- +------------------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------------------AATAGTACTTT---CCTGATTCCAG +CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCCTTTGTGTG-------- +------------------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATCAG-------------- +------------------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA----------------------- +------------------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------------------ACAGC---GACGAAGAGCT +CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGCAGTAAGTA-------- +----------------------------------------TTACAT---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_4.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,190 @@ +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCAAGCTTCACAGGAGTTAAA------------- +----AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT---------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +---------------------------------TCACAGGAGGTAAA------------- +----AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTA +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +------------TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAA +TTTTAAAAGCATTGGGACCAGC-------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +-----------------------------------------------------------A +TTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAG +-------------TAGGATGAC------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +-----------------CTACCTCTTCTTCTGCTAGACTGCC------------------ +ATTTAACAGCAGTTGAGTTGATA------------------------------------- +---------CTACTGGCCTAATTCCATGT----GT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +---TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA------------------ +GTCTAGCAGAAGAAGAGGTAGTA------------------------------------- +---------AT-------TAGATC----------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG--------------------------------------------------CC +ACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAAC---AA-----------G +CCCCAGAAGACGAAGGG------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +-----GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC--------------- +--TTGGCACTTATCTGGGA----------------------------------------- +------------------CGATCT----------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA--------------------------------------------------TC +GTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA------------- +CTCTGTCTCT-------------------------------------------------- +---------------------CTC----------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +--TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAA-----------T +CCTAGGAAAATGTCTA-------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +--TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAA-----------T +CCTAGGAAAATGTCTAAC------------------------------------------ +---------------------AGC----------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +--TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATA-----------T +CTTCCCTAAAAAATTAGC------------------------------------------ +---------------------CTGTCT-------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +----------------GCAATCTGATTCACCCGATTTCTTCC------------------ +AATTATGATGACAGGTGTAGGTC------------------------------------- +---------CTACTAATACAGT------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +----------------------------GGTTTTATAGACATCA---------------- +CTATGAAAGCCCTCATCCAAGAAA-----------------AAGTTCAGAAGTACACA-- +----------------TCCCACTAGG--------- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +-------------------------------TTTATCAAGAGCC---------------- +ATTTAAAAATCTGAAAACAGGAAA-----------------ATATGCAAGAATGAGGGG- +-------------TGCCCACACTAAT--------- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC---- +-----AGGAAGCAACCACCACTCTATT--------------------------------- +------TTGTGCATC--------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT---- +-----AGCCAGTAGATCCTAGACTAT---------------------------------- +-------AGCCCTGG--------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +--------------------------------------GGAGCT----AGAACGAT---- +-----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCT---------------- +GTAGACAAATACTGGGA------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC +TTGTGGGGCTGTTGGCTCTGGTCTGCT--------------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC +TGGTGGGGCAGTTGGCTCTGGTC------------------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A-------------------------------------GGGATTATGGAAAACAGA---- +-----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGG---------------- +ATTAGAACATGG------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC----------------------------ACT-------- +ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGG---------------- +GTTCCCTAG--TTAGC-------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +-CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGG---------------- +GTTCCCTAG--TTAGCCAGA---------------------------------------- +-----------------GAGCTCCCA--------- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------------------TGC +TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCC---------------- +ATCCAATCACACTACATATT---------------------------------------- +--------------------GACCAC--------- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC----------------------------ACCCTATCTTG +TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCC---------------- +ATCCAATCA--------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCA---------------- +ATTCTGAAA--CTGGATAAA---------------------------------------- +---------------CAGCAGTTGTT--------- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------------------TGCCAAGGATCC---------------- +GTTCACTAA--TCGAATGGA--------------------------TCTGTCTCTGTCTC +TCTCTCCACCTTCTTCTTCTATTCCT--------- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +TTCTGGGAAGTTCAAT----------------TAGGAATACCAC---------------- +ATCCCGCAGGGTTAAAAAAG--------------------------AAAAAATCAGT--- +---------------AACAGTACTGG--------- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +CTATG------TTTAC----------------TTCTAATCCCGA---------------- +ATCCTGCAAAGCTAGATAAAT---------------------TGCTTGTAACTCAGTC-- +---------------TTCTGATTTGT--------- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TCCCAAAGAAGACAAG----ATATCCTTGATC---------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA---------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------------------GGCTAATTCAC +TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACC---------------- +ACCCACAAG--------------------------------------------------- +----------------GCTACTTCCC--------- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------------------ACAACGGAATTGG---AGGAAATGAAC +CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACT---------------- +ATTTTT------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------------------AATAGTACTTT---CCTGATTCCAG +CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCC---------------- +TTTGTGTG---------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATC---------------- +AG---------------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA----------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------------------ACAGC---GACGAAGAGCT +CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGC---------------- +AGTAAGTA---------------------------------------------------- +-----------------TTACAT------------ +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +-------------------------------------AGCCATT---------------- +GCTCTCCAA--TTACTGTGA--------------------------TATTTCTCATGTTC +ATCTTGGGCCTT----AACTATTCCATCTAAAAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_40.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +--------------------------TTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +----------------GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAACACAGTGGGGGGACAT---------- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA--------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_41.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,21 @@ +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTA------CACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATT +CCCATACATTATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATG---------------------GGAATTGGCTGAAAGGATACCTTTGGACAGGC +CTGAGTAATGACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA-GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGGTCGTGTGATTCCA +ACTCTGTTCCAG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA-AATTTCAAA----------------------------AATTGGGCCTGAAAATCCAT +ACAATACTCCAGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC-CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCAC +CTAGCAATTCA------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +---------GGT----------------------------GATATGGGCTGATGTACCAT +TTGCCCCTGGATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_42.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,24 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT---------- +-------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC------------------------------------- +-------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT----- +-------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------------ +-------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAAGTCTTGAGTTCTCTTATTAA--- +---------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC---- +-------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTA +TGGCAAATACTGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_43.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,24 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +---------------------------------------------GATCCTGC------- +------ATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTG +AGCCTGGG +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +--------------------------------------------CAGATACCT------- +------AAATGATCAACAGCTCCTGGGGATT-TGGGGTTGCTCTGGAAAACTCATTTGCA +CCCCTGCT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCT------- +------AAAGGATCAACAGCTCC------------------------------------- +-------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------ACAGTAGAAAAATTCCCCTCCACC +ATTAAAACTGTGGTTACAATATC---------TGGGTCCCCTCC-------------TGA +GGATTGGT +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------ACAGTAGAAAAATTCCCCTCCACA +ATTAAAACTGTGGTTACAATTTC---------TGGGTCCCCTCC-------------TGA +GGATTGCT +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------ACTCCAA-----------TACTGTAGGAGATTCCAC------- +----------------CAATATT---------TGAGGGCTTCCCACCCCCTGCGTCCCAG +AAGTT---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_44.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,28 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTT +CTGTCACATTTAC---CAATACT------------------------------------- +--- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------TT--------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGAC +ATGGTAGA---AC---AGATGCA----------------------TGAGGATATAA---- +--- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +--------------------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGAC +ATGGTAGA---AC---AGATGCA----------------------TGAGGATATAAT--- +--C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +--------------------------------------------------TTAAAATTTT +CTGTCACATTTAC---CAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCAT +GTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +-------------------CACCCATCCAAAGGAATTGAGGTTCTTT---CTGATGTTTT +TTGTCTGGTGTGG---TAAGTCCCCACCTCGACAG------------------------- +--- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +C---CCCGCTTAA----------------------------------------------- +--- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--CTGTTCG--------GGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGT +CTGAGGGA---TCTCTAGTTACC------------------------------------- +---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_45.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------AGTAAGTAGTACCTGTAAC--GCAACCTATACCAATAGTAGCAA +TAGTAGCATTAGTAGTAGCACTAATAAT-------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------------------------CAACCTATACCAATAGTAGCAA +TAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG--------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_46.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC----------------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +-----------------------------------------------AGGATTTTACATA +ATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_47.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +--------------------------------------------ACTTTATATTTATATA +ATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTGAAGATCTCGG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT--------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_48.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGT +GGCGCATAGCTCTACAAGCTCCTTGTACTACTTCAATAA +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGT +GGCGAATAGCTCTACA----------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +-----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAA +TGCTGGTAGGGCT---------AT---------ACATTC +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +-----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGA +TGCTTCCAGGGCT---------CTCGTCTA-GGATCAAC +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +-----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGA +AATTGACAGATCTAATTACTACCTCTTCT----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_49.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----- +-TTGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--C +TCTGTCTCT------------CTC +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA-----TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATC +CTAGGAAAATGTCTA--------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA-----TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATC +CTAGGAAAATGTCTAAC----AGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_5.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,92 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +---------------------------------------------------------TTA +TCAGAAGG----------------AGCCACCCCACAAGATTTAAAC--ACCATGCTACAC +CC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +-----------------------------------------------GTTTTCAGCATTA +TCAGAAGG----------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAAAC +AC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +-------------------------------CAGAAGTGATACCCATGTTTTCAGCATTA +TCAGAAGG----------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAAA- +---------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +-------------------------------TGT-------------AACACCTCAGTCA +TTA------CACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCC--CATACATTATTG +TG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +-------------------------------ATG-------------TATG--------- +------------GGAATTGGCTGAAAGGATACCTTTGGACAGGCCT--GAGTAATGACTG +AGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +-------------------------------AA--------------GCTTGTGTAATTG +TTAATTTC---TCTGTCCCACTCCATCCAGGTCGTGTGATTCCAAC--TCTGTTCCAG-- +------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +-------------------------------AA--------------AATTTCAAA---- +------------------------AATTGGGCCTGAAAATCCATAC--AATACTCCAGTA +TT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +-------------------------------GC--------------CTGCATGGAATGG +ATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACCT--AGCAATTCA--- +---------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +-------------------------------GTA-------------CTTTCTATAGTGA +ATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCACCT--CCCAACCC---- +---------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +-----------------------------------------------------GGT---- +------------------------GATATGGGCTGATGTACCATTT--GCCCCTGGATGT +TC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +-------------------------------ATAGAG----------CTTCCTTTAGTTG +CCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAGTGACC--TG---------- +----------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +-------TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATAC--TGCATTTACCAT +ACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------ATAACCACAGAA-----------------AGCATAG +TAATATGG----------------GGAAAGACTCCTAAATTTAAACTGCCCATACAAAA- +--------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +---------------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCA +GTAGTAATACAAGATAATAGTGACATAAAAGTAGT------------------------- +---------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +---------------------------------GGAA----------AGGTGAAGGGGCA +GTAGTAATACAAGATAATAGTGACATAACAGTAGTG------------------------ +---------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------TTTTATGGTTCA +TAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT +---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTC +TAAAATAACCAGTACATGGAGTGTATTATGACC--------------------------- +---------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +-------------------------------------------------------CTCTA +GTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCT +CTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCT +CTATTAGTAACATATCCTGCTTTTCCTA-------------------------------- +---------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAA----------GTCTTGAGTTCTC +TTATTAA------------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCT +TTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +--------------------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCT +TTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACAT +AATAGCAACAGACATACAAACTAAAGAATTACAA-------------------------- +-------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +----------------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTC +ATCCTGTCTCCTTGCCACACAATCATCACCTG--
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_50.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCTATTATGGGGTACC----TGTGTGGC---------AGGA +AGCAACCACCACTCTATT-----------------------TTGTGCATC-- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCGACAGAGGAGAGCA----AGAAATGT---------AGCC +AGTAGATCCTAGACTAT-------------------------AGCCCTGG-- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-----------------------------GGAGCT----AGAACGAT---------TCGC +AGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCTGTACCCCAGACCT----GAAGCTCTCTTCTTGTGGGGC +TGTTGGCTCTGGTCTGCT---------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCT----GAAGCTCTCTTCTGGTGGGGC +AGTTGGCTCTGGTC-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A----------------------------GGGATTATGGAAAACAGA---------TGGC +AGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG-----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_51.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,64 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACAC----------------------------ACT--------ACTTGAAGCACT +CAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAG--TTAGC------------ +------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +-------------------------------------------------CTTGAAGCACT +CAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAG--TTAGCCAGA-------- +----------------------------GAGCTCCCA +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------TGCTGCTGGCTCAGC +TCGTCT---CATTCATTCCCTTACAGTAGGCCATCCAATCACACTACATATT-------- +-------------------------------GACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCC----------------------------ACCCTATCTTGTGCTGGCTCAGC +TCGTCT---CATTGTTTCCCTTACAGTAGGCCATCCAATCA------------------- +------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------TCCTCTGTCGAG +TAACGC---CTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGATAAA-------- +--------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------TGCCAAGGATCCGTTCACTAA--TCGAATGGA-----TCT +GTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------TTCTGGGAAGTT +CAAT----------------TAGGAATACCACATCCCGCAGGGTTAAAAAAG-----AAA +AAATCAGT------------------AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------CTATG------T +TTAC----------------TTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGT +AACTCAGTC-----------------TTCTGATTTGT +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGA +CAAG----ATATCCTTGATC---------------------------------------- +------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGA +CAAG----ATATCCTTGATCTGAGGA---------------------------------- +------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------GGCTAATTCACTCCCAACGAAGA +CAAG----ATATCCTTGATCTGTGGATGTACCACCCACAAG------------------- +---------------------------GCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------ACAACGGAATTGG---AGGAAATGAACCAGTAGATAAAT +TAGT----CAGTGCTGGAATCAGGAAAGTACTATTTTT---------------------- +------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------AATAGTACTTT---CCTGATTCCAGCACTGACTAAAT +TATC----TACTTGTTCATTTCCTCCAATTCCTTTGTGTG-------------------- +------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------GAAGAAGCGGAGACAGC---GACGAAGAGCTCATCAGAACAGT +CAGA----CTCATCAAGCTTCTCAATCAAATCAG-------------------------- +------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCTCATCAGAACAGT +CAGA----CTCATCAAGCTTCTGTA----------------------------------- +------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------ACAGC---GACGAAGAGCTCATCAGAACAGA +CAGA----CTCATCAAGCTTCTCTATCAAAGCAGTAAGTA-------------------- +----------------------------TTACAT---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_52.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTA------CACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATT +CCCATACATTATTGTG------------------------ +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATG---------------------GGAATTGGCTGAAAGGATACCTTTGGACAGGC +CTGAGTAATGACTGAGGTGTTACAA---------CTTGTC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA-GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGGTCGTGTGATTCCA +ACTCTGTTCCAG--------------------------AG +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA-AATTTCAAA----------------------------AATTGGGCCTGAAAATCCAT +ACAATACTCCAGTATT-TGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC-CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCAC +CTAGCAATTCA----------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_53.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT----- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC-------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA-------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_54.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC------------------------ +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTCTTTATGGCAAATACTGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_55.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +---------------------------------------------GATCCTGCATATAAG +CAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +--------------------------------------------CAGATACCTAAATGAT +CAACAGCTCCTGGGGATT-TGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC---------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_56.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +-------------ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATC +TGGGTCCCCTCC-------------TGAGGATTGGT +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +-------------ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTC +TGGGTCCCCTCC-------------TGAGGATTGCT +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCAC-----------------------CAATATT +TGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_57.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTT +CTGTCACATTTACCAATACT---------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------TT--------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGAC +ATGGTAGA---ACAGATGCA----------------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +--------------------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGAC +ATGGTAGA---ACAGATGCA----------------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +--------------------------------------------------TTAAAATTTT +CTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +-------------------CACCCATCCAAAGGAATTGAGGTTCTTT---CTGATGTTTT +TTGTCTGGTGTGGTAAGTCCCCACCTCGACAG---------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +C---CCCGCTTAA-----------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_58.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT-------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CAATAATAATAGCAATAGTTGAGTGGTCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_59.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +-----------------------TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCA +TAGCTCTACAAGCTCCTTGTACTACTTCAATAA +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA-----------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_6.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,130 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +--------------------GATCCTGC-------------ATATAAGCAGCAGCTTTTT +GCCTTT------------ACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG----- +------------------ +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +-------------------CAGATACCT-------------AAATGATCAACAGCTCCTG +GGGATT-------------TGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT----- +------------------ +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG----------------------------GGCATCAAGCAGCTCCAGG------- +CAAGAATGCTGGCTGTGGAAAGATACCT-------------AAAGGATCAACAGCTCC-- +------------------------------------------------------------ +------------------ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-----------ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATC-- +-------------------TGGGTCCCCTCC-------------TGAGGATTGGT----- +------------------ +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-----------ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTC-- +-------------------TGGGTCCCCTCC-------------TGAGGATTGCT----- +------------------ +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG----------------------------------------ACTCCAA-------- +----------TACTGTAGGAGATTCCAC-----------------------CAATATT-- +-------------------TGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT-------- +------------------ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +--------------------------------------------ATCCTCAT-------- +-----GCATCTGTTCTACCATGTCATTTTT-----------CCACATGTTAAAATTTTCT +GT-----------------CACATTTAC---CAATACT---------------------- +------------------ +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +--------------------------------------------TT-------------- +-------GGTAAATGTGACAGAAAATTTTA-----------ACATGTGGAAAAATGACAT +GG-----------------TAGA---AC---AGATGCA---------------------- +TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +-------GGTAAATGTGACAGAAAATTTTA-----------ACATGTGGAAAAATGACAT +GG-----------------TAGA---AC---AGATGCA---------------------- +TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------TTAAAATTTTCT +GT-----------------CACATTTAC---CAATACTACTTCTTGTGGGTTGGGGTCTG +TGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +------CACCCATCCAAAGGAATTGAGGTT-----------CTTT---CTGATGTTTTTT +GT-----------------CTGGTGTGG---TAAGTCCCCACCTCGACAG---------- +------------------ +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA----------------------------------TATTTTTTCTTAC-------- +-----CCCCTGGCCTTAACCGAATTTTTTC-----------CCATCGATCTAATTCTCC- +-------------------CCCGCTTAA-------------------------------- +------------------ +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC------------------------------------CTGTTCG-------------- +-------GGCGCCACTGCTAGAGATTTTCC-----------ACACTGACTAAAAGGGTCT +GA-----------------GGGA---TCTCTAGTTACC---------------------- +------------------ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------------------------AGTAAGTAGTACCTGTAAC--GCAAC +CTATACCAATAG-TAGCAATAGTAGCATTA-----------GTAGTAGCACTAATAAT-- +------------------------------------------------------------ +------------------ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +--------------------------------------------------------CAAC +CTATACCAATAG-TAGCAATAGTAGCATTA-----------GTAGTAGCAATAATAATAG +CAATAG------------TTGAGTGGTC-------------------------------- +------------CA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA----TTGGAG--------------AGCAATGGCTAGTGATTTTAACCTGCCAC +CTGTAGTAGCAA-AAGAAATAGTAGCCCG------------------------------- +------------------------------------------------------------ +------------------ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +-TATGGTACCAGTTAGAGAAAGAACCCCTA-----------GTAGGAGCAGAAACCTTCT +ATGTAG------------ATGGGGCAGC-------------------------------- +------------TAACAG +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +-------------------------------------AGTTCATGTATCCAGT------- +---GGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT--- +------------------------------------------------------------ +------------------ +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGT------- +---GGATATATAGAAGCAGA---------------------------------------- +------------------------------------------------------------ +------------------ +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +------TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTT +CTTTT--------------CAAATTAG-----------------------------CAG- +------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +------TGCTAA-----------------------------TTTTAAAAGACAATATTCT +GTTTC--------------CTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT- +------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +------GCCA---CAGAGGGAGCCACACAA-----------TGAATGGACACTATAGCTT +TTAGAG--GAGCTTAAGAATGAAGCTGTTA------------------------------ +---GA------------- +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +------CC--------------CCATAT---------------------TACTATGCTTT +CTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACATCATTAG------------ +--TGT------------- +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +--------------CAGAGGAGGTCTCT-------------------------------- +--------CGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGG- +CGACT------------- +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +--------GGAAACCAGAGGAGCTCTCT-------------------------------- +--------CGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCG-- +------------------ +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +------TAGGAACCAAAGAAAGATAGTT-------------------------------- +--------AAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG---- +------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_60.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CT---------AT--------ACATTC +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGG +CT---------CTCGTCTAGGATCAAC +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAAATTGACAGAT +CTAATTACTACCTCTTCT---------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_61.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCTATTATGGGGTACCTGTGTGGC---------AGGAAGCA +ACCACCACTCTATT-----------------------TTGTGCATC-- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGT---------AGCCAGTA +GATCCTAGACTAT-------------------------AGCCCTGG-- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-----------------------------GGAGCTAGAACGAT---------TCGCAGTT +AATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTT +GGCTCTGGTCTGCT---------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC--------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_62.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,32 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCA +GTGGGTTCCCTAG--TTAGC---------------------------------------- +--------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +---------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCA +GTGGGTTCCCTAG--TTAGCCAGA------------------------------------ +GAGCTCCCA +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +-----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTA +GGCCATCCAATCACACTACATATT------------------------------------ +---GACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTA +GGCCATCCAATCA----------------------------------------------- +--------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +--------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACA +CCCAATTCTGAAA--CTGGATAAA----------------------------------CA +GCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +----------------------------------------------------TGCCAAGG +ATCCGTTCACTAA--TCGAATGGA-----TCTGTCTCTGTCTCTCTCTCCACCTTCTTCT +TCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +--------------------TTCTGGGAAGTTCAAT----------------TAGGAATA +CCACATCCCGCAGGGTTAAAAAAG-----AAAAAATCAGT------------------AA +CAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +--------------------CTATG------TTTAC----------------TTCTAATC +CCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTC-----------------TT +CTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_63.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,24 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------GGCTAATTCACTCCCAACGAAGACAAGAT +ATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------ACAACGGAATTGG---AGGAAATGAACCAGTAGATAAATTAGTCA +GTGCTGGAATCAGGAAAGTACTATTTTT------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------AATAGTACTTT---CCTGATTCCAGCACTGACTAAATTATCTA +CTTGTTCATTTCCTCCAATTCCTTTGTGTG----------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------GAAGAAGCGGAGACAGC---GACGAAGAGCTCATCAGAACAGTCAGACT +CATCAAGCTTCTCAATCAAATCAG----------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCTCATCAGAACAGTCAGACT +CATCAAGCTTCTGTA-------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------ACAGC---GACGAAGAGCTCATCAGAACAGACAGACT +CATCAAGCTTCTCTATCAAAGCAGTAAGTA--TTACAT---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_64.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA-GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGGTCGTGTGATTCCA +ACTCTGTTCCAG-------------------------AG +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA-AATTTCAAA----------------------------AATTGGGCCTGAAAATCCAT +ACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC-CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCAC +CTAGCAATTCA---------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC-----------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_65.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +-------------------------TTTTATGGTTCATAATCCACTCCATGTACTGGTTC +TTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT----- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTG +TATTATGACC-------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +--------------------------------CTCTAGTGTCCATTCATTGTGTGGCTCC +CTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_66.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +-GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGAT +CTGAGCCTGGG +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATT-TGGGGTTGCTCTGGAAAACTCATTT +GCACCCCTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_67.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT---------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TT--------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCA----------------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +----------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCA----------------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +----------------------------------------TTAAAATTTTCTGTCACATT +TACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +---------CACCCATCCAAAGGAATTGAGGTTCTTT---CTGATGTTTTTTGTCTGGTG +TGGTAAGTCCCCACCTCGACAG----------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_68.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTAT--------ACATTC +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGG +CTCTCGTCTAGGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_69.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG--TGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCT +ATT-----------------------TTGTGCATC-- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +AT-------------------------AGCCCTGG-- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +---------------------------GGAGCTAGAACGATTCGCAGTTAATCCTGGCGT +GTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_7.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,48 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +A------TTGCCTTAC-------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +-----------------------------------------------AGGATTTTACATA +A------TTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCA +----------------CTA---------------- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +--------------------------------------------ACTTTATATTTATATA +A------TTCACTTCTCCAATTGTCC----------------CTCATCTCTCCTCCTCCA +GGTCTGAAG---ATCTCGG---------------- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +A------TTCCCTTCT-------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------TCCAAG +-----CCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTA +CTTCAATAA-------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +------------------------------ACCCATCTTATAGCA-AAATCCTTTCCAAG +-----CCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA-------------- +----------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +-----------------------------------------TCTACATAGTCTCTAAAGG +GTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCT---------AT------ +---ACATTC-------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +-----------------------------------------AATA-GCAATTTGTACAAG +-------CAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCT---------CTCGTCTA +-GGATCAAC-------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +-----------------------------------------TGTG-TTCAGCTGTACTAT +-------TATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT- +----------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +-----------CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTG +CTTTGATAGAGAAGCTTGAT--------------G +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +---------TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTA +A------TATTTGATT-------------------------------------------- +-----------AACATCTAA--------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +----------------------TTTGATTG--ACTAACTCTGATTCACTTTGATCTTGTA +G------TGCTTGAAT-------------------------------------------- +-----------GATTCCTAATGCATATTGTGAGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_70.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +-------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTC +CCTAGTTAGCCAGAGAGCTCCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_71.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,24 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +-----------------TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGC +CATCCAATCACACTACATATT--------------------------------------- +GACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA-------------------------------------------------- +------ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +--------------------TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCC +AATTCTGAAA--CTGGATAAA----------------------------------CAGCA +GTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +-------------------------------------------------TGCCAAGGATC +CGTTCACTAA--TCGAATGGA-----TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCT +ATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +--------------------TTCTGGGAAGTTCAAT-------------TAGGAATACCA +CATCCCGCAGGGTTAAAAAAG-----AAAAAATCAGT------------------AACAG +TACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +--------------------CTATG------TTTAC-------------TTCTAATCCCG +AATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTC-----------------TTCTG +ATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_72.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------GGCTAATTCACTCCCAACGAAGACAAGAT +ATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------ACAACGGAATTGG---AGGAAATGAACCAGTAGATAAATTAGTCA +GTGCTGGAATCAGGAAAGTACTATTTTT------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------AATAGTACTTT---CCTGATTCCAGCACTGACTAAATTATCTA +CTTGTTCATTTCCTCCAATTCCTTTGTGTG-----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_73.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +---------GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTCAATCAAATCAG------------ +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA--------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +---------------------ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCA +AGCTTCTCTATCAAAGCAGTAAGTATTACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_74.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAG-------------------------AG +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAA-------------------------AATTGGGCCTGAAAATCCATACAA +TACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_75.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC-CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCAC +CTAGCAATTCA +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_76.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT---------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TT--------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCA----------------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +----------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCA----------------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +----------------------------------------TTAAAATTTTCTGTCACATT +TACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_77.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG--TGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCT +ATTTTGTGCATC +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +AT--AGCCCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_78.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +-----------------TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGC +CATCCAATCACACTACATATTGACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA-----------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_79.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGATAA +A----------------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +-----------------------------TGCCAAGGATCCGTTCACTAA--TCGAATGG +A-----TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAAT-------------TAGGAATACCACATCCCGCAGGGTTAAAAAA +G-----AAAAAATCAGT------------------AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATG------TTTAC-------------TTCTAATCCCGAATCCTGCAAAGCTAGATAA +ATTGCTTGTAACTCAGTC-----------------TTCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_8.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT-------------------------------------------------- +----------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +----------TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGATTGTAAGACTA---------------------------------------- +----------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +--------------------------------TGACAGAAACCTAGTTGGTCCAAAATGC +GAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGC------------------ +----------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +-------------------ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAAT +GATGACAGCATGTCAGGGAGTAGGATGAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_80.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------GGCTAATTCACTCCCAACGAAGACAAGAT +ATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_81.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAA- +----------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +-----------------------------TGCCAAGGATCCGTTCACTAATCGAATGGAT +CTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_82.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAG-----AAAAAAT +CAGT-AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATG------TTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACT +CAGTCTTCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/NODE_9.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,170 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +-----------------CTACCTCTTCTTCTGCTAGACTGCC-------ATTTAACAGCA +GTTGAGTTGATA-----------------------------CTACTGGCCTAATTCCATG +T----GT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +---TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA-------GTCTAGCAGAA +GAAGAGGTAGTA-----------------------------AT-------TAGATC---- +------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG--------------------------------------------------CC +ACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAAC---AAGCCCCAGAAGAC +GAAGGG------------------------------------------------------ +------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +-----GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC------TTGGCACTT +ATCTGGGA------------------------------------------CGATCT---- +------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA--------------------------------------------------TC +GTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--CTCTGTCTCT- +-----------------------------------------------------CTC---- +------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +--TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGGAAAAT +GTCTA------------------------------------------------------- +------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +--TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAAT +GTCTAAC----------------------------------------------AGC---- +------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +--TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAA +AATTAGC----------------------------------------------CTGTCT- +------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +----------------GCAATCTGATTCACCCGATTTCTTCC-------AATTATGATGA +CAGGTGTAGGTC-----------------------------CTACTAATACAGT------ +------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +----------------------------GGTTTTATAGACATCA-----CTATGAAAGCC +CTCATCCAAGAAAAAGTTCAGAAGTACACA------------------TCCCACTAGG-- +------- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +-------------------------------TTTATCAAGAGCC-----ATTTAAAAATC +TGAAAACAGGAAAATATGCAAGAATGAGGGG--------------TGCCCACACTAAT-- +------- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC---- +-----AGGAAGCAACCACCACTCTATT----------------------------TTGTG +CATC-------------------------------------------------------- +------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT---- +-----AGCCAGTAGATCCTAGACTAT------------------------------AGCC +CTGG-------------------------------------------------------- +------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +--------------------------------------GGAGCT----AGAACGAT---- +-----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCT-----GTAGACAAATA +CTGGGA------------------------------------------------------ +------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC +TTGTGGGGCTGTTGGCTCTGGTCTGCT--------------------------------- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC +TGGTGGGGCAGTTGGCTCTGGTC------------------------------------- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A-------------------------------------GGGATTATGGAAAACAGA---- +-----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGG-----ATTAGAACATG +G----------------------------------------------------------- +------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC----------------------------ACT-------- +ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGG-----GTTCCCTAG-- +TTAGC------------------------------------------------------- +------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +-CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGG-----GTTCCCTAG-- +TTAGCCAGA----------------------------------------GAGCTCCCA-- +------- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------------------TGC +TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCC-----ATCCAATCACA +CTACATATT-------------------------------------------GACCAC-- +------- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC----------------------------ACCCTATCTTG +TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCC-----ATCCAATCA-- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCA-----ATTCTGAAA-- +CTGGATAAA--------------------------------------CAGCAGTTGTT-- +------- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------------------TGCCAAGGATCC-----GTTCACTAA-- +TCGAATGGA---------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT-- +------- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +TTCTGGGAAGTTCAAT----------------TAGGAATACCAC-----ATCCCGCAGGG +TTAAAAAAG---------AAAAAATCAGT------------------AACAGTACTGG-- +------- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +CTATG------TTTAC----------------TTCTAATCCCGA-----ATCCTGCAAAG +CTAGATAAAT----TGCTTGTAACTCAGTC-----------------TTCTGATTTGT-- +------- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TCCCAAAGAAGACAAG----ATATCCTTGATC---------------------------- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA---------------------- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------------------GGCTAATTCAC +TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACC-----ACCCACAAG-- +------------------------------------------------GCTACTTCCC-- +------- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------------------ACAACGGAATTGG---AGGAAATGAAC +CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACT-----ATTTTT----- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------------------AATAGTACTTT---CCTGATTCCAG +CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCC-----TTTGTGTG--- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATC-----AG--------- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA----------------------- +------------------------------------------------------------ +------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------------------ACAGC---GACGAAGAGCT +CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGC-----AGTAAGTA--- +-------------------------------------------------TTACAT----- +------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +-------------------------------------AGCCATT-----GCTCTCCAA-- +TTACTGTGA---------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTCCATC +TAAAAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.1 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 80 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.10 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 81 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.11 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 85 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.16 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 71 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.2 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +3 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 3 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 3 +done. + +Progressive alignment ... + STEP 1 /2 (thread 0) +Reallocating (by thread 0) ..done. *alloclen = 1142 + STEP 2 /2 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 3 +Segment 1/ 1 1- 84 +001-0000-0 (thread 1) identical 001-0000-0 (thread 1) better 001-0001-1 (thread 1) identical 001-0002-1 (thread 1) identical 001-0002-1 (thread 1) worse +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.20 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 77 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.29 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,63 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 82 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.38 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 75 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.39 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,63 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 100 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.4 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 76 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.40 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,63 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 86 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.51 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 77 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.64 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 81 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.69 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 96 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/align.log.8 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,65 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 73 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cdhit.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,35 @@ +================================================================ +Program: CD-HIT, V4.8.1 (+OpenMP), May 14 2019, 14:40:47 +Command: cd-hit-est -c 0.8 -n 5 -i long.good.fas -o grp -d 0 + -T 1 + +Started: Tue May 28 13:09:56 2019 +================================================================ + Output +---------------------------------------------------------------- +total seq: 100 +longest and shortest : 70 and 70 +Total letters: 7000 +Sequences have been sorted + +Approximated minimal memory consumption: +Sequence : 0M +Buffer : 1 X 12M = 12M +Table : 1 X 0M = 0M +Miscellaneous : 0M +Total : 12M + +Table limit with the given memory limit: +Max number of representatives: 4000000 +Max number of word counting entries: 98487020 + + comparing sequences from 0 to 100 + + 100 finished 84 clusters + +Approximated maximum memory consumption: 12M +writing new database +writing clustering information +program completed ! + +Total CPU time 0.04
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.0.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.1.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +---------GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTCAATCAAATCAG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA---------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.10.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +----------TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGT +GGGGGGACATCAAGCAGCCA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGT +GGGGGGACAT----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.11.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +--------------CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGA +TACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAG +TAAT-------TAGATC-------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.12.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.13.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.14.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.15.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.16.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCT +GAGGATTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.17.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.18.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.19.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.2.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TT--------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCATGAGGATATAA-- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +----------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCATGAGGATATAATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.20.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAG +GCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAG +GCGAGGGGCG------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.21.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.22.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.23.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.24.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.25.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.26.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.27.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.28.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.29.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----T +TGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTC +TGTCTCT------------CTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.3.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.30.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.31.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.32.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.33.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.34.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.35.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.36.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.37.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.38.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTT +GGCTCTGGTCTGCT +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.39.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAG-----------------------------CAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAA-----------------------------TTTTAAAAGACAATATTCTGTTTCC +TGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.4.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA----- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGG +AAAATGTCTAACAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.40.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG--------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATG---------------GGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGT +AATGACTGAGGTGTTACAACTTGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.41.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.42.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.43.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.44.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.45.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.46.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.47.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.48.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.49.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.5.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.50.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.51.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------ +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.52.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.53.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.54.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.55.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.56.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.57.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.58.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.59.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.6.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.60.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.61.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.62.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.63.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.64.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT---------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +----------TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGATTGTAAGACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.65.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.66.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.67.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.68.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.69.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +-------------------------TTTTATGGTTCATAATCCACTCCATGTACTGGTTC +TTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTG +TATTATGACC-------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.7.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.70.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.71.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.72.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.73.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.74.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.75.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.76.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.77.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.78.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.79.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.8.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT-- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +--AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAA +TTCCTTTGTGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.80.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.81.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.82.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.83.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/cls.9.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,588 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 +--------------------------CAGAAGTGATACCCATGTTTTCAG---------- +---------------------CATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCA +TGCTAAA----------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------GAAGA- +---------------AGCGGAGACAGCGACGAAGAGCTCA-------------------- +-------------TCAGAACAGTCAGACTCATCAAGCTTCTCAATCAAATCAG------- +----- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 +AT---C--CTCATGCATCTGTTCTACCATGTCATTTTTCCA------------------- +--------------------------------------CATGTTAAAATTTTCTGTCACA +TTTACCAATACT------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 +----------------------------------------------CTATGTTTACTTCT +A----------------------ATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAA +CTCAGTCTTCTGATTTGT------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 +------------------------------------------------------------ +----------------------CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTA +AGCCATGGAGCCAAATCCTAGGAAAATGT------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--CTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 +-------------------------------------CTACTATTGCTACTAATGGTA-- +--------------------------------TAGGTTGCGTTACATGTAC-------TA +CTTACTGCTTTGAT--------------------------AGAGAAGCTTGATG------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 +----------------------------------TCTTTGCCTTGGTTGGAGCAACTCCT +AA------------------------------TGGTTGAATTTTTACTACTTTATATTTA +TATAATTCCCTTCT---------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC-------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------ACAACGGAATTGGAGGA- +-------------------AATGAACCAGTAGATAAATTA-------------------- +GTCAGTGCTGGAATCAGGAAAGTACTATTTTT---------------------------- +----- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 +------------------------------------------------------------ +--------------------------------------------AGGATTT-------TA +CATAATTGCCTTAC--------------------------TTAAATCCCTGGGTAAATCT +GACTTGCCCAA-TTCAATTTCCCCACTA-------------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 +------------------------------------------------------------ +-----------------------TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCA +TGCTACACCC-------------------------------------------------- +-------------------AGTGGGGGGACATCAAGCAGCCA------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 +-------------------------------CTACCTCTTCTTCTGCTAGACTGCCATTT +AACA----------------------GCAGTTGAGTTGATACTACTGGCCT-------AA +TTCCATGTGT-------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 +------------------------------------------------------------ +---------------------TTCTCTGAAATCTACTAATTTTCTCCATTT-------AG +TACTGTCTTTTTTCTTTATGGCAAATACTGGAGTAT------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---TG +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 +--------------------------------------------TGCCAAGGATCCGTTC +ACT--------------------------AATCGAATGGATCTGTCTCTGTCTCTCTCTC +CACCTTCTTCTTCTATTCCT---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 +-------------------------CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTT +GC----------------------------------CCATACTATATGTTT-------TA +ATTTATATTTTTTCTT-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 +---------------------------------------------GCTGCTCCCACCCT- +------------------------ATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCT +TACAGTAGGCCATCCAATCA---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 +------------------------------------------------------------ +--------------------------------------------------------ACAG +TAGAAAAATTCCCCTCCACCA------------------TTAAAACTGTGGTTACAATAT +CTGGGTCCCC---------TCCTGAGGATTGGT--------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTA +GACAGGATGAGGATTAGAACA--------------------------------------- +--TGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 +------------------------------------------------------------ +----------------------------------------GATCCTGCATA-------TA +AGCAGCAGCTTTTT------------------------------------------GCCT +TTACTGGTTCT-CTCTGGTTAGACCAGATCTGA-GCCTGGG------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 +----------GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCG-- +-------------------------------------------------TTTGAGACCCA +CCTCCCAACCC------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------CAGAGGAGGTCTCTCGACGCAGGAC +TCGGCTTGCTG-----AAGGGCGCACGGCAAGAGGCGAGGGGCGGCGA------------ +------------------------------------------------------------ +---CT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 +------------------------------------GTCTGGGGCATCAAGCAGCTCCAG +GC--------------------------AAGAATGCTGGCTGTGGAAAGATACCTAAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 +------------------------------------------TTTTTCAG---------- +--------------------------------TTCGCTTAGATGAAGACTTCAGGCAGTA +TACTGCATTTACCATAC------------------------------------------- +-------------------CTAGTATAAACAATGAG------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------ACAGCGACGAAGAGCTCA-------------------- +-------------TCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAT +TACAT +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 +GGGGGG------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------AACAGTGCAGGGGAAAGAATAGTA------------------GA +CATAATAGCAACAGACATACAAACTAAAGAATTACAA----------------------- +----A +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 +------------------------------------------------------------ +----------------------------------------------TGCTCTGAAGAAAA +TTCCCTGGCCTTCCCTTGTAGTAAGGC-CATAT-CTTCCCTAAAAAATTAGCCTGTCT-- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 +------------------------------------------------------------ +---------------------------------------GGCTAATTCACTCCCAACGAA +GACAAGATATCCTTGATCT----------------------------------------- +----------------GTGGATGTACCACCCACAAGGCTACTTCCC-------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 +----------------------------------TGATTTGTTGTGTCAG---------- +--------------------TTAGGGTGACAACTTTTTGTGTTCCTCTATT-------AG +TAACATATCCTGCTTTTCCTA--------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 +------------------------------------------------------------ +---------------------------------------------------------TAA +CGCCACCTTTGCCTAGTGTTACGAAAC--------------------------------- +-------------------TGCCAGAGGATAGATGGAACAA-----------------G- +-----CCCCAGAAGACGAAGGG-------------------------------------- +----- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 +------------------------------------------------------------ +-----------------GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCCTTGGCACTTATCTGGGACGATCT--------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 +------------------------------------------------------------ +-------------------------------TTCTGGGAAGTT----------------- +------------------------------------------------------------ +-------------------CAATTAGGAATACCACATCCC-------------------- +-------GCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGG---------------- +----- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 +------------------------------CTCTAGTGTCCATTCATTGTGTGGCTCCCT +CT--------------------------GTGGCCCTTGGTCTTCTTGGGCT-------TG +TTCCATCTCTCC------------------------------------------------ +---------------------------------T-------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 +------------------------------------------------------------ +-------------A--------------------GCCATTGCTCTCCAATT-------AC +TGTGATATTTCTCATGTTCATCTTGG----------GCCTTAACTATTCCATCTAAAAAT +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 +------------------------------------------------------------ +---------------------------TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCT +TACAGTAGGCCATCCAATCAC---------------ACTACATATTGACCAC-------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 +-------------------------TCGGAGTCATTGTTGCTATTACCACCATCTTTTGT +TC------------------------------ATAGCAGCCCTGTAATATTTGATTAACA +TCTAA------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------ATAACCACAGAAAGCATA-------------------- +-------GTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACAT- +----- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 +------------------------------------------------------------ +--------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCT-------CA +TCCTGTCTCCTTGCCACACAATCATCACCTG----------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 +ACCCAT--CTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGG-- +--------------------------------CGAATAGCTCTACA-------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 +----------------------------------GAGGGGGAGTTGTTGTCTGTACCCCA +GACCTG-------AAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------TATAAAGACGCAGAAGTTATT-------------------- +-------CCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTCAAATTAGCAG---- +----- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 +----------------TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCC-- +-------------------------------------------------TTTGAGCCAAT +TCCCATACATTATTGTG------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------GGAAA- +-------------------GGTGAAGGGGCAGTAGTAATAC-----------------AA +GATAATAGTGACATAACAGTAGTGCGAAGAAGAAAAGCAAA------------------- +----- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 +------------------------------------------------------------ +--------------------------------AAGTGCAAGCAATCTGATT-------CA +CCCGATTTCTTCCAATTATGA--------------------------------------- +--------------TGACAGGTGTAGGTCCTACTAATACAGT------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------TATGGTACCAGTTAGAGAA- +---------------AGAACCCCTAGTAGGAGCAGAAACCT------------------- +-------TCTATGTAGATGGGGCAGCTAACAG---------------------------- +----- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 +------------------------------------------------------------ +--------------------------------------ATTGTACACATTT-------AG +AATGAAAAGTTATCCTGGTAG------------------CAGTTCATGTAGCCAGTGGA- +-------------------TATATAGAAGCAGA--------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 +------------------------------------------------------------ +----------------------------------------------------------TG +ACAGAAACCT------------------------------AGTTGGTCCAAAATGCGAAC +CCAGATTGTAA----GACAATTTTAAAAGCATTGGGACCA-------------------- +-------GC--------------------------------------------------- +----- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------GGTGATATGGGCTGATGTA +CCATTTGCCCC----TGGATGTTCTGCACTATAGGGTAATT-----------------TT +GGCTGACCTGAT------------------------------------------------ +----- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 +-----------GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGG-- +-------------------------------------------------TTTGAGAGCCA +CCTAGCAATTCA------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 +-------------------------------------------------------TCCTG +AC------------------------------TCCAATACTGTAGGAGATTCCACCAATA +TTTGAGGGCTTCCCACCCCCTGC------------------------------------- +-------------------GTCCCAGAAGTT----------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------ATTTTAAAAGCATTGGGACCAGCGGCTACACTAG---AAGA +AATGATGACAGCATGTCAGGGAGTAGGATGAC---------------------------- +----- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------CAACCTATACCAATAGTAGCAATA-------------------- +-------GTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTC--------- +---CA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 +------------------------------------------------------------ +--------CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAA +GACAAGATATCCTTGATC------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 +------------------------------------------------------------ +-------------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTA +ATCAGTGGGTTCCCTAGTTA----------------GCCAGAGAGCTCCCA--------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------ACAGT---------AATTGGAGAGCAATGGCTAGTGATT +TTAACCTGCCA--------CCTGTAGTAGCAAAAGAAATAGTAGCCCG------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 +------------------------------------------------------------ +------------------------------------------------------------ +-------AATTT----------------------------ATCAAGAGCCATTTAAAAAT +CTGAAAACAGG----AAAATATGCAAGAATGAGGGGTGCC-------------------- +CACACTAAT--------------------------------------------------- +----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 +------------------------------------------------------------ +------------------------------------------TTAAAATTTTCTGTCACA +TTTACCAATACTACTTCTTGTGGGTT---------------------------------- +---------------GGGGTCTGTGGGTACACAGGCATGTG------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 +-------------------------TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGG-- +--------------------------------CGCATAGCTCTACAAGCTC-------CT +TGTACTACTTCAATAA-------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 +-----------------------------------------TGTGTTCAGCTGTACTATT +ATGGTT-----------------ATAGCATTTTCCGTGAAATTGACAGATCTAATTACTA +CCTCTTCT---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 +------------------------------------------------------------ +------------------------------------------------------------ +---GATGGTTTT----------------------------ATAGACATCACTATGAAAGC +CCTCATCCAAG----AAAAAGTTCAGAAGTA-------CA-------------------- +CATCCCACTAGG------------------------------------------------ +----- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 +--------------------TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCC +A----------------------ATTCTGAAACTGGATAAACAGCAGTTGTT-------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------AGTTCATGTATCCAGTGGA- +-------------------TATATAGAAGCAGAAGTTATT-------------------- +-------CCAGCAGAAACAGGGGCTGAAACAGCATAT----------------------- +----- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 +------------------------------------------------------------ +---------------GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTT--------- +------------------------------------------------------------ +--------------AGAAACATCAGAAGGCTGTAGACAAATACTGGGA------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 +------------------------------------------------------------ +-----------------------AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATA +CTCCAGTATTTGCCATAAAGAAAAAAGACAGTA--------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 +------------------------------------------------------------ +------------------------------------------------------------ +---AGTAAGT------------------------------AGTACCTGTAAC--GCAA-- +-------------------CCTATACCAATAGTAGCAATA-------------------- +-------GTAGCATTAGTAGTAGCACTAATAAT--------------------------- +----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 +------------------------------------------------------------ +-----------------------------CG------------AGCAAGCTTCACAGGAG +TTAAAAAATTGGATGACAGAA---------------ACCTTGTTGGTCCAAAATGCGAAC +CCAGAT------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------GACCAGCAAAGCACCTCTGGAAA- +-------------------GGTGAAGGGGCAGTAGTAATAC-----------------AA +GATAATAGTGACATAAAAGTAGT------------------------------------- +----- +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 +C------------------------------------CCCATATTACTATGCTTTCTGTG +GT------------------------------------------TAATTTTTGCACTGCC +TCTGTTAATTGTTTTACATCATTAGTGT-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 +-----------------------------------------------CGGGCACACACT- +------------------------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTA +AGCAGTGGGTTCCCTAGTTA----------------GC---------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGG +TGTGGTAAGTCCCCACCTCGACAG------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 +------------------------------------------------------------ +---------------TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATC +TCTCATTTTTCTGCCCGTTCTAG------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---CT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 +--------------------------------------------CTTTATATTTTTTCTT +ACCCCC--------------------------TGGCCTTAACCGAATTTTTTCCCATCGA +TCTAATTCTCCCCCGCTTAA---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAG--GAACCAAAGAAAGATAGTTAAGTGTT +TCAATTGTGGC-ACAGAAGGGCACACAGCCAGAAATTGCAGG------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 +----------------------------------TCTACATAGTCTCTAAAGGGTTCCTT +TGGTCCT-------TGTCTTATGTCCAGAATGCTGGTAGGGCTATACATTC--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 +----------------------------------ATAGAGCTTCCTTTAGTTGCCCCCCT +ATCTTTATTGTG-AC--------------------------------------------- +------------------------------------------------------------ +----------------GAGGGGACGTTGCCAAAGAGTGACCTGAGG-------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 +G---------------------------AAGTCTTGAGTTCTCTTATTAA---------- +--------------------GTTCTCTGAAATCTACTAATTTTCTCCATTT-------AG +TACTGTCTTTTTTC---------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 +TTTGA------------------------------------------------------- +-----T----------TGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATT +CCTAATGCATATTGTGAGTC---------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 +------------------------------------------------------------ +--------------------------------------ACTTT---ATATT-------TA +TATAATTCACTTCTCCAATTGTCCCTCATCTCTCCT------------------------ +-----------CCTCCAGGTCTGAAGATCTCGG--------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 +------------------------------------------------------------ +------------------AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTA +GCCAGTAGATCCTAGACTATAGCCCTGG-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 +-------------------------------------CTTCTTCTGTTAGTGGTATTACT +TCT--------------------GTTAGTGCTTTGGTACCTCTAAGGAGTT-------TA +CATAATTGCCTTAC---------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 +----------------------------------AAGCTTGTGTAATTGTTAATTTCTCT +GTCCCACT------------------------CCATCCAGGTCGTGTGATTCCAACTCTG +TTCCAGAG---------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 +------------------------------------------------------------ +---------------------TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTG +ACTAA------------------------------------------------------- +--------------AAGGGTCTGAGGGATCTCTAGTTACC-------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 +------------------------------------------------------------ +----------GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTT-------- +------------------------------------------------------------ +--------------AGAGGAGCTTAAGAATGAAGCTGTTAGA------------------ +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 +------------------------------------------------------------ +----------------------------------------------CAGATACCTAAATG +ATCAACAGCTCCTGGGGATTTGGGGT---------TGCTCTGGAAAACTCATTTGCACCC +CTGCT------------------------------------------------------- +------------------------------------------------------------ +----- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 +------------------------------------------------------------ +--------------------AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCA +GGAAGCAACCACCACTCTATTTTGTGCATC------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.aln.bionj Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,1 @@ +((K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42:1.08382738,(K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25:0.38678554,K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11:0.46747664):0.28545681):0.33227873,((((((((((K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82:0.33019924,K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21:-0.23734134):0.31789154,(K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64:0.24097729,(K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49:0.79707563,K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45:-0.74851167):0.77584779):1.32894349):0.81661385,K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16:0.68299061):0.39482850,((K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51:-0.06422135,K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26:0.09239586):0.86857092,K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18:1.14412010):0.84795004):0.28669447,K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27:0.67261785):0.60126722,K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32:0.63477385):0.18692786,(K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74:-0.16093190,K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12:0.16093291):0.57964945):0.67246187,((((K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78:-0.04344772,K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9:0.09476592):0.37040287,(K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76:-0.05786514,K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6:0.28328022):0.55326849):0.59872919,K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34:0.27340084):0.40448800,((((K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67:-0.17074749,K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52:0.20956698):1.52105892,(K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62:1.28177524,K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54:0.17855203):0.68180287):0.28971612,(K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58:-0.27098528,K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48:0.97957110):0.06554447):0.45809147,K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66:0.89331114):0.21245918):0.13172832):0.24273634,((((K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80:0.20269507,(K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50:0.77435148,(K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24:0.00371471,K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4:-0.00371371):0.21016720):2.02702880):0.41420281,(K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72:0.68534267,((((K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71:0.95543969,((K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60:-0.13233471,K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39:0.32307261):0.86475265,K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46:1.34859216):0.51354015):0.30712959,((K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65:-0.11199759,K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41:0.13339269):0.88869047,((K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35:0.93511814,K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17:0.84248346):0.20386642,((K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23:0.05155873,K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1:0.00868567):0.61363840,K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8:0.76305079):0.26402888):0.34238318):0.44385353):0.24512014,(K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53:0.22552943,K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43:0.78767395):0.91552830):0.55719942,K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44:-0.55660146):1.02335250):0.64595079):0.76828027,K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14:-0.19931793):0.44801587,(K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70:1.35438824,(((K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59:1.36122406,(K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13:-0.08675730,K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7:1.41255224):0.63149464):0.73396337,K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3:0.39862660):0.54758346,((K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56:-0.14103474,(K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37:-0.11571378,K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29:1.73374462):0.27975333):0.93957406,K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5:0.66699010):0.59189928):0.48751685):0.27255732):0.10146419):0.19251713,((K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79:0.95977539,(((K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75:-0.12744217,K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73:0.12744318):1.16846502,(K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38:1.26209760,K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31:0.16246253):0.47137973):0.19725871,(K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69:-0.30324629,K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20:0.30324730):1.44542503):0.66402847):0.25500304,K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36:0.81059200):0.32113436):0.09836370,((((((((K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83:1.09870255,(K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77:1.00321472,K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63:-0.58553964):0.31580889):0.09470904,(K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33:0.20550822,K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15:-0.11599271):0.68516803):0.27381828,K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68:0.07779000):1.13107252,K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47:0.13239771):0.65484142,((K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61:0.34795883,K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19:-0.34795782):0.47106653,(K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55:-0.56689090,K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2:0.56689185):1.37990499):0.58266771):0.48182857,(K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10:-0.24484614,K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0:0.26969853):0.56252277):0.21004373,(K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81:0.03842903,K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40:-0.03842803):1.31178999):0.17807718,(((K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57:-0.06675175,K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30:0.44183204):0.77802974,K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28:0.89102417):0.66907573,K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22:1.12436128):0.56843060):0.39201805);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.aln.iqtree Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,259 @@ +IQ-TREE 1.6.10 built Mar 21 2019 + +Input file name: clsReps.aln +Type of analysis: tree reconstruction +Random seed number: 50990 + +REFERENCES +---------- + +To cite IQ-TREE please use: + +Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh +(2015) IQ-TREE: A fast and effective stochastic algorithm for estimating +maximum likelihood phylogenies. Mol Biol Evol, 32:268-274. +https://doi.org/10.1093/molbev/msu300 + +SEQUENCE ALIGNMENT +------------------ + +Input data: 84 sequences with 305 nucleotide sites +Number of constant sites: 15 (= 4.91803% of all sites) +Number of invariant (constant or ambiguous constant) sites: 15 (= 4.91803% of all sites) +Number of parsimony informative sites: 238 +Number of distinct site patterns: 301 + +SUBSTITUTION PROCESS +-------------------- + +Model of substitution: GTR+F+R4 + +Rate parameter R: + + A-C: 1.1368 + A-G: 3.5229 + A-T: 0.7423 + C-G: 0.8278 + C-T: 3.3869 + G-T: 1.0000 + +State frequencies: (empirical counts from alignment) + + pi(A) = 0.2808 + pi(C) = 0.2221 + pi(G) = 0.2104 + pi(T) = 0.2866 + +Rate matrix Q: + + A -0.9231 0.1932 0.5671 0.1628 + C 0.2443 -1.12 0.1333 0.7428 + G 0.757 0.1407 -1.117 0.2193 + T 0.1595 0.5757 0.161 -0.8962 + +Model of rate heterogeneity: FreeRate with 4 categories +Site proportion and rates: (0.05215,0.2261) (0.3403,0.5166) (0.301,0.5167) (0.3066,2.143) + + Category Relative_rate Proportion + 1 0.2261 0.05215 + 2 0.5166 0.3403 + 3 0.5167 0.301 + 4 2.143 0.3066 + +MAXIMUM LIKELIHOOD TREE +----------------------- + +Log-likelihood of the tree: -6705.2658 (s.e. 288.4958) +Unconstrained log-likelihood (without tree): -1739.1499 +Number of free parameters (#branches + #model parameters): 179 +Akaike information criterion (AIC) score: 13768.5317 +Corrected Akaike information criterion (AICc) score: 14284.0517 +Bayesian information criterion (BIC) score: 14434.4675 + +Total tree length (sum of branch lengths): 81.5600 +Sum of internal branch lengths: 34.1477 (41.8682% of tree length) + +WARNING: 8 near-zero internal branches (<0.0033) should be treated with caution + Such branches are denoted by '**' in the figure below + +NOTE: Tree is UNROOTED although outgroup taxon 'K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0' is drawn at root + ++--K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 +| +| +**K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 +| +--| +| | +--K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 +| +------| +| | | +-----K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 +| | +----| +| | | +**K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 +| | +---| +| | +--K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 +| +**| +| | | +**K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 +| | | +--| +| | | | +--K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 +| | | +---| +| | | | | +------------K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 +| | | | +--| +| | | | +--K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 +| | | +--| +| | | | | +--K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 +| | | | +-----| +| | | | +--K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 +| | +--| +| | | +**K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 +| | +--| +| | +--K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 +| +--| +| | | +-------K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 +| | +------| +| | | +-----------K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 +| | +--| +| | | +--K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 +| | +--| +| | | +----------------K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 +| | +---| +| | +---K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 +| +--| +| | | +-----K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 +| | +--| +| | +----K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 +| +--| +| | +-------K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 +| +**| +| | | +----------------K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 +| | | +---------| +| | | | +----K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 +| | | +--| +| | | | +--K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 +| | | +---| +| | | | | +--K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 +| | | | +**| +| | | | +--------K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 +| | +**| +| | +--------K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 +| +---| +| | | +--K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 +| | | +--| +| | | | +--K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 +| | +---------------| +| | +**K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 +| +--| +| | | +**K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 +| | | +-------| +| | | | +**K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 +| | | +----| +| | | | +-----K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 +| | | +**| +| | | | +-----------K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 +| | | +--| +| | | | +--K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 +| | | +--| +| | | | | +--K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 +| | | | | +--| +| | | | | | +-----------K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 +| | | | +--| +| | | | | +------------------K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 +| | | | | +--| +| | | | | | +**K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 +| | | | +--------------| +| | | | +**K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 +| | | +--| +| | | | | +-----K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 +| | | | +--| +| | | | | +--K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 +| | | | | +--------| +| | | | | | +**K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 +| | | | +--| +| | | | +--K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 +| | | +--| +| | | | | +--K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 +| | | | +-----| +| | | | | +**K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 +| | | | +--| +| | | | +--K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 +| | | +--| +| | | | | +------------K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 +| | | | | +--| +| | | | | | +-------K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 +| | | | +--| +| | | | | +**K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 +| | | | +-----| +| | | | +--K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 +| | +**| +| | | +--K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 +| | | +---| +| | | | | +-------------K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 +| | | | | +--| +| | | | | | +-------K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 +| | | | | +--| +| | | | | | +---------------K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 +| | | | +--| +| | | | | +**K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 +| | | | +------| +| | | | +--K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 +| | | +-------| +| | | | | +--K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 +| | | | | +-------| +| | | | | | +**K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 +| | | | +--| +| | | | | +--K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 +| | | | +-------| +| | | | +**K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 +| | | +--| +| | | | +**K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 +| | +--------| +| | +-------K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 +| +--| +| | +--K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 +| +--| +| | | +**K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 +| | | +**| +| | | | +**K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 +| | | +----| +| | | | | +-----------K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 +| | | | +--| +| | | | | +**K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 +| | | | +---------| +| | | | +--------------K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 +| | | +--| +| | | | +**K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 +| | | +--| +| | | | +----K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 +| | +--| +| | | +--K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 +| | +--| +| | +**K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 +| +----| +| | +---------K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 +| +--| +| | | +-------K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 +| | +-------| +| | +----K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 ++**| +| | +**K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 +| | +-------| +| | | +----------------K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 +| | +--| +| | | | +------------------K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 +| | | +----| +| | | +---K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 +| | +------| +| | | +-------K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 +| +--| +| +--------------------K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 +| ++**K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 + +Tree in newick format: + +(K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0:0.0208331911,((((((((((((((K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1:0.0000021264,K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23:0.0594553512):0.1296922788,(K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8:0.6920569038,(K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26:0.0000021772,K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51:0.0283525760):0.5331969251):0.6057681587):0.8607168852,((((K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3:0.0000028353,K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30:0.3916159776):0.2843786327,(K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13:1.4472688012,K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59:0.3619876765):0.3924140733):0.4787213037,(K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15:0.0247236298,K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33:0.0581588423):0.6929487305):0.3990922094,(K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52:0.0000020585,K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67:0.0383201285):0.3079742938):0.2597743406):0.0000022985,(K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17:0.9245053433,(K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38:1.3457435849,(K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61:0.3915429159,(K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77:1.8799018888,K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83:0.5038411641):0.5037750990):0.0271764262):0.0949221667):0.8212787266):0.3903288204,(K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54:0.6965753752,K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58:0.6412304658):0.3189483735):0.2390653662,K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32:0.9448908457):0.1277446238,((((K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4:1.9004804746,K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29:0.6520590566):1.1566050736,K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25:0.2692500204):0.3226998297,(K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11:0.2718098107,K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28:1.0520579555):0.0000025290):0.4867570590,K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42:1.0720754668):0.0000021108):0.0000026748,((K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45:0.0475485889,K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64:0.2329909782):0.0066766424,K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49:0.0000022583):1.7664057028):0.4398495866,(((((((((K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2:0.0000028742,K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55:0.0000029878):0.9536290679,K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68:0.7421118278):0.6353288885,K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70:1.3436451226):0.0000029501,K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80:0.3166720685):0.2918074414,((K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16:0.2598478941,K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48:1.4269996782):0.3164888696,((K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18:2.1630525675,K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82:0.0000024834):0.1020028419,K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21:0.0000021654):1.7140773364):0.2069120157):0.2042334412,(K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43:0.7155929162,((K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50:0.0252049664,K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63:0.0000023570):0.9934475786,K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53:0.0925475402):0.4322208720):0.4049833979):0.3817545617,(K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39:0.1062756132,(K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44:0.0000020765,K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60:0.0322744462):0.0823564084):0.7029217434):0.2354053948,((K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20:1.4442227491,K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71:0.9028043080):0.2004074130,(K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66:0.0000021492,K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81:0.4295448982):0.7256587050):0.0838503780):0.2033711616,((((K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5:0.3951526072,(((K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7:1.5853136692,K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72:0.9238586642):0.2856430831,K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57:1.7770622855):0.0349828150,(K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37:0.0000022539,K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56:0.0221564933):0.7978773936):0.1741143388):0.4687942454,((K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6:0.2766416992,K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76:0.0000026221):0.9737881350,(K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9:0.0668307423,K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78:0.0000023998):0.8962485506):0.3325230439):0.9732603709,K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34:0.0000026548):0.3407180311,K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75:0.8965290905):1.0313141689):0.0000020285):0.1368604217,K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14:0.2858560859):0.1965114888,(((((K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12:0.0000020229,K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74:0.0000029424):0.0000020783,(K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27:1.4158630182,(K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31:0.0000026705,K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69:1.7399481197):1.1476795814):0.3408538296):0.5834854608,K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24:0.0000024033):0.3025462633,K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36:0.6062263919):0.3980166535,(K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41:0.0254410497,K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65:0.0000025128):0.3640298759):0.1342885824):0.2799205018,K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35:1.1029338488):0.6396342694,(K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22:0.9656746254,K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73:0.5807206466):0.9096520535):0.1308637778,((((K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19:0.0000021878,K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47:1.9500839671):0.9137570016,(K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62:2.0983383341,K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79:0.4896914012):0.6190777654):0.3485939882,K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40:0.9233756271):0.8224062050,K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46:2.3808747943):0.0060670734):0.0000024163,K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10:0.0000024937); + +TIME STAMP +---------- + +Date and time: Tue May 28 13:11:57 2019 +Total CPU time used: 115.545 seconds (0h:1m:55s) +Total wall-clock time used: 120.015 seconds (0h:2m:0s) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.aln.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,354 @@ +IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019 +Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, +Heiko Schmidt, Dominik Schrempf, Michael Woodhams. + +Host: gaius (AVX2, FMA3, 15 GB RAM) +Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1 +Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue May 28 13:09:57 2019 +Kernel: AVX+FMA - 1 threads (8 CPU cores detected) + +HINT: Use -nt option to specify number of threads because your CPU has 8 cores! +HINT: -nt AUTO will automatically determine the best number of threads to use. + +Reading alignment file clsReps.aln ... Fasta format detected +Alignment most likely contains DNA/RNA sequences +Alignment has 84 sequences with 305 columns, 301 distinct patterns +238 parsimony-informative, 52 singleton sites, 15 constant sites +WARNING: Some sequence names are changed as follows: +K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 -> K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 +K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 -> K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 +K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 -> K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 +K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 -> K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 +K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 -> K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 +K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 -> K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 +K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 -> K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 +K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 -> K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 +K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 -> K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 +K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 -> K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 +K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 -> K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 +K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 -> K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 +K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 -> K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 +K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 -> K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 +K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 -> K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 +K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 -> K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 +K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 -> K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 +K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 -> K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 +K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 -> K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 +K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 -> K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 +K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 -> K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 +K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 -> K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 +K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 -> K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 +K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 -> K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 +K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 -> K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 +K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 -> K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 +K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 -> K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 +K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 -> K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 +K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 -> K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 +K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 -> K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 +K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 -> K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 +K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 -> K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 +K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 -> K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 +K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 -> K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 +K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 -> K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 +K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 -> K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 +K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 -> K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 +K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 -> K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 +K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 -> K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 +K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 -> K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 +K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 -> K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 +K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 -> K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 +K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 -> K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 +K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 -> K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 +K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 -> K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 +K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 -> K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 +K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 -> K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 +K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 -> K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 +K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 -> K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 +K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 -> K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 +K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 -> K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 +K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 -> K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 +K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 -> K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 +K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 -> K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 +K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 -> K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 +K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 -> K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 +K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 -> K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 +K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 -> K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 +K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 -> K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 +K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 -> K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 +K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 -> K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 +K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 -> K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 +K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 -> K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 +K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 -> K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 +K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 -> K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 +K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 -> K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 +K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 -> K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 +K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 -> K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 +K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 -> K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 +K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 -> K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 +K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 -> K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 +K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 -> K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 +K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 -> K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 +K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 -> K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 +K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 -> K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 +K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 -> K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 +K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 -> K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 +K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 -> K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 +K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 -> K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 +K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 -> K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 +K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 -> K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 +K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 -> K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 +K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 -> K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 +K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 -> K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 + + Gap/Ambiguity Composition p-value + 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90% + 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53% + 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21% + 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36% + 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86% + 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72% + 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71% + 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58% + 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28% + 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71% + 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76% + 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06% + 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72% + 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74% + 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54% + 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66% + 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47% + 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11% + 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61% + 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18% + 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00% + 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75% + 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23% + 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67% + 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02% + 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52% + 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05% + 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57% + 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98% + 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02% + 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08% + 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03% + 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47% + 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89% + 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36% + 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48% + 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92% + 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51% + 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24% + 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06% + 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06% + 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00% + 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90% + 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68% + 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88% + 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28% + 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89% + 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69% + 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81% + 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95% + 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20% + 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44% + 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71% + 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60% + 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49% + 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92% + 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75% + 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72% + 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57% + 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40% + 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77% + 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83% + 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48% + 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69% + 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64% + 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23% + 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65% + 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90% + 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19% + 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60% + 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10% + 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03% + 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28% + 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17% + 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26% + 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77% + 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37% + 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04% + 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16% + 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98% + 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70% + 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88% + 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25% + 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89% +WARNING: 84 sequences contain more than 50% gaps/ambiguity +**** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3) + +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds + +NOTE: 3 MB RAM (0 GB) is required! +Estimate model parameters (epsilon = 0.100) +1. Initial log-likelihood: -7393.152 +2. Current log-likelihood: -6850.590 +3. Current log-likelihood: -6814.795 +4. Current log-likelihood: -6812.204 +5. Current log-likelihood: -6811.732 +6. Current log-likelihood: -6811.618 +Optimal log-likelihood: -6811.491 +Rate parameters: A-C: 1.16582 A-G: 3.17373 A-T: 0.69428 C-G: 1.33012 C-T: 3.22998 G-T: 1.00000 +Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 +Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200) +Parameters optimization took 6 rounds (0.508 sec) +Computing ML distances based on estimated model parameters... 0.032 sec +WARNING: Some pairwise ML distances are too long (saturated) +Computing BIONJ tree... +0.003 seconds +Log-likelihood of BIONJ tree: -6859.680 +-------------------------------------------------------------------- +| INITIALIZING CANDIDATE TREE SET | +-------------------------------------------------------------------- +Generating 98 parsimony trees... 1.076 second +Computing log-likelihood of 98 initial trees ... 1.196 seconds +Current best score: -6803.399 + +Do NNI search on 20 best initial trees +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 1: -6746.667 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 4: -6743.453 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 8: -6739.399 +Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s +Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s +Finish initializing candidate tree set (20) +Current best tree score: -6739.399 / CPU time: 11.455 +Number of iterations: 20 +-------------------------------------------------------------------- +| OPTIMIZING CANDIDATE TREE SET | +-------------------------------------------------------------------- +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 24: -6738.697 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 25: -6730.006 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 27: -6728.392 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 29: -6725.172 +Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 31: -6723.283 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 37: -6720.321 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 39: -6717.689 +Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 41: -6717.333 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 44: -6715.754 +Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 56: -6714.598 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 59: -6714.257 +Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 66: -6713.872 +Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left) +Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left) +Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left) +Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left) +BETTER TREE FOUND at iteration 105: -6713.864 +Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left) +Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 123: -6712.300 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 126: -6710.985 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 127: -6710.445 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 130: -6709.739 +Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 136: -6709.364 +Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 142: -6709.294 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 147: -6708.895 +Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 160: -6708.749 +Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 163: -6708.686 +Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 173: -6708.554 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 180: -6708.518 +Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left) +Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 193: -6705.296 +BETTER TREE FOUND at iteration 200: -6705.295 +Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 202: -6705.270 +Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left) +Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left) +Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left) +Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left) +Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left) +Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left) +Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left) +Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left) +Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left) +BETTER TREE FOUND at iteration 293: -6705.270 +BETTER TREE FOUND at iteration 295: -6705.269 +Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left) +Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left) +Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left) +UPDATE BEST LOG-LIKELIHOOD: -6705.269 +Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left) +Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left) +Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left) +Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left) +Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left) +Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left) +Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left) +TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s + +-------------------------------------------------------------------- +| FINALIZING TREE SEARCH | +-------------------------------------------------------------------- +Performs final model parameters optimization +Estimate model parameters (epsilon = 0.010) +1. Initial log-likelihood: -6705.269 +Optimal log-likelihood: -6705.266 +Rate parameters: A-C: 1.13682 A-G: 3.52293 A-T: 0.74232 C-G: 0.82784 C-T: 3.38691 G-T: 1.00000 +Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 +Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143) +Parameters optimization took 1 rounds (0.062 sec) +BEST SCORE FOUND : -6705.266 +Total tree length: 81.560 + +Total number of iterations: 396 +CPU time used for tree search: 114.612 sec (0h:1m:54s) +Wall-clock time used for tree search: 119.058 sec (0h:1m:59s) +Total CPU time used: 115.545 sec (0h:1m:55s) +Total wall-clock time used: 120.013 sec (0h:2m:0s) + +Analysis results written to: + IQ-TREE report: clsReps.aln.iqtree + Maximum-likelihood tree: clsReps.aln.treefile + Likelihood distances: clsReps.aln.mldist + Screen log file: clsReps.aln.log + +Date and Time: Tue May 28 13:11:57 2019
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.aln.midpoint.treefile Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,1 @@ 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,252 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCA +ATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACAT +CAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAA +TTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGG +GGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCT +GGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCT +CTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAGCAG +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCC +CGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/final.all.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG---------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT---------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT---------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT---------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG--------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA--------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------------ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------------ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------------ +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG--------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------------ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------------ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +-------------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT----- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +-------------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +-------------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +-------------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +-------------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +-------------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------------ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------------ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------------ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------------ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------------ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------------ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------------ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------------ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +-------------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +--------------------------------------------------TTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +ACACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +----------------------------------------GTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------------------------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAA----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +------------------------TGT-------------AACACCTCAGTCATTA---- +--CACAGG--------------CCTGTCCAAAGGTATCCTTTGAGCCAATTCC------- +----------------------------------------------------CATACATT +ATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +------------------------ATG-------------TATG---------------- +-----GGA--------------ATTGGCTGAAAGGATACCTTTGGACAGGCCT------- +----------------------------------------------------GAGTAATG +ACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +------------------------AA--------------GCTTGTGTAATTGTTAATTT +C---TCTG--------------TCCCACTCCATCCAGGTCGTGTGATTCCAAC------- +----------------------------------------------------TCTGTTCC +AG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +------------------------AA--------------AATTTCAAA----------- +-------------------------------AATTGGGCCTGAAAATCCATAC------- +----------------------------------------------------AATACTCC +AGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +------------------------GC--------------CTGCATGGAATGGATGACCC +GGAGAGAG--------------AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT------- +----------------------------------------------------AGCAATTC +A------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +------------------------GTA-------------CTTTCTATAGTGAATAGAGT +TAGGCAGG--------------TATATTCACCATTATCGTTTGAGACCCACCT------- +----------------------------------------------------CCCAACCC +-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------------------------------------------GGT----------- +-------------------------------GATATGGGCTGATGTACCATTT------- +----------------------------------------------------GCCCCTGG +ATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +------------------------ATAGAG----------CTTCCTTTAGTTGCCCCCCT +ATCTTTAT--------------TGTGACGAGGGGACGTTGCCAAAGAGTGACC------- +----------------------------------------------------TG------ +--------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +------------------------------------------------------------ +TTTTTCAG--------------TTCGCTTAGATGAAGACTTCAGGCAGTATAC------- +----------------------------------------------------TGCATTTA +CCATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +-----------------ATAACCACAGAA-----------------AGCATAGTAATATG +G------------------------------GGAAAGACTCCTAAATTTAAACT------ +---------------------------------------------------GCCCATACA +AAA---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +--------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAAAAGTAGT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +--------------------------GGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAACAGTAGTG----------------- +------------------------------------------------------------ +-------------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +-----------------------------------------TTTTATGGTTCATAATCCA +CTCCATGT--------------ACTGGTTCTTTTAGAATCTCTCATTTTTCT-------- +---------------------------------------------------GCCCGTTCT +AGCT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTCTAAAATA +ACCAGTAC--------------ATGGAGTGTATTATGACC-------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------CTCTAGTGTCCA +TTCATTGT--------------GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGG------ +---------------------------------------------------GCTTGTTCC +ATCTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +-----------------------------------------------------TGATTTG +TTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCTCTATTAG +TAACATAT--------------CCTGCTTTTCCTA------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +---------------------------GAA----------GTCTTGAGTTCTCTTATTAA +--------------------------GTTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------TTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +--------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACATAATAGCA +ACAGACAT--------------ACAAACTAAAGAATTACAA------------------- +------------------------------------------------------------ +-----------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAAGGTGTTTTACTAAACTTTTCCA------ +---------------------------------------------------TGTTGTAAT +CCTCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +-----------------------------------------CAGGATTAACTGCGAATCT +T---TCTAG------------CTCCCTTGTTGCCCATACTATATGTTTTAATT------- +----------------------------------------------------TATATTTT +TT--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/final.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG---------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT---------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT---------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT---------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG--------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA--------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------------ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------------ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------------ +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG--------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------------ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------------ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +-------------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT----- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +-------------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +-------------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +-------------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +-------------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +-------------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------------ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------------ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------------ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------------ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------------ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------------ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------------ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------------ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +-------------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +--------------------------------------------------TTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +ACACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +----------------------------------------GTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------------------------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAA----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +------------------------TGT-------------AACACCTCAGTCATTA---- +--CACAGG--------------CCTGTCCAAAGGTATCCTTTGAGCCAATTCC------- +----------------------------------------------------CATACATT +ATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +------------------------ATG-------------TATG---------------- +-----GGA--------------ATTGGCTGAAAGGATACCTTTGGACAGGCCT------- +----------------------------------------------------GAGTAATG +ACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +------------------------AA--------------GCTTGTGTAATTGTTAATTT +C---TCTG--------------TCCCACTCCATCCAGGTCGTGTGATTCCAAC------- +----------------------------------------------------TCTGTTCC +AG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +------------------------AA--------------AATTTCAAA----------- +-------------------------------AATTGGGCCTGAAAATCCATAC------- +----------------------------------------------------AATACTCC +AGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +------------------------GC--------------CTGCATGGAATGGATGACCC +GGAGAGAG--------------AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT------- +----------------------------------------------------AGCAATTC +A------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +------------------------GTA-------------CTTTCTATAGTGAATAGAGT +TAGGCAGG--------------TATATTCACCATTATCGTTTGAGACCCACCT------- +----------------------------------------------------CCCAACCC +-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------------------------------------------GGT----------- +-------------------------------GATATGGGCTGATGTACCATTT------- +----------------------------------------------------GCCCCTGG +ATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +------------------------ATAGAG----------CTTCCTTTAGTTGCCCCCCT +ATCTTTAT--------------TGTGACGAGGGGACGTTGCCAAAGAGTGACC------- +----------------------------------------------------TG------ +--------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +------------------------------------------------------------ +TTTTTCAG--------------TTCGCTTAGATGAAGACTTCAGGCAGTATAC------- +----------------------------------------------------TGCATTTA +CCATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +-----------------ATAACCACAGAA-----------------AGCATAGTAATATG +G------------------------------GGAAAGACTCCTAAATTTAAACT------ +---------------------------------------------------GCCCATACA +AAA---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +--------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAAAAGTAGT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +--------------------------GGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAACAGTAGTG----------------- +------------------------------------------------------------ +-------------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +-----------------------------------------TTTTATGGTTCATAATCCA +CTCCATGT--------------ACTGGTTCTTTTAGAATCTCTCATTTTTCT-------- +---------------------------------------------------GCCCGTTCT +AGCT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTCTAAAATA +ACCAGTAC--------------ATGGAGTGTATTATGACC-------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------CTCTAGTGTCCA +TTCATTGT--------------GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGG------ +---------------------------------------------------GCTTGTTCC +ATCTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +-----------------------------------------------------TGATTTG +TTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCTCTATTAG +TAACATAT--------------CCTGCTTTTCCTA------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +---------------------------GAA----------GTCTTGAGTTCTCTTATTAA +--------------------------GTTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------TTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +--------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACATAATAGCA +ACAGACAT--------------ACAAACTAAAGAATTACAA------------------- +------------------------------------------------------------ +-----------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAAGGTGTTTTACTAAACTTTTCCA------ +---------------------------------------------------TGTTGTAAT +CCTCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +-----------------------------------------CAGGATTAACTGCGAATCT +T---TCTAG------------CTCCCTTGTTGCCCATACTATATGTTTTAATT------- +----------------------------------------------------TATATTTT +TT--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/final.noBadSeq.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG---------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT---------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT---------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT---------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG--------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA--------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------------ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------------ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------------ +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG--------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------------ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------------ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +-------------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT----- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +-------------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +-------------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +-------------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +-------------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +-------------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------------ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------------ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------------ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------------ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------------ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------------ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------------ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------------ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +-------------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +--------------------------------------------------TTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +ACACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +----------------------------------------GTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------------------------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAA----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +------------------------TGT-------------AACACCTCAGTCATTA---- +--CACAGG--------------CCTGTCCAAAGGTATCCTTTGAGCCAATTCC------- +----------------------------------------------------CATACATT +ATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +------------------------ATG-------------TATG---------------- +-----GGA--------------ATTGGCTGAAAGGATACCTTTGGACAGGCCT------- +----------------------------------------------------GAGTAATG +ACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +------------------------AA--------------GCTTGTGTAATTGTTAATTT +C---TCTG--------------TCCCACTCCATCCAGGTCGTGTGATTCCAAC------- +----------------------------------------------------TCTGTTCC +AG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +------------------------AA--------------AATTTCAAA----------- +-------------------------------AATTGGGCCTGAAAATCCATAC------- +----------------------------------------------------AATACTCC +AGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +------------------------GC--------------CTGCATGGAATGGATGACCC +GGAGAGAG--------------AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT------- +----------------------------------------------------AGCAATTC +A------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +------------------------GTA-------------CTTTCTATAGTGAATAGAGT +TAGGCAGG--------------TATATTCACCATTATCGTTTGAGACCCACCT------- +----------------------------------------------------CCCAACCC +-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------------------------------------------GGT----------- +-------------------------------GATATGGGCTGATGTACCATTT------- +----------------------------------------------------GCCCCTGG +ATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +------------------------ATAGAG----------CTTCCTTTAGTTGCCCCCCT +ATCTTTAT--------------TGTGACGAGGGGACGTTGCCAAAGAGTGACC------- +----------------------------------------------------TG------ +--------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +------------------------------------------------------------ +TTTTTCAG--------------TTCGCTTAGATGAAGACTTCAGGCAGTATAC------- +----------------------------------------------------TGCATTTA +CCATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +-----------------ATAACCACAGAA-----------------AGCATAGTAATATG +G------------------------------GGAAAGACTCCTAAATTTAAACT------ +---------------------------------------------------GCCCATACA +AAA---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +--------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAAAAGTAGT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +--------------------------GGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAACAGTAGTG----------------- +------------------------------------------------------------ +-------------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +-----------------------------------------TTTTATGGTTCATAATCCA +CTCCATGT--------------ACTGGTTCTTTTAGAATCTCTCATTTTTCT-------- +---------------------------------------------------GCCCGTTCT +AGCT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTCTAAAATA +ACCAGTAC--------------ATGGAGTGTATTATGACC-------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------CTCTAGTGTCCA +TTCATTGT--------------GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGG------ +---------------------------------------------------GCTTGTTCC +ATCTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +-----------------------------------------------------TGATTTG +TTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCTCTATTAG +TAACATAT--------------CCTGCTTTTCCTA------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +---------------------------GAA----------GTCTTGAGTTCTCTTATTAA +--------------------------GTTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------TTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +--------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACATAATAGCA +ACAGACAT--------------ACAAACTAAAGAATTACAA------------------- +------------------------------------------------------------ +-----------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAAGGTGTTTTACTAAACTTTTCCA------ +---------------------------------------------------TGTTGTAAT +CCTCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +-----------------------------------------CAGGATTAACTGCGAATCT +T---TCTAG------------CTCCCTTGTTGCCCATACTATATGTTTTAATT------- +----------------------------------------------------TATATTTT +TT--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/final.noOrphans.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG---------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT---------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT---------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT---------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG--------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA--------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------------ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------------ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------------ +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG--------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------------ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------------ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +-------------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT----- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +-------------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +-------------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +-------------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +-------------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +-------------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------------ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------------ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------------ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------------ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------------ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------------ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------------ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------------ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +-------------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +--------------------------------------------------TTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +ACACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +----------------------------------------GTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------------------------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAA----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +------------------------TGT-------------AACACCTCAGTCATTA---- +--CACAGG--------------CCTGTCCAAAGGTATCCTTTGAGCCAATTCC------- +----------------------------------------------------CATACATT +ATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +------------------------ATG-------------TATG---------------- +-----GGA--------------ATTGGCTGAAAGGATACCTTTGGACAGGCCT------- +----------------------------------------------------GAGTAATG +ACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +------------------------AA--------------GCTTGTGTAATTGTTAATTT +C---TCTG--------------TCCCACTCCATCCAGGTCGTGTGATTCCAAC------- +----------------------------------------------------TCTGTTCC +AG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +------------------------AA--------------AATTTCAAA----------- +-------------------------------AATTGGGCCTGAAAATCCATAC------- +----------------------------------------------------AATACTCC +AGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +------------------------GC--------------CTGCATGGAATGGATGACCC +GGAGAGAG--------------AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT------- +----------------------------------------------------AGCAATTC +A------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +------------------------GTA-------------CTTTCTATAGTGAATAGAGT +TAGGCAGG--------------TATATTCACCATTATCGTTTGAGACCCACCT------- +----------------------------------------------------CCCAACCC +-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------------------------------------------GGT----------- +-------------------------------GATATGGGCTGATGTACCATTT------- +----------------------------------------------------GCCCCTGG +ATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +------------------------ATAGAG----------CTTCCTTTAGTTGCCCCCCT +ATCTTTAT--------------TGTGACGAGGGGACGTTGCCAAAGAGTGACC------- +----------------------------------------------------TG------ +--------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +------------------------------------------------------------ +TTTTTCAG--------------TTCGCTTAGATGAAGACTTCAGGCAGTATAC------- +----------------------------------------------------TGCATTTA +CCATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +-----------------ATAACCACAGAA-----------------AGCATAGTAATATG +G------------------------------GGAAAGACTCCTAAATTTAAACT------ +---------------------------------------------------GCCCATACA +AAA---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +--------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAAAAGTAGT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +--------------------------GGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAACAGTAGTG----------------- +------------------------------------------------------------ +-------------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +-----------------------------------------TTTTATGGTTCATAATCCA +CTCCATGT--------------ACTGGTTCTTTTAGAATCTCTCATTTTTCT-------- +---------------------------------------------------GCCCGTTCT +AGCT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTCTAAAATA +ACCAGTAC--------------ATGGAGTGTATTATGACC-------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------CTCTAGTGTCCA +TTCATTGT--------------GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGG------ +---------------------------------------------------GCTTGTTCC +ATCTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +-----------------------------------------------------TGATTTG +TTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCTCTATTAG +TAACATAT--------------CCTGCTTTTCCTA------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +---------------------------GAA----------GTCTTGAGTTCTCTTATTAA +--------------------------GTTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------TTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +--------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACATAATAGCA +ACAGACAT--------------ACAAACTAAAGAATTACAA------------------- +------------------------------------------------------------ +-----------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAAGGTGTTTTACTAAACTTTTCCA------ +---------------------------------------------------TGTTGTAAT +CCTCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +-----------------------------------------CAGGATTAACTGCGAATCT +T---TCTAG------------CTCCCTTGTTGCCCATACTATATGTTTTAATT------- +----------------------------------------------------TATATTTT +TT--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/grp Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,252 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCA +ATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACAT +CAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAA +TTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGG +GGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCT +GGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCT +CTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAGCAG +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCC +CGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/grp.clstr Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,184 @@ +>Cluster 0 +0 70nt, >K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1... * +>Cluster 1 +0 70nt, >K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1... * +1 70nt, >K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1... at +/84.29% +>Cluster 2 +0 70nt, >K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1... * +1 70nt, >K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1... at -/94.29% +2 70nt, >K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1... at -/91.43% +>Cluster 3 +0 70nt, >K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1... * +>Cluster 4 +0 70nt, >K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1... * +1 70nt, >K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1... at +/88.57% +>Cluster 5 +0 70nt, >K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1... * +>Cluster 6 +0 70nt, >K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1... * +>Cluster 7 +0 70nt, >K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1... * +>Cluster 8 +0 70nt, >K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1... * +1 70nt, >K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1... at -/91.43% +>Cluster 9 +0 70nt, >K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1... * +>Cluster 10 +0 70nt, >K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1... * +1 70nt, >K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1... at +/82.86% +>Cluster 11 +0 70nt, >K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1... * +1 70nt, >K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1... at -/85.71% +>Cluster 12 +0 70nt, >K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1... * +>Cluster 13 +0 70nt, >K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1... * +>Cluster 14 +0 70nt, >K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1... * +>Cluster 15 +0 70nt, >K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1... * +>Cluster 16 +0 70nt, >K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1... * +1 70nt, >K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1... at +/95.71% +>Cluster 17 +0 70nt, >K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1... * +>Cluster 18 +0 70nt, >K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1... * +>Cluster 19 +0 70nt, >K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1... * +>Cluster 20 +0 70nt, >K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1... * +1 70nt, >K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1... at +/88.57% +>Cluster 21 +0 70nt, >K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1... * +>Cluster 22 +0 70nt, >K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1... * +>Cluster 23 +0 70nt, >K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1... * +>Cluster 24 +0 70nt, >K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1... * +>Cluster 25 +0 70nt, >K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1... * +>Cluster 26 +0 70nt, >K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1... * +>Cluster 27 +0 70nt, >K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1... * +>Cluster 28 +0 70nt, >K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1... * +>Cluster 29 +0 70nt, >K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1... * +1 70nt, >K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1... at -/90.00% +>Cluster 30 +0 70nt, >K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1... * +>Cluster 31 +0 70nt, >K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1... * +>Cluster 32 +0 70nt, >K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1... * +>Cluster 33 +0 70nt, >K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1... * +>Cluster 34 +0 70nt, >K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1... * +>Cluster 35 +0 70nt, >K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1... * +>Cluster 36 +0 70nt, >K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1... * +>Cluster 37 +0 70nt, >K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1... * +>Cluster 38 +0 70nt, >K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1... * +1 70nt, >K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1... at +/87.14% +>Cluster 39 +0 70nt, >K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1... * +1 70nt, >K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1... at -/88.57% +>Cluster 40 +0 70nt, >K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1... * +1 70nt, >K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1... at -/87.14% +>Cluster 41 +0 70nt, >K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1... * +>Cluster 42 +0 70nt, >K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1... * +>Cluster 43 +0 70nt, >K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1... * +>Cluster 44 +0 70nt, >K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1... * +>Cluster 45 +0 70nt, >K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1... * +>Cluster 46 +0 70nt, >K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1... * +>Cluster 47 +0 70nt, >K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1... * +>Cluster 48 +0 70nt, >K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1... * +>Cluster 49 +0 70nt, >K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1... * +>Cluster 50 +0 70nt, >K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1... * +>Cluster 51 +0 70nt, >K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1... * +1 70nt, >K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1... at +/90.00% +>Cluster 52 +0 70nt, >K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1... * +>Cluster 53 +0 70nt, >K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1... * +>Cluster 54 +0 70nt, >K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1... * +>Cluster 55 +0 70nt, >K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1... * +>Cluster 56 +0 70nt, >K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1... * +>Cluster 57 +0 70nt, >K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1... * +>Cluster 58 +0 70nt, >K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1... * +>Cluster 59 +0 70nt, >K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1... * +>Cluster 60 +0 70nt, >K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1... * +>Cluster 61 +0 70nt, >K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1... * +>Cluster 62 +0 70nt, >K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1... * +>Cluster 63 +0 70nt, >K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1... * +>Cluster 64 +0 70nt, >K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1... * +1 70nt, >K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1... at +/84.29% +>Cluster 65 +0 70nt, >K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1... * +>Cluster 66 +0 70nt, >K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1... * +>Cluster 67 +0 70nt, >K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1... * +>Cluster 68 +0 70nt, >K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1... * +>Cluster 69 +0 70nt, >K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1... * +1 70nt, >K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1... at -/81.43% +>Cluster 70 +0 70nt, >K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1... * +>Cluster 71 +0 70nt, >K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1... * +>Cluster 72 +0 70nt, >K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1... * +>Cluster 73 +0 70nt, >K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1... * +>Cluster 74 +0 70nt, >K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1... * +>Cluster 75 +0 70nt, >K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1... * +>Cluster 76 +0 70nt, >K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1... * +>Cluster 77 +0 70nt, >K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1... * +>Cluster 78 +0 70nt, >K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1... * +>Cluster 79 +0 70nt, >K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1... * +>Cluster 80 +0 70nt, >K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1... * +>Cluster 81 +0 70nt, >K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1... * +>Cluster 82 +0 70nt, >K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1... * +>Cluster 83 +0 70nt, >K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1... *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.0 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.0.aln.temp +# output HMM file: long.0.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.0.aln 2 72 70 160 2.00 0.745 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.1 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.1.aln.temp +# output HMM file: long.1.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.1.aln 2 79 79 173 2.00 0.656 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.10 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.10.aln.temp +# output HMM file: long.10.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.10.aln 2 80 80 174 2.00 0.637 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.11 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.11.aln.temp +# output HMM file: long.11.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.11.aln 2 84 84 179 2.00 0.444 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.12 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.12.aln.temp +# output HMM file: long.12.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.12.aln 2 72 70 160 2.00 0.708 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.06
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.13 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.13.aln.temp +# output HMM file: long.13.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.13.aln 2 72 70 160 2.00 0.707 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.14 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.14.aln.temp +# output HMM file: long.14.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.14.aln 2 72 70 160 2.00 0.704 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.16
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.15 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.15.aln.temp +# output HMM file: long.15.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.15.aln 2 72 70 160 2.00 0.720 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.16 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.16.aln.temp +# output HMM file: long.16.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.16.aln 2 71 70 160 2.00 0.709 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.17 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.17.aln.temp +# output HMM file: long.17.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.17.aln 2 72 70 160 2.00 0.780 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.18 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.18.aln.temp +# output HMM file: long.18.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.18.aln 2 72 70 160 2.00 0.736 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.19 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.19.aln.temp +# output HMM file: long.19.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.19.aln 2 72 70 160 2.00 0.732 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.2 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.2.aln.temp +# output HMM file: long.2.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.2.aln 3 83 70 188 3.00 0.614 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.20 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.20.aln.temp +# output HMM file: long.20.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.20.aln 2 76 76 168 2.00 0.702 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.21 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.21.aln.temp +# output HMM file: long.21.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.21.aln 2 72 70 160 2.00 0.766 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.22 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.22.aln.temp +# output HMM file: long.22.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.22.aln 2 72 70 160 2.00 0.735 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.23 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.23.aln.temp +# output HMM file: long.23.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.23.aln 2 72 70 160 2.00 0.750 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.24 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.24.aln.temp +# output HMM file: long.24.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.24.aln 2 72 70 160 2.00 0.782 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.25 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.25.aln.temp +# output HMM file: long.25.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.25.aln 2 72 70 160 2.00 0.727 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.26 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.26.aln.temp +# output HMM file: long.26.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.26.aln 2 72 70 160 2.00 0.738 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.27 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.27.aln.temp +# output HMM file: long.27.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.27.aln 2 72 70 160 2.00 0.716 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.28 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.28.aln.temp +# output HMM file: long.28.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.28.aln 2 72 70 160 2.00 0.767 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.29 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.29.aln.temp +# output HMM file: long.29.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.29.aln 2 82 82 176 2.00 0.404 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.3 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.3.aln.temp +# output HMM file: long.3.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.3.aln 2 72 70 160 2.00 0.720 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.30 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.30.aln.temp +# output HMM file: long.30.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.30.aln 2 72 70 160 2.00 0.759 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.31 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.31.aln.temp +# output HMM file: long.31.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.31.aln 2 72 70 160 2.00 0.711 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.32 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.32.aln.temp +# output HMM file: long.32.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.32.aln 2 72 70 160 2.00 0.714 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.04
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.33 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.33.aln.temp +# output HMM file: long.33.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.33.aln 2 72 70 160 2.00 0.723 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.34 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.34.aln.temp +# output HMM file: long.34.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.34.aln 2 72 70 160 2.00 0.720 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.06
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.35 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.35.aln.temp +# output HMM file: long.35.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.35.aln 2 72 70 160 2.00 0.757 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.36 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.36.aln.temp +# output HMM file: long.36.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.36.aln 2 72 70 160 2.00 0.712 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.04
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.37 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.37.aln.temp +# output HMM file: long.37.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.37.aln 2 72 70 160 2.00 0.723 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.38 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.38.aln.temp +# output HMM file: long.38.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.38.aln 2 74 74 165 2.00 0.662 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.39 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.39.aln.temp +# output HMM file: long.39.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.39.aln 2 99 99 200 2.00 0.366 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.4 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.4.aln.temp +# output HMM file: long.4.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.4.aln 2 75 75 167 2.00 0.662 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.14
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.40 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.40.aln.temp +# output HMM file: long.40.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.40.aln 2 85 85 180 2.00 0.380 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.41 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.41.aln.temp +# output HMM file: long.41.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.41.aln 2 72 70 160 2.00 0.788 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.42 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.42.aln.temp +# output HMM file: long.42.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.42.aln 2 72 70 160 2.00 0.738 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.43 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.43.aln.temp +# output HMM file: long.43.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.43.aln 2 72 70 160 2.00 0.766 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.44 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.44.aln.temp +# output HMM file: long.44.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.44.aln 2 72 70 160 2.00 0.753 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.45 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.45.aln.temp +# output HMM file: long.45.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.45.aln 2 72 70 160 2.00 0.756 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.46 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.46.aln.temp +# output HMM file: long.46.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.46.aln 2 72 70 160 2.00 0.743 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.47 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.47.aln.temp +# output HMM file: long.47.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.47.aln 2 72 70 160 2.00 0.774 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.48 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.48.aln.temp +# output HMM file: long.48.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.48.aln 2 72 70 160 2.00 0.734 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.49 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.49.aln.temp +# output HMM file: long.49.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.49.aln 2 72 70 160 2.00 0.770 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.5 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.5.aln.temp +# output HMM file: long.5.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.5.aln 2 72 70 160 2.00 0.734 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.04
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.50 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.50.aln.temp +# output HMM file: long.50.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.50.aln 2 72 70 160 2.00 0.751 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.51 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.51.aln.temp +# output HMM file: long.51.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.51.aln 2 76 76 168 2.00 0.693 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.52 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.52.aln.temp +# output HMM file: long.52.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.52.aln 2 72 70 160 2.00 0.746 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.53 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.53.aln.temp +# output HMM file: long.53.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.53.aln 2 72 70 160 2.00 0.758 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.54 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.54.aln.temp +# output HMM file: long.54.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.54.aln 2 72 70 160 2.00 0.758 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.55 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.55.aln.temp +# output HMM file: long.55.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.55.aln 2 72 70 160 2.00 0.736 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.56 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.56.aln.temp +# output HMM file: long.56.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.56.aln 2 72 70 160 2.00 0.722 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.57 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.57.aln.temp +# output HMM file: long.57.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.57.aln 2 72 70 160 2.00 0.719 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.58 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.58.aln.temp +# output HMM file: long.58.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.58.aln 2 72 70 160 2.00 0.747 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.59 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.59.aln.temp +# output HMM file: long.59.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.59.aln 2 72 70 160 2.00 0.736 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.06
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.6 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.6.aln.temp +# output HMM file: long.6.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.6.aln 2 72 70 160 2.00 0.707 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.60 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.60.aln.temp +# output HMM file: long.60.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.60.aln 2 72 70 160 2.00 0.761 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.06
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.61 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.61.aln.temp +# output HMM file: long.61.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.61.aln 2 72 70 160 2.00 0.766 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.08
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.62 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.62.aln.temp +# output HMM file: long.62.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.62.aln 2 72 70 160 2.00 0.749 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.63 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.63.aln.temp +# output HMM file: long.63.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.63.aln 2 72 70 160 2.00 0.748 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.06
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.64 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.64.aln.temp +# output HMM file: long.64.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.64.aln 2 80 80 174 2.00 0.649 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.07
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.65 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.65.aln.temp +# output HMM file: long.65.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.65.aln 2 72 70 160 2.00 0.775 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.66 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.66.aln.temp +# output HMM file: long.66.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.66.aln 2 72 70 160 2.00 0.707 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.67 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.67.aln.temp +# output HMM file: long.67.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.67.aln 2 72 70 160 2.00 0.751 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.68 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.68.aln.temp +# output HMM file: long.68.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.68.aln 2 72 70 160 2.00 0.734 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.69 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.69.aln.temp +# output HMM file: long.69.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.69.aln 2 95 95 195 2.00 0.357 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.18
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.7 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.7.aln.temp +# output HMM file: long.7.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.7.aln 2 72 70 160 2.00 0.743 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.70 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.70.aln.temp +# output HMM file: long.70.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.70.aln 2 72 70 160 2.00 0.697 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.71 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.71.aln.temp +# output HMM file: long.71.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.71.aln 2 72 70 160 2.00 0.771 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.72 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.72.aln.temp +# output HMM file: long.72.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.72.aln 2 72 70 160 2.00 0.729 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.15
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.73 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.73.aln.temp +# output HMM file: long.73.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.73.aln 2 72 70 160 2.00 0.747 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.22
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.74 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.74.aln.temp +# output HMM file: long.74.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.74.aln 2 72 70 160 2.00 0.703 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.23
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.75 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.75.aln.temp +# output HMM file: long.75.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.75.aln 2 72 70 160 2.00 0.722 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.17
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.76 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.76.aln.temp +# output HMM file: long.76.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.76.aln 2 72 70 160 2.00 0.707 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.77 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.77.aln.temp +# output HMM file: long.77.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.77.aln 2 72 70 160 2.00 0.770 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.18
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.78 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.78.aln.temp +# output HMM file: long.78.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.78.aln 2 72 70 160 2.00 0.717 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.79 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.79.aln.temp +# output HMM file: long.79.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.79.aln 2 72 70 160 2.00 0.724 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.17
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.8 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.8.aln.temp +# output HMM file: long.8.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.8.aln 2 72 72 163 2.00 0.376 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.80 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.80.aln.temp +# output HMM file: long.80.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.80.aln 2 72 70 160 2.00 0.742 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.14
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.81 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.81.aln.temp +# output HMM file: long.81.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.81.aln 2 72 70 160 2.00 0.767 + +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.82 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.82.aln.temp +# output HMM file: long.82.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.82.aln 2 72 70 160 2.00 0.742 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.83 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.83.aln.temp +# output HMM file: long.83.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.83.aln 2 72 70 160 2.00 0.745 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.14
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/hmmer.log.9 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,16 @@ +# hmmbuild :: profile HMM construction from multiple sequence alignments +# HMMER 3.2.1 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# input alignment file: long.9.aln.temp +# output HMM file: long.9.hmm +# input alignment is asserted as: DNA +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +# idx name nseq alen mlen W eff_nseq re/pos description +#---- -------------------- ----- ----- ----- ----- -------- ------ ----------- +1 long.9.aln 2 72 70 160 2.00 0.720 + +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.dealign.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,200 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCAATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATTTACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCTTCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATAATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTCTAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTGTA +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTATATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGCCATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCTGAGGATTGGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATC +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCACCTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTATAAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTATTACAT +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAATGTCTAACAGC +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACAT +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAATTAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCTGCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGAAGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCCATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACATATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGATTAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAATCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTCAAATTAGCAG +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTCTGTCTCTCTC +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAAGAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTACTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGA +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATC +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACCTAGCAATTCA +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCG +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAGAGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACATCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAACAGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACATCATTAGTGT +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTA +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTTGATCTGAGGA +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCTGAGGATTGCT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGC +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAACTTGTC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCGACAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTCCCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAGTGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCATATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTGAAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACTATAGCCCTGG +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTGTATTATGACC +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATAATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTCTGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATCTCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTG +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTATTTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,200 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCAATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATTTACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCTTCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATAATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTCTAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTGTA +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTATATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGCCATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCTGAGGATTGGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATC +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCACCTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTATAAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTATTACAT +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAATGTCTAACAGC +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACAT +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAATTAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCTGCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGAAGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCCATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACATATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGATTAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAATCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTCAAATTAGCAG +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTCTGTCTCTCTC +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAAGAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTACTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGA +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATC +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACCTAGCAATTCA +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCG +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAGAGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACATCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAACAGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACATCATTAGTGT +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTA +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTTGATCTGAGGA +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCTGAGGATTGCT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGC +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAACTTGTC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCGACAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTCCCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAGTGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCATATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTGAAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACTATAGCCCTGG +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTGTATTATGACC +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATAATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTCTGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATCTCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTG +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTATTTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.1.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,552 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG----------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT----------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT----------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT----------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT-------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG---------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA---- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------- +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------- +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------- +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------- +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------- +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG-------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG---------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA------------------------------ +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +--------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +--------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +--------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +--------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +--------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT------------------------------ +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +--------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +--------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +---------------------------------------------------------TTA +TCAGAAGG------------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAC +ACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +-----------------------------------------------GTTTTCAGCATTA +TCAGAAGG------------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAA +ACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +-------------------------------CAGAAGTGATACCCATGTTTTCAGCATTA +TCAGAAGG------------------AGCCACCCCACAAGATTTAAAC--ACCATGCTAA +A----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +-------------------------------TGT-------------AACACCTCAGTCA +TTA------CACAGG--CCTGTCCAAAGGTATCCTTTGAGCCAATTCC--CATACATTAT +TGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +-------------------------------ATG-------------TATG--------- +------------GGA--ATTGGCTGAAAGGATACCTTTGGACAGGCCT--GAGTAATGAC +TGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +-------------------------------AA--------------GCTTGTGTAATTG +TTAATTTC---TCTG--TCCCACTCCATCCAGGTCGTGTGATTCCAAC--TCTGTTCCAG +--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +-------------------------------AA--------------AATTTCAAA---- +--------------------------AATTGGGCCTGAAAATCCATAC--AATACTCCAG +TATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +-------------------------------GC--------------CTGCATGGAATGG +ATGACCCGGAGAGAG--AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT--AGCAATTCA- +------------------------------------ +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +-------------------------------GTA-------------CTTTCTATAGTGA +ATAGAGTTAGGCAGG--TATATTCACCATTATCGTTTGAGACCCACCT--CCCAACCC-- +------------------------------------ +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +-----------------------------------------------------GGT---- +--------------------------GATATGGGCTGATGTACCATTT--GCCCCTGGAT +GTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +-------------------------------ATAGAG----------CTTCCTTTAGTTG +CCCCCCTATCTTTAT--TGTGACGAGGGGACGTTGCCAAAGAGTGACC--TG-------- +------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +-------TTTTTCAG--TTCGCTTAGATGAAGACTTCAGGCAGTATAC--TGCATTTACC +ATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------ATAACCACAGAA-----------------AGCATAG +TAATATGG------------------GGAAAGACTCCTAAATTTAAACTGCCCATACAAA +A---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +---------------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCA +GTAGTAATACAAGAT--AATAGTGACATAAAAGTAGT----------------------- +------------------------------------ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +---------------------------------GGAA----------AGGTGAAGGGGCA +GTAGTAATACAAGAT--AATAGTGACATAACAGTAGTG---------------------- +-----------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------TTTTATGGTTCA +TAATCCACTCCATGT--ACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAG +CT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTC +TAAAATAACCAGTAC--ATGGAGTGTATTATGACC------------------------- +------------------------------------ +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +-------------------------------------------------------CTCTA +GTGTCCATTCATTGT--GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCAT +CTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCT +CTATTAGTAACATAT--CCTGCTTTTCCTA------------------------------ +------------------------------------ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAA----------GTCTTGAGTTCTC +TTATTAA--------------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGT +CTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------------------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGT +CTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACAT +AATAGCAACAGACAT--ACAAACTAAAGAATTACAA------------------------ +---------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCC +TCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------CAGGATTAACTG +CGAATCTT---TCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATT--TATATTTTTT +--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.10.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT----- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC-------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC------------------------ +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTCTTTATGGCAAATACTGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.11.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAA- +----------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +-----------------------------TGCCAAGGATCCGTTCACTAATCGAATGGAT +CTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAG-----AAAAAAT +CAGT-AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATG------TTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACT +CAGTCTTCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.12.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------GGCTAATTCACTCCCAACGAAGACAAGAT +ATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT-- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +--AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAA +TTCCTTTGTGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.13.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAG-------------------------AG +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAA-------------------------AATTGGGCCTGAAAATCCATACAA +TACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC-CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCAC +CTAGCAATTCA +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.14.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,12 @@ +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----T +TGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTC +TGTCTCT------------CTC +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA----- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGG +AAAATGTCTAACAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.2.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,152 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +---------------------------CTACCTCTTCTTCTGCTAGACTGCC-------A +TTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +-------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCA-------G +TCTAGCAGAAGAAGAGGTAGTAAT-------TAGATC------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAAC---AAGC +CCCAGAAGACGAAGGG---------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----- +-TTGGCACTTATCTGGGA-------------CGATCT------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGA--C +TCTGTCTCT-------------------------CTC------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA-----TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATC +CTAGGAAAATGTCTA----------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA-----TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATC +CTAGGAAAATGTCTAAC-----------------AGC------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC-----TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAAGGCCATATC +TTCCCTAAAAAATTAGC-----------------CTGTCT---- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA------------------GCAATCTGATTCACCCGATTTCTTCC-------A +ATTATGATGACAGGTGTAGGTCCTACTAATACAGT--------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +----------------------------GGTTTTATAGACATCACTATGAAAGCCCTCAT +CCAAGAAAAAGTTCAGAAGTACACA------------------TCCCACTAGG------- +-- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +-------------------------------TTTATCAAGAGCCATTTAAAAATCTGAAA +ACAGGAAAATATGCAAGAATGAGGGG--------------TGCCCACACTAAT------- +-- +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT---------ATTATGGGGTACC----TGTGTGGC---- +-----AGGAAGCAACCACCACTCTATT-----------------------TTGTGCATC- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG---------ACAGAGGAGAGCA----AGAAATGT---- +-----AGCCAGTAGATCCTAGACTAT-------------------------AGCCCTGG- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +--------------------------------------GGAGCT----AGAACGAT---- +-----TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGG +A----------------------------------------------------------- +-- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT---------GTACCCCAGACCT----GAAGCTCTCTTC +TTGTGGGGCTGTTGGCTCTGGTCTGCT--------------------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT---------CTAGCCCAGACCT----GAAGCTCTCTTC +TGGTGGGGCAGTTGGCTCTGGTC------------------------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A-------------------------------------GGGATTATGGAAAACAGA---- +-----TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG---- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC----------------------------ACT-------- +ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAG--TTAGC +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +-CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAG--TTAGC +CAGA----------------------------------------GAGCTCCCA------- +-- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +---------------------------------------------------------TGC +TGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATT-------------------------------------------GACCAC------- +-- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC----------------------------ACCCTATCTTG +TGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAGGCCATCCAATCA------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGA +TAAA--------------------------------------CAGCAGTTGTT------- +-- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +--------------------------------TGCCAAGGATCCGTTCACTAA--TCGAA +TGGA---------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT------- +-- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +TTCTGGGAAGTTCAAT----------------TAGGAATACCACATCCCGCAGGGTTAAA +AAAG---------AAAAAATCAGT------------------AACAGTACTGG------- +-- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +CTATG------TTTAC----------------TTCTAATCCCGAATCCTGCAAAGCTAGA +TAAAT----TGCTTGTAACTCAGTC-----------------TTCTGATTTGT------- +-- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TCCCAAAGAAGACAAG----ATATCCTTGATC---------------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC +TGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA---------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------------------------GGCTAATTCAC +TCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGTACCACCCACAAG------- +-------------------------------------------GCTACTTCCC------- +-- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------------------------ACAACGGAATTGG---AGGAAATGAAC +CAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGTACTATTTTT---------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------------------------AATAGTACTTT---CCTGATTCCAG +CACTGACTAAATTATC----TACTTGTTCATTTCCTCCAATTCCTTTGTGTG-------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +-----------------------------GAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAAATCAG-------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAGGAAGAAGCGGAGACAGC---GACGAAGAGCT +CATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA----------------------- +------------------------------------------------------------ +-- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +-----------------------------------------ACAGC---GACGAAGAGCT +CATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAAAGCAGTAAGTA-------- +--------------------------------------------TTACAT---------- +-- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +-------------------------------------AGCCATTGCTCTCCAA--TTACT +GTGA---------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTCCATCTAAAA +AT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.3.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,92 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +---------------------------------TTATCAGAAGG---------------- +AGCCACCCCACAAGATTTAAAC--ACCATGCTACACCC-------AGTGGGGGGACATCA +AGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +-----------------------GTTTTCAGCATTATCAGAAGG---------------- +AGCCACCCCACAAGATTTAAAC--ACCATGCTAAACAC-------AGTGGGGGGACAT-- +---------- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +-------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGG---------------- +AGCCACCCCACAAGATTTAAAC--ACCATGCTAAA------------------------- +---------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +-------TGT-------------AACACCTCAGTCATTA------CACAGGCCTGTCCAA +AGGTATCCTTTGAGCCAATTCC--CATACATTATTGTG---------------------- +---------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +-------ATG-------------TATG---------------------GGAATTGGCTGA +AAGGATACCTTTGGACAGGCCT--GAGTAATGACTGAGGTGTTACAA---------CTTG +TC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +-------AA--------------GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCC +ATCCAGGTCGTGTGATTCCAAC--TCTGTTCCAG-------------------------- +AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +-------AA--------------AATTTCAAA---------------------------- +AATTGGGCCTGAAAATCCATAC--AATACTCCAGTATT-TGCCATAAAGAAAAAAGACAG +TA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +-------GC--------------CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAG +AGTGGAGGTTTGAGAGCCACCT--AGCAATTCA--------------------------- +---------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +-------GTA-------------CTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCAC +CATTATCGTTTGAGACCCACCT--CCCAACCC---------------------------- +---------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +-----------------------------GGT---------------------------- +GATATGGGCTGATGTACCATTT--GCCCCTGGATGTTC-TGCACTATAGGGTAATTTTGG +CTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +-------ATAGAG----------CTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAG +GGGACGTTGCCAAAGAGTGACC--TG--------------------------AGG----- +---------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +-------------------------------------------TTTTTCAGTTCGCTTAG +ATGAAGACTTCAGGCAGTATAC--TGCATTTACCATACCTAGTATAAACAATGAG----- +---------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAA-----------------AGCATAGTAATATGG---------------- +GGAAAGACTCCTAAATTTAAACTGCCCATACAAAA---------------GGAAACAT-- +---------- +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +---------------GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATAC +AAGATAATAGTGACATAAAAGTAGT----------------------------------- +---------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +---------------------------------GGAAAGGTGAAGGGGCAGTAGTAATAC +AAGATAATAGTGACATAACAGTAGTG---------------------------------- +-----CGAAGAAGAAAAGCAAA +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT---------- +---------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC------------------------------------- +---------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT----- +---------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------------ +---------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAAGTCTTGAGTTCTCTTATTAA--- +---------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC---- +---------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTT- +-ATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACA +GACATACAAACTAAAGAATTACAA------------------------------------ +---------------------A +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTC +CTTGCCACACAATCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.4.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,46 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +--------------------------TTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTACACCC-------AGTGGGGGGACATCAAGCAGCCA- +- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +----------------GTTTTCAGCATTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTAAACAC-------AGTGGGGGGACAT----------- +- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGG----------------AGCCACC +CCACAAGATTTAAACACCATGCTAAA---------------------------------- +- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGT-------------AACACCTCAGTCATTA------CACAGGCCTGTCCAAAGGTATC +CTTTGAGCCAATTCCCATACATTATTGTG------------------------------- +- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATG-------------TATG---------------------GGAATTGGCTGAAAGGATA +CCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAA---------CTTGTC------- +- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA--------------GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGG +TCGTGTGATTCCAACTCTGTTCCAG--------------------------AG------- +- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA--------------AATTTCAAA----------------------------AATTGGG +CCTGAAAATCCATACAATACTCCAGTATT-TGCCATAAAGAAAAAAGACAGTA------- +- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC--------------CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAG +GTTTGAGAGCCACCTAGCAATTCA------------------------------------ +- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTA-------------CTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATC +GTTTGAGACCCACCTCCCAACCC------------------------------------- +- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +----------------------GGT----------------------------GATATGG +GCTGATGTACCATTTGCCCCTGGATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGA +T +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTG--------------------------AGG +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +--------------------------TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAG +TATACTGCATTTACCATACCTAGTATAAACAATGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.5.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,38 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT------------------ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAACAGTAGTGCGAAGAAGAAAAGCAAA +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +--------------------------------------TTTTATGGTTCATAATCCACTC +CATGTACTGGTTCTTTTAGAATCTCTCATTTTTCT--GCCCGTTCTAGCT---------- +---------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +-------------GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACC +AGTACATGGAGTGTATTATGACC------------------------------------- +---------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +---------------------------------------------CTCTAGTGTCCATTC +ATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT----- +---------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACT--------TTTTGTGTTCCTCTATTAGTAA +CATATCCTGCTTTTCCTA------------------------------------------ +---------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +----------------------------------GAAGTCTTGAGTTCTCTTATTAA--- +---------GTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC---- +---------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +----------TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTT- +-ATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +---------------GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACA +GACATACAAACTAAAGAATTACAA------------------------------------ +---------------------A +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTC +CTTGCCACACAATCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.6.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,15 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG--TGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCT +ATT-----------------------TTGTGCATC-- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +AT-------------------------AGCCCTGG-- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +---------------------------GGAGCTAGAACGATTCGCAGTTAATCCTGGCGT +GTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTT +GGCTCTGGTCTGCT +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.7.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +-----------------TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGC +CATCCAATCACACTACATATTGACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA----------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAA--CTGGATAA +A----------------------------------CAGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +-----------------------------TGCCAAGGATCCGTTCACTAA--TCGAATGG +A-----TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAAT-------------TAGGAATACCACATCCCGCAGGGTTAAAAAA +G-----AAAAAATCAGT------------------AACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATG------TTTAC-------------TTCTAATCCCGAATCCTGCAAAGCTAGATAA +ATTGCTTGTAACTCAGTC-----------------TTCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.8.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,24 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +-------------------------------GGCTAATTCACTCCCAACGAAGACAAGAT +ATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +---------------ACAACGGAATTGG---AGGAAATGAACCAGTAGATAAATTAGTCA +GTGCTGGAATCAGGAAAGTACTATTTTT------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +-----------------AATAGTACTTT---CCTGATTCCAGCACTGACTAAATTATCTA +CTTGTTCATTTCCTCCAATTCCTTTGTGTG----------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +---------GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTCAATCAAATCAG------------ +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA--------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +---------------------ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCA +AGCTTCTCTATCAAAGCAGTAAGTATTACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/input.merge.9.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,18 @@ +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG--------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATG---------------GGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGT +AATGACTGAGGTGTTACAACTTGTC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AA-GCTTGTGTAATTGTTAATTTC---TCTGTCCCACTCCATCCAGGTCGTGTGATTCCA +ACTCTGTTCCAG-------------------------AG +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AA-AATTTCAAA----------------------------AATTGGGCCTGAAAATCCAT +ACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GC-CTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCAC +CTAGCAATTCA---------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC-----------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.0.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.0.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.0.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.0.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2713552590 +STATS LOCAL MSV -7.8785 0.72075 +STATS LOCAL VITERBI -9.2080 0.72075 +STATS LOCAL FORWARD -3.7706 0.72075 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.11533 1.40204 1.61408 1.48269 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 5 0.28818 2.60848 2.42319 2.42940 5 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 6 2.38910 2.82844 0.25233 2.62837 6 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 7 2.31486 2.12647 2.41211 0.36768 7 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 8 2.38910 2.82844 0.25233 2.62837 8 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 9 0.28818 2.60848 2.42319 2.42940 9 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 10 2.31486 2.12647 2.41211 0.36768 10 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 11 0.28818 2.60848 2.42319 2.42940 11 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 12 2.46232 0.33808 2.58153 2.07174 12 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.1.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +---------GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTCAATCAAATCAG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA---------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.1.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCA +ATCAAATCAG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.1.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,260 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.1.aln +LENG 79 +MAXL 173 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 620049805 +STATS LOCAL MSV -7.9531 0.72095 +STATS LOCAL VITERBI -9.7409 0.72095 +STATS LOCAL FORWARD -3.6444 0.72095 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.15122 1.47367 1.35292 1.62872 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.98342 0.60779 2.04641 1.66785 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.91091 1.78233 1.95844 0.61114 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 0.56139 2.08489 1.86185 1.89791 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.91091 1.78233 1.95844 0.61114 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.10.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +----------TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGT +GGGGGGACATCAAGCAGCCA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGT +GGGGGGACAT----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.10.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACAT +CAAGCAGCCA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGT +GGGGGGACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.10.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,263 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.10.aln +LENG 80 +MAXL 174 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2350604415 +STATS LOCAL MSV -8.1786 0.72142 +STATS LOCAL VITERBI -9.7385 0.72142 +STATS LOCAL FORWARD -3.7323 0.72142 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.19661 1.39017 1.43397 1.55880 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.97267 2.25870 0.46443 2.05625 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.91091 1.78233 1.95844 0.61114 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 1.91091 1.78233 1.95844 0.61114 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.91091 1.78233 1.95844 0.61114 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.11.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +--------------CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGA +TACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAG +TAAT-------TAGATC-------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.11.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAA +TTCCATGTGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAG +TAATTAGATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.11.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,275 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.11.aln +LENG 84 +MAXL 179 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 423631681 +STATS LOCAL MSV -8.6084 0.73180 +STATS LOCAL VITERBI -10.4859 0.73180 +STATS LOCAL FORWARD -2.8117 0.73180 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.35581 1.49833 1.41970 1.28384 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.91091 1.78233 1.95844 0.61114 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.91091 1.78233 1.95844 0.61114 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 0.56139 2.08489 1.86185 1.89791 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.97267 2.25870 0.46443 2.05625 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.12.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.12.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.12.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.12.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1255752143 +STATS LOCAL MSV -8.3243 0.72219 +STATS LOCAL VITERBI -9.3425 0.72219 +STATS LOCAL FORWARD -3.3292 0.72219 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.40795 1.57292 1.70188 1.00628 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.13.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.13.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.13.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.13.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3041144465 +STATS LOCAL MSV -8.3628 0.72226 +STATS LOCAL VITERBI -9.5188 0.72226 +STATS LOCAL FORWARD -3.8436 0.72226 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.60546 1.22177 1.71091 1.12765 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.14.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.14.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.14.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.14.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1031720992 +STATS LOCAL MSV -8.3941 0.72237 +STATS LOCAL VITERBI -9.1821 0.72237 +STATS LOCAL FORWARD -3.5771 0.72237 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44271 1.49503 1.75234 1.00484 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.15.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.15.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.15.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.15.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 503286853 +STATS LOCAL MSV -8.0267 0.72173 +STATS LOCAL VITERBI -9.2116 0.72173 +STATS LOCAL FORWARD -3.7261 0.72173 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.60915 1.17831 1.57427 1.25532 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.16.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCT +GAGGATTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.16.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCT +GAGGATTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.16.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.16.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3834571115 +STATS LOCAL MSV -8.2739 0.72217 +STATS LOCAL VITERBI -9.2034 0.72217 +STATS LOCAL FORWARD -3.3554 0.72217 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.28694 1.39659 1.54629 1.33404 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.17.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.17.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.17.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.17.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3997138551 +STATS LOCAL MSV -8.0960 0.71951 +STATS LOCAL VITERBI -9.1776 0.71951 +STATS LOCAL FORWARD -3.5659 0.71951 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.16459 1.99242 1.12093 1.48895 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.18.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.18.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.18.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.18.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3982440997 +STATS LOCAL MSV -8.2321 0.72111 +STATS LOCAL VITERBI -9.3642 0.72111 +STATS LOCAL FORWARD -3.8226 0.72111 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.52296 1.42201 1.37492 1.24533 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.19.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.19.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.19.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.19.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2532513137 +STATS LOCAL MSV -8.0066 0.72124 +STATS LOCAL VITERBI -9.2158 0.72124 +STATS LOCAL FORWARD -3.4919 0.72124 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.31433 1.38953 1.56917 1.29487 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.2.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TT--------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCATGAGGATATAA-- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +----------GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGA-- +-ACAGATGCATGAGGATATAATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.2.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,9 @@ +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCAT +GAGGATATAA +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGA +GGATATAATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.2.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.2.aln +LENG 70 +MAXL 188 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 3 +EFFN 3.000000 +CKSUM 2903879936 +STATS LOCAL MSV -9.1232 0.72663 +STATS LOCAL VITERBI -9.3215 0.72663 +STATS LOCAL FORWARD -3.0734 0.72663 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.13844 1.68610 1.59008 1.23605 + 1.38629 1.38629 1.38629 1.38629 + 0.22977 3.95124 1.68173 1.46634 0.26236 0.00000 * + 1 0.96677 1.92013 1.91053 1.12362 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04726 3.76874 3.76874 1.46634 0.26236 1.55497 0.23724 + 2 2.36920 2.17182 2.47016 0.34545 2 t - - - + 1.83446 0.84257 1.83446 1.38629 + 0.42541 1.12882 3.76874 2.03997 0.13930 0.54886 0.86182 + 3 1.16410 2.43420 0.71774 2.18679 11 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 + 4 2.00446 2.13960 0.87914 1.10134 12 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.20.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAG +GCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAG +GCGAGGGGCG------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.20.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGG +GGCGGCGACT +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAG +GCGAGGGGCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.20.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,251 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.20.aln +LENG 76 +MAXL 168 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1469264720 +STATS LOCAL MSV -8.1344 0.72015 +STATS LOCAL VITERBI -9.5718 0.72015 +STATS LOCAL FORWARD -3.5802 0.72015 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44381 1.42833 1.04375 1.75948 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.97267 2.25870 0.46443 2.05625 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.97267 2.25870 0.46443 2.05625 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 0.56139 2.08489 1.86185 1.89791 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 0.56139 2.08489 1.86185 1.89791 4 a - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.03279 3.43399 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.21.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.21.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.21.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.21.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3352386187 +STATS LOCAL MSV -7.8693 0.72000 +STATS LOCAL VITERBI -9.1844 0.72000 +STATS LOCAL FORWARD -3.3420 0.72000 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.25619 1.45164 1.27473 1.60162 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.22.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.22.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.22.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.22.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3523423231 +STATS LOCAL MSV -7.9373 0.72115 +STATS LOCAL VITERBI -9.2441 0.72115 +STATS LOCAL FORWARD -3.3918 0.72115 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.22216 1.56504 1.56688 1.24607 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.23.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.23.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.23.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.23.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3211019947 +STATS LOCAL MSV -7.9072 0.72056 +STATS LOCAL VITERBI -9.2220 0.72056 +STATS LOCAL FORWARD -3.4510 0.72056 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.08931 1.43968 1.56997 1.52098 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.24.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.24.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.24.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.24.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4215457382 +STATS LOCAL MSV -7.8763 0.71945 +STATS LOCAL VITERBI -9.4044 0.71945 +STATS LOCAL FORWARD -3.0104 0.71945 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 0.92744 1.79235 1.33354 1.74684 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.25.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.25.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.25.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.25.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 648747008 +STATS LOCAL MSV -8.0253 0.72144 +STATS LOCAL VITERBI -9.3054 0.72144 +STATS LOCAL FORWARD -3.5454 0.72144 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34693 1.35348 1.61412 1.26387 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.26.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.26.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.26.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.26.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 497189614 +STATS LOCAL MSV -7.8241 0.72101 +STATS LOCAL VITERBI -9.1905 0.72101 +STATS LOCAL FORWARD -3.6608 0.72101 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.28628 1.27547 1.57145 1.44114 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.27.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.27.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.27.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.27.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3001191573 +STATS LOCAL MSV -8.4593 0.72188 +STATS LOCAL VITERBI -9.4223 0.72188 +STATS LOCAL FORWARD -3.4981 0.72188 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.51776 1.58057 1.52260 1.03059 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.28.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.28.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.28.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.28.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1508026264 +STATS LOCAL MSV -7.6335 0.71997 +STATS LOCAL VITERBI -9.1422 0.71997 +STATS LOCAL FORWARD -3.5559 0.71997 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.19716 1.45323 1.30893 1.63976 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.29.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA--------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC----T +TGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTC +TGTCTCT------------CTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.29.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCT +GGGACGATCT +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTC +TGTCTCTCTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.29.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,269 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.29.aln +LENG 82 +MAXL 176 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 793374180 +STATS LOCAL MSV -8.9232 0.73665 +STATS LOCAL VITERBI -10.8392 0.73665 +STATS LOCAL FORWARD -3.0454 0.73665 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.39622 1.43714 1.34448 1.36967 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 1.84050 1.95342 1.03654 1.06480 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.01896 1.01168 2.12953 0.95527 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 1.88401 1.14290 1.03416 1.75097 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.3.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.3.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.3.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.3.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1714318246 +STATS LOCAL MSV -8.2025 0.72173 +STATS LOCAL VITERBI -9.2815 0.72173 +STATS LOCAL FORWARD -3.3965 0.72173 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34339 1.47570 1.65715 1.14025 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.30.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.30.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.30.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.30.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4093262019 +STATS LOCAL MSV -7.9445 0.72024 +STATS LOCAL VITERBI -9.3105 0.72024 +STATS LOCAL FORWARD -3.3976 0.72024 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.06451 1.63146 1.44587 1.49647 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.31.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.31.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.31.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.31.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 994513381 +STATS LOCAL MSV -8.5121 0.72207 +STATS LOCAL VITERBI -9.3704 0.72207 +STATS LOCAL FORWARD -3.5012 0.72207 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.95498 1.24900 1.45266 1.08562 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.32.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.32.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.32.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.32.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2595042177 +STATS LOCAL MSV -8.2623 0.72196 +STATS LOCAL VITERBI -9.2330 0.72196 +STATS LOCAL FORWARD -3.2805 0.72196 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34295 1.40503 1.75567 1.13702 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.33.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.33.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.33.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.33.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2524839615 +STATS LOCAL MSV -8.0121 0.72159 +STATS LOCAL VITERBI -9.2643 0.72159 +STATS LOCAL FORWARD -3.5930 0.72159 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.41710 1.20864 1.66398 1.31083 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.34.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.34.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.34.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.34.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 195830549 +STATS LOCAL MSV -8.1832 0.72173 +STATS LOCAL VITERBI -9.2304 0.72173 +STATS LOCAL FORWARD -3.8439 0.72173 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34375 1.47628 1.65579 1.14035 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.35.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.35.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.35.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.35.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1613446834 +STATS LOCAL MSV -7.8105 0.72031 +STATS LOCAL VITERBI -9.1594 0.72031 +STATS LOCAL FORWARD -3.0929 0.72031 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 0.94738 1.59256 1.61110 1.56461 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.36.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.36.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.36.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.36.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1016574008 +STATS LOCAL MSV -8.2092 0.72204 +STATS LOCAL VITERBI -9.4140 0.72204 +STATS LOCAL FORWARD -3.0300 0.72204 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.41176 1.31197 1.75905 1.15585 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.37.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.37.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.37.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.37.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1060708763 +STATS LOCAL MSV -8.1362 0.72159 +STATS LOCAL VITERBI -9.1995 0.72159 +STATS LOCAL FORWARD -3.7336 0.72159 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34496 1.34940 1.66131 1.23731 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.38.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTT +GGCTCTGGTCTGCT +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.38.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCT +CTGGTCTGCT +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.38.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,245 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.38.aln +LENG 74 +MAXL 165 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1827060747 +STATS LOCAL MSV -8.2083 0.72255 +STATS LOCAL VITERBI -9.4166 0.72255 +STATS LOCAL FORWARD -3.6220 0.72255 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.72925 1.45913 1.16890 1.27499 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.91091 1.78233 1.95844 0.61114 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.91091 1.78233 1.95844 0.61114 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 1.98342 0.60779 2.04641 1.66785 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.91091 1.78233 1.95844 0.61114 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.39.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAG-----------------------------CAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAA-----------------------------TTTTAAAAGACAATATTCTGTTTCC +TGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.39.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAGCAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGC +TTCTATATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.39.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,320 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.39.aln +LENG 99 +MAXL 200 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3832268543 +STATS LOCAL MSV -9.7613 0.73289 +STATS LOCAL VITERBI -11.5188 0.73289 +STATS LOCAL FORWARD -2.6614 0.73289 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.28054 1.52683 1.53556 1.23942 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 1.12273 2.17004 0.88086 1.92408 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.01896 1.01168 2.12953 0.95527 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 1.09289 1.89038 1.88803 1.01509 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.4.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA----- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGG +AAAATGTCTAACAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.4.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAAT +GTCTAACAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.4.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,248 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.4.aln +LENG 75 +MAXL 167 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4254883388 +STATS LOCAL MSV -7.9031 0.72215 +STATS LOCAL VITERBI -9.4337 0.72215 +STATS LOCAL FORWARD -3.6540 0.72215 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.20862 1.43722 1.53118 1.39624 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.98342 0.60779 2.04641 1.66785 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.98342 0.60779 2.04641 1.66785 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 0.56139 2.08489 1.86185 1.89791 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 0.56139 2.08489 1.86185 1.89791 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.40.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG--------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATG---------------GGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGT +AATGACTGAGGTGTTACAACTTGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.40.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTT +ACAACTTGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.40.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,278 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.40.aln +LENG 85 +MAXL 180 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 850921081 +STATS LOCAL MSV -9.2442 0.73770 +STATS LOCAL VITERBI -10.9061 0.73770 +STATS LOCAL FORWARD -3.0276 0.73770 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34684 1.48715 1.41637 1.30441 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 1.09289 1.89038 1.88803 1.01509 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 1.84050 1.95342 1.03654 1.06480 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 1.84050 1.95342 1.03654 1.06480 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 1.09289 1.89038 1.88803 1.01509 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.41.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.41.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.41.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.41.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3655489519 +STATS LOCAL MSV -8.2137 0.71925 +STATS LOCAL VITERBI -9.4456 0.71925 +STATS LOCAL FORWARD -3.2467 0.71925 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 0.94751 1.95314 1.23648 1.71446 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.42.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.42.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.42.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.42.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1523439480 +STATS LOCAL MSV -7.9792 0.72102 +STATS LOCAL VITERBI -9.3053 0.72102 +STATS LOCAL FORWARD -3.4853 0.72102 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.25034 1.49541 1.52580 1.30200 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.43.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.43.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.43.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.43.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3312512886 +STATS LOCAL MSV -7.8819 0.72002 +STATS LOCAL VITERBI -9.2757 0.72002 +STATS LOCAL FORWARD -3.4162 0.72002 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.16793 1.59743 1.30588 1.53415 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.44.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.44.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.44.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.44.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2374664696 +STATS LOCAL MSV -8.0688 0.72046 +STATS LOCAL VITERBI -9.1038 0.72046 +STATS LOCAL FORWARD -3.5428 0.72046 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.13770 1.75158 1.40669 1.34326 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.45.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.45.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.45.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.45.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4135045782 +STATS LOCAL MSV -8.0188 0.72034 +STATS LOCAL VITERBI -9.0748 0.72034 +STATS LOCAL FORWARD -3.4332 0.72034 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.11475 1.55081 1.44662 1.49361 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.46.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.46.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.46.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.46.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4194640144 +STATS LOCAL MSV -8.2586 0.72083 +STATS LOCAL VITERBI -9.2349 0.72083 +STATS LOCAL FORWARD -3.5611 0.72083 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.52180 1.56997 1.27094 1.22737 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.47.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.47.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.47.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.47.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2191598282 +STATS LOCAL MSV -7.8363 0.71973 +STATS LOCAL VITERBI -9.1518 0.71973 +STATS LOCAL FORWARD -3.7787 0.71973 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.28422 1.64197 1.15255 1.54316 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.48.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.48.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.48.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.48.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 664434907 +STATS LOCAL MSV -7.9930 0.72119 +STATS LOCAL VITERBI -9.2272 0.72119 +STATS LOCAL FORWARD -3.6562 0.72119 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.41731 1.24184 1.53303 1.37475 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.49.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.49.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.49.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.49.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2518237207 +STATS LOCAL MSV -7.6534 0.71987 +STATS LOCAL VITERBI -9.2822 0.71987 +STATS LOCAL FORWARD -3.5503 0.71987 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.13983 1.68362 1.27304 1.53970 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.5.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.5.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.5.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.5.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1411486405 +STATS LOCAL MSV -8.2242 0.72116 +STATS LOCAL VITERBI -9.3853 0.72116 +STATS LOCAL FORWARD -3.9236 0.72116 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34233 1.63901 1.44518 1.17477 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.50.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.50.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.50.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.50.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3932738091 +STATS LOCAL MSV -8.6318 0.72054 +STATS LOCAL VITERBI -9.7767 0.72054 +STATS LOCAL FORWARD -3.3478 0.72054 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.06228 1.66134 1.52409 1.39987 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.51.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC------ +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGAT +ATCCTTGATCTGAGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.51.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTT +GATCTGAGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.51.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,251 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.51.aln +LENG 76 +MAXL 168 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3988988039 +STATS LOCAL MSV -8.1442 0.72049 +STATS LOCAL VITERBI -9.4670 0.72049 +STATS LOCAL FORWARD -3.5137 0.72049 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.10127 1.65526 1.33843 1.54060 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.98342 0.60779 2.04641 1.66785 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 0.56139 2.08489 1.86185 1.89791 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 1.98342 0.60779 2.04641 1.66785 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.91091 1.78233 1.95844 0.61114 4 t - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.03279 3.43399 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.52.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.52.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.52.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.52.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 62394181 +STATS LOCAL MSV -8.0100 0.72072 +STATS LOCAL VITERBI -9.3118 0.72072 +STATS LOCAL FORWARD -3.5566 0.72072 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.38092 1.39925 1.37704 1.38812 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.53.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.53.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.53.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.53.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4138962244 +STATS LOCAL MSV -7.9188 0.72028 +STATS LOCAL VITERBI -9.2113 0.72028 +STATS LOCAL FORWARD -3.4388 0.72028 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.16628 1.58889 1.37387 1.46448 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.54.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.54.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.54.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.54.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 677277550 +STATS LOCAL MSV -7.8511 0.72028 +STATS LOCAL VITERBI -9.3045 0.72028 +STATS LOCAL FORWARD -3.4387 0.72028 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 0.99121 1.67344 1.52419 1.49846 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.55.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.55.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.55.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.55.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 270279876 +STATS LOCAL MSV -8.2600 0.72111 +STATS LOCAL VITERBI -9.2516 0.72111 +STATS LOCAL FORWARD -3.7652 0.72111 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44455 1.60151 1.37316 1.17360 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.56.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.56.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.56.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.56.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3045280856 +STATS LOCAL MSV -8.0658 0.72163 +STATS LOCAL VITERBI -9.3021 0.72163 +STATS LOCAL FORWARD -3.6953 0.72163 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.41320 1.34805 1.61527 1.21049 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.57.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.57.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.57.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.57.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2156877472 +STATS LOCAL MSV -8.0137 0.72176 +STATS LOCAL VITERBI -9.3146 0.72176 +STATS LOCAL FORWARD -3.2022 0.72176 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.37567 1.54761 1.60818 1.09564 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.58.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.58.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.58.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.58.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 988802922 +STATS LOCAL MSV -7.9559 0.72068 +STATS LOCAL VITERBI -9.2724 0.72068 +STATS LOCAL FORWARD -3.4915 0.72068 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.11505 1.47137 1.56700 1.45320 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.59.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.59.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.59.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.59.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3210243743 +STATS LOCAL MSV -7.8918 0.72110 +STATS LOCAL VITERBI -9.2572 0.72110 +STATS LOCAL FORWARD -3.8308 0.72110 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.31529 1.39113 1.52918 1.32389 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 69 2.31486 2.12647 2.41211 0.36768 69 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 70 2.31486 2.12647 2.41211 0.36768 70 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.02469 3.71357 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.6.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.6.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.6.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.6.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2378325802 +STATS LOCAL MSV -8.3548 0.72225 +STATS LOCAL VITERBI -9.2925 0.72225 +STATS LOCAL FORWARD -3.4728 0.72225 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44379 1.53363 1.70267 1.00506 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.60.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.60.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.60.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.60.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1614228065 +STATS LOCAL MSV -8.0118 0.72018 +STATS LOCAL VITERBI -9.2620 0.72018 +STATS LOCAL FORWARD -3.4720 0.72018 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.11324 1.67408 1.37191 1.46793 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.61.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.61.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.61.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.61.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2408145248 +STATS LOCAL MSV -7.8359 0.72000 +STATS LOCAL VITERBI -9.0846 0.72000 +STATS LOCAL FORWARD -3.5699 0.72000 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.19531 1.63705 1.27077 1.50408 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.62.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.62.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.62.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.62.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1574236373 +STATS LOCAL MSV -7.9394 0.72062 +STATS LOCAL VITERBI -9.3943 0.72062 +STATS LOCAL FORWARD -3.3008 0.72062 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 0.94586 1.62365 1.70321 1.45938 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.63.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.63.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.63.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.63.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1581685751 +STATS LOCAL MSV -8.3992 0.72064 +STATS LOCAL VITERBI -9.5309 0.72064 +STATS LOCAL FORWARD -3.5039 0.72064 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.06213 1.62061 1.56496 1.39671 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.64.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT---------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +----------TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGATTGTAAGACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.64.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT +TGTAAGACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.64.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,263 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.64.aln +LENG 80 +MAXL 174 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1595177567 +STATS LOCAL MSV -8.1741 0.72087 +STATS LOCAL VITERBI -9.7059 0.72087 +STATS LOCAL FORWARD -3.6637 0.72087 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.12278 1.57946 1.40266 1.50238 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.98342 0.60779 2.04641 1.66785 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.97267 2.25870 0.46443 2.05625 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 0.56139 2.08489 1.86185 1.89791 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.97267 2.25870 0.46443 2.05625 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.65.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.65.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.65.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.65.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4203419393 +STATS LOCAL MSV -7.9742 0.71970 +STATS LOCAL VITERBI -9.3402 0.71970 +STATS LOCAL FORWARD -3.2406 0.71970 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.03960 1.73335 1.30313 1.61932 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.66.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.66.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.66.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.66.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 212902700 +STATS LOCAL MSV -8.4235 0.72226 +STATS LOCAL VITERBI -9.3579 0.72226 +STATS LOCAL FORWARD -3.4937 0.72226 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.51844 1.49446 1.65628 1.00586 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.67.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.67.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.67.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.67.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1592920432 +STATS LOCAL MSV -8.0355 0.72053 +STATS LOCAL VITERBI -9.2753 0.72053 +STATS LOCAL FORWARD -3.5978 0.72053 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34795 1.43634 1.34031 1.42433 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.68.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.68.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.68.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.68.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:04 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 197613389 +STATS LOCAL MSV -8.1343 0.72116 +STATS LOCAL VITERBI -9.1178 0.72116 +STATS LOCAL FORWARD -3.4711 0.72116 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.48462 1.41899 1.41252 1.24507 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.69.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +-------------------------TTTTATGGTTCATAATCCACTCCATGTACTGGTTC +TTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTG +TATTATGACC-------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.69.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCC +CGTTCTAGCT +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTG +TATTATGACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.69.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,308 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.69.aln +LENG 95 +MAXL 195 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3693886677 +STATS LOCAL MSV -9.3349 0.73564 +STATS LOCAL VITERBI -11.4690 0.73564 +STATS LOCAL FORWARD -2.9050 0.73564 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.31992 1.50669 1.46715 1.27076 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 1.97267 2.25870 0.46443 2.05625 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 0.56139 2.08489 1.86185 1.89791 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 3 0.56139 2.08489 1.86185 1.89791 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 4 1.97267 2.25870 0.46443 2.05625 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.7.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.7.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.7.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.7.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 4123557566 +STATS LOCAL MSV -8.0090 0.72082 +STATS LOCAL VITERBI -9.1696 0.72082 +STATS LOCAL FORWARD -3.9325 0.72082 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.37619 1.49875 1.37513 1.30474 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.70.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.70.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.70.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.70.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2654244890 +STATS LOCAL MSV -8.3785 0.72268 +STATS LOCAL VITERBI -9.4571 0.72268 +STATS LOCAL FORWARD -3.4371 0.72268 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.52355 1.21479 1.93188 1.07759 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.71.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.71.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.71.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.71.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1009151711 +STATS LOCAL MSV -7.9784 0.71983 +STATS LOCAL VITERBI -9.2979 0.71983 +STATS LOCAL FORWARD -3.3519 0.71983 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.08868 1.68568 1.30434 1.57664 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.72.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.72.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.72.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.72.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 295818489 +STATS LOCAL MSV -8.1681 0.72138 +STATS LOCAL VITERBI -9.1523 0.72138 +STATS LOCAL FORWARD -3.6764 0.72138 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.48326 1.48268 1.44801 1.16784 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.73.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.73.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.73.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.73.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1304963515 +STATS LOCAL MSV -7.9514 0.72069 +STATS LOCAL VITERBI -9.1535 0.72069 +STATS LOCAL FORWARD -3.8888 0.72069 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44728 1.46664 1.30757 1.33327 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.74.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.74.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.74.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.74.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1193822911 +STATS LOCAL MSV -8.5061 0.72241 +STATS LOCAL VITERBI -9.4253 0.72241 +STATS LOCAL FORWARD -3.1771 0.72241 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44165 1.53142 1.74981 0.98503 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.75.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.75.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.75.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.75.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3275121080 +STATS LOCAL MSV -8.4136 0.72163 +STATS LOCAL VITERBI -9.2547 0.72163 +STATS LOCAL FORWARD -3.4838 0.72163 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.40853 1.62732 1.52276 1.07607 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.38910 2.82844 0.25233 2.62837 4 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.76.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.76.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.76.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.76.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2027655957 +STATS LOCAL MSV -8.3586 0.72225 +STATS LOCAL VITERBI -9.4971 0.72225 +STATS LOCAL FORWARD -3.3563 0.72225 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.44704 1.27813 1.81427 1.12942 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.77.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.77.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.77.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.77.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 976848233 +STATS LOCAL MSV -7.7061 0.71985 +STATS LOCAL VITERBI -9.2820 0.71985 +STATS LOCAL FORWARD -3.6293 0.71985 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.16788 1.56354 1.27373 1.61046 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.78.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.78.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.78.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.78.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2522115511 +STATS LOCAL MSV -8.2929 0.72184 +STATS LOCAL VITERBI -9.4215 0.72184 +STATS LOCAL FORWARD -3.5618 0.72184 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.51931 1.54164 1.52480 1.05142 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.31486 2.12647 2.41211 0.36768 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.79.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.79.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.79.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.79.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1636119314 +STATS LOCAL MSV -8.2610 0.72156 +STATS LOCAL VITERBI -9.3322 0.72156 +STATS LOCAL FORWARD -3.1566 0.72156 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.48265 1.38100 1.52807 1.18848 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.8.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT-- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +--AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAA +TTCCTTTGTGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.8.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATT +CCTTTGTGTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.8.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,239 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.8.aln +LENG 72 +MAXL 163 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 3543576690 +STATS LOCAL MSV -9.0934 0.74635 +STATS LOCAL VITERBI -10.7285 0.74635 +STATS LOCAL FORWARD -2.0983 0.74635 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.24351 1.59287 1.56791 1.20462 + 1.38629 1.38629 1.38629 1.38629 + 0.33647 3.73767 1.33977 1.46634 0.26236 0.00000 * + 1 0.56139 2.08489 1.86185 1.89791 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 1.60944 0.22314 + 2 1.98342 0.60779 2.04641 1.66785 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.06454 3.46574 3.46574 1.46634 0.26236 0.51083 0.91629 + 3 0.28818 2.60848 2.42319 2.42940 3 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.80.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.80.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.80.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.80.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 1911820345 +STATS LOCAL MSV -7.7647 0.72086 +STATS LOCAL VITERBI -8.9877 0.72086 +STATS LOCAL FORWARD -3.6995 0.72086 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.45138 1.36359 1.37796 1.35511 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.31486 2.12647 2.41211 0.36768 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.46232 0.33808 2.58153 2.07174 4 c - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.81.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.81.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.81.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.81.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2860632243 +STATS LOCAL MSV -7.8884 0.71997 +STATS LOCAL VITERBI -9.2337 0.71997 +STATS LOCAL FORWARD -3.7511 0.71997 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.14114 1.63705 1.30427 1.53889 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.38910 2.82844 0.25233 2.62837 1 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.46232 0.33808 2.58153 2.07174 2 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.46232 0.33808 2.58153 2.07174 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.82.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.82.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.82.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.82.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2621139853 +STATS LOCAL MSV -7.9800 0.72086 +STATS LOCAL VITERBI -9.2405 0.72086 +STATS LOCAL FORWARD -3.6067 0.72086 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.37943 1.39613 1.41270 1.35774 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.83.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.83.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.83.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.83.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2205547240 +STATS LOCAL MSV -8.0191 0.72077 +STATS LOCAL VITERBI -9.1398 0.72077 +STATS LOCAL FORWARD -3.4631 0.72077 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.41098 1.49972 1.34037 1.30507 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.31486 2.12647 2.41211 0.36768 3 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 2.31486 2.12647 2.41211 0.36768 4 t - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.9.aln Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.9.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.9.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,233 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.9.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 158536290 +STATS LOCAL MSV -8.1021 0.72173 +STATS LOCAL VITERBI -9.2636 0.72173 +STATS LOCAL FORWARD -2.9700 0.72173 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.28100 1.37999 1.75596 1.21093 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 0.28818 2.60848 2.42319 2.42940 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 2.38910 2.82844 0.25233 2.62837 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 61 2.31486 2.12647 2.41211 0.36768 61 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 62 2.31486 2.12647 2.41211 0.36768 62 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 63 2.46232 0.33808 2.58153 2.07174 63 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 64 2.46232 0.33808 2.58153 2.07174 64 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 65 2.46232 0.33808 2.58153 2.07174 65 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 66 2.46232 0.33808 2.58153 2.07174 66 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 67 0.28818 2.60848 2.42319 2.42940 67 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 68 2.46232 0.33808 2.58153 2.07174 68 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 69 2.31486 2.12647 2.41211 0.36768 69 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 70 0.28818 2.60848 2.42319 2.42940 70 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.02469 3.71357 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.ClusterList.txt Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,100 @@ +K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 0 +K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 1 +K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 1 +K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 2 +K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 2 +K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 2 +K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 3 +K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 4 +K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 4 +K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 5 +K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 6 +K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 7 +K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 8 +K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 8 +K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 9 +K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 10 +K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 10 +K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 11 +K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 11 +K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 12 +K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 13 +K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 14 +K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 15 +K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 16 +K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 16 +K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 17 +K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 18 +K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 19 +K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 20 +K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 20 +K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 21 +K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 22 +K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 23 +K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 24 +K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 25 +K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 26 +K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 27 +K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 28 +K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 29 +K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 29 +K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 30 +K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 31 +K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 32 +K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 33 +K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 34 +K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 35 +K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 36 +K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 37 +K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 38 +K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 38 +K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 39 +K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 39 +K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 40 +K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 40 +K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 41 +K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 42 +K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 43 +K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 44 +K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 45 +K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 46 +K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 47 +K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 48 +K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 49 +K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 50 +K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 51 +K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 51 +K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 52 +K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 53 +K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 54 +K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 55 +K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 56 +K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 57 +K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 58 +K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 59 +K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 60 +K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 61 +K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 62 +K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 63 +K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 64 +K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 64 +K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 65 +K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 66 +K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 67 +K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 68 +K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 69 +K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 69 +K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 70 +K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 71 +K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 72 +K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 73 +K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 74 +K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 75 +K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 76 +K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 77 +K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 78 +K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 79 +K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 80 +K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 81 +K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 82 +K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 83
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,300 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCA +ATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACAT +CAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAA +TTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAG +TAATTAGATC +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGG +GGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAAT +GTCTAACAGC +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGT +GGGGGGACAT +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCT +GGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCT +CTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAGCAG +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTC +TGTCTCTCTC +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCAT +GAGGATATAA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGA +GGATATAATC +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAG +GCGAGGGGCG +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT +TGTAAGACTA +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTT +GATCTGAGGA +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCT +GAGGATTGCT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTT +ACAACTTGTC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGC +TTCTATATAT +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCC +CGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTG +TATTATGACC +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATT +CCTTTGTGTG +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/long.good.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,300 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACA +CCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCA +ATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +TACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGG +AAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAG +AAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAG +TACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACAT +CAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAA +TTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCA +AGCTTCTGTA +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTAT +ATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCT +GAGGATTGGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAG +TAATTAGATC +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGAT +TAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGG +GGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGAT +CAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTA +AGTATTACAT +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAAT +GTCTAACAGC +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAA +GAATTACAAA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGT +GGGGGGACAT +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAAT +TAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAG +GCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCT +GCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGA +AGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCT +GGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTC +CATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCC +ATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGAT +TAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAA +AAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAA +TCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCT +CTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTC +AAATTAGCAG +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTC +TGTCTCTCTC +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATA +CATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTA +CTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGG +CAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCAT +GAGGATATAA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCAT +TGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGG +CTGACCTGAT +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGA +GGATATAATC +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAG +GCGAGGGGCG +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGT +CCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGA +GTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT +ATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAA +TAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACA +CAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTAC +TACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACA +AATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGC +GAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT +TGTAAGACTA +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTT +GATCTGAGGA +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCT +GAGGATTGCT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTT +GGCTCTGGTC +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTT +ACAACTTGTC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCC +ACCTCGACAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGC +TTCTATATAT +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCC +CGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTC +CCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAG +AAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCAT +ATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTG +TATTATGACC +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATC +TCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATT +CCTTTGTGTG +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/merge.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6177 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 72 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 70 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 83 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 91 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 108 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 92 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 76 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 118 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 115 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 94 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 87 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 80 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 84 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 82 - 75 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 91 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-1 (thread 1) identical 001-0004-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 78 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 73 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 84 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 88 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 105 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 77 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 76 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 79 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 80 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 97 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 72 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 97 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 89 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 95 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 95 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 71 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 110 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 4 +njobc = 5 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 90 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 107 - 99 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### +Reallocated inconsistentpairlist, size=2 + +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 156 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-1 (thread 1) identical 001-0004-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 91 - 78 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 + -> OK +Segment 1/ 1 1- 108 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-1 (thread 1) identical 001-0006-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 117 - 114 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 2 1- 62 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-1 (thread 1) identical +Converged. + +Reached 1 +Segment 2/ 2 62- 134 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-1 (thread 1) identical 001-0004-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 78 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 102 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 84 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 4 +njobc = 5 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 72 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 99 - 76 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### + +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 103 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-1 (thread 1) identical 001-0004-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 101 - 72 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 + -> OK +Segment 1/ 1 1- 102 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 95 - 71 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 114 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-1 (thread 1) identical 001-0004-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 102 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 115 - 96 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 6 + -> OK +Segment 1/ 1 1- 154 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-1 (thread 1) identical 001-0008-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 110 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 5 +njobc = 6 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 108 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 93 - 87 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 + -> OK +Segment 1/ 1 1- 102 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-1 (thread 1) identical 001-0006-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 98 - 87 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 7 / 7 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 7 / 7 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 8 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 6 7 8 + -> OK +Segment 1/ 1 1- 105 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 97 - 74 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 + -> OK +Segment 1/ 1 1- 109 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-1 (thread 1) identical 001-0006-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 106 - 87 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 + -> OK +Segment 1/ 1 1- 127 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-1 (thread 1) identical 001-0008-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 101 - 91 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 7 / 7 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 7 / 7 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 8 + +Checking subalignment 1: + 1 2 3 4 5 + -> OK + +Checking subalignment 2: + 6 7 8 + -> OK +Segment 1/ 1 1- 102 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-1 (thread 1) identical 001-0012-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 99 - 85 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### +Reallocated inconsistentpairlist, size=2 + +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 + -> OK +Segment 1/ 1 1- 123 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-1 (thread 1) identical 001-0008-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 115 - 94 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 3 4 + -> OK + +Checking subalignment 2: + 5 6 + -> OK +Segment 1/ 1 1- 141 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +7 x 120 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 6 +njobc = 7 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 99 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 5 +njobc = 6 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +9 x 104 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 8 +njobc = 9 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 108 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 5 +njobc = 6 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 126 - 83 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 7 / 7 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 7 / 7 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 8 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 7 8 + -> OK +Segment 1/ 1 1- 130 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-1 (thread 1) identical 001-0012-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +7 x 100 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 6 +njobc = 7 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +7 x 140 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 6 +njobc = 7 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +13 x 128 - 123 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 13 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 13 10 / 13 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 12 / 12 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 13 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 13 10 / 13 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 12 / 12 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 13 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 13 10 / 13 + +Checking subalignment 1: + 1 2 3 4 5 6 + -> OK + +Checking subalignment 2: + 7 8 9 10 11 12 13 + -> OK +Segment 1/ 1 1- 163 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-1 (thread 1) identical 001-0022-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +10 x 130 - 111 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 9 / 9 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 9 / 9 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 10 + +Checking subalignment 1: + 1 2 3 4 + -> OK + +Checking subalignment 2: + 5 6 7 8 9 10 + -> OK +Segment 1/ 1 1- 142 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +16 x 129 - 101 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 16 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 16 10 / 16 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 15 / 15 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 16 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 16 10 / 16 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 15 / 15 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 16 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 16 10 / 16 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 + -> OK + +Checking subalignment 2: + 9 10 11 12 13 14 15 16 + -> OK +Segment 1/ 1 1- 152 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-1 (thread 1) identical 001-0028-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +10 x 108 - 96 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 9 / 9 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 9 / 9 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 10 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 6 7 8 9 10 + -> OK +Segment 1/ 1 1- 122 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-1 (thread 1) identical 001-0016-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 140 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 7 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 7 +njobc = 8 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +17 x 151 - 113 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 17 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 17 10 / 17 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 16 / 16 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 17 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 17 10 / 17 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 16 / 16 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 17 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 17 10 / 17 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 + -> OK + +Checking subalignment 2: + 14 15 16 17 + -> OK +Segment 1/ 1 1- 166 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-1 (thread 1) identical 001-0030-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +11 x 141 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 10 +njobc = 11 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +22 x 157 - 112 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 16 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 22 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 22 10 / 22 20 / 22 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 21 / 21 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 22 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 22 10 / 22 20 / 22 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 21 / 21 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 22 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 16 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 22 10 / 22 20 / 22 + +Checking subalignment 1: + 1 2 3 4 5 6 + -> OK + +Checking subalignment 2: + 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + -> OK +Segment 1/ 1 1- 170 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-1 (thread 1) identical 001-0040-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +12 x 121 - 96 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 10 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 12 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 12 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### +Reallocated inconsistentpairlist, size=2 + 10 / 12 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 11 / 11 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 12 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 12 10 / 12 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 11 / 11 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 12 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 10 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 12 10 / 12 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 + -> OK + +Checking subalignment 2: + 11 12 + -> OK +Segment 1/ 1 1- 122 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-1 (thread 1) identical 001-0020-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +10 x 142 - 88 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 9 / 9 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 9 / 9 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 10 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 7 8 9 10 + -> OK +Segment 1/ 1 1- 157 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-1 (thread 1) identical 001-0016-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +21 x 168 - 155 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 17 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 21 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 21 10 / 21 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 20 / 20 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 21 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 21 10 / 21 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 20 / 20 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 21 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 17 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 21 10 / 21 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + -> OK + +Checking subalignment 2: + 18 19 20 21 + -> OK +Segment 1/ 1 1- 209 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-1 (thread 1) identical 001-0038-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +12 x 141 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 11 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 10 / 11 (by thread 0) + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 11 +njobc = 12 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +24 x 169 - 74 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 22 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 24 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 24 10 / 24 20 / 24 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 23 / 23 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 24 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 24 10 / 24 20 / 24 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 23 / 23 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 24 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 22 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 24 10 / 24 20 / 24 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + -> OK +Segment 1/ 1 1- 174 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-1 (thread 1) identical 001-0044-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +13 x 121 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 12 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 12 +njobc = 13 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +26 x 186 - 107 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 21 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 26 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 26 10 / 26 20 / 26 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 25 / 25 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 26 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 26 10 / 26 20 / 26 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 25 / 25 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 26 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 21 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 26 10 / 26 20 / 26 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + -> OK + +Checking subalignment 2: + 22 23 24 25 26 + -> OK +Segment 1/ 1 1- 199 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-0 (thread 1) skip 001-0045-1 (thread 1) skip 001-0046-0 (thread 1) skip 001-0047-1 (thread 1) skip 001-0048-1 (thread 1) identical 001-0048-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +25 x 173 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 24 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 24 +njobc = 25 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +23 x 142 - 130 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 23 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 23 10 / 23 20 / 23 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 22 / 22 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 23 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 23 10 / 23 20 / 23 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 22 / 22 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 23 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 23 10 / 23 20 / 23 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 + -> OK + +Checking subalignment 2: + 14 15 16 17 18 19 20 21 22 23 + -> OK +Segment 1/ 1 1- 155 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +38 x 198 - 155 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 26 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 37 / 37 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 37 / 37 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 38 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 26 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 38 10 / 38 20 / 38 30 / 38 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 + -> OK + +Checking subalignment 2: + 27 28 29 30 31 32 33 34 35 36 37 38 + -> OK +Segment 1/ 1 1- 205 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-0 (thread 1) skip 001-0045-1 (thread 1) skip 001-0046-0 (thread 1) skip 001-0047-1 (thread 1) skip 001-0048-0 (thread 1) skip 001-0049-1 (thread 1) skip 001-0050-0 (thread 1) skip 001-0051-1 (thread 1) skip 001-0052-0 (thread 1) skip 001-0053-1 (thread 1) skip 001-0054-0 (thread 1) skip 001-0055-1 (thread 1) skip 001-0056-0 (thread 1) skip 001-0057-1 (thread 1) skip 001-0058-0 (thread 1) skip 001-0059-1 (thread 1) skip 001-0060-0 (thread 1) skip 001-0061-1 (thread 1) skip 001-0062-0 (thread 1) skip 001-0063-1 (thread 1) skip 001-0064-0 (thread 1) skip 001-0065-1 (thread 1) skip 001-0066-0 (thread 1) skip 001-0067-1 (thread 1) skip 001-0068-0 (thread 1) skip 001-0069-1 (thread 1) skip 001-0070-0 (thread 1) skip 001-0071-1 (thread 1) skip 001-0072-1 (thread 1) identical 001-0072-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +34 x 182 - 104 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 25 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 34 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 34 10 / 34 20 / 34 30 / 34 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 33 / 33 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 34 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 34 10 / 34 20 / 34 30 / 34 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 33 / 33 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 34 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 25 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 34 10 / 34 20 / 34 30 / 34 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 + -> OK + +Checking subalignment 2: + 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 + -> OK +Segment 1/ 1 1- 188 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-0 (thread 1) skip 001-0045-1 (thread 1) skip 001-0046-0 (thread 1) skip 001-0047-1 (thread 1) skip 001-0048-0 (thread 1) skip 001-0049-1 (thread 1) skip 001-0050-0 (thread 1) skip 001-0051-1 (thread 1) skip 001-0052-0 (thread 1) skip 001-0053-1 (thread 1) skip 001-0054-0 (thread 1) skip 001-0055-1 (thread 1) skip 001-0056-0 (thread 1) skip 001-0057-1 (thread 1) skip 001-0058-0 (thread 1) skip 001-0059-1 (thread 1) skip 001-0060-0 (thread 1) skip 001-0061-1 (thread 1) skip 001-0062-0 (thread 1) skip 001-0063-1 (thread 1) skip 001-0064-1 (thread 1) identical 001-0064-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +24 x 154 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 23 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 23 +njobc = 24 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +38 x 187 - 149 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 34 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 37 / 37 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 37 / 37 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 38 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 34 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 38 10 / 38 20 / 38 30 / 38 + +Checking subalignment 1: + 1 2 3 4 + -> OK + +Checking subalignment 2: + 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 + -> OK +Segment 1/ 1 1- 216 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-0 (thread 1) skip 001-0045-1 (thread 1) skip 001-0046-0 (thread 1) skip 001-0047-1 (thread 1) skip 001-0048-0 (thread 1) skip 001-0049-1 (thread 1) skip 001-0050-0 (thread 1) skip 001-0051-1 (thread 1) skip 001-0052-0 (thread 1) skip 001-0053-1 (thread 1) skip 001-0054-0 (thread 1) skip 001-0055-1 (thread 1) skip 001-0056-0 (thread 1) skip 001-0057-1 (thread 1) skip 001-0058-0 (thread 1) skip 001-0059-1 (thread 1) skip 001-0060-0 (thread 1) skip 001-0061-1 (thread 1) skip 001-0062-0 (thread 1) skip 001-0063-1 (thread 1) skip 001-0064-0 (thread 1) skip 001-0065-1 (thread 1) skip 001-0066-0 (thread 1) skip 001-0067-1 (thread 1) skip 001-0068-0 (thread 1) skip 001-0069-1 (thread 1) skip 001-0070-0 (thread 1) skip 001-0071-1 (thread 1) skip 001-0072-1 (thread 1) identical 001-0072-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +76 x 215 - 206 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 38 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 76 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 76 10 / 76 20 / 76 30 / 76 40 / 76 50 / 76 60 / 76 70 / 76 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 75 / 75 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 76 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 76 10 / 76 20 / 76 30 / 76 40 / 76 50 / 76 60 / 76 70 / 76 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 75 / 75 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 76 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 38 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 76 10 / 76 20 / 76 30 / 76 40 / 76 50 / 76 60 / 76 70 / 76 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 + -> OK + +Checking subalignment 2: + 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 + -> OK +Segment 1/ 1 1- 285 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-0 (thread 1) skip 001-0045-1 (thread 1) skip 001-0046-0 (thread 1) skip 001-0047-1 (thread 1) skip 001-0048-0 (thread 1) skip 001-0049-1 (thread 1) skip 001-0050-0 (thread 1) skip 001-0051-1 (thread 1) skip 001-0052-0 (thread 1) skip 001-0053-1 (thread 1) skip 001-0054-0 (thread 1) skip 001-0055-1 (thread 1) skip 001-0056-0 (thread 1) skip 001-0057-1 (thread 1) skip 001-0058-0 (thread 1) skip 001-0059-1 (thread 1) skip 001-0060-0 (thread 1) skip 001-0061-1 (thread 1) skip 001-0062-0 (thread 1) skip 001-0063-1 (thread 1) skip 001-0064-0 (thread 1) skip 001-0065-1 (thread 1) skip 001-0066-0 (thread 1) skip 001-0067-1 (thread 1) skip 001-0068-0 (thread 1) skip 001-0069-1 (thread 1) skip 001-0070-0 (thread 1) skip 001-0071-1 (thread 1) skip 001-0072-0 (thread 1) skip 001-0073-1 (thread 1) skip 001-0074-0 (thread 1) skip 001-0075-1 (thread 1) skip 001-0076-0 (thread 1) skip 001-0077-1 (thread 1) skip 001-0078-0 (thread 1) skip 001-0079-1 (thread 1) skip 001-0080-0 (thread 1) skip 001-0081-1 (thread 1) skip 001-0082-0 (thread 1) skip 001-0083-1 (thread 1) skip 001-0084-0 (thread 1) skip 001-0085-1 (thread 1) skip 001-0086-0 (thread 1) skip 001-0087-1 (thread 1) skip 001-0088-0 (thread 1) skip 001-0089-1 (thread 1) skip 001-0090-0 (thread 1) skip 001-0091-1 (thread 1) skip 001-0092-0 (thread 1) skip 001-0093-1 (thread 1) skip 001-0094-0 (thread 1) skip 001-0095-1 (thread 1) skip 001-0096-0 (thread 1) skip 001-0097-1 (thread 1) skip 001-0098-0 (thread 1) skip 001-0099-1 (thread 1) skip 001-0100-0 (thread 1) skip 001-0101-1 (thread 1) skip 001-0102-0 (thread 1) skip 001-0103-1 (thread 1) skip 001-0104-0 (thread 1) skip 001-0105-1 (thread 1) skip 001-0106-0 (thread 1) skip 001-0107-1 (thread 1) skip 001-0108-0 (thread 1) skip 001-0109-1 (thread 1) skip 001-0110-0 (thread 1) skip 001-0111-1 (thread 1) skip 001-0112-0 (thread 1) skip 001-0113-1 (thread 1) skip 001-0114-0 (thread 1) skip 001-0115-1 (thread 1) skip 001-0116-0 (thread 1) skip 001-0117-1 (thread 1) skip 001-0118-0 (thread 1) skip 001-0119-1 (thread 1) skip 001-0120-0 (thread 1) skip 001-0121-1 (thread 1) skip 001-0122-0 (thread 1) skip 001-0123-1 (thread 1) skip 001-0124-0 (thread 1) skip 001-0125-1 (thread 1) skip 001-0126-0 (thread 1) skip 001-0127-1 (thread 1) skip 001-0128-0 (thread 1) skip 001-0129-1 (thread 1) skip 001-0130-0 (thread 1) skip 001-0131-1 (thread 1) skip 001-0132-0 (thread 1) skip 001-0133-1 (thread 1) skip 001-0134-0 (thread 1) skip 001-0135-1 (thread 1) skip 001-0136-0 (thread 1) skip 001-0137-1 (thread 1) skip 001-0138-0 (thread 1) skip 001-0139-1 (thread 1) skip 001-0140-0 (thread 1) skip 001-0141-1 (thread 1) skip 001-0142-0 (thread 1) skip 001-0143-1 (thread 1) skip 001-0144-0 (thread 1) skip 001-0145-1 (thread 1) skip 001-0146-0 (thread 1) skip 001-0147-1 (thread 1) skip 001-0148-1 (thread 1) identical 001-0148-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +100 x 273 - 156 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 76 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 100 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 100 10 / 100 20 / 100 30 / 100 40 / 100 50 / 100 60 / 100 70 / 100 80 / 100 90 / 100 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 99 / 99 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 100 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 100 10 / 100 20 / 100 30 / 100 40 / 100 50 / 100 60 / 100 70 / 100 80 / 100 90 / 100 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 99 / 99 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 100 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 76 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 100 10 / 100 20 / 100 30 / 100 40 / 100 50 / 100 60 / 100 70 / 100 80 / 100 90 / 100 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 + -> OK + +Checking subalignment 2: + 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 + -> OK +Segment 1/ 1 1- 279 +001-0000-0 (thread 1) skip 001-0001-1 (thread 1) skip 001-0002-0 (thread 1) skip 001-0003-1 (thread 1) skip 001-0004-0 (thread 1) skip 001-0005-1 (thread 1) skip 001-0006-0 (thread 1) skip 001-0007-1 (thread 1) skip 001-0008-0 (thread 1) skip 001-0009-1 (thread 1) skip 001-0010-0 (thread 1) skip 001-0011-1 (thread 1) skip 001-0012-0 (thread 1) skip 001-0013-1 (thread 1) skip 001-0014-0 (thread 1) skip 001-0015-1 (thread 1) skip 001-0016-0 (thread 1) skip 001-0017-1 (thread 1) skip 001-0018-0 (thread 1) skip 001-0019-1 (thread 1) skip 001-0020-0 (thread 1) skip 001-0021-1 (thread 1) skip 001-0022-0 (thread 1) skip 001-0023-1 (thread 1) skip 001-0024-0 (thread 1) skip 001-0025-1 (thread 1) skip 001-0026-0 (thread 1) skip 001-0027-1 (thread 1) skip 001-0028-0 (thread 1) skip 001-0029-1 (thread 1) skip 001-0030-0 (thread 1) skip 001-0031-1 (thread 1) skip 001-0032-0 (thread 1) skip 001-0033-1 (thread 1) skip 001-0034-0 (thread 1) skip 001-0035-1 (thread 1) skip 001-0036-0 (thread 1) skip 001-0037-1 (thread 1) skip 001-0038-0 (thread 1) skip 001-0039-1 (thread 1) skip 001-0040-0 (thread 1) skip 001-0041-1 (thread 1) skip 001-0042-0 (thread 1) skip 001-0043-1 (thread 1) skip 001-0044-0 (thread 1) skip 001-0045-1 (thread 1) skip 001-0046-0 (thread 1) skip 001-0047-1 (thread 1) skip 001-0048-0 (thread 1) skip 001-0049-1 (thread 1) skip 001-0050-0 (thread 1) skip 001-0051-1 (thread 1) skip 001-0052-0 (thread 1) skip 001-0053-1 (thread 1) skip 001-0054-0 (thread 1) skip 001-0055-1 (thread 1) skip 001-0056-0 (thread 1) skip 001-0057-1 (thread 1) skip 001-0058-0 (thread 1) skip 001-0059-1 (thread 1) skip 001-0060-0 (thread 1) skip 001-0061-1 (thread 1) skip 001-0062-0 (thread 1) skip 001-0063-1 (thread 1) skip 001-0064-0 (thread 1) skip 001-0065-1 (thread 1) skip 001-0066-0 (thread 1) skip 001-0067-1 (thread 1) skip 001-0068-0 (thread 1) skip 001-0069-1 (thread 1) skip 001-0070-0 (thread 1) skip 001-0071-1 (thread 1) skip 001-0072-0 (thread 1) skip 001-0073-1 (thread 1) skip 001-0074-0 (thread 1) skip 001-0075-1 (thread 1) skip 001-0076-0 (thread 1) skip 001-0077-1 (thread 1) skip 001-0078-0 (thread 1) skip 001-0079-1 (thread 1) skip 001-0080-0 (thread 1) skip 001-0081-1 (thread 1) skip 001-0082-0 (thread 1) skip 001-0083-1 (thread 1) skip 001-0084-0 (thread 1) skip 001-0085-1 (thread 1) skip 001-0086-0 (thread 1) skip 001-0087-1 (thread 1) skip 001-0088-0 (thread 1) skip 001-0089-1 (thread 1) skip 001-0090-0 (thread 1) skip 001-0091-1 (thread 1) skip 001-0092-0 (thread 1) skip 001-0093-1 (thread 1) skip 001-0094-0 (thread 1) skip 001-0095-1 (thread 1) skip 001-0096-0 (thread 1) skip 001-0097-1 (thread 1) skip 001-0098-0 (thread 1) skip 001-0099-1 (thread 1) skip 001-0100-0 (thread 1) skip 001-0101-1 (thread 1) skip 001-0102-0 (thread 1) skip 001-0103-1 (thread 1) skip 001-0104-0 (thread 1) skip 001-0105-1 (thread 1) skip 001-0106-0 (thread 1) skip 001-0107-1 (thread 1) skip 001-0108-0 (thread 1) skip 001-0109-1 (thread 1) skip 001-0110-0 (thread 1) skip 001-0111-1 (thread 1) skip 001-0112-0 (thread 1) skip 001-0113-1 (thread 1) skip 001-0114-0 (thread 1) skip 001-0115-1 (thread 1) skip 001-0116-0 (thread 1) skip 001-0117-1 (thread 1) skip 001-0118-0 (thread 1) skip 001-0119-1 (thread 1) skip 001-0120-0 (thread 1) skip 001-0121-1 (thread 1) skip 001-0122-0 (thread 1) skip 001-0123-1 (thread 1) skip 001-0124-0 (thread 1) skip 001-0125-1 (thread 1) skip 001-0126-0 (thread 1) skip 001-0127-1 (thread 1) skip 001-0128-0 (thread 1) skip 001-0129-1 (thread 1) skip 001-0130-0 (thread 1) skip 001-0131-1 (thread 1) skip 001-0132-0 (thread 1) skip 001-0133-1 (thread 1) skip 001-0134-0 (thread 1) skip 001-0135-1 (thread 1) skip 001-0136-0 (thread 1) skip 001-0137-1 (thread 1) skip 001-0138-0 (thread 1) skip 001-0139-1 (thread 1) skip 001-0140-0 (thread 1) skip 001-0141-1 (thread 1) skip 001-0142-0 (thread 1) skip 001-0143-1 (thread 1) skip 001-0144-0 (thread 1) skip 001-0145-1 (thread 1) skip 001-0146-0 (thread 1) skip 001-0147-1 (thread 1) skip 001-0148-0 (thread 1) skip 001-0149-1 (thread 1) skip 001-0150-0 (thread 1) skip 001-0151-1 (thread 1) skip 001-0152-0 (thread 1) skip 001-0153-1 (thread 1) skip 001-0154-0 (thread 1) skip 001-0155-1 (thread 1) skip 001-0156-0 (thread 1) skip 001-0157-1 (thread 1) skip 001-0158-0 (thread 1) skip 001-0159-1 (thread 1) skip 001-0160-0 (thread 1) skip 001-0161-1 (thread 1) skip 001-0162-0 (thread 1) skip 001-0163-1 (thread 1) skip 001-0164-0 (thread 1) skip 001-0165-1 (thread 1) skip 001-0166-0 (thread 1) skip 001-0167-1 (thread 1) skip 001-0168-0 (thread 1) skip 001-0169-1 (thread 1) skip 001-0170-0 (thread 1) skip 001-0171-1 (thread 1) skip 001-0172-0 (thread 1) skip 001-0173-1 (thread 1) skip 001-0174-0 (thread 1) skip 001-0175-1 (thread 1) skip 001-0176-0 (thread 1) skip 001-0177-1 (thread 1) skip 001-0178-0 (thread 1) skip 001-0179-1 (thread 1) skip 001-0180-0 (thread 1) skip 001-0181-1 (thread 1) skip 001-0182-0 (thread 1) skip 001-0183-1 (thread 1) skip 001-0184-0 (thread 1) skip 001-0185-1 (thread 1) skip 001-0186-0 (thread 1) skip 001-0187-1 (thread 1) skip 001-0188-0 (thread 1) skip 001-0189-1 (thread 1) skip 001-0190-0 (thread 1) skip 001-0191-1 (thread 1) skip 001-0192-0 (thread 1) skip 001-0193-1 (thread 1) skip 001-0194-0 (thread 1) skip 001-0195-1 (thread 1) skip 001-0196-1 (thread 1) identical 001-0196-1 (thread 1) worse +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/mergeParallel.sh Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,56 @@ +#!/bin/bash + +my_func(){ + + ind1=$(($1*2-1)) + ind2=$(($1*2)) + + aln1=$(echo $4 | awk -v var="$ind1" '{print $var}') + aln2=$(echo $4 | awk -v var="$ind2" '{print $var}') + oName=$(echo $5 | awk -v var="$1" '{print $var}') + + echo "Merging $aln1.aln and $aln2.aln into $oName.aln" + + l1=$(grep -c ">" $aln1.aln) + l2=$(grep -c ">" $aln2.aln) + + if [ $l1 -eq "1" ] && [ $l2 -eq "1" ] + then + cat $aln1.aln $aln2.aln > temp.$6.$1.fas + mafft --localpair --preservecase --thread $2 --maxiterate $3 temp.$6.$1.fas > $oName.aln + elif [ $l1 -eq "1" ] + then + mafft --preservecase --thread $2 --maxiterate $3 --addfragments $aln1.aln $aln2.aln > $oName.aln + elif [ $l2 -eq "1" ] + then + mafft --preservecase --thread $2 --maxiterate $3 --addfragments $aln2.aln $aln1.aln > $oName.aln + else + cat $aln1.aln $aln2.aln > input.$6.$1.fas + str1="" + count=1 + gap=" " + + for i in $(seq 1 1 $l1) + do + str1=$str1$count$gap + count=$(($count+1)) + done + + echo $str1 > msaTable.$6.$1 + str2="" + for i in $(seq 1 1 $l2) + do + str2=$str2$count$gap + count=$(($count+1)) + done + + echo $str2 >> msaTable.$6.$1 + mafft --preservecase --thread $2 --maxiterate $3 --merge msaTable.$6.$1 input.$6.$1.fas > $oName.aln + + fi + +} + +export -f my_func + +parallel -j 1 my_func ::: $(seq 1 1 1) ::: 1 ::: 1 ::: "NODE_1 NODE_2" ::: "NODE_0" ::: "merge"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.1 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 +77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.10 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 4 +5 6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.11 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 +3 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.12 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 +4 5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.13 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 +3 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.14 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 +3 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.2 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 4 5 6 7 8 9 +10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.3 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 4 5 6 7 8 9 10 11 12 13 +14 15 16 17 18 19 20 21 22 23
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.4 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 4 5 6 7 8 9 10 +11 12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.5 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 +3 4 5 6 7 8 9 10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.6 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 +4 5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.7 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 +3 4 5 6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.8 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 3 4 5 +6 7 8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/msaTable.merge.9 Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2 @@ +1 2 +3 4 5 6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/pipelign.hmm Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,20013 @@ +HMMER3/f [3.2.1 | June 2018] +NAME long.0.aln +LENG 70 +MAXL 160 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:02 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 2713552590 +STATS LOCAL MSV -7.8785 0.72075 +STATS LOCAL VITERBI -9.2080 0.72075 +STATS LOCAL FORWARD -3.7706 0.72075 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.11533 1.40204 1.61408 1.48269 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 2.46232 0.33808 2.58153 2.07174 1 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 0.28818 2.60848 2.42319 2.42940 2 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 2.38910 2.82844 0.25233 2.62837 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 0.28818 2.60848 2.42319 2.42940 4 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 5 0.28818 2.60848 2.42319 2.42940 5 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 6 2.38910 2.82844 0.25233 2.62837 6 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 7 2.31486 2.12647 2.41211 0.36768 7 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 8 2.38910 2.82844 0.25233 2.62837 8 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 9 0.28818 2.60848 2.42319 2.42940 9 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 10 2.31486 2.12647 2.41211 0.36768 10 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 11 0.28818 2.60848 2.42319 2.42940 11 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 12 2.46232 0.33808 2.58153 2.07174 12 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 13 2.46232 0.33808 2.58153 2.07174 13 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 14 2.46232 0.33808 2.58153 2.07174 14 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 15 0.28818 2.60848 2.42319 2.42940 15 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 16 2.31486 2.12647 2.41211 0.36768 16 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 17 2.38910 2.82844 0.25233 2.62837 17 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 18 2.31486 2.12647 2.41211 0.36768 18 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 19 2.31486 2.12647 2.41211 0.36768 19 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 20 2.31486 2.12647 2.41211 0.36768 20 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 21 2.31486 2.12647 2.41211 0.36768 21 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 22 2.46232 0.33808 2.58153 2.07174 22 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 23 0.28818 2.60848 2.42319 2.42940 23 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 24 2.38910 2.82844 0.25233 2.62837 24 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 25 2.46232 0.33808 2.58153 2.07174 25 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 26 0.28818 2.60848 2.42319 2.42940 26 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 27 2.31486 2.12647 2.41211 0.36768 27 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 28 2.31486 2.12647 2.41211 0.36768 28 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 29 0.28818 2.60848 2.42319 2.42940 29 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 30 2.31486 2.12647 2.41211 0.36768 30 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 31 2.46232 0.33808 2.58153 2.07174 31 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 32 0.28818 2.60848 2.42319 2.42940 32 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 33 2.38910 2.82844 0.25233 2.62837 33 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 34 0.28818 2.60848 2.42319 2.42940 34 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 35 0.28818 2.60848 2.42319 2.42940 35 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 36 2.38910 2.82844 0.25233 2.62837 36 g - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.02469 3.71357 * 1.46634 0.26236 0.00000 * +// +HMMER3/f [3.2.1 | June 2018] +NAME long.40.aln +LENG 85 +MAXL 180 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Tue May 28 13:12:03 2019 +NSEQ 2 +EFFN 2.000000 +CKSUM 850921081 +STATS LOCAL MSV -9.2442 0.73770 +STATS LOCAL VITERBI -10.9061 0.73770 +STATS LOCAL FORWARD -3.0276 0.73770 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.34684 1.48715 1.41637 1.30441 + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * + 1 1.09289 1.89038 1.88803 1.01509 1 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 2 1.84050 1.95342 1.03654 1.06480 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 3 1.84050 1.95342 1.03654 1.06480 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 4 1.09289 1.89038 1.88803 1.01509 4 t - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 66 2.38910 2.82844 0.25233 2.62837 66 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 67 2.46232 0.33808 2.58153 2.07174 67 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 68 0.28818 2.60848 2.42319 2.42940 68 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 69 2.31486 2.12647 2.41211 0.36768 69 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 + 70 2.46232 0.33808 2.58153 2.07174 70 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.02469 3.71357 * 1.46634 0.26236 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/pipelign.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,1042 @@ + +[28 May 13:09:56] Pipelign started with sequence file <pipelign-in1.fasta> +================================================================ +Program: CD-HIT, V4.8.1 (+OpenMP), May 14 2019, 14:40:47 +Command: cd-hit-est -c 0.8 -n 5 -i long.good.fas -o grp -d 0 + -T 1 + +Started: Tue May 28 13:09:56 2019 +================================================================ + Output +---------------------------------------------------------------- +total seq: 100 +longest and shortest : 70 and 70 +Total letters: 7000 +Sequences have been sorted + +Approximated minimal memory consumption: +Sequence : 0M +Buffer : 1 X 12M = 12M +Table : 1 X 0M = 0M +Miscellaneous : 0M +Total : 12M + +Table limit with the given memory limit: +Max number of representatives: 4000000 +Max number of word counting entries: 98487020 + + +comparing sequences from 0 to 100 + + 100 finished 84 clusters + +Approximated maximum memory consumption: 12M +writing new database +writing clustering information +program completed ! + +Total CPU time 0.04 +inputfile = orig +84 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 84 (by thread 0) + 10 / 84 (by thread 0) + 20 / 84 (by thread 0) + 30 / 84 (by thread 0) + 40 / 84 (by thread 0) + 50 / 84 (by thread 0) + 60 / 84 (by thread 0) + 70 / 84 (by thread 0) + 80 / 84 (by thread 0) +tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + + 0 / 84 + 10 / 84 + 20 / 84 + 30 / 84 + 40 / 84 + 50 / 84 + 60 / 84 + 70 / 84 + 80 / 84 +done. + +Progressive alignment ... + +STEP 1 /83 (thread 0) +STEP 2 /83 (thread 0) +STEP 3 /83 (thread 0) +STEP 4 /83 (thread 0) +STEP 5 /83 (thread 0) +STEP 6 /83 (thread 0) +STEP 7 /83 (thread 0) +STEP 8 /83 (thread 0) +STEP 9 /83 (thread 0) +STEP 10 /83 (thread 0) +STEP 11 /83 (thread 0) +Reallocating (by thread 0) ..done. *alloclen = 1159 + +STEP 12 /83 (thread 0) +STEP 13 /83 (thread 0) +STEP 14 /83 (thread 0) +STEP 15 /83 (thread 0) +STEP 16 /83 (thread 0) +STEP 17 /83 (thread 0) +STEP 18 /83 (thread 0) +STEP 19 /83 (thread 0) +STEP 20 /83 (thread 0) +STEP 21 /83 (thread 0) +STEP 22 /83 (thread 0) +STEP 23 /83 (thread 0) +STEP 24 /83 (thread 0) +STEP 25 /83 (thread 0) +STEP 26 /83 (thread 0) +STEP 27 /83 (thread 0) +STEP 28 /83 (thread 0) +STEP 29 /83 (thread 0) +STEP 30 /83 (thread 0) +STEP 31 /83 (thread 0) +STEP 32 /83 (thread 0) +STEP 33 /83 (thread 0) +STEP 34 /83 (thread 0) +STEP 35 /83 (thread 0) +STEP 36 /83 (thread 0) +STEP 37 /83 (thread 0) +STEP 38 /83 (thread 0) +STEP 39 /83 (thread 0) +STEP 40 /83 (thread 0) +STEP 41 /83 (thread 0) +STEP 42 /83 (thread 0) +STEP 43 /83 (thread 0) +STEP 44 /83 (thread 0) +STEP 45 /83 (thread 0) +STEP 46 /83 (thread 0) +STEP 47 /83 (thread 0) +STEP 48 /83 (thread 0) +STEP 49 /83 (thread 0) +STEP 50 /83 (thread 0) +STEP 51 /83 (thread 0) +STEP 52 /83 (thread 0) +STEP 53 /83 (thread 0) +STEP 54 /83 (thread 0) +STEP 55 /83 (thread 0) +STEP 56 /83 (thread 0) +STEP 57 /83 (thread 0) +STEP 58 /83 (thread 0) +STEP 59 /83 (thread 0) +STEP 60 /83 (thread 0) +STEP 61 /83 (thread 0) +STEP 62 /83 (thread 0) +STEP 63 /83 (thread 0) +STEP 64 /83 (thread 0) +STEP 65 /83 (thread 0) +STEP 66 /83 (thread 0) +STEP 67 /83 (thread 0) +STEP 68 /83 (thread 0) +STEP 69 /83 (thread 0) +STEP 70 /83 (thread 0) +STEP 71 /83 (thread 0) +STEP 72 /83 (thread 0) +STEP 73 /83 (thread 0) +STEP 74 /83 (thread 0) +STEP 75 /83 (thread 0) +STEP 76 /83 (thread 0) +STEP 77 /83 (thread 0) +STEP 78 /83 (thread 0) +STEP 79 /83 (thread 0) +STEP 80 /83 (thread 0) +STEP 81 /83 (thread 0) +STEP 82 /83 (thread 0) +STEP 83 /83 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 84 + 10 / 84 + 20 / 84 + 30 / 84 + 40 / 84 + 50 / 84 + 60 / 84 + 70 / 84 + 80 / 84 +Segment 1/ 1 1- 271 +001-0000-0 (thread 1) identical +001-0000-0 (thread 1) worse + +001-0001-1 (thread 1) identical +001-0001-1 (thread 1) worse + +001-0002-0 (thread 1) identical +001-0002-0 (thread 1) worse + +001-0003-1 (thread 1) identical + +001-0004-0 (thread 1) identical +001-0004-0 (thread 1) worse + +001-0005-1 (thread 1) identical +001-0005-1 (thread 1) better + +001-0006-0 (thread 1) identical +001-0006-0 (thread 1) better + +001-0007-1 (thread 1) identical +001-0007-1 (thread 1) worse + +001-0008-0 (thread 1) identical +001-0008-0 (thread 1) worse + +001-0009-1 (thread 1) identical +001-0009-1 (thread 1) worse + +001-0010-0 (thread 1) identical +001-0010-0 (thread 1) worse + +001-0011-1 (thread 1) identical + +001-0012-0 (thread 1) identical + +001-0013-1 (thread 1) identical +001-0013-1 (thread 1) better + +001-0014-0 (thread 1) identical + +001-0015-1 (thread 1) identical +001-0015-1 (thread 1) worse + +001-0016-0 (thread 1) identical + +001-0017-1 (thread 1) identical + +001-0018-0 (thread 1) identical +001-0018-0 (thread 1) worse + +001-0019-1 (thread 1) identical +001-0019-1 (thread 1) better + +001-0020-0 (thread 1) identical +001-0020-0 (thread 1) worse + +001-0021-1 (thread 1) identical +001-0021-1 (thread 1) better + +001-0022-0 (thread 1) identical + +001-0023-1 (thread 1) identical +001-0023-1 (thread 1) better + +001-0024-0 (thread 1) identical +001-0024-0 (thread 1) worse + 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identical +001-0040-0 (thread 1) worse + +001-0041-1 (thread 1) identical +001-0041-1 (thread 1) better + +001-0042-0 (thread 1) identical +001-0042-0 (thread 1) worse + +001-0043-1 (thread 1) identical +001-0043-1 (thread 1) better + +001-0044-0 (thread 1) identical +001-0044-0 (thread 1) worse + +001-0045-1 (thread 1) identical +001-0045-1 (thread 1) better + +001-0046-0 (thread 1) identical +001-0046-0 (thread 1) worse + +001-0047-1 (thread 1) identical +001-0047-1 (thread 1) worse + +001-0048-0 (thread 1) identical +001-0048-0 (thread 1) worse + +001-0049-1 (thread 1) identical +001-0049-1 (thread 1) worse + +001-0050-0 (thread 1) identical +001-0050-0 (thread 1) worse + +001-0051-1 (thread 1) identical + +001-0052-0 (thread 1) identical +001-0052-0 (thread 1) worse + +001-0053-1 (thread 1) identical +001-0053-1 (thread 1) worse + +001-0054-0 (thread 1) identical +001-0054-0 (thread 1) better + +001-0055-1 (thread 1) identical +001-0055-1 (thread 1) better + +001-0056-0 (thread 1) identical +001-0056-0 (thread 1) worse + +001-0057-1 (thread 1) identical +001-0057-1 (thread 1) worse + +001-0058-0 (thread 1) identical + +001-0059-1 (thread 1) identical +001-0059-1 (thread 1) better + +001-0060-0 (thread 1) identical +001-0060-0 (thread 1) worse + +001-0061-1 (thread 1) identical +001-0061-1 (thread 1) worse + +001-0062-0 (thread 1) identical +001-0062-0 (thread 1) better + +001-0063-1 (thread 1) identical +001-0063-1 (thread 1) worse + +001-0064-0 (thread 1) identical +001-0064-0 (thread 1) worse + +001-0065-1 (thread 1) identical +001-0065-1 (thread 1) better + +001-0066-0 (thread 1) identical +001-0066-0 (thread 1) better + +001-0067-1 (thread 1) identical +001-0067-1 (thread 1) better + +001-0068-0 (thread 1) identical +001-0068-0 (thread 1) worse + +001-0069-1 (thread 1) identical +001-0069-1 (thread 1) worse + +001-0070-0 (thread 1) identical +001-0070-0 (thread 1) worse + +001-0071-1 (thread 1) identical +001-0071-1 (thread 1) better + +001-0072-0 (thread 1) identical + +001-0073-1 (thread 1) identical +001-0073-1 (thread 1) better + +001-0074-0 (thread 1) identical +001-0074-0 (thread 1) worse + +001-0075-1 (thread 1) identical +001-0075-1 (thread 1) better + +001-0076-0 (thread 1) identical +001-0076-0 (thread 1) better + +001-0077-1 (thread 1) identical +001-0077-1 (thread 1) better + +001-0078-0 (thread 1) identical +001-0078-0 (thread 1) worse + +001-0079-1 (thread 1) identical +001-0079-1 (thread 1) worse + +001-0080-0 (thread 1) identical +001-0080-0 (thread 1) worse + +001-0081-1 (thread 1) identical +001-0081-1 (thread 1) worse + +001-0082-0 (thread 1) identical + +001-0083-1 (thread 1) identical +001-0083-1 (thread 1) better + +001-0084-0 (thread 1) identical +001-0084-0 (thread 1) worse + +001-0085-1 (thread 1) identical +001-0085-1 (thread 1) worse + +001-0086-0 (thread 1) identical +001-0086-0 (thread 1) worse + +001-0087-1 (thread 1) identical + +001-0088-0 (thread 1) identical +001-0088-0 (thread 1) worse + +001-0089-1 (thread 1) identical +001-0089-1 (thread 1) worse + +001-0090-0 (thread 1) identical +001-0090-0 (thread 1) better + +001-0091-1 (thread 1) identical +001-0091-1 (thread 1) better + +001-0092-0 (thread 1) identical +001-0092-0 (thread 1) worse + +001-0093-1 (thread 1) identical +001-0093-1 (thread 1) better + +001-0094-0 (thread 1) identical +001-0094-0 (thread 1) better + +001-0095-1 (thread 1) identical +001-0095-1 (thread 1) better + +001-0096-0 (thread 1) identical +001-0096-0 (thread 1) worse + +001-0097-1 (thread 1) identical +001-0097-1 (thread 1) worse + +001-0098-0 (thread 1) identical +001-0098-0 (thread 1) worse + +001-0099-1 (thread 1) identical +001-0099-1 (thread 1) worse + +001-0100-0 (thread 1) identical +001-0100-0 (thread 1) worse + +001-0101-1 (thread 1) identical +001-0101-1 (thread 1) worse + +001-0102-0 (thread 1) identical + +001-0103-1 (thread 1) identical + +001-0104-0 (thread 1) identical +001-0104-0 (thread 1) worse + +001-0105-1 (thread 1) identical 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1) better + +001-0123-1 (thread 1) identical + +001-0124-0 (thread 1) identical +001-0124-0 (thread 1) better + +001-0125-1 (thread 1) identical +001-0125-1 (thread 1) better + +001-0126-0 (thread 1) identical + +001-0127-1 (thread 1) identical +001-0127-1 (thread 1) worse + +001-0128-0 (thread 1) identical +001-0128-0 (thread 1) worse + +001-0129-1 (thread 1) identical +001-0129-1 (thread 1) worse + +001-0130-0 (thread 1) identical +001-0130-0 (thread 1) better + +001-0131-1 (thread 1) identical +001-0131-1 (thread 1) better + +001-0132-0 (thread 1) identical +001-0132-0 (thread 1) better + +001-0133-1 (thread 1) identical + +001-0134-0 (thread 1) identical +001-0134-0 (thread 1) worse + +001-0135-1 (thread 1) identical + +001-0136-0 (thread 1) identical + +001-0137-1 (thread 1) identical +001-0137-1 (thread 1) worse + +001-0138-0 (thread 1) identical +001-0138-0 (thread 1) worse + +001-0139-1 (thread 1) identical +001-0139-1 (thread 1) better + +001-0140-0 (thread 1) identical + +001-0141-1 (thread 1) identical +001-0141-1 (thread 1) better + +001-0142-0 (thread 1) identical + +001-0143-1 (thread 1) identical +001-0143-1 (thread 1) worse + +001-0144-0 (thread 1) identical +001-0144-0 (thread 1) worse + +001-0145-1 (thread 1) identical +001-0145-1 (thread 1) better + +001-0146-0 (thread 1) identical +001-0146-0 (thread 1) better + +001-0147-1 (thread 1) identical +001-0147-1 (thread 1) worse + +001-0148-0 (thread 1) identical + +001-0149-1 (thread 1) identical +001-0149-1 (thread 1) better + +001-0150-0 (thread 1) identical + +001-0151-1 (thread 1) identical + +001-0152-0 (thread 1) identical + +001-0153-1 (thread 1) identical + +001-0154-0 (thread 1) identical + +001-0155-1 (thread 1) identical + +001-0156-0 (thread 1) identical + +001-0157-1 (thread 1) identical +001-0157-1 (thread 1) worse + +001-0158-0 (thread 1) identical + +001-0159-1 (thread 1) identical +001-0159-1 (thread 1) worse + +001-0160-0 (thread 1) identical +001-0160-0 (thread 1) worse + +001-0161-1 (thread 1) identical +001-0161-1 (thread 1) worse + +001-0162-0 (thread 1) identical +001-0162-0 (thread 1) worse + +001-0163-1 (thread 1) identical +001-0163-1 (thread 1) worse + +001-0164-1 (thread 1) identical +001-0164-1 (thread 1) worse + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019 +Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, +Heiko Schmidt, Dominik Schrempf, Michael Woodhams. + +Host: gaius (AVX2, FMA3, 15 GB RAM) +Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1 +Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue May 28 13:09:57 2019 +Kernel: AVX+FMA - 1 threads (8 CPU cores detected) + +HINT: Use -nt option to specify number of threads because your CPU has 8 cores! +HINT: -nt AUTO will automatically determine the best number of threads to use. + +Reading alignment file clsReps.aln ... Fasta format detected +Alignment most likely contains DNA/RNA sequences +Alignment has 84 sequences with 305 columns, 301 distinct patterns +238 parsimony-informative, 52 singleton sites, 15 constant sites +WARNING: Some sequence names are changed as follows: +K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 -> K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 +K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 -> K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 +K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 -> K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 +K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 -> K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 +K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 -> K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 +K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 -> K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 +K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 -> K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 +K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 -> K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 +K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 -> K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 +K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 -> K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 +K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 -> K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 +K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 -> K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 +K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 -> K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 +K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 -> K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 +K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 -> K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 +K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 -> K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 +K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 -> K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 +K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 -> K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 +K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 -> K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 +K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 -> K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 +K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 -> K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 +K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 -> K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 +K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 -> K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 +K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 -> K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 +K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 -> K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 +K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 -> K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 +K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 -> K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 +K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 -> K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 +K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 -> K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 +K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 -> K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 +K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 -> K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 +K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 -> K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 +K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 -> K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 +K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 -> K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 +K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 -> K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 +K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 -> K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 +K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 -> K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 +K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 -> K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 +K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 -> K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 +K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 -> K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 +K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 -> K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 +K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 -> K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 +K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 -> K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 +K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 -> K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 +K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 -> K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 +K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 -> K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 +K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 -> K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 +K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 -> K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 +K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 -> K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 +K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 -> K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 +K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 -> K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 +K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 -> K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 +K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 -> K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 +K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 -> K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 +K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 -> K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 +K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 -> K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 +K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 -> K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 +K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 -> K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 +K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 -> K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 +K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 -> K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 +K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 -> K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 +K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 -> K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 +K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 -> K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 +K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 -> K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 +K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 -> K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 +K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 -> K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 +K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 -> K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 +K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 -> K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 +K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 -> K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 +K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 -> K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 +K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 -> K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 +K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 -> K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 +K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 -> K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 +K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 -> K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 +K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 -> K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 +K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 -> K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 +K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 -> K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 +K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 -> K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 +K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 -> K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 +K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 -> K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 +K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 -> K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 +K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 -> K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 +K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 -> K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 +K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 -> K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 + + Gap/Ambiguity Composition p-value + 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90% + 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53% + 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21% + 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36% + 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86% + 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72% + 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71% + 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58% + 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28% + 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71% + 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76% + 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06% + 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72% + 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74% + 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54% + 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66% + 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47% + 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11% + 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61% + 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18% + 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00% + 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75% + 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23% + 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67% + 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02% + 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52% + 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05% + 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57% + 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98% + 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02% + 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08% + 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03% + 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47% + 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89% + 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36% + 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48% + 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92% + 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51% + 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24% + 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06% + 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06% + 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00% + 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90% + 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68% + 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88% + 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28% + 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89% + 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69% + 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81% + 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95% + 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20% + 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44% + 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71% + 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60% + 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49% + 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92% + 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75% + 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72% + 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57% + 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40% + 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77% + 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83% + 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48% + 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69% + 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64% + 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23% + 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65% + 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90% + 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19% + 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60% + 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10% + 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03% + 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28% + 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17% + 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26% + 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77% + 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37% + 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04% + 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16% + 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98% + 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70% + 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88% + 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25% + 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89% +WARNING: 84 sequences contain more than 50% gaps/ambiguity +**** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3) + +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds + +NOTE: 3 MB RAM (0 GB) is required! +Estimate model parameters (epsilon = 0.100) +1. Initial log-likelihood: -7393.152 +2. Current log-likelihood: -6850.590 +3. Current log-likelihood: -6814.795 +4. Current log-likelihood: -6812.204 +5. Current log-likelihood: -6811.732 +6. Current log-likelihood: -6811.618 +Optimal log-likelihood: -6811.491 +Rate parameters: A-C: 1.16582 A-G: 3.17373 A-T: 0.69428 C-G: 1.33012 C-T: 3.22998 G-T: 1.00000 +Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 +Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200) +Parameters optimization took 6 rounds (0.508 sec) +Computing ML distances based on estimated model parameters... 0.032 sec +WARNING: Some pairwise ML distances are too long (saturated) +Computing BIONJ tree... +0.003 seconds +Log-likelihood of BIONJ tree: -6859.680 +-------------------------------------------------------------------- +| INITIALIZING CANDIDATE TREE SET | +-------------------------------------------------------------------- +Generating 98 parsimony trees... 1.076 second +Computing log-likelihood of 98 initial trees ... 1.196 seconds +Current best score: -6803.399 + +Do NNI search on 20 best initial trees +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 1: -6746.667 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 4: -6743.453 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 8: -6739.399 +Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s +Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s +Finish initializing candidate tree set (20) +Current best tree score: -6739.399 / CPU time: 11.455 +Number of iterations: 20 +-------------------------------------------------------------------- +| OPTIMIZING CANDIDATE TREE SET | +-------------------------------------------------------------------- +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 24: -6738.697 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 25: -6730.006 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 27: -6728.392 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 29: -6725.172 +Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 31: -6723.283 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 37: -6720.321 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 39: -6717.689 +Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 41: -6717.333 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 44: -6715.754 +Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 56: -6714.598 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 59: -6714.257 +Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 66: -6713.872 +Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left) +Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left) +Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left) +Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left) +BETTER TREE FOUND at iteration 105: -6713.864 +Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left) +Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 123: -6712.300 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 126: -6710.985 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 127: -6710.445 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 130: -6709.739 +Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 136: -6709.364 +Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 142: -6709.294 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 147: -6708.895 +Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 160: -6708.749 +Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 163: -6708.686 +Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 173: -6708.554 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 180: -6708.518 +Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left) +Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 193: -6705.296 +BETTER TREE FOUND at iteration 200: -6705.295 +Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 202: -6705.270 +Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left) +Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left) +Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left) +Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left) +Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left) +Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left) +Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left) +Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left) +Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left) +BETTER TREE FOUND at iteration 293: -6705.270 +BETTER TREE FOUND at iteration 295: -6705.269 +Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left) +Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left) +Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left) +UPDATE BEST LOG-LIKELIHOOD: -6705.269 +Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left) +Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left) +Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left) +Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left) +Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left) +Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left) +Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left) +TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s + +-------------------------------------------------------------------- +| FINALIZING TREE SEARCH | +-------------------------------------------------------------------- +Performs final model parameters optimization +Estimate model parameters (epsilon = 0.010) +1. Initial log-likelihood: -6705.269 +Optimal log-likelihood: -6705.266 +Rate parameters: A-C: 1.13682 A-G: 3.52293 A-T: 0.74232 C-G: 0.82784 C-T: 3.38691 G-T: 1.00000 +Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 +Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143) +Parameters optimization took 1 rounds (0.062 sec) +BEST SCORE FOUND : -6705.266 +Total tree length: 81.560 + +Total number of iterations: 396 +CPU time used for tree search: 114.612 sec (0h:1m:54s) +Wall-clock time used for tree search: 119.058 sec (0h:1m:59s) +Total CPU time used: 115.545 sec (0h:1m:55s) +Total wall-clock time used: 120.013 sec (0h:2m:0s) + +Analysis results written to: + IQ-TREE report: clsReps.aln.iqtree + Maximum-likelihood tree: clsReps.aln.treefile + Likelihood distances: clsReps.aln.mldist + Screen log file: clsReps.aln.log + +Date and Time: Tue May 28 13:11:57 2019 +Working... done. +Pressed and indexed 84 HMMs (84 names). +Models pressed into binary file: pipelign.hmm.h3m +SSI index for binary model file: pipelign.hmm.h3i +Profiles (MSV part) pressed into: pipelign.hmm.h3f +Profiles (remainder) pressed into: pipelign.hmm.h3p + +Alignment files and HMMs can be found in <files> + Long sequence alignments have names <long.xx.aln> + HMM file written in <long.xx.hmm> + HMM database written in <pipelign.hmm> + +[28 May 13:12:16] Alignment with long sequences and fragments written in <final.noOrphans.aln> + +[28 May 13:12:16] <final.noBadSeq.aln> file created
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/pipeline.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,3 @@ + +Fragment file <frag.fas> does not exist. No fragments found for assigning clusters. +[28 May 13:12:04] Cluster alignments are written in <cls.xx.aln>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.1.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATC +TGAGCCTGGG +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTG +CACCCCTGCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.10.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACT +ACTTCAATAA +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAA +TAGCTCTACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.11.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGG +CTATACATTC +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTC +TAGGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.15.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACA +TCCCACTAGG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGC +CCACACTAAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.16.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTAT +TTTGTGCATC +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACT +ATAGCCCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.17.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTC +CCTAGTTAGC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAG +AGAGCTCCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.18.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACA +TATTGACCAC +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGC +CATCCAATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.19.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAAC +AGCAGTTGTT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTC +TTCTATTCCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.20.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTA +ACAGTACTGG +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCT +TCTGATTTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.24.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTC +TGTTCCAGAG +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAA +AAAGACAGTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.25.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACC +TAGCAATTCA +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCAC +CTCCCAACCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.26.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAG +TGACCTGAGG +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTAT +AAACAATGAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.27.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACA +TAAAAGTAGT +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAA +GAAAAGCAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.29.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACT +GTCTTTTTTC +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATAC +TGGAGTATTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.4.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAG +CACTAATAAT +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT +GAGTGGTCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.5.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGA +AACAGCATAT +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATA +TAGAAGCAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.6.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGA +AGCTGTTAGA +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACA +TCATTAGTGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.8.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATA +ATTGCCTTAC +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAAT +TTCCCCACTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/temp.merge.9.fas Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6 @@ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTG +AAGATCTCGG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATA +ATTCCCTTCT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +----------------------------GA------TCCTGC-------------ATATA +AGCAGCAGCTTTTTGCCTTT------------ACTGGTTCTCTCTGGTTAGAC------- +------------------------------------------------------CAGATC +TGAGCCTGGG---------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +---------------------------CAG------ATACCT-------------AAATG +ATCAACAGCTCCTGGGGATT-------------TGGGGTTGCTCTGGAAAACT------- +------------------------------------------------------CATTTG +CACCCCTGCT---------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGG------------------------------------GGCATCAAGCAGCTCCAG +G-------CAAGAATGCTGGCTGTGGAAAG------ATACCT-------------AAAGG +ATCAACAGCTCC------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACCATTAAAACTGT +GGTTACAATATC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGGT---------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +-------------------ACAGTAGAAAA------ATTCCCCTCCACAATTAAAACTGT +GGTTACAATTTC---------------------TGGGTCCCCTCC--------------- +-----------------------------------------------------------T +GAGGATTGCT---------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTG------------------------------------------------ACTCCAA +------------------TACTGTAGGAGA------TTCCAC------------------ +-----CAATATT---------------------TGAGGGCTTCCCACCCCCTG------- +------------------------------------------------------CGTCCC +AGAAGTT------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +----------------------------------------------------ATCCTCAT +-------------GCATCTGTTCTACCATG------TCATTTTT-----------CCACA +TGTTAAAATTTTCTGT-----------------CACATTTAC---CAATACT-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +----------------------------------------------------TT------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAA------------ +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +------------------------------------------------------------ +---------------GGTAAATGTGACAGA------AAATTTTA-----------ACATG +TGGAAAAATGACATGG-----------------TAGA---AC---AGATGCA-------- +------------------------------------------------------------ +---------------TGAGGATATAAT-----C----- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +--TTAAAATTTTCTGT-----------------CACATTTAC---CAATACTA------- +------------------------------------------------------CTTCTT +GTGGGTTGGGGTCTGTGGGTACACAGGCATGTG----- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +--------------CACCCATCCAAAGGAA------TTGAGGTT-----------CTTT- +--CTGATGTTTTTTGT-----------------CTGGTGTGG---TAAGTCCC------- +------------------------------------------------------CACCTC +GACAG--------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTA------------------------------------------TATTTTTTCTTAC +-------------CCCCTGGCCTTAACCGA------ATTTTTTC-----------CCATC +GATCTAATTCTCC--------------------CCCGCTTAA------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCC--------------------------------------------CTGTTCG------ +---------------GGCGCCACTGCTAGA------GATTTTCC-----------ACACT +GACTAAAAGGGTCTGA-----------------GGGA---TCTCTAGTTACC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +------------------------------------------AGTAAGTAGTACCTGTAA +C--GCAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCACTAATAAT------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +----CAACCTATACCAATAG-TAGCAATAG------TAGCATTA-----------GTAGT +AGCAATAATAATAGCAATAG------------TTGAGTGGTC------------------ +------------------------------------------------------------ +---------------------------CA--------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAA------------TTGGAG--------------AGCAATGGCTAGTGATTTTAA +CCTGCCACCTGTAGTAGCAA-AAGAAATAG------TAGCCCG----------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +---------TATGGTACCAGTTAGAGAAAG------AACCCCTA-----------GTAGG +AGCAGAAACCTTCTATGTAG------------ATGGGGCAGC------------------ +------------------------------------------------------------ +---------------------------TAACAG----- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +---------------------------------------------AGTTCATGTATCCAG +T----------GGATATATAGAAGCAGAAG------TTATTCCAGCAGAAACAGGGGCTG +AAACAGCATAT------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACA--------CATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAG +T----------GGATATATAGAAGCAGA-------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +--------------TATAAAGACGCAGAAG------TTATTCCAGCATACACAGGGCAGG +AAACAGCATATTTTCTTTT--------------CAAATTAG------------------- +------------------------------------------------------------ +-----------CAG------------------------ +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +--------------TGCTAA-----------------------------------TTTTA +AAAGACAATATTCTGTTTC--------------CTGCCCTGTTTCTGCTGGAA------- +------------------------------------------------------TAACTT +CTGCTTCTATATAT------------------------ +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +--------------GCCA---CAGAGGGAG------CCACACAA-----------TGAAT +GGACACTATAGCTTTTAGAG--GAGCTTAAGAATGAAGCTGTTA---------------- +------------------------------------------------------------ +------------------GA------------------ +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------------CC--------------------CCATAT------------------ +---TACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTA------- +------------------------------------------------------CATCAT +TAG--------------TGT------------------ +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +----------------------CAGAGGAG------GTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGGGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCGG-CGACT------------------ +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +----------------GGAAACCAGAGGAG------CTCTCT------------------ +----------------------CGACGCAGGACTCGGCTTGCTGAAGCGCGCA------- +------------------------------------------------------CGGCAA +GAGGCGAGGGGCG------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +--------------TAGGAACCAAAGAAAG------ATAGTT------------------ +----------------------AAGTGTTTCAATTGTGGCACAGAAGGGCACA------- +------------------------------------------------------CAGCCA +GAAATTGCAGG--------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTC-----------------------------TGTTAGTGGTATTACTTCTGTTAG +TGCTTTGGTACCTCTAAGGAGTTTACATAA------TTGCCTTAC--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +----------------AGGATTTTACATAA------TTGCCTTACTTAAATCCCTGGGTA +AATCTGACTTGCCCAATT---------------CAATTTCCCCA---------------- +-----------------------------------------------------------C +TA------------------------------------ +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +-------------ACTTTATATTTATATAA------TTCACTTCTCCAATTGTCC----- +-----------CTCATCT---------------CTCCTCCTCCAGGTCTGAAG------- +-------------------------------------------------------ATCTC +GG------------------------------------ +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGC-----------------------------CTTGGTTGGAGCAACTCCTAATGG +TTGAATTTTTACTACTTTATATTTATATAA------TTCCCTTCT--------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +-----------------------TCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGCATAGCTCTACAAGC---------------TCCTTGTACTACTTCAATAA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +-----------------------------------------------------------A +CCCATCTTATAGCA-AAATCCTTTCCAAG-----CCCTGTCTTATTCTTCTAGGTATGTG +GCGAATAGCTCTACA--------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +----------TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAAT +GCTGGTAGGGCT------------------------AT---------ACATTC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +----------AATA-GCAATTTGTACAAG-------CAGTTTTAGGCTGACTTCGTGGAT +GCTTCCAGGGCT------------------------CTCGTCTA-GGATCAAC------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +----------TGTG-TTCAGCTGTACTAT-------TATGGTTATAGCATTTTCCGTGAA +ATTGACAGATCTAATTAC---------------TACCTCTTCT----------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +----------------------------------------CTACTATTGCTACTAATGGT +ATAGGTTGCGTTACATGT---------------ACTACTTACTGCTTTGATAGA------ +-----------------------------------------------------GAAGCTT +GAT-----------------------------G----- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +--------------------------------------TCGGAGTCATTGTTGCTATTAC +CACCATCTTTTGTTCATAGCAGCCCTGTAA------TATTTGATT--------------- +------------------------------------------------------------ +------------------------------------------------------AACATC +TAA----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +---------------------------------------------------TTTGATTG- +-ACTAACTCTGATTCACTTTGATCTTGTAG------TGCTTGAAT--------------- +------------------------------------------------------------ +------------------------------------------------------GATTCC +TAATGCATAT-----TGTGA----------GTC----- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +-----------------------CGAGCA-----AGCTTCACAGGAGTTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGAT--------------------------------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +--------------------------------------TCACAGGAGGTAAA-------- +-----------------------AAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CTA------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +------------------------------------------------------------ +-------------------------------TGACAGAAACCTAGTTGGTCCAAAATGCG +AACCCAGATTGTAAGA-----------------CAATTTTAAAAGCATTGGGACCAGC-- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------ATTTTAAAAGCATTGGGACCAGCGG +CTACACTAGAAGAAATGATGACAGCATGTCAGGGAG-------------TAGGATGAC-- +-------------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------------------------------CTACCTCTTCTTCTGCTAGACTGC +C-----------------------------------ATTTAACAGCAGTTGAGTTGATA- +---------------------------------------------CTACTGGCCTAATTC +CATGT--------------------------GT----- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +------------------------------------------------------------ +----------------------TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGC +A-----------------------------------GTCTAGCAGAAGAAGAGGTAGTA- +---------------------------------------------AT-------TAGATC +-------------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +---TAACG---------------------------------------------------- +-----------------CCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGA +AC---AA----------------------------GCCCCAGAAGACGAAGGG------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGA----------------------------------------------------- +------------------------GAGAGACAGAGACAGATCCATTCGATTAGTGAACGG +ATCC----------------------------------TTGGCACTTATCTGGGA----- +------------------------------------------------------CGATCT +-------------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGA---------------------------------------------------- +-----------------TCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGG +ATCTGA------------------------------CTCTGTCTCT-------------- +---------------------------------------------------------CTC +-------------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTA-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +-----TA----------------------------------------------------- +---------------------TCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGG +AGCCAAA----------------------------TCCTAGGAAAATGTCTAAC------ +---------------------------------------------------------AGC +-------------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +----TGC----------------------------------------------------- +---------------------TCTGAAGAAAATTCCCTG----GCCTTCCCTTGTAGTAA +GGCCATA----------------------------TCTTCCCTAAAAAATTAGC------ +---------------------------------------------------------CTG +TCT----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAA---------------------------------------------------- +-----------------------------------GCAATCTGATTCACCCGATTTCTTC +C-----------------------------------AATTATGATGACAGGTGTAGGTC- +---------------------------------------------CTACTAATACAGT-- +-------------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GAT--------------------------------------------------------- +-----------------------------------------------GGTTTTATAGACA +TCA---------------------------------CTATGAAAGCCCTCATCCAAGAAA +-----------------AAGTTCAGAAGTACACA------------------TCCCACTA +GG------------------------------------ +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AA---------------------------------------------------------- +--------------------------------------------------TTTATCAAGA +GCC---------------------------------ATTTAAAAATCTGAAAACAGGAAA +-----------------ATATGCAAGAATGAGGGG--------------TGCCCACACTA +AT------------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTG----TGGGTCACAGTCT--------------ATTATGGGGTACC----------- +-------TGTGTGGC---------AGGAAGCAACCACCACTCTATT-------------- +------------------------------------------TTGTGCATC--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGA--ATAGGCGTTACTCG--------------ACAGAGGAGAGCA----------- +-------AGAAATGT---------AGCCAGTAGATCCTAGACTAT--------------- +-------------------------------------------AGCCCTGG--------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +-------------------------------------------GGAGCT----------- +-------AGAACGAT---------TCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAG +GCT---------------------------------GTAGACAAATACTGGGA------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +----GAGGGGGAGTTGTTGTCT--------------GTACCCCAGACCT----------- +-------GAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT-------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCT--------------CTAGCCCAGACCT----------- +-------GAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +A------------------------------------------GGGATTATG-------- +------GAAAACAGA---------TGGCAGGTGATGATTGTGTGGCAATTAGACAGGATG +AGG---------------------------------ATTAGAACATGG------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------CGGGCACAC--------------------------------------- +--------ACT--------ACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAG +TGG---------------------------------GTTCCCTAG--TTAGC-------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +--------------------CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAG +TGG---------------------------------GTTCCCTAG--TTAGCCAGA---- +-----------------------------------------------------GAGCTCC +CA------------------------------------ +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +----------------TGCTGCTGGCTCAGCTCGTCT---CATTCATTCCCTTACAGTAG +GCC---------------------------------ATCCAATCACACTACATATT---- +--------------------------------------------------------GACC +AC------------------------------------ +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------GCTGCTCCC--------------------------------------- +--------ACCCTATCTTGTGCTGGCTCAGCTCGTCT---CATTGTTTCCCTTACAGTAG +GCC---------------------------------ATCCAATCA--------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +-------------------TCCTCTGTCGAGTAACGC---CTATTCTGCTATGACGACAC +CCA---------------------------------ATTCTGAAA--CTGGATAAA---- +---------------------------------------------------CAGCAGTTG +TT------------------------------------ +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +---------------------------------------------------TGCCAAGGA +TCC---------------------------------GTTCACTAA--TCGAATGGA---- +----------------------TCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTC +CT------------------------------------ +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +-------------------TTCTGGGAAGTTCAAT----------------TAGGAATAC +CAC---------------------------------ATCCCGCAGGGTTAAAAAAG---- +----------------------AAAAAATCAGT------------------AACAGTACT +GG------------------------------------ +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +-------------------CTATG------TTTAC----------------TTCTAATCC +CGA---------------------------------ATCCTGCAAAGCTAGATAAAT--- +------------------TGCTTGTAACTCAGTC-----------------TTCTGATTT +GT------------------------------------ +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +------------C------ACTTATTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTCCCAAAGAAGACAAG----ATATCCTTGATC--------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +------------------------TTAAA-----AGAAAAGGGGGGACTGGA-------- +------AGGGCTAATTCACTGCCAAAGAAGACAAG----ATATCCTTGATCTGAGGA--- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +--------GGCTAATTCACTCCCAACGAAGACAAG----ATATCCTTGATCTGTGGATGT +ACC---------------------------------ACCCACAAG--------------- +----------------------------------------------------GCTACTTC +CC------------------------------------ +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +--------------------------------------ACAACGGAATTGG--------- +--------AGGAAATGAACCAGTAGATAAATTAGT----CAGTGCTGGAATCAGGAAAGT +ACT---------------------------------ATTTTT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +----------------------------------------AATAGTACTTT--------- +--------CCTGATTCCAGCACTGACTAAATTATC----TACTTGTTCATTTCCTCCAAT +TCC---------------------------------TTTGTGTG---------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +----------------------------------GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTCAATCAA +ATC---------------------------------AG---------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------CTATGGCAG-----GAAGAAGCGGAGACAGC--------- +--------GACGAAGAGCTCATCAGAACAGTCAGA----CTCATCAAGCTTCTGTA---- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +----------------------------------------------ACAGC--------- +--------GACGAAGAGCTCATCAGAACAGACAGA----CTCATCAAGCTTCTCTATCAA +AGC---------------------------------AGTAAGTA---------------- +-----------------------------------------------------TTACAT- +-------------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +--------------------------------------------------------AGCC +ATT---------------------------------GCTCTCCAA--TTACTGTGA---- +----------------------TATTTCTCATGTTCATCTTGGGCCTT----AACTATTC +CATCTA----------------------AAAAT----- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +--------------------------------------------------TTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +ACACCC-------AGTGGGGGGACATCAAGCAGCCA-- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +----------------------------------------GTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAACAC-------AGTGGGGGGACAT------------ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------------------------CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAG +G------------------------------AGCCACCCCACAAGATTTAAAC------- +----------------------------------------------------ACCATGCT +AAA----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +------------------------TGT-------------AACACCTCAGTCATTA---- +--CACAGG--------------CCTGTCCAAAGGTATCCTTTGAGCCAATTCC------- +----------------------------------------------------CATACATT +ATTGTG-------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +------------------------ATG-------------TATG---------------- +-----GGA--------------ATTGGCTGAAAGGATACCTTTGGACAGGCCT------- +----------------------------------------------------GAGTAATG +ACTGAGGTGTTACAA---------CTTGTC-------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +------------------------AA--------------GCTTGTGTAATTGTTAATTT +C---TCTG--------------TCCCACTCCATCCAGGTCGTGTGATTCCAAC------- +----------------------------------------------------TCTGTTCC +AG--------------------------AG-------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +------------------------AA--------------AATTTCAAA----------- +-------------------------------AATTGGGCCTGAAAATCCATAC------- +----------------------------------------------------AATACTCC +AGTATT-TGCCATAAAGAAAAAAGACAGTA-------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +------------------------GC--------------CTGCATGGAATGGATGACCC +GGAGAGAG--------------AAGTGTTAGAGTGGAGGTTTGAGAGCCACCT------- +----------------------------------------------------AGCAATTC +A------------------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +------------------------GTA-------------CTTTCTATAGTGAATAGAGT +TAGGCAGG--------------TATATTCACCATTATCGTTTGAGACCCACCT------- +----------------------------------------------------CCCAACCC +-------------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------------------------------------------GGT----------- +-------------------------------GATATGGGCTGATGTACCATTT------- +----------------------------------------------------GCCCCTGG +ATGTTC-TGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +------------------------ATAGAG----------CTTCCTTTAGTTGCCCCCCT +ATCTTTAT--------------TGTGACGAGGGGACGTTGCCAAAGAGTGACC------- +----------------------------------------------------TG------ +--------------------AGG--------------- +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +------------------------------------------------------------ +------------------------------------------------------------ +TTTTTCAG--------------TTCGCTTAGATGAAGACTTCAGGCAGTATAC------- +----------------------------------------------------TGCATTTA +CCATACCTAGTATAAACAATGAG--------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +-----------------ATAACCACAGAA-----------------AGCATAGTAATATG +G------------------------------GGAAAGACTCCTAAATTTAAACT------ +---------------------------------------------------GCCCATACA +AAA---------------GGAAACAT------------ +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +--------GACCAGCAAAGCACCTCTGGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAAAAGTAGT------------------ +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +--------------------------GGAA----------AGGTGAAGGGGCAGTAGTAA +TACAAGAT--------------AATAGTGACATAACAGTAGTG----------------- +------------------------------------------------------------ +-------------------CGAAGAAGAAAAGCAAA-- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +-----------------------------------------TTTTATGGTTCATAATCCA +CTCCATGT--------------ACTGGTTCTTTTAGAATCTCTCATTTTTCT-------- +---------------------------------------------------GCCCGTTCT +AGCT---------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------GAAGCAGAGCTAGAACTGGCAGAA----------AACAGAGAGATTCTAAAATA +ACCAGTAC--------------ATGGAGTGTATTATGACC-------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------CTCTAGTGTCCA +TTCATTGT--------------GTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGG------ +---------------------------------------------------GCTTGTTCC +ATCTCTCCT----------------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +-----------------------------------------------------TGATTTG +TTGTGTCAGTTAGGGTGACAACT------------------TTTTGTGTTCCTCTATTAG +TAACATAT--------------CCTGCTTTTCCTA------------------------- +------------------------------------------------------------ +-------------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +---------------------------GAA----------GTCTTGAGTTCTCTTATTAA +--------------------------GTTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTC---------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------TTCTCTGAAATCTACTAATTTTCTCCA------ +---------------------------------------------------TTTAGTACT +GTCTTTTTTCTTT--ATGGCAAATACTGGAGTATTG-- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +--------GGGGGGAACAGTGCAGGGGAAA----------GAATAGTAGACATAATAGCA +ACAGACAT--------------ACAAACTAAAGAATTACAA------------------- +------------------------------------------------------------ +-----------------------------------A-- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------TAAGGTGTTTTACTAAACTTTTCCA------ +---------------------------------------------------TGTTGTAAT +CCTCATCCTGTCTCCTTGCCACACAATCATCACCTG-- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +-----------------------------------------CAGGATTAACTGCGAATCT +T---TCTAG------------CTCCCTTGTTGCCCATACTATATGTTTTAATT------- +----------------------------------------------------TATATTTT +TT--------------------------CT-------T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pipelign-in1.fasta Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,200 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +CAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAA +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +GAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCAATCAAATCAG +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATTTACCAATACT +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +CTATGTTTACTTCTAATCCCGAATCCTGCAAAGCTAGATAAATTGCTTGTAACTCAGTCTTCTGATTTGT +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +CCAAGTATCCCCATAAGTTTCATAGATATGATGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTA +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +CTACTATTGCTACTAATGGTATAGGTTGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +TCTTTGCCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATAATTCCCTTCT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +AATAGCAATTTGTACAAGCAGTTTTAGGCTGACTTCGTGGATGCTTCCAGGGCTCTCGTCTAGGATCAAC +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +ACAACGGAATTGGAGGAAATGAACCAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +AGGATTTTACATAATTGCCTTACTTAAATCCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTA +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +TTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +CTACCTCTTCTTCTGCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGCCTAATTCCATGTGT +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +TTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTCTTTATGGCAAATACTGGAGTATTG +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +CTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTGTA +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +TGCCAAGGATCCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +CAGGATTAACTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATATGTTTTAATTTATATTTTTTCTT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +GCTGCTCCCACCCTATCTTGTGCTGGCTCAGCTCGTCTCATTGTTTCCCTTACAGTAGGCCATCCAATCA +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +ACAGTAGAAAAATTCCCCTCCACCATTAAAACTGTGGTTACAATATCTGGGTCCCCTCCTGAGGATTGGT +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +TTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATC +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +AGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAATTAGACAGGATGAGGATTAGAACATGG +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +GATCCTGCATATAAGCAGCAGCTTTTTGCCTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +GTACTTTCTATAGTGAATAGAGTTAGGCAGGTATATTCACCATTATCGTTTGAGACCCACCTCCCAACCC +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +CAGAGGAGGTCTCTCGACGCAGGACTCGGCTTGCTGAAGGGCGCACGGCAAGAGGCGAGGGGCGGCGACT +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +GTCTGGGGCATCAAGCAGCTCCAGGCAAGAATGCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCC +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTTTTCAGTTCGCTTAGATGAAGACTTCAGGCAGTATACTGCATTTACCATACCTAGTATAAACAATGAG +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +ACAGCGACGAAGAGCTCATCAGAACAGACAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTATTACAT +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +TATCCCCATAAGTTTCATCGATATGTTGCCCTAAGCGATGGAGCCAAATCCTAGGAAAATGTCTAACAGC +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +GGGGGGAACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAA +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +GTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACAT +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +TGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGTAAGGCCATATCTTCCCTAAAAAATTAGCCTGTCT +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +GGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATGTACCACCCACAAGGCTACTTCCC +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +TGATTTGTTGTGTCAGTTAGGGTGACAACTTTTTGTGTTCCTCTATTAGTAACATATCCTGCTTTTCCTA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +TAACGCCACCTTTGCCTAGTGTTACGAAACTGCCAGAGGATAGATGGAACAAGCCCCAGAAGACGAAGGG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +GTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +TTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGG +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +CTCTAGTGTCCATTCATTGTGTGGCTCCCTCTGTGGCCCTTGGTCTTCTTGGGCTTGTTCCATCTCTCCT +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +AGCCATTGCTCTCCAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTATTCCATCTAAAAAT +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +TGCTGCTGGCTCAGCTCGTCTCATTCATTCCCTTACAGTAGGCCATCCAATCACACTACATATTGACCAC +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTTGATTAACATCTAA +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +ATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACAT +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +TAAGGTGTTTTACTAAACTTTTCCATGTTGTAATCCTCATCCTGTCTCCTTGCCACACAATCATCACCTG +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +ACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +GAGGGGGAGTTGTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGGGGCTGTTGGCTCTGGTCTGCT +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +TATAAAGACGCAGAAGTTATTCCAGCATACACAGGGCAGGAAACAGCATATTTTCTTTTCAAATTAGCAG +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +TCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTACTCGAATGGATCTGACTCTGTCTCTCTC +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +TGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +GGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAACAGTAGTGCGAAGAAGAAAAGCAAA +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +AAGTGCAAGCAATCTGATTCACCCGATTTCTTCCAATTATGATGACAGGTGTAGGTCCTACTAATACAGT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +TATGGTACCAGTTAGAGAAAGAACCCCTAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAG +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +ATTGTACACATTTAGAATGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGA +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +TTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +TGACAGAAACCTAGTTGGTCCAAAATGCGAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +GGTGATATGGGCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTAATTTTGGCTGACCTGAT +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +GGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATC +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +GCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGAGAGCCACCTAGCAATTCA +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +GGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCG +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +TCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGTCCCAGAAGTT +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +ATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGATGAC +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +CAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGAGTGGTCCA +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +CACTTATTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATC +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +CTTGAAGCACTCAAGGCAAGCTTTATTGCGGCTTAATCAGTGGGTTCCCTAGTTAGCCAGAGAGCTCCCA +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCCG +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +AATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAAT +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +TTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +TCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACAAGCTCCTTGTACTACTTCAATAA +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +TGTGTTCAGCTGTACTATTATGGTTATAGCATTTTCCGTGAAATTGACAGATCTAATTACTACCTCTTCT +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +GATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAAAAAGTTCAGAAGTACACATCCCACTAGG +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +TCCTCTGTCGAGTAACGCCTATTCTGCTATGACGACACCCAATTCTGAAACTGGATAAACAGCAGTTGTT +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +AGTTCATGTATCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGGCTGAAACAGCATAT +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +GGAGCTAGAACGATTCGCAGTTAATCCTGGCGTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGA +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +AAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +AGTAAGTAGTACCTGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCACTAATAAT +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGAT +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +GACCAGCAAAGCACCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGT +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATTGTTTTACATCATTAGTGT +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +TCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTA +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +TTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTGCCAAAGAAGACAAGATATCCTTGATCTGAGGA +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +ACAGTAGAAAAATTCCCCTCCACAATTAAAACTGTGGTTACAATTTCTGGGTCCCCTCCTGAGGATTGCT +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +CGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGC +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +TTCTGAGGGGGAGATGTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGGGGCAGTTGGCTCTGGTC +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +ATGTATGGGAATTGGCTGAAAGGATACCTTTGGACAGGCCTGAGTAATGACTGAGGTGTTACAACTTGTC +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +CACCCATCCAAAGGAATTGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCGACAG +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +TGCTAATTTTAAAAGACAATATTCTGTTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATAT +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +TTTTATGGTTCATAATCCACTCCATGTACTGGTTCTTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CTTTATATTTTTTCTTACCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTCCCCCGCTTAA +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +TAGGAACCAAAGAAAGATAGTTAAGTGTTTCAATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +TCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGCTGGTAGGGCTATACATTC +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +ATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGGGACGTTGCCAAAGAGTGACCTGAGG +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +GAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTGTCTTTTTTC +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +TTTGATTGACTAACTCTGATTCACTTTGATCTTGTAGTGCTTGAATGATTCCTAATGCATATTGTGAGTC +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +ACTTTATATTTATATAATTCACTTCTCCAATTGTCCCTCATCTCTCCTCCTCCAGGTCTGAAGATCTCGG +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +AGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGTAGCCAGTAGATCCTAGACTATAGCCCTGG +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +GAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAATAACCAGTACATGGAGTGTATTATGACC +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +CTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATAATTGCCTTAC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +AAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAACTCTGTTCCAGAG +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCGGGCGCCACTGCTAGAGATTTTCCACACTGACTAAAAGGGTCTGAGGGATCTCTAGTTACC +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +GCCACAGAGGGAGCCACACAATGAATGGACACTATAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGA +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +CAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +AATAGTACTTTCCTGATTCCAGCACTGACTAAATTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTG +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +AATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGCAGGAAGCAACCACCACTCTATTTTGTGCATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pipelign-in2.fasta Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,2000 @@ +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/2 +TTCGCATTTTGGACCAACAAGGTTTCTGTCATCCAATTTTTTACCTGCAGTGAAGCTTGCTCGGCTCTAC +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/2 +TGGGTTGGGGTCTGTGTGTACACAGGCATGTGTGGCCCAAACATTATGTACCTCTGTATCATCTGCTTTA +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/2 +AACGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATA +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/2 +AGCCATTTAAAAATCTGAAAACATGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACA +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/2 +GGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGAT +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/2 +GAAGACCAAGGGCCACAGCGGGAGGCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATG +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/2 +GAGACCAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAAC +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/2 +GTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACG +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/2 +GTAATGTTTTTACTGGCCATCTTCCTGCTAATTTTAAAAGAAAAAATGCTTTTTCCTGCCCTGTTTCTGC +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/2 +CCACATCCCGCAGGGTTCAAAAAGAAAAAATCAGTAACAGTACTGGCTGTGGGTGATGCATATTTTTCCG +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/2 +ATGCTTTTAAAATAGTCTTACAATCTGGGTTCGCATTTTGGAGCAACAAGGTTTCTGTCATCCAATTTTT +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/2 +TTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCC +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/2 +CCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTA +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/2 +ACAAAATAGAGTGGTGTTTGCTTCCTTCCACACAGGTACCCCATAATAGACTGTGACCCACAATTTTTCT +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/2 +TGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCCCCAC +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/2 +CTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGCTCCTGGATATAAGCAGCT +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/2 +ACAGAGCCAGATCGATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTTCGGAGCGTGTG +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/2 +ACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGAGGTTCAATGGAACAGGACCA +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/2 +AATTTGTTTTATTCTGCATGGGAGGGTGATTGTGTCACTTCCTTCAGTGTTATTTGACCCTTCAGTACTC +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/2 +TCAGTTTCGTAACACTAGGCACCGGAGGCTTTATCTTTTTTGGTGTTATTAATGGTGCTAGTGCCAAGTA +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/2 +ATTAACTGCGAATCGTTCTAGCTCCCTGCTTGCCCATACTATATGTTTTAATTTATAATTTTTCTTTCCC +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/2 +TTTTTGACCACATGCCACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTATGTATGT +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/2 +CCTGGATTTTCTGCACTATAGGGTAATTTTGGCTGACCTGATTGCTGTGTCCTGTGTCAGCTGGTGCTTG +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/2 +GGGTCCCCTCGGGGTTGGGAGGTGGGTCTGAAACGATAATGGTGAATATCCCTGCCTAACTGTATTCACT +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/2 +GTATTTCTGCTATTAAGTCTTTTGATGGGTCATAATACACTCCATGTACTGGTTCTTTTAGAATCTCTCT +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/2 +ATCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCAGATTTACCAATACT +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/2 +AGAAGTACACATCCCACTAGGGGATGCTAGAATGGTAATAACAACATATTGGGGTCTGCATACAGGAGAA +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/2 +GTGTGCTATATCTCTTTTTCCTCCATTCTAAGGAGACTCCCTGACCCAAATGCCAGTCTCATTCTCCTGT +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/2 +AAAATAGTCTTAGAATCTGGGTTCGCATTTTGGACCAACAAGGTTTCTGTCATCCAATTTTTTACCTCCT +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/2 +GCCTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGTAGTTAAAAAATTGGATGA +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/2 +CAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGCCAGCGAGCTCCCAGGCTCAGATCTGGTCT +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/2 +GAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAA +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/2 +AATGCTTTTGTTATGAAACACACTTGGCAATGAAAGCAACACTTTTTACAATAGCAATTGGTACAAGCAG +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/2 +AGCTGCTGTATTGCTACTAGTGATTGCTCCATGTTTTTCCAGGTCTCGAGATGCTGCTCCCACCCTATCT +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/2 +GATGGAGTTCATAACCCATGCAAAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCC +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/2 +GTTTCGTAAAACACCATATGTATGTTTCAGGGAACGCTAGGGGATGGTTTTATAGAGATCACTATGAAAG +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/2 +AGATGGGGCAGCTCACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAC +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/2 +GTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTG +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/2 +ACAATACAAGAAAAAGAATCCGTATCCCGAGAGGACCAGGGATAGCATTTGTTACAATAGGAAAAATAAG +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/2 +TGCCAGATAGACCTTTTCCTTTTTTATTAACTGCTCTATAATTTGATTGACTAACTCTGATTCACTTTGA +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/2 +AATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAAT +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/2 +AGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGAGCCGACAGGCCCGAAG +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/2 +TTCGAGACTATTTAGACCGGTTCAATAAAACTCTAAGAGCCGAGCAAGCTTCAGAGGAGGTAAAAAATTG +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/2 +CTTTCCACAGTGGAATTCTGCTGTCCCTGTAATAAACCCGAAAATTTTGCATTTTTGTAATTTGTTTTTG +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/2 +CAAGAATCCTGGCTGTGGACAGATACCTAAAGGATCAACAGCTCCTGGGGATTAGGGGTTGCTCTGGAAA +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/2 +ATTGTTTTATTATTTCCAAATTGTTCTCTTAATTTGCTAGCTATCTGTTTTAAAGTGTTATTCCATTTTG +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/2 +TTGTTATGTCCTGCTTGATATTCACACCTAGTGCTAACTATGTGTCCTAATAAGGCCTTTCTTATAGCAG +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/2 +AAGGTCTGTTGGAAATGTGGAAAGGAAGGCCACCAAATGAAATATTGTACTGAGAGACAGGCTAATTTTT +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/2 +CTGACATTTATCACAGCTGGCTACTATTTCTTTTGCTACTACAGGTGGCAGGTTAAAATCACTAGCCATT +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/2 +ACCCGAAAATTTTGAATTTTTGTAATTTGTTTTAGTAATTCTTTAGTTTGTATGTCTGTTGCTATTATGT +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/2 +ATTTGTACATGGTCCTGTTCCATTGACCGTCTTATTATTACATATTAGAATCGCAAAACCAGCCGGGGCA +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/2 +GCCCTATCTTTATTGTGACGAGGGGTCGTTGCCCAAGAGTGACCTGAGGGAAGTTAAAGGATACAGTTCC +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/2 +AAACTTTTGACTAGCGGAGGCTAGAAGGAGATAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAA +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/2 +TTGTACTGTGCTGACATTTGTACATGGTCCTGTTCCATTGACCGTCTTATTATTACATTTTAGAATCGCA +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/2 +CTAGCCGTGCGCGCTTCAGCAAGCCGAGTCCTGCGTCGAGAGAGCTCCTCTGGTTTGCCTTTCGCTTTCA +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/2 +GTGTCCTGTGTCCGCTGCTGCTTGCTGTGCTTTTTTCTTACTTTTGTTTTGCTCTTCCTCTATCTTGTCT +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/2 +TAATAAATCTCTGGACCAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTAC +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/2 +CAAAGAGTGACCTGAGGGAAGTTAAAGGATACAGTTCCTTGTCTATCGGCTCCTGCTTCTTAGGGGGAGT +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/2 +CATGTTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCC +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/2 +CGGGCCACGTGATGACATTCTAGGCGGCTGTCACACCTCCACTCTAACACTTCTCTCTCCGGGACATCCA +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/2 +CACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGTGGTCAGCTATCCACTGACCT +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/2 +AAATTTTGAATATTTGTAATTTGTTTTTGTAATTCTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTA +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/2 +AGTGAGTCTGTTACTATGTTTACTTCTACTCCCGAATCCTGCACAGCTAGCTAAATTGCTTGTAACTCAG +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/2 +CAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTATTACATG +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/2 +TAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCGGAGGGGACCCGACAGG +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/2 +CTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAA +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/2 +CCTTGGTGTTCTGGGGCTTGTTCCATCTATCCTCTGTCCGTTTCGTAACACTAGGCAAAGGTGGCTTTAT +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/2 +GAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTATGACTGTTTTTCAGACTCTGCTA +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/2 +CCAGAGGAGCTTTGCTGGTCCTTTCCAAAGTGGATTTCTGCTGTCCCTGTAATAAACCCGAAAATTTTGA +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/2 +GAAGGTCTGTTTTAACATTTGCATGGCTGCTTGATGTCCCGCCACTGTGTTTAGCATGGTGTTTAAATCT +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/2 +AGTTCATAACCCATCCAAAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACC +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/2 +GGCTTTAGGCTTTGATCCCATAAACTGATTATATCCTCATGCATCTGTTCTAGCATGTCATTTTTCCACA +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/2 +GGGAGTTGATGTCTCTACCCGAGACCTGAAGCACTCTTCTGGTGGGGCTGTTGGCTCTGGTCTGCTCTGA +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/2 +GCTAACTATGTGTCCTAATAAGGCCTTTCTTATAGCAGAGTCTGAAAAACAGTCAAAGTAATACAGATGA +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/2 +CAGACAAAAAACATCAGAAAGAAGCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGCTAAATGGAC +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/2 +TACAGTTCCTTGTCTATCGGCTCCTGCTTCTGAGGTGGAGTTGTTGTCTCTACCCCCGACCTGAAGCTCT +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/2 +AGAGAGCTCCCAGGGTCAGATCTGGTCTAACCAGAGAGACCCAGTACAGGCAAAAAGCAGCTGCTTATAT +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/2 +CCATACATTATTGTGCCCCGGGTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGG +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/2 +CTACACACCAGGGCCAGGGGACAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAG +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/2 +AAGACAAGGACCAACGGAACGCTTTAGAGACTATGTAGACCGGTTCTATACAACTCTAAGAGGCGAGCAA +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/2 +ATTGTGGGTCACAGTCTATTAAGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCA +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/2 +GGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAAT +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/2 +GCATTAGGAATCATTCAAGCACACCCAGATCAAAGTGAATGAGAGTTAGTCAATCAAATAATAGAGCAGT +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/2 +TTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAAT +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/2 +AGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCG +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/2 +TATGTCCACAGATTTCTATGAGTATCTGATCATACTGTCTTACTTTGATAAAACCTCCAATTCCCCCTAT +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/2 +CTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCGAGAAGTGATAGCCCTGTT +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/2 +CATTTCAGGGAGTAGGATGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTACCAAA +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/2 +ACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACA +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/2 +GAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTCATGATGTAAAACAATTAACAGAGGCAGTG +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/2 +AAATGGAATAACACTTTAAAACCGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAA +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/2 +TAACCTGTCTATTTTTCTTTGTCTTAATATTTTCCTATATTCTATGATTACTATGGACCACACAACTATT +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/2 +TAGCTGCCCCATCTACATAGAAGGTTTCTGCTCCTACTATGGGTTCTTTCTCTAACTGGTACCATAATTT +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/2 +TATACAGCAATTACCATACCTAGTATAACCAATGAGACACCAGGGATTAGATATGATTACAATGTGCTTC +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/2 +ACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGTAGAAGTGAATTATATAA +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/2 +TGACGTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGA +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/2 +TGAGTCTGACTGTTCTGATGAGCTCTTCGTCGCTGTCTCCGCTTCTTCCTGCCATAGGAGATGCCTAAGG +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/2 +CGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCTACGGGCCTGTC +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/2 +AGACTCCTAAATTTAAACTGCCCCTACAAAAGGACACATGGGAAACATGGTGGACAGAGTATTGGCAAGC +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/2 +CAGGCCTGTGTAATGACTGAGGTGTTACAACTTGTCAACTTATAGCTGGTAGTATCATTATCTATTGTTA +>K03455|HIVHXB2CG_7370_7894_2_0_0_1_0_1_64/2 +CTCAGCAAATTGTTCTGCTGCTGCACTATACCCGACAATAATTGTCTGGCCTGTACCGTCAGCGTCAATT +>K03455|HIVHXB2CG_4615_5225_0_0_0_0_0_0_65/2 +GCATCCCCTAGTGGGATGTGTACTTCTGAACTTATTCTTGGATGAGGGCTTTCATAGTGATGTCTATAAA +>K03455|HIVHXB2CG_9032_9458_1_0_0_1_0_0_66/2 +TGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTCATTCA +>K03455|HIVHXB2CG_4421_5002_1_0_0_2_0_0_67/2 +TTTATGTCACTATTATCATGTATTACTACTGCCCCTTCACCTTTCCAGAGGAGCTTTGCTGGTCGTTTCC +>K03455|HIVHXB2CG_2487_3049_7_0_0_2_0_0_68/2 +CATTTTGTCATGCTACTTTGGAATATTGCTGGTGATCCTTTCCATCCCTGTGGAAGCACATTGTACTGAT +>K03455|HIVHXB2CG_1024_1606_1_0_0_2_0_0_69/2 +TTTTATTTAATCCCATGATTATCCATCTATTATAAATTTCTCCTACTGGGATAGGTGGATTATTTGTCAT +>K03455|HIVHXB2CG_1407_1938_1_0_0_0_0_0_6a/2 +TGAGGAAGCTGCAGAATGGGATAGAGTGCATGCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGA +>K03455|HIVHXB2CG_1875_2464_2_0_0_1_0_0_6b/2 +TTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGCGGCAATTATAGGAAC +>K03455|HIVHXB2CG_8342_8867_0_0_0_1_0_0_6c/2 +TAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGG +>K03455|HIVHXB2CG_1566_2129_4_0_0_1_0_0_6d/2 +TTCCCTGGCCTTCCCTTGTAGGAAGGCCAGATCTTCCCTAAAAAATTAGGCTGTCTCTCAGTACAATCTT +>K03455|HIVHXB2CG_1941_2422_1_0_0_2_0_0_6e/2 +GAACCAAAGAAAGATTGTTAAGTGTTTCAAATGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCC +>K03455|HIVHXB2CG_7782_8292_2_0_1_1_0_0_6f/2 +CTACTATCATTATTAATAATTTTATATACCACAGCCAATTTGTTATGTTAAACCAATTCCACAAACTTGC +>K03455|HIVHXB2CG_557_1109_4_0_0_0_0_0_70/2 +TCTTCCTCTATCTTGTCTAAAGCTTCCTTGGTGTCTTTTATCTCTATCCTTTGATGCACACAATAGAGGG +>K03455|HIVHXB2CG_4973_5502_0_0_0_0_0_0_71/2 +TATTAATGCTGCTAGTGCCAAGTATTGTAGAGATCCTACCTTGTTATGTCCTGCTTGATATTCACACCTA +>K03455|HIVHXB2CG_8830_9359_0_0_0_1_0_0_72/2 +CGGCTGTCAAACCTCCACTCTAACACTTCTCTCTCCGGGTCCTCCATCCCATGCAGGCTCACAGGGTGTA +>K03455|HIVHXB2CG_1265_1820_3_0_0_1_0_0_73/2 +TCTAGTGTAGCCGCTGGTCCCAATGCTTTTAAAATCGTCTTACAATCTGGGTTCGCATTTTGGACCAACA +>K03455|HIVHXB2CG_8172_8712_2_0_0_0_0_0_74/2 +CAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGGAAGTATGTGGAATTGGT +>K03455|HIVHXB2CG_280_759_1_0_0_1_0_0_75/2 +TTTTTGGCGTACTCACCAGACGCCGCCCCTCGCCTCTTGCCGTGCGCGCTTCAGCAAGCCGAGTCCTGCG +>K03455|HIVHXB2CG_7732_8231_2_0_0_1_0_0_76/2 +GAAGCGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATATGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGC +>K03455|HIVHXB2CG_8182_8678_1_0_0_3_0_1_77/2 +TGTGGCATTGAGCAAGCTCCCAGCACTATTCTTTAGTTCCTGACTCCAATAGCTGTAGGAGATTCCAGCA +>K03455|HIVHXB2CG_3939_4364_1_0_0_0_0_0_78/2 +TAGCTGACATTTATCACAGCTGGCTACTATTTCTTTTGCTACTACAGGTGGCAGGTTAAAATCACTAGCC +>K03455|HIVHXB2CG_3165_3604_2_1_0_1_0_0_79/2 +CCTGTTTTCAGATTTTTCAATGGCTCTTGATAAATTTGATATGTCCATTGGCCTTGCCCCTGCTTCTGTA +>K03455|HIVHXB2CG_3438_3961_2_0_0_0_0_0_7a/2 +TCAGTTAGGGTGACAACTTTTTGTCTTCCTCTATTAGTAACATATCCTGCTTTTCCTAATTTAGTCTCCC +>K03455|HIVHXB2CG_1067_1553_1_0_0_1_0_0_7b/2 +AGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCAGA +>K03455|HIVHXB2CG_3410_3966_2_0_0_1_0_0_7c/2 +AGCACTAACAGAAGTAATACGACTAACAGACGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTA +>K03455|HIVHXB2CG_894_1360_4_0_0_0_0_0_7d/2 +CTGTGTTTAGCATGGTGTTTAAATCTTGTGGGGTGGCTCCTTCTGATAATGCTGAAAACATGGGTATCAC +>K03455|HIVHXB2CG_7104_7541_1_1_0_1_0_0_7e/2 +ATTAATTGTACAAGACCCAAGAACAATACAAGAAAAAGAATCCGTATCCCGAGAGGACCAGGGAGAGCAT +>K03455|HIVHXB2CG_7759_8279_0_0_0_2_0_0_7f/2 +GAATAATTTTATATACCACAGCCAATTTGTTATGTTACACCAATTCCACACACTTGCCCATTTATCTAAT +>K03455|HIVHXB2CG_5863_6366_1_0_0_3_0_0_80/2 +CTTCGTTCCACACAGGTACCCCATAATAGACTGTGACGCACAATTTTTCTGTAGCACTACAGAACATCAA +>K03455|HIVHXB2CG_390_886_1_0_0_1_0_0_81/2 +GGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCAGCTTTTTGCCTGTACTGGGTCT +>K03455|HIVHXB2CG_6801_7291_0_0_0_2_0_0_82/2 +TTATTTCCAAATTGTTCTCTTAATTTGCAAGCTATCTGTTTTCAAGTGTTATTCCATTTTGCTCTACTAA +>K03455|HIVHXB2CG_3700_4187_4_0_0_1_0_0_83/2 +GAAAGACTCCTAAATTTCAACAGCCCATACAAACGTAAACATGGGAAACATGGTGGACAGAGTATTGGCA +>K03455|HIVHXB2CG_5426_5891_1_0_0_1_0_0_84/2 +TTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGTTAGGATCTCTACAATACTTGGCACTAGCAGC +>K03455|HIVHXB2CG_5306_5854_1_0_0_3_0_0_85/2 +TAGTCTAGGATCTCCTGGCTCCATTTCTTGCTCTCCTCTGTCGATTAACGCCTATTCTGGTATGTCGACA +>K03455|HIVHXB2CG_3832_4380_0_0_0_0_0_0_86/2 +GCATGGCTTCTCCTTTTAGCTGACATTTATCACAGCTGGCTACTATTTCTTTTGCTACTACAGGTGGCAG +>K03455|HIVHXB2CG_2238_2832_0_0_0_1_0_0_87/2 +GTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAAC +>K03455|HIVHXB2CG_6546_7031_1_0_0_1_0_0_88/2 +ATAATCAGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGT +>K03455|HIVHXB2CG_8948_9459_3_0_0_1_0_0_89/2 +TGGAAAGTCCCCCGCGGAAAGTCCCTTGTAGCAAGCTCGATGTCAGCAGTTCTTGAAGTACTCCGGATGC +>K03455|HIVHXB2CG_786_1264_1_0_0_1_0_0_8a/2 +AGAGATGGGTGCTAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGG +>K03455|HIVHXB2CG_6283_6804_0_0_0_0_1_0_8b/2 +TCAACTTATAGCTGGTAGTATCATTATCTATTGTTATTATATCAAGTTTATAAAAAAATGCATATTCTTT +>K03455|HIVHXB2CG_627_1115_2_0_0_0_0_0_8c/2 +CTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGCAACCCGAGGAGCTCTCTCGACGCAGGA +>K03455|HIVHXB2CG_5515_6018_3_0_0_2_0_0_8d/2 +ATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGAAATATGGAACAAGCCCCATAAGACCAAGG +>K03455|HIVHXB2CG_879_1356_1_0_0_1_0_0_8e/2 +GTTTAGCATGGTGTTTAAATCTTGTGGGGAGGCTCCTTCTGATAATGCTGAAAACATGGGTATCACTTCT +>K03455|HIVHXB2CG_6084_6555_1_0_0_2_0_0_8f/2 +AACTGATTATATCCTCATGGATGTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATT +>K03455|HIVHXB2CG_2582_3077_0_0_0_2_0_0_90/2 +TGGATTTTGTATTCTAAAAGGCTCTAAGATTTTTGTCATGCTACTTTGTAATATTGCTGGTGATCCTTTC +>K03455|HIVHXB2CG_4805_5372_1_0_0_2_0_0_91/2 +TGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAA +>K03455|HIVHXB2CG_4173_4655_0_0_0_3_0_0_92/2 +ATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAA +>K03455|HIVHXB2CG_1882_2390_2_0_0_2_0_0_93/2 +GAAGCAATGAGCGAAGTAACAAATTCAGCTACCATACTGATGCAGAGAGGCAATTTTAGGAACCAAAGAA +>K03455|HIVHXB2CG_3390_3956_1_0_0_2_0_0_94/2 +AAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGT +>K03455|HIVHXB2CG_7886_8323_0_0_0_1_0_0_95/2 +TTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAG +>K03455|HIVHXB2CG_9074_9539_3_0_0_3_0_0_96/2 +AAAAGGGGTGACTGGAAGGGCTAATTCACTCCCCAAGAAGACAATATATCCTTGATCTGTGGATCTACCA +>K03455|HIVHXB2CG_2043_2605_0_0_0_2_0_0_97/2 +GGGCCATCCATTCCTGGCTTTAATTTTACTGGTACAGTCTCACTAGGGCTAATGGGAAAATATAAAGTGC +>K03455|HIVHXB2CG_32_482_0_0_0_0_0_0_98/2 +AGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGG +>K03455|HIVHXB2CG_1777_2193_1_0_0_0_0_0_99/2 +CTCTACCCCAGACCTGAAGCTCTCTTCTGGTGGGGCTGTTGGCTCTGGTCTGCTCTGAAGAAAATTCCCT +>K03455|HIVHXB2CG_8654_9162_3_0_0_1_0_0_9a/2 +AGGGAAGTAGCCTTGTGTGTGGTAGATCCACAGATCAAGGATATCTTGTCTTCTTTGGGAGTGCATTAGC +>K03455|HIVHXB2CG_6451_6906_1_0_0_1_0_0_9b/2 +CCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAACTGA +>K03455|HIVHXB2CG_4835_5378_1_0_0_0_0_0_9c/2 +TCAAAGTAATACAGATGAATTAGTTGGTCTGCTAGTTCAGGGTCTACTTGTGTGCTATATCTCTTTTTCC +>K03455|HIVHXB2CG_1305_1792_0_0_0_3_0_0_9d/2 +TTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAA +>K03455|HIVHXB2CG_7199_7722_2_0_0_2_0_0_9e/2 +TGGTGGGTGCTACTCCTAATGGTTCAATTTTAACTACTTTATATTTATATAATTCAGTTCTCCAATTGTC +>K03455|HIVHXB2CG_3647_4111_2_0_0_0_0_0_9f/2 +ATTTGATTGACTAACTCTGATTCACTTTGATCTGGTTGTGCTTGAATGATTCCTAATGCATATTGTGAGT +>K03455|HIVHXB2CG_6704_7167_1_1_0_2_1_0_a0/2 +TCCCTGGTCCTCTCGGGATACGGATTCTATTTCTTGTATTGTTGTTGGGTCTTGTACAAATAATTTCTAC +>K03455|HIVHXB2CG_7976_8504_1_0_0_2_0_0_a1/2 +CAGATCGTCCCAGAAAAGTGCCAAGGATCCGTTCACTAATCGCATGGATCTGTCTCTGTCTCTCTCTCCA +>K03455|HIVHXB2CG_6024_6480_1_0_0_0_0_0_a2/2 +ATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTGTGGCCCAAACATTATGTACCTCTGT +>K03455|HIVHXB2CG_9058_9566_4_0_0_0_0_0_a3/2 +AGCCACTATTTAACAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGCTATCCTTT +>K03455|HIVHXB2CG_3403_3948_0_0_0_3_0_0_a4/2 +GAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGA +>K03455|HIVHXB2CG_3809_4318_1_0_0_1_0_0_a5/2 +TCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGAAGAT +>K03455|HIVHXB2CG_6743_7347_0_1_0_4_0_0_a6/2 +TGTGCGTTACAATTTCTGGGTCCCCTCGTGAGGATTGCTTAAAGATTATTGTTATAATATTTCGAAATTG +>K03455|HIVHXB2CG_8137_8696_1_0_0_1_0_1_a7/2 +ACCCAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATT +>K03455|HIVHXB2CG_6319_6805_0_0_0_1_1_0_a8/2 +AAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGC +>K03455|HIVHXB2CG_6614_7138_0_0_0_3_0_0_a9/2 +TTTCTTGTATTGTTGTTGGGTCATGTACAATTAATTTCTACCGATGTGTACAGCTGTACTATTATGGTTT +>K03455|HIVHXB2CG_6635_7182_3_0_0_2_1_0_aa/2 +TTGTAACCAATGCTCTCCCTGGTCCTCTCGGGATACGGATTCTTTTTGTTGTATTGTTGTTGGGTCTTGT +>K03455|HIVHXB2CG_8246_8705_1_0_0_1_0_0_ab/2 +ATCTGTCCCCTCAGCTACTGCTATGGGTGTGGCATTGAGCAAGCTAACAGCACTATTCTTTAGTTCCTGA +>K03455|HIVHXB2CG_4389_4839_1_0_0_3_0_0_ac/2 +TTAAGTCTACTATTCTTTCCCCTGCACTGTACCCCCCAATCCCCCCTTTAGTTTTAAAATTGTGGATGAA +>K03455|HIVHXB2CG_1984_2516_0_0_0_1_0_0_ad/2 +ATTTCTTCCAATTATGTTGACAGGTGTAGGTCCTACTAATACTGTACCTATAGCTTTATGTCCAGAGATT +>K03455|HIVHXB2CG_3915_4350_0_0_0_0_0_0_ae/2 +GGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGT +>K03455|HIVHXB2CG_8875_9410_1_0_0_0_0_0_af/2 +GCAGATAGGGTGGGATCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAG +>K03455|HIVHXB2CG_8844_9344_0_0_0_0_0_0_b0/2 +AAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAA +>K03455|HIVHXB2CG_2451_2932_3_0_0_3_0_0_b1/2 +TGTGGACATACAGCTATAGGTACAGTATTAGTAGGACCTACACCTGACAACATAATTGGAAGAAATGTGT +>K03455|HIVHXB2CG_2243_2751_0_0_0_1_0_0_b2/2 +CTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG +>K03455|HIVHXB2CG_5282_5798_2_0_0_1_0_0_b3/2 +CTGCTATGTCGACACCGAATTCTGAAAATGGATAAACAGCAGTTGTTGCAGAATTCTTATTATGGCTTCC +>K03455|HIVHXB2CG_5143_5599_2_0_0_1_0_0_b4/2 +GCTAGGGGATGGTTTTATAGAGATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACCCATCC +>K03455|HIVHXB2CG_7296_7871_3_0_1_5_0_1_b5/2 +ACAATAATCTTTCATCAATCCTCAGGAGGGGACCCAGAAATTGTAACCAGAGTTTTAATTGTGGAGGGGA +>K03455|HIVHXB2CG_897_1428_3_0_0_1_0_0_b6/2 +ATCCCATTCTGCAGCTTCGTCATTGATGGTCTCTTTTAACATTTGCATGGCTGCTTGATGTCCCCCCACT +>K03455|HIVHXB2CG_883_1488_0_0_0_2_0_0_b7/2 +TCCCCTTGGTTCTCTCATCTGGCCTGGTGCAATAGGCGCTGCAAGCACTGGATGCACTCTATCCCATTCT +>K03455|HIVHXB2CG_6394_6852_3_0_0_0_0_0_b8/2 +ATGCTAAAGGATATGATACAGAGGTACAAAATGTTTGGGCCACAGATGCCTGTGTACCCACAGACCCCAA +>K03455|HIVHXB2CG_3701_4127_2_0_0_3_0_0_b9/2 +AAAGAGTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGTCAA +>K03455|HIVHXB2CG_2765_3194_2_0_0_0_1_0_ba/2 +AAAATTAGTAGATTTCAGAGAAGTTAATAAGAGAACTCAAGACTTCTGGGCAGTTCAATTAGGAATACCA +>K03455|HIVHXB2CG_5464_5967_2_0_0_2_0_0_bb/2 +GTAGGATCTCTACAATACATGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCGTA +>K03455|HIVHXB2CG_7758_8278_2_0_0_1_0_0_bc/2 +GCCGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCCGGAAGCACTATGGGCGCAGCCTCAA +>K03455|HIVHXB2CG_9201_9703_3_0_0_1_0_0_bd/2 +CACTGACTAAAAGGTTCTGAGGGATCTCTAGTTACCAGAGTCACACAACAGACGGGCACACACTACTTGA +>K03455|HIVHXB2CG_4288_4773_1_0_0_1_0_0_be/2 +TGAATACTGCCATTTGTACAGCTGTCTTAAGATGTTCAGCCTGATCTCTTACCTGTCCTATAATTTTCTT +>K03455|HIVHXB2CG_239_747_2_1_0_1_0_0_bf/2 +GGAGAGAGAAGTGTTAGCGTGGAGGTTTGACATCCACCTAGCATTTCATCACATGGCCCGAGAGCTGCAT +>K03455|HIVHXB2CG_7489_7935_0_0_0_5_0_0_c0/2 +AGACTTTGCGTTGCAACAGATGCTGTTGCGCCTGAATATCCCTCAGCAAATTGTTCTGCTTCTGCACTAT +>K03455|HIVHXB2CG_2273_2889_3_0_0_2_0_0_c1/2 +ACGACCCCTCGTCACAATACCGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGCTGAT +>K03455|HIVHXB2CG_2463_3014_3_0_0_4_0_0_c2/2 +TCAATAGGAACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTG +>K03455|HIVHXB2CG_6656_7223_1_0_0_2_0_0_c3/2 +AAAGTTACAATGTGCTTGTCTCATATTTCCTATTATTCCTATTGTAACAAATGCTCTCCCTGGTCCTCTC +>K03455|HIVHXB2CG_4540_5074_0_0_0_2_0_0_c4/2 +GCCACACAATCCTCACGTGCCATCTGTTTTCCATAATCCCTAATGATCTTTGCTTTTCTTCTTGGCACTA +>K03455|HIVHXB2CG_5881_6321_1_0_0_0_1_0_c5/2 +TTTCTGTAGCACTACAGATCATCAACATCCCAAGGAGCATGGTGCCCCATCTCCACCCCCTTCTCCACAA +>K03455|HIVHXB2CG_4268_4878_1_0_0_1_0_0_c6/2 +TTTGTTTTTGTAATTCTTTAGTTTGTATGACTGTTGCTATTATGTCTACTATTCTTTCCCCTGCACTGTA +>K03455|HIVHXB2CG_8510_9088_2_0_0_1_0_0_c7/2 +CCAGTCCCCCCTTTTCTTTTAAAAAGTGGCTAAGATCTACAGCTGCCTTGTCAGTCATTGGTCTTAAAGG +>K03455|HIVHXB2CG_6316_6735_3_0_0_0_0_0_c8/2 +CAGAAACATTGTGGGTCAGAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCAATTTTG +>K03455|HIVHXB2CG_5231_5781_2_0_0_2_0_0_c9/2 +AATTCTGAAAATGGATAAAGAGCAGATGTTGCAGAATTCTTATTATGGCTTCCACTCCTGCCCAAGTATC +>K03455|HIVHXB2CG_7992_8490_1_0_0_2_0_0_ca/2 +CAACCGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTA +>K03455|HIVHXB2CG_6714_7281_0_1_0_1_0_0_cb/2 +AGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATAACAATAGATAATG +>K03455|HIVHXB2CG_7943_8387_0_0_0_2_0_0_cc/2 +TAGGTGGGTCTGCAACGATAATGGTGAATATCCCTGCCTAACTCTATTCACTATAGAAAGTACAGCAAAA +>K03455|HIVHXB2CG_5574_6076_3_0_0_4_0_0_cd/2 +TGGTATCGGTTGCGTTACATGTCCTACTTACTGGTTTGATAGATAAGCTTGATGAGTCTGACTGTTCTGA +>K03455|HIVHXB2CG_8946_9449_3_0_0_0_0_0_ce/2 +TACCAATGCTGCTTGTGCGTGGCTAGAAGCACAAGAGGAGGAGGAGGAGGGTTATCCAGTCACACCTCAG +>K03455|HIVHXB2CG_1665_2197_0_0_0_0_0_0_cf/2 +CTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAAT +>K03455|HIVHXB2CG_4856_5326_2_0_0_2_0_0_d0/2 +TGCTATATCTCTTTTACCTCCATTCTAAGGAGACTCCCTGACCCAAATGCCAGTCTCTTTCTCCTGTATG +>K03455|HIVHXB2CG_5664_6215_1_0_0_3_0_0_d1/2 +AGGAATTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAG +>K03455|HIVHXB2CG_8368_8837_2_0_0_1_0_0_d2/2 +TATCGTTTCAGACCCAGCTCCCAACCCCGAGGGGACCCGACAGGCCCTAAGGAATAGAAGAAGAAGGTGG +>K03455|HIVHXB2CG_5596_6081_3_0_0_3_0_0_d3/2 +ACTATTGGTATAGGTTGCGTTACAAGTACTACTTACTGCTTTGATAGAGAAGCTTGCTGAGTCTTACTGT +>K03455|HIVHXB2CG_6674_7183_1_0_0_1_1_0_d4/2 +ATTGTAACCAATGCTCTCCCTGGTCCTCTCGGGATACGGATTCTTTTTCTTGTATTGTTGTTGGGTCTTG +>K03455|HIVHXB2CG_2660_3191_3_0_0_1_1_0_d5/2 +AAGTCCCCACCTCCACAGATGTTGTCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTACTAAGTCA +>K03455|HIVHXB2CG_5213_5793_0_0_0_2_0_0_d6/2 +ATGTCGACACCCAATTCTGAAAATGGATAAACAGCAGTTGTTGCAGACTTCTTAATATGGCTTCCACTCC +>K03455|HIVHXB2CG_1972_2449_2_0_0_3_0_0_d7/2 +ATTTCTATGAGTATCTGATCATACTGTCTTACTTTGATACAACCTCCAATTCGCCCTATCAATTTTGGTT +>K03455|HIVHXB2CG_7594_8072_1_0_0_1_0_0_d8/2 +AATACTCCAACTAGCATTCCAAGGCACAGCAGTGGTGCAAATGAGTTTTCCAGAGCAACCCCAAATCCCC +>K03455|HIVHXB2CG_7422_7979_1_0_0_1_0_0_d9/2 +TGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACACA +>K03455|HIVHXB2CG_530_1128_0_0_0_1_0_0_da/2 +AAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCT +>K03455|HIVHXB2CG_8509_8968_1_0_0_2_0_0_db/2 +GCCTGTGCCTCTTCAGCTACGACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCT +>K03455|HIVHXB2CG_6749_7216_1_1_0_2_1_1_dc/2 +CAATGTGCTTGACTCATATTTCCTATTTTTTCCAATTGTAACAAATGCTCTCCCTGGTCCTCTCGGGATA +>K03455|HIVHXB2CG_5389_5891_1_0_0_1_0_0_dd/2 +GACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGATAGCCCTAGGTGTGAATATCAAGCAGGACATA +>K03455|HIVHXB2CG_8406_8858_2_0_0_1_0_0_de/2 +GACAGGCCCGAAGGACTAGAAGAAGAAGGTGGAGAGAGAGACATAGACAGATCCATTCGATTAGTGAACG +>K03455|HIVHXB2CG_1712_2135_2_0_0_0_0_0_df/2 +AGAAAATTCCCTGGCCTTCCCTTGTAGGAAGGCCAGATCTTCCCTAAAAAATTAGCCTGTCTCTCAGTAC +>K03455|HIVHXB2CG_6334_6809_1_0_0_2_1_0_e0/2 +CATTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGC +>K03455|HIVHXB2CG_452_867_1_0_0_6_0_0_e1/2 +CTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTACCTAGGGAACCCACTGCTTAA +>K03455|HIVHXB2CG_7942_8439_0_0_0_2_0_0_e2/2 +CTCCACCTTCTTCTTCTATTCCATCGGGCGTGTCGGGTCCCCTCGGGGTTGGGAGGTGGGTCTGAAACGA +>K03455|HIVHXB2CG_4384_4863_1_0_0_0_0_0_e3/2 +CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCCCCTGCACTGTACCCCCCAATCCCCCC +>K03455|HIVHXB2CG_1475_2064_3_0_0_1_0_0_e4/2 +GAGAACCAAGTGTAAGTGACATAGCAGGAACTCCTAGTACCCTTCAGGAACAAATAGGATGGATGACAAA +>K03455|HIVHXB2CG_3068_3605_1_0_0_2_0_0_e5/2 +TCCTGTTTTCATATTTTTAAATGGCTCTTGATAAATTTGATATGTCCATTGGCCTTGCCCCAGCTTCTGT +>K03455|HIVHXB2CG_8139_8621_0_0_0_4_0_0_e6/2 +GAGATTCCACCAATATTTGAGGGCTTCCCACCCCCAGCGTCCCAGAAGTTCGACCATCCTCGTTACAAAC +>K03455|HIVHXB2CG_2841_3356_1_0_0_0_0_0_e7/2 +CTGACTTGCCCAATTCAATTTCCCCACTAACTTCTGTATGTCATTGACAGTCCAGCTGTCTTTTTCTGGC +>K03455|HIVHXB2CG_1261_1762_3_0_0_1_0_0_e8/2 +GTATTAGAAGAGAAGGCTTACAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCCCCC +>K03455|HIVHXB2CG_2863_3382_0_0_0_1_0_0_e9/2 +TGCCTTACTTTAATGCCTGGGTAAATCTGACTTGCCCAATTCAATTTCCCCACTAACTTCTGTATGTCAT +>K03455|HIVHXB2CG_2173_2610_0_0_0_1_0_0_ea/2 +CTTTTGGGCCAACCATTCCTGGCTTTAATTTTACTGGTACAGTCTCAATAGGGCTAATGGGAAAATTTAA +>K03455|HIVHXB2CG_5528_6074_2_0_0_1_0_0_eb/2 +GTATAGGATGCGTTACATGTACTACTTACTGCTTTGATAGAGAAGCTTGATGAGTCTGACTGTTCTGATG +>K03455|HIVHXB2CG_6080_6617_0_0_0_1_0_0_ec/2 +GCACTTTAAACTAACACAGAGTGGGGTAAATTTTACACATGGCTTTAGGCTTTGATCCCATAAACTGATT +>K03455|HIVHXB2CG_4148_4748_2_0_0_0_0_0_ed/2 +GGCATGGGTCCCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAACTTAGTCAGTGCTGGAATC +>K03455|HIVHXB2CG_8777_9292_1_0_0_1_0_0_ee/2 +GTAACAAGCTGGTGTTCTCTCCTTTATTGGCCTCTACTATCTTATCTGGCTCAACTGGTACTAGCTTGTA +>K03455|HIVHXB2CG_5476_6014_1_0_0_2_0_0_ef/2 +CAATACTTGGCACTAGCAGCATTAATAACACCAACAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAAC +>K03455|HIVHXB2CG_7113_7671_1_1_0_2_0_0_f0/2 +ACAAGACCCAACCACAATACAAGAAAAAGAATCCGTATCCCGAGAGGACCAGGGAGAGCATTTGTTACAA +>K03455|HIVHXB2CG_8987_9481_2_0_0_1_0_0_f1/2 +TGCCGCCCAGGCCACGCCTCCCTGGAAAGTCCCCAGCGGAAAGTCCCTTGTAGCAAGCTCGATGTCAGCA +>K03455|HIVHXB2CG_2671_3153_0_0_0_2_0_0_f2/2 +TTATTGTTCTATGCTGCCCTATTTCTAATTCAGATCCTACATACAAATCATCCATGTATTGATAGATAAC +>K03455|HIVHXB2CG_4224_4679_2_0_0_2_0_0_f3/2 +GTCCTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAAATATCACAGTAATTGGAGAGCAA +>K03455|HIVHXB2CG_6035_6530_5_0_0_2_0_0_f4/2 +TTCTACCATGTCATATTTCCACATGTTAAAATTTTCTGTCACATTTACGAATACTACTTCTTGTGGGTTG +>K03455|HIVHXB2CG_3418_3942_0_0_0_1_0_0_f5/2 +CAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACC +>K03455|HIVHXB2CG_1464_1989_0_0_0_1_0_0_f6/2 +AGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGA +>K03455|HIVHXB2CG_6032_6496_0_0_0_2_0_0_f7/2 +TCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTGTGGCCGCAA +>K03455|HIVHXB2CG_5040_5549_2_0_0_0_0_0_f8/2 +TATGGAAAACAGATTGCAGGTGATGAATGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGT +>K03455|HIVHXB2CG_100_597_1_0_0_3_0_0_f9/2 +GGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGGTAGTACCAGTTGAGCCAGAGAAGTT +>K03455|HIVHXB2CG_4990_5509_1_0_0_1_0_0_fa/2 +TTGGTGTTATTAATGCTGCTAGTGCCAAGTATTGTAGAGATCCTACCTTGTTATGTCCTGCTTGATATTG +>K03455|HIVHXB2CG_3077_3581_0_0_0_1_0_0_fb/2 +AGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGA +>K03455|HIVHXB2CG_3622_4137_3_0_0_1_0_0_fc/2 +TTTCCTTTTTTATTAACTGCTCTATTATTTGATTGACTCACTCTGATTCACTTTGATCTGGTTGTGCTTG +>K03455|HIVHXB2CG_2195_2689_1_0_0_1_0_0_fd/2 +ATTTTCCCTTCCTTTTCCATCTGTGTACAAATTTCTACTAATGCTTTTATTTTTTCTTCTGTCAATGGCC +>K03455|HIVHXB2CG_1968_2454_2_0_0_3_0_0_fe/2 +CAATTGAGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTAGGAAATGT +>K03455|HIVHXB2CG_9059_9533_1_0_0_0_0_0_ff/2 +GCCACTTTTTAAAAGAAAAGGGGGGACTGGAATGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGA +>K03455|HIVHXB2CG_6521_7021_2_0_0_3_0_0_100/2 +GCTAGACTGCCATTTAACAGCAGTTGAGTTGATACTACTGGGCTAATTCCATGTGTCCATTGAACTGTGC +>K03455|HIVHXB2CG_8231_8672_3_0_0_1_0_0_101/2 +GTGGAATTGGTTTAACATAACAAATTGGCTGTGGTAAATAAAATTATTGATACTGATAGTAGGAGGCTTG +>K03455|HIVHXB2CG_8037_8549_2_0_0_0_0_0_102/2 +GAGTAAGTCTCTCAAGCGGTGGTAGCTGAAGAGGCACAGGCTCCGCAGATCGTCCCAGATAAGTGCCAAG +>K03455|HIVHXB2CG_1639_2119_4_0_0_0_0_0_103/2 +TTCCCTTGTAGGAAGGCCAGATCTTCCCTAAAAAATTAGCCTGTCTCTCAGTACAATCTTTCATTTGGTG +>K03455|HIVHXB2CG_6917_7381_2_0_0_6_0_0_104/2 +TTACAGTAGACCAATTCCCCTCGACAATTAAAACTGTGCGTTACAATTACTGGTTCCCCTCCTGAGTATT +>K03455|HIVHXB2CG_1460_1915_2_0_0_2_0_0_105/2 +CACCAGGCCCGATGAGAGAACCAAGGGGAAGAGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAAT +>K03455|HIVHXB2CG_6555_7009_1_0_0_1_0_0_106/2 +TTTAACAGCAGTTGAGTTGATACTACTTGCCTAATTCCATGTGTACATTGTACTGTGCTGACATTTGTAC +>K03455|HIVHXB2CG_2797_3237_0_0_0_1_1_0_107/2 +GAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGT +>K03455|HIVHXB2CG_7516_8078_1_0_0_1_0_0_108/2 +AGATTTATTACTCCAACTAGCATTCCAAGGCACAGCAGTGGTGCAAATGAGTTTTCCAGATCAACCCCAA +>K03455|HIVHXB2CG_6431_7042_1_0_0_1_0_0_109/2 +GGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAACT +>K03455|HIVHXB2CG_6815_7400_1_0_0_2_0_0_10a/2 +CACGTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCG +>K03455|HIVHXB2CG_3953_4426_3_0_0_0_0_0_10b/2 +GTACAATCTAGTTGCCATATTCCTGGACTACAGTCTACTTGTCCATGCATGGCTTCTCCTTTTAGCTGAC +>K03455|HIVHXB2CG_6268_6856_0_0_0_3_0_0_10c/2 +GGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGT +>K03455|HIVHXB2CG_1793_2313_1_0_0_2_0_0_10d/2 +CGTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGTGTCGTTGCCAAAGAGTGACCTGAGGGAAGTTAAA +>K03455|HIVHXB2CG_8464_8957_2_0_0_4_0_0_10e/2 +GATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATGTGCTGAGCCTGTGCCTCTTCAGCTACCACCG +>K03455|HIVHXB2CG_8912_9460_0_0_0_2_0_0_10f/2 +CTGGAAAGTCCCCAGCGGAAAGTCCCATGTAGCAAGCTCGATGTGAGCAGTTCTTGAAGTACTCCGGATG +>K03455|HIVHXB2CG_6899_7432_1_0_0_2_0_0_110/2 +TCAGTACTCCAAGTACTATTAAACCAAGTACTATTAAAGAGTTGTGTTGAATTACAGTATAAAAATTCCC +>K03455|HIVHXB2CG_289_745_1_0_0_6_0_0_111/2 +ACATTGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTC +>K03455|HIVHXB2CG_5871_6382_2_0_0_0_0_0_112/2 +CAGGAAGTCAGCCTAAAACTGCTTGTACGAATTGCTATTGTAAAACGTGTTGCTTTCATTGCCAAGTTTG +>K03455|HIVHXB2CG_351_782_0_0_0_1_0_0_113/2 +GGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT +>K03455|HIVHXB2CG_4140_4649_2_0_0_2_0_0_114/2 +TCCAAATTCCTGCTTGATACCCGCCCACCAACAGGCGGCCGTAACCGTAGCACCGGTGAAATTGCTGCCA +>K03455|HIVHXB2CG_948_1441_2_0_0_1_0_0_115/2 +CTGGATGCACTCTATCCGATTCTGCAGCTTCCTCATTGATGGTCTCTTTTAACATTTGCATGGCTGCTTG +>K03455|HIVHXB2CG_999_1523_0_0_0_0_0_0_116/2 +TCCTGAAGGGTACTAGTAGTTCCTGCTATGTCACTTCCCCTTGGTTCTCTCATCTGGCCTGGTGCAATAG +>K03455|HIVHXB2CG_4753_5246_2_0_0_0_0_0_117/2 +TATGTTGTTATTACCAATCTAGCATCCCCTAGTGGGATGTGTACTTCTGAACTTATTCTTGGATGAGGGC +>K03455|HIVHXB2CG_2861_3349_0_0_0_1_0_0_118/2 +GCCCAATTCAATTTCCCCACTAACTTCTGTATGTGATTGACAGTCCAGCTGTCTTTTTCTGGCAGCACTA +>K03455|HIVHXB2CG_7260_7810_2_0_0_3_0_0_119/2 +GCTAGGAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAAACCTCAGGAGGGGACC +>K03455|HIVHXB2CG_716_1185_3_0_0_3_0_0_11a/2 +GTAATTTTGGCTGACCTGATTGCTGTGTCCAGTGTCAGCTGCTGCTATCTGTGCTTTTTTCTTACTTTTG +>K03455|HIVHXB2CG_104_705_2_0_0_2_0_0_11b/2 +CAAGCCGAGTCCTGCGTCGAGCGAGCTCCTCTGGTTTCCCTTTCGCTTTCAGGTCCCTGTTCGGGCGCGA +>K03455|HIVHXB2CG_5965_6531_1_0_0_2_0_0_11c/2 +GTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCTGTCACATTTACGAATACTCCTTCTTGTGGGTT +>K03455|HIVHXB2CG_8570_9126_2_0_1_1_0_0_11d/2 +AAGGATATCTTGTCTTCTTTGGGAGTGAATTAGCCCTTGCAGTCCCCCCTTTTCTTTTAAAAAGTGGCTA +>K03455|HIVHXB2CG_1948_2399_2_0_0_3_0_0_11e/2 +TCCCCCTATCATTTTAGGTTTCCATCATCCTGGCAAACTCATTTCTTCTAATACTGTATCAACTGCTCCT +>K03455|HIVHXB2CG_3762_4342_1_0_0_0_0_0_11f/2 +TATTGGCAAGCCACCTGGATTCCTGAGTTGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACC +>K03455|HIVHXB2CG_8552_8964_2_0_0_4_0_0_120/2 +GAATGTAACGAGGATTGTGGAAGTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTC +>K03455|HIVHXB2CG_5253_5699_1_0_0_1_0_0_121/2 +TCTGCATAGAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATAT +>K03455|HIVHXB2CG_7528_8024_2_1_0_0_0_0_122/2 +TCCAGAGCAACCCCAAATCCCCAGGAGCTGTTGATCCTTTAGGTATCTTTCCACAGCCAGGATTCTTGCC +>K03455|HIVHXB2CG_2552_3101_2_0_0_3_0_0_123/2 +CATTAGCCCTATTGAGACTGTACCAGTAAAAAAAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGG +>K03455|HIVHXB2CG_5165_5666_3_0_0_3_0_0_124/2 +CCAAGTAAAATGTCTAACAGCTTCATTCTTAAGCTCCACTAAAAGCTCTAGTGTCCATTCATTGTGTGGC +>K03455|HIVHXB2CG_2208_2700_0_0_0_1_0_0_125/2 +TCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGAC +>K03455|HIVHXB2CG_4540_5029_1_0_0_2_0_0_126/2 +AACTTTGCTTTTCTTCTTGGCACTACTTTTCTGTCACTATTATCTTGTATTACTACTGCCCCTTCACCTT +>K03455|HIVHXB2CG_7530_8094_3_1_0_1_0_0_127/2 +TCCAAATCTGTTCCAGAGATTTATTACTCCAACTAGGATTCCAAGGCACAGCAGTGGTGCAAATGAGTTT +>K03455|HIVHXB2CG_727_1225_1_0_0_1_0_0_128/2 +CCTGATGTACCATTTGCCCCTGTATGTTCTGCACTATAGGGTAATTTTGGCTGACCTGATTGCTGTGTCC +>K03455|HIVHXB2CG_5377_5899_3_0_0_0_0_0_129/2 +GACTGTTTTTCAGACTCTGCTATAAGAAAGGCCATATTAGGACACATAGTTAGCCCTATGTTTGAATATC +>K03455|HIVHXB2CG_2159_2702_1_0_0_1_0_0_12a/2 +CCCAATTTTTGAAATTTTCCCTTCCTTATCCATCTCTGTACAAATTTCTACTAATGCTTTTATTTTTTCT +>K03455|HIVHXB2CG_7758_8226_2_0_0_0_0_0_12b/2 +GCAGTGGTAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCCCTATGGGCGCAGCCTCAA +>K03455|HIVHXB2CG_7660_8187_0_0_0_2_0_0_12c/2 +TTTCTAGCTGGATTTGCGATTCTTCAATTAAGGAGTGTATTAAGCTTGTGTAATTGTTAATTTCTCTGTC +>K03455|HIVHXB2CG_5148_5636_3_0_0_2_0_0_12d/2 +GGGATGGATTTATAGACATCACTATGAAATCCCTCATCCAAGAATAAGTTCAGAATTACACATCCCACTA +>K03455|HIVHXB2CG_4162_4644_1_0_0_4_0_0_12e/2 +ATTCCTGCTTTATTCCCGCCGACCAACAGGCTGCCCTAACCGTAGCACCGGTGAAATAGCTGCCATTGTC +>K03455|HIVHXB2CG_1938_2418_0_0_0_0_0_0_12f/2 +CTTTGATAAAACCTCCAATTCCCCCTATCATTTTTGGTTTCCATCTTCCTGGCAAACTCATTTCTTCTAA +>K03455|HIVHXB2CG_3121_3619_0_1_0_1_0_0_130/2 +CTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTGGAGGTGGGGACT +>K03455|HIVHXB2CG_3918_4436_2_0_0_0_0_0_131/2 +TATGTTACTAATAGAGGAAGACAAAAAGTAGTCACCCTAACTGACACAACAAATCAGAAGAGTGAGTTAC +>K03455|HIVHXB2CG_2303_2856_1_0_0_0_0_0_132/2 +GCAACTAAAGGAAGCTCTATTAGCTACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA +>K03455|HIVHXB2CG_7266_7716_1_0_0_1_0_0_133/2 +AAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATGCTCAGGAGGGGACCCAGAAA +>K03455|HIVHXB2CG_2417_2944_1_0_0_3_0_0_134/2 +ATGGTAAATGCAGTATACTTGCAGAAGTCTTCATCTAAGGGAACTGAAAAATATGCATCACCCAGATCCA +>K03455|HIVHXB2CG_2669_3299_0_0_0_3_0_0_135/2 +GATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATA +>K03455|HIVHXB2CG_3147_3654_2_1_0_1_0_0_136/2 +TTAATTGTTTTACAACATTAGTGTGGGCACCCCTCATTCTTGCATATTTTCCTGTTTTCAGATTTTTAAA +>K03455|HIVHXB2CG_8778_9283_2_0_0_3_0_0_137/2 +TGGTGTTCTCTCCTTTATTGGCGTCTTCTATGTTATCTGGCTCAACTGGTACTAGCTTGTAGGACCATCC +>K03455|HIVHXB2CG_8901_9430_1_0_0_2_0_0_138/2 +ATCAAGCTCGATGTGAGCAGTTCTTGAAGTACTCCGGATGCAGCTCTCGGGCCACGTGATGAAATGCTAG +>K03455|HIVHXB2CG_4885_5430_2_0_0_2_0_0_139/2 +GCTAACTATGTGTCCAAAAAAGGCCTTTCTTATAGCAGAGTCTGAAAAACAGTCAAAGTAATACAGATGA +>K03455|HIVHXB2CG_6229_6814_1_1_0_1_1_0_13a/2 +TTACAACTTGTCAACTTATAGCTGGTAGTATCATTATCTATTGTTCTTATATCAAGTTTATAAAAAAATG +>K03455|HIVHXB2CG_1603_2129_3_0_0_0_0_0_13b/2 +AAAATATTACGAATGTATAGCCCTACCAGCATTCTGGACATACGACAAGGACCAAAGGAACCCTTTAGAG +>K03455|HIVHXB2CG_29_524_1_0_0_0_0_0_13c/2 +ACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTACCCTGATTAGCAGAACTACACACCA +>K03455|HIVHXB2CG_4241_4725_1_0_0_1_0_0_13d/2 +AATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGAAATTGGAGAGCAATGGCTAGTGATTTTAAC +>K03455|HIVHXB2CG_3443_3904_0_0_0_4_0_0_13e/2 +AATTTAGACTCCCTGTTAGCTGCCCCATCTAGATAGAAGGTTTCTGCTCCAACTATGGGTACTTTCTCTA +>K03455|HIVHXB2CG_5770_6313_1_0_0_0_1_0_13f/2 +ATTTTCAGAATTGGGTGTCGACATAGCAGAAAAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCA +>K03455|HIVHXB2CG_3844_4342_1_0_0_3_0_0_140/2 +AACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAATC +>K03455|HIVHXB2CG_5920_6432_0_0_0_2_0_0_141/2 +TTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGA +>K03455|HIVHXB2CG_1729_2183_3_0_0_2_0_0_142/2 +AAAAATTGGATGACAGAAACCTTGTAGGTCCAAAATGCTAACCCAGATTGTAAGCCTATTTTAAAAGCAT +>K03455|HIVHXB2CG_3999_4500_1_0_0_3_0_0_143/2 +CTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTCGGAATCATTC +>K03455|HIVHXB2CG_1957_2347_0_0_0_0_0_0_144/2 +ACTGTATCATCTGCTCCTGTATCTAATAGAGCTTCCTTTAGTTGCCCCCCTATCTTTATTGTGACGAGGG +>K03455|HIVHXB2CG_5122_5660_0_0_0_0_0_0_145/2 +AAAATGTCTAACAGCTTCATTCTTAAGCTCCTCTAAAAGCTCTAGTGTCCATTCATTGTGTGGCTCCCTC +>K03455|HIVHXB2CG_2900_3431_0_0_0_3_0_0_146/2 +AGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCA +>K03455|HIVHXB2CG_1261_1838_0_0_0_1_0_0_147/2 +CATGCTTTCATCATTTCTTCTAGTGTAGCCGCTGGTCCCAATGCTTTTAAAATAGTCTTACAATCTGGGT +>K03455|HIVHXB2CG_6692_7225_3_0_0_4_0_1_148/2 +CTGCTCTTTCAAAATCAGCACAAGCATAATAGGTAAGGTGCAGAAAGAATATGCCTTTTTTTATAAACTT +>K03455|HIVHXB2CG_5897_6351_3_0_0_1_0_0_149/2 +GTACCCCATAATAGACTGTTACCCACAATTTTTCTGTAGCACTACAGATCATCAACATCCCAAGGAGCAT +>K03455|HIVHXB2CG_8569_9110_0_0_1_5_0_0_14a/2 +CTTTGGGAGTGAATTAGCCCTTCCAGACCCCCCTTTTCTTTTAAACAGTTGGTAATATCTACAGCTGCCT +>K03455|HIVHXB2CG_75_558_0_0_0_0_0_0_14b/2 +CCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGC +>K03455|HIVHXB2CG_884_1417_1_0_0_0_0_0_14c/2 +AACATATAGTATGGGCAAGCAGGGAGCAAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGA +>K03455|HIVHXB2CG_1034_1525_0_0_0_0_0_0_14d/2 +GTTCCTGAAGGGTACTAGTAGTTCCTGCTATGTCACTTCCCCTTGGTTCTCTCATCTGGCCTGGTGCAAT +>K03455|HIVHXB2CG_3680_4205_0_0_0_2_0_0_14e/2 +GACTAATTTATCTCCTTGTTCATTTCCTCCAATTCCTTTGTGTGCTGGTACCCATGCCAGATAGACCTTA +>K03455|HIVHXB2CG_2550_3000_2_0_0_2_0_0_14f/2 +CCCATTAGCCCTATTGAGAGTGTACGAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAAT +>K03455|HIVHXB2CG_8934_9441_2_0_0_1_0_0_150/2 +AAGTCCCTTGTAGCAAGCTCGATGTCAGCAGTTCTTGAAGAACTCCGGATGCAGCTCTCGGGCCACGTGA +>K03455|HIVHXB2CG_8209_8703_1_0_0_2_0_0_151/2 +CTGTGCCCTCAGCTACTGCTATGGCTGTGGCATTGAGCAATCTAACAGCACTATTCTTTAGTTCCTGACT +>K03455|HIVHXB2CG_7970_8547_3_0_0_4_1_0_152/2 +TGAGGAAAGATACCTAAATGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGGACC +>K03455|HIVHXB2CG_5040_5577_1_0_0_1_0_0_153/2 +TATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTATACAGGATGAGGATTAGAACATGGAAAAGT +>K03455|HIVHXB2CG_6463_6968_2_0_0_2_0_0_154/2 +ACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGAGGAAAAATGACATGGTCGAACA +>K03455|HIVHXB2CG_1975_2422_0_0_0_1_0_0_155/2 +GGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGG +>K03455|HIVHXB2CG_2291_2816_1_0_0_0_0_0_156/2 +AAAGATAGGGGGGCAACTAAAGGAAGCTCTATAAGATACAGGAGCAGATGATACAGTATTAGAAGAAATG +>K03455|HIVHXB2CG_8503_8930_3_0_0_1_0_0_157/2 +CTTGTGATTGCTCCATGTTTTTCCAGGTCTCGAGATGCTGCTCCCAGCCTATCTGCTGCTGGCTCAGCTC +>K03455|HIVHXB2CG_6907_7418_2_0_0_2_0_0_158/2 +GTAATAATAAGACGTTCAATGGAACAGTACCATGTACAAATGTGAGCACAGTACAATGTACACATGGAAT +>K03455|HIVHXB2CG_4606_5102_2_0_0_1_0_0_159/2 +TTATGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGTAATTCCCTACAATCCCCAAAGTCAAGG +>K03455|HIVHXB2CG_8024_8484_0_0_0_3_0_0_15a/2 +AAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGG +>K03455|HIVHXB2CG_5881_6370_2_0_0_0_0_0_15b/2 +GCCTAAAACTGCTTGTCCCAATTGCAATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACA +>K03455|HIVHXB2CG_4697_5306_1_0_0_1_0_0_15c/2 +AGAATTAAAGAAAATTATAGGACAGGTACGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCA +>K03455|HIVHXB2CG_6580_7006_0_0_0_1_0_0_15d/2 +GTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAG +>K03455|HIVHXB2CG_7983_8467_0_0_0_1_0_0_15e/2 +CTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTT +>K03455|HIVHXB2CG_8296_8680_1_0_0_0_0_0_15f/2 +GCTGTGGCATTGAGCAAGCTAACAGCACTATTCTTTAGTTCCTGACTCCAATACTGTAGGAGATTCCACC +>K03455|HIVHXB2CG_4711_5187_1_0_0_2_0_0_160/2 +TTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTCTTCATCCACAA +>K03455|HIVHXB2CG_31_595_1_0_0_1_0_0_161/2 +CTCTCTAGTTACCAGAGTCACACAACAGACGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTG +>K03455|HIVHXB2CG_2715_3244_0_0_0_1_1_0_162/2 +TAACCCATCCACAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCCACA +>K03455|HIVHXB2CG_5538_6026_0_0_0_1_0_0_163/2 +TACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATG +>K03455|HIVHXB2CG_8046_8607_5_0_0_4_0_0_164/2 +GTGCCATGGAATGCTAGTAGGAGTAATACATCTCTGGAACAGATATGGAATCAGACGACCTGGATGGAGT +>K03455|HIVHXB2CG_1513_2030_3_0_0_3_0_0_165/2 +CCAGAGCCCTTTTTCCTAGGGGCCCTGCAATTTCTGGCTGTGTGCCCTTCTTTGCCCCAATTGAAACACT +>K03455|HIVHXB2CG_848_1264_3_0_0_1_0_0_166/2 +CTACTTTTACCCATGCATTTAAAGTTCTCGGTGATATGGCCTGATGTACCATTTGCCCCTGGATGTTCTG +>K03455|HIVHXB2CG_1350_1835_2_0_0_0_0_0_167/2 +GCTGTCATCATTTCTTCTAGTGTAGCCGCTGGTCCCAATGCTTTTAAAATAGTCTTACAATCTGGGTTCG +>K03455|HIVHXB2CG_6668_7185_1_0_0_0_1_0_168/2 +CTATTGTAACAAATGCTCTCCCTGGTCCTCTCGGGATACGGATTCTTTTTCTTGTATTGTTGTTGGGTCT +>K03455|HIVHXB2CG_7973_8462_0_0_0_1_0_0_169/2 +AATGGATCTGTCTCTGTCTCTCTCTCGACCTTCTTCTTCTATTCCTTCGGGCCTGTCGGGTCCCCTCGGG +>K03455|HIVHXB2CG_4715_5183_4_0_0_1_0_0_16a/2 +AGGACCTGTAAGAGATCATGCTGAACATCTTAAGACAGCAGTACAAATGGCATTATTCATCCACAATTTT +>K03455|HIVHXB2CG_3636_4159_2_0_0_3_0_0_16b/2 +GGTACCCATGCGAGATAGACCTTTTCCTTTTTAATTAACTGCTCTATTATTTGATTGACTACCTCTGATT +>K03455|HIVHXB2CG_3200_3710_1_0_0_1_0_0_16c/2 +AGACAAAAAACATCAGACAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACA +>K03455|HIVHXB2CG_345_871_1_0_0_0_0_0_16d/2 +TTTTCTTTCCCCCTGGCCTTAACCGAATTTTTTCCCATCGATCTAATTCTCCCCCGCTTAATACTGACGC +>K03455|HIVHXB2CG_5062_5502_2_0_0_1_0_0_16e/2 +TATTACTGCTGCTAGTGCCAAGTATTGTAGAGATCCTACCTTGTTATGTCCTGCTTGATATTCACACCTA +>K03455|HIVHXB2CG_6433_6984_2_0_0_3_0_0_16f/2 +CTGGCCTAATTCCATGTTTACATTGTACTGTTCTGACATTTGTACATGGTCGTGTTCCATTGAACGTCTT +>K03455|HIVHXB2CG_947_1395_1_0_0_1_0_0_170/2 +CATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCATAAGAACTTAG +>K03455|HIVHXB2CG_1538_1952_4_0_0_1_0_0_171/2 +TTTCTTTGGTTCCTACAATTGCCTCTCTGCATCATTATGGTAGCTGAATTTGTTACTTGGCTCATTGCTT +>K03455|HIVHXB2CG_4131_4604_0_0_0_0_0_0_172/2 +CGTAGCACCGGTGAAATTGCTGCCATTGTCAGTATGTATTGTTTTTACTGGCCATCTTCCTGCTAATTTT +>K03455|HIVHXB2CG_1622_2187_0_0_0_0_0_0_173/2 +GCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTA +>K03455|HIVHXB2CG_7660_8199_2_0_0_1_0_0_174/2 +GGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCCTTAGGAGTAGCACCGACCAAGGCAAA +>K03455|HIVHXB2CG_5201_5696_1_0_0_1_0_0_175/2 +GATATGTTGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTAACAGCTTCATTCTTCAGCTCCTCT +>K03455|HIVHXB2CG_1313_1849_1_0_0_2_0_0_176/2 +TATCCGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCAT +>K03455|HIVHXB2CG_8074_8576_1_0_0_2_0_0_177/2 +AATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGACATTAACAATTACACAAG +>K03455|HIVHXB2CG_1395_1888_1_0_0_1_0_0_178/2 +TTGCTTCAGCCAAAACTCTTGCCTTATGGCCGGGTCCTCCTACTCCCTGACATGCTGTCATCCTTTCTTC +>K03455|HIVHXB2CG_6705_7209_0_1_0_0_1_0_179/2 +CTTGTCTCATATTTCCTATTTTTCCTATTGTAACAAATGCTCTCCCTGGTCCTCTCGGGATACGGATTCT +>K03455|HIVHXB2CG_1621_2215_0_0_0_0_0_0_17a/2 +AGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCT +>K03455|HIVHXB2CG_866_1330_1_0_0_1_0_0_17b/2 +GGGTGGCTCCTTCTGATAATGCTGAAAACATGGGTATCACTTCTGGGCTGAAAGCGTTCTCTTCTACTAC +>K03455|HIVHXB2CG_2463_3069_2_0_0_0_0_0_17c/2 +GCTCTAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGATGACTCAGATTG +>K03455|HIVHXB2CG_1521_2010_0_0_0_1_0_0_17d/2 +GGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATC +>K03455|HIVHXB2CG_6189_6630_1_0_0_0_0_0_17e/2 +TCTTCAAATCAGTGCACTTTAAACTAACACAGAGTGGGGTTAATTTTACACATGGCTTTAGGCTTTGATC +>K03455|HIVHXB2CG_5398_5947_3_0_0_0_0_0_17f/2 +ATAAGAAAGGCCTTCTTAGGACACATAGTTAGCCCTAGGTGTGAATATCCAGCAGGACATCACAAGGTAG +>K03455|HIVHXB2CG_8877_9290_0_0_0_1_0_0_180/2 +AGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCT +>K03455|HIVHXB2CG_8626_9276_0_0_0_2_0_0_181/2 +AGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGA +>K03455|HIVHXB2CG_3650_4171_1_0_0_1_0_0_182/2 +AATAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAA +>K03455|HIVHXB2CG_1589_2085_2_0_0_2_0_0_183/2 +ATTAGCCTGTCTCTCAGTACAATCTTTCATTTGGTGTCCTTCCTTTCCAGATTTCGAACAGCCCTTTTTC +>K03455|HIVHXB2CG_421_886_2_0_0_2_0_0_184/2 +CCTGCATATAAGCAGCTGCTTTTTGCCAGTACTTGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGC +>K03455|HIVHXB2CG_5949_6444_2_0_0_1_0_0_185/2 +AGGCATGTGTGGCCCACACATTATGTACCTCTGTATCATATGCTTTAGCATCTGATGCACAAAATAGAGT +>K03455|HIVHXB2CG_325_825_1_0_0_0_0_0_186/2 +ACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGTAGGCGTGGCCTGGGCGG +>K03455|HIVHXB2CG_6839_7374_3_0_0_4_0_0_187/2 +AGAACCATTCCCCTCCACAATTCAAACTGTGCGTTACACTTTCTGGGTCCCCTCCTGAGGATTGCTTAAA +>K03455|HIVHXB2CG_2871_3414_3_0_0_1_0_0_188/2 +GTACTGGATGTGGGTGATGCATCTTTTTCAGTTGCCTTCGATGAAGACTTCAGGAAGTATACTGCATTTA +>K03455|HIVHXB2CG_8429_8919_4_0_0_0_0_0_189/2 +AGAAGGTGGAGAGAGAGACAGAGACAGATCCCTTGTATTAGTGAACGGATCCTTGGCACTTATCTGTGAC +>K03455|HIVHXB2CG_6746_7253_1_1_0_2_0_1_18a/2 +TTTTAAAGTGTTATTCCATTTTGCTGTACTAATGTTACAATGTGCTTGTCACATATTTCCTATTTTTTCC +>K03455|HIVHXB2CG_5796_6223_2_0_0_1_0_0_18b/2 +GCCACTGACTTCTGCTCTTTCTATTAGTCTATCAATTAACCTGTCTATTTTTCTTTGTCTTAATATTTTC +>K03455|HIVHXB2CG_9082_9644_4_0_0_2_0_0_18c/2 +GGACTGTCAGGGGTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATGTACCACACACAAG +>K03455|HIVHXB2CG_471_993_2_0_0_0_0_0_18d/2 +AAGGGATGGTTGTAGCTGTCCCAGTATTTGTCTACAGCCTTCTGATGTTTCTAACAGGCCAGGATTAACT +>K03455|HIVHXB2CG_4573_5050_0_0_0_2_0_0_18e/2 +TGTTTTCCATAATCCCTAATGATCTTTGCTTTTGTTCTTGGCACTCCTTTTATGTCACTATTATCTTGTA +>K03455|HIVHXB2CG_7709_8278_1_0_0_1_0_0_18f/2 +AGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGATCTTTG +>K03455|HIVHXB2CG_6151_6676_3_0_0_3_0_0_190/2 +TAGGAAAATATTAAGACAAAGAAAAATCGACAGGTTAATTGATATACTAATAGAAAGAGCAGAAGACATT +>K03455|HIVHXB2CG_2717_3242_2_0_0_2_1_0_191/2 +ACGCATCCAAAGGCATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCCACAGA +>K03455|HIVHXB2CG_2244_2670_1_0_0_0_0_0_192/2 +TCTCTGTACAAATTTCTACTAATGCTTTTATTTTTTCTTCTGTCAATGGCCATTGTTTAACTTTTGGGCC +>K03455|HIVHXB2CG_4142_4627_0_0_0_2_0_0_193/2 +GCCCACCCACAGGCGGCCCTAACCGTAGCACCGTTGAAATTGCTGCCATTGTCAGTATGTATTGTTTTTA +>K03455|HIVHXB2CG_1829_2304_1_0_0_0_0_0_194/2 +GCCCCCCTATCTTTATTGTGACGAGGGGTCGTTGCCAAAGAGTGACCTGAGGGAAGTTAAAGGATACAGT +>K03455|HIVHXB2CG_3704_4200_0_0_0_1_0_0_195/2 +ATTTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTGCTGGTACCCATGCCAGATAGACCTTTTGCTT +>K03455|HIVHXB2CG_806_1271_2_0_0_0_0_0_196/2 +CAGTATTAAGCGTGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAACGAAAAAATA +>K03455|HIVHXB2CG_9098_9596_1_0_0_2_0_0_197/2 +GGTTGCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCATAGAGACCCAGTACAGGCAAA +>K03455|HIVHXB2CG_9169_9597_1_0_0_0_0_0_198/2 +GGGTTCCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACCCAGTACAGGCAA +>K03455|HIVHXB2CG_1475_1919_0_0_0_1_0_0_199/2 +ATTATGGTAGCTGAATTTGTTACTTGGCTCATTGCTTCAGCCAAAACTCTTGCCTTATGGCCTGGTCCTC +>K03455|HIVHXB2CG_813_1284_0_0_0_0_0_0_19a/2 +GCTGAAAGCCTTCTCTTCTACTACTTTTACCCATGCATTTAAAGTTCTAGGTGATATGGCCTGATGTACC +>K03455|HIVHXB2CG_4251_4712_1_0_0_0_0_0_19b/2 +AATTTTCTTTAATTCTTTATTCATAGATTCTACTACTCCTTGACTTTGGGGATTGTAGGGAATTCCAAAT +>K03455|HIVHXB2CG_7542_8077_2_1_0_1_0_0_19c/2 +GATTTATTACTCCAACTAGCATTCCAAGGCCCAGCAGTGGTGCAAATGAGTTTTCCAGAGCAACCCCAAA +>K03455|HIVHXB2CG_3530_3989_1_0_0_4_0_0_19d/2 +AGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATATATCAAGAGCCATTTAAAAATCTGAAA +>K03455|HIVHXB2CG_8033_8528_1_0_0_1_0_0_19e/2 +TTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCCCACG +>K03455|HIVHXB2CG_337_926_3_0_0_0_0_0_19f/2 +ACTGCGAATCGTTCTAGCTCCCTGCTTGCCCATACTATATGTTTTAATTTATATTTTTTCTTTCCCCCTG +>K03455|HIVHXB2CG_8847_9306_3_0_0_1_0_0_1a0/2 +GGAAAGACTGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCAGGAGACCTGGAAAAACAT +>K03455|HIVHXB2CG_7301_7811_3_0_1_0_0_0_1a1/2 +AATCTTTAAGCAATCCTCAGGCGGGGACCCAGACATTGTAACCACAGTATTAATTGTGGAGGGGAATTTT +>K03455|HIVHXB2CG_8140_8608_2_0_0_1_0_0_1a2/2 +CAAGCTTAATCCACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATAGGA +>K03455|HIVHXB2CG_3475_4047_2_0_0_5_0_0_1a3/2 +TTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCCTCAAAAGACTTAATAGCAGAAATACAGAATCA +>K03455|HIVHXB2CG_3285_3781_1_0_0_1_0_0_1a4/2 +CTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTATTGGGGAAATTGAATTGGGCAAGTC +>K03455|HIVHXB2CG_9043_9496_1_0_0_0_0_0_1a5/2 +GCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGAGTGGAAGGGCTAATTCACTCCCAAAGAA +>K03455|HIVHXB2CG_863_1405_3_0_0_3_0_0_1a6/2 +TTATTGTCTCTTTTAACATTTGCATGGCTGCTTGATGTCCCCCCACTGTGTTTAGCATGGTGATTAAATC +>K03455|HIVHXB2CG_7008_7508_0_0_0_3_0_0_1a7/2 +CTGCCAGATGTTTATAATTTGTTTTATTCTGGATGGGCGGGTGATTGTGTCACTTCCTTCAGTGTTATTT +>K03455|HIVHXB2CG_6055_6608_1_0_0_2_0_0_1a8/2 +ACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAAAAATAGCAATAGTT +>K03455|HIVHXB2CG_4082_4552_1_0_0_0_0_0_1a9/2 +TCAAAGTGCATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCA +>K03455|HIVHXB2CG_5607_6138_1_0_0_0_0_0_1aa/2 +ACTATGGACCACACAACTATTGCTATTATTATTGCTACTACTAATGCTACTATTGCTACTATTGGTATAG +>K03455|HIVHXB2CG_2372_2885_0_0_0_2_0_0_1ab/2 +ACCCACATCCAGTACTGTTACTGATTTTTTCATTTTTACCCCTGCGGGATGTGGTATTCCTAATTGAACT +>K03455|HIVHXB2CG_3491_4113_0_0_0_0_0_0_1ac/2 +TTATTTGATTGACTAACTCTGATTCACTTTGATCTGGTTGTGCTTGAATGATTCCTAATGCATATTGTGA +>K03455|HIVHXB2CG_8769_9258_0_0_0_1_0_0_1ad/2 +CAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCT +>K03455|HIVHXB2CG_4401_4889_1_0_0_1_0_0_1ae/2 +CCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTTGTAGCAGTTCATGTAGCCA +>K03455|HIVHXB2CG_1911_2405_2_0_0_0_0_0_1af/2 +TACCATAATGATGCAGAGAGGCAATATTAGGAACCAAAGAAAGATTGTTAAGTGTTTGAATTGTGGCAAA +>K03455|HIVHXB2CG_1158_1700_3_0_0_0_0_0_1b0/2 +AGAGTTTTATAGAACCGGTCTACATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCTTATGTCCAGAATGC +>K03455|HIVHXB2CG_1058_1450_1_0_0_1_0_0_1b1/2 +CTGCATGCACTGGATGCACTGTATCCCATTCTGCAGCTTCCTCATTGATGGTCTCTTTTAACATTTGCAT +>K03455|HIVHXB2CG_3869_4394_2_0_0_3_0_0_1b2/2 +GTCTACTTGTGCATGCCTGGCTTCTCCTTTTAGCTGACATTTATCAGAGCTGGCTACTATTTCTTTTGCT +>K03455|HIVHXB2CG_8021_8540_2_0_0_1_1_0_1b3/2 +TCTCAAGCGGTGGTAGGTGAAGAGGCACAGGCTCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTC +>K03455|HIVHXB2CG_1571_2094_0_0_0_1_0_0_1b4/2 +CCCTAAAAAATTAGCCTGTCTCTCAGTACAATCTTTCATTTGGTGTCCTTCCTTTCCCCATTTCCAACAG +>K03455|HIVHXB2CG_4445_4946_2_0_0_0_0_0_1b5/2 +TATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGACGTTATTCCCGCAGAAACAGGGCAG +>K03455|HIVHXB2CG_1620_2150_1_0_0_3_0_0_1b6/2 +TAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTATAGACTATGTAGACCGGTTC +>K03455|HIVHXB2CG_4371_4875_6_0_0_2_0_0_1b7/2 +GTTTTTGTAATTGTTTAGTTTGTATGTCTGTTGCTATTAAGTCTACTATTCTTTCCCCTGCACTGTACCC +>K03455|HIVHXB2CG_3895_4376_1_0_0_3_0_0_1b8/2 +AGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTGACCCTAACTGACAC +>K03455|HIVHXB2CG_7019_7507_1_0_0_1_0_0_1b9/2 +AGCAGAAGAAGAGGTAGTAATTAGATCTGTCCATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG +>K03455|HIVHXB2CG_8154_8649_0_0_0_1_0_0_1ba/2 +TCTTTCGTTCCTGACTCCAATACTGTAGGAGATTCCACCAATATTTGAGGGCTTCCCACCCCCTGCGTCC +>K03455|HIVHXB2CG_1930_2450_1_0_0_1_0_0_1bb/2 +GATATCTATGAGTATCTGATCATACTGTCTTACTTTGATAAAACCTCCAATTCCCCCTATCATTTTTGGT +>K03455|HIVHXB2CG_948_1424_2_0_0_2_0_0_1bc/2 +CATTCTGCAGCTTCCTCATTTATGGTCTCTTTTAACATTTGCATGGCAGCTTGATGTCCCCCCACTGTGT +>K03455|HIVHXB2CG_1234_1707_1_0_0_0_0_0_1bd/2 +CCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAATGCTTTCAGCCCAGAAGTGATACCCATGT +>K03455|HIVHXB2CG_4529_5013_0_0_0_1_0_0_1be/2 +TCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGT +>K03455|HIVHXB2CG_7824_8291_4_0_1_0_0_0_1bf/2 +TACTATCATTATGAATAATTTTATATACCACAGCCAATTTGTTATGTTAAACCAATTCCACAAACTTGCC +>K03455|HIVHXB2CG_265_763_3_1_0_2_0_0_1c0/2 +AAAATTTTTGGCGTACTCACCAGTCGCCGGCCCTCGCCTCTTGCCGTGCGCGCTTCATCAAGCCGAGTCC +>K03455|HIVHXB2CG_8600_9126_2_0_0_6_0_0_1c1/2 +AAGGATAACATGTGTTCTTTGGGAGTGCATTAGGCCTTCCAGTCCCCCCTATTCTTTTAAAAAGTGGCTA +>K03455|HIVHXB2CG_2940_3467_6_0_0_0_0_0_1c2/2 +GTTTTCTGCCAGTTCTAGCTCTGCTTCTTCTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTTCCTCTA +>K03455|HIVHXB2CG_5735_6168_1_0_0_0_0_0_1c3/2 +TGTCTTAATATTTTCCTATATTCTATGATTACTATGGACCACACAACTATTGCTATTATTATTGCTACTA +>K03455|HIVHXB2CG_596_1011_1_0_0_2_0_0_1c4/2 +TACTTCTGATCCTGTCTGAAGGGATGGTTGTAGCTGTCCCAGTATTTGTCTACAGCCTTCAGATGTTTCT +>K03455|HIVHXB2CG_8708_9162_0_0_0_1_0_0_1c5/2 +GGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTG +>K03455|HIVHXB2CG_7421_7885_1_0_0_2_0_1_1c6/2 +TTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGCATAAAACAA +>K03455|HIVHXB2CG_7126_7627_1_1_1_1_1_0_1c7/2 +ACAATACAAGAAAAAGAATCCGTATCCCGAGAGGACCAGGGAGATCATTTGTTACAATAGGAAAAATAAG +>K03455|HIVHXB2CG_2489_2936_0_0_0_0_0_0_1c8/2 +TACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGC +>K03455|HIVHXB2CG_9138_9654_2_0_0_2_0_0_1c9/2 +AGACGGGCACACACTACTTGAAGGCCTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTT +>K03455|HIVHXB2CG_7971_8443_2_0_0_0_0_0_1ca/2 +GTGGAAAGATACCTAAAGGATCAACCGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCAATTGCACCA +>K03455|HIVHXB2CG_3244_3776_2_0_0_0_0_0_1cb/2 +GGTGGCTTGCCAATACTCTGTCCACCATGTTTCCCATGTTTCCTTTTGTATGGGCAGTTTAAATTTAGGA +>K03455|HIVHXB2CG_6624_7212_0_0_0_1_1_0_1cc/2 +GTGCTTGTCTCATATTTCCTATTTTTCCTATTGTAACACATGCTCTCCCTGGTCCTCTCGGGATACGGAT +>K03455|HIVHXB2CG_5047_5581_1_0_0_1_0_0_1cd/2 +AACAGATGGCAGGTGATGATTGTGTGGCAAGTCGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAA +>K03455|HIVHXB2CG_8705_9169_2_0_0_3_0_0_1ce/2 +TAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGATCTATTCGCCACATACCTAGAAGAATAAGACCGGGC +>K03455|HIVHXB2CG_9111_9500_0_0_0_1_0_0_1cf/2 +AAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACA +>K03455|HIVHXB2CG_3087_3633_1_0_0_0_0_0_1d0/2 +TGTGGGCACCCCTCATTCTTGCATATTTTCCTGTTTTCAGATTTTTAAATGGCTCTTGATAAATTTGATA +>K03455|HIVHXB2CG_6205_6720_3_1_0_1_0_0_1d1/2 +AAGAGCAGAAGACAGTGGCAATGAGCGTGAAGTAGAAATATCCGCACTTGTGGAGAAGGGGGTGGAGATG +>K03455|HIVHXB2CG_7425_7891_2_0_0_1_0_1_1d2/2 +AGGAAATTGTTCTGCTGCTGCACTATACCAGACAATAATTGTCTGGCCTGTACCGTCAGCGTCAATTGAG +>K03455|HIVHXB2CG_8198_8657_0_0_0_2_0_1_1d3/2 +AGCACTATTCTTTAGTTCCTGACTCCAATAGGTGTAGGATATTCCACCAATATTTGAGGGCTTCCCACCC +>K03455|HIVHXB2CG_5477_5948_2_0_0_0_0_0_1d4/2 +AATACTTGGCACTCGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTATTGTTACGAAACT +>K03455|HIVHXB2CG_7950_8509_1_0_0_2_1_0_1d5/2 +GTCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCACTAATCGAATGGATCTGACTCTGTCTCTCT +>K03455|HIVHXB2CG_7340_7745_1_0_0_1_0_0_1d6/2 +AACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACATGG +>K03455|HIVHXB2CG_7428_7933_0_0_0_3_0_0_1d7/2 +ACTGTGAGTTGCAACAGATGGTGTTGCGCCTCAATAGCCCACAGGAAATTGTTCTGCTGCTGCACTATAC +>K03455|HIVHXB2CG_3336_3873_0_0_0_1_0_0_1d8/2 +CATAGAAGGTTTCTGCTCCTACTATGGGTTCTTTCTCTAACTGGTACCATAATTTCAGTAAGGGAGGGGT +>K03455|HIVHXB2CG_7557_8035_1_1_0_0_0_0_1d9/2 +TGTTCATCAAATATTACAGGGCTGCTATTAACAAAAGATGGTGGTAAAAGCAACAATGAGTCCGAGATCT +>K03455|HIVHXB2CG_8415_8932_1_0_0_1_0_0_1da/2 +TACTTGTGATTGCTCCATGTTTTTCCAGGTCTCGAGATGCTGCTCCCACCCTATCTGCTGCTGGCACAGC +>K03455|HIVHXB2CG_4067_4416_4_0_0_0_0_0_1db/2 +TCAAGCAGAACCCGATCAAAGTGAATCAGAGTTAGTCAATCAAATCATATAGCAGTTAATAAAAAAGGAA +>K03455|HIVHXB2CG_6036_6517_3_0_0_3_0_0_1dc/2 +TATCAAAGCAGTAAGTAGTCCATGTAACGCAACCTATAGCAAAAGTAGCAATAGTAGCATTAGTAGTAGC +>K03455|HIVHXB2CG_16_595_2_0_0_1_0_0_1dd/2 +ATCTCTAGTTACCAGAGTCACACAACAGACGGGCACACACTACTTGAAGCACTGAAGGCAAGCTTTATTG +>K03455|HIVHXB2CG_1274_1765_1_0_0_0_0_0_1de/2 +AGGCTTTCAGCCCAGAAGTGATACCCATGTTTTGAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAA +>K03455|HIVHXB2CG_8254_8808_2_0_0_3_0_0_1df/2 +ATTGGCTGTGGTATATAAAATTATTCATACTGATAGTAGGAGGCTTGGTAGGTTTAAGAATCGTTTTTGC +>K03455|HIVHXB2CG_2216_2792_1_0_0_1_0_0_1e0/2 +AGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACGCCTCGTC +>K03455|HIVHXB2CG_720_1152_0_0_0_1_0_0_1e1/2 +GCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAG +>K03455|HIVHXB2CG_2348_2868_0_0_0_2_0_0_1e2/2 +ATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAA +>K03455|HIVHXB2CG_5040_5570_1_0_0_3_0_0_1e3/2 +TATGGAAAACAGCTGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGT +>K03455|HIVHXB2CG_4494_5013_3_0_0_4_0_0_1e4/2 +TTGGCACTACTTTTATGTCAGTAATATGTTGTATTACTACTGCCCGTTCACCTTTCCAGAGGAGCTTTGC +>K03455|HIVHXB2CG_3516_4038_1_0_0_0_0_0_1e5/2 +AAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAATGCCAATGGACATATCAAATTTATCAAGAGCCAT +>K03455|HIVHXB2CG_5760_6259_2_0_0_0_0_0_1e6/2 +CATTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGA +>K03455|HIVHXB2CG_2682_3164_1_0_0_0_0_0_1e7/2 +CAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTACATACAAATCATCCATGTAT +>K03455|HIVHXB2CG_7198_7699_1_0_0_1_0_0_1e8/2 +TCAATTTTTACTACTTTATCTTTATATAATTCACTTCTCCAATTGTCCCTCATATCTCCTCCTCCAGGTC +>K03455|HIVHXB2CG_8714_9261_4_0_0_2_0_0_1e9/2 +AGACGTAGTACAAGGAGCTTGTAGAGCTATTCGCCAGAACCCTAGAAGAATAAGACAGGGCTTGGAAAGG +>K03455|HIVHXB2CG_7457_8063_2_0_0_1_0_0_1ea/2 +ACTAGCATTCCAAGGCACAGCAGTGGTGCAACTGAGTTTTCCAGAGCAACCCCAAATCCCCAGGAGCTGT +>K03455|HIVHXB2CG_6290_6823_1_0_0_2_1_0_1eb/2 +TGGGATGTTGATGATCTGTATTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGG +>K03455|HIVHXB2CG_2207_2739_2_0_0_0_0_0_1ec/2 +TTATGGCAAATACTGGAGTATTGTATGGATTTTCAGGCCCAATTTTTGAAATTTTCCCTTCCTTTTCCAT +>K03455|HIVHXB2CG_9181_9579_6_0_0_2_0_0_1ed/2 +GAGAGGTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACCCAGTACAGGCAAAAAGCAGCTGCTTAAATG +>K03455|HIVHXB2CG_22_472_3_0_0_1_0_0_1ee/2 +AACGAAGACAAGATATCGTTGATCTGTGGATCTACCACCCACAAGGCTACTTCCCTGATTATCAGAACTA +>K03455|HIVHXB2CG_2296_2821_0_0_0_4_0_0_1ef/2 +TAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTT +>K03455|HIVHXB2CG_609_1028_2_0_0_1_0_0_1f0/2 +TTATATAATGATCTAAGTTCTTCTGATCCTGTCTGAAGTGATGGTTGTAGCTGTCCCAGTATTTGTCTAC +>K03455|HIVHXB2CG_7436_7882_0_0_0_1_0_1_1f1/2 +GTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGG +>K03455|HIVHXB2CG_6483_7000_3_0_0_3_0_0_1f2/2 +GTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGAAGACCAGATTCATGAGGATATAATCA +>K03455|HIVHXB2CG_1900_2395_0_0_0_1_0_0_1f3/2 +ACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCA +>K03455|HIVHXB2CG_8675_9264_3_0_0_2_0_0_1f4/2 +GGCCTCTTCTATCTTATCTGGCTCACCTGGTACTAGCTTGTAGCACCATCCACAGGTCAGTGGATATCTG +>K03455|HIVHXB2CG_4075_4642_4_0_0_1_0_0_1f5/2 +TCCTGCTTGATTCCCGGCCACCAACAGGCGGCCCTAACCGTAGCACCGGTGAAATTGCTGCCATTGTCAG +>K03455|HIVHXB2CG_8686_9222_2_0_0_2_0_0_1f6/2 +GCACCAACCAAAGGTCAGTGGATCTCTGACCCCTGGCCCTGGTGTGTAGTTCTGCTAATCAGGGAAGTAG +>K03455|HIVHXB2CG_4244_4641_2_0_0_1_0_0_1f7/2 +AGATAAGGCCCAAGATGAACATGAGAAAAATCACAGTAATTTGAGAGCAATGGCTAGTGATTTTAACCTG +>K03455|HIVHXB2CG_1941_2479_0_0_0_2_0_0_1f8/2 +GAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCC +>K03455|HIVHXB2CG_1089_1580_0_0_0_1_0_0_1f9/2 +TTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGA +>K03455|HIVHXB2CG_609_1102_0_0_0_0_0_0_1fa/2 +TTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGG +>K03455|HIVHXB2CG_1663_2248_1_0_0_0_0_0_1fb/2 +TTAAAGGATACAGTTCCTTGTCTATCGGCTCCTGCTTCTGAGGGGGAGTTGTTGTCTCTACCCCAGACCT +>K03455|HIVHXB2CG_2027_2593_3_0_0_1_0_0_1fc/2 +CCTGGCTTTAATTTTACTGGTACAGTCTCAATAGGGCTAATGGGAAAATTTAAAGTGCAACCAAACTGAG +>K03455|HIVHXB2CG_3670_4063_3_0_0_6_0_0_1fd/2 +AAATAACCACAGAAAGGATAGTAATATGGGGAAAGACTCCAAAATTTAAACTGCCCATACAACAGGAAAC +>K03455|HIVHXB2CG_3259_3849_2_0_0_1_0_0_1fe/2 +CTAAATGGACAGTACAGCCTATAGTGCTGCCAGCAAAAGACAGCTGGACTGTCAATGACATACAGAAGTT +>K03455|HIVHXB2CG_3094_3634_2_0_0_0_0_0_1ff/2 +AATACATGGATGATTTTTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAAGAAAAATAGAGGAGCT +>K03455|HIVHXB2CG_3637_4259_4_0_0_1_0_0_200/2 +ATGATGTAACACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCCTATTAATAAGGGGAAAGAC +>K03455|HIVHXB2CG_3504_4036_0_0_0_2_0_0_201/2 +TATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTT +>K03455|HIVHXB2CG_453_934_0_0_0_5_0_0_202/2 +TGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAG +>K03455|HIVHXB2CG_1208_1762_3_0_0_1_0_0_203/2 +GGCAACTGGTACATCAGGCCATATCACCTAGAACTTTAAATGCCTGGGTAAAAGTAGTAGAATAGAAGGC +>K03455|HIVHXB2CG_2845_3325_1_0_0_0_0_0_204/2 +GGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAAGA +>K03455|HIVHXB2CG_8968_9485_1_0_0_1_0_0_205/2 +CTCGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTT +>K03455|HIVHXB2CG_2277_2793_1_0_0_0_0_0_206/2 +CCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGCGCAGATGATACAG +>K03455|HIVHXB2CG_607_1160_2_0_0_4_0_0_207/2 +ATTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGTAAACCAGA +>K03455|HIVHXB2CG_6142_6654_1_0_0_0_0_0_208/2 +CATAGAATATAGGAAAATATAAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCA +>K03455|HIVHXB2CG_5843_6315_2_0_0_1_1_0_209/2 +GATCCTAGACTAGAGCCCTGTAAGCATCCAGGAAGTCAGCCTAACACTGCTTGTACCAATTGCTATTGTA +>K03455|HIVHXB2CG_5774_6325_0_0_0_1_1_0_20a/2 +AATTTTTCTGTAGCACTACAGATCATCAACAACCCAAGGAGCATGGTGCCCCATCTCCACCCCCTTCTCC +>K03455|HIVHXB2CG_9092_9584_5_0_0_0_0_0_20b/2 +GGCTCCTTCACTCCCAAAGAAGACAAGATATCCTTTATCTTTGGATGTACCACACACAAGGCTACTTCCC +>K03455|HIVHXB2CG_1407_1918_2_0_0_0_0_0_20c/2 +TTATGGTAGCTGAATTTGTTACTTGGCTCATTGCTTCAGCCAAAACTCTTGCCTTATGGCCGGGTCCTCC +>K03455|HIVHXB2CG_2017_2451_0_0_0_0_0_0_20d/2 +AAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATT +>K03455|HIVHXB2CG_8060_8626_3_0_0_1_0_0_20e/2 +TGTAGGAGATTCCACCAATATTTGAGGGGTTCCCACCCCCTGCGTCCCAGAAGTTCCACAATCCTCGTTA +>K03455|HIVHXB2CG_6270_6648_3_0_0_1_0_0_20f/2 +TATTGGTATTAGTATCATTCTTCAAATCAGTGCACTTTAAACTAACACAGAGTGGGGTTAATTTTACAGA +>K03455|HIVHXB2CG_5023_5568_1_0_0_2_0_0_210/2 +CAAAGATCATTAGGGAATATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGA +>K03455|HIVHXB2CG_6484_6952_2_0_0_0_0_0_211/2 +CTGACATTTGTACATGGTCCTGTTCCATTGAACGTCTTATTATTACATTTTAGAATCGCAAAACCAGCCG +>K03455|HIVHXB2CG_9057_9594_1_0_0_1_0_0_212/2 +AAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTT +>K03455|HIVHXB2CG_5238_5745_1_0_0_1_0_0_213/2 +TTCTTATTATGGCATCCACTCCTGCCCAAGTATCCCCATAAGTTTCATAGATATGTTGCCCTAAGCCATG +>K03455|HIVHXB2CG_7438_7984_1_0_0_2_0_0_214/2 +AGGTATCTTTCCACAGCCAGGATTCTTGCCTGGATCTGCTTGAAGCCCCAGACTGTGAGTTGCAACAGAT +>K03455|HIVHXB2CG_7900_8303_1_0_0_0_0_0_215/2 +TTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGGAGCTCCAGGCAAGAATCCTGGC +>K03455|HIVHXB2CG_2534_3069_3_0_0_4_0_0_216/2 +GTTTTCTAAAATGCTCTAAGATTTTTGTCATGGTACTTTGGAATATTGCTGGTGATCCTTTCCAACGCTG +>K03455|HIVHXB2CG_7670_8163_2_0_0_1_0_0_217/2 +CAATTAAGGAGTGTATTAAGCTTTTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATT +>K03455|HIVHXB2CG_7532_7974_3_1_0_1_0_0_218/2 +CCCTCCCATCAGTGGACAAATTAGATGTTCCTCAAATATTCCAGGGCTGCTATTAACAAAAGATGGAGGT +>K03455|HIVHXB2CG_4036_4577_1_0_0_0_0_0_219/2 +GTCAGTATGTATTGTTTTTACTGGCCATCTTCCTGCTAATTTTAAAAGAAAATATGCTGTTTCCTGCCCT +>K03455|HIVHXB2CG_6840_7267_1_0_0_2_0_0_21a/2 +TTGCTAGCTATCTGTTTTAAAGTGTTATACCATTTTGCTCTACTACTGTTACAATGTGCTTGTCTCATAT +>K03455|HIVHXB2CG_1275_1753_2_0_0_1_0_0_21b/2 +ACAAGGTTTCTGACATCCAATTTTTTACCTCCTGTGAAGCTTGCTCGGCTCTTAGAGTTTTATAGAACCG +>K03455|HIVHXB2CG_5849_6413_2_0_0_2_0_0_21c/2 +AGAGTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCACTTGCTATTGTAAAAAGT +>K03455|HIVHXB2CG_3289_3687_2_0_0_1_0_0_21d/2 +TGCTTTCTGTGGTTATTTTTTGCACTGCCACTGTTAATTGTTTTACATCATTAGTGTGGGCACCCCTCAT +>K03455|HIVHXB2CG_8727_9223_0_0_0_2_0_0_21e/2 +AGCACCATCCAAAGGTCAGTTGATATCTGACCCCTGGCCCTGGTGTGTAGTTCTGCTAATCAGGGACGTA +>K03455|HIVHXB2CG_8268_8756_0_0_0_2_0_0_21f/2 +AGGTAAGTGGCGAATAGCTCTACAAGCTCCTTGAACTACTTCTATAACCCTATCTGTCCCCTCAGCTACT +>K03455|HIVHXB2CG_1456_1973_0_0_0_0_0_0_220/2 +ATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAAC +>K03455|HIVHXB2CG_8212_8688_0_0_0_0_0_1_221/2 +CTGCTATGGCTGTGGCATTGAGCAAGCTAACAGCACTATTCTTTAGTTCCTGACTCCAATAGCTGTAGGA +>K03455|HIVHXB2CG_954_1409_2_0_0_2_0_0_222/2 +TCATTGATGGTCTCTTTAAACATTTGCATGGCTGCTTGATGTCCCCCCACTTTGTTTAGCATGGTGTTTA +>K03455|HIVHXB2CG_6460_6905_2_0_0_1_0_0_223/2 +CCAACCCACAAGAAGTAGTATTGGTACATGTGACAGAAAATTTTAACATGTGGAAACATGACATGGTAGA +>K03455|HIVHXB2CG_1269_1765_3_0_0_2_0_0_224/2 +CATTTTGGACCAACAAGGTTTCTGTCATCCAATTTTATACCTCCTGTGAAGCTTGCTCGGCTCTTCGAGT +>K03455|HIVHXB2CG_7948_8476_2_0_0_1_0_0_225/2 +CCGTTCACTAATCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCTACGGGCCTGT +>K03455|HIVHXB2CG_5096_5615_3_0_0_5_0_0_226/2 +GAACATGGAAAAGTATAGTAACACACGATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACA +>K03455|HIVHXB2CG_1129_1547_1_0_0_1_0_0_227/2 +TTATTTGTCATCCATCCTATTTGTTCCTGAAGGGTACTAGTAGTACCTGCTATGTCACTTCCCCTTGGTT +>K03455|HIVHXB2CG_1681_2175_2_0_0_1_0_0_228/2 +GCTCTCTTCTGGTGGGGCTTTTGGCTCTGGTCTGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGGAA +>K03455|HIVHXB2CG_3121_3628_3_1_0_3_0_0_229/2 +GCACCCCTCATTCTTGCCTAATTTCCTGTTTTGAGATTTTTAAATGGCTCTTGATAAATTTGATATGTCC +>K03455|HIVHXB2CG_5909_6401_2_0_0_0_0_0_22a/2 +TTTAGCATCTGATGCACAAAATAGAGTGGTGGTTGCTTCCTTCCACACAGGTACCCCATAATAGACTGTG +>K03455|HIVHXB2CG_5183_5620_2_0_0_4_0_0_22b/2 +TCTAGTGACCATTCATTGTGTGGCTCCGTCTGTGGCGCTTGGTCTTCTGGGGCTTGTTCCATCTATCCAC +>K03455|HIVHXB2CG_4887_5366_1_0_0_0_0_0_22c/2 +AGATGAATTAGTTGGTCTGCTAGTTCAGGGTCTACTTGTGTGCTATATCTCTTTTTCCTCCATTCTATGG +>K03455|HIVHXB2CG_1930_2469_4_0_0_2_0_0_22d/2 +CTATCGCTTTATGTCCACAGATTTCTCTGAGTATCTGATCATACTGTCTTACTTTGATAAAACCTCCAAT +>K03455|HIVHXB2CG_4654_5228_1_0_0_0_0_0_22e/2 +CTAGCATCCCCTAGTGGGATGTGTACTTCTGAACTTATTCTTGGATGAGGGCTTTCATAGTGATGTCTAT +>K03455|HIVHXB2CG_3829_4380_1_0_0_1_0_0_22f/2 +ACCAGTTAGATAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGAC +>K03455|HIVHXB2CG_7309_7840_1_0_1_1_0_1_230/2 +AGCAATCCTCAGGAGGGGACCCAGAAATTGTAACCACAGTTTTCATTGTGGAGGGGAATTTTTCTACTGT +>K03455|HIVHXB2CG_6917_7359_1_0_0_2_0_1_231/2 +TACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTA +>K03455|HIVHXB2CG_8818_9376_0_0_0_2_0_0_232/2 +AGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGG +>K03455|HIVHXB2CG_7115_7619_0_1_0_2_1_0_233/2 +GGACTCATTGTTGCTATTACCACCATCTTTTGTTACTAGCAGCCCTGTAATATTTGAAGAACATCTAATT +>K03455|HIVHXB2CG_4988_5473_0_0_0_2_0_0_234/2 +TAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCA +>K03455|HIVHXB2CG_2513_3108_0_0_0_1_0_0_235/2 +AATGATCCATGTATTGATAGATAACTATGTCTGGATTTTGTTTTCTAAAAGGCTCTAAGATTTTTGTCAT +>K03455|HIVHXB2CG_7795_8206_0_0_1_2_0_0_236/2 +AATAATTCTTGTTCATTCTTTTCTTGCTGGTTTTGCGATTCTTCCATTAAGGAGTGTATTAAGCTTGTGA +>K03455|HIVHXB2CG_8839_9351_2_0_0_4_0_0_237/2 +CAACCTCCAGTCTAACACTACTCTCTCCGGGTCATCCATCGCATGCAGGCTCACAGGGTGTAACAAGCTG +>K03455|HIVHXB2CG_3576_3990_2_0_0_2_0_0_238/2 +CAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATTCAAGAATGATGGGTGCCCACACTAATGATGTAA +>K03455|HIVHXB2CG_4643_5146_1_0_0_0_0_0_239/2 +ATTTGGAATTCCCTACAATCCCCAAAGTCAAGGCGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATT +>K03455|HIVHXB2CG_5632_6125_3_0_0_4_0_0_23a/2 +AGCTTCAGAATGAAGCTGTTAGACATATTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTCTGA +>K03455|HIVHXB2CG_3291_3792_2_0_0_1_0_0_23b/2 +CCCACTCAGGAATCCATGTGGCTTGCCAATACTCTGTCCACCATGTTTCCCATGTTTCCTTTTGTATGGG +>K03455|HIVHXB2CG_6802_7237_0_0_0_3_0_0_23c/2 +TGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACA +>K03455|HIVHXB2CG_6455_6966_3_0_0_2_0_0_23d/2 +AGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTTACAGAAAATTTTAACCTGTGGAAAAATGAGATG +>K03455|HIVHXB2CG_3202_3735_0_0_0_1_0_0_23e/2 +CCTTTTGTATGGGCAGTTTAAATTTAGGAGTCTTTCCCCATATTACTATGCTTTCTGTGGTTATTATTTG +>K03455|HIVHXB2CG_619_1119_2_0_0_4_0_0_23f/2 +TTTGTTTTGCACTTCCTCTATCTTGTCTAAAGCTTCCTTGGTTTCTTTAATCTCTCTCCTTTGATGCACA +>K03455|HIVHXB2CG_2583_3121_3_0_0_1_0_0_240/2 +ATAAAGCCAGGAAAGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGGATTAG +>K03455|HIVHXB2CG_955_1412_3_0_0_1_0_0_241/2 +GGCTGTCGACAAATACTGGGACAGCTACCACCATCCCTTCAGACAGGATCAGAAGCACTTAGATCATTAT +>K03455|HIVHXB2CG_8040_8476_0_0_0_0_0_0_242/2 +ACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGA +>K03455|HIVHXB2CG_4085_4648_0_0_0_1_0_0_243/2 +CCAAATTCCTGCTTGATTCCCGCCCACCAACATGCGGCCCTAACCGTAGCACCGGTGAAATTGCTGCCAT +>K03455|HIVHXB2CG_3557_4033_1_0_0_4_0_0_244/2 +ATGTTTACTTCTAATCCCGAATGGTGCAACGCTAGATAAATTGGTTGTAACTCAGTCTTCTGATTTGTTG +>K03455|HIVHXB2CG_5404_5976_2_0_0_3_0_0_245/2 +AAGGCCTTATAAGGACACATAGTTAGCCCTAGGAGTGAATATCAAGCAGGACATAACAAGGTAGGATCTC +>K03455|HIVHXB2CG_3053_3501_1_0_0_1_0_0_246/2 +AGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGTATGATTTGTATGTAGGATCT +>K03455|HIVHXB2CG_2324_2780_3_0_0_0_0_0_247/2 +AGATACAGGATCATATGATACAGTATTAGAAGACATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATA +>K03455|HIVHXB2CG_8339_8879_4_0_0_2_0_0_248/2 +TCTTCTGCTGGCTCAGCTCGTCTCATTCTTTCCCTTACAGTAGGCCATCCACTCACACTACTTTTTGACC +>K03455|HIVHXB2CG_6559_7136_2_0_0_2_0_0_249/2 +GGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCGCACTCTGTGTTAGTTTAAAGTGCACTGCTTTGAA +>K03455|HIVHXB2CG_1902_2465_2_0_0_1_0_0_24a/2 +AGCTTTCTGTCCACAGATTTCTATGAGTATCTGATCATACTGTCTTACTTTGATAAAACCTCCAATTCCC +>K03455|HIVHXB2CG_8722_9206_2_0_0_5_0_0_24b/2 +AGTGGATATCTGAGCCCTGGCCGTGGTGTGTAGTTCTGCTAATGAGTGAAGTAGCCTTGTGTGAGGTAGA +>K03455|HIVHXB2CG_6036_6521_3_0_0_2_0_0_24c/2 +TATCCAAGCAGAAAGTAGTACATGTAACGCAACCAATACCAATAGTAGCAATAGTAGCATTAGTAGTAGC +>K03455|HIVHXB2CG_2167_2753_0_0_0_0_0_0_24d/2 +GAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAAC +>K03455|HIVHXB2CG_2981_3447_1_0_0_1_0_0_24e/2 +CTGCTTCTTCTGTTAGTGGAATTACTTCTGTTAGTGCTTTGGTTCCTCTAAGGAGTTTACATAATTGCCT +>K03455|HIVHXB2CG_1424_1880_1_0_0_1_0_0_24f/2 +GCCAAAACTCTTGCCTTATGGCCGGGTCCTCCTACTCCCTGAGATGCTGTCATCATTTCTTCTAGTGTAG +>K03455|HIVHXB2CG_2750_3245_0_0_0_0_1_0_250/2 +ATAACCCATCCAAAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCCAC +>K03455|HIVHXB2CG_4975_5506_3_0_0_1_0_0_251/2 +GTGTTATTAATGCTGCTAGTGCCAAGTATTGTAGAGATCCTACCTTGTTATGTCCTTCTTGATATTCACA +>K03455|HIVHXB2CG_955_1410_1_0_0_2_0_0_252/2 +GGCTGTAGACAAATACTGTGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTAT +>K03455|HIVHXB2CG_1363_1789_3_0_0_2_0_0_253/2 +AAATAGTCTTACAATCTGGTTTCGCATTTTGGACCAACAAGGTTTCTGTCATCCACTTTTTTACCTCCTG +>K03455|HIVHXB2CG_1065_1433_0_0_0_1_0_0_254/2 +ACTCTATCCCATTCTGCCGCTTCCTCATTGATGGTCTCTTTTAACATTTGCATGGCTGCTTGATGTCCCC +>K03455|HIVHXB2CG_1546_2079_1_0_0_1_0_0_255/2 +CTGTCTCTGAGTACAATCTTTCATTTGGTGTCCTTCCTTTCCACATTTCCAACAGCCCTTTTTCCTAGGG +>K03455|HIVHXB2CG_3293_3802_0_0_0_0_0_0_256/2 +AAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTAC +>K03455|HIVHXB2CG_8355_8894_2_0_0_2_0_0_257/2 +GCTGCTCCCACCCTATCTGCTTCTGGCTCAGCTCGACTCATTCTTTCCCTTACAGTAGGCCATCCAATCA +>K03455|HIVHXB2CG_1264_1714_1_0_0_2_0_0_258/2 +CTTGCTGGGCTCTTAGAGTTTTATAGAACCGGTCTCCATAGTCTCTAAAGGGTTCCTTTGGTCCTTGTCT +>K03455|HIVHXB2CG_6639_7088_2_0_0_1_0_0_259/2 +CAGCTGTACTATTATGGTTTTAGGATTGTCCGTGAAATTGACAGATCTAATTACTACCTCTTCTTCTGCT +>K03455|HIVHXB2CG_9072_9598_2_0_0_2_0_0_25a/2 +TGGGTTCCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGACTAACCAGAGAGACCGAGTACAGGCA +>K03455|HIVHXB2CG_6303_6921_0_0_0_0_0_0_25b/2 +ATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCA +>K03455|HIVHXB2CG_4346_4810_0_0_0_1_0_0_25c/2 +TACCCCCCAATCCCCCCTTTTCTTTTAAAATTGTGGATGAATACTGCCATTTGTACAGCTGTCTTAAGAT +>K03455|HIVHXB2CG_6622_7072_2_0_0_2_0_0_25d/2 +ATTTGAAGAATGAAACTAATACCAATAGTAGTAGCGTGAGAATGATAATGGAGAAAGGAGAGATAAAAAA +>K03455|HIVHXB2CG_2690_3183_1_0_0_0_1_0_25e/2 +ACCTCCACAGATGTTGTCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTAC +>K03455|HIVHXB2CG_1995_2516_0_0_0_1_0_0_25f/2 +ATTTCTTCCAATTAAGTTGACAGGTGTAGGTCCTACTAATACTGTACCTATAGCTTTATGTCCACAGATT +>K03455|HIVHXB2CG_1631_2095_1_0_0_4_0_0_260/2 +TCCCTAAAACATTCGCCTGTCTCTCAGTACAATCTTTCATTTGGAGTCCTTCCATTCCACATTTCCAACA +>K03455|HIVHXB2CG_7374_7848_0_0_0_1_0_1_261/2 +TACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATA +>K03455|HIVHXB2CG_1928_2330_1_0_0_1_0_0_262/2 +GAGTCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAG +>K03455|HIVHXB2CG_1853_2422_1_0_0_1_0_0_263/2 +GACCCGGCGATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGAT +>K03455|HIVHXB2CG_1895_2394_0_0_0_2_0_0_264/2 +CTATCATTTTTGGTTTCCATCTTCCTGGCAAACTCATTTCTTCTAATACTGTATGATCTGCTCCTTTATC +>K03455|HIVHXB2CG_664_1204_3_0_0_4_0_0_265/2 +GGATGTTCTGCACTATAGGTTAATTTTGTCTGACCTTATTTCTGTGTCCTGTGTCAGCTGCTGCTTGCTG +>K03455|HIVHXB2CG_7520_8033_2_0_0_3_0_0_266/2 +AGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATCTTACAGGGCTGCTATTACCA +>K03455|HIVHXB2CG_3542_3941_4_0_0_3_0_0_267/2 +GCAGGGGCAAGTCCAATGGACATATCAACTTTATCCAGAGCCATTTAAAAATCTGAAAACAGGACAATAT +>K03455|HIVHXB2CG_5944_6489_2_0_0_0_0_0_268/2 +CATAACAAAAGCCTTATGCATCTGCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAAC +>K03455|HIVHXB2CG_6448_6923_3_0_0_0_0_0_269/2 +TACCCACAGACCCCAACCCAGAAGAATTAGTATTGGTAAATGTGACAGAAAATTTAAACATGTGGAAAAA +>K03455|HIVHXB2CG_8381_8932_0_0_0_1_0_0_26a/2 +TACTTGTGATTGCTCCATGTTTTTCCAGGTCTCGAGATGCTGGTCCCACCCTATCTGCTGCTGGCTCAGC +>K03455|HIVHXB2CG_6904_7402_1_0_0_1_0_0_26b/2 +AATGTAATAATAAGACGTTCAATGGAACAGGAGCATGTACAAATGTCAGCACAGTACAATGTACACATGG +>K03455|HIVHXB2CG_1434_1973_3_0_0_0_0_0_26c/2 +GCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGCGAAGGAAGGGGAAGTGACATAGCAGGA +>K03455|HIVHXB2CG_7574_8148_0_1_0_1_0_0_26d/2 +TTAAGCTTGTTTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATTCCAAATCTGTTCCAG +>K03455|HIVHXB2CG_374_844_1_0_0_2_0_0_26e/2 +AGGGAGGGGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTT +>K03455|HIVHXB2CG_6893_7382_2_0_0_2_0_0_26f/2 +ATTACAGTAGAAAAATTCCCCTCCACAATTACAACTGTGCGTTACAATTTCTGGGTCCCCACCTGAGGAT +>K03455|HIVHXB2CG_4862_5316_2_0_0_1_0_0_270/2 +CTTTTTCCTCCATTCTATGGAGACTCCCTGACCCAAATGCCAGTCTCTTTCTCCTGTATGCCGACCCCAA +>K03455|HIVHXB2CG_6028_6490_2_0_0_2_0_0_271/2 +ACATTTACCAATAGTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTGTGGCCGAAACATTAT +>K03455|HIVHXB2CG_386_819_2_0_0_3_0_0_272/2 +CCTGGGCGGGCCTGGGGCGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGG +>K03455|HIVHXB2CG_5250_5792_3_0_0_0_0_0_273/2 +TGTCGACACCCAATTCTGAAAATGGATAAACAGCAGTTGTTGCAGAATTCTTATTATGGCTTCCACTCCT +>K03455|HIVHXB2CG_182_687_3_0_0_1_0_0_274/2 +GAGAGAGCTCCTCTGGTTTCCCTTTCGCTTTCAGGTGCCTGTTCGGGCGCCACTGCTAGAGATTTTCCAC +>K03455|HIVHXB2CG_1102_1559_1_0_0_0_0_0_275/2 +GAGGAAGAGCAAAACAAAAGTAAGAACAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGG +>K03455|HIVHXB2CG_3370_3805_2_0_0_1_0_0_276/2 +GTATTAACAAACTCCCAGTCAGGAATCCAGGTGGCTTGCCAATACTCTGTCCACCATGTTTCCCATGTTT +>K03455|HIVHXB2CG_790_1283_3_0_0_1_0_0_277/2 +CTGAAAGCCTTCTCTTCTACTACTTTTAGCCATGCATTTAAAGTTCTAGGTGATATGGCCTGATGTACCA +>K03455|HIVHXB2CG_3551_4063_2_0_0_2_0_0_278/2 +ATTCCTAATGCATATTGTGAGTCTGTTACTATGTTTACTTCAAATCCCGAATCCTGCAAAGCTATATAAA +>K03455|HIVHXB2CG_4273_4805_2_0_0_1_1_0_279/2 +ATCACAGTAATTGGATAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTATCAAAAGAAATAGTAGC +>K03455|HIVHXB2CG_6525_6995_3_0_0_3_0_0_27a/2 +GTAGAACAGATGCAAGAGGATCTAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTCACCC +>K03455|HIVHXB2CG_3526_3864_1_0_0_2_0_0_27b/2 +TAGCAGAAATACAGAAGCAGGGGCAATGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCT +>K03455|HIVHXB2CG_5468_5973_3_0_0_3_0_0_27c/2 +CCATAGGAGATGCCTAAGGCTTTTGTTATGAAACAAACTTGGCAATGACAGCAAGACATTTTACAATAGC +>K03455|HIVHXB2CG_3648_4180_4_0_0_2_0_0_27d/2 +CCTCCAATACCTTTGTGTGCTGGTACCCATGCCCGATAGACCTTTTCCTTTTTTATTAACTGCTCTATTA +>K03455|HIVHXB2CG_2566_3131_2_0_0_1_0_0_27e/2 +TTCTAAGTCAGATCCTCCATACAAATCATCCATGTATTGATAGATAACTATGTCTGGATTTTGTTTTCTA +>K03455|HIVHXB2CG_7605_7990_1_0_0_1_0_0_27f/2 +AGCAACAATGAGTCCGATATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTAT +>K03455|HIVHXB2CG_5456_6001_2_0_0_3_0_0_280/2 +TCTTGGTCGGTGTCTCCGCTTCTTCCTGCCATAGGAGATGCCTCAGGCTTTTGTTATGAAACAAACTTGG +>K03455|HIVHXB2CG_5995_6558_2_0_0_0_0_0_281/2 +ACGAAGAGCTCCTGAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACG +>K03455|HIVHXB2CG_4119_4651_1_0_0_2_0_0_282/2 +ATTCCAAATTCCTGCTTGATTCCCGCCGACCAACAGGCGGCCCTAACCGTAGCACCGGTGAAATTGCAGC +>K03455|HIVHXB2CG_1700_2109_1_0_0_1_0_0_283/2 +GGAAGGCCAGATCTTCCCTAAAAAATTAGCCTGTCTCTCAGTACAATCTTTGATTTGGTGTCCTTCCTTT +>K03455|HIVHXB2CG_8600_9168_1_0_1_0_0_0_284/2 +CTAATCAGGGAAGTAGCCTTGTGTGTGGTAGATCCACAGATCAAGGATATCTTGTCTTCTTTGGGAGTGA +>K03455|HIVHXB2CG_8525_8934_2_0_0_1_0_0_285/2 +CTACCACCGCTTGAGAGACTTACTCTTGATTGTACCGAGGATTGTGGAACTTCTGGGACTCAGGGGGTGG +>K03455|HIVHXB2CG_2918_3339_0_0_0_2_0_0_286/2 +CTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTAC +>K03455|HIVHXB2CG_6749_7307_0_1_0_1_0_0_287/2 +TTTTTATAAACTTGATATAATAACAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACC +>K03455|HIVHXB2CG_7328_7813_2_0_1_0_0_0_288/2 +CCCAGAAATTGTAACCACAGTTTTAATTGTGGATGGGAATTTTTCTACTGTAATACAACACAACTGTTTA +>K03455|HIVHXB2CG_5175_5715_0_0_0_1_0_0_289/2 +TATCCCCATAAGTTTCATAGCTATGTTGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTAACAGC +>K03455|HIVHXB2CG_7993_8437_0_0_0_2_0_0_28a/2 +CCACCTTCTTCTTCTATTCCTTCGGGGCTGTCGGGTCCCCTCGGGGTTGGGAGGTGGGTCTGACACGATA +>K03455|HIVHXB2CG_5047_5562_1_0_0_1_0_0_28b/2 +AACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATAAGAACATGGAAAAGTTTAGTAA +>K03455|HIVHXB2CG_8470_8969_1_1_0_0_0_0_28c/2 +TGAACGGATCCTTGTCACTTATCTGGGACGATCTTCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAG +>K03455|HIVHXB2CG_7312_7900_1_0_0_4_0_0_28d/2 +AATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATAGTGGAGGGGAATTTTTCTACTGTAA +>K03455|HIVHXB2CG_8031_8469_1_0_0_2_0_0_28e/2 +CTACTCGAATGGATCTGTCTCTGTCTCTCTCTCCACCTTCATCTTCTATTCCTTCGGGCCTGTCGGGTCC +>K03455|HIVHXB2CG_1463_1846_1_0_0_2_0_0_28f/2 +CTCCCTGACATGCTGTCATCATTTCTTCTAGTGTAGCGGCTGGTCCCAATGCTTTTACAATAGTCTTACA +>K03455|HIVHXB2CG_4205_4690_3_0_0_2_0_0_290/2 +CAGTGCTGGAATCAGGAAAGTAGTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGCAATAA +>K03455|HIVHXB2CG_8439_8937_1_0_0_0_0_0_291/2 +GAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGGACTTATCTGGGACGATCTGCGGA +>K03455|HIVHXB2CG_9079_9590_2_0_0_0_0_0_292/2 +CTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACCCAGTACAGGCAAAAAGCAG +>K03455|HIVHXB2CG_1377_1909_0_0_0_1_0_0_293/2 +AGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCAT +>K03455|HIVHXB2CG_9069_9505_0_0_0_0_0_0_294/2 +ATCTGAGGGCTCGCCACTCCCCAGTCCCGCCCAGGCCACGCCTCCCTGGAAAGTCCCCAGCGGAAAGTCC +>K03455|HIVHXB2CG_661_1118_1_0_0_1_0_0_295/2 +GGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGA +>K03455|HIVHXB2CG_2045_2564_2_0_0_2_0_0_296/2 +AATATGGCTAATGGGAAAATTTAAAGTGCAACCAAACTGAGTCAACAGATTTCTTCCAATTATGTTGACA +>K03455|HIVHXB2CG_7981_8474_4_0_0_2_0_0_297/2 +ACCTCAAGGATCAACAGCTCCTGTGGATTTGGTGTTGCTCTGGAAAACTCATTTGCACCACTGGTGTGCC +>K03455|HIVHXB2CG_6341_6881_0_0_0_2_0_0_298/2 +GGCACAATAATTTATGGGAATTGGCTCAAAGGATACCTTTGGACAGGCCTGTGTAATGACTTAGGTGTTA +>K03455|HIVHXB2CG_3619_4121_0_0_0_0_0_0_299/2 +TGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCAT +>K03455|HIVHXB2CG_6357_6846_1_0_0_0_0_0_29a/2 +CCTTTGGACAGGCCTGTGTAATGACTGAGGTGTTACAACTTGTCAACTTATAGCTGGTAGTATCATTATC +>K03455|HIVHXB2CG_382_894_0_0_0_2_0_0_29b/2 +TACTATATGTTTTAATATATATTTTTTCTTTCCCCCTGGCCTTAACCGAATTTATTCCCATCGATCTAAT +>K03455|HIVHXB2CG_1850_2381_1_0_0_4_0_0_29c/2 +GAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCACGTAACAAATTCAGCTACCATAAT +>K03455|HIVHXB2CG_598_1171_2_0_0_1_0_0_29d/2 +CTCAGAGCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCGCGAACAGGGACCTGAAAGCGAAAGG +>K03455|HIVHXB2CG_2243_2739_2_0_0_2_0_0_29e/2 +CTTTAACTTCCCTCAGGTCACTCTTTGGCAACTACCCCTCGTCACAATAAAGATAGGGGGGCAAGTAAAG +>K03455|HIVHXB2CG_4657_5203_1_0_0_1_0_0_29f/2 +CTTCTGAACTTATACTTGGATGAGGGCTTTCATAGTGATGTCTATAAAACCATCCCCTAGCTTTCCCTGA +>K03455|HIVHXB2CG_2785_3324_2_0_0_1_0_0_2a0/2 +TCTGTATGTCATTGACAGTCCAGCTGTCTTTTTCTGGCAGCCCTATAGGCTGTACTGTCCATTTATCAGG +>K03455|HIVHXB2CG_2631_3207_2_0_0_3_1_0_2a1/2 +TTTTGTCTTGTGTGGTAAGTCCCCACCTCCACAGATGTTGTGTCAGCTCCTCTATTTTAGTTCTATGCTG +>K03455|HIVHXB2CG_4204_4787_2_0_0_0_1_0_2a2/2 +TTTAAGATTGTGGATGAATACTGCCATTTGTACTGCTGTCTTAAGATGTTCAGCCTGATCTCTTACCTGT +>K03455|HIVHXB2CG_594_1110_0_0_0_1_0_0_2a3/2 +ATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGA +>K03455|HIVHXB2CG_8035_8568_4_0_0_1_1_0_2a4/2 +CAATCCTCGTTACAATCAAGAGTAAGTCTGTCAAGCGGTGGTAGCTGAAGAGGCACAGGCTCCGAAGATC +>K03455|HIVHXB2CG_3674_4152_1_0_0_0_0_0_2a5/2 +AACGACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGG +>K03455|HIVHXB2CG_4712_5257_0_0_0_2_0_0_2a6/2 +GCAGACCCCAATATGTTGTTATTACCCATGTAGCATCCCCTAGTGGGATGTGTACTTCTGAACTTATTCT +>K03455|HIVHXB2CG_6896_7341_2_0_0_2_0_0_2a7/2 +GATTCTAAAATGTAATAATAAGCCGTTCAATGGAACAGGACCATGTACAAATGTCAGGACAGTACAATGT +>K03455|HIVHXB2CG_7773_8226_0_0_1_3_0_0_2a8/2 +TTGCCCATTAATCTAAATCCAATAATTCTAGTTCATTCTTTTCTTGCTGGTTTTGCGATTCTTCAATTAA +>K03455|HIVHXB2CG_3204_3701_0_0_0_0_0_0_2a9/2 +AAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTAC +>K03455|HIVHXB2CG_3980_4427_2_0_0_1_0_0_2aa/2 +TGAGTTACAAGCAAATTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACACACAA +>K03455|HIVHXB2CG_3617_4228_0_0_0_1_0_0_2ab/2 +AGTACTTTCCTGATTCCAGGACTGACTAATTTATCTACTTGTTCATTTCCTCCAATTCCTTTGTGTGCTG +>K03455|HIVHXB2CG_6947_7480_3_0_0_0_0_0_2ac/2 +TGTCAGCACAGTACAATGTACAGATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATTGGAGT +>K03455|HIVHXB2CG_3539_3993_2_0_0_3_0_0_2ad/2 +GAAGCAGGGGCAAGGCCAATGGACATCTCAAATTTATCAAGAGCCATTTAAAAATCTGAACACAGGAAAA +>K03455|HIVHXB2CG_8034_8559_0_0_0_2_0_0_2ae/2 +TGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGA +>K03455|HIVHXB2CG_9000_9430_0_0_0_1_0_0_2af/2 +AGCAAGCTCGATGTCAGCAGTTCTTGAAGTACTCCGGATGCAGCTCTCTGGCCACGTGATGAAATGCTAG +>K03455|HIVHXB2CG_3903_4446_1_0_0_0_0_0_2b0/2 +TAACTTTTCCTTCTAAATGTGTACAATCTAGTTGCCATATTCCTGGACTACAGTCTACTTGTCCATGCAT +>K03455|HIVHXB2CG_338_720_0_0_0_1_0_0_2b1/2 +AGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGG +>K03455|HIVHXB2CG_5180_5698_3_0_0_1_0_0_2b2/2 +TAGATATGTTGCCCTAAGCCATGGAGCCAAATCCTAGGAAAATGTCTAACAGCTTGATTCTTAAGCTCCT +>K03455|HIVHXB2CG_1621_2150_3_0_0_0_0_0_2b3/2 +AGCCCTACCAGCATTCTGGACATAAGACAAGGAGCAAAGGAACCCTTTAGAGACTCTGTATACCGGTTCT +>K03455|HIVHXB2CG_1592_2200_0_0_0_1_0_0_2b4/2 +TTGTTGTCTCTACCCCAGACCTGAAGCTCTCTTCTGGTGGGGCTGTTGGCTCTGGTCTGCTCTGAAGACA +>K03455|HIVHXB2CG_1010_1471_1_0_0_2_0_0_2b5/2 +AACTTAGATCATTATATAATACAGTCGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACAC +>K03455|HIVHXB2CG_6467_6940_6_0_0_2_0_0_2b6/2 +CATGTTCCTGTTCCATTGAACGTCTTATTATTACATTTTAGAAACGCAAAACCAGCCGGGGCACAATAAT +>K03455|HIVHXB2CG_1019_1576_0_0_0_0_0_0_2b7/2 +CATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGC +>K03455|HIVHXB2CG_6081_6452_0_0_0_5_0_0_2b8/2 +GGGTACACAGGCATGTTTGGCGCAAACATTATGTACCTCTGTATCATATTCTTTAGCATGTGATGCCCAA +>K03455|HIVHXB2CG_319_791_0_0_0_0_0_0_2b9/2 +TCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCT +>K03455|HIVHXB2CG_7794_8338_1_0_1_2_0_0_2ba/2 +ACTATAGAAAGTCCAGCAAAAACTATTCTTAAACCTACCAAGCCTCCTACTAACATTATGAATAATTTTA +>K03455|HIVHXB2CG_238_718_2_0_0_4_0_0_2bb/2 +GTGCGCGCATCAGCAAGCCGAGTCCTGCTTCTAGAGAGCTCCTCTGGTTTCCCTTTCGCTTTCAGGTCGC +>K03455|HIVHXB2CG_4639_5202_0_0_0_1_0_0_2bc/2 +TTCTGAACTTATTCTTGGATGAGTGCTTTCATAGTGATGTCTATAAAACCATCCCCTAGCTTTCCCTGAA +>K03455|HIVHXB2CG_1116_1545_2_0_0_4_0_0_2bd/2 +CAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGTACACAGCAAACAGGTCAGCCAAAATTAC +>K03455|HIVHXB2CG_4071_4585_1_0_0_2_0_0_2be/2 +CTGCCATTGTCAGTATGTATTGTTTTTAGTGGCCATCTTCCTGCAAATTTTAAAAGAAAATATGCTGTTT +>K03455|HIVHXB2CG_20_496_1_0_0_1_0_0_2bf/2 +CAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACCCAGTACAGGCAAAAAGCAGCTGCTTAAA +>K03455|HIVHXB2CG_1379_1829_2_0_0_4_0_0_2c0/2 +CCATGCACATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGC +>K03455|HIVHXB2CG_4317_4787_2_0_0_2_1_0_2c1/2 +CCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATCCATGTCAGCTAAAAGGAGAAGCCATGCATGGAC +>K03455|HIVHXB2CG_4707_5311_3_0_0_3_0_0_2c2/2 +CAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACCTCAGTACAAATGGCAGTATTCATCC +>K03455|HIVHXB2CG_2978_3440_3_0_0_2_0_0_2c3/2 +ATATCAGTAGAATGTGCTTCCACAGGGATGGAAAGGATCAGCAGCAATATTCCACAGTAGCATGACAAAA +>K03455|HIVHXB2CG_1202_1696_1_0_0_0_0_0_2c4/2 +TCCAGGGGCAAATGGTACATCAGGCCATATCACCTATAACTTTAAATGCATGGGTAAAAGTAGTAGAAGA +>K03455|HIVHXB2CG_577_1039_1_0_0_1_0_0_2c5/2 +TTGCTACTGTATTATATAATGATGTAAGTTCTTCTGATCCTGTCTGAAGGGATGGTTGTAGCTGTCCCAG +>K03455|HIVHXB2CG_2831_3307_0_0_0_2_0_0_2c6/2 +GTCCAGCTGTCTTTTTCTGGCAGCACTATAGGCTGTACTGTCCATTTATCAGGCTGGAGTACATAACCCA +>K03455|HIVHXB2CG_3348_3833_1_0_0_1_0_0_2c7/2 +GCAAGTCAGATTTACCGAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAA +>K03455|HIVHXB2CG_3534_4089_3_0_0_1_0_0_2c8/2 +CACTTTGATCTGGTTGTGCTTGAATGATTCCTAATGCATATTGTGAGTCTGTTACTATTTTTACTTCTAA +>K03455|HIVHXB2CG_5769_6244_1_0_0_1_0_0_2c9/2 +TATTTCTCCTTCAGTCTCATTGCCACTGTCTTCTGCTCTTTCTATTAGTCTATCAATTAACCTGTCTATT +>K03455|HIVHXB2CG_3385_3934_0_0_0_4_0_0_2ca/2 +CCTCTATTAGTAACATATCCTTCTTTTCCTAATTTAGTCTCGCTGTTAGCTGCCCCATCTACATATACGG +>K03455|HIVHXB2CG_2455_2974_0_0_0_2_0_0_2cb/2 +CTCCCTGGTGTCTCATTGTTTAAACTAGGTATGGTAAATGCAGTATACTTCCTGAAGTCTTCATCTAAGG +>K03455|HIVHXB2CG_2733_3196_1_0_0_1_1_0_2cc/2 +GTGGTAAGTCCCCACCTCCACAGATGTTGTCTCAGCTCCTCTATTTTTGTTCAATGCTGCCCTATTTCTA +>K03455|HIVHXB2CG_2948_3516_5_0_0_0_0_0_2cd/2 +TTGATGGGTCATAATACACTCCATGTACTGGTTCTTTTAGAATCTCTCTGTTTTCTGCCAGTTCTAGCTC +>K03455|HIVHXB2CG_3037_3421_0_0_0_2_0_0_2ce/2 +GCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGA +>K03455|HIVHXB2CG_8103_8621_0_0_0_3_0_0_2cf/2 +ACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGC +>K03455|HIVHXB2CG_720_1201_0_0_0_0_0_0_2d0/2 +GCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAG +>K03455|HIVHXB2CG_766_1258_0_0_0_0_0_0_2d1/2 +CTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGAT +>K03455|HIVHXB2CG_9183_9675_1_0_0_4_0_0_2d2/2 +AGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCGAGATAAG +>K03455|HIVHXB2CG_1052_1583_0_0_0_1_0_0_2d3/2 +CATCTTTTATAAATTTCTCCTACTGGGATAGGTGGATTATTTGTCATCCATGCTATTTGTTCCTGAAGGG +>K03455|HIVHXB2CG_6690_7216_2_0_0_2_1_0_2d4/2 +GAATGTGCTTGTCTCATATTTCCTATTTTTCCAATTGTAACAAATGCTCTCCCTGGTCCTCTCGGGATAC +>K03455|HIVHXB2CG_3877_4404_0_0_0_2_0_0_2d5/2 +ATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGT +>K03455|HIVHXB2CG_3525_3980_5_0_0_2_0_0_2d6/2 +AGTCATCTGATTTGTTGTGTCAGTTAGGGTGACACCTTTTTGTCTTCCTCTATTAGTAACATATCCTGCT +>K03455|HIVHXB2CG_3070_3499_2_0_0_2_0_0_2d7/2 +AAAATCCAGAGATAGTTATCTATCAATACATGGATGATTTGTATGAAGGATCTGACTTAGAAATAGGGCA +>K03455|HIVHXB2CG_8197_8697_2_0_0_1_0_1_2d8/2 +AAGCATTATTGGAATTAGATAAATGGTCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTA +>K03455|HIVHXB2CG_25_502_3_0_0_2_0_0_2d9/2 +GAAGACACGATATCCTTGCTCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTAGAC +>K03455|HIVHXB2CG_6978_7494_0_0_0_2_0_0_2da/2 +TAATTTGTTTTATTCTGCATGGTAGGGTGATTGTGTCACTTCCTTCAGTGTTATTTGACCCTTGAGTACT +>K03455|HIVHXB2CG_4068_4550_3_0_0_1_0_0_2db/2 +TCTTCCTGCTAATTTTAAAAGAAAATATGCTGTTTCCAGCCCTGTTTCTGCTGGAATAACTTCTGCTTCT +>K03455|HIVHXB2CG_6065_6563_2_0_0_1_0_0_2dc/2 +ATCCCATAAACTGATTATCTCCTCATGCATCTGTTCTACCATGTCATTTTTCCACATGTTAAAATTTTCT +>K03455|HIVHXB2CG_2282_2751_1_0_0_0_0_0_2dd/2 +CGTCACAATAAAGATAGGGGGGCAACTAAAGTAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTA +>K03455|HIVHXB2CG_3883_4319_2_0_0_2_0_0_2de/2 +CAGCTAACAGGGAGAGTAAATTAGTAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCAC +>K03455|HIVHXB2CG_8898_9381_1_0_0_1_0_0_2df/2 +TCGAGACCTGGAAAAACATGGAGCCATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGG +>K03455|HIVHXB2CG_6495_6982_3_0_0_0_0_0_2e0/2 +GAAAATTTTACCATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTAATGGGAAC +>K03455|HIVHXB2CG_4627_5094_3_0_0_0_0_0_2e1/2 +CGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCGCCAAAGTCAAGGAGTAGTAGAATCTCTGAATAC +>K03455|HIVHXB2CG_7584_8117_1_1_0_4_0_0_2e2/2 +TTAACAAAAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACGTGGAGGAGGAGATATGAGGG +>K03455|HIVHXB2CG_3778_4298_2_0_0_0_0_0_2e3/2 +GGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTATTGAAATTATGGTCCCAGTTAGAGAAAGAACC +>K03455|HIVHXB2CG_8900_9429_0_0_0_2_0_0_2e4/2 +GAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCT +>K03455|HIVHXB2CG_2577_3046_1_0_0_1_0_0_2e5/2 +TTTGTCATGCTACTTTGGAATATTGCTGGTGATCCTTTCCATCCCTTTGGAAGCACATTGTACTGATATC +>K03455|HIVHXB2CG_6023_6519_3_0_0_3_0_0_2e6/2 +CATCAAGCTTCTCTATCAAAGCAGTACGTAGTACATGAAACGCAACCTCTACCAATAGTAGCAATAGTAG +>K03455|HIVHXB2CG_7870_8384_1_0_0_2_0_0_2e7/2 +GTTGGTCTGAAACGATAATGGTGAATATCCCTGCGTAACTCTATTCACTATAGAAAGTACAGCAAAAACT +>K03455|HIVHXB2CG_8258_8759_1_0_0_1_0_0_2e8/2 +GCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTACGAATAGTTTTTGCTGTA +>K03455|HIVHXB2CG_384_800_1_0_0_0_0_0_2e9/2 +GGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTGAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACT +>K03455|HIVHXB2CG_208_663_0_1_0_1_0_0_2ea/2 +ACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCACCT +>K03455|HIVHXB2CG_8385_8881_0_0_0_0_0_0_2eb/2 +TATCTGCTGCTGGCTCAGCTCGTCTCATTCTTTCCCTTACAGTAGGCCATCCAATCACACTACTTTTTGA +>K03455|HIVHXB2CG_7585_8210_2_1_0_2_0_0_2ec/2 +TAAGAAAAGATGGTGGAAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGA +>K03455|HIVHXB2CG_1726_2220_2_0_0_1_0_0_2ed/2 +GTAAAAAATTGGATGACAGAAACCATGTTGGTCCAAAATGCGAACCCAGATTGTAAGCCTATTTTAAAAG +>K03455|HIVHXB2CG_9159_9636_1_0_0_1_0_0_2ee/2 +TGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTTGGTTCCCTAGTTAGCCAGAGAGCTCCCAGG +>K03455|HIVHXB2CG_322_837_1_0_0_2_0_0_2ef/2 +CCATCTATCTAATTCTCCCCCGCTTAATACTGACGCTCTCGCACCCATCTCTCTCCTTCTATCCTCCGCT +>K03455|HIVHXB2CG_651_1155_1_0_0_0_0_0_2f0/2 +GACCTGAAAGCGAAAGGGACACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGG +>K03455|HIVHXB2CG_2967_3460_4_0_0_0_0_0_2f1/2 +CGAGGGATTAGATCTCAGTACAATGTGCTTCCACAGGGATGGAAAGTATCACCAGCAATATTCCAAATTA +>K03455|HIVHXB2CG_7416_7883_2_0_0_0_0_1_2f2/2 +GTTCTGCTGCTGCACTATACCAGACAATAATTGTCTGGCCTGTACCGTCAGCGTCAATTGAGGCTGCGCC +>K03455|HIVHXB2CG_8328_8858_0_0_0_3_0_0_2f3/2 +CTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGA +>K03455|HIVHXB2CG_8980_9481_1_0_0_3_0_0_2f4/2 +TCCCGCGCAGGCCCCGCCTCCCTGGAAAGTCCCCAGCGGAAAGTCCCTTGTCGCAAGCTCGATGTCAGCA +>K03455|HIVHXB2CG_3917_4431_1_0_0_2_0_0_2f5/2 +AATGTGTACAATCTAGTTGCCATCTTCCTGGACTACAGTCTACTTGTGCATGCATGGCTTCTCCTTTTAG +>K03455|HIVHXB2CG_4877_5329_1_0_0_4_0_0_2f6/2 +AATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGCAATCCACTTTGGAAAGGACCAGCA +>K03455|HIVHXB2CG_745_1273_1_0_0_3_0_0_2f7/2 +TCTCTTCTACTACTTTTACCCATTCATTTAAAGTTCTAGGTGATATGTCGTGATGTACCATTTGCCCCTG +>K03455|HIVHXB2CG_1627_2100_1_0_0_4_0_0_2f8/2 +ACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTATAGACTATGTAGACCGGTTCTATAAAA +>K03455|HIVHXB2CG_8595_9003_1_0_1_2_0_0_2f9/2 +TGGAAAACCCACCTGCTCCTCCTCTTGTGCTTCTAGCCAGGCACAAGCAGCATTGGTAGCTTCTGTATTG +>K03455|HIVHXB2CG_7806_8277_0_0_1_1_0_0_2fa/2 +ATAATTTTATATACCACATCCAATTTGTTATGTTAAACCAATTCCACAAACTTGCCCATTTATCTAATTC +>K03455|HIVHXB2CG_2838_3355_0_0_0_1_0_0_2fb/2 +TGACTTGCCCAATTCAATTTCCCCACTAACTTCTGTATGTCATTGAGAGTCCAGCTGTCTTTTTCTGGCA +>K03455|HIVHXB2CG_105_629_0_0_0_1_0_0_2fc/2 +GGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAG +>K03455|HIVHXB2CG_1400_1860_1_0_0_2_0_0_2fd/2 +CCATCAATGAGTAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCA +>K03455|HIVHXB2CG_3422_3959_1_0_0_2_0_0_2fe/2 +AGTTATGGTGACAACTTTTTGTCTTCCTCTATTCGTAACATATCCTGCTTTTCCTAATTTAGTCTCCCTG +>K03455|HIVHXB2CG_7624_8163_0_0_0_0_0_0_2ff/2 +CAATTAAGGAGTGTATTAAGCTTGTGTAATTGTTAATTTCTCTGTCCCACTCCATCCAGGTCGTGTGATT +>K03455|HIVHXB2CG_5241_5644_1_0_0_4_0_0_300/2 +TCATTCTTAAGCTCCTCTAACAGCTCTAGTGTCCATTCATTGTTAGGCACCCTCTGTGGCCCTTGGTCTT +>K03455|HIVHXB2CG_774_1282_3_0_0_2_0_0_301/2 +GGCTAGAAGGAGAGAGATGGGTGCGAGATCGTCAGAATTAAGCGGGGGAGAATTAGATCGATGGGAAACA +>K03455|HIVHXB2CG_5379_5864_2_0_0_2_0_0_302/2 +CTGTTTTTCAGCCTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTTAATATCAA +>K03455|HIVHXB2CG_1660_2159_2_0_0_2_0_0_303/2 +GCTGTAGGCTCTGGTGTGCTCTGAAGAAAATTCCCTGGCCTTCCCTTGTAGGAAGGCCAGATCTTCCCTA +>K03455|HIVHXB2CG_7376_7952_0_0_0_3_0_0_304/2 +CTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAAC +>K03455|HIVHXB2CG_6401_6914_2_0_0_2_0_0_305/2 +ATTAATACATTTTAGAATCGCAAAACCAGCCGGTGCACAATAATGTATGGGAATTGGCTCAAAGGATACC +>K03455|HIVHXB2CG_663_1172_1_0_0_0_0_0_306/2 +ACCTGATTGCTGTGTCCTGTGTCAGCTGCTGCTTGCTGTGCTTTTTTCTTACTTTTGTTTTGCTCTTCCT +>K03455|HIVHXB2CG_7623_8142_2_0_0_0_0_0_307/2 +ATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGCAGTGAATTATATAAATATAAATTAGTAA +>K03455|HIVHXB2CG_8624_9098_2_0_0_0_0_0_308/2 +ACCGTAATGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCT +>K03455|HIVHXB2CG_8175_8569_0_0_0_2_0_0_309/2 +ACAATCCTCTTTACAATCAAGAGTAAGTCTCTCAAGCGGTGGTAGCTGAAGAGGCACAGGCTCCGCATAT +>K03455|HIVHXB2CG_3691_4093_2_0_0_1_0_0_30a/2 +TCATATGGGGAAAGACTCCTAAATTTAAACAGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGA +>K03455|HIVHXB2CG_3439_3934_4_0_0_0_0_0_30b/2 +AAGAATCAGATGTAGACCTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGA +>K03455|HIVHXB2CG_4603_5012_3_0_0_1_0_0_30c/2 +CGGTTAGGGCCGGCTGTTGGTGGGCGGGACTCAAGCCGGAATTTGGAATTCCCTACAATCCCCAAAGTCA +>K03455|HIVHXB2CG_648_1222_2_0_0_0_0_0_30d/2 +ATGGACCTGAAAGGGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCA +>K03455|HIVHXB2CG_23_500_2_0_0_3_0_0_30e/2 +TAGCCAGAGAGCTCCCAGGCTGAGATCTTGTCTAAGCAGAGAGACCCAGTACAGGCAAAAAGCAGCTGCT +>K03455|HIVHXB2CG_5509_5907_2_0_0_1_0_0_30f/2 +TAGCAATTGGTACAAGCAGTTTTAGGCTGACTTCCTGGATGCTTCCAGGGCTGTAGTCTAGGATCTACTG +>K03455|HIVHXB2CG_115_623_2_0_0_1_0_0_310/2 +ATCCACTGACCTTTGGATGGTGCTACACGCTAGTACCAGTTGAGCCAGAGAATTTAGAAGAAGCCAACAA +>K03455|HIVHXB2CG_839_1295_1_0_0_1_0_0_311/2 +ATCACTTCTGGGCTGAAAGCCTTCTCTTCTAGTACTTTTACCCATGCATTTAAAGTTCTAGGTGATATGG +>K03455|HIVHXB2CG_3232_3737_2_0_0_1_0_0_312/2 +TTCCTTTTTTATGGGCAGTTTAAATTTAGGAGTCTTTCCCCATATTACTATGCTTTCTGTGGTTATTTTT +>K03455|HIVHXB2CG_6960_7485_0_0_0_2_0_0_313/2 +CAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAG +>K03455|HIVHXB2CG_1000_1549_3_0_0_1_0_0_314/2 +GGATCAGAAGAACTTAGATCAATATATAATACAGTAGCACCCCTCTATTGTGTGCATCAAAGGAAAGAGA +>K03455|HIVHXB2CG_9191_9669_3_0_0_0_0_0_315/2 +CCAGAGTCACACAACAGACGGGCACACACTACTTGAAGCACTCAAGGCAAGCTTTATTGAGGCTTAAGCA +>K03455|HIVHXB2CG_6354_6819_0_0_0_1_1_0_316/2 +AGGTGTTACAACTTGTCAACTTATAGCTGGTAGTATCATTATCTATTGTTATTATATCAAGTTTCTAAAA +>K03455|HIVHXB2CG_4710_5249_0_0_0_0_0_0_317/2 +CAATATGTTGTTATTACCAATCTAGCATCCCCTAGTGGGATGTGTACTTCTGAACTTATTCTTGGATGAG +>K03455|HIVHXB2CG_8738_9138_1_0_0_2_0_0_318/2 +AGCTATTCGCCACATACCAAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAA +>K03455|HIVHXB2CG_710_1241_0_0_0_4_0_0_319/2 +GTTCTAGGTGATATGGCCAGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGAAATATTTGCTGA +>K03455|HIVHXB2CG_7924_8475_4_0_0_1_0_0_31a/2 +AACTCACAGTCTGGGGCATCAAGCAGGACCAGGGAAGAATCCTGGCTGTGGAAAGATACCTAACGGATCA +>K03455|HIVHXB2CG_2684_3200_0_0_0_2_1_0_31b/2 +TGGTGTTGTAAGTCCCCAGCTCCACAGATGTTGTCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATT +>K03455|HIVHXB2CG_6249_6784_2_1_0_0_1_0_31c/2 +TCATTATCTATTGTTATTATATCAAGTTTATAAAAAAATGCATATTCTTTCTGCACCTTACCTCTTATGC +>K03455|HIVHXB2CG_8763_9288_0_0_0_1_0_0_31d/2 +ATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGA +>K03455|HIVHXB2CG_3032_3506_1_0_0_1_0_0_31e/2 +ATAATACACTCCATGTACTTGTTCTTTTAGAATCTCTCTGTTTTCTGCCAGTTCTAGCTCTGCTTCTTCT +>K03455|HIVHXB2CG_8063_8526_0_0_0_2_1_0_31f/2 +TTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAAC +>K03455|HIVHXB2CG_1135_1729_3_0_0_2_0_0_320/2 +TTACCTCCTTTGAAGCTTGCTCGGCTCTTAGAGTTTTATCGAACCGGTCTACATAGTCTCTAAAGGGTTC +>K03455|HIVHXB2CG_1777_2339_1_0_0_0_0_0_321/2 +TGTAAGACTATATTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAG +>K03455|HIVHXB2CG_7638_8151_1_0_0_1_0_0_322/2 +GGAGGAGATATGAGGGACAATAGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAG +>K03455|HIVHXB2CG_7693_8283_2_0_0_1_0_0_323/2 +TTATGAATAATTTTATATACCACCGCCAATTTGTTATGTTAAACCAATTCCACAAACTTGCCCATTTATC +>K03455|HIVHXB2CG_3933_4405_0_0_0_1_0_0_324/2 +GGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAG +>K03455|HIVHXB2CG_7631_8099_2_0_0_1_0_0_325/2 +GTGATTGCAAATCTGTTCCAGAGATTTATTACTCCAACTAGCATTCCAAGGCACAGCAGTGGTGCAAATG +>K03455|HIVHXB2CG_8371_8938_1_0_0_2_0_0_326/2 +TATTGCTACTTGTGAATGCTCCATGTATTTCCAGGTCTCGAGATGCTGCTCCCACCCTATCTGCTGCTGG +>K03455|HIVHXB2CG_7125_7622_1_1_0_5_1_0_327/2 +AACAATACAAGAAAAAGAATCCGTATCCCGAGAGGACCAGGGAGATCATTTGTTACAATAGGAAAAATAG +>K03455|HIVHXB2CG_5915_6412_1_0_0_3_0_0_328/2 +AAGTTTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGC +>K03455|HIVHXB2CG_1865_2367_1_0_0_0_0_0_329/2 +GCAAACTCATTTCTTCTAATACTGTATCATCTGCTCCTGTATCTAATAGAGCTTCCTTTAGTTGCCCCCC +>K03455|HIVHXB2CG_5755_6312_1_0_0_0_1_0_32a/2 +AACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGTCGTTACTCGACAGAGGAGAG +>K03455|HIVHXB2CG_9228_9698_1_0_0_1_0_0_32b/2 +GCTAGTACCAGTTGAGCCAGATAAGATAGAAGCGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCT +>K03455|HIVHXB2CG_3991_4524_2_0_0_1_0_0_32c/2 +CAATTAATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTCGG +>K03455|HIVHXB2CG_5672_6162_2_0_0_4_0_0_32d/2 +AATATTATCCTATATTCTCTGATTACTATGGACCACACAACTATTGCTATTATTATTGCTACTCCTAAAG +>K03455|HIVHXB2CG_9188_9692_0_0_0_1_0_0_32e/2 +CAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGA +>K03455|HIVHXB2CG_5238_5722_3_0_0_2_0_0_32f/2 +GCCCACGTATCCCCATAAGTTTCATAGATATGTTGCCCTAAGCCATGGAGCCCAATCCTAGGAAAATGTC +>K03455|HIVHXB2CG_9021_9485_4_0_0_2_0_0_330/2 +CCAGTCCCGCCCAGGCCACGCCTCCCTGGAAAGTCCCCAGCGGAACGTGCCTTGTAGCAAGCTCGATGTC +>K03455|HIVHXB2CG_4567_5019_2_0_0_0_0_0_331/2 +TACATACTGACAATGGCAGCAATTTCCCCGGTGCTACGGTTAGGGCCGCGTGTTGGTGGGCGGGAATCAA +>K03455|HIVHXB2CG_8323_8932_2_0_0_1_0_0_332/2 +GTGTACTTTCTATAGTGAATAGATTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAAC +>K03455|HIVHXB2CG_3021_3611_5_0_0_0_0_0_333/2 +ATATTTTCCTGTTTTCAGATTTTTAAATGGCTCTTGATAAATTTGATATGTCCATTGGCCTTGCCCCTGC +>K03455|HIVHXB2CG_1720_2196_1_0_0_1_0_0_334/2 +TGTCTCTACCCCAGACCTGAAGCTCTCTTCTGGTGGGGCTGTTGGCTCTGGTCTTCTCTGAAGAAAATTC +>K03455|HIVHXB2CG_7380_7893_1_0_0_2_0_1_335/2 +AATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTAGTTGGAGTACTGAAGGGTCAAATAACACTG +>K03455|HIVHXB2CG_8834_9304_3_0_0_0_0_0_336/2 +GGCCTAGTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGGAGATAGGGTGGGAGCAGCATCTCGAGC +>K03455|HIVHXB2CG_388_927_0_0_0_1_0_0_337/2 +AACTGCGAATCGTTCTAGCTCCCTGCTTGCCCATACTATATGTTTTAATTTATATTTTTACTTTCCCCCT +>K03455|HIVHXB2CG_9213_9708_2_0_0_1_0_0_338/2 +TTCCACACTGCCTAAAAGGGTCTGAGGGATCTCTAGTTACCAGAGTCACACAACAGACGGGCACACACTA +>K03455|HIVHXB2CG_8273_8774_2_0_0_2_0_0_339/2 +GCCCTGTCTTATACTTCTAGGTATGTGGCGAATAGCTCTACAAGCTCCTTTTACTACTTCTATAACCCTA +>K03455|HIVHXB2CG_1967_2518_2_0_0_1_0_0_33a/2 +TCAATTGTGGCAAAGAAGGGCAGACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGGTGTTGGAAATG +>K03455|HIVHXB2CG_110_604_0_0_0_0_0_0_33b/2 +GTCTGAGGGATCTCTAGTTACCAGAGTCACACAACAGACGGGCACACACTACTTGAAGCACTCAAGGCAA +>K03455|HIVHXB2CG_5131_5612_1_0_0_1_0_0_33c/2 +CCATTCATTGTGAGGCTCCCTCTGTGGCCCTTGGTCTTCTGGGGCTTGTTCCATCTATCCTCTGTCAGTT +>K03455|HIVHXB2CG_8221_8695_3_0_0_0_0_0_33d/2 +TCAGCTACTGCTATGGCTGTGGCATTGAGCAAGCTAACAGCACTATTCTTTAGTTCCTGACTCCAATACT +>K03455|HIVHXB2CG_837_1305_3_0_0_4_0_0_33e/2 +GGACAAAATTCGGTTAAGGCCAGGGGGCAAGAAAAAATATAAATTAAAACAAATAGTATGGGCAAGCAGG +>K03455|HIVHXB2CG_1393_1924_1_0_0_0_0_0_33f/2 +AAAGAGACCATCAATGAGGAAGGTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCAC +>K03455|HIVHXB2CG_7294_7810_3_0_0_1_0_0_340/2 +GTGCTTCCTGCTGCTCCCAAGAACCCAAGGAAGAAAGCTCCTATTCCCACTGCTCTTTTTTCTCTCTGCA +>K03455|HIVHXB2CG_6646_7084_2_0_0_2_0_0_341/2 +ATAGTAGTAGCGTGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAAAATCAGCACAAG +>K03455|HIVHXB2CG_4965_5498_2_0_0_5_0_0_342/2 +AATGCTGCAAGTGCCAAGTATTGTAGAGATCGTACCTTGTTATTTCCTGCTTGATAATCACACCTAGTGC +>K03455|HIVHXB2CG_8289_8777_0_0_0_1_0_0_343/2 +GTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGAT +>K03455|HIVHXB2CG_4372_4850_1_0_0_6_0_0_344/2 +AAGCCATGCATGGACAAGTAGACTGTAGTCCAGGACTATGGCAACTAGATTGTACACATTTAGAAGGAAA +>K03455|HIVHXB2CG_6054_6516_1_0_0_2_0_0_345/2 +TTTTCCACCTGTTAAAATTTTCTGTCACATTTACCAATACTACTTCTTGTGGGTTGGGGTCAGTGGGTAC +>K03455|HIVHXB2CG_8457_8957_2_0_0_1_0_0_346/2 +GCAGCATTGGTAGCTGCTGTATTGCTACTTGTGATTGCTCCATGTTTTTCCAGGTCTCGAGATGCAGCTC +>K03455|HIVHXB2CG_953_1436_1_0_0_1_0_0_347/2 +AAGGCTTTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATT +>K03455|HIVHXB2CG_7558_7993_2_1_0_2_0_0_348/2 +GTTCATCAAATATTACAGGGCTGCTATTAACAAAAGATGGTGGAAATAGCAACAATGAGTCCGAGAACTT +>K03455|HIVHXB2CG_3086_3611_0_0_0_0_0_0_349/2 +TATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATA +>K03455|HIVHXB2CG_2982_3454_2_0_0_2_0_0_34a/2 +CAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAAAATTCCAAAGTAGGATGACAAAAATCT +>K03455|HIVHXB2CG_2046_2539_4_0_0_5_0_0_34b/2 +AGGACACCAAATGAAAGATTGTAGTGAGAGACATGGTAATTTTTTAGGGAAGATCTGGCCATCCTACAAG +>K03455|HIVHXB2CG_807_1269_1_0_0_0_0_0_34c/2 +AGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAACTAT +>K03455|HIVHXB2CG_6467_7009_2_0_0_3_0_0_34d/2 +ACCAGAAGTAGTATTGGTAAATGTGACAGAAAATATTAACATGTGGAAAAATGACATGGTAGAACAGATG +>K03455|HIVHXB2CG_8460_8982_1_0_0_0_0_0_34e/2 +CTCTTGTGCTTCTAGCCAGGCACAAGCAGCATTGGTAGCTGCTGTATTGCTACTTGTGATTGCTCCATGT +>K03455|HIVHXB2CG_6919_7462_1_0_0_5_0_0_34f/2 +GTTTCACATCCTTCAGTGTTATTTGCCGCTTCAGTACTCCAAGTACTATTACACCAAGTACTATTAAACA +>K03455|HIVHXB2CG_4197_4724_1_0_0_0_0_0_350/2 +TACCTGTCCTATAATTTTCTTTAATTCTTTATTCATAGATTCTACTACTCCTTGACTTTGGGGATTGTAG +>K03455|HIVHXB2CG_119_585_2_0_0_0_0_0_351/2 +ACAGACCTTTGGATGGTGCTAGAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGA +>K03455|HIVHXB2CG_8349_8823_1_0_0_0_0_0_352/2 +ACTACTTTTTGACCACTTGCCACCCATCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGG +>K03455|HIVHXB2CG_494_1002_0_0_0_2_0_0_353/2 +TCCTGTCTGAAGGGATGGTTGTAGCTGTCCCAGTATTTGTCTACAGCGTTCTGATGTTTCTACCAGGCCA +>K03455|HIVHXB2CG_5766_6307_0_0_0_1_1_0_354/2 +CAGATCAACAACATCCCAAGGAGCATGGTGCCCCATCTCCACCCCCTTCTCCACAAGTGCTGATATTTCT +>K03455|HIVHXB2CG_5634_6083_0_0_0_1_0_0_355/2 +CTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAA +>K03455|HIVHXB2CG_740_1269_1_0_0_1_0_0_356/2 +TTCTACTACTTTTACCCATGCATTTAAAGTTCAAGGTGATATGGCCTGATGTACCATTTGCCCCTGGATG +>K03455|HIVHXB2CG_2894_3427_0_0_0_0_0_0_357/2 +TTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAG +>K03455|HIVHXB2CG_6926_7504_1_0_0_0_0_0_358/2 +TGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGGCAGTAGTATCAACT +>K03455|HIVHXB2CG_1573_2037_2_0_0_1_0_0_359/2 +TATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTCAGAATGTATAGCCCTCCCAGCATTCTGGACA +>K03455|HIVHXB2CG_4682_5173_2_0_0_0_0_0_35a/2 +AGACTCTATGAATCAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACA +>K03455|HIVHXB2CG_1430_1888_4_0_0_1_0_0_35b/2 +GAGTGCATCGAGTGCATGCAGGGCCTAATGCACCAGGGCATATGAGAGAACCAAGGGGAAGTGACATAGC +>K03455|HIVHXB2CG_8037_8509_2_0_0_1_1_0_35c/2 +CTCCGAAGATCGTCCCAGATAAGTGCCAAGGATCCGTTCAGTAATCGAATGGATCTGTCTCTGTCTCTCT +>K03455|HIVHXB2CG_2326_2844_0_0_0_1_0_0_35d/2 +CTGCGGGATGTGGTATTCCTAATTGAAGTTCCCAGAAGTCTTGAGTTCTCTTATTAAGTTCTCTGAAATC +>K03455|HIVHXB2CG_7564_8113_2_1_0_2_0_0_35e/2 +CAAATATTACAGGGCTGCTATTAACAACAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCCGACC +>K03455|HIVHXB2CG_8084_8561_0_0_0_2_0_0_35f/2 +ACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACAC +>K03455|HIVHXB2CG_8703_9200_2_0_0_3_0_0_360/2 +TATCTGACCCCTGGCCCTGGTGTTTAGTTCTGCTAATGAGGGAAGTAGCCTTGTGTGTGGAAGATCCACA +>K03455|HIVHXB2CG_7495_7869_0_0_0_2_0_1_361/2 +TAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATC +>K03455|HIVHXB2CG_2340_2840_3_0_0_1_0_0_362/2 +GGGATGTGGTATTCCTAATTGAACTTCCCAGAAGTCTTGAGTTCTCTTATTAAGTTCTCAGAAATCTACT +>K03455|HIVHXB2CG_5948_6340_1_0_0_2_0_0_363/2 +ACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGCCGAAGAGCTCATCAGAACAGTC +>K03455|HIVHXB2CG_7916_8406_1_0_0_0_0_0_364/2 +TCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCACGAATCCTGGCTGTGGAAAGATACCTA +>K03455|HIVHXB2CG_2839_3285_0_0_0_1_0_0_365/2 +CCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTT +>K03455|HIVHXB2CG_669_1141_0_0_0_0_0_0_366/2 +AAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGC +>K03455|HIVHXB2CG_1349_1879_0_0_0_1_0_0_367/2 +TGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGC +>K03455|HIVHXB2CG_6214_6685_0_1_0_2_0_0_368/2 +ATCTCTCCTTTCTCCATTATCATTGTCCCGCTACTACTATTGGTATTAGTATCATTCTTCAAATCATTGC +>K03455|HIVHXB2CG_3948_4530_0_0_0_1_0_0_369/2 +GTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGG +>K03455|HIVHXB2CG_3002_3515_2_0_0_1_0_0_36a/2 +GGGATGGAAAGGATCACCAGCAAAATTCCAAAGTAGCATGACAAAAATCTTCGAGCCTTTTAGAAAACAA +>K03455|HIVHXB2CG_7551_8016_2_1_0_0_0_0_36b/2 +ATTAGATGTTCATCAAATATTACAGGGCTGCTAATAACAAAAGATTGTGGTAATAGCAACAATGAGTCCG +>K03455|HIVHXB2CG_8918_9471_2_0_0_0_0_0_36c/2 +GATCAATCACAAGAAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGA +>K03455|HIVHXB2CG_3292_3838_1_0_0_3_0_0_36d/2 +TCTAACTGGTACCATAATATCACTAAGGGAGTGGTATTACCAAACTCCCACTCAGGAATCCAGGTGGCTT +>K03455|HIVHXB2CG_5273_5801_0_0_0_0_0_0_36e/2 +ATTCTGCTATGTCGACACCCAATTCTGAAAATGGATAAACAGCAGTTGTTGCAGAATTCTTATTATGGCT +>K03455|HIVHXB2CG_8550_9053_1_0_0_2_0_0_36f/2 +TTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAAAATTGGTGGAATC +>K03455|HIVHXB2CG_4171_4697_0_0_0_2_0_0_370/2 +TTTATTCATAGATTCTACTACTCCTTGACTTTGGTGATAGTAGGGAATTCCAAATTCCTGCTTGATTCCC +>K03455|HIVHXB2CG_3281_3669_1_0_0_1_0_0_371/2 +AGTGCTGCGAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCA +>K03455|HIVHXB2CG_1415_1907_0_0_0_5_0_0_372/2 +GCATTTGTTACTTGGCACATTGCATCAGCCAAAACTCTTGCCTTATGGCCGGGTCCACCAACTCCCTGAC +>K03455|HIVHXB2CG_7918_8409_0_0_0_1_0_0_373/2 +TGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAA +>K03455|HIVHXB2CG_8966_9480_3_0_0_2_0_0_374/2 +GGCTAGAAGCACAAGATGAGGAGGAGGTGGGTTTTCCAGTCACAGCTCAGGTACCTTTAAGCCCAATGAC +>K03455|HIVHXB2CG_4786_5302_3_0_0_4_0_0_375/2 +CTCTGGAGAGTCCCTGAGCCAAATGCCATTCTCTTTCTCCTGTATGCAGACCCCAATATGTTGTTATTAC +>K03455|HIVHXB2CG_1307_1822_3_0_0_2_0_0_376/2 +CAGCATTATCAGACGGAGCCACCCCACAATATTTAAACACCAAGCTAAACACAGTGGGGGGACATCAAGC +>K03455|HIVHXB2CG_5343_5849_2_0_0_3_0_0_377/2 +TAGGATGTACTGGCTCCATATCTTGCTCTCCTCTGTCGAGTAACGCCTATACTGCTATGTCGACACCCAA +>K03455|HIVHXB2CG_1146_1736_2_0_0_1_0_0_378/2 +CAATTTTTTACCTCCTGTGAAGCTTGCACGGCTCTTAGAGTTTTATAGAACCGGTCTACATAGTCTCTAA +>K03455|HIVHXB2CG_5039_5554_2_0_0_1_0_0_379/2 +CCTCTGTCAGTTTCGTAACACTAGGCAAAGGTGGCTTTATCTATTTTGGTGTTATTAATGCTGCTAGTGC +>K03455|HIVHXB2CG_395_841_1_0_0_2_0_0_37a/2 +GACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTGTCTG +>K03455|HIVHXB2CG_8189_8717_2_0_0_2_0_0_37b/2 +TTGTATAACCCTATCTTTCCCCTCAGCTACTGCTATGGCTGTGGCATTGAGCAAGCTAACAGCACTATTC +>K03455|HIVHXB2CG_3133_3762_1_1_0_3_0_0_37c/2 +TAGGGCAGCATAGAACAAACATAGAGGAGCTGAGACAACATCTGTGGAGGTGGGGACTTACCACACCAGA +>K03455|HIVHXB2CG_4528_4993_1_0_0_2_0_0_37d/2 +TTCTTTTAAAATTAGCAGGAATATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGG +>K03455|HIVHXB2CG_2630_3166_1_0_0_0_0_0_37e/2 +AGACGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATT +>K03455|HIVHXB2CG_3014_3443_0_0_0_2_0_0_37f/2 +TTCTTCTGTTAGTGGTCTTAGTTCTGTTAGTGCTTTGGTTCCTCTAAGGAGTTTACATAATTGCCTTACT +>K03455|HIVHXB2CG_1258_1708_3_0_0_3_0_0_380/2 +AAAGTAGTAGAAGAGAAGGCTATCATCCCAGAAGTGAAACCCATGTTTTCAGCATTATCAGAAGGAGCCA +>K03455|HIVHXB2CG_7847_8401_1_0_0_0_0_0_381/2 +CCCCTCGGGGTTGGGAGGTGGGTCTGAAACGATAATGGTGAATATCCCTGCCTAACTCTATTCACTATAG +>K03455|HIVHXB2CG_4785_5238_2_0_0_0_0_0_382/2 +TATTACCAATCTAGCATCCCCTAGTGGGATGTGTACTTCTGAACTTATTCTTGGATGAGGGCTTTCATAG +>K03455|HIVHXB2CG_6666_7168_1_0_0_2_1_0_383/2 +CTCGCTGGTCCTCTCGGGATACGGATTCTTTTTCTTGTATTGTTGTTGGGTCTTGTACAATTAAATTCTA +>K03455|HIVHXB2CG_8938_9529_2_0_0_1_0_0_384/2 +ACAGCAGCTCCCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGCGGAGGAGGTGGGTTTTCCAGTCA +>K03455|HIVHXB2CG_3393_3880_0_0_0_1_0_0_385/2 +CTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAG +>K03455|HIVHXB2CG_5530_6168_2_0_0_1_0_0_386/2 +TGTCTTAATATTATCCTATATTCTATGATTACTATGGACCACACAACTATTGCTATTATTATTGCTACTA +>K03455|HIVHXB2CG_4891_5352_1_0_0_0_0_0_387/2 +AAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTAGGAAAGGACCAGCAAAGCTCCTCTGGAA +>K03455|HIVHXB2CG_7983_8552_4_0_0_0_0_0_388/2 +CTAAAGGATCAAGAGCTCCTGGGGATTTGGTGTTGCTCTGGAAAACTCATTTGCACCCCTGCTGTTCCTT +>K03455|HIVHXB2CG_1488_1953_1_0_0_2_0_0_389/2 +CTTTCTTTGGTTCCTAAAATTGCCTCTCTGCATCATTATGGTCGCTGAATTTGTTACTTGGCTGATTGCT +>K03455|HIVHXB2CG_7369_7835_2_0_0_1_0_1_38a/2 +TTTTGTACTGTAATTCAACACAACTGTTTAATAGTACATGGTTTAATAGTACTTGGAGTACTGAAGGGTC +>K03455|HIVHXB2CG_3202_3646_1_0_0_1_0_0_38b/2 +ACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAAAGGACAGT +>K03455|HIVHXB2CG_7148_7652_5_1_0_1_1_0_38c/2 +CCTCCTATCTCCTCCTCCAGGTCTGAAGATCTCGGACTCATTGTTGCTATTACCACCATCTTTTGTTAAT +>K03455|HIVHXB2CG_2875_3431_0_0_0_0_0_0_38d/2 +TGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCAT +>K03455|HIVHXB2CG_5119_5669_0_0_0_3_0_0_38e/2 +AATGCTAGGAAAATGTCTAACAGCTTCATTCTTAAGCTCCTCTAAACGCTCTAGTGTCGATTCATTGTGT +>K03455|HIVHXB2CG_4431_4978_1_0_0_1_0_0_38f/2 +ACTACTGCCCCTTCACCTTTCCAGAGGAGCTTTGCTGGTCCTTTCCAAAGTGGATTTCTGCTGTCCCTGA +>K03455|HIVHXB2CG_8332_8839_4_0_0_1_0_0_390/2 +GTATAGTGAATAGAGTTAGGCAGGGAAATTCACCATTATCGTTTCAGACCCACCTCCCAAGCGCGAGGGG +>K03455|HIVHXB2CG_9154_9622_1_0_0_1_0_0_391/2 +CAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCTAGTTAGCCAGAGAGCTCCCAGGCACAGATCTGGTCT +>K03455|HIVHXB2CG_3930_4362_3_0_0_0_0_0_392/2 +GCTGACATTTATCACAGCTGGCTACTATTTCTTTTGCTACTACAGGTGGCAGGTTAAAATCACTAGCCAT +>K03455|HIVHXB2CG_2099_2640_1_0_0_0_0_0_393/2 +TTTTTTCTTCTGTCAATGGCCATTGTTTAACTTTTGGGCCATCCATTCCTGGCTTTAATTTTACTGGTAC +>K03455|HIVHXB2CG_775_1228_0_0_0_1_0_0_394/2 +TGGCCTGATGTACCATTTGCCCCTGGATGTTCTGCACTATAGGGTACTTTTGGCTGACCTGATTGCTGTG +>K03455|HIVHXB2CG_8244_8797_0_0_0_0_0_0_395/2 +TCTTATAGCAAAATCCTTTCCAAGCCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACAAGCTC +>K03455|HIVHXB2CG_8272_8826_2_0_0_2_0_0_396/2 +CATTATTCATAATGATAGTAGGAGGCTTGTTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAA +>K03455|HIVHXB2CG_466_962_0_0_0_3_0_0_397/2 +TTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCT +>K03455|HIVHXB2CG_6569_7123_2_0_0_2_0_0_398/2 +CCTAAATCCATGTGTAAAATTCACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACT +>K03455|HIVHXB2CG_1976_2423_1_0_0_1_0_0_399/2 +GCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGTAAATGTGGAAAGGA +>K03455|HIVHXB2CG_6632_7076_1_0_0_3_0_0_39a/2 +TATGGTTTTCGCATTGTCCGTGAAATTGACAGATCTAATTACTACCTCTTGTTCTGCTAGACTGCCAATT +>K03455|HIVHXB2CG_1589_2160_0_0_0_2_0_0_39b/2 +TCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAA +>K03455|HIVHXB2CG_3426_3883_2_0_0_5_0_0_39c/2 +ATACCCCTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGCGATTCTAAAAGAACCAGTACATG +>K03455|HIVHXB2CG_6842_7346_1_0_0_1_0_1_39d/2 +GTGGTTACAATTTCTGGGTCCCCTCCTGAGGATAGCTTAAAGATTATTGTTTTATTATTTCCAAATTGTT +>K03455|HIVHXB2CG_6758_7257_2_1_0_1_0_1_39e/2 +TCTGTTTTAAAGTGTTAATCCATTTTGCTCTACTAATGTTACAATGTGCTTGTCTCATATTTCCTATTTT +>K03455|HIVHXB2CG_3293_3770_1_0_0_4_0_0_39f/2 +AAAAGACAGCTGGACTGTCCATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTAC +>K03455|HIVHXB2CG_2499_2974_2_0_0_0_0_0_3a0/2 +AACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATAAGCCCTATTGATA +>K03455|HIVHXB2CG_5922_6477_0_0_0_2_0_0_3a1/2 +GCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACA +>K03455|HIVHXB2CG_435_1073_2_0_0_2_0_0_3a2/2 +GCTGCTTATTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGGTCTCTGGCTAACTA +>K03455|HIVHXB2CG_6447_6986_2_0_0_3_0_0_3a3/2 +GTACCCACAGAGCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAACATTTTAACATGTGGAAAA +>K03455|HIVHXB2CG_7991_8576_1_0_0_1_0_0_3a4/2 +AAGTTCCACAATCCTCGTAACAATCAAGAGTAAGTCTCTCAAGCGGTGGTAGCTGAAGAGGCACAGGCTC +>K03455|HIVHXB2CG_2305_2796_3_0_0_1_0_0_3a5/2 +TCTTATTAAGTTCTCTGAAATCTACTAATTTTCTCCATTTAGTACTTTCTTTTTTCTTTATGGCAAATAC +>K03455|HIVHXB2CG_6011_6523_2_0_0_0_0_0_3a6/2 +CACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCCATAG +>K03455|HIVHXB2CG_8380_8902_3_0_0_2_0_0_3a7/2 +CTCGAGCTGCTGCTCCCACCCTATCTGCTGCTGGCTCAGCTCGTCTCAATCTTTCCCTTACAGTAGGCCA +>K03455|HIVHXB2CG_8832_9354_0_0_0_2_0_0_3a8/2 +GTCAAACCTCCACTCTAACACTTGTCTCTCCGGGACATCCATCCCATGCAGGCTCACAGGGTGTAACAAG +>K03455|HIVHXB2CG_8560_9036_2_0_0_1_0_0_3a9/2 +AGTCATTGGTCTTAAAGGTACCTGAGGTGTGACTGGAAAACCCACCTCCTCGTCCTCTTGTGCTTCTAGC +>K03455|HIVHXB2CG_3089_3580_1_0_0_1_0_0_3aa/2 +CTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCAAAGAACAAAAATAGAG +>K03455|HIVHXB2CG_7035_7537_2_0_0_2_0_0_3ab/2 +GGATGGGCATACATTGCTTTTCCTACTTACTGCCACATGTTTATAATTTGTTTTATTCTGCATGGGAGGG +>K03455|HIVHXB2CG_320_805_1_0_0_3_0_0_3ac/2 +ACGCTCTCGCACCCATCTCTCTCCTAGTAGCCTCCGCTAGTCAAAATTATTGGCGTACTCACCAGTCGCC +>K03455|HIVHXB2CG_8424_8845_1_0_0_1_0_0_3ad/2 +TTACAGTAGGCCCTCCAATCACACTACTTTTTGACCACTTGCCACCCATCTTATAGCAAAATCCTTTCCA +>K03455|HIVHXB2CG_1664_2164_1_0_0_2_0_0_3ae/2 +GTGGGGCTGTTGGCTCTGGTCTGCTCTGACGAAAATTCCCTGGCCTTCCCTAGTAGGAAGGCCAGATCTT +>K03455|HIVHXB2CG_6966_7445_0_0_0_5_0_0_3af/2 +GTTATTTGACCCTTCAGTACTCCACGTACTATTAACCGACGTACTATTAAACAGTTGTGTAGAATTACAG +>K03455|HIVHXB2CG_594_1011_3_0_0_1_0_0_3b0/2 +TTCTTCTGATCCTGTCTGAAGGGATGGATGTAGCTGTCCCAGTATTTGTCTACAGCCTTCTGATGTTTCT +>K03455|HIVHXB2CG_26_546_2_0_0_0_0_0_3b1/2 +AAGACAAGATATCCTTGATCTGTGGATCTACCACACCCAAGGCTACTTCCCTGATTAGCAGAACTAGACA +>K03455|HIVHXB2CG_5179_5762_4_0_0_1_0_0_3b2/2 +CAGCAGTTGTTGCAGAATTCTTATTATGGCTTCCACTCCTGCCCAAGTATCCCCATACGTTTCATAGATA +>K03455|HIVHXB2CG_8167_8640_1_0_0_1_0_0_3b3/2 +AATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGAAAAATGGGCAAGTTTGTGGAA +>K03455|HIVHXB2CG_6183_6715_2_0_0_2_0_0_3b4/2 +CTTGTGCTGATATTGAAAGAGCAGTTTTTTATGTCTCCTTTCTCCAATATCATTCTCCCGCTACTACTAT +>K03455|HIVHXB2CG_4580_5127_1_0_0_0_0_0_3b5/2 +TGGCAGCACTTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGA +>K03455|HIVHXB2CG_4203_4642_0_0_0_0_0_0_3b6/2 +TCCTGCTTGATTCCCGCCCACCAACAGGCGGCCCTAACCGTAGCACCGGTGAAATTGCTGCCATTGTCAG +>K03455|HIVHXB2CG_5173_5711_0_0_0_2_0_0_3b7/2 +CCCATAAGTTTCATAGATATGTTGCCCTAAGCCATGGATCCAAATCCTAGGAAAATGTCTAACATCTTCA +>K03455|HIVHXB2CG_8718_9240_1_0_0_4_0_0_3b8/2 +ACCTGTTACTAGCATGTAGCACCATCCAAAGGTCAGTGGATATCTGACCCCTGGGCCTGGTGTGTAGTTC +>K03455|HIVHXB2CG_1646_2189_2_0_0_2_0_0_3b9/2 +GACAAGGACCAAAGGAACCCTTTAGAGACTAAGTATACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGC +>K03455|HIVHXB2CG_7104_7633_1_1_0_2_1_0_3ba/2 +ATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCCGATAGGACCAGGGAGAGCAT +>K03455|HIVHXB2CG_7577_8171_0_1_0_0_0_0_3bb/2 +GCTGCTATTAACAAAAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGAT +>K03455|HIVHXB2CG_9080_9612_1_0_0_1_0_0_3bc/2 +TGAGGCTTAAGCAGTGGGTTCCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCATAGAG +>K03455|HIVHXB2CG_7769_8242_1_0_1_4_0_0_3bd/2 +AACCAATTCCACAAACTTGCCCATTTATCTAATTCCAATACTTCTTGTTCAAACTTTTGTTGCTGGTTTT +>K03455|HIVHXB2CG_6774_7343_2_0_0_2_0_0_3be/2 +ATAGATAATGATACTACCAGCTATAAGTTTACAAGTTGTAACACCTGAGTCATTACACAGGCCTGTCCAA +>K03455|HIVHXB2CG_7419_7956_1_0_0_1_0_0_3bf/2 +ACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCGATGCAGAATAAAAC +>K03455|HIVHXB2CG_1584_2125_0_0_0_1_0_0_3c0/2 +GATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGA +>K03455|HIVHXB2CG_4726_5238_1_0_0_2_0_0_3c1/2 +GAGATCCGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGG +>K03455|HIVHXB2CG_987_1432_1_0_0_1_0_0_3c2/2 +CTCTATCCCATTCTGCAGCTTCCTCATTGATGGTCTCTTTTAACATTTGCATGGCAGCTTGATGTCCCCC +>K03455|HIVHXB2CG_7352_7839_2_0_0_1_0_1_3c3/2 +TAATTGTGGAGGGGAATTTTTCTACTGTAATTCCCCACAACTGTTTAATAGTACTTGGTTTAATAGTACT +>K03455|HIVHXB2CG_9112_9629_0_0_0_0_0_0_3c4/2 +AGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACAC +>K03455|HIVHXB2CG_8331_8894_1_0_0_3_0_0_3c5/2 +GCTGCTCGCACCCAATCTGCTGCTGGGTCAGCTCGTCTCATTCTTTCCCTTACAGTAGGCCATCCAATCA +>K03455|HIVHXB2CG_5746_6187_0_0_0_2_0_0_3c6/2 +TAACCTGTCTATTTTTCTTTGTCTTAATATTTTCCAATATTCTATGATTACTATGGACCACACACCTATT +>K03455|HIVHXB2CG_7839_8257_2_0_0_1_0_0_3c7/2 +CAATTTGTTATGTTAAACCAATTCCACAAACTTGCCCAATTATCTAATTCCAATAATTCTTGTTCATTCT +>K03455|HIVHXB2CG_5560_6023_0_0_0_2_0_0_3c8/2 +TGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGA +>K03455|HIVHXB2CG_2803_3242_2_0_0_1_1_0_3c9/2 +AAGACTTCTGGGAATTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGACAAAATCAGTAACAGT +>K03455|HIVHXB2CG_8178_8717_0_0_0_1_0_0_3ca/2 +TTCTATAACCCTATCTGTCCCCTCATCTACTGCTATGGCTGTGGCATTGAGCAAGCTAACAGCACTATTC +>K03455|HIVHXB2CG_4737_5275_0_1_0_1_0_0_3cb/2 +GAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATCTTAAAAGAAAAGGGGGGATTGGGG +>K03455|HIVHXB2CG_1092_1557_0_0_0_2_0_0_3cc/2 +GATAGGTGGATTATTTGTCATCCATCCTATTTGTTCCTGAAGGGTACTAGTCGTTCCTGCTAAGTCACTT +>K03455|HIVHXB2CG_1163_1606_1_0_0_0_0_0_3cd/2 +TTTTATTTAATCCCAGGATTATCCATCTTTTATAAATTTCTCCTACTGGGATAGGTGGATTATTTGTCAT +>K03455|HIVHXB2CG_5772_6285_2_0_0_0_1_0_3ce/2 +GCATGGTGCCCCATCTCCACCCCCTTCTCCACAAGTGCTGATATTTCTCCTTCACTCTCATTGCCACTGT +>K03455|HIVHXB2CG_8764_9250_0_0_0_1_0_0_3cf/2 +TAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGAT +>K03455|HIVHXB2CG_2064_2569_2_0_0_1_0_0_3d0/2 +TTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCAACAAGGGAAGGCCAGGGCATTTT +>K03455|HIVHXB2CG_5349_5796_4_0_0_1_0_0_3d1/2 +AGACCAACTAATTCATCTGTCTTACTTTGACAGTTTTTCAGACTCTGCTATAAGAAAGGGCTTATTCGGA +>K03455|HIVHXB2CG_9049_9567_1_0_0_2_0_0_3d2/2 +GCTCAGATCTGGTCTAACCAGAGAGACCCATTACAGGCAAAAAGCAGCTGCTTATATGCAGGATCTTAGG +>K03455|HIVHXB2CG_2549_3001_1_0_0_2_0_0_3d3/2 +TGTGGAAGCACATTGTACTGATCTCTAATCCCTGGTGTCTCATTGTTTATACTAGGTATGGTAACTGCAG +>K03455|HIVHXB2CG_5838_6416_1_0_0_1_0_0_3d4/2 +CAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTTCTTGTACCAATTGCTA +>K03455|HIVHXB2CG_8558_9075_3_0_0_0_0_0_3d5/2 +AACGAGGATTGTGGAACTTCTGGGACGCAGGTGGTGGGAATCCCTCAAATATTGGTGGAATCTGCTACAG +>K03455|HIVHXB2CG_490_935_0_0_0_2_0_0_3d6/2 +CCAGGATTAACTGCGAATCGTTCTAGCTCCCTGCATGCCCATACTATATGTTTAAATTTATATTTTTTCT +>K03455|HIVHXB2CG_4771_5396_0_1_0_2_0_0_3d7/2 +GCAGAGTCTGAAAAACAGTCAAAGTAATAGAGATGAATTCGTTGGTCTGCTAGTTCAGGGTCTACTTGTG +>K03455|HIVHXB2CG_2520_3028_0_0_0_3_0_0_3d8/2 +TTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGC +>K03455|HIVHXB2CG_6013_6503_4_0_0_2_0_0_3d9/2 +AAAATTTTCTGTCACAATTACCAATACTACTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTGTT +>K03455|HIVHXB2CG_6180_6655_2_0_0_3_0_0_3da/2 +CTAGTACTATTGGTATTAGAATCATTCTTCAAATCAGTGCACTTTAAACTAACACAGATTGGGGTTAATT +>K03455|HIVHXB2CG_5157_5665_0_0_0_0_0_0_3db/2 +CTAGGAAAATGTCTAACAGCTTCATTCTTAAGCTCCTCTAAAAGCTCTAGTGTCCATTCATTGTGTGGCT +>K03455|HIVHXB2CG_9240_9687_2_0_0_2_0_0_3dc/2 +CTGAGGGATCTCTAGTTACCAGAGTCACACAACAGACGGGCACAGACTACTTGAAGCACTCAAGTCAAGC +>K03455|HIVHXB2CG_2271_2792_2_0_0_3_0_0_3dd/2 +CAACGACCCCTCGTGACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGAAG +>K03455|HIVHXB2CG_7193_7746_2_0_0_3_0_0_3de/2 +ACAGCACCACTCTTCTCTTTGCCTTGGTGGGTGCTACTCCTAATGGTTCCATTTTTACTACTTTATATTT +>K03455|HIVHXB2CG_7272_7762_0_0_0_2_0_0_3df/2 +AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAA +>K03455|HIVHXB2CG_3679_4099_1_0_0_0_0_0_3e0/2 +AACTCTGATTCACTTTGATCTGGTTGTGCTTGAATGATTCCTAATGCATATTGTGAGTCTGTTACTATGT +>K03455|HIVHXB2CG_114_621_2_0_0_1_0_0_3e1/2 +CCACACTGACTAAAAGGGTCTGAGGGATCTCTAGTTACCAGAGTCACACAACAGACGGGCACACACAACT +>K03455|HIVHXB2CG_6142_6604_2_0_0_0_0_0_3e2/2 +ACACAGAGTGGGGTTAATTTTACACATGGCTTTAGGCTTTGATCCCATAAACTGATTATATCCTCATGCA +>K03455|HIVHXB2CG_1950_2465_1_0_0_2_0_0_3e3/2 +AAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAC +>K03455|HIVHXB2CG_5124_5602_4_0_0_4_0_0_3e4/2 +TATGTATGTTTCAGGGAAAGCTAGGGGATGGATTTCTAGACATCACTATGAAAGGCCTCATCCAAGAAAA +>K03455|HIVHXB2CG_7724_8235_1_0_0_1_0_0_3e5/2 +TCCACAAACTTGCCCATTTATCTAATTCCAATAATTCTTGTTCATTCTTTTGTTGCTGGTTTTGCGATTC +>K03455|HIVHXB2CG_2325_2763_1_0_0_2_0_0_3e6/2 +GATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCGAGGAAGATGGAAACCAAAAATGATAG +>K03455|HIVHXB2CG_2502_2971_0_0_0_0_0_0_3e7/2 +ATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pipelign-out1.fasta Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,600 @@ +>K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1 +------------------------------------------------------------ +------------------------------------------------------------ +-------------GATCCTGC----------------------------------ATATA +AGCAGCAGCTTTTTGC-CTTTACTGGTTCTCTCTGGTTAGACCAGATCTGAGCCTGGG-- +----------------------------------- +>K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1 +------------------------------------------------------------ +------------------------------------------------------------ +-------------AGCAGAATAGGCGTTACTC-----GACAGAGGAGAGCAAGAAATGTA +GCCAGTAGATCCTAGA-CTATA-----------------------------GCCCTGG-- +----------------------------------- +>K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1 +------------------------------------------------------------ +------------------------------------------------------------ +------------CAGATACCT----------------------------------AAATG +ATCAACAGCTCCTGGG-GATT-TGGGGTTGCTCTGGAAAACTCATTTGCACCCCTGCT-- +----------------------------------- +>K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1 +---------------------------------------------GTCTGGGGCATCAAG +CAGCTCCAGGCAAGAATGCTGGCTGT---------------------------------- +--------GG-AAAGATACCT----------------------------------AAAGG +ATCAACAGCTCC------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1 +---------------------------------------------TCCTGACTC------ +CAATACTGTAGGAGATTCC----------------------------------------- +-----------ACCAATATTT----------------------------------GAGGG +CTTCCCACCCCCTGCG-TCCC-AGAAGTT------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1 +------------CGAGCAAGCTTCACAGGAGTTAAAAAATTGGATGACAGAAAC-CTTGT +TGGTCCAAAATGCGAACCCAGAT------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1717_2240_0_0_0_2_0_0_4b/1 +----------------------TCACAGGAGGTAAAAAATTGGATGACAGAAAC-CTTGT +TGGTCCAAAATGCGAACCCAGATTGT---------------------------------- +-----------AAGACTA------------------------------------------ +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------ATTT--------------------------TAAAAGCATTGGG +ACCAGCGGCTAC----------ACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAT +GAC-------------------------------- +>K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1 +--------------------------------------------TGACAGAAAC-CTAGT +TGGTCCAAAATGCGAACCCAGATTGT---------------------------------- +-----------AAGACAATTT--------------------------TAAAAGCATTGGG +ACCAGC------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1 +-----------------------------------------------------CACTTAT +TAAAAGAAAAGGGGGGACTGGA-------------------------------------- +-----------AGGGCTAATT--------------------------CACTCCCAAAGAA +GACAAGATATCCTTGA-TC----------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_9067_9580_2_0_0_1_0_0_4c/1 +-----------------------------------------------------------T +TAAAAGAAAAGGGGGGACTGGA-------------------------------------- +-----------AGGGCTAATT--------------------------CACTGCCAAAGAA +GACAAGATATCCTTGA-TCTGAGGA----------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1 +------------------------------------------------------------ +------------------------------------------------------------ +-------------GGCTAATT--------------------------CACTCCCAACGAA +GACAAGATATCCTTGA-TCTGTGGATGTACCACCCACAAGGCTACTTCCC---------- +----------------------------------- +>K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1 +------------------------------------------------------------ +--------ACAACGGAATTGG--------------------------------------- +-------------AGGAAATG--------------------------AACCAGTAGATAA +ATTAGTCAGTGCTGGA-ATCAGGAAAGTACTATTTTT----------------------- +----------------------------------- +>K03455|HIVHXB2CG_3703_4231_2_0_0_1_0_0_62/1 +------------------------------------------------------------ +----------AATAGTACTTT--------------------------------------- +-------------CCTGATTC--------------------------CAGCACTGACTAA +ATTATCTACTTGTTCA-TTTCCTCCAATTCCTTTGTGTG--------------------- +----------------------------------- +>K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1 +------------------------------------------------------------ +-----GAAGAAGCGGAGACAGC-------------------------------------- +---------G-ACGAAGAGCT-----------------------CATCAGAACAGTCAGA +CTCATCAAGCTTCTCA-ATCAAATCAG--------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5968_6386_1_0_0_1_0_0_d/1 +--------------------------------------------------------CTAT +GGCAGGAAGAAGCGGAGACAGC-------------------------------------- +---------G-ACGAAGAGCT-----------------------CATCAGAACAGTCAGA +CTCATCAAGCTTCTGT-A------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1 +------------------------------------------------------------ +-----------------ACAGC-------------------------------------- +---------G-ACGAAGAGCT-----------------------CATCAGAACAGACAGA +CTCATCAAGCTTCTCT-ATCAAAGCAGTAAGTATTACAT--------------------- +----------------------------------- +>K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1 +------------------------------------------------------------ +-----------AAGCTTGTGTA-------------------------------------- +-----------ATTGTTAATT-----TCTCT-------------GTCCCACTCCATCCAG +GTCGTGTGATTCCAAC-TCTGTTCCAG-------------------------AG------ +----------------------------------- +>K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1 +------------------------------------------------------------ +-----------AAAATTTCAAA-------------------------------------- +------------------------------------------------------AATTGG +GCCTGAAAATCCATAC-AATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTA------ +----------------------------------- +>K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------AGCCAT--------------------------------------- +---------TGCTCTC-CAATTACTGTGATATTTCTCATGTTCATCTTGGGCCTTAACTA +TTCCATCTAAAAAT--------------------- +>K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------TGATTT-GTTGTGTCAG------------------TTAGGGTGAC +AACTTTTTGTGTTCCT-CTATTAGTAACATATCCTGCTTTTCC----------------- +------------TA--------------------- +>K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------G-AGGGGGAGTT-GTTGTCTGTACCCCAGACCTGAAGCTCTCTTCTTGTGG +GGCTGTTGGCTCTGGT-CTGCT-------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_1644_2213_4_0_0_3_0_0_4f/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----TTCTG-AGGGGGAGAT-GTTGTCTCTAGCCCAGACCTGAAGCTCTCTTCTGGTGG +GGCAGTTGGCTCTGGT-C------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1 +------------------------------------------------------------ +------------------------------------------------------------ +-------------------CT-CTAGTGTCCATTCATTGTGTGG------CTCCCTCTGT +GGCCCTTGGTCTTCTT-GGGCTTGTTCCATCTCTCCT----------------------- +----------------------------------- +>K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1 +------------------------------------------------------------ +---------ATAGAGCTTCCTTTAGTTGCCCCC-----------------------CTAT +CTTTATTGTG-ACGAGGGGAC-GTTGCCAAAGAGT--GACCTGAGG-------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------GAAGTCTTGAGTTCTCTTATTAA-----GTTCTCTGAA +ATCTACTAATTTTCTC-CATTTAGTACTGTCTTTTTTC---------------------- +----------------------------------- +>K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------TTCTCTGAA +ATCTACTAATTTTCTC-CATTTAGTACTGTCTTTTTTCTT------TATGGCAAATACTG +GAGTAT------TG--------------------- +>K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------TGCCAAGGATCC------------------------ +GTTCACTAATCGAATG-GATCTGTCTCTGTCTCTCTCTCCACCTTCTTCTTCTATTCCT- +----------------------------------- +>K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1 +------------------------------------------------------------ +----------GGTGATATGGGCTGATGTACC-------------ATTTGCCCCTGGATGT +TCTGCACTAT-AGGGTAATTTTGGCTGACCTGAT-------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1 +------------------------------------------------------------ +------CAGAAGTGATA----------------------------------CCCATGTTT +TCAGCATTAT-CAGAAGGAGCCACCCCACAAGATTT------------------------ +-AAACACCATGCTAAA-------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1 +------------------------------------------------------------ +------------------------------------------------------------ +------TTAT-CAGAAGGAGCCACCCCACAAGATTT------------------------ +-AAACACCATGCTACACCCAGTGGGGGGACATCAAGCAGCCA------------------ +----------------------------------- +>K03455|HIVHXB2CG_1302_1790_0_0_0_1_0_0_1c/1 +------------------------------------------------------------ +--------------------------------------------------------GTTT +TCAGCATTAT-CAGAAGGAGCCACCCCACAAGATTT------------------------ +-AAACACCATGCTAAACACAGTGGGGGGACAT---------------------------- +----------------------------------- +>K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1 +------------------------------------------------------------ +----------TGTAACACC------------------------------TCAGTCATTAC +ACAGGCCTGT-CCAAAGGTATCCTTTGAGCCAATTC------------------------ +-CCATACATTATTGTG-------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_6323_6872_1_0_0_2_0_0_50/1 +------------------------------------------------------------ +----------ATGTATG------------------------------------------- +--GGAATTGG-CTGAAAGGATACCTTTGGACAGGCC------------------------ +-TGAGTAATGACTGAG----GTGTTACAACTTGTC------------------------- +----------------------------------- +>K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1 +------------------------------------------------------------ +------------------------------------------------------------ +--------GA-CCAGCAAAGCACCTC---------T----GGAAAGGTGAAGGGGCAGTA +GTAATACAAGATAATA-GTGACATAAAAGTAGT--------------------------- +----------------------------------- +>K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------GGAAAGGTGAAGGGGCAGTA +GTAATACAAGATAATA-GTGACATAACAGTAGTGCGAAGAAGAAAAGCAAA--------- +----------------------------------- +>K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------GGGG--------------------GGAACAGTGCAGGGGAAAGA +ATAGTA-GACATAATA-GCAACAGACATACAAACTAAAGAATTACAAA------------ +----------------------------------- +>K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------TTTTATGGTTCATAA +TCCACTCCATGTACTG-GTTCTTTTAGAATCTCTCATTTTTCTGCCCGTTCTAGCT---- +----------------------------------- +>K03455|HIVHXB2CG_3441_3888_1_0_0_0_0_0_5c/1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------GAAGCAGAGCTAGAACTGGC----AGAAAACAGAGAGATTCTAA +AATAACCAGTACATGG-AGTGTATTATGACC----------------------------- +----------------------------------- +>K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1 +------------------------------------------------------------ +--------CAGAGGAGGTCT---------------------------------------- +-------------CTCGACGCAGGACTCGGCTTGCT----GAAGGGCGCACGG----CAA +GAGGCGAGGGGCGGCG-ACT---------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_667_1161_0_0_0_1_0_0_37/1 +------------------------------------------------------------ +--GGAAACCAGAGGAGCTCT---------------------------------------- +-------------CTCGACGCAGGACTCGGCTTGCT----GAAGCGCGCACGG----CAA +GAGGCGAGGGGCG----------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1 +------------------------------------------------------------ +-----------------------------------------------------------C +GGGCACACAC-TACTTGAAGCACTCA---------------------------------- +-AGGCAAGCTTTATTG-AGGCTTAAGCAGTGGGTTCCCTAGTTAGC-------------- +----------------------------------- +>K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1 +------------------------------------------------------------ +------------------------------------------------------------ +-------------CTTGAAGCACTCA---------------------------------- +-AGGCAAGCTTTATTG-CGGCTTAATCAGTGGGTTCCCTAGTTAGCCAGAGAGCT--CCC +A---------------------------------- +>K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------TGCTGCTGGCT---------------------------------- +-CAGCTCGTCTCATTC-ATTCCCTTACAGTAGGCCATCCAATCACACTACATATTGACCA +C---------------------------------- +>K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1 +------------------------------------------------------------ +------------------------------------------------------GC---T +GCTCCCACCC-TATCTTGTGCTGGCT---------------------------------- +-CAGCTCGTCTCATTG-TTTCCCTTACAGTAGGCCATCCAATCA---------------- +----------------------------------- +>K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1 +------------------------------------------------------------ +------------------------------------------------------CTATGT +TTACTTCTAA-T-CCCGAATCCTGCA---------------------------------- +-AAGCTAGATAAATTG-CTTGTAACTCAGT----CTTCTGATTTGT-------------- +----------------------------------- +>K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1 +------------------------------------------------------------ +TCCTCTGTCGAGTAACGCCTATTCT----------------------------GCTATGA +CGACACCCAA-T-TCTGAAACTGGAT---------------------------------- +-AAAC---AGCAGTTG-TT----------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1 +------------------------------------------------------------ +------------------------------------------------------------ +------------------TAGGAACCAAAGA--------------------------AAG +ATAGTTAAGTGTTTCA-ATTGTGGCACAGAAGGGCACACAGCCAGAAATTGCAGG----- +----------------------------------- +>K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1 +-------------TAAGGTGTTTTAC-----------------------------TAAAC +TTTTCCATGTTGTAATCCTCATCCT----------------------------GTCTCCT +TGCCACACAA-T-CATCACCTG-------------------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1 +------------------------------------------------------------ +------------------------------------------------------GCCACA +GAGGGAGCCA-CACAATGAATGGACA---------------------------------- +-CTATAGCTTTTAGAG-GAGCTTAAGAATGAAGCT-----GTTAGA-------------- +----------------------------------- +>K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1 +------------------------------------------------------------ +-------TAACGCCACCTTTGCCTA--------GTGTTACGAAACTGCCAGAGGA----- +-----------TAGATGGAACAAGCCC----------------------CAGAAG-ACGA +AGGG-------------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1 +------------------------------------------------------------ +-------AGGGATTA-------------------TGGAAAACAGATGGCAGGTGATGATT +GTGTGGCAAT-TAGACAGGATGAGGAT----------------------TAGAAC-ATG- +---G-------------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1 +------------------------------------------------------------ +------------CTACCTCTTCTTC---------TGCTAGACTGCCATTTAACAG----- +-----------CAGTTGAGTTGATACTACT---------------GGCCTAATTCCATG- +-TGT-------------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_6976_7493_0_0_0_0_0_0_12/1 +----------------------------------------------------------TT +AGGCCAGTAGTATCAACTCAACTGC---------TGTTAAATGGCAGTCTAGCAG----- +-----------AAGAAGAGGTAGTAAT----------------------TAGATC----- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1 +------------------------------------------------------------ +----GTGGAGA---------------------------GAGAGACAGAGACAGAT---CC +ATTCGATTAG-TGAACGGATCC---------------------------TTGGCACTTAT +CTGGGACGATCT------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_7957_8508_2_0_0_2_1_0_2c/1 +------------------------------------------------------------ +----TCCGAAGATCG-------------------TCCCAGATAAGTGCCAAGGAT---CC +GTTCACTACT-CGAATGGATCTGA--C---------------------TCTGTCTCT--- +---------CTC------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1 +------------------------------------------------------------ +----CCAAGTA------------------------TCCCCATAAGTTTCATAGAT---AT +GATGCCCTAA-GCCATGGAGCCAAATC---------------------CTAGGAAAATGT +CTA--------------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_5199_5715_1_0_0_2_0_0_1a/1 +------------------------------------------------------------ +---------TA------------------------TCCCCATAAGTTTCATCGAT---AT +GTTGCCCTAA-GCGATGGAGCCAAATC---------------------CTAGGAAAATGT +CTAAC----AGC------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1 +------------------------------------------------------------ +--------TGC------------------------TCTGAAGAAAATTCCCTG------- +GCCTTCCCTT-GTAGTAAGGCCATATC---------------------TTCCCTAAAAAA +TTAGC----CTGTCT--------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----CAGGATTAA--------CTGCGAATCTTTCTAGCTCCCTTGTTGCCCATACTATA +TGTTTTAATTTATATTTT------------TTCTT +>K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1 +------------------------------------------------------------ +-------------AATAGCAATT------------------------------------- +---------------------------------------------------------TGT +ACAAGCAGTTTTAGGC-TGACTTCGTGGATGCTTCCAGGGCTCTCGTC----------TA +GGATCAA---------------------------C +>K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------TGT +GTTCAGCTGTACTATT-ATGGTTATAGCATTTT-----CCGTGAAATTGACAGATCTAAT +TACTACCTCTTCT---------------------- +>K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------------T +TCTGGGAAGTTCAATT-AGGAATACCACATCCC-----GCAGGGTTAAAAAAGAAAAAAT +CAGTAACAGTACTGG-------------------- +>K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------TCCA-AGCCCTGTCTTATTCTTCTAGGTATGTGGCGCATAGCTCTACA +AGCTCCTTGTACTACTTCAATAA------------ +>K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1 +------------------------------------------------------------ +--------------ACC-CATCT------------------------------------- +---------------------------------------------------------TAT +AGCAAAATCCTTTCCA-AGCCCTGTCTTATTCTTCTAGGTATGTGGCGAATAGCTCTACA +----------------------------------- +>K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------CTACTATTGCTACTAATGGTATAGGTTGCGTTACA +TGTACTACTTACTGCTTTGATAGAGAAGCTTGATG +>K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1 +------------------------------------------------------------ +-------------TCTA-CATAG------------------------------------- +---------------------------------------------------------TCT +CTAAAGGGTTCCTTTG-GTCCTTGTCTTATGTC------CAGAATGCTGGTAGGGCTATA +CATTC------------------------------ +>K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1 +------------------------------------------------------------ +------------------------------------------A-----ATTGTGGGTCAC +AGTC------------TATTATGGGGTACCTGTGTG----GCAGGAAG------------ +-----CAACCACCAC--------------TCTATTTTGTGC--------ATC-------- +----------------------------------- +>K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1 +------------------------------------------------------------ +------------------------------------------GGAGCTAGAACGATTCGC +AGTT------------AATCCTGGCGTGTTAGAAAC----ATCAGAAGGC-------TG- +-TAGACAAATACTG-----------------------------------GGA-------- +----------------------------------- +>K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1 +-------------------------T---------------------------------- +---TTGATTGACTAACTCTGATT-----CACTTTGATCTTGTAGTGCTTGAATGATTCCT +AATG------------CATATTG-TGAGTC------------------------------ +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1 +-------------------------C-----------------------------TTCTT +CTGTTAGTGGTATTACTTCTGTTAGTGCTTTGGTACCTCTAAGGAGTTTACATAATTGCC +TTAC-------------------------------------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1 +------------------------------------------------------------ +-----------------------------------------AGGATTTTACATAATTGCC +TTAC------------TTAAATCCCTGGGT---------------AAATC-------TGA +CTTGCCCAATTCAAT--------------TTCCCCA-------------CTA-------- +----------------------------------- +>K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1 +------------------------------------------------------------ +--------------------------------------ACTTTATATTTATATAATTCAC +TTCT------------CCAATTGTCC---------------------------------- +----CTCATCTCTCC--------------TCCTCCAGGTCTGAAGATCTCGG-------- +----------------------------------- +>K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1 +-------------------------T-----------------------------CTTTG +CCTTGGTTGGAGCAACTCCTAATGGTTGAATTTTTACTACTTTATATTTATATAATTCCC +TTCT-------------------------------------------------------- +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1 +------------------------------------------------------------ +---TCGGAGTCATTGTTGCTATTACCACCATCTTTTGTTCATAGCAGCCCTGTAATATTT +GATT-------------------------------------------------------- +------------------------------------------AACATC-TAA-------- +----------------------------------- +>K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1 +------------------------------------------------------------ +-------------------------------------------------GATGGTTTTAT +AGACATCACT-ATGAAAGCCCTCATCCAAGAAAAAG----TTCAGAAGTA-------CA- +-CATCCCACTAGG----------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1 +------------------------------------------------------------ +-----------------------------------------------------AATTTAT +CAAGAGCCAT-TTAAAAATCTGAAAACAGGAAAATA----TGCAAGAATGAGGGGTGCC- +-CACACTAAT-------------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1 +------------------------------------------------------------ +--------CCCCATATTACTATGCTTTCTGTGGTTAATTTTTGCACTGCCTCTGTTAATT +GTTT-------------------------------------------------------- +------------------------------------------TACATC-ATTAGTGT--- +----------------------------------- +>K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1 +------------------------------------------------------------ +--------------------------------------------AGTTCATGTATCCAGT +GGATATATAG-AAGCAGAAGTTATTCCAGCAGAAAC---------------AGGGGCTG- +-AAACAGCATAT------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1 +-------------------ATTGTAC-----------------------------ACATT +TAGAATGAAAAGTTATCCTGGTA-------------------GCAGTTCATGTAGCCAGT +GGATATATAG-AAGCAGA------------------------------------------ +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1 +------------------------------------------------------------ +------------------------------------------------------------ +---TATAAAG-ACGCAGAAGTTATTCCAGCATACAC---------------AGGGCAGG- +-AAACAGCATATTTTC-TTTTCAAATTAG-----------------------------CA +G---------------------------------- +>K03455|HIVHXB2CG_4053_4544_2_0_0_2_0_0_52/1 +------------------------------------------------------------ +------------------------------------------------------------ +---TGCTAA---------------------------------------------TTTTA- +-AAAGACAATATTCTG-TTTCCTGCCCTGTTTCTGCTGGAATAACTTCTGCTTCTATATA +T---------------------------------- +>K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1 +------------------------------------------------------------ +---------GC-CTGCAT------------------------------------------ +---------G-GAATGGATGACCCGGAGAGAGA--------------------------- +------AGTGTTA-----------------GAGTGGAGGTTTGAGAGCCACCTAGCAATT +C------A--------------------------- +>K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1 +------------------------------------------------------------ +---------GTACTTTCT------------------------------------------ +---------A-TAGTGAATAGAGTTAGGCAGGT--------------------------- +------ATATTCA-----------------CCATTATCGTTTGAGACCCACCTCCCAACC +C---------------------------------- +>K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1 +------------------------------------------------------------ +-------CAAC-CTATACCAA--------------------------------------- +---TAG-TAG-CAATAGTAGCATTAGTAGTAGC--------------------------- +------AATAATA-----------------ATAGCAATAGTTGAGTGGTCCA-------- +----------------------------------- +>K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1 +----------------AGTAAGTAGT-----------------------------ACCTG +TAAC--GCAAC-CTATACCAA--------------------------------------- +---TAG-TAG-CAATAGTAGCATTAGTAGTAGC--------------------------- +------ACTAATA-----------------AT---------------------------- +----------------------------------- +>K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1 +------------------------------------------------------------ +---------CACCCATCC------------------------------------------ +---------A-AAGGAATTGAGGTTCTTTCTGA--------------------------- +------TGTTTTT-----------------TGTCTGGTGTGGTAAGTCCCCACCTCGACA +G---------------------------------- +>K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1 +ACAGTAATTGGAGAGCAATGGCTAGT-----------------------------GATTT +TAACCTGCCAC-CTGTAGTAG--------------------------------------- +---CAA-AAG-AAATAGTAGCCCG------------------------------------ +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1 +------------------------------------------------------------ +-------------TATGGTAC--------------------------------------- +---CAGTTAG-AGAAAGAACCCCTAGTAGGAGC--------------------------- +------AGAAACC-----------------TTCTATGTAGATGGGGCAGCTA-----ACA +G---------------------------------- +>K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1 +CT---------------------------------------------------------- +------------TTATATTTT--------------------------------------- +---TTCTT---------ACCCCCTGGCCTTAAC--------------------------- +------CGAATTT-----------------TTTCCCATCGATCTAATTCTCC-----CCC +GC--TTAA--------------------------- +>K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1 +------------------------------------------------------------ +---ACAGTAGAAAAATTCCCC--------------------------------------- +---TCCACCA-TTAAAACTGTGGTTACAATATC--------------------------- +-----TGGGTCCC-----------------CTCCTGAGGATTGGT--------------- +----------------------------------- +>K03455|HIVHXB2CG_6865_7379_1_0_0_0_0_1_4d/1 +------------------------------------------------------------ +---ACAGTAGAAAAATTCCCC--------------------------------------- +---TCCACAA-TTAAAACTGTGGTTACAATTTC--------------------------- +-----TGGGTCCC-----------------CTCCTGAGGATTGCT--------------- +----------------------------------- +>K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1 +--------ATC----------CTCAT-----------------------------GCATC +TGTTCTACCATGTCATTTTTC--------------------------------------- +---CACATGT-TAAAATTTTCTGTCACATTTAC--------------------------- +------CAATACT----------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_6480_6947_0_0_0_2_0_0_32/1 +--------TT-----------------------------------------------GGT +AAATGTGACAGAAAATTTTAA--------------------------------------- +---CATGTGG-AAAAATGACATGGTAGA---AC--------------------------- +------AGATGCA-------------------------------------TGAGGATATA +A---------------------------------- +>K03455|HIVHXB2CG_6482_6962_0_0_0_1_0_0_35/1 +---------------------------------------------------------GGT +AAATGTGACAGAAAATTTTAA--------------------------------------- +---CATGTGG-AAAAATGACATGGTAGA---AC--------------------------- +------AGATGCA-------------------------------------TGAGGATATA +AT-----C--------------------------- +>K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1 +------------------------------------------------------------ +------------------------------------------------------------ +---------T-TAAAATTTTCTGTCACATTTAC--------------------------- +------CAATACTA---------------CTTCTTGTGGGTTGGGGTCTGTGGGTACACA +GGCATGTG--------------------------- +>K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1 +TCCCTGTTCG-----------------------------------------------GGC +GCCACTGCTAGAGATTTTCCA--------------------------------------- +---CACTGAC-TAAAAGGGTCTGAGGGA---TCT-------------------------- +----CTAGTTACC----------------------------------------------- +----------------------------------- +>K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1 +----AAGTGCAAGCAATCTGATTCAC-----------------------------CCGAT +TTCTTCCAATTATGATGACAGGTGT----------------------------AGGTCCT +ACTAATACAG-T------------------------------------------------ +------------------------------------------------------------ +----------------------------------- +>K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1 +------------------------------------------------------------ +------------------------------------------------------------ +--ATAACCACAGAAAGCATAGTAATATGGGGAAAGA----CTCCTAAATTTAAACTGCC- +-CATACAAAAGGAAAC-------------------------------------------- +---------------------------AT------ +>K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1 +TTT--------------------------------------------------------- +------------------------------------------------------------ +-----------TTCAGTTCGCTTAGATGAAGACTTC----AGGCAGTATACTGCATTTAC +CATACCTAGTATAAAC-AATGAG------------------------------------- +-----------------------------------