Mercurial > repos > dfornika > match_plasmid_to_reference

annotate test-data/CP008719.gbk @ 4:826ddf832bef draft default tip

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 13:52:40 -0500
parents 8bb674372911
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8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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1 LOCUS CP008719 2101 bp DNA circular BCT 05-JAN-2016
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2 DEFINITION Escherichia coli strain ST648 plasmid pEC648_5, complete sequence.
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3 ACCESSION CP008719
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4 VERSION CP008719.1
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5 DBLINK BioProject: PRJNA248607
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6 BioSample: SAMN02800875
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7 KEYWORDS .
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8 SOURCE Escherichia coli
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9 ORGANISM Escherichia coli
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10 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
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11 Enterobacteriaceae; Escherichia.
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12 REFERENCE 1 (bases 1 to 2101)
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13 AUTHORS Gao,Z.
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14 TITLE Complete Genome Sequence of Multiple Antibiotic Resistant
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15 Escherichia coli Isolated from Pleural Effusion of Patients with
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16 Empyema Thoracis
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17 JOURNAL Unpublished
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18 REFERENCE 2 (bases 1 to 2101)
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19 AUTHORS Gao,Z.
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20 TITLE Direct Submission
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21 JOURNAL Submitted (09-JUN-2014) Department of Respiratory and Critical care
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22 medicine, Peking University People's hospital, Xizhimen South
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23 Street, Beijing, Beijing 100101, China
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24 COMMENT Annotation was added by the NCBI Prokaryotic Genome Annotation
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25 Pipeline (released 2013). Information about the Pipeline can be
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26 found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
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27
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28 ##Genome-Assembly-Data-START##
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29 Assembly Method :: Newbler v. 2.3; Consed
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30 Genome Coverage :: 40x; 350x
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31 Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000
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32 ##Genome-Assembly-Data-END##
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33
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34 ##Genome-Annotation-Data-START##
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35 Annotation Provider :: NCBI
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36 Annotation Date :: 06/13/2014 09:01:46
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37 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation
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38 Pipeline
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39 Annotation Method :: Best-placed reference protein set;
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40 GeneMarkS+
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41 Annotation Software revision :: 2.6 (rev. 437579)
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42 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;
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43 repeat_region
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44 Genes :: 4,807
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45 CDS :: 4,578
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46 Pseudo Genes :: 132
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47 CRISPR Arrays :: 2
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48 rRNAs :: 21 (5S, 16S, 23S)
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49 tRNAs :: 72
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50 ncRNA :: 4
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51 Frameshifted Genes :: 116
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52 ##Genome-Annotation-Data-END##
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53 FEATURES Location/Qualifiers
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54 source 1..2101
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55 /organism="Escherichia coli"
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56 /mol_type="genomic DNA"
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57 /strain="ST648"
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58 /db_xref="taxon:562"
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59 /plasmid="pEC648_5"
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60 gene join(1882..2101,1..47)
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61 /locus_tag="FH07_00765"
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62 CDS join(1882..2101,1..47)
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63 /locus_tag="FH07_00765"
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64 /inference="EXISTENCE: similar to AA
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65 sequence:RefSeq:WP_001024536.1"
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66 /note="Derived by automated computational analysis using
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67 gene prediction method: Protein Homology."
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68 /codon_start=1
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69 /transl_table=11
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70 /product="hypothetical protein"
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71 /protein_id="ALV71377.1"
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72 /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTF
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73 GFHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
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74 gene 913..1878
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75 /locus_tag="FH07_00775"
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76 CDS 913..1878
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77 /locus_tag="FH07_00775"
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78 /inference="EXISTENCE: similar to AA
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79 sequence:RefSeq:WP_012421200.1"
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80 /note="Derived by automated computational analysis using
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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81 gene prediction method: Protein Homology."
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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82 /codon_start=1
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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83 /transl_table=11
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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84 /product="Replication protein"
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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85 /protein_id="ALV71376.1"
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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86 /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRM
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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87 ASCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIV
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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88 VDYPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRG
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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89 KDGSAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGE
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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90 VVANVAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQL
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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91 DRETNEDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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92 ORIGIN
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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93 1 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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94 61 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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95 121 cctgcattat cctcagcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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96 181 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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97 241 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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98 301 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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99 361 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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100 421 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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101 481 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttgg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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102 541 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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103 601 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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104 661 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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105 721 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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106 781 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctggt gacatgtact
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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107 841 ggctcgcaat gcacaggtac gtgatgaata taccacatca aatcacagcc tgcccagatc
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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108 901 ggagcaggct taatgtcaga agataaattc ctttcggact acagcccccg tgatgcagtt
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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diff changeset
109 961 tgggataccc agcgcacgct taccgattct gtcgggggta tctaccagac tgctgctgaa
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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diff changeset
110 1021 ttcgagcgct atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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diff changeset
111 1081 accatcatgg aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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112 1141 cgtcattgcc ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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113 1201 gctctaccga aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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114 1261 gtcaggaact gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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115 1321 aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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116 1381 gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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117 1441 ccttcttggt ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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118 1501 gattgcttgc gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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119 1561 ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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120 1621 tactccgtta aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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diff changeset
121 1681 cagcttcaca agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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diff changeset
122 1741 gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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123 1801 gggaagcgga cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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124 1861 aaggataaat cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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diff changeset
125 1921 attggtttat tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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126 1981 ttgcttattg atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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127 2041 gatgaattaa ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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128 2101 a
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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129 //
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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130