Mercurial > repos > bgruening > rnaz_select_seqs
changeset 0:5f31010cdd15 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
| author | bgruening |
|---|---|
| date | Wed, 30 Jan 2019 03:58:28 -0500 |
| parents | |
| children | |
| files | AnnotateRNAz.py rnazSelectSeqs.xml test-data/Annotation.bed test-data/IRE.aln test-data/miRNA.maf test-data/notsorandom.aln test-data/randomize.aln test-data/snoRNA.aln test-data/tRNA.aln test-data/tRNA.aln.window test-data/tRNA.maf test-data/tRNA.maf.window test-data/tRNA.rnaz test-data/tRNA.rnaz.clustered test-data/tRNA.rnaz.clustered.annotated.bed test-data/tRNA.rnaz.clustered.annotated.rnaz test-data/tRNA_selected.aln test-data/unknown.aln test-data/unknown.aln.window test-data/unknown.rnaz test-data/unknown.rnaz.clustered test-data/unknown.rnaz.clustered.annotated.bed test-data/unknown.rnaz.clustered.annotated.rnaz |
| diffstat | 23 files changed, 1596 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotateRNAz.py Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,205 @@ +# AnnotateRnaz.py --- +# +# Filename: AnnotateRnaz.py +# Description: +# Author: Joerg Fallmann +# Maintainer: +# Created: Sat Jan 26 12:45:25 2019 (+0100) +# Version: +# Package-Requires: () +# Last-Updated: Tue Jan 29 13:52:57 2019 (+0100) +# By: Joerg Fallmann +# Update #: 188 +# URL: +# Doc URL: +# Keywords: +# Compatibility: +# +# + +# Commentary: +# This script is a replacement for rnazAnnotate.pl +# rnazAnnotate can not handle the output from version 2 adequatly +# This script uses the bedtools API to fast intersect an annotation Bed +# with output from RNAz + +# Change Log: +# +# +# +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or (at +# your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>. +# +# + +# Code: + +#!/usr/bin/env python3 + +import sys +import glob +import argparse +from io import StringIO +import gzip +import traceback as tb +import pybedtools +import re +import tempfile + +def parseargs(): + parser = argparse.ArgumentParser(description='Intersect RNAz output with Annotation from BED') + parser.add_argument("-b", "--bed", type=str, help='Annotation BED file') + parser.add_argument("-i", "--input", type=str, help='RNAz output') + parser.add_argument("-o", "--bedout", type=str, help='Annotation BED output') + parser.add_argument("-r", "--rnazout", type=str, help='Annotation rnaz output') + return parser.parse_args() + +def annotate(bed, input, bedout, rnazout): + try: + + pybedtools.set_tempdir('.') # Make sure we do not write somewhere we are not supposed to + anno = pybedtools.BedTool(bed) + rnaz=readrnaz(input) + tmpbed = pybedtools.BedTool(rnaztobed(rnaz), from_string=True) + + intersection = tmpbed.intersect(anno,wa=True,wb=True,s=True) # intersect strand specific, keep all info on a and b files + + bedtornaz(intersection, rnaz, bedout, rnazout) + + return 1 + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + +def readin(file): + try: + if '.gz' in file: + f = gzip.open(file,'rt') + else: + f = open(file,'rt') + return f + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + +def readrnaz(rnaz): + try: + toparse = readin(rnaz) + tointersect = {} + header = [] + for line in toparse: + if '#' in line[0]: + tointersect['header']=line.strip() + line = re.sub('^#','',line) + cont = line.strip().split('\t') + foi = cont.index('seqID') # need to find which column contains seqID + sf = cont.index('start') # need to find which column contains start + ef = cont.index('end') # need to find which column contains end + if 'strand' in cont:# need to find which column contains strand + df = cont.index('strand') + else: + df = None + else: + content = line.strip().split('\t') + newid=re.split('\.|\,|\s|\\|\/|\_', content[foi])[1] # I can only hope that we have species.chromosome.whatever as annotation in aln or maf, if not this is hardly parseable + if df: + longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', content[df]]) + tointersect[longid] = content + else: + longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '+']) + tointersect[longid] = content + longid = '_'.join([newid, content[sf], content[ef], 'RNAzresult', '0', '-']) + tointersect[longid] = content + + return tointersect + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + + +def rnaztobed(rnaz): + try: + tmpbed = [] + for key in rnaz: + if key != 'header': + tmpbed.append('\t'.join(key.split('_'))) + + return '\n'.join(tmpbed) + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + +def bedtornaz(bed, rnaz, bedout, rnazout): + try: + b = open(bedout,'w') + r = open(rnazout,'w') + + annotatedbed=[] + annotatedrnaz=[] + annotatedrnaz.append(str.join('\t',[rnaz['header'],'Annotation'])) + for line in open(bed.fn): + out = line.strip().split("\t") + annotatedbed.append(str.join('\t',out[0:3]+out[9:10]+out[4:6])) + key = str.join('_',out[0:6]) + annotatedrnaz.append(str.join('\t',rnaz[key]+out[9:10])) + + print(str.join('\n', annotatedbed),file=b) + print(str.join('\n', annotatedrnaz),file=r) + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + + +def closefile(file): + try: + file.close() + + except Exception as err: + exc_type, exc_value, exc_tb = sys.exc_info() + tbe = tb.TracebackException( + exc_type, exc_value, exc_tb, + ) + print(''.join(tbe.format()),file=sys.stderr) + + + + +#################### +#### MAIN #### +#################### +if __name__ == '__main__': + args=parseargs() + annotate(args.bed, args.input, args.bedout, args.rnazout) +###################################################################### +# AnnotateRnaz.py ends here
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnazSelectSeqs.xml Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,85 @@ +<tool id="rnaz_select_seqs" name="RNAz Select Seqs" version="2.1"> + <requirements> + <requirement type="package" version="2.1">rnaz</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + rnazSelectSeqs.pl + --num-seqs $numseqs + --num-samples $numsamples + --opt-id $optid + --max-id $maxid + #if $noref: + --no-ref $noref + #end if + '$input' + > '$output' + ]]></command> + <inputs> + <param format="txt" name="input" type="data" label="Input Alignment File" /> + <param argument="--num-seqs" name="numseqs" type="integer" value="6" label="Number of sequences in the output alignment(s). (Default:6)" /> + <param argument="--num-samples" name="numsamples" type="integer" value="1" label="Number of output alignments (Default: 1)" /> + <param argument="--opt-id" name="optid" type="integer" value="80" + label="The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80)" /> + <param argument="--max-id" name="maxid" type="integer" value="99" + label="Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences areremoved)" /> + <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue="" + label="By default the first sequence (=reference sequence) is always present in the output alignment(s). If you do not care having it removed, set this flag." /> + </inputs> + <outputs> + <data name="output" format="txt" /> + </outputs> + <tests> + <test> + <param name="input" value="tRNA.aln"/> + <param name="numseqs" value="1"/> + <output name="output" file="tRNA_selected.aln"/> + </test> + </tests> + <help><![CDATA[ RNAz up to version 1.0 was limited to alignments + of at most 6 sequences. As of version 2.0, there is no limit on + the maximum number of sequences. However, under some cirumstances + (e.g. for very large alignments) it is still useful to reduce the + number of sequences prior to running RNAz. You can select an + optimal subset of sequences using rnazSelectSeqs.pl before you + put it into RNAz: + + Usage: + rnazSelectSeqs.pl [options] [file] + + Options: + -n N, --num-seqs=N + Number of sequences in the output alignment(s). (Default:6) + + -a N, --num-samples=N + Number of output alignments (Default: 1) + + -i X, --opt-id=X + The resulting alignment(s) is (are) optimized for this value of + mean pairwise identity (in percent, default: 80) + + --max-id=X + Sequences from pairs with pairwise identity higher than X% are + removed (default: 99, i.e. only almost identical sequences are + removed) + + -x, --no-reference + By default the first sequence (=reference sequence) is always + present in the output alignment(s). If you do not care having it + removed, set this flag. + + -v, --version + Prints version information and exits. + + -h, --help + Prints a short help message and exits. + + --man Prints a detailed manual page and exits. + + + ]]></help> + + <citations> + <citation type="doi">10.1142/9789814295291_0009</citation> + </citations> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Annotation.bed Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,3 @@ +chr1 10 500 WhoKnows 0 + +chr1 90 900 WhoKnows2 0 - +chr4 1352400 1352700 tRNAContainer 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/IRE.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,17 @@ +CLUSTAL W(1.81) multiple sequence alignment + +393758_ENSMUSG00000025993_MOUSE_9754_9818/1-65 TAAGGCTTTGGCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAAAGAAGACAAAA +393758_SINFRUG00000122977_FUGU_3358_3422/1-65 TAAAAGCATTTCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAGGGGAGGAAAAC +393758_ENSRNOG00000003872_RAT_9703_9767/1-65 TAAGGCTTTAGCTTTCCAACTTCAGCTACAGTGTTAGCTAAGTTTGGAAAGAAGACATAA +393758_ENSDARG00000000241_ZEBRAFISH_9812_9874/1-65 -AAGGTTATTTCTCTCCGACTTCAGCTACAGTGATAGCTAAGTTTGGAGAGGAGAGAAGG + ** * ** *** *************** ************** * ** * + + +393758_ENSMUSG00000025993_MOUSE_9754_9818/1-65 AGAAG +393758_SINFRUG00000122977_FUGU_3358_3422/1-65 GGGAG +393758_ENSRNOG00000003872_RAT_9703_9767/1-65 AGAAG +393758_ENSDARG00000000241_ZEBRAFISH_9812_9874/1-65 GAGA- + * + + +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/miRNA.maf Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,15 @@ +##maf version=1 +a score=0 +s hg16.chr11 64433968 110 - 134482954 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s panTro1.chr9 65642342 110 - 136640551 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s baboon.1 349423 110 - 497844 GCTGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s rheMac1.SCAFFOLD120618 41607 110 - 48031 GCTGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s marmoset.1 290457 110 - 415896 GCCGAGACCGAGTGCACAAGGCTCTGACCTATGAGTTGACAGCCAGTGCTCTGGTCTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s galago.1 408904 110 - 511463 GCCAAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCATCTCCCCTCTGGCTGCCAATTACATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s rn3.chr1 58923176 110 + 268121971 GTCAAGATGGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTACTCTGATCTCGCCTCTGGCTGCCAGTTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s mm6.chr19 54573156 110 + 60626890 GCCAAGATGGCGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTACTCTTTTCTCTCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCACCTCAATGCCAGC +s canFam1.chr18 3536304 110 + 66173745 GCTGAGATCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCATCTCTCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s rfbat.1 111329 110 - 223543 GCCGAGACCGAGTGCACAGGGCTCTGACCTATGAATTGACAGCCAGTGCTCTCGTGTCCCCTCTGGCTGCCAATTCCATAGGTCACAGGTATGTTCGCCTCAATGCCAGC +s tenrec.32 717 110 - 2965 GCCCAGACCGAGTGCACAAGTCTCTGACCTATGAATTGACAGCCAGTGCCTTGGGCTCCCCTCTGGCTGCCAATACCATAGGTCACAGGTATGTTTGCCTCCATGCCAGC +s danRer2.chr10 14345337 107 + 36600514 GGTTAAGTCTAGGACACAGGGTGATGACCTATGAATTGACAGCCAGTGTTTGCAGT--CCAGCTGCCTGTCAGTTCTGTAGGCCACTGCCCTGTTTATCCTACTAAACA- +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/notsorandom.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,13 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +panTro1.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +canFam1.chr9 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +mm5.chr2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +rn3.chr3 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +galGal2.chr17 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +fr1.chrUn AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +danRer1.chr11 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/randomize.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,12 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +hg17.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +panTro1.chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +canFam1.chr9 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +mm5.chr2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +rn3.chr3 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +galGal2.chr17 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +fr1.chrUn AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +danRer1.chr11 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + ************************************************************ \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snoRNA.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,36 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 GTACCCTCGAGCACACCAGACTTGCAGAAAAAGCATACTCCAGAGGAAGCTGAGGCATGC +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 GTACCCTAGAGCACACCAGACTTGCAGAGAAAGCAGACAACAGAGGAAGCTGAGGCATGC +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 --------GGGCACAACAAGGTTGC--AGAAAGCAT-C-CCAAAGGATGAAAAGGCGTGA +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 -TACCCTCGAGCACACCAGACTTGCAGAAAAAGCATACTCCAGAGGAAGCTGAGGCATGC + * ***** ** **** * ****** * ** **** * **** ** + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 CTGCTCGAGAGCCAGCTGTTCCATGTGCAATTTTCCTCTGATAGTTTCTGGTCACTGTTG +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CTGCTCGAGAGGCAGCAGGCCCATGTGCAATTTTCCTCTGATAGGGCCTGGGTACTGTTG +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 CTTCCAGAGGTCTGGGAATTCCACGTGCGATGTT-CTTTGA-A---CAAACACCTGCTTT +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 CTGCTCGAGAGCCAGCGGTTCCATGTGCAATTTTCCTCTGATAAATCCTGGGTACTGTTG + ** * *** * *** **** ** ** ** *** * ** + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 CCACGGTGATAATGACTGGGCTATGTCATTATCTATCCGCCAACAGTAAGAGAAGCTTTG +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CCACGGTGATAATGGCTGTGCCGTGTCATTGTCGATCCACCAACAGTCAGAGAAGCTTGG +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 CCACGGTGGCGATGGCCTTGTTCTGTAGCCATCGCATTTCTTGAGGCAGGTAGAAAAAAA +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 CCACGGTGATAATGACTGTGCCGTGTCATTGTCGATCCACCAACAGTCAGAGAAGCTTTG + ******** *** * * *** ** * * * * + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 CAGTCGAGATATTGTTT--AGCAGATGGAGTGTTTTCTGTTGAACACTAAGTACTGCCAC +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 CAGTCAAGATATTGTTT--AGCAGACGGAGCGGTTTCTGTTGGACACTAAGTACTGCCAC +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 CAG-CATGATATTGTTTGAAGCGGGGAGAGCTGTTCCCGTCAGACACTGTCCGCTGTCAC +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 CAGTCAAGATATTGTTT--AGCAGACGGAGCGGTTTCTGTTGGACACTAAGTGCTGCTAC + *** * ********** *** * *** ** * ** ***** *** ** + + +470004_ENSG00000182512_HUMAN_8267_8506/1-243 AA- +470004_ENSMUSG00000021102_MOUSE_8376_8616/1-243 AAA +470004_SINFRUG00000145950_FUGU_5916_6140/1-243 AGC +470004_ENSRNOG00000004206_RAT_8331_8570/1-243 AAG + *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,14 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC +sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC + ** * * ** ** **** ** **** * *** ***** **** * ****** * + +sacCer1 CCCCTACAGGGCT +sacBay CCCCTACAGGGCT +sacKlu CCCCTACAGGGCT +sacCas CTCCCCTGGAGCA + * ** * **
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.aln.window Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,30 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1/0-73 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacBay/0-73 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC +sacKlu/0-73 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC +sacCas/0-73 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC + + +sacCer1/0-73 CCCCTACAGGGCT +sacBay/0-73 CCCCTACAGGGCT +sacKlu/0-73 CCCCTACAGGGCT +sacCas/0-73 CTCCCCTGGAGCA + + +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1_rev/0-73 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATT +sacBay_rev/0-73 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATT +sacKlu_rev/0-73 AGCCCTGTAGGGGGCTCGAACCCCTAGCCTTATGATTAAGAGTCATACGCGCTACCGATT +sacCas_rev/0-73 TGCTCCAGGGGAGGTTCGAACTCTCGACCTTCAGATTATGAGACTGACGCTCTTCCGACT + + +sacCer1_rev/0-73 GCGCCAACAAGGC +sacBay_rev/0-73 GCGCCAACAAGGC +sacKlu_rev/0-73 GCGCCAACAAGGC +sacCas_rev/0-73 GAGCTACTGAAGC + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.maf Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,6 @@ +##maf version=1 +a score=119673.000000 +s sacCer1.chr4 1352453 73 - 1531914 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacBay.contig_465 14962 73 - 57401 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacKlu.Contig1694 137 73 + 4878 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGCCCCCTACAGGGCT +s sacCas.Contig128 258 73 + 663 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAACCTCCCCTGGAGCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.maf.window Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,12 @@ +a score=0 +s sacCer1.chr4 1352453 73 - 1531914 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacBay.contig_465 14962 73 - 57401 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGCCCCCTACAGGGCT +s sacKlu.Contig1694 137 73 + 4878 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGCCCCCTACAGGGCT +s sacCas.Contig128 258 73 + 663 GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAACCTCCCCTGGAGCA + +a score=0 +s sacCer1.chr4 1352453 73 + 1531914 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC +s sacBay.contig_465 14962 73 + 57401 AGCCCTGTAGGGGGCTCGAACCCCTAACCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC +s sacKlu.Contig1694 137 73 - 4878 AGCCCTGTAGGGGGCTCGAACCCCTAGCCTTATGATTAAGAGTCATACGCGCTACCGATTGCGCCAACAAGGC +s sacCas.Contig128 258 73 - 663 TGCTCCAGGGGAGGTTCGAACTCTCGACCTTCAGATTATGAGACTGACGCTCTTCCGACTGAGCTACTGAAGC +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,156 @@ + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: forward + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -27.20 + Consensus MFE: -26.50 + Energy contribution: -23.63 + Covariance contribution: -2.87 + Combinations/Pair: 1.43 + Mean z-score: -1.82 + Structure conservation index: 0.97 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.15 + SVM RNA-class probability: 0.984068 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 - 1531914 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacBay.contig_465 14962 73 - 57401 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacKlu.Contig1694 137 73 + 4878 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R) +>sacCas.Contig128 258 73 + 663 +GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA +(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R) +>consensus +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87) + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: reverse + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -24.15 + Consensus MFE: -26.66 + Energy contribution: -23.35 + Covariance contribution: -3.31 + Combinations/Pair: 1.48 + Mean z-score: -1.79 + Structure conservation index: 1.10 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.58 + SVM RNA-class probability: 0.992927 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 + 1531914 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacBay.contig_465 14962 73 + 57401 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacKlu.Contig1694 137 73 - 4878 +AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R) +>sacCas.Contig128 258 73 - 663 +UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC +.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R) +>consensus +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31) + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: forward + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -24.15 + Consensus MFE: -26.66 + Energy contribution: -23.35 + Covariance contribution: -3.31 + Combinations/Pair: 1.48 + Mean z-score: -1.79 + Structure conservation index: 1.10 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.58 + SVM RNA-class probability: 0.992927 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 + 1531914 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacBay.contig_465 14962 73 + 57401 +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) +>sacKlu.Contig1694 137 73 - 4878 +AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R) +>sacCas.Contig128 258 73 - 663 +UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC +.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R) +>consensus +AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC +.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31) + +############################ RNAz 2.1 ############################## + + Sequences: 4 + Columns: 73 + Reading direction: reverse + Mean pairwise identity: 80.82 + Shannon entropy: 0.31118 + G+C content: 0.54795 + Mean single sequence MFE: -27.20 + Consensus MFE: -26.50 + Energy contribution: -23.63 + Covariance contribution: -2.87 + Combinations/Pair: 1.43 + Mean z-score: -1.82 + Structure conservation index: 0.97 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: 2.15 + SVM RNA-class probability: 0.984068 + Prediction: RNA + +###################################################################### + +>sacCer1.chr4 1352453 73 - 1531914 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacBay.contig_465 14962 73 - 57401 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) +>sacKlu.Contig1694 137 73 + 4878 +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R) +>sacCas.Contig128 258 73 + 663 +GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA +(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R) +>consensus +GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,2 @@ +# locusID seqID start end maxN maxIdentity maxP minZ +locus1 sacCer1.chr4 1352453 1352526 4 80.82 0.992927 -1.82
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered.annotated.bed Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,1 @@ +chr4 1352453 1352526 tRNAContainer 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz.clustered.annotated.rnaz Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,2 @@ +# locusID seqID start end maxN maxIdentity maxP minZ Annotation +locus1 sacCer1.chr4 1352453 1352526 4 80.82 0.992927 -1.82 tRNAContainer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_selected.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,9 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC + + +sacCer1 CCCCTACAGGGCT + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.aln Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,72 @@ +CLUSTAL W (1.83) multiple sequence alignment + + +hg17.chr1 TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGT +panTro1.chr1 TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTTGT +canFam1.chr9 TACAGCAGCTGCTATTGCTTACGGCTTGGATAAGAGGGAAGGGGAGAAGAATATCCTGGT +mm5.chr2 TACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTTGT +rn3.chr3 AACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTCGT +galGal2.chr17 AACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGT +fr1.chrUn AACCGCTGCTGCCATTGCTTATGGTCTGGACAAAAAGGACGGCGAGAAGAACATCCTCGT +danRer1.chr11 TACGGCGGCTGCCATTGCATACGGTCTGGACAAGAGGGACGGAGAGAAAAACATCCTGGT + ** ** ***** ***** ** ** **** ** * ** ** ** ** ** ***** ** + +hg17.chr1 GTTTGACCTGGGTGGTGGAACCTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +panTro1.chr1 GTTTGACCTGGGTGGTGGAACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +canFam1.chr9 GTTTGACCTGGGTGGTGGAACTTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +mm5.chr2 GTTTGACCTGGGTGGCGGCACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +rn3.chr3 GTTTGACCTGGGTGGTGGAACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +galGal2.chr17 ATTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTT +fr1.chrUn GTTCGATCTCGGTGGCGGCACCTTCGACGTGTCTCTGCTCACCATTGACAACGGTGTGTT +danRer1.chr11 GTTCGATCTGGGTGGTGGCACCTTTGACGTGTCTCTGCTGACCATCGATAACGGCGTGTT + ** ** ** ***** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** + +hg17.chr1 CAAAGTTGTGGCCACTAATGGAGATACTTATCTGGGTGGAGAAGACTTTGACCAGCGTGT +panTro1.chr1 CAAAGTTGTGGTCACTAATGGAGATACTCATCTGGGTGGAAAAGACTTTGACCAGCATGT +canFam1.chr9 TGAAGTTGTGGCTACTAATGGAGATACTCACCTGGGTGGAGAAGACTTTGACCAACGTGT +mm5.chr2 TGAAGTGGTGGCCACTAATGGAGATACTCACCTGGGTGGGGAAGACTTTGATCAGCGGGT +rn3.chr3 TGAAGTGGTGGCCACTAATGGAGACACTCATCTGGGTGGGGAAGACTTTGATCAGCGGGT +galGal2.chr17 TGAAGTTGTGGCTACAAATGGTGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGT +fr1.chrUn TGAAGTGGTGGCCACCAATGGTGACACTCACCTTGGAGGTGAAGACTTTGATCAGCGCGT +danRer1.chr11 TGAAGTGGTGGCCACAAACGGAGACACTCACCTGGGCGGAGAAGACTTCGACCAGCGCGT + **** **** ** ** ** ** ** * ** ** ** ******* ** ** * ** + +hg17.chr1 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCAGGAAAGACAA +panTro1.chr1 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCGGGAAAGACAA +canFam1.chr9 CATGGAACACTTCATCAAACTCTACAAAAAGAAGACTGGCAAAGATGTTAGGAAAGACAA +mm5.chr2 CATGGAACACTTCATCAAGTTGTACAAAAAGAAAACTGGTAAAGATGTTAGGAAAGACAA +rn3.chr3 CATGGAGCACTTCATCAAGCTGTACAAAAAGAAGACTGGGAAAGATGTCAGAAAGGACAA +galGal2.chr17 TATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAAAAGATGTCAGGAAGGATAA +fr1.chrUn CATGGAACACTTCATCAAGCTATACAAGAAGAAGACTGGCAAAGACGTGCGCAAAGACAA +danRer1.chr11 CATGGAGCACTTCATCAAGCTGTACAAGAAGAAGACGGGCAAAGATGTGCGCAAAGACAA + ***** *********** * ***** ***** ** ** ***** ** * ** ** ** + +hg17.chr1 TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA +panTro1.chr1 TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA +canFam1.chr9 CAGAGCTGTGCAGAAACTCCGGCGGGAGGTAGAAAAAGCCAAACGGGCCCTGTCTTCTCA +mm5.chr2 CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCTAAGAGAGCCTTGTCTTCTCA +rn3.chr3 CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCCAAGAGAGCCCTGTCTTCTCA +galGal2.chr17 CAGAGCTGTACAGAAACTAAGACGGGAAGTAGAGAAAGCGAAGCGGGCCCTGTCATCCCA +fr1.chrUn CCGTGCTGTCCAGAAGCTGCGTCGTGAGGTTGAGAAGGCAAAGAGGGCCCTGTCTGCCCA +danRer1.chr11 CCGCGCCGTGCAGAAGCTGCGCAGAGAGGTGGAGAAGGCTAAGAGAGCCCTGTCTGCCCA + * ** ** ***** ** * * * ** ** ** ** ** * *** **** * ** + +hg17.chr1 ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA +panTro1.chr1 ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA +canFam1.chr9 ACATCAAGCAAG----AATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTCTCTGAGA +mm5.chr2 GCATCAAGCAAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA +rn3.chr3 GCATCAAGCGAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA +galGal2.chr17 GCACCAAGCTAG----AATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGA +fr1.chrUn GCACCAGGCCCG----CATTGAGATCGAGTCTTTCTTTGAGGGAGAAGATTTCTCCGAGA +danRer1.chr11 GCATCAGGCCCG----CATCGAGATCGAGTCCTTCTTTGAGGGAGAAGATTTCTCTGAGA + ** ** ** * ** ** ** ** ** ** * ** ***** ** ** ** **** + +hg17.chr1 CCCTGACTCAGGCCAAATTTGAAGAGCTCAA +panTro1.chr1 CCCTGACTCAGGCCAAATTTGAAGAGCTCAA +canFam1.chr9 CTCTGACTCGGGCCAAATTTGAAGAGCTAAA +mm5.chr2 CCCTTACTCGGGCCAAATTTGAAGAGCTGAA +rn3.chr3 CCCTTACTCGGGCCAAATTTGAAGAGCTGAA +galGal2.chr17 CGCTTACTCGTGCCAAATTTGAAGAACTGAA +fr1.chrUn CACTGACCCGTGCCAAATTTGAAGAGCTTAA +danRer1.chr11 CTCTCACCAGAGCCAAGTTTGAAGAGCTCAA + * ** ** ***** ******** ** **
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.aln.window Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,152 @@ +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1/0-120 TACAGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGT +canFam1.chr9/0-120 TACAGCAGCTGCTATTGCTTACGGCTTGGATAAGAGGGAAGGGGAGAAGAATATCCTGGT +mm5.chr2/0-120 TACAGCAGCTGCTATTGCATATGGCCTGGATAAGAGAGAGGGAGAGAAGAACATCCTTGT +galGal2.chr17/0-120 AACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGT +fr1.chrUn/0-120 AACCGCTGCTGCCATTGCTTATGGTCTGGACAAAAAGGACGGCGAGAAGAACATCCTCGT +danRer1.chr11/0-120 TACGGCGGCTGCCATTGCATACGGTCTGGACAAGAGGGACGGAGAGAAAAACATCCTGGT + + +hg17.chr1/0-120 GTTTGACCTGGGTGGTGGAACCTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +canFam1.chr9/0-120 GTTTGACCTGGGTGGTGGAACTTTTGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +mm5.chr2/0-120 GTTTGACCTGGGTGGCGGCACCTTCGATGTGTCTCTTCTCACCATTGACAATGGTGTCTT +galGal2.chr17/0-120 ATTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTT +fr1.chrUn/0-120 GTTCGATCTCGGTGGCGGCACCTTCGACGTGTCTCTGCTCACCATTGACAACGGTGTGTT +danRer1.chr11/0-120 GTTCGATCTGGGTGGTGGCACCTTTGACGTGTCTCTGCTGACCATCGATAACGGCGTGTT + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1_rev/0-120 AAGACACCATTGTCAATGGTGAGAAGAGACACATCAAAGGTTCCACCACCCAGGTCAAAC +canFam1.chr9_rev/0-120 AAGACACCATTGTCAATGGTGAGAAGAGACACATCAAAAGTTCCACCACCCAGGTCAAAC +mm5.chr2_rev/0-120 AAGACACCATTGTCAATGGTGAGAAGAGACACATCGAAGGTGCCGCCACCCAGGTCAAAC +galGal2.chr17_rev/0-120 AAGACTCCGTTGTCAATTGTCAGGAGGGAGACATCAAAAGTTCCACCACCCAGGTCAAAT +fr1.chrUn_rev/0-120 AACACACCGTTGTCAATGGTGAGCAGAGACACGTCGAAGGTGCCGCCACCGAGATCGAAC +danRer1.chr11_rev/0-120 AACACGCCGTTATCGATGGTCAGCAGAGACACGTCAAAGGTGCCACCACCCAGATCGAAC + + +hg17.chr1_rev/0-120 ACCAGGATGTTCTTCTCCCCCTCCCTCTTATCCAGGCCATAAGCAATAGCAGCTGCTGTA +canFam1.chr9_rev/0-120 ACCAGGATATTCTTCTCCCCTTCCCTCTTATCCAAGCCGTAAGCAATAGCAGCTGCTGTA +mm5.chr2_rev/0-120 ACAAGGATGTTCTTCTCTCCCTCTCTCTTATCCAGGCCATATGCAATAGCAGCTGCTGTA +galGal2.chr17_rev/0-120 ACAAGGATGTTCTTTTCACCCTCTCTCTTGTCCAATCCGTATGCAATTGCAGCAGCAGTT +fr1.chrUn_rev/0-120 ACGAGGATGTTCTTCTCGCCGTCCTTTTTGTCCAGACCATAAGCAATGGCAGCAGCGGTT +danRer1.chr11_rev/0-120 ACCAGGATGTTTTTCTCTCCGTCCCTCTTGTCCAGACCGTATGCAATGGCAGCCGCCGTA + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1/120-240 CAAAGTTGTGGCCACTAATGGAGATACTTATCTGGGTGGAGAAGACTTTGACCAGCGTGT +panTro1.chr1/120-240 CAAAGTTGTGGTCACTAATGGAGATACTCATCTGGGTGGAAAAGACTTTGACCAGCATGT +rn3.chr3/120-240 TGAAGTGGTGGCCACTAATGGAGACACTCATCTGGGTGGGGAAGACTTTGATCAGCGGGT +galGal2.chr17/120-240 TGAAGTTGTGGCTACAAATGGTGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGT +fr1.chrUn/120-240 TGAAGTGGTGGCCACCAATGGTGACACTCACCTTGGAGGTGAAGACTTTGATCAGCGCGT +danRer1.chr11/120-240 TGAAGTGGTGGCCACAAACGGAGACACTCACCTGGGCGGAGAAGACTTCGACCAGCGCGT + + +hg17.chr1/120-240 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCAGGAAAGACAA +panTro1.chr1/120-240 CATGGAACACTTCATCAAACTGTACAAAAAGAAGACTGGCAAAGATGTCGGGAAAGACAA +rn3.chr3/120-240 CATGGAGCACTTCATCAAGCTGTACAAAAAGAAGACTGGGAAAGATGTCAGAAAGGACAA +galGal2.chr17/120-240 TATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAAAAGATGTCAGGAAGGATAA +fr1.chrUn/120-240 CATGGAACACTTCATCAAGCTATACAAGAAGAAGACTGGCAAAGACGTGCGCAAAGACAA +danRer1.chr11/120-240 CATGGAGCACTTCATCAAGCTGTACAAGAAGAAGACGGGCAAAGATGTGCGCAAAGACAA + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1_rev/120-240 TTGTCTTTCCTGACATCTTTGCCAGTCTTCTTTTTGTACAGTTTGATGAAGTGTTCCATG +panTro1.chr1_rev/120-240 TTGTCTTTCCCGACATCTTTGCCAGTCTTCTTTTTGTACAGTTTGATGAAGTGTTCCATG +rn3.chr3_rev/120-240 TTGTCCTTTCTGACATCTTTCCCAGTCTTCTTTTTGTACAGCTTGATGAAGTGCTCCATG +galGal2.chr17_rev/120-240 TTATCCTTCCTGACATCTTTTCCTGTTTTCTTCTTGTAGAGTTTGATGAAGTGCTCCATA +fr1.chrUn_rev/120-240 TTGTCTTTGCGCACGTCTTTGCCAGTCTTCTTCTTGTATAGCTTGATGAAGTGTTCCATG +danRer1.chr11_rev/120-240 TTGTCTTTGCGCACATCTTTGCCCGTCTTCTTCTTGTACAGCTTGATGAAGTGCTCCATG + + +hg17.chr1_rev/120-240 ACACGCTGGTCAAAGTCTTCTCCACCCAGATAAGTATCTCCATTAGTGGCCACAACTTTG +panTro1.chr1_rev/120-240 ACATGCTGGTCAAAGTCTTTTCCACCCAGATGAGTATCTCCATTAGTGACCACAACTTTG +rn3.chr3_rev/120-240 ACCCGCTGATCAAAGTCTTCCCCACCCAGATGAGTGTCTCCATTAGTGGCCACCACTTCA +galGal2.chr17_rev/120-240 ACACGCTGGTCAAAGTCTTCTCCACCCAGGTGTGTGTCACCATTTGTAGCCACAACTTCA +fr1.chrUn_rev/120-240 ACGCGCTGATCAAAGTCTTCACCTCCAAGGTGAGTGTCACCATTGGTGGCCACCACTTCA +danRer1.chr11_rev/120-240 ACGCGCTGGTCGAAGTCTTCTCCGCCCAGGTGAGTGTCTCCGTTTGTGGCCACCACTTCA + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1/240-360 TAGAGCTGTGCAGAAACTCTGGCGCAAGGTAGAAAAGGCCAAACGGGCCCTGTCTTCTCA +mm5.chr2/240-360 CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCTAAGAGAGCCTTGTCTTCTCA +rn3.chr3/240-360 CAGAGCTGTGCAGAAACTCCGGCGTGAGGTAGAAAAGGCCAAGAGAGCCCTGTCTTCTCA +galGal2.chr17/240-360 CAGAGCTGTACAGAAACTAAGACGGGAAGTAGAGAAAGCGAAGCGGGCCCTGTCATCCCA +fr1.chrUn/240-360 CCGTGCTGTCCAGAAGCTGCGTCGTGAGGTTGAGAAGGCAAAGAGGGCCCTGTCTGCCCA +danRer1.chr11/240-360 CCGCGCCGTGCAGAAGCTGCGCAGAGAGGTGGAGAAGGCTAAGAGAGCCCTGTCTGCCCA + + +hg17.chr1/240-360 ACATCAAGCAAGCAGTAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGA +mm5.chr2/240-360 GCATCAAGCAAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA +rn3.chr3/240-360 GCATCAAGCGAG----GATTGAAATTGAGTCCTTCTTCGAAGGAGAAGACTTCTCAGAGA +galGal2.chr17/240-360 GCACCAAGCTAG----AATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGA +fr1.chrUn/240-360 GCACCAGGCCCG----CATTGAGATCGAGTCTTTCTTTGAGGGAGAAGATTTCTCCGAGA +danRer1.chr11/240-360 GCATCAGGCCCG----CATCGAGATCGAGTCCTTCTTTGAGGGAGAAGATTTCTCTGAGA + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1_rev/240-360 TCTCAGAAAAGTCTTCTCCTTCATAGAAGGACTCAATTTCAATTACTGCTTGCTTGATGT +mm5.chr2_rev/240-360 TCTCTGAGAAGTCTTCTCCTTCGAAGAAGGACTCAATTTCAATC----CTTGCTTGATGC +rn3.chr3_rev/240-360 TCTCTGAGAAGTCTTCTCCTTCGAAGAAGGACTCAATTTCAATC----CTCGCTTGATGC +galGal2.chr17_rev/240-360 TCTCAGAGAAATCCTCTCCTTCAAAAAAGGATTCTATTTCAATT----CTAGCTTGGTGC +fr1.chrUn_rev/240-360 TCTCGGAGAAATCTTCTCCCTCAAAGAAAGACTCGATCTCAATG----CGGGCCTGGTGC +danRer1.chr11_rev/240-360 TCTCAGAGAAATCTTCTCCCTCAAAGAAGGACTCGATCTCGATG----CGGGCCTGATGC + + +hg17.chr1_rev/240-360 TGAGAAGACAGGGCCCGTTTGGCCTTTTCTACCTTGCGCCAGAGTTTCTGCACAGCTCTA +mm5.chr2_rev/240-360 TGAGAAGACAAGGCTCTCTTAGCCTTTTCTACCTCACGCCGGAGTTTCTGCACAGCTCTG +rn3.chr3_rev/240-360 TGAGAAGACAGGGCTCTCTTGGCCTTTTCTACCTCACGCCGGAGTTTCTGCACAGCTCTG +galGal2.chr17_rev/240-360 TGGGATGACAGGGCCCGCTTCGCTTTCTCTACTTCCCGTCTTAGTTTCTGTACAGCTCTG +fr1.chrUn_rev/240-360 TGGGCAGACAGGGCCCTCTTTGCCTTCTCAACCTCACGACGCAGCTTCTGGACAGCACGG +danRer1.chr11_rev/240-360 TGGGCAGACAGGGCTCTCTTAGCCTTCTCCACCTCTCTGCGCAGCTTCTGCACGGCGCGG + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1/271-391 GAAAAGGCCAAACGGGCCCTGTCTTCTCAACATCAAGCAAGCAGTAATTGAAATTGAGTC +mm5.chr2/271-391 GAAAAGGCTAAGAGAGCCTTGTCTTCTCAGCATCAAGCAAG----GATTGAAATTGAGTC +rn3.chr3/271-391 GAAAAGGCCAAGAGAGCCCTGTCTTCTCAGCATCAAGCGAG----GATTGAAATTGAGTC +galGal2.chr17/271-391 GAGAAAGCGAAGCGGGCCCTGTCATCCCAGCACCAAGCTAG----AATTGAAATAGAATC +fr1.chrUn/271-391 GAGAAGGCAAAGAGGGCCCTGTCTGCCCAGCACCAGGCCCG----CATTGAGATCGAGTC +danRer1.chr11/271-391 GAGAAGGCTAAGAGAGCCCTGTCTGCCCAGCATCAGGCCCG----CATCGAGATCGAGTC + + +hg17.chr1/271-391 CTTCTATGAAGGAGAAGACTTTTCTGAGACCCTGACTCAGGCCAAATTTGAAGAGCTCAA +mm5.chr2/271-391 CTTCTTCGAAGGAGAAGACTTCTCAGAGACCCTTACTCGGGCCAAATTTGAAGAGCTGAA +rn3.chr3/271-391 CTTCTTCGAAGGAGAAGACTTCTCAGAGACCCTTACTCGGGCCAAATTTGAAGAGCTGAA +galGal2.chr17/271-391 CTTTTTTGAAGGAGAGGATTTCTCTGAGACGCTTACTCGTGCCAAATTTGAAGAACTGAA +fr1.chrUn/271-391 TTTCTTTGAGGGAGAAGATTTCTCCGAGACACTGACCCGTGCCAAATTTGAAGAGCTTAA +danRer1.chr11/271-391 CTTCTTTGAGGGAGAAGATTTCTCTGAGACTCTCACCAGAGCCAAGTTTGAAGAGCTCAA + + +CLUSTAL W(1.81) multiple sequence alignment + + +hg17.chr1_rev/271-391 TTGAGCTCTTCAAATTTGGCCTGAGTCAGGGTCTCAGAAAAGTCTTCTCCTTCATAGAAG +mm5.chr2_rev/271-391 TTCAGCTCTTCAAATTTGGCCCGAGTAAGGGTCTCTGAGAAGTCTTCTCCTTCGAAGAAG +rn3.chr3_rev/271-391 TTCAGCTCTTCAAATTTGGCCCGAGTAAGGGTCTCTGAGAAGTCTTCTCCTTCGAAGAAG +galGal2.chr17_rev/271-391 TTCAGTTCTTCAAATTTGGCACGAGTAAGCGTCTCAGAGAAATCCTCTCCTTCAAAAAAG +fr1.chrUn_rev/271-391 TTAAGCTCTTCAAATTTGGCACGGGTCAGTGTCTCGGAGAAATCTTCTCCCTCAAAGAAA +danRer1.chr11_rev/271-391 TTGAGCTCTTCAAACTTGGCTCTGGTGAGAGTCTCAGAGAAATCTTCTCCCTCAAAGAAG + + +hg17.chr1_rev/271-391 GACTCAATTTCAATTACTGCTTGCTTGATGTTGAGAAGACAGGGCCCGTTTGGCCTTTTC +mm5.chr2_rev/271-391 GACTCAATTTCAATC----CTTGCTTGATGCTGAGAAGACAAGGCTCTCTTAGCCTTTTC +rn3.chr3_rev/271-391 GACTCAATTTCAATC----CTCGCTTGATGCTGAGAAGACAGGGCTCTCTTGGCCTTTTC +galGal2.chr17_rev/271-391 GATTCTATTTCAATT----CTAGCTTGGTGCTGGGATGACAGGGCCCGCTTCGCTTTCTC +fr1.chrUn_rev/271-391 GACTCGATCTCAATG----CGGGCCTGGTGCTGGGCAGACAGGGCCCTCTTTGCCTTCTC +danRer1.chr11_rev/271-391 GACTCGATCTCGATG----CGGGCCTGATGCTGGGCAGACAGGGCTCTCTTAGCCTTCTC + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,720 @@ + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -36.97 + Consensus MFE: -15.85 + Energy contribution: -15.72 + Covariance contribution: -0.13 + Combinations/Pair: 1.35 + Mean z-score: -0.44 + Structure conservation index: 0.43 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.76 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/0-120 +UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score = -0.87, R) +>canFam1.chr9/0-120 +UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score = -0.16, R) +>mm5.chr2/0-120 +UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score = 0.44, R) +>galGal2.chr17/0-120 +AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU +.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score = -0.79, R) +>fr1.chrUn/0-120 +AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU +.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score = -0.61, R) +>danRer1.chr11/0-120 +UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU +((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score = -0.64, R) +>consensus +UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU +....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 + -0.13) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -30.48 + Consensus MFE: -16.68 + Energy contribution: -16.27 + Covariance contribution: -0.41 + Combinations/Pair: 1.38 + Mean z-score: -0.85 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -2.64 + SVM RNA-class probability: 0.005929 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score = -1.08, R) +>canFam1.chr9/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-score = -1.16, R) +>mm5.chr2/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCGAAGGUGCCGCCACCCAGGUCAAACACAAGGAUGUUCUUCUCUCCCUCUCUCUUAUCCAGGCCAUAUGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((..(((.(((((....(((..(((.....)))....)))...))))))))..)))))).............(((....(((....)))...)))... ( -29.50, z-score = 0.11, R) +>galGal2.chr17/0-120 +AAGACUCCGUUGUCAAUUGUCAGGAGGGAGACAUCAAAAGUUCCACCACCCAGGUCAAAUACAAGGAUGUUCUUUUCACCCUCUCUCUUGUCCAAUCCGUAUGCAAUUGCAGCAGCAGUU +..(((((.((((.((((((((((((((((((((((....(((..(((.....)))..))).....)))))..........))))))))))............))))))))))).).)))) ( -31.10, z-score = -1.92, R) +>fr1.chrUn/0-120 +AACACACCGUUGUCAAUGGUGAGCAGAGACACGUCGAAGGUGCCGCCACCGAGAUCGAACACGAGGAUGUUCUUCUCGCCGUCCUUUUUGUCCAGACCAUAAGCAAUGGCAGCAGCGGUU +.....((((((((..((((((((..((((.(((((...((((....))))....(((....))).)))))))))))))))))............(.((((.....))))).)))))))). ( -37.70, z-score = -0.90, R) +>danRer1.chr11/0-120 +AACACGCCGUUAUCGAUGGUCAGCAGAGACACGUCAAAGGUGCCACCACCCAGAUCGAACACCAGGAUGUUUUUCUCUCCGUCCCUCUUGUCCAGACCGUAUGCAAUGGCAGCCGCCGUA +.....((((((....((((((.((((((...((((...((((....))))..)).)).......(((((..........)))))))).)))...))))))....)))))).......... ( -30.50, z-score = -0.16, R) +>consensus +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUGCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +....(((((((...)))))))....((((.(((((....((...(((.....)))...)).....)))))...))))............................(((((....))))). (-16.68 = -16.27 + -0.41) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -30.48 + Consensus MFE: -16.68 + Energy contribution: -16.27 + Covariance contribution: -0.41 + Combinations/Pair: 1.38 + Mean z-score: -0.85 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -2.64 + SVM RNA-class probability: 0.005929 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score = -1.08, R) +>canFam1.chr9_rev/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-score = -1.16, R) +>mm5.chr2_rev/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCGAAGGUGCCGCCACCCAGGUCAAACACAAGGAUGUUCUUCUCUCCCUCUCUCUUAUCCAGGCCAUAUGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((..(((.(((((....(((..(((.....)))....)))...))))))))..)))))).............(((....(((....)))...)))... ( -29.50, z-score = 0.11, R) +>galGal2.chr17_rev/0-120 +AAGACUCCGUUGUCAAUUGUCAGGAGGGAGACAUCAAAAGUUCCACCACCCAGGUCAAAUACAAGGAUGUUCUUUUCACCCUCUCUCUUGUCCAAUCCGUAUGCAAUUGCAGCAGCAGUU +..(((((.((((.((((((((((((((((((((((....(((..(((.....)))..))).....)))))..........))))))))))............))))))))))).).)))) ( -31.10, z-score = -1.92, R) +>fr1.chrUn_rev/0-120 +AACACACCGUUGUCAAUGGUGAGCAGAGACACGUCGAAGGUGCCGCCACCGAGAUCGAACACGAGGAUGUUCUUCUCGCCGUCCUUUUUGUCCAGACCAUAAGCAAUGGCAGCAGCGGUU +.....((((((((..((((((((..((((.(((((...((((....))))....(((....))).)))))))))))))))))............(.((((.....))))).)))))))). ( -37.70, z-score = -0.90, R) +>danRer1.chr11_rev/0-120 +AACACGCCGUUAUCGAUGGUCAGCAGAGACACGUCAAAGGUGCCACCACCCAGAUCGAACACCAGGAUGUUUUUCUCUCCGUCCCUCUUGUCCAGACCGUAUGCAAUGGCAGCCGCCGUA +.....((((((....((((((.((((((...((((...((((....))))..)).)).......(((((..........)))))))).)))...))))))....)))))).......... ( -30.50, z-score = -0.16, R) +>consensus +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUGCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +....(((((((...)))))))....((((.(((((....((...(((.....)))...)).....)))))...))))............................(((((....))))). (-16.68 = -16.27 + -0.41) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -36.97 + Consensus MFE: -15.85 + Energy contribution: -15.72 + Covariance contribution: -0.13 + Combinations/Pair: 1.35 + Mean z-score: -0.44 + Structure conservation index: 0.43 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.76 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/0-120 +UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score = -0.87, R) +>canFam1.chr9_rev/0-120 +UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score = -0.16, R) +>mm5.chr2_rev/0-120 +UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score = 0.44, R) +>galGal2.chr17_rev/0-120 +AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU +.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score = -0.79, R) +>fr1.chrUn_rev/0-120 +AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU +.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score = -0.61, R) +>danRer1.chr11_rev/0-120 +UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU +((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score = -0.64, R) +>consensus +UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU +....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 + -0.13) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -29.08 + Consensus MFE: -17.18 + Energy contribution: -17.27 + Covariance contribution: 0.09 + Combinations/Pair: 1.38 + Mean z-score: -0.03 + Structure conservation index: 0.59 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.58 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/120-240 +CAAAGUUGUGGCCACUAAUGGAGAUACUUAUCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +(((((((....(((((...(((........))).)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -29.23, z-score = -0.65, R) +>panTro1.chr1/120-240 +CAAAGUUGUGGUCACUAAUGGAGAUACUCAUCUGGGUGGAAAAGACUUUGACCAGCAUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCGGGAAAGACAA +(((((((....(((((....(((...))).....)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -26.53, z-score = -0.03, R) +>rn3.chr3/120-240 +UGAAGUGGUGGCCACUAAUGGAGACACUCAUCUGGGUGGGGAAGACUUUGAUCAGCGGGUCAUGGAGCACUUCAUCAAGCUGUACAAAAAGAAGACUGGGAAAGAUGUCAGAAAGGACAA +(((((((((((((.....((....))(((((....))))).................))))))....)))))))(((..((...........))..)))......((((......)))). ( -26.70, z-score = 0.92, R) +>galGal2.chr17/120-240 +UGAAGUUGUGGCUACAAAUGGUGACACACACCUGGGUGGAGAAGACUUUGACCAGCGUGUUAUGGAGCACUUCAUCAAACUCUACAAGAAGAAAACAGGAAAAGAUGUCAGGAAGGAUAA +((((((.((..(((....((....)).((((((((..((((....))))..)))).))))..))).))))))))...............................((((......)))). ( -24.20, z-score = 0.87, R) +>fr1.chrUn/120-240 +UGAAGUGGUGGCCACCAAUGGUGACACUCACCUUGGAGGUGAAGACUUUGAUCAGCGCGUCAUGGAACACUUCAUCAAGCUAUACAAGAAGAAGACUGGCAAAGACGUGCGCAAAGACAA +.(((((..(.(((.((((.((((.....)))))))).))).)..))))).....((((((((((((....)))))...((((..(........)..))))...))))))).......... ( -36.70, z-score = -1.77, R) +>danRer1.chr11/120-240 +UGAAGUGGUGGCCACAAACGGAGACACUCACCUGGGCGGAGAAGACUUCGACCAGCGCGUCAUGGAGCACUUCAUCAAGCUGUACAAGAAGAAGACGGGCAAAGAUGUGCGCAAAGACAA +....((((((.((......))...))).))).(((.(((((....))))).)))((((((((((((....)))))....((((.(........))))).....))))))).......... ( -31.10, z-score = 0.50, R) +>consensus +UGAAGUGGUGGCCACUAAUGGAGACACUCACCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +((((((..(..(((((...((.(.....).))..)))))..)..))))))....((.(((((((((....)))))....((........))..)))).)).....((((......)))). (-17.18 = -17.27 + 0.09) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -23.40 + Consensus MFE: -9.31 + Energy contribution: -9.48 + Covariance contribution: 0.17 + Combinations/Pair: 1.36 + Mean z-score: 0.40 + Structure conservation index: 0.40 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -7.30 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/120-240 +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUAAGUAUCUCCAUUAGUGGCCACAACUUUG +.((((......)))).....((((((............((......))..(((((....)))))))))))((((((.....((((..((((....))))......)))).....)))))) ( -22.90, z-score = -0.12, R) +>panTro1.chr1/120-240 +UUGUCUUUCCCGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACAUGCUGGUCAAAGUCUUUUCCACCCAGAUGAGUAUCUCCAUUAGUGACCACAACUUUG +.((((......)))).((((((((((((((.................))))((((....)))).))))).))))).......(((...((((........)))).)))............ ( -18.53, z-score = 1.10, R) +>rn3.chr3/120-240 +UUGUCCUUUCUGACAUCUUUCCCAGUCUUCUUUUUGUACAGCUUGAUGAAGUGCUCCAUGACCCGCUGAUCAAAGUCUUCCCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACCACUUCA +.((((......))))...............................(((((((..((((((..((((.(((.................))).))))..)).....))))....))))))) ( -19.43, z-score = 0.66, R) +>galGal2.chr17/120-240 +UUAUCCUUCCUGACAUCUUUUCCUGUUUUCUUCUUGUAGAGUUUGAUGAAGUGCUCCAUAACACGCUGGUCAAAGUCUUCUCCACCCAGGUGUGUGUCACCAUUUGUAGCCACAACUUCA +..........((((((.....((((............(((.((((((.(.(((........)))..).)))))).)))........))))...))))))....((((....))))..... ( -20.75, z-score = 0.35, R) +>fr1.chrUn/120-240 +UUGUCUUUGCGCACGUCUUUGCCAGUCUUCUUCUUGUAUAGCUUGAUGAAGUGUUCCAUGACGCGCUGAUCAAAGUCUUCACCUCCAAGGUGAGUGUCACCAUUGGUGGCCACCACUUCA +..(.(((((.((.((((..((.....((((.((..(.....)..)).)))).....)).)))).))....))))).).(((((.....)))))((((((((...))))).)))....... ( -31.40, z-score = -0.65, R) +>danRer1.chr11/120-240 +UUGUCUUUGCGCACAUCUUUGCCCGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACGCGCUGGUCGAAGUCUUCUCCGCCCAGGUGAGUGUCUCCGUUUGUGGCCACCACUUCA +..(((...(((((......)))..(((........).)).))..)))((((((..(((((((((.((((.((.((....)).)).))))....))))).......))))....)))))). ( -27.41, z-score = 1.03, R) +>consensus +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACAACUUCA +.((((......))))...........................(((((..(((((........))))).)))))(((.....((((...((((........)))).)))).....)))... ( -9.31 = -9.48 + 0.17) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -23.40 + Consensus MFE: -9.31 + Energy contribution: -9.48 + Covariance contribution: 0.17 + Combinations/Pair: 1.36 + Mean z-score: 0.40 + Structure conservation index: 0.40 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -7.30 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/120-240 +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUAAGUAUCUCCAUUAGUGGCCACAACUUUG +.((((......)))).....((((((............((......))..(((((....)))))))))))((((((.....((((..((((....))))......)))).....)))))) ( -22.90, z-score = -0.12, R) +>panTro1.chr1_rev/120-240 +UUGUCUUUCCCGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACAUGCUGGUCAAAGUCUUUUCCACCCAGAUGAGUAUCUCCAUUAGUGACCACAACUUUG +.((((......)))).((((((((((((((.................))))((((....)))).))))).))))).......(((...((((........)))).)))............ ( -18.53, z-score = 1.10, R) +>rn3.chr3_rev/120-240 +UUGUCCUUUCUGACAUCUUUCCCAGUCUUCUUUUUGUACAGCUUGAUGAAGUGCUCCAUGACCCGCUGAUCAAAGUCUUCCCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACCACUUCA +.((((......))))...............................(((((((..((((((..((((.(((.................))).))))..)).....))))....))))))) ( -19.43, z-score = 0.66, R) +>galGal2.chr17_rev/120-240 +UUAUCCUUCCUGACAUCUUUUCCUGUUUUCUUCUUGUAGAGUUUGAUGAAGUGCUCCAUAACACGCUGGUCAAAGUCUUCUCCACCCAGGUGUGUGUCACCAUUUGUAGCCACAACUUCA +..........((((((.....((((............(((.((((((.(.(((........)))..).)))))).)))........))))...))))))....((((....))))..... ( -20.75, z-score = 0.35, R) +>fr1.chrUn_rev/120-240 +UUGUCUUUGCGCACGUCUUUGCCAGUCUUCUUCUUGUAUAGCUUGAUGAAGUGUUCCAUGACGCGCUGAUCAAAGUCUUCACCUCCAAGGUGAGUGUCACCAUUGGUGGCCACCACUUCA +..(.(((((.((.((((..((.....((((.((..(.....)..)).)))).....)).)))).))....))))).).(((((.....)))))((((((((...))))).)))....... ( -31.40, z-score = -0.65, R) +>danRer1.chr11_rev/120-240 +UUGUCUUUGCGCACAUCUUUGCCCGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACGCGCUGGUCGAAGUCUUCUCCGCCCAGGUGAGUGUCUCCGUUUGUGGCCACCACUUCA +..(((...(((((......)))..(((........).)).))..)))((((((..(((((((((.((((.((.((....)).)).))))....))))).......))))....)))))). ( -27.41, z-score = 1.03, R) +>consensus +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACAACUUCA +.((((......))))...........................(((((..(((((........))))).)))))(((.....((((...((((........)))).)))).....)))... ( -9.31 = -9.48 + 0.17) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -29.08 + Consensus MFE: -17.18 + Energy contribution: -17.27 + Covariance contribution: 0.09 + Combinations/Pair: 1.38 + Mean z-score: -0.03 + Structure conservation index: 0.59 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.58 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/120-240 +CAAAGUUGUGGCCACUAAUGGAGAUACUUAUCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +(((((((....(((((...(((........))).)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -29.23, z-score = -0.65, R) +>panTro1.chr1_rev/120-240 +CAAAGUUGUGGUCACUAAUGGAGAUACUCAUCUGGGUGGAAAAGACUUUGACCAGCAUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCGGGAAAGACAA +(((((((....(((((....(((...))).....)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -26.53, z-score = -0.03, R) +>rn3.chr3_rev/120-240 +UGAAGUGGUGGCCACUAAUGGAGACACUCAUCUGGGUGGGGAAGACUUUGAUCAGCGGGUCAUGGAGCACUUCAUCAAGCUGUACAAAAAGAAGACUGGGAAAGAUGUCAGAAAGGACAA +(((((((((((((.....((....))(((((....))))).................))))))....)))))))(((..((...........))..)))......((((......)))). ( -26.70, z-score = 0.92, R) +>galGal2.chr17_rev/120-240 +UGAAGUUGUGGCUACAAAUGGUGACACACACCUGGGUGGAGAAGACUUUGACCAGCGUGUUAUGGAGCACUUCAUCAAACUCUACAAGAAGAAAACAGGAAAAGAUGUCAGGAAGGAUAA +((((((.((..(((....((....)).((((((((..((((....))))..)))).))))..))).))))))))...............................((((......)))). ( -24.20, z-score = 0.87, R) +>fr1.chrUn_rev/120-240 +UGAAGUGGUGGCCACCAAUGGUGACACUCACCUUGGAGGUGAAGACUUUGAUCAGCGCGUCAUGGAACACUUCAUCAAGCUAUACAAGAAGAAGACUGGCAAAGACGUGCGCAAAGACAA +.(((((..(.(((.((((.((((.....)))))))).))).)..))))).....((((((((((((....)))))...((((..(........)..))))...))))))).......... ( -36.70, z-score = -1.77, R) +>danRer1.chr11_rev/120-240 +UGAAGUGGUGGCCACAAACGGAGACACUCACCUGGGCGGAGAAGACUUCGACCAGCGCGUCAUGGAGCACUUCAUCAAGCUGUACAAGAAGAAGACGGGCAAAGAUGUGCGCAAAGACAA +....((((((.((......))...))).))).(((.(((((....))))).)))((((((((((((....)))))....((((.(........))))).....))))))).......... ( -31.10, z-score = 0.50, R) +>consensus +UGAAGUGGUGGCCACUAAUGGAGACACUCACCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +((((((..(..(((((...((.(.....).))..)))))..)..))))))....((.(((((((((....)))))....((........))..)))).)).....((((......)))). (-17.18 = -17.27 + 0.09) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -34.52 + Consensus MFE: -15.70 + Energy contribution: -14.52 + Covariance contribution: -1.19 + Combinations/Pair: 1.43 + Mean z-score: 0.11 + Structure conservation index: 0.45 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.92 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/240-360 +UAGAGCUGUGCAGAAACUCUGGCGCAAGGUAGAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGA +..........((((((.((((.(....).))))...((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))).))))))... ( -35.40, z-score = -1.05, R) +>mm5.chr2/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.((((.((.(((((.(((.((((((.....)))))).)))))))))).(((((.(((----((((.......)))))))))).)).)))).....)))))).)). ( -37.30, z-score = -0.73, R) +>rn3.chr3/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.(((.(((.(..........).)))..)))......((((((((....(((((.(((----((((.......)))))))))).))..)))))))))))))).)). ( -32.50, z-score = 0.75, R) +>galGal2.chr17/240-360 +CAGAGCUGUACAGAAACUAAGACGGGAAGUAGAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGA +(((((((((..............((((.((((.(...((...))...).))).).))))(((.....)))..----.......))))((((((((((....)))))))))).)))))... ( -27.10, z-score = 0.14, R) +>fr1.chrUn/240-360 +CCGUGCUGUCCAGAAGCUGCGUCGUGAGGUUGAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGA +..((((.........(((...(((......)))...))).....(((((.((..(((...))).))))))))----))).((((((...(((..(.....)..))).))))))....... ( -32.90, z-score = 1.69, R) +>danRer1.chr11/240-360 +CCGCGCCGUGCAGAAGCUGCGCAGAGAGGUGGAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGA +.((.(((((((((...))))))...(.((..((.(.((((.....)))).).))..))).......))).))----((..((((((...((((((...))))))...))))))..))... ( -41.90, z-score = -0.14, R) +>consensus +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGA +....(((((((....(((.(.....).))).((.(.(((.......))).).))......))))..)))...........(((.((...((((((...))))))...)).)))....... (-15.70 = -14.52 + -1.19) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -31.38 + Consensus MFE: -17.15 + Energy contribution: -16.27 + Covariance contribution: -0.88 + Combinations/Pair: 1.50 + Mean z-score: 0.17 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.07 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/240-360 +UCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUCUACCUUGCGCCAGAGUUUCUGCACAGCUCUA +....((((((((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))..((((.....))))))))))..........((((((.......)))))). ( -33.30, z-score = -1.00, R) +>mm5.chr2/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((..(((((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -33.90, z-score = -1.12, R) +>rn3.chr3/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((.((.(((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -31.90, z-score = 0.19, R) +>galGal2.chr17/240-360 +UCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUCUACUUCCCGUCUUAGUUUCUGUACAGCUCUG +.......(((((....(((((.....)))))....))))).(((----(((((.....))))))))..((((((..((...(((....(........)....)))....))...)))))) ( -23.50, z-score = 0.63, R) +>fr1.chrUn/240-360 +UCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUCAACCUCACGACGCAGCUUCUGGACAGCACGG +....(((((.....))))).........((.((((.........----)))).)).((((((((((((.((....)).)))))).................(((...)))..)))))).. ( -29.50, z-score = 1.62, R) +>danRer1.chr11/240-360 +UCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUCCACCUCUCUGCGCAGCUUCUGCACGGCGCGG +.....(((...((((((.......)))))).))).....((.((----(.(((..((.((((.(((((.((((((.....)))))).........))))).)))).)).)).).))))). ( -36.20, z-score = 0.69, R) +>consensus +UCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +.....((((((((((((.......)).))))))...))))..................((((....((.((((((.....)))))).))..............((....)).)))).... (-17.15 = -16.27 + -0.88) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -31.38 + Consensus MFE: -17.15 + Energy contribution: -16.27 + Covariance contribution: -0.88 + Combinations/Pair: 1.50 + Mean z-score: 0.17 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.07 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/240-360 +UCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUCUACCUUGCGCCAGAGUUUCUGCACAGCUCUA +....((((((((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))..((((.....))))))))))..........((((((.......)))))). ( -33.30, z-score = -1.00, R) +>mm5.chr2_rev/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((..(((((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -33.90, z-score = -1.12, R) +>rn3.chr3_rev/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((.((.(((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -31.90, z-score = 0.19, R) +>galGal2.chr17_rev/240-360 +UCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUCUACUUCCCGUCUUAGUUUCUGUACAGCUCUG +.......(((((....(((((.....)))))....))))).(((----(((((.....))))))))..((((((..((...(((....(........)....)))....))...)))))) ( -23.50, z-score = 0.63, R) +>fr1.chrUn_rev/240-360 +UCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUCAACCUCACGACGCAGCUUCUGGACAGCACGG +....(((((.....))))).........((.((((.........----)))).)).((((((((((((.((....)).)))))).................(((...)))..)))))).. ( -29.50, z-score = 1.62, R) +>danRer1.chr11_rev/240-360 +UCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUCCACCUCUCUGCGCAGCUUCUGCACGGCGCGG +.....(((...((((((.......)))))).))).....((.((----(.(((..((.((((.(((((.((((((.....)))))).........))))).)))).)).)).).))))). ( -36.20, z-score = 0.69, R) +>consensus +UCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +.....((((((((((((.......)).))))))...))))..................((((....((.((((((.....)))))).))..............((....)).)))).... (-17.15 = -16.27 + -0.88) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -34.52 + Consensus MFE: -15.70 + Energy contribution: -14.52 + Covariance contribution: -1.19 + Combinations/Pair: 1.43 + Mean z-score: 0.11 + Structure conservation index: 0.45 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.92 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/240-360 +UAGAGCUGUGCAGAAACUCUGGCGCAAGGUAGAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGA +..........((((((.((((.(....).))))...((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))).))))))... ( -35.40, z-score = -1.05, R) +>mm5.chr2_rev/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.((((.((.(((((.(((.((((((.....)))))).)))))))))).(((((.(((----((((.......)))))))))).)).)))).....)))))).)). ( -37.30, z-score = -0.73, R) +>rn3.chr3_rev/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.(((.(((.(..........).)))..)))......((((((((....(((((.(((----((((.......)))))))))).))..)))))))))))))).)). ( -32.50, z-score = 0.75, R) +>galGal2.chr17_rev/240-360 +CAGAGCUGUACAGAAACUAAGACGGGAAGUAGAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGA +(((((((((..............((((.((((.(...((...))...).))).).))))(((.....)))..----.......))))((((((((((....)))))))))).)))))... ( -27.10, z-score = 0.14, R) +>fr1.chrUn_rev/240-360 +CCGUGCUGUCCAGAAGCUGCGUCGUGAGGUUGAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGA +..((((.........(((...(((......)))...))).....(((((.((..(((...))).))))))))----))).((((((...(((..(.....)..))).))))))....... ( -32.90, z-score = 1.69, R) +>danRer1.chr11_rev/240-360 +CCGCGCCGUGCAGAAGCUGCGCAGAGAGGUGGAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGA +.((.(((((((((...))))))...(.((..((.(.((((.....)))).).))..))).......))).))----((..((((((...((((((...))))))...))))))..))... ( -41.90, z-score = -0.14, R) +>consensus +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGA +....(((((((....(((.(.....).))).((.(.(((.......))).).))......))))..)))...........(((.((...((((((...))))))...)).)))....... (-15.70 = -14.52 + -1.19) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -32.55 + Consensus MFE: -18.57 + Energy contribution: -18.10 + Covariance contribution: -0.47 + Combinations/Pair: 1.42 + Mean z-score: -0.11 + Structure conservation index: 0.57 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.82 + SVM RNA-class probability: 0.000001 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/271-391 +GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA +(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score = -0.31, R) +>mm5.chr2/271-391 +GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score = -0.98, R) +>rn3.chr3/271-391 +GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score = -0.51, R) +>galGal2.chr17/271-391 +GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA +(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score = 0.10, R) +>fr1.chrUn/271-391 +GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA +.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score = -0.02, R) +>danRer1.chr11/271-391 +GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA +((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score = 1.06, R) +>consensus +GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 + -0.47) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -33.18 + Consensus MFE: -22.01 + Energy contribution: -20.72 + Covariance contribution: -1.30 + Combinations/Pair: 1.48 + Mean z-score: 0.17 + Structure conservation index: 0.66 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.58 + SVM RNA-class probability: 0.000003 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/271-391 +UUGAGCUCUUCAAAUUUGGCCUGAGUCAGGGUCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUC +((((((((((((.........)))...)))).)))))....((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))((((((.....))))))... ( -34.00, z-score = -0.30, R) +>mm5.chr2/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUC +....(.(((((....(..((.(((((((((((...((((...(((((......)))))....))))......)))----))))))))..))..)))))))((((((.....))))))... ( -35.10, z-score = -0.81, R) +>rn3.chr3/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUC +((((((...((((....(((((......))))).....(((((....((((((...))))))....)))))....----.....)))).))))))..((.((((((.....)))))).)) ( -34.40, z-score = 0.10, R) +>galGal2.chr17/271-391 +UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC +....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score = 0.33, R) +>fr1.chrUn/271-391 +UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC +.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score = 0.29, R) +>danRer1.chr11/271-391 +UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC +..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score = 1.40, R) +>consensus +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC +...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 + -1.30) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -33.18 + Consensus MFE: -22.01 + Energy contribution: -20.72 + Covariance contribution: -1.30 + Combinations/Pair: 1.48 + Mean z-score: 0.17 + Structure conservation index: 0.66 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.58 + SVM RNA-class probability: 0.000003 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/271-391 +UUGAGCUCUUCAAAUUUGGCCUGAGUCAGGGUCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUC +((((((((((((.........)))...)))).)))))....((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))((((((.....))))))... ( -34.00, z-score = -0.30, R) +>mm5.chr2_rev/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUC +....(.(((((....(..((.(((((((((((...((((...(((((......)))))....))))......)))----))))))))..))..)))))))((((((.....))))))... ( -35.10, z-score = -0.81, R) +>rn3.chr3_rev/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUC +((((((...((((....(((((......))))).....(((((....((((((...))))))....)))))....----.....)))).))))))..((.((((((.....)))))).)) ( -34.40, z-score = 0.10, R) +>galGal2.chr17_rev/271-391 +UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC +....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score = 0.33, R) +>fr1.chrUn_rev/271-391 +UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC +.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score = 0.29, R) +>danRer1.chr11_rev/271-391 +UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC +..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score = 1.40, R) +>consensus +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC +...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 + -1.30) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -32.55 + Consensus MFE: -18.57 + Energy contribution: -18.10 + Covariance contribution: -0.47 + Combinations/Pair: 1.42 + Mean z-score: -0.11 + Structure conservation index: 0.57 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.82 + SVM RNA-class probability: 0.000001 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/271-391 +GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA +(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score = -0.31, R) +>mm5.chr2_rev/271-391 +GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score = -0.98, R) +>rn3.chr3_rev/271-391 +GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score = -0.51, R) +>galGal2.chr17_rev/271-391 +GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA +(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score = 0.10, R) +>fr1.chrUn_rev/271-391 +GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA +.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score = -0.02, R) +>danRer1.chr11_rev/271-391 +GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA +((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score = 1.06, R) +>consensus +GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 + -0.47)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,17 @@ +# windowID clusterID seqID start end strand N columns identity meanMFE consensusMFE energyTerm covarianceTerm combPerPair z SCI decValue P +GCwindow1 locus1 >hg17.chr1 0 120 + 6 120 83.72 -36.97 -15.85 -15.72 -0.13 1.35 -0.44 0.43 -4.76 0.000000 0.50000 +window2 locus1 >hg17.chr1 0 120 - 6 120 83.72 -30.48 -16.68 -16.27 -0.41 1.38 -0.85 0.55 -2.64 0.005929 0.50000 +window3 locus2 >hg17.chr1_rev 0 120 + 6 120 83.72 -30.48 -16.68 -16.27 -0.41 1.38 -0.85 0.55 -2.64 0.005929 0.50000 +window4 locus2 >hg17.chr1_rev 0 120 - 6 120 83.72 -36.97 -15.85 -15.72 -0.13 1.35 -0.44 0.43 -4.76 0.000000 0.50000 +window5 locus3 >hg17.chr1 120 240 + 6 120 85.83 -29.08 -17.18 -17.27 0.09 1.38 -0.03 0.59 -4.58 0.000000 0.46111 +window6 locus3 >hg17.chr1 120 240 - 6 120 85.83 -23.40 -9.31 -9.48 0.17 1.36 0.40 0.40 -7.30 0.000000 0.46111 +window7 locus4 >hg17.chr1_rev 120 240 + 6 120 85.83 -23.40 -9.31 -9.48 0.17 1.36 0.40 0.40 -7.30 0.000000 0.46111 +window8 locus4 >hg17.chr1_rev 120 240 - 6 120 85.83 -29.08 -17.18 -17.27 0.09 1.38 -0.03 0.59 -4.58 0.000000 0.46111 +window9 locus5 >hg17.chr1 240 360 + 6 120 80.00 -34.52 -15.70 -14.52 -1.19 1.43 0.11 0.45 -4.92 0.000000 0.50603 +window10 locus5 >hg17.chr1 240 360 - 6 120 80.00 -31.38 -17.15 -16.27 -0.88 1.50 0.17 0.55 -4.07 0.000000 0.50603 +window11 locus6 >hg17.chr1_rev 240 360 + 6 120 80.00 -31.38 -17.15 -16.27 -0.88 1.50 0.17 0.55 -4.07 0.000000 0.50603 +window12 locus6 >hg17.chr1_rev 240 360 - 6 120 80.00 -34.52 -15.70 -14.52 -1.19 1.43 0.11 0.45 -4.92 0.000000 0.50603 +window13 locus7 >hg17.chr1 271 391 + 6 120 82.22 -32.55 -18.57 -18.10 -0.47 1.42 -0.11 0.57 -3.82 0.000001 0.47735 +window14 locus7 >hg17.chr1 271 391 - 6 120 82.22 -33.18 -22.01 -20.72 -1.30 1.48 0.17 0.66 -3.58 0.000003 0.47735 +window15 locus8 >hg17.chr1_rev 271 391 + 6 120 82.22 -33.18 -22.01 -20.72 -1.30 1.48 0.17 0.66 -3.58 0.000003 0.47735 +window16 locus8 >hg17.chr1_rev 271 391 - 6 120 82.22 -32.55 -18.57 -18.10 -0.47 1.42 -0.11 0.57 -3.82 0.000001 0.47735
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered.annotated.bed Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,8 @@ +chr1 0 120 WhoKnows 0 + +chr1 0 120 WhoKnows2 0 - +chr1 120 240 WhoKnows 0 + +chr1 120 240 WhoKnows2 0 - +chr1 240 360 WhoKnows 0 + +chr1 240 360 WhoKnows2 0 - +chr1 271 391 WhoKnows 0 + +chr1 271 391 WhoKnows2 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz.clustered.annotated.rnaz Wed Jan 30 03:58:28 2019 -0500 @@ -0,0 +1,9 @@ +# windowID clusterID seqID start end strand N columns identity meanMFE consensusMFE energyTerm covarianceTerm combPerPair z SCI decValue P Annotation +window3 locus2 >hg17.chr1_rev 0 120 + 6 120 83.72 -30.48 -16.68 -16.27 -0.41 1.38 -0.85 0.55 -2.64 0.005929 0.50000 WhoKnows +window4 locus2 >hg17.chr1_rev 0 120 - 6 120 83.72 -36.97 -15.85 -15.72 -0.13 1.35 -0.44 0.43 -4.76 0.000000 0.50000 WhoKnows2 +window7 locus4 >hg17.chr1_rev 120 240 + 6 120 85.83 -23.40 -9.31 -9.48 0.17 1.36 0.40 0.40 -7.30 0.000000 0.46111 WhoKnows +window8 locus4 >hg17.chr1_rev 120 240 - 6 120 85.83 -29.08 -17.18 -17.27 0.09 1.38 -0.03 0.59 -4.58 0.000000 0.46111 WhoKnows2 +window11 locus6 >hg17.chr1_rev 240 360 + 6 120 80.00 -31.38 -17.15 -16.27 -0.88 1.50 0.17 0.55 -4.07 0.000000 0.50603 WhoKnows +window12 locus6 >hg17.chr1_rev 240 360 - 6 120 80.00 -34.52 -15.70 -14.52 -1.19 1.43 0.11 0.45 -4.92 0.000000 0.50603 WhoKnows2 +window15 locus8 >hg17.chr1_rev 271 391 + 6 120 82.22 -33.18 -22.01 -20.72 -1.30 1.48 0.17 0.66 -3.58 0.000003 0.47735 WhoKnows +window16 locus8 >hg17.chr1_rev 271 391 - 6 120 82.22 -32.55 -18.57 -18.10 -0.47 1.42 -0.11 0.57 -3.82 0.000001 0.47735 WhoKnows2