Mercurial > repos > drosofff > blastn_to_scaffold
changeset 0:ad9a1c117ac6 draft default tip
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Sun, 21 Jun 2015 14:41:10 -0400 |
| parents | |
| children | |
| files | blastn_to_scaffold.py blastn_to_scaffold.xml test-data/assembly.fa test-data/blastn.tab test-data/contigs.fa test-data/guideSequence.fa |
| diffstat | 6 files changed, 775 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blastn_to_scaffold.py Sun Jun 21 14:41:10 2015 -0400 @@ -0,0 +1,120 @@ +#!/usr/bin/python +import sys +import argparse + +def insert_newlines(string, every=60): + lines = [] + for i in xrange(0, len(string), every): + lines.append(string[i:i+every]) + return '\n'.join(lines) + +def getseq (fastadict, transcript, up, down, orientation="direct"): + def reverse (seq): + revdict = {"A":"T","T":"A","G":"C","C":"G","N":"N"} + revseq = [revdict[i] for i in seq[::-1]] + return "".join(revseq) + pickseq = fastadict[transcript][up-1:down] + if orientation == "direct": + return pickseq + else: + return reverse(pickseq) + +def Parser(): + the_parser = argparse.ArgumentParser( + description="Generate DNA scaffold from blastn alignment of Contigs") + the_parser.add_argument( + '--sequences', action="store", type=str, help="input sequence file in fasta format") + the_parser.add_argument( + '--guideSequence', action="store", type=str, help="the reference sequence to guide the scaffold assembly in fasta format") + the_parser.add_argument( + '--blastn-tab', dest="blastn_tab", action="store", type=str, help="13-columns tabular blastn output") + the_parser.add_argument( + '--output', action="store", type=str, help="output file path, fasta format") + args = the_parser.parse_args() + return args + +def blatnInfo (file): + blastlist = [] + with open(file, "r") as f: + for line in f: + minilist = [] + fields = line.rstrip().split() + minilist.append(fields[0]) + minilist.extend(fields[6:10]) + blastlist.append(minilist) + blastlist.sort(key=lambda x: x[3], reverse=True) + return blastlist + +def myContigs (file): + Contigs = {} + with open(file, "r") as f: + for line in f: + if line[0] == ">": + header = line[1:-1] + Contigs[header] = "" + else: + Contigs[header] += line[:-1] + return Contigs + +def myGuide (file): + Guide = {} + coordinate = 0 + with open(file, "r") as f: + for line in f: + if line[0] == ">": + continue + else: + for nucleotide in line[:-1]: + coordinate += 1 + Guide[coordinate] = nucleotide.lower() + return Guide + +def updateGuide (blastlist, GuideDict, ContigsDict): + ''' + the blastlist object is a list of list with + element [0] : name of the blasted Contig + element [1] : queryStart of the alignment to the reference + element [2] = queryStop of the alignment to the reference + element [3] : subjectStart of the alignment to the reference + element [4] = subjectStop of the alignment to the reference + ''' + for fields in blastlist: + seqHeader = fields[0] + queryStart = int(fields[1]) + queryStop = int(fields[2]) + subjectStart = int(fields[3]) + subjectStop = int(fields[4]) + if subjectStart > subjectStop: + subjectStart, subjectStop = subjectStop, subjectStart + orientation = "reverse" + else: + orientation = "direct" + sequence = getseq (ContigsDict, seqHeader, queryStart, queryStop, orientation) + for i in range(subjectStart, subjectStop+1): + try: + del GuideDict[i] + except KeyError: + continue + for i, nucleotide in enumerate(sequence): + GuideDict[i+subjectStart] = nucleotide + +def finalAssembly (GuideDict, outputfile): + finalSeqList = [] + for keys in sorted(GuideDict): + finalSeqList.append(GuideDict[keys]) + finalSequence = insert_newlines("".join(finalSeqList) ) + Out = open (outputfile, "w") + print >> Out, ">Scaffold" + print >> Out, finalSequence + Out.close() + +def __main__(): + args = Parser() + ContigsDict = myContigs (args.sequences) + GuideDict = myGuide (args.guideSequence) + blastlist = blatnInfo(args.blastn_tab) + updateGuide(blastlist, GuideDict, ContigsDict) + finalAssembly(GuideDict, args.output) + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blastn_to_scaffold.xml Sun Jun 21 14:41:10 2015 -0400 @@ -0,0 +1,47 @@ +<tool id="blastn2scaffold" name="blastn_to_scaffold" version="0.1.0"> +<description>Generate DNA scaffold from blastn alignment of Contigs</description> +<requirements> +</requirements> +<command interpreter="python"> + blastn_to_scaffold.py --sequences $sequences + --guideSequence $guideSequence + --blastn-tab $blastn_tab + --output $output +</command> +<inputs> +<param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> +<param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> +<param name="blastn_tab" type="data" format="tabular" label="Select a blastn output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> + +</inputs> +<outputs> + <data format="fasta" name="output"/> +</outputs> + + +<tests> + <test> + <param name="sequences" value="contigs.fa" ftype="fasta"/> + <param name="blastn_tab" value="blastn.tab" ftype="tabular"/> + <param name="guideSequence" value="guideSequence.fa" ftype="tabular"/> + <output name="output" file="assembly.fa" ftype="fasta"/> + </test> +</tests> + + +<help> + + +**What it Does** +This tool start from DNA contigs that aligned to a subject DNA sequence through blastn. +The contigs must be provided in fasta format. The blastn output must be tabular, the 12 standard column plus column 13 with the length of the blastn subject. +The sequence used to blastn the contigs must be provided to serve as a guide to the final assembly +The final assembly is a DNA sequence. +Nucleotides of the guide sequence which were not covered by contigs are in small letters in the output assembly. + + +**Attribution** +This Galaxy tool was created by drosofff@gmail.com on 9/06/2015 +</help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly.fa Sun Jun 21 14:41:10 2015 -0400 @@ -0,0 +1,207 @@ +>Scaffold +gcaaaaaggcccctgggGGGGGGTTAATGAGTACTGGAAAAAGAAGCGCGAGATACCACT +TCGCTGATTATGCTGATTCTGGTATTAAGGATTAGTAGAGTATCGGAAGTGCCGAAGGGA +ATAATGCTGGTCCGTTGTAAACAGGATACTTATGAGACCTCTTAACAGAAACTTTGAGCA +AACAACAAATAAACGAACAAAAAGAGTTATACATTGAACTTGAAAAAAATCAATGTCTTT +TATTTAGACTGATTTATATTGGTCTTTATAATCGTAAGGAATAATTCTCATCTAATGATA +TCGATGTAAAATGTATCATTCTAGCTATTCAATTATATTAATTGAGCTTAGCATCTGATT +AAATTTATTATAAAATAATATTTAATCCCCATCTTTGCAAGATGGAAACTCTCAATAAAT +CAGGAGTATAATAGATTTAAACCCTCACACTGAATCACGAGTATAAACAGATTCAAATAT +GATTAACAATCAAACAAACAAAAAGGGACCACAACTAGAGAGAGTACATTTTGGTAGTGC +GCAGGTTGTGGGAAAAAGTACCAAACGACGACAACGCGGAACCAAATTTGACATTGAATA +TACTGTTAAAAGGAACGATGCACCAAAAGAGCAGAAATTCTTAGTTTCAGAAATTTTTGA +TGAAAAGTTGGATAAACAAATAAAATATGAGAAGAAGCAAAATCATACTTTTATTAAACC +GAAATTAAATTTAGTTACTAGAGAAGAACAACACGTGACTAAGAAGGTTTTAAGAGGTAA +AGAACGAGCTGCAACTCATGCTTTTATGAAGGAAATGGTTGAATCTAACAAGATACAACC +TAGTTGGAATGTCGAATACGAAAAAGAAATAGATGAGGTTGATCTATTTTTTATGAAGAA +GAAAACCAAACCTTTCTCAGGTTTTTCTATTAAGGAATTAAGAGATAGTCTAATTGTGCA +GTCAGACGATAAAAACATGGCACAGCCAACCGTGATGAGTTCAACCAATGAAATTGTTAC +ACCCCGTGAGGAGATAAGCGTTTCTGCTATCTCTGAACAACTGGCATCCTTGATGGAGAG +AGTTGATAAACTCGAGAAGATGAATGCTGCTTTGGAGGAAGAAAACAAGCAGCTAAAGAA +AGAGAGAGAGGCGACTATTAAGTCAGTTAAGAAAGAGGCAAAGAGGACTAAACAAGAGAA +GCCTCAGATTGCGAAGAAAACGCAACACAAGAGTTTAGGAGTAAATCTTAAAATCACCAA +GACCAAAGTAGTTGGTCAGGAACAATGTTTGGAAATTGAAAATACTCAGCATAAGAAATT +TGTTGAGAAGCCAAGCATGCCATCCAAAGTGAGCAAGAAGATGAAGGGACAACAGTTGAA +AAAGACTATTCGTACTTGGTATGAATTTGATCCCTCTAAACTCGTTCAGCATCAAAAAGA +AGTGTTGAACAGTGTTGTTACCAACACAACCTTCGCAGATAAAGTCCGTGAAACTGGTAT +ACCTAAACAAAAGATTAGGTATACTGCAAAACCACCAGCAGAGGAGAAGAGGAGTATCCA +TTTCTATGGTTATAAGCCAAAAGGAATCCCTAACAAAGTTTGGTGGAATTGGGTCACCAC +TGGCACAGCTATGGACGCTTATGAAAAAGCTGACCATTATCTGTATCACCAATTTAAACG +AGAAATGATGGTATACAGAAATAAATGGGTCAAGTTTAGTAAGGAGTTCAATCCGTACCT +ATCGGAACCGAAAATGGTATGGGAAGAGAATACATGGGAATATGAATATAAAACAGACGT +TCCCTACAATTTTATTCTCAAATGGCGCCAGTTAGTGCAGACCTACAAGCCTAACACACC +AATCCAGGCTGATTGGTACAAAATCTCGCAGAAACAACAATGTTAATTGAAGTTTTCATT +AATTCTTTGTTGCAAAATCTAGGTATCATGATGTCTTTCCGTGACCTAGTGGCGAGCCCA +TGGATATTGCTAGTAATAGCTATACCCTTGTGTGCATTTGCCAGTTCAGCGTCTATGGTT +AGGGAGATGCTTTTCCGTCATAAAATTACAGAAAATATTTTAAAAGGAACAGGAGTAGAA +GAATTGTTTAatccattcgggataattattaaataTTTCCTTTATTTTGCAATTTTGTAT +GCTTTTATTAAATATATTAGAAATAACATTAACGTAATAACAGAGAAAGTTAATTTTATA +CGGAGAATAGTATCGAACCCAACTGGAACAACAGGACGTAGAGGTGTGTTAGGGCGATGT +GTAGAACAAATCATAGAATATCCAACATTCTTTATCACGATGGTCTACGAACTACAGCAA +ATTAAGAACAAAAAAGATCTTATCTCGAAAATTACGATGATAAGTAGTATTCTCAAGTTA +CCACTTGGTATTTGGGAAAGTACTGTAGGACGGATGCTAGATCGACCGGCGATAGAAGGA +ACAGAAGAAATGTTGGAAGATGTTCTACCTATGGTAGCAATGGGATTGACGATTACAAAG +ACTCAAATTGGAGATGTTCCAGTTGAAAGTTTTCTTGTGAATTTGGACCGTAATCAAAAG +GCTTGCGAAAATATAATAAAACGTATGCAGCCGTTGATGATTAAAATGGGAATGATGAAA +GATAGTTCATATGATACTATTTTGCAAGTTGCAAAAGAAGTTAATGAATTATCGGAAGCG +GAAACATGGATGAAAACAACGCTCAAATTAAACCCAAATGAGTTCTTACAAACACAAGGG +GCTGTAAGAGTTGGCGAAATCAGGGAAAAAGTTGCAACTTTGAGAAATAAGTTAAACACT +TTGCAAACGAAAGAACTTCGATCAGATAAAGTAGTAACAGAGTGCCAAAAACATCTGGCA +TCACTCGAAGTGCTACTTATTGAAGTTAAGGTGTTAGAGAACAGTAACCAAACCCGAGTA +AAACCCGTAGGAGTTACCATACAAGGCGAAAAACAAATCGGAAAGACAAACCTCGTAGCA +ATCCTCTCAAGAAAAGTGTGCGAGTATGTTCAGGAACATGGCGATATTTCTTTTAGAAAC +GCTACTAAATGGACAACTTGGTCTAGGCAGTGCAGAGATGAATTTGATACAGGATACACC +GGACAAGAAATAACTTACGTAGATGATGCCTTTCAACAAAAAGACAACAAGGATCATTTG +ATGTGGTTTACTTTTATTTCTAATACAGCAGTGGGAACAAACCAAGCTGATTTGAAACAA +AAAGGTTTACCATACAGAAGTAAGTTGGTGTTTACGACCTGTAACAAGTTGCCGGACAAA +AGCGTAACGATTGAGGATATCGAAGCATTACATGCTCGATTCCCTCATACAATTTGCTTG +AGGAGGAACAAGAACAAAATGCCAAAACGAGGAGCGATTGACGAGAGCTATGACTGGGTC +GATTTTTATTACGGACCAATGTCGAAAGCCGTCAGCGCTATTGGAAGCAACACGACCAGC +ACGCTAAAAACCATGTCTTTGAGTGAAATAGTGAAGATAATTGGAGATGATTTGATTATT +CAAAATAATTTCTATAACTCCACTATTAAAGATGTGGGAATCACCGGACAAGAACAAATG +GATGGAGCGCAATTAGAAAGAAGACAACGAATGCGCGAATTGAGGGATCACTTGTTGAGA +ATCCGCCCAGGAGACGAAAACATGCCTTTCCTTGATGAAACATTTGAGTTGAATAGCCGA +CCTATCCAGACAGATGAGAAATTTATACCGCTCAAAGATAACTTAGATGAAGAAGTTATG +TATGGCGGTATTTCAGATCAGTTGTTAACTAGATTTGATAATATCATCGAAAGGAGTTTA +GAAGGCTATGATGTTGAGTCGCGAGAGCTAGGTGTTGAACCTTTAACTACACTAAATCAC +GTGAGAAGTAATATGTTGAGTTATAGAGCGTGGAATCTCATTAATTCCATGTGTATTAAC +AAAACAGAAACTTTCAGTGCTTGGTTAGGAAGGTACATCACCGAATGTGTAGAAGGAGCA +GCAGAAAATCTAGTTACGACGAAAGTCAAAATTAGAGTTAATCCTTTTACAGGTTTGCAG +TTGATCGCGGCCAAACGAATGTTGCAAGAGAATAAATTGATCGATATGGATGAAATTCCA +TCGACATCAGCGAATTCATATGAAACAGTTTACGATCAAATCAAAAATTTCGTGAACGAT +GAACTGAGTCTGATGGAAACAGATATAGTTGATTTAGCTTTAGCAAAAATTAGCTTATCG +CAAATCCGAGGCAACATCAAGAGATCAACCTGGCTGGACGTAAATGATTGGATATTAGCT +TTGAAACATAAAATTTCAGGAAAAAGCTTTGCCAAACATATGGATCTGTATCCTAGCTCG +CTAGATTCTTTTCTTCTTACACTCAAAGATTGGGAGGTTGAAGACCGTATAAAGTTTAAC +TCTATTTACAAGCAAAAGGTATTGTTTGTTCAATCTAGATTTTCACTTTACTGTTGGTCT +CCTTTTATATCTCGTGGAACACGATTTGTGAAAGTGACTTCTCAGTTTAGAGAGTTAGTG +GATAAGTTAGAAACTGGCATTCTATTCCATGAAATAAAATCGGTTACAAATGGAATTAGA +TGGTTAGGAGGAGCAGGGAACAATGGACACGTTGGAGAAAGAGTAAGAGTTATTGCTCAT +ACAGCCCAATTTCCGAAAAAGAGTTACCCTCAGAATGGATTCCCTATAAACGAAGAACTA +CATAGGGAATGGATCCAACTTGTTATGAACTCGGACTATAAGTATCACTCACTTATAGGA +GAAGAAAAAGTAAATATTCTTTGGAACCTTATTAGGCTCCAACCTCAACATGAGGTGGAG +AATTTTAAGGTTTACTTAGAAGATTTGCAGGCGTCCCCGCCGAAAACTGGGACAATTTGT +GCAAAAGTAGTGAATGATATAAAAGCCGAAGTAACTTCAAGTTATAGGCAATTTAACAAT +TACTACACTCGTTTAACAAAAGATGGTATGCACACACTTTTATCAATGCTTTCTAGGATA +GGTGTTCCAATTTCAGATTATTGGAATGACCTTCTTGTCGACAAAGCGCCAGCTATTACA +GCGGTTACTGTTGGAGCAATAACAAGTTtagctattattacaatAGTAAAAACTTTTCAA +TATGCTATAGCTGGAGAAGAGCAAAGTAAAGGTGAAAAACGAGCCAAACAGAAGAACATC +GCAACAACTAAGCTTCAAAAATTGAAGTTTACACTTGGCAAAGAACAAGCTGAAGGGGAT +AGTATCGAACATGTTAAAGAATTTGACGGTGATGTTAAGTTCGAAACAATTGAGAAACTA +TTTGATCACATTGATGAACACCCCAACCTCAACATAGTAGGCTTAAACTTGGTAGCACCA +GAAAACCCAATTGCTATCTATGCCGCAAGAGAAGAATCGTACGACTTTTCATTTTCCGAA +CCGCGCCCGCCTCAATGGAAAAAGGTGGTAACGTTTAAGGAAGACAGTAAACGAATAATC +TCTCTACAGTTGCGAGGAGAAGATACTGAAGATAACATCCTTGATGAGATAGAACACGCT +ATAAAAGTCTCACATGGAATGCCGTATGCTGAATGGATATTCAATGGATGGTTTAAGAAA +GAGAGCAACGACAATATATTATATTGTGTCGAGTTGGACCTGGTGACCGCAAAAACCCAA +TCAGGCCCAGTTGGATGGACACGTGCTCAAACGAAAAACCTGAAAGATCTTGAAATTCAG +CTAAATAAAGGCAAACCGATCGATGTTAAATCAGTGGTTTTAGGTGCACCGCAAGCATCT +ACGCAGGCGACCGATACTATGGACGTGCTAGTGAATAAGCATTTAGTTAAAGTTCATTGT +CTGAGTTATGAAAATTTGAACAACTTAGCTTTGAACGGAACACAAGTGTTTGCTTTAGCA +TCCGACAATATATTGATCGTGCCTGCACATGCAGCCAGACAGAACAAGTGGATCCGATTT +AGTCGCGCAACACAAACTGGTCATTATGGAGTAGCGAAAGTTGATGAACGTAGAATTGAT +TTTACACGTGACATCGCTATAGCCGTTATTTTGACTAGAACCGAAGCAGAACAAAAATTG +TGCGAATTAGATTATTCGATCCAGTTGACGAATATTAGTAAAGAGAAATTCCACTTCCCT +CTTATTACGAAATATTTGTTAACCGCTGACCAGTCAGAAGTAGAATGGATGAATTGTACG +ACCCTACATTATTTTGCAAAGAATAGAACCGTGGGGTTAGGAAGAACAACATCATTCCAA +GTTTCTGAATTTCTATGTGGAAACGAGTACATATCCAAGAAACTGGTCGCATGCGCGCAA +GGACTCCAGTCAAGTGTCGAACTAAGCCGACTTGGTGATTGTGGAAGTCCAATTGTCTTG +GCGTCGGGAAAGAAGGCAGGAAAACTGATAGGTTTTCACGGTTATCACTCTCCAAATCTA +CAAACGTGGTATGGAGCAATGTTGACTGTTGAGGACTTGGGAATCATCAACGGCGTAGAA +GAACATTTTGATGACCCATGGGCCAAACTTATTACACAAGGATTACCTGTCGATTTGCCA +ATTGGACCAGAAGTTGAGTATGTTGGTAATCTAATAAGACCTAGTTTACCTGTGACAAAT +GACTCATTGGACCATTGGCACAAATCACCATTTGCTGATCAATTTGAAGAACAACTAGCA +CCTGGTCGATTGAATCCATATGATTCATATATTGAAGGAGATTTGCCAACTAATCTTGAG +GGCCGAAAAAGTTTAATCTTAGGCCCGAATAGTGAAATGGCAAAAACTCTTCCAGAATTG +GATCAAGGAATTATCGACTGGATTGTAGATCAGTTGGTGGTGGAACAAGTTGCAACTTTC +AAAGCAGAAAACCTTTTAACGAAAGTTAGTGACGATATTGACGAAATGCTTGATTATGCC +CTGAATGGAAATGTAGATAACACATATGTTAGGGGTATGGAAGTCAACAAAGCATCAGGA +TTACCTTGGAGTCTTTCAGGTAGTCCGAAAAAGAGTGACTTTATCGATGTAGATGAAGCT +ACTGGAGTCAGATCGTTTAAGGTTAATGCTAATGGAGACGCTCTTAAAAATAGAGTTATC +CTGAAGTTGCAACAGGCGAAGATGGGAAATAGAATCTTGAGTTTTTCAAGTTCGAAACTA +AAGGACCAACCCATCAAAATAGCGCAAGCGAAGAGTGGAAGGACGAGAGTATTCCATTGT +ATCCCAGTGGACTTAATCTTGTTTTCGGGAGCGCTGTACGGCCCGTACAAAGAAGCATAC +ACAAAGGCTGGACTGAAATGCTATCATGCTGTAGGAATAGATCCGAAATCAGTTGGTTGG +CAACAGTTGGCTACGTATATGACGAAGCATCCTAATTATTTTGATGCTGATTATAAGAAT +TACGATAAGTATTTGCATAGGCAGGTATTTAAAGCAGTTCGAAAAATTCAGCGATCAGTG +ATTCAACAGATGTGCCCAGATAAATGGGATAAAGCAAGAGCTGTTGAAGAATTAGATGCT 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+AGACACGTTGAACACAACAACAGAATCTCTTAGTAAACAAGTATTATTTAATACTGATGA +GATTACCGTGTTAAAGGTAGACGTAGCAACCGTCACACAAAAACAACAGGACGTAGAACA +TTCACTTGTGACAATGAAAGATGAGATAGGAGAATTGCACATATCAGTGAATGCCAATGC +TAACTCCATTGAGGCATTACGCACCAGAATTGCCGCGCTAGAGGTTAGAGATGTAGGACC +GTGGGTTTTGAAAAACAGAATTTACAAATTCGTGATCAATATGCCAAATGGAACTACTCG +CTATACTACAATATACTTTTTCGCCGATGTATATTATAGCACTGGAGTAAGAGCAGCACC +TACAAATGCGGGAACAACTACAAGCATATTGACGATTACTTCGTTGACAACATCATATAG +TTTGGCTAACGTCCCCGTTTTAAAAGGTGTACCTTATAGAGTCAATGGTTACTTTGCTAA +CGGAAATAGTATCGAAGATATAACCGGAAGCACGTCAGTGATTTACGACTCTATGTAAAC +CGGACATGACATGTCTATGACACGACATTAAACTGTCAGAACCTGTTTGGTTAACACAGA +GAGATTAACCGCAAGACGAGTATGCAGAATCCAACACAAACCATGCATATATACGACATG +CCCCTACGCGTCATCGCTGGCCTGTCAACCCTTGCCAAAACAACTGAAGAAGACGACAAC +ACCTCAACTGGAATAGTAGTTAGTGAAGTAGGAGAGCCACAAGTGGTCGACCATCCAGCA +TGGATTGATCCCTTTGTTGCTTATCAATTGCGAGCTCCACGTAAAAACATCACACCAGAT +TTTATATTTGGTCGAGCCGATATTGGTAATGCGTTTAGTGCTTTCTTACCGCGCCGCTTT +TCTGCTCCAGCAGTAGGAACCCGACTTGTGATAGACCCTGTTTTCACTTACCAACAGAAA +ACGGTGCTAGGACTATATAATTATTTCCATGCGGATTTTTATTATATAGTGCATGTTCCA +GCACCCTTGGGAACAGGTATCTATCTGAAGATCTATGCTCCTGAATTTGACACTACAACC +GTAACACGAGGAATTCGGTTTAAGCCAAGTGCATCTCCAACAATTGCACTTTCAGTCCCT +TGGAGCAACGATCTATCGACCGTAGAAACATCCGTAGGTCGAGTCGGACAGAGTGGAGGG +AGTATTGTTATCGAAACTATCGAAGATAACAGTAACGAGACGGTCAACACCCCACTCAGC +ATCACCGTTTGGTGTTGCATGGCGAATATTAAAGCCACAGGCTACAAAAATGCGGATACG +TCAGCTTACAACGAAAAAGGCATGAACTTTGTCCCAGTTCCAGTGCCAAAGCCGCCCGTT +CCCCCAACAAAACCAATTATGGGCGAGGAACAAGCTGACAATGAAGTTACAGCCGAAGGT +GGTAAACTTGTACAGGAATTGGTTTACGACCATTCTGCGATTCCTGTAGCGCCAGTCGTC +GAAACACAAGCAGAACAGCCGGAAGTCCCAGTTTCATCAGTGGCAACGCGAAAGAACGAT +ACGGGACATTTGGCAACAAAGTGGTATGATTTCGCCAAAATCAGTCTGTCAAACCCAGCT +AACATGAACTGGACCACGCTAACCATAGACCCGTACAACAATGTTACATTGTCTAGAGAT +GGTGAGTCGATGGTCCTACCATGGAGGCGAAATGTTTGGACAACCGGATCGAAAAGTATT +GGATATATCCGAACGATGGTTGCACAAATTAACATACCACGCCCGCCGCAGATCAGTGGA +GTGCTCGAAGTTAAAGATTCAATCAATAACTCAAGTATTTCACTGGTAGAATTTGGAGGA +AAAGTAGAGATTCCAATTATTCCGAAGGTTATGAACGGACTAGTAACAAGTGCTAGTTTG +CCAAGGCATAGACTAAACCCATGGATGAGAACCGCCGAAAGTAAGGTTGAATTGCAATAT +CGAATTATTGCTTTTAATCGAACTAGCGACATTGCTGACCTTAACGTTAGCGTTTTGTTG +CGACCTGGCGATTCGCAATTCCAATTGCCGATGAAACCTGACAATAGTGTGGATACACGT +CATTTTGAGCTTGTTGAAGCTTTAATGTACCACTACGATAGCCTCCGAATTCGAGGAGAA +GAACAGAGTCTGCCAGAAAATGCACCTAATGCAGTTTCAAACCCTCAGCAGTTCATTACA +CCCGCAACCGCTCTAAGTGCCGAAGAATATAATGTGCACGAGGCGTTGGGTGAAACTGAG +GAGTTGGAGCTGGATGAATTTCCGGTTCTGGTGTTCAAGGGAAATGTTCCCGTTGACTCA +GTGACGTCCATTCCTTTGGACCTCGCAACTATATACGACTTTGCTTGGGACGGAGAGCAG +AATGCAATTTCTCAGAAATTTCAGCGTTTTGCTCATCTGATACCGAAAAGCGCAGGTGGT +TTTGGCCCAGTGATTGGTAATTATACTATCACGGCTAACCTCCCCACCGGTGTAGCAGGT +CGTATTCTGCACAATTGTCTCCCAGGAGATTGTGTAGATCTAGCAGTATCGAGAATTTTT +GGCTTGAAGAGCCTTCTCGGTGTTGCAGGAACAGCAGTTTCAGCCATTGGTGGCCCACTC +CTTAACGGTTTGGTTAACACCGCAGCGCCTATCCTTAGTGGAGCAGCGCACGCCATTGGT +GGAAATGTTGTAGGAGGACTGGCTGATGCAGTGATCGACATTGGATCTAATTTGCTGACG +CCAAAAGAAAAAGAACAACCAAGCGCAAATTCAAGCGCGATTTCTGGAGATATTCCGATT +TCGCGTTTTGTAGAGATGCTCAAGTATGTCAAGGAGAATTACCAGGATAATCCTGTGTTC +CCGACTTTACTTGTTGAACCACAAAACTTCATCTCAAACGCAATGACCGCACTCAAAACA +ATTCCAATTGAGGTCTTTGCCAACATGCGCAATGTGAAAGTTGAACGAAATTTGTTCGAC +CGAACGGTTGTTCCAACTGTGAAGGAAGCTACTCTAGCTGATATTGTCATACCTAATCAT +ATGTATGGCTATATTCTCCGAGACTTCCTCCAAAACAAACGAGCGTTTCAATCTGGGACC +AAACAAAATGTGTACTTTCAGCAGTTTCTAACTGTTCTATCTCAACGTAATACCCGTACA +CATATTACGCTCAACGACATCACAAGTTGCTCTATTGATAGTGAGTCGATTGCAAACAAA +ATAGAGAGAGTAAAACGCTACTTGAGTGCAAACTCGAGTGGGGAGACCACGGAAGAATTT +TCGCGAACAGACACCGGTCTGCTACCTACTACGACCCGCAAAATCGTATTAGGTGAAAGT +AAACGCAGGACGGAACGAAACGTAGCAGAAACTGTTTTCCCTTCCGTGAGGCAGTAGATT +AAATCCAAAACTCGCCATGTGCGCGTCTCAGAAACTAATTTTTAAAATTGGTTTGCGCGT +ATGGTTAAAAAGTCACATTAAATATGAGGATGGTCGCTATAATTTTCTAGCAGAAGATTA +TAAAGGACGGTGTGATGATGTTTTGGAGCCCGCACTGGGTGTGGGTTCGTAGTGCTAGCA +ATTGCAACTTTTCCTGAAAGTTAATACCTATAGTTTATAGGAGAAAAATTAACATTTATT +GAGAATATCTGTGCAAACGACTCCCCACGCGGGGAGTAGTGGAATCTTGATAAACAGGTT +TTTTAAGCTTTTGCGTTTCCGAAAGGGTTACTCTGGCTGAACCAGCAGTTTTTATAACTG +TGGGTAGCCCCTCGGAAAATCAGGTTTGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn.tab Sun Jun 21 14:41:10 2015 -0400 @@ -0,0 +1,7 @@ +Contig1 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 100.00 2113 0 0 1 2113 4248 2136 0.0 3811 12333 +Contig2 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 99.89 1745 2 0 1 1745 366 2110 0.0 3139 12333 +Contig3 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 98.78 164 0 1 1 164 377 216 4e-80 284 12333 +Contig4 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 99.92 2476 2 0 1 2476 5145 7620 0.0 4457 12333 +Contig5 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 99.89 4714 1 2 6 4715 12333 7620 0.0 8473 12333 +Contig6 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 99.89 894 1 0 1 894 4235 5128 0.0 1608 12333 +Contig7 gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome 99.10 222 0 1 1 222 237 18 2e-111 389 12333
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fa Sun Jun 21 14:41:10 2015 -0400 @@ -0,0 +1,216 @@ +>Contig1 +TTTTGCTAAAGCTAAATCAACTATATCTGTTTCCATCAGACTCAGTTCATCGTTCACGAA +ATTTTTGATTTGATCGTAAACTGTTTCATATGAATTCGCTGATGTCGATGGAATTTCATC +CATATCGATCAATTTATTCTCTTGCAACATTCGTTTGGCCGCGATCAACTGCAAACCTGT +AAAAGGATTAACTCTAATTTTGACTTTCGTCGTAACTAGATTTTCTGCTGCTCCTTCTAC +ACATTCGGTGATGTACCTTCCTAACCAAGCACTGAAAGTTTCTGTTTTGTTAATACACAT +GGAATTAATGAGATTCCACGCTCTATAACTCAACATATTACTTCTCACGTGATTTAGTGT +AGTTAAAGGTTCAACACCTAGCTCTCGCGACTCAACATCATAGCCTTCTAAACTCCTTTC +GATGATATTATCAAATCTAGTTAACAACTGATCTGAAATACCGCCATACATAACTTCTTC +ATCTAAGTTATCTTTGAGCGGTATAAATTTCTCATCTGTCTGGATAGGTCGGCTATTCAA +CTCAAATGTTTCATCAAGGAAAGGCATGTTTTCGTCTCCTGGGCGGATTCTCAACAAGTG +ATCCCTCAATTCGCGCATTCGTTGTCTTCTTTCTAATTGCGCTCCATCCATTTGTTCTTG +TCCGGTGATTCCCACATCTTTAATAGTGGAGTTATAGAAATTATTTTGAATAATCAAATC +ATCTCCAATTATCTTCACTATTTCACTCAAAGACATGGTTTTTAGCGTGCTGGTCGTGTT +GCTTCCAATAGCGCTGACGGCTTTCGACATTGGTCCGTAATAAAAATCGACCCAGTCATA +GCTCTCGTCAATCGCTCCTCGTTTTGGCATTTTGTTCTTGTTCCTCCTCAAGCAAATTGT +ATGAGGGAATCGAGCATGTAATGCTTCGATATCCTCAATCGTTACGCTTTTGTCCGGCAA +CTTGTTACAGGTCGTAAACACCAACTTACTTCTGTATGGTAAACCTTTTTGTTTCAAATC +AGCTTGGTTTGTTCCCACTGCTGTATTAGAAATAAAAGTAAACCACATCAAATGATCCTT +GTTGTCTTTTTGTTGAAAGGCATCATCTACGTAAGTTATTTCTTGTCCGGTGTATCCTGT +ATCAAATTCATCTCTGCACTGCCTAGACCAAGTTGTCCATTTAGTAGCGTTTCTAAAAGA +AATATCGCCATGTTCCTGAACATACTCGCACACTTTTCTTGAGAGGATTGCTACGAGGTT +TGTCTTTCCGATTTGTTTTTCGCCTTGTATGGTAACTCCTACGGGTTTTACTCGGGTTTG +GTTACTGTTCTCTAACACCTTAACTTCAATAAGTAGCACTTCGAGTGATGCCAGATGTTT +TTGGCACTCTGTTACTACTTTATCTGATCGAAGTTCTTTCGTTTGCAAAGTGTTTAACTT +ATTTCTCAAAGTTGCAACTTTTTCCCTGATTTCGCCAACTCTTACAGCCCCTTGTGTTTG +TAAGAACTCATTTGGGTTTAATTTGAGCGTTGTTTTCATCCATGTTTCCGCTTCCGATAA +TTCATTAACTTCTTTTGCAACTTGCAAAATAGTATCATATGAACTATCTTTCATCATTCC +CATTTTAATCATCAACGGCTGCATACGTTTTATTATATTTTCGCAAGCCTTTTGATTACG +GTCCAAATTCACAAGAAAACTTTCAACTGGAACATCTCCAATTTGAGTCTTTGTAATCGT +CAATCCCATTGCTACCATAGGTAGAACATCTTCCAACATTTCTTCTGTTCCTTCTATCGC +CGGTCGATCTAGCATCCGTCCTACAGTACTTTCCCAAATACCAAGTGGTAACTTGAGAAT +ACTACTTATCATCGTAATTTTCGAGATAAGATCTTTTTTGTTCTTAATTTGCTGTAGTTC +GTAGACCATCGTGATAAAGAATGTTGGATATTCTATGATTTGTTCTACACATCGCCCTAA +CACACCTCTACGTCCTGTTGTTCCAGTTGGGTTCGATACTATTCTCCGTATAAAATTAAC +TTTCTCTGTTATTACGTTAATGTTATTTCTAATATATTTAATAAAAGCATACAAAATTGC +AAAATAAAGGAAA +>Contig2 +TATTATAAAATAATATTTAATCCCCATCTTTGCAAGATGGAAACTCTCAATAAATCAGGA +GTATAATAGATTTAAACCCTCACACTGAATCACGAGTATAAACAGATTCAAATATGATTA +ACAATCAAACAAACAAAAAGGGACCACAACTAGAGAGAGTACATTTTGGTAGTGCGCAGG +TTGTGGGAAAAAGTACCAAACGACGACAACGCGGAACCAAATTTGACATTGAATATACTG +TTAAAAGGAACGATGCACCAAAAGAGCAGAAATTCTTAGTTTCAGAAATTTTTGATGAAA +AGTTGGATAAACAAATAAAATATGAGAAGAAGCAAAATCATACTTTTATTAAACCGAAAT +TAAATTTAGTTACTAGAGAAGAACAACACGTGACTAAGAAGGTTTTAAGAGGTAAAGAAC +GAGCTGCAACTCATGCTTTTATGAAGGAAATGGTTGAATCTAACAAGATACAACCTAGTT +GGAATGTCGAATACGAAAAAGAAATAGATGAGGTTGATCTATTTTTTATGAAGAAGAAAA +CCAAACCTTTCTCAGGTTTTTCTATTAAGGAATTAAGAGATAGTCTAATTGTGCAGTCAG +ACGATAAAAACATGGCACAGCCAACCGTGATGAGTTCAACCAATGAAATTGTTACACCCC +GTGAGGAGATAAGCGTTTCTGCTATCTCTGAACAACTGGCATCCTTGATGGAGAGAGTTG +ATAAACTCGAGAAGATGAATGCTGCTTTGGAGGAAGAAAACAAGCAGCTAAAGAAAGAGA +GAGAGGCGACTATTAAGTCAGTTAAGAAAGAGGCAAAGAGGACTAAACAAGAGAAGCCTC +AGATTGCGAAGAAAACGCAACACAAGAGTTTAGGAGTAAATCTTAAAATCACCAAGACCA +AAGTAGTTGGTCAGGAACAATGTTTGGAAATTGAAAATACTCAGCATAAGAAATTTGTTG +AGAAGCCAAGCATGCCATCCAAAGTGAGCAAGAAGATGAAGGGACAACAGTTGAAAAAGA +CTATTCGTACTTGGTATGAATTTGATCCCTCTAAACTCGTTCAGCATCAAAAAGAAGTGT +TGAACAGTGTTGTTACCAACACAACCTTCGCAGATAAAGTCCGTGAAACTGGTATACCTA +AACAAAAGATTAGGTATACTGCAAAACCACCAGCAGAGGAGAAGAGGAGTATCCATTTCT +ATGGTTATAAGCCAAAAGGAATCCCTAACAAAGTTTGGTGGAATTGGGTCACCACTGGCA +CAGCTATGGACGCTTATGAAAAAGCTGACCATTATCTGTATCACCAATTTAAACGAGAAA +TGATGGTATACAGAAATAAATGGGTCAAGTTTAGTAAGGAGTTCAATCCGTACCTATCGG +AACCGAAAATGGTATGGGAAGAGAATACATGGGAATATGAATATAAAACAGACGTTCCCT +ACAATTTTATTCTCAAATGGCGCCAGTTAGTGCAGACCTACAAGCCTAACACACCAATCC +AGGCTGATTGGTACAAAATCTCGCAGAAACAACAATGTTAATTGAAGTTTTCATTAATTC +TTTGTTGCAAAATCTAGGTATCATGATGTCTTTCCGTGACCTAGTGGCGAGCCCATGGAT +ATTGCTAGTAATAGCTATACCCTTGTGTGCATTTGCCAGTTCAGCGTCTATGGTTAGGGA +GATGCTTTTCCGTCATAAAATTACAGAAAATATTTTAAAAGGAACAGGAGTAGAAGAATT +GTTTA +>Contig3 +TATTTTATAATAATAATTTAATCAGATGCTAAGCTCAATTAATATAATTGAATAGCTAGA +ATGATACATTTTACATCGATATCATTAGATGAGAATTATTCCTTACGATTATAAAGACCA +ATATAAATCAGTCTAAATAAAAGACATTGATTTTTTTCAAGTTC +>Contig4 +AGTAAAAACTTTTCAATATGCTATAGCTGGAGAAGAGCAAAGTAAAGGTGAAAAACGAGC +CAAACAGAAGAACATCGCAACAACTAAGCTTCAAAAATTGAAGTTTACACTTGGCAAAGA +ACAAGCTGAAGGGGATAGTATCGAACATGTTAAAGAATTTGACGGTGATGTTAAGTTCGA +AACAATTGAGAAACTATTTGATCACATTGATGAACACCCCAACCTCAACATAGTAGGCTT +AAACTTGGTAGCACCAGAAAACCCAATTGCTATCTATGCCGCAAGAGAAGAATCGTACGA +CTTTTCATTTTCCGAACCGCGCCCGCCTCAATGGAAAAAGGTGGTAACGTTTAAGGAAGA +CAGTAAACGAATAATCTCTCTACAGTTGCGAGGAGAAGATACTGAAGATAACATCCTTGA +TGAGATAGAACACGCTATAAAAGTCTCACATGGAATGCCGTATGCTGAATGGATATTCAA +TGGATGGTTTAAGAAAGAGAGCAACGACAATATATTATATTGTGTCGAGTTGGACCTGGT +GACCGCAAAAACCCAATCAGGCCCAGTTGGATGGACACGTGCTCAAACGAAAAACCTGAA +AGATCTTGAAATTCAGCTAAATAAAGGCAAACCGATCGATGTTAAATCAGTGGTTTTAGG +TGCACCGCAAGCATCTACGCAGGCGACCGATACTATGGACGTGCTAGTGAATAAGCATTT +AGTTAAAGTTCATTGTCTGAGTTATGAAAATTTGAACAACTTAGCTTTGAACGGAACACA +AGTGTTTGCTTTAGCATCCGACAATATATTGATCGTGCCTGCACATGCAGCCAGACAGAA +CAAGTGGATCCGATTTAGTCGCGCAACACAAACTGGTCATTATGGAGTAGCGAAAGTTGA +TGAACGTAGAATTGATTTTACACGTGACATCGCTATAGCCGTTATTTTGACTAGAACCGA +AGCAGAACAAAAATTGTGCGAATTAGATTATTCGATCCAGTTGACGAATATTAGTAAAGA +GAAATTCCACTTCCCTCTTATTACGAAATATTTGTTAACCGCTGACCAGTCAGAAGTAGA +ATGGATGAATTGTACGACCCTACATTATTTTGCAAAGAATAGAACCGTGGGGTTAGGAAG +AACAACATCATTCCAAGTTTCTGAATTTCTATGTGGAAACGAGTACATATCCAAGAAACT +GGTCGCATGCGCGCAAGGACTCCAGTCAAGTGTCGAACTAAGCCGACTTGGTGATTGTGG +AAGTCCAATTGTCTTGGCGTCGGGAAAGAAGGCAGGAAAACTGATAGGTTTTCACGGTTA +TCACTCTCCAAATCTACAAACGTGGTATGGAGCAATGTTGACTGTTGAGGACTTGGGAAT +CATCAACGGCGTAGAAGAACATTTTGATGACCCATGGGCCAAACTTATTACACAAGGATT +ACCTGTCGATTTGCCAATTGGACCAGAAGTTGAGTATGTTGGTAATCTAATAAGACCTAG +TTTACCTGTGACAAATGACTCATTGGACCATTGGCACAAATCACCATTTGCTGATCAATT +TGAAGAACAACTAGCACCTGGTCGATTGAATCCATATGATTCATATATTGAAGGAGATTT +GCCAACTAATCTTGAGGGCCGAAAAAGTTTAATCTTAGGCCCGAATAGTGAAATGGCAAA +AACTCTTCCAGAATTGGATCAAGGAATTATCGACTGGATTGTAGATCAGTTGGTGGTGGA +ACAAGTTGCAACTTTCAAAGCAGAAAACCTTTTAACGAAAGTTAGTGACGATATTGACGA +AATGCTTGATTATGCCCTGAATGGAAATGTAGATAACACATATGTTAGGGGTATGGAAGT +CAACAAAGCATCAGGATTACCTTGGAGTCTTTCAGGTAGTCCGAAAAAGAGTGACTTTAT +CGATGTAGATGAAGCTACTGGAGTCAGATCGTTTAAGGTTAATGCTAATGGAGACGCTCT +TAAAAATAGAGTTATCCTGAAGTTGCAACAGGCGAAGATGGGAAATAGAATCTTGAGTTT +TTCAAGTTCGAAACTAAAGGACCAACCCATCAAAATAGCGCAAGCGAAGAGTGGAAGGAC +GAGAGTATTCCATTGTATCCCAGTGGACTTAATCTTGTTTTCGGGAGCGCTGTACGGCCC +GTACAAAGAAGCATACACAAAGGCTGGACTGAAATGCTATCATGCTGTAGGAATAGATCC +GAAATCAGTTGGTTGGCAACAGTTGGCTACGTATATGACGAAGCATCCTAATTATTTTGA +TGCTGATTATAAGAATTACGATAAGTATTTGCATAGGCAGGTATTTAAAGCAGTTCGAAA +AATTCAGCGATCAGTGATTCAACAGATGTGCCCAGATAAATGGGATAAAGCAAGAGCTGT +TGAAGAATTAGATGCTATTGACACGTATGTAGTTGACTATCAAACAGTCTACAAAACCAG +TCGTGGTAACAAAAGT +>Contig5 +TTTTTGCAAACCTGATTTTCCGAGGGGCTACCCACAGTTATAAAAACTGCTGGTTCAGCC +AGAGTAACCCTTTCGGAAACGCAAAAGCTTAAAAAACCTGTTTATCAAGATTCCACTACT +CCCCGCGTGGGGAGTCGTTTGCACAGATATTCTCAATAAATGTTAATTTTTCTCCTATAA +ACTATAGGTATTAACTTTCAGGAAAAGTTGCAATTGCTAGCACTACGAACCCACACCCAG +TGCGGGCTCCAAAACATCATCACACCGTCCTTTATAATCTTCTGCTAGAAAATTATAGCG +ACCATCCTCATATTTAATGTGACTTTTTAACCATACGCGCAAACCAATTTTAAAAATTAG +TTTCTGAGACGCGCACATGGCGAGTTTTGGATTTAATCTACTGCCTCACGGAAGGGAAAA +CAGTTTCTGCTACGTTTCGTTCCGTCCTGCGTTTACTTTCACCTAATACGATTTTGCGGG +TCGTAGTAGGTAGCAGACCGGTGTCTGTTCGCGAAAATTCTTCCGTGGTCTCCCCACTCG +AGTTTGCACTCAAGTAGCGTTTTACTCTCTCTATTTTGTTTGCAATCGACTCACTATCAA +TAGAGCAACTTGTGATGTCGTTGAGCGTAATATGTGTACGGGTATTACGTTGAGATAGAA +CAGTTAGAAACTGCTGAAAGTACACATTTTGTTTGGTCCCAGATTGAAACGCTCGTTTGT +TTTGGAGGAAGTCTCGGAGAATATAGCCATACATATGATTAGGTATGACAATATCAGCTA +GAGTAGCTTCCTTCACAGTTGGAACAACCGTTCGGTCGAACAAATTTCGTTCAACTTTCA +CATTGCGCATGTTGGCAAAGACCTCAATTGGAATTGTTTTGAGTGCGGTCATTGCGTTTG +AGATGAAGTTTTGTGGTTCAACAAGTAAAGTCGGGAACACAGGATTATCCTGGTAATTCT +CCTTGACATACTTGAGCATCTCTACAAAACGCGAAATCGGAATATCTCCAGAAATCGCGC +TTGAATTTGCGCTTGGTTGTTCTTTTTCTTTTGGCGTCAGCAAATTAGATCCAATGTCGA +TCACTGCATCAGCCAGTCCTCCTACAACATTTCCACCAATGGCGTGCGCTGCTCCACTAA +GGATAGGCGCTGCGGTGTTAACCAAACCGTTAAGGAGTGGGCCACCAATGGCTGAAACTG +CTGTTCCTGCAACACCGAGAAGGCTCTTCAAGCCAAAAATTCTCGATACTGCTAGATCTA +CACAATCTCCTGGGAGACAATTGTGCAGAATACGACCTGCTACACCGGTGGGGAGGTTAG +CCGTGATAGTATAATTACCAATCACTGGGCCAAAACCACCTGCGCTTTTCGGTATCAGAT +GAGCAAAACGCTGAAATTTCTGAGAAATTGCATTCTGCTCTCCGTCCCAAGCAAAGTCGT +ATATAGTTGCGAGGTCCAAAGGAATGGACGTCACTGAGTCAACGGGAACATTTCCCTTGA +ACACCAGAACCGGAAATTCATCCAGCTCCAACTCCTCAGTTTCACCCAACGCCTCGTGCA +CATTATATTCTTCGGCACTTAGAGCGGTTGCGGGTGTAATGAACTGCTGAGGGTTTGAAA +CTGCATTAGGTGCATTTTCTGGCAGACTCTGTTCTTCTCCTCGAATTCGGAGGCTATCGT +AGTGGTACATTAAAGCTTCAACAAGCTCAAAATGACGTGTATCCACACTATTGTCAGGTT +TCATCGGCAATTGGAATTGCGAATCGCCAGGTCGCAACAAAACGCTAACGTTAAGGTCAG +CAATGTCGCTAGTTCGATTAAAAGCAATAATTCGATATTGCAATTCAACCTTACTTTCGG +CGGTTCTCATCCATGGGTTTAGTCTATGCCTTGGCAAACTAGCACTTGTTACTAGTCCGT +TCATAACCTTCGGAATAATTGGAATCTCTACTTTTCCTCCAAATTCTACCAGTGAAATAC +TTGAGTTATTGATTGAATCTTTAACTTCGAGCACTCCACTGATCTGCGGCGGGCGTGGTA +TGTTAATTTGTGCAACCATCGTTCGGATATATCCAATACTTTTCGATCCGGTTGTCCAAA +CATTTCGCCTCCATGGTAGGACCATCGACTCACCATCTCTAGACAATGTAACATTGTTGT +ACGGGTCTATGGTTAGCGTGGTCCAGTTCATGTTAGCTGGGTTTGACAGACTGATTTTGG +CGAAATCATACCACTTTGTTGCCAAATGTCCCGTATCGTTCTTTCGCGTTGCCACTGATG +AAACTGGGACTTCCGGCTGTTCTGCTTGTGTTTCGACGACTGGCGCTACAGGAATCGCAG +AATGGTCGTAAACCAATTCCTGTACAAGTTTACCACCTTCGGCTGTAACTTCATTGTCAG +CTTGTTCCTCGCCCATAATTGGTTTTGTTGGGGGAACGGGCGGCTTTGGCACTGGAACTG +GGACAAAGTTCATGCCTTTTTCGTTGTAAGCTGACGTATCCGCATTTTTGTAGCCTGTGG +CTTTAATATTCGCCATGCAACACCAAACGGTGATGCTGAGTGGGGTGTTGACCGTCTCGT +TACTGTTATCTTCGATAGTTTCGATAACAATACTCCCTCCACTCTGTCCGACTCGACCTA +CGGATGTTTCTACGGTCGATAGATCGTTGCTCCAAGGGACTGAAAGTGCAATTGTTGGAG +ATGCACTTGGCTTAAACCGAATTCCTCGTGTTACGGTTGTAGTGTCAAATTCAGGAGCAT +AGATCTTCAGATAGATACCTGTTCCCAAGGGTGCTGGAACATGCACTATATAATAAAAAT +CCGCATGGAAATAATTATATAGTCCTAGCACCGTTTTCTGTTGGTAAGTGAAAACAGGGT +CTATCACAAGTCGGGTTCCTACTGCTGGAGCAGAAAAGCGGCGCGGTAAGAAAGCACTAA +ACGCATTACCAATATCGGCTCGACCAAATATAAAATCTGGTGTGATGTTTTTACGTGGAG +CTCGCAATTGATAAGCAACAAAGGGATCAATCCATGCTGGATGGTCGACCACTTGTGGCT +CTCCTACTTCACTAACTACTATTCCAGTTGAGGTGTTGTCGTCTTCTTCAGTTGTTTTGG +CAAGGGTTGACAGGCCAGCGATGACGCGTAGGGGCATGTCGTATATATGCATGGTTTGTG +TTGGATTCTGCATACTCGTCTTGCGGTTAATCTCTCTGTGTTAACCAAACAGGTTCTGAC +AGTTTAATGTCGTGTCATAGACATGTCATGTCCGGTTTACATAGAGTCGTAAATCACTGA +CGTGCTTCCGGTTATATCTTCGATACTATTTCCGTTAGCAAAGTAACCATTGACTCTATA +AGGTACACCTTTTAAAACGGGGACGTTAGCCAAACTATATGATGTTGTCAACGAAGTAAT +CGTCAATATGCTTGTAGTTGTTCCCGCATTTGTAGGTGCTGCTCTTACTCCAGTGCTATA +ATATACATCGGCGAAAAAGTATATTGTAGTATAGCGAGTAGTTCCATTTGGCATATTGAT +CACGAATTTGTAAATTCTGTTTTTCAAAACCCACGGTCCTACATCTCTAACCTCTAGCGC +GGCAATTCTGGTGCGTAATGCCTCAATGGAGTTAGCATTGGCATTCACTGATATGTGCAA +TTCTCCTATCTCATCTTTCATTGTCACAAGTGAATGTTCTACGTCCTGTTGTTTTTGTGT +GACGGTTGCTACGTCTACCTTTAACACGGTAATCTCATCAGTATTAAATAATACTTGTTT +ACTAAGAGATTCTGTTGTTGTGTTCAACGTGTCTAAGGAGTCTTTCGTAGTTTGATCAAG +CTCGTTTAATGTTGTGGCAAGGGTGTTAATCTGTTTTGCCTGTTGACTTGTTGTTGTGGT +TAATTTGTCAACTTCTGAATTCATTTCTACCAATGCTGTATTGATATTAACGAATTGTTC +TTCATTTCGAGCTTGATTGTTGTCAACTACTTTAGCTAAACCGTCAAGTTGCAGTTTTTG +TTGATCGAGCTGGGTCTTTACTGCTGTTACTGAAGATTGAATTGACTTAATCTCAGTAAC +CTCGTTCTCGTCTAAAACGGTGAAAAGAGTGGTGTTCTGATCAAAGATCTCCTCTTTTAA +TGCCATAATAACGATTACAGAATTTTTGGAAAGTAACTTCCCAGCTCGTATTCAACAATA +CTGCTAATGCTCCATTCAAGGTTCTATTTGTACCACATTTTAGCTTTTGACAAAGCTCAT +TGTAATACTCCTCACCCCAAAGAGCGGCTTCGATCAACTGTTCTTGCACGAGATTTACCC +ACACAGTTATCTGATCTTCGCGGATATCAGTCCATACAAACGGTCCTTCAATAGATCGTT +GTAGTAATGGAGCTAAAACCATACCGTTTTCTAACTTAAATCCTCTTTTCAAGAATTGTA +GGTTTTCAAAAGAAGTAAATGGCTTCTCTTCTCCATCCTTTGAACCTGGTGTCATGATAT +GTCCTGTAGCATTTAGTACATCTCGATAAGTACAATAATTATACTTATCCTTATACTCAT +CGCTAACGCTTTTTATAATATCATCACCAAACGCGACGCTCGAGACATTCTGTCGGTAAT +CCCACAGTGATCTTAGGCCGGTTGTCTTCACCCACGCATACAAACCATAAATATCGTTCG +CCAGGCAATTATCAATTGTAGTAGTATAACTACCA +>Contig6 +TAGCTTTAGCAAAAATTAGCTTATCGCAAATCCGAGGCAACATCAAGAGATCAACCTGGC +TGGACGTAAATGATTGGATATTAGCTTTGAAACATAAAATTTCAGGAAAAAGCTTTGCCA +AACATATGGATCTGTATCCTAGCTCGCTAGATTCTTTTCTTCTTACACTCAAAGATTGGG +AGGTTGAAGACCGTATAAAGTTTAACTCTATTTACAAGCAAAAGGTATTGTTTGTTCAAT +CTAGATTTTCACTTTACTGTTGGTCTCCTTTTATATCTCGTGGAACACGATTTGTGAAAG +TGACTTCTCAGTTTAGAGAGTTAGTGGATAAGTTAGAAACTGGCATTCTATTCCATGAAA +TAAAATCGGTTACAAATGGAATTAGATGGTTAGGAGGAGCAGGGAACAATGGACACGTTG +GAGAAAGAGTAAGAGTTATTGCTCATACAGCCCAATTTCCGAAAAAGAGTTACCCTCAGA +ATGGATTCCCTATAAACGAAGAACTACATAGGGAATGGATCCAACTTGTTATGAACTCGG +ACTATAAGTATCACTCACTTATAGGAGAAGAAAAAGTAAATATTCTTTGGAACCTTATTA +GGCTCCAACCTCAACATGAGGTGGAGAATTTTAAGGTTTACTTAGAAGATTTGCAGGCGT +CCCCGCCGAAAACTGGGACAATTTGTGCAAAAGTAGTGAATGATATAAAAGCCGAAGTAA +CTTCAAGTTATAGGCAATTTAACAATTACTACACTCGTTTAACAAAAGATGGTATGCACA +CACTTTTATCAATGCTTTCTAGGATAGGTGTTCCAATTTCAGATTATTGGAATGACCTTC +TTGTCGACAAAGCGCCAGCTATTACAGCGGTTACTGTTGGAGCAATAACAAGTT +>Contig7 +AAGACATTGATTTTTTTCAAGTTCAATGTATAACTCTTTTTGTTCGTTTATTTGTTGTTT +GCTCAAAGTTTCTGTTAAGAGGTCTCATAAGTATCCTGTTTACAACGGACCAGCATTATT +CCCTTCGGCACTTCCGATACTCTACTAATCCTTAATACCAGAATCAGCATAATCAGCGAA +GTGGTATCTCGCGCTTCTTTTTCCAGTACTCATTAACCCCCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/guideSequence.fa Sun Jun 21 14:41:10 2015 -0400 @@ -0,0 +1,178 @@ +>gi|402295620|gb|JX220408.1|_Nora_virus_isolate_FR1,_complete_genome +GCAAAAAGGCCCCTGGGGGGGGGTTAATGAGTACTGGAAAAAGAAGCGCGAGATACCACTTCGCTGATTA +TGCTGATTCTGGTATTAAGGATTAGTAGAGTATCGGAAGTGCCGAAGGGAATAATGCTGGTCCGTTGTAA +ACAGGATACTTATGAGACCTCTTAACAGAAACTTTGAGCAAACAACAAATAAACGAACAAAAAGAGTTAT +ACATTGAACTTGAAAAATCAATGTCTTTTATTTAGACTGATTTATATTGGTCTTTATAATCGTAAGGAAT +AATTCTCATCTAATGATATCGATGTAAAATGTATCATTCTAGCTATTCAATTATATTAATTGAGCTTAGC +ATCTGATTAAATTATTATTATAAAATAATATTTAATCCCCATCTTTGCAAGATGGAAACTCTCAATAAAT +CAGGAGTATAATAGATTTAAACCCTCACACTGAATCACGAGTATAAACAGATTCAAATATGATTAACAAT +CAAACAAACAAAAAGGGACCACAACTAGAGAGAGTACATTTTGGTAGTGCGCAGGTTGTGGGAAAAAGTA +CCAAACGACGACAACGCGGAACCAAATTTGACATTGAATATACTGTTAAAAGGAACGATGCACCAAAAGA +GCAGAAATTCTTAGTTTCAGAAATTTTTGATGAAAAGTTGGATAAACAAATAAAATATGAGAAGAAGCAA +AATCATACTTTTATTAAACCGAAATTAAATTTAGTTACTAGAGAAGAACAACACGTGACTAAGAAGGTTT +TAAGAGGTAAAGAACGAGCTGCAACTCATGCTTTTATGAAGGAAATGGTTGAATCTAACAAGATACAACC +TAGTTGGAATGTCGAATACGAAAAAGAAATAGATGAGGTTGATCTATTTTTTATGAAGAAGAAAACCAAA +CCTTTCTCAGGTTTTTCTATTAAGGAATTAAGAGATAGTCTAATTGTGCAGTCAGACGATAAAAACATGG +CACAGCCAACCGTGATGAGTTCAACCAATGAAATTGTTACACCCCGTGAGGAGATAAGCGTTTCTGCTAT +CTCTGAACAACTGGCATCCTTGATGGAGAGAGTTGATAAACTCGAGAAGATGAATGCTGCTTTGGAGGAA +GAAAACAAGCAGCTAAAGAAAGAGAGAGAGGCGACTATTAAGTCAGTTAAGAAAGAGGCAAAGAGGACTA +AACAAGAGAAGCCTCAGATTGCGAAGAAAACGCAACACAAGAGTTTAGGAGTAAATCTTAAAATCACCAA +GACCAAAGTAGTTGGTCAGGAACAATGTTTGGAAATTGAAAATACTCAGCATAAGAAATTTGTTGAGAAG +CCAAGCATGCCATCCAAAGTGAGCAAGAAGATGAAGGGACAACAGTTGAAAAAGACTATTCGTACTTGGT +ATGAATTTGATCCCTCTAAACTCGTTCAGCATCAAAAAGAAGTGTTGAACAGTGTTGTTACTAACACAAC +CTTCGCAGATAAAGTCCGTGAAACTGGTATACCTAAACAAAAGATTAGGTATACTGCAAAACCACCAGCA +GAGGAGAAGAGGAGTATCCATTTCTATGGTTATAAGCCAAAAGGAATCCCTAACAAAGTTTGGTGGAATT +GGGTCACCACTGGCACAGCTATGGACGCTTATGAAAAAGCTGACCATTATCTGTATCACCAATTTAAACG +AGAAATGATGGTATACAGAAATAAATGGGTCAAGTTTAGTAAGGAGTTCAATCCGTACCTATCGGAACCG +AAAATGGTATGGGAAGAGAATACATGGGAATATGAATATAAAACAGACGTTCCCTACAATTTTATTCTCA +AATGGCGCCAGTTAGTGCAGACCTACAAGCCTAACACACCAATCCAGGCTGATTGGTACAAAATCTCGCA +GAAACAACAATGTTAATTGAAGTTTTCATTAATTCTTTGTTGCAAAATCTAGGTATCATGATGTCTTTCC +GTGACCTAGTGGCGAGCCCATGGATACTGCTAGTAATAGCTATACCCTTGTGTGCATTTGCCAGTTCAGC +GTCTATGGTTAGGGAGATGCTTTTCCGTCATAAAATTACAGAAAATATTTTAAAAGGAACAGGAGTAGAA +GAATTGTTTAATCCATTCGGGATAATTATTAAATATTTCCTTTATTTTGCAATTTTGTATGCTTTTATTA +AATATATTAGAAATAACATTAACGTAATAACAGAGAAAGTTAATTTTATACGGAGAATAGTATCGAACCC +AACTGGAACAACAGGACGTAGAGGTGTGTTAGGGCGATGTGTAGAACAAATCATAGAATATCCAACATTC +TTTATCACGATGGTCTACGAACTACAGCAAATTAAGAACAAAAAAGATCTTATCTCGAAAATTACGATGA +TAAGTAGTATTCTCAAGTTACCACTTGGTATTTGGGAAAGTACTGTAGGACGGATGCTAGATCGACCGGC +GATAGAAGGAACAGAAGAAATGTTGGAAGATGTTCTACCTATGGTAGCAATGGGATTGACGATTACAAAG +ACTCAAATTGGAGATGTTCCAGTTGAAAGTTTTCTTGTGAATTTGGACCGTAATCAAAAGGCTTGCGAAA +ATATAATAAAACGTATGCAGCCGTTGATGATTAAAATGGGAATGATGAAAGATAGTTCATATGATACTAT +TTTGCAAGTTGCAAAAGAAGTTAATGAATTATCGGAAGCGGAAACATGGATGAAAACAACGCTCAAATTA +AACCCAAATGAGTTCTTACAAACACAAGGGGCTGTAAGAGTTGGCGAAATCAGGGAAAAAGTTGCAACTT +TGAGAAATAAGTTAAACACTTTGCAAACGAAAGAACTTCGATCAGATAAAGTAGTAACAGAGTGCCAAAA +ACATCTGGCATCACTCGAAGTGCTACTTATTGAAGTTAAGGTGTTAGAGAACAGTAACCAAACCCGAGTA +AAACCCGTAGGAGTTACCATACAAGGCGAAAAACAAATCGGAAAGACAAACCTCGTAGCAATCCTCTCAA +GAAAAGTGTGCGAGTATGTTCAGGAACATGGCGATATTTCTTTTAGAAACGCTACTAAATGGACAACTTG +GTCTAGGCAGTGCAGAGATGAATTTGATACAGGATACACCGGACAAGAAATAACTTACGTAGATGATGCC +TTTCAACAAAAAGACAACAAGGATCATTTGATGTGGTTTACTTTTATTTCTAATACAGCAGTGGGAACAA +ACCAAGCTGATTTGAAACAAAAAGGTTTACCATACAGAAGTAAGTTGGTGTTTACGACCTGTAACAAGTT +GCCGGACAAAAGCGTAACGATTGAGGATATCGAAGCATTACATGCTCGATTCCCTCATACAATTTGCTTG +AGGAGGAACAAGAACAAAATGCCAAAACGAGGAGCGATTGACGAGAGCTATGACTGGGTCGATTTTTATT +ACGGACCAATGTCGAAAGCCGTCAGCGCTATTGGAAGCAACACGACCAGCACGCTAAAAACCATGTCTTT +GAGTGAAATAGTGAAGATAATTGGAGATGATTTGATTATTCAAAATAATTTCTATAACTCCACTATTAAA +GATGTGGGAATCACCGGACAAGAACAAATGGATGGAGCGCAATTAGAAAGAAGACAACGAATGCGCGAAT +TGAGGGATCACTTGTTGAGAATCCGCCCAGGAGACGAAAACATGCCTTTCCTTGATGAAACATTTGAGTT +GAATAGCCGACCTATCCAGACAGATGAGAAATTTATACCGCTCAAAGATAACTTAGATGAAGAAGTTATG +TATGGCGGTATTTCAGATCAGTTGTTAACTAGATTTGATAATATCATCGAAAGGAGTTTAGAAGGCTATG +ATGTTGAGTCGCGAGAGCTAGGTGTTGAACCTTTAACTACACTAAATCACGTGAGAAGTAATATGTTGAG +TTATAGAGCGTGGAATCTCATTAATTCCATGTGTATTAACAAAACAGAAACTTTCAGTGCTTGGTTAGGA +AGGTACATCACCGAATGTGTAGAAGGAGCAGCAGAAAATCTAGTTACGACGAAAGTCAAAATTAGAGTTA +ATCCTTTTACAGGTTTGCAGTTGATCGCGGCCAAACGAATGTTGCAAGAGAATAAATTGATCGATATGGA +TGAAATTCCATCGACATCAGCGAATTCATATGAAACAGTTTACGATCAAATCAAAAATTTCGTGAACGAT +GAACTGAGTCTGATGGAAACAGATATAGTTGATTTAGCTTTAGCAAAAATTAGCTTATCGCAAATCCGAG +GCAACATCAAAAGATCAACCTGGCTGGACGTAAATGATTGGATATTAGCTTTGAAACATAAAATTTCAGG +AAAAAGCTTTGCCAAACATATGGATCTGTATCCTAGCTCGCTAGATTCTTTTCTTCTTACACTCAAAGAT +TGGGAGGTTGAAGACCGTATAAAGTTTAACTCTATTTACAAGCAAAAGGTATTGTTTGTTCAATCTAGAT +TTTCACTTTACTGTTGGTCTCCTTTTATATCTCGTGGAACACGATTTGTGAAAGTGACTTCTCAGTTTAG +AGAGTTAGTGGATAAGTTAGAAACTGGCATTCTATTCCATGAAATAAAATCGGTTACAAATGGAATTAGA +TGGTTAGGAGGAGCAGGGAACAATGGACACGTTGGAGAAAGAGTAAGAGTTATTGCTCATACAGCCCAAT +TTCCGAAAAAGAGTTACCCTCAGAATGGATTCCCTATAAACGAAGAACTACATAGGGAATGGATCCAACT +TGTTATGAACTCGGACTATAAGTATCACTCACTTATAGGAGAAGAAAAAGTAAATATTCTTTGGAACCTT +ATTAGGCTCCAACCTCAACATGAGGTGGAGAATTTTAAGGTTTACTTAGAAGATTTGCAGGCGTCCCCGC +CGAAAACTGGGACAATTTGTGCAAAAGTAGTGAATGATATAAAAGCCGAAGTAACTTCAAGTTATAGGCA +ATTTAACAATTACTACACTCGTTTAACAAAAGATGGTATGCACACACTTTTATCAATGCTTTCTAGGATA +GGTGTTCCAATTTCAGATTATTGGAATGACCTTCTTGTCGACAAAGCGCCAGCTATTACAGCGGTTACTG +TTGGAGCAATAACAAGTTTAGCTATTATTACAATAGTAAAAACTTTTCAATATGCTATAGCTGGAGAAGA +GCAAAGTAAAGGTGAAAAACGAGCCAAACAGAAGAACATCGCAACAACTAAGCTTCAAAAATTGAAGTTT +ACACTTGGCAAAGAACAAGCTGAAGGGGATAGTATCGAACATGTTAAAGAATTTGACGGTGATGTTAAGT +TCGAAACAATTGAGAAACTATTTGATCACATTGATGAACACCCCAACCTCAACATAGTAGGCTTAAACTT +GGTAGCACCAGAAAACCCAATTGCTATCTATGCCGCAAGAGAAGAATCGTACGACTTTTCATTTTCCGAA +CCGCGCCCGCCTCAATGGAAAAAGGTGGTAACGTTTAAGGAAGACAGTAAACGAATAATCTCTCTACAGT +TGCGAGGAGAAGATACTGAAGATAACATCCTTGATGAGATAGAACACGCTATAAAAGTCTCACATGGAAT +GCCGTATGCTGAATGGATATTCAATGGATGGTTTAAGAAAGAGAGCAACGACAATATATTATATTGTGTC +GAGTTGGACCTGGTGACCGCAAAAACCCAATCAGGCCCAGTTGGATGGACACGTGCTCAAACGAAAAACC +TGAAAGATCTTGAAATTCAGCTAAATAAAGGCAAACCGATCGATGTTAAATCAGTGGTTTTAGGTGCACC +GCAAGCATCTACGCAGGCGACCGATACTATGGACGTGCTAGTGAATAAGCATTTAGTTAAAGTTCATTGT +CTGAGTTATGAAAATTTGAACAACTTAGCTTTGAACGGAACACAAGTGTTTGCTTTAGCATCCGACAATA +TATTGATCGTGCCTGCACATGCAGCCAGACAGAACAAGTGGATCCGATTTAGTCGCGCAACACAAACTGG +TCATTATGGAGTAGCGAAAGTTGATGAACGTAGAATTGATTTTACACGTGACATCGCTATAGCCGTTATT +TTGACTAGAACCGAAGCAGAACAAAAATTGTGCGAATTAGATTATTCGATCCAGTTGACGAATATTAGTA +AAGAGAAATTCCACTTCCCTCTTATTACGAAATATTTGTTAACCGCTGACCAGTCAGAAGTAGAATGGAT +GAATTGTACGACCCTACATTATTTTGCAAAGAATAGAACCGTGGGGTTAGGAAGAACAACATCATTCCAA +GTTTCTGAATTTCTATGTGGAAACGAGTACATATCCAAGAAACTGGTCGCATGCGCGCAAGGACTCCAGT +CAAGTGTCGAACTAAGCCGACTTGGTGATTGTGGAAGTCCAATTGTCTTGGCGTCGGGAAAGAAGGCAGG +AAAACTGATAGGTTTTCACGGTTATCACTCTCCAAATCTACAAACGTGGTATGGAGCAATGTTGACTGTT +GAGGACTTGGGAATCATCAACGGCGTAGAAGAACATTTTGATGACCCATGGGCCAAACTTATTACACAAG +GATTACCTGTCGATTTGCCAATTGGACCAGAAGTTGAGTATGTTGGTAATCTAATAAGACCTAGTTTACC +TGTGACAAATGACTCATTGGACCATTGGCACAAATCACCATTTGCTGATCAATTTGAAGAACAACTAGCA +CCTGGTCGATTGAATCCATATGATTCATATATTGAAGGAGATTTGCCAACTAATCTTGAGGGCCGAAAAA +GTTTAATCTTAGGCCCGAATAGTGAAATGGCAAAAACTCTTCCAGAATTGGATCAAGGAATTATCGACTG +GATTGTAGATCAGTTGGTGGTGGAACAAGTTGCAACTTTCAAAGCAGAAAACCTTTTAACGAAAGTTAGT +GACGATATTGACGAAATGCTTGATTATGCCCTGAATGGAAATGTAGATAACACATATGTTAGGGGTATGG +AAGTCAACAAAGCATCAGGATTACCTTGGAGTCTTTCAGGTAGTCCGAAAAAGAGTGACTTTATCGATGT +AGATGAAGCTACTGGAGTCAGATCGTTTAAGGTTAATGCTAATGGAGACGCTCTTAAAAATAGAGTTATC +CTGAAGTTGCAACAGGCGAAGATGGGAAATAGAATCTTGAGTTTTTCAAGTTCGAAACTAAAGGACCAAC +CCATCAAAATAGCGCAAGCGAAGAGTGGAAGGACGAGAGTATTCCATTGTATCCCAGTGGACTTAATCTT +GTTTTCGGGAGCGCTGTACGGCCCGTACAAAGAAGCATACACAAAGGCTGGACTGAAATGCTATCATGCT +GTAGGAATAGATCCGAAATCAGTTGGTTGGCAACAGTTGGCTACGTATATGACGAAGCATCCTAATTATT +TTGATGCTGATTATAAGAATTACGATAAGTATTTGCATAGGCAGGTATTTAAAGCAGTTCGAAAAATTCA +GCGATCAGTGATTCAACAGATGTGCCCAGATAAATGGGATAAAGCAAGAGCTGTTGAAGAATTAGATGCT +ATTGACACGTATGTAGTTGACTATCAAACAGTCTACAAAACCAATCGTGGCAACAAAAGTGGTAGTTATA +CTACTACAATTGATAATTGCCTGGCGAACGATATTTATGGTTTGTATGCGTGGGTGAAGACAACCGGCCT +AAGATCACTGTGGGATTACCGACAGAATGTCTCGAGCGTCGCGTTTGGTGATGATATTATAAAAAGCGTT +AGCGATGAGTATAAGGATAAGTATAATTATTGTACTTATCGAGATGTACTAAATGCTACAGGACATATCA +TGACACCAGGTTCAAAGGATGGAGAAGAGAAGCCATTTACTTCTTTTGAAAACCTACAATTCTTGAAAAG +AGGATTTAAGTTAGAAAACGGTATGGTTTTAGCTCCATTACTACAACGATCTATTGAAGGACCGTTTGTA +TGGACTGATATCCGCGAAGATCAGATAACTGTGTGGGTAAATCTCGTGCAAGAACAGTTGATCGAAGCCG +CTCTTTGGGGTGAGGAGTATTACAATGAGCTTTGTCAAAAGCTAAAATGTGGTACAAATAGAACCTTGAA +TGGAGCATTAGCAGTATTGTTGAATACGAGCTGGGAAGTTACTTTCCAAAAATTCTGTAATCGTTATTAT +GGCATTAAAAGAGGAGATCTTTGATCAGAACACCACTCTTTTCACCGTTTTAGACGAGAACGAGGTTACT +GAGATTAAGTCAATTCAATCTTCAGTAACAGCAGTAAAGACCCAGCTCGATCAACAAAAACTGCAACTTG +ACGGTTTAGCTAAAGTAGTTGACAACAATCAAGCTCGAAATGAAGAACAATTCGTTAATATCAATACAGC +ATTGGTAGAAATGAATTCAGAAGTTGACAAATTAACCACAACAACAAGTCAACAGGCAAAACAGATTAAC +ACCCTTGCCACAACATTAAACGAGCTTGATCAAACTACGAAAGACTCCTTAGACACGTTGAACACAACAA +CAGAATCTCTTAGTAAACAAGTATTATTTAATACTGATGAGATTACCGTGTTAAAGGTAGACGTAGCAAC +CGTCACACAAAAACAACAGGACGTAGAACATTCACTTGTGACAATGAAAGATGAGATAGGAGAATTGCAC +ATATCAGTGAATGCCAATGCTAACTCCATTGAGGCATTACGCACCAGAATTGCCGCGCTAGAGGTTAGAG +ATGTAGGACCGTGGGTTTTGAAAAACAGAATTTACAAATTCGTGATCAATATGCCAAATGGAACTACTCG +CTATACTACAATATACTTTTTCGCCGATGTATATTATAGCACTGGAGTAAGAGCAGCACCTACAAATGCG +GGAACAACTACAAGCATATTGACGATTACTTCGTTGACAACATCATATAGTTTGGCTAACGTCCCCGTTT +TAAAAGGTGTACCTTATAGAGTCAATGGTTACTTTGCTAACGGAAATAGTATCGAAGATATAACCGGAAG +CACGTCAGTGATTTACGACTCTATGTAAAAACCGGACATGACATGTCTATGACACGACATTAAACTGTCA +GAACCTGTTTGGTTAACACAGAGAGATTAACCGCAAGACGAGTATGCAGAATCCAACACAAACCATGCAT +ATATACGACATGCCCCTACGCGTCATCGCTGGCCTGTCAACCCTTGCCAAAACAACTGAAGAAGACGACA +ACACCTCAACTGGAATAGTAGTTAGTGAAGTAGGAGAGCCACAAGTGGTCGACCATCCAGCATGGATTGA +TCCCTTTGTTGCTTATCAATTGCGAGCTCCACGTAAAAACATCACACCAGATTTTATATTTGGTCGAGCC +GATATTGGTAATGCGTTTAGTGCTTTCTTACCGCGCCGCTTTTCTGCTCCAGCAGTAGGAACCCGACTTG +TGATAGACCCTGTTTTCACTTACCAACAGAAAACGGTGCTAGGACTATATAATTATTTCCATGCGGATTT +TTATTATATAGTGCATGTTCCAGCACCCTTGGGAACAGGTATCTATCTGAAGATCTATGCTCCTGAATTT +GACACTACAACCGTAACACGAGGAATTCGGTTTAAGCCAAGTGCATCTCCAACAATTGCACTTTCAGTCC +CTTGGAGCAACGATCTATCGACCGTAGAAACATCCGTAGGTCGAGTCGGACAGAGTGGAGGGAGTATTGT +TATCGAAACTATCGAAGATAACAGTAACGAGACGGTCAACACCCCACTCAGCATCACCGTTTGGTGTTGC +ATGGCGAACATTAAAGCCACAGGCTACAAAAATGCGGATACGTCAGCTTACAACGAAAAAGGCATGAACT +TTGTCCCAGTTCCAGTGCCAAAGCCGCCCGTTCCCCCAACAAAACCAATTATGGGCGAGGAACAAGCTGA +CAATGAAGTTACAGCCGAAGGTGGTAAACTTGTACAGGAATTGGTTTACGACCATTCTGCGATTCCTGTA +GCGCCAGTCGTCGAAACACAAGCAGAACAGCCGGAAGTCCCAGTTTCATCAGTGGCAACGCGAAAGAACG +ATACGGGACATTTGGCAACAAAGTGGTATGATTTCGCCAAAATCAGTCTGTCAAACCCAGCTAACATGAA +CTGGACCACGCTAACCATAGACCCGTACAACAATGTTACATTGTCTAGAGATGGTGAGTCGATGGTCCTA +CCATGGAGGCGAAATGTTTGGACAACCGGATCGAAAAGTATTGGATATATCCGAACGATGGTTGCACAAA +TTAACATACCACGCCCGCCGCAGATCAGTGGAGTGCTCGAAGTTAAAGATTCAATCAATAACTCAAGTAT +TTCACTGGTAGAATTTGGAGGAAAAGTAGAGATTCCAATTATTCCGAAGGTTATGAACGGACTAGTAACA +AGTGCTAGTTTGCCAAGGCATAGACTAAACCCATGGATGAGAACCGCCGAAAGTAAGGTTGAATTGCAAT +ATCGAATTATTGCTTTTAATCGAACTAGCGACATTGCTGACCTTAACGTTAGCGTTTTGTTGCGACCTGG +CGATTCGCAATTCCAATTGCCGATGAAACCTGACAATAGTGTGGATACACGTCATTTTGAGCTTGTTGAA +GCTTTAATGTACCACTACGATAGCCTCCGAATTCGAGGAGAAGAACAGAGTCTGCCAGAAAATGCACCTA +ATGCAGTTTCAAACCCTCAGCAGTTCATTACACCCGCAACCGCTCTAAGTGCCGAAGAATATAATGTGCA +CGAGGCGTTGGGTGAAACTGAGGAGTTGGAGCTGGATGAATTTCCGGTTCTGGTGTTCAAGGGAAATGTT +CCCGTTGACTCAGTGACGTCCATTCCTTTGGACCTCGCAACTATATACGACTTTGCTTGGGACGGAGAGC +AGAATGCAATTTCTCAGAAATTTCAGCGTTTTGCTCATCTGATACCGAAAAGCGCAGGTGGTTTTGGCCC +AGTGATTGGTAATTATACTATCACGGCTAACCTCCCCACCGGTGTAGCAGGTCGTATTCTGCACAATTGT +CTCCCAGGAGATTGTGTAGATCTAGCAGTATCGAGAATTTTTGGCTTGAAGAGCCTTCTCGGTGTTGCAG +GAACAGCAGTTTCAGCCATTGGTGGCCCACTCCTTAACGGTTTGGTTAACACCGCAGCGCCTATCCTTAG +TGGAGCAGCGCACGCCATTGGTGGAAATGTTGTAGGAGGACTGGCTGATGCAGTGATCGACATTGGATCT +AATTTGCTGACGCCAAAAGAAAAAGAACAACCAAGCGCAAATTCAAGCGCGATTTCTGGAGATATTCCGA +TTTCGCGTTTTGTAGAGATGCTCAAGTATGTCAAGGAGAATTACCAGGATAATCCTGTGTTCCCGACTTT +ACTTGTTGAACCACAAAACTTCATCTCAAACGCAATGACCGCACTCAAAACAATTCCAATTGAGGTCTTT +GCCAACATGCGCAATGTGAAAGTTGAACGAAATTTGTTCGACCGAACGGTTGTTCCAACTGTGAAGGAAG +CTACTCTAGCTGATATTGTCATACCTAATCATATGTATGGCTATATTCTCCGAGACTTCCTCCAAAACAA +ACGAGCGTTTCAATCTGGGACCAAACAAAATGTGTACTTTCAGCAGTTTCTAACTGTTCTATCTCAACGT +AATACCCGTACACATATTACGCTCAACGACATCACAAGTTGCTCTATTGATAGTGAGTCGATTGCAAACA +AAATAGAGAGAGTAAAACGCTACTTGAGTGCAAACTCGAGTGGGGAGACCACGGAAGAATTTTCGCGAAC +AGACACCGGTCTGCTACCTACTACGACCCGCAAAATCGTATTAGGTGAAAGTAAACGCAGGACGGAACGA +AACGTAGCAGAAACTGTTTTCCCTTCCGTGAGGCAGTAGATTAAATCCAAAACTCGCCATGTGCGCGTCT +CAGAAACTAATTTTTAAAATTGGTTTGCGCGTATGGTTAAAAAGAGTCACATTAAATATGAGGATGGTCG +CTATAATTTTCTAGCAGAAGATTATAAAGGACGGTGTGATGATGTTTTGGAGCCCGCACTGGGTGTGGGT +TCGTAGTGCTAGCAATTGCAACTTTTCCTGAAAGTTAATACCTATAGTTTATAGGAGAAAAATTAACATT +TATTGAGAATATCTGTGCAAACGACTCCCCACGCGGGGAGTAGTGGAATCTTGATAAACAGGTTTTTTAA +GCTTTTGCGTTTCCGAAAGGGTTACTCTGGCTGAACCAGCAGTTTTTATAACTGTGGGTAGCCCCTCGGA +AAATCAGGTTTGC