Mercurial > repos > drosofff > blastn_to_scaffold

--- /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
+ATTGACACGTATGTAGTTGACTATCAAACAGTCTACAAAACCAGTCGTGGTAACAAAAGT
+GGTAGTTATACTACTACAATTGATAATTGCCTGGCGAACGATATTTATGGTTTGTATGCG
+TGGGTGAAGACAACCGGCCTAAGATCACTGTGGGATTACCGACAGAATGTCTCGAGCGTC
+GCGTTTGGTGATGATATTATAAAAAGCGTTAGCGATGAGTATAAGGATAAGTATAATTAT
+TGTACTTATCGAGATGTACTAAATGCTACAGGACATATCATGACACCAGGTTCAAAGGAT
+GGAGAAGAGAAGCCATTTACTTCTTTTGAAAACCTACAATTCTTGAAAAGAGGATTTAAG
+TTAGAAAACGGTATGGTTTTAGCTCCATTACTACAACGATCTATTGAAGGACCGTTTGTA
+TGGACTGATATCCGCGAAGATCAGATAACTGTGTGGGTAAATCTCGTGCAAGAACAGTTG
+ATCGAAGCCGCTCTTTGGGGTGAGGAGTATTACAATGAGCTTTGTCAAAAGCTAAAATGT
+GGTACAAATAGAACCTTGAATGGAGCATTAGCAGTATTGTTGAATACGAGCTGGGAAGTT
+ACTTTCCAAAAATTCTGTAATCGTTATTATGGCATTAAAAGAGGAGATCTTTGATCAGAA
+CACCACTCTTTTCACCGTTTTAGACGAGAACGAGGTTACTGAGATTAAGTCAATTCAATC
+TTCAGTAACAGCAGTAAAGACCCAGCTCGATCAACAAAAACTGCAACTTGACGGTTTAGC
+TAAAGTAGTTGACAACAATCAAGCTCGAAATGAAGAACAATTCGTTAATATCAATACAGC
+ATTGGTAGAAATGAATTCAGAAGTTGACAAATTAACCACAACAACAAGTCAACAGGCAAA
+ACAGATTAACACCCTTGCCACAACATTAAACGAGCTTGATCAAACTACGAAAGACTCCTT
+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