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-rw-r--r--example/ref.fa81302
1 files changed, 81302 insertions, 0 deletions
diff --git a/example/ref.fa b/example/ref.fa
new file mode 100644
index 0000000..fdc51e6
--- /dev/null
+++ b/example/ref.fa
@@ -0,0 +1,81302 @@
+>SL1344 genome sequence
+agagattacgtctggttgcaagagatcatgacagggggaattggttgaaaataaatatat
+cgccagcagcacatgaacaagtttcggaatgtgatcaatttaaaaatttattgacttagg
+cgggcagatactttaaccaatataggaatacaagacagacaaataaaaatgacagagtac
+acaacatccatgaaccgcatcagcaccaccaccattaccaccatcaccattaccacaggt
+aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgaacagtgcgg
+gcttttttttcgaccagagatcacgaggtaacaaccatgcgagtgttgaagttcggcggt
+acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc
+aggcaagggcaggtagcgaccgtactttccgcccccgcgaaaattaccaaccatctggtg
+gcaatgattgaaaaaactatcggcggccaggatgctttgccgaatatcagcgatgcagaa
+cgtattttttctgacctgctcgcaggacttgccagcgcgcagccgggattcccgcttgca
+cggttgaaaatggttgtcgaacaagaattcgctcagatcaaacatgttctgcatggtatc
+agcctgctgggtcagtgcccggatagcatcaacgccgcgctgatttgccgtggcgaaaaa
+atgtcgatcgcgattatggcgggacttctggaggcgcgtgggcatcgcgtcacggtgatc
+gatccggtagaaaaattgctggcggtgggccattaccttgaatctaccgtcgatatcgcg
+gaatcgactcgccgtatcgccgccagccagatcccggccgatcacatgatcctgatggcg
+ggctttaccgccggtaatgaaaagggtgaactggtggtgctgggccgtaatggttccgac
+tattccgccgccgtgctggccgcctgtttacgcgctgactgctgtgaaatctggactgac
+gtcgatggcgtgtatacctgtgacccgcgccaggtgccggacgccaggctgctgaaatcg
+atgtcctaccaggaagcgatggaactctcttacttcggcgccaaagtccttcaccctcgc
+accattacgcccatcgcccagttccagatcccctgtctgattaaaaataccggtaatccg
+caggcgccaggaacgctgatcggcgcgtccagcgacgatgataacctgccggttaaaggg
+atctctaaccttaacaacatggcgatgtttagcgtctccggcccgggaatgaaagggatg
+attgggatggcggcgcgtgttttcgccgccatgtctcgcgccgggatctcggtggtgctc
+attacccagtcctcctctgagtacagcatcagtttctgtgtgccgcagagtgactgcgcg
+cgtgcccgccgtgcgatgcaggatgagttctatctggagctgaaagaggggctgctggag
+ccgctggcggttacggagcggttggcgattatctctgttgtcggcgacggtatgcgcacg
+ctacgcggcatttcagcgaaattcttcgccgcgctggcgcgggctaatatcaatatcgtg
+gcgatcgctcagggatcttctgagcgttctatttctgtggtggtgaataacgacgatgcc
+accaccggcgtgcgggtaacgcaccagatgctgttcaataccgatcaggtgattgaagtg
+tttgtcattggcgtcggcggcgtcggcggcgcgctactggaacagcttaaacgtcagcaa
+acctggctgaagaacaagcacatcgatctacgcgtgtgcggcgtggcgaactcaaaggcg
+ttgctaaccaatgtgcatggcctgaatctggacaactggcaggcggaactggcgcaagcg
+aacgcgccgttcaatctgggacgcttaattcgcctggtgaaagaatatcatctactcaat
+ccggtgattgttgattgtacctccagtcaggcggtggccgaccagtatgccgacttcctg
+cgtgaagggttccatgtggtgacgccaaacaagaaagcgaacacctcgtcaatggactac
+taccatcagctacgtttcgccgccgcgcaatcacggcgcaaattcttgtatgacaccaac
+gtcggcgccggtttgccggtaatcgaaaacctgcaaaacctgctgaatgccggtgatgaa
+ctgcaaaaattttccggcattctttccgggtcgctctcttttattttcggtaaactggaa
+gaggggatgagtctctcacaggcgaccgccctggcgcgcgagatgggctataccgaaccc
+gatccgcgcgacgatctttccggtatggatgtggcgcgtaaactgttgatcctcgcccgc
+gagacgggccgcgagctggagctttccgatattgtgattgaaccggtgttgccgaacgag
+tttgacgcctccggcgatgtgaccgcctttatggcacatctgccgcagcttgacgacgcg
+tttgccgcccgtgtggcgaaagctcgtgatgaaggtaaggtattgcgctatgtgggcaat
+atcgaagaggatggcgtgtgccgcgtgaaaattgccgaagttgatggtaacgatccgctc
+ttcaaagtgaaaaacggtgaaaacgcgctggcgttctacagccactattatcagcccttg
+ccgttggtgctgcgcggctacggcgcaggcaatgatgtgacggcggcgggcgtgtttgcc
+gatctgttacggaccctctcatggaagttaggagtttaacatggtgaaagtgtatgcccc
+ggcttccagcgcgaacatgagcgtcggtttcgacgtgttgggcgcagccgtcacacccgt
+tgacggcacgttgctgggcgatgtggtatccgttgaagcagcggaccatttccgtctgca
+taacctggggcgatttgccgataaactgccgccggagccgcgtgaaaatattgtttatca
+gtgctgggaacgtttttgccaggcattggggaaaaccatcccggtggcgatgacgctgga
+aaaaaatatgccgattggttccgggttagggtccagcgcctgttccgtcgtcgccgcgct
+ggtcgcgatgaatgagcactgcggcaaaccgttaaacgacacgcgtctgttggcgctgat
+gggcgagctggaaggccgtatctccggcagcatccattacgataacgtcgcgccgtgctt
+tcttggcggtatgcagttgatgattgaagaaaacggcattattagtcagcaggtgccggg
+ctttgatgagtggctatgggtactggcttatccgggcattaaagtttctaccgcagaagc
+acgggccattttgcctgcgcagtatcgccgtcaggattgcattgcgcatggacggcatct
+ggccggttttattcacgcctgttactcgcggcagccgcagcttgccgccgcgctgatgaa
+agatgttattgccgaaccataccgcgcgcgtttactgccgggctttagccaggcgcggca
+ggcggtgtcggagatcggcgcgctggcgagcgggatttccgggtcggggccgacgctgtt
+tgcgctatgcgataaaccggagacggcgcagcgcgtcgcggactggctgagcaaacatta
+tctgcaaaatcaggaaggcttcgttcatatttgccggctggatacggcgggcgcacgagt
+agtgggataatcaatgaaactctataatctgaaagaccataatgagcaggtcagctttgc
+gcaggccgtcacgcaaggactgggcaaacagcagggacttttttttccgcacgatctgcc
+ggagtttagcctgacggaaattgatgagatgctcaaccaggactttgtcagccgtagcgc
+aaagatcctctcggcatttattggcgatgaaataccgcagcaaattctggaagagcgcgt
+ccgcgcggcgtttgcgttcccggcaccggtagcgcaggtagaaagcgatgtcggctgcct
+ggagctgttccatggtccgacgctggcctttaaagacttcggcgggcgttttatggcgca
+aatgctgacgcatatcagcggcgacaaaccggtgacgattctgactgcaacgtcaggcga
+taccggcgcggcggtggctcacgcgttctatggcctggaaaatgtgcgggtcgtcattct
+ctacccgcgcggtaagatcagtccgttgcaggaaaaactgttctgtacgctgggcggcaa
+cattgaaaccgtggcgatcgacggcgatttcgacgcgtgccaggcgctggtgaaacaggc
+atttgatgacgaagaactgaaaacggcgctggggctgaattcggctaattcgattaatat
+cagccgcctgttggcgcaaatttgctactactttgaagccgtggcgcaactgccgcaggg
+ggcgcgtaaccaactggtgatctccgtccccagcggcaactttggcgatttgacggcagg
+gctgctggcgaagtcgttaggcctaccggtgaaacgttttatcgccgccaccaacgtcaa
+cgacacggtgccgcgttttctgcatgacggaaagtgggcgccgaaagcgacgcaggcgac
+cctgtcgaatgcgatggatgtcagccagccgaataactggccgcgcgtggaggagctatt
+ccgccgtaaaatctggcgcctgactgagctgggctatgcggcggtggatgatactacgac
+acagcagacgatgcgcgagctgaaagcgaaaggttatatctcggaacctcatgcggcggt
+agcgtatcgggcattacgcgaccagttaaaccctggcgagtatggcttgtttctcggaac
+ggcgcatccggcgaagtttaaagagagcgtggagtccattctgggagaaacgctggcctt
+gcctgaagcgctcgccgaacgcgccgacctgccgctgctttcacatcatctgcctgcgga
+ttttgccgccctgcgtaagctgatgatgacccgccaataaccattgcgcccggtggcgct
+gtcgcttaccgggcctatggggtggtgtcgatttgtaggccggataaggcgtaaccgcca
+tccggcgatgccgttactgctcgtagcgtttaaagaccagctcgtcttgtgtggaggttt
+cttcatcaaagaaatacccttcacggtcaaacgcggtaagctgttccggcttcgttaagc
+ggttttcaataataaaacggctcatcagtccgcgcgcttttttggcgtagaagcttacca
+ccttaaacttgccgtttttctcatcaaggaacacgggcttaatcagttcggcattcagtt
+tcttcggcttcaccgatttaaaatattcctcggaggccagattcaccaccacccgatcgc
+cctgcgcctcaagcgcttcgttgagcttatcggtaatgatatcgccccagaattgataaa
+gatctttgccgcgcggattctccaggcgaatccccatctccagacgataaggctgcatta
+aatccagcgggcgcaatacgccatacaagccagagagcatacgcagatgttgttgagcaa
+aatcaaaatccgcgtcgttgaacgtttccgcctgtaggccggtataaacatcgcctttga
+acgccagaatcgcctggcgtgcattatccggcgtaaaatgaggctgccagtcatgaaaac
+gcgtggcgttgagatccgccagtttgtcgctaattcccatcagcctggaaatttgcggcg
+ccgaaagctggcgggcctgttgaataagctgctggctgtgatccaacagctccggctggg
+tatagcgggtcgtggccagcgggctttgataatcaagcgtttttgcaggtgaaatcagaa
+tcagcatattcagtccttgcagggaattttctgcgactttagcaaaaaaacgccgcagag
+ttgaccgatggttgcgattgtcggcttaatcgcgcgatgccgcctcccaggtatctggcg
+ccagttgtggttcgatatccgggaagcgccgcggatcgaactgcggtcttacgcccagtt
+tccgttgtcgcagataatcgctggcgagggtatacaccaccggtgagagcaacaaaatcg
+ccgtcagattggtaatggccatacaggccatgatcatgtcagcgagctgccatatcagcg
+gaaaactgataagcgtaccggcgataaccatgccaagcgtcgcaaggcgtaatagccaga
+tagcctttgcgttatgtaaccgcagaaaaaacagattgttttcggcgtaaatatagttgg
+cgacgatagaactgaacgcgaacagaatgacgataagcgcgacaaaactggcgccccatt
+caccggtcaacgaaaccattgcatgttggagaagctgaatgccttctgttgacgagtggg
+acgcgtgattccccgccagcaggataatcatcgcgctggcggtacagatgataatggtgt
+cgctgaatacgccaatcatttgcacaatcccctgcgcgacagggtgagggggatacgacg
+ttgccgctgcggccgcattaggcgttgaccccattcccgcttcattagagaacatcccac
+gctgaaaaccgctggtaatagcctgggtgagcgtatatccggctgcgcctgccgcggctt
+cctgccagccaaatgcgcttttgactatcgaggcgataacgccaggcatttgctcaatat
+gccagaggcaaatgaatacgctgccggcgacccacaataacgcgatgaggggaatcagcc
+attgcatcagacgggcgacgcctttgatgccgcgaatgataattaacagggcacagaacg
+ccagagcaatgccggagataagcggcggaatgttgaaggcgaaatggagcgcgcgtgaga
+cggcattcgcctgcacgctattaaaaatcaacccgtaggcgacgagcagaaagagggcga
+aaaccacgcccatccagcgcattcccagcccacgcgccatataccacgccgggccgccgc
+ggaactggcctgtcgggtcacgttctttataaagctgggcaagcgaacactcggcgaagg
+aggtcgccatgccaatgatggccgagacccacatccagaataccgcgccgggaccgcctg
+cggcgatagccagcgccacgccggccaggttaccgctgccaatccgcgccgcgaggctgg
+tacacagagcctgaaatgacgtcaggccgcctggctgcgggctaaggctgcctttcagac
+tgcggctaaattggcgaatataacgaaactgaatgaatccggtacgccaggtaaaccaac
+atcctgcgccgagcagcaggtaaatcattaccgagccccagagtatttcgttaataaaac
+tgaaaaactcaggcattaacgtccctcttgttgatgccggcacgctttgataatcctgta
+taagcgtgacccatgatgtagatgaccttgtcagactaatattaacggcagtttaccata
+aatacggtggtatcctttaattgcgcatcaaccgtcggcagatacgcaaacagtgcacaa
+gggcagccaggtgcatgtaggcggttgcgctgtgagtgcgtcgtgttatcatcagggtag
+accggttacatcccctaacaagctgtttaaagagaaactctatcatgacggacaaattga
+cctcccttcgtcagttcaccaccgtagtggctgataccggagatatcgcggcaatgaaac
+tgtatcagccgcaggatgctacaactaacccttctctcattcttaacgcagcgcaaatcc
+cggaatatcgtaagctgattgacgatgctgtcgcctgggcgaaacagcagagcagcgacc
+gcgcgcagcaggttgttgacgcgaccgataagctggcggtgaatattggcctggagatcc
+tgaagctggtgccggggcgtatttctaccgaagttgacgcgcgtctgtcttatgacactg
+aagcgtctatcgccaaagcaaaacgtatcattaaactctacaatgatgcgggtatcagca
+acgatcgtatcctgatcaagctggcgtccacctggcagggcattcgtgcagccgaacagc
+tggaaaaagaaggcatcaactgtaacctgacgctgctgttctccttcgcgcaggcgcgtg
+cgtgcgccgaagcgggcgtctacctgatctcgccgttcgtaggtcgtattcttgactggt
+ataaagccaataccgacaagaaagactatgcgccagctgaagatccgggcgtggtttccg
+taacggaaatctacgagtactacaaacagcatggttacgaaaccgtcgttatgggcgcaa
+gcttccgtaacgtaggcgaaattctggagctggcgggctgcgaccgtctgactatcgcgc
+cggcattgctgaaagaactggcggaaagcgaaggggcgattgagcgtaagctctctttct
+ccggcgaagtcaaagcgcgcccggaacgcattaccgaagccgagttcctgtggcagcatc
+accaggaccccatggcggttgacaaactggcggatggtatccgtaagtttgcggtagacc
+aggaaaaactggaaaaaatgatcggcgatctgctgtaatcattaacgcgtggccctgata
+tgggtcacgctacctcttctgaaacctgtctgtccttcccttcgcagtgtatcattctgt
+ttaacgagactgtttaaacggaataatcatggataccttacgtattggcttagtttctat
+ctccgaccgcgcttcaagcggcgtttaccaggataaaggcattcctgcgcttgaggagtg
+gctcgcttctgcgctgaccacgcctttcgaggtccaacggcgcttaattcctgatgaaca
+ggaaattatcgagcaaacgttgtgtgaactggtcgatgagatgagctgtcatctggtgct
+gaccactggcggtaccggtccggcgcgtcgcgacgtcacgccggacgcgacccttgccat
+cgccgaccgtgaaatgccaggttttggcgagcagatgcgccagatcagcctgcgctttgt
+gccgaccgccattctttcccgccaggtgggcgttatccgtaaacaggcgttaattcttaa
+tctgcctggacagccaaaatcgatcaaagaaacgctggaaggcgtaaaagcggacgatgg
+cagcgttagcgtgccgggcatttttgcgagcgtgccgtattgcatacagctgcttgacgg
+gccgtatgtcgaaaccgcgccggaagtggttgccgctttccgtccaaagagcgccagacg
+tgagaatatgtcggactgaccggaaaatactgatagtagggttattcctcccggtgcggg
+aggaataaaagagatttagtgcgcctcgccgattggcagaatagtgcggccaaattgctc
+gtttagcacttcacccatcgccagataaatagcgctggcgccgcaaaccagaccaaccca
+gcctgcgatatggatagttgcttcgttaccggtgatattgccgaccgccagcagagcgaa
+cagtacggtcaggctcaggaaaacaaattgcagcgcgcgggcggctttcagcgtaccgaa
+gaacataaacagcgtgaacacgccccacagacctaaataagcgccgagtagctgagcgtc
+aggcgcatccgtcagacccattttcggcatcagcaggatagcgaccagcgtcagccagaa
+cgaaccgtaagaggtaaaggccgttaaaccaaaggtattgccttttttgtactccagcag
+accggcaaaaatttgcgcgataccgccgtagaaaatccccatcgccagaataataccgtc
+cagggcgaaaaaaccggcattgtgcaggttaagcagaatggtggtcatgccgaagcccat
+caggcccagcggtgccggattagccaacttagtgttgcccataattcctcaaaatcatca
+taattgaatggtgaaatagtttcccagaataacgagttccgtattcggggcgcggcataa
+taatcagggggaagaggactgtctatgatctaataagggggaaaagaaaatatttccccc
+agtgagggcattcacgcctgaacggctgccatcattcgtcgcaggcaggctatttgcaag
+accgccggaatagtcacgcgatacgcgctgccgctcatcgctttgacgccgtttaacgcc
+gcgccgaccgggccgccaagacctgcgccgcgcagcaatccgtggcccaggatgctcatt
+gcggcatgggtacgcaaaatgcgggtaagctgggtggaaagcaggtgggagacccctttt
+gccagactgcgatctttcatgagcagcggcagcagttcttccagttcagaaactttggcg
+tctacggcttgcagaaattcctgcttatgcgccgcgtccatcttctgccaggtatgacgt
+aaaaaatgctccagcagttgctgttctatttcaaacgtcgacatgcttttatctgctttg
+agttttagccgttttgcgacatccagcagaatcgcgcggtactgttttccgtgtccgcgc
+aatttgttggcgatactgtcgccgccgtaatgctgaaactcgccggcaatgagctgccag
+ttacggcggtgttgctccgggtgaccttccatcgctttgaacagctcgttatggctaaga
+acgctcgacaagcgagctttgcccttttcgttatgcgtcagcaaacgggcgaaatcggcg
+agttgttcttcgctacaatgctgaagaaagtctaaatcctcgtcgtgtaaataggtgacg
+ttcattttcagtctggcttttggaatagaaataacagcgattaatcgtcgccaatgactt
+taagtctcgccatatcggaagaatttaccgtatggcctgagaaggtaatctttgatacgc
+agcgtttgttgtcgttatcgctattaatattgatccagcctgttgtctggccctctttga
+ttgaggaagggacgttcaggctttggctggcgctacgcgcagttttaaaatagacggatg
+cgccgctaagttcgatgtcgccgtgatccgccgtgagttgaatgcgcttcacgatgcggc
+agacgggaattttcagcgtgagatcgttcgtttcatttctgggcatggcaataacaccca
+gtattttatggtcgttcgcgtgcgcgacgctacttaacgccaggccgaaaagcaggccga
+cggaaatcgttaacacagatcgcatggaatttctctttgacgggttcaataagcaatacc
+gtctatcatactctgctcatggcaacgattcagttttgtaatcttttctttttattacaa
+tttttctgtgaatggtattcgttatttaatttatttcatgaatatttatctgtctggttt
+tccatcgtgccctctcgtcactaaaaaattttttcatctcccccttgatgacgtgggtta
+cgaccccatcttgtagtcaaccgcagtggtgagtctgaaaaaaaacgattcagggtagtt
+gaaaccgcacgtttcgcccttattacagattcacaaccacatgatgaccgaatttttagt
+ggagacgtttagatgggtaaaattattggtatcgacctgggtactaccaactcttgtgta
+gcgattatggatggaacgcaggcacgcgtgctggagaacgccgagggcgatcgcactacg
+ccttctatcattgcttatacccaggatggtgaaactctggttggtcagccggctaaacgt
+caggcagtgacaaacccgcaaaacaccctgtttgcgattaaacgcctgattggccgccgc
+ttccaggacgaagaagttcaacgtgacgtttctatcatgccgtacaaaatcatcggcgcc
+gacaacggcgacgcatggcttgatgtgaaaggtcagaaaatggcgccgccgcagatttct
+gccgaagtgctgaagaaaatgaagaaaacggctgaagattatctgggcgaaccggtaact
+gaagcggttatcaccgtaccggcttactttaacgatgcgcagcgtcaggcaaccaaagat
+gctggtcgtatcgcggggctggaagttaaacgtatcatcaacgaaccgactgccgcagcg
+ctggcttacggtctggataaagaagtcggcaaccgtactatcgcggtttacgacctcggt
+ggtggtactttcgatatctctattatcgaaatcgacgaagttgatggcgaaaaaaccttt
+gaagttctggcaaccaacggtgatacccacctgggtggtgaagacttcgatacccgcctg
+atcaactacctcgttgacgagtttaagaaagatcagggcattgacctgcgtaacgatccg
+ctggctatgcagcgcctgaaagaagccgcagaaaaagccaaaatcgagctgtcttctgcg
+cagcagaccgacgtgaacctgccgtacattaccgcagatgccaccggtccgaaacacatg
+aacatcaaagtgactcgtgcgaaactggaaagcctggttgaagatctggtgaaccgttct
+atcgagccgctgaaagtcgcactgcaggacgctggcctgtccgtgtctgatatcaacgac
+gtgatcctcgttggcggtcagacccgtatgccaatggtgcagaaaaaagtggctgagttc
+tttggtaaagagccgcgtaaagacgttaacccggacgaagctgtggctatcggcgcagcg
+gtacagggcggcgtgttgaccggtgatgtgaaagacgtactgctgctggacgttaccccg
+ctgtctctgggtatcgaaacgatgggtggcgtgatgactccgcttatcaccaaaaacacc
+accatcccgaccaagcacagccaggtgttctctactgcggaagacaaccagtctgcggta
+accatccatgtgctgcagggtgagcgtaagcgtgcgtctgataacaaatctctgggtcag
+ttcaacctggatggcatcaacccggcgccgcgcggtatgccgcagatcgaagtcaccttc
+gatatcgatgctgacggtatcctgcacgtctccgcgaaagataaaaatagcggtaaagag
+cagaagatcactatcaaggcgtcttctggtctgaacgaggaagaaattcagaaaatggtt
+cgcgatgcagaagcgaacgctgaatccgaccgtaagttcgaagagctggttcagacccgt
+aaccagggcgaccatctgctgcacagcacccgtaagcaggttgaagaagcaggcgataaa
+ctgccggctgatgacaaaaccgctatcgagtctgccctgaacgcgctggaaactgccctg
+aaaggcgaagataaagccgctatcgaagcgaaaatgcaggaactggcgcaggtttcccag
+aaactgatggaaatcgctcagcagcaacatgcgcagcagcaggctggctccgctgacgct
+tctgcaaacaacgcgaaagatgacgacgttgtcgacgctgagtttgaagaagtaaaagat
+aaaaaataatcgccctttgaacgggtaattactggcacgggcgaagaggtttcctctccg
+cccgtgtatgcatgttaagggcagataaaaagagatggcgaaaagagattactacgagat
+tttaggcgtttccaaaacagcggaagagcgtgaaatcaaaaaggcgtataagcgcctggc
+catgaaatatcatccggaccgcaatcagggtgataaagaggccgaagctaagtttaaaga
+gattaaagaagcctacgaagtgctgaccgatgcgcaaaaacgcgcagcctacgatcagta
+tggtcacgccgcgtttgaacaaggcggtatgggcggcggatttggcggcggctttaatgg
+cggcgctgatttcagtgatatctttggtgacgtttttggcgatatctttggcggcgggcg
+tggtcgccaacgtgcggcgcgtggggctgatttgcgttataacatggatctcaccctgga
+agaagcggtgcgtggcgtgaccaaagagatccgtattccgacgctggaggagtgcgacgt
+ttgccacggcagcggcgcgaaagctggcacgcaaccgcaaacctgtccgacctgtcatgg
+ttctggtcaggtacagatgcgccagggattctttgctgtacagcagacctgcccacactg
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