--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out5.fasta	Sat Feb 21 16:33:42 2015 +0100
@@ -0,0 +1,258 @@
+>mm9_chr10_62044837_62045189_+
+AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACT
+TTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTT
+TTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTC
+TGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCG
+GGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTT
+CTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCC
+TCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTC
+GCT
+>mm9_chr10_75372919_75373002_+
+GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCAC
+CAGCACCTCAGGCTGTGACGCATTCTCATGGATC
+>mm9_chr10_80362428_80363292_-
+ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTT
+GGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGG
+CGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCC
+TCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCC
+GGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGT
+GTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCC
+ATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTA
+CAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGC
+CTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGT
+GTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATC
+GAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTG
+AGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCT
+CAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTC
+ACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGG
+TATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAG
+CATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAA
+GCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctg
+accttaactctgaat
+>mm9_chr11_7904565_7904642_+
+CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACT
+CACTGCATGTCCACTTGTCACAGGAGCC
+>mm9_chr11_78140156_78140259_+
+CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCC
+TGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAA
+ACAC
+>mm9_chr11_105616462_105616737_+
+TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCT
+GTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACAT
+GCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAAT
+TATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCAT
+GATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTT
+TGTAAATAACATGTTTGTTACTAGTA
+>mm9_chr12_30701762_30702509_+
+TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGA
+CATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCA
+TCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAG
+TGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGT
+GGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTG
+AGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAA
+AATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTG
+TCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAA
+GGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCT
+GTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAA
+ACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAG
+GCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCT
+TCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCC
+AACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGA
+GGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCA
+>mm9_chr13_49159496_49159569_+
+ttttcttttggattacttgatttttttttatttgatcttatttatgatga
+ttttgagtacatttttgaacagtt
+>mm9_chr13_100200304_100200330_+
+TCTCATATGAATAGCCACCCTCTTCTG
+>mm9_chr14_31949103_31949152_+
+GGATGCTATCCGCGATGTGCATGTAAAGGGCCTCATGTACCAGTGGATCG
+>mm9_chr14_67604227_67604668_+
+TTCACCGTGAGAGTTTTCTCCATTTCACTCTTCACTGTGCTGTTCTCTGT
+GCCGCTTTCCTCTTGACTTATAAACATCTGAGCCAGTTTTCAATAAACTT
+AAAACGAAGCCTGCTTCTCATCCCAAATTGTAAACAGGAATAAAGCTTTT
+TAAACCTTATCTTAAATTTTAACTTTGTTGAATTCTGCTTTGTGATAGGA
+CAATCTGTTTCACCCAACAAGAATCTGTGTAGGAGGATGAACATCCCGCA
+TGTTGGAGCTGCAAATCAGCACTGTACAAGCTCACTGATGGACAGCTGTT
+CTGTGATGTATTCCATGATTTTACTAATACTTTCAAAAATGGCAAAACTA
+ACTTCAGTTTTAATGTTGAAAGAAAATCATAAATGTTCCCATAGTTCAAT
+GGCACTGTCGATGAAACTGCTACTGAATTTAGAGAGAAAACG
+>mm9_chr14_75165582_75165744_+
+ggccctgggatgataTAACAGAAGAGTCTAAAGGAGGCTTCTGAGATGTG
+CAGTAGGAAAGCCTGGCACATAATAGGTTATTATCTAAATCCCTTCACTA
+CTCTTCAAAGACAGCAGGATGCCTCTGCTCCCATGTTTTATCTCTACTTA
+TGTGGAATTTATG
+>mm9_chr16_57154027_57154067_+
+GTTGAGGTTTATTTAAGTAAAATGATTTTTTAAAAAAGCAA
+>mm9_chr16_74862302_74862560_+
+GCATTGGCAGCAGATATTGGTACCCAGTGGCACTGCAGAGTACTTACAAT
+CAGGACTCGCTACTGTGCTTCATTCTGCTTTTCTCTCTGCTTCTATTACA
+GTTAAAGTGTTGCTAATTATAGAAACTCTCTGTTTATTGAACCTCGGTGT
+TAAGAAAAACTTGTAATCTTCAGATATGATCCGAAAGATTCCCAAACAAA
+TGTAACAAGGTCCACTTTTGTAGCCCTTTCTACCAGAAcactggttatca
+acctgtggg
+>mm9_chr16_98168779_98168914_+
+CCTATTTATTTCACTAAACATCTGCCTGCTAGCTGAGATAAACATTCTCT
+AAAAAACTGTTTACTGCAAAAAGTGATTACTGTTTTTTATTAGTTTCTTA
+GCATTTGAAATAGTTACATGAATGGAAGGATAGAGT
+>mm9_chr17_8483212_8483268_+
+AGACTTGTCAACAGCTCACCCAATGATGGAACTGAGGCTGCCCCTCAAGT
+GGCCAGA
+>mm9_chr17_30355791_30355913_+
+atctcatacccataagctcagaactcggggtggtaacataggaggactgc
+catgagtgtgactaacctgggctataggaggaggatctaccttaagcaaa
+tgaCCAACAAAACTAACAAGCTC
+>mm9_chr18_39571718_39571880_+
+TATAACATTCCATAAATGTACAATAATCTATTTTTGAGAAGCTCATTTTG
+AAACTTAACACTGTCATTGATAATCTTCAAGTGGTATTTCTTAGGCACCA
+TAAATTTCACATCCAGCTGGGTTACAATTATTTTAAAGTACTTTGAGACC
+AATTTAAACCATT
+>mm9_chr19_17633088_17633203_+
+TGGGAAATGAACTGCATGGCAATGAACCCCAGGGAATTTGGTGGTTAATT
+GTCTAAGGATAAGGACATCAGTTTTGTCTTTTGCATCACTGTGACCTTTG
+CCTCTAATTGTATAGA
+>mm9_chr19_41997624_41997859_+
+gctacacaacgactcacatagagggaagcaggcacacatcagataaaaca
+cAAAAGGATGGGTTGGTGATGGGCATAGTTAATGAGGGCCACTAGGTAAA
+TACACCTGATCCAAAAGTCACGCTACTACTTAGATTCTTCTCTCTGCTAA
+AGACAACAGAAgacatgttagccatgcttgtaatccctgcattggggaga
+tggagtcagaaatatcactgcaagttcacccaatag
+>mm9_chr19_56516515_56516684_+
+TGTATTCATTCACTATTCACTGATTTGTCAGATCATCCATCCACACAGGT
+GCTGAAGAGTAACCCATTTCACTTTGTATACAAGATAATGTTTTTGTACT
+TCAAATACATCTGGAATTCTTTCAAATATTCCAAGATTTTTTTTTTTTCT
+GAATAATCTTTGGTTACCTC
+>mm9_chr2_4543774_4543977_+
+gagccatttctccagccccTTTATGTGGAATATTAACAAGAGAAGACAAC
+ATAAAATGACTTACCATGCTGTGTGGCCTAACAGTGGATGAAGAATGAGT
+GATTTGGGCATTTCTGATAGTATTTATAAAGAAGACTTTTATGACCAAAC
+CACATGTCACAGTAGGGATTTGCTGCACATCTTATGAGAGTTTCTTCTTT
+GTCA
+>mm9_chr2_30200331_30200938_+
+CGCACACAAAGGATTTATTTGCCAGAGAGCAAGCAGACAGGCAGAGGTCA
+GAATGTTAGTTAGAAACTGAAGGAATGACTGCTGTAGCCACTGTGCCCAG
+CCAGAGCCATGAGGGAAGTGGGAGGCAGCACTTGGTGCTGCTGCTCTGGC
+TGACCCTTCTGGTTTCCTGCCACACTCCTAGCCCTGCCTGTGTGCTGCTG
+TCCCCCTCAACCTTCCACAGCCAGAAGGCAGATGTTCTTTCATGCCAAGA
+GCATCCATCCCCAGCATATCCTGGGCCCATGGTGGTGTCAAATGTAGTGA
+CCCTTCTGCCTTAAGGGAGCTGGGAAGCCTGGGGTGTGCAGGGTTGCAGG
+TCAGAAGCAGGACTAGCAGAGGGGCCTGGGGCCATTCTGTCTTGTGGGCT
+CTTTAATAGCTGAATGACGGGCACAGCCAGAAAAGGGTTAGGTCCCTTAT
+CCTAAGCAGCTCTGTGGCCAGCAGACGACTCTAAGTGGCAGAGCCTGGGA
+AGGGGCTGCTTAGCTGAGAAGTTCCAGGTAGGTGACAGGAACCTTGCCCT
+TCTTGTTGCCTCTCTCACCAATGAGCCAGTCGGGATCCATGCCTGGCAGG
+CTGTAGAC
+>mm9_chr2_106644220_106644341_+
+attcttaaggtaaatacctaggagtgatgtaacccagtcatagggaagaa
+ctacttttaatttgttgagcaacccccaacctgattttgacacaggtttg
+agtagtttacacttctactaac
+>mm9_chr2_125388931_125389219_+
+AGAGCACACAGCACATCACTTAGGCCTCCAACATTAAGGCAGCGCAAGTG
+CCTCAAGTAACTGAGAATACTTTACTCAGATACAAGGGTATCAAAAACAT
+GAGAACTGGCAGGAAGACCTCACAATGGTTTGTTAGCATCAAGTATTACC
+ATCCAGTTTCCTGTTTAAATAGTAATTAATGACTATTCTGAAATAAGGCA
+AATAATTACTCAAGCGGGCTGTCAAAGCCACTATCCTGTTGGCTGGGCAT
+CGGAGCAGTTAACTTTATCAAAGGCTTCTGACACAATGA
+>mm9_chr3_130936639_130936898_+
+CGAGGCTGCAGGCTGCAAATGTTCCCAGGCAGGCAAGACCTCACGTCCTA
+CTGGCTGCTGCCCTTGGGTGCATCTGTAGGCCCCGTGGCTCCTGCCCCTG
+GGGTTCAACACCGATAAACATAGAATACTCATTTTCAGAAGACCTGAGGG
+AATGAGTCTAAGCAACGCTTTTTACAAAAAGTGGCAAGGTTCAGGAAAAA
+AAAAAAAAAAGATGTTGCTCCAAGGCACCAAGGGTGTAATTTTTTTTCAG
+AAAAAGTCAG
+>mm9_chr3_136592671_136592771_+
+TGTCAGCCCATCACATTTTAGTGACAACAGTCATAGCCTTTATTTTCAGA
+TGACTTTCCTCTAAAACCACTGTCTATGAGTTGCCCCCCAAAACTCAAAA
+A
+>mm9_chr3_152861374_152861508_+
+ATCAAAAGCGACATGCAAGCATCTTGCTCTCACCACAGATCACTGAGACA
+TTAAGAGTGACGTCTCTTGAACTGTTGGCACGCCTAAGTTATTTCAGCAT
+TTCTTGCTCAGCAGTTGTTCTCTTGGCTTCCTCTG
+>mm9_chr4_13715310_13715630_+
+AACACATGGCCACATCATGTGATATTTTCAAAACACTTACACATAGCTTT
+GAGAAGGTCCCTGCAGGAATGATCCATCCTCTCACAGTTGGCCCATTTTT
+TAACAGCATATCTGCATTTTCCATTTAGGAGAGCTATATATTATTAGCTT
+ACATTTTTGGGTAGTAAAACAGTGCATTGCTGATTGTAAAACATGGACTT
+TATTATCTGCTGAAAATTGATTTGGCATTTATAGCCACTGTGTATTAGAC
+TGTTTTTCTGTTTTTAACATCAATGCTTAAAAGCGATGATTTGTGTTTaa
+aaaaattaaaaaaataaaata
+>mm9_chr4_147515029_147515097_+
+GCTGACGTGCTCTCCGAGTTCCTGGAGGTGGCCGTGCACCTGATTCTCTA
+TGTGCGCGAGGTCTACCCG
+>mm9_chr5_3949522_3949685_+
+AGTCCCAACCACCCCCTTGTTTAATGTATAACTTTCTGAAATGGGAGCGT
+TAGAATGGATTAAAATGGTTGGTAGGTGGTTGGATCACCAACCAAGACCA
+GAAATAGAGGGGTAGGCTGCTCAGGAGAGTATTGGGAGGGTAGCTATTAT
+TTGCATTTTGTGCT
+>mm9_chr5_68089694_68089831_+
+CAATGATAGAGAAGACTAAAATAAAAGCAGGCATGCTGGCACAAGCGACA
+GAAGGAAAAAGCCTCACCCGGCCCTGTTTGAGGCCACTCCTGGTGGCTCC
+TTTTCCAAGGACCATGCGGTCAAGCCTCTGAGTTGTTC
+>mm9_chr5_122819526_122819619_+
+CTTTAGAAAAGATGCATCTGTCATTGATTTAGGGATATGAATTGTTTGGA
+TTTGAGTAGTTTTCCATAACTCCTGCAGTTTGGCAATGTGTGCG
+>mm9_chr5_145619548_145619710_+
+CGGCGTTCTGAAAACTGTGCTCCGGGATGAGATCATTGCTTGGCACAAAA
+AGACACAGGAGGACACTTCCTCTCCACTGTCGGCCGCAGGGCAGCCTGAG
+AACATGGACAGCCAGCAGCTGGTTTCCTTAGTTCAGAAAGCCGTCACTGC
+CATCATGACCCGC
+>mm9_chr6_83928984_83929105_+
+ACAGGAACCATTATTTACATTTAATTTGGATGAATTTGTTACTGTGGATG
+AAGTCATAGAAGAAGTAAATCCTTCTCAAGCCAAGCAGAATCCATTAAAA
+GGAAAAAGAAAGGAAGCCCTCA
+>mm9_chr6_118857949_118858148_+
+CCAGGCTTGCTAGTTGGTGCAGTTAGCTACATCTCAGGACAGAGACAAGG
+TACTCTGAGCTCCCCTTGAACTGCCACACAAGCTGTCTCCTGGATGCCAA
+GCAGAGAAACCTGGAGACAACAATCATCATACTCAAAACCAGGATCTCTT
+TCTTAAGACTTTTGTATTTTGTCCCAGCCCTAACCCTGAGTTCTGCTGAA
+>mm9_chr7_85554210_85554343_+
+GTGAAACATCATGCTTCTGCATCAAGTTATTAGTGGGAAACCTGTAAAAG
+TTGACATTGAATGCTGATAACAAATTACTTTCATCCTGTCTCATAATGAA
+TCCTACATCAAGACAAGGCAAGTGAGAAAGAGGG
+>mm9_chr7_104055491_104055589_+
+ACATTTCTCCTCTCTTGGGGGAGCGCATCTCCTTGGGTGTGTCCACATCC
+GCCCCTAGGTACCCAGTGTGATGTGAGACACGAGTGTCTGTGCTAACTT
+>mm9_chr8_9970398_9970545_+
+AGTCTTCACCAAAATTAAGTCTCAGCTAACTTAAAAGTTGCAAGGATTTT
+TTTCAATAAAATTAATATCTTAAGTGTTTGGTGTTTAGATGATTCTCTCT
+CAACTTCCCCCACATTATCAAAAAACATTTGATGAACCTTAAAAACTC
+>mm9_chr9_20449846_20449932_+
+CCAGCACCGATGACACCATCGGCGACTTGAAGAAACTGATAGCTGCTCAA
+ACTGGCACCCGCTGGAACAAGATCGTTCTTAAAAAGT
+>mm9_chr9_107445870_107445930_+
+CAAGCAGAAGCTGGTGCCCATCATGACCATCCTGCTGGAAGAGCTGAATG
+CCTCCGGCCGC
+>mm9_chr9_120860476_120860606_+
+CTGCCATTGTACGCACCATGCAGAATACAAATGATGTAGAGACAGCTCGT
+TGTACTGCTGGGACTCTGCACAACCTTTCTCACCACCGCGAGGGCTTGCT
+GGCCATCTTTAAGTCTGGTGGCATCCCAGCG
+>mm9_chrX_10274057_10274087_+
+ACTTCGCTGTCATCATTTGTACAAACTCTTT
+>mm9_chrX_39881431_39881678_+
+AGCTAAAAAGAGTCCTTTTCTGACAGAAAGGCTGGACTTCTCCTTTTCAC
+CGTTTCTCTTACTGATGCTTTTGCCAGAAGAACAGTAAAGATTTAGACAC
+TGTCATGATTCATACACGTAAAATATTTTTCAAGGACACAATCTGATATA
+CTAACATTTATTTAAGAGGTTAAAGTCCACCACTAAATCTAAGGAAAGAT
+TTTTAACTGCCAAACACATTTCCTTTGACAAATAATGTAAGATGACAA
+>mm9_chrX_148249672_148249713_+
+AATGCTAGTATGAACAGTGGGAGGAATGAGCAAAATGTTACA
+>mm9_chrX_148481505_148482455_+
+CGCCACAACCTGCTACAGGCCTGTAAGATGCAGGACATCAAACTGCCACT
+GTCAAAGGGCACCATGGATGATATTAGTCAGGAAGAAGTGAGTATTATGG
+TGGGTGGTAGGAGTCATCTATGAATATTTAACCAGTAATGGGAGATTACA
+GATGGCCAGGAAGGGCAGGCAACAGATAGGACCACATAGAGTTGTGAGGG
+GCATAAAGATGGATGCAGAAGAAATGTGGCAAGGTGGAAGTAGTGAAGTC
+AGGCTTTGGTATGAGAGAGACATTGATTTGAGAGGAGAGCTGCAAGCCAG
+TGAGTACTCAGAAAGACCAAGAATGGGTCATTAATCTTAAGGATTTGAGC
+TCTTAGCTGCAGCAGATACTGGGCATGGGTAGGAGTGAGAATTGAGGAGC
+AGAGGAAGATGGGAAACTGGAGAACCTAAGGAGACTGATAGCTTAGCTGC
+AGTAAGGGAGGTTGGCCAGAAGAGGGTTGGGTAGGGGACTCAGCAAGGCA
+GAACTAAGGAAGCTTAGGTGGAGGGGAAGGAACAACATCTGAGCAACTAA
+AGCACTCTATCAACTGGAAGTGCAAGATGGTAGTGAGGGGTGGACAGGTG
+TAACTGAGTAACTCTTTGTAGGTAGCCTTTCAGTTTAATTCAGTAAAATA
+TTTTGAACACTAGTATTCCAGATACTGGTAGGCCATGACTTAACCATTCC
+TAATGTTAATCTCAGCTGTGCTAGCTGAGCTTGTGTTCACATTAGACATG
+AAGAAACTTAGTAAAAGGTAGAGCCCAGTTTTCGGTTTGGACCTTCCTGT
+TGGCCTCTGCTTCCGTGCCATCTAGCAAAGGAGTTCCTAATCTCTAGAGG
+GATACAAATGACTAGTCTGCTCCATCTGCCTCTTCCAACATTGCAGGGTA
+GCTCCCAGGGAGAAGAGTCAGTGAGTGGTTCCCAGAGAACATCCAGTATC
+T