Reverse complement benchmark from computer language shootout
slava
parent
df5f7cc4df
commit
a8853daf1d
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@ -0,0 +1,171 @@
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>ONE Homo sapiens alu
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GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA
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TCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACT
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AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG
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GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG
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CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGT
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GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA
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GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA
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TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAG
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AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA
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GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGT
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AATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACC
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AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTG
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GTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC
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CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAG
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AGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTT
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TGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA
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TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT
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GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGG
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TTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT
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CTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG
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CGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCG
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TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTA
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CTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG
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AGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCG
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GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACC
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TGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAA
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TACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA
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GGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT
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GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTC
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ACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGT
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TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC
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CGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG
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CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG
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GGCGACAGAGCGAGACTCCG
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>TWO IUB ambiguity codes
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cttBtatcatatgctaKggNcataaaSatgtaaaDcDRtBggDtctttataattcBgtcg
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tactDtDagcctatttSVHtHttKtgtHMaSattgWaHKHttttagacatWatgtRgaaa
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NtactMcSMtYtcMgRtacttctWBacgaaatatagScDtttgaagacacatagtVgYgt
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cattHWtMMWcStgttaggKtSgaYaaccWStcgBttgcgaMttBYatcWtgacaYcaga
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gtaBDtRacttttcWatMttDBcatWtatcttactaBgaYtcttgttttttttYaaScYa
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HgtgttNtSatcMtcVaaaStccRcctDaataataStcYtRDSaMtDttgttSagtRRca
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tttHatSttMtWgtcgtatSSagactYaaattcaMtWatttaSgYttaRgKaRtccactt
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tattRggaMcDaWaWagttttgacatgttctacaaaRaatataataaMttcgDacgaSSt
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acaStYRctVaNMtMgtaggcKatcttttattaaaaagVWaHKYagtttttatttaacct
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tacgtVtcVaattVMBcttaMtttaStgacttagattWWacVtgWYagWVRctDattBYt
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gtttaagaagattattgacVatMaacattVctgtBSgaVtgWWggaKHaatKWcBScSWa
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accRVacacaaactaccScattRatatKVtactatatttHttaagtttSKtRtacaaagt
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RDttcaaaaWgcacatWaDgtDKacgaacaattacaRNWaatHtttStgttattaaMtgt
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tgDcgtMgcatBtgcttcgcgaDWgagctgcgaggggVtaaScNatttacttaatgacag
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cccccacatYScaMgtaggtYaNgttctgaMaacNaMRaacaaacaKctacatagYWctg
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ttWaaataaaataRattagHacacaagcgKatacBttRttaagtatttccgatctHSaat
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actcNttMaagtattMtgRtgaMgcataatHcMtaBSaRattagttgatHtMttaaKagg
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YtaaBataSaVatactWtataVWgKgttaaaacagtgcgRatatacatVtHRtVYataSa
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KtWaStVcNKHKttactatccctcatgWHatWaRcttactaggatctataDtDHBttata
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aaaHgtacVtagaYttYaKcctattcttcttaataNDaaggaaaDYgcggctaaWSctBa
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aNtgctggMBaKctaMVKagBaactaWaDaMaccYVtNtaHtVWtKgRtcaaNtYaNacg
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gtttNattgVtttctgtBaWgtaattcaagtcaVWtactNggattctttaYtaaagccgc
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tcttagHVggaYtgtNcDaVagctctctKgacgtatagYcctRYHDtgBattDaaDgccK
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tcHaaStttMcctagtattgcRgWBaVatHaaaataYtgtttagMDMRtaataaggatMt
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ttctWgtNtgtgaaaaMaatatRtttMtDgHHtgtcattttcWattRSHcVagaagtacg
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ggtaKVattKYagactNaatgtttgKMMgYNtcccgSKttctaStatatNVataYHgtNa
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BKRgNacaactgatttcctttaNcgatttctctataScaHtataRagtcRVttacDSDtt
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aRtSatacHgtSKacYagttMHtWataggatgactNtatSaNctataVtttRNKtgRacc
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tttYtatgttactttttcctttaaacatacaHactMacacggtWataMtBVacRaSaatc
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cgtaBVttccagccBcttaRKtgtgcctttttRtgtcagcRttKtaaacKtaaatctcac
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aattgcaNtSBaaccgggttattaaBcKatDagttactcttcattVtttHaaggctKKga
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tacatcBggScagtVcacattttgaHaDSgHatRMaHWggtatatRgccDttcgtatcga
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aacaHtaagttaRatgaVacttagattVKtaaYttaaatcaNatccRttRRaMScNaaaD
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gttVHWgtcHaaHgacVaWtgttScactaagSgttatcttagggDtaccagWattWtRtg
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ttHWHacgattBtgVcaYatcggttgagKcWtKKcaVtgaYgWctgYggVctgtHgaNcV
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taBtWaaYatcDRaaRtSctgaHaYRttagatMatgcatttNattaDttaattgttctaa
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ccctcccctagaWBtttHtBccttagaVaatMcBHagaVcWcagBVttcBtaYMccagat
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gaaaaHctctaacgttagNWRtcggattNatcRaNHttcagtKttttgWatWttcSaNgg
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gaWtactKKMaacatKatacNattgctWtatctaVgagctatgtRaHtYcWcttagccaa
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tYttWttaWSSttaHcaaaaagVacVgtaVaRMgattaVcDactttcHHggHRtgNcctt
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tYatcatKgctcctctatVcaaaaKaaaagtatatctgMtWtaaaacaStttMtcgactt
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taSatcgDataaactaaacaagtaaVctaggaSccaatMVtaaSKNVattttgHccatca
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cBVctgcaVatVttRtactgtVcaattHgtaaattaaattttYtatattaaRSgYtgBag
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aHSBDgtagcacRHtYcBgtcacttacactaYcgctWtattgSHtSatcataaatataHt
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cgtYaaMNgBaatttaRgaMaatatttBtttaaaHHKaatctgatWatYaacttMctctt
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ttVctagctDaaagtaVaKaKRtaacBgtatccaaccactHHaagaagaaggaNaaatBW
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attccgStaMSaMatBttgcatgRSacgttVVtaaDMtcSgVatWcaSatcttttVatag
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ttactttacgatcaccNtaDVgSRcgVcgtgaacgaNtaNatatagtHtMgtHcMtagaa
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attBgtataRaaaacaYKgtRccYtatgaagtaataKgtaaMttgaaRVatgcagaKStc
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tHNaaatctBBtcttaYaBWHgtVtgacagcaRcataWctcaBcYacYgatDgtDHccta
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>THREE Homo sapiens frequency
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aacacttcaccaggtatcgtgaaggctcaagattacccagagaacctttgcaatataaga
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atatgtatgcagcattaccctaagtaattatattctttttctgactcaaagtgacaagcc
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ctagtgtatattaaatcggtatatttgggaaattcctcaaactatcctaatcaggtagcc
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atgaaagtgatcaaaaaagttcgtacttataccatacatgaattctggccaagtaaaaaa
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tagattgcgcaaaattcgtaccttaagtctctcgccaagatattaggatcctattactca
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tatcgtgtttttctttattgccgccatccccggagtatctcacccatccttctcttaaag
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gcctaatattacctatgcaaataaacatatattgttgaaaattgagaacctgatcgtgat
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tcttatgtgtaccatatgtatagtaatcacgcgactatatagtgctttagtatcgcccgt
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gggtgagtgaatattctgggctagcgtgagatagtttcttgtcctaatatttttcagatc
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gaatagcttctatttttgtgtttattgacatatgtcgaaactccttactcagtgaaagtc
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atgaccagatccacgaacaatcttcggaatcagtctcgttttacggcggaatcttgagtc
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taacttatatcccgtcgcttactttctaacaccccttatgtatttttaaaattacgttta
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ttcgaacgtacttggcggaagcgttattttttgaagtaagttacattgggcagactcttg
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acattttcgatacgactttctttcatccatcacaggactcgttcgtattgatatcagaag
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ctcgtgatgattagttgtcttctttaccaatactttgaggcctattctgcgaaatttttg
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ttgccctgcgaacttcacataccaaggaacacctcgcaacatgccttcatatccatcgtt
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cattgtaattcttacacaatgaatcctaagtaattacatccctgcgtaaaagatggtagg
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ggcactgaggatatattaccaagcatttagttatgagtaatcagcaatgtttcttgtatt
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aagttctctaaaatagttacatcgtaatgttatctcgggttccgcgaataaacgagatag
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attcattatatatggccctaagcaaaaacctcctcgtattctgttggtaattagaatcac
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acaatacgggttgagatattaattatttgtagtacgaagagatataaaaagatgaacaat
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tactcaagtcaagatgtatacgggatttataataaaaatcgggtagagatctgctttgca
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attcagacgtgccactaaatcgtaatatgtcgcgttacatcagaaagggtaactattatt
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aattaataaagggcttaatcactacatattagatcttatccgatagtcttatctattcgt
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tgtatttttaagcggttctaattcagtcattatatcagtgctccgagttctttattattg
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ttttaaggatgacaaaatgcctcttgttataacgctgggagaagcagactaagagtcgga
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gcagttggtagaatgaggctgcaaaagacggtctcgacgaatggacagactttactaaac
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caatgaaagacagaagtagagcaaagtctgaagtggtatcagcttaattatgacaaccct
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taatacttccctttcgccgaatactggcgtggaaaggttttaaaagtcgaagtagttaga
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ggcatctctcgctcataaataggtagactactcgcaatccaatgtgactatgtaatactg
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ggaacatcagtccgcgatgcagcgtgtttatcaaccgtccccactcgcctggggagacat
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gagaccacccccgtggggattattagtccgcagtaatcgactcttgacaatccttttcga
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ttatgtcatagcaatttacgacagttcagcgaagtgactactcggcgaaatggtattact
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aaagcattcgaacccacatgaatgtgattcttggcaatttctaatccactaaagcttttc
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cgttgaatctggttgtagatatttatataagttcactaattaagatcacggtagtatatt
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gatagtgatgtctttgcaagaggttggccgaggaatttacggattctctattgatacaat
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ttgtctggcttataactcttaaggctgaaccaggcgtttttagacgacttgatcagctgt
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tagaatggtttggactccctctttcatgtcagtaacatttcagccgttattgttacgata
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tgcttgaacaatattgatctaccacacacccatagtatattttataggtcatgctgttac
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ctacgagcatggtattccacttcccattcaatgagtattcaacatcactagcctcagaga
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tgatgacccacctctaataacgtcacgttgcggccatgtgaaacctgaacttgagtagac
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gatatcaagcgctttaaattgcatataacatttgagggtaaagctaagcggatgctttat
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ataatcaatactcaataataagatttgattgcattttagagttatgacacgacatagttc
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actaacgagttactattcccagatctagactgaagtactgatcgagacgatccttacgtc
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gatgatcgttagttatcgacttaggtcgggtctctagcggtattggtacttaaccggaca
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ctatactaataacccatgatcaaagcataacagaatacagacgataatttcgccaacata
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tatgtacagaccccaagcatgagaagctcattgaaagctatcattgaagtcccgctcaca
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atgtgtcttttccagacggtttaactggttcccgggagtcctggagtttcgacttacata
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aatggaaacaatgtattttgctaatttatctatagcgtcatttggaccaatacagaatat
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tatgttgcctagtaatccactataacccgcaagtgctgatagaaaatttttagacgattt
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ataaatgccccaagtatccctcccgtgaatcctccgttatactaattagtattcgttcat
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acgtataccgcgcatatatgaacatttggcgataaggcgcgtgaattgttacgtgacaga
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gatagcagtttcttgtgatatggttaacagacgtacatgaagggaaactttatatctata
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gtgatgcttccgtagaaataccgccactggtctgccaatgatgaagtatgtagctttagg
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tttgtactatgaggctttcgtttgtttgcagagtataacagttgcgagtgaaaaaccgac
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gaatttatactaatacgctttcactattggctacaaaatagggaagagtttcaatcatga
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gagggagtatatggatgctttgtagctaaaggtagaacgtatgtatatgctgccgttcat
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tcttgaaagatacataagcgataagttacgacaattataagcaacatccctaccttcgta
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acgatttcactgttactgcgcttgaaatacactatggggctattggcggagagaagcaga
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tcgcgccgagcatatacgagacctataatgttgatgatagagaaggcgtctgaattgata
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catcgaagtacactttctttcgtagtatctctcgtcctctttctatctccggacacaaga
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attaagttatatatatagagtcttaccaatcatgttgaatcctgattctcagagttcttt
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ggcgggccttgtgatgactgagaaacaatgcaatattgctccaaatttcctaagcaaatt
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ctcggttatgttatgttatcagcaaagcgttacgttatgttatttaaatctggaatgacg
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gagcgaagttcttatgtcggtgtgggaataattcttttgaagacagcactccttaaataa
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tatcgctccgtgtttgtatttatcgaatgggtctgtaaccttgcacaagcaaatcggtgg
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tgtatatatcggataacaattaatacgatgttcatagtgacagtatactgatcgagtcct
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ctaaagtcaattacctcacttaacaatctcattgatgttgtgtcattcccggtatcgccc
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gtagtatgtgctctgattgaccgagtgtgaaccaaggaacatctactaatgcctttgtta
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ggtaagatctctctgaattccttcgtgccaacttaaaacattatcaaaatttcttctact
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tggattaactacttttacgagcatggcaaattcccctgtggaagacggttcattattatc
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ggaaaccttatagaaattgcgtgttgactgaaattagatttttattgtaagagttgcatc
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tttgcgattcctctggtctagcttccaatgaacagtcctcccttctattcgacatcgggt
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ccttcgtacatgtctttgcgatgtaataattaggttcggagtgtggccttaatgggtgca
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actaggaatacaacgcaaatttgctgacatgatagcaaatcggtatgccggcaccaaaac
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gtgctccttgcttagcttgtgaatgagactcagtagttaaataaatccatatctgcaatc
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gattccacaggtattgtccactatctttgaactactctaagagatacaagcttagctgag
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accgaggtgtatatgactacgctgatatctgtaaggtaccaatgcaggcaaagtatgcga
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gaagctaataccggctgtttccagctttataagattaaaatttggctgtcctggcggcct
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cagaattgttctatcgtaatcagttggttcattaattagctaagtacgaggtacaactta
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tctgtcccagaacagctccacaagtttttttacagccgaaacccctgtgtgaatcttaat
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atccaagcgcgttatctgattagagtttacaactcagtattttatcagtacgttttgttt
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ccaacattacccggtatgacaaaatgacgccacgtgtcgaataatggtctgaccaatgta
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ggaagtgaaaagataaatat
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@ -0,0 +1,171 @@
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>ONE Homo sapiens alu
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CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAC
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CTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA
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GGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT
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GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA
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AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTC
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TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGG
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GTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC
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ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG
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GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA
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CAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT
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GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTC
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TCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT
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TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCT
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GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA
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CCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGC
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GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC
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TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA
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GTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT
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||||||
|
CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT
|
||||||
|
TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTC
|
||||||
|
ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG
|
||||||
|
GGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGT
|
||||||
|
TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG
|
||||||
|
CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAG
|
||||||
|
TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCG
|
||||||
|
CCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC
|
||||||
|
GCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG
|
||||||
|
CCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC
|
||||||
|
TGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCG
|
||||||
|
CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCA
|
||||||
|
AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC
|
||||||
|
CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTC
|
||||||
|
GAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC
|
||||||
|
GTGAGCCACCGCGCCCGGCC
|
||||||
|
>TWO IUB ambiguity codes
|
||||||
|
TAGGDHACHATCRGTRGVTGAGWTATGYTGCTGTCABACDWVTRTAAGAVVAGATTTNDA
|
||||||
|
GASMTCTGCATBYTTCAAKTTACMTATTACTTCATARGGYACMRTGTTTTYTATACVAAT
|
||||||
|
TTCTAKGDACKADACTATATNTANTCGTTCACGBCGYSCBHTANGGTGATCGTAAAGTAA
|
||||||
|
CTATBAAAAGATSTGWATBCSGAKHTTABBAACGTSYCATGCAAVATKTSKTASCGGAAT
|
||||||
|
WVATTTNTCCTTCTTCTTDDAGTGGTTGGATACVGTTAYMTMTBTACTTTHAGCTAGBAA
|
||||||
|
AAGAGKAAGTTRATWATCAGATTMDDTTTAAAVAAATATTKTCYTAAATTVCNKTTRACG
|
||||||
|
ADTATATTTATGATSADSCAATAWAGCGRTAGTGTAAGTGACVGRADYGTGCTACHVSDT
|
||||||
|
CTVCARCSYTTAATATARAAAATTTAATTTACDAATTGBACAGTAYAABATBTGCAGBVG
|
||||||
|
TGATGGDCAAAATBNMSTTABKATTGGSTCCTAGBTTACTTGTTTAGTTTATHCGATSTA
|
||||||
|
AAGTCGAKAAASTGTTTTAWAKCAGATATACTTTTMTTTTGBATAGAGGAGCMATGATRA
|
||||||
|
AAGGNCAYDCCDDGAAAGTHGBTAATCKYTBTACBGTBCTTTTTGDTAASSWTAAWAARA
|
||||||
|
TTGGCTAAGWGRADTYACATAGCTCBTAGATAWAGCAATNGTATMATGTTKMMAGTAWTC
|
||||||
|
CCNTSGAAWATWCAAAAMACTGAADNTYGATNAATCCGAYWNCTAACGTTAGAGDTTTTC
|
||||||
|
ATCTGGKRTAVGAABVCTGWGBTCTDVGKATTBTCTAAGGVADAAAVWTCTAGGGGAGGG
|
||||||
|
TTAGAACAATTAAHTAATNAAATGCATKATCTAAYRTDTCAGSAYTTYHGATRTTWAVTA
|
||||||
|
BGNTCDACAGBCCRCAGWCRTCABTGMMAWGMCTCAACCGATRTGBCAVAATCGTDWDAA
|
||||||
|
CAYAWAATWCTGGTAHCCCTAAGATAACSCTTAGTGSAACAWTBGTCDTTDGACWDBAAC
|
||||||
|
HTTTNGSKTYYAAYGGATNTGATTTAARTTAMBAATCTAAGTBTCATYTAACTTADTGTT
|
||||||
|
TCGATACGAAHGGCYATATACCWDTKYATDCSHTDTCAAAATGTGBACTGSCCVGATGTA
|
||||||
|
TCMMAGCCTTDAAABAATGAAGAGTAACTHATMGVTTAATAACCCGGTTVSANTGCAATT
|
||||||
|
GTGAGATTTAMGTTTAMAAYGCTGACAYAAAAAGGCACAMYTAAGVGGCTGGAABVTACG
|
||||||
|
GATTSTYGTBVAKTATWACCGTGTKAGTDTGTATGTTTAAAGGAAAAAGTAACATARAAA
|
||||||
|
GGTYCAMNYAAABTATAGNTSATANAGTCATCCTATWADKAACTRGTMSACDGTATSAYT
|
||||||
|
AAHSHGTAABYGACTYTATADTGSTATAGAGAAATCGNTAAAGGAAATCAGTTGTNCYMV
|
||||||
|
TNACDRTATBNATATASTAGAAMSCGGGANRCKKMCAAACATTNAGTCTRMAATBMTACC
|
||||||
|
CGTACTTCTBGDSYAATWGAAAATGACADDCHAKAAAYATATTKTTTTCACANACWAGAA
|
||||||
|
AKATCCTTATTAYKHKCTAAACARTATTTTDATBTVWCYGCAATACTAGGKAAASTTDGA
|
||||||
|
MGGCHTTHAATVCAHDRYAGGRCTATACGTCMAGAGAGCTBTHGNACARTCCBDCTAAGA
|
||||||
|
GCGGCTTTARTAAAGAATCCNAGTAWBTGACTTGAATTACWTVACAGAAABCAATNAAAC
|
||||||
|
CGTNTRANTTGAYCMAWBADTANABRGGTKTHTWTAGTTVCTMBKTAGMTVKCCAGCANT
|
||||||
|
TVAGSWTTAGCCGCRHTTTCCTTHNTATTAAGAAGAATAGGMTRAARTCTABGTACDTTT
|
||||||
|
TATAAVDHAHTATAGATCCTAGTAAGYTWATDWCATGAGGGATAGTAAMDMNGBASTWAM
|
||||||
|
TSTATRBAYDABATGTATATYCGCACTGTTTTAACMCWBTATAWAGTATBTSTATVTTAR
|
||||||
|
CCTMTTAAKADATCAACTAATYTSVTAKGDATTATGCKTCAYCAKAATACTTKAANGAGT
|
||||||
|
ATTSDAGATCGGAAATACTTAAYAAVGTATMCGCTTGTGTDCTAATYTATTTTATTTWAA
|
||||||
|
CAGWRCTATGTAGMTGTTTGTTYKTNGTTKTCAGAACNTRACCTACKTGSRATGTGGGGG
|
||||||
|
CTGTCATTAAGTAAATNGSTTABCCCCTCGCAGCTCWHTCGCGAAGCAVATGCKACGHCA
|
||||||
|
ACAKTTAATAACASAAADATTWNYTGTAATTGTTCGTMHACHTWATGTGCWTTTTGAAHY
|
||||||
|
ACTTTGTAYAMSAAACTTAADAAATATAGTABMATATYAATGSGGTAGTTTGTGTBYGGT
|
||||||
|
TWSGSVGWMATTDMTCCWWCABTCSVACAGBAATGTTKATBGTCAATAATCTTCTTAAAC
|
||||||
|
ARVAATHAGYBWCTRWCABGTWWAATCTAAGTCASTAAAKTAAGVKBAATTBGABACGTA
|
||||||
|
AGGTTAAATAAAAACTRMDTWBCTTTTTAATAAAAGATMGCCTACKAKNTBAGYRASTGT
|
||||||
|
ASSTCGTHCGAAKTTATTATATTYTTTGTAGAACATGTCAAAACTWTWTHGKTCCYAATA
|
||||||
|
AAGTGGAYTMCYTAARCSTAAATWAKTGAATTTRAGTCTSSATACGACWAKAASATDAAA
|
||||||
|
TGYYACTSAACAAHAKTSHYARGASTATTATTHAGGYGGASTTTBGAKGATSANAACACD
|
||||||
|
TRGSTTRAAAAAAAACAAGARTCVTAGTAAGATAWATGVHAAKATWGAAAAGTYAHVTAC
|
||||||
|
TCTGRTGTCAWGATRVAAKTCGCAAVCGASWGGTTRTCSAMCCTAACASGWKKAWDAATG
|
||||||
|
ACRCBACTATGTGTCTTCAAAHGSCTATATTTCGTVWAGAAGTAYCKGARAKSGKAGTAN
|
||||||
|
TTTCYACATWATGTCTAAAADMDTWCAATSTKDACAMAADADBSAAATAGGCTHAHAGTA
|
||||||
|
CGACVGAATTATAAAGAHCCVAYHGHTTTACATSTTTATGNCCMTAGCATATGATAVAAG
|
||||||
|
>THREE Homo sapiens frequency
|
||||||
|
ATATTTATCTTTTCACTTCCTACATTGGTCAGACCATTATTCGACACGTGGCGTCATTTT
|
||||||
|
GTCATACCGGGTAATGTTGGAAACAAAACGTACTGATAAAATACTGAGTTGTAAACTCTA
|
||||||
|
ATCAGATAACGCGCTTGGATATTAAGATTCACACAGGGGTTTCGGCTGTAAAAAAACTTG
|
||||||
|
TGGAGCTGTTCTGGGACAGATAAGTTGTACCTCGTACTTAGCTAATTAATGAACCAACTG
|
||||||
|
ATTACGATAGAACAATTCTGAGGCCGCCAGGACAGCCAAATTTTAATCTTATAAAGCTGG
|
||||||
|
AAACAGCCGGTATTAGCTTCTCGCATACTTTGCCTGCATTGGTACCTTACAGATATCAGC
|
||||||
|
GTAGTCATATACACCTCGGTCTCAGCTAAGCTTGTATCTCTTAGAGTAGTTCAAAGATAG
|
||||||
|
TGGACAATACCTGTGGAATCGATTGCAGATATGGATTTATTTAACTACTGAGTCTCATTC
|
||||||
|
ACAAGCTAAGCAAGGAGCACGTTTTGGTGCCGGCATACCGATTTGCTATCATGTCAGCAA
|
||||||
|
ATTTGCGTTGTATTCCTAGTTGCACCCATTAAGGCCACACTCCGAACCTAATTATTACAT
|
||||||
|
CGCAAAGACATGTACGAAGGACCCGATGTCGAATAGAAGGGAGGACTGTTCATTGGAAGC
|
||||||
|
TAGACCAGAGGAATCGCAAAGATGCAACTCTTACAATAAAAATCTAATTTCAGTCAACAC
|
||||||
|
GCAATTTCTATAAGGTTTCCGATAATAATGAACCGTCTTCCACAGGGGAATTTGCCATGC
|
||||||
|
TCGTAAAAGTAGTTAATCCAAGTAGAAGAAATTTTGATAATGTTTTAAGTTGGCACGAAG
|
||||||
|
GAATTCAGAGAGATCTTACCTAACAAAGGCATTAGTAGATGTTCCTTGGTTCACACTCGG
|
||||||
|
TCAATCAGAGCACATACTACGGGCGATACCGGGAATGACACAACATCAATGAGATTGTTA
|
||||||
|
AGTGAGGTAATTGACTTTAGAGGACTCGATCAGTATACTGTCACTATGAACATCGTATTA
|
||||||
|
ATTGTTATCCGATATATACACCACCGATTTGCTTGTGCAAGGTTACAGACCCATTCGATA
|
||||||
|
AATACAAACACGGAGCGATATTATTTAAGGAGTGCTGTCTTCAAAAGAATTATTCCCACA
|
||||||
|
CCGACATAAGAACTTCGCTCCGTCATTCCAGATTTAAATAACATAACGTAACGCTTTGCT
|
||||||
|
GATAACATAACATAACCGAGAATTTGCTTAGGAAATTTGGAGCAATATTGCATTGTTTCT
|
||||||
|
CAGTCATCACAAGGCCCGCCAAAGAACTCTGAGAATCAGGATTCAACATGATTGGTAAGA
|
||||||
|
CTCTATATATATAACTTAATTCTTGTGTCCGGAGATAGAAAGAGGACGAGAGATACTACG
|
||||||
|
AAAGAAAGTGTACTTCGATGTATCAATTCAGACGCCTTCTCTATCATCAACATTATAGGT
|
||||||
|
CTCGTATATGCTCGGCGCGATCTGCTTCTCTCCGCCAATAGCCCCATAGTGTATTTCAAG
|
||||||
|
CGCAGTAACAGTGAAATCGTTACGAAGGTAGGGATGTTGCTTATAATTGTCGTAACTTAT
|
||||||
|
CGCTTATGTATCTTTCAAGAATGAACGGCAGCATATACATACGTTCTACCTTTAGCTACA
|
||||||
|
AAGCATCCATATACTCCCTCTCATGATTGAAACTCTTCCCTATTTTGTAGCCAATAGTGA
|
||||||
|
AAGCGTATTAGTATAAATTCGTCGGTTTTTCACTCGCAACTGTTATACTCTGCAAACAAA
|
||||||
|
CGAAAGCCTCATAGTACAAACCTAAAGCTACATACTTCATCATTGGCAGACCAGTGGCGG
|
||||||
|
TATTTCTACGGAAGCATCACTATAGATATAAAGTTTCCCTTCATGTACGTCTGTTAACCA
|
||||||
|
TATCACAAGAAACTGCTATCTCTGTCACGTAACAATTCACGCGCCTTATCGCCAAATGTT
|
||||||
|
CATATATGCGCGGTATACGTATGAACGAATACTAATTAGTATAACGGAGGATTCACGGGA
|
||||||
|
GGGATACTTGGGGCATTTATAAATCGTCTAAAAATTTTCTATCAGCACTTGCGGGTTATA
|
||||||
|
GTGGATTACTAGGCAACATAATATTCTGTATTGGTCCAAATGACGCTATAGATAAATTAG
|
||||||
|
CAAAATACATTGTTTCCATTTATGTAAGTCGAAACTCCAGGACTCCCGGGAACCAGTTAA
|
||||||
|
ACCGTCTGGAAAAGACACATTGTGAGCGGGACTTCAATGATAGCTTTCAATGAGCTTCTC
|
||||||
|
ATGCTTGGGGTCTGTACATATATGTTGGCGAAATTATCGTCTGTATTCTGTTATGCTTTG
|
||||||
|
ATCATGGGTTATTAGTATAGTGTCCGGTTAAGTACCAATACCGCTAGAGACCCGACCTAA
|
||||||
|
GTCGATAACTAACGATCATCGACGTAAGGATCGTCTCGATCAGTACTTCAGTCTAGATCT
|
||||||
|
GGGAATAGTAACTCGTTAGTGAACTATGTCGTGTCATAACTCTAAAATGCAATCAAATCT
|
||||||
|
TATTATTGAGTATTGATTATATAAAGCATCCGCTTAGCTTTACCCTCAAATGTTATATGC
|
||||||
|
AATTTAAAGCGCTTGATATCGTCTACTCAAGTTCAGGTTTCACATGGCCGCAACGTGACG
|
||||||
|
TTATTAGAGGTGGGTCATCATCTCTGAGGCTAGTGATGTTGAATACTCATTGAATGGGAA
|
||||||
|
GTGGAATACCATGCTCGTAGGTAACAGCATGACCTATAAAATATACTATGGGTGTGTGGT
|
||||||
|
AGATCAATATTGTTCAAGCATATCGTAACAATAACGGCTGAAATGTTACTGACATGAAAG
|
||||||
|
AGGGAGTCCAAACCATTCTAACAGCTGATCAAGTCGTCTAAAAACGCCTGGTTCAGCCTT
|
||||||
|
AAGAGTTATAAGCCAGACAAATTGTATCAATAGAGAATCCGTAAATTCCTCGGCCAACCT
|
||||||
|
CTTGCAAAGACATCACTATCAATATACTACCGTGATCTTAATTAGTGAACTTATATAAAT
|
||||||
|
ATCTACAACCAGATTCAACGGAAAAGCTTTAGTGGATTAGAAATTGCCAAGAATCACATT
|
||||||
|
CATGTGGGTTCGAATGCTTTAGTAATACCATTTCGCCGAGTAGTCACTTCGCTGAACTGT
|
||||||
|
CGTAAATTGCTATGACATAATCGAAAAGGATTGTCAAGAGTCGATTACTGCGGACTAATA
|
||||||
|
ATCCCCACGGGGGTGGTCTCATGTCTCCCCAGGCGAGTGGGGACGGTTGATAAACACGCT
|
||||||
|
GCATCGCGGACTGATGTTCCCAGTATTACATAGTCACATTGGATTGCGAGTAGTCTACCT
|
||||||
|
ATTTATGAGCGAGAGATGCCTCTAACTACTTCGACTTTTAAAACCTTTCCACGCCAGTAT
|
||||||
|
TCGGCGAAAGGGAAGTATTAAGGGTTGTCATAATTAAGCTGATACCACTTCAGACTTTGC
|
||||||
|
TCTACTTCTGTCTTTCATTGGTTTAGTAAAGTCTGTCCATTCGTCGAGACCGTCTTTTGC
|
||||||
|
AGCCTCATTCTACCAACTGCTCCGACTCTTAGTCTGCTTCTCCCAGCGTTATAACAAGAG
|
||||||
|
GCATTTTGTCATCCTTAAAACAATAATAAAGAACTCGGAGCACTGATATAATGACTGAAT
|
||||||
|
TAGAACCGCTTAAAAATACAACGAATAGATAAGACTATCGGATAAGATCTAATATGTAGT
|
||||||
|
GATTAAGCCCTTTATTAATTAATAATAGTTACCCTTTCTGATGTAACGCGACATATTACG
|
||||||
|
ATTTAGTGGCACGTCTGAATTGCAAAGCAGATCTCTACCCGATTTTTATTATAAATCCCG
|
||||||
|
TATACATCTTGACTTGAGTAATTGTTCATCTTTTTATATCTCTTCGTACTACAAATAATT
|
||||||
|
AATATCTCAACCCGTATTGTGTGATTCTAATTACCAACAGAATACGAGGAGGTTTTTGCT
|
||||||
|
TAGGGCCATATATAATGAATCTATCTCGTTTATTCGCGGAACCCGAGATAACATTACGAT
|
||||||
|
GTAACTATTTTAGAGAACTTAATACAAGAAACATTGCTGATTACTCATAACTAAATGCTT
|
||||||
|
GGTAATATATCCTCAGTGCCCCTACCATCTTTTACGCAGGGATGTAATTACTTAGGATTC
|
||||||
|
ATTGTGTAAGAATTACAATGAACGATGGATATGAAGGCATGTTGCGAGGTGTTCCTTGGT
|
||||||
|
ATGTGAAGTTCGCAGGGCAACAAAAATTTCGCAGAATAGGCCTCAAAGTATTGGTAAAGA
|
||||||
|
AGACAACTAATCATCACGAGCTTCTGATATCAATACGAACGAGTCCTGTGATGGATGAAA
|
||||||
|
GAAAGTCGTATCGAAAATGTCAAGAGTCTGCCCAATGTAACTTACTTCAAAAAATAACGC
|
||||||
|
TTCCGCCAAGTACGTTCGAATAAACGTAATTTTAAAAATACATAAGGGGTGTTAGAAAGT
|
||||||
|
AAGCGACGGGATATAAGTTAGACTCAAGATTCCGCCGTAAAACGAGACTGATTCCGAAGA
|
||||||
|
TTGTTCGTGGATCTGGTCATGACTTTCACTGAGTAAGGAGTTTCGACATATGTCAATAAA
|
||||||
|
CACAAAAATAGAAGCTATTCGATCTGAAAAATATTAGGACAAGAAACTATCTCACGCTAG
|
||||||
|
CCCAGAATATTCACTCACCCACGGGCGATACTAAAGCACTATATAGTCGCGTGATTACTA
|
||||||
|
TACATATGGTACACATAAGAATCACGATCAGGTTCTCAATTTTCAACAATATATGTTTAT
|
||||||
|
TTGCATAGGTAATATTAGGCCTTTAAGAGAAGGATGGGTGAGATACTCCGGGGATGGCGG
|
||||||
|
CAATAAAGAAAAACACGATATGAGTAATAGGATCCTAATATCTTGGCGAGAGACTTAAGG
|
||||||
|
TACGAATTTTGCGCAATCTATTTTTTACTTGGCCAGAATTCATGTATGGTATAAGTACGA
|
||||||
|
ACTTTTTTGATCACTTTCATGGCTACCTGATTAGGATAGTTTGAGGAATTTCCCAAATAT
|
||||||
|
ACCGATTTAATATACACTAGGGCTTGTCACTTTGAGTCAGAAAAAGAATATAATTACTTA
|
||||||
|
GGGTAATGCTGCATACATATTCTTATATTGCAAAGGTTCTCTGGGTAATCTTGAGCCTTC
|
||||||
|
ACGATACCTGGTGAAGTGTT
|
||||||
|
|
@ -0,0 +1,59 @@
|
||||||
|
IN: temporary
|
||||||
|
USING: compiler hashtables io kernel math math namespaces
|
||||||
|
sequences strings vectors words words ;
|
||||||
|
|
||||||
|
! Instead of a variable, we define an inline word which pushes
|
||||||
|
! the hash on the stack, for performance.
|
||||||
|
DEFER: trans-hash
|
||||||
|
|
||||||
|
[
|
||||||
|
26 [ CHAR: A + dup set ] each
|
||||||
|
26 [ CHAR: a + dup set ] each
|
||||||
|
|
||||||
|
"TGCAAKYRMBDHV"
|
||||||
|
"ACGTUMRYKVHDB"
|
||||||
|
2dup
|
||||||
|
[ set ] 2each
|
||||||
|
[ ch>lower set ] 2each
|
||||||
|
] make-hash
|
||||||
|
|
||||||
|
\ trans-hash swap unit define-compound
|
||||||
|
\ trans-hash t "inline" set-word-prop
|
||||||
|
|
||||||
|
: translate-seq ( seq -- sbuf )
|
||||||
|
[
|
||||||
|
2000000 <sbuf> building set
|
||||||
|
<reversed> [ <reversed> % ] each
|
||||||
|
building get dup [ trans-hash hash ] inject
|
||||||
|
] with-scope ;
|
||||||
|
|
||||||
|
SYMBOL: out
|
||||||
|
|
||||||
|
: seg ( sbuf n -- str )
|
||||||
|
60 * dup 60 + pick length min rot <slice> >string ;
|
||||||
|
|
||||||
|
: show-seq ( seq -- )
|
||||||
|
translate-seq dup length 59 + 60 /i
|
||||||
|
[ seg out get stream-print ] each-with ;
|
||||||
|
|
||||||
|
: clear-seq ( seq -- ) 0 swap set-length ;
|
||||||
|
|
||||||
|
: do-line ( seq line -- seq )
|
||||||
|
dup first ">;" memq? [
|
||||||
|
over show-seq out get stream-print dup clear-seq
|
||||||
|
] [
|
||||||
|
over push
|
||||||
|
] if ;
|
||||||
|
|
||||||
|
: (reverse-complement) ( seq -- )
|
||||||
|
readln [ do-line (reverse-complement) ] [ show-seq ] if* ;
|
||||||
|
|
||||||
|
: reverse-complement ( infile outfile -- )
|
||||||
|
<file-writer> [
|
||||||
|
stdio get out set
|
||||||
|
<file-reader> [
|
||||||
|
500000 <vector> (reverse-complement)
|
||||||
|
] with-stream
|
||||||
|
] with-stream ;
|
||||||
|
|
||||||
|
{ translate-seq seg clear-seq } [ compile ] each
|
||||||
Loading…
Reference in New Issue