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Example Sequences for HCV Subtyping

>1a.COLONEL_NS3_AF290978
CTGGCGCCCATCACGGCGTACGCCCAGCAGACGAGAGGCCTCCTAGGGTGTATAATCACC
AGCCTGACTGGCCGGGACAAGAACCAAGTGGAGGGTGAGGTCCAGATCGTGTCAACTGCT
ACCCAAACCTTCCTGGCAACGTGCATCAATGGGGTATGCTGGACTGTCTACCACGGGGCC
GGAACGAGGACCATCGCATCACCCAAGGGTCCTGTCATCCAGATGTATACCAATGTGGAC
CAAGACCTTGTGGGCTGGCCCGCTCCTCAAGGTTCCCGCTCATTGACACCCTGCACCTGC
GGCTCCTCGGACCTTTACCTGGTCACG---AGGCAC---------GCCGATGTCATTCCT
GTGCGCCGGCAAGGTGATAGCAGGGGTAGCCTGCTTTCGCCCCGGCCCATTTCCTACTTG
AAAGGCTCCTCGGGGGGTCCGCTGTTGTGCCCCGCGGGACACGCCGTGGGCCTATTCAGG
GCCGCGGTGTGCACCCGTGGAGTGGCTAAGGCGGTGGACTTTATCCCTGTGGAGAACCTA
GAGACAACCATGAGATCCCCGGTGTTCACGGACAACTCCTCTCCACCAGCAGTGCCCCAG
AGCTTCCAGGTGGCCCACCTGCATGCTCCCACCGGCAGCGGTAAGAGCACCAAGGTCCCG
GCTGCGTACGCAGCTCAGGGCTATAAGGTGTTGGTGCTCAACCCTTCTGTTGCTGCAACG
CTGGGCTTTGGCGCTTACATGTCCAAGGCCCATGGGGTCGATCCTAATATCAGGACCGGG
GTGAGAACAATTACCACTGGCAGCCCTATCACGTACTCCACCTACGGCAAGTTCCTTGCC
GACGGCGGGTGCTCAGGAGGTGCTTATGACATAATAATTTGTGACGAGTGCCACTCCACG
GATGCCACATCCATCTTGGGCATCGGCACTGTCCTTGACCAAGCAGAGACTGCGGGGGCG
AGATTGGTTGTGCTCGCCACTGCTACCCCTCCGGGCTCCGTCACTGTGCCCCATCCTAAC
ATCGAGGAGGTTGCTCTGTCCACCACCGGAGAGATCCCTTTTTACGGCAAGGCCATCCCT
CTCGAGGTGATCAAGGGGGGAAGACATCTCATCTTCTGTCACTCAAAGAAGAAGTGCGAC
GAGCTCGCCGCGAAGCTGGTCGCACTGGGCATCAATGCCGTGGCCTACTACCGCGGTCTT
GACGTGTCTGTCATCCCGGCCAGCGGCGATGTTGTCGTCGTGTCGACCGATGCTCTCATG
ACTGGCTTTACTGGCGACTTCGACCCTGTGATAGACTGCAACACGTGTGTCACTCAGACA
GTCGATTTCAGCCTTGACCCTACCTTTACCATTGAGACAACCACG---CTCCCCCAGGAT
GCTGTCTCCAGGACTCAACGCCGGGGCAGGACTGGCAGGGGGAAGCCAGGCATCTACAGA
TTTGTTGCACCGGGGGAGCGCCCCTCCGGCATGTTCGACTCGTCCGTCCTCTGTGAGTGC
TATGACGCGGGCTGTGCTTGGTATGAGCTCACGCCCGCCGAGACTACAGTTAGGCTACGA
GCGTACATGAACACCCCGGGGCTTCCCGTGTGCCAGGACCATCTTGAATTTTGGGAGGGC
GTCTTTACGGGCCTCACTCATATAGATGCCCACTTTCTATCCCAGACAAAGCAGAGCGGG
GAGAACTTTCCTTACCTGGTAGCGTACCAAGCCACCGTGTGCGCTAGG
>AY587845
TTGCTGTGCCCCACTGACTGCTTCAGGAAGCACCCTGAGGCTACTTACACCAAATGTGGGGCCGGGCCATGGTTGACTCC
CAAATGCCTGGTTGATTACCCCTATAGATTGTGGCATTACCCGTGTACTGTCAACTTTACCATCTTCAAAATACGGATGT
TCATAGGGGGAGTCGAGCATAGGCTCAACGCGGCGTGCAATTTTACCCGTGGGGACCGTTGCAATCTGGAAGACCGGGAT
AGGAGTCAGCTCAGCCCCTTGCTGCATTCCACCACTGAATGGGCTATACTACCTTGCACCTACTCTGACATGCCGGCTTT
ATCTACCGGTCTCTTACACCTCCACCAAAACATTGTGGACGTGCAGTACCTGTATGGCCTATCGCCGGCTATTACCAAGT
TCATTGTCAAGTGGGAATGGGTGGTCCTCTTGTTTCTGCTCCTTGCGGACGCCAGAGTCTGCGCGTGCTTGTGGATGCTT
CTTCTGCTGGGGCAAGCCGAGGCGGCGCTGGAGAAGCTAGTCATTTTGCATGCGGCCAGCGCCGCAAGCTTTAATGGCAT
AATCTGCTTCACCATCTTCTTCATAGCCGCCTGGCACATCAAGGGTCGAGTGGTCCCCCTGGCTACTTACTCGTACCTCG
GCTTGTGGTCCTTCAGCCTTCTACTCCTGGCACTTCCCCAACAGGCCTATGCCCTTAATACAACAGAACAGGGGCAACTG
GGCTTGGTCCTTCTAGTGGTCATATCAGTCCTTACACTCAGCCCGGCTTATAAGATCCTCCTCTGCCGCAGCCTATGGTG
GCTGTCCTATCTATTGGTCCGAGCGGAAGCTTTGATCCAAGAGTGGGTACCGCCCTTGCAGGCGCGAGGCGGCCGCGATG
GCATCATATGGGCCGCCGTCATACTCTGTCCGGGCATAGTGTTTGACATAACCAAGTGGCTCCTGGCAGTCTTAGGACCT
GGTCACCTCCTTAGGAGTGTCCTAACAAGCGTGCCATACTTCGTCAGGGCGCAAGCTCTGTTGAGGATATGCGCTGCTGT
GAGACATCTCTCAGGTGGCAAGTACGTCCAGATGATGCTGCTGACCCTTGGCAGATGGACCGGCACCTACATTTATGACC
ATCTCACTCCACTGCAGGACTGGGCCCACGCGGGCCTACGAGACCTTGCGGTGGCAGTTGAGCCTGTTGTCTTCTCTGAC
ATGGAGACCAAGATCATCACCTGGGGGGCAGAAACCGCGGCGTGTGGGGACATCATTCTGGGCTTACCCGTCTCCGCCCG
AAGGGGGAGAGAGATACTTCTGGGGCCGGCCGATAGCCTTGAGGGCCAGGGGTGGCGGCTCCTCGCGCCTATCACGGCTT
ACTCCCAACAGACGCGGGGCTTACTTGGCTGCATCGTCACTAGCCTCACAGGCCGGGACAGGAACCAGGTCGAGGGGGAG
GTCCAAGTGGTCTCCACTGCAACACAATCTTTCCTCGCGACCTGTGTCAATGGTGTGTGTTGGACTGTTTACCACGGTGC
CGGCTCAAAGACCTTAGCTGGCCCAAAGGGTCCAATCATCCAAATGTATACCAATGTAGACCAGGACCTCGTCGGCTGGC
CGGCGCCCCCCGGGGCGCGTTCCTTGACACCATGCACCTGCGGCAGCTCGGACCTTTACTTGGTCACGAGGCATGCCGAT
GTCATTCCGGTGCGCCGGCGGGGCGACAGCAGGGGGAGCCTACTCTCCCCCAGGCCCATCTCCTACTTGAAGGGTTCTTC
GGGTGGTCCGCTGCTTTGCCCCTCGGGGCACGCTGTGGGCATCTTCCGGGCTGCTGTGTGCACCCGGGGGGTTGCAAAGG
CGGTGGACTTTGTACCCGTTGAGTCCATGGAAACTACTATGCGGTCTCCGGTCTTCACGGACAACTCGTCCCCCCCGGCC
GTACCGCAGACATTCCAAGTGGCCCATCTACATGCTCCCACTGGCAGCGGCAAGAGCACCAAGGTGCCGGCTGCGTATGC
GGCCCAGGGGTAC
>test
gtgGAAGTTAGAAACACCAGTTTTAGCTACTACGCCACCAATGATTGCTCGAACAACAGC
ATCACCTGGCAGCTCACCAACGCAGTTCTCCACCTTCCCGGATGCGTCCCATGTGAGAAT
GAC---AATGGCACCTTGCGCTGCTGGATACAAGTAACACCTAATGTGGCTGTGAAACAC
CGTGGCGCACTCACTCACAACCTGCGAACGCATGTCGACGTGATCGTAATGGCAGCTACG
GTCTGCTCGGCCTTGTATGTGGGGGACGTGTGCGGGGCCGTGATGATAGCGTCGCAGGCT
TTCATAATATCGCCAGAACGCCACAACTTCACCCAGGAGTGCAACTGTTCCATCTACCAA
GGTCATATCACCGGCCACCGCATGGCATGGGACATGATGCTGAACTGGTCACCAACTCTC
ACCATGATCCTCGCCTACGCTGCTCGTGTGCCTGAACTAGTCCTTGAAGTTGTCTTCGGC
GGCCATTGGGGCGTGGTGTTTGGCTTGGCCTATTTCTCCATGCAAGGAGCGTGGGCCAAA
GTCATCGCCATCCTCCTCCTTGTCGCAGGAGTGGACGCa
>3b.ST_E1_D11443
TTAGAGTACACGAACACGTCTGGCCTATATGTGCTTACCAACGACTGCTCTAATGGGAGC
ATTGTGTACGAGGCCGAAGATGTGATCTTGCACTTACCCGGATGCGTGCCCTGCGTCACA
ACC---GGCAACCAATCATCATGCTGGACAACGGTCTCAACGACGGTGGCCGTTAGGACC
CTTGGCGTGACCACCGCGTCGATCCGAACCCATGTGGATATGCTGGTAGGCGCACGACAA
CTGTGTTCGGCGCTGTACGTCGGGGACGCTTTCGGGGCTGTGTTTCTTGTGGGACAAGCG
TTCACCTTCAGACCTCGCCGCCACACGACCGTGCAGACGTGCAACTGCTCGATATACCCA
GGCCATGTTTCAGGACATCGTATGGCGTGGGATATGATGATGAACTGGTCCCCCACAATC
GGGCTAGTGATATCACATCTGATGCGGTTGCCCCAAACCCTCTTTGACTTGGTCTCGGGG
ACTCATTGGGGTGTGATGGCAGGTCTCGCCTACTTTTCCATGCAAGGCAATTGGGCCAAG
GTCGTCATCGTGCTGATCATGTTTTCAGGAGTAGATGCG


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Developed by: Tulio de Oliveira, Marco Salemi, Oliver Pybus, Sabrina Almeida,  Andrew Rambaut.

Developed by the Evolutionary Biology Group at University of Oxford, UK. Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, USA. Biotechnology department, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil.

Funded by the Marie Curie Fellowship, Royal Society and Wellcome Trus, UK.

Suggestions or problems on the program please contact:  Dr Tulio de Oliveira.