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Example Sequences for the REGA HIV-1 Automated Subtyping Tool 

>gi33300549
 
CCTCAAATCACTCTTTGGCAACGACCCCTAGTCACAATACAAGTAGGGGGACAGCTAAGGGAAGCTCTAT
TAGATACAGGAGCAGATGATACAGTATTAGAAGACATAAATTTGCCAGGAAAATGGAAACCAAAAATGAT
AGGGGGAATTGGAGGTTTTATCAAAGTAAAACAGTATGATAACATATGCATAGACATTTGTGGACACAAG
GCTATAGGTACAGTGTTGGTAGGACCTACACCTGCCAACATAATTGGAAGAAATATGTTGACTCAGATTG
GTTGTACTTTAAATTTTCCGATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGG
CCCAAAGGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATATGTACAGAAATG
GAAAAAGAAGGAAAAATTTCAAGAATTGGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGA
AAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTTTG
GGAGGTCCAATTAGGAATACCGCATCCTGCAGGGTTAAAAAAGAAAAAGTCAGTAACAGTACTGGATGTG
GGGGATGCATATTTTTCAGTTCCCTTAGATAAGGACTTCAGGAAGTACACTGCATTCACCATACCTAGTC
TCAACAATGAGACACCAGGAATTAGGTACCAGTACAATGTGCTTCCACAAGGATGGAAAGGATCACCAGC
AATATTCCAATGTAGCATGACAAAAATCTTAGATCCTTTTAGAGCAAAAAATCCAGACATAGTTATCTAC
CAATACGTGGATGATTTGTATGTAGGGTCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGT
TAAGAGAACATCTACTGAAATGGGGATTTTTTACACCAGACAAAAAACATCAAAAGGAGCCCCCATTCCT
TTGGATGGGGTATGAACTCCATCCTGATAAATGGGCAGTGCAG
 
>gi333005683 	
CCTCAAATCACTCTTTGGCAACGACCCCTAGTCACAATACAAGTAGGGGGACAGCTAAGGGAAGCTCTAT
TAGATACAGGAGCAGATGATACAGTATTAGAAGACATAAATTTGCCAGGAAAATGGAAACCAAAAATGAT
AGGGGGAATTGGAGGTTTTATCAAAGTAAAACAGTATGATAACATATGCATAGACATTTGTGGACACAAG
GCTATAGGTACAGTGTTGGTAGGACCTACACCTGCCAACATAATTGGAAGAAATATGTTGACTCAGATTG
GTTGTACTTTAAATTTTCCGATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGG
CCCAAAGGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATATGTACAGAAATG
GARAAAGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGA
AAAAAGAAAGTTCTAGTTCTAAATGGAGAAAGGTAGTAGATTTCAGAGAACTTAATAAAAGAACTCAAGA
CTTCTGTGAAGTCCAATTAGGAATACCACATCCTGCAGGATTAAAAAAGAACAAATCAGTAACARTACTR
GATGTGGGTGATGCATATTTTTCAATTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATAC
CTAGTATAAACAATGAGAAACCAGGGATTAGATATCAGTACAATGTGCTYCCACAGGGATGGAAAGGATC
ACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTATAGAAAACAAAATCCAGACATAGTT
ATCTGTCAATACATGGATGATTTGTATGTAGCATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAG
AGGAACTGAGACAACATTTGTGGAAGTGGGGATTCTACACACCAGACAAAAAATATCAGAAAGAACCCCC
ATTCCTTTGGATG
 
>gi|20136660|gb|AF493411.1
 
CCTCAGATCACTCTTTGGCAGCGACCCTTCGTTACAATAAAAATAGGGGGACAACTAATAGAAGCCCTAT
TAGATACAGGAGCAGATGATACAGTATTAGAAGACATAGATTTGCCAGGAAGATGGAAACCAAAAATAAT
AGGAGGAGTTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGGTACCTGTAGAAATCTGCGGACATAAA
GTTATAACTACAGTATTAGTAGGAGCTACACCTGTCAACATAATTGGAAGAAATCTGATGACTAAGATTG
GCTGCACTTTAAATTTTCCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGG
CCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGAAATTTGTACAGAATTG
GARAAAGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGA
AAAAAGAAAGTTCTAGTTCTAAATGGAGAAAGGTAGTAGATTTCAGAGAACTTAATAAAAGAACTCAAGA
CTTCTGTGAAGTCCAATTAGGAATACCACATCCTGCAGGATTAAAAAAGAACAAATCAGTAACARTACTR
GATGTGGGTGATGCATATTTTTCAATTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATAC
CTAGTATAAACAATGAGAAACCAGGGATTAGATATCAGTACAATGTGCTYCCACAGGGATGGAAAGGATC
ACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTATAGAAAACAAAATCCAGACATAGTT
ATCTGTCAATACATGGATGATTTGTATGTAGCATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAG
AGGAACTGAGACAACATTTGTGGAAGTGGGGATTCTACACACCAGACAAAAAATATCAGAAAGAACCCCC
ATTCCTTTGGATG
 
>HMDR4
 
CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAA
GTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAA
TTGGAAGAGGCAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTA
TTTGCCATAAGGAAAAAGAATAGTACTAAATGGAGAAAAATAGTAGATTTCAGAGAACTT
AATAAGAAAACTCAAGACTTTTGGGAAGTTCAATTAGGAATTCCACATCCCGGAGGGTTA
AAAAAGAAAAARTCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAATTCCCTTA
GATAAAGACTTCAGGAAGTATACTGCCTTTACCATACCTAGTATAAACAATGAGACACCA
GGGATTAGATATCAGTACAATGTGCTCCCACAGGGATGGAAAGGATCACCAGCAATATTC
CCAAGCTGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATC
TATCAATACGTGGATGATTTGTATGTAGGATCTGACTTAGAAATAGAGCAGCATAGAACA
AAAATAGAGGAACTAAGACAATATCTATGGAAATGGGGATTTTACACACCAGAGAACAAA
CATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACA
GTACAGCCTATAGTGCTACCAGAAAAAGA
 
>CRF02_AG.FR.DJ263
 
AAATTGGGCCTGAAAATCCATACAATACTCCAGTGTTTGGCATAAAGAAGAGAGATAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTCAATAAGAGA
ACTCAAGACTCCTGGGAGGTCCAATTAGGAATACCTCATCCCGCGGGATTAAAAAAGAAAAAATCAGTAACAGTACTAGATGTGGGTGATGCATATTTTTCAGT
CCCCTTAGATAAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTACAAATAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGAT
GGAAAGGATCACCAGCAATATTTCAGGCAAGCATGACAAACATCTTAGAGCACTATAGAATAAAAAATCCAGAGATAATGATCTACCAATATATGGATGATTTA
TATGTAGGATCTGACTTAGAGATAGAGCAGCATAGAGCAAAAATAGAGGAGTTGAGAGAACATCTACTAAAATGGGGATTTACCACACCAGATAAAAAACATCA
GAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTCCAGCCTATACAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATA
TACAGAAATTAGTGGGAAAACTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAAGCAACTGTGTAAACTCCTCAGGGGAGCCAAAGCATTAACAGAT
ATAGTACCACTGACTGAGGAAGCAGAATTAGAATTGGCAGAGAACAGGGAAATTCTAAAAGAACCTGTACATGGAGTATATTATGACCCAGCAAAAGACC
TAATAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTAAAAACAGGAAAATATGCAAAAAGGAGGTC
TGCCCACACTAATGATGTAAAACAATTAGCAGAGGTAGTGCAAAAAGTGGTTACAGAAAGCATAGTAATATGGGGAAAGACCCCTAAATTTAGACTACCCATAC
AAAGAGAAACATGGGAAGCATGGTGGATGGAGTATTGGCAGGCTACCTGGATTCCTGACTGGGAGTTCGTCAATACCCCTCCTCTAGTAAAATTGTGGTACCAG
TTAGAGAAAGACCCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAATAGGGAGACTAAGCTAGGAAAAGCGGGGTATGTCACTGACAGAGGAAG
ACAAAGGTTGTTTCCCTAACTGAGACAACAAATCAAAAGACTGAGTTACATGCAATTTATCTAGCCTTGCAGGACTCAGGATCAGAAGTAAATATAGTAACAGA
CTCACAGTATGCATTAGGAATCATTCAGGCACAACCAGACAGGAGTGAATCAGAGTTAGTCAATCAAATAATAGAGAAGCTAATAGAAAAGGACAAAGTCTAC
CTGTCATGGGTACCAGCACACAAAGGGATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTAATGGAATCAGGAAGGTACTATTTTTAGATGGCATAGATAA
AGCCCAAGAAGAGCATGGAAGATATCACAGCAATTGGAGAGCAATGGCTAGTGATTTTAATCTGCCACCTATAATAGCAAAAGAAATAGTGGCCTGCTGTGATC
AATGTCAGCTGAAAGGGGAAGCCATGCATGGACAAGTAGACTGTGGTCCAGGAATATGGCAATTAGATTGTACACATTTAGAAGGAAAAATTATCCTGGTAGCAG
TCCATGTAGCCAGTGGTTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAGGAGACAGCATACTTTATACTAAAATTAGCAGGAAGATGGCCAGTGAAAG
TAATACACACAGACAATGGCAGCAATTTTACCAGTGCTGCAGTAAAGGCAGCATGTTGGTGGGCAAATGTCACACAGGAATTTGGAATTCCCTACAATCCCCAAA
GCCAAGGAGTAGTGGAAGCTATGAATAAAGAATTAAAGAAAATCATAGGGCAGGTCAGGGATCAAGCTGAACACCTTAAGACAGCAGTACAGATGGCAGTATTCA
TTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCATCAGATATACAAACTAAAGAACTACAAAAACAGA
TTACAAAAATTCAAAATTTTCGGGTCTATTACAGGGACAGCAGAGACCCCATTTGGAAAGGACCAGCAAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACA
GGACAAGAGTGATATAAAGGTAGTACCAAGAAGAAAAGCAAAAATCATTAAAGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAGGTAGACAGGATGAGGA
 
>AF493411.1
 
CCTCAGATCACTCTTTGGCAGCGACCCTTCGTTACAATAAAAATAGGGGGACAACTAATAGAAGCCCTAT
TAGATACAGGAGCAGATGATACAGTATTAGAAGACATAGATTTGCCAGGAAGATGGAAACCAAAAATAAT
AGGAGGAGTTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGGTACCTGTAGAAATCTGCGGACATAAA
GTTATAACTACAGTATTAGTAGGAGCTACACCTGTCAACATAATTGGAAGAAATCTGATGACTAAGATTG
GCTGCACTTTAAATTTTCCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGG
CCCAAAAGTCAAACAATGGCCATTG

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Developed by: Tulio de Oliveira, Koen Deforche, Sharon Cassol, Andrew Rambaut and Anne-Mieke Vandamme.

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK., the HIV-1 Pathogenesis and Immunotherapeutics Program at University of Pretoria, South Africa, and the REGA Institute at the Katholieke Universiteit Leuven, Belgium.
Funded by the Marie Curie Fellowship, Flanders Bilateral Cooperation Program and the Wellcome Trust (grant # 061238 ).

For questions, suggestions or problems please contact:  Dr. Tulio de Oliveira.