HIV sequence database
Common Sequence Formats
Below are examples of some of the alignment formats our web interfaces recognize. In each example, two or more sequences are displayed in the given format. To convert the format of your sequence, we provide a Format Converter tool. More format descriptions can be found at the Pasteur Institute website: File Formats.
IMPORTANT! Do not convert your sequence files to a ".doc" file or open them in any word-processing program. One common reason for our web-based tools to fail is the corruption of the sequence format by changes introduced by word-processing programs.
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FastA: >CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG >U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
Table: CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGAAAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGAT U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACT
IG (IntelliGenetics): ; CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG ; U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
MSF:
1 50
CPZANT ATGGGAGCGG GGGCGTCTGT TTTGAGGGGA GAGAAGCTAG ATACATGGGA
U455 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG AAAAAATTAG ATTCATGGGA
BZ126B ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGAAAATTAG ATGCTTGGGA
IBNG ATGGGTGCGA GAGCGTCAGT ATTAAGTGGG GGAAAATTAG ATGCATGGGA
VI59 ATAGGTGCGA GAGCGTCAGT ATTAAGCGAG GGAAAATTAG ATGCATAGGA
VI310 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGAAAATTAG ATAAGTGGGA
SF2 ATGGGTGCGA GAGCGTCGGT ATTAAGCGGG GGAGAATTAG ATAAATGGGA
BZ167 ATGGGTGCGA GAGCGTCGGT ATTAAGCGGG GGAGAATTAG ATAGGTGGGA
PH153 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGGAAATTAG ATAGATGGGA
PH136 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGAGAATTAG ACAGATGGGA
TB132 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGACAATTAG ATAGATGGAA
GDE: #CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG #U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
PHYLIP (Interleaved):
11 1683 I
CPZANT ATGGGAGCGG GGGCGTCTGT TTTGAGGGGA GAGAAGCTAG ATACATGGGA
U455 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG AAAAAATTAG ATTCATGGGA
BZ126B ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGAAAATTAG ATGCTTGGGA
IBNG ATGGGTGCGA GAGCGTCAGT ATTAAGTGGG GGAAAATTAG ATGCATGGGA
VI59 ATAGGTGCGA GAGCGTCAGT ATTAAGCGAG GGAAAATTAG ATGCATAGGA
VI310 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGAAAATTAG ATAAGTGGGA
SF2 ATGGGTGCGA GAGCGTCGGT ATTAAGCGGG GGAGAATTAG ATAAATGGGA
BZ167 ATGGGTGCGA GAGCGTCGGT ATTAAGCGGG GGAGAATTAG ATAGGTGGGA
PH153 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGGAAATTAG ATAGATGGGA
PH136 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGAGAATTAG ACAGATGGGA
TB132 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG GGACAATTAG ATAGATGGAA
PHYLIP (Sequential):
11 1683
CPZANT ATGGGAGCGG GGGCGTCTGT TTTGAGGGGA GAGAAGCTAG ATACATGGGA
AAGTATCAGG CTTCGGCCCG GTGGCAAGAA AAAGTACATG ATAAAACATC
TGGTTTGGGC AAGATCGGAG CTGCAGCGTT TTGCGCTCAG CTCCTCCCTT
CTAGAAACAT CAGAAGGTTG TGAAAAGGCT ATCCATCAAT TGAGCCCTTC
CATAGAAATA AGATCCCCTG AAATAATATC TTTGTTTAAC ACCATTTGTG
TTCTGTGGTG CGTACATAAA GGGGAAAAGA TAAAAGACAC AGAACAAGCC
GTTAAAACAG TGAAAATGAA AGTAATGCAG ACACAAGCAG AAACAGGAAG
TAGCCAAACC GCAAGCAGAG GCATGCTTCT GCGGCTGCTC CTGTTAAACA
AACAGTGGTG TCAGCGACAT CTTAGTGGCG AAGGGAGAAA TTACCCCATC
ATAGTGGATG CAGGAGGAAT AGCAAGGCAT CAGCCACTGA CACCAAGAAC
CTTAAATGCC TGGGTAAAGT GTGTAGAAGA GAAAAATTTC AATCCAGAAG
TCATCCCTAT GTTTTCTGCT TTATCAGAAG GGGCAACTCC TCATGATTTA
AACACCATGC TTAATGCAGT TGGGGACCAT CAAGGAGCCA TGCAGGTGCT
AAAAGAAGTA ATCAATGAGG AAGCAGCTGA GTGGGATAGG TTACACCCCA
CTCATGCAGG ACCAGTACAG GCAGGACAAT TAAGGGAACC AACAGGAAGT
GATATAGCAG GGACAACAAG CACAGTGCAG GAGCAGATGC AATGGATGTC
AACACCTCAA CAGAATGGAG GAGTCCCAGT AGGGGACATC TATAAGAGAT
GGATCATCAT GGGATTAAAT AAGGTGGTCA GGANGTATAG TCCAGTCAGC
ATTCTAGAGA TAAAACAAGG ACCAAAAGAG CCCTTCAGAG ATTATGTGGA
TAGATTCTAT AAAACAATTA GAGCAGAACA GGCTTCACAG CCTGTGAAAG
CCTGGATGAC AGAAACCTTG TTAATCCAAA ATGCCAATCC AGATTGCAAA
CACATCCTGA AGGCTTTGGG AACAGGAGCC TCCTTAGAAG AAATGTTAAC
AGCTTGTCAA GGAGTAGGAG GCCCAGCCCA TAAGGCAAGA GTGTTGGCAG
AAGCTATGGC TTCTGCTAAT AAT---GCAC AG------GG AACCGCA---
GTCTTTCTGC AGAGAGGCAA TGGAAATAGA GGAGGAAAAA GACCTCTCAA
ATGTTTTAAC TGCGGTAAAG AGGGCCATAC TGCAAGAAAT TGCAAGGCCC
CAAGAAGGAA AGGCTGCTGG AGATGTGGAC AGGAAGGACA CCAGCTTAAA
AACTGTCCAG CAACAAATAC AGGAAAAGTA AATTTTTTAG GGAAACCGAC
CCCCACGTGG TGGGGGTGCA GACCAGGGAA CTTTGTGCAG AAGGAGGAAG
TAGTG----- ---------- ---------- ---------- -GAGCCAACA
GCTCCACCCA TAGAG----- ---------- ------ATCT AT--------
-CAGGAGGAG CACAAG---A GGACT----- -------CAG AAGGGTCTCA
AGGGGGAG-- ---------- GAGGAACTA- --CCTCCCTC GTATTCCCTG
AAATCCCTCT TTGGCAAAGA CCAATGA--- ---
U455 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG AAAAAATTAG ATTCATGGGA
GAAAATTCGG TTAAGGCCAG GGGGAAACAA AAAATATAGA CTGAAACATT
TAGTATGGGC AAGCAGGGAG CTGGAAAAAT TCACACTTAA CCCTGGCCTT
TTAGAAACAG CAGAAGGATG TCAGCAAATA CTGGGACAAT TACAACCAGC
TCTCCAGACA GGAACAGAAG AACTTAGATC ATTATATAAT ACAGTAGCAG
TCCTCTATTG TGTACATCAA AGGATAGATG TAAAAGACAC CAAGGAAGCT
TTAAATAAAA TAGAGGAAAT GCAAAATAAG AACAAGCAAA GG--------
---------- ACACAGCAGG CAGCAGCT-- ----AACACA ---GGAAGC-
---------- ---------- ---------- --AGTCAAAA TTACCCCATA
GTGCAAAATG CACAAGGGCA ACCAGTACAC CAGGCCTTAT CACCTAGGAC
CTTGAATGCA TGGGTGAAAG TAGTAGAAGA CAAGGCTTTC AGCCCAGAAG
TAATACCCAT GTTTTCAGCA TTATCAGAGG GAGCCACCCC ACAAGATTTA
AATATGATGC TGAATGTAGT GGGGGGACAC CAGGCAGCTA TGCAAATGTT
AAAAGATACC ATCAATGAGG AAGCTGCAGA GTGGGACAGG TTACATCCAG
TGCATGCAGG GCCTATTCCA CCAGGCCAGA TGAGAGAACC AAGGGGAAGT
GACATAGCAG GAACTACTAG CACCGTTCAA GAACAAATAG GATGGATGAC
AGGC------ ---AATCCAC CTATCCCAGT GGGAGACATC TATAGAAGAT
GGATAATCCT GGGATTAAAT AAAATAGTAA GAATGTATAG CCCTGTTAGC
ATTTTGGACA TAAGACAAGG GCCAAAAGAA CCCTTCAGGG ATTATGTAGA
TAGATTCTTT AAAACTCTCA GAGCTGAGCA AGCTACACAG GATGTAAAAA
ACTGGATGAC AGAAACCTTG CTGGTCCAAA ATGCGAATCC AGACTGTAAG
TCCATTTTAA GAGCATTAGG GCCAGGGGCT ACATTAGAAG AAATGATGAC
AGCATGCCAG GGAGTGGGAG GACCCGGCCA TAAAGCAAGG GTTTTGGCTG
AGGCAATGAG TCAAGTA--- ------CAAC AG---ACAAG C---------
ATAATGATGC AGAGAGGCAA TTTT---AGG GGCCCGAGAA GA---ATTAA
GTGTTTCAAC TGTGGCAAAG AAGGACACCT AGCCAAAAAT TGTAGGGCCC
CTAGGAAAAA GGGCTGTTGG AAATGCGGGA AAGAAGGACA CCAAATGAAA
GACTGCACT- -----GAG-- -AGACAGGCT AATTTTTTAG GGAAAATTTG
GCCTTCCAAC AAGGGG---A GGCCAGGGAA TTTTCCTCAG AGCAGACCA-
---------- ---------- ---------- ---------- -GAGCCAACA
GCCCCACCAG CAGAA----- ---------- ------ATCT TT---GGGAT
GGGGGAAAAG ATGACC---T CCCCT----- -------GCG AAACAGGAGC
TGAAAGAC-- ---------- AGGGAACAGA CT---CCTTT AGTTTCCCTC
AAATCACTCT TTGGCAACGA CCCCTTGTCA CAG
SLX: #=RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx DH123 .TGGAAGGGCTAATTTACTCCCAGAAAAGACAAGAtATCCTTGACCTGTG B-MANC .................................................. B-HAN .TGGAAGGGTTAATTTACTCCCCAAAAAGACAAGAgATCCTTGATCTGTG B-OYI .TGGAAGGGCTAATTTACTCCCAGAAAAGACAAGAtATTCTTGATCTGTG B-AUMBCC54 .TGGAAGGGCTAATACGCTCCCAAAGAAGACAAGAtATCCTTGATCTGTG F-93BR020 .TGGAAGGGTTAATTTACTCCAAGAGAAGACAAGAgATCCTTGATCTGTG BF-93BR029 .TGGAAGGGTTAATTTATTCCAAGAAAAGACAAGAgATCCTTGATCTGTG D-94UG114 .TGGAAGGGTTAGTTTGGTCCCCGAAAAGACAAGAgATCCTTGATCTTTG B-WR27 .TGGAAGGGCTAATTTACTCCCAGAAAAGACAAGAtATCCTTGATCTGTG D-ELI .TGGAAGGGCTAATTTGGTCCAAAAAGAGACAAGAgATCCTTGATCTTTG D-NDK .TGGAAGGGCTAATTTGGTCCAAGAAAAGACAAGAgATCCTTGATCTTTG B-LAI .TGGAAGGGCTAATTCACTCCCAACGAAGACAAGAtATCCTTGATCTGTG B-BCSG3 .TGGAAGGGCTAATTTTCTCCCAAAGAAGACAAGAtATCCTTGATCTGTG B-D31 .TGGAAGGGCTAGTTCACTCCCAAAAAAGACAAGAcATCCTTGACCTGTG B-RF .TGGATGGGCTAGTGTTCTCCCAGAAAAGACAAGAtATCCTTGATCTGTG B-JRFL .TGGAAGGGCTAATTCACTCACAGAAAAGACAAGAtATCCTTGATCTGTG D-84ZR085 .TGGAAGGGCTAGTTTACTCCCAGAAAAGACAAGAtATCCTTGATCTTTG B-HIVMN .TGGATGGGTTAATTTACTCCCAAAAGAGACAAGAcATCCTTGATCTGTG |
last modified: Tue Apr 22 12:43 2008