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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.
IMPORTANT! Do not convert your sequence files to a ".doc" file or open them in any word processing program. Sequence formats can be corrupted by cryptic changes introduced by word-processing programs and thus cause failures of sequence analysis tools.
Clustal W: CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA CPZANT AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC U455 GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT CPZANT TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT U455 TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT CPZANT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC U455 TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC CPZANT CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG U455 TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
FastA: >CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG >U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
GCG: cf:CPZANT Length: 250 Thu Apr 28 16:08:49 MDT 2011 Check: 751 .. 1 ATGGGAGCGG GGGCGTCTGT TTTGAGGGGA GAGAAGCTAG ATACATGGGA 51 AAGTATCAGG CTTCGGCCCG GTGGCAAGAA AAAGTACATG ATAAAACATC 101 TGGTTTGGGC AAGATCGGAG CTGCAGCGTT TTGCGCTCAG CTCCTCCCTT 151 CTAGAAACAT CAGAAGGTTG TGAAAAGGCT ATCCATCAAT TGAGCCCTTC 201 CATAGAAATA AGATCCCCTG AAATAATATC TTTGTTTAAC ACCATTTGTG 251
GDE: { name "CPZANT" sequence " ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG " } { name "U455" sequence " ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG " }
GDEFlat: #CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG #U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
IG (IntelliGenetics): ; CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG ; U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
Mase: ; CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG ; U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
Mega (Interleaved): #MEGA TITLE: Interleaved sequence data #CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA #U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA #CPZANT AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC #U455 GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT #CPZANT TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT #U455 TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT #CPZANT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC #U455 TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC #CPZANT CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG #U455 TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
Mega (Sequential): #MEGA TITLE: Noninterleaved sequence data #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
Nexus (interleaved): #NEXUS begin taxa; dimensions ntax=2; taxlabels CPZANT U455 ; end; begin characters; dimensions nchar=250; format interleave datatype=DNA gap=-; matrix CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA CPZANT AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC U455 GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT CPZANT TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT U455 TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT CPZANT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC U455 TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC CPZANT CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG U455 TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG ; end;
Nexus (Sequential): #NEXUS begin taxa; dimensions ntax=2; taxlabels CPZANT U455 ; end; begin characters; dimensions nchar=250; format datatype=dna gap=-; matrix CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGAAAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATCTGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTTCTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTCCATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTTTTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGCTCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG ; end;
PHYLIP (Interleaved): 2 250 i CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
PHYLIP (Sequential): 2 247 s CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTT U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAG
PIR: >DL;CPZANT CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG * >DL;U455 U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG *
Pretty Print: CPZANT ATGGGAGCGG GGGCGTCTGT TTTGAGGGGA GAGAAGCTAG ATACATGGGA 50 U455 ATGGGTGCGA GAGCGTCAGT ATTAAGCGGG AAAAAATTAG ATTCATGGGA CPZANT AAGTATCAGG CTTCGGCCCG GTGGCAAGAA AAAGTACATG ATAAAACATC 100 U455 GAAAATTCGG TTAAGGCCAG GGGGAAACAA AAAATATAGA CTGAAACATT CPZANT TGGTTTGGGC AAGATCGGAG CTGCAGCGTT TTGCGCTCAG CTCCTCCCTT 150 U455 TAGTATGGGC AAGCAGGGAG CTGGAAAAAT TCACACTTAA CCCTGGCCTT CPZANT CTAGAAACAT CAGAAGGTTG TGAAAAGGCT ATCCATCAAT TGAGCCCTTC 200 U455 TTAGAAACAG CAGAAGGATG TCAGCAAATA CTGGGACAAT TACAACCAGC CPZANT CATAGAAATA AGATCCCCTG AAATAATATC TTTGTTTAAC ACCATTTGTG 250 U455 TCTCCAGACA GGAACAGAAG AACTTAGATC ATTATATAAT ACAGTAGCAG Raw: One(!) sequence per line. ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGAAAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATCTGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTTCTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTCCATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTTTTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGCTCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
RSF: !!RICH_SEQUENCE 1.0 .. { name CPZANT sequence ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG } { name U455 sequence ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG }
SLX: CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA CPZANT AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC U455 GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT CPZANT TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT U455 TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT CPZANT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC U455 TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC CPZANT CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG U455 TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG
Stockholm: # STOCKHOLM 1.0 CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGA U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGA CPZANT AAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGATAAAACATC U455 GAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACTGAAACATT CPZANT TGGTTTGGGCAAGATCGGAGCTGCAGCGTTTTGCGCTCAGCTCCTCCCTT U455 TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCACACTTAACCCTGGCCTT CPZANT CTAGAAACATCAGAAGGTTGTGAAAAGGCTATCCATCAATTGAGCCCTTC U455 TTAGAAACAGCAGAAGGATGTCAGCAAATACTGGGACAATTACAACCAGC CPZANT CATAGAAATAAGATCCCCTGAAATAATATCTTTGTTTAACACCATTTGTG U455 TCTCCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAG //
Table: CPZANT ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACATGGGAAAGTATCAGGCTTCGGCCCGGTGGCAAGAAAAAGTACATGAT U455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGAAAAAATTAGATTCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAACAAAAAATATAGACT
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