[BioPython] aligning with clustalw fails

[Karin Lagesen]

i
I am trying to align some sequences using the clustalw in biopython.
For some reason it fails on some files, whereas on others it works
perfectly. Here is an example of where it fails:

adenine:11:40> python
Python 2.2.3 (#1, Oct  8 2003, 10:44:04)
[GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-112)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import Clustalw
>>> from Bio.Clustalw import MultipleAlignCL
>>> cline = MultipleAlignCL("/tmp/locatorfiles/11249")
>>> alignment = Clustalw.do_alignment(cline)
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File
"/tmp/biopython-1.21/build/lib.linux-i686-2.2/Bio/Clustalw/__init__.py",
line 121, in do_alignment
File
"/tmp/biopython-1.21/build/lib.linux-i686-2.2/Bio/Clustalw/__init__.py",
line 60, in parse_file
File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Martel/Parser.py",
line 328, in parseFile
File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Martel/Parser.py",
line 361, in parseString
File "/usr/local/lib/python2.2/xml/sax/handler.py", line 38, in
fatalError
    raise exception
Martel.Parser.ParserIncompleteException: error parsing at or beyond
character 221 (unparsed text remains)
>>> 

When I put the file into clustalw the normal way, everything works
just fine. The file I am trying to align is attached.

TIA,

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at labmed.uio.no
-------------- next part --------------
>+xylR to +malS 3733787 3735125
CGATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGT
GAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCT
CGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGG
CTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGC
GAACAGGTAGTTGTTATAACTCTTCCCTTTGGTCGAGTAGCCCTTCAGCTTGTGAATCAT
CGCTGTGGCAGTCACTTCCTGATCCGCTTTACGCAGCTGCGCACGCGATTTACGGAACGA
AGAGTAAGCCGGGTGCGTATTCAGGTTAGTGACATAGGCGCTCACCGATTCTTTGACAGA
ACTAAACTGTGAGTACCCTTTCACTTTACCTGGCGCATTGGTACAACGTCCTTTCATCGA
TTTCATGCCGAACAGGTTGTTGTTGTTGCGCGCCAGCTTCGACGTTCCCCAACCGCTTTC
TGCTGCAGCCATCGTCGCCACCATACTGGTGGGGATAATGTCTACGCGTTCAAGCAAGGT
ATTCCACGGGATTTTTCGCGTATTACCGGACCACTTCACCTTGTAGCGTTTGGCGATGTC
TTTCAGACGCGCACGCTCAGCAGGTGACCATTGGCCCTGATACTGTTTTGAAATGAGCCA
GTTACGTTCCGCAGTAATGGCCGCATTTTGGCTGGTAATGTAAGGCATTACGGTCCGGAG
AAACGCCTTTTTCCTTGGTGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTACT
CTTTGCACTATTGCGAGAATACTCTTGTTTACTGCTTACCTGTTTATTACTAGCTTTAGT
TAAGTGGGACTTTTGACTCGCTGTTGTTGTGTGCGTCTTCGCTAACACCTCACTCGAAAA
CACCAGAGTGAGTAACATAAGAATCATCGCCCCATATCGTCGTATGGGAGTCAAAATCAT
CAGGTCTCCTGGTCGGATTTAATCATTCCAACACCTTATATTTTTCACAAATTTGAGAGT
TGAATCTCAAATCATATCAAAAATAGCTGTCAAGAGCACCCCAAGGAATAGTCCAAATCT
GAAACTATGTCACGTGTTAACGATTCAGATTGGCGCTAAATCGCAGAAAATGTGGGGGTT
ATCGCAAAATTCAGCCGTTTTTTGCGCGAGATCGCTCACCCTTGCTTCTCATCCTGTGGA
CTTACCGCTCAGGGATGAGTTTTGTTTGGCTTATCGCTGGCAAACTGTCTGAAATCGCAG
CAATAAGGACTCATCCGCC
>0_-Salmonella_typhi_3998330_3999668
TTGGCGATAAACGAAATTTCGCAAATGTGCGGCTACCCGTCGCTGCAATATTTCTATTCG
GTGTTTAAAAAGGAGTACGTCACTACGCCTAAGGAGTATCGCGACCAGCATAGTGAAGCG
TTGTTGTAGTTTATCCAGCCTACAGATGCCTTGTAAGCCGGATAGCGTAGCGCCATCCGG
CACACAGAATTACATATGCGCGGCGATCAGACGCTGGTTGTCCTGGTACATCGCGAACAA
GTAGTTGTTATAGCGCGCCCCCTGGGTAGAGTAACCCTTTAGCTTATGAATCATCGCCGT
GGCGGTGACTTCCTGATCCGCCTTACGCAGTTGGGCGCGCGACTTGCGGAAAGAAGAATA
AGCCGGATGCGTGTTCAGGTTGGCGACATACGCGCTCACCGACTCCTCAACCGACGCGAA
TTGCGAGTAACCTTTCACCTTACCCGGCGTATTGGTACAACGCCCTTTCGTGCACTTCAT
GCCGAACAGGTTATTGTTGCTACGCGCCAGTTTAGAGGTTCCCCAGCCGCTTTCCGCCGC
CGCCATCGTCGCCACCATGCTGGTTGGGATAATGTCGACGCGCTCCAGCAACGTATTCCA
CGGAATACGACGCGTGTTGCCGGACCAGCTCACTTTATAGCGCTTCGCGATATCTTTCAT
ACGCGCGCGCTCAGACGGCGACCAGCGGTTCTGGTACTGTTTTGAGATCAGCCAATTACG
GTCCGCGGTAATCGCGGCATTTTGGCTGGTGATGTAAGGCATAACGGTCCGGAGAAACGC
TTTTTTTCTGGGGGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTGCTCTTTGC
ACTATTGCGAGAATACTCTTGTTTACTGCTAACCTGTTTATAACTTGTCTCAGTTATGTG
GGACTTTTGACTCGTTTGTGTTGCGCGCGTCTTTGCCAGCACCTCACCCGAAAATGCGAT
GGTGAGTAACATAAGAATCATTGCCCCATATCGTCGCATGGGAGTCAATATCATTAGGTC
TCCTGGTCGGATTGATACATTCCAACACCTTTTATTTTTCACGAAGTTGAGGTTTGAACC
CCAAATTCTAGCAAAAATAGGCTTAAAAAGCACCTCAGGGAATAGTCTTAATCCGAAACT
ATGTCAACTATTAACGATAACAGACAGCAATAATGCCAATAAAATGCGGCGTTTATCGCA
AATAGAGGCGTTTTTTTGCGCCTCGTCGCTCACCCTCGCGCCTCCTCCTGCGCGACTCTC
TGCTGGGGAGGAGTTCATTCGCCTAAAAACCAGGCAAGCTGATGAATATTGCCCACAAAG
GATAGCGTGATGAAACTTG
>1_-Salmonella_typhi_4356008_4357346
TTTATTATCGGCTTCGGCGCTATCATGCTGGTGGGGGCGAATCCCGCCTATAAAGATGCC
GCAGGCGCGCTGATTGGCGGCAATAACATGGCGGCGGTGCATCTGGCCAACGCGGTAGGC
GGCAACCTGTTCCTCGGCTTTATTTCGGCAGTGGCGTTTGCCACCATTCTGGCGGTGGTC
GCAGGTCTGACGCTGGCGGGCGCATCGGCGGTGTCGCATGACTTGTACGCCAACGTGTTC
CGCAAAGGCGCAACCGAACGTGAAGAGCTGAAGGTGTCGAAAATCACCGTCCTGGTGCTG
GACGTGATCGCCATTATCCTCGGCGTCCTGTTTGAAAATCAGAACATCGCCTTTATGGTG
GGCCTGGCATTTGCTATCGCCGCGAGCTGCAACTTCCCCATCATTCTGCTTTCCATGTAC
TGGTCAAAACTGACCACGCGCGGCGCTATGCTGGGCGGCTGGTTAGGTTTACTGACAGCG
GTGGTGCTGATGATTCTTGGCCCTACCATTTGGGTGCAGATCCTCGGCCACGAAAAAGCG
ATCTTCCCGTATGAGTATCCGGCGCTGTTCTCTATCAGCGTGGCGTTCCTGGGGATCTGG
TTCTTCTCGGCCACCGATAACTCGGCAGAAGGCAACCGTGAACGTGAGCAGTTCCGCGCT
CAGTTTATCCGCTCCCAAACGGGATTCGGCGTACAACAAGGGCGTGCGCATTAATCTTAC
CGTTTCCTCCGGCCCTGTGGGTCGGAGGAAAATCAGAACATCACCCTCGCCACCAGCGGG
GCTGCCAGCACCATCACCACGCCGGACAGCATCATTACCAGACTGGCGACGACGCCCTCC
TGCTGACCAAGTTCATAGGAACGCGCCGTGCCTGCCCCATGTGACGCCGCGCCGAATCCT
GCCCCTTTTGCCATGCCTTCCCGGATAGAGAGACGCAAAAATAGCGCGTCGCCGACCGCC
ATGCCAAACACGCCAGTGACGACCACGAACAGCGCCACCAGATCCGGCTGCCCGCCCAGG
GGTTCTGCCGCCGCCAGCGCAAACGGCGTAGTAACGGAACGTACCGCCAGACTACGCTGA
ATCTCATCCGATAACGTGAACAGACGCGCCAGCCAAACGGAACTGGTGACCGCCACCACC
GTCGCCGTCACTACACCCGCGGTGAGCGACATCCAGTGACGTTTGATAATCGCGAGGTTA
TCGTACACCGGCACCGCAAAGGCAATGGTCGCCGGGCCGAGCAGCCACAATAGCCAGTGC
GATTCGCTAATATAGTTTTGCCAGGAGATATGACCGAACACCAGCATTAACACCAGCAGT
GCCGGCGTCAACACTAATG
>2_Salmonella_typhi_3302673_3304011
CACGGTACTGATCCAGATCGCTGCTTTCCAGTTGCTGCTGAACTTTCGCGGCGAATTTTT
CCAGACGGCGTTTACCCAGCAGTTCTGCGTTCGGCAGTTCCACTTCTGGAATGGTCAGCT
TCATGGTGCGTTCGATGTTGCGCAGCAGACGACGCTCGCGGTTCTCAACGAACAGCAGCG
CGCGACCGGCGCGACCCGCACGACCGGTACGACCGATACGGTGAACGTAGGACTCGGAGT
CCATCGGAATATCGTAGTTCACCACCAGGCTGATACGTTCAACGTCCAGACCACGTGCCG
CAACATCGGTGGCGATCAGGATGTCCAGACGACCATCTTTCAGGCGTTCCAGAGTCTGCT
CACGCAGCGCCTGGTTCATATCGCCATTCAACGCGGCGCTGTTGTAGCCGTTACGTTCCA
GCGCTTCTGCTACTTCCAGGGTCGCGTTTTTGGTACGTACGAAGATAATCGCCGCATCAA
AGTCTTCCGCTTCCAGGAAACGCACCAGTGCTTCGTTTTTACGCATACCCCAGACAGTCC
AGTAGCTCTGGCTGATGTCAGGACGGGTAGTCACGCTGGACTGAATGCGCACTTCCTGCG
GCTCTTTCATAAAGCGGCGGGTAATGCGACGAATCGCTTCCGGCATGGTGGCGGAGAACA
GAGCGGTTTGATGACCTTCCGGGATCTGCGCCATAATAGTTTCAACGTCTTCGATGAAGC
CCATACGCAGCATTTCGTCGGCTTCATCCAGCACCAGACCACTCAGTTTAGAGAGGTCGA
GGGTGCCGCGTTTTAAGTGATCAAGCAGACGTCCCGGCGTACCGACAACGATCTGCGGCC
CCTGACGCAGGGCGCGTAACTGCACGTCATAACGCTGACCGCCGTACAGGGCAACCACGT
TTACGCCGCGCATGTGTTTAGAGAAATCCGTCATGGCTTCGGCAACCTGTACCGCCAGTT
CGCGGGTTGGCGCCAGCACCAGAATCTGAGGTGCCTTCAGCTCAGGATCAAGATTGTTGA
GCAGCGGTAAAGAGAACGCTGCGGTTTTGCCGCTACCGGTCTGGGCCATGCCCAGCACGT
CGCGACCGCCCAGCAGATGCGGAATGCACTCTGCCTGGATTGGAGATGGTTTTTCGTAAC
CCAGATCGGTAAGGGCTTCAAGGATAGGAGCCTTCAGCCCCAGATCTGCAAAAGTGGTTT
CGAATTCAGCCATGTAGTACGTGTGCCTCAAAATTAATGGCGGCCAGTCTACATAACTCA
TCATGAAATTGATCTGCAATTTTCATTGAAAAGTGTGAACCGGCTCAAAGTAGGTGTATT
AACGAACAACAACGCCCTC
>3_-Salmonella_typhi_767064_768402
TCTTTCCAATAACTGGCATTCAACTCTTTGATATAATTTTCTCCGGGAAAAAGTTTATCC
TTTAAAGGCAGTTTTTTGGCTAGCACGATTCTTTCTGCGTTAGATCCCGCGGACTCTGAA
TGTGTGAGGGAAGATAAGGCGTCCAGTTGAGCGCTTGAGGGTCTGGCTATCAATTCAAAA
AAAGGTTCTGACAATACAACACTACTAAGTGCTGCATAATTTCCTTTTTGTATGAGCGGT
TTGACGTACTCAAAAAAAGAAATAATCCCTGATTGCAATCTTGCCGCTTTTTTTAAATAC
TCAATTTCAGAACCACTGCTATCTTCACGTACAGGAATTATTCCATTATCCGTTTTTTTA
TAGCCAATTGTTGACCCAGTATTATCAGCCATAGCGAACTCCATTATTTCCACCCCTCCT
GATAAGAAAAGATCACACTTATCGTGGGGATGGCCATAGTTGGTTAGATAACCAAACATC
TTATTATAAATAGATCGGTTATCATTGGCGCCAGCAAAAGTTGCCAAATAAAACCCATGT
ATTTGTTTTTCTGCCCATTGCGCACCTAAAGAACGAGCAAATACTGATTGAATATTACCC
ATCCATCCTACATCGATAAGTGCTATATTTTTAAAACCTTCACAGGCCGTTTTAAAGTAG
ATGGAAAGCAGACACTTGTTTAAGTAATAAAGACTTACAAATAGATTCACCCATAATATC
TTTAGCTTTCCAATGATTAGATATCCCATGATTATACTCTGACCAATCAGCATGGAGAGT
ATTTATGCCGAGTTTTTTAGCATTCAGAATATCAGCATGAACATTATCGCCAACATGTAT
CCACGATGCAATATCTACATTTTCATTTTTCTTGACTATTGAAAATAATTTACCACTATT
TTTAGAGTACCGCTCTTCGCCAGATGAATAAACTGGAATGTTACTGATATCATAGCCACA
TGATGTTAACAACTCCTTTAATATTGCTGATGGAAGGTACATATCACTAATTAAAATGAC
TTTGCAACCATCACTAATAGCCTTTTCAAACAAACAGCTTCCACGCGCATTTTTATATAA
AACAATCTTCTCCATTTGTATTTCCAGATCGATTATCTTTTTTACTGTCGCTGGTGAAAG
CTGCGGATGCTTTTTTAAAATTTCATCGTATATTTCAGATATAAGTATTTCCGGCTCGCC
GCCAAAACGCCTGACCCTATTCTCTCTGGCACTTACTTCCGCCTGAACTCTTATCTCTGG
GAAATTATCAATAATACCAATCTCGTACGCTGATATAAAAAATTTCTCAGTTGCTAAAGT
TGATTGCATTAATGAAAAC
>4_-Salmonella_typhi_767064_768402
TCTTTCCAATAACTGGCATTCAACTCTTTGATATAATTTTCTCCGGGAAAAAGTTTATCC
TTTAAAGGCAGTTTTTTGGCTAGCACGATTCTTTCTGCGTTAGATCCCGCGGACTCTGAA
TGTGTGAGGGAAGATAAGGCGTCCAGTTGAGCGCTTGAGGGTCTGGCTATCAATTCAAAA
AAAGGTTCTGACAATACAACACTACTAAGTGCTGCATAATTTCCTTTTTGTATGAGCGGT
TTGACGTACTCAAAAAAAGAAATAATCCCTGATTGCAATCTTGCCGCTTTTTTTAAATAC
TCAATTTCAGAACCACTGCTATCTTCACGTACAGGAATTATTCCATTATCCGTTTTTTTA
TAGCCAATTGTTGACCCAGTATTATCAGCCATAGCGAACTCCATTATTTCCACCCCTCCT
GATAAGAAAAGATCACACTTATCGTGGGGATGGCCATAGTTGGTTAGATAACCAAACATC
TTATTATAAATAGATCGGTTATCATTGGCGCCAGCAAAAGTTGCCAAATAAAACCCATGT
ATTTGTTTTTCTGCCCATTGCGCACCTAAAGAACGAGCAAATACTGATTGAATATTACCC
ATCCATCCTACATCGATAAGTGCTATATTTTTAAAACCTTCACAGGCCGTTTTAAAGTAG
ATGGAAAGCAGACACTTGTTTAAGTAATAAAGACTTACAAATAGATTCACCCATAATATC
TTTAGCTTTCCAATGATTAGATATCCCATGATTATACTCTGACCAATCAGCATGGAGAGT
ATTTATGCCGAGTTTTTTAGCATTCAGAATATCAGCATGAACATTATCGCCAACATGTAT
CCACGATGCAATATCTACATTTTCATTTTTCTTGACTATTGAAAATAATTTACCACTATT
TTTAGAGTACCGCTCTTCGCCAGATGAATAAACTGGAATGTTACTGATATCATAGCCACA
TGATGTTAACAACTCCTTTAATATTGCTGATGGAAGGTACATATCACTAATTAAAATGAC
TTTGCAACCATCACTAATAGCCTTTTCAAACAAACAGCTTCCACGCGCATTTTTATATAA
AACAATCTTCTCCATTTGTATTTCCAGATCGATTATCTTTTTTACTGTCGCTGGTGAAAG
CTGCGGATGCTTTTTTAAAATTTCATCGTATATTTCAGATATAAGTATTTCCGGCTCGCC
GCCAAAACGCCTGACCCTATTCTCTCTGGCACTTACTTCCGCCTGAACTCTTATCTCTGG
GAAATTATCAATAATACCAATCTCGTACGCTGATATAAAAAATTTCTCAGTTGCTAAAGT
TGATTGCATTAATGAAAAC
>5_Salmonella_typhi_2966453_2967791
AGAGCCTTGCATAGTCCAGAAGTGCGGGTCCGCCAGCGGGATATCGACGGATTGCAGCGA
CAGCGTATGCCCCATCTGACGCCAGTCGGTGGCGATCATATTGGTGGCCGTCGGTAATCC
GGTCGCGCGACGGAATTCCGCCATCACTTCACGACCGGAAAAACCCTGCTCCGCGCCGCA
CGGATCTTCTGCATAGGCCAGAGAACCTTTTAGGTATTTACCAATGCTGATCGCTTCGTT
CAGCGACCAGGCACCGTTTGGATCGAGCGTGACGCGCGCTTGTGGGAAACGTTTCGCCAG
CGCCACGATTGACTCGGCCTCTTCTTCGCCCGCCAGCACGCCGCCTTTCAGTTTGAAGTC
GTTGAAGCCGTATTTTTCATACGCCGCTTCCGCCAGACGCACTACCGTTTCCGGCGTCAT
CGCCTCTTCATGGCGCAGACGATACCAGTCGCATTGCTCATCCGGCTGGCTTTGATACGG
CAGCGGCGTAACCTTGCGATTGCCGACAAAGAACAGATAACCCAGCATTTCGACTTCGCT
GCGCTGCTGACCGTCGCCTAACAGCGAAGCGACGTTGACGCCCAGATGTTGGCCCAAAAG
GTCAAGCATTGCCGCTTCAATGCCCGTCACCACATGGATAGTGGTACGGAGATCGAACGT
TTGTAAACCGCGTCCGCCCGCATCGCGATCGGCAAACTGGTTGCGAACGGCGGTCAGGAC
ATTTTTATATTCATCCAGCGTTTTTCCCACCACCAGTGGAATCGCATCTTCCAGCGTTTT
GCGAATTTTTTCGCCGCCCGGAATCTCGCCGACCCCAGTATGACCGGAGTTATCTTTAAC
AATGACGATGTTGCGCGTAAAGAACGGGGCGTGCGCGCCGCTCAGGTTCATCAGCATACT
GTCATGACCCGCAACCGGGATAACCTGCATTTCAGTCACTACAGGCGTGGTAAATTGAGT
ACTCATAACTGTGTCCTTATTCAGAATTAGTGACGACCAAAAACAGGGCGTTTGCGGTCA
AAAGTCCAGCCGGGGATCAGGTATTGCATCGGGCCTGCATCATTACGCGCGCCGCCTGGC
AGCTTTTTATACGCGTCATGCGCTTTTCGCACCTGTTCCCAGTCAAGCTCTACGCCCAGT
CCTGGCGCATCCGGAACGGCAATTTTGCCGTTTTTAATTTCCAGCGGATTTTTAGTCAGG
CGGCAATCGCCCTCCTGCCAGATCCAGTGCGTATCAATAGCGGTGGGTTTGCCTGGCGCC
GCCGCGCCGACATGGGTAAACATCGCCAGTGAAATATCAAAATGGTTATTCGAATGGCAG
CCCCAGGTTAGCCCCCAGT
>6_Salmonella_typhi_3089870_3091208
TTCAATCGCTAAGGTGGCGATATCAGGCACAGCATCGACGCTTGCTGTACCGGAAGTCAC
GATGTGCGGGCCTTCCGGCAATTCGCTTGCCTGCGCCGACATTGCACTTAAACCCACTAA
TGCCGCCAGGGCCATCACTTTGAACTTCACAGTCTCTCCTCCATATTGCAGTCATTGCCC
TGATATACAGGGCGCATGCAGGCAAGCTTAGCGGATATCGGTCTGTTGTCCATCAGACAA
CGCTTAGTTGAAAAGCGCGTGCATATGCGCGACGCCTTCCCGCGCCAGTTGGAAGGCGAT
AAGCCACATCACCACCCCTACCAGAATGTTGATAATGCGTTGAGCTTTCGCCGTACGCAG
TCGAGGCGCAAGCCAGGCCGCCAGTAGCGCTAACCCAAAAAACCATAAGAACGACGCGCT
AATCGTGCCGAGAGCAAACCAGCGCTTTGGCTCCATAGCCAGTTGTCCGCCGAGACTGCC
CAACACGACAAACGTATCCAGATAAACGTGCGGATTCAGCCAGGTTACCGCCAGCATCGT
AGCAATAATTTTCCAGCGCCCCTGCTTCATAACCTCGGCGCTGGCCAGCTCCAGATTACT
GCTCATTGCCGTTTTCAGCGCGCCAAAACCGTACCATAACAAGAACGCAACCCCGCCCCA
TGTGACCAGCGCCAGCAGCCACGGCGACTGCATCAGCAACGCGCTACCGCCAAAAATACC
GGCGCTAATCAGGACTAAATCACTTAACGCGCAAAGCAGCGCTATCATGAGGTGGTACTG
GCGACGAATTCCCTGATTCATCACAAACGCATTTTGCGGGCCAAGCGGAAGGATCATGGC
GGCGCCAAGGGCAACCCCTTGAAAATAATAAGATATCACGTTAACTACCCTGAGCTGTTT
TTCTTAAAGGCAGACTATAGCGCGGGAATATTATTAGCGGAAATTGATAATTTTAATCAC
TAATAAGAAAAGCTAATAAAGAGACTGAATAACGGATGGCGGCTACGCTTATCCGCTCAA
TAACCAGAGAATACTGGAGGCGGATAAGCGCAGCGCCGGCAGGCAGCACGGGAGGAAAAT
TACTCCGCGGCGTTATCTTTCACGCGTTTAAAATTGACGTCCATCTGCGGGTACGGGAAG
CTAATACCAGCGGCGTCGAATTCACGTTTAATACGTTCCAGCACGTCCCAATAGACATTT
TGCAGGTCGCTGCTTTTACTCCAGACACGCACCACAAAATTAATTGATGAGGCGCCCAGC
TCATTCAAACGCACCGTCATTTCGCGATCTTTTAAAATACGATCGTCGGACTCGATAATC
GTCGTTAGCAGCTGTTTCA
>0_-Salmonella_typhi_Ty2_3983042_3984380
ACGAAATTTCGCAAATGTGCGGCTACCCGTCGCTGCAATATTTCTATTCGGTGTTTAAAA
AGGAGTACGTCACTACGCCTAAGGAGTATCGCGACCAGCATAGTGAAGCGTTGTTGTAGT
TTATCCAGCCTACAGATGCCTTGTAAGCCGGATAGCGTAGCGCCATCCGGCACACAGAAT
TACATATGCGCGGCGATCAGACGCTGGTTGTCCTGGTACATCGCGAACAAGTAGTTGTTA
TAGCGCGCCCCCTGGGTAGAGTAACCCTTTAGCTTATGAATCATCGCCGTGGCGGTGACT
TCCTGATCCGCCTTACGCAGTTGGGCGCGCGACTTGCGGAAAGAAGAATAAGCCGGATGC
GTGTTCAGGTTGGCGACATACGCGCTCACCGACTCCTCAACCGACGCGAATTGCGAGTAA
CCTTTCACCTTACCCGGCGTATTGGTACAACGCCCTTTCGTGCACTTCATGCCGAACAGG
TTATTGTTGCTACGCGCCAGTTTAGAGGTTCCCCAGCCGCTTTCCGCCGCCGCCATCGTC
GCCACCATGCTGGTTGGGATAATGTCGACGCGCTCCAGCAACGTATTCCACGGAATACGA
CGCGTGTTGCCGGACCAGCTCACTTTATAGCGCTTCGCGATATCTTTCATACGCGCGCGC
TCAGACGGCGACCAGCGGTTCTGGTACTGTTTTGAGATCAGCCAATTACGGTCCGCGGTA
ATCGCGGCATTTTGGCTGGTGATGTAAGGCATAACGGTCCGGAGAAACGCTTTTTTTCTG
GGGGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTGCTCTTTGCACTATTGCGA
GAATACTCTTGTTTACTGCTAACCTGTTTATAACTTGTCTCAGTTATGTGGGACTTTTGA
CTCGTTTGTGTTGCGCGCGTCTTTGCCAGCACCTCACCCGAAAATGCGATGGTGAGTAAC
ATAAGAATCATTGCCCCATATCGTCGCATGGGAGTCAATATCATTAGGTCTCCTGGTCGG
ATTGATACATTCCAACACCTTTTATTTTTCACGAAGTTGAGGTTTGAACCCCAAATTCTA
GCAAAAATAGGCTTAAAAAGCACCTCAGGGAATAGTCTTAATCCGAAACTATGTCAACTA
TTAACGATAACAGACAGCAATAATGCCAATAAAATGCGGCGTTTATCGCAAATAGAGGCG
TTTTTTTGCGCCTCGTCGCTCACCCTCGCGCCTCCTCCTGCGCGACTCTCTGCTGGGGAG
GAGTTCATTCGCCTAAAAACCAGGCAAGCTGATGAATATTGCCCACAAAGGATAGCGTGA
TGAAACTTGCCGCCTTCGC
>1_-Salmonella_typhi_Ty2_4340648_4341986
GCTTCGGCGCTATCATGCTGGTGGGGGCGAATCCCGCCTATAAAGATGCCGCAGGCGCGC
TGATTGGCGGCAATAACATGGCGGCGGTGCATCTGGCCAACGCGGTAGGCGGCAACCTGT
TCCTCGGCTTTATTTCGGCAGTGGCGTTTGCCACCATTCTGGCGGTGGTCGCAGGTCTGA
CGCTGGCGGGCGCATCGGCGGTGTCGCATGACTTGTACGCCAACGTGTTCCGCAAAGGCG
CAACCGAACGTGAAGAGCTGAAGGTGTCGAAAATCACCGTCCTGGTGCTGGACGTGATCG
CCATTATCCTCGGCGTCCTGTTTGAAAATCAGAACATCGCCTTTATGGTGGGCCTGGCAT
TTGCTATCGCCGCGAGCTGCAACTTCCCCATCATTCTGCTTTCCATGTACTGGTCAAAAC
TGACCACGCGCGGCGCTATGCTGGGCGGCTGGTTAGGTTTACTGACAGCGGTGGTGCTGA
TGATTCTTGGCCCTACCATTTGGGTGCAGATCCTCGGCCACGAAAAAGCGATCTTCCCGT
ATGAGTATCCGGCGCTGTTCTCTATCAGCGTGGCGTTCCTGGGGATCTGGTTCTTCTCGG
CCACCGATAACTCGGCAGAAGGCAACCGTGAACGTGAGCAGTTCCGCGCTCAGTTTATCC
GCTCCCAAACGGGATTCGGCGTACAACAAGGGCGTGCGCATTAATCTTACCGTTTCCTCC
GGCCCTGTGGGTCGGAGGAAAATCAGAACATCACCCTCGCCACCAGCGGGGCTGCCAGCA
CCATCACCACGCCGGACAGCATCATTACCAGACTGGCGACGACGCCCTCCTGCTGACCAA
GTTCATAGGAACGCGCCGTGCCTGCCCCATGTGACGCCGCGCCGAATCCTGCCCCTTTTG
CCATGCCTTCCCGGATAGAGAGACGCAAAAATAGCGCGTCGCCGACCGCCATGCCAAACA
CGCCAGTGACGACCACGAACAGCGCCACCAGATCCGGCTGCCCGCCCAGGGGTTCTGCCG
CCGCCAGCGCAAACGGCGTAGTAACGGAACGTACCGCCAGACTACGCTGAATCTCATCCG
ATAACGTGAACAGACGCGCCAGCCAAACGGAACTGGTGACCGCCACCACCGTCGCCGTCA
CTACACCCGCGGTGAGCGACATCCAGTGACGTTTGATAATCGCGAGGTTATCGTACACCG
GCACCGCAAAGGCAATGGTCGCCGGGCCGAGCAGCCACAATAGCCAGTGCGATTCGCTAA
TATAGTTTTGCCAGGAGATATGACCGAACACCAGCATTAACACCAGCAGTGCCGGCGTCA
ACACTAATGGCATCAACGG
>2_Salmonella_typhi_Ty2_3288159_3289497
CCAGCAGCGCACGGTACTGATCCAGATCGCTGCTTTCCAGTTGCTGCTGAACTTTCGCGG
CGAATTTTTCCAGACGGCGTTTACCCAGCAGTTCTGCGTTCGGCAGTTCCACTTCTGGAA
TGGTCAGCTTCATGGTGCGTTCGATGTTGCGCAGCAGACGACGCTCGCGGTTCTCAACGA
ACAGCAGCGCGCGACCGGCGCGACCCGCACGACCGGTACGACCGATACGGTGAACGTAGG
ACTCGGAGTCCATCGGAATATCGTAGTTCACCACCAGGCTGATACGTTCAACGTCCAGAC
CACGTGCCGCAACATCGGTGGCGATCAGGATGTCCAGACGACCATCTTTCAGGCGTTCCA
GAGTCTGCTCACGCAGCGCCTGGTTCATATCGCCATTCAACGCGGCGCTGTTGTAGCCGT
TACGTTCCAGCGCTTCTGCTACTTCCAGGGTCGCGTTTTTGGTACGTACGAAGATAATCG
CCGCATCAAAGTCTTCCGCTTCCAGGAAACGCACCAGTGCTTCGTTTTTACGCATACCCC
AGACAGTCCAGTAGCTCTGGCTGATGTCAGGACGGGTAGTCACGCTGGACTGAATGCGCA
CTTCCTGCGGCTCTTTCATAAAGCGGCGGGTAATGCGACGAATCGCTTCCGGCATGGTGG
CGGAGAACAGAGCGGTTTGATGACCTTCCGGGATCTGCGCCATAATAGTTTCAACGTCTT
CGATGAAGCCCATACGCAGCATTTCGTCGGCTTCATCCAGCACCAGACCACTCAGTTTAG
AGAGGTCGAGGGTGCCGCGTTTTAAGTGATCAAGCAGACGTCCCGGCGTACCGACAACGA
TCTGCGGCCCCTGACGCAGGGCGCGTAACTGCACGTCATAACGCTGACCGCCGTACAGGG
CAACCACGTTTACGCCGCGCATGTGTTTAGAGAAATCCGTCATGGCTTCGGCAACCTGTA
CCGCCAGTTCGCGGGTTGGCGCCAGCACCAGAATCTGAGGTGCCTTCAGCTCAGGATCAA
GATTGTTGAGCAGCGGTAAAGAGAACGCTGCGGTTTTGCCGCTACCGGTCTGGGCCATGC
CCAGCACGTCGCGACCGCCCAGCAGATGCGGAATGCACTCTGCCTGGATTGGAGATGGTT
TTTCGTAACCCAGATCGGTAAGGGCTTCAAGGATAGGAGCCTTCAGCCCCAGATCTGCAA
AAGTGGTTTCGAATTCAGCCATGTAGTACGTGTGCCTCAAAATTAATGGCGGCCAGTCTA
CATAACTCATCATGAAATTGATCTGCAATTTTCATTGAAAAGTGTGAACCGGCTCAAAGT
AGGTGTATTAACGAACAAC
>3_Salmonella_typhi_Ty2_2186964_2188302
GGCGGCGTAACGTCTTATCTGGCCTACGTGAGCGGTGCCGTCTGTAGGCCTGATAAGCGC
AGCGCATCAGGCAAGACCCGAACCTGCGGCAGGTTCGAATCTTCCATATCGCAGATAGCA
AAAAAGCGCCTTTAGGGCGCTTTTTTACATTGGTGGGTCGTGCAGGATTCGAACCTGCGA
CCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCCTTGGATAAGGGTT
ACTGCTTCAATCATTCAGGATGGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTT
CGGGCCGTTGCTAAAGCAACATTATCCTTCACGTTCTCTACCAGTTACCACCTTGTATAT
TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCA
ACTGAGCTAACGACCCATACGGGTGCTGCCTGAAAGATTTTACTCGGACCATCTAAAGAT
GGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTACGGGCCGTTGCTGACGCAACG
TTATCCTTCACGTTCAACATCTGAGTTTGATGTTAAATTAGTGGGTCGTGCAGGATTCGA
ACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCACTTTT
ACGTTGCTTTCGAGTTGTTTAATATCCCGTGGCAACGGCGGCATATATTACTGATTTCAG
ATTTGAGCGCAACAAAAATTTCGACGCAGAGGGCTCAACTGCTTAGGAATCGCACGACGC
GACCAGAAAAAAGGCGTTTTCTGGTCGCATGGTACGCATTACATCGCGTTAAGACGCTTC
TGCGCCTGTTTCGCGCCATCAGTGCCAGGATATTTGTTAATCACCTGCTGATAAACCGCT
TTCGCTTTTGCCGTATCACCTTTGTCCTGCATGATAACGCCAACTTTGTACATCGCGTCC
GCAGCCTTCGGCGACTTAGGATAGTTTTTTACTACCGAGGCGAAATAATAGGCGGCGTCA
TCTTTTTTACCCTTGTTGTAATTCAACTGGCCCAGCCAATAATTGGCGTTCGGCTGATAA
GTAGAATCAGGGTATTTCTTGATGAAGTTCTGAAACGCCACAATCGCATCATCCTGGCGA
GACTTATCCTGCACCAGCGCAATTGCCGCATTGTAATCGGTATTCGCATCGCCACTTTGT
ACCGGCGCCCCTGAGGTTGCCGTACCGGCATCCGGAGCGGGGGTCGCAGCGGTTGCCGCC
CCGCTCTGGTCGCCAGCTGCTGGCTGCGCTGCGCCGCCATTATTTAAACTCCCCAGCTGC
AGCATAATTTGCTTCTGGC
>4_Salmonella_typhi_Ty2_2186964_2188302
GGCGGCGTAACGTCTTATCTGGCCTACGTGAGCGGTGCCGTCTGTAGGCCTGATAAGCGC
AGCGCATCAGGCAAGACCCGAACCTGCGGCAGGTTCGAATCTTCCATATCGCAGATAGCA
AAAAAGCGCCTTTAGGGCGCTTTTTTACATTGGTGGGTCGTGCAGGATTCGAACCTGCGA
CCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCCTTGGATAAGGGTT
ACTGCTTCAATCATTCAGGATGGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTT
CGGGCCGTTGCTAAAGCAACATTATCCTTCACGTTCTCTACCAGTTACCACCTTGTATAT
TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCA
ACTGAGCTAACGACCCATACGGGTGCTGCCTGAAAGATTTTACTCGGACCATCTAAAGAT
GGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTACGGGCCGTTGCTGACGCAACG
TTATCCTTCACGTTCAACATCTGAGTTTGATGTTAAATTAGTGGGTCGTGCAGGATTCGA
ACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCACTTTT
ACGTTGCTTTCGAGTTGTTTAATATCCCGTGGCAACGGCGGCATATATTACTGATTTCAG
ATTTGAGCGCAACAAAAATTTCGACGCAGAGGGCTCAACTGCTTAGGAATCGCACGACGC
GACCAGAAAAAAGGCGTTTTCTGGTCGCATGGTACGCATTACATCGCGTTAAGACGCTTC
TGCGCCTGTTTCGCGCCATCAGTGCCAGGATATTTGTTAATCACCTGCTGATAAACCGCT
TTCGCTTTTGCCGTATCACCTTTGTCCTGCATGATAACGCCAACTTTGTACATCGCGTCC
GCAGCCTTCGGCGACTTAGGATAGTTTTTTACTACCGAGGCGAAATAATAGGCGGCGTCA
TCTTTTTTACCCTTGTTGTAATTCAACTGGCCCAGCCAATAATTGGCGTTCGGCTGATAA
GTAGAATCAGGGTATTTCTTGATGAAGTTCTGAAACGCCACAATCGCATCATCCTGGCGA
GACTTATCCTGCACCAGCGCAATTGCCGCATTGTAATCGGTATTCGCATCGCCACTTTGT
ACCGGCGCCCCTGAGGTTGCCGTACCGGCATCCGGAGCGGGGGTCGCAGCGGTTGCCGCC
CCGCTCTGGTCGCCAGCTGCTGGCTGCGCTGCGCCGCCATTATTTAAACTCCCCAGCTGC
AGCATAATTTGCTTCTGGC
>5_Salmonella_typhi_Ty2_2952339_2953677
CACGCGTACAGAGCCTTGCATAGTCCAGAAGTGCGGGTCCGCCAGCGGGATATCGACGGA
TTGCAGCGACAGCGTATGCCCCATCTGACGCCAGTCGGTGGCGATCATATTGGTGGCCGT
CGGTAATCCGGTCGCGCGACGGAATTCCGCCATCACTTCACGACCGGAAAAACCCTGCTC
CGCGCCGCACGGATCTTCTGCATAGGCCAGAGAACCTTTTAGGTATTTACCAATGCTGAT
CGCTTCGTTCAGCGACCAGGCACCGTTTGGATCGAGCGTGACGCGCGCTTGTGGGAAACG
TTTCGCCAGCGCCACGATTGACTCGGCCTCTTCTTCGCCCGCCAGCACGCCGCCTTTCAG
TTTGAAGTCGTTGAAGCCGTATTTTTCATACGCCGCTTCCGCCAGACGCACTACCGTTTC
CGGCGTCATCGCCTCTTCATGGCGCAGACGATACCAGTCGCATTGCTCATCCGGCTGGCT
TTGATACGGCAGCGGCGTAACCTTGCGATTGCCGACAAAGAACAGATAACCCAGCATTTC
GACTTCGCTGCGCTGCTGACCGTCGCCTAACAGCGAAGCGACGTTGACGCCCAGATGTTG
GCCCAAAAGGTCAAGCATTGCCGCTTCAATGCCCGTCACCACATGGATAGTGGTACGGAG
ATCGAACGTTTGTAAACCGCGTCCGCCCGCATCGCGATCGGCAAACTGGTTGCGAACGGC
GGTCAGGACATTTTTATATTCATCCAGCGTTTTTCCCACCACCAGTGGAATCGCATCTTC
CAGCGTTTTGCGAATTTTTTCGCCGCCCGGAATCTCGCCGACCCCAGTATGACCGGAGTT
ATCTTTAACAATGACGATGTTGCGCGTAAAGAACGGGGCGTGCGCGCCGCTCAGGTTCAT
CAGCATACTGTCATGACCCGCAACCGGGATAACCTGCATTTCAGTCACTACAGGCGTGGT
AAATTGAGTACTCATAACTGTGTCCTTATTCAGAATTAGTGACGACCAAAAACAGGGCGT
TTGCGGTCAAAAGTCCAGCCGGGGATCAGGTATTGCATCGGGCCTGCATCATTACGCGCG
CCGCCTGGCAGCTTTTTATACGCGTCATGCGCTTTTCGCACCTGTTCCCAGTCAAGCTCT
ACGCCCAGTCCTGGCGCATCCGGAACGGCAATTTTGCCGTTTTTAATTTCCAGCGGATTT
TTAGTCAGGCGGCAATCGCCCTCCTGCCAGATCCAGTGCGTATCAATAGCGGTGGGTTTG
CCTGGCGCCGCCGCGCCGACATGGGTAAACATCGCCAGTGAAATATCAAAATGGTTATTC
GAATGGCAGCCCCAGGTTA
>6_Salmonella_typhi_Ty2_3075356_3076694
GACGTTCACTTCAATCGCTAAGGTGGCGATATCAGGCACAGCATCGACGCTTGCTGTACC
GGAAGTCACGATGTGCGGGCCTTCCGGCAATTCGCTTGCCTGCGCCGACATTGCACTTAA
ACCCACTAATGCCGCCAGGGCCATCACTTTGAACTTCACAGTCTCTCCTCCATATTGCAG
TCATTGCCCTGATATACAGGGCGCATGCAGGCAAGCTTAGCGGATATCGGTCTGTTGTCC
ATCAGACAACGCTTAGTTGAAAAGCGCGTGCATATGCGCGACGCCTTCCCGCGCCAGTTG
GAAGGCGATAAGCCACATCACCACCCCTACCAGAATGTTGATAATGCGTTGAGCTTTCGC
CGTACGCAGTCGAGGCGCAAGCCAGGCCGCCAGTAGCGCTAACCCAAAAAACCATAAGAA
CGACGCGCTAATCGTGCCGAGAGCAAACCAGCGCTTTGGCTCCATAGCCAGTTGTCCGCC
GAGACTGCCCAACACGACAAACGTATCCAGATAAACGTGCGGATTCAGCCAGGTTACCGC
CAGCATCGTAGCAATAATTTTCCAGCGCCCCTGCTTCATAACCTCGGCGCTGGCCAGCTC
CAGATTACTGCTCATTGCCGTTTTCAGCGCGCCAAAACCGTACCATAACAAGAACGCAAC
CCCGCCCCATGTGACCAGCGCCAGCAGCCACGGCGACTGCATCAGCAACGCGCTACCGCC
AAAAATACCGGCGCTAATCAGGACTAAATCACTTAACGCGCAAAGCAGCGCTATCATGAG
GTGGTACTGGCGACGAATTCCCTGATTCATCACAAACGCATTTTGCGGGCCAAGCGGAAG
GATCATGGCGGCGCCAAGGGCAACCCCTTGAAAATAATAAGATATCACGTTAACTACCCT
GAGCTGTTTTTCTTAAAGGCAGACTATAGCGCGGGAATATTATTAGCGGAAATTGATAAT
TTTAATCACTAATAAGAAAAGCTAATAAAGAGACTGAATAACGGATGGCGGCTACGCTTA
TCCGCTCAATAACCAGAGAATACTGGAGGCGGATAAGCGCAGCGCCGGCAGGCAGCACGG
GAGGAAAATTACTCCGCGGCGTTATCTTTCACGCGTTTAAAATTGACGTCCATCTGCGGG
TACGGGAAGCTAATACCAGCGGCGTCGAATTCACGTTTAATACGTTCCAGCACGTCCCAA
TAGACATTTTGCAGGTCGCTGCTTTTACTCCAGACACGCACCACAAAATTAATTGATGAG
GCGCCCAGCTCATTCAAACGCACCGTCATTTCGCGATCTTTTAAAATACGATCGTCGGAC
TCGATAATCGTCGTTAGCA