test_align testing reading and writing clustal format... CLUSTAL X (1.81) multiple sequence alignment gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA ******* **** ************************************* gi|6273285|gb|AF191659.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273284|gb|AF191658.1|AF191 TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273287|gb|AF191661.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA gi|6273286|gb|AF191660.1|AF191 TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA gi|6273290|gb|AF191664.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273289|gb|AF191663.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273291|gb|AF191665.1|AF191 TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA ****** ******** **** ********* ********* gi|6273285|gb|AF191659.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT gi|6273284|gb|AF191658.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273287|gb|AF191661.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273286|gb|AF191660.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273290|gb|AF191664.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273289|gb|AF191663.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT gi|6273291|gb|AF191665.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT ************************************ *********** * gi|6273285|gb|AF191659.1|AF191 ACCAGA gi|6273284|gb|AF191658.1|AF191 ACCAGA gi|6273287|gb|AF191661.1|AF191 ACCAGA gi|6273286|gb|AF191660.1|AF191 ACCAGA gi|6273290|gb|AF191664.1|AF191 ACCAGA gi|6273289|gb|AF191663.1|AF191 ACCAGA gi|6273291|gb|AF191665.1|AF191 ACCAGA ****** CLUSTAL X (1.81) multiple sequence alignment gi|4959044|gb|AAD34209.1|AF069 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNN gi|671626|emb|CAA85685.1| ---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFR * *: :: :. :* : :. : . :* :: . gi|4959044|gb|AAD34209.1|AF069 LLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW gi|671626|emb|CAA85685.1| VTPQPG-----------------VPPEEAGAAVAAESSTGT--------- : ** **:... *.*** .. gi|4959044|gb|AAD34209.1|AF069 LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQT gi|671626|emb|CAA85685.1| WTTVWTDGLTSLDRYKG-----RCYHIEPVPG------------------ .:* * *: .* :* : :* .* gi|4959044|gb|AAD34209.1|AF069 SENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE gi|671626|emb|CAA85685.1| -EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIP *::. . .:: :*..* :* .* .. . : . : gi|4959044|gb|AAD34209.1|AF069 VPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSEN gi|671626|emb|CAA85685.1| VAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE *. .:: : . .* . : *.: ..:: * . :: : gi|4959044|gb|AAD34209.1|AF069 EPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS gi|671626|emb|CAA85685.1| CLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN .*. :. :. . . .* **.*.. :.. *.. . . gi|4959044|gb|AAD34209.1|AF069 ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYE gi|671626|emb|CAA85685.1| ATAG-----------------------TCEEMIKRAIFARELGVPIVMHD ::* :.: .*: : * :: gi|4959044|gb|AAD34209.1|AF069 SERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLR gi|671626|emb|CAA85685.1| YLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKAL *** . * :. . . : *: .:: ::: .. . : : gi|4959044|gb|AAD34209.1|AF069 QIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGS gi|671626|emb|CAA85685.1| RLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDW :: * * : .. :.* . ::. :: * : : * * :.. gi|4959044|gb|AAD34209.1|AF069 SSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESG gi|671626|emb|CAA85685.1| VSLPGVIPVASG-----------------------------GIHVWHMPA * .. * :** . .:. .. gi|4959044|gb|AAD34209.1|AF069 SLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCI gi|671626|emb|CAA85685.1| LTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACV :*. ..: :. . .:* * : : * . ..*: gi|4959044|gb|AAD34209.1|AF069 TEYTEGDKLRKLPCSHEFHVHCIDRWLSE-NSTCPICRRAVLSSGNRESV gi|671626|emb|CAA85685.1| KARNEG---RDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD-- . .** *.*... : :: :* .* ::* : :. :. : gi|4959044|gb|AAD34209.1|AF069 V gi|671626|emb|CAA85685.1| - all_seqs... description: gi|6273285|gb|AF191659.1|AF191 seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', Gapped(IUPACUnambiguousDNA(), '-')) description: gi|6273284|gb|AF191658.1|AF191 seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA-- ...', Gapped(IUPACUnambiguousDNA(), '-')) description: gi|6273287|gb|AF191661.1|AF191 seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', Gapped(IUPACUnambiguousDNA(), '-')) description: gi|6273286|gb|AF191660.1|AF191 seq: Seq('TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', Gapped(IUPACUnambiguousDNA(), '-')) description: gi|6273290|gb|AF191664.1|AF191 seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', Gapped(IUPACUnambiguousDNA(), '-')) description: gi|6273289|gb|AF191663.1|AF191 seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', Gapped(IUPACUnambiguousDNA(), '-')) description: gi|6273291|gb|AF191665.1|AF191 seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', Gapped(IUPACUnambiguousDNA(), '-')) length: 156 Calculating summary information... consensus: Seq('TATACATTAAAGXAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', IUPACAmbiguousDNA()) Replacement dictionary ('A', 'A') : 1395.0 ('A', 'C') : 3.0 ('A', 'G') : 13.0 ('A', 'T') : 6.0 ('C', 'A') : 3.0 ('C', 'C') : 271.0 ('C', 'G') : 0 ('C', 'T') : 16.0 ('G', 'A') : 5.0 ('G', 'C') : 0 ('G', 'G') : 480.0 ('G', 'T') : 0 ('T', 'A') : 6.0 ('T', 'C') : 12.0 ('T', 'G') : 0 ('T', 'T') : 874.0 position specific score matrix. with a supplied consensus sequence... A C G T T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 1.0 0.0 0.0 6.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 X 4.0 0.0 3.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 4.0 A 4.0 0.0 0.0 0.0 T 0.0 0.0 0.0 3.0 A 3.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 C 1.0 6.0 0.0 0.0 A 6.0 0.0 0.0 1.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 X 0.0 3.0 0.0 4.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 2.0 0.0 5.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 1.0 0.0 6.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 T 0.0 0.0 0.0 7.0 G 1.0 0.0 6.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 defaulting to a consensus sequence... A C G T T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 1.0 0.0 0.0 6.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 X 4.0 0.0 3.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 4.0 A 4.0 0.0 0.0 0.0 T 0.0 0.0 0.0 3.0 A 3.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 T 0.0 0.0 0.0 1.0 A 1.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 C 1.0 6.0 0.0 0.0 A 6.0 0.0 0.0 1.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 X 0.0 3.0 0.0 4.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 2.0 0.0 5.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 1.0 0.0 6.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 T 0.0 0.0 0.0 7.0 G 1.0 0.0 6.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 with a selected sequence... A C G T T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 1.0 0.0 0.0 6.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 4.0 0.0 3.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 G 0.0 0.0 7.0 0.0 C 0.0 7.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 4.0 A 4.0 0.0 0.0 0.0 - 0.0 0.0 0.0 3.0 - 3.0 0.0 0.0 0.0 - 0.0 0.0 0.0 1.0 - 1.0 0.0 0.0 0.0 - 0.0 0.0 0.0 1.0 - 1.0 0.0 0.0 0.0 - 0.0 0.0 0.0 1.0 - 1.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 C 1.0 6.0 0.0 0.0 A 6.0 0.0 0.0 1.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 3.0 0.0 4.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 2.0 0.0 5.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 C 0.0 7.0 0.0 0.0 T 0.0 1.0 0.0 6.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 T 0.0 0.0 0.0 7.0 G 1.0 0.0 6.0 0.0 T 0.0 0.0 0.0 7.0 A 7.0 0.0 0.0 0.0 C 0.0 7.0 0.0 0.0 C 0.0 7.0 0.0 0.0 A 7.0 0.0 0.0 0.0 G 0.0 0.0 7.0 0.0 A 7.0 0.0 0.0 0.0 information content part of alignment: 88.4230990854 entire alignment: 287.54558449 relative information content relative information: 287.54558449 Column 1: AAAAAAA IC for column 1: 2.0 Column 7: TTTATTT IC for column 7: 1.40832722142 test print_info_content 0 T 2.000 1 A 2.000 2 T 2.000 3 A 2.000 4 C 2.000 5 A 2.000 6 T 2.000 7 T 1.408 8 A 2.000 9 A 2.000 10 A 2.000 11 G 2.000 12 A 1.015 13 A 2.000 14 G 2.000 15 G 2.000 16 G 2.000 17 G 2.000 18 G 2.000 19 A 2.000 20 T 2.000 21 G 2.000 22 C 2.000 23 G 2.000 24 G 2.000 25 A 2.000 26 T 2.000 27 A 2.000 28 A 2.000 29 A 2.000 30 T 2.000 31 G 2.000 32 G 2.000 33 A 2.000 34 A 2.000 35 A 2.000 36 G 2.000 37 G 2.000 38 C 2.000 39 G 2.000 40 A 2.000 41 A 2.000 42 A 2.000 43 G 2.000 44 A 2.000 45 A 2.000 46 A 2.000 47 G 2.000 48 A 2.000 49 A 2.000 50 T 2.000 51 A 2.000 52 T 2.000 53 A 2.000 54 T 2.000 55 A 2.000 56 - 0.682 57 - 0.682 58 - 0.333 59 - 0.333 60 - -0.115 61 - -0.115 62 - -0.115 63 - -0.115 64 - -0.115 65 - -0.115 66 A 2.000 67 T 2.000 68 A 2.000 69 T 2.000 70 A 2.000 71 T 2.000 72 T 2.000 73 T 2.000 74 C 1.408 75 A 1.408 76 A 2.000 77 A 2.000 78 T 2.000 79 T 2.000 80 T 1.015 81 C 2.000 82 C 2.000 83 T 2.000 84 T 2.000 85 A 2.000 86 T 2.000 87 A 2.000 88 T 2.000 89 A 2.000 90 C 1.137 91 C 2.000 92 C 2.000 93 A 2.000 94 A 2.000 95 A 2.000 96 T 2.000 97 A 2.000 98 T 2.000 99 A 2.000 100 A 2.000 101 A 2.000 102 A 2.000 103 A 2.000 104 T 2.000 105 A 2.000 106 T 2.000 107 C 2.000 108 T 2.000 109 A 2.000 110 A 2.000 111 T 2.000 112 A 2.000 113 A 2.000 114 A 2.000 115 T 2.000 116 T 2.000 117 A 2.000 118 G 2.000 119 A 2.000 120 T 2.000 121 G 2.000 122 A 2.000 123 A 2.000 124 T 2.000 125 A 2.000 126 T 2.000 127 C 2.000 128 A 2.000 129 A 2.000 130 A 2.000 131 G 2.000 132 A 2.000 133 A 2.000 134 T 2.000 135 C 2.000 136 C 1.408 137 A 2.000 138 T 2.000 139 T 2.000 140 G 2.000 141 A 2.000 142 T 2.000 143 T 2.000 144 T 2.000 145 A 2.000 146 G 2.000 147 T 2.000 148 G 1.408 149 T 2.000 150 A 2.000 151 C 2.000 152 C 2.000 153 A 2.000 154 G 2.000 155 A 2.000 testing reading and writing fasta format... all_seqs... description: AK1H_ECOLI/1-378 seq: Seq('CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE ...', Gapped(IUPACProtein(), '-')) description: AKH_HAEIN/1-382 seq: Seq('-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ ...', Gapped(IUPACProtein(), '-')) length: 382 consensus: Seq('CPDSINAALICRGEKMSXXXXXXXXXXXXXEXLSXXXXXXXXXXXXXGSHYXXXXXXXXX ...', IUPACProtein()) >AK1H_ECOLI/1-378 CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------ NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF--- ---FAALARANINIVAIA >AKH_HAEIN/1-382 -----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ LLAKG-GYLESSVEIEESTKRVDAANIA--K-DKVVLMAGF---TAGNEKGELVLLGRNG SDYSAAC-----------------LAACLGASVCEIWTDVDGVYTCDP--RLVPDARLLP TLSYREAMELSYFGAKVIHPRTIGPLLPQNIPCVIKNTGNPSAPGSI-ID--GNVKSESL Q----VKGITNLDNLAMFNVSGPGMQGM---VGMASRVFSAMSGAGISVILITQSSSEYS ---ISFCVPVKSAEVAKTVLETEFA-----NELNEHQLEPIEVIKDLSIISV-VGDGMKQ AKGIAARF------FSALAQAN Test format conversion... >gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCCATTGATTTAGTGTACCAGA >gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA-- ------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA >gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTATACCAGA >gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA TATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA CLUSTAL X (1.81) multiple sequence alignment gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273285|gb|AF191659.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273284|gb|AF191658.1|AF191 TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273287|gb|AF191661.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA gi|6273286|gb|AF191660.1|AF191 TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA gi|6273290|gb|AF191664.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273289|gb|AF191663.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273291|gb|AF191665.1|AF191 TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273285|gb|AF191659.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT gi|6273284|gb|AF191658.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273287|gb|AF191661.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273286|gb|AF191660.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273290|gb|AF191664.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273289|gb|AF191663.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT gi|6273291|gb|AF191665.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273285|gb|AF191659.1|AF191 ACCAGA gi|6273284|gb|AF191658.1|AF191 ACCAGA gi|6273287|gb|AF191661.1|AF191 ACCAGA gi|6273286|gb|AF191660.1|AF191 ACCAGA gi|6273290|gb|AF191664.1|AF191 ACCAGA gi|6273289|gb|AF191663.1|AF191 ACCAGA gi|6273291|gb|AF191665.1|AF191 ACCAGA