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|
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('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
description: gi|6273284|gb|AF191658.1|AF191
seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
description: gi|6273287|gb|AF191661.1|AF191
seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
description: gi|6273286|gb|AF191660.1|AF191
seq: Seq('TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
description: gi|6273290|gb|AF191664.1|AF191
seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
description: gi|6273289|gb|AF191663.1|AF191
seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
description: gi|6273291|gb|AF191665.1|AF191
seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', Gapped(IUPACUnambiguousDNA(), '-'))
length: 156
Calculating summary information...
consensus: Seq('TATACATTAAAGXAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATA...AGA', DNAAlphabet())
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: 88.42
entire alignment: 287.55
relative information content
relative information: 287.55
Column 1: AAAAAAA
IC for column 1: 2.00
Column 7: TTTATTT
IC for column 7: 1.41
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: EAS54_6_R1_2_1_413_324
seq: Seq('CCCTTCTTGTCTTCAGCGTTTCTCC', Gapped(IUPACAmbiguousDNA(), '-'))
description: EAS54_6_R1_2_1_540_792
seq: Seq('TTGGCAGGCCAAGGCCGATGGATCA', Gapped(IUPACAmbiguousDNA(), '-'))
description: EAS54_6_R1_2_1_443_348
seq: Seq('GTTGCTTCTGGCGTGGGTGGGGGGG', Gapped(IUPACAmbiguousDNA(), '-'))
length: 25
consensus: Seq('NTNGCNTNNNNNGNNGGNTGGNTCN', IUPACAmbiguousDNA())
Gapped(IUPACAmbiguousDNA(), '-') alignment with 3 rows and 25 columns
CCCTTCTTGTCTTCAGCGTTTCTCC EAS54_6_R1_2_1_413_324
TTGGCAGGCCAAGGCCGATGGATCA EAS54_6_R1_2_1_540_792
GTTGCTTCTGGCGTGGGTGGGGGGG EAS54_6_R1_2_1_443_348
Test format conversion...
As FASTA:
>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
As Clustal:
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
******
|
