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', 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-HYLES...AIA', Gapped(IUPACProtein(), '-'))
description: AKH_HAEIN/1-382
seq: Seq('-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHI...QAN', Gapped(IUPACProtein(), '-'))
length: 382
consensus: Seq('CPDSINAALICRGEKMSXXXXXXXXXXXXXEXLSXXXXXXXXXXXXXGSHYXXX...QAN', 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

