Fasta label (*)	Workbench label
Homosapiens	Homosapiens
Pttroglodytes	Pttroglodytes
Ptschweinfurthii	Ptschweinfurthii
Ptversus	Ptversus

(*) Clustalw cuts off Fasta labels after the first space (e.g. ">abc def" becomes ">abc").

Sequence alignment

Consensus key (see documentation for details)
* - single, fully conserved residue
  - no consensus


CLUSTAL W (1.81) multiple sequence alignment


Ptschweinfurthii      ------------------------------------------------------------
Pttroglodytes         ------------------------------------------------------------
Ptversus              ------------------------------------------------------------
Homosapiens           AGGGGCCACAGTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGT


Ptschweinfurthii      -----TAGCCCATAAAGGCTGTTGCTATGGTTGTGA-GCAAGAGGATGATGCCA-ATGTT
Pttroglodytes         -----TAGCCCATAAAGGCTGTTGCTATGGTTGTGA-GCAAGAGGATGATGCCA-ATGTT
Ptversus              -----TAGCCCATAAAGGCTGTTGCTATGGTTGTGA-GCAAGAGGATAATGCCA-ATGTT
Homosapiens           TCAATGAATCTGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTT
                            *  *     *****  *     *   **    *      *  ** *   *  **

Ptschweinfurthii      TCAGGTT-TCTAGG--TAGAGAAATG-AGCCGTAATA-TAGGCCTCGACCGATG--TGTA
Pttroglodytes         TCAGGTT-TCTAGG--TAGAGAAATG-AGCCGTAATA-TAGGCCTCGACCGATG--TGTA
Ptversus              TCAGGTT-TCTAGG--TAGAGAAATG-AGCCGTAATA-TAGACCTCGGCCGATG--TGTA
Homosapiens           TCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCA
                      ***  *  *** *   *  *  * ** **** **  *  *  ** *  ** **   ** *

Ptschweinfurthii      GGAAGAGGCAGATAAAAAATATTGAGGCGCCAT-TAGCGTGAAGGTAGCGG-ATGATCCA
Pttroglodytes         GGAAGAGGCAGATAAAAAATATTGAGGCGCCAT-TGGCGTGAAGGTAGCGG-ATGATCCA
Ptversus              GGAAGAGGCAGATAAAAAATATTGAGGCGCCGT-TAGCGTGGAGGTAGCGG-ATGNTCCA
Homosapiens           CGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCATCTTCCA
                       ***  ** *   ** **      ***   *   *  * *   * **     **  ****

Ptschweinfurthii      ACCATAGTTTACG-T---------------------------------------------
Pttroglodytes         GCCATAGTTTACG-TCTC------------------------------------------
Ptversus              ACCATAGTTTACG-TCTCGGGTGATGTGGGCGATCGACGAGAAGGCGGTTGAGGC-----
Homosapiens           CCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGAC
                       ** ** *  **  *                                             

Ptschweinfurthii      ------------------------------------------------------------
Pttroglodytes         ------------------------------------------------------------
Ptversus              ------------------------------------------------------------
Homosapiens           ATTAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCC


Ptschweinfurthii      ------------------------------------------------------------
Pttroglodytes         ------------------------------------------------------------
Ptversus              ------------------------------------------------------------
Homosapiens           CTTAAACACCCCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCT

Clustal W dendrogram

Phylip-format dendrogram

(
(
Ptversus:0.02653,
Homosapiens:0.88172)
:0.00680,
Ptschweinfurthii:0.00255,
Pttroglodytes:0.00868);

Clustal W options and diagnostic messages

Alignment type: Nucleic                 Alignment order: aligned                

                    Pairwise alignment parameters

Method: accurate                        
Matrix: IUB                             
Gap open penalty: 15.00                 Gap extension penalty: 6.66             

                    Multiple alignment parameters

Matrix: IUB                             Negative matrix?: no                    
Gap open penalty: 15.00                 Gap extension penalty: 6.66             
% identity for delay: 30                DNA transitions weighting: 0.5          




 CLUSTAL W (1.81) Multiple Sequence Alignments



Sequence type explicitly set to DNA
Sequence format is Pearson
Sequence 1: Ptversus              218 bp
Sequence 2: Ptschweinfurthii      178 bp
Sequence 3: Pttroglodytes         181 bp
Sequence 4: Homosapiens           420 bp
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  96
Sequences (1:3) Aligned. Score:  95
Sequences (1:4) Aligned. Score:  9
Sequences (2:3) Aligned. Score:  98
Sequences (2:4) Aligned. Score:  10
Sequences (3:4) Aligned. Score:  10
Time for pairwise alignment: 0.026714

Guide tree        file created:   [../tmp-dir/29565.CLUSTALW.dnd]
Start of Multiple Alignment
There are 3 groups
Aligning...
Group 1: Sequences:   2      Score:3361
Group 2: Sequences:   3      Score:3351
Group 3:                     Delayed
Sequence:4     Score:1655
Time for multiple alignment: 0.132071

Alignment Score 4450
CLUSTAL-Alignment file created  [../tmp-dir/29565.CLUSTALW.aln]

Citation

Algorithm Citation:

Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment. Computer Applications in the Biosciences (CABIOS), 8(2):189-191.

Thompson J.D., Higgins D.G., Gibson T.J. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 22:4673-4680(1994).

Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.

Program Citation:

CLUSTAL W: Julie D. Thompson, Desmond G. Higgins and Toby J. Gibson, modified; any errors are due to the modifications.

PHYLIP: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.