Sequences need to be in one of the following formats: MultAlin/Fasta, Genbank, Embl-Swissprotein.
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Paste in sequences

Optional Parameters

Graphical results: yes no

Sequence input format: auto mul
Sequence output format: msf mul doc

Scoring method: absolute percentage identity

Symbol comparison table - gap opening default value - gap extension default value :
Blosum62 - 12 - 2 AltDNA - 30 - 0 Dayhoff - 8 - 0 DNA - 5 - 0 Genetiq - 1 - 0 Identity - 1 - 0 Risler - 50 - 0

Gap penalties : (default: value from comparison table)

Gap penalty at opening:

Gap penalty at extension:

Gap penalty at extremities: none end beginning both

One iteration only: no yes

Text options

Text size Tiny Small MediumBold Large Giant Text color black red blue green grey white yellow pink orange violet brown cyan
Background color black red blue green grey white yellow pink orange violet brown cyan

Sequence options

High consensus color black red blue green grey white yellow pink orange violet brown cyan Low consensus color black red blue green grey white yellow pink orange violet brown cyan
Neutral color black red blue green grey white yellow pink orange violet brown cyan

High consensus value: % (default: 90%)
Low consensus value*: % (default: 50%)
*Must be less than first value.

Presentation options

Output style Normal Case Difference
Maximum line length
Graduation step

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For more information, contact sacs at cgl.ucsf.edu