Sequence Manipulation Suite:
Pairwise Align Protein
Pairwise Align Protein accepts two protein sequences and determines the optimal global alignment. Use Pairwise Align Protein to look for conserved sequence regions.

Paste sequence one (in raw sequence or FASTA format) into the text area below. Input limit is 20,000 characters.

Paste sequence two (in raw sequence or FASTA format) into the text area below. Input limit is 20,000 characters.


Use the following parameters to specify how alignments are scored.
  • Scoring matrix
  • Value for gaps preceding a sequence
  • Value for internal gaps
  • Value for gaps following a sequence
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