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 2000 characters.

Paste sequence two (in raw sequence or FASTA format) into the text area below. Input limit is 2000 characters.

Please check the browser compatibility page before using this program.

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