Sequence Manipulation Suite:
Pairwise Align DNA
Pairwise Align DNA accepts two DNA sequences and determines the optimal global alignment. Use Pairwise Align DNA 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.
  • Match value
  • Mismatch value
  • Penalty for gaps preceding a sequence
  • Penalty for internal gaps
  • Penalty for gaps following a sequence
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