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Paste a sequence to see the map.
About Pairwise Alignment · how to use, FAQ ▾
Align two DNA or protein sequences online with global (Needleman-Wunsch) or local (Smith-Waterman) alignment. Adjust the match, mismatch and gap scores and see percent identity and gaps — handy for comparing variants, checking a clone against a reference, or teaching alignment concepts.
How to use Pairwise Alignment
- 1Paste your two sequences into the input boxes.
- 2Choose global or local alignment and set the match, mismatch and gap scores.
- 3Read the aligned output along with percent identity and gap counts.
Frequently asked questions
What is the difference between global and local alignment?
Global (Needleman-Wunsch) aligns the sequences end to end. Local (Smith-Waterman) finds the best-matching subregion, which is better when only part of the sequences is similar.
Does it work for proteins?
Yes. It uses simple match/mismatch scoring, which works for DNA and protein. Substitution matrices such as BLOSUM are not yet supported.
Is there a length limit?
Very long sequences are capped to keep the alignment responsive. Use shorter sequences if you hit the limit.