Pairwise Align DNA
How to align two DNA sequences
- Paste the two DNA sequences.
- Set the match and mismatch scores and the gap opening and extension penalties, and tick Free end gaps if one sequence is inside the other.
- Click Align to see the alignment with the identity, gaps and score.
Frequently asked questions
Which method does it use?
A global alignment (Needleman-Wunsch) with affine gap penalties, so one long gap costs less than many short ones.
How long can the sequences be?
About 5,000 by 5,000 letters, since the whole alignment runs in your browser.
Is my sequence uploaded?
No. Everything runs in your browser, so your sequences never leave your device.
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