Pairwise Align

How to align two DNA or protein sequences

1. Choose DNA or protein and paste the two sequences.
2. Set the gap opening and extension penalties, and for DNA the match and mismatch scores. Tick Free end gaps if one sequence is inside the other.
3. Click Align to see the alignment with the identity, gaps and score, and for proteins the similarity.

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.

Which scoring matrix does it use?

BLOSUM62, with a global alignment (Needleman-Wunsch) and affine gap penalties.

What do the symbols between the lines mean?

A vertical bar marks identical residues and a colon marks similar 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.