AlignBench

Compare two DNA sequences. Global alignment (Needleman–Wunsch) matches them end to end; local alignment (Smith–Waterman) finds the best-matching region.

Sequence A

Sequence B Use the reverse complement of B

Alignment type

Match

Mismatch

Gap open

Gap extend

Default scores match EMBOSS needle and water for DNA (EDNAFULL: +5/−4, gap open 10, extend 0.5). Each sequence can be up to 10,000 bases.

About AlignBench

AlignBench is a free online tool for pairwise sequence alignment. Align two DNA sequences, globally or locally, with affine gaps. It runs entirely in your browser, so there is nothing to install and your data stays on your device.

Features

Global alignment (Needleman-Wunsch)
Local alignment (Smith-Waterman)
Affine gap penalties (Gotoh)
EMBOSS-compatible default scores
Identity, similarity, and gap statistics
Save results as text, spreadsheet, or sequence files
Installs on your phone and works offline

Common questions

Global or local: which should I use?

Use global when the two sequences should match end to end, such as comparing a gene to a variant. Use local to find the best-matching region, such as locating a read or fragment within a longer sequence.

Are the scores comparable to EMBOSS?

Yes. Defaults match EMBOSS needle and water for DNA: EDNAFULL +5/-4, gap open 10, gap extend 0.5.

How long can the sequences be?

Up to 10,000 bases each. Alignment runs in your browser, typically in well under a second.