Pairwise sequence aligner

This tool provides a simple and convenient way to check that your Sanger sequencing reads match the reference sequence. Paste a reference sequence in one box and a sequencing read (or another construct) in the other box and click Align. It can also align protein amino acid sequences.

Alignment uses the Needleman–Wunsch global algorithm — gaps are allowed and the full length of both sequences is aligned. Choose DNA or Protein before aligning; the scoring matrix matches the molecule type. FASTA header lines are optional and are skipped.

The aligned sequences appear with match indicators so you can spot substitutions and indels quickly. This is a teaching and troubleshooting aid, not a replacement for chromatogram base-calling software or large-scale BLAST searches. All processing runs in your browser.