Pairwise sequence alignment tool
Paste two sequences and the pairwise alignment tool lines them up, showing the score, the percent identity, the number of matches, mismatches and gaps, and the aligned sequences with a match line. Choose local alignment (Smith-Waterman) to find the best matching region, or global (Needleman-Wunsch) to align the sequences end to end.
What you get
- Local alignment (Smith-Waterman) or global alignment (Needleman-Wunsch)
- Score, percent identity, alignment length, matches, mismatches and gaps
- The aligned sequences with a match line and the range each covers
- DNA scoring of +2 for a match and −3 for a mismatch, gap open 5 and extend 2; proteins are scored with BLOSUM62
How to use it
- Open the Align tab and paste sequence 1 and sequence 2.
- Choose local or global.
- Run the alignment and read the identity and the gap count.
Worked example
Align GATTACAGATTACA with GCATGCTTACAGAT:
- Local: score 16, 100% identity over an 8-base region,
TTACAGATin both sequences. - Global: score −11, 50% identity, 8 gap positions, because the ends do not line up.
Local finds the shared core; global is forced to account for every base, so the same pair scores very differently.
Limits to know about
- Each sequence can be up to 10,000 residues.
- Both sequences must be the same kind: nucleotide with nucleotide, or protein with protein. RNA and DNA are compared on the same alphabet.
Common questions
What is the difference between local and global alignment?
Global alignment forces the whole of both sequences to line up; local alignment looks for the best matching piece. The alignment guide explains when to use each.
Can I align proteins?
Yes. Both sequences must be protein, and they are scored with the BLOSUM62 matrix.
How is this different from BLAST?
Pairwise alignment compares two sequences you supply. BLAST searches a whole database for sequences similar to yours; see the BLAST guide.
Are my sequences stored?
No. Sequences are processed in memory to produce your result and are not stored or logged. The privacy policy has the details, including what BLAST sends to NCBI and EMBL-EBI.