DNA Multiple Sequence Alignment (MSA)

Upload FASTA:

Upload or paste sequence(s) in FASTA format:

Input (FASTA)

Output (CLUSTAL)

CLUSTAL (Colored)

Output (Aligned FASTA)

Log

Alignment Parameters

k-mer size

Match

Mismatch

Gap

Banded DP width

Exact DP max columns

CLUSTAL block width

Paste DNA sequence(s) in FASTA format and click Generate. The tool will produce aligned output in CLUSTAL and FASTA formats.

Export: Select all (Ctrl+A), copy (Ctrl+C), paste into your editor (Ctrl+V)

Paste/upload FASTA sequences; for large inputs prefer files to reduce browser overhead.
Adjust k-mer size and scoring parameters for different alignment sensitivity.