Multiple Sequence Alignment
Sequence Alignment Tool
Protein–Protein · DNA–DNA · RNA–RNA · Smith-Waterman algorithm · BLOSUM62 scoring
Alignment Mode
Align all sequence pairs independently.
Scoring
ProteinBLOSUM62 matrix
DNA/RNAMatch +2 / Mismatch −1
Gap open−8
Gap extend−1
AlgorithmSmith-Waterman
Input Sequences (2)
SEQUENCE 1
SEQUENCE 2
Accepts FASTA format (with >header lines) or raw sequences. Sequence type (Protein/DNA/RNA) is auto-detected.