Enter two biological sequences into the Sequence Identity Calculator — choose your Sequence Type and, for proteins, a Substitution Matrix — and get back the Sequence Identity percentage alongside Sequence Similarity, Exact Matches, Total Positions, and Gap Positions to see exactly how closely your sequences align.
Sequence Identity
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Sequence Similarity
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Exact Matches
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Total Positions
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Gap Positions
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Identity measures the percentage of exact matches between aligned sequences, while similarity considers biochemically similar amino acids. For proteins, substitution matrices define which amino acids are considered similar based on evolutionary conservation.
Sequences must be pre-aligned and of equal length. Use dashes (-) or spaces to represent gaps. The tool does not perform alignment - it only calculates identity/similarity from existing alignments.
BLOSUM62 is recommended for comparing moderately divergent sequences (20-80% identity), while PAM250 is better for more distantly related sequences. BLOSUM62 is the most commonly used matrix.
Yes, select DNA/RNA sequence type for nucleotide sequences. The tool will calculate exact matches only, as nucleotides don't have similarity scoring like amino acids do.
Generally, >90% identity suggests very similar sequences, 50-90% indicates moderate similarity, and <50% suggests distant relationships. Context matters - functional domains may be conserved even in low-identity sequences.
Gaps are counted as non-matching positions and reduce both identity and similarity percentages. The tool reports the total number of gap positions found in the alignment.
The sequences must be the same length for proper comparison. If they differ in length, you need to align them first using alignment software, then use this calculator on the aligned result.