Sequence Identity Calculator

Sequence identity measures how similar two biological sequences are — a critical metric in genetics, evolutionary biology, and drug discovery. Paste your First Sequence and Second Sequence into the Sequence Identity Calculator, then select your Sequence Type (DNA/RNA or Protein) and substitution matrix to get Sequence Identity % as the primary result. Secondary outputs include Sequence Similarity, Exact Matches, Total Positions, and Gap Positions.

Sequence Type *

Paste the first sequence (gaps allowed with - or spaces)

Paste the second sequence (must be same length as first)

Results

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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Frequently Asked Questions

What is the difference between identity and similarity?

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.

How do I prepare sequences for analysis?

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.

What substitution matrix should I use?

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.

Can I analyze DNA and RNA sequences?

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.

What does a good sequence identity percentage mean?

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.

How are gaps handled in the calculation?

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.

What if my sequences are different lengths?

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.