Sequence Similarity Calculator

Work out sequence similarity instantly with clear inputs, formula shown and shareable results.

About Sequence Similarity Calculator

Divides identical positions by alignment length for identity, and adds conservative substitutions for similarity.

Formula

Identity and similarity

Identity (%) = identical positions / alignment length x 100; similarity adds conservatively substituted positions to the numerator

Worked example

With the default values below, Sequence Similarity Calculator returns Sequence identity of 87.000%. Change any input above and every figure here is recalculated in your browser.

Inputs used

Identical positionsaccepts 0–100,000: 87
Alignment lengthaccepts 1–100,000: 100
Conservatively substituted positionsaccepts 0–100,000: 6

Results

Sequence identity: 87.000%
Sequence similarity: 93.000%
Divergence: 13.000%
Unmatched positions: 7

Step by step

1Values used
2Identity and similarity
3Sequence identity= 87.000
4Sequence similarity= 93.000
5Divergence= 13.000
6Unmatched positions= 7

Assumptions and limits

The result is derived only from the 3 inputs listed above. Anything not among them is not part of the calculation.
In particular, this calculator does not take inflation, fees or charges or compounding frequency into account.
Figures are rounded for display to 3 decimal places, so totals built from several rounded parts can differ slightly from the unrounded arithmetic.

How these calculators are built and tested is described on the Methodology page. If a figure looks wrong, please report it.

Frequently Asked Questions

What identity implies homology?

Above about 30% identity over a long alignment usually indicates homology; below that lies the twilight zone.

Why report similarity separately?

Conservative substitutions preserve chemistry and function, so similarity better reflects structural conservation in proteins.