DNA Motif & Pattern Finder (IUPAC)
Search a sequence for a motif with IUPAC codes, mismatches and both strands.
🔒 Runs entirely in your browser — nothing is uploaded
Search a DNA sequence for any motif or pattern and get every position back. The motif can use IUPAC ambiguity codes (e.g. GGNCC or WGATAR), matches may overlap, and you can allow a few mismatches and scan the reverse strand too. Useful for locating binding sites, primer landing sites, recognition sequences and short sequence signatures.
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Matches
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Reverse (−)
Enter a sequence and a motif to search.
Matches may overlap. IUPAC codes in the motif expand to their base sets (e.g. N = A/C/G/T, R = A/G). Coordinates are 1-based on the forward sequence; reverse-strand hits report the forward substring they cover.
How to use the Motif Finder tool
- 1Paste your DNA sequence (FASTA accepted).
- 2Enter the motif, using IUPAC codes for degenerate positions if needed.
- 3Set allowed mismatches and reverse-strand search, then read the positions found.
Frequently asked questions
- Can I use ambiguity codes in the motif?
- Yes. IUPAC codes expand to their base sets — for example N matches any base, R matches A or G, and Y matches C or T — so degenerate motifs like WGATAR work directly.
- Does it find overlapping matches?
- Yes. The search slides one base at a time, so overlapping occurrences of the motif are all reported.
- What does the mismatch option do?
- It allows a match to differ from the motif at up to the chosen number of positions, which is useful for finding degenerate or imperfect sites.