DNA Motif Finder & Motif Discovery (IUPAC)
Search for a motif you have, or discover one shared by a set of sequences.
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. The page also answers the opposite question: paste two or more sequences — promoters of co-regulated genes, a set of binding regions — and it finds the short motif they share, reporting a consensus, a position-weight matrix and one site per sequence. Because a sampler of this kind returns a motif from any input, including random sequence, every run is scored against shuffled copies of your own sequences (same lengths, same base composition, no arrangement) and says plainly when the result does not stand out.
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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.
Find a motif you don't know yet
Paste two or more sequences — promoters of co-regulated genes, a set of binding regions — and this looks for the short pattern they share, rather than one you supply above.
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Gibbs site sampler (Lawrence et al. 1993), one site per sequence, both strands. A motif has no canonical orientation, so the consensus may come back as the reverse complement of the one you expect. Upper case marks a position one base holds; lower case marks one that is mixed. The search is deterministic — the same sequences give the same motif, so a result you save or share reproduces.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
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.
- 4Or, if you do not know the motif yet, paste a set of sequences lower down and let it find the one they share.
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.