Sequence motif finder
Locate overlapping literal or ambiguity-coded motifs in DNA or RNA FASTA, with explicit strand and matching rules.
Searches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds. Up to 500,000 characters. Review the settings before running.
Your result
How to use Sequence motif finder
- Paste gap-free DNA or RNA FASTA and enter an IUPAC motif.
- Choose literal, possible or certain matching and one or both strands.
- Review inclusive forward-source coordinates and download every match.
Useful next steps
Define ambiguity matching
Literal mode compares symbols. Possible mode accepts intersecting base sets. Certain mode requires every possible sequence base to be included in the motif.
Interpret strand rows explicitly
Both-strand mode searches the motif and its reverse complement. Overlapping matches are retained; palindromic motifs can produce two rows at one position. Matches do not establish biological significance.