Transcription factor binding scanner

This tool scans a DNA sequence for predicted transcription factor (TF) binding sites using position frequency matrices in MEME format. It is useful when you have a promoter region, enhancer, or other regulatory DNA and want to see which motifs from a curated library might bind there — on both the forward and reverse strands.

A bundled motif library (tf_elements.meme.txt) loads automatically when you open the page. You can optionally replace it with your own MEME file. Use the species filter to limit scanning to motifs annotated for human, mouse, rat, and other model organisms (JASPAR-style taxonomic links in matrix-tax-embedded.js).

Paste genomic DNA (A/C/G/T; FASTA header lines are ignored), set the minimum strength slider to control how strict matches must be relative to each motif’s score range, then click Scan. Results appear as a binding map along the sequence and a sortable table of hits (motif name, strand, coordinates, matched sequence, and score). Adjust the threshold after scanning — the map and table refresh without re-pasting your sequence.

For long regions, pan and zoom the binding map; hover blocks for scores. Enable hide weaker overlapping hits if the same motif name stacks repeatedly at nearly the same position. Sequences longer than about 35 kb are truncated for performance. All scanning runs in your browser; your DNA is not sent to a server.