Transcription Factor Binding Site Scanner — 2D Track View

This simulator renders a synthetic DNA molecule as a zoomable, pannable 2D sequence track — the same layout genome browsers use — and scans it with a position-weight-matrix (PWM) model of a transcription-factor binding motif, exactly the way bioinformatics tools like FIMO score candidate regulatory sites in a genome. Every window of the sequence — on both strands — is scored by summing log-odds terms that compare the local bases against the PWM's per-position frequencies, and any window that clears the score threshold is marked as a predicted binding site with a glowing gold highlight on the base track and a matching peak on the score curve beneath it. A cyan cursor sweeps continuously along the sequence at an adjustable speed, reading out the live window score, while switching between three archetypal motifs (TATA-box-like, GC-box/Sp1-like, CCAAT-box-like) shows how the shape and conservation of a motif changes how many — and how confident — the predicted sites are.