Transcription Factor Binding Site Scanner (2D Track View)

Motif Model (PWM)

Sequence length 180 bp

Score threshold 0.0 bits

Scan speed 14 bp/s

Scan Results

A C G T hit site

Drag the track to pan · scroll / pinch to zoom.

Sites above threshold

Best score

0.0 bits

Scanner position

Window score

0.0 bits

How it works

A transcription factor rarely binds one exact DNA word — it tolerates variation at each position. A position weight matrix (PWM) captures this as one base-frequency column per motif position, learned from real binding sites. Scanning a genome for candidate sites means sliding the PWM along the sequence and, at every offset, scoring how well that window matches the model versus random chance:

score = Σ log2( (f(i, b_i) + ε) / p_bg )   for i = 0 … L-1

f(i, b)  = model frequency of base b at motif position i
b_i      = the actual base in the window at position i
p_bg     = 0.25  (background probability of any base)
ε        = 0.01  (pseudocount, avoids log(0) for a never-seen base)

This is the log-odds scoring scheme used by real motif scanners such as FIMO and MAST. A window scores high only when its bases repeatedly land in the PWM's preferred columns; a single mismatch at a strongly-conserved position costs many bits. Because a transcription factor can bind either DNA strand, every window is also scored against its reverse complement, and the better of the two orientations is kept.

Motif model — switches the PWM (and its length) between three archetypal core-promoter/enhancer motifs.
Sequence length — regenerates a random synthetic sequence of the chosen length (each base drawn uniformly, matching the p_bg = 0.25 assumption above).
Score threshold — the log-odds cutoff a window must clear to be called a binding site; raising it demands a closer match and shrinks the hit count.
Scan speed / Pause — the cyan cursor sweeps the track at this rate, reading off the precomputed score at each offset live.

Gold bases mark every window whose best-strand score already clears the threshold — these are the simulator's predicted transcription-factor binding sites. The lower track plots the log-odds score curve itself, with the threshold drawn as a dashed line.

Transcription Factor Binding Site Scanner — 2D Track View