Figure 5

High stringency HB binding site predictions in the IAB7b CRM. PWMs corresponding to the 7 bp core predicted binding region (PBR, red) or the core PBR with flanking sequences of various sizes (black) were used to predict HB binding sites in the 828 bp IAB7b enhancer with an initial cutoff threshold ln(p-value) = -7.53 (corresponding to the 50^th percentile). For each individual PWM, a secondary cutoff at the 0^th, 25^th, 50^th or 75^th percentile of all the ranked sites (see Methods for details) was also applied. Note that at this primary cutoff score the core PBR fails to predict the true positive HB binding site (purple circle) and as the length of the PWM is increased more robust predictions are made.