between prediction X and the STE12 PWM across all aligned positions. Thus, scores ranged from zero, with no positions aligned, to seven, the length of the STE12 PWM. We observed a bimodal distribution of scores (Supplementary Figure S1) , and chose the alignment score corresponding to the minima of the distribution (alignment score ¼ 4.5) as the threshold to classify predictions as TP or FP.