Distributions of PWM scores and distances between BSs in real and random CEs. (A) Distribution of PWM scores for first and second BSs in real CEs (red) and random sequence CEs (blue). Scores S
define the rectangle OABC and perfectly separate high scoring CEs. By reducing the scores (dashed green lines), many additional true CEs, but also a large number of random CE are also covered by the rectangle OA′B′C′. Introduction of a sum of scores (diagonal EF) greatly improves the separation between real and random CEs (discontinuous line A′E′F′C′). (B) Distribution of distances between BSs and sum of matrix scores in real CEs (blue). Distance values were averaged in intervals of score values (1.75-1.80), (1.80-1.85), (1.85-1.90), (1.90-1.95) and (1.95-2.00) (red). The trend line reflects the dependence between PWM scores and distance between BSs.