Association improvements can compensate for reductions in PWM scores. In orthologous mouse–human pairs of 5′ss, association scores improve as PWM scores get weaker. The graph shows the average of the PWM-score differences (white bars) as well as association-score differences (black bars) for the orthologous 5′ss mouse–human pairs, organized by the number of nucleotide differences between the members of each pair (X-axis). A positive difference means a decrease in the score (and vice versa). The differences in PWM scores are always positive, as the 5′ss with the higher score within a pair is always considered first. Error bars, confidence intervals.
