the choice of binding partners [51], while different k-mers of the apparently degenerate RACRYNNNNNACG motif in yeast are associated with the regulatory regions of genes with different functions [52]. It is possible, therefore, that some mutations resulting in a loss of PWM match are, in fact, beneficial rather than deleterious and may be indicative of positive selection that was recently shown to occur at a fraction of Drosophila TFBSs by He et al. [12]. However, in line with the assumption of He et al., we believe that the predominant direction of positive selection would be towards increasing PWM scores, and such mutations will have a zero load according to our definition.
