Furthermore, regulatory modules often include multiple sites, none of which alone would be statistically significant in a genome-scale scan. Our procedure addresses this important case. In addition, our procedure permits use of a wide range of nucleotide substitution models, and it reports q-values [16], the fraction of intergenic regions of a given strength or better that are expected to be false, whereas MONKEY reports p-values, the fraction of false sites expected to show a given strength or better.