Supplementary Material Additional file 1 Additional Information. This file includes legends for Supplementary Tables 2–4, which are included as additional files (see below). It includes samples of calculations described in Methods. Click here for file Additional file 3 Supplementary Table 3. This table lists the sites and the q-values for each of the Crp binding site prediction experiments in Table 1 of the text. Click here for file Additional file 4 Supplementary Table 4. This table lists the sites and the q-values for each of the PurR binding site prediction experiments in Table 1 of the text. Click here for file Additional file 2 Supplementary Table 2. This table lists the orthologs and the orthologous intergenic regions used in this study. Click here for file