To test these sources of statistical power, we generated databases of promoter-containing E. coli intergenic regions, aligned E. coli-S. typhi intergenic regions, and motif models based on known Crp and PurR sites (see Methods). Specifically, the three databases contained: (1) the set of all E. coli intergenic regions, (2) the E. coli sequences extracted from the alignments of E. coli-S. typhi orthologous intergenic regions, and (3) the E. coli-S. typhi aligned intergenic regions data. Relative to the original method of Staden, our results show large improvement in the number of predicted transcription factor binding sites due to the alignment of two somewhat closely related species (Table 1 and Figures 4 and 5). Specifically, with a q-value cutoff of 0.001 (see Methods) the scanning of the set of all E. coli intergenic sequences results in only one Crp-significant intergenic region (with two predicted Crp sites), and one PurR-significant intergenic region (with one PurR site). No improvement was obtained in the reduced database of E. coli intergenic sequences. However, when the set of E. coli-S. typhi aligned sequences was scanned, 10 Crp-significant intergenic regions (with 13 Crp sites total), and 12 PurR-significant intergenic regions (with 13 PurR sites total) were predicted.