For example, PhyloScan identified a total of 10 Crp-significant intergenic regions in the E. coli-S. typhi aligned data, but after combination of the evidence from the remaining five species, a total of 29 Crp-significant intergenic regions were predicted, a near tripling. Compared to a simple search of the raw E. coli intergenic sequences (one Crp-significant intergenic region), this represents a tremendous increase in sensitivity. The results with the PurR model were also dramatic: the use of data from S. typhi, Y. pestis, H. influenzae, and V. cholerae provided a 50% increase in the number of PurR-significant intergenic regions (to 18 from 12), compared to the scanning of E. coli-S. typhi aligned intergenic sequences only. In the E. coli sequence alone there was only a single PurR-significant intergenic region. In the Supplementary Materials are tables listing the located sites for Crp [see Additional file 3] and PurR [see Additional file 4], as well as captions for these tables [see Additional file 1].