With only two closely related species in our set, we chose the Smith-Waterman [46] pairwise, gapped local alignment algorithm (implemented as BestFit in the Wisconsin Package Version 10.3, Accelrys Inc., San Diego, CA) to align their orthologous intergenic regions, using default parameters (match = 10.000; mismatch = -9.000; gap creation penalty = 50; gap extension penalty = 3). The alignment of E. coli and S. typhi orthologous upstream intergenic sequences resulted in 1662 unique aligned sequence pairs. The upstream intergenic sequences for an additional 836 E. coli genes that did not have orthologs in S. typhi remained. The combination of these two datasets (1662 + 836 = 2498) does not equal the above number of E. coli intergenic regions of interest (2379 sequences), due to the complication of divergently transcribed genes. Specifically, we observed that for some divergently transcribed genes in E. coli, the orthologous genes in S. typhi are not syntenic, thus S. typhi provided two separate intergenic regions for alignment to a single intergenic region of E. coli.