We used Gumby [65] to select conserved regions in our multiple alignments using a value of p < 0.5. In a multiple alignment of all 19 Mycobacterial genomes, we identified 4697 regions of conservation overlapping coding genes in the reference annotation, and 394 regions in intergenic regions. We also used the method of Ruzzo and Tompa [107] to identify conserved regions. Scores were normalized to the background inferred from the 3 rd-base frequencies.