The 31 organisms used in our analysis are described in Table 1 . These genome sequences are all contained in Table 7 Motifs passing our set of stringent filters, ranked by their degree of conservation (Continued) 50 k indicates the value of k in the k-means clustering process (50, 100, 200, or 250) b MAP score indicates the AlignACE MAP score [76] c Specificity score [77] d CompareACE score ≥ 0.7 to the alignment for this known motif e CompareACE score to its reverse complement f number of ScanACE hits in the genome that are conserved in ≥ 8 genomes g sequence logo [78] the TB database (TBDB) [75] . The three unpublished sequences generated at the Broad Institute (M. tuberculosis F11, M. tuberculosis Haarlem, and M. tuberculosis C) are high-quality genome sequences. M. tuberculosis F11 and M. tuberculosis Haarlem are finished, and M. tuberculosis C has 6.7× coverage and 4 scaffolds. The Broad Institute sequencing read pipeline interacts with the sample management system to ensure the read is associated with the correct sample. Vector identification, length checks and quality clipping were performed on all reads. Contamination checks and organism checks were also performed using a kmer-based algorithm that can compare sequence to a profile from any organism.