Within-genome DNA alignments. Plots of exactly matching sequences within four genomes as identified by the MUMmer program: (a) V. cholerae; (b) E. coli; (c) S. pyogenes; (d) S. pneumoniae. A point (x,y) indicates a DNA sequence that is repeated within the genome, occurring once at location x and again at location y. Points near the diagonal (y = x) correspond to tandem repeats. Points near the anti-diagonal (y = L - x, where L is genome length) correspond to repeats that occur at symmetric locations about the origin of location. The point (0,0) corresponds to the origin of replication in each plot. Statistically significant X-alignments occur in all four species (Table 1).