Figure 2

Dyad sweeping along the upstream region of the purR gene. Contiguous regions of overlapping matching dyads (ROMs) frequently overlap with the known binding sites. This example shows results after finding significant dyads in the 200+50 regions of the PurR regulon, and finding the ROMs within the same regions. The two ROMs with the highest peaks completely overlap with the two reported regulatory binding sites in this region (sites lie at positions -59 to -43 and at 29 to 45). The coordinates here are relative to the annotated first coding nucleotide of the gene. The known binding sites are illustrated as boxes below the figure. The lower line shows the different dyads coded in different colors. It can be seen, for instance, that blue dyads occur only in the two true binding sites.