For instance, in the collection of 10,000 synthetic data sets in which we planted two full-strength Crp transcription factor binding sites per intergenic region, we have 9,985 true positive intergenic regions at the 99.9% specificity level (see Figure 3). Of these true positives, in 6,287 of the E. coli intergenic regions two sites were predicted and the sites exactly coincided with the two planted sites. In 24 E. coli intergenic regions two sites were predicted and one of the two sites exactly coincided with a planted site. In 3,672 of these regions one site was predicted and it exactly coincided with one of the two planted sites, and in 2 of the E. coli intergenic regions, one site was predicted that did not exactly coincide with a planted site.