For a given input set of promoters, we ran the Gibbs sampler BioProspector (8) 400-550 times, evenly distributed across all motifs widths from 6-15 bp. We used a third-order background model derived from appropriate genomic promoters. We collected the best three results from each BioProspector run. We counted the number of times BioProspector identified each nucleotide in the input set. For each promoter, we identified the maximally occurring nucleotide, and extracted all positions identified by BioProspector >35% of the maximum. We clustered together neighboring positions into putative TFBS. As a dust filter, we removed all putative TFBSs <6 bp long ( Figure 1 ).