The second cutoff that our approach requires is the q-value cutoff that specifies which sites will be reported. We chose a default value of 0.001, meaning that according to our model, at most 0.1% of the intergenic sequences that we report as binding the transcription factor are chance false positives. While we have incorporated a fairly accurate phylogenetic model, we have not incorporated into this model such effects as the non-independence of the positions in a site (e.g., the effect of di- or tri-nucleotide energy terms, also known as stacking energies), nor effects from the cooperative binding of multiple transcription factors on the ability of a factor to bind to a DNA site. Because our model does not capture these and other features, the actual rate of false positives is likely to be higher than 0.1%.