A key focus of this work has been to combine evidence across transcription factor binding sites within an intergenic region and across orthologous regions in order to correctly identify intergenic regions that are likely to contain transcription factor binding sites, even when each of the identified transcription factor binding sites, considered in isolation, may not be sufficiently strong to be statistically significant. Accordingly, the individual sites included in our predictions are not necessarily statistically significant and individual site predictions may be false positives even within true-positive intergenic sequences.