304 short DNA regions (average ~400bp) were found to be significantly enriched in most Transcription Factor ChIP-seq experiments despite the fact that the 23 analysed TFs have diverse functions and expression patterns. These regions were bound by 15 or more factors at a q-value cutoff of 1e-5.
WU-BlastP BBH method with 10-9 as cutoff and at least 50% of the protein aligned. Only 1:1 pairs were used that had more than 10-29 better e-values than the next best hit.