The evidence for clustered adjacent binding sites. (A) The sketch illustrates the forward and reverse tag pileups and smoothed tag profiles resulting from an isolated binding site. (B) The sketch shows the forward and reverse tag pileups and smoothed tag profiles resulting from two nearby binding sites in a binding region. It can be seen that the overlapping of the forward and reverse tag pileups is mainly due to adjacent binding sites in the binding region. (C) A snapshot from CisGenome Browser showing an example of the overlapped forward and reverse tag pileups. The example is from the genomic regions of chr22:29885800-29886400 of the GABP ChIP-seq data. Also illustrated are the three distances (d1, d2 and d3) defined in the main text. (D) The average values and standard deviations of d1, d2 and d3 based on top 5% dense tag-enriched regions of GABP, STAT1 and NRSF ChIP-seq data, respectively.