Fig. 6
The problem of homotypic clusters: The TFBSs (t blue ) form an homotypic cluster within a certain interval on the sequence. The TFBS t red is also included in this interval. According to our definition to construct TFBS pairs and by following the DNA strand in 5’-3’ direction: i) we consider one t blue −t red pair in this interval indicating that an individual TFBS can only participate in one count of a specified pair (shown with black line); ii) if we consider t blue −t blue pairs, there are two pairs within this interval (shown with blue lines). The red (dashed) lines demonstrate that the remaining t blue −t blue and t blue −t red pairs are not taken into account in the calculation of pointwise mutual information of this pairs