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