Fig. 2

A cluster (a Set of Motifs with a Positional Preference Relative to the TSS). Each dashed horizontal line represents a sequence within our Proximal Promoter (PPR) Database, aligned so that all TSSs are in a single column. The dotted black horizontal line at the bottom represents the column coordinates within the alignment, running from −2000 bp to +1000 bp on the plus strand, as in Fig. 1. For any fixed TF (e.g., SP1), each solid vertical line indicates that the TF’s position-specific scoring matrix has a positive score, corresponding to a subsequence we call a “motif”. Each motif has a motif width, so for computational convenience we assigned the motif’s position and score to its 3′ base (not its 5′ base, as is more common). The top sequence, e.g., displays one motif as a horizontal dotted blue line; and the motif’s positive score, by a vertical solid red line at its 3’ base. Fig. 2 illustrates each positive score twice, once on top of its sequence, and vertically below once again on top of the column coordinates (dotted black horizontal line)