(A) SEL displays CSI intensities for all sequence permutations of a given binding site size (k-mers). Sequences are organized with respect to any selected seed motif; however, a k-mer representing PWM-derived motif is typically used. CSI intensities correlate with equilibrium binding affinities. As an example, the arrangement of 6-mer sequences for a simplified 4-mer seed motif is shown. The innermost circle displays the intensities for all sequences that have an exact match to the seed motif (0-mismatch ring). In this ring, sequences are arranged in a clockwise manner with sequences that include residues 5′ of the seed motif at the start, sequences with residues that flank both 5′ and 3′ ends in the middle, and 3′ flanking sequences at the end (context). The subsequent 1-mismatch ring contains the sequences that differ at one position from the seed. The sequences are organized clockwise starting with mismatches at the first position and ending with mismatches at the last position of the motif. Within each sector, the mismatches at a given position (indicated by x) are organized in alphabetical order (A, C, G, and T). The 2-mismatch ring contains all permutations with two positional differences with the seed, similarly ordered. (B) Left, SEL for JUN•ATF3 heterodimer using CRE (5′TGACGTCA3′) as the seed motif. By displaying the 10 bp sequence space, preferred sequences become apparent. Peaks corresponding to emergent and variably-spaced sites are identified by arrows. Right, SEL displaying 12 bp sequences for ATF4•CEBPG heterodimer using CRE-CAAT (5′ATGACGCAAT3′) as the seed motif. (C) Heatmap of the relative CSI intensities of 102 bZIP dimers (columns) for the 10 sites highlighted in Figure 2B as well as constituent half-sites of the six classic bZIP motifs (rows). Displayed is the maximum CSI intensity of all the 10 mers matching the site. bZIP dimers are listed in the same order as in Figure 1B. ATF3, ATF4, CEBPG, and JUN homodimers are marked by asterisks. While bZIPs do not bind as monomers to half-sites, the occurrence of bZIP half-sites within motifs is displayed in the second set of rows to enable comparison between the half-site preferences versus the CSI intensity for motifs that display these half-sites in different combinations or in different contexts.