The flanking sequences surrounding the core TFBS affect binding. For a set of sequences in which a single strong binding site was placed at different locations within a specific sequence context, the plot shows the log₂ of the ratio of the binding score attained by each sequence (with the x-coordinate marking the location of the center of the site) divided by the median binding score across all sequences in this set. (A) Gcn4 TFBS composed of 9 bp (in blue) or 23 bp, including fixed-flanks site (in red) placed along the HIS3-derived context. (B) Gcn4 TFBS of 9 bp (in blue) or 23 bp, including fixed-flanks site (in red) placed along the GAL1-10–derived context. (C) Gal4 TFBS of 17 bp (in blue) or 23 bp, including fixed-flanks site (in red) placed along the HIS3-derived context. (D) Gal4 TFBS of 17 bp (in blue) or 23 bp, including fixed-flanks site (in red) placed along the GAL1-10–derived context. (E) For each type of binding site, a boxplot shows a log₂ ratio of the binding score for sequences containing a site with fixed flanks within different sequence contexts divided by the median score across all contexts.