a, The co-crystal structure of upstream stimulatory factor (USF1) bound to its DNA ligand is juxtaposed above the average nucleotide-level DNase I cleavage pattern (blue) at motif instances of USF in DNase I footprints. Nucleotides that are sensitive to cleavage by DNase I are coloured blue on the co-crystal structure. The motif logo generated from USF DNase I footprints is displayed below the DNase I cleavage pattern. Below is a randomly ordered heat map showing the per-nucleotide DNase I cleavage for each motif instance of USF in DNase I footprints. b, The per-base DNase I hypersensitivity (blue) and vertebrate phylogenetic conservation (red) for all DNase I footprints in dermal fibroblasts matching three well-annotated transcription factor motifs. The white box indicates width of consensus motif. The number of motif occurrences within DNase I footprints is indicated below each graph.