Arrays of positioned nucleosomes flanking transcription factor (TF) binding sites.

A. Heatmaps of MNase midpoints (columns 1–2) and DNase I cuts (column 3) surrounding 1000 randomly sampled ChIP-seq peaks for CTCF, NF-kB, Irf4, GABP and C-fos. Heatmap rows are ordered from top to bottom by the nucleosome array log likelihood ratio (LLR). Columns 2 and 3 are aligned according to the most likely location of the upstream and downstream arrays of positioned nucleosomes. B. Aggregate MNase midpoint and DNase I cutsite depths across all regions and for the subset of regions with LLR>500.