De novo motif discovery accurately recovers known motifs. Examples of sequence motifs that are enriched in Stretch Enhancer (SE) DNase Hypersensitive Site (DHS) sequences or within DNase footprints (FP) across all ChromHMM concatenated enhancers (CEs). Sequences of motifs derived from EXTREME (bottom) are aligned to known motifs from two databases [20, 37] (top). Motif similarity was measured with TOMTOM, a tool that reports the significance of a match between a query motif and a database motif . Below each sequence logo, the cell type, sequence set, motif name, and significance of the TOMTOM match (E
) are displayed.