Preferential conservation of common binding by Dichaete and SoxN. (A). Venn diagram showing all Dichaete and SoxN binding intervals identified in D. melanogaster and D. simulans. The single largest category (7415 intervals) consists of commonly bound, conserved binding intervals. (B). Bar plots showing that commonly bound intervals are more likely to be conserved between D. melanogaster and D. simulans than intervals uniquely bound by either Dichaete or SoxN. The difference in conservation rates is highly significant for both D. melanogaster intervals (top, p < 2.2e-16 [approaches 0]) and D. simulans intervals (bottom, p < 2.2e-16 [approaches 0]). (C) MA plot showing binding intervals that are differentially bound between Dichaete (pink, fold change > 0) and SoxN (pink, fold change < 0) in both D. melanogaster and D. simulans. Fewer quantitative differences in binding are detected between the two TFs than between the binding profiles of one TF in two species. (D) Enriched motifs identified in intervals that are uniquely bound by SoxN or Dichaete in both D. melanogaster and D. simulans. A motif matching Ultraspiracle (Usp), a TF involved in axon pathfinding, was found in unique SoxN intervals, while a motif matching Brachyenteron (Byn), a TF critical for hindgut development, was found in unique Dichaete intervals.