Figure 5

Density and conservation of Sox motifs are higher in Dichaete intervals with binding conservation. (A) On average, Dichaete binding intervals that are conserved between all four species (“4-way conserved”) have more Sox motifs than intervals that are unique to D. melanogaster (“D. mel unique”) (p = 3.03e-193). (B) Dichaete binding intervals that are conserved between all four species do not show an increased rate of total nucleotide conservation on average than intervals that are unique to D. melanogaster. (C) Sox motifs in Dichaete intervals that are bound in all four species (“4-way Sox”) have a greater percentage of perfectly conserved nucleotides across all species than either Sox motifs in intervals that are unique to D. melanogaster (“D. mel Sox”, p = 9.56e-36), randomly shuffled control motifs in intervals that are bound in all four species (“4-way control”, p = 1.62e-43) or randomly shuffled control motifs in intervals that are unique to D. melanogaster (“D. mel control”, p = 1.67e-9). (D) On average, Dichaete intervals that are bound in all four species have more Sox motifs that are both positionally conserved and show 100% nucleotide conservation across all species than intervals that are only bound in D. melanogaster (p = 6.04e-28). The multiple alignment illustrates a positionally conserved Sox motif with 100% nucleotide conservation (highlighted in purple).