Motif tree of ChIP-seq-derived Cse4p binding sites in Yeast. Two distinct motif families were determined from the MotifCatcher analysis of 158 ChIP-seq derived Cse4p binding sites. Logos for the FPs of these two families taken with an FP frequency threshold of 1.0 are pictured above. At this threshold, all 158 sites naturally segregated into three non-intersecting groups (66 of the 158 into family 1, 47 of the 158 into family 2, and 45 of the 158 into neither family). While the associated motif in the first family does not resemble a readily recognizable sequence motif, the low E-value for this profile suggests that the position-specific distribution of sequence elements is highly different from the position-specific distribution of sequence elements in the whole Yeast genome. More than half of the sites in this family were also associated with highly ranked PolII targets, which supports the hypothesis put forth by that Cse4p is transiently localizing to regions of high histone turnover. The A/T-richness of the second motif family resembles the canonical CDEII motif, which is known to be responsible for the majority of direct interactions between Cse4p and DNA.