Original Data from El-Deiry et al., Used To Define The p53 Consensus Binding Site. The original DNA fragments collected from a genome-wide, p53-antibody immunoprecipitation, that were used to define the head-to-head (HH) p53 Consensus Binding Site, are graphically presented . The yellow columns corresponding to the 1stand 2ndhalf-sites were used to define the consensus p53 motif. The p53 binding site is highly degenerative. Within the yellow columns, notice that 7 of the 20 DNA target sites (35%) had at least one nucleotide insertion (green), deletion (red), or both (magenta) relative to the discovered 10 bp-spacer-10 bp consensus. Since insertions and deletions throw off the reading frame of a weight matrix, any PSSM approach will inherently mis-score at least 35% of these 20 sites. Alignments of the 160 experimentally validated p53 binding sites also reveal that any PSSM approach would inherently mis-score at least 30% of them as well. Another observation is that additional p53 half-sites are immediately adjacent (in yellow) to the ones used to define the consensus in 15 of the 20 target sites (75%). Since the genome-wide immunoprecipitation study was designed to pull down the highest affinity sites, the fact that 75% of the target sites are actually p53 cluster-sites is the first indication that cluster-sites of 3 or more half-sites confer higher binding affinity .