Base composition differs in active versus inactive ZFP target sites. A) Total base counts for active and inactive ZFP target sites (from ZFTS135, a dataset of 135 experimentally validated 9-bp target sites, see Additional File 1 - Table S1) reveal that variation in the average frequency of each base differentiates active versus inactive target sites. The total number of G and T residues relative to A and C is inflated because currently available OPEN pools are designed to target GNN and TNN triplets. B) Positional base counts, i.e., average base counts for each position within target site triplets (1st, 2nd, 3rd), suggest that thymine bases negatively impact ZFP binding at all three positions. C) An iceLogo  generated from ZFTS135 illustrates the difference in percentage composition of nucleotides at each position, from 1 - 9 (5' to 3'), between the positive class and the entire dataset. For example, 78% of all sites in ZFTS135 have a G in position 1, whereas 88% of all active sites have a G at position 1, resulting in a difference of 10%. Positive difference values indicate that, on average, the indicated bases are favored at those positions in active sites; negative difference values indicate that the indicated bases are disfavored. These position-specific differences in percentage composition also support the conclusion that thymine bases tend to occur in inactive targets (i.e., they have large negative propensities).