To address issues of generality, we repeated the procedure on additional sets of S.cerevisiae promoters (YAP1, TEC1, HAP4 and YDR026C). An added benefit is that we can evaluate the effect of information content of the binding motif and number of promoters on the improvement from positional clustering (22) . Repeating the analysis, we again find that independently of the set or sampling procedure, positional clustering improves accuracy through a broad range of random DSs (Figure 3 ). Improvement appears to be limited and unreliable only when sampling alone correctly identifies the binding site in fewer than 20% of results. This result is consistent with our analysis of STE12-bound promoters (Figure 2) , and may correspond to a lower limit for the efficacy of positional clustering.