Number of binding sites identified in treatment and control sample using different sets of parameters. (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the mononucleosome sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.