Nomenclature

Window A unique sub set of adjacent oligos, used for comparing between treatment samples and control samples. Windows have a user defined maximum bp length and minimum number of oligos, typically 675bp and 15 respectively. Adjacent windows invariably overlap by all but two oligos.
Interval A collection of one or more overlapping windows exceeding one or more score cutoffs: fold, intensity difference, or a Wilcoxon rank sum.
Binding Region A user selected portion of an Interval, what is the most probable binding region.
Binding Peak A peak of intensity within a Binding Region.

Overlapping Window(s) are collapsed into an Interval from which one or more Binding Regions and Binding Peaks are picked. (Window(s) -> Interval -> Binding Region(s) & Binding Peak(s))