FIG. 2.
Schematic of uncovered breakpoint computation. (a) Diagram of a small primer set in which there are initially 4 forward and 4 reverse primers. An additional forward primer (lightly shaded) is added at position i, which reduces the uncovered space. The difference in uncovered space between p(i −1)↱ to pi↱ is seen as the difference in total shaded area compared to darkly shaded area. (b) Uncovered space for the added primer at a specific reverse pair location, given by the dotted lines in (a). Uncovered breakpoints are the coordinates contained in the rectangle not contained in the triangle. The total number of such breakpoints is given by, |U| = |R − R ∩ T| = |R|− (|T| − |T1|,−|T2|).