Figure 2. The Effects of Stride versus Window Length on the Measure of Coverage.

In each graph a three-gene-length COT⁺ construct is evaluated for coverage. Cold (blue) colors indicate high levels of coverage, and hot (red) colors indicate low levels of coverage. The diagonal in the topography represents the transition from strides shorter than window length to strides longer than window length. The maximal coverage at three gene lengths occurs with a window size of 17 with a stride of 1 with no smoothing for both genes—where 82% of the 9mer area is captured for Gag (A) and 62% of the 9mer area is captured for Nef (B). It should be noted that in the area of window of 17 and a stride of 1 the surface is quite flat, and there are several pairs of parameters that give similar results.