Figure 5

Primer-primer compatibility probability and primer selection stringency. This figure shows how a number of primer selection criteria impact the overall probability that two primers will be mutually compatible. If compatible primers are connected by edges in a graph, the resulting probability is equivalent to the graph density. This figure plots graph density as a function of 3' ΔG interaction. Each point represents a single trial where additional primer compatibility thresholds were randomly chosen within specified ranges. Considered were the 3' tail ΔG interaction, complementary sequence local alignment score, and melting temperature (Tm) difference. Points that are more red allow for high Tm differences while points that are more blue require smaller Tm differences. The impact of local alignment score thresholds, while not shown explicitly, is indirectly revealed by the multiple tiers (bands) across the graph, the lowest corresponding to score = +4 and the highest to score = +6 to +10.