Figure 1

Diagram of the possible primer pairings allowed in the paired versus mux predictions of simulate_PCR. Heavier lines indicate F/R/IO combinations considered for paired reactions, and all lines indicate pairings considered for mux, which allows any combination of primers to pair up in a reaction with either primer behaving as the forward or reverse. Dashed lines indicate checks for a probe to land on an amplicon produced by a given primer pair. In the paired setting, primers listed as “|F” must act as forward primers and as “|R” as reverse primers, while in the mux setting either may act as forward and/or reverse. From a given set of BLAST results, the paired setting checks for two possible priming reactions of signature 1 and signature 2, and reports hits both with and without the probe. Mux checks for 16 possible priming reactions and reports all hits to either probe.