The Analyze - PCR window displays various data for PCR based on a user-selected PCR primer pair. The primer pair or set (TaqMan or nested primers) must be selected before this window can be called up.
Optimal annealing temperature for PCR TaOPT and the maximum annealing temperature (Tamax) are given. For an initial experiment, use TaOPT, since it usually gives the highest yield. The Tamax should be used mainly for diagnostic purposes because PCR is more specific in these conditions. PCR primers may be balanced by using their P.E. # or by their Tms. Excellent results have been obtained for multiplex PCR (10 pairs) when all the primers were within a 450-500 P.E. # range.
The picture above shows the window after nested primer set search. The real-time primer search yields 3 oligos per set.