Well, well, well. It looks like OpenPCR works much better than my ThermoCycler (which I just learned today is actually called PCR Sprint). The temperatures match pretty well between what the program is set for and what the recorded values are. I’ve discovered in the past that OpenPCR has a problem getting above 90C (see bottom of post), but I don’t think that is an issue here. If OpenPCR isn’t producing product then I may not have chosen the right annealing/extending temps or the problem may be elsewhere (unlikely).
ThermoCycler on the other hand is a piece of garbage. I’ve always hated this thing and now I have proof (again, I’ve done an experiment like this in the past, but it wasn’t as bad as these results show). Looking at the file “thermo-oil-3-cycles.png” you can see that ThermoCycler never gets below ~62C which is sad because it is set to anneal at 52C. It also extends at ~74C when it should be near 69C.
Tomorrow I’ll be taking some T measurements to try and get the program to be closer to the temps I want to run the pALS protocol at. OpenPCR will just need some slight modifications, but ThermoCycler needs a lot of help. Sigh…