That sort of "shouldered" peak can happen when you have 1 product that melts in 2 phases. How big is your amplified PCR product? Do you see one band or two when you run out your sample on an agarose gel?

Unless you are doing melt-curve based genotyping, the melt curve is the least informative part of a qPCR assay. The Ct values and the primer efficiency are the essential data.

I hope that helps!

Thanks Katie. My amplicon has 217 bp, a bit too big for qPCR. The point is I am using this melt curve for genotyping with allele specific PCRs and this kind of peak is very stable, despite the “shoulder”.