PCR not working - (Apr/09/2014 )

I use this tool, EMBOSS Cpgplot but usualy decrease windows size to around 20 to get higher resolution. It's not a simple GC content, but a graph of relative GC % over a set region. Amplicon may have average GC but at the same time have a high GC region, that makes problems.

You can't run them together. I just open two windows and compare them. If you are looking to find a common Tm, try NEB's Tm calculator.

You could always consult Emsembl or Genome Browser to see relative GC content across your gene of interest.