Primer design for PCR-based methylation analysis following bisulfite conversion of DNA is more complicated than the primer design for regular PCR. I attach this paper for you, it especially delicates to this topic by explaining how to design the primers and set the Tm. I hope it is helpful to your research.

Thanks! The paper is really interesting. I finally got some bands at higher annealing temperatures as the paper suggests but I had to adjust magnesium as well. :)