How to calculate base pair conservation for two species?

Question

[notsway]

Hi,

I'm trying to represent pair-wise conservation in the mitochondrial genome across a number of species. I want to create a diagram that looks like this. In the lower-right corner, there is a note that explains how conservation has been illustrated. I'd like to calculate average conservation for the genome and a given window.

I'd like to know how to get a conservation score for every base, given the sequences of two species. Is there an alternative for PhyloP or PhastCons which seem to require MSA?