We are interested in just pairwise conservation between putative regulatory elements identified from H3K27aC ChIP experiments in mice. I was able to use bnMapper to identify homology in humans, but cannot find any sort of tool/program in order to provide a conservation score. PhastCons requires at least three species for both PhastWeb and command line... I would even be happy with a program that just determines % matching/not matching that I could run from command line and not have to calculate a whole set (350+) of coordinates by hand. Anyone have any ideas? Thanks.

-Trevor-