I have a genome, and each position has a conservation score. I want to identify the conserved fragments from these scores. A naive way would be to setup two thresholds, one for the conservation score at each base and another one could be the length of the fragments. I want to calculate a P-value or sort of things to quantify the conservation of a fragment. It sounds a very common task, for example, like the peak calling. So I am wondering whether anyone can recommend some methods to calculate such a score.
I highly appreciate your help!