Pairwise alignment sliding window across the whole genome

Question

[dr_bantz]

There is a hexanucleotide motif found in arrays of tandem repeats throughout the genome. Some of these arrays have picked up mutations. I would like to annotate all the arrays in the genome, including degenerate arrays with a lot of mutations. As a first step, I was thinking to perform a pairwise sequence alignment between the motif (TTAGGC) and every hexamer in the genome (using a sliding window with a stride of 1) then assigning a score to each hexamer. I could easily write a python script to do this, but I was wondering if there may be some software out there that can do this faster?