Counting trinucleotide repeats

I have some amplicon sequence data from a number of different subjects. The amplicons contains come regions with trinucleotide repeats, specifically CAG. I’m trying to use the STR detector tool in the to detect and give me a count of the number of repeats, however, I’m finding that instead of the tool giving a count of the number of CAGs, it’s giving the count of the number of GCAs. Obviously, this is because the base before the first CAG is a G so the tool is detecting in the wrong frame. Is there a way to specify that I only want it to detect and count CAGs specifically?