I have been tackling with this for quite some time now and I think it is time for me to ask for help...
I have multiple paired samples (e.g. ID 1a,1b,2a,2b,3a,3b,4a,4b...) and their sequences for a specific locus, e.g. Locus 1. These are contingency loci and I am interested in the hyperpolymetric tract within this sequence, e.g. --GGGGGGGG-- and this can vary between sample i.e. ID 1a(8), 1b(9). I am interested in extracting where these tracts are within the loci (I have aligned the sequences) and somehow coding or calculating how many of these bases there are in a row for each sample as I need to compare between the pairs.
I currently use MEGA to visualise my sequences, and I know that the tract starts at for example site 2660 and finishes at 2669.
I am yet to find a quick way of being able to do this, so any help would be greatly appreciated. I am also very new to bioinformatics.