Microsatellites usually show different lengths for the alleles so when sequencing you can expect good sequence that then becomes a mess after the start of the microsatellite sequence. If you attach a .abi sequence file it would be easier to comment because sometimes low signal strength can look like mixed sequences

Paul Rutland Hello Paul, this is the image of the electropherogram of the microsatellites where four peaks appear, could each one be an allele considering tetraploidy?

These results look like stuttering to me. Often amplified alleles show structure....a shoulder on each peak,a range of peaks always geting less intense at larger sizes or a single strong peak with a plus and minus peak either side of it. You may find that all of your strongly amplifying samples shpe this effect of one major peak and 2 weaker stutter peaks/ In nature enzyme replication makes mistakes with long single ,double ,triple base sequences and the polymerase in your pcr makes the same type of error. You can often also see an N+1 peak when the taq adds an A base to the amplimer but yours looks like a dinucleotide repeat sequence with stutter bands

Paul Rutland thank you very much, your information has been beneficial and enlightening.