How are STR alleles identified?

Short Tandem Repeats (STR) alleles are primarily identified by analyzing the size of the PCR products that are generated from specific regions of the DNA containing these repeats. During the Polymerase Chain Reaction (PCR), primers that flank the STR regions amplify the DNA. The resulting PCR products vary in length depending on the number of repeat units present in each allele.

Once the PCR amplification is complete, the size of these products can be determined using gel electrophoresis or capillary electrophoresis. This method allows for the visualization and comparison of the lengths of the PCR products, which correspond to the number of repeats in the STR locus. The size differences are typically measured in base pairs (bp), enabling the identification of specific alleles based on their unique length.

While sequencing could provide detailed information about the exact nucleotide composition of the STRs, it is not the primary method used for allele identification in forensic and clinical contexts due to its complexity and cost. Similarly, direct observation under a microscope does not provide precise measurements of PCR product size, and the use of fluorescent dyes is typically part of the detection process in PCR but does not directly identify the alleles themselves without analyzing the size of the products.