You must use a text editor to create a custom reference file in .fasta format to carry out STR analysis. One reference .fasta file is required per locus, with one allele per .fasta line in the file. The file name must be the same as the name of the locus, for example, D18S51.fasta. In each .fasta file, each allele is identified by its name in the title line above the allele sequence line. The allele sequence line contains three parts: the pre-repeat flanking sequence, the allele repeat sequence, and the post-repeat flanking sequence.

Typically, the flanking sequences are identical for all the alleles for the locus but the repeat sequence region is specific for each allele. Also, typically, there is a difference in the length within the reference region for each allele, but there might be other differences as well such as a SNP within the region for one of the alleles.