**OutputFolderName**
The folder where the output files are stored.
**x.fasta**
The fasta file containing the loci's alleles.
**y.fasta**
The fasta file containing the loci's alleles.
**z.fasta**
The fasta file containing the loci's alleles.
**...**
Other fasta files containing the loci's alleles.
**short**
The folder containing the short loci's representative alleles.
**x_short.fasta**
The short fasta file containing the loci's representative alleles.
**y_short.fasta**
The short fasta file containing the loci's representative alleles.
**z_short.fasta**
The short fasta file containing the loci's representative alleles.
**...**
Other short fasta files containing the loci's representative alleles.