It supports the design of degenerate primers for amplifying a related set of nucleotide sequences for the detection of common traits amongst organisms, as well as to determine heredity.
[1] The software also designs tagged and nested primers for multiplex PCR reactions.
[2] The Primer Premier software supports motif analysis and ORF search along with finding restriction cut sites on the nucleotide sequence.
[3] The software also designs primers for flanking exons and introns in a gene, though there is no mention of it on the official Primer Premier page on the Premier Biosoft website.
The software calculates the hairpin structure stability and has been used to study its effect on PCR amplification.