DNA extraction and PCR amplification are essential steps in a number of different applications including forensics, sequencing, metagenomic analyses (i.e., study of community profiles) and comparison of ecosystems using their microbial profiles [1]. Design of primer pairs used in PCR depends on the target application and can be specific to a particular species, gene, ortholog group, taxon or community. In projects that aim to discover community composition and structure, primers are mainly required to (1) be universal in their ability to bind to a maximum number of different target species and (2) produce maximally distinguishable amplicons for the taxa of interest, which is the basis for the post PCR data analyses and species identification.