Sample output of PrimerSNP program. (A) SPEC output. (B) COMN output. The weight score and the free energy of melting (ΔG°) are displayed in addition to the PCR parameters of Primer3. The sequence alignment file is also available to the user by clicking the 'get alignment' button. The SNP and primer locations are highlighted within the multiple sequence alignment file. Red color highlights SNP locations; green color highlights the specific primer locations and blue color highlights the homologous regions of other stains/species.