Flow-chart showing the functional structure of SSR Locator. (A) Perl script to search SSRs; (B) text file where information from detected SSRs is stored; (C) module for the statistical calculations for SSR motif occurrence; (D) module that formats text files into standard Primer3 input files; (E) running of Primer3; (F) module for running Virtual-PCR (using a second sequence file as a template); (G) module performing global alignment between homologous amplicons; (H) identity and alignment score calculations between homologous amplicons; and (I) file containing SSR, primer, homologous amplicons, identity, and score information.