Abstract Motivation: We developed a technique and a tool for degenerate primer design based on multiple local alignments employing the MEME algorithm supported with electronic PCR. The objective is to find adequate primers starting from sequences with poor global similarity. We show an example of its application in our laboratory to find sequences in Brachiaria with similarity to ESTs related to apomixis. Contact: srestrep@uniandes.edu.co; j.tohme@cgiar.org Supplementary information: Supplementary data are available at Bioinformatics online.