BLAT (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.

1. Perform rapid mRNA/DNA and cross-species protein alignments using blat
2. Sort the output file
3. The output file can be filtered using UCSC pslCDnaFilter

Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).