AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. Such primers are usually selected so that they will amplify cDNA generated from mRNA but will not yield a product on the genomic DNA. This is achieved by taking advantage of the eucaryotic splicing system for mRNA. Either primer pairs are selected so that one of the primers matches the exon-exon border sequence that is not present in the genomic sequence or the pair is designed by placing each primer in a different exon so that a genomic product would include a long intronic sequence. AutoPrime provides these capabilities on top of the primer3 primer-design software.

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