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Cleaved Amplified Polymorphism Sequences (CAPS)

A CAPS marker represents a refinement of a STS marker. Where an STS assay shows no allelic variation in amplicon size, it may still be informative if the amplicon varies in sequence between individuals. If such sequence variation can be identified by treatment with a restriction enzyme after the PCR, the STS becomes a CAPs marker (note that the "C" in CAPS stands for "cleaved" to reflect the need for restriction digestion to identify the polymorphism). Since each restriction enzyme has its unique recognition site, a CAPs marker needs to specify both the primers and the specific restriction enzyme used.