 For instance, a hairpin loop with a fluorophore and quencher at the base of the stem is used.An unlabeled SNP specific PCR primer (one of many) with a specific 5' tail binds to the sequence to be probed, and the taq polymerase extends the sequence that will have a specific 5' end dependent on the SNP (insensitive to polymorphisms upstream of the SNP in question).In the next run a primer, complementary to that tail, with a hairpin loop is extended.