Outline of SRAP. In the SRAP reaction each primer contains a random filter sequence at the 5’end (blue box) and three variable selective nucleotides at the 3’ end. The core motif consists of CCGG in the forward primer and AATT in the reverse primer, both targeting gene related regions. Early cycles of PCR are carried out at a lower temperature (35°C) allowing mismatches to be incorporated in the amplicons. Late cycles at a higher annealing temperature (50°C) generate products from this pre-amplified pool.