Selective amplification: Depending on genome size, restriction-ligation generates thousands of adapted fragments. For visualization after electrophoresis, only a subset of these fragments is amplified. To achieve selective amplification of a subset of these fragments, primers are extendad into the unknown part of the fragments [underlined base pairs (bp)], usually one to three arbitrarlly chosen bases beyond the restriction site (c, in black). A primer extension of one, two or three bases reduces the number of amplified fragments by factors of 4, 16 and 64, respectively.