An outline of SSAP. DNA is digested with one frequently cutting and/or rarely cutting restriction enzyme (horizontal red lines marked ‘R’). Adapters (blue boxes) are ligated to restricted ends and then a pre-selective amplification is carried out (not illustrated). Selective PCR amplification, shown below, is carried out with LTR (red arrow) and adapter specific (blue arrow) primers. Both primers contain selective nucleotides (colored heads of the arrows) to ensure specific amplification and reduce the number of generated bands to a manageable level. Transposon amplification can only be carried out from the construct shown on the left as the primer at the 3’end contains a selective nucleotide that is absent from the one shown on the right. Generated PCR products of variable length are indicated by brown bars.