After amplification with PCR, samples are loaded into a gel (either agarose or polyacrylamide) for gel electrophoresis. The differing sizes created through random amplification will separate along the gel in a repeatable manner depending on the sample source. This creates a distinct DNA fingerprint.
Unlike traditional PCR analysis, RAPD does not require any specific knowledge of the DNA sequence of the target organism: the identical 10-mer primers will or will not amplify a segment of DNA, depending on positions that are complementary to the primers sequence. For example, no fragment is produced if primers annealed too far apart or 3 ends of the primers are not facing each other. Therefore, if a mutation has occurred in the template DNA at the site that was previously complementary to the primer, a PCR product will not be produced, resulting in a different pattern of amplified DNA segments on the gel.