PCR primers used to amplify three long NPCL markers together with the reference marker RAG1.

R = A+G; Y = C+T; W = A+T; M = A+C; K = G+T; D = A+T+G; H = A+C+T; N = A+G+C+T.
Each long NPCL marker is amplified in two contiguous and overlapping fragments (F1 and F2). * indicates NPCL marker that is amplified using both nested PCR and standard PCR in order to compare amplification difficulties between two PCR methods. For nested PCR, 1st PCR and 2nd PCR represent two separate runs, products of 1st PCR (no dilution) are used as amplification templates in 2nd PCR; For standard PCR, primers in 2nd PCR are used alone to amplify target fragments.