Schematic for adapter and primer design for the two rare cutters EcoRI and PstI and the frequent cutter MseI

Adapters consist of a core sequence (black) and an enzyme-specific sequence (red). The enzyme-specific sequence allows the ligation of the adapters to the resulting restriction fragments (green) without restoring the original restriction sites. In this way, ligated adapters create a target site for the AFLP primers in the subsequent amplification reactions. For this purpose, primer design matches the core (black), the enzyme-specific (red) and the restriction-site remnant (green) sequence. Primers may have one or a number of additional bases at the 3-end extending into the restriction fragments, called the selective nucleotides (represented by N, in blue). AFLP primers are named [+0] when they have no selective bases (only the core, enzyme-specific and restriction-site remnant sequence), [+1] when they have a single selective base, [+2] when they have two selective bases, and so on. Adapters and primers for other restriction enzymes are similar to these but have enzyme-specific parts corresponding to the respective enzymes.