Figure 2

Naming convention for FAPs. This example from chr1:154,126,854-154,134,237 (7,384 bp) illustrates the FAP naming convention. The central Alu is always the element being evaluated and the second member of the pair is designated by its sequential separation from the central Alu. The central Alu is designated with the number '0'. The absolute value of the sequential separation of a given Alu element from the central Alu is defined as its APSN. Additionally, Alu elements located 5' of the central Alu are assigned a negative value and with a positive value if located 3' of the central Alu. APSN: Alu pair sequence number; FAP: full-length Alu pair.