FIG 4.

Illustration of a “fuzzy” junction caused by an adjacent direct repeat. The black letters represent the sequence where the polymerase detaches (donor site), and the gray letters represent the sequence where polymerase reinitiates (acceptor site). The arrows represent the actual path of the polymerase, and the underlined letters denote the direct repeat sequence. The resulting DIP-associated sequences are represented by the black and gray letters to highlight the donor and acceptor sites, respectively. The junction sites reported by ViReMa are at the bottom and use the following nomenclature: DonorSite_AcceptorSite. Note that ViReMa was adjusted to push the junction site toward the 3′ site of the direct repeat. The left side illustrates a situation where no direct repeats are present and, as a result, ViReMa reports the correct junction. On the right, a situation where a direct repeat of 2 nucleotides is present, resulting in ambiguity. In this case, ViReMa pushes the junction toward the 3′ end of the repeat and incorrectly reports the junction as 5 to 7′ (5_7′). Shown are three possible paths for the polymerase that yield different junction locations with the same sequence. In all cases, the junction will be reported as 5_7′.