Organization of the Ty1 polypurine tracts. (A) A Ty1 element showing the locations of the long terminal repeats (triangles), the GAG and POL genes, the integrase-coding domain (IN), the central polypurine tract (cPPT), the central termination sequence (CTS), and the polypurine tract (PPT). The sequences of the wild-type cPPT and the cppt-74 mutant (30) are shown below. (B) The Ty1 central DNA flap is created when the 5′ end of the plus strand initiated at the cPPT is displaced by the 3′ end of plus-strand DNA. The size and position of the DNA flaps are determined by the CTS.