Analysis of chromosomes from FOARLYS+ cells generated in the presence of excess Rap1p. Chromosomes were isolated from the parent strain (YJS), a strain containing the C1–3A/TG1–3 direct repeat recombination assay 20 kb from the telomere on chromosome VII-L (YJS2) and the same strain expressing excess Rap1p (YJS2–FATRAP) (see Materials and Methods). Chromosomes were separated using a 1.5% agarose gel using a CHEF gel apparatus. The filter was hybridized with probe A. Chromosome II, which contains the endogenous LYS2 locus (chr II), and chromosome VII, where the LYS2 gene and C1–3A/TG1–3 direct repeats were integrated (chr VII), are indicated.