Deducing the fate of the parental form following recombination. (A) Graph depicting deep sequence coverage of the least predominant environment (the invading strand parental form) around each repeat. This is measured by quantifying the changes in read depth across flanking regions compared to wild type. Repeats were sorted by average activity, with first-generation msh1 repeats shown in gray and advanced-generation results shown in black. Class I repeats show significant reduction of the invading strand parental form in the resulting recombinant, and class II repeats retain the parental form in high copy numbers following recombination. Mapping of class I repeats gives the appearance of deletion in the recombinant. (B) DNA gel blot hybridization experiments with repeat DD and repeat F as probes show examples of class I and class II recombination outcomes in an advanced-generation msh1 mutant. P1 and P2 designate parental configurations, and R is the recombinant form. Additional bands in the msh1 lane probed with repeat F represent secondary recombinations, defined as events that depend on novel genomic environments created by primary recombination to occur.