Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity: recombinase sites are encoded in a synthetic chromosome, and tightly controlled induction of a modified recombinase creates a population of targeted structural variations. We used this method to scramble large regions of two yeast chromosomes: yeast synthetic chromosome arm synIXR, with 43 recombinase target sites, and synthetic region synVIL, with 5 recombinase sites. Deconvolving the scrambled genomes provides insight into genome structure and function and reveals whether off-target activity or ectopic recombinations interfere with the synthetic design