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We describe a method to make physical maps of genomes using correlative hybridization patterns of probes to random pools of BACs. We derive thereby an estimated distance between probes, and then use this estimated distance to order probes. To test the method, we used BAC libraries from Schizzosaccharomyces pombe. We compared our data to the known sequence assembly, in order to assess accuracy. We demonstrate a small number of significant discrepancies between our method and the map derived by sequence assembly. Some of these discrepancies may arise because genome order within a population is not stable; imposing a linear order on a population may not be biologically meaningful.