We are designing to generate a very complicated mouse model, basically we are trying to make conditional knockout models for 2 genes that are very close to each other. We're thinking about doing multiple rounds of ES cell targeting, but the question is how can we test if the changes are on the same allele? We are using Frt to flanking one gene and lox for the second gene. The closest Frt and lox are ~75 kb. If using Southern, is it possible to separate DNA more than 75 kb? If using FISH, can FISH detect such a small fragment as Frt site? Any other suggestions would be highly appreciated.