1. A method of mapping a region of a genome comprised of the steps: (a) obtaining nucleic acid material from a genome; (b) constructing a clone library and a long-range probe library from said nucleic acid material; (c) hybridizing labeled long-range probes to the clone library to form pairing between homologous nucleic acid sequences; (d) detecting the labels of the long-range probes paired with the clone library to form signals; (e) recording the signals to form a set of data; and (f) combining said set of data with calibration information in a computing device with memory to construct a map of the clones which covers the region of the genome.