The ordering of yeast artificial chromosome (YAC) clones by sequence-tagged site (STS)-content mapping has proven an effective means of constructing large, contiguously cloned arrays of DNA, some of which span almost entire human chromosomes (1). This method requires that each YAC clone be tested for the presence or absence of each STS in a simple binary fashion and ultimately results in a content map where each clone is identified and positioned relative to others based on its complement of STSs (2,3). The application of this technique to the long-range physical mapping of the genomes of more complex organisms, although powerful, is complicated by the fact that precise distance and positional information cannot be derived directly from the STS content of each clone.