Detecting rearrangements via ST-PGI. In order to evaluate resolution of mapping via ST-PGI, simulated experiments involving a single 24 × 24 array were performed and compared with theoretical calculations (for details, see Methods section). Sampling was performed at 40 tags per 200 kbp BAC in the first experiment (left) and at 80 tags per 200 kbp BAC in the second experiment (right). The percentage of mapped segments of particular lengths was observed. The theoretical calculation is overly optimistic because it assumes that every concatemer can be correctly parsed and every tag mapped.