False clone overlaps caused by repeated sequences. Each thin line represents a BAC clone, and clones with the same color are true overlapping pairs. False overlaps between clones (lines with different colors) are due to highly repeated sequences as well as duplications of small and large regions. Overlaps from highly repetitious sequences are largely dealt with by the overlapper and binner steps and further dealt with at the overlapping BAC detection step. The second and the third situations are dealt with at the bactig linearization step because conflicts can be detected between BACs. For example, in the second case, A/D and B/D clone pairs should overlap based on the clone layout, but this will not be validated.
