Figure 5.

Imperfect direct repeats can result in paired end tags (PETs) longer than expected. PETS for bases 10,941,077-10,960,123 of chromosome I are shown. Below the line in green are the normal sized PETs. Above the line longer, potentially aberrant, PETs are shown. The longer PETs are in regions lacking normal sequence coverage. Typically, the left end of the longer tags detects unique sequence and the right end is aligned with one of a group of imperfect direct repeats producing longer than normal PETs of differing sizes.