Figure 1.

The example of paired-end reads and their alignments in MEI regions. (A) A paired-end read consists of two mates from both ends of a DNA segment. The distance between two mates is determined. (B) An MEI is inserted between two mates, and because the MEI is not present in the reference genome, the distance between the two mates is shorter when mapping the mates to the reference genome. (C) The orange-colored mate is well mapped to the reference genome while the other mate is highly similar to a mobile-element sequence. (D) The blue-colored mate crosses an MEI breakpoint and thus alignment of it can be divided into two parts. The first partial alignment is still in the reference genome and the second partial alignment is in the mobile-element sequence.