Figure 3.

Example of possible distributions of repetitive elements. The top line represents a genome with three copies of the same repeat (white rectangular boxes). Smaller boxes represent reads. Gray parts of the reads indicate a repetition of this part of the read in the GSS dataset. Four different scenarios are shown: (i) No read (GSS) covers a repeat – no repetitive sequences can be found; (ii) one repeat is covered by three reads, but only the marked regions will occur twice; (iii) the beginning of two repeats is represented in the GSS dataset, but only this part can be found twice, from two different copies of the repeat; (iv) the initial parts of all repeats are covered, resulting in a partial coverage of the repeat.