Figure 12.

Example of hard and soft masks. Genomic sequences are shown below a read where open squares represent nucleotides. In the sequences, the open squares represent matches and the closed squares represent mismatches. The nucleotides contributing to the match length are represented as gray boxes. At the focus position, the match length of the target is 7. The first duplicate is a hard mask because its match length is 13 > 7. The second duplicate is a soft mask because its match length is 7, as the target. The third duplicate is not a mask because its match length is 2 < 7.