Figure 2

Examples of association of maximal repeats (MR). The MRs A and B are surrounded by rectangles. The spacer sequence between two MRs is denoted x or y and is underlined. Modules, created by the assembly of A, B and x or y, are surrounded by large rectangles. Case a) is the most simple case of association of maximal repeats A and B: the distance between them is always smaller than the size of the smallest MR B and they can be safely associated. Case b) shows that two occurrences of MR can be separated by any sequence, including the empty one. In case c), the distance between occurrences of A and B is equal to the size of the largest maximal repeat and spacers have to be checked for their similarity. The edit distance between sequences x and y equals 2, a value smaller than the sizes of A and B, and a module can be built. In case d), the size of x and y equals 4 as in case c), but x is at edit distance 4 from y, which is greater than 3, the size of B. The association of MRs A and B do not form a module in this case.