Fig. 1.

(Left) Simplified representation of a SD lifetime. Initially, a large-scale duplication forms an SD, at which point both the original region and the copy are identical. Then, both the original region and copy undergo various independent changes, such as large-scale deletions (in red), insertions (in blue), and small repeat insertions (in fuchsia). Finally, various germline mutations (in yellow) affect both regions. The resulting SD as seen today, defined as the pair $(G_{i:i+n},G_{j:j+m})$, is shown in the third row. (Right) Shows the idealized Jaccard similarity between the k-mer sets X_i and X_j corresponding to the G_i and G_j, respectively. Note that some repeats also increase the proportion of shared k-mers. Colors denote same as on Left