Bridging of repeat elements by paired read libraries. (a) The percentage of each repeat type per window of 1000 repeats (y-axis) is shown, relative to the size of each repeat on the x-axis. A higher density of dots indicates the presence of more repeats in the indicated size bin. (b) Pie chart of the largest classes of repetitive elements based on their total length (Mb) in the rat genome. Satellite repeats, RNA repeats, and low-complexity repeats are listed as “Other.” (c + d) Bridging by paired-tag libraries of all annotated LINEs (c) and LTRs (d) within contigs of RGSC 3.4. The size of LINE elements or LTRs (x-axis) is plotted against the percentage of elements of that specific size that were bridged by one or more read-pairs from each of the libraries. All single library datasets were normalized to 8.5× physical genome coverage.