Figure 1

Tartan-checked structure of SDs visualized using SHEAP. Diagonal lines aligned in the same column or row represent repetitive sequences. The lower left triangle of each panel shows a self-plot of the sequence after known repeat sequences have been masked using RepeatMasker. Each of the upper right triangles shows a self-plot of the intact sequence. (A) All of the SDs detected by SHEAP for all chromosomes except Chr Y. Rough estimates of the genomic positions of segmental duplications were: Chr. X-1, 33,454–43,954 (10,500); Chr. 12, 25,264–32,863 (7,599); Chr. 14–1, 8,647–14,424 (5,776); Chr. 7–1, 10,860–14,710 (3850); Chr. 7–4, 24,250–28,000 (3,750); Chr. 14–2, 45,553–49,106 (3,553); Chr. 2 T, 177,898–181,042 (3,144); Chr. 7–5, 34,938–37,919 (2,981); Chr. X-3, 122,800–125,582 (2,782); Chr. 5–2, 96,512–99,314 (2,802); Chr. X-4, 146,542–148,959 (2417); Chr. X-2, 53,082–54,812 (1730); Chr. 4–2, 61,950–64,050 (2,100); Chr. 13–2, 67,076–68,893 (1817); Chr. 4–1, 42,923–44,207 (1284); Chr. 7–2, 11,339–12,249 (910); Chr. 13–1, 62,919–64,168 (1,249); Chr. 5–1, 11,973–13,221 (1,249); Chr. 7–3, 12,327–13,309 (982); Chr. 13–3, 68,702–69,433 (730). Numbers in parentheses indicate the sizes of SDs (kbp). (B) Higher magnification for the self-plot of SD13M, located from 65,370,000 to 67,000,000 on Chr 13. The diagonal lines from top left to bottom right, which indicate a complete match between SD13M sequences, were eliminated by the algorithm. To remove redundant and overlapping sequences from 2,638 repetitive sequences, the sequences represented by diagonal lines that were located in the same column or in the same row (enclosed by two lines in the horizontal and vertical directions, respectively) were eliminated.