Dot plot- analysis of tandem arrays reveals higher-order structure. For each dot-plot shown, the type of repeat, chromosomal location and stringency (window size and % homology) are indicated. Black dots and horizontal lines represent tandem orientation, whereas blue dots and vertical lines represent inverted orientation. The repeat masker tracks for each region are shown below. A-G) Arrays are listed in Table 1. The Repeat Masker tracks indicate a large continuous domain of satellite DNA. A) 70.7 kb array of hsatII from 16q11.2 at low stringency, showing dense pattern indicative of homologous satellite DNA. A large inversion is seen in this array. ~20 kb of neighboring non-satellite DNA is also shown. B) 121 kb array of GsatII from 12p11.1, showing complex multiple inversions within this array. C) Same region as in B at increased stringency, showing 3 distinct domains of homology within overall array. D) Same array as in A at increased stringency, showing higher-order repeats in proximal 50 kb in both orientations. E) ~100 kb array of GAATG on Yq11.1, showing the 3.36 kb higher-order repeats in the distal 60 kb region. F) The 100 kb array of GAATG on Yq12, showing the 3.6 kb HOR across the entire sequenced array. G) The 61 bp VNTR from Xp22.33 at high stringency showing complex higher-order structure. H-L) Arrays listed in Table 2. The Repeat Masker tracks show repetitive patterns containing the different classes of transposable elements. H) The array containing the CT47 genes. I) The DMBT gene, showing the internal repetitive domain structure. J) The LPA gene, showing the internal repetitive domain structure. K) The 54.5 kb array of 5.4 kb megasatellite repeats, each of which contains a Mer33 repeat. L) The 51.4 kb array containing the ~6.0 kb Acro repeats. This array has an inversion in orientation of the repeat units, indicated by the vertical lines visible on the dotplot.