Table 1. Density of PONDS-forming repeats.
| Repeat type | Length (bp) | Spacer (bp) | Contr1 (n/kb) | Contr2 (n/kb) | Trans (n/kb) | Delet (n/kb) |
|---|---|---|---|---|---|---|
| DR | 3 – 100 | 0 | 0.2483 | 0.2678 | 0.3446 | 0.2766 |
| IR | 7 – 30 | 0 – 7 | 1.0639 | 1.0381 | 1.2008 | 1.1944 |
| H-DNA | 6 – 50 | 0 – 7 | 1.2274 | 1.2704 | 1.4444 | 1.2288 |
| G4-DNA | 15 – 90 | 1 – 7 | 0.1234 | 0.1457 | 0.1576 | 0.1316 |
| Z-DNA | 10 – 120 | 0 | 0.1120 | 0.1162 | 0.1239 | 0.1221 |
| Sum | 2.7750 | 2.8382 | 3.2713 | 2.9535 |
DR, direct repeats; IR, inverted repeats; H-DNA, triplex-forming homopurine•homopyrimidine runs with mirror repeat symmetry; G4-DNA, G-quartet-forming sequences of ≥4 runs of GGG each separated by 1–7 bases, but excluding homoG•homoC runs; Z-DNA, alternating purine-pyrimidine motifs (pure or mixed A-C, G-C, G-T runs). Length, min and max lengths of repeats. For DR, length refers to the length of each unit, for IR and H-DNA it signifies the length of each of the two stems, for G4-DNA it indicates the total length of a tract including spacer sequences between the G runs, and for Z-DNA it includes the total number of bases. For DR, the minimum number of repeat units was set to 5. Spacer, number of bases separating two units. Contr1, 1-kb bins flanking 20 222 randomly generated genomic coordinates; Contr2, 1-kb bins flanking 19 935 genomic coordinates, each located 3000 bp upstream (lower genomic coordinate; N-containing bins were excluded) of their respective translocation breakpoints; Trans, 1-kb bins flanking 19 947 translocation breakpoints; Delet, 1-kb bins flanking 46 365 deletion breakpoints; n/kb, density of motifs in number per kb; Sum, sum of all densities.