Table 3.
Read Pair Counts for Alternative Repeat Conformations
| Spanning Read Pairs |
||||
| Region ID | Region Environmenta | All | Fixed Distance | Compatible Conformations |
| A. Repeat R1 (28,763 bp) | ||||
| R1a | Violet-R1-Green | 72 | 58 | C1, C3, C4, C7 |
| R1b | Cyan-R1-Red | 59 | 53 | C1, C3, C4, C7 |
| R1c | Violet-R1-Red | 67 | 58 | C2, C5, C6, C8 |
| R1d | Cyan-R1-Green | 72 | 61 | C2, C5, C6, C8 |
| 230 | All (×2) | |||
| B. Repeat R2 (2,742 bp) | ||||
| R2a | Green-R2-Red | 283 | 54 | C1, C2, C4, C6 |
| R2b | Yellow-R2-Pink | 356 | 81 | C1, C2, C4, C6 |
| R2c | Green-R2-Pink | 202 | 33 | C3, C5, C7, C8 |
| R2d | Yellow-R2-Red | 196 | 37 | C3, C5, C7, C8 |
| 205 | All (×2) | |||
| C. Repeat R3 (9,620 bp) | ||||
| R3a | Violet-R3-Yellow | 130 | 27 | C1, C2, C3, C5 |
| R3b | Pink-R3-Cyan | 241 | 65 | C1, C2, C3, C5 |
| R3c | Violet-R3-Cyan | 217 | 52 | C4, C6, C7, C8 |
| R3d | Pink-R3-Yellow | 265 | 72 | C4, C6, C7, C8 |
| 216 | All (×2) | |||
| D. Segment R2 + R3 (29,250 bp) | ||||
| R3a + R2b | Violet-R3-Yellow-R2-Pink | 22 | 19 | C1, C2 |
| R3a + R2d | Violet-R3-Yellow-R2-Red | 16 | 14 | C3, C5 |
| R3d + R2b | Pink-R3-Yellow-R2-Pink | 54 | 48 | C4, C6 |
| R3d + R2d | Pink-R3-Yellow-R2-Red | 23 | 19 | C7, C8 |
| 100 | All | |||
| E. Single-copy regionsb | ||||
| SC1 | Red (40 kb) | 517 | 76 | All |
| SC2 | Red (110 kb) | 555 | 109 | All |
| SC3 | Green (190 kb) | 604 | 115 | All |
| SC4 | Violet (275 kb) | 529 | 91 | All |
| SC5 | Violet (355 kb) | 565 | 110 | All |
| SC6 | Pink (460 kb) | 646 | 136 | All |