Table 2.
Repeats Present at CNV Breakpointsa
| Subject | Left Breakpoint Repeat | Right Breakpoint Repeat | Microhomology (bp) | % Identity of Repeatsb |
|---|---|---|---|---|
| A1 | AluSxc | AluY | 26 | 81.7 |
| A2c | AluSx | AluSx1 | complex | complex |
| A3 | AluSx1c | AluY | 7 | 86.9 |
| A4 | AluSx1c | AluSp | 15 | 84.8 |
| A5 | AluSx1c | AluSp | 9 | 88.6 |
| A6 | AluY | AluSx3c | 21 | 84.6 |
| A8 | AluSx1c | AluSp | 15 | 84.8 |
| A9 | AluSx1c | AluSp | 15 | 84.8 |
| A10 | AluSz6 | AluSg | 31 | 80.1 |
| BAB 3166 | – | – | 6 | – |
| BAB 5112 | L1PA5 | L1PA7 | 21 | 90.6 |
| BAB 3200 | AluSc | – | complex | – |
| BAB 3327 | AluSxc | AluY | 26 | 81.7 |
| SPAST_1 | AluSx1c | AluSp | 15 | 84.8 |
| SPAST_3 | – | – | 4 | – |
| Spain 1 | L1PA5 | AluJb | 4 | – |
| Spain 2 | – | AluSp | 2 | – |
| Spain 3 | AluSz6 | – | 2 | – |
| Spain 4 | AluSq | L1M4 | 8 | – |
| Spain 5 | AluSz | AluSz | 26 | 80.6 |
| Spain 6 | AluSg4 | – | 1 | – |
| Spain 7 | AluSc | AluY | 15 | 84.6 |
| Spain 8 | AluSg4 | AluYc | 9 | 83.7 |
| Spain 9 | – | – | 6 | – |
| JKF B | AluSg | AluY | 14 | 82.1 |
| JKF C | AluSz | AluSxc | 35 | 82.8 |
| Ruhr 3 | AluJo | AluJb | 19 | 77.6 |
| Ruhr 4 | AluSz | AluY | 25 | 75.8 |
| Ruhr 5 | AluJo | AluJb | 19 | 77.6 |
| Ruhr 6 | Tigger4a | AT_rich | 1 bp ins | – |
| Ruhr 7 | AluSp | AluSp | 8 | 87.9 |
| Ruhr 9 | AluSx3 | AluSzc | 5 | 82.7 |
| Ruhr 10 | AluSx3 | AluSzc | 5 | 82.7 |
| Ruhr 11 | AluSx1 | AluSz | 38 | 82.7 |
| Ruhr 12 | AluSx | AluSx3 | 9 | 77.4 |
| Ruhr 13 | AluSz6 | AluSp | 24 | 84.4 |
| Ruhr 14 | AluJb | AluSzc | 18 | 77.6 |
| Ruhr 15 | AluJo | AluY | 22 | 79.9 |
| Ruhr 16 | AluSx | AluSp | 20 | 79.1 |
| Ruhr 17 | – | – | 3 | – |
| Ruhr 18 | AluSz6 | AluSp | 24 | 84.4 |
| Ruhr 21 | AluY | AluSp | 33 | 83.2 |
| Ruhr 23 | AluY | AluSz | 11 | 85.6 |
| Ruhr 26d | NA | NA | NA | NA |
| Ruhr 27 | AluY | AluSp | complex | complex |
| Ruhr 28 | – | L1M4 | 4 | – |
| Ruhr 29 | L1MC2 | L1M5 | 0 | – |
| Ruhr 31 | AluYc | AluY | 5 | 90.7 |
| Ruhr 32d | NA | NA | NA | NA |
| Park 1 | AluSx1 | AluSp | 7 | 80.7 |
| Park 2 | – | FLAM_C | 3 | – |
| Park 3 | AluYc | AluSxc | 8 | 81.1 |
| Park 4 | – | AluSq | 4 | – |
| A37 | AluY | AluY | 8 | 89.4 |
| A38 | AluY | AluSx3 | complex | complex |
| A39 | AluSxc | AluY | 26 | 81.7 |
| Iwanaga | – | AluSx3 | 1 | – |
| Mitne-Neto | – | L1M7 | 0 | – |
| Miura | AluSx1 | AluJb | 9 | 77.1 |
Left, telomeric; right, centromeric; –, not applicable or no repeat present.
a
All Alu-Alu and LINE-LINE pairs are in matching genomic orientation (both negative or both positive) (Table S1, Figure 2A), with the exception of Ruhr 29.
b
Number of identical bases divided by smaller repeat length. Comparison by Needleman-Wunsch Global Alignment algorithm.
c
Repeat contains the consensus 13-nt sequence associated with meiotic recombination hotspots, some NAHR breakpoint regions, and bound in vitro by PRDM9.42, 43, 44 The Alu from which the inserted sequence in the complex A2 rearrangement derives contains this sequence.
d
Breakpoint unable to be sequenced (Ruhr 26) or failed breakpoint PCR (Ruhr 32).