Table 1.
Datasets used in the study
| Species | VNTR composite family | Subfamilies | Number of elements analyzed | Remarks |
|---|---|---|---|---|
| Macaca mulatta (MMU) | SVA2MMU | 30 | ||
| Nomascus leucogenys (NLE) | SVA2NLE | 30 | ||
| SVANLE (SINE-R-VNTR-Alu) | 26 | |||
| PVA (PTGR2-VNTR-Alu) | 89 | Only elements displaying a 5’ complete VNTR (i.e. containing at least the 3’ part of the Alu-like region) | ||
| FVA (FRAM-VNTR-Alu) | 7 | |||
| LAVA (L1-Alu-VNTR-Alu) | LAVA_A – LAVA_F (22 subfamilies) | 5, 10 or 20 per subfamily, representing 5-10% of the subfamily members | Only elements displaying a 5’ complete VNTR (i.e. containing at least the 3’ part of the Alu-like region) | |
| Pongo abelii (PA) | SVA (SINE-R-VNTR-Alu) | SVAPA_1 - SVAPA_11 (11 subfamilies) | 5, 10 or 20 per subfamily | For the younger subfamilies SVAPA_7 to SVAPA_11 5’ truncated elements and elements with assembly gaps had to be taken into account to obtain consensus VNTR schemes with sufficient support |
| Pan troglodytes (Pt) | SVA (SINE-R-VNTR-Alu) | SVA_PtA | 83 | Only elements with full-length VNTR |
| Homo sapiens (HSA) | SVA (SINE-R-VNTR-Alu) | SVA_A – SVA_F (6 subfamilies) | 10 per subfamily | Only full-length elements |