Table 4.
Increase in number of annotated interspersed repeats, using Dfam + nhmmer
| Interspersed repeats (count) | All repeats (count) | Increase (count) | ||
|---|---|---|---|---|
| Human | Consensus | 3 743 222 | 4 532 893 | |
| Dfam | 4 007 051 | 4 708 414 | 175 521 | |
| Mouse | Consensus | 3 112 647 | 4 691 497 | |
| Dfam | 3 640 848 | 5 152 510 | 461 013 | |
| Zebrafish | Consensus | 2 757 001 | 3 577 995 | |
| Dfam | 3 058 971 | 3 790 149 | 212 154 | |
| Fly | Consensus | 22 819 | 119 232 | |
| Dfam | 24 676 | 120 868 | 1636 | |
| Nematode | Consensus | 46 566 | 80 064 | |
| Dfam | 71 855 | 103 212 | 23 148 |
For each organism, RepeatMasker was run using (i) cross_match with consensus sequences from the Repbase-derived RepeatMasker library and (ii) nhmmer with Dfam2. Interspersed repeats are shown separately, while the all repeats count also includes locally repetitive satellites and short tandem repeats.