Table 2.
Partial comparison of the proportion and detailed classification of detected repeats generated based on two databases of the Human genome
| Combination of RepBase and Dfam [bases masked: 45.62%] | msRepDB [bases masked: 47.29%] | |||||
|---|---|---|---|---|---|---|
| Repeat types | Number of elements | Length occupied | Percentage of sequences | Number of elements | Length occupied | Percentage of sequences |
| Retroelements | 2 800 814 | 1 236 215 277 bp | 37.78% | 3 852 568 | 1 291 793 390 bp | 39.48% |
| +SINEs | 1 453 130 | 369 205 643 bp | 11.28% | 1 602 909 | 329 745 622 bp | 10.08% |
| +Penelope | 75 | 14 277 bp | 0.00% | 75 | 14 225 bp | 0.00% |
| +LINEs | 807 771 | 588 058 432 bp | 17.97% | 1 630 986 | 696 100 321 bp | 21.27% |
| ++CRE/SLACS | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++L2/CR1/Rex | 193 908 | 56 822 264 bp | 1.74% | 294 645 | 69 266 031 bp | 2.12% |
| +++R1/LOA/Jockey | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++R2/R4/NeSL | 399 | 95 545 bp | 0.00% | 400 | 95 122 bp | 0.00% |
| +++RTE/Bov-B | 9 890 | 2 788 967 bp | 0.09% | 9 890 | 2 771 539 bp | 0.08% |
| +++L1/CIN4 | 603 337 | 528 287 954 bp | 16.15% | 1 325 814 | 623 904 329 bp | 19.07% |
| +LTR elements | 539 913 | 278 951 202 bp | 8.53% | 618 673 | 265 947 447 bp | 8.13% |
| ++BEL/Pao | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| ++Tyl/Copia | 0 | 0 bp | 0.00% | 12 | 3718 bp | 0.00% |
| ++Gypsy/DTRS1 | 14 309 | 3 767 626 bp | 0.12% | 15 125 | 3 750 523 bp | 0.11% |
| +++Retroviral | 515 395 | 272 547 814 bp | 8.33% | 593 203 | 259 578 662 bp | 7.93% |
| DNA transposons | 425 304 | 102 360 429 bp | 3.13% | 424 193 | 100 612 296 bp | 3.07% |
| +hobo-Activator | 280 952 | 57 692 527 bp | 1.76% | 280 102 | 56 974 131 bp | 1.74% |
| +Tc1-IS630-Pogo | 128 851 | 41 753 772 bp | 1.28% | 128 539 | 40 749 342 bp | 1.25% |
| +En-Spm | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +MuDR-IS905 | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +PiggyBac | 2310 | 554 582 bp | 0.02% | 2285 | 546 552 bp | 0.02% |
| +Tourist/Harbinger | 321 | 59 199 bp | 0.00% | 320 | 59 104 bp | 0.00% |
| +Other | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| Rolling circles | 1614 | 402 976 bp | 0.01% | 3664 | 1 046 162 bp | 0.03% |
| Unclassified | 122 691 | 24 233 010 bp | 0.74% | 225 158 | 30 427 467 bp | 0.93% |
| Total interspersed repeats | 1 362 808 716 bp | 41.65% | 1 422 833 153 bp | 43.48% | ||
| Small RNA | 12 650 | 1 358 026 bp | 0.04% | 10 142 | 979 175 bp | 0.03% |
| Satellites | 15 404 | 82 714 065 bp | 2.53% | 12 135 | 79 167 870 bp | 2.42% |
| Simple repeats | 710 220 | 39 030 544 bp | 1.19% | 663 652 | 37 699 053 bp | 1.15% |
| Low complexity | 102 465 | 6 353 924 bp | 0.19% | 92 549 | 5 565 612 bp | 0.17% |
The test results were obtained by using RepeatMasker based on the msRepDB database and the combination of Dfam and RepBase respectively under the default parameter settings.