Table 3.
Partial comparison of the proportion and detailed classification of detected repeats generated based on two databases of the Drosophila genome
| Combination of RepBase and Dfam [bases masked: 20.85%] | msRepDB [bases masked: 21.86%] | |||||
|---|---|---|---|---|---|---|
| Repeat types | Number of elements | Length occupied | Percentage of sequences | Number of elements | Length occupied | Percentage of sequences |
| Retroelements | 15 330 | 21 048 835 bp | 14.65% | 23 186 | 22 483 014 bp | 15.64% |
| +SINEs | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +Penelope | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +LINEs | 5293 | 5 447 560 bp | 4.49% | 6134 | 6 416 652 bp | 4.46% |
| ++CRE/SLACS | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++L2/CR1/Rex | 811 | 844 019 bp | 0.59% | 870 | 841 783 bp | 0.59% |
| +++R1/LOA/Jockey | 1014 | 1 562 240 bp | 1.09% | 1571 | 1 694 722 bp | 1.18% |
| +++R2/R4/NeSL | 38 | 39 896 bp | 0.03% | 38 | 39 900 bp | 0.03% |
| +++RTE/Bov-B | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++L1/CIN4 | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +LTR elements | 10 037 | 14 601 275 bp | 10.16% | 16 914 | 16 066 362 bp | 11.18% |
| ++BEL/Pao | 2326 | 3 123 105 bp | 2.17% | 2937 | 3 118 973 bp | 2.17% |
| ++Tyl/Copia | 500 | 740 782 bp | 0.52% | 784 | 733 449 bp | 0.51% |
| ++Gypsy/DTRS1 | 7211 | 10 737 388 bp | 7.47% | 13 243 | 12 190 939 bp | 8.48% |
| +++Retroviral | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| DNA transposons | 4135 | 1 870 086 bp | 1.30% | 4494 | 1 824 527 bp | 1.27% |
| +hobo-Activator | 189 | 75 919 bp | 0.05% | 168 | 76 244 bp | 0.05% |
| +Tc1-IS630-Pogo | 1112 | 609 344 bp | 0.42% | 1108 | 560 858 bp | 0.39% |
| +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 | 23 | 8619 bp | 0.01% | 23 | 8617 bp | 0.01% |
| +Tourist/Harbinger | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +Other | 2243 | 913 674 bp | 0.64% | 2454 | 894 197 bp | 0.62% |
| Rolling circles | 4662 | 999 082 bp | 0.70% | 5232 | 1 028 233 bp | 0.72% |
| Unclassified | 495 | 78 825 bp | 0.05% | 534 | 121 856 bp | 0.08% |
| Total interspersed repeats | 22 997 746 bp | 16.00% | 24 429 397 bp | 17.00% | ||
| Small RNA | 306 | 86 258 bp | 0.06% | 280 | 95 863 bp | 0.07% |
| Satellites | 1372 | 1 804 199 bp | 1.26% | 1828 | 1 862 670 bp | 1.30% |
| Simple repeats | 85 083 | 3 589 418 bp | 2.50% | 83 836 | 3 525 845 bp | 2.45% |
| Low complexity | 10 443 | 488 602 bp | 0.34% | 10 322 | 482 327 bp | 0.34% |
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.