Table 1 Summary of different repeat types and their prevalence
Type | Subclass | Superfamily | No. of families | No. of elements | Length (Mb) | % of genome |
|---|---|---|---|---|---|---|
Class I: Retroelements | LTR-RT | Gypsy | 1345 | 277,258 | 349.9 | 31.5 |
Copia | 422 | 117,165 | 153.7 | 13.8 | ||
Unknown | 161 | 78,351 | 80 | 7.2 | ||
LINE | LINE | 4655 | 92,325 | 26.3 | 2.4 | |
SINE | SINE | 41 | 7378 | 1.3 | 0.1 | |
Class II: DNA Transposons | TIR | Mutator | 35 | 5549 | 1 | 0.1 |
PIF | 72 | 8778 | 1.8 | 0.2 | ||
hAT | 89 | 13,004 | 2.6 | 0.2 | ||
CACTA | 215 | 26,852 | 4.7 | 0.4 | ||
Tc1 | 959 | 112,087 | 20.8 | 1.9 | ||
Other | 1 | 143,640 | 6 | 0.5 | ||
Helitron | – | 362 | 123,538 | 27.4 | 2.5 | |
Tandem repeats | – | 1 | 143,640 | 6 | 0.5 | |
Total | – | 681.5 | 61.3 |
