Table 3 Different types of repeat sequences found in the Suijing18 (SJ18) assembly (version 1).
Repeat_Type | SJ18 | Nipponbare | R498 | |||
|---|---|---|---|---|---|---|
Length (bp) | % | Length (bp) | % | Length (bp) | % | |
Class I: Retrotransposon | 94,087,436 | 22.3 | 105,098,791 | 28.2 | 117,509,061 | 30.1 |
LTR-Retrotransposon | 88,392,161 | 21.0 | 98,903,987 | 26.5 | 111,173,484 | 28.4 |
LTR/Gypsy | 72,477,718 | 17.2 | 65,915,787 | 17.7 | 80,330,011 | 20.6 |
LTR/Copia | 14,161,220 | 3.4 | 17,931,866 | 4.8 | 15,079,454 | 3.9 |
LTR/Other | 1,753,223 | 0.4 | 15,056,334 | 4.0 | 15,764,019 | 4.0 |
Non-LTR Retrotransposon | 5,695,275 | 1.4 | 6,194,804 | 1.7 | 6,335,577 | 1.6 |
SINE | 362,005 | 0.1 | 796,311 | 0.2 | 848,061 | 0.2 |
LINE | 5,333,270 | 1.3 | 5,398,493 | 1.5 | 5,487,516 | 1.4 |
Class II: DNA Transposon | 69,249,868 | 16.4 | 40,716,340 | 10.9 | 40,743,536 | 10.4 |
EnSpm/CACTA | 10,690,200 | 2.5 | 14,117,095 | 3.8 | 13,264,041 | 3.4 |
hAT | 5,494,725 | 1.3 | 1,641,580 | 0.4 | 1,897,505 | 0.5 |
Harbinger | 9,746,844 | 2.3 | 3,729,352 | 1.0 | 3,882,866 | 1.0 |
Tc1/Mariner | 6,525,750 | 1.6 | 462,697 | 0.1 | 607,903 | 0.2 |
MuDR | 16,081,157 | 3.8 | 5,872,349 | 1.6 | 5,993,554 | 1.5 |
Helitron | 12,538,290 | 3.0 | 1,850,232 | 0.5 | 1,702,664 | 0.4 |
Other | 8,172,902 | 1.9 | 13,043,035 | 3.5 | 13,395,003 | 3.4 |
Other tandem repeat | 18,811,934 | 4.5 | 3,935,022 | 1.1 | 4,548,484 | 1.2 |
Low Complexity | 313,050 | 0.1 | 22,478 | 0.0 | 17,672 | 0.0 |
Unclassified | 13,830,076 | 3.3 | 1,117,819 | 0.3 | 1,607,036 | 0.4 |
Total | 196,292,364 | 46.5 | 150,890,450 | 40.4 | 164,425,789 | 42.1 |
