Table 2. Transposable elements (TEs) in the R. oryzae genome.
| Elements | Total basesa | % of assembly | Sequence identity (%)b | ESTc |
| Class I transposons | 5,589,511 | 12.13 | ||
| LTR elements / Ty3 | 3,700,795 | 8.03 | 97% | Yes |
| LINES | 1,742,093 | 3.78 | 97% | Yes |
| DIRS | 146,622 | 0.32 | 97% | Yes |
| Class II transposons | 3,462,307 | 7.50 | ||
| Mariners | 1,666,728 | 3.62 | 98% | Yes |
| En/Spn | 314,481 | 0.68 | 98% | No |
| Tigger | 262,307 | 0.57 | 94% | No |
| Crypton | 191,823 | 0.42 | 98% | No |
| Helitron | 66,534 | 0.14 | 99% | No |
| Total | 9,051,818 | 19.63 |
a
The genomic distribution of the representative elements was identified using the sensitive mode of RepeatMasker version open-3.0.8, with cross_match version 0.990329.
b
Sequence identity was computed based on the average identity of the full-length copies of each representative against the consensus sequence of each group.
c
EST reads overlap with the identified TEs (see Table S6).