Table 2.
Compared with RepeatMasker, LongRepMarker found repeat families and their detailed numbers on the Ant dataset
| LongRepMarker (reference-assisted mode) | LongRepMarker (de novomode) | RepeatMasker | ||||||
|---|---|---|---|---|---|---|---|---|
| Super-Family | Family | Amount | Super-Family | Family | Amount | Super-Family | Family | Amount |
| LTR | Copia | 150 | LTR | Copia | 18 | LTR | Copia | 4 |
| LTR | Gypsy | 1608 | LTR | Gypsy | 145 | LTR | Gypsy | 17 |
| LTR | Pao | 981 | LTR | Pao | 69 | LTR | Pao | 17 |
| LTR | DIRs | 4 | LTR | DIRs | 1 | LTR | DIRs | 0 |
| LTR | ERV1 | 2 | LTR | ERV1 | 1 | LTR | ERV1 | 3 |
| LTR | Gypsy-Cigr | 1 | LTR | Gypsy-Cigr | 1 | LTR | Gypsy-Cigr | 1 |
| LTR | Caulimovirus | 1 | LTR | Caulimovirus | 1 | LTR | Caulimovirus | 0 |
| LTR | Ngaro | 1 | LTR | Ngaro | 1 | LTR | Ngaro | 1 |
| LTR | ERVL-MaLR | 1 | LTR | ERVL-MaLR | 1 | LTR | ERVL-MaLR | 1 |
| LTR | Other | 4 | LTR | Other | 1 | LTR | Other | 0 |
| LINE | Penelope | 1007 | LINE | Penelope | 172 | LINE | Penelope | 5 |
| LINE | CR1 | 6 | LINE | CR1 | 5 | LINE | CR1 | 9 |
| LINE | I | 40 | LINE | I | 6 | LINE | I | 0 |
| LINE | R1 | 269 | LINE | R1 | 34 | LINE | R1 | 5 |
| LINE | RTE-X | 20 | LINE | RTE-X | 12 | LINE | RTE-X | 6 |
| LINE | R2-NeSL | 7 | LINE | R2-NeSL | 11 | LINE | R2-NeSL | 0 |
| LINE | Other | 5 | LINE | Other | 1 | LINE | Other | 3 |
| DNA | Maverick | 2381 | DNA | Maverick | 136 | DNA | Maverick | 4 |
| DNA | Kolobok-Hydra | 81 | DNA | Kolobok-Hydra | 5 | DNA | Kolobok-Hydra | 0 |
| DNA | Kolobok-T2 | 1122 | DNA | Kolobok-T2 | 97 | DNA | Kolobok-T2 | 26 |
| DNA | TcMar-Mariner | 2275 | DNA | TcMar-Mariner | 257 | DNA | TcMar-Mariner | 2228 |
| DNA | TcMar-Tc4 | 185 | DNA | TcMar-Tc4 | 78 | DNA | TcMar-Tc4 | 3 |
| DNA | TcMar | 49 | DNA | TcMar | 21 | DNA | TcMar | 1 |
| DNA | TcMar-Tc1 | 1317 | DNA | TcMar-Tc1 | 227 | DNA | TcMar-Tc1 | 136 |
| DNA | Merlin | 16 | DNA | Merlin | 18 | DNA | Merlin | 1 |
| DNA | hAT | 14 | DNA | hAT | 16 | DNA | hAT | 8 |
| DNA | hAT-Blackjack | 37 | DNA | hAT-Blackjack | 41 | DNA | hAT-Blackjack | 2 |
| DNA | Other | 119 | DNA | Other | 96 | DNA | Other | 10 |
| RC | Helitron | 153 | RC | Helitron | 37 | RC | Helitron | 16 |
| Unknown | Other | 13308 | Unknown | Other | 7400 | Unknown | Other | 8332 |