Table 3.
Number of sequences classified into each category from each search method.
| PR | RVP | RT | RVT_1 | |||||
|---|---|---|---|---|---|---|---|---|
| NT | AA | NT | AA | NT | AA | NT | AA | |
| ERVP | 12 | 12 | 1 | 1 | ||||
| ERV9 | 34 | 31 | 114 | 114 | 22 | 22 | ||
| ERVW | 13 | 13 | 53 | 53 | 10 | 9 | ||
| ERVH | 24 | 22 | 62 | 61 | 11 | 9 | ||
| ERVF | 2 | 2 | ||||||
| ERVFXA | 7 | 7 | ||||||
| ERVFB | 1 | 1 | ||||||
| ERVRB | 1 | 2 | 2 | |||||
| ERVI | 20 | 18 | ||||||
| ERVE | 3 | 3 | 20 | 20 | 3 | 3 | ||
| ERV3 | 2 | 2 | 2 | 2 | 1 | 1 | ||
| ERVT | 4 | 4 | 4 | 4 | ||||
| Gammaretrovirus total | 81 | 75 | 283 | 280 | 51 | 48 | ||
| HK1 | 39 | 39 | 1 | 1 | 16 | 16 | 2 | 2 |
| HK2 | 62 | 60 | 32 | 20 | 53 | 53 | 36 | 35 |
| HK4 | 7 | 7 | 2 | 2 | 6 | 6 | 2 | 2 |
| HK9 (K14C) | 15 | 12 | 2 | 2 | 5 | 5 | 2 | 2 |
| HK10 (KC4) | 5 | 1 | 1 | |||||
| HK3 | 216 | 215 | 22 | 22 | 81 | 80 | 14 | 14 |
| HK5 | 36 | 36 | 38 | 38 | 1 | 1 | ||
| HK6 | 52 | 54 | 11 | 11 | ||||
| HK7 | 3 | 3 | 2 | 2 | 10 | 10 | 7 | 7 |
| HK8 | 34 | 35 | 8 | 8 | 35 | 34 | 17 | 16 |
| Betaretrovirus total | 464 | 461 | 69 | 57 | 260 | 254 | 82 | 79 |
| ERVL | 6 | 6 | 5 | 4 | ||||
| UNPLACED | 16 | 19 | 0 | 18 | 10 | 19 | 10 | 17 |
| INTERNAL | 1 | 1 | ||||||
| Total | 480 | 150 | 572 | 149 | ||||
PR, results from BLAST for HK2 protease; RT, results from BLAST for Phoenix RVT_1 domain of reverse transcriptase; RVP, results from LTRdigest for RVP domain; RVT_1, results from LTRdigest for RVT_1 domain; NT, results classified by their nucleic acid sequence; AA, results classified by their translation.