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| Subtype in the env region of CRFs | Predicted #CRFs having subtype X | Predicted #CRFs using jpHMM | Actual #CRFs containing the subtype | Predicted #sequences containing subtype X | Actual #sequences containing subtype X | Sensitivity |
| A | 16 | 17 | 18 | 376 | 383 | 98.17% |
| B | 11 | 12 | 16 | 59 | 86 | 68.61% |
| C | 4 | 4 | 4 | 24 | 24 | 100.0% |
| D | 3 | 3 | 5 | 9 | 23 | 39.13% |
| F | 9 | 9 | 10 | 52 | 54 | 96.30% |
| G | 10 | 13 | 14 | 59 | 69 | 85.51% |
| H | 2 | 2 | 2 | 8 | 8 | 100% |
| J | 2 | 2 | 3 | 20 | 23 | 86.96% |
