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Quality of the predictions involving multiple alignments. The weights assigned to the aligned sequences are calculated using a BLOSUM weight scheme at a fractional identity of 0.80. LRG and PHAT columns correspond to the substitution matrices used by the SVM.
| Substitution Matrix | LRG | PHAT |
| Accuracy | 95.0 | 95.0 |
| Sensitivity | 31.3 | 31.3 |
| Specificity | 99.8 | 99.8 |
| Pnon-IPM | 92.3 | 93.8 |
| PIPM | 95.0 | 95.0 |
| CPM | 0.52 | 0.53 |
