| Hairpin | Positiona | Regionb | Scorec | Mature 5’arm | Mature 3’arm |
| MD11 | 2086 - 2179 | NS5A | 209.6 | AUCCGGAUCCCCAGGCUCCCCC | AAGAAUAGGACUCAACGUCGGA |
| MD36 | 8468 - 8563 | E1 | 201.7 | GCUCCCGACAAGCAGAUCGAUA | GGGGAGUUUGCCGUCCCUGGUG |
| MD19 | 4340 - 4458 | E2 | 188.2 | GUGAUUGGGUGCGUCAGGGUGA | UGUAUAGCAGGGGUGUUGGCCC |
| MD18 | 4062 - 4146 | NS4B | 179.5 | GGGACGCGGUCUGCAGGAGGCC | UGAACUGCUCAGCGAGCAUCAU |
| MD3 | 968 - 1086 | NS5B | 164.8 | GGCGGAGUACCUGGUCAUAGCC | GCCGCGUCCUCCUGGACCCCCG |
| MD39 | 9406 - 9490 | 5’-UTR | 164.2 | UCCAGGCAUUGAGCGGGUUUAU | CAAUUCCGGUGUACUCACCG |
| MD30 | 7705 - 7783 | E2 | 158.5 | CUGUAGGUAGGCGCGCCCGACC | CCACGGGGCUGGGAGUGAAGC |
| MD1 | 432 - 533 | NS5B | 152.9 | UUGAAGAGGUACUUGCCACAUA | CUCUGGACAGAAGCCUAGCGCG |
| MD26 | 5952 - 6053 | NS3 | 148.1 | AAGGUCUUGGUCCACAUUGGUA | CUUGGGUGAUGCGAUGGUCCUC |
| MD14 | 2348 - 2414 | NS5A | 144.5 | UAGCGGGCAGCCAUGGACCACA | AGGCUUUUUCCACGUCUCUAC |