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Interactions in the unbound RNA
| Interaction | Unbound RNA (MD − LES) | Unbound RNA (MD + LES) | Unbound RNA (experiment) |
| G35–C41 base pair | Lost (only K1) | Lost (K1, K2) | Lost |
| G32–A44 base pair | Preserved | Lost | Lost |
| G43–A33 base pair | Preserved | Lost | No data |
| A30–A44 stack | Lost | Lost | No data |
| A30–A29 stack | Formed | Formed | No data |
| O2′ (A29)–H–N1(A44) | Lost | Lost | Lost |
| N2(G45)–H–O3′ (A33) | Preserved | Lost | No data |
