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3.4 Case Studies

1. HIV‑1 TAR RNA (58 nt) – FPRE080 recovers the canonical hairpin with 100 % base‑pair agreement, while LinearFold misses the GU wobble at the loop closure.
2. Ribosomal RNA fragment (274 nt) – The method correctly predicts a large internal bulge that is energetically unfavorable in the full Turner model but is captured after parameter pruning.

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