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Table 7 Free energy parameters for internal loops.

From: Computational RNA secondary structure design: empirical complexity and improved methods

Parameter Explanation Values
ΔG-length-I(n) Destabilizing energy of internal loop of size n (n = 4, 5, 6,...) 1.7, 1.8, 2.0,...
ΔG-length-B(n) Destabilizing energy of bulge of size n (n = 1, 2, 3,...) 3.8, 2.8, 3.2,...
ΔG-Internal-n (s i , s j , si+1, sj-1) Terminal mismatch free energy of closing base pair (s i ·s j ) and neighbouring free bases si+1and sj-1 -1.1, -0.7, -0.4, 0.0 and 0.7
ΔG-Asymmetry(l1, l2) Penalty for asymmetric internal loops m i n = { 3 0.5 | l 1 l 2 | MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaieGacqWFTbqBcqWFPbqAcqWFUbGBcqGH9aqpdaGabeqaauaabaqaceaaaeaacqaIZaWmaeaacqaIWaamcqGGUaGlcqaI1aqncqGHflY1daabdaqaaiabdYgaSnaaBaaaleaacqaIXaqmaeqaaOGaeyOeI0IaemiBaW2aaSbaaSqaaiabikdaYaqabaaakiaawEa7caGLiWoaaaaacaGL7baaaaa@4222@