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Tutorials:

Turner 2004:

Watson-Crick pairs, self complementary duplex

Watson-Crick pairs, non-self complementary duplex

Terminal mismatches

Hairpin loop, 6 nucleotide hairpin loop with no special stacking terms

Hairpin loop, 5 nucleotide hairpin loop with GG first mismatch

Hairpin loop, 4 nucleotide special hairpin loop

Hairpin loop, 6 nucleotide all C loop

Hairpin loop, 5 nucleotide loop with special GU closure

Bulge loop, single C bulge with multiple states

Bulge loop, 3 nucleotide bulge

Internal loop, 2×2 internal loop

Internal loop, 1×5 internal loop

Internal loop, 2×3 internal loop with stabilizing mismatches

Coaxial stacking, flush coaxial stacking

Coaxial stacking, mismatch-mediated coaxial stacking

Multibranch loops

Turner 1999:

Watson-Crick pairs, self complementary duplex

Watson-Crick pairs, non-self complementary duplex

Terminal mismatches

Hairpin loop, 6 nucleotide hairpin loop with no special stacking terms

Hairpin loop, 5 nucleotide hairpin loop with GA first mismatch

Hairpin loop, 4 nucleotide hairpin loop with tetraloop bonus

Hairpin loop, 6 nucleotide all C loop

Hairpin loop, 5 nucleotide loop with special GU closure

Bulge loop, single C bulge

Bulge loop, 3 nucleotide bulge

Internal loop, 2×2 internal loop

Internal loop, 1×5 internal loop

Internal loop, 2×3 internal loop with stabilizing mismatches

Coaxial stacking, flush coaxial stacking

Coaxial stacking, mismatch-mediated coaxial stacking

Multibranch loops