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(Color online) Interaction energies (in arbitrary units) between pairs of nucleotides. We use the color code shown on the right to represent interaction strengths. We obtained the singlestrand stacking energies from experimental data reported in Ref. [60] (Chap. 8), and the hydrogen bonding and cross-stacking energies from the duplex stacking enthalpies used in the Turner Rules [60] (Chap. 8).
