Figure 4.

Profile scoring used to encode caloric values from the NN thermodynamic model at 37°C with 1 M NaCl. The base and its 5′ NN determine the score for a match; C scores 1300 in positions 1, 10 and 17 of the top sequence (the oligo) because T preceeds it and it scores 1830 in position 18, because C proceeds it. The score position 8 is the sum of the two 5′–3′ mismatch NN values, minus the NN value overcounted in the following match. The AG/TA mismatch data is inverted to demonstrate that the actual 3′–5′ mismatch is equivalent to this standard 5′–3′ representation. The profile score summation, minus the standard initiation penalty of 1.0 kcal/mol is the duplex's free energy summation, 20.91 kcal/mol.