Last modified on 18 April 2012.
Table 2. Base-Pair Stack Statistics
| Base pair 1 | Base pair 2 | Decomp base-pair SE | Decomp stacking SE | Decomp. base pair + stack SE | BP-ST SE | Exp BP-ST energy | Difference of decomp. BP-ST SE and exp BP-ST energy |
|---|---|---|---|---|---|---|---|
| CG | CG | -3.1814 | -0.2416 | -3.01 | -2.43 | -2.40 | 0.61 |
| GC | CG | -3.2819 | -0.2444 | -3.12 | -3.40 | -3.30 | -0.18 |
| GC | GC | -3.3824 | -0.0578 | -3.03 | -2.70 | -3.40 | -0.37 |
| GU | CG | -1.7603 | -0.1206 | -1.47 | -2.32 | -2.10 | -0.63 |
| GU | GC | -1.8608 | -0.1169 | -1.57 | -2.35 | -2.50 | -0.93 |
| GU | GU | -0.3392 | -0.1761 | -0.11 | 0.14 | 1.30 | 1.41 |
| UG | CG | -1.7240 | -0.2009 | -1.52 | -1.76 | -1.40 | 0.12 |
| UG | GC | -1.8245 | -0.2202 | -1.64 | -1.93 | -1.50 | 0.14 |
| UG | GU | -0.3029 | -0.0461 | 0.06 | -0.83 | -0.50 | -0.56 |
| UG | UG | -0.2667 | -0.1602 | -0.02 | -1.22 | 0.30 | 0.32 |
| AU | CG | -2.6577 | 0.1496 | -2.10 | -3.19 | -2.10 | 0.00 |
| AU | GC | -2.7583 | -0.0203 | -2.37 | -3.09 | -2.20 | 0.17 |
| AU | GU | -1.2367 | 0.1435 | -0.68 | -2.03 | -1.40 | -0.72 |
| AU | UG | -1.2004 | 0.2242 | -0.57 | -1.33 | -0.60 | -0.03 |
| AU | AU | -2.1341 | 0.4631 | -1.26 | -1.65 | -1.10 | 0.16 |
| UA | CG | -2.8042 | 0.0226 | -2.37 | -3.19 | -2.10 | 0.27 |
| UA | GC | -2.9048 | -0.0084 | -2.50 | -2.91 | -2.40 | 0.10 |
| UA | GU | -1.3832 | 0.1658 | -0.81 | -1.62 | -1.30 | -0.49 |
| UA | UG | -1.3469 | 0.1261 | -0.81 | -1.07 | -1.00 | -0.19 |
| UA | AU | -2.2806 | 0.4795 | -1.39 | -2.53 | -0.90 | 0.49 |
| UA | UA | -2.4271 | 0.4124 | -1.61 | -2.04 | -1.30 | 0.31 |
For each base-pair stack, the decomposed base-pair SE, decomposed stacking SE, base-pair stack energy computed from the decomposition model (Eq. (6)), base-pair stack SE, experimental base-pair stack energy (kcal/mol), and the difference between the sum of decomposed base-pair and stack SEs and experimental base-pair stack energy derived from experiment are presented. SE are in units of kcal/mol and are derived from statistics using all sequences.
