The 4 × 4 tables for stacking and terminal stacking energies are indexed as follows: X refers to row and Y to column. Thus an energy for the stacked pair
|| Y
|| ------------------
\/ A C G U
would be found in row 2 (C) ------------------
5' --> 3' and column 3 (G). This position 5' --> 3'
AC ----> is marked by an '*' in the AX
UG table on the right. UY
3' <-- 5' 3' <-- 5'
. . . .
. . * .
. . . .
. . . .
An entry containing a single dot ('.') refers to a not yet assigned
energy. All Watson-Crick and wobble stacking energies are defined.
Stacking energies for non-canonical base pairs are not yet available.
Each 1 × 4 table for single base stacking at the ends of helices contains 4 entries, corresponding to the unpaired base. These are also referred to as dangling base energies.
These energies are purely from entropic effects, and there are consequently no enthalpies. The energies for internal, bulge and hairpin loops depend on the numbers in the loop table, plus other terms. The details may be found here.