#Data table for symetric interior loops of size 2 #Free energies at 37 degrees for RNA #Data Arrangement: #For the 4x4 tables, each starting pair needs its own table. #This is the AA table: # 5' --> 3' # X # A A # U U # Y # 3' <-- 5' # Y-> # ---------------------------- # (X) A C G U # | ---------------------------- # V # (A) 1.9 1.9 1.9 1.9 # (C) 1.9 1.9 1.9 1.9 # (G) 1.9 1.9 -0.7 1.9 # (U) 1.9 1.9 1.9 1.5 #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' X A A U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.5 # 5' --> 3' X A C U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 0.8 # 5' --> 3' X A G U C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 0.8 # 5' --> 3' X A U U A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.2 # 5' --> 3' X A G U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.6 # 5' --> 3' X A U U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.2 # 5' --> 3' X C A G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.2 # 5' --> 3' X C C G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 0.9 -0.4 0.5 0.5 C 0.3 0.5 0.5 0.6 G -0.1 0.5 -2.2 0.5 U 0.5 0.0 0.5 -0.1 # 5' --> 3' X C G G C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 0.9 0.5 0.5 0.5 C 0.5 0.5 0.5 0.5 G 0.5 0.5 -1.4 0.5 U 0.5 0.5 0.5 0.4 # 5' --> 3' X C U G A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 0.8 # 5' --> 3' X C G G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.2 1.3 1.2 1.2 C 1.2 1.7 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.1 # 5' --> 3' X C U G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 0.6 0.5 1.2 1.2 C 1.2 1.2 1.2 1.2 G -0.2 1.2 -1.4 1.2 U 1.2 1.0 1.2 1.1 # 5' --> 3' X G A C U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.2 # 5' --> 3' X G C C G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 0.8 0.5 0.5 0.5 C 0.5 0.5 0.5 0.5 G 0.5 0.5 -2.3 0.5 U 0.5 0.5 0.5 -0.6 # 5' --> 3' X G G C C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 0.9 0.3 -0.1 0.5 C -0.4 0.5 0.5 0.0 G 0.5 0.5 -2.2 0.5 U 0.5 0.6 0.5 -0.1 # 5' --> 3' X G U C A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 0.8 # 5' --> 3' X G G C U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.6 1.2 1.0 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 0.7 # 5' --> 3' X G U C G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.2 1.5 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.5 # 5' --> 3' X U A A U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.7 # 5' --> 3' X U C A G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.2 # 5' --> 3' X U G A C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.2 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.2 # 5' --> 3' X U U A A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.5 # 5' --> 3' X U G A U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.9 # 5' --> 3' X U U A G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.6 # 5' --> 3' X G A U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.6 # 5' --> 3' X G C U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.5 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.5 # 5' --> 3' X G G U C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 0.6 1.2 -0.2 1.2 C 0.5 1.2 1.2 1.0 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.1 # 5' --> 3' X G U U A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.2 # 5' --> 3' X G G U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.6 # 5' --> 3' X G U U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.2 # 5' --> 3' X U A G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.9 # 5' --> 3' X U C G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.6 1.2 1.2 1.2 C 1.2 1.2 1.2 1.2 G 1.0 1.2 -1.4 1.2 U 1.2 1.2 1.2 0.7 # 5' --> 3' X U G G C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.2 1.2 1.2 1.2 C 1.3 1.7 1.2 1.2 G 1.2 1.2 -1.4 1.2 U 1.2 1.2 1.2 1.1 # 5' --> 3' X U U G A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.6 # 5' --> 3' X U G G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.9 # 5' --> 3' X U U G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 1.9 1.9 1.9 1.9 C 1.9 1.9 1.9 1.9 G 1.9 1.9 -0.7 1.9 U 1.9 1.9 1.9 1.6