#Data Arrangement: #For the 4x4 tables, each starting pair needs its own table. #This is the AA table: # 5' --> 3' # AX # TY # 3' <-- 5' # Y-> # ---------------------------- # (X) A C G U # | ---------------------------- # V # (A) 4.0 5.2 4.7 4.3 # (C) 4.0 5.2 4.7 4.3 # (G) 4.0 5.2 4.7 4.3 # (U) 4.0 5.2 4.7 4.3 #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' AX TY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 4.0 5.2 4.7 4.3 C 4.0 5.2 4.7 4.3 G 4.0 5.2 4.7 4.3 U 4.0 5.2 4.7 4.3 # 5' --> 3' CX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -4.6 -4.2 -4.7 -5.0 C -4.6 -4.2 -4.7 -5.0 G -4.6 -4.2 -4.7 -5.0 U -4.6 -4.2 -4.7 -5.0 # 5' --> 3' GX CY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -6.2 -3.3 -5.1 -0.9 C -6.2 -3.3 -5.1 -0.9 G -6.2 -3.3 -5.1 -0.9 U -6.2 -3.3 -5.1 -0.9 # 5' --> 3' GX TY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -3.0 -0.1 -1.9 2.3 C -3.0 -0.1 -1.9 2.3 G -3.0 -0.1 -1.9 2.3 U -3.0 -0.1 -1.9 2.3 # 5' --> 3' TX AY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.3 1.7 0.7 -5.8 C 2.3 1.7 0.7 -5.8 G 2.3 1.7 0.7 -5.8 U 2.3 1.7 0.7 -5.8 # 5' --> 3' TX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.3 1.7 0.7 -5.8 C 2.3 1.7 0.7 -5.8 G 2.3 1.7 0.7 -5.8 U 2.3 1.7 0.7 -5.8