#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) -0.7 -0.3 -0.5 0.0 # (C) -0.6 -0.2 0.0 -0.3 # (G) -0.6 0.0 -0.4 -0.5 # (U) 0.0 -0.3 -0.5 -0.4 #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' AX TY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.7 -0.3 -0.5 0.0 C -0.6 -0.2 0.0 -0.3 G -0.6 0.0 -0.4 -0.5 U 0.0 -0.3 -0.5 -0.4 # 5' --> 3' CX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -1.0 -0.8 -0.9 0.0 C -0.8 -0.5 0.0 -0.7 G -1.0 0.0 -0.9 -1.0 U 0.0 -0.6 -0.9 -0.9 # 5' --> 3' GX CY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -1.0 -0.7 -0.8 0.0 C -1.0 -0.6 0.0 -0.7 G -1.0 0.0 -1.0 -0.8 U 0.0 -0.6 -0.9 -0.9 # 5' --> 3' GX TY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.2 -0.5 -0.6 C -0.2 -0.2 -0.9 -0.2 G -0.5 -0.9 -0.5 -0.5 U -0.5 -0.2 -0.5 -0.2 # 5' --> 3' TX AY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 -0.4 -0.5 0.0 C -0.5 -0.2 0.0 -0.5 G -0.6 -0.0 -0.4 -0.5 U 0.0 -0.3 -0.6 -0.3 # 5' --> 3' TX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.2 -0.5 -0.5 C -0.2 -0.2 -0.8 -0.2 G -0.5 -1.0 -0.5 -0.5 U -0.5 -0.2 -0.5 -0.2