#Data Arrangement: #For the 4x4 tables, each starting pair needs its own table. #This is the AA table: # 5' --> 3' # AX # UY # 3' <-- 5' # Y-> # ---------------------------- # (X) A C G U # | ---------------------------- # V # (A) -3.9 2.0 -3.5 2.0 # (C) -2.3 6.0 -2.3 -0.3 # (G) -3.1 2.0 -3.5 2.0 # (U) -2.3 4.6 -2.3 -1.7 #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' AX UY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -3.9 2.0 -3.5 2.0 C -2.3 6.0 -2.3 -0.3 G -3.1 2.0 -3.5 2.0 U -2.3 4.6 -2.3 -1.7 # 5' --> 3' CX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -9.1 -5.6 -5.6 -5.6 C -5.7 -3.4 -5.7 -2.7 G -8.2 -5.6 -9.2 -5.6 U -5.7 -5.3 -5.7 -8.6 # 5' --> 3' GX CY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.2 -4.0 -5.6 -4.0 C -7.2 0.5 -7.2 -4.2 G -7.1 -4.0 -6.2 -4.0 U -7.2 -0.3 -7.2 -5.0 # 5' --> 3' GX UY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -3.4 2.0 -3.5 2.0 C -2.3 6.0 -2.3 -0.3 G -0.6 2.0 -3.5 2.0 U -2.3 4.6 -2.3 1.6 # 5' --> 3' UX AY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -4.0 -6.3 -8.9 -6.3 C -4.3 -5.1 -4.3 -1.8 G -3.8 -6.3 -8.9 -6.3 U -4.3 -1.4 -4.3 1.4 # 5' --> 3' UX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -4.8 -6.3 -8.9 -6.3 C -4.3 -5.1 -4.3 -1.8 G 3.1 -6.3 -1.5 -6.3 U -4.3 -1.4 -4.3 1.4