#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) . . . -1.0 # (C) . . -1.4 . # (G) . -1.3 . +0.7 # (U) -0.9 . +0.1 . #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' AX TY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A . . . -1.0 C . . -1.4 . G . -1.3 . +0.7 U -0.9 . +0.1 . # 5' --> 3' CX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A . . . -1.5 C . . -1.8 . G . -2.2 . -0.5 U -1.3 . -0.3 . # 5' --> 3' GX CY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A . . . -1.3 C . . -2.2 . G . -1.8 . +0.1 U -1.4 . -0.6 . # 5' --> 3' GX TY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A . . . +0.3 C . . -0.6 . G . -0.3 . +0.7 U +0.1 . +1.2 . # 5' --> 3' TX AY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A . . . -0.6 C . . -1.3 . G . -1.5 . +0.4 U -1.0 . +0.3 . # 5' --> 3' TX GY # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A . . . +0.4 C . . +0.1 . G . -0.5 . +0.5 U +0.7 . +0.7 .