#Data table for symetric interior loops of size 2 #Free energies at 37 degrees for DNA #Data Arrangement: #For the 4x4 tables, each starting pair needs its own table. #This is the AA table: # 5' --> 3' # X # A A # T T # Y # 3' <-- 5' # Y-> # ---------------------------- # (X) A C G U # | ---------------------------- # V # (A) 12.9 1.5 10.7 1.5 # (C) 10.4 14.7 10.4 -1.6 # (G) 1.8 1.5 1.6 1.5 # (U) 10.4 3.5 10.4 -4.8 #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' X A A T T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 12.9 1.5 10.7 1.5 C 10.4 14.7 10.4 -1.6 G 1.8 1.5 1.6 1.5 U 10.4 3.5 10.4 -4.8 # 5' --> 3' X A C T G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 10.9 8.9 10.9 C 4.1 12.8 4.1 1.3 G 4.5 10.9 -5.0 10.9 U 4.1 11.6 4.1 0.5 # 5' --> 3' X A G T C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 5.0 3.9 -6.3 3.9 C 5.3 2.6 5.3 -4.9 G -2.2 3.9 -9.9 3.9 U 5.3 -12.3 5.3 -7.5 # 5' --> 3' X A T T A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 4.9 9.8 7.1 9.8 C 9.8 7.5 9.8 4.3 G 7.1 9.8 4.1 9.8 U 9.8 4.3 9.8 5.7 # 5' --> 3' X A G T T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 5.0 3.9 -6.3 3.9 C 5.3 2.6 5.3 -4.9 G -2.2 3.9 -9.9 3.9 U 5.3 -12.3 5.3 -7.5 # 5' --> 3' X A T T G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 10.9 8.9 10.9 C 4.1 12.8 4.1 1.3 G 4.5 10.9 -5.0 10.9 U 4.1 11.6 4.1 0.5 # 5' --> 3' X C A G T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 13.2 11.3 13.2 C 9.6 5.9 9.6 0.1 G 6.9 13.2 -1.1 13.2 U 9.6 3.0 9.6 0.7 # 5' --> 3' X C C G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 4.6 1.3 4.6 C 9.3 7.5 9.3 1.9 G 3.9 4.6 -0.9 4.6 U 9.3 0.5 9.3 2.1 # 5' --> 3' X C G G C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 4.0 5.1 6.1 5.1 C 5.1 4.1 5.1 1.6 G 6.1 5.1 0.1 5.1 U 5.1 1.6 5.1 -2.7 # 5' --> 3' X C T G A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 5.0 5.3 -2.2 5.3 C 3.9 2.6 3.9 -12.3 G -6.3 5.3 -9.9 5.3 U 3.9 -4.9 3.9 -7.5 # 5' --> 3' X C G G T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 4.0 5.1 6.1 5.1 C 5.1 4.1 5.1 1.6 G 6.1 5.1 0.1 5.1 U 5.1 1.6 5.1 -2.7 # 5' --> 3' X C T G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 4.6 1.3 4.6 C 9.3 7.5 9.3 1.9 G 3.9 4.6 -0.9 4.6 U 9.3 0.5 9.3 2.1 # 5' --> 3' X G A C T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -1.4 13.2 11.3 13.2 C 4.2 12.9 4.2 -0.4 G 6.9 13.2 3.4 13.2 U 4.2 3.7 4.2 -10.0 # 5' --> 3' X G C C G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.6 3.9 2.4 3.9 C 3.9 6.0 3.9 -0.6 G 2.4 3.9 -2.8 3.9 U 3.9 -0.6 3.9 0.3 # 5' --> 3' X G G C C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 9.3 3.9 9.3 C 4.6 7.5 4.6 0.5 G 1.3 9.3 -0.9 9.3 U 4.6 1.9 4.6 2.1 # 5' --> 3' X G T C A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 4.1 4.5 4.1 C 10.9 12.8 10.9 11.6 G 8.9 4.1 -5.0 4.1 U 10.9 1.3 10.9 0.5 # 5' --> 3' X G G C T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 9.3 3.9 9.3 C 4.6 7.5 4.6 0.5 G 1.3 9.3 -0.9 9.3 U 4.6 1.9 4.6 2.1 # 5' --> 3' X G T C G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.6 3.9 2.4 3.9 C 3.9 6.0 3.9 -0.6 G 2.4 3.9 -2.8 3.9 U 3.9 -0.6 3.9 0.3 # 5' --> 3' X T A A T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 12.1 14.3 11.9 14.3 C 14.3 17.4 14.3 2.5 G 11.9 14.3 8.4 14.3 U 14.3 2.5 14.3 6.2 # 5' --> 3' X T C A G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -1.4 4.2 6.9 4.2 C 13.2 12.9 13.2 3.7 G 11.3 4.2 3.4 4.2 U 13.2 -0.4 13.2 -10.0 # 5' --> 3' X T G A C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 9.6 6.9 9.6 C 13.2 5.9 13.2 3.0 G 11.3 9.6 -1.1 9.6 U 13.2 0.1 13.2 0.7 # 5' --> 3' X T T A A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 12.9 10.4 1.8 10.4 C 1.5 14.7 1.5 3.5 G 10.7 10.4 1.6 10.4 U 1.5 -1.6 1.5 -4.8 # 5' --> 3' X T G A T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 9.6 6.9 9.6 C 13.2 5.9 13.2 3.0 G 11.3 9.6 -1.1 9.6 U 13.2 0.1 13.2 0.7 # 5' --> 3' X T T A G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -1.4 4.2 6.9 4.2 C 13.2 12.9 13.2 3.7 G 11.3 4.2 3.4 4.2 U 13.2 -0.4 13.2 -10.0 # 5' --> 3' X G A T T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -1.4 13.2 11.3 13.2 C 4.2 12.9 4.2 -0.4 G 6.9 13.2 3.4 13.2 U 4.2 3.7 4.2 -10.0 # 5' --> 3' X G C T G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.6 3.9 2.4 3.9 C 3.9 6.0 3.9 -0.6 G 2.4 3.9 -2.8 3.9 U 3.9 -0.6 3.9 0.3 # 5' --> 3' X G G T C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 9.3 3.9 9.3 C 4.6 7.5 4.6 0.5 G 1.3 9.3 -0.9 9.3 U 4.6 1.9 4.6 2.1 # 5' --> 3' X G T T A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 4.1 4.5 4.1 C 10.9 12.8 10.9 11.6 G 8.9 4.1 -5.0 4.1 U 10.9 1.3 10.9 0.5 # 5' --> 3' X G G T T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 9.3 3.9 9.3 C 4.6 7.5 4.6 0.5 G 1.3 9.3 -0.9 9.3 U 4.6 1.9 4.6 2.1 # 5' --> 3' X G T T G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 2.6 3.9 2.4 3.9 C 3.9 6.0 3.9 -0.6 G 2.4 3.9 -2.8 3.9 U 3.9 -0.6 3.9 0.3 # 5' --> 3' X T A G T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 10.0 13.2 11.3 13.2 C 9.6 5.9 9.6 0.1 G 6.9 13.2 -1.1 13.2 U 9.6 3.0 9.6 0.7 # 5' --> 3' X T C G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 4.6 1.3 4.6 C 9.3 7.5 9.3 1.9 G 3.9 4.6 -0.9 4.6 U 9.3 0.5 9.3 2.1 # 5' --> 3' X T G G C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 4.0 5.1 6.1 5.1 C 5.1 4.1 5.1 1.6 G 6.1 5.1 0.1 5.1 U 5.1 1.6 5.1 -2.7 # 5' --> 3' X T T G A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 5.0 5.3 -2.2 5.3 C 3.9 2.6 3.9 -12.3 G -6.3 5.3 -9.9 5.3 U 3.9 -4.9 3.9 -7.5 # 5' --> 3' X T G G T Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A 4.0 5.1 6.1 5.1 C 5.1 4.1 5.1 1.6 G 6.1 5.1 0.1 5.1 U 5.1 1.6 5.1 -2.7 # 5' --> 3' X T T G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.6 4.6 1.3 4.6 C 9.3 7.5 9.3 1.9 G 3.9 4.6 -0.9 4.6 U 9.3 0.5 9.3 2.1