#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