#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