#Data table for symmetric interior loops of size 2 #The Enthalpies at 37 degrees for RNA #Data Arrangement: #For the 4x4 tables, each starting pair needs its own table. #This is the AA table: # 5' --> 3' # X # A A # U U # Y # 3' <-- 5' # Y-> # ---------------------------- # (X) A C G U # | ---------------------------- # V # (A) -0.5 -0.5 -0.5 -0.5 # (C) -0.5 -0.5 -0.5 -0.5 # (G) -0.5 -0.5 -8.3 -0.5 # (U) -0.5 -0.5 -0.5 -3.9 #An energy of "." is "infinity," i.e. not allowed. # 5' --> 3' X A A U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X A C U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -12.3 # 5' --> 3' X A G U C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X A U U A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -7.3 # 5' --> 3' X A G U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X A U U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -7.3 # 5' --> 3' X C A G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -5.5 # 5' --> 3' X C C G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -10.5 -10.5 -10.5 -10.5 C -10.5 -10.5 -10.5 -10.5 G -10.5 -10.5 -18.4 -10.5 U -10.5 -10.5 -10.5 -13.9 # 5' --> 3' X C G G C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -10.5 -10.5 -10.5 -10.5 C -10.5 -10.5 -10.5 -10.5 G -10.5 -10.5 -18.4 -10.5 U -10.5 -10.5 -10.5 -10.5 # 5' --> 3' X C U G A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X C G G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -5.5 # 5' --> 3' X C U G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X G A C U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X G C C G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -10.5 -10.5 -10.5 -10.5 C -10.5 -10.5 -10.5 -10.5 G -10.5 -10.5 -18.4 -10.5 U -10.5 -10.5 -10.5 -17.3 # 5' --> 3' X G G C C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -10.5 -10.5 -10.5 -10.5 C -10.5 -10.5 -10.5 -10.5 G -10.5 -10.5 -18.4 -10.5 U -10.5 -10.5 -10.5 -13.9 # 5' --> 3' X G U C A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -12.3 # 5' --> 3' X G G C U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X G U C G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -12.3 # 5' --> 3' X U A A U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -0.5 # 5' --> 3' X U C A G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X U G A C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -5.5 # 5' --> 3' X U U A A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X U G A U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -0.5 # 5' --> 3' X U U A G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X G A U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X G C U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -12.3 # 5' --> 3' X G G U C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X G U U A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -7.3 # 5' --> 3' X G G U U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X G U U G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -7.3 # 5' --> 3' X U A G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -0.5 # 5' --> 3' X U C G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -8.9 # 5' --> 3' X U G G C Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -5.5 -5.5 -5.5 -5.5 C -5.5 -5.5 -5.5 -5.5 G -5.5 -5.5 -13.4 -5.5 U -5.5 -5.5 -5.5 -5.5 # 5' --> 3' X U U G A Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9 # 5' --> 3' X U G G U Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -0.5 # 5' --> 3' X U U G G Y # 3' <-- 5' # Y # ---------------------------- A C G U # ---------------------------- A -0.5 -0.5 -0.5 -0.5 C -0.5 -0.5 -0.5 -0.5 G -0.5 -0.5 -8.3 -0.5 U -0.5 -0.5 -0.5 -3.9