tstacki.dg

mfold

Data Arangement: 
  
                 Y 
         ------------------ 
     (X)  A    C    G    U 
         ------------------ 
             5' ==> 3' 
                AX 
                AY 
             3' <== 5' 
     (A)   .     .     .     . 
     (C)   .     .     .     . 
     (G)   .     .     .     . 
     (U) -0.70 -0.10 -0.70 -0.10 
  
-------------------------------- 
STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. 
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         AX                      AX                      AX                      AX 
         AY                      CY                      GY                      UY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .   -1.00   .     .     .   -1.00   .     .     .   -2.20 -1.00 -1.00 -2.20 -0.50 
  .     .   -1.50   .     .     .   -1.50   .     .     .   -2.70   .   -1.00 -1.00 -0.20 -1.00 
  .   -1.50   .   -1.00   .   -1.50   .   -1.00   .   -2.70   .   -2.20 -2.20 -0.50 -1.00 -0.50 
-1.00   .   -1.50   .   -1.00   .   -1.50   .   -2.20   .   -2.70   .   -0.30 -1.00 -0.30 -2.00 
  
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         CX                      CX                      CX                      CX 
         AY                      CY                      GY                      UY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .   -1.00   .     .     .   -1.00 -1.50 -1.50 -2.70 -1.90   .     .     .   -1.00 
  .     .   -1.50   .     .     .   -1.50   .   -1.50 -1.50 -1.00 -1.50   .     .   -1.50   . 
  .   -1.50   .   -1.00   .   -1.50   .   -1.00 -2.70 -1.90 -1.50 -1.90   .   -1.50   .   -1.00 
-1.00   .   -1.50   .   -1.00   .   -1.50   .   -1.40 -1.50 -1.40 -2.50 -1.00   .   -1.50   . 
  
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         GX                      GX                      GX                      GX 
         AY                      CY                      GY                      UY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .   -2.20 -1.50 -1.50 -2.70 -1.30   .     .     .   -1.00 -1.50 -1.50 -2.70 -1.30 
  .     .   -2.70   .   -1.50 -1.50 -0.60 -1.50   .     .   -1.50   .   -1.50 -1.50 -0.60 -1.50 
  .   -2.70   .   -2.20 -2.70 -1.50 -1.50 -1.50   .   -1.50   .   -1.00 -2.70 -1.50 -1.50 -1.50 
-2.20   .   -2.70   .   -0.80 -1.50 -0.80 -2.50 -1.00   .   -1.50   .   -0.80 -1.50 -0.80 -2.50 
  
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         UX                      UX                      UX                      UX 
         AY                      CY                      GY                      UY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-1.00 -1.00 -2.20 -0.40   .     .     .   -1.00 -1.00 -1.00 -2.20 -0.40   .     .     .   -2.00 
-1.00 -1.00 +0.20 -1.00   .     .   -1.50   .   -1.00 -1.00 +0.20 -1.00   .     .   -2.50   . 
-2.20 -0.40 -1.00 -0.40   .   -1.50   .   -1.00 -2.20 -0.40 -1.00 -0.40   .   -2.50   .   -2.00 
+0.20 -1.00 +0.20 -2.00 -1.00   .   -1.50   .   +0.20 -1.00 +0.20 -2.00 -2.00   .   -2.50   .