tstackh.dgd

mfold

Data Arangement: v 3.1a 
  
                 Y 
         ------------------ 
     (X)  A    C    G    T 
         ------------------ 
             5' ==> 3' 
                AX 
                AY 
             3' <== 5' 
     (A)   .     .     .     . 
     (C)   .     .     .     . 
     (G)   .     .     .     . 
     (T) -0.70 -0.10 -0.70 -0.10 
  
-------------------------------- 
STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. 
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    T        A    C    G    T        A    C    G    T        A    C    G    T 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         AX                      AX                      AX                      AX 
         AY                      CY                      GY                      TY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
   .     .     .   -0.60   .     .     .   -0.50   .     .     .   -0.60 -0.70 -0.30 -0.50 -0.90  
   .     .   -1.00   .     .     .   -1.00   .     .     .   -1.00   .   -0.60 -0.20 -1.00 -0.30 
   .   -1.00   .   -0.50   .   -0.80   .   -0.20   .   -1.00   .   -0.50 -0.60 -1.00 -0.40 -0.50 
 -0.70   .   -0.50   .   -0.60   .   -0.20   .   -0.60   .   -0.50   .   -0.78 -0.30 -0.50 -0.40 
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    T        A    C    G    T        A    C    G    T        A    C    G    T 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         CX                      CX                      CX                      CX 
         AY                      CY                      GY                      TY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
   .     .     .   -0.40   .     .     .   -0.20 -1.00 -0.80 -0.90 -1.00   .     .     .   -0.30 
   .     .   -0.70   .     .     .   -0.60   .   -0.80 -0.50 -1.00 -0.70   .     .   -0.60   .  
   .   -0.80   .   -0.20   .   -0.50   .   -0.20 -1.00 -1.00 -0.90 -1.00   .   -0.60   .   -0.20 
 -0.30   .   -0.20   .   -0.20   .   -0.20   .   -1.00 -0.60 -0.90 -0.90 -0.30   .   -0.20   .  
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    T        A    C    G    T        A    C    G    T        A    C    G    T 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         GX                      GX                      GX                      GX 
         AY                      CY                      GY                      TY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
   .     .     .   -0.50 -1.00 -0.70 -0.80 -1.00   .     .     .   -0.40 -0.50 -0.20 -0.50 -0.60 
   .     .   -0.80   .   -1.00 -0.60 -1.00 -0.70   .     .   -1.00   .   -0.20 -0.20 -0.90 -0.20 
   .   -0.90   .   -0.50 -1.00 -1.00 -1.00 -0.80   .   -0.90   .   -0.50 -0.50 -0.90 -0.50 -0.50 
 -0.50   .   -0.50   .   -1.00 -0.60 -0.90 -0.90 -0.40   .   -0.50   .   -0.50 -0.20 -0.50 -0.20 
  
  
          Y                       Y                       Y                       Y 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    T        A    C    G    T        A    C    G    T        A    C    G    T 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         TX                      TX                      TX                      TX 
         AY                      CY                      GY                      TY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
 -0.60 -0.40 -0.50 -0.60   .     .     .   -0.50 -0.50 -0.20 -0.50 -0.50   .     .     .   -0.30 
 -0.50 -0.20 -1.00 -0.50   .     .   -0.70   .   -0.20 -0.20 -0.80 -0.20   .     .   -0.90   .  
 -0.60 -1.00 -0.40 -0.50   .   -0.70   .   -0.20 -0.50 -1.00 -0.50 -0.50   .   -0.90   .   -0.20 
 -0.80 -0.30 -0.60 -0.30 -0.30   .   -0.20   .   -0.50 -0.20 -0.50 -0.20 -0.40   .   -0.20   .