tstacki.ent

mfold

Data Arangement:                                                                                
                                                                                                
                 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'         
   .     .     .   -0.68   .     .     .   -0.68   .     .     .   -0.42 -0.81 -0.19 -0.58  0.00
   .     .   -1.61   .     .     .   -0.58   .     .     .   -0.97   .   -0.52 -0.10  0.00 -0.29
   .   -0.58   .    0.16   .   -0.52   .    0.06   .   -1.32   .    0.16 -0.68  0.00 -0.29 -0.77
 -0.81   .    0.16   .   -0.52   .    0.06   .   -0.68   .    0.16   .    0.00 -0.81 -0.97 -0.64
                                                                                                
                                                                                                
          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'         
   .     .     .   -0.71   .     .     .   -0.39 -0.58 -0.39 -0.68  0.00   .     .     .   -0.35
   .     .   -1.06   .     .     .   -0.61   .   -0.52 -0.29  0.00 -0.55   .     .   -0.61   .  
   .   -0.39   .    0.06   .   -0.29   .    0.06 -1.32  0.00 -0.64 -0.61   .   -0.81   .    0.06
 -0.19   .    0.06   .   -0.10   .    0.06   .    0.00 -0.81 -1.61 -1.42 -0.81   .    0.06   .  
                                                                                                
                                                                                                
          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'         
   .     .     .   -0.61 -1.61 -1.06 -0.84  0.00   .     .     .   -0.35  0.16  0.06  0.16 -1.00
   .     .   -0.84   .   -0.58 -0.61  0.00 -0.84   .     .   -1.39   .    0.06  0.06 -1.16  0.06
   .   -0.68   .    0.16 -0.97  0.00 -1.39 -0.94   .   -0.64   .    0.16  0.16 -1.61  0.16 -0.48
 -0.58   .    0.16   .    0.00 -0.61 -1.16 -1.68 -0.29   .    0.16   .   -0.97  0.06 -0.48  0.06
                                                                                                
                                                                                                
          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'         
 -0.68 -0.71 -0.61  0.00   .     .     .   -0.71  0.16  0.06  0.16 -0.58   .     .     .   -0.64
 -0.68 -0.10  0.00 -0.71   .     .   -0.84   .    0.06  0.06 -0.94  0.06   .     .   -1.68   .  
 -0.42  0.00 -0.35 -0.58   .   -0.55   .    0.06  0.16 -0.61  0.16 -0.48   .   -1.42   .    0.06
  0.00 -0.35 -1.00 -0.64 -0.29   .    0.06   .   -0.77  0.06 -0.48  0.06 -0.64   .    0.06   .