Version 3.0 free energy parameters for RNA folding at 37°

Stacking energies
Terminal mismatch stacking energies (hairpin loops)
Terminal mismatch stacking energies (interior loops)
Single base stacking energies
Loop destabilizing energies
Tetra-loops
Miscellaneous energies

Stacking energies at 37 ° :

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 : 
 
          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'   
   .     .     .     .     .     .     .     .     .     .     .     .     .     .     .   -0.90 
   .     .     .     .     .     .     .     .     .     .     .     .     .     .   -2.20   .   
   .     .     .     .     .     .     .     .     .     .     .     .     .   -2.10   .   -0.60 
   .     .     .     .     .     .     .     .     .     .     .     .   -1.10   .   -1.40   .    
 
          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'   
   .     .     .     .     .     .     .     .     .     .     .   -2.10   .     .     .     .   
   .     .     .     .     .     .     .     .     .     .   -3.30   .     .     .     .     .    
   .     .     .     .     .     .     .     .     .   -2.40   .   -1.40   .     .     .     .   
   .     .     .     .     .     .     .     .   -2.10   .   -2.10   .     .     .     .     .    
 
          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'   
   .     .     .     .     .     .     .   -2.40   .     .     .     .     .     .     .   -1.30 
   .     .     .     .     .     .   -3.40   .     .     .     .     .     .     .   -2.50   .   
   .     .     .     .     .   -3.30   .   -1.50   .     .     .     .     .   -2.10   .   -0.50  
   .     .     .     .   -2.20   .   -2.50   .     .     .     .     .   -1.40   .    1.30   .     
 
          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'   
   .     .     .   -1.30   .     .     .     .     .     .     .   -1.00   .     .     .     .   
   .     .   -2.40   .     .     .     .     .     .     .   -1.50   .     .     .     .     .    
   .   -2.10   .   -1.00   .     .     .     .     .   -1.40   .    0.30   .     .     .     .   
 -0.90   .   -1.30   .     .     .     .     .   -0.60   .   -0.50   .     .     .     .     .

Terminal mismatch stacking energies at 37 ° (hairpin loops):

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'   
   .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.50 -0.30 -0.30 
   .     .     .     .     .     .     .     .     .     .     .     .   -0.10 -0.20 -1.50 -0.20 
   .     .     .     .     .     .     .     .     .     .     .     .   -1.10 -1.20 -0.20  0.20 
   .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.30 -0.60 -1.10 
 
          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'   
   .     .     .     .     .     .     .     .   -1.50 -1.50 -1.40 -1.80   .     .     .     .  
   .     .     .     .     .     .     .     .   -1.00 -0.90 -2.90 -0.80   .     .     .     . 
   .     .     .     .     .     .     .     .   -2.20 -2.00 -1.60 -1.10   .     .     .     .  
   .     .     .     .     .     .     .     .   -1.70 -1.40 -1.80 -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'     
         GX                      GX                      GX                      GX 
         AY                      CY                      GY                      UY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
   .     .     .     .   -1.10 -1.50 -1.30 -2.10   .     .     .     .    0.20 -0.50 -0.30 -0.30 
   .     .     .     .   -1.10 -0.70 -2.40 -0.50   .     .     .     .   -0.10 -0.20 -1.50 -0.20 
   .     .     .     .   -2.40 -2.90 -1.40 -1.20   .     .     .     .   -0.90 -1.10 -0.30  0.00 
   .     .     .     .   -1.90 -1.00 -2.20 -1.50   .     .     .     .   -0.30 -0.30 -0.40 -1.10 
 
          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'   
 -0.50 -0.30 -0.60 -0.50   .     .     .     .   -0.50 -0.30 -0.60 -0.50   .     .     .     .  
 -0.20 -0.10 -1.20 -0.00   .     .     .     .   -0.20 -0.10 -1.70  0.00   .     .     .     . 
 -1.40 -1.20 -0.70 -0.20   .     .     .     .   -0.80 -1.20 -0.30 -0.70   .     .     .     .  
 -0.30 -0.10 -0.50 -0.80   .     .     .     .   -0.60 -0.10 -0.60 -0.80   .     .     .     .

Terminal mismatch stacking energies at 37 ° (interior loops):

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'   
   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70 -0.40  0.70 
   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70  0.70  0.70 
   .     .     .     .     .     .     .     .     .     .     .     .   -0.40  0.70  0.70  0.70 
   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70  0.70  0.00 
 
          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'   
   .     .     .     .     .     .     .     .   -0.00 -0.00 -1.10 -0.00   .     .     .     .  
   .     .     .     .     .     .     .     .   -0.00 -0.00 -0.00 -0.00   .     .     .     . 
   .     .     .     .     .     .     .     .   -1.10 -0.00 -0.00 -0.00   .     .     .     .  
   .     .     .     .     .     .     .     .   -0.00 -0.00 -0.00 -0.70   .     .     .     . 
 
          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'   
   .     .     .     .   -0.00 -0.00 -1.10 -0.00   .     .     .     .    0.70  0.70 -0.40  0.70 
   .     .     .     .   -0.00 -0.00 -0.00 -0.00   .     .     .     .    0.70  0.70  0.70  0.70 
   .     .     .     .   -1.10 -0.00 -0.00 -0.00   .     .     .     .   -0.40  0.70  0.70  0.70 
   .     .     .     .   -0.00 -0.00 -0.00 -0.70   .     .     .     .    0.70  0.70  0.70  0.00 
 
          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'     
         UX                      UX                      UX                      UX 
         AY                      CY                      GY                      UY 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
  0.70  0.70 -0.40  0.70   .     .     .     .    0.70  0.70 -0.40  0.70   .     .     .     .  
  0.70  0.70  0.70  0.70   .     .     .     .    0.70  0.70  0.70  0.70   .     .     .     . 
 -0.40  0.70  0.70  0.70   .     .     .     .   -0.40  0.70  0.70  0.70   .     .     .     .  
  0.70  0.70  0.70  0.00   .     .     .     .    0.70  0.70  0.70  0.00   .     .     .     .

Single base stacking energies at 37 ° :

          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   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 
         A                       C                       G                       U 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .     .     .     .     .     .     .     .     .     .   -0.80 -0.50 -0.80 -0.60 

          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   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 
         A                       C                       G                       U 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .     .     .     .     .     .   -1.70 -0.80 -1.70 -1.20   .     .     .     . 
 
          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   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 
         A                       C                       G                       U 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .     .   -1.10 -0.40 -1.30 -0.60   .     .     .     .   -0.80 -0.50 -0.80 -0.60 
 
          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   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 
         A                       C                       G                       U 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-0.70 -0.10 -0.70 -0.10   .     .     .     .   -0.70 -0.10 -0.70 -0.10   .     .     .     . 
 
          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         A                       A                       A                       A 
         AX                      CX                      GX                      UX 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.10 -0.20 -0.20 
 
          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         C                       C                       C                       C 
         AX                      CX                      GX                      UX 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .     .     .     .     .     .   -0.20 -0.30 -0.00 -0.00   .     .     .     . 
  
          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         G                       G                       G                       G 
         AX                      CX                      GX                      UX 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
  .     .     .     .   -0.50 -0.30 -0.20 -0.10   .     .     .     .   -0.30 -0.10 -0.20 -0.20 
 
          X                       X                       X                       X 
  ------------------      ------------------      ------------------      ------------------ 
   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
  ------------------      ------------------      ------------------      ------------------ 
      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
         U                       U                       U                       U 
         AX                      CX                      GX                      UX 
      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-0.30 -0.30 -0.40 -0.20   .     .     .     .   -0.30 -0.30 -0.40 -0.20   .     .     .     .

Loop free energies at 37 ° :

DESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED) 
hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges 
SIZE         INTERNAL            BULGE            HAIRPIN 
------------------------------------------------------- 
1                .                3.80                . 
2                .                2.80                . 
3                .                3.20              5.70  
4              1.70               3.60              5.60 
5              1.80               4.00              5.60 
6              2.00               4.40              5.40 
7              2.20               4.60              5.90 
8              2.30               4.70              5.60 
9              2.40               4.80              6.40 
10             2.50               4.90              6.50 
11             2.60               5.00              6.60 
12             2.70               5.10              6.70 
13             2.80               5.20              6.80 
14             2.90               5.30              6.90 
15             3.00               5.40              6.90 
16             3.00               5.40              7.00 
17             3.10               5.50              7.10 
18             3.10               5.50              7.10 
19             3.20               5.60              7.20 
20             3.30               5.70              7.20 
21             3.30               5.70              7.30 
22             3.40               5.80              7.30 
23             3.40               5.80              7.40 
24             3.40               5.80              7.40 
25             3.50               5.90              7.50 
26             3.50               5.90              7.50 
27             3.60               6.00              7.50 
28             3.60               6.00              7.60 
29             3.60               6.00              7.60 
30             3.70               6.10              7.70

Ultrastable tetra-loops & energy bonus at 37 ° :

 Seq    Energy 
 ------------- 
 GGGGAC -3.00 
 GGUGAC -3.00 
 CGAAAG -3.00 
 GGAGAC -3.00 
 CGCAAG -3.00 
 GGAAAC -3.00 
 CGGAAG -3.00 
 CUUCGG -3.00 
 CGUGAG -3.00 
 CGAAGG -2.50 
 CUACGG -2.50 
 GGCAAC -2.50 
 CGCGAG -2.50 
 UGAGAG -2.50 
 CGAGAG -2.00 
 AGAAAU -2.00 
 CGUAAG -2.00 
 CUAACG -2.00 
 UGAAAG -2.00 
 GGAAGC -1.50 
 GGGAAC -1.50 
 UGAAAA -1.50 
 AGCAAU -1.50 
 AGUAAU -1.50 
 CGGGAG -1.50 
 AGUGAU -1.50 
 GGCGAC -1.50 
 GGGAGC -1.50 
 GUGAAC -1.50 
 UGGAAA -1.50

Miscellaneous free energies at 37 °

Miscellaneous free energy rules 
------------------------------- 
 
Extrapolation for large loops based on polymer theory 
internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) 
-->  
1.079 
 
asymmetric internal loops: the ninio equation 
the maximum correction 
-->  
3.00 
 
the f(m) array (see Ninio for details) 
--> 
 .50  .50  .50  .50 
 
multibranched loops 
  offset,  free base penalty,  helix penalty 
-->  
    3.40          .00                 .40 
 
efn2 multibranched loops 
   offset,  free base penalty,  helix penalty 
--> 
     10.10         -0.30              -0.30  
 
terminal AU penalty 
-->  
 0.50 
 
bonus for GGG hairpin 
-->  
-2.20 
 
c hairpin slope 
-->  
0.30 
 
c hairpin intercept 
-->  
1.60 
 
c hairpin of 3 
-->  
1.40 
 
Intermolecular initiation free energy 
-->  
4.10 
 
GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) 
-->  
1