mdv1.out

mfold

Structure    1

Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -145.30

         10         20           30     
-    A       UUC-     .-UCA  -|       C 
 GGGG ACCCCCC    GGGGG     CC UCGCGCAG G
 CCCC UGGGGGG    CCCCC     GG AGCGCGUC G
A    -       CCUU     \ ---  A^       G 
 .        210                     40    


                          50        60 
                        .-G          G 
                           GCCACGCUGC \
                           CGGUGCGACG A
                        \ -          A 
                            70         


                                  80         
                          .-GGUUC         AC 
                                 UCGUGCGUU  \
                                 AGCACGCAA  C
                          \ -----         AG 
                               100        90 


                                     110     
                            .-A   C       UU 
                               GGU GCGCCUC  \
                               CCA UGCGGAG  C
                            \ -   C       CA 
                                     120     


                               130         140 
                              .-U     .-A    G 
                                 GGGAG   GCGC A
                                 CCCUC   CGCG A
                              \ -     \ -    A 
                                               


                                        150          
                                        UAGC-      C 
                                             CCGUGA U
                                             GGCACU C
                                        AAGCU      G 
                                        170       160


                                180         
                                GU        C 
                                  ACGAGGUG C
                                  UGCUCCAC C
                                C-        G 
                              200        190



Structure    2

Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -141.80

         10         20          30     
-    A       UUC-     .-UCACC        C 
 GGGG ACCCCCC    GGGGG       UCGCGCAG G
 CCCC UGGGGGG    CCCCC       AGCGCGUC G
A    -       CCUU     \ -----        G 
 .        210                    40    


                               50        60 
                        .-A|              G 
                           GGG--GCCACGCUGC \
                           CCC  CGGUGCGACG A
                        \ -^  \           A 
                                 70         


                                        80         
                                G    .-U        AC 
                                 GUUC   CGUGCGUU  \
                                 CAAG   GCACGCAA  C
                                U    \ -        AG 
                                  170           90 


                                       100       110     
                                       .-A    C       UU 
                                          AGGU GCGCCUC  \
                                          UCCA UGCGGAG  C
                                       \ -    C       CA 
                                                 120     


                                         130       140 
                                              AG     G 
                                         --GGG  AGCGC A
                                           CCC  UCGCG A
                                         \    GA     A 
                                            150        


                                                     
                                           ----    C 
                                               GUGA U
                                               CACU C
                                           CUGG    G 
                                                  160


                          180         
                          GU        C 
                            ACGAGGUG C
                            UGCUCCAC C
                          C-        G 
                        200        190



Structure    3

Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -140.80

           10    
-     .-ACC    U 
 GGGGA     CCCC U
 CCCCU     GGGG C
A     \ ---    G 
 .        20     


                   30     
        .-UCA   -       C 
             CCU CGCGCAG G
             GGA GCGCGUC G
        \ ---   A       G 
                    40    


            50        60 
          .-G          G 
             GCCACGCUGC \
             CGGUGCGACG A
          \ -          A 
              70         


                    80         
            .-GGUUC         AC 
                   UCGUGCGUU  \
                   AGCACGCAA  C
            \ -----         AG 
                 100        90 


                       110     
              .-A   C       UU 
                 GGU GCGCCUC  \
                 CCA UGCGGAG  C
              \ -   C       CA 
                       120     


                 130         140 
                .-U     .-A    G 
                   GGGAG   GCGC A
                   CCCUC   CGCG A
                \ -     \ -    A 
                                 


                          150          
                          UAGC-      C 
                               CCGUGA U
                               GGCACU C
                          AAGCU      G 
                          170       160


                    180         
                  .-GU        C 
                      ACGAGGUG C
                      UGCUCCAC C
                  \ --        G 
                             190


                  200       
                    |     U 
                    CCCCCC U
                    GGGGGG C
                    ^     C 
                       210  



Structure    4

Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -139.70

         10          20           30     
-    A       .-UU|      .-CA   -       C 
 GGGG ACCCCCC    CGGGGGU    CCU CGCGCAG G
 CCCC UGGGGGG    GCCCUCA    GGA GCGCGUC G
A    -       \ --^      \ --   A       G 
 .        210                      40    


                            50        60 
                          .-G          G 
                             GCCACGCUGC \
                             CGGUGCGACG A
                          \ -          A 
                              70         


                                    80         
                            .-GGUUC         AC 
                                   UCGUGCGUU  \
                                   AGCACGCAA  C
                            \ -----         AG 
                                 100        90 


                                       110     
                              .-A   C       UU 
                                 GGU GCGCCUC  \
                                 CCA UGCGGAG  C
                              \ -   C       CA 
                                       120     


                                 130       140 
                                .-U   AG     G 
                                   GGG  AGCGC A
                                   CCC  UCGCG A
                                \ -   GA     A 
                                    150        


                                      160  
                                  GU    CG 
                                    GACU  U
                                    CUGG  C
                                  AG    CA 
                                 170       


                       180         
               U---------        C 
                         ACGAGGUG C
                         UGCUCCAC C
               CCUUCCCCCC        G 
                      200       190



Structure    5

Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -139.50

         10          20 
-    A       .-UUC|   G 
 GGGG ACCCCCC     GGGG U
 CCCC UGGGGGG     CUCC C
A    -       \ ---^   A 
 .        210           


                  30     
                       C 
               --GCGCAG G
                 CGCGUC G
               \       G 
                   40    


                         50        60 
                 -                  G 
                  GAAGGG--GCCACGCUGC \
                  CUUCCC  CGGUGCGACG A
                 C      \           A 
                           70         


                                  80         
                          .-GGUUC         AC 
                                 UCGUGCGUU  \
                                 AGCACGCAA  C
                          \ -----         AG 
                               100        90 


                                     110     
                            .-A   C       UU 
                               GGU GCGCCUC  \
                               CCA UGCGGAG  C
                            \ -   C       CA 
                                     120     


                               130         140 
                              .-U     .-A    G 
                                 GGGAG   GCGC A
                                 CCCUC   CGCG A
                              \ -     \ -    A 
                                               


                                        150          
                                        UAGC-      C 
                                             CCGUGA U
                                             GGCACU C
                                        AAGCU      G 
                                        170       160


                                 180         
                                GU-        C 
                                   ACGAGGUG C
                                   UGCUCCAC C
                                CCC        G 
                                200       190



Structure    6

Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -138.50

         10         20           30     
-    A       UUC-     .-UCA   -       C 
 GGGG ACCCCCC    GGGGG     CCU CGCGCAG G
 CCCC UGGGGGG    CCCCC     GGA GCGCGUC G
A    -       CCUU     \ ---   A       G 
 .        210                     40    


                          50        60 
                        .-G          G 
                           GCCACGCUGC \
                           CGGUGCGACG A
                        \ -          A 
                            70         


                                    80         
                          .-G   .-C         AC 
                             GUU   UCGUGCGUU  \
                             CAG   AGCACGCAA  C
                          \ -   \ -         AG 
                                 100        90 


                                           110     
                                  .-A   C       UU 
                                     GGU GCGCCUC  \
                                     CCA UGCGGAG  C
                                  \ -   C       CA 
                                           120     


                                    130       140 
                                    U-   AG     G 
                                      GGG  AGCGC A
                                      CCC  UCGCG A
                                    UG   GA     A 
                                       150        


                             160       170 
                            .-UCGUC|   UCG 
                                   ACGG   A
                                   UGCC   A
                            \ -----^   CUC 
                                           


                             180         
                              -        C 
                               ACGAGGUG C
                               UGCUCCAC C
                              C        G 
                            200       190