Structure 1
Folding bases      1 to    221 of MDV-1 (-) RNA                                     
 Initial dG =   -145.3

         10         20           30     
-    |A      UUC-     .-UCA   -       C 
 GGGGA CCCCCC    GGGGG     CCU CGCGCAG G
 CCCCU GGGGGG    CCCCC     GGA GCGCGUC 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 = -141.8 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 = -140.8 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 = -139.7 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 = -139.5 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 = -138.5 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


mfold version 3.1
M. Zuker, Rensselaer Polytechnic Institute