Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C2p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C2p_exo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C2p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward pairing A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 24 Number of adjacent stackings = 23 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Bs/Ww pairing antiparallel cis one_hbond A39-A40 : G-A O2'/Hh adjacent_5p upward pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C3p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C4p_exo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C4p_exo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward pairing A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 24 Number of adjacent stackings = 23 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A21-A27 : C-C Ws/Hh pairing parallel trans one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond A31-A35 : G-A Ss/Wh O2'/Bh pairing parallel trans one_hbond A39-A40 : G-A O2'/Hh adjacent_5p upward pairing Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C4p_exo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 26 Number of adjacent stackings = 25 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A10 : C-A Ws/Hw pairing antiparallel trans one_hbond A7-A9 : U-A Hh/O2P pairing A7-A10 : U-A Ww/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A34 : G-C O2P/Bh pairing A32-A35 : G-A O2'/Bh pairing Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 26 Number of adjacent stackings = 25 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh O2'/C8 adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel trans one_hbond A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A34 : G-C O2P/Bh pairing A32-A35 : G-A O2'/Bh pairing Residue conformations ------------------------------------------- A1 : G O4p_endo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C4p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C4p_exo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C2p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C1p_exo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A18-A19 : adjacent_5p upward A19-A20 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 27 Number of adjacent stackings = 26 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A O2'/Ss pairing A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A22-A25 : U-U Ww/O2P pairing A24-A41 : U-A Ws/Wh pairing antiparallel cis one_hbond 46 A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond A39-A40 : G-A O2'/Hh adjacent_5p pairing A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C4p_exo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C2p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C1p_exo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 24 Number of adjacent stackings = 23 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A4 : G-A O2'/Hh adjacent_5p pairing A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel trans 137 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A35 : G-A O2'/Bh pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C O4p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C4p_exo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 24 Number of adjacent stackings = 23 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A24-A41 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A35 : G-A O2'/Bh pairing A39-A40 : G-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C2p_exo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C2p_exo anti A35 : A C1p_exo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 25 Number of adjacent stackings = 24 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel cis one_hbond 131 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A24-A41 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond A32-A35 : G-A O2'/Bh pairing A39-A40 : G-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C4p_exo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C2p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C2p_exo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C2p_exo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C1p_exo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 23 Number of adjacent stackings = 22 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A4 : G-A O2'/Hh adjacent_5p pairing A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Bh O2'/Bh pairing parallel trans one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A35 : G-A O2'/Bh pairing A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C4p_exo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C4p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C2p_exo anti A39 : G C3p_endo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A23-A24 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ Number of stackings = 25 Number of adjacent stackings = 25 Number of non adjacent stackings = 0 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A4 : G-A O2'/Hh adjacent_5p pairing A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel cis 137 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Bh O2'/Bh pairing parallel trans one_hbond A24-A41 : U-A Ww/Ww pairing antiparallel cis XX A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A35 : G-A O2'/Bh pairing Residue conformations ------------------------------------------- A1 : G O4p_endo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C4p_exo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 25 Number of adjacent stackings = 24 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel trans one_hbond A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A35 : G-A O2'/Bh pairing Residue conformations ------------------------------------------- A1 : G C3p_endo anti A2 : G C4p_exo anti A3 : G C4p_exo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C3p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C4p_exo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C4p_exo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C4p_exo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 22 Number of adjacent stackings = 21 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A3 : G-G O2'/C8 adjacent_5p pairing A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A7-A9 : U-A Hh/O2P Ww/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A21-A37 : C-C O2'/Bh pairing A24-A41 : U-A Ww/Ww pairing antiparallel cis XX A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A39-A40 : G-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G O4p_endo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C O4p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C2p_exo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C4p_exo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A2-A3 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 22 Number of adjacent stackings = 21 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A10 : C-A Bh/O2P Bh/O2P pairing A7-A9 : U-A Hh/O2P pairing A7-A10 : U-A Ww/O2P pairing A8-A9 : C-A O2'/Hh adjacent_5p pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond A39-A40 : G-A O2'/Hh adjacent_5p pairing A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G O4p_endo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C2p_exo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C4p_exo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C1p_exo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C2p_exo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A18-A19 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 23 Number of adjacent stackings = 22 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs O2'/Ss pairing parallel cis one_hbond A21-A27 : C-C Ws/Wh pairing antiparallel trans one_hbond 137 A24-A41 : U-A Ww/Ww pairing antiparallel cis XX A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond A32-A34 : G-C O2P/Bh pairing Residue conformations ------------------------------------------- A1 : G C3p_endo anti A2 : G C2p_exo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C2p_exo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C4p_exo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward pairing A19-A20 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 24 Number of adjacent stackings = 23 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh O2'/C8 adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A7-A10 : U-A Ww/O2P pairing A16-A17 : C-C O2'/Hh adjacent_5p pairing A17-A18 : C-C O2P/Bh adjacent_5p upward pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A22 : C-U O2'/Hh adjacent_5p pairing A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX Residue conformations ------------------------------------------- A1 : G C1p_exo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C2p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C4p_exo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C4p_exo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward pairing A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A16-A17 : adjacent_5p upward A17-A18 : adjacent_5p upward A25-A26 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 21 Number of adjacent stackings = 20 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A2 : G-G O2'/Hh adjacent_5p upward pairing A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond A22-A24 : U-U Hh/O2P pairing A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A34 : G-C O2P/Bh pairing A32-A35 : G-A O2'/Bh pairing A39-A40 : G-A O2'/Hh adjacent_5p pairing A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C3p_endo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C2p_exo anti A25 : U C3p_endo anti A26 : C C4p_exo anti A27 : C C4p_exo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C2p_exo anti A31 : G C3p_endo anti A32 : G C4p_exo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C1p_exo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 24 Number of adjacent stackings = 23 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A10 : C-A Ws/Hw pairing antiparallel trans one_hbond A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A32-A35 : G-A O2'/Bh pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C O4p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C2p_exo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A24-A25 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward pairing A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 28 Number of adjacent stackings = 27 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel trans 137 A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A19-A35 : C-A Ws/Wh pairing parallel trans one_hbond 79 A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs O2'/Ss pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A22-A36 : U-U Ww/O2P pairing A24-A41 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A39-A40 : G-A O2'/Hh adjacent_5p upward pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C2p_exo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C3p_endo anti A33 : U C3p_exo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ Number of stackings = 21 Number of adjacent stackings = 21 Number of non adjacent stackings = 0 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A10 : C-A Ws/Wh pairing antiparallel trans one_hbond 78 A7-A9 : U-A Hh/O2P pairing A7-A10 : U-A Ww/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A27 : C-C Ws/Hw pairing antiparallel trans one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C4p_exo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C1p_exo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C4p_exo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C3p_endo anti A33 : U C3p_exo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ Number of stackings = 25 Number of adjacent stackings = 25 Number of non adjacent stackings = 0 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A4 : G-A O2'/Hh adjacent_5p pairing A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Hw pairing antiparallel trans one_hbond A7-A9 : U-A Hh/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A19-A35 : C-A Ws/Wh pairing parallel trans one_hbond 79 A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Bs/Bs pairing parallel cis one_hbond A21-A27 : C-C O2'/Bh pairing A21-A37 : C-C O2'/Bh pairing A22-A37 : U-C O2P/Bh pairing A23-A26 : U-C O2P/Bh pairing A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C3p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C4p_exo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C4p_exo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A18-A19 : adjacent_5p upward A25-A26 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 20 Number of adjacent stackings = 19 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A21-A37 : C-C O2'/Bh pairing A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Bs/Ww pairing antiparallel cis one_hbond A31-A35 : G-A Ss/Wh pairing antiparallel trans one_hbond 63 A35-A36 : A-U O2'/Hh adjacent_5p pairing A39-A40 : G-A O2'/Hh adjacent_5p pairing A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C2p_exo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C2p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C2p_exo anti A20 : C C3p_endo anti A21 : C C4p_exo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C2p_exo anti A33 : U C3p_exo anti A34 : C C2p_exo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ Number of stackings = 23 Number of adjacent stackings = 23 Number of non adjacent stackings = 0 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond A21-A27 : C-C O2'/Bh pairing A21-A37 : C-C O2'/Bh pairing A24-A25 : U-U Hh/Hw adjacent_5p pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Bs/Ww pairing antiparallel cis one_hbond A34-A35 : C-A O2P/Hh adjacent_5p pairing A35-A36 : A-U O2'/Hh adjacent_5p pairing A43-A44 : C-A O2'/Hh adjacent_5p pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C C3p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C3p_endo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C4p_exo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C3p_endo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C4p_exo anti A38 : G C3p_endo anti A39 : G C4p_exo anti A40 : A C2p_exo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A3-A4 : adjacent_5p upward A4-A5 : adjacent_5p upward A9-A10 : adjacent_5p upward A10-A11 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A23-A24 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward pairing A40-A41 : adjacent_5p upward A41-A42 : adjacent_5p upward Non-Adjacent stackings ------------------------------------------ A28-A38 : outward Number of stackings = 23 Number of adjacent stackings = 22 Number of non adjacent stackings = 1 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A1-A18 : G-C Bs/O2' pairing A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A6-A11 : C-C Ww/Bh pairing antiparallel trans 137 A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX A30-A35 : G-A Bs/Ww pairing parallel cis one_hbond 56 A31-A35 : G-A Ss/Wh O2'/Bh pairing parallel trans one_hbond A39-A40 : G-A O2'/Hh adjacent_5p upward pairing Residue conformations ------------------------------------------- A1 : G C2p_exo anti A2 : G C4p_exo anti A3 : G C3p_endo anti A4 : A C3p_endo anti A5 : G C3p_endo anti A6 : C C3p_endo anti A7 : U C3p_endo anti A8 : C O4p_endo anti A9 : A C3p_endo anti A10 : A C3p_endo anti A11 : C C3p_endo anti A12 : U C3p_endo anti A13 : C C2p_exo anti A14 : U C3p_endo anti A15 : C C3p_endo anti A16 : C C3p_endo anti A17 : C C3p_endo anti A18 : C C3p_endo anti A19 : C C3p_endo anti A20 : C C3p_endo anti A21 : C C3p_endo anti A22 : U C2p_endo anti A23 : U C3p_endo anti A24 : U C3p_endo anti A25 : U C3p_endo anti A26 : C C3p_endo anti A27 : C C3p_endo anti A28 : G C3p_endo anti A29 : A C3p_endo anti A30 : G C3p_endo anti A31 : G C2p_exo anti A32 : G C3p_endo anti A33 : U C2p_endo anti A34 : C C3p_endo anti A35 : A C2p_endo anti A36 : U C3p_endo anti A37 : C C3p_endo anti A38 : G C3p_endo anti A39 : G C3p_endo anti A40 : A C3p_endo anti A41 : A C3p_endo anti A42 : C C3p_endo anti A43 : C C3p_endo anti A44 : A O4p_endo anti Adjacent stackings ---------------------------------------------- A1-A2 : adjacent_5p upward A2-A3 : adjacent_5p upward A4-A5 : adjacent_5p upward A6-A7 : adjacent_5p upward A10-A11 : adjacent_5p upward A11-A12 : adjacent_5p upward A12-A13 : adjacent_5p upward A13-A14 : adjacent_5p upward A14-A15 : adjacent_5p upward A15-A16 : adjacent_5p upward A17-A18 : adjacent_5p upward A19-A20 : adjacent_5p upward A25-A26 : adjacent_5p upward A26-A27 : adjacent_5p upward A27-A28 : adjacent_5p upward A28-A29 : adjacent_5p upward A29-A30 : adjacent_5p upward A30-A31 : adjacent_5p upward A31-A32 : adjacent_5p upward A36-A37 : adjacent_5p upward A38-A39 : adjacent_5p upward A39-A40 : adjacent_5p upward A41-A42 : adjacent_5p upward A42-A43 : adjacent_5p upward A43-A44 : adjacent_5p inward Non-Adjacent stackings ------------------------------------------ Number of stackings = 25 Number of adjacent stackings = 25 Number of non adjacent stackings = 0 Base-pairs ------------------------------------------------------ A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX A4-A14 : A-U Ww/Ww pairing antiparallel cis XX A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX A7-A9 : U-A Hh/O2P pairing A7-A10 : U-A Ww/O2P pairing A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX A19-A35 : C-A Ws/Wh pairing parallel trans one_hbond 79 A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX A20-A35 : C-A Bs/Bs O2'/Ss pairing parallel cis one_hbond A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel trans one_hbond A22-A24 : U-U Hh/O2P pairing A24-A25 : U-U Hh/Hw adjacent_5p pairing parallel cis one_hbond A25-A40 : U-A Ww/Ww pairing antiparallel cis XX A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX A29-A36 : A-U Ww/Ww pairing antiparallel cis XX