Loop Free-Energy Decomposition

Structure 1
MDV-1 (-) RNA
Initial dG = -145.30

Structural elementddGInformation
External loop -1.70 1 ss bases & 1 closing helices.
Stack -3.30External closing pair is G 1-C 220
Stack -3.30External closing pair is G 2-C 219
Stack -3.30External closing pair is G 3-C 218
Stack -2.40External closing pair is G 4-C 217
Helix -12.30 5 base pairs.
Bulge loop 1.60External closing pair is A 5-U 216
Stack -3.30External closing pair is C 7-G 215
Stack -3.30External closing pair is C 8-G 214
Stack -3.30External closing pair is C 9-G 213
Stack -3.30External closing pair is C 10-G 212
Stack -3.30External closing pair is C 11-G 211
Helix -16.50 6 base pairs.
Interior loop 2.70External closing pair is C 12-G 210
Stack -3.30External closing pair is G 16-C 205
Stack -3.30External closing pair is G 17-C 204
Stack -3.30External closing pair is G 18-C 203
Stack -3.30External closing pair is G 19-C 202
Helix -13.20 5 base pairs.
Multi-loop -1.20External closing pair is G 20-C 201
14 ss bases & 7 closing helices.
Stack -2.20External closing pair is A 180-U 199
Stack -2.40External closing pair is C 181-G 198
Stack -2.40External closing pair is G 182-C 197
Stack -2.10External closing pair is A 183-U 196
Stack -3.30External closing pair is G 184-C 195
Stack -2.20External closing pair is G 185-C 194
Stack -2.10External closing pair is U 186-A 193
Helix -16.70 8 base pairs.
Hairpin loop 3.20Closing pair is G 187-C 192
Stack -3.30External closing pair is G 130-C 177
Stack -3.30External closing pair is G 131-C 176
Stack -2.40External closing pair is G 132-C 175
Stack -2.10External closing pair is A 133-U 174
Helix -11.10 5 base pairs.
Multi-loop 0.90External closing pair is G 134-C 173
10 ss bases & 3 closing helices.
Stack -3.30External closing pair is C 152-G 167
Stack -2.40External closing pair is C 153-G 166
Stack -2.20External closing pair is G 154-C 165
Stack -2.10External closing pair is U 155-A 164
Stack -2.40External closing pair is G 156-C 163
Helix -12.40 6 base pairs.
Hairpin loop 4.10Closing pair is A 157-U 162
Stack -3.40External closing pair is G 136-C 147
Stack -2.40External closing pair is C 137-G 146
Stack -3.40External closing pair is G 138-C 145
Helix -9.20 4 base pairs.
Hairpin loop 0.40Closing pair is C 139-G 144
Stack -3.30External closing pair is G 102-C 128
Stack -2.20External closing pair is G 103-C 127
Helix -5.50 3 base pairs.
Interior loop 1.70External closing pair is U 104-A 126
Stack -2.50External closing pair is G 106-U 124
Stack -2.40External closing pair is C 107-G 123
Stack -3.40External closing pair is G 108-C 122
Stack -3.30External closing pair is C 109-G 121
Stack -2.10External closing pair is C 110-G 120
Stack -2.40External closing pair is U 111-A 119
Helix -16.10 7 base pairs.
Hairpin loop 4.20Closing pair is C 112-G 118
Stack -2.40External closing pair is U 78-A 100
Stack -2.40External closing pair is C 79-G 99
Stack -2.20External closing pair is G 80-C 98
Stack -2.10External closing pair is U 81-A 97
Stack -3.40External closing pair is G 82-C 96
Stack -2.40External closing pair is C 83-G 95
Stack -2.20External closing pair is G 84-C 94
Stack -0.90External closing pair is U 85-A 93
Helix -18.00 9 base pairs.
Hairpin loop 5.10Closing pair is U 86-A 92
Stack -3.40External closing pair is G 50-C 72
Stack -3.30External closing pair is C 51-G 71
Stack -2.10External closing pair is C 52-G 70
Stack -2.20External closing pair is A 53-U 69
Stack -2.40External closing pair is C 54-G 68
Stack -3.40External closing pair is G 55-C 67
Stack -2.10External closing pair is C 56-G 66
Stack -2.10External closing pair is U 57-A 65
Stack -3.40External closing pair is G 58-C 64
Helix -24.40 10 base pairs.
Hairpin loop 5.70Closing pair is C 59-G 63
Stack -3.30External closing pair is C 24-G 48
Stack -2.10External closing pair is C 25-G 47
Helix -5.40 3 base pairs.
Bulge loop 1.40External closing pair is U 26-A 46
Stack -2.40External closing pair is C 27-G 44
Stack -3.40External closing pair is G 28-C 43
Stack -2.40External closing pair is C 29-G 42
Stack -3.40External closing pair is G 30-C 41
Stack -2.10External closing pair is C 31-G 40
Stack -2.10External closing pair is A 32-U 39
Helix -15.80 7 base pairs.
Hairpin loop 3.20Closing pair is G 33-C 38


Structure 2
MDV-1 (-) RNA
Initial dG = -141.80

Structural elementddGInformation
External loop -1.70 1 ss bases & 1 closing helices.
Stack -3.30External closing pair is G 1-C 220
Stack -3.30External closing pair is G 2-C 219
Stack -3.30External closing pair is G 3-C 218
Helix -9.90 4 base pairs.
Bulge loop 1.40External closing pair is G 4-C 217
Stack -2.20External closing pair is A 6-U 216
Stack -3.30External closing pair is C 7-G 215
Stack -3.30External closing pair is C 8-G 214
Stack -3.30External closing pair is C 9-G 213
Stack -3.30External closing pair is C 10-G 212
Stack -3.30External closing pair is C 11-G 211
Helix -18.70 7 base pairs.
Interior loop 2.70External closing pair is C 12-G 210
Stack -3.30External closing pair is G 16-C 205
Stack -3.30External closing pair is G 17-C 204
Stack -3.30External closing pair is G 18-C 203
Stack -3.30External closing pair is G 19-C 202
Helix -13.20 5 base pairs.
Multi-loop 2.30External closing pair is G 20-C 201
9 ss bases & 4 closing helices.
Stack -2.20External closing pair is A 180-U 199
Stack -2.40External closing pair is C 181-G 198
Stack -2.40External closing pair is G 182-C 197
Stack -2.10External closing pair is A 183-U 196
Stack -3.30External closing pair is G 184-C 195
Stack -2.20External closing pair is G 185-C 194
Stack -2.10External closing pair is U 186-A 193
Helix -16.70 8 base pairs.
Hairpin loop 3.20Closing pair is G 187-C 192
Stack -3.30External closing pair is G 47-C 177
Stack -3.30External closing pair is G 48-C 176
Helix -6.60 3 base pairs.
Multi-loop 1.70External closing pair is G 49-C 175
2 ss bases & 3 closing helices.
Stack -2.20External closing pair is G 74-C 173
Stack -0.90External closing pair is U 75-A 172
Stack -2.40External closing pair is U 76-A 171
Helix -5.50 4 base pairs.
Multi-loop 1.60External closing pair is C 77-G 170
6 ss bases & 5 closing helices.
Stack -2.20External closing pair is G 154-C 165
Stack -2.10External closing pair is U 155-A 164
Stack -2.40External closing pair is G 156-C 163
Helix -6.70 4 base pairs.
Hairpin loop 4.10Closing pair is A 157-U 162
Stack -3.30External closing pair is G 130-C 153
Stack -3.30External closing pair is G 131-C 152
Helix -6.60 3 base pairs.
Interior loop -0.30External closing pair is G 132-C 151
Stack -2.10External closing pair is A 135-U 148
Stack -3.40External closing pair is G 136-C 147
Stack -2.40External closing pair is C 137-G 146
Stack -3.40External closing pair is G 138-C 145
Helix -11.30 5 base pairs.
Hairpin loop 0.40Closing pair is C 139-G 144
Stack -2.10External closing pair is A 101-U 129
Stack -3.30External closing pair is G 102-C 128
Stack -2.20External closing pair is G 103-C 127
Helix -7.60 4 base pairs.
Interior loop 1.70External closing pair is U 104-A 126
Stack -2.50External closing pair is G 106-U 124
Stack -2.40External closing pair is C 107-G 123
Stack -3.40External closing pair is G 108-C 122
Stack -3.30External closing pair is C 109-G 121
Stack -2.10External closing pair is C 110-G 120
Stack -2.40External closing pair is U 111-A 119
Helix -16.10 7 base pairs.
Hairpin loop 4.20Closing pair is C 112-G 118
Stack -2.40External closing pair is C 79-G 99
Stack -2.20External closing pair is G 80-C 98
Stack -2.10External closing pair is U 81-A 97
Stack -3.40External closing pair is G 82-C 96
Stack -2.40External closing pair is C 83-G 95
Stack -2.20External closing pair is G 84-C 94
Stack -0.90External closing pair is U 85-A 93
Helix -15.60 8 base pairs.
Hairpin loop 5.10Closing pair is U 86-A 92
Stack -3.40External closing pair is G 50-C 72
Stack -3.30External closing pair is C 51-G 71
Stack -2.10External closing pair is C 52-G 70
Stack -2.20External closing pair is A 53-U 69
Stack -2.40External closing pair is C 54-G 68
Stack -3.40External closing pair is G 55-C 67
Stack -2.10External closing pair is C 56-G 66
Stack -2.10External closing pair is U 57-A 65
Stack -3.40External closing pair is G 58-C 64
Helix -24.40 10 base pairs.
Hairpin loop 5.70Closing pair is C 59-G 63
Stack -2.40External closing pair is U 26-A 45
Stack -2.40External closing pair is C 27-G 44
Stack -3.40External closing pair is G 28-C 43
Stack -2.40External closing pair is C 29-G 42
Stack -3.40External closing pair is G 30-C 41
Stack -2.10External closing pair is C 31-G 40
Stack -2.10External closing pair is A 32-U 39
Helix -18.20 8 base pairs.
Hairpin loop 3.20Closing pair is G 33-C 38


Structure 3
MDV-1 (-) RNA
Initial dG = -140.80

Structural elementddGInformation
External loop -1.70 1 ss bases & 1 closing helices.
Stack -3.30External closing pair is G 1-C 220
Stack -3.30External closing pair is G 2-C 219
Stack -3.30External closing pair is G 3-C 218
Stack -2.40External closing pair is G 4-C 217
Helix -12.30 5 base pairs.
Multi-loop -0.70External closing pair is A 5-U 216
16 ss bases & 9 closing helices.
Stack -3.30External closing pair is C 200-G 215
Stack -3.30External closing pair is C 201-G 214
Stack -3.30External closing pair is C 202-G 213
Stack -3.30External closing pair is C 203-G 212
Stack -3.30External closing pair is C 204-G 211
Helix -16.50 6 base pairs.
Hairpin loop 4.20Closing pair is C 205-G 210
Stack -2.20External closing pair is A 180-U 199
Stack -2.40External closing pair is C 181-G 198
Stack -2.40External closing pair is G 182-C 197
Stack -2.10External closing pair is A 183-U 196
Stack -3.30External closing pair is G 184-C 195
Stack -2.20External closing pair is G 185-C 194
Stack -2.10External closing pair is U 186-A 193
Helix -16.70 8 base pairs.
Hairpin loop 3.20Closing pair is G 187-C 192
Stack -3.30External closing pair is G 130-C 177
Stack -3.30External closing pair is G 131-C 176
Stack -2.40External closing pair is G 132-C 175
Stack -2.10External closing pair is A 133-U 174
Helix -11.10 5 base pairs.
Multi-loop 0.90External closing pair is G 134-C 173
10 ss bases & 3 closing helices.
Stack -3.30External closing pair is C 152-G 167
Stack -2.40External closing pair is C 153-G 166
Stack -2.20External closing pair is G 154-C 165
Stack -2.10External closing pair is U 155-A 164
Stack -2.40External closing pair is G 156-C 163
Helix -12.40 6 base pairs.
Hairpin loop 4.10Closing pair is A 157-U 162
Stack -3.40External closing pair is G 136-C 147
Stack -2.40External closing pair is C 137-G 146
Stack -3.40External closing pair is G 138-C 145
Helix -9.20 4 base pairs.
Hairpin loop 0.40Closing pair is C 139-G 144
Stack -3.30External closing pair is G 102-C 128
Stack -2.20External closing pair is G 103-C 127
Helix -5.50 3 base pairs.
Interior loop 1.70External closing pair is U 104-A 126
Stack -2.50External closing pair is G 106-U 124
Stack -2.40External closing pair is C 107-G 123
Stack -3.40External closing pair is G 108-C 122
Stack -3.30External closing pair is C 109-G 121
Stack -2.10External closing pair is C 110-G 120
Stack -2.40External closing pair is U 111-A 119
Helix -16.10 7 base pairs.
Hairpin loop 4.20Closing pair is C 112-G 118
Stack -2.40External closing pair is U 78-A 100
Stack -2.40External closing pair is C 79-G 99
Stack -2.20External closing pair is G 80-C 98
Stack -2.10External closing pair is U 81-A 97
Stack -3.40External closing pair is G 82-C 96
Stack -2.40External closing pair is C 83-G 95
Stack -2.20External closing pair is G 84-C 94
Stack -0.90External closing pair is U 85-A 93
Helix -18.00 9 base pairs.
Hairpin loop 5.10Closing pair is U 86-A 92
Stack -3.40External closing pair is G 50-C 72
Stack -3.30External closing pair is C 51-G 71
Stack -2.10External closing pair is C 52-G 70
Stack -2.20External closing pair is A 53-U 69
Stack -2.40External closing pair is C 54-G 68
Stack -3.40External closing pair is G 55-C 67
Stack -2.10External closing pair is C 56-G 66
Stack -2.10External closing pair is U 57-A 65
Stack -3.40External closing pair is G 58-C 64
Helix -24.40 10 base pairs.
Hairpin loop 5.70Closing pair is C 59-G 63
Stack -3.30External closing pair is C 24-G 48
Stack -2.10External closing pair is C 25-G 47
Helix -5.40 3 base pairs.
Bulge loop 1.40External closing pair is U 26-A 46
Stack -2.40External closing pair is C 27-G 44
Stack -3.40External closing pair is G 28-C 43
Stack -2.40External closing pair is C 29-G 42
Stack -3.40External closing pair is G 30-C 41
Stack -2.10External closing pair is C 31-G 40
Stack -2.10External closing pair is A 32-U 39
Helix -15.80 7 base pairs.
Hairpin loop 3.20Closing pair is G 33-C 38
Stack -3.30External closing pair is C 9-G 20
Stack -3.30External closing pair is C 10-G 19
Stack -3.30External closing pair is C 11-G 18
Helix -9.90 4 base pairs.
Hairpin loop 0.80Closing pair is C 12-G 17


Structure 4
MDV-1 (-) RNA
Initial dG = -139.70

Structural elementddGInformation
External loop -1.70 1 ss bases & 1 closing helices.
Stack -3.30External closing pair is G 1-C 220
Stack -3.30External closing pair is G 2-C 219
Stack -3.30External closing pair is G 3-C 218
Helix -9.90 4 base pairs.
Bulge loop 1.40External closing pair is G 4-C 217
Stack -2.20External closing pair is A 6-U 216
Stack -3.30External closing pair is C 7-G 215
Stack -3.30External closing pair is C 8-G 214
Stack -3.30External closing pair is C 9-G 213
Stack -3.30External closing pair is C 10-G 212
Stack -3.30External closing pair is C 11-G 211
Helix -18.70 7 base pairs.
Multi-loop 2.80External closing pair is C 12-G 210
13 ss bases & 3 closing helices.
Stack -2.20External closing pair is A 180-U 199
Stack -2.40External closing pair is C 181-G 198
Stack -2.40External closing pair is G 182-C 197
Stack -2.10External closing pair is A 183-U 196
Stack -3.30External closing pair is G 184-C 195
Stack -2.20External closing pair is G 185-C 194
Stack -2.10External closing pair is U 186-A 193
Helix -16.70 8 base pairs.
Hairpin loop 3.20Closing pair is G 187-C 192
Stack -2.40External closing pair is C 15-G 178
Stack -3.30External closing pair is G 16-C 177
Stack -3.30External closing pair is G 17-C 176
Stack -1.50External closing pair is G 18-C 175
Stack -2.10External closing pair is G 19-U 174
Stack -2.20External closing pair is G 20-C 173
Helix -14.80 7 base pairs.
Multi-loop -2.20External closing pair is U 21-A 172
14 ss bases & 7 closing helices.
Stack -2.40External closing pair is G 156-C 169
Stack -2.20External closing pair is A 157-U 168
Stack -2.10External closing pair is C 158-G 167
Helix -6.70 4 base pairs.
Hairpin loop 5.30Closing pair is U 159-G 166
Stack -3.30External closing pair is G 130-C 153
Stack -3.30External closing pair is G 131-C 152
Helix -6.60 3 base pairs.
Interior loop -0.30External closing pair is G 132-C 151
Stack -2.10External closing pair is A 135-U 148
Stack -3.40External closing pair is G 136-C 147
Stack -2.40External closing pair is C 137-G 146
Stack -3.40External closing pair is G 138-C 145
Helix -11.30 5 base pairs.
Hairpin loop 0.40Closing pair is C 139-G 144
Stack -3.30External closing pair is G 102-C 128
Stack -2.20External closing pair is G 103-C 127
Helix -5.50 3 base pairs.
Interior loop 1.70External closing pair is U 104-A 126
Stack -2.50External closing pair is G 106-U 124
Stack -2.40External closing pair is C 107-G 123
Stack -3.40External closing pair is G 108-C 122
Stack -3.30External closing pair is C 109-G 121
Stack -2.10External closing pair is C 110-G 120
Stack -2.40External closing pair is U 111-A 119
Helix -16.10 7 base pairs.
Hairpin loop 4.20Closing pair is C 112-G 118
Stack -2.40External closing pair is U 78-A 100
Stack -2.40External closing pair is C 79-G 99
Stack -2.20External closing pair is G 80-C 98
Stack -2.10External closing pair is U 81-A 97
Stack -3.40External closing pair is G 82-C 96
Stack -2.40External closing pair is C 83-G 95
Stack -2.20External closing pair is G 84-C 94
Stack -0.90External closing pair is U 85-A 93
Helix -18.00 9 base pairs.
Hairpin loop 5.10Closing pair is U 86-A 92
Stack -3.40External closing pair is G 50-C 72
Stack -3.30External closing pair is C 51-G 71
Stack -2.10External closing pair is C 52-G 70
Stack -2.20External closing pair is A 53-U 69
Stack -2.40External closing pair is C 54-G 68
Stack -3.40External closing pair is G 55-C 67
Stack -2.10External closing pair is C 56-G 66
Stack -2.10External closing pair is U 57-A 65
Stack -3.40External closing pair is G 58-C 64
Helix -24.40 10 base pairs.
Hairpin loop 5.70Closing pair is C 59-G 63
Stack -3.30External closing pair is C 24-G 48
Stack -2.10External closing pair is C 25-G 47
Helix -5.40 3 base pairs.
Bulge loop 1.40External closing pair is U 26-A 46
Stack -2.40External closing pair is C 27-G 44
Stack -3.40External closing pair is G 28-C 43
Stack -2.40External closing pair is C 29-G 42
Stack -3.40External closing pair is G 30-C 41
Stack -2.10External closing pair is C 31-G 40
Stack -2.10External closing pair is A 32-U 39
Helix -15.80 7 base pairs.
Hairpin loop 3.20Closing pair is G 33-C 38


Structure 5
MDV-1 (-) RNA
Initial dG = -139.50

Structural elementddGInformation
External loop -1.70 1 ss bases & 1 closing helices.
Stack -3.30External closing pair is G 1-C 220
Stack -3.30External closing pair is G 2-C 219
Stack -3.30External closing pair is G 3-C 218
Helix -9.90 4 base pairs.
Bulge loop 1.40External closing pair is G 4-C 217
Stack -2.20External closing pair is A 6-U 216
Stack -3.30External closing pair is C 7-G 215
Stack -3.30External closing pair is C 8-G 214
Stack -3.30External closing pair is C 9-G 213
Stack -3.30External closing pair is C 10-G 212
Stack -3.30External closing pair is C 11-G 211
Helix -18.70 7 base pairs.
Multi-loop 2.70External closing pair is C 12-G 210
4 ss bases & 4 closing helices.
Stack -2.40External closing pair is G 44-C 208
Stack -0.90External closing pair is A 45-U 207
Stack -2.10External closing pair is A 46-U 206
Stack -3.30External closing pair is G 47-C 205
Stack -3.30External closing pair is G 48-C 204
Helix -12.00 6 base pairs.
Multi-loop 0.70External closing pair is G 49-C 203
12 ss bases & 6 closing helices.
Stack -2.20External closing pair is A 180-U 199
Stack -2.40External closing pair is C 181-G 198
Stack -2.40External closing pair is G 182-C 197
Stack -2.10External closing pair is A 183-U 196
Stack -3.30External closing pair is G 184-C 195
Stack -2.20External closing pair is G 185-C 194
Stack -2.10External closing pair is U 186-A 193
Helix -16.70 8 base pairs.
Hairpin loop 3.20Closing pair is G 187-C 192
Stack -3.30External closing pair is G 130-C 177
Stack -3.30External closing pair is G 131-C 176
Stack -2.40External closing pair is G 132-C 175
Stack -2.10External closing pair is A 133-U 174
Helix -11.10 5 base pairs.
Multi-loop 0.90External closing pair is G 134-C 173
10 ss bases & 3 closing helices.
Stack -3.30External closing pair is C 152-G 167
Stack -2.40External closing pair is C 153-G 166
Stack -2.20External closing pair is G 154-C 165
Stack -2.10External closing pair is U 155-A 164
Stack -2.40External closing pair is G 156-C 163
Helix -12.40 6 base pairs.
Hairpin loop 4.10Closing pair is A 157-U 162
Stack -3.40External closing pair is G 136-C 147
Stack -2.40External closing pair is C 137-G 146
Stack -3.40External closing pair is G 138-C 145
Helix -9.20 4 base pairs.
Hairpin loop 0.40Closing pair is C 139-G 144
Stack -3.30External closing pair is G 102-C 128
Stack -2.20External closing pair is G 103-C 127
Helix -5.50 3 base pairs.
Interior loop 1.70External closing pair is U 104-A 126
Stack -2.50External closing pair is G 106-U 124
Stack -2.40External closing pair is C 107-G 123
Stack -3.40External closing pair is G 108-C 122
Stack -3.30External closing pair is C 109-G 121
Stack -2.10External closing pair is C 110-G 120
Stack -2.40External closing pair is U 111-A 119
Helix -16.10 7 base pairs.
Hairpin loop 4.20Closing pair is C 112-G 118
Stack -2.40External closing pair is U 78-A 100
Stack -2.40External closing pair is C 79-G 99
Stack -2.20External closing pair is G 80-C 98
Stack -2.10External closing pair is U 81-A 97
Stack -3.40External closing pair is G 82-C 96
Stack -2.40External closing pair is C 83-G 95
Stack -2.20External closing pair is G 84-C 94
Stack -0.90External closing pair is U 85-A 93
Helix -18.00 9 base pairs.
Hairpin loop 5.10Closing pair is U 86-A 92
Stack -3.40External closing pair is G 50-C 72
Stack -3.30External closing pair is C 51-G 71
Stack -2.10External closing pair is C 52-G 70
Stack -2.20External closing pair is A 53-U 69
Stack -2.40External closing pair is C 54-G 68
Stack -3.40External closing pair is G 55-C 67
Stack -2.10External closing pair is C 56-G 66
Stack -2.10External closing pair is U 57-A 65
Stack -3.40External closing pair is G 58-C 64
Helix -24.40 10 base pairs.
Hairpin loop 5.70Closing pair is C 59-G 63
Stack -3.40External closing pair is G 28-C 43
Stack -2.40External closing pair is C 29-G 42
Stack -3.40External closing pair is G 30-C 41
Stack -2.10External closing pair is C 31-G 40
Stack -2.10External closing pair is A 32-U 39
Helix -13.40 6 base pairs.
Hairpin loop 3.20Closing pair is G 33-C 38
Stack -1.50External closing pair is G 16-C 27
Stack -2.10External closing pair is G 17-U 26
Stack -3.30External closing pair is G 18-C 25
Helix -6.90 4 base pairs.
Hairpin loop 3.20Closing pair is G 19-C 24


Structure 6
MDV-1 (-) RNA
Initial dG = -138.50

Structural elementddGInformation
External loop -1.70 1 ss bases & 1 closing helices.
Stack -3.30External closing pair is G 1-C 220
Stack -3.30External closing pair is G 2-C 219
Stack -3.30External closing pair is G 3-C 218
Helix -9.90 4 base pairs.
Bulge loop 1.40External closing pair is G 4-C 217
Stack -2.20External closing pair is A 6-U 216
Stack -3.30External closing pair is C 7-G 215
Stack -3.30External closing pair is C 8-G 214
Stack -3.30External closing pair is C 9-G 213
Stack -3.30External closing pair is C 10-G 212
Stack -3.30External closing pair is C 11-G 211
Helix -18.70 7 base pairs.
Interior loop 2.70External closing pair is C 12-G 210
Stack -3.30External closing pair is G 16-C 205
Stack -3.30External closing pair is G 17-C 204
Stack -3.30External closing pair is G 18-C 203
Stack -3.30External closing pair is G 19-C 202
Helix -13.20 5 base pairs.
Multi-loop 0.90External closing pair is G 20-C 201
11 ss bases & 6 closing helices.
Stack -2.20External closing pair is A 180-U 199
Stack -2.40External closing pair is C 181-G 198
Stack -2.40External closing pair is G 182-C 197
Stack -2.10External closing pair is A 183-U 196
Stack -3.30External closing pair is G 184-C 195
Stack -2.20External closing pair is G 185-C 194
Stack -2.10External closing pair is U 186-A 193
Helix -16.70 8 base pairs.
Hairpin loop 3.20Closing pair is G 187-C 192
Stack -2.20External closing pair is A 164-U 179
Stack -2.40External closing pair is C 165-G 178
Stack -3.30External closing pair is G 166-C 177
Helix -7.90 4 base pairs.
Hairpin loop 4.60Closing pair is G 167-C 176
Stack -2.20External closing pair is G 74-C 158
Stack -1.30External closing pair is U 75-A 157
Helix -3.50 3 base pairs.
Multi-loop 2.00External closing pair is U 76-G 156
5 ss bases & 4 closing helices.
Stack -3.30External closing pair is G 130-C 153
Stack -3.30External closing pair is G 131-C 152
Helix -6.60 3 base pairs.
Interior loop -0.30External closing pair is G 132-C 151
Stack -2.10External closing pair is A 135-U 148
Stack -3.40External closing pair is G 136-C 147
Stack -2.40External closing pair is C 137-G 146
Stack -3.40External closing pair is G 138-C 145
Helix -11.30 5 base pairs.
Hairpin loop 0.40Closing pair is C 139-G 144
Stack -3.30External closing pair is G 102-C 128
Stack -2.20External closing pair is G 103-C 127
Helix -5.50 3 base pairs.
Interior loop 1.70External closing pair is U 104-A 126
Stack -2.50External closing pair is G 106-U 124
Stack -2.40External closing pair is C 107-G 123
Stack -3.40External closing pair is G 108-C 122
Stack -3.30External closing pair is C 109-G 121
Stack -2.10External closing pair is C 110-G 120
Stack -2.40External closing pair is U 111-A 119
Helix -16.10 7 base pairs.
Hairpin loop 4.20Closing pair is C 112-G 118
Stack -2.40External closing pair is U 78-A 100
Stack -2.40External closing pair is C 79-G 99
Stack -2.20External closing pair is G 80-C 98
Stack -2.10External closing pair is U 81-A 97
Stack -3.40External closing pair is G 82-C 96
Stack -2.40External closing pair is C 83-G 95
Stack -2.20External closing pair is G 84-C 94
Stack -0.90External closing pair is U 85-A 93
Helix -18.00 9 base pairs.
Hairpin loop 5.10Closing pair is U 86-A 92
Stack -3.40External closing pair is G 50-C 72
Stack -3.30External closing pair is C 51-G 71
Stack -2.10External closing pair is C 52-G 70
Stack -2.20External closing pair is A 53-U 69
Stack -2.40External closing pair is C 54-G 68
Stack -3.40External closing pair is G 55-C 67
Stack -2.10External closing pair is C 56-G 66
Stack -2.10External closing pair is U 57-A 65
Stack -3.40External closing pair is G 58-C 64
Helix -24.40 10 base pairs.
Hairpin loop 5.70Closing pair is C 59-G 63
Stack -3.30External closing pair is C 24-G 48
Stack -2.10External closing pair is C 25-G 47
Helix -5.40 3 base pairs.
Bulge loop 1.40External closing pair is U 26-A 46
Stack -2.40External closing pair is C 27-G 44
Stack -3.40External closing pair is G 28-C 43
Stack -2.40External closing pair is C 29-G 42
Stack -3.40External closing pair is G 30-C 41
Stack -2.10External closing pair is C 31-G 40
Stack -2.10External closing pair is A 32-U 39
Helix -15.80 7 base pairs.
Hairpin loop 3.20Closing pair is G 33-C 38