X~ MFOLD.BCK̂ MFOLD.BCK6BACKUP/LOG [MFOLD...] PUBLIC2:[ANONYMOUS]MFOLD.BCK/SAV CHERRY kiV5.5 _OPAL::  _AMBER$DKA0: V5.5 ~ *[MFOLD]ALU.CONNECT;1+,+./ 4DN-*0123KPWO56VJ7/Bi89GHJDFOLD of: alu.gcg Check: 7822 from: 1 to: 311 January 4, 1990 22:34Length: 311 Energy: -121.0 .. 1 S 0 2 0 1 2 A 1 3 0 2 3 M 2 4 0 3 4 P 3 5 0 4 5 L 4 6 0 5 6 E 5 7 0 6 7 A 6 8 0 7 8 L 7 9 0 8 9 U 8 10 0 9 10 S 9 11 0 10 11 E 10 12 0 11 12 Q 11 13 0 12 13 U 12 14 0 13 14 E 13 15 0 14 15 N 14 16 0 15 16 C 15 17 0 16 17 E 16 18 0 17 18 A 17 19 0 18 19 C 18 20 0 19 20 J 19 21 0 20 21 L 20 22 0 21 22 G 21 23 0 22 23 G 22 24 203 23 24 C 23 25 202 24 25 C 24 26 201 25 26 G 25 27 180 26 27 G 26 28 179 27 28 G 27 29 178 28 29 C 28 30 177 29 30 G 29 31 176 30 31 C 30 32 175 31 32 G 31 33 174 32 33 G 32 34 172 33 34 C 33 35 171 34 35 G 34 36 0 35 36 G 35 37 169 36 37 C 36 38 168 37 38 U 37 39 0 38 39 C 38 40 167 39 40 A 39 41 166 40 41 C 40 42 165 41 42 G 41 43 164 42 43 C 42 44 163 43 44 C 43 45 162 44 45 U 44 46 141 45 46 G 45 47 140 46 47 U 46 48 139 47 48 A 47 49 138 48 49 A 48 50 0 49 50 U 49 51 65 50 51 C 50 52 64 51 52 C 51 53 63 52 53 C 52 54 62 53 54 A 53 55 0 54 55 G 54 56 0 55 56 C 55 57 0 56 57 A 56 58 0 57 58 C 57 59 0 58 59 U 58 60 0 59 60 U 59 61 0 60 61 C 60 62 0 61 62 G 61 63 53 62 63 G 62 64 52 63 64 G 63 65 51 64 65 A 64 66 50 65 66 G 65 67 0 66 67 G 66 68 0 67 68 C 67 69 0 68 69 C 68 70 0 69 70 G 69 71 137 70 71 A 70 72 136 71 72 G 71 73 135 72 73 G 72 74 134 73 74 C 73 75 133 74 75 G 74 76 132 75 76 G 75 77 131 76 77 G 76 78 130 77 78 A 77 79 0 78 79 G 78 80 0 79 80 G 79 81 0 80 81 A 80 82 0 81 82 U 81 83 126 82 83 U 82 84 125 83 84 G 83 85 124 84 85 C 84 86 123 85 86 U 85 87 122 86 87 U 86 88 120 87 88 G 87 89 119 88 89 A 88 90 0 89 90 G 89 91 116 90 91 C 90 92 115 91 92 C 91 93 114 92 93 C 92 94 113 93 94 A 93 95 112 94 95 G 94 96 111 95 96 G 95 97 110 96 97 A 96 98 0 97 98 G 97 99 106 98 99 U 98 100 105 99 100 U 99 101 0 100 101 C 100 102 0 101 102 G 101 103 0 102 103 A 102 104 0 103 104 G 103 105 0 104 105 A 104 106 99 105 106 C 105 107 98 106 107 C 106 108 0 107 108 A 107 109 0 108 109 G 108 110 0 109 110 C 109 111 96 110 111 C 110 112 95 111 112 U 111 113 94 112 113 G 112 114 93 113 114 G 113 115 92 114 115 G 114 116 91 115 116 C 115 117 90 116 117 G 116 118 0 117 118 A 117 119 0 118 119 C 118 120 88 119 120 A 119 121 87 120 121 U 120 122 0 121 122 A 121 123 86 122 123 G 122 124 85 123 124 C 123 125 84 124 125 G 124 126 83 125 126 A 125 127 82 126 127 G 126 128 0 127 128 A 127 129 0 128 129 C 128 130 0 129 130 C 129 131 77 130 131 C 130 132 76 131 132 C 131 133 75 132 133 G 132 134 74 133 134 U 133 135 73 134 135 C 134 136 72 135 136 U 135 137 71 136 137 C 136 138 70 137 138 U 137 139 48 138 139 A 138 140 47 139 140 C 139 141 46 140 141 A 140  142 45 141 142 A 141 143 0 142 143 A 142 144 0 143 144 A 143 145 0 144 145 A 144 146 156 145 146 A 145 147 155 146 147 U 146 148 154 147 148 A 147 149 0 148 149 C 148 150 0 149 150 A 149 151 0 150 151 A 150 152 0 151 152 A 151 153 0 152 153 A 152 154 0 153 154 A 153 155 147 154 155 U 154 156 146 155 156 U 155 157 145 156 157 A 156 158 0 157 158 G 157 159 0 158 159 C 158 160 0 159 160 C 159 161 0 160 161 G 160 162 0 161 162 G 161 163 44 162 163 G 162 164 43 163 164 C 163 165 42 164 165 G 164 166 41 165 166 U 165 167 40 166 167 G 166 168 39 167 168 G 167 169 37 168 169 U 168 170 36 169 170 G 169 171 0 170 171 G 170 172 34 171 172 C 171 173 33 172 173 G 172 174 0 173 174 C 173 175 32 174 175 G 174 176 31 175 176 C 175 177 30 176 177 G 176 178 29 177 178 C 177 179 28 178 179 C 178 180 27 179 180 U 179 181 26 180 181 G 180 182 0 181 182 U 181 183 0 182 183 A 182 184 0 183 184 A 183 185 0 184 185 U 184 186 200 185 186 C 185 187 199 186 187 C 186 188 198 187 188 C 187 189 197 188 189 A 188 190 0 189 190 G 189 191 0 190 191 C 190 192 0 191 192 U 191 193 0 192 193 A 192 194 0 193 194 C 193 195 0 194 195 U 194 196 0 195 196 C 195 197 0 196 197 G 196 198 188 197 198 G 197 199 187 198 199 G 198 200 186 199 200 A 199 201 185 200 201 G 200 202 25 201 202 G 201 203 24 202 203 C 202 204 23 203 204 U 203 205 304 204 205 G 204 206 303 205 206 A 205 207 302 206 207 G 206 208 301 207 208 G 207 209 300 208 209 C 208 210 299 209 210 G 209 211 298 210 211 G 210 212 297 211 212 G 211 213 296 212 213 A 212 214 0 213 214 G 213 215 0 214 215 G 214 216 0 215 216 A 215 217 0 216 217 U 216 218 292 217 218 C 217 219 291 218 219 G 218 220 290 219 220 C 219 221 289 220 221 U 220 222 288 221 222 U 221 223 287 222 223 G 222 224 0 223 224 A 223 225 0 224 225 G 224 226 282 225 226 C 225 227 281 226 227 C 226 228 280 227 228 C 227 229 279 228 229 G 228 230 278 229 230 G 229 231 277 230 231 G 230 232 276 231 232 A 231 233 0 232 233 G 232 234 0 233 234 G 233 235 0 234 235 C 234 236 274 235 236 G 235 237 273 236 237 G 236  238 272 237 238 A 237 239 271 238 239 G 238 240 270 239 240 G 239 241 0 240 241 C 240 242 0 241 242 U 241 243 269 242 243 G 242 244 268 243 244 C 243 245 267 244 245 A 244 246 266 245 246 G 245 247 265 246 247 U 246 248 264 247 248 G 247 249 263 248 249 A 248 250 0 249 250 G 249 251 262 250 251 C 250 252 261 251 252 C 251 253 0 252 253 G 252 254 0 253 254 U 253 255 0 254 255 G 254 256 0 255 256 A 255 257 0 256 257 U 256 258 0 257 258 C 257 259 0 258 259 G 258 260 0 259 260 C 259 261 0 260 261 G 260 262 251 261 262 C 261 263 250 262 263 C 262 264 248 263 264 A 263 265 247 264 265 C 264 266 246 265 266 U 265 267 245 266 267 G 266 268 244 267 268 C 267 269 243 268 269 A 268 270 242 269 270 C 269 271 239 270 271 U 270 272 238 271 272 C 271 273 237 272 273 C 272 274 236 273 274 G 273 275 235 274 275 G 274 276 0 275 276 C 275 277 231 276 277 C 276 278 230 277 278 U 277 279 229 278 279 G 278 280 228 279 280 G 279 281 227 280 281 G 280 282 226 281 282 C 281 283 225 282 283 G 282 284 0 283 284 A 283 285 0 284 285 C 284 286 0 285 286 G 285 287 0 286 287 G 286 288 222 287 288 A 287 289 221 288 289 G 288 290 220 289 290 C 289 291 219 290 291 G 290 292 218 291 292 A 291 293 217 292 293 G 292 294 0 293 294 A 293 295 0 294 295 C 294 296 0 295 296 C 295 297 212 296 297 C 296 298 211 297 298 C 297 299 210 298 299 G 298 300 209 299 300 U 299 301 208 300 301 C 300 302 207 301 302 U 301 303 206 302 303 C 302 304 205 303 304 A 303 305 204 304 305 A 304 306 0 305 306 A 305 307 0 306 307 A 306 308 0 307 308 A 307 309 0 308 309 A 308 310 0 309 310 A 309 311 0 310 311 A 310 0 0 311*[MFOLD]ALU.CT;1+,0.&/ 48&$-*0123KPWO%5 6@IM7Li89GHJ8 290 ENERGY = -114.1 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 0 25 26 T 25 27 0 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 139 45 46 G 45 47 138 46 4<7 C 46 48 137 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 135 124 125 A 124 126 134 125 126 T 125 127 133 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 126 133 134 T 133 135 125 134 135 T 134 136 124 135 136 A 135 137 0 136 137 G 136 138 47 137 138 C 137 139 46 138 139 C 138 140 45 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -112.9 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 120 24 25 G 24 26 119 25 26 T 25 27 118 26 27 A 26 28 117 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 0 45 46 G 45 47 0 46 47 C 46 48 0 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 27 117 118 A 117 119 26 118 119 C 118 120 25 119 120 A 119 121 24 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 0 136 137 G 136 138 0 137 138 C 137 139 0 138 139 C 138 140 0 139 140 G 139 141 0 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A " 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -112.4 ACJL  1 G 0 2 183 1 2 G 1 3 182 2 3 C 2 4 181 3 4 C 3 5 180 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 0 25 26 T 25 27 0 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 139 45 46 G 45 47 138 46 47 C 46 48 137 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 pI~ MFOLD.BCK0*[MFOLD]ALU.CT;18& ) 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 135 124 125 A 124 126 134 125 126 T 125 127 133 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 126 133 134 T 133 135 125 134 135 T 134 . 136 124 135 136 A 135 137 0 136 137 G 136 138 47 137 138 C 137 139 46 138 139 C 138 140 45 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 0 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 4 180 181 G 180 182 3 181 182 C 181 183 2 182 183 T 182 184 1 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 $7 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 0 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -111.9 ACJL  1 G 0 2 48 1 2 G 1 3 47 2 3 C 2 4 46 3 4 C 3 5 45 4 5 G 4 6 0 5 6 G 5 7 0 6 7 G 6 8 26 7 8 C 7 9 25 8 9 G 8 10 24 9 10 C 9 11 0 10 11 G 10 12 23 11 12 G 11 13 22 12 13 C 12 14 21 13 14 G 13 15 20 14 15 G 14 16 0 15 16 C 15 17 0 16 17 T 16 18 0 17 18 C 17 19 0 18 19 A 18 20 0 19 20 C 19 21 14 20 21 G 20 22 13 21 22 C 21 23 12 22 23 C 22 24 11 23 24 T 23 25 9 24 25 G 24 26 8 25 26 T 25 27 7 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 4 45 46 G 45 47 3 46 47 C 46 48 2 47 48 C 47 49 1 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 0 136 137 G 136 138 0 137 138 C 137 139 0 138 139 C 138 140 160 139 140 G 139 141 159 140 141 G 140 142 158 141 142 G 141 143 157 142 143 C 142 144 156 143 144 G 143 145 155 144 145 T 144 146 154 145 146 G 145 147 153 146 147 G 146 148 0 147 148 T 147 149 0 148 149 G 148 150 0 149 150 G 149 151 0 150 151 C 150 152 0 151 152 G 151 153 0 152 153 C 152 154 146 153 154 G 153 155 145 154 155 C 154 156 144 155 156 G 155 157 143 156 157 C 156 158 142 157 158 C 157 159 141 158 159 T 158 160 140 159 160 G 159 161 139 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 I191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -110.6 ACJL  1 G 0 2 48 1 2 G 1 3 47 2 3 C 2 4 46 3 4 C 3 5 45 4 5 G 4 6 0 5 6 G 5 7 0 6 7 G 6 8 26 7 8 C 7 9 25 8 9 G 8 10 24 9 10 C 9 11 0 10 11 G 10 12 23 11 12 G 11 13 22 12 13 C 12 14 21 13 14 G 13 15 20 14 15 G 14 16 0 15 16 C 15 17 0 16 17 T 16 18 0 17 18 C 17 19 0 18 19 A 18 20 0 19 20 C 19 21 14 20 21 G 20 22 13 21 22 C 21 23 12 22 23 C 22 24 11 23 24 T 23 25 9 24 25 G 24 26 8 25 26 T 25 27 7 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 L31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 4 45 46 G 45 47 3 46 47 C 46 48 2 47 48 C 47 49 1 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 183 136 137 G 136 138 182 137 138 C 137 139 181 138 139 C 138 140 180 139 140 G 139 141 159 140 141 G 140 142 158 141 142 G 141 143 157 142 143 C 142 144 156 143 144 G 143 145 155 144 145 T 144 146 154 145 146 G 145 147 153 146 147 G 146 148 0 147 148 T 147 149 0 148 149 G 148 150 0 149 150 G 149 151 0 150 151 C 150 152 0 151 152 G 151 153 0 152 153 C 152 154 146 153 154 G 153 155 145 154 155 C 154 156 144 155 156 G 155 157 143 156 157 C 156 158 142 157 158 C 157 159 141 158 159 T 158 160 140 159 160 G 159 161 0 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 139 180 181 G 180 182 138 181 182 C 181 183 137 182 183 T 182 184 136 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 2[71 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 0 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -109.1 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 64 25 26 T 25 27 63 26 27 A 26 28 62 27 ^ 28 A 27 29 61 28 29 T 28 30 60 29 30 C 29 31 59 30 31 C 30 32 58 31 32 C 31 33 56 32 33 A 32 34 0 33 34 G 33 35 53 34 35 C 34 36 52 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 51 38 39 T 38 40 50 39 40 C 39 41 49 40 41 G 40 42 48 41 42 G 41 43 47 42 43 G 42 44 0 43 44 A 43 45 0 44 45 G 44 46 0 45 46 G 45 47 0 46 47 C 46 48 42 47 48 C 47 49 41 48 49 G 48 50 40 49 50 A 49 51 39 50 51 G 50 52 38 51 52 G 51 53 35 52 53 C 52 54 34 53 54 G 53 55 0 54 55 G 54 56 0 55 56 G 55 57 32 56 57 A 56 58 0 57 58 G 57 59 31 58 59 G 58 60 30 59 60 A 59 61 29 60 61 T 60 62 28 61 62 T 61 63 27 62 63 G 62 64 26 63 64 C 63 65 25 64 65 T 64 66 0 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 0 101 102 G 101 103 138 102 103 C 102 104 137 103 104 G 103 105 116 104 105 A 104 106 115 105 106 G 105 107 114 106 107 A 106 108 113 107 108 C 107 109 112 108 109 C 108 110 0 109 110 C 109 111 0 110 111 C 110 112 0 111 112 G 111 113 108 112 113 T 112 114 107 113 114 C 113 115 106 114 115 T 114 116 105 115 116 C 115 117 104 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 0 136 137 G 136 138 103 137 138 C 137 139 102 138 139 C 138 140 0 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 VZ~ MFOLD.BCK0*[MFOLD]ALU.CT;18&Qy|g172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -107.2 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 0 25 26 T 25 27 0 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 139 45 46 G 45 47 138 46 47 C 46 48 137 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 135 124 125 A 124 126 134 125 126 T 125 127 133 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 126 133 134 T 133 135 125 134 135 T 134 136 124 135 136 A 135 137 0 136 137 G 136 138 47 137 138 C 137 139 46 138 139 C 138 140 45 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 284 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 161 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -106.7 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 0 25 26 T 25 27 0 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 139 45 46 G 45 47 138 46 47 C 46 48 137 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 62 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 0 61 62 T 61 63 58 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 0 104 105 A 104 106 0 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 0 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 135 124 125 A 124 126 134 125 126 T 125 127 133 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 126 133 134 T 133 135 125 134 135 T 134 136 124 135 136 A 135 137 0 136 137 G 136 138 47 137 138 C 137 139 46 138 139 C 138 140 45 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -106.4 ACJL  1 G 0 2 183 1 2 G 1 3 182 2 3 C 2 4 181 3 4 C 3 5 180 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 0 25 26 T 25 27 0 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 139 45 46 G 45 47 138 46 47 C 46 48 137 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 135 124 125 A 124 126 134 125 126 T 125 127 133 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 126 133 134 T 133 135 125 134 135 T 134 136 124 135 136 A 135 137 0 136 137 G 136 138 47 137 138 C 137 139 46 138 139 C 138 140 45 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 0 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 4 180 181 G 180 182 3 181 182 C 181 183 2 182 183 T 182 184 1 183 184 G 183 185 0 184 185 A 184 186 201 185 186 G 185 187 200 186 187 G 186 188 199 187 188 C 187 189 198 188 189 G 188 190 197 189 190 G 189 191 196 190 191 G 190 192 0 191 192 A 191 193 0 192 193 G 192 194 0 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 190 196 197 C 196 198 189 197 198 G 197 199 188 198 199 C 198 200 187 199 200 T 199 201 186 200 201 T 200 202 185 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 0 266 267 A 266 268 0 267 268 G 267 269 0 268 269 C 268 270 0 269 270 G 269 271 282 270 271 A 270 272 281 271 272 G 271 273 280 272 273 A 272 274 279 273 274 C 273 275 278 274 275 C 274 276 0 275 276 C 275 277 0 276 277 C 276 278 0 277 278 G 277 279 274 278 279 T 278 280 273 279 280 C 279 281 272 280 281 T 280 282 271 281 282 C 281 283 270 282 283 A 282 284 0 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289w5~ MFOLD.BCK0*[MFOLD]ALU.CT;18&u| 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -106.4 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 139 25 26 T 25 27 0 26 27 A 26 28 62 27 28 A 27 29 61 28 29 T 28 30 60 29 30 C 29 31 59 30 31 C 30 32 58 31 32 C 31 33 56 32 33 A 32 34 0 33 34 G 33 35 53 34 35 C 34 36 52 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 51 38 39 T 38 40 50 39 40 C 39 41 49 40 41 G 40 42 48 41 42 G 41 43 47 42 43 G 42 44 0 43 44 A 43 45 0 44 45 G 44 46 0 45 46 G 45 47 0 46 47 C 46 48 42 47 48 C 47 49 41 48 49 G 48 50 40 49 50 A 49 51 39 50 51 G 50 52 38 51 52 G 51 53 35 52 53 C 52 54 34 53 54 G 53 55 0 54 55 G 54 56 0 55 56 G 55 57 32 56 57 A 56 58 0 57 58 G 57 59 31 58 59 G 58 60 30 59 60 A 59 61 29 60 61 T 60 62 28 61 62 T 61 63 27 62 63 G 62 64 138 63 64 C 63 65 137 64 65 T 64 66 136 65 66 T 65 67 120 66 67 G 66 68 119 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 0 98 99 A 98 100 0 99 100 T 99 101 0 100 101 A 100 102 0 101 102 G 101 103 0 102 103 C 102 104 0 103 104 G 103 105 116 104 105 A 104 106 115 105 106 G 105 107 114 106 107 A 106 108 113 107 108 C 107 109 112 108 109 C 108 110 0 109 110 C 109 111 0 110 111 C 110 112 0 111 112 G 111 113 108 112 113 T 112 114 107 113 114 C 113 115 106 114 115 T 114 116 105 115 116 C 115 117 104 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 67 119 120 A 119 121 66 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 65 136 137 G 136 138 64 137 138 C 137 139 63 138 139 C 138 140 25 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -106.4 ACJL  1 G 0 2 48 1 2 G 1 3 47 2 3 C 2 4 46 3 4 C 3 5 45 4 5 G 4 6 0 5 6 G 5 7 0 6 7 G 6 8 26 7 8 C 7 9 25 8 9 G 8 10 24 9 10 C 9 11 0 10 11 G 10 12 23 11 12 G 11 13 22 12 13 C 12 14 21 13 14 G 13 15 20 14 15 G 14 16 0 15 16 C 15 17 0 16 17 T 16 18 0 17 18 C 17 19 0 18 19 A 18 20 0 19 20 C 19 21 14 20 21 G 20 22 13 21 22 C 21 23 12 22 23 C 22 24 11 23 24 T 23 25 9 24 25 G 24 26 8 25 26 T 25 27 7 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 4 45 46 G 45 47 3 46 47 C 46 48 2 47 48 C 47 49 1 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 161 118 119 C 118 120 160 119 120 A 119 121 159 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 0 136 137 G 136 138 0 137 138 C 137 139 0 138 139 C 138 140 0 139 140 G 139 141 0 140 141 G 140 142 158 141 142 G 141 143 157 142 143 C 142 144 156 143 144 G 143 145 155 144 145 T 144 146 154 145 146 G 145 147 153 146 147 G 146 148 0 147 148 T 147 149 0 148 149 G 148 150 0 149 150 G 149 151 0 150 151 C 150 152 0 151 152 G 151 153 0 152 153 C 152 154 146 153 154 G 153 155 145 154 155 C 154 156 144 155 156 G 155 157 143 156 157 C 156 158 142 157 158 C 157 159 141 158 159 T 158 160 120 159 160 G 159 161 119 160 161 T 160 162 118 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -106.0 ACJL  1 G 0 2 48 1 2 G 1 3 47 2 3 C 2 4 46 3 4 C 3 5 45 4 5 G 4 6 0 5 6 G 5 7 0 6 7 G 6 8 26 7 8 C 7 9 25 8 9 G 8 10 24 9 10 C 9 11 0 10 11 G 10 12 23 11 12 G 11 13 22 12 13 C 12 14 21 13 14 G 13 15 20 14 15 G 14 16 0 15 16 C 15 17 0 16 17 T 16 18 0 17 18 C 17 19 0 18 19 A 18 20 0 19 20 C 19 21 14 20 21 G 20 22 13 21 22 C 21 23 12 22 23 C 22 24 11 23 24 T 23 25 9 24 25 G 24 26 8 25 26 T 25 27 7 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 4 45 46 G 45 47 3 46 47 C 46 48 2 47 48 C 47 49 1 48 49 G 48 50 282 49 50 A 49 51 281 50 51 G 50 52 280 51 52 G 51 53 279 52 53 C 52 54 278 53 54 G 53 55 277 54 55 G 54 56 276 55 56 G 55 57 275 56 57 A 56 58 0 57 58 G 57 59 274 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 271 61 62 T 61 63 270 62 63 G 62 64 269 63 64 C 63 65 268 64 65 T 64 66 267 65 66 T 65 67 266 66 67 G 66 68 0 67 68 A 67 69 0 68 69 G 68 70 261 69 70 C 69 71 260 70 71 C 70 72 259 71 72 C 71 73 258 72 73 A 72 74 257 73 74 G 73 75 256 74 75 G 74 76 255 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 213 85 86 C 85 87 212 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 210 89 90 C 89 91 209 90 91 T 90 92 208 91 92 G 91 93 207 92 93 G 92 94 206 93 94 G 93 95 205 94 95 C 94 96 204 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 202 98 99 A 98 100 201 99 100 T 99 101 0 100 101 A 100 102 200 101 102 G 101 103 199 102 103 C 102 104 198 103 104 G 103 105 197 104 105 A 104 106 196 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 193 108 109 C 108 110 191 109 110 C 109 111 190 110 111 C 110 112 189 111 112 G 111 113 188 112 113 T 112 114 187 113 114 C 113 115 186 114 115 T 114 116 185 115 116 C 115 117 184 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 183 136 137 G 136 138 182 137 138 C 137 139 181 138 139 C 138 140 180 139 140 G 139 141 159 140 141 G 140 142 158 141 142 G 141 143 157 142 143 C 142 144 156 143 144 G 143 145 155 144 145 T 144 146 154 145 146 G 145 147 153 146 147 G 146 148 0 147 148 T 147 149 0 148 149 G 148 150 0 149 150 G 149 151 0 150 151 C 150 152 0 151 152 G 151 153 0 152 153 C 152 154 146 153 154 G 153 155 145 154 155 C 154 156 144 155 156 G 155 157 143 156 157 C 156 158 142 157 158 C 157 159 141 158 159 T 158 160 140 159 160 G 159 161 0 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 139 180 181 G 180 182 138 181 182 C 181 183 137 182 183 T 182 184 136 183 184 G 183 185 116 184 185 A 184 186 115 185 186 G 185 187 114 186 187 G 186 188 113 187 188 C 187 189 112 188 189 G 188 190 111 189 190 G 189 191 110 190 191 G 190 192 109 191 192 A 191 193 0 192 193 G 192 194 108 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 105 196 197 C 196 198 104 197 198 G 197 199 103 198 199 C 198 200 102 199 200 T 199 201 101 200 201 T 200 202 99 201 202 G 201 203 98 202 203 A 202 204 0 203 204 G 203 205 95 204 205 C 204 206 94 205 206 C 205 207 93 206 207 C 206 208 92 207 208 G 207 209 91 208 209 G 208 210 90 209 210 G 209 211 89 210 211 A 210 212 0 211 212 G 211 213 86 212 213 G 212 214 85 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 75 255 256 C 255 257 74 256 257 T 256 258 73 257 258 G 257 259 72 258 259 G 258 260 71 259 260 G 259 261 70 260 261 C 260 262 69 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 66 266 267 A 266 268 65 267 268 G 267 269 64 268 269 C 268 270 63 269 270 G 269 271 62 270 271 A 270 272 61 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 58 274 275 C 274 276 56 275 276 C 275 277 55 276 277 C 276 278 54 277 278 G 277 279 53 278 279 T 278 280 52 279 280 C 279 281 51 280 281 T 280 282 50 281 282 C 281 283 49 282 283 A 282 284 0 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -105.9 ACJL  1 G 0 2 48 1 2 G 1 3 47 2 3 C 2 4 46 3 4 C 3 5 45 4 5 G 4 6 0 5 6 G 5 7 0 6 7 G 6 8 26 7 8 C 7 9 25 8 9 G 8 10 24 9 10 C 9 11 0 10 11 G 10 12 23 11 12 G 11 13 22 12 13 C 12 14 21 13 14 G 13 15 20 14 15 G 14 16 0 15 16 C 15 17 0 16 17 T 16 18 0 17 18 C 17 19 0 18 19 A 18 20 0 19 20 C 19 21 14 20 21 G 20 22 13 21 22 C 21 23 12 22 23 C 22 24 11 23 24 T 23 25 9 24 25 G 24 26 8 25 26 T 25 27 7 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 4 45 46 G 45 47 3 46 47 C 46 48 2 47 48 C 47 49 1 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T E Q~ MFOLD.BCK0*[MFOLD]ALU.CT;18&L112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 284 134 135 T 134 136 0 135 136 A 135 137 183 136 137 G 136 138 182 137 138 C 137 139 181 138 139 C 138 140 180 139 140 G 139 141 159 140 141 G 140 142 158 141 142 G 141 143 157 142 143 C 142 144 156 143 144 G 143 145 155 144 145 T 144 146 154 145 146 G 145 147 153 146 147 G 146 148 0 147 148 T 147 149 0 148 149 G 148 150 0 149 150 G 149 151 0 150 151 C 150 152 0 151 152 G 151 153 0 152 153 C 152 154 146 153 154 G 153 155 145 154 155 C 154 156 144 155 156 G 155 157 143 156 157 C 156 158 142 157 158 C 157 159 141 158 159 T 158 160 140 159 160 G 159 161 0 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 139 180 181 G 180 182 138 181 182 C 181 183 137 182 183 T 182 184 136 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 0 283 284 A 283 285 134 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -105.8 ACJL  1 G 0 2 119 1 2 G 1 3 47 2 3 C 2 4 46 3 4 C 3 5 45 4 5 G 4 6 0 5 6 G 5 7 0 6 7 G 6 8 26 7 8 C 7 9 25 8 9 G 8 10 24 9 10 C 9 11 0 10 11 G 10 12 23 11 12 G 11 13 22 12 13 C 12 14 21 13 14 G 13 15 20 14 15 G 14 16 0 15 16 C 15 17 0 16 17 T 16 18 0 17 18 C 17 19 0 18 19 A 18 20 0 19 20 C 19 21 14 20 21 G 20 22 13 21 22 C 21 23 12 22 23 C 22 24 11 23 24 T 23 25 9 24 25 G 24 26 8 25 26 T 25 27 7 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 4 45 46 G 45 47 3 46 47 C 46 48 2 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 1 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 0 136 137 G 136 138 0 137 138 C 137 139 0 138 139 C 138 140 160 139 140 G 139 141 159 140 141 G 140 142 158 141 142 G 141 143 157 142 143 C 142 144 156 143 144 G 143 145 155 144 145 T 144 146 154 145 146 G 145 147 153 146 147 G 146 148 0 147 148 T 147 149 0 148 149 G 148 150 0 149 150 G 149 151 0 150 151 C 150 152 0 151 152 G 151 153 0 152 153 C 152 154 146 153 154 G 153 155 145 154 155 C 154 156 144 155 156 G 155 157 143 156 157 C 156 158 142 157 158 C 157 159 141 158 159 T 158 160 140 159 160 G 159 161 139 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -105.6 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 148 15 16 C 15 17 147 16 17 T 16 18 0 17 18 C 17 19 146 18 19 A 18 20 145 19 20 C 19 21 144 20 21 G 20 22 143 21 22 C 21 23 142 22 23 C 22 24 141 23 24 T 23 25 140 24 25 G 24 26 0 25 26 T 25 27 0 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 139 45 46 G 45 47 138 46 47 C 46 48 137 47 48 C 47 49 0 48 49 G 48 50 116 49 50 A 49 51 115 50 51 G 50 52 114 51 52 G 51 53 113 52 53 C 52 54 112 53 54 G 53 55 111 54 55 G 54 56 110 55 56 G 55 57 109 56 57 A 56 58 0 57 58 G 57 59 108 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 105 61 62 T 61 63 104 62 63 G 62 64 103 63 64 C 63 65 102 64 65 T 64 66 101 65 66 T 65 67 99 66 67 G 66 68 98 67 68 A 67 69 0 68 69 G 68 70 95 69 70 C 69 71 94 70 71 C 70 72 93 71 72 C 71 73 92 72 73 A 72 74 91 73 74 G 73 75 90 74 75 G 74 76 89 75 76 A 75 77 0 76 77 G 76 78 0 77 78 T 77 79 0 78 79 T 78 80 0 79 80 C 79 81 0 80 81 G 80 82 0 81 82 A 81 83 0 82 83 G 82 84 0 83 84 A 83 85 0 84 85 C 84 86 0 85 86 C 85 87 0 86 87 A 86 88 0 87 88 G 87 89 0 88 89 C 88 90 75 89 90 C 89 91 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 94 71 93 94 G 93 95 70 94 95 C 94 96 69 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 67 98 99 A 98 100 66 99 100 T 99 101 0 100 101 A 100 102 65 101 102 G 101 103 64 102 103 C 102 104 63 103 104 G 103 105 62 104 105 A 104 106 61 105 106 G 105 107 0 106 107 A 106 108 0 107 108 C 107 109 58 108 109 C 108 110 56 109 110 C 109 111 55 110 111 C 110 112 54 111 112 G 111 113 53 112 113 T 112 114 52 113 114 C 113 115 51 114 115 T 114 116 50 115 116 C 115 117 49 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 135 124 125 A 124 126 134 125 126 T 125 127 133 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 126 133 134 T 133 135 125 134 135 T 134 136 124 135 136 A 135 137 0 136 137 G 136 138 40 7 137 138 C 137 139 46 138 139 C 138 140 45 139 140 G 139 141 24 140 141 G 140 142 23 141 142 G 141 143 22 142 143 C 142 144 21 143 144 G 143 145 20 144 145 T 144 146 19 145 146 G 145 147 18 146 147 G 146 148 16 147 148 T 147 149 15 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 221 212 213 G 212 214 220 213 214 C 213 215 219 214 215 G 214 216 0 215 216 G 215 217 0 216 217 A 216 218 0 217 218 G 217 219 0 218 219 G 218 220 214 219 220 C 219 221 213 220 221 T 220 222 212 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 0 248 249 C 248 250 0 249 250 T 249 251 0 250 251 C 250 252 0 251 252 C 251 253 0 252 253 G 252 254 0 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 2908 290 ENERGY = -105.3 ACJL  1 G 0 2 0 1 2 G 1 3 0 2 3 C 2 4 0 3 4 C 3 5 160 4 5 G 4 6 159 5 6 G 5 7 158 6 7 G 6 8 157 7 8 C 7 9 156 8 9 G 8 10 155 9 10 C 9 11 154 10 11 G 10 12 153 11 12 G 11 13 151 12 13 C 12 14 150 13 14 G 13 15 0 14 15 G 14 16 0 15 16 C 15 17 58 16 17 T 16 18 57 17 18 C 17 19 56 18 19 A 18 20 0 19 20 C 19 21 54 20 21 G 20 22 53 21 22 C 21 23 52 22 23 C 22 24 51 23 24 T 23 25 50 24 25 G 24 26 47 25 26 T 25 27 46 26 27 A 26 28 0 27 28 A 27 29 0 28 29 T 28 30 44 29 30 C 29 31 43 30 31 C 30 32 42 31 32 C 31 33 41 32 33 A 32 34 0 33 34 G 33 35 0 34 35 C 34 36 0 35 36 A 35 37 0 36 37 C 36 38 0 37 38 T 37 39 0 38 39 T 38 40 0 39 40 C 39 41 0 40 41 G 40 42 32 41 42 G 41 43 31 42 43 G 42 44 30 43 44 A 43 45 29 44 45 G 44 46 0 45 46 G 45 47 26 46 47 C 46 48 25 47 48 C 47 49 0 48 49 G 48 50 0 49 50 A 49 51 24 50 51 G 50 52 23 51 52 G 51 53 22 52 53 C 52 54 21 53 54 G 53 55 20 54 55 G 54 56 0 55 56 G 55 57 18 56 57 A 56 58 17 57 58 G 57 59 16 58 59 G 58 60 0 59 60 A 59 61 0 60 61 T 60 62 0 61 62 T 61 63 0 62 63 G 62 64 0 63 64 C 63 65 83 64 65 T 64 66 82 65 66 T 65 67 81 66 67 G 66 68 80 67 68 A 67 69 79 68 69 G 68 70 78 69 70 C 69 71 77 70 71 C 70 72 0 71 72 C 71 73 0 72 73 A 72 74 0 73 74 G 73 75 0 74 75 G 74 76 0 75 76 A 75 77 0 76 77 G 76 78 70 77 78 T 77 79 69 78 79 T 78 80 68 79 80 C 79 81 67 80 81 G 80 82 66 81 82 A 81 83 65 82 83 G 82 84 64 83 84 A 83 85 148 84 85 C 84 86 147 85 86 C 85 87 146 86 87 A 86 88 145 87 88 G 87 89 143 88 89 C 88 90 142 89 90 C 89 91 141 90 91 T 90 92 140 91 92 G 91 93 139 92 93 G 92 94 138 93 94 G 93 95 0 94 95 C 94 96 137 95 96 G 95 97 0 96 97 A 96 98 0 97 98 C 97 99 0 98 99 A 98 100 0 99 100 T 99 101 0 100 101 A 100 102 0 101 102 G 101 103 0 102 103 C 102 104 0 103 104 G 103 105 116 104 105 A 104 106 115 105 106 G 105 107 114 106 107 A 106 108 113 107 108 C 107 109 112 108 109 C 108 110 0 109 110 C 109 111 0 110 111 C 110 112 0 111 112 G 111 113 108 112 113 T 112 114 107 113 114 C 113 115 106 114 115 T 114 116 105 115 116 C 115 117 104 116 117 T 116 118 0 117 118 A 117 119 0 118 119 C 118 120 0 119 120 A 119 121 0 120 121 A 120 122 0 121 122 A 121 123 0 122 123 A 122 124 0 123 124 A 123 125 0 124 125 A 124 126 0 125 126 T 125 127 0 126 127 A 126 128 0 127 128 C 127 129 0 128 129 A 128 130 0 129 130 A 129 131 0 130 131 A 130 132 0 131 132 A 131 133 0 132 133 A 132 134 0 133 134 T 133 135 0 134 135 T 134 136 0 135 136 A 135 137 0 136 137 G 136 138 95 137 138 C 137 139 93 138 139 C 138 140 92 139 140 G 139 141 91 140 141 G 140 142 90 141 142 G 141 143 89 142 143 C 142 144 88 143 144 G 143 145 0 144 145 T 144 146 87 145 146 G 145 147 86 146 147 G 146 148 85 147 148 T 147 149 84 148 149 G 148 150 0 149 150 G 149 151 13 150 151 C 150 152 12 151 152 G 151 153 0 152 153 C 152 154 11 153 154 G 153 155 10 154 155 C 154 156 9 155 156 G 155 157 8 156 157 C 156 158 7 157 158 C 157 159 6 158 159 T 158 160 5 159 160 G 159 161 4 160 161 T 160 162 0 161 162 A 161 163 0 162 163 A 162 164 0 163 164 T 163 165 179 164 165 C 164 166 178 165 166 C 165 167 177 166 167 C 166 168 176 167 168 A 167 169 0 168 169 G 168 170 0 169 170 C 169 171 0 170 171 T 170 172 0 171 172 A 171 173 0 172 173 C 172 174 0 173 174 T 173 175 0 174 175 C 174 176 0 175 176 G 175 177 167 176 177 G 176 178 166 177 178 G 177 179 165 178 179 A 178 180 164 179 180 G 179 181 0 180 181 G 180 182 0 181 182 C 181 183 0 182 183 T 182 184 283 183 184 G 183 185 282 184 185 A 184 186 281 185 186 G 185 187 280 186 187 G 186 188 279 187 188 C 187 189 278 188 189 G 188 190 277 189 190 G 189 191 276 190 191 G 190 192 275 191 192 A 191 193 0 192 193 G 192 194 274 193 194 G 193 195 0 194 195 A 194 196 0 195 196 T 195 197 271 196 197 C 196 198 270 197 198 G 197 199 269 198 199 C 198 200 268 199 200 T 199 201 267 200 201 T 200 202 266 201 202 G 201 203 0 202 203 A 202 204 0 203 204 G 203 205 261 204 205 C 204 206 260 205 206 C 205 207 259 206 207 C 206 208 258 207 208 G 207 209 257 208 209 G 208 210 256 209 210 G 209 211 255 210 211 A 210 212 0 211 212 G 211 213 0 212 213 G 212 214 0 213 214 C 213 215 253 214 215 G 214 216 252 215 216 G 215 217 251 216 217 A 216 218 250 217 218 G 217 219 249 218 219 G 218 220 0 219 220 C 219 221 0 220 221 T 220 222 248 221 222 G 221 223 247 222 223 C 222 224 246 223 224 A 223 225 245 224 225 G 224 226 244 225 226 T 225 227 243 226 227 G 226 228 242 227 228 A 227 229 0 228 229 G 228 230 241 229Y~ MFOLD.BCK0*[MFOLD]ALU.CT;18&! 230 C 229 231 240 230 231 C 230 232 238 231 232 G 231 233 237 232 233 T 232 234 0 233 234 G 233 235 0 234 235 A 234 236 0 235 236 T 235 237 0 236 237 C 236 238 232 237 238 G 237 239 231 238 239 C 238 240 0 239 240 G 239 241 230 240 241 C 240 242 229 241 242 C 241 243 227 242 243 A 242 244 226 243 244 C 243 245 225 244 245 T 244 246 224 245 246 G 245 247 223 246 247 C 246 248 222 247 248 A 247 249 221 248 249 C 248 250 218 249 250 T 249 251 217 250 251 C 250 252 216 251 252 C 251 253 215 252 253 G 252 254 214 253 254 G 253 255 0 254 255 C 254 256 210 255 256 C 255 257 209 256 257 T 256 258 208 257 258 G 257 259 207 258 259 G 258 260 206 259 260 G 259 261 205 260 261 C 260 262 204 261 262 G 261 263 0 262 263 A 262 264 0 263 264 C 263 265 0 264 265 G 264 266 0 265 266 G 265 267 201 266 267 A 266 268 200 267 268 G 267 269 199 268 269 C 268 270 198 269 270 G 269 271 197 270 271 A 270 272 196 271 272 G 271 273 0 272 273 A 272 274 0 273 274 C 273 275 193 274 275 C 274 276 191 275 276 C 275 277 190 276 277 C 276 278 189 277$ 278 G 277 279 188 278 279 T 278 280 187 279 280 C 279 281 186 280 281 T 280 282 185 281 282 C 281 283 184 282 283 A 282 284 183 283 284 A 283 285 0 284 285 A 284 286 0 285 286 A 285 287 0 286 287 A 286 288 0 287 288 A 287 289 0 288 289 A 288 290 0 289 290 A 289 0 0 290 74 90 91 T 90 92 73 91 92 G 91 93 72 92 93 G 92 *[MFOLD]ALU.DISTANCE;1+,1./ 4P-*0123KPWO56`-l N7Ti89GHJG Program DISTANCE computes the distance between pairs of RNA structuresM File: alu.ct P 1 290 bases ENERGY = -114.1 ACJL P 2 290 bases ENERGY = -112.9 ACJL P 3 290 bases ENERGY = -112.4 ACJL P 4 290 bases ENERGY = -111.9 ACJL P 5 290 bases ENERGY = -110.6 ACJL P 6 290 bases ENERGY = -109.1 ACJL P 7 290 bases ENERGY = -107.2 ACJL P 8 290 bases ENERGY = -106.7 ACJL P 9 290 bases ENERGY = -106.4 ACJL P 10 290 bases ENERGY = -106.4 ACJL P 11 290 bases ENERGY = -106.4 ACJL P 12 290 bases ENERGY = -106.0 ACJL P 13 290 bases ENERGY = -105.9 ACJL P 14 290 bases ENERGY = -105.8 ACJL P 15 290 bases ENERGY = -105.6 ACJL % Too many structures in input file...$ Only the first 15 will be processed DistancesP 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 1 0 2 43 0 3 23 43 0 4 45 45 67 0 5 45 45 67 23 0# 6 23 38 23 45 45 0( 7 22 43 23 45 45 23 0- 8 26 43 26 45 45 23 26 02 9 42 43 42 67 67 42 43 42 07 10 21 33 23 45 45 39 22 21 42 0< 11 45 46 67 21 22 45 45 45 67 45 0A 12 115 115 99 115 99 115 112 115 99 115 115 0F 13 49 49 67 49 50 49 45 49 70 49 49 85 0K 14 41 41 64 48 48 41 41 41 64 41 48 115 49 0P 15 19 43 23 45 45 23 22 26 42 21 45 115 49 41 0*[MFOLD]ALU.FIGURE;1+,;.-/ 4#-,-*0123KPWO-56b74 \i89GHJ.vp 20.455 129.545 100.0 0.0#.wn -29.00 319.00 319.00 -29.00.ls 1 30.m 290 0 .d 290 290.d 0 0.d 290 0.to 2 .m 290 10.reld 2.90 0.00.m 304.50 10.00.pt 10 .m 290 20.reld 2.90 0.00.m 304.50 20.00.pt 20 .m 290 30.reld 2.90 0.00.m 304.50 30.00.pt 30 .m 290 40.reld 2.90 0.00.m 304.50 40.00.pt 40 .m 290 50.reld 2.90 0.00.m 304.50 50.00.pt 50 .m 290 60.reld 2.90 0.00.m 304.50 60.00.pt 60 .m 290 70.reld 2.90 0.00.m 304.50 70.00.pt 70 .m 290 80.reld 2.90 0.00.m 304.50 80.00.pt 80 .m 290 90.reld 2.90 0.00.m 304.50 90.00.pt 90 .m 290 100.reld 2.90 0.00.m 304.50 100.00.pt 100 .m 290 110.reld 2.90 0.00.m 304.50 110.00.pt 110 .m 290 120.reld 2.90 0.00.m 304.50 120.00.pt 120 .m 290 130.reld 2.90 0.00.m 304.50 130.00.pt 130 .m 290 140.reld 2.90 0.00.m 304.50 140.00.pt 140 .m 290 150.reld 2.90 0.00.m 304.50 150.00.pt 150 .m 290 160.reld 2.90 0.00.m 304.50 160.00.pt 160 .m 290 170.reld 2.90 0.00.m 304.50 170.00.pt 170 .m 290 180.reld 2.90 0.00.m 304.50 180.00.pt 180 .m 290 190.reld 2.90 0.00.m 304.50 190.00.pt 190 .m 290 200.reld 2.90 0.00.m 304.50 200.00.pt 200 .m 290 210.reld 2.90 0.00.m 304.50 210.00.pt 210 .m 290 220.reld 2.90 0.00.m 304.50 220.00.pt 220 .m 290 230.reld 2.90 0.00.m 304.50 230.00.pt 230 .m 290 240.reld 2.90 0.00.m 304.50 240.00.pt 240 .m 290 250.reld 2.90 0.00.m 304.50 250.00.pt 250 .m 290 260.reld 2.90 0.00.m 304.50 260.00.pt 260 .m 290 270.reld 2.90 0.00.m 304.50 270.00.pt 270 .m 290 280.reld 2.90 0.00.m 304.50 280.00.pt 280.to 4 .m 10 0.reld 0.00 -2.90.m 10.00 -14.50.pt 10 .m 20 0.reld 0.00 -2.90.m 20.00 -14.50.pt 20 .m 30 0.reld 0.00 -2.90.m 30.00 -14.50.pt 30 .m 40 0.reld 0.00 -2.90.m 40.00 -14.50.pt 40 .m 50 0.reld 0.00 -2.90.m 50.00 -14.50.pt 50 .m 60 0.reld 0.00 -2.90.m 60.00 -14.50.pt 60 .m 70 0.reld 0.00 -2.90.m 70.00 -14.50.pt 70 .m 80 0.reld 0.00 -2.90.m 80.00 -14.50.pt 80 .m 90 0.reld 0.00 -2.90.m 90.00 -14.50.pt 90 .m 100 0.reld 0.00 -2.90.m 100.00 -14.50.pt 100 .m 110 0.reld 0.00 -2.90.m 110.00 -14.50.pt 110 .m 120 0.reld 0.00 -2.90.m 120.00 -14.50.pt 120 .m 130 0.reld 0.00 -2.90.m 130.00 -14.50.pt 130 .m 140 0.reld 0.00 -2.90.m 140.00 -14.50.pt 140 .m 150 0.reld 0.00 -2.90.m 150.00 -14.50.pt 150 .m 160 0.reld 0.00 -2.90.m 160.00 -14.50.pt 160 .m 170 0.reld 0.00 -2.90.m 170.00 -14.50.pt 170 .m 180 0.reld 0.00 -2.90.m 180.00 -14.50.pt 180 .m 190 0.reld 0.00 -2.90.m 190.00 -14.50.pt 190 .m 200 0.reld 0.00 -2.90.m 200.00 -14.50.pt 200 .m 210 0.reld 0.00 -2.90.m 210.00 -14.50.pt 210 .m 220 0.reld 0.00 -2.90.m 220.00 -14.50.pt 220 .m 230 0.reld 0.00 -2.90.m 230.00 -14.50.pt 230 .m 240 0.reld 0.00 -2.90.m 240.00 -14.50.pt 240 .m 250 0.reld 0.00 -2.90.m 250.00 -14.50.pt 250 .m 260 0.reld 0.00 -2.90.m 260.00 -14.50.pt 260 .m 270 0.reld 0.00 -2.90.m 270.00 -14.50.pt 270 .m 280 0.reld 0.00 -2.90.m 280.00 -14.50.pt 280 .m 290 134 .d 289 135 .p 290 161 .p 290 183 .m 289 134 .d 288 135 .p 289 161 .p 289 164 .p 289 183 .p 289 281 .m 288 134 .d 287 135 .p 288 161 .p 288 164 .p 288 183 .p 288 281 .m 287 134 .d 286 135 .p 287 161 .p 287 164 .p 287 183 .p 287 281 .m 286 134 .d 285 135 .p 286 161 .p 286 164 .p 286 183 .p 286 281 .m 285 134 .d 284 135 .p 285 161 .p 285 164 .p 285 183 .p 285 281 .m 284 134 .d 283 135 .p 284 161 .p 284 164 .p 284 183 .p 283 134 .p 283 161 .m 283 183 .d 275 191 .p 282 1 .m 282 49 .d 275 56 .m 282 180 .d 281 181 .p 282 181 .m 282 186 .d 281 187 .m 282 189 .d 279 192 .m 282 270 .d 278 274 .m 282 272 .d 281 273 .p 281 184 .m 281 186 .d 280 187 .m 280 184 .d 279 185 .m 280 262 .d 276 266 .m 277 190 .d 276 191 .p 277 191 .m 277 193 .d 276 194 .m 276 189 .d 274 191 .m 276 193 .d 275 194 .m 275 189 .d 274 190 .m 275 193 .d 274 194 .p 274 58 .p 274 193 .m 273 196 .d 272 197 .p 272 196 .m 271 61 .d 266 66 .m 271 196 .d 266 201 .p 270 196 .p 270 199 .p 269 194 .m 268 200 .d 267 201 .p 268 201 .m 267 164 .d 265 166 .m 267 196 .d 266 197 .m 266 65 .d 264 67 .m 266 182 .d 264 184 .m 266 196 .d 264 198 .m 266 199 .d 265 200 .m 266 200 .d 264 202 .m 266 206 .d 264 208 .p 265 199 .p 265 261 .p 264 204 .m 263 200 .d 261 202 .p 263 201 .p 262 199 .p 262 200 .p 262 205 .m 262 207 .d 261 208 .m 261 69 .d 255 75 .m 261 204 .d 255 210 .m 260 206 .d 259 207 .m 259 205 .d 258 206 .m 257 209 .d 256 210 .p 257 210 .m 257 211 .d 254 214 .m 257 212 .d 256 213 .m 256 208 .d 255 209 .p 255 212 .m 254 244 .d 252 246 .m 253 214 .d 249 218 .p 253 249 .m 252 209 .d 249 212 .m 252 212 .d 251 213 .p 252 213 .p 252 216 .m 252 218 .d 251 219 .m 251 215 .d 250 216 .m 251 218 .d 250 219 .m 250 215 .d 249 216 .m 250 218 .d 249 219 .p 249 215 .m 248 2@ 21 .d 242 227 .m 247 213 .d 244 216 .m 247 219 .d 246 220 .m 247 238 .d 245 240 .m 246 221 .d 245 222 .p 244 222 .m 244 232 .d 242 234 .m 243 221 .d 242 222 .m 242 212 .d 239 215 .m 242 218 .d 240 220 .p 242 225 .p 242 229 .p 242 232 .m 241 222 .d 240 223 .m 241 225 .d 239 227 .p 241 227 .m 241 229 .d 240 230 .m 241 232 .d 239 234 .p 241 234 .m 240 221 .d 238 223 .m 240 231 .d 238 233 .p 240 236 .m 239 225 .d 236 228 .m 239 229 .d 238 230 .m 238 231 .d 237 232 .m 237 216 .d 236 217 .p 237 229 .m 236 225 .d 235 226 .p 236 229 .p 236 232 .m 234 226 .d 233 227 .p 234 230 .m 233 225 .d 231 227 .p 233 228 .p 233 229 .m 231 218 .d 228 221 .m 230 222 .d 229 223 .m 221 212 .d 219 214 .p 214 83 .m 213 85 .d 212 86 .m 210 89 .d 204 95 .m 203 196 .d 202 197 .m 202 98 .d 201 99 .m 201 185 .d 196 190 .m 200 101 .d 196 105 .p 197 193 .p 196 192 .p 193 108 .m 192 164 .d 189 167 .m 191 109 .d 184 116 .m 188 169 .d 186 171 .m 188 181 .d 187 182 .m 187 165 .d 186 166 .m 186 173 .d 182 177 .m 185 134 .d 180 139 .m 185 164 .d 184 165 .m 184 161 .d 183 162 .p 184 166 .m 184 167 .d 180 171 .m 183 1 .d 180 4 .p 183 2 .p 183 131 .p 183 132 .p 183 133 .p 183 160 .p 183 163 .m 183 177 .d 182 178 .p 183 179 .p 182 1 .p 182 5 .m 182 46 .d 180 48 .m 182 156 .d 179 159 .m 182 160 .d 181 161 .p 182 176 .p 181 4 .p 181 128 .m 181 134 .d 180 135 .p 181 135 .p 181 139 .p 181 159 .m 181 164 .d 180 165 .m 181 165 .d 180 166 .m 181 166 .d 180 167 .p 181 167 .p 181 171 .m 181 173 .d 180 174 .m 181 174 .d 180 175 .p 181 175 .p 180 3 .p 180 119 .p 180 128 .p 180 134 .p 180 138 .p 180 159 .p 180 161 .p 180 164 .m 180 170 .d 179 171 .m 180 173 .d 179 174 .p 179 161 .m 179 164 .d 176 167 .m 178 3 .d 177 4 .m 178 157 .d 175 160 .p 178 161 .m 178 164 .d 176 166 .m 178 166 .d 177 167 .p 178 167 .m 178 170 .d 177 171 .p 178 171 .p 178 173 .p 178 174 .m 177 3 .d 175 5 .p 177 128 .m 177 138 .d 175 140 .m 177 164 .d 176 165 .m 177 170 .d 176 171 .p 177 173 .p 176 128 .p 176 164 .p 176 170 .p 175 169 .p 174 133 .m 174 168 .d 173 169 .p 174 169 .m 173 160 .d 171 162 .m 172 135 .d 169 138 .p 172 164 .m 171 1 .d 169 3 .p 171 163 .m 170 160 .d 169 161 .p 169 164 .p 169 165 .m 168 159 .d 167 160 .p 168 161 .p 168 164 .m 167 1 .d 166 2 .m 167 5 .d 166 6 .m 166 1 .d 165 2 .p 166 160 .m 165 1 .d 164 2 .p 165 160 .p 164 1 .p 164 5 .p 164 130 .p 164 131 .p 164 132 .m 164 133 .d 161 136 .p 164 136 .p 164 137 .p 164 160 .p 163 135 .p 163 159 .m 162 117 .d 159 120 .m 162 126 .d 159 129 .p 162 134 .p 161 1 .m 161 2 .d 160 3 .p 161 5 .p 161 6 .m 161 7 .d 159 9 .p 161 120 .p 161 121 .p 161 122 .p 161 123 .p 161 124 .m 161 125 .d 159 127 .p 161 129 .p 161 130 .p 161 131 .p 161 132 .m 161 133 .d 160 134 .m 161 137 .d 160 138 .p 161 140 .p 161 141 .m 161 142 .d 159 144 .m 161 154 .d 160 155 .m 160 4 .d 153 11 .m 160 135 .d 158 137 .m 160 139 .d 153 146 .m 159 1 .d 158 2 .p 159 2 .m 159 6 .d 158 7 .p 159 130 .p 159 137 .m 159 141 .d 158 142 .m 158 1 .d 156 3 .m 158 5 .d 157 6 .m 158 11 .d 155 14 .m 158 140 .d 157 141 .m 158 146 .d 155 149 .m 158 149 .d 156 151 .p 157 5 .m 157 137 .d 156 138 .p 157 140 .m 156 4 .d 155 5 .m 156 139 .d 155 140 .p 155 6 .m 155 7 .d 151 11 .m 155 12 .d 153 14 .m 155 137 .d 154 138 .p 155 141 .m 155 142 .d 151 146 .m 155 147 .d 153 149 .m 154 139 .d 153 140 .m 153 7 .d 150 10 .m 153 12 .d 151 14 .m 153 15 .d 152 16 .m 153 142 .d 150 145 .m 153 147 .d 152 148 .m 151 2 .d 148 5 .m 151 12 .d 150 13 .m 151 15 .d 149 17 .m 151 137 .d 148 140 .m 151 142 .d 150 143 .p 151 147 .m 150 17 .d 147 20 .m 149 13 .d 148 14 .p 149 16 .m 149 20 .d 146 23 .m 148 12 .d 147 13 .m 148 15 .d 146 17 .m 148 84 .d 145 87 .m 148 107 .d 146 109 .m 148 137 .d 145 140 .m 147 17 .d 139 25 .p 147 18 .p 146 16 .m 145 7 .d 142 10 .p 144 18 .m 144 24 .d 142 26 .m 144 111 .d 140 115 .m 143 46 .d 141 48 .m 143 88 .d 138 93 .m 143 137 .d 142 138 .m 142 23 .d 141 24 .p 142 24 .m 142 30 .d 140 32 .m 141 22 .d 140 23 .p 141 26 .p 141 29 .m 141 39 .d 138 42 .m 141 47 .d 139 49 .m 141 116 .d 140 117 .p 141 117 .p 141 119 .p 141 126 .p 141 128 .m 141 134 .d 140 135 .p 141 135 .m 140 13 .d 136 17 .p 140 26 .p 140 29 .p 140 39 .p 140 47 .m 140 66 .d 139 67 .p 140 98 .p 140 100 .p 140 103 .p 140 116 .p 140 119 .p 140 126 .p 140 128 .p 140 134 .m 139 42 .d 138 43 .m 139 45 .d 137 47 .p 139 46 .m 139 51 .d 137 53 .m 139 58 .d 138 59 .m 139 93 .d 137 95 .p 139 96 .p 139 102 .m 138 25 .d 137 26 .m 138 34 .d 137 35 .p 138 41 .p 138 45 .p 138 49 .p 138 58 .m 138 63 .d 136 65 .p 138 96 .m 138 102 .d 137 103 .p 138 106 .m 138 112 .d 137 113 .m 137 23 .d 135 25 .p 137 24 .p 137 29 .p 137 30 .p 137 31 .p 137 32 .m 137 37 .d 136 38 .m 137 38 .d 136 39 .p 137 40 .p 137 48 .m 137 61 .d 136 62 .p 137 98 .p 137 108 .p 137 109 .p 137 110 .p 137 111 .m 137 114 .d 136 115 .p 137 115 .m 137 116 .d 135 118 .p 137 117 .p 137 119 .p 137 126 .p 137 128 .m 136 26 .d 133 29 .p 136 29 .m 136 100 .d 135 101 .p 136 113 .m 136 126 .d 135 127 .p 135 28 .m 135 33 .d 134 34 .p 135 34 .p 135 36 .m 135 41 .d 134 42 .m 135 42 .d 134 43 .m 135 43 .d 134 44 .m 135 44 .d 134 45 .m 135 45 .d 134 46 .p 135 46 .m 135 49 .d 134 50 .m 135 50 .d 134 51 .m 135 51 .d 134 52 .p 135 52 .m 135 59 .d 132 62 .p 135 60 .m 135 96 .d 134 97 .p 135 97 .p 135 99 .p 135 104 .m 135 105 .d 134 106 .m 135 106 .d 134 107 .p 135 107 .p 135 112 .m 135 120 .d 134 121 .m 135 121 .d 134 122 .m 135 122 .d 134 123 .m 135 123 .d 134 124 .m 135 124 .d 133 126 .p 135 125 .m 135 129 .d 134 130 .p 135 130 .p 135 131 .m 134 25 .d 133 26 .p 134 27 .p 134 33 .p 134 36 .p 134 41 .p 134 49 .m 134 112 .d 133 113 .p 134 118 .p 134 120 .p 134 127 .p 134 129 .p 133 24 .m 133 38 .d 132 39 .p 133 39 .p 133 115 .p 133 117 .p 132 24 .p 132 26 .p 132 29 .m 132 38 .d 131 39 .m 132 61 .d 131 62 .p 132 113 .p 132 115 .p 132 117 .p 132 126 .p 131 24 .p 131 26 .p 131 29 .m 131 38 .d 130 39 .m 131 61 .d 130 62 .p 131 113 .p 131 115 .p 131 117 .p 131 126 .p 130 24 .p 130 26 .p 130 29 .m 130 38 .d 129 39 .m 130 61 .d 128 63 .m 130 65 .d 128 67 .p 130 113 .p 130 115 .p 130 117 .p 130 126 .m 129 24 .d 126 27 .p 129 26 .p 129 29 .p 129 38 .p 129 115 .p 129 117 .p 128 34 .p 128 41 .p 128 42 .p 128 43 .p 128 45 .p 128 46 .p 128 49 .p 128 51 .p 128 52 .p 128 58 .p 128 59 .p 128 106 .m 128 112 .d 127 113 .m 127 24 .d 125 26 .p 127 29 .p 127 38 .p 127 39 .m 127 100 .d 126 101 .p 127 115 .m 127 117 .d 126 118 .m 126 28 .d 125 29 .p 126 33 .p 126 34 .p 126 36 .p 126 41 .p 126 42 .p 126 43 .p 126 44 .p 126 45 .p 126 46 .p 126 49 .p 126 50 .p 126 51 .p 126 52 .m 126 60 .d 124 62 .p 126 96 .p 126 97 .m 126 99 .d 125 100 .m 126 112 .d 125 113 .p 126 120 .p 126 121 .p 126 122 .p 125 24 .m 125 38 .d 124 39 .p 125 39 .p 125 115 .p 125 117 .p 124 24 .p 124 26 .p 124 29 .m 124 38 .d 123 39 .m 124 61 .d 123 62 .p 124 100 .p 124 115 .p 124 117 .p 123 24 .p 123 26 .p 123 29 .m 123 38 .d 122 39 .m 123 61 .d 122 62 .p 123 100 .p 123 115 .p 123 117 .p 122 24 .p 122 26 .p 122 29 .m 122 38 .d 121 39 .m 122 61 .d 121 62 .p 122 100 .p 122 115 .p 122 117 .p 121 24 .p 121 26 .p 121 29 .m 121 38 .d 120 39 .m 121 61 .d 119 63 .m 121 65 .d 119 67 .p 121 100 .p 121 115 .p 121 117 .m 120 24 .d 117 27 .p 120 26 .p 120 29 .p 120 38 .p 120 61 .p 120 100 .p 120 115 .p 119 1 .p 119 34 .p 119 41 .p 119 42 .p 119 43 .p 119 45 .p 119 46 .p 119 49 .p 119 51 .p 119 52 .p 119 58 .p 119 59 .p 119 102 .m 119 112 .d 118 113 .m 118 24 .d 117 25 .p 118 29 .p 118 38 .p 118 39 .p 118 61 .p 118 62 .p 118 65 .m 118 100 .d 116 102 .p 117 1 .p 117 28 .m 117 33 .d 116 34 .p 117 34 .p 117 36 .m 117 41 .d 115 43 .m 117 42 .d 112 47 .p 117 43 .m 117 44 .d 115 46 .m 117 45 .d 116 46 .p 117 46 .p 117 49 .m 117 50 .d 115 52 .m 117 51 .d 116 52 .p 117 52 .m 117 55 .d 113 59 .m 117 58 .d 115 60 .p 117 59 .p 117 60 .p 117 102 .m 117 105 .d 115 107 .p 116 25 .m 116 41 .d 113 44 .m 116 49 .d 109 56 .m 116 54 .d 113 57 .m 116 104 .d 112 108 .p 115 27 .p 115 28 .m 115 33 .d 114 34 .p 115 36 .m 115 45 .d 114 46 .p 115 49 .m 115 51 .d 114 52 .m 115 54 .d 113 56 .m 115 58 .d 112 61 .m 115 101 .d 114 102 .m 114 49 .d 113 50 .m 114 96 .d 112 98 .m 113 25 .d 112 26 .m 113 34 .d 112 35 .p 113 51 .m 113 102 .d 111 104 .m 112 48 .d 111 49 .m 111 51 .d 110 52 .p 111 52 .m 111 55 .d 110 56 .p 111 56 .m 111 58 .d 110 59 .m 110 54 .d 108 56 .m 110 58 .d 109 59 .m 109 54 .d 108 55 .m 109 58 .d 108 59 .p 108 58 .p 108 63 .p 108 104 .m 107 61 .d 106 62 .p 107 62 .m 106 61 .d 105 62 .m 106 64 .d 103 67 .p 106 98 .m 105 61 .d 101 65 .p 104 61 .p 104 64 .p 104 65 .p 104 98 .p 103 58 .p 103 59 .m 102 61 .d 100 63 .p 102 62 .m 102 65 .d 100 67 .p 102 66 .p 102 98 .p 101 61 .p 100 58 .p 100 59 .m 100 60 .d 99 61 .p 100 68 .p 100 69 .p 100 96 .m 99 24 .d 97 26 .m 99 62 .d 98 63 .p 99 65 .m 99 66 .d 98 67 .p 98 69 .m 97 65 .d 95 67 .p 97 66 .p 96 64 .p 96 65 .p 96 70 .m 95 46 .d 93 48 .m 95 69 .d 89 75 .m 91 50 .d 88 53 .m 91 74 .d 90 75 .p 91 75 .m 91 76 .d 90 77 .m 91 82 .d 90 83 .m 90 58 .d 89 59 .p 90 81 .p 89 74 .m 89 77 .d 87 79 .p 89 81 .p 89 83 .m 88 61 .d 86 63 .p 88 79 .p 88 80 .p 87 78 .m 86 54 .d 85 55 .m 86 55 .d 85 56 .m 86 58 .d 85 59 .m 86 74 .d 85 75 .p 86 75 .p 86 77 .p 86 81 .p 85 74 .m 85 77 .d 83 79 .p 85 81 .p 84 61 .p 84 62 .p 84 79 .m 83 64 .d 77 70 .p 83 78 .p 82 78 .m 80 58 .d 76 62 .m 80 74 .d 79 75 .p 80 75 .p 79 74 .p 78 74 .m 75 64 .d 72 67 .p 75 71 .m 67 4 .d 62 9 .m 67 26 .d 65 28 .m 67 53 .d 64 56 .p 67 61 .p 67 62 .m 66 50 .d 61 55 .p 66 51 .m 66 56 .d 64 58 .m 66 57 .d 64 59 .m 66 58 .d 65 59 .m 66 59 .d 65 60 .p 66 60 .m 65 11 .d 61 15 .m 64 15 .d 63 16 .m 64 25 .d 58 31 .p 62 28 .p 62 57 .p 62 58 .m 61 25 .d 60 26 .p 61 27 .p 61 57 .p 59 26 .m 59 29 .d 58 30 .m 59 31 .d 58 32 .m 58 16 .d 56 18 .p 58 26 .m 57 29 .d 54 32 .m 56 31 .d 55 32 .p 56 32 .p 56 35 .p 55 35 .m 55 37 .d 54 38 .m 54 20 .d 50 24 .p 54 35 .m 53 2 .d 51 4 .m 53 34 .d 52 35 .m 53 46 .d 52 47 .m 52 37 .d 47 42 .p 51 35 .m 51 37 .d 49 39 .p 51 47 .p 50 26 .m 50 29 .d 49 30 .m 49 24 .d 48 25 .p 49 26 .p 49 29 .p 49 32 .m 48 1 .d 45 4 .p 48 2 .m 48 5 .d 47 6 .m 48 6 .d 46 8 .m 48 11 .d 46 13 .m 48 14 .d 45 17 .p 48 21 .m 48 42 .d 47 43 .p 48 43 .p 47 1 .m 47 9 .d 46 10 .m 47 21 .d 44 24 .m 47 25 .d 46 26 .m 47 34 .d 46 35 .p 47 41 .p 46 4 .m 46 23 .d 45 24 .p 46 24 .m 46 29 .d 45 30 .m 46 30 .d 45 31 .m 46 31 .d 45 32 .m 46 37 .d 44 39 .m 46 38 .d 45 39 .m 46 39 .d 45 40 .p 46 40 .p 45 10 .p 45 26 .p 45 29 .p 45 35 .m 45 37 .d 43 39 .p 44 26 .m 44 29 .d 41 32 .m 43 22 .d 40 25 .p 43 24 .p 43 26 .m 43 29 .d 41 31 .m 43 31 .d 42 32 .p 43 32 .p 43 35 .m 43 37 .d 42 38 .p 43 38 .m 42 3 .d 38 7 .p 42 24 .p 42 26 .m 42 29 .d 41 30 .p 42 35 .p 42 37 .p 41 26 .p 41 29 .p 41 35 .p 41 37 .p 40 34 .p 39 25 .m 39 27 .d 38 28 .m 39 33 .d 38 34 .p 39 34 .p 38 25 .p 38 27 .p 38 33 .p 37 1 .m 37 25 .d 36 26 .m 36 24 .d 34 26 .p 36 29 .m 35 2 .d 34 3 .m 35 9 .d 34 10 .m 34 23 .d 32 25 .p 34 29 .p 33 26 .p 33 29 .m 32 5 .d 30 7 .m 31 5 .d 29 7 .p 31 25 .p 30 25 .p 29 5 .p 29 6 .p 29 25 .p 28 24 .p 26 1 .m 26 2 .d 25 3 .p 26 5 .p 26 6 .m 26 7 .d 24 9 .m 26 9 .d 23 12 .p 26 11 .m 26 12 .d 23 15 .m 26 15 .d 25 16 .m 26 19 .d 25 20 .p 26 21 .m 25 4 .d 20 9 .m 25 18 .d 24 19 .m 24 1 .d 23 2 .m 24 6 .d 23 7 .p 24 7 .p 24 12 .m 23 1 .d 21 3 .p 23 9 .m 23 11 .d 20 14 .m 23 14 .d 21 16 .m 22 9 .d 20 11 .p 22 11 .p 22 14 .m 21 4 .d 20 5 .p 20 2 .p 20 12 .p 20 15 .m 18 1 .d 17 2 .m 18 5 .d 15 8 .m 18 6 .d 17 7 .m 18 11 .d 17 12 .p 18 12 .p 18 14 .m 17 1 .d 13 5 .m 17 11 .d 16 12 .p 16 1 .m 16 9 .d 15 10 .p 16 11 .m 14 8 .d 13 9 .p 14 10 .p 13 1 .m 13 2 .d 10 5 .p 13 6 .m 13 7 .d 12 8 .p 10 1 .m 10 2 .d 9 3 .p 10 6 .p 9 4 .p 8 1 .m 8 2 .d 7 318 .d 250 219 .m 250 215 .d 249 216 .m 250 218 .d 249 219 .p 249 215 .m 248 2*[MFOLD]ALU.FLD;1+,g./ 4h,-*0123KPWO56pJ7Tci89GHJ DFOLD of: alu.gcg check: 7822 from: 1 to: 311 January 4, 1990 22:34Energy: -121.0..G 10 20 30 40 50 GSAMPLEALUSEQUENCEACJLG - G U ----- A AGC G GCC GGGCGCG GC GC CACGCC UGUA UCCC AG CGG UCCGCGC CG UG GUGCGG ACAU AGGG CG---------------AAAAAAA G G - GCCGA - CUU G 310 180 170 160 140 60 h 70 80 90 100 h GGCC AGGA - -A --A UC h GAGGCGGG UUGCU UG GCCCAGG GU h CUCUGCCC AGCGA AC CGGGUCC CA Gh ---- -CAG U AG GAC GA h 130 120 110 A 150A AAA AC A AAU AA UUA AA --- AA A ) 190 ) GUAA AGC ) UCCC U) AGGG A) ---- CUC ) 200 O 210 220 230 240 250 O AGGA --GA AGG GC A CGUG O UGAGGCGGG UCGCUU GCCCGGG CGGAG UGCAGUG GC O ACUCUGCCC AGCGAG CGGGUCC GCCUC ACGUCAC CG AO -CAG GCAG --G -- - CGCU O 300 290 280 270 260 *[MFOLD]ALU.GCG;1+,@ ./ 4Ll-*0123KPWO56@b7li89GHJL REFORMAT of: Alu.Seq check: 7822 from: 1 to: 311 January 4, 1990 22:18 (No documentation)B Alu.Gcg Length: 311 January 4, 1990 22:18 Check: 7822 ..A 1 SampleALUs equenceACJ LGGCCGGGCG CGGCGGCTCA CGCCTGTAAT A 51 CCCAGCACTT CGGGAGGCCG AGGCGGGAGG ATTGCTTGAG CCCAGGAGTT A 101 CGAGACCAGC CTGGGCGACA TAGCGAGACC CCGTCTCTAC AAAAAATACA A 151 AAAATTAGCC GGGCGTGGTG GCGCGCGCCT GTAATCCCAG CTACTCGGGA A 201 GGCTGAGGCG GGAGGATCGC TTGAGCCCGG GAGGCGGAGG CTGCAGTGAG A 251 CCGTGATCGC GCCACTGCAC TCCGGCCTGG GCGACGGAGC GAGACCCCGT  301 CTCAAAAAAA At.~ MFOLD.BCKG *[MFOLD]ALU.OUT;1x?B*[MFOLD]ALU.OUT;1+,G .?/ 4x?=-*0123KPWO>56`ŀM7vi89GHJz= FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -114.1 - 10 20 30 -----GGC -| G T GTAA AGC - CGGGCGCG GC GC CACGCCT TCCC A- GTCCGCGC CG TG GTGCGGG AGGG C-AAAAAAA G^ G - ---- CTT -. 160 150 140 40  O 50 60 70 80 O C A GA - -A AGTTCG O GGC GAGGCGGG G TTGCT TG GCCCAGG O CCG CTCTGCCC C AGCGA AC CGGGTCC AO A - AG T AG GACCAG O 110 100 90  8 120 8 TACAAAA AC 8 AAT A8 TTA A8 ------- AA 8 130  170  TAA AGC  TCCC T AGGG A --- CTC   H 180 190 200 210 220 230 H GGC A GA --GA AGG GC A - T H TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GH ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AH --- - AG GCAG --G -- - C T H 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -112.9 A 10 20 30 A----GGC - G T -------------------- |A AGC A CGGGCGCG GC GC CACGCC TGTA TCCC AA GTCCGCGC CG TG GTGCGG ACAT AGGG CAAAAAAAA G G - GCCGATTAAAAACATAAAAA ^- CTT A. 160 150 140 130 120 40  a 50 60 70 80 a GGCC A GA - -A AGTTCG a GAGGCGGG G TTGCT TG GCCCAGG a CTCTGCCC C AGCGA AC CGGGTCC Aa ---- - AG T AG GACCAG a 110 100 90   170  TAA AGC  TCCC T AGGG A --- CTC   H 180 190 200 210 220 230 H GGC A GA --GA AGG GC A - T H TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GH ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AH --- - AG GCAG --G -- - C T H 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -112.4 3 10 20 30 3-------- | - G T GTAA AGC 3 GGCC GGGCGCG GC GC CACGCCT TCCC A3 TCGG TCCGCGC CG TG GTGCGGG AGGG C3AAAAAAAA ^ G G - ---- CTT 3. 180 150 140 40  U 50 60 70 80 U C A GA - -A AGTTCG U GGC GAGGCGGG G TTGCT TG GCCCAGG U CCG CTCTGCCC C AGCGA AC CGGGTCC AU A - AG T AG GACCAG U 110 100 90  > 120 > TACAAAA AC > AAT A> TTA A> ------- AA > 130  160 170  GTAA AGC  TCCC T AGGG A ---- CTC   @ 190 200 210 220 230 @ A GA --GA AGG GC A - T @ GAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG G@ CTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC A@ - AG GCAG --G -- - C T @ 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -111.9  10 ------- |GG C GC  GGCC GCG GGCG  CCGG TGT CCGC TAAAAAAA ^-- - AC . 20   30  AA AGC  TCCC A AGGG C -- CTT  40  / 50 60 70 80 / A GA - -A AGTTCG / GAGGCGGG G TTGCT TG GCCCAGG / CTCTGCCC C AGCGA AC CGGGTCC A/ - AG T AG GACCAG / 110 100 90  . 120 130 140 . TACAAAAAATACAAAAATTAGC GT . CGGGCGTG G. GTCCGCGC G. ---------------------- GC . 160 150 0 170 0 TAA AGC 0 TCCC T0 AGGG A0 --- CTC 0  b 180 190 200 210 220 230 b GGC A GA --GA AGG GC A - T b TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG Gb ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC Ab --- - AG GCAG --G -- - C T b 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -110.6  10 -------- GG C GC  GGCC GCG GGCG  CCGG TGT CCGC TAAAAAAAA -- - AC . 20   30  AA AGC  TCCC A AGGG C -- CTT  40  0 50 60 70 80 0 A GA - -A AGTTCG 0 GAGGCGGG G TTGCT TG GCCCAGG 0 CTCTGCCC C AGCGA AC CGGGTCC A0 - AG T AG GACCAG 0 110 100 90  1 120 130 140 1 TACAAAAAATACAAAAATT | GT 1 AGCC GGGCGTG G1 TCGG TCCGCGC G1 ------------------- ^ GC 1 180 150 3 160 170 3 GTAA AGC 3 TCCC T3 AGGG A3 ---- CTC 3  W 190 200 210 220 230 W A GA --GA AGG GC A - T W GAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GW CTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AW - AG GCAG --G -- - C T W 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -109.1 8 10 20 30 40 8----GGC - G T - - -A AC G 8 CGGGCGCG GC GC CACGCCT GTAATCC C GC TTCGG A8 GTCCGCGC CG TG GTGCGGG CGTTAGG G CG GAGCC G8AAAAAAA G G - C A GG -- G 8. 160 150 140 60 50  7 70 80 7 T -A AGTTCG 7 TG GCCCAGG 7 AC CGGGTCC A7 - AG GACCAG 7 90  D 100 D TA| -------------------- C D GC GAGAC D CG CTCTG CD --^ ATTAAAAACATAAAAAACAT C D 130 120 110  170  TAA AGC  TCCC T AGGG A --- CTC   H 180 190 200 210 220 230 H GGC A GA --GA AGG GC A - T H TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GH ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AH --- - AG GCAG --G -- - C T H 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -107.2 , 10 20 30 ,---GGC - G T GTAA AGC , CGGGCGCG GC GC CACGCCT TCCC A, GTCCGCGC CG TG GTGCGGG AGGG C,AAAAAA G G - ---- CTT ,. 160 150 140 40  N 50 60 70 80 N C A GA - -A AGTTCG N GGC GAGGCGGG G TTGCT TG GCCCAGG N CCG CTCTGCCC C AGCGA AC CGGGTCC AN A - AG T AG GACCAG N 110 100 90  7 120 7 TACAAAA AC 7 AAT A7 TTA A7 ------- AA 7 130  170  |AA AGC  T TCCC T A AGGG A ^-- CTC   G 180 190 200 210 220 230 G GGC A GA --GA AGG GC A - T G TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GG ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AG --- - AG GCAG --G -- - C T G 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -106.7 - 10 20 30 -----GGC - G T GTAA AGC - CGGGCGCG GC GC CACGCCT TCCC A- GTCCGCGC CG TG GTGCGGG AGGG C-AAAAAAA G G - ---- CTT -. 160 150 140 40  = 50 = C ----A |G = GGC GAGGCGGG G = CCG CTCTGCCC T A= A CAGAG ^T = 110 60 P 70 80 P - -A AGTTCG P GCT TG GCCCAGG P CGA AC CGGGTCC AP T AG GACCAG P 100 90  8 120 8 TACAAAA AC 8 AAT A8 TTA A8 ------- AA 8 130  170  TAA AGC  TCCC T AGGG A --- CTC   H 180 190 200 210 220 230 H GGC A GA --GA AGG GC A - T H TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GH ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AH --- - AG GCAG --G -- - C T H 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -106.4 3 10 20 30 3-------- - G T GTAA AGC 3 GGCC GGGCGCG GC GC CACGCCT TCCC A3 TCGG TCCGCGC CG TG GTGCGGG AGGG C3AAAAAAAA G G - ---- CTT 3. 180 150 140 40  U 50 60 70 80 U C A GA - -A AGTTCG U GGC GAGGCGGG G TTGCT TG GCCCAGG U CCG CTCTGCCC C AGCGA AC CGGGTCC AU A - AG T AG GACCAG U 110 100 90  > 120 > TACAAAA AC > AAT A> TTA A> ------- AA > 130  160 170  GTAA AGC  TCCC T AGGG A ---- CTC    190  G GA  AGGCGG  TTCGCT G - AG  200  1 210 220 230 1 GA AGG GC A - T A1 GCCCGGG CGGAG TGCAGTG GC CG G 1 CGGGTCC GCCTC ACGTCAC CG GC A 1 -- --G -- - C T -1 260 250 240  270 GACGGAGC | C GAGAC CTCTG C -------- ^ C 280 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -106.4 7 10 20 30 40 7----GGC - G T T - -A AC G 27 CGGGCGCG GC GC CACGCCTG AATCC C GC TTCGG A 7 GTCCGCGC CG TG GTGCGGGC TTAGG G CG GAGCC G 7AAAAAAA G G - - A GG -- G 7. 160 150 140 60 50  I 70 80 I | --------------- -A AGTTCG I GCT TG GCCCAGG I CGA AC CGGGTCC A I ^ TTAAAAACATAAAAA AT GACCAG I 130 120 90  J 100 J GACATAGC C J GAGAC J CTCTG CJ -------- C J 110 C 170  TAA AGC  TCCC T AGGG A --- CTC   H 180 190 200 210 220 230 H GGC A GA --GA AGG GC A - T H TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GH ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AH --- - AG GCAG --G -- - C T H 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -106.4  10 ------- GG C GC  GGCC GCG GGCG  CCGG TGT CCGC TAAAAAAA -- - AC . 20   30 G AA AGC  TCCC AG AGGG CC -- CTT  40 - / 50 60 70 80 / A GA - -A AGTTCG L/ GAGGCGGG G TTGCT TG GCCCAGG / CTCTGCCC C AGCGA AC CGGGTCC A1/ - AG T AG GACCAG / 110 100 90 C C. 120 130 140 . T | AAAAATACAAAAATTAGCCG GT . ACA GGCGTG G. TGT CCGCGC G. - ^ -------------------- GC . 160 150  170  AA AGC  TCCC T AGGG A -- CTC   CL 180 190 200 210 220 230 L GGC A GA --GA AGG GC A - T L TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GL ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AL --- - AG GCAG --G -- - C T L 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -106.0  10 -------- GG C GC G GGCC GCG GGCG  CCGG TGT CCGC T AAAAAAAA -- - AC . 20   30  AA AGC  TCCC A AGGG C -- CTT  40  Av 50 60 70 80 90 100 110 120 130 140 v A GA --GA AGTTCGAGA | AG GA T GA - TACAAAAAATACAAAAATT GT v GAGGCGGG G TTGCTT GCCCAGG CC CCTGGGC CA AGCGA C CCCGTCTC AGCC GGGCGTG Gv CTCTGCCC C AGCGAG CGGGTCC GG GGGCCCG GT TCGCT G GGGCGGAG TCGG TCCGCGC Gv - AG GCAG --------G ^ -A -A - AG A ------------------- GC v 280 270 260 210 200 190 180 150 x 160 170 x GTAA AGC x TCCC Tx AGGG Ax ---- CTC x  H 220 230 H GC A - T H CGGAG TGCAGTG GC CG GH GCCTC ACGTCAC CG GC AH -- - C T H 250 240 = FOLDING BASES 1 TO 290 OF ACJL 8 ENERGY = -105.9  10 ------ GG C GC  GGCC GCG GGCG G CCGG TGT CCGC T AAAAAA -- - AC C. 20 G  30  AA AGC  TCCC A AGGG C -- CTT  40  . 50 60 70 80 . A GA - -A AGTTCG . GAGGCGGG G TTGCT TG GCCCAGG . CTCTGCCC C AGCGA AC CGGGTCC A. - AG T AG GACCAG . 110 100 90  C/ 120 130 140 / TACAAAAAATACAAAAA|T GT -/ T AGCC GGGCGTG G / A TCGG TCCGCGC G / -----------------^A GC / 180 150  1 160 170 1 GTAA AGC 1 TCCC T 1 AGGG AG1 ---- CTC 1  U 190 200 210 220 230 U A GA --GA AGG GC A - T U GAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG G U CTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC A U - AG GCAG --G -- - C T U 280 270 260 250 240 = FOLDING BASES 1 TO 290 OF ACJL A ENERGY = -105.8 10 ------- |-- GG C GC G GCC GCG GGCG C CGG TGT CCGC T AAAAAAA ^AT -- - AC . 20   30  AA AGC  TCCC A  AGGG CC -- CTT  40  C3 50 60 70 80 3 C A GA - -A AGTTCG 3 GAGGCGGG G TTGCT TG GCCCAGG 3 CTCTGCCC C AGCGA AC CGGGTCC A 3 - - AG T AG GACCAG 3 110 100 90  ) 120 130 140 ) AAAAAATACAAAAATTAGC GT ) CGGGCGTG G ) GTCCGCGC G ) ------------------- GC ) 160 150 + 170 + TAA AGC + TCCC T + AGGG A + --- CTC + C T] 180 190 200 210 220 230 A] GGC A GA --GA AGG GC A - T ] TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG G ] ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC A ] --- - AG GCAG --G -- - C T A] 280 270 260 250 240 T= FOLDING BASES 1 TO 290 OF ACJL G ENERGY = -105.6 A- 10 20 30 -----GGC - G T GTAA AGC - CGGGCGCG GC GC CACGCCT TCCC A - GTCCGCGC CG TG GTGCGGG AGGG C -AAAAAAA G G - ---- CTT -. 160 150 140 40 G GO 50 60 70 80 TO C A GA - -A AGTTCG O GGC GAGGCGGG G TTGCT TG GCCCAGG O CCG CTCTGCCC C AGCGA AC CGGGTCC A O A - AG T AG GACCAG O 110 100 90  G8 120 8 TACAAAA AC 8 AAT A8 TTA A8 ------- AA 8 130 C 170  TAA AGC  TCCC T AGGG A --- CTC   = 180 190 200 210 = GGC A GA --GA ------A |G = TGAGGCGGG G TCGCTT GCCCGGG GGC G = ACTCTGCCC C AGCGAG CGGGTCC TCG A= --- - AG GCAG GGCCTCA ^G = 280 270 260 250 220  1F 230 F A - T F GCAGTG GC CG GF CGTCAC CG GC AF - C T F 240 = FOLDING BASES 1 TO 290 OF ACJL  ENERGY = -105.3 / 10 20 30 /----GGC - GG A -- AA AGC / CGGGCGCG GC CTC CGCCT GT TCCC A / GTCCGCGC CG GAG GCGGA CG AGGG C /AAAAAAA G -G G GC -G CTT /. 160 150 50 40  ) 60 70 ) GATTG CC ) CTTGAGC A ) GAGCTTG GT) ----- AG ) 80  -G 90 100 G | - G ------------GACATAGC C G ACCA GCCTGG C GAGAC AG TGGT CGGGCC G CTCTG CCG ^ G - ATTAAAAACATAAAAAACAT C G 140 130 120 110L G 170  TAA AGC  TCCC T AGGG A --- CTC   H 180 190 200 210 220 230 H GGC A GA --GA AGG GC A - T H TGAGGCGGG G TCGCTT GCCCGGG CGGAG TGCAGTG GC CG GH ACTCTGCCC C AGCGAG CGGGTCC GCCTC ACGTCAC CG GC AH --- - AG GCAG --G -- - C T H 280 270 260 250 240 / CTCTGCCC C AGCGA AC CGGGTCC A/ - AG T AG GACCAG*[MFOLD]ALU.PLOT1;1+,.W/ 4PWV-*0123KPWOW56@!_L N7}i89GHJ稤~ MFOLD.BCK*[MFOLD]ALU.PLOT1;1PWf<Alu RNA, 4 levels, energy increment = 11.4 kcal/mole $ 290 20 20 2 2 1000000000000000000000003000043000000 003400000 4300340000 00030000000 003000030000 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yrrrrrrq^O/'''''g____ZIIIIC==0(((vk_VJEEEEEEEE=66666666655555555...."zzzzsssrnnnjRJJJHGGGGA>>>* |uuuuuutaT6.....oggggZIIIICCA80((%$vk_ZRHHHHHHHHE>>>>>>>>>>>>>>>>>6666*{{{zvvvrZRRRPOOOOIFFF2 }}}}}}|i\>66666!$GGCCGGGCGCGGCGGCTCACGCCTGTAATCCCAGCACTTCGGGAGGCCGAGGCGGGAGGATTGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCGACATAGCGAGACCCCGTCTCTACAAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCGGGAGGATCGCTTGAGCCCGGGAGGCGGAGGCTGCAGTGAGCCGTGATCGCGCCACTGCACTCCGGCCTGGGCGACGGAGCGAGACCCCGTCTCAAAAAAAAS[KLc uXGGGGGGGGGGGGGGC# ummmmtttttttttrrrrrrrrrj\C;;6... sbbbbbbbaPHBB80000000(w^VV*[MFOLD]ALU.SEQ;1+,./ 4<J-*0123KPWO56B47i89GHJ;Sample ALU sequenceACJL<GGCCGGGCGCGGCGGCTCACGCCTGTAATCCCAGCACTTCGGGAGGCCGAGGCGGGAGGA<TTGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCGACATAGCGAGACCCCGTCTCTACA<AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG<GCTGAGGCGGGAGGATCGCTTGAGCCCGGGAGGCGGAGGCTGCAGTGAGCCGTGATCGCG3CCACTGCACTCCGGCCTGGGCGACGGAGCGAGACCCCGTCTCAAAAAAAA1*[MFOLD]ALU.UWGCG;1+,.N/ 4#NL-*0123KPWOM56` X N74^i89GHJ@.vp 20.455 129.545 100.0 0.0#.wn -29.00 319.00 319.00 -29.00.ls 1 30.m 290 0 .d 290 290.d 0 0.d 290 0.m 0 0.d 0 290 .d 290 290.to 2 .m 290 20.reld 2.90 0.00.m 304.50 20.00.pt 20 .m 0 20.reld -2.90 0.00 .m 290 40.reld 2.90 0.00.m 304.50 40.00.pt 40 .m 0 40.reld -2.90 0.00 .m 290 60.reld 2.90 0.00.m 304.50 60.00.pt 60 .m 0 60.reld -2.90 0.00 .m 290 80.reld 2.90 0.00.m 304.50 80.00.pt 80 .m 0 80.reld -2.90 0.00 .m 290 100.reld 2.90 0.00.m 304.50 100.00.pt 100 .m 0 100.reld -2.90 0.00 .m 290 120.reld 2.90 0.00.m 304.50 120.00.pt 120 .m 0 120.reld -2.90 0.00 .m 290 140.reld 2.90 0.00.m 304.50 140.00.pt 140 .m 0 140.reld -2.90 0.00 .m 290 160.reld 2.90 0.00.m 304.50 160.00.pt 160 .m 0 160.reld -2.90 0.00 .m 290 180.reld 2.90 0.00.m 304.50 180.00.pt 180 .m 0 180.reld -2.90 0.00 .m 290 200.reld 2.90 0.00.m 304.50 200.00.pt 200 .m 0 200.reld -2.90 0.00 .m 290 220.reld 2.90 0.00.m 304.50 220.00.pt 220 .m 0 220.reld -2.90 0.00 .m 290 240.reld 2.90 0.00.m 304.50 240.00.pt 240 .m 0 240.reld -2.90 0.00 .m 290 260.reld 2.90 0.00.m 304.50 260.00.pt 260 .m 0 260.reld -2.90 0.00 .m 290 280.reld 2.90 0.00.m 304.50 280.00.pt 280 .m 0 280.reld -2.90 0.00.to 4 .m 20 0.reld 0.00 -2.90.m 20.00 -14.50.pt 20 .m 20 290.reld 0.00 2.90 .m 40 0.reld 0.00 -2.90.m 40.00 -14.50.pt 40 .m 40 290.reld 0.00 2.90 .m 60 0.reld 0.00 -2.90.m 60.00 -14.50.pt 60 .m 60 290.reld 0.00 2.90 .m 80 0.reld 0.00 -2.90.m 80.00 -14.50.pt 80 .m 80 290.reld 0.00 2.90 .m 100 0.reld 0.00 -2.90.m 100.00 -14.50.pt 100 .m 100 290.reld 0.00 2.90 .m 120 0.reld 0.00 -2.90.m 120.00 -14.50.pt 120 .m 120 290.reld 0.00 2.90 .m 140 0.reld 0.00 -2.90.m 140.00 -14.50.pt 140 .m 140 290.reld 0.00 2.90 .m 160 0.reld 0.00 -2.90.m 160.00 -14.50.pt 160 .m 160 290.reld 0.00 2.90 .m 180 0.reld 0.00 -2.90.m 180.00 -14.50.pt 180 .m 180 290.reld 0.00 2.90 .m 200 0.reld 0.00 -2.90.m 200.00 -14.50.pt 200 .m 200 290.reld 0.00 2.90 .m 220 0.reld 0.00 -2.90.m 220.00 -14.50.pt 220 .m 220 290.reld 0.00 2.90 .m 240 0.reld 0.00 -2.90.m 240.00 -14.50.pt 240 .m 240 290.reld 0.00 2.90 .m 260 0.reld 0.00 -2.90.m 260.00 -14.50.pt 260 .m 260 290.reld 0.00 2.90 .m 280 0.reld 0.00 -2.90.m 280.00 -14.50.pt 280 .m 280 290.reld 0.00 2.90 .m 290 134 .d 289 135 .p 290 135 .p 290 161 .p 290 164 .p 290 183 .p 290 281 .m 289 134 .d 288 135 .p 289 161 .p 289 164 .p 289 171 .p 289 174 .p 289 183 .p 289 281 .m 288 134 .d 287 135 .p 288 159 .p 288 161 .p 288 164 .p 288 171 .p 288 174 .p 288 183 .p 288 281 .m 287 134 .d 286 135 .p 287 159 .p 287 161 .p 287 164 .p 287 174 .p 287 183 .p 287 281 .p 286 126 .m 286 134 .d 285 135 .p 286 159 .p 286 161 .p 286 164 .p 286 183 .p 286 281 .p 285 126 .m 285 134 .d 284 135 .p 285 159 .p 285 161 .p 285 164 .p 285 183 .p 285 281 .p 284 126 .m 284 134 .d 283 135 .p 284 159 .p 284 161 .p 284 164 .p 284 171 .p 284 174 .p 284 183 .m 284 200 .d 281 203 .p 283 134 .p 283 161 .p 283 164 .m 283 183 .d 275 191 .p 282 1 .p 282 2 .m 282 49 .d 275 56 .m 282 104 .d 278 108 .m 282 180 .d 281 181 .p 282 181 .m 282 186 .d 281 187 .p 282 187 .m 282 189 .d 279 192 .m 282 194 .d 281 195 .m 282 266 .d 280 268 .m 282 270 .d 278 274 .m 282 272 .d 281 273 .p 282 278 .p 281 184 .m 281 186 .d 280 187 .m 281 193 .d 279 195 .m 280 184 .d 279 185 .m 280 262 .d 276 266 .p 279 186 .p 279 189 .m 278 269 .d 277 270 .m 277 186 .d 276 187 .p 277 187 .m 277 190 .d 276 191 .p 277 191 .m 277 193 .d 276 194 .m 276 189 .d 274 191 .m 276 193 .d 275 194 .m 275 58 .d 274 59 .m 275 189 .d 274 190 .m 275 193 .d 274 194 .p 275 268 .p 274 58 .p 274 193 .p 274 198 .p 274 268 .p 274 270 .m 273 196 .d 272 197 .p 272 196 .m 272 199 .d 269 202 .p 272 264 .m 271 61 .d 266 66 .m 271 196 .d 266 201 .p 270 196 .p 270 199 .m 270 264 .d 269 265 .m 269 181 .d 267 183 .p 269 193 .p 269 194 .p 268 197 .m 268 200 .d 267 201 .p 268 201 .m 267 164 .d 265 166 .m 267 196 .d 266 197 .m 266 65 .d 264 67 .m 266 182 .d 264 184 .m 266 196 .d 264 198 .m 266 199 .d 265 200 .m 266 200 .d 264 202 .m 266 205 .d 265 206 .m 266 206 .d 264 208 .p 266 261 .p 265 199 .p 265 261 .p 264 204 .p 263 66 .m 263 200 .d 261 202 .p 263 201 .p 262 199 .p 262 200 .p 262 205 .m 262 207 .d 261 208 .m 261 69 .d 255 75 .m 261 204 .d 255 210 .p 261 210 .m 260 206 .d 259 207 .m 259 205 .d 258 206 .m 257 209 .d 256 210 .p 257 210 .m 257 211 .d 254 214 .m 257 212 .d 256 213 .p 257 213 .m 257 217 .d 253 221 .m 256 208 .d 255 209 .p 255 208 .p 255 212 .m 255 246 .d 254 247 .p 254 78 .m 254 79 .d 252 81 .p 254 80 .m 254 241 .d 253 242 .m 254 244 .d 252 246 .p 254 249 .p 254 250 .m 253 214 .d 249 218 .p 253 244 .p 253 247 .p 253 249 .m 252 209 .d 249 212 .m 252 212 .d 251 213 .p 252 213 .p 252 216 .m 252 218 .d 251 219 .p 252 219 .p 251 212 .m 251 215 .d 250 216 .m 251 218 .d 250 219 .m 250 212 .d 249 213 .m 250 215 .d 249 216 .m 250 218 .d 249 219 .p 249 215 .p 249 222 .m 248 221 .d 242 227 .m 247 213 .d 244 216 .p 247 218 .m 247 219 .d 246 220 .m 247 238 .d 245 240 .m 246 221 .d 245 222 .p 245 225 .p 244 222 .p 244 227 .m 244 232 .d 242 234 .m 243 221 .d 242 222 .m 242 212 .d 239 215 .m 242 218 .d 240 220 .p 242 225 .p 242 229 .p 242 232 .p 242 238 .m 241 222 .d 240 223 .m 241 225 .d 239 227 .p 241 227 .m 241 229 .d 240 230 .m 241 232 .d 239 234 .p 241 234 .m 240 221 .d 238 223 .m 240 231 .d 238 233 .p 240 236 .m 239 213 .d 236 216 .m 239 225 .d 236 228 .m 239 229 .d 238 230 .m 238 231 .d 237 232 .m 237 216 .d 236 217 .p 237 225 .p 237 229 .p 236 224 .m 236 225 .d 235 226 .p 236 227 .p 236 229 .p 236 232 .m 234 221 .d 232 223 .m 234 226 .d 233 227 .p 234 230 .m 233 219 .d 232 220 .m 233 225 .d 231 227 .p 233 228 .p 233 229 .m 231 218 .d 228 221 .m 230 222 .d 229 223 .p 227 223 .m 221 212 .d 219 214 .m 221 215 .d 220 216 .p 220 215 .p 218 214 .p 214 83 .p 214 210 .m 213 85 .d 212 86 .p 213 86 .m 212 78 .d 211 79 .m 210 89 .d 204 95 .m 206 180 .d 203 183 .m 203 196 .d 202 197 .m 202 98 .d 201 99 .p 202 182 .m 202 183 .d 199 186 .p 201 97 .m 201 185 .d 196 190 .p 201 186 .m 200 1 .d 198 3 .m 200 101 .d 196 105 .m 197 191 .d 196 192 .p 197 193 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40 .m 141 47 .d 139 49 .p 141 117 .p 141 119 .p 141 126 .p 141 128 .m 141 134 .d 140 135 .p 141 135 .m 140 10 .d 137 13 .m 140 13 .d 136 17 .p 140 26 .p 140 29 .p 140 37 .p 140 47 .p 140 65 .m 140 66 .d 139 67 .p 140 98 .p 140 100 .m 140 103 .d 139 104 .p 140 114 .p 140 119 .p 140 126 .p 140 128 .p 140 134 .m 139 1 .d 137 3 .m 139 6 .d 137 8 .p 139 34 .m 139 42 .d 138 43 .p 139 43 .m 139 45 .d 137 47 .p 139 46 .m 139 51 .d 137 53 .m 139 58 .d 138 59 .p 139 59 .m 139 93 .d 137 95 .p 139 96 .p 139 102 .p 139 106 .m 138 21 .d 137 22 .m 138 25 .d 137 26 .m 138 34 .d 137 35 .p 138 41 .p 138 45 .p 138 49 .p 138 51 .p 138 58 .m 138 63 .d 136 65 .p 138 67 .p 138 96 .m 138 102 .d 137 103 .p 138 104 .p 138 106 .m 138 112 .d 137 113 .m 137 23 .d 135 25 .p 137 24 .p 137 29 .p 137 30 .p 137 31 .p 137 32 .m 137 37 .d 136 38 .m 137 38 .d 136 39 .p 137 39 .p 137 40 .p 137 48 .m 137 61 .d 135 63 .p 137 62 .m 137 65 .d 134 68 .p 137 66 .p 137 98 .p 137 100 .p 137 108 .p 137 109 .p 137 110 .p 137 111 .m 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119 5 .p 119 15 .p 119 34 .p 119 41 .p 119 42 .p 119 43 .p 119 45 .p 119 46 .p 119 49 .p 119 51 .p 119 52 .p 119 54 .p 119 58 .p 119 59 .p 119 96 .p 119 102 .p 119 104 .p 119 106 .m 119 112 .d 118 113 .m 118 24 .d 117 25 .p 118 29 .p 118 38 .p 118 39 .p 118 61 .p 118 62 .p 118 65 .m 118 66 .d 117 67 .m 118 100 .d 116 102 .p 117 1 .m 117 5 .d 115 7 .p 117 19 .p 117 28 .m 117 33 .d 116 34 .p 117 34 .p 117 36 .m 117 41 .d 115 43 .m 117 42 .d 112 47 .p 117 43 .m 117 44 .d 115 46 .m 117 45 .d 116 46 .p 117 46 .p 117 49 .m 117 50 .d 115 52 .m 117 51 .d 116 52 .p 117 52 .m 117 54 .d 115 56 .m 117 55 .d 113 59 .m 117 58 .d 115 60 .p 117 59 .p 117 60 .p 117 68 .p 117 97 .p 117 99 .p 117 102 .p 117 104 .m 117 105 .d 115 107 .p 117 112 .m 116 5 .d 114 7 .p 116 25 .m 116 41 .d 113 44 .m 116 49 .d 109 56 .m 116 54 .d 113 57 .m 116 58 .d 115 59 .m 116 104 .d 112 108 .p 116 112 .p 115 25 .p 115 27 .p 115 28 .m 115 33 .d 114 34 .p 115 34 .p 115 36 .m 115 45 .d 114 46 .p 115 49 .m 115 51 .d 114 52 .m 115 54 .d 113 56 .m 115 58 .d 112 61 .m 115 101 .d 114 102 .p 115 104 .p 115 106 .m 114 49 .d 113 50 .p 114 54 .m 114 96 .d 112 98 .m 114 104 .d 113 105 .m 113 9 .d 110 12 .m 113 25 .d 112 26 .p 113 27 .m 113 28 .d 112 29 .m 113 34 .d 112 35 .p 113 36 .p 113 49 .p 113 51 .p 113 54 .m 113 102 .d 111 104 .p 113 106 .m 112 24 .d 111 25 .m 112 48 .d 111 49 .m 111 51 .d 110 52 .p 111 52 .m 111 55 .d 110 56 .p 111 56 .m 111 58 .d 110 59 .p 111 59 .p 111 106 .p 110 25 .p 110 49 .m 110 51 .d 109 52 .m 110 54 .d 108 56 .m 110 58 .d 109 59 .p 110 106 .m 109 14 .d 108 15 .m 109 51 .d 108 52 .m 109 54 .d 108 55 .m 109 58 .d 108 59 .m 108 25 .d 107 26 .p 108 54 .p 108 58 .p 108 63 .p 108 67 .p 108 102 .p 108 104 .m 107 61 .d 106 62 .p 107 62 .m 107 65 .d 106 66 .p 107 100 .p 106 53 .m 106 61 .d 105 62 .m 106 64 .d 103 67 .m 106 65 .d 105 66 .m 106 90 .d 105 91 .p 106 98 .p 106 100 .p 105 26 .m 105 61 .d 101 65 .p 104 61 .p 104 64 .p 104 65 .p 104 98 .m 103 46 .d 102 47 .p 103 58 .p 103 59 .m 103 94 .d 102 95 .p 103 96 .m 102 61 .d 100 63 .p 102 62 .m 102 65 .d 100 67 .p 102 66 .p 102 98 .m 101 26 .d 100 27 .p 101 61 .m 100 25 .d 99 26 .p 100 57 .p 100 58 .p 100 59 .m 100 60 .d 99 61 .p 100 68 .p 100 69 .p 100 96 .m 99 24 .d 97 26 .m 99 62 .d 98 63 .p 99 65 .m 99 66 .d 98 67 .p 98 45 .p 98 46 .p 98 58 .p 98 59 .p 98 69 .m 97 61 .d 96 62 .p 97 62 .m 97 65 .d 95 67 .p 97 66 .p 96 61 .p 96 64 .p 96 65 .p 96 70 .m 95 46 .d 93 48 .m 95 69 .d 89 75 .p 95 83 .m 94 71 .d 93 72 .m 94 85 .d 93 86 .m 93 47 .d 92 48 .m 93 70 .d 92 71 .m 93 85 .d 91 87 .m 91 50 .d 88 53 .m 91 57 .d 89 59 .m 91 58 .d 90 59 .m 91 74 .d 90 75 .p 91 75 .m 91 76 .d 90 77 .p 91 77 .m 91 82 .d 90 83 .p 91 83 .p 90 81 .p 89 74 .m 89 77 .d 87 79 .p 89 81 .p 89 83 .m 88 61 .d 86 63 .p 88 72 .p 88 79 .p 88 80 .p 87 78 .m 86 54 .d 85 55 .m 86 55 .d 85 56 .p 86 56 .m 86 58 .d 85 59 .m 86 74 .d 85 75 .p 86 75 .p 86 77 .p 86 81 .p 85 58 .p 85 63 .p 85 74 .m 85 77 .d 83 79 .p 85 81 .m 84 61 .d 83 62 .p 84 62 .p 84 79 .m 83 64 .d 77 70 .p 83 78 .p 82 78 .m 80 58 .d 76 62 .m 80 59 .d 79 60 .m 80 74 .d 79 75 .p 80 75 .m 79 73 .d 78 74 .p 79 74 .m 78 63 .d 75 66 .m 75 64 .d 72 67 .p 75 71 .m 71 14 .d 66 19 .m 71 45 .d 69 47 .m 68 29 .d 67 30 .m 68 61 .d 67 62 .p 68 62 .m 67 4 .d 62 9 .m 67 8 .d 66 9 .m 67 10 .d 66 11 .m 67 20 .d 66 21 .m 67 24 .d 66 25 .m 67 26 .d 65 28 .p 67 47 .m 67 48 .d 64 51 .m 67 53 .d 64 56 .p 67 61 .m 66 50 .d 61 55 .p 66 51 .m 66 56 .d 64 58 .m 66 57 .d 64 59 .m 66 58 .d 65 59 .m 66 59 .d 65 60 .p 66 60 .m 65 11 .d 61 15 .m 65 14 .d 63 16 .p 65 25 .m 65 33 .d 62 36 .m 64 9 .d 61 12 .m 64 21 .d 63 22 .m 64 25 .d 58 31 .p 62 15 .p 62 25 .p 62 28 .m 62 55 .d 61 56 .m 62 56 .d 61 57 .p 62 57 .p 62 58 .p 61 14 .m 61 25 .d 60 26 .p 61 27 .p 61 54 .m 60 17 .d 59 18 .m 59 3 .d 58 4 .p 59 13 .p 59 16 .m 59 17 .d 58 18 .p 59 26 .m 59 29 .d 58 30 .m 59 31 .d 58 32 .m 59 47 .d 58 48 .m 58 16 .d 56 18 .p 58 26 .p 58 29 .p 57 26 .m 57 29 .d 54 32 .m 56 17 .d 55 18 .m 56 29 .d 54 31 .m 56 31 .d 55 32 .p 56 32 .p 56 35 .m 56 47 .d 55 48 .p 55 20 .p 55 35 .m 55 37 .d 54 38 .m 55 47 .d 53 49 .m 54 20 .d 50 24 .p 54 35 .p 54 37 .m 53 2 .d 51 4 .m 53 34 .d 52 35 .m 53 46 .d 52 47 .m 52 37 .d 47 42 .m 51 16 .d 49 18 .p 51 26 .p 51 35 .m 51 37 .d 49 39 .p 51 39 .p 51 47 .p 50 26 .m 50 29 .d 49 30 .m 49 4 .d 47 6 .m 49 10 .d 46 13 .m 49 20 .d 48 21 .m 49 24 .d 48 25 .p 49 26 .p 49 29 .p 49 31 .p 49 32 .m 48 1 .d 45 4 .p 48 2 .m 48 6 .d 46 8 .m 48 14 .d 45 17 .p 48 34 .m 48 42 .d 47 43 .p 48 43 .p 47 1 .p 47 5 .m 47 9 .d 46 10 .m 47 21 .d 44 24 .m 47 25 .d 46 26 .m 47 34 .d 46 35 .p 47 41 .p 46 4 .m 46 23 .d 45 24 .p 46 24 .m 46 29 .d 45 30 .m 46 30 .d 45 31 .m 46 31 .d 45 32 .p 46 32 .m 46 37 .d 44 39 .m 46 38 .d 45 39 .m 46 39 .d 45 40 .p 46 40 .p 45 3 .p 45 8 .p 45 10 .m 45 16 .d 43 18 .p 45 18 .p 45 20 .p 45 22 .p 45 26 .p 45 29 .p 45 35 .m 45 37 .d 43 39 .p 44 26 .m 44 29 .d 41 32 .m 43 22 .d 40 25 .m 43 23 .d 42 24 .p 43 24 .p 43 26 .m 43 29 .d 41 31 .m 43 31 .d 42 32 .p 43 32 .p 43 35 .m 43 37 .d 42 38 .p 43 38 .m 42 3 .d 38 7 .p 42 26 .m 42 29 .d 41 30 .p 42 35 .p 42 37 .m 41 8 .d 40 9 .m 41 20 .d 40 21 .p 41 26 .p 41 29 .p 41 35 .p 41 37 .m 40 6 .d 39 7 .p 40 34 .m 39 5 .d 37 7 .p 39 25 .m 39 27 .d 38 28 .p 39 28 .m 39 33 .d 38 34 .p 39 34 .m 38 5 .d 37 6 .p 38 25 .p 38 27 .p 38 33 .p 37 1 .m 37 25 .d 36 26 .m 36 24 .d 34 26 .p 36 29 .p 35 1 .m 35 2 .d 34 3 .m 35 7 .d 34 8 .m 35 9 .d 34 10 .m 35 21 .d 34 22 .m 34 23 .d 32 25 .p 34 24 .p 34 29 .p 34 30 .p 33 26 .p 33 29 .m 32 1 .d 31 2 .m 32 5 .d 30 7 .m 32 6 .d 31 7 .m 31 5 .d 29 7 .p 31 25 .m 30 5 .d 29 6 .p 30 25 .p 29 5 .p 29 9 .p 29 25 .p 28 17 .p 28 24 .p 27 17 .p 26 1 .m 26 2 .d 25 3 .p 26 5 .p 26 6 .m 26 7 .d 24 9 .m 26 9 .d 23 12 .p 26 11 .m 26 12 .d 23 15 .m 26 15 .d 25 16 .m 26 19 .d 25 20 .p 26 21 .m 25 4 .d 20 9 .p 25 17 .m 25 18 .d 24 19 .m 24 1 .d 23 2 .p 24 2 .m 24 6 .d 23 7 .p 24 7 .p 24 12 .p 24 15 .m 23 1 .d 21 3 .m 23 5 .d 22 6 .p 23 9 .m 23 11 .d 20 14 .m 23 14 .d 21 16 .p 22 1 .m 22 9 .d 20 11 .p 22 11 .p 22 14 .m 21 4 .d 20 5 .p 21 17 .p 20 1 .p 20 2 .p 20 6 .p 20 12 .p 20 15 .m 18 1 .d 17 2 .m 18 5 .d 15 8 .m 18 6 .d 17 7 .p 18 7 .p 18 9 .m 18 11 .d 17 12 .p 18 12 .p 18 14 .m 17 1 .d 13 5 .m 17 5 .d 16 6 .p 17 9 .m 17 11 .d 16 12 .p 16 1 .m 16 9 .d 15 10 .p 16 11 .m 14 8 .d 13 9 .p 14 10 .p 13 1 .m 13 2 .d 10 5 .p 13 6 .m 13 7 .d 12 8 .p 10 1 .m 10 2 .d 9 3 .p 10 6 .p 9 4 .p 8 1 .m 8 2 .d 7 3 .p 183 289 .p 161 288 .p 183 288 .m 134 287 .d 135 286 .p 161 287 .p 183 287 .m 134 286 .d 135 285 .p 161 286 .p 183 286 .m 134 285 .d 135 284 .p 161 285 .p 183 285 .p 161 284 .p 183 284 .m 183 283 .d 191 275 .p 181 282 .p 187 280 .m 190 277 .d 191 276 .m 189 276 .d 191 274 .m 193 276 .d 194 275 .m 193 275 .d 194 274 .p 193 274 .m 196 273 .d 197 272 .p 196 272 .m 196 271 .d 201 266 .p 196 270 .p 201 267 .m 199 266 .d 200 265 .m 200 266 .d 202 264 .p 204 264 .m 200 263 .d 202 261 .p 201 263 .m 204 261 .d 210 255 .m 209 257 .d 210 256 .p 210 257 .m 211 257 .d 214 254 .m 208 256 .d 209 255 .p 212 255 .m 214 253 .d 218 249 .m 212 252 .d 213 251 .p 213 252 .p 216 252 .m 218 252 .d 219 251 .m 218 251 .d 219 250 .m 215 250 .d 216 249 .m 218 250 .d 219 249 .m 221 248 .d 227 242 .m 219 247 .d 220 246 .p 229 242 .m 222 241 .d 223 240 .p 227 241 .m 229 241 .d 230 240 .m 232 241 .d 234 239 .p 234 241 .m 231 240 .d 233 238 .m 225 239 .d 228 236 .m 229 239 .d 230 238 .m 231 238 .d 232 237 .p 229 237 .p 232 236 .m 134 185 .d 139 180 .m 167 184 .d 171 180 .m 1 183 .d 4 180 .p 162 183 .p 163 183 .p 1 182 .m 156 182 .d 158 180 .m 160 182 .d 161 181 .p 4 181 .m 164 181 .d 165 180 .m 165 181 .d 166 180 .m 166 181 .d 167 180 .m 173 181 .d 174 180 .m 174 181 .d 175 180 .p 3 180 .p 161 180 .p 164 180 .m 170 180 .d 171 179 .m 173 180 .d 174 179 .p 161 179 .m 164 179 .d 167 176 .m 164 178 .d 166 176 .m 166 178 .d 167 177 .p 167 178 .m 170 178 .d 171 177 .p 173 178 .p 174 178 .m 170 177 .d 171 176 .p 173 177 .p 170 176 .p 169 175 .m 168 174 .d 169 173 .p 169 174 .m 135 172 .d 138 169 .m 1 171 .d 3 169 .m 1 167 .d 2 166 .m 1 166 .d 2 165 .m 1 165 .d 2 164 .p 1 164 .m 133 164 .d 136 161 .p 160 164 .p 135 163 .p 159 163 .m 126 162 .d 129 159 .p 134 162 .p 1 161 .m 2 161 .d 3 160 .p 5 161 .p 6 161 .p 129 161 .p 130 161 .p 131 161 .p 132 161 .m 133 161 .d 134 160 .m 137 161 .d 138 160 .p 140 161 .m 142 161 .d 144 159 .m 4 160 .d 11 153 .m 139 160 .d 146 153 .p 1 159 .p 2 159 .m 6 159 .d 7 158 .m 1 158 .d 3 156 .m 5 158 .d 6 157 .m 140 158 .d 141 157 .m 146 158 .d 149 155 .m 7 155 .d 11 151 .m 12 155 .d 14 153 .m 142 155 .d 146 151 .m 12 153 .d 14 151 .m 147 153 .d 148 152 .m 12 151 .d 13 150 .m 15 151 .d 17 149 .m 137 151 .d 140 148 .p 147 151 .m 13 149 .d 14 148 .p 16 149 .m 15 148 .d 17 146 .m 17 147 .d 25 139 .p 18 147 .p 16 146 .m 23 142 .d 24 141 .m 22 141 .d 23 140 .p 26 141 .m 39 141 .d 42 138 .m 47 141 .d 49 139 .p 119 141 .p 26 140 .p 116 140 .p 117 140 .p 119 140 .p 126 140 .p 128 140 .p 134 140 .p 135 140 .m 42 139 .d 43 138 .m 45 139 .d 47 137 .p 46 139 .m 25 138 .d 26 137 .m 34 138 .d 35 137 .p 45 138 .p 49 138 .m 102 138 .d 103 137 .m 112 138 .d 113 137 .p 24 137 .p 29 137 .p 48 137 .p 98 137 .m 116 137 .d 118 135 .p 117 137 .p 119 137 .p 126 137 .p 128 137 .m 24 136 .d 25 135 .m 26 136 .d 29 133 .p 29 136 .p 115 136 .m 126 136 .d 127 135 .p 28 135 .p 36 135 .m 44 135 .d 45 134 .m 45 135 .d 46 134 .p 46 135 .m 49 135 .d 50 134 .m 50 135 .d 51 134 .p 51 135 .m 59 135 .d 62 132 .m 120 135 .d 121 134 .m 121 135 .d 122 134 .m 122 135 .d 123 134 .m 123 135 .d 124 134 .m 124 135 .d 126 133 .p 125 135 .m 129 135 .d 130 134 .p 130 135 .p 131 135 .m 25 134 .d 26 133 .p 27 134 .p 36 134 .p 44 134 .p 49 134 .p 118 134 .p 120 134 .p 127 134 .p 129 134 .m 38 133 .d 39 132 .p 39 133 .p 115 133 .p 117 133 .p 24 132 .p 26 132 .p 29 132 .m 38 132 .d 39 131 .p 115 132 .p 117 132 .p 126 132 .p 24 131 .p 26 131 .p 29 131 .m 38 131 .d 39 130 .p 117 131 .p 126 131 .p 24 130 .p 26 130 .p 29 130 .m 38 130 .d 39 129 .m 65 130 .d 67 128 .p 117 130 .p 126 130 .m 24 129 .d 27 126 .p 26 129 .p 38 129 .p 117 129 .p 34 128 .p 41 128 .p 42 128 .p 43 128 .p 45 128 .p 46 128 .p 49 128 .m 112 128 .d 113 127 .m 24 127 .d 26 125 .p 38 127 .p 39 127 .m 117 127 .d 118 126 .m 28 126 .d 29 125 .p 33 126 .p 34 126 .p 36 126 .p 41 126 .p 42 126 .p 43 126 .p 44 126 .p 45 126 .p 46 126 .p 49 126 .m 99 126 .d 100 125 .p 120 126 .p 121 126 .p 122 126 .p 24 125 .m 38 125 .d 39 124 .p 39 125 .p 117 125 .p 24 124 .p 26 124 .p 29 124 .m 38 124 .d 39 123 .p 117 124 .p 24 123 .p 26 123 .p 29 123 .m 38 123 .d 39 122 .p 117 123 .p 24 122 .p 26 122 .p 29 122 .m 38 122 .d 39 121 .p 115 122 .p 117 122 .p 24 121 .p 26 121 .p 29 121 .m 38 121 .d 39 120 .m 61 121 .d 62 120 .p 115 121 .p 117 121 .m 24 120 .d 27 117 .p 26 120 .p 29 120 .p 34 119 .p 41 119 .p 42 119 .p 43 119 .p 45 119 .p 46 119 .p 49 119 .p 59 119 .p 102 119 .m 24 118 .d 25 117 .p 29 118 .p 28 117 .p 41 117 .m 42 117 .d 47 112 .p 43 117 .m 44 117 .d 46 115 .m 45 117 .d 46 116 .p 46 117 .p 49 117 .m 50 117 .d 52 115 .m 49 116 .d 56 109 .m 104 116 .d 108 112 .p 49 115 .m 51 115 .d 52 114 .m 58 115 .d 61 112 .m 55 111 .d 56 110 .m 58 111 .d 59 110 .m 54 110 .d 56 108 .m 58 110 .d 59 109 .m 58 109 .d 59 108 .p 58 108 .p 63 108 .m 61 107 .d 62 106 .p 62 107 .m 61 106 .d 62 105 .m 64 106 .d 67 103 .m 61 105 .d 65 101 .p 61 104 .m 61 102 .d 63 100 .m 65 102 .d 67 100 .p 68 100 .p 96 100 .m 62 99 .d 63 98 .p 65 99 .m 66 99 .d 67 98 .p 69 98 .m 65 97 .d 67 95 .p 66 97 .p 65 96 .m 69 95 .d 75 89 .m 74 91 .d 75 90 .p 74 89 .m 77 89 .d 79 87 .p 81 89 .p 83 89 .p 79 88 .p 80 88 .p 78 87 .m 74 86 .d 75 85 .p 75 86 .p 77 86 .p 81 86 .m 77 85 .d 79 83 .p 81 85 .p 79 84 .p 78 83 .p 78 82 .p 75 80 .m 50 66 .d 55 61 .m 25 64 .d 31 58 .p 58 62 .p 57 61 .p 26 60 .p 26 59 .m 16 58 .d 18 56 .m 29 57 .d 32 54 .m 31 56 .d 32 55 .p 32 56 .p 35 55 .m 20 54 .d 24 50 .p 35 54 .m 34 53 .d 35 52 .m 37 52 .d 42 47 .m 37 51 .d 38 50 .p 26 49 .m 1 48 .d 4 45 .m 6 48 .d 8 46 .p 25 48 .m 42 48 .d 43 47 .m 21 47 .d 24 44 .m 25 47 .d 26 46 .m 34 47 .d 35 46 .m 29 46 .d 30 45 .m 31 46 .d 32 45 .p 26 45 .p 29 45 .m 37 45 .d 39 43 .p 26 44 .m 29 44 .d 32 41 .m 29 43 .d 31 41 .m 31 43 .d 32 42 .m 37 43 .d 38 42 .p 37 42 .p 35 41 .p 34 40 .m 33 39 .d 34 38 .p 34 39 .p 33 38 .m 25 37 .d 26 36 .m 24 36 .d 26 34 .m 2 35 .d 3 34 .m 5 32 .d 7 30 .p 6 29 .p 25 29 .p 24 28 .m 2 26 .d 3 25 .p 6 26 .m 7 26 .d 9 24 .m 9 26 .d 12 23 .m 19 26 .d 20 25 .m 4 25 .d 9 20 .m 6 24 .d 7 23 .p 7 24 .m 1 23 .d 3 21 .m 11 23 .d 14 20 .m 14 23 .d 16 21 .m 9 22 .d 11 20 .p 15 20 .p 1 18 .m 5 18 .d 8 15 .m 11 18 .d 12 17 .p 12 18 .m 1 17 .d 5 13 .m 11 17 .d 12 16 .m 9 16 .d 10 15 .p 11 16 .m 8 14 .d 9 13 .p 10 14 .m 2 13 .d 5 10 .m 7 13 .d 8 12 .m 2 10 .d 3 9 .m 2 8 .d 3 7135 285 .p 161 286 .p 183 286 .m 134 285 .d 135 284 .p 161 285 .p 183 285 .p 161 284 .p 183 284 .m 183 283 .d 191 275 .p 181 282 .p 187 280 .m 190 277 .d 191 276 .m 189 276 .d 191 274 .m 193 276 .d 194 275 .m 193 275 .d 194 274 *[MFOLD]BATGEN.EXE;7+,.-/ 4---*0123 KPWO.56Gi7c_i89GHJ"0D`0205ih)BATGEN01i05-09 etz ( ?B!d FORRTL_001! LIBRTL_001O! MTHRTL_001$R LRNA$R CRNA0Run the folding program again in the batch file?8)Enter folding program type 1 Linear 2 CircularBatch file name? Default:(Header file name? Default:(.This program generates batch files for the RNA.folding programs LRNA and CRNA. Put the start,up information (like changing directories..)into HEADER.DAT.2At each prompt, you may type in your own response,!or hit return to use the default.Enter run type0 Regular run 1 Save run2 Continuation runEnter run mode 1 N best2 Multiple molecules$What is the save file name? Default:(That save file doesn't exist.Continue anyway?$What is the save file name? Default:(N15' end?3' end?Sequence file? Default:( Single Force Double Force Closed ExcisionOpen Excision Single ProhibitDouble Prohibit*Do you have Force or Excision information? (2 Single Force 6 Single Prohibit (3 Double Force 7 Double Prohibit (4 Closed Excision 8 Exit Force Info %5 Open Excision 9 Show current!10 Clear CurrentChoice?Starting location and length?Out of bounds. Range: to 5' base, 3' base and length?5' base and 3' base?Dangle Loop StackTStack TLoop MiscloopUse default energy files? file name? Default:(!The files you type in here become the new defaults. P does not exist. Try again.  > Premature end of Miscloop file.$Change any of the energy parameters? 2* All energy values are 10X integers. For example * -3.2 is -32 in this table. . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair []5Enter Parameter and new value ( to main menu)1 )d''Within how many percent of the minimum?#Maximum number of structures found?1Distance between structures must be greater than:(YNMake a structure file?Make a CT file?Make a REGION file?Structure file name? Default:(Printer width? Default:CT file name? Default:(REGION file name? Default:(Default= -> Please enter an integer between  and (Y,N) Default:->))->)Number too big to convert: PINPUT SEQUENCE FILE NAME ( / to end): 12 ) NO SEQUENCE IDENTIFIERS FOUND IN THIS FILE AVAILABLE SEQUENCES IN . CHOOSE SEQUENCE by NUMBER or NAME , or ? for RELIST; DEFAULTS TO THE FIRST ONE, / for NEW file. NUMBER CHOICE BETWEEN 1 AND THIS ENTRY DOES NOT MATCH WITH ANY IN GIVEN LIST SEQUENCE TRUNCATED TO ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE*2P22< LOCUSORIGIN//ID SQ SequenceNRC GENBANK Header.DatPP0P PTXpHLp PP(PxPPPhPPX@P8PPP(XhhDHhPX`XPP8PPPxPPPhPPXXXPP8PPPxPPPhPPXXXP   (P t,tt((pp,t,   @Xpt|xxPPPPPPtz pppppp  ( @8<TD@8<tD@8<D@8<D L<DD<DD (h l p t h l PPP (p  t   t  | |    HPpazAPPPPHPP& BT d d d d,  <8N0B $Fold.Com Fold.Seq Fold.Out Fold.CT Fold.Reg Fold.Sav Stack.Dat Loop.Dat ^l~ MFOLD.BCK*[MFOLD]BATGEN.EXE;7-T6 Dangle.Dat TStack.Dat TLoop.Dat Miscloop.Dat P. H[\\1# L$ .$3$! )$ $$kkRR!B ##2R ## RN3 ##$P\15PH[ \#M# F#7# 0#!## ##":"" """$"P " ""DLLP"P-~Q d"J"O"l( ="."kkxIPkPPH[q !!޼޼k !ݼ!!H[y !!k !mV!c!Y _FHP[k! HH[-  ! @H'T_dˀː H[Z  ,   $o t 48<@ kDp PB G V X( - N`lPhY  t HH[P X_h˄~ ˘˨ H[P'` h˄> ˘|Hp[}PQЬЬ $ 0޻0Pՠ<Ѡ6 ?!&<DZ1 ޻Vަ Xަ\P ަ lަp` Ц kަ|ަ ˄t ˈ,n P| ߦcpTTUE TUPPTPTT,PE T˔|' 1TP@U߅TO[Ь ,Ь4Ï@ЫVN4 LP1޻@W޻,Xk4 T k1м RSռ 1eP@@TфѤA9 RUdSP@@YiYU> UdSP@@YiYUdSP@@P`PRSTԼ Vkk1ּ м SkCǐ: ~kT߫J߫@MkPPѫk kk0 )ߨߨ 1oм Pk@ м PЫ@ǰм PЫ@@1 k1<ּ м Pk@ǐkkz kz߫p}kk - jߨD߫FG1 9*z1k߫kk  kPP 0m ߨ߫1м Pk@ м PЫ@ǰм P@@1k 1м Sռ 1~eP@@Rт3zhLŒ9V,=11Ѣ:ApŒxP1Ѣ2˄ŒV1Ѣ2ˌŒVz1Ѣ2˔bŒOVBSHѢAY˜*P@@ˤP S-м R$м RRYeZJ@XP^QRYSXTԼ 1 VH[}PQ}PQ } PQ}PQ}PQ$}PQ,Yp8P1[LE@'"H XPX &`kh pxQ ~ˀ_ UZˈ gˠˬ~˸ulcZP(&ː(˘1e|HD[Ь$H P ߫X ߫]fhR P ߫xq [߫-6ˈ! P˘? '߫߫ ߫߫˨P ˸ ߫߫ ߫iE"P޻$VJPE" QJQE"PJP(Q$PޫRЀ QNAQBP1,.RP@$S߃ R,n 䟯(kkPP`PRnPSR1dR 1\SB$JlRCS:K1,)A2PޫS$RЃ PH[Ь޻Rޢ ޢ $ޢ,ޢ8(ޢ$@ޢ$L< }ߢ WߢMߢ$CPHD[}PQ}PQ } PQЬ(Y4IP1e<EDkL\޻(Rߢ _lޢ Xޢ dThKߢ %2 )t N|9PVX˄ˌl˔"ˠnsNAgX˨PXE˰&+x$ ˸=$bnk}PIR WZ>V2VPZ@b4P, @KB~m?JJ8?ZP˔@<˘˔16WJb4WB~1SWk110ZZ2ZPP@ Z2ZPPXH11H91HP0P ZP2PPPXH HP0P XXP Z2ZZZJ JP0P ZZP 2VPѼ P-aN/2V~*YqPP   Y\?RԼ ZV"2ZXXP)@<X Y=VZռ !Y1\B~P1hм P@b4YZY_(AKB~pV[-k&.O˜05V1=YZ)1м P2@J8Ѽ'1ݼ<'ϋό2 P@vB~2P@s<м P2@J8PP@816Yk34>B~cIN) PPPZPXPP12YWW'1k12XPP@GsؑGs*/Gs1Gs2 GsأYP2PkKW'7<'kݼ Gs Y2kWz [ݼEV=ZX(k1V Q(E@@(@@ 8 (  @FORRTLLIBRTLMTHRTL BATGEN BATGEN%Q BATGEN$DATA INIT INIT)h GETRUNTYPEp GETRUNTYPE Q REGULARRUN REGULARRUNm FINISH 8FINISH SAVERUNXSAVERUN\CONTINUATIONRUNCONTINUATIONRUN ONESEQ ONESEQ =MULTISEQMULTISEQ  4SEQINFOSEQINFO$ u FORCEINFOp FORCEINFOr 9 EFILES EFILES(  EPARAMSEPARAMS5 NBEST `NBEST  OUTPUTFILES( OUTPUTFILES2 z GETINT GETINT  CONVT XCONVTf YESSIR YESSIR UPCASE p UPCASE FWRITESTR WRITESTR  GETSTR @ GETSTR j PARSE PARSE FIND h FIND  GETSEQ GETSEQ¹U Y *+ XO *[MFOLD]BATGEN.FOR;5+,.B/ 4OB@-*0123KPWOC56i7ti89GHJD program batgen* ** Batch file generator for RNA.>** Design: As each subroutine is called, it asks for it's own@** particular parameter. Before exiting, it writes out@** it's answers (data, file name, whatever) to file 20,?** the batch file. At the same time, these values areB** stored in the program, so that if the user runs again,?** the defaults are the answers from the previous run.@** Parameters between main, high level and intermediateB** level routines are passed in COMMON blocks and by nameE** to low and basement level routines (exception:GetRunType)**:** Tried to stay as close as possible to variableC** definitions listed in MFOLD.DOC ( RNA.DOC in version 1)*6** Synopsis of routines (sub=subroutine, fun=function)*** HIGH LEVEL ROUTINES-** blank Block Data - initial default set upE** Sub INIT - Intro!, gets batch file name, header info, andB** whether Circular or Linear folding program.B** Sub GetRunType - gets run type (Regular, Save, Continuation)C** Sub RegularRun - gets run mode (nbest or multiple), and calls9** Sub Finish - KP. Closes files. Could do more.** INTERMEDIATE LEVEL ROUTINESC** Sub SaveRun - gets save run file name, then the other dataB** Sub ContinuationRun - gets old save file name, then other info=** Sub OneSeq - Regular run, one sequence. Get stuff.A** Sub MultiSeq - Regular run, multiple sequence. Go to it.** LOW LEVEL ROUTINESB** Sub SeqInfo - gets seq (from GetSeq, which is FORMID withA** different vars passed back), and begin/end$** if necessary.@** Sub ForceInfo - Gets force info, EXCEPT for EParam stuff..** Sub EFiles - Gets energy file names.>** Sub EParams - EParam menu, separated from Force menu.L** Sub NBest - get the 3 nbest parameters: how many % within minimum@** energy, max # of structures and distance.C** Sub OutputFiles - inquires of 3 output files: Structure,CT and** REGION** THE BASEMENTH** Sub GetInt - gets an integer within limits, returns default if6** user hits return. Has default.J** Fun Convt - converts a Char*5 string to an integer, if possibleD** Fun YesSir - returns .TRUE. if user types Y. Has default.9** Fun UpCase - "uppercases" character sent to it.B** Sub WriteStr - writes a string to desired unit, leaves out&** trailing blanks=** Sub GetStr - gets a string from user. Has default./** NEEDS THIS OTHER ROUTINE (not in this file).H** Sub GetSeq - altered version of FORMID to return file name and"** seq number.**&** -John Jaeger Dec88D** -modified for version 2 by Michael Zuker Nov89* ** Files:** Unit Description;** 10 Header file - contains info specific to your site1** (i.e. set default [....])0** 20 Batch file - where all this stuff goes*D** Main program: Figures out RunType (Regular, Save or Continuation)*** and calls proper routine.*$ integer inunit,outunit,runtype$ parameter (inunit=5,outunit=6) character*1 ch logical finished,yessir*B integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop*; common/ints/cntrl,eparam,list,listsz,seqlimits,linear2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloop*B** Open batch file, put in header info, get linear or circular run* call init finished=.false. 10 if (finished) goto 20 if (linear) then& write (20,5) '$R LRNA' else& write (20,5) '$R CRNA' endif runtype=cntrl(1) call getruntype(runtype) cntrl(1)=runtype if (runtype.eq.0) then call regularrun write (20,2)" elseif (runtype.eq.1) then call saverun write (20,2)" elseif (runtype.eq.2) then call continuationrun endif ch='N' write (outunit,1) finished=.not.yessir(ch) goto 1020 continue call finishD1 format (1x,'Run the folding program again in the batch file?')2 format ('8')5 format (a7/1x) end  block data*@** Initializes variables in COMMON blocks. Change these to suit** your own tastes.*B integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop*; common/ints/cntrl,eparam,list,listsz,seqlimits,linear2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloop*G data cntrl/1,1,80,0,0,1,1,0,0,0/eparam/0,0,0,0,46,4,30,30,-500,1/4 data listsz/0/linear/.true./seqlimits/1,1,999/ data batch/'Fold.Com'/ data stack/'Stack.Dat'/ data loop/'Loop.Dat'/ data dangle/'Dangle.Dat'/ data tstack/'TStack.Dat'/ data tloop/'TLoop.Dat'/= data sequence/'Fold.Seq'/struc/'Fold.Out'/ct/'Fold.CT'/1 data region/'Fold.Reg'/savefile/'Fold.Sav'/# data miscloop/'Miscloop.Dat'/* end )* High level routines - called by main  subroutine init*?** Greet user. Get batch file and open as unit 20. Get headerB** file (unit 10) and put it's info into the batch file. Find out7** if we're running linear or circular folding program.* integer inunit,outunit$ parameter (inunit=5,outunit=6) integer i*B integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear@ character*80 batch,sequence,struc,ct,region,hfile,savefile@ character*80 stack,loop,dangle,tstack,tloop,miscloop,buffa*; common/ints/cntrl,eparam,list,listsz,seqlimits,linear2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloop*$ data hfile(1:10)/'Header.Dat'/* ** Intro.* write (outunit,100) write (outunit,101) write (outunit,102) write (outunit,103) write (outunit,104) write (outunit,105)*** Get Batch file name*20 write (outunit,3) batch call getstr(batch)3 open (unit=20,status='new',err=20,file=batch,# 1 carriagecontrol='list')*** Get default header file*10 write (outunit,4) hfile call getstr(hfile)3 open (unit=10,status='old',err=10,file=hfile,# 1 carriagecontrol='list')*)** write header file to top of batch file*30 read (10,1,end=40) buffa call writestr(20,buffa) goto 30*/** Get type of program run (linear or circular)*40 write (outunit,2) if (linear) then i=1 else i=2 endif call getint(i,1,2,i) linear=(i.eq.1) return*1 format (a)02 format (1x,'Enter folding program type',/, 1 5x,'1 Linear',/, 2 5x,'2 Circular')13 format (1x,'Batch file name? Default:',a40)24 format (1x,'Header file name? Default:',a40)B100 format (3x,'This program generates batch files for the RNA')B101 format (1x,'folding programs LRNA and CRNA. Put the start')@102 format (1x,'up information (like changing directories..)')$103 format (1x,'into HEADER.DAT.')F104 format (3x,'At each prompt, you may type in your own response,')7105 format (1x,'or hit return to use the default.',/) end  subroutine getruntype(rt)*=** Gets Run type (regular, save or continuation), and returns)** the right value (Reg=0,Save=1,Cont=2).l*e integer inunit,outunit$ parameter (inunit=5,outunit=6) integer rt write (outunit,1)t call getint(rt,0,2,rt) write (20,2) rta return$1 format (1x,'Enter run type',/,$ 1 5x,'0 Regular run',/,! 2 5x,'1 Save run',/, ' 3 5x,'2 Continuation run')r2 format (i1) ende l subroutine regularrunr*o<** User wants a regular run, but there are two modes: single=** and multiple (can't run plots from batch). Get mode type,l=** (nbest=1, multiple=2) write to file, then call appropriates** subroutine.*y integer inunit,outunit$ parameter (inunit=5,outunit=6)**B integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop*N; common/ints/cntrl,eparam,list,listsz,seqlimits,linear2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloopS*,C** Get Run Mode a.k.a. Cntrl(7). Either 1 (N best) or 2 (Multiple)l*  write (outunit,1)h( call getint(cntrl(7),1,2,cntrl(7)) write (20,2) cntrl(7)T*S if (cntrl(7).eq.1) thena call oneseqn" else if (cntrl(7).eq.2) then call multiseqi endif return$1 format (1x,'Enter run mode',/, 1 5x,'1 N best',/,* 2 5x,'2 Multiple molecules')2 format (i1)W endI  subroutine finishg* ** Close shopq*h# close (unit=10,status='keep') # close (unit=20,status='keep') return end  * Medium level routinesu subroutine saverun*n@** User wants a save run. Ask for save file name, write it out,A** then call appropriate subroutines to get the rest of the data.e*n integer inunit,outunit$ parameter (inunit=5,outunit=6)*nB integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop* ; common/ints/cntrl,eparam,list,listsz,seqlimits,linear 2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloop *s** Get the Save file name*t write (outunit,1) savefile call getstr(savefile) call writestr(20,savefile)*** Ask for all the right info *t, call seqinfo(sequence,seqlimits,cntrl): call efiles(stack,loop,dangle,tstack,tloop,miscloop)+ call forceinfo(seqlimits,list,listsz)  call eparams(eparam) return<1 format (1x,'What is the save file name? Default:',a40) end  subroutine continuationrun* <** User wants a continuation run. Get NBest parameters, theA** old save file name, put the continuation dump in the log file,e'** then ask for the other output files.i*i integer inunit,outunit$ parameter (inunit=5,outunit=6) logical itexists,yessire character*1 ch*oB integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop*c; common/ints/cntrl,eparam,list,listsz,seqlimits,linearn2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloopt*g9** Since we're writing a batch file, assume "n best" model** for the continuation runn*t write (20,3) call nbest(cntrl)* 0** Get the save file name, and see if it exists.*1 10 write (outunit,1) savefile call getstr(savefile)*+ inquire(file=savefile,exist=itexists)e if (.not.itexists) thena9 write (inunit,*) 'That save file doesn''t exist.'o+ write (inunit,*) 'Continue anyway?'  ch='N'$ if (.not.yessir(ch)) goto 10 endif) call writestr(20,savefile)*u write (20,2)- call outputfiles(struc,ct,region,cntrl)r return<1 format (1x,'What is the save file name? Default:',a40)2 format (/,'N')3 format ('1') end   subroutine oneseq *r*** User wants a regular run, one sequence.*B integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop*r; common/ints/cntrl,eparam,list,listsz,seqlimits,linearo2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloopt** call nbest(cntrl) , call seqinfo(sequence,seqlimits,cntrl): call efiles(stack,loop,dangle,tstack,tloop,miscloop)- call outputfiles(struc,ct,region,cntrl) + call forceinfo(seqlimits,list,listsz)i call eparams(eparam) return endz q subroutine multiseqn*a** Regular run, many sequences.,* B integer cntrl(10),eparam(10),list(100,4),listsz,seqlimits(3) logical linear: character*80 batch,sequence,struc,ct,region,savefile: character*80 stack,loop,dangle,tstack,tloop,miscloop*o; common/ints/cntrl,eparam,list,listsz,seqlimits,linearo2 common/fnams/batch,sequence,struc,ct,region,= 1 savefile,stack,loop,dangle,tstack,tloop,miscloop *a, call seqinfo(sequence,seqlimits,cntrl) call nbest(cntrl)/: call efiles(stack,loop,dangle,tstack,tloop,miscloop)- call outputfiles(struc,ct,region,cntrl)  call eparams(eparam) return end * Low level routines- subroutine seqinfo(seq,seqlimits,cntrl)l*uE** Get sequence file name, sequence #, and folding limits (5' to 3').uC** Use a slightly altered version of FORMID to do most of the dirtyo** work.* integer inunit,outunit,ptr$ parameter (inunit=5,outunit=6)*0 character*80 seq,seqnumbuf= integer seqlimits(3),cntrl(10),i,seqsize,numofseqs,tempe*,/ if (cntrl(1).eq.0.and.cntrl(7).eq.2) then0*a/** Just get seq, because it's a multi-seq run *  write (outunit,3) seqi call getstr(seq) call writestr(20,seq), else*,** Get seq, number and limits.*d2 call getseq(seq,seqlimits(3),seqlimits(1)) write (outunit,1)I2 call getint(1,1,seqlimits(3),seqlimits(2)) write (outunit,2)  temp=seqlimits(3) 9 call getint(temp,seqlimits(2),temp,seqlimits(3))t call writestr(20,seq)l*aE** Have to encode and WriteStr the seq #, since FORMID is picky about ** this sort of thing.*e seqnumbuf=' ' + encode (5,5,seqnumbuf) seqlimits(1)d ptr=1i, do while (seqnumbuf(ptr:ptr).eq.' ') ptr=ptr+1p enddot/ seqnumbuf(1:80-ptr+1)=seqnumbuf(ptr:80)e# call writestr(20,seqnumbuf) 1 write (20,6) (seqlimits(i),i=2,3)d endif return1 format (1x,'5'' end?')2 format (1x,'3'' end?')/3 format (1x,'Sequence file? Default:',a40)t5 format (i5)e6 format (i5,/,i5) end 1 subroutine forceinfo(seqlimits,list,listsz)* @** Get the information found in the FORCE menu - except option 1A** (change energy parameters), which is a separate routine. Menu'0** is slighly changed from RNA - check format 2.*( integer inunit,outunit$ parameter (inunit=5,outunit=6)*e3 integer seqlimits(3),list(100,4),listsz,i,j,kr logical yessir character*1 ch ch='N' i=8N*n:** Ask user if they have any info. If they don't just go.*e write (outunit,1)) if (yessir(ch)) then10 i=8m write(outunit,2) call getint(i,2,10,i)*** it's ugly but it workst*  if (i.eq.8) then* "** write info to batch file, exit.*( do i=1,listszuB if (list(i,1).eq.3.or.list(i,1).eq.7) then? write (20,12) (list(i,j),j=1,4)e else? write (20,12) (list(i,j),j=1,3)) endif do j=1,4+ list(i,j)=0, enddou enddox listsz=0 return& elseif (i.eq.3.or.i.eq.7) then*o ** Double force, double prohibit*e listsz=listsz+1m list(listsz,1)=i!30 write (outunit,5)m, read (inunit,*,err=10) i,j,k3 if (i.lt.seqlimits(2).or.i.gt.j.or.( 1 j.lt.i.or.i+k.gt.j) thenC write (outunit,4) seqlimits(2),seqlimits(3)  goto 30e endifu list(listsz,2)=i list(listsz,3)=j list(listsz,4)=k else if (i.lt.8) theni+* note that 3,7 were taken 4~ MFOLD.BCK*[MFOLD]BATGEN.FOR;5OB}<# care of above...c listsz=listsz+1s list(listsz,1)=i*20 if (i.eq.4.or.i.eq.5) then*l** Excision info*t) write (outunit,7)t2 read (inunit,*,err=10) i,jH if (i.lt.seqlimits(2).or.i.gt.seqlimits(3)) thenK write (outunit,4) seqlimits(2),seqlimits(3)n' goto 20e endifx else* !** Single force, single prohibit.* ) write (outunit,3)u2 read (inunit,*,err=10) i,jF if (i.lt.seqlimits(2).or.i.gt.seqlimits(3).or., 1 i+j.gt.seqlimits(3)) thenK write (outunit,4) seqlimits(2),seqlimits(3)m' goto 20e endif  endifn list(listsz,2)=i list(listsz,3)=j list(listsz,4)=0 else if (i.eq.9) then * ** Output info to the user** do 40 j=1,listsz+ if (list(j,1).eq.2) theneN write (outunit,*) 'Single Force ',list(j,2),list(j,3)/ elseif (list(j,1).eq.3) then,O write (outunit,*) 'Double Force ',list(j,2),list(j,3),*- 1 list(j,4)n/ elseif (list(j,1).eq.4) then N write (outunit,*) 'Closed Excision',list(j,2),list(j,3)/ elseif (list(j,1).eq.5) theniN write (outunit,*) 'Open Excision ',list(j,2),list(j,3)/ elseif (list(j,1).eq.6) thenuN write (outunit,*) 'Single Prohibit',list(j,2),list(j,3)/ elseif (list(j,1).eq.7) thenaO write (outunit,*) 'Double Prohibit',list(j,2),list(j,3),e- 1 list(j,4)s endif40 continue else*a** clear the arrrayi*) do 99 i=1,listsz# list(i,1)=0e99 continue listsz=0 endifa goto 10h endift>1 format (1x,'Do you have Force or Excision information?')2 format(/,,9 . 10x,'2 Single Force 6 Single Prohibit',/,t9 . 10x,'3 Double Force 7 Double Prohibit',/,u9 . 10x,'4 Closed Excision 8 Exit Force Info',/,k6 . 10x,'5 Open Excision 9 Show current',/," . 33x,'10 Clear Current',/, . 1x,'Choice?')13 format (1x,'Starting location and length?')*74 format (1x,'Out of bounds. Range:',i5,' to ',i5) 25 format (1x,'5'' base, 3'' base and length?')*6 format (1x,a15,' :',i5,2x,i5,2x,i5)*7 format (1x,'5'' base and 3'' base?')12 format (i1,/,i5,2(1x,i5))i end  s@ subroutine efiles(stack,loop,dangle,tstack,tloop,miscloop)* ?** Get the energy file info. Ask the user if they want defaulte=** files. If so, then write out defaults. Otherwise get news@** energy file names (WHICH BECOME THE NEW DEFAULTS!!) and write ** them out.*e integer inunit,outunit$ parameter (inunit=5,outunit=6): character*80 stack,loop,dangle,tstack,tloop,miscloop logical yessir character*1 ch*0 ch='Y' write (outunit,1)t if (.not.yessir(ch)) then  write (outunit,3),) write (outunit,2) 'Dangle',dangle0 call getstr(dangle)o& write (outunit,2) ' Loop',loop call getstr(loop)s( write (outunit,2) ' Stack',stack call getstr(stack)) write (outunit,2) 'TStack',tstackp call getstr(tstack)e( write (outunit,2) ' TLoop',tloop call getstr(tloop).50 write (outunit,2) ' Miscloop',miscloop call getstr(miscloop), endif  call writestr(20,dangle) call writestr(20,loop) call writestr(20,stack)  call writestr(20,tstack) call writestr(20,tloop)y call writestr(20,miscloop)0 open(32,file=miscloop,status='old',err=60) return60 write(6,4) miscloop0 go to 50-1 format (1x,'Use default energy files?')a/2 format (1x,a6,' file name? Default:',a40)o73 format (/,1x,'The files you type in here become', $ 1 ' the new defaults.')54 format (' ',a80/' does not exist. Try again.'/)k endl subroutine eparams(eparam)*l6** Get the energy parameters. Usually this is part of3** the Force/Excision menu, but I separated them tol** speed things up a bit.n*t integer inunit,outunit$ parameter (inunit=5,outunit=6)6 integer eparam(10),i,j,oldep(10),start,fin,convt logical yessir,findq character*20 inbuf character*5 token character*1 ch real a,b,c ;c Get misc loop info - discard all but the EPARAM data.eA if(find(32,3,' > ')) stop 'Premature end of Miscloop file.'  read (32,*) aqA if(find(32,3,' > ')) stop 'Premature end of Miscloop file.'m read (32,*) arA if(find(32,3,' > ')) stop 'Premature end of Miscloop file.'i read (32,*) a,b,c,a A if(find(32,3,' > ')) stop 'Premature end of Miscloop file.'l read (32,*) a,b,c  close (32) eparam(5)=int(a*10) eparam(6)=int(b*10)l eparam(10)=int(c*10) do i=1,10t oldep(i)=eparam(i) enddo) ch='N' write (outunit,1)2 if (yessir(ch)) then write (20,4),10 write (outunit,2) (eparam(i),i=1,10) inbuf=' '0% read (outunit,7,err=10) inbufS*t start=1O fin=20* call parse (start,fin,inbuf,token)# if (start-1.eq.fin) goto 20n i=convt(token)* call parse (start,fin,inbuf,token) j=convt(token)* & if (i.lt.1.or.i.gt.10) goto 10 eparam(i)=j= write (20,3) i,j goto 100*q** TERMINATOR=CR right here...*,20 write (20,5) endifn do i=1,10n eparam(i)=oldep(i)? enddom return81 format (1x,'Change any of the energy parameters?')2 format(/,C . 10x,'* All energy values are 10X integers. For example',/,q. . 10x,'* -3.2 is -32 in this table.',//,F . 10x,' 1 Extra stack energy [',i5,']',/,F . 10x,' 2 Extra bulge energy [',i5,']',/,F . 10x,' 3 Extra loop energy (interior) [',i5,']',/,F . 10x,' 4 Extra loop energy (hairpin) [',i5,']',/,F . 10x,' 5 Extra loop energy (multi) [',i5,']',/,F . 10x,' 6 Multi loop energy/single-stranded base [',i5,']',/,F . 10x,' 7 Maximum size of interior loop [',i5,']',/,F . 10x,' 8 Maximum lopsidedness of an interior loop [',i5,']',/,F . 10x,' 9 Bonus Energy [',i5,']',/,G . 10x,'10 Multi loop energy/closing base-pair [',i5,']',//, C . 1x,'Enter Parameter and new value ( to main menu)') 3 format (i2/i5)4 format ('1')5 format (' ')6 format () 7 format (a) endt 2 subroutine nbest(cntrl) * A** Get the three NBest parameters - %,# structures, and distance. >** Stick them in Cntrl, where they belong, and write them out.*  integer inunit,outunit$ parameter (inunit=5,outunit=6)* integer cntrl(10),i,jq*  write (outunit,1),* call getint(cntrl(8),0,100,cntrl(8)) write (outunit,2) + call getint(cntrl(6),1,9999,cntrl(6))t write (outunit,3) * call getint(cntrl(9),0,100,cntrl(9))*f- write (20,4) cntrl(8),cntrl(6),cntrl(9) * return;1 format (1x,'Within how many percent of the minimum?')t72 format (1x,'Maximum number of structures found?') E3 format (1x,'Distance between structures must be greater than:')i4 format (i4,2(/,i4)) ends ,3 subroutine outputfiles(struc,ct,region,cntrl) *e1** Ask the user for the kind of output files theys1** want. Defaults here are imbedded in the code. *  integer inunit,outunit$ parameter (inunit=5,outunit=6) integer cntrl(10)t" character*80 struc,ct,region logical yessir character*1 ch*f** Structure file?*i ch='Y' write (outunit,1)  if (yessir(ch)) then*49** If a structure file is desired, don't stick the output ** into the log file. *  write (20,9) 'Y' write (20,9) 'N' write (outunit,4) struc  call getstr(struc)" write (outunit,5) cntrl(3)- call getint(cntrl(3),40,144,cntrl(3))  call writestr(20,struc). write (20,6) cntrl(3) else write (20,9) 'N' endif * ** CT file? *t ch='N' write (outunit,2)  if (yessir(ch)) then write (20,9) 'Y' write (outunit,7) ct call getstr(ct)  call writestr (20,ct) else write (20,9) 'N' endif0* ** Region file?e*) ch='N' write (outunit,3) if (yessir(ch)) then write (20,9) 'Y' write (outunit,8) region call getstr(region)u call writestr(20,region) else write (20,9) 'N' endif. return* *1 format (1x,'Make a structure file?')#2 format (1x,'Make a CT file?') '3 format (1x,'Make a REGION file?') 54 format (1x,'Structure file name? Default:',a40) .5 format (1x,'Printer width? Default:',i3)6 format (i3),.7 format (1x,'CT file name? Default:',a40)28 format (1x,'REGION file name? Default:',a40)9 format (a1), end)* <** BASEMENT ROUTINES (should be in a tool box some where...)* 2 subroutine getint(default,minimum,maximum,i)*(3** Get an integer from the user. Make sure it's ina1** bounds (Minimum <= I <= Maximum). If the userP2** hits return, use the default. Uses the routine** Convt, stolen from RNA.*  integer inunit,outunit$ parameter (inunit=5,outunit=6)- integer default,minimum,maximum,i,convto character*5 inbuf *  inbuf=' '110 write (outunit,1) default " read (inunit,2,err=10) inbuf if (inbuf.eq.' ') then i=default( else i=convt(inbuf) endif, if (i.lt.minimum.or.i.gt.maximum) then) write (outunit,3) minimum,maximum, goto 10 endife return* '1 format (1x,'Default=',i4,' ->',$)F2 format (a5) B3 format (1x,'Please enter an integer between ',i4,' and ',i4) ende ,! integer function convt(str)o*t7** Convert a buffer STR to an integer. Stolen from RNA'*  integer i,place' character*5 strt logical neg  e neg = .false.  place = 0  convt = 0)  do 10 i = 5,1,-1! if (str(i:i).eq.'-') then/ neg = .true. else7 if (str(i:i).ge.'0'.and.str(i:i).le.'9') then)G convt = convt + 10**place * (ichar(str(i:i)) - ichar('0'))* place = place+1 endifw endif* 10 continue! if (neg) convt = convt * -1a return ende  & logical function yessir(default)*u4** Ask for, and get either a Y or N response. If Y,4** this function returns .TRUE., .PHALSE. otherwise.*c integer inunit,outunit$ parameter (inunit=5,outunit=6)# character*1 default,ch,upcaset ch=' '10 write (outunit,1) defaultn read (inunit,2,err=10) cho if (ch.eq.' ') then  yessir=(default.eq.'Y')( else ch=upcase(ch)  yessir=(ch.eq.'Y')# if (ch.ne.'Y') then2& if (ch.ne.'N') goto 10 endif endifn,1 format (1x,'(Y,N) Default:',a1,'->',$)2 format (a1)o return endc p' character*1 function upcase (ch)n* ** Stolen from MYLIB.FOR'** Change Ch to upper case if necessary *a character*1 ch' character*1 lowera,lowerz,upperal*i- data lowera/'a'/lowerz/'z'/uppera/'A'/o*F if (lle(lowera(1:1),ch(1:1)).and.lge(lowerz(1:1),ch(1:1))) then; upcase=char(ichar(uppera)+ichar(ch)-ichar(lowera))a elsel upcase=ch endif return' end o% subroutine writestr(unit,buffa)b*m5** Write out what's ever in the buffer to UNIT. Killt7** trailing spaces. Special format for screen (unit=6) -** since it requires line control characters.t*e integer outunitl parameter (outunit=6)r integer unit,ptr,i character*80 buffa*i i=80$10 if (buffa(i:i).ne.' ') goto 20 i=i-1e goto 10u*=20 if (unit.eq.outunit) theno! write (unit,1) buffa(1:i)i else! write (unit,2) buffa(1:i) endif return1 format (1x,a) 2 format (a) endc o subroutine getstr(default)*a5** Get string from the user. If it bombs, try again. *c integer inunit,outunit$ parameter (inunit=5,outunit=6) character*80 default,inbuf* 10 inbuf=' 'r write (outunit,1)'" read (inunit,2,err=10) inbuf% if (inbuf.ne.' ') default=inbuf return1 format (1x,'->',$)2 format (a) end / subroutine parse(start,fin,inbuf,token)m/ integer start,fin,i,tokenstart,tokenfin  character*20 inbuf character*5 token)*a i=startd token=' ' 1 do while (i.le.fin.and.inbuf(i:i).eq.' ') i=i+1, enddot tokenstart=i1 do while (i.le.fin.and.inbuf(i:i).ne.' ')i i=i+1 enddoO tokenfin=i-1* if (tokenfin-tokenstart+1.gt.5) then start=finf0 write (*,1) inbuf(tokenstart:tokenfin) elseA token(1:tokenfin-tokenstart+1)=inbuf(tokenstart:tokenfin)o endif  start=im return51 format (1x,'Number too big to convert: ',a20)R end.'c Used in reading the energy files. Bc Locates markers in the energy files so that data can be readc properly.(! function find(unit,len,str)t implicit integer (a-z) logical find,flagu character*20 str character*80 inrec * find = .false. flag = .false. do while(.not.flag)% read(unit,100,end=200) inrec. count = 1 do i = 1,80-len+13 if (inrec(i:i).eq.str(count:count)) theni count = count + 1, if (count.gt.len) flag = .true.> if (inrec(i+1:i+1).ne.str(count:count)) count = 1 endif enddo enddo0 return100 format(a80)r200 find = .true.] return endim size of interior loop [',i5,']',/,F . 10x,' 8 Maximum lopsidedness of an interior loop [',i5,']',/,F . 10x,' 9 Bonus Energy [',i5,']',/,G . 10x,'10 Multi loop energy/closing base-pair [',i5,']',//, C . 1x,'Enter *[MFOLD]BATGEN.OBJ;3+,.3/ 431-*0123KPWO456i7Ai89GHJ>1BATGEN0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 BATGENTP$R LRNA$R CRNA0Run the folding program again in the batch file?8 BATGENPPH[INIT\\1G FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_ENDG FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDk GETRUNTYPEkRR REGULARRUNC FOR$WRITE_SF FOR$IO_ENDRSAVERUNC FOR$WRITE_SF FOR$IO_ENDRCONTINUATIONRUNN FOR$WRITE_SF FOR$IO_END$YESSIRP\1FINISHP HBATGENYESSIRINIT GETRUNTYPE REGULARRUNSAVERUNCONTINUATIONRUNFINISH$CODEM$PDATA0$LOCALINTSFNAMS FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF>P P#BP!~P!P2PP P1%Q6 BATGEN$DATA0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 BATGEN$DATABPP. Q@Q QPFold.Com H'QStack.Dat G'Loop.Dat H'Dangle.Dat F'TStack.Dat F'TLoop.Dat G'QFold.Seq H'Fold.Out H'Fold.CT I'Fold.Reg H'Fold.Sav H'QMiscloop.Dat D'INTSFNAMS/INIT0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 INITP)Enter folding program type 1 Linear 2 CircularBatch file name? Default:(Header file name? Default:(.This program generates batch files for the RNA.folding programs LRNA and CRNA. Put the start,up information (like changing directories..)into HEADER.DAT.2At each prompt, you may type in your own response,!or hit return to use the default. INITSPPPPP QHeader.DatPH[ FOR$WRITE_SF FOR$IO_END FOR$WRITE_SF FOR$IO_END FOR$WRITE_SF FOR$IO_END# FOR$WRITE_SF FOR$IO_END8 FOR$WRITE_SF FOR$IO_ENDo FOR$WRITE_SF FOR$IO_ENDK FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDGETSTR$FOR$OPENPk FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_ENDDGETSTRLFOR$OPENP~   FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDlWRITESTR FOR$WRITE_SF FOR$IO_ENDkkxGETINTPkPP HINITGETSTRFOR$OPENWRITESTRGETINTh$CODE$PDATA,$LOCALINTSFNAMS FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SFP-DPIP5)h5 GETRUNTYPE0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 GETRUNTYPE`PEnter run type0 Regular run 1 Save run2 Continuation run GETRUNTYPEPPH[ FOR$WRITE_SF FOR$IO_END޼޼kGETINTV FOR$WRITE_SFݼ FOR$IO_L_V FOR$IO_END H GETRUNTYPEGETINTQ$CODEY$PDATA$LOCAL FOR$IO_END FOR$IO_L_V FOR$WRITE_SF Q5 REGULARRUN0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 REGULARRUNOPEnter run mode 1 N best2 Multiple molecules REGULARRUNPPH[ FOR$WRITE_SF FOR$IO_ENDkGETINTE FOR$WRITE_SF FOR$IO_L_R FOR$IO_ENDONESEQMULTISEQ H REGULARRUNGETINTONESEQMULTISEQm$CODEH$PDATA$LOCALINTSFNAMS FOR$IO_END FOR$IO_L_R FOR$WRITE_SFQP ZPdPm1FINISH0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 FINISH FINISHOP PH[k FOR$CLOSE FOR$CLOSEM HFINISH FOR$CLOSE$CODE$PDATA$LOCAL 2SAVERUN0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133SAVERUN6P$What is the save file name? Default:(SAVERUNvPPPPPP0PPP Pp (08P(PH[ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END@GETSTRHWRITESTRTSEQINFOdEFILESˀ FORCEINFOːEPARAMS HSAVERUNGETSTRWRITESTRSEQINFOEFILES FORCEINFOEPARAMS\$CODE/$PDATA$LOCALINTSFNAMS FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF\:CONTINUATIONRUN0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133CONTINUATIONRUNlPThat save file doesn't exist.Continue anyway?$What is the save file name? Default:(N1CONTINUATIONRUN,PPPP@P((!( PH[a FOR$WRITE_SF FOR$IO_END,NBEST1 FOR$WRITE_SF$ FOR$IO_T_DS FOR$IO_END4GETSTR< FOR$INQUIREk FOR$WRITE_SLP FOR$IO_T_DS FOR$IO_END FOR$WRITE_SLX FOR$IO_T_DS FOR$IO_ENDN`YESSIRPhWRITESTR\ FOR$WRITE_SF FOR$IO_ENDt OUTPUTFILES HCONTINUATIONRUNYESSIRNBESTGETSTR FOR$INQUIREWRITESTR OUTPUTFILES$CODEe$PDATA$LOCALINTSFNAMS FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SLZPD'1ONESEQ0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 ONESEQ ONESEQYPPPPPP@PP0PPP Pp (08@HP(PH[PNBESTXSEQINFOhEFILES˄ OUTPUTFILES˘ FORCEINFO˨EPARAMS HONESEQNBESTSEQINFOEFILES OUTPUTFILES FORCEINFOEPARAMS=$CODE$PDATA$LOCALINTSFNAMS =3MULTISEQ0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133MULTISEQMULTISEQ2PPPPPP@PP0PPP Pp (08@H(PH[PSEQINFO`NBESThEFILES˄ OUTPUTFILES˘EPARAMS HMULTISEQSEQINFONBESTEFILES OUTPUTFILESEPARAMS4$CODE$PDATA$LOCALINTSFNAMS  42SEQINFO0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133SEQINFONP5' end?3' end?Sequence file? Default:(SEQINFOTPP   (PTTTPPTP|HP[}PQЬЬ $ 0޻0PՠѠ  FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END<GETSTRDWRITESTR1޻Vަ Xަ\PGETSEQ FOR$WRITE_SF FOR$IO_ENDަ lަp`GETINT FOR$WRITE_SF FOR$IO_ENDЦ kަ|ަ ˄tGETINTˈWRITESTR,n P> FOR$ENCODE_MFߦ FOR$IO_L_R FOR$IO_ENDTTUE TUPPTPTT,PE T˔WRITESTRA FOR$WRITE_SFTP@U߅ FOR$IO_L_RT FOR$IO_END |HSEQINFOGETSTRWRITESTRGETSEQGETINTu$CODEG$PDATA$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$WRITE_SF FOR$ENCODE_MF/P<5P6gP P0$ u4 FORCEINFO0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 FORCEINFOP Single Force Double Force Closed ExcisionOpen Excision Single ProhibitDouble Prohibit*Do you have Force or Excision information? (2 Single Force 6 Single Prohibit (3 Double Force 7 Double Prohibit (4 Closed Excision 8 Exit Force Info %5 Open Excision 9 Show current!10 Clear CurrentChoice?Starting location and length?Out of bounds. Range: to 5' base, 3' base and length?5' base and 3' base? FORCEINFO P   @H *9HWPO[Ь ,Ь4Ï@ЫVNf FOR$WRITE_SF FOR$IO_ENDLYESSIRP1޻@W޻,Xk FOR$WRITE_SF FOR$IO_ENDTGETINTk1м RSռ 1eP@@TфѤ FOR$WRITE_SFUdSP@@Yi FOR$IO_L_RYU FOR$IO_END FOR$WRITE_SFUdSP@@Yi FOR$IO_L_RYU FOR$IO_ENDdSP@@P`PRSTԼ Vkk1ּ м SkCǐ FOR$WRITE_SF FOR$IO_END FOR$READ_SLk FOR$IO_L_R߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_ENDkPPѫkkk FOR$WRITE_SFߨ FOR$IO_L_Rߨ  FOR$IO_L_R FOR$IO_END1oм Pk@ м PЫ@ǰм PЫ@@1k1ּ м Pk@ǐkk FOR$WRITE_SF FOR$IO_END FOR$READ_SLk FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_ENDkk  FOR$WRITE_SFߨ FOR$IO_L_R߫ FOR$IO_X_DA FOR$IO_END1i FOR$WRITE_SF FOR$IO_ENDz FOR$READ_SLk FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_ENDkk kPP  FOR$WRITE_SFߨ FOR$IO_L_R߫ FOR$IO_X_DA FOR$IO_END1м Pk@ м PЫ@ǰм P@@1k 1м Sռ 1eP@@Rт FOR$WRITE_SLh FOR$IO_T_DSŒ FOR$IO_L_RV FOR$IO_L_V FOR$IO_END1Ѣ FOR$WRITE_SLp FOR$IO_T_DSŒ FOR$IO_L_RxLISLISTP FOR$IO_L_V FOR$IO_END1Ѣ FOR$WRITE_SL˄ FOR$IO_T_DSŒ FOR$IO_L_RV FOR$IO_L_V FOR$IO_END1Ѣ FOR$WRITE_SLˌ FOR$IO_T_DSŒ FOR$IO_L_RV FOR$IO_L_V FOR$IO_END1Ѣ FOR$WRITE_SL˔ FOR$IO_T_DSŒ FOR$IO_L_RV FOR$IO_L_V FOR$IO_ENDѢ FOR$WRITE_SL˜ FOR$IO_T_DSP@@ FOR$IO_L_RˤLISLISTP FOR$IO_L_V FOR$IO_ENDSм Rм RRYeZJ@XP^QRYSXT OTS$MOVE5_R5Լ 1 V O FORCEINFOYESSIRGETINTLISLIST9$CODE$PDATA$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$IO_X_DA FOR$READ_SL FOR$WRITE_SF FOR$WRITE_SL OTS$MOVE5_R5=NPPPPPAP>XP_PPP PP0%P .P<DPIPzPP-PP P P0gPrPP~P3P1P: PP2BPIP2zPP2PHPAP- P$~r 91EFILES0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 EFILESPDangle Loop StackTStack TLoop MiscloopUse default energy files? file name? Default:(!The files you type in here become the new defaults. P does not exist. Try again. EFILESPPPPPPP4  $ !, $, ,PH[}PQ}PQ } PQ}PQ}PQ$}PQ,Y* FOR$WRITE_SF FOR$IO_END8YESSIRP1e FOR$WRITE_SF FOR$IO_ENDH FOR$WRITE_SF@ FOR$IO_T_DS FOR$IO_T_DS FOR$IO_ENDHGETSTRH FOR$WRITE_SFP FOR$IO_T_DS FOR$IO_T_DS FOR$IO_ENDXGETSTRH FOR$WRITE_SF` FOR$IO_T_DSk FOR$IO_T_DS FOR$IO_ENDhGETSTRH FOR$WRITE_SFp FOR$IO_T_DS FOR$IO_T_DS FOR$IO_ENDxGETSTRH FOR$WRITE_SFˀ FOR$IO_T_DS  FOR$IO_T_DS FOR$IO_ENDˈGETSTRˠWRITESTRˬ WRITESTR˸WRITESTRWRITESTRWRITESTRWRITESTRFOR$OPENP FOR$WRITE_SF( FOR$IO_T_DS FOR$IO_ENDH FOR$WRITE_SFː FOR$IO_T_DS( FOR$IO_T_DS FOR$IO_END˘GETSTR1e HEFILESYESSIRGETSTRWRITESTRFOR$OPEN$CODE$PDATA$LOCAL FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF`PtPgP4(  2EPARAMS0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133EPARAMS6P  > Premature end of Miscloop file.$Change any of the energy parameters? 2* All energy values are 10X integers. For example * -3.2 is -32 in this table. . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair []5Enter Parameter and new value ( to main menu)1 )EPARAMSXP ((<A FIND@  FIND@  FIND@  FIND@!B4 {a,1hja&+ر}d/q !Il.!fsf dURɒXiٿƝٞʯزHRN.v+a%#6%-%3@c,ۛݣۑѿƼܶՔ:v.g#0##2nY#1O".pW cM't7L;drLsph`݀2ڭɃځߋڔg~9ዯ+#"_m62/[،˘ЗϽbэ7hu/dL%(:x!=i3ގE?]gUG4 )fGWo @}Q B|_nk5)_9ݣ4ݞߓC!+o<(/'CD`|gMTޥ^N{N 0g'DWTWW'bf'*Z̴߷QpO{QZPswa܏7n\G _ˑE+?/! 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Default:(Printer width? Default:CT file name? Default:(REGION file name? Default:(r OUTPUTFILESPPPP (0   0    0  PH[}PQ}PQ } PQЬ(Y FOR$WRITE_SF FOR$IO_END4YESSIRP1 FOR$WRITE_SF< FOR$IO_T_DS FOR$IO_END FOR$WRITE_SFD FOR$IO_T_DS FOR$IO_ENDU FOR$WRITE_SFk FOR$IO_T_DS FOR$IO_ENDLGETSTR޻(Ry FOR$WRITE_SFߢ  FOR$IO_L_R FOR$IO_ENDޢ Xޢ dTGETINThWRITESTR FOR$WRITE_SFߢ  FOR$IO_L_R FOR$IO_END FOR$WRITE_SFt FOR$IO_T_DS FOR$IO_ENDN) FOR$WRITE_SF FOR$IO_END|YESSIRP FOR$WRITE_SF˄ FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_T_DS  FOR$IO_ENDˌGETSTR˔WRITESTR FOR$WRITE_SFˠ FOR$IO_T_DS FOR$IO_ENDN= FOR$WRITE_SF FOR$IO_END˨YESSIRP FOR$WRITE_SF˰ FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END˸GETSTRWRITESTR FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END H OUTPUTFILESYESSIRGETSTRGETINTWRITESTRz$CODE$PDATA$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$WRITE_SF1SPP aPVP"PXTP$i>2 z1GETINT0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 GETINTOPDefault= -> Please enter an integer between  and  GETINT8PP YESSIR#PPH[}PQ  FOR$WRITE_SFk FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDߑ TYTT~UPCASEאTYTTYN1tЫP HYESSIRUPCASE$CODE$PDATA,$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SF_PpP3P "1UPCASE0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 UPCASE UPCASEmPQazAPH[}PQ}PQ  P QQPQQPP TE HUPCASEF$CODE$PDATA$LOCALP &P>P F3WRITESTR0123-Feb-1992 02:2023-Feb-1992 02:20 VAX FORTRAN V5.7-133WRITESTR P))EWRITESTRPPP0H[}PQPTTUE UTѼݼ FOR$WRITE_SFT  FOR$IO_T_DS FOR$IO_ENDݼ FOR$WRITE_SFT FOR$IO_T_DS FOR$IO_ENDw 0HWRITESTR$CODE$PDATA$LOCAL FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF0"P-P.YP,! 31GETSTR0123-Feb-1992 02:2023-Feb-1992 02:20VAX FORTRAN V5.7-133 GETSTRP->) GETSTRPPPPP FOR$ENCODE_MF*[MFOLD]BEGIN.DAT;1+,./ 4K|-*0123KPWO56Oh7i89GHJKMFOLD - Prediction of RNA secondary structure by free energy minimization. D - Version 2.0 : suboptimal folding with temperature dependence& - Michael Zuker and John Jaeger ) - LRNA : folds linear RNA sequences+ - CRNA : folds circular RNA sequences3Any research that uses these programs should cite : M. Zuker 9 On Finding All Suboptimal Foldings of an RNA Molecule. Science, 244, 48-52, (1989)+ J. A. Jaeger, D. H. Turner and M. Zuker 8 Improved Predictions of Secondary Structures for RNA.B Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989)+ J. A. Jaeger, D. H. Turner and M. Zuker A Predicting Optimal and Suboptimal Secondary Structure for RNA.< in "Molecular Evolution: Computer Analysis of Protein and/ Nucleic Acid Sequences", R. F. Doolittle ed.- Methods in Enzymology, 183, 281-306 (1989)*[MFOLD]BPIN.FOR;1+,./ 4B$-*0123KPWO56h74i89GHJ$ subroutine bpin(n,l,bp,indeof)c c (FS382)c character*70 l integer*4 bp(1000)c2c READ BASE PAIR INFORMATION FOR ONE STRUCTUREc indeof = 0 read (2,101,end=20) n,l, read (2,102,end=90) (k,bp(k), i = 1,n) returncc EXPECTED END OF FILE 20 indeof = 1 returncc UNEXPECTED END OF FILE 90 write (6,190) stopc 101 format (i5,1x,a70) 102 format (i5,15x,i5)B 190 format (/' Unexpected end of file: no data following label') end*[MFOLD]BPIN.OBJ;1+,./ 4S-*0123KPWO56Tu i7Ti89GHJ/BPIN0123-Feb-1992 01:5123-Feb-1992 01:51VAX FORTRAN V5.7-133 BPINIPF0 Unexpected end of file: no data following label BPINS PF P H[}PQЬ  $Լ~ FOR$READ_SF߼ FOR$IO_L_R  FOR$IO_T_DS FOR$IO_END~ FOR$READ_SFмRR޻$Sk FOR$IO_L_RkP@c FOR$IO_L_RR FOR$IO_END FOR$WRITE_SF FOR$IO_ENDFOR$STOP HBPIN$CODEB$PDATA($LOCALFOR$STOP FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SF!PQPFnP й *[MFOLD]BPSRCH.FOR;1+,./ 4Ct-*0123KPWO56Th7t?i89GHJ* subroutine bpsrch(nb1,bp1,nb2,bp2,d)c c (FS383)c, integer*4 d,d1,d2, bp1(1000),bp2(1000)cCc OBTAIN LARGEST MINIMAL DISTANCE WHERE DISTANCE IS THE GREATERBc OF THE DIFFERENCES BETWEEN THE I's AND THE J's, RESPECTIVELYc do i1 = 1,nb1 d1 = nb1 j1 = bp1(i1)/ if (j1.gt.i1.and.bp2(i1).ne.j1) then do i2 = 1,nb2 j2 = bp2(i2)% if (j2.gt.i2) then8 d2 = max0(iabs(i1-i2),iabs(j1-j2))& d1 = min0(d1,d2)( if (d1.eq.d2) then;c SAVE INDICES OF CRITICAL BASE PAIRS is1 = i1 js1 = j1 is2 = i2 js2 = j2 end if end if end do d = max0(d,d1) if (d.eq.d1) then3c SAVE INDICES OF CRITICAL BASE PAIRS ip1 = is1 jp1 = js1 ip2 = is2 jp2 = js2 end if end if end docBc WRITE OUT INDICES OF CRITICAL BASE PAIRS AND RETURN DISTANCEc VALUE TO MAIN PROGRAMc%! WRITE (4,101) IP1,JP1,IP2,JP2,D! 101 format (/ 2i5,5x,2i5,5x,i5) return end*[MFOLD]BPSRCH.OBJ;1+,./ 4H-*0123KPWO564v i7i89GHJ1BPSRCH0123-Feb-1992 01:5123-Feb-1992 01:51VAX FORTRAN V5.7-133 BPSRCH BPSRCHP  PO[^Ь$Ь,8мUռ1$WмXЇYYU1E8Y1м ZSZ8RЂQQSSUPPTPTQYPPVPVTPPVVPXTTPPTTXXPUYS QZSмSSXXSSѼXUaK OBPSRCH$CODE$PDATA<$LOCAL70PIPSP_P^sPFPP1%*[MFOLD]CDOT.OBJ;1+,.!/ 4!-*0123KPWO"56yli7i89GHJ 1DOTPLT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 DOTPLTiP@  Minimum Energy = Increment = Enter New Increment ENTER NEW VINC: BASE = N = Base-pair = ( , )Score = +[14;1HMinimum energy = [16;1HIncrement = #[18;1HEnter New Increment [18;24H+[18;24H +0 ENTER PLOT FILE NAME : ) ENTER PLOT LABEL (UP TO 59 CHARACTERS) :</ ENTER TICK MARK INTERVAL & NUMBER OF LEVELS : P+"[2;1HEnter New Increment "[3;1H [2;24H+[2;24H +[2;1HBase = [3;1HN = +[21;1HBase-pair = ,[22;1HEnergy =  DOTPLTP  <\z T T AOUT@s s AOUT@$ AOUT@ <@D AOUT@D AOUT@H<@H(4 AOUT@ 8P AOUT@d AOUT@ 0 AOUT@L AOUT@// AOUT@44 AOUT@6P6 AOUT@P. PO[ЫDVWXϼ 1˘TEKRESETˠSCURSRN(PhQNQQDQPN RFRP@PN,RDQRNQFQR@R@RJRR@PJP4hPRP0Ы0Ы4˰VPR0h~^˼V^PR8RSR0TT^S4UU^V^PZU^0hPRP~^V^ZPP8TUP8SRѫ$R1ѫ$r1ѫ$Qѫ$qVT100VDѫ$Tѫ$tNEWPAGVT100FOR$STOPѫ$P0ѫ$p1VT100 FOR$WRITE_SF FOR$IO_END FOR$READ_SFt FOR$IO_T_DS FOR$IO_ENDFOR$OPEN$ FOR$WRITE_SF FOR$IO_END* FOR$READ_SFRB FOR$IO_T_DS;R FOR$IO_END/ FOR$WRITE_SF FOR$IO_END FOR$READ_SL߫< FOR$IO_L_R߫@ FOR$IO_L_R FOR$IO_END* FOR$WRITE_SFd FOR$IO_X_DA FOR$IO_ENDb FOR$WRITE_SFh FOR$IO_L_Vݫ< FOR$IO_L_Vݫ< FOR$IO_L_V FOR$IO_L_V FOR$IO_L_V FOR$IO_L_V FOR$IO_ENDѫ@@PPVhRh1ЫSTի1hPTUUPTP@TVPUЫTTh~^0(V^UPѫ@VPUU¨UVUUU@hZTQQZTZUJZPZhZTPPZTZJSTlg FOR$WRITE_SFի4VP FOR$IO_L_V FOR$IO_ENDR@ FOR$CLOSE1ѫ$Gѫ$g1NhPP^PP^XHDWINDO^NEWPAG\SETMRGHOMENEWLINpAOUTNEWLIN˄AOUTHOMELINEFLINEFALFMODːVT100l FOR$WRITE_SF, FOR$IO_L_R, FOR$IO_L_R, FOR$IO_L_R FOR$IO_END FOR$REWINDMI FOR$READ_SF| FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF, FOR$IO_L_R FOR$IO_END˘TEKTZTTP@ TTP@-ZTTUE0E91dTEKlSCURSRѫ$Tѫ$tNEWPAG|VT100FOR$STOPѫ$R1sѫ$r1fѫ$Qѫ$q1˄SETMRG˄TEKˌINITT˔TERMˠSETBUF<< < <˨TWINDONhPP^P^˼DWINDO^NEWPAGTRIAXISTWINDOԫHOMETLINEFTAOUT IOUTNEWLIN0AOUT<IOUT:NEWLINNEWLINLAOUTNEWLINALFMOD¹+p+ 1XVT100L FOR$WRITE_SF, FOR$IO_L_R FOR$IO_L_V, FOR$IO_L_Rݫ FOR$IO_L_V, FOR$IO_L_R, FOR$IO_L_R FOR$IO_END FOR$REWINDϵϱ FOR$READ_SF| FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF, FOR$IO_L_R FOR$IO_END`TEKTZTTP@ TTP@-ZTTUE0E91UTYI0I9IP0P UYYPUTZU1UYYԫhVECTORUYYUUˀVECTORYU FOR$WRITE_SF, FOR$IO_L_R4 FOR$IO_L_R FOR$IO_END1Ï(P PNPPhUNUUDUPN UFUP@PJPUU^˔U^˘ːV^NPYHOMENEWLINˤAOUTEs˴˰IOUTAOUTNEWLINAOUTJY~^IOUT^AOUT1VT100 FOR$WRITE_SF, FOR$IO_L_REs FOR$IO_L_R, FOR$IO_L_RJY~ FOR$IO_L_V FOR$IO_END1YTUE0E9EP0P YUUPYTZYNEWPAG<P< PԫThYh1hPUUPP@hUh1ѫ1ˠVPZh~^˴ˬV^PZ˸VPTh~^V^PTZPZPVPhZTTZZPJUqVPTVPTY&SETMRGGAXISSETMRG VNP,MOVEAhYhNk8VNPDDRAWAYNhYY^XY^`PDWINDO^11HOMEHOMEYNEWLINYNEWLIN AOUTмP@sIOUT(AOUTмP@s84IOUTDAOUTNEWLINNEWLINXAOUTdIOUT1lVT100# FOR$WRITE_SF, FOR$IO_L_RмP@s FOR$IO_L_RмP@s FOR$IO_L_R, FOR$IO_L_Rݫ8 FOR$IO_L_V FOR$IO_END1~S ODOTPLTTEKINITTTERMSETBUFTWINDODWINDONEWPAGTRIAXISHOMELINEFAOUTIOUTNEWLINALFMODVT100VECTORRESETSCURSRVFOR$OPEN FOR$CLOSESETMRGGAXISMOVEADRAWA $CODE\$PDATA $LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSFOR$STOP FOR$REWIND FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$IO_X_DA FOR$READ_SF FOR$READ_SF FOR$READ_SL FOR$WRITE_SF P"P%PP 'P4P?P IPaP kPP PMP PPKP,`PuP PPP P P+P @PGPHP,@PKPZPjP sPgP PP P P.P PkPmP,PPPP PP%PWPPP0$ Pc P P P $ P = Pc Pp P~s P( P' P# P 4 P _ P P " .TRI0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  TRI TRIPPH[޼޼kMOVABS޼޼ DRWABS޼޼ DRWABS޼(޼,$DRWABS\ HTRIMOVABSDRWABSQ$CODE$PDATA0$LOCAL Q/AXIS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 AXISP@  AXIS@P(,0  ,8 $8P. PH [(PPP2PǏP QPPQRRRPQQQQSNQNRPGPQTNSPGPQU CHRSIZ(CSIZEV << ޼ <޼@4TWINDOWRNWPDTPJPP@sNPPAPkNPGPkPQPx@QHMOVEATDRWRELV~^d`MOVREL^lIOUT2RW޼ x޼˄tTWINDORSNRPDUPJPP@sNTNPPCPTGTTQT=ˈMOVEA˔DRWRELV~^ˤΫ ~^˨ˠMOVREL^ˬIOUT2SR˴CHRSIZV HAXISCHRSIZCSIZETWINDOMOVEADRWRELMOVRELIOUT2$CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSTPP P&PPP PP]P*?PlnP9PD*0GAXIS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 GAXIS#P@ GAXISPp.TEK0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  TEK3P%!KALZMG+++ TEKP  PH[Ѽ1 FOR$WRITE_SF FOR$IO_L_Rk FOR$IO_T_DS FOR$IO_T_DS FOR$IO_L_R FOR$IO_END FOR$WRITE_SF FOR$IO_L_R FOR$IO_T_DS FOR$IO_T_DS FOR$IO_L_R FOR$IO_END FOR$WRITE_SF FOR$IO_L_R  FOR$IO_T_DS( FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_L_R0 FOR$IO_T_DS8 FOR$IO_T_DS FOR$IO_L_R FOR$IO_ENDѼ& FOR$WRITE_SF FOR$IO_L_R FOR$IO_END HTEK>$CODE,$PDATA@$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$WRITE_SFPP#>1VECTOR0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 VECTOR VECTOR4P ($, ($,P. P H [ЫRPP1׼ּ޼0޼4,MARKP޼޼VPS޼$~^( V^PS PSPRPNPP¼PNP 8MOVEADDRAWARRRNk#Li0~ MFOLD.BCK*[MFOLD]CDOT.OBJ;1!4P¼PNP1FRPNPP¼PNP PMOVEA\DRAWAR HVECTORVMARKMOVEADRAWA$CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS6P8P@xP3~P)PPP)1%)*[MFOLD]CIRC.FOR;1+,.$/ 4S$$<-*0123KPWO%56nh7ti89GHJHc Energy funtion.@c ERG is the energy of a loop closed by I,J (new numbering).>c IP,JP is the other closing base-pair when MODE = 2 or 3.cc 1/2 Asym. loop correction3c Extrapolate loops with dG(n)=dG(30)+1.75*ln(n/30)'c Hairpins of 3 have no terminal stack.c" function erg(mode,i,j,ip,jp) include 'rfd.inc' dimension e(4) integer*2 tlink,tlptr 100 if (mode.eq.1) thenc Read energy files call ergread erg = 0 return endif erg = 0,c Do not allow prohibited bases to pair.. if (force(i).eq.1.or.force(j).eq.1) then erg = infinity return endif  if (mode.lt.6) then+c Add bonus energy to force base-pairs.= if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) then! erg = erg + eparam(9) endif endif - goto (100,200,300,400,500,600,700),mode 'c Nucleotide accesssibility option./200 if (force(i).eq.3.or.force(jp).eq.3) then erg = infinity return endifc Stacking energy.B erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp)) . + eparam(1) return 300 size1 = ip - i - 1 size2 = j - jp - 1( if (size1.eq.0.or.size2.eq.0) then)c Check for nucleotide accessibility.0 if (size1.eq.0.and.force(i).eq.3) then erg = infinity return endif1 if (size2.eq.0.and.force(jp).eq.3) then erg = infinity return endif size = size1+size2c Bulge loop. if (size.eq.1) thenJ erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))* . + bulge(1) + eparam(2)# else if (size.gt.30) then: loginc = int(prelog*log((float(size)/30.0)))8 erg = erg + bulge(30) + loginc + eparam(2) else1 erg = erg + bulge(size) + eparam(2) endif return else size = size1+size2% lopsid = abs((size1-size2))c Interior loop. if (size.gt.30) then: loginc = int(prelog*log((float(size)/30.0)))K erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))E . + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1)). . + inter(30) + loginc + eparam(3)A . + min0(maxpen,(lopsid*poppen(min0(4,size1,size2)))) elseJ erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))E . + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))' . + inter(size) + eparam(3)A . + min0(maxpen,(lopsid*poppen(min0(4,size1,size2)))) endif return endif 400 size = j-i-1c Hairpin loop.D if ((size.eq.3).and.fce(i,j).and.seq(hstnum(i+1)).eq.' ') thenc Closed excision erg = eparam(9) return endif if (size.gt.30) then6 loginc = int(prelog*log((float(size)/30.0)))G erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))2 . + hairpin(30) + loginc + eparam(4) else if (size.lt.4) then) erg=erg+hairpin(size)+eparam(4) elsec tlink=0 if (size.eq.4) thenJ key=((numseq(i+4)*8+numseq(i+3))*8+numseq(i+2))*8+numseq(i+1) tlptr=1J do while ((tlptr.le.numoftloops).and.(tloop(tlptr,1).ne.key)) tlptr=tlptr+1 enddo; if (tlptr.le.numoftloops) tlink=tloop(tlptr,2) endifG erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))3 . + hairpin(size) + eparam(4) + tlink endif return c Multi-branch loop.500 do 501 ii = 1,4501 e(ii) = infinity  if (i.le.n-2) then  ind1 = (n-1)*i ind2 = (n-1)*(i+1)  else if (i.eq.n-1) then  ind1 = (n-1)*i ind2 = -n else  ind1 = -n ind2 = -1 endif   do k = i+2,j-3Cc EPARAM(6) is the energy penalty for each single-stranded baseJc in a multi-loop. EPARAM(10) is the energy penalty for each base-pairc closing a multi-loop.1c No dangling ends next to the I,J base-pair.; e(1) = min0(e(1),wst(ind1+k)+work(k+1,mod(j-1,3)))'c I+1 dangles on the I,J base-pair.C e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1)K . + wst(ind2+k) + work(k+1,mod(j-1,3)) + eparam(6))'c J-1 dangles on the I,J base-pair.C e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2)K . + wst(ind1+k) + work(k+1,mod(j-2,3)) + eparam(6))3c Both I+1 and J-1 dangle on the I,J base-pair.C e(4) = min0(e(4),dangle(numseq(i),numseq(j),numseq(i+1),1)C . + dangle(numseq(i),numseq(j),numseq(j-1),2)M . + wst(ind2+k) + work(k+1,mod(j-2,3)) + 2*eparam(6)) enddo?c EPARAM(5) is the energy penalty for closing a multi-loop.D erg = erg + eparam(5) + eparam(10) + min0(e(1),e(2),e(3),e(4)) return <c Dangling base stacking energy. IP dangles over the I,J=c base-pair. 3' or 5' dangle if JP = 1 or 2 respectively.;600 erg = erg + dangle(numseq(i),numseq(j),numseq(ip),jp) return /700 if (force(i).eq.3.or.force(jp).eq.3) then erg = infinity return endif(c Terminal stack or mismatch energy.A erg = erg + tstk(numseq(i),numseq(j),numseq(ip),numseq(jp)) return end     subroutine fill>c This subroutine computes the arrays of optimal energies. include 'rfd.inc' dimension inc(5,5)H data loop/3/,inc/0,0,0,1,0,0,0,1,0,0,0,1,0,1,0,1,0,1,0,0,0,0,0,0,0 ./  vmin = infinity if (n.le.80) then pinc = 5 elseif (n.le.100) then pinc = 2 else pinc = 1 endif pcnt = pinc crit = n*n*n/50  do j = 1,2*n-1'c How far along is the computation? if (n.gt.10) then if (j.le.n) then) if (j**3.ge.pcnt*crit) then$ write (6,1000) pcnt# pcnt = pcnt + pinc endif else5 if ((2*n-j)**3.le.(100-pcnt)*crit) then$ write (6,1000) pcnt# pcnt = pcnt + pinc endif endif endif1000 format ('+',i4,'%') * do i = min0(j,n),max0(1,j-n+1),-1 vij = infinity wij = infinity$ if (j-i.le.loop) goto 300Fc Test for a prohibited base-pair or a pair which cannot formc a base-pair.Q if (vst((n-1)*(i-1)+j).eq.1.or.inc(numseq(i),numseq(j)).eq.0) goto 200Fc Compute VIJ, the minimum energy of the fragment from I to J>c inclusive where I and J base-pair with one another.-c Perhaps I,J closes a hairpin loop.) vij = min0(vij,erg(4,i,j,i,j))$ if (j-i-1.ge.loop+2) then+c Perhaps I,J stacks over I+1,J-1.; vij = min0(vij,erg(2,i,j,i+1,j-1)+v(i+1,j-1)) endif/c Search for a bulge or interior loop.$ if (j-i-1.ge.loop+3) then do d = j-i-3,1,-1" do ip = i+1,j-1-d jp = d+ip6 if (j-i-2-d.gt.eparam(7)) goto 1009 if (abs(ip-i+jp-j).le.eparam(8)) then( if (ip.gt.n) thenS vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*(ip-n-1)+jp-n)) elseO vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*(ip-1)+jp)) endif endif enddo enddo endif &100 if (j-i-1.ge.2*loop+4) then.c Perhaps I,J closes a multi-loop.* vij=min0(vij,erg(5,i,j,i,j)) endif s aIc Compute WIJ, the minimum energy of a non-empty folding on I topIc J inclusive. This is the circular folding program and so there!c are no exterior bases.pK200 wij = min0 ( wij, eparam(10)+vij, v(i+1,j)+eparam(6)+eparam(10)+lG . erg(6,j,i+1,i,2), v(i,j-1)+eparam(6)+eparam(10)+aK . erg(6,j-1,i,j,1), v(i+1,j-1)+2*eparam(6)+eparam(10)+= . erg(6,j-1,i+1,i,2)+erg(6,j-1,i+1,j,1),(? . w(i+1,j)+eparam(6), w(i,j-1)+eparam(6) )  t& if (j-i-1.gt.2*loop+2) then! index = (n-1)*(i-1)t)c Check for open bifurcation.. do k = i,j-1? wij = min0(wij,wst(index+k)+work(k+1,mod(j,3))) enddo  endif 0Ec Store VIJ and WIJ. They can be regarded as elements V(I,J) Cc and W(I,J) in a two dimensional array. They are actuallyGc stored in the one dimensional arrays VST and WST in position c (N-1)*(I-1) + J.uIc Columns J,J-1 and J-2 of W are stored again in the WORK array. 7c This is done to reduce virtual memory swaps.i#300 vst((n-1)*(i-1)+j) = vijh# wst((n-1)*(i-1)+j) = wij ! work(i,mod(j,3)) = wij. if (j.gt.n) then=Ec VMIN is the minimum folding energy of the entire sequence..G vmin = min0(vmin,vst((n-1)*(i-1)+j)+vst((n-1)*(j-n-1)+i))  endif enddo if (j.ge.n) then  do k = j+1,n+1,-1Ic Fill in some WORK array values before beginning work on theqc next column.; work(k,mod(j+1,3)) = wst((k-n-1)*(n-1)+j+1-n)3 enddo endif enddo( return end  Bc Used to recall values of V which are actually stored in VST. function v(i,j)  include 'rfd.inc'  if (i.gt.n) then" v = vst((n-1)*(i-n-1)+j-n) else v = vst((n-1)*(i-1)+j) endif return end  f iBc Used to recall values of W which are actually stored in WST. function w(i,j)r include 'rfd.inc'n e if (i.gt.n) then" w = wst((n-1)*(i-n-1)+j-n) else w = wst((n-1)*(i-1)+j) endif return enda ( Ec Computes an optimal structure on the subsequence II to JI where Dc II and JI must base-pair with one another. ERROR = 0 is normalc termination.Mc NFORCE is the number of forced base-pairs encountered in the traceback. * subroutine trace(ii,ji,nforce,error) include 'rfd.inc'o n error = 0e ),c Zero the appropriate region of BASEPR. if (ji.le.n) thenj do k=ii,ji basepr(k) = 0q enddo) else do k=1,ji-nn basepr(k) = 0n enddo= do k = ii,nr basepr(k) = 0 enddo0 endif =c Initialize the stack of outstanding base-pairs and push Dc II, JI and V(II,JI) on to the stack. The fourth stack position#c is unused in this subroutine.( call initsts! call push(ii,ji,v(ii,ji),0)a nforce = 0 =c Pull a fragment and its expected energy from the stack.t)c End if there are no fragments left.e100 stz = pull(i,j,e,xx) if (stz.ne.0) return ,c Do I and J base-pair with one another? if (e.eq.v(i,j)) goto 300  tst = w(i+1,j) + eparam(6) do while (e.eq.tst)t%c Whittle away from the 5' end.2 i = i + 1 if (i.ge.j) goto 100 e = w(i,j)" tst = w(i+1,j) + eparam(6) enddoi i tst = w(i,j-1) + eparam(6) do while (e.eq.tst) %c Whittle away from the 3' end.  j = j - 1  if (i.ge.j) goto 100 e = w(i,j)" tst = w(i,j-1) + eparam(6) enddo 0 tst1 = v(i+1,j) + eparam(6) + eparam(10) +7 . dangle(numseq(j),numseq(i+1),numseq(i),2)n0 tst2 = v(i,j-1) + eparam(6) + eparam(10) +7 . dangle(numseq(j-1),numseq(i),numseq(j),1) 4 tst3 = v(i+1,j-1) + 2*eparam(6) + eparam(10) +: . dangle(numseq(j-1),numseq(i+1),numseq(i),2): . + dangle(numseq(j-1),numseq(i+1),numseq(j),1) if (e.eq.tst1) then c I dangles over I+1,J. i = i + 1 e = v(i,j)e else if (e.eq.tst2) thenc J dangles over I,J-1. j = j - 1 e = v(i,j)  else if (e.eq.tst3) then*c Both I and J dangle over I+1,J-1. i = i + 1 j = j - 1 e = v(i,j)a endif)*c Check for stem closing a multi-loop., if (e.eq.v(i,j)+eparam(10)) e = v(i,j) e if (e.ne.v(i,j)) thendDc Cannot chop away at ends any more and still the ends do notEc base-pair with one another. Structure MUST bifurcate (OPEN).m k = i+1200 if (k.eq.j) then *c Structure will not split. Error ii = hstnum(i)  ji = hstnum(j)s error = 10  returnp endif) if (e.eq.w(i,k) + w(k+1,j)) then2Hc Best structure on I,J splits into best structures on I,K and8c K+1,J. Push these fragments on to the stack.# call push(i,k,w(i,k),0) ' call push(k+1,j,w(k+1,j),0)p goto 100 elseo k = k + 1) goto 200 endif endift Jc Base-pair found. Base-pairs are stored in the range 1 <= I < J <= N.300 if (j.le.n) then basepr(i) = j basepr(j) = i else if (i.gt.n) thenr basepr(i-n) = j-n basepr(j-n) = i-n i = i - n j = j - n else basepr(j-n) = i basepr(i) = j-n endif0*c Check if this is a forced base-pair.I if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) nforce = nforce + 1 &c Perhaps I,J stacks over I+1,J-1?! if (e.eq.erg(2,i,j,i+1,j-1) . + v(i+1,j-1)) thenp i = i + 1 j = j - 1 e = v(i,j)  goto 300e endif(c Perhaps I,J closes a hairpin loop?' if (e.eq.erg(4,i,j,i,j)) goto 100g c<c Define E' ( EP in the program ) to be E corrected by a4c possible bonus energy for forced base-pairing.c ep = eI if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) ep = ep - eparam(9)e , k = i+2 &c Perhaps I,J closes a multi-loop?400 if (k.ge.j-3) goto 500D if (ep.eq.w(i+1,k) + w(k+1,j-1) + eparam(10) + eparam(5)) then-c Multi-loop. No dangling ends on I,J.n$ call push(i+1,k,w(i+1,k),0)( call push(k+1,j-1,w(k+1,j-1),0) goto 100hE else if (ep.eq.erg(6,i,j,i+1,1)+w(i+2,k)+w(k+1,j-1)+eparam(10)+4 . eparam(6)+eparam(5)) then4c Multi-loop. I+1 dangles over I,J base-pair.$ call push(i+2,k,w(i+2,k),0)( call push(k+1,j-1,w(k+1,j-1),0) goto 100nE else if (ep.eq.erg(6,i,j,j-1,2)+w(i+1,k)+w(k+1,j-2)+eparam(10)+v4 . eparam(6)+eparam(5)) then4c Multi-loop. J-1 dangles over I,J base-pair.$ call push(i+1,k,w(i+1,k),0)( call push(k+1,j-2,w(k+1,j-2),0) goto 100SJ else if (ep.eq.erg(6,i,j,i+1,1)+erg(6,i,j,j-1,2)+w(i+2,k)+w(k+1,j-2); . + eparam(10)+2*eparam(6)+eparam(5)) then1Dc Multi-loop. Both I+1 and J-1 dangle over the I,J base-pair.$ call push(i+2,k,w(i+2,k),0)( call push(k+1,j-2,w(k+1,j-2),0) goto 100 else k = k + 1 goto 400 endifv e 3Fc None of the above work. I,J MUST close a bulge or interior loop.500 do d = j-i-3,1,-1i do ip = i+1,j-1-dp jp = d+ip) if (j-i-2-d.gt.eparam(7)) then 6c Error, bulge or interior loop not found. ii = hstnum(i) ji = hstnum(j) error = 11 return endif0 if (abs(ip-i+jp-j).le.eparam(8)) then6 if (e.eq.erg(3,i,j,ip,jp)+v(ip,jp)) then i = ipI j = jpi e = v(i,j)i goto 300  endifi endif enddo enddo(.c Error, bulge or interior loop not found. ii = hstnum(i) ji = hstnum(j) error = 11 return end  e 69c Store results of a SAVE run for a CONTINUATION run.  subroutine putcont include 'rfd.inc'( * write(30) n,nsave,vmin,listsz,seqlab< write(30) stack,tstk,dangle,hairpin,bulge,inter,eparam write(30) (vst(i),i=1,n*n) write(30) (wst(i),i=1,n*n), write(30) (seq(i),i=nsave(1),nsave(2))+ write(30) ((list(i,j),i=1,100),j=1,4)k! write(30) tloop,numoftloops / write(30) (poppen(i),i=1,4),maxpen,prelogW return enda l8c Read results of a SAVE run for a CONTINUATION run. subroutine getcont include 'rfd.inc'e e0 read(30,end=10) n,nsave,vmin,listsz,seqlabB read(30,end=10) stack,tstk,dangle,hairpin,bulge,inter,eparam& read(30,end=10) (vst(i),i=1,n*n)& read(30,end=10) (wst(i),i=1,n*n)2 read(30,end=10) (seq(i),i=nsave(1),nsave(2))1 read(30,end=10) ((list(i,j),i=1,100),j=1,4)(' read(30,err=10) tloop,numoftloops)5 read(30,err=10) (poppen(i),i=1,4),maxpen,prelogf goto 11u e10 call errmsg(40,0,0)n m 11 return end( 1*[MFOLD]CIRC.INC;1+,./ 4M -*0123KPWO56Eyh74i89GHJ implicit integer (a-z) ( parameter (maxn=625,fldmax=2*maxn). parameter (infinity=16000,sortmax=30000). parameter (mxbits=(maxn*(maxn+1)+31)/32) parameter (maxtloops=40) parameter (maxsiz=10000) - integer*2 vst(maxn*maxn),wst(maxn*maxn) integer poppen(4),maxpen real prelog, data eparam/0,0,0,0,46,4,30,30,-500,1/K dimension newnum(maxsiz),hstnum(fldmax),force(fldmax),numseq(fldmax), . work(fldmax,0:2),J . stack(5,5,5,5),tstk(5,5,5,5),dangle(5,5,5,2),hairpin(30),bulge(30),. . inter(30),eparam(10),cntrl(10),nsave(2)G common /main/ vst,wst,newnum,hstnum,force,numseq,work,stack,tstk,I . dangle,hairpin,bulge,inter,eparam,cntrl,nsave,poppen,maxpen,prelog  character*1 seq(maxsiz) character*5 inbuf character*30 seqlab common /seq/ seq,seqlab  dimension list(100,4) common /list/ list,listsz common /nm/ n,vmin  dimension basepr(maxn) common /trace/ basepr 6 integer*2 two(0:15),marks(mxbits),force2(mxbits) common/bits/marks,force2 . integer*2 tloop(maxtloops,2),numoftloops% common/tloops/tloop,numoftloops M data two/1,2,4,8,16,32,64,128,256,512,1024,2048,4096,8192,16384,-32768/*[MFOLD]CIRC.OBJ;1+,.!/ 4!L-*0123KPWO"56Lddi7Tri89GHJ)$<~ MFOLD.BCK*[MFOLD]CIRC.OBJ;1!u*.ERG0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133  ERG ERGPѼмP@Hм QAH޼ ޼ FCEPϼVмP@HмQAH<>PмQAКQмPQ@КPPм QPAКQQмPQ@КP@PPüPPWü PPXVWX1WмP@H<>PXмP@H<>PXWYYмP@КPмQPAКQQм PQ@КPPмQPAКQAQQQYNYQG/QP MTH$ALOG_R5D8PJPPPQPQQIYYЫPXWYXWPPZPZY1NYPF/P MTH$ALOG_R5D8PJPPм QA̚RмSCԚRRRAКQQQCКSCHSмQA̚RмTDԚRRRAКQQQDКTDHSSPSSPPWWPPTTXXTD ZT4PPTTPPS1м P@̚SмTDԚSSS@КPPPDКTDHūTмP@̚SмQAԚSSS@КPPPAКQAHTIPTTYYWWYYWWXXWG Z4WWZZWWTЫPü PPWVW޼޼ FCEPмP@sP@ PWNWPF/P MTH$ALOG_R5D8PJPPм TD̚ZмXHԚZZZDКTTTHКXHHXXPXX1WG`XX1XWмP@T@ܚTT@ؚTT@ԚTPTT 2TZ2J ZZPTT 2TTD NXм TD̚PмZJԚPPPDКTTTJКZJHZG`ZZ2XXXZЫPPޫX<>PPѼPPżPkZZPZѼZżZkZZk WW1 TzTT{TTTŏTмYIԚYм QYAКQQмYQIКYм QA̚Qм SCКQQмRBКQ UzUU{UUUŏUAIWRB\RWVF\VWS>C SWkTX2D TTbPѫPP2PPIZZZѫZZATfTTѫTTPPPѫPPWWWЫQQЫQQRRЫRRQQЫQQWWPPмWPGКWWм PW@КPPмWPGКWG WWPмP@HмWGH<>PмWGКWмPW@КPPм WPGКWWмPW@КP@HP OERGERGREADFCEMTH$ALOG$CODE$PDATAT$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS MTH$ALOG_R5nP ,P:P IP:WP#ePzP PPP/PPPPP*P0P5PCPOP]PlPWPHP/P&PPP6P!P PgnPtPPPePPP nPP.PPP9PP*/FILL0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133 FILL(P+% FILLP    P. PQxPO[^\<>lPldЫllPlP2P lѭ1Vl 1ѫlݫ OTS$POWJJū QPQ FOR$WRITE_SFݫ FOR$IO_L_V FOR$IO_ENDlPëP~ OTS$POWJJëdQī QPQ FOR$WRITE_SFݫ FOR$IO_L_V FOR$IO_ENDlPPWWPPWЫPPllPPѫW1<>X<>YëPP1ЫP@КPЫQPAКQAd1lQPPQQA1$ERG<>QQPPQQXëQQQ~^L~^P<ERG^PZ~^X~^\TV^PZXPPZZPPXëPPZZ1PZ1PZPUѫU1Z ëPPZPP1ëP P«PPQPQQѫl`ERGlQlTTTQ QlQ2AQQPXQQPPQQXxERGlQTTQ Q2AQQPXQQPPQQXUSZ14ëZZZ ːERGXZZPPZZXZZ^ˬ˨V^PPUZ^˴ERG^PUXP<>ZZPPZZTTUUTUU^V^PPZU^ERG^PZTUUZZUTT^ZZ^V^QQPPRZ^T^ERG^PRZ^ZZ^ ERG^PRUTTRRTZ^0,W^PTZZPPZ~^@8W^PZTTPPTTYëTTTlTPTPЫTѫzQ{QQQďQTPZ>J ZQTRB\R2SSUYSSUUSSYTPTPTTXDYD zQ{QQQďQQYAXѫQQQPP@DT2TTPPTTPPW}ѫllWPPTTWlQzPY{YYYďYlTPPQPPPlP>@ PQXďXYTRB\R2`rXPWT1 OFILLERGVW$CODE!$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_V FOR$WRITE_SF OTS$POWJJ!P'P0P6P]P|nPuP>P%PIP%&P9>PbP|P~PNP P"P@P`PifP5P.P~P[PD"P3fPiwPXt,v,V0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133 V VP. PH$[ѼPQQQPPP2@PQQPP2@ЫP HVb$CODE$PDATA$$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSP->P(b,W0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133 W WP. PH$[ѼPQQQPPP2@ PQQPP2@ ЫP HWb$CODE$PDATA$$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSP->P(b0TRACE0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133 TRACEP TRACEDP(,04(,,(,,((,(,((,(,(,(,(,(,( ,( ( ,,(, (,(,(,(,(,   (,   (,    (,(,    (,8@8@(,P. PO [ЫVԼѼмPмYѼPPPPZIWP^QRZSWT OTS$MOVE5_R5PPWYP^QRWSYT OTS$MOVE5_R5мWѼPPPPYGZP^QRYSZT OTS$MOVE5_R5INITST޼4޼8޼(޼,$VP^<0PUSH^Լ WYVDPULLЫVPVXVVP1~^hdW^PZVZ֫ѫ pWPV~^ˀ|W^PZ ~^ːˈW^PZVZ׫ ѫ 1J˔WPV ~^˨ˠW^PZ~^˰ˬV^Ы ZPPЫQAКRRAԚQQJКQAPRZSS^˸V^PPJКQЫTDКQQJ̚QAPUTT^S^V^QQPPЫQAКQЫXHԚQQJ̚QAPJКQQHԚXXJ̚XHPXVRTZ VЫ ZPVVUS VЫ ZPVVXTS VЫ ZPVZ VPVPVPV VVP1kk ЫP@sЫ P@s VWPZkSS^($W^PZVZ0WP^H<PUSH^kPP^`P^TPW^P^h\PUSH^1Sk1Rѫ iЫSЫ CЫ SЫCѫS PPCS@SP  PЫ@ЫSPCЫSCHЫ SCHpFCEPּ ~^ˌ ~^ː|ERG^PSZZ^˘ TT^˜˔V^PSVSZT ˠVPV1ˬERGVP1VTЫP@HЫ P@HFCEPVTk PkP1ZZ^W^PSk~^ XX^W^PSSSTSZ^Z^W^P^PUSH^kPP^X^P^ X^W^P^ PUSH ^1Z^8(ERG^PZXX^D@W^PZk~^P SS^TLW^PZZZZTZX^hX^\XW^P^pdPUSH^kPP^ˈS^ˌP^|S^ˀxW^P^ː˄PUSH ^1S^˨˘ERG^PSXX^˴˰W^PSk~^ ZZ^˼W^PSSSSTSX^X^W^P^PUSH^kPP^Z^P^Z^W^P^PUSH ^1X^ERG^PX ~^0 ERG^PXZZ^<8W^PXkSS^H UU^LDW^PXXPPXXTXZ^`Z^TPW^P^h\PUSH^kPP^ˀU^˄P^tU^xpW^P^ˈ|PUSH ^1Sk1jë TT1 STSѫS1T ë PPTPPЫP@s¹(Ы P@s VëP P« PPUPUUːERGPU˨VPUVUЫЫ ˴VPV1SSaT1BЫTDsЫ TDs V OTRACEINITSTPUSHVPULLWFCEERG) $CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS OTS$MOVE5_R5:P:(P)SPc^PP,P&P HP7P;P!P;(P>PDPuP PP&PQMPiPXuP.P PP P;PuPP PPPqPqPqPrD P] Pz P% P9 P#) 2PUTCONT0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133PUTCONTPUTCONT$P (    | d x xT x '  dP. PH [ FOR$WRITE_SU FOR$IO_L_V߫t FOR$IO_X_DA FOR$IO_L_V@ FOR$IO_L_V˄ FOR$IO_T_DS FOR$IO_END FOR$WRITE_SU߫ FOR$IO_X_DA߫$ FOR$IO_X_DA߫4 FOR$IO_X_DA߫D FOR$IO_X_DA߫T FOR$IO_X_DA߫d FOR$IO_X_DA߫ FOR$IO_X_DA FOR$IO_END FOR$WRITE_SU>˨\\ˬˤ FOR$IO_X_SE FOR$IO_END FOR$WRITE_SU> ˨\ˬˤ FOR$IO_X_SE FOR$IO_END FOR$WRITE_SU \RR\˜Bˠ˜ FOR$IO_T_DS\R FOR$IO_END FOR$WRITE_SUR\l˴˰ FOR$IO_X_SB\R FOR$IO_END FOR$WRITE_SU?ˌ FOR$IO_X_DA2 ~ FOR$IO_W_V FOR$IO_END FOR$WRITE_SU$˼ FOR$IO_X_SB4 FOR$IO_L_V8 FOR$IO_F_V FOR$IO_END( HPUTCONT$CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_W_V FOR$IO_L_V FOR$IO_F_V FOR$IO_T_DS FOR$IO_X_DA FOR$IO_X_SB FOR$IO_X_SE FOR$WRITE_SU $P!(׼2GETCONT0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133GETCONTP(GETCONT,P (    | d x xT x '  dP. P H [Ы\kRS~ FOR$READ_SUc FOR$IO_L_R߫| FOR$IO_X_DAߣ FOR$IO_L_R@ FOR$IO_L_Rˌ FOR$IO_T_DS FOR$IO_END~ FOR$READ_SU߫ FOR$IO_X_DA߫, FOR$IO_X_DA߫< FOR$IO_X_DA߫L FOR$IO_X_DA߫\ FOR$IO_X_DA߫l FOR$IO_X_DA߫  FOR$IO_X_DA FOR$IO_END~ FOR$READ_SU>ccPP˼ FOR$IO_X_SEccPPR FOR$IO_END~ FOR$READ_SU> ccPP˼ FOR$IO_X_SEccSSR FOR$IO_END~ FOR$READ_SU SRRSˤB˨ˤ FOR$IO_T_DSSR FOR$IO_END~ FOR$READ_SU\Sc FOR$IO_X_SBeRS\ FOR$IO_END FOR$READ_SU?˔ FOR$IO_X_DA?  FOR$IO_W_R FOR$IO_END FOR$READ_SU$ FOR$IO_X_SBR4 FOR$IO_L_R8 FOR$IO_F_R FOR$IO_ENDˬERRMSG\Rk2 HGETCONTERRMSGA$CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_W_R FOR$IO_L_R FOR$IO_F_R FOR$IO_T_DS FOR$IO_X_DA FOR$IO_X_SB FOR$IO_X_SE FOR$READ_SUUPdPPnP36PUP PPoPD.P "(ŷռA*[MFOLD]CMISC.OBJ;1+,.H/ 4HH-*0123KPWOI56gi7t i89GHJ<2PROCESS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133PROCESSPROCESS4PP. PO [ PVVPVQQPPWFXP^QRWSXT OTS$MOVE5_R5PP@P@@@W@XXWHQWX@Q@WWQGXQW PQQPAXՈԨPQPP1XYXPPZLWP^QRZSWT OTS$MOVE5_R5YPYWYPZYQQZYQQPP\WZ>JWP^QR\SWT OTS$MOVE5_R5XY XWWX1ZYG\ЌT1WDsDКGADКGBDКDHGCDКGZDКDHGGDКGHDКDHGUGTDКGVGWDКDHXW2WW@1WG\GXGZGGXZGZ\T\PPT@QЁRBHTPTZLRHLSނsSFCEZT1UL$H( SFCE\V\YYV IVY1Z\V\YYVIPЀRBHVY1PZVLYHRiTVTrTDbQVQQQAZP1WVWԚX\LԚ\xxЈWV OPROCESSSFCE:$CODE$PDATAL$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS OTS$MOVE5_R5EP&LPsXP;bP|PPP&PPP& P{PPG`P7PPPPPP7PGP_PgPwPPP\P PPP6PfPPPP&jP PPNPH P+* 8 :0CONVT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 CONVT CONVTPPH[}PQTUԫVVWG-TG0G9U  OTS$POWJJߚGQ0QQPPUVTΫЫPP HCONVTf$CODE$PDATA $LOCAL OTS$POWJJ$&P+P*2P#9P[P&f3ENEFILES0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133ENEFILESvPEnter dangle energy file name (default dangle.dat)DANGLE.DATEnter loop energy file name (default loop.dat)LOOP.DATEnter stack energy file name (default stack.dat)STACK.DATEnter tstack energy file name (default tstack.dat)TSTACK.DATEnter tloop energy file name (default tloop.dat)Tloop.DATEnter misc. loop energy file name (default miscloop.dat)miscloop.DAT(ENEFILES(P(2 2 (82 FOR$OPEN@.=k (lk FOR$OPEN@0t  ( FOR$OPEN@2  ( FOR$OPEN@0 ( FOR$OPEN@8% ] (<] FOR$OPEN@PH([ FOR$WRITE_SL FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDFOR$OPENP FOR$WRITE_SL< FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDLFOR$OPENP FOR$WRITE_SLp FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDˀFOR$OPENP FOR$WRITE_SLˤ FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_END˴FOR$OPENP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDFOR$OPENP FOR$WRITE_SL  FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDFOR$OPENPFOR$EXIT HENEFILESFOR$OPENFOR$EXIT$CODEm$PDATAh$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SL;(PtPbP PYP~P2P 4(1ERRMSG0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 ERRMSGP0u$ Open bifurcation not found between  and # Bulge or interior loop closed by (, ) not found& Closed bifurcation not found between  and  Base pair between  and  conflicts with at least one other pair Buffer overflow in lineout End reached at traceback  More than  basepairs in sort at (,) Premature end of save file ERRMSGP. PH [Ѽ  FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDѼ 6 FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDѼ p FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDѼ FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDFOR$STOPѼ FOR$WRITE_SF FOR$IO_ENDԼѼ FOR$WRITE_SFݼ FOR$IO_L_V FOR$IO_ENDѼ- FOR$WRITE_SF FOR$IO_L_Rݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDԼѼ(` FOR$WRITE_SF FOR$IO_ENDFOR$STOP HERRMSGy$CODE~$PDATA $LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSFOR$STOP FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$WRITE_SF>P*>P*nP*P1PP P:ZP*(y1INITST0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 INITST INITSTP@ K @INITST $CODE$PDATA$LOCAL$STK  /PUSH0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 PUSHPERROR - STACK OVERFLOW PUSHPPH[R  2 FOR$WRITE_SLk FOR$IO_T_DS FOR$IO_ENDFOR$STOP Pм@м@м @Œм@T HPUSH]$CODE$PDATA$LOCAL$STKFOR$STOP FOR$IO_END FOR$IO_T_DS FOR$WRITE_SLP!]/PULL0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 PULL PULL[PH[Q P P@ P@ P@ P@T PS HPULLR$CODE$PDATA$LOCAL$STKP R1LINOUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 LINOUT\P FOLDING BASES  TO  OF  ENERGY =    LINOUT|P' LPDTld@pd@lD@pD@PD\D@`D@P. 8P- .QPO<[^ЫVЫWkмP@sRмP@sS k FOR$WRITE_SFR FOR$IO_L_VS FOR$IO_L_V@ FOR$IO_T_DSݼ  FOR$IO_F_V FOR$IO_ENDINITST޼x޼|tPUSHZիVZXXVP@VZVW˘PULLЫWЫVPVWWZVJ1ZZVWV1WVPPP8WYV$Ы8 խ1Y׫$֫ѫVWIsP@ 1Is0Ы$XHs4 0P PP0Y$DIGIT 4P PP4DIGITѫ 8XЫ0P@HЫ4P@HXY$Ы0P@HЫ4P@H 'YIꐫIQk FOR$WRITE_SF FOR$IO_ENDЫYYXkHk FOR$WRITE_SFWYWPXPˈ@ˌˈ FOR$IO_T_DSYW FOR$IO_ENDkBk FOR$WRITE_SFWYWPXPː@˔ː FOR$IO_T_DSYW FOR$IO_ENDXlѫ1 V YYVXHꐫHVꐫIꐫI YPPWWYVWYXVPXVS@CVWY1ЫXH׫WZ ëVPP P ի 1ZYЫX (ѫ(VW,ի 1׫(YXYWIs0(PЫ0SC@ 0P PP0ˬDIGIT(P@XVHs4(PЫ4SC@ 4P PP4DIGIT(P@ ,`ЭZWЫVJ1ЫYIJIZJJsJYIsӼVWѫVWJ~^V PUSH^JV֫ѫVWGsZFsYXJHIH ZP PPZZ DIGIT YP PPYY$8DIGITWVY|Iꐏ^IWVGV11X OLINOUTINITSTPUSHPULLDIGIT$CODEU$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_V FOR$IO_F_V FOR$IO_T_DS FOR$WRITE_SF`PP PPP P2P SPxP~P P P&P*PPP;PLPAbP$PCP&4P.xPPPP PP8P P$P7OP ZP PPP P*P %PjP P PP0!% B'0DIGIT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 DIGIT DIGIT8PQ Q0123456789Q.PO4[м4}PQޫ PFOR$INI_DES2_R3VмP PQ QRRPRRFQQPV䞻WѼ VVTUVU PPī PP@gTUм XYVޫZЊTū XUUDEgXVYū XXHg^ ODIGIT$CODE$PDATAl$LOCALFOR$INI_DES2_R3$ for main menu)  Enter new value  Enter base and length  Enter base pair and length  Enter begining and end  01 Energy Parameter 6 Single Prohibit 02 Single Force 7 Double Prohibit 03 Double Force 8 Begin Folding  04 Closed Excision 9 Show current  K05 Open Excision 10 Clear current  Enter Choice  MENU8PP. @PPH [\@d1 FOR$WRITE_SF FOR$IO_END# FOR$WRITE_SF FOR$IO_END FOR$READ_SLk FOR$IO_L_R FOR$IO_ENDkk k LISTOUT1y@1q FOR$WRITE_SF FOR$IO_ENDVR FOR$READ_SL߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_END@@Pk@Ы@̌Ы@@̬1  FOR$WRITE_SF FOR$IO_END FOR$READ_SL߫ FOR$IO_L_R߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_END@@Pk@Ы@̌Ы@Ы@̬1 FOR$WRITE_SF FOR$IO_ENDzv FOR$READ_SL߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_END@@Pk@Ы@̌Ы@@̬1-FOR$EXIT FOR$WRITE_SFR߂ FOR$IO_L_R  FOR$IO_ENDc FOR$WRITE_SF FOR$IO_END FOR$READ_SF߫ FOR$IO_L_R FOR$IO_ENDի1ѫ 1 FOR$WRITE_SF FOR$IO_ENDϊφ FOR$REA%̸~ MFOLD.BCK*[MFOLD]CMISC.OBJ;1H!0D_SL߫  FOR$IO_L_R FOR$IO_ENDЫPЫ @18 HMENULISTOUTFOR$EXIT$CODE7$PDATA@$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_R FOR$READ_SF FOR$READ_SL FOR$WRITE_SFoPLPPPxPszP(|P~PPP(PP<PP RF* =.2LISTOUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133LISTOUT]P No choices currently defined Current Choices : (,)  : ,LISTOUTPQDEnergy Parameter  'Single Force  'Double Force  'Closed Excision  'Open Excision  'Single Prohibit  'Double Prohibit  'PH[R@ݼ FOR$WRITE_SLk FOR$IO_T_DS FOR$IO_END1ݼ FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDݼ FOR$WRITE_SL FOR$IO_T_DS FOR$IO_END@STS1bUхѥ.ݼ FOR$WRITE_SFP@` FOR$IO_T_DSVDŒWg FOR$IO_L_RWV FOR$IO_ENDEݼ FOR$WRITE_SFP @`$  FOR$IO_T_DSVDŒWg FOR$IO_L_RWV FOR$IO_ENDSTKݼ FOR$WRITE_SL( FOR$IO_T_DS FOR$IO_END HLISTOUTM$CODEV$PDATA$LOCALDLIST FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SLP0P1PwPPPUPR& M1DEVICE0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 DEVICEP' Combination of continuation run and multiple foldings disallowedFOLD.SAVEnter start of fragment (default 1)Enter terminal type 1 VGT1002 Visual 102 (default)3 Tektronics 41051 Enter minimum vector size for plot (default 1) Enter run mode0 Sub-optimal plot (default) 1 N Best2 Multiple Molecules) Enter number of tracebacks (default 1) ( Enter percentage for sort (default 0)  Enter window size (default 0) Enter run type0 Regular run (default) 1 Save run2 Continuation run( Enter save file name (default fold.sav)  nucleotides Enter end of fragment (default ) DEVICEtP''''( (H@E E FOR$OPEN@tp#NP. PpP yPP PPP PPAP8VPfPqP&P#P PP`PUPm@PDP"rPPPPn$P1P IPKP ]PoP{PPP+P<XP cW+p/MSEQ0123-Feb-1992 02:2423-Feb-1992 02:24OVAX FORTRAN V5.7-133 MSEQ&P'   nucleotides MSEQ$P''''D$ D$ P.  PPH [k޼D,MULTID FOR$WRITE_SLH FOR$IO_T_DS FOR$IO_END޼hPMULTID FOR$WRITE_SF$ FOR$IO_T_DS FOR$IO_L_V FOR$IO_END B HMSEQMULTID$CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_V FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SLO P,4P=*2OUTPUTS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133OUTPUTSDQP (# Do you want printer output? (Y,n)  Output to terminal? (Y,n) ! Enter output file name (default #)2 Enter number of columns on printer (default 80)   Do you want ct file? (y,N)  Enter ct file name (default #)! Do you want region table? (y,N) ' Enter region table file name (default #)OOUTPUTStP( (H t| t| t|P. PKp[\V\TD'AD'ZD'aD'z\\PTTPPTTWWTD' TWX\Y\WY\L'0L'9L'AL'ZL'aL'zXTL'DXP_@XWY FOR$REWINDY FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkN 1kn 1. FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkN kn (HHM FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDFOR$OPENPv FOR$WRITE_SF FOR$IO_END~ FOR$READ_SF@  FOR$IO_L_R FOR$IO_ENDP FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkY ky PP(LH1 FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkY ky 1(PH FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDhFOR$OPENP FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_END@FOR$OPENP1 FOR$WRITE_SLː FOR$IO_T_DS FOR$IO_ENDFOR$EXITHP.OUT.CT .REG4 KOUTPUTSFOR$OPENFOR$EXIT$CODET$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$REWIND FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$READ_SF FOR$READ_SF FOR$WRITE_SF FOR$WRITE_SL P )P2P ;P_PrPYPP$P PPPP P'P3P TPP P_PP5PVPP PPPP PP  PkPmPRP fZ+ c2ERGREAD0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133ERGREAD!P  > Premature end of MISCLOOP.DAT<--ERROR - DANGLE ENERGY FILE NOT FOUNDERROR - PREMATURE END OF DANGLE ENERGY FILE-----ERROR - STACK ENERGY FILE NOT FOUNDSTACK ERROR - PREMATURE END OF STACK ENERGY FILEERROR - PREMATURE END OF TSTACK ENERGY FILEPRERGREAD_PP p FIND@  FIND@ FIND@( FIND@= @= FIND@= `= FIND@$A+e FIND@== FIND@== FIND@# STEST@*== FIND@=$= FIND@#    +P. POx[ GETTLOOPShFINDP߫xFOR$STOP  FOR$READ_SL8 FOR$IO_F_R FOR$IO_ENDD"8ˈFIND  FOR$READ_SL߫ FOR$IO_F_R FOR$IO_ENDE"PJP4ˠFIND  FOR$READ_SL߫ FOR$IO_F_R߫ FOR$IO_F_R߫  FOR$IO_F_R߫ FOR$IO_F_R FOR$IO_ENDE"PJP$E"PJP(E" PJP,E"PJP0˸FIND  FOR$READ_SL߫ FOR$IO_F_R߫ FOR$IO_F_R߫  FOR$IO_F_R FOR$IO_ENDE"PJPE"PJPE" PJPPPQRPSJQTUPVJSWXPYJVZJY\\Z\\W\\T\<>L @YX@VU@SR@QPFINDPkk1$(k1~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDX$\YXPPW\PPXPP(P@ VZYPPWPPP(@TTP)@<>ZT瑫..<>ZZCONVTPZZfdVYXrFINDPk(+$ FINDX~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDVWVVYI V(IYZZP)@<>YZ瑫..<>YY(CONVTPYWYHPWYHWYH`WyXX1CXPVWPYJVPZPTJYQSPRJTUJR\\U\\Q\\P\<>L@RS@TZ@YW@VX8FINDPkk1(Yk1~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDWZWPP\YPPWPP(P@VXZPP\PPP(@TTP)@<>XT瑫..<>XXHCONVTPXXfVZWrYEH@YQ@ \@W@P˔$7FINDPkk1(,k1~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDVZVPPX,PPVPP(P@HW\ZPPXPPP(@TTP)@<>\T瑫..<>\\ˤCONVTP\\gWZVn,7˴FINDPk(  FOR$CLOSE FOR$CLOSE FOR$CLOSE FOR$CLOSEY FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SL˄ FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SLh FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFù.     obFOR$STOP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFOR$STOPP . @ OERGREAD GETTLOOPSFINDCONVTSTEST FOR$CLOSE*$CODE$PDATAl$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSFOR$STOP FOR$IO_END FOR$IO_F_R FOR$IO_T_DS FOR$READ_SF FOR$READ_SL FOR$WRITE_SLP PKPPKPZP`PiP PP PP P)P :PGPTPPPPkPzPPP BP4PPJTPPPPP   h*0STEST0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 STEST1PSYMMETRY ERROR(,) =  2 STEST2FP  PxO[^ЬÏp}PQk޻STkVTPPXVPPYVPPTPPkP@ZYP@Uj1 FOR$WRITE_SL  FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_T_DSk FOR$IO_L_VT FOR$IO_L_VV FOR$IO_L_VX FOR$IO_L_Vj FOR$IO_L_R FOR$IO_END FOR$WRITE_SF FOR$IO_T_DSX FOR$IO_L_VV FOR$IO_L_VT FOR$IO_L_Vk FOR$IO_L_Vߥ FOR$IO_L_R FOR$IO_ENDFOR$STOPZX/VTk xOSTESTT$CODE*$PDATA($LOCALFOR$STOP FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SL vPl"泲T.OUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  OUTisPDANGLETSTACKSTACKINTERBULGEHAIRPINTLoops(++* <-l OUT $P  "P. PO$[(ݼ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDRSRTUVTPPUPPSP@ WgXX>/ݼ FOR$WRITE_SFX FOR$IO_L_V FOR$IO_END8ݼ FOR$WRITE_SF FOR$IO_ENDdWVUG FOR$WRITE_SF FOR$IO_ENDSnK FOR$WRITE_SF FOR$IO_ENDRJ(ݼ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDRSTUSPPTPPRP@HVfWW>/ݼ FOR$WRITE_SFW FOR$IO_L_V FOR$IO_END8ݼ FOR$WRITE_SF FOR$IO_ENDVUTG FOR$WRITE_SF FOR$IO_ENDSnK FOR$WRITE_SF FOR$IO_ENDRN(ݼ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDRSTUSPPTPPRP@VfWW>/ݼ FOR$WRITE_SFW FOR$IO_L_V FOR$IO_END8ݼ FOR$WRITE_SF FOR$IO_ENDVUTG FOR$WRITE_SF FOR$IO_ENDSnK FOR$WRITE_SF FOR$IO_ENDRNMݼ FOR$WRITE_SF  FOR$IO_T_DS( FOR$IO_T_DS0 FOR$IO_T_DS FOR$IO_ENDRdS\ݼ FOR$WRITE_SFR FOR$IO_L_V FOR$IO_L_Rߣx FOR$IO_L_R߃ FOR$IO_L_R FOR$IO_ENDR(ݼ FOR$WRITE_SF8 FOR$IO_T_DS FOR$IO_ENDW 12WXH YZ2YPzPP{PPPPVYP2PPPYV2ZPPA@V2ZPPC@V2ZVVGF2ZPPU@=Zeݼ FOR$WRITE_SFk FOR$IO_T_DS?H N FOR$IO_W_R FOR$IO_END= WS OOUT$CODEl$PDATAd$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_W_R FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$WRITE_SFicP$P;P$]PP$5PGPzP P3PP!PP ma- /FIND0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 FIND PP FINDTPPPHT[} PQԫTT~ݼ FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDUüPPPVWVWPUR@BUUTUQGAUVWPPRt HFIND$CODE$PDATAd$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF,PuPnWP0hPpPP+ 0CDUMP0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 CDUMPLPEnter file name for continuation dump (return for terminal)Energy ParametersListing of energy files? (y/N) . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair []e CDUMPaPP (( H;`L;LLP. P HL[ FOR$WRITE_SL$ FOR$IO_T_DS FOR$IO_END~j FOR$READ_SF FOR$IO_T_DS FOR$IO_END-( nkk,FOR$OPENDLISTOUTmk FOR$WRITE_SFL FOR$IO_T_DS FOR$IO_ENDtk FOR$WRITE_SF߫ FOR$IO_X_DA FOR$IO_END FOR$WRITE_SLT FOR$IO_T_DS FOR$IO_ENDq FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDYy\OUTFOR$EXIT8 HCDUMPFOR$OPENLISTOUTOUTFOR$EXIT$CODE$PDATA$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_T_DS FOR$IO_X_DA FOR$READ_SF FOR$READ_SF FOR$WRITE_SF FOR$WRITE_SL'%PQPVP PPD+*I4 GETTLOOPS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 GETTLOOPS[P)4Too many characters in numeric field of this line oftloop.dat file: )O GETTLOOPS`PP ``P|H`[ FOR$READ_SF FOR$IO_END~ FOR$READ_SF FOR$IO_T_DS FOR$IO_END\M\PQP:2\PP@ \2\PP(@ TONUMPPPPP2QPAҠ\M\QQQ:2\QQA \\V2VPP@ ~ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END2\\\(L CONVT2\PLN\V2\PP @=V\1$ FOR$CLOSE |H GETTLOOPSCONVTTONUM FOR$CLOSEE$CODET$PDATA$LOCALTLOOPS FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$READ_SF FOR$WRITE_SF7*P_PkPPPP!&P<0 E0TONUM0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 TONUMI*PUnknown base in TLOOP file:  TONUMP PH[}PQЬ T>U2TVVWGAFeGCFeGGFeGUFeGTFe=T~ FOR$WRITE_SFG  FOR$IO_T_DS FOR$IO_ENDFOR$STOP HTONUM$CODE#$PDATA$$LOCALFOR$STOP FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF@2P 8P?CPIP.SPYPcPiPsP ,  _DS FOR$READ_SF FO*[MFOLD]CON.FOR;1+,./ 4<-*0123KPWO56Nh74;i89GHJ  implicit integer (a-z) character*132 in character*72 out1,out2 character*40 fle character*6 cont,comm data cont/' .'/ data comm/'C '/ *1 write (6,*) 'Enter source file name' read (5,100) fle+ open (10,err=1,status='OLD',file=fle)*10 write (6,*) 'Enter target file name'$ read (5,100,end=10,err=10) fle if (fle.eq.' ') goto 10< open (20,carriagecontrol='LIST',status='NEW',file=fle)  do while (1) do i = 1,72 out1(i:i) = ' ' out2(i:i) = ' ' enddo do i = 1,132 in(i:i) = ' ' enddo! read (10,1000,end=11) in  ptr = 7& do while (in(ptr:ptr).eq.' ') ptr = ptr + 1 enddo  last = 132( do while (in(last:last).eq.' ') last = last - 1 enddo   if (last.le.72) then$ write (20,1001) in(1:72)# write (6,1003) in(1:72) else write (6,1010) write (6,1100) write (6,1110)$ write (6,1111) in(50:80) bp = 73+ do while (bp.lt.20.or.bp.gt.72)- write (6,*) 'Enter breakpoint' read (5,*) bp enddo ! out1(1:bp) = in(1:bp) write (6,1003) out1 write (20,1001) out1 $ if (in(1:1).eq.'C') then out2(1:6) = comm st = ptr else out2(1:6) = cont st = ptr+3 endif 1 out2(st:st+last-bp-1) = in(bp+1:last)  write (6,1003) out2 write (20,1001) out2 write (6,1010)  endif enddo 11 close(10) close(20) stop 100 format(a40)1000 format(a132)1001 format(a72)1002 format(1x,a132)1003 format(1x,a72)1010 format(/,70('-'),/)31100 format(20x,'5 5 6 6 7 7 8')31110 format(20x,'0 5 0 5 0 5 0')1111 format(20x,a31,/) end*[MFOLD]CRNA.EXE;2+,./ 4-*0123 KPWO56wui7hi89GHJ0D`0205si hvCRNA01T8si05-09   Q,}$ U& 78  9 S;  ?B!d FORRTL_001! LIBRTL_001O! MTHRTL_001Segment larger than +begin.dat [H[J[1mP P [0m%[24;20HPress to continue ...) Author and reference file not available.+%(Enter dangle energy file name (default dangle.dat)DANGLE.DATEnter loop energy file name (default loop.dat)LOOP.DATEnter stack energy file name (default stack.dat)STACK.DATEnter tstack energy file name (default tstack.dat)TSTACK.DATEnter tloop energy file name (default tloop.dat)Tloop.DATEnter misc. loop energy file name (default miscloop.dat)miscloop.DAT(0u$ Open bifurcation not found between  and # Bulge or interior loop closed by (, ) not found& Closed bifurcation not found between  and  Base pair between  and  conflicts with at least one other pair Buffer overflow in lineout End reached at traceback  More than  basepairs in sort at (,) Premature end of save fileERROR - STACK OVERFLOW FOLDING BASES  TO  OF  ENERGY =    () ENERGY =  & Energy Parameters (10ths kcal/mole) . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair []9 Enter Parameter to be changed ( for main menu)  Enter new value  Enter base and length  Enter base pair and length  Enter begining and end  01 Energy Parameter 6 Single Prohibit 02 Single Force 7 Double Prohibit 03 Double Force 8 Begin Folding  04 Closed Excision 9 Show current  05 Open Excision 10 Clear current  Enter Choice  No choices currently defined Current Choices : (,)  : ,' Combination of continuation run and multiple foldings disallowedFOLD.SAVEnter start of fragment (default 1)Enter terminal type 1 VGT1002 Visual 102 (default)3 Tektronics 41051 Enter minimum vector size for plot (default 1) Enter run mode0 Sub-optimal plot (default) 1 N Best2 Multiple Molecules) Enter number of tracebacks (default 1) ( Enter percentage for sort (default 0)  Enter window size (default 0) Enter run type0 Regular run (default) 1 Save run2 Continuation run( Enter save file name (default fold.sav)  nucleotides Enter end of fragment (default )NEWOLD'   nucleotides (# Do you want printer output? (Y,n)  Output to terminal? (Y,n) ! Enter output file name (default #)2 Enter number of columns on printer (default 80)   Do you want ct file? (y,N)  Enter ct file name (default #)! Do you want region table? (y,N) ' Enter region table file name (default #).OUT.CT .REG  > Premature end of MISCLOOP.DAT<--ERROR - DANGLE ENERGY FILE NOT FOUNDERROR - PREMATURE END OF DANGLE ENERGY FILE-----ERROR - STACK ENERGY FILE NOT FOUNDSTACK ERROR - PREMATURE END OF STACK ENERGY FILEERROR - PREMATURE END OF TSTACK ENERGY FILEP . SYMMETRY ERROR(,) =  DANGLETSTACKSTACKINTERBULGEHAIRPINTLoops(++* <-PEnter file name for continuation dump (return for terminal)Energy ParametersListing of energy files? (y/N) . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair [])4Too many characters in numeric field of this line oftloop.dat file: )Unknown base in TLOOP file: @  Minimum Energy = Increment = Enter New Increment ENTER NEW VINC: BASE = N = Base-pair = ( , )Score = +[14;1HMinimum energy = [16;1HIncrement = #[18;1HEnter New Increment [18;24H+[18;24H +0 ENTER PLOT FILE NAME : ) ENTER PLOT LABEL (UP TO 59 CHARACTERS) :</ ENTER TICK MARK INTERVAL & NUMBER OF LEVELS : P+"[2;1HEnter New Increment "[3;1H [2;24H+[2;24H +[2;1HBase = [3;1HN = +[21;1HBase-pair = ,[22;1HEnergy = @ @%!K+++%!KALZMG+++Input sequence file name (/ to end) 12 ) No sequence identifiers found in this file Available sequences in .Choose sequence by number or name , or ? for relist; defaults to the first one, / for new file. NUMBER CHOICE BETWEEN 1 AND This entry does not match with any in given list Sequence truncated to ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE%2P22< LOCUSORIGIN//ID SQ SequenceNRC GENBANK Input sequence file name (/ to end) 12 ) No sequence identifiers found in this file ERROR IN MULTID, SEQUENCE REQUESTED NOT FOUND Sequence truncated to ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE&2P2 &9s~ MFOLD.BCK*[MFOLD]CRNA.EXE;2| LOCUSORIGIN//ID SQ Sequence NRC GENBANK PLOT  D  @H$48,48(0048<00488@D008@488HHP< 480048  @ @ @ @ @ @ @ @ P ,d !|!!|!!|!!|!!!!|!!!!|!!|!|!|!!!!|!!|!|!!(#,#0#4#(#,#,#(#,#,#(#(#,#(#,#(#(#,#(#,#(#,#(#,#(#,#(#,#(# #,#(# #(# #,#,#(#,#(#,#(#,#(#,#(#,#(#,# # # #(#,# # # #(#,# # # #(#,#(#,# # # #(#,#8#@#8#@#(#,#; (#  ,  6 t: x: xd; x,< hci d; (#  ,  6 t: x: xd; x,< hci d(()2 : P)`).Es P))0|  P))2  P))0 #P)0*8- e P)d*- .hc** @@@@,@$@@D@0@$@@D@,@@@D@0@@@D@@@@@@D@ @@@D@0123456789 .hAhcEnergy Parameter Single Force Double Force Closed Excision Open Excision Single Prohibit Double Prohibit     X<'W<''hc(PC(xCD @E D D <D  C DCCCP<@ C# X<'W<''hcDDP< D DDP< D(E(8E dElE dElE dElEPFhFptFptFptGpt G|t8GF|tXG$+xGFtGFtG#)#G*0tGFtH#    +Z  HPH; ((II;8IIsIJPJpJJpJ KK K8^XL <LL<`dhltLtLxxtLtLppLLtLtLMT<MLN<<LLT<L<LLT<L<<LLLMMM<<<DMLLLLLxx8OLO<<LLLLLLLLLLLLt MLL$MppxLLLLLxx<LLL<t3lP HPT|P fP<tPpPp Q QM<QQQQQQQQRRxRR|RRSSUHUS  <=>?@ABCUUUUUUUUX2vP%`B@HtHHH,;9 E0c2XP%B (T(h(|(,.!OOOm(1H+, A1,$)   pZf~H & ^ 41j @/ g$̡?W/ H0-E ќ;2ҁU p' y`!%Ȯ$ J`uaGD5[aIi2 =pg11n) Q|DDs!z B9}*Gg#<N"Vd}}Y,a,) lipi8X3R"50DiHitTxlipilipi:/P" h{D{_ JPTTIGEC{P|FGL:NrVZ}E]{"YWCSV!g!Zi`o1HeH/NL{EL/" LJC LKGE{_{EGNHE{LNLK{EG{ELI5140MeCGbH LJ/h{TUXY6GL{"CjLKGE{d{EJG|fCfd{EHINCC"N{ENNUCCNCCNLE{LJCEL{LJC{EGLN"{ENNONNCNNC]{GICoW:"7ZOGE{oWCKeZC]{GIC6  {EICoW:"8{ErO/""K "K@]{GICGE{`{D_{ECNFG{De"xBIG{EGC8 5yLaC/"UGCGCGE{GE{]{GI@{DE~HU{ {EIC I OII C I IC RrZCH|!TJE{rZI{:3 " RC {ELrZHHq!|O WJ6CO\_fmty}.3?HQY`kqw~DOSVYdnw$(.C`!<=>?\]^6DOC` " I3Me " .I3Mo " DIC` " :IC`6 DI=[z6DIC` (hl |Ti-J?W BCD(,40H plipii pplipiTipi    hhhhl #   \ li    . 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DRAWA DRAWAf DRWABS |DRWABSS DRWREL DRWREL% DWINDO DWINDO * EMCHAR $EMCHAR4u HOME HOMET INITT INITT LINEF LINEF LVLCHT LVLCHT + MOVABS MOVABS( MOVEA MOVEA ; MOVREL $MOVREL% NEWLIN LNEWLIN NEWPAG `NEWPAGu PLCHAR PLCHAR RESCAL RESCAL&R RESET $ RESET" REVCOT REVCOT/ SCURSR  SCURSR & SETBUF 4 SETBUFd SETMRG  SETMRG TERM  TERM * TKSYNC  TKSYNCB TOUTPT  TOUTPT TOUTST 4 TOUTST9 TWINDO p TWINDO * V2ST  V2ST VECMOD d VECMOD C WINCOT  WINCOT XYCNVT  XYCNVT9  BUFFPK  BUFFPK CARTN | CARTN&f CLIPT  CLIPTR2 CWSEND  CWSEND) DIGPAK D DIGPAK\ DMGIN  DMGIN8$ IOWAIT  IOWAIT0 PARCLT  PARCLTJ PCLIPT @ PCLIPT / PLTCHR p PLTCHR PSCAL  PSCAL5 RECOVR ` RECOVR} TINSTR  TINSTR TSEND  TSEND ADEIN  ADEINU PNTMOD  PNTMOD <*[MFOLD]CRNA.OBJ;1+,. / 4 ,-*0123KPWO 56tbi7t}"i89GHJ3RNA$MAIN0123-Feb-1992 02:2323-Feb-1992 02:23VAX FORTRAN V5.7-133RNA$MAIN*PSegment larger than +RNA$MAIN\P$48,48(0048<00488@D008@488HH 480048 P. PO [BEGINDEVICE\ENEFILES<ERGCDUMPOUTPUTSMENU TMSEQ,n_,n__PROCESSPP FOR$WRITE_SL\ FOR$IO_T_DS to continue ...) Author and reference file not available. BEGIN<TPP d FOR$OPEN@PHT[FOR$OPENP1 FOR$WRITE_SF FOR$IO_L_R FOR$IO_L_R FOR$IO_L_R FOR$IO_END~% FOR$READ_SF FOR$IO_T_DS FOR$IO_END( FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END. FOR$WRITE_SF FOR$IO_L_R FOR$IO_L_R FOR$IO_ENDc FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDf FOR$WRITE_SF FOR$IO_END HBEGINFOR$OPEN$CODE$PDATA$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$READ_SF FOR$READ_SF FOR$WRITE_SFPVPE)*[MFOLD]CSORT.OBJ;1+,. / 4 \-*0123KPWO 56Zki7(i89GHJ2SORTOUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133SORTOUTSORTOUT$PP. PH [kRԼѼ   BUILD_HEAP HEAP_SORT RB B  MARKPRRkRB B Rk HSORTOUT BUILD_HEAP HEAP_SORTMARKz$CODE$PDATA0$LOCAL<MAIN.'SEQDLISTNM TRACE BITSTLOOPSHEAPP PPPUP '+z5 BUILD_HEAP0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 BUILD_HEAP BUILD_HEAP0P $(P. PK [PPPPƏdPP\ V戩RSR1SRkENEkRЫSP\戩0uBs$Cs(ERRMSG1戩戩PR@S@SPPSSRRSSSRRS1\戩\\WW1u\2uRRXGYP^QRXSYT OTS$MOVE5_R5\2u\\GXP^QR\SXT OTS$MOVE5_R5戩WX戩1X\XYYL0L4,ENEPRI region,c input : ct file name ( .ct assumed )$c ct file of that name1c output : region table ( [same name].reg )6c raw sequence data ([same name].seq )c region --> ct/c input : region file name ( .reg assumed )&c region file of that name0c raw sequence file ( .seq assumed ),c raw sequence file of that name0c output : ct file ( [same name as reg].ct )c implicit integer(a-z)) integer nbases,region,iprime,jprime0 integer x/'X'/,seqk,regsiz,j,k,k1,k2,k3,k4$ integer seq(8000),primes(8000) integer ct(8000,2)# integer i,line(80),blank/' '/ real r/0.0/) character*50 ctname,seqname,regname character*70 label logical used1,used2,flag6 data used1/.false./,used2/.false./,flag/.false./cc1 write(5,111) read(6,112) t if ( t.eq.1 ) go to 34 if ( t.ne.2 ) go to 1cc CT-->REGcc READ IN CT FILE1c COL 1: BASE PAIR (SEQUENTIAL NUMBER) OR 0 c COL 2: HISTORICAL NUMBERc9 if (.not.used1) then write(6,1010)*1010 format(' Enter CT file name : '$)# read(5,1020,end=99) ctname1020 format(a50)N open(1,file=ctname,readonly,status='old',defaultfile='fold.ct',err=9) pos = 1G regname = ' 'G seqname = ' 'E do while (ctname(pos:pos).ne.'.'.and.ctname(pos:pos).ne.' '. . and.pos.lt.40). regname(pos:pos) = ctname(pos:pos). seqname(pos:pos) = ctname(pos:pos) pos = pos + 1 enddo$ regname(pos:pos+3) = '.reg'$ seqname(pos:pos+3) = '.seq'A open(2,file=regname,status='new',carriagecontrol='list')A open(3,file=seqname,status='new',carriagecontrol='list') endif seqpos = 0 read(1,101,end=99) n,label do 15 i=1,n410 read(1,102,end=32) k,elt,k1,k2,ct(i,1),ct(i,2) start=seqpos+1 finish=ct(i,2) do 12 j=start,finish12 seq(j)=x seqpos=ct(i,2)15 seq(seqpos)=eltcc FIND STACKING REGIONSc region=1 i=0 18 i=i+119 if ( i.gt.n ) go to 32 subscr=ct(i,1)! if ( subscr.eq.0 ) go to 18- if ( ct(i,2).gt.ct(subscr,2) ) go to 18 iprime=ct(i,2) jprime=ct(subscr,2) regsiz=1 j=jprime-1 20 i=i+1 subscr=ct(i,1)! if ( subscr.eq.0 ) go to 30& if ( ct(i,2).gt.ct(subscr,2).or.' x j.ne.ct(subscr,2) ) go to 30 regsiz=regsiz+1 j=j-1 go to 20030 write(2,103) region,iprime,jprime,regsiz,r region=region+1 go to 19532 if(.not.used1) write(3,106) (seq(i),i=1,seqpos) used1 = .true. go to 9cc REG-->CTc34 if (.not.used1) then write(6,1030).1030 format(' Enter REGION file name : '$)$ read(5,1020,end=99) regnameJ open(2,file=regname,readonly,status='old',defaultfile='fold.reg', . err=34)67 write(6,1040)01040 format(' Enter SEQUENCE file name : '$)$ read(5,1020,end=99) seqname? open(3,file=seqname,readonly,status='old',defaultfile= . 'fold.seq',err=67) pos = 1F ctname = ' 'G do while (regname(pos:pos).ne.'.'.and.regname(pos:pos).ne.' '. . and.pos.lt.40). ctname(pos:pos) = regname(pos:pos) pos = pos + 1 enddo" ctname(pos:pos+3) = '.ct'@ open(1,file=ctname,status='new',carriagecontrol='list') nbases=0 35 read(3,107,end=38) line j=1)37 if ( line(j).eq.blank ) go to 35 nbases=nbases+1 seq(nbases)=line(j) j=j+1 if ( j.gt.80 ) go to 35 go to 37 endif38 do k=1,nbases primes(k)=0 enddo k=1 if(used1) go to 41640 read(2,104,end=90) region,iprime,jprime,regsiz,r( if(used1.and.region.eq.1) go to 9141 used1 = .true.!50 if ( k.eq.iprime ) go to 60 k=k+1! if ( k.gt.nbases ) go to 90 go to 5060 k3=jprime+iprime-k primes(k)=k3 primes(k3)=k k=k+1( if ( k-iprime.lt.regsiz ) go to 60 go to 4090 flag = .true.91 if (.not.used2) then used2 = .true. write(6,201) read(5,202) offset if(i.le.0) i = 1 write(6,203) read(5,204) label% nbases = nbases - offset + 1 endif write(1,105) nbases,label do 95 k=1,nbases k1=k-1 k2=k+1 if ( k.eq.nbases ) k2=0 kk1 = k + offset - 1 k3 = 02 if(primes(kk1).ne.0) k3=primes(kk1)-offset+1 k4=kk1)95 write(1,102) k,seq(kk1),k1,k2,k3,k4 if(flag) go to 99 go to 34 99 stopc101 format(i5,1x,a70)102 format(i5,1x,a1,3x,4i5)*103 format(' (',i5,')',3x,3(i5,3x),f7.1)$104 format(2x,i5,4x,3(i5,3x),f7.1)105 format(i5,' ',a70)106 format(60a1)107 format(80a1)1111 format(/,' INPUT 1 - FOR REG --> CT, OR'/ 1 /,' 2 - FOR CT --> REG: ')112 format(i1)C201 format(' Enter historical numbering of first base [ 1 ] : '$)202 format(i) 203 format(' Enter label : '$)204 format(a70) end*[MFOLD]CT_GCG.FOR;1+,./ 4C-*0123KPWO56nF*h7T{?i89GHJ-C Generates a CT file. (Richard Feldmann) SUBROUTINE CT(R) INCLUDE 'RFD.DAT' REAL R 2 WRITE(21,100) SEQLAB,HSTNUM(1),HSTNUM(N),N,R DO K = 1,N K1 = K+1 IF (K.EQ.N) K1 = 0C WRITE (21,200) K, SEQ(HSTNUM(K)),K-1,K1,BASEPR(K),HSTNUM(K) ENDDO RETURNA100 FORMAT('FOLD of: ',A30,' Check: 0 from: ',I5,' to: ',I5,/,4 . 'Length: ',I5,' Energy: ',F7.1,/,'..')200 FORMAT(I5,1X,A1,3X,4I5) END*[MFOLD]CVTCT.EXE;3+,. / 4 -*0123 KPWO 56Tڙ i7,pi89GHJ0D`0205[ ih CVTCT01J[ i05-09 GILO  ?B!d FORRTL_001! LIBRTL_001%Convert a CT file to a UWGCG CT file.FOLD of: Check: 0 from: to:Length: Energy:.. "Make MaxSiz bigger in the program.) file name? )File does not exist.SYS$OUTPUTFile already exists. Continue) (Y or N)? )GCG CT PPP`LhXd\TTLhXdTP`LhXdPX .CT )y~ MFOLD.BCK*[MFOLD]CVTCT.EXE;3 Q   .PPHL PPPPl`tYNPȗazAPHD[i\MTh\\TDB T\V\VTDB _DB\Vtˈ˨3!PI[} PQ}PQ QЬ,8޻8RMiݼknߢ XP@HU=iݼMݼ#ݼ!*мSTS[UiݼT-P n, Tg Pk,Jg P8PVVV1DH[}PQR*g~lHIg~='(~ PPR QPQQPRQQPHl[}PQ}PQ  P QQPQQPP @@ (@@ 8  @FORRTLLIBRTL CVTCT CVTCT$ GCG_CT GCG_CT CTIN CTIN%$ BUFLEN КBUFLEN 0 GETFIL GETFIL'  YES YES UPCASE pUPCASEF*[MFOLD]CVTCT.FOR;3+,. / 4C -*0123KPWO 56Vh7Ni89GHJ program cvtct*>** Convert a normal CT file to a .DAT file format that UWGCG's** SQUIGGLES will accept.7** -John Jaeger 13Feb89-* parameter maxsiz=1750*1 integer bpair(maxsiz),size,pinfo(4,maxsiz)4 integer inunit,outunit,comunit,fnum,tsiz,csiz integer i,j character*1 base(maxsiz) character*2 buffer character*30 seqlab' character*80 text,gcgfname,ctext logical inopen,isnew real eng*> data inopen/.false./inunit/1/outopen/.false./outunit/2/ data isnew/.false./& data fnum/0/tsiz/4/text/'.COM'/" data csiz/6/ctext/'GCG CT'/*.** Get CT file name and the first set of data.* write (6,1); call ctin (inunit,inopen,size,seqlab,base,pinfo,eng)*5** Open a .COM file to put the SQUIGGLES commands in.* do while (inopen)*=** Remove spaces so that squiggles parse routine doesn't read** the wrong numbers.* j=30' do while (seqlab(j:j).eq.' ') j=j-1 enddo do i=1,j2 if(seqlab(i:i).eq.' ') seqlab(i:i)='_' enddo*2 call getfil(csiz,ctext,gcgfname,.false.)B open (unit=outunit,name=gcgfname,carriagecontrol='LIST', 1 status='NEW')9 call gcg_ct(outunit,size,seqlab,base,pinfo,eng), close (unit=outunit,status='KEEP')> call ctin (inunit,inopen,size,seqlab,base,pinfo,eng) enddo*( close (unit=inunit,status='KEEP')) close (unit=comunit,status='KEEP')*:1 format (1x,'Convert a CT file to a UWGCG CT file.')3 format (i2) end : subroutine gcg_ct(funit,size,seqlab,base,pinfo,eng)* parameter maxsiz=750*- integer funit,size,pinfo(4,maxsiz),i,j real eng character*1 base(maxsiz) character*30 seqlab*7 write (funit,10) seqlab,pinfo(4,1),pinfo(4,size) write (funit,20) size,eng* do i=1,size7 write (funit,30) i,base(i),(pinfo(j,i),j=1,4) enddo*@10 format ('FOLD of:',a30,' Check: 0 from:',i3,' to:',i3,//)320 format ('Length:',i3,' Energy:',f7.1,/,'..')30 format (i5,1x,a1,3x,4i5)* return end @ subroutine ctin(myunit,isopen,size,seqlab,base,pinfo,eng)@** Read in a CT file. Use the unit MYUNIT as the file so we can@** read in multiple CT data sets from one big file. ISOPEN will;** return .FALSE. when we reach the end of the CT data set.C** This routine requires the GETFIL subroutine, found in MYLIB.FOR.* parameter maxsiz=750* integer pinfo(4,maxsiz),size,myunit character*1 base(maxsiz) character*30 seqlab logical isopen real eng* integer i,tsiz,j logical old character*80 filnam,title*) data old/.true./title/'CT'/tsiz/2/7********************************************************** CT file header=** CTSUM - integer - total number of bases, lines of CT data<** SEQLAB - character*50 - label that goes with the sequence* 510 format(i5,10x,f7.1,4x,a30)*7********************************************************** CT file data section&** SEQCT - character*1 - base (AGCTU):** K2 - integer - who K5 is basepaired to (0=unpaired)"** full format : (I5,1X,A1,3X,4I5)*520 format(6x,a1,3x,4i5)*&** if the file isn't open, then get it* if (.not.isopen) then- call getfil (tsiz,title,filnam,old)5 open (unit=myunit,name=filnam,status='OLD',& 1 carriagecontrol='LIST') isopen=.true. endif*'** Make sure we can fit it in the array*0 read (myunit,510,end=700) size,eng,seqlab if (size.gt.maxsiz) then write (6,505):505 format (1x,'Make MaxSiz bigger in the program.') stop else*** Get the stuff* do 10 i=1,size9 read (myunit,520) base(i),(pinfo(j,i),j=1,4)10 continue endif goto 800*'700 close(unit=myunit,status='KEEP') isopen=.false.* 800 return end % integer function buflen(inbuf)*?** Return the position of the last non-blank character in InBuf* character*1 sp character*80 inbuf integer i* data sp/' '/* i=801 do while ((i.gt.0).and.(inbuf(i:i).eq.sp)) i=i-1 enddo buflen=i return end*[MFOLD]CVTCT.OBJ;1+,. / 4 -*0123KPWO56T i7^Vi89GHJ0CVTCT0123-Feb-1992 01:4923-Feb-1992 01:49VAX FORTRAN V5.7-133 CVTCT5P%Convert a CT file to a UWGCG CT file. CVTCThPPPP`LhXd\TTLhXdTP`LhXdPXQQQQGCG CT J'PPHL[ FOR$WRITE_SF FOR$IO_ENDTCTIN\\TDB T\V\VTDB _DB\VtGETFILˈFOR$OPEN˨GCG_CT FOR$CLOSECTIN FOR$CLOSE FOR$CLOSEP PHCVTCTCTINGETFILFOR$OPENGCG_CT FOR$CLOSE$CODE.$PDATA`$LOCAL FOR$IO_END FOR$WRITE_SF+Ph;PJPWP0$1GCG_CT0123-Feb-1992 01:4923-Feb-1992 01:49VAX FORTRAN V5.7-133 GCG_CT\PFOLD of: Check: 0 from: to:Length: Energy:.. GCG_CTP .PI[} PQ}PQ QЬ,8޻8Rݼ FOR$WRITE_SFk FOR$IO_T_DSߢ  FOR$IO_L_RP@ FOR$IO_L_R FOR$IO_END*ݼ FOR$WRITE_SFݼ FOR$IO_L_Vݼ FOR$IO_F_V FOR$IO_ENDмSTSUHݼ FOR$WRITE_SFT FOR$IO_L_V$PDATAT$LOCALFOR$STOP FOR$IO_END FOR$IO_L_R FOR$IO_F_R FOR$IO_T_DS FOR$IO_X_NL FOR$READ_SF FOR$READ_SF FOR$WRITE_SF(,PHPPPT P1%$1BUFLEN0123-Feb-1992 01:4923-Feb-1992 01:49VAX FORTRAN V5.7-133 BUFLEN BUFLENMPPQ PH[}PQPTTTP@TTPC HBUFLEN0$CODE$PDATA$LOCALP'P 0*[MFOLD]DANGLE.DAT;1+,. / 4O -*0123KPWO 56h7]i89GHJE X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E AX AX AX AXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . . . . . . . . . -0.8 -0.5 -0.8 -0.6E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E CX CX CX CXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M . . . . . . . . -1.7 -0.8 -1.7 -1.2 . . . .E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E GX GX GX GXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . -1.1 -0.4 -1.3 -0.6 . . . . -0.8 -0.5 -0.8 -0.6E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E UX UX UX UXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M-0.7 -0.1 -0.7 -0.1 . . . . -1.2 -0.5 -1.2 -0.7 . . . .E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D A A A AE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . . . . . . . . . -0.3 -0.1 -0.2 -0.2E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D C C C CE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M . . . . . . . . -0.2 -0.3 -0.0 -0.0 . . . . E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D G G G GE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . -0.5 -0.2 -0.2 -0.1 . . . . -0.2 -0.2 -0.2 -0.2E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D U U U UE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M-0.3 -0.3 -0.4 -0.2 . . . . -0.2 -0.2 -0.2 -0.2 . . . . *[MFOLD]DANGLE.DH;1+, . / 4O -*0123KPWO 56h7ei89GHJNDANGLE ENTHALPIES - mostly from Turner et al. Ann. Rev. Biophys. Biophys. Chem( (1988) 17 pp 167-92.E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E AX AX AX AXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . . . . . . . . . -4.9 -0.9 -5.5 -2.3E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E CX CX CX CXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M . . . . . . . . -9.0 -4.1 -8.6 -7.5 . . . .E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E GX GX GX GXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . -7.4 -2.8 -6.4 -3.6 . . . . -4.9 -0.9 -5.5 -2.3E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E UX UX UX UXD A C G UI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M-5.7 -0.7 -5.8 -2.2 . . . . -7.4 -2.4 -7.2 -4.9 . . . .E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D A A A AE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . . . . . . . . . -0.5 6.9 -0.6 -0.6E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D C C C CE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M . . . . . . . . -1.6 0.7 -4.6 -0.4 . . . . E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D G G G GE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . -2.4 3.3 0.8 -1.4 . . . . -1.5 5.1 0.1 1.0E X X X XN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'D U U U UE AX CX GX UXI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M 1.6 2.2 0.7 3.1 . . . . 1.6 2.2 0.7 3.1 . . . . *[MFOLD]DISTANCE.EXE;5+,. / 4 -*0123 KPWO 56tH i74Gvi89GHJ0D`0205 i2h, DISTANCE01Y i05-09   ?B!d FORRTL_001! LIBRTL_0016 Program DISTANCE computes the distance between pairs of RNA structures Enter name of input data file: P File: F4 For distance between 1st structure and every other one in the file, enter 1 For distance between all 2possible pairs of structures in the file, enter 2 ?  Enter name of output file (enter term if you wish output to terminal):  bases < Distances 1  No data in input file! Only one structure in input file% Too many structures in input file... Only the first 15 will be processedF0 Unexpected end of file: no data following labelTERMtermP(P)Fd)))))))))))))))  F H[Ы \TUV<-%+ $$<P߫ЫWc{p,^[TE-P` N-P` AVX "$Upի 1UTT3VUݫ4U˄ի {U[T3VwUZݫP4NKk˘˰TPUPk@LTV U1BU1WUPTPTU1VUTRTRTRVW=VUWRWˌT߄cWR`iRUf\P\P@LV=R \RBˈTd c (THIS REQUIRES TWO SEARCH LOOPS, ONE FOR EACH STRUCTURE)c d = 0( call bpsrch(nbases,bp1,nbs2,bp2,d)( call bpsrch(nbs2,bp2,nbases,bp1,d) dm(nstr,ns1) = dc&c GO ON TO NEXT STRUCTURE (IF ANY)! WRITE (4,111) go to 30c0c END OF FILE FOUND - DECIDE WHAT TO DO NEXTc 50 nstr = nstr - 1c"c CHECK FOR INSUFFICIENT INPUT if (nstr.eq.0) go to 90 if (nstr.eq.1) go to 91c)c CHECK FOR COMPLETION OF COMPARISONS if (ins.eq.1) go to 60# if (ns1.eq.(nstr-1)) go to 60cDc SET CONTROLS FOR NEXT SET OF COMPARISONS AND REWIND INPUT UNIT ns1 = ns1 + 1 nstr = 0 rewind 2 go to 20c c OUTPUTc% 60 write (iout,120) (j,j = 1,nstr) write (iout,111) if (ins.eq.2) go to 65+ write (iout,121) (dm(j,1),j = 1,nstr) stopc 65 do j = 1,nstr dm(i,i) = 0. write (iout,125) j,(dm(j,i),i = 1,j) write (iout,111) end do stopcc ERROR CONDITIONSc@c NOT ENOUGH DATA IN INPUT FILE TO DO DIFFERENCE CALCULATION 90 write (6,190) stop 91 write (6,191) stopc+c GREATER THAN MAX ALLOWABLE STRUCTURESHc WRITE MESSAGE (1st ENCOUNTER ONLY) AND PROCEED AS FOR END OF INPUT$ 92 if (ns1.eq.1) write (iout,192) go to 50cH 101 format (//' Program DISTANCE computes the distance between pairs ' 1 'of RNA structures')4 105 format (/' Enter name of input data file: ',$) 106 format (a80) 107 format (/' File: ',a70/)D 110 format (' For distance between 1st structure and every other '@ 1 'one in the file, enter 1' / ' For distance between all 'D 2 'possible pairs of structures in the file, enter 2'/' ? ',$) 111 format (i1)E 112 format (/' Enter name of output file'/' (enter term if you '& 1 'wish output to terminal): ',$) 113 format (/)* 115 format ( 1x,i2,i6,' bases ',a60)+ 120 format (//' Distances'// 5x,15i5) 121 format (' 1 ',15i5) 125 format (1x,i2,2x,15i5)c( 190 format (/' No data in input file')3 191 format (/' Only one structure in input file')E 192 format (/ ' Too many structures in input file...'/ ' Only the '$ 1 'first 15 will be processed') end*[MFOLD]DISTANCE.OBJ;1+,. / 4 >-*0123KPWO564U i7T|i89GHJ8 DISTANCE$MAIN0123-Feb-1992 01:5023-Feb-1992 01:50VAX FORTRAN V5.7-133 DISTANCE$MAINkP6 Program DISTANCE computes the distance between pairs of RNA structures Enter name of input data file: P File: F4 For distance between 1st structure and every other one in the file, enter 1 For distance between all 2possible pairs of structures in the file, enter 2 ?  Enter name of output file (enter term if you wish output to terminal):  bases < Distances 1  No data in input file! Only one structure in input file% Too many structures in input file... Only the first 15 will be processed DISTANCE$MAIN#PP"P#Fd###############Q.TERMtermPH#[Ы \TUV FOR$WRITE_SF FOR$IO_ENDN FOR$WRITE_SF FOR$IO_ENDs FOR$READ_SF$ FOR$IO_T_DS FOR$IO_ENDv FOR$WRITE_SF$ FOR$IO_T_DS FOR$IO_END<FOR$OPENP FOR$WRITE_SF FOR$IO_END- FOR$READ_SF߫ FOR$IO_L_RЫW FOR$IO_END0 FOR$WRITE_SF FOR$IO_ENDs FOR$READ_SF, FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_END-P` -P` VXFOR$OPEN FOR$WRITE_SF FOR$IO_ENDv FOR$WRITE_SF$ FOR$IO_T_DS FOR$IO_ENDUpBPINի 1UTTV FOR$WRITE_SFU FOR$IO_L_Vݫe FOR$IO_L_V4 FOR$IO_T_DS FOR$IO_ENDU˄BPINի UTV FOR$WRITE_SFU FOR$IO_L_Vݫ FOR$IO_L_V4 FOR$IO_T_DS FOR$IO_ENDk˘BPSRCH˰BPSRCHTPUPk@LTV FOR$WRITE_SF FOR$IO_ENDU1U1WUPTPTU FOR$REWIND1V FOR$WRITE_SFUTRTR FOR$IO_L_VTR FOR$IO_END-V FOR$WRITE_SF FOR$IO_ENDWV FOR$WRITE_SFUWRWˌT߄ FOR$IO_L_RWR FOR$IO_ENDFOR$STOPRU\P\P@LV FOR$WRITE_SFR FOR$IO_L_V\RBˈTd FOR$IO_L_R if ((choice(i:i).lt.'0').or.(choice(i:i).gt.'9')) then goto 200 else vinc = 0B do while ((choice(i:i).ge.'0').and.(choice(i:i).le.'9'))> vinc = ichar(choice(i:i)) - ichar('0') + 10 * vinc i = i + 1 enddo endif vinc = vinc * mult  if(vinc.lt.0) go to 10  c Compute and plot vectors  do 122 jstrt = 1,n j = jstrt + 1 i = 0- call vector(i,j,vmin,vinc,cntrl(6)) 122 continue do 124 istrt = 2,n j = n + 1 i = istrt - 1- call vector(i,j,vmin,vinc,cntrl(6)) 124 continue if (cntrl(5).eq.1) then*c GRAPHICS DUMP IF PRINTER ENABLED# write(6,2025) 27,232025 format('+'2a1$) end if go to 120  c,c DISPLAY CROSS HAIRS AND RETRIEVE I,Jc200 call tek(cntrl(5)) call reset call scursr(cha,ixa,iya)7 x = float(ixa) * float((n-1))/float(maxx) + 1.09 y = float(iya) * float((n-1)) / float(maxy) + 1.0 iget = y + 0.5 jget = x + 0.5 iget = n + 1 - iget iret = iget jret = jget- vbest = v(iget,jget) + v(jget,n+iget) do 350 i=-1,1 do 350 j=-1,18 check = v(iget+i,jget+j) + v(jget+j,n+iget+i)' if(check.ge.vbest) go to 350 iret = iget + i jret = jget + j vbest = check350 continue ; if(cha.eq.ichar('R').or.cha.eq.ichar('r')) go to 107 if(cha.eq.ichar('Q').or.cha.eq.ichar('q')) then call vt100(cntrl(5)) return endif7 if(cha.eq.ichar('T').or.cha.eq.ichar('t')) then call newpag call vt100(cntrl(5)) stop end if7 if(cha.eq.ichar('P').or.cha.eq.ichar('p')) then call vt100(cntrl(5)) write(6,4010)/4010 format('0 ENTER PLOT FILE NAME : '$) read(5,4015) plotfile4015 format(a30); open(unit=7,file=plotfile,carriagecontrol='LIST' 1 ,status='NEW') label(60) = '$' write(6,4020)>4020 format(' ENTER PLOT LABEL (UP TO 59 CHARACTERS) :')) read(5,4030) (label(i),i=1,59)4030 format(60a1) write(6,4040)E4040 format(' ENTER TICK MARK INTERVAL & NUMBER OF LEVELS : '$) read(5,*) nt,levels ihaf = 2 iclr = 2 mode = 1 write(7,4030) label/ write(7,4050) n,nt,nt,ihaf,iclr,mode4050 format(6i5)2 if(levels.gt.1) icrit = vinc/(levels-1) do 300 j=1,n do 290 i=1,j' vst((n-1)*(i-1)+i) = 0( check = v(i,j)+v(j,n+i)% if(levels.gt.1) then< k = (check + icrit - 1 - vmin)/icrit + 1: if(k.le.levels) vst((n-1)*(i-1)+i) = k elseA if(check.le.vmin+vinc) vst((n-1)*(i-1)+i) = 1 end if290 continue* write(7,4060) (v(i,i),i=1,j)4060 format(80i1)300 continue close(7) go to 10 end if7 if(cha.eq.ichar('G').or.cha.eq.ichar('g')) then 1 call dwindo(1.0,float(n),1.0,float(n)) call newpag4 if (cntrl(5).eq.1) call setmrg(1040,1223) &301 if (cntrl(5).ne.3) goto 307 call home call newlin0 call aout(15,'ENTER NEW VINC: ') call newlin0 call aout(15,' ') call home call linef call linef call alfmod goto 303 307 call vt100(cntrl(5)) write(6,3030) 27,27,27;3030 format('+',a1,'[2;1HEnter New Increment ',; 1 a1,'[3;1H ',! 1 a1,'[2;24H',$) 303 rewind(5), read (5,2050,end=200,err=200) choice if (cntrl(5).ne.3) then write(6,3025) 27 call tek(cntrl(5)) endif)3025 format('+',a1,'[2;24H ') i = 1 mult = 11 do while (choice(i:i).eq.' '.and.i.lt.30) i = i + 1 enddo $ if (choice(i:i).eq.'-') then mult = -1 i = i + 1 endif > if ((choice(i:i).lt.'0').or.(choice(i:i).gt.'9')) then goto 330 else vinc = 0B do while ((choice(i:i).ge.'0').and.(choice(i:i).le.'9'))> vinc = ichar(choice(i:i)) - ichar('0') + 10 * vinc i = i + 1 enddo endif vinc = vinc * mult   call newpag " if (cntrl(5).eq.1) then my = 959 else my = 779 endif maxvi = 0 do 310 i=1,n$ vst((n-1)*(i-1)+i) = 0 do 309 j=1,n$ if(j-i) 302,309,304*302 check = v(j,i) + v(i,n+j) go to 306*304 check = v(i,j) + v(j,n+i)1306 if(check.gt.vmin+vinc) go to 3090 vst((n-1)*(i-1)+i) = v(i,i) + 1309 continue0 if(v(i,i).gt.maxvi) maxvi = v(i,i)310 continue call setmrg(0,1023)) call gaxis(my,maxx,maxy,maxvi)4 if (cntrl(5).eq.1) call setmrg(1040,1223) y = float(v(1,1)) call movea(1.0,y) do 320 i=2,n x = float(i) y = float(v(i,i))320 call drawa(x,y)1 call dwindo(1.0,float(n),1.0,float(n)) go to 301 330 call tek(cntrl(5))# call scursr(cha,ixa,iya); if (cha.eq.ichar('T').or.cha.eq.ichar('t')) then call newpag! call vt100(cntrl(5)) stop endif? if (cha.eq.ichar('R').or.cha.eq.ichar('r')) goto 301; if (cha.eq.ichar('Q').or.cha.eq.ichar('q')) thenn! call setmrg(0,1023)* goto 10  endifD x = float(ixa-1024+maxx) * float((n-1))/float(maxx) + 1.0& y = float(v(int(x),int(x))) l& if (cntrl(5).ne.3) goto 247 call home call newlin. call aout(6,'BASE = ')$ call iout(hstnum(int(x)))% call aout(7,' ')a call newlin + call aout(3,'N = ')l call iout(int(y))( call aout(10,' ') goto 330  247 call vt100(cntrl(5)) 4 write(6,3040) 27,hstnum(int(x)),27,int(y)93040 format('+',a1,'[2;1HBase = ',i6,f9 1 a1,'[3;1HN = ',i6)= goto 330l endif  d# if (cntrl(5).ne.3) goto 224  call home  call homei do 223 ii = 1,22 call newlinl223 continue  call newlin 2 call aout(13,'Base-pair = ( ') call iout(hstnum(iret))u call aout(1,', ')  call iout(hstnum(jret))  call aout(1,')') call newlina call newlin  , call aout(8,'Score = ') call iout(vbest) goto 200 ,224 call vt100(cntrl(5)); write(6,3020) 27,hstnum(iret),hstnum(jret),27,vbest453020 format('+',a1,'[21;1HBase-pair = ',i5,',',i5,2. 1 a1,'[22;1HEnergy = ',i6) t go to 200w end2    0 subroutine tri (xone,xlimit,yone,ylimit)' integer xone,yone,xlimit,ylimit  m call movabs(xone,ylimit)" call drwabs(xlimit,ylimit) call drwabs(xlimit,yone) call drwabs(xone,ylimit) return endi ." subroutine axis(n0,m0,x,y) include 'rfd.inc' 5 real xo,xplace,yo,yplace,endbit,scalex,scaleyc : xspc = 80  if (cntrl(5).eq.2) then  yspc = 40 else# if (cntrl(5).eq.1) then. yspc = 80 else yspc = 50 endif endif  numx = x/xspc numy = y/yspc  numx = min0(numx,n)0 numy = min0(numy,n)o% scalex = float(n)/float(numx)1% scaley = float(n)/float(numy) ) if (cntrl(5).eq.2) call chrsiz(4)m call csize(ihorz,ivert)n ihorz = ihorz/2= ivert = ivert/2 endbit = .97 if (cntrl(5).eq.1) thenm maxy = 959 else maxy = 779t endif  P call twindo(0,x,y,maxy)  do 100 i=0,numx  xo = float(i)*scalex io = hstnum(int(xo)+1)' xplace = float(int(xo)) + 1.0R/ if ((xplace/float(n)).lt.endbit) thenc# call movea(xplace,1.0)  call drwrel(0,10)& call movrel(-ihorz,ivert) call iout2(io)l endif(100 continue call twindo(x,1024,0,y) do 200 i=0,numy yo = float(i) * scaley io = hstnum(int(yo)+1)% yplace = n - float(int(yo))e5 if ((yplace/float(n)).gt.(1.0-endbit)) then,# call movea(1.0,yplace)j call drwrel(10,0). call movrel((ihorz*2),(ivert*-1)) call iout2(io)  endif 200 continue call chrsiz(1) return endo h q( subroutine gaxis(maxy,x,y,maxvi) include 'rfd.inc''2 real scalex,endbit,xo,xplace,yplace,scaley e numx = x/80 numx = min0(numx,int(n))% scalex = float(n)/float(numx)  p) if (cntrl(5).eq.2) call chrsiz(4)  call csize(ihorz,ivert)  endbit = .97 .) call twindo(1024-x,1024,0,maxy-y)t call movea(1.0,float(n))% call drawa(float(n),float(n))  do 100 i=0,numx  xo = float(i)*scalex io = hstnum(int(xo)+1)' xplace = float(int(xo)) + 1.0T/ if ((xplace/float(n)).lt.endbit) thenb( call movea(xplace,float(n)) call drwrel(0,-10)L+ call movrel(-ihorz,(-2*ivert)), call iout2(io)0 endif1100 continue) call twindo(0,1024-x,maxy-y,maxy)M6 call dwindo(1.0,float(n),0.0,float(maxvi)*1.3) call movea(float(n),0.0)) call drawa(float(n),float(maxvi))  numy = min0(y/80,maxvi)l+ scaley = float(maxvi) / float(numy)m do 200 i = 0,numy)% io = int(float(i) * scaley)n yplace = float(io)% call movea(float(n),yplace)  call drwrel(-10,0), call movrel((ihorz*-4),(ivert/-2)) call iout2(io)200 continue, call twindo(1024-x,1024,maxy-y,maxy) call chrsiz(1) return end  ( 1 subroutine iout2 (intt)e integer str(7),out(7)e l int = intt if (intt.eq.0) then  out(1) = ichar('0') i = 7 else do i = 7,1,-1. str(i) = mod(int,10) + ichar('0') int = int / 10  enddo i = 1* do while (str(i).eq.ichar('0')) i = i + 1 enddo do j = i,7 out(j-i+1) = str(j) enddo endif) call anstr(7-i+1,out)e return end  e  subroutine iout (intt) integer intt,int integer str(5) logical neg  c neg = .false.  int = intt if (int.lt.0) then int = int * -1 neg = .true. endif  do 100 i = 5,1,-1 + str(i) = mod(int,10) + ichar('0')7 int = int / 10100 continue i = 1 3 do while (i .lt.5.and.str(i).eq.ichar('0'))  str(i) = ichar(' ')  i = i+1 enddoe if (neg) then( str(i-1) = ichar('-') endif( call adeout(5,str) return endc subroutine aout(int,str) integer out(86)4 character*85 str   do j = 1,85  out(j) = ichar(' ')' enddo  i = 0  do 100 j = 1,int i = i + 1q" out(i) = ichar(str(i:i))100 continue call adeout(i,out) return end. o subroutine vt100(iterm)  o call alfmod  if (iterm.eq.2) then write(6,1001) 24a endif. if (iterm.eq.3) then% write(6,1002) 27,'%','!',2i write(6,1003) 27,'K' endif 1001 format('+',a1,$)1002 format('+',3a1,i1,$)1003 format('+',2a1,$)  return end   subroutine tek(iterm)e  if (iterm.eq.3) then$ write(6,111) 27,'%','!',0$ write(6,111) 27,'K','A',0" write(6,112) 27,'L','Z'$ write(6,111) 27,'M','G',0 endif4 if (iterm.eq.2) then write(6,222) 28 endif111 format('+',3a1,i1)112 format('+',3a1) 222 format('+',a1) return end  - subroutine vector (i,j,vopt,vinc,ina)  include 'rfd.inc'v real x1,x2,y1,y2 ) do while (i+2.le.j)  j = j - 1 i = i + 1> if (v(i,j)+v(j,n+i).gt.vopt+vinc.or.mark(i,j)) then# if (flag.ge.ina) thenv x2 = float(j+1)" y2 = float(n+2-i)" call movea(x1,y1)" call drawa(x2,y2) endif  flag = 0 else flag = flag + 1 ! if (flag.eq.1) then  x1 = float(j)" y1 = float(n+1-i) endif endif enddo  if (flag.ge.ina) then  x2 = float(j+1) y2 = float(n+2-i) call movea(x1,y1) call drawa(x2,y2) endifo return end *[MFOLD]EFN.FOR;1+,.N/ 4ONM-*0123KPWON56h7Ƌi89GHJ=c Program efn - RNA folding energy function for linear or c circular RNAc9c Input - a CT file containing one or more structures7c - energy files : stack.???, tstack.??? etc.;c Output - the energy of each of the foldings according$c to the input datasetsCc - optional lineprinter output and REGion table output:c Objective - this program serves as a check on energy0c calculations performed by lrnaCc - energies can be calculated according to different1c rules (e.g. temperature change)c include 'efn.inc' real energy character*1 ans logical flag,circular data circular/.false./ c Linear or circular RNA  write(6,1005)@1005 format(' Linear or circular RNA ? (L [default] or C) : '$) read(5,1007) ans1007 format(a1)6 if (ans.eq.'C'.or.ans.eq.'c') circular = .true. =c Initial setup for run : get CT file name and open file. 5 write(6,1010)91010 format(' Enter CT file name (default=fold.ct) : '$) read(5,1020,end=999) ctnam1020 format(a50)O open(unit=7,file=ctnam,defaultfile='fold.ct',readonly,status='old',err=5) iter = 0c&c Determine output specifications.c call outputscc Read energy informationc call enefiles call erg(1,0,0,0,0)cc Read foldings one by one.c$10 read(7,1030,end=999) n,ctlabel1030 format(i5,a50) do i = 1,n basepr(i) = 0 enddo do i = 1,nB read(7,1040,end=998,err=997) k,seq(i),basepr(i),hstnum(i)!1040 format(i5,1x,a1,13x,2i5) if (i.ne.k) go to 9972 if (basepr(i).gt.0) basepr(basepr(i)) = i enddo iter = iter + 1c*c Process sequence to find base types.c call processcc Double up if circularc if (circular) then do i = 1,n basepr(i+n) = 0 seq(i+n) = seq(i)! force(i+n) = force(i)# hstnum(i+n) = hstnum(i)# numseq(i+n) = numseq(i) enddo endifcc Compute energy of foldingc if (circular) thenc2c Find a base pair that closes a hairpin loop.c First find a base pair.c i = 1- do while (basepr(i).eq.0.and.i.le.n) i = i + 1 enddo if (i.gt.n) thencc No structure !c& write(6,1050) iter,ctlabel<1050 format(' ',i5,'. ',a50/' No structure found.'/) go to 10 endifc flag = .false. do while (.not.flag) j = i + 18 do while (basepr(j).eq.0.and.j.lt.basepr(i)) j = j + 1 enddo# if(j.eq.basepr(i)) then flag = .true. else i = j endif enddoc&c i.basepr(i) close a hairpin loopc/ energy = float(erg(4,i,basepr(i),i,i))c<c Circular permutation of structure : start at basepr(i)c do j = 1,i$ if (basepr(j).gt.0) then' if (basepr(j).lt.i) then- basepr(n+j) = basepr(j) + n- basepr(n+basepr(j)) = n + j else+ basepr(basepr(j)) = n + j) basepr(n+j) = basepr(j) endif endif enddo( call efn(nergy,basepr(i),n+i,0)0 energy = ( energy + float(nergy) )/10.0cc Restore foldingc do j = n + 1,n + i8 if(basepr(j).le.n) basepr(basepr(j)) = j - n enddo elsecc linear moleculec call efn(nergy,1,n,1)# energy = float(nergy)/10.0c endifc' write(6,2010) iter,ctlabel,energy:2010 format(' ',i5,'. ',a50/' Computed energy = ',f8.1/)cc Line printer output.cN if(cntrl(2).eq.1.or.cntrl(2).eq.3) call linout(1,n,energy,iret,jret,err)cc Region table output.c# if(cntrl(2).gt.1) call regtabcc Read next structurec go to 10cc Error in CT file.c997 write(6,9080)"9080 format(' Error in CT file.') stopc!c Error - incomplete CT file.c998 write(6,9090)*9090 format(' Premature end of CT file.')c 999 stop end & subroutine efn(e,ii,ji,ext_open) include 'efn.inc' e = 0 error = 0  call initst! call push(ii,ji,ext_open,0) 100 stz = pull(i,j,open,null) if (stz.ne.0) return ,c Do I and J base-pair with one another?" if (basepr(i).eq.j) goto 300  if (open.eq.0) then 7 do while (basepr(i).eq.0.and.basepr(i+1).eq.0)*c Whittle away from the 5' end. i = i + 1 e = e+eparam(6)# if (i.ge.j-1) goto 100 enddo7 do while (basepr(j).eq.0.and.basepr(j-1).eq.0)*c Whittle away from the 3' end. j = j - 1 e = e+eparam(6)# if (i.ge.j-1) goto 100 enddo 8 if (basepr(i).eq.0.and.basepr(i+1).gt.i+1) then"c I dangles over I+1,J.C e = e + min0(0,erg(6,basepr(i+1),i+1,i,2)) + eparam(6) i = i + 1 endifM if (basepr(j).eq.0.and.basepr(j-1).ne.0.and.basepr(j-1).lt.j-1) then"c J dangles over I,J-1.C e = e + min0(0,erg(6,j-1,basepr(j-1),j,1)) + eparam(6) j = j - 1 endif else 7 do while (basepr(i).eq.0.and.basepr(i+1).eq.0)*c Whittle away from the 5' end. i = i + 1# if (i.ge.j-1) goto 100 enddo7 do while (basepr(j).eq.0.and.basepr(j-1).eq.0)*c Whittle away from the 3' end. j = j - 1# if (i.ge.j-1) goto 100 enddo 8 if (basepr(i).eq.0.and.basepr(i+1).gt.i+1) then"c I dangles over I+1,J.7 e = e + min0(0,erg(6,basepr(i+1),i+1,i,2)) i = i + 1 endifM if (basepr(j).eq.0.and.basepr(j-1).ne.0.and.basepr(j-1).lt.j-1) then"c J dangles over I,J-1.7 e = e + min0(0,erg(6,j-1,basepr(j-1),j,1)) j = j - 1 endif endif  if (basepr(i).ne.j) thenHc Cannot chop away at the ends any more and still the ends do notDc base-pair with one another. Structure MUST bifucate (OPEN). k = basepr(i) kp = basepr(j) if (k .ge. kp) then error = 50, write (6,*) 'ERROR - KNOT FOUND' e = infinity return endif# if (basepr(k+1).ne.0) then! call push(i,k,open,0)# call push(k+1,j,open,0)' elseif (basepr(k+2).eq.0) then# call push(i,k+1,open,0)# call push(k+2,j,open,0)G elseif (erg(6,k,i,k+1,1).le.erg(6,basepr(k+2),k+2,k+1,2)) then# call push(i,k+1,open,0)# call push(k+2,j,open,0) else! call push(i,k,open,0)# call push(k+1,j,open,0) endif goto 100 endifc;c Add penalty for accessible base pair in a multi=loop.c&300 if(open.eq.0) e = e + eparam(10)310 open = 0 &c Perhaps I,J stacks over I+1,J-1?" if (basepr(i+1).eq.j-1) then# e = e + erg(2,i,j,i+1,j-1) i = i ++>fQ~ MFOLD.BCK*[MFOLD]EFN.FOR;1ON"| 1 j = j - 1 goto 310 endif sum = 0 k = i + 1 do while (k.lt.j)! if (basepr(k).gt.k) then sum = sum + 1 ip = k k = basepr(k) + 1 jp = k - 1 if (k.gt.j) then" write (6,*) 'ERROR' error = 51 e = infinity return endif% elseif (basepr(k).eq.0) then k = k + 1 endif enddo  if (sum.eq.0) then e = e + erg(4,i,j,i,j)  goto 100R elseif (sum.eq.1) then! e = e + erg(3,i,j,ip,jp) i = ipn j = jpk goto 310c else is = i+1f js = j-1g' e = e + eparam(5) + eparam(10) 8 if (basepr(i+1).eq.0.and.basepr(i+2).ne.0) thenF if (erg(6,i,j,i+1,1).le.erg(6,basepr(i+2),i+2,i+1,2)) then is = i+2 ; e = e + min0(0,erg(6,i,j,i+1,1)) + eparam(6)c endifc endif8 if (basepr(i+1).eq.0.and.basepr(i+2).eq.0) then is = i+28 e = e + min0(0,erg(6,i,j,i+1,1)) + eparam(6) endif8 if (basepr(j-1).eq.0.and.basepr(j-2).ne.0) thenF if (erg(6,i,j,j-1,2).le.erg(6,j-2,basepr(j-2),j-1,1)) then js = j-2); e = e + min0(0,erg(6,i,j,j-1,2)) + eparam(6)n endif' endif8 if (basepr(j-1).eq.0.and.basepr(j-2).eq.0) then js = j-28 e = e + min0(0,erg(6,i,j,j-1,2)) + eparam(6) endif call push (is,js,0,0) goto 100m endif end= i c mc Energy funtion.r@c ERG is the energy of a loop closed by I,J (new numbering).>c IP,JP is the other closing base-pair when MODE = 2 or 3.Fc The ends of the sequence cannot be contained in a hairpin, bulgeCc or interior loop. By convention, the ends of the sequence are)Bc put into a special kind of multi-loop. This can be called an*c exterior loop or an open multi-loop.c c 1/2 Asym. loop correction 3c Extrapolate loops with dG(n)=dG(30)+1.75*ln(n/30)1cx(c* Hairpins of 3 have no terminal stack.c " function erg(mode,i,j,ip,jp) include 'efn.inc'  integer*2 tlink,tlptr cr s100 if (mode.eq.1) thenec Read energy files. call ergread erg = 0  return endif  d erg = 0  - goto (100,200,300,400,500,600,700),modeq &c Nucleotide accessibility option./200 if (force(i).eq.3.or.force(jp).eq.3) thenu erg = infinity  return endifc Stacking energy.B erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp)) . + eparam(1) return bc c Interior or bulge loop. c 300 size1 = ip - i - 1 size2 = j - jp - 1( if (size1.eq.0.or.size2.eq.0) then-c Check for nucleotide accessibility. 0 if (size1.eq.0.and.force(i).eq.3) then erg = infinityr return  endif1 if (size2.eq.0.and.force(jp).eq.3) then  erg = infinity  return  endife size = size1+size2c Bulge loop energy. if (size.eq.1) then I erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))e- . + bulge(size) + eparam(2) " elseif (size.gt.30) then9 loginc = int(prelog*log((float(size)/30.0)))e7 erg = erg + bulge(30) + loginc + eparam(2)  else0 erg = erg + bulge(size) + eparam(2) endifn return else size = size1+size2% lopsid = abs((size1-size2)) c Interior loop. if (size.gt.30) then9 loginc = int(prelog*log((float(size)/30.0))) J erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))E . + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))g. . + inter(30) + loginc + eparam(3)A . + min0(maxpen,(lopsid*poppen(min0(4,size1,size2))))s elseJ erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))E . + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))g' . + inter(size) + eparam(3)tA . + min0(maxpen,(lopsid*poppen(min0(4,size1,size2))))p endif8 return endift .cc Hairpin loop.qco400 size = j-i-1 if (size.eq.3) thene"c Check for closed excisionI if(seq(i+1).eq.' '.and.seq(i+2).eq.' '.and.seq(i+3).eq.' ') then erg = eparam(9)  return endif endif0 if (size.gt.30) then5 loginc = int(prelog*log((float(size)/30.0)))F erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))2 . + hairpin(30) + loginc + eparam(4) else if (size .lt. 4) thencn c* Special case for hairpin of 3c . erg = erg + hairpin(size) + eparam(4) elsec tlink=0 if (size.eq.4) thenI key=((numseq(i+4)*8+numseq(i+3))*8+numseq(i+2))*8+numseq(i+1)  tlptr=1oI do while ((tlptr.le.numoftloops).and.(tloop(tlptr,1).ne.key)). tlptr=tlptr+1 enddoa: if (tlptr.le.numoftloops) tlink=tloop(tlptr,2) endifC erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1)) 3 . + hairpin(size) + eparam(4) + tlinkW endifr returnc c This is impossible. c '500 stop ' Impossible option in erg.'. )Gc Dangling base stacking energy. IP dangles over the I,J base-pair.12c 3' or 5' dangle if JP = 1 or 2 respectively.;600 erg = erg + dangle(numseq(i),numseq(j),numseq(ip),jp)r return /700 if (force(i).eq.3.or.force(jp).eq.3) then( erg = infinitye return) endif(c Terminal stack or mismatch energy.A erg = erg + tstk(numseq(i),numseq(j),numseq(ip),numseq(jp)) return end   subroutine process(c Process RNA sequence to be folded. include 'efn.inc' Dc Selected fragment is from hstnum(1) to hstnum(n) in historical1c numbering. ( 1 to n in internal numbering )   do k = 1,n7c Bases are examined to determine their type.mc A - type 14c B - an A accessible to nuclease cleavagec C - type 23c Z - a C accessible to nuclease cleavage c G - type 33c H - a G accessible to nuclease cleavage1c U/T - type 47c V/W - a U/T accessible to nuclease cleavagen"c anything else - type 5*c NUMSEQ stores nucleotide type. numseq(k) = 5m force(k) = 0. if (seq(k) .eq. 'A') numseq(k) = 1% if (seq(k) .eq. 'B') then. numseq(k) = 1 force(k) = 3a endifo. if (seq(k) .eq. 'C') numseq(k) = 2% if (seq(k) .eq. 'Z') then= numseq(k) = 2 force(k) = 3p endif . if (seq(k) .eq. 'G') numseq(k) = 3% if (seq(k) .eq. 'H') then  numseq(k) = 3 force(k) = 3. endif ? if (seq(k) .eq. 'U'.or.seq(k).eq.'T') numseq(k) = 4 6 if (seq(k) .eq. 'V'.or.seq(k).eq.'W') then numseq(k) = 4 force(k) = 3 endifg enddo. return endk 2 t'c Used in reading the energy files. function convt(str), implicit integer (a-z) character*5 str, logical neg  a neg = .false. place = 0 convt = 0  do i = 5,1,-1 ! if (str(i:i).eq.'-') thenr neg = .true. else7 if (str(i:i).ge.'0'.and.str(i:i).le.'9') thenpG convt = convt + 10**place * (ichar(str(i:i)) - ichar('0'))e place = place+1 endif endif- enddog! if (neg) convt = convt * -1u return end =c Reads energy file names and open the files for reading.  subroutine enefiles  character*40 filen F10 write (6,*) 'Enter dangle energy file name (default dangle.dat)' read (5,100,end=1) filenF open(10,file=filen,defaultfile='DANGLE.DAT',status='OLD',err=10) B20 write (6,*) 'Enter loop energy file name (default loop.dat)' read (5,100,end=1) filenD open(11,file=filen,defaultfile='LOOP.DAT',status='OLD',err=20) gD30 write (6,*) 'Enter stack energy file name (default stack.dat)' read (5,100,end=1) filenE open(12,file=filen,defaultfile='STACK.DAT',status='OLD',err=30)  iF40 write (6,*) 'Enter tstack energy file name (default tstack.dat)' read (5,100,end=1) filenF open(13,file=filen,defaultfile='TSTACK.DAT',status='OLD',err=40) iD50 write (6,*) 'Enter tloop energy file name (default tloop.dat)' read (5,100,end=1) filenE open(29,file=filen,defaultfile='Tloop.DAT',status='OLD',err=50). nL60 write (6,*) 'Enter misc. loop energy file name (default miscloop.dat)' read (5,100,end=1) filenH open(32,file=filen,defaultfile='miscloop.DAT',status='OLD',err=60) 100 format(a40)- goto 21 call exit- 2 return end  c Initialize the stack.+ subroutine initst  implicit integer (a-z) dimension stk(50,4)  common /stk/ stk,spa r sp = 0 return end-c Add A,B,C,D to the bottom of the stack.e subroutine push(a,b,c,d) implicit integer (a-z) dimension stk(50,4)  common /stk/ stk,sp   sp = sp + 1  if (sp.gt.50) then- write (6,*) 'ERROR - STACK OVERFLOW'J stopc endifa stk(sp,1) = a. stk(sp,2) = bh stk(sp,3) = cc stk(sp,4) = d, return end Dc Retrieve A,B,C,D from the bottom of the stack and decrease thec stack size by one. function pull(a,b,c,d) implicit integer (a-z) dimension stk(50,4)p common /stk/ stk,sp  p if (sp.eq.0) thenl pull = 1i returno endifc a = stk(sp,1)n b = stk(sp,2) c = stk(sp,3)c d = stk(sp,4)l sp = sp - 1 pull = 0 return ende g i3c Line printer output of a secondary structure. 5 subroutine linout(n1,n2,energy,iret,jret,error)oc0 include 'efn.inc')( character array(6,900),dash,bl,dot real energy( integer unitcj/ data dash/'-'/,bl/' '/,dot/'.'/,amax/900/ ct&c WRITE SEQUENCE LABEL AND ENERGYc unit = cntrl(4)( hstn1 = hstnum(n1) hstn2 = hstnum(n2)0 write(unit,103) hstn1,hstn2,ctlabel,energycec INITIALIZE TRACEBACK ci call initst  call push(n1,n2,0,0) nstem = 0o go to 3hc"c OUTPUT PORTION OF STRUCTUREci5 do while (1.eq.1)e write(unit,106) ll = countr) if(cntrl(3).lt.ll) ll = cntrl(3)  do k = 1,6f@ if(unit.eq.6) write(unit,105) (array(k,i),i = 1,ll)@ if(unit.ne.6) write(unit,104) (array(k,i),i = 1,ll) enddo' if(countr.le.cntrl(3)) go to 3e do k = 1,5  do j = 1,6 array(j,k) = bl array(j,k+5) = bl enddo2 array(2,k+5) = dot array(5,k+5) = dot enddo k = 10e ll = cntrl(3)+1 do i = ll,countrm k = k+1 do j = 1,6g$ array(j,k) = array(j,i) enddo enddo countr = ks enddo c 3 do k = 1,amaxe do j = 1,6 array(j,k) = bl enddo0 enddo c c FILL IN OUTPUT MATRIXc(! nstem = pull(i,j,countr,xx)e if (nstem.ne.0) returncsc LOOK FOR DANGLING ENDS c 12 ip = i jp = j do while (basepr(ip).eq.0) ip = ip+1 if(ip.ge.j) go to 16 enddom do while (basepr(jp).eq.0) jp = jp-1 enddo  k = ip-i if(j-jp.gt.k) k = j-jp if(k.eq.0) go to 17 ii = ipk jj = jps pos = countr+k+1 if(pos.gt.amax) then error = 21 return endif, do kk = 1,k( pos = pos-1 ii = ii-1 jj = jj+1 if(ii.ge.i) theni i2 = hstnum(ii)i" array(2,pos) = seq(ii)@ if(10*(i2/10).eq.i2) call digit(1,i2,pos,amax,array) elsen array(2,pos) = dash  endif if(jj.le.j) then  j2 = hstnum(jj) " array(5,pos) = seq(jj)@ if(10*(j2/10).eq.j2) call digit(6,j2,pos,amax,array) else, array(5,pos) = dash) endif enddo0 countr = countr+k  go to 17clc HAIRPIN LOOPecl16 if(i.ge.j) go to 5 half = (j-i+2)/2 ii = i-1 jj = j+1 do k = 1,halfi ii = ii+1 jj = jj-1 countr = countr+1 if(countr.gt.amax) then error = 21 return endif$ if(seq(ii).eq.' ') go to 40 i2 = hstnum(ii) j2 = hstnum(jj)M if(10*(i2/10).eq.i2.and.ii.lt.jj) call digit(1,i2,countr,amax,array)d@ if(10*(j2/10).eq.j2) call digit(6,j2,countr,amax,array) if(k.ne.half) thenr% array(2,countr) = seq(ii)n% array(5,countr) = seq(jj)m else2 if(ii.lt.jj) array(3,countr) = seq(ii)% array(4,countr) = seq(jj)e endif 22 enddo go to 5nc c 'CLOSED' EXCISION FOUNDc 40 array(3,countr) = dash array(4,countr) = dash go to 50c c STACKING OR BIFURCATIONc) 17 i = ip j = jp! if(basepr(i).eq.j) go to 24c c CHECK FOR KNOTictI if(basepr(i).ge.basepr(j).or.i.ge.basepr(i).or.basepr(j).ge.j) then) iret = hstnum(i) ! jret = hstnum(basepr(i))  error = 20e return endifecic BIFURCATION MUST OCCURsco countr = countr+2i if(countr.gt.amax) then( error = 21u return endifn' call push(basepr(i)+1,j,countr,0)m j = basepr(i) c c STACKING REGIONc 24 countr = countr+1c if(countr.gt.amax) then  error = 21  returnt endife ii = hstnum(i) jj = hstnum(j) array(3,countr) = seq(i) array(4,countr) = seq(j)= if(10*(ii/10).eq.ii) call digit(1,ii,countr,amax,array) = if(10*(jj/10).eq.jj) call digit(6,jj,countr,amax,array)l& if(i.eq.iret.and.j.eq.jret) then array(2,countr) = '|' array(5,countr) = '^' end if i = i+1e j = j-1t if(basepr(i)-j) 12,24,12 L103 format(' FOLDING BASES ',i4,' TO ',i4,' OF ',a50,/' ENERGY = ',f8.1)104 format(220a1) 105 format(' ',220a1) 106 format(' ') ende )Fc Puts the number COLUMN in row ROW and column POS of the array B.Fc The least significant digit ends up in column POS. If the numberEc is too large to fit, a period is put in column POS and row ROW. - subroutine digit(row,column,pos,bmax,b)k implicit integer (a-z)# integer pos,column,bmax,d(10).( character*1 b(6,bmax),bl,c(10),dotF data bl/' '/,c/'0','1','2','3','4','5','6','7','8','9'/,dot/'.'/cu size=1 n=column 1 p=n/10 q=n-10*p d(size)=qi if(p.eq.0) go to 2 n=pr size=size+1c go to 1 2 if(pos-size.lt.0) go to 3f do k=1,size  q=pos-k+1# if(b(row,q).ne.bl) go to 3 enddoe p=pos do 4 k=1,size. q=d(k) b(row,p)=c(q+1)) 4 p=p-1t return3 b(row,pos)=dot return end* cGc Generates a region table for the Shapiro and Maizel DRAW program.i subroutine regtab  include 'efn.inc'n real r k = 1 region = 1 do while (k.lt.n)e r = 0.0 regsz = 1 kst = k! if (k.lt.basepr(k)) then ; do while (basepr(k+1).eq.basepr(k)-1.and.k.lt.n)a regsz = regsz + 1=F r = r + float(erg(2,k,basepr(k),k+1,basepr(k+1))) / 10.0 k = k + 1  enddoH write (22,100) region,hstnum(kst),hstnum(basepr(kst)),regsz,r region = region + 1 endif k = k + 1 enddo return k*100 format(' (',i5,')',3x,3(i5,3x),f8.1) end0 n4c Set up output units and files for RNA folding. subroutine outputs include 'efn.inc'  character*40 str,dstre eAc Examine CT file name to get default names for output files.i f k = 1i= do while ((ctnam(k:k).lt.'A'.or.ctnam(k:k).gt.'Z').and.t9 . (ctnam(k:k).lt.'a'.or.ctnam(k:k).gt.'z'))( k = k + 1 enddo, slen = min0(30,25+k)( do while (ctnam(slen:slen).eq.' ') slen = slen - 1 enddo j = 1  do i = k,slen : if ((ctnam(i:i).ge.'A'.and.ctnam(i:i).le.'Z').or.: . (ctnam(i:i).ge.'a'.and.ctnam(i:i).le.'z').or.< . (ctnam(i:i).ge.'0'.and.ctnam(i:i).le.'9')) then " dstr(j:j) = ctnam(i:i) elses dstr(j:j) = '_'- endif j = j + 1 enddo/ slen = j <c Line printer output. Get name and open file for write. rewind(5)e cntrl(2) = 0 write (6,5010) read (5,5000,end=1) in' if (in.ne.'N'.and.in.ne.'n') thenk cntrl(2) = 1 write (6,5011) read (5,5000,end=1) in* if (in.eq.'N'.or.in.eq.'n') then) dstr(slen+1:slen+4) = '.OUT' 51 write (6,5012) dstr read (5,5001) str cntrl(4) = 208 open(20,file=str,defaultfile=dstr,recl=255,= . status='NEW',err=51,carriagecontrol='LIST')t else cntrl(4) = 6 endif/ write (6,5013)& read (5,5014,end=1) cntrl(3)+ if (cntrl(3).eq. 0) cntrl(3) = 80n endift p<c Region table output. Get name and open file for write. write (6,5030) read (5,5000,end=1) in& if (in.eq.'Y'.or.in.eq.'y') then cntrl(2) = cntrl(2) + 2% dstr(slen+1:slen+4) = '.REG'o53 write (6,5031) dstr read (5,5001) strO open(22,file=str,defaultfile=dstr,status='NEW',carriagecontrol='LIST')b endif' write (6,*) ' ' return1 call exitY5000 format(a1)5001 format(a40)s55010 format(' Do you want printer output? (Y,n) ',$)(-5011 format(' Output to terminal? (Y,n) ',$) 95012 format(' Enter output file name (default ',a35,')')pD5013 format(' Enter number of columns on printer (default 80) ',$)5014 format(i10)35030 format(' Do you want region table? (y,N) ',$))?5031 format(' Enter region table file name (default ',a35,')') endd c Reads energy files.t subroutine ergread ( include 'efn.inc'  logical endfile character*80 inrec character*5 temp real a,b,c,d rc TLoop INFORMATION IN call gettloops jc Get misc loop info? if(find(32,3,' > ')) stop 'Premature end of MISCLOOP.DAT'2 read (32,*) prelog prelog=prelog*10 endfile = find(32,3,' > ') read (32,*) a  maxpen=int(a*10) endfile = find(32,3,' > ') read (32,*) a,b,c,d  poppen(1)=int(a*10)k poppen(2)=int(b*10)e poppen(3)=int(c*10)  poppen(4)=int(d*10) endfile = find(32,3,' > ') read (32,*) a,b,cr eparam(5)=int(a*10)0 eparam(6)=int(b*10)F eparam(10)=int(c*10) c DANGLE INc t do a = 1,5 do b = 1,5 do c = 1,5 do d = 1,2( dangle(a,b,c,d) = infinity enddo  enddo enddo) enddo endfile = find(10,3,'<--') if (.not.endfile) then do var4 = 1,2 do var1 = 1,4 $ if (endfile) goto 150) read(10,100,end=150) inrec  do var2 = 1,4 do var3 = 1,4  j = 0: tstart = (var2-1)*20 + (var3-1)*5 + 12 temp = inrec(tstart:tstart+4) do i = 2,4 @ if (temp(i-1:i+1).eq.' . ') j = infinity enddoK if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') j = infinity 0 if (j.eq.0) j = convt(temp)4 dangle(var1,var2,var3,var4) = j enddo( enddo) endfile = find(10,3,'<--')d enddof enddo else; write (6,*) 'ERROR - DANGLE ENERGY FILE NOT FOUND'6 stopg endif  f100 format(a80)  goto 200 =?150 write (6,*) 'ERROR - PREMATURE END OF DANGLE ENERGY FILE'1 stop t "c INTERNAL,BULGE AND HAIRPIN IN h"200 endfile = find(11,5,'-----') i = 1 201 read(11,100,end=300) inrec j = -1 do ii = 1,3s j = j + 6% do while (inrec(j:j).eq.' ')e j = j + 1  enddo temp = inrec(j:j+4) k = 0 do jj = 2,46 if (temp(jj-1:jj+1).eq.' . ') k = infinity enddo? if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') k = infinity$ if (k.eq.0) k = convt(temp)" if (ii.eq.1) inter(i) = k" if (ii.eq.2) bulge(i) = k$ if (ii.eq.3) hairpin(i) = k enddoX i = i + 1 if (i.le.30) goto 201 c STACK IN 300 do a = 1,5 do b = 1,5 do c = 1,5 do d = 1,5' stack(a,b,c,d) = infinity enddoR enddo enddo. enddoi endfile = find(12,3,'<--') if (.not.endfile) then do var1 = 1,4 do var3 = 1,4r$ if (endfile) goto 350) read(12,100,end=350) inrec do var2 = 1,4 do var4 = 1,4  j = 0: tstart = (var2-1)*20 + (var4-1)*5 + 12 temp = inrec(tstart:tstart+4) do i = 2,4 @ if (temp(i-1:i+1).eq.' . ') j = infinity enddoK if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') j = infinity,0 if (j.eq.0) j = convt(temp)3 stack(var1,var2,var3,var4) = jq enddot enddo enddoe& endfile = find(12,3,'<--') enddo else: write (6,*) 'ERROR - STACK ENERGY FILE NOT FOUND' stopj endif call stest(stack,'STACK ')  goto 400 />350 write (6,*) 'ERROR - PREMATURE END OF STACK ENERGY FILE' stop m400 do a = 1,5 do b = 1,5 do c = 1,5 do d = 1,5& tstk(a,b,c,d) = infinity enddoc enddo enddos enddo endfile = find(13,3,'<--') if (.not.endfile) then do var1 = 1,4 do var3 = 1,4t$ if (endfile) goto 350) read(13,100,end=450) inrecc do var2 = 1,4 do var4 = 1,4' j = 0: tstart = (var2-1)*20 + (var4-1)*5 + 12 temp = inrec(tstart:tstart+4) do i = 2,4@ if (temp(i-1:i+1).eq.' . ') j = infinity enddoK if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') j = infinity(0 if (j.eq.0) j = convt(temp)2 tstk(var1,var2,var3,var4) = j enddoe enddo enddoW& endfile = find(13,3,'<--') enddo else: write (6,*) 'ERROR - STACK ENERGY FILE NOT FOUND' stop endifc** CALL STEST(TSTK,'TSTACK')=  close(10). close(11) close(12)l close(13). goto 500 t?450 write (6,*) 'ERROR - PREMATURE END OF TSTACK ENERGY FILE'a stop r 500 return end0?c Symmetry test on stacking and terminal stacking energies.(@c For all i,j,k,l between 1 and 4, STACK(i,j,k,l) MUST equalBc STACK(l,k,j,i). If this fails at some i,j,k,l; these numbers@c are printed out and the programs grinds to an abrupt halt!# subroutine stest(stack,sname)n$ integer stack(5,5,5,5),a,b,c,d character*6 sname  l do a = 1,4 do b = 1,4 do c = 1,4 do d = 1,48 if (stack(a,b,c,d).ne.stack(d,c,b,a)) then- write (6,*) 'SYMMETRY ERROR'Z; write (6,101) sname,a,b,c,d,stack(a,b,c,d).; write (6,101) sname,d,c,b,a,stack(d,c,b,a)0 stop( endif  enddo  enddon enddo enddoi return/101 format(5x,a6,'(',3(i1,','),i1,') = ',i10)Z end  Ic Writes out the numbers in the energy arrays of the folding program.) subroutine out(u). include 'efn.inc' $ integer*2 tlptr,key,bptr,nbase character*4 tlbuf  _5c used for testing contents of energy arrays only $c not used in the mature program u write (u,100) 'DANGLE' do var4 = 1,25 do var1 = 1,4 do var2 = 1,4  do var3 = 1,4 . o = dangle(var1,var2,var3,var4)& if (o.ne.infinity) then! write (u,101) o elseN write (u,102)  endif enddo  enddo  write (6,103)5 enddo  write (6,104) enddoo ( f write (u,100) 'TSTACK' do var1 = 1,4  do var3 = 1,4a do var2 = 1,4  do var4 = 1,4c, o = tstk(var1,var2,var3,var4)& if (o.ne.infinity) then! write (u,101) oe else write (u,102)b endif enddot enddo6 write (6,103)0 enddo  write (6,104)q enddo   write (u,100) 'STACK'  do var1 = 1,4e do var3 = 1,4  do var2 = 1,4  do var4 = 1,4 - o = stack(var1,var2,var3,var4)N& if (o.ne.infinity) then! write (u,101) oe elseY write (u,102)a endif enddoo enddo( write (6,103)o enddo) write (6,104)E enddoi n- write (u,200) 'INTER','BULGE','HAIRPIN'n do i = 1,30 4 write (u,201) i,inter(i),bulge(i),hairpin(i) enddoo a write (u,100) 'TLoops' do tlptr=1,numoftloops key=tloop(tlptr,1) do bptr=1,4 nbase=mod(key,8) key=int(key/8) if (nbase.eq.1) then# tlbuf(bptr:bptr)='A'0$ elseif (nbase.eq.2) then# tlbuf(bptr:bptr)='C'T$ elseif (nbase.eq.3) then# tlbuf(bptr:bptr)='G'2 else# tlbuf(bptr:bptr)='U'  endif enddo( write (u,205) tlbuf,tloop(tlptr,2) enddo( return100 format(//,a40,//) 101 format('+',i4,1x,$)102 format('+',4('*'),1x,$) 103 format(' ')0104 format(/)2200 format(3a20,/,60('-'),/)201 format(i4,i16,2i20)n205 format(a4,2x,i8) end, 'c Used in reading the energy files.mBc Locates markers in the energy files so that data can be readc properly.G! function find(unit,len,str)  implicit integer (a-z) logical find,flag1 character*20 str character*80 inrec  find = .false. flag = .false. do while(.not.flag)% read(unit,100,end=200) inrecd count = 1 do 101 i = 1,80-len+13 if (inrec(i:i).eq.str(count:count)) then  count = count + 1, if (count.gt.len) flag = .true.> if (inrec(i+1:i+1).ne.str(count:count)) count = 1 endif101 continuer enddo  return100 format(a80)t200 find = .true. return end   subroutine gettloopsci8c* Read in TLoop sequences, convert to numeric form, and%c* convert energy to an integer (*10).ct( parameter (maxtloops=40,bufsiz=80)0 integer*2 i,ptr,tloop(maxtloops,2),nseq(4) integer*2 numoftloops,fptr integer*2 convt  character*5 buffa  character*80 inbufce& common /tloops/tloop,numoftloopsc  numoftloops=0lcc* Throw out header'cO read (29,1)IcNCc* Read a line and convert to numeric sequence and energy until EOF co10 read (29,2,end=99) inbuf ptr=1E! numoftloops=numoftloops+1 & do while ((ptr.lt.bufsiz).and.+ 2 (inbuf(ptr:ptr).eq.' '))- ptr=ptr+1d enddo);c Only take first four characters, since they're TETRAloops# buffa(1:4)=inbuf(ptr:ptr+3)e buffa(5:5)=' ' call tonum(buffa,nseq)F tloop(numoftloops,1)=((nseq(4)*8+nseq(3))*8+nseq(2))*8+nseq(1) ptr=ptr+4.& do while ((ptr.lt.bufsiz).and.+ 2 (inbuf(ptr:ptr).eq.' '))k ptr=ptr+1k enddotc Simple error check..+ if (inbuf(ptr+4:ptr+4).ne.' ') theng! write (*,5) inbufr endif # buffa(1:4)=inbuf(ptr:ptr+3)( buffa(5:5)=' ') tloop(numoftloops,2)=convt(buffa)  do i=1,ptr+4 inbuf(i:i)=' ' enddo goto 10,c=c* Normal endingc "99 close(unit=29,status='KEEP') return1 format(//)2 format (a)J5 format (1x,'Too many characters in numeric field of this line of',/,& 1 1x,'tloop.dat file: ',a) end  ( subroutine tonum(tloopseq,numeric)c 1c* Convert TLoopSeq to numeric format in Numeric.,c character*5 tloopseq integer*2 i,numeric(4)cr do i=1,4* if (tloopseq(i:i).eq.'A') then numeric(i)=1* elseif (tloopseq(i:i).eq.'C') then numeric(i)=2* elseif (tloopseq(i:i).eq.'G') then numeric(i)=3* elseif (tloopseq(i:i).eq.'U') then numeric(i)=4* elseif (tloopseq(i:i).eq.'T') then numeric(i)=4 else) write (*,1) tloopseq(i:i) =1 format (1x,'Unknown base in TLOOP file: ',a1)d stop endif' enddo return end *[MFOLD]EFN.INC;1+,./ 4H-*0123KPWO56 h7gi89GHJ,~Go {{ mni>va;3jnS9|" +~=t~,!C:FaNz5m}Y tz5fr7)[3gDGG*0IRM!.(q?XT|VyLE D)(S\HU5ly&5 ֈ HI[啽C8!3G̞۟^DT &Tj5Me̬'^2:yUhN _o:89j*}^Ӝݪp=UT(i[ VڏmfUt7m3bfAC\(ěl4Xx\ix\ǹ0r@C98A2ypR \Fmݻo)/.&Pkkl(dѸ|Ct\BnT-g_$ࡼ`F@1`* 9)賦xqJ ~x+<!~w oP+E#{QSYví A֧F ._R|ʟ{>DՠӾfC%?N-Z޷5 S{DcSf+LIf;5M("/vhroh-O})!)߇9!GF tr녃} G2uOj(/ϩ[@T`uNIr:J&;y~K !\絑ޕVRx?b~/NfaNł,xT]s $멶`R*k;%G.BAo@.ͷd(ItNuA@Vv)~'jvm J7)Jy$W6/dAN<V\OZM[f*O[|jGkݫ Zz-obsܞL9sҵl;Ar{y"='cxrgzi9 +{yDLq|*4Y2Ԣe%|ТCє[l s:gJ˱Y(W $ '>6P q=:cC4K?Dȵחw}7T afקŘm 97NwV}oDP~ցs즬pZ8cMD[<,dmfҁmPG$/ Sclhn4~7Iݿ %(As}kN/(}A%bAd k@ywK84S/06LExOM/Ec҄ҕrR%\!{Yͨu8&w2IZzN) Mݓg>e0bp'! \/_"I.fA편B@ }szMF)@?k.v"lr9<% و4vSbfOX|(VP!"49<$j:y!60E _ >78u2@ӶpGu؆P/\P%-L2Ě/٫O&#mJݰ T{?2)?Xo+Տҟo~&,Sw-U(C|5dQܷgHXw逮0##K]%lⱎ? 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FigDot has no external subroutines'or functions, and can be compiled by... $FOR/nocheck figdot $link figdot$del figdot.obj;*/noconf Operation AUpper case is what the computer prints, lower case is your reply. C1) Make a energy dot plot dump file using LRNA or CRNA (see notes).? The only data FigDot will read from the file will be the TicA increment - it ignores the rest. For this example, assume the" file produced is called RNA.TRI 2) Run FigDot $r figdotINPUT TRIANGULAR FILE? rna.triOUTPUT FIGURE FILE? rna.figure F3) Make sure that the UWGCG enviroment has been set to the appropriateA graphics output device (for example TEK4014, QMS, etc..). For this example, assume TEK4014. 4) Run UWGCG's Figure program $figure/in=rna.figure =FIGURE makes figures and posters by drawing graphics and textDtogether. You can include output from other GCG graphics programs aspart of a figure. ) When the TEK4014 is ready, press . A4) (continued...) hit return. The plot will be displayed at your> terminal or sent to your plotter (depending on what you did for step 3). -John Jaeger January 1989.*[MFOLD]FIGDOT.EXE;2+,./ 4-*0123 KPWO564 i7T}i89GHJ0D`0205p i h FIGDOT01tp i05-09 z}  ?B!d FORRTL_001! LIBRTL_001This program only works for square dotplotsMatrix too big! Resize nmax and recompileFull matrix not implementedIHaf must be either 1 or 2!NDotplots are different sizes!Only square dotplots workMatrix too big!Triangular file name? )POutput Figure file name? .vp 20.455 129.545 100.0 0.0.wn .ls 1 30.m  0.d .d 0 0.d  0.m 0 0.d 0 .d .m .reld .m .pt .to .p .m .d Do you want a double dotplot+Change numbering on axes (currently 1..N)?  Graph start:. Enter new start.(Y,N) Default:->P PpPP +*;e  e TazAOx[~T E ~9 ' $ $ P     ? T? U? V? ? ? UV ߫D 2TPP ߫L  ߫Tx 1RTK I SR(2RPŏPW2SPWP?@ =RS =TRd ~ xP1kL~ Q~  ˀ{ P$  w t  i ?G ?= ?3 ?) ? ? " T ˠ%  ˨ 2PP ˰ ˸ bRTMW  SR'2RW2SPďPWP?@u =RS| =TRM q &~T E P=3~1 2~  ~ ?~u~PsMTWE>WPRPRRE@WSSuSlRc2T~M2T~C2T~92T~/@k4`62T~ 2T~2T~ UP2PPP2URRPPXXYTZfqYZ1,>2Y~\2\PP@ \2T~WYR2R~HE#= WSSC:;4E@ffW~MR~\R\ 2R\\L=RkD#p2Y~RS~KUY1 hqXZ1,b2X~4EY2YPP@ Yr)XU2U~E#= WSRS~>MU~EL>WPRP~YUY2UYYI =Uk@~2X~T2T~JMS@EVX1TW1XW12WZďZ2XVZVF1VVXP2PPVWS2SSďSSP@ @VԷV,\2W~2X~E<2W~{2X~qVWP2P~cXV2V~Vg=WXA=W%k1TW1TW12WX2TZďZXZJ1ZZWP2PPZTV2VVďVVP@ @ZԷZ,p2T~2W~FP2T~2W~ZTP2P~wZWZ2Z~iz=WT<=W$CP߫\fH[}PQ Z1kR  TYTT3~0TYTTY N1tЫPH[}PQ}PQ  P QQPQQPP @@(@8  @FORRTLLIBRTL DOTFILTER DOTFILTER ?ԻԺ %  YESSIR YESSIR UPCASE UPCASE  F*[MFOLD]FIGDOT.FOR;5+,./ 4H-*0123KPWO564 i7ri89GHJ program dotfilter*B** Take a energy dot plot dump file from LRNA or CRNA and reformat@** (sic) as a file for UWGCG's FIGURE program. This program has** no external calls.*B** note that matrix is a little different: j goes left to right in+** drawing, and i goes up - down in drawing* parameter (nmax=700); integer*2 n,nit,njt,ihaf,iclr,mode,m(nmax,nmax),i,j,x5 integer*2 n2,nit2,njt2,ihaf2,iclr2,mode2,istart integer*2 start,k,ticstart2 character*80 trifile1,trifile2,figfile,inbuf character*4 label logical double,yessir data double/.false./*** open file, get data*10 write (*,1) read (*,2) trifile1/ open (unit=10,file=trifile1,status='old',* 1 carriagecontrol='list',err=10) read (10,2) inbuf* read (10,6) n,nit,njt,ihaf,iclr,mode*H if (nit.ne.njt) stop 'This program only works for square dotplots'F if (n.gt.nmax) stop 'Matrix too big! Resize nmax and recompile'* if (ihaf.eq.1) then* stop 'Full matrix not implemented' else if (ihaf.eq.2) then do j=1,n& read (10,11) (m(i,j),i=1,j) enddo else* stop 'IHaf must be either 1 or 2!' endif# close (unit=10,status='keep')* write (*,30) if (yessir('N')) then double=.true.12 write (*,1) read (*,2) trifile29 open (unit=12,file=trifile2,status='old',, 1 carriagecontrol='list',err=12) read (12,2) inbuf2 read (12,6) n2,nit2,njt2,ihaf2,iclr2,mode2*9 if (n2.ne.n) stop 'Dotplots are different sizes!': if (nit2.ne.njt2) stop 'Only square dotplots work'. if (n2.gt.nmax) stop 'Matrix too big!'c Resize nmax and recompile'* if (ihaf2.eq.1) then2 stop 'Full matrix not implemented'( else if (ihaf.eq.2) then do j=1,n. read (12,11) (m(j,i),i=1,j) enddo else2 stop 'IHaf must be either 1 or 2!' endif% close (unit=12,status='keep') endif**** write (*,98) if (yessir('N')) then write (*,99) ticstart read (*,*) ticstart endif*-** open figure file, write header (format 14)*20 write (*,13) read (*,2) figfile. open (unit=15,status='new',file=figfile,* 1 carriagecontrol='list',err=20)5 write (15,14) -(.1*n),1.1*n,1.1*n,-.1*n,n,n,n,n% if (double) write (15,15) n,n,n*** Tics and labels*! i=(int(ticstart/nit)+1)*nit write (15,21) 2*9** i axis (up to down in uppper triangle) tics and labels* do while (i.lt.n+ticstart) encode (4,22,label) i start=1, do while (label(start:start).eq.' ') start=start+1 enddo0 write (15,16) n,i-ticstart,(0.01*n),0.00E write (15,18) 1.05*n,float(i-ticstart),(label(k:k),k=start,4)4 if (double) write (15,16) 0,i,-(0.01*n),0.00 i=i+nit enddo! j=(int(ticstart/nit)+1)*nit write (15,21) 4*;** j axis (left to right in upper triangle) tics and labels* do while (j.lt.n+ticstart) encode (4,22,label) j start=1, do while (label(start:start).eq.' ') start=start+1 enddo1 write (15,16) j-ticstart,0,0.00,-(0.01*n)F write (15,18) float(j-ticstart),-0.05*n,(label(k:k),k=start,4)1 if (double) write (15,16) j,n,0.00,0.01*n j=j+njt enddo*** Points and Lines* do j=n,1,-1 do i=1,j% if (m(i,j).ne.0) then6* if we've found a point, see if we can draw a line... x=12 do while (m(i+x,j-x).ne.0), m(i+x,j-x)=0% x=x+1 enddo x=x-1( if (x.eq.0) then&* isolated base pair; put a dot at j,i1 write (15,24) j,i else7* series of base pairs; draw a line from j,i to j-x,i+x9 write (15,26) j,i,j-x,i+x endif endif enddo enddo* if (double) then do j=n,1,-1 do i=1,j% if (m(j,i).ne.0) then6* if we've found a point, see if we can draw a line... x=12 do while (m(j-x,i+x).ne.0), m(j-x,i+x)=0% x=x+1 enddo x=x-1( if (x.eq.0) then&* isolated base pair; put a dot at i,j1 write (15,24) i,j else7* series of base pairs; draw a line from i,j to i+x,j-x9 write (15,26) i,j,i+x,j-x endif endif enddo enddo endif*# close (unit=15,status='keep')*,1 format (1x,'Triangular file name? ',$)2 format (a)5 format (/)6 format (6i5)11 format (80i1)/13 format (1x,'Output Figure file name? ',$)0* Header section - continuation 3 draws triangle/14 format ('.vp 20.455 129.545 100.0 0.0',/," 1 '.wn ',4(f7.2,1x),/, 2 '.ls 1 30',/,H 3 '.m ',i3,' 0',/,'.d ',i3,1x,i3,/,'.d 0 0',/,'.d ',i3,' 0')515 format ('.m 0 0',/,'.d 0 ',i3,/,'.d ',i3,1x,i3)* Tic format (both directions)516 format ('.m ',i4,1x,i4,/,'.reld ',f7.2,1x,f7.2)* Label for tics.18 format ('.m ',f7.2,1x,f7.2,/,'.pt ',4a1) * Text origin21 format ('.to ',i1)22 format (i4)* Point format24 format ('.p ',i4,1x,i4) * Line format.26 format ('.m ',i4,1x,i4,/,'.d ',i4,1x,i4)230 format (1x,'Do you want a double dotplot',$)?98 format (1x,'Change numbering on axes (currently 1..N)? ')999 format (1x,'Graph start:',i5,'. Enter new start.') end& logical function yessir(default)*4** Ask for, and get either a Y or N response. If Y,4** this function returns .TRUE., .PHALSE. otherwise.* integer inunit,outunit$ parameter (inunit=5,outunit=6)# character*1 default,ch,upcase ch=' '10 write (outunit,1) default read (inunit,2,err=10) ch if (ch.eq.' ') then yessir=(default.eq.'Y') else ch=upcase(ch) yessir=(ch.eq.'Y')# if (ch.ne.'Y') then& if (ch.ne.'N') goto 10 endif endif,1 format (1x,'(Y,N) Default:',a1,'->',$)2 format (a1) return end' character*1 function upcase (ch)*** Stolen from MYLIB.FOR'** Change Ch to upper case if necessary* character*1 ch' character*1 lowera,lowerz,uppera*- data lowera/'a'/lowerz/'z'/uppera/'A'/*F if (lle(lowera(1:1),ch(1:1)).and.lge(lowerz(1:1),ch(1:1))) then; upcase=char(ichar(uppera)+ichar(ch)-ichar(lowera)) else upcase=ch endif return end *[MFOLD]FIGDOT.OBJ;4+,./ 4-*0123KPWO56T i7i89GHJ4 DOTFILTER0123-Feb-1992 01:5823-Feb-1992 01:58VAX FORTRAN V5.7-133 DOTFILTERPThis program only works for square dotplotsMatrix too big! Resize nmax and recompileFull matrix not implementedIHaf must be either 1 or 2!NDotplots are different sizes!Only square dotplots workMatrix too big!Triangular file name? )POutput Figure file name? .vp 20.455 129.545 100.0 0.0.wn .ls 1 30.m  0.d .d 0 0.d  0.m 0 0.d 0 .d .m .reld .m .pt .to .p .m .d Do you want a double dotplot+Change numbering on axes (currently 1..N)?  Graph start:. Enter new start. DOTFILTERPP PpPP +*;e  YESSIR@ e T YESSIR@QPO[~ FOR$WRITE_SF FOR$IO_END~ FOR$READ_SF FOR$IO_T_DS FOR$IO_END$FOR$OPENP  FOR$READ_SF FOR$IO_T_DS FOR$IO_END  FOR$READ_SF? FOR$IO_W_RT? FOR$IO_W_RU? FOR$IO_W_RV? FOR$IO_W_R? FOR$IO_W_R? FOR$IO_W_R FOR$IO_ENDUV߫DFOR$STOP2TPP߫LFOR$STOP߫TFOR$STOP1RT  FOR$READ_SFܰSR2RPŏPW2SPWP?@ FOR$IO_W_R=RS FOR$IO_END=TRd FOR$CLOSE~ FOR$WRITE_SF FOR$IO_ENDxYESSIRP1k~ FOR$WRITE_SF FOR$IO_END~ FOR$READ_SF  FOR$IO_T_DS FOR$IO_ENDˀFOR$OPENP  FOR$READ_SF FOR$IO_T_DS FOR$IO_END  FOR$READ_SF? FOR$IO_W_R? FOR$IO_W_R? FOR$IO_W_R? FOR$IO_W_R? FOR$IO_W_R? FOR$IO_W_R FOR$IO_ENDTˠFOR$STOP˨FOR$STOP2PP˰FOR$STOP˸FOR$STOPRT  FOR$READ_SFݰSR2RW2SPďPWP?@ FOR$IO_W_R=RS FOR$IO_END=TR FOR$CLOSEFOR$STOP8~ FOR$WRITE_SF FOR$IO_ENDYESSIRPh~ FOR$WRITE_SF2~ FOR$IO_W_V FOR$IO_END~ FOR$READ_SL? FOR$IO_W_R FOR$IO_END ~ FOR$WRITE_SF FOR$IO_END~ FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDFOR$OPENP) FOR$WRITE_SFMTWE>WPRPRR FOR$IO_F_VE@WSS FOR$IO_F_VS FOR$IO_F_VR FOR$IO_F_V2T~ FOR$IO_W_V2T~ FOR$IO_W_V2T~ FOR$IO_W_V2T~ FOR$IO_W_V FOR$IO_ENDk FOR$WRITE_SF2T~ FOR$IO_W_V2T~ FOR$IO_W_V2T~ FOR$IO_W_V FOR$IO_ENDUP2PPP2URRPPXXYTZ FOR$WRITE_SF FOR$IO_L_R FOR$IO_ENDYZ1 FOR$ENCODE_MF2Y~ FOR$IO_W_V FOR$IO_END\2\PP@ \ FOR$WRITE_SF2T~ FOR$IO_W_VYR2R~ FOR$IO_W_VE#= WSS FOR$IO_F_V FOR$IO_F_R FOR$IO_END FOR$WRITE_SFE@ffW~ FOR$IO_F_VMR~ FOR$IO_F_V\R\2R\\L FOR$IO_T_DS=R FOR$IO_ENDk FOR$WRITE_SF  FOR$IO_L_R2Y~ FOR$IO_W_VRS~ FOR$IO_F_V FOR$IO_F_R FOR$IO_ENDUY1 FOR$WRITE_SF FOR$IO_L_R FOR$IO_ENDXZ1 FOR$ENCODE_MF2X~ FOR$IO_W_V FOR$IO_ENDY2YPP@ Y FOR$WRITE_SFXU2U~ FOR$IO_W_V  FOR$IO_L_R FOR$IO_F_RE#= WSRS~ FOR$IO_F_V FOR$IO_END FOR$WRITE_SFMU~ FOR$IO_F_VEL>WPRP~ FOR$IO_F_VYUY2UYYI  FOR$IO_T_DS=U FOR$IO_ENDk FOR$WRITE_SF2X~ FOR$IO_W_V2T~ FOR$IO_W_V FOR$IO_F_RS FOR$IO_F_V FOR$IO_ENDVX1TW1XW12WZďZ2XVZVF1VVXP2PPVWS2SSďSSP@@VԷV FOR$WRITE_SF2W~ FOR$IO_W_V2X~ FOR$IO_W_V FOR$IO_END FOR$WRITE_SF2W~ FOR$IO_W_V2X~ FOR$IO_W_VVWP2P~ FOR$IO_W_VXV2V~ FOR$IO_W_V FOR$IO_END=WXA=W%k1TW1TW12WX2TZďZXZJ1ZZWP2PPZTV2VVďVVP@@ZԷZ FOR$WRITE_SF2T~ FOR$IO_W_V2W~ FOR$IO_W_V FOR$IO_END FOR$WRITE_SF2T~ FOR$IO_W_V2W~ FOR$IO_W_VZTP2P~ FOR$IO_W_VZWZ2Z~ FOR$IO_W_V FOR$IO_END=WT<=W$ FOR$CLOSEP߫\FOR$STOP" O DOTFILTERYESSIRFOR$OPEN FOR$CLOSE $CODE$PDATA$LOCALFOR$STOP FOR$IO_END FOR$IO_W_R FOR$IO_W_V FOR$IO_L_R FOR$IO_F_R FOR$IO_F_V FOR$IO_T_DS FOR$READ_SF FOR$READ_SL FOR$WRITE_SF FOR$ENCODE_MF<P P P  PPK)P(PKP ^P xP PPbPMP'P.P=*P4P,P\P PDP,3PPP@2P<PXPP P,PEPP(PGPlP {P,PF ?ԻԺ % 1YESSIR0123-Feb-1992 01:5823-Feb-1992 01:58VAX FORTRAN V5.7-133 YESSIR$P(Y,N) Default:-> YESSIR#PPH[}PQ  FOR$WRITE_SFk FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDߑ TYTT~UPCASEאTYTTYN1tЫP HYESSIRUPCASE$CODE$PDATA,$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SF_PpP3P 1UPCASE0123-Feb-1992 01:5823-Feb-1992 01:58VAX FORTRAN V5.7-133 UPCASE UPCASEmPQazAPH[}PQ}PQ  P QQPQQPP E HUPCASEF$CODE$PDATA$LOCALP &P>P  F*[MFOLD]FILES.LIS;1+,./ 4M-*0123KPWO569h7i89GHJ- Directory of filesK Suboptimal RNA folding package - M. Zuker, J. A. Jaeger, D. H. Turner( Version 2.0FALU.CT - A concatenation of 15 CT files containing part of the output D produced by executing the BAT2.COM command file. These are B 15 foldings of an ALU RNA sequence. The first is optimal.HALU.DISTANCE - The output of the DISTANCE program using ALU.CT as input.E This file contains all the pairwise distances between 8 15 different foldings of an ALU sequence.JALU.OUT - Structure output file (120 record length) containing part of theH output produced by executing the BAT2.COM command file. These G are 15 foldings of an ALU RNA sequence. The first is optimal./ Selected base pairs are marked by |1 ^ .GALU.PLOT1 - This is an ASCII dot plot file created using the P optionD when the cross hairs are displayed while running LRNA inE suboptimal plot mode. The run is a continuation using theE ALU.SAV file. The energy increment selected is 114 ( 11.4I kcal/mole ) which is 10% of the minimum computed free energy.G 4 levels were selected. The first level is for optimal baseE pairs. Levels 2, 3, and 4 correspond to energy increments9 of 3.8, 7.6, and 11.4 kcal/mole respectively.JALU.PLOT2 - Similar to ALU.PLOT1. Only three levels are used up to a totalD energy increment of 7.6 kcal/mole ( 6.6% from minimum ).JALU.REG - A concatenation of 15 REGion files containing part of the ouput G produced by executing the BAT2.COM command file. These are 15@ foldings of an ALU RNA sequence. The first is optimal.GALU.SAV - The unformatted save file created by executing BAT1.COM. ThisK file can be used for a continuation run of LRNA (as in BAT2.COM).C This file is for the folding of an ALU RNA sequence usingG default energy files and no auxiliary information which would7 either force or prohibit specific base pairs.FALU.SEQ - Sequence used in sample foldings. Note that A, C, G and U/T@ are in uppercase letters. Bases that are in lowercase9 letters will not be recognized by the program!HALU.UWGCG - Output of FIGDOT using ALU.PLOT1 and ALU.PLOT2 as input. TheI title is not included in this file. The FIGURE program in theM University of Wisconsin Genetics Computer Group package ( UWGCG )K can be used to transform this device independent plot file intoK a device specific plot file. The output is two energy dot plotsH for the folding of the ALU sequence ( BAT1.COM & BAT2.COM ).L You could also write your own program to create energy dot plotsG with labels and using multiple colors for different levels.J NB : The FIGURE program in version 5 of UWGCG works with theseI files; it DOES NOT work with version 6 (sorry about that, but it's not my fault).EBAT1.COM - Sample command file for folding an ALU RNA sequence. This H command file is the output of the BATGEN program and produces" the save file ALU1.SAV.DBAT2.COM - Sample command file for folding an ALU RNA sequence. ThisE command file executes the LRNA program which reads in the B ALU1.SAV save file and computes optimal and suboptimal B foldings of an ALU RNA sequence. Up to 200 foldings areE allowed, although only 15 are generated. All foldings mustD be within 10% of the minimum computed free energy and the< distance between any pair must be greater than 5.(BATGEN.EXE - Executable code for BATGEN.IBATGEN.FOR - Source code for BATGEN. This program creates batch files for RNA folding.$BATGEN.OBJ - Object file for BATGEN.@BEGIN.DAT - Author and reference information that are displayed % before program execution.:BPIN.FOR - Source code for a subroutine used by DISTANCE. BPIN.OBJ - Object file for BPIN.;BPSRCH.FOR - Source code for a subroutine used by DISTANCE."BPSRCH.OBJ - Object file for BPIN.DCDOT.OBJ - Object file for DOTPLT. Similar to LDOT.OBJ. This file is1 linked with others to create CRNA.EXE.ICIRC.COM - Command file for compiling and linking the circular version ofH the folding program. This file should be copied into TEMP.COME and edited to eliminate unnecessary compilations. TEMP.COM? should then be executed. Note that it erases itself.ECIRC.FOR - Source code for main; circular version of folding program.BCIRC.INC - An include file for the circular version of the foldingE program. Note (see CIRC.COM and LIN.COM) that it is copied> into a temporary file called RFD.INC (Rna FolDing). CIRC.OBJ - Object file for CIRC.CCMISC.OBp.~ MFOLD.BCK*[MFOLD]FILES.LIS;1MU( J - Object file for MRNA.FOR. This is similar to LMISC.OBJ 9 and is linked with others to create CRNA.EXE."CON.EXE - Executable file for CON.DCON.FOR - Source code for CON. This program is used interactively toJ convert FORTRAN source code from long record lengths to standard$ record lengths (up to 72).CON.OBJ - Object file for CON.FCRNA.EXE - The circular verision of the RNA folding program (FORTRAN). CRNA.OBJ - Object file for CRNA.;CSORT.OBJ - Object file for SORT.FOR. Similar to LSORT.OBJ.(CTTOBP.EXE - Executable file for CTTOBP.CCTTOBP.FOR - Source code for a program that converts a CT file into; a REGion and a sequence file, and vice versa. $CTTOBP.OBJ - Object file for CTTOBP.DCT_GCG.FOR - This file contains an alternte for of the CT subroutineB in MFOLD.FOR . This alternate generates CT files that4 can be read directly by UWGCG software.&CVTCT.EXE - Executable file for CVTCT.GCVTCT.FOR - Source code for CVTCT. This program converts a CT file intoE a .DAT file used by the University of Wisconsin packageC for displaying RNA foldings (eg. SQUIGGLES accepts this7 file format). Needs JJLIB.OBJ at link time."CVTCT.OBJ - Object file for CVTCT.MDANGLE.DAT - Energy file for single base stacking (dangling ends) at 37 deg. G Entries marked "." should be interpreted as plus infinity.F In such cases, no single base stacking occurs. Equivalent to DANGLE.037 .DDANGLE.DH - Enthalpy file for single base stacking (dangling ends). F This file is used by the NEWTEMP program together with theB DANGLE.DAT file to produce energy files for folding atE arbitrary temperatures between 0 and 100 deg. Some singleA base stacking energies may come out positive for high? temperatures. The program only includes single base9 stacking if the energy increment is negative.F Entries marked "." should be interpreted as plus infinity.,DISTANCE.EXE - Executable file for DISTANCE.HDISTANCE.FOR - Source code for DISTANCE. This program reads in a CT fileF containing between 2 and 15 structures and computes theF distance between the first and all the rest or else the* distance between all pairs.(DISTANCE.OBJ - Object file for DISTANCE.4DOTPLT.FOR - Source code for the DOTPLOT subroutine.#EFN.EXE - Executable file for EFN. DEFN.FOR - An independent program to compute the energies of foldingsF using a CT file as input. This program requires energy tableC input. The output consists of the computed energy of eachH folding found in the input CT file. Line printer output and/or* region table output are options.AEFN.INC - Include file for EFN. Needed when EFN.FOR is compiled.IEFN.OBJ - Object file for EFN.FOR. This single file is all that is needed to create EFN.EXE. CERRATA2.LIST - List of errata found in folding programs with dates.M&FIGDOT.DOC - Documentation for FIGDOT.(FIGDOT.EXE - Executable file for FIGDOT.EFIGDOT.FOR - Source code for FIGDOT. This program takes an ASCII plot E file (produced by CRNA or LRNA using the P (plot) option D in DOTPLT and converts it into a device inependent plotG file for use by the FIGURE program from the University of E Wisconsin package. The net result is to create an energy  dot plot.$FIGDOT.OBJ - Object file for FIGDOT.FILES.LIST - This file.rIFORMID.FOR - Source code for FORMID. This subroutine reads and interpretst sequence data.sIFORMID.OBJ - Object file for FORMID. Linked to create both the linear andG circular versions of the folding programs (FORTRAN and C). =GETSEQ.FOR - Almost the same as FORMID.FOR. Used with BATGEN.o$GETSEQ.OBJ - Object file for GETSEQ.EHEADER.DAT - Default header for batch files created by BATGEN. Please 5 modify this file to suit your own needs.sAINIT.COM - This command file must be executed before running the 1A folding program in dot plot mode. If this command filepC is not executed, the energy dot plot will go into a filee8 PLOT.DAT and the program will probably crash.EJJLIB.FOR - Some subroutines by John Jaeger that are needed by CVTCT.c@JJLIB.OBJ - Object file for JJLIB. Needed by CVTCT at link time.DLDOT.OBJ - Object file for DOTPLT. Similar to CDOT.OBJ. This file is1 linked with others to create LRNA.EXE.tFLIN.COM - Command file for compiling and linking the linear version ofG the folding program. This file should be copied into TEMP.COMnD and edited to eliminate unnecessary compilations. TEMP.COM> should then be executed. Note that it erases itself.FLIN.FOR - Source code for main; linear version of the folding program.?LIN.INC - An include file for the linear version of the folding D program. Note (see CIRC.COM and LIN.COM) that it is copied= into a temporary file called RFD.INC (Rna FolDing).LLIN.OBJ - Object file for LIN.FLMISC.OBJ - Object file for MRNA.FOR. This is similar to CMISC.OBJ and9 is linked with other files to create LRNA.EXErGLOOP.DAT - Energy data for hairpin, bulge and interior loops at 37 deg.a! Equivalent to LOOP.037 HLRNA.EXE - Executable file for the linear version of the folding program (FORTRAN).n LRNA.OBJ - Object file for LRNA.;LSORT.OBJ - Object file for SORT.FOR. Similar to CSORT.OBJ.dGMFOLD.DOC - A glossary of subroutines and functions used in the foldingu? programs as well as a list of some of the varibles.UGMFOLD.FLOW - A flow chart for the main routine of the folding programs.w?MFOLD.USER - A user's manual. Another description will appear :nJ Predicting Optimal and Suboptimal Secondary Structure for RNA; by J. A. Jaeger, D. H. Turner and M. Zuker, iniD "Molecular Evolution: Computer Analysis of Protein and 9 Nucleic Acid Sequences", R. F. Doolittle ed.l9 Methods in Enzymology, 183, 281-306, (1990).s<MISCLOOP.DAT - Miscellaneous loop file at 37 deg. Contains :C i. a paramater for extrapolating bulge, interior andL. hairpin loop size beyond 30.E ii. parameters for the Ninio "asymmetric interior loop"f correction.bG iii. parameters used in computing the destabilizing effecta* of multi-branched loops.EMRNA.FOR - Miscellaneous subroutines for both the linear and circularo+ versions of the folding program.cCMULTID.FOR - This subroutine reads and interprets sequence data. ItoA differs from FORMID in that it automatically returns F one sequence after another to the calling routine instead< of requesting a sequence number of identifier. IMULTID.OBJ - Object file for MULTID. Linked to create both the linear andRG circular versions of the folding programs (FORTRAN and C).i*NEWTEMP.EXE - Executable file for NEWTEMP.ENEWTEMP.FOR - Source code for NEWTEMP. This program reads the 37 deg.D energy files :D STACK.DAT, TSTACK.DAT, LOOP.DAT, DANGLE.DAT, TLOOP.DAT & MISCLOOP.DAT- as well as the enthalpy files :i8 STACK.DH, TSTACK.DH, DANGLE.DH & TLOOP.DH > and computes new energy files for folding at anyA user defined temperature between 0 and 100 degrees.b@ The output files are labelled with the appropriateC temperature. For example, if 25 deg. is selected, thel1 output energy files will be named : D STACK.025, TSTACK.025, LOOP.025, DANGLE.025, TLOOP.025 & MISCLOOP.025&NEWTEMP.OBJ - Object file for NEWTEMP.!READ_ME.FIRST - To be read first.B9RFD.INC - A temporary copy of either CIRC.INC or LIN.INC.4RNA.FOR - FORTRAN source code (main)for RNA folding.3SORT.FOR - Source code for the sorting subroutine. oHSTACK.DAT - Energy file for base pair stacking within helices at 37 deg.F Entries marked "." should be interpreted as plus infinity.% Equivalent to STACK.037 .e:STACK.DH - Enthalpy file for base pair stacking. This fileE is used by the NEWTEMP program together with the STACK.DATR@ file to produce energy files for folding at arbitraryA temperatures between 0 and 100 deg. Entries marked "."a3 should be interpreted as plus infinity. aDTLOOP.DAT - A list of distiguished tetraloops and the bonus energiesG given to them at 37 deg. These bonus energies are included C* in the final folding energies.# Equivalent to TLOOP.037@TLOOP.DH - Enthalpy file for distinguished tetraloops. This fileE is used by the NEWTEMP program together with the TLOOP.DATr@ file to produce bonus energies for listed tetraloops.ETSTACK.DAT - Energy file for terminal mismatched pairs in hairpin andiD interior loops at 37 deg. Entries marked "." should be E interpreted as plus infinity. Equivalent to TSTACK.037 .TFTSTACK.DH - Enthalpy file for terminal mismatched pairs in hairpin and4 interior loops. This file is used by the@ NEWTEMP program together with the TSTACK.DAT file to9 produce energy files for folding at arbitraryEB temperatures between 0 and 100 deg. Entries marked "."4 should be interpreted as plus infinity. GZP.OLB - Graphics object library for creating the interactive dot plotsn and P-Num plots. *[MFOLD]FORMID.FOR;1+,.$/ 4I$$-*0123KPWO%56Eh74Vi89GHJH2 subroutine formid(seqid,seq,nseq,nmax,used)c RESEARCHER: M. ZUKERc JUN 1986c DS TUDHOPEEc WRITTEN TO WORK ON VAX-11-750 UNDER VMS4.3 USING STANDARD F-77Ec #### NOTE #### USE OF CARRIAGE CONTROL LINE FEED SUPPRESSIONCc IS USED IN THIS PROGRAM AND IS NOT STANDARD"c FORTRAN-777c SEE '$' IN FORMAT STATEMENT 102 implicit integer*2 (a-z)& logical found,endfil,valid,used1 integer*2 sline(500),seqnum(500),nseq,nmax character*8 stype character*30 seqids(500) character*30 choice,seqid& character*50 filnam,fmtseq(500) character*80 reclin character*1 seq(nmax) data found/.false./, . endfil/.false./, . valid/.false./Ec **************************************************************6c subroutine number FS372, test main driver FP475?c biomath program catalogued as FS372.FOR named formid.forEc **************************************************************c PURPOSE:8c subroutine used to extract sequences from various"c format type files including(c STANFORD,GENBANK,EMBL,PIR,and,NRCEc **************************************************************c variable list table:2c * -- sent down from main returned unchanged,c ** - returned to main from subroutine4c ***- sent down from main and returned changedBc INTEGERS:IDCNT -- to keep track of the number of sequence8c identifiers found in the file(c I,K -- loop countersGc LINE -- to point to the record line number of a fileCc N -- counter to extract the correct number of,c sequence elementsFc * NMAX -- maximum length of sequence expected by userEc ** NSEQ -- length of the sequence retrieved from fileBc POINTR -- pointer to point to sequence identifier;c chosen from array of identifiersBc SEQNUM -- an ARRAY of the length of the sequencesDc for the sequence identifiers found in the0c NRC-format type filesDc SLINE -- an ARRAY of the record-line numbers where6c a sequence starts in a fileCc START -- defines what column of a record to start3c reading the sequence in.Cc CHARACTERS:CHOICE-- character string of length 20 to read inEc choice for sequence identifier to retrieveCc FILNAM -- character string of length 50 to read in(c the filename.Bc FMTSEQ -- an ARRAY of characters, each length 50,Dc describing how the sequence is to be readCc RECLIN -- a record of a file, length 80 charactersBc ** SEQ -- an ARRAY of characters each length 1 to-c store the sequence9c ** SEQID -- retrieved name of the sequenceCc SEQIDS -- an ARRAY of retrieved names of sequencesDc STYPE -- character string of length 8 defining the3c format type of the file.Ac LOGICALS:FOUND -- logical variable used in looping until.c something retrievedFc *** USED -- logical variable used in determining if the@c subroutine has been previously calledAc VALID -- logical variable used in looping until+c some input validcc4c if the subroutine has NOT been USED then must;c input the filename and do error checking on filenameBc else branch to listing the sequences available in this file if (.not.used) then10 found = .false. valid = .false. used = .false.:c initialize for a new file by setting variables back)c to zero and blanking out old names! if (nmax.eq.0) nmax = 9999 nseq = 0 stype = ' '% seqid = ' 'C filnam= ' ' do 500 i = 1,500 sline(i) = 0 seqnum(i)= 0* seqids(i)=' 'F fmtseq(i)= ' '500 continue;111 write(6,102) 'Input sequence file name (/ to end) '102 format(1x,a37$)) read(5,110,end=111,err=111) filnam# if (filnam(1:1).eq.'/') then goto 999 endif110 format(a50)Cc open the file only after a valid filename has been retrievedAc error in filename results in prompting for the input again/ open(66,file=filnam,status='OLD',err=10)Bc find sequence file format type and the sequence identifiers idcnt = 0 line = 1c DO WHILE (.NOT.FOUND)1600 read(66,120,end = 410,err = 991) reclin120 format(a80)=c STANFORD format, recognized by the ';' in the first columnc of the record& if (reclin(1:1).eq.';') then#c DO WHILE (.NOT.ENDFIL)610 line = line + 14 read(66,120,end = 410,err=991) reclin;c to find the next sequence identifer scroll through the:c file until the first character in the line is not ';'+ if (reclin(1:1).ne.';') then% found = .true.( stype ='STANFORD'( idcnt = idcnt + 1) sline(idcnt)= line/ seqids(idcnt) = reclin(1:30)" line = line + 18 read(66,120,end = 410,err=991) reclin;c DO WHILE ((INDEX(RECLIN,'1').EQ.0).AND.7c . (INDEX(RECLIN,'2').EQ.0))c ENDDO6615 if (index(reclin,'1').eq.0) then7 if (index(reclin,'2').eq.0) then' line = line + 1= read(66,120,end = 410,err=991) reclin! goto 615 endif endif=c assume at least one line not a sequence identifier occursAc after last sequence read in to get around the CTRL-L problem.=c therefore, after reading in the record containing the end2c of sequence identifier, read in another record" line = line + 18 read(66,120,end = 410,err=991) reclin endifc ENDDO& if (.not.endfil) goto 610@c GENBANK format, recognized by the word LOCUS starting in the c first position of the record. elseif (reclin(1:5).eq.'LOCUS') then found = .true.# stype = 'GENBANK ' idcnt = 1. seqids(idcnt) = reclin(13:27)'c DO WHILE (.NOT.ENDFIL)$620 line = line + 1: read(66,120,end = 410,err=991) reclin;c scrolling through to find the key phrase ORIGIN becauseCc the line after this key phrase occurrance is where the sequencec occurs in the file;@c read through the file obtaining other sequences by scrolling9c through to the '//' which signals the end of sequence7c Then start looking for another sequence identifier.5 if (reclin(1:6).eq.'ORIGIN') then+ sline(idcnt) = line6c DO WHILE (RECLIN(1:2).NE.'//')5625 if (reclin(1:2).ne.'//') then* line = line + 1@ read(66,120,end = 410,err=991) reclin# goto 625c ENDDO endif9 elseif (reclin(1:5).eq.'LOCUS') then, idcnt = idcnt + 18 seqids(idcnt) = reclin(13:27) endifc ENDDO, if (.not.endfil) goto 620?c PIR format, recognized by the '>' occurring in column 1 of aUBc record. The sequence itself start 2 lines down from the recordc containing '>'.* elseif (reclin(1:1).eq.'>') then found = .true.S# stype = 'PIR 'T'c DO WHILE (.NOT.ENDFIL)N0630 if (reclin(1:1).eq.'>') then) idcnt = idcnt + 1s/ sline(idcnt) = line + 1n4 seqids(idcnt) = reclin(5:25) endift# line = line + 159 read(66,120,end = 410,err=991) reclinac ENDDO, if (.not.endfil) goto 630Ac EMBL (european) format, recognized by the key phrase ID in the*c first column of the record.. elseif (reclin(1:5).eq.'ID ') then found = .true.b# stype = 'EMBL 'RDc scrolling through to find the key phrase 'SQ Sequence' becauseCc the line after this key phrase occurrance is where the sequencerc occurs in the file;s(c DO WHILE (.NOT.ENDFIL)5640 if (reclin(1:5).eq.'ID ') then*, idcnt = idcnt + 1@ seqids(idcnt) = reclin(6:index(reclin,' '))B elseif (reclin(1:13).eq.'SQ Sequence') then. sline(idcnt) = line endif$ line = line + 1: read(66,120,end = 410,err=991) reclinc ENDDO, if (.not.endfil) goto 640Ac NRC format, recognized by '(' occurring in the first column of Bc a record. The record line following this line holds the number@c of elements in the sequence and the name of the sequence. The8c following line signals the beginning of the sequence.:c The sequence itself is read in by using variable formatBc described by the '(' record line. This format statement on the1c record containing '(' ,must also be retrieved.* elseif (reclin(1:1).eq.'(') then found = .true.$ stype = 'NRC '(c DO WHILE (.NOT.ENDFIL)1650 if (reclin(1:1).eq.'(') thenN) idcnt = idcnt + 1wC fmtseq(idcnt) = reclin(1:index(reclin,')')) ' line = line + 1 8 read(66,140,end = 410,err = 991)3 . seqnum(idcnt),seqids(idcnt)s+ sline(idcnt) = line  endif$ line = line + 1: read(66,120,end = 410,err=991) reclinc ENDDO"140 format(i4,5x,a30)* if (.not.endfil) goto 650 endif Dc keep scrolling through the file until a key phrase signalling>c a format type is recognized or the end of file is found line = line + 1 c ENDDO if (.not.found) goto 600 @c if a format type has not been found then this cannot be a(c sequence file and return to main.410 if (.not.found) thenrD write(6,105) ' No sequence identifiers found in this file '105 format(a50) return endif-c if this is a valid format type proceedO used = .true. endif<c IF USED this call before start at listing identifiers'c listing the sequence identifiersl3c allow the user to input the number requested 0c or control Z to finish here and return toc entering a new filename valid = .false.7c keep outputting the list of sequence identifiers@c while NOT VALID choice of sequence identifier is inputtedc DO WHILE (.NOT.VALID)k4660 write(6,150) 'Available sequences in ',filnam150 format(/,1x,a23,a50)e do 525 k = 1,idcnt,2$ if (sline(k).ne.0) then# if (k .eq. idcnt) then - write (6,151) k,'.',seqids(k)  elseoA write (6,191) k,'.',seqids(k),k+1,'.',seqids(k+1)  endif$151 format(1x,i3,a1,1x,a30)4191 format(1x,i3,a1,1x,a30,3x,i3,a1,1x,a30) endif525 continue& choice = ' '& seqid = ' ' pointr = 0  write(6,152) C .'Choose sequence by number or name , or ? for relist; ' write(6,152) A .' defaults to the first one, / for new file.'r152 format(1x,a60)a read(5,153,end=10) choice153 format(a30)<c error checking of the inputted CHOICE and determiningDc if this input is a number, a default value, a relist command-c or the name of the sequence identifierr i = 1/ do while (choice(i:i).eq.' '.and.i.lt.6)= i = i + 1 enddo> if ((choice(i:i).ge.'1').and.(choice(i:i).le.'9')) thenDc using COLLATING sequence to convert character to number value2 pointr = ichar(choice(i:i)) - ichar('0')* if (choice(i+1:i+1).ne.' ') thenG pointr = ichar(choice(i+1:i+1)) - ichar('0') + 10 * pointr' endif * if (choice(i+2:i+2).ne.' ') thenG pointr = ichar(choice(i+2:i+2)) - ichar('0') + 10 * pointr  endif # if (pointr.gt.idcnt) then@ write(6,154) ' NUMBER CHOICE BETWEEN 1 AND ',idcnt154 format(a30,i2). else% seqid = seqids(pointr)  valid = .true.A endif - elseif (ichar(choice(6:6)).eq.32) then  pointr = 1 seqid = seqids(1)( valid = .true.' elseif (choice(1:1).eq.'?') then  continue elserIc find out if the inputted choice is in the list of seq identifiers. pointr = 0 do 535 k = 1,idcnt* if (seqids(k).eq.choice) then$ seqid = seqids(k) pointr = k ! valid = .true. endif535 continue if (pointr.eq.0) then,F write(6,105) 'This entry does not match with any in given list' endif endif c ENDDO  if (.not.valid) goto 660i<c having obtained a valid sequence choice or default of?c one available sequence, rewind the file and retrieve therc sequenceo rewind(66,err = 992)f>c having retrieved the line number in the file where this>c identifier occurs from SLINE(POINTR) scroll through the&c file until this line is reached& do 550 i = 1,sline(pointr)3 read(66,120,end = 410,err=991) reclind550 continue>c if nrc type then read sequence according to format type$ if (stype.eq.'NRC ') then# nseq = seqnum(pointr)e8c if the number in the NRC sequence is greater than3c the maximum number sent down from main, then 9c truncate to NMAX and output a message to the user.$ if (nseq.gt.nmax) thenC write(6,160) ' Sequence truncated to ',nseqI"160 format(1x,a30,i5) nseq = nmax endif 7 read(66,fmtseq(pointr),end = 420,err=991) - . (seq(k),k=1,seqnum(pointr))e<c Else if not type NRC then find the sequence by taking<c each letter of the next records until end-of-sequence@c indicator found or number in the sequence NMAX is reached else n = 1 found = .false.c DO WHILE (.NOT.FOUND) 1670 read(66,120,end = 420,err=991) reclin Ac there is a need for the two positions to start reading the1Cc sequence; to accommodate the GENBANK format and the STANFORD c end-of-sequence checks.) if (stype.eq.'GENBANK ') then  start = 10 else start = 1i endif  do 565 i = start,80d=c if the number in the sequence is less than the desired ?c number, NMAX sent down from main, then retrieve sequencef" if (n.le.nmax) then& if (.not.found) then& seq(n) = reclin(i:i))c check if an early end of sequencee> if ((seq(n).eq.'1').or.(seq(n).eq.'2').or.A . (reclin(1:1).eq.'/').or.(seq(n).eq.'*')) thenO$ seq(n) = ' '$ nseq = n - 1& found = .true.<c if not an end-of-sequence character but have gone far$c enough, then truncate to NMAX+ elseif (n.eq.nmax) thene# nseq = nmaxd& found = .true.C write(6,160) ' Sequence truncated to ',nseq @c if not a end-of-sequence character, check to see if it is@c not a blank character. Blank characters will not be addedc to the sequence. / elseif (seq(n).ne.' ') thenM" n = n + 1 endif endifaAc if the number of sequence characters found is Greater thani4c NMAX then all of the sequence has been found. else " found = .true. nseq = n write(6,160)9 . ' Sequence truncated to ',nseq  endifc565 continuec ENDDO# if (.not.found) goto 670  endif 420 return'991 stop ' ERROR IN READING FILE ' '992 stop ' ERROR IN REWINDING FILE'9)999 stop ' END of SESSION...GOOD BYE' end*[MFOLD]FORMID.OBJ;3+,./ 4 -*0123KPWO56.&i7Ti89GHJ 1FORMID0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 FORMIDPInput sequence file name (/ to end) 12 ) No sequence identifiers found in this file Available sequences in .Choose sequence by number or name , or ? for relist; defaults to the first one, / for new file. NUMBER CHOICE BETWEEN 1 AND This entry does not match with any in given list Sequence truncated to ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE%2P22< FORMIDȤP26Ph%B%4'H)\+p,-Yppp;q90333QjQPO[}PQV2PP8}PQ ޫPFOR$INI_DES1_R21ԫ FOR$WRITE_SF FOR$IO_T_DSD FOR$IO_T_DS FOR$IO_ENDݰRV12RSCB[1RV FOR$WRITE_SF2R~ FOR$IO_W_V FOR$IO_T_DSSP@b FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF2R~ FOR$IO_W_V FOR$IO_T_DSSCb FOR$IO_T_DSRP2P~ FOR$IO_W_V FOR$IO_T_DSCc  FOR$IO_T_DS FOR$IO_END=VR, \, Z FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END~ FOR$READ_SF< FOR$IO_T_DS FOR$IO_END1kԼ' } T, (2z<WX2XYIB[I*_YP, @b2Y(2Iz=WX FOR$WRITE_SFT FOR$IO_T_DS FOR$IO_ENDݟ FOR$READ_SFD FOR$IO_T_DS FOR$IO_ENDz/XFOR$STOP\FOR$OPENP1"VWB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDꑫ;1WB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END;1k}STANFORDTV2VPW@B[P(@bWB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDˀ LIB$INDEXP˔ LIB$INDEXPWB~ FO/(.:~ MFOLD.BCK*[MFOLD]FORMID.OBJ;35R$READ_SFL FOR$IO_T_DS FOR$IO_ENDWB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END11)61k}GENBANK TV2PP, @bWB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END);2VPW@B[)AWB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END)6V2VPP, @b1V1>k}PIR TWX>V2VPX@B[P, @bXWB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END1)C1k}EMBL T)CV˨ LIB$INDEXP2VXX,P Hb) H2VPW@B[WB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END1(1k}NRC T(V˼ LIB$INDEX2VX2XY,P 2IzW¹9( L5 aB~ FOR$READ_SF?H*_ FOR$IO_W_RXP@b FOR$IO_T_DS FOR$IO_ENDWHB[WB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END1UWk11XX2XPP@\ X2XPPYI\11I\91I\P0PPZXP2PPPYI\ I\P0P ZY2YYYPPZX2XXXH\ H\P0P ZX2XXXPPZZV FOR$WRITE_SF  FOR$IO_T_DS2V~ FOR$IO_W_V FOR$IO_END2ZPP(@b1aPP Z(c\?ZXV2XPPY)Ib\(IbXZ=VXZ FOR$WRITE_SF( FOR$IO_T_DS FOR$IO_END1 B~ FOR$REWINDP12ZZJB[XYXB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDk FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDV1=XY,X)TU1J*_  FOR$WRITE_SF0 FOR$IO_T_DS2 ~ FOR$IO_W_V FOR$IO_END갼 2ZP@zB~ FOR$READ_SO2P@hd2J*_ZZh` FOR$IO_X_NL FOR$IO_END1ZkB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END)T] PPPWPP1Z1k2WPP2ZY@IhIh*/Ih1Ih2 IhZ kZ k FOR$WRITE_SF8 FOR$IO_T_DS2 ~ FOR$IO_W_V FOR$IO_ENDIh ZkZ  FOR$WRITE_SF@ FOR$IO_T_DS2 ~ FOR$IO_W_V FOR$IO_END=PW=k1VHFOR$STOPPFOR$STOPP LOCUSQ"GENBANK QORIGIN//ID SQ SequenceNRC  OFORMIDFOR$OPEN LIB$INDEX $CODEe$PDATA,$LOCALFOR$STOP FOR$REWIND FOR$IO_END FOR$IO_W_R FOR$IO_W_V FOR$IO_T_DS FOR$IO_X_NL FOR$READ_SF FOR$READ_SO FOR$WRITE_SFFOR$INI_DES1_R272P4PoPPPLP|P%PPP PPP PP#PSP.WP#P;P.PPPPPP4PM8PBfPM~P1PPP!PPPnP#P^'PSPPe`P~P%PP PPPPPr2PO6PDPPPPPPPPAP\P/PP PPhPP_P.PP!APETPeZP(]PP1P&PP1 Pc PfS P b Pf P P P P P Px P P  P P PD P6' P- P1 P5-+ W *[MFOLD]GETSEQ.FOR;1+,O.'/ 4I'%-*0123KPWO&56n88h7ti89GHJJ+ subroutine getseq(filnam,nseq,pointr)>* Different name to Formid to return file name, index (Pointr)-* Changes in code marked by **()** around it.3* SUBROUTINE FORMID(SEQID,SEQ,NSEQ,NMAX,USED)c RESEARCHER: M. ZUKERc JUN 1986c DS TUDHOPEEc WRITTEN TO WORK ON VAX-11-750 UNDER VMS4.3 USING STANDARD F-77Ec #### NOTE #### USE OF CARRIAGE CONTROL LINE FEED SUPPRESSIONCc IS USED IN THIS PROGRAM AND IS NOT STANDARD"c FORTRAN-777c SEE '$' IN FORMAT STATEMENT 102 implicit integer*2 (a-z)& logical found,endfil,valid,used' integer*2 sline(500),seqnum(500) integer*4 nseq,nmax**()** parameter (nmax=10000) integer*4 pointr**()** character*8 stype character*30 seqids(500) character*30 choice,seqid**()** character*50 fmtseq(500)! character*80 filnam,reclin**()** character*1 seq(nmax) data found/.false./, . endfil/.false./, . valid/.false./Ec **************************************************************6c subroutine number FS372, test main driver FP475?c biomath program catalogued as FS372.FOR named formid.forEc **************************************************************c PURPOSE:8c subroutine used to extract sequences from various"c format type files including(c STANFORD,GENBANK,EMBL,PIR,and,NRCEc **************************************************************c variable list table:2c * -- sent down from main returned unchanged,c ** - returned to main from subroutine4c ***- sent down from main and returned changedBc INTEGERS:IDCNT -- to keep track of the number of sequence8c identifiers found in the file(c I,K -- loop countersGc LINE -- to point to the record line number of a fileCc N -- counter to extract the correct number of,c sequence elementsFc * NMAX -- maximum length of sequence expected by userEc ** NSEQ -- length of the sequence retrieved from fileBc POINTR -- pointer to point to sequence identifier;c chosen from array of identifiersBc SEQNUM -- an ARRAY of the length of the sequencesDc for the sequence identifiers found in the0c NRC-format type filesDc SLINE -- an ARRAY of the record-line numbers where6c a sequence starts in a fileCc START -- defines what column of a record to start3c reading the sequence in.Cc CHARACTERS:CHOICE-- character string of length 20 to read inEc choice for sequence identifier to retrieveCc FILNAM -- character string of length 50 to read in(c the filename.Bc FMTSEQ -- an ARRAY of characters, each length 50,Dc describing how the sequence is to be readCc RECLIN -- a record of a file, length 80 charactersBc ** SEQ -- an ARRAY of characters each length 1 to-c store the sequence9c ** SEQID -- retrieved name of the sequenceCc SEQIDS -- an ARRAY of retrieved names of sequencesDc STYPE -- character string of length 8 defining the3c format type of the file.Ac LOGICALS:FOUND -- logical variable used in looping until.c something retrievedFc *** USED -- logical variable used in determining if the@c subroutine has been previously calledAc VALID -- logical variable used in looping until+c some input validcc4c if the subroutine has NOT been USED then must;c input the filename and do error checking on filenameBc else branch to listing the sequences available in this file**()** used=.false.**()** if (.not.used) then10 found = .false. valid = .false. used = .false.:c initialize for a new file by setting variables back)c to zero and blanking out old names**()**"* IF (NMAX.EQ.0) NMAX = 9999**()** nseq = 0 stype = ' '% seqid = ' 'C filnam= ' ' do 500 i = 1,500 sline(i) = 0 seqnum(i)= 0* seqids(i)=' 'F fmtseq(i)= ' '500 continue< write(6,102) 'INPUT SEQUENCE FILE NAME ( / to end): '102 format(5x,a42$)( read(5,110,end=999,err=10) filnam110 format(a50)& if(filnam(1:1).eq.'/') goto 999Cc open the file only after a valid filename has been retrievedAc error in filename results in prompting for the input again/ open(66,file=filnam,status='OLD',err=10)Bc find sequence file format type and the sequence identifiers idcnt = 0 line = 1c DO WHILE (.NOT.FOUND)1600 read(66,120,end = 410,err = 991) reclin120 format(a80)=c STANFORD format, recognized by the ';' in the first columnc of the record& if (reclin(1:1).eq.';') then#c DO WHILE (.NOT.ENDFIL)610 line = line + 14 read(66,120,end = 410,err=991) reclin;c to find the next sequence identifer scroll through the:c file until the first character in the line is not ';'+ if (reclin(1:1).ne.';') then% found = .true.( stype ='STANFORD'( idcnt = idcnt + 1) sline(idcnt)= line/ seqids(idcnt) = reclin(1:30)" line = line + 18 read(66,120,end = 410,err=991) reclin;c DO WHILE ((INDEX(RECLIN,'1').EQ.0).AND.7c . (INDEX(RECLIN,'2').EQ.0))c ENDDO6615 if (index(reclin,'1').eq.0) then7 if (index(reclin,'2').eq.0) then' line = line + 1= read(66,120,end = 410,err=991) reclin! goto 615 endif endif=c assume at least one line not a sequence identifier occursAc after last sequence read in to get around the CTRL-L problem.=c therefore, after reading in the record containing the end2c of sequence identifier, read in another record" line = line + 18 read(66,120,end = 410,err=991) reclin endifc ENDDO& if (.not.endfil) goto 610@c GENBANK format, recognized by the word LOCUS starting in the c first position of the record. elseif (reclin(1:5).eq.'LOCUS') then found = .true.# stype = 'GENBANK ' idcnt = 1. seqids(idcnt) = reclin(13:27)'c DO WHILE (.NOT.ENDFIL)$620 line = line + 1: read(66,120,end = 410,err=991) reclin;c scrolling through to find the key phrase ORIGIN becauseCc the line after this key phrase occurrance is where the sequencec occurs in the file;@c read through the file obtaining other sequences by scrolling9c through to the '//' which signals the end of sequence7c Then start looking for another sequence identifier.5 if (reclin(1:6).eq.'ORIGIN') then+ sline(idcnt) = line6c DO WHILE (RECLIN(1:2).NE.'//')5625 if (reclin(1:2).ne.'//') then* line = line + 1@ read(66,120,end = 410,err=991) reclin# goto 625 c ENDDOu endif 9 elseif (reclin(1:5).eq.'LOCUS') thenU, idcnt = idcnt + 18 seqids(idcnt) = reclin(13:27) endifc ENDDO, if (.not.endfil) goto 620?c PIR format, recognized by the '>' occurring in column 1 of a Bc record. The sequence itself start 2 lines down from the recordc containing '>'.* elseif (reclin(1:1).eq.'>') then found = .true.e# stype = 'PIR 'd'c DO WHILE (.NOT.ENDFIL)00630 if (reclin(1:1).eq.'>') then) idcnt = idcnt + 1e/ sline(idcnt) = line + 1 4 seqids(idcnt) = reclin(5:25) endifc# line = line + 1a9 read(66,120,end = 410,err=991) reclinxc ENDDO, if (.not.endfil) goto 630Ac EMBL (european) format, recognized by the key phrase ID in the*c first column of the record.. elseif (reclin(1:5).eq.'ID ') then found = .true.t# stype = 'EMBL 'Dc scrolling through to find the key phrase 'SQ Sequence' becauseCc the line after this key phrase occurrance is where the sequencemc occurs in the file;y(c DO WHILE (.NOT.ENDFIL)5640 if (reclin(1:5).eq.'ID ') then*, idcnt = idcnt + 1@ seqids(idcnt) = reclin(6:index(reclin,' '))B elseif (reclin(1:13).eq.'SQ Sequence') then. sline(idcnt) = line endif$ line = line + 1: read(66,120,end = 410,err=991) reclinc ENDDO, if (.not.endfil) goto 640Ac NRC format, recognized by '(' occurring in the first column ofrBc a record. The record line following this line holds the number@c of elements in the sequence and the name of the sequence. The8c following line signals the beginning of the sequence.:c The sequence itself is read in by using variable formatBc described by the '(' record line. This format statement on the1c record containing '(' ,must also be retrieved. * elseif (reclin(1:1).eq.'(') then found = .true.$ stype = 'NRC '(c DO WHILE (.NOT.ENDFIL)1650 if (reclin(1:1).eq.'(') thenf) idcnt = idcnt + 1 C fmtseq(idcnt) = reclin(1:index(reclin,')'))-' line = line + 18 read(66,140,end = 410,err = 991)3 . seqnum(idcnt),seqids(idcnt)0+ sline(idcnt) = linec endif$ line = line + 1: read(66,120,end = 410,err=991) reclinc ENDDO"140 format(i4,5x,a30)* if (.not.endfil) goto 650 endifsDc keep scrolling through the file until a key phrase signalling>c a format type is recognized or the end of file is found line = line + 1 c ENDDO if (.not.found) goto 600s@c if a format type has not been found then this cannot be a(c sequence file and return to main.410 if (.not.found) then D write(6,105) ' NO SEQUENCE IDENTIFIERS FOUND IN THIS FILE '105 format(5x,a50)  returna endif-c if this is a valid format type proceeda used = .true. endif<c IF USED this call before start at listing identifiers'c listing the sequence identifiers 3c allow the user to input the number requestedn0c or control Z to finish here and return toc entering a new filename valid = .false.7c keep outputting the list of sequence identifiersi@c while NOT VALID choice of sequence identifier is inputtedc DO WHILE (.NOT.VALID) 4660 write(6,150) 'AVAILABLE SEQUENCES IN ',filnam150 format(1x,a23,a50)d do 525 k = 1,idcnt,2$ if (sline(k).ne.0) then# if (k .eq. idcnt) then=- write (6,151) k,'.',seqids(k)e elsekA write (6,191) k,'.',seqids(k),k+1,'.',seqids(k+1)M endif$151 format(1x,i3,a1,1x,a30)4191 format(1x,i3,a1,1x,a30,3x,i3,a1,1x,a30) endif525 continue& choice = ' '& seqid = ' ' pointr = 0m write(6,152)iD .' CHOOSE SEQUENCE by NUMBER or NAME , or ? for RELIST; ' write(6,152) @ .' DEFAULTS TO THE FIRST ONE, / for NEW file.'152 format(1x,a60) read(5,153,end=10) choice153 format(a30)% if(choice(1:1).eq.'/') goto 10i<c error checking of the inputted CHOICE and determiningDc if this input is a number, a default value, a relist command-c or the name of the sequence identifiere i = 1/ do while (choice(i:i).eq.' '.and.i.lt.6)l i = i + 1 enddo> if ((choice(i:i).ge.'1').and.(choice(i:i).le.'9')) thenDc using COLLATING sequence to convert character to number value2 pointr = ichar(choice(i:i)) - ichar('0')* if (choice(i+1:i+1).ne.' ') thenG pointr = ichar(choice(i+1:i+1)) - ichar('0') + 10 * pointrF endif * if (choice(i+2:i+2).ne.' ') thenG pointr = ichar(choice(i+2:i+2)) - ichar('0') + 10 * pointrr endif# if (pointr.gt.idcnt) thenn@ write(6,154) ' NUMBER CHOICE BETWEEN 1 AND ',idcnt154 format(a30,i2)d else% seqid = seqids(pointr)  valid = .true.i endif - elseif (ichar(choice(6:6)).eq.32) then  pointr = 1 seqid = seqids(1)  valid = .true.' elseif (choice(1:1).eq.'?') then  continue elseIIc find out if the inputted choice is in the list of seq identifiers.C pointr = 0 do 535 k = 1,idcnt* if (seqids(k).eq.choice) then$ seqid = seqids(k) pointr = k ! valid = .true. endif535 continue if (pointr.eq.0) then F write(6,105) 'THIS ENTRY DOES NOT MATCH WITH ANY IN GIVEN LIST' endif endif c ENDDOt if (.not.valid) goto 660 <c having obtained a valid sequence choice or default of?c one available sequence, rewind the file and retrieve thec sequence  rewind(66,err = 992)e>c having retrieved the line number in the file where this>c identifier occurs from SLINE(POINTR) scroll through the&c file until this line is reached& do 550 i = 1,sline(pointr)3 read(66,120,end = 410,err=991) reclini550 continue>c if nrc type then read sequence according to format type$ if (stype.eq.'NRC ') then# nseq = seqnum(pointr)=8c if the number in the NRC sequence is greater than3c the maximum number sent down from main, then 9c truncate to NMAX and output a message to the user.4$ if (nseq.gt.nmax) thenC write(6,160) ' SEQUENCE TRUNCATED TO ',nseqe"160 format(1x,a30,i5) nseq = nmax endift7 read(66,fmtseq(pointr),end = 420,err=991)g- . (seq(k),k=1,seqnum(pointr))<c Else if not type NRC then find the sequence by taking<c each letter of the next records until end-of-sequence@c indicator found or number in the sequence NMAX is reached else1 n = 1 found = .false.c DO WHILE (.NOT.FOUND)1670 read(66,120,end = 420,err=991) reclin Ac there is a need for the two positions to start reading the Cc sequence; to accommodate the GENBANK format and the STANFORD c end-of-sequence checks.) if (stype.eq.'GENBANK ') thent start = 10 else start = 1  endif= do 565 i = start,80 =c if the number in the sequence is less than the desired.?c number, NMAX sent down from main, then retrieve sequencei" if (n.le.nmax) then& if (.not.found) then& seq(n) = reclin(i:i))c check if an early end of sequence > if ((seq(n).eq.'1').or.(seq(n).eq.'2').or.A . (reclin(1:1).eq.'/').or.(seq(n).eq.'*')) thenl$ seq(n) = ' '$ nseq = n - 1& found = .true.<c if not an end-of-sequence character but have gone far$c enough, then truncate to NMAX+ elseif (n.eq.nmax) then6# nseq = nmax & found = .true.C write(6,160) ' SEQUENCE TRUNCATED TO ',nseqt@c if not a end-of-sequence character, check to see if it is@c not a blank character. Blank characters will not be addedc to the sequence.s/ elseif (seq(n).ne.' ') then " n = n + 1 endif endifeAc if the number of sequence characters found is Greater thanE4c NMAX then all of the sequence has been found. else " found = .true. nseq = n write(6,160)9 . ' SEQUENCE TRUNCATED TO ',nseqS endif 565 continuec ENDDO# if (.not.found) goto 670  endifn% close(unit=66,status='keep')(420 return'991 stop ' ERROR IN READING FILE ''992 stop ' ERROR IN REWINDING FILE'6)999 stop ' END of SESSION...GOOD BYE'i end*[MFOLD]GETSEQ.OBJ;1+,P./ 4 f-*0123KPWO56Fi74i89GHJ1GETSEQ0123-Feb-1992 00:5023-Feb-1992 00:50VAX FORTRAN V5.7-133 GETSEQPINPUT SEQUENCE FILE NAME ( / to end): 12 ) NO SEQUENCE IDENTIFIERS FOUND IN THIS FILE AVAILABLE SEQUENCES IN . CHOOSE SEQUENCE by NUMBER or NAME , or ? for RELIST; DEFAULTS TO THE FIRST ONE, / for NEW file. NUMBER CHOICE BETWEEN 1 AND THIS ENTRY DOES NOT MATCH WITH ANY IN GIVEN LIST SEQUENCE TRUNCATED TO ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE*2P22< GETSEQPP(PF&B&(*,,.Zqqq<r80444BRkQPO[}PQ VPP1Y FOR$WRITE_SFˤ FOR$IO_T_DS FOR$IO_T_DS FOR$IO_ENDݰRV12RSCb41RV FOR$WRITE_SF2R~ FOR$IO_W_Vˬ FOR$IO_T_DSSP˴@<˸˴ FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF2R~ FOR$IO_W_V˼ FOR$IO_T_DSSC< FOR$IO_T_DSRP2P~ FOR$IO_W_V FOR$IO_T_DSC4< FOR$IO_T_DS FOR$IO_END=VR, Լ  FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END~ FOR$READ_SF FOR$IO_T_DS FOR$IO_END㑫/1kԼ} ,2 P <ZW2WXHb4HJ8XP, @<2X(2Hv=ZW FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_ENDv FOR$READ_SF FOR$IO_T_DS FOR$IO_END /1(FOR$OPENP1?VWB~ FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDꑫ;1WB~ FOR$READ_SF FOR$IO_T_DS FOR$IO_END‘;1k}STANFORDV2VPW@b4P(@k}PIR WZ>V2VPZ@b4P, @JPNPPPPPPPPP-KPPPq\P eP\mPoPRyP"PP!PhP_P(PAP-P&ZPrP1PPP6P3 P40 P5 PJ PY P_ Pu P{ P P P PK P7 P  P P2 *+ XO *[MFOLD]HEADER.DAT;2+,U./ 4@j-*0123KPWO56Իi7Tai89GHJ@$! header.dat is used for initialization of the batch file. For$! example....$ set default [.mfold]*[MFOLD]JJLIB.FOR;1+,W./ 4M`-*0123KPWO56!h7ti89GHJ***** ;** MYLIB.FOR is the library of routines written in fortran.'** Name Type CommentK** GetFil Sub Get a file name and see if it's old or new.=** Yes L. Func Query and wait for the answer Y or N.M** UpCase C*1 Func Take a single char and convert to upper case.**+** - John Jaeger 28Aug87*0 subroutine getfil (tsiz,text,fname,isold)5** Get the name of a file and see if it's old or new.*+ 0~ MFOLD.BCKW*[MFOLD]JJLIB.FOR;1Mf character*80 fname,inbuf,query,text integer tsiz logical isold,nofile,yes character*1 ans,upcase* nofile=.true."103 write (6,1) text(1:tsiz) read (5,2) fname*9** Try to open the old FName to see if it already exists.B** This is to prevent writing over a previous data file by mistake*+ inquire (file=fname,exist=itexists) if (isold) then" if (itexists) then. nofile=.false. else+ write (6,5) endif else4 if (fname.eq.' ') then2 fname='SYS$OUTPUT'& return endif* if (itexists) thenF query='File already exists. Continue'0 if (yes(31,query)) nofile=.false. else. nofile=.false. endif endif if (nofile) goto 103*% 1 format (1x,a,' file name? '$) 2 format (a)) 5 format (1x,'File does not exist.') return end ( logical function yes(qsiz,query)* character*80 query integer qsiz,ich$ character*1 inbuf,y,n,upcase data y/'Y'/n/'N'/*!10 write (*,1) query(1:qsiz) read (*,2) inbuf ich=ichar(upcase(inbuf))8 if (ich.ne.ichar(y).and.ich.ne.ichar(n)) goto 10 yes=ich.eq.ichar(y)%1 format (1x,a,' (Y or N)? ',$)2 format (a) return end ' character*1 function upcase (ch)'** Change Ch to upper case if necessary character*1 ch' character*1 lowera,lowerz,uppera*- data lowera/'a'/lowerz/'z'/uppera/'A'/*F if (lle(lowera(1:1),ch(1:1)).and.lge(lowerz(1:1),ch(1:1))) then; upcase=char(ichar(uppera)+ichar(ch)-ichar(lowera)) else upcase=ch endif return end*[MFOLD]JJLIB.OBJ;1+,[ ./ 4N-*0123KPWO56U i7i89GHJ1GETFIL0123-Feb-1992 01:5023-Feb-1992 01:50VAX FORTRAN V5.7-133 GETFIL9P) file name? )File does not exist. GETFILTPPPP\PdP|HP[}PQ} PQV FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF  FOR$IO_T_DS FOR$IO_END$ FOR$INQUIREkV FOR$WRITE_SF FOR$IO_END-P n, 2 Pk,< P8YESPVVV1D2PSYS$OUTPUTFile already exists. Continue |HGETFILYES FOR$INQUIRE$CODEZ$PDATA$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SF>qP"tPxPP>PPPP3' .YES0123-Feb-1992 01:5023-Feb-1992 01:50VAX FORTRAN V5.7-133  YESP) (Y or N)? ) YESPP QYNPH[}PQR~ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END~ FOR$READ_SF FOR$IO_T_DS FOR$IO_END~ UPCASE⚎PPRQPQQPRQQP HYESUPCASE$CODE$PDATA4$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SFwP 1UPCASE0123-Feb-1992 01:5023-Feb-1992 01:50VAX FORTRAN V5.7-133 UPCASE UPCASEmPQazAPH[}PQ}PQ  P QQPQQPP E HUPCASEF$CODE$PDATA$LOCALP &P>PF*[MFOLD]LDOT.OBJ;2+,.!/ 4!-*0123KPWO"56݁i7Di89GHJ1DOTPLT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 DOTPLTiP@  Minimum Energy = Increment = Enter New Increment ENTER NEW VINC: BASE = N = Base-pair = ( , )Score = +[14;1HMinimum energy = [16;1HIncrement = #[18;1HEnter New Increment [18;24H+[18;24H +0 ENTER PLOT FILE NAME : ) ENTER PLOT LABEL (UP TO 59 CHARACTERS) :</ ENTER TICK MARK INTERVAL & NUMBER OF LEVELS : P+"[2;1HEnter New Increment "[3;1H [2;24H+[2;24H +[2;1HBase = [3;1HN = +[21;1HBase-pair = ,[22;1HEnergy =  DOTPLTP  <\z$ T T AOUT@s s AOUT@$ AOUT@$$$$$$$$ <@D AOUT@D AOUT@$$H<@$$H(4 AOUT@ 8P AOUT@d AOUT@ 0 AOUT@$L AOUT@// AOUT@44 AOUT@6P6 AOUT@$$P. PO[ЫDVWϼ 1˘TEKRESETˠSCURSRN(P$QNQQDQPN RFRP@PN,RDQRNQFQR@R@RJRR@PJP4$PRP0Ы0Ы4˰VPR0$~^˼V^PRXRSR0TT^S4UU^V^PYU^0$PRP~^V^YPPXTUPXSRѫ$R1ѫ$r1ѫ$Qѫ$qVT100VDѫ$Tѫ$tNEWPAGVT100FOR$STOPѫ$Pѫ$p1VT100 FOR$WRITE_SF FOR$IO_END FOR$READ_SFt FOR$IO_T_DS FOR$IO_ENDFOR$OPEN$ FOR$WRITE_SF FOR$IO_END* FOR$READ_SFRB FOR$IO_T_DS;R FOR$IO_END/ FOR$WRITE_SF FOR$IO_END FOR$READ_SL߫< FOR$IO_L_R߫@ FOR$IO_L_R FOR$IO_END* FOR$WRITE_SFd FOR$IO_X_DA FOR$IO_ENDb FOR$WRITE_SF$ FOR$IO_L_Vݫ< FOR$IO_L_Vݫ< FOR$IO_L_V FOR$IO_L_V FOR$IO_L_V FOR$IO_L_V FOR$IO_ENDѫ@@PPV$R$1ЫSTի1$PTUUPTP@TVPUЫTT$~^0(V^UPѫ@VPUUUVUUU@$YTQQYTYUIYPY$YTPPYTYISTUg FOR$WRITE_SFի4VP FOR$IO_L_V FOR$IO_ENDR@ FOR$CLOSE1ѫ$Gѫ$g1N$PP^PP^XHDWINDO^NEWPAG$\SETMRG$HOMENEWLINpAOUTNEWLIN˄AOUTHOMELINEFLINEFALFMODːVT100l FOR$WRITE_SF, FOR$IO_L_R, FOR$IO_L_R, FOR$IO_L_R FOR$IO_END FOR$REWIND FOR$READ_SF| FOR$IO_T_DS FOR$IO_END$ FOR$WRITE_SF, FOR$IO_L_R FOR$IO_END˘TEKTYTTP@ TTP@-YTTUE0E91dTEKlSCURSRѫ$Tѫ$tNEWPAG|VT100FOR$STOPѫ$R1sѫ$r1fѫ$Qѫ$q1˄SETMRG˄TEKˌINITT˔TERMˠSETBUF$<< < <˨TWINDON$PP^P^˼DWINDO^NEWPAGTRIAXISTWINDOԫ$HOMETLINEFTtAOUT IOUTNEWLIN0AOUT<IOUTNEWLINNEWLINLAOUTNEWLINALFMOD¹,p+ 2XVT100L FOR$WRITE_SF, FOR$IO_L_R FOR$IO_L_V, FOR$IO_L_Rݫ FOR$IO_L_V, FOR$IO_L_R, FOR$IO_L_R FOR$IO_END FOR$REWINDyu FOR$READ_SF| FOR$IO_T_DS FOR$IO_END$ FOR$WRITE_SF, FOR$IO_L_R FOR$IO_END`TEKTYTTP@ TTP@-YTTUE0E91UTZJ0J9JP0P UZZPUTYU1$UZ$ZԫhVECTORUZ$ZU$$UˀVECTORZU$ FOR$WRITE_SF, FOR$IO_L_R4 FOR$IO_L_R FOR$IO_END1Ï(P PNPP$UNUUDUPN UFUP@PJPUU^˔U^˘ːV^NPZ$HOMENEWLINˤAOUTE_$˴˰IOUTAOUTNEWLINAOUTJZ~^IOUT^AOUT1VT100 FOR$WRITE_SF, FOR$IO_L_RE_$ FOR$IO_L_R, FOR$IO_L_RJZ~ FOR$IO_L_V FOR$IO_END1ZTUE0E9EP0P ZUUPZTYZNEWPAG$<P< PԫT$Z$1$PUUPP@$U$1ѫ1ˠVPY$~^˴ˬV^PY˸VPT$~^V^PTYPYPVP$YTTYYPIUeVPTVPTZSETMRGGAXIS$SETMRG VNP,MOVEA$Z$Nk8VNPDDRAWAZN$ZZ^XZ^`PDWINDO^1i$1HOMEHOMEZNEWLINZNEWLIN AOUTмP@_$IOUT(AOUTмP@_$84IOUTDAOUTNEWLINNEWLINXAOUTX8dIOUT1~lVT100# FOR$WRITE_SF, FOR$IO_L_RмP@_$ FOR$IO_L_RмP@_$ FOR$IO_L_R, FOR$IO_L_RX FOR$IO_L_V FOR$IO_END1S ODOTPLTTEKINITTTERMSETBUFTWINDODWINDONEWPAGTRIAXISHOMELINEFAOUTIOUTNEWLINALFMODVT100VECTORRESETSCURSRVFOR$OPEN FOR$CLOSESETMRGGAXISMOVEADRAWA $CODE\$PDATA $LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSFOR$STOP FOR$REWIND FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$IO_X_DA FOR$READ_SF FOR$READ_SF FOR$READ_SL FOR$WRITE_SFP PPP -P:PEP OPiP sPP PqP  PPgP4PP(PPPP )P[P pPGPH7P,pP{PPP PoP P P PPP^P Pk,PmP, PP&P6P=PRPYPPPP0\ Pc" P) PT P \ P } P P P P, P+ P$Y P  P  P P " .TRI0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  TRI TRIPPH[޼޼kMOVABS޼޼ DRWABS޼޼ DRWABS޼(޼,$DRWABS\ HTRIMOVABSDRWABSQ$CODE$PDATA0$LOCAL Q/AXIS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 AXISP@  AXIS@P(,0  ,8 $8$P. PI [R$(P$PP2PǏP QPPQSS$$SPQQ$$QQTN$QNSPGPQUNTPGPQV$ CHRSIZ(CSIZEW $<< ޼ <޼@4TWINDOXSNXPDUPJPP@_$NPPAPkN$PGPkPQPx@QHMOVEATDRWRELW~^d`MOVREL^lIOUT2SX޼ x޼˄tTWINDOSTNSPDVPJPP@_$N$UNPPCPUGUUQU=ˈMOVEA˔DRWRELW~^ˤΫ ~^˨ˠMOVREL^ˬIOUT2TS˴CHRSIZW IAXISCHRSIZCSIZETWINDOMOVEADRWRELMOVRELIOUT2$CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSUPP(P.PPP PP]P*GPlvP9PD+0GAXIS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 GAXIS#P@ GAXISPp.TEK0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  TEK3P%!KALZMG+++ TEKP  PH[Ѽ1 FOR$WRITE_SF FOR$IO_L_Rk FOR$IO_T_DS FOR$IO_T_DS FOR$IO_L_R FOR$IO_END FOR$WRITE_SF FOR$IO_L_R FOR$IO_T_DS FOR$IO_T_DS FOR$IO_L_R FOR$IO_END FOR$WRITE_SF FOR$IO_L_R  FOR$IO_T_DS( FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_L_R0 FOR$IO_T_DS8 FOR$IO_T_DS FOR$IO_L_R FOR$IO_ENDѼ& FOR$WRITE_SF FOR$IO_L_R FOR$IO_END HTEK>$CODE,$PDATA@$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$WRITE_SFPP#>1VECTOR0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 VECTOR VECTOR4P ($, ($,$P. P H [ЫRPP1׼ּ޼0޼4,MARKP޼޼VPS޼$$~^( V^PS PSPRPNP$P¼PNP 8MOVEADDRAWARRRNk$P¼PNP1FRPNP$P¼PNP PMOVEA\DRAWAR HVECTORVMARKMOVEADRAWA$CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS6P8P@xP3~P)PPP)1%**[MFOLD]LIN.FOR;1+,h.9/ 4S99-*0123KPWO:56Ω[h7tl i89GHJ(c Energy funtion.@c ERG is the energy of a loop closed by I,J (new numbering).>c IP,JP is the other closing base-pair when MODE = 2 or 3.Fc The ends of the sequence cannot be contained in a hairpin, bulgeCc or interior loop. By convention, the ends of the sequence areBc put into a special kind of multi-loop. This can be called an*c exterior loop or an open multi-loop.cc 1/2 Asym. loop correction3c Extrapolate loops with dG(n)=dG(30)+1.75*ln(n/30)c(c* Hairpins of 3 have no terminal stack.c" function erg(mode,i,j,ip,jp) include 'rfd.inc' dimension e(4) integer*2 tlink,tlptrc 100 if (mode.eq.1) thenc Read energy files. call ergread erg = 0 return endif erg = 0+c Do not allow prohibited base to pair.. if (force(i).eq.1.or.force(j).eq.1) then erg = infinity return endif  if (mode.lt.6) then.c Add bonus energy to force base-pairs.= if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) then! erg = erg + eparam(9) endif endif - goto (100,200,300,400,500,600,700),mode &c Nucleotide accessibility option./200 if (force(i).eq.3.or.force(jp).eq.3) then erg = infinity return endifBc Molecule is not circular. N is not covalently bonded to N+1." if (i.eq.n.or.j.eq.n+1) then erg = infinity return endifc Stacking energy.B erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp)) . + eparam(1) return  <300 if ((i.le.n.and.ip.gt.n).or.(jp.le.n.and.j.gt.n)) thenCc Loop is not allowed to contain the ends of the sequence. erg = infinity return endifc size1 = ip - i - 1 size2 = j - jp - 1( if (size1.eq.0.or.size2.eq.0) then-c Check for nucleotide accessibility.0 if (size1.eq.0.and.force(i).eq.3) then erg = infinity return endif1 if (size2.eq.0.and.force(jp).eq.3) then erg = infinity return endif size = size1+size2c Bulge loop energy. if (size.eq.1) thenI erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))- . + bulge(size) + eparam(2)" elseif (size.gt.30) then9 loginc = int(prelog*log((float(size)/30.0)))7 erg = erg + bulge(30) + loginc + eparam(2) else0 erg = erg + bulge(size) + eparam(2) endif return else size = size1+size2% lopsid = abs((size1-size2))c Interior loop. if (size.gt.30) then9 loginc = int(prelog*log((float(size)/30.0)))J erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))E . + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1)). . + inter(30) + loginc + eparam(3)A . + min0(maxpen,(lopsid*poppen(min0(4,size1,size2)))) elseJ erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))E . + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))' . + inter(size) + eparam(3)A . + min0(maxpen,(lopsid*poppen(min0(4,size1,size2)))) endif return endif !400 if (i.le.n.and.j.gt.n) thenAc Hairpin loop must not contain the ends of the sequence. erg = infinity return endifc size = j-i-1D if ((size.eq.3).and.fce(i,j).and.seq(hstnum(i+1)).eq.' ') thenc Closed excision erg = eparam(9) return endif if (size.gt.30) then5 loginc = int(prelog*log((float(size)/30.0)))F erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))2 . + hairpin(30) + loginc + eparam(4) else if (size .lt. 4) thenc c* Special case for hairpin of 3c. erg = erg + hairpin(size) + eparam(4) elsec tlink=0 if (size.eq.4) thenI key=((numseq(i+4)*8+numseq(i+3))*8+numseq(i+2))*8+numseq(i+1) tlptr=1I do while ((tlptr.le.numoftloops).and.(tloop(tlptr,1).ne.key)) tlptr=tlptr+1 enddo: if (tlptr.le.numoftloops) tlink=tloop(tlptr,2) endifC erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))3 . + hairpin(size) + eparam(4) + tlink endif return 3c Multi-branch (or multi-) loop closed by I,J.500 do 501 ii = 1,4501 e(ii) = infinity  if (i+2.gt.j-3) thenEc There are at most 3 bases between I and J. The fragment from.c I to J inclusive contains the origen. e(1) = 0E if (i.ne.n) e(2) = dangle(numseq(i),numseq(j),numseq(i+1),1)G if (j.ne.n+1) e(3) = dangle(numseq(i),numseq(j),numseq(j-1),2)& if (i.ne.n.and.j.ne.n+1) then= e(4) = dangle(numseq(i),numseq(j),numseq(i+1),1) +; . dangle(numseq(i),numseq(j),numseq(j-1),2) endif else if (i.ge.n-1) then4c I is at or next to the end of the sequence. e(1) = w2(n+1,j-1) if (i.ne.n) thenI e(2) = dangle(numseq(i),numseq(j),numseq(i+1),1) + w2(n+1,j-1)= e(4) = dangle(numseq(i),numseq(j),numseq(i+1),1) +I . dangle(numseq(i),numseq(j),numseq(j-1),2) + w2(n+1,j-2) endifG e(3) = dangle(numseq(i),numseq(j),numseq(j-1),2) + w2(n+1,j-2)) else if (j.eq.n+1.or.j.eq.n+2) then4c J is at or next to the end of the sequence. e(1) = wst2((n-1)*i+n)O e(2) = dangle(numseq(i),numseq(j),numseq(i+1),1) + wst2((n-1)*(i+1)+n) if (j.ne.n+1) thenK e(3) = dangle(numseq(i),numseq(j),numseq(j-1),2)+wst2((n-1)*i+n)= e(4) = dangle(numseq(i),numseq(j),numseq(i+1),1) +Q . dangle(numseq(i),numseq(j),numseq(j-1),2) + wst2((n-1)*(i+1)+n) endif else ind1 = (n-1)*i ind2 = ind1 + n - 1 do k = i+2,j-3 if (k.eq.n) thenCc When K = N, the structure splits into two disconnectedLc pieces. This open multi-loop ( exterior loop ) is not given theMc usual EPARAM(5),EPARAM(6) and EPARAM(10) destabilizing energies.c ind3 = -n8c No dangling ends next to the I,J base-pair.: e(1) = min0(e(1),wst2(ind1+k)+wst2(ind3+j-1)).c I+1 dangles on the I,J base-pair.G e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1): . + wst2(ind2+k) + wst2(ind3+j-1)).c J-1 dangles on the I,J base-pair.G e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2): . + wst2(ind1+k) + wst2(ind3+j-2)):c Both I+1 and J-1 dangle on the I,J base-pair.G e(4) = min0(e(4),dangle(numseq(i),numseq(j),numseq(i+1),1)C . + dangle(numseq(i),numseq(j),numseq(j-1),2): . + wst2(ind2+k) + wst2(ind3+j-2)) elseEc When K is not N, the ends of the sequence are not in theJc loop. This is a proper multi-loop with an energy of EPARAM(6)Gc for each single-stranded base, an energy of EPARAM(10) forHc each closing base-pair, plus and extra energy of EPARAM(5).8c No dangling ends next to the I,J base-pair.J e(1) = min0(e(1),wst1(ind1+k)+work1(k+1,mod(j-1,3))+eparam(5)& . +eparam(10)).c I+1 dangles on the I,J base-pair.G e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1)L . + wst1(ind2+k) + work1(k+1,mod(j-1,3)) + eparam(5)4 . + eparam(6) + eparam(10) ).c J-1 dangles on the I,J base-pair.G e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2)sL . + wst1(ind1+k) + work1(k+1,mod(j-2,3)) + eparam(5)4 . + eparam(6) + eparam(10) ):c Both I+1 and J-1 dangle on the I,J base-pair.G e(4) = min0(e(4),dangle(numseq(i),numseq(j),numseq(i+1),1)fC . + dangle(numseq(i),numseq(j),numseq(j-1),2)lL . + wst1(ind2+k) + work1(k+1,mod(j-2,3)) + eparam(5)8 . + 2*eparam(6) + eparam(10) ) endifu enddo endif  + erg = erg + min0(e(1),e(2),e(3),e(4)) return ,Gc Dangling base stacking energy. IP dangles over the I,J base-pair. 2c 3' or 5' dangle if JP = 1 or 2 respectively.;600 erg = erg + dangle(numseq(i),numseq(j),numseq(ip),jp)i return /700 if (force(i).eq.3.or.force(jp).eq.3) then erg = infinity return endif(c Terminal stack or mismatch energy.A erg = erg + tstk(numseq(i),numseq(j),numseq(ip),numseq(jp)). return end) e    subroutine fill9>c This subroutine computes the arrays of optimal energies. include 'rfd.inc'$ dimension inc(5,5),e1(5),e2(5)H data loop/3/,inc/0,0,0,1,0,0,0,1,0,0,0,1,0,1,0,1,0,1,0,0,0,0,0,0,0 ./  r vmin = infinity  if (n.le.80) thenl pinc = 5n elseif (n.le.100) then pinc = 2 else pinc = 1 endifr pcnt = pinc  crit = n*n*n/50   do j = 1,2*n-1*c How far along is the computation? if (n.gt.10) then if (j.le.n) then() if (j**3.ge.pcnt*crit) then)$ write (6,1000) pcnt# pcnt = pcnt + pinc endiff else 5 if ((2*n-j)**3.le.(100-pcnt)*crit) then $ write (6,1000) pcnt# pcnt = pcnt + pinc  endifa endif endif1ѻ~ MFOLD.BCKh*[MFOLD]LIN.FOR;1S9rJ1000 format ('+',i4,'%') * do i = min0(j,n),max0(1,j-n+1),-1 vij = infinity w1ij = infinity w2ij = 0  if (j.le.n) then ' if (j-i.le.loop) goto 300  else1. if (i.eq.n.or.j.eq.n+1) goto 100 endifGc Test for a prohibited base-pair or a pair which cannot form.jQ if (vst((n-1)*(i-1)+j).eq.1.or.inc(numseq(i),numseq(j)).eq.0) goto 200 Fc Compute VIJ, the minimum energy of the fragment from I to J>c inclusive where I and J base-pair with one another.-c Perhaps I,J closes a hairpin loop.a) vij = min0(vij,erg(4,i,j,i,j)) . if (j-i-1.ge.loop+2.or.j.gt.n) then.c Perhaps I,J stacks over I+1,J-1.; vij = min0(vij,erg(2,i,j,i+1,j-1)+v(i+1,j-1))  endifDc Search for the best bulge or interior loop closed by I,J.. if (j-i-1.ge.loop+3.or.j.gt.n) then do d = j-i-3,1,-11" do ip = i+1,j-1-d jp = d+ip 6 if (j-i-2-d.gt.eparam(7)) goto 1009 if (abs(ip-i+jp-j).le.eparam(8)) thens( if (ip.gt.n) thenS vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*(ip-n-1)+jp-n))  else O vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*(ip-1)+jp)) endif endifd enddo enddoo endif 0100 if (j-i-1.ge.2*loop+4.or.j.gt.n) then;c Search for the best multi-loop closed by I,J.z* vij=min0(vij,erg(5,i,j,i,j)) endif!c Compute W1IJ and W2IJ.eGc A multi-loop containing N and 1 (ie. N+1) as single-stranded Hc bases is called an exterior loop. W1IJ is the minimum foldingEc energy of a non-empty folding on I to J inclusive where anrGc exterior loop is given an energy of EPARAM(5) plus EPARAM(6)e@c per single-stranded exterior base plus EPARAM(10) per<c double-stranded exterior base-pair in addition to=c possible dangling base energies. W2IJ is similarlynCc defined except that the folding can be empty and that aneHc exterior loop is given no energy other than possible danglingc base energies.d200 do ii = 1,5 e1(ii) = infinity e2(ii) = infinity enddo if (i.ne.n) thennEc Add single-stranded I to an optimal structure containing c the base-pair I,J. I e1(1) = v(i+1,j) + eparam(10) + eparam(6) + erg(6,j,i+1,i,2) * e1(4) = w1(i+1,j) + eparam(6)0 e2(1) = v(i+1,j) + erg(6,j,i+1,i,2) e2(4) = w2(i+1,j) endif if (j.ne.n+1) then Ec Add single-stranded J to an optimal structure containing)c the base-pair I,J.nI e1(2) = v(i,j-1) + eparam(10) + eparam(6) + erg(6,j-1,i,j,1).* e1(5) = w1(i,j-1) + eparam(6)0 e2(2) = v(i,j-1) + erg(6,j-1,i,j,1) e2(5) = w2(i,j-1) endif( if (i.ne.n.and.j.ne.n+1) thenKc Add single-stranded I and J to an optimal structure containing #c the base-pair I+1,J-1.t< e1(3) = v(i+1,j-1) + eparam(10) + 2*eparam(6) +> . erg(6,j-1,i+1,i,2) + erg(6,j-1,i+1,j,1)4 e2(3) = v(i+1,j-1) + erg(6,j-1,i+1,i,2)( . + erg(6,j-1,i+1,j,1) endif D w1ij = min0(eparam(10)+vij,e1(1),e1(2),e1(3),e1(4),e1(5))> w2ij = min0(vij,w2ij,e2(1),e2(2),e2(3),e2(4),e2(5)) t0 if (j-i-1.gt.2*loop+2.or.j.gt.n) then! index = (n-1)*(i-1)n-c Search for an open bifurcation.( do k = i,j-1 if (k.eq.n) then= w1ij = min0(w1ij,wst2(index+k)+work2(k+1))  elseF w1ij = min0(w1ij,wst1(index+k)+work1(k+1,mod(j,3)))= w2ij = min0(w2ij,wst2(index+k)+work2(k+1))  endifd enddo  endif Ec Store VIJ, W1IJ and W2IJ. They can be regarded as elementseFc V(I,J), W1(I,J) and W2(I,J) in two dimensional arrays. TheyFc are actually stored in one dimensional arrays VST, WST1 and,c WST2 is position (N-1)*(I-1) + J.Ic Columns J,J-1 and J-2 of W1 are also stored in the work array,eIc WORK1. Column J of W2 is stored again in the work array WORK2.w7c This is done to reduce virtual memory swaps.p#300 vst((n-1)*(i-1)+j) = vija% wst1((n-1)*(i-1)+j) = w1ij% wst2((n-1)*(i-1)+j) = w2ij+# work1(i,mod(j,3)) = w1ij1 work2(i) = w2ij if (j.gt.n) theneHc VMIN is the minimum folding energy of the entire sequence.G vmin = min0(vmin,vst((n-1)*(i-1)+j)+vst((n-1)*(j-n-1)+i))  endif enddo if (j.ge.n) thene do k = j+1,n+1,-1Ac Fill in some work array values before beginning onc the next column.2> work1(k,mod(j+1,3)) = wst1((k-n-1)*(n-1)+j+1-n)3 work2(k) = wst2((k-n-1)*(n-1)+j+1-n) enddoT endif enddot return endBc Used to recall values of V which are actually stored in VST. function v(i,j)  include 'rfd.inc'n x if (i.gt.n) then" v = vst((n-1)*(i-n-1)+j-n) else v = vst((n-1)*(i-1)+j) endif1 return end1 )Dc Used to recall values of W1 which are actually stored in WST1. function w1(i,j) include 'rfd.inc'  0 if (i.gt.n) then$ w1 = wst1((n-1)*(i-n-1)+j-n) else w1 = wst1((n-1)*(i-1)+j) endifa return end  Dc Used to recall values of W2 which are actually stored in WST2. function w2(i,j) include 'rfd.inc'e ) if (i.gt.n) then$ w2 = wst2((n-1)*(i-n-1)+j-n) else w2 = wst2((n-1)*(i-1)+j) endif return endp m )   Dc Computes an optimal structure on the subsequence from II to JI?c where II and JI must base-pair with each other. ERROR = 0 %c indicates a normal termination.(Fc NFORCE is the number of forced base-pairs encountered during thec traceback.:c Base-pair information is stored in the array BASEPR.* subroutine trace(ii,ji,nforce,error) include 'rfd.inc'  r error = 0) 3,c Zero the appropriate region of BASEPR. if (ji.le.n) theng do k=ii,ji basepr(k) = 0d enddo else do k=1,ji-nr basepr(k) = 0e enddo, do k = ii,n basepr(k) = 0. enddo. endif Dc Initialize the stack of outstanding base-pairs and push II,JI,%c V(II,JI) and 0 on to the stack.r call initstn! call push(ii,ji,v(ii,ji),0)  nforce = 0 ) 100 i = j do while (i.eq.j)9Ec Pull a fragment ( I to J ) and its expected energy ( E ) from Ec the stack. OPEN = 1 indicates that the free bases are part ofoBc an exterior loop. OPEN = 0 (ie. closed) indicates that the,c free bases are part of a multi-loop. stz = pull(i,j,e,open) if (stz.ne.0) return enddo ,c Do I and J base-pair with one another? if (e.eq.v(i,j)) goto 300t n if (open.eq.0) then1 n0 do while (e.eq.w1(i+1,j)+eparam(6))*c Whittle away from the 5' end. i = i + 1 e = w1(i,j)! if (i.ge.j) goto 1000 enddo, do while (e.eq.w1(i,j-1)+eparam(6))*c Whittle away from the 3' end. j = j - 1 e = w1(i,j)! if (i.ge.j) goto 100  enddo pF if (e.eq.v(i+1,j)+eparam(10)+eparam(6)+erg(6,j,i+1,i,2)) then"c I dangles over I+1,J. i = i + 1 e = v(i,j) J elseif (e.eq.v(i,j-1)+eparam(10)+eparam(6)+erg(6,j-1,i,j,1)) then"c J dangles over I,J-1. j = j - 1 e = v(i,j) = elseif (e.eq.v(i+1,j-1) + eparam(10) + 2*eparam(6) + D . erg(6,j-1,i+1,i,2) + erg(6,j-1,i+1,j,1) ) then.c Both I and J dangle over I+1,J-1. i = i + 1 j = j - 1 e = v(i,j)o endif-c Check for stem closing a multi-loop.b/ if (e.eq.v(i,j)+eparam(10)) e = v(i,j)J o else o" do while (e.eq.w2(i+1,j))(c Whittle away at the 5' end. i = i + 1! if (i.ge.j) goto 100+ enddo" do while (e.eq.w2(i,j-1))(c Whittle away at the 3' end. j = j - 1! if (i.ge.j) goto 100, enddo j1 if (e.eq.v(i+1,j)+erg(6,j,i+1,i,2)) then="c I dangles over I+1,J. i = i + 1 e = v(i,j) 7 elseif (e.eq.v(i,j-1) + erg(6,j-1,i,j,1)) then "c J dangles over I,J-1. j = j - 1 e = v(i,j)tL elseif (e.eq.v(i+1,j-1)+erg(6,j-1,i+1,i,2)+erg(6,j-1,i+1,j,1)) then/c Bothe I and J dangle over I+1,J-1.  i = i + 1 j = j - 1 e = v(i,j)j endif endife f if (e.ne.v(i,j)) thenHc Cannot chop away at the ends any more and still the ends do notDc base-pair with one another. Structure MUST bifucate (OPEN). k = i200 if (k.eq.j) then *c Structure will not split. Error ii = hstnum(i)e ji = hstnum(j)  error = 10g returna endif9 if (open.eq.0.and.e.eq.w1(i,k) + w1(k+1,j)) theneDc Best structure on I,J splits into best structures on I,KGc and K+1,J. Push these fragments on to the stack. (OPEN = 0)($ call push(i,k,w1(i,k),0)( call push(k+1,j,w1(k+1,j),0) goto 100> else if (open.eq.1.and.e.eq.w2(i,k) + w2(k+1,j)) thenDc Best structure on I,J splits into best structures on I,KGc and K+1,J. Push these fragments on to the stack. (OPEN = 1) $ call push(i,k,w2(i,k),1)( call push(k+1,j,w2(k+1,j),1) goto 100 else  k = k + 1  goto 200 endif endif  nNc Base-pair found. All base-pairs are stored in the range 1 <= I < J <= N.Hc If I and J form a base-pair, then BASEPR(I) = J and BASEPR(J) = I.300 if (j.le.n) then basepr(i) = j basepr(j) = i else if (i.gt.n) then) basepr(i-n) = j-n basepr(j-n) = i-n i = i - n j = j - n else basepr(j-n) = i basepr(i) = j-n endifc open = 0*c Check if this is a forced base-pair.I if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) nforce = nforce + 1e&c Perhaps I,J stacks over I+1,J-1?# if (i.ne.n.and.j.ne.n+1) then)$ if (e.eq.erg(2,i,j,i+1,j-1) . + v(i+1,j-1)) then i = i + 1n j = j - 1l e = v(i,j) goto 300 endif endifs a(c Perhaps I,J closes a hairpin loop?' if (e.eq.erg(4,i,j,i,j)) goto 100  @c E' ( EP in the program ) is E corrcted for possible forcedc base-pairs. c( ep = eI if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) ep = ep - eparam(9)  i if (i+2.gt.j-3) then&c Tidy up loose ends (trivial).A if (ep.eq.0.or.(i.ne.n.and.ep.eq.erg(6,i,j,i+1,1))) theni j goto 100t : elseif (j.ne.n+1.and.ep.eq.erg(6,i,j,j-1,2)) then f goto 100( ) elseif (i.ne.n.and.j.ne.n+1.and.f@ . ep.eq.erg(6,i,j,i+1,1) + erg(6,i,j,j-1,2)) then k goto 100  l else  ii = hstnum(i)i ji = hstnum(j) error = 12  returnk endif  else if (i.ge.n-1) then (c Up to one base hanging on to I.$ if (ep.eq.w2(n+1,j-1)) then+ call push(n+1,j-1,w2(n+1,j-1),1)( goto 100w elseif (i.ne.n) then  9 if (ep.eq.erg(6,i,j,i+1,1) + w2(n+1,j-1)) thena. call push(n+1,j-1,w2(n+1,j-1),1) goto 100O else if (ep.eq.erg(6,i,j,i+1,1)+erg(6,i,j,j-1,2) + w2(n+1,j-2)) theno. call push(n+1,j-2,w2(n+1,j-2),1) goto 100 endif o; elseif (ep.eq.erg(6,i,j,j-1,2) + w2(n+1,j-2)) thenw+ call push(n+1,j-2,w2(n+1,j-2),1)n goto 100 elsem ii = hstnum(i)  ji = hstnum(j)  error = 12  returnh endif n) else if (j.eq.n+1.or.j.eq.n+2) then (c Up to one base hanging on to J." if (ep.eq.w2(i+1,n)) then( call push(i+1,n,w2(i+1,n),1) goto 100 n9 elseif (ep.eq.erg(6,i,j,i+1,1) + w2(i+2,n)) thene( call push(i+2,n,w2(i+2,n),1) goto 100 r elseif (j.ne.n+1) thenn +5 if (ep.eq.erg(6,i,j,j-1,2)+w2(i+1,n)) then1* call push(i+1,n,w2(i+1,n),1) goto 100N elseif (ep.eq.erg(6,i,j,i+1,1) + erg(6,i,j,j-1,2) + w2(i+2,n)) then* call push(i+2,n,w2(i+2,n),1) goto 100 endif elsen ii = hstnum(i)  ji = hstnum(j)  error = 12n return  endif v else c k = i+2)c Perhaps I,J closes a multi-loop? 400 do while (k.le.j-3) if (k.ne.n) thenO if (ep.eq.w1(i+1,k) + w1(k+1,j-1) + eparam(10) + eparam(5)) theni6c Multi-loop. No dangling ends on I,J.. call push(i+1,k,w1(i+1,k),0)2 call push(k+1,j-1,w1(k+1,j-1),0) goto 100F else if (ep.eq.erg(6,i,j,i+1,1)+w1(i+2,k)+w1(k+1,j-1) +A . eparam(10) + eparam(6) + eparam(5)) then Ac Multi-loop. I+1 dangles over the I,J base-pair. . call push(i+2,k,w1(i+2,k),0)2 call push(k+1,j-1,w1(k+1,j-1),0) goto 100F else if (ep.eq.erg(6,i,j,j-1,2)+w1(i+1,k)+w1(k+1,j-2) +A . eparam(10) + eparam(6) + eparam(5)) thenuAc Multi-loop. J-1 dangles over the I,J base-pair. . call push(i+1,k,w1(i+1,k),0)2 call push(k+1,j-2,w1(k+1,j-2),0) goto 100I else if (ep.eq.erg(6,i,j,i+1,1)+erg(6,i,j,j-1,2)+w1(i+2,k)rE . +w1(k+1,j-2)+eparam(10)+2*eparam(6)+eparam(5)) then.Mc Multi-loop. Both I+1 and J-1 dangle over the I,J base-pair.p. call push(i+2,k,w1(i+2,k),0)2 call push(k+1,j-2,w1(k+1,j-2),0) goto 100 endif else6 if (ep.eq.w2(i+1,k) + w2(k+1,j-1)) then9c Exterior loop. No ends dangling on I,J.i. call push(i+1,k,w2(i+1,k),1)2 call push(k+1,j-1,w2(k+1,j-1),1) goto 100J else if (ep.eq.erg(6,i,j,i+1,1)+w2(i+2,k)+w2(k+1,j-1)) thenDc Exterior loop. I+1 dangles over the I,J base-pair.. call push(i+2,k,w2(i+2,k),1)2 call push(k+1,j-1,w2(k+1,j-1),1) goto 100J else if (ep.eq.erg(6,i,j,j-1,2)+w2(i+1,k)+w2(k+1,j-2)) thenDc Exterior loop. J-1 dangles over the I,J base-pair.. call push(i+1,k,w2(i+1,k),1)2 call push(k+1,j-2,w2(k+1,j-2),1) goto 100/ else if (ep.eq.erg(6,i,j,i+1,1)+ B . erg(6,i,j,j-1,2)+w2(i+2,k)+w2(k+1,j-2)) thenPc Exterior loop. Both I+1 and J-1 dangle over the I,J base-pair.. call push(i+2,k,w2(i+2,k),1)2 call push(k+1,j-2,w2(k+1,j-2),1) goto 100 endif endife k = k + 1s enddo ) endif  *Fc None of the above work. I,J MUST close a bulge or interior loop.500 do d = j-i-3,1,-1B do ip = i+1,j-1-d, jp = d+ip) if (j-i-2-d.gt.eparam(7)) then 6c Error, bulge or interior loop not found. ii = hstnum(i) ji = hstnum(j) error = 11 return endif0 if (abs(ip-i+jp-j).le.eparam(8)) then6 if (e.eq.erg(3,i,j,ip,jp)+v(ip,jp)) then i = ip  j = jp  e = v(i,j)e goto 300j endif  endif enddoo enddo -c Error, bulge or interior loop not found.  ii = hstnum(i) ji = hstnum(j) error = 11 return end  e i e .9c Store results of a SAVE run for a continuation run.o subroutine putcont include 'rfd.inc'= i* write(30) n,nsave,vmin,listsz,seqlab< write(30) stack,tstk,dangle,hairpin,bulge,inter,eparam write(30) (vst(i),i=1,n*n)! write(30) (wst1(i),i=1,n*n)j! write(30) (wst2(i),i=1,n*n) , write(30) (seq(i),i=nsave(1),nsave(2)). write(30) ((list(i,j),i=1,listsz),j=1,4)! write(30) tloop,numoftloopsn/ write(30) (poppen(i),i=1,4),maxpen,preloge return end :c Read results from a SAVE run for a CONTINUATION run. subroutine getcont include 'rfd.inc'e 0 read(30,err=10) n,nsave,vmin,listsz,seqlabB read(30,err=10) stack,tstk,dangle,hairpin,bulge,inter,eparam& read(30,err=10) (vst(i),i=1,n*n)' read(30,err=10) (wst1(i),i=1,n*n)r' read(30,err=10) (wst2(i),i=1,n*n)s2 read(30,err=10) (seq(i),i=nsave(1),nsave(2))4 read(30,err=10) ((list(i,j),i=1,listsz),j=1,4)' read(30,err=10) tloop,numoftloops05 read(30,err=10) (poppen(i),i=1,4),maxpen,prelog, goto 11  10 call errmsg(40,0,0)i i 11 return endK *[MFOLD]LIN.INC;1+,l./ 4MV-*0123KPWO56&h7 i89GHJ implicit integer (a-z) ( parameter (maxn=625,fldmax=2*maxn). parameter (infinity=16000,sortmax=30000). parameter (mxbits=(maxn*(maxn+1)+31)/32) parameter (maxtloops=40) parameter (maxsiz=10000) > integer*2 vst(maxn*maxn),wst1(maxn*maxn),wst2(maxn*maxn) integer poppen(4),maxpen real prelogK dimension newnum(maxsiz),hstnum(maxn*2),force(maxn*2),numseq(maxn*2),' . work1(maxn*2,0:2),work2(maxn*2),J . stack(5,5,5,5),tstk(5,5,5,5),dangle(5,5,5,2),hairpin(30),bulge(30),. . inter(30),eparam(10),cntrl(10),nsave(2), data eparam/0,0,0,0,46,4,30,30,-500,1/B common /main/ vst,wst1,wst2,newnum,hstnum,force,work1,work2,I . stack,tstk,dangle,hairpin,bulge,inter,eparam,cntrl,nsave,n,numseq, . poppen,prelog,maxpen  character*1 seq(maxsiz) character*5 inbuf character*30 seqlab common /seq/ seq,seqlab  dimension list(100,4) common /list/ list,listsz common /nm/ vmin  dimension basepr(maxn) common /trace/ basepr 6 integer*2 two(0:15),marks(mxbits),force2(mxbits) common/bits/marks,force2 . integer*2 tloop(maxtloops,2),numoftloops% common/tloops/tloop,numoftloops M data two/1,2,4,8,16,32,64,128,256,512,1024,2048,4096,8192,16384,-32768/*[MFOLD]LIN.OBJ;2+,.0/ 40/`-*0123KPWO156xi7i89GHJ*.ERG0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  ERG ERG8P$P. PO4[^ѼERGREADPԫмP@ s$м QA s$<>PѼмP@ s$м QA s$޼޼ FCEP$ϼVмP@ s$мQA s$<>PѼ$$PѼ P<>PмQA$QмPQ@$PPм QPA$QQмPQ@$P@F$P$PVѼ$Ѽ$Ѽ$Ѽ $<>PüPPWü PPXWX1WмP@ s$<>PXмP@ s$<>PXWYYмP@$PмQPA$QQм PQ@$PPмQPA$QAF$QI$Q$QYNYQG/QP MTH$ALOG_R5D%PJPP$QPQ$QI$Y$YЫPXWYXWPPZPZY1NYPF/P MTH$ALOG_R5D%PJPPм QA$RмSC$RRRA$QQQC$SC $SмQA$RмTD$RRRA$QQQD$TD $SĊ$SPS$SPPWWPPTTXXTDn%ZT%PPTTPPS1м P@$SмTD$SSS@$PPPD$TD $TмP@$SмQA$SSS@$PPPA$QA $TI$T$TYYWWYYWWXXWGn%Z%WWZZWWTЫPVѼ$Ѽ $<>Pü PPWW޼޼ FCEPмP@_$P@ $PWNWPF/P MTH$ALOG_R5D%PJPPм TD$ZмXH$ZZZD$TTTH$XH $X$XPX$X1WG"$X$X1XWмP@$T@$TT@$TT@$TPTT 2TZ2J ZZPTT 2TTD NXм TD$PмZJ$PPPD$TTTJ$ZJ $ZG"$Z$Z2XXXZЫPPޫX<>PX X1ԫVѼ$мP@$Wм TWD$TTT@$P@$$PѼ Pм TD$WWD$TTмWTG$WG$Ѽ$Ѽ PмP@$Wм TD$WW@$WD$YYD$TTT@$P@$G$1$WѼW1V$~^  ~^$W2^PѼ$1$~^, ~^0(W2^мTD$Yм QYA$QQQD$TD$P$~^8 ~^<4W2^мTD$Qм YI$QQD$QI$SSI$YYYD$TD$A$QQP$~^D ~^H@W2^м QA$TTA$QQмTQD$TD$P1$PѼ P$TѼ T1VżWT$T2DTTQWQ$Q2AQмYI$Sм RB$SSI$SC$QѼ PB$PB$PPI$PT@$@$C$SQS1ļWWk$kQQX1мYI$Sм RB$SSI$SB$PB$PPI$P@$C$TX$1¹ ,$UXkY UEIR2RRѫRRXQR2BRRC$V2EZZVѫVV2IY@$Y2E~UUYѫYYTRURѫRR1 RzRU{UUUďUXUXkRY2B RRE閆$V$V$VѫVVXQV2F C$ZE閆$Z$Z$Z$ZѫZZ@$R ZzZV{VVVĀVXVF閆$R$R$R$RѫRRTRF閆$R$R$VVR$RѫRRX^ЫQQЫQQTTЫTTQQЫQQQPPмQPA$QQм PQ@$PPмQPA$QA$QQPмP@ s$мQA s$<>PмQA$QмPQ@$PPм QPA$QQмPQ@$P@ $P OERGERGREADFCEMTH$ALOGW2 $CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS MTH$ALOG_R5P ,P:P IP:WP#ePzP PPPP3P P PPPP<P FPPPZP {PPPPPPPWPGP/FPvPGPP"P :P5OP eP tPgPPPPe8PHPXP PP/1P/jPWpPQP9PSP'P9PIPP9P  Pf P P} P P=1 /FILL0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 FILL(P+% FILLP        $P. PQPPO[^<>\$P$dЫS$$P$P2P$ ѭ1$ 1ѫ $ݫ  OTS$POWJJūSQPQ FOR$WRITE_SFS FOR$IO_L_V FOR$IO_ENDS$Pë P~ OTS$POWJJSdQīQPQ FOR$WRITE_SFS FOR$IO_L_V FOR$IO_ENDS$ PPVVPPVЫ PP$$PPѫV1ЫWG.$W<>X<>YZѫ $ë PP1ѫ$1$Pѫ P1Ы P@$PǸ,P@<1$PQQP P@1 ERG<>QQPPQQXѫ $ë QQQ~^H ~^L8ERG^PU~^T ~^XPV^PUXPPUUPPXѫ $ë PPP1ë PPU1 PUPTѫT1Uë PPUPP$1ëPPܫ PPQPQQ$1ѫ$\ERG$Q$RRRQQ$Q2AQQPXQQPPQQXtERG$QRRQQ2AQQPXQQPPQQXT;U1ѫ $ë UUU ˌERGXUUPPUUXUޫP<><>Uѫ$1UU^˨ˤV^$P$PTU^˼˰ERG^PTTT^W1^$PT^V^PUT^ERG^PU~^W2^P$Pѫ P1 UU^ V^$P$PTU^ERG^PT TT^0(W1^$PT^<4V^PUT^H@ERG^PU ~^`XW2^Pѫ$1$Pѫ P1UU^h TT^ldV^$P$QQPRT^xU^|pERG^PRT^ːTT^˔ˈERG^PRT^ˤ RR^˨ˠV^PUR^˴T^˸ˬERG^PUR^~^ERG^PUX$PPUUЫUUPPЫPPUUЫUUPPЫPPUUЫUUYXUUUPPЫPPUUЫUUPPЫPPUUЫUUPPЫPPZѫ $ë PPP1$PUUPЫUѫ 1U$UPR2BRE.$RYTTRRTTYz Q{QQQďQUQUPT2D RRA얆$QYRRQQRRY2DTE.$TZRRTTRRZ U1p$PUPU UXEYE ZEz Q{QQQďQQYA쒆$Zwѫ $$ ZZZPP@EU2UUPPUUPPVVѫ $1$V WWPPV$UzWW{WWWďW$PZZUZ ZZ$Z>J ZUQď<QWPYI얆$Y@.$X2jy2 xQZVP 1 OFILLERGVW1W2$CODE!$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_V FOR$WRITE_SF OTS$POWJJ`(P.PP#PMP#OPuPPP PPPPP PNfPuPPPPP~PB*P3uP PPwP,P=PPPPP'PYP3P+Ps- ,V0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 V V$P. PH$[Ѽ$$P$QQQPP$P2@$PQQPP2@ЫP HVb$CODE$PDATA$$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSP->P)b-W10123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  W1 W1$P. PH$[Ѽ$$P$QQQPP$P2@ $PQQPP2@ ЫP HW1b$CODE$PDATA$$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSP->P)b-W20123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  W2 W2$P. PH$[Ѽ$$P$QQQPP$P2@$PQQPP2@ЫP HW2b$CODE$PDATA$$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSP->P)b0TRACE0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 TRACEP TRACEDP(,04(,,(,((,,,( (,((,(,( ,(,(,(,,(,,( (,((,(,2Yd<~ MFOLD.BCK*[MFOLD]LIN.OBJ;20u4( ,(,(,( ,( ( ,,( ,( ( ,,(, (,(,(,(,(,(,(, (,(, (,(,(, (, $$$(,$$$(, $$$(,(, $$$   (,   (,    (,(,       (,   (,    (,(,    (,8@8@(,$P. PO [ЫVЫ WԼѼ$мPмZѼPPPPXJYP^QRXSYT OTS$MOVE5_R5$PPXYP^QRXSYT OTS$MOVE5_R5мXѼ$PP$PPYHZP^QRYSZT OTS$MOVE5_R5INITST޼4޼8޼(޼,$VP^<0PUSH^Լ XWѫWVW DPULLЫ WЫVPVW W XVЫ WVP1ի1YY^hW dW1^Ы W$PVPYW pW1Ы WPVѫW1bWYY^˄|W1^$PVPY ˈW1Ы WPVѫW1!YY^˘W ˔V^$P$PZY^ˬˠERG^PZVZ֫˸VPV1 ZZ^V^$P$PYZ^ERG^PYVY׫ VPV1YY^ ZZ^V^$P$QQPRZ^Y^ ERG^PRZ^ ZZ^$ERG^PRVRZ׫ 0VPV<V$PVPHVPV1ZZ^XW TW2^Ы WVPZѫW1WZZ^h`W2^VPZWѫW1`ZZ^pW lV^PRZ^˄xERG^PRVR֫ːVPV1 RR^ˤ˜V^PZR^˰˨ERG^PZVZ׫ VPVZZ^ RR^V^PYR^Z^ERG^PYR^RR^ERG^PYVYR׫ VPVVЫ WVP1ЫkkWЫP@_$G_$ VW ի1 W1PRk~^0W ,W1^Ы WPRVR8W1P^PDPUSH^kPP^hP^\W XW1^P^pdPUSH^Ы W1wѫ1xW2PRk~^ˈW ˄W2^Ы WPRVRːW2P^˨˜PUSH^kPP^P^˴W ˰W2^P^˼PUSH^Ы W1k1W$ЫPW@ЫGѫ$$P$WRR@PBPRW$WRЫBЫPR@ԫЫP@ s$G s$W FCEЫ WPּ ѫ$1$PWP~^W~^W ERG^PRЫ WYY^WZZ^V^PRVRYZ VЫ WPV1W ERGЫ WVP1VZЫP@ s$G s$W $FCEЫ WP$VZYWPYP1Zѫ$~^@W 0ERG^Ы WZP1Ĺ )$PWPW~^XW HERG^Ы WZP1ѫ$$PWP~^pW `ERG^PRЫ WW~^ˈW xERG^Ы WPRZR1|ЫRB_$G_$ VW $RѫR1$~^˔WRR^˘ːW2^ZP$PP^ˬR^˰P^ˠR^ˤ˜W2^P^˴˨PUSH ^1ѫ$1~^W ˼ERG^PSЫ W$~^WTT^W2^PSZS$SS^T^S^T^W2^P^PUSH ^18~^W ERG^PT ~^(ERG^Ы WPT$~^4WSS^80W2^PTZT$TT^LS^PT^@S^D<W2^P^THPUSH ^11R^lW \ERG^PRЫ W$~^xWSS^|tW2^PRZR$RR^ːS^˔R^˄S^ˈˀW2^P^˘ˌPUSH ^1ЫP@_$G_$ VW $PWP$PWP1SS^ˤˠW2^ZPS^˼S^˰ˬW2^P^˸PUSH^1jS^W ERG^PSЫ WRR^W2^PSZSR^R^W2^P^PUSH^1$PWP1W~^ W ERG^PRЫ WSS^,(W2^PRZRS^DS^84W2^P^L@PUSH^1xS^dW TERG^PS ~^|lERG^Ы WPSRR^ˈ˄W2^PSZSR^ˠR^˔ːW2^P^˨˜PUSH^11ЫP@_$G_$ VW YkWYkY1k$1YY^˴˰W1^PRk~^WSS^˼W1^PR$R$RZRY^Y^W1^P^PUSH^kPP^S^P^S^W1^P^PUSH ^1Y^W ERG^PYЫ WSS^$ W1^PYk~^0WRR^4,W1^PY$Y$Y$YZYS^HS^<8W1^P^PDPUSH^kPP^hR^lP^\R^`XW1^P^pdPUSH ^1R^ˈW xERG^PRЫ WSS^˔ːW1^PRk~^ˠWYY^ˤ˜W1^PR$R$R$RZRS^˸S^ˬ˨W1^P^˴PUSH^kPP^Y^P^Y^W1^P^PUSH ^1S^W ERG^PS ~^ERG^Ы WPSYY^W1^PSk~^(WRR^,$W1^PS$S$PPS$SZSY^@Y^40W1^P^H<PUSH^kPP^`R^dP^TR^XPW1^P^h\PUSH ^11RR^tpW2^PYk~^ˀWSS^˄|W2^PYZYR^˘R^ˌˈW2^P^ˠ˔PUSH^kPP^˸S^˼P^ˬS^˰˨W2^P^˴PUSH ^1bR^W ERG^PRЫ WSS^W2^PRk~^WYY^W2^PRZRS^S^W2^P^PUSH^kPP^(Y^,P^Y^ W2^P^0$PUSH ^1Y^HW 8ERG^PYЫ WSS^TPW2^PYk~^`WRR^d\W2^PYZYS^xS^lhW2^P^ˀtPUSH^kPP^˘R^˜P^ˌR^ːˈ !W2^P^ˠ˔PUSH ^1S^˸W ˨ERG^PS ~^ERG^Ы WPSRR^W2^PSk~^WYY^W2^PSZSR^ R^W2^P^ PUSH^kPP^ Y^$ P^ Y^  W2^P^(  PUSH ^1k1 ëWZZ1WPZPYѫY1Z ëWPPZPP$ЫP@_$G_$ VW ëP PWPPRPRR$W 0 ERGPRЫ WH VPRVRЫЫ T VЫ WPV1,YYZ1:ЫZJ_$G_$ VW Q OTRACEINITSTPUSHVPULLW1ERGW2FCE)$CODE$PDATA $LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS OTS$MOVE5_R5P:,P)WPcbPP,P*!P FPNPyP"P"%P6PyPPP.P <PtdPPPP!P2PPP]P#P,P[PPZ,PCPQMP*wPPPPPPs5P}PPPPP-P)PP'P)PV6PI|PPsPF/ PC} PF) PFq P  PF4 PC Pa P2 P2 PS P0 P1 P!B PN P PoPrmPrrPqPA*PqPoPoPr;PUPqP&PBP׽   )2PUTCONT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133PUTCONTPUTCONTS$P$  z$  >$ &$ x$ x$ x$ ($ '  $P. P H [\ FOR$WRITE_SU$ FOR$IO_L_V߫t FOR$IO_X_DA FOR$IO_L_V@ FOR$IO_L_V˄ FOR$IO_T_DS FOR$IO_END FOR$WRITE_SU߫ FOR$IO_X_DA߫ FOR$IO_X_DA߫$ FOR$IO_X_DA߫4 FOR$IO_X_DA߫D FOR$IO_X_DA߫T FOR$IO_X_DA߫d FOR$IO_X_DA FOR$IO_END FOR$WRITE_SU>l˨$$RRˬˤ FOR$IO_X_SE FOR$IO_END FOR$WRITE_SU> ˨Rˬˤ FOR$IO_X_SE FOR$IO_END FOR$WRITE_SU>˨Rˬˤ FOR$IO_X_SE FOR$IO_END FOR$WRITE_SU$R$SSR˜Cˠ˜ FOR$IO_T_DSRS FOR$IO_END FOR$WRITE_SURSc˴@˸˰ FOR$IO_X_SBSR FOR$IO_END FOR$WRITE_SU?ˌ FOR$IO_X_DA2 ~ FOR$IO_W_V FOR$IO_END FOR$WRITE_SUr%˼ FOR$IO_X_SB% FOR$IO_L_V% FOR$IO_F_V FOR$IO_END( HPUTCONT$CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_W_V FOR$IO_L_V FOR$IO_F_V FOR$IO_T_DS FOR$IO_X_DA FOR$IO_X_SB FOR$IO_X_SE FOR$WRITE_SU PP!)׼2GETCONT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133GETCONTJP(GETCONT,P$  z$  >$ &$ x$ x$ x$ ($ '  $P. PH [Ы\kRS FOR$READ_SU$ FOR$IO_L_R߫| FOR$IO_X_DA FOR$IO_L_R@ FOR$IO_L_Rˌ FOR$IO_T_DS FOR$IO_END FOR$READ_SU߫  FOR$IO_X_DA߫ FOR$IO_X_DA߫, FOR$IO_X_DA߫< FOR$IO_X_DA߫L FOR$IO_X_DA߫\ FOR$IO_X_DA߫l FOR$IO_X_DA FOR$IO_END FOR$READ_SU>c$$PP˼ FOR$IO_X_SE$$PPR FOR$IO_END FOR$READ_SU> $$PP˼ FOR$IO_X_SE$$PPR FOR$IO_END FOR$READ_SU>$$PP˼ FOR$IO_X_SE$$PPR FOR$IO_END FOR$READ_SU$T$RRTˤB˨ˤ FOR$IO_T_DSTR FOR$IO_END FOR$READ_SU\Td@ FOR$IO_X_SB@RT\ FOR$IO_END FOR$READ_SU?˔ FOR$IO_X_DA?  FOR$IO_W_R FOR$IO_END FOR$READ_SUr% FOR$IO_X_SBR% FOR$IO_L_R% FOR$IO_F_R FOR$IO_ENDˬERRMSG\Rk2 HGETCONTERRMSG$CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_W_R FOR$IO_L_R FOR$IO_F_R FOR$IO_T_DS FOR$IO_X_DA FOR$IO_X_SB FOR$IO_X_SE FOR$READ_SU^P}iP-PPQPEPPP)PnTPCP #)𩦻ռYZEz Q{QQQďQQYA쒆$Zwѫ $$ ZZZPP@EU2UUPPUUPPVVѫ $1$V WWPPV$Uz*[MFOLD]LMISC.OBJ;2+,.K/ 4KI-*0123KPWOL56!1|i7t"i89GHJF2PROCESS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133PROCESSPROCESS4P$P. PO [$P$VVPVQQPPWFB#XP^QRWSXT OTS$MOVE5_R5PP@P@@@W@XXWHB#QWX@Q@WWQGB#XQW$$P$QQPAB#WՇ$$ԧPQ$PP1$WXW$PPYs$ZP^QRYSZT OTS$MOVE5_R5$$XPXYXP$ZXQQZXQQPP\YZ>JYP^QR\SYT OTS$MOVE5_R5WX$W$YYW1ZXIB#\ЌT1YD_$D$IAD$IBD$D s$ICD$IZD$D s$IGD$IHD$D s$IUITD$IVIWD$D s$WY2WW@1WGYG\GZGG\ZGZYTYPPT@B#QЁRB s$TPfTZIB#RLF#SނsSFCEZT1UIB#$LB#( SFCEYVYXXV HVX1ZYVYXXVHB#PЀRB s$VX1P$VZ$XIB#RLF#SbQXQsQAcUXUU$UEZV1W$PXP$Y$\L$\qq$$ЉPX OPROCESSSFCEN$CODE$PDATAL$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS OTS$MOVE5_R5EP&LPsXP;bP|PPP&PPP: P{PPG`P7PPPPPP7PGP_PgPwPPPdP PPP6PfPPPP&jP PPOPIP0+ 9 N0CONVT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 CONVT CONVTPPH[}PQTUԫVVWG-TG0G9U  OTS$POWJJߚGQ0QQPPUVTΫЫPP HCONVTf$CODE$PDATA $LOCAL OTS$POWJJ$&P+P*2P#9P[P&f3ENEFILES0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133ENEFILESvPEnter dangle energy file name (default dangle.dat)DANGLE.DATEnter loop energy file name (default loop.dat)LOOP.DATEnter stack energy file name (default stack.dat)STACK.DATEnter tstack energy file name (default tstack.dat)TSTACK.DATEnter tloop energy file name (default tloop.dat)Tloop.DATEnter misc. loop energy file name (default miscloop.dat)miscloop.DAT(ENEFILES(P(2 2 (82 FOR$OPEN@.=k (lk FOR$OPEN@0t  ( FOR$OPEN@2  ( FOR$OPEN@0 ( FOR$OPEN@8% ] (<] FOR$OPEN@PH([ FOR$WRITE_SL FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDFOR$OPENP FOR$WRITE_SL< FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDLFOR$OPENP FOR$WRITE_SLp FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDˀFOR$OPENP FOR$WRITE_SLˤ FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_END˴FOR$OPENP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDFOR$OPENP FOR$WRITE_SL  FOR$IO_T_DS FOR$IO_END~j FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDFOR$OPENPFOR$EXIT HENEFILESFOR$OPENFOR$EXIT$CODEm$PDATAh$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$WRITE_SL;(PtPbP PYP~P2P 4(1ERRMSG0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 ERRMSGP0u$ Open bifurcation not found between  and # Bulge or interior loop closed by (, ) not found& Closed bifurcation not found between  and  Base pair between  and  conflicts with at least one other pair Buffer overflow in lineout End reached at traceback  More than  basepairs in sort at (,) Premature end of save file ERRMSG$P. PH [Ѽ  FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDѼ 6 FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDѼ p FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDѼ FOR$WRITE_SFݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDFOR$STOPѼ FOR$WRITE_SF FOR$IO_ENDԼѼ FOR$WRITE_SFݼ FOR$IO_L_V FOR$IO_ENDѼ- FOR$WRITE_SF FOR$IO_L_Rݼ FOR$IO_L_Vݼ  FOR$IO_L_V FOR$IO_ENDԼѼ(` FOR$WRITE_SF FOR$IO_ENDFOR$STOP HERRMSGy$CODE~$PDATA $LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSFOR$STOP FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$WRITE_SF>P*>P*nP*P1PP P:ZP*)y1INITST0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 INITST INITSTP@ K @INITST $CODE$PDATA$LOCAL$STK  /PUSH0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 PUSHPERROR - STACK OVERFLOW PUSHPPH[R  2 FOR$WRITE_SLk FOR$IO_T_DS FOR$IO_ENDFOR$STOP Pм@м@м @Œм@T HPUSH]$CODE$PDATA$LOCAL$STKFOR$STOP FOR$IO_END FOR$IO_T_DS FOR$WRITE_SLP!]/PULL0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 PULL PULL[PH[Q P P@ P@ P@ P@T PS HPULLR$CODE$PDATA$LOCAL$STKP R1LINOUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 LINOUT\P FOLDING BASES  TO  OF  ENERGY =    LINOUT|P' LPDTld@pd@lD@pD@PD\D@`D@$P. 8P- .QPO<[^ЫVЫW$kмP@_$RмP@_$S k FOR$WRITE_SFR FOR$IO_L_VS FOR$IO_L_V@ FOR$IO_T_DSݼ  FOR$IO_F_V FOR$IO_ENDINITST޼x޼|tPUSHZիVZXXVP@VZVW˘PULLЫWЫVPVWWZVJ1ZZVWV1WVPPP8WYV$Ы8 խ1Y׫$֫ѫVWI_$P@ 1I_$0Ы$XH_$4 0P PP0Y$DIGIT 4P PP4DIGITѫ 8XЫ0P@HЫ4P@HXY$Ы0P@HЫ4P@H 'YIꐫIQk FOR$WRITE_SF FOR$IO_ENDЫY$$YXkHk FOR$WRITE_SFWYWPXPˈ@ˌˈ FOR$IO_T_DSYW FOR$IO_ENDkBk FOR$WRITE_SFWYWPXPː@˔ː FOR$IO_T_DSYW FOR$IO_ENDXlѫ$1 V YYVXHꐫHVꐫIꐫI Y$PPWWYVWYXVPXVS@CVWY1ЫXH׫WZ ëVPP P ի 1ZYЫX (ѫ(VW,ի 1׫(YXYWI_$0(PЫ0SC@ 0P PP0ˬDIGIT(P@XVH_$4(PЫ4SC@ 4P PP4DIGIT(P@ ,`ЭZWЫVJ1ЫYIJIZJJ_$JYI_$ӼVWѫVWJ~^V PUSH^JV֫ѫVWG_$ZF_$YXJHIH ZP PPZZ DIGIT YP PPYY$8DIGITWVY|Iꐏ^IWVGV11X OLINOUTINITSTPUSHPULLDIGIT$CODEU$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_V FOR$IO_F_V FOR$IO_T_DS FOR$WRITE_SF`PP PPP P2P SPxP~P P P&P*PPP;PLPAbP$PCP&4P.xPPPP PP8P P$P7OP ZP PPP P*P %PjP P PP1!% C'0DIGIT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 DIGIT DIGIT8PQ Q0123456789Q.PO4[м4}PQޫ PFOR$INI_DES2_R3VмP PQ QRRPRRFQQPV䞻WѼ VVTUVU PPī PP@gTUм XYVޫZЊTū XUUDEgXVYū XXHg^ ODIGIT$CODE$PDATAl$LOCALFOR$INI_DES2_R3$ for main menu)  Enter new value  Enter base and length  Enter base pair and length  Enter begining and end  01 Energy Parameter 6 Single Prohibit 02 Single Force 7 Double Prohibit 03 Double Force 8 Begin Folding  04 Closed Excision 9 Show current  K05 Open Excision 10 Clear current  Enter Choice  MENU8P$P. @PPH [\@d1 FOR$WRITE_SF FOR$IO_END# FOR$WRITE_SF FOR$IO_END FOR$READ_SLk FOR$IO_L_R FOR$IO_ENDkk k LISTOUT1y@1q FOR$WRITE_SF FOR$IO_ENDVR FOR$READ_SL߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_END@@Pk@Ы@̌Ы@@̬1  FOR$WRITE_SF FOR$IO_END FOR$READ_SL߫ FOR$IO_L_R߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_END@@Pk@Ы@̌Ы@Ы@̬1 FOR$WRITE_SF FOR$IO_ENDzv FOR$READ_SL߫ FOR$IO_L_R߫ FOR$IO_L_R FOR$IO_END@@Pk@Ы@̌Ы@@̬1-FOR$EXIT FOR$WRITE_SF$R߂ FOR$IO_L_R  FOR$IO_ENDc FOR$WRITE_SF FOR$IO_END FOR$READ_SF߫ FOR$IO_L_R FOR$IO_ENDի1ѫ 1 FOR$WRITE_SF FOR$IO_ENDϊφ FOR$READ_SL߫  FOR$IO_L_R FOR$IO_ENDЫPЫ @$18 HMENULISTOUTFOR$EXIT$CODE7$PDATA@$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_R FOR$READ_SF FOR$READ_SL FOR$WRITE_SFoPLPPPxPszP(|P~PPP(PP<PP RF+ >.2LISTOUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133LISTOUT]P No choices currently defined Current Choices : (,)  : ,LISTOUTPQDEnergy Parameter  'Single Force  'Double Force  'Closed Excision  'Open Excision  'Single Prohibit  'Double Prohibit  'PH[R@ݼ FOR$WRITE_SLk FOR$IO_T_DS FOR$IO_END1ݼ FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDݼ FOR$WRITE_SL FOR$IO_T_DS FOR$IO_END@STS1bUхѥ.ݼ FOR$WRITE_SFP@` FOR$IO_T_DSVDŒWg FOR$IO_L_RWV FOR$IO_ENDEݼ FOR$WRITE_SFP @`$  FOR$IO_T_DSVDŒWg FOR$IO_L_RWV FOR$IO_ENDSTKݼ FOR$WRITE_SL( FOR$IO_T_DS FOR$IO_ENDѡ HLISTOUTM$CODEV$PDATA$LOCALDLIST FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SL0P1PwPPPUPR& M1DEVICE0123-Feb-1992 02:2423-Feb-1992 02:24 VAX FORTRAN V5.7-133 DEVICEP' Combination of continuation run and multiple foldings disallowedFOLD.SAVEnter start of fragment (default 1)Enter terminal type 1 VGT1002 Visual 102 (default)3 Tektronics 41051 Enter minimum vector size for plot (default 1) Enter run mode0 Sub-optimal plot (default) 1 N Best2 Multiple Molecules) Enter number of tracebacks (default 1) ( Enter percentage for sort (default 0)  Enter window size (default 0) Enter run type0 Regular run (default) 1 Save run2 Continuation run( Enter save file name (default fold.sav)  nu3lU~ MFOLD.BCK*[MFOLD]LMISC.OBJ;2KL$cleotides Enter end of fragment (default ) DEVICEtP''''( (H@$E E FOR$OPEN@t$p#N$P. PpP yPP PPP PPAP8VPfPqP&P#P PP`PUPm@PDP"rPPPPn$P1P IPKP ]PoP{PPP+P<XP cW,p/MSEQ0123-Feb-1992 02:2423-Feb-1992 02:24IVAX FORTRAN V5.7-133 MSEQ&P'   nucleotides MSEQ$P''''D$$ D$$ $P.  PPH [k޼D,MULTID FOR$WRITE_SLH FOR$IO_T_DS FOR$IO_END޼hPMULTID FOR$WRITE_SF$ FOR$IO_T_DS$ FOR$IO_L_V FOR$IO_END$$$t HMSEQMULTID$CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_L_V FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SL_ P,4P=O+62OUTPUTS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133OUTPUTS$QP (# Do you want printer output? (Y,n)  Output to terminal? (Y,n) ! Enter output file name (default #)2 Enter number of columns on printer (default 80)   Do you want ct file? (y,N)  Enter ct file name (default #)! Do you want region table? (y,N) ' Enter region table file name (default #)ROUTPUTSOtP( (H t| t| t|$P. PKp[\V\TD'AD'ZD'aD'z\\PTTPPTTWWTD' TWX\Y\WY\L'0L'9L'AL'ZL'aL'zXTL'DXP_@XWY FOR$REWINDY$ FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkN 1kn 1$. FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkN kn (HHM FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_END$FOR$OPENP$v FOR$WRITE_SF FOR$IO_END~ FOR$READ_SF$  FOR$IO_L_R FOR$IO_END$P$ FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkY ky $PP$(LH1 FOR$WRITE_SF FOR$IO_END~ FOR$READ_SFk FOR$IO_L_R FOR$IO_ENDkY ky 1$$$$(PH FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDhFOR$OPENP FOR$WRITE_SF  FOR$IO_T_DS FOR$IO_END FOR$READ_SF FOR$IO_T_DS FOR$IO_END@FOR$OPENP1 FOR$WRITE_SLː FOR$IO_T_DS FOR$IO_ENDFOR$EXITHP.OUT.CT .REG4 KOUTPUTSFOR$OPENFOR$EXIT$CODET$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$REWIND FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$READ_SF FOR$READ_SF FOR$WRITE_SF FOR$WRITE_SL P )P2P ;P_PrPYPP$P PPPP P'P3P TPP P_PP5PVPP PPPP PP  PkPmPRP fZ, d2ERGREAD0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133ERGREAD!P  > Premature end of MISCLOOP.DAT<--ERROR - DANGLE ENERGY FILE NOT FOUNDERROR - PREMATURE END OF DANGLE ENERGY FILE-----ERROR - STACK ENERGY FILE NOT FOUNDSTACK ERROR - PREMATURE END OF STACK ENERGY FILEERROR - PREMATURE END OF TSTACK ENERGY FILEPERGREADPP p FIND@  FIND@ FIND@( FIND@= @= FIND@= `= FIND@$A+e FIND@== FIND@== FIND@#$ STEST@*== FIND@=$= FIND@#    +$P. POx[ GETTLOOPShFINDP߫xFOR$STOP  FOR$READ_SL% FOR$IO_F_R FOR$IO_ENDD"%ˈFIND  FOR$READ_SL߫ FOR$IO_F_R FOR$IO_ENDE"PJP%ˠFIND  FOR$READ_SL߫ FOR$IO_F_R߫ FOR$IO_F_R߫  FOR$IO_F_R߫ FOR$IO_F_R FOR$IO_ENDE"PJPr%E"PJPv%E" PJPz%E"PJP~%˸FIND  FOR$READ_SL߫ FOR$IO_F_R߫ FOR$IO_F_R߫  FOR$IO_F_R FOR$IO_ENDE"PJP$E"PJP$E" PJP$PPQRPSJQTUPVJSWXPYJVZJY\\Z\\W\\T\<>L$@YX@VU@SR@QPFINDPkk1$(k1~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDX$\YXPPW\PPXPP(P@$VZYPPWPPP(@TTP)@<>ZT瑫..<>ZZCONVTPZZfdVYXrFINDPk(+$ FINDX~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDVWVVYI V(IYZZP)@<>YZ瑫..<>YY(CONVTPYWYH$WYH$WYH"$WyXX1CXPVWPYJVPZPTJYQSPRJTUJR\\U\\Q\\P\<>LF$@RS@TZ@YW@VX8FINDPkk1(Yk1~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDWZWPP\YPPWPP(P@F$VXZPP\PPP(@TTP)@<>XT瑫..<>XXHCONVTPXXfVZWrYE $@YQ@ \@W@P˔FINDPkk1(,k1~  FOR$READ_SFP FOR$IO_T_DS FOR$IO_ENDVZVPPX,PPVPP(P@ $W\ZPPXPPP(@TTP)@<>\T瑫..<>\\ˤCONVTP\\gWZVn,7˴FINDPk(  FOR$CLOSE FOR$CLOSE FOR$CLOSE FOR$CLOSEY FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SL˄ FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SLh FOR$IO_T_DS FOR$IO_ENDFOR$STOP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDOù/     p3bFOR$STOP FOR$WRITE_SL FOR$IO_T_DS FOR$IO_ENDFOR$STOPP . @ OERGREAD GETTLOOPSFINDCONVTSTEST FOR$CLOSE*$CODE$PDATAl$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSFOR$STOP FOR$IO_END FOR$IO_F_R FOR$IO_T_DS FOR$READ_SF FOR$READ_SL FOR$WRITE_SLP PKPPKPZP`PiP PP PP P)P :PGPTPPPPkPzPPP BP4PPJTPPPPP   i*0STEST0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 STEST1PSYMMETRY ERROR(,) =  b STEST FP  PxO[^ЬÏp}PQk޻STkVTPPXVPPYVPPTPPkP@ZYP@Uj1 FOR$WRITE_SL  FOR$IO_T_DS FOR$IO_END FOR$WRITE_SF FOR$IO_T_DSk FOR$IO_L_VT FOR$IO_L_VV FOR$IO_L_VX FOR$IO_L_Vj FOR$IO_L_R FOR$IO_END FOR$WRITE_SF FOR$IO_T_DSX FOR$IO_L_VV FOR$IO_L_VT FOR$IO_L_Vk FOR$IO_L_Vߥ FOR$IO_L_R FOR$IO_ENDFOR$STOPZX/VTk xOSTESTT$CODE*$PDATA($LOCALFOR$STOP FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$WRITE_SF FOR$WRITE_SL vP "泲T.OUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133  OUTnsPDANGLETSTACKSTACKINTERBULGEHAIRPINTLoops(++* <-o OUTh$P  "$P. PO$[(ݼ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDRSRTUVTPPUPPSP@$WgXX>/ݼ FOR$WRITE_SFX FOR$IO_L_V FOR$IO_END8ݼ FOR$WRITE_SF FOR$IO_ENDdWVUG FOR$WRITE_SF FOR$IO_ENDSnK FOR$WRITE_SF FOR$IO_ENDRJ(ݼ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDRSTUSPPTPPRP@ $VfWW>/ݼ FOR$WRITE_SFW FOR$IO_L_V FOR$IO_END8ݼ FOR$WRITE_SF FOR$IO_ENDVUTG FOR$WRITE_SF FOR$IO_ENDSnK FOR$WRITE_SF FOR$IO_ENDRN(ݼ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDRSTUSPPTPPRP@F$VfWW>/ݼ FOR$WRITE_SFW FOR$IO_L_V FOR$IO_END8ݼ FOR$WRITE_SF FOR$IO_ENDVUTG FOR$WRITE_SF FOR$IO_ENDSnK FOR$WRITE_SF FOR$IO_ENDRNMݼ FOR$WRITE_SF  FOR$IO_T_DS( FOR$IO_T_DS0 FOR$IO_T_DS FOR$IO_ENDR&$S\ݼ FOR$WRITE_SFR FOR$IO_L_V FOR$IO_L_Rߣx FOR$IO_L_R߃ FOR$IO_L_R FOR$IO_ENDR(ݼ FOR$WRITE_SF8 FOR$IO_T_DS FOR$IO_ENDW 12WXH YZ2YPzPP{PPPPVYP2PPPYV2ZPPA@V2ZPPC@V2ZVVGF2ZPPU@=Zeݼ FOR$WRITE_SFk FOR$IO_T_DS?H N FOR$IO_W_R FOR$IO_END= WS OOUT$CODEl$PDATAd$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_W_R FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$WRITE_SFicP$P;P$]PP$5PGPzP P3PP!PP ma. /FIND0123-Feb-1992 02:2423-Feb-1992 02:24SVAX FORTRAN V5.7-133 FIND PP FINDTPPPHT[} PQԫTT~ݼ FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDUüPPPVWVWPUR@BUUTUQGAUVWPPt HFIND$CODE$PDATAd$LOCAL FOR$IO_END FOR$IO_T_DS FOR$READ_SF,PuPnWP0hPpPP+ D0CDUMP0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 CDUMP$PEnter file name for continuation dump (return for terminal)Energy ParametersListing of energy files? (y/N) . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair []o CDUMPPP$ (( H;`L;LL$P. P HL[ FOR$WRITE_SL$ FOR$IO_T_DS FOR$IO_END~j FOR$READ_SF FOR$IO_T_DS FOR$IO_END-( nkk,FOR$OPENDLISTOUTmk FOR$WRITE_SFL FOR$IO_T_DS FOR$IO_ENDtk FOR$WRITE_SF߫ FOR$IO_X_DA FOR$IO_END FOR$WRITE_SLT FOR$IO_T_DS FOR$IO_ENDq FOR$READ_SF FOR$IO_T_DS FOR$IO_ENDYy\OUTFOR$EXIT8 HCDUMPFOR$OPENLISTOUTOUTFOR$EXIT$CODE$PDATA$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPS FOR$IO_END FOR$IO_T_DS FOR$IO_X_DA FOR$READ_SF FOR$READ_SF FOR$WRITE_SF FOR$WRITE_SL'%PQPVP PPI++4 GETTLOOPS0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 GETTLOOPS[P)4Too many characters in numeric field of this line oftloop.dat file: )F GETTLOOPS_`PP ``P|H`[ FOR$READ_SF FOR$IO_END~ FOR$READ_SF FOR$IO_T_DS FOR$IO_END\M\PQP:2\PP@ \2\PP(@ TONUMPPPPP2QPAҠ\M\QQQ:2\QQA \\V2VPP@ ~ FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END2\\\(L CONVT2\PLN\V2\PP @=V\1$ FOR$CLOSE |H GETTLOOPSCONVTTONUM FOR$CLOSEE$CODET$PDATA$LOCALTLOOPS FOR$IO_END FOR$IO_T_DS FOR$READ_SF FOR$READ_SF FOR$WRITE_SF7*P_PkPPPP!&P<0 E0TONUM0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 TONUM*PUnknown base in TLOOP file:  TONUM_P PH[}PQЬ T>U2TVVWGAFeGCFeGGFeGUFeGTFe=T~ FOR$WRITE_SFG  FOR$IO_T_DS FOR$IO_ENDFOR$STOP HTONUM$CODE#$PDATA$$LOCALFOR$STOP FOR$IO_END FOR$IO_T_DS FOR$WRITE_SF@2P 8P?CPIP.SPYPcPiPsP ,  READ_SF FOR$WRITE_SF FOR$WRITE_SLO*(P>pP yPP PPP PPAP8VPfPqP&P#P PP`PUPm@PDP"rPPPPn$P1P IPKP ]PoP{PPP+P<XP cW,p/MSEQ0123-Feb-1992 02:2423-Feb*[MFOLD]LOOP.DAT;1+,w./ 4A-*0123KPWO56.|Zh7w*i89GHJADESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED)9hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges7SIZE INTERNAL BULGE HAIRPIN7-------------------------------------------------------41 . 3.9 .42 4.1 3.1 .53 4.5 3.5 4.554 4.9 4.2 5.555 5.3 4.8 4.956 5.7 5.0 5.157 5.9 5.2 5.258 6.0 5.3 5.559 6.1 5.4 5.8510 6.3 5.5 5.9511 6.4 5.7 6.0512 6.4 5.7 6.1513 6.5 5.8 6.2514 6.6 5.9 6.3515 6.7 6.0 6.4516 6.8 6.1 6.4517 6.8 6.1 6.5518 6.9 6.2 6.5519 6.9 6.2 6.6520 7.0 6.3 6.7521 7.1 6.3 6.7522 7.1 6.4 6.8523 7.1 6.4 6.8524 7.2 6.5 6.9525 7.2 6.5 6.9526 7.3 6.5 6.9527 7.3 6.6 7.0528 7.4 6.7 7.0529 7.4 6.7 7.1530 7.4 6.7 7.1*[MFOLD]LRNA.EXE;3+,./ 4-*0123 KPWO56i7i89GHJ&0D`0205i4,h|+LRNA011i05-09   # Q/& U( 7 : v!; &\<  ?B!d FORRTL_001! LIBRTL_001O! MTHRTL_001Segment larger than +begin.dat [H[J[1mP P [0m%[24;20HPress to continue ...) Author and reference file not available.+%(Enter dangle energy file name (default dangle.dat)DANGLE.DATEnter loop energy file name (default loop.dat)LOOP.DATEnter stack energy file name (default stack.dat)STACK.DATEnter tstack energy file name (default tstack.dat)TSTACK.DATEnter tloop energy file name (default tloop.dat)Tloop.DATEnter misc. loop energy file name (default miscloop.dat)miscloop.DAT(0u$ Open bifurcation not found between  and # Bulge or interior loop closed by (, ) not found& Closed bifurcation not found between  and  Base pair between  and  conflicts with at least one other pair Buffer overflow in lineout End reached at traceback  More than  basepairs in sort at (,) Premature end of save fileERROR - STACK OVERFLOW FOLDING BASES  TO  OF  ENERGY =    () ENERGY =  & Energy Parameters (10ths kcal/mole) . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair []9 Enter Parameter to be changed ( for main menu)  Enter new value  Enter base and length  Enter base pair and length  Enter begining and end  01 Energy Parameter 6 Single Prohibit 02 Single Force 7 Double Prohibit 03 Double Force 8 Begin Folding  04 Closed Excision 9 Show current  05 Open Excision 10 Clear current  Enter Choice  No choices currently defined Current Choices : (,)  : ,' Combination of continuation run and multiple foldings disallowedFOLD.SAVEnter start of fragment (default 1)Enter terminal type 1 VGT1002 Visual 102 (default)3 Tektronics 41051 Enter minimum vector size for plot (default 1) Enter run mode0 Sub-optimal plot (default) 1 N Best2 Multiple Molecules) Enter number of tracebacks (default 1) ( Enter percentage for sort (default 0)  Enter window size (default 0) Enter run type0 Regular run (default) 1 Save run2 Continuation run( Enter save file name (default fold.sav)  nucleotides Enter end of fragment (default )NEWOLD'   nucleotides (# Do you want printer output? (Y,n)  Output to terminal? (Y,n) ! Enter output file name (default #)2 Enter number of columns on printer (default 80)   Do you want ct file? (y,N)  Enter ct file name (default #)! Do you want region table? (y,N) ' Enter region table file name (default #).OUT.CT .REG  > Premature end of MISCLOOP.DAT<--ERROR - DANGLE ENERGY FILE NOT FOUNDERROR - PREMATURE END OF DANGLE ENERGY FILE-----ERROR - STACK ENERGY FILE NOT FOUNDSTACK ERROR - PREMATURE END OF STACK ENERGY FILEERROR - PREMATURE END OF TSTACK ENERGY FILEP . SYMMETRY ERROR(,) =  DANGLETSTACKSTACKINTERBULGEHAIRPINTLoops(++* <-PEnter file name for continuation dump (return for terminal)Energy ParametersListing of energy files? (y/N) . 1 Extra stack energy [] . 2 Extra bulge energy [] . 3 Extra loop energy (interior) [] . 4 Extra loop energy (hairpin) [] . 5 Extra loop energy (multi) [] . 6 Multi loop energy/single-stranded base [] . 7 Maximum size of interior loop [] . 8 Maximum lopsidedness of an interior loop [] . 9 Bonus Energy [] .10 Multi loop energy/closing base-pair [])4Too many characters in numeric field of this line oftloop.dat file: )Unknown base in TLOOP file: @  Minimum Energy = Increment = Enter New Increment ENTER NEW VINC: BASE = N = Base-pair = ( , )Score = +[14;1HMinimum energy = [16;1HIncrement = #[18;1HEnter New Increment [18;24H+[18;24H +0 ENTER PLOT FILE NAME : ) ENTER PLOT LABEL (UP TO 59 CHARACTERS) :</ ENTER TICK MARK INTERVAL & NUMBER OF LEVELS : P+"[2;1HEnter New Increment "[3;1H [2;24H+[2;24H +[2;1HBase = [3;1HN = +[21;1HBase-pair = ,[22;1HEnergy = @ @%!K+++%!KALZMG+++Input sequence file name (/ to end) 12 ) No sequence identifiers found in this file Available sequences in .Choose sequence by number or name , or ? for relist; defaults to the first one, / for new file. NUMBER CHOICE BETWEEN 1 AND This entry does not match with any in given list Sequence truncated to ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE%2P22< LOCUSORIGIN//ID SQ SequenceNRC GENBANK Input sequence file name (/ to end) 12 ) No sequence identifiers found in this file ERROR IN MULTID, SEQUENCE REQUESTED NOT FOUND Sequence truncated to ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE&2P2 LOCUSORIGIN//ID SQ Sequence NRC GENBANK PLOT  D  @H$48,48(0048<00488@D008@488HH.+ 480048  @ @ @ @ @ @ @ @ P ,d !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!8$<$@$D$8$<$<$8$<$8$8$<$<$<$8$8$<$8$8$<$8$<$8$<$8$<$8$<$8$<$<$8$<$<$8$8$<$8$8$<$8$<$4?~ MFOLD.BCK*[MFOLD]LRNA.EXE;3|8$<$8$<$8$<$8$0$<$8$0$8$0$<$<$8$0$<$8$0$8$0$<$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$8$<$.+.+.+8$<$.+.+.+8$<$.+.+.+8$<$8$<$.+.+.+0$0$0$8$<$0$0$0$8$<$0$0$0$8$<$8$<$0$0$0$0$0$0$8$<$0$0$0$8$<$0$0$0$8$<$8$<$0$0$0$8$<$H$P$H$P$8$<$v+  :+  (+ ,+ x^-+ x-+ xN.+ (.+ hi+o+ v+  :+  (+ ,+ x^-+ x-+ xN.+ (.+ hi+o+ (/2 : 00.Es 0D00|  0x02  000 #008- e 01- .hi+11FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF0123456789 .hHhi+Energy Parameter Single Force Double Force Closed Excision Open Excision Single Prohibit Double Prohibit     XB+'WB+''hi+(J((JD @E D D .+D  |JJJtJTJ.+@ PJ# XB+'WB+''hi+TK4K.+ 0K TK4K.+ 0K(K(K LL LL LLPLMptMptMptMptM|tMxM|tN$+x0NxMtPNxMtpN#)v+N*0tNxMtN#    +Z  `OPON.+ ((0PXP;8pP\Ps\PPPP QP Q QQQeS <DSbS.+`dhltStSxxtStSppSStStSTPB+TST.+.+SSPB+S.+SSPB+S.+.+SSSSSS.+.+.+SSSSSSxxUU.+.+SSSSSSSSSSSStSSSSppxSSSSSxx.+SSS.+t3W H8WT|LW fhW.+tWpWpWWS.+PXTXXXHXTX`XLX`X0Y4Y(Y?@ABC\\\\\\\\2&PX%`B$8L`,;9 E0c2P:%BЯددد,د@,.!OOOm(1H+, A1,$)   pZf~H & ^ 41j @/ g$̡?W/ H0-E ќ;2ҁU p' y`!%Ȯ$ J`uaGD5[aIi2 =pg11n) Q|DDs!z B9}*Gg#<N"Vd}}Y,a,) lo+po+h8X3R"50Do+Ho+txHLlo+po+HLlo+po+:/P" h{D{_ JPTTIGEC{P|FGL:NrVZ}E]{"YWCSV!g!Zi`o1HeH/NL{EL/" LJC LKGE{_{EGNHE{LNLK{EG{ELI5140MeCGbH LJ/h{TUXY6GL{"CjLKGE{d{EJG|fCfd{EHINCC"N{ENNUCCNCCNLE{LJCEL{LJC{EGLN"{ENNONNCNNC]{GICoW:"7ZOGE{oWCKeZC]{GIC6  {EICoW:"8{ErO/""K "K@]{GICGE{`{D_{ECNFG{De"xBIG{EGC8 5yLaC/"UGCGCGE{GE{]{GI@{DE~HU{ {EIC I OII C I IC RrZCH|!TJE{rZI{:3 " RC {ELrZHHq!|O WJ6CO\_fmty}.3?HQY`kqw~DOSVYdnw$(.C`!<=>?\]^6DOC` " I3Me " .I3Mo " DIC` " :IC`6 DI=[z6DIC` ( |@To+-J?W BCDtH x lo+po+o+@T  lo+po+To+po+    n+n+n+n+ #   LTtT  @LTX@P\`DLdhDPlp@TXD\`lo+4  hD  . 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FIND +FIND  CDUMP H+CDUMP+ GETTLOOPSP+ GETTLOOPS0 E TONUM +TONUM  SORTOUTH+SORTOUT,z BUILD_HEAP+ BUILD_HEAP8+ HEAP_SORT+ HEAP_SORT"+ ENE +ENE-A SWAP +SWAP  DOTPLT +DOTPLT¹,p+ 2 "  TRI +TRI Q AXIS x+AXISD+ GAXIS @+GAXIS0*x IOUT2 +IOUT2 IOUT H+IOUT` AOUT +AOUTR VT100 +VT100 TEK +TEK> VECTOR +VECTOR%* FORMID +FORMID¹9( L5 a桹-+ W  MULTID ,MULTID¹Bd + W ADEOUT < ,ADEOUT w ALFMOD ,ALFMOD - ANSTR ,ANSTR>d CHRSIZ ,CHRSIZ w CSIZE D,CSIZE. DRAWA t,DRAWAf DRWABS ,DRWABSS DRWREL 0,DRWREL% DWINDO X,DWINDO * EMCHAR ,EMCHAR4u HOME ,HOMET INITT P,INITT LINEF ,LINEF LVLCHT ,LVLCHT + MOVABS ,MOVABS( MOVEA H,MOVEA ; MOVREL ,MOVREL% NEWLIN ,NEWLIN NEWPAG ,NEWPAGu PLCHAR 8,PLCHAR RESCAL 0,RESCAL&R RESET ,RESET" REVCOT L,REVCOT/ SCURSR l,SCURSR & SETBUF ,SETBUFd SETMRG ,SETMRG TERM ,TERM * TKSYNC 8,TKSYNCB TOUTPT |,TOUTPT TOUTST ,TOUTST9 TWINDO ,TWINDO * V2ST ,V2ST VECMOD ,VECMOD C WINCOT ,WINCOT XYCNVT $ ,XYCNVT9  BUFFPK 0",BUFFPK CARTN &,CARTN&f CLIPT D(,CLIPTR2 CWSEND x*,CWSEND) DIGPAK *,DIGPAK\ DMGIN +,DMGIN8$ IOWAIT $-,IOWAIT0 PARCLT T-,PARCLTJ PCLIPT -,PCLIPT / PLTCHR -,PLTCHR PSCAL .,PSCAL5 RECOVR 1,RECOVR} TINSTR @2,TINSTR TSEND 2,TSEND ADEIN 3,ADEINU PNTMOD X3,PNTMOD <*[MFOLD]LRNA.OBJ;2+,. / 4 `-*0123KPWO 56tvi7t@;i89GHJ3RNA$MAIN0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133RNA$MAIN*PSegment larger than +RNA$MAIN\P$48,48(0048<00488@D008@488HH$ 480048 $P. PO [BEGINDEVICE\$ENEFILES<ERGCDUMP$OUTPUTS$MENU$TMSEQ,n_,n__PROCESS$PP FOR$WRITE_SL\ FOR$IO_T_DS to continue ...) Author and reference file not available. BEGIN<TPP d FOR$OPEN@PHT[FOR$OPENP1 FOR$WRITE_SF FOR$IO_L_R FOR$IO_L_R FOR$IO_L_R FOR$IO_END~% FOR$READ_SF FOR$IO_T_DS FOR$IO_END( FOR$WRITE_SF FOR$IO_T_DS FOR$IO_END. FOR$WRITE_SF FOR$IO_L_R FOR$IO_L_R FOR$IO_ENDc FOR$READ_SFk FOR$IO_T_DS FOR$IO_ENDf FOR$WRITE_SF FOR$IO_END HBEGINFOR$OPEN$CODE$PDATA$LOCAL FOR$IO_END FOR$IO_L_R FOR$IO_T_DS FOR$READ_SF FOR$READ_SF FOR$WRITE_SFPVPE)*[MFOLD]LSORT.OBJ;2+,. / 4 h-*0123KPWO 56~i7Bi89GHJ2SORTOUT0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133SORTOUTSORTOUT$P$P. PH [kRԼѼ $ BUILD_HEAP HEAP_SORT RB B  MARKPRRkRB B Rk HSORTOUT BUILD_HEAP HEAP_SORTMARKz$CODE$PDATA0$LOCAL%MAIN.'SEQDLISTNM TRACE BITSTLOOPSHEAPP PPPUP ',z5 BUILD_HEAP0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 BUILD_HEAP BUILD_HEAP0P $($P. PK [PPP$PƏdPP\ V戩RSR$1SRkENEkRЫSP\戩0uB_$$C_$(ERRMSG1戩戩PR@S@$SPPSS$RRSSS$RRS1\戩\\WW1u\2uRRXGYP^QRXSYT OTS$MOVE5_R5\2u\\GXP^QR\SXT OTS$MOVE5_R5戩WX戩1X\XYYL0L4,ENEPRI I ). INTER(30)& Table of interior loop energies. J7 Mainly used to designate the 3' end of a segment. JPE J' - used mainly to designate the 5' end of a segment beginning with J ( J' < J ). LIST(100,4)B List of options selected in MENU. Up to 100 can be selected. LISTSZ3 The number of options selected from the MENU. MAXN5 Maximum size of a fragment which can be folded. MARKS(maxbits) {int*2}= Pair marking array for preventing identical tracebacks.@ Accessed through MARK and SMARK. A base pair i.j is mappedA into a single bit of this array. Any base pair which occurs? in a structure which is computed is "set" from 0 to 1. In> addition, base pairs close to these base pairs (within aD distance of WINDOW) are also "set". Base pairs which are "set"4 will not be chosen for computing new foldings. NA The size of the fragment to be folded after processing. The= fragment is doubled in size for computational purposes. NEWNUM(5000)C NEWNUM(I) is the numbering of the Ith element in the originalB sequence in the fragment to be folded. If the Ith element is5 not in the chosen fragment, then NEWNUM(I) = 0. NSAVE(2)I 5' and 3' ends of the fragment to be folded (historical numbering). NUMSEQ(2 * maxn); Holds sequence converted from characters to integers. 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SEQLAB {char*30} Sequence label. STACK(5,5,5,5)! Table of stacking energies. TSTK(5,5,5,5) * Table of terminal stacking energies. VST(maxn squared) {int*2}E Energy array V(i,j) is stored as VST((n-1)*(i-1)+j). V(i,j) isC the minimum folding energy of the segment closed by the base  pair i.j. WORK(2 * maxn,0:2)? Holds columns of WST to minimize paging during multi-loopA searchs. In the linear version there is WORK1(2*maxn,0:2)  and WORK2(2*maxn). WST(maxn squrard) {int*2}B Energy array mapped as V(i,j) is, in the linear version thisG array is split into WST1(maxn sq) and WST2(maxn sq). W(i,j) is ?E Energy array W(i,j) is stored as WST((n-1)*(i-1)+j). W(i,j) isC the minimum folding energy of the segment from i to j. In theD linear version of the program, WSTis split into WST1 and WST2.@ WST1 penalizes all exterior single-stranded bases and baseG pairs as if they were in an interior loop. WST2 does not do this. Routines: AOUT(INT,STR) {dotplt module}E Prints a character string of length INT to the graphics screen.! AXIS(N0,M0,X,Y) {dotplt module}* Prints out axis along vector region. BUILD_HEAP(ERR)D Reads in all the V energies within a user-specified percentageB (up to an upper limit built into the program) and sorts themF into inverse partial order (a heap with the lowest value at the top).% var heap(sortmax) : heap array CONVT(STR)C Returns the value of the integer held in the character string STR. CT(R)/ Puts the results of TRACE into a ct file. DEVICE; Gets terminal, printer and run information from user. DIGIT(ROW,COLUMN,POS,BMAX,B)6 Adds the sequence numbers to the lineout result. DOTPLT(IRET,JRET,JUMP) Sub-optimal plot option. ENE(I,J) Returns V(i,j) + V(j,i+n). ENEFILES1 Reads in the appropriate energy file names. ERG(MODE,I,J,IP,JP)? Returns the value from the energy tables indicated by the parameter values.; var e(4) : (linear only) array for minimum energies  ERGREAD8 Reads in the appropriate energy rules from a file. ERRMSG(ERR,I,J)A Prints error message number (err) and stops if appropriate.= I and J are numbers passed to be included in some error messages. FILLA Uses the energy function (erg) to fill the matrices V and WA (or W1 and W2) with the folding energies. The matrices areA accessed by the rest of the program by either the functionsB V(i,j) and W(i,j) {or W1,W2}, or by VST(k) and WST(k) {WST1,( WST2} where k = (n-1)*(i-1)+j. C var inc(5,5) : base pair possibilities - 1,2,3,4,5 correspondE to A,C,G,U and X (other) respectively. Inc(i,j) = 1 if and onlyC if base types i and j can form a base pair. Thus the program 9 allows one to define G.G as a base pair if desired.t FIND(UNIT,LEN,STR)A Searches the file under unit number UNIT until it finds thev! string STR (of length LEN).d FCE(II,JI)I Returns .TRUE. if SFCE has been called on (i,j), .FALSE. otherwise.; This is how information on forced base pairs is used. " FORMID(SEQID,SEQ,NSEQ,NMAX,USED)0 Standard routine for reading in sequences.' GAXIS(MAXY,X,Y,MAXVI) {dotplt module} @ Prints out axis for the graph terminator option of dotplt. GETCONT9 Reads a save file. HEAP_SORTr8 Sorts the results of BUILD_HEAP into linear order.= var sort(sortmax) : the heap is sorted into this array  INITST2 Initializes the program stack. The stack is2 four integers wide and up to 50 levels deep.4 The stack is used to keep track of outstanding% fragments during the traceback.d IOUT (INTT) {dotplt module}1 Right justified integer to graphics screen. IOUT2 (INTT) {dotplt module}4 Left justified integer to graphics screen. & LINOUT(N1,N2,ENERGY,IRET,JRET,ERROR): Puts the results of TRACE into line printer format. LISTOUTC Prints the options selected already by the user. Called from MENU. MARK(I,J) J Returns .TRUE. if SMARK has been called on (i,j), .FALSE. otherwise.E Used to determine which base pairs have occurred in structures o7 already computed or are close to such base pairs.  MENU( Gets run options required by user. MSEQ(I)iD On first call, opens a sequence file and returns the number ofF sequences as I. On subsequent calls, reads in sequence number I  using MULTID. ' MULTID(SEQID,SEQ,NSEQ,NMAX,USED,RNUM) 4 Modified FORMID for use with multiple folding. OUT > Debug routine, not used during normal program execution.A Will print out the energy tables in a semi-readable format. OUTPUTS B Gets output options desired by user (enables some or all of ' lineout, region table, ct file). PROCESS > Converts the initial rna data into forms useable by the  program. PULL(A,B,C,D)p@ Pulls the four parameters off the stack. Returns 0 if the  stack was not empty. PUSH(A,B,C,D)1 Pushes the four parameters onto the stack. n PUTCONT(A Saves the program information into a "save file" after filla is called. REGTAB4 Puts the results of TRACE into a region table. SFCE(II,JI) A Sets a mark on a point i,j so that the program will include B it in any folding by giving this base pair a bonus energy of EPARAM(9). SMARK(I,J)A Sets a mark on a point (base pair) i.j so that the program p> knows the point has been included in an already computed. structure or is "close" to such a point. SORTOUT(I,J,REP,ERR)A Used for "N Best" run. On the first pass this routine willp> call BUILD_HEAP and HEAP_SORT, and return the (i,j) pairC with the lowest energy. From then on the routine will returnF the (i,j) pair with the lowest energy that hasn't been SMARK'ed. STEST(STACK,SNAME)> Tests the stack tables for symmetry, used after ergread. SWAP(I,J)n Puts (I = J) and (J = I) TRACE(II,JI,NFORCE,ERROR) e> Computes the best folding containing the basepair II.JI.C The output is put into the BASEPR(k) array. If BASEPR(k) = 0, > then k is single-stranded. If BASEPR(k) = k' > 0, then k pairs with k'./ TRI (XONE,XLIMIT,YONE,YLIMIT) {dotplt module} + Prints out triangular vector region. d, VECTOR (I,J,VOPT,VINC,INA) {dotplt module}D Prints out all the stacking regions within VINC energy of VOPTC along the diagonal starting with the point (i,j) {along axis, " top right corner is origion} VT100(ITERM) {dotplt module}8 Returns a terminal of type (ITERM) to vt100 mode.  V(I,J): Returns the v-energy value of (i,j) mapped into VST. W(I,J)B Returns the w-energy value of (i,j) mapped into WST, in the> linear version of the program this routine is split into7 W1(i,j) and W2(i,j) which map into WST1 and WST2.*[MFOLD]MFOLD.USE;1+,./ 4I\-*0123KPWO56Fh7Tsdi89GHJ0   9 Sub-optimal RNA Folding Program Users Manual9 -------------------------------------------- : Michael Zuker, Eric Nelson and John Jaeger   Start: &Initially, the following menu appears   Enter run type! 0 Regular run (default) 1 Save run 2 Continuation run FIn a regular run the program takes an RNA sequence as input, computesFthe energy matrix for the molecule, and produces various foldings asFoutput. Since the computation of the energy matrix uses a great dealFof time and resourses, the matrix can be saved before any output isFgenerated (a save run) and later used to produce output (acontinuation run). %Regular or Continuation run -> step b  Step a: FAt this point a prompt will appear asking for the name of the file)into which the save matrix can be stored. -> step f Step b: $The following menu will be displayed  Enter run mode& 0 Sub-optimal plot (default) 1 N best 2 Multiple molecules GIf the program is run in 'Sub-optimal plot' ("dot plot") mode, theFenergy matrix will be displayed graphically after it is computed. In?'N-best' mode the program will generate the suboptimal foldings<within a certain percentage of the minimum energy. IfB'Multiple molecules' ("multi") mode is chosen the program willErun the N-best mode with every complete sequence in a file. This last+option MUST be done in a regular run mode.  N best or multi mode -> step d  Step c: The following menu now appears:  Enter terminal type 1 VGT100 2 Visual 102 (default) 3 Tektronics 4105   Fnext is a prompt for the minimum size of displayed vectors (used to+avoid isolated single points in the graph). -> step e  Step d: FTwo prompts asking for values of 'N-best' parameters now appear: theFpercentage above the optimal energy which foldings must be within, andN.  Step e: HA prompt for the window parameter. The distance between any pair of >computed foldings must be more than window. A simpler distancefunction is defined in: 1. Zuker M9 On Finding All Suboptimal Foldings of an RNA Molecule. Science, 244, 48-52, (1989) 2. Zuker M= The Use of Dynamic Programming Algorithms in RNA Secondary Structure Prediction.B in "Mathematical Methods for DNA Sequences", M. S. Waterman ed.$ CRC PRESS, INC., 159-184, (1989)>The new definition of distance requires that any two computed Dfoldings must contain more than 'window' base pairs that are in one folding and not in the other. Continuation run -> step h  Step f: FAt this point a prompt for the name of a file containing one or moreFsequences (in Stanford, Genbank, EMBL, PIR, or NRC format) willFappear. If the program is being run in 'multi' mode all of theFsequences in the file will be folded, otherwise the program will askCfor a selection from the file's contents (a portion of a sequence).ESequence data must be in upper case. The program recognizes A, C, G, Dand T or U. The characters B, Z, H, and V or W are recognized as A, FC, G, and T or U respectively; but they are flagged by the program as Cbeing accessible to nuclease cleavage. A flagged base can pair only'if its 3' neighbor is single stranded.   Step g: =Six files containing energy information are needed to run the?program, and the names of these files are now requested. The/default energy files are organized as follows: !Dangle.Dat - single base stacking,Loop.Dat - hairpin, bulge and interior loops'Stack.Dat - base pair stacking energies?TStack.Dat - stacking energies for terminal mismatched pairs in' interior and hairpin loopsETLoop.Dat - a list of distinguished tetra-loops and the bonus eneriesF given to them. If you do not want to use this file, createI a dummy file containing a few blank lines and use it instead.=MiscLoop.Dat - some miscellaneous energies (see FILES.LIST).DThese files can be replaced by Dangle.025, Loop.025, Stack.025 etc. $for folding at (for example) 25 deg. -> step i  Step h: FFor a continuation run, a file previously created by a save run needsFto be read in at this point. A prompt will appear asking forFidentification of this file. After the file is read, the energy rulesFand parameters used during the save run are output either to a file or the screen. Step i: FThree different types of folding output formats can be produced:Fprinter (which shows the secondary structure in a rough, but directlyFreadable format), CT file, and Region table (both CT files and regionFtables can be used as input to certain other programs). Prompts will8appear asking which types of output need to be produced.  Step j: Main menu (see apendix A) Save run -> halt/N-best and multi mode -> produce folding output  Step k: &Enter Dotplot section (see appendix B)    ( Appendix A' Main Menu  The following menu will appear:  9 1 Energy Parameter 6 Single Prohibit9 2 Single Force 7 Double Prohibit9 3 Double Force 8 Begin Folding 9 4 Closed Excision 9 Show current 9 5 Open Excision 10 Clear current  FSelections 2 through 7 provide a way for the user to directly alterFthe possible secondary structure by forcing or prohibiting particularFbase-pairs. Each time one of these parameters is chosen, it is addedFto a list held in memory - selection 8 will print the list and 10 willFerase the list. If '8' is chosen from the menu the program willcontinue past this section. /NB : Options 2 and 3 force base pairs to occur.EBase pairs are forced by giving them a bonus energy (EPARAM(9) in theAprogram code). These energies are subtracted during the tracebackDalgorithm so that the computed structures have the correct energies.BUnfortunately, there is no way to subtract the bonus energies fromAthe energy dot plots. Moreover, each forced base pair contain twoCbonus energies because of the nature of the algorithm. For example,@suppose that an optimal folding of an RNA contains 3 forced baseDpairs ( default bonus energy is 50.0 kcal per forced base pair ) andDthat the correct folding energy is -180.0 kcal/mole. Internally, the@energy will be -180.0 - (3+1) x 50.0 = -380.0 kcal/mole. To find?foldings within 10% of the correct energy, one needs to computeEfoldings to within 18.0 kcal of -180.0 - 3 x 50.0 = -330.0 kcal/mole.DThis comes out to -312.0 kcal/mole. The ratio of -312.0 to -380.0 isC82%, so that one would request the 18% level of suboptimality! This>confustion only exists when base pairs are forced. Each closed)excision counts as one forced base pair. DChoosing '1' from the above menu will result in the following (when 4the default 37 deg. energy files have been chosen) :  / Energy Parameters (10ths kcal/mole) = 1 Extra stack energy [ 0]= 2 Extra bulge energy [ 0]= 3 Extra loop energy (interior) [ 0]= 4 Extra loop energy (hairpin) [ 0]= 5 Extra loop energy (multi) [ 46]= 6 Multi loop energy/single-stranded base [ 4]= 7 Maximum size of interior loop [ 30]= 8 Maximum lopsidedness of an interior loop [ 30]= 9 Bonus Energy [ -500]= 10 Multi loop energy/closing base-pair [ 1]  FThe energy parameters (along with the energy rules, which are read inFfrom files) decide what a given folding will look like. For example,Fone could reduce the probability of a bulge loop by increasing parameter 2. ENote that parameters 7 and 8 limit the maximum size and lopsidedness h@of bulge and interior loops. The default values of 30 should be Fsufficient for folding at 37 deg or less. If you wish to fold at high Etemperatures, it would be wise to increase these parameters to 60 or i5even 100. Note that this will increase folding times!e n a n , o( Appendix B& Dotplot t SFWhen the dotplot section is entered, a triangular graph is drawn in1the upper right part of the screen and the prompto u# Minimum energy =  Increment = 0n i! Enter new increment o uFappears under the graph. Associated with each energy increment valueFe is a set S(e) such that S contains all (and only) the base-pairsFthat exist in foldings within e 10ths kcal/mole of the lowest energy.FWhen an increment value x is entered in response to the prompt, allFthe base-pairs in S(x) are added to the graph. If a negitive value is:entered as an increment the graph is cleared and re-drawn.FIf the prompt is responded to with no value (just a ) aFcross-hair cursor will appear, at this time the user can pick off aFpoint in the graph and, by selecting the key used to terminate theFcross-hair state, can select one of several options. The cross-hair,termination keys have the following effects:  Key | Option= ------------|----------------------------------------p/ r | clear and re-draw graph  |? q | generate folding output considering the > | cross-hair selected point as forced to! | base-pairo | ( t | exit the program | C p | generate an ASCII file which has simplifiedeD | the energy matrix by classifing the energiesB | into a number of levels. FIGDOT reads thisC | output file and creates a plot file for thei- | UWGCG program FIGURE.n |i5 g | enter graph mode (see below) S |8? others | display location and energy informationN) | on selected pointi<When graph mode is entered a similar (to main dotplot mode) <situation exists. For every energy increment e and everyDnucleotide i, there exists a number n of base pairs in which i takesBpart and for which the energy of the best folding containing thatFbase pair is within e of the optimal energy. This is the P-Num plot. AEgraph of n vs i is plotted for each entered energy increment, and(B will produce a cross-hair cursor. The cross hair *termination keys result in the following:  e Key | Option= ------------|----------------------------------------e/ r | clear and re-draw graphs |t3 q | return to main dotplot mode  |h( t | exit the program |r( others | display i and n 5 | information on selected pointA aDNote : A 'p' option for creating a hard copy of the Pnum plot is not? in the program yet. The entire plotting section will be e> completely redone when the program is ported to a UNIX  environment.e*[MFOLD]MISCLOOP.DAT;1+,./ 4E-*0123KPWO56h7tli89GHJFREE ENERGY BY SIZE OF LOOPmisc. loop functionsE > internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) 1.079-asymmetric internal loops: the ninio equation > the maximum correction 3.0) > the f(m) array (see ninio for details) .4 .3 .2 .1multibranched loops. > offset, free base penalty, helix penalty' 4.6 .4 .1*[MFOLD]MRNA.FOR;1+,.Q/ 4ZQO~-*0123KPWOP56h7si89GHJ( subroutine process(c Process RNA sequence to be folded. include 'rfd.inc'Bc Selected fragment is from NSAVE(1) to NSAVE(2) in historicalc numbering. do i = nsave(1),nsave(2) newnum(i) = 0 enddoIc LIST contains information on excisions, and on forced or prohibitedc base-pairs. ptr = 0!100 if (ptr.eq.listsz) goto 400 ptr = ptr + 1$ if (list(ptr,1).eq.4) goto 200$ if (list(ptr,1).eq.5) goto 300 goto 100Ec Closed excision beween LIST(PTR,2) and LIST(PTR,3) ( historicalc numbering ) .(200 do i = list(ptr,2)+4,list(ptr,3)-1 newnum(i) = 1 enddo goto 100Cc Open excision beween LIST(PTR,2) and LIST(PTR,3) ( historicalc numbering ) .$300 do i = list(ptr,2),list(ptr,3) newnum(i) = 1 enddo goto 100 400 n = 0 do k = nsave(1),nsave(2)4c Generate new numbering of fragment ( 1 to N ).! if (newnum(k).eq.0) then n = n+1 newnum(k) = n else6c An excised base gets a new numbering of 0. newnum(k) = 0 endif enddo ! if (n*2.gt.fldmax) goto 700 $c Zero the FORCE and VST arrays. do i = 1,n force(i) = 0 if (cntrl(1).ne.2) then do j = i,i+n-1# vst((n-1)*(i-1)+j) = 0 enddo endif enddo  do k = nsave(1),nsave(2) i = newnum(k) if (i.gt.0) thenCc Non-excised bases are examined to determine their type.c A - type 14c B - an A accessible to nuclease cleavagec C - type 23c Z - a C accessible to nuclease cleavagec G - type 33c H - a G accessible to nuclease cleavagec U/T - type 47c V/W - a U/T accessible to nuclease cleavage"c anything else - type 5.c HSTNUM stores historical numbering*c NUMSEQ stores nucleotide type. hstnum(i) = k numseq(i) = 5. if (seq(k) .eq. 'A') numseq(i) = 1% if (seq(k) .eq. 'B') then numseq(i) = 1 force(i) = 3 endif. if (seq(k) .eq. 'C') numseq(i) = 2% if (seq(k) .eq. 'Z') then numseq(i) = 2 force(i) = 3 endif. if (seq(k) .eq. 'G') numseq(i) = 3% if (seq(k) .eq. 'H') then numseq(i) = 3 force(i) = 3 endif? if (seq(k) .eq. 'U'.or.seq(k).eq.'T') numseq(i) = 46 if (seq(k) .eq. 'V'.or.seq(k).eq.'W') then numseq(i) = 4 force(i) = 3 endif endif enddo ptr = 0!500 if (ptr.eq.listsz) goto 600 ptr = ptr + 1 i = list(ptr,2) j = list(ptr,3) k = list(ptr,4)5 if (list(ptr,1).eq.2.or.list(ptr,1).eq.6) k = j4 goto (500,520,530,540,500,560,570),list(ptr,1)3c Force bases I to I+K-1 to be double-stranded.520 do x = i,i+k-1 force(newnum(x)) = 2 enddo goto 5007c Force base-pairs I.J , I+1.J-1 , ... I+K-1.J-K+1.530 do x = 0,k-1* call sfce(newnum(i+x),newnum(j-x)) enddo goto 5007c Force the ends of a closed excision to base-pair.$540 call sfce(newnum(i),newnum(j)) do ii = i+1,i+3 seq(ii) = ' ' enddo goto 5002c Prohibit bases I to I+K-1 from base-pairing.560 do ii = i,i+k-1 force(newnum(ii)) = 1 enddo goto 500>c Prohibit the base-pairs I.J , I+1,J-1 , ... I+K-1.J-K+1.570 if (cntrl(1).ne.2) then do x = 0,k-15 vst((n-1)*(newnum(i+x)-1)+newnum(j-x)) = 17 vst((n-1)*(newnum(j-x)-1)+newnum(i+x)+n) = 1 enddo endif goto 500c Double up the sequence.600 do i = 1,n hstnum(i+n) = hstnum(i) force(i+n) = force(i) numseq(i+n) = numseq(i) enddo 700 return end  'c Used in reading the energy files. function convt(str) implicit integer (a-z) character*5 str logical neg  neg = .false. place = 0 convt = 0  do i = 5,1,-1! if (str(i:i).eq.'-') then neg = .true. else7 if (str(i:i).ge.'0'.and.str(i:i).le.'9') thenG convt = convt + 10**place * (ichar(str(i:i)) - ichar('0')) place = place+1 endif endif enddo! if (neg) convt = convt * -1 return end =c Reads energy file names and open the files for reading. subroutine enefiles character*40 filen F10 write (6,*) 'Enter dangle energy file name (default dangle.dat)' read (5,100,end=1) filenF open(10,file=filen,defaultfile='DANGLE.DAT',status='OLD',err=10) B20 write (6,*) 'Enter loop energy file name (default loop.dat)' read (5,100,end=1) filenD open(11,file=filen,defaultfile='LOOP.DAT',status='OLD',err=20) D30 write (6,*) 'Enter stack energy file name (default stack.dat)' read (5,100,end=1) filenE open(12,file=filen,defaultfile='STACK.DAT',status='OLD',err=30) F40 write (6,*) 'Enter tstack energy file name (default tstack.dat)' read (5,100,end=1) filenF open(13,file=filen,defaultfile='TSTACK.DAT',status='OLD',err=40) D50 write (6,*) 'Enter tloop energy file name (default tloop.dat)' read (5,100,end=1) filenE open(29,file=filen,defaultfile='Tloop.DAT',status='OLD',err=50) L60 write (6,*) 'Enter misc. loop energy file name (default miscloop.dat)' read (5,100,end=1) filenH open(32,file=filen,defaultfile='miscloop.DAT',status='OLD',err=60) 100 format(a40) goto 21 call exit 2 return end c Error message subroutine. subroutine errmsg(err,i,j) include 'rfd.inc' % if (err.eq.10) write (6,10) i,j% if (err.eq.11) write (6,11) i,j% if (err.eq.12) write (6,12) i,j if (err.eq.20) then write (6,20) i,j stop endif if (err.eq.21) then write (6,21) err = 0 endif# if (err.eq.30) write (6,30) i if (err.eq.31) then! write (6,31) sortmax,i,j err = 0 endif if (err.eq.40) then write (6,40) stop endif return B10 format(' Open bifurcation not found between ',i4,' and ',i4)J11 format(' Bulge or interior loop closed by (',i4,',',i4') not found')D12 format(' Closed bifurcation not found between ',i4,' and ',i4)D20 format(' Base pair between ',i3,' and ',i3,' conflicts with ',! . 'at least one other pair')+21 format(' Buffer overflow in lineout')-30 format(' End reached at traceback ',i4)F31 format(' More than ',i5,' basepairs in sort at (',i4,',',i4,')')+40 format(' Premature end of save file') endc Initialize the stack. subroutine initst implicit integer (a-z) dimension stk(50,4) common /stk/ stk,sp sp = 0 return end-c Add A,B,C,D to the bottom of the stack. subroutine push(a,b,c,d) implicit integer (a-z) dimension stk(50,4) common /stk/ stk,sp  sp = sp + 1 if (sp.gt.50) then- write (6,*) 'ERROR - STACK OVERFLOW' stop endif stk(sp,1) = a stk(sp,2) = b stk(sp,3) = c stk(sp,4) = d return endDc Retrieve A,B,C,D from the bottom of the stack and decrease thec stack size by one. function pull(a,b,c,d) implicit integer (a-z) dimension stk(50,4) common /stk/ stk,sp  if (sp.eq.0) then pull = 1 return endif a = stk(sp,1) b = stk(sp,2) c = stk(sp,3)  d = stk(sp,4) sp = sp - 1e pull = 0 return endi  3c Line printer output of a secondary structure. 5 subroutine linout(n1,n2,energy,iret,jret,error)vc) include 'rfd.inc'( character array(6,900),dash,bl,dot real energyn integer unitce/ data dash/'-'/,bl/' '/,dot/'.'/,amax/900/(c.&c WRITE SEQUENCE LABEL AND ENERGYc unit = cntrl(4)q hstn1 = hstnum(n1) hstn2 = hstnum(n2)/ write(unit,103) hstn1,hstn2,seqlab,energy(c,c INITIALIZE TRACEBACKac call initst call push(n1,n2,0,0) nstem = 0 go to 3)c1"c OUTPUT PORTION OF STRUCTUREcp5 do while (1.eq.1)T write(unit,106) ll = countr) if(cntrl(3).lt.ll) ll = cntrl(3), do k = 1,6)@ if(unit.eq.6) write(unit,105) (array(k,i),i = 1,ll)@ if(unit.ne.6) write(unit,104) (array(k,i),i = 1,ll) enddo' if(countr.le.cntrl(3)) go to 3  do k = 1,5e do j = 1,6 array(j,k) = bl array(j,k+5) = bl enddo  array(2,k+5) = dot array(5,k+5) = dot enddo k = 10E ll = cntrl(3)+1 do i = ll,countr= k = k+1 do j = 1,6 $ array(j,k) = array(j,i) enddo enddo countr = k enddoc3 do k = 1,amax, do j = 1,6 array(j,k) = bl enddo enddoocxc FILL IN OUTPUT MATRIXcm! nstem = pull(i,j,countr,xx)y if (nstem.ne.0) returncic LOOK FOR DANGLING ENDS c 12 ip = i jp = j do while (basepr(ip).eq.0) ip = ip+1 if(ip.ge.j) go to 16c enddou do while (basepr(jp).eq.0) jp = jp-1 enddo  k = ip-i if(j-jp.gt.k) k = j-jp if(k.eq.0) go to 17 ii = ips jj = jpl pos = countr+k9X8~ MFOLD.BCK*[MFOLD]MRNA.FOR;1ZQOv+1 if(pos.gt.amax) then error = 21 return endif  do kk = 1,kf pos = pos-1 ii = ii-1 jj = jj+1 if(ii.ge.i) thenn i2 = hstnum(ii)f" array(2,pos) = seq(i2)@ if(10*(i2/10).eq.i2) call digit(1,i2,pos,amax,array) elsee array(2,pos) = dash endif if(jj.le.j) thenn j2 = hstnum(jj)." array(5,pos) = seq(j2)@ if(10*(j2/10).eq.j2) call digit(6,j2,pos,amax,array) else  array(5,pos) = dash  endif enddoq countr = countr+k go to 17cec HAIRPIN LOOPkcq16 if(i.ge.j) go to 5 half = (j-i+2)/2 ii = i-1 jj = j+1 do k = 1,halfd ii = ii+1 jj = jj-1 countr = countr+1 if(countr.gt.amax) then error = 21 return endif, if(seq(hstnum(ii)).eq.' ') go to 40 i2 = hstnum(ii) j2 = hstnum(jj)M if(10*(i2/10).eq.i2.and.ii.lt.jj) call digit(1,i2,countr,amax,array)o@ if(10*(j2/10).eq.j2) call digit(6,j2,countr,amax,array) if(k.ne.half) theni% array(2,countr) = seq(i2)3% array(5,countr) = seq(j2)n elsej2 if(ii.lt.jj) array(3,countr) = seq(i2)% array(4,countr) = seq(j2) endif 22 enddoe go to 5 cic 'CLOSED' EXCISION FOUNDc40 array(3,countr) = dash array(4,countr) = dash go to 5acnc STACKING OR BIFURCATIONc 17 i = ip j = jp! if(basepr(i).eq.j) go to 24rcbc CHECK FOR KNOT c,I if(basepr(i).ge.basepr(j).or.i.ge.basepr(i).or.basepr(j).ge.j) then- iret = hstnum(i)e! jret = hstnum(basepr(i))  error = 20n return( endifc c BIFURCATION MUST OCCUR co countr = countr+2  if(countr.gt.amax) then  error = 21s return endiff' call push(basepr(i)+1,j,countr,0) j = basepr(i) cuc STACKING REGIONc 24 countr = countr+1r if(countr.gt.amax) thent error = 21t return endif* ii = hstnum(i) jj = hstnum(j) array(3,countr) = seq(ii)  array(4,countr) = seq(jj)-= if(10*(ii/10).eq.ii) call digit(1,ii,countr,amax,array)= if(10*(jj/10).eq.jj) call digit(6,jj,countr,amax,array))& if(i.eq.iret.and.j.eq.jret) then array(2,countr) = '|' array(5,countr) = '^' end if i = i+1 j = j-1  if(basepr(i)-j) 12,24,12 nL103 format(' FOLDING BASES ',i4,' TO ',i4,' OF ',a30,/' ENERGY = ',f8.1)104 format(220a1)g105 format(' ',220a1)i106 format(' ')e end Fc Puts the number COLUMN in row ROW and column POS of the array B.Fc The least significant digit ends up in column POS. If the numberEc is too large to fit, a period is put in column POS and row ROW.y- subroutine digit(row,column,pos,bmax,b)0 implicit integer (a-z)# integer pos,column,bmax,d(10)t( character*1 b(6,bmax),bl,c(10),dotF data bl/' '/,c/'0','1','2','3','4','5','6','7','8','9'/,dot/'.'/cf size=1 n=column 1 p=n/10 q=n-10*p d(size)=q if(p.eq.0) go to 2 n=pn size=size+1a go to 1'2 if(pos-size.lt.0) go to 3 do k=1,sizef q=pos-k+1# if(b(row,q).ne.bl) go to 30 enddo* p=posp do 4 k=1,sizef q=d(k) b(row,p)=c(q+1)n 4 p=p-1 return3 b(row,pos)=dot return endr 0Gc Generates a region table for the Shapiro and Maizel DRAW program.c subroutine regtab, include 'rfd.inc'p real r d k = 1i region = 1 do while (k.lt.n)  r = 0.0 regsz = 1 kst = k! if (k.lt.basepr(k)) thens; do while (basepr(k+1).eq.basepr(k)-1.and.k.lt.n)l regsz = regsz + 1.F r = r + float(erg(2,k,basepr(k),k+1,basepr(k+1))) / 10.0 k = k + 12 enddoH write (22,100) region,hstnum(kst),hstnum(basepr(kst)),regsz,r region = region + 1 endif k = k + 1 enddoi return .*100 format(' (',i5,')',3x,3(i5,3x),f7.1) end  -c Generates a CT file. (Richard Feldmann)  subroutine ct(r) include 'rfd.inc'w real r  write(21,100) n,r,seqlab do k = 1,n k1 = k+1 if (k.eq.n) k1 = 0C write (21,200) k, seq(hstnum(k)),k-1,k1,basepr(k),hstnum(k), enddof return m+100 format(i5,1x,'ENERGY = ',f7.1,4x,a30)4200 format(i5,1x,a1,3x,4i5)s ende ' , n.c Menu subroutine for RNA folding program.5c Allows the user to set energy parameters and tou c add auxiliary information. subroutine menu  o include 'rfd.inc'a data listsz/0/ '!10 if (listsz.ge.100) goto 800e write (6,900)50 write (6,901)t$ read (5,*,end=1,err=1) choice. if (choice.lt.1.or.choice.gt.10) goto 509 goto (100,200,300,400,400,200,300,800,60,70),choice= 60 call listout(6) goto 10, 70 listsz = 0 goto 10 1 call exit( , )'100 write (6,1000) (eparam(i),i=1,10)e101 write (6,1001)& read (5,1002,end=10,err=10) parm* if (parm.lt.1.or.parm.gt.10) goto 10 write (6,1003)" read (5,*,end=10,err=10) val eparam(parm) = val goto 1001000 format(/, 8 . 10x,' Energy Parameters (10ths kcal/mole)',//,F . 10x,' 1 Extra stack energy [',i5,']',/,F . 10x,' 2 Extra bulge energy [',i5,']',/,F . 10x,' 3 Extra loop energy (interior) [',i5,']',/,F . 10x,' 4 Extra loop energy (hairpin) [',i5,']',/,F . 10x,' 5 Extra loop energy (multi) [',i5,']',/,F . 10x,' 6 Multi loop energy/single-stranded base [',i5,']',/,F . 10x,' 7 Maximum size of interior loop [',i5,']',/,F . 10x,' 8 Maximum lopsidedness of an interior loop [',i5,']',/,F . 10x,' 9 Bonus Energy [',i5,']',/,G . 10x,'10 Multi loop energy/closing base-pair [',i5,']',//),L1001 format(' Enter Parameter to be changed ( for main menu) ',$)1002 format(i6) %1003 format(' Enter new value ',$)  200 write (6,2001)" read (5,*,end=10,err=10) i,k listsz = listsz + 1  list(listsz,1) = choice( list(listsz,2) = i list(listsz,3) = k list(listsz,4) = -1C goto 10 *2001 format(' Enter base and length ',$) 300 write (6,3001)$ read (5,*,end=10,err=10) i,j,k listsz = listsz + 1  list(listsz,1) = choiceu list(listsz,2) = i list(listsz,3) = j list(listsz,4) = k goto 10l13001 format(' Enter base pair and length ',$)  t400 write (6,4001)" read (5,*,end=10,err=10) i,j listsz = listsz + 1  list(listsz,1) = choice list(listsz,2) = i list(listsz,3) = j list(listsz,4) = -1d goto 10d-4001 format(' Enter begining and end ',$) 800 return u900 format(/,kA . 10x,'1 Energy Parameter 6 Single Prohibit',/,)A . 10x,'2 Single Force 7 Double Prohibit',/,dA . 10x,'3 Double Force 8 Begin Folding ',/,kA . 10x,'4 Closed Excision 9 Show current ',/,RB . 10x,'5 Open Excision 10 Clear current ',//)"901 format(' Enter Choice ',$) end2  = subroutine listout(u)i?c This subroutine lists current choices on excisions and on &c forced or prohibited base-pairs. integer u  common /list/ list,listsz  dimension list(100,4)t character*20 choices(7)g? data choices/'Energy Parameter ','Single Force ',H .'Double Force ','Closed Excision ','Open Excision ',2 .'Single Prohibit ','Double Prohibit '/  if (listsz.eq.0) thenj3 write(u,*) ' No choices currently defined'u else write(u,*) ' 'q& write(u,*) ' Current Choices' do 100 i = 1,listsz7 if (list(i,1).eq.3.or.list(i,1).eq.7) then D write(u,1000) choices(list(i,1)),(list(i,k),k = 2,4) elseoD write(u,1001) choices(list(i,1)),(list(i,k),k = 2,3) endif100 continuer write(u,*) ' ' endif return-1000 format(10x,a20,': (',i4,',',i4,') ',i4) %1001 format(10x,a20,': ',i4,',',i4) end  f)c Control subroutine for RNA folding.1 subroutine device  include 'rfd.inc'  character*40 sfile,str character in oAc What kind of run is this? ( regular, save or continuation )  write (6,2000)" read (5,2001,end=1) cntrl(1) write (6,*) ' ')6 if (cntrl(1).lt.0.or.cntrl(1).gt.2) cntrl(1) = 0 d if (cntrl(1).eq.1) thent cntrl(7) = 1 else/c What mode is the program to be run in? >c dot plot, automatic sorted tracebacks of one sequence:c fragment or suboptimal foldings of every completec sequence in a file.9 write (6,1002) % read (5,2001,end=1) cntrl(7) 9 if (cntrl(7).lt.0.or.cntrl(7).gt.2) cntrl(7) = 0 2 if (cntrl(1).eq.2.and.cntrl(7).eq.2) thenZ write (6,*) 'Combination of continuation run and multiple foldings disallowed' write (6,*) ' 'b goto 9 endif write (6,*) ' ' endif):c Folding multiple sequences is treated as a sort run.?c Find total number of sequences to be folded in a multiple c sequence run.  / if (cntrl(7).eq.2) call mseq(cntrl(5))S C if (cntrl(7).eq.0) then%c Prompt for terminal type.  write (6,1000). read (5,2001,end=7,err=7) cntrl(5)<7 if (cntrl(5).lt.1.or.cntrl(5).gt.3) cntrl(5) = 2 write (6,1001)$ elseif (cntrl(1).ne.1) then(c Prompt for controls on sort. write (6,1004)( read (5,2001,end=1) cntrl(8) write (6,1003) endif if (cntrl(1).ne.1) then( read (5,2001,end=1) cntrl(6)+ if (cntrl(6).lt.1) cntrl(6) = 1, x write (6,1005)( read (5,2001,end=1) cntrl(9) write (6,*) ' 'c endif?c Prompt for SAVE file name for a save/continuation run. if (cntrl(1).ne.0) then4 write (6,3000)% read (5,3001,end=1) sfilem# if (cntrl(1).eq.1) then str = 'NEW' else str = 'OLD'n endif Z open(30,err=2,file=sfile,defaultfile='FOLD.SAV',status=str,form='UNFORMATTED') goto 3%2 if (cntrl(1).eq.2) goto 4y+3 if (cntrl(1).eq.2) call getcontb endif/c Obtain sequence. Original length is N.(:c A fragment from NSAVE(1) to NSAVE(2) is selected.Fc After PROCESS, N becomes the length of the processed sequencec to be folded.2 if (cntrl(1).ne.2.and.cntrl(7).ne.2) then1 call formid(seqlab,seq,n,maxsiz,used)" write(6,4000) seqlab,n= write (6,*) 'Enter start of fragment (default 1)'i( read (5,4001,end=1) nsave(1)+ if (nsave(1).le.0) nsave(1) = 1( write (6,4002) n( read (5,4001,end=1) nsave(2)+ if (nsave(2).le.0) nsave(2) = ne endif e71000 format(1x,'Enter terminal type',/,5x,'1 VGT100',iB . /,5x,'2 Visual 102 (default)',/,5x,'3 Tektronics 4105')E1001 format(/,' Enter minimum vector size for plot (default 1) ',$) F1002 format(1x,'Enter run mode',/,5x,'0 Sub-optimal plot (default)',7 . /,5x,'1 N Best',/,5x,'2 Multiple Molecules') =1003 format(/,' Enter number of tracebacks (default 1) ',$)(<1004 format(/,' Enter percentage for sort (default 0) ',$)41005 format(/,' Enter window size (default 0) ',$)A2000 format(1x,'Enter run type',/,5x,'0 Regular run (default)',n7 . /,5x,'1 Save run',/,5x,'2 Continuation run') 2001 format(i6)83000 format(' Enter save file name (default fold.sav)')3001 format(a30)T.4000 format(/,' ',a30,5x,i5,' nucleotides',/)4001 format(i10)r94002 format(1x,'Enter end of fragment (default ',i5,')') return1 call exitk end  (Bc Obtain multiple sequences from a sequence file using MULTID. subroutine mseq(i) include 'rfd.inc'0 logical used data used/.false./  if (.not.used) then 0 call multid(seqlab,seq,n,maxsiz,used,i) write (6,*) ' ' else0 call multid(seqlab,seq,n,maxsiz,used,i) write(6,4000) seqlab,nu endifo nsave(1) = 1 nsave(2) = n return.4000 format(/,' ',a30,5x,i5,' nucleotides',/) end0 4c Set up output units and files for RNA folding. subroutine outputs include 'rfd.inc'  character*40 str,dstr0 0Cc Examine sequence label to get default names for output files. k = 1? do while ((seqlab(k:k).lt.'A'.or.seqlab(k:k).gt.'Z').and.p; . (seqlab(k:k).lt.'a'.or.seqlab(k:k).gt.'z'))d k = k + 1 enddol slen = min0(30,25+k)) do while (seqlab(slen:slen).eq.' ')0 slen = slen - 1 enddo j = 10 do i = k,slen < if ((seqlab(i:i).ge.'A'.and.seqlab(i:i).le.'Z').or.< . (seqlab(i:i).ge.'a'.and.seqlab(i:i).le.'z').or.> . (seqlab(i:i).ge.'0'.and.seqlab(i:i).le.'9')) then ,# dstr(j:j) = seqlab(i:i)e else  dstr(j:j) = '_'  endif j = j + 1 enddo  slen = j <c Line printer output. Get name and open file for write. rewind(5)0 cntrl(2) = 0 write (6,5010) read (5,5000,end=1) in' if (in.ne.'N'.and.in.ne.'n') then  cntrl(2) = 1 write (6,5011) read (5,5000,end=1) in* if (in.eq.'N'.or.in.eq.'n') then) dstr(slen+1:slen+4) = '.OUT' 51 write (6,5012) dstr read (5,5001) str cntrl(4) = 208 open(20,file=str,defaultfile=dstr,recl=255,= . status='NEW',err=51,carriagecontrol='LIST')r else cntrl(4) = 6) endifz write (6,5013)& read (5,5014,end=1) cntrl(3)+ if (cntrl(3).eq. 0) cntrl(3) = 80l endifC 7c CT file output. Get name and open file for write. write (6,5020) read (5,5000,end=1) in& if (in.eq.'Y'.or.in.eq.'y') then" cntrl(2) = 2 + 2*cntrl(2)% dstr(slen+1:slen+4) = '.CT ',52 write (6,5021) dstr read (5,5001) str+ open(21,file=str,defaultfile=dstr,t9 . status='NEW',err=52,carriagecontrol='LIST') endif= s<c Region table output. Get name and open file for write. write (6,5030) read (5,5000,end=1) in& if (in.eq.'Y'.or.in.eq.'y') thenD if (cntrl(2).eq.1.or.cntrl(2).eq.2) cntrl(2) = cntrl(2) + 1 cntrl(2) = cntrl(2) + 3% dstr(slen+1:slen+4) = '.REG' 53 write (6,5031) dstr read (5,5001) str+ open(22,file=str,defaultfile=dstr, 9 . status='NEW',err=52,carriagecontrol='LIST') endif  write (6,*) ' '  . if (1.ne.1) then1 call exit endif/ return t5000 format(a1)5001 format(a40)55010 format(' Do you want printer output? (Y,n) ',$)t-5011 format(' Output to terminal? (Y,n) ',$)o95012 format(' Enter output file name (default ',a35,')')mD5013 format(' Enter number of columns on printer (default 80) ',$)5014 format(i10) .5020 format(' Do you want ct file? (y,N) ',$)55021 format(' Enter ct file name (default ',a35,')')i35030 format(' Do you want region table? (y,N) ',$)t?5031 format(' Enter region table file name (default ',a35,')')  end* c Reads energy files.d subroutine ergread e include 'rfd.inc'e logical endfile character*80 inrec character*5 temp real a,b,c,d ,c TLoop INFORMATION IN call gettloops (c Get misc loop info? if(find(32,3,' > ')) stop 'Premature end of MISCLOOP.DAT'i read (32,*) prelog prelog=prelog*10 endfile = find(32,3,' > ') read (32,*) ai maxpen=int(a*10) endfile = find(32,3,' > ') read (32,*) a,b,c,d0 poppen(1)=int(a*10)n poppen(2)=int(b*10)u poppen(3)=int(c*10)  poppen(4)=int(d*10) endfile = find(32,3,' > ') read (32,*) a,b,cr eparam(5)=int(a*10)n eparam(6)=int(b*10), eparam(10)=int(c*10) c DANGLE IN   do a = 1,5 do b = 1,5 do c = 1,5 do d = 1,2( dangle(a,b,c,d) = infinity enddo enddo enddoe enddoa endfile = find(10,3,'<--') if (.not.endfile) then do var4 = 1,2 do var1 = 1,4m$ if (endfile) goto 150) read(10,100,end=150) inrec  do var2 = 1,4 do var3 = 1,4  j = 0: tstart = (var2-1)*20 + (var3-1)*5 + 12 temp = inrec(tstart:tstart+4) do i = 2,4i@ if (temp(i-1:i+1).eq.' . ') j = infinity enddoK if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') j = infinitya0 if (j.eq.0) j = convt(temp)4 dangle(var1,var2,var3,var4) = j enddol enddo) endfile = find(10,3,'<--')h enddom enddo else; write (6,*) 'ERROR - DANGLE ENERGY FILE NOT FOUND' stop endifr )100 format(a80)t goto 200 ?150 write (6,*) 'ERROR - PREMATURE END OF DANGLE ENERGY FILE' stop t r"c INTERNAL,BULGE AND HAIRPIN IN 6"200 endfile = find(11,5,'-----') i = 1 201 read(11,100,end=300) inrec j = -1 do ii = 1,3e j = j + 6% do while (inrec(j:j).eq.' ')  j = j + 1c enddo temp = inrec(j:j+4) k = 0 do jj = 2,46 if (temp(jj-1:jj+1).eq.' . ') k = infinity enddo? if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') k = infinity.$ if (k.eq.0) k = convt(temp)" if (ii.eq.1) inter(i) = k" if (ii.eq.2) bulge(i) = k$ if (ii.eq.3) hairpin(i) = k enddol i = i + 1  if (i.le.30) goto 201n c STACK IN 3300 do a = 1,5 do b = 1,5 do c = 1,5 do d = 1,5' stack(a,b,c,d) = infinityg enddo  enddo) enddo enddof endfile = find(12,3,'<--') if (.not.endfile) then do var1 = 1,4 do var3 = 1,4 $ if (endfile) goto 350) read(12,100,end=350) inrece do var2 = 1,4 do var4 = 1,4  j = 0: tstart = (var2-1)*20 + (var4-1)*5 + 12 temp = inrec(tstart:tstart+4) do i = 2,41@ if (temp(i-1:i+1).eq.' . ') j = infinity enddoK if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') j = infinitye0 if (j.eq.0) j = convt(temp)3 stack(var1,var2,var3,var4) = j2 enddo, enddo enddo'& endfile = find(12,3,'<--') enddo else: write (6,*) 'ERROR - STACK ENERGY FILE NOT FOUND' stop1 endifx call stest(stack,'STACK ') m goto 400 >350 write (6,*) 'ERROR - PREMATURE END OF STACK ENERGY FILE' stop e400 do a = 1,5 do b = 1,5 do c = 1,5 do d = 1,5& tstk(a,b,c,d) = infinity enddo. enddor enddon enddo' endfile = find(13,3,'<--') if (.not.endfile) then do var1 = 1,4 do var3 = 1,4'$ if (endfile) goto 350) read(13,100,end=450) inrec  do var2 = 1,4 do var4 = 1,4  j = 0: tstart = (var2-1)*20 + (var4-1)*5 + 12 temp = inrec(tstart:tstart+4) do i = 2,4l@ if (temp(i-1:i+1).eq.' . ') j = infinity enddoK if (temp(1:1).eq.'.'.or.temp(5:5).eq.'.') j = infinity,0 if (j.eq.0) j = convt(temp)2 tstk(var1,var2,var3,var4) = j enddo0 enddo enddo& endfile = find(13,3,'<--') enddo else: write (6,*) 'ERROR - STACK ENERGY FILE NOT FOUND' stop endifuc** CALL STEST(TSTK,'TSTACK')o u close(10) close(11)  close(12)a close(13)s goto 500 a?450 write (6,*) 'ERROR - PREMATURE END OF TSTACK ENERGY FILE'd stop k 500 return end ?c Symmetry test on stacking and terminal stacking energies.@c For all i,j,k,l between 1 and 4, STACK(i,j,k,l) MUST equalBc STACK(l,k,j,i). If this fails at some i,j,k,l; these numbers@c are printed out and the programs grinds to an abrupt halt!# subroutine stest(stack,sname)s$ integer stack(5,5,5,5),a,b,c,d character*6 snamei  do a = 1,4 do b = 1,4 do c = 1,4 do d = 1,48 if (stack(a,b,c,d).ne.stack(d,c,b,a)) then- write (6,*) 'SYMMETRY ERROR'd; write (6,101) sname,a,b,c,d,stack(a,b,c,d),; write (6,101) sname,d,c,b,a,stack(d,c,b,a)  stop  endif enddo0 enddo enddo. enddo' return/101 format(5x,a6,'(',3(i1,','),i1,') = ',i10) end, 2Ic Writes out the numbers in the energy arrays of the folding program.  subroutine out(u)a include 'rfd.inc' $ integer*2 tlptr,key,bptr,nbase character*4 tlbuf  5c used for testing contents of energy arrays only$c not used in the mature program ( write (u,100) 'DANGLE' do var4 = 1,20 do var1 = 1,4  do var2 = 1,4  do var3 = 1,4i. o = dangle(var1,var2,var3,var4)& if (o.ne.infinity) then! write (u,101) o2 else  write (u,102)  endif enddo  enddor write (6,103)t enddos write (6,104)t enddo5 a a write (u,100) 'TSTACK' do var1 = 1,4t do var3 = 1,4n do var2 = 1,4  do var4 = 1,4e, o = tstk(var1,var2,var3,var4)& if (o.ne.infinity) then! write (u,101) or elset write (u,102)t endif enddoe enddo  write (6,103) enddo2 write (6,104)s enddo   write (u,100) 'STACK'e do var1 = 1,4  do var3 = 1,46 do var2 = 1,4. do var4 = 1,4x- o = stack(var1,var2,var3,var4)o& if (o.ne.infinity) then! write (u,101) o, elset write (u,102)o endif enddod enddom write (6,103)m enddoo write (6,104) enddoo t- write (u,200) 'INTER','BULGE','HAIRPIN'N do i = 1,30t4 write (u,201) i,inter(i),bulge(i),hairpin(i) enddoa r write (u,100) 'TLoops' do tlptr=1,numoftloops key=tloop(tlptr,1) do bptr=1,4 nbase=mod(key,8) key=int(key/8) if (nbase.eq.1) then# tlbuf(bptr:bptr)='A'0$ elseif (nbase.eq.2) then# tlbuf(bptr:bptr)='C'T$ elseif (nbase.eq.3) then# tlbuf(bptr:bptr)='G'2 else# tlbuf(bptr:bptr)='U'  endif enddo( write (u,205) tlbuf,tloop(tlptr,2) enddo( return100 format(//,a40,//) 101 format('+',i4,1x,$)102 format('+',4('*'),1x,$) 103 format(' ')0104 format(/)2200 format(3a20,/,60('-'),/)201 format(i4,i16,2i20)n205 format(a4,2x,i8) end, 'c Used in reading the energy files.mBc Locates markers in the energy files so that data can be readc properly.G! function find(unit,len,str)  implicit integer (a-z) logical find,flag1 character*20 str character*80 inrec  find = .false. flag = .false. do while(.not.flag)% read(unit,100,end=200) inrecd count = 1 do 101 i = 1,80-len+13 if (inrec(i:i).eq.str(count:count)) then  count = count + 1, if (count.gt.len) flag = .true.> if (inrec(i+1:i+1).ne.str(count:count)) count = 1 endif101 continuer enddo  return100 format(a80)t200 find = .true. return end    subroutine cdump include 'rfd.inc'i character*40 name  character yn O write (6,*) 'Enter file name for continuation dump (return for terminal)'  read (5,100,end=1) name  if (name.eq.' ') then1 u = 6 else u = 31l( open(31,status='NEW',file=name) endif0 call listout(u) ' write (u,101) 'Energy Parameters'  write (u,1000) eparamE2 write (6,*) 'Listing of energy files? (y/N)' read(5,102) yn& if (yn.eq.'Y'.or.yn.eq.'y') then call out(u) endifE return1 call exit100 format(a30)U101 format(a20,/)6102 format(a1)1000 format(/,)F . 10x,' 1 Extra stack energy [',i5,']',/,F . 10x,' 2 Extra bulge energy [',i5,']',/,F . 10x,' 3 Extra loop energy (interior) [',i5,']',/,F . 10x,' 4 Extra loop energy (hairpin) [',i5,']',/,F . 10x,' 5 Extra loop energy (multi) [',i5,']',/,F . 10x,' 6 Multi loop energy/single-stranded base [',i5,']',/,F . 10x,' 7 Maximum size of interior loop [',i5,']',/,F . 10x,' 8 Maximum lopsidedness of an interior loop [',i5,']',/,F . 10x,' 9 Bonus Energy [',i5,']',/,G . 10x,'10 Multi loop energy/closing base-pair [',i5,']',//) end, subroutine gettloopscd8c* Read in TLoop sequences, convert to numeric form, and%c* convert energy to an integer (*10)nce( parameter (maxtloops=40,bufsiz=80)0 integer*2 i,ptr,tloop(maxtloops,2),nseq(4) integer*2 numoftloops,fptr integer*2 convt  character*5 buffa4 character*80 inbufc & common /tloops/tloop,numoftloopsc  numoftloops=0vc-c* Throw out header1c  read (29,1)tc Cc* Read a line and convert to numeric sequence and energy until EOF c 10 read (29,2,end=99) inbuf ptr=1i! numoftloops=numoftloops+1 & do while ((ptr.lt.bufsiz).and.+ 2 (inbuf(ptr:ptr).eq.' '))  ptr=ptr+1n enddo ;c Only take first four characters, since they're TETRAloops # buffa(1:4)=inbuf(ptr:ptr+3)  buffa(5:5)=' ' call tonum(buffa,nseq)F tloop(numoftloops,1)=((nseq(4)*8+nseq(3))*8+nseq(2))*8+nseq(1) ptr=ptr+4 & do while ((ptr.lt.bufsiz).and.+ 2 (inbuf(ptr:ptr).eq.' '))5 ptr=ptr+1E enddoTc Simple error czeck. + if (inbuf(ptr+4:ptr+4).ne.' ') then5! write (*,5) inbuf endif # buffa(1:4)=inbuf(ptr:ptr+3)  buffa(5:5)=' ') tloop(numoftloops,2)=convt(buffa)  do i=1,ptr+4 inbuf(i:i)=' ' enddo goto 10c c* Normal endingc'"99 close(unit=29,status='KEEP') return1 format(//)2 format (a)J5 format (1x,'Too many characters in numeric field of this line of',/,& 1 1x,'tloop.dat file: ',a) end) ( subroutine tonum(tloopseq,numeric)c 1c* Convert TLoopSeq to numeric format in Numeric. cl character*5 tloopseq integer*2 i,numeric(4)ci do i=1,4* if (tloopseq(i:i).eq.'A') then numeric(i)=1* elseif (tloopseq(i:i).eq.'C') then numeric(i)=2* elseif (tloopseq(i:i).eq.'G') then numeric(i)=3* elseif (tloopseq(i:i).eq.'U') then numeric(i)=4* elseif (tloopseq(i:i).eq.'T') then numeric(i)=4 else) write (*,1) tloopseq(i:i) =1 format (1x,'Unknown base in TLOOP file: ',a1)( stop endif3 enddoo return end**[MFOLD]MULTID.FOR;1+,.!/ 4G! L-*0123KPWO!56. h7V{i89GHJ7 subroutine multid(seqid,seq,nseq,nmax,used,rnum)Dc REVISED VERSION OF FORMID -- TO WORK WITH MULTIPLE ALIGNMENTSc RESEARCHER: M. ZUKERc JUN 1986c DS TUDHOPEEc WRITTEN TO WORK ON VAX-11-750 UNDER VMS4.3 USING STANDARD F-77Dc #### NOTE #### USE OF CARRIAGE CONTROL LINE FEED SUPPRESSIONBc IS USED IN THIS PROGRAM AND IS NOT STANDARD!c FORTRAN-776c SEE '$' IN FORMAT STATEMENT 102 implicit integer (a-z)& logical found,endfil,valid,used4 integer sline(500),seqnum(500),nseq,nmax,rnum character*8 stype character*30 seqids(500) character*30 choice,seqid& character*50 filnam,fmtseq(500) character*80 reclin character*1 seq(nmax) data found/.false./, . endfil/.false./, . valid/.false./Ec **************************************************************c subroutine MULTIDEc *:D~ MFOLD.BCK*[MFOLD]MULTID.FOR;1G!<*************************************************************c PURPOSE:8c subroutine used to extract sequences from various"c format type files including(c STANFORD,GENBANK,EMBL,PIR,and,NRC:c This revised version of FORMID is shorter. Another;c variable RNUM is passed first into the subroutine on>c the first call to return the number of sequences in the@c file. The same variable is then used to request specific1c sequences in do_loops of the main program.Bc This eliminates the task of having to select the sequences.Ec **************************************************************c variable list table:2c * -- sent down from main returned unchanged,c ** - returned to main from subroutine4c ***- sent down from main and returned changedBc INTEGERS:IDCNT -- to keep track of the number of sequence8c identifiers found in the file(c I,K -- loop countersGc LINE -- to point to the record line number of a fileCc N -- counter to extract the correct number of,c sequence elementsFc * NMAX -- maximum length of sequence expected by userEc ** NSEQ -- length of the sequence retrieved from fileBc POINTR -- pointer to point to sequence identifier;c chosen from array of identifiersFc RNUM -- the number of identified sequences returnedBc to main if first use of the subroutine,Fc the number sent down from main, identifying@c a sequence if not the first time usedBc SEQNUM -- an ARRAY of the length of the sequencesDc for the sequence identifiers found in the0c NRC-format type filesDc SLINE -- an ARRAY of the record-line numbers where6c a sequence starts in a fileCc START -- defines what column of a record to start3c reading the sequence in.Cc CHARACTERS:CHOICE-- character string of length 20 to read inEc choice for sequence identifier to retrieveCc FILNAM -- character string of length 50 to read in(c the filename.Bc FMTSEQ -- an ARRAY of characters, each length 50,Dc describing how the sequence is to be readCc RECLIN -- a record of a file, length 80 charactersBc ** SEQ -- an ARRAY of characters each length 1 to-c store the sequence9c ** SEQID -- retrieved name of the sequenceCc SEQIDS -- an ARRAY of retrieved names of sequencesDc STYPE -- character string of length 8 defining the3c format type of the file.Ac LOGICALS:FOUND -- logical variable used in looping until.c something retrievedFc *** USED -- logical variable used in determining if the@c subroutine has been previously calledAc VALID -- logical variable used in looping until+c some input validcc4c if the subroutine has NOT been USED then must;c input the filename and do error checking on filenameBc else branch to listing the sequences available in this file if (.not.used) then10 found = .false. valid = .false. used = .false.:c initialize for a new file by setting variables back)c to zero and blanking out old names! if (nmax.eq.0) nmax = 9999 nseq = 0 stype = ' '/ seqid = ' 'C filnam= ' ' do 500 i = 1,100 sline(i) = 0 seqnum(i)= 04 seqids(i)=' 'F fmtseq(i)= ' '500 continue;111 write(6,102) 'Input sequence file name (/ to end) '102 format(1x,a38,$)) read(5,110,end=999,err=999) filnam' if (filnam(1:1).eq.'/') goto 999110 format(a50)Cc open the file only after a valid filename has been retrievedAc error in filename results in prompting for the input again/ open(66,file=filnam,status='OLD',err=10)Bc find sequence file format type and the sequence identifiers idcnt = 0 line = 1c DO WHILE (.NOT.FOUND)1600 read(66,120,end = 410,err = 991) reclin120 format(a80)=c STANFORD format, recognized by the ';' in the first columnc of the record& if (reclin(1:1).eq.';') then#c DO WHILE (.NOT.ENDFIL)610 line = line + 14 read(66,120,end = 410,err=991) reclin;c to find the next sequence identifer scroll through the:c file until the first character in the line is not ';'+ if (reclin(1:1).ne.';') then% found = .true.( stype ='STANFORD'( idcnt = idcnt + 1) sline(idcnt)= line/ seqids(idcnt) = reclin(1:30)" line = line + 18 read(66,120,end = 410,err=991) reclin;c DO WHILE ((INDEX(RECLIN,'1').EQ.0).AND.7c . (INDEX(RECLIN,'2').EQ.0))c ENDDO6615 if (index(reclin,'1').eq.0) then7 if (index(reclin,'2').eq.0) then' line = line + 1= read(66,120,end = 410,err=991) reclin! goto 615 endif endif=c assume at least one line not a sequence identifier occursAc after last sequence read in to get around the CTRL-L problem.=c therefore, after reading in the record containing the end2c of sequence identifier, read in another record" line = line + 18 read(66,120,end = 410,err=991) reclin endifc ENDDO& if (.not.endfil) goto 610@c GENBANK format, recognized by the word LOCUS starting in the c first position of the record. elseif (reclin(1:5).eq.'LOCUS') then found = .true.# stype = 'GENBANK ' idcnt = 1. seqids(idcnt) = reclin(13:27)'c DO WHILE (.NOT.ENDFIL)$620 line = line + 1: read(66,120,end = 410,err=991) reclin;c scrolling through to find the key phrase ORIGIN becauseCc the line after this key phrase occurrance is where the sequencec occurs in the file;@c read through the file obtaining other sequences by scrolling9c through to the '//' which signals the end of sequence7c Then start looking for another sequence identifier. 5 if (reclin(1:6).eq.'ORIGIN') thenV+ sline(idcnt) = lineG6c DO WHILE (RECLIN(1:2).NE.'//')5625 if (reclin(1:2).ne.'//') then0* line = line + 1@ read(66,120,end = 410,err=991) reclin# goto 625Oc ENDDO  endif 9 elseif (reclin(1:5).eq.'LOCUS') then , idcnt = idcnt + 18 seqids(idcnt) = reclin(13:27) endifc ENDDO, if (.not.endfil) goto 620?c PIR format, recognized by the '>' occurring in column 1 of atBc record. The sequence itself start 2 lines down from the recordc containing '>'.* elseif (reclin(1:1).eq.'>') then found = .true.*# stype = 'PIR '*'c DO WHILE (.NOT.ENDFIL) 0630 if (reclin(1:1).eq.'>') then) idcnt = idcnt + 1b/ sline(idcnt) = line + 1 4 seqids(idcnt) = reclin(5:25) endif # line = line + 1o9 read(66,120,end = 410,err=991) reclinhc ENDDO, if (.not.endfil) goto 630Ac EMBL (european) format, recognized by the key phrase ID in thepc first column of the record.. elseif (reclin(1:5).eq.'ID ') then found = .true.h# stype = 'EMBL '*Dc scrolling through to find the key phrase 'SQ Sequence' becauseCc the line after this key phrase occurrance is where the sequence c occurs in the file;u(c DO WHILE (.NOT.ENDFIL)5640 if (reclin(1:5).eq.'ID ') thenp, idcnt = idcnt + 1@ seqids(idcnt) = reclin(6:index(reclin,' '))B elseif (reclin(1:13).eq.'SQ Sequence') then. sline(idcnt) = line endif$ line = line + 1: read(66,120,end = 410,err=991) reclinc ENDDO, if (.not.endfil) goto 640Ac NRC format, recognized by '(' occurring in the first column of-Bc a record. The record line following this line holds the number@c of elements in the sequence and the name of the sequence. The8c following line signals the beginning of the sequence.:c The sequence itself is read in by using variable formatBc described by the '(' record line. This format statement on the1c record containing '(' ,must also be retrieved.t* elseif (reclin(1:1).eq.'(') then found = .true.$ stype = 'NRC '(c DO WHILE (.NOT.ENDFIL)1650 if (reclin(1:1).eq.'(') then ) idcnt = idcnt + 1nC fmtseq(idcnt) = reclin(1:index(reclin,')'))' line = line + 1o8 read(66,140,end = 410,err = 991)3 . seqnum(idcnt),seqids(idcnt)a+ sline(idcnt) = line  endif$ line = line + 1: read(66,120,end = 410,err=991) reclinc ENDDO"140 format(i4,5x,a30)* if (.not.endfil) goto 650 endif Dc keep scrolling through the file until a key phrase signalling>c a format type is recognized or the end of file is found line = line + 1 c ENDDO if (.not.found) goto 600 @c if a format type has not been found then this cannot be a(c sequence file and return to main.410 if (.not.found) thenRD write(6,105) ' No sequence identifiers found in this file '105 format(a50) return endif-c if this is a valid format type proceedG used = .true.9c if this is the first time used then return to main @c with RNUM, the number of identified sequences in the file rnum = idcnt endif>c IF USED this call before retreive a sequence using RNUM& seqid = ' ' pointr = rnum3 if ((pointr.lt.1).or.(pointr.gt.idcnt)) thenB stop ' ERROR IN MULTID, SEQUENCE REQUESTED NOT FOUND' else % seqid = seqids(pointr) endif<c having obtained a valid sequence choice or default of?c one available sequence, rewind the file and retrieve the c sequences rewind(66,err = 992)e>c having retrieved the line number in the file where this>c identifier occurs from SLINE(POINTR) scroll through the&c file until this line is reached& do 550 i = 1,sline(pointr)3 read(66,120,end = 410,err=991) reclin 550 continue>c if nrc type then read sequence according to format type$ if (stype.eq.'NRC ') then# nseq = seqnum(pointr))8c if the number in the NRC sequence is greater than3c the maximum number sent down from main, theni9c truncate to NMAX and output a message to the user.a$ if (nseq.gt.nmax) thenC write(6,160) ' Sequence truncated to ',nseq "160 format(1x,a30,i4) nseq = nmax endifl7 read(66,fmtseq(pointr),end = 420,err=991)=- . (seq(k),k=1,seqnum(pointr))n<c Else if not type NRC then find the sequence by taking<c each letter of the next records until end-of-sequence@c indicator found or number in the sequence NMAX is reached else n = 1 found = .false.c DO WHILE (.NOT.FOUND)1670 read(66,120,end = 420,err=991) reclin Ac there is a need for the two positions to start reading the Cc sequence; to accommodate the GENBANK format and the STANFORDuc end-of-sequence checks.) if (stype.eq.'GENBANK ') thent start = 10 else start = 1  endifd do 565 i = start,80 =c if the number in the sequence is less than the desired ?c number, NMAX sent down from main, then retrieve sequenced" if (n.le.nmax) then& if (.not.found) then& seq(n) = reclin(i:i))c check if an early end of sequenceC> if ((seq(n).eq.'1').or.(seq(n).eq.'2').or.A . (reclin(1:1).eq.'/').or.(seq(n).eq.'*')) thenf$ seq(n) = ' '$ nseq = n - 1& found = .true.<c if not an end-of-sequence character but have gone far$c enough, then truncate to NMAX+ elseif (n.eq.nmax) then# nseq = nmaxu& found = .true.C write(6,160) ' Sequence truncated to ',nseqL@c if not a end-of-sequence character, check to see if it is@c not a blank character. Blank characters will not be addedc to the sequence.i/ elseif (seq(n).ne.' ') thene" n = n + 1 endif endif0Ac if the number of sequence characters found is Greater than4c NMAX then all of the sequence has been found. else " found = .true. nseq = n write(6,160)9 . ' Sequence truncated to ',nseq  endif 565 continuec ENDDO# if (.not.found) goto 670a endif0420 return'991 stop ' ERROR IN READING FILE 'a'992 stop ' ERROR IN REWINDING FILE'i)999 stop ' END of SESSION...GOOD BYE'c end*[MFOLD]MULTID.OBJ;3+,. / 4 -*0123KPWO 56Tqi7i89GHJ1MULTID0123-Feb-1992 02:2423-Feb-1992 02:24VAX FORTRAN V5.7-133 MULTIDPInput sequence file name (/ to end) 12 ) No sequence identifiers found in this file ERROR IN MULTID, SEQUENCE REQUESTED NOT FOUND Sequence truncated to ERROR IN READING FILE ERROR IN REWINDING FILE END of SESSION...GOOD BYE&2P2 MULTIDP2P%B%') + ,-.YQPOl[}PQЫ VЫWkXм@}PQ(ޫ$PFOR$INI_DES1_R21XԼռ<'Լ } t((2-|dYZ,nS,nd[ZP(@c2ZP(2-@˚YZ FOR$WRITE_SFT FOR$IO_T_DS FOR$IO_END FOR$READ_SFD FOR$IO_T_DS FOR$IO_END|/1\FOR$OPENP1(VZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDꑫ;1ZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDÑ;1X}STANFORDtVZFSVP(@cZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDˀ LIB$INDEXP˔ LIB$INDEXPZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDW11)_1X}GENBANK tV, 4cZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END)dZFS)jZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END)_VVP, @cW1]1>X}PIR tZY>VYFSVP, @cYZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDW1)l1X}EMBL t)lV˨ LIB$INDEXPVY,P Ic) qZFSZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDW1(1X}NRC t(V˼ LIB$INDEX2VY,P 2I˚ZB~ FOR$READ_SFF`[y FOR$IO_L_RVP@c FOR$IO_T_DS FOR$IO_ENDZFSZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDW1YZX11FOR$STOP,~ мYѼVFOR$STOPP(@cB~ FOR$REWINDP1ISZRZB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_ENDX¹Bd +  FOR$WRITE_SF FOR$IO_T_DS FOR$IO_ENDV WXkV1AZR)t1I`[ Ѽ  FOR$WRITE_SF FOR$IO_T_DSݼ  FOR$IO_L_V FOR$IO_ENDм 2YP@˚B~ FOR$READ_SOP@4I`[ FOR$IO_X_NL FOR$IO_END1YXB~ FOR$READ_SFL FOR$IO_T_DS FOR$IO_END)t PPPPP1Y1XP4Z@IjIj*/Ij1Ij2 IjY XYм X FOR$WRITE_SF FOR$IO_T_DSݼ  FOR$IO_L_V FOR$IO_ENDIj YXY  FOR$WRITE_SF FOR$IO_T_DSݼ  FOR$IO_L_V FOR$IO_ENDP7X1V WXkFOR$STOPFOR$STOPP LOCUSQ6GENBANK QORIGIN//ID SQ SequenceQNRC Q  OMULTIDFOR$OPEN LIB$INDEX$CODE$PDATA$LOCALFOR$STOP FOR$REWIND FOR$IO_END FOR$IO_L_R FOR$IO_L_V FOR$IO_T_DS FOR$IO_X_NL FOR$READ_SF FOR$READ_SO FOR$WRITE_SFFOR$INI_DES1_R28PEPP,P(PPs"PxMP TP=XPBPPPP;P.PP(Pi,PnWPhPPP PIP1PPPP,P5PjQPqP uP%PXPP!PPPP/P;PUPosPwP#PPP P&P UPQePnjP(mP-P=P.PP0%Ph)PqfP'rPvP$PPPPP|PP PPPG P6>P EPIP4cW*[MFOLD]NEWTEMP.FOR;1+,./ 4G-*0123KPWO56n3h7Ti89GHJ* program newtempD* Create a new set of energy files for LRNA/CRNA at some temperature* other than 37C.7* -John Jaeger 10/89$ integer dgunit,dhunit,outunit real temperature,tratio character*80 fname character*3 extension*+ data dgunit/10/dhunit/12/outunit/14/* Introduction write (*,100)* Get temperature1 write (*,110) read (*,*) temperature; if (temperature.gt.100.0.or.temperature.lt.0.0) then? write (*,*) 'Temperature out of range. Keep between'( write (*,*) '0.0 and 100.0 C.' goto 1 endif$ if (temperature.eq.37.0) then write (*,120) stop endif0 tratio=(temperature+273.15)/(37.0+273.15)0 encode (3,130,extension) int(temperature)5 if (extension(1:1).eq.' ') extension(1:1)='0'5 if (extension(2:2).eq.' ') extension(2:2)='0'5 if (extension(3:3).eq.' ') extension(3:3)='0'* Stacks write (*,*) 'Stacks' fname=' ' fname(1:6)='STACK.' fname(7:9)=extension> open(unit=dgunit,name='STACK.DAT',status='OLD',err=200,# 1 carriagecontrol='LIST')= open(unit=dhunit,name='STACK.DH',status='OLD',err=200,# 1 carriagecontrol='LIST')1 open(unit=outunit,name=fname,status='NEW',# 1 carriagecontrol='LIST')0 call stacks(dgunit,dhunit,tratio,outunit)# close (dgunit,status='KEEP')# close (dhunit,status='KEEP')$ close (outunit,status='KEEP')* Terminal Stacks( write (*,*) 'Terminal mismatches' fname=' ' fname(1:7)='TSTACK.' fname(8:10)=extension? open(unit=dgunit,name='TSTACK.DAT',status='OLD',err=200,# 1 carriagecontrol='LIST')> open(unit=dhunit,name='TSTACK.DH',status='OLD',err=200,# 1 carriagecontrol='LIST')1 open(unit=outunit,name=fname,status='NEW',# 1 carriagecontrol='LIST')0 call stacks(dgunit,dhunit,tratio,outunit)# close (dgunit,status='KEEP')# close (dhunit,status='KEEP')$ close (outunit,status='KEEP') * Dangles write (*,*) 'Dangles' fname=' ' fname(1:7)='DANGLE.' fname(8:10)=extension? open(unit=dgunit,name='dangle.DAT',status='OLD',err=200,# 1 carriagecontrol='LIST')> open(unit=dhunit,name='dangle.DH',status='OLD',err=200,# 1 carriagecontrol='LIST')1 open(unit=outunit,name=fname,status='NEW',# 1 carriagecontrol='LIST')1 call dangles(dgunit,dhunit,tratio,outunit)# close (dgunit,status='KEEP')# close (dhunit,status='KEEP')$ close (outunit,status='KEEP')* Loops write (*,*) 'Loops' fname=' ' fname(1:5)='LOOP.' fname(6:8)=extension= open(unit=dgunit,name='loop.DAT',status='OLD',err=200,# 1 carriagecontrol='LIST')1 open(unit=outunit,name=fname,status='NEW',# 1 carriagecontrol='LIST')( call loops(dgunit,tratio,outunit)# close (dgunit,status='KEEP')$ close (outunit,status='KEEP') * Tetraloops fname=' ' fname(1:6)='TLOOP.' fname(7:9)=extension> open(unit=dgunit,name='Tloop.DAT',status='OLD',err=200,# 1 carriagecontrol='LIST')= open(unit=dhunit,name='Tloop.DH',status='OLD',err=200,# 1 carriagecontrol='LIST')1 open(unit=outunit,name=fname,status='NEW',# 1 carriagecontrol='LIST')0 call tloops(dgunit,dhunit,tratio,outunit)# close (dgunit,status='KEEP')# close (dhunit,status='KEEP')$ close (outunit,status='KEEP')* Other loop parameters fname=' ' fname(1:9)='MISCLOOP.' fname(10:12)=extensionA open(unit=dgunit,name='Miscloop.DAT',status='OLD',err=200,# 1 carriagecontrol='LIST')1 open(unit=outunit,name=fname,status='NEW',# 1 carriagecontrol='LIST')- call otherloops(dgunit,tratio,outunit)# close (dgunit,status='KEEP')$ close (outunit,status='KEEP') stop*?200 write (*,*) 'Trouble opening files. Make sure all .DAT'9 write (*,*) 'and .DH files are in this directory.' stop*D100 format (1x,'Create a new set of energy files for LRNA/CRNA.')6110 format (1x,'New temperature (in celcius) ? ',$)>120 format (1x,'Default files already calculated for 37C.')130 format (i3) end 1 subroutine dangles(indg,indh,tratio,outdg)*-* Dangle calculations - similar to Stack code* real tratio,dg,dh,dgnew# integer indg,indh,outdg,sets& character*80 dgbuf,dhbuf,outbuf logical myfind*3* Dangle data is in the form of 8 "sets", each with'* 1 line of data - hense the loop name.* do sets=1,84* Since the header info is needed, copy header stuff1* until (inclusive) a line with a '<--' is found.*) call misclines(indg,outdg,'<--')"* get the enthalpy file up to date) if (myfind(indh,'<--')) goto 200*& read (indg,100,err=200) dgbuf& read (indh,100,err=200) dhbuf. call getdg(dgbuf,dhbuf,tratio,outbuf)! write (outdg,100) outbuf enddo return%* Error reading one of the data linesB200 write (*,*) 'OOPS! Can''t read one of the lines of data in'- write (*,*) 'one of the dangle files.' stop*100 format (a80)* end 0 subroutine stacks(indg,indh,tratio,outdg)** Stack/TStack calculations* real tratio,dg,dh,dgnew) integer indg,indh,outdg,sets,lines& character*80 dgbuf,dhbuf,outbuf logical myfind*=* Stack und TStack data is in the form of 4 "sets", each with+* 4 "lines" of data - hense the loop names.* do sets=1,44* Since the header info is needed, copy header stuff1* until (inclusive) a line with a '<--' is found.*) call misclines(indg,outdg,'<--')"* get the enthalpy file up to date) if (myfind(indh,'<--')) goto 200* do lines=1,4( read (indg,100,err=200) dgbuf( read (indh,100,err=200) dhbuf0 call getdg(dgbuf,dhbuf,tratio,outbuf)# write (outdg,100) outbuf enddo enddo return%* Error reading one of the data linesA200 write (*,*) 'OOPS! Can''t read one of the lines of data in'0 write (*,*) 'one of the (t)stack files.' stop*100 format (a80)* end / subroutine loops (loopdg,tratio,newloop)** Loop calcuations$ integer loopdg,newloop,j,size0 real tratio,internal,bulge,hairpin,round1 character*80 inbuf* Copy header info+ call misclines(loopdg,newloop,'---')* First line only has bulges( read (loopdg,110,end=200) j,bulge1 write (newloop,111) j,round1(bulge*tratio)0* Second line only has bulges and internal loops1 read (loopdg,120,end=200) j,internal,bulge5 write (newloop,121) j,round1(internal*tratio),0 1 round1(bulge*tratio)* Ok after that do size=3,30: read(loopdg,100,end=200) j,internal,bulge,hairpin) internal=round1(internal*tratio)# bulge=round1(bulge*tratio)' hairpin=round1(hairpin*tratio)4 write(newloop,100) j,internal,bulge,hairpin enddo return* Errors>200 write (*,*) 'Error in reading loop file. End of file?' stop*-100 format (i2,11x,f5.1,13x,f5.1,12x,f5.1)110 format (i2,29x,f5.1)+111 format (i2,14x,'.',14x,f5.1,15x,'.')$120 format (i2,11x,f5.1,13x,f5.1),121 format (i2,11x,f5.1,13x,f5.1,15x,'.')* end 3 subroutine otherloops(infile,tratio,outfile)6* This file is in a weird format. Numbers are written integer infile,outfile! real tratio,a,b,c,d,round1* Loop > 30 parameter+ call misclines(infile,outfile,' > ') read (infile,*) a# write (outfile,100) a*tratio)* Max asymmetric internal loop correction+ call misclines(infile,outfile,' > ')R read (infile,*) a% write (outfile,110) (a*tratio) * Ninio's f(m) array+ call misclines(infile,outfile,' > ')t read (infile,*) a,b,c,d= write (outfile,120) round1(a*tratio),round1(b*tratio),; 1 round1(c*tratio),round1(d*tratio)i+ call misclines(infile,outfile,' > ')&* and the linear bifurcation function. read (infile,*) a,b,c= write (outfile,130) round1(a*tratio),round1(b*tratio),** 1 round1(c*tratio)* return 100 format (f5.3)110 format (f5.1)120 format (4(3x,f5.1))130 format (3(3x,f5.1)) end 24 subroutine tloops (indg,indh,tratio,tloopout)*u* Tetraloop conversion* ! integer indg,indh,tloopoute real tratio,dh,dg,round11 character*4 seq logical myfindt*i* call misclines(indg,tloopout,'---')' if (myfind(indh,'---')) goto 2003*0B* while (not eof(indg)) - sorry, my pascal is showing through...*a,10 read (indg,100,end=50,err=200) seq,dg read (indh,100) seq,dh'9 write (tloopout,100) seq,round1(dh-(dh-dg)*tratio)o goto 10*o50 continuea returnt100 format (1x,a4,2x,f4.1) *a:200 write (*,*) 'Error reading one of the tloop files.' stop end a1 subroutine misclines(inunit,outunit,token)hE* Copy misc. lines from InUnit to OutUnit, until (inclusive, that is)e* a line with Token is found. *o integer inunit,outunitm character*3 token character*80 copybuf *f copybuf=' '- do while (index(copybuf,token).eq.0), read (inunit,100,err=200) copybuf& write (outunit,100) copybuf enddo returnn9200 write (*,*) 'Error in reading text info in files.' stopt100 format (a80)o end t3 subroutine getdg (dgbuf,dhbuf,tratio,outbuf)o?* Convert the data in dGBuf and dHBuf to a free energy at a new @* temperature, as governed by TRatio. Put the result in OutBuf.*0 integer dgstart,dgend,dhstart,dhend,convt& character*80 dgbuf,dhbuf,outbuf" character*5 dgtoken,dhtoken% real tratio,dg,dh,dgnew,round1 *e outbuf=' '' dgstart=1 dgend=80 dhstart=1 dhend=80" do while (dgend.gt.dgstart)1 call parse (dgstart,dgend,dgbuf,dgtoken)o1 call parse (dhstart,dhend,dhbuf,dhtoken;q~ MFOLD.BCK*[MFOLD]NEWTEMP.FOR;1G# ),& if (dgtoken(1:1).ne.' ') then& if (dgtoken(1:1).ne.'.') then$ dg = convt(dgtoken)/10.0$ dh = convt(dhtoken)/10.01 dgnew = round1(dh - (dh - dg)*tratio)t)* convert to token, put in output buffer.o,* The lazy way is VAX specific, using ENCODE( encode (5,120,dgtoken) dgnew- outbuf(dgstart-5:dgstart)=dgtokene else1+ outbuf(dgstart-1:dgstart-1)='.'n endif endif enddo returnt120 format (f5.1) end t* logical function myfind (unit,token)*K8* Returns .TRUE. if there is some error in reading Unit.*  integer unit character*3 token  character*80 inbuf*  inbuf=' 'u( do while (index(inbuf,token).eq.0)- read (unit,100,err=200,end=200) inbufo enddoi myfind=.false. return*200 myfind=.true.e return100 format (a80) endm n# real function round1 (numba)a3* Round "Numba" to 1 place after the decimal point.t*i real numba,temp integer sign'* if (numba.lt.0) thenK sign=-1e temp=abs(numba) elser sign=1 temp=numba endif# round1 = int(temp*10.0)/10.02 if (temp-round1.ge. 0.05) round1=round1+0.1 round1=round1*sign return= end - subroutine parse(start,fin,inbuf,token) :* Stolen from BATGEN, but now with active ingredient Z7!!!3* (actually, just increased InBuf to Character*80).K- integer start,fin,i,tokenstart,tokenfin  character*80 inbuf character*5 token *e i=startl token=' 'w/ do while (i.le.fin.and.inbuf(i:i).eq.' ') i=i+1 enddor if (i.lt.fin) then tokenstart=i1 do while (i.le.fin.and.inbuf(i:i).ne.' ')c i=i+12 enddo, tokenfin=i-1, if (tokenfin-tokenstart+1.gt.5) then0 write (*,1) inbuf(tokenstart:tokenfin) stop elseC token(1:tokenfin-tokenstart+1)=inbuf(tokenstart:tokenfin)n endifg7 else if ((i.eq.fin).and.(inbuf(i:i).ne.' ')) then, token(1:1)=inbuf(i:i) endift start=im! if (start.gt.fin) start=fino return?1 format (1x,'Number too big to convert in line:',/,1x,a80) endc  d! integer function convt(str)e*t7** Convert a buffer STR to an integer. Stolen from RNAt*' integer i,placel character*5 str  logical negh - neg = .false.  place = 0, convt = 0f  do 10 i = 5,1,-1! if (str(i:i).eq.'-') theng neg = .true. else7 if (str(i:i).ge.'0'.and.str(i:i).le.'9') thenrG convt = convt + 10**place * (ichar(str(i:i)) - ichar('0'))  place = place+1 endif) endifn 10 continue! if (neg) convt = convt * -1 return end *[MFOLD]PLOT.DAT;1+,./ 4-*0123KPWO56Rh7:i89GHJ 7 @ 7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @7 @8 6k @k=L `L6k @@u@7`@16k"UuU7`N276k%IuI7`B536k(AuA7`'Z806k*VuV7`O1066k-JuJ7`C1326k0BuB7`/[1596k2VuV7`O1856k5KuK7`D2116k8CuC7`7\2386k:WuW7`P2646k=LV`>D14z=LVo>D213f=LV2{>D421r=LVg>D630`=LV/u>D83.l=LVa>D104,x=LVm>D125*[MFOLD]READ_ME.FIRST;1+,. / 4I ^-*0123KPWO 5634h74ۙi89GHJD MFOLD - Prediction of RNA secondary structure by free energy  minimization. - Version 2.0 - - Michael Zuker and John Jaeger 0 - LRNA : folds linear RNA sequences2 - CRNA : folds circular RNA sequences <The original version (1.0) was designed by Michael Zuker andBprogrammed by Eric Nelson in the summer of 1987 in the Division ofDBiological Sciences at the National Research Council of Canada. John?Jaeger added the tetraloop bonus energy feature and created the*BATGEN program for batch file generation.  =Version 2.0 corrects a number of small bugs from the original:program. These were added to version 1 and itemized in theEERRATA.LIST file that was distributed along with version 1. The major improvements of version 2 are : B1. During the generation of suboptimal foldings, the number of newDbase pairs that are sufficiently different from base pairs that haveBalready been found must be greater than the WINDOW parameter. ThisAfeature was added during the summer of 1989, and was made part of@version 1 (item 11 in the ERRATA.LIST file distributed with thisCversion). The effect is to eliminate structures that contain just afew new base pairs. D2. Temperature dependent folding. This was added in the fall of 1989&and was never a feature of version 1. E3. The multiple sequence option will now generate suboptimal foldings=of all the sequences in an input file. This can be used (for Cexample), to compute all foldings within 10% of the minimum energy .for all the 5S RNAs conained in a single file. DMETHOD : A dynamic programming algorithm is used to find optimal andDsuboptimal foldings of an RNA molecule starting from linear sequenceBdata. Auxiliary information can be used to constrain the folding.  Energy data from : ES.M. Freier et al., Proc. Natl. Acad. Sci. USA, 83, 9373-9377, 1986. ID.H. Turner et al., Cold Spring Harbor Symposia on Quantitative Biology, 52, 123-133, 1987.ID.H. Turner et al., Annu. Rev. Biophys. Biophys. Chem 17, 167-192 (1988).HThis last reference has all the dangling end and terminal mismatch data. References : M. Zuker 6On Finding All Suboptimal Foldings of an RNA Molecule.Science, 244, 48-52, (1989)(J. A. Jaeger, D. H. Turner and M. Zuker 5Improved Predictions of Secondary Structures for RNA.?Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989) (J. A. Jaeger, D. H. Turner and M. Zuker >Predicting Optimal and Suboptimal Secondary Structure for RNA.9in "Molecular Evolution: Computer Analysis of Protein and,Nucleic Acid Sequences", R. F. Doolittle ed.*Methods in Enzymology, 183, 281-306 (1989) see also: M. Zuker %Computer Prediction of RNA Structure.:in "RNA Processing", J. E. Dahlberg and J. N. Abelson eds.+Methods in Enzymology, 180, 262-288, (1989) M. Zuker :The Use of Dynamic Programming Algorithms in RNA SecondaryStructure Prediction.?in "Mathematical Methods for DNA Sequences", M. S. Waterman ed.!CRC Press, Inc., 159-184, (1989))A.B. Jacobson, M. Zuker and A. Hirashima =Comparitive Studies on the Secondary Structure of the RNAs ofRelated RNA Coliphages.>in "Molecular Biology of RNA: New Perspectives", M. Inouye andB. S. Dudock eds.%Academic Press, Inc., 331-354, (1987)Use :?LRNA and CRNA are ready to use. They can be run by issuing the commands : $ Run LRNA or $ Run CRNAEYou must execute the command file INIT.COM before attempting any run with energy dot plots.AThe files LIN.COM and CIRC.COM are command files that compile andBlink LRNA and CRNA respectively. These files should be copied intoBthe temporary file TEMP.COM. TEMP.COM can then be edited to removeAredundant compilations. The dimensions can be altered by changingCLIN.INC (linear RNA folding) or CIRC.INC (circular RNA folding). IfDLIN.INC or CIRC.INC is changed, then ALL subroutines used by LRNA orACRNA must be recompiled with the exception of FORMID and MULTID. AFILES.LIST contains a list and description of all files used for Ffolding. Note the sample runs of the ALU sequence and the batch files +(BAT1.COM and BAT2.COM that produced them).MFOLD.USER is a user's manual.@MFOLD.DOC is a glossary of functions, subroutines and variables.>MFOLD.FLOW is a crude flow chart of the MAIN program of MFOLD.*[MFOLD]RFD.INC;7+,J./ 4MV-*0123KPWO564vi7T|i89GHJ implicit integer (a-z) ( parameter (maxn=625,fldmax=2*maxn). parameter (infinity=16000,sortmax=30000). parameter (mxbits=(maxn*(maxn+1)+31)/32) parameter (maxtloops=40) parameter (maxsiz=10000) > integer*2 vst(maxn*maxn),wst1(maxn*maxn),wst2(maxn*maxn) integer poppen(4),maxpen real prelogK dimension newnum(maxsiz),hstnum(maxn*2),force(maxn*2),numseq(maxn*2),' . work1(maxn*2,0:2),work2(maxn*2),J . stack(5,5,5,5),tstk(5,5,5,5),dangle(5,5,5,2),hairpin(30),bulge(30),. . inter(30),eparam(10),cntrl(10),nsave(2), data eparam/0,0,0,0,46,4,30,30,-500,1/B common /main/ vst,wst1,wst2,newnum,hstnum,force,work1,work2,I . stack,tstk,dangle,hairpin,bulge,inter,eparam,cntrl,nsave,n,numseq, . poppen,prelog,maxpen  character*1 seq(maxsiz) character*5 inbuf character*30 seqlab common /seq/ seq,seqlab  dimension list(100,4) common /list/ list,listsz common /nm/ vmin  dimension basepr(maxn) common /trace/ basepr 6 integer*2 two(0:15),marks(mxbits),force2(mxbits) common/bits/marks,force2 . integer*2 tloop(maxtloops,2),numoftloops% common/tloops/tloop,numoftloops M data two/1,2,4,8,16,32,64,128,256,512,1024,2048,4096,8192,16384,-32768/*[MFOLD]RNA.FOR;3+,./ 4Pb-*0123KPWO564 i7ti89GHJ0Cc MFOLD - Prediction of RNA secondary structure by free energyc minimization.c - Version 2.0,c - Michael Zuker and John Jaeger0c - LRNA : folds linear RNA sequences2c - CRNA : folds circular RNA sequencescCc The original version (1.0) was designed by Michael Zuker andIc programmed by Eric Nelson in the summer of 1987 in the Division ofKc Biological Sciences at the National Research Council of Canada. JohnFc Jaeger added the tetraloop bonus energy feature and created the0c BATGEN program for batch file generation.cDc Version 2.0 corrects a number of small bugs from the originalAc program. These were added to version 1 and itemized in theLc ERRATA.LIST file that was distributed along with version 1. The majorBc improvements of version 2 are : 1. During the generation ofAc suboptimal foldings, the number of new base pairs that areJc sufficiently different from base pairs that have already been foundHc must be greater than the WINDOW parameter. This feature was addedLc during the summer of 1989, and was made part of version 1 (item 11 inLc the ERRATA.LIST file distributed with this version). The effect is toFc eliminate structures that contain just a few new base pairs. 2.Lc Temperature dependent folding. This was added in the fall of 1989 and(c was never a feature of version 1.cKc METHOD : A dynamic programming algorithm is used to find optimal andKc suboptimal foldings of an RNA molecule starting from linear sequenceHc data. Auxiliary information can be used to constrain the folding.cJc NB : Base pairs are forced by giving them a bonus energy (EPARAM(9)Ec in the program code). These energies are subtracted during theKc traceback algorithm so that the computed sturctures have the correctEc energies. Unfortunately, there is no way to subtract the bonusJc energies from the energy dot plots. Moreover, each forced base pairIc contain two bonus energies because of the nature of the algorithm.Hc For example, suppose that an optimal folding of an RNA contains 3Lc forced base pairs ( default bonus energy is 50.0 kcal per forced baseFc pair ) and that the correct folding energy is -180.0 kcal/mole.Dc Internally, the energy will be -180.0 - (3+1) x 50.0 = -380.0Hc kcal/mole. To find foldings within 10% of the correct energy, oneKc needs to compute foldings to within 18.0 kcal of -180.0 - 3 x 50.0 =Ic -330.0 kcal/mole. This comes out to -312.0 kcal/mole. The ratio ofJc -312.0 to -380.0 is 82%, so that one would request the 18% level ofEc suboptimality! This confustion only exists when base pairs areCc forced. Each closed excision counts as one forced base pair.cc Energy data from :Kc S.M. Freier et al., Proc. Natl. Acad. Sci. USA, 83, 9373-9377, 1986.Oc D.H. Turner et al., Cold Spring Harbor Symposia on Quantitative Biology,c 52, 123-133, 1987.Pc D.H. Turner et al., Annu. Rev. Biophys. Biophys. Chem 17, 167-192 (1988).Oc This last reference has all the dangling end and terminal mismatch data.cc References :c M. Zuker=c On Finding All Suboptimal Foldings of an RNA Molecule."c Science, 244, 48-52, (1989)c.c J. A. Jaeger, D. H. Turner and M. Zuker<c Improved Predictions of Secondary Structures for RNA.Fc Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989)c.c J. A. Jaeger, D. H. Turner and M. ZukerEc Predicting Optimal and Suboptimal Secondary Structure for RNA.@c in "Molecular Evolution: Computer Analysis of Protein and3c Nucleic Acid Sequences", R. F. Doolittle ed.1c Methods in Enzymology, 183, 281-306 (1989)c include 'rfd.inc' real energy logical flag1c Fill screen with author and reference data. call beginc Initial setup for run.5 call device if (cntrl(1).ne.2) thenCc Read energy information if this is not a continuation run. call enefiles call erg(1,0,0,0,0) else<c dump out information read in from continuation file call cdump endif@c Determine output specifications if this is not a save run.% if (cntrl(1).ne.1) call outputs6c Call the menu if this is not a continuation run." if (cntrl(1).ne.2) call menu mrep = 1*c CNTRL(7) = 0 - suboptimal dot plot.c 1 - N best sorted by energy?c 2 - best folding for all sequences in a file(10 if (cntrl(7).eq.2) call mseq(mrep)&c Process sequence before folding. do i = 1,mxbits marks(i) = 0 force2(i) = 0 enddo call process if (n*2.gt.fldmax) then tt = fldmax/2)c Fragment is too long. Try again.. write (6,*) 'Segment larger than ',tt stop endif if (cntrl(1).ne.2) thenEc Fill the optimal energy arrays except in a continuation run. call fill endif  if (cntrl(1).eq.1) then@c Save the results from FILL in a SAVE run and then stop. call putcont stop endif  rep = 1 jump = 1 flag = .true. err = 0  do while (flag) if (cntrl(7).eq.0) thenDc Interactive dot plot returns IRET, JRET (new numbering).' call dotplt(iret,jret,jump) jump = 2 else=c Automatic sort returns IRET,JRET (new numbering).+ call sortout(iret,jret,rep,err) if (err.eq.30) then flag = .false.( call errmsg(err,rep-1,0) err = 0 endif rep = rep + 1 endifKc First traceback yields the best structure on the included fragmentc from IRET to JRET.3 if (flag) call trace(iret,jret,nforc1,err)1 if (err.ne.0) call errmsg(err,iret,jret) if (flag) then it = iret+nLc Second traceback yields the best structure on the excluded fragmentc from IRET to JRET.) call trace(jret,it,nforc2,err) if (err.ne.0) then% call errmsg(err,jret,it) elseLc The energy of the best structure containing the base-pair IRET,Gc JRET is the sum of the energies of the optimal foldings onJc the included and excluded fragments. A correction is made forc forced base-pairs.c* CALL EFN(ENE,1,N)*c* WRITE (6,*) 'NEW ENERGY ',ENEN ene = v(iret,jret) + v(jret,iret+n) - eparam(9) * (nforc1+nforc2)' energy = float(ene) / 10.0Ac Count the number of new base pairs not within WINDOW$c of existing base pairs. numbp = 0 do k = 1,n& if(k.lt.basepr(k)) then> if(.not.mark(k,basepr(k))) numbp = numbp + 1 endif enddo do k = 1,n& if(k.lt.basepr(k)) thenCc Mark "traced-back" base pairs and also base-pairs>c which are close (within WINDOW = CNTRL(9) ).) call smark(k,basepr(k))( if(cntrl(9).gt.0) then/ do k1 = -cntrl(9),cntrl(9)2 do k2 = -cntrl(9),cntrl(9)D if(k+k1.gt.0.and.k+k1.lt.basepr(k)+k2.and.L 1 basepr(k)+k2.le.n) call smark(k+k1,basepr(k)+k2) enddo enddo endif endif enddo' if(numbp.le.cntrl(9)) then rep = rep - 1 go to 900 endif# write (6,1010) rep - 11010 format('+',i5$)H if (cntrl(2).ne.2.and.cntrl(2).ne.3.and.cntrl(2).ne.6) then$c Line printer output.5 call linout(1,n,energy,iret,jret,err)o endif if (err.ne.0) thenl* call errmsg(err,iret,jret) elses9 if (cntrl(2).ge.3.and.cntrl(2).ne.4) thens'c Region table output.a call regtab endifE? if (mod(cntrl(2),2).eq.0.or.cntrl(2).eq.7) theno"c CT file output." call ct(energy) endifl endif endif endif> if (cntrl(7).eq.1.and.rep.gt.cntrl(6)) flag = .false.900 continuem enddo c -c Multiple sequence option (CNTRL(7) = 2)e>c If sequence number (MREP) is < total number of sequences*c (CNTRL(5)), go get another sequence.c 2 if (cntrl(7).eq.2.and.mrep.lt.cntrl(5)) then mrep = mrep + 1 goto 10 endif stop end   f ic Marks a base-pair I,J.$c Assumes that 1 <= I <= J <= N.<c The information is stored in a single bit in the MARKS c array.Cc The conversion from double dimension to single is through the/c transformation I,J ==> (J-1)*J/2 + I .  subroutine smark(i,j)  include 'rfd.inc'  t posn = (((j-1)*j)/2) + i word = (posn+15) / 16p bit = mod(posn,16)+ marks(word) = marks(word).or.two(bit)r return end #c Marks a forced base-pair I,J. 9c The incoming base-pair II,JI is processed to an I,Jo,c base-pair satisfying 1 <= I <= J <= N.=c The information is stored in a single bit in the FORCE2o c array.Cc The conversion from double dimension to single is through thee/c transformation I,J ==> (J-1)*J/2 + I .e subroutine sfce(ii,ji) include 'rfd.inc'k g if (ii.gt.n) thene i = ii - n j = ji - n elseif (ji.gt.n) then  i = ji-n j = ii else i = ii j = ji endif  c b posn = (((j-1)*j)/2) + i word = (posn+15) / 16t bit = mod(posn,16) - force2(word) = force2(word).or.two(bit)f return end  r?c Retrieves information on whether or not the base-pair I,Je@c has been marked by a traceback passing through or close toc this pair. function mark(i,j) include 'rfd.inc'  logical mark e posn = (((j-1)*j)/2) + i word = (posn+15) / 16  bit = mod(posn,16) t$ set = marks(word).and.two(bit) mark = .false.! if (set.ne.0) mark = .true.c return end   1?c Retrieves information on whether or not the base-pair I,Jc has been forced. function fce(ii,ji)h include 'rfd.inc'  logical fced c if (ii.gt.n) thend i = ii - n j = ji - n elseif (ji.gt.n) thenl i = ji-n j = ii else i = ii j = ji endifg r posn = (((j-1)*j)/2) + i word = (posn+15) / 16, bit = mod(posn,16) % set = force2(word).and.two(bit)1 fce = .false. if (set.ne.0) fce = .true. return endn m8c fills screen with author and reference information subroutine begin character*1 ansa character*80 recordi: open(3,file='begin.dat',status='old',readonly,err=5) write(6,1010) 27,27,27)1010 format(' ',a1,'[H',a1,'[J'a1,'[1m') 1 read(3,1020,end=2) recordi1020 format(a80), write(6,1030) record1030 format(' ',a80) go to 1.2 write(6,1040) 27,27pF1040 format(' ',a1,'[0m',a1,'[24;20HPress to continue ...'$) read(5,1050) ans1050 format(a1) return5 write(6,1060) =1060 format(//' Author and reference file not available.'//)6 return endd'rfd.inc' real energy logical flag1c Fill screen with author and reference data. call beginc Initial setup for run.5 *[MFOLD]SETUP1.COM;2+,./ 47-*0123KPWO564tZi74Ei89GHJ$ set term/nowrap$ assign tt plot$ gcg$ !$ ! Tek for the Mac$ tek versa tt$ !"$ ! Tek for MS-Kermit on an IBM-PC$ ! tek tek4014 tt$ !2$ rnabatgen :== $disk$public3:[applic.zuker]batgen+$ lrna :== $disk$public3:[applic.zuker]lrna+$ crna :== $disk$public3:[applic.zuker]crna7$ rnadist*ance :== $disk$public3:[applic.zuker]distance/$ figdot :== $disk$public3:[applic.zuker]figdot-$ cvtct :== $disk$public3:[applic.zuker]cvtct2$ notek :== type disk$public3:[applic.zuker]ctrl.x$ exit*[MFOLD]SETUP2.COM;2+,./ 43-*0123KPWO56Zi7Ti89GHJ$ set term/nowrap$ assign tt plot$ gcg$ !$ ! Tek for the Mac$ ! tek versa tt$ !"$ ! Tek for MS-Kermit on an IBM-PC$ tek tek4014 tt$ ! $ ! Symbols$ !2$ rnabatgen :== $disk$public3:[applic.zuker]batgen+$ lrna :== $disk$public3:[applic.zuker]lrna+$ crna :== $disk$public3:[applic.zuker]crna3$ distance :== $disk$public3:[applic.zuker]distance/$ figdot :== $disk$public3:[applic.zuker]figdot-$ cvtct :== $disk$public3:[applic.zuker]cvtct2$ notek :== type disk$public3:[applic.zuker]ctrl.x$ exit*[MFOLD]SETUP_ZUKER.COM;3+,./ 47-*0123KPWO56TZi7i89GHJ$ set term/nowrap$ assign tt plot$ gcg$ !$ ! Tek for the Mac$ ! tek versa tt$ !"$ ! Tek for MS-Kermit on an IBM-PC$ tek tek4014 tt$ !2$ rnabatgen :== $disk$public3:[applic.zuker]batgen+$ lrna :== $disk$public3:[applic.zuker]lrna+$ crna :== $disk$public3:[applic.zuker]crna7$ rnadist*ance :== $disk$public3:[applic.zuker]distance/$ figdot :== $disk$public3:[applic.zuker]figdot-$ cvtct :== $disk$public3:[applic.zuker]cvtct2$ notek :== type disk$public3:[applic.zuker]ctrl.x$ exit*[MFOLD]SORT.FOR;1+,. / 4V -*0123KPWO56nr.h7(i89GHJ % subroutine sortout(i,j,rep,err) include 'rfd.inc'1 dimension heapi(sortmax+1),heapj(sortmax+1)# common /heap/ heapi,heapj,num;c The first time in (REP = 1), valid I,J base-pairs arec sorted by energy. err = 0) if (rep.eq.1.or.cntrl(7).eq.2) then call build_heap call heap_sort cntr = num endif.c Select the next valid unmarked base-pair. do while (mark(heapi(cntr),heapj(cntr))) if (cntr.eq.1) then err = 30 return endif cntr = cntr - 1 enddo9c The base-pair I,J will be used to create a folding. i = heapi(cntr) j = heapj(cntr) return end  Kc Add I,J to HEAPI and HEAPJ if the best energy of a folding containingHc I,J is no greater than a given percent ( CNTRL(8) ) of the minimumc folding energy. subroutine build_heap include 'rfd.inc'# common /heap/ heapi,heapj,num1 dimension heapi(sortmax+1),heapj(sortmax+1) * crit = vmin + abs(vmin)*cntrl(8)/100 num = 0 i = 1 j = 2 do while (i.lt.n)# if (ene(i,j).le.crit) then$ if (num.eq.sortmax) then err = 313 call errmsg(err,hstnum(i),hstnum(j)) goto 10 endif num = num + 1 heapi(num) = i heapj(num) = j j = j + cntrl(9) + 1 if (j.gt.n) then i = i + 1 j = i + 1 endif else j = j +1 if (j.gt.n) then i = i + 1 j = i + 1 endif endif enddo  do i = num+1,sortmax+1 heapi(i) = 0 heapj(i) = 0 enddo 10 do q = 2,num cur = q up = cur/2V do while (ene(heapi(cur),heapj(cur)).lt.ene(heapi(up),heapj(up)).and.up.ge.1)- call swap(heapi(cur),heapi(up))- call swap(heapj(cur),heapj(up)) cur = cur/2 up = cur/2 enddo enddo return end  c Efficient sort of heap. subroutine heap_sort include 'rfd.inc'# common /heap/ heapi,heapj,num1 dimension heapi(sortmax+1),heapj(sortmax+1)  do ir = num-1,2,-1( call swap(heapi(ir+1),heapi(1))( call swap(heapj(ir+1),heapj(1))  <!x]~ MFOLD.BCK*[MFOLD]SORT.FOR;1V =b up = 1 c = 2 do while (c.le.ir) if (c.ne.ir) thenK if (ene(heapi(c+1),heapj(c+1)).lt.ene(heapi(c),heapj(c))) then c = c + 1 endif endifG if (ene(heapi(c),heapj(c)).lt.ene(heapi(up),heapj(up))) then+ call swap(heapi(c),heapi(up))+ call swap(heapj(c),heapj(up)) up = c c = 2 * c else c = ir+1 endif enddo enddo return end Hc ENE(k) is the minimum energy of a folding containing the base-pairc I,J at heap(k). function ene(i,j) include 'rfd.inc'# common /heap/ heapi,heapj,num1 dimension heapi(sortmax+1),heapj(sortmax+1)  ene = v(i,j)+ v(j,i+n) return end    subroutine swap(i,j) k = i i = j j = k return end*[MFOLD]STACK.DAT;1+,. / 4P -*0123KPWO 56fh7Ci89GHJData Arangement: Y  ------------------  (X) A C G U  ------------------  5' ==> 3'  AX  AY 3' <== 5'  (A) . . . .  (C) . . . .  (G) . . . .  (U) -0.7 -0.1 -0.7 -0.1 --------------------------------STACKING ENERGIES :E Y Y Y YP------------------ ------------------ ------------------ ------------------ N A C G U A C G U A C G U A C G U P------------------ ------------------ ------------------ ------------------ M 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' E AX AX AX AXE AY CY GY UYK 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' O . . . . . . . . . . . . . . . -0.9O . . . . . . . . . . . . . . -2.1 . O . . . . . . . . . . . . . -1.7 . -0.5O . . . . . . . . . . . . -0.9 . -0.7 . E Y Y Y YP------------------ ------------------ ------------------ ------------------ N A C G U A C G U A C G U A C G U P------------------ ------------------ ------------------ ------------------ M 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' E CX CX CX CXE AY CY GY UYK 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' O . . . . . . . . . . . -1.8 . . . . P . . . . . . . . . . -2.9 . . . . . P . . . . . . . . . -2.0 . -1.5 . . . . P . . . . . . . . -1.7 . -1.5 . . . . . E Y Y Y YP------------------ ------------------ ------------------ ------------------ N A C G U A C G U A C G U A C G U P------------------ ------------------ ------------------ ------------------ M 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' E GX GX GX GXE AY CY GY UYK 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' O . . . . . . . -2.3 . . . . . . . -0.5P . . . . . . -3.4 . . . . . . . -1.9 . P . . . . . -2.9 . -1.3 . . . . . -1.5 . -0.5 P . . . . -2.1 . -1.9 . . . . . -0.7 . -0.5 . E Y Y Y YP------------------ ------------------ ------------------ ------------------ N A C G U A C G U A C G U A C G U P------------------ ------------------ ------------------ ------------------ M 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' E UX UX UX UXE AY CY GY UYK 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' P . . . -1.1 . . . . . . . -0.7 . . . . P . . -2.3 . . . . . . . -1.3 . . . . . P . -1.8 . -0.7 . . . . . -1.5 . -0.6 . . . . P-0.9 . -0.5 . . . . . -0.5 . -0.5 . . . . . *[MFOLD]STACK.DH;1+,. / 4O -*0123KPWO 56ih74i89GHJData Arangement: Y ------------------ (X) A C G U ------------------ 5' ==> 3' AX AY 3' <== 5' (A) . . . . (C) . . . . (G) . . . . (U) -0.7 -0.1 -0.7 -0.1 --------------------------------STACKING ENTHALPIES :E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E AX AX AX AXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . . . . . . . . . . . . -6.6M . . . . . . . . . . . . . . -10.2 .O . . . . . . . . . . . . . -7.6 . -3.6M . . . . . . . . . . . . -5.7 . -4.0 .E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E CX CX CX CXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M . . . . . . . . . . . -10.5 . . . .M . . . . . . . . . . -12.2 . . . . .M . . . . . . . . . -8.0 . -1.8 . . . .M . . . . . . . . -7.6 . -12.7 . . . . .E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E GX GX GX GXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . . . . . -13.3 . . . . . . . -3.6M . . . . . . -14.2 . . . . . . . -9.7 .O . . . . . -12.2 . -5.3 . . . . . -12.7 . -3.6M . . . . -10.2 . -9.7 . . . . . -4.0 . -2.7 .E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E UX UX UX UXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'M . . . -8.1 . . . . . . . -4.0 . . . .M . . -13.3 . . . . . . . -5.3 . . . . .M . -10.5 . -4.0 . . . . . -1.8 . -5.3 . . . .M-6.6 . -3.6 . . . . . -3.6 . -3.6 . . . . .*[MFOLD]TLOOP.DAT;1+,./ 4 -*0123KPWO56h7Ti89GHJ Seq Energy ----------- GAAA -2.0 GCAA -2.0 GAGA -2.0 GUGA -2.0 GGAA -2.0 UUCG -2.0 UACG -2.0 GCGA -2.0*[MFOLD]TLOOP.DH;1+,./ 4"-*0123KPWO56ch7t&i89GHJ" Seq Energy tetraloop enthalpies ----------- GAAA -4.0 GCAA -4.0 GAGA -4.0 GUGA -4.0 GGAA -4.0 UUCG -4.0 UACG -4.0 GCGA -4.0L=sk`~ MFOLD.BCK*[MFOLD]TSTACK.DAT;1O  *[MFOLD]TSTACK.DAT;1+,. / 4O p-*0123KPWO 56.h7i89GHJData Arangement:  Y ------------------ (X) A C G U ------------------ 5' ==> 3' AX AY 3' <== 5' (A) . . . . (C) . . . . (G) . . . . (U) -0.7 -0.1 -0.7 -0.1 --------------------------------7STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E AX AX AX AXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . -1.0 . . . -0.7 . . . -1.1 -0.8 -1.0 -1.0 -1.0O . . -1.1 . . . -1.1 . . . -1.6 . -0.7 -0.7 -0.7 -0.7O . -1.9 . -1.5 . -1.0 . -0.9 . -1.9 . -1.5 -0.8 -1.0 -1.0 -1.0O-0.8 . -0.8 . -0.7 . -0.7 . -0.8 . -0.8 . -0.8 -0.8 -0.8 -0.8   E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E CX CX CX CXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . -0.8 . . . -0.6 -1.9 -2.0 -1.9 -1.9 . . . -0.6M . . -1.3 . . . -0.6 . -1.0 -1.1 -1.0 -0.8 . . -0.8 .O . -2.0 . -1.4 . -1.1 . -0.9 -1.9 -1.9 -1.9 -1.9 . -1.5 . -1.1M-1.0 . -1.0 . -0.7 . -0.7 . -1.4 -1.5 -1.4 -1.2 -0.8 . -0.8 .   E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E GX GX GX GXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . -1.1 -1.1 -1.3 -1.3 -1.3 . . . -1.2 -0.8 -1.0 -1.0 -1.0O . . -1.3 . -1.1 -0.6 -0.6 -0.5 . . -1.4 . -0.7 -0.7 -0.7 -0.7O . -1.9 . -1.5 -1.6 -1.5 -1.4 -1.5 . -1.9 . -1.6 -0.8 -1.0 -1.0 -1.0O-1.0 . -1.0 . -0.8 -0.8 -0.8 -0.7 -1.0 . -1.0 . -0.8 -0.8 -0.8 -0.8   E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E UX UX UX UXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O-1.0 -0.8 -1.1 -0.9 . . . -0.5 -1.5 -1.4 -1.5 -1.4 . . . -0.5M-0.7 -0.6 -0.3 -0.5 . . -0.5 . -0.9 -0.9 -0.7 -0.7 . . -0.7 .O-1.1 -0.9 -1.2 -0.9 . -0.8 . -0.7 -1.5 -1.4 -1.6 -1.4 . -1.2 . -0.9M-0.3 -0.6 -0.3 -0.5 -0.7 . -0.7 . -0.9 -1.1 -0.9 -0.9 -0.8 . -0.8 . *[MFOLD]TSTACK.DH;1+,. / 4O .-*0123KPWO 56Th7hi89GHJData Arangement: Y ------------------ (X) A C G U ------------------ 5' ==> 3' AX AY 3' <== 5' (A) . . . . (C) . . . . (G) . . . . (U) -0.7 -0.1 -0.7 -0.1 --------------------------------)STACKING ENTHALPIES : TERMINAL MISMATCHESE Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E AX AX AX AXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . -4.0 . . . -4.3 . . . -3.8 -4.3 -6.0 -6.0 -6.0O . . -5.2 . . . -7.2 . . . -7.1 . -2.6 -2.4 -2.4 -2.4O . -10.3 . -7.2 . -5.2 . -4.8 . -9.4 . -6.6 -3.4 -6.9 -6.9 -6.9O-4.3 . -4.3 . -2.6 . -2.6 . -3.4 . -3.4 . -3.3 -3.3 -3.3 -3.3E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E CX CX CX CXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . -6.3 . . . -5.1 -10.3 -9.5 -10.3 -10.3 . . . -1.4M . . -8.8 . . . -3.1 . -5.2 -4.5 -5.2 -6.7 . . -5.0 .O . -9.5 . -7.9 . -4.5 . -4.8 -9.4 -9.4 -9.4 -9.4 . -7.4 . -4.4M-6.0 . -6.0 . -2.4 . -2.4 . -8.1 -7.4 -8.1 -8.6 -3.3 . -3.3 .E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E GX GX GX GXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O . . . -8.9 -5.2 -8.8 -5.6 -8.8 . . . -8.9 -4.3 -6.0 -6.0 -6.0O . . -5.6 . -7.2 -3.1 -3.1 -3.9 . . -6.2 . -2.6 -2.4 -2.4 -2.4O . -10.3 . -9.6 -7.1 -7.4 -6.2 -7.4 . -9.4 . -9.2 -3.4 -6.9 -6.9 -6.9O-6.0 . -6.0 . -5.0 -5.0 -5.0 -5.7 -6.9 . -6.9 . -3.3 -3.3 -3.3 -3.3E Y Y Y YN------------------ ------------------ ------------------ ------------------M A C G U A C G U A C G U A C G UN------------------ ------------------ ------------------ ------------------I 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3'E UX UX UX UXE AY CY GY UYI 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5'O-4.0 -6.3 -8.9 -5.9 . . . -1.8 -7.2 -7.9 -9.6 -8.1 . . . 1.4M-4.3 -5.1 -2.0 -1.8 . . -3.9 . -4.8 -4.8 -3.6 -4.8 . . -5.7 .O-3.8 -6.8 -8.9 -6.8 . -6.7 . -4.8 -6.6 -8.1 -9.2 -8.1 . -8.6 . -3.6M-2.8 -1.4 -2.8 -1.4 -2.4 . -2.4 . -5.5 -4.4 -5.5 -3.6 -3.3 . -3.3 .*[MFOLD]ZP.OLB;2+,./ 4-*0123 KPWO56 ް-￑7 i89GHJTq[VAX-11 Librarian V2A.00F`^F!}DBBZX # %A1INEV=A1OUTVvADEINVwADEOUTCAG2LEV%AINSTTZALFMOD<ALFSET=8ANCHOEXANMODE?.ANSTRT>lAOUTSTUBAKSPT%A1INEV=A1OUTVvADEINVwADEOUTCAG2LEV%AINSTTZALFMOD<ALFSET=8ANCHOEXANMODE?.ANSTRT>lAOUTSTUBAKSPT)W"XETYPPTLXFRMTPSDXLABTPSXLENTPQ&XLOCTPHHXLOCTPVXMFRMTUXMTCSTOXNEATTRXTICSTORXTYPETPXZEROTIBYLOCRT BAKSPT\BINITT@CALPNT)CMNMXT:COMSET,DATGETDLIMXKDSPLAY&ERRECLGLINEL6HLABEL$INFINS&MONPOS+W"XETYPPTLXFRMTPSDXLABTPSXLENTPQ&XLOCTPHHXLOCTPVXMFRMTUXMTCSTOXNEATTRXTICSTORXTYPETPXZEROTIBYLOCRT#BAKSPT]BINITTACALPNT*CMNMXT;COMSET-DATGETDLIMXKDSPLAY'ERRECLGLINEL8HLABEL%INFINS'MONPOSNXWDTHTdzXYCNVTPXZEROTWYDENRTYDYMDT``YETYPT_4YFRMRT]&YLABRT^YLENRT\YLOCRTIBYLOCRTYMDYDaYMFRM"NXWDTHTdzXYCNVTPXZEROTWYDENRTYDYMDT``YETYPT_4YFRMRT]&YLABRT^YLENRT\YLOCRTIBYLOCRTYMDYDaYMFRMrY8YTYPEXYWDTH[rYZEROr"Y8YTYPEXYWDTH[rYZERO).VSVSTATSWCHARSWINDOcSYMBLT SYMOUTTABHORTABVERTCSLEVTEKSYMhTERMKT(~TINPUT+TINSTRTKDASH+.VSVSTATSWCHARSWINDOcSYMBLT SYMOUTTABHORTABVERTCSLEVTEKSYMhTERMKT(~TINPUT+TINSTRTKDASH)L"SLIMYTSOFTEK<SPREADdSTEPLTcSTEPST+L"SLIMYTSOFTEK<SPREADdSTEPLTcSTEPST72ROUNDDROUNDUVRROTATRSCALERSTTAB~SAVCOM!SCURSR2vSEEBUFSEEDWG18SEELOCSEEMODSEEMRGZSEETRN92ROUNDDROUNDUVRROTATRSCALERSTTAB~SAVCOM!SCURSR2vSEEBUFSEEDWG18SEELOCSEEMODSEEMRGZSEETRN80INITTRIOTHER^IOWAITaIPMODRIUBGCRJUSTERy.KA12AS|KAM2ASxKAS2A1yKAS2AM KCMSETKINELTLABELT:0INITTRIOTHER^IOWAITaIPMODRIUBGCRJUSTERy.KA12AS|KAM2ASxKAS2A1yKAS2AM KCMSETKINELTLABELTESPLITFEXPOUTFFORMXBFILBOX,FINDGEFINDLE FINITTFONLYTFONTEToFRAMET<GENFLGGLINETtHLABELESPLITFEXPOUTFFORMXBFILBOX,FINDGEFINDLE FINITTFONLYTFONTEToFRAMET<GENFLGGLINETtHLABELJDLIMYT".DMGINAdDRAWAADRAWRA8DRAWSADRAWSRPDRWABSDRWRELfDSHABSDSHMODDSHRELDSPLAYnERRECTJDLIMYT".DMGINAdDRAWAADRAWRA8DRAWSADRAWSRPDRWABSDRWRELfDSHABSDSHMODDSHRELDSPLAYnERRECT!PDCURSRsDIGPAKCZDINITXDBDINITYJ<DLIMXT!PDCURSRsDIGPAKCZDINITXDBDINITYJ<DLIMXT?pOPTIMKNOUBGCBPARCLTPCLIPTPENLOCPLACEBiPLCHAR~PLCOPY6PLINIT PLOFFDnPLONEDPNTRELvPOINTAApOPTIMKNOUBGCBPARCLTPCLIPTPENLOCPLACEBiPLCHAR~PLCOPY6PLINIT PLOFFDnPLONEDPNTRELvPOINTAr_YMTCSZYNEAT\YTICSr"_YMTCSZYNEAT\YTICS|?[NMOVABSMOVEANMOVERN@MOVRELQNEWLINYhNEWPAGNEWPENNOTATEf NPTSXTNUMSETr YMFRMTYTICS YZEROINFINS8MONPOS?RGCHEK7SLIMX)XTYPEYZERO|A[NMOVABSMOVEANMOVERN@MOVRELQNEWLINYhNEWPAGNEWPENNOTATEf NPTSXTNUMSETr# YMFRMTYTICS YZEROINFINS:MONPOSARGCHEK9SLIMX+XTYPE"YZERO0VjHOMEINFHSTRINIBASECIBASEX8IBASEY>IFORMTINCPLTe~INFINT0VjHOMEINFHSTRINIBASECIBASEX8IBASEY>IFORMTINCPLTe~INFINT8 LVLCHTLWIDTH|MNMXXTMONPOS: LVLCHTLWIDTH|MNMXXTMONPOS)VMGINNVSTRINBVWINDO`WIDTHP WINCOTMXDENTP0 STEPST TKDASH,TTBLSZULINEL2USERSL0VLABEL(XDENETXTYPET+VMGINNVSTRINBVWINDO`WIDTHP WINCOTMXDENTP>:~ MFOLD.BCK*[MFOLD]ZP.OLB;2|+0#STEPST TKDASH-TTBLSZULINEL3USERSL1VLABEL*XDENETXTYPET|uCOPTIMCPLOTX`CSIZEAkCWSENDjPCZAXISDASHAAxDASHRADASHSAPDASHSRDATGET|uCOPTIMCPLOTX`CSIZEAkCWSENDjPCZAXISDASHAAxDASHRADASHSAPDASHSRDATGETr7gSIZELTfSIZESTKrSLIMXTr9gSIZELTfSIZESTKrSLIMXT)USESET V2STSTFVBARSTzVCURSR_dVECMOD\VLABEL+USESET V2STSTFVBARSTzVCURSR_dVECMOD\VLABELr)0UMNMXTrUPOINTUSERSTr+0UMNMXTrUPOINTUSERST7xSEETWN2SETBUFSETMRGLSETSIGSETTABSETWIN9xSEETWN2SETBUFSETMRGLSETSIGSETTABSETWINGRIDSTE*HBARSTHDCOPYtHLABEL SEEMRG3SEETRN4SETWIN.SLIMXLGRIDSTE*HBARSTHDCOPYtHLABEL#SEEMRG4SEETRN5SETWIN/SLIMXLrCOMDMPlCOMGETCOMSETrCOMDMPlCOMGETCOMSETV?X(RECOVR$REL2ABJREMLABRESCALRESCOM6RESETT/RESTAT@REVCOTjRGCHEKVAX(RECOVR$REL2ABJREMLABRESCALRESCOM6RESETT/RESTAT@REVCOTjRGCHEK8LOCLEXLOGTIXLOGTRNqLOPTIM NUMSETPLONTAbPOINTABPSPEED<RGCHEK:LOCLEXLOGTIXLOGTRNqLOPTIM#!NUMSETPLONTAcPOINTA PSPEED=RGCHEK?POINTRLPOLTRNHPSCALD PSPEEDD1+F011AG2LEV01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 AG2LEV AG2LEVGP  PL[Ь޻ZN<,  C LAG2LEV($CODE$PDATA$LOCAL(ww1F011DINITX01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 DINITX DINITX EPPPH[IBASEXP\ \~^ COMSET^ \~^ COMSET^\~^ COMSET^ \~^ COMSET^\~\k^ COMSETU HDINITXIBASEXCOMSETt$CODE$PDATA$LOCAL tww1F011DINITY01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 DINITY DINITYPP FPH[IBASEYP\ \~^ COMSET^ \~^ COMSET^\~^ COMSET^ \~^ COMSET^\~\k^ COMSETU HDINITYIBASEYCOMSETt$CODE$PDATA$LOCAL tww1F011HBARST01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 HBARST HBARSTP@PGPN[IBASECPkCOMSETkYռѼY~^ N~^$COMSET^Y~^ N~^$COMSET^Y~^ N ~^$COMSET^IBASEYPYIZQZPZQZPZZY~Yk^,(COMSETw NHBARSTIBASECCOMSETIBASEY$CODE$PDATA4$LOCAL@BPPCOM#P!)PPPww1)F011VBARST01 8-ApHr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 VBARST VBARSTPPPN[IBASECPkCOMSETkYռѼY~^ N~^$COMSET^Y~^ N~^$COMSET^Y~^ N ~^$COMSET^IBASEXPYIZQZPZQZPZZY~Yk^,(COMSETw NVBARSTIBASECCOMSETIBASEX$CODE$PDATA4$LOCAL@BPPCOM I#P!)PPPww1@F011XLOCTP01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XLOCTP XLOCTPP  PPH[ IBASEYPkIBASEYPkQC@AQQJQIBASEXP^(PNP~^,$COMSETs HXLOCTPIBASEYCOMSETIBASEX^$CODE $PDATA0 J$LOCAL@BPPCOM ^ww1F011YLOCRT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YLOCRT YLOCRTP  PPH[ IBASEXPkIBASEXPkQC@AQQJQIBASEYP^(PNP~^,$COMSETs HYLOCRTIBASEXCOMSETIBASEY^$CODE $PDATA0$LKOCAL@BPPCOM ^ww1F010DLIMX01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 DLIMX DLIMXzPPPH[IBASEXPk k~^޼ COMSET^ k~^޼ COMSETZ HDLIMXIBASEXCOMSETB$CODE$PDATA$LOCALBww1 F01 L0DLIMY01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 DLIMY DLIMYzPPPH[IBASEYPk k~^޼ COMSET^ k~^޼ COMSETZ HDLIMYIBASEYCOMSETB$CODE$PDATA$LOCALBww1 F010SLIMX01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 SL MIMX SLIMXP PPH[NkN IBASEXP ~^COMSET^~^$ COMSETZ HSLIMXIBASEXCOMSETD$CODE$PDATA,$LOCAL Dww14%F010SLIMY01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 SLIMY SLIMYP PPH N[NkN IBASEYP ~^COMSET^~^$ COMSETZ HSLIMYIBASEYCOMSETD$CODE$PDATA,$LOCAL Dww1)F01/XDEN01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XDEN XDENPPPL[NkQk"IBASEXPZZ~^COMSET^Z~^ COMSET^ OZ~Z^ COMSET^W LXDENIBASEXCOMSET]$CODE$PDATA($LOCAL PMPH ]ww1,F010XWDTH01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XWDTH XWDTHlPPPH[NkQkCIBASEXP~^COMSET^X HXWDTHIBASEXCOMSET9$CODEP$PDATA$LOCAL P)P  9ww1i1F010XTYPE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XTYPE XTYPEoPPPH[NkQkQkCIBASEXP~^COMSET^X HXTYPEIBASEXCOMSET<$CODE$PDATA$LOCAL P)P  <ww15F Q010XNEAT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XNEAT XNEATfPPPH[NkQkIBASEXPݫ^COMSET^X HXNEATIBASEXCOMSET3$CODE$PDATA$LOCAL P#P 3ww1=F010XZERO01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTR RAN V2.0-2 XZERO XZEROhPPPH[NkQkIBASEXP~^COMSET^X HXZEROIBASEXCOMSET5$CODE$PDATA$LOCAL P%P  5ww12BF01/XLOC01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XLOC XLOC]PPPH[IBA SSEXPkNk~^COMSETW HXLOCIBASEXCOMSET*$CODE$PDATA$LOCAL*ww1?EF010XTICS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XTICS XTICSlPPPH[NkQkCIBASEXP~^COMSET^X HXTICSIBASEXCOMSET9$CODE$PDATAT$LOCAL P)P  9ww1 MHF01/XLAB01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XLAB XLAB^PPPH[NkIBASEXP~^COMSETW HXLABIBASEXCOMSET+$CODE$PDATA$LOCAL+ww1LF01/XLEN01 U8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XLEN XLENcPPPH[NkIBASEXP~^COMSET^W HXLENIBASEXCOMSET0$CODE$PDATA$LOCALP  0ww1@OF01/XFRM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XFRM XFRMhPP VPH[NkQkIBASEXP~^COMSET^W HXFRMIBASEXCOMSET5$CODE$PDATA$LOCAL P%P  5ww1 TF010XMTCS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XMTCS XMTCSlPPPH[NkQkCIBASEXP~^COMSET^X WHXMTCSIBASEXCOMSET9$CODE$PDATA$LOCAL P)P  9ww1YF010XMFRM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XMFRM XMFRMhPPPH[NkQkIBASEXP ~^COMSET^X HXMFRMIBASEXCOMSET5$CODE$PDATA$LOCAL P%P  X5ww10_F010XETYP01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 XETYP XETYPhPPPH[NkQkIBASEXP~^COMSET^X HXETYPIBASEXCOMSET5$CODE$PDATA$LOCAL P%P  5ww1`cF01/YDEN01 8-Ap Yr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YDEN YDENPPPL[NkQk"IBASEYPZZ~^COMSET^Z~^ COMSET^Z~Z^ COMSET^W LYDENIBASEYCOMSET]$CODE$PDATA($LOCAL PMPH ]ww1fF010YWDTH01 8-Apr-1981 13:18 8-Apr-1981 13:18 ZVAX-11 FORTRAN V2.0-2 YWDTH YWDTHlPPPH[IBASEYPkNQCk~^COMSET^X HYWDTHIBASEYCOMSET9$CODE$PDATA$LOCAL P$P 9ww1ekF010YTYPE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YTYPE YTYPElPP [PH[IBASEYPkNQCk~^COMSET^X HYTYPEIBASEYCOMSET9$CODE$PDATA$LOCAL P$P 9ww1qF010YNEAT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YNEAT YNEATfPPPH[NkQkIBASEYPݫ^COMSET^X HYNEATIBA\SEYCOMSET3$CODE$PDATA$LOCAL P#P 3ww1vF010YZERO01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YZERO YZEROhPPPH[IBASEYPkNQk~^COMSET^X HYZEROIBASEYCOMSET5$CODE$PDATA$LOCAL P P 5]ww1zF01/YLOC01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YLOC YLOC]PPPH[IBASEYPkNk~^COMSETW HYLOCIBASEYCOMSET*$CODE$PDATA$LOCAL*ww1}F010YTICS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V ^2.0-2 YTICS YTICSlPPPH[IBASEYPkNQCk~^COMSET^X HYTICSIBASEYCOMSET9$CODE$PDATA$LOCAL P$P 9ww1HF01/YLAB01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YLAB YLAB^PPPH[Nk _IBASEYP~^COMSETW HYLABIBASEYCOMSET+$CODE$PDATA$LOCAL+ww1 VF01/YLEN01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YLEN YLENcPPPH[NkIBASEYP~^COMSET^W HYLENIBASEYCOMSET0$CODE$PDATA$LOCA`LP  0ww1@F01/YFRM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YFRM YFRMhPPPH[NkQkIBASEYP~^COMSET^W HYFRMIBASEYCOMSET5$CODE$PDATA$LOCAL P%P  5ww1F010 aYMTCS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YMTCS YMTCSjPPPH[NkQkCIBASEYP~^COMSET^X HYMTCSIBASEYCOMSET7$CODE$PDATA$LOCALP  7ww1`F010YETYP01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YETYP YETYP bhPPPH[NkQkIBASEYP~^COMSET^X HYETYPIBASEYCOMSET5$CODE$PDATA$LOCAL P%P  5ww1@,F010YMFRM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YMFRM YMFRMhPPPH[NkQkIBASEYP ~^COMSET c^X HYMFRMIBASEYCOMSET5$CODE$PDATA$LOCAL P%P  5ww1 F01/LINE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 LINE LINEWPPPH[NkIBASECP^ COMSETW HLINECOMSETIBASEC$$CODE$PDATA$LOCAL$dww1`͠F010SYMBL01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 SYMBL SYMBLYPPPH[NkIBASECP~^ COMSETX HSYMBLCOMSETIBASEC&$CODE$PDATA$LOCAL&ww1F010STEPS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V e2.0-2 STEPS STEPSYPPPH[NkIBASECP~^ COMSETX HSTEPSCOMSETIBASEC&$CODE$PDATA$LOCAL&ww1 F010STEPL01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 STEPL STEPLYPPPH[NkIBASECP~^ COMSETX f HSTEPLCOMSETIBASEC&$CODE$PDATA$LOCAL&ww1F010INFIN01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 INFIN INFINaPPPH[SkIBASECP~^ ޼COMSET^X HINFINCOMSETIBASEC.$CODE$PDATA$LOCAL P. gww1F01/NPTS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 NPTS NPTSYPPPH[NkIBASECP~^ COMSETW HNPTSCOMSETIBASEC&$CODE$PDATA$LOCAL&ww1 *F010SIZES01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 h SIZES SIZESYPPPH[kIBASECP~^ ޼COMSETX HSIZESCOMSETIBASEC&$CODE$PDATA$LOCAL&ww1F010SIZEL01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 SIZEL SIZELYPPPH[kIBASECP~^ ޼COMSETX iHSIZELCOMSETIBASEC&$CODE$PDATA$LOCAL&ww1QF010CHECK01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 CHECK CHECKwP P    PN[ЬЬ$0QHCBINITT4ERREC<IBASEXPkZZ޼LDTYPCKZ޼LDTYPCK?.l~ MFOLD.BCK*[MFOLD]ZP.OLB;2*|ijZ޼LDRGCHEKZ޼LDRGCHEKPOPTIMPWIDTHkP@LYQYPSPREADPTSET<IBASEYPkZwYZ NCHECKBINITTERRECIBASEXTYPCKRGCHEKOPTIMWIDTHSPREADTSETIBASEY$CODE$PDATAX$LOCAL@BPPCOM'+PMP _P qP P P!ww1F010TYPCK01 8-Apr-1981 13:18 k8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 TYPCK TYPCKP P  PN[Ь IBASECPk޻ZS@QJ YЫZYZY ZYmZY4ZY ZYZY~^,NZ~Z^0(COMSET^i NTYPCKIBASECCOMSET$CODE$PDATA4$LOCAL@BPPCOM1+Pi5P_BPJPVP^PfPnPww1l@F011RGCHEK01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 RGCHEK RGCHEKPP  PN[Ь ,0IBASECPk@мP@(@, C YЫZJ@QQZRZZ޼<8MNMXCYB@ ~^LHCOMSET^ ~^XTCOMSET^Ys NRGCHEKIBASECMNMXCOMSET$ mCODE$PDATA`$LOCAL@BPPCOMEP_UPtP!ww1F011BINITT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 BINITT BINITTPx P PN[ CSIZEk,INITTk4ERRECYP!P.ЩPA\\A\ZZAZ A iԩԩ P$PIr(ԩ,P0ԩ4P8PQQQPx~^Nx~^COMSET^~^Np~^COMSET^~^COMSET^~^ COMSET^ݫ$P"~ OTS$POWRRP$ݫ P"~ OTS$POWRRP ~^COMSET^ ~^ COMSET OLOPTIMIBASEC MTH$ALOG10SEETRMLINWDTROUNDUROUNDDFINDGECOMSETvLINHGTW$CODE $PDATAd$LOCAL@BPPCOM OTS$POWRJ OTS$POWRR MTH$ALOG10_R58P

P8MPxww1 HF011SYMOUT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 SYMOUT SYMOUTP PH[SEELOCѼ!ѼCSIZENPD?PJPN PD?PJP Ϋ~^,Ϋ ~^0(MOVREL^ALFMOD޼84TOUTPTѼ ޼@޼D<TEKSYM޼84SOFTEKMOVABS HSYMOUTSEELOCCSIZEMOVRELALFMODTOUTPTTEKSYMSOFTEKMOVABS$CODE$PDATAH$LOCAL Pa PqwP'}P!P ww1:MF011TEKSYM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 TEKSYM TEKSYMPDPxQ cG<BPO[TSEETRMPǏPѼ 1Ѽ1ѼkQ1EPNQEQP J $$(мkмϼ ԫ,01Z,x01-,Z01Z,,401Z,Z01Z,0,41<,x01hMOVRELΫ(ZZ^xZ^|tDRWREL^ˀMOVRELΫ(~^˔ˌDRWREL^1˘MOVRELΫ(~^ˬˤDRWREL^Ϋ$~^˴˰MOVREL^˼DRWREL1ЫXXPPZZ^xXYY~^|tDRWREL^X~^DRWREL^Z^xY^|tDRWREL^Ϋ(~^ˬˤDRWREL^1ЫXXPPZZ^xXYY^|tDRWREL^X~^DRWREL^Z^xY~^|tDRWREL^ˀDRWREL1h,4Zԫ<ԫ@ë,4P0Pǫ0PUЫ,VUNVPE=MPYZYP MTH$COS_R4D PJPXYP MTH$SIN_R4D PJPWë@XJ ëP }ww1~F010LABEL01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 LABEL LABELPHP $  ,   04<00@DQD Qls|os|oAPCPB@BARCPOp[IBASEXkѼPkkWмPJ@$ѫ$J@8$ի$1IBASECP(@,Ы,Ы,мPJ@0޼IOTHERPZJJ08JJ4PPAP@LP PPP0PPP*P%P6PAPbVpww15F010WIDTH01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 WIDTH WIDTHP@APP2ww1@F011NUMSET01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 NUMSET NUMSET6PQ9 P PH[Ьм PJ@$kJ@8׫ѫkѫ޼$޼(޼,޼0 IFORM޼8޼<޼D޼H4FFORM޼TLMTH$SIGN@PJP޼ \޼d޼h޼lXEXPOUT HNUMSETIFORMFFORMMTH$SIGNEXPOUT$CODE$PDATAp$LOCAL@BPPCOM.PF2P8P VPOtP1ww1`&F011ALFSET01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 ALFSET ALFSET2\P PQ!%+4;CKQXaiow}JANUARYFEBRUARYMARCHAPRILMAYJUNEJULYAUGUSTSEPTEMBEROCTOBERNOVEMBERDECEMBERMONDAYTUESDAYWEDNESDAYTHURSDAYFRIDAYSATURDAYSUNDAYPO@[Ь ,kZѼ ZѼ ZQѼ ԼJPZPPZJ˼ëJPZkPЫPPмPP PЫZ޻,YZ JiZZPZPЫZЫY޻,XZ ZYI JhZYZI OALFSET$CODE$PDATAp$LOCAL'P%P.P 4PPP$ww1@F011MONPOS01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 MONPOS MONPOSPP PH[J k޼ k~^$YMDYD^,IUBGCN ޼@޼H <GLINEg HMONPOSYMDYDIUBGCGLINEE$CODE$PDATAL$LOCAL Eww1 NF010GLINE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 GLINE GLINE0PP  PH[мPJ@TJ@XëPPPkPkP IBASEY ѼP޼$ WINCOTN k4MOVABS@DRWABS޼TLWINCOTN k`MOVABSlDRWABS HGLINEIBASEYWINCOTMOVABSDRWABS$CODE$PDATAx$LOCAL@BPPCOMDP'YP7kP%P!ww1F011EXPOUT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 EXPOUT EXPOUT;P QD TENSHUNDREDS THOUSANDSMILLIONSPO|[Ь 0 <мPJ@PJ@8м Ϋ мѫ 1ի 1ѫ1ѫѫ1ѫ11Ѽ1ϫ 11       111Ы YYVЫXXVЫZ޻~PPP,P8PNPdPp PsPvPPPxP+PP@PPPP7PFPnP P5P PPdP2P P(P;P@IP2UPPk_ww1F011HSTRIN01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 HSTRIN HSTRINZP  PL[Ь޻ZުުANSTRM LHSTRINANSTR+$CODE$PDATA $LOCAL+ww1`F011NOTATE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 NOTATE NOTATENPP  QPO[Ь(,CSIZE޼<޼@8MOVABS Xм WZ޻(YZWJiJiXZ~^HHiLDANSTR^Jik ~^XPMOVREL^Ji PP~^XPMOVREL^ZXWZZX PP~^HHiLXDANSTRs ONOTATECSIZEMOVABSANSTRMOVREL$CODE$PDATA\$LOCAL @PgEP^OPTmPPww1 F011HLABEL01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2  HLABEL HLABELVP PH[Ь޼޼ANSTRO HHLABELANSTR'$CODE$PDATA $LOCAL'ww1F011VSTRIN01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 VSTRIN VSTRIN[P PL[Ь޻ZުުVLABELN LVSTRIN VLABEL+$CODE$PDATA $LOCAL+ww1fF011VLABEL01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 VLABEL VLABELtP PH[ЬkkLINEFkP@ANCHOBAKSPkc HVLABELLINEFANCHOBAKSPA$CODE$PDATA $LOCALP Aww1`F010FFORM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 FFORM FFORMP PL[Ьü PPZSZZZkP"~ OTS$POWRJˏZQZP PP~P"~ OTS$POWRJQZPQZJ޼޼ ޼ $޼(޼,FONLY޼޼ ޼ $޼(޼,EFORMl LFFORMFONLYEFORM$CODE$PDATA0 $LOCAL OTS$POWRJ "PAPCXP aP#P! ww1F010EFORM01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 EFORM EFORM8P0P PN[Ь ޼ ޼$޼ (ESPLITkYYPNP~P"~ OTS$POWRRPE~^4~^8޼ <޼@޼D0FONLY^޻ZмPE@ мP+@YмP-@NYPˏP~^LмP@THIFORMw NEFORMESPLITFONLYIFORM$CODE$PDATA\$LOCAL OTS$POWRRP  ww1`/F010FONLY01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 FONLY FONLYVP0P PN[Ь$ ~P"~ OTS$POWRJEPk޼0(MTH$SIGN@PJPPNPݼ P"~ OTS$POWRJCQQDQP@PJPPNPü   ~^<޼@޼D4IFORM^ ZˏP޻$YQPSZ-JiZЫ P.@iѼ ޼ PЫ P@THIFORMo NFONLYMTH$SIGNIFORM$CODE$PDATA\$LOCAL OTS$POWRJPP PPww1@F011ESPLIT01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 ESPLIT ESPLITXPPA&@ffP$N PD$PJP(,0ѫ(k0 (ѫ(ѫ,ѫ 1Aѫ 18֫,~^`N,~^d\COMSET^~^`N0~^d\COMSET^~^`N~^d\COMSET^ LSPREADCSIZ EIBASEYLINWDTMTH$AMODCOMSET$CODE$PDATAh$LOCAL@BPPCOMCPg2P6P_P gP{PP1P)PP/#ww1 F011IOTHER01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 IOTHER IOTHER_P PPH[IBASEXPkIBASEYPѼkPѼPkЫPY HIOTHERIBASEXIBASEY9$CODE$PDATA$LOCAL %P/P 9ww1 F011JUSTER01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 JUSTER JUSTERP PO[Ь kмYѫY޻ ZЫP@jYëPPмWЫZkXZW޻ YJiJiXWZZX Xkռ Լ PP~^($LINWDT^P P PP~^($LINWDT^PPX OJUSTERLINWDT$CODE$PDATA,$LOCAL9#P2PRP[P eP}PP&P@P ww1@-F010PLACE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 PLACE PLACEdP P QSTD UPH LOH UL4 UR4 LL4 LR4 UL6 UC6 UR6 LL6 LC6 LR6 DaEC/EDTEE@/EDTEDDDDE@/E"EmEE@/EDDDD"EmEDDDDE@/ED"EE@/EHEsEE@/EDDDDD"EDDHEsEDDPN[мkѼ ռkkPѼ@ k1SEETRMǏPNPY,IBASEXP^8kZEYJ ~^<4COMSET^@IBASEXP^8EYJ$~^<4COMSET^,IBASEYP^8EYJ(~^<4COMSET^@IBASEYP^8EYJ,~Y^<4COMSET^n  NPLACESEETRMCOMSETIBASEXIBASEY$CODE$PDATAL$LOCALPP&P,Pww1F010YMDYD01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YMDYD YMDYD4PQ;Zx0NPH0[м ммkk׼ kk ּ kѼ޼LEAPkk kP@̼` HYMDYDLEAPc$CODE$PDATA<$LOCALBPP1P'P9P KP PP!cww1 F010YDYMD01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 YDYMD YDYMD7lPQ;Zx0Nm<[y1OnPNh[м Ѽ  LEAPYռ׼ ޼ LEAPmPPmPѼPּ ÏmPéPNPFBP@PJPZ PZPѼ@ZZ PZPZk@` NYDYMDLEAP$CODE$PDATAt$LOCALBPP1P 0P!`PP!ww1F01/LEAP01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 LEAP LEAP^PH[ zP{PPkzP{dPPzP{PPkիիN HLEAPX$CODE$PDATA $LOCALBPP1EPJPOPXww1F010IUBGC01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 IUBGC IUBGCPO[NYNGDYPJPŏPNP C YPFCPJPXŏdXPNPA ZCZYPD?PJPWWPNP@ZCZYZYkJZ PD $E$PAP(EB(PCP,E,PAP0ZX@ZNPE0P8WXBZNXPE,P"'-]39>|D1JOUP[afol$rw}C?Bk ?"'-^39>}D2JOUQ[afpl%rw}D?BnH?BoI?B:cuv% '` ?BQPND[N P@)J`PJP(LOCLEPkPQQ8LOCLEPPQQ ZЫ YYZJPHLOCLEP PQQZѫYZJ`ZXLOCLEP$PQQPďPYQďdQQPQQQPPPP NOUBGCLOCLE$CODE$PDATA$LOCALNPwP|Pww1"F011FINDGE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 FINDGE FINDGE[P  PL[Ь м PQ@׼ ּ ޻Zм PQ@j@jPG LFINDGE<$CODE$PDATA$LOCALP <ww1`m'F011FINDLE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 FINDLE FINDLEiP  PL[ЬA67kм PQ@k׼ ּ ޻Zм PQ@jk׼ м P@jPG LFINDLEJ$CODE$PDATA$LOCAL'PJww1/F010LOCGE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 LOCGE LOCGE[P PL[Ьм P@׼ ּ ޻Zм P@j@jPF LLOCGE<$CODE$PDATA$LOCALP <ww12F010LOCLE01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 LOCLE LOCLEbP PL[Ьм P@׼ ּ ޻Zм P@j׼ м P@jPF LLOCLEC$CODE$PDATA$LOCALP Cww1@68F011ROUNDD01 8-Apr-1981 13:18 8-Apr-1981 13:18VAX-11 FORTRAN V2.0-2 ROUNDD ROUNDDAPL[GZSB@XZJZPZkNPPEPQмЫPE LROUNDD;$CODE$PDATA$LOCAL P0P ;ww1 P HPJPTP ^P`PkP uPwPP PPPP^PP AP#PPPLP<Pv'P1P8PDBPiPvPP'PPMP=P]PPPP*P)P^R2ww1hF011PARCLT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 PARCLT PARCLTPP@Q QмQ м QмммQ м M @PARCLTJ$CODE$PDATA$LOCAL+PP(P(P)P0P7PJww1 F011LINTRN0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 LINTRN LINTRNP@RESCALY @LINTRNRESCAL$CODE$PDATA$LOCALTKTRNXww1`F011LOGTRN0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 LOGTRN LOGTRN%P@N4RESCAL] @LOGTRNRESCAL$CODE$PDATA$LOCALTKTRNXww1F011POLTRN0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 POLTRN POLTRN4P@ м4м8м DPSCAL` @POLTRNPSCAL)$CODE$PDATA$LOCALTKTRNX )ww1F011RESCAL0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 RESCAL RESCALPPY@PBPDPFP SPjPPPPP(ww1 F011LVLCHT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 LVLCHT LVLCHTQPPH[\լxkREVCOTЬЬxY HLVLCHTREVCOT+$CODE$PDATA$LOCAL TKTRNXP +ww1<F011REVCOT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 REVCOT REVCOTPD P P N[P-ATZPNPPG,PPNPPG0P ϫN N1A A 1YJ4ZAi A ZZA8~ݫ OTS$POWRRP ZZA< ~ݫ OTS$POWRRPZ1NPC<PNPC@P MTH$ATAN2EeC.PE PEQ@QP MTH$SQRT_R3F,PADP kQ4@DZQ8BDkkQ4@DSjA4D4~^0,MTH$AMOD^PA4D8~^0,MTH$AMOD^PQPЫPQPЫPQPЫPQPA4D~^0,MTH$AMOD^PR G0PAHP޼ <޼@8PCLIPT NREVCOT MTH$ATAN2MTH$SQRTMTH$AMODPCLIPT$CODE$PDATAD$LOCAL TKTRNX OTS$POWRR MTH$SQRT_R3DPOPYP[P.]P_PaP nPPPPPPP(=P UP ePlPxP}P5P! P;/ww1VF011PCLIPT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 PCLIPT PCLIPT5PDZԪtQjQQQ tT DPCLIPT/$CODE$PDATA$LOCALTKTRNXPPP&P /ww1`F011PNTREL0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 PNTREL PNTRELCPPH[kPNTABS_ HPNTRELPNTABS%$CODE$PDATA$LOCALTKTRNX%ww1 F011PNTABS0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 PNTABS PNTABSRPPH[PNTMOD޼޼kTKPNTxi HPNTABSPNTMODTKPNT1$CODE$PDATA $LOCALTKTRNXP1ww1`(F011DRWREL0130-Jul-1981 15:0830-Jul-1981 15:08VAX- 11 FORTRAN V2.2-40 DRWREL DRWRELCPPH[kDRWABS_ HDRWRELDRWABS%$CODE$PDATA$LOCALTKTRNX%ww1@,F011SETMRG0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 SETMRG SETMRGP@ммT @SETMRG$CODE$PDATA$LOCALTKTRNXww1 G1F011MOVREL0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 MOVREL MOVRELCPPH[kMOVABS_ HMOVRELMOVABS%$CODE$PDATA$LOCALTKTRNX%ww1`T4F011SETTAB0130-Jul-1981 15: 0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 SETTAB SETTAB P PN[Ьtռk޻ZkP@jѼ@j@jkkt޻ZkYIjмIjիkk޻ZkP@jЫ@jЫT NSETTAB$CODE$PDATA $LOCALTKTRNXP//P6P;P#ww1@8F011RSTTAB0130-Jul-1981 15:0830-Jul -1981 15:08VAX-11 FORTRAN V2.2-40 RSTTAB RSTTABP PO[Ь ռkk޻ ZkPѼ@jkXkZ޻ YZXJJiXZXZP@iXZZX޻ YJiXZZ T ORSTTAB$CODE$PDATA$$LOCALTKTRNX1PvPV&P4P >PPRP pPP ww1`@F011TABHOR0130- Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TABHOR TABHORP PN[Ь kѫ޻ZЫP@jk@jkNEWLIN޻ZЫYIjIj MOVABSALFMODs NTABHORNEWLINMOVABSALFMOD{$CODE$PDATA($LOCALTKTRNX#P#0P=PJP/SP&{ww1FF01r)"TWINDOiTYPCKTULINETr+"TWINDOiTYPCKTULINET 1TABVER0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TABVER TABVERP PL[Ь kk޻ZkPPЫP@j@jkЫP@$MOVABSALFMODh LTABVERMOVABSALFMODh$CODE$PDATA($LOCALTKTRNXP,9P CP MP hww17KF01 1DSHMOD0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 DSHMOD DSHMODPPPN[YɀɀTOUTPT TOUTPTɴZJɴZZkXYCNVTмh NDSHMODTOUTPTXYCNVTP$CODE$PDATA $LOCALTKTRNXP2Pww1OF011TKDASH0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TKDASH TKDASHqPPQ y 4QܠA B BHCHQ<QtPO[Z1ʠ1P@ʤʤCWSEND1CWSEND11k1 ի  P PP  իЫPЫQA@  WXXWWYXYZJHxWXZ|WVWZZVJxYEJ|YPEYPBJxBJ|VZY(V Z$kԫԫ,ѫ11ѫѫԫ,ԫN0N4PNP8PNPPFZPJPZkЫP^ LKINb$CODE$PDATA$LOCALTKTRNXTKPLOT (P@P bww1 bF01.KCM0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 KCM KCMmPL[NZEWD33PFZPJPECPFZPJPE!>pBPNQDQPFZPJPZkЫP^ LKCMc$CODE$PDATA$LOCAL"TKTRNXTKPLOT (P@P cww1fF011DCURSR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 DCURSR DCURSR@PPH[޼޼޼ kSCURSRR HDCURSRSCURSR $CODE$PDATA$LOCAL ww1 PnF011SCURSR0130-Jul-1981 15:0830 #-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 SCURSR SCURSRVPP PH [DMGINkЫЫ Ы` HSCURSRDMGIN&$CODE$PDATA($LOCALTKPLOT &ww1rF010DMGIN0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 DMGIN DMGINPTP Bn=vO lc rc;1p\ Ws9eD-@A& \J,v|\TJ_Cye"x:)|671bc>/k&JZ$[9wts%},8z cQH7=E#H6}_r|o,U:L]IM}AH(nO5F9)ݔcl4q'&vk)|7.ɥv2\ =zIp#8ai'\DK# !Za >Y2?YkL)>jNWx4dtLH* +@+<2qnen{6mCZk6UtC|jcS n7{2 8ֈ|co!W@6=Suy>GCP[󫊠»񀖋4Ԟ볧L.ҷCei_7XK^! }X- ~f{Z¸_Q!j[]=y1poui]bi\Q JBo{n<"p3w].vwV+dy]~:%dPdj=2m1qUnJdcApmcw{@ zN)tEc BBߥO .s$z螎 U =CW}l/D*HV(l~O@HO-vE]^M1m!]7Mbo%yRLGx$f j AyRu̺!9iQKG+x>z3s':EeU)Ve6=\7*Ɣ@l-m[U( ^t ▚@~CXdS r|u/ٸwM(]QRYI6WSXNʘGp37@A8 }ܹ{43+ٖ]VW ';\|, rPwp)\=#tbWlw{q#j8X [> LJLNTV;!- W~zzBKzFVE3}lH)E-Os,]Z` ')=RSJzDRTGxK]A&ޒjf#ߌn/Lp$hfhi56Vа2k p3'L WZ.^j;t#߄4,/סb-is}nGdw:z8E/['(!Cy!:PZYCY(i)d Ѿ,jaTo&7K7zCG*Sqh iB1@),]EQfiupirV']qG +[a6 -IlS*>?K- wwW)ps5bys88t*T`ltj|/gq q|!~yf~$NR,4YZ"1 ;?}%2ryFnvYX͐7S]E1OD,!j?nzXi3T~yw3_uqP 4Wm6ѤFV3N& lJ[A 0>#ڐ+_HkKzRa{tK4-RG8if0۠{5W[$!_i]\yȃF=q:53~P}¨wI"Dh}^s`@C,KF"Q@JV)-Dp97ar7^ǐU#;'_ }Bi]DC6h @h4 $=Yߌ'\ ^ÿB~_I,,b>ϫ>7oIB j~ʹYo[߬x7 +A׵0{n֑vɞjae50HA6t8o_҈3qT-=.m3 Q=(U*ȇ]gCifМKsb|$T-Ib,¨ w1f7yLCIw )d]|6 K!vM?ӾNEӵXPúK7Cj/LeA΍nyt#q΅# Ӝ6f+}zjb!MGL>;p*u_9D+a.x^"1SFf~Tc  aO2C6o} 2 ('Z)Od¤%W>Dv w t baWsS [Hk{!H[-GjNP1Lv&`,8xQb^ ql!PL }2N-*Z=s4":%Ern$QHp4#~[XJ:j9詅EJbB+v43g7Au9^~Yw>l{@uħm+(2#|o#eiSHe֝n5pe(?qAj.t4guB4wgO  0_I6!/AzWAÿ|LGuf~v߯bflA%w:^]v!`qFt+&in4>>xdnc@DKl[`s%z6>e> :nk7k#zpÉo~R;}.%f@>yɲA_'O**7#fI.b0@RTJ }ހG~1M!s=a 1&k=C~g̀ԯ!LE?)w9|ZG*_ 'SK)l"+FKoH$u4M]P M4,1:`C&38! &Z+f=FeMr=6uI5>M#}<jk29#" gd;~o1d0 $ & 8-.ʇ,Cq_X8Ɓ7P 539%ZJu#Pq\ʻ̹u\&!Ba.T#*ϖ}N֬fFߪ;j ܝr" [Q#r8%sN1DHZX6y3o6t .l^gM>*\KjMZ_ږʖne0ߺf_cn P@j浸+93*gaSn7{&c]ȕkoP [v \h7L*TCqugM Q>6*R|vZ{z~l4YO}P~eseSϜBjc4cp,-IfWv-7^y#[݅#XqrvJ&{K H?0b :>x1ÓQ֔4pNQwT>}"snc${ k w9-8C C{\sYj@ 7\ ZYw)ZB*ڏ@zMDVDl [Dtu~X ǗR_i'D.}BFОrL23<ʕWJujPn#EKsH)v)яw*wªgy.9֟!^wʭ(*)ì8$\|WBc&Clwa!nlx4]tf=Sj(`FIi!c1z(gG5y!9!k_!'#WRs42K!S/fi!P:w 4a G?7W6!|AI"U ?fd; վS犺ΏcKH%MBs OȹB`teHg;kB))*JeimTv2.PJfKP@`g<)Q&Tu R+*[wdjcb&/Vs9~osc2&p?&&}4nktZ$6]7J`EQYZ<šHmLEb~8Y\T}b!".n%0#@xVDR]b0b$g#-Q7{z<.6Ubޖ'"[[rBS^Y]I:5!V&T/{ c,>EZJRQ0y!'UESG'L*R[}&}l<8"Z&Jd ~)RPpH`^D$ln:yKfɡPM\{J *fqrhU`Y$%BNr(Y2P``}Lz%z+@4.ax:W\ELSc*hop@Pv\9w,9*AuQ^ zg iR`m76<|Ԕ2Uq|^ 2?:L^T ^ B$!< A^E~@@QIO_CkQL.K.Dfa#Pq\i\l`2vOcs.2n@gck8_6^L 60 Q H(B/_w`|Q*\BRY1 .ӣ@Lǘ.! + %.?K86:>fi(VKH#Rz{pX;t?j":8 39*E?DKGWSRFAmIGMbu <iB8{BG@ m[t 01*44|y8gh,l*?2ϕX 4 :\ShRvV 98םM"5a-b[h ෑfw>_Y:Bt,6n̛y {u+km#E#v9=4K+jhv=rܰZ9.*#MW2i䰪xhpMf \<0<ΟMi 0\0clbwJ^LW?\P(WF݈)sbj9#@RCBE$nQPi" 5" ve@d%828r 4n0cz}xBNGQVvE|Hqa ab22ly={8 wzxE XIfJnA_>^s4u/(3? 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HRESETMOVABSCWSENDCHRSIZALFMOD$CODE$PDATA$LOCALTKTRNXPP."ww1 F010TKPNT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TKPNT TKPNTPP =PH[kTOUTPT޼ ޼XYCNVT޼ ޼XYCNVTi HTKPNTTOUTPTXYCNVTE$CODE$PDATA$LOCALTKTRNXP  Eww1F011GENFLG0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 GENFLG GENFLGPH[PtPR HGENFLG$CODE$PDATA$>LOCALTKTRNXww1qF010ANCHO0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 ANCHO ANCHO:PPPH[мkANSTRL HANCHOANSTR$CODE$PDATA$LOCALww1`F010A1OUT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2- ?40 A1OUT A1OUT,P ((PO [ЬмYмWZZW޻XHYHYJh( KA12AS0ANSTRHYWHZYkZY OA1OUTKA12ASANSTRh$CODE$PDATA\$LOCAL #P<5P hww1@F011AOUTST0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 AOUTST B AOUTST(P $$QHPL [Ь мZZkkZZ޼$KAM2AS,ANSTRZ LAOUTSTKAM2ASANSTR:$CODE$PDATAX$LOCALP :ww1F010ANSTR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 ANSTR ANSTRP BSYMSNohBUFFPKy CALCONCALPNTBSYMSNohBUFFPKy CALCONCALPNTCQZf~H & ^ 41j @/ g$̡?W/ H0-E ќ;2ҁU p' y`!%Ȯ$ J`uaGD5[aIi2 =pg11n) Q|DDs!z B9}*Gg#<N"Vd}}Y,a,)PO[Ь`l1\kALFMODD1ZʬʘʜPʬPʔʬʜPʈPʜPPʰЪ|ʰpMOVABSALFMODNEWLINYɬɘPɜPɄPZZZZkkZЫXZXPP ѫ XPPZZHl˄|TOUTSTɄPɜQQPɜPPɬɜZɬZZɬXXѫ 11ԫ ֫ ѫ 1N ZEZPJP$XȜYY$PȜPP(DZJZ,,YȜYY0ѫ(1ի(1ѫ01ի01Ы P@l4ˈTOUTPTЫ(ȬЫ0EȰ1^ȈȄPP8Ы4ZǏdJ<Ǐd<@ŏd@PPdww1F011EMCHAR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 EMCHAR EMCHARtP (lpQl:/P" h{D{_ JPTTGIGEC{P|FGL:NrVZ}E]{"YWCSV!g!Zi`o1HeH/NL{EL/" LJC LKGE{H_{EGNHE{LNLK{EG{ELI5140MeCGbH LJ/h{TUXY6IGL{"CjLKGE{d{EJG|fCfd{EHINCC"N{ENNUCCNCCNLE{LJJCEL{LJC{EGLN"{ENNONNCNNC]{GICoW:"7ZOGE{oWCKeZC]K{GIC6  {EICoW:"8{ErO/""K "K@]{GICGE{`{D_{ECNFG{De"xBILG{EGC8 5yLaC/"UGCGCGE{GE{]{GI@{DE~HU{ {EICM I OII C I IC RrZCH|!TJE{rZI{:3 " RC {ELrZHHq!|O WJQ N6CO\_fmty}.3?HQY`kqw~DOSVYdnw$(.C`!<=>?\]^6DOC` " I3Me " O.I3Mo " DIC` " :IC`6 DI=[z6DIC`PO[Ь\hkkZ kYZYPJ˼Q@A@ ZZԫ ZNʬNʰʬʰNʜ ֫ѫ1ЫP@h$ѫ$ ѫ$~NPZEZPJP(XȜYY(PȜPP,DZJZ00YȜYY4ȜPѫ,P1ի,1ȜPѫ4P1ի41Ы$P@8֫8Ы8P@<PǏd,P=P'CP]P2&fww1`CF010LINEF0130-Jul-1981 15:0830-JuUl-1981 15:08VAX-11 FORTRAN V2.2-40 LINEF LINEFKP PPN[ZʀALFMODTOUTPTY1ʜkʜNʜ\G\PJPʬG\\J\ ʰʬʬkʰʰʬPPPkkPPʬʰQQQЫQQʰPQ ʜPʈPʜPPʰЪ|ʰMOVABSALFMODCWSEND NLINEFALFMODTOUTPTMOVABSCWSEND$CODE$PDATA$ V$LOCALTKTRNXTKPLOTCP3PrPyPPP8PP<PP'ww1@ F010BAKSP0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 BAKSP BAKSP PPPN[ZʀALFMODʠTOUTPTYNʜ\G\iPJPkkʬG\\J\ʰʜʜ ʬЫʬʰ Ы WʰʬʬʰʰʜPʄPޜPPʬʜPPʬʠMOVABSALFMOD} NBAKSPALFMODTOUTPTMOVABS$CODE$PDATA$$LOCALTKTRNXTKPLOTJP"P7PlsPPPPP.P;PP&ww1 k%F01/HOME0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 HOME  XHOMEPP|Q PH[| kTOUTST| MOVABSALFMOD| HHOMETOUTSTMOVABSALFMODT$CODE$PDATA $LOCALTKTRNXTKPLOTP3)PCPTww1.F010ERASE0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 ERAS YE ERASEtP PQ PH[kTOUTST IOWAITRECOVRn HERASETOUTSTIOWAITRECOVR)$CODE$PDATA$LOCALTKPLOTP )ww1&3F011RECOVR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 RECOVR RECOVR PPH[\Ьxk̴ Z̰̀ALFMOD MOVABS̠CWSENDѫѫϫALFMODPNTMODkxz HRECOVRALFMODMOVABSCWSENDPNTMOD}$CODE$PDATA$LOCALTKTRNX<:PGPQP[P ]P_PaP cPmP}ww17F011NEWPAG0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 NEWPAG [NEWPAGP P|Q PH[ALFMODkTOUTST IOWAIT| MOVABSALFMOD| HNEWPAGALFMODTOUTSTIOWAITMOVABSu$CODE$PDATA($LOCALTKTRNXTKPLOTP.PAPIPZPuww1Na dMODrPPPH[TOUTPT\L\\k TOUTPTY HPNTMODTOUTPT<$CODE$PDATA$LOCALTKTRNX2P <ww1`F010IPMOD0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 IPMOD IPMODRPPQPH[kTOUTSTxX ?tPLTCHRPNTABS``PNTMODPNTRELvPOINTAAtPLTCHRPNTABS``PNTMODPNTRELvPOINTA eHIPMODTOUTST$CODE$PDATA$LOCALTKTRNXww1`eF011XYCNVT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 XYCNVT XYCNVTPdhplQQ;:Vo:=>-J?W BCDPOX[YɜZмPPPZZPP мPPZPPZZ0PLTCHRԫԫɸЫɸЫɠfɼ֫ЫɼЫPЫ@֫ЫЫPЫ@֫ЫЫPЫ@իԫѫ1֫XЫЫPЫ@@TOUTST11Ȭ ZZPZPȜPZȰYYPYPȜPYZYZYZkȴPPPNP$ȴkZYdZYZNYPY BJPDJPAJP,Z(E#> ׫$P@,PNQDQPNQBQPJPȴԫȴЫ ЫիLTKSYNC OXYCNVTPLTCHRTOUTSTTKSYNC  g$CODE$PDATA$LOCALTKTRNXTKPLOTWPmP vP~PPP P4P9PPP P+P6PfPPPPPE9 ww1/pF011LINWDT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 LINWDT LINWDT.PH[żPQQPPR hHLINWDT%$CODE$PDATA$LOCALTKTRNX%ww1tF011LINHGT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 LINHGT LINHGT.PH[żPQQPPR HLINHGT%$CODE$PDATA$LOCALTKTRNX%ww1WyF011CHRSIZ0130-Jul-i1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 CHRSIZ CHRSIZP,PQ8X3R"50QPO([мYXȠYYYYYYZJȄJȈYȐPLCHAR7YȠTOUTSTYkw OCHRSIZPLCHARTOUTSTw$CODE$PDATAD$LOCALTKTRNXTKPLOT+P "P*P2PTP ^PjP jwww1`}F011PLCHAR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 PLCHAR PLCHARP\P @@DQhQIPO@[X1YмɈмɄ޼ DIGPAKkZ,JZ޼4J<0DIGPAKkZPPDTOUTSTPTOUTPTɀGeC.ЫP MTH$COS_R4P ЫP MTH$SIN_R4PN kNɄE hEPEPE PRP ɈPPPPɜQQPɜP| OPLCHARDIGPAKTOUTSTTOUTPTMTH$COSMTH$SIN$CODE$PDATA$LOCALTKTRNXTKPLOT MTH$SIN_R4 MTH$COS_R4P6PN)ww1F011CZAXIS0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 CZAXIS CZAXIS;PD lZʠмʨʨʨʨCWSEND] DCZAXISCWSEND0$CODE$PDATA$LOCALTKTRNXPP"P 0ww1F011CWSEND0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 CWSEND CWSENDZPPQPH[P`PPkTOUTSTY HCWSENDTOUTST)$CODEm$PDATA$LOCALTKTRNX)ww1-F010TSEND0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TSEND TSEND6PPPH[kBUFFPKI HTSENDBUFFPK$CODE$PDATA$LOCALww1F011TOUTPT0130-Jul-1981 15:0830-Jul-1981 15:08 nVAX-11 FORTRAN V2.2-40 TOUTPT TOUTPT;PPPH[мkTOUTSTN HTOUTPTTOUTST$CODE$PDATA$LOCALww1`UF011TOUTST0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TOUTST TOUTSTjP PL[ЬмZZ\\ZZk޼ BUFFPK_ o LTOUTSTBUFFPK9$CODE$PDATA$$LOCALTKTRNX P9ww1F011TKSYNC0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 TKSYNC TKSYNCP 4P,QPL([ k kPPԫЫZZk BUFFPKZZիBUFFPKN LTKSYNCBUFFPK pB$CODE$PDATAL$LOCAL #P 8PBww1`F011BUFFPK0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 BUFFPK BUFFPKPP XlX 4Q4HQQ0POT[qЬP\ѫdмëkPdP1ռѫXɫZ$P@\Ы PP$Ы$PPZPZP(Z ѫ(1ѫ1ϫ֫ЫP@˨`ADEOUTZZJ˨xlPLTCHRJ˨˰ZYZ,ˬZZlI˨YlZYZ0ͫ4ѫ44ѫ44ϫ4ЫP@˨1Zʴ׫ʤʨ1֫ЫP@˨֫ʨP`PЫQʤPA˨1ЫP@˨֫ЫZJ˨ZPJ˨ JrZ1ռT1֫ЫP@˨`ADEOUTˬ1`ADEOUTԫ1ի`ADEOUTի޼˄|ADEOUTXˈADEOUTXԫ1ѫ1֫ЫP@˨@ˬЫP)@˨XYYI˨ZZZXYZE-e*-BB @MODr"PP R_MUTPP^WE]^cSq TOtQTY P N|LH3XeD:*DՈWPpLQE1$NEUTW nP\OCTV@ZRNoTRmSԉ@0ZJі@M SxzR{ RRRRQQɜQ@DzJ0Q{ QQUi703bVj'>c9cd4iJ$,i514,ը*K.Rߒ@$:2-2bXCJ^0MLSFK=PK USVUUQEND԰˛QVNի  kЭ\Uծ Q d݌ּЫP@PTThQ@Q Q Q@Q1P<XI_ЫPÏ@@YYPPR֫֫PʜQQPкQZDPʜRRPʜPAXP:PP&YGE1#LtTOUTSTԪTTSENDЫ NDMGINTOUTSTTINSTRRECOVRTSENDADEIN$$CODE $PDATA$LOCALTKTRNXTKPLOT2;PTPP P+8PfP-PMD8$wwi1v| HP01PaTABSA1IN0130-Jul-1981 15:P930MKs-J?W BCDPOX[YɜZмPPPZZPP мPPZPPZZ0PLTCHRԫԫɸЫɸЫɠaWWO֫ЫɼЫPЫ@CLMH֫ЫЫPЫ@YRR֫ЫЫPЫ@۹EKWTԫѫ1֫]ꍋTЫPЫ@@TOUTST11Ȭ ZZPZPȜPZȰYYPYPȜPYZYZYZkȴPPPNP$ȴkZYdZYZNYPY BJPDJPAJP,Z(E#> ׫$P@,PNQDQPNQBQPJPȴԫȴЫ ЫիLTKSYNC OXYCNVTPLTCHRTOUTSTTKSYNC L5piun1981 7jtygq-Hm1987}zyqtAX-7ek RC!B0.2+`{MLJWPNMN>vPA7AU<PuPPP9P$TP $T+PfIP6PLXլ\<NC_[iEk_=Cݸ.DQ]ʷ񥗲 UNQTQw2ya81 15:08VAX-11 FORTR)N VF.7n|u\K] CHRSIZ C/SSICJVRI ,PXHKPO8X3R"HEC}NMXPO([мYXȠYYYYYYZJȄJȈYȐPLCHAR7YȠTOUTSTYkw OCHRSIZPLCHARTOUTSTw$CODE$PDATAD$LOCALTKTRNXTKPLOT+P "P*P2PTP ^PjP D WIMP"Tz1TIN0)}`PPH3[oV P,qh-9927;5:0830-s8dime!07:1/TH 13FYRTRDjcvk2/0 PEATARBXAR $HOCZPIOPP_Pw1ؗDВ01@DO&+130|Nul-p81 55:`/Nw,1b5$1)hgAX52 Z IV60C֜O$ nX-CRڼ4J<0DKGPANp^RcTTOUTST-Nul6?kgsetn0d^\-;5 FORTRaOV2.2-40NT})@ J?J9ZXJHNL-X^kK[мJ8TGNTVST=N3IODEHTOSp@UC TOSpCC$CITPXR@v=$MCCLpuR*DG1w1`UF011RESTAT0130-Jul-981 11 *G6ԋP7֩vRL<"4 튣Q01NINITTFOR$OPENbETBUFJUCGd0$8-L;)zax1"50835 :(h1;1)15:6P\AT@VC,1 FIvlV0340QYNYVWFFVFLKT2HDSYVW#ww1X]l52l1X&R^HOC5326Ntd6981 472#2-Jui/;#4"4!:VZ\/1*DORTV@J;R0.)| SEELOC SESLOCP@T3C/LGVTQDЬP_GL YмŏT/EfP8FBO1PGN(ګ[~$'7mЫPP+;PRjPZP(Z ѫ(1ѫ91RMV4130-Jul-19$>`,p∖Q9>pdtzod$ZSB--#_OVυJן\UYHSL̻Z]ZN鿅DZZlLDʤO>YYZ0VFBI5ӫ44ԏwJQE4ϫ4$PDATAЫP; }c\ROJ[n+2[ʨ3֨sP@fԫP`0aЫQʤPA˨1ЫP@˨ҭWTÒBX/y6ir?33,KglspEZSAQP1֫ЫP@˨`DEOqTS1`ADEOUTԫ1իO%ER EOUTի޼˄|ADEOUTXˈADEOUTXԫ1ѫ1֫ЫP@˨@ˬЫP)@˨XYYI˨ZZZXYZdXi41G OKA12AS2Jp 230-Juj a}yea17130-LQ brxt1'17>0HCA]8"B&2d2-41wweKPT 4NVO1PP1~P?HTP]WkTOUTPT)޼v NYXYCNVT޼ ޼bXYNRUAX= HTKPNTTOUTPTXYCNVTE$CODE$PDATA$LOCALTKTRNXP  Eww1F011GENFLG0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 GENFLG GENFLGPH[PtPR HGENFLG$CODE$PDATA$bLOCALPJ  X6w7LETIMqF01bLINEXT0ANCHO0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 ANCHO ANCHO:PPPH[мkANSTRL HANCHOANSTR$CODE$PDATA$LOCALww1`F010A1OUT0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-B40N_AL016q 8!9<1 *?q |eyJl/4;0p1:8<VaY)11 FORTQAN S0360NC{3ZIKV0aLR[Ҩ @ мYМVZZW޳XHXH]hh:[VBHK$`м!VՙZYZVDDKYZEaUXXY߬ Xx)XM_*JTSh$ IS0M$RDAVc\$CI` OAL $shE7p@AC¯hNPuWa@31ww1`^F011AOUTST0130-Jul-19 1 15:4>xq`x4?/  {@V 9 1 0c{h :>ycxvv 0[X,11 @B-2*2-/AJYTIiLbW k@I2ASLP$ "%QHT#MGwh o {w|gϯt{ZY2*DJ CYPY(XB[ZRk AL1VYANRAOAi&CMDEa"gTCX$V` ANvVOOVAIӤ P a}EuG10ANSTR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 ANSTR ANSTRP = pf CALPNT= pf CALPNT>CQZf~H & ^ 41j @/ g$̡?W/ H0-E ќ;2ҁU p' y`!%Ȯ$ J`uaGD5[aIi2 =pg11n) Q|DDs!z B9}*Gg#<N"Vd}}Y,a,)PO[Ь`l1\kALFMODD1ZʬʘʜPʬPʔʬʜPʈPʜPPʰЪ|ʰpMOVABSALFMODNEWLINYɬɘPɜPɄPZZZZkkZЫXZXPP ѫ XPPZZHl˄|TOUTSTɄPɜQQPɜPPɬɜZɬZZɬXXѫ 11ԫ ֫ ѫ 1N ZEZPJP$XȜYY$PȜPP(DZJZ,,YȜYY0ѫ(1ի(1ѫ01ի01Ы P@l4ˈTOUTPTЫ(ȬЫ0EȰ1^ȈȄPP8Ы4ZǏdJ<Ǐd<@ŏd@PPdww1F011EMCHAR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 EMCHAR EMCHARtP (lpQl:/P" h{D{_ JPTTGIGEC{P|FGL:NrVZ}E]{"YWCSV!g!Zi`o1HeH/NL{EL/" LJC LKGE{H_{EGNHE{LNLK{EG{ELI5140MeCGbH LJ/h{TUXY6IGL{"CjLKGE{d{EJG|fCfd{EHINCC"N{ENNUCCNCCNLE{LJJCEL{LJC{EGLN"{ENNONNCNNC]{GICoW:"7ZOGE{oWCKeZC]K{GIC6  {EICoW:"8{ErO/""K "K@]{GICGE{`{D_{ECNFG{De"xBILG{EGC8 5yLaC/"UGCGCGE{GE{]{GI@{DE~HU{ {EICM I OII C I IC RrZCH|!TJE{rZI{:3 " RC {ELrZHHq!|O WJQ N6CO\_fmty}.3?HQY`kqw~DOSVYdnw$(.C`!<=>?\]^6DOC` " I3Me " O.I3Mo " DIC` " :IC`6 DI=[z6DIC`PO[Ь\hkkZ kYZYPJ˼Q@A@ ZZԫ ZNʬNʰʬʰNʜ ֫ѫ1ЫP@h$ѫ$ ѫ$~NPZEZPJP(XȜYY(PȜPP,DZJZ00YȜYY4ȜPѫ,P1ի,1ȜPѫ4P1ի41Ы$P@8֫8Ы8P@<PǏd,P=P'CP]P2&fww1`CF010LINEF0130-Jul-1981 15:0830-JuUl-1981 15:08VAX-11 FORTRAN V2.2-40 LINEF LINEFKP PPN[ZʀALFMODTOUTPTY1ʜkʜNʜ\G\PJPʬG\\J\ ʰʬʬkʰʰʬPPPkkPPʬʰQQQЫQQʰPQ ʜPʈPʜPPʰЪ|ʰMOVABSALFMODCWSEND NLINEFALFMODTOUTPTMOVABSCWSEND$CODE$PDATA$ V$LOCALTKTRNXTKPLOTCP3PrPyPPP8PP<PP'ww1@ F010BAKSP0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 BAKSP BAKSP PPPN[ZʀALFMODʠTOUTPTYNʜ\G\iPJPkkʬG\\J\ʰʜʜ ʬЫʬʰ Ы WʰʬʬʰʰʜPʄPޜPPʬʜPPʬʠMOVABSALFMOD} NBAKSPALFMODTOUTPTMOVABS$CODE$PDATA$$LOCALTKTRNXTKPLOTJP"P7PlsPPPPP.P;PP&ww1 k%F01/HOME0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 HOME  XHOMEPP|Q PH[| kTOUTST| MOVABSALFMOD| HHOMETOUTSTMOVABSALFMODT$CODE$PDATA $LOCALTKTRNXTKPLOTP3)PCPTww1.F010ERASE0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 ERAS YE ERASEtP PQ PH[kTOUTST IOWAITRECOVRn HERASETOUTSTIOWAITRECOVR)$CODE$PDATA$LOCALTKPLOTP )ww1&3F011RECOVR0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 RECOVR RECOVR PPH[\Ьxk̴ Z̰̀ALFMOD MOVABS̠CWSENDѫѫϫALFMODPNTMODkxz HRECOVRALFMODMOVABSCWSENDPNTMOD}$CODE$PDATA$LOCALTKTRNX<:PGPQP[P ]P_PaP cPmP}ww17F011NEWPAG0130-Jul-1981 15:0830-Jul-1981 15:08VAX-11 FORTRAN V2.2-40 NEWPAG [NEWPAGP P|Q PH[ALFMODkTOUTST IOWAIT| MOVABSALFMOD| HNEWPAGALFMODTOUTSTIOWAITMOVABSu$CODE$PDATA($LOCALTKTRNXTKPLOTP.PAPIPZPuww1N