Prediction results legend pp - predicted # of base-pairs cp - predicted # of base-pairs that are correct incp - predicted # of base-pairs that are incorrect pu - predicted # of unpaired bases cu - predicted # of unpaired bases that are correct incu - predicted # of unpaired bases that are incorrect aaaa and bbbb represent that the base-pairing partner is the same as expected. Pairing partner 0 means unpaired. true pairs: 106 true unpairs: 150 pp cp incp pu cu incu ilm 126 93 33 110 94 16 mwm 171 73 98 20 16 4 tmRNA.e.coli.bpseq ilm.pairs.nogap mwm.pairs.nogap 1 359 aaaa bbbb 2 358 aaaa bbbb 3 357 aaaa bbbb 4 356 aaaa bbbb 5 355 aaaa bbbb 6 354 aaaa bbbb 7 353 aaaa bbbb 8 0 347 16 9 0 346 345 10 0 aaaa 155 11 0 345 346 12 0 344 360 13 0 343 343 14 0 342 342 15 0 341 341 16 0 340 8 17 0 339 344 18 0 338 338 19 0 337 348 20 0 aaaa 347 21 332 aaaa 351 22 331 aaaa bbbb 23 330 aaaa bbbb 24 329 aaaa bbbb 25 328 aaaa bbbb 26 327 aaaa bbbb 27 326 aaaa 285 28 325 aaaa 322 29 0 324 111 30 0 aaaa 108 31 0 aaaa 89 32 0 aaaa 232 33 0 aaaa bbbb 34 320 aaaa 288 35 0 319 339 36 318 aaaa bbbb 37 317 aaaa bbbb 38 316 296 39 315 153 40 314 aaaa bbbb 41 313 aaaa bbbb 42 312 309 92 43 311 308 91 44 307 aaaa bbbb 45 306 aaaa bbbb 46 305 aaaa bbbb 47 304 aaaa bbbb 48 303 aaaa bbbb 49 67 aaaa bbbb 50 66 aaaa bbbb 51 65 aaaa bbbb 52 64 aaaa bbbb 53 63 aaaa bbbb 54 0 aaaa bbbb 55 78 aaaa bbbb 56 77 aaaa bbbb 57 76 aaaa bbbb 58 75 aaaa bbbb 59 74 aaaa bbbb 60 73 0 163 61 0 aaaa 292 62 0 aaaa 126 63 53 aaaa bbbb 64 52 aaaa bbbb 65 51 aaaa bbbb 66 50 aaaa bbbb 67 49 aaaa bbbb 68 0 aaaa 94 69 0 aaaa 237 70 0 aaaa 120 71 0 aaaa bbbb 72 0 aaaa 291 73 60 0 83 74 59 aaaa bbbb 75 58 aaaa bbbb 76 57 aaaa bbbb 77 56 aaaa bbbb 78 55 aaaa bbbb 79 0 aaaa bbbb 80 0 aaaa bbbb 81 0 aaaa 290 82 0 aaaa bbbb 83 0 aaaa 73 84 0 aaaa 122 85 0 aaaa 301 86 0 aaaa 300 87 0 98 229 88 0 97 97 89 0 96 31 90 0 95 95 91 0 aaaa 43 92 0 aaaa 42 93 0 aaaa bbbb 94 0 aaaa 68 95 0 90 90 96 0 89 183 97 0 88 88 98 0 87 332 99 0 aaaa 107 100 0 aaaa 198 101 0 aaaa 149 102 0 aaaa bbbb 103 0 aaaa bbbb 104 0 aaaa 134 105 0 aaaa 309 106 0 aaaa 308 107 0 aaaa 99 108 137 0 30 109 136 aaaa 200 110 135 aaaa 323 111 134 aaaa 29 112 133 aaaa 231 113 132 aaaa 246 114 130 aaaa bbbb 115 129 aaaa bbbb 116 128 aaaa 325 117 127 aaaa bbbb 118 0 126 150 119 0 125 225 120 0 124 70 121 0 aaaa 161 122 0 aaaa 84 123 0 aaaa 247 124 0 120 289 125 0 119 326 126 0 118 62 127 117 aaaa bbbb 128 116 aaaa 284 129 115 aaaa bbbb 130 114 aaaa bbbb 131 0 aaaa 235 132 113 aaaa 239 133 112 aaaa 321 134 111 aaaa 104 135 110 aaaa 171 136 109 aaaa 151 137 108 0 0 138 181 aaaa bbbb 139 180 aaaa bbbb 140 179 aaaa bbbb 141 178 aaaa bbbb 142 177 aaaa bbbb 143 176 aaaa bbbb 144 175 aaaa bbbb 145 170 aaaa bbbb 146 169 aaaa bbbb 147 168 aaaa bbbb 148 167 aaaa bbbb 149 0 166 101 150 0 aaaa 118 151 164 0 136 152 163 0 0 153 162 0 39 154 0 aaaa 186 155 0 aaaa 10 156 0 197 166 157 196 aaaa bbbb 158 195 aaaa bbbb 159 194 aaaa bbbb 160 193 aaaa bbbb 161 192 aaaa 121 162 153 191 191 163 152 190 60 164 151 0 185 165 0 aaaa 236 166 0 149 156 167 148 aaaa bbbb 168 147 aaaa bbbb 169 146 aaaa bbbb 170 145 aaaa bbbb 171 0 aaaa 135 172 0 aaaa 190 173 0 aaaa 223 174 0 aaaa 222 175 144 aaaa bbbb 176 143 aaaa bbbb 177 142 aaaa bbbb 178 141 aaaa bbbb 179 140 aaaa bbbb 180 139 aaaa bbbb 181 138 aaaa bbbb 182 0 aaaa 294 183 0 aaaa 96 184 0 aaaa bbbb 185 0 aaaa 164 186 0 aaaa 154 187 0 aaaa 205 188 0 aaaa 204 189 0 aaaa 337 190 0 163 172 191 0 162 162 192 161 aaaa 0 193 160 aaaa bbbb 194 159 aaaa bbbb 195 158 aaaa bbbb 196 157 aaaa bbbb 197 0 156 bbbb 198 0 aaaa 100 199 0 230 315 200 229 aaaa 109 201 228 aaaa bbbb 202 227 aaaa bbbb 203 226 aaaa bbbb 204 0 aaaa 188 205 0 aaaa 187 206 0 aaaa 233 207 222 aaaa 230 208 221 aaaa bbbb 209 220 aaaa bbbb 210 219 aaaa bbbb 211 0 237 274 212 0 236 218 213 245 aaaa bbbb 214 244 aaaa bbbb 215 243 aaaa bbbb 216 242 aaaa bbbb 217 241 aaaa bbbb 218 240 aaaa 212 219 210 aaaa bbbb 220 209 aaaa bbbb 221 208 aaaa bbbb 222 207 aaaa 174 223 0 aaaa 173 224 0 aaaa 264 225 0 aaaa 119 226 203 aaaa bbbb 227 202 aaaa bbbb 228 201 aaaa bbbb 229 200 aaaa 87 230 0 199 207 231 0 aaaa 112 232 0 aaaa 32 233 0 aaaa 206 234 0 aaaa bbbb 235 0 aaaa 131 236 0 212 165 237 0 211 69 238 0 aaaa 257 239 0 aaaa 132 240 218 aaaa 316 241 217 aaaa bbbb 242 216 aaaa bbbb 243 215 aaaa bbbb 244 214 aaaa bbbb 245 213 aaaa bbbb 246 0 aaaa 113 247 0 aaaa 123 248 283 aaaa bbbb 249 282 aaaa bbbb 250 281 aaaa bbbb 251 280 aaaa bbbb 252 279 aaaa bbbb 253 278 aaaa bbbb 254 277 aaaa bbbb 255 276 aaaa bbbb 256 275 aaaa 287 257 274 aaaa 238 258 0 273 275 259 272 aaaa bbbb 260 271 aaaa bbbb 261 270 aaaa bbbb 262 0 aaaa 336 263 299 aaaa 335 264 298 aaaa 224 265 297 aaaa bbbb 266 0 296 324 267 295 aaaa bbbb 268 294 aaaa 334 269 293 aaaa 333 270 261 aaaa bbbb 271 260 aaaa bbbb 272 259 aaaa bbbb 273 0 258 bbbb 274 257 aaaa 211 275 256 aaaa 258 276 255 aaaa bbbb 277 254 aaaa bbbb 278 253 aaaa bbbb 279 252 aaaa bbbb 280 251 aaaa bbbb 281 250 aaaa bbbb 282 249 aaaa bbbb 283 248 aaaa bbbb 284 0 aaaa 128 285 0 aaaa 27 286 0 aaaa bbbb 287 0 aaaa 256 288 0 aaaa 34 289 0 aaaa 124 290 0 aaaa 81 291 0 aaaa 72 292 0 aaaa 61 293 269 aaaa 0 294 268 aaaa 182 295 267 aaaa bbbb 296 0 266 38 297 265 aaaa bbbb 298 264 aaaa 311 299 263 aaaa 310 300 0 aaaa 86 301 0 aaaa 85 302 0 aaaa bbbb 303 48 aaaa bbbb 304 47 aaaa bbbb 305 46 aaaa bbbb 306 45 aaaa bbbb 307 44 aaaa bbbb 308 0 43 106 309 0 42 105 310 0 aaaa 299 311 43 0 298 312 42 0 320 313 41 aaaa bbbb 314 40 aaaa bbbb 315 0 39 199 316 0 38 240 317 37 aaaa bbbb 318 36 aaaa bbbb 319 0 35 bbbb 320 34 aaaa 312 321 0 aaaa 133 322 0 aaaa 28 323 0 aaaa 110 324 0 29 266 325 28 aaaa 116 326 27 aaaa 125 327 26 aaaa bbbb 328 25 aaaa bbbb 329 24 aaaa bbbb 330 23 aaaa bbbb 331 22 aaaa bbbb 332 21 aaaa 98 333 0 aaaa 269 334 0 aaaa 268 335 0 aaaa 263 336 352 0 262 337 351 19 189 338 350 18 18 339 349 17 35 340 348 16 349 341 0 15 15 342 0 14 14 343 0 13 13 344 0 12 17 345 0 11 9 346 0 9 11 347 0 8 20 348 340 0 19 349 339 0 340 350 338 0 361 351 337 0 21 352 336 0 362 353 7 aaaa bbbb 354 6 aaaa bbbb 355 5 aaaa bbbb 356 4 aaaa bbbb 357 3 aaaa bbbb 358 2 aaaa bbbb 359 1 aaaa bbbb 360 0 aaaa 12 361 0 aaaa 350 362 0 aaaa 352