**************************************************************************** File name: 7ptk.pdb no. of DNA/RNA chains: 1 [B=720] no. of nucleotides: 720 no. of atoms: 23080 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 359 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.G1 B.C355 G-C WC 19-XIX cWW cW-W 2 B.G2 B.C354 G-C WC 19-XIX cWW cW-W 3 B.G3 B.C353 G-C WC 19-XIX cWW cW-W 4 B.A4 B.U352 A-U WC 20-XX cWW cW-W 5 B.G5 B.C351 G-C WC 19-XIX cWW cW-W 6 B.A6 B.U350 A-U WC 20-XX cWW cW-W 7 B.G7 B.C349 G-C WC 19-XIX cWW cW-W 8 B.U8 B.G348 U-G Wobble 28-XXVIII cWW cW-W 9 B.A9 B.U347 A-U WC 20-XX cWW cW-W 10 B.C10 B.G346 C-G WC 19-XIX cWW cW-W 11 B.U11 B.G345 U-G Wobble 28-XXVIII cWW cW-W 12 B.A12 B.U344 A-U WC 20-XX cWW cW-W 13 B.U13 B.A343 U-A WC 20-XX cWW cW-W 14 B.U14 B.G342 U-G -- -- cWW cW-W 15 B.C15 B.G341 C-G WC 19-XIX cWW cW-W 16 B.A16 B.U50 A-U WC 20-XX cWW cW-W 17 B.G17 B.C49 G-C WC 19-XIX cWW cW-W 18 B.A18 B.U48 A-U WC 20-XX cWW cW-W 19 B.U19 B.A47 U-A WC 20-XX cWW cW-W 20 B.G20 B.C46 G-C WC 19-XIX cWW cW-W 21 B.C21 B.G45 C-G WC 19-XIX cWW cW-W 22 B.A22 B.U44 A-U WC 20-XX cWW cW-W 23 B.G23 B.U43 G-U Wobble 28-XXVIII cWW cW-W 24 B.A24 B.U42 A-U WC 20-XX cWW cW-W 25 B.C25 B.G41 C-G WC 19-XIX cWW cW-W 26 B.C26 B.G40 C-G WC 19-XIX cWW cW-W 27 B.G27 B.C39 G-C WC 19-XIX cWW cW-W 28 B.C28 B.G38 C-G WC 19-XIX cWW cW-W 29 B.A29 B.A37 A+A -- -- cWH cW+M 30 B.A30 B.C34 A-C -- -- cHH cM-M 31 B.A30 B.U524 A+U -- -- cWH cW+M 32 B.A30 B.G525 A+G -- -- .HH .M+M 33 B.G31 B.C528 G-C WC 19-XIX cWW cW-W 34 B.U32 B.A522 U+A -- -- cH. cM+. 35 B.U32 B.A527 U-A WC 20-XX cWW cW-W 36 B.U33 B.A526 U-A WC 20-XX cWW cW-W 37 B.C34 B.G525 C-G WC 19-XIX cWW cW-W 38 B.A35 B.U524 A-U WC 20-XX cWW cW-W 39 B.G36 B.C523 G-C WC 19-XIX cWW cW-W 40 B.A51 B.U74 A-U WC 20-XX cWW cW-W 41 B.G52 B.C73 G-C WC 19-XIX cWW cW-W 42 B.G53 B.C72 G-C WC 19-XIX cWW cW-W 43 B.G54 B.U71 G-U Wobble 28-XXVIII cWW cW-W 44 B.U55 B.A70 U-A WC 20-XX cWW cW-W 45 B.A56 B.U69 A-U WC 20-XX cWW cW-W 46 B.C57 B.G68 C-G WC 19-XIX cWW cW-W 47 B.G58 B.C67 G-C WC 19-XIX cWW cW-W 48 B.U59 B.A66 U-A WC 20-XX cWW cW-W 49 B.U60 B.A65 U-A WC 20-XX cWW cW-W 50 B.U61 B.G64 U+G -- -- tSW tm+W 51 B.C75 B.G340 C-G WC 19-XIX cWW cW-W 52 B.C76 B.G339 C-G WC 19-XIX cWW cW-W 53 B.G77 B.C338 G-C WC 19-XIX cWW cW-W 54 B.A78 B.U101 A-U WC 20-XX cWW cW-W 55 B.C79 B.G100 C-G WC 19-XIX cWW cW-W 56 B.U80 B.A99 U-A WC 20-XX cWW cW-W 57 B.A81 B.U98 A-U WC 20-XX cWW cW-W 58 B.A82 B.U97 A-U WC 20-XX cWW cW-W 59 B.G83 B.C96 G-C WC 19-XIX cWW cW-W 60 B.U84 B.A95 U-A WC 20-XX cWW cW-W 61 B.G85 B.U94 G-U Wobble 28-XXVIII cWW cW-W 62 B.U86 B.A93 U-A WC 20-XX cWW cW-W 63 B.A87 B.U92 A-U WC 20-XX cWW cW-W 64 B.U88 B.G91 U+G -- -- tSW tm+W 65 B.G102 B.C308 G-C WC 19-XIX cWW cW-W 66 B.C103 B.G307 C-G WC 19-XIX cWW cW-W 67 B.C104 B.G306 C-G WC 19-XIX cWW cW-W 68 B.U105 B.A128 U-A WC 20-XX cWW cW-W 69 B.U106 B.G127 U-G Wobble 28-XXVIII cWW cW-W 70 B.G107 B.U126 G-U -- -- cWW cW-W 71 B.U108 B.A125 U-A WC 20-XX cWW cW-W 72 B.U108 B.U126 U-U -- 16-XVI cWW cW-W 73 B.G109 B.C124 G-C WC 19-XIX cWW cW-W 74 B.C110 B.G123 C-G WC 19-XIX cWW cW-W 75 B.C111 B.G122 C-G WC 19-XIX cWW cW-W 76 B.U112 B.A121 U-A WC 20-XX cWW cW-W 77 B.G113 B.C120 G-C WC 19-XIX cWW cW-W 78 B.C114 B.G119 C-G WC 19-XIX cWW cW-W 79 B.U115 B.G118 U+G -- -- tSW tm+W 80 B.C129 B.G276 C-G WC 19-XIX cWW cW-W 81 B.C130 B.G275 C-G WC 19-XIX cWW cW-W 82 B.C131 B.G274 C-G WC 19-XIX cWW cW-W 83 B.A132 B.U155 A-U WC 20-XX cWW cW-W 84 B.A133 B.U154 A-U WC 20-XX cWW cW-W 85 B.A134 B.U153 A-U WC 20-XX cWW cW-W 86 B.U135 B.A152 U-A WC 20-XX cWW cW-W 87 B.G136 B.C151 G-C WC 19-XIX cWW cW-W 88 B.U137 B.A150 U-A WC 20-XX cWW cW-W 89 B.G138 B.C149 G-C WC 19-XIX cWW cW-W 90 B.C139 B.G148 C-G WC 19-XIX cWW cW-W 91 B.C140 B.G147 C-G WC 19-XIX cWW cW-W 92 B.U141 B.G146 U-G Wobble 28-XXVIII cWW cW-W 93 B.U142 B.G145 U+G -- -- tSW tm+W 94 B.C156 B.G244 C-G WC 19-XIX cWW cW-W 95 B.C157 B.G243 C-G WC 19-XIX cWW cW-W 96 B.G158 B.C242 G-C WC 19-XIX cWW cW-W 97 B.G159 B.U182 G-U Wobble 28-XXVIII cWW cW-W 98 B.U160 B.A181 U-A WC 20-XX cWW cW-W 99 B.C161 B.G180 C-G WC 19-XIX cWW cW-W 100 B.A162 B.U179 A-U WC 20-XX cWW cW-W 101 B.U163 B.G178 U-G Wobble 28-XXVIII cWW cW-W 102 B.C164 B.G177 C-G WC 19-XIX cWW cW-W 103 B.C165 B.G176 C-G WC 19-XIX cWW cW-W 104 B.A166 B.U175 A-U WC 20-XX cWW cW-W 105 B.A167 B.U174 A-U WC 20-XX cWW cW-W 106 B.G168 B.C173 G-C WC 19-XIX cWW cW-W 107 B.U169 B.G172 U+G -- -- tSW tm+W 108 B.G183 B.C212 G-C WC 19-XIX cWW cW-W 109 B.C184 B.G211 C-G WC 19-XIX cWW cW-W 110 B.G185 B.C210 G-C WC 19-XIX cWW cW-W 111 B.G186 B.C209 G-C WC 19-XIX cWW cW-W 112 B.G187 B.U208 G-U Wobble 28-XXVIII cWW cW-W 113 B.C188 B.G207 C-G WC 19-XIX cWW cW-W 114 B.G189 B.C206 G-C WC 19-XIX cWW cW-W 115 B.U190 B.A205 U-A WC 20-XX cWW cW-W 116 B.A191 B.U204 A-U WC 20-XX cWW cW-W 117 B.U192 B.A203 U-A WC 20-XX cWW cW-W 118 B.A193 B.U202 A-U WC 20-XX cWW cW-W 119 B.G194 B.C201 G-C WC 19-XIX cWW cW-W 120 B.G195 B.U200 G-U Wobble 28-XXVIII cWW cW-W 121 B.U196 B.G199 U+G -- -- tSW tm+W 122 B.G213 B.C241 G-C WC 19-XIX cWW cW-W 123 B.U214 B.A240 U-A WC 20-XX cWW cW-W 124 B.U215 B.A239 U-A WC 20-XX cWW cW-W 125 B.U216 B.A238 U-A WC 20-XX cWW cW-W 126 B.U217 B.G237 U-G Wobble 28-XXVIII cWW cW-W 127 B.C218 B.G236 C-G WC 19-XIX cWW cW-W 128 B.C219 B.G235 C-G WC 19-XIX cWW cW-W 129 B.G220 B.C234 G-C WC 19-XIX cWW cW-W 130 B.A221 B.U233 A-U WC 20-XX cWW cW-W 131 B.G222 B.C232 G-C WC 19-XIX cWW cW-W 132 B.A223 B.A231 A+A -- 01-I tWW tW+W 133 B.G225 B.A488 G+A -- -- cHW cM+W 134 B.G225 B.C494 G-C WC 19-XIX cWW cW-W 135 B.A226 B.U493 A-U WC 20-XX cWW cW-W 136 B.G227 B.C492 G-C WC 19-XIX cWW cW-W 137 B.G228 B.C491 G-C WC 19-XIX cWW cW-W 138 B.U229 B.A490 U-A WC 20-XX cWW cW-W 139 B.A230 B.U489 A-U WC 20-XX cWW cW-W 140 B.U245 B.A273 U-A WC 20-XX cWW cW-W 141 B.C246 B.G272 C-G WC 19-XIX cWW cW-W 142 B.C247 B.G271 C-G WC 19-XIX cWW cW-W 143 B.A248 B.U270 A-U WC 20-XX cWW cW-W 144 B.C249 B.G269 C-G WC 19-XIX cWW cW-W 145 B.G250 B.C268 G-C WC 19-XIX cWW cW-W 146 B.U251 B.A267 U-A WC 20-XX cWW cW-W 147 B.G252 B.U266 G-U Wobble 28-XXVIII cWW cW-W 148 B.A253 B.U265 A-U WC 20-XX cWW cW-W 149 B.C254 B.G264 C-G WC 19-XIX cWW cW-W 150 B.A255 B.A263 A+A -- 01-I tWW tW+W 151 B.A257 B.A454 A+A -- -- cHW cM+W 152 B.A257 B.U460 A-U WC 20-XX cWW cW-W 153 B.G258 B.C459 G-C WC 19-XIX cWW cW-W 154 B.G259 B.C458 G-C WC 19-XIX cWW cW-W 155 B.U260 B.A457 U-A WC 20-XX cWW cW-W 156 B.A261 B.U456 A-U WC 20-XX cWW cW-W 157 B.G262 B.C455 G-C WC 19-XIX cWW cW-W 158 B.A277 B.U305 A-U WC 20-XX cWW cW-W 159 B.G278 B.C304 G-C WC 19-XIX cWW cW-W 160 B.C279 B.G303 C-G WC 19-XIX cWW cW-W 161 B.A280 B.U302 A-U WC 20-XX cWW cW-W 162 B.G281 B.U301 G-U Wobble 28-XXVIII cWW cW-W 163 B.C282 B.G300 C-G WC 19-XIX cWW cW-W 164 B.U283 B.A299 U-A WC 20-XX cWW cW-W 165 B.G284 B.C298 G-C WC 19-XIX cWW cW-W 166 B.C285 B.G297 C-G WC 19-XIX cWW cW-W 167 B.A287 B.U296 A-U rHoogsteen 24-XXIV tHW tM-W 168 B.A288 B.U293 A-U -- -- cW. cW-. 169 B.A288 B.A422 A+A -- -- cWH cW+M 170 B.G289 B.C426 G-C WC 19-XIX cWW cW-W 171 B.G290 B.A420 G+A -- 09-IX cHW cM+W 172 B.G290 B.C425 G-C WC 19-XIX cWW cW-W 173 B.G291 B.C424 G-C ~Wobble -- cWW cW-W 174 B.A292 B.U423 A-U WC 20-XX cWW cW-W 175 B.U293 B.A422 U-A WC 20-XX cWW cW-W 176 B.A294 B.U421 A-U WC 20-XX cWW cW-W 177 B.U309 B.A337 U-A WC 20-XX cWW cW-W 178 B.G310 B.U336 G-U Wobble 28-XXVIII cWW cW-W 179 B.G311 B.C335 G-C WC 19-XIX cWW cW-W 180 B.A312 B.U334 A-U WC 20-XX cWW cW-W 181 B.U313 B.A333 U-A WC 20-XX cWW cW-W 182 B.G314 B.C332 G-C WC 19-XIX cWW cW-W 183 B.C315 B.G331 C-G WC 19-XIX cWW cW-W 184 B.C316 B.G330 C-G WC 19-XIX cWW cW-W 185 B.A317 B.U329 A-U WC 20-XX cWW cW-W 186 B.G318 B.C328 G-C WC 19-XIX cWW cW-W 187 B.A319 B.A327 A+A -- 01-I tWW tW+W 188 B.A320 B.G388 A+G -- -- .WH .W+M 189 B.A320 B.U389 A+U -- -- -- -- 190 B.C321 B.A386 C+A -- -- cHW cM+W 191 B.C321 B.G392 C-G WC 19-XIX cWW cW-W 192 B.U322 B.A391 U-A WC 20-XX cWW cW-W 193 B.C323 B.G390 C-G WC 19-XIX cWW cW-W 194 B.A324 B.U389 A-U WC 20-XX cWW cW-W 195 B.C325 B.G388 C-G WC 19-XIX cWW cW-W 196 B.G326 B.C387 G-C WC 19-XIX cWW cW-W 197 B.A356 B.U720 A-U WC 20-XX cWW cW-W 198 B.A357 B.U719 A-U WC 20-XX cWW cW-W 199 B.U358 B.A718 U-A WC 20-XX cWW cW-W 200 B.U359 B.A717 U-A WC 20-XX cWW cW-W 201 B.C360 B.G716 C-G WC 19-XIX cWW cW-W 202 B.U361 B.A715 U-A WC 20-XX cWW cW-W 203 B.C362 B.G714 C-G WC 19-XIX cWW cW-W 204 B.C363 B.G713 C-G WC 19-XIX cWW cW-W 205 B.A364 B.U712 A-U WC 20-XX cWW cW-W 206 B.U365 B.A711 U-A WC 20-XX cWW cW-W 207 B.U366 B.G710 U-G Wobble 28-XXVIII cWW cW-W 208 B.U367 B.A709 U-A WC 20-XX cWW cW-W 209 B.A368 B.U708 A-U WC 20-XX cWW cW-W 210 B.C369 B.G707 C-G WC 19-XIX cWW cW-W 211 B.C370 B.G706 C-G WC 19-XIX cWW cW-W 212 B.G371 B.C651 G-C WC 19-XIX cWW cW-W 213 B.C372 B.G650 C-G WC 19-XIX cWW cW-W 214 B.C373 B.G649 C-G WC 19-XIX cWW cW-W 215 B.G374 B.C404 G-C WC 19-XIX cWW cW-W 216 B.A375 B.U403 A-U WC 20-XX cWW cW-W 217 B.A376 B.U402 A-U WC 20-XX cWW cW-W 218 B.U377 B.G401 U-G Wobble 28-XXVIII cWW cW-W 219 B.C378 B.G400 C-G WC 19-XIX cWW cW-W 220 B.G379 B.C399 G-C WC 19-XIX cWW cW-W 221 B.A380 B.U398 A-U WC 20-XX cWW cW-W 222 B.C381 B.G397 C-G WC 19-XIX cWW cW-W 223 B.C382 B.G396 C-G WC 19-XIX cWW cW-W 224 B.C383 B.G395 C-G WC 19-XIX cWW cW-W 225 B.C384 B.G394 C-G WC 19-XIX cWW cW-W 226 B.A385 B.A393 A+A -- -- cWH cW+M 227 B.A386 B.G392 A-G -- -- -- -- 228 B.C405 B.G624 C-G WC 19-XIX cWW cW-W 229 B.C406 B.G623 C-G WC 19-XIX cWW cW-W 230 B.C407 B.G622 C-G WC 19-XIX cWW cW-W 231 B.G408 B.C438 G-C WC 19-XIX cWW cW-W 232 B.A409 B.U437 A-U WC 20-XX cWW cW-W 233 B.G410 B.C436 G-C WC 19-XIX cWW cW-W 234 B.C411 B.G435 C-G WC 19-XIX cWW cW-W 235 B.A412 B.U434 A-U WC 20-XX cWW cW-W 236 B.U413 B.A433 U-A WC 20-XX cWW cW-W 237 B.U413 B.U434 U-U -- 16-XVI cWW cW-W 238 B.A414 B.U432 A-U WC 20-XX cWW cW-W 239 B.G415 B.U431 G-U Wobble 28-XXVIII cWW cW-W 240 B.A416 B.U430 A-U WC 20-XX cWW cW-W 241 B.C417 B.G429 C-G WC 19-XIX cWW cW-W 242 B.C418 B.G428 C-G WC 19-XIX cWW cW-W 243 B.A419 B.A427 A+A -- 01-I tWW tW+W 244 B.C439 B.G597 C-G WC 19-XIX cWW cW-W 245 B.C440 B.G596 C-G WC 19-XIX cWW cW-W 246 B.C441 B.G595 C-G WC 19-XIX cWW cW-W 247 B.A442 B.U472 A-U WC 20-XX cWW cW-W 248 B.A443 B.U471 A-U WC 20-XX cWW cW-W 249 B.C444 B.G470 C-G WC 19-XIX cWW cW-W 250 B.G445 B.C469 G-C WC 19-XIX cWW cW-W 251 B.C446 B.G468 C-G WC 19-XIX cWW cW-W 252 B.U447 B.A467 U-A WC 20-XX cWW cW-W 253 B.G448 B.U466 G-U -- -- cWW cW-W 254 B.G449 B.C465 G-C WC 19-XIX cWW cW-W 255 B.A450 B.U464 A-U WC 20-XX cWW cW-W 256 B.C451 B.G463 C-G WC 19-XIX cWW cW-W 257 B.G452 B.C462 G-C WC 19-XIX cWW cW-W 258 B.A453 B.A461 A+A -- 01-I tWW tW+W 259 B.C473 B.G570 C-G WC 19-XIX cWW cW-W 260 B.C474 B.G569 C-G WC 19-XIX cWW cW-W 261 B.G475 B.C568 G-C WC 19-XIX cWW cW-W 262 B.G476 B.C506 G-C WC 19-XIX cWW cW-W 263 B.C477 B.G505 C-G WC 19-XIX cWW cW-W 264 B.A478 B.U504 A-U WC 20-XX cWW cW-W 265 B.A479 B.U503 A-U WC 20-XX cWW cW-W 266 B.A480 B.U502 A-U WC 20-XX cWW cW-W 267 B.U481 B.A501 U-A WC 20-XX cWW cW-W 268 B.G482 B.U500 G-U -- -- cWW cW-W 269 B.A483 B.U499 A-U WC 20-XX cWW cW-W 270 B.G484 B.C498 G-C WC 19-XIX cWW cW-W 271 B.U485 B.A497 U-A WC 20-XX cWW cW-W 272 B.C486 B.G496 C-G WC 19-XIX cWW cW-W 273 B.A487 B.A495 A+A -- 01-I tWW tW+W 274 B.G507 B.C543 G-C WC 19-XIX cWW cW-W 275 B.G508 B.U542 G-U Wobble 28-XXVIII cWW cW-W 276 B.U509 B.A541 U-A WC 20-XX cWW cW-W 277 B.G510 B.C540 G-C WC 19-XIX cWW cW-W 278 B.C511 B.G539 C-G WC 19-XIX cWW cW-W 279 B.C512 B.G538 C-G WC 19-XIX cWW cW-W 280 B.U513 B.A537 U-A WC 20-XX cWW cW-W 281 B.G514 B.C536 G-C WC 19-XIX cWW cW-W 282 B.A515 B.U535 A-U WC 20-XX cWW cW-W 283 B.G516 B.U534 G-U -- -- cWW cW-W 284 B.C517 B.G533 C-G WC 19-XIX cWW cW-W 285 B.C518 B.G532 C-G WC 19-XIX cWW cW-W 286 B.U519 B.G531 U-G Wobble 28-XXVIII cWW cW-W 287 B.A520 B.U530 A-U WC 20-XX cWW cW-W 288 B.A521 B.A529 A-A -- -- ..W ..-W 289 B.U544 B.A567 U-A WC 20-XX cWW cW-W 290 B.U545 B.G566 U+G rWobble 27-XXVII tWW tW+W 291 B.G546 B.C565 G-C WC 19-XIX cWW cW-W 292 B.G547 B.C564 G-C WC 19-XIX cWW cW-W 293 B.C548 B.G563 C-G WC 19-XIX cWW cW-W 294 B.U549 B.A562 U-A WC 20-XX cWW cW-W 295 B.C550 B.G561 C-G WC 19-XIX cWW cW-W 296 B.C551 B.G560 C-G WC 19-XIX cWW cW-W 297 B.A552 B.U559 A-U WC 20-XX cWW cW-W 298 B.G553 B.C558 G-C WC 19-XIX cWW cW-W 299 B.U554 B.G557 U+G -- -- tSW tm+W 300 B.U571 B.A594 U-A WC 20-XX cWW cW-W 301 B.A572 B.U593 A-U WC 20-XX cWW cW-W 302 B.G573 B.C592 G-C WC 19-XIX cWW cW-W 303 B.C574 B.G591 C-G WC 19-XIX cWW cW-W 304 B.G575 B.U590 G-U -- -- cWW cW-W 305 B.C576 B.G589 C-G WC 19-XIX cWW cW-W 306 B.C576 B.U590 C-U -- -- cWW cW-W 307 B.U577 B.A588 U-A WC 20-XX cWW cW-W 308 B.G578 B.C587 G-C WC 19-XIX cWW cW-W 309 B.C579 B.G586 C-G WC 19-XIX cWW cW-W 310 B.G580 B.C585 G-C WC 19-XIX cWW cW-W 311 B.U581 B.G584 U+G -- -- tSW tm+W 312 B.A598 B.U621 A-U WC 20-XX cWW cW-W 313 B.G599 B.C620 G-C WC 19-XIX cWW cW-W 314 B.C600 B.G619 C-G WC 19-XIX cWW cW-W 315 B.A601 B.U618 A-U WC 20-XX cWW cW-W 316 B.U602 B.A617 U-A WC 20-XX cWW cW-W 317 B.C603 B.G616 C-G WC 19-XIX cWW cW-W 318 B.C604 B.G615 C-G WC 19-XIX cWW cW-W 319 B.G605 B.C614 G-C WC 19-XIX cWW cW-W 320 B.U606 B.G613 U-G -- -- cWW cW-W 321 B.U607 B.A612 U-A WC 20-XX cWW cW-W 322 B.U608 B.G611 U+G -- -- tSW tm+W 323 B.C625 B.G648 C-G WC 19-XIX cWW cW-W 324 B.G626 B.C647 G-C WC 19-XIX cWW cW-W 325 B.G627 B.U646 G-U -- -- cWW cW-W 326 B.U628 B.A645 U-A WC 20-XX cWW cW-W 327 B.U628 B.U646 U-U -- 16-XVI cWW cW-W 328 B.U629 B.A644 U-A WC 20-XX cWW cW-W 329 B.G630 B.C643 G-C WC 19-XIX cWW cW-W 330 B.C631 B.G642 C-G WC 19-XIX cWW cW-W 331 B.C632 B.G641 C-G WC 19-XIX cWW cW-W 332 B.U633 B.A640 U-A WC 20-XX cWW cW-W 333 B.G634 B.C639 G-C WC 19-XIX cWW cW-W 334 B.U635 B.G638 U+G -- -- tSW tm+W 335 B.C652 B.G675 C-G WC 19-XIX cWW cW-W 336 B.U653 B.G674 U-G Wobble 28-XXVIII cWW cW-W 337 B.A654 B.U673 A-U WC 20-XX cWW cW-W 338 B.C655 B.G672 C-G WC 19-XIX cWW cW-W 339 B.U656 B.A671 U-A WC 20-XX cWW cW-W 340 B.C657 B.G670 C-G WC 19-XIX cWW cW-W 341 B.A658 B.U669 A-U WC 20-XX cWW cW-W 342 B.U659 B.A668 U-A WC 20-XX cWW cW-W 343 B.G660 B.C667 G-C WC 19-XIX cWW cW-W 344 B.A661 B.U666 A-U WC 20-XX cWW cW-W 345 B.U662 B.G665 U+G -- -- tSW tm+W 346 B.U676 B.G705 U-G Wobble 28-XXVIII cWW cW-W 347 B.G677 B.C704 G-C WC 19-XIX cWW cW-W 348 B.A678 B.U703 A-U WC 20-XX cWW cW-W 349 B.C679 B.G702 C-G WC 19-XIX cWW cW-W 350 B.A680 B.U701 A-U WC 20-XX cWW cW-W 351 B.G681 B.C700 G-C WC 19-XIX cWW cW-W 352 B.C682 B.G699 C-G WC 19-XIX cWW cW-W 353 B.G683 B.C698 G-C WC 19-XIX cWW cW-W 354 B.U684 B.A697 U-A WC 20-XX cWW cW-W 355 B.G685 B.U696 G-U Wobble 28-XXVIII cWW cW-W 356 B.A686 B.U695 A-U WC 20-XX cWW cW-W 357 B.U687 B.A694 U-A WC 20-XX cWW cW-W 358 B.G688 B.C693 G-C WC 19-XIX cWW cW-W 359 B.U689 B.G692 U+G -- -- tSW tm+W **************************************************************************** List of 10 multiplets 1 nts=3 ACG B.A30,B.C34,B.G525 2 nts=3 AAU B.A30,B.A35,B.U524 3 nts=3 UAA B.U32,B.A522,B.A527 4 nts=3 GAC B.G225,B.A488,B.C494 5 nts=3 AAU B.A257,B.A454,B.U460 6 nts=3 AUA B.A288,B.U293,B.A422 7 nts=3 GAC B.G290,B.A420,B.C425 8 nts=3 AAU B.A320,B.A324,B.U389 9 nts=3 ACG B.A320,B.C325,B.G388 10 nts=3 CAG B.C321,B.A386,B.G392 **************************************************************************** List of 6 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[6] bps=57 strand-1 5'-GAACGUAUCCUAGAUGCAGACCGCACUGAACAUGGGUUCAGGCAUCUUGGCUCCAGU-3' bp-type .|||||||||||||||||||||||.||||||.||||.||||||||||.||||||||. strand-2 3'-UUUGCAUGGGAUCUACGUUUGGCGAGACUUGAAUCCGAGUCCGUGGAGCCGAGGUCG-5' helix-form .AA......Ax.A.......AAA.xAA...x.A.A..A.......x..AA..AAA. 1 B.G64 B.U61 G+U -- -- tWS tW+m 2 B.A65 B.U60 A-U WC 20-XX cWW cW-W 3 B.A66 B.U59 A-U WC 20-XX cWW cW-W 4 B.C67 B.G58 C-G WC 19-XIX cWW cW-W 5 B.G68 B.C57 G-C WC 19-XIX cWW cW-W 6 B.U69 B.A56 U-A WC 20-XX cWW cW-W 7 B.A70 B.U55 A-U WC 20-XX cWW cW-W 8 B.U71 B.G54 U-G Wobble 28-XXVIII cWW cW-W 9 B.C72 B.G53 C-G WC 19-XIX cWW cW-W 10 B.C73 B.G52 C-G WC 19-XIX cWW cW-W 11 B.U74 B.A51 U-A WC 20-XX cWW cW-W 12 B.A16 B.U50 A-U WC 20-XX cWW cW-W 13 B.G17 B.C49 G-C WC 19-XIX cWW cW-W 14 B.A18 B.U48 A-U WC 20-XX cWW cW-W 15 B.U19 B.A47 U-A WC 20-XX cWW cW-W 16 B.G20 B.C46 G-C WC 19-XIX cWW cW-W 17 B.C21 B.G45 C-G WC 19-XIX cWW cW-W 18 B.A22 B.U44 A-U WC 20-XX cWW cW-W 19 B.G23 B.U43 G-U Wobble 28-XXVIII cWW cW-W 20 B.A24 B.U42 A-U WC 20-XX cWW cW-W 21 B.C25 B.G41 C-G WC 19-XIX cWW cW-W 22 B.C26 B.G40 C-G WC 19-XIX cWW cW-W 23 B.G27 B.C39 G-C WC 19-XIX cWW cW-W 24 B.C28 B.G38 C-G WC 19-XIX cWW cW-W 25 B.A29 B.A37 A+A -- -- cWH cW+M 26 B.C523 B.G36 C-G WC 19-XIX cWW cW-W 27 B.U524 B.A35 U-A WC 20-XX cWW cW-W 28 B.G525 B.C34 G-C WC 19-XIX cWW cW-W 29 B.A526 B.U33 A-U WC 20-XX cWW cW-W 30 B.A527 B.U32 A-U WC 20-XX cWW cW-W 31 B.C528 B.G31 C-G WC 19-XIX cWW cW-W 32 B.A529 B.A521 A-A -- -- .W. .W-. 33 B.U530 B.A520 U-A WC 20-XX cWW cW-W 34 B.G531 B.U519 G-U Wobble 28-XXVIII cWW cW-W 35 B.G532 B.C518 G-C WC 19-XIX cWW cW-W 36 B.G533 B.C517 G-C WC 19-XIX cWW cW-W 37 B.U534 B.G516 U-G -- -- cWW cW-W 38 B.U535 B.A515 U-A WC 20-XX cWW cW-W 39 B.C536 B.G514 C-G WC 19-XIX cWW cW-W 40 B.A537 B.U513 A-U WC 20-XX cWW cW-W 41 B.G538 B.C512 G-C WC 19-XIX cWW cW-W 42 B.G539 B.C511 G-C WC 19-XIX cWW cW-W 43 B.C540 B.G510 C-G WC 19-XIX cWW cW-W 44 B.A541 B.U509 A-U WC 20-XX cWW cW-W 45 B.U542 B.G508 U-G Wobble 28-XXVIII cWW cW-W 46 B.C543 B.G507 C-G WC 19-XIX cWW cW-W 47 B.U544 B.A567 U-A WC 20-XX cWW cW-W 48 B.U545 B.G566 U+G rWobble 27-XXVII tWW tW+W 49 B.G546 B.C565 G-C WC 19-XIX cWW cW-W 50 B.G547 B.C564 G-C WC 19-XIX cWW cW-W 51 B.C548 B.G563 C-G WC 19-XIX cWW cW-W 52 B.U549 B.A562 U-A WC 20-XX cWW cW-W 53 B.C550 B.G561 C-G WC 19-XIX cWW cW-W 54 B.C551 B.G560 C-G WC 19-XIX cWW cW-W 55 B.A552 B.U559 A-U WC 20-XX cWW cW-W 56 B.G553 B.C558 G-C WC 19-XIX cWW cW-W 57 B.U554 B.G557 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#2[5] bps=58 strand-1 5'-GUAUACUUAGUCGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCUGACAGCGUGAUGU-3' bp-type .||||||||||||||.|||||||||||||||||||||||||||||||||||||||||. strand-2 3'-UAUGUGAAUCAGCCCUUAUCAUGAGAGGGUUAAGAGGUAGAUGGGCUGUCGCAUUACG-5' helix-form .A....AAAAxA.x..A..A......AAxAAAAA......AA.x.....A....AA. 1 B.G91 B.U88 G+U -- -- tWS tW+m 2 B.U92 B.A87 U-A WC 20-XX cWW cW-W 3 B.A93 B.U86 A-U WC 20-XX cWW cW-W 4 B.U94 B.G85 U-G Wobble 28-XXVIII cWW cW-W 5 B.A95 B.U84 A-U WC 20-XX cWW cW-W 6 B.C96 B.G83 C-G WC 19-XIX cWW cW-W 7 B.U97 B.A82 U-A WC 20-XX cWW cW-W 8 B.U98 B.A81 U-A WC 20-XX cWW cW-W 9 B.A99 B.U80 A-U WC 20-XX cWW cW-W 10 B.G100 B.C79 G-C WC 19-XIX cWW cW-W 11 B.U101 B.A78 U-A WC 20-XX cWW cW-W 12 B.C338 B.G77 C-G WC 19-XIX cWW cW-W 13 B.G339 B.C76 G-C WC 19-XIX cWW cW-W 14 B.G340 B.C75 G-C WC 19-XIX cWW cW-W 15 B.G341 B.C15 G-C WC 19-XIX cWW cW-W 16 B.G342 B.U14 G-U -- -- cWW cW-W 17 B.A343 B.U13 A-U WC 20-XX cWW cW-W 18 B.U344 B.A12 U-A WC 20-XX cWW cW-W 19 B.G345 B.U11 G-U Wobble 28-XXVIII cWW cW-W 20 B.G346 B.C10 G-C WC 19-XIX cWW cW-W 21 B.U347 B.A9 U-A WC 20-XX cWW cW-W 22 B.G348 B.U8 G-U Wobble 28-XXVIII cWW cW-W 23 B.C349 B.G7 C-G WC 19-XIX cWW cW-W 24 B.U350 B.A6 U-A WC 20-XX cWW cW-W 25 B.C351 B.G5 C-G WC 19-XIX cWW cW-W 26 B.U352 B.A4 U-A WC 20-XX cWW cW-W 27 B.C353 B.G3 C-G WC 19-XIX cWW cW-W 28 B.C354 B.G2 C-G WC 19-XIX cWW cW-W 29 B.C355 B.G1 C-G WC 19-XIX cWW cW-W 30 B.A356 B.U720 A-U WC 20-XX cWW cW-W 31 B.A357 B.U719 A-U WC 20-XX cWW cW-W 32 B.U358 B.A718 U-A WC 20-XX cWW cW-W 33 B.U359 B.A717 U-A WC 20-XX cWW cW-W 34 B.C360 B.G716 C-G WC 19-XIX cWW cW-W 35 B.U361 B.A715 U-A WC 20-XX cWW cW-W 36 B.C362 B.G714 C-G WC 19-XIX cWW cW-W 37 B.C363 B.G713 C-G WC 19-XIX cWW cW-W 38 B.A364 B.U712 A-U WC 20-XX cWW cW-W 39 B.U365 B.A711 U-A WC 20-XX cWW cW-W 40 B.U366 B.G710 U-G Wobble 28-XXVIII cWW cW-W 41 B.U367 B.A709 U-A WC 20-XX cWW cW-W 42 B.A368 B.U708 A-U WC 20-XX cWW cW-W 43 B.C369 B.G707 C-G WC 19-XIX cWW cW-W 44 B.C370 B.G706 C-G WC 19-XIX cWW cW-W 45 B.U676 B.G705 U-G Wobble 28-XXVIII cWW cW-W 46 B.G677 B.C704 G-C WC 19-XIX cWW cW-W 47 B.A678 B.U703 A-U WC 20-XX cWW cW-W 48 B.C679 B.G702 C-G WC 19-XIX cWW cW-W 49 B.A680 B.U701 A-U WC 20-XX cWW cW-W 50 B.G681 B.C700 G-C WC 19-XIX cWW cW-W 51 B.C682 B.G699 C-G WC 19-XIX cWW cW-W 52 B.G683 B.C698 G-C WC 19-XIX cWW cW-W 53 B.U684 B.A697 U-A WC 20-XX cWW cW-W 54 B.G685 B.U696 G-U Wobble 28-XXVIII cWW cW-W 55 B.A686 B.U695 A-U WC 20-XX cWW cW-W 56 B.U687 B.A694 U-A WC 20-XX cWW cW-W 57 B.G688 B.C693 G-C WC 19-XIX cWW cW-W 58 B.U689 B.G692 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#3[8] bps=57 strand-1 5'-GGCAGGCAUGAGGCUGGAUGCCAGACGUGAGAGGGGUCGGUUCGGCCUACUCAUGAU-3' bp-type .|||||||.|||||||||||||||.||||||.||||||||||||||||||||||||. strand-2 3'-UCGUCCGUGUUCCGAUCUACGGUCAGCACUCACCCCAGCUAAGCCGGGUGAGUACUG-5' helix-form .AAAAAA...x..x..A.AAAA..x..A..x.A...AA..AAx..x..AAAAAAA. 1 B.G118 B.U115 G+U -- -- tWS tW+m 2 B.G119 B.C114 G-C WC 19-XIX cWW cW-W 3 B.C120 B.G113 C-G WC 19-XIX cWW cW-W 4 B.A121 B.U112 A-U WC 20-XX cWW cW-W 5 B.G122 B.C111 G-C WC 19-XIX cWW cW-W 6 B.G123 B.C110 G-C WC 19-XIX cWW cW-W 7 B.C124 B.G109 C-G WC 19-XIX cWW cW-W 8 B.A125 B.U108 A-U WC 20-XX cWW cW-W 9 B.U126 B.G107 U-G -- -- cWW cW-W 10 B.G127 B.U106 G-U Wobble 28-XXVIII cWW cW-W 11 B.A128 B.U105 A-U WC 20-XX cWW cW-W 12 B.G306 B.C104 G-C WC 19-XIX cWW cW-W 13 B.G307 B.C103 G-C WC 19-XIX cWW cW-W 14 B.C308 B.G102 C-G WC 19-XIX cWW cW-W 15 B.U309 B.A337 U-A WC 20-XX cWW cW-W 16 B.G310 B.U336 G-U Wobble 28-XXVIII cWW cW-W 17 B.G311 B.C335 G-C WC 19-XIX cWW cW-W 18 B.A312 B.U334 A-U WC 20-XX cWW cW-W 19 B.U313 B.A333 U-A WC 20-XX cWW cW-W 20 B.G314 B.C332 G-C WC 19-XIX cWW cW-W 21 B.C315 B.G331 C-G WC 19-XIX cWW cW-W 22 B.C316 B.G330 C-G WC 19-XIX cWW cW-W 23 B.A317 B.U329 A-U WC 20-XX cWW cW-W 24 B.G318 B.C328 G-C WC 19-XIX cWW cW-W 25 B.A319 B.A327 A+A -- 01-I tWW tW+W 26 B.C387 B.G326 C-G WC 19-XIX cWW cW-W 27 B.G388 B.C325 G-C WC 19-XIX cWW cW-W 28 B.U389 B.A324 U-A WC 20-XX cWW cW-W 29 B.G390 B.C323 G-C WC 19-XIX cWW cW-W 30 B.A391 B.U322 A-U WC 20-XX cWW cW-W 31 B.G392 B.C321 G-C WC 19-XIX cWW cW-W 32 B.A393 B.A385 A+A -- -- cHW cM+W 33 B.G394 B.C384 G-C WC 19-XIX cWW cW-W 34 B.G395 B.C383 G-C WC 19-XIX cWW cW-W 35 B.G396 B.C382 G-C WC 19-XIX cWW cW-W 36 B.G397 B.C381 G-C WC 19-XIX cWW cW-W 37 B.U398 B.A380 U-A WC 20-XX cWW cW-W 38 B.C399 B.G379 C-G WC 19-XIX cWW cW-W 39 B.G400 B.C378 G-C WC 19-XIX cWW cW-W 40 B.G401 B.U377 G-U Wobble 28-XXVIII cWW cW-W 41 B.U402 B.A376 U-A WC 20-XX cWW cW-W 42 B.U403 B.A375 U-A WC 20-XX cWW cW-W 43 B.C404 B.G374 C-G WC 19-XIX cWW cW-W 44 B.G649 B.C373 G-C WC 19-XIX cWW cW-W 45 B.G650 B.C372 G-C WC 19-XIX cWW cW-W 46 B.C651 B.G371 C-G WC 19-XIX cWW cW-W 47 B.C652 B.G675 C-G WC 19-XIX cWW cW-W 48 B.U653 B.G674 U-G Wobble 28-XXVIII cWW cW-W 49 B.A654 B.U673 A-U WC 20-XX cWW cW-W 50 B.C655 B.G672 C-G WC 19-XIX cWW cW-W 51 B.U656 B.A671 U-A WC 20-XX cWW cW-W 52 B.C657 B.G670 C-G WC 19-XIX cWW cW-W 53 B.A658 B.U669 A-U WC 20-XX cWW cW-W 54 B.U659 B.A668 U-A WC 20-XX cWW cW-W 55 B.G660 B.C667 G-C WC 19-XIX cWW cW-W 56 B.A661 B.U666 A-U WC 20-XX cWW cW-W 57 B.U662 B.G665 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#4[9] bps=56 strand-1 5'-GGGGCACAUUUGGGAGCAGCUGCAUAUCCCAGGUUUAUGCUCGGGCGGUUGCCUGU-3' bp-type .||||||||||||||||||||||.|||.||.||||||||||||||||.|||||||. strand-2 3'-UUCCGUGUAAACCCUCGUUGACGUAUAGGGACCAGAUACGAGCCCGCUAACGGACG-5' helix-form ..AAAAA...x..x.....A..xx.....x..........Ax..x...AAAAAA. 1 B.G145 B.U142 G+U -- -- tWS tW+m 2 B.G146 B.U141 G-U Wobble 28-XXVIII cWW cW-W 3 B.G147 B.C140 G-C WC 19-XIX cWW cW-W 4 B.G148 B.C139 G-C WC 19-XIX cWW cW-W 5 B.C149 B.G138 C-G WC 19-XIX cWW cW-W 6 B.A150 B.U137 A-U WC 20-XX cWW cW-W 7 B.C151 B.G136 C-G WC 19-XIX cWW cW-W 8 B.A152 B.U135 A-U WC 20-XX cWW cW-W 9 B.U153 B.A134 U-A WC 20-XX cWW cW-W 10 B.U154 B.A133 U-A WC 20-XX cWW cW-W 11 B.U155 B.A132 U-A WC 20-XX cWW cW-W 12 B.G274 B.C131 G-C WC 19-XIX cWW cW-W 13 B.G275 B.C130 G-C WC 19-XIX cWW cW-W 14 B.G276 B.C129 G-C WC 19-XIX cWW cW-W 15 B.A277 B.U305 A-U WC 20-XX cWW cW-W 16 B.G278 B.C304 G-C WC 19-XIX cWW cW-W 17 B.C279 B.G303 C-G WC 19-XIX cWW cW-W 18 B.A280 B.U302 A-U WC 20-XX cWW cW-W 19 B.G281 B.U301 G-U Wobble 28-XXVIII cWW cW-W 20 B.C282 B.G300 C-G WC 19-XIX cWW cW-W 21 B.U283 B.A299 U-A WC 20-XX cWW cW-W 22 B.G284 B.C298 G-C WC 19-XIX cWW cW-W 23 B.C285 B.G297 C-G WC 19-XIX cWW cW-W 24 B.A287 B.U296 A-U rHoogsteen 24-XXIV tHW tM-W 25 B.U421 B.A294 U-A WC 20-XX cWW cW-W 26 B.A422 B.U293 A-U WC 20-XX cWW cW-W 27 B.U423 B.A292 U-A WC 20-XX cWW cW-W 28 B.C424 B.G291 C-G ~Wobble -- cWW cW-W 29 B.C425 B.G290 C-G WC 19-XIX cWW cW-W 30 B.C426 B.G289 C-G WC 19-XIX cWW cW-W 31 B.A427 B.A419 A+A -- 01-I tWW tW+W 32 B.G428 B.C418 G-C WC 19-XIX cWW cW-W 33 B.G429 B.C417 G-C WC 19-XIX cWW cW-W 34 B.U430 B.A416 U-A WC 20-XX cWW cW-W 35 B.U431 B.G415 U-G Wobble 28-XXVIII cWW cW-W 36 B.U432 B.A414 U-A WC 20-XX cWW cW-W 37 B.A433 B.U413 A-U WC 20-XX cWW cW-W 38 B.U434 B.A412 U-A WC 20-XX cWW cW-W 39 B.G435 B.C411 G-C WC 19-XIX cWW cW-W 40 B.C436 B.G410 C-G WC 19-XIX cWW cW-W 41 B.U437 B.A409 U-A WC 20-XX cWW cW-W 42 B.C438 B.G408 C-G WC 19-XIX cWW cW-W 43 B.G622 B.C407 G-C WC 19-XIX cWW cW-W 44 B.G623 B.C406 G-C WC 19-XIX cWW cW-W 45 B.G624 B.C405 G-C WC 19-XIX cWW cW-W 46 B.C625 B.G648 C-G WC 19-XIX cWW cW-W 47 B.G626 B.C647 G-C WC 19-XIX cWW cW-W 48 B.G627 B.U646 G-U -- -- cWW cW-W 49 B.U628 B.A645 U-A WC 20-XX cWW cW-W 50 B.U629 B.A644 U-A WC 20-XX cWW cW-W 51 B.G630 B.C643 G-C WC 19-XIX cWW cW-W 52 B.C631 B.G642 C-G WC 19-XIX cWW cW-W 53 B.C632 B.G641 C-G WC 19-XIX cWW cW-W 54 B.U633 B.A640 U-A WC 20-XX cWW cW-W 55 B.G634 B.C639 G-C WC 19-XIX cWW cW-W 56 B.U635 B.G638 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#5[8] bps=57 strand-1 5'-GCUUGGGUGAUCGGUCCACGUGACACUACCUACGUCUAGCGUUGGGAGCAUCCGUUU-3' bp-type .|||||||||||||||||||||||.||||||.||||.|||||||||||||||||.|. strand-2 3'-UGAACCUACUGGCCAGGUGCAUUGAGAUGGAAGCAGGUCGCAACCCUCGUAGGCGAG-5' helix-form .AAAA.....x..xAAAA......x.AAAAx........A..x..x.AAAAAA... 1 B.G172 B.U169 G+U -- -- tWS tW+m 2 B.C173 B.G168 C-G WC 19-XIX cWW cW-W 3 B.U174 B.A167 U-A WC 20-XX cWW cW-W 4 B.U175 B.A166 U-A WC 20-XX cWW cW-W 5 B.G176 B.C165 G-C WC 19-XIX cWW cW-W 6 B.G177 B.C164 G-C WC 19-XIX cWW cW-W 7 B.G178 B.U163 G-U Wobble 28-XXVIII cWW cW-W 8 B.U179 B.A162 U-A WC 20-XX cWW cW-W 9 B.G180 B.C161 G-C WC 19-XIX cWW cW-W 10 B.A181 B.U160 A-U WC 20-XX cWW cW-W 11 B.U182 B.G159 U-G Wobble 28-XXVIII cWW cW-W 12 B.C242 B.G158 C-G WC 19-XIX cWW cW-W 13 B.G243 B.C157 G-C WC 19-XIX cWW cW-W 14 B.G244 B.C156 G-C WC 19-XIX cWW cW-W 15 B.U245 B.A273 U-A WC 20-XX cWW cW-W 16 B.C246 B.G272 C-G WC 19-XIX cWW cW-W 17 B.C247 B.G271 C-G WC 19-XIX cWW cW-W 18 B.A248 B.U270 A-U WC 20-XX cWW cW-W 19 B.C249 B.G269 C-G WC 19-XIX cWW cW-W 20 B.G250 B.C268 G-C WC 19-XIX cWW cW-W 21 B.U251 B.A267 U-A WC 20-XX cWW cW-W 22 B.G252 B.U266 G-U Wobble 28-XXVIII cWW cW-W 23 B.A253 B.U265 A-U WC 20-XX cWW cW-W 24 B.C254 B.G264 C-G WC 19-XIX cWW cW-W 25 B.A255 B.A263 A+A -- 01-I tWW tW+W 26 B.C455 B.G262 C-G WC 19-XIX cWW cW-W 27 B.U456 B.A261 U-A WC 20-XX cWW cW-W 28 B.A457 B.U260 A-U WC 20-XX cWW cW-W 29 B.C458 B.G259 C-G WC 19-XIX cWW cW-W 30 B.C459 B.G258 C-G WC 19-XIX cWW cW-W 31 B.U460 B.A257 U-A WC 20-XX cWW cW-W 32 B.A461 B.A453 A+A -- 01-I tWW tW+W 33 B.C462 B.G452 C-G WC 19-XIX cWW cW-W 34 B.G463 B.C451 G-C WC 19-XIX cWW cW-W 35 B.U464 B.A450 U-A WC 20-XX cWW cW-W 36 B.C465 B.G449 C-G WC 19-XIX cWW cW-W 37 B.U466 B.G448 U-G -- -- cWW cW-W 38 B.A467 B.U447 A-U WC 20-XX cWW cW-W 39 B.G468 B.C446 G-C WC 19-XIX cWW cW-W 40 B.C469 B.G445 C-G WC 19-XIX cWW cW-W 41 B.G470 B.C444 G-C WC 19-XIX cWW cW-W 42 B.U471 B.A443 U-A WC 20-XX cWW cW-W 43 B.U472 B.A442 U-A WC 20-XX cWW cW-W 44 B.G595 B.C441 G-C WC 19-XIX cWW cW-W 45 B.G596 B.C440 G-C WC 19-XIX cWW cW-W 46 B.G597 B.C439 G-C WC 19-XIX cWW cW-W 47 B.A598 B.U621 A-U WC 20-XX cWW cW-W 48 B.G599 B.C620 G-C WC 19-XIX cWW cW-W 49 B.C600 B.G619 C-G WC 19-XIX cWW cW-W 50 B.A601 B.U618 A-U WC 20-XX cWW cW-W 51 B.U602 B.A617 U-A WC 20-XX cWW cW-W 52 B.C603 B.G616 C-G WC 19-XIX cWW cW-W 53 B.C604 B.G615 C-G WC 19-XIX cWW cW-W 54 B.G605 B.C614 G-C WC 19-XIX cWW cW-W 55 B.U606 B.G613 U-G -- -- cWW cW-W 56 B.U607 B.A612 U-A WC 20-XX cWW cW-W 57 B.U608 B.G611 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#6[8] bps=57 strand-1 5'-GUCUAUACGUCCGCGUUUUCCGAGAUACCUCAGACUUAUUUGCCGGUAGCGCUGCGU-3' bp-type .|||||||||||||||||||||||.||||||.||||.|||||||||||||.|||||. strand-2 3'-UGGAUAUGCGGGCGCAAAGGGCUCAAUGGAGACUGAGUAAACGGCCAUCGUGACGCG-5' helix-form ...AA........x.AA.......xAAAAAx...A..AAA..x..x.AA....AA. 1 B.G199 B.U196 G+U -- -- tWS tW+m 2 B.U200 B.G195 U-G Wobble 28-XXVIII cWW cW-W 3 B.C201 B.G194 C-G WC 19-XIX cWW cW-W 4 B.U202 B.A193 U-A WC 20-XX cWW cW-W 5 B.A203 B.U192 A-U WC 20-XX cWW cW-W 6 B.U204 B.A191 U-A WC 20-XX cWW cW-W 7 B.A205 B.U190 A-U WC 20-XX cWW cW-W 8 B.C206 B.G189 C-G WC 19-XIX cWW cW-W 9 B.G207 B.C188 G-C WC 19-XIX cWW cW-W 10 B.U208 B.G187 U-G Wobble 28-XXVIII cWW cW-W 11 B.C209 B.G186 C-G WC 19-XIX cWW cW-W 12 B.C210 B.G185 C-G WC 19-XIX cWW cW-W 13 B.G211 B.C184 G-C WC 19-XIX cWW cW-W 14 B.C212 B.G183 C-G WC 19-XIX cWW cW-W 15 B.G213 B.C241 G-C WC 19-XIX cWW cW-W 16 B.U214 B.A240 U-A WC 20-XX cWW cW-W 17 B.U215 B.A239 U-A WC 20-XX cWW cW-W 18 B.U216 B.A238 U-A WC 20-XX cWW cW-W 19 B.U217 B.G237 U-G Wobble 28-XXVIII cWW cW-W 20 B.C218 B.G236 C-G WC 19-XIX cWW cW-W 21 B.C219 B.G235 C-G WC 19-XIX cWW cW-W 22 B.G220 B.C234 G-C WC 19-XIX cWW cW-W 23 B.A221 B.U233 A-U WC 20-XX cWW cW-W 24 B.G222 B.C232 G-C WC 19-XIX cWW cW-W 25 B.A223 B.A231 A+A -- 01-I tWW tW+W 26 B.U489 B.A230 U-A WC 20-XX cWW cW-W 27 B.A490 B.U229 A-U WC 20-XX cWW cW-W 28 B.C491 B.G228 C-G WC 19-XIX cWW cW-W 29 B.C492 B.G227 C-G WC 19-XIX cWW cW-W 30 B.U493 B.A226 U-A WC 20-XX cWW cW-W 31 B.C494 B.G225 C-G WC 19-XIX cWW cW-W 32 B.A495 B.A487 A+A -- 01-I tWW tW+W 33 B.G496 B.C486 G-C WC 19-XIX cWW cW-W 34 B.A497 B.U485 A-U WC 20-XX cWW cW-W 35 B.C498 B.G484 C-G WC 19-XIX cWW cW-W 36 B.U499 B.A483 U-A WC 20-XX cWW cW-W 37 B.U500 B.G482 U-G -- -- cWW cW-W 38 B.A501 B.U481 A-U WC 20-XX cWW cW-W 39 B.U502 B.A480 U-A WC 20-XX cWW cW-W 40 B.U503 B.A479 U-A WC 20-XX cWW cW-W 41 B.U504 B.A478 U-A WC 20-XX cWW cW-W 42 B.G505 B.C477 G-C WC 19-XIX cWW cW-W 43 B.C506 B.G476 C-G WC 19-XIX cWW cW-W 44 B.C568 B.G475 C-G WC 19-XIX cWW cW-W 45 B.G569 B.C474 G-C WC 19-XIX cWW cW-W 46 B.G570 B.C473 G-C WC 19-XIX cWW cW-W 47 B.U571 B.A594 U-A WC 20-XX cWW cW-W 48 B.A572 B.U593 A-U WC 20-XX cWW cW-W 49 B.G573 B.C592 G-C WC 19-XIX cWW cW-W 50 B.C574 B.G591 C-G WC 19-XIX cWW cW-W 51 B.G575 B.U590 G-U -- -- cWW cW-W 52 B.C576 B.G589 C-G WC 19-XIX cWW cW-W 53 B.U577 B.A588 U-A WC 20-XX cWW cW-W 54 B.G578 B.C587 G-C WC 19-XIX cWW cW-W 55 B.C579 B.G586 C-G WC 19-XIX cWW cW-W 56 B.G580 B.C585 G-C WC 19-XIX cWW cW-W 57 B.U581 B.G584 U+G -- -- tSW tm+W **************************************************************************** List of 44 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#2] bps=13 strand-1 5'-GGGAGAGUACUAU-3' bp-type ||||||||||||| strand-2 3'-CCCUCUCGUGGUA-5' helix-form AA......A..A 1 B.G1 B.C355 G-C WC 19-XIX cWW cW-W 2 B.G2 B.C354 G-C WC 19-XIX cWW cW-W 3 B.G3 B.C353 G-C WC 19-XIX cWW cW-W 4 B.A4 B.U352 A-U WC 20-XX cWW cW-W 5 B.G5 B.C351 G-C WC 19-XIX cWW cW-W 6 B.A6 B.U350 A-U WC 20-XX cWW cW-W 7 B.G7 B.C349 G-C WC 19-XIX cWW cW-W 8 B.U8 B.G348 U-G Wobble 28-XXVIII cWW cW-W 9 B.A9 B.U347 A-U WC 20-XX cWW cW-W 10 B.C10 B.G346 C-G WC 19-XIX cWW cW-W 11 B.U11 B.G345 U-G Wobble 28-XXVIII cWW cW-W 12 B.A12 B.U344 A-U WC 20-XX cWW cW-W 13 B.U13 B.A343 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=13 strand-1 5'-AGAUGCAGACCGC-3' bp-type ||||||||||||| strand-2 3'-UCUACGUUUGGCG-5' helix-form .A.......AAA 1 B.A16 B.U50 A-U WC 20-XX cWW cW-W 2 B.G17 B.C49 G-C WC 19-XIX cWW cW-W 3 B.A18 B.U48 A-U WC 20-XX cWW cW-W 4 B.U19 B.A47 U-A WC 20-XX cWW cW-W 5 B.G20 B.C46 G-C WC 19-XIX cWW cW-W 6 B.C21 B.G45 C-G WC 19-XIX cWW cW-W 7 B.A22 B.U44 A-U WC 20-XX cWW cW-W 8 B.G23 B.U43 G-U Wobble 28-XXVIII cWW cW-W 9 B.A24 B.U42 A-U WC 20-XX cWW cW-W 10 B.C25 B.G41 C-G WC 19-XIX cWW cW-W 11 B.C26 B.G40 C-G WC 19-XIX cWW cW-W 12 B.G27 B.C39 G-C WC 19-XIX cWW cW-W 13 B.C28 B.G38 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=6 strand-1 5'-GUUCAG-3' bp-type |||||| strand-2 3'-CAAGUC-5' helix-form ...AA 1 B.G31 B.C528 G-C WC 19-XIX cWW cW-W 2 B.U32 B.A527 U-A WC 20-XX cWW cW-W 3 B.U33 B.A526 U-A WC 20-XX cWW cW-W 4 B.C34 B.G525 C-G WC 19-XIX cWW cW-W 5 B.A35 B.U524 A-U WC 20-XX cWW cW-W 6 B.G36 B.C523 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=10 strand-1 5'-AGGGUACGUU-3' bp-type |||||||||| strand-2 3'-UCCUAUGCAA-5' helix-form A......AA 1 B.A51 B.U74 A-U WC 20-XX cWW cW-W 2 B.G52 B.C73 G-C WC 19-XIX cWW cW-W 3 B.G53 B.C72 G-C WC 19-XIX cWW cW-W 4 B.G54 B.U71 G-U Wobble 28-XXVIII cWW cW-W 5 B.U55 B.A70 U-A WC 20-XX cWW cW-W 6 B.A56 B.U69 A-U WC 20-XX cWW cW-W 7 B.C57 B.G68 C-G WC 19-XIX cWW cW-W 8 B.G58 B.C67 G-C WC 19-XIX cWW cW-W 9 B.U59 B.A66 U-A WC 20-XX cWW cW-W 10 B.U60 B.A65 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#2] bps=3 strand-1 5'-CCG-3' bp-type ||| strand-2 3'-GGC-5' helix-form .A 1 B.C75 B.G340 C-G WC 19-XIX cWW cW-W 2 B.C76 B.G339 C-G WC 19-XIX cWW cW-W 3 B.G77 B.C338 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#2] bps=10 strand-1 5'-ACUAAGUGUA-3' bp-type |||||||||| strand-2 3'-UGAUUCAUAU-5' helix-form AAAA....A 1 B.A78 B.U101 A-U WC 20-XX cWW cW-W 2 B.C79 B.G100 C-G WC 19-XIX cWW cW-W 3 B.U80 B.A99 U-A WC 20-XX cWW cW-W 4 B.A81 B.U98 A-U WC 20-XX cWW cW-W 5 B.A82 B.U97 A-U WC 20-XX cWW cW-W 6 B.G83 B.C96 G-C WC 19-XIX cWW cW-W 7 B.U84 B.A95 U-A WC 20-XX cWW cW-W 8 B.G85 B.U94 G-U Wobble 28-XXVIII cWW cW-W 9 B.U86 B.A93 U-A WC 20-XX cWW cW-W 10 B.A87 B.U92 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#7[#3] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-CGG-5' helix-form .. 1 B.G102 B.C308 G-C WC 19-XIX cWW cW-W 2 B.C103 B.G307 C-G WC 19-XIX cWW cW-W 3 B.C104 B.G306 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#3] bps=2 strand-1 5'-UU-3' bp-type || strand-2 3'-AG-5' helix-form . 1 B.U105 B.A128 U-A WC 20-XX cWW cW-W 2 B.U106 B.G127 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#9[#3] bps=7 strand-1 5'-UGCCUGC-3' bp-type ||||||| strand-2 3'-ACGGACG-5' helix-form AAAAAA 1 B.U108 B.A125 U-A WC 20-XX cWW cW-W 2 B.G109 B.C124 G-C WC 19-XIX cWW cW-W 3 B.C110 B.G123 C-G WC 19-XIX cWW cW-W 4 B.C111 B.G122 C-G WC 19-XIX cWW cW-W 5 B.U112 B.A121 U-A WC 20-XX cWW cW-W 6 B.G113 B.C120 G-C WC 19-XIX cWW cW-W 7 B.C114 B.G119 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#10[#4] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form .. 1 B.C129 B.G276 C-G WC 19-XIX cWW cW-W 2 B.C130 B.G275 C-G WC 19-XIX cWW cW-W 3 B.C131 B.G274 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#4] bps=10 strand-1 5'-AAAUGUGCCU-3' bp-type |||||||||| strand-2 3'-UUUACACGGG-5' helix-form ...AAAAA. 1 B.A132 B.U155 A-U WC 20-XX cWW cW-W 2 B.A133 B.U154 A-U WC 20-XX cWW cW-W 3 B.A134 B.U153 A-U WC 20-XX cWW cW-W 4 B.U135 B.A152 U-A WC 20-XX cWW cW-W 5 B.G136 B.C151 G-C WC 19-XIX cWW cW-W 6 B.U137 B.A150 U-A WC 20-XX cWW cW-W 7 B.G138 B.C149 G-C WC 19-XIX cWW cW-W 8 B.C139 B.G148 C-G WC 19-XIX cWW cW-W 9 B.C140 B.G147 C-G WC 19-XIX cWW cW-W 10 B.U141 B.G146 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#12[#5] bps=3 strand-1 5'-CCG-3' bp-type ||| strand-2 3'-GGC-5' helix-form .. 1 B.C156 B.G244 C-G WC 19-XIX cWW cW-W 2 B.C157 B.G243 C-G WC 19-XIX cWW cW-W 3 B.G158 B.C242 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#13[#5] bps=10 strand-1 5'-GUCAUCCAAG-3' bp-type |||||||||| strand-2 3'-UAGUGGGUUC-5' helix-form .....AAAA 1 B.G159 B.U182 G-U Wobble 28-XXVIII cWW cW-W 2 B.U160 B.A181 U-A WC 20-XX cWW cW-W 3 B.C161 B.G180 C-G WC 19-XIX cWW cW-W 4 B.A162 B.U179 A-U WC 20-XX cWW cW-W 5 B.U163 B.G178 U-G Wobble 28-XXVIII cWW cW-W 6 B.C164 B.G177 C-G WC 19-XIX cWW cW-W 7 B.C165 B.G176 C-G WC 19-XIX cWW cW-W 8 B.A166 B.U175 A-U WC 20-XX cWW cW-W 9 B.A167 B.U174 A-U WC 20-XX cWW cW-W 10 B.G168 B.C173 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#14[#6] bps=13 strand-1 5'-GCGGGCGUAUAGG-3' bp-type ||||||||||||| strand-2 3'-CGCCUGCAUAUCU-5' helix-form ........AA.. 1 B.G183 B.C212 G-C WC 19-XIX cWW cW-W 2 B.C184 B.G211 C-G WC 19-XIX cWW cW-W 3 B.G185 B.C210 G-C WC 19-XIX cWW cW-W 4 B.G186 B.C209 G-C WC 19-XIX cWW cW-W 5 B.G187 B.U208 G-U Wobble 28-XXVIII cWW cW-W 6 B.C188 B.G207 C-G WC 19-XIX cWW cW-W 7 B.G189 B.C206 G-C WC 19-XIX cWW cW-W 8 B.U190 B.A205 U-A WC 20-XX cWW cW-W 9 B.A191 B.U204 A-U WC 20-XX cWW cW-W 10 B.U192 B.A203 U-A WC 20-XX cWW cW-W 11 B.A193 B.U202 A-U WC 20-XX cWW cW-W 12 B.G194 B.C201 G-C WC 19-XIX cWW cW-W 13 B.G195 B.U200 G-U Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#15[#6] bps=10 strand-1 5'-GUUUUCCGAG-3' bp-type |||||||||| strand-2 3'-CAAAGGGCUC-5' helix-form .AA...... 1 B.G213 B.C241 G-C WC 19-XIX cWW cW-W 2 B.U214 B.A240 U-A WC 20-XX cWW cW-W 3 B.U215 B.A239 U-A WC 20-XX cWW cW-W 4 B.U216 B.A238 U-A WC 20-XX cWW cW-W 5 B.U217 B.G237 U-G Wobble 28-XXVIII cWW cW-W 6 B.C218 B.G236 C-G WC 19-XIX cWW cW-W 7 B.C219 B.G235 C-G WC 19-XIX cWW cW-W 8 B.G220 B.C234 G-C WC 19-XIX cWW cW-W 9 B.A221 B.U233 A-U WC 20-XX cWW cW-W 10 B.G222 B.C232 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#16[#6] bps=6 strand-1 5'-GAGGUA-3' bp-type |||||| strand-2 3'-CUCCAU-5' helix-form AAAAA 1 B.G225 B.C494 G-C WC 19-XIX cWW cW-W 2 B.A226 B.U493 A-U WC 20-XX cWW cW-W 3 B.G227 B.C492 G-C WC 19-XIX cWW cW-W 4 B.G228 B.C491 G-C WC 19-XIX cWW cW-W 5 B.U229 B.A490 U-A WC 20-XX cWW cW-W 6 B.A230 B.U489 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#17[#5] bps=10 strand-1 5'-UCCACGUGAC-3' bp-type |||||||||| strand-2 3'-AGGUGCAUUG-5' helix-form AAAA..... 1 B.U245 B.A273 U-A WC 20-XX cWW cW-W 2 B.C246 B.G272 C-G WC 19-XIX cWW cW-W 3 B.C247 B.G271 C-G WC 19-XIX cWW cW-W 4 B.A248 B.U270 A-U WC 20-XX cWW cW-W 5 B.C249 B.G269 C-G WC 19-XIX cWW cW-W 6 B.G250 B.C268 G-C WC 19-XIX cWW cW-W 7 B.U251 B.A267 U-A WC 20-XX cWW cW-W 8 B.G252 B.U266 G-U Wobble 28-XXVIII cWW cW-W 9 B.A253 B.U265 A-U WC 20-XX cWW cW-W 10 B.C254 B.G264 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#18[#5] bps=6 strand-1 5'-AGGUAG-3' bp-type |||||| strand-2 3'-UCCAUC-5' helix-form AAAA. 1 B.A257 B.U460 A-U WC 20-XX cWW cW-W 2 B.G258 B.C459 G-C WC 19-XIX cWW cW-W 3 B.G259 B.C458 G-C WC 19-XIX cWW cW-W 4 B.U260 B.A457 U-A WC 20-XX cWW cW-W 5 B.A261 B.U456 A-U WC 20-XX cWW cW-W 6 B.G262 B.C455 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#19[#4] bps=9 strand-1 5'-AGCAGCUGC-3' bp-type ||||||||| strand-2 3'-UCGUUGACG-5' helix-form .....A.. 1 B.A277 B.U305 A-U WC 20-XX cWW cW-W 2 B.G278 B.C304 G-C WC 19-XIX cWW cW-W 3 B.C279 B.G303 C-G WC 19-XIX cWW cW-W 4 B.A280 B.U302 A-U WC 20-XX cWW cW-W 5 B.G281 B.U301 G-U Wobble 28-XXVIII cWW cW-W 6 B.C282 B.G300 C-G WC 19-XIX cWW cW-W 7 B.U283 B.A299 U-A WC 20-XX cWW cW-W 8 B.G284 B.C298 G-C WC 19-XIX cWW cW-W 9 B.C285 B.G297 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#20[#4] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form . 1 B.G289 B.C426 G-C WC 19-XIX cWW cW-W 2 B.G290 B.C425 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#21[#4] bps=3 strand-1 5'-AUA-3' bp-type ||| strand-2 3'-UAU-5' helix-form .. 1 B.A292 B.U423 A-U WC 20-XX cWW cW-W 2 B.U293 B.A422 U-A WC 20-XX cWW cW-W 3 B.A294 B.U421 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#22[#3] bps=10 strand-1 5'-UGGAUGCCAG-3' bp-type |||||||||| strand-2 3'-AUCUACGGUC-5' helix-form ..A.AAAA. 1 B.U309 B.A337 U-A WC 20-XX cWW cW-W 2 B.G310 B.U336 G-U Wobble 28-XXVIII cWW cW-W 3 B.G311 B.C335 G-C WC 19-XIX cWW cW-W 4 B.A312 B.U334 A-U WC 20-XX cWW cW-W 5 B.U313 B.A333 U-A WC 20-XX cWW cW-W 6 B.G314 B.C332 G-C WC 19-XIX cWW cW-W 7 B.C315 B.G331 C-G WC 19-XIX cWW cW-W 8 B.C316 B.G330 C-G WC 19-XIX cWW cW-W 9 B.A317 B.U329 A-U WC 20-XX cWW cW-W 10 B.G318 B.C328 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#23[#3] bps=6 strand-1 5'-CUCACG-3' bp-type |||||| strand-2 3'-GAGUGC-5' helix-form ..A.. 1 B.C321 B.G392 C-G WC 19-XIX cWW cW-W 2 B.U322 B.A391 U-A WC 20-XX cWW cW-W 3 B.C323 B.G390 C-G WC 19-XIX cWW cW-W 4 B.A324 B.U389 A-U WC 20-XX cWW cW-W 5 B.C325 B.G388 C-G WC 19-XIX cWW cW-W 6 B.G326 B.C387 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#24[#2] bps=15 strand-1 5'-AAUUCUCCAUUUACC-3' bp-type ||||||||||||||| strand-2 3'-UUAAGAGGUAGAUGG-5' helix-form AAAAA......AA. 1 B.A356 B.U720 A-U WC 20-XX cWW cW-W 2 B.A357 B.U719 A-U WC 20-XX cWW cW-W 3 B.U358 B.A718 U-A WC 20-XX cWW cW-W 4 B.U359 B.A717 U-A WC 20-XX cWW cW-W 5 B.C360 B.G716 C-G WC 19-XIX cWW cW-W 6 B.U361 B.A715 U-A WC 20-XX cWW cW-W 7 B.C362 B.G714 C-G WC 19-XIX cWW cW-W 8 B.C363 B.G713 C-G WC 19-XIX cWW cW-W 9 B.A364 B.U712 A-U WC 20-XX cWW cW-W 10 B.U365 B.A711 U-A WC 20-XX cWW cW-W 11 B.U366 B.G710 U-G Wobble 28-XXVIII cWW cW-W 12 B.U367 B.A709 U-A WC 20-XX cWW cW-W 13 B.A368 B.U708 A-U WC 20-XX cWW cW-W 14 B.C369 B.G707 C-G WC 19-XIX cWW cW-W 15 B.C370 B.G706 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#25[#3] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-CGG-5' helix-form .. 1 B.G371 B.C651 G-C WC 19-XIX cWW cW-W 2 B.C372 B.G650 C-G WC 19-XIX cWW cW-W 3 B.C373 B.G649 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#26[#3] bps=11 strand-1 5'-GAAUCGACCCC-3' bp-type ||||||||||| strand-2 3'-CUUGGCUGGGG-5' helix-form AA..AA...A 1 B.G374 B.C404 G-C WC 19-XIX cWW cW-W 2 B.A375 B.U403 A-U WC 20-XX cWW cW-W 3 B.A376 B.U402 A-U WC 20-XX cWW cW-W 4 B.U377 B.G401 U-G Wobble 28-XXVIII cWW cW-W 5 B.C378 B.G400 C-G WC 19-XIX cWW cW-W 6 B.G379 B.C399 G-C WC 19-XIX cWW cW-W 7 B.A380 B.U398 A-U WC 20-XX cWW cW-W 8 B.C381 B.G397 C-G WC 19-XIX cWW cW-W 9 B.C382 B.G396 C-G WC 19-XIX cWW cW-W 10 B.C383 B.G395 C-G WC 19-XIX cWW cW-W 11 B.C384 B.G394 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#27[#4] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form .. 1 B.C405 B.G624 C-G WC 19-XIX cWW cW-W 2 B.C406 B.G623 C-G WC 19-XIX cWW cW-W 3 B.C407 B.G622 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#28[#4] bps=11 strand-1 5'-GAGCAUAGACC-3' bp-type ||||||||||| strand-2 3'-CUCGUAUUUGG-5' helix-form A......... 1 B.G408 B.C438 G-C WC 19-XIX cWW cW-W 2 B.A409 B.U437 A-U WC 20-XX cWW cW-W 3 B.G410 B.C436 G-C WC 19-XIX cWW cW-W 4 B.C411 B.G435 C-G WC 19-XIX cWW cW-W 5 B.A412 B.U434 A-U WC 20-XX cWW cW-W 6 B.U413 B.A433 U-A WC 20-XX cWW cW-W 7 B.A414 B.U432 A-U WC 20-XX cWW cW-W 8 B.G415 B.U431 G-U Wobble 28-XXVIII cWW cW-W 9 B.A416 B.U430 A-U WC 20-XX cWW cW-W 10 B.C417 B.G429 C-G WC 19-XIX cWW cW-W 11 B.C418 B.G428 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#29[#5] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form .. 1 B.C439 B.G597 C-G WC 19-XIX cWW cW-W 2 B.C440 B.G596 C-G WC 19-XIX cWW cW-W 3 B.C441 B.G595 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#30[#5] bps=6 strand-1 5'-AACGCU-3' bp-type |||||| strand-2 3'-UUGCGA-5' helix-form ..A.. 1 B.A442 B.U472 A-U WC 20-XX cWW cW-W 2 B.A443 B.U471 A-U WC 20-XX cWW cW-W 3 B.C444 B.G470 C-G WC 19-XIX cWW cW-W 4 B.G445 B.C469 G-C WC 19-XIX cWW cW-W 5 B.C446 B.G468 C-G WC 19-XIX cWW cW-W 6 B.U447 B.A467 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#31[#5] bps=4 strand-1 5'-GACG-3' bp-type |||| strand-2 3'-CUGC-5' helix-form ... 1 B.G449 B.C465 G-C WC 19-XIX cWW cW-W 2 B.A450 B.U464 A-U WC 20-XX cWW cW-W 3 B.C451 B.G463 C-G WC 19-XIX cWW cW-W 4 B.G452 B.C462 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#32[#6] bps=3 strand-1 5'-CCG-3' bp-type ||| strand-2 3'-GGC-5' helix-form .. 1 B.C473 B.G570 C-G WC 19-XIX cWW cW-W 2 B.C474 B.G569 C-G WC 19-XIX cWW cW-W 3 B.G475 B.C568 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#33[#6] bps=6 strand-1 5'-GCAAAU-3' bp-type |||||| strand-2 3'-CGUUUA-5' helix-form ..AAA 1 B.G476 B.C506 G-C WC 19-XIX cWW cW-W 2 B.C477 B.G505 C-G WC 19-XIX cWW cW-W 3 B.A478 B.U504 A-U WC 20-XX cWW cW-W 4 B.A479 B.U503 A-U WC 20-XX cWW cW-W 5 B.A480 B.U502 A-U WC 20-XX cWW cW-W 6 B.U481 B.A501 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#34[#6] bps=4 strand-1 5'-AGUC-3' bp-type |||| strand-2 3'-UCAG-5' helix-form A.. 1 B.A483 B.U499 A-U WC 20-XX cWW cW-W 2 B.G484 B.C498 G-C WC 19-XIX cWW cW-W 3 B.U485 B.A497 U-A WC 20-XX cWW cW-W 4 B.C486 B.G496 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#35[#1] bps=9 strand-1 5'-GGUGCCUGA-3' bp-type ||||||||| strand-2 3'-CUACGGACU-5' helix-form .......A 1 B.G507 B.C543 G-C WC 19-XIX cWW cW-W 2 B.G508 B.U542 G-U Wobble 28-XXVIII cWW cW-W 3 B.U509 B.A541 U-A WC 20-XX cWW cW-W 4 B.G510 B.C540 G-C WC 19-XIX cWW cW-W 5 B.C511 B.G539 C-G WC 19-XIX cWW cW-W 6 B.C512 B.G538 C-G WC 19-XIX cWW cW-W 7 B.U513 B.A537 U-A WC 20-XX cWW cW-W 8 B.G514 B.C536 G-C WC 19-XIX cWW cW-W 9 B.A515 B.U535 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#36[#1] bps=4 strand-1 5'-CCUA-3' bp-type |||| strand-2 3'-GGGU-5' helix-form A.A 1 B.C517 B.G533 C-G WC 19-XIX cWW cW-W 2 B.C518 B.G532 C-G WC 19-XIX cWW cW-W 3 B.U519 B.G531 U-G Wobble 28-XXVIII cWW cW-W 4 B.A520 B.U530 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#37[#1] bps=8 strand-1 5'-GGCUCCAG-3' bp-type |||||||| strand-2 3'-CCGAGGUC-5' helix-form AA..AAA 1 B.G546 B.C565 G-C WC 19-XIX cWW cW-W 2 B.G547 B.C564 G-C WC 19-XIX cWW cW-W 3 B.C548 B.G563 C-G WC 19-XIX cWW cW-W 4 B.U549 B.A562 U-A WC 20-XX cWW cW-W 5 B.C550 B.G561 C-G WC 19-XIX cWW cW-W 6 B.C551 B.G560 C-G WC 19-XIX cWW cW-W 7 B.A552 B.U559 A-U WC 20-XX cWW cW-W 8 B.G553 B.C558 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#38[#6] bps=4 strand-1 5'-UAGC-3' bp-type |||| strand-2 3'-AUCG-5' helix-form .AA 1 B.U571 B.A594 U-A WC 20-XX cWW cW-W 2 B.A572 B.U593 A-U WC 20-XX cWW cW-W 3 B.G573 B.C592 G-C WC 19-XIX cWW cW-W 4 B.C574 B.G591 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#39[#6] bps=5 strand-1 5'-CUGCG-3' bp-type ||||| strand-2 3'-GACGC-5' helix-form ..AA 1 B.C576 B.G589 C-G WC 19-XIX cWW cW-W 2 B.U577 B.A588 U-A WC 20-XX cWW cW-W 3 B.G578 B.C587 G-C WC 19-XIX cWW cW-W 4 B.C579 B.G586 C-G WC 19-XIX cWW cW-W 5 B.G580 B.C585 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#40[#5] bps=8 strand-1 5'-AGCAUCCG-3' bp-type |||||||| strand-2 3'-UCGUAGGC-5' helix-form .AAAAAA 1 B.A598 B.U621 A-U WC 20-XX cWW cW-W 2 B.G599 B.C620 G-C WC 19-XIX cWW cW-W 3 B.C600 B.G619 C-G WC 19-XIX cWW cW-W 4 B.A601 B.U618 A-U WC 20-XX cWW cW-W 5 B.U602 B.A617 U-A WC 20-XX cWW cW-W 6 B.C603 B.G616 C-G WC 19-XIX cWW cW-W 7 B.C604 B.G615 C-G WC 19-XIX cWW cW-W 8 B.G605 B.C614 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#41[#4] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form . 1 B.C625 B.G648 C-G WC 19-XIX cWW cW-W 2 B.G626 B.C647 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#42[#4] bps=7 strand-1 5'-UUGCCUG-3' bp-type ||||||| strand-2 3'-AACGGAC-5' helix-form AAAAAA 1 B.U628 B.A645 U-A WC 20-XX cWW cW-W 2 B.U629 B.A644 U-A WC 20-XX cWW cW-W 3 B.G630 B.C643 G-C WC 19-XIX cWW cW-W 4 B.C631 B.G642 C-G WC 19-XIX cWW cW-W 5 B.C632 B.G641 C-G WC 19-XIX cWW cW-W 6 B.U633 B.A640 U-A WC 20-XX cWW cW-W 7 B.G634 B.C639 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#43[#3] bps=10 strand-1 5'-CUACUCAUGA-3' bp-type |||||||||| strand-2 3'-GGUGAGUACU-5' helix-form ..AAAAAAA 1 B.C652 B.G675 C-G WC 19-XIX cWW cW-W 2 B.U653 B.G674 U-G Wobble 28-XXVIII cWW cW-W 3 B.A654 B.U673 A-U WC 20-XX cWW cW-W 4 B.C655 B.G672 C-G WC 19-XIX cWW cW-W 5 B.U656 B.A671 U-A WC 20-XX cWW cW-W 6 B.C657 B.G670 C-G WC 19-XIX cWW cW-W 7 B.A658 B.U669 A-U WC 20-XX cWW cW-W 8 B.U659 B.A668 U-A WC 20-XX cWW cW-W 9 B.G660 B.C667 G-C WC 19-XIX cWW cW-W 10 B.A661 B.U666 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#44[#2] bps=13 strand-1 5'-UGACAGCGUGAUG-3' bp-type ||||||||||||| strand-2 3'-GCUGUCGCAUUAC-5' helix-form .....A....AA 1 B.U676 B.G705 U-G Wobble 28-XXVIII cWW cW-W 2 B.G677 B.C704 G-C WC 19-XIX cWW cW-W 3 B.A678 B.U703 A-U WC 20-XX cWW cW-W 4 B.C679 B.G702 C-G WC 19-XIX cWW cW-W 5 B.A680 B.U701 A-U WC 20-XX cWW cW-W 6 B.G681 B.C700 G-C WC 19-XIX cWW cW-W 7 B.C682 B.G699 C-G WC 19-XIX cWW cW-W 8 B.G683 B.C698 G-C WC 19-XIX cWW cW-W 9 B.U684 B.A697 U-A WC 20-XX cWW cW-W 10 B.G685 B.U696 G-U Wobble 28-XXVIII cWW cW-W 11 B.A686 B.U695 A-U WC 20-XX cWW cW-W 12 B.U687 B.A694 U-A WC 20-XX cWW cW-W 13 B.G688 B.C693 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 3 isolated WC/wobble pairs Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#2] -1 B.C15 B.G341 C-G WC 19-XIX cWW cW-W [#1] -2 B.U544 B.A567 U-A WC 20-XX cWW cW-W [#5] -3 B.U607 B.A612 U-A WC 20-XX cWW cW-W **************************************************************************** List of 6 coaxial stacks 1 Helix#1 contains 6 stems: [#4,#2,#3,#36,#35,#37] 2 Helix#2 contains 5 stems: [#6,#5,#1,#24,#44] 3 Helix#3 contains 8 stems: [#9,#8,#7,#22,#23,#26,#25,#43] 4 Helix#4 contains 9 stems: [#11,#10,#19,#21,#20,#28,#27,#41,#42] 5 Helix#5 contains 8 stems: [#13,#12,#17,#18,#31,#30,#29,#40] 6 Helix#6 contains 8 stems: [#14,#15,#16,#34,#33,#32,#38,#39] **************************************************************************** List of 89 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 GA B.G1,B.A356 2 nts=2 AA B.A16,B.A51 3 nts=2 GA B.G77,B.A78 4 nts=2 GA B.G102,B.A337 5 nts=2 AU B.A125,B.U126 6 nts=2 AG B.A128,B.G306 7 nts=2 AG B.A132,B.G274 8 nts=2 CA B.C156,B.A273 9 nts=2 GG B.G158,B.G159 10 nts=2 UC B.U182,B.C242 11 nts=2 GG B.G183,B.G213 12 nts=2 GU B.G199,B.U200 13 nts=2 GU B.G244,B.U245 14 nts=2 GA B.G276,B.A277 15 nts=2 CA B.C285,B.A286 16 nts=2 AU B.A287,B.U421 17 nts=2 CU B.C370,B.U676 18 nts=2 GG B.G371,B.G675 19 nts=2 GG B.G374,B.G649 20 nts=2 CG B.C405,B.G648 21 nts=2 GG B.G408,B.G622 22 nts=2 CA B.C418,B.A419 23 nts=2 CU B.C439,B.U621 24 nts=2 AG B.A442,B.G595 25 nts=2 UG B.U447,B.G448 26 nts=2 GU B.G449,B.U466 27 nts=2 CA B.C473,B.A594 28 nts=2 GG B.G475,B.G476 29 nts=2 UU B.U499,B.U500 30 nts=2 CC B.C506,B.C568 31 nts=2 CU B.C543,B.U544 32 nts=2 GC B.G557,B.C558 33 nts=2 CG B.C565,B.G566 34 nts=2 GU B.G570,B.U571 35 nts=2 GC B.G584,B.C585 36 nts=2 GU B.G589,B.U590 37 nts=2 GA B.G597,B.A598 38 nts=2 GC B.G624,B.C625 39 nts=2 GU B.G665,B.U666 40 nts=2 GC B.G692,B.C693 41 nts=2 GG B.G705,B.G706 42 nts=3 UCC B.U14,B.C15,B.C75 43 nts=3 CAC B.C28,B.A29,B.C523 44 nts=3 GAU B.G31,B.A529,B.U530 45 nts=3 GAG B.G36,B.A37,B.G38 46 nts=3 UUC B.U60,B.U61,B.C63 47 nts=3 UGA B.U62,B.G64,B.A65 48 nts=3 AUC B.A87,B.U88,B.C90 49 nts=3 UGU B.U89,B.G91,B.U92 50 nts=3 UGG B.U108,B.G107,B.G127 51 nts=3 CUC B.C114,B.U115,B.C117 52 nts=3 UGG B.U116,B.G118,B.G119 53 nts=3 UUC B.U141,B.U142,B.C144 54 nts=3 UGG B.U143,B.G145,B.G146 55 nts=3 GUC B.G168,B.U169,B.C171 56 nts=3 UGC B.U170,B.G172,B.C173 57 nts=3 GUC B.G195,B.U196,B.C198 58 nts=3 GAG B.G225,B.A495,B.G496 59 nts=3 AAC B.A230,B.A231,B.C232 60 nts=3 CAC B.C254,B.A255,B.C455 61 nts=3 AAC B.A257,B.A461,B.C462 62 nts=3 GAG B.G262,B.A263,B.G264 63 nts=3 GAG B.G289,B.A427,B.G428 64 nts=3 GGA B.G290,B.G291,B.A292 65 nts=3 GAC B.G318,B.A319,B.C387 66 nts=3 GAC B.G326,B.A327,B.C328 67 nts=3 CAA B.C384,B.A385,B.A386 68 nts=3 GAG B.G392,B.A393,B.G394 69 nts=3 UCC B.U423,B.C424,B.C425 70 nts=3 AGA B.A483,B.G482,B.A501 71 nts=3 AGC B.A515,B.G516,B.C517 72 nts=3 GUU B.G533,B.U534,B.U535 73 nts=3 GUC B.G553,B.U554,B.C556 74 nts=3 CGG B.C576,B.G575,B.G591 75 nts=3 GUC B.G580,B.U581,B.C583 76 nts=3 GGU B.G626,B.G627,B.U628 77 nts=3 GUC B.G634,B.U635,B.C637 78 nts=3 UGC B.U636,B.G638,B.C639 79 nts=3 AUC B.A645,B.U646,B.C647 80 nts=3 AUC B.A661,B.U662,B.C664 81 nts=3 GUC B.G688,B.U689,B.C691 82 nts=4 AAAA B.A30,B.A522,B.A521,B.A520 83 nts=4 AAAG B.A256,B.A454,B.A453,B.G452 84 nts=4 AAUG B.A294,B.A295,B.U296,B.G297 85 nts=4 GGGA B.G340,B.G341,B.G342,B.A343 86 nts=4 GAUG B.G507,B.A567,B.U545,B.G546 87 nts=5 GUUUC B.G605,B.U606,B.U607,B.U608,B.C610 88 nts=5 UGAGC B.U609,B.G611,B.A612,B.G613,B.C614 89 nts=6 GAAAAC B.G222,B.A223,B.A224,B.A488,B.A487,B.C486 **************************************************************************** Nucleotides not involved in stacking interactions nts=19 CUUAACCCCUCCAUCUCUU B.C129,B.U197,B.U215,B.A288,B.A320,B.C321,B.C338,B.C351,B.C353,B.U359,B.C360,B.C362,B.A420,B.U504,B.C550,B.U582,B.C603,B.U663,B.U690 **************************************************************************** List of 27 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O2'@B.U62 B.G64 3.19 2 sugar O2'@B.U89 B.G91 2.97 3 sugar O4'@B.U92 B.G91 3.44 4 sugar O2'@B.U116 B.G118 3.16 5 sugar O4'@B.G119 B.G118 3.43 6 sugar O2'@B.U143 B.G145 3.24 7 sugar O4'@B.G146 B.G145 3.48 8 sugar O4'@B.G274 B.U155 3.28 9 sugar O2'@B.U170 B.G172 3.11 10 sugar O4'@B.C173 B.G172 3.46 11 sugar O4'@B.G186 B.G185 3.32 12 sugar O2'@B.U197 B.G199 3.04 13 sugar O4'@B.U200 B.G199 3.33 14 sugar O4'@B.U421 B.A287 3.22 15 sugar O2'@B.A287 B.A288 3.39 16 sugar O4'@B.U676 B.C370 3.47 17 sugar O4'@B.G289 B.A419 3.06 18 sugar O4'@B.A487 B.A488 3.07 19 sugar O2'@B.U555 B.G557 3.03 20 sugar O2'@B.U582 B.G584 3.11 21 sugar O4'@B.C585 B.G584 3.43 22 sugar O2'@B.U609 B.G611 3.15 23 sugar O4'@B.A612 B.G611 3.46 24 sugar O2'@B.U636 B.G638 3.14 25 sugar O4'@B.C639 B.G638 3.47 26 sugar O2'@B.U663 B.G665 3.16 27 sugar O2'@B.U690 B.G692 3.23 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 23 hairpin loops 1 hairpin loop: nts=11; [9]; linked by [#2] summary: [1] 9 [B.28 B.38] 13 nts=11 CAAGUUCAGAG B.C28,B.A29,B.A30,B.G31,B.U32,B.U33,B.C34,B.A35,B.G36,B.A37,B.G38 nts=9 AAGUUCAGA B.A29,B.A30,B.G31,B.U32,B.U33,B.C34,B.A35,B.G36,B.A37 2 hairpin loop: nts=6; [4]; linked by [#4] summary: [1] 4 [B.60 B.65] 10 nts=6 UUUCGA B.U60,B.U61,B.U62,B.C63,B.G64,B.A65 nts=4 UUCG B.U61,B.U62,B.C63,B.G64 3 hairpin loop: nts=6; [4]; linked by [#6] summary: [1] 4 [B.87 B.92] 10 nts=6 AUUCGU B.A87,B.U88,B.U89,B.C90,B.G91,B.U92 nts=4 UUCG B.U88,B.U89,B.C90,B.G91 4 hairpin loop: nts=6; [4]; linked by [#9] summary: [1] 4 [B.114 B.119] 7 nts=6 CUUCGG B.C114,B.U115,B.U116,B.C117,B.G118,B.G119 nts=4 UUCG B.U115,B.U116,B.C117,B.G118 5 hairpin loop: nts=6; [4]; linked by [#11] summary: [1] 4 [B.141 B.146] 10 nts=6 UUUCGG B.U141,B.U142,B.U143,B.C144,B.G145,B.G146 nts=4 UUCG B.U142,B.U143,B.C144,B.G145 6 hairpin loop: nts=6; [4]; linked by [#13] summary: [1] 4 [B.168 B.173] 10 nts=6 GUUCGC B.G168,B.U169,B.U170,B.C171,B.G172,B.C173 nts=4 UUCG B.U169,B.U170,B.C171,B.G172 7 hairpin loop: nts=6; [4]; linked by [#14] summary: [1] 4 [B.195 B.200] 13 nts=6 GUUCGU B.G195,B.U196,B.U197,B.C198,B.G199,B.U200 nts=4 UUCG B.U196,B.U197,B.C198,B.G199 8 hairpin loop: nts=11; [9]; linked by [#15] summary: [1] 9 [B.222 B.232] 10 nts=11 GAAGAGGUAAC B.G222,B.A223,B.A224,B.G225,B.A226,B.G227,B.G228,B.U229,B.A230,B.A231,B.C232 nts=9 AAGAGGUAA B.A223,B.A224,B.G225,B.A226,B.G227,B.G228,B.U229,B.A230,B.A231 9 hairpin loop: nts=11; [9]; linked by [#17] summary: [1] 9 [B.254 B.264] 10 nts=11 CAAAGGUAGAG B.C254,B.A255,B.A256,B.A257,B.G258,B.G259,B.U260,B.A261,B.G262,B.A263,B.G264 nts=9 AAAGGUAGA B.A255,B.A256,B.A257,B.G258,B.G259,B.U260,B.A261,B.G262,B.A263 10 hairpin loop: nts=13; [11]; linked by [#19] summary: [1] 11 [B.285 B.297] 9 nts=13 CAAAGGGAUAAUG B.C285,B.A286,B.A287,B.A288,B.G289,B.G290,B.G291,B.A292,B.U293,B.A294,B.A295,B.U296,B.G297 nts=11 AAAGGGAUAAU B.A286,B.A287,B.A288,B.G289,B.G290,B.G291,B.A292,B.U293,B.A294,B.A295,B.U296 11 hairpin loop: nts=11; [9]; linked by [#22] summary: [1] 9 [B.318 B.328] 10 nts=11 GAACUCACGAC B.G318,B.A319,B.A320,B.C321,B.U322,B.C323,B.A324,B.C325,B.G326,B.A327,B.C328 nts=9 AACUCACGA B.A319,B.A320,B.C321,B.U322,B.C323,B.A324,B.C325,B.G326,B.A327 12 hairpin loop: nts=62; [60]; linked by [#23] summary: [1] 60 [B.326 B.387] 6 nts=62 GACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAAC B.G326,B.A327,B.C328,B.U329,B.G330,B.G331,B.C332,B.A333,B.U334,B.C335,B.U336,B.A337,B.C338,B.G339,B.G340,B.G341,B.G342,B.A343,B.U344,B.G345,B.G346,B.U347,B.G348,B.C349,B.U350,B.C351,B.U352,B.C353,B.C354,B.C355,B.A356,B.A357,B.U358,B.U359,B.C360,B.U361,B.C362,B.C363,B.A364,B.U365,B.U366,B.U367,B.A368,B.C369,B.C370,B.G371,B.C372,B.C373,B.G374,B.A375,B.A376,B.U377,B.C378,B.G379,B.A380,B.C381,B.C382,B.C383,B.C384,B.A385,B.A386,B.C387 nts=60 ACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAA B.A327,B.C328,B.U329,B.G330,B.G331,B.C332,B.A333,B.U334,B.C335,B.U336,B.A337,B.C338,B.G339,B.G340,B.G341,B.G342,B.A343,B.U344,B.G345,B.G346,B.U347,B.G348,B.C349,B.U350,B.C351,B.U352,B.C353,B.C354,B.C355,B.A356,B.A357,B.U358,B.U359,B.C360,B.U361,B.C362,B.C363,B.A364,B.U365,B.U366,B.U367,B.A368,B.C369,B.C370,B.G371,B.C372,B.C373,B.G374,B.A375,B.A376,B.U377,B.C378,B.G379,B.A380,B.C381,B.C382,B.C383,B.C384,B.A385,B.A386 13 hairpin loop: nts=11; [9]; linked by [#26] summary: [1] 9 [B.384 B.394] 11 nts=11 CAACGUGAGAG B.C384,B.A385,B.A386,B.C387,B.G388,B.U389,B.G390,B.A391,B.G392,B.A393,B.G394 nts=9 AACGUGAGA B.A385,B.A386,B.C387,B.G388,B.U389,B.G390,B.A391,B.G392,B.A393 14 hairpin loop: nts=11; [9]; linked by [#28] summary: [1] 9 [B.418 B.428] 11 nts=11 CAAUAUCCCAG B.C418,B.A419,B.A420,B.U421,B.A422,B.U423,B.C424,B.C425,B.C426,B.A427,B.G428 nts=9 AAUAUCCCA B.A419,B.A420,B.U421,B.A422,B.U423,B.C424,B.C425,B.C426,B.A427 15 hairpin loop: nts=11; [9]; linked by [#31] summary: [1] 9 [B.452 B.462] 4 nts=11 GAACUACCUAC B.G452,B.A453,B.A454,B.C455,B.U456,B.A457,B.C458,B.C459,B.U460,B.A461,B.C462 nts=9 AACUACCUA B.A453,B.A454,B.C455,B.U456,B.A457,B.C458,B.C459,B.U460,B.A461 16 hairpin loop: nts=11; [9]; linked by [#34] summary: [1] 9 [B.486 B.496] 4 nts=11 CAAUACCUCAG B.C486,B.A487,B.A488,B.U489,B.A490,B.C491,B.C492,B.U493,B.C494,B.A495,B.G496 nts=9 AAUACCUCA B.A487,B.A488,B.U489,B.A490,B.C491,B.C492,B.U493,B.C494,B.A495 17 hairpin loop: nts=11; [9]; linked by [#36] summary: [1] 9 [B.520 B.530] 4 nts=11 AAACUGAACAU B.A520,B.A521,B.A522,B.C523,B.U524,B.G525,B.A526,B.A527,B.C528,B.A529,B.U530 nts=9 AACUGAACA B.A521,B.A522,B.C523,B.U524,B.G525,B.A526,B.A527,B.C528,B.A529 18 hairpin loop: nts=6; [4]; linked by [#37] summary: [1] 4 [B.553 B.558] 8 nts=6 GUUCGC B.G553,B.U554,B.U555,B.C556,B.G557,B.C558 nts=4 UUCG B.U554,B.U555,B.C556,B.G557 19 hairpin loop: nts=6; [4]; linked by [#39] summary: [1] 4 [B.580 B.585] 5 nts=6 GUUCGC B.G580,B.U581,B.U582,B.C583,B.G584,B.C585 nts=4 UUCG B.U581,B.U582,B.C583,B.G584 20 hairpin loop: nts=6; [4]; linked by [#-3] summary: [1] 4 [B.607 B.612] 1 nts=6 UUUCGA B.U607,B.U608,B.U609,B.C610,B.G611,B.A612 nts=4 UUCG B.U608,B.U609,B.C610,B.G611 21 hairpin loop: nts=6; [4]; linked by [#42] summary: [1] 4 [B.634 B.639] 7 nts=6 GUUCGC B.G634,B.U635,B.U636,B.C637,B.G638,B.C639 nts=4 UUCG B.U635,B.U636,B.C637,B.G638 22 hairpin loop: nts=6; [4]; linked by [#43] summary: [1] 4 [B.661 B.666] 10 nts=6 AUUCGU B.A661,B.U662,B.U663,B.C664,B.G665,B.U666 nts=4 UUCG B.U662,B.U663,B.C664,B.G665 23 hairpin loop: nts=6; [4]; linked by [#44] summary: [1] 4 [B.688 B.693] 13 nts=6 GUUCGC B.G688,B.U689,B.U690,B.C691,B.G692,B.C693 nts=4 UUCG B.U689,B.U690,B.C691,B.G692 **************************************************************************** List of 10 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#-1] summary: [2] 1 1 [B.13 B.343 B.15 B.341] 13 1 nts=6 UUCGGA B.U13,B.U14,B.C15,B.G341,B.G342,B.A343 nts=1 U B.U14 nts=1 G B.G342 2 symmetric internal loop: nts=6; [1,1]; linked by [#8,#9] summary: [2] 1 1 [B.106 B.127 B.108 B.125] 2 7 nts=6 UGUAUG B.U106,B.G107,B.U108,B.A125,B.U126,B.G127 nts=1 G B.G107 nts=1 U B.U126 3 symmetric internal loop: nts=6; [1,1]; linked by [#20,#21] summary: [2] 1 1 [B.290 B.425 B.292 B.423] 2 3 nts=6 GGAUCC B.G290,B.G291,B.A292,B.U423,B.C424,B.C425 nts=1 G B.G291 nts=1 C B.C424 4 symmetric internal loop: nts=6; [1,1]; linked by [#30,#31] summary: [2] 1 1 [B.447 B.467 B.449 B.465] 6 4 nts=6 UGGCUA B.U447,B.G448,B.G449,B.C465,B.U466,B.A467 nts=1 G B.G448 nts=1 U B.U466 5 symmetric internal loop: nts=6; [1,1]; linked by [#33,#34] summary: [2] 1 1 [B.481 B.501 B.483 B.499] 6 4 nts=6 UGAUUA B.U481,B.G482,B.A483,B.U499,B.U500,B.A501 nts=1 G B.G482 nts=1 U B.U500 6 symmetric internal loop: nts=6; [1,1]; linked by [#35,#36] summary: [2] 1 1 [B.515 B.535 B.517 B.533] 9 4 nts=6 AGCGUU B.A515,B.G516,B.C517,B.G533,B.U534,B.U535 nts=1 G B.G516 nts=1 U B.U534 7 symmetric internal loop: nts=6; [1,1]; linked by [#-2,#37] summary: [2] 1 1 [B.544 B.567 B.546 B.565] 1 8 nts=6 UUGCGA B.U544,B.U545,B.G546,B.C565,B.G566,B.A567 nts=1 U B.U545 nts=1 G B.G566 8 symmetric internal loop: nts=6; [1,1]; linked by [#38,#39] summary: [2] 1 1 [B.574 B.591 B.576 B.589] 4 5 nts=6 CGCGUG B.C574,B.G575,B.C576,B.G589,B.U590,B.G591 nts=1 G B.G575 nts=1 U B.U590 9 symmetric internal loop: nts=6; [1,1]; linked by [#40,#-3] summary: [2] 1 1 [B.605 B.614 B.607 B.612] 8 1 nts=6 GUUAGC B.G605,B.U606,B.U607,B.A612,B.G613,B.C614 nts=1 U B.U606 nts=1 G B.G613 10 symmetric internal loop: nts=6; [1,1]; linked by [#41,#42] summary: [2] 1 1 [B.626 B.647 B.628 B.645] 2 7 nts=6 GGUAUC B.G626,B.G627,B.U628,B.A645,B.U646,B.C647 nts=1 G B.G627 nts=1 U B.U646 **************************************************************************** List of 15 junctions 1 4-way junction: nts=8; [0,0,0,0]; linked by [#-1,#2,#4,#5] summary: [4] 0 0 0 0 [B.15 B.341 B.16 B.50 B.51 B.74 B.75 B.340] 1 13 10 3 nts=8 CAUAUCGG B.C15,B.A16,B.U50,B.A51,B.U74,B.C75,B.G340,B.G341 nts=0 nts=0 nts=0 nts=0 2 4-way junction: nts=8; [0,0,0,0]; linked by [#5,#6,#7,#22] summary: [4] 0 0 0 0 [B.77 B.338 B.78 B.101 B.102 B.308 B.309 B.337] 3 10 3 10 nts=8 GAUGCUAC B.G77,B.A78,B.U101,B.G102,B.C308,B.U309,B.A337,B.C338 nts=0 nts=0 nts=0 nts=0 3 4-way junction: nts=8; [0,0,0,0]; linked by [#7,#8,#10,#19] summary: [4] 0 0 0 0 [B.104 B.306 B.105 B.128 B.129 B.276 B.277 B.305] 3 2 3 9 nts=8 CUACGAUG B.C104,B.U105,B.A128,B.C129,B.G276,B.A277,B.U305,B.G306 nts=0 nts=0 nts=0 nts=0 4 4-way junction: nts=8; [0,0,0,0]; linked by [#10,#11,#12,#17] summary: [4] 0 0 0 0 [B.131 B.274 B.132 B.155 B.156 B.244 B.245 B.273] 3 10 3 10 nts=8 CAUCGUAG B.C131,B.A132,B.U155,B.C156,B.G244,B.U245,B.A273,B.G274 nts=0 nts=0 nts=0 nts=0 5 4-way junction: nts=8; [0,0,0,0]; linked by [#12,#13,#14,#15] summary: [4] 0 0 0 0 [B.158 B.242 B.159 B.182 B.183 B.212 B.213 B.241] 3 10 13 10 nts=8 GGUGCGCC B.G158,B.G159,B.U182,B.G183,B.C212,B.G213,B.C241,B.C242 nts=0 nts=0 nts=0 nts=0 6 4-way junction: nts=8; [0,0,0,0]; linked by [#24,#25,#43,#44] summary: [4] 0 0 0 0 [B.370 B.706 B.371 B.651 B.652 B.675 B.676 B.705] 15 3 10 13 nts=8 CGCCGUGG B.C370,B.G371,B.C651,B.C652,B.G675,B.U676,B.G705,B.G706 nts=0 nts=0 nts=0 nts=0 7 4-way junction: nts=8; [0,0,0,0]; linked by [#25,#26,#27,#41] summary: [4] 0 0 0 0 [B.373 B.649 B.374 B.404 B.405 B.624 B.625 B.648] 3 11 3 2 nts=8 CGCCGCGG B.C373,B.G374,B.C404,B.C405,B.G624,B.C625,B.G648,B.G649 nts=0 nts=0 nts=0 nts=0 8 4-way junction: nts=8; [0,0,0,0]; linked by [#27,#28,#29,#40] summary: [4] 0 0 0 0 [B.407 B.622 B.408 B.438 B.439 B.597 B.598 B.621] 3 11 3 8 nts=8 CGCCGAUG B.C407,B.G408,B.C438,B.C439,B.G597,B.A598,B.U621,B.G622 nts=0 nts=0 nts=0 nts=0 9 4-way junction: nts=8; [0,0,0,0]; linked by [#29,#30,#32,#38] summary: [4] 0 0 0 0 [B.441 B.595 B.442 B.472 B.473 B.570 B.571 B.594] 3 6 3 4 nts=8 CAUCGUAG B.C441,B.A442,B.U472,B.C473,B.G570,B.U571,B.A594,B.G595 nts=0 nts=0 nts=0 nts=0 10 4-way junction: nts=8; [0,0,0,0]; linked by [#32,#33,#35,#-2] summary: [4] 0 0 0 0 [B.475 B.568 B.476 B.506 B.507 B.543 B.544 B.567] 3 6 9 1 nts=8 GGCGCUAC B.G475,B.G476,B.C506,B.G507,B.C543,B.U544,B.A567,B.C568 nts=0 nts=0 nts=0 nts=0 11* 4-way junction: nts=14; [2,1,2,1]; linked by [#2,#3,#36,#3] summary: [4] 2 1 2 1 [B.28 B.38 B.31 B.528 B.530 B.520 B.523 B.36] 13 6 4 6 nts=14 CAAGCAUAAACGAG B.C28,B.A29,B.A30,B.G31,B.C528,B.A529,B.U530,B.A520,B.A521,B.A522,B.C523,B.G36,B.A37,B.G38 nts=2 AA B.A29,B.A30 nts=1 A B.A529 nts=2 AA B.A521,B.A522 nts=1 A B.A37 12* 4-way junction: nts=14; [2,1,2,1]; linked by [#15,#16,#34,#16] summary: [4] 2 1 2 1 [B.222 B.232 B.225 B.494 B.496 B.486 B.489 B.230] 10 6 4 6 nts=14 GAAGCAGCAAUAAC B.G222,B.A223,B.A224,B.G225,B.C494,B.A495,B.G496,B.C486,B.A487,B.A488,B.U489,B.A230,B.A231,B.C232 nts=2 AA B.A223,B.A224 nts=1 A B.A495 nts=2 AA B.A487,B.A488 nts=1 A B.A231 13* 4-way junction: nts=14; [2,1,2,1]; linked by [#17,#18,#31,#18] summary: [4] 2 1 2 1 [B.254 B.264 B.257 B.460 B.462 B.452 B.455 B.262] 10 6 4 6 nts=14 CAAAUACGAACGAG B.C254,B.A255,B.A256,B.A257,B.U460,B.A461,B.C462,B.G452,B.A453,B.A454,B.C455,B.G262,B.A263,B.G264 nts=2 AA B.A255,B.A256 nts=1 A B.A461 nts=2 AA B.A453,B.A454 nts=1 A B.A263 14* 4-way junction: nts=14; [2,1,2,1]; linked by [#22,#23,#26,#23] summary: [4] 2 1 2 1 [B.318 B.328 B.321 B.392 B.394 B.384 B.387 B.326] 10 6 11 6 nts=14 GAACGAGCAACGAC B.G318,B.A319,B.A320,B.C321,B.G392,B.A393,B.G394,B.C384,B.A385,B.A386,B.C387,B.G326,B.A327,B.C328 nts=2 AA B.A319,B.A320 nts=1 A B.A393 nts=2 AA B.A385,B.A386 nts=1 A B.A327 15 4-way junction: nts=16; [3,1,2,2]; linked by [#19,#20,#28,#21] summary: [4] 3 1 2 2 [B.285 B.297 B.289 B.426 B.428 B.418 B.421 B.294] 9 2 11 3 nts=16 CAAAGCAGCAAUAAUG B.C285,B.A286,B.A287,B.A288,B.G289,B.C426,B.A427,B.G428,B.C418,B.A419,B.A420,B.U421,B.A294,B.A295,B.U296,B.G297 nts=3 AAA B.A286,B.A287,B.A288 nts=1 A B.A427 nts=2 AA B.A419,B.A420 nts=2 AU B.A295,B.U296 **************************************************************************** List of 6 kissing loop interactions 1 stem #3 between hairpin loops #1 and #17 2 stem #16 between hairpin loops #8 and #16 3 stem #18 between hairpin loops #9 and #15 4 stem #20 between hairpin loops #10 and #14 5 stem #21 between hairpin loops #10 and #14 6 stem #23 between hairpin loops #11 and #13 **************************************************************************** List of 39 splayed-apart dinucleotides 1 B.C15 B.A16 angle=98 distance=13.9 ratio=0.76 2 B.U62 B.C63 angle=87 distance=13.1 ratio=0.69 3 B.U74 B.C75 angle=87 distance=14.7 ratio=0.69 4 B.U88 B.U89 angle=92 distance=13.6 ratio=0.72 5 B.U89 B.C90 angle=89 distance=13.9 ratio=0.70 6 B.U101 B.G102 angle=135 distance=17.8 ratio=0.93 7 B.U115 B.U116 angle=85 distance=13.3 ratio=0.68 8 B.U116 B.C117 angle=88 distance=13.2 ratio=0.70 9 B.A128 B.C129 angle=162 distance=17.7 ratio=0.99 10 B.U143 B.C144 angle=89 distance=13.3 ratio=0.70 11 B.U155 B.C156 angle=158 distance=18.6 ratio=0.98 12 B.U169 B.U170 angle=86 distance=13.4 ratio=0.68 13 B.U170 B.C171 angle=87 distance=13.1 ratio=0.69 14 B.U182 B.G183 angle=135 distance=19.6 ratio=0.92 15 B.U196 B.U197 angle=94 distance=13.7 ratio=0.73 16 B.U197 B.C198 angle=86 distance=13.3 ratio=0.68 17 B.C241 B.C242 angle=163 distance=18.3 ratio=0.99 18 B.A273 B.G274 angle=136 distance=18.7 ratio=0.93 19 B.U305 B.G306 angle=160 distance=18.0 ratio=0.99 20 B.A337 B.C338 angle=135 distance=17.0 ratio=0.92 21 B.C370 B.G371 angle=161 distance=18.7 ratio=0.99 22 B.A386 B.C387 angle=96 distance=14.5 ratio=0.74 23 B.C404 B.C405 angle=158 distance=18.8 ratio=0.98 24 B.C438 B.C439 angle=156 distance=19.4 ratio=0.98 25 B.U472 B.C473 angle=152 distance=18.5 ratio=0.97 26 B.U554 B.U555 angle=86 distance=13.4 ratio=0.68 27 B.U555 B.C556 angle=87 distance=13.2 ratio=0.69 28 B.U581 B.U582 angle=95 distance=13.8 ratio=0.74 29 B.U582 B.C583 angle=86 distance=13.2 ratio=0.68 30 B.A594 B.G595 angle=146 distance=18.9 ratio=0.96 31 B.U609 B.C610 angle=87 distance=13.3 ratio=0.69 32 B.U621 B.G622 angle=165 distance=19.2 ratio=0.99 33 B.U635 B.U636 angle=86 distance=13.3 ratio=0.68 34 B.U636 B.C637 angle=87 distance=13.1 ratio=0.69 35 B.G648 B.G649 angle=147 distance=18.8 ratio=0.96 36 B.U662 B.U663 angle=90 distance=13.4 ratio=0.71 37 B.G675 B.U676 angle=131 distance=19.3 ratio=0.91 38 B.U689 B.U690 angle=88 distance=13.0 ratio=0.70 39 B.U690 B.C691 angle=88 distance=13.4 ratio=0.69 ---------------------------------------------------------------- Summary of 31 splayed-apart units 1 nts=2 CA B.C15,B.A16 2 nts=2 UC B.U62,B.C63 3 nts=2 UC B.U74,B.C75 4 nts=3 UUC B.U88,B.U89,B.C90 5 nts=2 UG B.U101,B.G102 6 nts=3 UUC B.U115,B.U116,B.C117 7 nts=2 AC B.A128,B.C129 8 nts=2 UC B.U143,B.C144 9 nts=2 UC B.U155,B.C156 10 nts=3 UUC B.U169,B.U170,B.C171 11 nts=2 UG B.U182,B.G183 12 nts=3 UUC B.U196,B.U197,B.C198 13 nts=2 CC B.C241,B.C242 14 nts=2 AG B.A273,B.G274 15 nts=2 UG B.U305,B.G306 16 nts=2 AC B.A337,B.C338 17 nts=2 CG B.C370,B.G371 18 nts=2 AC B.A386,B.C387 19 nts=2 CC B.C404,B.C405 20 nts=2 CC B.C438,B.C439 21 nts=2 UC B.U472,B.C473 22 nts=3 UUC B.U554,B.U555,B.C556 23 nts=3 UUC B.U581,B.U582,B.C583 24 nts=2 AG B.A594,B.G595 25 nts=2 UC B.U609,B.C610 26 nts=2 UG B.U621,B.G622 27 nts=3 UUC B.U635,B.U636,B.C637 28 nts=2 GG B.G648,B.G649 29 nts=2 UU B.U662,B.U663 30 nts=2 GU B.G675,B.U676 31 nts=3 UUC B.U689,B.U690,B.C691 **************************************************************************** This structure contains 1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. **************************************************************************** List of 3 H-type pseudoknot loop segments 1 stem#22(hairpin#11) vs stem#23(hairpin#12) L1 groove=MAJOR nts=2 AA B.A319,B.A320 2 stem#22(hairpin#11) vs stem#23(hairpin#12) L2 groove=----- nts=1 A B.A327 3 stem#22(hairpin#11) vs stem#23(hairpin#12) L3 groove=----- nts=49 CGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAA B.C338,B.G339,B.G340,B.G341,B.G342,B.A343,B.U344,B.G345,B.G346,B.U347,B.G348,B.C349,B.U350,B.C351,B.U352,B.C353,B.C354,B.C355,B.A356,B.A357,B.U358,B.U359,B.C360,B.U361,B.C362,B.C363,B.A364,B.U365,B.U366,B.U367,B.A368,B.C369,B.C370,B.G371,B.C372,B.C373,B.G374,B.A375,B.A376,B.U377,B.C378,B.G379,B.A380,B.C381,B.C382,B.C383,B.C384,B.A385,B.A386 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7ptk nts=720 [whole] GGGAGAGUACUAUUCAGAUGCAGACCGCAAGUUCAGAGCGGUUUGCAUCUAGGGUACGUUUUCGAACGUAUCCUCCGACUAAGUGUAUUCGUAUACUUAGUGCCUUGUGCCUGCUUCGGCAGGCAUGACCCAAAUGUGCCUUUCGGGGCACAUUUCCGGUCAUCCAAGUUCGCUUGGGUGAUGCGGGCGUAUAGGUUCGUCUAUACGUCCGCGUUUUCCGAGAAGAGGUAACUCGGGAAACCGGUCCACGUGACAAAGGUAGAGUUACGUGGAGGGAGCAGCUGCAAAGGGAUAAUGCAGUUGCUGGCUGGAUGCCAGAACUCACGACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAACGUGAGAGGGGUCGGUUCCCCGAGCAUAGACCAAUAUCCCAGGUUUAUGCUCCCCAACGCUGGACGAACUACCUACGUCUAGCGUUCCGGCAAAUGAGUCAAUACCUCAGACUUAUUUGCGGUGCCUGAGCCUAAACUGAACAUGGGUUCAGGCAUCUUGGCUCCAGUUCGCUGGAGCCGACGGUAGCGCUGCGUUCGCGCAGUGCUAGGGAGCAUCCGUUUUCGAGCGGAUGCUGGGCGGUUGCCUGUUCGCAGGCAAUCGGGCCUACUCAUGAUUCGUCAUGAGUGGUGACAGCGUGAUGUUCGCAUUACGCUGUCGGGUAGAUGGAGAAUU (((((((((((((.((((((((((((((..[[[[[[.)))))))))))))((((((((((....))))))))))(((((((((((((....))))))))))(((((.(((((((....))))))).))(((((((((((((....))))))))))(((((((((((((....))))))))))(((((((((((((....)))))))))))))((((((((((..[[[[[[.)))))))))))))((((((((((..[[[[[[.)))))))))))))(((((((((...[[.[[[..))))))))))))((((((((((..[[[[[[.)))))))))))))).)))))))))))))(((((((((((((((((((((((((((((..]]]]]].)))))))))))((((((((((((((..]]].]].)))))))))))(((((((((.((((..]]]]]].)))).))))))(((((((((.((((..]]]]]].)))).))))))(((((((((.((((..]]]]]].)))).)))))))))(.((((((((....)))))))).))))((((.(((((....))))).)))))))((((((((.(....).)))))))))))((.(((((((....))))))).)))))((((((((((....))))))))))(((((((((((((....)))))))))))))))))))))))))))) >7ptk-B #1 nts=720 0.00(2.86) [chain] RNA GGGAGAGUACUAUUCAGAUGCAGACCGCAAGUUCAGAGCGGUUUGCAUCUAGGGUACGUUUUCGAACGUAUCCUCCGACUAAGUGUAUUCGUAUACUUAGUGCCUUGUGCCUGCUUCGGCAGGCAUGACCCAAAUGUGCCUUUCGGGGCACAUUUCCGGUCAUCCAAGUUCGCUUGGGUGAUGCGGGCGUAUAGGUUCGUCUAUACGUCCGCGUUUUCCGAGAAGAGGUAACUCGGGAAACCGGUCCACGUGACAAAGGUAGAGUUACGUGGAGGGAGCAGCUGCAAAGGGAUAAUGCAGUUGCUGGCUGGAUGCCAGAACUCACGACUGGCAUCUACGGGGAUGGUGCUCUCCCAAUUCUCCAUUUACCGCCGAAUCGACCCCAACGUGAGAGGGGUCGGUUCCCCGAGCAUAGACCAAUAUCCCAGGUUUAUGCUCCCCAACGCUGGACGAACUACCUACGUCUAGCGUUCCGGCAAAUGAGUCAAUACCUCAGACUUAUUUGCGGUGCCUGAGCCUAAACUGAACAUGGGUUCAGGCAUCUUGGCUCCAGUUCGCUGGAGCCGACGGUAGCGCUGCGUUCGCGCAGUGCUAGGGAGCAUCCGUUUUCGAGCGGAUGCUGGGCGGUUGCCUGUUCGCAGGCAAUCGGGCCUACUCAUGAUUCGUCAUGAGUGGUGACAGCGUGAUGUUCGCAUUACGCUGUCGGGUAGAUGGAGAAUU (((((((((((((.((((((((((((((..[[[[[[.)))))))))))))((((((((((....))))))))))(((((((((((((....))))))))))(((((.(((((((....))))))).))(((((((((((((....))))))))))(((((((((((((....))))))))))(((((((((((((....)))))))))))))((((((((((..[[[[[[.)))))))))))))((((((((((..[[[[[[.)))))))))))))(((((((((...[[.[[[..))))))))))))((((((((((..[[[[[[.)))))))))))))).)))))))))))))(((((((((((((((((((((((((((((..]]]]]].)))))))))))((((((((((((((..]]].]].)))))))))))(((((((((.((((..]]]]]].)))).))))))(((((((((.((((..]]]]]].)))).))))))(((((((((.((((..]]]]]].)))).)))))))))(.((((((((....)))))))).))))((((.(((((....))))).)))))))((((((((.(....).)))))))))))((.(((((((....))))))).)))))((((((((((....))))))))))(((((((((((((....)))))))))))))))))))))))))))) **************************************************************************** Summary of structural features of 720 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G ( B.G1 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 2 G ( B.G2 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 G ( B.G3 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 A ( B.A4 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( B.G5 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 A ( B.A6 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( B.G7 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 8 U ( B.U8 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 A ( B.A9 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 C ( B.C10 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 U ( B.U11 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 A ( B.A12 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 U ( B.U13 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 14 U . B.U14 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 15 C ( B.C15 0.019 anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,splayed-apart 16 A ( B.A16 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 17 G ( B.G17 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 A ( B.A18 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 U ( B.U19 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 G ( B.G20 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 C ( B.C21 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 A ( B.A22 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 G ( B.G23 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 A ( B.A24 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ( B.C25 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 C ( B.C26 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 G ( B.G27 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 C ( B.C28 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,phosphate 29 A . B.A29 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 30 A . B.A30 0.006 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop 31 G [ B.G31 0.021 pseudoknotted,turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 32 U [ B.U32 0.015 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 33 U [ B.U33 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 34 C [ B.C34 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 35 A [ B.A35 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 36 G [ B.G36 0.004 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 37 A . B.A37 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 38 G ) B.G38 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 39 C ) B.C39 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 G ) B.G40 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 41 G ) B.G41 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 U ) B.U42 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 43 U ) B.U43 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 44 U ) B.U44 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 45 G ) B.G45 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 46 C ) B.C46 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 A ) B.A47 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 48 U ) B.U48 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 49 C ) B.C49 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 50 U ) B.U50 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 51 A ( B.A51 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 52 G ( B.G52 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 53 G ( B.G53 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 G ( B.G54 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 55 U ( B.U55 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 56 A ( B.A56 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 57 C ( B.C57 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 58 G ( B.G58 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 59 U ( B.U59 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 U ( B.U60 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 61 U . B.U61 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 62 U . B.U62 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 63 C . B.C63 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 64 G . B.G64 0.007 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 65 A ) B.A65 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 66 A ) B.A66 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 67 C ) B.C67 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 G ) B.G68 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 69 U ) B.U69 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 70 A ) B.A70 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 71 U ) B.U71 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 72 C ) B.C72 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 73 C ) B.C73 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 74 U ) B.U74 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 75 C ( B.C75 0.021 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 76 C ( B.C76 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 77 G ( B.G77 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 78 A ( B.A78 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 79 C ( B.C79 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 80 U ( B.U80 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 81 A ( B.A81 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 82 A ( B.A82 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 83 G ( B.G83 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 84 U ( B.U84 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 85 G ( B.G85 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 86 U ( B.U86 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 87 A ( B.A87 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 88 U . B.U88 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 89 U . B.U89 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 90 C . B.C90 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 91 G . B.G91 0.006 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 92 U ) B.U92 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 93 A ) B.A93 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 94 U ) B.U94 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 95 A ) B.A95 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 96 C ) B.C96 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 97 U ) B.U97 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 98 U ) B.U98 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 99 A ) B.A99 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 100 G ) B.G100 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 101 U ) B.U101 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 102 G ( B.G102 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 103 C ( B.C103 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 104 C ( B.C104 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 105 U ( B.U105 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 106 U ( B.U106 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 107 G . B.G107 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 108 U ( B.U108 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 109 G ( B.G109 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 110 C ( B.C110 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 111 C ( B.C111 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 112 U ( B.U112 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 113 G ( B.G113 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 114 C ( B.C114 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 115 U . B.U115 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 116 U . B.U116 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 117 C . B.C117 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 118 G . B.G118 0.005 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 119 G ) B.G119 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 120 C ) B.C120 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 121 A ) B.A121 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 122 G ) B.G122 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 123 G ) B.G123 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 124 C ) B.C124 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 125 A ) B.A125 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 126 U . B.U126 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 127 G ) B.G127 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 128 A ) B.A128 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 129 C ( B.C129 0.027 ~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 130 C ( B.C130 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 131 C ( B.C131 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 132 A ( B.A132 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 133 A ( B.A133 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 134 A ( B.A134 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 135 U ( B.U135 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 136 G ( B.G136 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 137 U ( B.U137 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 138 G ( B.G138 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 139 C ( B.C139 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 140 C ( B.C140 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 141 U ( B.U141 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 142 U . B.U142 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 143 U . B.U143 0.004 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 144 C . B.C144 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 145 G . B.G145 0.005 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 146 G ) B.G146 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 147 G ) B.G147 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 148 G ) B.G148 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 149 C ) B.C149 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 150 A ) B.A150 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 151 C ) B.C151 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 152 A ) B.A152 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 153 U ) B.U153 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 154 U ) B.U154 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 155 U ) B.U155 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-acceptor,splayed-apart 156 C ( B.C156 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 157 C ( B.C157 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 158 G ( B.G158 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 159 G ( B.G159 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 160 U ( B.U160 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 161 C ( B.C161 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 162 A ( B.A162 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 163 U ( B.U163 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 164 C ( B.C164 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 165 C ( B.C165 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 166 A ( B.A166 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 167 A ( B.A167 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 168 G ( B.G168 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 169 U . B.U169 0.001 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 170 U . B.U170 0.004 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 171 C . B.C171 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 172 G . B.G172 0.005 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 173 C ) B.C173 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 174 U ) B.U174 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 175 U ) B.U175 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 176 G ) B.G176 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 177 G ) B.G177 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 178 G ) B.G178 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 179 U ) B.U179 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 180 G ) B.G180 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 181 A ) B.A181 0.016 turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 182 U ) B.U182 0.007 turn,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 183 G ( B.G183 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 184 C ( B.C184 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 185 G ( B.G185 0.009 turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-acceptor,phosphate 186 G ( B.G186 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 187 G ( B.G187 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 188 C ( B.C188 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 189 G ( B.G189 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 190 U ( B.U190 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 191 A ( B.A191 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 192 U ( B.U192 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 193 A ( B.A193 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 194 G ( B.G194 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 195 G ( B.G195 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 196 U . B.U196 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 197 U . B.U197 0.005 turn,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 198 C . B.C198 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 199 G . B.G199 0.007 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 200 U ) B.U200 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 201 C ) B.C201 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 202 U ) B.U202 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 203 A ) B.A203 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 204 U ) B.U204 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 205 A ) B.A205 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 206 C ) B.C206 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 207 G ) B.G207 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 208 U ) B.U208 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 209 C ) B.C209 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 210 C ) B.C210 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 211 G ) B.G211 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 212 C ) B.C212 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 213 G ( B.G213 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 214 U ( B.U214 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 215 U ( B.U215 0.015 anti,~C3'-endo,BI,non-stack,canonical,helix,stem,coaxial-stack 216 U ( B.U216 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 217 U ( B.U217 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 218 C ( B.C218 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 219 C ( B.C219 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 220 G ( B.G220 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 221 A ( B.A221 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 222 G ( B.G222 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 223 A . B.A223 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 224 A . B.A224 0.007 ~C2'-endo,non-pair-contact,hairpin-loop,junction-loop,kissing-loop 225 G [ B.G225 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop 226 A [ B.A226 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 227 G [ B.G227 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 228 G [ B.G228 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 229 U [ B.U229 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 230 A [ B.A230 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 231 A . B.A231 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 232 C ) B.C232 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 233 U ) B.U233 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 234 C ) B.C234 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 235 G ) B.G235 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 236 G ) B.G236 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 237 G ) B.G237 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 238 A ) B.A238 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 239 A ) B.A239 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 240 A ) B.A240 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 241 C ) B.C241 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 242 C ) B.C242 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 243 G ) B.G243 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 244 G ) B.G244 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 245 U ( B.U245 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 246 C ( B.C246 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 247 C ( B.C247 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 248 A ( B.A248 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 249 C ( B.C249 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 250 G ( B.G250 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 251 U ( B.U251 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 252 G ( B.G252 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 253 A ( B.A253 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 254 C ( B.C254 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 255 A . B.A255 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,phosphate 256 A . B.A256 0.007 ~C2'-endo,non-pair-contact,hairpin-loop,junction-loop,kissing-loop 257 A [ B.A257 0.008 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop 258 G [ B.G258 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 259 G [ B.G259 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 260 U [ B.U260 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 261 A [ B.A261 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 262 G [ B.G262 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 263 A . B.A263 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 264 G ) B.G264 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 265 U ) B.U265 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 266 U ) B.U266 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 267 A ) B.A267 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 268 C ) B.C268 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 269 G ) B.G269 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 270 U ) B.U270 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 271 G ) B.G271 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 272 G ) B.G272 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 273 A ) B.A273 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 274 G ) B.G274 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 275 G ) B.G275 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 276 G ) B.G276 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 277 A ( B.A277 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 278 G ( B.G278 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 279 C ( B.C279 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 280 A ( B.A280 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 281 G ( B.G281 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 282 C ( B.C282 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 283 U ( B.U283 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 284 G ( B.G284 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 285 C ( B.C285 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 286 A . B.A286 0.007 anti,~C2'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,kissing-loop 287 A . B.A287 0.010 BII,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,cap-donor,cap-acceptor 288 A . B.A288 0.005 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop,cap-acceptor,phosphate 289 G [ B.G289 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,cap-donor 290 G [ B.G290 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,internal-loop,kissing-loop,phosphate 291 G . B.G291 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,kissing-loop 292 A [ B.A292 0.011 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop,kissing-loop 293 U [ B.U293 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 294 A [ B.A294 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 295 A . B.A295 0.002 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,kissing-loop 296 U . B.U296 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 297 G ) B.G297 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 298 C ) B.C298 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 299 A ) B.A299 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 300 G ) B.G300 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 301 U ) B.U301 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 302 U ) B.U302 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 303 G ) B.G303 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 304 C ) B.C304 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 305 U ) B.U305 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 306 G ) B.G306 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 307 G ) B.G307 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 308 C ) B.C308 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 309 U ( B.U309 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 310 G ( B.G310 0.009 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 311 G ( B.G311 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 312 A ( B.A312 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 313 U ( B.U313 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 314 G ( B.G314 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 315 C ( B.C315 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 316 C ( B.C316 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 317 A ( B.A317 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 318 G ( B.G318 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 319 A . B.A319 0.019 ~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,phosphate 320 A . B.A320 0.006 ~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop 321 C [ B.C321 0.020 pseudoknotted,turn,anti,~C3'-endo,non-stack,canonical,non-canonical,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop 322 U [ B.U322 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop,phosphate 323 C [ B.C323 0.014 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 324 A [ B.A324 0.017 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 325 C [ B.C325 0.024 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 326 G [ B.G326 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 327 A . B.A327 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 328 C ) B.C328 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 329 U ) B.U329 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 330 G ) B.G330 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 331 G ) B.G331 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 332 C ) B.C332 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 333 A ) B.A333 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 334 U ) B.U334 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 335 C ) B.C335 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 336 U ) B.U336 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 337 A ) B.A337 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,splayed-apart 338 C ) B.C338 0.004 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate,splayed-apart 339 G ) B.G339 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 340 G ) B.G340 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 341 G ) B.G341 0.011 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,junction-loop 342 G . B.G342 0.015 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,internal-loop 343 A ) B.A343 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop,phosphate 344 U ) B.U344 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 345 G ) B.G345 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 346 G ) B.G346 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 347 U ) B.U347 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 348 G ) B.G348 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 349 C ) B.C349 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 350 U ) B.U350 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 351 C ) B.C351 0.004 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 352 U ) B.U352 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 353 C ) B.C353 0.005 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 354 C ) B.C354 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 355 C ) B.C355 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 356 A ( B.A356 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 357 A ( B.A357 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 358 U ( B.U358 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 359 U ( B.U359 0.011 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 360 C ( B.C360 0.012 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 361 U ( B.U361 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 362 C ( B.C362 0.004 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 363 C ( B.C363 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 364 A ( B.A364 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 365 U ( B.U365 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 366 U ( B.U366 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 367 U ( B.U367 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 368 A ( B.A368 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 369 C ( B.C369 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 370 C ( B.C370 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,cap-acceptor,splayed-apart 371 G ( B.G371 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate,splayed-apart 372 C ( B.C372 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 373 C ( B.C373 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 374 G ( B.G374 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 375 A ( B.A375 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 376 A ( B.A376 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 377 U ( B.U377 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 378 C ( B.C378 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 379 G ( B.G379 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 380 A ( B.A380 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 381 C ( B.C381 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 382 C ( B.C382 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 383 C ( B.C383 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 384 C ( B.C384 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 385 A . B.A385 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,phosphate 386 A . B.A386 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop,splayed-apart 387 C ] B.C387 0.011 pseudoknotted,turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,phosphate,splayed-apart 388 G ] B.G388 0.018 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 389 U ] B.U389 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 390 G ] B.G390 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 391 A ] B.A391 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 392 G ] B.G392 0.003 pseudoknotted,anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop 393 A . B.A393 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 394 G ) B.G394 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 395 G ) B.G395 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 396 G ) B.G396 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 397 G ) B.G397 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 398 U ) B.U398 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 399 C ) B.C399 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 400 G ) B.G400 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 401 G ) B.G401 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 402 U ) B.U402 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 403 U ) B.U403 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 404 C ) B.C404 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 405 C ( B.C405 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 406 C ( B.C406 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 407 C ( B.C407 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 408 G ( B.G408 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 409 A ( B.A409 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 410 G ( B.G410 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 411 C ( B.C411 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 412 A ( B.A412 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 413 U ( B.U413 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 414 A ( B.A414 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 415 G ( B.G415 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 416 A ( B.A416 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 417 C ( B.C417 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 418 C ( B.C418 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 419 A . B.A419 0.022 anti,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,cap-acceptor,phosphate 420 A . B.A420 0.007 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop,phosphate 421 U ] B.U421 0.005 pseudoknotted,turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,cap-donor 422 A ] B.A422 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 423 U ] B.U423 0.007 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop,kissing-loop 424 C . B.C424 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,kissing-loop 425 C ] B.C425 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,internal-loop,kissing-loop 426 C ] B.C426 0.002 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 427 A . B.A427 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 428 G ) B.G428 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 429 G ) B.G429 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 430 U ) B.U430 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 431 U ) B.U431 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 432 U ) B.U432 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 433 A ) B.A433 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 434 U ) B.U434 0.002 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 435 G ) B.G435 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 436 C ) B.C436 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 437 U ) B.U437 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 438 C ) B.C438 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 439 C ( B.C439 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 440 C ( B.C440 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 441 C ( B.C441 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 442 A ( B.A442 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 443 A ( B.A443 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 444 C ( B.C444 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 445 G ( B.G445 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 446 C ( B.C446 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 447 U ( B.U447 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 448 G . B.G448 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 449 G ( B.G449 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 450 A ( B.A450 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 451 C ( B.C451 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 452 G ( B.G452 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 453 A . B.A453 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 454 A . B.A454 0.007 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop 455 C ] B.C455 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 456 U ] B.U456 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop,phosphate 457 A ] B.A457 0.011 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 458 C ] B.C458 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 459 C ] B.C459 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 460 U ] B.U460 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop 461 A . B.A461 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 462 C ) B.C462 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 463 G ) B.G463 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 464 U ) B.U464 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 465 C ) B.C465 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 466 U . B.U466 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 467 A ) B.A467 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 468 G ) B.G468 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 469 C ) B.C469 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 470 G ) B.G470 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 471 U ) B.U471 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 472 U ) B.U472 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 473 C ( B.C473 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 474 C ( B.C474 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 475 G ( B.G475 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 476 G ( B.G476 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 477 C ( B.C477 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 478 A ( B.A478 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 479 A ( B.A479 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 480 A ( B.A480 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 481 U ( B.U481 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 482 G . B.G482 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 483 A ( B.A483 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 484 G ( B.G484 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 485 U ( B.U485 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 486 C ( B.C486 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 487 A . B.A487 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop,cap-donor,phosphate 488 A . B.A488 0.010 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop,cap-acceptor 489 U ] B.U489 0.015 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 490 A ] B.A490 0.012 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 491 C ] B.C491 0.012 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop,phosphate 492 C ] B.C492 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 493 U ] B.U493 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 494 C ] B.C494 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop 495 A . B.A495 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 496 G ) B.G496 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 497 A ) B.A497 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 498 C ) B.C498 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 499 U ) B.U499 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 500 U . B.U500 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 501 A ) B.A501 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 502 U ) B.U502 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 503 U ) B.U503 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 504 U ) B.U504 0.008 anti,~C3'-endo,non-stack,canonical,helix,stem,coaxial-stack 505 G ) B.G505 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 506 C ) B.C506 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 507 G ( B.G507 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 508 G ( B.G508 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 509 U ( B.U509 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 510 G ( B.G510 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 511 C ( B.C511 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 512 C ( B.C512 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 513 U ( B.U513 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 514 G ( B.G514 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 515 A ( B.A515 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 516 G . B.G516 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 517 C ( B.C517 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 518 C ( B.C518 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 519 U ( B.U519 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 520 A ( B.A520 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 521 A . B.A521 0.013 ~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 522 A . B.A522 0.005 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop,phosphate 523 C ] B.C523 0.017 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 524 U ] B.U524 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 525 G ] B.G525 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 526 A ] B.A526 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 527 A ] B.A527 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,kissing-loop 528 C ] B.C528 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 529 A . B.A529 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop,kissing-loop 530 U ) B.U530 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 531 G ) B.G531 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 532 G ) B.G532 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 533 G ) B.G533 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 534 U . B.U534 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 535 U ) B.U535 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 536 C ) B.C536 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 537 A ) B.A537 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 538 G ) B.G538 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 539 G ) B.G539 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 540 C ) B.C540 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 541 A ) B.A541 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 542 U ) B.U542 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 543 C ) B.C543 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 544 U ( B.U544 0.004 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 545 U . B.U545 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 546 G ( B.G546 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 547 G ( B.G547 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 548 C ( B.C548 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 549 U ( B.U549 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 550 C ( B.C550 0.006 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack 551 C ( B.C551 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 552 A ( B.A552 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 553 G ( B.G553 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 554 U . B.U554 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 555 U . B.U555 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 556 C . B.C556 0.005 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 557 G . B.G557 0.005 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 558 C ) B.C558 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 559 U ) B.U559 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 560 G ) B.G560 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 561 G ) B.G561 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 562 A ) B.A562 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 563 G ) B.G563 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 564 C ) B.C564 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 565 C ) B.C565 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 566 G . B.G566 0.014 ~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 567 A ) B.A567 0.009 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 568 C ) B.C568 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 569 G ) B.G569 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 570 G ) B.G570 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 571 U ( B.U571 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 572 A ( B.A572 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 573 G ( B.G573 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 574 C ( B.C574 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 575 G . B.G575 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 576 C ( B.C576 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 577 U ( B.U577 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 578 G ( B.G578 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 579 C ( B.C579 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 580 G ( B.G580 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 581 U . B.U581 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 582 U . B.U582 0.006 turn,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 583 C . B.C583 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 584 G . B.G584 0.006 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 585 C ) B.C585 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 586 G ) B.G586 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 587 C ) B.C587 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 588 A ) B.A588 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 589 G ) B.G589 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 590 U . B.U590 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 591 G ) B.G591 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 592 C ) B.C592 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 593 U ) B.U593 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 594 A ) B.A594 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 595 G ) B.G595 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 596 G ) B.G596 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 597 G ) B.G597 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 598 A ( B.A598 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 599 G ( B.G599 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 600 C ( B.C600 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 601 A ( B.A601 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 602 U ( B.U602 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 603 C ( B.C603 0.003 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack 604 C ( B.C604 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 605 G ( B.G605 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 606 U . B.U606 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 607 U ( B.U607 0.005 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop 608 U . B.U608 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 609 U . B.U609 0.004 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 610 C . B.C610 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 611 G . B.G611 0.011 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 612 A ) B.A612 0.005 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,cap-donor,phosphate 613 G . B.G613 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 614 C ) B.C614 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 615 G ) B.G615 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 616 G ) B.G616 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 617 A ) B.A617 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 618 U ) B.U618 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 619 G ) B.G619 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 620 C ) B.C620 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 621 U ) B.U621 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 622 G ) B.G622 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 623 G ) B.G623 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 624 G ) B.G624 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 625 C ( B.C625 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 626 G ( B.G626 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 627 G . B.G627 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 628 U ( B.U628 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 629 U ( B.U629 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 630 G ( B.G630 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 631 C ( B.C631 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 632 C ( B.C632 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 633 U ( B.U633 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 634 G ( B.G634 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 635 U . B.U635 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 636 U . B.U636 0.004 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 637 C . B.C637 0.004 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 638 G . B.G638 0.005 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 639 C ) B.C639 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 640 A ) B.A640 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 641 G ) B.G641 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 642 G ) B.G642 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 643 C ) B.C643 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 644 A ) B.A644 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 645 A ) B.A645 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 646 U . B.U646 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 647 C ) B.C647 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 648 G ) B.G648 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 649 G ) B.G649 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 650 G ) B.G650 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 651 C ) B.C651 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 652 C ( B.C652 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 653 U ( B.U653 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 654 A ( B.A654 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 655 C ( B.C655 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 656 U ( B.U656 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 657 C ( B.C657 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 658 A ( B.A658 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 659 U ( B.U659 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 660 G ( B.G660 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 661 A ( B.A661 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 662 U . B.U662 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 663 U . B.U663 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 664 C . B.C664 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop 665 G . B.G665 0.006 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 666 U ) B.U666 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 667 C ) B.C667 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 668 A ) B.A668 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 669 U ) B.U669 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 670 G ) B.G670 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 671 A ) B.A671 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 672 G ) B.G672 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 673 U ) B.U673 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 674 G ) B.G674 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 675 G ) B.G675 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 676 U ( B.U676 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 677 G ( B.G677 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 678 A ( B.A678 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 679 C ( B.C679 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 680 A ( B.A680 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 681 G ( B.G681 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 682 C ( B.C682 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 683 G ( B.G683 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 684 U ( B.U684 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 685 G ( B.G685 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 686 A ( B.A686 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 687 U ( B.U687 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 688 G ( B.G688 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 689 U . B.U689 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 690 U . B.U690 0.002 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 691 C . B.C691 0.002 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 692 G . B.G692 0.009 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 693 C ) B.C693 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 694 A ) B.A694 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 695 U ) B.U695 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 696 U ) B.U696 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 697 A ) B.A697 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 698 C ) B.C698 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 699 G ) B.G699 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 700 C ) B.C700 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 701 U ) B.U701 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 702 G ) B.G702 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 703 U ) B.U703 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 704 C ) B.C704 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 705 G ) B.G705 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 706 G ) B.G706 0.013 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 707 G ) B.G707 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 708 U ) B.U708 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 709 A ) B.A709 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 710 G ) B.G710 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 711 A ) B.A711 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 712 U ) B.U712 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 713 G ) B.G713 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 714 G ) B.G714 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 715 A ) B.A715 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 716 G ) B.G716 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 717 A ) B.A717 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 718 A ) B.A718 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 719 U ) B.U719 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 720 U ) B.U720 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack **************************************************************************** List of 18 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-iloops.pdb -- an ensemble of internal loops 7 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 8 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 9 dssr-2ndstrs.ct -- secondary structure in connectivity table format 10 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 11 dssr-torsions.txt -- backbone torsion angles and suite names 12 dssr-splays.pdb -- an ensemble of splayed-apart units 13 dssr-stacks.pdb -- an ensemble of base stacks 14 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 15 dssr-rotmat.txt -- position vector and rotation matrix 16 dssr-viewV.pdb -- vertical view of the principal moment of inertia 17 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 18 dssr-viewT.pdb -- top view of the principal moment of inertia