**************************************************************************** File name: 7nas.pdb no. of DNA/RNA chains: 1 [A=974] no. of nucleotides: 974 no. of atoms: 32390 no. of waters: 0 no. of metals: 43 [Mg=43] **************************************************************************** List of 4 types of 5 modified nucleotides nt count list 1 2MG-g 1 A.2MG1516 2 G7M-g 1 A.G7M527 3 MA6-a 2 A.MA6/1518,A.MA6/1519 4 PSU-P 1 A.PSU516 **************************************************************************** List of 492 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.A3 A.C613 A-C -- -- cSS cm-m 2 A.A3 A.G628 A+G Linker -- tSS tm+m 3 A.G9 A.C25 G-C WC 19-XIX cWW cW-W 4 A.A10 A.U24 A-U WC 20-XX cWW cW-W 5 A.G11 A.C23 G-C WC 19-XIX cWW cW-W 6 A.U12 A.G22 U-G Wobble 28-XXVIII cWW cW-W 7 A.U13 A.U20 U-U Calcutta -- tHW tM-W 8 A.U13 A.A915 U+A Hoogsteen 23-XXIII cWH cW+M 9 A.G15 A.U920 G-U Wobble 28-XXVIII cWW cW-W 10 A.A16 A.A919 A-A -- -- cWW cW-W 11 A.U17 A.A918 U-A WC 20-XX cWW cW-W 12 A.C18 A.G917 C-G WC 19-XIX cWW cW-W 13 A.A19 A.U916 A-U WC 20-XX cWW cW-W 14 A.U20 A.A915 U-A -- -- cWW cW-W 15 A.G21 A.A914 G-A Sheared 11-XI tSH tm-M 16 A.G22 A.A913 G+A Linker -- tSS tm+m 17 A.C23 A.U561 C+U -- -- cHW cM+W 18 A.C25 A.A559 C-A -- -- tHW tM-W 19 A.A26 A.G558 A-G Sheared 11-XI tHS tM-m 20 A.G27 A.C556 G-C WC 19-XIX cWW cW-W 21 A.A28 A.U555 A-U WC 20-XX cWW cW-W 22 A.U29 A.A554 U-A WC 20-XX cWW cW-W 23 A.U30 A.A553 U-A WC 20-XX cWW cW-W 24 A.A32 A.U552 A-U WC 20-XX cWW cW-W 25 A.A33 A.U551 A-U WC 20-XX cWW cW-W 26 A.C34 A.G550 C-G WC 19-XIX cWW cW-W 27 A.G35 A.C549 G-C WC 19-XIX cWW cW-W 28 A.C36 A.G548 C-G WC 19-XIX cWW cW-W 29 A.U37 A.A397 U+A rWC 21-XXI tWW tW+W 30 A.G39 A.C403 G-C WC 19-XIX cWW cW-W 31 A.C40 A.G402 C-G WC 19-XIX cWW cW-W 32 A.G41 A.C401 G-C WC 19-XIX cWW cW-W 33 A.G42 A.C400 G-C WC 19-XIX cWW cW-W 34 A.G42 A.A622 G+A Linker -- tSS tm+m 35 A.C43 A.G399 C-G WC 19-XIX cWW cW-W 36 A.A44 A.U398 A-U WC 20-XX cWW cW-W 37 A.G45 A.C396 G-C WC 19-XIX cWW cW-W 38 A.G46 A.C395 G-C WC 19-XIX cWW cW-W 39 A.C47 A.G361 C-G WC 19-XIX cWW cW-W 40 A.U49 A.G362 U-G -- -- cWS cW-m 41 A.U49 A.U365 U-U Calcutta -- tHW tM-W 42 A.A50 A.G360 A+G Linker -- tSS tm+m 43 A.A51 A.U114 A+U -- -- cHS cM+m 44 A.A51 A.C314 A-C -- -- cWS cW-m 45 A.C52 A.G359 C-G WC 19-XIX cWW cW-W 46 A.A53 A.U358 A-U WC 20-XX cWW cW-W 47 A.C54 A.G357 C-G WC 19-XIX cWW cW-W 48 A.A55 A.G357 A-G Sheared 11-XI tHS tM-m 49 A.A55 A.U368 A+U rWC 21-XXI tWW tW+W 50 A.U56 A.C352 U-C -- -- ..W ..-W 51 A.U56 A.A356 U-A WC 20-XX cWW cW-W 52 A.G57 A.C355 G-C WC 19-XIX cWW cW-W 53 A.C58 A.G354 C-G WC 19-XIX cWW cW-W 54 A.G61 A.C106 G-C WC 19-XIX cWW cW-W 55 A.U62 A.G105 U-G Wobble 28-XXVIII cWW cW-W 56 A.C63 A.G104 C-G WC 19-XIX cWW cW-W 57 A.G64 A.G68 G+G -- 06-VI cWH cW+M 58 A.G64 A.A101 G-A -- -- t.H t.-M 59 A.A66 A.U103 A-U WC 20-XX cWW cW-W 60 A.C67 A.G102 C-G WC 19-XIX cWW cW-W 61 A.G68 A.A101 G-A Imino 08-VIII cWW cW-W 62 A.G69 A.C99 G-C WC 19-XIX cWW cW-W 63 A.G69 A.G100 G-G -- -- tSH tm-M 64 A.U70 A.A71 U+A Platform -- cSH cm+M 65 A.U70 A.A98 U-A WC 20-XX cWW cW-W 66 A.A71 A.C99 A-C -- -- cWS cW-m 67 A.A72 A.G94 A-G -- -- tH. tM-. 68 A.A72 A.A98 A-A -- -- tWS tW-m 69 A.C73 A.G94 C-G -- -- t.W t.-W 70 A.C73 A.G97 C-G WC 19-XIX cWW cW-W 71 A.A74 A.U96 A-U WC 20-XX cWW cW-W 72 A.G75 A.C95 G-C WC 19-XIX cWW cW-W 73 A.G76 A.U93 G-U Wobble 28-XXVIII cWW cW-W 74 A.A77 A.U92 A-U WC 20-XX cWW cW-W 75 A.A78 A.U91 A-U WC 20-XX cWW cW-W 76 A.G79 A.C90 G-C WC 19-XIX cWW cW-W 77 A.A80 A.U89 A-U WC 20-XX cWW cW-W 78 A.A81 A.U88 A-U WC 20-XX cWW cW-W 79 A.G82 A.U84 G-U -- -- tWH tW-M 80 A.G82 A.C87 G-C WC 19-XIX cWW cW-W 81 A.G94 A.G97 G+G -- 06-VI cWH cW+M 82 A.C99 A.G100 C+G Platform -- cSH cm+M 83 A.G102 A.A151 G-A -- -- cSW cm-W 84 A.U103 A.A172 U+A -- -- tSW tm+W 85 A.A109 A.G324 A-G Sheared 11-XI tHS tM-m 86 A.G111 A.G331 G-G -- -- tWH tW-M 87 A.G112 A.A315 G-A -- -- cWW cW-W 88 A.G113 A.C314 G-C WC 19-XIX cWW cW-W 89 A.G113 A.A353 G-A -- -- cSS cm-m 90 A.U114 A.A313 U-A WC 20-XX cWW cW-W 91 A.G115 A.A116 G+A Platform -- cSH cm+M 92 A.G115 A.G117 G+G -- -- .SH .m+M 93 A.G115 A.C312 G-C WC 19-XIX cWW cW-W 94 A.A116 A.A313 A-A -- -- tWS tW-m 95 A.A119 A.U287 A-U rHoogsteen 24-XXIV tHW tM-W 96 A.G122 A.U239 G-U Wobble 28-XXVIII cWW cW-W 97 A.U123 A.A238 U-A WC 20-XX cWW cW-W 98 A.C124 A.G237 C-G WC 19-XIX cWW cW-W 99 A.U125 A.A236 U-A WC 20-XX cWW cW-W 100 A.G126 A.C235 G-C WC 19-XIX cWW cW-W 101 A.G127 A.C234 G-C WC 19-XIX cWW cW-W 102 A.G128 A.C233 G-C WC 19-XIX cWW cW-W 103 A.A129 A.G232 A-G Imino 08-VIII cWW cW-W 104 A.A130 A.C233 A-C -- -- .WS .W-m 105 A.A131 A.U231 A-U WC 20-XX cWW cW-W 106 A.C132 A.G230 C-G WC 19-XIX cWW cW-W 107 A.U133 A.U229 U-U -- 16-XVI cWW cW-W 108 A.C136 A.G227 C-G WC 19-XIX cWW cW-W 109 A.U137 A.G226 U-G Wobble 28-XXVIII cWW cW-W 110 A.G138 A.C225 G-C WC 19-XIX cWW cW-W 111 A.A139 A.U224 A-U WC 20-XX cWW cW-W 112 A.U140 A.A223 U-A WC 20-XX cWW cW-W 113 A.G141 A.C222 G-C WC 19-XIX cWW cW-W 114 A.G142 A.A196 G+A Linker -- tSW tm+W 115 A.G142 A.C221 G-C WC 19-XIX cWW cW-W 116 A.G144 A.C178 G-C WC 19-XIX cWW cW-W 117 A.G145 A.G177 G+G -- 06-VI cWH cW+M 118 A.G146 A.C176 G-C WC 19-XIX cWW cW-W 119 A.G147 A.C175 G-C WC 19-XIX cWW cW-W 120 A.G148 A.A174 G-A Imino 08-VIII cWW cW-W 121 A.A149 A.A172 A-A -- 05-V tWH tW-M 122 A.U150 A.A171 U-A rHoogsteen 24-XXIV tWH tW-M 123 A.A151 A.U170 A-U rHoogsteen 24-XXIV tHW tM-W 124 A.A152 A.C169 A-C -- -- tHW tM-W 125 A.C153 A.G168 C-G WC 19-XIX cWW cW-W 126 A.U154 A.A167 U-A WC 20-XX cWW cW-W 127 A.A155 A.U166 A-U WC 20-XX cWW cW-W 128 A.C156 A.G165 C-G WC 19-XIX cWW cW-W 129 A.U157 A.G164 U-G Wobble 28-XXVIII cWW cW-W 130 A.G158 A.C163 G-C WC 19-XIX cWW cW-W 131 A.G159 A.A162 G-A Sheared 11-XI tSH tm-M 132 A.A160 A.G347 A+G -- 10-X tWS tW+m 133 A.U173 A.G198 U+G -- -- cHS cM+m 134 A.A179 A.A196 A-A -- 05-V tWH tW-M 135 A.A182 A.C194 A-C ~rHoogsteen 25-XXV tHW tM-W 136 A.G184 A.C193 G-C WC 19-XIX cWW cW-W 137 A.U185 A.A192 U-A WC 20-XX cWW cW-W 138 A.C186 A.G191 C-G WC 19-XIX cWW cW-W 139 A.G187 A.A190 G-A Sheared 11-XI tSH tm-M 140 A.A197 A.G220 A+G Linker -- t.S t.+m 141 A.G198 A.U219 G-U Wobble 28-XXVIII cWW cW-W 142 A.A199 A.U218 A-U WC 20-XX cWW cW-W 143 A.G200 A.C217 G-C WC 19-XIX cWW cW-W 144 A.G201 A.U216 G-U Wobble 28-XXVIII cWW cW-W 145 A.G201 A.A468 G+A -- -- cWH cW+M 146 A.G202 A.C215 G-C WC 19-XIX cWW cW-W 147 A.G202 A.A465 G-A -- -- c.W c.-W 148 A.G202 A.A466 G-A -- -- cSW cm-W 149 A.G203 A.G204 G+G Platform -- cSH cm+M 150 A.G203 A.C214 G-C WC 19-XIX cWW cW-W 151 A.G203 A.A465 G-A -- -- cSW cm-W 152 A.A205 A.C214 A-C -- -- .W. .W-. 153 A.C206 A.G213 C-G WC 19-XIX cWW cW-W 154 A.C207 A.G212 C-G WC 19-XIX cWW cW-W 155 A.U208 A.G211 U+G -- -- tSW tm+W 156 A.C215 A.A466 C+A -- -- ..W ..+W 157 A.G232 A.A263 G+A Linker -- tSS tm+m 158 A.G240 A.C286 G-C WC 19-XIX cWW cW-W 159 A.G241 A.C285 G-C WC 19-XIX cWW cW-W 160 A.G242 A.C284 G-C WC 19-XIX cWW cW-W 161 A.A243 A.A282 A-A -- 05-V tWH tW-M 162 A.U244 A.C893 U-C -- 18-XVIII cWW cW-W 163 A.U244 A.A906 U+A -- -- cHS cM+m 164 A.U245 A.U283 U-U -- 16-XVI cWW cW-W 165 A.A246 A.G281 A-G Sheared 11-XI tHS tM-m 166 A.G247 A.C277 G-C WC 19-XIX cWW cW-W 167 A.G247 A.A282 G+A Linker -- tSS tm+m 168 A.C248 A.G276 C-G WC 19-XIX cWW cW-W 169 A.U249 A.G275 U-G Wobble 28-XXVIII cWW cW-W 170 A.G251 A.G254 G+G -- 06-VI cWH cW+M 171 A.G251 A.G255 G+G -- -- cWH cW+M 172 A.G251 A.C272 G-C -- -- .W. .W-. 173 A.U252 A.A274 U-A WC 20-XX cWW cW-W 174 A.A253 A.U273 A-U WC 20-XX cWW cW-W 175 A.G254 A.C272 G-C WC 19-XIX cWW cW-W 176 A.G255 A.G266 G+G -- 06-VI cHW cM+W 177 A.G255 A.C271 G-C WC 19-XIX cWW cW-W 178 A.U256 A.G266 U+G -- -- cHW cM+W 179 A.U256 A.A270 U-A WC 20-XX cWW cW-W 180 A.G257 A.C269 G-C WC 19-XIX cWW cW-W 181 A.G258 A.U268 G-U Wobble 28-XXVIII cWW cW-W 182 A.G259 A.C267 G-C WC 19-XIX cWW cW-W 183 A.G260 A.G265 G-G -- -- tWH tW-M 184 A.U261 A.A263 U-A -- -- tSH tm-M 185 A.G266 A.C271 G-C -- -- -- -- 186 A.G289 A.C311 G-C WC 19-XIX cWW cW-W 187 A.C290 A.G310 C-G WC 19-XIX cWW cW-W 188 A.U291 A.A309 U-A WC 20-XX cWW cW-W 189 A.G292 A.G305 G-G -- -- tHS tM-m 190 A.G292 A.C308 G-C WC 19-XIX cWW cW-W 191 A.G292 A.A608 G+A -- 10-X tSW tm+W 192 A.G293 A.U304 G-U Wobble 28-XXVIII cWW cW-W 193 A.U294 A.A303 U-A WC 20-XX cWW cW-W 194 A.C295 A.G302 C-G WC 19-XIX cWW cW-W 195 A.U296 A.G301 U-G Wobble 28-XXVIII cWW cW-W 196 A.G297 A.A300 G-A Sheared 11-XI tSH tm-M 197 A.G299 A.G566 G+G -- 06-VI cWH cW+M 198 A.A300 A.U565 A-U -- -- cSW cm-W 199 A.A309 A.A607 A-A -- -- cSW cm-W 200 A.C316 A.G337 C-G WC 19-XIX cWW cW-W 201 A.U317 A.A336 U-A WC 20-XX cWW cW-W 202 A.G318 A.C335 G-C WC 19-XIX cWW cW-W 203 A.G319 A.C334 G-C WC 19-XIX cWW cW-W 204 A.A320 A.U333 A-U WC 20-XX cWW cW-W 205 A.A321 A.G332 A-G Imino 08-VIII cWW cW-W 206 A.C322 A.A329 C-A ~rHoogsteen 25-XXV tWH tW-M 207 A.U323 A.A327 U-A rHoogsteen 24-XXIV tWH tW-M 208 A.A338 A.G351 A-G -- -- cWW cW-W 209 A.C339 A.G350 C-G WC 19-XIX cWW cW-W 210 A.U340 A.A349 U-A WC 20-XX cWW cW-W 211 A.C341 A.G348 C-G WC 19-XIX cWW cW-W 212 A.C342 A.G347 C-G WC 19-XIX cWW cW-W 213 A.U343 A.G346 U+G -- -- tSW tm+W 214 A.C352 A.A356 C+A -- -- cWH cW+M 215 A.G362 A.U365 G+U -- -- tWW tW+W 216 A.A366 A.G394 A-G -- -- cSW cm-W 217 A.U367 A.A393 U-A WC 20-XX cWW cW-W 218 A.G369 A.C392 G-C WC 19-XIX cWW cW-W 219 A.C370 A.G391 C-G WC 19-XIX cWW cW-W 220 A.A371 A.A373 A+A -- -- cSH cm+M 221 A.A371 A.U390 A-U WC 20-XX cWW cW-W 222 A.C372 A.A389 C-A ~rHoogsteen 25-XXV tWH tW-M 223 A.A373 A.G391 A-G -- -- cWS cW-m 224 A.A373 A.G481 A-G -- -- tSS tm-m 225 A.A374 A.U390 A-U -- -- cWS cW-m 226 A.U375 A.A389 U-A WC 20-XX cWW cW-W 227 A.G376 A.U387 G-U Wobble 28-XXVIII cWW cW-W 228 A.G377 A.C386 G-C WC 19-XIX cWW cW-W 229 A.G378 A.C385 G-C WC 19-XIX cWW cW-W 230 A.C379 A.G384 C-G WC 19-XIX cWW cW-W 231 A.G380 A.A383 G-A Sheared 11-XI tSH tm-M 232 A.G391 A.A482 G+A -- -- tSS tm+m 233 A.A397 A.A547 A+A -- -- cHS cM+m 234 A.G404 A.A498 G+A Linker -- tSS tm+m 235 A.G404 A.A499 G+A -- 09-IX cWH cW+M 236 A.U405 A.A499 U+A Hoogsteen 23-XXIII cWH cW+M 237 A.G406 A.C436 G-C WC 19-XIX cWW cW-W 238 A.U407 A.A435 U-A WC 20-XX cWW cW-W 239 A.A408 A.U434 A-U WC 20-XX cWW cW-W 240 A.U409 A.G433 U-G Wobble 28-XXVIII cWW cW-W 241 A.G410 A.A432 G-A Sheared 11-XI tSH tm-M 242 A.A411 A.A430 A-A -- 05-V tWH tW-M 243 A.A412 A.A431 A-A -- 05-V tHW tM-W 244 A.G413 A.G428 G+G -- 04-IV tSS tm+m 245 A.A414 A.A430 A-A -- 05-V tHW tM-W 246 A.A415 A.G428 A+G -- -- cHH cM+M 247 A.G416 A.U427 G-U Wobble 28-XXVIII cWW cW-W 248 A.G417 A.U426 G-U Wobble 28-XXVIII cWW cW-W 249 A.C418 A.G425 C-G WC 19-XIX cWW cW-W 250 A.C419 A.G424 C-G WC 19-XIX cWW cW-W 251 A.U420 A.C422 U+C -- -- .WW .W+W 252 A.U420 A.G423 U+G -- -- tWW tW+W 253 A.U429 A.A431 U+A Hoogsteen 23-XXIII cWH cW+M 254 A.U437 A.A495 U-A rHoogsteen 24-XXIV tWH tW-M 255 A.U438 A.A496 U-A rHoogsteen 24-XXIV tWH tW-M 256 A.U439 A.A496 U-A -- -- tHW tM-W 257 A.U439 A.A498 U-A WC 20-XX cWW cW-W 258 A.C440 A.G497 C-G WC 19-XIX cWW cW-W 259 A.A441 A.A493 A-A -- -- cWW cW-W 260 A.G442 A.C492 G-C WC 19-XIX cWW cW-W 261 A.C443 A.G491 C-G WC 19-XIX cWW cW-W 262 A.G444 A.C490 G-C WC 19-XIX cWW cW-W 263 A.G445 A.C489 G-C WC 19-XIX cWW cW-W 264 A.G446 A.C488 G-C WC 19-XIX cWW cW-W 265 A.G447 A.A487 G-A Sheared 11-XI tSH tm-M 266 A.A448 A.U486 A-U rHoogsteen 24-XXIV tHW tM-W 267 A.G449 A.G484 G+G -- 03-III tWW tW+W 268 A.G450 A.C483 G-C WC 19-XIX cWW cW-W 269 A.A452 A.U480 A+U rWC 21-XXI tWW tW+W 270 A.G453 A.U479 G-U -- -- cHW cM-W 271 A.G454 A.A478 G-A -- -- cWW cW-W 272 A.G455 A.C477 G-C WC 19-XIX cWW cW-W 273 A.A456 A.U476 A-U WC 20-XX cWW cW-W 274 A.G457 A.C475 G-C WC 19-XIX cWW cW-W 275 A.U458 A.G474 U-G Wobble 28-XXVIII cWW cW-W 276 A.A459 A.U473 A-U WC 20-XX cWW cW-W 277 A.A460 A.U472 A-U WC 20-XX cWW cW-W 278 A.A461 A.U471 A-U WC 20-XX cWW cW-W 279 A.G462 A.C470 G-C WC 19-XIX cWW cW-W 280 A.U463 A.C469 U-C -- -- cWW cW-W 281 A.U464 A.A468 U+A -- -- tSW tm+W 282 A.G494 A.G497 G+G -- -- cSH cm+M 283 A.A496 A.A498 A+A -- -- cWH cW+M 284 A.G500 A.C545 G-C WC 19-XIX cWW cW-W 285 A.C501 A.G544 C-G WC 19-XIX cWW cW-W 286 A.A502 A.U543 A-U WC 20-XX cWW cW-W 287 A.C503 A.G542 C-G WC 19-XIX cWW cW-W 288 A.C503 A.U543 C-U -- 18-XVIII cWW cW-W 289 A.C504 A.G541 C-G WC 19-XIX cWW cW-W 290 A.G505 A.C526 G-C WC 19-XIX cWW cW-W 291 A.G506 A.C525 G-C WC 19-XIX cWW cW-W 292 A.C507 A.G524 C-G WC 19-XIX cWW cW-W 293 A.U508 A.A509 U+A Platform -- cSH cm+M 294 A.U508 A.A510 U+A -- -- cSH cm+M 295 A.A509 A.U543 A-U -- -- cWS cW-m 296 A.A510 A.G542 A-G -- -- cSS cm-m 297 A.C511 A.G540 C-G WC 19-XIX cWW cW-W 298 A.U512 A.A539 U-A WC 20-XX cWW cW-W 299 A.C513 A.G538 C-G WC 19-XIX cWW cW-W 300 A.C514 A.G537 C-G WC 19-XIX cWW cW-W 301 A.G515 A.C536 G-C WC 19-XIX cWW cW-W 302 A.PSU516 A.A533 P-A -- -- tWH tW-M 303 A.PSU516 A.C536 P-C -- -- cWW cW-W 304 A.G521 A.C528 G-C WC 19-XIX cWW cW-W 305 A.C522 A.G7M527 C-g WC 19-XIX cWW cW-W 306 A.G7M527 A.A535 g+A Linker -- tSW tm+W 307 A.A563 A.U884 A+U rWC 21-XXI tWW tW+W 308 A.G567 A.C883 G-C WC 19-XIX cWW cW-W 309 A.G568 A.A574 G+A Linker -- tSS tm+m 310 A.G568 A.C882 G-C WC 19-XIX cWW cW-W 311 A.C569 A.G881 C-G WC 19-XIX cWW cW-W 312 A.G570 A.C866 G-C WC 19-XIX cWW cW-W 313 A.U571 A.A865 U-A WC 20-XX cWW cW-W 314 A.A572 A.A574 A-A -- -- cHH cM-M 315 A.A573 A.C883 A-C -- -- cWS cW-m 316 A.G575 A.C880 G-C WC 19-XIX cWW cW-W 317 A.G577 A.C764 G-C WC 19-XIX cWW cW-W 318 A.C578 A.G763 C-G WC 19-XIX cWW cW-W 319 A.A579 A.U762 A-U WC 20-XX cWW cW-W 320 A.C580 A.G761 C-G WC 19-XIX cWW cW-W 321 A.G581 A.G760 G-G -- -- t.H t.-M 322 A.C582 A.C758 C-C -- -- tHW tM-W 323 A.C582 A.A759 C-A ~rHoogsteen 25-XXV tWH tW-M 324 A.A583 A.C758 A-C ~Sheared -- tHS tM-m 325 A.G584 A.U757 G-U Wobble 28-XXVIII cWW cW-W 326 A.G585 A.C756 G-C WC 19-XIX cWW cW-W 327 A.C586 A.G755 C-G WC 19-XIX cWW cW-W 328 A.G588 A.C651 G-C WC 19-XIX cWW cW-W 329 A.U589 A.G650 U-G Wobble 28-XXVIII cWW cW-W 330 A.U590 A.A649 U-A WC 20-XX cWW cW-W 331 A.U591 A.A648 U-A WC 20-XX cWW cW-W 332 A.G592 A.C647 G-C WC 19-XIX cWW cW-W 333 A.U593 A.G646 U-G Wobble 28-XXVIII cWW cW-W 334 A.U594 A.G645 U-G Wobble 28-XXVIII cWW cW-W 335 A.A595 A.A596 A+A Platform -- cSH cm+M 336 A.A596 A.U644 A-U WC 20-XX cWW cW-W 337 A.G597 A.C643 G-C WC 19-XIX cWW cW-W 338 A.U598 A.A640 U-A WC 20-XX cWW cW-W 339 A.U598 A.A642 U-A -- -- cSW cm-W 340 A.C599 A.G639 C-G WC 19-XIX cWW cW-W 341 A.A600 A.U638 A-U WC 20-XX cWW cW-W 342 A.G601 A.C637 G-C WC 19-XIX cWW cW-W 343 A.A602 A.U636 A-U WC 20-XX cWW cW-W 344 A.U603 A.A635 U-A WC 20-XX cWW cW-W 345 A.G604 A.C634 G-C WC 19-XIX cWW cW-W 346 A.U605 A.G633 U-G Wobble 28-XXVIII cWW cW-W 347 A.C611 A.A629 C-A -- -- cWW cW-W 348 A.C612 A.G628 C-G WC 19-XIX cWW cW-W 349 A.C613 A.G627 C-G WC 19-XIX cWW cW-W 350 A.C614 A.G626 C-G WC 19-XIX cWW cW-W 351 A.G615 A.U625 G-U Wobble 28-XXVIII cWW cW-W 352 A.G616 A.C624 G-C WC 19-XIX cWW cW-W 353 A.G617 A.C623 G-C WC 19-XIX cWW cW-W 354 A.C618 A.A622 C-A ~rHoogsteen 25-XXV tWH tW-M 355 A.U641 A.C643 U+C -- -- cSH cm+M 356 A.U652 A.A753 U-A rHoogsteen 24-XXIV tWH tW-M 357 A.G654 A.G752 G-G -- -- tHS tM-m 358 A.G654 A.C754 G-C WC 19-XIX cWW cW-W 359 A.A655 A.U751 A-U WC 20-XX cWW cW-W 360 A.G656 A.C750 G-C WC 19-XIX cWW cW-W 361 A.U657 A.A749 U-A WC 20-XX cWW cW-W 362 A.C658 A.G748 C-G WC 19-XIX cWW cW-W 363 A.U659 A.A747 U-A WC 20-XX cWW cW-W 364 A.C660 A.G745 C-G WC 19-XIX cWW cW-W 365 A.G661 A.C744 G-C WC 19-XIX cWW cW-W 366 A.U662 A.A743 U-A WC 20-XX cWW cW-W 367 A.A663 A.G742 A-G Imino 08-VIII cWW cW-W 368 A.G664 A.G741 G-G -- -- cWW cW-W 369 A.A665 A.G724 A+G -- 09-IX cHW cM+W 370 A.G666 A.U740 G-U Wobble 28-XXVIII cWW cW-W 371 A.G667 A.C739 G-C WC 19-XIX cWW cW-W 372 A.G668 A.C738 G-C WC 19-XIX cWW cW-W 373 A.G669 A.C737 G-C WC 19-XIX cWW cW-W 374 A.G670 A.C736 G-C WC 19-XIX cWW cW-W 375 A.G671 A.C735 G-C WC 19-XIX cWW cW-W 376 A.U672 A.G734 U-G Wobble 28-XXVIII cWW cW-W 377 A.A673 A.U717 A-U WC 20-XX cWW cW-W 378 A.G674 A.A716 G-A -- -- cWW cW-W 379 A.A675 A.A715 A-A -- -- c.W c.-W 380 A.A676 A.G714 A-G Imino 08-VIII cWW cW-W 381 A.U677 A.G713 U-G sWobble -- cWW cW-W 382 A.U678 A.A712 U-A WC 20-XX cWW cW-W 383 A.C679 A.G711 C-G WC 19-XIX cWW cW-W 384 A.C680 A.G710 C-G WC 19-XIX cWW cW-W 385 A.A681 A.U709 A-U WC 20-XX cWW cW-W 386 A.G682 A.C708 G-C WC 19-XIX cWW cW-W 387 A.G683 A.U707 G-U Wobble 28-XXVIII cWW cW-W 388 A.U684 A.A706 U-A WC 20-XX cWW cW-W 389 A.G685 A.A704 G-A -- -- tWH tW-M 390 A.G685 A.G705 G-G -- -- tWH tW-M 391 A.U686 A.A704 U-A rHoogsteen 24-XXIV tWH tW-M 392 A.A687 A.G700 A+G Linker -- tWS tW+m 393 A.A687 A.G703 A-G Sheared 11-XI tHS tM-m 394 A.G688 A.C699 G-C WC 19-XIX cWW cW-W 395 A.G688 A.A704 G+A Linker -- tSS tm+m 396 A.C689 A.G698 C-G WC 19-XIX cWW cW-W 397 A.G690 A.A696 G-A -- -- tWH tW-M 398 A.U692 A.A695 U-A -- -- tSH tm-M 399 A.A695 A.G786 A-G -- -- cWS cW-m 400 A.G722 A.G733 G+G -- 03-III tWW tW+W 401 A.G725 A.C732 G-C WC 19-XIX cWW cW-W 402 A.C726 A.G731 C-G WC 19-XIX cWW cW-W 403 A.G727 A.G730 G-G -- -- tSH tm-M 404 A.G752 A.C754 G+C -- -- cSH cm+M 405 A.G765 A.A816 G-A -- -- cSW cm-W 406 A.A767 A.U813 A-U -- -- .HW .M-W 407 A.A768 A.C811 A-C -- -- cWW cW-W 408 A.G769 A.C810 G-C WC 19-XIX cWW cW-W 409 A.G769 A.A900 G-A -- -- cSW cm-W 410 A.C770 A.G809 C-G WC 19-XIX cWW cW-W 411 A.C770 A.C899 C-C -- -- cSW cm-W 412 A.G771 A.C808 G-C WC 19-XIX cWW cW-W 413 A.U772 A.A807 U-A WC 20-XX cWW cW-W 414 A.G773 A.C806 G-C WC 19-XIX cWW cW-W 415 A.G774 A.C805 G-C WC 19-XIX cWW cW-W 416 A.G775 A.U804 G-U -- -- cWH cW-M 417 A.G776 A.G803 G-G -- -- tWH tW-M 418 A.G776 A.U804 G-U -- -- cSW cm-W 419 A.G778 A.U804 G-U Wobble 28-XXVIII cWW cW-W 420 A.C779 A.G803 C-G WC 19-XIX cWW cW-W 421 A.A780 A.A802 A-A ~Sheared -- tSH tm-M 422 A.A781 A.U801 A-U rHoogsteen 24-XXIV tHW tM-W 423 A.A782 A.G800 A-G Sheared 11-XI tHS tM-m 424 A.C783 A.G799 C-G WC 19-XIX cWW cW-W 425 A.A784 A.U798 A-U WC 20-XX cWW cW-W 426 A.G785 A.C797 G-C WC 19-XIX cWW cW-W 427 A.G786 A.C796 G-C WC 19-XIX cWW cW-W 428 A.A787 A.C795 A-C -- -- cWH cW-M 429 A.U788 A.A794 U-A -- -- tWH tW-M 430 A.U788 A.C795 U-C -- -- cSW cm-W 431 A.C817 A.G1529 C-G WC 19-XIX cWW cW-W 432 A.U820 A.A873 U+A Hoogsteen 23-XXIII cWH cW+M 433 A.G821 A.C879 G-C WC 19-XIX cWW cW-W 434 A.U822 A.A878 U-A WC 20-XX cWW cW-W 435 A.C823 A.G877 C-G WC 19-XIX cWW cW-W 436 A.G824 A.C876 G-C WC 19-XIX cWW cW-W 437 A.A825 A.U875 A-U WC 20-XX cWW cW-W 438 A.C826 A.G874 C-G WC 19-XIX cWW cW-W 439 A.U827 A.A872 U+A rWC 21-XXI tWW tW+W 440 A.U828 A.G858 U-G -- -- t.S t.-m 441 A.G829 A.C857 G-C WC 19-XIX cWW cW-W 442 A.G830 A.C856 G-C WC 19-XIX cWW cW-W 443 A.A831 A.U855 A-U WC 20-XX cWW cW-W 444 A.G832 A.U854 G-U Wobble 28-XXVIII cWW cW-W 445 A.G833 A.C853 G-C WC 19-XIX cWW cW-W 446 A.U834 A.G852 U-G Wobble 28-XXVIII cWW cW-W 447 A.U835 A.G851 U-G Wobble 28-XXVIII cWW cW-W 448 A.G836 A.U850 G-U Wobble 28-XXVIII cWW cW-W 449 A.U837 A.G849 U-G Wobble 28-XXVIII cWW cW-W 450 A.G838 A.C848 G-C WC 19-XIX cWW cW-W 451 A.C839 A.G847 C-G WC 19-XIX cWW cW-W 452 A.C840 A.G846 C-G WC 19-XIX cWW cW-W 453 A.C841 A.A845 C-A ~rHoogsteen 25-XXV tWH tW-M 454 A.A860 A.G869 A-G Sheared 11-XI tHS tM-m 455 A.A860 A.A872 A-A -- 05-V tWH tW-M 456 A.G861 A.C868 G-C WC 19-XIX cWW cW-W 457 A.C862 A.G867 C-G WC 19-XIX cWW cW-W 458 A.U863 A.C866 U-C -- -- tWH tW-M 459 A.A864 A.G917 A+G Linker -- tSS tm+m 460 A.G867 A.A873 G+A Linker -- tSW tm+W 461 A.G885 A.C912 G-C WC 19-XIX cWW cW-W 462 A.G886 A.U911 G-U Wobble 28-XXVIII cWW cW-W 463 A.G887 A.C910 G-C WC 19-XIX cWW cW-W 464 A.G888 A.A909 G-A Sheared 11-XI tSH tm-M 465 A.A889 A.A908 A+A -- 02-II tHH tM+M 466 A.G890 A.U891 G+U Platform -- cSH cm+M 467 A.U891 A.A908 U-A -- -- tWH tW-M 468 A.A892 A.A906 A-A ~Sheared -- tHS tM-m 469 A.C893 A.A906 C-A -- -- cWS cW-m 470 A.G894 A.U905 G-U Wobble 28-XXVIII cWW cW-W 471 A.G895 A.U904 G-U Wobble 28-XXVIII cWW cW-W 472 A.C896 A.G903 C-G WC 19-XIX cWW cW-W 473 A.C897 A.G902 C-G WC 19-XIX cWW cW-W 474 A.G898 A.A901 G-A Sheared 11-XI tSH tm-M 475 A.U921 A.A1534 U-A WC 20-XX cWW cW-W 476 A.G922 A.C1533 G-C WC 19-XIX cWW cW-W 477 A.A923 A.U1532 A-U WC 20-XX cWW cW-W 478 A.G925 A.U1390 G-U -- -- tHW tM-W 479 A.G925 A.A1531 G-A -- -- cWW cW-W 480 A.G928 A.C1389 G-C WC 19-XIX cWW cW-W 481 A.G929 A.C1388 G-C WC 19-XIX cWW cW-W 482 A.C930 A.G1387 C-G WC 19-XIX cWW cW-W 483 A.G1392 A.A1503 G+A -- -- tHH tM+M 484 A.A1507 A.U1528 A-U WC 20-XX cWW cW-W 485 A.A1508 A.U1527 A-U WC 20-XX cWW cW-W 486 A.C1509 A.G1526 C-G WC 19-XIX cWW cW-W 487 A.C1510 A.G1525 C-G WC 19-XIX cWW cW-W 488 A.G1511 A.C1524 G-C WC 19-XIX cWW cW-W 489 A.U1512 A.G1523 U-G Wobble 28-XXVIII cWW cW-W 490 A.A1513 A.U1522 A-U WC 20-XX cWW cW-W 491 A.G1514 A.C1521 G-C WC 19-XIX cWW cW-W 492 A.G1515 A.C1520 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 67 multiplets 1 nts=3 ACG A.A3,A.C612,A.G628 2 nts=3 ACG A.A3,A.C613,A.G627 3 nts=3 GCA A.G9,A.C25,A.A559 4 nts=3 GCU A.G11,A.C23,A.U561 5 nts=3 UGA A.U12,A.G22,A.A913 6 nts=3 UUA A.U13,A.U20,A.A915 7 nts=3 CAG A.C18,A.A864,A.G917 8 nts=3 UAA A.U37,A.A397,A.A547 9 nts=3 UGU A.U49,A.G362,A.U365 10 nts=3* AUC A.A51,A.U114,A.C314 11 nts=3 UCA A.U56,A.C352,A.A356 12 nts=3 GGA A.G64,A.G68,A.A101 13 nts=3 GCG A.G69,A.C99,A.G100 14 nts=3 UAC A.U70,A.A71,A.C99 15 nts=3 UAA A.U70,A.A72,A.A98 16 nts=3 CGG A.C73,A.G94,A.G97 17 nts=3 GUC A.G82,A.U84,A.C87 18 nts=3 GCA A.G113,A.C314,A.A353 19 nts=3 UAA A.U114,A.A116,A.A313 20 nts=3 GGC A.G115,A.G117,A.C312 21 nts=3 GAC A.G128,A.A130,A.C233 22 nts=3 ACG A.A160,A.C342,A.G347 23 nts=3 UGU A.U173,A.G198,A.U219 24 nts=3 GCA A.G202,A.C215,A.A466 25 nts=3 UCA A.U244,A.C893,A.A906 26 nts=3 GGC A.G251,A.G254,A.C272 27 nts=3 GGC A.G255,A.G266,A.C271 28 nts=3 UAA A.U291,A.A309,A.A607 29 nts=3 GAU A.G297,A.A300,A.U565 30 nts=3 CGA A.C370,A.G391,A.A482 31 nts=3 CUA A.C372,A.U375,A.A389 32 nts=3 AAA A.A411,A.A414,A.A430 33 nts=3 AUA A.A412,A.U429,A.A431 34 nts=3 GAG A.G413,A.A415,A.G428 35 nts=3 UCG A.U420,A.C422,A.G423 36 nts=3 CGG A.C440,A.G494,A.G497 37 nts=3 CgA A.C522,A.G7M527,A.A535 38 nts=3 GAC A.G567,A.A573,A.C883 39 nts=3 GUC A.G570,A.U863,A.C866 40 nts=3 CCA A.C582,A.C758,A.A759 41 nts=3 AAU A.A595,A.A596,A.U644 42 nts=3 GUC A.G597,A.U641,A.C643 43 nts=3 UAA A.U598,A.A640,A.A642 44 nts=3 GGC A.G654,A.G752,A.C754 45 nts=3 AGG A.A687,A.G700,A.G703 46 nts=3 GCA A.G769,A.C810,A.A900 47 nts=3 CGC A.C770,A.G809,A.C899 48 nts=3 GGU A.G776,A.G778,A.U804 49 nts=3 GUA A.G925,A.U1390,A.A1531 50 nts=4 GCCA A.G42,A.C400,A.C618,A.A622 51 nts=4 CAGU A.C54,A.A55,A.G357,A.U368 52 nts=4 AUAA A.A66,A.U103,A.A149,A.A172 53 nts=4 CGAU A.C67,A.G102,A.A151,A.U170 54 nts=4 AGUA A.A129,A.G232,A.U261,A.A263 55 nts=4 GAAC A.G142,A.A179,A.A196,A.C221 56 nts=4 GUUA A.G201,A.U216,A.U464,A.A468 57 nts=4 GACA A.G203,A.A205,A.C214,A.A465 58 nts=4 AGCA A.A243,A.G247,A.C277,A.A282 59 nts=4 GGCA A.G292,A.G305,A.C308,A.A608 60 nts=4 AAUG A.A371,A.A373,A.U390,A.G481 61 nts=4 AUAU A.A502,A.U508,A.A509,A.U543 62 nts=4 CUAG A.C503,A.U508,A.A510,A.G542 63 nts=4 GAAC A.G568,A.A572,A.A574,A.C882 64 nts=4 GGCA A.G685,A.G688,A.C699,A.A704 65 nts=4 UAGC A.U692,A.A695,A.G786,A.C796 66 nts=4 UCGA A.U820,A.C862,A.G867,A.A873 67 nts=6 GUUAAA A.G404,A.U438,A.U439,A.A496,A.A498,A.A499 **************************************************************************** List of 27 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[1] bps=6 strand-1 5'-UCACAC-3' bp-type .|.||| strand-2 3'-GGGGUG-5' helix-form xxxA. 1 A.U49 A.G362 U-G -- -- cWS cW-m 2 A.C47 A.G361 C-G WC 19-XIX cWW cW-W 3 A.A50 A.G360 A+G Linker -- tSS tm+m 4 A.C52 A.G359 C-G WC 19-XIX cWW cW-W 5 A.A53 A.U358 A-U WC 20-XX cWW cW-W 6 A.C54 A.G357 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=4 strand-1 5'-AUGC-3' bp-type .||| strand-2 3'-UACG-5' helix-form x.. 1 A.A55 A.U368 A+U rWC 21-XXI tWW tW+W 2 A.U56 A.A356 U-A WC 20-XX cWW cW-W 3 A.G57 A.C355 G-C WC 19-XIX cWW cW-W 4 A.C58 A.G354 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[5] bps=19 strand-1 5'-GUCACGGUACAGGAAGAAG-3' bp-type |||||.||.|||||||||| strand-2 3'-CGGUGACAGGUCUUUCUUC-5' helix-form ..xA.x.xx.Ax.A.... 1 A.G61 A.C106 G-C WC 19-XIX cWW cW-W 2 A.U62 A.G105 U-G Wobble 28-XXVIII cWW cW-W 3 A.C63 A.G104 C-G WC 19-XIX cWW cW-W 4 A.A66 A.U103 A-U WC 20-XX cWW cW-W 5 A.C67 A.G102 C-G WC 19-XIX cWW cW-W 6 A.G68 A.A101 G-A Imino 08-VIII cWW cW-W 7 A.G69 A.C99 G-C WC 19-XIX cWW cW-W 8 A.U70 A.A98 U-A WC 20-XX cWW cW-W 9 A.A72 A.G94 A-G -- -- tH. tM-. 10 A.C73 A.G97 C-G WC 19-XIX cWW cW-W 11 A.A74 A.U96 A-U WC 20-XX cWW cW-W 12 A.G75 A.C95 G-C WC 19-XIX cWW cW-W 13 A.G76 A.U93 G-U Wobble 28-XXVIII cWW cW-W 14 A.A77 A.U92 A-U WC 20-XX cWW cW-W 15 A.A78 A.U91 A-U WC 20-XX cWW cW-W 16 A.G79 A.C90 G-C WC 19-XIX cWW cW-W 17 A.A80 A.U89 A-U WC 20-XX cWW cW-W 18 A.A81 A.U88 A-U WC 20-XX cWW cW-W 19 A.G82 A.C87 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[2] bps=15 strand-1 5'-AAAGUCCAGACUCCU-3' bp-type ....|||||.||||. strand-2 3'-GUCAAGGUCGGAGGG-5' helix-form xxx.A.AAx.AA.. 1 A.A109 A.G324 A-G Sheared 11-XI tHS tM-m 2 A.A327 A.U323 A-U rHoogsteen 24-XXIV tHW tM-W 3 A.A329 A.C322 A-C ~rHoogsteen 25-XXV tHW tM-W 4 A.G332 A.A321 G-A Imino 08-VIII cWW cW-W 5 A.U333 A.A320 U-A WC 20-XX cWW cW-W 6 A.C334 A.G319 C-G WC 19-XIX cWW cW-W 7 A.C335 A.G318 C-G WC 19-XIX cWW cW-W 8 A.A336 A.U317 A-U WC 20-XX cWW cW-W 9 A.G337 A.C316 G-C WC 19-XIX cWW cW-W 10 A.A338 A.G351 A-G -- -- cWW cW-W 11 A.C339 A.G350 C-G WC 19-XIX cWW cW-W 12 A.U340 A.A349 U-A WC 20-XX cWW cW-W 13 A.C341 A.G348 C-G WC 19-XIX cWW cW-W 14 A.C342 A.G347 C-G WC 19-XIX cWW cW-W 15 A.U343 A.G346 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#5[3] bps=15 strand-1 5'-GGGUGGCUGGUCUUG-3' bp-type ..|||||||||||.. strand-2 3'-GACACCGACUAGGAG-5' helix-form xA.AxAAAx.A.x. 1 A.G111 A.G331 G-G -- -- tWH tW-M 2 A.G112 A.A315 G-A -- -- cWW cW-W 3 A.G113 A.C314 G-C WC 19-XIX cWW cW-W 4 A.U114 A.A313 U-A WC 20-XX cWW cW-W 5 A.G115 A.C312 G-C WC 19-XIX cWW cW-W 6 A.G289 A.C311 G-C WC 19-XIX cWW cW-W 7 A.C290 A.G310 C-G WC 19-XIX cWW cW-W 8 A.U291 A.A309 U-A WC 20-XX cWW cW-W 9 A.G292 A.C308 G-C WC 19-XIX cWW cW-W 10 A.G293 A.U304 G-U Wobble 28-XXVIII cWW cW-W 11 A.U294 A.A303 U-A WC 20-XX cWW cW-W 12 A.C295 A.G302 C-G WC 19-XIX cWW cW-W 13 A.U296 A.G301 U-G Wobble 28-XXVIII cWW cW-W 14 A.U565 A.A300 U-A -- -- cWS cW-m 15 A.G566 A.G299 G+G -- 06-VI cHW cM+W -------------------------------------------------------------------------- helix#6[1] bps=7 strand-1 5'-AGGGUAA-3' bp-type .|||... strand-2 3'-UCCCUAG-5' helix-form xAAxxx 1 A.A119 A.U287 A-U rHoogsteen 24-XXIV tHW tM-W 2 A.G240 A.C286 G-C WC 19-XIX cWW cW-W 3 A.G241 A.C285 G-C WC 19-XIX cWW cW-W 4 A.G242 A.C284 G-C WC 19-XIX cWW cW-W 5 A.U245 A.U283 U-U -- 16-XVI cWW cW-W 6 A.A243 A.A282 A-A -- 05-V tWH tW-M 7 A.A246 A.G281 A-G Sheared 11-XI tHS tM-m -------------------------------------------------------------------------- helix#7[5] bps=28 strand-1 5'-GUCUGGGAACUCUGAUGGAGAGGGGCCU-3' bp-type |||||||.||.|||||||.||||||||. strand-2 3'-UAGACCCGUGUGGCUACCGUUCUCCGGG-5' helix-form .AA.A..xA.x..AAA.x..A..AxA. 1 A.G122 A.U239 G-U Wobble 28-XXVIII cWW cW-W 2 A.U123 A.A238 U-A WC 20-XX cWW cW-W 3 A.C124 A.G237 C-G WC 19-XIX cWW cW-W 4 A.U125 A.A236 U-A WC 20-XX cWW cW-W 5 A.G126 A.C235 G-C WC 19-XIX cWW cW-W 6 A.G127 A.C234 G-C WC 19-XIX cWW cW-W 7 A.G128 A.C233 G-C WC 19-XIX cWW cW-W 8 A.A129 A.G232 A-G Imino 08-VIII cWW cW-W 9 A.A131 A.U231 A-U WC 20-XX cWW cW-W 10 A.C132 A.G230 C-G WC 19-XIX cWW cW-W 11 A.U133 A.U229 U-U -- 16-XVI cWW cW-W 12 A.C136 A.G227 C-G WC 19-XIX cWW cW-W 13 A.U137 A.G226 U-G Wobble 28-XXVIII cWW cW-W 14 A.G138 A.C225 G-C WC 19-XIX cWW cW-W 15 A.A139 A.U224 A-U WC 20-XX cWW cW-W 16 A.U140 A.A223 U-A WC 20-XX cWW cW-W 17 A.G141 A.C222 G-C WC 19-XIX cWW cW-W 18 A.G142 A.C221 G-C WC 19-XIX cWW cW-W 19 A.A197 A.G220 A+G Linker -- t.S t.+m 20 A.G198 A.U219 G-U Wobble 28-XXVIII cWW cW-W 21 A.A199 A.U218 A-U WC 20-XX cWW cW-W 22 A.G200 A.C217 G-C WC 19-XIX cWW cW-W 23 A.G201 A.U216 G-U Wobble 28-XXVIII cWW cW-W 24 A.G202 A.C215 G-C WC 19-XIX cWW cW-W 25 A.G203 A.C214 G-C WC 19-XIX cWW cW-W 26 A.C206 A.G213 C-G WC 19-XIX cWW cW-W 27 A.C207 A.G212 C-G WC 19-XIX cWW cW-W 28 A.U208 A.G211 U+G -- -- tSW tm+W -------------------------------------------------------------------------- helix#8[2] bps=17 strand-1 5'-ACGGUAGCUAAACCGCA-3' bp-type .||||||.....||.|. strand-2 3'-GGUCAUCAAUAGGGGGA-5' helix-form ...AAA....xAA..x 1 A.A162 A.G159 A-G Sheared 11-XI tHS tM-m 2 A.C163 A.G158 C-G WC 19-XIX cWW cW-W 3 A.G164 A.U157 G-U Wobble 28-XXVIII cWW cW-W 4 A.G165 A.C156 G-C WC 19-XIX cWW cW-W 5 A.U166 A.A155 U-A WC 20-XX cWW cW-W 6 A.A167 A.U154 A-U WC 20-XX cWW cW-W 7 A.G168 A.C153 G-C WC 19-XIX cWW cW-W 8 A.C169 A.A152 C-A -- -- tWH tW-M 9 A.U170 A.A151 U-A rHoogsteen 24-XXIV tWH tW-M 10 A.A171 A.U150 A-U rHoogsteen 24-XXIV tHW tM-W 11 A.A172 A.A149 A-A -- 05-V tHW tM-W 12 A.A174 A.G148 A-G Imino 08-VIII cWW cW-W 13 A.C175 A.G147 C-G WC 19-XIX cWW cW-W 14 A.C176 A.G146 C-G WC 19-XIX cWW cW-W 15 A.G177 A.G145 G+G -- 06-VI cHW cM+W 16 A.C178 A.G144 C-G WC 19-XIX cWW cW-W 17 A.A179 A.A196 A-A -- 05-V tWH tW-M -------------------------------------------------------------------------- helix#9[1] bps=5 strand-1 5'-AGUCG-3' bp-type .|||. strand-2 3'-CCAGA-5' helix-form x.A. 1 A.A182 A.C194 A-C ~rHoogsteen 25-XXV tHW tM-W 2 A.G184 A.C193 G-C WC 19-XIX cWW cW-W 3 A.U185 A.A192 U-A WC 20-XX cWW cW-W 4 A.C186 A.G191 C-G WC 19-XIX cWW cW-W 5 A.G187 A.A190 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#10[2] bps=13 strand-1 5'-GCUUAGGUGGGGU-3' bp-type |||||||||||.. strand-2 3'-CGGAUCCACUCGA-5' helix-form ..x.AA.A..xx 1 A.G247 A.C277 G-C WC 19-XIX cWW cW-W 2 A.C248 A.G276 C-G WC 19-XIX cWW cW-W 3 A.U249 A.G275 U-G Wobble 28-XXVIII cWW cW-W 4 A.U252 A.A274 U-A WC 20-XX cWW cW-W 5 A.A253 A.U273 A-U WC 20-XX cWW cW-W 6 A.G254 A.C272 G-C WC 19-XIX cWW cW-W 7 A.G255 A.C271 G-C WC 19-XIX cWW cW-W 8 A.U256 A.A270 U-A WC 20-XX cWW cW-W 9 A.G257 A.C269 G-C WC 19-XIX cWW cW-W 10 A.G258 A.U268 G-U Wobble 28-XXVIII cWW cW-W 11 A.G259 A.C267 G-C WC 19-XIX cWW cW-W 12 A.G260 A.G265 G-G -- -- tWH tW-M 13 A.U261 A.A263 U-A -- -- tSH tm-M -------------------------------------------------------------------------- helix#11[6] bps=31 strand-1 5'-AGCCUAUGCAGCCUGCCGCAGCACCCUCCGP-3' bp-type .|||||||||.||||||||.||||||||||. strand-2 3'-GCGGGUACGUAGGACGGCGUCGUGGGAGGCA-5' helix-form .AA.xxA.x.x.xAAAAAxxAA..x.AA.x 1 A.A383 A.G380 A-G Sheared 11-XI tHS tM-m 2 A.G384 A.C379 G-C WC 19-XIX cWW cW-W 3 A.C385 A.G378 C-G WC 19-XIX cWW cW-W 4 A.C386 A.G377 C-G WC 19-XIX cWW cW-W 5 A.U387 A.G376 U-G Wobble 28-XXVIII cWW cW-W 6 A.A389 A.U375 A-U WC 20-XX cWW cW-W 7 A.U390 A.A371 U-A WC 20-XX cWW cW-W 8 A.G391 A.C370 G-C WC 19-XIX cWW cW-W 9 A.C392 A.G369 C-G WC 19-XIX cWW cW-W 10 A.A393 A.U367 A-U WC 20-XX cWW cW-W 11 A.G394 A.A366 G-A -- -- cWS cW-m 12 A.C395 A.G46 C-G WC 19-XIX cWW cW-W 13 A.C396 A.G45 C-G WC 19-XIX cWW cW-W 14 A.U398 A.A44 U-A WC 20-XX cWW cW-W 15 A.G399 A.C43 G-C WC 19-XIX cWW cW-W 16 A.C400 A.G42 C-G WC 19-XIX cWW cW-W 17 A.C401 A.G41 C-G WC 19-XIX cWW cW-W 18 A.G402 A.C40 G-C WC 19-XIX cWW cW-W 19 A.C403 A.G39 C-G WC 19-XIX cWW cW-W 20 A.A499 A.U405 A+U Hoogsteen 23-XXIII cHW cM+W 21 A.G500 A.C545 G-C WC 19-XIX cWW cW-W 22 A.C501 A.G544 C-G WC 19-XIX cWW cW-W 23 A.A502 A.U543 A-U WC 20-XX cWW cW-W 24 A.C503 A.G542 C-G WC 19-XIX cWW cW-W 25 A.C504 A.G541 C-G WC 19-XIX cWW cW-W 26 A.C511 A.G540 C-G WC 19-XIX cWW cW-W 27 A.U512 A.A539 U-A WC 20-XX cWW cW-W 28 A.C513 A.G538 C-G WC 19-XIX cWW cW-W 29 A.C514 A.G537 C-G WC 19-XIX cWW cW-W 30 A.G515 A.C536 G-C WC 19-XIX cWW cW-W 31 A.PSU516 A.A533 P-A -- -- tWH tW-M -------------------------------------------------------------------------- helix#12[6] bps=29 strand-1 5'-AGCGUUAAUCGGAGUAAUGAAUUGAGGGC-3' bp-type .|||||||||.||||..|||.||||.||| strand-2 3'-UCGCAAUUAGACUCGGUACUAGACUUCCG-5' helix-form xA.AAx..AxxAA.x...A..x.Axx.. 1 A.A397 A.U37 A+U rWC 21-XXI tWW tW+W 2 A.G548 A.C36 G-C WC 19-XIX cWW cW-W 3 A.C549 A.G35 C-G WC 19-XIX cWW cW-W 4 A.G550 A.C34 G-C WC 19-XIX cWW cW-W 5 A.U551 A.A33 U-A WC 20-XX cWW cW-W 6 A.U552 A.A32 U-A WC 20-XX cWW cW-W 7 A.A553 A.U30 A-U WC 20-XX cWW cW-W 8 A.A554 A.U29 A-U WC 20-XX cWW cW-W 9 A.U555 A.A28 U-A WC 20-XX cWW cW-W 10 A.C556 A.G27 C-G WC 19-XIX cWW cW-W 11 A.G558 A.A26 G-A Sheared 11-XI tSH tm-M 12 A.G9 A.C25 G-C WC 19-XIX cWW cW-W 13 A.A10 A.U24 A-U WC 20-XX cWW cW-W 14 A.G11 A.C23 G-C WC 19-XIX cWW cW-W 15 A.U12 A.G22 U-G Wobble 28-XXVIII cWW cW-W 16 A.A914 A.G21 A-G Sheared 11-XI tHS tM-m 17 A.A915 A.U20 A-U -- -- cWW cW-W 18 A.U916 A.A19 U-A WC 20-XX cWW cW-W 19 A.G917 A.C18 G-C WC 19-XIX cWW cW-W 20 A.A918 A.U17 A-U WC 20-XX cWW cW-W 21 A.A919 A.A16 A-A -- -- cWW cW-W 22 A.U920 A.G15 U-G Wobble 28-XXVIII cWW cW-W 23 A.U921 A.A1534 U-A WC 20-XX cWW cW-W 24 A.G922 A.C1533 G-C WC 19-XIX cWW cW-W 25 A.A923 A.U1532 A-U WC 20-XX cWW cW-W 26 A.G925 A.U1390 G-U -- -- tHW tM-W 27 A.G928 A.C1389 G-C WC 19-XIX cWW cW-W 28 A.G929 A.C1388 G-C WC 19-XIX cWW cW-W 29 A.C930 A.G1387 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#13[2] bps=15 strand-1 5'-CGGUUGAAAGUACUU-3' bp-type .||||....||||.. strand-2 3'-UCCGGAAUGUAUGAA-5' helix-form xA...xxx..AAx. 1 A.C422 A.U420 C+U -- -- .WW .W+W 2 A.G424 A.C419 G-C WC 19-XIX cWW cW-W 3 A.G425 A.C418 G-C WC 19-XIX cWW cW-W 4 A.U426 A.G417 U-G Wobble 28-XXVIII cWW cW-W 5 A.U427 A.G416 U-G Wobble 28-XXVIII cWW cW-W 6 A.G428 A.A415 G+A -- -- cHH cM+M 7 A.A430 A.A411 A-A -- 05-V tHW tM-W 8 A.A431 A.U429 A+U Hoogsteen 23-XXIII cHW cM+W 9 A.A432 A.G410 A-G Sheared 11-XI tHS tM-m 10 A.G433 A.U409 G-U Wobble 28-XXVIII cWW cW-W 11 A.U434 A.A408 U-A WC 20-XX cWW cW-W 12 A.A435 A.U407 A-U WC 20-XX cWW cW-W 13 A.C436 A.G406 C-G WC 19-XIX cWW cW-W 14 A.U437 A.A495 U-A rHoogsteen 24-XXIV tWH tW-M 15 A.U438 A.A496 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#14[2] bps=12 strand-1 5'-UCAGCGGGGAGG-3' bp-type ||.|||||...| strand-2 3'-AGACGCCCAUGC-5' helix-form .x.AAAA..x. 1 A.U439 A.A498 U-A WC 20-XX cWW cW-W 2 A.C440 A.G497 C-G WC 19-XIX cWW cW-W 3 A.A441 A.A493 A-A -- -- cWW cW-W 4 A.G442 A.C492 G-C WC 19-XIX cWW cW-W 5 A.C443 A.G491 C-G WC 19-XIX cWW cW-W 6 A.G444 A.C490 G-C WC 19-XIX cWW cW-W 7 A.G445 A.C489 G-C WC 19-XIX cWW cW-W 8 A.G446 A.C488 G-C WC 19-XIX cWW cW-W 9 A.G447 A.A487 G-A Sheared 11-XI tSH tm-M 10 A.A448 A.U486 A-U rHoogsteen 24-XXIV tHW tM-W 11 A.G449 A.G484 G+G -- 03-III tWW tW+W 12 A.G450 A.C483 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#15[1] bps=13 strand-1 5'-AGGGAGUAAAGUU-3' bp-type ...||||||||.. strand-2 3'-UUACUCGUUUCCA-5' helix-form ..AAA..AAA.. 1 A.A452 A.U480 A+U rWC 21-XXI tWW tW+W 2 A.G453 A.U479 G-U -- -- cHW cM-W 3 A.G454 A.A478 G-A -- -- cWW cW-W 4 A.G455 A.C477 G-C WC 19-XIX cWW cW-W 5 A.A456 A.U476 A-U WC 20-XX cWW cW-W 6 A.G457 A.C475 G-C WC 19-XIX cWW cW-W 7 A.U458 A.G474 U-G Wobble 28-XXVIII cWW cW-W 8 A.A459 A.U473 A-U WC 20-XX cWW cW-W 9 A.A460 A.U472 A-U WC 20-XX cWW cW-W 10 A.A461 A.U471 A-U WC 20-XX cWW cW-W 11 A.G462 A.C470 G-C WC 19-XIX cWW cW-W 12 A.U463 A.C469 U-C -- -- cWW cW-W 13 A.U464 A.A468 U+A -- -- tSW tm+W -------------------------------------------------------------------------- helix#16[2] bps=6 strand-1 5'-AGCCgC-3' bp-type .||||| strand-2 3'-UCGGCG-5' helix-form xA.x. 1 A.A510 A.U508 A+U -- -- cHS cM+m 2 A.G524 A.C507 G-C WC 19-XIX cWW cW-W 3 A.C525 A.G506 C-G WC 19-XIX cWW cW-W 4 A.C526 A.G505 C-G WC 19-XIX cWW cW-W 5 A.G7M527 A.C522 g-C WC 19-XIX cWW cW-W 6 A.C528 A.G521 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#17[2] bps=12 strand-1 5'-AGGCGGUCGACU-3' bp-type .||||||||||. strand-2 3'-UCCGCCAGCUGA-5' helix-form x.AxxAAA..x 1 A.A563 A.U884 A+U rWC 21-XXI tWW tW+W 2 A.G567 A.C883 G-C WC 19-XIX cWW cW-W 3 A.G568 A.C882 G-C WC 19-XIX cWW cW-W 4 A.C569 A.G881 C-G WC 19-XIX cWW cW-W 5 A.G575 A.C880 G-C WC 19-XIX cWW cW-W 6 A.G821 A.C879 G-C WC 19-XIX cWW cW-W 7 A.U822 A.A878 U-A WC 20-XX cWW cW-W 8 A.C823 A.G877 C-G WC 19-XIX cWW cW-W 9 A.G824 A.C876 G-C WC 19-XIX cWW cW-W 10 A.A825 A.U875 A-U WC 20-XX cWW cW-W 11 A.C826 A.G874 C-G WC 19-XIX cWW cW-W 12 A.U827 A.A872 U+A rWC 21-XXI tWW tW+W -------------------------------------------------------------------------- helix#18[1] bps=3 strand-1 5'-GUA-3' bp-type ||. strand-2 3'-CAA-5' helix-form Ax 1 A.G570 A.C866 G-C WC 19-XIX cWW cW-W 2 A.U571 A.A865 U-A WC 20-XX cWW cW-W 3 A.A572 A.A574 A-A -- -- cHH cM-M -------------------------------------------------------------------------- helix#19[1] bps=8 strand-1 5'-CCCCGGGC-3' bp-type .||||||. strand-2 3'-AGGGUCCA-5' helix-form .AA..A. 1 A.C611 A.A629 C-A -- -- cWW cW-W 2 A.C612 A.G628 C-G WC 19-XIX cWW cW-W 3 A.C613 A.G627 C-G WC 19-XIX cWW cW-W 4 A.C614 A.G626 C-G WC 19-XIX cWW cW-W 5 A.G615 A.U625 G-U Wobble 28-XXVIII cWW cW-W 6 A.G616 A.C624 G-C WC 19-XIX cWW cW-W 7 A.G617 A.C623 G-C WC 19-XIX cWW cW-W 8 A.C618 A.A622 C-A ~rHoogsteen 25-XXV tWH tW-M -------------------------------------------------------------------------- helix#20[7] bps=51 strand-1 5'-GCAUCUGACUGGCAAGCUGAGUCUCGUAGGGGGGGUAGAAUUCCAGGUGUA-3' bp-type |||||||||||||||||.|||||||||..||||||||....|||||||... strand-2 3'-UGUAGACUGAUUGUUUGACUCAGAGCAGGUCCCCCGUAAGGAGGUCUAGAG-5' helix-form .AAAA..x.x..AA..xxx.AA.xAA..x....A.xA....A..A..... 1 A.G633 A.U605 G-U Wobble 28-XXVIII cWW cW-W 2 A.C634 A.G604 C-G WC 19-XIX cWW cW-W 3 A.A635 A.U603 A-U WC 20-XX cWW cW-W 4 A.U636 A.A602 U-A WC 20-XX cWW cW-W 5 A.C637 A.G601 C-G WC 19-XIX cWW cW-W 6 A.U638 A.A600 U-A WC 20-XX cWW cW-W 7 A.G639 A.C599 G-C WC 19-XIX cWW cW-W 8 A.A640 A.U598 A-U WC 20-XX cWW cW-W 9 A.C643 A.G597 C-G WC 19-XIX cWW cW-W 10 A.U644 A.A596 U-A WC 20-XX cWW cW-W 11 A.G645 A.U594 G-U Wobble 28-XXVIII cWW cW-W 12 A.G646 A.U593 G-U Wobble 28-XXVIII cWW cW-W 13 A.C647 A.G592 C-G WC 19-XIX cWW cW-W 14 A.A648 A.U591 A-U WC 20-XX cWW cW-W 15 A.A649 A.U590 A-U WC 20-XX cWW cW-W 16 A.G650 A.U589 G-U Wobble 28-XXVIII cWW cW-W 17 A.C651 A.G588 C-G WC 19-XIX cWW cW-W 18 A.U652 A.A753 U-A rHoogsteen 24-XXIV tWH tW-M 19 A.G654 A.C754 G-C WC 19-XIX cWW cW-W 20 A.A655 A.U751 A-U WC 20-XX cWW cW-W 21 A.G656 A.C750 G-C WC 19-XIX cWW cW-W 22 A.U657 A.A749 U-A WC 20-XX cWW cW-W 23 A.C658 A.G748 C-G WC 19-XIX cWW cW-W 24 A.U659 A.A747 U-A WC 20-XX cWW cW-W 25 A.C660 A.G745 C-G WC 19-XIX cWW cW-W 26 A.G661 A.C744 G-C WC 19-XIX cWW cW-W 27 A.U662 A.A743 U-A WC 20-XX cWW cW-W 28 A.A663 A.G742 A-G Imino 08-VIII cWW cW-W 29 A.G664 A.G741 G-G -- -- cWW cW-W 30 A.G666 A.U740 G-U Wobble 28-XXVIII cWW cW-W 31 A.G667 A.C739 G-C WC 19-XIX cWW cW-W 32 A.G668 A.C738 G-C WC 19-XIX cWW cW-W 33 A.G669 A.C737 G-C WC 19-XIX cWW cW-W 34 A.G670 A.C736 G-C WC 19-XIX cWW cW-W 35 A.G671 A.C735 G-C WC 19-XIX cWW cW-W 36 A.U672 A.G734 U-G Wobble 28-XXVIII cWW cW-W 37 A.A673 A.U717 A-U WC 20-XX cWW cW-W 38 A.G674 A.A716 G-A -- -- cWW cW-W 39 A.A675 A.A715 A-A -- -- c.W c.-W 40 A.A676 A.G714 A-G Imino 08-VIII cWW cW-W 41 A.U677 A.G713 U-G sWobble -- cWW cW-W 42 A.U678 A.A712 U-A WC 20-XX cWW cW-W 43 A.C679 A.G711 C-G WC 19-XIX cWW cW-W 44 A.C680 A.G710 C-G WC 19-XIX cWW cW-W 45 A.A681 A.U709 A-U WC 20-XX cWW cW-W 46 A.G682 A.C708 G-C WC 19-XIX cWW cW-W 47 A.G683 A.U707 G-U Wobble 28-XXVIII cWW cW-W 48 A.U684 A.A706 U-A WC 20-XX cWW cW-W 49 A.G685 A.G705 G-G -- -- tWH tW-M 50 A.U686 A.A704 U-A rHoogsteen 24-XXIV tWH tW-M 51 A.A687 A.G703 A-G Sheared 11-XI tHS tM-m -------------------------------------------------------------------------- helix#21[1] bps=4 strand-1 5'-GCGU-3' bp-type ||.. strand-2 3'-CGAA-5' helix-form .xx 1 A.G688 A.C699 G-C WC 19-XIX cWW cW-W 2 A.C689 A.G698 C-G WC 19-XIX cWW cW-W 3 A.G690 A.A696 G-A -- -- tWH tW-M 4 A.U692 A.A695 U-A -- -- tSH tm-M -------------------------------------------------------------------------- helix#22[1] bps=5 strand-1 5'-GGGCG-3' bp-type ..||. strand-2 3'-GACGG-5' helix-form xxA. 1 A.G722 A.G733 G+G -- 03-III tWW tW+W 2 A.G724 A.A665 G+A -- 09-IX cWH cW+M 3 A.G725 A.C732 G-C WC 19-XIX cWW cW-W 4 A.C726 A.G731 C-G WC 19-XIX cWW cW-W 5 A.G727 A.G730 G-G -- -- tSH tm-M -------------------------------------------------------------------------- helix#23[2] bps=11 strand-1 5'-GCUCAGGUGCG-3' bp-type |||...||||. strand-2 3'-CGGACGCACGA-5' helix-form A.....AAAx 1 A.G755 A.C586 G-C WC 19-XIX cWW cW-W 2 A.C756 A.G585 C-G WC 19-XIX cWW cW-W 3 A.U757 A.G584 U-G Wobble 28-XXVIII cWW cW-W 4 A.C758 A.A583 C-A ~Sheared -- tSH tm-M 5 A.A759 A.C582 A-C ~rHoogsteen 25-XXV tHW tM-W 6 A.G760 A.G581 G-G -- -- tH. tM-. 7 A.G761 A.C580 G-C WC 19-XIX cWW cW-W 8 A.U762 A.A579 U-A WC 20-XX cWW cW-W 9 A.G763 A.C578 G-C WC 19-XIX cWW cW-W 10 A.C764 A.G577 C-G WC 19-XIX cWW cW-W 11 A.G765 A.A816 G-A -- -- cSW cm-W -------------------------------------------------------------------------- helix#24[3] bps=17 strand-1 5'-AAGCGUGGGCAAACAGG-3' bp-type ..||||||||...|||| strand-2 3'-UCCGCACCUGAUGGUCC-5' helix-form x....A.x.......A 1 A.A767 A.U813 A-U -- -- .HW .M-W 2 A.A768 A.C811 A-C -- -- cWW cW-W 3 A.G769 A.C810 G-C WC 19-XIX cWW cW-W 4 A.C770 A.G809 C-G WC 19-XIX cWW cW-W 5 A.G771 A.C808 G-C WC 19-XIX cWW cW-W 6 A.U772 A.A807 U-A WC 20-XX cWW cW-W 7 A.G773 A.C806 G-C WC 19-XIX cWW cW-W 8 A.G774 A.C805 G-C WC 19-XIX cWW cW-W 9 A.G778 A.U804 G-U Wobble 28-XXVIII cWW cW-W 10 A.C779 A.G803 C-G WC 19-XIX cWW cW-W 11 A.A780 A.A802 A-A ~Sheared -- tSH tm-M 12 A.A781 A.U801 A-U rHoogsteen 24-XXIV tHW tM-W 13 A.A782 A.G800 A-G Sheared 11-XI tHS tM-m 14 A.C783 A.G799 C-G WC 19-XIX cWW cW-W 15 A.A784 A.U798 A-U WC 20-XX cWW cW-W 16 A.G785 A.C797 G-C WC 19-XIX cWW cW-W 17 A.G786 A.C796 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#25[2] bps=17 strand-1 5'-AGGCGUGGCUUCCGAGC-3' bp-type .||||||||||||..|| strand-2 3'-CCCGUGUUGGAGGUGCG-5' helix-form .AA..........x.. 1 A.A845 A.C841 A-C ~rHoogsteen 25-XXV tHW tM-W 2 A.G846 A.C840 G-C WC 19-XIX cWW cW-W 3 A.G847 A.C839 G-C WC 19-XIX cWW cW-W 4 A.C848 A.G838 C-G WC 19-XIX cWW cW-W 5 A.G849 A.U837 G-U Wobble 28-XXVIII cWW cW-W 6 A.U850 A.G836 U-G Wobble 28-XXVIII cWW cW-W 7 A.G851 A.U835 G-U Wobble 28-XXVIII cWW cW-W 8 A.G852 A.U834 G-U Wobble 28-XXVIII cWW cW-W 9 A.C853 A.G833 C-G WC 19-XIX cWW cW-W 10 A.U854 A.G832 U-G Wobble 28-XXVIII cWW cW-W 11 A.U855 A.A831 U-A WC 20-XX cWW cW-W 12 A.C856 A.G830 C-G WC 19-XIX cWW cW-W 13 A.C857 A.G829 C-G WC 19-XIX cWW cW-W 14 A.G858 A.U828 G-U -- -- tS. tm-. 15 A.A860 A.G869 A-G Sheared 11-XI tHS tM-m 16 A.G861 A.C868 G-C WC 19-XIX cWW cW-W 17 A.C862 A.G867 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#26[2] bps=12 strand-1 5'-GGGGUACGGCCG-3' bp-type |||....||||. strand-2 3'-CUCAAAUUUGGA-5' helix-form ...xxxx..A. 1 A.G885 A.C912 G-C WC 19-XIX cWW cW-W 2 A.G886 A.U911 G-U Wobble 28-XXVIII cWW cW-W 3 A.G887 A.C910 G-C WC 19-XIX cWW cW-W 4 A.G888 A.A909 G-A Sheared 11-XI tSH tm-M 5 A.U891 A.A908 U-A -- -- tWH tW-M 6 A.A892 A.A906 A-A ~Sheared -- tHS tM-m 7 A.C893 A.U244 C-U -- 18-XVIII cWW cW-W 8 A.G894 A.U905 G-U Wobble 28-XXVIII cWW cW-W 9 A.G895 A.U904 G-U Wobble 28-XXVIII cWW cW-W 10 A.C896 A.G903 C-G WC 19-XIX cWW cW-W 11 A.C897 A.G902 C-G WC 19-XIX cWW cW-W 12 A.G898 A.A901 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#27[1] bps=9 strand-1 5'-AACCGUAGG-3' bp-type ||||||||| strand-2 3'-UUGGCGUCC-5' helix-form A..A..AA 1 A.A1507 A.U1528 A-U WC 20-XX cWW cW-W 2 A.A1508 A.U1527 A-U WC 20-XX cWW cW-W 3 A.C1509 A.G1526 C-G WC 19-XIX cWW cW-W 4 A.C1510 A.G1525 C-G WC 19-XIX cWW cW-W 5 A.G1511 A.C1524 G-C WC 19-XIX cWW cW-W 6 A.U1512 A.G1523 U-G Wobble 28-XXVIII cWW cW-W 7 A.A1513 A.U1522 A-U WC 20-XX cWW cW-W 8 A.G1514 A.C1521 G-C WC 19-XIX cWW cW-W 9 A.G1515 A.C1520 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 65 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[#12] bps=4 strand-1 5'-GAGU-3' bp-type |||| strand-2 3'-CUCG-5' helix-form AA. 1 A.G9 A.C25 G-C WC 19-XIX cWW cW-W 2 A.A10 A.U24 A-U WC 20-XX cWW cW-W 3 A.G11 A.C23 G-C WC 19-XIX cWW cW-W 4 A.U12 A.G22 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#2[#12] bps=3 strand-1 5'-UCA-3' bp-type ||| strand-2 3'-AGU-5' helix-form A. 1 A.U17 A.A918 U-A WC 20-XX cWW cW-W 2 A.C18 A.G917 C-G WC 19-XIX cWW cW-W 3 A.A19 A.U916 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#12] bps=4 strand-1 5'-GAUU-3' bp-type |||| strand-2 3'-CUAA-5' helix-form A.. 1 A.G27 A.C556 G-C WC 19-XIX cWW cW-W 2 A.A28 A.U555 A-U WC 20-XX cWW cW-W 3 A.U29 A.A554 U-A WC 20-XX cWW cW-W 4 A.U30 A.A553 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#4[#12] bps=5 strand-1 5'-AACGC-3' bp-type ||||| strand-2 3'-UUGCG-5' helix-form AA.A 1 A.A32 A.U552 A-U WC 20-XX cWW cW-W 2 A.A33 A.U551 A-U WC 20-XX cWW cW-W 3 A.C34 A.G550 C-G WC 19-XIX cWW cW-W 4 A.G35 A.C549 G-C WC 19-XIX cWW cW-W 5 A.C36 A.G548 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#11] bps=6 strand-1 5'-GCGGCA-3' bp-type |||||| strand-2 3'-CGCCGU-5' helix-form AAAAA 1 A.G39 A.C403 G-C WC 19-XIX cWW cW-W 2 A.C40 A.G402 C-G WC 19-XIX cWW cW-W 3 A.G41 A.C401 G-C WC 19-XIX cWW cW-W 4 A.G42 A.C400 G-C WC 19-XIX cWW cW-W 5 A.C43 A.G399 C-G WC 19-XIX cWW cW-W 6 A.A44 A.U398 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#11] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form . 1 A.G45 A.C396 G-C WC 19-XIX cWW cW-W 2 A.G46 A.C395 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#1] bps=3 strand-1 5'-CAC-3' bp-type ||| strand-2 3'-GUG-5' helix-form A. 1 A.C52 A.G359 C-G WC 19-XIX cWW cW-W 2 A.A53 A.U358 A-U WC 20-XX cWW cW-W 3 A.C54 A.G357 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#2] bps=3 strand-1 5'-UGC-3' bp-type ||| strand-2 3'-ACG-5' helix-form .. 1 A.U56 A.A356 U-A WC 20-XX cWW cW-W 2 A.G57 A.C355 G-C WC 19-XIX cWW cW-W 3 A.C58 A.G354 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#3] bps=3 strand-1 5'-GUC-3' bp-type ||| strand-2 3'-CGG-5' helix-form .. 1 A.G61 A.C106 G-C WC 19-XIX cWW cW-W 2 A.U62 A.G105 U-G Wobble 28-XXVIII cWW cW-W 3 A.C63 A.G104 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#10[#3] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A66 A.U103 A-U WC 20-XX cWW cW-W 2 A.C67 A.G102 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#3] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form . 1 A.G69 A.C99 G-C WC 19-XIX cWW cW-W 2 A.U70 A.A98 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#12[#3] bps=3 strand-1 5'-CAG-3' bp-type ||| strand-2 3'-GUC-5' helix-form .A 1 A.C73 A.G97 C-G WC 19-XIX cWW cW-W 2 A.A74 A.U96 A-U WC 20-XX cWW cW-W 3 A.G75 A.C95 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#13[#3] bps=7 strand-1 5'-GAAGAAG-3' bp-type ||||||| strand-2 3'-UUUCUUC-5' helix-form .A.... 1 A.G76 A.U93 G-U Wobble 28-XXVIII cWW cW-W 2 A.A77 A.U92 A-U WC 20-XX cWW cW-W 3 A.A78 A.U91 A-U WC 20-XX cWW cW-W 4 A.G79 A.C90 G-C WC 19-XIX cWW cW-W 5 A.A80 A.U89 A-U WC 20-XX cWW cW-W 6 A.A81 A.U88 A-U WC 20-XX cWW cW-W 7 A.G82 A.C87 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#14[#5] bps=3 strand-1 5'-GUG-3' bp-type ||| strand-2 3'-CAC-5' helix-form .A 1 A.G113 A.C314 G-C WC 19-XIX cWW cW-W 2 A.U114 A.A313 U-A WC 20-XX cWW cW-W 3 A.G115 A.C312 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#15[#7] bps=7 strand-1 5'-GUCUGGG-3' bp-type ||||||| strand-2 3'-UAGACCC-5' helix-form .AA.A. 1 A.G122 A.U239 G-U Wobble 28-XXVIII cWW cW-W 2 A.U123 A.A238 U-A WC 20-XX cWW cW-W 3 A.C124 A.G237 C-G WC 19-XIX cWW cW-W 4 A.U125 A.A236 U-A WC 20-XX cWW cW-W 5 A.G126 A.C235 G-C WC 19-XIX cWW cW-W 6 A.G127 A.C234 G-C WC 19-XIX cWW cW-W 7 A.G128 A.C233 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#16[#7] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A131 A.U231 A-U WC 20-XX cWW cW-W 2 A.C132 A.G230 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#17[#7] bps=7 strand-1 5'-CUGAUGG-3' bp-type ||||||| strand-2 3'-GGCUACC-5' helix-form ..AAA. 1 A.C136 A.G227 C-G WC 19-XIX cWW cW-W 2 A.U137 A.G226 U-G Wobble 28-XXVIII cWW cW-W 3 A.G138 A.C225 G-C WC 19-XIX cWW cW-W 4 A.A139 A.U224 A-U WC 20-XX cWW cW-W 5 A.U140 A.A223 U-A WC 20-XX cWW cW-W 6 A.G141 A.C222 G-C WC 19-XIX cWW cW-W 7 A.G142 A.C221 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#18[#8] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 A.G146 A.C176 G-C WC 19-XIX cWW cW-W 2 A.G147 A.C175 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#19[#8] bps=6 strand-1 5'-CUACUG-3' bp-type |||||| strand-2 3'-GAUGGC-5' helix-form AAA.. 1 A.C153 A.G168 C-G WC 19-XIX cWW cW-W 2 A.U154 A.A167 U-A WC 20-XX cWW cW-W 3 A.A155 A.U166 A-U WC 20-XX cWW cW-W 4 A.C156 A.G165 C-G WC 19-XIX cWW cW-W 5 A.U157 A.G164 U-G Wobble 28-XXVIII cWW cW-W 6 A.G158 A.C163 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#20[#9] bps=3 strand-1 5'-GUC-3' bp-type ||| strand-2 3'-CAG-5' helix-form .A 1 A.G184 A.C193 G-C WC 19-XIX cWW cW-W 2 A.U185 A.A192 U-A WC 20-XX cWW cW-W 3 A.C186 A.G191 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#21[#7] bps=6 strand-1 5'-GAGGGG-3' bp-type |||||| strand-2 3'-UUCUCC-5' helix-form .A..A 1 A.G198 A.U219 G-U Wobble 28-XXVIII cWW cW-W 2 A.A199 A.U218 A-U WC 20-XX cWW cW-W 3 A.G200 A.C217 G-C WC 19-XIX cWW cW-W 4 A.G201 A.U216 G-U Wobble 28-XXVIII cWW cW-W 5 A.G202 A.C215 G-C WC 19-XIX cWW cW-W 6 A.G203 A.C214 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#22[#7] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form A 1 A.C206 A.G213 C-G WC 19-XIX cWW cW-W 2 A.C207 A.G212 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#23[#6] bps=3 strand-1 5'-GGG-3' bp-type ||| strand-2 3'-CCC-5' helix-form AA 1 A.G240 A.C286 G-C WC 19-XIX cWW cW-W 2 A.G241 A.C285 G-C WC 19-XIX cWW cW-W 3 A.G242 A.C284 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#24[#10] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-CGG-5' helix-form .. 1 A.G247 A.C277 G-C WC 19-XIX cWW cW-W 2 A.C248 A.G276 C-G WC 19-XIX cWW cW-W 3 A.U249 A.G275 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#25[#10] bps=8 strand-1 5'-UAGGUGGG-3' bp-type |||||||| strand-2 3'-AUCCACUC-5' helix-form .AA.A.. 1 A.U252 A.A274 U-A WC 20-XX cWW cW-W 2 A.A253 A.U273 A-U WC 20-XX cWW cW-W 3 A.G254 A.C272 G-C WC 19-XIX cWW cW-W 4 A.G255 A.C271 G-C WC 19-XIX cWW cW-W 5 A.U256 A.A270 U-A WC 20-XX cWW cW-W 6 A.G257 A.C269 G-C WC 19-XIX cWW cW-W 7 A.G258 A.U268 G-U Wobble 28-XXVIII cWW cW-W 8 A.G259 A.C267 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#26[#5] bps=4 strand-1 5'-GCUG-3' bp-type |||| strand-2 3'-CGAC-5' helix-form AAA 1 A.G289 A.C311 G-C WC 19-XIX cWW cW-W 2 A.C290 A.G310 C-G WC 19-XIX cWW cW-W 3 A.U291 A.A309 U-A WC 20-XX cWW cW-W 4 A.G292 A.C308 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#27[#5] bps=4 strand-1 5'-GUCU-3' bp-type |||| strand-2 3'-UAGG-5' helix-form .A. 1 A.G293 A.U304 G-U Wobble 28-XXVIII cWW cW-W 2 A.U294 A.A303 U-A WC 20-XX cWW cW-W 3 A.C295 A.G302 C-G WC 19-XIX cWW cW-W 4 A.U296 A.G301 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#28[#4] bps=5 strand-1 5'-CUGGA-3' bp-type ||||| strand-2 3'-GACCU-5' helix-form AA.A 1 A.C316 A.G337 C-G WC 19-XIX cWW cW-W 2 A.U317 A.A336 U-A WC 20-XX cWW cW-W 3 A.G318 A.C335 G-C WC 19-XIX cWW cW-W 4 A.G319 A.C334 G-C WC 19-XIX cWW cW-W 5 A.A320 A.U333 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#29[#4] bps=4 strand-1 5'-CUCC-3' bp-type |||| strand-2 3'-GAGG-5' helix-form AA. 1 A.C339 A.G350 C-G WC 19-XIX cWW cW-W 2 A.U340 A.A349 U-A WC 20-XX cWW cW-W 3 A.C341 A.G348 C-G WC 19-XIX cWW cW-W 4 A.C342 A.G347 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#30[#11] bps=3 strand-1 5'-GCA-3' bp-type ||| strand-2 3'-CGU-5' helix-form .A 1 A.G369 A.C392 G-C WC 19-XIX cWW cW-W 2 A.C370 A.G391 C-G WC 19-XIX cWW cW-W 3 A.A371 A.U390 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#31[#11] bps=4 strand-1 5'-GGGC-3' bp-type |||| strand-2 3'-UCCG-5' helix-form .AA 1 A.G376 A.U387 G-U Wobble 28-XXVIII cWW cW-W 2 A.G377 A.C386 G-C WC 19-XIX cWW cW-W 3 A.G378 A.C385 G-C WC 19-XIX cWW cW-W 4 A.C379 A.G384 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#32[#13] bps=4 strand-1 5'-GUAU-3' bp-type |||| strand-2 3'-CAUG-5' helix-form AA. 1 A.G406 A.C436 G-C WC 19-XIX cWW cW-W 2 A.U407 A.A435 U-A WC 20-XX cWW cW-W 3 A.A408 A.U434 A-U WC 20-XX cWW cW-W 4 A.U409 A.G433 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#33[#13] bps=4 strand-1 5'-GGCC-3' bp-type |||| strand-2 3'-UUGG-5' helix-form ..A 1 A.G416 A.U427 G-U Wobble 28-XXVIII cWW cW-W 2 A.G417 A.U426 G-U Wobble 28-XXVIII cWW cW-W 3 A.C418 A.G425 C-G WC 19-XIX cWW cW-W 4 A.C419 A.G424 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#34[#14] bps=2 strand-1 5'-UC-3' bp-type || strand-2 3'-AG-5' helix-form . 1 A.U439 A.A498 U-A WC 20-XX cWW cW-W 2 A.C440 A.G497 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#35[#14] bps=5 strand-1 5'-GCGGG-3' bp-type ||||| strand-2 3'-CGCCC-5' helix-form AAAA 1 A.G442 A.C492 G-C WC 19-XIX cWW cW-W 2 A.C443 A.G491 C-G WC 19-XIX cWW cW-W 3 A.G444 A.C490 G-C WC 19-XIX cWW cW-W 4 A.G445 A.C489 G-C WC 19-XIX cWW cW-W 5 A.G446 A.C488 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#36[#15] bps=8 strand-1 5'-GAGUAAAG-3' bp-type |||||||| strand-2 3'-CUCGUUUC-5' helix-form AA..AAA 1 A.G455 A.C477 G-C WC 19-XIX cWW cW-W 2 A.A456 A.U476 A-U WC 20-XX cWW cW-W 3 A.G457 A.C475 G-C WC 19-XIX cWW cW-W 4 A.U458 A.G474 U-G Wobble 28-XXVIII cWW cW-W 5 A.A459 A.U473 A-U WC 20-XX cWW cW-W 6 A.A460 A.U472 A-U WC 20-XX cWW cW-W 7 A.A461 A.U471 A-U WC 20-XX cWW cW-W 8 A.G462 A.C470 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#37[#11] bps=5 strand-1 5'-GCACC-3' bp-type ||||| strand-2 3'-CGUGG-5' helix-form AA.. 1 A.G500 A.C545 G-C WC 19-XIX cWW cW-W 2 A.C501 A.G544 C-G WC 19-XIX cWW cW-W 3 A.A502 A.U543 A-U WC 20-XX cWW cW-W 4 A.C503 A.G542 C-G WC 19-XIX cWW cW-W 5 A.C504 A.G541 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#38[#16] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form .A 1 A.G505 A.C526 G-C WC 19-XIX cWW cW-W 2 A.G506 A.C525 G-C WC 19-XIX cWW cW-W 3 A.C507 A.G524 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#39[#11] bps=5 strand-1 5'-CUCCG-3' bp-type ||||| strand-2 3'-GAGGC-5' helix-form .AA. 1 A.C511 A.G540 C-G WC 19-XIX cWW cW-W 2 A.U512 A.A539 U-A WC 20-XX cWW cW-W 3 A.C513 A.G538 C-G WC 19-XIX cWW cW-W 4 A.C514 A.G537 C-G WC 19-XIX cWW cW-W 5 A.G515 A.C536 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#40[#16] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-Cg-5' helix-form . 1 A.G521 A.C528 G-C WC 19-XIX cWW cW-W 2 A.C522 A.G7M527 C-g WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#41[#17] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form .A 1 A.G567 A.C883 G-C WC 19-XIX cWW cW-W 2 A.G568 A.C882 G-C WC 19-XIX cWW cW-W 3 A.C569 A.G881 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#42[#18] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form A 1 A.G570 A.C866 G-C WC 19-XIX cWW cW-W 2 A.U571 A.A865 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#43[#23] bps=4 strand-1 5'-GCAC-3' bp-type |||| strand-2 3'-CGUG-5' helix-form AAA 1 A.G577 A.C764 G-C WC 19-XIX cWW cW-W 2 A.C578 A.G763 C-G WC 19-XIX cWW cW-W 3 A.A579 A.U762 A-U WC 20-XX cWW cW-W 4 A.C580 A.G761 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#44[#23] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-UCG-5' helix-form .A 1 A.G584 A.U757 G-U Wobble 28-XXVIII cWW cW-W 2 A.G585 A.C756 G-C WC 19-XIX cWW cW-W 3 A.C586 A.G755 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#45[#20] bps=7 strand-1 5'-GUUUGUU-3' bp-type ||||||| strand-2 3'-CGAACGG-5' helix-form ..AA.. 1 A.G588 A.C651 G-C WC 19-XIX cWW cW-W 2 A.U589 A.G650 U-G Wobble 28-XXVIII cWW cW-W 3 A.U590 A.A649 U-A WC 20-XX cWW cW-W 4 A.U591 A.A648 U-A WC 20-XX cWW cW-W 5 A.G592 A.C647 G-C WC 19-XIX cWW cW-W 6 A.U593 A.G646 U-G Wobble 28-XXVIII cWW cW-W 7 A.U594 A.G645 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#46[#20] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form . 1 A.A596 A.U644 A-U WC 20-XX cWW cW-W 2 A.G597 A.C643 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#47[#20] bps=8 strand-1 5'-UCAGAUGU-3' bp-type |||||||| strand-2 3'-AGUCUACG-5' helix-form ..AAAA. 1 A.U598 A.A640 U-A WC 20-XX cWW cW-W 2 A.C599 A.G639 C-G WC 19-XIX cWW cW-W 3 A.A600 A.U638 A-U WC 20-XX cWW cW-W 4 A.G601 A.C637 G-C WC 19-XIX cWW cW-W 5 A.A602 A.U636 A-U WC 20-XX cWW cW-W 6 A.U603 A.A635 U-A WC 20-XX cWW cW-W 7 A.G604 A.C634 G-C WC 19-XIX cWW cW-W 8 A.U605 A.G633 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#48[#19] bps=6 strand-1 5'-CCCGGG-3' bp-type |||||| strand-2 3'-GGGUCC-5' helix-form AA..A 1 A.C612 A.G628 C-G WC 19-XIX cWW cW-W 2 A.C613 A.G627 C-G WC 19-XIX cWW cW-W 3 A.C614 A.G626 C-G WC 19-XIX cWW cW-W 4 A.G615 A.U625 G-U Wobble 28-XXVIII cWW cW-W 5 A.G616 A.C624 G-C WC 19-XIX cWW cW-W 6 A.G617 A.C623 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#49[#20] bps=5 strand-1 5'-AGUCU-3' bp-type ||||| strand-2 3'-UCAGA-5' helix-form .AA. 1 A.A655 A.U751 A-U WC 20-XX cWW cW-W 2 A.G656 A.C750 G-C WC 19-XIX cWW cW-W 3 A.U657 A.A749 U-A WC 20-XX cWW cW-W 4 A.C658 A.G748 C-G WC 19-XIX cWW cW-W 5 A.U659 A.A747 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#50[#20] bps=3 strand-1 5'-CGU-3' bp-type ||| strand-2 3'-GCA-5' helix-form AA 1 A.C660 A.G745 C-G WC 19-XIX cWW cW-W 2 A.G661 A.C744 G-C WC 19-XIX cWW cW-W 3 A.U662 A.A743 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#51[#20] bps=7 strand-1 5'-GGGGGGU-3' bp-type ||||||| strand-2 3'-UCCCCCG-5' helix-form ....A. 1 A.G666 A.U740 G-U Wobble 28-XXVIII cWW cW-W 2 A.G667 A.C739 G-C WC 19-XIX cWW cW-W 3 A.G668 A.C738 G-C WC 19-XIX cWW cW-W 4 A.G669 A.C737 G-C WC 19-XIX cWW cW-W 5 A.G670 A.C736 G-C WC 19-XIX cWW cW-W 6 A.G671 A.C735 G-C WC 19-XIX cWW cW-W 7 A.U672 A.G734 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#52[#20] bps=7 strand-1 5'-UCCAGGU-3' bp-type ||||||| strand-2 3'-AGGUCUA-5' helix-form A..A.. 1 A.U678 A.A712 U-A WC 20-XX cWW cW-W 2 A.C679 A.G711 C-G WC 19-XIX cWW cW-W 3 A.C680 A.G710 C-G WC 19-XIX cWW cW-W 4 A.A681 A.U709 A-U WC 20-XX cWW cW-W 5 A.G682 A.C708 G-C WC 19-XIX cWW cW-W 6 A.G683 A.U707 G-U Wobble 28-XXVIII cWW cW-W 7 A.U684 A.A706 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#53[#21] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G688 A.C699 G-C WC 19-XIX cWW cW-W 2 A.C689 A.G698 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#54[#22] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G725 A.C732 G-C WC 19-XIX cWW cW-W 2 A.C726 A.G731 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#55[#24] bps=6 strand-1 5'-GCGUGG-3' bp-type |||||| strand-2 3'-CGCACC-5' helix-form ...A. 1 A.G769 A.C810 G-C WC 19-XIX cWW cW-W 2 A.C770 A.G809 C-G WC 19-XIX cWW cW-W 3 A.G771 A.C808 G-C WC 19-XIX cWW cW-W 4 A.U772 A.A807 U-A WC 20-XX cWW cW-W 5 A.G773 A.C806 G-C WC 19-XIX cWW cW-W 6 A.G774 A.C805 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#56[#24] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-UG-5' helix-form . 1 A.G778 A.U804 G-U Wobble 28-XXVIII cWW cW-W 2 A.C779 A.G803 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#57[#24] bps=4 strand-1 5'-CAGG-3' bp-type |||| strand-2 3'-GUCC-5' helix-form ..A 1 A.C783 A.G799 C-G WC 19-XIX cWW cW-W 2 A.A784 A.U798 A-U WC 20-XX cWW cW-W 3 A.G785 A.C797 G-C WC 19-XIX cWW cW-W 4 A.G786 A.C796 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#58[#17] bps=6 strand-1 5'-GUCGAC-3' bp-type |||||| strand-2 3'-CAGCUG-5' helix-form AAA.. 1 A.G821 A.C879 G-C WC 19-XIX cWW cW-W 2 A.U822 A.A878 U-A WC 20-XX cWW cW-W 3 A.C823 A.G877 C-G WC 19-XIX cWW cW-W 4 A.G824 A.C876 G-C WC 19-XIX cWW cW-W 5 A.A825 A.U875 A-U WC 20-XX cWW cW-W 6 A.C826 A.G874 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#59[#25] bps=12 strand-1 5'-GGAGGUUGUGCC-3' bp-type |||||||||||| strand-2 3'-CCUUCGGUGCGG-5' helix-form .........AA 1 A.G829 A.C857 G-C WC 19-XIX cWW cW-W 2 A.G830 A.C856 G-C WC 19-XIX cWW cW-W 3 A.A831 A.U855 A-U WC 20-XX cWW cW-W 4 A.G832 A.U854 G-U Wobble 28-XXVIII cWW cW-W 5 A.G833 A.C853 G-C WC 19-XIX cWW cW-W 6 A.U834 A.G852 U-G Wobble 28-XXVIII cWW cW-W 7 A.U835 A.G851 U-G Wobble 28-XXVIII cWW cW-W 8 A.G836 A.U850 G-U Wobble 28-XXVIII cWW cW-W 9 A.U837 A.G849 U-G Wobble 28-XXVIII cWW cW-W 10 A.G838 A.C848 G-C WC 19-XIX cWW cW-W 11 A.C839 A.G847 C-G WC 19-XIX cWW cW-W 12 A.C840 A.G846 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#60[#25] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G861 A.C868 G-C WC 19-XIX cWW cW-W 2 A.C862 A.G867 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#61[#26] bps=3 strand-1 5'-GGG-3' bp-type ||| strand-2 3'-CUC-5' helix-form .. 1 A.G885 A.C912 G-C WC 19-XIX cWW cW-W 2 A.G886 A.U911 G-U Wobble 28-XXVIII cWW cW-W 3 A.G887 A.C910 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#62[#26] bps=4 strand-1 5'-GGCC-3' bp-type |||| strand-2 3'-UUGG-5' helix-form ..A 1 A.G894 A.U905 G-U Wobble 28-XXVIII cWW cW-W 2 A.G895 A.U904 G-U Wobble 28-XXVIII cWW cW-W 3 A.C896 A.G903 C-G WC 19-XIX cWW cW-W 4 A.C897 A.G902 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#63[#12] bps=3 strand-1 5'-UGA-3' bp-type ||| strand-2 3'-ACU-5' helix-form .A 1 A.U921 A.A1534 U-A WC 20-XX cWW cW-W 2 A.G922 A.C1533 G-C WC 19-XIX cWW cW-W 3 A.A923 A.U1532 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#64[#12] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form .. 1 A.G928 A.C1389 G-C WC 19-XIX cWW cW-W 2 A.G929 A.C1388 G-C WC 19-XIX cWW cW-W 3 A.C930 A.G1387 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#65[#27] bps=9 strand-1 5'-AACCGUAGG-3' bp-type ||||||||| strand-2 3'-UUGGCGUCC-5' helix-form A..A..AA 1 A.A1507 A.U1528 A-U WC 20-XX cWW cW-W 2 A.A1508 A.U1527 A-U WC 20-XX cWW cW-W 3 A.C1509 A.G1526 C-G WC 19-XIX cWW cW-W 4 A.C1510 A.G1525 C-G WC 19-XIX cWW cW-W 5 A.G1511 A.C1524 G-C WC 19-XIX cWW cW-W 6 A.U1512 A.G1523 U-G Wobble 28-XXVIII cWW cW-W 7 A.A1513 A.U1522 A-U WC 20-XX cWW cW-W 8 A.G1514 A.C1521 G-C WC 19-XIX cWW cW-W 9 A.G1515 A.C1520 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 10 isolated WC/wobble pairs Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#12] -1 A.G15 A.U920 G-U Wobble 28-XXVIII cWW cW-W [#1] -2 A.C47 A.G361 C-G WC 19-XIX cWW cW-W [#8] -3 A.G144 A.C178 G-C WC 19-XIX cWW cW-W [#11] -4 A.U367 A.A393 U-A WC 20-XX cWW cW-W [#11] -5 A.U375 A.A389 U-A WC 20-XX cWW cW-W [#14] -6 A.G450 A.C483 G-C WC 19-XIX cWW cW-W [#17] -7 A.G575 A.C880 G-C WC 19-XIX cWW cW-W [#20] -8 A.G654 A.C754 G-C WC 19-XIX cWW cW-W [#20] -9 A.A673 A.U717 A-U WC 20-XX cWW cW-W -- -10 A.C817 A.G1529 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 17 coaxial stacks 1 Helix#3 contains 5 stems: [#9,#10,#11,#12,#13] 2 Helix#4 contains 2 stems: [#28,#29] 3 Helix#5 contains 3 stems: [#14,#26,#27] 4 Helix#7 contains 5 stems: [#15,#16,#17,#21,#22] 5 Helix#8 contains 2 stems: [#19,#18] 6 Helix#10 contains 2 stems: [#24,#25] 7 Helix#11 contains 6 stems: [#31,#30,#6,#5,#37,#39] 8 Helix#12 contains 6 stems: [#4,#3,#1,#2,#63,#64] 9 Helix#13 contains 2 stems: [#33,#32] 10 Helix#14 contains 2 stems: [#34,#35] 11 Helix#16 contains 2 stems: [#38,#40] 12 Helix#17 contains 2 stems: [#41,#58] 13 Helix#20 contains 7 stems: [#47,#46,#45,#49,#50,#51,#52] 14 Helix#23 contains 2 stems: [#44,#43] 15 Helix#24 contains 3 stems: [#55,#56,#57] 16 Helix#25 contains 2 stems: [#59,#60] 17 Helix#26 contains 2 stems: [#61,#62] **************************************************************************** List of 176 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 A.G9,A.A26 2 nts=2 GC A.G31,A.C48 3 nts=2 AA A.A32,A.A553 4 nts=2 CU A.C36,A.U37 5 nts=2 AG A.A44,A.G45 6 nts=2 GA A.G46,A.A366 7 nts=2 CC A.C54,A.C352 8 nts=2 AU A.A55,A.U56 9 nts=2 GG A.G61,A.G107 10 nts=2 UG A.U70,A.G94 11 nts=2 GG A.G75,A.G76 12 nts=2 UG A.U85,A.G86 13 nts=2 GA A.G97,A.A98 14 nts=2 UG A.U103,A.G104 15 nts=2 GR A.G108,T.ARG10 16 nts=2 GG A.G115,A.G289 17 nts=2 AG A.A120,A.G122 18 nts=2 GA A.G128,A.A129 19 nts=2 CU A.C132,A.U133 20 nts=2 GA A.G142,A.A143 21 nts=2 GG A.G158,A.G159 22 nts=2 GC A.G168,A.C169 23 nts=2 UA A.U173,A.A197 24 nts=2 AG A.A182,A.G184 25 nts=2 CG A.C186,A.G187 26 nts=2 AA A.A195,A.A196 27 nts=2 CU A.C207,A.U208 28 nts=2 GG A.G211,A.G212 29 nts=2 GC A.G213,A.C214 30 nts=2 UG A.U244,A.G894 31 nts=2 GG A.G247,A.G278 32 nts=2 AG A.A250,A.G275 33 nts=2 GG A.G251,A.G266 34 nts=2 AA A.A262,A.A263 35 nts=2 CR A.C280,Q.ARG40 36 nts=2 CU A.C286,A.U287 37 nts=2 GG A.G293,A.G305 38 nts=2 UG A.U296,A.G297 39 nts=2 AG A.A356,A.G357 40 nts=2 GA A.G369,A.A393 41 nts=2 GG A.G380,A.G384 42 nts=2 CU A.C419,A.U420 43 nts=2 GG A.G423,A.G424 44 nts=2 GG A.G446,A.G447 45 nts=2 AA A.A499,A.A547 46 nts=2 GA A.G505,A.A535 47 nts=2 CU A.C507,A.U508 48 nts=2 AA A.A509,A.A510 49 nts=2 CG A.C518,A.G529 50 nts=2 CA A.C522,A.A523 51 nts=2 Cg A.C526,A.G7M527 52 nts=2 GU A.G530,A.U531 53 nts=2 AC A.A533,A.C536 54 nts=2 GG A.G540,A.G541 55 nts=2 CA A.C545,A.A546 56 nts=2 AG A.A563,A.G567 57 nts=2 GA A.G570,A.A873 58 nts=2 AA A.A573,A.A574 59 nts=2 GA A.G577,A.A816 60 nts=2 GG A.G587,A.G755 61 nts=2 AG A.A596,A.G645 62 nts=2 GU A.G597,A.U598 63 nts=2 GC A.G617,A.C618 64 nts=2 AC A.A642,A.C643 65 nts=2 AG A.A663,A.G664 66 nts=2 GG A.G688,A.G700 67 nts=2 UG A.U701,A.G703 68 nts=2 GG A.G727,A.G731 69 nts=2 AG A.A777,A.G778 70 nts=2 GU A.G818,A.U820 71 nts=2 CG A.C841,A.G846 72 nts=2 CU A.C862,A.U863 73 nts=2 AG A.A872,A.G874 74 nts=2 GA A.G885,A.A913 75 nts=2 GG A.G898,A.G902 76 nts=2 UA A.U905,A.A906 77 nts=2 AC A.A923,A.C924 78 nts=2 GG A.G925,A.G927 79 nts=2 GA A.G926,A.A1531 80 nts=2 CU A.C1389,A.U1390 81 nts=2 Gg A.G1515,A.2MG1516 82 nts=3 AAA A.A1,A.A2,A.A3 83 nts=3 GAU A.G15,A.A16,A.U17 84 nts=3 GAG A.G38,A.A397,A.G548 85 nts=3 GGU A.G39,A.G404,A.U405 86 nts=3 UAA A.U49,A.A364,A.A363 87 nts=3 CGC A.C67,A.G64,A.C99 88 nts=3 GGG A.G69,A.G68,A.G102 89 nts=3 AGC A.A131,A.G232,A.C233 90 nts=3 CGC A.C176,A.G177,A.C178 91 nts=3 GGC A.G198,A.G220,A.C221 92 nts=3 GAU A.G227,A.A228,A.U229 93 nts=3 GGU A.G259,A.G260,A.U261 94 nts=3 ACC A.A306,A.C307,A.C308 95 nts=3 CAC A.C314,A.A315,A.C330 96 nts=3 CGG A.C316,A.G351,A.G350 97 nts=3 GAG A.G331,A.A59,A.G354 98 nts=3 GAC A.G337,A.A338,A.C339 99 nts=3 CUG A.C345,A.U343,A.G347 100 nts=3 UGC A.U367,A.G394,A.C395 101 nts=3 ACU A.A371,A.C372,A.U387 102 nts=3 GAU A.G376,A.A389,A.U390 103 nts=3 GAA A.G406,A.A495,A.A496 104 nts=3 GAG A.G442,A.A441,A.G497 105 nts=3 GUU A.G462,A.U463,A.U464 106 nts=3 CAU A.C477,A.A478,A.U479 107 nts=3 GPG A.G515,A.PSU516,A.G517 108 nts=3 CAG A.C519,A.A520,A.G521 109 nts=3 UUC A.U562,A.U884,A.C883 110 nts=3 AAA A.A572,A.A864,A.A865 111 nts=3 UGU A.U684,A.G685,A.U686 112 nts=3 GGG A.G722,A.G724,A.G725 113 nts=3 AAG A.A728,A.A729,A.G730 114 nts=3 GAA A.G745,A.A746,A.A747 115 nts=3 GGG A.G774,A.G775,A.G776 116 nts=3 AGA A.A815,A.G1529,A.A819 117 nts=3 GGG A.G821,A.G575,A.G881 118 nts=3 CUU A.C826,A.U827,A.U870 119 nts=3 CAA A.C899,A.A900,A.A901 120 nts=3 AAU A.A914,A.A915,A.U916 121 nts=3 Gaa A.G1517,A.MA6/1518,A.MA6/1519 122 nts=3 CUC A.C1536,A.U1537,A.C1538 123 nts=4 AUGG A.A19,A.U20,A.G21,A.G22 124 nts=4 ACAA A.A65,A.C381,A.A382,A.A383 125 nts=4 CGGG A.C110,A.G111,A.G112,A.G113 126 nts=4 ACGC A.A130,A.C264,A.G265,A.C267 127 nts=4 AAAA A.A162,A.A161,A.A160,A.A344 128 nts=4 CAAG A.C188,A.A189,A.A190,A.G191 129 nts=4 GUAG A.G242,A.U245,A.A243,A.G281 130 nts=4 GGGG A.G359,A.G360,A.G361,A.G362 131 nts=4 AAAG A.A412,A.A414,A.A415,A.G416 132 nts=4 CGCU A.C580,A.G581,A.C758,A.U757 133 nts=4 GAGA A.G588,A.A753,A.G654,A.A655 134 nts=4 UAUA A.U594,A.A595,A.U641,A.A640 135 nts=4 CAAC A.C620,A.A621,A.A622,A.C623 136 nts=4 CUGU A.C651,A.U652,A.G752,A.U751 137 nts=4 GGGA A.G666,A.G741,A.G742,A.A743 138 nts=4 AAGA A.A687,A.A704,A.G705,A.A706 139 nts=4 CGGU A.C689,A.G690,A.G691,A.U692 140 nts=4 CAGG A.C779,A.A780,A.G800,A.G799 141 nts=4 GAUU A.G786,A.A787,A.U788,A.U789 142 nts=4 UUGA A.U842,A.U843,A.G844,A.A845 143 nts=4 CGGC A.C857,A.G858,A.G869,A.C868 144 nts=4 GGAU A.G887,A.G888,A.A889,A.U891 145 nts=4 AAUU A.A918,A.A919,A.U920,A.U921 146 nts=5 AAGAG A.A7,A.A298,A.G299,A.A300,A.G301 147 nts=5 GGGAU A.G27,A.G557,A.G558,A.A559,A.U561 148 nts=5 CAAGA A.C73,A.A72,A.A71,A.G100,A.A101 149 nts=5 GGAUU A.G147,A.G148,A.A149,A.U150,A.U170 150 nts=5 AAAUC A.A279,A.A246,A.A282,A.U283,A.C284 151 nts=5 AACUG A.A320,A.A321,A.C322,A.U323,A.G324 152 nts=5 UGUAG A.U409,A.G410,A.U429,A.A411,A.G413 153 nts=5 CUGAY A.C564,A.U565,A.G566,A.A560,E.TYR128 154 nts=5 GAAGG A.G584,A.A583,A.A759,A.G760,A.G761 155 nts=5 CGGCC A.C764,A.G765,A.G812,A.C811,A.C810 156 nts=5 GAAAA A.G769,A.A768,A.A767,A.A766,A.A814 157 nts=5 CAUAG A.C783,A.A782,A.U801,A.A802,A.G803 158 nts=5 AGAAC A.A790,A.G791,A.A792,A.A794,A.C795 159 nts=5 GUGAG A.G829,A.U828,A.G859,A.A860,A.G861 160 nts=6 UGAAAG A.U427,A.G428,A.A430,A.A431,A.A432,A.G433 161 nts=6 CUUGAC A.C436,A.U437,A.U438,A.G494,A.A493,A.C492 162 nts=6 AAAUCC A.A607,A.A608,A.A609,A.U610,A.C611,A.C612 163 nts=6 GAACGG A.G628,A.A629,A.A630,A.C631,A.G606,A.G633 164 nts=6 GAAAUG A.G693,A.A694,A.A695,A.A696,A.U697,A.G698 165 nts=6 AGGAAU A.A712,A.G713,A.G714,A.A715,A.A716,A.U717 166 nts=6 CAAAAC A.C893,A.A892,A.A907,A.A908,A.A909,A.C910 167 nts=6 UGGUGA A.U1391,A.G1504,A.G1505,A.U1506,A.G1530,A.A1507 168 nts=7 CAAAAAC A.C153,A.A152,A.A151,A.A171,A.A172,A.A174,A.C175 169 nts=7 UAAACGU A.U375,A.A374,A.A373,A.A482,A.C483,A.G484,A.U486 170 nts=7 UUAAGAG A.U678,A.U677,A.A676,A.A675,A.G674,A.A673,A.G734 171 nts=8 GGGAUACC A.G146,A.G145,A.G144,A.A179,A.U180,A.A181,A.C194,A.C193 172 nts=8 CAGAAACC A.C206,A.A205,A.G204,A.A465,A.A466,A.A468,A.C469,A.C470 173 nts=8 GAAUGAAA A.G240,A.A119,A.A288,A.U118,A.G117,A.A116,A.A51,A.A353 174 nts=8 CAGGCCAH A.C732,A.A665,A.G733,A.G721,A.C720,A.C719,A.A718,K.HIS118 175 nts=9 CGAGAAAGU A.C135,A.G134,A.A325,A.G326,A.A109,A.A327,A.A329,A.G332,A.U333 176 nts=11 GGGAAGGGAAC A.G455,A.G454,A.G453,A.A452,A.A451,A.G481,A.G450,A.G449,A.A448,A.A487,A.C488 **************************************************************************** Nucleotides not involved in stacking interactions nts=42 UUGAUUCAACUUCUCUUGUCUUAUCUUUAUCUCUUGGGACCU A.U4,A.U5,A.G6,A.A8,A.U13,A.U14,A.C47,A.A50,A.A60,A.C83,A.U84,A.U121,A.C183,A.U209,A.C210,A.U365,A.U368,A.G388,A.U421,A.C422,A.U467,A.U485,A.A532,A.U534,A.C576,A.U619,A.U632,A.U653,A.A702,A.U723,A.C754,A.U793,A.C805,A.U813,A.U871,A.G890,A.G928,A.G1392,A.A1503,A.C1535,A.C1539,A.U1540 **************************************************************************** List of 69 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.A629 A.A3 3.07 2 sugar O2'@A.A629 A.A3 3.24 3 sugar O4'@A.U5 A.G6 2.79 4 phosphate OP2@A.A16 A.U14 3.16 5 sugar O2'@A.A306 A.G31 3.18 6 sugar O2'@A.G200 A.A65 3.21 7 sugar O4'@A.G69 A.G68 3.30 8 sugar O4'@A.A119 A.A120 3.48 9 phosphate OP2@A.A161 A.G159 2.76 10 sugar O4'@A.C163 A.A162 3.32 11 sugar O4'@A.U180 A.A179 2.94 12 phosphate OP2@A.A189 A.G187 2.97 13 sugar O4'@A.U173 A.A197 2.76 14 sugar O4'@A.C221 A.A197 3.13 15 phosphate OP2@A.U209 A.C210 2.96 16 phosphate OP1@A.C210 A.G211 3.00 17 sugar O4'@A.C210 A.G211 3.34 18 sugar O4'@A.A250 A.U252 2.65 19 sugar O4'@A.A279 A.G281 3.09 20 sugar O4'@A.U283 A.A282 3.30 21 phosphate OP2@A.G299 A.G297 2.95 22 sugar O4'@A.C330 A.A315 3.21 23 phosphate OP2@A.G326 A.G324 3.14 24 sugar O4'@A.A160 A.A344 2.92 25 sugar O4'@A.C345 A.G346 2.87 26 phosphate OP2@A.A364 A.G362 3.19 27 sugar O4'@A.C47 A.U365 2.93 28 phosphate OP2@A.A382 A.G380 3.21 29 sugar O4'@A.G384 A.A383 3.43 30 sugar O4'@A.U390 A.A389 2.89 31 sugar O4'@A.A414 A.A412 2.77 32 sugar O4'@A.C422 A.G423 3.46 33 sugar O4'@A.A451 A.A452 3.18 34 phosphate OP2@A.A466 A.U464 3.08 35 sugar O4'@A.U486 A.G484 3.04 36 sugar O4'@A.U405 A.A498 3.24 37 sugar O2'@A.U405 A.A498 3.22 38 sugar O4'@A.C504 A.A510 2.95 39 phosphate OP1@A.A532 A.A532 2.87 40 sugar O4'@A.G529 A.A533 2.90 41 sugar O4'@A.C528 A.A535 3.29 42 sugar O4'@A.G566 A.A560 2.95 43 sugar O4'@A.C569 A.A574 2.82 44 sugar O4'@A.U598 A.G597 3.46 45 phosphate OP2@A.A694 A.U692 2.90 46 sugar O4'@A.U701 A.G703 3.22 47 sugar O4'@A.G721 A.G722 2.84 48 phosphate OP2@A.A729 A.G727 2.97 49 sugar O4'@A.G761 A.G760 3.35 50 sugar O4'@A.A782 A.A781 3.42 51 other P@A.G791 A.U789 3.18 52 phosphate OP2@A.G791 A.U789 2.77 53 sugar O4'@A.A816 A.A814 3.03 54 sugar O4'@A.G577 A.A816 2.90 55 sugar O4'@A.A819 A.C817 2.90 56 sugar O2'@A.U820 A.G818 3.11 57 sugar O4'@A.G570 A.U820 3.17 58 sugar O4'@A.G846 A.A845 3.38 59 sugar O4'@A.C868 A.A873 3.06 60 sugar O2'@A.G22 A.G885 2.74 61 phosphate OP2@A.A900 A.G898 2.90 62 sugar O2'@A.C924 A.G925 2.76 63 sugar O2'@A.G926 A.G925 3.06 64 phosphate OP2@A.U1391 A.G928 2.80 65 phosphate O3'@A.G1504 A.A1503 2.96 66 other P@A.MA6/1518 A.2MG1516 3.37 67 phosphate OP1@A.MA6/1518 A.2MG1516 2.72 68 phosphate OP2@A.MA6/1518 A.2MG1516 2.62 69 other NZ@U.LYS40 A.G1525 2.77 **************************************************************************** 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 22 hairpin loops 1 hairpin loop: nts=11; [9]; linked by [#1] summary: [1] 9 [A.12 A.22] 4 nts=11 UUUGAUCAUGG A.U12,A.U13,A.U14,A.G15,A.A16,A.U17,A.C18,A.A19,A.U20,A.G21,A.G22 nts=9 UUGAUCAUG A.U13,A.U14,A.G15,A.A16,A.U17,A.C18,A.A19,A.U20,A.G21 2 hairpin loop: nts=6; [4]; linked by [#13] summary: [1] 4 [A.82 A.87] 7 nts=6 GCUUGC A.G82,A.C83,A.U84,A.U85,A.G86,A.C87 nts=4 CUUG A.C83,A.U84,A.U85,A.G86 3 hairpin loop: nts=6; [4]; linked by [#19] summary: [1] 4 [A.158 A.163] 6 nts=6 GGAAAC A.G158,A.G159,A.A160,A.A161,A.A162,A.C163 nts=4 GAAA A.G159,A.A160,A.A161,A.A162 4 hairpin loop: nts=6; [4]; linked by [#20] summary: [1] 4 [A.186 A.191] 3 nts=6 CGCAAG A.C186,A.G187,A.C188,A.A189,A.A190,A.G191 nts=4 GCAA A.G187,A.C188,A.A189,A.A190 5 hairpin loop: nts=6; [4]; linked by [#22] summary: [1] 4 [A.207 A.212] 2 nts=6 CUUCGG A.C207,A.U208,A.U209,A.C210,A.G211,A.G212 nts=4 UUCG A.U208,A.U209,A.C210,A.G211 6 hairpin loop: nts=9; [7]; linked by [#25] summary: [1] 7 [A.259 A.267] 8 nts=9 GGUAACGGC A.G259,A.G260,A.U261,A.A262,A.A263,A.C264,A.G265,A.G266,A.C267 nts=7 GUAACGG A.G260,A.U261,A.A262,A.A263,A.C264,A.G265,A.G266 7 hairpin loop: nts=6; [4]; linked by [#27] summary: [1] 4 [A.296 A.301] 4 nts=6 UGAGAG A.U296,A.G297,A.A298,A.G299,A.A300,A.G301 nts=4 GAGA A.G297,A.A298,A.G299,A.A300 8 hairpin loop: nts=14; [12]; linked by [#28] summary: [1] 12 [A.320 A.333] 5 nts=14 AACUGAGACACGGU A.A320,A.A321,A.C322,A.U323,A.G324,A.A325,A.G326,A.A327,A.C328,A.A329,A.C330,A.G331,A.G332,A.U333 nts=12 ACUGAGACACGG A.A321,A.C322,A.U323,A.G324,A.A325,A.G326,A.A327,A.C328,A.A329,A.C330,A.G331,A.G332 9 hairpin loop: nts=6; [4]; linked by [#29] summary: [1] 4 [A.342 A.347] 4 nts=6 CUACGG A.C342,A.U343,A.A344,A.C345,A.G346,A.G347 nts=4 UACG A.U343,A.A344,A.C345,A.G346 10 hairpin loop: nts=6; [4]; linked by [#31] summary: [1] 4 [A.379 A.384] 4 nts=6 CGCAAG A.C379,A.G380,A.C381,A.A382,A.A383,A.G384 nts=4 GCAA A.G380,A.C381,A.A382,A.A383 11 hairpin loop: nts=6; [4]; linked by [#33] summary: [1] 4 [A.419 A.424] 4 nts=6 CUUCGG A.C419,A.U420,A.U421,A.C422,A.G423,A.G424 nts=4 UUCG A.U420,A.U421,A.C422,A.G423 12 hairpin loop: nts=9; [7]; linked by [#36] summary: [1] 7 [A.462 A.470] 8 nts=9 GUUAAUACC A.G462,A.U463,A.U464,A.A465,A.A466,A.U467,A.A468,A.C469,A.C470 nts=7 UUAAUAC A.U463,A.U464,A.A465,A.A466,A.U467,A.A468,A.C469 13 hairpin loop: nts=18; [16]; linked by [#38] summary: [1] 16 [A.507 A.524] 3 nts=18 CUAACUCCGPGCCAGCAG A.C507,A.U508,A.A509,A.A510,A.C511,A.U512,A.C513,A.C514,A.G515,A.PSU516,A.G517,A.C518,A.C519,A.A520,A.G521,A.C522,A.A523,A.G524 nts=16 UAACUCCGPGCCAGCA A.U508,A.A509,A.A510,A.C511,A.U512,A.C513,A.C514,A.G515,A.PSU516,A.G517,A.C518,A.C519,A.A520,A.G521,A.C522,A.A523 14 hairpin loop: nts=6; [4]; linked by [#40] summary: [1] 4 [A.522 A.527] 2 nts=6 CAGCCg A.C522,A.A523,A.G524,A.C525,A.C526,A.G7M527 nts=4 AGCC A.A523,A.G524,A.C525,A.C526 15 hairpin loop: nts=7; [5]; linked by [#48] summary: [1] 5 [A.617 A.623] 6 nts=7 GCUCAAC A.G617,A.C618,A.U619,A.C620,A.A621,A.A622,A.C623 nts=5 CUCAA A.C618,A.U619,A.C620,A.A621,A.A622 16 hairpin loop: nts=10; [8]; linked by [#53] summary: [1] 8 [A.689 A.698] 2 nts=10 CGGUGAAAUG A.C689,A.G690,A.G691,A.U692,A.G693,A.A694,A.A695,A.A696,A.U697,A.G698 nts=8 GGUGAAAU A.G690,A.G691,A.U692,A.G693,A.A694,A.A695,A.A696,A.U697 17 hairpin loop: nts=6; [4]; linked by [#54] summary: [1] 4 [A.726 A.731] 2 nts=6 CGAAGG A.C726,A.G727,A.A728,A.A729,A.G730,A.G731 nts=4 GAAG A.G727,A.A728,A.A729,A.G730 18 hairpin loop: nts=11; [9]; linked by [#57] summary: [1] 9 [A.786 A.796] 4 nts=11 GAUUAGAUACC A.G786,A.A787,A.U788,A.U789,A.A790,A.G791,A.A792,A.U793,A.A794,A.C795,A.C796 nts=9 AUUAGAUAC A.A787,A.U788,A.U789,A.A790,A.G791,A.A792,A.U793,A.A794,A.C795 19 hairpin loop: nts=7; [5]; linked by [#59] summary: [1] 5 [A.840 A.846] 12 nts=7 CCUUGAG A.C840,A.C841,A.U842,A.U843,A.G844,A.A845,A.G846 nts=5 CUUGA A.C841,A.U842,A.U843,A.G844,A.A845 20 hairpin loop: nts=6; [4]; linked by [#60] summary: [1] 4 [A.862 A.867] 2 nts=6 CUAACG A.C862,A.U863,A.A864,A.A865,A.C866,A.G867 nts=4 UAAC A.U863,A.A864,A.A865,A.C866 21 hairpin loop: nts=6; [4]; linked by [#62] summary: [1] 4 [A.897 A.902] 4 nts=6 CGCAAG A.C897,A.G898,A.C899,A.A900,A.A901,A.G902 nts=4 GCAA A.G898,A.C899,A.A900,A.A901 22 hairpin loop: nts=6; [4]; linked by [#65] summary: [1] 4 [A.1515 A.1520] 9 nts=6 GgGaaC A.G1515,A.2MG1516,A.G1517,A.MA6/1518,A.MA6/1519,A.C1520 nts=4 gGaa A.2MG1516,A.G1517,A.MA6/1518,A.MA6/1519 **************************************************************************** List of 17 bulges 1 bulge: nts=5; [1,0]; linked by [#3,#4] summary: [2] 1 0 [A.30 A.553 A.32 A.552] 4 5 nts=5 UGAUA A.U30,A.G31,A.A32,A.U552,A.A553 nts=1 G A.G31 nts=0 2 bulge: nts=5; [0,1]; linked by [#5,#6] summary: [2] 0 1 [A.44 A.398 A.45 A.396] 6 2 nts=5 AGCAU A.A44,A.G45,A.C396,A.A397,A.U398 nts=0 nts=1 A A.A397 3 bulge: nts=5; [1,0]; linked by [#7,#8] summary: [2] 1 0 [A.54 A.357 A.56 A.356] 3 3 nts=5 CAUAG A.C54,A.A55,A.U56,A.A356,A.G357 nts=1 A A.A55 nts=0 4 bulge: nts=5; [0,1]; linked by [#12,#13] summary: [2] 0 1 [A.75 A.95 A.76 A.93] 3 7 nts=5 GGUGC A.G75,A.G76,A.U93,A.G94,A.C95 nts=0 nts=1 G A.G94 5 bulge: nts=5; [1,0]; linked by [#-4,#30] summary: [2] 1 0 [A.367 A.393 A.369 A.392] 1 3 nts=5 UUGCA A.U367,A.U368,A.G369,A.C392,A.A393 nts=1 U A.U368 nts=0 6 bulge: nts=5; [0,1]; linked by [#-5,#31] summary: [2] 0 1 [A.375 A.389 A.376 A.387] 1 4 nts=5 UGUGA A.U375,A.G376,A.U387,A.G388,A.A389 nts=0 nts=1 G A.G388 7 bulge: nts=5; [1,0]; linked by [#45,#46] summary: [2] 1 0 [A.594 A.645 A.596 A.644] 7 2 nts=5 UAAUG A.U594,A.A595,A.A596,A.U644,A.G645 nts=1 A A.A595 nts=0 8 bulge: nts=5; [0,1]; linked by [#49,#50] summary: [2] 0 1 [A.659 A.747 A.660 A.745] 5 3 nts=5 UCGAA A.U659,A.C660,A.G745,A.A746,A.A747 nts=0 nts=1 A A.A746 9 bulge: nts=6; [2,0]; linked by [#9,#10] summary: [2] 2 0 [A.63 A.104 A.66 A.103] 3 2 nts=6 CGAAUG A.C63,A.G64,A.A65,A.A66,A.U103,A.G104 nts=2 GA A.G64,A.A65 nts=0 10 bulge: nts=6; [2,0]; linked by [#11,#12] summary: [2] 2 0 [A.70 A.98 A.73 A.97] 2 3 nts=6 UAACGA A.U70,A.A71,A.A72,A.C73,A.G97,A.A98 nts=2 AA A.A71,A.A72 nts=0 11 bulge: nts=6; [2,0]; linked by [#21,#22] summary: [2] 2 0 [A.203 A.214 A.206 A.213] 6 2 nts=6 GGACGC A.G203,A.G204,A.A205,A.C206,A.G213,A.C214 nts=2 GA A.G204,A.A205 nts=0 12 bulge: nts=6; [2,0]; linked by [#24,#25] summary: [2] 2 0 [A.249 A.275 A.252 A.274] 3 8 nts=6 UAGUAG A.U249,A.A250,A.G251,A.U252,A.A274,A.G275 nts=2 AG A.A250,A.G251 nts=0 13 bulge: nts=6; [0,2]; linked by [#46,#47] summary: [2] 0 2 [A.597 A.643 A.598 A.640] 2 8 nts=6 GUAUAC A.G597,A.U598,A.A640,A.U641,A.A642,A.C643 nts=0 nts=2 UA A.U641,A.A642 14 bulge: nts=6; [0,2]; linked by [#-8,#49] summary: [2] 0 2 [A.654 A.754 A.655 A.751] 1 5 nts=6 GAUGAC A.G654,A.A655,A.U751,A.G752,A.A753,A.C754 nts=0 nts=2 GA A.G752,A.A753 15 bulge: nts=7; [0,3]; linked by [#26,#27] summary: [2] 0 3 [A.292 A.308 A.293 A.304] 4 4 nts=7 GGUGACC A.G292,A.G293,A.U304,A.G305,A.A306,A.C307,A.C308 nts=0 nts=3 GAC A.G305,A.A306,A.C307 16 bulge: nts=7; [3,0]; linked by [#30,#-5] summary: [2] 3 0 [A.371 A.390 A.375 A.389] 3 1 nts=7 ACAAUAU A.A371,A.C372,A.A373,A.A374,A.U375,A.A389,A.U390 nts=3 CAA A.C372,A.A373,A.A374 nts=0 17 bulge: nts=7; [3,0]; linked by [#55,#56] summary: [2] 3 0 [A.774 A.805 A.778 A.804] 6 2 nts=7 GGGAGUC A.G774,A.G775,A.G776,A.A777,A.G778,A.U804,A.C805 nts=3 GGA A.G775,A.G776,A.A777 nts=0 **************************************************************************** List of 20 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#-1,#2] summary: [2] 1 1 [A.15 A.920 A.17 A.918] 1 3 nts=6 GAUAAU A.G15,A.A16,A.U17,A.A918,A.A919,A.U920 nts=1 A A.A16 nts=1 A A.A919 2 symmetric internal loop: nts=6; [1,1]; linked by [#-3,#18] summary: [2] 1 1 [A.144 A.178 A.146 A.176] 1 2 nts=6 GGGCGC A.G144,A.G145,A.G146,A.C176,A.G177,A.C178 nts=1 G A.G145 nts=1 G A.G177 3 asymmetric internal loop: nts=7; [1,2]; linked by [#10,#11] summary: [2] 1 2 [A.67 A.102 A.69 A.99] 2 2 nts=7 CGGCGAG A.C67,A.G68,A.G69,A.C99,A.G100,A.A101,A.G102 nts=1 G A.G68 nts=2 GA A.G100,A.A101 4 asymmetric internal loop: nts=7; [2,1]; linked by [#15,#16] summary: [2] 2 1 [A.128 A.233 A.131 A.231] 7 2 nts=7 GAAAUGC A.G128,A.A129,A.A130,A.A131,A.U231,A.G232,A.C233 nts=2 AA A.A129,A.A130 nts=1 G A.G232 5 asymmetric internal loop: nts=9; [4,1]; linked by [#-2,#7] summary: [2] 4 1 [A.47 A.361 A.52 A.359] 1 3 nts=9 CCUAACGGG A.C47,A.C48,A.U49,A.A50,A.A51,A.C52,A.G359,A.G360,A.G361 nts=4 CUAA A.C48,A.U49,A.A50,A.A51 nts=1 G A.G360 6 asymmetric internal loop: nts=9; [3,2]; linked by [#16,#17] summary: [2] 3 2 [A.132 A.230 A.136 A.227] 2 7 nts=9 CUGCCGAUG A.C132,A.U133,A.G134,A.C135,A.C136,A.G227,A.A228,A.U229,A.G230 nts=3 UGC A.U133,A.G134,A.C135 nts=2 AU A.A228,A.U229 7 asymmetric internal loop: nts=9; [1,4]; linked by [#34,#35] summary: [2] 1 4 [A.440 A.497 A.442 A.492] 2 5 nts=9 CAGCAGAAG A.C440,A.A441,A.G442,A.C492,A.A493,A.G494,A.A495,A.A496,A.G497 nts=1 A A.A441 nts=4 AGAA A.A493,A.G494,A.A495,A.A496 8 asymmetric internal loop: nts=9; [3,2]; linked by [#50,#51] summary: [2] 3 2 [A.662 A.743 A.666 A.740] 3 7 nts=9 UAGAGUGGA A.U662,A.A663,A.G664,A.A665,A.G666,A.U740,A.G741,A.G742,A.A743 nts=3 AGA A.A663,A.G664,A.A665 nts=2 GG A.G741,A.G742 9 symmetric internal loop: nts=10; [3,3]; linked by [#43,#44] summary: [2] 3 3 [A.580 A.761 A.584 A.757] 4 3 nts=10 CGCAGUCAGG A.C580,A.G581,A.C582,A.A583,A.G584,A.U757,A.C758,A.A759,A.G760,A.G761 nts=3 GCA A.G581,A.C582,A.A583 nts=3 CAG A.C758,A.A759,A.G760 10 symmetric internal loop: nts=10; [3,3]; linked by [#56,#57] summary: [2] 3 3 [A.779 A.803 A.783 A.799] 2 4 nts=10 CAAACGGUAG A.C779,A.A780,A.A781,A.A782,A.C783,A.G799,A.G800,A.U801,A.A802,A.G803 nts=3 AAA A.A780,A.A781,A.A782 nts=3 GUA A.G800,A.U801,A.A802 11 asymmetric internal loop: nts=11; [3,4]; linked by [#35,#-6] summary: [2] 3 4 [A.446 A.488 A.450 A.483] 5 1 nts=11 GGAGGCGUUAC A.G446,A.G447,A.A448,A.G449,A.G450,A.C483,A.G484,A.U485,A.U486,A.A487,A.C488 nts=3 GAG A.G447,A.A448,A.G449 nts=4 GUUA A.G484,A.U485,A.U486,A.A487 12 symmetric internal loop: nts=12; [4,4]; linked by [#-9,#52] summary: [2] 4 4 [A.673 A.717 A.678 A.712] 1 7 nts=12 AGAAUUAGGAAU A.A673,A.G674,A.A675,A.A676,A.U677,A.U678,A.A712,A.G713,A.G714,A.A715,A.A716,A.U717 nts=4 GAAU A.G674,A.A675,A.A676,A.U677 nts=4 GGAA A.G713,A.G714,A.A715,A.A716 13 asymmetric internal loop: nts=13; [4,5]; linked by [#-6,#36] summary: [2] 4 5 [A.450 A.483 A.455 A.477] 1 8 nts=13 GAAGGGCAUUGAC A.G450,A.A451,A.A452,A.G453,A.G454,A.G455,A.C477,A.A478,A.U479,A.U480,A.G481,A.A482,A.C483 nts=4 AAGG A.A451,A.A452,A.G453,A.G454 nts=5 AUUGA A.A478,A.U479,A.U480,A.G481,A.A482 14 asymmetric internal loop: nts=13; [3,6]; linked by [#52,#53] summary: [2] 3 6 [A.684 A.706 A.688 A.699] 7 2 k-turn:normal nts=13 UGUAGCGUAGAGA A.U684,A.G685,A.U686,A.A687,A.G688,A.C699,A.G700,A.U701,A.A702,A.G703,A.A704,A.G705,A.A706 nts=3 GUA A.G685,A.U686,A.A687 nts=6 GUAGAG A.G700,A.U701,A.A702,A.G703,A.A704,A.G705 15 asymmetric internal loop: nts=14; [4,6]; linked by [#23,#24] summary: [2] 4 6 [A.242 A.284 A.247 A.277] 3 3 k-turn:normal nts=14 GAUUAGCGACGAUC A.G242,A.A243,A.U244,A.U245,A.A246,A.G247,A.C277,A.G278,A.A279,A.C280,A.G281,A.A282,A.U283,A.C284 nts=4 AUUA A.A243,A.U244,A.U245,A.A246 nts=6 GACGAU A.G278,A.A279,A.C280,A.G281,A.A282,A.U283 16 asymmetric internal loop: nts=14; [6,4]; linked by [#47,#48] summary: [2] 6 4 [A.605 A.633 A.612 A.628] 8 6 nts=14 UGAAAUCCGAACUG A.U605,A.G606,A.A607,A.A608,A.A609,A.U610,A.C611,A.C612,A.G628,A.A629,A.A630,A.C631,A.U632,A.G633 nts=6 GAAAUC A.G606,A.A607,A.A608,A.A609,A.U610,A.C611 nts=4 AACU A.A629,A.A630,A.C631,A.U632 17 asymmetric internal loop: nts=14; [6,4]; linked by [#61,#62] summary: [2] 6 4 [A.887 A.910 A.894 A.905] 3 4 nts=14 GGAGUACGUAAAAC A.G887,A.G888,A.A889,A.G890,A.U891,A.A892,A.C893,A.G894,A.U905,A.A906,A.A907,A.A908,A.A909,A.C910 nts=6 GAGUAC A.G888,A.A889,A.G890,A.U891,A.A892,A.C893 nts=4 AAAA A.A906,A.A907,A.A908,A.A909 18 asymmetric internal loop: nts=15; [5,6]; linked by [#18,#19] summary: [2] 5 6 [A.147 A.175 A.153 A.168] 2 6 nts=15 GGAUAACGCUAAUAC A.G147,A.G148,A.A149,A.U150,A.A151,A.A152,A.C153,A.G168,A.C169,A.U170,A.A171,A.A172,A.U173,A.A174,A.C175 nts=5 GAUAA A.G148,A.A149,A.U150,A.A151,A.A152 nts=6 CUAAUA A.C169,A.U170,A.A171,A.A172,A.U173,A.A174 19 asymmetric internal loop: nts=15; [6,5]; linked by [#32,#33] summary: [2] 6 5 [A.409 A.433 A.416 A.427] 4 4 k-turn:reverse nts=15 UGAAGAAGUGUAAAG A.U409,A.G410,A.A411,A.A412,A.G413,A.A414,A.A415,A.G416,A.U427,A.G428,A.U429,A.A430,A.A431,A.A432,A.G433 nts=6 GAAGAA A.G410,A.A411,A.A412,A.G413,A.A414,A.A415 nts=5 GUAAA A.G428,A.U429,A.A430,A.A431,A.A432 20 asymmetric internal loop: nts=16; [5,7]; linked by [#39,#40] summary: [2] 5 7 [A.515 A.536 A.521 A.528] 5 2 nts=16 GPGCCAGCGGUAAUAC A.G515,A.PSU516,A.G517,A.C518,A.C519,A.A520,A.G521,A.C528,A.G529,A.G530,A.U531,A.A532,A.A533,A.U534,A.A535,A.C536 nts=5 PGCCA A.PSU516,A.G517,A.C518,A.C519,A.A520 nts=7 GGUAAUA A.G529,A.G530,A.U531,A.A532,A.A533,A.U534,A.A535 **************************************************************************** List of 10 junctions 1 3-way junction: nts=9; [1,2,0]; linked by [#44,#45,#-8] summary: [3] 1 2 0 [A.586 A.755 A.588 A.651 A.654 A.754] 3 7 1 nts=9 CGGCUUGCG A.C586,A.G587,A.G588,A.C651,A.U652,A.U653,A.G654,A.C754,A.G755 nts=1 G A.G587 nts=2 UU A.U652,A.U653 nts=0 2 3-way junction: nts=12; [0,5,1]; linked by [#6,#-2,#-4] summary: [3] 0 5 1 [A.46 A.395 A.47 A.361 A.367 A.393] 2 1 1 nts=12 GCGGAAUAUAGC A.G46,A.C47,A.G361,A.G362,A.A363,A.A364,A.U365,A.A366,A.U367,A.A393,A.G394,A.C395 nts=0 nts=5 GAAUA A.G362,A.A363,A.A364,A.U365,A.A366 nts=1 G A.G394 3 3-way junction: nts=14; [0,7,1]; linked by [#51,#-9,#54] summary: [3] 0 7 1 [A.672 A.734 A.673 A.717 A.725 A.732] 7 1 2 nts=14 UAUACCGGUGGCGG A.U672,A.A673,A.U717,A.A718,A.C719,A.C720,A.G721,A.G722,A.U723,A.G724,A.G725,A.C732,A.G733,A.G734 nts=0 nts=7 ACCGGUG A.A718,A.C719,A.C720,A.G721,A.G722,A.U723,A.G724 nts=1 G A.G733 4 3-way junction: nts=16; [2,3,5]; linked by [#58,#59,#60] summary: [3] 2 3 5 [A.826 A.874 A.829 A.857 A.861 A.868] 6 12 2 nts=16 CUUGCGGAGCGUUAAG A.C826,A.U827,A.U828,A.G829,A.C857,A.G858,A.G859,A.A860,A.G861,A.C868,A.G869,A.U870,A.U871,A.A872,A.A873,A.G874 nts=2 UU A.U827,A.U828 nts=3 GGA A.G858,A.G859,A.A860 nts=5 GUUAA A.G869,A.U870,A.U871,A.A872,A.A873 5 4-way junction: nts=16; [6,0,2,0]; linked by [#14,#15,#23,#26] summary: [4] 6 0 2 0 [A.115 A.312 A.122 A.239 A.240 A.286 A.289 A.311] 3 7 3 4 nts=16 GAGUAAUGUGCUAGCC A.G115,A.A116,A.G117,A.U118,A.A119,A.A120,A.U121,A.G122,A.U239,A.G240,A.C286,A.U287,A.A288,A.G289,A.C311,A.C312 nts=6 AGUAAU A.A116,A.G117,A.U118,A.A119,A.A120,A.U121 nts=0 nts=2 UA A.U287,A.A288 nts=0 6 4-way junction: nts=19; [1,5,4,1]; linked by [#17,#-3,#20,#21] summary: [4] 1 5 4 1 [A.142 A.221 A.144 A.178 A.184 A.193 A.198 A.219] 7 1 3 6 nts=19 GAGCAUAACGCCAAAGUGC A.G142,A.A143,A.G144,A.C178,A.A179,A.U180,A.A181,A.A182,A.C183,A.G184,A.C193,A.C194,A.A195,A.A196,A.A197,A.G198,A.U219,A.G220,A.C221 nts=1 A A.A143 nts=5 AUAAC A.A179,A.U180,A.A181,A.A182,A.C183 nts=4 CAAA A.C194,A.A195,A.A196,A.A197 nts=1 G A.G220 7* 5-way junction: nts=14; [0,0,1,3,0]; linked by [#37,#38,#40,#38,#39] summary: [5] 0 0 1 3 0 [A.504 A.541 A.505 A.526 A.527 A.522 A.524 A.507 A.511 A.540] 5 3 2 3 5 nts=14 CGCgCAGCUAACGG A.C504,A.G505,A.C526,A.G7M527,A.C522,A.A523,A.G524,A.C507,A.U508,A.A509,A.A510,A.C511,A.G540,A.G541 nts=0 nts=0 nts=1 A A.A523 nts=3 UAA A.U508,A.A509,A.A510 nts=0 8* 5-way junction: nts=15; [0,0,2,3,0]; linked by [#41,#42,#60,#42,#-7] summary: [5] 0 0 2 3 0 [A.569 A.881 A.570 A.866 A.867 A.862 A.865 A.571 A.575 A.880] 3 2 2 2 1 nts=15 CGCGCUAAUAAAGCG A.C569,A.G570,A.C866,A.G867,A.C862,A.U863,A.A864,A.A865,A.U571,A.A572,A.A573,A.A574,A.G575,A.C880,A.G881 nts=0 nts=0 nts=2 UA A.U863,A.A864 nts=3 AAA A.A572,A.A573,A.A574 nts=0 9 5-way junction: nts=19; [2,2,2,1,2]; linked by [#4,#5,#32,#34,#37] summary: [5] 2 2 2 1 2 [A.36 A.548 A.39 A.403 A.406 A.436 A.439 A.498 A.500 A.545] 5 6 4 2 5 nts=19 CUGGCGUGCUUUAAGCAAG A.C36,A.U37,A.G38,A.G39,A.C403,A.G404,A.U405,A.G406,A.C436,A.U437,A.U438,A.U439,A.A498,A.A499,A.G500,A.C545,A.A546,A.A547,A.G548 nts=2 UG A.U37,A.G38 nts=2 GU A.G404,A.U405 nts=2 UU A.U437,A.U438 nts=1 A A.A499 nts=2 AA A.A546,A.A547 10 5-way junction: nts=23; [2,6,1,1,3]; linked by [#8,#9,#14,#28,#29] summary: [5] 2 6 1 1 3 [A.58 A.354 A.61 A.106 A.113 A.314 A.316 A.337 A.339 A.350] 3 3 3 5 4 nts=23 CAAGCGGACGGGCACGACGGCAG A.C58,A.A59,A.A60,A.G61,A.C106,A.G107,A.G108,A.A109,A.C110,A.G111,A.G112,A.G113,A.C314,A.A315,A.C316,A.G337,A.A338,A.C339,A.G350,A.G351,A.C352,A.A353,A.G354 nts=2 AA A.A59,A.A60 nts=6 GGACGG A.G107,A.G108,A.A109,A.C110,A.G111,A.G112 nts=1 A A.A315 nts=1 A A.A338 nts=3 GCA A.G351,A.C352,A.A353 **************************************************************************** List of 13 non-loop single-stranded segments 1 nts=8 AAAUUGAA A.A1,A.A2,A.A3,A.U4,A.U5,A.G6,A.A7,A.A8 2 nts=1 A A.A26 3 nts=10 GGAAUUACUG A.G557,A.G558,A.A559,A.A560,A.U561,A.U562,A.A563,A.C564,A.U565,A.G566 4 nts=1 C A.C576 5 nts=4 GAAA A.G765,A.A766,A.A767,A.A768 6 nts=6 CGUAAA A.C811,A.G812,A.U813,A.A814,A.A815,A.A816 7 nts=3 GAU A.G818,A.A819,A.U820 8 nts=1 U A.U884 9 nts=3 AAA A.A913,A.A914,A.A915 10 nts=4 CGGG A.C924,A.G925,A.G926,A.G927 11 nts=7* UUGAGGU A.U1390,A.U1391,A.G1392,A.A1503,A.G1504,A.G1505,A.U1506 12 nts=2 GA A.G1530,A.A1531 13 nts=6 CCUCCU A.C1535,A.C1536,A.U1537,A.C1538,A.C1539,A.U1540 **************************************************************************** List of 51 A-minor motifs (types I, II, or X) 1 type=II A|C-G A.A2|A.C613,A.G627 WC -A.C613 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.94],N3-O2'(hydroxyl)[2.47]" +A.G627 H-bonds[0]: "" 2 type=I A|C-G A.A3|A.C612,A.G628 WC -A.C612 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.00]" +A.G628 H-bonds[2]: "N1-O2'(hydroxyl)[2.77],N3-N2(amino)[3.04]" 3 type=X A|G-C A.A51|A.G113,A.C314 WC +A.G113 H-bonds[0]: "" -A.C314 H-bonds[2]: "N6(amino)-O2(carbonyl)[3.11],N1-O2'(hydroxyl)[2.90]" 4 type=X A|U-A A.A51|A.U114,A.A313 WC +A.U114 H-bonds[2]: "N7-O2'(hydroxyl)[2.49],N6(amino)-O2(carbonyl)[2.79]" -A.A313 H-bonds[0]: "" 5 type=X A|G-C A.A71|A.G69,A.C99 WC +A.G69 H-bonds[0]: "" -A.C99 H-bonds[2]: "N6(amino)-O2(carbonyl)[2.52],N1-O2'(hydroxyl)[2.88]" 6 type=X A|U-A A.A71|A.U70,A.A98 WC +A.U70 H-bonds[2]: "N7*O2(carbonyl)[3.17],N6(amino)-O2(carbonyl)[3.34]" -A.A98 H-bonds[0]: "" 7 type=X A|U-A A.A72|A.U70,A.A98 WC +A.U70 H-bonds[0]: "" -A.A98 H-bonds[1]: "N6(amino)-N3[2.81]" 8 type=X A|U-A A.A116|A.U114,A.A313 WC +A.U114 H-bonds[0]: "" -A.A313 H-bonds[2]: "N6(amino)-N3[2.93],N1-O2'(hydroxyl)[2.62]" 9 type=X A|C-G A.A151|A.C67,A.G102 WC +A.C67 H-bonds[0]: "" -A.G102 H-bonds[2]: "N1-N2(amino)[3.23],N3-O2'(hydroxyl)[2.68]" 10 type=X A|G-A A.A151|A.G68,A.A101 Imino +A.G68 H-bonds[1]: "N6(amino)-O2'(hydroxyl)[3.55]" -A.A101 H-bonds[0]: "" 11 type=X A|C-G A.A160|A.C342,A.G347 WC -A.C342 H-bonds[0]: "" +A.G347 H-bonds[1]: "N6(amino)-O2'(hydroxyl)[2.67]" 12 type=X A|C-G A.A161|A.C342,A.G347 WC -A.C342 H-bonds[0]: "" +A.G347 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.09],N1-O2'(hydroxyl)[2.49]" 13 type=II A|C-G A.A171|A.C67,A.G102 WC -A.C67 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.52],N3-O2'(hydroxyl)[3.26]" +A.G102 H-bonds[0]: "" 14 type=I A|A-U A.A172|A.A66,A.U103 WC -A.A66 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.75]" +A.U103 H-bonds[1]: "N1-O2'(hydroxyl)[3.04]" 15 type=II A|G-C A.A195|A.G141,A.C222 WC +A.G141 H-bonds[0]: "" -A.C222 H-bonds[1]: "N3-O2'(hydroxyl)[2.53]" 16 type=I A|G-C A.A196|A.G142,A.C221 WC +A.G142 H-bonds[2]: "N1-O2'(hydroxyl)[2.50],N3-N2(amino)[3.04]" -A.C221 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.64]" 17 type=X A|G-C A.A205|A.G203,A.C214 WC +A.G203 H-bonds[0]: "" -A.C214 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.61]" 18 type=II A|A-U A.A262|A.A131,A.U231 WC -A.A131 H-bonds[3]: "O2'(hydroxyl)-O3'[3.05],O2'(hydroxyl)-O2'(hydroxyl)[3.18],N3-O2'(hydroxyl)[2.46]" +A.U231 H-bonds[0]: "" 19 type=X A|G-C A.A282|A.G247,A.C277 WC +A.G247 H-bonds[2]: "N1-O2'(hydroxyl)[2.53],N3-N2(amino)[3.34]" -A.C277 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.62]" 20 type=I A|G-C A.A353|A.G113,A.C314 WC -A.G113 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.50],O2'(hydroxyl)-N3[2.85],N3-N2(amino)[3.12]" +A.C314 H-bonds[0]: "" 21 type=X A|C-G A.A373|A.C370,A.G391 WC +A.C370 H-bonds[0]: "" -A.G391 H-bonds[2]: "N6(amino)-N3[3.14],N1-O2'(hydroxyl)[2.76]" 22 type=X A|A-U A.A373|A.A371,A.U390 WC +A.A371 H-bonds[2]: "N7-O2'(hydroxyl)[2.63],N6(amino)-N3[3.00]" -A.U390 H-bonds[0]: "" 23 type=X A|A-U A.A374|A.A371,A.U390 WC +A.A371 H-bonds[0]: "" -A.U390 H-bonds[2]: "N6(amino)-O2(carbonyl)[2.59],N1-O2'(hydroxyl)[2.36]" 24 type=X A|G-C A.A465|A.G202,A.C215 WC -A.G202 H-bonds[1]: "N6(amino)*N2(amino)[2.88]" +A.C215 H-bonds[2]: "N7-O2'(hydroxyl)[2.37],N6(amino)-O2(carbonyl)[2.38]" 25 type=X A|G-C A.A465|A.G203,A.C214 WC -A.G203 H-bonds[2]: "N6(amino)-N3[2.81],N1-O2'(hydroxyl)[2.36]" +A.C214 H-bonds[0]: "" 26 type=X A|G-C A.A466|A.G202,A.C215 WC -A.G202 H-bonds[1]: "N1-N2(amino)[3.22]" +A.C215 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.50]" 27 type=X A|G-U A.A468|A.G201,A.U216 Wobble +A.G201 H-bonds[1]: "N7-N2(amino)[3.12]" -A.U216 H-bonds[0]: "" 28 type=II A|A-U A.A509|A.A502,A.U543 WC +A.A502 H-bonds[0]: "" -A.U543 H-bonds[1]: "N3-O2'(hydroxyl)[2.29]" 29 type=I A|C-G A.A510|A.C503,A.G542 WC +A.C503 H-bonds[1]: "N1-O2'(hydroxyl)[2.41]" -A.G542 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.35],N3-N2(amino)[2.86]" 30 type=II A|C-U A.A510|A.C503,A.U543 -- +A.C503 H-bonds[1]: "N1-O2'(hydroxyl)[2.41]" -A.U543 H-bonds[1]: "O2'(hydroxyl)-O4'[3.54]" 31 type=X A|C-g A.A535|A.C522,A.G7M527 WC -A.C522 H-bonds[0]: "" +A.G7M527 H-bonds[2]: "N1-O2'(hydroxyl)[2.86],N3-N2(amino)[3.31]" 32 type=I A|A-U A.A572|A.A19,A.U916 WC +A.A19 H-bonds[1]: "N1-O2'(hydroxyl)[3.04]" -A.U916 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.49]" 33 type=X A|G-C A.A573|A.G567,A.C883 WC +A.G567 H-bonds[0]: "" -A.C883 H-bonds[1]: "N3-O2'(hydroxyl)[2.47]" 34 type=I A|G-C A.A574|A.G568,A.C882 WC +A.G568 H-bonds[2]: "N1-O2'(hydroxyl)[2.70],N3-N2(amino)[2.68]" -A.C882 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.38],O2'(hydroxyl)-O2(carbonyl)[3.09]" 35 type=X A|U-A A.A607|A.U291,A.A309 WC +A.U291 H-bonds[0]: "" -A.A309 H-bonds[3]: "N6(amino)-O2'(hydroxyl)[3.30],N6(amino)-N3[3.17],N1-O2'(hydroxyl)[2.31]" 36 type=X A|G-C A.A608|A.G292,A.C308 WC +A.G292 H-bonds[3]: "N6(amino)-O2'(hydroxyl)[3.07],N6(amino)-N3[2.67],N1-N2(amino)[2.51]" -A.C308 H-bonds[0]: "" 37 type=II A|G-C A.A621|A.G41,A.C401 WC +A.G41 H-bonds[0]: "" -A.C401 H-bonds[3]: "O2'(hydroxyl)-O3'[3.17],O2'(hydroxyl)-O2'(hydroxyl)[2.76],N3-O2'(hydroxyl)[2.32]" 38 type=I A|G-C A.A622|A.G42,A.C400 WC +A.G42 H-bonds[2]: "N1-O2'(hydroxyl)[2.96],N3-N2(amino)[3.42]" -A.C400 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.24]" 39 type=X A|U-A A.A642|A.U598,A.A640 WC -A.U598 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.39]" +A.A640 H-bonds[0]: "" 40 type=X A|G-C A.A695|A.G785,A.C797 WC -A.G785 H-bonds[0]: "" +A.C797 H-bonds[1]: "N6(amino)-O2'(hydroxyl)[3.32]" 41 type=X A|G-C A.A695|A.G786,A.C796 WC -A.G786 H-bonds[1]: "N1-N2(amino)[3.45]" +A.C796 H-bonds[0]: "" 42 type=X A|G-C A.A696|A.G785,A.C797 WC -A.G785 H-bonds[0]: "" +A.C797 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[2.38],N1-O2'(hydroxyl)[3.13]" 43 type=I A|G-C A.A704|A.G688,A.C699 WC +A.G688 H-bonds[2]: "N1-O2'(hydroxyl)[2.27],N3-N2(amino)[3.52]" -A.C699 H-bonds[0]: "" 44 type=II A|C-G A.A728|A.C578,A.G763 WC -A.C578 H-bonds[1]: "N3-O2'(hydroxyl)[2.55]" +A.G763 H-bonds[0]: "" 45 type=I A|G-C A.A729|A.G577,A.C764 WC -A.G577 H-bonds[1]: "N3-N2(amino)[3.54]" +A.C764 H-bonds[1]: "N1-O2'(hydroxyl)[3.09]" 46 type=I A|G-C A.A767|A.G1511,A.C1524 WC +A.G1511 H-bonds[0]: "" -A.C1524 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.70],O2'(hydroxyl)-O2(carbonyl)[2.87]" 47 type=X A|A-G A.A777|A.A676,A.G714 Imino +A.A676 H-bonds[0]: "" -A.G714 H-bonds[1]: "N3-N2(amino)[3.31]" 48 type=I A|C-G A.A864|A.C18,A.G917 WC -A.C18 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.06]" +A.G917 H-bonds[2]: "N1-O2'(hydroxyl)[2.59],N3-N2(amino)[3.19]" 49 type=X A|C-G A.A873|A.C862,A.G867 WC -A.C862 H-bonds[0]: "" +A.G867 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.39],N1-O2'(hydroxyl)[2.34]" 50 type=X A|G-C A.A900|A.G769,A.C810 WC -A.G769 H-bonds[1]: "N1-N2(amino)[3.09]" +A.C810 H-bonds[0]: "" 51 type=I A|U-G A.A913|A.U12,A.G22 Wobble -A.U12 H-bonds[0]: "" +A.G22 H-bonds[2]: "N1-O2'(hydroxyl)[2.83],N3-N2(amino)[3.37]" **************************************************************************** List of 9 ribose zippers 1 nts=4 AACC A.A2,A.A3,A.C612,A.C613 2 nts=4 ACAA A.A66,A.C67,A.A171,A.A172 3 nts=4 GGAG A.G112,A.G113,A.A353,A.G354 4 nts=4 AAAA A.A130,A.A131,A.A262,A.A263 5 nts=4 AACC A.A195,A.A196,A.C221,A.C222 6 nts=4 GGAC A.G201,A.G202,A.A468,A.C469 7 nts=4 CCAA A.C400,A.C401,A.A621,A.A622 8 nts=4 AAGU A.A509,A.A510,A.G542,A.U543 9 nts=4 AUGG A.A696,A.U697,A.G785,A.G786 **************************************************************************** List of 3 kink turns 1 Normal k-turn; iloop#14; between stems [#53,#52]; bending-angle=58 C#53[CG A.C699,A.G688] [GA A.G703,A.A687] NC#52[AU A.A706,A.U684] strand1 nts=15; GCGUAGAGAUCUGGA A.G698,A.C699,A.G700,A.U701,A.A702,A.G703,A.A704,A.G705,A.A706,A.U707,A.C708,A.U709,A.G710,A.G711,A.A712 strand2 nts=12; UCCAGGUGUAGC A.U678,A.C679,A.C680,A.A681,A.G682,A.G683,A.U684,A.G685,A.U686,A.A687,A.G688,A.C689 2 Normal k-turn; iloop#15; between stems [#24,#23]; bending-angle=44 C#24[CG A.C277,A.G247] [GA A.G281,A.A246] NC#23[CG A.C284,A.G242] strand1 nts=12; GGCGACGAUCCC A.G275,A.G276,A.C277,A.G278,A.A279,A.C280,A.G281,A.A282,A.U283,A.C284,A.C285,A.C286 strand2 nts=10; GGGAUUAGCU A.G240,A.G241,A.G242,A.A243,A.U244,A.U245,A.A246,A.G247,A.C248,A.U249 3 REVERSE k-turn; iloop#19; between stems [#32,#33]; bending-angle=61 C#32[UG A.U409,A.G433] [GA A.G410,A.A432] NC#33[GU A.G416,A.U427] strand1 nts=14; GUAUGAAGAAGGCC A.G406,A.U407,A.A408,A.U409,A.G410,A.A411,A.A412,A.G413,A.A414,A.A415,A.G416,A.G417,A.C418,A.C419 strand2 nts=13; GGUUGUAAAGUAC A.G424,A.G425,A.U426,A.U427,A.G428,A.U429,A.A430,A.A431,A.A432,A.G433,A.U434,A.A435,A.C436 **************************************************************************** List of 103 splayed-apart dinucleotides 1 A.A3 A.U4 angle=142 distance=17.3 ratio=0.95 2 A.U4 A.U5 angle=104 distance=13.8 ratio=0.79 3 A.G6 A.A7 angle=91 distance=13.1 ratio=0.72 4 A.A7 A.A8 angle=148 distance=18.3 ratio=0.96 5 A.U13 A.U14 angle=97 distance=14.5 ratio=0.75 6 A.U30 A.G31 angle=112 distance=16.0 ratio=0.83 7 A.G31 A.A32 angle=106 distance=16.8 ratio=0.80 8 A.G38 A.G39 angle=88 distance=13.8 ratio=0.70 9 A.G46 A.C47 angle=111 distance=16.8 ratio=0.83 10 A.C47 A.C48 angle=87 distance=14.6 ratio=0.69 11 A.A50 A.A51 angle=142 distance=20.1 ratio=0.95 12 A.A51 A.C52 angle=113 distance=17.9 ratio=0.84 13 A.A59 A.A60 angle=124 distance=14.4 ratio=0.88 14 A.G64 A.A65 angle=153 distance=18.5 ratio=0.97 15 A.A65 A.A66 angle=163 distance=18.2 ratio=0.99 16 A.U84 A.U85 angle=100 distance=11.9 ratio=0.77 17 A.U133 A.G134 angle=87 distance=12.2 ratio=0.69 18 A.A143 A.G144 angle=134 distance=16.8 ratio=0.92 19 A.A172 A.U173 angle=89 distance=14.6 ratio=0.70 20 A.U173 A.A174 angle=147 distance=17.8 ratio=0.96 21 A.A182 A.C183 angle=98 distance=11.9 ratio=0.77 22 A.C183 A.G184 angle=97 distance=14.2 ratio=0.75 23 A.A196 A.A197 angle=105 distance=15.1 ratio=0.79 24 A.U208 A.U209 angle=117 distance=15.8 ratio=0.86 25 A.U209 A.C210 angle=92 distance=13.5 ratio=0.72 26 A.U239 A.G240 angle=96 distance=15.2 ratio=0.75 27 A.A243 A.U244 angle=139 distance=19.3 ratio=0.94 28 A.U244 A.U245 angle=161 distance=19.5 ratio=0.99 29 A.G265 A.G266 angle=129 distance=14.2 ratio=0.90 30 A.A279 A.C280 angle=142 distance=18.9 ratio=0.94 31 A.C280 A.G281 angle=119 distance=16.7 ratio=0.86 32 A.G305 A.A306 angle=89 distance=13.7 ratio=0.70 33 A.A315 A.C316 angle=170 distance=19.1 ratio=1.00 34 A.A329 A.C330 angle=104 distance=16.0 ratio=0.79 35 A.G331 A.G332 angle=117 distance=17.1 ratio=0.85 36 A.U343 A.A344 angle=129 distance=15.6 ratio=0.90 37 A.A344 A.C345 angle=88 distance=13.2 ratio=0.70 38 A.G351 A.C352 angle=117 distance=17.1 ratio=0.85 39 A.C352 A.A353 angle=151 distance=17.3 ratio=0.97 40 A.A353 A.G354 angle=154 distance=17.5 ratio=0.97 41 A.U365 A.A366 angle=109 distance=13.9 ratio=0.82 42 A.U367 A.U368 angle=119 distance=17.6 ratio=0.86 43 A.U368 A.G369 angle=151 distance=18.8 ratio=0.97 44 A.U387 A.G388 angle=152 distance=17.3 ratio=0.97 45 A.G388 A.A389 angle=106 distance=16.9 ratio=0.80 46 A.C396 A.A397 angle=129 distance=15.5 ratio=0.90 47 A.A397 A.U398 angle=121 distance=14.6 ratio=0.87 48 A.U405 A.G406 angle=148 distance=18.2 ratio=0.96 49 A.A412 A.G413 angle=91 distance=14.9 ratio=0.71 50 A.G413 A.A414 angle=107 distance=15.6 ratio=0.80 51 A.U420 A.U421 angle=108 distance=14.9 ratio=0.81 52 A.U421 A.C422 angle=92 distance=13.1 ratio=0.72 53 A.A466 A.U467 angle=100 distance=14.0 ratio=0.77 54 A.U467 A.A468 angle=100 distance=13.2 ratio=0.77 55 A.G484 A.U485 angle=116 distance=16.4 ratio=0.85 56 A.U485 A.U486 angle=170 distance=17.7 ratio=1.00 57 A.C504 A.G505 angle=158 distance=18.6 ratio=0.98 58 A.A523 A.G524 angle=108 distance=14.3 ratio=0.81 59 A.U531 A.A532 angle=137 distance=13.2 ratio=0.94 60 A.A532 A.A533 angle=173 distance=15.1 ratio=1.00 61 A.A533 A.U534 angle=120 distance=16.8 ratio=0.87 62 A.A535 A.C536 angle=104 distance=15.0 ratio=0.79 63 A.A559 A.A560 angle=135 distance=17.5 ratio=0.92 64 A.A560 A.U561 angle=160 distance=18.8 ratio=0.98 65 A.U561 A.U562 angle=101 distance=15.4 ratio=0.77 66 A.A563 A.C564 angle=122 distance=15.1 ratio=0.87 67 A.G566 A.G567 angle=94 distance=14.4 ratio=0.73 68 A.C569 A.G570 angle=169 distance=17.7 ratio=1.00 69 A.G606 A.A607 angle=154 distance=17.4 ratio=0.97 70 A.C618 A.U619 angle=98 distance=13.7 ratio=0.76 71 A.C631 A.U632 angle=140 distance=16.3 ratio=0.94 72 A.U632 A.G633 angle=118 distance=15.9 ratio=0.86 73 A.U653 A.G654 angle=87 distance=13.4 ratio=0.69 74 A.G664 A.A665 angle=112 distance=16.6 ratio=0.83 75 A.A665 A.G666 angle=144 distance=17.6 ratio=0.95 76 A.U701 A.A702 angle=131 distance=17.0 ratio=0.91 77 A.A702 A.G703 angle=115 distance=15.2 ratio=0.84 78 A.G722 A.U723 angle=128 distance=14.0 ratio=0.90 79 A.U723 A.G724 angle=123 distance=15.6 ratio=0.88 80 A.G733 A.G734 angle=148 distance=18.2 ratio=0.96 81 A.C754 A.G755 angle=95 distance=12.7 ratio=0.74 82 A.G765 A.A766 angle=86 distance=12.8 ratio=0.68 83 A.G776 A.A777 angle=90 distance=12.8 ratio=0.71 84 A.A814 A.A815 angle=101 distance=15.7 ratio=0.77 85 A.A815 A.A816 angle=142 distance=19.5 ratio=0.95 86 A.A816 A.C817 angle=118 distance=16.0 ratio=0.86 87 A.C817 A.G818 angle=100 distance=15.5 ratio=0.77 88 A.G818 A.A819 angle=122 distance=17.0 ratio=0.87 89 A.A819 A.U820 angle=88 distance=13.5 ratio=0.69 90 A.U820 A.G821 angle=142 distance=17.4 ratio=0.95 91 A.U863 A.A864 angle=86 distance=12.1 ratio=0.68 92 A.G869 A.U870 angle=111 distance=15.0 ratio=0.82 93 A.U870 A.U871 angle=151 distance=18.3 ratio=0.97 94 A.U871 A.A872 angle=118 distance=15.7 ratio=0.86 95 A.A872 A.A873 angle=107 distance=15.4 ratio=0.80 96 A.A873 A.G874 angle=128 distance=17.3 ratio=0.90 97 A.U884 A.G885 angle=157 distance=18.6 ratio=0.98 98 A.G898 A.C899 angle=100 distance=13.1 ratio=0.77 99 A.U1390 A.U1391 angle=146 distance=18.1 ratio=0.96 100 A.G1529 A.G1530 angle=102 distance=16.5 ratio=0.78 101 A.G1530 A.A1531 angle=121 distance=15.2 ratio=0.87 102 A.A1534 A.C1535 angle=104 distance=14.7 ratio=0.79 103 A.C1538 A.C1539 angle=108 distance=15.1 ratio=0.81 ---------------------------------------------------------------- Summary of 63 splayed-apart units 1 nts=3 AUU A.A3,A.U4,A.U5 2 nts=3 GAA A.G6,A.A7,A.A8 3 nts=2 UU A.U13,A.U14 4 nts=3 UGA A.U30,A.G31,A.A32 5 nts=2 GG A.G38,A.G39 6 nts=3 GCC A.G46,A.C47,A.C48 7 nts=3 AAC A.A50,A.A51,A.C52 8 nts=2 AA A.A59,A.A60 9 nts=3 GAA A.G64,A.A65,A.A66 10 nts=2 UU A.U84,A.U85 11 nts=2 UG A.U133,A.G134 12 nts=2 AG A.A143,A.G144 13 nts=3 AUA A.A172,A.U173,A.A174 14 nts=3 ACG A.A182,A.C183,A.G184 15 nts=2 AA A.A196,A.A197 16 nts=3 UUC A.U208,A.U209,A.C210 17 nts=2 UG A.U239,A.G240 18 nts=3 AUU A.A243,A.U244,A.U245 19 nts=2 GG A.G265,A.G266 20 nts=3 ACG A.A279,A.C280,A.G281 21 nts=2 GA A.G305,A.A306 22 nts=2 AC A.A315,A.C316 23 nts=2 AC A.A329,A.C330 24 nts=2 GG A.G331,A.G332 25 nts=3 UAC A.U343,A.A344,A.C345 26 nts=4 GCAG A.G351,A.C352,A.A353,A.G354 27 nts=2 UA A.U365,A.A366 28 nts=3 UUG A.U367,A.U368,A.G369 29 nts=3 UGA A.U387,A.G388,A.A389 30 nts=3 CAU A.C396,A.A397,A.U398 31 nts=2 UG A.U405,A.G406 32 nts=3 AGA A.A412,A.G413,A.A414 33 nts=3 UUC A.U420,A.U421,A.C422 34 nts=3 AUA A.A466,A.U467,A.A468 35 nts=3 GUU A.G484,A.U485,A.U486 36 nts=2 CG A.C504,A.G505 37 nts=2 AG A.A523,A.G524 38 nts=4 UAAU A.U531,A.A532,A.A533,A.U534 39 nts=2 AC A.A535,A.C536 40 nts=4 AAUU A.A559,A.A560,A.U561,A.U562 41 nts=2 AC A.A563,A.C564 42 nts=2 GG A.G566,A.G567 43 nts=2 CG A.C569,A.G570 44 nts=2 GA A.G606,A.A607 45 nts=2 CU A.C618,A.U619 46 nts=3 CUG A.C631,A.U632,A.G633 47 nts=2 UG A.U653,A.G654 48 nts=3 GAG A.G664,A.A665,A.G666 49 nts=3 UAG A.U701,A.A702,A.G703 50 nts=3 GUG A.G722,A.U723,A.G724 51 nts=2 GG A.G733,A.G734 52 nts=2 CG A.C754,A.G755 53 nts=2 GA A.G765,A.A766 54 nts=2 GA A.G776,A.A777 55 nts=8 AAACGAUG A.A814,A.A815,A.A816,A.C817,A.G818,A.A819,A.U820,A.G821 56 nts=2 UA A.U863,A.A864 57 nts=6 GUUAAG A.G869,A.U870,A.U871,A.A872,A.A873,A.G874 58 nts=2 UG A.U884,A.G885 59 nts=2 GC A.G898,A.C899 60 nts=2 UU A.U1390,A.U1391 61 nts=3 GGA A.G1529,A.G1530,A.A1531 62 nts=2 AC A.A1534,A.C1535 63 nts=2 CC A.C1538,A.C1539 **************************************************************************** This structure contains 2-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. **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7nas nts=974 [whole] AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGPGCCAGCAGCCgCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGC&GCCUUG&AGGUAACCGUAGGgGaaCCUGCGGUUGGAUCACCUCCU ........((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((..((((((((((....))))))).)))))..)))))......(((......(((((((..((...(((((((.(.((.....((((((....))))))......)).).....(((....)))....((((((..((....)))))))).)))))))..)).)))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...(((((....)))).))))).)).))))))..((((......((((....)))).....))))..((.(((((...(....((((((((.......)))))))).....)....)))))....)).((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((((((((...((((((((....(((((((...((........))......)))))))....).......((....)).)))))))..))).)))))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((((.....))))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((....(((&)))...&....(((((((((....)))))))))}..)))...... >7nas-A #1 nts=974 0.00(3.25) [chain] RNA* AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGPGCCAGCAGCCgCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGC&GCCUUG&AGGUAACCGUAGGgGaaCCUGCGGUUGGAUCACCUCCU ........((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((..((((((((((....))))))).)))))..)))))......(((......(((((((..((...(((((((.(.((.....((((((....))))))......)).).....(((....)))....((((((..((....)))))))).)))))))..)).)))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...(((((....)))).))))).)).))))))..((((......((((....)))).....))))..((.(((((...(....((((((((.......)))))))).....)....)))))....)).((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((((((((...((((((((....(((((((...((........))......)))))))....).......((....)).)))))))..))).)))))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((((.....))))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((....(((&)))...&....(((((((((....)))))))))}..)))...... **************************************************************************** Summary of structural features of 974 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 A . A.A1 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop 2 A . A.A2 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop,A-minor,ribose-zipper 3 A . A.A3 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,ribose-zipper,cap-acceptor,splayed-apart 4 U . A.U4 0.004 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop,splayed-apart 5 U . A.U5 0.006 anti,~C2'-endo,non-stack,ss-non-loop,cap-donor,splayed-apart 6 G . A.G6 0.019 syn,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 7 A . A.A7 0.012 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 8 A . A.A8 0.015 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 9 G ( A.G9 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,phosphate 10 A ( A.A10 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 G ( A.G11 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 12 U ( A.U12 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 13 U . A.U13 0.009 anti,~C2'-endo,non-stack,non-canonical,multiplet,hairpin-loop,splayed-apart 14 U . A.U14 0.015 u-turn,anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 15 G [ A.G15 0.015 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,phosphate 16 A . A.A16 0.016 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,cap-donor,phosphate 17 U [ A.U17 0.014 pseudoknotted,u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop,phosphate 18 C [ A.C18 0.015 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,phosphate 19 A [ A.A19 0.017 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,A-minor,phosphate 20 U . A.U20 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop 21 G . A.G21 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 22 G ) A.G22 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,cap-donor 23 C ) A.C23 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 24 U ) A.U24 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ) A.C25 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet 26 A . A.A26 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 27 G ( A.G27 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 28 A ( A.A28 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 29 U ( A.U29 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 U ( A.U30 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 31 G . A.G31 0.016 turn,anti,~C2'-endo,non-pair-contact,bulge,cap-acceptor,splayed-apart 32 A ( A.A32 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 33 A ( A.A33 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 C ( A.C34 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 G ( A.G35 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 C ( A.C36 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 37 U . A.U37 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 38 G . A.G38 0.020 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 39 G ( A.G39 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 40 C ( A.C40 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 41 G ( A.G41 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 42 G ( A.G42 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 43 C ( A.C43 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 A ( A.A44 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 45 G ( A.G45 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 46 G ( A.G46 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 47 C ( A.C47 0.013 turn,anti,~C2'-endo,BII,non-stack,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,cap-donor,phosphate,splayed-apart 48 C . A.C48 0.012 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 49 U . A.U49 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 50 A . A.A50 0.015 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 51 A . A.A51 0.017 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,splayed-apart 52 C ( A.C52 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,splayed-apart 53 A ( A.A53 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 54 C ( A.C54 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,bulge,phosphate 55 A . A.A55 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,bulge,phosphate 56 U ( A.U56 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge 57 G ( A.G57 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 58 C ( A.C58 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 59 A . A.A59 0.019 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 60 A . A.A60 0.012 ~C2'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 61 G ( A.G61 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 62 U ( A.U62 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 63 C ( A.C63 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 64 G . A.G64 0.013 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,phosphate,splayed-apart 65 A . A.A65 0.015 turn,anti,~C2'-endo,non-pair-contact,bulge,cap-acceptor,splayed-apart 66 A ( A.A66 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,ribose-zipper,phosphate,splayed-apart 67 C ( A.C67 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,ribose-zipper 68 G . A.G68 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,cap-acceptor 69 G ( A.G69 0.012 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,cap-donor 70 U ( A.U70 0.012 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 71 A . A.A71 0.012 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor 72 A . A.A72 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,bulge,A-minor 73 C ( A.C73 0.016 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 74 A ( A.A74 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 75 G ( A.G75 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 76 G ( A.G76 0.016 ~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 77 A ( A.A77 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 78 A ( A.A78 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 79 G ( A.G79 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 80 A ( A.A80 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 81 A ( A.A81 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 82 G ( A.G82 0.020 turn,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop 83 C . A.C83 0.007 anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop 84 U . A.U84 0.009 turn,anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 85 U . A.U85 0.004 turn,syn,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 86 G . A.G86 0.007 ~C2'-endo,non-pair-contact,hairpin-loop,phosphate 87 C ) A.C87 0.016 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop 88 U ) A.U88 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 89 U ) A.U89 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 90 C ) A.C90 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 91 U ) A.U91 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 92 U ) A.U92 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 93 U ) A.U93 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 94 G . A.G94 0.021 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,bulge 95 C ) A.C95 0.006 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 96 U ) A.U96 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 97 G ) A.G97 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 98 A ) A.A98 0.010 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 99 C ) A.C99 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 100 G . A.G100 0.022 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 101 A . A.A101 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,phosphate 102 G ) A.G102 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 103 U ) A.U103 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 104 G ) A.G104 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 105 G ) A.G105 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 106 C ) A.C106 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 107 G . A.G107 0.020 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 108 G . A.G108 0.029 syn,~C3'-endo,non-pair-contact,junction-loop,phosphate 109 A . A.A109 0.024 turn,syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 110 C . A.C110 0.010 anti,~C3'-endo,BI,non-pair-contact,junction-loop 111 G . A.G111 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 112 G . A.G112 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,ribose-zipper 113 G ( A.G113 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,ribose-zipper 114 U ( A.U114 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 115 G ( A.G115 0.015 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 116 A . A.A116 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor 117 G . A.G117 0.022 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop 118 U . A.U118 0.013 anti,~C3'-endo,BI,non-pair-contact,junction-loop 119 A . A.A119 0.016 turn,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,phosphate 120 A . A.A120 0.021 anti,~C2'-endo,BI,non-pair-contact,junction-loop,cap-acceptor,phosphate 121 U . A.U121 0.004 turn,anti,~C3'-endo,non-stack,non-pair-contact,junction-loop 122 G ( A.G122 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 123 U ( A.U123 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 124 C ( A.C124 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 125 U ( A.U125 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 126 G ( A.G126 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 127 G ( A.G127 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 128 G ( A.G128 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 129 A . A.A129 0.014 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 130 A . A.A130 0.018 anti,~C2'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,ribose-zipper 131 A ( A.A131 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor,ribose-zipper,phosphate 132 C ( A.C132 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 133 U . A.U133 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 134 G . A.G134 0.021 anti,~C3'-endo,BI,non-pair-contact,internal-loop,splayed-apart 135 C . A.C135 0.013 anti,~C3'-endo,BI,non-pair-contact,internal-loop 136 C ( A.C136 0.011 ~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 137 U ( A.U137 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 138 G ( A.G138 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 139 A ( A.A139 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 140 U ( A.U140 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 141 G ( A.G141 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 142 G ( A.G142 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 143 A . A.A143 0.012 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 144 G ( A.G144 0.019 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,splayed-apart 145 G . A.G145 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 146 G ( A.G146 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 147 G ( A.G147 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 148 G . A.G148 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 149 A . A.A149 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 150 U . A.U150 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 151 A . A.A151 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 152 A . A.A152 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 153 C ( A.C153 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 154 U ( A.U154 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 155 A ( A.A155 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 156 C ( A.C156 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 157 U ( A.U157 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 158 G ( A.G158 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 159 G . A.G159 0.014 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 160 A . A.A160 0.008 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor 161 A . A.A161 0.011 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,cap-donor,phosphate 162 A . A.A162 0.017 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 163 C ) A.C163 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 164 G ) A.G164 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 165 G ) A.G165 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 166 U ) A.U166 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 167 A ) A.A167 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 168 G ) A.G168 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 169 C . A.C169 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 170 U . A.U170 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 171 A . A.A171 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor,ribose-zipper 172 A . A.A172 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper,splayed-apart 173 U . A.U173 0.014 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,cap-donor,splayed-apart 174 A . A.A174 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 175 C ) A.C175 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 176 C ) A.C176 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 177 G . A.G177 0.014 syn,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 178 C ) A.C178 0.013 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 179 A . A.A179 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor 180 U . A.U180 0.011 anti,~C3'-endo,non-pair-contact,junction-loop,cap-donor 181 A . A.A181 0.012 anti,~C2'-endo,non-pair-contact,junction-loop 182 A . A.A182 0.016 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 183 C . A.C183 0.005 turn,syn,~C2'-endo,BI,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 184 G ( A.G184 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 185 U ( A.U185 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 186 C ( A.C186 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 187 G . A.G187 0.018 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 188 C . A.C188 0.006 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 189 A . A.A189 0.012 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 190 A . A.A190 0.016 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 191 G ) A.G191 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 192 A ) A.A192 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 193 C ) A.C193 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop 194 C . A.C194 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 195 A . A.A195 0.017 anti,~C3'-endo,BI,non-pair-contact,junction-loop,A-minor,ribose-zipper,phosphate 196 A . A.A196 0.015 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,ribose-zipper,phosphate,splayed-apart 197 A . A.A197 0.018 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor,splayed-apart 198 G ( A.G198 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 199 A ( A.A199 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 200 G ( A.G200 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 201 G ( A.G201 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 202 G ( A.G202 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 203 G ( A.G203 0.011 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 204 G . A.G204 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,bulge 205 A . A.A205 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,A-minor 206 C ( A.C206 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 207 C ( A.C207 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 208 U . A.U208 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 209 U . A.U209 0.009 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 210 C . A.C210 0.006 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 211 G . A.G211 0.011 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 212 G ) A.G212 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 213 G ) A.G213 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 214 C ) A.C214 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 215 C ) A.C215 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 216 U ) A.U216 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 217 C ) A.C217 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 218 U ) A.U218 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 219 U ) A.U219 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 220 G . A.G220 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 221 C ) A.C221 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,ribose-zipper,cap-donor 222 C ) A.C222 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper 223 A ) A.A223 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 224 U ) A.U224 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 225 C ) A.C225 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 226 G ) A.G226 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 227 G ) A.G227 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 228 A . A.A228 0.016 anti,~C3'-endo,non-pair-contact,internal-loop 229 U . A.U229 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 230 G ) A.G230 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 231 U ) A.U231 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor 232 G . A.G232 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 233 C ) A.C233 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 234 C ) A.C234 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 235 C ) A.C235 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 236 A ) A.A236 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 237 G ) A.G237 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 238 A ) A.A238 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 239 U ) A.U239 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 240 G ( A.G240 0.020 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 241 G ( A.G241 0.018 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 242 G ( A.G242 0.014 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 243 A . A.A243 0.014 turn,k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 244 U . A.U244 0.012 turn,k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 245 U . A.U245 0.013 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 246 A . A.A246 0.020 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 247 G ( A.G247 0.016 k-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 248 C ( A.C248 0.010 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 249 U ( A.U249 0.013 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 250 A . A.A250 0.005 syn,~C2'-endo,non-pair-contact,bulge,cap-donor 251 G . A.G251 0.015 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge 252 U ( A.U252 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,cap-acceptor 253 A ( A.A253 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 254 G ( A.G254 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 255 G ( A.G255 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 256 U ( A.U256 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 257 G ( A.G257 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 258 G ( A.G258 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 259 G ( A.G259 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 260 G . A.G260 0.019 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop 261 U . A.U261 0.013 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,phosphate 262 A . A.A262 0.015 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper 263 A . A.A263 0.015 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,ribose-zipper,phosphate 264 C . A.C264 0.010 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 265 G . A.G265 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate,splayed-apart 266 G . A.G266 0.021 turn,syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate,splayed-apart 267 C ) A.C267 0.010 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 268 U ) A.U268 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 269 C ) A.C269 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 270 A ) A.A270 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 271 C ) A.C271 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 272 C ) A.C272 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 273 U ) A.U273 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 274 A ) A.A274 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 275 G ) A.G275 0.011 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 276 G ) A.G276 0.018 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 277 C ) A.C277 0.015 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,phosphate 278 G . A.G278 0.016 k-turn,anti,~C3'-endo,BII,non-pair-contact,internal-loop,phosphate 279 A . A.A279 0.019 turn,k-turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 280 C . A.C280 0.013 turn,k-turn,anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 281 G . A.G281 0.014 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,splayed-apart 282 A . A.A282 0.018 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,cap-acceptor 283 U . A.U283 0.010 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,cap-donor 284 C ) A.C284 0.009 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 285 C ) A.C285 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 286 C ) A.C286 0.014 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 287 U . A.U287 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 288 A . A.A288 0.015 anti,~C3'-endo,BI,non-pair-contact,junction-loop 289 G ( A.G289 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 290 C ( A.C290 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 291 U ( A.U291 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 292 G ( A.G292 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 293 G ( A.G293 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 294 U ( A.U294 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 295 C ( A.C295 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 296 U ( A.U296 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 297 G . A.G297 0.018 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor,phosphate 298 A . A.A298 0.017 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 299 G . A.G299 0.020 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,phosphate 300 A . A.A300 0.020 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate 301 G ) A.G301 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 302 G ) A.G302 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 303 A ) A.A303 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 304 U ) A.U304 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 305 G . A.G305 0.018 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,splayed-apart 306 A . A.A306 0.014 anti,~C3'-endo,BI,non-pair-contact,bulge,cap-donor,splayed-apart 307 C . A.C307 0.010 anti,~C3'-endo,non-pair-contact,bulge,phosphate 308 C ) A.C308 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 309 A ) A.A309 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 310 G ) A.G310 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 311 C ) A.C311 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 312 C ) A.C312 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 313 A ) A.A313 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 314 C ) A.C314 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 315 A . A.A315 0.017 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor,splayed-apart 316 C ( A.C316 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 317 U ( A.U317 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 318 G ( A.G318 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 319 G ( A.G319 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 320 A ( A.A320 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 321 A . A.A321 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 322 C . A.C322 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 323 U . A.U323 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 324 G . A.G324 0.021 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 325 A . A.A325 0.016 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 326 G . A.G326 0.020 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 327 A . A.A327 0.020 u-turn,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 328 C . A.C328 0.013 turn,~C2'-endo,non-pair-contact,hairpin-loop,phosphate 329 A . A.A329 0.021 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,splayed-apart 330 C . A.C330 0.013 anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 331 G . A.G331 0.020 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 332 G . A.G332 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate,splayed-apart 333 U ) A.U333 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 334 C ) A.C334 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 335 C ) A.C335 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 336 A ) A.A336 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 337 G ) A.G337 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 338 A . A.A338 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 339 C ( A.C339 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 340 U ( A.U340 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 341 C ( A.C341 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 342 C ( A.C342 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 343 U . A.U343 0.009 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 344 A . A.A344 0.010 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 345 C . A.C345 0.006 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 346 G . A.G346 0.014 turn,syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 347 G ) A.G347 0.016 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 348 G ) A.G348 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 349 A ) A.A349 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 350 G ) A.G350 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 351 G . A.G351 0.016 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 352 C . A.C352 0.010 turn,anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 353 A . A.A353 0.016 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,phosphate,splayed-apart 354 G ) A.G354 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop,ribose-zipper,phosphate,splayed-apart 355 C ) A.C355 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 356 A ) A.A356 0.018 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge 357 G ) A.G357 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,bulge,phosphate 358 U ) A.U358 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 359 G ) A.G359 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 360 G . A.G360 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 361 G ) A.G361 0.015 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 362 G . A.G362 0.022 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,phosphate 363 A . A.A363 0.018 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 364 A . A.A364 0.019 u-turn,anti,~C3'-endo,non-pair-contact,junction-loop,cap-donor,phosphate 365 U . A.U365 0.011 u-turn,syn,~C3'-endo,BII,non-stack,non-canonical,non-pair-contact,multiplet,junction-loop,cap-acceptor,phosphate,splayed-apart 366 A . A.A366 0.017 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 367 U ( A.U367 0.018 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate,splayed-apart 368 U . A.U368 0.014 turn,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,bulge,splayed-apart 369 G ( A.G369 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 370 C ( A.C370 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 371 A ( A.A371 0.015 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 372 C . A.C372 0.013 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge 373 A . A.A373 0.019 turn,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor 374 A . A.A374 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,bulge,A-minor,phosphate 375 U ( A.U375 0.015 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,multiplet,bulge,phosphate 376 G ( A.G376 0.020 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 377 G ( A.G377 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 378 G ( A.G378 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 379 C ( A.C379 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 380 G . A.G380 0.016 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 381 C . A.C381 0.011 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 382 A . A.A382 0.018 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 383 A . A.A383 0.016 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 384 G ) A.G384 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 385 C ) A.C385 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 386 C ) A.C386 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 387 U ) A.U387 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 388 G . A.G388 0.016 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,phosphate,splayed-apart 389 A ) A.A389 0.017 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,cap-acceptor,phosphate,splayed-apart 390 U ) A.U390 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,cap-donor 391 G ) A.G391 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 392 C ) A.C392 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 393 A ) A.A393 0.019 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate 394 G . A.G394 0.022 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 395 C ) A.C395 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 396 C ) A.C396 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 397 A . A.A397 0.021 turn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,bulge,phosphate,splayed-apart 398 U ) A.U398 0.013 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 399 G ) A.G399 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 400 C ) A.C400 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 401 C ) A.C401 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper,phosphate 402 G ) A.G402 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 403 C ) A.C403 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 404 G . A.G404 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 405 U . A.U405 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-donor,phosphate,splayed-apart 406 G ( A.G406 0.013 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 407 U ( A.U407 0.013 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 408 A ( A.A408 0.012 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 409 U ( A.U409 0.009 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 410 G . A.G410 0.015 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 411 A . A.A411 0.016 k-turn,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 412 A . A.A412 0.012 turn,k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,cap-acceptor,splayed-apart 413 G . A.G413 0.011 turn,k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 414 A . A.A414 0.010 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,cap-donor,splayed-apart 415 A . A.A415 0.011 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 416 G ( A.G416 0.016 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 417 G ( A.G417 0.014 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 418 C ( A.C418 0.012 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 419 C ( A.C419 0.010 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 420 U . A.U420 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 421 U . A.U421 0.005 turn,anti,~C3'-endo,non-stack,hairpin-loop,splayed-apart 422 C . A.C422 0.006 turn,anti,~C2'-endo,BII,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-donor,splayed-apart 423 G . A.G423 0.012 turn,syn,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor 424 G ) A.G424 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 425 G ) A.G425 0.013 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 426 U ) A.U426 0.008 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 427 U ) A.U427 0.008 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 428 G . A.G428 0.021 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 429 U . A.U429 0.010 turn,k-turn,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 430 A . A.A430 0.015 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 431 A . A.A431 0.015 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 432 A . A.A432 0.014 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 433 G ) A.G433 0.009 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 434 U ) A.U434 0.009 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 435 A ) A.A435 0.013 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 436 C ) A.C436 0.013 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 437 U . A.U437 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 438 U . A.U438 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 439 U ( A.U439 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop 440 C ( A.C440 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 441 A . A.A441 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 442 G ( A.G442 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 443 C ( A.C443 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 444 G ( A.G444 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 445 G ( A.G445 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 446 G ( A.G446 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 447 G . A.G447 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 448 A . A.A448 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 449 G . A.G449 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 450 G ( A.G450 0.016 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate 451 A . A.A451 0.018 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate 452 A . A.A452 0.018 turn,syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 453 G . A.G453 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 454 G . A.G454 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 455 G ( A.G455 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 456 A ( A.A456 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 457 G ( A.G457 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 458 U ( A.U458 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 459 A ( A.A459 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 460 A ( A.A460 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 461 A ( A.A461 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 462 G ( A.G462 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 463 U . A.U463 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop 464 U . A.U464 0.008 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor 465 A . A.A465 0.012 turn,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor 466 A . A.A466 0.011 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,phosphate,splayed-apart 467 U . A.U467 0.007 turn,u-turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 468 A . A.A468 0.014 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,splayed-apart 469 C . A.C469 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,ribose-zipper 470 C ) A.C470 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 471 U ) A.U471 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 472 U ) A.U472 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 473 U ) A.U473 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 474 G ) A.G474 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 475 C ) A.C475 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 476 U ) A.U476 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 477 C ) A.C477 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 478 A . A.A478 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 479 U . A.U479 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 480 U . A.U480 0.011 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop 481 G . A.G481 0.014 ~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,internal-loop 482 A . A.A482 0.016 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 483 C ) A.C483 0.016 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate 484 G . A.G484 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,splayed-apart 485 U . A.U485 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 486 U . A.U486 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate,splayed-apart 487 A . A.A487 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 488 C ) A.C488 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 489 C ) A.C489 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 490 C ) A.C490 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 491 G ) A.G491 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 492 C ) A.C492 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 493 A . A.A493 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 494 G . A.G494 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 495 A . A.A495 0.021 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 496 A . A.A496 0.017 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 497 G ) A.G497 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 498 A ) A.A498 0.017 anti,~C3'-endo,BII,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,cap-acceptor 499 A . A.A499 0.018 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 500 G ( A.G500 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 501 C ( A.C501 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 502 A ( A.A502 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 503 C ( A.C503 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 504 C ( A.C504 0.011 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 505 G [ A.G505 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 506 G [ A.G506 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 507 C [ A.C507 0.013 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate 508 U . A.U508 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop 509 A . A.A509 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,phosphate 510 A . A.A510 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 511 C ( A.C511 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 512 U ( A.U512 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 513 C ( A.C513 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 514 C ( A.C514 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 515 G ( A.G515 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop 516 P . A.PSU516 0.065 modified,anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,internal-loop 517 G . A.G517 0.016 anti,~C2'-endo,non-pair-contact,hairpin-loop,internal-loop 518 C . A.C518 0.009 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,internal-loop,phosphate 519 C . A.C519 0.010 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,internal-loop 520 A . A.A520 0.007 anti,~C3'-endo,non-pair-contact,hairpin-loop,internal-loop 521 G ( A.G521 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop,internal-loop,phosphate 522 C ( A.C522 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor,phosphate 523 A . A.A523 0.012 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,splayed-apart 524 G ] A.G524 0.001 pseudoknotted,turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,splayed-apart 525 C ] A.C525 0.002 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 526 C ] A.C526 0.001 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 527 g ) A.G7M527 0.013 modified,anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor 528 C ) A.C528 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,cap-donor 529 G . A.G529 0.004 anti,~C3'-endo,non-pair-contact,internal-loop,cap-donor 530 G . A.G530 0.012 syn,~C3'-endo,non-pair-contact,internal-loop,phosphate 531 U . A.U531 0.010 turn,anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 532 A . A.A532 0.015 syn,~C3'-endo,non-stack,non-pair-contact,internal-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 533 A . A.A533 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate,splayed-apart 534 U . A.U534 0.005 turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 535 A . A.A535 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,cap-acceptor,splayed-apart 536 C ) A.C536 0.008 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,splayed-apart 537 G ) A.G537 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 538 G ) A.G538 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 539 A ) A.A539 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 540 G ) A.G540 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 541 G ) A.G541 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 542 G ) A.G542 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 543 U ) A.U543 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 544 G ) A.G544 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 545 C ) A.C545 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 546 A . A.A546 0.013 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 547 A . A.A547 0.015 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 548 G ) A.G548 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 549 C ) A.C549 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 550 G ) A.G550 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 551 U ) A.U551 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 552 U ) A.U552 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 553 A ) A.A553 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 554 A ) A.A554 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 555 U ) A.U555 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 556 C ) A.C556 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 557 G . A.G557 0.017 anti,~C3'-endo,non-pair-contact,ss-non-loop 558 G . A.G558 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 559 A . A.A559 0.017 syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate,splayed-apart 560 A . A.A560 0.017 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-acceptor,phosphate,splayed-apart 561 U . A.U561 0.011 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,splayed-apart 562 U . A.U562 0.013 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 563 A . A.A563 0.021 syn,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate,splayed-apart 564 C . A.C564 0.010 turn,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 565 U . A.U565 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,phosphate 566 G . A.G566 0.016 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop,cap-donor,splayed-apart 567 G ( A.G567 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,splayed-apart 568 G ( A.G568 0.016 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 569 C ( A.C569 0.014 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 570 G [ A.G570 0.018 pseudoknotted,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,cap-donor,splayed-apart 571 U [ A.U571 0.018 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 572 A . A.A572 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,phosphate 573 A . A.A573 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 574 A . A.A574 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,cap-acceptor 575 G ( A.G575 0.019 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,junction-loop 576 C . A.C576 0.012 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate 577 G ( A.G577 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,A-minor,cap-donor 578 C ( A.C578 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,phosphate 579 A ( A.A579 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 580 C ( A.C580 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 581 G . A.G581 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 582 C . A.C582 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 583 A . A.A583 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 584 G ( A.G584 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 585 G ( A.G585 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 586 C ( A.C586 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 587 G . A.G587 0.017 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 588 G ( A.G588 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 589 U ( A.U589 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 590 U ( A.U590 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 591 U ( A.U591 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 592 G ( A.G592 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 593 U ( A.U593 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 594 U ( A.U594 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 595 A . A.A595 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge 596 A ( A.A596 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 597 G ( A.G597 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,cap-acceptor 598 U ( A.U598 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,cap-donor 599 C ( A.C599 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 600 A ( A.A600 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 601 G ( A.G601 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 602 A ( A.A602 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 603 U ( A.U603 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 604 G ( A.G604 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 605 U ( A.U605 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 606 G . A.G606 0.018 anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 607 A . A.A607 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,splayed-apart 608 A . A.A608 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,phosphate 609 A . A.A609 0.018 anti,~C3'-endo,BI,non-pair-contact,internal-loop 610 U . A.U610 0.012 anti,~C3'-endo,non-pair-contact,internal-loop 611 C . A.C611 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 612 C ( A.C612 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,ribose-zipper 613 C ( A.C613 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 614 C ( A.C614 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 615 G ( A.G615 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 616 G ( A.G616 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 617 G ( A.G617 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 618 C . A.C618 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 619 U . A.U619 0.010 turn,anti,~C3'-endo,BI,non-stack,hairpin-loop,splayed-apart 620 C . A.C620 0.010 anti,~C3'-endo,non-pair-contact,hairpin-loop 621 A . A.A621 0.016 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,phosphate 622 A . A.A622 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 623 C ) A.C623 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 624 C ) A.C624 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 625 U ) A.U625 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 626 G ) A.G626 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 627 G ) A.G627 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor 628 G ) A.G628 0.018 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor 629 A . A.A629 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-donor 630 A . A.A630 0.016 anti,~C3'-endo,BI,non-pair-contact,internal-loop 631 C . A.C631 0.011 turn,anti,~C3'-endo,non-pair-contact,internal-loop,splayed-apart 632 U . A.U632 0.009 turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,phosphate,splayed-apart 633 G ) A.G633 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,splayed-apart 634 C ) A.C634 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 635 A ) A.A635 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 636 U ) A.U636 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 637 C ) A.C637 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 638 U ) A.U638 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 639 G ) A.G639 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 640 A ) A.A640 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 641 U . A.U641 0.016 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge 642 A . A.A642 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor,phosphate 643 C ) A.C643 0.013 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 644 U ) A.U644 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 645 G ) A.G645 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 646 G ) A.G646 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 647 C ) A.C647 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 648 A ) A.A648 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 649 A ) A.A649 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 650 G ) A.G650 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 651 C ) A.C651 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 652 U . A.U652 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop 653 U . A.U653 0.007 anti,~C2'-endo,BI,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 654 G ( A.G654 0.016 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,splayed-apart 655 A ( A.A655 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 656 G ( A.G656 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 657 U ( A.U657 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 658 C ( A.C658 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 659 U ( A.U659 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 660 C ( A.C660 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 661 G ( A.G661 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 662 U ( A.U662 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 663 A . A.A663 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 664 G . A.G664 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 665 A . A.A665 0.021 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 666 G ( A.G666 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 667 G ( A.G667 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 668 G ( A.G668 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 669 G ( A.G669 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 670 G ( A.G670 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 671 G ( A.G671 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 672 U ( A.U672 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 673 A ( A.A673 0.014 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 674 G . A.G674 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 675 A . A.A675 0.014 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 676 A . A.A676 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 677 U . A.U677 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 678 U ( A.U678 0.012 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 679 C ( A.C679 0.012 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 680 C ( A.C680 0.010 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 681 A ( A.A681 0.013 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 682 G ( A.G682 0.014 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 683 G ( A.G683 0.013 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 684 U ( A.U684 0.009 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 685 G . A.G685 0.011 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop 686 U . A.U686 0.008 k-turn,anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 687 A . A.A687 0.015 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 688 G ( A.G688 0.007 k-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,A-minor 689 C ( A.C689 0.008 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 690 G . A.G690 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 691 G . A.G691 0.016 anti,~C3'-endo,non-pair-contact,hairpin-loop 692 U . A.U692 0.010 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor,phosphate 693 G . A.G693 0.010 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 694 A . A.A694 0.012 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 695 A . A.A695 0.013 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,phosphate 696 A . A.A696 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,A-minor,ribose-zipper 697 U . A.U697 0.006 anti,~C3'-endo,non-pair-contact,hairpin-loop,ribose-zipper 698 G ) A.G698 0.011 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,hairpin-loop 699 C ) A.C699 0.012 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,A-minor 700 G . A.G700 0.013 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 701 U . A.U701 0.010 turn,k-turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 702 A . A.A702 0.009 turn,k-turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 703 G . A.G703 0.010 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,cap-acceptor,phosphate,splayed-apart 704 A . A.A704 0.013 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,phosphate 705 G . A.G705 0.013 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 706 A ) A.A706 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 707 U ) A.U707 0.012 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 708 C ) A.C708 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 709 U ) A.U709 0.010 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 710 G ) A.G710 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 711 G ) A.G711 0.013 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 712 A ) A.A712 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 713 G . A.G713 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 714 G . A.G714 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 715 A . A.A715 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 716 A . A.A716 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 717 U ) A.U717 0.013 anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate 718 A . A.A718 0.019 syn,~C3'-endo,non-pair-contact,junction-loop,phosphate 719 C . A.C719 0.013 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 720 C . A.C720 0.012 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 721 G . A.G721 0.016 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,phosphate 722 G . A.G722 0.019 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,splayed-apart 723 U . A.U723 0.009 turn,anti,~C3'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 724 G . A.G724 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 725 G ( A.G725 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 726 C ( A.C726 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 727 G . A.G727 0.015 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 728 A . A.A728 0.015 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor 729 A . A.A729 0.018 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,cap-donor,phosphate 730 G . A.G730 0.016 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 731 G ) A.G731 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 732 C ) A.C732 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop 733 G . A.G733 0.016 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 734 G ) A.G734 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 735 C ) A.C735 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 736 C ) A.C736 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 737 C ) A.C737 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 738 C ) A.C738 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 739 C ) A.C739 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 740 U ) A.U740 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 741 G . A.G741 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 742 G . A.G742 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 743 A ) A.A743 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 744 C ) A.C744 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 745 G ) A.G745 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 746 A . A.A746 0.011 anti,~C3'-endo,non-pair-contact,bulge 747 A ) A.A747 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 748 G ) A.G748 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 749 A ) A.A749 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 750 C ) A.C750 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 751 U ) A.U751 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 752 G . A.G752 0.017 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge 753 A . A.A753 0.019 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,bulge,phosphate 754 C ) A.C754 0.009 turn,syn,~C3'-endo,non-stack,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,phosphate,splayed-apart 755 G ) A.G755 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 756 C ) A.C756 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 757 U ) A.U757 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 758 C . A.C758 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 759 A . A.A759 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 760 G . A.G760 0.020 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor 761 G ) A.G761 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 762 U ) A.U762 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 763 G ) A.G763 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 764 C ) A.C764 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,A-minor 765 G . A.G765 0.017 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 766 A . A.A766 0.023 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 767 A . A.A767 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,A-minor 768 A . A.A768 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 769 G ( A.G769 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,phosphate 770 C ( A.C770 0.016 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 771 G ( A.G771 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 772 U ( A.U772 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 773 G ( A.G773 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 774 G ( A.G774 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 775 G . A.G775 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,bulge 776 G . A.G776 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,bulge,splayed-apart 777 A . A.A777 0.020 anti,~C3'-endo,BI,non-pair-contact,bulge,A-minor,splayed-apart 778 G ( A.G778 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 779 C ( A.C779 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 780 A . A.A780 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 781 A . A.A781 0.015 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,phosphate 782 A . A.A782 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate 783 C ( A.C783 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 784 A ( A.A784 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 785 G ( A.G785 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper 786 G ( A.G786 0.015 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,ribose-zipper 787 A . A.A787 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,hairpin-loop 788 U . A.U788 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop 789 U . A.U789 0.006 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-acceptor 790 A . A.A790 0.006 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 791 G . A.G791 0.012 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 792 A . A.A792 0.007 u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate 793 U . A.U793 0.003 turn,anti,~C3'-endo,non-stack,hairpin-loop 794 A . A.A794 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop 795 C . A.C795 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,phosphate 796 C ) A.C796 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,phosphate 797 C ) A.C797 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 798 U ) A.U798 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 799 G ) A.G799 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 800 G . A.G800 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 801 U . A.U801 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 802 A . A.A802 0.017 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 803 G ) A.G803 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 804 U ) A.U804 0.014 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 805 C ) A.C805 0.011 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 806 C ) A.C806 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 807 A ) A.A807 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 808 C ) A.C808 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 809 G ) A.G809 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 810 C ) A.C810 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor 811 C . A.C811 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 812 G . A.G812 0.021 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 813 U . A.U813 0.012 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 814 A . A.A814 0.016 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor,phosphate,splayed-apart 815 A . A.A815 0.017 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 816 A . A.A816 0.018 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 817 C { A.C817 0.017 pseudoknotted,anti,~C2'-endo,isolated-canonical,non-pair-contact,cap-acceptor,phosphate,splayed-apart 818 G . A.G818 0.014 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 819 A . A.A819 0.019 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,splayed-apart 820 U . A.U820 0.018 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 821 G ( A.G821 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate,splayed-apart 822 U ( A.U822 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 823 C ( A.C823 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 824 G ( A.G824 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 825 A ( A.A825 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 826 C ( A.C826 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 827 U . A.U827 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 828 U . A.U828 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 829 G ( A.G829 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 830 G ( A.G830 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 831 A ( A.A831 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 832 G ( A.G832 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 833 G ( A.G833 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 834 U ( A.U834 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 835 U ( A.U835 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 836 G ( A.G836 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 837 U ( A.U837 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 838 G ( A.G838 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 839 C ( A.C839 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 840 C ( A.C840 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 841 C . A.C841 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop 842 U . A.U842 0.006 turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 843 U . A.U843 0.009 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 844 G . A.G844 0.010 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 845 A . A.A845 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 846 G ) A.G846 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 847 G ) A.G847 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 848 C ) A.C848 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 849 G ) A.G849 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 850 U ) A.U850 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 851 G ) A.G851 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 852 G ) A.G852 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 853 C ) A.C853 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 854 U ) A.U854 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 855 U ) A.U855 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 856 C ) A.C856 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 857 C ) A.C857 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 858 G . A.G858 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 859 G . A.G859 0.016 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 860 A . A.A860 0.022 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop 861 G ( A.G861 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 862 C ( A.C862 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor 863 U . A.U863 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,splayed-apart 864 A . A.A864 0.020 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,splayed-apart 865 A ] A.A865 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,junction-loop 866 C ] A.C866 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,hairpin-loop,junction-loop 867 G ) A.G867 0.020 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor 868 C ) A.C868 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor 869 G . A.G869 0.025 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 870 U . A.U870 0.020 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 871 U . A.U871 0.010 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 872 A . A.A872 0.019 syn,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 873 A . A.A873 0.017 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 874 G ) A.G874 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 875 U ) A.U875 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 876 C ) A.C876 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 877 G ) A.G877 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 878 A ) A.A878 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 879 C ) A.C879 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 880 C ) A.C880 0.014 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,junction-loop,phosphate 881 G ) A.G881 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 882 C ) A.C882 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 883 C ) A.C883 0.014 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor 884 U . A.U884 0.014 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 885 G ( A.G885 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,cap-acceptor,phosphate,splayed-apart 886 G ( A.G886 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 887 G ( A.G887 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 888 G . A.G888 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 889 A . A.A889 0.016 anti,~C2'-endo,BII,non-canonical,non-pair-contact,internal-loop 890 G . A.G890 0.014 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,internal-loop 891 U . A.U891 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 892 A . A.A892 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 893 C . A.C893 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 894 G ( A.G894 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 895 G ( A.G895 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 896 C ( A.C896 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 897 C ( A.C897 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 898 G . A.G898 0.016 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,splayed-apart 899 C . A.C899 0.009 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 900 A . A.A900 0.018 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,phosphate 901 A . A.A901 0.018 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 902 G ) A.G902 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 903 G ) A.G903 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 904 U ) A.U904 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 905 U ) A.U905 0.012 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 906 A . A.A906 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 907 A . A.A907 0.014 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate 908 A . A.A908 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 909 A . A.A909 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 910 C ) A.C910 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 911 U ) A.U911 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 912 C ) A.C912 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 913 A . A.A913 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,phosphate 914 A . A.A914 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 915 A . A.A915 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop 916 U ] A.U916 0.012 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,A-minor 917 G ] A.G917 0.018 pseudoknotted,anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 918 A ] A.A918 0.016 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 919 A . A.A919 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 920 U ] A.U920 0.013 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 921 U ( A.U921 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 922 G ( A.G922 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 923 A ( A.A923 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 924 C . A.C924 0.014 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate 925 G . A.G925 0.013 syn,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,cap-acceptor,phosphate 926 G . A.G926 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor 927 G . A.G927 0.008 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 928 G ( A.G928 0.015 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor 929 G ( A.G929 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 930 C ( A.C930 0.007 break,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 931 G ) A.G1387 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 932 C ) A.C1388 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 933 C ) A.C1389 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 934 U . A.U1390 0.014 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,splayed-apart 935 U . A.U1391 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate,splayed-apart 936 G . A.G1392 0.008 break,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,ss-non-loop,phosphate 937 A . A.A1503 0.007 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,ss-non-loop,cap-acceptor,phosphate 938 G . A.G1504 0.006 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-donor 939 G . A.G1505 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop 940 U . A.U1506 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 941 A ( A.A1507 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 942 A ( A.A1508 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 943 C ( A.C1509 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 944 C ( A.C1510 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 945 G ( A.G1511 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 946 U ( A.U1512 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 947 A ( A.A1513 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 948 G ( A.G1514 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 949 G ( A.G1515 0.018 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 950 g . A.2MG1516 0.068 modified,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-acceptor 951 G . A.G1517 0.010 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 952 a . A.MA6/1518 0.063 modified,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 953 a . A.MA6/1519 0.058 modified,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 954 C ) A.C1520 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 955 C ) A.C1521 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 956 U ) A.U1522 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 957 G ) A.G1523 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 958 C ) A.C1524 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 959 G ) A.G1525 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor,phosphate 960 G ) A.G1526 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 961 U ) A.U1527 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 962 U ) A.U1528 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end 963 G } A.G1529 0.025 pseudoknotted,turn,syn,~C2'-endo,isolated-canonical,non-pair-contact,splayed-apart 964 G . A.G1530 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 965 A . A.A1531 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,splayed-apart 966 U ) A.U1532 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 967 C ) A.C1533 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 968 A ) A.A1534 0.011 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,splayed-apart 969 C . A.C1535 0.007 anti,~C3'-endo,BII,non-stack,non-pair-contact,ss-non-loop,splayed-apart 970 C . A.C1536 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 971 U . A.U1537 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 972 C . A.C1538 0.008 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 973 C . A.C1539 0.007 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 974 U . A.U1540 0.005 syn,~C2'-endo,non-stack,ss-non-loop **************************************************************************** List of 21 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-bulges.pdb -- an ensemble of bulges 7 dssr-iloops.pdb -- an ensemble of internal loops 8 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 9 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 10 dssr-2ndstrs.ct -- secondary structure in connectivity table format 11 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 12 dssr-torsions.txt -- backbone torsion angles and suite names 13 dssr-splays.pdb -- an ensemble of splayed-apart units 14 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 15 dssr-Kturns.pdb -- an ensemble of kink-turn motifs 16 dssr-stacks.pdb -- an ensemble of base stacks 17 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 18 dssr-rotmat.txt -- position vector and rotation matrix 19 dssr-viewV.pdb -- vertical view of the principal moment of inertia 20 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 21 dssr-viewT.pdb -- top view of the principal moment of inertia