**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=4lfb.pdb -o=4lfb.out File name: 4lfb.pdb no. of DNA/RNA chains: 1 [A=1512] no. of nucleotides: 1512 no. of atoms: 52046 no. of waters: 24 no. of metals: 239 [Mg=213,K=24,Zn=2] **************************************************************************** List of 8 types of 14 modified nucleotides nt count list 1 2MG-g 1 A.2MG1207 2 4OC-c 1 A.4OC1402 3 5MC-c 4 A.5MC967,A.5MC1400,A.5MC1404,A.5MC1407 4 7MG-g 1 A.7MG527 5 M2G-g 1 A.M2G966 6 MA6-a 2 A.MA6/1518,A.MA6/1519 7 PSU-P 3 A.PSU516,A.PSU1540,A.PSU1541 8 UR3-u 1 A.UR3/1498 **************************************************************************** List of 767 base pairs nt1 nt2 bp name Saenger LW DSSR 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 5 A.U13 A.U20 U-U Calcutta -- tHW tM-W 6 A.U13 A.A915 U+A Hoogsteen 23-XXIII cWH cW+M 7 A.G15 A.U920 G-U Wobble 28-XXVIII cWW cW-W 8 A.A16 A.A919 A-A -- -- cWW cW-W 9 A.A16 A.A1080 A-A -- -- cWS cW-m 10 A.U17 A.A918 U-A WC 20-XX cWW cW-W 11 A.U17 A.G1079 U-G -- -- cSS cm-m 12 A.C18 A.G917 C-G WC 19-XIX cWW cW-W 13 A.C19 A.G916 C-G WC 19-XIX 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.G28 A.C555 G-C WC 19-XIX cWW cW-W 22 A.G29 A.C554 G-C WC 19-XIX 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.G44 A.C398 G-C WC 19-XIX cWW cW-W 37 A.U45 A.G396 U-G Wobble 28-XXVIII 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.A51 A.U114 A+U -- -- cHS cM+m 43 A.A51 A.C314 A-C -- -- cWS cW-m 44 A.G52 A.U359 G-U Wobble 28-XXVIII cWW cW-W 45 A.A53 A.U358 A-U WC 20-XX cWW cW-W 46 A.C54 A.G357 C-G WC 19-XIX cWW cW-W 47 A.A55 A.G357 A-G Sheared 11-XI tHS tM-m 48 A.A55 A.U368 A+U rWC 21-XXI tWW tW+W 49 A.U56 A.C352 U-C -- -- t.W t.-W 50 A.U56 A.A356 U-A WC 20-XX cWW cW-W 51 A.G57 A.C355 G-C WC 19-XIX cWW cW-W 52 A.C58 A.G354 C-G WC 19-XIX cWW cW-W 53 A.A60 A.G107 A+G Linker -- t.S t.+m 54 A.A60 A.C110 A-C ~rHoogsteen 25-XXV tHW tM-W 55 A.G61 A.C106 G-C WC 19-XIX cWW cW-W 56 A.U62 A.G105 U-G Wobble 28-XXVIII cWW cW-W 57 A.C63 A.G104 C-G WC 19-XIX cWW cW-W 58 A.G64 A.G68 G+G -- 06-VI cWH cW+M 59 A.G64 A.A101 G-A -- -- t.H t.-M 60 A.U65 A.G199 U-G -- -- c.S c.-m 61 A.G66 A.C103 G-C WC 19-XIX cWW cW-W 62 A.G66 A.A172 G-A -- -- cSS cm-m 63 A.C67 A.G102 C-G WC 19-XIX cWW cW-W 64 A.G68 A.A101 G-A Imino 08-VIII cWW cW-W 65 A.G68 A.A152 G+A Linker -- tSS tm+m 66 A.G69 A.C99 G-C WC 19-XIX cWW cW-W 67 A.G70 A.U98 G-U Wobble 28-XXVIII cWW cW-W 68 A.C73 A.G97 C-G WC 19-XIX cWW cW-W 69 A.C74 A.G96 C-G WC 19-XIX cWW cW-W 70 A.G75 A.U95 G-U Wobble 28-XXVIII cWW cW-W 71 A.C76 A.G93 C-G WC 19-XIX cWW cW-W 72 A.G77 A.C92 G-C WC 19-XIX cWW cW-W 73 A.G78 A.C91 G-C WC 19-XIX cWW cW-W 74 A.G79 A.U90 G-U Wobble 28-XXVIII cWW cW-W 75 A.G80 A.C89 G-C WC 19-XIX cWW cW-W 76 A.G102 A.A151 G-A -- -- cSW cm-W 77 A.C103 A.A171 C+A -- -- tSW tm+W 78 A.A109 A.G324 A-G Sheared 11-XI tHS tM-m 79 A.C110 A.G331 C-G -- -- t.H t.-M 80 A.G111 A.G331 G-G -- -- tWH tW-M 81 A.G112 A.A315 G-A Imino 08-VIII cWW cW-W 82 A.G113 A.C314 G-C WC 19-XIX cWW cW-W 83 A.G113 A.A353 G-A -- -- cSS cm-m 84 A.U114 A.A313 U-A WC 20-XX cWW cW-W 85 A.G115 A.A116 G+A Platform -- cSH cm+M 86 A.G115 A.G117 G+G -- -- cSH cm+M 87 A.G115 A.C312 G-C WC 19-XIX cWW cW-W 88 A.A116 A.A313 A-A -- -- tWS tW-m 89 A.A119 A.U287 A-U rHoogsteen 24-XXIV tHW tM-W 90 A.C121 A.G236 C-G Metal -- tWH tW-M 91 A.G122 A.U239 G-U Wobble 28-XXVIII cWW cW-W 92 A.C123 A.G238 C-G WC 19-XIX cWW cW-W 93 A.G124 A.C237 G-C WC 19-XIX cWW cW-W 94 A.U125 A.G236 U-G Wobble 28-XXVIII cWW cW-W 95 A.G126 A.C235 G-C WC 19-XIX cWW cW-W 96 A.G127 A.C234 G-C WC 19-XIX cWW cW-W 97 A.G128 A.C233 G-C WC 19-XIX cWW cW-W 98 A.U129 A.G232 U-G Wobble 28-XXVIII cWW cW-W 99 A.G129^A A.C190^C G+C -- -- tW. tW+. 100 A.A130 A.C233 A-C -- -- tWS tW-m 101 A.C131 A.G231 C-G WC 19-XIX cWW cW-W 102 A.C132 A.G230 C-G WC 19-XIX cWW cW-W 103 A.U133 A.U229 U-U -- 16-XVI cWW cW-W 104 A.C135 A.A228 C-A -- -- c.W c.-W 105 A.C136 A.G227 C-G WC 19-XIX cWW cW-W 106 A.C137 A.G226 C-G WC 19-XIX cWW cW-W 107 A.G138 A.C225 G-C WC 19-XIX cWW cW-W 108 A.G139 A.C224 G-C WC 19-XIX cWW cW-W 109 A.A140 A.U223 A-U WC 20-XX cWW cW-W 110 A.A141 A.U222 A-U WC 20-XX cWW cW-W 111 A.G142 A.A196 G+A Linker -- tSS tm+m 112 A.G142 A.C221 G-C WC 19-XIX cWW cW-W 113 A.A143 A.G220 A-G Imino 08-VIII cWW cW-W 114 A.G144 A.C178 G-C WC 19-XIX cWW cW-W 115 A.G145 A.C177 G-C WC 19-XIX cWW cW-W 116 A.G146 A.C176 G-C WC 19-XIX cWW cW-W 117 A.G147 A.C175 G-C WC 19-XIX cWW cW-W 118 A.G148 A.C174 G-C WC 19-XIX cWW cW-W 119 A.A149 A.A172 A-A -- 05-V tWH tW-M 120 A.C150 A.A171 C-A ~rHoogsteen 25-XXV tWH tW-M 121 A.A151 A.U170 A-U rHoogsteen 24-XXIV tHW tM-W 122 A.A152 A.C169 A-C ~rHoogsteen 25-XXV tHW tM-W 123 A.C153 A.G168 C-G WC 19-XIX cWW cW-W 124 A.C154 A.G167 C-G WC 19-XIX cWW cW-W 125 A.C155 A.G166 C-G WC 19-XIX cWW cW-W 126 A.G156 A.C165 G-C WC 19-XIX cWW cW-W 127 A.G157 A.U164 G-U Wobble 28-XXVIII cWW cW-W 128 A.G158 A.C163 G-C WC 19-XIX cWW cW-W 129 A.G159 A.A162 G-A Sheared 11-XI tSH tm-M 130 A.A160 A.G347 A+G -- 10-X tWS tW+m 131 A.U173 A.G198 U+G -- -- cHS cM+m 132 A.A179 A.A196 A-A -- 05-V tWH tW-M 133 A.U180 A.A195 U-A rHoogsteen 24-XXIV tWH tW-M 134 A.U180 A.A196 U-A -- -- tWH tW-M 135 A.G181 A.U182 G+U Platform -- cSH cm+M 136 A.U182 A.U223 U+U -- -- tWS tW+m 137 A.G183 A.C194 G-C WC 19-XIX cWW cW-W 138 A.G184 A.C193 G-C WC 19-XIX cWW cW-W 139 A.A185 A.U192 A-U WC 20-XX cWW cW-W 140 A.C186 A.G191 C-G WC 19-XIX cWW cW-W 141 A.C187 A.U190^L C-U -- -- cWW cW-W 142 A.C188 A.G190^K C-G WC 19-XIX cWW cW-W 143 A.G189 A.U190^J G-U Wobble 28-XXVIII cWW cW-W 144 A.C190 A.G190^I C-G WC 19-XIX cWW cW-W 145 A.C190^A A.G190^H C-G WC 19-XIX cWW cW-W 146 A.C190^B A.G190^G C-G WC 19-XIX cWW cW-W 147 A.A197 A.G220 A+G Linker -- tSS tm+m 148 A.G198 A.C219 G-C WC 19-XIX cWW cW-W 149 A.G199 A.C218 G-C WC 19-XIX cWW cW-W 150 A.G200 A.C217 G-C WC 19-XIX cWW cW-W 151 A.C201 A.G216 C-G WC 19-XIX cWW cW-W 152 A.G232 A.A263 G+A Linker -- tSS tm+m 153 A.C240 A.G286 C-G WC 19-XIX cWW cW-W 154 A.C241 A.G285 C-G WC 19-XIX cWW cW-W 155 A.C242 A.G284 C-G WC 19-XIX cWW cW-W 156 A.A243 A.A282 A-A -- 05-V tWH tW-M 157 A.U244 A.C893 U-C -- 18-XVIII cWW cW-W 158 A.C245 A.C283 C-C -- -- cWW cW-W 159 A.A246 A.G281 A-G Sheared 11-XI tHS tM-m 160 A.G247 A.C277 G-C WC 19-XIX cWW cW-W 161 A.G247 A.A282 G+A Linker -- tSS tm+m 162 A.C248 A.G276 C-G WC 19-XIX cWW cW-W 163 A.U249 A.G275 U-G Wobble 28-XXVIII cWW cW-W 164 A.G251 A.G254 G+G -- 06-VI cWH cW+M 165 A.G251 A.C271 G-C -- -- -- -- 166 A.G251 A.C272 G-C -- -- tW. tW-. 167 A.U252 A.A274 U-A WC 20-XX cWW cW-W 168 A.U253 A.A273 U-A WC 20-XX cWW cW-W 169 A.G254 A.C272 G-C WC 19-XIX cWW cW-W 170 A.G255 A.G266 G-G -- -- cHH cM-M 171 A.G255 A.C271 G-C WC 19-XIX cWW cW-W 172 A.U256 A.A270 U-A WC 20-XX cWW cW-W 173 A.G257 A.C269 G-C WC 19-XIX cWW cW-W 174 A.G258 A.C268 G-C WC 19-XIX cWW cW-W 175 A.G259 A.C267 G-C WC 19-XIX cWW cW-W 176 A.G260 A.G265 G-G -- -- tWH tW-M 177 A.G266 A.A270 G+A -- -- cWH cW+M 178 A.G266 A.C271 G+C -- -- -- -- 179 A.G278 A.A279 G-A Platform -- cSW cm-W 180 A.G289 A.C311 G-C WC 19-XIX cWW cW-W 181 A.C290 A.G310 C-G WC 19-XIX cWW cW-W 182 A.C291 A.G309 C-G WC 19-XIX cWW cW-W 183 A.G292 A.G305 G-G -- -- tHS tM-m 184 A.G292 A.C308 G-C WC 19-XIX cWW cW-W 185 A.G292 A.A608 G+A -- 10-X tSW tm+W 186 A.G293 A.U304 G-U Wobble 28-XXVIII cWW cW-W 187 A.U294 A.A303 U-A WC 20-XX cWW cW-W 188 A.C295 A.G302 C-G WC 19-XIX cWW cW-W 189 A.U296 A.G301 U-G Wobble 28-XXVIII cWW cW-W 190 A.G297 A.A300 G-A Sheared 11-XI tSH tm-M 191 A.A298 A.U560 A-U -- -- t.H t.-M 192 A.G299 A.G566 G+G -- 06-VI cWH cW+M 193 A.A300 A.U565 A-U -- -- cSW cm-W 194 A.G316 A.C337 G-C WC 19-XIX cWW cW-W 195 A.G317 A.C336 G-C WC 19-XIX cWW cW-W 196 A.G318 A.C335 G-C WC 19-XIX cWW cW-W 197 A.G319 A.C334 G-C WC 19-XIX cWW cW-W 198 A.G319 A.A1434 G+A Linker -- tSS tm+m 199 A.C320 A.G333 C-G WC 19-XIX cWW cW-W 200 A.A321 A.G332 A-G Imino 08-VIII cWW cW-W 201 A.C322 A.A329 C-A ~rHoogsteen 25-XXV tWH tW-M 202 A.U323 A.A327 U-A rHoogsteen 24-XXIV tWH tW-M 203 A.C335 A.A1433 C-A -- -- cSS cm-m 204 A.A338 A.G351 A-G Imino 08-VIII cWW cW-W 205 A.C339 A.G350 C-G WC 19-XIX cWW cW-W 206 A.U340 A.A349 U-A WC 20-XX cWW cW-W 207 A.C341 A.G348 C-G WC 19-XIX cWW cW-W 208 A.C342 A.G347 C-G WC 19-XIX cWW cW-W 209 A.U343 A.G346 U+G -- -- t.W t.+W 210 A.C352 A.A356 C+A -- -- cWH cW+M 211 A.G362 A.U365 G+U -- -- tWW tW+W 212 A.C366 A.G394 C-G -- -- cSW cm-W 213 A.U367 A.A393 U-A WC 20-XX cWW cW-W 214 A.C369 A.G392 C-G WC 19-XIX cWW cW-W 215 A.C370 A.G391 C-G WC 19-XIX cWW cW-W 216 A.G371 A.A374 G+A -- -- c.H c.+M 217 A.G371 A.C390 G-C WC 19-XIX cWW cW-W 218 A.C372 A.A389 C-A -- -- tWH tW-M 219 A.A373 A.G391 A-G -- -- cWS cW-m 220 A.A373 A.G481 A-G -- -- tSS tm-m 221 A.A374 A.C390 A-C -- -- cWS cW-m 222 A.U375 A.A389 U-A WC 20-XX cWW cW-W 223 A.G376 A.U387 G-U Wobble 28-XXVIII cWW cW-W 224 A.G377 A.C386 G-C WC 19-XIX cWW cW-W 225 A.G378 A.C385 G-C WC 19-XIX cWW cW-W 226 A.C379 A.G384 C-G WC 19-XIX cWW cW-W 227 A.G380 A.A383 G-A Sheared 11-XI tSH tm-M 228 A.A397 A.A547 A+A -- -- cHS cM+m 229 A.C401 A.A621 C-A -- -- cSS cm-m 230 A.U404 A.U498 U+U -- -- cWH cW+M 231 A.U405 A.A499 U+A Hoogsteen 23-XXIII cWH cW+M 232 A.G406 A.C436 G-C WC 19-XIX cWW cW-W 233 A.G407 A.C435 G-C WC 19-XIX cWW cW-W 234 A.A408 A.U434 A-U WC 20-XX cWW cW-W 235 A.G409 A.C433 G-C WC 19-XIX cWW cW-W 236 A.G410 A.A432 G-A Sheared 11-XI tSH tm-M 237 A.A411 A.A430 A-A -- 05-V tWH tW-M 238 A.G413 A.G428 G+G -- 04-IV tSS tm+m 239 A.A414 A.A430 A-A -- 05-V tHW tM-W 240 A.A415 A.G428 A+G -- -- cH. cM+. 241 A.G416 A.U427 G-U Wobble 28-XXVIII cWW cW-W 242 A.C417 A.G426 C-G WC 19-XIX cWW cW-W 243 A.C418 A.G425 C-G WC 19-XIX cWW cW-W 244 A.C419 A.G424 C-G WC 19-XIX cWW cW-W 245 A.U420 A.G423 U+G -- -- tSW tm+W 246 A.U429 A.A431 U+A Hoogsteen 23-XXIII cWH cW+M 247 A.U437 A.A496 U-A rHoogsteen 24-XXIV tWH tW-M 248 A.G438 A.A497 G-A Sheared 11-XI tSH tm-M 249 A.A439 A.U495 A-U rHoogsteen 24-XXIV tHW tM-W 250 A.A440 A.G494 A-G Sheared 11-XI tHS tM-m 251 A.C442 A.G492 C-G WC 19-XIX cWW cW-W 252 A.C443 A.G491 C-G WC 19-XIX cWW cW-W 253 A.C444 A.G490 C-G WC 19-XIX cWW cW-W 254 A.G445 A.C489 G-C WC 19-XIX cWW cW-W 255 A.G446 A.C488 G-C WC 19-XIX cWW cW-W 256 A.G447 A.A487 G-A Sheared 11-XI tSH tm-M 257 A.A448 A.U486 A-U rHoogsteen 24-XXIV tHW tM-W 258 A.C449 A.G484 C+G -- -- cHW cM+W 259 A.G450 A.C483 G-C WC 19-XIX cWW cW-W 260 A.A452 A.U480 A-U rHoogsteen 24-XXIV tHW tM-W 261 A.A453 A.C479 A-C ~rHoogsteen 25-XXV tHW tM-W 262 A.C454 A.A478 C-A -- -- tHW tM-W 263 A.C455 A.G477 C-G WC 19-XIX cWW cW-W 264 A.C456 A.G476 C-G WC 19-XIX cWW cW-W 265 A.C457 A.G475 C-G WC 19-XIX cWW cW-W 266 A.C458 A.G474 C-G WC 19-XIX cWW cW-W 267 A.G459 A.A463 G-A Sheared 11-XI tSH tm-M 268 A.G485 A.U486 G+U Platform -- cSH cm+M 269 A.U498 A.A547 U-A rHoogsteen 24-XXIV tWH tW-M 270 A.G500 A.C545 G-C WC 19-XIX cWW cW-W 271 A.C501 A.G544 C-G WC 19-XIX cWW cW-W 272 A.G502 A.C543 G-C WC 19-XIX cWW cW-W 273 A.C503 A.A510 C+A -- -- tSW tm+W 274 A.C503 A.G542 C-G WC 19-XIX cWW cW-W 275 A.C504 A.G541 C-G WC 19-XIX cWW cW-W 276 A.G505 A.C526 G-C WC 19-XIX cWW cW-W 277 A.G506 A.C525 G-C WC 19-XIX cWW cW-W 278 A.C507 A.G524 C-G WC 19-XIX cWW cW-W 279 A.C508 A.A509 C+A Platform -- cSH cm+M 280 A.C508 A.A510 C+A -- -- cSH cm+M 281 A.A509 A.C543 A-C -- -- cSS cm-m 282 A.A510 A.G542 A-G -- -- cSS cm-m 283 A.C511 A.G540 C-G WC 19-XIX cWW cW-W 284 A.U512 A.A539 U-A WC 20-XX cWW cW-W 285 A.C513 A.G538 C-G WC 19-XIX cWW cW-W 286 A.C514 A.G537 C-G WC 19-XIX cWW cW-W 287 A.G515 A.C536 G-C WC 19-XIX cWW cW-W 288 A.PSU516 A.C519 P-C -- -- cSW cm-W 289 A.PSU516 A.A533 P-A ~rHoogsteen -- tWH tW-M 290 A.C519 A.A533 C+A -- -- -- -- 291 A.A520 A.G529 A-G Sheared 11-XI tHS tM-m 292 A.A520 A.A533 A+A -- -- tWW tW+W 293 A.G521 A.C528 G-C WC 19-XIX cWW cW-W 294 A.C522 A.7MG527 C-g WC 19-XIX cWW cW-W 295 A.7MG527 A.A535 g+A Linker -- tSW tm+W 296 A.A563 A.U884 A+U rWC 21-XXI tWW tW+W 297 A.G567 A.C883 G-C WC 19-XIX cWW cW-W 298 A.G568 A.A574 G+A Linker -- tSS tm+m 299 A.G568 A.C882 G-C WC 19-XIX cWW cW-W 300 A.C569 A.G881 C-G WC 19-XIX cWW cW-W 301 A.G570 A.C866 G-C WC 19-XIX cWW cW-W 302 A.U571 A.A865 U-A WC 20-XX cWW cW-W 303 A.A572 A.A574 A-A -- -- cHH cM-M 304 A.A572 A.G916 A-G -- -- cSS cm-m 305 A.A573 A.C883 A-C -- -- cSS cm-m 306 A.G575 A.G576 G+G Platform -- cSH cm+M 307 A.G575 A.C880 G-C WC 19-XIX cWW cW-W 308 A.G577 A.A729 G-A -- -- cSS cm-m 309 A.G577 A.C764 G-C WC 19-XIX cWW cW-W 310 A.C578 A.G763 C-G WC 19-XIX cWW cW-W 311 A.G579 A.C762 G-C WC 19-XIX cWW cW-W 312 A.U580 A.G761 U-G Wobble 28-XXVIII cWW cW-W 313 A.G581 A.G760 G-G -- -- tSH tm-M 314 A.U582 A.A759 U-A rHoogsteen 24-XXIV tWH tW-M 315 A.A583 A.G758 A-G Sheared 11-XI tHS tM-m 316 A.G584 A.U757 G-U Wobble 28-XXVIII cWW cW-W 317 A.G585 A.C756 G-C WC 19-XIX cWW cW-W 318 A.C586 A.G755 C-G WC 19-XIX cWW cW-W 319 A.G588 A.C651 G-C WC 19-XIX cWW cW-W 320 A.C589 A.G650 C-G WC 19-XIX cWW cW-W 321 A.C590 A.G649 C-G WC 19-XIX cWW cW-W 322 A.U591 A.A648 U-A WC 20-XX cWW cW-W 323 A.G592 A.C647 G-C WC 19-XIX cWW cW-W 324 A.G593 A.U646 G-U Wobble 28-XXVIII cWW cW-W 325 A.G594 A.C645 G-C WC 19-XIX cWW cW-W 326 A.G595 A.C596 G+C Platform -- cSH cm+M 327 A.G595 A.G644 G-G -- -- c.W c.-W 328 A.C596 A.G644 C-G WC 19-XIX cWW cW-W 329 A.G597 A.C643 G-C WC 19-XIX cWW cW-W 330 A.U598 A.A640 U-A WC 20-XX cWW cW-W 331 A.U598 A.A642 U-A -- -- cWW cW-W 332 A.C599 A.G639 C-G WC 19-XIX cWW cW-W 333 A.C600 A.G638 C-G WC 19-XIX cWW cW-W 334 A.C601 A.G637 C-G WC 19-XIX cWW cW-W 335 A.A602 A.U636 A-U WC 20-XX cWW cW-W 336 A.U603 A.G635 U-G Wobble 28-XXVIII cWW cW-W 337 A.G604 A.C634 G-C WC 19-XIX cWW cW-W 338 A.U605 A.G633 U-G Wobble 28-XXVIII cWW cW-W 339 A.G606 A.A632 G-A Sheared 11-XI tSH tm-M 340 A.A611 A.G629 A-G Imino 08-VIII cWW cW-W 341 A.C612 A.G628 C-G WC 19-XIX cWW cW-W 342 A.C613 A.G627 C-G WC 19-XIX cWW cW-W 343 A.A614 A.U626 A-U WC 20-XX cWW cW-W 344 A.C615 A.G625 C-G WC 19-XIX cWW cW-W 345 A.G616 A.C624 G-C WC 19-XIX cWW cW-W 346 A.G617 A.C623 G-C WC 19-XIX cWW cW-W 347 A.C618 A.A622 C-A ~rHoogsteen 25-XXV tWH tW-M 348 A.U641 A.C643 U+C -- -- cSH cm+M 349 A.U652 A.A753 U-A rHoogsteen 24-XXIV tWH tW-M 350 A.G654 A.G752 G-G -- -- tHS tM-m 351 A.G654 A.C754 G-C WC 19-XIX cWW cW-W 352 A.A655 A.U751 A-U WC 20-XX cWW cW-W 353 A.C656 A.G750 C-G WC 19-XIX cWW cW-W 354 A.G657 A.C749 G-C WC 19-XIX cWW cW-W 355 A.G658 A.C747 G-C WC 19-XIX cWW cW-W 356 A.U659 A.A746 U-A WC 20-XX cWW cW-W 357 A.G660 A.C745 G-C WC 19-XIX cWW cW-W 358 A.G661 A.C744 G-C WC 19-XIX cWW cW-W 359 A.G662 A.U743 G-U Wobble 28-XXVIII cWW cW-W 360 A.A663 A.G742 A-G Imino 08-VIII cWW cW-W 361 A.G664 A.G741 G-G -- -- cWW cW-W 362 A.A665 A.G724 A+G -- 09-IX cHW cM+W 363 A.G666 A.U740 G-U Wobble 28-XXVIII cWW cW-W 364 A.G667 A.C739 G-C WC 19-XIX cWW cW-W 365 A.G668 A.C738 G-C WC 19-XIX cWW cW-W 366 A.U669 A.A737 U-A WC 20-XX cWW cW-W 367 A.G670 A.C736 G-C WC 19-XIX cWW cW-W 368 A.G671 A.C735 G-C WC 19-XIX cWW cW-W 369 A.U672 A.G734 U-G Wobble 28-XXVIII cWW cW-W 370 A.G673 A.C717 G-C WC 19-XIX cWW cW-W 371 A.G674 A.A716 G-A Imino 08-VIII cWW cW-W 372 A.A675 A.A715 A-A -- -- cWW cW-W 373 A.A676 A.G714 A-G Imino 08-VIII cWW cW-W 374 A.U677 A.G713 U-G ~Wobble -- cWW cW-W 375 A.U678 A.A712 U-A WC 20-XX cWW cW-W 376 A.C679 A.G711 C-G WC 19-XIX cWW cW-W 377 A.C680 A.G710 C-G WC 19-XIX cWW cW-W 378 A.C681 A.G709 C-G WC 19-XIX cWW cW-W 379 A.G682 A.C708 G-C WC 19-XIX cWW cW-W 380 A.G683 A.C707 G-C WC 19-XIX cWW cW-W 381 A.A684 A.A706 A-A -- -- cWW cW-W 382 A.G685 A.U705 G-U -- -- tSH tm-M 383 A.U686 A.A704 U-A rHoogsteen 24-XXIV tWH tW-M 384 A.A687 A.G700 A+G Linker -- tWS tW+m 385 A.A687 A.G703 A-G Sheared 11-XI tHS tM-m 386 A.G688 A.C699 G-C WC 19-XIX cWW cW-W 387 A.G688 A.A704 G+A Linker -- tSS tm+m 388 A.C689 A.G698 C-G WC 19-XIX cWW cW-W 389 A.G690 A.U697 G-U -- -- t.H t.-M 390 A.G691 A.A696 G-A Sheared 11-XI tSH tm-M 391 A.A695 A.G786 A-G -- -- cWS cW-m 392 A.G714 A.A777 G-A -- -- tSS tm-m 393 A.A722 A.A733 A+A -- 01-I tWW tW+W 394 A.G725 A.C732 G-C WC 19-XIX cWW cW-W 395 A.C726 A.G731 C-G WC 19-XIX cWW cW-W 396 A.G727 A.G730 G-G -- -- tSH tm-M 397 A.G752 A.C754 G+C -- -- cSH cm+M 398 A.G765 A.A816 G-A -- -- cSW cm-W 399 A.A766 A.U813 A-U rHoogsteen 24-XXIV tHW tM-W 400 A.A766 A.G1525 A-G -- -- cWS cW-m 401 A.A767 A.G1511 A+G Linker -- tSS tm+m 402 A.A768 A.C811 A-C -- -- cWW cW-W 403 A.G769 A.C810 G-C WC 19-XIX cWW cW-W 404 A.G769 A.A900 G-A -- -- cSW cm-W 405 A.C770 A.G809 C-G WC 19-XIX cWW cW-W 406 A.C770 A.C899 C-C -- -- cSW cm-W 407 A.G771 A.C808 G-C WC 19-XIX cWW cW-W 408 A.U772 A.A807 U-A WC 20-XX cWW cW-W 409 A.G773 A.C806 G-C WC 19-XIX cWW cW-W 410 A.G774 A.C805 G-C WC 19-XIX cWW cW-W 411 A.G776 A.G803 G-G -- -- tWH tW-M 412 A.G776 A.U804 G-U -- -- tSW tm-W 413 A.G778 A.U804 G-U Wobble 28-XXVIII cWW cW-W 414 A.C779 A.G803 C-G WC 19-XIX cWW cW-W 415 A.A780 A.A802 A-A ~Sheared -- tSH tm-M 416 A.A781 A.U801 A-U rHoogsteen 24-XXIV tHW tM-W 417 A.A782 A.G800 A-G Sheared 11-XI tHS tM-m 418 A.C783 A.G799 C-G WC 19-XIX cWW cW-W 419 A.C784 A.G798 C-G WC 19-XIX cWW cW-W 420 A.G785 A.C797 G-C WC 19-XIX cWW cW-W 421 A.G786 A.C796 G-C WC 19-XIX cWW cW-W 422 A.A787 A.C795 A-C -- -- cWH cW-M 423 A.U788 A.A794 U-A -- -- tWH tW-M 424 A.U788 A.C795 U-C -- -- cSW cm-W 425 A.C810 A.C899 C+C -- -- cSH cm+M 426 A.C817 A.G1529 C-G WC 19-XIX cWW cW-W 427 A.U820 A.A873 U+A Hoogsteen 23-XXIII cWH cW+M 428 A.G821 A.C879 G-C WC 19-XIX cWW cW-W 429 A.C822 A.G878 C-G WC 19-XIX cWW cW-W 430 A.G823 A.C877 G-C WC 19-XIX cWW cW-W 431 A.C824 A.G876 C-G WC 19-XIX cWW cW-W 432 A.G825 A.C875 G-C WC 19-XIX cWW cW-W 433 A.C826 A.G874 C-G WC 19-XIX cWW cW-W 434 A.U827 A.A859 U-A -- -- cSW cm-W 435 A.U827 A.A872 U+A rWC 21-XXI tWW tW+W 436 A.A828 A.G858 A-G Sheared 11-XI tHS tM-m 437 A.G829 A.C857 G-C WC 19-XIX cWW cW-W 438 A.G830 A.C856 G-C WC 19-XIX cWW cW-W 439 A.U831 A.G855 U-G Wobble 28-XXVIII cWW cW-W 440 A.C832 A.G854 C-G WC 19-XIX cWW cW-W 441 A.U833 A.G853 U-G Wobble 28-XXVIII cWW cW-W 442 A.C834 A.G852 C-G WC 19-XIX cWW cW-W 443 A.U835 A.G851 U-G Wobble 28-XXVIII cWW cW-W 444 A.G836 A.U850 G-U Wobble 28-XXVIII cWW cW-W 445 A.G837 A.C849 G-C WC 19-XIX cWW cW-W 446 A.G838 A.C848 G-C WC 19-XIX cWW cW-W 447 A.A860 A.G869 A-G Sheared 11-XI tHS tM-m 448 A.A860 A.A872 A-A -- 05-V tWH tW-M 449 A.G861 A.C868 G-C WC 19-XIX cWW cW-W 450 A.C862 A.G867 C-G WC 19-XIX cWW cW-W 451 A.U863 A.C866 U-C ~Sheared -- tSH tm-M 452 A.A864 A.G917 A+G Linker -- tWS tW+m 453 A.G867 A.A873 G+A Linker -- tSW tm+W 454 A.G885 A.C912 G-C WC 19-XIX cWW cW-W 455 A.G885 A.A914 G+A Linker -- tSS tm+m 456 A.G886 A.U911 G-U Wobble 28-XXVIII cWW cW-W 457 A.G887 A.C910 G-C WC 19-XIX cWW cW-W 458 A.G888 A.A909 G-A Sheared 11-XI tSH tm-M 459 A.A889 A.A908 A+A -- 02-II tHH tM+M 460 A.G890 A.U891 G+U Platform -- cSH cm+M 461 A.U891 A.A907 U-A rHoogsteen 24-XXIV tWH tW-M 462 A.A892 A.G906 A-G Sheared 11-XI tHS tM-m 463 A.G894 A.U905 G-U Wobble 28-XXVIII cWW cW-W 464 A.G895 A.C904 G-C WC 19-XIX cWW cW-W 465 A.C896 A.G903 C-G WC 19-XIX cWW cW-W 466 A.C897 A.G902 C-G WC 19-XIX cWW cW-W 467 A.G898 A.A901 G-A Sheared 11-XI tSH tm-M 468 A.A919 A.A1080 A+A -- -- tSW tm+W 469 A.U921 A.A1396 U-A WC 20-XX cWW cW-W 470 A.G922 A.C1395 G-C WC 19-XIX cWW cW-W 471 A.G922 A.A1398 G+A Linker -- tSS tm+m 472 A.A923 A.U1393 A-U WC 20-XX cWW cW-W 473 A.C924 A.G1392 C-G WC 19-XIX cWW cW-W 474 A.C924 A.A1502 C-A -- -- tSH tm-M 475 A.G925 A.U1391 G-U Wobble 28-XXVIII cWW cW-W 476 A.G927 A.U1390 G-U Wobble 28-XXVIII cWW cW-W 477 A.G928 A.C1389 G-C WC 19-XIX cWW cW-W 478 A.G929 A.C1388 G-C WC 19-XIX cWW cW-W 479 A.C930 A.G1387 C-G WC 19-XIX cWW cW-W 480 A.C931 A.G1386 C-G WC 19-XIX cWW cW-W 481 A.C932 A.G1385 C-G WC 19-XIX cWW cW-W 482 A.G933 A.C1384 G-C WC 19-XIX cWW cW-W 483 A.C934 A.A938 C+A ~rWobble 26-XXVI tWW tW+W 484 A.A935 A.U1380 A-U WC 20-XX cWW cW-W 485 A.A935 A.C1383 A-C -- -- cSW cm-W 486 A.C936 A.G1379 C-G WC 19-XIX cWW cW-W 487 A.C936 A.C1382 C-C -- -- cSW cm-W 488 A.A937 A.U1345 A-U -- -- tW. tW-. 489 A.A937 A.C1378 A-C ~Sheared -- tSH tm-M 490 A.G939 A.C1344 G-C WC 19-XIX cWW cW-W 491 A.C940 A.G1343 C-G WC 19-XIX cWW cW-W 492 A.G941 A.C1342 G-C WC 19-XIX cWW cW-W 493 A.G942 A.U1341 G-U Wobble 28-XXVIII cWW cW-W 494 A.U943 A.A1340 U-A WC 20-XX cWW cW-W 495 A.G944 A.A1339 G-A Sheared 11-XI tSH tm-M 496 A.G945 A.A1236 G-A Imino 08-VIII cWW cW-W 497 A.A946 A.U1235 A-U WC 20-XX cWW cW-W 498 A.A946 A.A1333 A-A -- -- cSS cm-m 499 A.G947 A.C1234 G-C WC 19-XIX cWW cW-W 500 A.C948 A.G1233 C-G WC 19-XIX cWW cW-W 501 A.A949 A.U1232 A-U WC 20-XX cWW cW-W 502 A.U950 A.G1231 U-G Wobble 28-XXVIII cWW cW-W 503 A.G951 A.C970 G-C -- -- cSS cm-m 504 A.G951 A.C1230 G-C WC 19-XIX cWW cW-W 505 A.U952 A.A1229 U-A WC 20-XX cWW cW-W 506 A.G953 A.C1228 G-C WC 19-XIX cWW cW-W 507 A.G954 A.C1226 G-C WC 19-XIX cWW cW-W 508 A.G954 A.A1227 G-A Sheared 11-XI tSH tm-M 509 A.U955 A.A1225 U-A WC 20-XX cWW cW-W 510 A.U956 A.U960 U+U -- 13-XIII tWW tW+W 511 A.A959 A.G1221 A+G Linker -- tWS tW+m 512 A.U961 A.A974 U+A -- -- t.W t.+W 513 A.U961 A.A1201 U+A rWC 21-XXI tWW tW+W 514 A.C962 A.G973 C-G WC 19-XIX cWW cW-W 515 A.G963 A.C972 G-C WC 19-XIX cWW cW-W 516 A.A978 A.G1316 A+G -- 10-X tWS tW+m 517 A.A978 A.A1360 A-A -- 05-V tHW tM-W 518 A.C984 A.G1221 C-G WC 19-XIX cWW cW-W 519 A.C985 A.G1220 C-G WC 19-XIX cWW cW-W 520 A.A986 A.U1219 A-U WC 20-XX cWW cW-W 521 A.G987 A.C1218 G-C WC 19-XIX cWW cW-W 522 A.G988 A.A1016 G+A Linker -- tSS tm+m 523 A.G988 A.C1217 G-C WC 19-XIX cWW cW-W 524 A.C989 A.G1216 C-G WC 19-XIX cWW cW-W 525 A.C990 A.G1215 C-G WC 19-XIX cWW cW-W 526 A.U991 A.G993 U+G -- -- cSH cm+M 527 A.U991 A.A1213 U-A rHoogsteen 24-XXIV tWH tW-M 528 A.G993 A.A996 G+A -- -- cWH cW+M 529 A.G993 A.C1045 G-C WC 19-XIX cWW cW-W 530 A.C995 A.A1046 C-A -- -- cWS cW-m 531 A.A996 A.C1045 A-C -- -- cWS cW-m 532 A.U997 A.A1044 U-A WC 20-XX cWW cW-W 533 A.G998 A.C1043 G-C -- -- cWW cW-W 534 A.C999 A.G1042 C-G WC 19-XIX cWW cW-W 535 A.U1000 A.A1041 U-A WC 20-XX cWW cW-W 536 A.A1001 A.U1040 A-U WC 20-XX cWW cW-W 537 A.G1002 A.C1039 G-C WC 19-XIX cWW cW-W 538 A.G1003^A A.C1038 G-C WC 19-XIX cWW cW-W 539 A.A1004 A.G1036 A+G -- -- cHH cM+M 540 A.A1005 A.C1027 A-C ~Sheared -- tSH tm-M 541 A.C1006 A.G1023 C-G WC 19-XIX cWW cW-W 542 A.C1007 A.G1022 C-G WC 19-XIX cWW cW-W 543 A.G1009 A.U1020 G-U Wobble 28-XXVIII cWW cW-W 544 A.G1010 A.C1019 G-C WC 19-XIX cWW cW-W 545 A.G1011 A.C1018 G-C WC 19-XIX cWW cW-W 546 A.U1012 A.G1017 U-G Wobble 28-XXVIII cWW cW-W 547 A.G1013 A.A1016 G-A Sheared 11-XI tSH tm-M 548 A.C1028 A.G1033 C-G WC 19-XIX cWW cW-W 549 A.C1029 A.G1032 C-G WC 19-XIX cWW cW-W 550 A.C1030 A.G1031 C-G WC 19-XIX cWW cW-W 551 A.A1046 A.U1211 A-U -- -- tHW tM-W 552 A.A1046 A.A1213 A+A -- -- tWW tW+W 553 A.G1047 A.C1210 G-C WC 19-XIX cWW cW-W 554 A.G1048 A.C1209 G-C WC 19-XIX cWW cW-W 555 A.G1048 A.C1214 G-C -- -- cSW cm-W 556 A.G1050 A.C1208 G-C WC 19-XIX cWW cW-W 557 A.C1051 A.2MG1207 C-g WC 19-XIX cWW cW-W 558 A.U1052 A.G1206 U-G Wobble 28-XXVIII cWW cW-W 559 A.G1053 A.G1057 G+G -- 06-VI cWH cW+M 560 A.G1053 A.C1203 G-C -- -- cW. cW-. 561 A.A1055 A.C1200 A-C ~rHoogsteen 25-XXV tHW tM-W 562 A.A1055 A.U1205 A-U -- -- cWW cW-W 563 A.U1056 A.A1204 U-A WC 20-XX cWW cW-W 564 A.G1057 A.C1203 G-C WC 19-XIX cWW cW-W 565 A.G1058 A.U1199 G-U Wobble 28-XXVIII cWW cW-W 566 A.G1058 A.G1202 G-G -- -- tSH tm-M 567 A.C1059 A.G1198 C-G WC 19-XIX cWW cW-W 568 A.C1060 A.G1197 C-G WC 19-XIX cWW cW-W 569 A.G1061 A.C1195 G-C WC 19-XIX cWW cW-W 570 A.U1062 A.U1194 U-U -- 16-XVI cWW cW-W 571 A.C1063 A.G1193 C-G WC 19-XIX cWW cW-W 572 A.G1064 A.C1192 G+C -- -- c.H c.+M 573 A.C1066 A.A1191 C-A ~rHoogsteen 25-XXV tWH tW-M 574 A.G1068 A.C1107 G-C WC 19-XIX cWW cW-W 575 A.G1068 A.A1191 G+A Linker -- tSS tm+m 576 A.C1069 A.G1106 C-G WC 19-XIX cWW cW-W 577 A.U1070 A.G1094 U-G -- -- tHW tM-W 578 A.U1070 A.A1105 U-A WC 20-XX cWW cW-W 579 A.C1071 A.U1085 C+U -- -- cHH cM+M 580 A.C1071 A.G1104 C-G WC 19-XIX cWW cW-W 581 A.G1072 A.G1084 G-G -- -- tH. tM-. 582 A.G1072 A.C1103 G-C WC 19-XIX cWW cW-W 583 A.U1073 A.G1084 U-G -- -- cW. cW-. 584 A.U1073 A.A1102 U-A WC 20-XX cWW cW-W 585 A.G1074 A.U1083 G-U Wobble 28-XXVIII cWW cW-W 586 A.G1074 A.A1101 G+A Linker -- tS. tm+. 587 A.C1075 A.G1082 C-G WC 19-XIX cWW cW-W 588 A.C1076 A.G1081 C-G WC 19-XIX cWW cW-W 589 A.G1077 A.A1080 G-A -- -- tSH tm-M 590 A.G1084 A.A1102 G+A -- -- cSH cm+M 591 A.U1086 A.G1099 U-G ~Wobble -- cWW cW-W 592 A.G1087 A.C1098 G-C WC 19-XIX cWW cW-W 593 A.G1088 A.C1097 G-C WC 19-XIX cWW cW-W 594 A.G1088 A.A1167 G+A -- -- tSW tm+W 595 A.G1089 A.C1096 G-C WC 19-XIX cWW cW-W 596 A.G1089 A.A1169 G+A Linker -- tSS tm+m 597 A.U1090 A.U1095 U-U -- 16-XVI cWW cW-W 598 A.U1091 A.A1093 U-A -- -- tSH tm-M 599 A.C1113 A.G1187 C-G WC 19-XIX cWW cW-W 600 A.C1114 A.G1186 C-G WC 19-XIX cWW cW-W 601 A.C1115 A.G1185 C-G WC 19-XIX cWW cW-W 602 A.C1116 A.G1184 C-G WC 19-XIX cWW cW-W 603 A.C1118 A.G1155 C-G WC 19-XIX cWW cW-W 604 A.C1119 A.G1154 C-G WC 19-XIX cWW cW-W 605 A.G1120 A.C1153 G-C WC 19-XIX cWW cW-W 606 A.U1121 A.A1152 U-A WC 20-XX cWW cW-W 607 A.U1122 A.A1151 U-A WC 20-XX cWW cW-W 608 A.A1123 A.U1150 A-U WC 20-XX cWW cW-W 609 A.G1124 A.C1149 G-C WC 19-XIX cWW cW-W 610 A.U1126 A.C1145 U-C -- -- cWW cW-W 611 A.U1126 A.U1148 U-U -- -- cWW cW-W 612 A.G1127 A.G1144 G-G -- -- cWW cW-W 613 A.G1127 A.C1145 G-C WC 19-XIX cWW cW-W 614 A.G1127 A.A1146 G-A -- -- cSH cm-M 615 A.G1127 A.C1147 G-C -- -- cSW cm-W 616 A.C1128 A.G1131 C+G -- -- tSH tm+M 617 A.C1128 A.G1143 C-G WC 19-XIX cWW cW-W 618 A.C1129 A.U1135 C+U -- -- t.W t.+W 619 A.G1131 A.G1143 G-G -- -- cWS cW-m 620 A.C1132 A.G1142 C-G WC 19-XIX cWW cW-W 621 A.G1133 A.C1141 G-C WC 19-XIX cWW cW-W 622 A.G1134 A.C1140 G-C WC 19-XIX cWW cW-W 623 A.U1135 A.G1138 U+G -- -- t.W t.+W 624 A.G1139 A.G1142 G+G -- 06-VI cWH cW+M 625 A.C1145 A.C1147 C+C -- -- cSH cm+M 626 A.C1149 A.A1280 C-A -- -- cSW cm-W 627 A.G1156 A.A1179 G+A -- 10-X tSW tm+W 628 A.A1157 A.G1178 A+G -- 10-X tWS tW+m 629 A.C1158 A.G1181 C-G WC 19-XIX cWW cW-W 630 A.G1160 A.A1176 G-A Imino 08-VIII cWW cW-W 631 A.G1160 A.G1182 G+G -- 06-VI cHW cM+W 632 A.C1161 A.G1175 C-G WC 19-XIX cWW cW-W 633 A.C1162 A.G1174 C-G WC 19-XIX cWW cW-W 634 A.C1163 A.G1173 C-G WC 19-XIX cWW cW-W 635 A.G1164 A.C1172 G-C WC 19-XIX cWW cW-W 636 A.C1165 A.G1171 C-G WC 19-XIX cWW cW-W 637 A.G1166 A.A1169 G-A Sheared 11-XI tSH tm-M 638 A.G1175 A.G1182 G-G -- -- cHH cM-M 639 A.A1176 A.G1181 A-G -- -- t.H t.-M 640 A.A1176 A.G1182 A-G -- -- -- -- 641 A.G1177 A.G1181 G-G -- -- tWH tW-M 642 A.C1200 A.U1205 C+U -- -- tSW tm+W 643 A.G1224 A.C1362 G-C WC 19-XIX cWW cW-W 644 A.G1233 A.U1364 G-U -- -- cSS cm-m 645 A.C1237 A.G1337 C-G WC 19-XIX cWW cW-W 646 A.A1238 A.G1241 A-G -- -- cWS cW-m 647 A.A1238 A.U1301 A-U rHoogsteen 24-XXIV tHW tM-W 648 A.A1239 A.A1299 A+A -- -- tHH tM+M 649 A.G1241 A.C1296 G-C WC 19-XIX cWW cW-W 650 A.C1242 A.G1295 C-G WC 19-XIX cWW cW-W 651 A.C1243 A.G1294 C-G WC 19-XIX cWW cW-W 652 A.C1244 A.G1293 C-G WC 19-XIX cWW cW-W 653 A.A1245 A.U1292 A-U WC 20-XX cWW cW-W 654 A.C1246 A.G1291 C-G WC 19-XIX cWW cW-W 655 A.U1247 A.G1290 U-G Wobble 28-XXVIII cWW cW-W 656 A.A1248 A.A1289 A-A -- 05-V tWH tW-M 657 A.C1249 A.A1288 C-A ~rHoogsteen 25-XXV tWH tW-M 658 A.A1250 A.G1353 A+G -- -- tWS tW+m 659 A.A1252 A.A1285 A+A -- 01-I tWW tW+W 660 A.G1253 A.C1284 G-C WC 19-XIX cWW cW-W 661 A.C1254 A.G1283 C-G WC 19-XIX cWW cW-W 662 A.G1255 A.G1258 G-G -- -- cSS cm-m 663 A.G1255 A.C1259 G-C -- -- cSS cm-m 664 A.G1255 A.C1282 G-C WC 19-XIX cWW cW-W 665 A.G1258 A.C1277 G-C WC 19-XIX cWW cW-W 666 A.C1259 A.G1276 C-G WC 19-XIX cWW cW-W 667 A.C1260 A.A1275 C-A -- -- t.H t.-M 668 A.A1261 A.G1274 A-G Sheared 11-XI tHS tM-m 669 A.C1262 A.G1273 C-G WC 19-XIX cWW cW-W 670 A.C1263 A.G1272 C-G WC 19-XIX cWW cW-W 671 A.C1264 A.G1271 C-G WC 19-XIX cWW cW-W 672 A.G1265 A.C1270 G-C WC 19-XIX cWW cW-W 673 A.G1266 A.A1269 G-A Sheared 11-XI tSH tm-M 674 A.A1268 A.C1326 A-C -- -- cSS cm-m 675 A.A1269 A.G1312 A+G Linker -- tSS tm+m 676 A.G1276 A.C1282 G-C -- -- cSS cm-m 677 A.A1287 A.G1370 A+G -- -- tWS tW+m 678 A.A1289 A.G1371 A+G Linker -- tSS tm+m 679 A.C1297 A.C1298 C+C Platform -- cSH cm+M 680 A.G1300 A.U1301 G+U Platform -- cSH cm+M 681 A.C1303 A.G1334 C-G WC 19-XIX cWW cW-W 682 A.G1304 A.A1333 G-A Sheared 11-XI tSH tm-M 683 A.G1305 A.A1332 G-A Sheared 11-XI tSH tm-M 684 A.A1306 A.G1331 A-G Sheared 11-XI tHS tM-m 685 A.U1307 A.U1330 U-U -- 16-XVI cWW cW-W 686 A.U1308 A.A1329 U-A WC 20-XX cWW cW-W 687 A.G1309 A.C1328 G-C WC 19-XIX cWW cW-W 688 A.G1310 A.C1327 G-C WC 19-XIX cWW cW-W 689 A.G1311 A.C1326 G-C WC 19-XIX cWW cW-W 690 A.G1312 A.C1325 G-C WC 19-XIX cWW cW-W 691 A.U1313 A.A1324 U-A WC 20-XX cWW cW-W 692 A.C1314 A.G1323 C-G WC 19-XIX cWW cW-W 693 A.U1315 A.A1319 U-A rHoogsteen 24-XXIV tWH tW-M 694 A.A1319 A.G1361 A+G -- 10-X tWS tW+m 695 A.U1345 A.U1376 U+U -- 13-XIII tWW tW+W 696 A.A1346 A.A1375 A+A -- 02-II tHH tM+M 697 A.G1347 A.U1348 G+U Platform -- cSH cm+M 698 A.U1348 A.A1374 U-A rHoogsteen 24-XXIV tWH tW-M 699 A.A1349 A.G1373 A-G Sheared 11-XI tHS tM-m 700 A.A1350 A.U1372 A-U WC 20-XX cWW cW-W 701 A.U1351 A.G1371 U-G Wobble 28-XXVIII cWW cW-W 702 A.C1352 A.G1370 C-G WC 19-XIX cWW cW-W 703 A.G1353 A.C1369 G-C WC 19-XIX cWW cW-W 704 A.C1354 A.G1368 C-G WC 19-XIX cWW cW-W 705 A.G1355 A.C1367 G-C WC 19-XIX cWW cW-W 706 A.G1356 A.C1366 G-C WC 19-XIX cWW cW-W 707 A.A1357 A.G1365 A-G Imino 08-VIII cWW cW-W 708 A.U1358 A.A1363 U+A rWC 21-XXI tWW tW+W 709 A.G1379 A.U1381 G+U -- -- cSH cm+M 710 A.G1392 A.A1502 G+A -- -- cSS cm+m 711 A.C1399 A.G1504 C-G WC 19-XIX cWW cW-W 712 A.G1401 A.C1501 G-C WC 19-XIX cWW cW-W 713 A.4OC1402 A.A1500 c-A -- -- cWW cW-W 714 A.C1403 A.A1499 C-A -- -- cSW cm-W 715 A.5MC1404 A.G1497 c-G WC 19-XIX cWW cW-W 716 A.G1405 A.C1496 G-C WC 19-XIX cWW cW-W 717 A.U1406 A.U1495 U-U -- -- cWW cW-W 718 A.U1406 A.G1517 U-G -- -- cSS cm-m 719 A.5MC1407 A.G1494 c-G WC 19-XIX cWW cW-W 720 A.C1409 A.G1491 C-G WC 19-XIX cWW cW-W 721 A.G1410 A.C1490 G-C WC 19-XIX cWW cW-W 722 A.C1411 A.G1489 C-G WC 19-XIX cWW cW-W 723 A.C1412 A.G1488 C-G WC 19-XIX cWW cW-W 724 A.A1413 A.G1487 A-G Imino 08-VIII cWW cW-W 725 A.U1414 A.G1486 U-G Wobble 28-XXVIII cWW cW-W 726 A.G1415 A.U1485 G-U Wobble 28-XXVIII cWW cW-W 727 A.G1416 A.C1484 G-C WC 19-XIX cWW cW-W 728 A.G1417 A.A1483 G-A Sheared 11-XI tSH tm-M 729 A.A1418 A.G1482 A-G Sheared 11-XI tHS tM-m 730 A.G1419 A.U1481 G-U Wobble 28-XXVIII cWW cW-W 731 A.C1420 A.G1480 C-G WC 19-XIX cWW cW-W 732 A.G1421 A.C1479 G-C WC 19-XIX cWW cW-W 733 A.G1422 A.C1478 G-C WC 19-XIX cWW cW-W 734 A.G1423 A.C1477 G-C WC 19-XIX cWW cW-W 735 A.C1424 A.G1476 C-G WC 19-XIX cWW cW-W 736 A.U1425 A.G1475 U-G -- -- cWW cW-W 737 A.C1426 A.G1474 C-G WC 19-XIX cWW cW-W 738 A.U1427 A.A1473 U-A WC 20-XX cWW cW-W 739 A.A1428 A.U1472 A-U WC 20-XX cWW cW-W 740 A.C1429 A.G1471 C-G WC 19-XIX cWW cW-W 741 A.C1430 A.G1470 C-G WC 19-XIX cWW cW-W 742 A.C1431 A.G1469 C-G WC 19-XIX cWW cW-W 743 A.G1432 A.A1468 G-A Sheared 11-XI tSH tm-M 744 A.A1434 A.G1467 A-G Sheared 11-XI tHS tM-m 745 A.G1435 A.C1466 G-C WC 19-XIX cWW cW-W 746 A.U1436 A.C1465 U-C -- -- cWW cW-W 747 A.C1437 A.G1464 C-G WC 19-XIX cWW cW-W 748 A.G1438 A.C1463 G-C WC 19-XIX cWW cW-W 749 A.C1439 A.G1462 C-G WC 19-XIX cWW cW-W 750 A.C1440 A.G1461 C-G WC 19-XIX cWW cW-W 751 A.G1441 A.A1460 G-A Sheared 11-XI tSH tm-M 752 A.G1442 A.G1461 G-G -- -- tWS tW-m 753 A.G1447 A.C1459 G-C WC 19-XIX cWW cW-W 754 A.C1448 A.G1455 C-G WC 19-XIX cWW cW-W 755 A.C1449 A.G1454 C-G WC 19-XIX cWW cW-W 756 A.U1450 A.G1453 U+G -- -- t.W t.+W 757 A.UR3/1498 A.A1499 u+A Platform -- cSH cm+M 758 A.A1507 A.U1528 A-U WC 20-XX cWW cW-W 759 A.G1508 A.C1527 G-C WC 19-XIX cWW cW-W 760 A.C1509 A.G1526 C-G WC 19-XIX cWW cW-W 761 A.U1510 A.G1525 U-G Wobble 28-XXVIII cWW cW-W 762 A.G1511 A.C1524 G-C WC 19-XIX cWW cW-W 763 A.U1512 A.G1523 U-G Wobble 28-XXVIII cWW cW-W 764 A.A1513 A.U1522 A-U WC 20-XX cWW cW-W 765 A.C1514 A.G1521 C-G WC 19-XIX cWW cW-W 766 A.C1515 A.G1520 C-G WC 19-XIX cWW cW-W 767 A.G1516 A.MA6/1519 G-a -- -- tWH tW-M **************************************************************************** List of 119 multiplets 1 nts=3 GCA A.G9,A.C25,A.A559 2 nts=3 GCU A.G11,A.C23,A.U561 3 nts=3 UGA A.U12,A.G22,A.A913 4 nts=3 UUA A.U13,A.U20,A.A915 5 nts=3 UAG A.U17,A.A918,A.G1079 6 nts=3 CAG A.C18,A.A864,A.G917 7 nts=3 GCA A.G41,A.C401,A.A621 8 nts=3 UGU A.U49,A.G362,A.U365 9 nts=3* AUC A.A51,A.U114,A.C314 10 nts=3 UCA A.U56,A.C352,A.A356 11 nts=3 AGC A.A60,A.G107,A.C110 12 nts=3 GCA A.G113,A.C314,A.A353 13 nts=3 UAA A.U114,A.A116,A.A313 14 nts=3 GGC A.G115,A.G117,A.C312 15 nts=3 CUG A.C121,A.U125,A.G236 16 nts=3 GAC A.G128,A.A130,A.C233 17 nts=3 UGA A.U129,A.G232,A.A263 18 nts=3 AAG A.A143,A.A197,A.G220 19 nts=3 ACG A.A160,A.C342,A.G347 20 nts=3 UGC A.U173,A.G198,A.C219 21 nts=3 GGC A.G251,A.G254,A.C272 22 nts=3 GGC A.G255,A.G266,A.C271 23 nts=3 GAU A.G297,A.A300,A.U565 24 nts=3 GCA A.G318,A.C335,A.A1433 25 nts=3 GAC A.G371,A.A374,A.C390 26 nts=3 CUA A.C372,A.U375,A.A389 27 nts=3 AAA A.A411,A.A414,A.A430 28 nts=3 GAG A.G413,A.A415,A.G428 29 nts=3 AGU A.A448,A.G485,A.U486 30 nts=3 PCA A.PSU516,A.C519,A.A533 31 nts=3 CgA A.C522,A.7MG527,A.A535 32 nts=3 GAC A.G567,A.A573,A.C883 33 nts=3 GUC A.G570,A.U863,A.C866 34 nts=3 GGC A.G575,A.G576,A.C880 35 nts=3 GAC A.G577,A.A729,A.C764 36 nts=3 GCG A.G595,A.C596,A.G644 37 nts=3 GUC A.G597,A.U641,A.C643 38 nts=3 UAA A.U598,A.A640,A.A642 39 nts=3 GGC A.G654,A.G752,A.C754 40 nts=3 AGA A.A676,A.G714,A.A777 41 nts=3 AGG A.A687,A.G700,A.G703 42 nts=3 AGC A.A695,A.G786,A.C796 43 nts=3 AGC A.A767,A.G1511,A.C1524 44 nts=3 GCA A.G769,A.C810,A.A900 45 nts=3 CGC A.C770,A.G809,A.C899 46 nts=3 GGU A.G776,A.G778,A.U804 47 nts=3 GCG A.G776,A.C779,A.G803 48 nts=3 UAA A.U827,A.A859,A.A872 49 nts=3 GUA A.G890,A.U891,A.A907 50 nts=3 GCA A.G922,A.C1395,A.A1398 51 nts=3 CGA A.C924,A.G1392,A.A1502 52 nts=3 AUC A.A935,A.U1380,A.C1383 53 nts=3 CGC A.C936,A.G1379,A.C1382 54 nts=3 CGU A.C948,A.G1233,A.U1364 55 nts=3 GCC A.G951,A.C970,A.C1230 56 nts=3 GCA A.G954,A.C1226,A.A1227 57 nts=3 ACG A.A959,A.C984,A.G1221 58 nts=3 UAA A.U961,A.A974,A.A1201 59 nts=3 AGA A.A978,A.G1316,A.A1360 60 nts=3 CAU A.C995,A.A1046,A.U1211 61 nts=3 GCC A.G1048,A.C1209,A.C1214 62 nts=3 GGC A.G1053,A.G1057,A.C1203 63 nts=3 ACU A.A1055,A.C1200,A.U1205 64 nts=3 GUG A.G1058,A.U1199,A.G1202 65 nts=3 UGA A.U1070,A.G1094,A.A1105 66 nts=3 CUG A.C1071,A.U1085,A.G1104 67 nts=3 GGC A.G1072,A.G1084,A.C1103 68 nts=3 UGA A.U1073,A.G1084,A.A1102 69 nts=3 GUA A.G1074,A.U1083,A.A1101 70 nts=3 GCA A.G1124,A.C1149,A.A1280 71 nts=3 UCU A.U1126,A.C1145,A.U1148 72 nts=3 GGA A.G1127,A.G1144,A.A1146 73 nts=3 GCC A.G1127,A.C1145,A.C1147 74 nts=3 CGG A.C1128,A.G1131,A.G1143 75 nts=3 CUG A.C1129,A.U1135,A.G1138 76 nts=3 CGG A.C1132,A.G1139,A.G1142 77 nts=3 GAG A.G1160,A.A1176,A.G1182 78 nts=3 AGC A.A1250,A.G1353,A.C1369 79 nts=3 AGC A.A1268,A.G1311,A.C1326 80 nts=3 ACG A.A1287,A.C1352,A.G1370 81 nts=3 UAG A.U1315,A.A1319,A.G1361 82 nts=3 GUA A.G1347,A.U1348,A.A1374 83 nts=3 CuA A.C1403,A.UR3/1498,A.A1499 84 nts=3 UUG A.U1406,A.U1495,A.G1517 85 nts=3 CGG A.C1440,A.G1442,A.G1461 86 nts=4 AAGA A.A16,A.A919,A.G1077,A.A1080 87 nts=4 GGCA A.G21,A.G885,A.C912,A.A914 88 nts=4 GCCA A.G42,A.C400,A.C618,A.A622 89 nts=4 CAGU A.C54,A.A55,A.G357,A.U368 90 nts=4 GCAA A.G66,A.C103,A.A149,A.A172 91 nts=4 GCCA A.G66,A.C103,A.C150,A.A171 92 nts=4 CGAU A.C67,A.G102,A.A151,A.U170 93 nts=4 AGUU A.A140,A.G181,A.U182,A.U223 94 nts=4 GAAC A.G142,A.A179,A.A196,A.C221 95 nts=4 AGCA A.A243,A.G247,A.C277,A.A282 96 nts=4 GGCA A.G292,A.G305,A.C308,A.A608 97 nts=4 GCAG A.G319,A.C334,A.A1434,A.G1467 98 nts=4 CAGG A.C370,A.A373,A.G391,A.G481 99 nts=4 GCAC A.G502,A.C508,A.A509,A.C543 100 nts=4 CCAG A.C503,A.C508,A.A510,A.G542 101 nts=4 PAGA A.PSU516,A.A520,A.G529,A.A533 102 nts=4 UGCA A.U686,A.G688,A.C699,A.A704 103 nts=4 AUUG A.A766,A.U813,A.U1510,A.G1525 104 nts=4 UCGA A.U820,A.C862,A.G867,A.A873 105 nts=4 UAGA A.U827,A.A860,A.G869,A.A872 106 nts=4 AUUC A.A937,A.U1345,A.U1376,A.C1378 107 nts=4 AUGA A.A946,A.U1235,A.G1304,A.A1333 108 nts=4 GGAC A.G988,A.G1013,A.A1016,A.C1217 109 nts=4 CGCA A.C1066,A.G1068,A.C1107,A.A1191 110 nts=4 GCGA A.G1089,A.C1096,A.G1166,A.A1169 111 nts=4 AAUG A.A1248,A.A1289,A.U1351,A.G1371 112 nts=4 GGCC A.G1255,A.G1258,A.C1277,A.C1282 113 nts=4 GCGC A.G1255,A.C1259,A.G1276,A.C1282 114 nts=4 GAGC A.G1266,A.A1269,A.G1312,A.C1325 115 nts=5 UAUUA A.U37,A.A397,A.U404,A.U498,A.A547 116 nts=5 GGAAC A.G64,A.G68,A.A101,A.A152,A.C169 117 nts=5 UGACA A.U991,A.G993,A.A996,A.C1045,A.A1213 118 nts=5 AGCGU A.A1238,A.G1241,A.C1296,A.G1300,A.U1301 119 nts=6 CGAACG A.C19,A.G568,A.A572,A.A574,A.C882,A.G916 **************************************************************************** List of 43 helices Note: a helix is defined by base-stacking interactions, regardless of bp 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[4] bps=19 strand-1 5'-GCGGCGUGCUCCGUGGGCG-3' bp-type ||||||||.|||||||||. strand-2 3'-CGCCGCGCGAGGCAUCCGA-5' helix-form AAAAAx.x.x.Axx.AA. 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.G44 A.C398 G-C WC 19-XIX cWW cW-W 7 A.U45 A.G396 U-G Wobble 28-XXVIII cWW cW-W 8 A.G46 A.C395 G-C WC 19-XIX cWW cW-W 9 A.C366 A.G394 C-G -- -- cSW cm-W 10 A.U367 A.A393 U-A WC 20-XX cWW cW-W 11 A.C369 A.G392 C-G WC 19-XIX cWW cW-W 12 A.C370 A.G391 C-G WC 19-XIX cWW cW-W 13 A.G371 A.C390 G-C WC 19-XIX cWW cW-W 14 A.U375 A.A389 U-A WC 20-XX cWW cW-W 15 A.G376 A.U387 G-U Wobble 28-XXVIII cWW cW-W 16 A.G377 A.C386 G-C WC 19-XIX cWW cW-W 17 A.G378 A.C385 G-C WC 19-XIX cWW cW-W 18 A.C379 A.G384 C-G WC 19-XIX cWW cW-W 19 A.G380 A.A383 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#2[1] bps=5 strand-1 5'-UCGAC-3' bp-type .|||| strand-2 3'-GGUUG-5' helix-form xx.. 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.G52 A.U359 G-U Wobble 28-XXVIII cWW cW-W 4 A.A53 A.U358 A-U WC 20-XX cWW cW-W 5 A.C54 A.G357 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=4 strand-1 5'-AUGC-3' bp-type .||| strand-2 3'-UACG-5' helix-form xA. 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#4[3] bps=16 strand-1 5'-GUCGCGGGCCGCGGGG-3' bp-type |||||.|||||||||| strand-2 3'-CGGCGACUGGUGCCUC-5' helix-form ..x...AAA.AAA.. 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.G66 A.C103 G-C WC 19-XIX 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.G70 A.U98 G-U Wobble 28-XXVIII cWW cW-W 9 A.C73 A.G97 C-G WC 19-XIX cWW cW-W 10 A.C74 A.G96 C-G WC 19-XIX cWW cW-W 11 A.G75 A.U95 G-U Wobble 28-XXVIII cWW cW-W 12 A.C76 A.G93 C-G WC 19-XIX cWW cW-W 13 A.G77 A.C92 G-C WC 19-XIX cWW cW-W 14 A.G78 A.C91 G-C WC 19-XIX cWW cW-W 15 A.G79 A.U90 G-U Wobble 28-XXVIII cWW cW-W 16 A.G80 A.C89 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#5[2] bps=15 strand-1 5'-AAAGGCCCCACUCCU-3' bp-type ....|||||.||||. strand-2 3'-GUCACGGGGGGAGGG-5' helix-form xxxAAAAAxAAAA. 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.G333 A.C320 G-C WC 19-XIX 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.C336 A.G317 C-G WC 19-XIX cWW cW-W 9 A.C337 A.G316 C-G WC 19-XIX cWW cW-W 10 A.A338 A.G351 A-G Imino 08-VIII 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 -- -- t.W t.+W -------------------------------------------------------------------------- helix#6[3] bps=17 strand-1 5'-CGGGUGGCCGGUCUUGU-3' bp-type ...|||||||||||... strand-2 3'-AGACACCGGCUAGGAGA-5' helix-form xx.AAxAAAx.A.x.x 1 A.C110 A.A60 C-A ~rHoogsteen 25-XXV tWH tW-M 2 A.G111 A.G331 G-G -- -- tWH tW-M 3 A.G112 A.A315 G-A Imino 08-VIII cWW cW-W 4 A.G113 A.C314 G-C WC 19-XIX cWW cW-W 5 A.U114 A.A313 U-A WC 20-XX cWW cW-W 6 A.G115 A.C312 G-C WC 19-XIX cWW cW-W 7 A.G289 A.C311 G-C WC 19-XIX cWW cW-W 8 A.C290 A.G310 C-G WC 19-XIX cWW cW-W 9 A.C291 A.G309 C-G WC 19-XIX cWW cW-W 10 A.G292 A.C308 G-C WC 19-XIX cWW cW-W 11 A.G293 A.U304 G-U Wobble 28-XXVIII cWW cW-W 12 A.U294 A.A303 U-A WC 20-XX cWW cW-W 13 A.C295 A.G302 C-G WC 19-XIX cWW cW-W 14 A.U296 A.G301 U-G Wobble 28-XXVIII cWW cW-W 15 A.U565 A.A300 U-A -- -- cWS cW-m 16 A.G566 A.G299 G+G -- 06-VI cHW cM+W 17 A.U560 A.A298 U-A -- -- tH. tM-. -------------------------------------------------------------------------- helix#7[1] bps=7 strand-1 5'-ACCCCAA-3' bp-type .|||... strand-2 3'-UGGGCAG-5' helix-form xAAxxx 1 A.A119 A.U287 A-U rHoogsteen 24-XXIV tHW tM-W 2 A.C240 A.G286 C-G WC 19-XIX cWW cW-W 3 A.C241 A.G285 C-G WC 19-XIX cWW cW-W 4 A.C242 A.G284 C-G WC 19-XIX cWW cW-W 5 A.C245 A.C283 C-C -- -- 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#8[4] bps=24 strand-1 5'-GCGUGGGUCCUCCCGGAAGAGGGC-3' bp-type ||||||||||..|||||||.|||| strand-2 3'-UGCGCCCGGGUAGGCCUUCGCCCG-5' helix-form .A..AA.x..x.AAAAAA.xAA. 1 A.G122 A.U239 G-U Wobble 28-XXVIII cWW cW-W 2 A.C123 A.G238 C-G WC 19-XIX cWW cW-W 3 A.G124 A.C237 G-C WC 19-XIX cWW cW-W 4 A.U125 A.G236 U-G Wobble 28-XXVIII 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.U129 A.G232 U-G Wobble 28-XXVIII cWW cW-W 9 A.C131 A.G231 C-G WC 19-XIX 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.C135 A.A228 C-A -- -- c.W c.-W 13 A.C136 A.G227 C-G WC 19-XIX cWW cW-W 14 A.C137 A.G226 C-G WC 19-XIX cWW cW-W 15 A.G138 A.C225 G-C WC 19-XIX cWW cW-W 16 A.G139 A.C224 G-C WC 19-XIX cWW cW-W 17 A.A140 A.U223 A-U WC 20-XX cWW cW-W 18 A.A141 A.U222 A-U WC 20-XX cWW cW-W 19 A.G142 A.C221 G-C WC 19-XIX cWW cW-W 20 A.A143 A.G220 A-G Imino 08-VIII cWW cW-W 21 A.G198 A.C219 G-C WC 19-XIX cWW cW-W 22 A.G199 A.C218 G-C WC 19-XIX cWW cW-W 23 A.G200 A.C217 G-C WC 19-XIX cWW cW-W 24 A.C201 A.G216 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#9[4] bps=30 strand-1 5'-GGGGUGUGUCCGAAGGGGGACAACCCGGGG-3' bp-type .|||||.||||...|||||....||||||. strand-2 3'-CCCCGCCCAGGUUACCCCCAAUCGGGCUCA-5' helix-form xAA.AAAAAAxx.xAAAAx....AAA... 1 A.G129^A A.C190^C G+C -- -- tW. tW+. 2 A.G190^G A.C190^B G-C WC 19-XIX cWW cW-W 3 A.G190^H A.C190^A G-C WC 19-XIX cWW cW-W 4 A.G190^I A.C190 G-C WC 19-XIX cWW cW-W 5 A.U190^J A.G189 U-G Wobble 28-XXVIII cWW cW-W 6 A.G190^K A.C188 G-C WC 19-XIX cWW cW-W 7 A.U190^L A.C187 U-C -- -- cWW cW-W 8 A.G191 A.C186 G-C WC 19-XIX cWW cW-W 9 A.U192 A.A185 U-A WC 20-XX cWW cW-W 10 A.C193 A.G184 C-G WC 19-XIX cWW cW-W 11 A.C194 A.G183 C-G WC 19-XIX cWW cW-W 12 A.G181 A.U182 G+U Platform -- cSH cm+M 13 A.A195 A.U180 A-U rHoogsteen 24-XXIV tHW tM-W 14 A.A196 A.A179 A-A -- 05-V tHW tM-W 15 A.G144 A.C178 G-C WC 19-XIX cWW cW-W 16 A.G145 A.C177 G-C WC 19-XIX cWW cW-W 17 A.G146 A.C176 G-C WC 19-XIX cWW cW-W 18 A.G147 A.C175 G-C WC 19-XIX cWW cW-W 19 A.G148 A.C174 G-C WC 19-XIX cWW cW-W 20 A.A149 A.A172 A-A -- 05-V tWH tW-M 21 A.C150 A.A171 C-A ~rHoogsteen 25-XXV tWH tW-M 22 A.A151 A.U170 A-U rHoogsteen 24-XXIV tHW tM-W 23 A.A152 A.C169 A-C ~rHoogsteen 25-XXV tHW tM-W 24 A.C153 A.G168 C-G WC 19-XIX cWW cW-W 25 A.C154 A.G167 C-G WC 19-XIX cWW cW-W 26 A.C155 A.G166 C-G WC 19-XIX cWW cW-W 27 A.G156 A.C165 G-C WC 19-XIX cWW cW-W 28 A.G157 A.U164 G-U Wobble 28-XXVIII cWW cW-W 29 A.G158 A.C163 G-C WC 19-XIX cWW cW-W 30 A.G159 A.A162 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#10[1] bps=9 strand-1 5'-UUGGUGGGG-3' bp-type ||||||||. strand-2 3'-AACCACCCG-5' helix-form .AAAAA.x 1 A.U252 A.A274 U-A WC 20-XX cWW cW-W 2 A.U253 A.A273 U-A 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.C268 G-C WC 19-XIX cWW cW-W 8 A.G259 A.C267 G-C WC 19-XIX cWW cW-W 9 A.G260 A.G265 G-G -- -- tWH tW-M -------------------------------------------------------------------------- helix#11[1] bps=4 strand-1 5'-GGCG-3' bp-type |||. strand-2 3'-UCGA-5' helix-form .Ax 1 A.G275 A.U249 G-U Wobble 28-XXVIII cWW cW-W 2 A.G276 A.C248 G-C WC 19-XIX cWW cW-W 3 A.C277 A.G247 C-G WC 19-XIX cWW cW-W 4 A.G278 A.A279 G-A Platform -- cSW cm-W -------------------------------------------------------------------------- helix#12[9] bps=44 strand-1 5'-AGCGUUACCCGGAGUAAGGAAUUGACGGGGCCCGACAAGCGGUG-3' bp-type .|||||||||.||||..|||.|||||||||||||||..|||||. strand-2 3'-UCGCAAUGGGACUCGGUCCUAGACUGUUCCGGGCUGCCCGCUAA-5' helix-form xAAAAx.AAxxAA.xxxAA..x.xA.x.AAAAAxA.xx.A... 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.C554 A.G29 C-G WC 19-XIX cWW cW-W 9 A.C555 A.G28 C-G WC 19-XIX 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.U13 A+U Hoogsteen 23-XXIII cHW cM+W 18 A.G916 A.C19 G-C WC 19-XIX 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.A1396 U-A WC 20-XX cWW cW-W 24 A.G922 A.C1395 G-C WC 19-XIX cWW cW-W 25 A.A923 A.U1393 A-U WC 20-XX cWW cW-W 26 A.C924 A.G1392 C-G WC 19-XIX cWW cW-W 27 A.G925 A.U1391 G-U Wobble 28-XXVIII cWW cW-W 28 A.G927 A.U1390 G-U Wobble 28-XXVIII cWW cW-W 29 A.G928 A.C1389 G-C WC 19-XIX cWW cW-W 30 A.G929 A.C1388 G-C WC 19-XIX cWW cW-W 31 A.C930 A.G1387 C-G WC 19-XIX cWW cW-W 32 A.C931 A.G1386 C-G WC 19-XIX cWW cW-W 33 A.C932 A.G1385 C-G WC 19-XIX cWW cW-W 34 A.G933 A.C1384 G-C WC 19-XIX cWW cW-W 35 A.A935 A.U1380 A-U WC 20-XX cWW cW-W 36 A.C936 A.G1379 C-G WC 19-XIX cWW cW-W 37 A.A937 A.C1378 A-C ~Sheared -- tSH tm-M 38 A.A938 A.C934 A+C ~rWobble 26-XXVI tWW tW+W 39 A.G939 A.C1344 G-C WC 19-XIX cWW cW-W 40 A.C940 A.G1343 C-G WC 19-XIX cWW cW-W 41 A.G941 A.C1342 G-C WC 19-XIX cWW cW-W 42 A.G942 A.U1341 G-U Wobble 28-XXVIII cWW cW-W 43 A.U943 A.A1340 U-A WC 20-XX cWW cW-W 44 A.G944 A.A1339 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#13[4] bps=35 strand-1 5'-GGGGUGAAACUCCUGAACCCGGGACGAAACCCCCG-3' bp-type .||||....||||....|||||...|....||||. strand-2 3'-UCCCGGAUGGAGGAAUGGGGCCAUGCGUCAGGGGA-5' helix-form .AA.xxxx.AAAx.x...AAA..x.xx...AAA. 1 A.G423 A.U420 G+U -- -- tWS tW+m 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.G426 A.C417 G-C WC 19-XIX cWW cW-W 5 A.U427 A.G416 U-G Wobble 28-XXVIII cWW cW-W 6 A.G428 A.G413 G+G -- 04-IV tSS tm+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.C433 A.G409 C-G WC 19-XIX cWW cW-W 11 A.U434 A.A408 U-A WC 20-XX cWW cW-W 12 A.C435 A.G407 C-G WC 19-XIX cWW cW-W 13 A.C436 A.G406 C-G WC 19-XIX cWW cW-W 14 A.U437 A.A496 U-A rHoogsteen 24-XXIV tWH tW-M 15 A.G438 A.A497 G-A Sheared 11-XI tSH tm-M 16 A.A439 A.U495 A-U rHoogsteen 24-XXIV tHW tM-W 17 A.A440 A.G494 A-G Sheared 11-XI tHS tM-m 18 A.C442 A.G492 C-G WC 19-XIX cWW cW-W 19 A.C443 A.G491 C-G WC 19-XIX cWW cW-W 20 A.C444 A.G490 C-G WC 19-XIX cWW cW-W 21 A.G445 A.C489 G-C WC 19-XIX cWW cW-W 22 A.G446 A.C488 G-C WC 19-XIX cWW cW-W 23 A.G447 A.A487 G-A Sheared 11-XI tSH tm-M 24 A.A448 A.U486 A-U rHoogsteen 24-XXIV tHW tM-W 25 A.C449 A.G484 C+G -- -- cHW cM+W 26 A.G450 A.C483 G-C WC 19-XIX cWW cW-W 27 A.A373 A.G481 A-G -- -- tSS tm-m 28 A.A452 A.U480 A-U rHoogsteen 24-XXIV tHW tM-W 29 A.A453 A.C479 A-C ~rHoogsteen 25-XXV tHW tM-W 30 A.C454 A.A478 C-A -- -- tHW tM-W 31 A.C455 A.G477 C-G WC 19-XIX cWW cW-W 32 A.C456 A.G476 C-G WC 19-XIX cWW cW-W 33 A.C457 A.G475 C-G WC 19-XIX cWW cW-W 34 A.C458 A.G474 C-G WC 19-XIX cWW cW-W 35 A.G459 A.A463 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#14[0] bps=2 strand-1 5'-UA-3' bp-type .. strand-2 5'-AU-3' helix-form x 1 A.U498 A.A547 U-A rHoogsteen 24-XXIV tWH tW-M 2 A.A499 A.U405 A+U Hoogsteen 23-XXIII cHW cM+W -------------------------------------------------------------------------- helix#15[2] bps=11 strand-1 5'-GCGCCCUCCGP-3' bp-type ||||||||||. strand-2 3'-CGCGGGAGGCA-5' helix-form AAAAx.AAAx 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.G502 A.C543 G-C WC 19-XIX 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 6 A.C511 A.G540 C-G WC 19-XIX cWW cW-W 7 A.U512 A.A539 U-A WC 20-XX cWW cW-W 8 A.C513 A.G538 C-G WC 19-XIX cWW cW-W 9 A.C514 A.G537 C-G WC 19-XIX cWW cW-W 10 A.G515 A.C536 G-C WC 19-XIX cWW cW-W 11 A.PSU516 A.A533 P-A ~rHoogsteen -- tWH tW-M -------------------------------------------------------------------------- helix#16[2] bps=7 strand-1 5'-AGCCgCG-3' bp-type .|||||. strand-2 3'-CCGGCGA-5' helix-form xAAx.. 1 A.A509 A.C508 A+C Platform -- 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.7MG527 A.C522 g-C WC 19-XIX cWW cW-W 6 A.C528 A.G521 C-G WC 19-XIX cWW cW-W 7 A.G529 A.A520 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#17[2] bps=12 strand-1 5'-AGGCGGCGCGCU-3' bp-type .||||||||||. strand-2 3'-UCCGCCGCGCGA-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.C822 A.G878 C-G WC 19-XIX cWW cW-W 8 A.G823 A.C877 G-C WC 19-XIX cWW cW-W 9 A.C824 A.G876 C-G WC 19-XIX cWW cW-W 10 A.G825 A.C875 G-C WC 19-XIX 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'-ACCACGGC-3' bp-type .||||||. strand-2 3'-GGGUGCCA-5' helix-form .AAA.A. 1 A.A611 A.G629 A-G Imino 08-VIII 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.A614 A.U626 A-U WC 20-XX cWW cW-W 5 A.C615 A.G625 C-G WC 19-XIX 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=52 strand-1 5'-AGCGUGGGACGCUCAGGCUGACGGUGGGAGGGGUGGUGGAAUUCCCGGAGUA-3' bp-type .|||||||||||||||||.|||||||||..||||||||....||||||.... strand-2 3'-GUGUACCCUGCGGGUCCGACUGCCACCUGGUCCACCGCAAGGAGGGCCAUAG-5' helix-form ....AAAAx.xAAAAA.xxxA.xAAA...x.AAAA.xA....AAAAA.... 1 A.A632 A.G606 A-G Sheared 11-XI tHS tM-m 2 A.G633 A.U605 G-U Wobble 28-XXVIII cWW cW-W 3 A.C634 A.G604 C-G WC 19-XIX cWW cW-W 4 A.G635 A.U603 G-U Wobble 28-XXVIII cWW cW-W 5 A.U636 A.A602 U-A WC 20-XX cWW cW-W 6 A.G637 A.C601 G-C WC 19-XIX cWW cW-W 7 A.G638 A.C600 G-C WC 19-XIX cWW cW-W 8 A.G639 A.C599 G-C WC 19-XIX cWW cW-W 9 A.A640 A.U598 A-U WC 20-XX cWW cW-W 10 A.C643 A.G597 C-G WC 19-XIX cWW cW-W 11 A.G644 A.C596 G-C WC 19-XIX cWW cW-W 12 A.C645 A.G594 C-G WC 19-XIX cWW cW-W 13 A.U646 A.G593 U-G Wobble 28-XXVIII cWW cW-W 14 A.C647 A.G592 C-G WC 19-XIX cWW cW-W 15 A.A648 A.U591 A-U WC 20-XX cWW cW-W 16 A.G649 A.C590 G-C WC 19-XIX cWW cW-W 17 A.G650 A.C589 G-C WC 19-XIX cWW cW-W 18 A.C651 A.G588 C-G WC 19-XIX cWW cW-W 19 A.U652 A.A753 U-A rHoogsteen 24-XXIV tWH tW-M 20 A.G654 A.C754 G-C WC 19-XIX cWW cW-W 21 A.A655 A.U751 A-U WC 20-XX cWW cW-W 22 A.C656 A.G750 C-G WC 19-XIX cWW cW-W 23 A.G657 A.C749 G-C WC 19-XIX cWW cW-W 24 A.G658 A.C747 G-C WC 19-XIX cWW cW-W 25 A.U659 A.A746 U-A WC 20-XX cWW cW-W 26 A.G660 A.C745 G-C WC 19-XIX cWW cW-W 27 A.G661 A.C744 G-C WC 19-XIX cWW cW-W 28 A.G662 A.U743 G-U Wobble 28-XXVIII cWW cW-W 29 A.A663 A.G742 A-G Imino 08-VIII cWW cW-W 30 A.G664 A.G741 G-G -- -- cWW cW-W 31 A.G666 A.U740 G-U Wobble 28-XXVIII cWW cW-W 32 A.G667 A.C739 G-C WC 19-XIX cWW cW-W 33 A.G668 A.C738 G-C WC 19-XIX cWW cW-W 34 A.U669 A.A737 U-A WC 20-XX cWW cW-W 35 A.G670 A.C736 G-C WC 19-XIX cWW cW-W 36 A.G671 A.C735 G-C WC 19-XIX cWW cW-W 37 A.U672 A.G734 U-G Wobble 28-XXVIII cWW cW-W 38 A.G673 A.C717 G-C WC 19-XIX cWW cW-W 39 A.G674 A.A716 G-A Imino 08-VIII cWW cW-W 40 A.A675 A.A715 A-A -- -- cWW cW-W 41 A.A676 A.G714 A-G Imino 08-VIII cWW cW-W 42 A.U677 A.G713 U-G ~Wobble -- cWW cW-W 43 A.U678 A.A712 U-A WC 20-XX cWW cW-W 44 A.C679 A.G711 C-G WC 19-XIX cWW cW-W 45 A.C680 A.G710 C-G WC 19-XIX cWW cW-W 46 A.C681 A.G709 C-G WC 19-XIX cWW cW-W 47 A.G682 A.C708 G-C WC 19-XIX cWW cW-W 48 A.G683 A.C707 G-C WC 19-XIX cWW cW-W 49 A.A684 A.A706 A-A -- -- cWW cW-W 50 A.G685 A.U705 G-U -- -- tSH tm-M 51 A.U686 A.A704 U-A rHoogsteen 24-XXIV tWH tW-M 52 A.A687 A.G703 A-G Sheared 11-XI tHS tM-m -------------------------------------------------------------------------- helix#21[1] bps=4 strand-1 5'-GCGG-3' bp-type ||.. strand-2 3'-CGUA-5' helix-form A.. 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.U697 G-U -- -- t.H t.-M 4 A.G691 A.A696 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#22[1] bps=5 strand-1 5'-AGGCG-3' bp-type ..||. strand-2 3'-AACGG-5' helix-form xxA. 1 A.A722 A.A733 A+A -- 01-I 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[5] bps=29 strand-1 5'-GCUGAGGCGCGAAGCGUGGGCAAACCGGU-3' bp-type |||...||||...||||||||...||||. strand-2 3'-CGGAUGUGCGAUCCGCACCUGAUGGGCCC-5' helix-form A......AAxxx..AAAAx.....A.Ax 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.G758 A.A583 G-A Sheared 11-XI tSH tm-M 5 A.A759 A.U582 A-U rHoogsteen 24-XXIV tHW tM-W 6 A.G760 A.G581 G-G -- -- tHS tM-m 7 A.G761 A.U580 G-U Wobble 28-XXVIII cWW cW-W 8 A.C762 A.G579 C-G WC 19-XIX 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 12 A.A766 A.U813 A-U rHoogsteen 24-XXIV tHW tM-W 13 A.A768 A.C811 A-C -- -- cWW cW-W 14 A.G769 A.C810 G-C WC 19-XIX cWW cW-W 15 A.C770 A.G809 C-G WC 19-XIX cWW cW-W 16 A.G771 A.C808 G-C WC 19-XIX cWW cW-W 17 A.U772 A.A807 U-A WC 20-XX cWW cW-W 18 A.G773 A.C806 G-C WC 19-XIX cWW cW-W 19 A.G774 A.C805 G-C WC 19-XIX cWW cW-W 20 A.G778 A.U804 G-U Wobble 28-XXVIII cWW cW-W 21 A.C779 A.G803 C-G WC 19-XIX cWW cW-W 22 A.A780 A.A802 A-A ~Sheared -- tSH tm-M 23 A.A781 A.U801 A-U rHoogsteen 24-XXIV tHW tM-W 24 A.A782 A.G800 A-G Sheared 11-XI tHS tM-m 25 A.C783 A.G799 C-G WC 19-XIX cWW cW-W 26 A.C784 A.G798 C-G WC 19-XIX cWW cW-W 27 A.G785 A.C797 G-C WC 19-XIX cWW cW-W 28 A.G786 A.C796 G-C WC 19-XIX cWW cW-W 29 A.U788 A.C795 U-C -- -- cSW cm-W -------------------------------------------------------------------------- helix#24[2] bps=14 strand-1 5'-CCUGGGGGCCGAGC-3' bp-type ||||||||||..|| strand-2 3'-GGGUCUCUGGAGCG-5' helix-form ...A....A.x.A 1 A.C848 A.G838 C-G WC 19-XIX cWW cW-W 2 A.C849 A.G837 C-G WC 19-XIX cWW cW-W 3 A.U850 A.G836 U-G Wobble 28-XXVIII cWW cW-W 4 A.G851 A.U835 G-U Wobble 28-XXVIII cWW cW-W 5 A.G852 A.C834 G-C WC 19-XIX cWW cW-W 6 A.G853 A.U833 G-U Wobble 28-XXVIII cWW cW-W 7 A.G854 A.C832 G-C WC 19-XIX cWW cW-W 8 A.G855 A.U831 G-U Wobble 28-XXVIII cWW cW-W 9 A.C856 A.G830 C-G WC 19-XIX cWW cW-W 10 A.C857 A.G829 C-G WC 19-XIX cWW cW-W 11 A.G858 A.A828 G-A Sheared 11-XI tSH tm-M 12 A.A860 A.G869 A-G Sheared 11-XI tHS tM-m 13 A.G861 A.C868 G-C WC 19-XIX cWW cW-W 14 A.C862 A.G867 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#25[2] bps=13 strand-1 5'-GGGGAUACGGCCG-3' bp-type |||.....||||. strand-2 3'-CUCAAAGUUCGGA-5' helix-form ....x.xx.AA. 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.A889 A.A908 A+A -- 02-II tHH tM+M 6 A.U891 A.A907 U-A rHoogsteen 24-XXIV tWH tW-M 7 A.A892 A.G906 A-G Sheared 11-XI tHS tM-m 8 A.C893 A.U244 C-U -- 18-XVIII cWW cW-W 9 A.G894 A.U905 G-U Wobble 28-XXVIII cWW cW-W 10 A.G895 A.C904 G-C WC 19-XIX cWW cW-W 11 A.C896 A.G903 C-G WC 19-XIX cWW cW-W 12 A.C897 A.G902 C-G WC 19-XIX cWW cW-W 13 A.G898 A.A901 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#26[2] bps=13 strand-1 5'-UACCACGUGCUAC-3' bp-type .||||||||||.| strand-2 3'-UUGGUGUACGAGG-5' helix-form xBxAA......x 1 A.U960 A.U956 U+U -- 13-XIII tWW tW+W 2 A.A1225 A.U955 A-U WC 20-XX cWW cW-W 3 A.C1226 A.G954 C-G WC 19-XIX cWW cW-W 4 A.C1228 A.G953 C-G WC 19-XIX cWW cW-W 5 A.A1229 A.U952 A-U WC 20-XX cWW cW-W 6 A.C1230 A.G951 C-G WC 19-XIX cWW cW-W 7 A.G1231 A.U950 G-U Wobble 28-XXVIII cWW cW-W 8 A.U1232 A.A949 U-A WC 20-XX cWW cW-W 9 A.G1233 A.C948 G-C WC 19-XIX cWW cW-W 10 A.C1234 A.G947 C-G WC 19-XIX cWW cW-W 11 A.U1235 A.A946 U-A WC 20-XX cWW cW-W 12 A.A1236 A.G945 A-G Imino 08-VIII cWW cW-W 13 A.C1237 A.G1337 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#27[1] bps=3 strand-1 5'-UCG-3' bp-type .|| strand-2 3'-AGC-5' helix-form xA 1 A.U961 A.A1201 U+A rWC 21-XXI tWW tW+W 2 A.C962 A.G973 C-G WC 19-XIX cWW cW-W 3 A.G963 A.C972 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#28[1] bps=16 strand-1 5'-AAGACCCCAUGAAGAA-3' bp-type ..|||||||....|.. strand-2 3'-AUCUGGGGUUAGGCUA-5' helix-form xxAA.AAA.....xx 1 A.A978 A.A1360 A-A -- 05-V tHW tM-W 2 A.A1319 A.U1315 A-U rHoogsteen 24-XXIV tHW tM-W 3 A.G1323 A.C1314 G-C WC 19-XIX cWW cW-W 4 A.A1324 A.U1313 A-U WC 20-XX cWW cW-W 5 A.C1325 A.G1312 C-G WC 19-XIX cWW cW-W 6 A.C1326 A.G1311 C-G WC 19-XIX cWW cW-W 7 A.C1327 A.G1310 C-G WC 19-XIX cWW cW-W 8 A.C1328 A.G1309 C-G WC 19-XIX cWW cW-W 9 A.A1329 A.U1308 A-U WC 20-XX cWW cW-W 10 A.U1330 A.U1307 U-U -- 16-XVI cWW cW-W 11 A.G1331 A.A1306 G-A Sheared 11-XI tSH tm-M 12 A.A1332 A.G1305 A-G Sheared 11-XI tHS tM-m 13 A.A1333 A.G1304 A-G Sheared 11-XI tHS tM-m 14 A.G1334 A.C1303 G-C WC 19-XIX cWW cW-W 15 A.A1238 A.U1301 A-U rHoogsteen 24-XXIV tHW tM-W 16 A.A1239 A.A1299 A+A -- -- tHH tM+M -------------------------------------------------------------------------- helix#29[1] bps=8 strand-1 5'-CCAGGCCU-3' bp-type |||||||. strand-2 3'-GGUCCGGA-5' helix-form AAAA..x 1 A.C984 A.G1221 C-G WC 19-XIX cWW cW-W 2 A.C985 A.G1220 C-G WC 19-XIX cWW cW-W 3 A.A986 A.U1219 A-U WC 20-XX cWW cW-W 4 A.G987 A.C1218 G-C WC 19-XIX cWW cW-W 5 A.G988 A.C1217 G-C WC 19-XIX cWW cW-W 6 A.C989 A.G1216 C-G WC 19-XIX cWW cW-W 7 A.C990 A.G1215 C-G WC 19-XIX cWW cW-W 8 A.U991 A.A1213 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#30[2] bps=7 strand-1 5'-CCGGGUG-3' bp-type ||||||. strand-2 3'-GGUCCGA-5' helix-form .x.A.. 1 A.C1006 A.G1023 C-G WC 19-XIX cWW cW-W 2 A.C1007 A.G1022 C-G WC 19-XIX cWW cW-W 3 A.G1009 A.U1020 G-U Wobble 28-XXVIII cWW cW-W 4 A.G1010 A.C1019 G-C WC 19-XIX cWW cW-W 5 A.G1011 A.C1018 G-C WC 19-XIX cWW cW-W 6 A.U1012 A.G1017 U-G Wobble 28-XXVIII cWW cW-W 7 A.G1013 A.A1016 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#31[1] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form AA 1 A.C1028 A.G1033 C-G WC 19-XIX cWW cW-W 2 A.C1029 A.G1032 C-G WC 19-XIX cWW cW-W 3 A.C1030 A.G1031 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#32[5] bps=25 strand-1 5'-CCUAGCACAGGGCUAUGGCCGUCGC-3' bp-type |||||.||.|||||.||||||.|.. strand-2 3'-GGAUCGUGCCCCgGCACUGGCUGCA-5' helix-form x.A...xxx.xAAxx.x.Ax...x 1 A.C1038 A.G1003^A C-G WC 19-XIX cWW cW-W 2 A.C1039 A.G1002 C-G WC 19-XIX cWW cW-W 3 A.U1040 A.A1001 U-A WC 20-XX cWW cW-W 4 A.A1041 A.U1000 A-U WC 20-XX cWW cW-W 5 A.G1042 A.C999 G-C WC 19-XIX cWW cW-W 6 A.C1043 A.G998 C-G -- -- cWW cW-W 7 A.A1044 A.U997 A-U WC 20-XX cWW cW-W 8 A.C1045 A.G993 C-G WC 19-XIX cWW cW-W 9 A.A1046 A.C995 A-C -- -- cSW cm-W 10 A.G1047 A.C1210 G-C WC 19-XIX cWW cW-W 11 A.G1048 A.C1209 G-C WC 19-XIX cWW cW-W 12 A.G1050 A.C1208 G-C WC 19-XIX cWW cW-W 13 A.C1051 A.2MG1207 C-g WC 19-XIX cWW cW-W 14 A.U1052 A.G1206 U-G Wobble 28-XXVIII cWW cW-W 15 A.A1055 A.C1200 A-C ~rHoogsteen 25-XXV tHW tM-W 16 A.U1056 A.A1204 U-A WC 20-XX cWW cW-W 17 A.G1057 A.C1203 G-C WC 19-XIX cWW cW-W 18 A.G1058 A.U1199 G-U Wobble 28-XXVIII cWW cW-W 19 A.C1059 A.G1198 C-G WC 19-XIX cWW cW-W 20 A.C1060 A.G1197 C-G WC 19-XIX cWW cW-W 21 A.G1061 A.C1195 G-C WC 19-XIX cWW cW-W 22 A.U1062 A.U1194 U-U -- 16-XVI cWW cW-W 23 A.C1063 A.G1193 C-G WC 19-XIX cWW cW-W 24 A.G1064 A.C1192 G+C -- -- c.H c.+M 25 A.C1066 A.A1191 C-A ~rHoogsteen 25-XXV tWH tW-M -------------------------------------------------------------------------- helix#33[2] bps=10 strand-1 5'-GCUCGUGCCG-3' bp-type |||||||||. strand-2 3'-CGAGCAUGGA-5' helix-form A.AAAx.A. 1 A.G1068 A.C1107 G-C WC 19-XIX cWW cW-W 2 A.C1069 A.G1106 C-G WC 19-XIX cWW cW-W 3 A.U1070 A.A1105 U-A WC 20-XX cWW cW-W 4 A.C1071 A.G1104 C-G WC 19-XIX cWW cW-W 5 A.G1072 A.C1103 G-C WC 19-XIX cWW cW-W 6 A.U1073 A.A1102 U-A WC 20-XX cWW cW-W 7 A.G1074 A.U1083 G-U Wobble 28-XXVIII cWW cW-W 8 A.C1075 A.G1082 C-G WC 19-XIX cWW cW-W 9 A.C1076 A.G1081 C-G WC 19-XIX cWW cW-W 10 A.G1077 A.A1080 G-A -- -- tSH tm-M -------------------------------------------------------------------------- helix#34[1] bps=6 strand-1 5'-UGGGUU-3' bp-type .|||.. strand-2 3'-GCCCUA-5' helix-form .AA.x 1 A.U1086 A.G1099 U-G ~Wobble -- cWW cW-W 2 A.G1087 A.C1098 G-C WC 19-XIX cWW cW-W 3 A.G1088 A.C1097 G-C WC 19-XIX cWW cW-W 4 A.G1089 A.C1096 G-C WC 19-XIX cWW cW-W 5 A.U1090 A.U1095 U-U -- 16-XVI cWW cW-W 6 A.U1091 A.A1093 U-A -- -- tSH tm-M -------------------------------------------------------------------------- helix#35[1] bps=4 strand-1 5'-CCCC-3' bp-type |||| strand-2 3'-GGGG-5' helix-form .AA 1 A.C1113 A.G1187 C-G WC 19-XIX cWW cW-W 2 A.C1114 A.G1186 C-G WC 19-XIX cWW cW-W 3 A.C1115 A.G1185 C-G WC 19-XIX cWW cW-W 4 A.C1116 A.G1184 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#36[2] bps=15 strand-1 5'-GCCGGCUCUAACGGG-3' bp-type .|||||.|||||||. strand-2 3'-UGGCCGUGAUUGCCA-5' helix-form x..xxxx...A.Ax 1 A.G1138 A.U1135 G+U -- -- tW. tW+. 2 A.C1140 A.G1134 C-G WC 19-XIX cWW cW-W 3 A.C1141 A.G1133 C-G WC 19-XIX cWW cW-W 4 A.G1142 A.C1132 G-C WC 19-XIX cWW cW-W 5 A.G1143 A.C1128 G-C WC 19-XIX cWW cW-W 6 A.C1145 A.G1127 C-G WC 19-XIX cWW cW-W 7 A.U1148 A.U1126 U-U -- -- cWW cW-W 8 A.C1149 A.G1124 C-G WC 19-XIX cWW cW-W 9 A.U1150 A.A1123 U-A WC 20-XX cWW cW-W 10 A.A1151 A.U1122 A-U WC 20-XX cWW cW-W 11 A.A1152 A.U1121 A-U WC 20-XX cWW cW-W 12 A.C1153 A.G1120 C-G WC 19-XIX cWW cW-W 13 A.G1154 A.C1119 G-C WC 19-XIX cWW cW-W 14 A.G1155 A.C1118 G-C WC 19-XIX cWW cW-W 15 A.G1156 A.A1179 G+A -- 10-X tSW tm+W -------------------------------------------------------------------------- helix#37[1] bps=9 strand-1 5'-ACGCCCGCG-3' bp-type .|.|||||. strand-2 3'-GGAGGGCGA-5' helix-form xx.AAAA. 1 A.A1157 A.G1178 A+G -- 10-X tWS tW+m 2 A.C1158 A.G1181 C-G WC 19-XIX cWW cW-W 3 A.G1160 A.A1176 G-A Imino 08-VIII cWW cW-W 4 A.C1161 A.G1175 C-G WC 19-XIX cWW cW-W 5 A.C1162 A.G1174 C-G WC 19-XIX cWW cW-W 6 A.C1163 A.G1173 C-G WC 19-XIX cWW cW-W 7 A.G1164 A.C1172 G-C WC 19-XIX cWW cW-W 8 A.C1165 A.G1171 C-G WC 19-XIX cWW cW-W 9 A.G1166 A.A1169 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#38[1] bps=4 strand-1 5'-AGCG-3' bp-type .||| strand-2 3'-ACGC-5' helix-form .AA 1 A.A1252 A.A1285 A+A -- 01-I tWW tW+W 2 A.G1253 A.C1284 G-C WC 19-XIX cWW cW-W 3 A.C1254 A.G1283 C-G WC 19-XIX cWW cW-W 4 A.G1255 A.C1282 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#39[2] bps=9 strand-1 5'-GCCACCCGG-3' bp-type ||..||||. strand-2 3'-CGAGGGGCA-5' helix-form A...AAA. 1 A.G1258 A.C1277 G-C WC 19-XIX cWW cW-W 2 A.C1259 A.G1276 C-G WC 19-XIX cWW cW-W 3 A.C1260 A.A1275 C-A -- -- t.H t.-M 4 A.A1261 A.G1274 A-G Sheared 11-XI tHS tM-m 5 A.C1262 A.G1273 C-G WC 19-XIX cWW cW-W 6 A.C1263 A.G1272 C-G WC 19-XIX cWW cW-W 7 A.C1264 A.G1271 C-G WC 19-XIX cWW cW-W 8 A.G1265 A.C1270 G-C WC 19-XIX cWW cW-W 9 A.G1266 A.A1269 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#40[1] bps=10 strand-1 5'-AAGGUGGGCC-3' bp-type ..|||||||. strand-2 3'-CAUCACCCGC-5' helix-form ...AAAAAx 1 A.A1288 A.C1249 A-C ~rHoogsteen 25-XXV tHW tM-W 2 A.A1289 A.A1248 A-A -- 05-V tHW tM-W 3 A.G1290 A.U1247 G-U Wobble 28-XXVIII cWW cW-W 4 A.G1291 A.C1246 G-C WC 19-XIX cWW cW-W 5 A.U1292 A.A1245 U-A WC 20-XX cWW cW-W 6 A.G1293 A.C1244 G-C WC 19-XIX cWW cW-W 7 A.G1294 A.C1243 G-C WC 19-XIX cWW cW-W 8 A.G1295 A.C1242 G-C WC 19-XIX cWW cW-W 9 A.C1296 A.G1241 C-G WC 19-XIX cWW cW-W 10 A.C1297 A.C1298 C+C Platform -- cSH cm+M -------------------------------------------------------------------------- helix#41[1] bps=13 strand-1 5'-UAUAAUCGCGGAU-3' bp-type ....|||||||.. strand-2 3'-UAAGUGGCGCCGA-5' helix-form .x....AA.A.x 1 A.U1345 A.U1376 U+U -- 13-XIII tWW tW+W 2 A.A1346 A.A1375 A+A -- 02-II tHH tM+M 3 A.U1348 A.A1374 U-A rHoogsteen 24-XXIV tWH tW-M 4 A.A1349 A.G1373 A-G Sheared 11-XI tHS tM-m 5 A.A1350 A.U1372 A-U WC 20-XX cWW cW-W 6 A.U1351 A.G1371 U-G Wobble 28-XXVIII cWW cW-W 7 A.C1352 A.G1370 C-G WC 19-XIX cWW cW-W 8 A.G1353 A.C1369 G-C WC 19-XIX cWW cW-W 9 A.C1354 A.G1368 C-G WC 19-XIX cWW cW-W 10 A.G1355 A.C1367 G-C WC 19-XIX cWW cW-W 11 A.G1356 A.C1366 G-C WC 19-XIX cWW cW-W 12 A.A1357 A.G1365 A-G Imino 08-VIII cWW cW-W 13 A.U1358 A.A1363 U+A rWC 21-XXI tWW tW+W -------------------------------------------------------------------------- helix#42[7] bps=44 strand-1 5'-CGcCcGUcCGCCAUGGGAGCGGGCUCUACCCGAGUCGCCGGCCU-3' bp-type ||..||.|||||.|||..||||||.||||||..|.||||.|||. strand-2 3'-GCAAGCUGGCGGGGUCAGUGCCCGGGAUGGGAGCCGCGGACGGG-5' helix-form x..xA..xAAAA..........AAAAAAAA.x..AAAA.xAA. 1 A.C1399 A.G1504 C-G WC 19-XIX cWW cW-W 2 A.G1401 A.C1501 G-C WC 19-XIX cWW cW-W 3 A.4OC1402 A.A1500 c-A -- -- cWW cW-W 4 A.C1403 A.A1499 C-A -- -- cSW cm-W 5 A.5MC1404 A.G1497 c-G WC 19-XIX cWW cW-W 6 A.G1405 A.C1496 G-C WC 19-XIX cWW cW-W 7 A.U1406 A.U1495 U-U -- -- cWW cW-W 8 A.5MC1407 A.G1494 c-G WC 19-XIX cWW cW-W 9 A.C1409 A.G1491 C-G WC 19-XIX cWW cW-W 10 A.G1410 A.C1490 G-C WC 19-XIX cWW cW-W 11 A.C1411 A.G1489 C-G WC 19-XIX cWW cW-W 12 A.C1412 A.G1488 C-G WC 19-XIX cWW cW-W 13 A.A1413 A.G1487 A-G Imino 08-VIII cWW cW-W 14 A.U1414 A.G1486 U-G Wobble 28-XXVIII cWW cW-W 15 A.G1415 A.U1485 G-U Wobble 28-XXVIII cWW cW-W 16 A.G1416 A.C1484 G-C WC 19-XIX cWW cW-W 17 A.G1417 A.A1483 G-A Sheared 11-XI tSH tm-M 18 A.A1418 A.G1482 A-G Sheared 11-XI tHS tM-m 19 A.G1419 A.U1481 G-U Wobble 28-XXVIII cWW cW-W 20 A.C1420 A.G1480 C-G WC 19-XIX cWW cW-W 21 A.G1421 A.C1479 G-C WC 19-XIX cWW cW-W 22 A.G1422 A.C1478 G-C WC 19-XIX cWW cW-W 23 A.G1423 A.C1477 G-C WC 19-XIX cWW cW-W 24 A.C1424 A.G1476 C-G WC 19-XIX cWW cW-W 25 A.U1425 A.G1475 U-G -- -- cWW cW-W 26 A.C1426 A.G1474 C-G WC 19-XIX cWW cW-W 27 A.U1427 A.A1473 U-A WC 20-XX cWW cW-W 28 A.A1428 A.U1472 A-U WC 20-XX cWW cW-W 29 A.C1429 A.G1471 C-G WC 19-XIX cWW cW-W 30 A.C1430 A.G1470 C-G WC 19-XIX cWW cW-W 31 A.C1431 A.G1469 C-G WC 19-XIX cWW cW-W 32 A.G1432 A.A1468 G-A Sheared 11-XI tSH tm-M 33 A.A1434 A.G1467 A-G Sheared 11-XI tHS tM-m 34 A.G1435 A.C1466 G-C WC 19-XIX cWW cW-W 35 A.U1436 A.C1465 U-C -- -- cWW cW-W 36 A.C1437 A.G1464 C-G WC 19-XIX cWW cW-W 37 A.G1438 A.C1463 G-C WC 19-XIX cWW cW-W 38 A.C1439 A.G1462 C-G WC 19-XIX cWW cW-W 39 A.C1440 A.G1461 C-G WC 19-XIX cWW cW-W 40 A.G1441 A.A1460 G-A Sheared 11-XI tSH tm-M 41 A.G1447 A.C1459 G-C WC 19-XIX cWW cW-W 42 A.C1448 A.G1455 C-G WC 19-XIX cWW cW-W 43 A.C1449 A.G1454 C-G WC 19-XIX cWW cW-W 44 A.U1450 A.G1453 U+G -- -- t.W t.+W -------------------------------------------------------------------------- helix#43[1] bps=10 strand-1 5'-AGCUGUACCG-3' bp-type |||||||||. strand-2 3'-UCGGCGUGGa-5' helix-form AA....AA. 1 A.A1507 A.U1528 A-U WC 20-XX cWW cW-W 2 A.G1508 A.C1527 G-C WC 19-XIX cWW cW-W 3 A.C1509 A.G1526 C-G WC 19-XIX cWW cW-W 4 A.U1510 A.G1525 U-G Wobble 28-XXVIII 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.C1514 A.G1521 C-G WC 19-XIX cWW cW-W 9 A.C1515 A.G1520 C-G WC 19-XIX cWW cW-W 10 A.G1516 A.MA6/1519 G-a -- -- tWH tW-M **************************************************************************** List of 97 stems Note: a stem is defined as a helix consisting of only 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'-UCC-3' bp-type ||| strand-2 3'-AGG-5' helix-form AA 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.C19 A.G916 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#12] bps=4 strand-1 5'-GGGU-3' bp-type |||| strand-2 3'-CCCA-5' helix-form AA. 1 A.G27 A.C556 G-C WC 19-XIX cWW cW-W 2 A.G28 A.C555 G-C WC 19-XIX cWW cW-W 3 A.G29 A.C554 G-C WC 19-XIX 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 AAAA 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[#1] bps=6 strand-1 5'-GCGGCG-3' bp-type |||||| strand-2 3'-CGCCGC-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.G44 A.C398 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#1] bps=2 strand-1 5'-UG-3' bp-type || strand-2 3'-GC-5' helix-form . 1 A.U45 A.G396 U-G Wobble 28-XXVIII cWW cW-W 2 A.G46 A.C395 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#2] bps=3 strand-1 5'-GAC-3' bp-type ||| strand-2 3'-UUG-5' helix-form .. 1 A.G52 A.U359 G-U Wobble 28-XXVIII 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[#3] bps=3 strand-1 5'-UGC-3' bp-type ||| strand-2 3'-ACG-5' helix-form A. 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[#4] 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[#4] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.G66 A.C103 G-C WC 19-XIX cWW cW-W 2 A.C67 A.G102 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#4] bps=10 strand-1 5'-GGCCGCGGGG-3' bp-type |||||||||| strand-2 3'-CUGGUGCCUC-5' helix-form AAA.AAA.. 1 A.G69 A.C99 G-C WC 19-XIX cWW cW-W 2 A.G70 A.U98 G-U Wobble 28-XXVIII cWW cW-W 3 A.C73 A.G97 C-G WC 19-XIX cWW cW-W 4 A.C74 A.G96 C-G WC 19-XIX cWW cW-W 5 A.G75 A.U95 G-U Wobble 28-XXVIII cWW cW-W 6 A.C76 A.G93 C-G WC 19-XIX cWW cW-W 7 A.G77 A.C92 G-C WC 19-XIX cWW cW-W 8 A.G78 A.C91 G-C WC 19-XIX cWW cW-W 9 A.G79 A.U90 G-U Wobble 28-XXVIII cWW cW-W 10 A.G80 A.C89 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#12[#6] bps=3 strand-1 5'-GUG-3' bp-type ||| strand-2 3'-CAC-5' helix-form AA 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#13[#8] bps=8 strand-1 5'-GCGUGGGU-3' bp-type |||||||| strand-2 3'-UGCGCCCG-5' helix-form .A..AA. 1 A.G122 A.U239 G-U Wobble 28-XXVIII cWW cW-W 2 A.C123 A.G238 C-G WC 19-XIX cWW cW-W 3 A.G124 A.C237 G-C WC 19-XIX cWW cW-W 4 A.U125 A.G236 U-G Wobble 28-XXVIII 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.U129 A.G232 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#14[#8] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form . 1 A.C131 A.G231 C-G WC 19-XIX cWW cW-W 2 A.C132 A.G230 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#15[#8] bps=7 strand-1 5'-CCGGAAG-3' bp-type ||||||| strand-2 3'-GGCCUUC-5' helix-form AAAAAA 1 A.C136 A.G227 C-G WC 19-XIX cWW cW-W 2 A.C137 A.G226 C-G WC 19-XIX cWW cW-W 3 A.G138 A.C225 G-C WC 19-XIX cWW cW-W 4 A.G139 A.C224 G-C WC 19-XIX cWW cW-W 5 A.A140 A.U223 A-U WC 20-XX cWW cW-W 6 A.A141 A.U222 A-U WC 20-XX cWW cW-W 7 A.G142 A.C221 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#16[#9] bps=5 strand-1 5'-GGGGG-3' bp-type ||||| strand-2 3'-CCCCC-5' helix-form AAAA 1 A.G144 A.C178 G-C WC 19-XIX cWW cW-W 2 A.G145 A.C177 G-C WC 19-XIX cWW cW-W 3 A.G146 A.C176 G-C WC 19-XIX cWW cW-W 4 A.G147 A.C175 G-C WC 19-XIX cWW cW-W 5 A.G148 A.C174 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#17[#9] bps=6 strand-1 5'-CCCGGG-3' bp-type |||||| strand-2 3'-GGGCUC-5' helix-form AAA.. 1 A.C153 A.G168 C-G WC 19-XIX cWW cW-W 2 A.C154 A.G167 C-G WC 19-XIX cWW cW-W 3 A.C155 A.G166 C-G WC 19-XIX cWW cW-W 4 A.G156 A.C165 G-C WC 19-XIX cWW cW-W 5 A.G157 A.U164 G-U Wobble 28-XXVIII cWW cW-W 6 A.G158 A.C163 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#18[#9] bps=4 strand-1 5'-GGAC-3' bp-type |||| strand-2 3'-CCUG-5' helix-form AAA 1 A.G183 A.C194 G-C WC 19-XIX cWW cW-W 2 A.G184 A.C193 G-C WC 19-XIX cWW cW-W 3 A.A185 A.U192 A-U WC 20-XX cWW cW-W 4 A.C186 A.G191 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#19[#9] bps=5 strand-1 5'-CGCCC-3' bp-type ||||| strand-2 3'-GUGGG-5' helix-form A.AA 1 A.C188 A.G190^K C-G WC 19-XIX cWW cW-W 2 A.G189 A.U190^J G-U Wobble 28-XXVIII cWW cW-W 3 A.C190 A.G190^I C-G WC 19-XIX cWW cW-W 4 A.C190^A A.G190^H C-G WC 19-XIX cWW cW-W 5 A.C190^B A.G190^G C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#20[#8] bps=4 strand-1 5'-GGGC-3' bp-type |||| strand-2 3'-CCCG-5' helix-form AA. 1 A.G198 A.C219 G-C WC 19-XIX cWW cW-W 2 A.G199 A.C218 G-C WC 19-XIX cWW cW-W 3 A.G200 A.C217 G-C WC 19-XIX cWW cW-W 4 A.C201 A.G216 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#21[#7] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form AA 1 A.C240 A.G286 C-G WC 19-XIX cWW cW-W 2 A.C241 A.G285 C-G WC 19-XIX cWW cW-W 3 A.C242 A.G284 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#22[#11] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-CGG-5' helix-form A. 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#23[#10] bps=8 strand-1 5'-UUGGUGGG-3' bp-type |||||||| strand-2 3'-AACCACCC-5' helix-form .AAAAA. 1 A.U252 A.A274 U-A WC 20-XX cWW cW-W 2 A.U253 A.A273 U-A 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.C268 G-C WC 19-XIX cWW cW-W 8 A.G259 A.C267 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#24[#6] bps=4 strand-1 5'-GCCG-3' bp-type |||| strand-2 3'-CGGC-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.C291 A.G309 C-G WC 19-XIX cWW cW-W 4 A.G292 A.C308 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#25[#6] 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#26[#5] bps=5 strand-1 5'-GGGGC-3' bp-type ||||| strand-2 3'-CCCCG-5' helix-form AAAA 1 A.G316 A.C337 G-C WC 19-XIX cWW cW-W 2 A.G317 A.C336 G-C WC 19-XIX 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.C320 A.G333 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#27[#5] bps=4 strand-1 5'-CUCC-3' bp-type |||| strand-2 3'-GAGG-5' helix-form AAA 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#28[#1] bps=3 strand-1 5'-CCG-3' bp-type ||| strand-2 3'-GGC-5' helix-form .A 1 A.C369 A.G392 C-G WC 19-XIX cWW cW-W 2 A.C370 A.G391 C-G WC 19-XIX cWW cW-W 3 A.G371 A.C390 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#29[#1] 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#30[#13] bps=4 strand-1 5'-GGAG-3' bp-type |||| strand-2 3'-CCUC-5' helix-form AAA 1 A.G406 A.C436 G-C WC 19-XIX cWW cW-W 2 A.G407 A.C435 G-C WC 19-XIX cWW cW-W 3 A.A408 A.U434 A-U WC 20-XX cWW cW-W 4 A.G409 A.C433 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#31[#13] bps=4 strand-1 5'-GCCC-3' bp-type |||| strand-2 3'-UGGG-5' helix-form .AA 1 A.G416 A.U427 G-U Wobble 28-XXVIII cWW cW-W 2 A.C417 A.G426 C-G WC 19-XIX 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#32[#13] bps=5 strand-1 5'-CCCGG-3' bp-type ||||| strand-2 3'-GGGCC-5' helix-form .AAA 1 A.C442 A.G492 C-G WC 19-XIX cWW cW-W 2 A.C443 A.G491 C-G WC 19-XIX cWW cW-W 3 A.C444 A.G490 C-G 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#33[#13] bps=4 strand-1 5'-CCCC-3' bp-type |||| strand-2 3'-GGGG-5' helix-form AAA 1 A.C455 A.G477 C-G WC 19-XIX cWW cW-W 2 A.C456 A.G476 C-G WC 19-XIX cWW cW-W 3 A.C457 A.G475 C-G WC 19-XIX cWW cW-W 4 A.C458 A.G474 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#34[#15] bps=5 strand-1 5'-GCGCC-3' bp-type ||||| strand-2 3'-CGCGG-5' helix-form AAAA 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.G502 A.C543 G-C WC 19-XIX 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#35[#16] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form AA 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#36[#15] bps=5 strand-1 5'-CUCCG-3' bp-type ||||| strand-2 3'-GAGGC-5' helix-form .AAA 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#37[#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.7MG527 C-g WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#38[#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#39[#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#40[#23] bps=4 strand-1 5'-GCGU-3' bp-type |||| strand-2 3'-CGCG-5' helix-form AA. 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.G579 A.C762 G-C WC 19-XIX cWW cW-W 4 A.U580 A.G761 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#41[#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#42[#20] bps=7 strand-1 5'-GCCUGGG-3' bp-type ||||||| strand-2 3'-CGGACUC-5' helix-form .AAAAA 1 A.G588 A.C651 G-C WC 19-XIX cWW cW-W 2 A.C589 A.G650 C-G WC 19-XIX cWW cW-W 3 A.C590 A.G649 C-G WC 19-XIX 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.G593 A.U646 G-U Wobble 28-XXVIII cWW cW-W 7 A.G594 A.C645 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#43[#20] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form . 1 A.C596 A.G644 C-G WC 19-XIX cWW cW-W 2 A.G597 A.C643 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#44[#20] bps=8 strand-1 5'-UCCCAUGU-3' bp-type |||||||| strand-2 3'-AGGGUGCG-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.C600 A.G638 C-G WC 19-XIX cWW cW-W 4 A.C601 A.G637 C-G WC 19-XIX cWW cW-W 5 A.A602 A.U636 A-U WC 20-XX cWW cW-W 6 A.U603 A.G635 U-G Wobble 28-XXVIII 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#45[#19] bps=6 strand-1 5'-CCACGG-3' bp-type |||||| strand-2 3'-GGUGCC-5' helix-form AAA.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.A614 A.U626 A-U WC 20-XX cWW cW-W 4 A.C615 A.G625 C-G WC 19-XIX 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#46[#20] bps=3 strand-1 5'-ACG-3' bp-type ||| strand-2 3'-UGC-5' helix-form A. 1 A.A655 A.U751 A-U WC 20-XX cWW cW-W 2 A.C656 A.G750 C-G WC 19-XIX cWW cW-W 3 A.G657 A.C749 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#47[#20] bps=5 strand-1 5'-GUGGG-3' bp-type ||||| strand-2 3'-CACCU-5' helix-form AAA. 1 A.G658 A.C747 G-C WC 19-XIX cWW cW-W 2 A.U659 A.A746 U-A WC 20-XX cWW cW-W 3 A.G660 A.C745 G-C WC 19-XIX cWW cW-W 4 A.G661 A.C744 G-C WC 19-XIX cWW cW-W 5 A.G662 A.U743 G-U Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#48[#20] bps=7 strand-1 5'-GGGUGGU-3' bp-type ||||||| strand-2 3'-UCCACCG-5' helix-form .AAAA. 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.U669 A.A737 U-A WC 20-XX 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#49[#20] bps=6 strand-1 5'-UCCCGG-3' bp-type |||||| strand-2 3'-AGGGCC-5' helix-form AAAAA 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.C681 A.G709 C-G WC 19-XIX cWW cW-W 5 A.G682 A.C708 G-C WC 19-XIX cWW cW-W 6 A.G683 A.C707 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#50[#21] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 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#51[#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#52[#23] bps=6 strand-1 5'-GCGUGG-3' bp-type |||||| strand-2 3'-CGCACC-5' helix-form .AAAA 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#53[#23] 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#54[#23] bps=4 strand-1 5'-CCGG-3' bp-type |||| strand-2 3'-GGCC-5' helix-form A.A 1 A.C783 A.G799 C-G WC 19-XIX cWW cW-W 2 A.C784 A.G798 C-G WC 19-XIX 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#55[#17] bps=6 strand-1 5'-GCGCGC-3' bp-type |||||| strand-2 3'-CGCGCG-5' helix-form AAA.. 1 A.G821 A.C879 G-C WC 19-XIX cWW cW-W 2 A.C822 A.G878 C-G WC 19-XIX cWW cW-W 3 A.G823 A.C877 G-C WC 19-XIX cWW cW-W 4 A.C824 A.G876 C-G WC 19-XIX cWW cW-W 5 A.G825 A.C875 G-C WC 19-XIX cWW cW-W 6 A.C826 A.G874 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#56[#24] bps=10 strand-1 5'-GGUCUCUGGG-3' bp-type |||||||||| strand-2 3'-CCGGGGGUCC-5' helix-form A....A... 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.U831 A.G855 U-G Wobble 28-XXVIII cWW cW-W 4 A.C832 A.G854 C-G WC 19-XIX cWW cW-W 5 A.U833 A.G853 U-G Wobble 28-XXVIII cWW cW-W 6 A.C834 A.G852 C-G WC 19-XIX 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.G837 A.C849 G-C WC 19-XIX cWW cW-W 10 A.G838 A.C848 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#57[#24] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 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#58[#25] 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#59[#25] bps=4 strand-1 5'-GGCC-3' bp-type |||| strand-2 3'-UCGG-5' helix-form .AA 1 A.G894 A.U905 G-U Wobble 28-XXVIII cWW cW-W 2 A.G895 A.C904 G-C WC 19-XIX 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#60[#12] bps=2 strand-1 5'-UG-3' bp-type || strand-2 3'-AC-5' helix-form . 1 A.U921 A.A1396 U-A WC 20-XX cWW cW-W 2 A.G922 A.C1395 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#61[#12] bps=3 strand-1 5'-ACG-3' bp-type ||| strand-2 3'-UGU-5' helix-form A. 1 A.A923 A.U1393 A-U WC 20-XX cWW cW-W 2 A.C924 A.G1392 C-G WC 19-XIX cWW cW-W 3 A.G925 A.U1391 G-U Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#62[#12] bps=7 strand-1 5'-GGGCCCG-3' bp-type ||||||| strand-2 3'-UCCGGGC-5' helix-form .AAAAA 1 A.G927 A.U1390 G-U Wobble 28-XXVIII cWW cW-W 2 A.G928 A.C1389 G-C WC 19-XIX cWW cW-W 3 A.G929 A.C1388 G-C WC 19-XIX cWW cW-W 4 A.C930 A.G1387 C-G WC 19-XIX cWW cW-W 5 A.C931 A.G1386 C-G WC 19-XIX cWW cW-W 6 A.C932 A.G1385 C-G WC 19-XIX cWW cW-W 7 A.G933 A.C1384 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#63[#12] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-UG-5' helix-form A 1 A.A935 A.U1380 A-U WC 20-XX cWW cW-W 2 A.C936 A.G1379 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#64[#12] bps=5 strand-1 5'-GCGGU-3' bp-type ||||| strand-2 3'-CGCUA-5' helix-form .A.. 1 A.G939 A.C1344 G-C WC 19-XIX cWW cW-W 2 A.C940 A.G1343 C-G WC 19-XIX cWW cW-W 3 A.G941 A.C1342 G-C WC 19-XIX cWW cW-W 4 A.G942 A.U1341 G-U Wobble 28-XXVIII cWW cW-W 5 A.U943 A.A1340 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#65[#26] bps=8 strand-1 5'-AGCAUGUG-3' bp-type |||||||| strand-2 3'-UCGUGCAC-5' helix-form .....AA 1 A.A946 A.U1235 A-U WC 20-XX cWW cW-W 2 A.G947 A.C1234 G-C WC 19-XIX cWW cW-W 3 A.C948 A.G1233 C-G WC 19-XIX cWW cW-W 4 A.A949 A.U1232 A-U WC 20-XX cWW cW-W 5 A.U950 A.G1231 U-G Wobble 28-XXVIII cWW cW-W 6 A.G951 A.C1230 G-C WC 19-XIX cWW cW-W 7 A.U952 A.A1229 U-A WC 20-XX cWW cW-W 8 A.G953 A.C1228 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#66[#26] bps=2 strand-1 5'-GU-3' bp-type || strand-2 3'-CA-5' helix-form B 1 A.G954 A.C1226 G-C WC 19-XIX cWW cW-W 2 A.U955 A.A1225 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#67[#27] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form A 1 A.C962 A.G973 C-G WC 19-XIX cWW cW-W 2 A.G963 A.C972 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#68[#29] bps=7 strand-1 5'-CCAGGCC-3' bp-type ||||||| strand-2 3'-GGUCCGG-5' helix-form AAAA.. 1 A.C984 A.G1221 C-G WC 19-XIX cWW cW-W 2 A.C985 A.G1220 C-G WC 19-XIX cWW cW-W 3 A.A986 A.U1219 A-U WC 20-XX cWW cW-W 4 A.G987 A.C1218 G-C WC 19-XIX cWW cW-W 5 A.G988 A.C1217 G-C WC 19-XIX cWW cW-W 6 A.C989 A.G1216 C-G WC 19-XIX cWW cW-W 7 A.C990 A.G1215 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#69[#32] bps=4 strand-1 5'-CUAG-3' bp-type |||| strand-2 3'-GAUC-5' helix-form .A. 1 A.C999 A.G1042 C-G WC 19-XIX cWW cW-W 2 A.U1000 A.A1041 U-A WC 20-XX cWW cW-W 3 A.A1001 A.U1040 A-U WC 20-XX cWW cW-W 4 A.G1002 A.C1039 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#70[#30] bps=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form . 1 A.C1006 A.G1023 C-G WC 19-XIX cWW cW-W 2 A.C1007 A.G1022 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#71[#30] bps=4 strand-1 5'-GGGU-3' bp-type |||| strand-2 3'-UCCG-5' helix-form .A. 1 A.G1009 A.U1020 G-U Wobble 28-XXVIII cWW cW-W 2 A.G1010 A.C1019 G-C WC 19-XIX cWW cW-W 3 A.G1011 A.C1018 G-C WC 19-XIX cWW cW-W 4 A.U1012 A.G1017 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#72[#31] bps=3 strand-1 5'-CCC-3' bp-type ||| strand-2 3'-GGG-5' helix-form AA 1 A.C1028 A.G1033 C-G WC 19-XIX cWW cW-W 2 A.C1029 A.G1032 C-G WC 19-XIX cWW cW-W 3 A.C1030 A.G1031 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#73[#32] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form . 1 A.G1047 A.C1210 G-C WC 19-XIX cWW cW-W 2 A.G1048 A.C1209 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#74[#32] bps=3 strand-1 5'-GCU-3' bp-type ||| strand-2 3'-CgG-5' helix-form AA 1 A.G1050 A.C1208 G-C WC 19-XIX cWW cW-W 2 A.C1051 A.2MG1207 C-g WC 19-XIX cWW cW-W 3 A.U1052 A.G1206 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#75[#32] bps=2 strand-1 5'-UG-3' bp-type || strand-2 3'-AC-5' helix-form . 1 A.U1056 A.A1204 U-A WC 20-XX cWW cW-W 2 A.G1057 A.C1203 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#76[#32] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-UGG-5' helix-form .A 1 A.G1058 A.U1199 G-U Wobble 28-XXVIII cWW cW-W 2 A.C1059 A.G1198 C-G WC 19-XIX cWW cW-W 3 A.C1060 A.G1197 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#77[#33] bps=6 strand-1 5'-GCUCGU-3' bp-type |||||| strand-2 3'-CGAGCA-5' helix-form A.AAA 1 A.G1068 A.C1107 G-C WC 19-XIX cWW cW-W 2 A.C1069 A.G1106 C-G WC 19-XIX cWW cW-W 3 A.U1070 A.A1105 U-A WC 20-XX cWW cW-W 4 A.C1071 A.G1104 C-G WC 19-XIX cWW cW-W 5 A.G1072 A.C1103 G-C WC 19-XIX cWW cW-W 6 A.U1073 A.A1102 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#78[#33] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-UGG-5' helix-form .A 1 A.G1074 A.U1083 G-U Wobble 28-XXVIII cWW cW-W 2 A.C1075 A.G1082 C-G WC 19-XIX cWW cW-W 3 A.C1076 A.G1081 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#79[#34] bps=3 strand-1 5'-GGG-3' bp-type ||| strand-2 3'-CCC-5' helix-form AA 1 A.G1087 A.C1098 G-C WC 19-XIX cWW cW-W 2 A.G1088 A.C1097 G-C WC 19-XIX cWW cW-W 3 A.G1089 A.C1096 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#80[#35] bps=4 strand-1 5'-CCCC-3' bp-type |||| strand-2 3'-GGGG-5' helix-form .AA 1 A.C1113 A.G1187 C-G WC 19-XIX cWW cW-W 2 A.C1114 A.G1186 C-G WC 19-XIX cWW cW-W 3 A.C1115 A.G1185 C-G WC 19-XIX cWW cW-W 4 A.C1116 A.G1184 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#81[#36] bps=7 strand-1 5'-CCGUUAG-3' bp-type ||||||| strand-2 3'-GGCAAUC-5' helix-form A.A... 1 A.C1118 A.G1155 C-G WC 19-XIX cWW cW-W 2 A.C1119 A.G1154 C-G WC 19-XIX cWW cW-W 3 A.G1120 A.C1153 G-C WC 19-XIX cWW cW-W 4 A.U1121 A.A1152 U-A WC 20-XX cWW cW-W 5 A.U1122 A.A1151 U-A WC 20-XX cWW cW-W 6 A.A1123 A.U1150 A-U WC 20-XX cWW cW-W 7 A.G1124 A.C1149 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#82[#36] bps=3 strand-1 5'-CGG-3' bp-type ||| strand-2 3'-GCC-5' helix-form .. 1 A.C1132 A.G1142 C-G WC 19-XIX cWW cW-W 2 A.G1133 A.C1141 G-C WC 19-XIX cWW cW-W 3 A.G1134 A.C1140 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#83[#37] bps=5 strand-1 5'-CCCGC-3' bp-type ||||| strand-2 3'-GGGCG-5' helix-form AAAA 1 A.C1161 A.G1175 C-G WC 19-XIX cWW cW-W 2 A.C1162 A.G1174 C-G WC 19-XIX cWW cW-W 3 A.C1163 A.G1173 C-G WC 19-XIX cWW cW-W 4 A.G1164 A.C1172 G-C WC 19-XIX cWW cW-W 5 A.C1165 A.G1171 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#84[#40] bps=7 strand-1 5'-GCCCACU-3' bp-type ||||||| strand-2 3'-CGGGUGG-5' helix-form AAAA.. 1 A.G1241 A.C1296 G-C WC 19-XIX cWW cW-W 2 A.C1242 A.G1295 C-G WC 19-XIX cWW cW-W 3 A.C1243 A.G1294 C-G WC 19-XIX cWW cW-W 4 A.C1244 A.G1293 C-G WC 19-XIX cWW cW-W 5 A.A1245 A.U1292 A-U WC 20-XX cWW cW-W 6 A.C1246 A.G1291 C-G WC 19-XIX cWW cW-W 7 A.U1247 A.G1290 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#85[#38] bps=3 strand-1 5'-GCG-3' bp-type ||| strand-2 3'-CGC-5' helix-form AA 1 A.G1253 A.C1284 G-C WC 19-XIX cWW cW-W 2 A.C1254 A.G1283 C-G WC 19-XIX cWW cW-W 3 A.G1255 A.C1282 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#86[#39] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G1258 A.C1277 G-C WC 19-XIX cWW cW-W 2 A.C1259 A.G1276 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#87[#39] bps=4 strand-1 5'-CCCG-3' bp-type |||| strand-2 3'-GGGC-5' helix-form AAA 1 A.C1262 A.G1273 C-G WC 19-XIX cWW cW-W 2 A.C1263 A.G1272 C-G WC 19-XIX cWW cW-W 3 A.C1264 A.G1271 C-G WC 19-XIX cWW cW-W 4 A.G1265 A.C1270 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#88[#28] bps=7 strand-1 5'-UGGGGUC-3' bp-type ||||||| strand-2 3'-ACCCCAG-5' helix-form AAA.AA 1 A.U1308 A.A1329 U-A WC 20-XX cWW cW-W 2 A.G1309 A.C1328 G-C WC 19-XIX cWW cW-W 3 A.G1310 A.C1327 G-C WC 19-XIX cWW cW-W 4 A.G1311 A.C1326 G-C WC 19-XIX cWW cW-W 5 A.G1312 A.C1325 G-C WC 19-XIX cWW cW-W 6 A.U1313 A.A1324 U-A WC 20-XX cWW cW-W 7 A.C1314 A.G1323 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#89[#41] bps=7 strand-1 5'-AUCGCGG-3' bp-type ||||||| strand-2 3'-UGGCGCC-5' helix-form ..AA.A 1 A.A1350 A.U1372 A-U WC 20-XX cWW cW-W 2 A.U1351 A.G1371 U-G Wobble 28-XXVIII cWW cW-W 3 A.C1352 A.G1370 C-G WC 19-XIX cWW cW-W 4 A.G1353 A.C1369 G-C WC 19-XIX cWW cW-W 5 A.C1354 A.G1368 C-G WC 19-XIX cWW cW-W 6 A.G1355 A.C1367 G-C WC 19-XIX cWW cW-W 7 A.G1356 A.C1366 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#90[#42] bps=2 strand-1 5'-cG-3' bp-type || strand-2 3'-GC-5' helix-form A 1 A.5MC1404 A.G1497 c-G WC 19-XIX cWW cW-W 2 A.G1405 A.C1496 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#91[#42] bps=4 strand-1 5'-CGCC-3' bp-type |||| strand-2 3'-GCGG-5' helix-form AAA 1 A.C1409 A.G1491 C-G WC 19-XIX cWW cW-W 2 A.G1410 A.C1490 G-C WC 19-XIX cWW cW-W 3 A.C1411 A.G1489 C-G WC 19-XIX cWW cW-W 4 A.C1412 A.G1488 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#92[#42] bps=3 strand-1 5'-UGG-3' bp-type ||| strand-2 3'-GUC-5' helix-form .. 1 A.U1414 A.G1486 U-G Wobble 28-XXVIII cWW cW-W 2 A.G1415 A.U1485 G-U Wobble 28-XXVIII cWW cW-W 3 A.G1416 A.C1484 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#93[#42] bps=6 strand-1 5'-GCGGGC-3' bp-type |||||| strand-2 3'-UGCCCG-5' helix-form ....A 1 A.G1419 A.U1481 G-U Wobble 28-XXVIII cWW cW-W 2 A.C1420 A.G1480 C-G WC 19-XIX cWW cW-W 3 A.G1421 A.C1479 G-C WC 19-XIX cWW cW-W 4 A.G1422 A.C1478 G-C WC 19-XIX cWW cW-W 5 A.G1423 A.C1477 G-C WC 19-XIX cWW cW-W 6 A.C1424 A.G1476 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#94[#42] bps=6 strand-1 5'-CUACCC-3' bp-type |||||| strand-2 3'-GAUGGG-5' helix-form AAAAA 1 A.C1426 A.G1474 C-G WC 19-XIX cWW cW-W 2 A.U1427 A.A1473 U-A WC 20-XX cWW cW-W 3 A.A1428 A.U1472 A-U WC 20-XX cWW cW-W 4 A.C1429 A.G1471 C-G WC 19-XIX cWW cW-W 5 A.C1430 A.G1470 C-G WC 19-XIX cWW cW-W 6 A.C1431 A.G1469 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#95[#42] bps=4 strand-1 5'-CGCC-3' bp-type |||| strand-2 3'-GCGG-5' helix-form AAA 1 A.C1437 A.G1464 C-G WC 19-XIX cWW cW-W 2 A.G1438 A.C1463 G-C WC 19-XIX cWW cW-W 3 A.C1439 A.G1462 C-G WC 19-XIX cWW cW-W 4 A.C1440 A.G1461 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#96[#42] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-CGG-5' helix-form AA 1 A.G1447 A.C1459 G-C WC 19-XIX cWW cW-W 2 A.C1448 A.G1455 C-G WC 19-XIX cWW cW-W 3 A.C1449 A.G1454 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#97[#43] bps=9 strand-1 5'-AGCUGUACC-3' bp-type ||||||||| strand-2 3'-UCGGCGUGG-5' helix-form AA....AA 1 A.A1507 A.U1528 A-U WC 20-XX cWW cW-W 2 A.G1508 A.C1527 G-C WC 19-XIX cWW cW-W 3 A.C1509 A.G1526 C-G WC 19-XIX cWW cW-W 4 A.U1510 A.G1525 U-G Wobble 28-XXVIII 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.C1514 A.G1521 C-G WC 19-XIX cWW cW-W 9 A.C1515 A.G1520 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 24 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 [#2] -2 A.C47 A.G361 C-G WC 19-XIX cWW cW-W [#1] -3 A.U367 A.A393 U-A WC 20-XX cWW cW-W [#1] -4 A.U375 A.A389 U-A WC 20-XX cWW cW-W [#13] -5 A.G450 A.C483 G-C WC 19-XIX cWW cW-W [#17] -6 A.G575 A.C880 G-C WC 19-XIX cWW cW-W [#20] -7 A.G654 A.C754 G-C WC 19-XIX cWW cW-W [#20] -8 A.G673 A.C717 G-C WC 19-XIX cWW cW-W -- -9 A.C817 A.G1529 C-G WC 19-XIX cWW cW-W [#32] -10 A.G993 A.C1045 G-C WC 19-XIX cWW cW-W [#32] -11 A.U997 A.A1044 U-A WC 20-XX cWW cW-W [#32] -12 A.G1003^A A.C1038 G-C WC 19-XIX cWW cW-W [#32] -13 A.G1061 A.C1195 G-C WC 19-XIX cWW cW-W [#32] -14 A.C1063 A.G1193 C-G WC 19-XIX cWW cW-W [#36] -15 A.G1127 A.C1145 G-C WC 19-XIX cWW cW-W [#36] -16 A.C1128 A.G1143 C-G WC 19-XIX cWW cW-W [#37] -17 A.C1158 A.G1181 C-G WC 19-XIX cWW cW-W -- -18 A.G1224 A.C1362 G-C WC 19-XIX cWW cW-W [#26] -19 A.C1237 A.G1337 C-G WC 19-XIX cWW cW-W [#28] -20 A.C1303 A.G1334 C-G WC 19-XIX cWW cW-W [#42] -21 A.C1399 A.G1504 C-G WC 19-XIX cWW cW-W [#42] -22 A.G1401 A.C1501 G-C WC 19-XIX cWW cW-W [#42] -23 A.5MC1407 A.G1494 c-G WC 19-XIX cWW cW-W [#42] -24 A.G1435 A.C1466 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 22 coaxial stacks 1 Helix#1 contains 4 stems: [#5,#6,#28,#29] 2 Helix#4 contains 3 stems: [#9,#10,#11] 3 Helix#5 contains 2 stems: [#26,#27] 4 Helix#6 contains 3 stems: [#12,#24,#25] 5 Helix#8 contains 4 stems: [#13,#14,#15,#20] 6 Helix#9 contains 4 stems: [#19,#18,#16,#17] 7 Helix#12 contains 9 stems: [#4,#3,#1,#2,#60,#61,#62,#63,#64] 8 Helix#13 contains 4 stems: [#31,#30,#32,#33] 9 Helix#15 contains 2 stems: [#34,#36] 10 Helix#16 contains 2 stems: [#35,#37] 11 Helix#17 contains 2 stems: [#38,#55] 12 Helix#20 contains 7 stems: [#44,#43,#42,#46,#47,#48,#49] 13 Helix#23 contains 5 stems: [#41,#40,#52,#53,#54] 14 Helix#24 contains 2 stems: [#56,#57] 15 Helix#25 contains 2 stems: [#58,#59] 16 Helix#26 contains 2 stems: [#66,#65] 17 Helix#30 contains 2 stems: [#70,#71] 18 Helix#32 contains 5 stems: [#69,#73,#74,#75,#76] 19 Helix#33 contains 2 stems: [#77,#78] 20 Helix#36 contains 2 stems: [#82,#81] 21 Helix#39 contains 2 stems: [#86,#87] 22 Helix#42 contains 7 stems: [#90,#91,#92,#93,#94,#95,#96] **************************************************************************** List of 289 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 UG A.U5,A.G6 2 nts=2 GA A.G9,A.A26 3 nts=2 GC A.G31,A.C48 4 nts=2 CU A.C36,A.U37 5 nts=2 GU A.G44,A.U45 6 nts=2 GC A.G46,A.C366 7 nts=2 CU A.C47,A.U365 8 nts=2 CC A.C54,A.C352 9 nts=2 AU A.A55,A.U56 10 nts=2 GC A.G64,A.C67 11 nts=2 GU A.G80,A.U81 12 nts=2 CA A.C99,A.A101 13 nts=2 CG A.C103,A.G104 14 nts=2 GG A.G115,A.G289 15 nts=2 GG A.G129^A,A.G190^G 16 nts=2 CU A.C132,A.U133 17 nts=2 GA A.G142,A.A143 18 nts=2 GG A.G158,A.G159 19 nts=2 UA A.U173,A.A197 20 nts=2 UG A.U182,A.G183 21 nts=2 CC A.C187,A.C188 22 nts=2 UR A.U190^E,Q.ARG72 23 nts=2 GR A.G190^F,Q.ARG63 24 nts=2 CU A.C201,A.U203 25 nts=2 GG A.G231,A.G232 26 nts=2 AC A.A243,A.C245 27 nts=2 UG A.U244,A.G894 28 nts=2 CR A.C280,Q.ARG38 29 nts=2 GG A.G293,A.G305 30 nts=2 UG A.U296,A.G297 31 nts=2 GG A.G346,A.G347 32 nts=2 GG A.G350,A.G351 33 nts=2 AG A.A356,A.G357 34 nts=2 GG A.G380,A.G384 35 nts=2 GA A.G392,A.A393 36 nts=2 GC A.G396,A.C398 37 nts=2 UR A.U421,C.ARG127 38 nts=2 GG A.G423,A.G424 39 nts=2 CG A.C458,A.G459 40 nts=2 GG A.G492,A.G494 41 nts=2 AA A.A499,A.A547 42 nts=2 GA A.G505,A.A535 43 nts=2 CC A.C507,A.C508 44 nts=2 AA A.A509,A.A510 45 nts=2 CA A.C522,A.A523 46 nts=2 AC A.A533,A.C536 47 nts=2 GG A.G540,A.G541 48 nts=2 CG A.C545,A.G546 49 nts=2 UA A.U552,A.A553 50 nts=2 AG A.A563,A.G567 51 nts=2 GA A.G570,A.A873 52 nts=2 AA A.A573,A.A574 53 nts=2 GG A.G587,A.G755 54 nts=2 GU A.G597,A.U598 55 nts=2 GC A.G617,A.C618 56 nts=2 AG A.A632,A.G633 57 nts=2 AC A.A642,A.C643 58 nts=2 GC A.G644,A.C645 59 nts=2 GG A.G657,A.G658 60 nts=2 GG A.G688,A.G700 61 nts=2 CG A.C701,A.G703 62 nts=2 GG A.G727,A.G731 63 nts=2 CC A.C747,A.C748 64 nts=2 AG A.A777,A.G778 65 nts=2 UC A.U804,A.C805 66 nts=2 GU A.G818,A.U820 67 nts=2 GC A.G838,A.C840 68 nts=2 CU A.C862,A.U863 69 nts=2 CG A.C866,A.G867 70 nts=2 AG A.A872,A.G874 71 nts=2 CC A.C879,A.C880 72 nts=2 GG A.G898,A.G902 73 nts=2 CA A.C912,A.A913 74 nts=2 GA A.G922,A.A923 75 nts=2 GG A.G925,A.G927 76 nts=2 GG A.G926,A.G1505 77 nts=2 GA A.G933,A.A935 78 nts=2 UG A.U943,A.G944 79 nts=2 GG A.G945,A.G1337 80 nts=2 GG A.G953,A.G954 81 nts=2 UU A.U955,A.U956 82 nts=2 AA A.A958,A.A959 83 nts=2 AC A.A969,A.C970 84 nts=2 CU A.C990,A.U991 85 nts=2 AC A.A994,A.C995 86 nts=2 AG A.A1005,A.G1026 87 nts=2 CC A.C1007,A.C1008 88 nts=2 UG A.U1012,A.G1013 89 nts=2 CG A.C1030,A.G1030^A 90 nts=2 GG A.G1033,A.G1034 91 nts=2 GG A.G1048,A.G1050 92 nts=2 UA A.U1049,A.A1201 93 nts=2 CU A.C1054,A.U1196 94 nts=2 GG A.G1057,A.G1058 95 nts=2 GA A.G1074,A.A1102 96 nts=2 GG A.G1077,A.G1081 97 nts=2 GU A.G1089,A.U1090 98 nts=2 GG A.G1117,A.G1184 99 nts=2 GC A.G1138,A.C1140 100 nts=2 GG A.G1155,A.G1156 101 nts=2 CG A.C1165,A.G1166 102 nts=2 GC A.G1202,A.C1203 103 nts=2 AU A.A1204,A.U1205 104 nts=2 CC A.C1208,A.C1209 105 nts=2 CU A.C1210,A.U1211 106 nts=2 AG A.A1213,A.G1215 107 nts=2 AC A.A1227,A.C1228 108 nts=2 AG A.A1239,A.G1241 109 nts=2 UR A.U1240,G.ARG32 110 nts=2 GA A.G1255,A.A1279 111 nts=2 CC A.C1259,A.C1260 112 nts=2 GG A.G1265,A.G1266 113 nts=2 GG A.G1273,A.G1274 114 nts=2 CA A.C1284,A.A1285 115 nts=2 CC A.C1296,A.C1297 116 nts=2 CG A.C1378,A.G1379 117 nts=2 UR A.U1380,G.ARG3 118 nts=2 UC A.U1381,A.C1382 119 nts=2 UU A.U1390,A.U1391 120 nts=2 CG A.C1440,A.G1441 121 nts=2 GA A.G1442,A.A1446 122 nts=2 GG A.G1453,A.G1454 123 nts=2 AA A.A1492,A.A1493 124 nts=2 Gu A.G1497,A.UR3/1498 125 nts=2 AG A.A1507,A.G1530 126 nts=2 GG A.G1516,A.G1520 127 nts=2 AU A.A1531,A.U1532 128 nts=3 GAG A.G38,A.A397,A.G548 129 nts=3 GUU A.G39,A.U498,A.U405 130 nts=3 UAA A.U49,A.A364,A.A363 131 nts=3 GGG A.G61,A.G107,A.G108 132 nts=3 GGG A.G69,A.G68,A.G102 133 nts=3 GAU A.G144,A.A179,A.U180 134 nts=3 GAC A.G148,A.A149,A.C150 135 nts=3 GCU A.G168,A.C169,A.U170 136 nts=3 CCU A.C190^B,A.C190^C,A.U190^D 137 nts=3 GUG A.G190^K,A.U190^L,A.G191 138 nts=3 GGC A.G198,A.G220,A.C221 139 nts=3 GGY A.G247,A.G278,Q.TYR95 140 nts=3 GGU A.G259,A.G260,A.U261 141 nts=3 GCC A.G306,A.C307,A.C308 142 nts=3 CAC A.C314,A.A315,A.C330 143 nts=3 GAC A.G316,A.A338,A.C339 144 nts=3 GAG A.G331,A.A59,A.G354 145 nts=3 CUC A.C342,A.U343,A.C345 146 nts=3 GCU A.G371,A.C372,A.U387 147 nts=3 GAC A.G376,A.A389,A.C390 148 nts=3 AAG A.A414,A.A415,A.G416 149 nts=3 CUC A.C419,A.U420,A.C422 150 nts=3 GGG A.G446,A.G447,A.G485 151 nts=3 CAG A.C519,A.A520,A.G521 152 nts=3 CUC A.C562,A.U884,A.C883 153 nts=3 AAA A.A572,A.A864,A.A865 154 nts=3 GAU A.G577,A.A816,A.U813 155 nts=3 GAG A.G662,A.A663,A.G664 156 nts=3 CAA A.C732,A.A665,A.A733 157 nts=3 GGG A.G774,A.G775,A.G776 158 nts=3 AGA A.A815,A.G1529,A.A819 159 nts=3 GGG A.G821,A.G575,A.G881 160 nts=3 CUU A.C826,A.U827,A.U870 161 nts=3 GGU A.G890,A.G906,A.U905 162 nts=3 CAA A.C899,A.A900,A.A901 163 nts=3 AAG A.A914,A.A915,A.G916 164 nts=3 UUA A.U957,A.U960,A.A1225 165 nts=3 GAA A.G963,A.A964,A.A965 166 nts=3 gcA A.M2G966,A.5MC967,A.A968 167 nts=3 GAR A.G973,A.A974,N.ARG31 168 nts=3 GAG A.G993,A.A1046,A.G1047 169 nts=3 GGG A.G1002,A.G1003,A.G1003^A 170 nts=3 GGG A.G1009,A.G1021,A.G1022 171 nts=3 GGU A.G1023,A.G1024,A.U1025 172 nts=3 UAG A.U1056,A.A1055,A.G1206 173 nts=3 UGA A.U1078,A.G1079,A.A1080 174 nts=3 GGC A.G1087,A.G1099,A.C1100 175 nts=3 UUC A.U1091,A.U1095,A.C1096 176 nts=3 AAA A.A1093,A.A1092,A.A1183 177 nts=3 GUC A.G1134,A.U1135,A.C1137 178 nts=3 CGC A.C1158,A.G1160,A.C1161 179 nts=3 GAC A.G1187,A.A1188,A.C1189 180 nts=3 CAG A.C1249,A.A1248,A.G1290 181 nts=3 CAA A.C1267,A.A1268,A.A1269 182 nts=3 CUG A.C1314,A.U1315,A.G1316 183 nts=3 GAA A.G1338,A.A1339,A.A1340 184 nts=3 UAR A.U1348,A.A1346,G.ARG10 185 nts=3 GUc A.G1405,A.U1406,A.5MC1407 186 nts=3 CAU A.C1412,A.A1413,A.U1414 187 nts=3 CUC A.C1424,A.U1425,A.C1426 188 nts=3 GAG A.G1447,A.A1460,A.G1461 189 nts=3 CUC A.C1449,A.U1450,A.C1452 190 nts=3 GGG A.G1474,A.G1475,A.G1476 191 nts=3 GGG A.G1486,A.G1487,A.G1488 192 nts=3 Gaa A.G1517,A.MA6/1518,A.MA6/1519 193 nts=3 UCU A.U1542,A.C1543,A.U1544 194 nts=4 UAGA A.U17,A.A16,A.G15,A.A1396 195 nts=4 CUGG A.C19,A.U20,A.G21,A.G22 196 nts=4 GGGA A.G27,A.G557,A.G558,A.A559 197 nts=4 GAGG A.G52,A.A360,A.G361,A.G362 198 nts=4 UCAA A.U65,A.C381,A.A382,A.A383 199 nts=4 CGGG A.C110,A.G111,A.G112,A.G113 200 nts=4 GAAC A.G122,A.A120,A.A119,A.C240 201 nts=4 AAAA A.A162,A.A161,A.A160,A.A344 202 nts=4 CGAA A.C194,A.G181,A.A195,A.A196 203 nts=4 GAUG A.G227,A.A228,A.U229,A.G230 204 nts=4 AUGG A.A250,A.U252,A.G251,A.G266 205 nts=4 CUGC A.C369,A.U367,A.G394,A.C395 206 nts=4 CUGU A.C436,A.U437,A.G438,A.U495 207 nts=4 AACC A.A452,A.A453,A.C454,A.C455 208 nts=4 AGAG A.A460,A.G462,A.A463,A.G474 209 nts=4 GPGU A.G515,A.PSU516,A.G517,A.U531 210 nts=4 CGCG A.C528,A.G529,A.C518,A.G530 211 nts=4 UGUC A.U560,A.G566,A.U565,A.C564 212 nts=4 UGGU A.U580,A.G581,A.G758,A.U757 213 nts=4 GAGA A.G588,A.A753,A.G654,A.A655 214 nts=4 GGUA A.G594,A.G595,A.U641,A.A640 215 nts=4 CAAC A.C620,A.A621,A.A622,A.C623 216 nts=4 CUGU A.C651,A.U652,A.G752,A.U751 217 nts=4 GGGU A.G666,A.G741,A.G742,A.U743 218 nts=4 GAGU A.G683,A.A684,A.G685,A.U686 219 nts=4 CGGU A.C689,A.G690,A.G691,A.U692 220 nts=4 GAAR A.G730,A.A729,A.A728,O.ARG54 221 nts=4 CAGG A.C779,A.A780,A.G800,A.G799 222 nts=4 GAUU A.G786,A.A787,A.U788,A.U789 223 nts=4 CGGC A.C857,A.G858,A.G869,A.C868 224 nts=4 GGAU A.G887,A.G888,A.A889,A.U891 225 nts=4 AAUU A.A918,A.A919,A.U920,A.U921 226 nts=4 CAAG A.C936,A.A937,A.A938,A.G939 227 nts=4 AACC A.A946,A.A1236,A.C1237,A.C1336 228 nts=4 ACGG A.A977,A.C1223,A.G1222,A.G1221 229 nts=4 AUGC A.A996,A.U997,A.G998,A.C999 230 nts=4 CGAG A.C1030^B,A.G1030^C,A.A1030^D,A.G1031 231 nts=4 GCUC A.G1042,A.C1043,A.U992,A.C1045 232 nts=4 UCGU A.U1052,A.C1200,A.G1053,A.U1199 233 nts=4 UGCG A.U1126,A.G1127,A.C1128,A.G1139 234 nts=4 AAAG A.A1167,A.A1168,A.A1169,A.G1171 235 nts=4 GAGG A.G1175,A.A1176,A.G1177,A.G1178 236 nts=4 GCCC A.G1224,A.C1322,A.C1321,A.C1320 237 nts=4 CAAG A.C1262,A.A1261,A.A1275,A.G1276 238 nts=4 CCUA A.C1344,A.C934,A.U1345,A.A1377 239 nts=4 GAUC A.G1356,A.A1357,A.U1358,A.C1359 240 nts=4 UGGR A.U1372,A.G1373,A.G1347,I.ARG107 241 nts=4 CGcC A.C1399,A.G1401,A.4OC1402,A.C1403 242 nts=4 CAGU A.C1409,A.A1408,A.G1494,A.U1495 243 nts=4 GGGU A.G1416,A.G1417,A.G1482,A.U1481 244 nts=4 GAAC A.G1419,A.A1418,A.A1483,A.C1484 245 nts=5 GAGAG A.G7,A.A298,A.G299,A.A300,A.G301 246 nts=5 UUUAC A.U82,A.U83,A.U84,A.A88,A.C89 247 nts=5 AAUGC A.A262,A.A263,A.U264,A.G265,A.C267 248 nts=5 AAACG A.A279,A.A246,A.A282,A.C283,A.G284 249 nts=5 CACUG A.C320,A.A321,A.C322,A.U323,A.G324 250 nts=5 GGUAG A.G409,A.G410,A.U429,A.A411,A.G413 251 nts=5 GAAGG A.G584,A.A583,A.A759,A.G760,A.G761 252 nts=5 AAUAC A.A687,A.A704,A.U705,A.A706,A.C707 253 nts=5 CGCCC A.C764,A.G765,A.C812,A.C811,A.C810 254 nts=5 GAAAA A.G769,A.A768,A.A767,A.A766,A.A814 255 nts=5 CAUAG A.C783,A.A782,A.U801,A.A802,A.G803 256 nts=5 GAAAG A.G829,A.A828,A.A859,A.A860,A.G861 257 nts=5 GAAAW A.G1017,A.A1016,A.A1015,A.A1014,S.TRP34 258 nts=5 AGCCC A.A1035,A.G1036,A.C1037,A.C1038,A.C1039 259 nts=5 GCGGG A.G1124,A.C1145,A.G1144,A.G1143,A.G1142 260 nts=5 ACGUC A.A1191,A.C1192,A.G1193,A.U1194,A.C1195 261 nts=5 AAAAU A.A1350,A.A1349,A.A1374,A.A1375,A.U1376 262 nts=6 CAAAAC A.C153,A.A152,A.A151,A.A171,A.A172,A.C174 263 nts=6 GAAAAC A.G406,A.A496,A.A497,A.A439,A.A440,A.C442 264 nts=6 UGAAAC A.U427,A.G428,A.A430,A.A431,A.A432,A.C433 265 nts=6 UGGGGG A.U605,A.G606,A.G631,A.G630,A.G629,A.G628 266 nts=6 AAAGAC A.A607,A.A608,A.A609,A.G610,A.A611,A.C612 267 nts=6 AGGAAC A.A712,A.G713,A.G714,A.A715,A.A716,A.C717 268 nts=6 AGAACC A.A790,A.G791,A.A792,A.A794,A.C795,A.C796 269 nts=6 CAAAAC A.C893,A.A892,A.A907,A.A908,A.A909,A.C910 270 nts=6 GAAACF A.G1323,A.A1319,A.A978,A.A1318,A.C1317,N.PHE16 271 nts=6 cAACGA A.5MC1404,A.A1499,A.A1500,A.C1501,A.G1504,A.A1502 272 nts=6 CGGCCG A.C1431,A.G1432,A.G1467,A.C1466,A.C1465,A.G1464 273 nts=7 UAAACGU A.U375,A.A374,A.A373,A.A482,A.C483,A.G484,A.U486 274 nts=7 UUAAGGG A.U678,A.U677,A.A676,A.A675,A.G674,A.G673,A.G734 275 nts=7 CUAUUCC A.C962,A.U961,A.A983,A.U982,A.U981,A.C980,A.C979 276 nts=7 ACGCUGG A.A1067,A.C1066,A.G1064,A.C1063,A.U1062,A.G1061,A.G1197 277 nts=7 CAAAGGU A.C1118,A.A1179,A.A1180,A.A1157,A.G1181,A.G1182,A.U1159 278 nts=7 CGAACUC A.C1132,A.G1131,A.A1130,A.A1146,A.C1147,A.U1148,A.C1149 279 nts=7 GAAAAAA A.G1253,A.A1252,A.A1251,A.A1250,A.A1287,A.A1288,A.A1289 280 nts=7 AGCGAGC A.A1360,A.G1361,A.C1361^A,A.G976,A.A1363,A.G1365,A.C1366 281 nts=7 CUGAAAG A.C1437,A.U1436,A.G1435,A.A1434,A.A1433,A.A1468,A.G1469 282 nts=8 GUAUGAAA A.G286,A.U287,A.A288,A.U118,A.G117,A.A116,A.A51,A.A353 283 nts=8 GGAGCCGH A.G725,A.G724,A.A722,A.G721,A.C720,A.C719,A.G718,K.HIS116 284 nts=9 GUAAAGCPP A.G698,A.U697,A.A696,A.A695,A.A694,A.G693,A.C1539,A.PSU1540,A.PSU1541 285 nts=9 CGGAAAUUR A.C1335,A.G1300,A.G1334,A.A1333,A.A1332,A.A1306,A.U1307,A.U1308,M.ARG99 286 nts=10 CCAAGAAAGG A.C136,A.C135,A.A134,A.A325,A.G326,A.A109,A.A327,A.A329,A.G332,A.G333 287 nts=10 UGUGGGCAAC A.U1083,A.G1084,A.U1085,A.G1094,A.G1068,A.G1108,A.C1109,A.A1110,A.A1111,A.C1112 288 nts=10 AUGGGCUACR A.A1329,A.U1330,A.G1331,A.G1305,A.G1304,A.C1303,A.U1301,A.A1299,A.C1298,G.ARG114 289 nts=11 GACUAGGCAAC A.G477,A.A478,A.C479,A.U480,A.A451,A.G481,A.G450,A.C449,A.A448,A.A487,A.C488 **************************************************************************** Nucleotides not involved in stacking interactions nts=61 AUAAUUUGACAUUGCUAAUCUUUUGCACUCUCUCUGUCAAUCUAUCAUCUCACCAcGAAUC A.A8,A.U14,A.A50,A.A60,A.U202,A.U204,A.U368,A.G388,A.A412,A.C461,A.A532,A.U534,A.U561,A.G576,A.C596,A.U619,A.A653,A.A702,A.U723,A.C754,A.U793,A.U839,A.U841,A.U871,A.G971,A.C972,A.A975,A.C1027,A.U1065,A.C1071,A.U1086,A.C1113,A.U1125,A.C1129,A.U1136,A.G1190,A.U1212,A.C1214,A.A1238,A.A1256,A.U1257,A.C1270,A.U1278,A.A1280,A.U1281,A.C1282,A.A1286,A.U1302,A.C1362,A.U1364,A.C1383,A.A1394,A.C1395,A.C1397,A.A1398,A.5MC1400,A.G1443,A.A1451,A.A1503,A.U1506,A.C1533 **************************************************************************** List of 95 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.A16 A.U14 3.24 2 sugar O2'@A.G200 A.U65 3.04 3 sugar O4'@A.G108 A.G107 3.39 4 sugar O4'@A.A119 A.A120 3.25 5 phosphate O3'@A.U190^D A.G129^A 3.44 6 phosphate OP1@A.U190^E A.G129^A 3.41 7 sugar O4'@A.G190^G A.G129^A 3.03 8 phosphate OP2@A.A161 A.G159 3.01 9 sugar O2'@A.U343 A.A160 3.29 10 sugar O4'@A.G66 A.U173 3.12 11 phosphate OP1@A.A130 A.U190^E 3.28 12 sugar O4'@A.A143 A.A196 3.15 13 sugar O4'@A.U173 A.A197 2.95 14 sugar O4'@A.C221 A.A197 3.29 15 phosphate OP2@A.A263 A.U261 3.18 16 sugar O4'@A.A279 A.G281 3.15 17 phosphate OP2@A.G299 A.G297 3.18 18 sugar O4'@A.G301 A.A300 3.46 19 sugar O4'@A.C330 A.A315 3.34 20 phosphate OP2@A.G326 A.G324 3.17 21 sugar O4'@A.A134 A.A325 3.12 22 sugar O4'@A.A160 A.A344 3.40 23 sugar O4'@A.C345 A.G346 3.39 24 phosphate OP2@A.A364 A.G362 3.41 25 sugar O4'@A.C47 A.U365 2.93 26 phosphate OP2@A.A382 A.G380 3.08 27 sugar O4'@A.G384 A.A383 3.40 28 sugar O4'@A.C390 A.A389 3.02 29 sugar O4'@A.C422 A.G423 3.43 30 sugar O4'@A.A451 A.A452 3.06 31 sugar O2'@A.A460 A.G459 3.44 32 sugar O2'@A.G438 A.G494 2.81 33 sugar O4'@A.C504 A.A510 2.92 34 sugar O4'@A.U531 A.G517 2.98 35 sugar O4'@A.C518 A.G529 3.43 36 sugar O4'@A.C528 A.A535 3.25 37 sugar O4'@A.U20 A.A572 3.20 38 sugar O4'@A.C569 A.A574 2.93 39 sugar O2'@A.G881 A.G576 3.47 40 sugar O4'@A.U598 A.G597 3.40 41 sugar O4'@A.C701 A.G703 3.35 42 sugar O4'@A.G721 A.A722 3.06 43 sugar O2'@A.A722 A.U723 3.33 44 phosphate OP2@A.A729 A.G727 3.14 45 sugar O4'@A.G761 A.G760 3.39 46 phosphate OP2@A.G791 A.U789 3.12 47 sugar O2'@A.G1516 A.U793 3.17 48 sugar O4'@A.A816 A.A814 2.98 49 sugar O4'@A.G577 A.A816 3.10 50 sugar O4'@A.A819 A.C817 2.73 51 sugar O2'@A.U820 A.G818 3.02 52 sugar O4'@A.G570 A.U820 3.11 53 sugar O4'@A.A859 A.A828 2.99 54 sugar O4'@A.C868 A.A873 3.00 55 sugar O2'@A.G22 A.G885 3.19 56 phosphate OP2@A.A900 A.G898 3.08 57 phosphate OP2@A.A959 A.U957 3.35 58 other MG@A.MG1784 A.M2G966 3.17 59 sugar O2'@A.U1062 A.A968 2.93 60 sugar O4'@A.U950 A.G971 3.28 61 sugar O4'@A.G1365 A.G971 3.31 62 sugar O4'@A.U982 A.A983 3.20 63 phosphate OP2@A.A1015 A.G1013 3.46 64 phosphate OP2@A.G1030^C A.G1030^A 2.90 65 sugar O4'@A.G1047 A.A1046 3.37 66 sugar O4'@A.A1201 A.U1049 3.32 67 phosphate OP2@A.G1079 A.G1077 3.37 68 sugar O4'@A.U920 A.A1080 3.02 69 phosphate OP1@A.G1084 A.U1086 2.83 70 phosphate OP2@A.A1093 A.U1091 2.98 71 sugar O4'@A.U1095 A.A1093 2.91 72 sugar O4'@A.U1085 A.G1094 2.96 73 sugar O4'@A.C1075 A.A1101 3.09 74 phosphate OP2@A.U1136 A.C1137 3.10 75 sugar O4'@A.C1137 A.G1138 3.43 76 sugar O4'@A.C1140 A.G1138 3.48 77 sugar O4'@A.A1157 A.C1158 3.05 78 phosphate OP2@A.A1168 A.G1166 3.08 79 phosphate OP2@A.A1180 A.G1178 3.19 80 sugar O2'@A.U1211 A.A1213 2.74 81 sugar O4'@A.C1322 A.G1224 3.15 82 sugar O2'@A.C1303 A.A1238 3.09 83 sugar O4'@A.A1239 A.G1241 2.84 84 phosphate OP2@A.A1268 A.G1266 3.27 85 sugar O4'@A.U1126 A.A1280 3.21 86 sugar O2'@A.C1277 A.C1282 3.49 87 sugar O4'@A.A1285 A.A1286 3.01 88 sugar O4'@A.C1298 A.A1299 3.05 89 phosphate OP2@A.A1318 A.G1316 3.27 90 sugar O4'@A.C1336 A.G1337 3.00 91 sugar O4'@A.C1501 A.A1394 3.16 92 sugar O4'@A.C1452 A.G1453 2.94 93 other O3@A.NMY1822 A.G1491 3.47 94 phosphate OP2@A.G927 A.A1503 3.28 95 sugar O4'@A.G1504 A.G1505 3.41 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 33 hairpin loops 1 hairpin loop: nts=11; [9]; linked by [#1] summary: [1] 9 [A.12 A.22] 4 nts=11 UUUGAUCCUGG A.U12,A.U13,A.U14,A.G15,A.A16,A.U17,A.C18,A.C19,A.U20,A.G21,A.G22 nts=9 UUGAUCCUG A.U13,A.U14,A.G15,A.A16,A.U17,A.C18,A.C19,A.U20,A.G21 2 hairpin loop: nts=7; [5]; linked by [#11] summary: [1] 5 [A.80 A.89] 10 nts=7 GUUUUAC A.G80,A.U81,A.U82,A.U83,A.U84,A.A88,A.C89 nts=5 UUUUA A.U81,A.U82,A.U83,A.U84,A.A88 3 hairpin loop: nts=6; [4]; linked by [#17] 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 [#19] summary: [1] 4 [A.190 A.190] 5 nts=6 CCUUGG A.C190^B,A.C190^C,A.U190^D,A.U190^E,A.G190^F,A.G190^G nts=4 CUUG A.C190^C,A.U190^D,A.U190^E,A.G190^F 5 hairpin loop: nts=5; [3]; linked by [#20] summary: [1] 3 [A.201 A.216] 4 nts=5 CUUUG A.C201,A.U202,A.U203,A.U204,A.G216 nts=3 UUU A.U202,A.U203,A.U204 6 hairpin loop: nts=9; [7]; linked by [#23] summary: [1] 7 [A.259 A.267] 8 nts=9 GGUAAUGGC A.G259,A.G260,A.U261,A.A262,A.A263,A.U264,A.G265,A.G266,A.C267 nts=7 GUAAUGG A.G260,A.U261,A.A262,A.A263,A.U264,A.G265,A.G266 7 hairpin loop: nts=6; [4]; linked by [#25] 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 [#26] summary: [1] 12 [A.320 A.333] 5 nts=14 CACUGAGACACGGG A.C320,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.G333 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 [#27] 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 [#29] 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 [#31] 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=7; [5]; linked by [#33] summary: [1] 5 [A.458 A.474] 4 nts=7 CGACGAG A.C458,A.G459,A.A460,A.C461,A.G462,A.A463,A.G474 nts=5 GACGA A.G459,A.A460,A.C461,A.G462,A.A463 13 hairpin loop: nts=18; [16]; linked by [#35] summary: [1] 16 [A.507 A.524] 3 nts=18 CCAACUCCGPGCCAGCAG A.C507,A.C508,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 CAACUCCGPGCCAGCA A.C508,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 [#37] summary: [1] 4 [A.522 A.527] 2 nts=6 CAGCCg A.C522,A.A523,A.G524,A.C525,A.C526,A.7MG527 nts=4 AGCC A.A523,A.G524,A.C525,A.C526 15 hairpin loop: nts=7; [5]; linked by [#45] 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 [#50] 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 [#51] 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 [#54] 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=5; [3]; linked by [#56] summary: [1] 3 [A.838 A.848] 10 nts=5 GUCUC A.G838,A.U839,A.C840,A.U841,A.C848 nts=3 UCU A.U839,A.C840,A.U841 20 hairpin loop: nts=6; [4]; linked by [#57] 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 [#59] 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=10; [8]; linked by [#67] summary: [1] 8 [A.963 A.972] 2 nts=10 GAAgcAACGC A.G963,A.A964,A.A965,A.M2G966,A.5MC967,A.A968,A.A969,A.C970,A.G971,A.C972 nts=8 AAgcAACG A.A964,A.A965,A.M2G966,A.5MC967,A.A968,A.A969,A.C970,A.G971 23 hairpin loop: nts=6; [4]; linked by [#71] summary: [1] 4 [A.1012 A.1017] 4 nts=6 UGAAAG A.U1012,A.G1013,A.A1014,A.A1015,A.A1016,A.G1017 nts=4 GAAA A.G1013,A.A1014,A.A1015,A.A1016 24 hairpin loop: nts=6; [4]; linked by [#72] summary: [1] 4 [A.1030 A.1031] 3 nts=6 CGCGAG A.C1030,A.G1030^A,A.C1030^B,A.G1030^C,A.A1030^D,A.G1031 nts=4 GCGA A.G1030^A,A.C1030^B,A.G1030^C,A.A1030^D 25 hairpin loop: nts=6; [4]; linked by [#78] summary: [1] 4 [A.1076 A.1081] 3 nts=6 CGUGAG A.C1076,A.G1077,A.U1078,A.G1079,A.A1080,A.G1081 nts=4 GUGA A.G1077,A.U1078,A.G1079,A.A1080 26 hairpin loop: nts=8; [6]; linked by [#79] summary: [1] 6 [A.1089 A.1096] 3 nts=8 GUUAAGUC A.G1089,A.U1090,A.U1091,A.A1092,A.A1093,A.G1094,A.U1095,A.C1096 nts=6 UUAAGU A.U1090,A.U1091,A.A1092,A.A1093,A.G1094,A.U1095 27 hairpin loop: nts=7; [5]; linked by [#82] summary: [1] 5 [A.1134 A.1140] 3 nts=7 GUUCGGC A.G1134,A.U1135,A.U1136,A.C1137,A.G1138,A.G1139,A.C1140 nts=5 UUCGG A.U1135,A.U1136,A.C1137,A.G1138,A.G1139 28 hairpin loop: nts=6; [4]; linked by [#83] summary: [1] 4 [A.1165 A.1171] 5 nts=6 CGAAAG A.C1165,A.G1166,A.A1167,A.A1168,A.A1169,A.G1171 nts=4 GAAA A.G1166,A.A1167,A.A1168,A.A1169 29 hairpin loop: nts=6; [4]; linked by [#87] summary: [1] 4 [A.1265 A.1270] 4 nts=6 GGCAAC A.G1265,A.G1266,A.C1267,A.A1268,A.A1269,A.C1270 nts=4 GCAA A.G1266,A.C1267,A.A1268,A.A1269 30 hairpin loop: nts=10; [8]; linked by [#88] summary: [1] 8 [A.1314 A.1323] 7 nts=10 CUGCAACCCG A.C1314,A.U1315,A.G1316,A.C1317,A.A1318,A.A1319,A.C1320,A.C1321,A.C1322,A.G1323 nts=8 UGCAACCC A.U1315,A.G1316,A.C1317,A.A1318,A.A1319,A.C1320,A.C1321,A.C1322 31 hairpin loop: nts=12; [10]; linked by [#89] summary: [1] 10 [A.1356 A.1366] 7 nts=12 GAUCAGCCAUGC A.G1356,A.A1357,A.U1358,A.C1359,A.A1360,A.G1361,A.C1361^A,A.C1362,A.A1363,A.U1364,A.G1365,A.C1366 nts=10 AUCAGCCAUG A.A1357,A.U1358,A.C1359,A.A1360,A.G1361,A.C1361^A,A.C1362,A.A1363,A.U1364,A.G1365 32 hairpin loop: nts=6; [4]; linked by [#96] summary: [1] 4 [A.1449 A.1454] 3 nts=6 CUACGG A.C1449,A.U1450,A.A1451,A.C1452,A.G1453,A.G1454 nts=4 UACG A.U1450,A.A1451,A.C1452,A.G1453 33 hairpin loop: nts=6; [4]; linked by [#97] summary: [1] 4 [A.1515 A.1520] 9 nts=6 CGGaaG A.C1515,A.G1516,A.G1517,A.MA6/1518,A.MA6/1519,A.G1520 nts=4 GGaa A.G1516,A.G1517,A.MA6/1518,A.MA6/1519 **************************************************************************** List of 25 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 GUGAC A.G44,A.U45,A.G396,A.A397,A.C398 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; [1,0]; linked by [#-3,#28] summary: [2] 1 0 [A.367 A.393 A.369 A.392] 1 3 nts=5 UUCGA A.U367,A.U368,A.C369,A.G392,A.A393 nts=1 U A.U368 nts=0 5 bulge: nts=5; [0,1]; linked by [#-4,#29] 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 6 bulge: nts=5; [1,0]; linked by [#42,#43] summary: [2] 1 0 [A.594 A.645 A.596 A.644] 7 2 nts=5 GGCGC A.G594,A.G595,A.C596,A.G644,A.C645 nts=1 G A.G595 nts=0 7 bulge: nts=5; [0,1]; linked by [#46,#47] summary: [2] 0 1 [A.657 A.749 A.658 A.747] 3 5 nts=5 GGCCC A.G657,A.G658,A.C747,A.C748,A.C749 nts=0 nts=1 C A.C748 8 bulge: nts=5; [0,1]; linked by [#60,#61] summary: [2] 0 1 [A.922 A.1395 A.923 A.1393] 2 3 nts=5 GAUAC A.G922,A.A923,A.U1393,A.A1394,A.C1395 nts=0 nts=1 A A.A1394 9 bulge: nts=5; [1,0]; linked by [#61,#62] summary: [2] 1 0 [A.925 A.1391 A.927 A.1390] 3 7 nts=5 GGGUU A.G925,A.G926,A.G927,A.U1390,A.U1391 nts=1 G A.G926 nts=0 10 bulge: nts=5; [0,1]; linked by [#65,#66] summary: [2] 0 1 [A.953 A.1228 A.954 A.1226] 8 2 nts=5 GGCAC A.G953,A.G954,A.C1226,A.A1227,A.C1228 nts=0 nts=1 A A.A1227 11 bulge: nts=5; [1,0]; linked by [#69,#-12] summary: [2] 1 0 [A.1002 A.1039 A.1003 A.1038] 4 1 nts=5 GGGCC A.G1002,A.G1003,A.G1003^A,A.C1038,A.C1039 nts=1 G A.G1003 nts=0 12 bulge: nts=5; [1,0]; linked by [#73,#74] summary: [2] 1 0 [A.1048 A.1209 A.1050 A.1208] 2 3 nts=5 GUGCC A.G1048,A.U1049,A.G1050,A.C1208,A.C1209 nts=1 U A.U1049 nts=0 13 bulge: nts=5; [0,1]; linked by [#76,#-13] summary: [2] 0 1 [A.1060 A.1197 A.1061 A.1195] 3 1 nts=5 CGCUG A.C1060,A.G1061,A.C1195,A.U1196,A.G1197 nts=0 nts=1 U A.U1196 14 bulge: nts=5; [0,1]; linked by [#-15,#-16] summary: [2] 0 1 [A.1127 A.1145 A.1128 A.1143] 1 1 nts=5 GCGGC A.G1127,A.C1128,A.G1143,A.G1144,A.C1145 nts=0 nts=1 G A.G1144 15 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 CGUGCG A.C63,A.G64,A.U65,A.G66,A.C103,A.G104 nts=2 GU A.G64,A.U65 nts=0 16 bulge: nts=6; [2,0]; linked by [#13,#14] summary: [2] 2 0 [A.129 A.232 A.131 A.231] 8 2 nts=6 UGACGG A.U129,A.G129^A,A.A130,A.C131,A.G231,A.G232 nts=2 GA A.G129^A,A.A130 nts=0 17 bulge: nts=6; [2,0]; linked by [#22,#23] 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 18 bulge: nts=6; [0,2]; linked by [#43,#44] 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 19 bulge: nts=6; [0,2]; linked by [#-7,#46] summary: [2] 0 2 [A.654 A.754 A.655 A.751] 1 3 nts=6 GAUGAC A.G654,A.A655,A.U751,A.G752,A.A753,A.C754 nts=0 nts=2 GA A.G752,A.A753 20 bulge: nts=7; [0,3]; linked by [#24,#25] summary: [2] 0 3 [A.292 A.308 A.293 A.304] 4 4 nts=7 GGUGGCC A.G292,A.G293,A.U304,A.G305,A.G306,A.C307,A.C308 nts=0 nts=3 GGC A.G305,A.G306,A.C307 21 bulge: nts=7; [3,0]; linked by [#28,#-4] summary: [2] 3 0 [A.371 A.390 A.375 A.389] 3 1 nts=7 GCAAUAC A.G371,A.C372,A.A373,A.A374,A.U375,A.A389,A.C390 nts=3 CAA A.C372,A.A373,A.A374 nts=0 22 bulge: nts=7; [3,0]; linked by [#52,#53] 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 23 bulge: nts=7; [3,0]; linked by [#-10,#-11] summary: [2] 3 0 [A.993 A.1045 A.997 A.1044] 1 1 nts=7 GACAUAC A.G993,A.A994,A.C995,A.A996,A.U997,A.A1044,A.C1045 nts=3 ACA A.A994,A.C995,A.A996 nts=0 24 bulge: nts=7; [0,3]; linked by [#75,#76] summary: [2] 0 3 [A.1057 A.1203 A.1058 A.1199] 2 3 nts=7 GGUCAGC A.G1057,A.G1058,A.U1199,A.C1200,A.A1201,A.G1202,A.C1203 nts=0 nts=3 CAG A.C1200,A.A1201,A.G1202 25 bulge: nts=7; [3,0]; linked by [#-16,#82] summary: [2] 3 0 [A.1128 A.1143 A.1132 A.1142] 1 3 nts=7 CCAGCGG A.C1128,A.C1129,A.A1130,A.G1131,A.C1132,A.G1142,A.G1143 nts=3 CAG A.C1129,A.A1130,A.G1131 nts=0 **************************************************************************** List of 39 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 [#10,#11] summary: [2] 1 1 [A.67 A.102 A.69 A.99] 2 10 nts=6 CGGCAG A.C67,A.G68,A.G69,A.C99,A.A101,A.G102 nts=1 G A.G68 nts=1 A A.A101 3 symmetric internal loop: nts=6; [1,1]; linked by [#18,#19] summary: [2] 1 1 [A.186 A.191 A.188 A.190] 4 5 nts=6 CCCGUG A.C186,A.C187,A.C188,A.G190^K,A.U190^L,A.G191 nts=1 C A.C187 nts=1 U A.U190^L 4 symmetric internal loop: nts=6; [1,1]; linked by [#-11,#69] summary: [2] 1 1 [A.997 A.1044 A.999 A.1042] 1 4 nts=6 UGCGCA A.U997,A.G998,A.C999,A.G1042,A.C1043,A.A1044 nts=1 G A.G998 nts=1 C A.C1043 5 symmetric internal loop: nts=6; [1,1]; linked by [#70,#71] summary: [2] 1 1 [A.1007 A.1022 A.1009 A.1020] 2 4 nts=6 CCGUGG A.C1007,A.C1008,A.G1009,A.U1020,A.G1021,A.G1022 nts=1 C A.C1008 nts=1 G A.G1021 6 symmetric internal loop: nts=6; [1,1]; linked by [#-13,#-14] summary: [2] 1 1 [A.1061 A.1195 A.1063 A.1193] 1 1 nts=6 GUCGUC A.G1061,A.U1062,A.C1063,A.G1193,A.U1194,A.C1195 nts=1 U A.U1062 nts=1 U A.U1194 7 symmetric internal loop: nts=6; [1,1]; linked by [#90,#-23] summary: [2] 1 1 [A.1405 A.1496 A.1407 A.1494] 2 1 nts=6 GUcGUC A.G1405,A.U1406,A.5MC1407,A.G1494,A.U1495,A.C1496 nts=1 U A.U1406 nts=1 U A.U1495 8 symmetric internal loop: nts=6; [1,1]; linked by [#91,#92] summary: [2] 1 1 [A.1412 A.1488 A.1414 A.1486] 4 3 nts=6 CAUGGG A.C1412,A.A1413,A.U1414,A.G1486,A.G1487,A.G1488 nts=1 A A.A1413 nts=1 G A.G1487 9 symmetric internal loop: nts=6; [1,1]; linked by [#93,#94] summary: [2] 1 1 [A.1424 A.1476 A.1426 A.1474] 6 6 nts=6 CUCGGG A.C1424,A.U1425,A.C1426,A.G1474,A.G1475,A.G1476 nts=1 U A.U1425 nts=1 G A.G1475 10 symmetric internal loop: nts=6; [1,1]; linked by [#-24,#95] summary: [2] 1 1 [A.1435 A.1466 A.1437 A.1464] 1 4 nts=6 GUCGCC A.G1435,A.U1436,A.C1437,A.G1464,A.C1465,A.C1466 nts=1 U A.U1436 nts=1 C A.C1465 11 asymmetric internal loop: nts=7; [1,2]; linked by [#-21,#-22] summary: [2] 1 2 [A.1399 A.1504 A.1401 A.1501] 1 1 nts=7 CcGCAAG A.C1399,A.5MC1400,A.G1401,A.C1501,A.A1502,A.A1503,A.G1504 nts=1 c A.5MC1400 nts=2 AA A.A1502,A.A1503 12 asymmetric internal loop: nts=7; [1,2]; linked by [#-23,#91] summary: [2] 1 2 [A.1407 A.1494 A.1409 A.1491] 1 4 nts=7 cACGAAG A.5MC1407,A.A1408,A.C1409,A.G1491,A.A1492,A.A1493,A.G1494 nts=1 A A.A1408 nts=2 AA A.A1492,A.A1493 13 asymmetric internal loop: nts=8; [1,3]; linked by [#62,#63] summary: [2] 1 3 [A.933 A.1384 A.935 A.1380] 7 2 nts=8 GCAUUCCC A.G933,A.C934,A.A935,A.U1380,A.U1381,A.C1382,A.C1383,A.C1384 nts=1 C A.C934 nts=3 UCC A.U1381,A.C1382,A.C1383 14 asymmetric internal loop: nts=8; [3,1]; linked by [#74,#75] summary: [2] 3 1 [A.1052 A.1206 A.1056 A.1204] 3 2 nts=8 UGCAUAUG A.U1052,A.G1053,A.C1054,A.A1055,A.U1056,A.A1204,A.U1205,A.G1206 nts=3 GCA A.G1053,A.C1054,A.A1055 nts=1 U A.U1205 15 symmetric internal loop: nts=8; [2,2]; linked by [#86,#87] summary: [2] 2 2 [A.1259 A.1276 A.1262 A.1273] 2 4 nts=8 CCACGGAG A.C1259,A.C1260,A.A1261,A.C1262,A.G1273,A.G1274,A.A1275,A.G1276 nts=2 CA A.C1260,A.A1261 nts=2 GA A.G1274,A.A1275 16 symmetric internal loop: nts=8; [2,2]; linked by [#92,#93] summary: [2] 2 2 [A.1416 A.1484 A.1419 A.1481] 3 6 nts=8 GGAGUGAC A.G1416,A.G1417,A.A1418,A.G1419,A.U1481,A.G1482,A.A1483,A.C1484 nts=2 GA A.G1417,A.A1418 nts=2 GA A.G1482,A.A1483 17 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 CCUAAGUAG A.C47,A.C48,A.U49,A.A50,A.A51,A.G52,A.U359,A.A360,A.G361 nts=4 CUAA A.C48,A.U49,A.A50,A.A51 nts=1 A A.A360 18 asymmetric internal loop: nts=9; [3,2]; linked by [#14,#15] summary: [2] 3 2 [A.132 A.230 A.136 A.227] 2 7 nts=9 CUACCGAUG A.C132,A.U133,A.A134,A.C135,A.C136,A.G227,A.A228,A.U229,A.G230 nts=3 UAC A.U133,A.A134,A.C135 nts=2 AU A.A228,A.U229 19 asymmetric internal loop: nts=9; [3,2]; linked by [#47,#48] summary: [2] 3 2 [A.662 A.743 A.666 A.740] 5 7 nts=9 GAGAGUGGU A.G662,A.A663,A.G664,A.A665,A.G666,A.U740,A.G741,A.G742,A.U743 nts=3 AGA A.A663,A.G664,A.A665 nts=2 GG A.G741,A.G742 20 asymmetric internal loop: nts=9; [2,3]; linked by [#81,#-15] summary: [2] 2 3 [A.1124 A.1149 A.1127 A.1145] 7 1 nts=9 GUUGCACUC A.G1124,A.U1125,A.U1126,A.G1127,A.C1145,A.A1146,A.C1147,A.U1148,A.C1149 nts=2 UU A.U1125,A.U1126 nts=3 ACU A.A1146,A.C1147,A.U1148 21 asymmetric internal loop: nts=9; [2,3]; linked by [#-22,#90] summary: [2] 2 3 [A.1401 A.1501 A.1404 A.1497] 1 2 nts=9 GcCcGuAAC A.G1401,A.4OC1402,A.C1403,A.5MC1404,A.G1497,A.UR3/1498,A.A1499,A.A1500,A.C1501 nts=2 cC A.4OC1402,A.C1403 nts=3 uAA A.UR3/1498,A.A1499,A.A1500 22 asymmetric internal loop: nts=9; [3,2]; linked by [#94,#-24] summary: [2] 3 2 [A.1431 A.1469 A.1435 A.1466] 6 1 nts=9 CGAAGCGAG A.C1431,A.G1432,A.A1433,A.A1434,A.G1435,A.C1466,A.G1467,A.A1468,A.G1469 nts=3 GAA A.G1432,A.A1433,A.A1434 nts=2 GA A.G1467,A.A1468 23 asymmetric internal loop: nts=9; [4,1]; linked by [#95,#96] summary: [2] 4 1 [A.1440 A.1461 A.1447 A.1459] 4 3 nts=9 CGGGAGCAG A.C1440,A.G1441,A.G1442,A.G1443,A.A1446,A.G1447,A.C1459,A.A1460,A.G1461 nts=4 GGGA A.G1441,A.G1442,A.G1443,A.A1446 nts=1 A A.A1460 24 symmetric internal loop: nts=10; [3,3]; linked by [#40,#41] summary: [2] 3 3 [A.580 A.761 A.584 A.757] 4 3 nts=10 UGUAGUGAGG A.U580,A.G581,A.U582,A.A583,A.G584,A.U757,A.G758,A.A759,A.G760,A.G761 nts=3 GUA A.G581,A.U582,A.A583 nts=3 GAG A.G758,A.A759,A.G760 25 symmetric internal loop: nts=10; [3,3]; linked by [#53,#54] 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 26 asymmetric internal loop: nts=10; [2,4]; linked by [#85,#86] summary: [2] 2 4 [A.1255 A.1282 A.1258 A.1277] 3 2 nts=10 GAUGCUAAUC A.G1255,A.A1256,A.U1257,A.G1258,A.C1277,A.U1278,A.A1279,A.A1280,A.U1281,A.C1282 nts=2 AU A.A1256,A.U1257 nts=4 UAAU A.U1278,A.A1279,A.A1280,A.U1281 27 asymmetric internal loop: nts=11; [3,4]; linked by [#32,#-5] summary: [2] 3 4 [A.446 A.488 A.450 A.483] 5 1 nts=11 GGACGCGGUAC A.G446,A.G447,A.A448,A.C449,A.G450,A.C483,A.G484,A.G485,A.U486,A.A487,A.C488 nts=3 GAC A.G447,A.A448,A.C449 nts=4 GGUA A.G484,A.G485,A.U486,A.A487 28 asymmetric internal loop: nts=11; [2,5]; linked by [#-17,#83] summary: [2] 2 5 [A.1158 A.1181 A.1161 A.1175] 1 5 nts=11 CUGCGAGGAAG A.C1158,A.U1159,A.G1160,A.C1161,A.G1175,A.A1176,A.G1177,A.G1178,A.A1179,A.A1180,A.G1181 nts=2 UG A.U1159,A.G1160 nts=5 AGGAA A.A1176,A.G1177,A.G1178,A.A1179,A.A1180 29 symmetric internal loop: nts=12; [4,4]; linked by [#-8,#49] summary: [2] 4 4 [A.673 A.717 A.678 A.712] 1 6 nts=12 GGAAUUAGGAAC A.G673,A.G674,A.A675,A.A676,A.U677,A.U678,A.A712,A.G713,A.G714,A.A715,A.A716,A.C717 nts=4 GAAU A.G674,A.A675,A.A676,A.U677 nts=4 GGAA A.G713,A.G714,A.A715,A.A716 30 symmetric internal loop: nts=12; [4,4]; linked by [#-20,#88] summary: [2] 4 4 [A.1303 A.1334 A.1308 A.1329] 1 7 nts=12 CGGAUUAUGAAG A.C1303,A.G1304,A.G1305,A.A1306,A.U1307,A.U1308,A.A1329,A.U1330,A.G1331,A.A1332,A.A1333,A.G1334 nts=4 GGAU A.G1304,A.G1305,A.A1306,A.U1307 nts=4 UGAA A.U1330,A.G1331,A.A1332,A.A1333 31 asymmetric internal loop: nts=13; [4,5]; linked by [#16,#17] summary: [2] 4 5 [A.148 A.174 A.153 A.168] 5 6 nts=13 GACAACGCUAAUC A.G148,A.A149,A.C150,A.A151,A.A152,A.C153,A.G168,A.C169,A.U170,A.A171,A.A172,A.U173,A.C174 nts=4 ACAA A.A149,A.C150,A.A151,A.A152 nts=5 CUAAU A.C169,A.U170,A.A171,A.A172,A.U173 32 asymmetric internal loop: nts=13; [4,5]; linked by [#-5,#33] summary: [2] 4 5 [A.450 A.483 A.455 A.477] 1 4 nts=13 GAAACCGACUGAC A.G450,A.A451,A.A452,A.A453,A.C454,A.C455,A.G477,A.A478,A.C479,A.U480,A.G481,A.A482,A.C483 nts=4 AAAC A.A451,A.A452,A.A453,A.C454 nts=5 ACUGA A.A478,A.C479,A.U480,A.G481,A.A482 33 asymmetric internal loop: nts=14; [4,6]; linked by [#21,#22] summary: [2] 4 6 [A.242 A.284 A.247 A.277] 3 3 k-turn:normal nts=14 CAUCAGCGACGACG A.C242,A.A243,A.U244,A.C245,A.A246,A.G247,A.C277,A.G278,A.A279,A.C280,A.G281,A.A282,A.C283,A.G284 nts=4 AUCA A.A243,A.U244,A.C245,A.A246 nts=6 GACGAC A.G278,A.A279,A.C280,A.G281,A.A282,A.C283 34 asymmetric internal loop: nts=14; [6,4]; linked by [#44,#45] summary: [2] 6 4 [A.605 A.633 A.612 A.628] 8 6 nts=14 UGAAAGACGGGGAG A.U605,A.G606,A.A607,A.A608,A.A609,A.G610,A.A611,A.C612,A.G628,A.G629,A.G630,A.G631,A.A632,A.G633 nts=6 GAAAGA A.G606,A.A607,A.A608,A.A609,A.G610,A.A611 nts=4 GGGA A.G629,A.G630,A.G631,A.A632 35 asymmetric internal loop: nts=14; [6,4]; linked by [#58,#59] summary: [2] 6 4 [A.887 A.910 A.894 A.905] 3 4 nts=14 GGAGUACGUGAAAC A.G887,A.G888,A.A889,A.G890,A.U891,A.A892,A.C893,A.G894,A.U905,A.G906,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 GAAA A.G906,A.A907,A.A908,A.A909 36 symmetric internal loop: nts=14; [5,5]; linked by [#84,#85] summary: [2] 5 5 [A.1247 A.1290 A.1253 A.1284] 7 3 nts=14 UACAAAGCAAAAAG A.U1247,A.A1248,A.C1249,A.A1250,A.A1251,A.A1252,A.G1253,A.C1284,A.A1285,A.A1286,A.A1287,A.A1288,A.A1289,A.G1290 nts=5 ACAAA A.A1248,A.C1249,A.A1250,A.A1251,A.A1252 nts=5 AAAAA A.A1285,A.A1286,A.A1287,A.A1288,A.A1289 37 asymmetric internal loop: nts=15; [6,5]; linked by [#30,#31] summary: [2] 6 5 [A.409 A.433 A.416 A.427] 4 4 k-turn:reverse nts=15 GGAAGAAGUGUAAAC A.G409,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.C433 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 38 asymmetric internal loop: nts=15; [4,7]; linked by [#49,#50] summary: [2] 4 7 [A.683 A.707 A.688 A.699] 6 2 k-turn:normal nts=15 GAGUAGCGCAGAUAC A.G683,A.A684,A.G685,A.U686,A.A687,A.G688,A.C699,A.G700,A.C701,A.A702,A.G703,A.A704,A.U705,A.A706,A.C707 nts=4 AGUA A.A684,A.G685,A.U686,A.A687 nts=7 GCAGAUA A.G700,A.C701,A.A702,A.G703,A.A704,A.U705,A.A706 39 asymmetric internal loop: nts=16; [5,7]; linked by [#36,#37] summary: [2] 5 7 [A.515 A.536 A.521 A.528] 5 2 k-turn:normal 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 19 junctions 1 3-way junction: nts=9; [1,2,0]; linked by [#41,#42,#-7] summary: [3] 1 2 0 [A.586 A.755 A.588 A.651 A.654 A.754] 3 7 1 nts=9 CGGCUAGCG A.C586,A.G587,A.G588,A.C651,A.U652,A.A653,A.G654,A.C754,A.G755 nts=1 G A.G587 nts=2 UA A.U652,A.A653 nts=0 2 3-way junction: nts=11; [2,1,2]; linked by [#64,#65,#-19] summary: [3] 2 1 2 [A.943 A.1340 A.946 A.1235 A.1237 A.1337] 5 8 1 nts=11 UGGAUACGGAA A.U943,A.G944,A.G945,A.A946,A.U1235,A.A1236,A.C1237,A.G1337,A.G1338,A.A1339,A.A1340 nts=2 GG A.G944,A.G945 nts=1 A A.A1236 nts=2 GA A.G1338,A.A1339 3 3-way junction: nts=11; [1,2,2]; linked by [#80,#81,#-17] summary: [3] 1 2 2 [A.1116 A.1184 A.1118 A.1155 A.1158 A.1181] 4 7 1 nts=11 CGCGGACGGAG A.C1116,A.G1117,A.C1118,A.G1155,A.G1156,A.A1157,A.C1158,A.G1181,A.G1182,A.A1183,A.G1184 nts=1 G A.G1117 nts=2 GA A.G1156,A.A1157 nts=2 GA A.G1182,A.A1183 4 3-way junction: nts=12; [0,5,1]; linked by [#6,#-2,#-3] summary: [3] 0 5 1 [A.46 A.395 A.47 A.361 A.367 A.393] 2 1 1 nts=12 GCGGAAUCUAGC A.G46,A.C47,A.G361,A.G362,A.A363,A.A364,A.U365,A.C366,A.U367,A.A393,A.G394,A.C395 nts=0 nts=5 GAAUC A.G362,A.A363,A.A364,A.U365,A.C366 nts=1 G A.G394 5 3-way junction: nts=12; [0,3,3]; linked by [#77,#78,#79] summary: [3] 0 3 3 [A.1073 A.1102 A.1074 A.1083 A.1087 A.1098] 6 3 3 nts=12 UGUGUUGCGCAA A.U1073,A.G1074,A.U1083,A.G1084,A.U1085,A.U1086,A.G1087,A.C1098,A.G1099,A.C1100,A.A1101,A.A1102 nts=0 nts=3 GUU A.G1084,A.U1085,A.U1086 nts=3 GCA A.G1099,A.C1100,A.A1101 6 3-way junction: nts=13; [2,1,4]; linked by [#68,#-10,#73] summary: [3] 2 1 4 [A.990 A.1215 A.993 A.1045 A.1047 A.1210] 7 1 2 nts=13 CUUGCAGCUUACG A.C990,A.U991,A.U992,A.G993,A.C1045,A.A1046,A.G1047,A.C1210,A.U1211,A.U1212,A.A1213,A.C1214,A.G1215 nts=2 UU A.U991,A.U992 nts=1 A A.A1046 nts=4 UUAC A.U1211,A.U1212,A.A1213,A.C1214 7 3-way junction: nts=14; [0,7,1]; linked by [#48,#-8,#51] summary: [3] 0 7 1 [A.672 A.734 A.673 A.717 A.725 A.732] 7 1 2 nts=14 UGCGCCGAUGGCAG A.U672,A.G673,A.C717,A.G718,A.C719,A.C720,A.G721,A.A722,A.U723,A.G724,A.G725,A.C732,A.A733,A.G734 nts=0 nts=7 GCCGAUG A.G718,A.C719,A.C720,A.G721,A.A722,A.U723,A.G724 nts=1 A A.A733 8 3-way junction: nts=16; [2,3,5]; linked by [#55,#56,#57] summary: [3] 2 3 5 [A.826 A.874 A.829 A.857 A.861 A.868] 6 10 2 nts=16 CUAGCGAAGCGUUAAG A.C826,A.U827,A.A828,A.G829,A.C857,A.G858,A.A859,A.A860,A.G861,A.C868,A.G869,A.U870,A.U871,A.A872,A.A873,A.G874 nts=2 UA A.U827,A.A828 nts=3 GAA A.G858,A.A859,A.A860 nts=5 GUUAA A.G869,A.U870,A.U871,A.A872,A.A873 9 3-way junction: nts=16; [2,4,4]; linked by [#-12,#70,#72] summary: [3] 2 4 4 [A.1003 A.1038 A.1006 A.1023 A.1028 A.1033] 1 2 3 nts=16 GAACGGUGCCGGAGCC A.G1003^A,A.A1004,A.A1005,A.C1006,A.G1023,A.G1024,A.U1025,A.G1026,A.C1027,A.C1028,A.G1033,A.G1034,A.A1035,A.G1036,A.C1037,A.C1038 nts=2 AA A.A1004,A.A1005 nts=4 GUGC A.G1024,A.U1025,A.G1026,A.C1027 nts=4 GAGC A.G1034,A.A1035,A.G1036,A.C1037 10 3-way junction: nts=17; [3,6,2]; linked by [#-19,#84,#-20] summary: [3] 3 6 2 [A.1237 A.1337 A.1241 A.1296 A.1303 A.1334] 1 7 1 nts=17 CAAUGCCCAGUUCGCCG A.C1237,A.A1238,A.A1239,A.U1240,A.G1241,A.C1296,A.C1297,A.C1298,A.A1299,A.G1300,A.U1301,A.U1302,A.C1303,A.G1334,A.C1335,A.C1336,A.G1337 nts=3 AAU A.A1238,A.A1239,A.U1240 nts=6 CCAGUU A.C1297,A.C1298,A.A1299,A.G1300,A.U1301,A.U1302 nts=2 CC A.C1335,A.C1336 11 3-way junction: nts=19; [2,5,6]; linked by [#63,#64,#89] summary: [3] 2 5 6 [A.936 A.1379 A.939 A.1344 A.1350 A.1372] 2 5 7 nts=19 CAAGCUAGUAAUGAAUACG A.C936,A.A937,A.A938,A.G939,A.C1344,A.U1345,A.A1346,A.G1347,A.U1348,A.A1349,A.A1350,A.U1372,A.G1373,A.A1374,A.A1375,A.U1376,A.A1377,A.C1378,A.G1379 nts=2 AA A.A937,A.A938 nts=5 UAGUA A.U1345,A.A1346,A.G1347,A.U1348,A.A1349 nts=6 GAAUAC A.G1373,A.A1374,A.A1375,A.U1376,A.A1377,A.C1378 12 3-way junction: nts=20; [4,5,5]; linked by [#-14,#77,#80] summary: [3] 4 5 5 [A.1063 A.1193 A.1068 A.1107 A.1113 A.1187] 1 6 4 nts=20 CGUCAGCGCAACCGACGACG A.C1063,A.G1064,A.U1065,A.C1066,A.A1067,A.G1068,A.C1107,A.G1108,A.C1109,A.A1110,A.A1111,A.C1112,A.C1113,A.G1187,A.A1188,A.C1189,A.G1190,A.A1191,A.C1192,A.G1193 nts=4 GUCA A.G1064,A.U1065,A.C1066,A.A1067 nts=5 GCAAC A.G1108,A.C1109,A.A1110,A.A1111,A.C1112 nts=5 ACGAC A.A1188,A.C1189,A.G1190,A.A1191,A.C1192 13 4-way junction: nts=16; [6,0,2,0]; linked by [#12,#13,#21,#24] summary: [4] 6 0 2 0 [A.115 A.312 A.122 A.239 A.240 A.286 A.289 A.311] 3 8 3 4 nts=16 GAGUAACGUCGUAGCC A.G115,A.A116,A.G117,A.U118,A.A119,A.A120,A.C121,A.G122,A.U239,A.C240,A.G286,A.U287,A.A288,A.G289,A.C311,A.C312 nts=6 AGUAAC A.A116,A.G117,A.U118,A.A119,A.A120,A.C121 nts=0 nts=2 UA A.U287,A.A288 nts=0 14 4-way junction: nts=17; [1,4,3,1]; linked by [#15,#16,#18,#20] summary: [4] 1 4 3 1 [A.142 A.221 A.144 A.178 A.183 A.194 A.198 A.219] 7 5 4 4 nts=17 GAGCAUGUGCAAAGCGC A.G142,A.A143,A.G144,A.C178,A.A179,A.U180,A.G181,A.U182,A.G183,A.C194,A.A195,A.A196,A.A197,A.G198,A.C219,A.G220,A.C221 nts=1 A A.A143 nts=4 AUGU A.A179,A.U180,A.G181,A.U182 nts=3 AAA A.A195,A.A196,A.A197 nts=1 G A.G220 15 4-way junction: nts=23; [1,4,10,0]; linked by [#-6,#40,#52,#55] summary: [4] 1 4 10 0 [A.575 A.880 A.577 A.764 A.769 A.810 A.821 A.879] 1 4 6 6 nts=23 GGGCGAAAGCCCUAAACGAUGCC A.G575,A.G576,A.G577,A.C764,A.G765,A.A766,A.A767,A.A768,A.G769,A.C810,A.C811,A.C812,A.U813,A.A814,A.A815,A.A816,A.C817,A.G818,A.A819,A.U820,A.G821,A.C879,A.C880 nts=1 G A.G576 nts=4 GAAA A.G765,A.A766,A.A767,A.A768 nts=10 CCUAAACGAU A.C811,A.C812,A.U813,A.A814,A.A815,A.A816,A.C817,A.G818,A.A819,A.U820 nts=0 16* 5-way junction: nts=14; [0,0,1,3,0]; linked by [#34,#35,#37,#35,#36] 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 CGCgCAGCCAACGG A.C504,A.G505,A.C526,A.7MG527,A.C522,A.A523,A.G524,A.C507,A.C508,A.A509,A.A510,A.C511,A.G540,A.G541 nts=0 nts=0 nts=1 A A.A523 nts=3 CAA A.C508,A.A509,A.A510 nts=0 17* 5-way junction: nts=15; [0,0,2,3,0]; linked by [#38,#39,#57,#39,#-6] 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 18 5-way junction: nts=23; [2,6,1,1,3]; linked by [#8,#9,#12,#26,#27] 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 CAAGCGGACGGGCAGCACGGCAG 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.G316,A.C337,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 19 5-way junction: nts=26; [2,2,4,6,2]; linked by [#4,#5,#30,#32,#34] summary: [5] 2 2 4 6 2 [A.36 A.548 A.39 A.403 A.406 A.436 A.442 A.492 A.500 A.545] 5 6 4 5 5 nts=26 CUGGCUUGCUGAACGGUAAUAGCGAG A.C36,A.U37,A.G38,A.G39,A.C403,A.U404,A.U405,A.G406,A.C436,A.U437,A.G438,A.A439,A.A440,A.C442,A.G492,A.G494,A.U495,A.A496,A.A497,A.U498,A.A499,A.G500,A.C545,A.G546,A.A547,A.G548 nts=2 UG A.U37,A.G38 nts=2 UU A.U404,A.U405 nts=4 UGAA A.U437,A.G438,A.A439,A.A440 nts=6 GUAAUA A.G494,A.U495,A.A496,A.A497,A.U498,A.A499 nts=2 GA A.G546,A.A547 **************************************************************************** List of 11 non-loop single-stranded segments 1 nts=4 UGGA A.U5,A.G6,A.G7,A.A8 2 nts=1 A A.A26 3 nts=10 GGAUUCACUG A.G557,A.G558,A.A559,A.U560,A.U561,A.C562,A.A563,A.C564,A.U565,A.G566 4 nts=1 U A.U884 5 nts=3 AAA A.A913,A.A914,A.A915 6 nts=6 UUAAUU A.U956,A.U957,A.A958,A.A959,A.U960,A.U961 7 nts=10 AAGAACCUUA A.A974,A.A975,A.G976,A.A977,A.A978,A.C979,A.C980,A.U981,A.U982,A.A983 8 nts=2 GC A.G1222,A.C1223 9 nts=2 CA A.C1397,A.A1398 10 nts=2 GU A.G1505,A.U1506 11 nts=10* GAUCCPPUCU A.G1530,A.A1531,A.U1532,A.C1533,A.C1539,A.PSU1540,A.PSU1541,A.U1542,A.C1543,A.U1544 **************************************************************************** List of 67 A-minor motifs (types I, II, or X) 1 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)[3.19],N1-O2'(hydroxyl)[2.78]" 2 type=X A|U-A A.A51|A.U114,A.A313 WC +A.U114 H-bonds[2]: "N7-O2'(hydroxyl)[2.74],N6(amino)-O2(carbonyl)[3.23]" -A.A313 H-bonds[0]: "" 3 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[2.61],N1-O2'(hydroxyl)[2.82]" 4 type=X A|G-C A.A130|A.G128,A.C233 WC +A.G128 H-bonds[0]: "" -A.C233 H-bonds[2]: "N6(amino)-O2(carbonyl)[3.25],N1-O2'(hydroxyl)[2.71]" 5 type=II A|C-G A.A151|A.C67,A.G102 WC +A.C67 H-bonds[0]: "" -A.G102 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.93],N1-N2(amino)[3.44],N3-O2'(hydroxyl)[2.69]" 6 type=X A|C-G A.A160|A.C342,A.G347 WC -A.C342 H-bonds[0]: "" +A.G347 H-bonds[2]: "N6(amino)-N3[3.45],N1-N2(amino)[3.36]" 7 type=X A|C-G A.A161|A.C342,A.G347 WC -A.C342 H-bonds[0]: "" +A.G347 H-bonds[1]: "N1-O2'(hydroxyl)[2.92]" 8 type=II A|C-G A.A171|A.C67,A.G102 WC -A.C67 H-bonds[3]: "O2'(hydroxyl)-O3'[3.19],O2'(hydroxyl)-O2'(hydroxyl)[2.90],N3-O2'(hydroxyl)[2.53]" +A.G102 H-bonds[0]: "" 9 type=I A|G-C A.A172|A.G66,A.C103 WC -A.G66 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.89],N3-N2(amino)[3.00]" +A.C103 H-bonds[1]: "N1-O2'(hydroxyl)[2.78]" 10 type=II A|A-U A.A195|A.A141,A.U222 WC +A.A141 H-bonds[0]: "" -A.U222 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.65],N3-O2'(hydroxyl)[2.88]" 11 type=I A|G-C A.A196|A.G142,A.C221 WC +A.G142 H-bonds[2]: "N1-O2'(hydroxyl)[2.41],N3-N2(amino)[3.09]" -A.C221 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.84]" 12 type=II A|C-G A.A262|A.C131,A.G231 WC -A.C131 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.63],N3-O2'(hydroxyl)[2.69]" +A.G231 H-bonds[0]: "" 13 type=I A|U-G A.A263|A.U129,A.G232 Wobble -A.U129 H-bonds[0]: "" +A.G232 H-bonds[2]: "N1-O2'(hydroxyl)[2.71],N3-N2(amino)[3.55]" 14 type=I A|G-C A.A282|A.G247,A.C277 WC +A.G247 H-bonds[2]: "N1-O2'(hydroxyl)[2.83],N3-N2(amino)[3.07]" -A.C277 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.88]" 15 type=I A|G-C A.A353|A.G113,A.C314 WC -A.G113 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.70],O2'(hydroxyl)-N3[2.78],N3-N2(amino)[3.03]" +A.C314 H-bonds[1]: "N1-O2'(hydroxyl)[3.43]" 16 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[2.80],N1-O2'(hydroxyl)[3.06]" 17 type=X A|G-C A.A374|A.G371,A.C390 WC +A.G371 H-bonds[1]: "N6(amino)*N2(amino)[3.27]" -A.C390 H-bonds[2]: "N6(amino)-O2(carbonyl)[2.86],N1-O2'(hydroxyl)[2.72]" 18 type=X A|G-C A.A389|A.G371,A.C390 WC -A.G371 H-bonds[0]: "" +A.C390 H-bonds[1]: "O2'(hydroxyl)-OP1[2.84]" 19 type=I A|C-G A.A482|A.C370,A.G391 WC -A.C370 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.09],O2'(hydroxyl)-O2(carbonyl)[2.97]" +A.G391 H-bonds[1]: "N3-N2(amino)[3.50]" 20 type=II A|G-C A.A509|A.G502,A.C543 WC +A.G502 H-bonds[0]: "" -A.C543 H-bonds[1]: "N3-O2'(hydroxyl)[2.54]" 21 type=I A|C-G A.A510|A.C503,A.G542 WC +A.C503 H-bonds[1]: "N1-O2'(hydroxyl)[2.68]" -A.G542 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.80],O2'(hydroxyl)-N3[3.35],N3-N2(amino)[2.67]" 22 type=X A|C-g A.A535|A.C522,A.7MG527 WC -A.C522 H-bonds[0]: "" +A.7MG527 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.27],N1-O2'(hydroxyl)[2.40]" 23 type=I A|C-G A.A572|A.C19,A.G916 WC +A.C19 H-bonds[1]: "N1-O2'(hydroxyl)[2.82]" -A.G916 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.02],N3-N2(amino)[3.38]" 24 type=II A|G-C A.A573|A.G567,A.C883 WC +A.G567 H-bonds[0]: "" -A.C883 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.02],N3-O2'(hydroxyl)[2.79]" 25 type=I A|G-C A.A574|A.G568,A.C882 WC +A.G568 H-bonds[2]: "N1-O2'(hydroxyl)[2.67],N3-N2(amino)[2.94]" -A.C882 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.68],O2'(hydroxyl)-O2(carbonyl)[2.83]" 26 type=X A|C-G A.A607|A.C291,A.G309 WC +A.C291 H-bonds[0]: "" -A.G309 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.16],N1-O2'(hydroxyl)[2.93]" 27 type=X A|G-C A.A608|A.G292,A.C308 WC +A.G292 H-bonds[3]: "N6(amino)-O2'(hydroxyl)[3.22],N6(amino)-N3[3.06],N1-N2(amino)[2.86]" -A.C308 H-bonds[0]: "" 28 type=II A|G-C A.A621|A.G41,A.C401 WC +A.G41 H-bonds[0]: "" -A.C401 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.93],N3-O2'(hydroxyl)[2.52]" 29 type=I A|G-C A.A622|A.G42,A.C400 WC +A.G42 H-bonds[2]: "N1-O2'(hydroxyl)[2.92],N3-N2(amino)[3.34]" -A.C400 H-bonds[1]: "O2'(hydroxyl)-O2(carbonyl)[3.23]" 30 type=X A|U-A A.A642|A.U598,A.A640 WC -A.U598 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.98]" +A.A640 H-bonds[0]: "" 31 type=X A|G-C A.A695|A.G786,A.C796 WC -A.G786 H-bonds[1]: "N1-N2(amino)[3.06]" +A.C796 H-bonds[0]: "" 32 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)[3.03],N1-O2'(hydroxyl)[2.76]" 33 type=X A|G-C A.A704|A.G688,A.C699 WC +A.G688 H-bonds[2]: "N1-O2'(hydroxyl)[2.59],N3-N2(amino)[3.43]" -A.C699 H-bonds[0]: "" 34 type=II A|C-G A.A728|A.C578,A.G763 WC -A.C578 H-bonds[3]: "O2'(hydroxyl)-O3'[3.04],O2'(hydroxyl)-O2'(hydroxyl)[2.93],N3-O2'(hydroxyl)[2.62]" +A.G763 H-bonds[0]: "" 35 type=I A|G-C A.A729|A.G577,A.C764 WC -A.G577 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.30],N3-N2(amino)[3.27]" +A.C764 H-bonds[1]: "N1-O2'(hydroxyl)[2.77]" 36 type=X A|U-G A.A766|A.U1510,A.G1525 Wobble +A.U1510 H-bonds[0]: "" -A.G1525 H-bonds[2]: "N1-N2(amino)[2.96],N3-O2'(hydroxyl)[3.07]" 37 type=I A|G-C A.A767|A.G1511,A.C1524 WC +A.G1511 H-bonds[1]: "N3-N2(amino)[3.11]" -A.C1524 H-bonds[3]: "O3'-O2'(hydroxyl)[2.92],O2'(hydroxyl)-O2'(hydroxyl)[3.11],O2'(hydroxyl)-O2(carbonyl)[2.72]" 38 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)[2.84]" 39 type=I A|C-G A.A864|A.C18,A.G917 WC -A.C18 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.04]" +A.G917 H-bonds[2]: "N1-O2'(hydroxyl)[2.98],N3-N2(amino)[3.11]" 40 type=I A|C-G A.A873|A.C862,A.G867 WC -A.C862 H-bonds[0]: "" +A.G867 H-bonds[1]: "N1-O2'(hydroxyl)[2.68]" 41 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]: "" 42 type=X A|A-G A.A909|A.A1413,A.G1487 Imino -A.A1413 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.94],N3-O2'(hydroxyl)[3.11]" +A.G1487 H-bonds[0]: "" 43 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)[2.86],N3-N2(amino)[3.05]" 44 type=II A|C-G A.A958|A.C985,A.G1220 WC -A.C985 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.86],N3-O2'(hydroxyl)[2.78]" +A.G1220 H-bonds[0]: "" 45 type=I A|C-G A.A959|A.C984,A.G1221 WC -A.C984 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.65],O2'(hydroxyl)-O2(carbonyl)[3.27]" +A.G1221 H-bonds[2]: "N1-O2'(hydroxyl)[2.82],N3-N2(amino)[3.25]" 46 type=X A|G-C A.A996|A.G993,A.C1045 WC +A.G993 H-bonds[1]: "N6(amino)*N2(amino)[3.25]" -A.C1045 H-bonds[2]: "N6(amino)-O2(carbonyl)[3.09],N1-O2'(hydroxyl)[3.07]" 47 type=II A|G-C A.A1015|A.G987,A.C1218 WC +A.G987 H-bonds[0]: "" -A.C1218 H-bonds[3]: "O2'(hydroxyl)-O3'[2.72],O2'(hydroxyl)-O2'(hydroxyl)[2.83],N3-O2'(hydroxyl)[2.70]" 48 type=I A|G-C A.A1016|A.G988,A.C1217 WC +A.G988 H-bonds[2]: "N1-O2'(hydroxyl)[3.49],N3-N2(amino)[3.09]" -A.C1217 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.51],O2'(hydroxyl)-O2(carbonyl)[3.30]" 49 type=I A|A-A A.A1080|A.A16,A.A919 -- -A.A16 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.68],O2'(hydroxyl)-N3[3.00]" +A.A919 H-bonds[2]: "N6(amino)-O2'(hydroxyl)[3.27],N1-O2'(hydroxyl)[2.79]" 50 type=I A|G-U A.A1101|A.G1074,A.U1083 Wobble +A.G1074 H-bonds[2]: "N1-O2'(hydroxyl)[2.57],N3-N2(amino)[3.25]" -A.U1083 H-bonds[1]: "O3'-O2'(hydroxyl)[3.60]" 51 type=II A|G-C A.A1168|A.G1088,A.C1097 WC +A.G1088 H-bonds[0]: "" -A.C1097 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.92],N3-O2'(hydroxyl)[2.66]" 52 type=I A|G-C A.A1169|A.G1089,A.C1096 WC +A.G1089 H-bonds[2]: "N1-O2'(hydroxyl)[2.94],N3-N2(amino)[3.11]" -A.C1096 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.71],O2'(hydroxyl)-O2(carbonyl)[2.92]" 53 type=X A|C-G A.A1213|A.C990,A.G1215 WC -A.C990 H-bonds[0]: "" +A.G1215 H-bonds[1]: "O2'(hydroxyl)-N7[3.12]" 54 type=X A|G-C A.A1238|A.G1241,A.C1296 WC -A.G1241 H-bonds[2]: "N1-N2(amino)[3.26],N3-O2'(hydroxyl)[2.62]" +A.C1296 H-bonds[0]: "" 55 type=II A|G-C A.A1251|A.G1353,A.C1369 WC +A.G1353 H-bonds[0]: "" -A.C1369 H-bonds[3]: "O2'(hydroxyl)-O3'[2.78],O2'(hydroxyl)-O2'(hydroxyl)[2.98],N3-O2'(hydroxyl)[2.63]" 56 type=II A|G-C A.A1268|A.G1311,A.C1326 WC +A.G1311 H-bonds[0]: "" -A.C1326 H-bonds[3]: "O2'(hydroxyl)-O3'[3.15],O2'(hydroxyl)-O2'(hydroxyl)[2.80],N3-O2'(hydroxyl)[2.56]" 57 type=I A|G-C A.A1269|A.G1312,A.C1325 WC +A.G1312 H-bonds[2]: "N1-O2'(hydroxyl)[2.68],N3-N2(amino)[3.02]" -A.C1325 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[2.90]" 58 type=X A|G-C A.A1280|A.G1124,A.C1149 WC +A.G1124 H-bonds[0]: "" -A.C1149 H-bonds[2]: "N6(amino)-O2(carbonyl)[2.97],N1-O2'(hydroxyl)[2.60]" 59 type=X A|C-G A.A1287|A.C1352,A.G1370 WC -A.C1352 H-bonds[0]: "" +A.G1370 H-bonds[1]: "N1-N2(amino)[3.30]" 60 type=II A|C-G A.A1288|A.C1352,A.G1370 WC -A.C1352 H-bonds[3]: "O2'(hydroxyl)-O3'[3.09],O2'(hydroxyl)-O2'(hydroxyl)[2.86],N3-O2'(hydroxyl)[2.68]" +A.G1370 H-bonds[0]: "" 61 type=I A|U-G A.A1289|A.U1351,A.G1371 Wobble -A.U1351 H-bonds[0]: "" +A.G1371 H-bonds[2]: "N1-O2'(hydroxyl)[2.86],N3-N2(amino)[3.27]" 62 type=II A|A-U A.A1333|A.A946,A.U1235 WC -A.A946 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.51],N3-O2'(hydroxyl)[2.82]" +A.U1235 H-bonds[0]: "" 63 type=I A|G-C A.A1398|A.G922,A.C1395 WC +A.G922 H-bonds[2]: "N1-O2'(hydroxyl)[2.70],N3-N2(amino)[2.85]" -A.C1395 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.80],O2'(hydroxyl)-O2(carbonyl)[3.36]" 64 type=II A|G-C A.A1433|A.G318,A.C335 WC +A.G318 H-bonds[0]: "" -A.C335 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.85],N3-O2'(hydroxyl)[2.75]" 65 type=I A|G-C A.A1434|A.G319,A.C334 WC +A.G319 H-bonds[1]: "N3-N2(amino)[3.44]" -A.C334 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[3.01],O2'(hydroxyl)-O2(carbonyl)[3.02]" 66 type=I a|c-G A.MA6/1518|A.5MC1404,A.G1497 WC -A.5MC1404 H-bonds[0]: "" +A.G1497 H-bonds[1]: "N1-O2'(hydroxyl)[2.73]" 67 type=I a|c-G A.MA6/1519|A.5MC1404,A.G1497 WC -A.5MC1404 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.65],O2'(hydroxyl)-O2(carbonyl)[2.60]" +A.G1497 H-bonds[1]: "N3-N2(amino)[2.89]" **************************************************************************** List of 20 ribose zippers 1 nts=4 AUGA A.A16,A.U17,A.G1079,A.A1080 2 nts=4 GCAA A.G66,A.C67,A.A171,A.A172 3 nts=4 GGAG A.G112,A.G113,A.A353,A.G354 4 nts=4 AACU A.A195,A.A196,A.C221,A.U222 5 nts=4 CCAA A.C334,A.C335,A.A1433,A.A1434 6 nts=4 CCAA A.C400,A.C401,A.A621,A.A622 7 nts=4 AAGC A.A509,A.A510,A.G542,A.C543 8 nts=4 AACC A.A573,A.A574,A.C882,A.C883 9 nts=4 GCAA A.G577,A.C578,A.A728,A.A729 10 nts=4 AUGG A.A696,A.U697,A.G785,A.G786 11 nts=4 AACG A.A766,A.A767,A.C1524,A.G1525 12 nts=4 UAUG A.U813,A.A814,A.U1510,A.G1511 13 nts=4 AGAU A.A938,A.G939,A.A1375,A.U1376 14 nts=4 AACC A.A958,A.A959,A.C984,A.C985 15 nts=4 AACC A.A1015,A.A1016,A.C1217,A.C1218 16 nts=4 CCAA A.C1096,A.C1097,A.A1168,A.A1169 17 nts=4 AACG A.A1250,A.A1251,A.C1369,A.G1370 18 nts=4 AACC A.A1268,A.A1269,A.C1325,A.C1326 19 nts=4 AACG A.A1287,A.A1288,A.C1352,A.G1353 20 nts=4 cGaa A.5MC1404,A.G1405,A.MA6/1518,A.MA6/1519 **************************************************************************** List of 4 possible kink turns 1 Normal k-turn; iloop#33; between stems [#22,#21]; bending-angle=52 C#22[CG A.C277,A.G247] [GA A.G281,A.A246] NC#21[GC A.G284,A.C242] strand1 nts=12; GGCGACGACGGG A.G275,A.G276,A.C277,A.G278,A.A279,A.C280,A.G281,A.A282,A.C283,A.G284,A.G285,A.G286 strand2 nts=10; CCCAUCAGCU A.C240,A.C241,A.C242,A.A243,A.U244,A.C245,A.A246,A.G247,A.C248,A.U249 2 Normal k-turn; iloop#38; between stems [#50,#49]; bending-angle=56 C#50[CG A.C699,A.G688] [GA A.G703,A.A687] NC#49[CG A.C707,A.G683] strand1 nts=15; GCGCAGAUACCGGGA A.G698,A.C699,A.G700,A.C701,A.A702,A.G703,A.A704,A.U705,A.A706,A.C707,A.C708,A.G709,A.G710,A.G711,A.A712 strand2 nts=12; UCCCGGAGUAGC A.U678,A.C679,A.C680,A.C681,A.G682,A.G683,A.A684,A.G685,A.U686,A.A687,A.G688,A.C689 3 Normal k-turn; iloop#39; between stems [#37,#36]; bending-angle=34 C#37[CG A.C528,A.G521] [GA A.G529,A.A520] NC#36[CG A.C536,A.G515] strand1 nts=14; gCGGUAAUACGGAG A.7MG527,A.C528,A.G529,A.G530,A.U531,A.A532,A.A533,A.U534,A.A535,A.C536,A.G537,A.G538,A.A539,A.G540 strand2 nts=12; CUCCGPGCCAGC A.C511,A.U512,A.C513,A.C514,A.G515,A.PSU516,A.G517,A.C518,A.C519,A.A520,A.G521,A.C522 4 REVERSE k-turn; iloop#37; between stems [#30,#31]; bending-angle=54 C#30[GC A.G409,A.C433] [GA A.G410,A.A432] NC#31[GU A.G416,A.U427] strand1 nts=14; GGAGGAAGAAGCCC A.G406,A.G407,A.A408,A.G409,A.G410,A.A411,A.A412,A.G413,A.A414,A.A415,A.G416,A.C417,A.C418,A.C419 strand2 nts=13; GGGUGUAAACUCC A.G424,A.G425,A.G426,A.U427,A.G428,A.U429,A.A430,A.A431,A.A432,A.C433,A.U434,A.C435,A.C436 **************************************************************************** List of 178 splayed-apart dinucleotides 1 A.G6 A.G7 angle=93 distance=13.7 ratio=0.74 2 A.G7 A.A8 angle=150 distance=18.7 ratio=0.97 3 A.U13 A.U14 angle=100 distance=15.0 ratio=0.77 4 A.U30 A.G31 angle=111 distance=15.5 ratio=0.82 5 A.G31 A.A32 angle=99 distance=15.9 ratio=0.76 6 A.G38 A.G39 angle=86 distance=13.3 ratio=0.68 7 A.G46 A.C47 angle=108 distance=16.7 ratio=0.81 8 A.C47 A.C48 angle=95 distance=15.2 ratio=0.74 9 A.A50 A.A51 angle=140 distance=20.1 ratio=0.94 10 A.A51 A.G52 angle=118 distance=18.3 ratio=0.86 11 A.A59 A.A60 angle=124 distance=14.6 ratio=0.88 12 A.G64 A.U65 angle=150 distance=19.1 ratio=0.97 13 A.U65 A.G66 angle=175 distance=18.3 ratio=1.00 14 A.U81 A.U82 angle=96 distance=13.6 ratio=0.74 15 A.A120 A.C121 angle=87 distance=14.1 ratio=0.69 16 A.U129 A.G129^A angle=174 distance=19.0 ratio=1.00 17 A.G129^A A.A130 angle=161 distance=18.7 ratio=0.99 18 A.A143 A.G144 angle=114 distance=14.9 ratio=0.84 19 A.U173 A.C174 angle=139 distance=17.4 ratio=0.94 20 A.U190^D A.U190^E angle=112 distance=15.3 ratio=0.83 21 A.G190^F A.G190^G angle=133 distance=16.9 ratio=0.92 22 A.A196 A.A197 angle=104 distance=15.4 ratio=0.79 23 A.U202 A.U203 angle=131 distance=18.2 ratio=0.91 24 A.U239 A.C240 angle=89 distance=13.3 ratio=0.70 25 A.A243 A.U244 angle=133 distance=18.0 ratio=0.92 26 A.U244 A.C245 angle=160 distance=18.7 ratio=0.98 27 A.G265 A.G266 angle=104 distance=13.9 ratio=0.79 28 A.A279 A.C280 angle=114 distance=16.3 ratio=0.84 29 A.C280 A.G281 angle=113 distance=16.1 ratio=0.83 30 A.G297 A.A298 angle=86 distance=12.2 ratio=0.68 31 A.G305 A.G306 angle=88 distance=13.5 ratio=0.69 32 A.A315 A.G316 angle=165 distance=18.4 ratio=0.99 33 A.A327 A.C328 angle=94 distance=14.8 ratio=0.73 34 A.C328 A.A329 angle=92 distance=13.8 ratio=0.72 35 A.A329 A.C330 angle=105 distance=16.2 ratio=0.80 36 A.G331 A.G332 angle=116 distance=17.2 ratio=0.85 37 A.U343 A.A344 angle=133 distance=15.9 ratio=0.92 38 A.A344 A.C345 angle=100 distance=14.9 ratio=0.76 39 A.G351 A.C352 angle=121 distance=17.4 ratio=0.87 40 A.C352 A.A353 angle=149 distance=17.3 ratio=0.96 41 A.A353 A.G354 angle=151 distance=17.5 ratio=0.97 42 A.U365 A.C366 angle=107 distance=14.5 ratio=0.80 43 A.U367 A.U368 angle=120 distance=18.0 ratio=0.87 44 A.U368 A.C369 angle=151 distance=18.6 ratio=0.97 45 A.U387 A.G388 angle=151 distance=17.4 ratio=0.97 46 A.G388 A.A389 angle=105 distance=16.5 ratio=0.79 47 A.G396 A.A397 angle=122 distance=15.4 ratio=0.87 48 A.A397 A.C398 angle=126 distance=14.6 ratio=0.89 49 A.U405 A.G406 angle=152 distance=18.0 ratio=0.97 50 A.G413 A.A414 angle=104 distance=14.9 ratio=0.79 51 A.U420 A.U421 angle=99 distance=11.9 ratio=0.77 52 A.A460 A.C461 angle=112 distance=15.8 ratio=0.83 53 A.C461 A.G462 angle=127 distance=17.3 ratio=0.89 54 A.A497 A.U498 angle=86 distance=14.6 ratio=0.69 55 A.C504 A.G505 angle=157 distance=18.4 ratio=0.98 56 A.G517 A.C518 angle=91 distance=15.2 ratio=0.72 57 A.C518 A.C519 angle=90 distance=14.8 ratio=0.71 58 A.A523 A.G524 angle=112 distance=14.9 ratio=0.83 59 A.G530 A.U531 angle=149 distance=18.8 ratio=0.96 60 A.U531 A.A532 angle=113 distance=16.1 ratio=0.83 61 A.A532 A.A533 angle=158 distance=18.5 ratio=0.98 62 A.A533 A.U534 angle=116 distance=16.8 ratio=0.85 63 A.A535 A.C536 angle=110 distance=15.3 ratio=0.82 64 A.A559 A.U560 angle=138 distance=17.9 ratio=0.93 65 A.U560 A.U561 angle=159 distance=19.4 ratio=0.98 66 A.U561 A.C562 angle=103 distance=15.1 ratio=0.79 67 A.A563 A.C564 angle=120 distance=15.2 ratio=0.86 68 A.G566 A.G567 angle=89 distance=13.8 ratio=0.70 69 A.C569 A.G570 angle=169 distance=18.0 ratio=1.00 70 A.G606 A.A607 angle=167 distance=18.0 ratio=0.99 71 A.C618 A.U619 angle=94 distance=13.4 ratio=0.73 72 A.G664 A.A665 angle=108 distance=16.3 ratio=0.81 73 A.A665 A.G666 angle=141 distance=17.2 ratio=0.94 74 A.C701 A.A702 angle=163 distance=19.0 ratio=0.99 75 A.A702 A.G703 angle=120 distance=16.8 ratio=0.87 76 A.A722 A.U723 angle=102 distance=12.3 ratio=0.78 77 A.U723 A.G724 angle=106 distance=14.2 ratio=0.80 78 A.A733 A.G734 angle=149 distance=17.7 ratio=0.96 79 A.C754 A.G755 angle=102 distance=13.2 ratio=0.78 80 A.G765 A.A766 angle=89 distance=13.6 ratio=0.70 81 A.G776 A.A777 angle=87 distance=12.7 ratio=0.69 82 A.A792 A.U793 angle=95 distance=15.0 ratio=0.74 83 A.U793 A.A794 angle=102 distance=16.5 ratio=0.78 84 A.A814 A.A815 angle=100 distance=15.9 ratio=0.77 85 A.A815 A.A816 angle=141 distance=19.9 ratio=0.94 86 A.A816 A.C817 angle=118 distance=16.1 ratio=0.86 87 A.C817 A.G818 angle=106 distance=15.9 ratio=0.80 88 A.G818 A.A819 angle=130 distance=17.7 ratio=0.90 89 A.A819 A.U820 angle=90 distance=14.1 ratio=0.70 90 A.U820 A.G821 angle=137 distance=17.4 ratio=0.93 91 A.U839 A.C840 angle=111 distance=15.2 ratio=0.82 92 A.C840 A.U841 angle=127 distance=17.6 ratio=0.89 93 A.U863 A.A864 angle=86 distance=12.5 ratio=0.69 94 A.G869 A.U870 angle=107 distance=15.3 ratio=0.81 95 A.U870 A.U871 angle=161 distance=19.4 ratio=0.99 96 A.U871 A.A872 angle=128 distance=16.4 ratio=0.90 97 A.A872 A.A873 angle=104 distance=15.1 ratio=0.79 98 A.A873 A.G874 angle=124 distance=16.8 ratio=0.88 99 A.U884 A.G885 angle=161 distance=18.7 ratio=0.99 100 A.G898 A.C899 angle=90 distance=12.4 ratio=0.71 101 A.G925 A.G926 angle=121 distance=16.3 ratio=0.87 102 A.G926 A.G927 angle=136 distance=19.3 ratio=0.93 103 A.G933 A.C934 angle=86 distance=13.5 ratio=0.68 104 A.U960 A.U961 angle=172 distance=19.0 ratio=1.00 105 A.A965 A.M2G966 angle=145 distance=18.2 ratio=0.95 106 A.A968 A.A969 angle=108 distance=17.3 ratio=0.81 107 A.C970 A.G971 angle=126 distance=17.8 ratio=0.89 108 A.G971 A.C972 angle=99 distance=16.2 ratio=0.76 109 A.A974 A.A975 angle=145 distance=19.1 ratio=0.95 110 A.G976 A.A977 angle=87 distance=13.6 ratio=0.69 111 A.A977 A.A978 angle=125 distance=14.8 ratio=0.89 112 A.U991 A.U992 angle=95 distance=13.8 ratio=0.74 113 A.A1004 A.A1005 angle=87 distance=12.1 ratio=0.70 114 A.G1013 A.A1014 angle=100 distance=13.2 ratio=0.76 115 A.G1048 A.U1049 angle=156 distance=18.4 ratio=0.98 116 A.U1049 A.G1050 angle=124 distance=17.8 ratio=0.89 117 A.G1053 A.C1054 angle=139 distance=19.3 ratio=0.94 118 A.C1054 A.A1055 angle=148 distance=17.0 ratio=0.96 119 A.U1085 A.U1086 angle=107 distance=15.0 ratio=0.80 120 A.A1093 A.G1094 angle=106 distance=17.1 ratio=0.80 121 A.G1094 A.U1095 angle=111 distance=15.7 ratio=0.82 122 A.G1124 A.U1125 angle=134 distance=18.2 ratio=0.92 123 A.U1125 A.U1126 angle=125 distance=15.9 ratio=0.89 124 A.C1129 A.A1130 angle=96 distance=14.2 ratio=0.74 125 A.U1135 A.U1136 angle=98 distance=13.4 ratio=0.75 126 A.U1136 A.C1137 angle=103 distance=14.7 ratio=0.78 127 A.G1182 A.A1183 angle=153 distance=19.7 ratio=0.97 128 A.A1183 A.G1184 angle=102 distance=14.9 ratio=0.78 129 A.G1190 A.A1191 angle=94 distance=13.4 ratio=0.73 130 A.C1195 A.U1196 angle=105 distance=17.0 ratio=0.79 131 A.U1196 A.G1197 angle=135 distance=17.0 ratio=0.92 132 A.C1200 A.A1201 angle=150 distance=18.9 ratio=0.97 133 A.A1201 A.G1202 angle=160 distance=17.6 ratio=0.98 134 A.U1211 A.U1212 angle=139 distance=18.9 ratio=0.94 135 A.U1212 A.A1213 angle=89 distance=12.8 ratio=0.70 136 A.C1214 A.G1215 angle=125 distance=16.7 ratio=0.89 137 A.G1224 A.A1225 angle=140 distance=17.3 ratio=0.94 138 A.C1237 A.A1238 angle=129 distance=16.9 ratio=0.90 139 A.A1239 A.U1240 angle=163 distance=19.2 ratio=0.99 140 A.U1240 A.G1241 angle=129 distance=17.2 ratio=0.90 141 A.A1256 A.U1257 angle=129 distance=17.9 ratio=0.90 142 A.U1257 A.G1258 angle=122 distance=16.6 ratio=0.87 143 A.G1266 A.C1267 angle=87 distance=12.3 ratio=0.69 144 A.C1277 A.U1278 angle=116 distance=15.1 ratio=0.85 145 A.U1278 A.A1279 angle=145 distance=13.6 ratio=0.95 146 A.A1279 A.A1280 angle=130 distance=17.3 ratio=0.91 147 A.A1280 A.U1281 angle=90 distance=14.0 ratio=0.71 148 A.U1281 A.C1282 angle=88 distance=13.6 ratio=0.70 149 A.U1301 A.U1302 angle=93 distance=13.7 ratio=0.73 150 A.U1302 A.C1303 angle=156 distance=18.4 ratio=0.98 151 A.A1319 A.C1320 angle=89 distance=13.6 ratio=0.71 152 A.C1322 A.G1323 angle=91 distance=13.9 ratio=0.71 153 A.C1335 A.C1336 angle=93 distance=14.0 ratio=0.72 154 A.G1337 A.G1338 angle=101 distance=15.2 ratio=0.77 155 A.C1359 A.A1360 angle=116 distance=15.4 ratio=0.85 156 A.C1362 A.A1363 angle=105 distance=14.7 ratio=0.80 157 A.A1363 A.U1364 angle=119 distance=16.5 ratio=0.86 158 A.U1364 A.G1365 angle=111 distance=15.9 ratio=0.83 159 A.A1377 A.C1378 angle=115 distance=14.9 ratio=0.84 160 A.U1393 A.A1394 angle=124 distance=15.8 ratio=0.88 161 A.A1394 A.C1395 angle=113 distance=15.8 ratio=0.84 162 A.A1396 A.C1397 angle=162 distance=19.0 ratio=0.99 163 A.C1397 A.A1398 angle=93 distance=14.9 ratio=0.72 164 A.A1398 A.C1399 angle=119 distance=15.5 ratio=0.86 165 A.C1399 A.5MC1400 angle=149 distance=18.8 ratio=0.96 166 A.5MC1400 A.G1401 angle=143 distance=18.1 ratio=0.95 167 A.G1442 A.G1443 angle=172 distance=16.3 ratio=1.00 168 A.G1443 A.A1446 angle=143 distance=16.8 ratio=0.95 169 A.U1450 A.A1451 angle=117 distance=15.1 ratio=0.85 170 A.A1451 A.C1452 angle=95 distance=14.6 ratio=0.74 171 A.G1491 A.A1492 angle=107 distance=16.4 ratio=0.81 172 A.A1493 A.G1494 angle=142 distance=16.9 ratio=0.95 173 A.A1502 A.A1503 angle=102 distance=15.0 ratio=0.78 174 A.A1503 A.G1504 angle=109 distance=17.0 ratio=0.82 175 A.G1505 A.U1506 angle=133 distance=17.9 ratio=0.92 176 A.U1506 A.A1507 angle=99 distance=15.6 ratio=0.76 177 A.G1529 A.G1530 angle=99 distance=16.3 ratio=0.76 178 A.PSU1541 A.U1542 angle=93 distance=13.7 ratio=0.73 ---------------------------------------------------------------- Summary of 110 splayed-apart units 1 nts=3 GGA A.G6,A.G7,A.A8 2 nts=2 UU A.U13,A.U14 3 nts=3 UGA A.U30,A.G31,A.A32 4 nts=2 GG A.G38,A.G39 5 nts=3 GCC A.G46,A.C47,A.C48 6 nts=3 AAG A.A50,A.A51,A.G52 7 nts=2 AA A.A59,A.A60 8 nts=3 GUG A.G64,A.U65,A.G66 9 nts=2 UU A.U81,A.U82 10 nts=2 AC A.A120,A.C121 11 nts=3 UGA A.U129,A.G129^A,A.A130 12 nts=2 AG A.A143,A.G144 13 nts=2 UC A.U173,A.C174 14 nts=2 UU A.U190^D,A.U190^E 15 nts=2 GG A.G190^F,A.G190^G 16 nts=2 AA A.A196,A.A197 17 nts=2 UU A.U202,A.U203 18 nts=2 UC A.U239,A.C240 19 nts=3 AUC A.A243,A.U244,A.C245 20 nts=2 GG A.G265,A.G266 21 nts=3 ACG A.A279,A.C280,A.G281 22 nts=2 GA A.G297,A.A298 23 nts=2 GG A.G305,A.G306 24 nts=2 AG A.A315,A.G316 25 nts=4 ACAC A.A327,A.C328,A.A329,A.C330 26 nts=2 GG A.G331,A.G332 27 nts=3 UAC A.U343,A.A344,A.C345 28 nts=4 GCAG A.G351,A.C352,A.A353,A.G354 29 nts=2 UC A.U365,A.C366 30 nts=3 UUC A.U367,A.U368,A.C369 31 nts=3 UGA A.U387,A.G388,A.A389 32 nts=3 GAC A.G396,A.A397,A.C398 33 nts=2 UG A.U405,A.G406 34 nts=2 GA A.G413,A.A414 35 nts=2 UU A.U420,A.U421 36 nts=3 ACG A.A460,A.C461,A.G462 37 nts=2 AU A.A497,A.U498 38 nts=2 CG A.C504,A.G505 39 nts=3 GCC A.G517,A.C518,A.C519 40 nts=2 AG A.A523,A.G524 41 nts=5 GUAAU A.G530,A.U531,A.A532,A.A533,A.U534 42 nts=2 AC A.A535,A.C536 43 nts=4 AUUC A.A559,A.U560,A.U561,A.C562 44 nts=2 AC A.A563,A.C564 45 nts=2 GG A.G566,A.G567 46 nts=2 CG A.C569,A.G570 47 nts=2 GA A.G606,A.A607 48 nts=2 CU A.C618,A.U619 49 nts=3 GAG A.G664,A.A665,A.G666 50 nts=3 CAG A.C701,A.A702,A.G703 51 nts=3 AUG A.A722,A.U723,A.G724 52 nts=2 AG A.A733,A.G734 53 nts=2 CG A.C754,A.G755 54 nts=2 GA A.G765,A.A766 55 nts=2 GA A.G776,A.A777 56 nts=3 AUA A.A792,A.U793,A.A794 57 nts=8 AAACGAUG A.A814,A.A815,A.A816,A.C817,A.G818,A.A819,A.U820,A.G821 58 nts=3 UCU A.U839,A.C840,A.U841 59 nts=2 UA A.U863,A.A864 60 nts=6 GUUAAG A.G869,A.U870,A.U871,A.A872,A.A873,A.G874 61 nts=2 UG A.U884,A.G885 62 nts=2 GC A.G898,A.C899 63 nts=3 GGG A.G925,A.G926,A.G927 64 nts=2 GC A.G933,A.C934 65 nts=2 UU A.U960,A.U961 66 nts=2 Ag A.A965,A.M2G966 67 nts=2 AA A.A968,A.A969 68 nts=3 CGC A.C970,A.G971,A.C972 69 nts=2 AA A.A974,A.A975 70 nts=3 GAA A.G976,A.A977,A.A978 71 nts=2 UU A.U991,A.U992 72 nts=2 AA A.A1004,A.A1005 73 nts=2 GA A.G1013,A.A1014 74 nts=3 GUG A.G1048,A.U1049,A.G1050 75 nts=3 GCA A.G1053,A.C1054,A.A1055 76 nts=2 UU A.U1085,A.U1086 77 nts=3 AGU A.A1093,A.G1094,A.U1095 78 nts=3 GUU A.G1124,A.U1125,A.U1126 79 nts=2 CA A.C1129,A.A1130 80 nts=3 UUC A.U1135,A.U1136,A.C1137 81 nts=3 GAG A.G1182,A.A1183,A.G1184 82 nts=2 GA A.G1190,A.A1191 83 nts=3 CUG A.C1195,A.U1196,A.G1197 84 nts=3 CAG A.C1200,A.A1201,A.G1202 85 nts=3 UUA A.U1211,A.U1212,A.A1213 86 nts=2 CG A.C1214,A.G1215 87 nts=2 GA A.G1224,A.A1225 88 nts=2 CA A.C1237,A.A1238 89 nts=3 AUG A.A1239,A.U1240,A.G1241 90 nts=3 AUG A.A1256,A.U1257,A.G1258 91 nts=2 GC A.G1266,A.C1267 92 nts=6 CUAAUC A.C1277,A.U1278,A.A1279,A.A1280,A.U1281,A.C1282 93 nts=3 UUC A.U1301,A.U1302,A.C1303 94 nts=2 AC A.A1319,A.C1320 95 nts=2 CG A.C1322,A.G1323 96 nts=2 CC A.C1335,A.C1336 97 nts=2 GG A.G1337,A.G1338 98 nts=2 CA A.C1359,A.A1360 99 nts=4 CAUG A.C1362,A.A1363,A.U1364,A.G1365 100 nts=2 AC A.A1377,A.C1378 101 nts=3 UAC A.U1393,A.A1394,A.C1395 102 nts=6 ACACcG A.A1396,A.C1397,A.A1398,A.C1399,A.5MC1400,A.G1401 103 nts=3 GGA A.G1442,A.G1443,A.A1446 104 nts=3 UAC A.U1450,A.A1451,A.C1452 105 nts=2 GA A.G1491,A.A1492 106 nts=2 AG A.A1493,A.G1494 107 nts=3 AAG A.A1502,A.A1503,A.G1504 108 nts=3 GUA A.G1505,A.U1506,A.A1507 109 nts=2 GG A.G1529,A.G1530 110 nts=2 PU A.PSU1541,A.U1542 **************************************************************************** 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 >4lfb nts=1512 [whole] UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGPGCCAGCAGCCgCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAgcAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGgCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACcGcCcGUcACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGuAACAAGGUAGCUGUACCGGaaGGUGCGGCUGGAUC&CPPUCU ....((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((((((((((.....)))))))))).)))))......(((......((((((((..((...(((((((.(((((....((((((....)))))).....)))))....((((.(((((....))))).))))...((((...)))).)))))))..))))))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...(((((....)))).))))).)).))))))..((((......((((....)))).....))))....(((((...(....((((.....)))).....)....)))))......((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((((((((...((((((((....((((((....((........)).......))))))....).......((....)).)))))))..))))).)))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((...))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((((.(((((((.((..(((((..((((((((((......((........))..........(((((((..(...(.((((.(..((.((((....)))).))....(((....)))....))))).)).((.(((...((((((.(....(((((((((....)))...(((......)))...)))))).....((((.(((((((..((...(((.....)))).)...)))))))..(..(((((....))))).....)..)))).....).).)))...)).)))))....)))))))..[)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((......]...)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((((((.((((((...(.((((....(((....))).)))).)..)))))).))))))..))).))))..).))...)..)..(((((((((....)))))))))}....&...... >4lfb-A #1 nts=1512 0.00(3.40) [chain] RNA* UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGPGCCAGCAGCCgCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAgcAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGgCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACcGcCcGUcACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGuAACAAGGUAGCUGUACCGGaaGGUGCGGCUGGAUC&CPPUCU ....((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((((((((((.....)))))))))).)))))......(((......((((((((..((...(((((((.(((((....((((((....)))))).....)))))....((((.(((((....))))).))))...((((...)))).)))))))..))))))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...(((((....)))).))))).)).))))))..((((......((((....)))).....))))....(((((...(....((((.....)))).....)....)))))......((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((((((((...((((((((....((((((....((........)).......))))))....).......((....)).)))))))..))))).)))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((...))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((((.(((((((.((..(((((..((((((((((......((........))..........(((((((..(...(.((((.(..((.((((....)))).))....(((....)))....))))).)).((.(((...((((((.(....(((((((((....)))...(((......)))...)))))).....((((.(((((((..((...(((.....)))).)...)))))))..(..(((((....))))).....)..)))).....).).)))...)).)))))....)))))))..[)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((......]...)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((((((.((((((...(.((((....(((....))).)))).)..)))))).))))))..))).))))..).))...)..)..(((((((((....)))))))))}....&...... **************************************************************************** Summary of structural features of 1512 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 U . A.U5 0.004 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 2 G . A.G6 0.010 syn,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 3 G . A.G7 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 4 A . A.A8 0.008 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 5 G ( A.G9 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,phosphate 6 A ( A.A10 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( A.G11 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 8 U ( A.U12 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 9 U . A.U13 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,splayed-apart 10 U . A.U14 0.003 u-turn,anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 11 G [ A.G15 0.009 pseudoknotted,turn,u-turn,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,hairpin-loop,internal-loop,phosphate 12 A . A.A16 0.009 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,internal-loop,A-minor,ribose-zipper,cap-donor,phosphate 13 U [ A.U17 0.009 pseudoknotted,u-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,internal-loop,ribose-zipper,phosphate 14 C [ A.C18 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,phosphate 15 C [ A.C19 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,phosphate 16 U . A.U20 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-donor 17 G . A.G21 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate 18 G ) A.G22 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,cap-donor 19 C ) A.C23 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 20 U ) A.U24 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 21 C ) A.C25 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet 22 A . A.A26 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 23 G ( A.G27 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 24 G ( A.G28 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ( A.G29 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 U ( A.U30 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 27 G . A.G31 0.003 turn,anti,~C2'-endo,non-pair-contact,bulge,splayed-apart 28 A ( A.A32 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 29 A ( A.A33 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 C ( A.C34 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 G ( A.G35 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 C ( A.C36 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 33 U . A.U37 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 34 G . A.G38 0.004 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 35 G ( A.G39 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 36 C ( A.C40 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 37 G ( A.G41 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 38 G ( A.G42 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 39 C ( A.C43 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 G ( A.G44 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 41 U ( A.U45 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 42 G ( A.G46 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 43 C ( A.C47 0.006 turn,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,cap-donor,phosphate,splayed-apart 44 C . A.C48 0.004 turn,anti,~C2'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 45 U . A.U49 0.008 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 46 A . A.A50 0.006 anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 47 A . A.A51 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,splayed-apart 48 G ( A.G52 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,splayed-apart 49 A ( A.A53 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 50 C ( A.C54 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,bulge 51 A . A.A55 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,bulge,phosphate 52 U ( A.U56 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge 53 G ( A.G57 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 54 C ( A.C58 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 55 A . A.A59 0.005 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 56 A . A.A60 0.006 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate,splayed-apart 57 G ( A.G61 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 58 U ( A.U62 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 59 C ( A.C63 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 60 G . A.G64 0.011 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,phosphate,splayed-apart 61 U . A.U65 0.004 turn,anti,~C2'-endo,non-canonical,non-pair-contact,bulge,cap-acceptor,splayed-apart 62 G ( A.G66 0.002 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,ribose-zipper,cap-donor,splayed-apart 63 C ( A.C67 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,ribose-zipper 64 G . A.G68 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 65 G ( A.G69 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 66 G ( A.G70 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 67 C ( A.C73 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 C ( A.C74 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 69 G ( A.G75 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 C ( A.C76 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 71 G ( A.G77 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 72 G ( A.G78 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 73 G ( A.G79 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 74 G ( A.G80 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 75 U . A.U81 0.005 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 76 U . A.U82 0.006 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 77 U . A.U83 0.005 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 78 U . A.U84 0.004 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 79 A . A.A88 0.005 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 80 C ) A.C89 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 81 U ) A.U90 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 82 C ) A.C91 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 83 C ) A.C92 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 84 G ) A.G93 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 85 U ) A.U95 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 86 G ) A.G96 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 87 G ) A.G97 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 88 U ) A.U98 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 89 C ) A.C99 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 90 A . A.A101 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 91 G ) A.G102 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,phosphate 92 C ) A.C103 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 93 G ) A.G104 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 94 G ) A.G105 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 95 C ) A.C106 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 96 G . A.G107 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,cap-acceptor,phosphate 97 G . A.G108 0.021 syn,~C3'-endo,non-pair-contact,junction-loop,cap-donor,phosphate 98 A . A.A109 0.009 turn,syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 99 C . A.C110 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 100 G . A.G111 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 101 G . A.G112 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,ribose-zipper 102 G ( A.G113 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,ribose-zipper,phosphate 103 U ( A.U114 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 104 G ( A.G115 0.020 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 105 A . A.A116 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,phosphate 106 G . A.G117 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 107 U . A.U118 0.005 anti,~C3'-endo,BI,non-pair-contact,junction-loop 108 A . A.A119 0.007 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,phosphate 109 A . A.A120 0.008 anti,~C3'-endo,BI,non-pair-contact,junction-loop,cap-acceptor,splayed-apart 110 C . A.C121 0.004 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 111 G ( A.G122 0.007 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 112 C ( A.C123 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 113 G ( A.G124 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 114 U ( A.U125 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 115 G ( A.G126 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 116 G ( A.G127 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 117 G ( A.G128 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 118 U ( A.U129 0.005 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate,splayed-apart 119 G . A.G129^A 0.014 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,bulge,cap-acceptor,splayed-apart 120 A . A.A130 0.009 anti,~C2'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor,cap-donor,phosphate,splayed-apart 121 C ( A.C131 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,A-minor,phosphate 122 C ( A.C132 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 123 U . A.U133 0.010 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop,phosphate 124 A . A.A134 0.006 anti,~C3'-endo,non-pair-contact,internal-loop,cap-donor 125 C . A.C135 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 126 C ( A.C136 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 127 C ( A.C137 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 128 G ( A.G138 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 129 G ( A.G139 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 130 A ( A.A140 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 131 A ( A.A141 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 132 G ( A.G142 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 133 A . A.A143 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,cap-donor,splayed-apart 134 G ( A.G144 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 135 G ( A.G145 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 136 G ( A.G146 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 137 G ( A.G147 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 138 G ( A.G148 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 139 A . A.A149 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 140 C . A.C150 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 141 A . A.A151 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 142 A . A.A152 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 143 C ( A.C153 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 144 C ( A.C154 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 145 C ( A.C155 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 146 G ( A.G156 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 147 G ( A.G157 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 148 G ( A.G158 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 149 G . A.G159 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 150 A . A.A160 0.005 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,cap-acceptor 151 A . A.A161 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,cap-donor,phosphate 152 A . A.A162 0.003 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 153 C ) A.C163 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 154 U ) A.U164 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 155 C ) A.C165 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 156 G ) A.G166 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 157 G ) A.G167 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 158 G ) A.G168 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 159 C . A.C169 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 160 U . A.U170 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 161 A . A.A171 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper 162 A . A.A172 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper 163 U . A.U173 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 164 C ) A.C174 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 165 C ) A.C175 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 166 C ) A.C176 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 167 C ) A.C177 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 168 C ) A.C178 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 169 A . A.A179 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop 170 U . A.U180 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 171 G . A.G181 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 172 U . A.U182 0.005 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 173 G ( A.G183 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 174 G ( A.G184 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 175 A ( A.A185 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 176 C ( A.C186 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 177 C . A.C187 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 178 C ( A.C188 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 179 G ( A.G189 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 180 C ( A.C190 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 181 C ( A.C190^A 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 182 C ( A.C190^B 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 183 C . A.C190^C 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 184 U . A.U190^D 0.006 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 185 U . A.U190^E 0.006 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 186 G . A.G190^F 0.008 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 187 G ) A.G190^G 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,splayed-apart 188 G ) A.G190^H 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 189 G ) A.G190^I 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 190 U ) A.U190^J 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 191 G ) A.G190^K 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 192 U . A.U190^L 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 193 G ) A.G191 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 194 U ) A.U192 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 195 C ) A.C193 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 196 C ) A.C194 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 197 A . A.A195 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,A-minor,ribose-zipper,phosphate 198 A . A.A196 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate,splayed-apart 199 A . A.A197 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-acceptor,splayed-apart 200 G ( A.G198 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 201 G ( A.G199 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 202 G ( A.G200 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 203 C ( A.C201 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 204 U . A.U202 0.002 turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 205 U . A.U203 0.004 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 206 U . A.U204 0.003 turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop 207 G ) A.G216 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 208 C ) A.C217 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 209 C ) A.C218 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 210 C ) A.C219 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 211 G . A.G220 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop 212 C ) A.C221 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,ribose-zipper,cap-donor 213 U ) A.U222 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper 214 U ) A.U223 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 215 C ) A.C224 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 216 C ) A.C225 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 217 G ) A.G226 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 218 G ) A.G227 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 219 A . A.A228 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 220 U . A.U229 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 221 G ) A.G230 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 222 G ) A.G231 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,A-minor 223 G ) A.G232 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 224 C ) A.C233 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 225 C ) A.C234 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 226 C ) A.C235 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 227 G ) A.G236 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 228 C ) A.C237 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 229 G ) A.G238 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 230 U ) A.U239 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,splayed-apart 231 C ( A.C240 0.009 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,splayed-apart 232 C ( A.C241 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 233 C ( A.C242 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 234 A . A.A243 0.010 turn,k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,splayed-apart 235 U . A.U244 0.006 turn,k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 236 C . A.C245 0.005 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 237 A . A.A246 0.007 k-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop 238 G ( A.G247 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,phosphate 239 C ( A.C248 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 240 U ( A.U249 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,bulge 241 A . A.A250 0.007 anti,~C2'-endo,non-pair-contact,bulge 242 G . A.G251 0.010 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge 243 U ( A.U252 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,bulge 244 U ( A.U253 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 245 G ( A.G254 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,phosphate 246 G ( A.G255 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,phosphate 247 U ( A.U256 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 248 G ( A.G257 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 249 G ( A.G258 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 250 G ( A.G259 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 251 G . A.G260 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 252 U . A.U261 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 253 A . A.A262 0.006 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor 254 A . A.A263 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,phosphate 255 U . A.U264 0.006 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 256 G . A.G265 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 257 G . A.G266 0.019 turn,u-turn,anti,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate,splayed-apart 258 C ) A.C267 0.008 turn,u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 259 C ) A.C268 0.003 u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 260 C ) A.C269 0.005 u-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 261 A ) A.A270 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 262 C ) A.C271 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 263 C ) A.C272 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet 264 A ) A.A273 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 265 A ) A.A274 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,bulge 266 G ) A.G275 0.011 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,bulge,phosphate 267 G ) A.G276 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 268 C ) A.C277 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,internal-loop,A-minor,phosphate 269 G . A.G278 0.004 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 270 A . A.A279 0.009 turn,k-turn,syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-donor,phosphate,splayed-apart 271 C . A.C280 0.005 turn,k-turn,anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 272 G . A.G281 0.005 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,splayed-apart 273 A . A.A282 0.005 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,phosphate 274 C . A.C283 0.008 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 275 G ) A.G284 0.010 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 276 G ) A.G285 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 277 G ) A.G286 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 278 U . A.U287 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop 279 A . A.A288 0.004 anti,~C3'-endo,BI,non-pair-contact,junction-loop 280 G ( A.G289 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 281 C ( A.C290 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 282 C ( A.C291 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 283 G ( A.G292 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 284 G ( A.G293 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 285 U ( A.U294 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 286 C ( A.C295 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 287 U ( A.U296 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 288 G . A.G297 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor,phosphate,splayed-apart 289 A . A.A298 0.010 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 290 G . A.G299 0.013 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate 291 A . A.A300 0.012 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,cap-acceptor,phosphate 292 G ) A.G301 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 293 G ) A.G302 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 294 A ) A.A303 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 295 U ) A.U304 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 296 G . A.G305 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge,splayed-apart 297 G . A.G306 0.007 anti,~C3'-endo,BI,non-pair-contact,bulge,splayed-apart 298 C . A.C307 0.004 anti,~C3'-endo,non-pair-contact,bulge 299 C ) A.C308 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,phosphate 300 G ) A.G309 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,phosphate 301 G ) A.G310 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 302 C ) A.C311 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 303 C ) A.C312 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 304 A ) A.A313 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 305 C ) A.C314 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 306 A . A.A315 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor,phosphate,splayed-apart 307 G ( A.G316 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 308 G ( A.G317 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 309 G ( A.G318 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 310 G ( A.G319 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 311 C ( A.C320 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 312 A . A.A321 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 313 C . A.C322 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 314 U . A.U323 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 315 G . A.G324 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 316 A . A.A325 0.011 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 317 G . A.G326 0.013 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 318 A . A.A327 0.011 u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate,splayed-apart 319 C . A.C328 0.013 turn,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 320 A . A.A329 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate,splayed-apart 321 C . A.C330 0.002 anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 322 G . A.G331 0.003 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate,splayed-apart 323 G . A.G332 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,splayed-apart 324 G ) A.G333 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 325 C ) A.C334 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 326 C ) A.C335 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper 327 C ) A.C336 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 328 C ) A.C337 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 329 A . A.A338 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 330 C ( A.C339 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 331 U ( A.U340 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 332 C ( A.C341 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 333 C ( A.C342 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 334 U . A.U343 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,splayed-apart 335 A . A.A344 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 336 C . A.C345 0.005 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 337 G . A.G346 0.009 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 338 G ) A.G347 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 339 G ) A.G348 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 340 A ) A.A349 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 341 G ) A.G350 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 342 G . A.G351 0.011 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 343 C . A.C352 0.005 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate,splayed-apart 344 A . A.A353 0.014 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,phosphate,splayed-apart 345 G ) A.G354 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop,ribose-zipper,phosphate,splayed-apart 346 C ) A.C355 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 347 A ) A.A356 0.005 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge,phosphate 348 G ) A.G357 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,bulge,phosphate 349 U ) A.U358 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 350 U ) A.U359 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 351 A . A.A360 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop 352 G ) A.G361 0.008 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 353 G . A.G362 0.009 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,phosphate 354 A . A.A363 0.006 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 355 A . A.A364 0.008 u-turn,anti,~C3'-endo,BI,non-pair-contact,junction-loop,cap-donor,phosphate 356 U . A.U365 0.009 u-turn,syn,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,cap-acceptor,phosphate,splayed-apart 357 C . A.C366 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 358 U ( A.U367 0.005 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate,splayed-apart 359 U . A.U368 0.008 turn,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,helix-end,multiplet,bulge,splayed-apart 360 C ( A.C369 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 361 C ( A.C370 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 362 G ( A.G371 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 363 C . A.C372 0.008 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,bulge 364 A . A.A373 0.009 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,bulge,A-minor 365 A . A.A374 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor,phosphate 366 U ( A.U375 0.006 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,multiplet,bulge,phosphate 367 G ( A.G376 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 368 G ( A.G377 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 369 G ( A.G378 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 370 C ( A.C379 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 371 G . A.G380 0.008 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 372 C . A.C381 0.004 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 373 A . A.A382 0.005 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 374 A . A.A383 0.006 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 375 G ) A.G384 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor 376 C ) A.C385 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 377 C ) A.C386 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 378 U ) A.U387 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 379 G . A.G388 0.006 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,phosphate,splayed-apart 380 A ) A.A389 0.007 turn,anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,A-minor,cap-acceptor,phosphate,splayed-apart 381 C ) A.C390 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,cap-donor,phosphate 382 G ) A.G391 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 383 G ) A.G392 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 384 A ) A.A393 0.006 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,junction-loop,phosphate 385 G . A.G394 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 386 C ) A.C395 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 387 G ) A.G396 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 388 A . A.A397 0.013 turn,syn,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,bulge,phosphate,splayed-apart 389 C ) A.C398 0.004 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 390 G ) A.G399 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 391 C ) A.C400 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 392 C ) A.C401 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 393 G ) A.G402 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 394 C ) A.C403 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 395 U . A.U404 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 396 U . A.U405 0.008 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 397 G ( A.G406 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 398 G ( A.G407 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 399 A ( A.A408 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 400 G ( A.G409 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 401 G . A.G410 0.004 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 402 A . A.A411 0.002 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 403 A . A.A412 0.006 turn,k-turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop 404 G . A.G413 0.008 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate,splayed-apart 405 A . A.A414 0.002 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 406 A . A.A415 0.002 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 407 G ( A.G416 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 408 C ( A.C417 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 409 C ( A.C418 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 410 C ( A.C419 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 411 U . A.U420 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 412 U . A.U421 0.004 turn,syn,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 413 C . A.C422 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor 414 G . A.G423 0.010 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 415 G ) A.G424 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 416 G ) A.G425 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 417 G ) A.G426 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 418 U ) A.U427 0.005 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 419 G . A.G428 0.003 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 420 U . A.U429 0.008 turn,k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 421 A . A.A430 0.004 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 422 A . A.A431 0.003 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 423 A . A.A432 0.005 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 424 C ) A.C433 0.010 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 425 U ) A.U434 0.002 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 426 C ) A.C435 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 427 C ) A.C436 0.002 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 428 U . A.U437 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 429 G . A.G438 0.005 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,cap-donor 430 A . A.A439 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 431 A . A.A440 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop 432 C ( A.C442 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 433 C ( A.C443 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 434 C ( A.C444 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 435 G ( A.G445 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 436 G ( A.G446 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 437 G . A.G447 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 438 A . A.A448 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 439 C . A.C449 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 440 G ( A.G450 0.005 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate 441 A . A.A451 0.009 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate 442 A . A.A452 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,phosphate 443 A . A.A453 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 444 C . A.C454 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 445 C ( A.C455 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 446 C ( A.C456 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 447 C ( A.C457 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 448 C ( A.C458 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 449 G . A.G459 0.003 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 450 A . A.A460 0.006 u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 451 C . A.C461 0.004 turn,u-turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 452 G . A.G462 0.005 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 453 A . A.A463 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 454 G ) A.G474 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 455 G ) A.G475 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 456 G ) A.G476 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 457 G ) A.G477 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 458 A . A.A478 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 459 C . A.C479 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 460 U . A.U480 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 461 G . A.G481 0.006 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,internal-loop 462 A . A.A482 0.006 turn,anti,~C3'-endo,non-pair-contact,internal-loop,A-minor 463 C ) A.C483 0.004 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate 464 G . A.G484 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 465 G . A.G485 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 466 U . A.U486 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 467 A . A.A487 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 468 C ) A.C488 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 469 C ) A.C489 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 470 G ) A.G490 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 471 G ) A.G491 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 472 G ) A.G492 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 473 G . A.G494 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor 474 U . A.U495 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 475 A . A.A496 0.007 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate 476 A . A.A497 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 477 U . A.U498 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,splayed-apart 478 A . A.A499 0.008 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop 479 G ( A.G500 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 480 C ( A.C501 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 481 G ( A.G502 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 482 C ( A.C503 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,phosphate 483 C ( A.C504 0.004 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,phosphate,splayed-apart 484 G [ A.G505 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 485 G [ A.G506 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 486 C [ A.C507 0.006 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate 487 C . A.C508 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop,phosphate 488 A . A.A509 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,phosphate 489 A . A.A510 0.006 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 490 C ( A.C511 0.010 k-turn,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop 491 U ( A.U512 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 492 C ( A.C513 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 493 C ( A.C514 0.002 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop 494 G ( A.G515 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop 495 P . A.PSU516 0.038 modified,k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,internal-loop 496 G . A.G517 0.002 k-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,internal-loop,cap-acceptor,splayed-apart 497 C . A.C518 0.003 turn,k-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,internal-loop,cap-donor,phosphate,splayed-apart 498 C . A.C519 0.006 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,internal-loop,phosphate,splayed-apart 499 A . A.A520 0.005 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,internal-loop,phosphate 500 G ( A.G521 0.007 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,internal-loop,phosphate 501 C ( A.C522 0.008 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor,phosphate 502 A . A.A523 0.006 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,splayed-apart 503 G ] A.G524 0.008 pseudoknotted,turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,splayed-apart 504 C ] A.C525 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,phosphate 505 C ] A.C526 0.006 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,phosphate 506 g ) A.7MG527 0.087 modified,k-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor 507 C ) A.C528 0.007 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 508 G . A.G529 0.004 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,cap-acceptor 509 G . A.G530 0.005 turn,k-turn,anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 510 U . A.U531 0.004 k-turn,anti,~C2'-endo,BII,non-pair-contact,internal-loop,cap-donor,splayed-apart 511 A . A.A532 0.004 turn,k-turn,syn,~C2'-endo,non-stack,internal-loop,splayed-apart 512 A . A.A533 0.006 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate,splayed-apart 513 U . A.U534 0.003 turn,k-turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 514 A . A.A535 0.007 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,cap-acceptor,phosphate,splayed-apart 515 C ) A.C536 0.006 k-turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 516 G ) A.G537 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 517 G ) A.G538 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 518 A ) A.A539 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 519 G ) A.G540 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 520 G ) A.G541 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 521 G ) A.G542 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 522 C ) A.C543 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 523 G ) A.G544 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 524 C ) A.C545 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate 525 G . A.G546 0.005 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 526 A . A.A547 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 527 G ) A.G548 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 528 C ) A.C549 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 529 G ) A.G550 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 530 U ) A.U551 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 531 U ) A.U552 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 532 A ) A.A553 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 533 C ) A.C554 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 534 C ) A.C555 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 535 C ) A.C556 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 536 G . A.G557 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop 537 G . A.G558 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 538 A . A.A559 0.014 syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate,splayed-apart 539 U . A.U560 0.009 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate,splayed-apart 540 U . A.U561 0.009 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,ss-non-loop,splayed-apart 541 C . A.C562 0.005 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 542 A . A.A563 0.009 syn,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 543 C . A.C564 0.003 turn,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 544 U . A.U565 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,phosphate 545 G . A.G566 0.012 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,ss-non-loop,splayed-apart 546 G ( A.G567 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,phosphate,splayed-apart 547 G ( A.G568 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 548 C ( A.C569 0.007 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 549 G [ A.G570 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,junction-loop,cap-donor,splayed-apart 550 U [ A.U571 0.007 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 551 A . A.A572 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,cap-acceptor,phosphate 552 A . A.A573 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper,phosphate 553 A . A.A574 0.011 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 554 G ( A.G575 0.007 anti,~C2'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,junction-loop 555 G . A.G576 0.009 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,junction-loop,cap-acceptor,phosphate 556 G ( A.G577 0.014 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,ribose-zipper,cap-donor,phosphate 557 C ( A.C578 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper,phosphate 558 G ( A.G579 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 559 U ( A.U580 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 560 G . A.G581 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 561 U . A.U582 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 562 A . A.A583 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 563 G ( A.G584 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 564 G ( A.G585 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 565 C ( A.C586 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 566 G . A.G587 0.010 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate 567 G ( A.G588 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 568 C ( A.C589 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 569 C ( A.C590 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 570 U ( A.U591 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 571 G ( A.G592 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 572 G ( A.G593 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 573 G ( A.G594 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 574 G . A.G595 0.009 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge 575 C ( A.C596 0.002 anti,~C3'-endo,BI,non-stack,canonical,non-canonical,helix,stem-end,coaxial-stack,multiplet,bulge 576 G ( A.G597 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,cap-acceptor,phosphate 577 U ( A.U598 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,cap-donor 578 C ( A.C599 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 579 C ( A.C600 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 580 C ( A.C601 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 581 A ( A.A602 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 582 U ( A.U603 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 583 G ( A.G604 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 584 U ( A.U605 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 585 G . A.G606 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,splayed-apart 586 A . A.A607 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop,A-minor,phosphate,splayed-apart 587 A . A.A608 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,phosphate 588 A . A.A609 0.007 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate 589 G . A.G610 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop 590 A . A.A611 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 591 C ( A.C612 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 592 C ( A.C613 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 593 A ( A.A614 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 594 C ( A.C615 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 595 G ( A.G616 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 596 G ( A.G617 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 597 C . A.C618 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 598 U . A.U619 0.006 turn,anti,~C3'-endo,non-stack,hairpin-loop,splayed-apart 599 C . A.C620 0.003 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 600 A . A.A621 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 601 A . A.A622 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 602 C ) A.C623 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 603 C ) A.C624 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 604 G ) A.G625 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 605 U ) A.U626 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 606 G ) A.G627 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 607 G ) A.G628 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 608 G . A.G629 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 609 G . A.G630 0.007 anti,~C3'-endo,non-pair-contact,internal-loop 610 G . A.G631 0.003 anti,~C3'-endo,BII,non-pair-contact,internal-loop 611 A . A.A632 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 612 G ) A.G633 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 613 C ) A.C634 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 614 G ) A.G635 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 615 U ) A.U636 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 616 G ) A.G637 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 617 G ) A.G638 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 618 G ) A.G639 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 619 A ) A.A640 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 620 U . A.U641 0.008 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge 621 A . A.A642 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor 622 C ) A.C643 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 623 G ) A.G644 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 624 C ) A.C645 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 625 U ) A.U646 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 626 C ) A.C647 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 627 A ) A.A648 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 628 G ) A.G649 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 629 G ) A.G650 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 630 C ) A.C651 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 631 U . A.U652 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop 632 A . A.A653 0.008 turn,syn,~C2'-endo,non-stack,non-pair-contact,junction-loop,phosphate 633 G ( A.G654 0.007 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop 634 A ( A.A655 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 635 C ( A.C656 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 636 G ( A.G657 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 637 G ( A.G658 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 638 U ( A.U659 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 639 G ( A.G660 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 640 G ( A.G661 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 641 G ( A.G662 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 642 A . A.A663 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 643 G . A.G664 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 644 A . A.A665 0.009 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 645 G ( A.G666 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 646 G ( A.G667 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 647 G ( A.G668 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 648 U ( A.U669 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 649 G ( A.G670 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 650 G ( A.G671 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 651 U ( A.U672 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 652 G ( A.G673 0.010 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 653 G . A.G674 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 654 A . A.A675 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 655 A . A.A676 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 656 U . A.U677 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 657 U ( A.U678 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 658 C ( A.C679 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 659 C ( A.C680 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 660 C ( A.C681 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 661 G ( A.G682 0.002 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 662 G ( A.G683 0.007 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 663 A . A.A684 0.006 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 664 G . A.G685 0.009 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 665 U . A.U686 0.011 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop 666 A . A.A687 0.007 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,phosphate 667 G ( A.G688 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,A-minor,phosphate 668 C ( A.C689 0.006 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 669 G . A.G690 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 670 G . A.G691 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 671 U . A.U692 0.007 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 672 G . A.G693 0.010 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 673 A . A.A694 0.007 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 674 A . A.A695 0.010 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,phosphate 675 A . A.A696 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,A-minor,ribose-zipper,phosphate 676 U . A.U697 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,ribose-zipper 677 G ) A.G698 0.011 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 678 C ) A.C699 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,A-minor 679 G . A.G700 0.006 k-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 680 C . A.C701 0.005 turn,k-turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 681 A . A.A702 0.005 turn,k-turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 682 G . A.G703 0.005 k-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,cap-acceptor,splayed-apart 683 A . A.A704 0.006 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,phosphate 684 U . A.U705 0.007 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 685 A . A.A706 0.010 k-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 686 C ) A.C707 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 687 C ) A.C708 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 688 G ) A.G709 0.005 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 689 G ) A.G710 0.004 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 690 G ) A.G711 0.003 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 691 A ) A.A712 0.007 k-turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 692 G . A.G713 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 693 G . A.G714 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 694 A . A.A715 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 695 A . A.A716 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 696 C ) A.C717 0.007 anti,~C2'-endo,BII,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 697 G . A.G718 0.007 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 698 C . A.C719 0.006 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 699 C . A.C720 0.003 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 700 G . A.G721 0.011 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,phosphate 701 A . A.A722 0.015 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,cap-acceptor,splayed-apart 702 U . A.U723 0.010 turn,anti,~C3'-endo,non-stack,junction-loop,cap-acceptor,splayed-apart 703 G . A.G724 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate,splayed-apart 704 G ( A.G725 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 705 C ( A.C726 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 706 G . A.G727 0.008 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 707 A . A.A728 0.006 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,phosphate 708 A . A.A729 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 709 G . A.G730 0.007 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 710 G ) A.G731 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate 711 C ) A.C732 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop 712 A . A.A733 0.007 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop,splayed-apart 713 G ) A.G734 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 714 C ) A.C735 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 715 C ) A.C736 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 716 A ) A.A737 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 717 C ) A.C738 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 718 C ) A.C739 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 719 U ) A.U740 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 720 G . A.G741 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 721 G . A.G742 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 722 U ) A.U743 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 723 C ) A.C744 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 724 C ) A.C745 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 725 A ) A.A746 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 726 C ) A.C747 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 727 C . A.C748 0.004 turn,anti,~C2'-endo,non-pair-contact,bulge 728 C ) A.C749 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 729 G ) A.G750 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 730 U ) A.U751 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 731 G . A.G752 0.005 anti,~C2'-endo,BII,non-canonical,non-pair-contact,multiplet,bulge 732 A . A.A753 0.008 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,bulge,phosphate 733 C ) A.C754 0.007 turn,syn,~C3'-endo,non-stack,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,phosphate,splayed-apart 734 G ) A.G755 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 735 C ) A.C756 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 736 U ) A.U757 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 737 G . A.G758 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 738 A . A.A759 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 739 G . A.G760 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,cap-acceptor,phosphate 740 G ) A.G761 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor 741 C ) A.C762 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 742 G ) A.G763 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 743 C ) A.C764 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 744 G . A.G765 0.009 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 745 A . A.A766 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,ribose-zipper,phosphate,splayed-apart 746 A . A.A767 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,ribose-zipper 747 A . A.A768 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 748 G ( A.G769 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 749 C ( A.C770 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 750 G ( A.G771 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 751 U ( A.U772 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 752 G ( A.G773 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 753 G ( A.G774 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 754 G . A.G775 0.004 anti,~C3'-endo,BI,non-pair-contact,bulge 755 G . A.G776 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,splayed-apart 756 A . A.A777 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor,splayed-apart 757 G ( A.G778 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 758 C ( A.C779 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 759 A . A.A780 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 760 A . A.A781 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 761 A . A.A782 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 762 C ( A.C783 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 763 C ( A.C784 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 764 G ( A.G785 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor,ribose-zipper 765 G ( A.G786 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor,ribose-zipper 766 A . A.A787 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop 767 U . A.U788 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 768 U . A.U789 0.008 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 769 A . A.A790 0.006 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop 770 G . A.G791 0.012 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 771 A . A.A792 0.009 u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 772 U . A.U793 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 773 A . A.A794 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop,splayed-apart 774 C . A.C795 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 775 C ) A.C796 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,A-minor 776 C ) A.C797 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,A-minor 777 G ) A.G798 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 778 G ) A.G799 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 779 G . A.G800 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 780 U . A.U801 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 781 A . A.A802 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 782 G ) A.G803 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 783 U ) A.U804 0.009 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 784 C ) A.C805 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 785 C ) A.C806 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 786 A ) A.A807 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 787 C ) A.C808 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 788 G ) A.G809 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 789 C ) A.C810 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 790 C . A.C811 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 791 C . A.C812 0.009 anti,~C2'-endo,non-pair-contact,junction-loop,phosphate 792 U . A.U813 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,ribose-zipper,phosphate 793 A . A.A814 0.009 anti,~C3'-endo,BI,non-pair-contact,junction-loop,ribose-zipper,cap-acceptor,phosphate,splayed-apart 794 A . A.A815 0.010 turn,anti,~C2'-endo,non-pair-contact,junction-loop,splayed-apart 795 A . A.A816 0.011 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 796 C { A.C817 0.008 pseudoknotted,anti,~C2'-endo,isolated-canonical,non-pair-contact,junction-loop,cap-acceptor,splayed-apart 797 G . A.G818 0.009 turn,anti,~C2'-endo,non-pair-contact,junction-loop,cap-acceptor,splayed-apart 798 A . A.A819 0.009 turn,anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 799 U . A.U820 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 800 G ( A.G821 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 801 C ( A.C822 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 802 G ( A.G823 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 803 C ( A.C824 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 804 G ( A.G825 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 805 C ( A.C826 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 806 U . A.U827 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop 807 A . A.A828 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor,phosphate 808 G ( A.G829 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 809 G ( A.G830 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 810 U ( A.U831 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 811 C ( A.C832 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 812 U ( A.U833 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 813 C ( A.C834 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 814 U ( A.U835 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 815 G ( A.G836 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 816 G ( A.G837 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 817 G ( A.G838 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 818 U . A.U839 0.006 turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 819 C . A.C840 0.002 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 820 U . A.U841 0.004 turn,anti,~C3'-endo,non-stack,hairpin-loop,splayed-apart 821 C ) A.C848 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,hairpin-loop 822 C ) A.C849 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 823 U ) A.U850 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 824 G ) A.G851 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 825 G ) A.G852 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 826 G ) A.G853 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 827 G ) A.G854 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 828 G ) A.G855 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 829 C ) A.C856 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 830 C ) A.C857 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 831 G . A.G858 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 832 A . A.A859 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,phosphate 833 A . A.A860 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 834 G ( A.G861 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 835 C ( A.C862 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor 836 U . A.U863 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,splayed-apart 837 A . A.A864 0.009 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,A-minor,splayed-apart 838 A ] A.A865 0.011 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,junction-loop 839 C ] A.C866 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,hairpin-loop,junction-loop 840 G ) A.G867 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,A-minor 841 C ) A.C868 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor 842 G . A.G869 0.014 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,junction-loop,splayed-apart 843 U . A.U870 0.006 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 844 U . A.U871 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 845 A . A.A872 0.014 syn,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,splayed-apart 846 A . A.A873 0.015 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 847 G ) A.G874 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,splayed-apart 848 C ) A.C875 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 849 G ) A.G876 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 850 C ) A.C877 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 851 G ) A.G878 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 852 C ) A.C879 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 853 C ) A.C880 0.006 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 854 G ) A.G881 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,phosphate 855 C ) A.C882 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor,ribose-zipper,phosphate 856 C ) A.C883 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor,ribose-zipper 857 U . A.U884 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 858 G ( A.G885 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,cap-acceptor,splayed-apart 859 G ( A.G886 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 860 G ( A.G887 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 861 G . A.G888 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 862 A . A.A889 0.007 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 863 G . A.G890 0.008 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop 864 U . A.U891 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 865 A . A.A892 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 866 C . A.C893 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 867 G ( A.G894 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 868 G ( A.G895 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 869 C ( A.C896 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 870 C ( A.C897 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 871 G . A.G898 0.004 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,splayed-apart 872 C . A.C899 0.005 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 873 A . A.A900 0.007 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,cap-donor,phosphate 874 A . A.A901 0.007 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 875 G ) A.G902 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 876 G ) A.G903 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 877 C ) A.C904 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 878 U ) A.U905 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 879 G . A.G906 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 880 A . A.A907 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 881 A . A.A908 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 882 A . A.A909 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 883 C ) A.C910 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 884 U ) A.U911 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 885 C ) A.C912 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,phosphate 886 A . A.A913 0.010 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor 887 A . A.A914 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,phosphate 888 A . A.A915 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop 889 G ] A.G916 0.010 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,A-minor 890 G ] A.G917 0.008 pseudoknotted,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 891 A ] A.A918 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 892 A . A.A919 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,phosphate 893 U ] A.U920 0.005 pseudoknotted,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,cap-donor 894 U ( A.U921 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 895 G ( A.G922 0.009 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor 896 A ( A.A923 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 897 C ( A.C924 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 898 G ( A.G925 0.006 anti,~C3'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 899 G . A.G926 0.006 turn,anti,~C3'-endo,non-pair-contact,bulge,splayed-apart 900 G ( A.G927 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,cap-donor,phosphate,splayed-apart 901 G ( A.G928 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 902 G ( A.G929 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 903 C ( A.C930 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 904 C ( A.C931 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 905 C ( A.C932 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 906 G ( A.G933 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 907 C . A.C934 0.006 turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 908 A ( A.A935 0.006 turn,anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 909 C ( A.C936 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 910 A . A.A937 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 911 A . A.A938 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,ribose-zipper 912 G ( A.G939 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,ribose-zipper,phosphate 913 C ( A.C940 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 914 G ( A.G941 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 915 G ( A.G942 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 916 U ( A.U943 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 917 G . A.G944 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 918 G . A.G945 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 919 A ( A.A946 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor 920 G ( A.G947 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 921 C ( A.C948 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 922 A ( A.A949 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 923 U ( A.U950 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor,phosphate 924 G ( A.G951 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 925 U ( A.U952 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 926 G ( A.G953 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 927 G ( A.G954 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 928 U ( A.U955 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 929 U . A.U956 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 930 U . A.U957 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor 931 A . A.A958 0.005 turn,u-turn,anti,~C3'-endo,non-pair-contact,ss-non-loop,A-minor,ribose-zipper 932 A . A.A959 0.004 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,ribose-zipper,cap-donor,phosphate 933 U . A.U960 0.008 turn,u-turn,syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate,splayed-apart 934 U . A.U961 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,phosphate,splayed-apart 935 C ( A.C962 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end 936 G ( A.G963 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 937 A . A.A964 0.006 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 938 A . A.A965 0.012 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,splayed-apart 939 g . A.M2G966 0.048 modified,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 940 c . A.5MC967 0.031 modified,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 941 A . A.A968 0.006 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 942 A . A.A969 0.003 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate,splayed-apart 943 C . A.C970 0.003 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 944 G . A.G971 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,cap-acceptor,phosphate,splayed-apart 945 C ) A.C972 0.005 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,phosphate,splayed-apart 946 G ) A.G973 0.013 turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 947 A . A.A974 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate,splayed-apart 948 A . A.A975 0.021 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 949 G . A.G976 0.008 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 950 A . A.A977 0.010 syn,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 951 A . A.A978 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,phosphate,splayed-apart 952 C . A.C979 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 953 C . A.C980 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 954 U . A.U981 0.008 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 955 U . A.U982 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,phosphate 956 A . A.A983 0.008 turn,syn,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor 957 C ( A.C984 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,multiplet,A-minor,ribose-zipper 958 C ( A.C985 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,ribose-zipper 959 A ( A.A986 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 960 G ( A.G987 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 961 G ( A.G988 0.002 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 962 C ( A.C989 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 963 C ( A.C990 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,junction-loop,A-minor 964 U . A.U991 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,splayed-apart 965 U . A.U992 0.004 turn,anti,~C2'-endo,BII,non-pair-contact,junction-loop,splayed-apart 966 G ( A.G993 0.010 syn,~C2'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,A-minor 967 A . A.A994 0.013 turn,anti,~C3'-endo,BI,non-pair-contact,bulge,phosphate 968 C . A.C995 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,bulge 969 A . A.A996 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor 970 U ( A.U997 0.003 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,internal-loop 971 G . A.G998 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 972 C ( A.C999 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 973 U ( A.U1000 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 974 A ( A.A1001 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 975 G ( A.G1002 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 976 G . A.G1003 0.004 anti,~C3'-endo,BI,non-pair-contact,bulge 977 G ( A.G1003^A 0.003 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,junction-loop 978 A . A.A1004 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 979 A . A.A1005 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,junction-loop,phosphate,splayed-apart 980 C ( A.C1006 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 981 C ( A.C1007 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 982 C . A.C1008 0.003 anti,~C3'-endo,BI,non-pair-contact,internal-loop 983 G ( A.G1009 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 984 G ( A.G1010 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 985 G ( A.G1011 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 986 U ( A.U1012 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 987 G . A.G1013 0.004 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor,splayed-apart 988 A . A.A1014 0.005 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 989 A . A.A1015 0.006 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 990 A . A.A1016 0.004 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 991 G ) A.G1017 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 992 C ) A.C1018 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 993 C ) A.C1019 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 994 U ) A.U1020 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 995 G . A.G1021 0.003 anti,~C3'-endo,BI,non-pair-contact,internal-loop 996 G ) A.G1022 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 997 G ) A.G1023 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,junction-loop 998 G . A.G1024 0.002 anti,~C3'-endo,BII,non-pair-contact,junction-loop 999 U . A.U1025 0.003 turn,anti,~C2'-endo,BII,non-pair-contact,junction-loop 1000 G . A.G1026 0.004 anti,~C3'-endo,non-pair-contact,junction-loop 1001 C . A.C1027 0.002 anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,junction-loop 1002 C ( A.C1028 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 1003 C ( A.C1029 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1004 C ( A.C1030 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 1005 G . A.G1030^A 0.002 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor 1006 C . A.C1030^B 0.003 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1007 G . A.G1030^C 0.002 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 1008 A . A.A1030^D 0.003 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 1009 G ) A.G1031 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop 1010 G ) A.G1032 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1011 G ) A.G1033 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 1012 G . A.G1034 0.002 anti,~C3'-endo,BI,non-pair-contact,junction-loop 1013 A . A.A1035 0.002 anti,~C3'-endo,BI,non-pair-contact,junction-loop 1014 G . A.G1036 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-loop 1015 C . A.C1037 0.004 anti,~C3'-endo,non-pair-contact,junction-loop 1016 C ) A.C1038 0.003 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,bulge,junction-loop 1017 C ) A.C1039 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 1018 U ) A.U1040 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1019 A ) A.A1041 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1020 G ) A.G1042 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1021 C . A.C1043 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1022 A ) A.A1044 0.004 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,internal-loop 1023 C ) A.C1045 0.002 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,junction-loop,A-minor 1024 A . A.A1046 0.002 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,cap-acceptor 1025 G ( A.G1047 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor 1026 G ( A.G1048 0.006 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate,splayed-apart 1027 U . A.U1049 0.003 turn,anti,~C2'-endo,non-pair-contact,bulge,cap-acceptor,splayed-apart 1028 G ( A.G1050 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 1029 C ( A.C1051 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1030 U ( A.U1052 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1031 G . A.G1053 0.007 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,splayed-apart 1032 C . A.C1054 0.006 turn,anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate,splayed-apart 1033 A . A.A1055 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate,splayed-apart 1034 U ( A.U1056 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 1035 G ( A.G1057 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 1036 G ( A.G1058 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 1037 C ( A.C1059 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1038 C ( A.C1060 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 1039 G ( A.G1061 0.006 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,internal-loop 1040 U . A.U1062 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-donor 1041 C ( A.C1063 0.004 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,phosphate 1042 G . A.G1064 0.014 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,junction-loop,phosphate 1043 U . A.U1065 0.005 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop 1044 C . A.C1066 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 1045 A . A.A1067 0.013 anti,~C2'-endo,non-pair-contact,junction-loop 1046 G ( A.G1068 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 1047 C ( A.C1069 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1048 U ( A.U1070 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1049 C ( A.C1071 0.006 anti,~C3'-endo,BI,non-stack,canonical,non-canonical,helix,stem,coaxial-stack,multiplet 1050 G ( A.G1072 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 1051 U ( A.U1073 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 1052 G ( A.G1074 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 1053 C ( A.C1075 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor,phosphate 1054 C ( A.C1076 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 1055 G . A.G1077 0.008 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor 1056 U . A.U1078 0.008 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1057 G . A.G1079 0.011 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,ribose-zipper,cap-donor,phosphate 1058 A . A.A1080 0.010 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-acceptor,phosphate 1059 G ) A.G1081 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 1060 G ) A.G1082 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1061 U ) A.U1083 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 1062 G . A.G1084 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,phosphate 1063 U . A.U1085 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,splayed-apart 1064 U . A.U1086 0.008 anti,~C3'-endo,BI,non-stack,non-canonical,helix-end,junction-loop,cap-acceptor,splayed-apart 1065 G ( A.G1087 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 1066 G ( A.G1088 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,A-minor 1067 G ( A.G1089 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,hairpin-loop,A-minor 1068 U . A.U1090 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 1069 U . A.U1091 0.005 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 1070 A . A.A1092 0.009 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1071 A . A.A1093 0.006 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 1072 G . A.G1094 0.007 turn,u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor,phosphate,splayed-apart 1073 U . A.U1095 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate,splayed-apart 1074 C ) A.C1096 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,hairpin-loop,A-minor,ribose-zipper 1075 C ) A.C1097 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,ribose-zipper 1076 C ) A.C1098 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 1077 G . A.G1099 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 1078 C . A.C1100 0.004 anti,~C3'-endo,BI,non-pair-contact,junction-loop 1079 A . A.A1101 0.005 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,A-minor,cap-acceptor,phosphate 1080 A ) A.A1102 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 1081 C ) A.C1103 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1082 G ) A.G1104 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1083 A ) A.A1105 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 1084 G ) A.G1106 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1085 C ) A.C1107 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,junction-loop,phosphate 1086 G . A.G1108 0.006 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 1087 C . A.C1109 0.003 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 1088 A . A.A1110 0.006 anti,~C3'-endo,BI,non-pair-contact,junction-loop,phosphate 1089 A . A.A1111 0.008 anti,~C3'-endo,BI,non-pair-contact,junction-loop 1090 C . A.C1112 0.004 anti,~C3'-endo,non-pair-contact,junction-loop 1091 C ( A.C1113 0.003 anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end,junction-loop 1092 C ( A.C1114 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1093 C ( A.C1115 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1094 C ( A.C1116 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop 1095 G . A.G1117 0.008 anti,~C3'-endo,non-pair-contact,junction-loop 1096 C ( A.C1118 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 1097 C ( A.C1119 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1098 G ( A.G1120 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1099 U ( A.U1121 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1100 U ( A.U1122 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1101 A ( A.A1123 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1102 G ( A.G1124 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,splayed-apart 1103 U . A.U1125 0.008 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 1104 U . A.U1126 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,cap-donor,phosphate,splayed-apart 1105 G ( A.G1127 0.010 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,internal-loop 1106 C ( A.C1128 0.004 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge 1107 C . A.C1129 0.007 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,bulge,splayed-apart 1108 A . A.A1130 0.006 turn,anti,~C3'-endo,BI,non-pair-contact,bulge,splayed-apart 1109 G . A.G1131 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge 1110 C ( A.C1132 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 1111 G ( A.G1133 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1112 G ( A.G1134 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 1113 U . A.U1135 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 1114 U . A.U1136 0.004 turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 1115 C . A.C1137 0.002 turn,anti,~C3'-endo,BII,non-pair-contact,hairpin-loop,cap-donor,cap-acceptor,splayed-apart 1116 G . A.G1138 0.009 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor 1117 G . A.G1139 0.005 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop 1118 C ) A.C1140 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,cap-donor,phosphate 1119 C ) A.C1141 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1120 G ) A.G1142 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 1121 G ) A.G1143 0.003 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge 1122 G . A.G1144 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge 1123 C ) A.C1145 0.006 anti,~C2'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,bulge,internal-loop 1124 A . A.A1146 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 1125 C . A.C1147 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 1126 U . A.U1148 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 1127 C ) A.C1149 0.002 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor,phosphate 1128 U ) A.U1150 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1129 A ) A.A1151 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1130 A ) A.A1152 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1131 C ) A.C1153 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1132 G ) A.G1154 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1133 G ) A.G1155 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 1134 G . A.G1156 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 1135 A . A.A1157 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor 1136 C ( A.C1158 0.013 syn,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,cap-acceptor 1137 U . A.U1159 0.006 turn,anti,~C2'-endo,BII,non-pair-contact,internal-loop 1138 G . A.G1160 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 1139 C ( A.C1161 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 1140 C ( A.C1162 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1141 C ( A.C1163 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1142 G ( A.G1164 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1143 C ( A.C1165 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1144 G . A.G1166 0.003 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor 1145 A . A.A1167 0.005 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,hairpin-loop 1146 A . A.A1168 0.005 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 1147 A . A.A1169 0.004 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 1148 G ) A.G1171 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1149 C ) A.C1172 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1150 G ) A.G1173 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1151 G ) A.G1174 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1152 G ) A.G1175 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,internal-loop 1153 A . A.A1176 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 1154 G . A.G1177 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop,phosphate 1155 G . A.G1178 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 1156 A . A.A1179 0.005 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,phosphate 1157 A . A.A1180 0.004 anti,~C3'-endo,non-pair-contact,internal-loop,cap-donor,phosphate 1158 G ) A.G1181 0.011 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,internal-loop,junction-loop 1159 G . A.G1182 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 1160 A . A.A1183 0.007 turn,anti,~C2'-endo,non-pair-contact,junction-loop,splayed-apart 1161 G ) A.G1184 0.006 turn,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,junction-loop,splayed-apart 1162 G ) A.G1185 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1163 G ) A.G1186 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1164 G ) A.G1187 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,junction-loop,phosphate 1165 A . A.A1188 0.007 anti,~C3'-endo,non-pair-contact,junction-loop 1166 C . A.C1189 0.002 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate 1167 G . A.G1190 0.010 anti,~C3'-endo,non-stack,non-pair-contact,junction-loop,phosphate,splayed-apart 1168 A . A.A1191 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate,splayed-apart 1169 C . A.C1192 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 1170 G ) A.G1193 0.003 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 1171 U . A.U1194 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1172 C ) A.C1195 0.006 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,bulge,internal-loop,splayed-apart 1173 U . A.U1196 0.003 turn,anti,~C2'-endo,non-pair-contact,bulge,splayed-apart 1174 G ) A.G1197 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 1175 G ) A.G1198 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1176 U ) A.U1199 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 1177 C . A.C1200 0.008 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,bulge,phosphate,splayed-apart 1178 A . A.A1201 0.004 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,bulge,cap-donor,splayed-apart 1179 G . A.G1202 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,phosphate,splayed-apart 1180 C ) A.C1203 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 1181 A ) A.A1204 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1182 U . A.U1205 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 1183 G ) A.G1206 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 1184 g ) A.2MG1207 0.060 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1185 C ) A.C1208 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 1186 C ) A.C1209 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge 1187 C ) A.C1210 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 1188 U . A.U1211 0.006 anti,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,junction-loop,cap-donor,splayed-apart 1189 U . A.U1212 0.004 turn,anti,~C3'-endo,BI,non-stack,non-pair-contact,junction-loop,splayed-apart 1190 A . A.A1213 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,cap-acceptor,splayed-apart 1191 C . A.C1214 0.004 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 1192 G ) A.G1215 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,A-minor,splayed-apart 1193 G ) A.G1216 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1194 C ) A.C1217 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 1195 C ) A.C1218 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor,ribose-zipper 1196 U ) A.U1219 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1197 G ) A.G1220 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,A-minor 1198 G ) A.G1221 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,A-minor,phosphate 1199 G . A.G1222 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1200 C . A.C1223 0.006 turn,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 1201 G [ A.G1224 0.010 pseudoknotted,turn,anti,~C2'-endo,isolated-canonical,non-pair-contact,cap-acceptor,phosphate,splayed-apart 1202 A ) A.A1225 0.011 ~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate,splayed-apart 1203 C ) A.C1226 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,phosphate 1204 A . A.A1227 0.014 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,phosphate 1205 C ) A.C1228 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 1206 A ) A.A1229 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1207 C ) A.C1230 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 1208 G ) A.G1231 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1209 U ) A.U1232 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1210 G ) A.G1233 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 1211 C ) A.C1234 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1212 U ) A.U1235 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop,A-minor,phosphate 1213 A . A.A1236 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate 1214 C ( A.C1237 0.004 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,junction-loop,phosphate,splayed-apart 1215 A . A.A1238 0.007 anti,~C3'-endo,BI,non-stack,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 1216 A . A.A1239 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,splayed-apart 1217 U . A.U1240 0.006 turn,anti,~C2'-endo,junction-loop,phosphate,splayed-apart 1218 G ( A.G1241 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,junction-loop,A-minor,cap-acceptor,phosphate,splayed-apart 1219 C ( A.C1242 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1220 C ( A.C1243 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1221 C ( A.C1244 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1222 A ( A.A1245 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1223 C ( A.C1246 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1224 U ( A.U1247 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 1225 A . A.A1248 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 1226 C . A.C1249 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 1227 A . A.A1250 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,ribose-zipper,phosphate 1228 A . A.A1251 0.006 anti,~C3'-endo,BI,non-pair-contact,internal-loop,A-minor,ribose-zipper 1229 A . A.A1252 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 1230 G ( A.G1253 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 1231 C ( A.C1254 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1232 G ( A.G1255 0.004 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,phosphate 1233 A . A.A1256 0.005 anti,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,splayed-apart 1234 U . A.U1257 0.003 turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 1235 G ( A.G1258 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,internal-loop,phosphate,splayed-apart 1236 C ( A.C1259 0.001 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 1237 C . A.C1260 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1238 A . A.A1261 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1239 C ( A.C1262 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1240 C ( A.C1263 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1241 C ( A.C1264 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1242 G ( A.G1265 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 1243 G . A.G1266 0.004 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,cap-acceptor,splayed-apart 1244 C . A.C1267 0.001 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,splayed-apart 1245 A . A.A1268 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 1246 A . A.A1269 0.003 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,A-minor,ribose-zipper,phosphate 1247 C ) A.C1270 0.003 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 1248 G ) A.G1271 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1249 G ) A.G1272 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1250 G ) A.G1273 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1251 G . A.G1274 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1252 A . A.A1275 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1253 G ) A.G1276 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 1254 C ) A.C1277 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,internal-loop,cap-donor,splayed-apart 1255 U . A.U1278 0.007 turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 1256 A . A.A1279 0.007 syn,~C3'-endo,BII,non-pair-contact,internal-loop,splayed-apart 1257 A . A.A1280 0.004 turn,anti,~C2'-endo,non-stack,non-canonical,multiplet,internal-loop,A-minor,cap-acceptor,phosphate,splayed-apart 1258 U . A.U1281 0.009 anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,phosphate,splayed-apart 1259 C ) A.C1282 0.004 anti,~C3'-endo,BI,non-stack,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet,internal-loop,cap-acceptor,splayed-apart 1260 G ) A.G1283 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1261 C ) A.C1284 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 1262 A . A.A1285 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-donor,phosphate 1263 A . A.A1286 0.007 turn,anti,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,cap-acceptor,phosphate 1264 A . A.A1287 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,ribose-zipper 1265 A . A.A1288 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,ribose-zipper,phosphate 1266 A . A.A1289 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 1267 G ) A.G1290 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 1268 G ) A.G1291 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1269 U ) A.U1292 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1270 G ) A.G1293 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1271 G ) A.G1294 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1272 G ) A.G1295 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1273 C ) A.C1296 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,multiplet,junction-loop,A-minor 1274 C . A.C1297 0.005 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,junction-loop,phosphate 1275 C . A.C1298 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,junction-loop,cap-donor,phosphate 1276 A . A.A1299 0.019 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor 1277 G . A.G1300 0.015 turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 1278 U . A.U1301 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate,splayed-apart 1279 U . A.U1302 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 1280 C ( A.C1303 0.005 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop,cap-donor,phosphate,splayed-apart 1281 G . A.G1304 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 1282 G . A.G1305 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1283 A . A.A1306 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1284 U . A.U1307 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1285 U ( A.U1308 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 1286 G ( A.G1309 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1287 G ( A.G1310 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1288 G ( A.G1311 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor 1289 G ( A.G1312 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 1290 U ( A.U1313 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1291 C ( A.C1314 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1292 U . A.U1315 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop 1293 G . A.G1316 0.009 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,cap-acceptor 1294 C . A.C1317 0.004 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1295 A . A.A1318 0.006 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 1296 A . A.A1319 0.004 u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,phosphate,splayed-apart 1297 C . A.C1320 0.003 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 1298 C . A.C1321 0.006 anti,~C3'-endo,non-pair-contact,hairpin-loop,phosphate 1299 C . A.C1322 0.006 anti,~C2'-endo,BII,non-pair-contact,hairpin-loop,cap-donor,phosphate,splayed-apart 1300 G ) A.G1323 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,splayed-apart 1301 A ) A.A1324 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1302 C ) A.C1325 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1303 C ) A.C1326 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1304 C ) A.C1327 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1305 C ) A.C1328 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1306 A ) A.A1329 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 1307 U . A.U1330 0.008 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1308 G . A.G1331 0.014 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 1309 A . A.A1332 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1310 A . A.A1333 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor 1311 G ) A.G1334 0.007 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,junction-loop 1312 C . A.C1335 0.007 turn,anti,~C2'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 1313 C . A.C1336 0.006 anti,~C2'-endo,non-pair-contact,junction-loop,cap-donor,splayed-apart 1314 G ) A.G1337 0.006 anti,~C3'-endo,BII,isolated-canonical,non-pair-contact,helix-end,junction-loop,cap-acceptor,splayed-apart 1315 G . A.G1338 0.006 anti,~C3'-endo,non-pair-contact,junction-loop,phosphate,splayed-apart 1316 A . A.A1339 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,junction-loop 1317 A ) A.A1340 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 1318 U ) A.U1341 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1319 C ) A.C1342 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1320 G ) A.G1343 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1321 C ) A.C1344 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 1322 U . A.U1345 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,phosphate 1323 A . A.A1346 0.006 anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,phosphate 1324 G . A.G1347 0.006 turn,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop 1325 U . A.U1348 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 1326 A . A.A1349 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 1327 A ( A.A1350 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 1328 U ( A.U1351 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor 1329 C ( A.C1352 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1330 G ( A.G1353 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1331 C ( A.C1354 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1332 G ( A.G1355 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1333 G ( A.G1356 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1334 A . A.A1357 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,phosphate 1335 U . A.U1358 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 1336 C . A.C1359 0.006 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 1337 A . A.A1360 0.007 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,splayed-apart 1338 G . A.G1361 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,phosphate 1339 C . A.C1361^A 0.002 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 1340 C ] A.C1362 0.007 pseudoknotted,turn,anti,~C3'-endo,non-stack,isolated-canonical,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1341 A . A.A1363 0.005 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate,splayed-apart 1342 U . A.U1364 0.005 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,multiplet,hairpin-loop,splayed-apart 1343 G . A.G1365 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,cap-donor,phosphate,splayed-apart 1344 C ) A.C1366 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1345 C ) A.C1367 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1346 G ) A.G1368 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1347 C ) A.C1369 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1348 G ) A.G1370 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 1349 G ) A.G1371 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 1350 U ) A.U1372 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop,phosphate 1351 G . A.G1373 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,phosphate 1352 A . A.A1374 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,phosphate 1353 A . A.A1375 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,ribose-zipper,phosphate 1354 U . A.U1376 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,ribose-zipper,phosphate 1355 A . A.A1377 0.005 anti,~C3'-endo,non-pair-contact,junction-loop,splayed-apart 1356 C . A.C1378 0.008 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,junction-loop,splayed-apart 1357 G ) A.G1379 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 1358 U ) A.U1380 0.010 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 1359 U . A.U1381 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,internal-loop 1360 C . A.C1382 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop 1361 C . A.C1383 0.002 anti,~C3'-endo,BI,non-stack,non-canonical,multiplet,internal-loop 1362 C ) A.C1384 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1363 G ) A.G1385 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1364 G ) A.G1386 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1365 G ) A.G1387 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1366 C ) A.C1388 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1367 C ) A.C1389 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1368 U ) A.U1390 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 1369 U ) A.U1391 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 1370 G ) A.G1392 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 1371 U ) A.U1393 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 1372 A . A.A1394 0.010 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,cap-acceptor,splayed-apart 1373 C ) A.C1395 0.012 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,bulge,A-minor,splayed-apart 1374 A ) A.A1396 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,splayed-apart 1375 C . A.C1397 0.002 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 1376 A . A.A1398 0.004 anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,ss-non-loop,A-minor,phosphate,splayed-apart 1377 C ( A.C1399 0.009 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate,splayed-apart 1378 c . A.5MC1400 0.032 modified,turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 1379 G ( A.G1401 0.008 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 1380 c . A.4OC1402 0.025 modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1381 C . A.C1403 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 1382 c ( A.5MC1404 0.027 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor,ribose-zipper 1383 G ( A.G1405 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,ribose-zipper,phosphate 1384 U . A.U1406 0.009 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 1385 c ( A.5MC1407 0.028 modified,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 1386 A . A.A1408 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop 1387 C ( A.C1409 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1388 G ( A.G1410 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1389 C ( A.C1411 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1390 C ( A.C1412 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1391 A . A.A1413 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 1392 U ( A.U1414 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1393 G ( A.G1415 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1394 G ( A.G1416 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1395 G . A.G1417 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1396 A . A.A1418 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1397 G ( A.G1419 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1398 C ( A.C1420 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1399 G ( A.G1421 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 1400 G ( A.G1422 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1401 G ( A.G1423 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1402 C ( A.C1424 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1403 U . A.U1425 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1404 C ( A.C1426 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1405 U ( A.U1427 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1406 A ( A.A1428 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1407 C ( A.C1429 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1408 C ( A.C1430 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1409 C ( A.C1431 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1410 G . A.G1432 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1411 A . A.A1433 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,internal-loop,A-minor,ribose-zipper,phosphate 1412 A . A.A1434 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,A-minor,ribose-zipper 1413 G ( A.G1435 0.010 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 1414 U . A.U1436 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1415 C ( A.C1437 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1416 G ( A.G1438 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1417 C ( A.C1439 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1418 C ( A.C1440 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 1419 G . A.G1441 0.004 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1420 G . A.G1442 0.015 syn,~C3'-endo,BII,non-canonical,non-pair-contact,multiplet,internal-loop,splayed-apart 1421 G . A.G1443 0.005 turn,syn,~C2'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 1422 A . A.A1446 0.006 anti,~C3'-endo,non-pair-contact,internal-loop,phosphate,splayed-apart 1423 G ( A.G1447 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1424 C ( A.C1448 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1425 C ( A.C1449 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 1426 U . A.U1450 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 1427 A . A.A1451 0.003 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 1428 C . A.C1452 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,splayed-apart 1429 G . A.G1453 0.008 turn,syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 1430 G ) A.G1454 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate 1431 G ) A.G1455 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1432 C ) A.C1459 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 1433 A . A.A1460 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1434 G ) A.G1461 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 1435 G ) A.G1462 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1436 C ) A.C1463 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1437 G ) A.G1464 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1438 C . A.C1465 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1439 C ) A.C1466 0.004 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 1440 G . A.G1467 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop 1441 A . A.A1468 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1442 G ) A.G1469 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1443 G ) A.G1470 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1444 G ) A.G1471 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1445 U ) A.U1472 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1446 A ) A.A1473 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1447 G ) A.G1474 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1448 G . A.G1475 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 1449 G ) A.G1476 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1450 C ) A.C1477 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1451 C ) A.C1478 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1452 C ) A.C1479 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1453 G ) A.G1480 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1454 U ) A.U1481 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1455 G . A.G1482 0.006 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1456 A . A.A1483 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 1457 C ) A.C1484 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1458 U ) A.U1485 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1459 G ) A.G1486 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1460 G . A.G1487 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,A-minor 1461 G ) A.G1488 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1462 G ) A.G1489 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 1463 C ) A.C1490 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 1464 G ) A.G1491 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-acceptor,phosphate,splayed-apart 1465 A . A.A1492 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate,splayed-apart 1466 A . A.A1493 0.005 anti,~C3'-endo,BII,non-pair-contact,internal-loop,phosphate,splayed-apart 1467 G ) A.G1494 0.011 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate,splayed-apart 1468 U . A.U1495 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 1469 C ) A.C1496 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 1470 G ) A.G1497 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor 1471 u . A.UR3/1498 0.034 modified,anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate 1472 A . A.A1499 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,phosphate 1473 A . A.A1500 0.010 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 1474 C ) A.C1501 0.007 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,cap-donor,phosphate 1475 A . A.A1502 0.030 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,internal-loop,splayed-apart 1476 A . A.A1503 0.004 turn,anti,~C2'-endo,non-stack,non-pair-contact,internal-loop,cap-acceptor,phosphate,splayed-apart 1477 G ) A.G1504 0.010 turn,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop,cap-donor,phosphate,splayed-apart 1478 G . A.G1505 0.018 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor,phosphate,splayed-apart 1479 U . A.U1506 0.009 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 1480 A ( A.A1507 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 1481 G ( A.G1508 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1482 C ( A.C1509 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1483 U ( A.U1510 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 1484 G ( A.G1511 0.009 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 1485 U ( A.U1512 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1486 A ( A.A1513 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1487 C ( A.C1514 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1488 C ( A.C1515 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1489 G . A.G1516 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor 1490 G . A.G1517 0.006 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop 1491 a . A.MA6/1518 0.033 modified,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper 1492 a . A.MA6/1519 0.042 modified,u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,A-minor,ribose-zipper,phosphate 1493 G ) A.G1520 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 1494 G ) A.G1521 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1495 U ) A.U1522 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1496 G ) A.G1523 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 1497 C ) A.C1524 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1498 G ) A.G1525 0.011 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper,phosphate 1499 G ) A.G1526 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1500 C ) A.C1527 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 1501 U ) A.U1528 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 1502 G } A.G1529 0.008 pseudoknotted,turn,syn,~C2'-endo,isolated-canonical,non-pair-contact,splayed-apart 1503 G . A.G1530 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 1504 A . A.A1531 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1505 U . A.U1532 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1506 C . A.C1533 0.003 break,anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate 1507 C . A.C1539 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 1508 P . A.PSU1540 0.039 modified,anti,~C3'-endo,non-pair-contact,ss-non-loop 1509 P . A.PSU1541 0.041 modified,anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 1510 U . A.U1542 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 1511 C . A.C1543 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 1512 U . A.U1544 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate **************************************************************************** List of 17 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