examples/testdata/rna-alignment.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <!DOCTYPE rnaml SYSTEM "rnaml.dtd">
  21
  22 <rnaml version="1.0">
  23
  24    <molecule id="1">
  25       <sequence>
  26          <numbering-system id="1" used-in-file="false">
  27             <numbering-range>
  28                <start>1</start>
  29                <end>249</end>
  30             </numbering-range>
  31          </numbering-system>
  32          <seq-data>
  33             gaggaaaguc cggacUUCGC AGAAAAAGGU GCCAGUGAAA AACUGGGGGC CGUAAGGCUA
  34             CGGAAAGUGU AACAGAAAAC AAACCGCUAA UUCUACCUAG GUAAGAUUAG ACAGGAUGAA
  35             AAUGUCGAGC UUAUGGCUCG ACCUCUUUGU GGAAACACAA GGACGCUGCA AACCCCACCU
  36             GAAGCAAGAA AGAGUUCGUU UCAGUUUUUC GCUCAGGAAC UCUUAGAGUC GCUCGAGGAU
  37             UUUGGUGAC
  38          </seq-data>
  39       </sequence>
  40       <structure>
  41          <model id="?">
  42             <str-annotation>
  43                <base-pair comment="?">
  44                   <base-id-5p>
  45                      <base-id><position>15</position></base-id>
  46                   </base-id-5p>
  47                   <base-id-3p>
  48                      <base-id><position>184</position></base-id>
  49                   </base-id-3p>
  50                </base-pair>
  51                <base-pair comment="?">
  52                   <base-id-5p>
  53                      <base-id><position>16</position></base-id>
  54                   </base-id-5p>
  55                   <base-id-3p>
  56                      <base-id><position>183</position></base-id>
  57                   </base-id-3p>
  58                </base-pair>
  59                <base-pair comment="?">
  60                   <base-id-5p>
  61                      <base-id><position>17</position></base-id>
  62                   </base-id-5p>
  63                   <base-id-3p>
  64                      <base-id><position>182</position></base-id>
  65                   </base-id-3p>
  66                </base-pair>
  67                <base-pair comment="?">
  68                   <base-id-5p>
  69                      <base-id><position>18</position></base-id>
  70                   </base-id-5p>
  71                   <base-id-3p>
  72                      <base-id><position>181</position></base-id>
  73                   </base-id-3p>
  74                </base-pair>
  75                <base-pair comment="?">
  76                   <base-id-5p>
  77                      <base-id><position>22</position></base-id>
  78                   </base-id-5p>
  79                   <base-id-3p>
  80                      <base-id><position>210</position></base-id>
  81                   </base-id-3p>
  82                </base-pair>
  83                <base-pair comment="?">
  84                   <base-id-5p>
  85                      <base-id><position>23</position></base-id>
  86                   </base-id-5p>
  87                   <base-id-3p>
  88                      <base-id><position>209</position></base-id>
  89                   </base-id-3p>
  90                </base-pair>
  91                <base-pair comment="?">
  92                   <base-id-5p>
  93                      <base-id><position>24</position></base-id>
  94                   </base-id-5p>
  95                   <base-id-3p>
  96                      <base-id><position>208</position></base-id>
  97                   </base-id-3p>
  98                </base-pair>
  99                <base-pair comment="?">
 100                   <base-id-5p>
 101                      <base-id><position>25</position></base-id>
 102                   </base-id-5p>
 103                   <base-id-3p>
 104                      <base-id><position>207</position></base-id>
 105                   </base-id-3p>
 106                </base-pair>
 107                <base-pair comment="?">
 108                   <base-id-5p>
 109                      <base-id><position>27</position></base-id>
 110                   </base-id-5p>
 111                   <base-id-3p>
 112                      <base-id><position>180</position></base-id>
 113                   </base-id-3p>
 114                </base-pair>
 115                <base-pair comment="?">
 116                   <base-id-5p>
 117                      <base-id><position>28</position></base-id>
 118                   </base-id-5p>
 119                   <base-id-3p>
 120                      <base-id><position>179</position></base-id>
 121                   </base-id-3p>
 122                </base-pair>
 123                <base-pair comment="?">
 124                   <base-id-5p>
 125                      <base-id><position>29</position></base-id>
 126                   </base-id-5p>
 127                   <base-id-3p>
 128                      <base-id><position>178</position></base-id>
 129                   </base-id-3p>
 130                </base-pair>
 131                <base-pair comment="?">
 132                   <base-id-5p>
 133                      <base-id><position>30</position></base-id>
 134                   </base-id-5p>
 135                   <base-id-3p>
 136                      <base-id><position>177</position></base-id>
 137                   </base-id-3p>
 138                </base-pair>
 139                <base-pair comment="?">
 140                   <base-id-5p>
 141                      <base-id><position>31</position></base-id>
 142                   </base-id-5p>
 143                   <base-id-3p>
 144                      <base-id><position>176</position></base-id>
 145                   </base-id-3p>
 146                </base-pair>
 147                <base-pair comment="?">
 148                   <base-id-5p>
 149                      <base-id><position>32</position></base-id>
 150                   </base-id-5p>
 151                   <base-id-3p>
 152                      <base-id><position>46</position></base-id>
 153                   </base-id-3p>
 154                </base-pair>
 155                <base-pair comment="?">
 156                   <base-id-5p>
 157                      <base-id><position>33</position></base-id>
 158                   </base-id-5p>
 159                   <base-id-3p>
 160                      <base-id><position>45</position></base-id>
 161                   </base-id-3p>
 162                </base-pair>
 163                <base-pair comment="?">
 164                   <base-id-5p>
 165                      <base-id><position>34</position></base-id>
 166                   </base-id-5p>
 167                   <base-id-3p>
 168                      <base-id><position>44</position></base-id>
 169                   </base-id-3p>
 170                </base-pair>
 171                <base-pair comment="?">
 172                   <base-id-5p>
 173                      <base-id><position>35</position></base-id>
 174                   </base-id-5p>
 175                   <base-id-3p>
 176                      <base-id><position>43</position></base-id>
 177                   </base-id-3p>
 178                </base-pair>
 179                <base-pair comment="?">
 180                   <base-id-5p>
 181                      <base-id><position>36</position></base-id>
 182                   </base-id-5p>
 183                   <base-id-3p>
 184                      <base-id><position>42</position></base-id>
 185                   </base-id-3p>
 186                </base-pair>
 187                <base-pair comment="?">
 188                   <base-id-5p>
 189                      <base-id><position>47</position></base-id>
 190                   </base-id-5p>
 191                   <base-id-3p>
 192                      <base-id><position>61</position></base-id>
 193                   </base-id-3p>
 194                </base-pair>
 195                <base-pair comment="?">
 196                   <base-id-5p>
 197                      <base-id><position>48</position></base-id>
 198                   </base-id-5p>
 199                   <base-id-3p>
 200                      <base-id><position>59</position></base-id>
 201                   </base-id-3p>
 202                </base-pair>
 203                <base-pair comment="?">
 204                   <base-id-5p>
 205                      <base-id><position>49</position></base-id>
 206                   </base-id-5p>
 207                   <base-id-3p>
 208                      <base-id><position>58</position></base-id>
 209                   </base-id-3p>
 210                </base-pair>
 211                <base-pair comment="?">
 212                   <base-id-5p>
 213                      <base-id><position>50</position></base-id>
 214                   </base-id-5p>
 215                   <base-id-3p>
 216                      <base-id><position>57</position></base-id>
 217                   </base-id-3p>
 218                </base-pair>
 219                <base-pair comment="?">
 220                   <base-id-5p>
 221                      <base-id><position>51</position></base-id>
 222                   </base-id-5p>
 223                   <base-id-3p>
 224                      <base-id><position>56</position></base-id>
 225                   </base-id-3p>
 226                </base-pair>
 227                <base-pair comment="?">
 228                   <base-id-5p>
 229                      <base-id><position>62</position></base-id>
 230                   </base-id-5p>
 231                   <base-id-3p>
 232                      <base-id><position>175</position></base-id>
 233                   </base-id-3p>
 234                </base-pair>
 235                <base-pair comment="?">
 236                   <base-id-5p>
 237                      <base-id><position>63</position></base-id>
 238                   </base-id-5p>
 239                   <base-id-3p>
 240                      <base-id><position>174</position></base-id>
 241                   </base-id-3p>
 242                </base-pair>
 243                <base-pair comment="?">
 244                   <base-id-5p>
 245                      <base-id><position>67</position></base-id>
 246                   </base-id-5p>
 247                   <base-id-3p>
 248                      <base-id><position>173</position></base-id>
 249                   </base-id-3p>
 250                </base-pair>
 251                <base-pair comment="?">
 252                   <base-id-5p>
 253                      <base-id><position>68</position></base-id>
 254                   </base-id-5p>
 255                   <base-id-3p>
 256                      <base-id><position>172</position></base-id>
 257                   </base-id-3p>
 258                </base-pair>
 259                <base-pair comment="?">
 260                   <base-id-5p>
 261                      <base-id><position>69</position></base-id>
 262                   </base-id-5p>
 263                   <base-id-3p>
 264                      <base-id><position>169</position></base-id>
 265                   </base-id-3p>
 266                </base-pair>
 267                <base-pair comment="?">
 268                   <base-id-5p>
 269                      <base-id><position>70</position></base-id>
 270                   </base-id-5p>
 271                   <base-id-3p>
 272                      <base-id><position>168</position></base-id>
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 274                </base-pair>
 275                <base-pair comment="?">
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 278                   </base-id-5p>
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 282                </base-pair>
 283                <base-pair comment="?">
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 285                      <base-id><position>84</position></base-id>
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 290                </base-pair>
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 293                      <base-id><position>85</position></base-id>
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 298                </base-pair>
 299                <base-pair comment="?">
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 301                      <base-id><position>86</position></base-id>
 302                   </base-id-5p>
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 306                </base-pair>
 307                <base-pair comment="?">
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 309                      <base-id><position>87</position></base-id>
 310                   </base-id-5p>
 311                   <base-id-3p>
 312                      <base-id><position>110</position></base-id>
 313                   </base-id-3p>
 314                </base-pair>
 315                <base-pair comment="?">
 316                   <base-id-5p>
 317                      <base-id><position>88</position></base-id>
 318                   </base-id-5p>
 319                   <base-id-3p>
 320                      <base-id><position>109</position></base-id>
 321                   </base-id-3p>
 322                </base-pair>
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 325                      <base-id><position>89</position></base-id>
 326                   </base-id-5p>
 327                   <base-id-3p>
 328                      <base-id><position>108</position></base-id>
 329                   </base-id-3p>
 330                </base-pair>
 331                <base-pair comment="?">
 332                   <base-id-5p>
 333                      <base-id><position>90</position></base-id>
 334                   </base-id-5p>
 335                   <base-id-3p>
 336                      <base-id><position>107</position></base-id>
 337                   </base-id-3p>
 338                </base-pair>
 339                <base-pair comment="?">
 340                   <base-id-5p>
 341                      <base-id><position>91</position></base-id>
 342                   </base-id-5p>
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 344                      <base-id><position>106</position></base-id>
 345                   </base-id-3p>
 346                </base-pair>
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 348                   <base-id-5p>
 349                      <base-id><position>92</position></base-id>
 350                   </base-id-5p>
 351                   <base-id-3p>
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 353                   </base-id-3p>
 354                </base-pair>
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 356                   <base-id-5p>
 357                      <base-id><position>93</position></base-id>
 358                   </base-id-5p>
 359                   <base-id-3p>
 360                      <base-id><position>104</position></base-id>
 361                   </base-id-3p>
 362                </base-pair>
 363                <base-pair comment="?">
 364                   <base-id-5p>
 365                      <base-id><position>94</position></base-id>
 366                   </base-id-5p>
 367                   <base-id-3p>
 368                      <base-id><position>103</position></base-id>
 369                   </base-id-3p>
 370                </base-pair>
 371                <base-pair comment="?">
 372                   <base-id-5p>
 373                      <base-id><position>95</position></base-id>
 374                   </base-id-5p>
 375                   <base-id-3p>
 376                      <base-id><position>102</position></base-id>
 377                   </base-id-3p>
 378                </base-pair>
 379                <base-pair comment="?">
 380                   <base-id-5p>
 381                      <base-id><position>96</position></base-id>
 382                   </base-id-5p>
 383                   <base-id-3p>
 384                      <base-id><position>101</position></base-id>
 385                   </base-id-3p>
 386                </base-pair>
 387                <base-pair comment="?">
 388                   <base-id-5p>
 389                      <base-id><position>124</position></base-id>
 390                   </base-id-5p>
 391                   <base-id-3p>
 392                      <base-id><position>142</position></base-id>
 393                   </base-id-3p>
 394                </base-pair>
 395                <base-pair comment="?">
 396                   <base-id-5p>
 397                      <base-id><position>125</position></base-id>
 398                   </base-id-5p>
 399                   <base-id-3p>
 400                      <base-id><position>141</position></base-id>
 401                   </base-id-3p>
 402                </base-pair>
 403                <base-pair comment="?">
 404                   <base-id-5p>
 405                      <base-id><position>126</position></base-id>
 406                   </base-id-5p>
 407                   <base-id-3p>
 408                      <base-id><position>140</position></base-id>
 409                   </base-id-3p>
 410                </base-pair>
 411                <base-pair comment="?">
 412                   <base-id-5p>
 413                      <base-id><position>127</position></base-id>
 414                   </base-id-5p>
 415                   <base-id-3p>
 416                      <base-id><position>139</position></base-id>
 417                   </base-id-3p>
 418                </base-pair>
 419                <base-pair comment="?">
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 421                      <base-id><position>128</position></base-id>
 422                   </base-id-5p>
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 424                      <base-id><position>138</position></base-id>
 425                   </base-id-3p>
 426                </base-pair>
 427                <base-pair comment="?">
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 429                      <base-id><position>129</position></base-id>
 430                   </base-id-5p>
 431                   <base-id-3p>
 432                      <base-id><position>137</position></base-id>
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 434                </base-pair>
 435                <base-pair comment="?">
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 437                      <base-id><position>143</position></base-id>
 438                   </base-id-5p>
 439                   <base-id-3p>
 440                      <base-id><position>165</position></base-id>
 441                   </base-id-3p>
 442                </base-pair>
 443                <base-pair comment="?">
 444                   <base-id-5p>
 445                      <base-id><position>144</position></base-id>
 446                   </base-id-5p>
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 448                      <base-id><position>163</position></base-id>
 449                   </base-id-3p>
 450                </base-pair>
 451                <base-pair comment="?">
 452                   <base-id-5p>
 453                      <base-id><position>145</position></base-id>
 454                   </base-id-5p>
 455                   <base-id-3p>
 456                      <base-id><position>162</position></base-id>
 457                   </base-id-3p>
 458                </base-pair>
 459                <base-pair comment="?">
 460                   <base-id-5p>
 461                      <base-id><position>146</position></base-id>
 462                   </base-id-5p>
 463                   <base-id-3p>
 464                      <base-id><position>161</position></base-id>
 465                   </base-id-3p>
 466                </base-pair>
 467                <base-pair comment="?">
 468                   <base-id-5p>
 469                      <base-id><position>147</position></base-id>
 470                   </base-id-5p>
 471                   <base-id-3p>
 472                      <base-id><position>160</position></base-id>
 473                   </base-id-3p>
 474                </base-pair>
 475                <base-pair comment="?">
 476                   <base-id-5p>
 477                      <base-id><position>148</position></base-id>
 478                   </base-id-5p>
 479                   <base-id-3p>
 480                      <base-id><position>159</position></base-id>
 481                   </base-id-3p>
 482                </base-pair>
 483                <base-pair comment="?">
 484                   <base-id-5p>
 485                      <base-id><position>149</position></base-id>
 486                   </base-id-5p>
 487                   <base-id-3p>
 488                      <base-id><position>158</position></base-id>
 489                   </base-id-3p>
 490                </base-pair>
 491                <base-pair comment="?">
 492                   <base-id-5p>
 493                      <base-id><position>150</position></base-id>
 494                   </base-id-5p>
 495                   <base-id-3p>
 496                      <base-id><position>157</position></base-id>
 497                   </base-id-3p>
 498                </base-pair>
 499                <base-pair comment="?">
 500                   <base-id-5p>
 501                      <base-id><position>151</position></base-id>
 502                   </base-id-5p>
 503                   <base-id-3p>
 504                      <base-id><position>156</position></base-id>
 505                   </base-id-3p>
 506                </base-pair>
 507                <base-pair comment="?">
 508                   <base-id-5p>
 509                      <base-id><position>188</position></base-id>
 510                   </base-id-5p>
 511                   <base-id-3p>
 512                      <base-id><position>230</position></base-id>
 513                   </base-id-3p>
 514                </base-pair>
 515                <base-pair comment="?">
 516                   <base-id-5p>
 517                      <base-id><position>189</position></base-id>
 518                   </base-id-5p>
 519                   <base-id-3p>
 520                      <base-id><position>229</position></base-id>
 521                   </base-id-3p>
 522                </base-pair>
 523                <base-pair comment="?">
 524                   <base-id-5p>
 525                      <base-id><position>190</position></base-id>
 526                   </base-id-5p>
 527                   <base-id-3p>
 528                      <base-id><position>224</position></base-id>
 529                   </base-id-3p>
 530                </base-pair>
 531                <base-pair comment="?">
 532                   <base-id-5p>
 533                      <base-id><position>191</position></base-id>
 534                   </base-id-5p>
 535                   <base-id-3p>
 536                      <base-id><position>223</position></base-id>
 537                   </base-id-3p>
 538                </base-pair>
 539                <base-pair comment="?">
 540                   <base-id-5p>
 541                      <base-id><position>192</position></base-id>
 542                   </base-id-5p>
 543                   <base-id-3p>
 544                      <base-id><position>222</position></base-id>
 545                   </base-id-3p>
 546                </base-pair>
 547                <base-pair comment="?">
 548                   <base-id-5p>
 549                      <base-id><position>193</position></base-id>
 550                   </base-id-5p>
 551                   <base-id-3p>
 552                      <base-id><position>221</position></base-id>
 553                   </base-id-3p>
 554                </base-pair>
 555                <base-pair comment="?">
 556                   <base-id-5p>
 557                      <base-id><position>194</position></base-id>
 558                   </base-id-5p>
 559                   <base-id-3p>
 560                      <base-id><position>220</position></base-id>
 561                   </base-id-3p>
 562                </base-pair>
 563                <base-pair comment="?">
 564                   <base-id-5p>
 565                      <base-id><position>195</position></base-id>
 566                   </base-id-5p>
 567                   <base-id-3p>
 568                      <base-id><position>219</position></base-id>
 569                   </base-id-3p>
 570                </base-pair>
 571                <base-pair comment="?">
 572                   <base-id-5p>
 573                      <base-id><position>196</position></base-id>
 574                   </base-id-5p>
 575                   <base-id-3p>
 576                      <base-id><position>218</position></base-id>
 577                   </base-id-3p>
 578                </base-pair>
 579                <base-pair comment="?">
 580                   <base-id-5p>
 581                      <base-id><position>197</position></base-id>
 582                   </base-id-5p>
 583                   <base-id-3p>
 584                      <base-id><position>217</position></base-id>
 585                   </base-id-3p>
 586                </base-pair>
 587                <base-pair comment="?">
 588                   <base-id-5p>
 589                      <base-id><position>203</position></base-id>
 590                   </base-id-5p>
 591                   <base-id-3p>
 592                      <base-id><position>213</position></base-id>
 593                   </base-id-3p>
 594                </base-pair>
 595                <base-pair comment="?">
 596                   <base-id-5p>
 597                      <base-id><position>204</position></base-id>
 598                   </base-id-5p>
 599                   <base-id-3p>
 600                      <base-id><position>212</position></base-id>
 601                   </base-id-3p>
 602                </base-pair>
 603                <base-pair comment="?">
 604                   <base-id-5p>
 605                      <base-id><position>205</position></base-id>
 606                   </base-id-5p>
 607                   <base-id-3p>
 608                      <base-id><position>211</position></base-id>
 609                   </base-id-3p>
 610                </base-pair>
 611                <base-pair comment="?">
 612                   <base-id-5p>
 613                      <base-id><position>244</position></base-id>
 614                   </base-id-5p>
 615                   <base-id-3p>
 616                      <base-id><position>249</position></base-id>
 617                   </base-id-3p>
 618                </base-pair>
 619             </str-annotation>
 620          </model>
 621       </structure>
 622    </molecule>
 623 <molecule id="2">
 624       <sequence>
 625          <numbering-system id="2" used-in-file="false">
 626             <numbering-range>
 627                <start>1</start>
 628                <end>294</end>
 629             </numbering-range>
 630          </numbering-system>
 631          <seq-data>
 632             gaggaaaguc cgggCUCCAU AGGGCAGAGU GCCAGGUAAC GCCUGGGAGG CGCGAGCCUA
 633             CGGAAAGUGC CACAGAAAAC AACCGCCUAA GCGCGCAAGC GCCGGUAAGG GUGAAAAGGU
 634             GCGGUAAGAG CGCACCGCAC GGCUGGCAAC AGUUCGUGGC UAGGUAAACC CCACUCGGAG
 635             CAAGACCAAA UAGGGAUCCA UUGGCGUGGC CCGCGCUGGA UCCGGGUAGG UUGCUAAAGG
 636             CGGCCAGCGA UGGUCGUCGU AGAGGAAUGA CUGUCCUCGa cagaacccgg cuua
 637          </seq-data>
 638       </sequence>
 639       <structure>
 640          <model id="?">
 641             <str-annotation>
 642                <base-pair comment="?">
 643                   <base-id-5p>
 644                      <base-id><position>6</position></base-id>
 645                   </base-id-5p>
 646                   <base-id-3p>
 647                      <base-id><position>293</position></base-id>
 648                   </base-id-3p>
 649                </base-pair>
 650                <base-pair comment="?">
 651                   <base-id-5p>
 652                      <base-id><position>7</position></base-id>
 653                   </base-id-5p>
 654                   <base-id-3p>
 655                      <base-id><position>292</position></base-id>
 656                   </base-id-3p>
 657                </base-pair>
 658                <base-pair comment="?">
 659                   <base-id-5p>
 660                      <base-id><position>8</position></base-id>
 661                   </base-id-5p>
 662                   <base-id-3p>
 663                      <base-id><position>291</position></base-id>
 664                   </base-id-3p>
 665                </base-pair>
 666                <base-pair comment="?">
 667                   <base-id-5p>
 668                      <base-id><position>10</position></base-id>
 669                   </base-id-5p>
 670                   <base-id-3p>
 671                      <base-id><position>290</position></base-id>
 672                   </base-id-3p>
 673                </base-pair>
 674                <base-pair comment="?">
 675                   <base-id-5p>
 676                      <base-id><position>11</position></base-id>
 677                   </base-id-5p>
 678                   <base-id-3p>
 679                      <base-id><position>289</position></base-id>
 680                   </base-id-3p>
 681                </base-pair>
 682                <base-pair comment="?">
 683                   <base-id-5p>
 684                      <base-id><position>12</position></base-id>
 685                   </base-id-5p>
 686                   <base-id-3p>
 687                      <base-id><position>288</position></base-id>
 688                   </base-id-3p>
 689                </base-pair>
 690                <base-pair comment="?">
 691                   <base-id-5p>
 692                      <base-id><position>13</position></base-id>
 693                   </base-id-5p>
 694                   <base-id-3p>
 695                      <base-id><position>287</position></base-id>
 696                   </base-id-3p>
 697                </base-pair>
 698                <base-pair comment="?">
 699                   <base-id-5p>
 700                      <base-id><position>14</position></base-id>
 701                   </base-id-5p>
 702                   <base-id-3p>
 703                      <base-id><position>286</position></base-id>
 704                   </base-id-3p>
 705                </base-pair>
 706                <base-pair comment="?">
 707                   <base-id-5p>
 708                      <base-id><position>15</position></base-id>
 709                   </base-id-5p>
 710                   <base-id-3p>
 711                      <base-id><position>180</position></base-id>
 712                   </base-id-3p>
 713                </base-pair>
 714                <base-pair comment="?">
 715                   <base-id-5p>
 716                      <base-id><position>16</position></base-id>
 717                   </base-id-5p>
 718                   <base-id-3p>
 719                      <base-id><position>179</position></base-id>
 720                   </base-id-3p>
 721                </base-pair>
 722                <base-pair comment="?">
 723                   <base-id-5p>
 724                      <base-id><position>17</position></base-id>
 725                   </base-id-5p>
 726                   <base-id-3p>
 727                      <base-id><position>178</position></base-id>
 728                   </base-id-3p>
 729                </base-pair>
 730                <base-pair comment="?">
 731                   <base-id-5p>
 732                      <base-id><position>18</position></base-id>
 733                   </base-id-5p>
 734                   <base-id-3p>
 735                      <base-id><position>177</position></base-id>
 736                   </base-id-3p>
 737                </base-pair>
 738                <base-pair comment="?">
 739                   <base-id-5p>
 740                      <base-id><position>22</position></base-id>
 741                   </base-id-5p>
 742                   <base-id-3p>
 743                      <base-id><position>212</position></base-id>
 744                   </base-id-3p>
 745                </base-pair>
 746                <base-pair comment="?">
 747                   <base-id-5p>
 748                      <base-id><position>23</position></base-id>
 749                   </base-id-5p>
 750                   <base-id-3p>
 751                      <base-id><position>211</position></base-id>
 752                   </base-id-3p>
 753                </base-pair>
 754                <base-pair comment="?">
 755                   <base-id-5p>
 756                      <base-id><position>24</position></base-id>
 757                   </base-id-5p>
 758                   <base-id-3p>
 759                      <base-id><position>210</position></base-id>
 760                   </base-id-3p>
 761                </base-pair>
 762                <base-pair comment="?">
 763                   <base-id-5p>
 764                      <base-id><position>25</position></base-id>
 765                   </base-id-5p>
 766                   <base-id-3p>
 767                      <base-id><position>209</position></base-id>
 768                   </base-id-3p>
 769                </base-pair>
 770                <base-pair comment="?">
 771                   <base-id-5p>
 772                      <base-id><position>27</position></base-id>
 773                   </base-id-5p>
 774                   <base-id-3p>
 775                      <base-id><position>176</position></base-id>
 776                   </base-id-3p>
 777                </base-pair>
 778                <base-pair comment="?">
 779                   <base-id-5p>
 780                      <base-id><position>28</position></base-id>
 781                   </base-id-5p>
 782                   <base-id-3p>
 783                      <base-id><position>175</position></base-id>
 784                   </base-id-3p>
 785                </base-pair>
 786                <base-pair comment="?">
 787                   <base-id-5p>
 788                      <base-id><position>29</position></base-id>
 789                   </base-id-5p>
 790                   <base-id-3p>
 791                      <base-id><position>174</position></base-id>
 792                   </base-id-3p>
 793                </base-pair>
 794                <base-pair comment="?">
 795                   <base-id-5p>
 796                      <base-id><position>30</position></base-id>
 797                   </base-id-5p>
 798                   <base-id-3p>
 799                      <base-id><position>173</position></base-id>
 800                   </base-id-3p>
 801                </base-pair>
 802                <base-pair comment="?">
 803                   <base-id-5p>
 804                      <base-id><position>31</position></base-id>
 805                   </base-id-5p>
 806                   <base-id-3p>
 807                      <base-id><position>172</position></base-id>
 808                   </base-id-3p>
 809                </base-pair>
 810                <base-pair comment="?">
 811                   <base-id-5p>
 812                      <base-id><position>32</position></base-id>
 813                   </base-id-5p>
 814                   <base-id-3p>
 815                      <base-id><position>46</position></base-id>
 816                   </base-id-3p>
 817                </base-pair>
 818                <base-pair comment="?">
 819                   <base-id-5p>
 820                      <base-id><position>33</position></base-id>
 821                   </base-id-5p>
 822                   <base-id-3p>
 823                      <base-id><position>45</position></base-id>
 824                   </base-id-3p>
 825                </base-pair>
 826                <base-pair comment="?">
 827                   <base-id-5p>
 828                      <base-id><position>34</position></base-id>
 829                   </base-id-5p>
 830                   <base-id-3p>
 831                      <base-id><position>44</position></base-id>
 832                   </base-id-3p>
 833                </base-pair>
 834                <base-pair comment="?">
 835                   <base-id-5p>
 836                      <base-id><position>35</position></base-id>
 837                   </base-id-5p>
 838                   <base-id-3p>
 839                      <base-id><position>43</position></base-id>
 840                   </base-id-3p>
 841                </base-pair>
 842                <base-pair comment="?">
 843                   <base-id-5p>
 844                      <base-id><position>36</position></base-id>
 845                   </base-id-5p>
 846                   <base-id-3p>
 847                      <base-id><position>42</position></base-id>
 848                   </base-id-3p>
 849                </base-pair>
 850                <base-pair comment="?">
 851                   <base-id-5p>
 852                      <base-id><position>47</position></base-id>
 853                   </base-id-5p>
 854                   <base-id-3p>
 855                      <base-id><position>61</position></base-id>
 856                   </base-id-3p>
 857                </base-pair>
 858                <base-pair comment="?">
 859                   <base-id-5p>
 860                      <base-id><position>48</position></base-id>
 861                   </base-id-5p>
 862                   <base-id-3p>
 863                      <base-id><position>59</position></base-id>
 864                   </base-id-3p>
 865                </base-pair>
 866                <base-pair comment="?">
 867                   <base-id-5p>
 868                      <base-id><position>49</position></base-id>
 869                   </base-id-5p>
 870                   <base-id-3p>
 871                      <base-id><position>58</position></base-id>
 872                   </base-id-3p>
 873                </base-pair>
 874                <base-pair comment="?">
 875                   <base-id-5p>
 876                      <base-id><position>50</position></base-id>
 877                   </base-id-5p>
 878                   <base-id-3p>
 879                      <base-id><position>57</position></base-id>
 880                   </base-id-3p>
 881                </base-pair>
 882                <base-pair comment="?">
 883                   <base-id-5p>
 884                      <base-id><position>51</position></base-id>
 885                   </base-id-5p>
 886                   <base-id-3p>
 887                      <base-id><position>56</position></base-id>
 888                   </base-id-3p>
 889                </base-pair>
 890                <base-pair comment="?">
 891                   <base-id-5p>
 892                      <base-id><position>62</position></base-id>
 893                   </base-id-5p>
 894                   <base-id-3p>
 895                      <base-id><position>171</position></base-id>
 896                   </base-id-3p>
 897                </base-pair>
 898                <base-pair comment="?">
 899                   <base-id-5p>
 900                      <base-id><position>63</position></base-id>
 901                   </base-id-5p>
 902                   <base-id-3p>
 903                      <base-id><position>170</position></base-id>
 904                   </base-id-3p>
 905                </base-pair>
 906                <base-pair comment="?">
 907                   <base-id-5p>
 908                      <base-id><position>67</position></base-id>
 909                   </base-id-5p>
 910                   <base-id-3p>
 911                      <base-id><position>169</position></base-id>
 912                   </base-id-3p>
 913                </base-pair>
 914                <base-pair comment="?">
 915                   <base-id-5p>
 916                      <base-id><position>68</position></base-id>
 917                   </base-id-5p>
 918                   <base-id-3p>
 919                      <base-id><position>168</position></base-id>
 920                   </base-id-3p>
 921                </base-pair>
 922                <base-pair comment="?">
 923                   <base-id-5p>
 924                      <base-id><position>69</position></base-id>
 925                   </base-id-5p>
 926                   <base-id-3p>
 927                      <base-id><position>165</position></base-id>
 928                   </base-id-3p>
 929                </base-pair>
 930                <base-pair comment="?">
 931                   <base-id-5p>
 932                      <base-id><position>70</position></base-id>
 933                   </base-id-5p>
 934                   <base-id-3p>
 935                      <base-id><position>164</position></base-id>
 936                   </base-id-3p>
 937                </base-pair>
 938                <base-pair comment="?">
 939                   <base-id-5p>
 940                      <base-id><position>71</position></base-id>
 941                   </base-id-5p>
 942                   <base-id-3p>
 943                      <base-id><position>163</position></base-id>
 944                   </base-id-3p>
 945                </base-pair>
 946                <base-pair comment="?">
 947                   <base-id-5p>
 948                      <base-id><position>83</position></base-id>
 949                   </base-id-5p>
 950                   <base-id-3p>
 951                      <base-id><position>110</position></base-id>
 952                   </base-id-3p>
 953                </base-pair>
 954                <base-pair comment="?">
 955                   <base-id-5p>
 956                      <base-id><position>84</position></base-id>
 957                   </base-id-5p>
 958                   <base-id-3p>
 959                      <base-id><position>109</position></base-id>
 960                   </base-id-3p>
 961                </base-pair>
 962                <base-pair comment="?">
 963                   <base-id-5p>
 964                      <base-id><position>85</position></base-id>
 965                   </base-id-5p>
 966                   <base-id-3p>
 967                      <base-id><position>106</position></base-id>
 968                   </base-id-3p>
 969                </base-pair>
 970                <base-pair comment="?">
 971                   <base-id-5p>
 972                      <base-id><position>86</position></base-id>
 973                   </base-id-5p>
 974                   <base-id-3p>
 975                      <base-id><position>105</position></base-id>
 976                   </base-id-3p>
 977                </base-pair>
 978                <base-pair comment="?">
 979                   <base-id-5p>
 980                      <base-id><position>87</position></base-id>
 981                   </base-id-5p>
 982                   <base-id-3p>
 983                      <base-id><position>104</position></base-id>
 984                   </base-id-3p>
 985                </base-pair>
 986                <base-pair comment="?">
 987                   <base-id-5p>
 988                      <base-id><position>91</position></base-id>
 989                   </base-id-5p>
 990                   <base-id-3p>
 991                      <base-id><position>102</position></base-id>
 992                   </base-id-3p>
 993                </base-pair>
 994                <base-pair comment="?">
 995                   <base-id-5p>
 996                      <base-id><position>92</position></base-id>
 997                   </base-id-5p>
 998                   <base-id-3p>
 999                      <base-id><position>101</position></base-id>
1000                   </base-id-3p>
1001                </base-pair>
1002                <base-pair comment="?">
1003                   <base-id-5p>
1004                      <base-id><position>93</position></base-id>
1005                   </base-id-5p>
1006                   <base-id-3p>
1007                      <base-id><position>100</position></base-id>
1008                   </base-id-3p>
1009                </base-pair>
1010                <base-pair comment="?">
1011                   <base-id-5p>
1012                      <base-id><position>94</position></base-id>
1013                   </base-id-5p>
1014                   <base-id-3p>
1015                      <base-id><position>99</position></base-id>
1016                   </base-id-3p>
1017                </base-pair>
1018                <base-pair comment="?">
1019                   <base-id-5p>
1020                      <base-id><position>118</position></base-id>
1021                   </base-id-5p>
1022                   <base-id-3p>
1023                      <base-id><position>136</position></base-id>
1024                   </base-id-3p>
1025                </base-pair>
1026                <base-pair comment="?">
1027                   <base-id-5p>
1028                      <base-id><position>119</position></base-id>
1029                   </base-id-5p>
1030                   <base-id-3p>
1031                      <base-id><position>135</position></base-id>
1032                   </base-id-3p>
1033                </base-pair>
1034                <base-pair comment="?">
1035                   <base-id-5p>
1036                      <base-id><position>120</position></base-id>
1037                   </base-id-5p>
1038                   <base-id-3p>
1039                      <base-id><position>134</position></base-id>
1040                   </base-id-3p>
1041                </base-pair>
1042                <base-pair comment="?">
1043                   <base-id-5p>
1044                      <base-id><position>121</position></base-id>
1045                   </base-id-5p>
1046                   <base-id-3p>
1047                      <base-id><position>133</position></base-id>
1048                   </base-id-3p>
1049                </base-pair>
1050                <base-pair comment="?">
1051                   <base-id-5p>
1052                      <base-id><position>122</position></base-id>
1053                   </base-id-5p>
1054                   <base-id-3p>
1055                      <base-id><position>132</position></base-id>
1056                   </base-id-3p>
1057                </base-pair>
1058                <base-pair comment="?">
1059                   <base-id-5p>
1060                      <base-id><position>123</position></base-id>
1061                   </base-id-5p>
1062                   <base-id-3p>
1063                      <base-id><position>131</position></base-id>
1064                   </base-id-3p>
1065                </base-pair>
1066                <base-pair comment="?">
1067                   <base-id-5p>
1068                      <base-id><position>137</position></base-id>
1069                   </base-id-5p>
1070                   <base-id-3p>
1071                      <base-id><position>160</position></base-id>
1072                   </base-id-3p>
1073                </base-pair>
1074                <base-pair comment="?">
1075                   <base-id-5p>
1076                      <base-id><position>138</position></base-id>
1077                   </base-id-5p>
1078                   <base-id-3p>
1079                      <base-id><position>158</position></base-id>
1080                   </base-id-3p>
1081                </base-pair>
1082                <base-pair comment="?">
1083                   <base-id-5p>
1084                      <base-id><position>139</position></base-id>
1085                   </base-id-5p>
1086                   <base-id-3p>
1087                      <base-id><position>157</position></base-id>
1088                   </base-id-3p>
1089                </base-pair>
1090                <base-pair comment="?">
1091                   <base-id-5p>
1092                      <base-id><position>140</position></base-id>
1093                   </base-id-5p>
1094                   <base-id-3p>
1095                      <base-id><position>156</position></base-id>
1096                   </base-id-3p>
1097                </base-pair>
1098                <base-pair comment="?">
1099                   <base-id-5p>
1100                      <base-id><position>141</position></base-id>
1101                   </base-id-5p>
1102                   <base-id-3p>
1103                      <base-id><position>155</position></base-id>
1104                   </base-id-3p>
1105                </base-pair>
1106                <base-pair comment="?">
1107                   <base-id-5p>
1108                      <base-id><position>142</position></base-id>
1109                   </base-id-5p>
1110                   <base-id-3p>
1111                      <base-id><position>154</position></base-id>
1112                   </base-id-3p>
1113                </base-pair>
1114                <base-pair comment="?">
1115                   <base-id-5p>
1116                      <base-id><position>143</position></base-id>
1117                   </base-id-5p>
1118                   <base-id-3p>
1119                      <base-id><position>152</position></base-id>
1120                   </base-id-3p>
1121                </base-pair>
1122                <base-pair comment="?">
1123                   <base-id-5p>
1124                      <base-id><position>144</position></base-id>
1125                   </base-id-5p>
1126                   <base-id-3p>
1127                      <base-id><position>151</position></base-id>
1128                   </base-id-3p>
1129                </base-pair>
1130                <base-pair comment="?">
1131                   <base-id-5p>
1132                      <base-id><position>145</position></base-id>
1133                   </base-id-5p>
1134                   <base-id-3p>
1135                      <base-id><position>150</position></base-id>
1136                   </base-id-3p>
1137                </base-pair>
1138                <base-pair comment="?">
1139                   <base-id-5p>
1140                      <base-id><position>184</position></base-id>
1141                   </base-id-5p>
1142                   <base-id-3p>
1143                      <base-id><position>232</position></base-id>
1144                   </base-id-3p>
1145                </base-pair>
1146                <base-pair comment="?">
1147                   <base-id-5p>
1148                      <base-id><position>185</position></base-id>
1149                   </base-id-5p>
1150                   <base-id-3p>
1151                      <base-id><position>231</position></base-id>
1152                   </base-id-3p>
1153                </base-pair>
1154                <base-pair comment="?">
1155                   <base-id-5p>
1156                      <base-id><position>186</position></base-id>
1157                   </base-id-5p>
1158                   <base-id-3p>
1159                      <base-id><position>230</position></base-id>
1160                   </base-id-3p>
1161                </base-pair>
1162                <base-pair comment="?">
1163                   <base-id-5p>
1164                      <base-id><position>187</position></base-id>
1165                   </base-id-5p>
1166                   <base-id-3p>
1167                      <base-id><position>229</position></base-id>
1168                   </base-id-3p>
1169                </base-pair>
1170                <base-pair comment="?">
1171                   <base-id-5p>
1172                      <base-id><position>194</position></base-id>
1173                   </base-id-5p>
1174                   <base-id-3p>
1175                      <base-id><position>223</position></base-id>
1176                   </base-id-3p>
1177                </base-pair>
1178                <base-pair comment="?">
1179                   <base-id-5p>
1180                      <base-id><position>195</position></base-id>
1181                   </base-id-5p>
1182                   <base-id-3p>
1183                      <base-id><position>222</position></base-id>
1184                   </base-id-3p>
1185                </base-pair>
1186                <base-pair comment="?">
1187                   <base-id-5p>
1188                      <base-id><position>196</position></base-id>
1189                   </base-id-5p>
1190                   <base-id-3p>
1191                      <base-id><position>221</position></base-id>
1192                   </base-id-3p>
1193                </base-pair>
1194                <base-pair comment="?">
1195                   <base-id-5p>
1196                      <base-id><position>197</position></base-id>
1197                   </base-id-5p>
1198                   <base-id-3p>
1199                      <base-id><position>220</position></base-id>
1200                   </base-id-3p>
1201                </base-pair>
1202                <base-pair comment="?">
1203                   <base-id-5p>
1204                      <base-id><position>198</position></base-id>
1205                   </base-id-5p>
1206                   <base-id-3p>
1207                      <base-id><position>219</position></base-id>
1208                   </base-id-3p>
1209                </base-pair>
1210                <base-pair comment="?">
1211                   <base-id-5p>
1212                      <base-id><position>199</position></base-id>
1213                   </base-id-5p>
1214                   <base-id-3p>
1215                      <base-id><position>218</position></base-id>
1216                   </base-id-3p>
1217                </base-pair>
1218                <base-pair comment="?">
1219                   <base-id-5p>
1220                      <base-id><position>203</position></base-id>
1221                   </base-id-5p>
1222                   <base-id-3p>
1223                      <base-id><position>217</position></base-id>
1224                   </base-id-3p>
1225                </base-pair>
1226                <base-pair comment="?">
1227                   <base-id-5p>
1228                      <base-id><position>204</position></base-id>
1229                   </base-id-5p>
1230                   <base-id-3p>
1231                      <base-id><position>216</position></base-id>
1232                   </base-id-3p>
1233                </base-pair>
1234                <base-pair comment="?">
1235                   <base-id-5p>
1236                      <base-id><position>205</position></base-id>
1237                   </base-id-5p>
1238                   <base-id-3p>
1239                      <base-id><position>215</position></base-id>
1240                   </base-id-3p>
1241                </base-pair>
1242                <base-pair comment="?">
1243                   <base-id-5p>
1244                      <base-id><position>206</position></base-id>
1245                   </base-id-5p>
1246                   <base-id-3p>
1247                      <base-id><position>214</position></base-id>
1248                   </base-id-3p>
1249                </base-pair>
1250                <base-pair comment="?">
1251                   <base-id-5p>
1252                      <base-id><position>207</position></base-id>
1253                   </base-id-5p>
1254                   <base-id-3p>
1255                      <base-id><position>213</position></base-id>
1256                   </base-id-3p>
1257                </base-pair>
1258                <base-pair comment="?">
1259                   <base-id-5p>
1260                      <base-id><position>239</position></base-id>
1261                   </base-id-5p>
1262                   <base-id-3p>
1263                      <base-id><position>258</position></base-id>
1264                   </base-id-3p>
1265                </base-pair>
1266                <base-pair comment="?">
1267                   <base-id-5p>
1268                      <base-id><position>240</position></base-id>
1269                   </base-id-5p>
1270                   <base-id-3p>
1271                      <base-id><position>257</position></base-id>
1272                   </base-id-3p>
1273                </base-pair>
1274                <base-pair comment="?">
1275                   <base-id-5p>
1276                      <base-id><position>241</position></base-id>
1277                   </base-id-5p>
1278                   <base-id-3p>
1279                      <base-id><position>256</position></base-id>
1280                   </base-id-3p>
1281                </base-pair>
1282                <base-pair comment="?">
1283                   <base-id-5p>
1284                      <base-id><position>242</position></base-id>
1285                   </base-id-5p>
1286                   <base-id-3p>
1287                      <base-id><position>255</position></base-id>
1288                   </base-id-3p>
1289                </base-pair>
1290                <base-pair comment="?">
1291                   <base-id-5p>
1292                      <base-id><position>243</position></base-id>
1293                   </base-id-5p>
1294                   <base-id-3p>
1295                      <base-id><position>254</position></base-id>
1296                   </base-id-3p>
1297                </base-pair>
1298                <base-pair comment="?">
1299                   <base-id-5p>
1300                      <base-id><position>244</position></base-id>
1301                   </base-id-5p>
1302                   <base-id-3p>
1303                      <base-id><position>253</position></base-id>
1304                   </base-id-3p>
1305                </base-pair>
1306                <base-pair comment="?">
1307                   <base-id-5p>
1308                      <base-id><position>245</position></base-id>
1309                   </base-id-5p>
1310                   <base-id-3p>
1311                      <base-id><position>252</position></base-id>
1312                   </base-id-3p>
1313                </base-pair>
1314                <base-pair comment="?">
1315                   <base-id-5p>
1316                      <base-id><position>246</position></base-id>
1317                   </base-id-5p>
1318                   <base-id-3p>
1319                      <base-id><position>251</position></base-id>
1320                   </base-id-3p>
1321                </base-pair>
1322             </str-annotation>
1323          </model>
1324       </structure>
1325    </molecule>
1326 </rnaml>