*Details for Individual Sequences in the Dataset are Available Under the Respective Links

  Overall Archaea Bacteria Eukaryotic Chloroplast Eukaryotic Mitochondrion Eukaryotic Nuclear
16S rRNA            
Comparative            
Hairpin Loop Closing 65,697 3,986 27,393 4,525 10,319 19,474
Average 132 173 140 137 92 146
2-100 65,254 3,986 27,392 4,525 10,168 19,453
101-500 173 0 1 0 151 21
501+ 0 0 0 0 0 0
Internal Loop Closing 45,193 2,110 20,196 3,009 6,252 13,626
Average 91 92 104 91 56 102
2-100 37,912 1,790 17,617 2,765 4,841 10,899
101-500 7,164 320 2,578 244 1,386 2,636
501+ 117 0 1 0 25 91
Multistem Loop Closing 40,161 2,421 18,296 2,857 6,214 10,373
Average 81 105 94 87 55 78
2-100 18,533 1,066 9,911 1,357 2,204 3,995
101-500 18,771 1,286 7,465 1,413 3,515 5,092
501+ 2,857 69 920 87 495 1,286
Bulge Loop Closing 40,943 1,694 17,500 3,015 7,194 11,540
Average 83 74 90 91 64 87
2-100 23,089 869 9,019 1,666 4,324 7,211
101-500 16,896 825 8,044 1,339 2,649 4,047
501+ 958 0 437 20 221 282
Mfold Matches4            
Hairpin Loop Closing 39,857 3,287 19,011 2,716 5,000 9,843
Average 80 143 97 82 45 74
2-100 39,809 3,287 19,011 2,716 4,952 9,843
101-500 48 0 0 0 48 0
501+ 0 0 0 0 0 0
Internal Loop Closing 20,108 1,302 10,061 1,267 2,043 5,435
Average 41 57 52 38 18 41
2-100 18,895 1,224 9,691 1,238 1,719 5,023
101-500 1,201 78 370 29 324 400
501+ 12 0 0 0 0 12
Multistem Loop Closing 9,647 1,084 5,696 822 976 1,069
Average 19 47 29 25 9 8
2-100 7,322 612 4,644 608 577 881
101-500 2,205 472 1,015 214 393 111
501+ 120 0 37 0 6 77
Bulge Loop Closing 10,506 657 5,234 788 1,451 2,376
Average 21 29 27 24 13 18
2-100 8,078 449 3,647 557 1,168 2,257
101-500 2,376 208 1,555 227 267 119
501+ 52 0 32 4 16 0
Total Mfold Predicted            
Hairpin Loop Closing 61,119 3,546 25,305 4,092 10,460 17,716
Average 123 154 130 124 93 133
2-100 61,119 3,546 25,305 4,092 10,460 17,716
101-500 0 0 0 0 0 0
501+ 0 0 0 0 0 0
Internal Loop Closing 73,450 3,382 28,671 4,846 11,632 24,919
Average 148 147 147 147 104 187
2-100 48,954 2,501 20,314 3,250 7,060 15,829
101-500 15,387 686 4,049 1,066 3,314 6,272
501+ 9,109 195 4,308 530 1,258 2,818
Multistem Loop Closing 50,581 2,370 21,449 3,464 8,685 14,613
Average 102 103 110 105 78 110
2-100 14,287 727 6,566 1,051 2,258 3,685
101-500 20,633 1,160 7,177 1,496 4,322 6,478
501+ 15,661 483 7,706 917 2,105 4,450
Bulge Loop Closing 37,997 1,812 14,756 2,343 6,112 12,974
Average 77 79 76 71 55 98
2-100 22,387 1,223 8,465 1,249 3,559 7,891
101-500 9,273 445 3,346 718 1,704 3,060
501+ 6,337 144 2,945 376 849 2,023
Predicted Correctly5            
Hairpin Loop Closing 34,905 2,762 17,163 2,398 4,394 8,188
Average 70 120 88 73 39 62
2-100 34,905 2,762 17,163 2,398 4,394 8,188
101-500 0 0 0 0 0 0
501+ 0 0 0 0 0 0
Internal Loop Closing 16,879 971 8,831 1,139 1,442 4,496
Average 34 42 45 35 13 34
2-100 15,913 913 8,518 1,116 1,219 4,147
101-500 966 58 313 23 223 349
501+ 0 0 0 0 0 0
Multistem Loop Closing 7,515 800 4,597 680 754 684
Average 15 35 24 21 7 5
2-100 5,527 432 3,601 524 450 520
101-500 1,868 368 959 156 298 87
501+ 120 0 37 0 6 77
Bulge Loop Closing 5,714 363 2,740 373 680 1,558
Average 12 16 14 11 6 12
2-100 4,179 234 1,726 223 514 1,482
101-500 1,491 129 982 146 158 76
501+ 44 0 32 4 8 0
23S rRNA            
Comparative            
Hairpin Loop Closing 64,927 5,148 20,698 8,627 13,852 16,602
Average 254 303 276 278 171 319
2-100 64,478 5,148 20,691 8,618 13,754 16,273
101-500 400 0 7 9 90 294
501+ 49 0 0 0 8 35
Internal Loop Closing 44,856 3,815 15,484 6,304 7,668 11,585
Average 175 224 206 203 95 223
2-100 31,189 2,691 11,207 4,430 5,027 7,834
101-500 11,327 889 3,387 1,520 2,466 3,065
501+ 2,340 235 890 354 175 686
Multistem Loop Closing 32,856 2,497 13,242 4,069 5,560 7,488
Average 128 147 177 131 69 144
2-100 12,826 899 5,882 1,606 2,218 2,221
101-500 16,514 1,351 5,841 2,002 2,780 4,540
501+ 3,516 247 1,519 461 562 727
Bulge Loop Closing 36,319 2,633 11,677 5,226 7,174 9,609
Average 142 155 156 169 89 185
2-100 25,592 1,923 8,204 3,440 5,044 6,981
101-500 8,880 581 2,847 1,455 1,788 2,209
501+ 1,847 129 626 331 342 419
Mfold Matches            
Hairpin Loop Closing 35,099 3,319 13,376 4,564 5,727 8,113
Average 137 195 178 147 71 156
2-100 34,924 3,319 13,376 4,558 5,699 7,972
101-500 159 0 0 6 28 125
501+ 16 0 0 0 0 16
Internal Loop Closing 16,218 1,978 6,361 1,795 1,948 4,136
Average 63 116 85 58 24 80
2-100 13,187 1,518 5,464 1,584 1,573 3,048
101-500 2,728 401 751 190 367 1,019
501+ 303 59 146 21 8 69
Multistem Loop Closing 9,639 1,065 4,246 1,003 1,353 1,972
Average 38 63 57 32 17 38
2-100 4,897 493 2,409 607 673 715
101-500 3,981 518 1,344 346 550 1,223
501+ 761 54 493 50 130 34
Bulge Loop Closing 14,552 1,571 5,186 1,478 2,364 3,953
Average 57 92 69 48 29 76
2-100 12,186 1,242 4,341 1,268 2,053 3,282
101-500 2,157 276 772 172 274 663
501+ 209 53 73 38 37 8
Total Mfold Predicted            
Hairpin Loop Closing 59,145 4,754 19,058 7,770 12,999 14,564
Average 231 280 254 251 160 280
2-100 59,145 4,754 19,058 7,770 12,999 14,564
101-500 0 0 0 0 0 0
501+ 0 0 0 0 0 0
Internal Loop Closing 68,243 5,009 20,451 8,503 14,604 19,676
Average 267 295 273 274 180 378
2-100 40,828 3,151 12,477 4,994 8,653 11,553
101-500 14,876 1,202 3,894 2,013 3,267 4,500
501+ 12,539 656 4,080 1,496 2,684 3,623
Multistem Loop Closing 52,932 3,753 16,680 7,165 12,328 13,006
Average 207 221 222 231 152 250
2-100 13,266 1,019 4,193 2,084 3,157 2,813
101-500 20,836 1,566 6,296 2,717 4,937 5,320
501+ 18,830 1,168 6,191 2,364 4,234 4,873
Bulge Loop Closing 38,032 2,620 11,105 4,246 7,453 12,608
Average 149 154 148 137 92 242
2-100 22,575 1,684 6,690 2,540 4,361 7,300
101-500 8,190 494 2,258 849 1,589 3,000
501+ 7,267 442 2,157 857 1,503 2,308
Predicted Correctly            
Hairpin Loop Closing 31,871 3,086 12,564 4,240 5,023 6,958
Average 124 182 168 137 62 134
2-100 31,871 3,086 12,564 4,240 5,023 6,958
101-500 0 0 0 0 0 0
501+ 0 0 0 0 0 0
Internal Loop Closing 12,362 1,609 4,980 1,469 1,297 3,007
Average 48 95 66 47 16 58
2-100 10,580 1,243 4,468 1,335 1,160 2,374
101-500 1,695 307 500 134 134 620
501+ 87 59 12 0 3 13
Multistem Loop Closing 7,398 832 3,109 877 1,019 1,561
Average 29 49 41 28 13 30
2-100 3,549 377 1,570 523 500 579
101-500 3,228 410 1,107 305 451 955
501+ 621 45 432 49 68 27
Bulge Loop Closing 8,386 839 2,927 906 1,171 2,543
Average 33 49 39 29 14 49
2-100 7,075 718 2,496 793 1,012 2,056
101-500 1,222 113 404 85 137 483
501+ 89 8 27 28 22 4
  1. RNA Contact Distance is defined as the number of nucleotides intervening between the 5' and 3' nucleotides in a base-pair.
  2. Only canonical base-pairs (G-C,C-G,A-U,U-A,G-U,U-G) are considered.
  3. Loop environment for a base-pair is defined here.
  4. Number of comparative base-pairs in a given loop environment predicted correctly by Mfold 3.1. No consideration is given to the loop environment of the Mfold prediction.
  5. Base-pairs predicted by Mfold 3.1 not only meet the criteria for a match to a comparative base-pair, but are in the same loop environment as the comparative base-pair they match.