Base-pair frequencies

predominant_types
Base-pair types shown in bold in the published table (most frequent).
covarying_types
Base-pair types marked * in the published table (involved in a covariation).
header_format
legacy = entry not yet revised to the v4 layout (no type / conformation).

85 rows where strength = "Significant" sorted by position_1

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Suggested facets: helix_number, position_1, position_2, reference_base_pair, CG, GU, AA, AC, AG, CA, CU, GA, GG, UC, UU, covarying_types

group_code 7

  • 3 13
  • A 13
  • B 13
  • E 13
  • C 11
  • M 11
  • T 11

conformation 4

tertiary_type 2

molecule 2

header_format 2

strength 1

  • Significant · 85 ✖
Link rowid molecule helix_number position_1 ▼ position_2 pair_note header_format reference_base_pair conformation ai_code tertiary_type header_extra strength group_code GC CG UA AU GU UG AA AC AG CA CC CU GA GG UC UU gap Seq predominant_types covarying_types
3753 3753 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant T   0.4 1.5 2.1     0.8 0.3 66.2         0.1   0.3 28.1 719 AU,AG UA,AG
3754 3754 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant 3   0.5   1.5         97.5         0.2     0.2 405 AG  
3755 3755 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant B                 100.0                 252 AG  
3756 3756 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant A   5.6   11.1         83.3                 36 CG,AU,AG  
3757 3757 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant C             6.2   93.8                 81 AA,AG  
3758 3758 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant E       1.7         96.6         0.9     0.9 117 AG  
3759 3759 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant M   0.4 4.7 3.9     0.4 0.9 2.1             0.9 86.6 233 UA,AU,AG CG,UA,AU
3816 3816 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant T 7.8 3.0 0.5 13.6 0.1 0.1 23.2 4.6 0.7   0.3 0.3 0.4 0.3   0.5 44.5 740 GC,CG,AU,AA,AC GC,CG,AA,UU
3817 3817 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant 3 14.1 5.1 0.7 22.1   0.2 29.0             0.2     28.4 411 GC,CG,AU,AA GC,CG,AA
3818 3818 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant B 22.6 8.2 0.8 35.4   0.4 32.3             0.4       257 GC,CG,AU,AA GC,CG,UA,AU
3819 3819 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant A             100.0                     36 AA  
3820 3820 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant C       5.2     54.2 34.4 1.0         1.0   1.0 3.1 96 AU,AA,AC AA,GG,UU
3821 3821 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant E     0.8                           99.1 118    
3822 3822 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant M   0.4 0.4 2.1 0.4   0.4 0.4 1.7   0.9 0.9 1.3     1.3 89.7 233 AU AU,CC,GA
133 133 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant 3     0.3 0.5     5.2 0.3 92.3 0.7     0.2 0.3     0.2 611 AA,AG AG,CA
134 134 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant B     0.3 1.3     10.6 0.7 85.8       0.3 0.7     0.3 302 AA,AG AG,GA
135 135 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant A     2.3       2.3   86.4 9.1               44 UA,AA,AG,CA AG,CA
136 136 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant E                 100.0                 298 AG  
141 141 5S 3 80 96   v4 U:G cWW       Significant 3 0.3 8.5 0.2   0.2 89.2           0.2   0.2 0.2 1.1   611 CG,UG GC,UG,CU
142 142 5S 3 80 96   v4 U:G cWW       Significant B 0.3 3.6 0.3     94.7               0.7   0.3   302 CG,UG GC,UG
143 143 5S 3 80 96   v4 U:G cWW       Significant A           100.0                       44 UG  
144 144 5S 3 80 96   v4 U:G cWW       Significant E 0.7 14.8     0.3 80.9           0.3     0.3 2.7   298 CG,UG,UU GC,UG,CU
4152 4152 23S 13 239 258   v4 C:G cWW       Significant T 5.7 5.5 22.5 12.1 2.5 21.2 1.4   0.1 4.4 5.9 0.3 0.3 0.2 9.6 4.7 3.3 866 GC,CG,UA,AU,GU,UG,CA,CC,UC,UU UA,AU,CC,GG
4153 4153 23S 13 239 258   v4 C:G cWW       Significant 3 3.3 8.2 20.3 4.9 1.0 31.6       3.9 9.8   0.2 0.4 13.9 2.1 0.4 512 GC,CG,UA,AU,UG,CA,CC,UC,UU AU,UG,CC,GA
4154 4154 23S 13 239 258   v4 C:G cWW       Significant B 5.1 14.9 15.6 8.7 0.7 46.7         0.7       7.2   0.4 276 GC,CG,UA,AU,UG,UC GC,AU,UG
4155 4155 23S 13 239 258   v4 C:G cWW       Significant A 5.6 2.8 8.3     77.8       5.6               36 GC,CG,UA,UG,CA GC,UG,CA
4156 4156 23S 13 239 258   v4 C:G cWW       Significant C 29.0   8.0 5.0 17.0 5.0 3.0     4.0     1.0   12.0 16.0   100 GC,UA,AU,GU,UG,AA,CA,UC,UU GC,CA,UU
4157 4157 23S 13 239 258   v4 C:G cWW       Significant E 0.5   29.0 0.5 1.5 2.5       9.0 24.0   0.5 1.0 25.5 5.5 0.5 200 UA,UG,CA,CC,UC,UU UA,GU,CC
4158 4158 23S 13 239 258   v4 C:G cWW       Significant M 1.2 2.4 32.7 29.5   6.7 3.5   0.4 5.5 0.4 1.2 0.4     5.5 10.7 254 CG,UA,AU,UG,AA,CA,UU GC,CG,UA,AU
4271 4271 23S 18 287 353   v4 G:C cWW       Significant T 7.6 3.9 8.3 10.7 4.1 1.8 7.2 0.9 1.8 0.7 1.7 3.1 2.5 4.1 0.8 2.4 38.3 877 GC,CG,UA,AU,GU,AA,CU,GA,GG,UU GC,CG,UA,AU
4272 4272 23S 18 287 353   v4 G:C cWW       Significant 3 12.4 6.5 9.4 14.5 6.5 3.1 8.2 1.1 1.5 0.2 2.9 4.8 3.4 6.9 1.0 2.7 14.9 523 GC,CG,UA,AU,GU,UG,AA,CC,CU,GA,GG,UU GC,CG,UA,AU
4273 4273 23S 18 287 353   v4 G:C cWW       Significant B 8.4 6.2 15.3 21.8 4.7 4.4 14.2 0.4 1.1 0.4   8.7 2.9 5.5 0.7 4.0 1.5 275 GC,CG,UA,AU,GU,UG,AA,CU,GA,GG,UU GC,CG,UA,AU
4274 4274 23S 18 287 353   v4 G:C cWW       Significant A 5.6 38.9   27.8   11.1   2.8     5.6   5.6     2.8   36 GC,CG,AU,UG,AC,CC,GA,UU GC,CG,AU
4275 4275 23S 18 287 353   v4 G:C cWW       Significant C 2.0   23.0 12.0 1.0   18.0 2.0 7.0 5.0   2.0 3.0   2.0 4.0 19.0 100 GC,UA,AU,AA,AC,AG,CA,CU,GA,UC,UU GC,UA,AU
4276 4276 23S 18 287 353   v4 G:C cWW       Significant E 18.9 1.4 3.3 2.8 9.9   1.9 1.9 2.4   6.1 0.5 3.8 9.9 1.4 0.9 35.0 212 GC,UA,AU,GU,AG,CC,GA,GG GC,CG,UA,AU
4277 4277 23S 18 287 353   v4 G:C cWW       Significant M     0.4 2.4 0.4   0.8   0.4       0.4     1.2 94.1 254 AU UA,AU
4999 4999 23S 33 688 774   v4 U:G No BP       Significant T     90.9 1.5 0.1 3.6       0.1         3.3 0.3 0.2 886 UA,UG,UC UA,AU
5000 5000 23S 33 688 774   v4 U:G No BP       Significant 3     89.5     5.3                 5.0 0.2   524 UA,UG,UC  
5001 5001 23S 33 688 774   v4 U:G No BP       Significant B     88.7     9.2                 2.1     282 UA,UG,UC  
5002 5002 23S 33 688 774   v4 U:G No BP       Significant A     100.0                             37 UA  
5003 5003 23S 33 688 774   v4 U:G No BP       Significant C     100.0                             100 UA  
5004 5004 23S 33 688 774   v4 U:G No BP       Significant E     88.8     1.0                 9.8 0.5   205 UA,UC  
5005 5005 23S 33 688 774   v4 U:G No BP       Significant M     90.1 5.0 0.4 1.5       0.4         1.1 0.8 0.8 262 UA,AU UA,AU
5496 5496 23S 38 874 903   v4 G:C cWW       Significant T 29.1 1.5 2.2 2.6 12.9 0.3 0.6 0.3         22.8   0.2 0.5 26.8 859 GC,UA,AU,GU,GA GC,CG,UA,AU
5497 5497 23S 38 874 903   v4 G:C cWW       Significant 3 30.6 2.6 1.2 2.4 21.3   0.4 0.2         39.8       1.4 493 GC,CG,AU,GU,GA CG,AU,GA
5498 5498 23S 38 874 903   v4 G:C cWW       Significant B 53.7 4.5 2.5 4.9 34.4                         244 GC,CG,UA,AU,GU GC,CG,UA,AU
5499 5499 23S 38 874 903   v4 G:C cWW       Significant A 40.5       45.9     2.7         10.8         37 GC,GU,AC,GA GU,AC
5500 5500 23S 38 874 903   v4 G:C cWW       Significant C 91.0     1.0 2.0 2.0   2.0             2.0     100 GC,GU,UG,AC,UC GC,AU,UG
5501 5501 23S 38 874 903   v4 G:C cWW       Significant E 2.4 0.9     1.9   0.9           90.6       3.3 212 GC,GA CG,GA
5502 5502 23S 38 874 903   v4 G:C cWW       Significant M 3.0   4.9 3.8 1.5 0.4 0.8                 1.5 84.3 266 GC,UA,AU GC,UA,AU
5811 5811 23S 42 1035 1120   v4 U:G cWW       Significant T 0.2 0.2 1.5 0.7 0.2 69.2 0.1 0.2         0.1     0.6 26.8 858 UG GC,AU,UG
5812 5812 23S 42 1035 1120   v4 U:G cWW       Significant 3   0.2 0.2     98.3                   0.8 0.4 482 UG  
5813 5813 23S 42 1035 1120   v4 U:G cWW       Significant B           100.0                       239 UG  
5814 5814 23S 42 1035 1120   v4 U:G cWW       Significant A           97.3                     2.7 37 UG  
5815 5815 23S 42 1035 1120   v4 U:G cWW       Significant C     1.0     98.0                   1.0   100 UG  
5816 5816 23S 42 1035 1120   v4 U:G cWW       Significant E   0.5 0.5     96.6                   1.9 0.5 206 UG  
5817 5817 23S 42 1035 1120   v4 U:G cWW       Significant M 0.7 0.4 4.0 2.2 0.7 8.0 0.4 0.7         0.4       82.6 276 UA,AU,UG GC,AU,UG
6406 6406 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant T 29.1   7.8 1.3 0.6 0.5 1.5 0.8 0.1 15.5 0.6 0.2 0.1     0.1 41.5 844 GC,UA,CA GC,AU,UG,CA
6407 6407 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant 3 32.1   4.3 0.4 0.6 0.4 0.9     19.7             41.6 468 GC,UA,CA GC,AU,UG,CA
6408 6408 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant B 57.0   5.3 0.8 1.1 0.8       35.0               263 GC,UA,CA GC,AU,UG,CA
6409 6409 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant A                                 99.9 41    
6410 6410 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant C 96.0     2.0 2.0                         100 GC,AU,GU GC,AU
6411 6411 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant E     3.7       2.4                   93.9 164 UA,AA  
6412 6412 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant M     16.7 2.5   0.7 3.3 2.5 0.4 14.1 1.8 0.7 0.4     0.4 56.6 276 UA,AU,AA,AC,CA UA,AC,CU
7099 7099 23S 61 1667 1993   v4 G:U tSH       Significant T 0.1   1.2 0.6 97.3   0.1           0.1 0.1   0.1 0.2 807 GU UA,GU
7100 7100 23S 61 1667 1993   v4 G:U tSH       Significant 3 0.2     0.2 99.3                     0.2   430 GU  
7101 7101 23S 61 1667 1993   v4 G:U tSH       Significant B 0.4       99.2                     0.4   236 GU  
7102 7102 23S 61 1667 1993   v4 G:U tSH       Significant A         100.0                         41 GU  
7103 7103 23S 61 1667 1993   v4 G:U tSH       Significant C         100.0                         101 GU  
7104 7104 23S 61 1667 1993   v4 G:U tSH       Significant E       0.7 99.3                         153 GU  
7105 7105 23S 61 1667 1993   v4 G:U tSH       Significant M     3.6 1.4 93.1   0.4           0.4 0.4     0.7 276 UA,GU UA,GU
8184 8184 23S 77 2124 2174   v4 G:C cWW       Significant T 67.5   0.2     0.1   0.1             0.2 0.1 31.6 847 GC GC,UA
8185 8185 23S 77 2124 2174   v4 G:C cWW       Significant 3 100.0                                 437 GC  
8186 8186 23S 77 2124 2174   v4 G:C cWW       Significant B 100.0                                 241 GC  
8187 8187 23S 77 2124 2174   v4 G:C cWW       Significant A 100.0                                 41 GC  
8188 8188 23S 77 2124 2174   v4 G:C cWW       Significant C 99.0             1.0                   101 GC  
8189 8189 23S 77 2124 2174   v4 G:C cWW       Significant E 100.0                                 155 GC  
8190 8190 23S 77 2124 2174   v4 G:C cWW       Significant M 11.3   0.6     0.3                 0.6 0.3 86.7 309 GC GC,UA
8709 8709 23S 88 2401 2415   v4 U:G cWW       Significant T 1.3 15.7 2.4 1.4   45.0     2.1 0.4     0.2   0.4 0.6 30.6 847 CG,UA,UG,AG GC,AU,UG,CA
8710 8710 23S 88 2401 2415   v4 U:G cWW       Significant 3 2.3 29.5 1.6 1.6   59.3     4.1           0.5 1.1   437 GC,CG,UG,AG GC,AU,UG
8711 8711 23S 88 2401 2415   v4 U:G cWW       Significant B   6.6       92.9     0.4                 241 CG,UG  
8712 8712 23S 88 2401 2415   v4 U:G cWW       Significant A 12.2 70.7       12.2                 4.9     41 GC,CG,UG,UC GC,CG
8713 8713 23S 88 2401 2415   v4 U:G cWW       Significant C     2.0     93.1       3.0     1.0   1.0     101 UA,UG,CA UG,CA
8714 8714 23S 88 2401 2415   v4 U:G cWW       Significant E 3.2 54.2 4.5 4.5   19.4     11.0             3.2   155 GC,CG,UA,AU,UG,AG,UU GC,CG,UA,AU
8715 8715 23S 88 2401 2415   v4 U:G cWW       Significant M 0.3 1.3 3.6 1.6   9.1             0.3       83.8 309 UA,UG GC,AU,UG

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CREATE TABLE "basepair_frequency" (
   "molecule" TEXT,
   "helix_number" TEXT,
   "position_1" INTEGER,
   "position_2" INTEGER,
   "pair_note" TEXT,
   "header_format" TEXT,
   "reference_base_pair" TEXT,
   "conformation" TEXT,
   "ai_code" TEXT,
   "tertiary_type" TEXT,
   "header_extra" TEXT,
   "strength" TEXT,
   "group_code" TEXT,
   "GC" REAL,
   "CG" REAL,
   "UA" REAL,
   "AU" REAL,
   "GU" REAL,
   "UG" REAL,
   "AA" REAL,
   "AC" REAL,
   "AG" REAL,
   "CA" REAL,
   "CC" REAL,
   "CU" REAL,
   "GA" REAL,
   "GG" REAL,
   "UC" REAL,
   "UU" REAL,
   "gap" REAL,
   "Seq" INTEGER,
   "predominant_types" TEXT,
   "covarying_types" TEXT
);
CREATE INDEX "idx_basepair_frequency_molecule_position_1_position_2"
    ON "basepair_frequency" ("molecule", "position_1", "position_2");