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).

86 rows where group_code = "E" and tertiary_type = "3°: base pair" sorted by position_1

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Suggested facets: reference_base_pair, GU, UG, AA, AC, AG, CA, CU, GA, GG, UC, UU, gap, covarying_types

conformation 7

strength 5

molecule 3

header_format 2

tertiary_type 1

  • 3°: base pair · 86 ✖

group_code 1

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
3646 3646 23S 2 30 510   v4 G:C cWW   3°: base pair   Strong E 30.8 44.4 1.7 17.1   4.3                     1.8 117 GC,CG,AU,UG GC,CG,UA,AU
356 356 16S 5 47 361   v4 C:G cWW   3°: base pair   Strong E 97.6   1.7 0.1       0.1         0.1   0.1   0.2 936 GC GC,UA,AU
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  
440 440 16S 6 68 101   v4 G:A cWW   3°: base pair   Weak E   1.5 93.1 2.6   0.3 0.2   0.2 0.2   0.1 0.2 0.1   1.3 0.1 973 UA,AU CG,UA,AU
124 124 5S 3 75 101 Tertiary legacy     B 3°: base pair   Strong E       57.7     2.7 20.8 18.8                 298 AU,AA,AC,AG  
128 128 5S 3 76 100 Tertiary legacy     B 3°: base pair   Strong E                         99.7 0.3       298 GA  
132 132 5S 3 77 99 Tertiary legacy     B 3°: base pair   Strong E     99.7     0.3                       298 UA  
136 136 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant E                 100.0                 298 AG  
601 601 16S 7 129 232   v4 A:G cWW   3°: base pair   Strong E 0.1 0.8 72.3   0.1 25.7 0.1   0.4       0.1 0.1   0.2 0.1 1015 UA,UG CG,UA,GU
678 678 16S 8 145 177   v4 G:G cWW   3°: base pair   Strong E 0.3 0.3 0.1 24.8 1.2   1.3 0.9 0.2 0.1   2.0     0.1 64.6 4.3 1018 AU,CU,UU GC,CG,AA,UU
699 699 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong E 0.4     0.1   0.2 1.3 83.6 1.0 0.6 9.8   0.9   1.4 0.2 0.6 1021 AC,CC UG,AC,GA
846 846 16S 11 245 283   v4 U:U cWW   3°: base pair   Strong E               0.1   0.1 99.2         0.6   1024 CC CC,UU
4395 4395 23S 19.2 319 323   v4 G:C cWW   3°: base pair   Strong E 1.4 88.7 1.8 0.5   5.0 0.5   0.5               1.9 221 CG,UG GC,CG,UA,AU
1021 1021 16S 13 321 332   v4 A:G cWW   3°: base pair   Strong E   99.7               0.2       0.1       1025 CG  
1056 1056 16S 15 367 393   v4 U:A cWW   3°: base pair   Strong E 0.1 0.1 98.0     1.8                       1017 UA GC,CG,UA
4479 4479 23S 21 383 391   v4 C:A cWW   3°: base pair   ??? E     0.5                           99.6 221    
1175 1175 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong E                                 100.0 1030    
1182 1182 16S 17 440 497   v4 C:G cWW   3°: base pair   Strong E                                 100.0 1030    
1189 1189 16S 17 441 493   v4 A:A cWW   3°: base pair   Strong E                                 100.0 1030    
1231 1231 16S 17 450 483   v4 G:C cWW   3°: base pair   Strong E                                 100.0 1030    
4591 4591 23S 24.1 531 2018   v4 C:G cWW   3°: base pair   Strong E 0.7           93.3     1.3     3.3       1.3 150 AA,GA GC,AA
4626 4626 23S 25 537 556   v4 G:A cWW   3°: base pair   Strong E 8.7 1.4 67.8 9.1 0.5   1.4   1.0     0.5   0.5   1.9 7.3 208 GC,UA,AU GC,CG,UA,AU
4633 4633 23S 25 538 555   v4 A:G cWW   3°: base pair   Weak E 38.2 2.4   9.2 20.8 13.0               0.5   5.8 10.1 207 GC,CG,AU,GU,UG,UU GC,AU,UG
4682 4682 23S 25.1 563 578   v4 A:G cWW   3°: base pair   Strong E   95.2 1.9     2.4                     0.5 207 CG,UG CG,UA
4696 4696 23S 25.1 565 576   v4 C:U cWW   3°: base pair   Strong E 98.6             1.4                   207 GC  
1434 1434 16S 19.1 575 880   v4 G:C cWW   3°: base pair   Strong E 0.6   0.1 96.0 3.0   0.1 0.1 0.1                 1005 AU,GU GC,UA,AU
1469 1469 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong E 0.3   0.9     1.2   0.2             97.4   0.1 1032 UC  
1623 1623 16S 21 611 629   v4 C:A cWW   3°: base pair   Strong E                                 100.0 1042    
4899 4899 23S 31 637 651   v4 A:G cWW   3°: base pair   Strong E                                 100.0 203    
1728 1728 16S 22 663 742   v4 A:G cWW   3°: base pair   Strong E   33.9 15.5 0.1   49.5   0.3         0.1 0.2 0.3   0.2 1029 CG,UA,UG UG,AC,GA
1791 1791 16S 23 674 716   v4 G:A cWW   3°: base pair   Strong E 93.1 0.5   4.7 0.4 0.5             0.4 0.2     0.3 1026 GC,AU GC,CG,AU
4948 4948 23S 32 674 806   v4 G:C cWW   3°: base pair   ??? E 99.5       0.5                         202 GC  
5074 5074 23S 33 698 763   v4 C:G cWW   3°: base pair   Strong E 2.0 45.4 43.4 1.0   2.0       2.9 1.0 1.0 0.5 1.0       205 GC,CG,UA,UG,CA GC,CG,UA,AU
5151 5151 23S 34 713 718   v4 G:A cWW   3°: base pair   Strong E 85.3 10.3 1.5 2.5       0.5                   204 GC,CG,AU GC,CG,UA,AU
1875 1875 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong E 0.1 0.1 12.2 0.3 3.3 0.1 56.2 0.2 0.7       5.9 20.6     0.3 1033 UA,GU,AA,GA,GG AA,GG
5368 5368 23S 38 847 933   v4 U:A cWW   3°: base pair   Strong E 0.9 15.2 1.4 9.0   2.8 0.5   0.9         2.8     66.4 211 CG,AU,UG,GG GC,CG,UA,AU
5438 5438 23S 38 857 920   v4 G:A cWW   3°: base pair   Strong E   27.4 9.0 5.2 0.9 12.7 15.1 0.5 13.7   0.5   12.3     1.4 1.5 212 CG,UA,AU,UG,AA,AG,GA CG,AA,UU
2309 2309 16S 30 945 1236   v4 G:A cWW   3°: base pair   Strong E 0.1       0.1   0.1     0.2     98.9 0.1     0.5 976 GA  
2575 2575 16S 33.2 1026 1035   v4 G:A cWW   3°: base pair   Strong E                                 100.0 1029    
5802 5802 23S 42 1032 1122   v4 A:G cWW   3°: base pair   Strong E 92.9 0.5   3.0   2.0             1.0       0.5 197 GC,AU,UG GC,AU,UG
5844 5844 23S 42 1039 1116   v4 A:G cWW   3°: base pair   Strong E   3.4 95.1     0.5                 0.5   0.5 203 CG,UA CG,UA
5851 5851 23S 42 1040 1115   v4 A:G cWW   3°: base pair   Strong E 9.8 2.4 66.8 2.0   2.9       15.6             0.5 205 GC,CG,UA,AU,UG,CA GC,CG,UA,AU
2673 2673 16S 34 1061 1195   v4 G:C cWW   3°: base pair   No Support E 99.3       0.2           0.2     0.1     0.2 998 GC  
2680 2680 16S 34 1062 1194   v4 U:U cWW   3°: base pair   Strong E   2.6 96.2   0.1 0.5             0.2     0.2 0.2 998 CG,UA CG,UA,GU
5956 5956 23S 43.1 1082 1086   v4 U:A tWW   3°: base pair   Strong E   98.6       0.5                     1.0 211 CG  
5963 5963 23S 44 1087 1102   v4 G:C cWW   3°: base pair   Strong E 95.6     3.4 0.5                       0.5 206 GC,AU GC,AU
6047 6047 23S 46 1196 1250   v4 C:G cWW   3°: base pair   Strong E 0.5 84.9 9.7   0.5 1.6 0.5   0.5         1.1     0.5 185 CG,UA GC,CG,UA
6089 6089 23S 46 1203 1242   v4 U:U cWW   3°: base pair   Strong E 71.2 2.1 2.6 19.9 1.0                   0.5 2.1 0.5 191 GC,CG,UA,AU,UU GC,CG,UA,AU
6096 6096 23S 46 1204 1241   v4 A:A cWW   3°: base pair   Strong E 1.6 4.7 14.1 0.5   70.8     0.5           0.5 5.7 1.5 192 CG,UA,UG,UU GC,AU,UG
6187 6187 23S 46.1 1263 2016   v4 U:U cWW   3°: base pair   Strong E 100.0                                 150 GC  
3065 3065 16S 42 1303 1334   v4 C:G cWW   3°: base pair   Strong E 98.6   0.5 0.3       0.2           0.3     0.1 1021 GC GC,UA,AU
3072 3072 16S 42 1307 1330   v4 U:U cWW   3°: base pair   Strong E         0.1       0.3   3.1       0.7 95.6 0.2 1022 CC,UU AG,CC,UU
6411 6411 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant E     3.7       2.4                   93.9 164 UA,AA  
3177 3177 16S 43 1357 1365   v4 A:G cWW   3°: base pair   Strong E 84.4 0.9 4.7 3.5 0.1 3.1     0.2 1.6       1.1 0.1   0.4 1023 GC,UA,AU,UG GC,CG,UA,AU
6453 6453 23S 52 1359 1372   v4 A:U cWW   3°: base pair   Strong E                                 100.0 181    
3184 3184 16S 44 1399 1504   v4 C:G cWW   3°: base pair   Strong E   99.0       0.1       0.2   0.1   0.1     0.3 837 CG  
3198 3198 16S 44 1402 1500   v4 C:A cWW   3°: base pair   Strong E     0.2     0.1       99.4   0.1         0.1 861 CA UG,CA
3219 3219 16S 44 1407 1494   v4 C:G cWW   3°: base pair   ??? E   99.2       0.3         0.1 0.1         0.2 883 CG  
3254 3254 16S 44 1413 1487   v4 A:G cWW   3°: base pair   Strong E   5.5 92.7 0.4   0.1   0.1             1.0   0.1 908 CG,UA CG,UA,AU
6642 6642 23S 55 1425 1573   v4 G:G cWW   3°: base pair   Strong E 2.8 10.6 12.3 70.4   2.8 0.6                   0.6 179 GC,CG,UA,AU,UG GC,CG,UA,AU
6915 6915 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong E 2.8 67.8 4.4 0.6 15.6       0.6         0.6     7.8 180 GC,CG,UA,GU CG,UA,GU
6922 6922 23S 59 1528 1543   v4 A:G tHS   3°: base pair   Strong E 17.2 18.9 2.2 51.7 0.6 0.6     1.1               7.8 180 GC,CG,UA,AU GC,CG,UA,AU
7146 7146 23S 62 1690 1697   v4 A:G tHS   3°: base pair   Strong E         0.6   4.5   93.5 0.6   0.6           155 AA,AG GU,AG,CA
7251 7251 23S 63.1 1752 1756   v4 C:G cWW   3°: base pair   Strong E 88.5 0.6 3.2   2.6           0.6     0.6 2.6   1.2 156 GC,UA,GU,UC GC,CG,UA
7405 7405 23S 66 1800 1817   v4 C:G tWW   3°: base pair   Strong E   1.3 5.8 87.1 0.6 0.6 1.3 1.3 0.6               1.3 155 UA,AU CG,UA,AU
7412 7412 23S 66 1803 1814   v4 A:G tHS   3°: base pair   Weak E 2.6 1.9 0.6 1.9 89.1     0.6                 3.2 156 GC,GU CG,UA,GU,AC
7559 7559 23S 68 1855 1887   v4 U:C cWW   3°: base pair   Strong E                                 100.0 155    
7566 7566 23S 68 1856 1886   v4 U:U cWW   3°: base pair   Strong E                                 100.0 155    
7573 7573 23S 68 1858 1884   v4 A:G tHS/tSH   3°: base pair   Strong E                                 100.0 155    
7580 7580 23S 68 1859 1883   v4 U:U cWW   3°: base pair   Strong E                                 99.9 155    
7678 7678 23S 69.1 1925 1929   v4 C:G tWW   3°: base pair   Strong E           99.4                     0.6 155 UG  
7979 7979 23S 75 2086 2233   v4 U:U cWW   3°: base pair   Strong E   3.2 53.5 2.6           38.7     0.6     0.6 0.6 155 CG,UA,AU,CA CG,UA,AU
8091 8091 23S 76 2104 2185   v4 C:U cWW   3°: base pair   Strong E   5.2 85.2 2.6 1.3 3.9   0.6               1.3   155 CG,UA,AU,UG CG,UA,AU
8126 8126 23S 76 2109 2180   v4 U:U cWW   3°: base pair   Weak E 96.1     0.6   2.6                     0.6 155 GC,UG GC,AU,UG
8413 8413 23S 81.1 2282 2427   v4 G:C cWW   3°: base pair   Strong E 94.8 2.6     2.6                         155 GC,CG,GU GC,CG
8609 8609 23S 86 2351 2366   v4 G:A cWW   3°: base pair   Weak E 16.1 3.9 3.9 2.6 1.9 1.3             70.3         155 GC,CG,UA,AU,GA CG,AU,GA
8616 8616 23S 86 2352 2365   v4 A:G cWW   3°: base pair   Strong E 3.9   4.5 91.0               0.6           155 GC,UA,AU GC,UA,AU
8826 8826 23S 90 2507 2582   v4 C:G cWW   3°: base pair   Strong E   100.0                               135 CG  
8861 8861 23S 90 2512 2574   v4 C:G cWW   3°: base pair   Strong E   97.8               2.2               135 CG,CA  
9183 9183 23S 96 2675 2732   v4 A:G cWW   3°: base pair   Strong E   2.2 4.3 1.4 2.9 1.4   1.4       1.4 0.7 2.2 33.3 47.8 0.7 138 CG,UA,GU,GG,UC,UU CG,AC,GA,UU
9421 9421 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? E   7.1   2.4 1.2 9.5     4.8       4.8     2.4 67.9 84 CG,AU,UG,AG,GA,UU AU,UG,GA
9442 9442 23S 99 2813 2887   v4 A:A cWW   3°: base pair   Strong E 2.4 21.2 60.0 1.2 1.2             1.2 1.2 1.2   4.7 6.0 85 GC,CG,UA,UU GC,CG,UA,AU
9449 9449 23S 99 2814 2886   v4 A:A cWW   3°: base pair   Strong E 3.5 72.9 1.2 3.5     5.9     1.2 4.7 2.4       1.2 3.6 85 GC,CG,AU,AA,CC,CU GC,CG,AA,UU
9547 9547 23S 101 2844 2872   v4 G:A cWW   3°: base pair   Strong E 1.1   4.5 1.1 2.2 1.1         3.4       1.1 77.5 7.9 89 UA,GU,CC,UU CC,UU
9554 9554 23S 101 2845 2871   v4 U:U cWW   3°: base pair   No Support E 22.7 3.4   52.3 3.4 11.4       1.1   1.1   1.1   2.3 1.1 88 GC,CG,AU,GU,UG,UU GC,AU,UG,CA
9568 9568 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong E           1.8       0.9   0.9   0.9 0.9 87.2 7.4 109 UU CA,GG,UU

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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");