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).

47 rows where group_code = "B", molecule = "16S" and strength = "Weak" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, UA, AU, GU, UG, AA, AC, AG, CA, CC, CU, GA, GG, UC, UU, gap, predominant_types, covarying_types

conformation 4

tertiary_type 2

strength 1

  • Weak · 47 ✖

molecule 1

  • 16S · 47 ✖

header_format 1

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
199 199 16S 1 13 21   v4 U:G No BP       Weak B     0.2     98.9     0.2         0.1   0.1 0.1 2128 UG  
276 276 16S 3 35 549   v4 G:C cWW       Weak B 98.8 0.1     0.1     0.2     0.4       0.1   0.2 3467 GC GC,CG
290 290 16S 3 37 547   v4 U:A tWS       Weak B     98.7     0.7 0.1     0.2     0.1     0.1 0.1 3570 UA  
297 297 16S 4 39 403   v4 G:C cWW       Weak B 96.4   1.0 0.5 1.0     0.2     0.2   0.1 0.1 0.3   0.1 3830 GC GC,UA,AU
374 374 16S 5 54 357   v4 C:G cWW       Weak B   99.3 0.4     0.1     0.1                 4138 CG CG,UA
381 381 16S 5 56 356   v4 U:A cWW       Weak B     99.8                   0.1     0.1   4124 UA  
395 395 16S 5 58 354   v4 C:G cWW       Weak B   99.3       0.1     0.1 0.1 0.2     0.1     0.1 4221 CG  
409 409 16S 6 62 105   v4 U:G cWW       Weak B   0.4 0.2     98.6                 0.4 0.2 0.1 4404 UG  
437 437 16S 6 68 101   v4 G:A cWW   3°: base pair   Weak B 0.7   0.1   0.2 0.3 0.2     0.3     97.0 0.5     0.6 4427 GA UG,GA
948 948 16S 12 292 308   v4 G:C cWW       Weak B 99.2     0.2 0.1     0.1     0.1       0.2     4920 GC GC,AU
1046 1046 16S 14 342 347   v4 C:G cWW       Weak B   98.1       0.4               0.1     1.4 4889 CG  
1081 1081 16S 15 375 388   v4 U:G No BP       Weak B     0.3     98.8     0.1           0.2 0.5   4613 UG  
1116 1116 16S 16 406 436   v4 G:C cWW       Weak B 99.1       0.5                 0.1 0.1   0.1 4861 GC  
1144 1144 16S 16 416 427   v4 G:U cWW       Weak B 16.8     0.5 79.5     1.0       0.1       1.8 0.1 4982 GC,GU GU,AC
1165 1165 16S 16 419 424   v4 C:G cWW       Weak B 0.4 78.2 0.4 0.2   17.3               0.1     3.2 4957 CG,UG GC,CG,UA,AU
1424 1424 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak B     99.7                             4553 UA  
1473 1473 16S 20 584 757   v4 G:U cWW       Weak B       0.1 99.6             0.1 0.1       0.1 4742 GU  
1536 1536 16S 21 594 645   v4 U:G cWW       Weak B 0.5 29.2 6.8 1.5   57.9 1.3 0.6 0.5 1.1   0.1 0.1 0.1 0.2 0.1 0.1 4747 CG,UA,UG GC,AU,UG,CA
1550 1550 16S 21 597 643   v4 G:C cWW       Weak B 99.2       0.1           0.1   0.1 0.3 0.1   0.1 4778 GC  
1606 1606 16S 21 605 633   v4 U:G cWW       Weak B 0.1 0.1 1.5     88.4     0.1           1.5 7.1 1.1 4799 UG,UU GC,UG
1613 1613 16S 21 606 632   v4 G:U No BP       Weak B 2.2 1.0 1.0 2.3 69.1 1.9 0.4 0.1 0.5   0.5 0.4 2.9 12.1 1.8 2.0 1.7 4794 GC,AU,GU,GA,GG,UU GU,UG,AA,CC
1690 1690 16S 22 658 748   v4 C:G cWW       Weak B 7.8 7.7 5.7 20.6 8.5 0.8 9.6 0.5 0.4 1.5 0.3 5.1 21.3 1.0 0.8 8.4   4701 GC,CG,UA,AU,GU,AA,CU,GA,UU CG,AU,GA,UC
1732 1732 16S 22 666 740   v4 G:U cWW       Weak B 0.8 0.5 0.1 2.9 95.5                     0.1 0.1 4805 AU,GU CG,UA,GU
1795 1795 16S 23 677 713   v4 U:G cWW       Weak B   2.4 19.5     72.3       5.6         0.1     4843 CG,UA,UG,CA UG,CA
1844 1844 16S 23 684 706   v4 U:A cWW       Weak B     98.0       1.7               0.1     4857 UA  
1865 1865 16S 23 690 697   v4 G:U tSH       Weak B       8.0 91.6             0.1       0.1 0.1 4853 AU,GU  
2040 2040 16S 26 832 854   v4 G:U cWW       Weak B 8.3 0.9 0.5 3.2 83.9 0.3           0.1 0.1 2.5   0.1   4735 GC,AU,GU,GG CG,UA,GU
2103 2103 16S 26.1 861 868   v4 G:C cWW       Weak B 80.3 2.6     7.5     0.7     5.5   0.1 0.1 0.1   3.0 4493 GC,CG,GU,CC GC,CG
2194 2194 16S 28 925 1391   v4 G:U cWW       Weak B         99.4             0.1 0.2 0.1   0.1 0.2 3712 GU  
2250 2250 16S 28 935 1380   v4 A:U cWW       Weak B       99.5 0.1   0.1   0.1     0.2       0.1 0.1 3978 AU  
2285 2285 16S 29 942 1341   v4 G:U cWW       Weak B       0.1 97.9                     0.2 1.8 4157 GU  
2341 2341 16S 30 950 1231   v4 U:G cWW       Weak B   0.2 19.1     80.2       0.1           0.1 0.2 4184 UA,UG UG,CA
2383 2383 16S 31 960 975   v4 U:A No BP       Weak B     92.1     7.5                     0.2 4347 UA,UG  
2390 2390 16S 31 961 974   v4 U:A No BP       Weak B 0.1   86.4     0.3         0.1       11.3 1.2 0.4 4330 UA,UC GC,UA
2621 2621 16S 34 1052 1206   v4 U:G cWW       Weak B   0.1 0.2     99.3     0.1               0.2 4234 UG  
2628 2628 16S 34 1053 1205   v4 G:U No BP       Weak B 3.8       95.6             0.2         0.2 4383 GC,GU  
2649 2649 16S 34 1058 1199   v4 G:U cWW       Weak B 0.1       99.3             0.2       0.1 0.2 4395 GU  
2901 2901 16S 40 1158 1178   v4 C:G No BP       Weak B   99.8                               4605 CG  
2908 2908 16S 40 1159 1177   v4 U:G No BP       Weak B   5.7 0.1     93.5     0.5               0.1 4600 CG,UG  
3020 3020 16S 41 1255 1282   v4 G:C cWW       Weak B 99.0       0.6     0.1     0.1   0.1 0.1     0.1 4668 GC  
3188 3188 16S 44 1401 1501   v4 G:C cWW       Weak B 99.3                   0.1   0.3   0.1   0.2 1817 GC  
3321 3321 16S 44 1425 1475   v4 U:G cWW       Weak B 0.1 2.9 5.6 0.4 0.1 36.1 2.0 0.4 42.6 0.2     5.4 3.6 0.2 0.1 0.3 3285 CG,UA,UG,AA,AG,GA,GG GC,UA,AG
3363 3363 16S 44 1435 1466   v4 G:C cWW       Weak B 89.8     1.1 4.8     2.6     0.2   0.1 0.2   0.1 1.0 3404 GC,GU,AC GC,AU
3405 3405 16S 44 1442 1460   v4 G:C cWW       Weak B 25.9 1.7 5.1 0.6 0.3 1.0 16.7 0.3 0.6 9.2   0.1 28.9 0.5 0.4 3.4 5.5 3464 GC,UA,AA,CA,GA,UU CG,AC,GA,UU
3447 3447 16S 45 1506 1529   v4 U:G No BP       Weak B     0.3     98.1         0.1     0.4 0.7 0.3 0.1 718 UG UG,CC
3482 3482 16S 45 1511 1524   v4 G:C cWW       Weak B 83.6 1.1 0.3 0.1 5.7     0.1     0.5   0.2 1.0     7.3 917 GC,GU GC,CG,UA,AU
3489 3489 16S 45 1512 1523   v4 U:G cWW       Weak B   0.2 0.2     96.9   0.1 0.1       0.1   1.3 0.5 0.5 948 UG UG,AC,GA

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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");