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 = 3, 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
198 198 16S 1 13 21   v4 U:G No BP       Weak 3   0.1 0.2     99.0     0.1         0.1   0.1 0.4 3097 UG  
275 275 16S 3 35 549   v4 G:C cWW       Weak 3 93.4 0.1     5.3     0.2     0.3   0.1   0.2   0.4 4555 GC,GU GC,CG
289 289 16S 3 37 547   v4 U:A tWS       Weak 3     98.6     0.7 0.1     0.2     0.1     0.1 0.2 4665 UA  
296 296 16S 4 39 403   v4 G:C cWW       Weak 3 75.2   5.4 0.4 1.1   0.1 0.2     0.2   16.7 0.1 0.3   0.3 4942 GC,UA,GA GC,UA,AU
373 373 16S 5 54 357   v4 C:G cWW       Weak 3   99.3 0.3     0.1     0.1 0.1               5285 CG CG,UA
380 380 16S 5 56 356   v4 U:A cWW       Weak 3     99.6                   0.1     0.1 0.1 5283 UA  
394 394 16S 5 58 354   v4 C:G cWW       Weak 3 0.7 98.5       0.1     0.1 0.1 0.2     0.1     0.2 5381 CG GC,CG
408 408 16S 6 62 105   v4 U:G cWW       Weak 3   1.0 0.7     97.6               0.1 0.3 0.1 0.1 5571 UG  
436 436 16S 6 68 101   v4 G:A cWW   3°: base pair   Weak 3 3.4 0.3 16.3 0.7 0.2 0.3 0.2   0.1 0.3     77.1 0.4   0.2 0.6 5599 GC,UA,GA CG,AU,GA
947 947 16S 12 292 308   v4 G:C cWW       Weak 3 82.8     7.4 8.6     0.3         0.3   0.1 0.3   6174 GC,AU,GU GC,AU
1045 1045 16S 14 342 347   v4 C:G cWW       Weak 3 0.1 98.2       0.3               0.1     1.3 6131 CG GC,CG
1080 1080 16S 15 375 388   v4 U:G No BP       Weak 3   0.1 0.4     98.5     0.1           0.1 0.4 0.3 5867 UG  
1115 1115 16S 16 406 436   v4 G:C cWW       Weak 3 82.4       0.4                 0.1 0.1   16.9 6109 GC  
1143 1143 16S 16 416 427   v4 G:U cWW       Weak 3 13.4     0.4 63.4     0.8       0.1       1.5 20.4 6249 GC,GU GU,AC
1164 1164 16S 16 419 424   v4 C:G cWW       Weak 3 0.3 62.3 0.4 0.2   13.8                     23.0 6225 CG,UG GC,CG,UA,AU
1423 1423 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak 3     99.7     0.1                       5788 UA  
1472 1472 16S 20 584 757   v4 G:U cWW       Weak 3 0.1     0.1 99.2             0.1 0.4       0.1 5994 GU  
1535 1535 16S 21 594 645   v4 U:G cWW       Weak 3 0.4 24.0 5.9 1.3   47.7 1.1 0.4 0.4 0.9   0.1   0.1 0.1 0.1 17.3 6020 CG,UA,UG GC,AU,UG,CA
1549 1549 16S 21 597 643   v4 G:C cWW       Weak 3 82.0       0.1     0.2     0.1   0.1 0.2     17.3 6053 GC  
1605 1605 16S 21 605 633   v4 U:G cWW       Weak 3 1.2 0.5 1.2 0.1 0.3 71.7                 1.2 5.6 18.0 6071 UG,UU GC,AU,UG
1612 1612 16S 21 606 632   v4 G:U No BP       Weak 3 2.0 0.8 0.8 1.9 56.4 1.6 0.3 0.1 0.4   0.4 0.3 2.4 9.7 1.5 2.8 18.4 6068 GC,GU,GA,GG,UU GU,UG,AA,CC
1689 1689 16S 22 658 748   v4 C:G cWW       Weak 3 6.2 7.2 4.8 30.5 7.5 0.6 7.8 0.8 0.4 2.4 0.5 4.1 17.1 2.1 1.2 6.7   5948 GC,CG,UA,AU,GU,AA,CA,CU,GA,GG,UU CG,AU,GA,UC
1731 1731 16S 22 666 740   v4 G:U cWW       Weak 3 2.0 1.0 0.1 2.4 78.8       0.1       15.4         6055 GC,AU,GU,GA CG,UA,GU
1794 1794 16S 23 677 713   v4 U:G cWW       Weak 3   5.2 29.7     58.8 0.1     5.4   0.5     0.2     6104 CG,UA,UG,CA UG,CA
1843 1843 16S 23 684 706   v4 U:A cWW       Weak 3 8.2   77.9 0.2 11.6   1.5 0.4             0.1     6115 GC,UA,GU UA,GU,AC
1864 1864 16S 23 690 697   v4 G:U tSH       Weak 3 0.1     7.7 91.8             0.1 0.1     0.1 0.1 6118 AU,GU  
2039 2039 16S 26 832 854   v4 G:U cWW       Weak 3 6.8 0.8 0.4 2.7 70.5 0.3 13.1 1.1 0.7       0.6 2.0 0.2 0.7   6004 GC,AU,GU,AA,GG CG,GU,AA,UC
2102 2102 16S 26.1 861 868   v4 G:C cWW       Weak 3 83.1 2.1   0.1 6.8     0.6     4.3   0.1 0.1 0.1 0.3 2.3 5743 GC,CG,GU,CC GC,CG,UU
2193 2193 16S 28 925 1391   v4 G:U cWW       Weak 3         99.5             0.1 0.1 0.1   0.1 0.1 4863 GU  
2249 2249 16S 28 935 1380   v4 A:U cWW       Weak 3       99.5 0.1       0.1     0.2       0.1 0.1 5140 AU  
2284 2284 16S 29 942 1341   v4 G:U cWW       Weak 3 0.1     0.1 98.2                     0.2 1.4 5323 GU  
2340 2340 16S 30 950 1231   v4 U:G cWW       Weak 3   0.2 15.0     84.1       0.1       0.2   0.1 0.3 5342 UA,UG UG,CA
2382 2382 16S 31 960 975   v4 U:A No BP       Weak 3     72.2     27.5                     0.1 5561 UA,UG  
2389 2389 16S 31 961 974   v4 U:A No BP       Weak 3 0.1 0.1 68.1     20.8         0.2       8.9 1.5 0.3 5546 UA,UG,UC UA,CC
2620 2620 16S 34 1052 1206   v4 U:G cWW       Weak 3   0.2 0.2     99.2     0.1             0.1 0.3 5423 UG  
2627 2627 16S 34 1053 1205   v4 G:U No BP       Weak 3 3.0     0.1 96.4             0.2         0.3 5581 GC,GU  
2648 2648 16S 34 1058 1199   v4 G:U cWW       Weak 3 0.1       99.2             0.3       0.1 0.2 5594 GU  
2900 2900 16S 40 1158 1178   v4 C:G No BP       Weak 3   96.4       0.5       0.2 2.2 0.1     0.2   0.2 5825 CG,CC CG,UC
2907 2907 16S 40 1159 1177   v4 U:G No BP       Weak 3   6.6 0.2 0.1   87.0 1.8 0.4 1.8 0.4   0.1 0.1 0.9 0.1 0.4 0.3 5822 CG,UG UG,AA,CU
3019 3019 16S 41 1255 1282   v4 G:C cWW       Weak 3 81.8       0.5     0.1     0.1   0.1 0.1     17.4 5904 GC  
3187 3187 16S 44 1401 1501   v4 G:C cWW       Weak 3 99.4                   0.1   0.2   0.1   0.2 2784 GC  
3320 3320 16S 44 1425 1475   v4 U:G cWW       Weak 3 2.3 3.1 5.4 6.2 11.1 28.6 1.6 0.8 31.7 0.2     4.1 2.7 1.3 0.1 0.8 4419 GC,CG,UA,AU,GU,UG,AG,GA,GG UA,GU,AG
3362 3362 16S 44 1435 1466   v4 G:C cWW       Weak 3 75.9 1.0 0.2 6.1 10.4 1.8   2.1 0.1   0.2   0.7 0.2 0.1 0.1 1.0 4557 GC,AU,GU,AC GC,AU,UG
3404 3404 16S 44 1442 1460   v4 G:C cWW       Weak 3 20.3 1.9 3.9 1.1 0.7 1.4 19.2 0.3 0.5 6.8   0.1 34.9 0.4 0.3 2.5 5.7 4635 GC,UA,AA,CA,GA,UU CG,AC,GA,UU
3446 3446 16S 45 1506 1529   v4 U:G No BP       Weak 3   0.9 0.3     96.7     0.1   0.1     0.2 0.7 0.1 0.9 1484 UG UG,CC
3481 3481 16S 45 1511 1524   v4 G:C cWW       Weak 3 88.5 0.6 0.2 0.1 5.0     0.2     0.3   0.2 0.8     4.2 1707 GC,GU GC,CG,UA,AU
3488 3488 16S 45 1512 1523   v4 U:G cWW       Weak 3   0.2 0.5     95.7   0.1 0.1 0.1     0.1 0.1 0.8 2.0 0.5 1743 UG,UU UG,AC,CA

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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");