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).

36 rows where group_code = 3 and tertiary_type = "3°: pseudoknot" sorted by position_1

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

strength 5

conformation 4

molecule 2

tertiary_type 1

  • 3°: pseudoknot · 36 ✖

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
205 205 16S 2 17 918   v4 U:A cWW   3°: pseudoknot   Strong 3     98.5     0.5       0.1     0.1   0.2 0.2 0.3 3123 UA  
212 212 16S 2 18 917   v4 C:G cWW   3°: pseudoknot   Strong 3   92.8 3.9     0.7     0.2 2.1   0.1         0.2 3137 CG,UA,CA CG,UA
219 219 16S 2 19 916   v4 A:U cWW   3°: pseudoknot   Strong 3   85.3 0.9 9.6   0.3     1.2 0.3 0.1 2.2   0.1     0.2 3166 CG,AU,CU CG,UA,AU
3803 3803 23S 6.1 61 93   v4 C:G cWW   3°: pseudoknot   Strong 3 26.0 14.3 8.8 15.7   0.5   5.7         0.2 0.2     28.5 407 GC,CG,UA,AU,AC GC,CG,UA,AU
3810 3810 23S 6.1 62 92   v4   cWW   3°: pseudoknot   Strong 3 5.6 25.1 19.8 1.0 0.2 0.5 4.1   1.2 0.2 0.2   1.0 0.2   12.2 28.5 410 GC,CG,UA,AA,UU GC,CG,UA,AU
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
3824 3824 23S 6.1 65 89   v4 U:A cWW   3°: pseudoknot   Strong 3 18.5 24.8 7.1 15.1 5.1                 0.5 0.2 0.2 28.5 411 GC,CG,UA,AU,GU GC,CG,UA,AU
3831 3831 23S 6.1 66 88   v4 C:G cWW   3°: pseudoknot   Weak 3   67.4 1.5     1.5 0.2   0.2 0.2       0.5     28.5 411 CG CG,UA
3838 3838 23S 6.2 67 74   v4 U:A cWH   3°: pseudoknot   Strong 3 2.2 2.2 60.3 8.5 6.3 1.5       0.7 1.0   0.2   13.1 2.7 1.1 411 GC,CG,UA,AU,GU,UC,UU GC,CG,UA,AU
4377 4377 23S 19.1 317 334   v4 G:C cWW   3°: pseudoknot   Strong 3 52.7 6.5 3.4 27.5 7.1 1.3   0.2 0.4   0.7 0.2           535 GC,CG,UA,AU,GU GC,CG,UA,AU
4384 4384 23S 19.1 318 333   v4 C:G cWW   3°: pseudoknot   Strong 3 3.0 71.2 15.7 2.6 0.4 4.9 0.6   0.2   0.6         0.7 0.2 535 GC,CG,UA,AU,UG GC,CG,UA,AU
4517 4517 23S 22.1 413 2410   v4 C:G cWW   3°: pseudoknot   Strong 3 0.2 57.3 1.4 37.2 2.6       0.2     0.2 0.2 0.5       419 CG,AU,GU GC,CG,UA,AU
4524 4524 23S 22.1 414 2409   v4 C:G cWW   3°: pseudoknot   Strong 3 4.1 58.5 6.7 27.4 0.7 1.7     0.2 0.2     0.2       0.2 419 GC,CG,UA,AU GC,CG,UA,AU
4531 4531 23S 22.1 415 2408   v4 A:U cWW   3°: pseudoknot   Strong 3 3.6 15.5 23.2 56.3 0.2 0.5     0.2   0.5             419 GC,CG,UA,AU GC,CG,UA,AU
4538 4538 23S 22.1 416 2407   v4 U:A cWW   3°: pseudoknot   Strong 3 4.3 31.0 54.5 2.9 1.4 4.8   0.5               0.7   420 GC,CG,UA,AU,UG GC,CG,UA,AU
1325 1325 16S 18.1 505 526   v4 G:C cWW   3°: pseudoknot   Strong 3 98.8 0.2 0.1   0.4           0.1     0.1 0.1   0.1 5536 GC GC,CG,UA
1332 1332 16S 18.1 506 525   v4 G:C cWW   3°: pseudoknot   Strong 3 98.7     0.3       0.5     0.1     0.1 0.1   0.2 5579 GC GC,AU
1339 1339 16S 18.1 507 524   v4 C:G cWW   3°: pseudoknot   Strong 3   98.4       0.3   0.1 0.3 0.1 0.6 0.1         0.2 5544 CG CG,AC
1381 1381 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support 3 99.5       0.1     0.1           0.1     0.1 5577 GC  
1388 1388 16S 18 522 527   v4 C:G cWW   3°: pseudoknot   Strong 3   99.3   0.3           0.1 0.1 0.1         0.1 5452 CG CG,AU
1423 1423 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak 3     99.7     0.1                       5788 UA  
5721 5721 23S 41.1 1005 1138   v4 C:G cWW   3°: pseudoknot   Strong 3 39.0 59.1 0.8                     0.2   0.2 0.6 472 GC,CG GC,CG,UA
5728 5728 23S 41.1 1006 1137   v4 C:G cWW   3°: pseudoknot   Strong 3   94.1 4.2     1.1     0.2               0.4 472 CG,UA CG,UA
6372 6372 23S 50.1 1343 1404   v4 G:C cWW   3°: pseudoknot   Strong 3 90.6 1.6 2.3 1.2 3.5     0.2 0.2         0.2     0.2 487 GC,UA,GU GC,CG,UA,AU
6379 6379 23S 50.1 1344 1403   v4 U:A cWW   3°: pseudoknot   Strong 3 0.6 17.7 81.1     0.2                     0.4 486 CG,UA GC,CG,UA
7338 7338 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong 3                     37.9         61.9 0.2 412 CC,UU CC,UU
8136 8136 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong 3 0.2     2.1 0.9       20.1       76.7         437 AU,AG,GA AG,GA
8143 8143 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong 3   27.5 66.8     0.9       2.5     2.1     0.2   437 CG,UA,CA,GA CG,UA
8150 8150 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong 3 8.9     88.8 0.2         0.7   0.5 0.9         437 GC,AU GC,AU,CA
8416 8416 23S 81.2 2283 2325   v4 C:G cWW   3°: pseudoknot   ??? 3   51.0 41.4     7.6                       437 CG,UA,UG CG,UA
8549 8549 23S 85.1 2326 2389   v4 C:G cWW   3°: pseudoknot   Strong 3 0.7 34.3 2.5 24.9 0.2 31.8             5.3 0.2       437 CG,UA,AU,UG,GA CG,AU,GA
8556 8556 23S 85.1 2328 2387   v4 A:U cWW   3°: pseudoknot   Weak 3       99.1       0.9                   437 AU  
8563 8563 23S 85.1 2329 2386   v4 U:A cWW   3°: pseudoknot   Strong 3 49.9   19.0 30.2                 0.5   0.5     437 GC,UA,AU GC,UA,AU
8570 8570 23S 85.1 2330 2385   v4 G:C cWW   3°: pseudoknot   Strong 3 89.9 0.7 5.7 2.7 0.5                       0.5 437 GC,UA,AU GC,CG,UA,AU
8640 8640 23S 86.1 2359 2428   v4 C:G cWW   3°: pseudoknot   Strong 3   55.0 36.1 1.6 0.5   1.4     5.5               438 CG,UA,CA CG,UA,AU
9039 9039 23S 93.1 2626 2777   v4 C:G cWW   3°: pseudoknot   Strong 3   58.7 16.1     3.2 1.3 0.3 6.1 0.5   0.8 1.1 0.8     11.2 380 CG,UA,UG,AG CG,UA,AC

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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");