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 = "C" and tertiary_type = "3°: pseudoknot" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, UA, AU, AA, CA, 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
208 208 16S 2 17 918   v4 U:A cWW   3°: pseudoknot   Strong C     100.0                             117 UA  
215 215 16S 2 18 917   v4 C:G cWW   3°: pseudoknot   Strong C   99.2             0.8                 118 CG  
222 222 16S 2 19 916   v4 A:U cWW   3°: pseudoknot   Strong C   91.5             8.5                 117 CG,AG  
3806 3806 23S 6.1 61 93   v4 C:G cWW   3°: pseudoknot   Strong C 67.0 3.2   7.4 16.0               2.1   2.1   2.2 94 GC,CG,AU,GU,GA,UC GC,CG,AU
3813 3813 23S 6.1 62 92   v4   cWW   3°: pseudoknot   Strong C   8.4 15.8 2.1     57.9   4.2 6.3       1.1   3.2 1.1 95 CG,UA,AU,AA,AG,CA,UU CG,AA,UU
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
3827 3827 23S 6.1 65 89   v4 U:A cWW   3°: pseudoknot   Strong C   81.2 6.2 2.1                 8.3   1.0   1.0 96 CG,UA,AU,GA CG,AU,GA,UC
3834 3834 23S 6.1 66 88   v4 C:G cWW   3°: pseudoknot   Weak C   92.7 3.1               1.0       2.1   1.0 96 CG,UA,UC CG,UA
3841 3841 23S 6.2 67 74   v4 U:A cWH   3°: pseudoknot   Strong C 63.5 2.1 3.1 9.4 19.8   1.0           1.0         96 GC,CG,UA,AU,GU GC,CG,UA,AU
4380 4380 23S 19.1 317 334   v4 G:C cWW   3°: pseudoknot   Strong C 6.0     90.0                       1.0 3.0 100 GC,AU GC,AU
4387 4387 23S 19.1 318 333   v4 C:G cWW   3°: pseudoknot   Strong C   92.0 2.0       1.0     1.0 2.0           2.0 100 CG,UA,CC CG,UA
4520 4520 23S 22.1 413 2410   v4 C:G cWW   3°: pseudoknot   Strong C   99.0 1.0                             98 CG CG,UA
4527 4527 23S 22.1 414 2409   v4 C:G cWW   3°: pseudoknot   Strong C   96.9 1.0     2.0                       98 CG,UG CG,UA
4534 4534 23S 22.1 415 2408   v4 A:U cWW   3°: pseudoknot   Strong C       98.0                       2.0   98 AU,UU  
4541 4541 23S 22.1 416 2407   v4 U:A cWW   3°: pseudoknot   Strong C   96.9 3.1                             98 CG,UA CG,UA
1328 1328 16S 18.1 505 526   v4 G:C cWW   3°: pseudoknot   Strong C 99.4   0.6                             161 GC GC,UA
1335 1335 16S 18.1 506 525   v4 G:C cWW   3°: pseudoknot   Strong C 98.1   1.2   0.6                         160 GC GC,UA
1342 1342 16S 18.1 507 524   v4 C:G cWW   3°: pseudoknot   Strong C   100.0                               160 CG  
1384 1384 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support C 99.4                   0.6             170 GC  
1391 1391 16S 18 522 527   v4 C:G cWW   3°: pseudoknot   Strong C   99.4                     0.6         168 CG CG,GA
1426 1426 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak C     98.8                         0.6 0.6 162 UA  
5724 5724 23S 41.1 1005 1138   v4 C:G cWW   3°: pseudoknot   Strong C   96.0 2.0 2.0                           100 CG,UA,AU CG,UA,AU
5731 5731 23S 41.1 1006 1137   v4 C:G cWW   3°: pseudoknot   Strong C   97.0 1.0       2.0                     100 CG,AA CG,AA
6375 6375 23S 50.1 1343 1404   v4 G:C cWW   3°: pseudoknot   Strong C 98.0     2.0                           100 GC,AU GC,AU
6382 6382 23S 50.1 1344 1403   v4 U:A cWW   3°: pseudoknot   Strong C     97.0   3.0                         100 UA,GU UA,GU
7341 7341 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong C                     100.0             95 CC  
8139 8139 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong C             3.0           97.0         101 AA,GA  
8146 8146 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong C   96.0 3.0             1.0               101 CG,UA CG,UA
8153 8153 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong C 2.0 64.4   11.9 1.0                     20.8   101 GC,CG,AU,UU GC,CG,UU
8419 8419 23S 81.2 2283 2325   v4 C:G cWW   3°: pseudoknot   ??? C   14.7 7.8     77.5                       102 CG,UA,UG  
8552 8552 23S 85.1 2326 2389   v4 C:G cWW   3°: pseudoknot   Strong C   31.4 2.9     65.7                       102 CG,UA,UG  
8559 8559 23S 85.1 2328 2387   v4 A:U cWW   3°: pseudoknot   Weak C       100.0                           102 AU  
8566 8566 23S 85.1 2329 2386   v4 U:A cWW   3°: pseudoknot   Strong C     2.0 98.0                           102 UA,AU UA,AU
8573 8573 23S 85.1 2330 2385   v4 G:C cWW   3°: pseudoknot   Strong C 94.1     5.9                           102 GC,AU GC,AU
8643 8643 23S 86.1 2359 2428   v4 C:G cWW   3°: pseudoknot   Strong C   97.0 3.0                             101 CG,UA CG,UA
9042 9042 23S 93.1 2626 2777   v4 C:G cWW   3°: pseudoknot   Strong C   98.2 1.8                             56 CG CG,UA

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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");