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).

11 rows where group_code = 3, molecule = "23S" and strength = "Significant" sorted by position_1

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Suggested facets: reference_base_pair, GG, UU, gap, Seq

conformation 4

tertiary_type 2

strength 1

  • Significant · 11 ✖

molecule 1

  • 23S · 11 ✖

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
3754 3754 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant 3   0.5   1.5         97.5         0.2     0.2 405 AG  
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
4153 4153 23S 13 239 258   v4 C:G cWW       Significant 3 3.3 8.2 20.3 4.9 1.0 31.6       3.9 9.8   0.2 0.4 13.9 2.1 0.4 512 GC,CG,UA,AU,UG,CA,CC,UC,UU AU,UG,CC,GA
4272 4272 23S 18 287 353   v4 G:C cWW       Significant 3 12.4 6.5 9.4 14.5 6.5 3.1 8.2 1.1 1.5 0.2 2.9 4.8 3.4 6.9 1.0 2.7 14.9 523 GC,CG,UA,AU,GU,UG,AA,CC,CU,GA,GG,UU GC,CG,UA,AU
5000 5000 23S 33 688 774   v4 U:G No BP       Significant 3     89.5     5.3                 5.0 0.2   524 UA,UG,UC  
5497 5497 23S 38 874 903   v4 G:C cWW       Significant 3 30.6 2.6 1.2 2.4 21.3   0.4 0.2         39.8       1.4 493 GC,CG,AU,GU,GA CG,AU,GA
5812 5812 23S 42 1035 1120   v4 U:G cWW       Significant 3   0.2 0.2     98.3                   0.8 0.4 482 UG  
6407 6407 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant 3 32.1   4.3 0.4 0.6 0.4 0.9     19.7             41.6 468 GC,UA,CA GC,AU,UG,CA
7100 7100 23S 61 1667 1993   v4 G:U tSH       Significant 3 0.2     0.2 99.3                     0.2   430 GU  
8185 8185 23S 77 2124 2174   v4 G:C cWW       Significant 3 100.0                                 437 GC  
8710 8710 23S 88 2401 2415   v4 U:G cWW       Significant 3 2.3 29.5 1.6 1.6   59.3     4.1           0.5 1.1   437 GC,CG,UG,AG GC,AU,UG

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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");