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 = "A", molecule = "23S" and strength = "Significant" sorted by position_1

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Suggested facets: reference_base_pair, GC, 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
3756 3756 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant A   5.6   11.1         83.3                 36 CG,AU,AG  
3819 3819 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant A             100.0                     36 AA  
4155 4155 23S 13 239 258   v4 C:G cWW       Significant A 5.6 2.8 8.3     77.8       5.6               36 GC,CG,UA,UG,CA GC,UG,CA
4274 4274 23S 18 287 353   v4 G:C cWW       Significant A 5.6 38.9   27.8   11.1   2.8     5.6   5.6     2.8   36 GC,CG,AU,UG,AC,CC,GA,UU GC,CG,AU
5002 5002 23S 33 688 774   v4 U:G No BP       Significant A     100.0                             37 UA  
5499 5499 23S 38 874 903   v4 G:C cWW       Significant A 40.5       45.9     2.7         10.8         37 GC,GU,AC,GA GU,AC
5814 5814 23S 42 1035 1120   v4 U:G cWW       Significant A           97.3                     2.7 37 UG  
6409 6409 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant A                                 99.9 41    
7102 7102 23S 61 1667 1993   v4 G:U tSH       Significant A         100.0                         41 GU  
8187 8187 23S 77 2124 2174   v4 G:C cWW       Significant A 100.0                                 41 GC  
8712 8712 23S 88 2401 2415   v4 U:G cWW       Significant A 12.2 70.7       12.2                 4.9     41 GC,CG,UG,UC GC,CG

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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");