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

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Suggested facets: reference_base_pair, GU, AC, GA, UC, UU, 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
3757 3757 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant C             6.2   93.8                 81 AA,AG  
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
4156 4156 23S 13 239 258   v4 C:G cWW       Significant C 29.0   8.0 5.0 17.0 5.0 3.0     4.0     1.0   12.0 16.0   100 GC,UA,AU,GU,UG,AA,CA,UC,UU GC,CA,UU
4275 4275 23S 18 287 353   v4 G:C cWW       Significant C 2.0   23.0 12.0 1.0   18.0 2.0 7.0 5.0   2.0 3.0   2.0 4.0 19.0 100 GC,UA,AU,AA,AC,AG,CA,CU,GA,UC,UU GC,UA,AU
5003 5003 23S 33 688 774   v4 U:G No BP       Significant C     100.0                             100 UA  
5500 5500 23S 38 874 903   v4 G:C cWW       Significant C 91.0     1.0 2.0 2.0   2.0             2.0     100 GC,GU,UG,AC,UC GC,AU,UG
5815 5815 23S 42 1035 1120   v4 U:G cWW       Significant C     1.0     98.0                   1.0   100 UG  
6410 6410 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant C 96.0     2.0 2.0                         100 GC,AU,GU GC,AU
7103 7103 23S 61 1667 1993   v4 G:U tSH       Significant C         100.0                         101 GU  
8188 8188 23S 77 2124 2174   v4 G:C cWW       Significant C 99.0             1.0                   101 GC  
8713 8713 23S 88 2401 2415   v4 U:G cWW       Significant C     2.0     93.1       3.0     1.0   1.0     101 UA,UG,CA UG,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");