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).

5 rows where conformation = "tSH", group_code = "C" and molecule = "23S" sorted by position_1

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Suggested facets: reference_base_pair, Seq

strength 2

molecule 1

header_format 1

group_code 1

conformation 1

tertiary_type 0

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
3890 3890 23S 7 82 104   v4 U:A tSH       Strong C     2.0 2.0 91.8           2.0   1.0 1.0       98 UA,AU,GU,CC UA,GU,CC
4100 4100 23S 11 195 200   v4 A:U tSH       Strong C       100.0                           100 AU  
7103 7103 23S 61 1667 1993   v4 G:U tSH       Significant C         100.0                         101 GU  
8272 8272 23S 78 2144 2147   v4 G:A tSH       Strong C   1.0       93.1     2.0           2.0 2.0   101 UG,AG,UC,UU  
9371 9371 23S 97 2746 2758   v4 U:A tSH       Strong C     96.6             3.4               58 UA,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");