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).

7 rows where conformation = "tSH", header_format = "v4" and molecule = "16S" sorted by position_1

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Suggested facets: GC, GA, UU, gap, predominant_types, covarying_types

group_code 7

strength 1

molecule 1

header_format 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
1863 1863 16S 23 690 697   v4 G:U tSH       Weak T 0.1 0.1 4.2 7.5 81.9   0.1     1.6 0.8 0.1 0.1   3.1 0.2 0.1 7180 UA,AU,GU,UC UA,GU,CC
1864 1864 16S 23 690 697   v4 G:U tSH       Weak 3 0.1     7.7 91.8             0.1 0.1     0.1 0.1 6118 AU,GU  
1865 1865 16S 23 690 697   v4 G:U tSH       Weak B       8.0 91.6             0.1       0.1 0.1 4853 AU,GU  
1866 1866 16S 23 690 697   v4 G:U tSH       Weak A       34.3 65.7                         233 AU,GU  
1867 1867 16S 23 690 697   v4 G:U tSH       Weak C       10.1 88.8   0.6                   0.6 169 AU,GU GU,AA
1868 1868 16S 23 690 697   v4 G:U tSH       Weak E 0.6     0.4 98.4               0.5 0.1       1032 GU  
1869 1869 16S 23 690 697   v4 G:U tSH       Weak M 0.2 0.4 33.7 5.1 13.8 0.1 0.7 0.2   13.0 6.3 0.1 0.4   24.8 0.8 0.3 901 UA,AU,GU,CA,CC,UC UA,GU,CC

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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");