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 group_code = 3, molecule = "16S" and strength = "No Support" sorted by position_1

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Suggested facets: reference_base_pair, GC, gap, predominant_types

tertiary_type 2

conformation 2

strength 1

  • No Support · 5 ✖

molecule 1

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
1381 1381 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support 3 99.5       0.1     0.1           0.1     0.1 5577 GC  
2186 2186 16S 28 924 1392   v4 C:G cWW       No Support 3   99.6       0.1           0.1         0.1 4928 CG  
2298 2298 16S 30 944 1237   v4 G:C No BP       No Support 3 99.6             0.1                 0.2 5326 GC  
2403 2403 16S 31 963 972   v4 G:C cWW       No Support 3 99.5             0.1     0.1           0.3 5549 GC  
2669 2669 16S 34 1061 1195   v4 G:C cWW   3°: base pair   No Support 3 97.0     0.3 2.3           0.1     0.1     0.1 5466 GC,GU GC,AU

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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");