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

✎ View and edit SQL

This data as json, CSV (advanced)

Suggested facets: reference_base_pair, GU, GG, 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
1386 1386 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support M 99.6       0.1                 0.1     0.1 831 GC  
2191 2191 16S 28 924 1392   v4 C:G cWW       No Support M 0.2 98.3     0.1 0.2       0.1       1.0       899 CG GC,CG
2303 2303 16S 30 944 1237   v4 G:C No BP       No Support M 98.4       1.1     0.2         0.1       0.3 1152 GC  
2408 2408 16S 31 963 972   v4 G:C cWW       No Support M 99.9       0.1                         1153 GC  
2674 2674 16S 34 1061 1195   v4 G:C cWW   3°: base pair   No Support M 63.7     35.5 0.3     0.2           0.1 0.1   0.2 1151 GC,AU GC,AU

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");