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 = "tWW", molecule = "16S" and strength = "Strong" sorted by position_1

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Suggested facets: GC, UG, gap, predominant_types, covarying_types

group_code 7

tertiary_type 1

strength 1

  • Strong · 7 ✖

molecule 1

header_format 1

conformation 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
1870 1870 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong T 0.2 0.7 3.0 1.6 0.9 0.7 29.5 0.3 5.1 0.4 0.1 0.1 1.3 55.1 0.1 0.2 0.7 7189 UA,AA,AG,GG AA,CC,GG,UU
1871 1871 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong 3 0.1   2.1 0.1 0.7 0.1 29.7 0.1 2.4       1.4 63.1     0.1 6134 UA,AA,AG,GG AA,GG
1872 1872 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong B 0.2       0.2 0.1 24.5   2.9       0.5 71.3     0.1 4860 AA,AG,GG AA,GG
1873 1873 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong A         0.8   20.3   0.4         78.4       241 AA,GG AA,GG
1874 1874 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong C           0.6 75.4   1.8         21.6     0.6 167 AA,GG AA,GG
1875 1875 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong E 0.1 0.1 12.2 0.3 3.3 0.1 56.2 0.2 0.7       5.9 20.6     0.3 1033 UA,GU,AA,GA,GG AA,GG
1876 1876 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong M 0.2 5.2 10.2 12.1 1.8 4.4 19.3 1.9 24.0 3.3 0.9 1.0 1.2 6.0 1.1 2.8 4.5 896 CG,UA,AU,UG,AA,AG,CA,GG,UU UA,GU,AG,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");