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).

6 rows where conformation = "tWW", group_code = "M" and header_format = "v4" sorted by position_1

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Suggested facets: reference_base_pair, AA, CA, predominant_types, covarying_types

tertiary_type 2

molecule 2

strength 1

header_format 1

group_code 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
4123 4123 23S 12.1 234 430   v4 U:A tWW       Strong M   3.5 9.4 0.4   0.4 1.2 0.4   0.4     0.4     0.8 83.1 254 CG,UA CG,UA,AU
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
5957 5957 23S 43.1 1082 1086   v4 U:A tWW   3°: base pair   Strong M 0.4 0.7 13.1 3.3 0.4   0.4     0.4       0.4 0.4 2.5 78.2 275 UA,AU,UU GC,CG,UA,AU
7343 7343 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong M   0.4 6.1             0.4 81.0         11.0 1.2 263 UA,CC,UU CC,UU
7406 7406 23S 66 1800 1817   v4 C:G tWW   3°: base pair   Strong M   70.3 1.8 1.4     0.4     2.8 1.1 0.7         21.6 283 CG,CA CG,UA,AU
7679 7679 23S 69.1 1925 1929   v4 C:G tWW   3°: base pair   Strong M   93.9 3.2 1.3   1.0                   0.6   311 CG,UA CG,UA,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");