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 conformation = "tHS", group_code = "T" and molecule = "23S" sorted by position_1

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Suggested facets: reference_base_pair, CG, AU, CA, CU

strength 3

tertiary_type 1

molecule 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
3753 3753 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant T   0.4 1.5 2.1     0.8 0.3 66.2         0.1   0.3 28.1 719 AU,AG UA,AG
6917 6917 23S 59 1528 1543   v4 A:G tHS   3°: base pair   Strong T 5.7 7.2 4.7 11.2 0.6 1.0 0.9 0.2 21.4 0.2 0.1 0.1       1.5 44.9 859 GC,CG,UA,AU,AG GC,UA,AG,CU
7141 7141 23S 62 1690 1697   v4 A:G tHS   3°: base pair   Strong T       0.4 0.4   10.8   53.5 2.9   0.4 0.1     3.9 27.7 836 AA,AG,CA,UU AG,CA,UU
7316 7316 23S 65 1775 1789   v4 U:A tHS       Weak T   1.0 97.3 0.4     0.1               0.5 0.8   842 UA CG,UA,AU
7407 7407 23S 66 1803 1814   v4 A:G tHS   3°: base pair   Weak T 0.5 0.4 0.6 1.5 20.2 0.1 7.6 2.6 37.5 0.2 0.1 0.1       0.2 28.2 840 GU,AA,AC,AG 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");