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 = "tSH", group_code = "M" and header_format = "v4" sorted by position_1

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Suggested facets: reference_base_pair, AA, GA, predominant_types

strength 3

molecule 2

header_format 1

group_code 1

conformation 1

tertiary_type 0

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
3892 3892 23S 7 82 104   v4 U:A tSH       Strong M     3.8 1.7 3.8 0.4 0.4   0.4             0.9 88.4 234 UA,GU UA,GU,AG
4102 4102 23S 11 195 200   v4 A:U tSH       Strong M     3.9 87.0     1.6 0.8                 6.7 254 UA,AU UA,AU
1869 1869 16S 23 690 697   v4 G:U tSH       Weak M 0.2 0.4 33.7 5.1 13.8 0.1 0.7 0.2   13.0 6.3 0.1 0.4   24.8 0.8 0.3 901 UA,AU,GU,CA,CC,UC UA,GU,CC
7105 7105 23S 61 1667 1993   v4 G:U tSH       Significant M     3.6 1.4 93.1   0.4           0.4 0.4     0.7 276 UA,GU UA,GU
8274 8274 23S 78 2144 2147   v4 G:A tSH       Strong M     1.9     0.3 1.0 1.0   1.3   0.3 3.9     1.3 89.0 309 GA AC,GA,UU
9373 9373 23S 97 2746 2758   v4 U:A tSH       Strong M   0.8 85.0 2.9 0.8 1.7 0.4               2.9 0.4 5.0 240 UA,AU,UC 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");