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 = "tHW", header_format = "v4" and molecule = "16S" sorted by position_1

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Suggested facets: GC, AU, UG, AG, CA, CC, CU, GA, UU, gap, predominant_types, covarying_types

group_code 7

tertiary_type 1

strength 1

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
694 694 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong T 0.2     0.4 7.2 0.2 2.5 69.9 0.4 0.1 2.1 0.4 0.7 3.7 0.2 0.1 11.9 7096 GU,AA,AC,CC,GG GU,UG,AC,CA
695 695 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong 3 0.2     0.4 8.4 0.3 2.8 78.7 0.4 0.2 2.5 0.5 0.8 4.3 0.3 0.1 0.3 6105 GU,AA,AC,CC,GG GU,UG,AC,CA
696 696 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong B 0.1     0.4 10.5 0.3 1.1 79.6 0.2 0.1 0.6 0.5 0.8 5.4 0.1   0.3 4869 GU,AC,GG GU,UG,AC,CA
697 697 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong A       0.5     47.9 35.8 0.9   11.2 2.3       1.4   215 AA,AC,CC,CU AA,CC,UU
698 698 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong C     0.6 3.0     1.8 89.9 1.8   0.6     0.6     1.8 168 AU,AC UA,AC,GG
699 699 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong E 0.4     0.1   0.2 1.3 83.6 1.0 0.6 9.8   0.9   1.4 0.2 0.6 1021 AC,CC UG,AC,GA
700 700 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong M     0.1   0.1 0.1 0.2   0.2               99.2 832   GU,UG,AA

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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");