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).

14 rows where conformation = "tWH" and header_format = "v4" sorted by position_1

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Suggested facets: helix_number, position_1, position_2, UA, UG, AA, AG, CA, GA, UC, UU, predominant_types, covarying_types

group_code 7

molecule 2

tertiary_type 1

strength 1

header_format 1

conformation 1

  • tWH · 14 ✖
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
1170 1170 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong T     53.9     0.2 1.5   0.3       1.5 16.2   0.2 25.9 6924 UA,GG UA,GG
1171 1171 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong 3     59.6     0.2 1.5   0.4       1.7 18.9 0.1 0.2 17.5 5934 UA,GG UA,GG
1172 1172 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong B     71.9     0.2 1.9   0.5       2.2 22.9 0.1 0.2   4678 UA,GA,GG UA,GG
1173 1173 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong A     77.0     0.4       0.4       21.7     0.4 226 UA,GG UA,GG
1174 1174 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong C     98.8     0.6             0.6         163 UA  
1175 1175 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong E                                 100.0 1030    
1176 1176 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong M     4.3 0.1     1.7           0.4     0.2 93.3 835 UA UA,AU
4859 4859 23S 28 607 621   v4 U:A tWH       Strong T 0.8 1.0 52.8 4.1 1.5 3.3 3.9 1.2 0.8 0.2 0.5   1.0 1.6 0.3 0.2 26.8 883 UA,AU,UG,AA UA,AU,CC,GG
4860 4860 23S 28 607 621   v4 U:A tWH       Strong 3 1.3 1.7 67.6 4.8 2.5 5.6 6.0 2.1 1.2 0.2 0.8   1.5 2.7 0.6   1.6 521 UA,AU,GU,UG,AA,AC,GG UA,AU,CC,GG
4861 4861 23S 28 607 621   v4 U:A tWH       Strong B     100.0                             282 UA  
4862 4862 23S 28 607 621   v4 U:A tWH       Strong A     97.3     2.7                       37 UA,UG  
4863 4863 23S 28 607 621   v4 U:A tWH       Strong C     100.0                             100 UA  
4864 4864 23S 28 607 621   v4 U:A tWH       Strong E 3.5 4.5 16.8 12.4 6.4 13.9 15.3 5.4 3.0 0.5 2.0   4.0 6.9 1.5   4.0 202 GC,CG,UA,AU,GU,UG,AA,AC,AG,CC,GA,GG UA,AU,CC,GG
4865 4865 23S 28 607 621   v4 U:A tWH       Strong M     5.3 4.2     1.1   0.4 0.4     0.4     0.8 87.5 262 UA,AU 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");