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).

9 rows where conformation = "cWW", group_code = "E" and strength = "Significant" sorted by position_1

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Suggested facets: reference_base_pair, gap, Seq, covarying_types

tertiary_type 2

molecule 2

strength 1

  • Significant · 9 ✖

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
3821 3821 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant E     0.8                           99.1 118    
144 144 5S 3 80 96   v4 U:G cWW       Significant E 0.7 14.8     0.3 80.9           0.3     0.3 2.7   298 CG,UG,UU GC,UG,CU
4157 4157 23S 13 239 258   v4 C:G cWW       Significant E 0.5   29.0 0.5 1.5 2.5       9.0 24.0   0.5 1.0 25.5 5.5 0.5 200 UA,UG,CA,CC,UC,UU UA,GU,CC
4276 4276 23S 18 287 353   v4 G:C cWW       Significant E 18.9 1.4 3.3 2.8 9.9   1.9 1.9 2.4   6.1 0.5 3.8 9.9 1.4 0.9 35.0 212 GC,UA,AU,GU,AG,CC,GA,GG GC,CG,UA,AU
5501 5501 23S 38 874 903   v4 G:C cWW       Significant E 2.4 0.9     1.9   0.9           90.6       3.3 212 GC,GA CG,GA
5816 5816 23S 42 1035 1120   v4 U:G cWW       Significant E   0.5 0.5     96.6                   1.9 0.5 206 UG  
6411 6411 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant E     3.7       2.4                   93.9 164 UA,AA  
8189 8189 23S 77 2124 2174   v4 G:C cWW       Significant E 100.0                                 155 GC  
8714 8714 23S 88 2401 2415   v4 U:G cWW       Significant E 3.2 54.2 4.5 4.5   19.4     11.0             3.2   155 GC,CG,UA,AU,UG,AG,UU GC,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");