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).

15 rows where conformation = "No BP", group_code = "B" and strength = "Weak" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, UA, AG, CC, gap, Seq, predominant_types

molecule 2

strength 1

  • Weak · 15 ✖

header_format 1

group_code 1

conformation 1

  • No BP · 15 ✖

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
199 199 16S 1 13 21   v4 U:G No BP       Weak B     0.2     98.9     0.2         0.1   0.1 0.1 2128 UG  
1081 1081 16S 15 375 388   v4 U:G No BP       Weak B     0.3     98.8     0.1           0.2 0.5   4613 UG  
1613 1613 16S 21 606 632   v4 G:U No BP       Weak B 2.2 1.0 1.0 2.3 69.1 1.9 0.4 0.1 0.5   0.5 0.4 2.9 12.1 1.8 2.0 1.7 4794 GC,AU,GU,GA,GG,UU GU,UG,AA,CC
4994 4994 23S 33 687 775   v4 C:G No BP       Weak B   99.3               0.4 0.4             282 CG  
5099 5099 23S 34 703 729   v4 U:G No BP       Weak B   1.8       98.2                       282 UG  
2383 2383 16S 31 960 975   v4 U:A No BP       Weak B     92.1     7.5                     0.2 4347 UA,UG  
2390 2390 16S 31 961 974   v4 U:A No BP       Weak B 0.1   86.4     0.3         0.1       11.3 1.2 0.4 4330 UA,UC GC,UA
2628 2628 16S 34 1053 1205   v4 G:U No BP       Weak B 3.8       95.6             0.2         0.2 4383 GC,GU  
2901 2901 16S 40 1158 1178   v4 C:G No BP       Weak B   99.8                               4605 CG  
2908 2908 16S 40 1159 1177   v4 U:G No BP       Weak B   5.7 0.1     93.5     0.5               0.1 4600 CG,UG  
3447 3447 16S 45 1506 1529   v4 U:G No BP       Weak B     0.3     98.1         0.1     0.4 0.7 0.3 0.1 718 UG UG,CC
7395 7395 23S 66 1799 1820   v4 G:U No BP       Weak B         100.0                         262 GU  
7668 7668 23S 69 1911 1919   v4 U:A No BP       Weak B     98.0             1.6             0.4 244 UA  
7927 7927 23S 74 2075 2434   v4 U:A No BP       Weak B     100.0                             241 UA  
8361 8361 23S 80 2249 2255   v4 U:G No BP       Weak B           99.6                     0.4 238 UG  

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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");