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).

12 rows where conformation = "No BP", group_code = "E" and molecule = "16S" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, UA, AG, GA, GG, UC, UU, gap, predominant_types

strength 3

tertiary_type 1

molecule 1

  • 16S · 12 ✖

header_format 1

group_code 1

conformation 1

  • No BP · 12 ✖
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
202 202 16S 1 13 21   v4 U:G No BP       Weak E   0.1 0.1     98.9                     0.8 815 UG  
1084 1084 16S 15 375 388   v4 U:G No BP       Weak E 0.1 0.2 0.1     98.0             0.1 0.2   0.1 1.3 1026 UG GC,UG
1469 1469 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong E 0.3   0.9     1.2   0.2             97.4   0.1 1032 UC  
1616 1616 16S 21 606 632   v4 G:U No BP       Weak E                                 100.0 1042    
2302 2302 16S 30 944 1237   v4 G:C No BP       No Support E 99.2                       0.1     0.1 0.6 972 GC GC,UU
2386 2386 16S 31 960 975   v4 U:A No BP       Weak E     0.7     99.0     0.1         0.2       1006 UG  
2393 2393 16S 31 961 974   v4 U:A No BP       Weak E   0.1 2.4     96.7         0.4     0.1 0.3     1007 UA,UG UG,CC
2631 2631 16S 34 1053 1205   v4 G:U No BP       Weak E         99.8                       0.2 997 GU  
2694 2694 16S 34 1064 1192   v4 G:C No BP       Strong E   0.1 2.2   1.0 1.3     0.3 0.1 0.1 89.3     4.3 1.1 0.2 1000 UA,CU,UC AG,CU,UC
2904 2904 16S 40 1158 1178   v4 C:G No BP       Weak E   80.9 0.1     2.7   0.1 0.1 0.8 12.7 0.7   0.2 1.2 0.1 0.5 1019 CG,UG,CC CG,UC
2911 2911 16S 40 1159 1177   v4 U:G No BP       Weak E 0.1 1.6 0.7 0.4   65.6 10.1 2.2 8.0 2.3 0.2 0.2 0.4 5.1 0.3 2.3 0.7 1018 UG,AA,AC,AG,CA,GG,UU UG,AA,CC
3450 3450 16S 45 1506 1529   v4 U:G No BP       Weak E   2.0 0.4     95.8     0.1           0.1   1.4 684 CG,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");