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 = "A" and molecule = "16S" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, UG, Seq, 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
200 200 16S 1 13 21   v4 U:G No BP       Weak A           100.0                       154 UG  
1082 1082 16S 15 375 388   v4 U:G No BP       Weak A     2.2     95.6                     2.2 228 UA,UG  
1467 1467 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong A     1.8     94.9                 3.2     217 UG,UC  
1614 1614 16S 21 606 632   v4 G:U No BP       Weak A 5.2     2.2 47.0 4.3           0.4 0.9 3.9 4.3 31.0 0.9 232 GC,AU,GU,UG,GG,UC,UU GU,UC
2300 2300 16S 30 944 1237   v4 G:C No BP       No Support A 99.5             0.5                   191 GC  
2384 2384 16S 31 960 975   v4 U:A No BP       Weak A           100.0                       208 UG  
2391 2391 16S 31 961 974   v4 U:A No BP       Weak A   3.3 3.3     78.5                   14.8   209 CG,UA,UG,UU  
2629 2629 16S 34 1053 1205   v4 G:U No BP       Weak A 1.0     0.5 98.5                         197 GU  
2692 2692 16S 34 1064 1192   v4 G:C No BP       Strong A 100.0                                 198 GC  
2902 2902 16S 40 1158 1178   v4 C:G No BP       Weak A   99.5       0.5                       195 CG  
2909 2909 16S 40 1159 1177   v4 U:G No BP       Weak A   53.0       46.0           0.5       0.5   198 CG,UG CG,UU
3448 3448 16S 45 1506 1529   v4 U:G No BP       Weak A           95.0                 5.0     80 UG,UC  

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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");