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).

31 rows where conformation = "No BP" and group_code = "B" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, UA, UG, AG, CC, UU, gap, Seq, predominant_types, covarying_types

strength 5

tertiary_type 2

molecule 2

header_format 1

group_code 1

conformation 1

  • No BP · 31 ✖
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  
1466 1466 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong B 0.1 11.2 2.6     68.4   0.1   0.2 15.6 0.8     0.6 0.3   4697 CG,UA,UG,CC UG,CC
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  
5001 5001 23S 33 688 774   v4 U:G No BP       Significant B     88.7     9.2                 2.1     282 UA,UG,UC  
5099 5099 23S 34 703 729   v4 U:G No BP       Weak B   1.8       98.2                       282 UG  
2299 2299 16S 30 944 1237   v4 G:C No BP       No Support B 99.7                               0.1 4162 GC  
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  
2691 2691 16S 34 1064 1192   v4 G:C No BP       Strong B 97.1       2.1     0.1         0.1 0.6       4404 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  
6604 6604 23S 55 1420 1578   v4 A:U No BP       Strong B       11.4 0.4 0.8     1.5     2.3       72.3 11.5 264 AU,CU,UU AG,UU
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
6912 6912 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong B 3.4 13.6 5.7 0.4 2.7   1.5           62.1     0.8 9.9 264 GC,CG,UA,GU,GA CG,GA,UU
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  
7682 7682 23S 71 1935 1962   v4 G:C No BP       Strong B 99.6         0.4                       240 GC GC,UG
7927 7927 23S 74 2075 2434   v4 U:A No BP       Weak B     100.0                             241 UA  
8137 8137 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong B                 34.4       65.6         241 AG,GA AG,GA
8144 8144 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong B   41.9 53.9             1.7     2.5         241 CG,UA,GA CG,UA
8151 8151 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong B       100.0                           241 AU  
8361 8361 23S 80 2249 2255   v4 U:G No BP       Weak B           99.6                     0.4 238 UG  
8480 8480 23S 84 2296 2322   v4 U:A No BP       Strong B     96.7                       2.5 0.8   241 UA,UC  
8851 8851 23S 90 2511 2577   v4 U:A No BP       No Support B     100.0                             241 UA  
9096 9096 23S 94 2637 2781   v4 U:A No BP       Strong B     99.5     0.5                       213 UA  
9411 9411 23S 98 2796 2800   v4 U:A No BP       Strong B   1.4 12.4 0.9   0.5       2.8           0.5 81.7 218 UA,CA CG,UA,AU
9418 9418 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? B     63.1 10.8 19.7 3.9             0.5       2.0 203 UA,AU,GU,UG UA,GU
9565 9565 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong B         3.4 1.5     0.5     1.0 1.0 51.7   41.0   205 GU,GG,UU GG,UU

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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");