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 = "T" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, UA, AU, GU, UG, AA, AC, AG, CA, CC, CU, GA, GG, UC, 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
197 197 16S 1 13 21   v4 U:G No BP       Weak T   0.1 8.8 0.1   88.5 0.1   1.5 0.1     0.1 0.1   0.3 0.5 3890 UA,UG UG,AA
1079 1079 16S 15 375 388   v4 U:G No BP       Weak T   0.1 0.9     97.8     0.1         0.1 0.1 0.4 0.4 6852 UG  
1464 1464 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong T 0.1 7.6 7.8 0.1   52.0 0.9 0.2 0.1 0.5 10.5 0.5   0.1 15.3 0.3 3.9 6988 CG,UA,UG,CC,UC UG,AA,CC
1611 1611 16S 21 606 632   v4 G:U No BP       Weak T 1.7 1.7 1.4 1.7 47.5 1.7 0.4 0.1 0.4   0.3 0.3 2.0 8.1 1.4 2.4 28.8 7251 GU,GA,GG,UU GU,UG,AA,CC
4992 4992 23S 33 687 775   v4 C:G No BP       Weak T   95.8 0.2 0.9   1.2   0.1 0.3 0.1 0.1 0.3 0.1 0.3     0.3 886 CG CG,UA,AU
4999 4999 23S 33 688 774   v4 U:G No BP       Significant T     90.9 1.5 0.1 3.6       0.1         3.3 0.3 0.2 886 UA,UG,UC UA,AU
5097 5097 23S 34 703 729   v4 U:G No BP       Weak T   15.1 0.1 0.1 0.1 71.4 0.2   5.1 0.1   0.1   0.6     7.1 887 CG,UG,AG GU,UG,AA
2297 2297 16S 30 944 1237   v4 G:C No BP       No Support T 99.3       0.2     0.1                 0.3 6633 GC  
2381 2381 16S 31 960 975   v4 U:A No BP       Weak T     61.8 14.8   22.4 0.2   0.1           0.2 0.2 0.3 6871 UA,AU,UG UA,AU
2388 2388 16S 31 961 974   v4 U:A No BP       Weak T 0.1 0.1 66.4 0.1 0.1 16.8 0.3     0.6 0.2 2.1     8.7 4.1 0.3 6856 UA,UG,CU,UC,UU GC,UA,CU
2626 2626 16S 34 1053 1205   v4 G:U No BP       Weak T 2.6     15.1 81.7     0.1       0.1         0.3 6891 GC,AU,GU GU,AC
2689 2689 16S 34 1064 1192   v4 G:C No BP       Strong T 73.2   2.5 0.4 1.8 0.2 0.2 0.1 0.1 0.7 0.1 12.9 2.5 0.5 4.2 0.4 0.1 6914 GC,UA,CU,GA,UC GC,UA,AG,CU
2899 2899 16S 40 1158 1178   v4 C:G No BP       Weak T   81.2 0.4 0.1   0.5       0.1 1.8 0.2   0.1 0.2 0.1 15.2 7138 CG CG,UA,AU
2906 2906 16S 40 1159 1177   v4 U:G No BP       Weak T   5.5 0.2 0.1   73.5 1.5 0.3 1.5 0.4 0.4 0.1 0.1 0.8   0.4 15.2 7135 CG,UG UG,AA,CC
6602 6602 23S 55 1420 1578   v4 A:U No BP       Strong T 4.5 10.9 5.9 7.0 0.8 0.2 0.1 0.2 0.6 0.2   0.8       22.3 46.3 860 GC,CG,UA,AU,UU GC,CG,AA,UU
3445 3445 16S 45 1506 1529   v4 U:G No BP       Weak T   0.6 4.6     93.0               0.2 0.5 0.4 0.7 2260 UA,UG  
6910 6910 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong T 1.9 18.8 3.7 1.6 7.7 0.3 1.0   0.2 2.8 0.2 0.1 20.0 0.2 0.1 0.3 40.8 861 CG,UA,GU,CA,GA CG,AU,GA,UC
7393 7393 23S 66 1799 1820   v4 G:U No BP       Weak T 22.1   0.1 0.6 73.2     0.1         0.4       3.5 842 GC,GU UA,GU,AC
7666 7666 23S 69 1911 1919   v4 U:A No BP       Weak T     97.9             0.5           0.1 1.5 852 UA  
7680 7680 23S 71 1935 1962   v4 G:C No BP       Strong T 51.6 20.5   16.5 5.7 0.2 0.2 2.6 1.1       0.2 0.7 0.2 0.4   847 GC,CG,AU,GU,AC GC,CG,AU
7925 7925 23S 74 2075 2434   v4 U:A No BP       Weak T   0.1 97.8     0.4 0.2         0.1     0.2 1.2   845 UA CG,UA
8135 8135 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong T 0.1 0.2 0.9 1.1 0.5   1.3   11.0 0.1     53.0   0.1   31.6 847 AG,GA AG,GA,UC
8142 8142 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong T   26.0 37.7     1.1 0.1     1.8     1.3     0.1 32.0 847 CG,UA CG,UA
8149 8149 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong T 5.4 7.7 0.6 49.2 0.4   0.7   0.5 0.4   0.2 0.8     2.5 31.6 847 GC,CG,AU,UU GC,CG,UA,AU
8359 8359 23S 80 2249 2255   v4 U:G No BP       Weak T     4.1     94.6       0.6       0.4 0.1 0.1 0.1 845 UA,UG UG,CA
8478 8478 23S 84 2296 2322   v4 U:A No BP       Strong T   0.4 63.4 0.1   0.2 0.1 0.1   0.1 0.1   0.5   2.7 0.5 31.7 848 UA,UC CG,UA,AU
8849 8849 23S 90 2511 2577   v4 U:A No BP       No Support T     99.1             0.9               778 UA  
9094 9094 23S 94 2637 2781   v4 U:A No BP       Strong T 0.9 11.6 51.8 1.7   0.8 0.8 0.2 0.3 1.1 0.6 0.2 0.8   0.8 0.5 28.3 662 CG,UA GC,CG,UA,AU
9409 9409 23S 98 2796 2800   v4 U:A No BP       Strong T 1.7 0.6 4.2 0.6   0.4       0.9           0.1 91.4 693 UA GC,CG,UA,AU
9416 9416 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? T 0.7 1.7 39.9 7.6 9.7 4.3 1.7 0.2 1.4 3.3     2.4 0.5   1.0 25.5 421 UA,AU,GU,UG,CA,GA CG,UA,GU,AC
9563 9563 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong T     0.7   1.8 3.8   0.4 0.2 0.2   0.9 0.4 26.2 1.1 57.5 6.7 447 UG,GG,UU AC,CA,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");