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", group_code = "E" and header_format = "v4" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, UA, GU, AC, AG, 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
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    
4997 4997 23S 33 687 775   v4 C:G No BP       Weak E   98.5                       1.0     0.5 205 CG  
5004 5004 23S 33 688 774   v4 U:G No BP       Significant E     88.8     1.0                 9.8 0.5   205 UA,UC  
5102 5102 23S 34 703 729   v4 U:G No BP       Weak E   49.3       50.2       0.5               205 CG,UG UG,CA
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
6607 6607 23S 55 1420 1578   v4 A:U No BP       Strong E 12.8 50.8 24.6 5.0 0.6     0.6   1.1             4.6 179 GC,CG,UA,AU GC,CG,UA,AU
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  
6915 6915 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong E 2.8 67.8 4.4 0.6 15.6       0.6         0.6     7.8 180 GC,CG,UA,GU CG,UA,GU
7398 7398 23S 66 1799 1820   v4 G:U No BP       Weak E 97.4       0.6     0.6                 1.2 155 GC  
7671 7671 23S 69 1911 1919   v4 U:A No BP       Weak E     99.4                         0.6   155 UA  
7685 7685 23S 71 1935 1962   v4 G:C No BP       Strong E   98.7       0.6   0.6                   155 CG CG,AC
7930 7930 23S 74 2075 2434   v4 U:A No BP       Weak E     98.1                         1.9   155 UA  
8140 8140 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong E 0.6     4.5 2.6               92.3         155 AU,GU,GA AU,GA
8147 8147 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong E   4.5 91.6     2.6             0.6     0.6   155 CG,UA,UG CG,UA
8154 8154 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong E 2.6     91.0 0.6         1.9   1.3 2.6         155 GC,AU,GA GC,AU,CA
8364 8364 23S 80 2249 2255   v4 U:G No BP       Weak E           98.1               1.9       155 UG  
8483 8483 23S 84 2296 2322   v4 U:A No BP       Strong E     85.2         0.6   0.6     2.6   10.3 0.6   155 UA,GA,UC UA,AC
8854 8854 23S 90 2511 2577   v4 U:A No BP       No Support E     100.0                             135 UA  
9099 9099 23S 94 2637 2781   v4 U:A No BP       Strong E 1.6 68.0 12.8 1.6   3.2 0.8 0.8   1.6 3.2   0.8   4.0 1.6   125 CG,UA,UG,CC,UC GC,CG,UA,AU
9414 9414 23S 98 2796 2800   v4 U:A No BP       Strong E                                 100.0 126    
9421 9421 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? E   7.1   2.4 1.2 9.5     4.8       4.8     2.4 67.9 84 CG,AU,UG,AG,GA,UU AU,UG,GA
9568 9568 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong E           1.8       0.9   0.9   0.9 0.9 87.2 7.4 109 UU 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");