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 = "C" and header_format = "v4" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, UA, AU, GU, UG, AA, AG, CU, GG, UU, Seq, predominant_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
201 201 16S 1 13 21   v4 U:G No BP       Weak C     0.8     94.4                   4.8   126 UG,UU  
1083 1083 16S 15 375 388   v4 U:G No BP       Weak C     0.6     99.4                       164 UG  
1468 1468 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong C   0.6 3.0 1.2   73.8   0.6 0.6   1.8     1.2 15.9 1.2   164 UA,UG,UC AU,UG,CC
1615 1615 16S 21 606 632   v4 G:U No BP       Weak C 2.4 44.7 27.1 2.4 1.8 12.4 1.2   1.2     0.6     4.1 1.8 0.6 170 GC,CG,UA,AU,UG,UC GC,CG,UA,AU
4996 4996 23S 33 687 775   v4 C:G No BP       Weak C   95.0             2.0     3.0           100 CG,AG,CU  
5003 5003 23S 33 688 774   v4 U:G No BP       Significant C     100.0                             100 UA  
5101 5101 23S 34 703 729   v4 U:G No BP       Weak C           100.0                       100 UG  
2301 2301 16S 30 944 1237   v4 G:C No BP       No Support C 100.0                                 160 GC  
2385 2385 16S 31 960 975   v4 U:A No BP       Weak C     96.9                         3.1   162 UA,UU  
2392 2392 16S 31 961 974   v4 U:A No BP       Weak C     96.9             2.5           0.6   163 UA,CA  
2630 2630 16S 34 1053 1205   v4 G:U No BP       Weak C 0.6       99.4                         163 GU  
2693 2693 16S 34 1064 1192   v4 G:C No BP       Strong C 89.6       6.1   0.6             3.7       163 GC,GU,GG GC,AA
2903 2903 16S 40 1158 1178   v4 C:G No BP       Weak C   91.0   0.6   3.0 0.6   0.6     0.6         3.6 167 CG,UG CG,AU
2910 2910 16S 40 1159 1177   v4 U:G No BP       Weak C   3.0 0.6 0.6   90.4     1.2 0.6       0.6   0.6 2.4 167 CG,UG AU,UG,CA
6606 6606 23S 55 1420 1578   v4 A:U No BP       Strong C     3.0 3.0 2.0   1.0 1.0       1.0       1.0 88.0 100 UA,AU,GU UA,AU
3449 3449 16S 45 1506 1529   v4 U:G No BP       Weak C           100.0                       108 UG  
6914 6914 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong C 2.0 4.0 9.0 11.0 1.0 3.0 5.0   1.0 24.0 2.0 1.0 8.0 1.0 1.0 1.0 26.0 100 GC,CG,UA,AU,UG,AA,CA,CC,GA GC,AU,UG,CA
7397 7397 23S 66 1799 1820   v4 G:U No BP       Weak C 1.0       96.0               3.0         101 GU,GA  
7670 7670 23S 69 1911 1919   v4 U:A No BP       Weak C     100.0                             101 UA  
7684 7684 23S 71 1935 1962   v4 G:C No BP       Strong C 97.0             2.0           1.0       101 GC,AC  
7929 7929 23S 74 2075 2434   v4 U:A No BP       Weak C     100.0                             99 UA  
8139 8139 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong C             3.0           97.0         101 AA,GA  
8146 8146 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong C   96.0 3.0             1.0               101 CG,UA CG,UA
8153 8153 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong C 2.0 64.4   11.9 1.0                     20.8   101 GC,CG,AU,UU GC,CG,UU
8363 8363 23S 80 2249 2255   v4 U:G No BP       Weak C     2.0     98.0                       102 UA,UG  
8482 8482 23S 84 2296 2322   v4 U:A No BP       Strong C     99.0                           1.0 102 UA  
8853 8853 23S 90 2511 2577   v4 U:A No BP       No Support C     100.0                             98 UA  
9098 9098 23S 94 2637 2781   v4 U:A No BP       Strong C     100.0                             56 UA  
9413 9413 23S 98 2796 2800   v4 U:A No BP       Strong C     2.2                           97.8 90 UA  
9420 9420 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? C     71.2 13.5   3.8               3.8   1.9 5.7 52 UA,AU,UG,GG UA,AU,GG
9567 9567 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong C         2.0 10.0               20.0   68.0   50 GU,UG,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");