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 = "A" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, UA, UG, 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
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
4995 4995 23S 33 687 775   v4 C:G No BP       Weak A   100.0                               37 CG  
5002 5002 23S 33 688 774   v4 U:G No BP       Significant A     100.0                             37 UA  
5100 5100 23S 34 703 729   v4 U:G No BP       Weak A   32.4       67.6                       37 CG,UG  
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
6605 6605 23S 55 1420 1578   v4 A:U No BP       Strong A 39.0     29.3 7.3                       24.4 41 GC,AU,GU GC,AU
3448 3448 16S 45 1506 1529   v4 U:G No BP       Weak A           95.0                 5.0     80 UG,UC  
6913 6913 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong A         73.2                       26.8 41 GU  
7396 7396 23S 66 1799 1820   v4 G:U No BP       Weak A 90.2       9.8                         41 GC,GU  
7669 7669 23S 69 1911 1919   v4 U:A No BP       Weak A     100.0                             41 UA  
7683 7683 23S 71 1935 1962   v4 G:C No BP       Strong A 22.0 51.2     26.8                         41 GC,CG,GU CG,GU
7928 7928 23S 74 2075 2434   v4 U:A No BP       Weak A     100.0                             41 UA  
8138 8138 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong A       4.9         12.2       82.9         41 AU,AG,GA AG,GA
8145 8145 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong A   29.3 48.8             17.1     4.9         41 CG,UA,CA,GA CG,UA
8152 8152 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong A 85.4     14.6                           41 GC,AU GC,AU
8362 8362 23S 80 2249 2255   v4 U:G No BP       Weak A           100.0                       41 UG  
8481 8481 23S 84 2296 2322   v4 U:A No BP       Strong A     100.0                             41 UA  
8852 8852 23S 90 2511 2577   v4 U:A No BP       No Support A     100.0                             41 UA  
9097 9097 23S 94 2637 2781   v4 U:A No BP       Strong A     100.0                             41 UA  
9412 9412 23S 98 2796 2800   v4 U:A No BP       Strong A 30.0 2.5   5.0   5.0                     57.5 40 GC,CG,AU,UG GC,AU,UG
9419 9419 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? A 7.9 2.6 2.6       2.6     36.8     13.2       34.3 38 GC,CG,UA,AA,CA,GA GC,CA
9566 9566 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong A     2.6     10.5                   78.9 7.9 38 UA,UG,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");