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 = "M" and header_format = "v4" 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
203 203 16S 1 13 21   v4 U:G No BP       Weak M     50.2 0.1   38.6 0.4   8.1 0.7     0.4 0.1   0.6 0.6 669 UA,UG,AG UA,AG
1085 1085 16S 15 375 388   v4 U:G No BP       Weak M 0.2 0.4 5.1     92.9 0.4   0.1         0.2   0.1 0.6 829 UA,UG GC,UG,AA
1470 1470 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong M 0.1 0.3 45.6 0.7 0.2 9.1 7.2 1.1 0.7 3.2 0.1     0.1 0.5 0.1 31.0 886 UA,UG,AA,CA CG,UA,GU,AC
1617 1617 16S 21 606 632   v4 G:U No BP       Weak M   0.1 0.6 0.2 2.0 0.2 0.4   0.2 0.1     0.1     0.4 95.8 1021 GU UA,GU,AG
4998 4998 23S 33 687 775   v4 C:G No BP       Weak M   89.7 0.8 3.1   4.2   0.4 0.4       0.4 0.4     0.8 262 CG,AU,UG CG,UA,AU
5005 5005 23S 33 688 774   v4 U:G No BP       Significant M     90.1 5.0 0.4 1.5       0.4         1.1 0.8 0.8 262 UA,AU UA,AU
5103 5103 23S 34 703 729   v4 U:G No BP       Weak M   6.1 0.4 0.4 0.4 48.7 0.8   17.1     0.4   1.9     24.0 263 CG,UG,AG GU,UG,AA
2303 2303 16S 30 944 1237   v4 G:C No BP       No Support M 98.4       1.1     0.2         0.1       0.3 1152 GC  
2387 2387 16S 31 960 975   v4 U:A No BP       Weak M     6.5 89.1   0.6 0.9 0.3 0.6   0.1 0.3     1.0 0.7 0.1 1153 UA,AU UA,AU,CC
2394 2394 16S 31 961 974   v4 U:A No BP       Weak M 0.6   54.6 0.6 0.4 0.1 1.5 0.1   3.3 0.3 12.3 0.1   8.9 17.3   1151 UA,CA,CU,UC,UU GC,UA,CU
2632 2632 16S 34 1053 1205   v4 G:U No BP       Weak M 0.5     90.9 7.8     0.5       0.1       0.1 0.1 1152 AU,GU GC,AU
2695 2695 16S 34 1064 1192   v4 G:C No BP       Strong M 38.0 0.1 12.9 3.0 1.0   1.0 0.2 0.3 3.9 0.7   15.0 0.3 21.7 1.6 0.5 1150 GC,UA,AU,CA,GA,UC GC,CG,UA,AU
2905 2905 16S 40 1158 1178   v4 C:G No BP       Weak M 0.1 2.5 2.3 0.3     0.2   0.1     0.3   0.2   0.4 93.5 1152 CG,UA GC,CG,UA,AU
2912 2912 16S 40 1159 1177   v4 U:G No BP       Weak M   0.3 0.3 0.2 0.1 2.5 0.1   0.1 0.3 2.0 0.2   0.2   0.4 93.6 1152 UG,CC AU,UG,CC
6608 6608 23S 55 1420 1578   v4 A:U No BP       Strong M   1.1 1.4 2.2         0.4               94.9 276 AU CG,UA,AU
3451 3451 16S 45 1506 1529   v4 U:G No BP       Weak M     15.6     83.0               0.1 0.1 0.9 0.1 672 UA,UG  
6916 6916 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong M       0.4                         99.7 276    
7399 7399 23S 66 1799 1820   v4 G:U No BP       Weak M 0.7   0.4 1.8 89.0                       8.1 283 GU UA,GU
7672 7672 23S 69 1911 1919   v4 U:A No BP       Weak M     96.1                           3.8 311 UA  
7686 7686 23S 71 1935 1962   v4 G:C No BP       Strong M 29.4     45.2 11.9   0.6 6.1 2.9       0.6 1.6 0.6 1.0   310 GC,AU,GU,AC,AG GC,AU
7931 7931 23S 74 2075 2434   v4 U:A No BP       Weak M   0.3 94.8     1.0 0.6         0.3     0.6 2.3   309 UA,UU CG,UA
8141 8141 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong M   0.6 2.6       2.6   1.6 0.3     5.2   0.3   86.7 309 UA,AA,GA AG,GA,UC
8148 8148 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong M   1.0 7.8     1.6 0.3     1.0     0.6       87.7 309 UA CG,UA
8155 8155 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong M 1.6   1.6 5.5 0.3   1.9   1.3       1.0       86.7 309 AU GC,UA,AU
8365 8365 23S 80 2249 2255   v4 U:G No BP       Weak M     10.7     87.1       1.6         0.3 0.3   309 UA,UG UG,CA
8484 8484 23S 84 2296 2322   v4 U:A No BP       Strong M   1.0 10.0 0.3   0.6 0.3       0.3       0.3 0.3 86.7 309 UA CG,UA,AU
8855 8855 23S 90 2511 2577   v4 U:A No BP       No Support M     97.3             2.7               263 UA,CA  
9100 9100 23S 94 2637 2781   v4 U:A No BP       Strong M 0.9   7.9 3.5   0.4 1.8   0.9       1.8     0.4 82.3 227 UA,AU GC,UA,AU
9415 9415 23S 98 2796 2800   v4 U:A No BP       Strong M                                 100.0 219    
9422 9422 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? M     4.5 2.3     13.6 2.3 4.5             2.3 70.4 44 UA,AU,AA,AC,AG,UU AA,UU
9569 9569 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong M     4.4     6.7   4.4       2.2     8.9 31.1 42.2 45 UA,UG,AC,CU,UC,UU AC,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");