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 = 3 and header_format = "v4" sorted by position_1

✎ View and edit SQL

This data as json, CSV (advanced)

Suggested facets: helix_number, reference_base_pair, GC, CG, UA, AU, 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
198 198 16S 1 13 21   v4 U:G No BP       Weak 3   0.1 0.2     99.0     0.1         0.1   0.1 0.4 3097 UG  
1080 1080 16S 15 375 388   v4 U:G No BP       Weak 3   0.1 0.4     98.5     0.1           0.1 0.4 0.3 5867 UG  
1465 1465 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong 3 0.1 8.9 2.3     57.7   0.1   0.1 12.3 0.6     17.5 0.3   5946 CG,UA,UG,CC,UC UG,CC
1612 1612 16S 21 606 632   v4 G:U No BP       Weak 3 2.0 0.8 0.8 1.9 56.4 1.6 0.3 0.1 0.4   0.4 0.3 2.4 9.7 1.5 2.8 18.4 6068 GC,GU,GA,GG,UU GU,UG,AA,CC
4993 4993 23S 33 687 775   v4 C:G No BP       Weak 3   99.0               0.2 0.2     0.4     0.2 524 CG  
5000 5000 23S 33 688 774   v4 U:G No BP       Significant 3     89.5     5.3                 5.0 0.2   524 UA,UG,UC  
5098 5098 23S 34 703 729   v4 U:G No BP       Weak 3   22.5       77.3       0.2               524 CG,UG UG,CA
2298 2298 16S 30 944 1237   v4 G:C No BP       No Support 3 99.6             0.1                 0.2 5326 GC  
2382 2382 16S 31 960 975   v4 U:A No BP       Weak 3     72.2     27.5                     0.1 5561 UA,UG  
2389 2389 16S 31 961 974   v4 U:A No BP       Weak 3 0.1 0.1 68.1     20.8         0.2       8.9 1.5 0.3 5546 UA,UG,UC UA,CC
2627 2627 16S 34 1053 1205   v4 G:U No BP       Weak 3 3.0     0.1 96.4             0.2         0.3 5581 GC,GU  
2690 2690 16S 34 1064 1192   v4 G:C No BP       Strong 3 79.8   0.4   1.8 0.2   0.1 0.1     15.9 0.1 0.4 0.8 0.2 0.1 5606 GC,CU GC,UA,AG,CU
2900 2900 16S 40 1158 1178   v4 C:G No BP       Weak 3   96.4       0.5       0.2 2.2 0.1     0.2   0.2 5825 CG,CC CG,UC
2907 2907 16S 40 1159 1177   v4 U:G No BP       Weak 3   6.6 0.2 0.1   87.0 1.8 0.4 1.8 0.4   0.1 0.1 0.9 0.1 0.4 0.3 5822 CG,UG UG,AA,CU
6603 6603 23S 55 1420 1578   v4 A:U No BP       Strong 3 8.1 18.8 9.1 10.5 1.0 0.4   0.2 0.8 0.4   1.2       39.5 9.8 484 GC,CG,UA,AU,UU GC,CG,UU
3446 3446 16S 45 1506 1529   v4 U:G No BP       Weak 3   0.9 0.3     96.7     0.1   0.1     0.2 0.7 0.1 0.9 1484 UG UG,CC
6911 6911 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong 3 2.9 32.6 4.7 0.4 13.4   0.8   0.2       33.8 0.2   0.4 10.4 485 GC,CG,UA,GU,GA CG,AU,GA
7394 7394 23S 66 1799 1820   v4 G:U No BP       Weak 3 40.0       58.3     0.2                 1.5 458 GC,GU GU,AC
7667 7667 23S 69 1911 1919   v4 U:A No BP       Weak 3     98.6             0.9           0.2 0.2 440 UA  
7681 7681 23S 71 1935 1962   v4 G:C No BP       Strong 3 56.9 39.9     2.5 0.5   0.2                   436 GC,CG,GU GC,CG
7926 7926 23S 74 2075 2434   v4 U:A No BP       Weak 3     99.3                         0.7   437 UA  
8136 8136 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong 3 0.2     2.1 0.9       20.1       76.7         437 AU,AG,GA AG,GA
8143 8143 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong 3   27.5 66.8     0.9       2.5     2.1     0.2   437 CG,UA,CA,GA CG,UA
8150 8150 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong 3 8.9     88.8 0.2         0.7   0.5 0.9         437 GC,AU GC,AU,CA
8360 8360 23S 80 2249 2255   v4 U:G No BP       Weak 3           99.1               0.7     0.2 434 UG  
8479 8479 23S 84 2296 2322   v4 U:A No BP       Strong 3     92.9         0.2   0.2     0.9   5.0 0.7   437 UA,UC UA,AC
8850 8850 23S 90 2511 2577   v4 U:A No BP       No Support 3     100.0                             417 UA  
9095 9095 23S 94 2637 2781   v4 U:A No BP       Strong 3 1.1 20.3 71.0 0.8   1.1 0.3 0.3   1.8 1.1 0.3 0.3   1.3 0.5   379 CG,UA GC,CG,UA,AU
9410 9410 23S 98 2796 2800   v4 U:A No BP       Strong 3 3.1 1.0 7.0 1.0   0.8       1.6           0.3 85.2 384 GC,UA GC,CG,UA,AU
9417 9417 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? 3 0.9 2.2 39.7 7.4 12.6 4.9 0.3   1.2 4.3     3.1     0.6 22.7 325 CG,UA,AU,GU,UG,CA,GA CG,UA,GU
9564 9564 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong 3     0.3   2.0 2.6     0.3 0.3   0.9 0.6 30.4 0.3 59.4 3.2 352 GU,UG,GG,UU CA,GG,UU

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");