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).

82 rows where group_code = "C" and tertiary_type = "3°: base pair" sorted by position_1

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Suggested facets: reference_base_pair, GC, CG, UA, AU, GU, UG, AA, AC, AG, CA, CC, CU, GA, GG, UC, UU, gap, Seq, covarying_types

conformation 7

strength 5

molecule 2

tertiary_type 1

  • 3°: base pair · 82 ✖

header_format 1

group_code 1

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
3645 3645 23S 2 30 510   v4 G:C cWW   3°: base pair   Strong C 6.5   6.5       80.4   6.5                 46 GC,UA,AA,AG GC,AA
355 355 16S 5 47 361   v4 C:G cWW   3°: base pair   Strong C   96.8               0.6 1.3     0.6     0.6 156 CG  
3757 3757 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant C             6.2   93.8                 81 AA,AG  
439 439 16S 6 68 101   v4 G:A cWW   3°: base pair   Weak C 1.8   2.4 0.6 0.6               92.7 1.8       164 UA,GA AU,GA
600 600 16S 7 129 232   v4 A:G cWW   3°: base pair   Strong C     0.6 4.8   1.8     91.0       0.6 0.6     0.6 167 AU,AG UA,AG
677 677 16S 8 145 177   v4 G:G cWW   3°: base pair   Strong C 72.6     17.9 1.8   0.6 0.6         0.6 3.6     2.4 168 GC,AU,GG GC,AU
698 698 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong C     0.6 3.0     1.8 89.9 1.8   0.6     0.6     1.8 168 AU,AC UA,AC,GG
845 845 16S 11 245 283   v4 U:U cWW   3°: base pair   Strong C           0.6           0.6       98.8   170 UU  
4394 4394 23S 19.2 319 323   v4 G:C cWW   3°: base pair   Strong C 3.0 94.0       1.0                     2.0 100 GC,CG GC,CG
1020 1020 16S 13 321 332   v4 A:G cWW   3°: base pair   Strong C             1.2   98.8                 166 AG  
1055 1055 16S 15 367 393   v4 U:A cWW   3°: base pair   Strong C     98.2     1.8                       165 UA  
4478 4478 23S 21 383 391   v4 C:A cWW   3°: base pair   ??? C     1.0             96.0             3.0 100 CA  
1174 1174 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong C     98.8     0.6             0.6         163 UA  
1181 1181 16S 17 440 497   v4 C:G cWW   3°: base pair   Strong C   0.6 2.5 0.6                       95.7 0.6 162 UA,UU CG,UU
1188 1188 16S 17 441 493   v4 A:A cWW   3°: base pair   Strong C 3.1 67.5 11.0 4.3 1.2   0.6   4.3 4.9     2.5       0.6 163 GC,CG,UA,AU,AG,CA,GA GC,CG,UA,AU
1230 1230 16S 17 450 483   v4 G:C cWW   3°: base pair   Strong C 93.2   0.6 1.9       1.2             2.5   0.6 162 GC,UC GC,UA,AU
4590 4590 23S 24.1 531 2018   v4 C:G cWW   3°: base pair   Strong C   97.0 2.0       1.0                     100 CG,UA CG,UA
4625 4625 23S 25 537 556   v4 G:A cWW   3°: base pair   Strong C     1.0       7.0 1.0   1.0     90.0         100 AA,GA AC,GA
4632 4632 23S 25 538 555   v4 A:G cWW   3°: base pair   Weak C       1.0     5.0   94.0                 100 AA,AG  
4681 4681 23S 25.1 563 578   v4 A:G cWW   3°: base pair   Strong C     4.0       3.0   1.0       92.0         100 UA,AA,GA AG,GA
4695 4695 23S 25.1 565 576   v4 C:U cWW   3°: base pair   Strong C   2.0 1.0 3.0               94.0           100 CG,AU,CU UA,CU
1433 1433 16S 19.1 575 880   v4 G:C cWW   3°: base pair   Strong C 98.8     1.2                           162 GC GC,AU
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
1622 1622 16S 21 611 629   v4 C:A cWW   3°: base pair   Strong C   1.2   4.1 0.6 0.6 22.4 1.2 15.9 40.0 0.6 2.9 5.9     1.2 3.6 170 AU,AA,AG,CA,CU,GA AG,CA,UU
4898 4898 23S 31 637 651   v4 A:G cWW   3°: base pair   Strong C     1.0 12.0   1.0 20.0 5.0 58.0             1.0 2.0 100 AU,AA,AC,AG UA,AG
1727 1727 16S 22 663 742   v4 A:G cWW   3°: base pair   Strong C   0.6 0.6 2.4 0.6 1.2 0.6   93.5               0.6 168 AU,AG UA,GU,AG
1790 1790 16S 23 674 716   v4 G:A cWW   3°: base pair   Strong C 2.4           0.6           96.4       0.6 169 GC,GA  
4947 4947 23S 32 674 806   v4 G:C cWW   3°: base pair   ??? C 100.0                                 100 GC  
5073 5073 23S 33 698 763   v4 C:G cWW   3°: base pair   Strong C   99.0 1.0                             100 CG CG,UA
5150 5150 23S 34 713 718   v4 G:A cWW   3°: base pair   Strong C     2.0 2.0 2.0   4.0           88.0 1.0 1.0     100 UA,AU,GU,AA,GA AU,GA,UC
1874 1874 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong C           0.6 75.4   1.8         21.6     0.6 167 AA,GG AA,GG
5367 5367 23S 38 847 933   v4 U:A cWW   3°: base pair   Strong C 64.0   4.0 6.0 3.0 1.0 1.0 1.0 2.0 5.0       11.0 1.0   1.0 100 GC,UA,AU,GU,AG,CA,GG GC,AU,UG,CA
5437 5437 23S 38 857 920   v4 G:A cWW   3°: base pair   Strong C     2.0       7.0   1.0       89.0     1.0   100 UA,AA,GA AG,GA,UU
2308 2308 16S 30 945 1236   v4 G:A cWW   3°: base pair   Strong C                 1.9 0.6     97.5         160 GA AG,GA
2574 2574 16S 33.2 1026 1035   v4 G:A cWW   3°: base pair   Strong C 0.6 1.2 5.0 5.0     2.5   0.6       67.7 1.2   0.6 15.5 161 UA,AU,AA,GA CG,AU,GA
5801 5801 23S 42 1032 1122   v4 A:G cWW   3°: base pair   Strong C       1.0     5.0   94.0                 100 AA,AG  
5843 5843 23S 42 1039 1116   v4 A:G cWW   3°: base pair   Strong C 3.0     78.0 13.0   3.0         1.0     2.0     100 GC,AU,GU,AA,UC GC,AU
5850 5850 23S 42 1040 1115   v4 A:G cWW   3°: base pair   Strong C 22.0   7.0 62.0 1.0   5.0 2.0         1.0         100 GC,UA,AU,AA,AC GC,UA,AU
2672 2672 16S 34 1061 1195   v4 G:C cWW   3°: base pair   No Support C 100.0                                 162 GC  
2679 2679 16S 34 1062 1194   v4 U:U cWW   3°: base pair   Strong C     1.2                       1.8 96.9   163 UU  
5955 5955 23S 43.1 1082 1086   v4 U:A tWW   3°: base pair   Strong C     98.0                       2.0     100 UA,UC  
5962 5962 23S 44 1087 1102   v4 G:C cWW   3°: base pair   Strong C 92.0     6.0 1.0                     1.0   100 GC,AU GC,AU
6046 6046 23S 46 1196 1250   v4 C:G cWW   3°: base pair   Strong C   100.0                               100 CG  
6088 6088 23S 46 1203 1242   v4 U:U cWW   3°: base pair   Strong C 1.0 57.0 23.0 3.0   7.0       1.0           8.0   100 CG,UA,AU,UG,UU GC,CG,UA,AU
6095 6095 23S 46 1204 1241   v4 A:A cWW   3°: base pair   Strong C 1.0 6.0 51.0 4.0   3.0 9.0     11.0   1.0 2.0 1.0 5.0 6.0   100 CG,UA,AU,UG,AA,CA,GA,UC,UU GC,CG,UA,AU
6186 6186 23S 46.1 1263 2016   v4 U:U cWW   3°: base pair   Strong C                               100.0   100 UU  
3064 3064 16S 42 1303 1334   v4 C:G cWW   3°: base pair   Strong C   98.8                       0.6     0.6 169 CG  
3071 3071 16S 42 1307 1330   v4 U:U cWW   3°: base pair   Strong C       5.9                     1.2 92.9   169 AU,UU  
6410 6410 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant C 96.0     2.0 2.0                         100 GC,AU,GU GC,AU
3176 3176 16S 43 1357 1365   v4 A:G cWW   3°: base pair   Strong C     0.6       2.4   3.0       93.5       0.6 169 AA,AG,GA AG,GA
6452 6452 23S 52 1359 1372   v4 A:U cWW   3°: base pair   Strong C       92.0   2.0 2.0 4.0                   100 AU,UG,AA,AC AU,UG
3183 3183 16S 44 1399 1504   v4 C:G cWW   3°: base pair   Strong C   99.3                             0.7 135 CG  
3197 3197 16S 44 1402 1500   v4 C:A cWW   3°: base pair   Strong C                   100.0               142 CA  
3218 3218 16S 44 1407 1494   v4 C:G cWW   3°: base pair   ??? C   100.0                               148 CG  
3253 3253 16S 44 1413 1487   v4 A:G cWW   3°: base pair   Strong C   5.4 3.4 3.4     1.3   83.9 2.0   0.7           149 CG,UA,AU,AG,CA UA,AG,CU
6641 6641 23S 55 1425 1573   v4 G:G cWW   3°: base pair   Strong C 1.0   3.0 1.0 3.0 12.0               80.0       100 UA,GU,UG,GG UA,AU,GG
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
6921 6921 23S 59 1528 1543   v4 A:G tHS   3°: base pair   Strong C   3.0 4.0 3.0   4.0 5.0   9.0 2.0   1.0       13.0 56.0 100 CG,UA,AU,UG,AA,AG,CA,UU AG,CA,UU
7145 7145 23S 62 1690 1697   v4 A:G tHS   3°: base pair   Strong C       1.0     46.5   50.5 1.0             1.0 101 AA,AG AG,CA
7250 7250 23S 63.1 1752 1756   v4 C:G cWW   3°: base pair   Strong C   82.2 10.9     5.9               1.0       101 CG,UA,UG CG,UA
7404 7404 23S 66 1800 1817   v4 C:G tWW   3°: base pair   Strong C   39.6               60.4               101 CG,CA  
7411 7411 23S 66 1803 1814   v4 A:G tHS   3°: base pair   Weak C       4.0     53.5 11.9 29.7               1.0 101 AU,AA,AC,AG  
7558 7558 23S 68 1855 1887   v4 U:C cWW   3°: base pair   Strong C 68.3     17.8 9.9   3.0 1.0                   101 GC,AU,GU,AA GC,AU
7565 7565 23S 68 1856 1886   v4 U:U cWW   3°: base pair   Strong C 97.0     3.0                           101 GC,AU GC,AU
7572 7572 23S 68 1858 1884   v4 A:G tHS/tSH   3°: base pair   Strong C       3.0     21.8   75.2                 101 AU,AA,AG  
7579 7579 23S 68 1859 1883   v4 U:U cWW   3°: base pair   Strong C 88.1     5.0 5.9   1.0                     101 GC,AU,GU GC,AU
7677 7677 23S 69.1 1925 1929   v4 C:G tWW   3°: base pair   Strong C   100.0                               101 CG  
7978 7978 23S 75 2086 2233   v4 U:U cWW   3°: base pair   Strong C     97.0 2.0                       1.0   100 UA,AU UA,AU
8090 8090 23S 76 2104 2185   v4 C:U cWW   3°: base pair   Strong C   24.8 25.7   1.0 48.5                       101 CG,UA,UG GU,UG
8125 8125 23S 76 2109 2180   v4 U:U cWW   3°: base pair   Weak C       1.0               1.0     1.0 97.0   101 UU  
8412 8412 23S 81.1 2282 2427   v4 G:C cWW   3°: base pair   Strong C 100.0                                 101 GC  
8608 8608 23S 86 2351 2366   v4 G:A cWW   3°: base pair   Weak C             83.3           16.7         102 AA,GA  
8615 8615 23S 86 2352 2365   v4 A:G cWW   3°: base pair   Strong C             12.7   87.3                 102 AA,AG  
8825 8825 23S 90 2507 2582   v4 C:G cWW   3°: base pair   Strong C   100.0                               97 CG  
8860 8860 23S 90 2512 2574   v4 C:G cWW   3°: base pair   Strong C   89.9 7.1     3.0                       99 CG,UA,UG CG,UA
9182 9182 23S 96 2675 2732   v4 A:G cWW   3°: base pair   Strong C   3.4 5.2   12.1       79.3                 58 CG,UA,GU,AG UA,GU,AG
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
9441 9441 23S 99 2813 2887   v4 A:A cWW   3°: base pair   Strong C   18.0 78.0 4.0                           50 CG,UA,AU CG,UA,AU
9448 9448 23S 99 2814 2886   v4 A:A cWW   3°: base pair   Strong C   84.0 6.0       2.0   6.0             2.0   50 CG,UA,AA,AG,UU CG,UA
9546 9546 23S 101 2844 2872   v4 G:A cWW   3°: base pair   Strong C     4.0 4.0 2.0   8.0   82.0                 50 UA,AU,GU,AA,AG UA,GU,AG
9553 9553 23S 101 2845 2871   v4 U:U cWW   3°: base pair   No Support C 30.0   4.0 42.0 16.0 2.0   2.0       4.0           50 GC,UA,AU,GU,UG,AC,CU GC,UA,AU
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");