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).

86 rows where group_code = "B" and tertiary_type = "3°: base pair" sorted by position_1

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Suggested facets: reference_base_pair, AU, GU, UG, AA, AC, CA, CC, CU, GA, GG, UC, UU, gap

conformation 7

strength 5

molecule 3

header_format 2

tertiary_type 1

  • 3°: base pair · 86 ✖

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
3643 3643 23S 2 30 510   v4 G:C cWW   3°: base pair   Strong B 97.6       1.2   1.2                     250 GC GC,AA
353 353 16S 5 47 361   v4 C:G cWW   3°: base pair   Strong B   92.6 3.9     0.5             1.6 0.7     0.3 4038 CG,UA CG,UA
3755 3755 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant B                 100.0                 252 AG  
437 437 16S 6 68 101   v4 G:A cWW   3°: base pair   Weak B 0.7   0.1   0.2 0.3 0.2     0.3     97.0 0.5     0.6 4427 GA UG,GA
122 122 5S 3 75 101 Tertiary legacy     B 3°: base pair   Strong B     2.6 0.3     3.0 0.3 5.0   0.3   88.1 0.3       302 UA,AA,AG,GA AG,CC,GA
126 126 5S 3 76 100 Tertiary legacy     B 3°: base pair   Strong B         0.3   29.8 0.3 0.7 0.3     1.0 67.5       302 AA,GG AA,GG
130 130 5S 3 77 99 Tertiary legacy     B 3°: base pair   Strong B     98.7     0.3 0.3                   0.7 302 UA  
134 134 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant B     0.3 1.3     10.6 0.7 85.8       0.3 0.7     0.3 302 AA,AG AG,GA
598 598 16S 7 129 232   v4 A:G cWW   3°: base pair   Strong B 1.5 17.8 11.5 1.0 0.4 25.1 0.1 0.1 38.0 0.2 0.2   2.4 0.3 0.1   1.2 4743 CG,UA,UG,AG,GA GC,UA,AG
675 675 16S 8 145 177   v4 G:G cWW   3°: base pair   Strong B 6.7 24.1 2.4 2.8 0.2 21.8 0.1 0.1 0.3 0.1   0.1 0.1 40.8   0.1 0.3 4809 GC,CG,UA,AU,UG,GG UA,AU,GG
696 696 16S 8 152 169   v4 A:C tHW   3°: base pair   Strong B 0.1     0.4 10.5 0.3 1.1 79.6 0.2 0.1 0.6 0.5 0.8 5.4 0.1   0.3 4869 GU,AC,GG GU,UG,AC,CA
843 843 16S 11 245 283   v4 U:U cWW   3°: base pair   Strong B                     25.2 0.1     0.1 74.3   4985 CC,UU CC,UU
4392 4392 23S 19.2 319 323   v4 G:C cWW   3°: base pair   Strong B 27.4 68.7     0.4 1.8             1.1 0.7       281 GC,CG GC,CG
1018 1018 16S 13 321 332   v4 A:G cWW   3°: base pair   Strong B   0.1         0.1 0.1 99.3               0.1 5065 AG  
1053 1053 16S 15 367 393   v4 U:A cWW   3°: base pair   Strong B 0.4   99.2 0.2           0.1               4947 UA GC,UA,AU
4476 4476 23S 21 383 391   v4 C:A cWW   3°: base pair   ??? B   0.4       1.4       96.8             1.4 281 CA UG,CA
1172 1172 16S 17 438 496   v4 U:A tWH   3°: base pair   Strong B     71.9     0.2 1.9   0.5       2.2 22.9 0.1 0.2   4678 UA,GA,GG UA,GG
1179 1179 16S 17 440 497   v4 C:G cWW   3°: base pair   Strong B 0.4 51.4 15.3 3.9   2.8 0.6   0.1 0.5 0.1 0.1 0.9 0.1 0.1 22.0 1.6 4693 CG,UA,AU,UG,UU CG,GA,UU
1186 1186 16S 17 441 493   v4 A:A cWW   3°: base pair   Strong B 14.1 4.2 0.6 8.8 3.5 2.9 41.7 2.4 1.0       18.0 1.4 0.1   1.1 4684 GC,CG,AU,GU,UG,AA,AC,GA GC,CG,AA
1228 1228 16S 17 450 483   v4 G:C cWW   3°: base pair   Strong B 94.0 1.1 2.6 1.3   0.2   0.1     0.1   0.1 0.1     0.2 4780 GC,UA GC,CG,UA,AU
4588 4588 23S 24.1 531 2018   v4 C:G cWW   3°: base pair   Strong B 1.7 63.9 21.0 8.6   3.0     0.9       0.4       0.4 233 CG,UA,AU,UG GC,CG,UA,AU
4623 4623 23S 25 537 556   v4 G:A cWW   3°: base pair   Strong B   1.8         14.5           83.0       0.7 282 AA,GA CG,GA
4630 4630 23S 25 538 555   v4 A:G cWW   3°: base pair   Weak B         0.7   1.1   97.5         0.4     0.4 281 AG GU,AG
4679 4679 23S 25.1 563 578   v4 A:G cWW   3°: base pair   Strong B             1.1   31.9       66.7 0.4       282 AG,GA AG,GA
4693 4693 23S 25.1 565 576   v4 C:U cWW   3°: base pair   Strong B       0.7 1.4         0.4   93.3     3.5 0.7   282 CU,UC CU,UC
1431 1431 16S 19.1 575 880   v4 G:C cWW   3°: base pair   Strong B 98.6     0.4 0.2     0.1           0.2     0.4 4383 GC GC,AU
1466 1466 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong B 0.1 11.2 2.6     68.4   0.1   0.2 15.6 0.8     0.6 0.3   4697 CG,UA,UG,CC UG,CC
1620 1620 16S 21 611 629   v4 C:A cWW   3°: base pair   Strong B 0.5 18.5 4.8 2.2 3.2 4.2 2.8 0.5 3.0 51.1 2.0 1.8 1.7 0.9 0.9 0.8 1.1 4598 CG,UA,AU,GU,UG,AA,AG,CA,CC GU,UG,AC,CA
4896 4896 23S 31 637 651   v4 A:G cWW   3°: base pair   Strong B       0.7     0.4   97.9         1.1       281 AG  
1725 1725 16S 22 663 742   v4 A:G cWW   3°: base pair   Strong B 0.8 0.9 2.3 0.1 0.3 0.5 0.3 0.1 94.3         0.2     0.1 4794 UA,AG GC,UA,AG
1788 1788 16S 23 674 716   v4 G:A cWW   3°: base pair   Strong B 0.1                       99.7         4834 GA  
4945 4945 23S 32 674 806   v4 G:C cWW   3°: base pair   ??? B 98.8             0.4                 0.8 242 GC  
5071 5071 23S 33 698 763   v4 C:G cWW   3°: base pair   Strong B   98.9                       0.7     0.4 282 CG  
5148 5148 23S 34 713 718   v4 G:A cWW   3°: base pair   Strong B     0.7                   97.9 0.7 0.4   0.4 282 GA GA,UC
1872 1872 16S 23.1 722 733   v4 G:G tWW   3°: base pair   Strong B 0.2       0.2 0.1 24.5   2.9       0.5 71.3     0.1 4860 AA,AG,GG AA,GG
5365 5365 23S 38 847 933   v4 U:A cWW   3°: base pair   Strong B     49.6 44.2 1.7 2.5 0.4 1.2   0.4               242 UA,AU,UG UA,AU
5435 5435 23S 38 857 920   v4 G:A cWW   3°: base pair   Strong B 0.4 1.2   1.7     0.4   46.3       50.0         242 AG,GA AG,GA
2306 2306 16S 30 945 1236   v4 G:A cWW   3°: base pair   Strong B             0.4     0.1     99.2       0.2 4190 GA  
2572 2572 16S 33.2 1026 1035   v4 G:A cWW   3°: base pair   Strong B 0.9 23.6 3.0 0.4 0.1 1.1 0.2     0.1     29.6 0.2     40.7 4412 CG,UA,GA CG,AU,GA
5799 5799 23S 42 1032 1122   v4 A:G cWW   3°: base pair   Strong B     0.4     2.9 0.8 0.8 94.6 0.4               239 UG,AG UA,AG
5841 5841 23S 42 1039 1116   v4 A:G cWW   3°: base pair   Strong B 32.4 0.8 0.4 26.1 18.3   0.4 3.3 17.4         0.8       241 GC,AU,GU,AC,AG GC,CG,UA,AU
5848 5848 23S 42 1040 1115   v4 A:G cWW   3°: base pair   Strong B 6.2 6.6 46.1 11.6 0.8 1.2 0.8   24.9 0.4     1.2         241 GC,CG,UA,AU,AG GC,UA,AG
2670 2670 16S 34 1061 1195   v4 G:C cWW   3°: base pair   No Support B 99.4       0.4                 0.1       4267 GC  
2677 2677 16S 34 1062 1194   v4 U:U cWW   3°: base pair   Strong B       0.1   0.1           0.1       99.5 0.1 4400 UU  
5953 5953 23S 43.1 1082 1086   v4 U:A tWW   3°: base pair   Strong B   0.8 98.8                   0.4         247 UA CG,UA
5960 5960 23S 44 1087 1102   v4 G:C cWW   3°: base pair   Strong B 98.4 0.8   0.4             0.4             248 GC GC,CG,AU
6044 6044 23S 46 1196 1250   v4 C:G cWW   3°: base pair   Strong B   98.5 0.4     0.4       0.4   0.4           266 CG CG,UA
6086 6086 23S 46 1203 1242   v4 U:U cWW   3°: base pair   Strong B 2.3 7.5 24.8 25.9             0.4   0.8     38.0 0.4 266 GC,CG,UA,AU,UU GC,CG,UU
6093 6093 23S 46 1204 1241   v4 A:A cWW   3°: base pair   Strong B 27.0 3.0 9.9 8.7 2.3 9.9 34.2     0.8   0.8 1.9 1.1     0.4 263 GC,CG,UA,AU,GU,UG,AA GC,UG,AA,CU
6184 6184 23S 46.1 1263 2016   v4 U:U cWW   3°: base pair   Strong B     0.4                         99.6   236 UU  
3062 3062 16S 42 1303 1334   v4 C:G cWW   3°: base pair   Strong B 0.2 99.5       0.1       0.1               4645 CG GC,CG
3069 3069 16S 42 1307 1330   v4 U:U cWW   3°: base pair   Strong B           0.1         2.3         97.5   4656 CC,UU CC,UU
6408 6408 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant B 57.0   5.3 0.8 1.1 0.8       35.0               263 GC,UA,CA GC,AU,UG,CA
3174 3174 16S 43 1357 1365   v4 A:G cWW   3°: base pair   Strong B           0.1 0.1 0.1 93.0       6.4 0.1       4572 AG,GA AG,GA
6450 6450 23S 52 1359 1372   v4 A:U cWW   3°: base pair   Strong B     0.4 99.2                 0.4         264 AU UA,AU
3181 3181 16S 44 1399 1504   v4 C:G cWW   3°: base pair   Strong B   99.4       0.1     0.1 0.1 0.2 0.2         0.2 1733 CG  
3195 3195 16S 44 1402 1500   v4 C:A cWW   3°: base pair   Strong B   0.3 0.1             99.4     0.1       0.2 1871 CA  
3216 3216 16S 44 1407 1494   v4 C:G cWW   3°: base pair   ??? B   99.0               0.5 0.2 0.1   0.2       1855 CG  
3251 3251 16S 44 1413 1487   v4 A:G cWW   3°: base pair   Strong B   0.3   0.2     0.1   99.3               0.1 2752 AG  
6639 6639 23S 55 1425 1573   v4 G:G cWW   3°: base pair   Strong B 0.8 0.4 15.2   0.4 22.0 0.4     0.4       60.6       264 UA,UG,GG UA,GG
6912 6912 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong B 3.4 13.6 5.7 0.4 2.7   1.5           62.1     0.8 9.9 264 GC,CG,UA,GU,GA CG,GA,UU
6919 6919 23S 59 1528 1543   v4 A:G tHS   3°: base pair   Strong B 5.3 0.4 12.1   1.1 1.5 1.1 0.8 65.5               12.1 264 GC,UA,AG GC,UA,AG
7143 7143 23S 62 1690 1697   v4 A:G tHS   3°: base pair   Strong B             11.1   74.8 2.3           11.5 0.4 262 AA,AG,CA,UU AG,CA,UU
7248 7248 23S 63.1 1752 1756   v4 C:G cWW   3°: base pair   Strong B 9.9 67.9 15.3 1.9   3.4               1.1     0.4 262 GC,CG,UA,UG GC,CG,UA,AU
7402 7402 23S 66 1800 1817   v4 C:G tWW   3°: base pair   Strong B   100.0                               262 CG  
7409 7409 23S 66 1803 1814   v4 A:G tHS   3°: base pair   Weak B       0.4     0.4 0.4 98.5               0.4 259 AG  
7556 7556 23S 68 1855 1887   v4 U:C cWW   3°: base pair   Strong B 15.4     15.1 39.4     3.5   0.4 0.8 1.2     23.9 0.4   259 GC,AU,GU,AC,UC GU,CA,UC
7563 7563 23S 68 1856 1886   v4 U:U cWW   3°: base pair   Strong B 23.2 0.8 0.4 42.5                       33.2   259 GC,AU,UU GC,CG,UA,AU
7570 7570 23S 68 1858 1884   v4 A:G tHS/tSH   3°: base pair   Strong B   0.8         1.2   35.8       61.9       0.4 260 AG,GA AG,GA
7577 7577 23S 68 1859 1883   v4 U:U cWW   3°: base pair   Strong B 2.3 0.8   0.4 1.1   0.8 0.8 60.9         0.4   32.6   261 GC,AG,UU GC,AG,UU
7675 7675 23S 69.1 1925 1929   v4 C:G tWW   3°: base pair   Strong B   99.2                   0.4         0.4 241 CG  
7976 7976 23S 75 2086 2233   v4 U:U cWW   3°: base pair   Strong B     39.8                         60.2   241 UA,UU  
8088 8088 23S 76 2104 2185   v4 C:U cWW   3°: base pair   Strong B 0.8 37.9 16.7 11.2   8.8           19.2     4.2 1.2   240 CG,UA,AU,UG,CU,UC GC,CG,UA,AU
8123 8123 23S 76 2109 2180   v4 U:U cWW   3°: base pair   Weak B                       0.4       99.6   241 UU  
8410 8410 23S 81.1 2282 2427   v4 G:C cWW   3°: base pair   Strong B 94.1   5.5 0.4                           238 GC,UA GC,UA,AU
8606 8606 23S 86 2351 2366   v4 G:A cWW   3°: base pair   Weak B 0.8       0.8   12.8   0.4       84.3 0.4     0.4 242 AA,GA AG,GA
8613 8613 23S 86 2352 2365   v4 A:G cWW   3°: base pair   Strong B             8.7   90.9       0.4         242 AA,AG AG,GA
8823 8823 23S 90 2507 2582   v4 C:G cWW   3°: base pair   Strong B   100.0                               242 CG  
8858 8858 23S 90 2512 2574   v4 C:G cWW   3°: base pair   Strong B   97.9                 1.2           0.8 243 CG  
9180 9180 23S 96 2675 2732   v4 A:G cWW   3°: base pair   Strong B 0.4     0.4 2.5   0.4   95.8               0.4 236 GU,AG GU,AG
9418 9418 23S 99 2808 2891   v4 G:U No BP   3°: base pair   ??? B     63.1 10.8 19.7 3.9             0.5       2.0 203 UA,AU,GU,UG UA,GU
9439 9439 23S 99 2813 2887   v4 A:A cWW   3°: base pair   Strong B 29.1 30.0 25.1 5.4     8.9         1.0   0.5       203 GC,CG,UA,AU,AA GC,CG,UA,AU
9446 9446 23S 99 2814 2886   v4 A:A cWW   3°: base pair   Strong B   59.1 13.3 1.0   15.3 10.3   0.5 0.5               203 CG,UA,UG,AA CG,UA,AU
9544 9544 23S 101 2844 2872   v4 G:A cWW   3°: base pair   Strong B 0.5   0.5 1.0 3.4 1.0 7.3   48.8       27.8 9.3     0.5 205 GU,AA,AG,GA,GG AG,GA
9551 9551 23S 101 2845 2871   v4 U:U cWW   3°: base pair   No Support B 6.3 3.9   3.4 29.3       10.7     0.5       45.9   205 GC,CG,AU,GU,AG,UU GC,AG,UU
9565 9565 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong B         3.4 1.5     0.5     1.0 1.0 51.7   41.0   205 GU,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");