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).

36 rows where group_code = "M" and tertiary_type = "3°: pseudoknot" 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

conformation 4

molecule 2

tertiary_type 1

  • 3°: pseudoknot · 36 ✖

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
210 210 16S 2 17 918   v4 U:A cWW   3°: pseudoknot   Strong M   0.4 97.3 0.4   0.1 0.3     0.1     0.1 0.1 0.3 0.3 0.3 672 UA CG,UA,AU
217 217 16S 2 18 917   v4 C:G cWW   3°: pseudoknot   Strong M 3.4 90.1 4.7 0.1   0.1 0.1   0.6 0.1     0.1     0.1 0.3 675 GC,CG,UA GC,CG,UA,AU
224 224 16S 2 19 916   v4 A:U cWW   3°: pseudoknot   Strong M 0.4 90.7 4.4 1.9   0.1 0.3   0.4 0.9   0.1   0.3     0.3 676 CG,UA GC,CG,UA,AU
3808 3808 23S 6.1 61 93   v4 C:G cWW   3°: pseudoknot   Strong M     0.4 0.9     1.3   0.9   0.4   0.9 0.9 0.4 2.6 91.5 233 UU AA,CC,GG,UU
3815 3815 23S 6.1 62 92   v4   cWW   3°: pseudoknot   Strong M   0.4 0.9 2.1 0.4 1.3 2.1       0.9 0.9 0.4 0.4   2.1 88.0 233 AU,AA,UU AU,UG,CC,GA
3822 3822 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant M   0.4 0.4 2.1 0.4   0.4 0.4 1.7   0.9 0.9 1.3     1.3 89.7 233 AU AU,CC,GA
3829 3829 23S 6.1 65 89   v4 U:A cWW   3°: pseudoknot   Strong M 0.4 0.4 0.4 1.3     0.4 0.4 1.3 0.4     2.6       92.1 233 GA AG,GA
3836 3836 23S 6.1 66 88   v4 C:G cWW   3°: pseudoknot   Weak M 0.4   0.9 1.7 0.4       2.6   0.4   0.9     0.9 91.7 233 AG UA,GU,AG,CC
3843 3843 23S 6.2 67 74   v4 U:A cWH   3°: pseudoknot   Strong M 1.3   2.6 3.0 0.4   1.7 0.4 0.4 0.4   1.3 1.7 1.7   0.9 84.1 233 UA,AU UA,AU,GG
4382 4382 23S 19.1 317 334   v4 G:C cWW   3°: pseudoknot   Strong M 5.9     4.3 1.2                     0.4 88.2 254 GC,AU GC,AU
4389 4389 23S 19.1 318 333   v4 C:G cWW   3°: pseudoknot   Strong M   9.8 0.4 0.8   0.4 0.8                   87.8 254 CG CG,UA,AU
4522 4522 23S 22.1 413 2410   v4 C:G cWW   3°: pseudoknot   Strong M   12.2 1.6 0.4     0.8       0.4 0.4         84.2 254 CG CG,UA,AU
4529 4529 23S 22.1 414 2409   v4 C:G cWW   3°: pseudoknot   Strong M   13.0 0.8 0.4   0.8   0.4 0.4               84.2 254 CG CG,UA,AU
4536 4536 23S 22.1 415 2408   v4 A:U cWW   3°: pseudoknot   Strong M     2.8 13.0                         84.3 254 UA,AU UA,AU
4543 4543 23S 22.1 416 2407   v4 U:A cWW   3°: pseudoknot   Strong M   6.7 6.7 2.0                         84.8 254 CG,UA,AU CG,UA,AU
1330 1330 16S 18.1 505 526   v4 G:C cWW   3°: pseudoknot   Strong M 97.0 0.1 0.5 0.6 1.3               0.4       0.1 831 GC GC,CG,UA,AU
1337 1337 16S 18.1 506 525   v4 G:C cWW   3°: pseudoknot   Strong M 89.3 0.2 0.8 8.1 0.1   0.1 0.2             0.7 0.4   832 GC,AU GC,CG,UA,AU
1344 1344 16S 18.1 507 524   v4 C:G cWW   3°: pseudoknot   Strong M   28.8 68.2 0.4   2.2       0.1     0.1     0.2   831 CG,UA,UG CG,UA,AU
1386 1386 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support M 99.6       0.1                 0.1     0.1 831 GC  
1393 1393 16S 18 522 527   v4 C:G cWW   3°: pseudoknot   Strong M   99.0   0.8             0.1             832 CG CG,AU
1428 1428 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak M   2.3 93.0 0.7 0.6 0.8 0.7     0.1   0.1 0.1   0.1 0.2 1.3 881 CG,UA CG,UA,AU
5726 5726 23S 41.1 1005 1138   v4 C:G cWW   3°: pseudoknot   Strong M 1.5 10.5 4.7     0.4                     83.0 275 CG,UA GC,CG,UA
5733 5733 23S 41.1 1006 1137   v4 C:G cWW   3°: pseudoknot   Strong M   13.0 3.6 0.4   0.4                     82.5 276 CG,UA CG,UA,AU
6377 6377 23S 50.1 1343 1404   v4 G:C cWW   3°: pseudoknot   Strong M 1.8 0.7 0.7 2.5   0.4 0.7                 0.4 92.7 276 AU GC,CG,UA,AU
6384 6384 23S 50.1 1344 1403   v4 U:A cWW   3°: pseudoknot   Strong M 0.7 0.4 4.0 1.1 0.4       0.4             0.4 92.7 276 UA GC,CG,UA,AU
7343 7343 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong M   0.4 6.1             0.4 81.0         11.0 1.2 263 UA,CC,UU CC,UU
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
8421 8421 23S 81.2 2283 2325   v4 C:G cWW   3°: pseudoknot   ??? M   1.0 3.9 0.3   5.5 0.3                 2.9 86.0 309 UA,UG,UU UG,AA
8554 8554 23S 85.1 2326 2389   v4 C:G cWW   3°: pseudoknot   Strong M   3.2 3.6 0.6   5.8 0.6                   86.1 309 CG,UA,UG AU,UG
8561 8561 23S 85.1 2328 2387   v4 A:U cWW   3°: pseudoknot   Weak M     0.3 14.6                         85.1 309 AU UA,AU
8568 8568 23S 85.1 2329 2386   v4 U:A cWW   3°: pseudoknot   Strong M 0.3 0.3 13.3 1.0                         85.1 309 UA GC,CG,UA,AU
8575 8575 23S 85.1 2330 2385   v4 G:C cWW   3°: pseudoknot   Strong M 11.7 0.3 1.0 1.9                         85.1 309 GC GC,CG,UA,AU
8645 8645 23S 86.1 2359 2428   v4 C:G cWW   3°: pseudoknot   Strong M   74.1 9.4 1.9   0.6       1.9             11.9 309 CG,UA CG,UA,AU
9044 9044 23S 93.1 2626 2777   v4 C:G cWW   3°: pseudoknot   Strong M   0.4 2.2 1.8 0.4 0.4 0.9 1.8               2.2 89.9 227 UA,UU CG,UA,GU,AC

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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");