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 = "T" and tertiary_type = "3°: pseudoknot" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, 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
204 204 16S 2 17 918   v4 U:A cWW   3°: pseudoknot   Strong T   0.1 98.3 0.1   0.4 0.1     0.1     0.1   0.2 0.2 0.4 3912 UA CG,UA,AU
211 211 16S 2 18 917   v4 C:G cWW   3°: pseudoknot   Strong T 0.6 92.5 3.9     0.6     0.3 1.7   0.1 0.1       0.2 3930 CG,UA GC,CG,UA
218 218 16S 2 19 916   v4 A:U cWW   3°: pseudoknot   Strong T 0.1 86.3 1.4 8.0   0.2 0.1   1.3 0.4 0.1 1.8   0.1     0.4 3959 CG,AU GC,CG,UA,AU
3802 3802 23S 6.1 61 93   v4 C:G cWW   3°: pseudoknot   Strong T 23.0 8.3 5.0 9.9 2.0 0.3 0.4 3.1 0.3   0.1   0.7 0.4 0.4 0.8 45.0 734 GC,CG,UA,AU,GU,AC GC,CG,UA,AU
3809 3809 23S 6.1 62 92   v4   cWW   3°: pseudoknot   Strong T 3.1 15.2 13.3 1.5 0.3 0.7 10.4   1.2 0.9 0.4 0.3 0.7 0.4   7.9 43.8 738 GC,CG,UA,AA,UU GC,CG,UA,AU
3816 3816 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant T 7.8 3.0 0.5 13.6 0.1 0.1 23.2 4.6 0.7   0.3 0.3 0.4 0.3   0.5 44.5 740 GC,CG,AU,AA,AC GC,CG,AA,UU
3823 3823 23S 6.1 65 89   v4 U:A cWW   3°: pseudoknot   Strong T 10.4 24.5 4.9 9.1 2.8   0.1 0.1 0.4 0.1     1.9 0.3 0.3 0.1 44.9 740 GC,CG,UA,AU,GU GC,CG,UA,AU
3830 3830 23S 6.1 66 88   v4 C:G cWW   3°: pseudoknot   Weak T 0.1 49.5 1.5 0.5 0.1 0.8 0.1   0.9 0.1 0.3   0.3 0.3 0.3 0.3 44.8 740 CG GC,CG,UA,AU
3837 3837 23S 6.2 67 74   v4 U:A cWH   3°: pseudoknot   Strong T 9.9 1.5 34.7 6.9 6.2 0.8 0.7 0.1 0.1 0.5 0.5 0.4 0.8 0.5 7.3 1.8 27.1 740 GC,UA,AU,GU,UC GC,CG,UA,AU
4376 4376 23S 19.1 317 334   v4 G:C cWW   3°: pseudoknot   Strong T 34.1 3.9 2.0 27.9 4.6 0.8   0.1 0.2   0.4 0.1       0.2 25.5 889 GC,CG,UA,AU,GU GC,CG,UA,AU
4383 4383 23S 19.1 318 333   v4 C:G cWW   3°: pseudoknot   Strong T 1.8 56.0 9.8 1.8 0.2 3.0 0.7   0.1 0.1 0.6         0.4 25.4 889 CG,UA,UG GC,CG,UA,AU
4516 4516 23S 22.1 413 2410   v4 C:G cWW   3°: pseudoknot   Strong T 0.1 47.7 1.4 20.4 1.4   0.3   0.1   0.1 0.3 0.1 0.3     27.9 771 CG,AU GC,CG,UA,AU
4523 4523 23S 22.1 414 2409   v4 C:G cWW   3°: pseudoknot   Strong T 2.2 48.4 4.0 15.0 0.4 1.4   0.1 0.3 0.1     0.1       27.8 771 GC,CG,UA,AU GC,CG,UA,AU
4530 4530 23S 22.1 415 2408   v4 A:U cWW   3°: pseudoknot   Strong T 1.9 8.4 13.5 47.3 0.1 0.3     0.1   0.3         0.3 27.8 771 CG,UA,AU GC,CG,UA,AU
4537 4537 23S 22.1 416 2407   v4 U:A cWW   3°: pseudoknot   Strong T 2.3 31.3 32.3 2.2 0.8 2.6   0.3               0.4 27.7 772 GC,CG,UA,AU,UG GC,CG,UA,AU
1324 1324 16S 18.1 505 526   v4 G:C cWW   3°: pseudoknot   Strong T 98.6 0.2 0.2 0.1 0.4               0.1 0.1 0.1   0.1 6520 GC GC,CG,UA,AU
1331 1331 16S 18.1 506 525   v4 G:C cWW   3°: pseudoknot   Strong T 97.6   0.1 1.1       0.5     0.1       0.1   0.2 6563 GC GC,UA,AU
1338 1338 16S 18.1 507 524   v4 C:G cWW   3°: pseudoknot   Strong T   89.5 8.7     0.5     0.2 0.1 0.5 0.1         0.1 6527 CG,UA CG,UA
1380 1380 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support T 99.5       0.1     0.1           0.1     0.2 6570 GC  
1387 1387 16S 18 522 527   v4 C:G cWW   3°: pseudoknot   Strong T   99.3   0.4             0.1           0.1 6444 CG CG,AU
1422 1422 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak T   0.3 98.8 0.1 0.1 0.2 0.1                   0.1 6825 UA CG,UA,GU
5720 5720 23S 41.1 1005 1138   v4 C:G cWW   3°: pseudoknot   Strong T 22.2 47.7 2.2 0.2   0.1               0.1   0.1 27.4 847 GC,CG,UA GC,CG,UA,AU
5727 5727 23S 41.1 1006 1137   v4 C:G cWW   3°: pseudoknot   Strong T   68.0 3.7 0.1   0.7 0.2   0.1               27.2 848 CG,UA CG,UA,AU
6371 6371 23S 50.1 1343 1404   v4 G:C cWW   3°: pseudoknot   Strong T 63.0 1.2 1.5 1.7 2.0 0.1 0.2 0.1 0.1         0.1   0.1 29.7 863 GC,GU GC,CG,UA,AU
6378 6378 23S 50.1 1344 1403   v4 U:A cWW   3°: pseudoknot   Strong T 0.6 10.1 58.2 0.3 0.5 0.1     0.1             0.1 29.9 862 CG,UA GC,CG,UA,AU
7337 7337 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong T   0.1 2.1             0.1 60.3         36.9 0.5 770 UA,CC,UU CC,UU
8135 8135 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong T 0.1 0.2 0.9 1.1 0.5   1.3   11.0 0.1     53.0   0.1   31.6 847 AG,GA AG,GA,UC
8142 8142 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong T   26.0 37.7     1.1 0.1     1.8     1.3     0.1 32.0 847 CG,UA CG,UA
8149 8149 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong T 5.4 7.7 0.6 49.2 0.4   0.7   0.5 0.4   0.2 0.8     2.5 31.6 847 GC,CG,AU,UU GC,CG,UA,AU
8415 8415 23S 81.2 2283 2325   v4 C:G cWW   3°: pseudoknot   ??? T   28.4 23.7 0.1   15.2 0.1                 1.1 31.4 848 CG,UA,UG CG,UA,AU
8548 8548 23S 85.1 2326 2389   v4 C:G cWW   3°: pseudoknot   Strong T 0.4 22.6 2.9 13.1 0.1 26.4 0.2           2.7 0.1     31.3 848 CG,UA,AU,UG,GA AU,UG,GA
8555 8555 23S 85.1 2328 2387   v4 A:U cWW   3°: pseudoknot   Weak T     0.1 68.4       0.5                 31.0 848 AU UA,AU
8562 8562 23S 85.1 2329 2386   v4 U:A cWW   3°: pseudoknot   Strong T 25.8 0.1 14.9 27.7                 0.2   0.2   31.0 848 GC,UA,AU GC,CG,UA,AU
8569 8569 23S 85.1 2330 2385   v4 G:C cWW   3°: pseudoknot   Strong T 61.9 0.5 3.3 2.8 0.2                       31.3 848 GC,UA,AU GC,CG,UA,AU
8639 8639 23S 86.1 2359 2428   v4 C:G cWW   3°: pseudoknot   Strong T   67.0 22.4 1.5 0.2 0.2 0.7     3.5             4.4 848 CG,UA,CA CG,UA,AU
9038 9038 23S 93.1 2626 2777   v4 C:G cWW   3°: pseudoknot   Strong T   42.1 10.1 0.6 0.2 2.0 1.1 0.8 3.5 0.3   0.5 0.6 0.5   0.8 37.4 663 CG,UA,UG,AG 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");