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

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Suggested facets: helix_number, reference_base_pair, GC, CG, AU, GG, 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
207 207 16S 2 17 918   v4 U:A cWW   3°: pseudoknot   Strong A     98.6     1.4                       148 UA  
214 214 16S 2 18 917   v4 C:G cWW   3°: pseudoknot   Strong A   99.3       0.7                       149 CG  
221 221 16S 2 19 916   v4 A:U cWW   3°: pseudoknot   Strong A   100.0                               150 CG  
3805 3805 23S 6.1 61 93   v4 C:G cWW   3°: pseudoknot   Strong A 63.9 30.6                     2.8 2.8       36 GC,CG,GA,GG GC,CG
3812 3812 23S 6.1 62 92   v4   cWW   3°: pseudoknot   Strong A   94.4 2.8               2.8             36 CG,UA,CC CG,UA
3819 3819 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant A             100.0                     36 AA  
3826 3826 23S 6.1 65 89   v4 U:A cWW   3°: pseudoknot   Strong A 100.0                                 36 GC  
3833 3833 23S 6.1 66 88   v4 C:G cWW   3°: pseudoknot   Weak A   94.4 5.6                             36 CG,UA CG,UA
3840 3840 23S 6.2 67 74   v4 U:A cWH   3°: pseudoknot   Strong A 2.8   75.0 8.3 11.1                       2.8 36 GC,UA,AU,GU UA,GU
4379 4379 23S 19.1 317 334   v4 G:C cWW   3°: pseudoknot   Strong A 80.6     11.1             8.3             36 GC,AU,CC GC,AU
4386 4386 23S 19.1 318 333   v4 C:G cWW   3°: pseudoknot   Strong A 5.6 80.6 13.9                             36 GC,CG,UA GC,CG,UA
4519 4519 23S 22.1 413 2410   v4 C:G cWW   3°: pseudoknot   Strong A       100.0                           37 AU  
4526 4526 23S 22.1 414 2409   v4 C:G cWW   3°: pseudoknot   Strong A   37.8 35.1   5.4 18.9       2.7               37 CG,UA,GU,UG,CA CG,UA,GU
4533 4533 23S 22.1 415 2408   v4 A:U cWW   3°: pseudoknot   Strong A 18.9 56.8 13.5   2.7 5.4         2.7             37 GC,CG,UA,GU,UG,CC GC,CG,UA
4540 4540 23S 22.1 416 2407   v4 U:A cWW   3°: pseudoknot   Strong A 35.1 2.7 18.9 21.6 16.2     5.4                   37 GC,CG,UA,AU,GU,AC GC,CG,UA,AU
1327 1327 16S 18.1 505 526   v4 G:C cWW   3°: pseudoknot   Strong A 99.5                         0.5       205 GC  
1334 1334 16S 18.1 506 525   v4 G:C cWW   3°: pseudoknot   Strong A 100.0                                 204 GC  
1341 1341 16S 18.1 507 524   v4 C:G cWW   3°: pseudoknot   Strong A   93.5       4.5     2.0                 201 CG,UG,AG  
1383 1383 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support A 99.5                         0.5       203 GC  
1390 1390 16S 18 522 527   v4 C:G cWW   3°: pseudoknot   Strong A   99.5       0.5                       200 CG  
1425 1425 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak A     100.0                             220 UA  
5723 5723 23S 41.1 1005 1138   v4 C:G cWW   3°: pseudoknot   Strong A   100.0                               36 CG  
5730 5730 23S 41.1 1006 1137   v4 C:G cWW   3°: pseudoknot   Strong A   100.0                               36 CG  
6374 6374 23S 50.1 1343 1404   v4 G:C cWW   3°: pseudoknot   Strong A 97.6             2.4                   41 GC,AC  
6381 6381 23S 50.1 1344 1403   v4 U:A cWW   3°: pseudoknot   Strong A   68.3 31.7                             41 CG,UA CG,UA
7340 7340 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong A                     17.1         82.9   41 CC,UU CC,UU
8138 8138 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong A       4.9         12.2       82.9         41 AU,AG,GA AG,GA
8145 8145 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong A   29.3 48.8             17.1     4.9         41 CG,UA,CA,GA CG,UA
8152 8152 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong A 85.4     14.6                           41 GC,AU GC,AU
8418 8418 23S 81.2 2283 2325   v4 C:G cWW   3°: pseudoknot   ??? A   100.0                               41 CG  
8551 8551 23S 85.1 2326 2389   v4 C:G cWW   3°: pseudoknot   Strong A   82.9 4.9     12.2                       41 CG,UA,UG CG,UA
8558 8558 23S 85.1 2328 2387   v4 A:U cWW   3°: pseudoknot   Weak A       100.0                           41 AU  
8565 8565 23S 85.1 2329 2386   v4 U:A cWW   3°: pseudoknot   Strong A 92.7     7.3                           41 GC,AU GC,AU
8572 8572 23S 85.1 2330 2385   v4 G:C cWW   3°: pseudoknot   Strong A 78.0     22.0                           41 GC,AU GC,AU
8642 8642 23S 86.1 2359 2428   v4 C:G cWW   3°: pseudoknot   Strong A     26.8       14.6     58.5               41 UA,AA,CA  
9041 9041 23S 93.1 2626 2777   v4 C:G cWW   3°: pseudoknot   Strong A   12.2 85.4             2.4               41 CG,UA,CA CG,UA

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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");