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

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Suggested facets: helix_number, reference_base_pair, UA, AU, GU, UG, AC, AG, GA, GG, 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
209 209 16S 2 17 918   v4 U:A cWW   3°: pseudoknot   Strong E     96.8 0.1   1.4       0.4         0.7 0.1 0.5 812 UA UA,AU
216 216 16S 2 18 917   v4 C:G cWW   3°: pseudoknot   Strong E   85.5 7.2     0.6       6.5             0.2 825 CG,UA,CA CG,UA
223 223 16S 2 19 916   v4 A:U cWW   3°: pseudoknot   Strong E   97.0 2.4             0.5             0.1 826 CG,UA CG,UA
3807 3807 23S 6.1 61 93   v4 C:G cWW   3°: pseudoknot   Strong E           0.9                     99.1 117    
3814 3814 23S 6.1 62 92   v4   cWW   3°: pseudoknot   Strong E                           0.9     99.1 117    
3821 3821 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant E     0.8                           99.1 118    
3828 3828 23S 6.1 65 89   v4 U:A cWW   3°: pseudoknot   Strong E                             0.8   99.1 118    
3835 3835 23S 6.1 66 88   v4 C:G cWW   3°: pseudoknot   Weak E                   0.8             99.1 118    
3842 3842 23S 6.2 67 74   v4 U:A cWH   3°: pseudoknot   Strong E 0.8 1.7 31.1 4.2 4.2 5.0       1.7 3.4       44.5 0.8 2.5 119 UA,AU,GU,UG,CC,UC CG,AU,UC
4381 4381 23S 19.1 317 334   v4 G:C cWW   3°: pseudoknot   Strong E 41.7 15.6 8.3 15.6 14.2 2.8   0.5 0.9     0.5           218 GC,CG,UA,AU,GU,UG GC,CG,UA,AU
4388 4388 23S 19.1 318 333   v4 C:G cWW   3°: pseudoknot   Strong E 2.3 55.7 27.4 4.1 0.9 4.1 1.4   0.5   1.4         1.8 0.5 219 GC,CG,UA,AU,UG GC,CG,UA,AU
4521 4521 23S 22.1 413 2410   v4 C:G cWW   3°: pseudoknot   Strong E 0.7 5.3 4.0 79.3 7.3       0.7     0.7 0.7 1.3       150 CG,UA,AU,GU GC,CG,UA,AU
4528 4528 23S 22.1 414 2409   v4 C:G cWW   3°: pseudoknot   Strong E 11.3   10.0 76.7 0.7       0.7       0.7         150 GC,UA,AU GC,UA,AU
4535 4535 23S 22.1 415 2408   v4 A:U cWW   3°: pseudoknot   Strong E 5.3 29.3 61.3 2.7         0.7   0.7             150 GC,CG,UA,AU GC,CG,UA,AU
4542 4542 23S 22.1 416 2407   v4 U:A cWW   3°: pseudoknot   Strong E 3.3 17.3 61.3 2.7   13.3                   2.0   150 GC,CG,UA,AU,UG,UU GC,CG,UA,AU
1329 1329 16S 18.1 505 526   v4 G:C cWW   3°: pseudoknot   Strong E 99.7       0.2                       0.1 1002 GC  
1336 1336 16S 18.1 506 525   v4 G:C cWW   3°: pseudoknot   Strong E 96.9             2.6           0.1 0.2   0.2 998 GC,AC  
1343 1343 16S 18.1 507 524   v4 C:G cWW   3°: pseudoknot   Strong E   96.2           0.3 0.8   2.3 0.2         0.2 999 CG,CC CG,AC
1385 1385 16S 18 521 528   v4 G:C cWW   3°: pseudoknot   No Support E 99.8             0.1                 0.1 1001 GC  
1392 1392 16S 18 522 527   v4 C:G cWW   3°: pseudoknot   Strong E   99.8                       0.1     0.1 1000 CG  
1427 1427 16S 19.1 571 865   v4 U:A cWW   3°: pseudoknot   Weak E     99.6     0.3       0.1               1015 UA  
5725 5725 23S 41.1 1005 1138   v4 C:G cWW   3°: pseudoknot   Strong E 94.4 1.0 2.1                     0.5   0.5 1.5 195 GC,UA GC,CG,UA
5732 5732 23S 41.1 1006 1137   v4 C:G cWW   3°: pseudoknot   Strong E   88.2 10.3           0.5               1.0 195 CG,UA CG,UA
6376 6376 23S 50.1 1343 1404   v4 G:C cWW   3°: pseudoknot   Strong E 75.1 4.4 6.1 3.3 9.4       0.6         0.6     0.6 181 GC,CG,UA,AU,GU GC,CG,UA,AU
6383 6383 23S 50.1 1344 1403   v4 U:A cWW   3°: pseudoknot   Strong E   19.3 79.0     0.6                     1.2 181 CG,UA CG,UA
7342 7342 23S 65.1 1782 2586   v4 U:U tWW   3°: pseudoknot   Strong E                               99.3 0.7 135 UU  
8140 8140 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong E 0.6     4.5 2.6               92.3         155 AU,GU,GA AU,GA
8147 8147 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong E   4.5 91.6     2.6             0.6     0.6   155 CG,UA,UG CG,UA
8154 8154 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong E 2.6     91.0 0.6         1.9   1.3 2.6         155 GC,AU,GA GC,AU,CA
8420 8420 23S 81.2 2283 2325   v4 C:G cWW   3°: pseudoknot   ??? E     100.0                             155 UA  
8553 8553 23S 85.1 2326 2389   v4 C:G cWW   3°: pseudoknot   Strong E 1.9 2.6 5.8 70.3 0.6 3.2             14.8 0.6       155 CG,UA,AU,UG,GA AU,UG,GA
8560 8560 23S 85.1 2328 2387   v4 A:U cWW   3°: pseudoknot   Weak E       97.4       2.6                   155 AU,AC  
8567 8567 23S 85.1 2329 2386   v4 U:A cWW   3°: pseudoknot   Strong E 95.5     1.9                 1.3   1.3     155 GC GC,AU
8574 8574 23S 85.1 2330 2385   v4 G:C cWW   3°: pseudoknot   Strong E 94.8 1.9   1.3 1.3                       0.6 155 GC GC,CG,AU
8644 8644 23S 86.1 2359 2428   v4 C:G cWW   3°: pseudoknot   Strong E     94.2 4.5 1.3                         155 UA,AU UA,AU
9043 9043 23S 93.1 2626 2777   v4 C:G cWW   3°: pseudoknot   Strong E   23.8 5.6     8.7 4.0 0.8 19.0   0.8 2.4 4.0 2.4     28.7 126 CG,UA,UG,AA,AG,CU,GA,GG CG,UA,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");