Base-pair statistics (frequencies and scores together) (view)

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).
sequences
Number of sequences in the group.

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, sequences, predominant_types, covarying_types, Xch, Ych, PE, PES, Cov1, Cov3, C1_C3, WC, WCGU, YCons, DfDel, PNuc

strength 5

conformation 4

molecule 2

tertiary_type 1

  • 3°: pseudoknot · 36 ✖

group_code 1

molecule helix_number position_1 ▼ position_2 reference_base_pair conformation tertiary_type strength group_code GC CG UA AU GU UG AA AC AG CA CC CU GA GG UC UU gap sequences predominant_types covarying_types Xch Ych PE PES Cov1 Cov3 C1_C3 WC WCGU XCons YCons DfDel PNuc
16S 2 17 918 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 2 2 1 0.5 0.04 0.0 0.04 0.97 0.99 1.91 1.81 0.0 0.77
16S 2 18 917 C:G cWW 3°: pseudoknot Strong E   85.5 7.2     0.6       6.5             0.2 825 CG,UA,CA CG,UA 2 5 1 0.29 0.5 0.93 1.43 0.93 0.93 1.58 1.34 0.0 0.78
16S 2 19 916 A:U cWW 3°: pseudoknot Strong E   97.0 2.4             0.5             0.1 826 CG,UA CG,UA 0 3 0 0.0 0.83 0.99 1.83 0.99 0.99 1.82 1.79 0.0 0.78
23S 6.1 61 93 C:G cWW 3°: pseudoknot Strong E           0.9                     99.1 117     5 0 0 0.0 0.0 0.0 0.0 0.0 1.0 1.38 -0.05 0.45 0.0
23S 6.1 62 92   cWW 3°: pseudoknot Strong E                           0.9     99.1 117     7 0 0 0.0 0.0 0.0 0.0 0.0 0.0 1.23 -0.05 0.45 0.0
23S 6.1 64 90 A:U cWW 3°: pseudoknot Significant E     0.8                           99.1 118     4 0 0 0.0 0.0 0.0 0.0 1.0 1.0 1.04 -0.05 0.45 0.0
23S 6.1 65 89 U:A cWW 3°: pseudoknot Strong E                             0.8   99.1 118     0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 1.26 -0.05 0.45 0.0
23S 6.1 66 88 C:G cWW 3°: pseudoknot Weak E                   0.8             99.1 118     7 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.25 -0.05 0.45 0.0
23S 6.2 67 74 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 7 8 2 0.27 0.11 0.0 0.11 0.39 0.48 0.97 0.16 0.01 0.44
23S 19.1 317 334 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 14 9 8 0.7 0.68 0.81 1.49 0.81 0.98 0.33 0.15 0.0 0.83
23S 19.1 318 333 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 6 13 5 0.53 0.77 0.9 1.67 0.9 0.95 0.52 0.59 0.01 0.83
23S 22.1 413 2410 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 11 7 5 0.56 0.48 0.89 1.38 0.89 0.97 0.86 1.27 0.0 0.57
23S 22.1 414 2409 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 6 5 3 0.55 0.91 0.98 1.89 0.98 0.99 0.83 0.89 0.0 0.57
23S 22.1 415 2408 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 13 9 8 0.73 0.97 0.99 1.95 0.99 0.99 0.57 0.63 0.0 0.57
23S 22.1 416 2407 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 8 6 4 0.57 0.6 0.85 1.45 0.85 0.98 0.65 0.64 0.0 0.57
16S 18.1 505 526 G:C cWW 3°: pseudoknot Strong E 99.7       0.2                       0.1 1002 GC   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 2.0 1.97 0.0 0.95
16S 18.1 506 525 G:C cWW 3°: pseudoknot Strong E 96.9             2.6           0.1 0.2   0.2 998 GC,AC   4 0 0 0.0 0.0 0.0 0.0 0.97 0.97 1.77 1.99 0.0 0.94
16S 18.1 507 524 C:G cWW 3°: pseudoknot Strong E   96.2           0.3 0.8   2.3 0.2         0.2 999 CG,CC CG,AC 2 3 0 0.0 0.08 0.0 0.08 0.96 0.96 1.9 1.79 0.0 0.95
16S 18 521 528 G:C cWW 3°: pseudoknot No Support E 99.8             0.1                 0.1 1001 GC   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 1.99 1.99 0.0 0.95
16S 18 522 527 C:G cWW 3°: pseudoknot Strong E   99.8                       0.1     0.1 1000 CG   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 1.99 1.99 0.0 0.95
16S 19.1 571 865 U:A cWW 3°: pseudoknot Weak E     99.6     0.3       0.1               1015 UA   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 1.99 1.97 0.0 0.96
23S 41.1 1005 1138 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 2 2 2 1.0 0.75 0.99 1.74 0.99 0.99 1.71 1.55 0.01 0.73
23S 41.1 1006 1137 C:G cWW 3°: pseudoknot Strong E   88.2 10.3           0.5               1.0 195 CG,UA CG,UA 2 4 3 1.0 0.95 0.99 1.95 0.99 0.99 1.31 1.42 0.0 0.73
23S 50.1 1343 1404 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 3 8 5 0.91 0.57 0.89 1.46 0.89 0.99 1.12 0.84 0.0 0.68
23S 50.1 1344 1403 U:A cWW 3°: pseudoknot Strong E   19.3 79.0     0.6                     1.2 181 CG,UA CG,UA 5 4 4 0.89 0.97 0.99 1.97 0.99 1.0 1.19 1.22 0.0 0.68
23S 65.1 1782 2586 U:U tWW 3°: pseudoknot Strong E                               99.3 0.7 135 UU   0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 1.93 2.0 0.0 0.51
23S 76.1 2112 2169 G:A No BP 3°: pseudoknot Strong E 0.6     4.5 2.6               92.3         155 AU,GU,GA AU,GA 3 3 2 0.67 0.58 0.97 1.55 0.05 0.08 1.74 1.57 0.0 0.59
23S 76.1 2113 2170 U:A No BP 3°: pseudoknot Strong E   4.5 91.6     2.6             0.6     0.6   155 CG,UA,UG CG,UA 2 4 2 0.67 0.54 0.96 1.5 0.96 0.99 1.68 1.57 0.0 0.59
23S 76.1 2117 2172 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 4 3 1 0.29 0.29 0.94 1.22 0.94 0.94 1.48 1.56 0.0 0.59
23S 81.2 2283 2325 C:G cWW 3°: pseudoknot ??? E     100.0                             155 UA   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 2.0 2.0 0.0 0.59
23S 85.1 2326 2389 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 6 6 4 0.67 0.61 0.88 1.49 0.81 0.84 0.75 0.81 0.0 0.59
23S 85.1 2328 2387 A:U cWW 3°: pseudoknot Weak E       97.4       2.6                   155 AU,AC   0 1 0 0.0 0.0 0.0 0.0 0.97 0.97 2.0 1.76 0.0 0.59
23S 85.1 2329 2386 U:A cWW 3°: pseudoknot Strong E 95.5     1.9                 1.3   1.3     155 GC GC,AU 2 2 1 0.5 0.43 0.97 1.4 0.97 0.97 1.76 1.7 0.0 0.59
23S 85.1 2330 2385 G:C cWW 3°: pseudoknot Strong E 94.8 1.9   1.3 1.3                       0.6 155 GC GC,CG,AU 2 3 2 0.8 0.71 0.99 1.7 0.99 1.0 1.69 1.62 0.0 0.59
23S 86.1 2359 2428 C:G cWW 3°: pseudoknot Strong E     94.2 4.5 1.3                         155 UA,AU UA,AU 2 2 1 0.5 0.78 0.99 1.76 0.99 1.0 1.64 1.61 0.0 0.59
23S 93.1 2626 2777 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 14 5 4 0.42 0.13 0.0 0.13 0.41 0.53 -0.47 -0.12 0.07 0.34

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CREATE VIEW basepair_combined as
select f.molecule, f.helix_number, f.position_1, f.position_2,
       f.reference_base_pair, f.conformation, f.tertiary_type, f.strength, f.group_code,
       f.GC, f.CG, f.UA, f.AU, f.GU, f.UG, f.AA, f.AC, f.AG, f.CA, f.CC, f.CU, f.GA, f.GG, f.UC, f.UU, f.gap, f.Seq as sequences,
       f.predominant_types, f.covarying_types,
       s.Xch, s.Ych, s.PE, s.PES, s.Cov1, s.Cov3, s."C1+C3" as C1_C3,
       s.WC, s.WCGU, s.XCons, s.YCons, s.DfDel, s.PNuc
from basepair_frequency f
left join basepair_collective_score s
  on s.molecule = f.molecule and s.position_1 = f.position_1
 and s.position_2 = f.position_2 and s.group_code = f.group_code;