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

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Suggested facets: helix_number, reference_base_pair, GC, CG, UA, AU, AA, CA, UC, UU, gap, sequences, predominant_types, covarying_types, Xch, Ych, PE, PES, Cov1, Cov3, C1_C3, WC, WCGU, XCons, 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 C     100.0                             117 UA   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 2.0 1.93 0.01 0.64
16S 2 18 917 C:G cWW 3°: pseudoknot Strong C   99.2             0.8                 118 CG   1 1 0 0.0 0.0 0.0 0.0 0.99 0.99 1.94 1.93 0.01 0.65
16S 2 19 916 A:U cWW 3°: pseudoknot Strong C   91.5             8.5                 117 CG,AG   5 2 1 0.29 0.0 0.0 0.0 0.92 0.92 1.4 1.93 0.0 0.64
23S 6.1 61 93 C:G cWW 3°: pseudoknot Strong C 67.0 3.2   7.4 16.0               2.1   2.1   2.2 94 GC,CG,AU,GU,GA,UC GC,CG,AU 5 7 3 0.5 0.34 0.79 1.14 0.79 0.96 1.13 0.8 0.0 0.89
23S 6.1 62 92   cWW 3°: pseudoknot Strong C   8.4 15.8 2.1     57.9   4.2 6.3       1.1   3.2 1.1 95 CG,UA,AU,AA,AG,CA,UU CG,AA,UU 10 7 4 0.47 0.28 0.7 0.98 0.27 0.27 0.65 1.02 0.01 0.91
23S 6.1 64 90 A:U cWW 3°: pseudoknot Significant C       5.2     54.2 34.4 1.0         1.0   1.0 3.1 96 AU,AA,AC AA,GG,UU 2 8 1 0.2 0.05 0.0 0.05 0.05 0.05 1.57 0.66 0.03 0.9
23S 6.1 65 89 U:A cWW 3°: pseudoknot Strong C   81.2 6.2 2.1                 8.3   1.0   1.0 96 CG,UA,AU,GA CG,AU,GA,UC 5 4 4 0.89 0.65 0.94 1.58 0.91 0.91 0.98 1.2 0.01 0.92
23S 6.1 66 88 C:G cWW 3°: pseudoknot Weak C   92.7 3.1               1.0       2.1   1.0 96 CG,UA,UC CG,UA 2 2 1 0.5 0.5 0.97 1.47 0.97 0.97 1.66 1.51 0.01 0.92
23S 6.2 67 74 U:A cWH 3°: pseudoknot Strong C 63.5 2.1 3.1 9.4 19.8   1.0           1.0         96 GC,CG,UA,AU,GU GC,CG,UA,AU 8 11 7 0.74 0.4 0.78 1.18 0.78 0.98 1.18 0.73 0.0 0.93
23S 19.1 317 334 G:C cWW 3°: pseudoknot Strong C 6.0     90.0                       1.0 3.0 100 GC,AU GC,AU 4 3 3 0.86 0.86 0.99 1.85 0.99 0.99 1.41 1.42 0.01 0.94
23S 19.1 318 333 C:G cWW 3°: pseudoknot Strong C   92.0 2.0       1.0     1.0 2.0           2.0 100 CG,UA,CC CG,UA 2 4 2 0.67 0.33 0.96 1.29 0.96 0.96 1.6 1.44 0.0 0.95
23S 22.1 413 2410 C:G cWW 3°: pseudoknot Strong C   99.0 1.0                             98 CG CG,UA 1 1 1 1.0 1.0 1.0 2.0 1.0 1.0 1.92 1.92 0.0 0.95
23S 22.1 414 2409 C:G cWW 3°: pseudoknot Strong C   96.9 1.0     2.0                       98 CG,UG CG,UA 1 1 0 0.0 0.33 0.98 1.31 0.98 1.0 1.81 1.92 0.0 0.95
23S 22.1 415 2408 A:U cWW 3°: pseudoknot Strong C       98.0                       2.0   98 AU,UU   1 0 0 0.0 0.0 0.0 0.0 0.98 0.98 1.86 2.0 0.0 0.95
23S 22.1 416 2407 U:A cWW 3°: pseudoknot Strong C   96.9 3.1                             98 CG,UA CG,UA 1 1 1 1.0 1.0 1.0 2.0 1.0 1.0 1.81 1.81 0.0 0.95
16S 18.1 505 526 G:C cWW 3°: pseudoknot Strong C 99.4   0.6                             161 GC GC,UA 1 2 0 0.0 1.0 1.0 2.0 1.0 1.0 1.95 1.78 0.0 0.89
16S 18.1 506 525 G:C cWW 3°: pseudoknot Strong C 98.1   1.2   0.6                         160 GC GC,UA 0 1 0 0.0 0.67 0.99 1.66 0.99 1.0 1.9 1.85 0.0 0.88
16S 18.1 507 524 C:G cWW 3°: pseudoknot Strong C   100.0                               160 CG   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 2.0 2.0 0.0 0.88
16S 18 521 528 G:C cWW 3°: pseudoknot No Support C 99.4                   0.6             170 GC   0 1 0 0.0 0.0 0.0 0.0 0.99 0.99 1.95 2.0 0.0 0.93
16S 18 522 527 C:G cWW 3°: pseudoknot Strong C   99.4                     0.6         168 CG CG,GA 0 0 0 0.0 1.0 1.0 2.0 0.99 0.99 1.95 1.95 0.0 0.92
16S 19.1 571 865 U:A cWW 3°: pseudoknot Weak C     98.8                         0.6 0.6 162 UA   0 1 0 0.0 0.0 0.0 0.0 0.99 0.99 1.94 1.89 0.01 0.89
23S 41.1 1005 1138 C:G cWW 3°: pseudoknot Strong C   96.0 2.0 2.0                           100 CG,UA,AU CG,UA,AU 2 2 2 1.0 1.0 1.0 2.0 1.0 1.0 1.72 1.72 0.0 0.97
23S 41.1 1006 1137 C:G cWW 3°: pseudoknot Strong C   97.0 1.0       2.0                     100 CG,AA CG,AA 1 1 0 0.0 0.67 0.99 1.66 0.98 0.98 1.78 1.81 0.0 0.97
23S 50.1 1343 1404 G:C cWW 3°: pseudoknot Strong C 98.0     2.0                           100 GC,AU GC,AU 1 1 1 1.0 1.0 1.0 2.0 1.0 1.0 1.86 1.86 0.0 0.97
23S 50.1 1344 1403 U:A cWW 3°: pseudoknot Strong C     97.0   3.0                         100 UA,GU UA,GU 1 1 1 1.0 1.0 1.0 2.0 0.97 1.0 1.81 1.81 0.0 0.97
23S 65.1 1782 2586 U:U tWW 3°: pseudoknot Strong C                     100.0             95 CC   0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 2.0 0.0 0.92
23S 76.1 2112 2169 G:A No BP 3°: pseudoknot Strong C             3.0           97.0         101 AA,GA   1 0 0 0.0 0.0 0.0 0.0 0.0 0.0 1.81 2.0 0.0 0.98
23S 76.1 2113 2170 U:A No BP 3°: pseudoknot Strong C   96.0 3.0             1.0               101 CG,UA CG,UA 1 2 1 0.67 0.75 0.99 1.74 0.99 0.99 1.81 1.76 0.0 0.98
23S 76.1 2117 2172 A:U No BP 3°: pseudoknot Strong C 2.0 64.4   11.9 1.0                     20.8   101 GC,CG,AU,UU GC,CG,UU 5 4 4 0.89 0.64 0.87 1.51 0.78 0.79 0.6 0.95 0.0 0.98
23S 81.2 2283 2325 C:G cWW 3°: pseudoknot ??? C   14.7 7.8     77.5                       102 CG,UA,UG   8 5 2 0.31 0.0 0.0 0.0 0.23 1.0 1.4 1.6 0.0 0.99
23S 85.1 2326 2389 C:G cWW 3°: pseudoknot Strong C   31.4 2.9     65.7                       102 CG,UA,UG   8 2 0 0.0 0.0 0.0 0.0 0.34 1.0 1.1 1.81 0.0 0.99
23S 85.1 2328 2387 A:U cWW 3°: pseudoknot Weak C       100.0                           102 AU   0 0 0 0.0 0.0 0.0 0.0 1.0 1.0 2.0 2.0 0.0 0.99
23S 85.1 2329 2386 U:A cWW 3°: pseudoknot Strong C     2.0 98.0                           102 UA,AU UA,AU 1 1 1 1.0 1.0 1.0 2.0 1.0 1.0 1.86 1.86 0.0 0.99
23S 85.1 2330 2385 G:C cWW 3°: pseudoknot Strong C 94.1     5.9                           102 GC,AU GC,AU 3 3 3 1.0 1.0 1.0 2.0 1.0 1.0 1.68 1.68 0.0 0.99
23S 86.1 2359 2428 C:G cWW 3°: pseudoknot Strong C   97.0 3.0                             101 CG,UA CG,UA 1 1 1 1.0 1.0 1.0 2.0 1.0 1.0 1.81 1.81 0.0 0.98
23S 93.1 2626 2777 C:G cWW 3°: pseudoknot Strong C   98.2 1.8                             56 CG CG,UA 1 1 1 1.0 1.0 1.0 2.0 1.0 1.0 1.87 1.87 0.0 0.54

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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;