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.

12 rows where conformation = "No BP", group_code = "T" and molecule = "16S" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, GC, CG, AU, AA, AC, AG, CA, CU, GA, GG, UC, UU, gap, predominant_types, covarying_types, Xch, PE, PES, Cov1, Cov3, C1_C3, WC, WCGU, XCons, YCons, DfDel, PNuc

strength 3

tertiary_type 1

molecule 1

  • 16S · 12 ✖

group_code 1

conformation 1

  • No BP · 12 ✖
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 1 13 21 U:G No BP   Weak T   0.1 8.8 0.1   88.5 0.1   1.5 0.1     0.1 0.1   0.3 0.5 3890 UA,UG UG,AA 14 68 3 0.07 0.02 0.0 0.02 0.09 0.98 1.8 1.5 0.0 0.46
16S 15 375 388 U:G No BP   Weak T   0.1 0.9     97.8     0.1         0.1 0.1 0.4 0.4 6852 UG   10 30 4 0.2 0.05 0.0 0.05 0.01 0.99 1.94 1.68 0.02 0.8
16S 20 582 758 C:C No BP 3°: base pair Strong T 0.1 7.6 7.8 0.1   52.0 0.9 0.2 0.1 0.5 10.5 0.5   0.1 15.3 0.3 3.9 6988 CG,UA,UG,CC,UC UG,AA,CC 95 111 26 0.25 0.26 0.66 0.92 0.16 0.7 0.79 0.52 0.03 0.79
16S 21 606 632 G:U No BP   Weak T 1.7 1.7 1.4 1.7 47.5 1.7 0.4 0.1 0.4   0.3 0.3 2.0 8.1 1.4 2.4 28.8 7251 GU,GA,GG,UU GU,UG,AA,CC 89 148 18 0.15 0.15 0.0 0.15 0.09 0.78 -0.06 -0.3 0.01 0.61
16S 30 944 1237 G:C No BP   No Support T 99.3       0.2     0.1                 0.3 6633 GC   3 4 0 0.0 0.04 0.0 0.04 1.0 1.0 1.95 1.97 0.0 0.78
16S 31 960 975 U:A No BP   Weak T     61.8 14.8   22.4 0.2   0.1           0.2 0.2 0.3 6871 UA,AU,UG UA,AU 10 32 1 0.05 0.39 0.77 1.16 0.77 0.99 1.35 0.64 0.0 0.81
16S 31 961 974 U:A No BP   Weak T 0.1 0.1 66.4 0.1 0.1 16.8 0.3     0.6 0.2 2.1     8.7 4.1 0.3 6856 UA,UG,CU,UC,UU GC,UA,CU 48 99 4 0.05 0.07 0.0 0.07 0.67 0.84 1.73 0.59 0.0 0.8
16S 34 1053 1205 G:U No BP   Weak T 2.6     15.1 81.7     0.1       0.1         0.3 6891 GC,AU,GU GU,AC 7 20 0 0.0 0.01 0.0 0.01 0.18 1.0 1.35 1.79 0.0 0.81
16S 34 1064 1192 G:C No BP   Strong T 73.2   2.5 0.4 1.8 0.2 0.2 0.1 0.1 0.7 0.1 12.9 2.5 0.5 4.2 0.4 0.1 6914 GC,UA,CU,GA,UC GC,UA,AG,CU 53 71 16 0.26 0.58 0.89 1.47 0.76 0.78 0.99 1.0 0.0 0.81
16S 40 1158 1178 C:G No BP   Weak T   81.2 0.4 0.1   0.5       0.1 1.8 0.2   0.1 0.2 0.1 15.2 7138 CG CG,UA,AU 12 156 4 0.05 0.13 0.0 0.13 0.96 0.97 0.97 1.02 0.12 0.71
16S 40 1159 1177 U:G No BP   Weak T   5.5 0.2 0.1   73.5 1.5 0.3 1.5 0.4 0.4 0.1 0.1 0.8   0.4 15.2 7135 CG,UG UG,AA,CC 80 167 11 0.09 0.16 0.0 0.16 0.07 0.94 0.49 1.0 0.12 0.71
16S 45 1506 1529 U:G No BP   Weak T   0.6 4.6     93.0               0.2 0.5 0.4 0.7 2260 UA,UG   7 19 0 0.0 0.01 0.0 0.01 0.05 0.99 1.9 1.58 0.0 0.26

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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;