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).

13 rows where group_code = "B" and strength = "Significant" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, UA, GG, Seq, predominant_types, covarying_types

conformation 4

tertiary_type 2

molecule 2

header_format 2

strength 1

  • Significant · 13 ✖

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
3755 3755 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant B                 100.0                 252 AG  
3818 3818 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant B 22.6 8.2 0.8 35.4   0.4 32.3             0.4       257 GC,CG,AU,AA GC,CG,UA,AU
134 134 5S 3 78 98 Tertiary legacy     B 3°: base pair   Significant B     0.3 1.3     10.6 0.7 85.8       0.3 0.7     0.3 302 AA,AG AG,GA
142 142 5S 3 80 96   v4 U:G cWW       Significant B 0.3 3.6 0.3     94.7               0.7   0.3   302 CG,UG GC,UG
4154 4154 23S 13 239 258   v4 C:G cWW       Significant B 5.1 14.9 15.6 8.7 0.7 46.7         0.7       7.2   0.4 276 GC,CG,UA,AU,UG,UC GC,AU,UG
4273 4273 23S 18 287 353   v4 G:C cWW       Significant B 8.4 6.2 15.3 21.8 4.7 4.4 14.2 0.4 1.1 0.4   8.7 2.9 5.5 0.7 4.0 1.5 275 GC,CG,UA,AU,GU,UG,AA,CU,GA,GG,UU GC,CG,UA,AU
5001 5001 23S 33 688 774   v4 U:G No BP       Significant B     88.7     9.2                 2.1     282 UA,UG,UC  
5498 5498 23S 38 874 903   v4 G:C cWW       Significant B 53.7 4.5 2.5 4.9 34.4                         244 GC,CG,UA,AU,GU GC,CG,UA,AU
5813 5813 23S 42 1035 1120   v4 U:G cWW       Significant B           100.0                       239 UG  
6408 6408 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant B 57.0   5.3 0.8 1.1 0.8       35.0               263 GC,UA,CA GC,AU,UG,CA
7101 7101 23S 61 1667 1993   v4 G:U tSH       Significant B 0.4       99.2                     0.4   236 GU  
8186 8186 23S 77 2124 2174   v4 G:C cWW       Significant B 100.0                                 241 GC  
8711 8711 23S 88 2401 2415   v4 U:G cWW       Significant B   6.6       92.9     0.4                 241 CG,UG  

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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");