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).

21 rows where conformation = "No BP" and tertiary_type = "3°: pseudoknot" sorted by position_1

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Suggested facets: position_1, position_2, reference_base_pair, CA, GA, gap, Seq, predominant_types, covarying_types

group_code 7

tertiary_type 1

  • 3°: pseudoknot · 21 ✖

strength 1

molecule 1

header_format 1

conformation 1

  • No BP · 21 ✖
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
8135 8135 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong T 0.1 0.2 0.9 1.1 0.5   1.3   11.0 0.1     53.0   0.1   31.6 847 AG,GA AG,GA,UC
8136 8136 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong 3 0.2     2.1 0.9       20.1       76.7         437 AU,AG,GA AG,GA
8137 8137 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong B                 34.4       65.6         241 AG,GA AG,GA
8138 8138 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong A       4.9         12.2       82.9         41 AU,AG,GA AG,GA
8139 8139 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong C             3.0           97.0         101 AA,GA  
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
8141 8141 23S 76.1 2112 2169   v4 G:A No BP   3°: pseudoknot   Strong M   0.6 2.6       2.6   1.6 0.3     5.2   0.3   86.7 309 UA,AA,GA AG,GA,UC
8142 8142 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong T   26.0 37.7     1.1 0.1     1.8     1.3     0.1 32.0 847 CG,UA CG,UA
8143 8143 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong 3   27.5 66.8     0.9       2.5     2.1     0.2   437 CG,UA,CA,GA CG,UA
8144 8144 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong B   41.9 53.9             1.7     2.5         241 CG,UA,GA CG,UA
8145 8145 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong A   29.3 48.8             17.1     4.9         41 CG,UA,CA,GA CG,UA
8146 8146 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong C   96.0 3.0             1.0               101 CG,UA CG,UA
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
8148 8148 23S 76.1 2113 2170   v4 U:A No BP   3°: pseudoknot   Strong M   1.0 7.8     1.6 0.3     1.0     0.6       87.7 309 UA CG,UA
8149 8149 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong T 5.4 7.7 0.6 49.2 0.4   0.7   0.5 0.4   0.2 0.8     2.5 31.6 847 GC,CG,AU,UU GC,CG,UA,AU
8150 8150 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong 3 8.9     88.8 0.2         0.7   0.5 0.9         437 GC,AU GC,AU,CA
8151 8151 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong B       100.0                           241 AU  
8152 8152 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong A 85.4     14.6                           41 GC,AU GC,AU
8153 8153 23S 76.1 2117 2172   v4 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
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
8155 8155 23S 76.1 2117 2172   v4 A:U No BP   3°: pseudoknot   Strong M 1.6   1.6 5.5 0.3   1.9   1.3       1.0       86.7 309 AU GC,UA,AU

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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");