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).

12 rows where conformation = "No BP", group_code = "M" and strength = "Strong" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, CG, AA, GA, UC, gap, Seq, predominant_types, covarying_types

tertiary_type 2

molecule 2

strength 1

  • Strong · 12 ✖

header_format 1

group_code 1

conformation 1

  • No BP · 12 ✖
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
1470 1470 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong M 0.1 0.3 45.6 0.7 0.2 9.1 7.2 1.1 0.7 3.2 0.1     0.1 0.5 0.1 31.0 886 UA,UG,AA,CA CG,UA,GU,AC
2695 2695 16S 34 1064 1192   v4 G:C No BP       Strong M 38.0 0.1 12.9 3.0 1.0   1.0 0.2 0.3 3.9 0.7   15.0 0.3 21.7 1.6 0.5 1150 GC,UA,AU,CA,GA,UC GC,CG,UA,AU
6608 6608 23S 55 1420 1578   v4 A:U No BP       Strong M   1.1 1.4 2.2         0.4               94.9 276 AU CG,UA,AU
6916 6916 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong M       0.4                         99.7 276    
7686 7686 23S 71 1935 1962   v4 G:C No BP       Strong M 29.4     45.2 11.9   0.6 6.1 2.9       0.6 1.6 0.6 1.0   310 GC,AU,GU,AC,AG GC,AU
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
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
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
8484 8484 23S 84 2296 2322   v4 U:A No BP       Strong M   1.0 10.0 0.3   0.6 0.3       0.3       0.3 0.3 86.7 309 UA CG,UA,AU
9100 9100 23S 94 2637 2781   v4 U:A No BP       Strong M 0.9   7.9 3.5   0.4 1.8   0.9       1.8     0.4 82.3 227 UA,AU GC,UA,AU
9415 9415 23S 98 2796 2800   v4 U:A No BP       Strong M                                 100.0 219    
9569 9569 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong M     4.4     6.7   4.4       2.2     8.9 31.1 42.2 45 UA,UG,AC,CU,UC,UU AC,UU

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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");