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 = 3 and strength = "Strong" sorted by position_1

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Suggested facets: helix_number, reference_base_pair, AC, GA, UU, Seq, 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
1465 1465 16S 20 582 758   v4 C:C No BP   3°: base pair   Strong 3 0.1 8.9 2.3     57.7   0.1   0.1 12.3 0.6     17.5 0.3   5946 CG,UA,UG,CC,UC UG,CC
2690 2690 16S 34 1064 1192   v4 G:C No BP       Strong 3 79.8   0.4   1.8 0.2   0.1 0.1     15.9 0.1 0.4 0.8 0.2 0.1 5606 GC,CU GC,UA,AG,CU
6603 6603 23S 55 1420 1578   v4 A:U No BP       Strong 3 8.1 18.8 9.1 10.5 1.0 0.4   0.2 0.8 0.4   1.2       39.5 9.8 484 GC,CG,UA,AU,UU GC,CG,UU
6911 6911 23S 59 1527 1544   v4 G:A No BP   3°: base pair   Strong 3 2.9 32.6 4.7 0.4 13.4   0.8   0.2       33.8 0.2   0.4 10.4 485 GC,CG,UA,GU,GA CG,AU,GA
7681 7681 23S 71 1935 1962   v4 G:C No BP       Strong 3 56.9 39.9     2.5 0.5   0.2                   436 GC,CG,GU GC,CG
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
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
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
8479 8479 23S 84 2296 2322   v4 U:A No BP       Strong 3     92.9         0.2   0.2     0.9   5.0 0.7   437 UA,UC UA,AC
9095 9095 23S 94 2637 2781   v4 U:A No BP       Strong 3 1.1 20.3 71.0 0.8   1.1 0.3 0.3   1.8 1.1 0.3 0.3   1.3 0.5   379 CG,UA GC,CG,UA,AU
9410 9410 23S 98 2796 2800   v4 U:A No BP       Strong 3 3.1 1.0 7.0 1.0   0.8       1.6           0.3 85.2 384 GC,UA GC,CG,UA,AU
9564 9564 23S 101 2849 2866   v4 U:U No BP   3°: base pair   Strong 3     0.3   2.0 2.6     0.3 0.3   0.9 0.6 30.4 0.3 59.4 3.2 352 GU,UG,GG,UU CA,GG,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");