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).

11 rows where group_code = "M", header_format = "v4" and strength = "Significant" sorted by position_1

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Suggested facets: reference_base_pair, CG, UA, GU, AA, AG, GA, Seq, predominant_types, covarying_types

conformation 4

tertiary_type 2

strength 1

  • Significant · 11 ✖

molecule 1

header_format 1

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
3759 3759 23S 5 53 117   v4 A:G tHS   3°: base pair   Significant M   0.4 4.7 3.9     0.4 0.9 2.1             0.9 86.6 233 UA,AU,AG CG,UA,AU
3822 3822 23S 6.1 64 90   v4 A:U cWW   3°: pseudoknot   Significant M   0.4 0.4 2.1 0.4   0.4 0.4 1.7   0.9 0.9 1.3     1.3 89.7 233 AU AU,CC,GA
4158 4158 23S 13 239 258   v4 C:G cWW       Significant M 1.2 2.4 32.7 29.5   6.7 3.5   0.4 5.5 0.4 1.2 0.4     5.5 10.7 254 CG,UA,AU,UG,AA,CA,UU GC,CG,UA,AU
4277 4277 23S 18 287 353   v4 G:C cWW       Significant M     0.4 2.4 0.4   0.8   0.4       0.4     1.2 94.1 254 AU UA,AU
5005 5005 23S 33 688 774   v4 U:G No BP       Significant M     90.1 5.0 0.4 1.5       0.4         1.1 0.8 0.8 262 UA,AU UA,AU
5502 5502 23S 38 874 903   v4 G:C cWW       Significant M 3.0   4.9 3.8 1.5 0.4 0.8                 1.5 84.3 266 GC,UA,AU GC,UA,AU
5817 5817 23S 42 1035 1120   v4 U:G cWW       Significant M 0.7 0.4 4.0 2.2 0.7 8.0 0.4 0.7         0.4       82.6 276 UA,AU,UG GC,AU,UG
6412 6412 23S 51 1348 1598   v4 C:A cWW   3°: base pair   Significant M     16.7 2.5   0.7 3.3 2.5 0.4 14.1 1.8 0.7 0.4     0.4 56.6 276 UA,AU,AA,AC,CA UA,AC,CU
7105 7105 23S 61 1667 1993   v4 G:U tSH       Significant M     3.6 1.4 93.1   0.4           0.4 0.4     0.7 276 UA,GU UA,GU
8190 8190 23S 77 2124 2174   v4 G:C cWW       Significant M 11.3   0.6     0.3                 0.6 0.3 86.7 309 GC GC,UA
8715 8715 23S 88 2401 2415   v4 U:G cWW       Significant M 0.3 1.3 3.6 1.6   9.1             0.3       83.8 309 UA,UG GC,AU,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");