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).

42 rows where conformation = "tSH" sorted by position_1

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Suggested facets: helix_number, position_1, position_2, reference_base_pair, GC, CG, UA, AU, GU, AA, AC, CU, GA, GG, UU, gap, predominant_types, covarying_types

group_code 7

strength 3

molecule 2

header_format 1

conformation 1

  • tSH · 42 ✖

tertiary_type 0

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
3886 3886 23S 7 82 104   v4 U:A tSH       Strong T   0.1 4.3 0.8 35.6 1.2 0.1 0.1 0.1 0.4 6.2   3.6 0.8 2.6 0.3 43.7 745 UA,GU,CC,GA,UC UA,GU,AG,CC
3887 3887 23S 7 82 104   v4 U:A tSH       Strong 3   0.2 5.1   40.2 1.9   0.2   0.7 10.7   6.3 1.2 4.6   28.8 413 UA,GU,CC,GA,UC UA,GU,CC
3888 3888 23S 7 82 104   v4 U:A tSH       Strong B   0.4 8.1   60.9 2.7   0.4     17.1   2.3 1.9 5.8   0.4 258 UA,GU,UG,CC,GA,UC UA,GU,CC
3889 3889 23S 7 82 104   v4 U:A tSH       Strong A         25.0         8.3     55.6   11.1     36 GU,CA,GA,UC GA,UC
3890 3890 23S 7 82 104   v4 U:A tSH       Strong C     2.0 2.0 91.8           2.0   1.0 1.0       98 UA,AU,GU,CC UA,GU,CC
3891 3891 23S 7 82 104   v4 U:A tSH       Strong E           0.8                     99.1 119    
3892 3892 23S 7 82 104   v4 U:A tSH       Strong M     3.8 1.7 3.8 0.4 0.4   0.4             0.9 88.4 234 UA,GU UA,GU,AG
4096 4096 23S 11 195 200   v4 A:U tSH       Strong T     1.2 95.8 0.1   0.5 0.2                 2.1 840 AU UA,AU
4097 4097 23S 11 195 200   v4 A:U tSH       Strong 3       99.6 0.2                       0.2 486 AU  
4098 4098 23S 11 195 200   v4 A:U tSH       Strong B       100.0                           271 AU  
4099 4099 23S 11 195 200   v4 A:U tSH       Strong A       100.0                           36 AU  
4100 4100 23S 11 195 200   v4 A:U tSH       Strong C       100.0                           100 AU  
4101 4101 23S 11 195 200   v4 A:U tSH       Strong E       98.9 0.6                       0.6 179 AU  
4102 4102 23S 11 195 200   v4 A:U tSH       Strong M     3.9 87.0     1.6 0.8                 6.7 254 UA,AU UA,AU
1863 1863 16S 23 690 697   v4 G:U tSH       Weak T 0.1 0.1 4.2 7.5 81.9   0.1     1.6 0.8 0.1 0.1   3.1 0.2 0.1 7180 UA,AU,GU,UC UA,GU,CC
1864 1864 16S 23 690 697   v4 G:U tSH       Weak 3 0.1     7.7 91.8             0.1 0.1     0.1 0.1 6118 AU,GU  
1865 1865 16S 23 690 697   v4 G:U tSH       Weak B       8.0 91.6             0.1       0.1 0.1 4853 AU,GU  
1866 1866 16S 23 690 697   v4 G:U tSH       Weak A       34.3 65.7                         233 AU,GU  
1867 1867 16S 23 690 697   v4 G:U tSH       Weak C       10.1 88.8   0.6                   0.6 169 AU,GU GU,AA
1868 1868 16S 23 690 697   v4 G:U tSH       Weak E 0.6     0.4 98.4               0.5 0.1       1032 GU  
1869 1869 16S 23 690 697   v4 G:U tSH       Weak M 0.2 0.4 33.7 5.1 13.8 0.1 0.7 0.2   13.0 6.3 0.1 0.4   24.8 0.8 0.3 901 UA,AU,GU,CA,CC,UC UA,GU,CC
7099 7099 23S 61 1667 1993   v4 G:U tSH       Significant T 0.1   1.2 0.6 97.3   0.1           0.1 0.1   0.1 0.2 807 GU UA,GU
7100 7100 23S 61 1667 1993   v4 G:U tSH       Significant 3 0.2     0.2 99.3                     0.2   430 GU  
7101 7101 23S 61 1667 1993   v4 G:U tSH       Significant B 0.4       99.2                     0.4   236 GU  
7102 7102 23S 61 1667 1993   v4 G:U tSH       Significant A         100.0                         41 GU  
7103 7103 23S 61 1667 1993   v4 G:U tSH       Significant C         100.0                         101 GU  
7104 7104 23S 61 1667 1993   v4 G:U tSH       Significant E       0.7 99.3                         153 GU  
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
8268 8268 23S 78 2144 2147   v4 G:A tSH       Strong T 0.1 3.2 1.2   0.2 21.9 0.4 0.5 0.2 0.5   0.5 32.4 0.4 0.4 0.7 37.6 848 CG,UG,GA UG,AC,CU,GA
8269 8269 23S 78 2144 2147   v4 G:A tSH       Strong 3 0.2 5.9 0.9   0.5 20.8   0.2       0.7 60.0 0.7 0.2   9.7 438 CG,UG,GA UG,AC,CU,GA
8270 8270 23S 78 2144 2147   v4 G:A tSH       Strong B 0.4   1.2     4.5             93.8         242 UG,GA UG,GA
8271 8271 23S 78 2144 2147   v4 G:A tSH       Strong A           73.2             26.8         41 UG,GA UG,GA
8272 8272 23S 78 2144 2147   v4 G:A tSH       Strong C   1.0       93.1     2.0           2.0 2.0   101 UG,AG,UC,UU  
8273 8273 23S 78 2144 2147   v4 G:A tSH       Strong E   16.8 0.6   1.3 32.3   0.6       1.9 16.1 1.9 0.6   27.7 155 CG,UG,GA UG,AC,CU,GA
8274 8274 23S 78 2144 2147   v4 G:A tSH       Strong M     1.9     0.3 1.0 1.0   1.3   0.3 3.9     1.3 89.0 309 GA AC,GA,UU
9367 9367 23S 97 2746 2758   v4 U:A tSH       Strong T   0.3 94.4 1.1 0.3 0.6 0.1     0.3         1.0 0.1 1.7 697 UA CG,UA,AU
9368 9368 23S 97 2746 2758   v4 U:A tSH       Strong 3     100.0                             399 UA  
9369 9369 23S 97 2746 2758   v4 U:A tSH       Strong B     100.0                             227 UA  
9370 9370 23S 97 2746 2758   v4 U:A tSH       Strong A     100.0                             41 UA  
9371 9371 23S 97 2746 2758   v4 U:A tSH       Strong C     96.6             3.4               58 UA,CA  
9372 9372 23S 97 2746 2758   v4 U:A tSH       Strong E     100.0                             131 UA  
9373 9373 23S 97 2746 2758   v4 U:A tSH       Strong M   0.8 85.0 2.9 0.8 1.7 0.4               2.9 0.4 5.0 240 UA,AU,UC CG,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");