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Table 5 Tetra-nucleotide bias for three RNA viruses. The tetra-nucleotide bias in three viruses. z value quantifies the tetra-nucleotide bias, as defined in equation (1). N (w) and E (w) are actual and expected frequency of occurrence for word w.

From: Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling

  BCoV MHV SARS   BCoV MHV SARS
Tetra-nucleotide N(w) E(w) z N(w) E(w) z N(w) E(w) z Tetra-nucleotide N(w) E(w) z N(w) E(w) z N(w) E(w) z
AAAA 148 206.2 -7.4 147 145.8 0.2 222 216.5 0.7 UAAA 264 226.2 4.6 187 170.9 2.2 170 183 -1.7
AAAC 110 103.7 1.1 98 91.2 1.3 154 148.1 0.9 UAAC 78 105.1 -4.8 85 122.4 -6.1 123 128 -0.8
AAAG 184 169.7 2.0 173 133.6 6.2 165 158.8 0.9 UAAG 205 171.7 4.6 193 165.3 3.9 107 134.4 -4.3
AAAU 217 220 -0.4 179 164.9 2.0 213 200.6 1.6 UAAU 322 309.9 1.3 245 259.8 -1.7 166 193.9 -3.6
AACA 133 114.1 3.2 113 112.1 0.2 215 175.7 5.4 UACA 178 163.7 2.0 122 123.4 -0.2 230 200.3 3.8
AACC 76 61.3 3.4 107 75.2 6.7 102 92.5 1.8 UACC 97 82.9 2.8 106 98.5 1.4 118 97.1 3.8
AACG 29 40.7 -3.3 35 61.8 -6.2 44 66.3 -5.0 UACG 50 54.4 -1.1 58 72.6 -3.1 46 63.3 -3.9
AACU 91 121.5 -5.0 84 106.5 -4.0 171 168.5 0.4 UACU 196 205.2 -1.2 153 168.2 -2.1 195 192.2 0.4
AAGA 172 157.9 2.0 176 136.4 6.2 184 161.8 3.2 UAGA 128 123.4 0.8 119 124.7 -0.9 102 119.6 -2.9
AAGC 137 103.8 5.9 140 103 6.6 96 112.8 -2.9 UAGC 79 98.7 -3.6 82 118.7 -6.1 71 84.8 -2.7
AAGG 133 121.3 1.9 159 122.4 6.0 140 117.3 3.8 UAGG 73 78.8 -1.2 67 121.3 -9.0 74 75.6 -0.3
AAGU 191 180.6 1.4 179 163.1 2.3 136 139.4 -0.5 UAGU 171 213 -5.2 161 190.7 -3.9 101 126.8 -4.2
AAUA 189 215.2 -3.2 148 182.1 -4.6 113 154.1 -6.0 UAUA 251 237 1.7 192 189 0.4 99 136.5 -5.8
AAUC 100 104.5 -0.8 75 93.2 -3.4 93 121.9 -4.8 UAUC 84 112.3 -4.9 86 99.9 -2.5 84 116.1 -5.4
AAUG 246 229.3 2.0 234 232.1 0.2 230 201.5 3.7 UAUG 310 271.5 4.3 278 238.1 4.7 189 190.3 -0.2
AAUU 265 265.5 -0.1 212 207.8 0.5 211 212 -0.1 UAUU 314 345 -3.0 253 248.5 0.5 190 211.8 -2.7
ACAA 144 137.1 1.1 115 114.1 0.2 269 204.1 8.3 UCAA 131 130 0.2 136 117.7 3.1 202 174.1 3.8
ACAC 84 66.4 3.9 88 75.4 2.6 168 142.2 3.9 UCAC 53 60.4 -1.7 57 67.1 -2.2 130 109.6 3.5
ACAG 118 105.7 2.2 108 104.9 0.5 151 145.1 0.9 UCAG 107 122.1 -2.5 105 106.7 -0.3 110 121.4 -1.9
ACAU 128 123.5 0.7 106 122.7 -2.7 186 172.9 1.8 UCAU 84 124.6 -6.6 88 117.8 -5.0 153 146.7 0.9
ACCA 105 76.9 5.8 116 85 6.1 161 117.7 7.3 UCCA 68 73.4 -1.1 74 80.6 -1.3 76 95.4 -3.6
ACCC 56 37.3 5.6 84 57.6 6.3 54 60.7 -1.6 UCCC 31 37.4 -1.9 45 56 -2.7 31 44.6 -3.7
ACCG 24 35.5 -3.5 52 57.4 -1.3 31 48.8 -4.6 UCCG 15 26 -3.9 37 55.1 -4.4 19 29.7 -3.5
ACCU 83 77.7 1.1 97 97.7 -0.1 139 111.2 4.8 UCCU 74 101.4 -4.9 103 102.4 0.1 80 107.1 -4.8
ACGA 32 44.5 -3.4 31 56.5 -6.2 40 64.4 -5.5 UCGA 18 41.4 -6.6 42 50.4 -2.2 43 67.5 -5.4
ACGC 29 34.1 -1.6 49 52.5 -0.9 31 54.8 -5.8 UCGC 30 34.1 -1.3 45 54 -2.2 38 56.2 -4.4
ACGG 26 31.3 -1.7 46 48.5 -0.7 26 41 -4.2 UCGG 19 29.1 -3.4 33 49.8 -4.3 16 39.9 -6.9
ACGU 47 60.5 -3.1 53 72.1 -4.1 53 72.6 -4.2 UCGU 51 74.1 -4.9 59 74.8 -3.3 73 84.4 -2.3
ACUA 141 127.9 2.1 119 121.3 -0.4 166 167.3 -0.2 UCUA 116 130.2 -2.3 115 124.5 -1.5 130 140.9 -1.7
ACUC 49 68.2 -4.2 61 68.9 -1.7 119 115 0.7 UCUC 52 67.1 -3.3 69 69.6 -0.1 82 108.4 -4.6
ACUG 144 131.5 2.0 126 141.4 -2.4 159 163.3 -0.6 UCUG 119 135.5 -2.6 117 135.5 -2.9 133 141.4 -1.3
ACUU 142 160.9 -2.7 116 132.1 -2.5 207 184.9 3.0 UCUU 195 191.8 0.4 153 142.8 1.6 219 182.6 4.9
AGAA 147 141.6 0.8 162 126.6 5.7 144 158.7 -2.1 UGAA 174 195.3 -2.8 154 176.8 -3.1 164 180.2 -2.2
AGAC 67 71.9 -1.1 87 80.6 1.3 114 117.2 -0.5 UGAC 86 101.8 -2.8 118 127.6 -1.5 153 151.9 0.2
AGAG 107 88.9 3.5 115 103.4 2.1 146 112.3 5.8 UGAG 96 127.7 -5.1 144 167 -3.2 117 136.2 -3.0
AGAU 177 170.4 0.9 158 145.2 1.9 128 141.1 -2.0 UGAU 314 311.7 0.2 243 261 -2.0 215 196.5 2.4
AGCA 113 105.8 1.3 102 112.1 -1.7 105 118.8 -2.3 UGCA 181 166.3 2.1 187 161.5 3.6 166 182 -2.2
AGCC 77 54.1 5.7 91 80.7 2.1 68 55.4 3.1 UGCC 102 81.6 4.1 144 122.4 3.6 114 81.6 6.5
AGCG 48 44.9 0.8 62 71.2 -2.0 32 46.4 -3.8 UGCG 52 65.5 -3.0 86 97.6 -2.1 58 58.5 -0.1
AGCU 126 122.6 0.6 132 132 0.0 140 146.9 -1.0 UGCU 270 218.4 6.4 254 226.8 3.3 315 224.5 11.0
AGGA 116 96.4 3.6 114 117.8 -0.6 138 99.5 7.0 UGGA 171 154.4 2.4 187 147.4 5.9 152 126 4.2
AGGC 65 61.9 0.7 114 104.6 1.7 92 80.3 2.4 UGGC 144 103.8 7.2 184 144.4 6.0 141 103.4 6.7
AGGG 55 59.1 -1.0 88 79.5 1.7 53 60.7 -1.8 UGGG 81 105 -4.3 90 118.9 -4.8 59 74.4 -3.2
AGGU 137 143.8 -1.0 128 150 -3.3 129 119.5 1.6 UGGU 307 302.3 0.5 260 236.3 2.8 200 173.5 3.7
AGUA 137 159.2 -3.2 124 155.6 -4.6 115 116.9 -0.3 UGUA 228 233.8 -0.7 202 215.5 -1.7 161 165.6 -0.6
AGUC 62 77.6 -3.2 75 93.9 -3.5 76 87.3 -2.2 UGUC 116 116.5 -0.1 159 143.6 2.3 141 129.8 1.8
AGUG 152 156.2 -0.6 187 173.8 1.8 127 120.7 1.0 UGUG 266 246.9 2.2 300 255.8 5.0 214 170.9 6.0
AGUU 222 239.6 -2.1 214 206 1.0 126 161.7 -5.1 UGUU 498 407.8 8.1 415 346.1 6.7 274 252 2.5
AUAA 228 220.7 0.9 189 188.5 0.1 129 152.4 -3.4 UUAA 322 269.8 5.8 258 235.5 2.7 195 202.8 -1.0
AUAC 124 129.2 -0.8 100 112.8 -2.2 100 132.3 -5.1 UUAC 185 173.5 1.6 158 155.6 0.3 186 179.8 0.8
AUAG 120 141.9 -3.3 120 135 -2.3 65 91.7 -5.1 UUAG 141 177.5 -5.0 131 183 -7.0 112 119.5 -1.2
AUAU 205 237.9 -3.9 151 185.9 -4.7 99 144.4 -6.9 UUAU 397 385.6 1.1 309 269.1 4.4 191 226.5 -4.3
AUCA 105 122 -2.8 77 99.2 -4.1 139 136.8 0.3 UUCA 127 155 -4.1 132 126.1 1.0 206 180 3.5
AUCC 59 62.9 -0.9 63 65.5 -0.6 54 65.9 -2.7 UUCC 66 80.1 -2.9 75 90.9 -3.0 71 87.9 -3.3
AUCG 31 46.9 -4.2 42 57.2 -3.7 31 59.6 -6.7 UUCG 33 55.3 -5.5 64 69.3 -1.2 56 71.8 -3.4
AUCU 108 129.1 -3.4 87 109.2 -3.9 108 137.1 -4.5 UUCU 193 201.6 -1.1 133 151.2 -2.7 226 189.5 4.8
AUGA 204 212.3 -1.0 203 202.8 0.0 189 198.6 -1.2 UUGA 237 239.3 -0.3 197 213.4 -2.0 189 186.8 0.3
AUGC 186 151.1 5.2 194 164.2 4.2 179 154.3 3.6 UUGC 197 174.1 3.2 188 184.4 0.5 185 162.5 3.2
AUGG 211 180.8 4.1 197 179.4 2.4 185 143.1 6.4 UUGG 213 230.6 -2.1 208 185.6 3.0 153 143.2 1.5
AUGU 296 273.3 2.5 275 269.9 0.6 218 197.4 2.7 UUGU 415 363.3 4.9 368 298 7.4 245 204.3 5.2
AUUA 239 253.9 -1.7 191 216 -3.1 190 192 -0.3 UUUA 407 345.3 6.0 303 257.1 5.2 204 204.1 0.0
AUUC 106 126.1 -3.3 100 110.2 -1.8 127 136.8 -1.5 UUUC 141 161.3 -2.9 109 146.1 -5.6 187 162.4 3.5
AUUG 245 253.5 -1.0 206 211.6 -0.7 208 176 4.4 UUUG 367 357.7 0.9 318 271.3 5.2 207 194.8 1.6
AUUU 361 337.8 2.3 287 251.6 4.1 197 205.6 -1.1 UUUU 454 495.8 -3.4 296 325 -2.9 215 245.2 -3.5
GAAA 118 124 -1.0 104 111.4 -1.3 142 140.8 0.2 CAAA 128 133.8 -0.9 160 108.5 9.0 221 182.3 5.2
GAAC 58 64.6 -1.5 63 75.1 -2.5 89 96.9 -1.5 CAAC 83 71 2.6 93 74.9 3.8 166 128.5 6.0
GAAG 136 125.8 1.7 153 123.2 4.9 126 117.7 1.4 CAAG 108 111 -0.5 135 111.5 4.0 158 132.5 4.0
GAAU 118 140.8 -3.5 119 142.4 -3.6 90 125.7 -5.8 CAAU 144 147.5 -0.5 126 139.1 -2.0 178 170.2 1.1
GACA 82 83 -0.2 99 91 1.5 162 128.5 5.4 CACA 82 78.3 0.8 84 80.6 0.7 168 150.9 2.5
GACC 37 39.2 -0.6 61 69.1 -1.8 66 68.5 -0.5 CACC 59 44 4.1 76 59.3 3.9 98 80.1 3.6
GACG 27 33 -1.9 46 51 -1.3 33 52.9 -5.0 CACG 28 31.5 -1.1 40 46 -1.6 27 50.4 -6.0
GACU 82 86.6 -0.9 88 94.7 -1.3 101 115.3 -2.4 CACU 108 75.3 6.8 97 93.1 0.7 184 151.4 4.8
GAGA 73 77.8 -1.0 104 100.3 0.7 105 111.8 -1.2 CAGA 125 106.4 3.3 123 98.1 4.6 141 128.8 2.0
GAGC 52 60.1 -1.9 66 90.9 -4.8 83 74.9 1.7 CAGC 96 71.9 5.2 99 82.8 3.2 95 96.6 -0.3
GAGG 73 68.6 1.0 112 108.6 0.6 95 89.1 1.1 CAGG 94 84.9 1.8 106 93.4 2.4 102 93.4 1.6
GAGU 103 100.9 0.4 128 134 -0.9 108 98.6 1.7 CAGU 108 128.7 -3.3 132 127.4 0.7 98 127.2 -4.7
GAUA 149 172.1 -3.2 127 145.4 -2.8 81 111 -5.2 CAUA 88 110.8 -3.9 92 112.5 -3.5 99 118.2 -3.2
GAUC 70 86.1 -3.2 63 73 -2.1 55 75.7 -4.3 CAUC 49 56.5 -1.8 45 67.1 -4.9 100 91.9 1.5
GAUG 231 209.7 2.7 237 199.5 4.8 198 159 5.6 CAUG 110 117.8 -1.3 119 143.9 -3.8 153 138.3 2.3
GAUU 205 201.7 0.4 159 176.8 -2.4 125 128.6 -0.6 CAUU 166 149 2.5 160 159 0.1 196 173 3.2
GCAA 104 114.7 -1.8 137 123.3 2.2 133 131 0.3 CCAA 84 81.4 0.5 126 90.8 6.7 119 107.2 2.1
GCAC 70 65.3 1.1 77 74.2 0.6 99 92 1.3 CCAC 71 41.7 8.2 74 55.9 4.4 81 77.7 0.7
GCAG 131 102.4 5.1 157 113.3 7.5 80 100.5 -3.7 CCAG 67 64.5 0.6 90 80.7 1.9 95 77.5 3.6
GCAU 120 109.4 1.8 128 140.9 -2.0 112 104.2 1.4 CCAU 81 71.9 1.9 94 97.4 -0.6 97 91 1.1
GCCA 84 57.8 6.2 111 97.4 2.5 99 76.5 4.7 CCCA 46 41.6 1.2 83 62.7 4.7 56 60.1 -1.0
GCCC 34 34.5 -0.2 75 63.8 2.5 35 36.6 -0.5 CCCC 28 22.2 2.2 43 47.5 -1.2 18 28.8 -3.6
GCCG 29 29.7 -0.2 51 60.5 -2.2 21 31.7 -3.4 CCCG 17 20.4 -1.4 45 39.4 1.6 16 20.1 -1.6
GCCU 84 66.8 3.8 122 106.2 2.8 75 71.9 0.7 CCCU 58 43.9 3.8 76 78 -0.4 48 60.7 -3.0
GCGA 30 38.9 -2.6 42 57.3 -3.7 36 43.5 -2.1 CCGA 25 27.9 -1.0 45 47.1 -0.6 16 36.2 -6.0
GCGC 31 31.7 -0.2 65 57.4 1.8 38 41 -0.8 CCGC 20 21.8 -0.7 50 47 0.8 21 32.1 -3.6
GCGG 21 31.7 -3.4 43 56.8 -3.3 23 29.6 -2.2 CCGG 11 20.9 -3.9 36 44.9 -2.4 13 21.2 -3.2
GCGU 63 55.9 1.7 87 82.1 1.0 47 52.9 -1.5 CCGU 29 38.2 -2.7 54 68.1 -3.1 37 41.8 -1.3
GCUA 165 131.3 5.4 162 144.3 2.7 153 140.7 1.9 CCUA 85 77 1.7 83 96.5 -2.5 104 88.6 3.0
GCUC 58 58.8 -0.2 75 80.5 -1.1 89 98.1 -1.7 CCUC 38 40.1 -0.6 79 58.6 4.8 63 65.2 -0.5
GCUG 136 131.5 0.7 187 173.4 1.9 196 145.3 7.6 CCUG 89 80.4 1.7 118 108.1 1.7 70 89 -3.7
GCUU 167 147.3 3.0 158 162.5 -0.6 180 149.5 4.5 CCUU 86 97.4 -2.1 119 113.3 1.0 105 104.6 0.1
GGAA 86 82.1 0.8 83 103.4 -3.7 103 86 3.3 CGAA 23 42.7 -5.5 40 58.5 -4.4 37 55.5 -4.5
GGAC 51 48.4 0.7 57 67.7 -2.4 68 72.3 -0.9 CGAC 24 22.5 0.6 32 34.3 -0.7 27 46.9 -5.3
GGAG 81 66.6 3.2 109 95.9 2.4 92 70.1 4.8 CGAG 17 29.5 -4.2 42 53.5 -2.9 35 49.8 -3.8
GGAU 122 127 -0.8 139 124.7 2.3 80 83.7 -0.7 CGAU 41 63.1 -5.0 46 63.3 -4.0 36 56 -4.9
GGCA 93 70 5.0 142 99.4 7.7 108 83.7 4.8 CGCA 38 40.7 -0.8 67 63.3 0.8 46 58.2 -2.9
GGCC 34 33.7 0.1 74 74.8 -0.2 33 39.1 -1.8 CGCC 19 17.1 0.8 50 45.6 1.2 15 27.1 -4.2
GGCG 28 32.2 -1.3 57 62.9 -1.4 33 40.5 -2.1 CGCG 17 14.9 1.0 32 39.2 -2.1 21 23.4 -0.9
GGCU 95 88.7 1.2 135 117.9 2.9 115 94.9 3.8 CGCU 36 44.4 -2.3 61 73.5 -2.7 46 74.1 -5.9
GGGA 38 53 -3.7 52 65.7 -3.1 36 48.5 -3.3 CGGA 15 26.4 -4.0 35 51 -4.1 18 33.8 -4.9
GGGC 20 37.4 -5.1 64 68.8 -1.1 36 38.3 -0.7 CGGC 21 19 0.8 45 47.2 -0.6 20 29.3 -3.1
GGGG 26 41.9 -4.5 23 53.8 -7.6 20 31.4 -3.7 CGGG 10 19.9 -4.0 27 39.1 -3.5 12 17.5 -2.4
GGGU 88 95 -1.3 88 100.4 -2.2 52 63.8 -2.7 CGGU 31 50.2 -4.9 52 67.2 -3.4 28 55.5 -6.7
GGUA 147 153.8 -1.0 113 130.8 -2.8 106 102.8 0.6 CGUA 55 53.6 0.3 52 71.6 -4.2 52 60.2 -1.9
GGUC 51 70.4 -4.2 61 76.8 -3.3 40 71.3 -6.7 CGUC 16 24.9 -3.2 29 41.9 -3.6 36 41.9 -1.6
GGUG 160 161.8 -0.3 179 171.9 1.0 135 119.9 2.5 CGUG 60 64.9 -1.1 84 90.6 -1.3 69 71.3 -0.5
GGUU 205 201.3 0.5 175 181.2 -0.8 127 123.2 0.6 CGUU 59 83.2 -4.8 88 104.4 -2.9 53 81.6 -5.8
GUAA 165 174.4 -1.3 135 160.2 -3.6 101 130.5 -4.7 CUAA 154 145.5 1.3 128 140 -1.8 141 153.8 -1.9
GUAC 99 109.2 -1.8 86 110.2 -4.2 143 109 5.9 CUAC 112 88.1 4.6 95 87.5 1.5 160 140.2 3.0
GUAG 112 118.4 -1.1 104 136.9 -5.1 96 88.6 1.4 CUAG 78 86.6 -1.7 74 103.6 -5.3 75 99.2 -4.4
GUAU 191 195.4 -0.6 166 172 -0.8 94 118.6 -4.1 CUAU 163 148.3 2.2 182 150.6 4.7 177 162 2.1
GUCA 85 95.2 -1.9 105 98.5 1.2 114 113.3 0.1 CUCA 59 75 -3.4 73 82.5 -1.9 137 130.2 1.1
GUCC 30 52.2 -5.6 59 73.4 -3.1 35 52.7 -4.4 CUCC 33 41 -2.3 62 58.7 0.8 46 62.3 -3.7
GUCG 33 39.6 -1.9 35 59 -5.7 40 51.3 -2.9 CUCG 21 32 -3.5 39 46 -1.9 43 59.9 -4.0
GUCU 97 109.1 -2.1 125 120.1 0.8 104 112.9 -1.5 CUCU 84 82 0.4 110 94.8 2.8 126 136.9 -1.7
GUGA 122 162.3 -5.8 152 163.3 -1.6 131 127 0.6 CUGA 107 124.3 -2.8 108 139.4 -4.8 141 150.6 -1.4
GUGC 113 115.2 -0.4 149 148.5 0.1 130 110.9 3.3 CUGC 109 91.9 3.2 141 110.9 5.2 159 128.2 4.9
GUGG 158 146.3 1.8 180 158.8 3.1 109 101 1.4 CUGG 121 98.1 4.2 136 123.2 2.1 106 104.8 0.2
GUGU 245 218.3 3.3 269 223.8 5.5 174 129.3 7.2 CUGU 151 157.5 -0.9 164 179.7 -2.1 152 159.3 -1.1
GUUA 255 244.6 1.2 237 225.1 1.4 126 168.7 -6.0 CUUA 143 152.3 -1.4 125 150.3 -3.8 164 163.1 0.1
GUUC 104 123 -3.1 119 116.6 0.4 97 114.8 -3.0 CUUC 68 80.6 -2.5 76 81.3 -1.1 148 124.3 3.9
GUUG 280 254.7 2.9 283 248 4.0 165 169.1 -0.6 CUUG 168 147.9 3.0 154 152.9 0.2 190 154.7 5.2
GUUU 344 316.4 2.8 253 239.5 1.6 192 171 2.9 CUUU 211 212.4 -0.2 191 177.1 1.9 209 183.8 3.4
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