Multiple sequence alignment - TraesCS3D01G167200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G167200 chr3D 100.000 2597 0 0 1 2597 141474814 141472218 0.000000e+00 4796
1 TraesCS3D01G167200 chr3D 97.186 1315 18 7 265 1579 405523360 405522065 0.000000e+00 2206
2 TraesCS3D01G167200 chr3D 97.879 990 17 2 1609 2597 405522071 405521085 0.000000e+00 1709
3 TraesCS3D01G167200 chr3D 97.222 144 4 0 121 264 778991 779134 7.180000e-61 244
4 TraesCS3D01G167200 chr3D 96.721 122 2 1 1 120 405523473 405523352 4.380000e-48 202
5 TraesCS3D01G167200 chr6D 97.170 2332 51 7 265 2595 38564351 38566668 0.000000e+00 3927
6 TraesCS3D01G167200 chr6D 96.667 120 4 0 1 120 38564240 38564359 1.580000e-47 200
7 TraesCS3D01G167200 chr4A 95.287 2334 102 6 265 2595 350846821 350844493 0.000000e+00 3694
8 TraesCS3D01G167200 chr4A 97.226 1622 41 3 715 2335 466147605 466145987 0.000000e+00 2743
9 TraesCS3D01G167200 chr4A 96.783 1461 38 4 1141 2595 309476171 309474714 0.000000e+00 2429
10 TraesCS3D01G167200 chr4A 89.128 1628 117 27 265 1858 621289305 621287704 0.000000e+00 1971
11 TraesCS3D01G167200 chr4A 96.240 851 31 1 265 1115 309477012 309476163 0.000000e+00 1393
12 TraesCS3D01G167200 chr4A 97.156 422 7 2 265 686 466148008 466147592 0.000000e+00 708
13 TraesCS3D01G167200 chr4A 95.833 120 5 0 1 120 309477123 309477004 7.330000e-46 195
14 TraesCS3D01G167200 chr4A 94.167 120 7 0 1 120 350846932 350846813 1.590000e-42 183
15 TraesCS3D01G167200 chr6B 97.249 2072 51 3 265 2335 280037424 280035358 0.000000e+00 3506
16 TraesCS3D01G167200 chr6B 88.033 1571 136 25 266 1791 90024351 90025914 0.000000e+00 1812
17 TraesCS3D01G167200 chr6B 90.566 689 42 6 265 930 266830253 266829565 0.000000e+00 891
18 TraesCS3D01G167200 chr6B 98.333 120 2 0 1 120 280037535 280037416 7.280000e-51 211
19 TraesCS3D01G167200 chr6B 94.118 119 5 2 2 120 90024242 90024358 2.050000e-41 180
20 TraesCS3D01G167200 chr6B 93.333 120 6 1 1 118 266830366 266830247 2.660000e-40 176
21 TraesCS3D01G167200 chr7B 96.525 2072 58 6 265 2335 78125166 78123108 0.000000e+00 3415
22 TraesCS3D01G167200 chr7B 98.333 120 2 0 1 120 78125277 78125158 7.280000e-51 211
23 TraesCS3D01G167200 chr7A 94.623 1432 72 2 1168 2595 455697505 455698935 0.000000e+00 2213
24 TraesCS3D01G167200 chr7A 91.480 939 42 13 265 1169 455696409 455697343 0.000000e+00 1256
25 TraesCS3D01G167200 chr2B 87.415 1319 105 23 265 1531 75732387 75733696 0.000000e+00 1459
26 TraesCS3D01G167200 chr4B 87.418 1216 88 29 367 1531 429608816 429607615 0.000000e+00 1338
27 TraesCS3D01G167200 chr4B 92.517 882 53 5 1723 2595 552767621 552768498 0.000000e+00 1251
28 TraesCS3D01G167200 chr5D 97.222 144 4 0 121 264 520347004 520346861 7.180000e-61 244
29 TraesCS3D01G167200 chr5D 95.172 145 7 0 121 265 520346855 520346711 2.010000e-56 230
30 TraesCS3D01G167200 chr5D 96.269 134 5 0 131 264 520347143 520347010 1.210000e-53 220
31 TraesCS3D01G167200 chr5D 89.474 152 15 1 117 267 428574332 428574483 9.490000e-45 191
32 TraesCS3D01G167200 chr5A 91.667 144 12 0 121 264 597943842 597943985 1.580000e-47 200
33 TraesCS3D01G167200 chr4D 90.066 151 13 1 121 269 50885912 50885762 7.330000e-46 195
34 TraesCS3D01G167200 chr5B 90.411 146 14 0 120 265 700942127 700942272 2.640000e-45 193
35 TraesCS3D01G167200 chr2D 90.345 145 14 0 121 265 18769131 18768987 9.490000e-45 191
36 TraesCS3D01G167200 chr3A 94.915 118 6 0 1 118 6672937 6672820 4.410000e-43 185


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G167200 chr3D 141472218 141474814 2596 True 4796.000000 4796 100.000000 1 2597 1 chr3D.!!$R1 2596
1 TraesCS3D01G167200 chr3D 405521085 405523473 2388 True 1372.333333 2206 97.262000 1 2597 3 chr3D.!!$R2 2596
2 TraesCS3D01G167200 chr6D 38564240 38566668 2428 False 2063.500000 3927 96.918500 1 2595 2 chr6D.!!$F1 2594
3 TraesCS3D01G167200 chr4A 621287704 621289305 1601 True 1971.000000 1971 89.128000 265 1858 1 chr4A.!!$R1 1593
4 TraesCS3D01G167200 chr4A 350844493 350846932 2439 True 1938.500000 3694 94.727000 1 2595 2 chr4A.!!$R3 2594
5 TraesCS3D01G167200 chr4A 466145987 466148008 2021 True 1725.500000 2743 97.191000 265 2335 2 chr4A.!!$R4 2070
6 TraesCS3D01G167200 chr4A 309474714 309477123 2409 True 1339.000000 2429 96.285333 1 2595 3 chr4A.!!$R2 2594
7 TraesCS3D01G167200 chr6B 280035358 280037535 2177 True 1858.500000 3506 97.791000 1 2335 2 chr6B.!!$R2 2334
8 TraesCS3D01G167200 chr6B 90024242 90025914 1672 False 996.000000 1812 91.075500 2 1791 2 chr6B.!!$F1 1789
9 TraesCS3D01G167200 chr6B 266829565 266830366 801 True 533.500000 891 91.949500 1 930 2 chr6B.!!$R1 929
10 TraesCS3D01G167200 chr7B 78123108 78125277 2169 True 1813.000000 3415 97.429000 1 2335 2 chr7B.!!$R1 2334
11 TraesCS3D01G167200 chr7A 455696409 455698935 2526 False 1734.500000 2213 93.051500 265 2595 2 chr7A.!!$F1 2330
12 TraesCS3D01G167200 chr2B 75732387 75733696 1309 False 1459.000000 1459 87.415000 265 1531 1 chr2B.!!$F1 1266
13 TraesCS3D01G167200 chr4B 429607615 429608816 1201 True 1338.000000 1338 87.418000 367 1531 1 chr4B.!!$R1 1164
14 TraesCS3D01G167200 chr4B 552767621 552768498 877 False 1251.000000 1251 92.517000 1723 2595 1 chr4B.!!$F1 872

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
180 183 0.034059 CGACAAGAGACAGGCCTGTT 59.966 55.0 37.98 26.55 45.05 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1933 1.067364 TCAGTGTTCAACTACGCCGAA 59.933 47.619 0.0 0.0 36.83 4.3 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.452990 TGTCCAACAGTCCAACTTAGACA 59.547 43.478 0.00 0.00 36.68 3.41
79 80 6.037610 CCAACTTAGACAGCTCCATCAAATAC 59.962 42.308 0.00 0.00 0.00 1.89
120 123 8.970691 ACAAATCATACACTGTAATTTGAAGC 57.029 30.769 22.27 0.00 38.83 3.86
121 124 7.750458 ACAAATCATACACTGTAATTTGAAGCG 59.250 33.333 22.27 7.46 38.83 4.68
122 125 7.609760 AATCATACACTGTAATTTGAAGCGA 57.390 32.000 0.00 0.00 0.00 4.93
123 126 7.609760 ATCATACACTGTAATTTGAAGCGAA 57.390 32.000 0.00 0.00 0.00 4.70
124 127 7.428282 TCATACACTGTAATTTGAAGCGAAA 57.572 32.000 0.00 0.00 0.00 3.46
125 128 7.295201 TCATACACTGTAATTTGAAGCGAAAC 58.705 34.615 0.00 0.00 0.00 2.78
126 129 5.751243 ACACTGTAATTTGAAGCGAAACT 57.249 34.783 0.00 0.00 0.00 2.66
127 130 5.510671 ACACTGTAATTTGAAGCGAAACTG 58.489 37.500 0.00 0.00 0.00 3.16
128 131 4.379793 CACTGTAATTTGAAGCGAAACTGC 59.620 41.667 0.00 0.00 0.00 4.40
129 132 3.896122 TGTAATTTGAAGCGAAACTGCC 58.104 40.909 0.00 0.00 34.65 4.85
130 133 3.568007 TGTAATTTGAAGCGAAACTGCCT 59.432 39.130 0.00 0.00 34.65 4.75
131 134 2.997485 ATTTGAAGCGAAACTGCCTC 57.003 45.000 0.00 0.00 34.65 4.70
132 135 1.674359 TTTGAAGCGAAACTGCCTCA 58.326 45.000 0.00 0.00 33.66 3.86
133 136 1.896220 TTGAAGCGAAACTGCCTCAT 58.104 45.000 0.00 0.00 35.39 2.90
134 137 1.159285 TGAAGCGAAACTGCCTCATG 58.841 50.000 0.00 0.00 30.64 3.07
135 138 1.160137 GAAGCGAAACTGCCTCATGT 58.840 50.000 0.00 0.00 34.65 3.21
136 139 2.289382 TGAAGCGAAACTGCCTCATGTA 60.289 45.455 0.00 0.00 30.64 2.29
137 140 1.726853 AGCGAAACTGCCTCATGTAC 58.273 50.000 0.00 0.00 34.65 2.90
138 141 0.370273 GCGAAACTGCCTCATGTACG 59.630 55.000 0.00 0.00 0.00 3.67
139 142 1.990799 CGAAACTGCCTCATGTACGA 58.009 50.000 0.00 0.00 0.00 3.43
140 143 2.540515 CGAAACTGCCTCATGTACGAT 58.459 47.619 0.00 0.00 0.00 3.73
141 144 2.535984 CGAAACTGCCTCATGTACGATC 59.464 50.000 0.00 0.00 0.00 3.69
142 145 3.735208 CGAAACTGCCTCATGTACGATCT 60.735 47.826 0.00 0.00 0.00 2.75
143 146 4.497507 CGAAACTGCCTCATGTACGATCTA 60.498 45.833 0.00 0.00 0.00 1.98
144 147 5.533482 GAAACTGCCTCATGTACGATCTAT 58.467 41.667 0.00 0.00 0.00 1.98
145 148 5.537300 AACTGCCTCATGTACGATCTATT 57.463 39.130 0.00 0.00 0.00 1.73
146 149 6.650427 AACTGCCTCATGTACGATCTATTA 57.350 37.500 0.00 0.00 0.00 0.98
147 150 6.842437 ACTGCCTCATGTACGATCTATTAT 57.158 37.500 0.00 0.00 0.00 1.28
148 151 6.857956 ACTGCCTCATGTACGATCTATTATC 58.142 40.000 0.00 0.00 0.00 1.75
149 152 6.434340 ACTGCCTCATGTACGATCTATTATCA 59.566 38.462 0.00 0.00 0.00 2.15
150 153 7.123397 ACTGCCTCATGTACGATCTATTATCAT 59.877 37.037 0.00 0.00 0.00 2.45
151 154 8.519799 TGCCTCATGTACGATCTATTATCATA 57.480 34.615 0.00 0.00 0.00 2.15
152 155 8.406297 TGCCTCATGTACGATCTATTATCATAC 58.594 37.037 0.00 0.00 0.00 2.39
153 156 7.588123 GCCTCATGTACGATCTATTATCATACG 59.412 40.741 0.00 0.00 0.00 3.06
154 157 8.827677 CCTCATGTACGATCTATTATCATACGA 58.172 37.037 0.00 0.00 0.00 3.43
162 165 9.486857 ACGATCTATTATCATACGATTTGTACG 57.513 33.333 0.00 0.00 35.44 3.67
163 166 9.698617 CGATCTATTATCATACGATTTGTACGA 57.301 33.333 0.00 0.00 35.44 3.43
169 172 8.556517 TTATCATACGATTTGTACGACAAGAG 57.443 34.615 0.00 0.00 39.53 2.85
170 173 6.185852 TCATACGATTTGTACGACAAGAGA 57.814 37.500 0.00 0.00 39.53 3.10
171 174 6.025896 TCATACGATTTGTACGACAAGAGAC 58.974 40.000 0.00 0.00 39.53 3.36
172 175 4.233123 ACGATTTGTACGACAAGAGACA 57.767 40.909 0.00 0.00 39.53 3.41
173 176 4.227538 ACGATTTGTACGACAAGAGACAG 58.772 43.478 0.00 0.00 39.53 3.51
174 177 3.608506 CGATTTGTACGACAAGAGACAGG 59.391 47.826 0.00 0.00 39.53 4.00
175 178 2.433868 TTGTACGACAAGAGACAGGC 57.566 50.000 0.00 0.00 32.34 4.85
176 179 0.601558 TGTACGACAAGAGACAGGCC 59.398 55.000 0.00 0.00 0.00 5.19
177 180 0.889306 GTACGACAAGAGACAGGCCT 59.111 55.000 0.00 0.00 0.00 5.19
178 181 0.888619 TACGACAAGAGACAGGCCTG 59.111 55.000 31.60 31.60 0.00 4.85
180 183 0.034059 CGACAAGAGACAGGCCTGTT 59.966 55.000 37.98 26.55 45.05 3.16
181 184 1.541233 CGACAAGAGACAGGCCTGTTT 60.541 52.381 37.98 33.02 45.05 2.83
182 185 2.147150 GACAAGAGACAGGCCTGTTTC 58.853 52.381 37.36 37.36 45.05 2.78
183 186 1.202818 ACAAGAGACAGGCCTGTTTCC 60.203 52.381 39.17 29.18 43.34 3.13
184 187 1.072965 CAAGAGACAGGCCTGTTTCCT 59.927 52.381 39.17 31.33 43.34 3.36
189 192 4.339335 AGGCCTGTTTCCTGAGGT 57.661 55.556 3.11 0.00 31.53 3.85
190 193 2.556849 AGGCCTGTTTCCTGAGGTT 58.443 52.632 3.11 0.00 31.53 3.50
191 194 0.853530 AGGCCTGTTTCCTGAGGTTT 59.146 50.000 3.11 0.00 31.53 3.27
192 195 0.961753 GGCCTGTTTCCTGAGGTTTG 59.038 55.000 0.00 0.00 0.00 2.93
193 196 0.961753 GCCTGTTTCCTGAGGTTTGG 59.038 55.000 0.00 0.00 0.00 3.28
194 197 1.620822 CCTGTTTCCTGAGGTTTGGG 58.379 55.000 0.00 0.00 0.00 4.12
195 198 0.961753 CTGTTTCCTGAGGTTTGGGC 59.038 55.000 0.00 0.00 0.00 5.36
196 199 0.469144 TGTTTCCTGAGGTTTGGGCC 60.469 55.000 0.00 0.00 0.00 5.80
197 200 1.155155 TTTCCTGAGGTTTGGGCCC 59.845 57.895 17.59 17.59 0.00 5.80
198 201 1.660019 TTTCCTGAGGTTTGGGCCCA 61.660 55.000 24.45 24.45 0.00 5.36
199 202 2.283173 CCTGAGGTTTGGGCCCAC 60.283 66.667 28.70 15.02 0.00 4.61
200 203 2.283173 CTGAGGTTTGGGCCCACC 60.283 66.667 28.70 24.53 40.81 4.61
209 212 3.661648 GGGCCCACCACACCAGAT 61.662 66.667 19.95 0.00 39.85 2.90
210 213 2.361610 GGCCCACCACACCAGATG 60.362 66.667 0.00 0.00 35.26 2.90
211 214 2.756400 GCCCACCACACCAGATGA 59.244 61.111 0.00 0.00 0.00 2.92
212 215 1.377725 GCCCACCACACCAGATGAG 60.378 63.158 0.00 0.00 0.00 2.90
213 216 2.069776 CCCACCACACCAGATGAGT 58.930 57.895 0.00 0.00 0.00 3.41
214 217 0.036010 CCCACCACACCAGATGAGTC 60.036 60.000 0.00 0.00 0.00 3.36
215 218 0.979665 CCACCACACCAGATGAGTCT 59.020 55.000 0.00 0.00 34.14 3.24
216 219 1.349026 CCACCACACCAGATGAGTCTT 59.651 52.381 0.00 0.00 30.42 3.01
217 220 2.420642 CACCACACCAGATGAGTCTTG 58.579 52.381 0.00 0.00 30.42 3.02
218 221 2.050144 ACCACACCAGATGAGTCTTGT 58.950 47.619 0.00 0.00 30.96 3.16
219 222 2.037772 ACCACACCAGATGAGTCTTGTC 59.962 50.000 0.00 0.00 28.51 3.18
220 223 2.332104 CACACCAGATGAGTCTTGTCG 58.668 52.381 0.00 0.00 28.51 4.35
221 224 1.964223 ACACCAGATGAGTCTTGTCGT 59.036 47.619 0.00 0.00 28.51 4.34
222 225 2.288457 ACACCAGATGAGTCTTGTCGTG 60.288 50.000 0.62 0.62 28.51 4.35
223 226 1.337260 ACCAGATGAGTCTTGTCGTGC 60.337 52.381 0.00 0.00 30.42 5.34
224 227 1.337167 CCAGATGAGTCTTGTCGTGCA 60.337 52.381 0.00 0.00 30.42 4.57
225 228 2.407090 CAGATGAGTCTTGTCGTGCAA 58.593 47.619 0.00 0.00 35.50 4.08
226 229 2.802247 CAGATGAGTCTTGTCGTGCAAA 59.198 45.455 0.00 0.00 36.53 3.68
227 230 3.062763 AGATGAGTCTTGTCGTGCAAAG 58.937 45.455 0.00 0.00 36.53 2.77
228 231 2.595124 TGAGTCTTGTCGTGCAAAGA 57.405 45.000 0.00 0.00 36.53 2.52
229 232 3.111853 TGAGTCTTGTCGTGCAAAGAT 57.888 42.857 2.07 0.00 36.53 2.40
230 233 3.059884 TGAGTCTTGTCGTGCAAAGATC 58.940 45.455 2.07 2.86 36.53 2.75
231 234 2.061773 AGTCTTGTCGTGCAAAGATCG 58.938 47.619 2.07 0.00 36.53 3.69
232 235 1.792949 GTCTTGTCGTGCAAAGATCGT 59.207 47.619 2.07 0.00 36.53 3.73
233 236 2.984471 GTCTTGTCGTGCAAAGATCGTA 59.016 45.455 2.07 0.00 36.53 3.43
234 237 2.984471 TCTTGTCGTGCAAAGATCGTAC 59.016 45.455 0.00 0.00 36.53 3.67
235 238 2.425578 TGTCGTGCAAAGATCGTACA 57.574 45.000 0.00 0.00 0.00 2.90
236 239 2.954316 TGTCGTGCAAAGATCGTACAT 58.046 42.857 0.00 0.00 0.00 2.29
237 240 4.099380 TGTCGTGCAAAGATCGTACATA 57.901 40.909 0.00 0.00 0.00 2.29
238 241 4.487019 TGTCGTGCAAAGATCGTACATAA 58.513 39.130 0.00 0.00 0.00 1.90
239 242 5.106442 TGTCGTGCAAAGATCGTACATAAT 58.894 37.500 0.00 0.00 0.00 1.28
240 243 5.579119 TGTCGTGCAAAGATCGTACATAATT 59.421 36.000 0.00 0.00 0.00 1.40
241 244 6.091577 TGTCGTGCAAAGATCGTACATAATTT 59.908 34.615 0.00 0.00 0.00 1.82
242 245 6.408039 GTCGTGCAAAGATCGTACATAATTTG 59.592 38.462 0.00 0.32 0.00 2.32
243 246 6.311690 TCGTGCAAAGATCGTACATAATTTGA 59.688 34.615 12.29 0.00 31.01 2.69
244 247 7.011016 TCGTGCAAAGATCGTACATAATTTGAT 59.989 33.333 12.29 0.00 31.01 2.57
245 248 7.318909 CGTGCAAAGATCGTACATAATTTGATC 59.681 37.037 12.29 5.91 36.55 2.92
246 249 7.318909 GTGCAAAGATCGTACATAATTTGATCG 59.681 37.037 12.29 0.00 40.21 3.69
247 250 7.011016 TGCAAAGATCGTACATAATTTGATCGT 59.989 33.333 12.29 2.41 40.21 3.73
248 251 8.484799 GCAAAGATCGTACATAATTTGATCGTA 58.515 33.333 12.29 0.00 40.21 3.43
249 252 9.779237 CAAAGATCGTACATAATTTGATCGTAC 57.221 33.333 0.00 0.00 40.21 3.67
256 259 8.510714 CGTACATAATTTGATCGTACGTATAGC 58.489 37.037 16.05 0.00 46.23 2.97
257 260 9.333497 GTACATAATTTGATCGTACGTATAGCA 57.667 33.333 16.05 1.77 0.00 3.49
258 261 8.449085 ACATAATTTGATCGTACGTATAGCAG 57.551 34.615 16.05 0.84 0.00 4.24
259 262 5.824243 AATTTGATCGTACGTATAGCAGC 57.176 39.130 16.05 0.00 0.00 5.25
260 263 4.563337 TTTGATCGTACGTATAGCAGCT 57.437 40.909 16.05 0.00 0.00 4.24
261 264 3.808116 TGATCGTACGTATAGCAGCTC 57.192 47.619 16.05 0.90 0.00 4.09
262 265 3.400255 TGATCGTACGTATAGCAGCTCT 58.600 45.455 16.05 0.00 0.00 4.09
263 266 3.432592 TGATCGTACGTATAGCAGCTCTC 59.567 47.826 16.05 0.00 0.00 3.20
465 473 5.898174 TCGACAGATGAAACATTACGGTAT 58.102 37.500 0.00 0.00 0.00 2.73
750 831 2.280524 CCACGGCAAGTCGTTCCA 60.281 61.111 0.00 0.00 41.86 3.53
1374 1659 5.398122 ACAAAACGATTCGCAAAATGTACAG 59.602 36.000 5.86 0.00 0.00 2.74
1581 1869 1.133606 GGAAAGGAACAACTGACCCCA 60.134 52.381 0.00 0.00 0.00 4.96
1845 2137 1.420430 AGTTTTCAGAGGACCCGTGA 58.580 50.000 0.00 0.00 0.00 4.35
2392 2695 5.129485 ACACATCGATGTAATCCCTTCTTCT 59.871 40.000 29.52 0.00 41.39 2.85
2393 2696 6.051717 CACATCGATGTAATCCCTTCTTCTT 58.948 40.000 29.52 0.00 41.39 2.52
2394 2697 6.201806 CACATCGATGTAATCCCTTCTTCTTC 59.798 42.308 29.52 0.00 41.39 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 7.739825 ACACTACATATGTATTTGATGGAGCT 58.260 34.615 22.51 0.00 35.28 4.09
79 80 9.935682 GTATGATTTGTTTGGACACTACATATG 57.064 33.333 0.00 0.00 34.98 1.78
120 123 1.990799 TCGTACATGAGGCAGTTTCG 58.009 50.000 0.00 0.00 0.00 3.46
121 124 3.786635 AGATCGTACATGAGGCAGTTTC 58.213 45.455 0.00 0.00 0.00 2.78
122 125 3.895232 AGATCGTACATGAGGCAGTTT 57.105 42.857 0.00 0.00 0.00 2.66
123 126 5.537300 AATAGATCGTACATGAGGCAGTT 57.463 39.130 0.00 0.00 0.00 3.16
124 127 6.434340 TGATAATAGATCGTACATGAGGCAGT 59.566 38.462 0.00 0.00 0.00 4.40
125 128 6.856895 TGATAATAGATCGTACATGAGGCAG 58.143 40.000 0.00 0.00 0.00 4.85
126 129 6.834168 TGATAATAGATCGTACATGAGGCA 57.166 37.500 0.00 0.00 0.00 4.75
127 130 7.588123 CGTATGATAATAGATCGTACATGAGGC 59.412 40.741 14.25 0.00 39.34 4.70
128 131 8.827677 TCGTATGATAATAGATCGTACATGAGG 58.172 37.037 14.25 0.00 39.34 3.86
136 139 9.486857 CGTACAAATCGTATGATAATAGATCGT 57.513 33.333 0.00 0.00 39.14 3.73
137 140 9.698617 TCGTACAAATCGTATGATAATAGATCG 57.301 33.333 0.00 0.00 40.49 3.69
143 146 9.181805 CTCTTGTCGTACAAATCGTATGATAAT 57.818 33.333 0.00 0.00 45.62 1.28
144 147 8.400186 TCTCTTGTCGTACAAATCGTATGATAA 58.600 33.333 0.00 0.00 45.62 1.75
145 148 7.854422 GTCTCTTGTCGTACAAATCGTATGATA 59.146 37.037 0.00 0.00 45.62 2.15
146 149 6.691818 GTCTCTTGTCGTACAAATCGTATGAT 59.308 38.462 0.00 0.00 45.62 2.45
147 150 6.025896 GTCTCTTGTCGTACAAATCGTATGA 58.974 40.000 0.00 0.00 42.63 2.15
148 151 5.798434 TGTCTCTTGTCGTACAAATCGTATG 59.202 40.000 0.00 0.00 37.69 2.39
149 152 5.946298 TGTCTCTTGTCGTACAAATCGTAT 58.054 37.500 0.00 0.00 37.69 3.06
150 153 5.361135 TGTCTCTTGTCGTACAAATCGTA 57.639 39.130 0.00 0.00 37.69 3.43
151 154 4.227538 CTGTCTCTTGTCGTACAAATCGT 58.772 43.478 0.00 0.00 37.69 3.73
152 155 3.608506 CCTGTCTCTTGTCGTACAAATCG 59.391 47.826 0.00 0.00 37.69 3.34
153 156 3.368236 GCCTGTCTCTTGTCGTACAAATC 59.632 47.826 0.00 0.00 37.69 2.17
154 157 3.326747 GCCTGTCTCTTGTCGTACAAAT 58.673 45.455 0.00 0.00 37.69 2.32
155 158 2.547218 GGCCTGTCTCTTGTCGTACAAA 60.547 50.000 0.00 0.00 37.69 2.83
156 159 1.000506 GGCCTGTCTCTTGTCGTACAA 59.999 52.381 0.00 0.00 36.54 2.41
157 160 0.601558 GGCCTGTCTCTTGTCGTACA 59.398 55.000 0.00 0.00 0.00 2.90
158 161 0.889306 AGGCCTGTCTCTTGTCGTAC 59.111 55.000 3.11 0.00 0.00 3.67
159 162 0.888619 CAGGCCTGTCTCTTGTCGTA 59.111 55.000 25.53 0.00 0.00 3.43
160 163 1.115930 ACAGGCCTGTCTCTTGTCGT 61.116 55.000 33.20 5.90 40.24 4.34
161 164 0.034059 AACAGGCCTGTCTCTTGTCG 59.966 55.000 37.75 8.46 44.13 4.35
162 165 2.147150 GAAACAGGCCTGTCTCTTGTC 58.853 52.381 37.75 22.22 44.13 3.18
163 166 1.202818 GGAAACAGGCCTGTCTCTTGT 60.203 52.381 37.75 19.30 44.13 3.16
164 167 1.072965 AGGAAACAGGCCTGTCTCTTG 59.927 52.381 37.75 11.91 44.13 3.02
165 168 1.072965 CAGGAAACAGGCCTGTCTCTT 59.927 52.381 37.75 27.73 46.19 2.85
166 169 0.689623 CAGGAAACAGGCCTGTCTCT 59.310 55.000 37.75 28.66 46.19 3.10
167 170 3.239861 CAGGAAACAGGCCTGTCTC 57.760 57.895 37.75 32.77 46.19 3.36
172 175 0.853530 AAACCTCAGGAAACAGGCCT 59.146 50.000 0.00 0.00 35.75 5.19
173 176 0.961753 CAAACCTCAGGAAACAGGCC 59.038 55.000 0.00 0.00 32.32 5.19
174 177 0.961753 CCAAACCTCAGGAAACAGGC 59.038 55.000 0.00 0.00 32.32 4.85
175 178 1.620822 CCCAAACCTCAGGAAACAGG 58.379 55.000 0.00 0.00 35.69 4.00
176 179 0.961753 GCCCAAACCTCAGGAAACAG 59.038 55.000 0.00 0.00 0.00 3.16
177 180 0.469144 GGCCCAAACCTCAGGAAACA 60.469 55.000 0.00 0.00 0.00 2.83
178 181 1.185618 GGGCCCAAACCTCAGGAAAC 61.186 60.000 19.95 0.00 0.00 2.78
179 182 1.155155 GGGCCCAAACCTCAGGAAA 59.845 57.895 19.95 0.00 0.00 3.13
180 183 2.088096 TGGGCCCAAACCTCAGGAA 61.088 57.895 26.33 0.00 0.00 3.36
181 184 2.451493 TGGGCCCAAACCTCAGGA 60.451 61.111 26.33 0.00 0.00 3.86
182 185 2.283173 GTGGGCCCAAACCTCAGG 60.283 66.667 30.64 0.00 0.00 3.86
183 186 2.283173 GGTGGGCCCAAACCTCAG 60.283 66.667 30.64 0.00 33.40 3.35
184 187 3.106609 TGGTGGGCCCAAACCTCA 61.107 61.111 30.64 16.92 41.50 3.86
192 195 3.661648 ATCTGGTGTGGTGGGCCC 61.662 66.667 17.59 17.59 0.00 5.80
193 196 2.361610 CATCTGGTGTGGTGGGCC 60.362 66.667 0.00 0.00 0.00 5.80
194 197 1.377725 CTCATCTGGTGTGGTGGGC 60.378 63.158 0.00 0.00 0.00 5.36
195 198 0.036010 GACTCATCTGGTGTGGTGGG 60.036 60.000 0.00 0.00 0.00 4.61
196 199 0.979665 AGACTCATCTGGTGTGGTGG 59.020 55.000 0.00 0.00 32.29 4.61
197 200 2.224378 ACAAGACTCATCTGGTGTGGTG 60.224 50.000 0.00 0.00 37.75 4.17
198 201 2.037772 GACAAGACTCATCTGGTGTGGT 59.962 50.000 0.00 0.00 39.42 4.16
199 202 2.693069 GACAAGACTCATCTGGTGTGG 58.307 52.381 0.00 0.00 39.42 4.17
200 203 2.288457 ACGACAAGACTCATCTGGTGTG 60.288 50.000 0.00 0.00 39.42 3.82
201 204 1.964223 ACGACAAGACTCATCTGGTGT 59.036 47.619 0.00 0.00 39.42 4.16
202 205 2.332104 CACGACAAGACTCATCTGGTG 58.668 52.381 0.00 0.00 39.42 4.17
203 206 1.337260 GCACGACAAGACTCATCTGGT 60.337 52.381 0.00 0.00 42.30 4.00
204 207 1.337167 TGCACGACAAGACTCATCTGG 60.337 52.381 0.00 0.00 34.48 3.86
205 208 2.070262 TGCACGACAAGACTCATCTG 57.930 50.000 0.00 0.00 34.48 2.90
206 209 2.820059 TTGCACGACAAGACTCATCT 57.180 45.000 0.00 0.00 36.42 2.90
207 210 3.059884 TCTTTGCACGACAAGACTCATC 58.940 45.455 0.00 0.00 40.06 2.92
208 211 3.111853 TCTTTGCACGACAAGACTCAT 57.888 42.857 0.00 0.00 40.06 2.90
209 212 2.595124 TCTTTGCACGACAAGACTCA 57.405 45.000 0.00 0.00 40.06 3.41
210 213 2.091277 CGATCTTTGCACGACAAGACTC 59.909 50.000 0.72 1.15 40.06 3.36
211 214 2.061773 CGATCTTTGCACGACAAGACT 58.938 47.619 0.72 0.00 40.06 3.24
212 215 1.792949 ACGATCTTTGCACGACAAGAC 59.207 47.619 0.72 0.00 40.06 3.01
213 216 2.148916 ACGATCTTTGCACGACAAGA 57.851 45.000 1.21 1.21 40.06 3.02
214 217 2.729360 TGTACGATCTTTGCACGACAAG 59.271 45.455 0.24 0.00 40.06 3.16
215 218 2.745102 TGTACGATCTTTGCACGACAA 58.255 42.857 0.24 0.00 36.13 3.18
216 219 2.425578 TGTACGATCTTTGCACGACA 57.574 45.000 0.24 0.00 0.00 4.35
217 220 5.637104 ATTATGTACGATCTTTGCACGAC 57.363 39.130 0.24 0.00 0.00 4.34
218 221 6.311690 TCAAATTATGTACGATCTTTGCACGA 59.688 34.615 0.24 0.00 0.00 4.35
219 222 6.474364 TCAAATTATGTACGATCTTTGCACG 58.526 36.000 0.00 0.00 0.00 5.34
220 223 7.318909 CGATCAAATTATGTACGATCTTTGCAC 59.681 37.037 0.00 3.44 32.16 4.57
221 224 7.011016 ACGATCAAATTATGTACGATCTTTGCA 59.989 33.333 0.00 0.00 34.67 4.08
222 225 7.345192 ACGATCAAATTATGTACGATCTTTGC 58.655 34.615 0.00 0.00 34.67 3.68
223 226 9.779237 GTACGATCAAATTATGTACGATCTTTG 57.221 33.333 0.00 5.07 34.67 2.77
231 234 9.333497 TGCTATACGTACGATCAAATTATGTAC 57.667 33.333 24.41 2.68 33.74 2.90
232 235 9.550811 CTGCTATACGTACGATCAAATTATGTA 57.449 33.333 24.41 0.00 0.00 2.29
233 236 7.061905 GCTGCTATACGTACGATCAAATTATGT 59.938 37.037 24.41 0.00 0.00 2.29
234 237 7.273598 AGCTGCTATACGTACGATCAAATTATG 59.726 37.037 24.41 3.95 0.00 1.90
235 238 7.313646 AGCTGCTATACGTACGATCAAATTAT 58.686 34.615 24.41 9.74 0.00 1.28
236 239 6.675026 AGCTGCTATACGTACGATCAAATTA 58.325 36.000 24.41 1.68 0.00 1.40
237 240 5.529791 AGCTGCTATACGTACGATCAAATT 58.470 37.500 24.41 0.00 0.00 1.82
238 241 5.048643 AGAGCTGCTATACGTACGATCAAAT 60.049 40.000 24.41 9.29 0.00 2.32
239 242 4.275196 AGAGCTGCTATACGTACGATCAAA 59.725 41.667 24.41 1.85 0.00 2.69
240 243 3.813724 AGAGCTGCTATACGTACGATCAA 59.186 43.478 24.41 4.52 0.00 2.57
241 244 3.400255 AGAGCTGCTATACGTACGATCA 58.600 45.455 24.41 6.86 0.00 2.92
242 245 3.432592 TGAGAGCTGCTATACGTACGATC 59.567 47.826 24.41 6.19 0.00 3.69
243 246 3.400255 TGAGAGCTGCTATACGTACGAT 58.600 45.455 24.41 13.27 0.00 3.73
244 247 2.830104 TGAGAGCTGCTATACGTACGA 58.170 47.619 24.41 6.04 0.00 3.43
245 248 3.604065 TTGAGAGCTGCTATACGTACG 57.396 47.619 15.01 15.01 0.00 3.67
246 249 5.977725 TCAAATTGAGAGCTGCTATACGTAC 59.022 40.000 0.15 0.00 0.00 3.67
247 250 6.144078 TCAAATTGAGAGCTGCTATACGTA 57.856 37.500 0.15 0.00 0.00 3.57
248 251 5.011090 TCAAATTGAGAGCTGCTATACGT 57.989 39.130 0.15 0.00 0.00 3.57
249 252 5.521735 ACTTCAAATTGAGAGCTGCTATACG 59.478 40.000 0.15 0.00 0.00 3.06
250 253 6.917217 ACTTCAAATTGAGAGCTGCTATAC 57.083 37.500 0.15 0.00 0.00 1.47
251 254 7.555965 TGTACTTCAAATTGAGAGCTGCTATA 58.444 34.615 0.15 0.00 0.00 1.31
252 255 6.409704 TGTACTTCAAATTGAGAGCTGCTAT 58.590 36.000 0.15 0.00 0.00 2.97
253 256 5.793817 TGTACTTCAAATTGAGAGCTGCTA 58.206 37.500 0.15 0.00 0.00 3.49
254 257 4.645535 TGTACTTCAAATTGAGAGCTGCT 58.354 39.130 0.00 0.00 0.00 4.24
255 258 4.692625 TCTGTACTTCAAATTGAGAGCTGC 59.307 41.667 0.00 0.00 0.00 5.25
256 259 6.981762 ATCTGTACTTCAAATTGAGAGCTG 57.018 37.500 0.00 0.00 0.00 4.24
257 260 8.535335 TCTAATCTGTACTTCAAATTGAGAGCT 58.465 33.333 0.00 0.00 0.00 4.09
258 261 8.599774 GTCTAATCTGTACTTCAAATTGAGAGC 58.400 37.037 0.00 0.00 0.00 4.09
259 262 9.868277 AGTCTAATCTGTACTTCAAATTGAGAG 57.132 33.333 0.00 0.31 0.00 3.20
260 263 9.645059 CAGTCTAATCTGTACTTCAAATTGAGA 57.355 33.333 0.00 0.00 0.00 3.27
261 264 9.645059 TCAGTCTAATCTGTACTTCAAATTGAG 57.355 33.333 0.00 0.00 36.85 3.02
365 371 2.340328 GGTCGTGGGCAATGGAACC 61.340 63.158 0.00 0.00 0.00 3.62
465 473 4.899457 CAGGTCCCCAGAACTACATGTATA 59.101 45.833 5.91 0.00 38.27 1.47
750 831 4.578898 TGCTGTCGCGTGGTCGTT 62.579 61.111 5.77 0.00 39.65 3.85
1191 1469 1.970917 GAAGGGACGCTGCATGTTCG 61.971 60.000 0.00 0.00 0.00 3.95
1374 1659 4.174762 CGGAGGCTGTAGAGTTAAGTTTC 58.825 47.826 0.00 0.00 0.00 2.78
1480 1768 2.149578 GCTGACAGAGTGCAGAACATT 58.850 47.619 6.65 0.00 34.06 2.71
1581 1869 9.628500 GAAAGAGGTATTTATGTGGTAAAGGAT 57.372 33.333 0.00 0.00 35.83 3.24
1644 1933 1.067364 TCAGTGTTCAACTACGCCGAA 59.933 47.619 0.00 0.00 36.83 4.30
1845 2137 4.563061 GTTTTGCAATCCATCTCAAGCTT 58.437 39.130 0.00 0.00 0.00 3.74
2235 2535 5.041940 CGCACAACTATCCTCCTACTTAAC 58.958 45.833 0.00 0.00 0.00 2.01
2392 2695 9.621629 TGTTCTTTTATTTAGTTCTGTGAGGAA 57.378 29.630 0.00 0.00 0.00 3.36
2393 2696 9.052759 GTGTTCTTTTATTTAGTTCTGTGAGGA 57.947 33.333 0.00 0.00 0.00 3.71
2394 2697 8.836413 TGTGTTCTTTTATTTAGTTCTGTGAGG 58.164 33.333 0.00 0.00 0.00 3.86
2441 2744 6.619801 AGTCCTGTGTGTTCTTTTATTCAC 57.380 37.500 0.00 0.00 0.00 3.18
2537 2840 8.279970 TGTATTTGATTCTGTTGAATACCCAG 57.720 34.615 0.00 0.00 42.43 4.45


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.