Multiple sequence alignment - TraesCS6B01G258200

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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 TraesCS6B01G258200 chr6B 100.000 2969 0 0 1 2969 463401283 463404251 0.000000e+00 5483.0
1 TraesCS6B01G258200 chr6B 97.914 2493 43 8 360 2847 132949366 132946878 0.000000e+00 4307.0
2 TraesCS6B01G258200 chr6B 89.731 1821 125 27 991 2805 536157639 536155875 0.000000e+00 2270.0
3 TraesCS6B01G258200 chr6B 86.449 214 17 11 439 652 536157870 536157669 1.070000e-54 224.0
4 TraesCS6B01G258200 chr5A 96.997 2564 61 12 361 2913 680744136 680746694 0.000000e+00 4294.0
5 TraesCS6B01G258200 chr5A 95.198 354 17 0 1 354 544229312 544229665 7.190000e-156 560.0
6 TraesCS6B01G258200 chr5A 94.721 341 18 0 1 341 549294646 549294306 5.630000e-147 531.0
7 TraesCS6B01G258200 chr5A 94.135 341 20 0 1 341 549315267 549314927 1.220000e-143 520.0
8 TraesCS6B01G258200 chr7A 99.279 2359 17 0 447 2805 9493199 9490841 0.000000e+00 4263.0
9 TraesCS6B01G258200 chr7A 82.188 320 36 17 101 408 13396662 13396972 3.800000e-64 255.0
10 TraesCS6B01G258200 chr7A 87.143 140 5 13 258 397 56199442 56199316 2.380000e-31 147.0
11 TraesCS6B01G258200 chr4B 96.322 2556 53 10 400 2921 245452923 245455471 0.000000e+00 4161.0
12 TraesCS6B01G258200 chr1A 99.274 1929 14 0 429 2357 517178424 517180352 0.000000e+00 3485.0
13 TraesCS6B01G258200 chr3B 87.988 2406 167 57 406 2805 145883009 145880720 0.000000e+00 2730.0
14 TraesCS6B01G258200 chr3B 99.413 341 2 0 1 341 736491878 736492218 1.170000e-173 619.0
15 TraesCS6B01G258200 chr3B 95.044 343 15 1 1 341 609326681 609326339 3.370000e-149 538.0
16 TraesCS6B01G258200 chr3B 96.774 155 4 1 2813 2966 431146087 431146241 1.060000e-64 257.0
17 TraesCS6B01G258200 chr3B 94.231 156 7 2 2813 2966 431126249 431126404 1.380000e-58 237.0
18 TraesCS6B01G258200 chr3B 93.210 162 9 2 2805 2965 686698201 686698361 1.380000e-58 237.0
19 TraesCS6B01G258200 chr3B 91.870 123 5 5 258 379 736483296 736483414 1.830000e-37 167.0
20 TraesCS6B01G258200 chr3B 81.373 102 13 6 426 524 773733962 773733864 8.820000e-11 78.7
21 TraesCS6B01G258200 chr2B 89.711 1837 125 28 976 2805 706803192 706801413 0.000000e+00 2287.0
22 TraesCS6B01G258200 chr2B 97.965 344 6 1 1 344 622910654 622910996 1.970000e-166 595.0
23 TraesCS6B01G258200 chr2B 94.215 363 17 4 1 363 690782289 690782647 4.330000e-153 551.0
24 TraesCS6B01G258200 chr2B 91.830 306 21 4 625 929 706803998 706803696 9.840000e-115 424.0
25 TraesCS6B01G258200 chr2B 89.151 212 12 10 441 652 706804143 706803943 1.370000e-63 254.0
26 TraesCS6B01G258200 chr2B 90.000 190 13 5 2780 2964 340551466 340551654 1.060000e-59 241.0
27 TraesCS6B01G258200 chr2B 92.025 163 12 1 2805 2966 584101928 584102090 8.280000e-56 228.0
28 TraesCS6B01G258200 chr2B 82.906 234 23 13 159 379 127182295 127182524 8.400000e-46 195.0
29 TraesCS6B01G258200 chr7B 84.384 1364 147 33 1454 2805 610363571 610364880 0.000000e+00 1279.0
30 TraesCS6B01G258200 chr7B 80.042 942 120 33 448 1366 610360874 610361770 1.160000e-178 636.0
31 TraesCS6B01G258200 chr7B 91.005 189 12 3 2786 2969 220958944 220958756 1.770000e-62 250.0
32 TraesCS6B01G258200 chr7B 91.617 167 10 4 2806 2969 747168692 747168527 8.280000e-56 228.0
33 TraesCS6B01G258200 chr5D 93.483 844 52 2 1961 2804 22455910 22456750 0.000000e+00 1251.0
34 TraesCS6B01G258200 chr3D 91.930 855 57 8 1958 2805 159125439 159126288 0.000000e+00 1186.0
35 TraesCS6B01G258200 chr3D 94.842 349 17 1 1 349 434915593 434915246 7.240000e-151 544.0
36 TraesCS6B01G258200 chr3D 89.726 146 8 7 258 402 32153145 32153284 2.350000e-41 180.0
37 TraesCS6B01G258200 chr3D 91.346 104 0 8 304 402 53821727 53821628 1.860000e-27 134.0
38 TraesCS6B01G258200 chr2A 86.977 860 87 10 927 1770 545739371 545738521 0.000000e+00 944.0
39 TraesCS6B01G258200 chr1D 80.840 1310 154 58 447 1715 404274534 404275787 0.000000e+00 939.0
40 TraesCS6B01G258200 chr1D 84.559 272 27 10 127 388 164852734 164852468 3.800000e-64 255.0
41 TraesCS6B01G258200 chr4A 83.793 907 113 22 1914 2805 699588360 699589247 0.000000e+00 830.0
42 TraesCS6B01G258200 chr4A 95.601 341 15 0 1 341 701695412 701695072 5.600000e-152 547.0
43 TraesCS6B01G258200 chr4A 93.038 158 10 1 2813 2969 737849435 737849278 2.300000e-56 230.0
44 TraesCS6B01G258200 chr5B 85.714 126 13 5 261 384 166668878 166668756 8.640000e-26 128.0
45 TraesCS6B01G258200 chr1B 84.127 126 4 13 341 463 675865023 675865135 1.130000e-19 108.0


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 TraesCS6B01G258200 chr6B 463401283 463404251 2968 False 5483.000000 5483 100.000000 1 2969 1 chr6B.!!$F1 2968
1 TraesCS6B01G258200 chr6B 132946878 132949366 2488 True 4307.000000 4307 97.914000 360 2847 1 chr6B.!!$R1 2487
2 TraesCS6B01G258200 chr6B 536155875 536157870 1995 True 1247.000000 2270 88.090000 439 2805 2 chr6B.!!$R2 2366
3 TraesCS6B01G258200 chr5A 680744136 680746694 2558 False 4294.000000 4294 96.997000 361 2913 1 chr5A.!!$F2 2552
4 TraesCS6B01G258200 chr7A 9490841 9493199 2358 True 4263.000000 4263 99.279000 447 2805 1 chr7A.!!$R1 2358
5 TraesCS6B01G258200 chr4B 245452923 245455471 2548 False 4161.000000 4161 96.322000 400 2921 1 chr4B.!!$F1 2521
6 TraesCS6B01G258200 chr1A 517178424 517180352 1928 False 3485.000000 3485 99.274000 429 2357 1 chr1A.!!$F1 1928
7 TraesCS6B01G258200 chr3B 145880720 145883009 2289 True 2730.000000 2730 87.988000 406 2805 1 chr3B.!!$R1 2399
8 TraesCS6B01G258200 chr2B 706801413 706804143 2730 True 988.333333 2287 90.230667 441 2805 3 chr2B.!!$R1 2364
9 TraesCS6B01G258200 chr7B 610360874 610364880 4006 False 957.500000 1279 82.213000 448 2805 2 chr7B.!!$F1 2357
10 TraesCS6B01G258200 chr5D 22455910 22456750 840 False 1251.000000 1251 93.483000 1961 2804 1 chr5D.!!$F1 843
11 TraesCS6B01G258200 chr3D 159125439 159126288 849 False 1186.000000 1186 91.930000 1958 2805 1 chr3D.!!$F2 847
12 TraesCS6B01G258200 chr2A 545738521 545739371 850 True 944.000000 944 86.977000 927 1770 1 chr2A.!!$R1 843
13 TraesCS6B01G258200 chr1D 404274534 404275787 1253 False 939.000000 939 80.840000 447 1715 1 chr1D.!!$F1 1268
14 TraesCS6B01G258200 chr4A 699588360 699589247 887 False 830.000000 830 83.793000 1914 2805 1 chr4A.!!$F1 891

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
338 339 0.037139 ACGCACGGGCATTTGTACTA 60.037 50.0 11.77 0.0 41.24 1.82 F
339 340 0.650512 CGCACGGGCATTTGTACTAG 59.349 55.0 11.77 0.0 41.24 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 3941 1.065491 TGCTTGCCTTATCCACATCGT 60.065 47.619 0.0 0.0 0.0 3.73 R
2469 4804 4.661125 TGCGAAAGTAATTGTGCATCATC 58.339 39.130 0.0 0.0 0.0 2.92 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
22 23 3.824414 ATTCCGAAAAATGACCGTCAC 57.176 42.857 2.57 0.00 0.00 3.67
23 24 1.515081 TCCGAAAAATGACCGTCACC 58.485 50.000 2.57 0.00 0.00 4.02
24 25 1.202663 TCCGAAAAATGACCGTCACCA 60.203 47.619 2.57 0.00 0.00 4.17
25 26 1.810151 CCGAAAAATGACCGTCACCAT 59.190 47.619 2.57 0.00 0.00 3.55
26 27 3.004171 CCGAAAAATGACCGTCACCATA 58.996 45.455 2.57 0.00 0.00 2.74
27 28 3.437395 CCGAAAAATGACCGTCACCATAA 59.563 43.478 2.57 0.00 0.00 1.90
28 29 4.083217 CCGAAAAATGACCGTCACCATAAA 60.083 41.667 2.57 0.00 0.00 1.40
29 30 5.453648 CGAAAAATGACCGTCACCATAAAA 58.546 37.500 2.57 0.00 0.00 1.52
30 31 5.915758 CGAAAAATGACCGTCACCATAAAAA 59.084 36.000 2.57 0.00 0.00 1.94
31 32 6.584563 CGAAAAATGACCGTCACCATAAAAAT 59.415 34.615 2.57 0.00 0.00 1.82
32 33 7.751348 CGAAAAATGACCGTCACCATAAAAATA 59.249 33.333 2.57 0.00 0.00 1.40
33 34 9.413048 GAAAAATGACCGTCACCATAAAAATAA 57.587 29.630 2.57 0.00 0.00 1.40
34 35 9.936759 AAAAATGACCGTCACCATAAAAATAAT 57.063 25.926 2.57 0.00 0.00 1.28
35 36 9.936759 AAAATGACCGTCACCATAAAAATAATT 57.063 25.926 2.57 0.00 0.00 1.40
36 37 9.581099 AAATGACCGTCACCATAAAAATAATTC 57.419 29.630 2.57 0.00 0.00 2.17
37 38 7.090953 TGACCGTCACCATAAAAATAATTCC 57.909 36.000 0.00 0.00 0.00 3.01
38 39 6.659668 TGACCGTCACCATAAAAATAATTCCA 59.340 34.615 0.00 0.00 0.00 3.53
39 40 7.340743 TGACCGTCACCATAAAAATAATTCCAT 59.659 33.333 0.00 0.00 0.00 3.41
40 41 7.712797 ACCGTCACCATAAAAATAATTCCATC 58.287 34.615 0.00 0.00 0.00 3.51
41 42 7.559897 ACCGTCACCATAAAAATAATTCCATCT 59.440 33.333 0.00 0.00 0.00 2.90
42 43 8.413229 CCGTCACCATAAAAATAATTCCATCTT 58.587 33.333 0.00 0.00 0.00 2.40
43 44 9.450807 CGTCACCATAAAAATAATTCCATCTTC 57.549 33.333 0.00 0.00 0.00 2.87
94 95 9.495572 AAACACCTTTTCAAAGTACAAAAATGA 57.504 25.926 0.00 0.00 34.20 2.57
95 96 9.665719 AACACCTTTTCAAAGTACAAAAATGAT 57.334 25.926 0.00 0.00 34.20 2.45
96 97 9.313118 ACACCTTTTCAAAGTACAAAAATGATC 57.687 29.630 0.00 0.00 34.20 2.92
97 98 9.311916 CACCTTTTCAAAGTACAAAAATGATCA 57.688 29.630 0.00 0.00 34.20 2.92
142 143 9.429109 TCCATACACAACTACTATTTCATAGGA 57.571 33.333 0.00 0.00 37.18 2.94
160 161 8.687292 TCATAGGATGAAATGAAAATGAGGAG 57.313 34.615 0.00 0.00 36.11 3.69
161 162 5.848833 AGGATGAAATGAAAATGAGGAGC 57.151 39.130 0.00 0.00 0.00 4.70
162 163 5.516984 AGGATGAAATGAAAATGAGGAGCT 58.483 37.500 0.00 0.00 0.00 4.09
163 164 5.360144 AGGATGAAATGAAAATGAGGAGCTG 59.640 40.000 0.00 0.00 0.00 4.24
164 165 5.359009 GGATGAAATGAAAATGAGGAGCTGA 59.641 40.000 0.00 0.00 0.00 4.26
165 166 6.127535 GGATGAAATGAAAATGAGGAGCTGAA 60.128 38.462 0.00 0.00 0.00 3.02
166 167 6.653526 TGAAATGAAAATGAGGAGCTGAAA 57.346 33.333 0.00 0.00 0.00 2.69
167 168 7.235935 TGAAATGAAAATGAGGAGCTGAAAT 57.764 32.000 0.00 0.00 0.00 2.17
168 169 8.352137 TGAAATGAAAATGAGGAGCTGAAATA 57.648 30.769 0.00 0.00 0.00 1.40
169 170 8.464404 TGAAATGAAAATGAGGAGCTGAAATAG 58.536 33.333 0.00 0.00 0.00 1.73
170 171 6.956202 ATGAAAATGAGGAGCTGAAATAGG 57.044 37.500 0.00 0.00 0.00 2.57
171 172 5.819991 TGAAAATGAGGAGCTGAAATAGGT 58.180 37.500 0.00 0.00 40.52 3.08
184 185 8.757982 AGCTGAAATAGGTCATGATAAACATT 57.242 30.769 0.00 0.00 37.07 2.71
185 186 8.627403 AGCTGAAATAGGTCATGATAAACATTG 58.373 33.333 0.00 0.00 37.07 2.82
186 187 8.408601 GCTGAAATAGGTCATGATAAACATTGT 58.591 33.333 0.00 0.00 37.07 2.71
192 193 9.920946 ATAGGTCATGATAAACATTGTTAAGGT 57.079 29.630 1.76 0.00 37.07 3.50
194 195 9.174166 AGGTCATGATAAACATTGTTAAGGTAC 57.826 33.333 1.76 0.00 37.07 3.34
195 196 8.952278 GGTCATGATAAACATTGTTAAGGTACA 58.048 33.333 1.76 0.00 37.07 2.90
213 214 7.095695 AGGTACATAAAAATTTCATGGTCCG 57.904 36.000 14.09 0.00 0.00 4.79
214 215 6.887545 AGGTACATAAAAATTTCATGGTCCGA 59.112 34.615 14.09 0.00 0.00 4.55
215 216 7.394923 AGGTACATAAAAATTTCATGGTCCGAA 59.605 33.333 14.09 0.00 0.00 4.30
216 217 8.030106 GGTACATAAAAATTTCATGGTCCGAAA 58.970 33.333 14.09 0.00 36.83 3.46
217 218 9.413048 GTACATAAAAATTTCATGGTCCGAAAA 57.587 29.630 14.09 0.00 36.06 2.29
218 219 8.532977 ACATAAAAATTTCATGGTCCGAAAAG 57.467 30.769 14.09 0.00 36.06 2.27
219 220 8.364142 ACATAAAAATTTCATGGTCCGAAAAGA 58.636 29.630 14.09 0.00 36.06 2.52
220 221 9.202273 CATAAAAATTTCATGGTCCGAAAAGAA 57.798 29.630 0.00 0.00 36.06 2.52
221 222 9.771534 ATAAAAATTTCATGGTCCGAAAAGAAA 57.228 25.926 0.00 0.00 36.06 2.52
222 223 8.675705 AAAAATTTCATGGTCCGAAAAGAAAT 57.324 26.923 0.00 0.00 37.31 2.17
223 224 9.771534 AAAAATTTCATGGTCCGAAAAGAAATA 57.228 25.926 0.00 0.00 35.38 1.40
224 225 8.757164 AAATTTCATGGTCCGAAAAGAAATAC 57.243 30.769 0.00 0.00 35.38 1.89
225 226 7.703058 ATTTCATGGTCCGAAAAGAAATACT 57.297 32.000 0.00 0.00 36.06 2.12
226 227 6.737254 TTCATGGTCCGAAAAGAAATACTC 57.263 37.500 0.00 0.00 0.00 2.59
227 228 5.800296 TCATGGTCCGAAAAGAAATACTCA 58.200 37.500 0.00 0.00 0.00 3.41
228 229 5.874810 TCATGGTCCGAAAAGAAATACTCAG 59.125 40.000 0.00 0.00 0.00 3.35
229 230 5.223449 TGGTCCGAAAAGAAATACTCAGT 57.777 39.130 0.00 0.00 0.00 3.41
230 231 4.994852 TGGTCCGAAAAGAAATACTCAGTG 59.005 41.667 0.00 0.00 0.00 3.66
231 232 4.995487 GGTCCGAAAAGAAATACTCAGTGT 59.005 41.667 0.00 0.00 0.00 3.55
232 233 6.161381 GGTCCGAAAAGAAATACTCAGTGTA 58.839 40.000 0.00 0.00 35.37 2.90
233 234 6.647895 GGTCCGAAAAGAAATACTCAGTGTAA 59.352 38.462 0.00 0.00 34.45 2.41
234 235 7.359849 GGTCCGAAAAGAAATACTCAGTGTAAC 60.360 40.741 0.00 0.00 34.45 2.50
235 236 6.647895 TCCGAAAAGAAATACTCAGTGTAACC 59.352 38.462 0.00 0.00 37.80 2.85
236 237 6.649557 CCGAAAAGAAATACTCAGTGTAACCT 59.350 38.462 0.00 0.00 37.80 3.50
237 238 7.172703 CCGAAAAGAAATACTCAGTGTAACCTT 59.827 37.037 0.00 0.00 37.80 3.50
238 239 9.199982 CGAAAAGAAATACTCAGTGTAACCTTA 57.800 33.333 0.00 0.00 37.80 2.69
281 282 3.932545 AAAAAGTGTCGCATAATGGCA 57.067 38.095 0.00 0.00 0.00 4.92
282 283 2.919666 AAAGTGTCGCATAATGGCAC 57.080 45.000 0.00 0.00 0.00 5.01
332 333 3.600694 TGCAACGCACGGGCATTT 61.601 55.556 11.77 0.00 41.24 2.32
333 334 3.105157 GCAACGCACGGGCATTTG 61.105 61.111 11.77 13.80 41.24 2.32
334 335 2.334653 CAACGCACGGGCATTTGT 59.665 55.556 11.77 0.00 41.24 2.83
335 336 1.576920 CAACGCACGGGCATTTGTA 59.423 52.632 11.77 0.00 41.24 2.41
336 337 0.727793 CAACGCACGGGCATTTGTAC 60.728 55.000 11.77 0.00 41.24 2.90
337 338 0.887387 AACGCACGGGCATTTGTACT 60.887 50.000 11.77 0.00 41.24 2.73
338 339 0.037139 ACGCACGGGCATTTGTACTA 60.037 50.000 11.77 0.00 41.24 1.82
339 340 0.650512 CGCACGGGCATTTGTACTAG 59.349 55.000 11.77 0.00 41.24 2.57
340 341 1.734163 GCACGGGCATTTGTACTAGT 58.266 50.000 3.77 0.00 40.72 2.57
341 342 2.736081 CGCACGGGCATTTGTACTAGTA 60.736 50.000 11.77 0.00 41.24 1.82
342 343 3.264104 GCACGGGCATTTGTACTAGTAA 58.736 45.455 3.77 0.00 40.72 2.24
343 344 3.875134 GCACGGGCATTTGTACTAGTAAT 59.125 43.478 3.77 0.00 40.72 1.89
344 345 5.051816 GCACGGGCATTTGTACTAGTAATA 58.948 41.667 3.77 0.00 40.72 0.98
345 346 5.524646 GCACGGGCATTTGTACTAGTAATAA 59.475 40.000 3.77 2.43 40.72 1.40
346 347 6.204108 GCACGGGCATTTGTACTAGTAATAAT 59.796 38.462 3.77 4.72 40.72 1.28
347 348 7.385752 GCACGGGCATTTGTACTAGTAATAATA 59.614 37.037 3.77 0.00 40.72 0.98
348 349 9.263538 CACGGGCATTTGTACTAGTAATAATAA 57.736 33.333 3.61 0.00 0.00 1.40
1122 1695 2.742372 GTGCACCGCCAGTTCGAT 60.742 61.111 5.22 0.00 0.00 3.59
1640 3941 2.560542 GCTGAGTGAGAAGAAGGAGTGA 59.439 50.000 0.00 0.00 0.00 3.41
2382 4717 7.113437 TCCGTCCATCATATTTTTAAAGTGGA 58.887 34.615 0.00 0.00 32.48 4.02
2469 4804 5.412526 TTGAAACTGTTACAAGTAAGCGG 57.587 39.130 0.00 0.00 0.00 5.52
2805 5149 4.560856 GTTGCAACGCACGGGCAA 62.561 61.111 14.90 16.74 44.50 4.52
2807 5151 2.261586 TTGCAACGCACGGGCAATA 61.262 52.632 11.77 1.08 42.12 1.90
2808 5152 1.796190 TTGCAACGCACGGGCAATAA 61.796 50.000 11.77 0.00 42.12 1.40
2811 5158 1.202200 GCAACGCACGGGCAATAATAA 60.202 47.619 11.77 0.00 41.24 1.40
2842 5191 2.871096 AGAATTGGGTTTCTGCCGTA 57.129 45.000 0.00 0.00 34.68 4.02
2854 5203 4.650545 TTCTGCCGTACGTCATAAAAAC 57.349 40.909 15.21 0.00 0.00 2.43
2862 5211 4.496895 CGTACGTCATAAAAACTACCCTCG 59.503 45.833 7.22 0.00 0.00 4.63
2865 5214 5.540911 ACGTCATAAAAACTACCCTCGAAA 58.459 37.500 0.00 0.00 0.00 3.46
2870 5219 4.514781 AAAAACTACCCTCGAAATTGCC 57.485 40.909 0.00 0.00 0.00 4.52
2871 5220 2.124277 AACTACCCTCGAAATTGCCC 57.876 50.000 0.00 0.00 0.00 5.36
2899 5250 2.026262 ACCCACTATGCCACCTTAAGTG 60.026 50.000 0.97 0.29 46.83 3.16
2927 5278 8.980143 AAAAACGATTCAGTTCTTTTTCTTGA 57.020 26.923 0.00 0.00 32.43 3.02
2928 5279 8.980143 AAAACGATTCAGTTCTTTTTCTTGAA 57.020 26.923 0.00 0.00 32.43 2.69
2929 5280 8.620533 AAACGATTCAGTTCTTTTTCTTGAAG 57.379 30.769 0.00 0.00 32.43 3.02
2930 5281 6.729187 ACGATTCAGTTCTTTTTCTTGAAGG 58.271 36.000 0.00 0.00 0.00 3.46
2931 5282 5.626955 CGATTCAGTTCTTTTTCTTGAAGGC 59.373 40.000 0.00 0.00 0.00 4.35
2932 5283 4.918810 TCAGTTCTTTTTCTTGAAGGCC 57.081 40.909 0.00 0.00 0.00 5.19
2933 5284 3.315191 TCAGTTCTTTTTCTTGAAGGCCG 59.685 43.478 0.00 0.00 0.00 6.13
2934 5285 2.034685 AGTTCTTTTTCTTGAAGGCCGC 59.965 45.455 0.00 0.00 0.00 6.53
2935 5286 0.958822 TCTTTTTCTTGAAGGCCGCC 59.041 50.000 0.00 0.00 0.00 6.13
2936 5287 0.387239 CTTTTTCTTGAAGGCCGCCG 60.387 55.000 3.05 0.00 0.00 6.46
2937 5288 2.414840 TTTTTCTTGAAGGCCGCCGC 62.415 55.000 3.05 0.69 0.00 6.53
2950 5301 2.752640 GCCGCGGGGTTTGGTTAT 60.753 61.111 29.38 0.00 34.97 1.89
2951 5302 2.344981 GCCGCGGGGTTTGGTTATT 61.345 57.895 29.38 0.00 34.97 1.40
2952 5303 1.031029 GCCGCGGGGTTTGGTTATTA 61.031 55.000 29.38 0.00 34.97 0.98
2953 5304 1.682740 CCGCGGGGTTTGGTTATTAT 58.317 50.000 20.10 0.00 0.00 1.28
2954 5305 2.848691 CCGCGGGGTTTGGTTATTATA 58.151 47.619 20.10 0.00 0.00 0.98
2955 5306 2.809696 CCGCGGGGTTTGGTTATTATAG 59.190 50.000 20.10 0.00 0.00 1.31
2956 5307 3.494749 CCGCGGGGTTTGGTTATTATAGA 60.495 47.826 20.10 0.00 0.00 1.98
2957 5308 3.744426 CGCGGGGTTTGGTTATTATAGAG 59.256 47.826 0.00 0.00 0.00 2.43
2958 5309 4.711399 GCGGGGTTTGGTTATTATAGAGT 58.289 43.478 0.00 0.00 0.00 3.24
2959 5310 4.514066 GCGGGGTTTGGTTATTATAGAGTG 59.486 45.833 0.00 0.00 0.00 3.51
2960 5311 5.061179 CGGGGTTTGGTTATTATAGAGTGG 58.939 45.833 0.00 0.00 0.00 4.00
2961 5312 5.397109 CGGGGTTTGGTTATTATAGAGTGGT 60.397 44.000 0.00 0.00 0.00 4.16
2962 5313 6.183360 CGGGGTTTGGTTATTATAGAGTGGTA 60.183 42.308 0.00 0.00 0.00 3.25
2963 5314 6.994496 GGGGTTTGGTTATTATAGAGTGGTAC 59.006 42.308 0.00 0.00 0.00 3.34
2964 5315 6.994496 GGGTTTGGTTATTATAGAGTGGTACC 59.006 42.308 4.43 4.43 0.00 3.34
2965 5316 6.994496 GGTTTGGTTATTATAGAGTGGTACCC 59.006 42.308 10.07 0.32 0.00 3.69
2966 5317 7.365831 GGTTTGGTTATTATAGAGTGGTACCCA 60.366 40.741 10.07 0.00 0.00 4.51
2967 5318 7.752518 TTGGTTATTATAGAGTGGTACCCAA 57.247 36.000 10.07 0.00 34.18 4.12
2968 5319 7.752518 TGGTTATTATAGAGTGGTACCCAAA 57.247 36.000 10.07 0.00 34.18 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.231221 TGGTGACGGTCATTTTTCGG 58.769 50.000 14.78 0.00 0.00 4.30
6 7 4.671880 TTATGGTGACGGTCATTTTTCG 57.328 40.909 14.78 0.00 0.00 3.46
7 8 7.883229 ATTTTTATGGTGACGGTCATTTTTC 57.117 32.000 14.78 0.46 0.00 2.29
9 10 9.936759 AATTATTTTTATGGTGACGGTCATTTT 57.063 25.926 14.78 4.68 0.00 1.82
11 12 8.194769 GGAATTATTTTTATGGTGACGGTCATT 58.805 33.333 14.78 5.38 0.00 2.57
14 15 7.090953 TGGAATTATTTTTATGGTGACGGTC 57.909 36.000 0.00 0.00 0.00 4.79
15 16 7.559897 AGATGGAATTATTTTTATGGTGACGGT 59.440 33.333 0.00 0.00 0.00 4.83
16 17 7.940850 AGATGGAATTATTTTTATGGTGACGG 58.059 34.615 0.00 0.00 0.00 4.79
17 18 9.450807 GAAGATGGAATTATTTTTATGGTGACG 57.549 33.333 0.00 0.00 0.00 4.35
68 69 9.495572 TCATTTTTGTACTTTGAAAAGGTGTTT 57.504 25.926 7.65 0.00 36.53 2.83
69 70 9.665719 ATCATTTTTGTACTTTGAAAAGGTGTT 57.334 25.926 7.65 0.00 36.53 3.32
70 71 9.313118 GATCATTTTTGTACTTTGAAAAGGTGT 57.687 29.630 7.65 0.00 36.53 4.16
71 72 9.311916 TGATCATTTTTGTACTTTGAAAAGGTG 57.688 29.630 7.65 0.00 36.53 4.00
116 117 9.429109 TCCTATGAAATAGTAGTTGTGTATGGA 57.571 33.333 0.00 0.00 45.54 3.41
134 135 9.128404 CTCCTCATTTTCATTTCATCCTATGAA 57.872 33.333 0.00 0.00 46.77 2.57
135 136 7.230108 GCTCCTCATTTTCATTTCATCCTATGA 59.770 37.037 0.00 0.00 37.55 2.15
136 137 7.230913 AGCTCCTCATTTTCATTTCATCCTATG 59.769 37.037 0.00 0.00 0.00 2.23
137 138 7.230913 CAGCTCCTCATTTTCATTTCATCCTAT 59.769 37.037 0.00 0.00 0.00 2.57
138 139 6.544931 CAGCTCCTCATTTTCATTTCATCCTA 59.455 38.462 0.00 0.00 0.00 2.94
139 140 5.360144 CAGCTCCTCATTTTCATTTCATCCT 59.640 40.000 0.00 0.00 0.00 3.24
140 141 5.359009 TCAGCTCCTCATTTTCATTTCATCC 59.641 40.000 0.00 0.00 0.00 3.51
141 142 6.446781 TCAGCTCCTCATTTTCATTTCATC 57.553 37.500 0.00 0.00 0.00 2.92
142 143 6.845758 TTCAGCTCCTCATTTTCATTTCAT 57.154 33.333 0.00 0.00 0.00 2.57
143 144 6.653526 TTTCAGCTCCTCATTTTCATTTCA 57.346 33.333 0.00 0.00 0.00 2.69
144 145 7.919621 CCTATTTCAGCTCCTCATTTTCATTTC 59.080 37.037 0.00 0.00 0.00 2.17
145 146 7.398332 ACCTATTTCAGCTCCTCATTTTCATTT 59.602 33.333 0.00 0.00 0.00 2.32
146 147 6.894103 ACCTATTTCAGCTCCTCATTTTCATT 59.106 34.615 0.00 0.00 0.00 2.57
147 148 6.430007 ACCTATTTCAGCTCCTCATTTTCAT 58.570 36.000 0.00 0.00 0.00 2.57
148 149 5.819991 ACCTATTTCAGCTCCTCATTTTCA 58.180 37.500 0.00 0.00 0.00 2.69
149 150 5.882557 TGACCTATTTCAGCTCCTCATTTTC 59.117 40.000 0.00 0.00 0.00 2.29
150 151 5.819991 TGACCTATTTCAGCTCCTCATTTT 58.180 37.500 0.00 0.00 0.00 1.82
151 152 5.441718 TGACCTATTTCAGCTCCTCATTT 57.558 39.130 0.00 0.00 0.00 2.32
152 153 5.131642 TCATGACCTATTTCAGCTCCTCATT 59.868 40.000 0.00 0.00 0.00 2.57
153 154 4.657504 TCATGACCTATTTCAGCTCCTCAT 59.342 41.667 0.00 0.00 0.00 2.90
154 155 4.033009 TCATGACCTATTTCAGCTCCTCA 58.967 43.478 0.00 0.00 0.00 3.86
155 156 4.679373 TCATGACCTATTTCAGCTCCTC 57.321 45.455 0.00 0.00 0.00 3.71
156 157 6.753913 TTATCATGACCTATTTCAGCTCCT 57.246 37.500 0.00 0.00 0.00 3.69
157 158 6.767902 TGTTTATCATGACCTATTTCAGCTCC 59.232 38.462 0.00 0.00 0.00 4.70
158 159 7.792374 TGTTTATCATGACCTATTTCAGCTC 57.208 36.000 0.00 0.00 0.00 4.09
159 160 8.627403 CAATGTTTATCATGACCTATTTCAGCT 58.373 33.333 0.00 0.00 36.81 4.24
160 161 8.408601 ACAATGTTTATCATGACCTATTTCAGC 58.591 33.333 0.00 0.00 36.81 4.26
166 167 9.920946 ACCTTAACAATGTTTATCATGACCTAT 57.079 29.630 3.17 0.00 36.81 2.57
168 169 9.174166 GTACCTTAACAATGTTTATCATGACCT 57.826 33.333 3.17 0.00 36.81 3.85
169 170 8.952278 TGTACCTTAACAATGTTTATCATGACC 58.048 33.333 3.17 0.00 36.81 4.02
187 188 8.679100 CGGACCATGAAATTTTTATGTACCTTA 58.321 33.333 11.57 0.00 0.00 2.69
188 189 7.394923 TCGGACCATGAAATTTTTATGTACCTT 59.605 33.333 11.57 0.00 0.00 3.50
189 190 6.887545 TCGGACCATGAAATTTTTATGTACCT 59.112 34.615 11.57 0.00 0.00 3.08
190 191 7.090953 TCGGACCATGAAATTTTTATGTACC 57.909 36.000 11.57 12.00 0.00 3.34
191 192 8.973835 TTTCGGACCATGAAATTTTTATGTAC 57.026 30.769 11.57 6.24 30.75 2.90
192 193 9.632807 CTTTTCGGACCATGAAATTTTTATGTA 57.367 29.630 11.57 0.00 35.43 2.29
193 194 8.364142 TCTTTTCGGACCATGAAATTTTTATGT 58.636 29.630 11.57 2.36 35.43 2.29
194 195 8.755696 TCTTTTCGGACCATGAAATTTTTATG 57.244 30.769 6.87 6.87 35.43 1.90
195 196 9.771534 TTTCTTTTCGGACCATGAAATTTTTAT 57.228 25.926 0.00 0.00 35.43 1.40
196 197 9.771534 ATTTCTTTTCGGACCATGAAATTTTTA 57.228 25.926 0.00 0.00 35.43 1.52
197 198 8.675705 ATTTCTTTTCGGACCATGAAATTTTT 57.324 26.923 0.00 0.00 35.43 1.94
198 199 9.203421 GTATTTCTTTTCGGACCATGAAATTTT 57.797 29.630 12.05 0.00 35.43 1.82
199 200 8.585018 AGTATTTCTTTTCGGACCATGAAATTT 58.415 29.630 12.05 0.00 35.43 1.82
200 201 8.122472 AGTATTTCTTTTCGGACCATGAAATT 57.878 30.769 12.05 0.00 35.43 1.82
201 202 7.393234 TGAGTATTTCTTTTCGGACCATGAAAT 59.607 33.333 0.00 0.00 35.43 2.17
202 203 6.712998 TGAGTATTTCTTTTCGGACCATGAAA 59.287 34.615 0.00 0.00 33.73 2.69
203 204 6.234920 TGAGTATTTCTTTTCGGACCATGAA 58.765 36.000 0.00 0.00 0.00 2.57
204 205 5.800296 TGAGTATTTCTTTTCGGACCATGA 58.200 37.500 0.00 0.00 0.00 3.07
205 206 5.643777 ACTGAGTATTTCTTTTCGGACCATG 59.356 40.000 0.00 0.00 0.00 3.66
206 207 5.643777 CACTGAGTATTTCTTTTCGGACCAT 59.356 40.000 0.00 0.00 0.00 3.55
207 208 4.994852 CACTGAGTATTTCTTTTCGGACCA 59.005 41.667 0.00 0.00 0.00 4.02
208 209 4.995487 ACACTGAGTATTTCTTTTCGGACC 59.005 41.667 0.00 0.00 0.00 4.46
209 210 7.359849 GGTTACACTGAGTATTTCTTTTCGGAC 60.360 40.741 0.00 0.00 31.53 4.79
210 211 6.647895 GGTTACACTGAGTATTTCTTTTCGGA 59.352 38.462 0.00 0.00 31.53 4.55
211 212 6.649557 AGGTTACACTGAGTATTTCTTTTCGG 59.350 38.462 0.00 0.00 31.53 4.30
212 213 7.653767 AGGTTACACTGAGTATTTCTTTTCG 57.346 36.000 0.00 0.00 31.53 3.46
261 262 3.005261 TGTGCCATTATGCGACACTTTTT 59.995 39.130 10.80 0.00 32.49 1.94
262 263 2.556189 TGTGCCATTATGCGACACTTTT 59.444 40.909 10.80 0.00 32.49 2.27
263 264 2.158559 TGTGCCATTATGCGACACTTT 58.841 42.857 10.80 0.00 32.49 2.66
264 265 1.819928 TGTGCCATTATGCGACACTT 58.180 45.000 10.80 0.00 32.49 3.16
265 266 1.672363 CATGTGCCATTATGCGACACT 59.328 47.619 10.80 0.00 32.49 3.55
266 267 1.268692 CCATGTGCCATTATGCGACAC 60.269 52.381 0.00 4.89 0.00 3.67
267 268 1.023502 CCATGTGCCATTATGCGACA 58.976 50.000 0.00 0.00 0.00 4.35
268 269 1.265095 CTCCATGTGCCATTATGCGAC 59.735 52.381 0.00 0.00 0.00 5.19
269 270 1.596603 CTCCATGTGCCATTATGCGA 58.403 50.000 0.00 0.00 0.00 5.10
270 271 0.039798 GCTCCATGTGCCATTATGCG 60.040 55.000 0.00 0.00 0.00 4.73
271 272 1.034356 TGCTCCATGTGCCATTATGC 58.966 50.000 5.64 0.00 0.00 3.14
272 273 3.297830 CATGCTCCATGTGCCATTATG 57.702 47.619 5.64 0.00 37.12 1.90
315 316 3.600694 AAATGCCCGTGCGTTGCA 61.601 55.556 0.00 8.11 45.88 4.08
316 317 2.465097 TACAAATGCCCGTGCGTTGC 62.465 55.000 0.00 0.00 45.88 4.17
317 318 0.727793 GTACAAATGCCCGTGCGTTG 60.728 55.000 0.00 1.29 45.88 4.10
319 320 0.037139 TAGTACAAATGCCCGTGCGT 60.037 50.000 0.00 0.00 41.78 5.24
320 321 0.650512 CTAGTACAAATGCCCGTGCG 59.349 55.000 0.00 0.00 41.78 5.34
321 322 1.734163 ACTAGTACAAATGCCCGTGC 58.266 50.000 0.00 0.00 38.26 5.34
322 323 7.724305 ATTATTACTAGTACAAATGCCCGTG 57.276 36.000 0.91 0.00 0.00 4.94
1122 1695 1.597854 CAGCTTCGTGTTGAGCCCA 60.598 57.895 0.00 0.00 0.00 5.36
1640 3941 1.065491 TGCTTGCCTTATCCACATCGT 60.065 47.619 0.00 0.00 0.00 3.73
2469 4804 4.661125 TGCGAAAGTAATTGTGCATCATC 58.339 39.130 0.00 0.00 0.00 2.92
2768 5112 6.879993 TGCAACGGGTATAAAGTAAATCTGAA 59.120 34.615 0.00 0.00 0.00 3.02
2822 5170 1.995376 ACGGCAGAAACCCAATTCTT 58.005 45.000 0.00 0.00 37.56 2.52
2838 5187 4.747810 AGGGTAGTTTTTATGACGTACGG 58.252 43.478 21.06 1.43 0.00 4.02
2842 5191 4.789012 TCGAGGGTAGTTTTTATGACGT 57.211 40.909 0.00 0.00 0.00 4.34
2854 5203 3.553828 TTAGGGCAATTTCGAGGGTAG 57.446 47.619 0.00 0.00 0.00 3.18
2862 5211 5.932619 AGTGGGTAATTTAGGGCAATTTC 57.067 39.130 0.00 0.00 0.00 2.17
2865 5214 4.832823 GCATAGTGGGTAATTTAGGGCAAT 59.167 41.667 0.00 0.00 0.00 3.56
2870 5219 4.141251 AGGTGGCATAGTGGGTAATTTAGG 60.141 45.833 0.00 0.00 0.00 2.69
2871 5220 5.048846 AGGTGGCATAGTGGGTAATTTAG 57.951 43.478 0.00 0.00 0.00 1.85
2913 5264 2.034685 GCGGCCTTCAAGAAAAAGAACT 59.965 45.455 0.00 0.00 0.00 3.01
2914 5265 2.394708 GCGGCCTTCAAGAAAAAGAAC 58.605 47.619 0.00 0.00 0.00 3.01
2917 5268 0.387239 CGGCGGCCTTCAAGAAAAAG 60.387 55.000 18.34 0.00 0.00 2.27
2919 5270 2.914908 GCGGCGGCCTTCAAGAAAA 61.915 57.895 18.34 0.00 0.00 2.29
2920 5271 3.361977 GCGGCGGCCTTCAAGAAA 61.362 61.111 18.34 0.00 0.00 2.52
2933 5284 1.031029 TAATAACCAAACCCCGCGGC 61.031 55.000 22.85 0.00 0.00 6.53
2934 5285 1.682740 ATAATAACCAAACCCCGCGG 58.317 50.000 21.04 21.04 0.00 6.46
2935 5286 3.731089 TCTATAATAACCAAACCCCGCG 58.269 45.455 0.00 0.00 0.00 6.46
2936 5287 4.514066 CACTCTATAATAACCAAACCCCGC 59.486 45.833 0.00 0.00 0.00 6.13
2937 5288 5.061179 CCACTCTATAATAACCAAACCCCG 58.939 45.833 0.00 0.00 0.00 5.73
2938 5289 6.009908 ACCACTCTATAATAACCAAACCCC 57.990 41.667 0.00 0.00 0.00 4.95
2939 5290 6.994496 GGTACCACTCTATAATAACCAAACCC 59.006 42.308 7.15 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.