Multiple sequence alignment - TraesCS1D01G287900

Loading Multiple Alignment...

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 TraesCS1D01G287900 chr1D 100.000 4721 0 0 1 4721 386420281 386425001 0.000000e+00 8719
1 TraesCS1D01G287900 chr1D 96.970 66 2 0 4404 4469 386424749 386424684 1.390000e-20 111
2 TraesCS1D01G287900 chr1A 96.827 3719 92 13 659 4362 486330633 486334340 0.000000e+00 6191
3 TraesCS1D01G287900 chr1A 94.760 668 24 6 6 666 486329863 486330526 0.000000e+00 1029
4 TraesCS1D01G287900 chr1B 97.443 2542 51 5 416 2953 518799517 518802048 0.000000e+00 4322
5 TraesCS1D01G287900 chr1B 94.822 1429 54 12 2950 4362 518802256 518803680 0.000000e+00 2211
6 TraesCS1D01G287900 chr1B 89.937 477 25 8 1 467 518799049 518799512 1.130000e-165 593
7 TraesCS1D01G287900 chr1B 88.177 203 18 3 4468 4664 518803758 518803960 2.200000e-58 237
8 TraesCS1D01G287900 chr1B 89.412 85 6 2 4394 4478 586281825 586281744 2.320000e-18 104
9 TraesCS1D01G287900 chr7B 94.937 79 2 2 4399 4475 713303791 713303713 6.420000e-24 122
10 TraesCS1D01G287900 chr5B 97.059 68 1 1 4403 4469 572349915 572349982 3.860000e-21 113
11 TraesCS1D01G287900 chr3A 91.667 84 4 2 4389 4470 41115031 41114949 3.860000e-21 113
12 TraesCS1D01G287900 chr2D 95.775 71 1 1 4401 4469 334331508 334331578 3.860000e-21 113
13 TraesCS1D01G287900 chr2A 97.015 67 1 1 4404 4469 18609719 18609653 1.390000e-20 111
14 TraesCS1D01G287900 chr2A 94.366 71 3 1 4401 4470 18609650 18609720 1.800000e-19 108
15 TraesCS1D01G287900 chr2B 93.333 75 2 2 4395 4469 693327336 693327265 1.800000e-19 108


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 TraesCS1D01G287900 chr1D 386420281 386425001 4720 False 8719.00 8719 100.00000 1 4721 1 chr1D.!!$F1 4720
1 TraesCS1D01G287900 chr1A 486329863 486334340 4477 False 3610.00 6191 95.79350 6 4362 2 chr1A.!!$F1 4356
2 TraesCS1D01G287900 chr1B 518799049 518803960 4911 False 1840.75 4322 92.59475 1 4664 4 chr1B.!!$F1 4663

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
535 603 0.888736 TGGCTTGGTGGTTGTGATCG 60.889 55.000 0.0 0.0 0.00 3.69 F
1552 1734 0.324614 TCCTTCAAATGGCTGAGCGA 59.675 50.000 0.0 0.0 0.00 4.93 F
2797 2979 1.004745 AGTTCTGCACTTGGTATGGGG 59.995 52.381 0.0 0.0 27.32 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 2463 0.039256 CATGTGGTTGCGGAAAGGTG 60.039 55.0 0.00 0.00 0.0 4.00 R
3436 3837 0.475475 TGCTGCCTCCTAATCCATGG 59.525 55.0 4.97 4.97 0.0 3.66 R
4688 5145 0.178961 GGGAACTGTTGGAGGCCTTT 60.179 55.0 6.77 0.00 0.0 3.11 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
41 42 4.567385 GCAGCTAGCTCGCTCGCT 62.567 66.667 23.51 11.59 44.34 4.93
150 151 1.507174 GTCCGTCCTTCTCTCCGTG 59.493 63.158 0.00 0.00 0.00 4.94
203 206 4.742201 CGCACCAGTCCAGTCCCG 62.742 72.222 0.00 0.00 0.00 5.14
204 207 3.311110 GCACCAGTCCAGTCCCGA 61.311 66.667 0.00 0.00 0.00 5.14
205 208 2.660064 GCACCAGTCCAGTCCCGAT 61.660 63.158 0.00 0.00 0.00 4.18
206 209 1.517832 CACCAGTCCAGTCCCGATC 59.482 63.158 0.00 0.00 0.00 3.69
295 304 2.439880 GCTGGTAAGGAAGCCCTATCTT 59.560 50.000 0.00 0.00 43.48 2.40
535 603 0.888736 TGGCTTGGTGGTTGTGATCG 60.889 55.000 0.00 0.00 0.00 3.69
740 922 2.095567 ACTGAGCATGCGAATGTTGTTC 60.096 45.455 13.01 1.16 0.00 3.18
743 925 1.881973 AGCATGCGAATGTTGTTCACT 59.118 42.857 13.01 0.00 0.00 3.41
744 926 1.980844 GCATGCGAATGTTGTTCACTG 59.019 47.619 0.00 0.00 0.00 3.66
820 1002 6.605849 TCTATGTCGGCGTGTTAGTATATTC 58.394 40.000 6.85 0.00 0.00 1.75
985 1167 7.549488 AGTGATCTTTAAATAGTTTCCACCTCG 59.451 37.037 0.00 0.00 0.00 4.63
1174 1356 0.909610 AAGAGAGAACGCCCCCATCA 60.910 55.000 0.00 0.00 0.00 3.07
1351 1533 6.594159 GCACTGGTACAAGAGTGTATGTTTAT 59.406 38.462 3.64 0.00 42.18 1.40
1525 1707 5.415701 TGAAACTGGTATGAAGAAGGCAATC 59.584 40.000 0.00 0.00 0.00 2.67
1552 1734 0.324614 TCCTTCAAATGGCTGAGCGA 59.675 50.000 0.00 0.00 0.00 4.93
1843 2025 2.439507 AGGCGGATCATCATTACAGGTT 59.560 45.455 0.00 0.00 0.00 3.50
1981 2163 5.529581 TCGATAAATCTGTGGCACATCTA 57.470 39.130 22.35 10.28 44.52 1.98
2281 2463 1.458639 AACCTTGTGCTCTTGCCAGC 61.459 55.000 0.00 0.00 40.13 4.85
2512 2694 1.898472 CTTCTGAGAGAGGGACTGCAA 59.102 52.381 0.00 0.00 41.55 4.08
2797 2979 1.004745 AGTTCTGCACTTGGTATGGGG 59.995 52.381 0.00 0.00 27.32 4.96
2909 3091 3.119291 CTCTATCGTGTAAAGGCTGCAG 58.881 50.000 10.11 10.11 0.00 4.41
3196 3594 5.593679 TTCTACCCATTACAGCACTCTAC 57.406 43.478 0.00 0.00 0.00 2.59
3205 3603 7.360946 CCCATTACAGCACTCTACTTTTGTAAC 60.361 40.741 0.00 0.00 34.86 2.50
3212 3610 5.176223 GCACTCTACTTTTGTAACGCTGTTA 59.824 40.000 0.00 0.00 34.06 2.41
3216 3614 9.084164 ACTCTACTTTTGTAACGCTGTTATATG 57.916 33.333 4.83 0.92 34.06 1.78
3403 3804 1.705186 ACACCATTGAGCCCTACTGTT 59.295 47.619 0.00 0.00 0.00 3.16
3679 4080 2.019249 ACATTTCAGGATGGCATGACG 58.981 47.619 3.81 0.00 34.09 4.35
3700 4101 3.079578 GAGTATGTGATCCCATGCCATG 58.920 50.000 0.36 0.00 0.00 3.66
3707 4108 0.184451 ATCCCATGCCATGACAGACC 59.816 55.000 6.18 0.00 0.00 3.85
3729 4130 5.372661 ACCCCATGTAAATAATAGCTCCAGT 59.627 40.000 0.00 0.00 0.00 4.00
3899 4300 5.678107 GCCATAAAGAAAGATGGTCTTGCAG 60.678 44.000 3.04 0.00 43.94 4.41
3940 4342 5.460646 CAAAGAAATGTTACATGGTTCGCT 58.539 37.500 0.00 0.00 0.00 4.93
3945 4347 3.052455 TGTTACATGGTTCGCTGATGT 57.948 42.857 0.00 0.00 34.68 3.06
4020 4430 2.578021 ACATCCAAGGCTACCAGACATT 59.422 45.455 0.00 0.00 0.00 2.71
4065 4475 5.963594 ACTCGTATACTCTTCAAAGGTTCC 58.036 41.667 0.56 0.00 0.00 3.62
4257 4671 8.991275 TGATTGCCCTTATTTAGATGGAAATTT 58.009 29.630 0.00 0.00 31.51 1.82
4284 4698 2.756829 TCGACCAGTAATTCGTTTGCA 58.243 42.857 0.00 0.00 0.00 4.08
4285 4699 3.331150 TCGACCAGTAATTCGTTTGCAT 58.669 40.909 0.00 0.00 0.00 3.96
4286 4700 4.496360 TCGACCAGTAATTCGTTTGCATA 58.504 39.130 0.00 0.00 0.00 3.14
4357 4776 8.441312 ACTTATTTCTTCCGTTTGTCTACAAA 57.559 30.769 4.19 4.19 42.90 2.83
4358 4777 8.557029 ACTTATTTCTTCCGTTTGTCTACAAAG 58.443 33.333 8.48 3.94 45.36 2.77
4359 4778 4.806342 TTCTTCCGTTTGTCTACAAAGC 57.194 40.909 8.48 3.96 45.36 3.51
4362 4781 4.272504 TCTTCCGTTTGTCTACAAAGCTTG 59.727 41.667 8.48 0.00 45.36 4.01
4363 4782 3.799366 TCCGTTTGTCTACAAAGCTTGA 58.201 40.909 8.48 0.00 45.36 3.02
4364 4783 3.558418 TCCGTTTGTCTACAAAGCTTGAC 59.442 43.478 8.48 3.49 45.36 3.18
4365 4784 3.311322 CCGTTTGTCTACAAAGCTTGACA 59.689 43.478 12.03 12.03 45.36 3.58
4366 4785 4.024048 CCGTTTGTCTACAAAGCTTGACAT 60.024 41.667 15.65 0.00 45.36 3.06
4368 4787 5.504010 CGTTTGTCTACAAAGCTTGACATGT 60.504 40.000 15.65 11.44 45.36 3.21
4390 4841 5.470437 TGTTCAAATAACACCGTGCATCTTA 59.530 36.000 0.00 0.00 0.00 2.10
4409 4860 9.899226 GCATCTTATACAAATTCAAATACTCCC 57.101 33.333 0.00 0.00 0.00 4.30
4412 4863 9.847224 TCTTATACAAATTCAAATACTCCCTCC 57.153 33.333 0.00 0.00 0.00 4.30
4413 4864 8.671384 TTATACAAATTCAAATACTCCCTCCG 57.329 34.615 0.00 0.00 0.00 4.63
4414 4865 4.918588 ACAAATTCAAATACTCCCTCCGT 58.081 39.130 0.00 0.00 0.00 4.69
4415 4866 4.941873 ACAAATTCAAATACTCCCTCCGTC 59.058 41.667 0.00 0.00 0.00 4.79
4416 4867 3.840124 ATTCAAATACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
4417 4868 1.492764 TCAAATACTCCCTCCGTCCC 58.507 55.000 0.00 0.00 0.00 4.46
4418 4869 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
4419 4870 1.557832 CAAATACTCCCTCCGTCCCAA 59.442 52.381 0.00 0.00 0.00 4.12
4420 4871 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
4421 4872 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4422 4873 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4423 4874 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4424 4875 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4425 4876 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4426 4877 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4427 4878 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4428 4879 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4429 4880 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
4430 4881 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4431 4882 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
4432 4883 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
4433 4884 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4434 4885 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4435 4886 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
4436 4887 5.334105 CGTCCCAAAATAAGTGTCTCAACTG 60.334 44.000 0.00 0.00 0.00 3.16
4437 4888 5.048713 GTCCCAAAATAAGTGTCTCAACTGG 60.049 44.000 0.00 0.00 0.00 4.00
4438 4889 4.827284 CCCAAAATAAGTGTCTCAACTGGT 59.173 41.667 0.00 0.00 0.00 4.00
4439 4890 5.301805 CCCAAAATAAGTGTCTCAACTGGTT 59.698 40.000 0.00 0.00 0.00 3.67
4440 4891 6.208644 CCAAAATAAGTGTCTCAACTGGTTG 58.791 40.000 7.10 7.10 41.71 3.77
4441 4892 6.039270 CCAAAATAAGTGTCTCAACTGGTTGA 59.961 38.462 14.30 14.30 46.27 3.18
4454 4905 7.026631 TCAACTGGTTGAGACACTTATTTTG 57.973 36.000 11.53 0.00 43.90 2.44
4455 4906 6.039270 TCAACTGGTTGAGACACTTATTTTGG 59.961 38.462 11.53 0.00 43.90 3.28
4456 4907 4.827284 ACTGGTTGAGACACTTATTTTGGG 59.173 41.667 0.00 0.00 0.00 4.12
4457 4908 5.055265 TGGTTGAGACACTTATTTTGGGA 57.945 39.130 0.00 0.00 0.00 4.37
4458 4909 4.825085 TGGTTGAGACACTTATTTTGGGAC 59.175 41.667 0.00 0.00 0.00 4.46
4459 4910 4.083484 GGTTGAGACACTTATTTTGGGACG 60.083 45.833 0.00 0.00 0.00 4.79
4460 4911 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
4461 4912 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
4462 4913 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
4463 4914 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4464 4915 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4465 4916 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4466 4917 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4467 4918 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4474 4925 1.320507 GGACGGAGGGAGTAGATCAC 58.679 60.000 0.00 0.00 0.00 3.06
4492 4943 1.596260 CACTAGCATCATCGGTGCAAG 59.404 52.381 1.56 0.00 44.87 4.01
4535 4988 7.860918 TTTACCACCGTGCATATTATACAAA 57.139 32.000 0.00 0.00 0.00 2.83
4571 5024 3.314541 ACTTCGACTTGGATGTGGTAC 57.685 47.619 0.00 0.00 0.00 3.34
4576 5029 2.478894 CGACTTGGATGTGGTACAACAC 59.521 50.000 4.87 0.00 44.16 3.32
4593 5050 2.996631 ACACAATTCCTGAGATCTGCC 58.003 47.619 0.00 0.00 0.00 4.85
4606 5063 4.940046 TGAGATCTGCCTCTGATTTTTGAC 59.060 41.667 0.00 0.00 34.38 3.18
4609 5066 3.819368 TCTGCCTCTGATTTTTGACACA 58.181 40.909 0.00 0.00 0.00 3.72
4612 5069 3.256383 TGCCTCTGATTTTTGACACATGG 59.744 43.478 0.00 0.00 0.00 3.66
4636 5093 7.768240 GGAAGTTTCCTTTTCTGAACAACTTA 58.232 34.615 3.63 0.00 44.11 2.24
4645 5102 7.391148 TTTTCTGAACAACTTAGAGCAACTT 57.609 32.000 0.00 0.00 0.00 2.66
4648 5105 6.112734 TCTGAACAACTTAGAGCAACTTCAA 58.887 36.000 0.00 0.00 0.00 2.69
4654 5111 8.485976 ACAACTTAGAGCAACTTCAATAGATC 57.514 34.615 0.00 0.00 0.00 2.75
4664 5121 6.525629 CAACTTCAATAGATCCCGTATCCTT 58.474 40.000 0.00 0.00 34.90 3.36
4665 5122 7.667557 CAACTTCAATAGATCCCGTATCCTTA 58.332 38.462 0.00 0.00 34.90 2.69
4666 5123 7.850935 ACTTCAATAGATCCCGTATCCTTAA 57.149 36.000 0.00 0.00 34.90 1.85
4667 5124 8.258850 ACTTCAATAGATCCCGTATCCTTAAA 57.741 34.615 0.00 0.00 34.90 1.52
4668 5125 8.711170 ACTTCAATAGATCCCGTATCCTTAAAA 58.289 33.333 0.00 0.00 34.90 1.52
4669 5126 9.209175 CTTCAATAGATCCCGTATCCTTAAAAG 57.791 37.037 0.00 0.00 34.90 2.27
4670 5127 8.486942 TCAATAGATCCCGTATCCTTAAAAGA 57.513 34.615 0.00 0.00 34.90 2.52
4671 5128 9.101325 TCAATAGATCCCGTATCCTTAAAAGAT 57.899 33.333 0.00 0.00 34.90 2.40
4672 5129 9.726438 CAATAGATCCCGTATCCTTAAAAGATT 57.274 33.333 0.00 0.00 34.90 2.40
4675 5132 7.677892 AGATCCCGTATCCTTAAAAGATTACC 58.322 38.462 0.00 0.00 34.90 2.85
4676 5133 5.846203 TCCCGTATCCTTAAAAGATTACCG 58.154 41.667 0.00 0.00 0.00 4.02
4677 5134 4.992951 CCCGTATCCTTAAAAGATTACCGG 59.007 45.833 0.00 0.00 0.00 5.28
4678 5135 5.453762 CCCGTATCCTTAAAAGATTACCGGT 60.454 44.000 13.98 13.98 0.00 5.28
4679 5136 6.051074 CCGTATCCTTAAAAGATTACCGGTT 58.949 40.000 15.04 0.00 0.00 4.44
4680 5137 7.209475 CCGTATCCTTAAAAGATTACCGGTTA 58.791 38.462 15.04 2.98 0.00 2.85
4681 5138 7.710475 CCGTATCCTTAAAAGATTACCGGTTAA 59.290 37.037 15.04 5.61 0.00 2.01
4682 5139 8.758715 CGTATCCTTAAAAGATTACCGGTTAAG 58.241 37.037 15.04 12.66 33.49 1.85
4683 5140 9.049523 GTATCCTTAAAAGATTACCGGTTAAGG 57.950 37.037 24.15 24.15 46.47 2.69
4684 5141 6.417258 TCCTTAAAAGATTACCGGTTAAGGG 58.583 40.000 27.21 15.44 45.71 3.95
4685 5142 6.215227 TCCTTAAAAGATTACCGGTTAAGGGA 59.785 38.462 27.21 16.86 45.71 4.20
4686 5143 6.885918 CCTTAAAAGATTACCGGTTAAGGGAA 59.114 38.462 23.07 8.99 43.57 3.97
4687 5144 7.394077 CCTTAAAAGATTACCGGTTAAGGGAAA 59.606 37.037 23.07 8.34 43.57 3.13
4688 5145 8.703378 TTAAAAGATTACCGGTTAAGGGAAAA 57.297 30.769 15.04 0.00 37.70 2.29
4689 5146 7.600231 AAAAGATTACCGGTTAAGGGAAAAA 57.400 32.000 15.04 0.00 37.70 1.94
4706 5163 1.704641 AAAAGGCCTCCAACAGTTCC 58.295 50.000 5.23 0.00 0.00 3.62
4707 5164 0.178961 AAAGGCCTCCAACAGTTCCC 60.179 55.000 5.23 0.00 0.00 3.97
4708 5165 2.359975 GGCCTCCAACAGTTCCCG 60.360 66.667 0.00 0.00 0.00 5.14
4709 5166 2.430367 GCCTCCAACAGTTCCCGT 59.570 61.111 0.00 0.00 0.00 5.28
4710 5167 1.675219 GCCTCCAACAGTTCCCGTA 59.325 57.895 0.00 0.00 0.00 4.02
4711 5168 0.035739 GCCTCCAACAGTTCCCGTAA 59.964 55.000 0.00 0.00 0.00 3.18
4712 5169 1.543871 GCCTCCAACAGTTCCCGTAAA 60.544 52.381 0.00 0.00 0.00 2.01
4713 5170 2.148768 CCTCCAACAGTTCCCGTAAAC 58.851 52.381 0.00 0.00 0.00 2.01
4714 5171 2.148768 CTCCAACAGTTCCCGTAAACC 58.851 52.381 0.00 0.00 0.00 3.27
4715 5172 1.770061 TCCAACAGTTCCCGTAAACCT 59.230 47.619 0.00 0.00 0.00 3.50
4716 5173 1.877443 CCAACAGTTCCCGTAAACCTG 59.123 52.381 0.00 0.00 0.00 4.00
4717 5174 2.485835 CCAACAGTTCCCGTAAACCTGA 60.486 50.000 0.00 0.00 0.00 3.86
4718 5175 3.408634 CAACAGTTCCCGTAAACCTGAT 58.591 45.455 0.00 0.00 0.00 2.90
4719 5176 3.782656 ACAGTTCCCGTAAACCTGATT 57.217 42.857 0.00 0.00 0.00 2.57
4720 5177 3.671716 ACAGTTCCCGTAAACCTGATTC 58.328 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 2.413765 GATCGAGACGGACAGGGC 59.586 66.667 0.00 0.00 0.00 5.19
189 190 1.686110 GGATCGGGACTGGACTGGT 60.686 63.158 0.00 0.00 0.00 4.00
203 206 3.866582 CACCAGCGGAGGGGGATC 61.867 72.222 1.50 0.00 0.00 3.36
295 304 2.011222 ACGAGACAAAAACCAAAGCGA 58.989 42.857 0.00 0.00 0.00 4.93
498 565 1.228552 ACCGACAAATGGCAGGCTT 60.229 52.632 0.00 0.00 0.00 4.35
549 617 0.806492 GCCGACTTTCCATCGACTCC 60.806 60.000 0.00 0.00 42.25 3.85
671 853 8.986847 GCGACTAGGATAATATTACGCTATCTA 58.013 37.037 13.85 3.98 40.28 1.98
694 876 2.032030 GTGCAAAGCAAAAGACTAGCGA 60.032 45.455 0.00 0.00 41.47 4.93
740 922 5.634896 GCTGGACATTCAGAAATTACAGTG 58.365 41.667 7.96 0.00 36.93 3.66
743 925 4.154015 CACGCTGGACATTCAGAAATTACA 59.846 41.667 0.00 0.00 36.93 2.41
744 926 4.154195 ACACGCTGGACATTCAGAAATTAC 59.846 41.667 0.00 0.00 36.93 1.89
798 980 5.474532 AGGAATATACTAACACGCCGACATA 59.525 40.000 0.00 0.00 0.00 2.29
820 1002 8.892723 TGCAACAAATTCTGTATGTTAGATAGG 58.107 33.333 0.00 0.00 37.23 2.57
869 1051 5.354234 AGCCAGACAGTAAATTAATCCAACG 59.646 40.000 0.00 0.00 0.00 4.10
985 1167 4.493220 CGCATAGCTGCTTCTTTTGTAGTC 60.493 45.833 7.79 0.00 46.65 2.59
1174 1356 6.015519 TCCATTTCTTTCGATTTGTTGGTGAT 60.016 34.615 0.00 0.00 0.00 3.06
1351 1533 6.251255 TCATTATGATTGATGGACCACTCA 57.749 37.500 0.00 0.00 31.74 3.41
1525 1707 0.749454 CCATTTGAAGGAGGGGCTCG 60.749 60.000 0.00 0.00 0.00 5.03
1552 1734 2.125512 GCGCGTCTTGGGATCTGT 60.126 61.111 8.43 0.00 0.00 3.41
1843 2025 3.745975 CGGCTTTGTCAGTCTCAAATGTA 59.254 43.478 0.00 0.00 34.88 2.29
1981 2163 1.280421 GTTCCTCCCAGCATCTTCACT 59.720 52.381 0.00 0.00 0.00 3.41
2281 2463 0.039256 CATGTGGTTGCGGAAAGGTG 60.039 55.000 0.00 0.00 0.00 4.00
2512 2694 8.840321 CCGATTATCACTTGGTTATCTTTGATT 58.160 33.333 0.00 0.00 0.00 2.57
2536 2718 3.446161 TCCAAGTGATACTACCTGAACCG 59.554 47.826 0.00 0.00 0.00 4.44
2785 2967 1.205460 AAGGCGACCCCATACCAAGT 61.205 55.000 0.00 0.00 35.39 3.16
2797 2979 5.973565 CCATAAATGAAATCTGAAAGGCGAC 59.026 40.000 0.00 0.00 0.00 5.19
2909 3091 5.728351 TGTGAGTAAAACAACACTAGCAC 57.272 39.130 0.00 0.00 34.81 4.40
3002 3399 7.221259 GGTTAAGTGGTGTAACAAATTTGACAC 59.779 37.037 24.56 24.56 39.98 3.67
3149 3547 4.880759 ACTCACTGAAGTCTCATCACAAG 58.119 43.478 0.00 0.00 0.00 3.16
3205 3603 7.618442 ACGTTACTGATTTTCATATAACAGCG 58.382 34.615 0.00 0.00 32.07 5.18
3212 3610 8.330466 TCCAACAACGTTACTGATTTTCATAT 57.670 30.769 0.00 0.00 0.00 1.78
3216 3614 6.295039 TCTCCAACAACGTTACTGATTTTC 57.705 37.500 0.00 0.00 0.00 2.29
3436 3837 0.475475 TGCTGCCTCCTAATCCATGG 59.525 55.000 4.97 4.97 0.00 3.66
3679 4080 2.936919 TGGCATGGGATCACATACTC 57.063 50.000 10.88 3.89 0.00 2.59
3700 4101 6.534634 AGCTATTATTTACATGGGGTCTGTC 58.465 40.000 0.00 0.00 0.00 3.51
3707 4108 6.652481 CAGACTGGAGCTATTATTTACATGGG 59.348 42.308 0.00 0.00 0.00 4.00
3729 4130 5.641209 GCTAGACAAGAAGAAATCAAGCAGA 59.359 40.000 0.00 0.00 0.00 4.26
3899 4300 1.971695 GGTACAACACCCAGCTGCC 60.972 63.158 8.66 0.00 42.07 4.85
3940 4342 2.507213 GCCATGGCCAATCACATCA 58.493 52.632 27.24 0.00 34.56 3.07
3959 4361 2.345760 GGTGACCTTGCAGGCCATG 61.346 63.158 5.01 0.97 39.63 3.66
3960 4362 2.036256 GGTGACCTTGCAGGCCAT 59.964 61.111 5.01 0.00 39.63 4.40
3961 4363 3.496309 CTGGTGACCTTGCAGGCCA 62.496 63.158 5.01 0.00 39.63 5.36
3962 4364 2.674380 CTGGTGACCTTGCAGGCC 60.674 66.667 2.11 0.00 39.63 5.19
3963 4365 3.368571 GCTGGTGACCTTGCAGGC 61.369 66.667 13.52 1.17 39.63 4.85
3964 4366 1.673665 GAGCTGGTGACCTTGCAGG 60.674 63.158 18.77 1.16 42.49 4.85
4020 4430 2.503331 CCGGATGGTTGCAGCAATATA 58.497 47.619 11.96 1.14 0.00 0.86
4194 4608 7.919091 CGATGATCTCAATTTCCATTTGACATT 59.081 33.333 0.00 0.00 0.00 2.71
4257 4671 3.949754 ACGAATTACTGGTCGATGGTCTA 59.050 43.478 0.00 0.00 39.64 2.59
4284 4698 9.228949 GAAACAGATTCATATGGAGCATCTTAT 57.771 33.333 1.33 0.00 37.99 1.73
4285 4699 7.386025 CGAAACAGATTCATATGGAGCATCTTA 59.614 37.037 1.33 0.00 37.96 2.10
4286 4700 6.204301 CGAAACAGATTCATATGGAGCATCTT 59.796 38.462 1.33 0.00 37.96 2.40
4296 4715 6.173339 ACTTGTGACCGAAACAGATTCATAT 58.827 36.000 0.00 0.00 37.96 1.78
4357 4776 5.562696 CGGTGTTATTTGAACATGTCAAGCT 60.563 40.000 0.00 0.67 46.85 3.74
4358 4777 4.616802 CGGTGTTATTTGAACATGTCAAGC 59.383 41.667 0.00 0.00 46.85 4.01
4359 4778 5.624900 CACGGTGTTATTTGAACATGTCAAG 59.375 40.000 0.00 0.00 46.85 3.02
4362 4781 3.911964 GCACGGTGTTATTTGAACATGTC 59.088 43.478 10.24 0.00 32.23 3.06
4363 4782 3.316588 TGCACGGTGTTATTTGAACATGT 59.683 39.130 10.24 0.00 32.23 3.21
4364 4783 3.894920 TGCACGGTGTTATTTGAACATG 58.105 40.909 10.24 0.00 32.23 3.21
4365 4784 4.458989 AGATGCACGGTGTTATTTGAACAT 59.541 37.500 10.24 1.13 32.23 2.71
4366 4785 3.818210 AGATGCACGGTGTTATTTGAACA 59.182 39.130 10.24 0.00 0.00 3.18
4368 4787 6.751514 ATAAGATGCACGGTGTTATTTGAA 57.248 33.333 10.24 0.00 0.00 2.69
4390 4841 6.659824 ACGGAGGGAGTATTTGAATTTGTAT 58.340 36.000 0.00 0.00 0.00 2.29
4407 4858 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4408 4859 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4409 4860 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
4410 4861 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
4411 4862 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
4412 4863 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
4413 4864 5.048713 CCAGTTGAGACACTTATTTTGGGAC 60.049 44.000 0.00 0.00 0.00 4.46
4414 4865 5.070001 CCAGTTGAGACACTTATTTTGGGA 58.930 41.667 0.00 0.00 0.00 4.37
4415 4866 4.827284 ACCAGTTGAGACACTTATTTTGGG 59.173 41.667 0.00 0.00 0.00 4.12
4416 4867 6.039270 TCAACCAGTTGAGACACTTATTTTGG 59.961 38.462 9.12 0.00 43.90 3.28
4417 4868 7.026631 TCAACCAGTTGAGACACTTATTTTG 57.973 36.000 9.12 0.00 43.90 2.44
4430 4881 6.039270 CCAAAATAAGTGTCTCAACCAGTTGA 59.961 38.462 12.40 12.40 46.27 3.18
4431 4882 6.208644 CCAAAATAAGTGTCTCAACCAGTTG 58.791 40.000 4.09 4.09 41.71 3.16
4432 4883 5.301805 CCCAAAATAAGTGTCTCAACCAGTT 59.698 40.000 0.00 0.00 0.00 3.16
4433 4884 4.827284 CCCAAAATAAGTGTCTCAACCAGT 59.173 41.667 0.00 0.00 0.00 4.00
4434 4885 5.048713 GTCCCAAAATAAGTGTCTCAACCAG 60.049 44.000 0.00 0.00 0.00 4.00
4435 4886 4.825085 GTCCCAAAATAAGTGTCTCAACCA 59.175 41.667 0.00 0.00 0.00 3.67
4436 4887 4.083484 CGTCCCAAAATAAGTGTCTCAACC 60.083 45.833 0.00 0.00 0.00 3.77
4437 4888 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4438 4889 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4439 4890 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
4440 4891 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
4441 4892 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4442 4893 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
4443 4894 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4444 4895 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4445 4896 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4446 4897 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4447 4898 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4448 4899 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4449 4900 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
4450 4901 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
4451 4902 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
4452 4903 0.635009 ATCTACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
4453 4904 0.185416 GATCTACTCCCTCCGTCCCA 59.815 60.000 0.00 0.00 0.00 4.37
4454 4905 0.185416 TGATCTACTCCCTCCGTCCC 59.815 60.000 0.00 0.00 0.00 4.46
4455 4906 1.133730 AGTGATCTACTCCCTCCGTCC 60.134 57.143 0.00 0.00 33.17 4.79
4456 4907 2.351706 AGTGATCTACTCCCTCCGTC 57.648 55.000 0.00 0.00 33.17 4.79
4457 4908 2.487625 GCTAGTGATCTACTCCCTCCGT 60.488 54.545 0.00 0.00 40.89 4.69
4458 4909 2.156098 GCTAGTGATCTACTCCCTCCG 58.844 57.143 0.00 0.00 40.89 4.63
4459 4910 3.231207 TGCTAGTGATCTACTCCCTCC 57.769 52.381 0.00 0.00 40.89 4.30
4460 4911 4.402829 TGATGCTAGTGATCTACTCCCTC 58.597 47.826 0.00 0.00 40.89 4.30
4461 4912 4.461450 TGATGCTAGTGATCTACTCCCT 57.539 45.455 0.00 0.00 40.89 4.20
4462 4913 4.142491 CGATGATGCTAGTGATCTACTCCC 60.142 50.000 0.00 0.00 40.89 4.30
4463 4914 4.142491 CCGATGATGCTAGTGATCTACTCC 60.142 50.000 0.00 0.00 40.89 3.85
4464 4915 4.457603 ACCGATGATGCTAGTGATCTACTC 59.542 45.833 0.00 0.00 40.89 2.59
4465 4916 4.217334 CACCGATGATGCTAGTGATCTACT 59.783 45.833 0.00 0.00 43.56 2.57
4466 4917 4.480541 CACCGATGATGCTAGTGATCTAC 58.519 47.826 0.00 0.00 0.00 2.59
4467 4918 3.057245 GCACCGATGATGCTAGTGATCTA 60.057 47.826 0.00 0.00 40.08 1.98
4474 4925 0.585357 GCTTGCACCGATGATGCTAG 59.415 55.000 4.40 4.40 45.20 3.42
4492 4943 1.156736 ATACAGGACAAGTTGCACGC 58.843 50.000 1.81 0.00 0.00 5.34
4535 4988 5.125739 AGTCGAAGTTACTGATCCTTTCGAT 59.874 40.000 9.84 0.00 0.00 3.59
4551 5004 2.631062 TGTACCACATCCAAGTCGAAGT 59.369 45.455 0.00 0.00 0.00 3.01
4571 5024 3.128242 GGCAGATCTCAGGAATTGTGTTG 59.872 47.826 0.00 0.00 0.00 3.33
4576 5029 3.134262 TCAGAGGCAGATCTCAGGAATTG 59.866 47.826 0.00 0.00 36.30 2.32
4579 5032 2.539432 TCAGAGGCAGATCTCAGGAA 57.461 50.000 0.00 0.00 36.30 3.36
4581 5034 3.842007 AAATCAGAGGCAGATCTCAGG 57.158 47.619 0.00 0.00 36.30 3.86
4582 5035 5.064962 GTCAAAAATCAGAGGCAGATCTCAG 59.935 44.000 0.00 0.00 36.30 3.35
4583 5036 4.940046 GTCAAAAATCAGAGGCAGATCTCA 59.060 41.667 0.00 0.00 36.30 3.27
4584 5037 4.940046 TGTCAAAAATCAGAGGCAGATCTC 59.060 41.667 0.00 0.00 0.00 2.75
4593 5050 6.323203 ACTTCCATGTGTCAAAAATCAGAG 57.677 37.500 0.00 0.00 0.00 3.35
4630 5087 7.011857 GGGATCTATTGAAGTTGCTCTAAGTTG 59.988 40.741 0.00 0.00 32.13 3.16
4631 5088 7.051000 GGGATCTATTGAAGTTGCTCTAAGTT 58.949 38.462 0.00 0.00 34.65 2.66
4632 5089 6.587273 GGGATCTATTGAAGTTGCTCTAAGT 58.413 40.000 0.00 0.00 0.00 2.24
4636 5093 3.452627 ACGGGATCTATTGAAGTTGCTCT 59.547 43.478 0.00 0.00 0.00 4.09
4645 5102 8.486942 TCTTTTAAGGATACGGGATCTATTGA 57.513 34.615 0.00 0.00 46.39 2.57
4654 5111 4.992951 CCGGTAATCTTTTAAGGATACGGG 59.007 45.833 14.90 13.07 46.39 5.28
4664 5121 8.703378 TTTTTCCCTTAACCGGTAATCTTTTA 57.297 30.769 8.00 0.00 0.00 1.52
4665 5122 7.600231 TTTTTCCCTTAACCGGTAATCTTTT 57.400 32.000 8.00 0.00 0.00 2.27
4686 5143 2.039418 GGAACTGTTGGAGGCCTTTTT 58.961 47.619 6.77 0.00 0.00 1.94
4687 5144 1.704641 GGAACTGTTGGAGGCCTTTT 58.295 50.000 6.77 0.00 0.00 2.27
4688 5145 0.178961 GGGAACTGTTGGAGGCCTTT 60.179 55.000 6.77 0.00 0.00 3.11
4689 5146 1.460699 GGGAACTGTTGGAGGCCTT 59.539 57.895 6.77 0.00 0.00 4.35
4690 5147 2.895424 CGGGAACTGTTGGAGGCCT 61.895 63.158 3.86 3.86 0.00 5.19
4691 5148 2.359975 CGGGAACTGTTGGAGGCC 60.360 66.667 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.