Multiple sequence alignment - TraesCS3B01G483600

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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 TraesCS3B01G483600 chr3B 100.000 4724 0 0 1 4724 730282387 730287110 0.000000e+00 8724
1 TraesCS3B01G483600 chr3B 83.884 3419 456 64 389 3757 730308862 730312235 0.000000e+00 3173
2 TraesCS3B01G483600 chr3B 97.531 243 4 2 4483 4724 17613476 17613235 9.460000e-112 414
3 TraesCS3B01G483600 chr3B 89.157 332 27 4 3922 4247 730312330 730312658 5.690000e-109 405
4 TraesCS3B01G483600 chr3D 96.185 4430 129 15 1 4394 550659156 550663581 0.000000e+00 7208
5 TraesCS3B01G483600 chr3D 84.019 3429 459 55 389 3777 550667623 550671002 0.000000e+00 3214
6 TraesCS3B01G483600 chr3D 83.624 287 37 7 3812 4094 550671142 550671422 1.300000e-65 261
7 TraesCS3B01G483600 chr3A 96.203 3266 94 5 758 4019 687592657 687595896 0.000000e+00 5317
8 TraesCS3B01G483600 chr3A 88.727 1579 135 14 2818 4379 687614129 687615681 0.000000e+00 1890
9 TraesCS3B01G483600 chr3A 85.838 692 54 12 1 667 687591983 687592655 0.000000e+00 695
10 TraesCS3B01G483600 chr3A 89.931 288 19 3 4105 4382 687595895 687596182 3.470000e-96 363
11 TraesCS3B01G483600 chr4A 77.796 1788 340 39 2012 3781 532216194 532217942 0.000000e+00 1050
12 TraesCS3B01G483600 chr4A 96.296 243 8 1 4483 4724 740519471 740519229 9.530000e-107 398
13 TraesCS3B01G483600 chr2B 97.942 243 4 1 4483 4724 549651563 549651805 2.030000e-113 420
14 TraesCS3B01G483600 chr2B 96.907 97 3 0 4393 4489 549651377 549651473 3.780000e-36 163
15 TraesCS3B01G483600 chr6B 97.521 242 4 2 4483 4723 122684030 122684270 3.400000e-111 412
16 TraesCS3B01G483600 chr6B 97.046 237 5 1 4489 4723 515091919 515092155 9.530000e-107 398
17 TraesCS3B01G483600 chr6B 96.875 96 3 0 4394 4489 122683845 122683940 1.360000e-35 161
18 TraesCS3B01G483600 chr6B 95.876 97 4 0 4393 4489 515091726 515091822 1.760000e-34 158
19 TraesCS3B01G483600 chr1B 97.845 232 5 0 4492 4723 27240063 27239832 7.360000e-108 401
20 TraesCS3B01G483600 chr1B 95.885 243 6 4 4483 4723 665286883 665286643 1.590000e-104 390
21 TraesCS3B01G483600 chr1B 96.875 96 3 0 4394 4489 27240258 27240163 1.360000e-35 161
22 TraesCS3B01G483600 chr1B 96.875 96 3 0 4394 4489 665287068 665286973 1.360000e-35 161
23 TraesCS3B01G483600 chr4B 96.296 243 7 2 4483 4723 245460543 245460301 9.530000e-107 398
24 TraesCS3B01G483600 chr4B 95.833 96 4 0 4394 4489 245460729 245460634 6.330000e-34 156
25 TraesCS3B01G483600 chr7B 96.281 242 7 2 4483 4723 144478598 144478358 3.430000e-106 396
26 TraesCS3B01G483600 chr7B 96.875 96 3 0 4394 4489 144478783 144478688 1.360000e-35 161
27 TraesCS3B01G483600 chr6A 92.929 99 7 0 4391 4489 119296759 119296661 1.370000e-30 145
28 TraesCS3B01G483600 chr7D 91.000 100 7 2 4390 4489 170971286 170971383 2.970000e-27 134


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 TraesCS3B01G483600 chr3B 730282387 730287110 4723 False 8724.0 8724 100.000000 1 4724 1 chr3B.!!$F1 4723
1 TraesCS3B01G483600 chr3B 730308862 730312658 3796 False 1789.0 3173 86.520500 389 4247 2 chr3B.!!$F2 3858
2 TraesCS3B01G483600 chr3D 550659156 550663581 4425 False 7208.0 7208 96.185000 1 4394 1 chr3D.!!$F1 4393
3 TraesCS3B01G483600 chr3D 550667623 550671422 3799 False 1737.5 3214 83.821500 389 4094 2 chr3D.!!$F2 3705
4 TraesCS3B01G483600 chr3A 687591983 687596182 4199 False 2125.0 5317 90.657333 1 4382 3 chr3A.!!$F2 4381
5 TraesCS3B01G483600 chr3A 687614129 687615681 1552 False 1890.0 1890 88.727000 2818 4379 1 chr3A.!!$F1 1561
6 TraesCS3B01G483600 chr4A 532216194 532217942 1748 False 1050.0 1050 77.796000 2012 3781 1 chr4A.!!$F1 1769

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
178 179 0.035343 TTCACCAACACGTGTTCCCA 60.035 50.0 30.24 12.27 35.83 4.37 F
491 507 1.722011 AAAGTTCCATAGCGGACACG 58.278 50.0 0.00 0.00 46.36 4.49 F
521 538 7.667043 ATTTAAGCGATTAAGTCAAGTCACA 57.333 32.0 5.94 0.00 0.00 3.58 F
2333 2419 0.320771 ATGTCACGTGAGACCCTTGC 60.321 55.0 20.73 4.95 37.73 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1034 1111 4.702131 CCTCATCAGTTAAAACCTTCCCAG 59.298 45.833 0.00 0.0 0.00 4.45 R
2333 2419 2.435586 CTGCAACCCAGAGCCTCG 60.436 66.667 0.00 0.0 44.64 4.63 R
3006 3107 3.453717 TCTGCAGCTCTTCAATACTGGAT 59.546 43.478 9.47 0.0 29.78 3.41 R
4473 4724 0.108138 TAGCTTTCCTTCCTCAGCGC 60.108 55.000 0.00 0.0 37.35 5.92 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
70 71 8.175716 GGTAACGATTTTTCTCTTTCAGTATGG 58.824 37.037 0.00 0.00 36.16 2.74
81 82 7.212976 TCTCTTTCAGTATGGATGTATCAAGC 58.787 38.462 0.00 0.00 36.16 4.01
164 165 3.247886 GGAAGAACGAGAAACACTTCACC 59.752 47.826 0.00 0.00 38.73 4.02
178 179 0.035343 TTCACCAACACGTGTTCCCA 60.035 50.000 30.24 12.27 35.83 4.37
196 197 4.376223 TCCCATACCAGGTTTAATCCTCA 58.624 43.478 0.00 0.00 35.37 3.86
200 201 5.532406 CCATACCAGGTTTAATCCTCATGTG 59.468 44.000 0.00 3.08 35.37 3.21
205 206 1.742831 GTTTAATCCTCATGTGCGGCA 59.257 47.619 0.00 0.00 0.00 5.69
274 286 4.156373 CACACAATGCCTATGACATGTTGA 59.844 41.667 0.00 0.00 0.00 3.18
281 293 4.130118 GCCTATGACATGTTGACTTAGGG 58.870 47.826 18.81 8.63 38.96 3.53
430 445 9.199982 CATAGAAGAACATTTCAATTTTGCTGT 57.800 29.630 0.00 0.00 0.00 4.40
491 507 1.722011 AAAGTTCCATAGCGGACACG 58.278 50.000 0.00 0.00 46.36 4.49
521 538 7.667043 ATTTAAGCGATTAAGTCAAGTCACA 57.333 32.000 5.94 0.00 0.00 3.58
578 606 9.696917 ACATGACTTAAATTTTCCTTCATTCAC 57.303 29.630 0.00 0.00 0.00 3.18
2333 2419 0.320771 ATGTCACGTGAGACCCTTGC 60.321 55.000 20.73 4.95 37.73 4.01
2527 2613 3.084786 GCTCTTTGTATTGCAAGGGAGT 58.915 45.455 4.94 0.00 39.09 3.85
2820 2921 1.218316 CCGCACTAAGGTCAGGTCC 59.782 63.158 0.00 0.00 0.00 4.46
3006 3107 5.548406 GGAGTTCAAGCACCTAAAGAACTA 58.452 41.667 6.15 0.00 46.23 2.24
3057 3158 0.396695 CCATCCAAGCCAGCAAGGAT 60.397 55.000 9.33 9.33 41.40 3.24
3354 3455 1.941668 GCACTAAGCTGGTGTCACCTC 60.942 57.143 22.56 13.95 39.58 3.85
3372 3473 1.000283 CTCGGGGAAGATGAAGATCCG 60.000 57.143 0.00 0.00 37.61 4.18
3394 3495 2.639327 GGGATGCTTGCACCACACC 61.639 63.158 13.27 0.00 0.00 4.16
3540 3641 0.769873 AGATCATGGATGGTGCCCTC 59.230 55.000 0.00 0.00 0.00 4.30
3824 4046 6.908825 TGGCATGTTACAATTCTTAAGACAC 58.091 36.000 4.18 0.00 0.00 3.67
3845 4070 4.024048 CACCATTTGCGAGTCTTGTACTTT 60.024 41.667 0.00 0.00 39.07 2.66
3869 4094 5.472148 TGTATCGTGATACGGTTTCTGTTT 58.528 37.500 13.66 0.00 44.97 2.83
3878 4103 6.419413 TGATACGGTTTCTGTTTTGAAAATGC 59.581 34.615 0.00 0.00 37.63 3.56
4009 4238 9.432077 CAATGTTGTAAAATTTGTTTACCTTGC 57.568 29.630 6.53 0.00 34.81 4.01
4052 4284 4.697514 TCTATGTTTCTACTGCATCCTGC 58.302 43.478 0.00 0.00 45.29 4.85
4057 4289 3.423539 TTCTACTGCATCCTGCTTGTT 57.576 42.857 0.34 0.00 45.31 2.83
4114 4346 1.071471 CGTGTCCAAGTGAAGCCCT 59.929 57.895 0.00 0.00 0.00 5.19
4153 4385 0.620700 AGAGGCGGGATTTGGTAGGT 60.621 55.000 0.00 0.00 0.00 3.08
4385 4636 1.811965 TGATGGCCATTTCAAGTGTCG 59.188 47.619 21.84 0.00 0.00 4.35
4394 4645 3.328382 TTTCAAGTGTCGTATGGAGGG 57.672 47.619 0.00 0.00 0.00 4.30
4395 4646 1.191535 TCAAGTGTCGTATGGAGGGG 58.808 55.000 0.00 0.00 0.00 4.79
4396 4647 1.191535 CAAGTGTCGTATGGAGGGGA 58.808 55.000 0.00 0.00 0.00 4.81
4397 4648 1.137086 CAAGTGTCGTATGGAGGGGAG 59.863 57.143 0.00 0.00 0.00 4.30
4398 4649 1.043673 AGTGTCGTATGGAGGGGAGC 61.044 60.000 0.00 0.00 0.00 4.70
4399 4650 1.043673 GTGTCGTATGGAGGGGAGCT 61.044 60.000 0.00 0.00 0.00 4.09
4400 4651 0.755698 TGTCGTATGGAGGGGAGCTC 60.756 60.000 4.71 4.71 0.00 4.09
4401 4652 1.152525 TCGTATGGAGGGGAGCTCC 60.153 63.158 25.59 25.59 41.21 4.70
4402 4653 1.152440 CGTATGGAGGGGAGCTCCT 60.152 63.158 31.36 13.94 41.39 3.69
4403 4654 0.112606 CGTATGGAGGGGAGCTCCTA 59.887 60.000 31.36 12.70 41.39 2.94
4404 4655 1.480683 CGTATGGAGGGGAGCTCCTAA 60.481 57.143 31.36 13.40 41.39 2.69
4405 4656 1.972075 GTATGGAGGGGAGCTCCTAAC 59.028 57.143 31.36 21.09 41.39 2.34
4406 4657 0.400670 ATGGAGGGGAGCTCCTAACC 60.401 60.000 31.36 27.39 41.39 2.85
4407 4658 2.134933 GGAGGGGAGCTCCTAACCG 61.135 68.421 31.36 0.00 37.25 4.44
4408 4659 2.041819 AGGGGAGCTCCTAACCGG 60.042 66.667 31.36 0.00 34.92 5.28
4409 4660 3.862991 GGGGAGCTCCTAACCGGC 61.863 72.222 31.36 13.25 35.95 6.13
4410 4661 4.222847 GGGAGCTCCTAACCGGCG 62.223 72.222 31.36 0.00 35.95 6.46
4411 4662 4.893601 GGAGCTCCTAACCGGCGC 62.894 72.222 26.25 0.00 43.98 6.53
4412 4663 4.893601 GAGCTCCTAACCGGCGCC 62.894 72.222 19.07 19.07 44.75 6.53
4414 4665 4.468689 GCTCCTAACCGGCGCCTT 62.469 66.667 26.68 15.87 37.54 4.35
4415 4666 3.085119 GCTCCTAACCGGCGCCTTA 62.085 63.158 26.68 16.18 37.54 2.69
4416 4667 1.518774 CTCCTAACCGGCGCCTTAA 59.481 57.895 26.68 6.15 0.00 1.85
4417 4668 0.529992 CTCCTAACCGGCGCCTTAAG 60.530 60.000 26.68 15.67 0.00 1.85
4418 4669 2.178235 CCTAACCGGCGCCTTAAGC 61.178 63.158 26.68 0.00 38.52 3.09
4427 4678 2.744709 GCCTTAAGCGCCGGTTCA 60.745 61.111 4.18 0.00 0.00 3.18
4428 4679 2.750888 GCCTTAAGCGCCGGTTCAG 61.751 63.158 4.18 3.71 0.00 3.02
4429 4680 2.106683 CCTTAAGCGCCGGTTCAGG 61.107 63.158 14.08 14.08 29.99 3.86
4430 4681 1.079405 CTTAAGCGCCGGTTCAGGA 60.079 57.895 4.18 0.00 0.00 3.86
4431 4682 0.672401 CTTAAGCGCCGGTTCAGGAA 60.672 55.000 4.18 0.00 0.00 3.36
4432 4683 0.672401 TTAAGCGCCGGTTCAGGAAG 60.672 55.000 4.18 0.00 0.00 3.46
4435 4686 3.121030 CGCCGGTTCAGGAAGCTG 61.121 66.667 1.90 4.29 36.72 4.24
4436 4687 2.747855 GCCGGTTCAGGAAGCTGG 60.748 66.667 1.90 11.85 36.72 4.85
4437 4688 2.747855 CCGGTTCAGGAAGCTGGC 60.748 66.667 9.27 0.00 36.72 4.85
4438 4689 2.032528 CGGTTCAGGAAGCTGGCA 59.967 61.111 9.27 0.00 36.72 4.92
4439 4690 2.037136 CGGTTCAGGAAGCTGGCAG 61.037 63.158 10.94 10.94 36.72 4.85
4440 4691 1.073897 GGTTCAGGAAGCTGGCAGT 59.926 57.895 17.16 0.00 36.02 4.40
4441 4692 0.957888 GGTTCAGGAAGCTGGCAGTC 60.958 60.000 17.16 6.46 36.02 3.51
4442 4693 0.250467 GTTCAGGAAGCTGGCAGTCA 60.250 55.000 17.16 0.00 0.00 3.41
4443 4694 0.250467 TTCAGGAAGCTGGCAGTCAC 60.250 55.000 17.16 7.33 0.00 3.67
4444 4695 1.071987 CAGGAAGCTGGCAGTCACA 59.928 57.895 17.16 0.00 0.00 3.58
4445 4696 1.072159 AGGAAGCTGGCAGTCACAC 59.928 57.895 17.16 3.44 0.00 3.82
4446 4697 2.320587 GGAAGCTGGCAGTCACACG 61.321 63.158 17.16 0.00 0.00 4.49
4447 4698 2.959357 GAAGCTGGCAGTCACACGC 61.959 63.158 17.16 0.00 0.00 5.34
4454 4705 4.969196 CAGTCACACGCCGCACCT 62.969 66.667 0.00 0.00 0.00 4.00
4455 4706 4.664677 AGTCACACGCCGCACCTC 62.665 66.667 0.00 0.00 0.00 3.85
4456 4707 4.961511 GTCACACGCCGCACCTCA 62.962 66.667 0.00 0.00 0.00 3.86
4457 4708 4.002506 TCACACGCCGCACCTCAT 62.003 61.111 0.00 0.00 0.00 2.90
4458 4709 3.792047 CACACGCCGCACCTCATG 61.792 66.667 0.00 0.00 0.00 3.07
4483 4734 4.680237 CCACCACGCGCTGAGGAA 62.680 66.667 18.72 0.00 31.87 3.36
4484 4735 3.114616 CACCACGCGCTGAGGAAG 61.115 66.667 18.72 9.41 31.87 3.46
4485 4736 4.379243 ACCACGCGCTGAGGAAGG 62.379 66.667 18.72 8.21 31.87 3.46
4486 4737 4.069232 CCACGCGCTGAGGAAGGA 62.069 66.667 5.73 0.00 0.00 3.36
4487 4738 2.048222 CACGCGCTGAGGAAGGAA 60.048 61.111 5.73 0.00 0.00 3.36
4488 4739 1.667830 CACGCGCTGAGGAAGGAAA 60.668 57.895 5.73 0.00 0.00 3.13
4489 4740 1.374758 ACGCGCTGAGGAAGGAAAG 60.375 57.895 5.73 0.00 0.00 2.62
4490 4741 2.744768 CGCGCTGAGGAAGGAAAGC 61.745 63.158 5.56 0.00 0.00 3.51
4491 4742 1.376553 GCGCTGAGGAAGGAAAGCT 60.377 57.895 0.00 0.00 33.41 3.74
4492 4743 0.108138 GCGCTGAGGAAGGAAAGCTA 60.108 55.000 0.00 0.00 33.41 3.32
4493 4744 1.933247 CGCTGAGGAAGGAAAGCTAG 58.067 55.000 0.00 0.00 33.41 3.42
4494 4745 1.205893 CGCTGAGGAAGGAAAGCTAGT 59.794 52.381 0.00 0.00 33.41 2.57
4495 4746 2.626840 GCTGAGGAAGGAAAGCTAGTG 58.373 52.381 0.00 0.00 32.82 2.74
4496 4747 2.234908 GCTGAGGAAGGAAAGCTAGTGA 59.765 50.000 0.00 0.00 32.82 3.41
4497 4748 3.855858 CTGAGGAAGGAAAGCTAGTGAC 58.144 50.000 0.00 0.00 0.00 3.67
4498 4749 3.511477 TGAGGAAGGAAAGCTAGTGACT 58.489 45.455 0.00 0.00 0.00 3.41
4499 4750 4.673968 TGAGGAAGGAAAGCTAGTGACTA 58.326 43.478 0.00 0.00 0.00 2.59
4500 4751 4.463186 TGAGGAAGGAAAGCTAGTGACTAC 59.537 45.833 0.00 0.00 0.00 2.73
4501 4752 4.417437 AGGAAGGAAAGCTAGTGACTACA 58.583 43.478 0.00 0.00 0.00 2.74
4502 4753 4.838986 AGGAAGGAAAGCTAGTGACTACAA 59.161 41.667 0.00 0.00 0.00 2.41
4503 4754 4.930405 GGAAGGAAAGCTAGTGACTACAAC 59.070 45.833 0.00 0.00 0.00 3.32
4504 4755 4.175787 AGGAAAGCTAGTGACTACAACG 57.824 45.455 0.00 0.00 0.00 4.10
4505 4756 3.825014 AGGAAAGCTAGTGACTACAACGA 59.175 43.478 0.00 0.00 0.00 3.85
4506 4757 4.280174 AGGAAAGCTAGTGACTACAACGAA 59.720 41.667 0.00 0.00 0.00 3.85
4507 4758 4.385146 GGAAAGCTAGTGACTACAACGAAC 59.615 45.833 0.00 0.00 0.00 3.95
4508 4759 3.198863 AGCTAGTGACTACAACGAACG 57.801 47.619 0.00 0.00 0.00 3.95
4509 4760 2.551459 AGCTAGTGACTACAACGAACGT 59.449 45.455 0.00 0.00 0.00 3.99
4510 4761 2.655474 GCTAGTGACTACAACGAACGTG 59.345 50.000 0.00 0.00 0.00 4.49
4511 4762 3.607775 GCTAGTGACTACAACGAACGTGA 60.608 47.826 0.00 0.00 0.00 4.35
4512 4763 3.425577 AGTGACTACAACGAACGTGAA 57.574 42.857 0.00 0.00 0.00 3.18
4513 4764 3.772932 AGTGACTACAACGAACGTGAAA 58.227 40.909 0.00 0.00 0.00 2.69
4514 4765 4.365723 AGTGACTACAACGAACGTGAAAT 58.634 39.130 0.00 0.00 0.00 2.17
4515 4766 4.208460 AGTGACTACAACGAACGTGAAATG 59.792 41.667 0.00 0.00 0.00 2.32
4516 4767 4.026310 GTGACTACAACGAACGTGAAATGT 60.026 41.667 0.00 4.33 38.00 2.71
4517 4768 5.173673 GTGACTACAACGAACGTGAAATGTA 59.826 40.000 0.00 5.24 32.67 2.29
4518 4769 5.921976 TGACTACAACGAACGTGAAATGTAT 59.078 36.000 0.00 0.00 32.67 2.29
4519 4770 7.060979 GTGACTACAACGAACGTGAAATGTATA 59.939 37.037 0.00 0.00 32.67 1.47
4520 4771 7.594386 TGACTACAACGAACGTGAAATGTATAA 59.406 33.333 0.00 0.00 32.67 0.98
4521 4772 7.946043 ACTACAACGAACGTGAAATGTATAAG 58.054 34.615 0.00 0.00 32.67 1.73
4522 4773 7.809331 ACTACAACGAACGTGAAATGTATAAGA 59.191 33.333 0.00 0.00 32.67 2.10
4523 4774 7.410800 ACAACGAACGTGAAATGTATAAGAA 57.589 32.000 0.00 0.00 32.67 2.52
4524 4775 7.285788 ACAACGAACGTGAAATGTATAAGAAC 58.714 34.615 0.00 0.00 32.67 3.01
4525 4776 6.399204 ACGAACGTGAAATGTATAAGAACC 57.601 37.500 0.00 0.00 32.67 3.62
4526 4777 5.927689 ACGAACGTGAAATGTATAAGAACCA 59.072 36.000 0.00 0.00 32.67 3.67
4527 4778 6.424509 ACGAACGTGAAATGTATAAGAACCAA 59.575 34.615 0.00 0.00 32.67 3.67
4528 4779 7.118680 ACGAACGTGAAATGTATAAGAACCAAT 59.881 33.333 0.00 0.00 32.67 3.16
4529 4780 8.597227 CGAACGTGAAATGTATAAGAACCAATA 58.403 33.333 0.00 0.00 32.67 1.90
4538 4789 9.893305 AATGTATAAGAACCAATAAATTAGCGC 57.107 29.630 0.00 0.00 0.00 5.92
4539 4790 8.671384 TGTATAAGAACCAATAAATTAGCGCT 57.329 30.769 17.26 17.26 0.00 5.92
4540 4791 9.767228 TGTATAAGAACCAATAAATTAGCGCTA 57.233 29.630 14.45 14.45 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.803380 CGAAACTAGTAACCGGGCCG 60.803 60.000 21.46 21.46 0.00 6.13
21 22 5.792468 CCTAACTGACGACGAAACTAGTAAC 59.208 44.000 0.00 0.00 0.00 2.50
70 71 4.280677 AGAGCTAGTCTGGCTTGATACATC 59.719 45.833 12.50 0.00 40.40 3.06
178 179 5.133221 GCACATGAGGATTAAACCTGGTAT 58.867 41.667 9.33 0.00 40.73 2.73
200 201 0.110192 GTGTCTAACTTTGCTGCCGC 60.110 55.000 0.00 0.00 0.00 6.53
205 206 3.206150 CACAGTGGTGTCTAACTTTGCT 58.794 45.455 0.00 0.00 40.24 3.91
229 238 5.011586 TGCCCCATATGTCAATATGTCATG 58.988 41.667 1.24 0.00 42.85 3.07
312 324 4.406648 AAGATGTCGAACCTCATATGCA 57.593 40.909 0.00 0.00 0.00 3.96
521 538 7.429636 ACATAACTAAACGCAGTACATTTGT 57.570 32.000 0.00 0.00 45.00 2.83
578 606 4.734854 GCGTTGTGCTGATAAATGGTATTG 59.265 41.667 0.00 0.00 41.73 1.90
629 666 7.130099 TCTGATAGAACTACTAATTGGGTCCA 58.870 38.462 0.00 0.00 34.56 4.02
706 753 6.101150 TGAAGATACCTTATGCCAATGTACCT 59.899 38.462 0.00 0.00 31.62 3.08
716 763 9.664332 AATATCATGAGTGAAGATACCTTATGC 57.336 33.333 0.09 0.00 38.01 3.14
910 986 8.904099 AAAATTAGGTCGCAAACTAGCTATAT 57.096 30.769 0.00 0.00 0.00 0.86
911 987 8.726870 AAAAATTAGGTCGCAAACTAGCTATA 57.273 30.769 0.00 0.00 0.00 1.31
950 1026 4.628333 CACGTGTTAAATGGGACGATAACT 59.372 41.667 7.58 0.00 35.77 2.24
1034 1111 4.702131 CCTCATCAGTTAAAACCTTCCCAG 59.298 45.833 0.00 0.00 0.00 4.45
2333 2419 2.435586 CTGCAACCCAGAGCCTCG 60.436 66.667 0.00 0.00 44.64 4.63
3006 3107 3.453717 TCTGCAGCTCTTCAATACTGGAT 59.546 43.478 9.47 0.00 29.78 3.41
3057 3158 1.968017 CTTCAGCTGCTCGGCCAAA 60.968 57.895 9.47 0.00 0.00 3.28
3354 3455 0.601311 GCGGATCTTCATCTTCCCCG 60.601 60.000 0.00 0.00 38.58 5.73
3372 3473 1.077501 TGGTGCAAGCATCCCTAGC 60.078 57.895 2.42 0.00 40.88 3.42
3394 3495 2.101415 TCAGATATGTGAGGTTCCGCAG 59.899 50.000 0.00 0.00 0.00 5.18
3540 3641 4.141892 ACATACAAACCATCAATGCATGGG 60.142 41.667 0.00 2.48 46.98 4.00
3810 4032 5.698832 TCGCAAATGGTGTCTTAAGAATTG 58.301 37.500 6.78 7.24 0.00 2.32
3815 4037 3.997021 AGACTCGCAAATGGTGTCTTAAG 59.003 43.478 0.00 0.00 34.78 1.85
3824 4046 4.749245 AAAGTACAAGACTCGCAAATGG 57.251 40.909 0.00 0.00 37.44 3.16
3845 4070 5.063180 ACAGAAACCGTATCACGATACAA 57.937 39.130 15.55 0.00 46.05 2.41
3869 4094 3.388308 CAATGAACACCGGCATTTTCAA 58.612 40.909 0.00 0.00 32.74 2.69
3878 4103 0.523072 CTGAAGGCAATGAACACCGG 59.477 55.000 0.00 0.00 0.00 5.28
3931 4160 5.183713 TCCTGAAATCAGTTTTACAGCATGG 59.816 40.000 9.43 0.00 40.96 3.66
4009 4238 6.320494 AGATTGAGCGGTATCTACTAACAG 57.680 41.667 0.00 0.00 29.56 3.16
4052 4284 1.457303 CGCCTCTTCGAGAACAACAAG 59.543 52.381 0.00 0.00 0.00 3.16
4057 4289 0.458543 GATGCGCCTCTTCGAGAACA 60.459 55.000 4.18 0.00 0.00 3.18
4081 4313 2.251893 GACACGGAAATCAGTCTCGAC 58.748 52.381 0.00 0.00 0.00 4.20
4114 4346 1.686587 TCGGACTCTCAACTCAAGCAA 59.313 47.619 0.00 0.00 0.00 3.91
4153 4385 1.462616 AACACTGCAGTTGTTGAGCA 58.537 45.000 24.44 0.00 36.72 4.26
4371 4622 3.623060 CCTCCATACGACACTTGAAATGG 59.377 47.826 0.00 0.00 36.11 3.16
4398 4649 0.529992 CTTAAGGCGCCGGTTAGGAG 60.530 60.000 23.20 9.54 45.00 3.69
4399 4650 1.518774 CTTAAGGCGCCGGTTAGGA 59.481 57.895 23.20 3.11 45.00 2.94
4400 4651 2.178235 GCTTAAGGCGCCGGTTAGG 61.178 63.158 23.20 16.37 44.97 2.69
4401 4652 3.406559 GCTTAAGGCGCCGGTTAG 58.593 61.111 23.20 17.07 0.00 2.34
4410 4661 2.744709 TGAACCGGCGCTTAAGGC 60.745 61.111 7.64 6.03 37.64 4.35
4411 4662 2.106683 CCTGAACCGGCGCTTAAGG 61.107 63.158 7.64 3.97 0.00 2.69
4412 4663 0.672401 TTCCTGAACCGGCGCTTAAG 60.672 55.000 7.64 0.00 0.00 1.85
4413 4664 0.672401 CTTCCTGAACCGGCGCTTAA 60.672 55.000 7.64 0.00 0.00 1.85
4414 4665 1.079405 CTTCCTGAACCGGCGCTTA 60.079 57.895 7.64 0.00 0.00 3.09
4415 4666 2.358737 CTTCCTGAACCGGCGCTT 60.359 61.111 7.64 0.00 0.00 4.68
4418 4669 3.121030 CAGCTTCCTGAACCGGCG 61.121 66.667 0.00 0.00 41.77 6.46
4419 4670 2.747855 CCAGCTTCCTGAACCGGC 60.748 66.667 0.00 0.00 41.77 6.13
4420 4671 2.747855 GCCAGCTTCCTGAACCGG 60.748 66.667 0.00 0.00 41.77 5.28
4421 4672 2.032528 TGCCAGCTTCCTGAACCG 59.967 61.111 0.00 0.00 41.77 4.44
4422 4673 0.957888 GACTGCCAGCTTCCTGAACC 60.958 60.000 0.00 0.00 41.77 3.62
4423 4674 0.250467 TGACTGCCAGCTTCCTGAAC 60.250 55.000 0.00 0.00 41.77 3.18
4424 4675 0.250467 GTGACTGCCAGCTTCCTGAA 60.250 55.000 0.00 0.00 41.77 3.02
4425 4676 1.372683 GTGACTGCCAGCTTCCTGA 59.627 57.895 0.00 0.00 41.77 3.86
4426 4677 1.071987 TGTGACTGCCAGCTTCCTG 59.928 57.895 0.00 0.00 38.85 3.86
4427 4678 1.072159 GTGTGACTGCCAGCTTCCT 59.928 57.895 0.00 0.00 0.00 3.36
4428 4679 2.320587 CGTGTGACTGCCAGCTTCC 61.321 63.158 0.00 0.00 0.00 3.46
4429 4680 2.959357 GCGTGTGACTGCCAGCTTC 61.959 63.158 0.00 0.00 0.00 3.86
4430 4681 2.974698 GCGTGTGACTGCCAGCTT 60.975 61.111 0.00 0.00 0.00 3.74
4437 4688 4.969196 AGGTGCGGCGTGTGACTG 62.969 66.667 9.37 0.00 0.00 3.51
4438 4689 4.664677 GAGGTGCGGCGTGTGACT 62.665 66.667 9.37 0.00 0.00 3.41
4439 4690 4.961511 TGAGGTGCGGCGTGTGAC 62.962 66.667 9.37 0.08 0.00 3.67
4440 4691 4.002506 ATGAGGTGCGGCGTGTGA 62.003 61.111 9.37 0.00 0.00 3.58
4441 4692 3.792047 CATGAGGTGCGGCGTGTG 61.792 66.667 9.37 0.00 0.00 3.82
4466 4717 4.680237 TTCCTCAGCGCGTGGTGG 62.680 66.667 26.18 16.83 43.77 4.61
4467 4718 3.114616 CTTCCTCAGCGCGTGGTG 61.115 66.667 21.60 21.60 44.96 4.17
4468 4719 4.379243 CCTTCCTCAGCGCGTGGT 62.379 66.667 8.43 0.00 0.00 4.16
4469 4720 3.589654 TTCCTTCCTCAGCGCGTGG 62.590 63.158 8.43 7.87 0.00 4.94
4470 4721 1.630244 CTTTCCTTCCTCAGCGCGTG 61.630 60.000 8.43 5.06 0.00 5.34
4471 4722 1.374758 CTTTCCTTCCTCAGCGCGT 60.375 57.895 8.43 0.00 0.00 6.01
4472 4723 2.744768 GCTTTCCTTCCTCAGCGCG 61.745 63.158 0.00 0.00 0.00 6.86
4473 4724 0.108138 TAGCTTTCCTTCCTCAGCGC 60.108 55.000 0.00 0.00 37.35 5.92
4474 4725 1.205893 ACTAGCTTTCCTTCCTCAGCG 59.794 52.381 0.00 0.00 37.35 5.18
4475 4726 2.234908 TCACTAGCTTTCCTTCCTCAGC 59.765 50.000 0.00 0.00 0.00 4.26
4476 4727 3.513515 AGTCACTAGCTTTCCTTCCTCAG 59.486 47.826 0.00 0.00 0.00 3.35
4477 4728 3.511477 AGTCACTAGCTTTCCTTCCTCA 58.489 45.455 0.00 0.00 0.00 3.86
4478 4729 4.463186 TGTAGTCACTAGCTTTCCTTCCTC 59.537 45.833 0.00 0.00 0.00 3.71
4479 4730 4.417437 TGTAGTCACTAGCTTTCCTTCCT 58.583 43.478 0.00 0.00 0.00 3.36
4480 4731 4.803098 TGTAGTCACTAGCTTTCCTTCC 57.197 45.455 0.00 0.00 0.00 3.46
4481 4732 4.621886 CGTTGTAGTCACTAGCTTTCCTTC 59.378 45.833 0.00 0.00 0.00 3.46
4482 4733 4.280174 TCGTTGTAGTCACTAGCTTTCCTT 59.720 41.667 0.00 0.00 0.00 3.36
4483 4734 3.825014 TCGTTGTAGTCACTAGCTTTCCT 59.175 43.478 0.00 0.00 0.00 3.36
4484 4735 4.170292 TCGTTGTAGTCACTAGCTTTCC 57.830 45.455 0.00 0.00 0.00 3.13
4485 4736 4.088213 CGTTCGTTGTAGTCACTAGCTTTC 59.912 45.833 0.00 0.00 0.00 2.62
4486 4737 3.979495 CGTTCGTTGTAGTCACTAGCTTT 59.021 43.478 0.00 0.00 0.00 3.51
4487 4738 3.004106 ACGTTCGTTGTAGTCACTAGCTT 59.996 43.478 0.00 0.00 0.00 3.74
4488 4739 2.551459 ACGTTCGTTGTAGTCACTAGCT 59.449 45.455 0.00 0.00 0.00 3.32
4489 4740 2.655474 CACGTTCGTTGTAGTCACTAGC 59.345 50.000 0.00 0.00 0.00 3.42
4490 4741 4.137849 TCACGTTCGTTGTAGTCACTAG 57.862 45.455 0.00 0.00 0.00 2.57
4491 4742 4.550577 TTCACGTTCGTTGTAGTCACTA 57.449 40.909 0.00 0.00 0.00 2.74
4492 4743 3.425577 TTCACGTTCGTTGTAGTCACT 57.574 42.857 0.00 0.00 0.00 3.41
4493 4744 4.026310 ACATTTCACGTTCGTTGTAGTCAC 60.026 41.667 0.00 0.00 0.00 3.67
4494 4745 4.114073 ACATTTCACGTTCGTTGTAGTCA 58.886 39.130 0.00 0.00 0.00 3.41
4495 4746 4.703899 ACATTTCACGTTCGTTGTAGTC 57.296 40.909 0.00 0.00 0.00 2.59
4496 4747 7.809331 TCTTATACATTTCACGTTCGTTGTAGT 59.191 33.333 11.34 4.20 0.00 2.73
4497 4748 8.165212 TCTTATACATTTCACGTTCGTTGTAG 57.835 34.615 11.34 3.37 0.00 2.74
4498 4749 8.427012 GTTCTTATACATTTCACGTTCGTTGTA 58.573 33.333 9.08 9.08 0.00 2.41
4499 4750 7.285788 GTTCTTATACATTTCACGTTCGTTGT 58.714 34.615 0.00 0.71 0.00 3.32
4500 4751 6.735063 GGTTCTTATACATTTCACGTTCGTTG 59.265 38.462 0.00 0.00 0.00 4.10
4501 4752 6.424509 TGGTTCTTATACATTTCACGTTCGTT 59.575 34.615 0.00 0.00 0.00 3.85
4502 4753 5.927689 TGGTTCTTATACATTTCACGTTCGT 59.072 36.000 0.00 0.00 0.00 3.85
4503 4754 6.397831 TGGTTCTTATACATTTCACGTTCG 57.602 37.500 0.00 0.00 0.00 3.95
4512 4763 9.893305 GCGCTAATTTATTGGTTCTTATACATT 57.107 29.630 0.00 0.00 0.00 2.71
4513 4764 9.284968 AGCGCTAATTTATTGGTTCTTATACAT 57.715 29.630 8.99 0.00 0.00 2.29
4514 4765 8.671384 AGCGCTAATTTATTGGTTCTTATACA 57.329 30.769 8.99 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.