Multiple sequence alignment - TraesCS1D01G090400

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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 TraesCS1D01G090400 chr1D 100.000 4808 0 0 1 4808 76801321 76796514 0.000000e+00 8879.0
1 TraesCS1D01G090400 chr1A 97.514 3218 53 12 1190 4386 108079947 108076736 0.000000e+00 5474.0
2 TraesCS1D01G090400 chr1A 97.346 1168 15 2 1 1163 108081098 108079942 0.000000e+00 1971.0
3 TraesCS1D01G090400 chr1A 89.941 169 11 3 4382 4550 108076488 108076326 3.770000e-51 213.0
4 TraesCS1D01G090400 chr1B 96.170 2402 69 15 2119 4504 120407203 120404809 0.000000e+00 3904.0
5 TraesCS1D01G090400 chr1B 95.442 2150 64 14 1 2121 120409610 120407466 0.000000e+00 3397.0
6 TraesCS1D01G090400 chr1B 94.922 256 13 0 4550 4805 679397911 679398166 7.500000e-108 401.0
7 TraesCS1D01G090400 chr1B 96.774 31 1 0 4518 4548 120404554 120404524 9.000000e-03 52.8
8 TraesCS1D01G090400 chr6B 96.484 256 9 0 4550 4805 116426896 116427151 1.600000e-114 424.0
9 TraesCS1D01G090400 chr7A 95.367 259 12 0 4550 4808 680755935 680755677 3.460000e-111 412.0
10 TraesCS1D01G090400 chr7A 80.423 189 33 3 4365 4551 688994286 688994100 1.800000e-29 141.0
11 TraesCS1D01G090400 chr6D 95.331 257 12 0 4549 4805 299218532 299218276 4.480000e-110 409.0
12 TraesCS1D01G090400 chrUn 94.922 256 13 0 4550 4805 318893440 318893185 7.500000e-108 401.0
13 TraesCS1D01G090400 chrUn 95.257 253 12 0 4550 4802 358455033 358455285 7.500000e-108 401.0
14 TraesCS1D01G090400 chrUn 94.208 259 15 0 4550 4808 258410282 258410024 3.490000e-106 396.0
15 TraesCS1D01G090400 chrUn 94.208 259 15 0 4550 4808 336703253 336702995 3.490000e-106 396.0
16 TraesCS1D01G090400 chr4D 94.922 256 13 0 4550 4805 69344596 69344851 7.500000e-108 401.0
17 TraesCS1D01G090400 chr2A 82.540 189 25 6 4363 4550 74118281 74118462 4.980000e-35 159.0
18 TraesCS1D01G090400 chr2B 95.349 43 2 0 4509 4551 114055284 114055326 8.630000e-08 69.4
19 TraesCS1D01G090400 chr5D 81.081 74 10 2 4433 4504 443803065 443803136 6.720000e-04 56.5


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 TraesCS1D01G090400 chr1D 76796514 76801321 4807 True 8879.000000 8879 100.000000 1 4808 1 chr1D.!!$R1 4807
1 TraesCS1D01G090400 chr1A 108076326 108081098 4772 True 2552.666667 5474 94.933667 1 4550 3 chr1A.!!$R1 4549
2 TraesCS1D01G090400 chr1B 120404524 120409610 5086 True 2451.266667 3904 96.128667 1 4548 3 chr1B.!!$R1 4547

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
860 880 0.994247 TGCTTGGTGGATGAGGATGT 59.006 50.000 0.00 0.00 0.00 3.06 F
1765 1790 2.509052 TATAGTCAGCATGCACCGTC 57.491 50.000 21.98 5.72 34.76 4.79 F
1827 1859 3.825143 AATAATTGGGAACATGCCAGC 57.175 42.857 0.00 0.00 39.66 4.85 F
1970 2004 6.985117 AGCTGTCTTTTCATATGAAGCAAAA 58.015 32.000 21.13 11.98 35.21 2.44 F
3104 3403 2.037772 CCACTGGATTTAGGATCCGAGG 59.962 54.545 5.98 0.00 41.03 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2569 2868 1.153005 GCAAGCCTGGAGATGGAGG 60.153 63.158 0.00 0.0 0.00 4.30 R
3049 3348 0.872021 CTCCTATCCGTTGTCTGCGC 60.872 60.000 0.00 0.0 0.00 6.09 R
3104 3403 1.372087 CCGCAAGATCTTCCCAGCAC 61.372 60.000 4.57 0.0 43.02 4.40 R
3306 3605 2.239681 TCTTCTCAGGGGAAGAGTCC 57.760 55.000 7.51 0.0 44.37 3.85 R
4550 5374 0.102481 ACGCACGGGCATTCTACTAG 59.898 55.000 11.77 0.0 41.24 2.57 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
179 184 7.094634 CCACAACACATTAGTAAAAGATGCTCT 60.095 37.037 0.00 0.00 0.00 4.09
799 819 7.656412 TGAGTAGCTATTCTTCTTGCTGATAG 58.344 38.462 16.27 0.00 37.02 2.08
815 835 8.437360 TTGCTGATAGAAAGTATACCATGTTG 57.563 34.615 0.00 0.00 0.00 3.33
860 880 0.994247 TGCTTGGTGGATGAGGATGT 59.006 50.000 0.00 0.00 0.00 3.06
1608 1633 8.604640 ATCTCATATCATAGTGCTGTTCAAAG 57.395 34.615 0.00 0.00 0.00 2.77
1765 1790 2.509052 TATAGTCAGCATGCACCGTC 57.491 50.000 21.98 5.72 34.76 4.79
1827 1859 3.825143 AATAATTGGGAACATGCCAGC 57.175 42.857 0.00 0.00 39.66 4.85
1970 2004 6.985117 AGCTGTCTTTTCATATGAAGCAAAA 58.015 32.000 21.13 11.98 35.21 2.44
1971 2005 7.609056 AGCTGTCTTTTCATATGAAGCAAAAT 58.391 30.769 21.13 3.91 35.21 1.82
2039 2073 7.939588 ACTCTATACCCAGCATATTTCCTTTTC 59.060 37.037 0.00 0.00 0.00 2.29
2050 2084 8.515414 AGCATATTTCCTTTTCTGAAGTTACAC 58.485 33.333 0.00 0.00 0.00 2.90
2569 2868 7.250569 TCAAAAAGTTGATGAGTTGTTGAGTC 58.749 34.615 0.00 0.00 39.11 3.36
3104 3403 2.037772 CCACTGGATTTAGGATCCGAGG 59.962 54.545 5.98 0.00 41.03 4.63
3822 4121 8.871686 ACAAACAATAACAATTCAAGAGTTCC 57.128 30.769 0.00 0.00 0.00 3.62
3873 4189 0.329261 TCAAGGGCAGTGAATCCCAG 59.671 55.000 7.03 0.05 45.07 4.45
4000 4316 6.486253 TTTTCTTGAGAGTCATCATTTCGG 57.514 37.500 0.00 0.00 0.00 4.30
4003 4319 1.212616 GAGAGTCATCATTTCGGCCG 58.787 55.000 22.12 22.12 0.00 6.13
4291 4619 3.134081 GGCTTACATCTGCTTGGTACCTA 59.866 47.826 14.36 4.36 0.00 3.08
4305 4633 6.039382 GCTTGGTACCTATTTTTCAGTATGGG 59.961 42.308 14.36 0.00 36.16 4.00
4408 4991 2.547218 CCCACGTGTATCCCTAAATCGG 60.547 54.545 15.65 0.00 0.00 4.18
4415 4998 7.011669 CACGTGTATCCCTAAATCGGTAATTTT 59.988 37.037 7.58 0.00 38.53 1.82
4545 5369 9.575868 TTACATTGGTAAAATTGACAACCTAGA 57.424 29.630 0.00 0.00 36.57 2.43
4550 5374 9.444600 TTGGTAAAATTGACAACCTAGAGATAC 57.555 33.333 0.00 0.00 32.99 2.24
4551 5375 8.822805 TGGTAAAATTGACAACCTAGAGATACT 58.177 33.333 0.00 0.00 32.99 2.12
4560 5384 9.562408 TGACAACCTAGAGATACTAGTAGAATG 57.438 37.037 8.85 1.22 45.01 2.67
4561 5385 8.398878 ACAACCTAGAGATACTAGTAGAATGC 57.601 38.462 8.85 0.00 45.01 3.56
4562 5386 7.449086 ACAACCTAGAGATACTAGTAGAATGCC 59.551 40.741 8.85 0.00 45.01 4.40
4563 5387 6.486941 ACCTAGAGATACTAGTAGAATGCCC 58.513 44.000 8.85 0.00 45.01 5.36
4564 5388 5.587043 CCTAGAGATACTAGTAGAATGCCCG 59.413 48.000 8.85 0.00 45.01 6.13
4565 5389 4.988029 AGAGATACTAGTAGAATGCCCGT 58.012 43.478 8.85 0.00 0.00 5.28
4566 5390 4.762765 AGAGATACTAGTAGAATGCCCGTG 59.237 45.833 8.85 0.00 0.00 4.94
4567 5391 3.256136 AGATACTAGTAGAATGCCCGTGC 59.744 47.826 8.85 0.00 38.26 5.34
4568 5392 0.102481 ACTAGTAGAATGCCCGTGCG 59.898 55.000 3.59 0.00 41.78 5.34
4569 5393 0.102481 CTAGTAGAATGCCCGTGCGT 59.898 55.000 0.00 0.00 41.78 5.24
4571 5395 1.019278 AGTAGAATGCCCGTGCGTTG 61.019 55.000 0.86 0.00 46.55 4.10
4572 5396 2.395360 TAGAATGCCCGTGCGTTGC 61.395 57.895 0.86 0.00 46.55 4.17
4573 5397 4.776647 GAATGCCCGTGCGTTGCC 62.777 66.667 0.86 0.00 46.55 4.52
4584 5408 2.430582 CGTTGCCACGGCCATTTG 60.431 61.111 2.24 0.00 43.16 2.32
4585 5409 2.913765 CGTTGCCACGGCCATTTGA 61.914 57.895 2.24 0.00 43.16 2.69
4586 5410 1.365633 GTTGCCACGGCCATTTGAA 59.634 52.632 2.24 0.00 41.09 2.69
4587 5411 0.249657 GTTGCCACGGCCATTTGAAA 60.250 50.000 2.24 0.00 41.09 2.69
4588 5412 0.683973 TTGCCACGGCCATTTGAAAT 59.316 45.000 2.24 0.00 41.09 2.17
4589 5413 1.550327 TGCCACGGCCATTTGAAATA 58.450 45.000 2.24 0.00 41.09 1.40
4590 5414 2.106566 TGCCACGGCCATTTGAAATAT 58.893 42.857 2.24 0.00 41.09 1.28
4591 5415 2.499289 TGCCACGGCCATTTGAAATATT 59.501 40.909 2.24 0.00 41.09 1.28
4592 5416 3.055530 TGCCACGGCCATTTGAAATATTT 60.056 39.130 2.24 0.00 41.09 1.40
4593 5417 3.938334 GCCACGGCCATTTGAAATATTTT 59.062 39.130 2.24 0.00 34.56 1.82
4594 5418 4.201802 GCCACGGCCATTTGAAATATTTTG 60.202 41.667 2.24 0.00 34.56 2.44
4595 5419 4.934602 CCACGGCCATTTGAAATATTTTGT 59.065 37.500 2.24 0.00 0.00 2.83
4596 5420 5.411053 CCACGGCCATTTGAAATATTTTGTT 59.589 36.000 2.24 0.00 0.00 2.83
4597 5421 6.305639 CACGGCCATTTGAAATATTTTGTTG 58.694 36.000 2.24 0.00 0.00 3.33
4598 5422 5.411053 ACGGCCATTTGAAATATTTTGTTGG 59.589 36.000 2.24 8.62 0.00 3.77
4599 5423 5.641209 CGGCCATTTGAAATATTTTGTTGGA 59.359 36.000 17.58 0.01 0.00 3.53
4600 5424 6.183360 CGGCCATTTGAAATATTTTGTTGGAG 60.183 38.462 17.58 10.46 0.00 3.86
4601 5425 6.654582 GGCCATTTGAAATATTTTGTTGGAGT 59.345 34.615 17.58 0.00 0.00 3.85
4602 5426 7.174772 GGCCATTTGAAATATTTTGTTGGAGTT 59.825 33.333 17.58 0.00 0.00 3.01
4603 5427 8.229811 GCCATTTGAAATATTTTGTTGGAGTTC 58.770 33.333 17.58 0.00 0.00 3.01
4604 5428 9.492973 CCATTTGAAATATTTTGTTGGAGTTCT 57.507 29.630 1.43 0.00 0.00 3.01
4692 5516 8.934023 ATTGAAAACTACTTTTCTACATGGGA 57.066 30.769 0.00 0.00 43.97 4.37
4693 5517 8.754991 TTGAAAACTACTTTTCTACATGGGAA 57.245 30.769 0.00 0.00 43.97 3.97
4694 5518 8.754991 TGAAAACTACTTTTCTACATGGGAAA 57.245 30.769 10.64 10.64 43.97 3.13
4695 5519 8.626526 TGAAAACTACTTTTCTACATGGGAAAC 58.373 33.333 13.24 3.32 43.97 2.78
4696 5520 8.762481 AAAACTACTTTTCTACATGGGAAACT 57.238 30.769 13.24 6.75 33.22 2.66
4697 5521 8.762481 AAACTACTTTTCTACATGGGAAACTT 57.238 30.769 13.24 7.81 33.22 2.66
4698 5522 8.762481 AACTACTTTTCTACATGGGAAACTTT 57.238 30.769 13.24 6.03 33.22 2.66
4699 5523 8.392372 ACTACTTTTCTACATGGGAAACTTTC 57.608 34.615 13.24 0.00 33.22 2.62
4700 5524 7.996644 ACTACTTTTCTACATGGGAAACTTTCA 59.003 33.333 13.24 1.94 33.22 2.69
4701 5525 7.654022 ACTTTTCTACATGGGAAACTTTCAA 57.346 32.000 13.24 1.41 33.22 2.69
4702 5526 8.250143 ACTTTTCTACATGGGAAACTTTCAAT 57.750 30.769 13.24 0.00 33.22 2.57
4703 5527 8.360390 ACTTTTCTACATGGGAAACTTTCAATC 58.640 33.333 13.24 0.00 33.22 2.67
4704 5528 8.477419 TTTTCTACATGGGAAACTTTCAATCT 57.523 30.769 13.24 0.00 33.22 2.40
4705 5529 9.581289 TTTTCTACATGGGAAACTTTCAATCTA 57.419 29.630 13.24 0.00 33.22 1.98
4706 5530 9.753674 TTTCTACATGGGAAACTTTCAATCTAT 57.246 29.630 10.64 0.00 0.00 1.98
4707 5531 9.753674 TTCTACATGGGAAACTTTCAATCTATT 57.246 29.630 0.00 0.00 0.00 1.73
4708 5532 9.396022 TCTACATGGGAAACTTTCAATCTATTC 57.604 33.333 0.00 0.00 0.00 1.75
4709 5533 9.177608 CTACATGGGAAACTTTCAATCTATTCA 57.822 33.333 0.00 0.00 0.00 2.57
4710 5534 8.599624 ACATGGGAAACTTTCAATCTATTCAT 57.400 30.769 0.00 0.00 0.00 2.57
4711 5535 8.689972 ACATGGGAAACTTTCAATCTATTCATC 58.310 33.333 0.00 0.00 0.00 2.92
4712 5536 8.910944 CATGGGAAACTTTCAATCTATTCATCT 58.089 33.333 3.93 0.00 0.00 2.90
4713 5537 8.884124 TGGGAAACTTTCAATCTATTCATCTT 57.116 30.769 3.93 0.00 0.00 2.40
4714 5538 9.312904 TGGGAAACTTTCAATCTATTCATCTTT 57.687 29.630 3.93 0.00 0.00 2.52
4731 5555 9.661563 ATTCATCTTTAAACATGGTAGTACGAA 57.338 29.630 3.95 0.00 0.00 3.85
4732 5556 8.697846 TCATCTTTAAACATGGTAGTACGAAG 57.302 34.615 3.95 0.00 0.00 3.79
4733 5557 8.525316 TCATCTTTAAACATGGTAGTACGAAGA 58.475 33.333 3.95 0.00 0.00 2.87
4734 5558 9.146984 CATCTTTAAACATGGTAGTACGAAGAA 57.853 33.333 0.00 0.00 0.00 2.52
4735 5559 8.524870 TCTTTAAACATGGTAGTACGAAGAAC 57.475 34.615 0.00 0.00 0.00 3.01
4736 5560 8.143193 TCTTTAAACATGGTAGTACGAAGAACA 58.857 33.333 0.00 0.00 0.00 3.18
4737 5561 8.836268 TTTAAACATGGTAGTACGAAGAACAT 57.164 30.769 0.00 0.00 0.00 2.71
4738 5562 6.963049 AAACATGGTAGTACGAAGAACATC 57.037 37.500 0.00 0.00 0.00 3.06
4740 5564 3.770263 TGGTAGTACGAAGAACATCGG 57.230 47.619 4.63 0.00 46.82 4.18
4741 5565 3.346315 TGGTAGTACGAAGAACATCGGA 58.654 45.455 4.63 0.00 46.82 4.55
4742 5566 3.376234 TGGTAGTACGAAGAACATCGGAG 59.624 47.826 4.63 0.00 46.82 4.63
4743 5567 3.624861 GGTAGTACGAAGAACATCGGAGA 59.375 47.826 4.63 0.00 46.82 3.71
4744 5568 4.275443 GGTAGTACGAAGAACATCGGAGAT 59.725 45.833 4.63 0.00 46.82 2.75
4745 5569 5.468072 GGTAGTACGAAGAACATCGGAGATA 59.532 44.000 4.63 0.00 46.82 1.98
4746 5570 6.017605 GGTAGTACGAAGAACATCGGAGATAA 60.018 42.308 4.63 0.00 46.82 1.75
4747 5571 6.636562 AGTACGAAGAACATCGGAGATAAT 57.363 37.500 4.63 0.00 46.82 1.28
4748 5572 7.741027 AGTACGAAGAACATCGGAGATAATA 57.259 36.000 4.63 0.00 46.82 0.98
4749 5573 7.808672 AGTACGAAGAACATCGGAGATAATAG 58.191 38.462 4.63 0.00 46.82 1.73
4750 5574 6.879276 ACGAAGAACATCGGAGATAATAGA 57.121 37.500 4.63 0.00 46.82 1.98
4751 5575 7.273320 ACGAAGAACATCGGAGATAATAGAA 57.727 36.000 4.63 0.00 46.82 2.10
4752 5576 7.713750 ACGAAGAACATCGGAGATAATAGAAA 58.286 34.615 4.63 0.00 46.82 2.52
4753 5577 8.361139 ACGAAGAACATCGGAGATAATAGAAAT 58.639 33.333 4.63 0.00 46.82 2.17
4754 5578 9.197694 CGAAGAACATCGGAGATAATAGAAATT 57.802 33.333 0.00 0.00 45.12 1.82
4764 5588 9.946165 CGGAGATAATAGAAATTAAAAACCACC 57.054 33.333 0.00 0.00 31.44 4.61
4770 5594 8.570068 AATAGAAATTAAAAACCACCTAGCGA 57.430 30.769 0.00 0.00 0.00 4.93
4771 5595 6.250344 AGAAATTAAAAACCACCTAGCGAC 57.750 37.500 0.00 0.00 0.00 5.19
4772 5596 4.673534 AATTAAAAACCACCTAGCGACG 57.326 40.909 0.00 0.00 0.00 5.12
4773 5597 3.383620 TTAAAAACCACCTAGCGACGA 57.616 42.857 0.00 0.00 0.00 4.20
4774 5598 1.505425 AAAAACCACCTAGCGACGAC 58.495 50.000 0.00 0.00 0.00 4.34
4775 5599 0.677842 AAAACCACCTAGCGACGACT 59.322 50.000 0.00 0.00 0.00 4.18
4776 5600 1.538047 AAACCACCTAGCGACGACTA 58.462 50.000 0.00 0.00 0.00 2.59
4777 5601 0.807496 AACCACCTAGCGACGACTAC 59.193 55.000 0.00 0.00 0.00 2.73
4778 5602 0.321919 ACCACCTAGCGACGACTACA 60.322 55.000 0.00 0.00 0.00 2.74
4779 5603 1.022735 CCACCTAGCGACGACTACAT 58.977 55.000 0.00 0.00 0.00 2.29
4780 5604 2.216046 CCACCTAGCGACGACTACATA 58.784 52.381 0.00 0.00 0.00 2.29
4781 5605 2.812591 CCACCTAGCGACGACTACATAT 59.187 50.000 0.00 0.00 0.00 1.78
4782 5606 3.999001 CCACCTAGCGACGACTACATATA 59.001 47.826 0.00 0.00 0.00 0.86
4783 5607 4.142945 CCACCTAGCGACGACTACATATAC 60.143 50.000 0.00 0.00 0.00 1.47
4784 5608 4.689812 CACCTAGCGACGACTACATATACT 59.310 45.833 0.00 0.00 0.00 2.12
4785 5609 4.689812 ACCTAGCGACGACTACATATACTG 59.310 45.833 0.00 0.00 0.00 2.74
4786 5610 4.093115 CCTAGCGACGACTACATATACTGG 59.907 50.000 0.00 0.00 0.00 4.00
4787 5611 3.736720 AGCGACGACTACATATACTGGA 58.263 45.455 0.00 0.00 0.00 3.86
4788 5612 3.747010 AGCGACGACTACATATACTGGAG 59.253 47.826 0.00 0.00 42.13 3.86
4789 5613 3.667430 GCGACGACTACATATACTGGAGC 60.667 52.174 0.00 0.00 39.74 4.70
4790 5614 3.423253 CGACGACTACATATACTGGAGCG 60.423 52.174 0.00 0.00 39.74 5.03
4791 5615 3.736720 ACGACTACATATACTGGAGCGA 58.263 45.455 0.00 0.00 39.74 4.93
4792 5616 3.747010 ACGACTACATATACTGGAGCGAG 59.253 47.826 0.00 0.00 39.74 5.03
4793 5617 3.995048 CGACTACATATACTGGAGCGAGA 59.005 47.826 0.00 0.00 39.74 4.04
4794 5618 4.143073 CGACTACATATACTGGAGCGAGAC 60.143 50.000 0.00 0.00 39.74 3.36
4795 5619 3.747010 ACTACATATACTGGAGCGAGACG 59.253 47.826 0.00 0.00 39.74 4.18
4796 5620 2.847441 ACATATACTGGAGCGAGACGA 58.153 47.619 0.00 0.00 0.00 4.20
4797 5621 3.211865 ACATATACTGGAGCGAGACGAA 58.788 45.455 0.00 0.00 0.00 3.85
4798 5622 3.251245 ACATATACTGGAGCGAGACGAAG 59.749 47.826 0.00 0.00 0.00 3.79
4799 5623 1.025812 ATACTGGAGCGAGACGAAGG 58.974 55.000 0.00 0.00 0.00 3.46
4800 5624 0.322277 TACTGGAGCGAGACGAAGGT 60.322 55.000 0.00 0.00 0.00 3.50
4801 5625 1.153939 CTGGAGCGAGACGAAGGTG 60.154 63.158 0.00 0.00 0.00 4.00
4802 5626 1.867919 CTGGAGCGAGACGAAGGTGT 61.868 60.000 0.00 0.00 0.00 4.16
4803 5627 1.444553 GGAGCGAGACGAAGGTGTG 60.445 63.158 0.00 0.00 0.00 3.82
4804 5628 2.049063 AGCGAGACGAAGGTGTGC 60.049 61.111 0.00 0.00 0.00 4.57
4805 5629 2.355837 GCGAGACGAAGGTGTGCA 60.356 61.111 0.00 0.00 0.00 4.57
4806 5630 2.375766 GCGAGACGAAGGTGTGCAG 61.376 63.158 0.00 0.00 0.00 4.41
4807 5631 2.375766 CGAGACGAAGGTGTGCAGC 61.376 63.158 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
525 531 9.023967 CAAACTTTCCTTATGTTCAAGAAAGTG 57.976 33.333 14.99 3.11 36.76 3.16
860 880 1.638589 CCCCCACCCTCTTTATTGTGA 59.361 52.381 0.00 0.00 0.00 3.58
1765 1790 5.470777 TGTGTTAATACCGTCCCAAAGAAAG 59.529 40.000 0.00 0.00 0.00 2.62
1827 1859 1.838112 TAGGGCCAATGCAAAGACAG 58.162 50.000 6.18 0.00 40.13 3.51
1970 2004 7.802117 TCGTCCAAATTTCCTCCTCTAATTAT 58.198 34.615 0.00 0.00 0.00 1.28
1971 2005 7.093024 ACTCGTCCAAATTTCCTCCTCTAATTA 60.093 37.037 0.00 0.00 0.00 1.40
1980 2014 4.142881 GCTACAACTCGTCCAAATTTCCTC 60.143 45.833 0.00 0.00 0.00 3.71
2050 2084 8.553459 AAATTGTAGGAAGTAACACTGAGATG 57.447 34.615 0.00 0.00 0.00 2.90
2066 2100 8.110860 AGTAGAATTTGTGGTGAAATTGTAGG 57.889 34.615 0.00 0.00 36.00 3.18
2569 2868 1.153005 GCAAGCCTGGAGATGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
2631 2930 7.286313 TCACCATGACAATTATTATGGCAGTA 58.714 34.615 7.40 0.00 42.98 2.74
2745 3044 8.781951 TCTTTTAGGATGATAACAAGGGAAGAT 58.218 33.333 0.00 0.00 0.00 2.40
3049 3348 0.872021 CTCCTATCCGTTGTCTGCGC 60.872 60.000 0.00 0.00 0.00 6.09
3104 3403 1.372087 CCGCAAGATCTTCCCAGCAC 61.372 60.000 4.57 0.00 43.02 4.40
3306 3605 2.239681 TCTTCTCAGGGGAAGAGTCC 57.760 55.000 7.51 0.00 44.37 3.85
3838 4137 4.515567 GCCCTTGATCGGAAAAACTATAGG 59.484 45.833 4.43 0.00 0.00 2.57
3873 4189 3.459969 ACCTAACCCCCTCATTCTCATTC 59.540 47.826 0.00 0.00 0.00 2.67
4000 4316 5.846203 TGAACTTATAAGGTATGGTACGGC 58.154 41.667 16.73 0.00 0.00 5.68
4003 4319 8.027771 CCGATCTGAACTTATAAGGTATGGTAC 58.972 40.741 16.73 0.00 0.00 3.34
4219 4546 5.076182 CAGGGCTCTGACAGAATATAGAGA 58.924 45.833 8.28 0.00 43.49 3.10
4220 4547 4.220382 CCAGGGCTCTGACAGAATATAGAG 59.780 50.000 17.43 0.00 43.49 2.43
4408 4991 8.840833 ACCCAAATTATGTTGGTCAAAATTAC 57.159 30.769 3.44 0.00 45.72 1.89
4545 5369 3.256136 GCACGGGCATTCTACTAGTATCT 59.744 47.826 3.77 0.00 40.72 1.98
4550 5374 0.102481 ACGCACGGGCATTCTACTAG 59.898 55.000 11.77 0.00 41.24 2.57
4551 5375 0.533491 AACGCACGGGCATTCTACTA 59.467 50.000 11.77 0.00 41.24 1.82
4552 5376 1.019278 CAACGCACGGGCATTCTACT 61.019 55.000 11.77 0.00 41.24 2.57
4553 5377 1.423845 CAACGCACGGGCATTCTAC 59.576 57.895 11.77 0.00 41.24 2.59
4554 5378 2.395360 GCAACGCACGGGCATTCTA 61.395 57.895 11.77 0.00 41.24 2.10
4555 5379 3.737172 GCAACGCACGGGCATTCT 61.737 61.111 11.77 0.00 41.24 2.40
4556 5380 4.776647 GGCAACGCACGGGCATTC 62.777 66.667 11.77 0.00 41.24 2.67
4568 5392 0.249657 TTTCAAATGGCCGTGGCAAC 60.250 50.000 13.76 0.00 42.43 4.17
4569 5393 0.683973 ATTTCAAATGGCCGTGGCAA 59.316 45.000 13.76 0.56 42.43 4.52
4570 5394 1.550327 TATTTCAAATGGCCGTGGCA 58.450 45.000 13.76 1.08 44.11 4.92
4571 5395 2.888834 ATATTTCAAATGGCCGTGGC 57.111 45.000 0.00 1.16 41.06 5.01
4572 5396 4.934602 ACAAAATATTTCAAATGGCCGTGG 59.065 37.500 0.00 0.00 0.00 4.94
4573 5397 6.305639 CAACAAAATATTTCAAATGGCCGTG 58.694 36.000 0.00 0.00 0.00 4.94
4574 5398 5.411053 CCAACAAAATATTTCAAATGGCCGT 59.589 36.000 0.10 0.00 0.00 5.68
4575 5399 5.641209 TCCAACAAAATATTTCAAATGGCCG 59.359 36.000 0.10 0.00 0.00 6.13
4576 5400 6.654582 ACTCCAACAAAATATTTCAAATGGCC 59.345 34.615 0.10 0.00 0.00 5.36
4577 5401 7.671495 ACTCCAACAAAATATTTCAAATGGC 57.329 32.000 0.10 0.00 0.00 4.40
4578 5402 9.492973 AGAACTCCAACAAAATATTTCAAATGG 57.507 29.630 0.10 8.22 0.00 3.16
4671 5495 8.762481 AGTTTCCCATGTAGAAAAGTAGTTTT 57.238 30.769 8.02 8.02 38.65 2.43
4672 5496 8.762481 AAGTTTCCCATGTAGAAAAGTAGTTT 57.238 30.769 9.12 0.00 35.13 2.66
4673 5497 8.762481 AAAGTTTCCCATGTAGAAAAGTAGTT 57.238 30.769 9.12 0.00 35.13 2.24
4674 5498 7.996644 TGAAAGTTTCCCATGTAGAAAAGTAGT 59.003 33.333 13.01 0.00 35.13 2.73
4675 5499 8.391075 TGAAAGTTTCCCATGTAGAAAAGTAG 57.609 34.615 13.01 0.00 35.13 2.57
4676 5500 8.754991 TTGAAAGTTTCCCATGTAGAAAAGTA 57.245 30.769 13.01 0.00 35.13 2.24
4677 5501 7.654022 TTGAAAGTTTCCCATGTAGAAAAGT 57.346 32.000 13.01 0.00 35.13 2.66
4678 5502 8.579863 AGATTGAAAGTTTCCCATGTAGAAAAG 58.420 33.333 13.01 0.00 35.13 2.27
4679 5503 8.477419 AGATTGAAAGTTTCCCATGTAGAAAA 57.523 30.769 13.01 0.00 35.13 2.29
4680 5504 9.753674 ATAGATTGAAAGTTTCCCATGTAGAAA 57.246 29.630 13.01 4.49 0.00 2.52
4681 5505 9.753674 AATAGATTGAAAGTTTCCCATGTAGAA 57.246 29.630 13.01 0.00 0.00 2.10
4682 5506 9.396022 GAATAGATTGAAAGTTTCCCATGTAGA 57.604 33.333 13.01 0.00 0.00 2.59
4683 5507 9.177608 TGAATAGATTGAAAGTTTCCCATGTAG 57.822 33.333 13.01 0.00 0.00 2.74
4684 5508 9.699410 ATGAATAGATTGAAAGTTTCCCATGTA 57.301 29.630 13.01 8.29 0.00 2.29
4685 5509 8.599624 ATGAATAGATTGAAAGTTTCCCATGT 57.400 30.769 13.01 6.48 0.00 3.21
4686 5510 8.910944 AGATGAATAGATTGAAAGTTTCCCATG 58.089 33.333 13.01 0.00 0.00 3.66
4687 5511 9.484806 AAGATGAATAGATTGAAAGTTTCCCAT 57.515 29.630 13.01 5.24 0.00 4.00
4688 5512 8.884124 AAGATGAATAGATTGAAAGTTTCCCA 57.116 30.769 13.01 0.26 0.00 4.37
4705 5529 9.661563 TTCGTACTACCATGTTTAAAGATGAAT 57.338 29.630 23.11 14.44 31.83 2.57
4706 5530 9.146984 CTTCGTACTACCATGTTTAAAGATGAA 57.853 33.333 23.11 11.85 31.83 2.57
4707 5531 8.525316 TCTTCGTACTACCATGTTTAAAGATGA 58.475 33.333 23.11 6.71 31.83 2.92
4708 5532 8.697846 TCTTCGTACTACCATGTTTAAAGATG 57.302 34.615 16.42 16.42 0.00 2.90
4709 5533 9.148104 GTTCTTCGTACTACCATGTTTAAAGAT 57.852 33.333 0.00 0.00 0.00 2.40
4710 5534 8.143193 TGTTCTTCGTACTACCATGTTTAAAGA 58.857 33.333 0.00 0.00 0.00 2.52
4711 5535 8.301730 TGTTCTTCGTACTACCATGTTTAAAG 57.698 34.615 0.00 0.00 0.00 1.85
4712 5536 8.836268 ATGTTCTTCGTACTACCATGTTTAAA 57.164 30.769 0.00 0.00 0.00 1.52
4713 5537 7.274033 CGATGTTCTTCGTACTACCATGTTTAA 59.726 37.037 0.00 0.00 34.46 1.52
4714 5538 6.748658 CGATGTTCTTCGTACTACCATGTTTA 59.251 38.462 0.00 0.00 34.46 2.01
4715 5539 5.575606 CGATGTTCTTCGTACTACCATGTTT 59.424 40.000 0.00 0.00 34.46 2.83
4716 5540 5.100259 CGATGTTCTTCGTACTACCATGTT 58.900 41.667 0.00 0.00 34.46 2.71
4717 5541 4.439700 CCGATGTTCTTCGTACTACCATGT 60.440 45.833 7.19 0.00 37.42 3.21
4718 5542 4.042398 CCGATGTTCTTCGTACTACCATG 58.958 47.826 7.19 0.00 37.42 3.66
4719 5543 3.949754 TCCGATGTTCTTCGTACTACCAT 59.050 43.478 7.19 0.00 37.42 3.55
4720 5544 3.346315 TCCGATGTTCTTCGTACTACCA 58.654 45.455 7.19 0.00 37.42 3.25
4721 5545 3.624861 TCTCCGATGTTCTTCGTACTACC 59.375 47.826 7.19 0.00 37.42 3.18
4722 5546 4.871993 TCTCCGATGTTCTTCGTACTAC 57.128 45.455 7.19 0.00 37.42 2.73
4723 5547 7.741027 ATTATCTCCGATGTTCTTCGTACTA 57.259 36.000 7.19 0.00 37.42 1.82
4724 5548 6.636562 ATTATCTCCGATGTTCTTCGTACT 57.363 37.500 7.19 0.00 37.42 2.73
4725 5549 7.804712 TCTATTATCTCCGATGTTCTTCGTAC 58.195 38.462 7.19 0.00 37.42 3.67
4726 5550 7.974482 TCTATTATCTCCGATGTTCTTCGTA 57.026 36.000 7.19 0.00 37.42 3.43
4727 5551 6.879276 TCTATTATCTCCGATGTTCTTCGT 57.121 37.500 7.19 0.00 37.42 3.85
4728 5552 8.749841 ATTTCTATTATCTCCGATGTTCTTCG 57.250 34.615 0.00 1.95 38.83 3.79
4738 5562 9.946165 GGTGGTTTTTAATTTCTATTATCTCCG 57.054 33.333 0.00 0.00 0.00 4.63
4744 5568 9.669887 TCGCTAGGTGGTTTTTAATTTCTATTA 57.330 29.630 0.00 0.00 0.00 0.98
4745 5569 8.456471 GTCGCTAGGTGGTTTTTAATTTCTATT 58.544 33.333 0.00 0.00 0.00 1.73
4746 5570 7.201582 CGTCGCTAGGTGGTTTTTAATTTCTAT 60.202 37.037 0.00 0.00 0.00 1.98
4747 5571 6.091169 CGTCGCTAGGTGGTTTTTAATTTCTA 59.909 38.462 0.00 0.00 0.00 2.10
4748 5572 5.106830 CGTCGCTAGGTGGTTTTTAATTTCT 60.107 40.000 0.00 0.00 0.00 2.52
4749 5573 5.084055 CGTCGCTAGGTGGTTTTTAATTTC 58.916 41.667 0.00 0.00 0.00 2.17
4750 5574 4.756135 TCGTCGCTAGGTGGTTTTTAATTT 59.244 37.500 0.00 0.00 0.00 1.82
4751 5575 4.152938 GTCGTCGCTAGGTGGTTTTTAATT 59.847 41.667 0.00 0.00 0.00 1.40
4752 5576 3.681417 GTCGTCGCTAGGTGGTTTTTAAT 59.319 43.478 0.00 0.00 0.00 1.40
4753 5577 3.059166 GTCGTCGCTAGGTGGTTTTTAA 58.941 45.455 0.00 0.00 0.00 1.52
4754 5578 2.297033 AGTCGTCGCTAGGTGGTTTTTA 59.703 45.455 0.00 0.00 0.00 1.52
4755 5579 1.069668 AGTCGTCGCTAGGTGGTTTTT 59.930 47.619 0.00 0.00 0.00 1.94
4756 5580 0.677842 AGTCGTCGCTAGGTGGTTTT 59.322 50.000 0.00 0.00 0.00 2.43
4757 5581 1.200948 GTAGTCGTCGCTAGGTGGTTT 59.799 52.381 0.00 0.00 0.00 3.27
4758 5582 0.807496 GTAGTCGTCGCTAGGTGGTT 59.193 55.000 0.00 0.00 0.00 3.67
4759 5583 0.321919 TGTAGTCGTCGCTAGGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
4760 5584 1.022735 ATGTAGTCGTCGCTAGGTGG 58.977 55.000 0.00 0.00 0.00 4.61
4761 5585 4.689812 AGTATATGTAGTCGTCGCTAGGTG 59.310 45.833 0.00 0.00 0.00 4.00
4762 5586 4.689812 CAGTATATGTAGTCGTCGCTAGGT 59.310 45.833 0.00 0.00 0.00 3.08
4763 5587 4.093115 CCAGTATATGTAGTCGTCGCTAGG 59.907 50.000 0.00 0.00 0.00 3.02
4764 5588 4.928020 TCCAGTATATGTAGTCGTCGCTAG 59.072 45.833 0.00 0.00 0.00 3.42
4765 5589 4.886579 TCCAGTATATGTAGTCGTCGCTA 58.113 43.478 0.00 0.00 0.00 4.26
4766 5590 3.736720 TCCAGTATATGTAGTCGTCGCT 58.263 45.455 0.00 0.00 0.00 4.93
4767 5591 3.667430 GCTCCAGTATATGTAGTCGTCGC 60.667 52.174 0.00 0.00 0.00 5.19
4768 5592 3.423253 CGCTCCAGTATATGTAGTCGTCG 60.423 52.174 0.00 0.00 0.00 5.12
4769 5593 3.744942 TCGCTCCAGTATATGTAGTCGTC 59.255 47.826 0.00 0.00 0.00 4.20
4770 5594 3.736720 TCGCTCCAGTATATGTAGTCGT 58.263 45.455 0.00 0.00 0.00 4.34
4771 5595 3.995048 TCTCGCTCCAGTATATGTAGTCG 59.005 47.826 0.00 0.00 0.00 4.18
4772 5596 4.143073 CGTCTCGCTCCAGTATATGTAGTC 60.143 50.000 0.00 0.00 0.00 2.59
4773 5597 3.747010 CGTCTCGCTCCAGTATATGTAGT 59.253 47.826 0.00 0.00 0.00 2.73
4774 5598 3.995048 TCGTCTCGCTCCAGTATATGTAG 59.005 47.826 0.00 0.00 0.00 2.74
4775 5599 3.999046 TCGTCTCGCTCCAGTATATGTA 58.001 45.455 0.00 0.00 0.00 2.29
4776 5600 2.847441 TCGTCTCGCTCCAGTATATGT 58.153 47.619 0.00 0.00 0.00 2.29
4777 5601 3.365465 CCTTCGTCTCGCTCCAGTATATG 60.365 52.174 0.00 0.00 0.00 1.78
4778 5602 2.814919 CCTTCGTCTCGCTCCAGTATAT 59.185 50.000 0.00 0.00 0.00 0.86
4779 5603 2.219458 CCTTCGTCTCGCTCCAGTATA 58.781 52.381 0.00 0.00 0.00 1.47
4780 5604 1.025812 CCTTCGTCTCGCTCCAGTAT 58.974 55.000 0.00 0.00 0.00 2.12
4781 5605 0.322277 ACCTTCGTCTCGCTCCAGTA 60.322 55.000 0.00 0.00 0.00 2.74
4782 5606 1.604023 ACCTTCGTCTCGCTCCAGT 60.604 57.895 0.00 0.00 0.00 4.00
4783 5607 1.153939 CACCTTCGTCTCGCTCCAG 60.154 63.158 0.00 0.00 0.00 3.86
4784 5608 1.901948 ACACCTTCGTCTCGCTCCA 60.902 57.895 0.00 0.00 0.00 3.86
4785 5609 1.444553 CACACCTTCGTCTCGCTCC 60.445 63.158 0.00 0.00 0.00 4.70
4786 5610 2.089349 GCACACCTTCGTCTCGCTC 61.089 63.158 0.00 0.00 0.00 5.03
4787 5611 2.049063 GCACACCTTCGTCTCGCT 60.049 61.111 0.00 0.00 0.00 4.93
4788 5612 2.355837 TGCACACCTTCGTCTCGC 60.356 61.111 0.00 0.00 0.00 5.03
4789 5613 2.375766 GCTGCACACCTTCGTCTCG 61.376 63.158 0.00 0.00 0.00 4.04
4790 5614 3.555428 GCTGCACACCTTCGTCTC 58.445 61.111 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.