Multiple sequence alignment - TraesCS7D01G289200

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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 TraesCS7D01G289200 chr7D 100.000 6303 0 0 1 6303 329809272 329802970 0.000000e+00 11640.0
1 TraesCS7D01G289200 chr7D 95.363 496 20 2 5800 6294 303584630 303585123 0.000000e+00 785.0
2 TraesCS7D01G289200 chr7D 94.071 506 26 3 5800 6303 187264952 187264449 0.000000e+00 765.0
3 TraesCS7D01G289200 chr7D 94.153 496 26 2 5800 6294 90316840 90317333 0.000000e+00 752.0
4 TraesCS7D01G289200 chr7D 93.663 505 29 2 5800 6303 601162964 601162462 0.000000e+00 752.0
5 TraesCS7D01G289200 chr7D 94.828 116 6 0 5696 5811 86479565 86479450 1.400000e-41 182.0
6 TraesCS7D01G289200 chr7D 94.048 84 4 1 1 84 257034350 257034432 6.630000e-25 126.0
7 TraesCS7D01G289200 chr7D 93.671 79 5 0 4715 4793 329804522 329804444 1.110000e-22 119.0
8 TraesCS7D01G289200 chr7D 93.671 79 5 0 4751 4829 329804558 329804480 1.110000e-22 119.0
9 TraesCS7D01G289200 chr7A 96.732 4468 101 18 886 5326 333107921 333103472 0.000000e+00 7400.0
10 TraesCS7D01G289200 chr7A 94.000 550 26 5 108 655 333114833 333114289 0.000000e+00 826.0
11 TraesCS7D01G289200 chr7A 88.988 336 17 6 5362 5693 333103324 333103005 1.270000e-106 398.0
12 TraesCS7D01G289200 chr7A 93.966 116 7 0 5696 5811 114267300 114267415 6.490000e-40 176.0
13 TraesCS7D01G289200 chr7A 93.966 116 7 0 5696 5811 172309060 172308945 6.490000e-40 176.0
14 TraesCS7D01G289200 chr7A 96.203 79 3 0 4751 4829 333104080 333104002 5.130000e-26 130.0
15 TraesCS7D01G289200 chr7A 90.110 91 9 0 4703 4793 333104056 333103966 1.110000e-22 119.0
16 TraesCS7D01G289200 chr7A 94.444 54 1 1 817 868 333107974 333107921 1.460000e-11 82.4
17 TraesCS7D01G289200 chr7A 92.727 55 4 0 4775 4829 333104092 333104038 5.240000e-11 80.5
18 TraesCS7D01G289200 chr7A 97.297 37 1 0 5324 5360 333103380 333103344 5.280000e-06 63.9
19 TraesCS7D01G289200 chr7B 93.526 3661 109 41 782 4392 290956993 290960575 0.000000e+00 5330.0
20 TraesCS7D01G289200 chr7B 92.842 950 37 9 4413 5359 290960567 290961488 0.000000e+00 1349.0
21 TraesCS7D01G289200 chr7B 87.123 730 41 15 83 787 290951439 290952140 0.000000e+00 778.0
22 TraesCS7D01G289200 chr7B 81.285 358 27 12 5360 5693 290961572 290961913 2.920000e-63 254.0
23 TraesCS7D01G289200 chr7B 94.118 51 3 0 4766 4816 290960833 290960883 1.880000e-10 78.7
24 TraesCS7D01G289200 chr3D 95.122 492 22 1 5812 6303 72912703 72913192 0.000000e+00 774.0
25 TraesCS7D01G289200 chr3D 95.041 484 21 2 5812 6294 604973450 604973931 0.000000e+00 758.0
26 TraesCS7D01G289200 chr3D 93.966 116 7 0 5696 5811 302622620 302622505 6.490000e-40 176.0
27 TraesCS7D01G289200 chr3D 93.333 60 3 1 25 84 105095629 105095571 3.130000e-13 87.9
28 TraesCS7D01G289200 chr6D 94.523 493 24 2 5812 6303 455801271 455800781 0.000000e+00 758.0
29 TraesCS7D01G289200 chr5D 94.355 496 24 3 5800 6294 537622447 537621955 0.000000e+00 758.0
30 TraesCS7D01G289200 chr4D 93.861 505 27 3 5800 6303 411804983 411804482 0.000000e+00 758.0
31 TraesCS7D01G289200 chr4D 98.000 50 1 0 35 84 454160624 454160673 3.130000e-13 87.9
32 TraesCS7D01G289200 chr2B 82.810 605 64 22 117 691 569265794 569266388 7.290000e-139 505.0
33 TraesCS7D01G289200 chr3A 93.966 116 7 0 5696 5811 129969174 129969289 6.490000e-40 176.0
34 TraesCS7D01G289200 chr3A 93.333 60 4 0 25 84 64622047 64621988 8.700000e-14 89.8
35 TraesCS7D01G289200 chr2D 93.966 116 7 0 5696 5811 290386899 290387014 6.490000e-40 176.0
36 TraesCS7D01G289200 chr1D 93.966 116 7 0 5696 5811 9626247 9626362 6.490000e-40 176.0
37 TraesCS7D01G289200 chr1D 93.103 116 8 0 5696 5811 465920594 465920479 3.020000e-38 171.0
38 TraesCS7D01G289200 chr1D 89.552 67 6 1 19 84 465062658 465062724 4.050000e-12 84.2
39 TraesCS7D01G289200 chr1A 93.966 116 7 0 5696 5811 191630049 191630164 6.490000e-40 176.0
40 TraesCS7D01G289200 chr6B 96.923 65 2 0 19 83 471316268 471316332 6.680000e-20 110.0
41 TraesCS7D01G289200 chrUn 95.161 62 3 0 3430 3491 100172226 100172165 1.450000e-16 99.0
42 TraesCS7D01G289200 chr5A 93.548 62 4 0 3430 3491 709675790 709675851 6.730000e-15 93.5
43 TraesCS7D01G289200 chr5A 90.476 63 6 0 3428 3490 143027575 143027637 4.050000e-12 84.2
44 TraesCS7D01G289200 chr5A 92.982 57 4 0 25 81 613766250 613766194 4.050000e-12 84.2
45 TraesCS7D01G289200 chr3B 92.308 65 4 1 20 84 23411735 23411798 2.420000e-14 91.6
46 TraesCS7D01G289200 chr5B 92.063 63 5 0 3428 3490 140746759 140746821 8.700000e-14 89.8
47 TraesCS7D01G289200 chr6A 98.000 50 1 0 35 84 188309267 188309316 3.130000e-13 87.9
48 TraesCS7D01G289200 chr1B 91.803 61 5 0 3430 3490 370729936 370729876 1.130000e-12 86.1
49 TraesCS7D01G289200 chr4B 89.062 64 7 0 3430 3493 107661156 107661219 5.240000e-11 80.5
50 TraesCS7D01G289200 chr4A 89.062 64 7 0 3430 3493 628941933 628941870 5.240000e-11 80.5


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 TraesCS7D01G289200 chr7D 329802970 329809272 6302 True 11640.000000 11640 100.000000 1 6303 1 chr7D.!!$R3 6302
1 TraesCS7D01G289200 chr7D 187264449 187264952 503 True 765.000000 765 94.071000 5800 6303 1 chr7D.!!$R2 503
2 TraesCS7D01G289200 chr7D 601162462 601162964 502 True 752.000000 752 93.663000 5800 6303 1 chr7D.!!$R4 503
3 TraesCS7D01G289200 chr7A 333103005 333107974 4969 True 1181.971429 7400 93.785857 817 5693 7 chr7A.!!$R3 4876
4 TraesCS7D01G289200 chr7A 333114289 333114833 544 True 826.000000 826 94.000000 108 655 1 chr7A.!!$R2 547
5 TraesCS7D01G289200 chr7B 290956993 290961913 4920 False 1752.925000 5330 90.442750 782 5693 4 chr7B.!!$F2 4911
6 TraesCS7D01G289200 chr7B 290951439 290952140 701 False 778.000000 778 87.123000 83 787 1 chr7B.!!$F1 704
7 TraesCS7D01G289200 chr4D 411804482 411804983 501 True 758.000000 758 93.861000 5800 6303 1 chr4D.!!$R1 503
8 TraesCS7D01G289200 chr2B 569265794 569266388 594 False 505.000000 505 82.810000 117 691 1 chr2B.!!$F1 574

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
787 900 1.202463 AGCCGAGTTCGATTCATGGAG 60.202 52.381 2.59 0.00 43.02 3.86 F
1815 1934 0.834612 AACTTCACCGTCCCAACTCA 59.165 50.000 0.00 0.00 0.00 3.41 F
2303 2439 1.762419 CATGTTTGCAGTGCTGTGAC 58.238 50.000 17.60 9.80 0.00 3.67 F
3804 3969 1.078709 TTCTTCAGGCGCTTGATTCG 58.921 50.000 23.70 14.26 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2045 2.083002 CTCTCAGGCTTGCCTTTCTTC 58.917 52.381 11.99 0.0 0.00 2.87 R
2682 2818 2.124403 GCAGCATCCTGTGGAGGG 60.124 66.667 0.45 0.0 41.26 4.30 R
3834 3999 1.879372 GCAGCCATGTCAAGTCTCACA 60.879 52.381 0.00 0.0 0.00 3.58 R
5733 6131 0.029700 ACCAACGTGCGTTTTTAGCC 59.970 50.000 7.27 0.0 36.00 3.93 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
59 60 4.877323 GGGACGAAACCAAGAATATCAC 57.123 45.455 0.00 0.00 0.00 3.06
60 61 3.626217 GGGACGAAACCAAGAATATCACC 59.374 47.826 0.00 0.00 0.00 4.02
61 62 4.514401 GGACGAAACCAAGAATATCACCT 58.486 43.478 0.00 0.00 0.00 4.00
62 63 4.941873 GGACGAAACCAAGAATATCACCTT 59.058 41.667 0.00 0.00 0.00 3.50
63 64 5.414765 GGACGAAACCAAGAATATCACCTTT 59.585 40.000 0.00 0.00 0.00 3.11
64 65 6.403309 GGACGAAACCAAGAATATCACCTTTC 60.403 42.308 0.00 0.00 0.00 2.62
65 66 6.238648 ACGAAACCAAGAATATCACCTTTCT 58.761 36.000 0.00 0.00 33.69 2.52
66 67 6.715264 ACGAAACCAAGAATATCACCTTTCTT 59.285 34.615 0.00 0.00 41.61 2.52
67 68 7.230712 ACGAAACCAAGAATATCACCTTTCTTT 59.769 33.333 0.00 0.00 39.53 2.52
68 69 8.726988 CGAAACCAAGAATATCACCTTTCTTTA 58.273 33.333 0.00 0.00 39.53 1.85
115 116 6.013725 ACTTTTTGTCCTTTCCCTTTTTGTCT 60.014 34.615 0.00 0.00 0.00 3.41
290 351 9.528847 GTGAACTTTTCTTCAAAATTGTTGAAC 57.471 29.630 0.00 0.00 34.96 3.18
412 491 5.476599 TGAACCTGTTTTCAAATCCGATGAT 59.523 36.000 0.00 0.00 32.42 2.45
669 778 9.653287 ATTCGAAAATCTAAGTGATACAACAGA 57.347 29.630 0.00 0.00 34.45 3.41
671 780 8.085909 TCGAAAATCTAAGTGATACAACAGACA 58.914 33.333 0.00 0.00 34.45 3.41
697 806 1.299089 GCAATGAATAACGCGGCCC 60.299 57.895 12.47 0.00 0.00 5.80
712 821 1.610624 CGGCCCCGCTTGTTCATATAT 60.611 52.381 0.00 0.00 0.00 0.86
714 823 2.890945 GGCCCCGCTTGTTCATATATTT 59.109 45.455 0.00 0.00 0.00 1.40
725 834 6.726258 TGTTCATATATTTCTGGCGCTATG 57.274 37.500 7.64 4.98 0.00 2.23
732 841 9.049523 CATATATTTCTGGCGCTATGATGTATT 57.950 33.333 7.64 0.00 0.00 1.89
752 861 2.862541 TGCTAGTGCACAATGGTTCTT 58.137 42.857 21.04 0.00 45.31 2.52
787 900 1.202463 AGCCGAGTTCGATTCATGGAG 60.202 52.381 2.59 0.00 43.02 3.86
792 905 3.452474 GAGTTCGATTCATGGAGACCAG 58.548 50.000 0.00 0.00 36.75 4.00
804 917 2.104111 TGGAGACCAGCTTTCTTTTCGA 59.896 45.455 0.00 0.00 0.00 3.71
815 928 7.044052 CCAGCTTTCTTTTCGAAGTTTTGTAAG 60.044 37.037 0.00 0.00 32.21 2.34
876 991 4.629115 GCTGTGTGCGCCCAACAC 62.629 66.667 19.40 19.40 38.55 3.32
877 992 3.208383 CTGTGTGCGCCCAACACA 61.208 61.111 25.04 25.04 45.42 3.72
880 995 4.182433 TGTGCGCCCAACACAGGA 62.182 61.111 4.18 0.00 42.88 3.86
881 996 3.357079 GTGCGCCCAACACAGGAG 61.357 66.667 4.18 0.00 37.96 3.69
884 999 2.281761 CGCCCAACACAGGAGCTT 60.282 61.111 0.00 0.00 0.00 3.74
941 1056 4.323562 GGGCTACTTCCTTAAGAGAAGCAA 60.324 45.833 23.00 15.26 43.75 3.91
1461 1577 7.674471 TTTCGTGTATCATGGTTAATGTTCA 57.326 32.000 0.00 0.00 37.56 3.18
1502 1618 0.981183 TGGACGTGGCATAGGTTCTT 59.019 50.000 0.00 0.00 0.00 2.52
1503 1619 1.349688 TGGACGTGGCATAGGTTCTTT 59.650 47.619 0.00 0.00 0.00 2.52
1598 1714 6.842437 ATTGCTCCGTGACAGATATATACT 57.158 37.500 0.00 0.00 0.00 2.12
1784 1903 1.153549 GCAGCGACGATTCCTCCTT 60.154 57.895 0.00 0.00 0.00 3.36
1815 1934 0.834612 AACTTCACCGTCCCAACTCA 59.165 50.000 0.00 0.00 0.00 3.41
1832 1951 6.434028 CCCAACTCAAAAGATGTCTCCATTTA 59.566 38.462 0.00 0.00 0.00 1.40
2265 2386 2.275318 GCTCAGATGAGGTTAGTGCAC 58.725 52.381 9.40 9.40 42.29 4.57
2303 2439 1.762419 CATGTTTGCAGTGCTGTGAC 58.238 50.000 17.60 9.80 0.00 3.67
3454 3615 7.013369 TGACGTATTTCAGTGCTAGATACATCT 59.987 37.037 0.00 0.00 40.86 2.90
3462 3623 6.153510 TCAGTGCTAGATACATCTGTTTGAGT 59.846 38.462 1.88 0.00 37.76 3.41
3663 3825 6.848451 TCTGTTTTCAAGTACTGGTTGTTTC 58.152 36.000 0.00 0.00 0.00 2.78
3804 3969 1.078709 TTCTTCAGGCGCTTGATTCG 58.921 50.000 23.70 14.26 0.00 3.34
3834 3999 1.343069 GAGATCTAATGGGCCGTCCT 58.657 55.000 0.00 0.00 36.20 3.85
3867 4032 2.684843 GGCTGCTGAAAGAGGTGCG 61.685 63.158 0.00 0.00 34.07 5.34
4122 4291 2.636768 GCAATTGTGTGCCTACCTTC 57.363 50.000 7.40 0.00 38.66 3.46
4132 4305 2.093921 GTGCCTACCTTCTCTGAGTTCC 60.094 54.545 4.32 0.00 0.00 3.62
4277 4450 8.613482 GCTAAACCTTCTCTAAACATTGTATCC 58.387 37.037 0.00 0.00 0.00 2.59
4368 4541 8.721133 AAAATAAACAACCTGGTCTTATCCTT 57.279 30.769 0.00 0.27 0.00 3.36
4373 4546 6.176014 ACAACCTGGTCTTATCCTTATAGC 57.824 41.667 0.00 0.00 0.00 2.97
4442 4615 2.684881 CAAGGGATACTTCAGCGCAAAT 59.315 45.455 11.47 0.00 37.29 2.32
4493 4666 8.359642 TGAATTAAAATGAAGAACCTGGTCTTG 58.640 33.333 13.76 0.00 37.98 3.02
4602 4775 2.774439 TCCTTTTCGAAAGCACTTGC 57.226 45.000 10.98 0.00 42.49 4.01
4756 4929 4.388499 GGTGGTCGTGATGGCGGT 62.388 66.667 0.00 0.00 0.00 5.68
4941 5115 6.088016 ACTTGTTTGATGCATGCTAGAAAA 57.912 33.333 20.33 11.19 0.00 2.29
4996 5170 4.632538 AACTTTGGTTGGTTCTTTCTCG 57.367 40.909 0.00 0.00 33.96 4.04
5063 5237 0.250295 TTGCAGGGAAGAAGACCACG 60.250 55.000 0.00 0.00 0.00 4.94
5488 5846 3.072915 TCAGCTTCCTGTTTCCTCAATCA 59.927 43.478 0.00 0.00 40.09 2.57
5557 5936 7.415206 GCACTACTAATTAGGGATTGTTTGGTG 60.415 40.741 16.73 11.23 32.03 4.17
5560 5939 7.933215 ACTAATTAGGGATTGTTTGGTGTAC 57.067 36.000 16.73 0.00 0.00 2.90
5614 5993 7.950496 GTCAATTGTTTGTACTGATCGACTTAC 59.050 37.037 5.13 0.00 34.32 2.34
5616 5995 7.813852 ATTGTTTGTACTGATCGACTTACTC 57.186 36.000 0.00 0.00 0.00 2.59
5617 5996 5.388111 TGTTTGTACTGATCGACTTACTCG 58.612 41.667 0.00 0.00 44.44 4.18
5624 6022 0.747283 ATCGACTTACTCGCTCCCGT 60.747 55.000 0.00 0.00 42.62 5.28
5647 6045 5.990386 GTCCTTTCTACGTCTTCCTCTTTTT 59.010 40.000 0.00 0.00 0.00 1.94
5657 6055 8.350852 ACGTCTTCCTCTTTTTAATCTCTCTA 57.649 34.615 0.00 0.00 0.00 2.43
5658 6056 8.973182 ACGTCTTCCTCTTTTTAATCTCTCTAT 58.027 33.333 0.00 0.00 0.00 1.98
5693 6091 5.473931 TGTCTTCCTCTTTTCAATCTCTCG 58.526 41.667 0.00 0.00 0.00 4.04
5694 6092 4.328712 GTCTTCCTCTTTTCAATCTCTCGC 59.671 45.833 0.00 0.00 0.00 5.03
5695 6093 3.961480 TCCTCTTTTCAATCTCTCGCA 57.039 42.857 0.00 0.00 0.00 5.10
5696 6094 3.854666 TCCTCTTTTCAATCTCTCGCAG 58.145 45.455 0.00 0.00 0.00 5.18
5697 6095 2.935201 CCTCTTTTCAATCTCTCGCAGG 59.065 50.000 0.00 0.00 0.00 4.85
5698 6096 2.935201 CTCTTTTCAATCTCTCGCAGGG 59.065 50.000 0.00 0.00 0.00 4.45
5699 6097 2.567169 TCTTTTCAATCTCTCGCAGGGA 59.433 45.455 0.00 0.00 0.00 4.20
5700 6098 3.007940 TCTTTTCAATCTCTCGCAGGGAA 59.992 43.478 0.00 0.00 0.00 3.97
5701 6099 3.417069 TTTCAATCTCTCGCAGGGAAA 57.583 42.857 0.00 0.00 0.00 3.13
5702 6100 3.417069 TTCAATCTCTCGCAGGGAAAA 57.583 42.857 0.00 0.00 0.00 2.29
5703 6101 2.699954 TCAATCTCTCGCAGGGAAAAC 58.300 47.619 0.00 0.00 0.00 2.43
5704 6102 1.740025 CAATCTCTCGCAGGGAAAACC 59.260 52.381 0.00 0.00 40.67 3.27
5720 6118 7.462571 GGGAAAACCTTATACACAGAACATT 57.537 36.000 0.00 0.00 35.85 2.71
5721 6119 8.570068 GGGAAAACCTTATACACAGAACATTA 57.430 34.615 0.00 0.00 35.85 1.90
5722 6120 8.674607 GGGAAAACCTTATACACAGAACATTAG 58.325 37.037 0.00 0.00 35.85 1.73
5723 6121 8.182227 GGAAAACCTTATACACAGAACATTAGC 58.818 37.037 0.00 0.00 0.00 3.09
5724 6122 8.630054 AAAACCTTATACACAGAACATTAGCA 57.370 30.769 0.00 0.00 0.00 3.49
5725 6123 7.849804 AACCTTATACACAGAACATTAGCAG 57.150 36.000 0.00 0.00 0.00 4.24
5726 6124 5.817816 ACCTTATACACAGAACATTAGCAGC 59.182 40.000 0.00 0.00 0.00 5.25
5727 6125 5.817296 CCTTATACACAGAACATTAGCAGCA 59.183 40.000 0.00 0.00 0.00 4.41
5728 6126 6.018425 CCTTATACACAGAACATTAGCAGCAG 60.018 42.308 0.00 0.00 0.00 4.24
5729 6127 1.808945 ACACAGAACATTAGCAGCAGC 59.191 47.619 0.00 0.00 42.56 5.25
5730 6128 1.808343 CACAGAACATTAGCAGCAGCA 59.192 47.619 3.17 0.00 45.49 4.41
5731 6129 1.808945 ACAGAACATTAGCAGCAGCAC 59.191 47.619 3.17 0.00 45.49 4.40
5732 6130 1.081892 AGAACATTAGCAGCAGCACG 58.918 50.000 3.17 0.00 45.49 5.34
5733 6131 0.097674 GAACATTAGCAGCAGCACGG 59.902 55.000 3.17 0.00 45.49 4.94
5734 6132 1.308069 AACATTAGCAGCAGCACGGG 61.308 55.000 3.17 0.00 45.49 5.28
5735 6133 2.825836 ATTAGCAGCAGCACGGGC 60.826 61.111 0.00 0.00 45.49 6.13
5745 6143 2.640421 GCACGGGCTAAAAACGCA 59.360 55.556 0.00 0.00 36.96 5.24
5746 6144 1.728074 GCACGGGCTAAAAACGCAC 60.728 57.895 0.00 0.00 36.96 5.34
5750 6148 2.791092 GGGCTAAAAACGCACGTTG 58.209 52.632 9.46 0.00 38.47 4.10
5751 6149 0.662077 GGGCTAAAAACGCACGTTGG 60.662 55.000 9.46 2.26 38.47 3.77
5752 6150 0.029700 GGCTAAAAACGCACGTTGGT 59.970 50.000 9.46 3.22 38.47 3.67
5779 6177 3.041351 CAGCAGCGCGGTGTTGTA 61.041 61.111 36.54 0.00 38.36 2.41
5780 6178 2.280524 AGCAGCGCGGTGTTGTAA 60.281 55.556 35.36 0.00 0.00 2.41
5781 6179 1.890041 AGCAGCGCGGTGTTGTAAA 60.890 52.632 35.36 0.00 0.00 2.01
5799 6197 8.693542 GTTGTAAACCGTGTTACAGATATAGT 57.306 34.615 7.86 0.00 43.11 2.12
5800 6198 9.143631 GTTGTAAACCGTGTTACAGATATAGTT 57.856 33.333 7.86 0.00 43.11 2.24
5808 6206 8.512956 CCGTGTTACAGATATAGTTATAGCAGT 58.487 37.037 0.00 0.00 31.01 4.40
5844 6242 1.572447 GGCTAAAAACGCACGCTGA 59.428 52.632 0.00 0.00 0.00 4.26
5898 6296 4.083431 CCGCGCTACAGATACAGTTATAGT 60.083 45.833 5.56 0.00 0.00 2.12
6050 6448 4.341487 TGAGAGGTGCTACTGCTAAAGTA 58.659 43.478 0.00 0.00 40.56 2.24
6051 6449 4.770531 TGAGAGGTGCTACTGCTAAAGTAA 59.229 41.667 0.00 0.00 40.92 2.24
6234 6633 1.079819 GCAGTAGCGCACTTCCTGA 60.080 57.895 11.47 0.00 34.26 3.86
6267 6666 3.006537 TGCTACTTCTGACTAAACCGCTT 59.993 43.478 0.00 0.00 0.00 4.68
6294 6693 2.002018 TTTCCCCAACGGCCACTTCT 62.002 55.000 2.24 0.00 0.00 2.85
6295 6694 2.002018 TTCCCCAACGGCCACTTCTT 62.002 55.000 2.24 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.938670 CGTCCCGTTTTGATGATTTTATATTTA 57.061 29.630 0.00 0.00 0.00 1.40
18 19 8.679100 TCGTCCCGTTTTGATGATTTTATATTT 58.321 29.630 0.00 0.00 0.00 1.40
19 20 8.215926 TCGTCCCGTTTTGATGATTTTATATT 57.784 30.769 0.00 0.00 0.00 1.28
20 21 7.795482 TCGTCCCGTTTTGATGATTTTATAT 57.205 32.000 0.00 0.00 0.00 0.86
21 22 7.612668 TTCGTCCCGTTTTGATGATTTTATA 57.387 32.000 0.00 0.00 0.00 0.98
22 23 6.503589 TTCGTCCCGTTTTGATGATTTTAT 57.496 33.333 0.00 0.00 0.00 1.40
23 24 5.943706 TTCGTCCCGTTTTGATGATTTTA 57.056 34.783 0.00 0.00 0.00 1.52
24 25 4.839668 TTCGTCCCGTTTTGATGATTTT 57.160 36.364 0.00 0.00 0.00 1.82
25 26 4.542735 GTTTCGTCCCGTTTTGATGATTT 58.457 39.130 0.00 0.00 0.00 2.17
26 27 3.057806 GGTTTCGTCCCGTTTTGATGATT 60.058 43.478 0.00 0.00 0.00 2.57
27 28 2.486592 GGTTTCGTCCCGTTTTGATGAT 59.513 45.455 0.00 0.00 0.00 2.45
28 29 1.874872 GGTTTCGTCCCGTTTTGATGA 59.125 47.619 0.00 0.00 0.00 2.92
29 30 1.604755 TGGTTTCGTCCCGTTTTGATG 59.395 47.619 0.00 0.00 0.00 3.07
30 31 1.970092 TGGTTTCGTCCCGTTTTGAT 58.030 45.000 0.00 0.00 0.00 2.57
31 32 1.671845 CTTGGTTTCGTCCCGTTTTGA 59.328 47.619 0.00 0.00 0.00 2.69
32 33 1.671845 TCTTGGTTTCGTCCCGTTTTG 59.328 47.619 0.00 0.00 0.00 2.44
33 34 2.041251 TCTTGGTTTCGTCCCGTTTT 57.959 45.000 0.00 0.00 0.00 2.43
34 35 2.041251 TTCTTGGTTTCGTCCCGTTT 57.959 45.000 0.00 0.00 0.00 3.60
35 36 2.265589 ATTCTTGGTTTCGTCCCGTT 57.734 45.000 0.00 0.00 0.00 4.44
36 37 3.055675 TGATATTCTTGGTTTCGTCCCGT 60.056 43.478 0.00 0.00 0.00 5.28
37 38 3.308866 GTGATATTCTTGGTTTCGTCCCG 59.691 47.826 0.00 0.00 0.00 5.14
38 39 3.626217 GGTGATATTCTTGGTTTCGTCCC 59.374 47.826 0.00 0.00 0.00 4.46
39 40 4.514401 AGGTGATATTCTTGGTTTCGTCC 58.486 43.478 0.00 0.00 0.00 4.79
40 41 6.371825 AGAAAGGTGATATTCTTGGTTTCGTC 59.628 38.462 0.00 0.00 32.05 4.20
41 42 6.238648 AGAAAGGTGATATTCTTGGTTTCGT 58.761 36.000 0.00 0.00 32.05 3.85
42 43 6.743575 AGAAAGGTGATATTCTTGGTTTCG 57.256 37.500 0.00 0.00 32.05 3.46
80 81 8.421784 GGGAAAGGACAAAAAGTAAAGAAATCT 58.578 33.333 0.00 0.00 0.00 2.40
81 82 8.421784 AGGGAAAGGACAAAAAGTAAAGAAATC 58.578 33.333 0.00 0.00 0.00 2.17
91 92 6.406370 AGACAAAAAGGGAAAGGACAAAAAG 58.594 36.000 0.00 0.00 0.00 2.27
92 93 6.367374 AGACAAAAAGGGAAAGGACAAAAA 57.633 33.333 0.00 0.00 0.00 1.94
93 94 6.367374 AAGACAAAAAGGGAAAGGACAAAA 57.633 33.333 0.00 0.00 0.00 2.44
94 95 6.367374 AAAGACAAAAAGGGAAAGGACAAA 57.633 33.333 0.00 0.00 0.00 2.83
95 96 6.367374 AAAAGACAAAAAGGGAAAGGACAA 57.633 33.333 0.00 0.00 0.00 3.18
96 97 6.212589 AGAAAAAGACAAAAAGGGAAAGGACA 59.787 34.615 0.00 0.00 0.00 4.02
97 98 6.640518 AGAAAAAGACAAAAAGGGAAAGGAC 58.359 36.000 0.00 0.00 0.00 3.85
98 99 6.867519 AGAAAAAGACAAAAAGGGAAAGGA 57.132 33.333 0.00 0.00 0.00 3.36
99 100 7.921786 AAAGAAAAAGACAAAAAGGGAAAGG 57.078 32.000 0.00 0.00 0.00 3.11
100 101 9.219603 AGAAAAGAAAAAGACAAAAAGGGAAAG 57.780 29.630 0.00 0.00 0.00 2.62
101 102 9.214957 GAGAAAAGAAAAAGACAAAAAGGGAAA 57.785 29.630 0.00 0.00 0.00 3.13
102 103 8.593679 AGAGAAAAGAAAAAGACAAAAAGGGAA 58.406 29.630 0.00 0.00 0.00 3.97
103 104 8.134202 AGAGAAAAGAAAAAGACAAAAAGGGA 57.866 30.769 0.00 0.00 0.00 4.20
104 105 9.521503 CTAGAGAAAAGAAAAAGACAAAAAGGG 57.478 33.333 0.00 0.00 0.00 3.95
115 116 9.783256 CGAAAAAGGAACTAGAGAAAAGAAAAA 57.217 29.630 0.00 0.00 38.49 1.94
290 351 7.389803 AAAAGTTCACCAATTTGGGAAAAAG 57.610 32.000 19.39 2.84 43.37 2.27
666 775 6.358822 CGTTATTCATTGCATAATGCTGTCTG 59.641 38.462 0.00 0.00 45.31 3.51
669 778 4.977963 GCGTTATTCATTGCATAATGCTGT 59.022 37.500 19.56 0.00 45.31 4.40
671 780 4.221342 CGCGTTATTCATTGCATAATGCT 58.779 39.130 22.30 0.95 45.31 3.79
697 806 4.611355 CGCCAGAAATATATGAACAAGCGG 60.611 45.833 0.00 0.00 35.38 5.52
712 821 3.250762 GCAATACATCATAGCGCCAGAAA 59.749 43.478 2.29 0.00 0.00 2.52
714 823 2.037641 AGCAATACATCATAGCGCCAGA 59.962 45.455 2.29 0.00 0.00 3.86
752 861 3.767673 ACTCGGCTAGTTGATTAACCAGA 59.232 43.478 0.00 0.00 37.52 3.86
787 900 4.553756 AACTTCGAAAAGAAAGCTGGTC 57.446 40.909 0.00 0.00 38.57 4.02
792 905 6.472486 AGCTTACAAAACTTCGAAAAGAAAGC 59.528 34.615 0.00 8.39 38.57 3.51
804 917 7.433708 AAACTGCAAAAAGCTTACAAAACTT 57.566 28.000 0.00 0.00 45.94 2.66
815 928 4.811208 GAAACTTCGAAACTGCAAAAAGC 58.189 39.130 0.00 0.00 45.96 3.51
1327 1443 0.464735 ACTCGGATGACTCCTCCTCG 60.465 60.000 0.00 0.00 39.65 4.63
1461 1577 6.096423 TCCAGAAATTAGTACTACATCGCACT 59.904 38.462 0.91 0.00 0.00 4.40
1651 1770 5.163764 GCATGGATCGTGAATACAGACAAAA 60.164 40.000 0.00 0.00 29.42 2.44
1652 1771 4.332543 GCATGGATCGTGAATACAGACAAA 59.667 41.667 0.00 0.00 29.42 2.83
1657 1776 4.122046 TGAAGCATGGATCGTGAATACAG 58.878 43.478 0.00 0.00 29.42 2.74
1784 1903 3.507233 ACGGTGAAGTTATACCTCGTCAA 59.493 43.478 7.08 0.00 34.77 3.18
1832 1951 8.406297 GGAAAAAGAAGATAATTAGGATGCGTT 58.594 33.333 0.00 0.00 0.00 4.84
1926 2045 2.083002 CTCTCAGGCTTGCCTTTCTTC 58.917 52.381 11.99 0.00 0.00 2.87
2265 2386 2.959516 TGCATAGAAGAGAACCACACG 58.040 47.619 0.00 0.00 0.00 4.49
2662 2798 4.830600 AGGGAAAATGTGTAAACAACGGAT 59.169 37.500 0.00 0.00 0.00 4.18
2666 2802 5.163499 TGTGGAGGGAAAATGTGTAAACAAC 60.163 40.000 0.00 0.00 0.00 3.32
2682 2818 2.124403 GCAGCATCCTGTGGAGGG 60.124 66.667 0.45 0.00 41.26 4.30
2915 3053 6.597832 TGGAAACTTGGAAGAACAGAAAAA 57.402 33.333 0.00 0.00 0.00 1.94
2922 3060 6.581171 ATTCAGATGGAAACTTGGAAGAAC 57.419 37.500 0.00 0.00 39.39 3.01
3106 3244 2.637872 ACCTTTGTTGCTAGCAGGAGTA 59.362 45.455 22.83 4.49 0.00 2.59
3454 3615 8.227119 CGTCACATATTAATTGACACTCAAACA 58.773 33.333 15.59 0.00 40.12 2.83
3462 3623 4.814234 GCCTCCGTCACATATTAATTGACA 59.186 41.667 15.59 1.09 39.77 3.58
3595 3756 8.204160 TGAAAACTCTAGAACTGAGAAATCACA 58.796 33.333 0.00 0.00 35.66 3.58
3663 3825 9.559958 GTTGAAAATGTACCATATTTCTGTCAG 57.440 33.333 0.00 0.00 33.90 3.51
3804 3969 4.823989 CCCATTAGATCTCCACCATTCAAC 59.176 45.833 0.00 0.00 0.00 3.18
3834 3999 1.879372 GCAGCCATGTCAAGTCTCACA 60.879 52.381 0.00 0.00 0.00 3.58
4132 4305 6.073873 GCTCCGAATCTAGAATTCACAATGAG 60.074 42.308 8.44 4.43 0.00 2.90
4277 4450 4.515191 TGCTTGCCTAGTGTTCTTGTTAAG 59.485 41.667 0.00 0.00 0.00 1.85
4408 4581 9.753674 TGAAGTATCCCTTGATTTATCAAAGTT 57.246 29.630 6.61 1.50 45.26 2.66
4419 4592 1.486310 TGCGCTGAAGTATCCCTTGAT 59.514 47.619 9.73 0.00 32.03 2.57
4425 4598 3.873952 AGAAGATTTGCGCTGAAGTATCC 59.126 43.478 9.73 0.00 0.00 2.59
4433 4606 4.668576 TGTTTAGAGAAGATTTGCGCTG 57.331 40.909 9.73 0.00 0.00 5.18
4481 4654 3.323979 TCACTTAGGACAAGACCAGGTTC 59.676 47.826 0.00 0.00 0.00 3.62
4522 4695 9.393249 CAGAATTCACGTAAAACATACACAAAT 57.607 29.630 8.44 0.00 0.00 2.32
4538 4711 2.831333 AGCTATCCTGCAGAATTCACG 58.169 47.619 17.39 0.00 34.99 4.35
4602 4775 2.294791 CCTAGGTCAGATCCACTAAGCG 59.705 54.545 0.00 0.00 0.00 4.68
4941 5115 5.527582 GTCTTTTCCATGCTATACCGACAAT 59.472 40.000 0.00 0.00 0.00 2.71
4996 5170 9.043079 GTTAGTTAGCAAATCTATACAACTCCC 57.957 37.037 0.00 0.00 0.00 4.30
5063 5237 5.668558 ACAGTTTCTAATCGTCACCAAAC 57.331 39.130 0.00 0.00 0.00 2.93
5488 5846 9.547279 AGGTATGGTTCAAAATTAAAAGAGGAT 57.453 29.630 0.00 0.00 0.00 3.24
5557 5936 7.603404 TGCTAGTAGAAGATTAGATCCTCGTAC 59.397 40.741 0.00 0.00 0.00 3.67
5560 5939 6.401688 CGTGCTAGTAGAAGATTAGATCCTCG 60.402 46.154 0.00 0.00 0.00 4.63
5614 5993 0.100861 GTAGAAAGGACGGGAGCGAG 59.899 60.000 0.00 0.00 0.00 5.03
5616 5995 1.226603 CGTAGAAAGGACGGGAGCG 60.227 63.158 0.00 0.00 36.66 5.03
5617 5996 0.179142 GACGTAGAAAGGACGGGAGC 60.179 60.000 0.00 0.00 44.58 4.70
5624 6022 5.803237 AAAAGAGGAAGACGTAGAAAGGA 57.197 39.130 0.00 0.00 0.00 3.36
5657 6055 9.981460 AAAAGAGGAAGACATAGTATGGAAAAT 57.019 29.630 14.59 0.00 33.60 1.82
5658 6056 9.449719 GAAAAGAGGAAGACATAGTATGGAAAA 57.550 33.333 14.59 0.00 33.60 2.29
5670 6068 5.473931 CGAGAGATTGAAAAGAGGAAGACA 58.526 41.667 0.00 0.00 0.00 3.41
5693 6091 4.585879 TCTGTGTATAAGGTTTTCCCTGC 58.414 43.478 0.00 0.00 45.47 4.85
5694 6092 6.001460 TGTTCTGTGTATAAGGTTTTCCCTG 58.999 40.000 0.00 0.00 45.47 4.45
5696 6094 7.462571 AATGTTCTGTGTATAAGGTTTTCCC 57.537 36.000 0.00 0.00 41.86 3.97
5697 6095 8.182227 GCTAATGTTCTGTGTATAAGGTTTTCC 58.818 37.037 0.00 0.00 41.05 3.13
5698 6096 8.726988 TGCTAATGTTCTGTGTATAAGGTTTTC 58.273 33.333 0.00 0.00 0.00 2.29
5699 6097 8.630054 TGCTAATGTTCTGTGTATAAGGTTTT 57.370 30.769 0.00 0.00 0.00 2.43
5700 6098 7.148239 GCTGCTAATGTTCTGTGTATAAGGTTT 60.148 37.037 0.00 0.00 0.00 3.27
5701 6099 6.316390 GCTGCTAATGTTCTGTGTATAAGGTT 59.684 38.462 0.00 0.00 0.00 3.50
5702 6100 5.817816 GCTGCTAATGTTCTGTGTATAAGGT 59.182 40.000 0.00 0.00 0.00 3.50
5703 6101 5.817296 TGCTGCTAATGTTCTGTGTATAAGG 59.183 40.000 0.00 0.00 0.00 2.69
5704 6102 6.510799 GCTGCTGCTAATGTTCTGTGTATAAG 60.511 42.308 8.53 0.00 36.03 1.73
5705 6103 5.294306 GCTGCTGCTAATGTTCTGTGTATAA 59.706 40.000 8.53 0.00 36.03 0.98
5706 6104 4.811024 GCTGCTGCTAATGTTCTGTGTATA 59.189 41.667 8.53 0.00 36.03 1.47
5707 6105 3.624861 GCTGCTGCTAATGTTCTGTGTAT 59.375 43.478 8.53 0.00 36.03 2.29
5708 6106 3.002791 GCTGCTGCTAATGTTCTGTGTA 58.997 45.455 8.53 0.00 36.03 2.90
5709 6107 1.808945 GCTGCTGCTAATGTTCTGTGT 59.191 47.619 8.53 0.00 36.03 3.72
5710 6108 1.808343 TGCTGCTGCTAATGTTCTGTG 59.192 47.619 17.00 0.00 40.48 3.66
5711 6109 1.808945 GTGCTGCTGCTAATGTTCTGT 59.191 47.619 17.00 0.00 40.48 3.41
5712 6110 1.201998 CGTGCTGCTGCTAATGTTCTG 60.202 52.381 17.00 0.00 40.48 3.02
5713 6111 1.081892 CGTGCTGCTGCTAATGTTCT 58.918 50.000 17.00 0.00 40.48 3.01
5714 6112 0.097674 CCGTGCTGCTGCTAATGTTC 59.902 55.000 17.00 0.00 40.48 3.18
5715 6113 1.308069 CCCGTGCTGCTGCTAATGTT 61.308 55.000 17.00 0.00 40.48 2.71
5716 6114 1.746615 CCCGTGCTGCTGCTAATGT 60.747 57.895 17.00 0.00 40.48 2.71
5717 6115 3.104766 CCCGTGCTGCTGCTAATG 58.895 61.111 17.00 2.81 40.48 1.90
5718 6116 2.825836 GCCCGTGCTGCTGCTAAT 60.826 61.111 17.00 0.00 40.48 1.73
5728 6126 1.728074 GTGCGTTTTTAGCCCGTGC 60.728 57.895 0.00 0.00 37.95 5.34
5729 6127 1.439693 CGTGCGTTTTTAGCCCGTG 60.440 57.895 0.00 0.00 31.22 4.94
5730 6128 1.888638 ACGTGCGTTTTTAGCCCGT 60.889 52.632 0.00 0.00 43.22 5.28
5731 6129 0.994737 CAACGTGCGTTTTTAGCCCG 60.995 55.000 7.27 0.00 41.05 6.13
5732 6130 0.662077 CCAACGTGCGTTTTTAGCCC 60.662 55.000 7.27 0.00 36.00 5.19
5733 6131 0.029700 ACCAACGTGCGTTTTTAGCC 59.970 50.000 7.27 0.00 36.00 3.93
5734 6132 1.117234 CACCAACGTGCGTTTTTAGC 58.883 50.000 7.27 0.00 36.00 3.09
5754 6152 1.154205 ACCGCGCTGCTGCTAATTAG 61.154 55.000 14.03 8.20 36.97 1.73
5755 6153 1.153449 ACCGCGCTGCTGCTAATTA 60.153 52.632 14.03 0.00 36.97 1.40
5756 6154 2.436646 ACCGCGCTGCTGCTAATT 60.437 55.556 14.03 0.00 36.97 1.40
5757 6155 3.197790 CACCGCGCTGCTGCTAAT 61.198 61.111 14.03 0.00 36.97 1.73
5758 6156 4.680237 ACACCGCGCTGCTGCTAA 62.680 61.111 14.03 0.00 36.97 3.09
5759 6157 4.680237 AACACCGCGCTGCTGCTA 62.680 61.111 14.03 0.00 36.97 3.49
5762 6160 2.111932 TTTACAACACCGCGCTGCTG 62.112 55.000 5.56 0.95 0.00 4.41
5763 6161 1.890041 TTTACAACACCGCGCTGCT 60.890 52.632 5.56 0.00 0.00 4.24
5764 6162 1.724581 GTTTACAACACCGCGCTGC 60.725 57.895 5.56 0.00 0.00 5.25
5765 6163 1.082366 GGTTTACAACACCGCGCTG 60.082 57.895 5.56 0.00 0.00 5.18
5766 6164 3.336566 GGTTTACAACACCGCGCT 58.663 55.556 5.56 0.00 0.00 5.92
5771 6169 3.870419 TCTGTAACACGGTTTACAACACC 59.130 43.478 11.05 0.00 40.59 4.16
5772 6170 5.662211 ATCTGTAACACGGTTTACAACAC 57.338 39.130 11.05 0.00 40.59 3.32
5773 6171 8.306038 ACTATATCTGTAACACGGTTTACAACA 58.694 33.333 11.05 3.57 40.59 3.33
5774 6172 8.693542 ACTATATCTGTAACACGGTTTACAAC 57.306 34.615 11.05 0.00 40.59 3.32
5779 6177 9.688592 GCTATAACTATATCTGTAACACGGTTT 57.311 33.333 0.00 0.00 0.00 3.27
5780 6178 8.853126 TGCTATAACTATATCTGTAACACGGTT 58.147 33.333 0.00 0.00 0.00 4.44
5781 6179 8.400184 TGCTATAACTATATCTGTAACACGGT 57.600 34.615 0.00 0.00 0.00 4.83
5782 6180 8.512956 ACTGCTATAACTATATCTGTAACACGG 58.487 37.037 0.00 0.00 0.00 4.94
5794 6192 9.462606 TGCTGCTAATCTACTGCTATAACTATA 57.537 33.333 0.00 0.00 0.00 1.31
5795 6193 8.354711 TGCTGCTAATCTACTGCTATAACTAT 57.645 34.615 0.00 0.00 0.00 2.12
5796 6194 7.575909 GCTGCTGCTAATCTACTGCTATAACTA 60.576 40.741 8.53 0.00 36.03 2.24
5797 6195 6.656632 TGCTGCTAATCTACTGCTATAACT 57.343 37.500 0.00 0.00 0.00 2.24
5798 6196 5.347364 GCTGCTGCTAATCTACTGCTATAAC 59.653 44.000 8.53 0.00 36.03 1.89
5799 6197 5.473931 GCTGCTGCTAATCTACTGCTATAA 58.526 41.667 8.53 0.00 36.03 0.98
5800 6198 4.379918 CGCTGCTGCTAATCTACTGCTATA 60.380 45.833 14.03 0.00 36.97 1.31
5801 6199 3.613671 CGCTGCTGCTAATCTACTGCTAT 60.614 47.826 14.03 0.00 36.97 2.97
5802 6200 2.287849 CGCTGCTGCTAATCTACTGCTA 60.288 50.000 14.03 0.00 36.97 3.49
5803 6201 1.537776 CGCTGCTGCTAATCTACTGCT 60.538 52.381 14.03 0.00 36.97 4.24
5804 6202 0.857935 CGCTGCTGCTAATCTACTGC 59.142 55.000 14.03 0.00 36.97 4.40
5808 6206 1.300156 CCGCGCTGCTGCTAATCTA 60.300 57.895 14.03 0.00 36.97 1.98
5810 6208 3.643978 CCCGCGCTGCTGCTAATC 61.644 66.667 14.03 0.00 36.97 1.75
5898 6296 2.203056 TACTCGGGCGCGCTACTA 60.203 61.111 32.29 15.11 0.00 1.82


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

AutoCloner maintained by Alex Coulton.