Multiple sequence alignment - TraesCS3A01G167800

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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 TraesCS3A01G167800 chr3A 100.000 3016 0 0 1 3016 174294997 174291982 0.000000e+00 5570.0
1 TraesCS3A01G167800 chr3A 87.832 715 46 22 120 810 678000632 678001329 0.000000e+00 800.0
2 TraesCS3A01G167800 chr3D 94.668 2138 67 13 899 3016 155594570 155592460 0.000000e+00 3273.0
3 TraesCS3A01G167800 chr3D 82.143 112 13 3 1 112 309928683 309928787 4.140000e-14 89.8
4 TraesCS3A01G167800 chr3B 94.767 1414 47 5 899 2304 226078030 226079424 0.000000e+00 2176.0
5 TraesCS3A01G167800 chr3B 95.753 259 11 0 2758 3016 226081336 226081594 4.650000e-113 418.0
6 TraesCS3A01G167800 chr3B 85.714 294 30 8 119 403 242744048 242743758 1.760000e-77 300.0
7 TraesCS3A01G167800 chr3B 94.737 57 2 1 2498 2553 226079730 226079786 1.490000e-13 87.9
8 TraesCS3A01G167800 chr4D 89.356 714 55 17 117 818 289666012 289665308 0.000000e+00 878.0
9 TraesCS3A01G167800 chr4D 91.549 71 5 1 43 112 278290003 278289933 2.470000e-16 97.1
10 TraesCS3A01G167800 chr5A 88.952 706 54 12 118 817 84674364 84673677 0.000000e+00 850.0
11 TraesCS3A01G167800 chr5A 87.349 332 22 5 120 447 323998952 323999267 2.210000e-96 363.0
12 TraesCS3A01G167800 chr4A 88.794 705 58 15 120 817 465897779 465897089 0.000000e+00 845.0
13 TraesCS3A01G167800 chr4A 83.665 704 60 27 120 818 33856853 33857506 1.990000e-171 612.0
14 TraesCS3A01G167800 chr1A 88.011 709 53 15 120 816 215012285 215012973 0.000000e+00 809.0
15 TraesCS3A01G167800 chr1A 87.092 705 65 19 120 817 261434045 261433360 0.000000e+00 774.0
16 TraesCS3A01G167800 chr1A 89.474 342 28 6 119 453 400270793 400270453 2.780000e-115 425.0
17 TraesCS3A01G167800 chr1A 94.643 112 5 1 1 112 574215787 574215897 4.000000e-39 172.0
18 TraesCS3A01G167800 chr7A 87.569 724 57 22 120 817 526126164 526125448 0.000000e+00 808.0
19 TraesCS3A01G167800 chr7A 87.642 704 56 21 120 818 643182339 643181662 0.000000e+00 789.0
20 TraesCS3A01G167800 chr7A 87.968 374 22 11 120 476 128162087 128161720 1.290000e-113 420.0
21 TraesCS3A01G167800 chr7A 97.273 110 3 0 1 110 676422517 676422408 1.430000e-43 187.0
22 TraesCS3A01G167800 chr7A 96.396 111 4 0 1 111 543809654 543809544 1.850000e-42 183.0
23 TraesCS3A01G167800 chr6A 86.030 723 71 22 110 824 389761942 389761242 0.000000e+00 749.0
24 TraesCS3A01G167800 chr7D 84.358 716 74 33 121 818 75314352 75315047 0.000000e+00 667.0
25 TraesCS3A01G167800 chr7D 84.821 112 15 2 1 112 566198827 566198936 8.840000e-21 111.0
26 TraesCS3A01G167800 chr2A 84.714 700 62 19 119 816 646824118 646824774 0.000000e+00 658.0
27 TraesCS3A01G167800 chr2A 86.013 479 40 12 120 596 539693477 539693930 3.490000e-134 488.0
28 TraesCS3A01G167800 chr2A 83.810 105 14 3 11 113 11239707 11239810 2.470000e-16 97.1
29 TraesCS3A01G167800 chr1B 81.516 752 75 46 120 818 217314152 217313412 7.300000e-156 560.0
30 TraesCS3A01G167800 chr2D 95.455 66 2 1 48 112 109553219 109553284 1.480000e-18 104.0
31 TraesCS3A01G167800 chr7B 86.207 87 10 2 28 113 615307074 615307159 3.200000e-15 93.5


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 TraesCS3A01G167800 chr3A 174291982 174294997 3015 True 5570.000000 5570 100.000000 1 3016 1 chr3A.!!$R1 3015
1 TraesCS3A01G167800 chr3A 678000632 678001329 697 False 800.000000 800 87.832000 120 810 1 chr3A.!!$F1 690
2 TraesCS3A01G167800 chr3D 155592460 155594570 2110 True 3273.000000 3273 94.668000 899 3016 1 chr3D.!!$R1 2117
3 TraesCS3A01G167800 chr3B 226078030 226081594 3564 False 893.966667 2176 95.085667 899 3016 3 chr3B.!!$F1 2117
4 TraesCS3A01G167800 chr4D 289665308 289666012 704 True 878.000000 878 89.356000 117 818 1 chr4D.!!$R2 701
5 TraesCS3A01G167800 chr5A 84673677 84674364 687 True 850.000000 850 88.952000 118 817 1 chr5A.!!$R1 699
6 TraesCS3A01G167800 chr4A 465897089 465897779 690 True 845.000000 845 88.794000 120 817 1 chr4A.!!$R1 697
7 TraesCS3A01G167800 chr4A 33856853 33857506 653 False 612.000000 612 83.665000 120 818 1 chr4A.!!$F1 698
8 TraesCS3A01G167800 chr1A 215012285 215012973 688 False 809.000000 809 88.011000 120 816 1 chr1A.!!$F1 696
9 TraesCS3A01G167800 chr1A 261433360 261434045 685 True 774.000000 774 87.092000 120 817 1 chr1A.!!$R1 697
10 TraesCS3A01G167800 chr7A 526125448 526126164 716 True 808.000000 808 87.569000 120 817 1 chr7A.!!$R2 697
11 TraesCS3A01G167800 chr7A 643181662 643182339 677 True 789.000000 789 87.642000 120 818 1 chr7A.!!$R4 698
12 TraesCS3A01G167800 chr6A 389761242 389761942 700 True 749.000000 749 86.030000 110 824 1 chr6A.!!$R1 714
13 TraesCS3A01G167800 chr7D 75314352 75315047 695 False 667.000000 667 84.358000 121 818 1 chr7D.!!$F1 697
14 TraesCS3A01G167800 chr2A 646824118 646824774 656 False 658.000000 658 84.714000 119 816 1 chr2A.!!$F3 697
15 TraesCS3A01G167800 chr1B 217313412 217314152 740 True 560.000000 560 81.516000 120 818 1 chr1B.!!$R1 698

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
896 1075 0.036765 TTCCCGTACTTCGCATTGCT 60.037 50.0 7.12 0.0 38.35 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2231 1.186917 TGGAACCAAATGCTGCAGGG 61.187 55.0 17.12 10.2 0.0 4.45 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
21 22 2.473530 TGCAAAGCAGTGAAAAGACG 57.526 45.000 0.00 0.00 33.32 4.18
22 23 1.742831 TGCAAAGCAGTGAAAAGACGT 59.257 42.857 0.00 0.00 33.32 4.34
23 24 2.163412 TGCAAAGCAGTGAAAAGACGTT 59.837 40.909 0.00 0.00 33.32 3.99
24 25 2.783832 GCAAAGCAGTGAAAAGACGTTC 59.216 45.455 0.00 0.00 0.00 3.95
25 26 3.029074 CAAAGCAGTGAAAAGACGTTCG 58.971 45.455 0.00 0.00 0.00 3.95
26 27 0.582005 AGCAGTGAAAAGACGTTCGC 59.418 50.000 0.00 0.00 38.12 4.70
27 28 0.384353 GCAGTGAAAAGACGTTCGCC 60.384 55.000 0.00 0.00 38.53 5.54
28 29 0.234884 CAGTGAAAAGACGTTCGCCC 59.765 55.000 0.00 0.00 38.53 6.13
29 30 1.203313 GTGAAAAGACGTTCGCCCG 59.797 57.895 0.00 0.00 32.89 6.13
30 31 2.172659 GAAAAGACGTTCGCCCGC 59.827 61.111 0.00 0.00 0.00 6.13
31 32 2.280592 AAAAGACGTTCGCCCGCT 60.281 55.556 0.00 0.00 0.00 5.52
32 33 1.005867 AAAAGACGTTCGCCCGCTA 60.006 52.632 0.00 0.00 0.00 4.26
33 34 0.600782 AAAAGACGTTCGCCCGCTAA 60.601 50.000 0.00 0.00 0.00 3.09
34 35 0.600782 AAAGACGTTCGCCCGCTAAA 60.601 50.000 0.00 0.00 0.00 1.85
35 36 0.390735 AAGACGTTCGCCCGCTAAAT 60.391 50.000 0.00 0.00 0.00 1.40
36 37 0.390735 AGACGTTCGCCCGCTAAATT 60.391 50.000 0.00 0.00 0.00 1.82
37 38 0.445043 GACGTTCGCCCGCTAAATTT 59.555 50.000 0.00 0.00 0.00 1.82
38 39 0.167251 ACGTTCGCCCGCTAAATTTG 59.833 50.000 0.00 0.00 0.00 2.32
39 40 0.167251 CGTTCGCCCGCTAAATTTGT 59.833 50.000 0.00 0.00 0.00 2.83
40 41 1.613270 GTTCGCCCGCTAAATTTGTG 58.387 50.000 0.00 0.00 0.00 3.33
41 42 1.068816 GTTCGCCCGCTAAATTTGTGT 60.069 47.619 0.00 0.00 0.00 3.72
42 43 0.800012 TCGCCCGCTAAATTTGTGTC 59.200 50.000 0.00 0.00 0.00 3.67
43 44 0.519519 CGCCCGCTAAATTTGTGTCA 59.480 50.000 0.00 0.00 0.00 3.58
44 45 1.465689 CGCCCGCTAAATTTGTGTCAG 60.466 52.381 0.00 0.00 0.00 3.51
45 46 1.810151 GCCCGCTAAATTTGTGTCAGA 59.190 47.619 0.00 0.00 0.00 3.27
46 47 2.423538 GCCCGCTAAATTTGTGTCAGAT 59.576 45.455 0.00 0.00 0.00 2.90
47 48 3.119495 GCCCGCTAAATTTGTGTCAGATT 60.119 43.478 0.00 0.00 0.00 2.40
48 49 4.662145 CCCGCTAAATTTGTGTCAGATTC 58.338 43.478 0.00 0.00 0.00 2.52
49 50 4.334443 CCGCTAAATTTGTGTCAGATTCG 58.666 43.478 0.00 0.00 0.00 3.34
50 51 4.092821 CCGCTAAATTTGTGTCAGATTCGA 59.907 41.667 0.00 0.00 0.00 3.71
51 52 5.220662 CCGCTAAATTTGTGTCAGATTCGAT 60.221 40.000 0.00 0.00 0.00 3.59
52 53 5.674148 CGCTAAATTTGTGTCAGATTCGATG 59.326 40.000 0.00 0.00 0.00 3.84
53 54 5.967674 GCTAAATTTGTGTCAGATTCGATGG 59.032 40.000 0.00 0.00 0.00 3.51
54 55 4.361451 AATTTGTGTCAGATTCGATGGC 57.639 40.909 0.00 0.00 0.00 4.40
55 56 2.768253 TTGTGTCAGATTCGATGGCT 57.232 45.000 0.00 0.00 0.00 4.75
56 57 2.299993 TGTGTCAGATTCGATGGCTC 57.700 50.000 0.00 0.00 0.00 4.70
57 58 1.203928 GTGTCAGATTCGATGGCTCG 58.796 55.000 0.00 0.77 46.41 5.03
58 59 0.528466 TGTCAGATTCGATGGCTCGC 60.528 55.000 0.00 0.00 44.65 5.03
59 60 1.299392 TCAGATTCGATGGCTCGCG 60.299 57.895 0.00 0.00 44.65 5.87
60 61 1.299392 CAGATTCGATGGCTCGCGA 60.299 57.895 9.26 9.26 44.65 5.87
61 62 1.007964 AGATTCGATGGCTCGCGAG 60.008 57.895 31.37 31.37 44.65 5.03
62 63 2.018866 GATTCGATGGCTCGCGAGG 61.019 63.158 35.10 19.37 44.65 4.63
75 76 2.511600 CGAGGCGGCGGATCTTTT 60.512 61.111 9.78 0.00 0.00 2.27
76 77 2.106683 CGAGGCGGCGGATCTTTTT 61.107 57.895 9.78 0.00 0.00 1.94
77 78 0.808453 CGAGGCGGCGGATCTTTTTA 60.808 55.000 9.78 0.00 0.00 1.52
78 79 0.938008 GAGGCGGCGGATCTTTTTAG 59.062 55.000 9.78 0.00 0.00 1.85
79 80 0.539986 AGGCGGCGGATCTTTTTAGA 59.460 50.000 9.78 0.00 0.00 2.10
80 81 1.065709 AGGCGGCGGATCTTTTTAGAA 60.066 47.619 9.78 0.00 0.00 2.10
81 82 1.330829 GGCGGCGGATCTTTTTAGAAG 59.669 52.381 9.78 0.00 0.00 2.85
82 83 2.277084 GCGGCGGATCTTTTTAGAAGA 58.723 47.619 9.78 0.00 0.00 2.87
83 84 2.872858 GCGGCGGATCTTTTTAGAAGAT 59.127 45.455 9.78 0.00 39.53 2.40
90 91 5.993106 GATCTTTTTAGAAGATCCACCGG 57.007 43.478 12.74 0.00 44.17 5.28
91 92 3.606687 TCTTTTTAGAAGATCCACCGGC 58.393 45.455 0.00 0.00 0.00 6.13
92 93 2.413310 TTTTAGAAGATCCACCGGCC 57.587 50.000 0.00 0.00 0.00 6.13
93 94 0.177141 TTTAGAAGATCCACCGGCCG 59.823 55.000 21.04 21.04 0.00 6.13
94 95 0.685131 TTAGAAGATCCACCGGCCGA 60.685 55.000 30.73 6.75 0.00 5.54
95 96 1.389609 TAGAAGATCCACCGGCCGAC 61.390 60.000 30.73 10.34 0.00 4.79
96 97 4.143333 AAGATCCACCGGCCGACG 62.143 66.667 30.73 17.26 43.80 5.12
114 115 2.911143 CGTAGCAGCCCCCTTGAT 59.089 61.111 0.00 0.00 0.00 2.57
115 116 2.133195 CGTAGCAGCCCCCTTGATA 58.867 57.895 0.00 0.00 0.00 2.15
159 160 6.591935 TGACACTGTCTTAAAATCTGGTTCT 58.408 36.000 10.54 0.00 33.15 3.01
282 283 1.534729 AAGACGATTTTGCCCCTCAC 58.465 50.000 0.00 0.00 0.00 3.51
283 284 0.400213 AGACGATTTTGCCCCTCACA 59.600 50.000 0.00 0.00 0.00 3.58
336 371 3.359523 CACATGTGTGCCGCTGCT 61.360 61.111 18.03 0.00 39.39 4.24
337 372 3.359523 ACATGTGTGCCGCTGCTG 61.360 61.111 0.00 0.00 38.71 4.41
338 373 4.771356 CATGTGTGCCGCTGCTGC 62.771 66.667 9.23 9.23 38.71 5.25
341 376 4.771356 GTGTGCCGCTGCTGCATG 62.771 66.667 21.24 7.04 41.46 4.06
343 378 4.771356 GTGCCGCTGCTGCATGTG 62.771 66.667 21.24 4.29 41.46 3.21
361 404 4.796314 TGCTGCTGCATGTGTGTA 57.204 50.000 14.93 0.00 45.31 2.90
433 496 1.136565 GTGTGTGTGCTGTTGCGTT 59.863 52.632 0.00 0.00 43.34 4.84
509 589 2.663520 CGTGCGTGTGGGTTGCTA 60.664 61.111 0.00 0.00 0.00 3.49
547 721 2.580966 TGTGTTGCTACGTGTGTGTA 57.419 45.000 0.00 0.00 0.00 2.90
551 725 1.795872 GTTGCTACGTGTGTGTATGCA 59.204 47.619 0.00 0.00 31.38 3.96
626 800 2.826277 CACTGATGCTGCGTGTGTA 58.174 52.632 0.00 0.00 0.00 2.90
670 848 7.230108 CACATATCATATGAGGGCAAAAGAGTT 59.770 37.037 11.87 0.00 0.00 3.01
723 901 6.817140 GGACGGAAATGTCATATAGGGAATAC 59.183 42.308 0.00 0.00 40.72 1.89
753 932 5.998363 AGAGTTTGTGTCAAATAGGGAAGAC 59.002 40.000 0.00 0.00 0.00 3.01
763 942 7.978975 TGTCAAATAGGGAAGACAAACTTTTTG 59.021 33.333 0.00 0.00 37.99 2.44
800 979 6.758886 AGGAAGCAGATTTTAAGATAGTGTCG 59.241 38.462 0.00 0.00 0.00 4.35
819 998 8.034058 AGTGTCGAATAAGGAATTTTCTCTTG 57.966 34.615 0.00 0.00 0.00 3.02
820 999 7.878127 AGTGTCGAATAAGGAATTTTCTCTTGA 59.122 33.333 0.00 0.00 0.00 3.02
824 1003 9.884636 TCGAATAAGGAATTTTCTCTTGATACA 57.115 29.630 0.00 0.00 0.00 2.29
829 1008 8.414629 AAGGAATTTTCTCTTGATACAAAGCT 57.585 30.769 0.00 0.00 0.00 3.74
830 1009 8.414629 AGGAATTTTCTCTTGATACAAAGCTT 57.585 30.769 0.00 0.00 0.00 3.74
831 1010 8.864087 AGGAATTTTCTCTTGATACAAAGCTTT 58.136 29.630 5.69 5.69 0.00 3.51
836 1015 9.897744 TTTTCTCTTGATACAAAGCTTTACATG 57.102 29.630 12.25 2.49 0.00 3.21
837 1016 8.846943 TTCTCTTGATACAAAGCTTTACATGA 57.153 30.769 12.25 14.39 0.00 3.07
838 1017 8.846943 TCTCTTGATACAAAGCTTTACATGAA 57.153 30.769 12.25 7.52 0.00 2.57
839 1018 8.939929 TCTCTTGATACAAAGCTTTACATGAAG 58.060 33.333 12.25 15.91 0.00 3.02
840 1019 8.846943 TCTTGATACAAAGCTTTACATGAAGA 57.153 30.769 20.42 20.42 0.00 2.87
841 1020 9.283768 TCTTGATACAAAGCTTTACATGAAGAA 57.716 29.630 21.30 11.70 0.00 2.52
842 1021 9.897744 CTTGATACAAAGCTTTACATGAAGAAA 57.102 29.630 18.51 0.00 0.00 2.52
844 1023 9.677567 TGATACAAAGCTTTACATGAAGAAAAC 57.322 29.630 12.25 0.00 0.00 2.43
845 1024 9.677567 GATACAAAGCTTTACATGAAGAAAACA 57.322 29.630 12.25 0.00 0.00 2.83
847 1026 8.356533 ACAAAGCTTTACATGAAGAAAACATG 57.643 30.769 12.25 0.00 46.96 3.21
848 1027 7.439056 ACAAAGCTTTACATGAAGAAAACATGG 59.561 33.333 12.25 0.00 46.19 3.66
849 1028 5.473039 AGCTTTACATGAAGAAAACATGGC 58.527 37.500 0.00 0.00 46.19 4.40
850 1029 4.627035 GCTTTACATGAAGAAAACATGGCC 59.373 41.667 0.00 0.00 46.19 5.36
851 1030 4.799564 TTACATGAAGAAAACATGGCCC 57.200 40.909 0.00 0.00 46.19 5.80
852 1031 2.607499 ACATGAAGAAAACATGGCCCA 58.393 42.857 0.00 0.00 46.19 5.36
853 1032 3.175594 ACATGAAGAAAACATGGCCCAT 58.824 40.909 0.00 0.00 46.19 4.00
854 1033 3.196254 ACATGAAGAAAACATGGCCCATC 59.804 43.478 0.00 0.00 46.19 3.51
855 1034 2.886913 TGAAGAAAACATGGCCCATCA 58.113 42.857 0.00 0.00 0.00 3.07
856 1035 2.827322 TGAAGAAAACATGGCCCATCAG 59.173 45.455 0.00 0.00 0.00 2.90
857 1036 1.188863 AGAAAACATGGCCCATCAGC 58.811 50.000 0.00 0.00 0.00 4.26
865 1044 2.516225 GCCCATCAGCCCCGTAAC 60.516 66.667 0.00 0.00 0.00 2.50
866 1045 2.192175 CCCATCAGCCCCGTAACC 59.808 66.667 0.00 0.00 0.00 2.85
867 1046 2.375345 CCCATCAGCCCCGTAACCT 61.375 63.158 0.00 0.00 0.00 3.50
868 1047 1.146263 CCATCAGCCCCGTAACCTC 59.854 63.158 0.00 0.00 0.00 3.85
869 1048 1.146263 CATCAGCCCCGTAACCTCC 59.854 63.158 0.00 0.00 0.00 4.30
870 1049 2.070650 ATCAGCCCCGTAACCTCCC 61.071 63.158 0.00 0.00 0.00 4.30
871 1050 4.157120 CAGCCCCGTAACCTCCCG 62.157 72.222 0.00 0.00 0.00 5.14
874 1053 2.043046 CCCCGTAACCTCCCGGTA 60.043 66.667 0.00 0.00 44.73 4.02
875 1054 1.685421 CCCCGTAACCTCCCGGTAA 60.685 63.158 0.00 0.00 44.73 2.85
876 1055 1.517361 CCCGTAACCTCCCGGTAAC 59.483 63.158 0.00 0.00 44.73 2.50
877 1056 0.972471 CCCGTAACCTCCCGGTAACT 60.972 60.000 0.00 0.00 44.73 2.24
878 1057 0.897621 CCGTAACCTCCCGGTAACTT 59.102 55.000 0.00 0.00 44.73 2.66
879 1058 1.134995 CCGTAACCTCCCGGTAACTTC 60.135 57.143 0.00 0.00 44.73 3.01
880 1059 1.134995 CGTAACCTCCCGGTAACTTCC 60.135 57.143 0.00 0.00 44.73 3.46
881 1060 1.208052 GTAACCTCCCGGTAACTTCCC 59.792 57.143 0.00 0.00 44.73 3.97
882 1061 1.547472 AACCTCCCGGTAACTTCCCG 61.547 60.000 0.00 0.00 44.73 5.14
883 1062 1.986210 CCTCCCGGTAACTTCCCGT 60.986 63.158 0.00 0.00 43.98 5.28
884 1063 0.684153 CCTCCCGGTAACTTCCCGTA 60.684 60.000 0.00 0.00 43.98 4.02
885 1064 0.457443 CTCCCGGTAACTTCCCGTAC 59.543 60.000 0.00 0.00 43.98 3.67
886 1065 0.039618 TCCCGGTAACTTCCCGTACT 59.960 55.000 0.00 0.00 43.98 2.73
887 1066 0.897621 CCCGGTAACTTCCCGTACTT 59.102 55.000 0.00 0.00 43.98 2.24
888 1067 1.134995 CCCGGTAACTTCCCGTACTTC 60.135 57.143 0.00 0.00 43.98 3.01
889 1068 1.468054 CCGGTAACTTCCCGTACTTCG 60.468 57.143 0.00 0.00 43.98 3.79
890 1069 1.633561 GGTAACTTCCCGTACTTCGC 58.366 55.000 0.00 0.00 38.35 4.70
891 1070 1.067635 GGTAACTTCCCGTACTTCGCA 60.068 52.381 0.00 0.00 38.35 5.10
892 1071 2.417787 GGTAACTTCCCGTACTTCGCAT 60.418 50.000 0.00 0.00 38.35 4.73
893 1072 2.467566 AACTTCCCGTACTTCGCATT 57.532 45.000 0.00 0.00 38.35 3.56
894 1073 1.722011 ACTTCCCGTACTTCGCATTG 58.278 50.000 0.00 0.00 38.35 2.82
895 1074 0.373716 CTTCCCGTACTTCGCATTGC 59.626 55.000 0.00 0.00 38.35 3.56
896 1075 0.036765 TTCCCGTACTTCGCATTGCT 60.037 50.000 7.12 0.00 38.35 3.91
897 1076 0.459585 TCCCGTACTTCGCATTGCTC 60.460 55.000 7.12 0.00 38.35 4.26
983 1162 3.411517 CTCCCCACCCGCAATCCT 61.412 66.667 0.00 0.00 0.00 3.24
984 1163 3.406595 CTCCCCACCCGCAATCCTC 62.407 68.421 0.00 0.00 0.00 3.71
1006 1186 2.802667 GCGATTGCAGCGATGACGT 61.803 57.895 4.02 0.00 42.15 4.34
1222 1402 3.636231 CCTCCCGTGAAGCCCACA 61.636 66.667 7.49 0.00 45.98 4.17
1364 1544 1.067060 CATGCCCTTCTCGTACGATCA 59.933 52.381 19.87 5.64 0.00 2.92
1636 1816 2.670414 CAGCTTAAGAAGAAGACGCCTG 59.330 50.000 6.67 0.00 0.00 4.85
1859 2045 1.439353 ATGCCGTCATCGACATTGGC 61.439 55.000 12.28 12.28 36.85 4.52
2171 2359 4.132336 TGTTAGCCGATCGTATCTACACT 58.868 43.478 15.09 1.01 0.00 3.55
2292 2480 2.197577 GAGAAAGATCCGTGCTGCTAC 58.802 52.381 0.00 0.00 0.00 3.58
2367 2635 3.355626 CATCTGGCTGATGCATCAAAG 57.644 47.619 28.39 23.63 44.96 2.77
2368 2636 1.100510 TCTGGCTGATGCATCAAAGC 58.899 50.000 28.39 26.65 41.91 3.51
2380 2648 5.494632 TGCATCAAAGCACTCTATCATTG 57.505 39.130 0.00 0.00 40.11 2.82
2381 2649 4.201980 TGCATCAAAGCACTCTATCATTGC 60.202 41.667 0.00 0.00 40.11 3.56
2382 2650 4.201980 GCATCAAAGCACTCTATCATTGCA 60.202 41.667 0.00 0.00 38.81 4.08
2383 2651 4.952262 TCAAAGCACTCTATCATTGCAC 57.048 40.909 0.00 0.00 38.81 4.57
2384 2652 4.582869 TCAAAGCACTCTATCATTGCACT 58.417 39.130 0.00 0.00 38.81 4.40
2385 2653 5.005740 TCAAAGCACTCTATCATTGCACTT 58.994 37.500 0.00 0.00 38.81 3.16
2484 2752 3.322254 ACTGGAGAAACGAGATGAAGTGT 59.678 43.478 0.00 0.00 0.00 3.55
2774 4477 1.066303 CTCTGAAGCAGCCTACCTACG 59.934 57.143 0.00 0.00 0.00 3.51
2828 4531 0.461961 ACCCAGACAAGATCTAGCGC 59.538 55.000 0.00 0.00 35.15 5.92
2832 4535 0.526524 AGACAAGATCTAGCGCGCAC 60.527 55.000 35.10 17.81 35.15 5.34
2882 4592 8.420374 TTTTCCGCAAAAATGTTGTACATAAA 57.580 26.923 0.00 0.00 37.97 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.531508 CGTCTTTTCACTGCTTTGCAAC 59.468 45.455 0.00 0.00 38.41 4.17
4 5 3.029074 CGAACGTCTTTTCACTGCTTTG 58.971 45.455 0.00 0.00 0.00 2.77
6 7 1.003866 GCGAACGTCTTTTCACTGCTT 60.004 47.619 0.00 0.00 0.00 3.91
7 8 0.582005 GCGAACGTCTTTTCACTGCT 59.418 50.000 0.00 0.00 0.00 4.24
8 9 0.384353 GGCGAACGTCTTTTCACTGC 60.384 55.000 0.00 0.00 0.00 4.40
9 10 0.234884 GGGCGAACGTCTTTTCACTG 59.765 55.000 0.00 0.00 0.00 3.66
10 11 1.219522 CGGGCGAACGTCTTTTCACT 61.220 55.000 0.00 0.00 0.00 3.41
11 12 1.203313 CGGGCGAACGTCTTTTCAC 59.797 57.895 0.00 0.00 0.00 3.18
12 13 2.600475 GCGGGCGAACGTCTTTTCA 61.600 57.895 0.00 0.00 35.98 2.69
13 14 1.010419 TAGCGGGCGAACGTCTTTTC 61.010 55.000 0.00 0.00 35.98 2.29
14 15 0.600782 TTAGCGGGCGAACGTCTTTT 60.601 50.000 0.00 0.00 35.98 2.27
15 16 0.600782 TTTAGCGGGCGAACGTCTTT 60.601 50.000 0.00 0.00 35.98 2.52
16 17 0.390735 ATTTAGCGGGCGAACGTCTT 60.391 50.000 0.00 0.00 35.98 3.01
17 18 0.390735 AATTTAGCGGGCGAACGTCT 60.391 50.000 0.00 0.00 35.98 4.18
18 19 0.445043 AAATTTAGCGGGCGAACGTC 59.555 50.000 0.00 0.00 35.98 4.34
19 20 0.167251 CAAATTTAGCGGGCGAACGT 59.833 50.000 0.00 0.00 35.98 3.99
20 21 0.167251 ACAAATTTAGCGGGCGAACG 59.833 50.000 0.00 0.00 0.00 3.95
21 22 1.068816 ACACAAATTTAGCGGGCGAAC 60.069 47.619 0.00 0.00 0.00 3.95
22 23 1.198178 GACACAAATTTAGCGGGCGAA 59.802 47.619 0.00 0.00 0.00 4.70
23 24 0.800012 GACACAAATTTAGCGGGCGA 59.200 50.000 0.00 0.00 0.00 5.54
24 25 0.519519 TGACACAAATTTAGCGGGCG 59.480 50.000 0.00 0.00 0.00 6.13
25 26 1.810151 TCTGACACAAATTTAGCGGGC 59.190 47.619 0.00 0.00 0.00 6.13
26 27 4.662145 GAATCTGACACAAATTTAGCGGG 58.338 43.478 0.00 0.00 0.00 6.13
27 28 4.092821 TCGAATCTGACACAAATTTAGCGG 59.907 41.667 0.00 0.00 0.00 5.52
28 29 5.203358 TCGAATCTGACACAAATTTAGCG 57.797 39.130 0.00 0.00 0.00 4.26
29 30 5.967674 CCATCGAATCTGACACAAATTTAGC 59.032 40.000 0.00 0.00 0.00 3.09
30 31 5.967674 GCCATCGAATCTGACACAAATTTAG 59.032 40.000 0.00 0.00 0.00 1.85
31 32 5.647658 AGCCATCGAATCTGACACAAATTTA 59.352 36.000 0.00 0.00 0.00 1.40
32 33 4.460382 AGCCATCGAATCTGACACAAATTT 59.540 37.500 0.00 0.00 0.00 1.82
33 34 4.012374 AGCCATCGAATCTGACACAAATT 58.988 39.130 0.00 0.00 0.00 1.82
34 35 3.614092 AGCCATCGAATCTGACACAAAT 58.386 40.909 0.00 0.00 0.00 2.32
35 36 3.002791 GAGCCATCGAATCTGACACAAA 58.997 45.455 0.00 0.00 0.00 2.83
36 37 2.621338 GAGCCATCGAATCTGACACAA 58.379 47.619 0.00 0.00 0.00 3.33
37 38 2.299993 GAGCCATCGAATCTGACACA 57.700 50.000 0.00 0.00 0.00 3.72
58 59 0.808453 TAAAAAGATCCGCCGCCTCG 60.808 55.000 0.00 0.00 0.00 4.63
59 60 0.938008 CTAAAAAGATCCGCCGCCTC 59.062 55.000 0.00 0.00 0.00 4.70
60 61 0.539986 TCTAAAAAGATCCGCCGCCT 59.460 50.000 0.00 0.00 0.00 5.52
61 62 1.330829 CTTCTAAAAAGATCCGCCGCC 59.669 52.381 0.00 0.00 0.00 6.13
62 63 2.277084 TCTTCTAAAAAGATCCGCCGC 58.723 47.619 0.00 0.00 0.00 6.53
63 64 4.717188 GATCTTCTAAAAAGATCCGCCG 57.283 45.455 14.16 0.00 44.17 6.46
69 70 4.200092 GCCGGTGGATCTTCTAAAAAGAT 58.800 43.478 1.90 0.06 39.53 2.40
70 71 3.606687 GCCGGTGGATCTTCTAAAAAGA 58.393 45.455 1.90 0.00 0.00 2.52
71 72 2.683362 GGCCGGTGGATCTTCTAAAAAG 59.317 50.000 1.90 0.00 0.00 2.27
72 73 2.718563 GGCCGGTGGATCTTCTAAAAA 58.281 47.619 1.90 0.00 0.00 1.94
73 74 1.406341 CGGCCGGTGGATCTTCTAAAA 60.406 52.381 20.10 0.00 0.00 1.52
74 75 0.177141 CGGCCGGTGGATCTTCTAAA 59.823 55.000 20.10 0.00 0.00 1.85
75 76 0.685131 TCGGCCGGTGGATCTTCTAA 60.685 55.000 27.83 0.00 0.00 2.10
76 77 1.076559 TCGGCCGGTGGATCTTCTA 60.077 57.895 27.83 0.00 0.00 2.10
77 78 2.363795 TCGGCCGGTGGATCTTCT 60.364 61.111 27.83 0.00 0.00 2.85
78 79 2.202892 GTCGGCCGGTGGATCTTC 60.203 66.667 27.83 1.14 0.00 2.87
79 80 4.143333 CGTCGGCCGGTGGATCTT 62.143 66.667 27.83 0.00 0.00 2.40
96 97 2.040009 TATCAAGGGGGCTGCTACGC 62.040 60.000 0.00 1.67 0.00 4.42
97 98 0.249911 GTATCAAGGGGGCTGCTACG 60.250 60.000 0.00 0.00 0.00 3.51
98 99 0.837272 TGTATCAAGGGGGCTGCTAC 59.163 55.000 0.00 0.00 0.00 3.58
99 100 1.490490 CTTGTATCAAGGGGGCTGCTA 59.510 52.381 0.00 0.00 0.00 3.49
100 101 0.257039 CTTGTATCAAGGGGGCTGCT 59.743 55.000 0.00 0.00 0.00 4.24
101 102 0.255890 TCTTGTATCAAGGGGGCTGC 59.744 55.000 9.18 0.00 0.00 5.25
102 103 1.839994 TCTCTTGTATCAAGGGGGCTG 59.160 52.381 9.11 0.00 0.00 4.85
103 104 2.270434 TCTCTTGTATCAAGGGGGCT 57.730 50.000 9.11 0.00 0.00 5.19
104 105 3.366052 TTTCTCTTGTATCAAGGGGGC 57.634 47.619 9.11 0.00 0.00 5.80
105 106 5.360999 GGAATTTTCTCTTGTATCAAGGGGG 59.639 44.000 9.11 2.12 0.00 5.40
106 107 6.190587 AGGAATTTTCTCTTGTATCAAGGGG 58.809 40.000 9.11 4.10 0.00 4.79
107 108 7.709149 AAGGAATTTTCTCTTGTATCAAGGG 57.291 36.000 9.18 6.37 0.00 3.95
115 116 9.136323 AGTGTCAAATAAGGAATTTTCTCTTGT 57.864 29.630 0.00 0.00 35.54 3.16
406 459 4.918060 CACACACACACACGCGCG 62.918 66.667 30.96 30.96 0.00 6.86
433 496 2.187685 CGCAGGCAGCACATAGGA 59.812 61.111 1.96 0.00 46.13 2.94
464 527 2.158682 ACACCCACATACACACACACAT 60.159 45.455 0.00 0.00 0.00 3.21
502 582 1.278637 GCACACACACGTAGCAACC 59.721 57.895 0.00 0.00 0.00 3.77
531 705 1.795872 TGCATACACACACGTAGCAAC 59.204 47.619 0.00 0.00 0.00 4.17
532 706 1.795872 GTGCATACACACACGTAGCAA 59.204 47.619 0.00 0.00 46.61 3.91
551 725 2.435234 ACCAACACACACGCACGT 60.435 55.556 0.00 0.00 0.00 4.49
650 827 6.916360 AAAAACTCTTTTGCCCTCATATGA 57.084 33.333 5.07 5.07 33.39 2.15
723 901 8.792633 TCCCTATTTGACACAAACTCTAAATTG 58.207 33.333 0.00 0.00 0.00 2.32
732 910 6.385649 TTGTCTTCCCTATTTGACACAAAC 57.614 37.500 0.00 0.00 38.87 2.93
763 942 6.749923 AATCTGCTTCCTTATTTGACACTC 57.250 37.500 0.00 0.00 0.00 3.51
819 998 9.677567 TGTTTTCTTCATGTAAAGCTTTGTATC 57.322 29.630 22.02 9.68 0.00 2.24
824 1003 6.424812 GCCATGTTTTCTTCATGTAAAGCTTT 59.575 34.615 17.30 17.30 40.43 3.51
825 1004 5.928264 GCCATGTTTTCTTCATGTAAAGCTT 59.072 36.000 0.00 0.00 40.43 3.74
826 1005 5.473039 GCCATGTTTTCTTCATGTAAAGCT 58.527 37.500 0.00 0.00 40.43 3.74
827 1006 4.627035 GGCCATGTTTTCTTCATGTAAAGC 59.373 41.667 0.00 0.00 40.43 3.51
828 1007 5.170748 GGGCCATGTTTTCTTCATGTAAAG 58.829 41.667 4.39 0.00 40.43 1.85
829 1008 4.590647 TGGGCCATGTTTTCTTCATGTAAA 59.409 37.500 0.00 0.00 40.43 2.01
830 1009 4.155709 TGGGCCATGTTTTCTTCATGTAA 58.844 39.130 0.00 0.00 40.43 2.41
831 1010 3.772387 TGGGCCATGTTTTCTTCATGTA 58.228 40.909 0.00 0.00 40.43 2.29
832 1011 2.607499 TGGGCCATGTTTTCTTCATGT 58.393 42.857 0.00 0.00 40.43 3.21
833 1012 3.196039 TGATGGGCCATGTTTTCTTCATG 59.804 43.478 26.77 0.00 41.34 3.07
834 1013 3.443052 TGATGGGCCATGTTTTCTTCAT 58.557 40.909 26.77 0.00 0.00 2.57
835 1014 2.827322 CTGATGGGCCATGTTTTCTTCA 59.173 45.455 26.77 12.96 0.00 3.02
836 1015 2.417787 GCTGATGGGCCATGTTTTCTTC 60.418 50.000 26.77 8.28 0.00 2.87
837 1016 1.551883 GCTGATGGGCCATGTTTTCTT 59.448 47.619 26.77 0.00 0.00 2.52
838 1017 1.188863 GCTGATGGGCCATGTTTTCT 58.811 50.000 26.77 0.00 0.00 2.52
839 1018 3.746900 GCTGATGGGCCATGTTTTC 57.253 52.632 26.77 10.80 0.00 2.29
848 1027 2.516225 GTTACGGGGCTGATGGGC 60.516 66.667 0.00 0.00 40.05 5.36
849 1028 2.192175 GGTTACGGGGCTGATGGG 59.808 66.667 0.00 0.00 0.00 4.00
850 1029 1.146263 GAGGTTACGGGGCTGATGG 59.854 63.158 0.00 0.00 0.00 3.51
851 1030 1.146263 GGAGGTTACGGGGCTGATG 59.854 63.158 0.00 0.00 0.00 3.07
852 1031 2.070650 GGGAGGTTACGGGGCTGAT 61.071 63.158 0.00 0.00 0.00 2.90
853 1032 2.686106 GGGAGGTTACGGGGCTGA 60.686 66.667 0.00 0.00 0.00 4.26
854 1033 4.157120 CGGGAGGTTACGGGGCTG 62.157 72.222 0.00 0.00 0.00 4.85
871 1050 1.067635 TGCGAAGTACGGGAAGTTACC 60.068 52.381 0.00 0.00 42.83 2.85
872 1051 2.352503 TGCGAAGTACGGGAAGTTAC 57.647 50.000 0.00 0.00 42.83 2.50
873 1052 3.255725 CAATGCGAAGTACGGGAAGTTA 58.744 45.455 0.00 0.00 42.83 2.24
874 1053 2.073816 CAATGCGAAGTACGGGAAGTT 58.926 47.619 0.00 0.00 42.83 2.66
875 1054 1.722011 CAATGCGAAGTACGGGAAGT 58.278 50.000 0.00 0.00 42.83 3.01
876 1055 0.373716 GCAATGCGAAGTACGGGAAG 59.626 55.000 0.00 0.00 42.83 3.46
877 1056 0.036765 AGCAATGCGAAGTACGGGAA 60.037 50.000 0.00 0.00 42.83 3.97
878 1057 0.459585 GAGCAATGCGAAGTACGGGA 60.460 55.000 0.00 0.00 42.83 5.14
879 1058 0.739462 TGAGCAATGCGAAGTACGGG 60.739 55.000 0.00 0.00 42.83 5.28
880 1059 1.075542 TTGAGCAATGCGAAGTACGG 58.924 50.000 0.00 0.00 42.83 4.02
881 1060 2.873170 TTTGAGCAATGCGAAGTACG 57.127 45.000 0.00 0.00 45.66 3.67
882 1061 4.098416 GGATTTTGAGCAATGCGAAGTAC 58.902 43.478 0.00 0.00 0.00 2.73
883 1062 3.128589 GGGATTTTGAGCAATGCGAAGTA 59.871 43.478 0.00 0.00 0.00 2.24
884 1063 2.094545 GGGATTTTGAGCAATGCGAAGT 60.095 45.455 0.00 0.00 0.00 3.01
885 1064 2.533266 GGGATTTTGAGCAATGCGAAG 58.467 47.619 0.00 0.00 0.00 3.79
886 1065 1.135431 CGGGATTTTGAGCAATGCGAA 60.135 47.619 0.00 0.00 0.00 4.70
887 1066 0.451383 CGGGATTTTGAGCAATGCGA 59.549 50.000 0.00 0.00 0.00 5.10
888 1067 0.171007 ACGGGATTTTGAGCAATGCG 59.829 50.000 0.00 0.00 0.00 4.73
889 1068 1.795162 CGACGGGATTTTGAGCAATGC 60.795 52.381 0.00 0.00 0.00 3.56
890 1069 1.468520 ACGACGGGATTTTGAGCAATG 59.531 47.619 0.00 0.00 0.00 2.82
891 1070 1.737793 GACGACGGGATTTTGAGCAAT 59.262 47.619 0.00 0.00 0.00 3.56
892 1071 1.153353 GACGACGGGATTTTGAGCAA 58.847 50.000 0.00 0.00 0.00 3.91
893 1072 0.034198 TGACGACGGGATTTTGAGCA 59.966 50.000 0.00 0.00 0.00 4.26
894 1073 1.153353 TTGACGACGGGATTTTGAGC 58.847 50.000 0.00 0.00 0.00 4.26
895 1074 3.000041 TGATTGACGACGGGATTTTGAG 59.000 45.455 0.00 0.00 0.00 3.02
896 1075 3.000041 CTGATTGACGACGGGATTTTGA 59.000 45.455 0.00 0.00 0.00 2.69
897 1076 2.095853 CCTGATTGACGACGGGATTTTG 59.904 50.000 0.00 0.00 34.76 2.44
1340 1520 0.727398 GTACGAGAAGGGCATGTTGC 59.273 55.000 0.00 0.00 44.08 4.17
1345 1525 1.067212 GTGATCGTACGAGAAGGGCAT 59.933 52.381 23.89 3.57 0.00 4.40
1620 1800 4.021229 TGGTATCAGGCGTCTTCTTCTTA 58.979 43.478 0.00 0.00 0.00 2.10
1636 1816 1.369625 CTCTTGTGCCCGTTGGTATC 58.630 55.000 0.00 0.00 0.00 2.24
1859 2045 1.887707 GCTTATTCACCTCCGCGGG 60.888 63.158 27.83 16.14 36.97 6.13
2043 2231 1.186917 TGGAACCAAATGCTGCAGGG 61.187 55.000 17.12 10.20 0.00 4.45
2139 2327 4.220821 ACGATCGGCTAACATATCCTCAAT 59.779 41.667 20.98 0.00 0.00 2.57
2171 2359 9.698309 GAGCAGCTATATAAGATGAAAACAGTA 57.302 33.333 0.00 0.00 44.73 2.74
2355 2623 4.773013 TGATAGAGTGCTTTGATGCATCA 58.227 39.130 25.42 25.42 45.23 3.07
2356 2624 5.943706 ATGATAGAGTGCTTTGATGCATC 57.056 39.130 20.14 20.14 45.23 3.91
2357 2625 5.507482 GCAATGATAGAGTGCTTTGATGCAT 60.507 40.000 0.00 0.00 45.23 3.96
2360 2628 5.066117 AGTGCAATGATAGAGTGCTTTGATG 59.934 40.000 0.00 0.00 46.14 3.07
2361 2629 5.191426 AGTGCAATGATAGAGTGCTTTGAT 58.809 37.500 0.00 0.00 46.14 2.57
2362 2630 4.582869 AGTGCAATGATAGAGTGCTTTGA 58.417 39.130 0.00 0.00 46.14 2.69
2363 2631 4.959596 AGTGCAATGATAGAGTGCTTTG 57.040 40.909 0.00 0.00 46.14 2.77
2364 2632 4.157289 CCAAGTGCAATGATAGAGTGCTTT 59.843 41.667 2.43 0.00 46.14 3.51
2365 2633 3.693085 CCAAGTGCAATGATAGAGTGCTT 59.307 43.478 2.43 0.00 46.14 3.91
2366 2634 3.276857 CCAAGTGCAATGATAGAGTGCT 58.723 45.455 2.43 0.00 46.14 4.40
2367 2635 2.357009 CCCAAGTGCAATGATAGAGTGC 59.643 50.000 2.43 0.00 46.17 4.40
2368 2636 3.376234 CACCCAAGTGCAATGATAGAGTG 59.624 47.826 2.43 0.00 37.14 3.51
2369 2637 3.614092 CACCCAAGTGCAATGATAGAGT 58.386 45.455 2.43 0.00 37.14 3.24
2382 2650 4.406456 TGAAAGAACATATGCACCCAAGT 58.594 39.130 1.58 0.00 0.00 3.16
2383 2651 5.587388 ATGAAAGAACATATGCACCCAAG 57.413 39.130 1.58 0.00 0.00 3.61
2384 2652 5.479724 TGAATGAAAGAACATATGCACCCAA 59.520 36.000 1.58 0.00 0.00 4.12
2385 2653 5.015515 TGAATGAAAGAACATATGCACCCA 58.984 37.500 1.58 0.00 0.00 4.51
2440 2708 8.097662 CCAGTCTTCCTAGTAGTCTTGAAAAAT 58.902 37.037 0.00 0.00 0.00 1.82
2484 2752 3.320626 CAGCAACACGAAAGATCAGAGA 58.679 45.455 0.00 0.00 0.00 3.10
2882 4592 3.736433 GCTCTAGTGCTTCACGATGATGT 60.736 47.826 9.52 0.00 39.64 3.06


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

AutoCloner maintained by Alex Coulton.