Multiple sequence alignment - TraesCS5A01G520000

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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 TraesCS5A01G520000 chr5A 100.000 5543 0 0 1 5543 680980188 680985730 0.000000e+00 10237.0
1 TraesCS5A01G520000 chr5A 88.261 3646 401 13 900 4532 680921191 680924822 0.000000e+00 4337.0
2 TraesCS5A01G520000 chr5A 80.707 622 73 24 4887 5498 680869208 680869792 1.830000e-119 440.0
3 TraesCS5A01G520000 chr4D 96.570 4636 149 8 66 4694 500300015 500304647 0.000000e+00 7672.0
4 TraesCS5A01G520000 chr4D 88.293 3767 396 28 948 4688 500197145 500200892 0.000000e+00 4471.0
5 TraesCS5A01G520000 chr4D 97.892 664 13 1 4880 5543 500304638 500305300 0.000000e+00 1147.0
6 TraesCS5A01G520000 chr4D 80.588 680 88 19 4886 5543 500200892 500201549 8.350000e-133 484.0
7 TraesCS5A01G520000 chr4D 82.051 546 59 19 5008 5543 500155372 500155888 3.970000e-116 429.0
8 TraesCS5A01G520000 chr4B 93.494 4719 276 20 1 4694 643628095 643632807 0.000000e+00 6985.0
9 TraesCS5A01G520000 chr4B 88.045 3806 422 19 900 4688 643528092 643531881 0.000000e+00 4477.0
10 TraesCS5A01G520000 chr4B 88.328 3727 396 22 948 4650 643481805 643485516 0.000000e+00 4436.0
11 TraesCS5A01G520000 chr4B 90.628 2785 247 9 66 2843 643534561 643537338 0.000000e+00 3685.0
12 TraesCS5A01G520000 chr4B 96.687 664 20 2 4880 5543 643632798 643633459 0.000000e+00 1103.0
13 TraesCS5A01G520000 chr4B 79.508 610 90 15 4886 5490 643531881 643532460 8.650000e-108 401.0
14 TraesCS5A01G520000 chrUn 88.470 3764 406 16 900 4650 60417303 60413555 0.000000e+00 4521.0
15 TraesCS5A01G520000 chrUn 88.198 3745 416 14 900 4631 16761275 16757544 0.000000e+00 4444.0
16 TraesCS5A01G520000 chrUn 89.566 2722 256 21 1986 4688 60473866 60471154 0.000000e+00 3428.0
17 TraesCS5A01G520000 chrUn 80.299 670 88 23 4886 5542 60413515 60412877 3.020000e-127 466.0
18 TraesCS5A01G520000 chrUn 79.463 633 85 22 4932 5543 60471115 60470507 1.860000e-109 407.0
19 TraesCS5A01G520000 chrUn 85.185 135 16 2 368 499 277589979 277589846 9.690000e-28 135.0
20 TraesCS5A01G520000 chrUn 100.000 44 0 0 76 119 277590257 277590214 1.280000e-11 82.4
21 TraesCS5A01G520000 chr7A 92.718 206 12 2 4678 4883 610942742 610942944 1.510000e-75 294.0
22 TraesCS5A01G520000 chr7D 93.750 192 11 1 4694 4884 552968244 552968435 2.530000e-73 287.0
23 TraesCS5A01G520000 chr1A 91.919 198 14 2 4686 4882 398057996 398057800 5.470000e-70 276.0
24 TraesCS5A01G520000 chr1A 93.085 188 11 2 4692 4879 586291459 586291274 1.970000e-69 274.0
25 TraesCS5A01G520000 chr2D 93.514 185 11 1 4694 4878 620298290 620298107 1.970000e-69 274.0
26 TraesCS5A01G520000 chr2B 92.973 185 12 1 4694 4878 796458726 796458543 9.150000e-68 268.0
27 TraesCS5A01G520000 chr5D 90.955 199 16 2 4690 4888 488352507 488352311 3.290000e-67 267.0
28 TraesCS5A01G520000 chr3A 90.099 202 15 4 4683 4882 157724170 157724368 1.980000e-64 257.0
29 TraesCS5A01G520000 chr2A 87.773 229 13 11 4672 4896 3113657 3113440 2.560000e-63 254.0


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 TraesCS5A01G520000 chr5A 680980188 680985730 5542 False 10237.000000 10237 100.000000 1 5543 1 chr5A.!!$F3 5542
1 TraesCS5A01G520000 chr5A 680921191 680924822 3631 False 4337.000000 4337 88.261000 900 4532 1 chr5A.!!$F2 3632
2 TraesCS5A01G520000 chr5A 680869208 680869792 584 False 440.000000 440 80.707000 4887 5498 1 chr5A.!!$F1 611
3 TraesCS5A01G520000 chr4D 500300015 500305300 5285 False 4409.500000 7672 97.231000 66 5543 2 chr4D.!!$F3 5477
4 TraesCS5A01G520000 chr4D 500197145 500201549 4404 False 2477.500000 4471 84.440500 948 5543 2 chr4D.!!$F2 4595
5 TraesCS5A01G520000 chr4D 500155372 500155888 516 False 429.000000 429 82.051000 5008 5543 1 chr4D.!!$F1 535
6 TraesCS5A01G520000 chr4B 643481805 643485516 3711 False 4436.000000 4436 88.328000 948 4650 1 chr4B.!!$F1 3702
7 TraesCS5A01G520000 chr4B 643628095 643633459 5364 False 4044.000000 6985 95.090500 1 5543 2 chr4B.!!$F3 5542
8 TraesCS5A01G520000 chr4B 643528092 643537338 9246 False 2854.333333 4477 86.060333 66 5490 3 chr4B.!!$F2 5424
9 TraesCS5A01G520000 chrUn 16757544 16761275 3731 True 4444.000000 4444 88.198000 900 4631 1 chrUn.!!$R1 3731
10 TraesCS5A01G520000 chrUn 60412877 60417303 4426 True 2493.500000 4521 84.384500 900 5542 2 chrUn.!!$R2 4642
11 TraesCS5A01G520000 chrUn 60470507 60473866 3359 True 1917.500000 3428 84.514500 1986 5543 2 chrUn.!!$R3 3557

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
489 505 0.465460 AACAACCGCTTCCAGCTGAA 60.465 50.0 17.39 6.85 39.60 3.02 F
2172 2201 0.866061 CCTTCGACATCGGCTACACG 60.866 60.0 0.73 0.00 40.29 4.49 F
2659 2688 0.174389 TGCGCAAAACAGGCTTTCAA 59.826 45.0 8.16 0.00 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2489 0.234884 GACTGTTCGAAAGGTTGCCG 59.765 55.0 0.00 0.0 0.00 5.69 R
4084 4127 5.765182 ACAACTCCATAAGGAACAAACAGAG 59.235 40.0 0.00 0.0 45.19 3.35 R
4593 4645 5.532406 TGACTCAAACTGGATTCAGAAAAGG 59.468 40.0 8.39 0.0 43.49 3.11 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.037641 GCTTGGGCTCTTTGGAATGTTT 59.962 45.455 0.00 0.00 35.22 2.83
26 27 3.656559 CTTGGGCTCTTTGGAATGTTTG 58.343 45.455 0.00 0.00 0.00 2.93
43 44 8.275632 GGAATGTTTGAAACAAAGCTTTGATAC 58.724 33.333 38.78 27.35 45.86 2.24
123 127 2.831526 GGTATCCCCAGCAAAACATGTT 59.168 45.455 4.92 4.92 0.00 2.71
231 235 2.897969 AGTCAACGGTCTACAAGGATGT 59.102 45.455 0.00 0.00 43.74 3.06
232 236 3.056749 AGTCAACGGTCTACAAGGATGTC 60.057 47.826 0.00 0.00 41.05 3.06
236 240 0.527817 GGTCTACAAGGATGTCGCGG 60.528 60.000 6.13 0.00 41.05 6.46
262 266 2.978824 CAATCGTCAGGACCCCGT 59.021 61.111 0.00 0.00 0.00 5.28
391 407 5.458015 TCATCCAATGCGTCTTATACTACG 58.542 41.667 2.41 2.41 41.92 3.51
489 505 0.465460 AACAACCGCTTCCAGCTGAA 60.465 50.000 17.39 6.85 39.60 3.02
553 569 1.843206 TCATATGCACCTGCCCTGTTA 59.157 47.619 0.00 0.00 41.18 2.41
560 576 1.472480 CACCTGCCCTGTTAATTTCCG 59.528 52.381 0.00 0.00 0.00 4.30
623 639 0.875728 CCAGAGATAGTACGCTCCGG 59.124 60.000 0.00 0.00 0.00 5.14
632 648 3.001902 TACGCTCCGGGTTGCAGAG 62.002 63.158 0.00 0.00 0.00 3.35
648 664 1.950828 AGAGATCATCTGCTTTGGCG 58.049 50.000 0.00 0.00 42.25 5.69
673 689 1.061735 AGGACCCCAACCAAACCATTT 60.062 47.619 0.00 0.00 0.00 2.32
682 698 4.690280 CCAACCAAACCATTTGTTCTATGC 59.310 41.667 0.97 0.00 38.98 3.14
716 732 3.829948 CTCATGACTTGCAACAATGACC 58.170 45.455 0.00 0.00 0.00 4.02
738 754 4.386711 CTGCAGATATCATTGCTGGAAGA 58.613 43.478 8.42 0.00 40.87 2.87
757 773 3.554934 AGACTGGAACAATGACTTGCAA 58.445 40.909 0.00 0.00 38.70 4.08
762 778 6.624423 ACTGGAACAATGACTTGCAAATATC 58.376 36.000 0.00 0.00 38.70 1.63
792 808 4.670765 AGTTTCAGGCAGATTTTCCAGAT 58.329 39.130 0.00 0.00 0.00 2.90
873 890 3.725459 CACAGTCGCATTGCCGCA 61.725 61.111 2.41 0.00 0.00 5.69
894 911 6.190264 CGCACATTATGATATCATAGCTTGC 58.810 40.000 26.21 26.21 39.69 4.01
906 923 4.333417 GCTTGCTGCTCCAATCCT 57.667 55.556 0.00 0.00 38.95 3.24
1011 1040 5.450550 CGATAGCTGAGTAATGGTGTCTTCA 60.451 44.000 0.00 0.00 0.00 3.02
1012 1041 4.623932 AGCTGAGTAATGGTGTCTTCAA 57.376 40.909 0.00 0.00 0.00 2.69
1020 1049 2.435372 TGGTGTCTTCAAGTGCCTTT 57.565 45.000 0.00 0.00 0.00 3.11
1037 1066 3.496331 CCTTTTTGTTTCCAGGCCTCTA 58.504 45.455 0.00 0.00 0.00 2.43
1041 1070 1.568504 TGTTTCCAGGCCTCTATCGT 58.431 50.000 0.00 0.00 0.00 3.73
1234 1263 2.359107 CCTGCAGCGTGACACCAT 60.359 61.111 8.66 0.00 0.00 3.55
1335 1364 2.350514 GCAAGGCTCCAGCTGTCT 59.649 61.111 13.81 1.67 41.70 3.41
1606 1635 1.821061 CGGAGACCTTCCTGCACTGT 61.821 60.000 0.00 0.00 44.41 3.55
1659 1688 1.084289 GCACCATACCACCGTCTTTC 58.916 55.000 0.00 0.00 0.00 2.62
1842 1871 3.305720 TGGTACCATTAGCCTCGAAGAT 58.694 45.455 11.60 0.00 33.89 2.40
2172 2201 0.866061 CCTTCGACATCGGCTACACG 60.866 60.000 0.73 0.00 40.29 4.49
2203 2232 7.255660 CCAATATCCAGAACCTACTACTCTCAC 60.256 44.444 0.00 0.00 0.00 3.51
2235 2264 0.920763 ATGGACCAATCCCAGCCTCA 60.921 55.000 0.00 0.00 45.59 3.86
2401 2430 5.918011 GTCTCTTCACTATCTAATTGCTCCG 59.082 44.000 0.00 0.00 0.00 4.63
2460 2489 5.921962 AAGGGAAATTGCCAAGTTCTATC 57.078 39.130 16.17 7.55 35.90 2.08
2659 2688 0.174389 TGCGCAAAACAGGCTTTCAA 59.826 45.000 8.16 0.00 0.00 2.69
3326 3364 4.097286 GCTACTGCTTCTAGTTCTACTGCT 59.903 45.833 0.00 0.00 36.03 4.24
3360 3398 4.158394 GCCACTGCAATCCTTTTCTCATTA 59.842 41.667 0.00 0.00 37.47 1.90
3417 3455 3.118186 CCAATCCCCATTTGCAACATGAT 60.118 43.478 17.70 6.71 0.00 2.45
4084 4127 4.907879 AGCTTATTTGCAAGATACTGGC 57.092 40.909 0.00 5.98 34.99 4.85
4673 4735 3.925913 GCTTTGCACAGTTTTGTTTCTGA 59.074 39.130 1.15 0.00 34.62 3.27
4707 4769 8.977505 TGTTTTTCATATCAGTTTTGCTAAAGC 58.022 29.630 0.00 0.00 42.50 3.51
4733 4795 8.498054 ACATATAGATGTGCCATAAGTATTGC 57.502 34.615 1.31 0.00 44.90 3.56
4734 4796 8.102676 ACATATAGATGTGCCATAAGTATTGCA 58.897 33.333 1.31 0.00 44.90 4.08
4742 4804 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
4743 4805 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
4744 4806 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
4745 4807 6.073003 GCCATAAGTATTGCACATCTAAGTCC 60.073 42.308 0.00 0.00 0.00 3.85
4746 4808 7.220030 CCATAAGTATTGCACATCTAAGTCCT 58.780 38.462 0.00 0.00 0.00 3.85
4747 4809 8.367911 CCATAAGTATTGCACATCTAAGTCCTA 58.632 37.037 0.00 0.00 0.00 2.94
4748 4810 9.935241 CATAAGTATTGCACATCTAAGTCCTAT 57.065 33.333 0.00 0.00 0.00 2.57
4749 4811 9.935241 ATAAGTATTGCACATCTAAGTCCTATG 57.065 33.333 0.00 0.00 0.00 2.23
4750 4812 7.366847 AGTATTGCACATCTAAGTCCTATGT 57.633 36.000 0.00 0.00 34.22 2.29
4751 4813 7.437748 AGTATTGCACATCTAAGTCCTATGTC 58.562 38.462 0.00 0.00 31.60 3.06
4752 4814 5.675684 TTGCACATCTAAGTCCTATGTCA 57.324 39.130 0.00 0.00 31.60 3.58
4753 4815 5.876651 TGCACATCTAAGTCCTATGTCAT 57.123 39.130 0.00 0.00 31.60 3.06
4754 4816 6.239217 TGCACATCTAAGTCCTATGTCATT 57.761 37.500 0.00 0.00 31.60 2.57
4755 4817 6.051074 TGCACATCTAAGTCCTATGTCATTG 58.949 40.000 0.00 0.00 31.60 2.82
4756 4818 6.127083 TGCACATCTAAGTCCTATGTCATTGA 60.127 38.462 0.00 0.00 31.60 2.57
4757 4819 6.933521 GCACATCTAAGTCCTATGTCATTGAT 59.066 38.462 0.00 0.00 31.60 2.57
4758 4820 7.117523 GCACATCTAAGTCCTATGTCATTGATC 59.882 40.741 0.00 0.00 31.60 2.92
4759 4821 8.366401 CACATCTAAGTCCTATGTCATTGATCT 58.634 37.037 0.00 0.00 31.60 2.75
4760 4822 8.932610 ACATCTAAGTCCTATGTCATTGATCTT 58.067 33.333 0.00 0.82 0.00 2.40
4765 4827 8.899427 AAGTCCTATGTCATTGATCTTATGTG 57.101 34.615 0.00 0.00 0.00 3.21
4766 4828 7.448420 AGTCCTATGTCATTGATCTTATGTGG 58.552 38.462 0.00 0.00 0.00 4.17
4767 4829 7.290948 AGTCCTATGTCATTGATCTTATGTGGA 59.709 37.037 0.00 0.00 0.00 4.02
4768 4830 7.601886 GTCCTATGTCATTGATCTTATGTGGAG 59.398 40.741 0.00 0.00 0.00 3.86
4769 4831 7.510343 TCCTATGTCATTGATCTTATGTGGAGA 59.490 37.037 0.00 0.00 0.00 3.71
4770 4832 8.319881 CCTATGTCATTGATCTTATGTGGAGAT 58.680 37.037 0.00 0.00 36.60 2.75
4771 4833 9.722184 CTATGTCATTGATCTTATGTGGAGATT 57.278 33.333 0.00 0.00 34.13 2.40
4772 4834 8.618702 ATGTCATTGATCTTATGTGGAGATTC 57.381 34.615 0.00 0.00 34.13 2.52
4773 4835 6.703165 TGTCATTGATCTTATGTGGAGATTCG 59.297 38.462 0.00 0.00 34.13 3.34
4774 4836 6.703607 GTCATTGATCTTATGTGGAGATTCGT 59.296 38.462 0.00 0.00 34.13 3.85
4775 4837 6.703165 TCATTGATCTTATGTGGAGATTCGTG 59.297 38.462 0.00 0.00 34.13 4.35
4776 4838 5.598416 TGATCTTATGTGGAGATTCGTGT 57.402 39.130 0.00 0.00 34.13 4.49
4777 4839 5.351458 TGATCTTATGTGGAGATTCGTGTG 58.649 41.667 0.00 0.00 34.13 3.82
4778 4840 4.123497 TCTTATGTGGAGATTCGTGTGG 57.877 45.455 0.00 0.00 0.00 4.17
4779 4841 3.767131 TCTTATGTGGAGATTCGTGTGGA 59.233 43.478 0.00 0.00 0.00 4.02
4780 4842 4.221924 TCTTATGTGGAGATTCGTGTGGAA 59.778 41.667 0.00 0.00 39.42 3.53
4781 4843 2.920724 TGTGGAGATTCGTGTGGAAA 57.079 45.000 0.00 0.00 38.36 3.13
4782 4844 3.417069 TGTGGAGATTCGTGTGGAAAT 57.583 42.857 0.00 0.00 38.36 2.17
4783 4845 3.750371 TGTGGAGATTCGTGTGGAAATT 58.250 40.909 0.00 0.00 38.36 1.82
4784 4846 4.141287 TGTGGAGATTCGTGTGGAAATTT 58.859 39.130 0.00 0.00 38.36 1.82
4785 4847 4.582656 TGTGGAGATTCGTGTGGAAATTTT 59.417 37.500 0.00 0.00 38.36 1.82
4786 4848 5.154222 GTGGAGATTCGTGTGGAAATTTTC 58.846 41.667 0.24 0.24 38.36 2.29
4787 4849 5.048713 GTGGAGATTCGTGTGGAAATTTTCT 60.049 40.000 8.93 0.00 38.36 2.52
4788 4850 5.534654 TGGAGATTCGTGTGGAAATTTTCTT 59.465 36.000 8.93 0.00 38.36 2.52
4789 4851 6.040391 TGGAGATTCGTGTGGAAATTTTCTTT 59.960 34.615 8.93 0.00 38.36 2.52
4790 4852 6.923508 GGAGATTCGTGTGGAAATTTTCTTTT 59.076 34.615 8.93 0.00 38.36 2.27
4791 4853 7.096065 GGAGATTCGTGTGGAAATTTTCTTTTG 60.096 37.037 8.93 0.00 38.36 2.44
4792 4854 6.701400 AGATTCGTGTGGAAATTTTCTTTTGG 59.299 34.615 8.93 0.00 38.36 3.28
4793 4855 4.688021 TCGTGTGGAAATTTTCTTTTGGG 58.312 39.130 8.93 0.00 0.00 4.12
4794 4856 4.160626 TCGTGTGGAAATTTTCTTTTGGGT 59.839 37.500 8.93 0.00 0.00 4.51
4795 4857 4.873259 CGTGTGGAAATTTTCTTTTGGGTT 59.127 37.500 8.93 0.00 0.00 4.11
4796 4858 5.352846 CGTGTGGAAATTTTCTTTTGGGTTT 59.647 36.000 8.93 0.00 0.00 3.27
4797 4859 6.128145 CGTGTGGAAATTTTCTTTTGGGTTTT 60.128 34.615 8.93 0.00 0.00 2.43
4798 4860 7.574030 CGTGTGGAAATTTTCTTTTGGGTTTTT 60.574 33.333 8.93 0.00 0.00 1.94
4822 4884 9.981114 TTTTCTTTTCCTTTCCATACTTGATTC 57.019 29.630 0.00 0.00 0.00 2.52
4823 4885 8.940397 TTCTTTTCCTTTCCATACTTGATTCT 57.060 30.769 0.00 0.00 0.00 2.40
4824 4886 8.340618 TCTTTTCCTTTCCATACTTGATTCTG 57.659 34.615 0.00 0.00 0.00 3.02
4825 4887 7.944554 TCTTTTCCTTTCCATACTTGATTCTGT 59.055 33.333 0.00 0.00 0.00 3.41
4826 4888 7.687941 TTTCCTTTCCATACTTGATTCTGTC 57.312 36.000 0.00 0.00 0.00 3.51
4827 4889 6.373005 TCCTTTCCATACTTGATTCTGTCA 57.627 37.500 0.00 0.00 34.25 3.58
4828 4890 6.173339 TCCTTTCCATACTTGATTCTGTCAC 58.827 40.000 0.00 0.00 36.32 3.67
4829 4891 6.013379 TCCTTTCCATACTTGATTCTGTCACT 60.013 38.462 0.00 0.00 36.32 3.41
4830 4892 6.656693 CCTTTCCATACTTGATTCTGTCACTT 59.343 38.462 0.00 0.00 36.32 3.16
4831 4893 7.824289 CCTTTCCATACTTGATTCTGTCACTTA 59.176 37.037 0.00 0.00 36.32 2.24
4832 4894 8.777865 TTTCCATACTTGATTCTGTCACTTAG 57.222 34.615 0.00 0.00 36.32 2.18
4833 4895 7.718334 TCCATACTTGATTCTGTCACTTAGA 57.282 36.000 0.00 0.00 36.32 2.10
4834 4896 8.311395 TCCATACTTGATTCTGTCACTTAGAT 57.689 34.615 0.00 0.00 36.32 1.98
4835 4897 8.200120 TCCATACTTGATTCTGTCACTTAGATG 58.800 37.037 0.00 0.00 36.32 2.90
4836 4898 7.984050 CCATACTTGATTCTGTCACTTAGATGT 59.016 37.037 0.00 0.00 36.32 3.06
4837 4899 8.815189 CATACTTGATTCTGTCACTTAGATGTG 58.185 37.037 0.00 0.00 36.32 3.21
4838 4900 5.641209 ACTTGATTCTGTCACTTAGATGTGC 59.359 40.000 0.00 0.00 36.32 4.57
4839 4901 5.151297 TGATTCTGTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
4840 4902 5.550290 TGATTCTGTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
4841 4903 6.175471 TGATTCTGTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
4842 4904 7.330262 TGATTCTGTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
4843 4905 7.823799 TGATTCTGTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
4844 4906 6.968131 TCTGTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
4845 4907 6.701340 TCTGTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
4846 4908 7.836842 TCTGTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
4847 4909 8.478066 TCTGTCACTTAGATGTGCAATAACTAT 58.522 33.333 0.00 0.00 37.81 2.12
4848 4910 9.750125 CTGTCACTTAGATGTGCAATAACTATA 57.250 33.333 0.00 0.00 37.81 1.31
4849 4911 9.750125 TGTCACTTAGATGTGCAATAACTATAG 57.250 33.333 0.00 0.00 37.81 1.31
4850 4912 8.704234 GTCACTTAGATGTGCAATAACTATAGC 58.296 37.037 0.00 0.00 37.81 2.97
4851 4913 8.421002 TCACTTAGATGTGCAATAACTATAGCA 58.579 33.333 0.00 0.00 37.81 3.49
4861 4923 8.992835 TGCAATAACTATAGCACATCTAGATG 57.007 34.615 27.63 27.63 44.15 2.90
4873 4935 4.944619 CATCTAGATGTGCCCTAGACAA 57.055 45.455 22.42 0.00 43.57 3.18
4874 4936 5.282055 CATCTAGATGTGCCCTAGACAAA 57.718 43.478 22.42 0.00 43.57 2.83
4875 4937 4.737855 TCTAGATGTGCCCTAGACAAAC 57.262 45.455 0.00 0.00 38.08 2.93
4876 4938 2.789409 AGATGTGCCCTAGACAAACC 57.211 50.000 0.00 0.00 0.00 3.27
4877 4939 1.282157 AGATGTGCCCTAGACAAACCC 59.718 52.381 0.00 0.00 0.00 4.11
4878 4940 0.331616 ATGTGCCCTAGACAAACCCC 59.668 55.000 0.00 0.00 0.00 4.95
5029 5098 6.203723 ACAAGCAAGTTTCACTCAAGTAGATC 59.796 38.462 0.00 0.00 0.00 2.75
5059 5132 9.897744 CAACAAGAGCTCAAAAATAAATCAGTA 57.102 29.630 17.77 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.660887 TCAAAGCTTTGTTTCAAACATTCC 57.339 33.333 32.46 0.00 41.79 3.01
25 26 6.826893 GCTTTGTATCAAAGCTTTGTTTCA 57.173 33.333 32.46 25.58 46.64 2.69
60 61 4.574599 AGTTTTTCTGTCAGTTGGATGC 57.425 40.909 0.00 0.00 0.00 3.91
165 169 9.515020 GATTCAGACTGAGAAAGTAACAGATAG 57.485 37.037 5.10 0.00 40.07 2.08
231 235 1.771073 CGATTGCTAAATGGCCGCGA 61.771 55.000 8.23 0.00 0.00 5.87
232 236 1.369209 CGATTGCTAAATGGCCGCG 60.369 57.895 0.00 0.00 0.00 6.46
236 240 2.032178 GTCCTGACGATTGCTAAATGGC 59.968 50.000 0.00 0.00 0.00 4.40
262 266 4.584743 TCTGCAGAGTCAACTAGAGAAACA 59.415 41.667 13.74 0.00 0.00 2.83
341 357 9.822727 TGGTATATCTCAAGGTACTAATCATCA 57.177 33.333 0.00 0.00 38.49 3.07
366 382 6.033937 CGTAGTATAAGACGCATTGGATGATG 59.966 42.308 0.00 0.00 31.49 3.07
391 407 5.146010 TGCTGTTGGATTATTTGGGAAAC 57.854 39.130 0.00 0.00 0.00 2.78
489 505 2.270205 CTGCTGGCGACCCTTGAT 59.730 61.111 0.00 0.00 0.00 2.57
515 531 3.822594 TGAGCGCGTGATTAATTTGTT 57.177 38.095 8.43 0.00 0.00 2.83
516 532 5.443261 CATATGAGCGCGTGATTAATTTGT 58.557 37.500 8.43 0.00 0.00 2.83
553 569 5.395642 CAGTTTAACGGTAATGCGGAAATT 58.604 37.500 0.00 0.00 0.00 1.82
560 576 6.093082 ACATACTTCCAGTTTAACGGTAATGC 59.907 38.462 0.00 0.00 0.00 3.56
632 648 0.464373 TCCCGCCAAAGCAGATGATC 60.464 55.000 0.00 0.00 39.83 2.92
648 664 2.014033 TTTGGTTGGGGTCCTGTCCC 62.014 60.000 0.00 0.00 46.31 4.46
673 689 1.289160 AGCTTCCAGGGCATAGAACA 58.711 50.000 0.00 0.00 0.00 3.18
682 698 1.126488 TCATGAGCTAGCTTCCAGGG 58.874 55.000 20.42 9.69 0.00 4.45
716 732 4.213694 GTCTTCCAGCAATGATATCTGCAG 59.786 45.833 16.66 7.63 41.17 4.41
738 754 4.942761 ATTTGCAAGTCATTGTTCCAGT 57.057 36.364 0.00 0.00 38.76 4.00
757 773 8.985315 TCTGCCTGAAACTCAATAATGATATT 57.015 30.769 0.00 0.00 34.37 1.28
762 778 7.490402 GGAAAATCTGCCTGAAACTCAATAATG 59.510 37.037 0.00 0.00 0.00 1.90
859 876 1.024046 TAATGTGCGGCAATGCGACT 61.024 50.000 3.23 0.00 37.81 4.18
873 890 7.317842 GCAGCAAGCTATGATATCATAATGT 57.682 36.000 22.62 10.08 38.26 2.71
894 911 8.207545 ACTTTAAATAGTAGAGGATTGGAGCAG 58.792 37.037 0.00 0.00 0.00 4.24
906 923 7.897565 AGTACCTCACCCACTTTAAATAGTAGA 59.102 37.037 0.00 0.00 0.00 2.59
1012 1041 1.138859 GCCTGGAAACAAAAAGGCACT 59.861 47.619 7.65 0.00 44.88 4.40
1020 1049 2.304761 ACGATAGAGGCCTGGAAACAAA 59.695 45.455 12.00 0.00 39.45 2.83
1037 1066 3.971245 AGAAGAGGCAGAGAAAACGAT 57.029 42.857 0.00 0.00 0.00 3.73
1041 1070 3.146104 CCCAAGAAGAGGCAGAGAAAA 57.854 47.619 0.00 0.00 0.00 2.29
1335 1364 2.571212 CCACCACTGAAGCTGTTGTTA 58.429 47.619 0.00 0.00 0.00 2.41
1581 1610 4.187056 GGAAGGTCTCCGAAAGCG 57.813 61.111 0.00 0.00 33.37 4.68
1606 1635 3.603158 TTTGGCGAGAACTAGTATGCA 57.397 42.857 0.00 0.00 0.00 3.96
1659 1688 0.457443 TGAGATGACAGCTACTGCCG 59.543 55.000 0.00 0.00 40.80 5.69
1870 1899 6.831664 AATAGGGGAAGATGTGACAGTAAT 57.168 37.500 0.00 0.00 0.00 1.89
2172 2201 1.777272 AGGTTCTGGATATTGGGGAGC 59.223 52.381 0.00 0.00 0.00 4.70
2203 2232 7.832503 GGATTGGTCCATCAAAACTATTTTG 57.167 36.000 7.56 7.56 45.66 2.44
2235 2264 4.560919 CGTAGGTGGTAAGCTTTGAGAAGT 60.561 45.833 3.20 0.00 35.29 3.01
2460 2489 0.234884 GACTGTTCGAAAGGTTGCCG 59.765 55.000 0.00 0.00 0.00 5.69
2659 2688 7.187824 TGCTAAAAGTATCTGGAATCTGACT 57.812 36.000 0.00 0.00 0.00 3.41
2680 2709 2.590821 ACTCAGCTGGACAAAATTGCT 58.409 42.857 15.13 0.00 0.00 3.91
2769 2798 1.230324 GAGCAAGGTTGAGTGTGGTC 58.770 55.000 0.00 0.00 0.00 4.02
3310 3339 7.371936 ACAACAGTTAGCAGTAGAACTAGAAG 58.628 38.462 0.00 0.00 34.13 2.85
3360 3398 6.998968 TTCCTCAAACAAATTGTTGCAATT 57.001 29.167 12.50 1.68 40.14 2.32
4084 4127 5.765182 ACAACTCCATAAGGAACAAACAGAG 59.235 40.000 0.00 0.00 45.19 3.35
4593 4645 5.532406 TGACTCAAACTGGATTCAGAAAAGG 59.468 40.000 8.39 0.00 43.49 3.11
4594 4646 6.624352 TGACTCAAACTGGATTCAGAAAAG 57.376 37.500 8.39 2.21 43.49 2.27
4719 4781 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
4720 4782 6.073003 GGACTTAGATGTGCAATACTTATGGC 60.073 42.308 0.00 0.00 33.16 4.40
4721 4783 7.220030 AGGACTTAGATGTGCAATACTTATGG 58.780 38.462 0.00 0.00 0.00 2.74
4722 4784 9.935241 ATAGGACTTAGATGTGCAATACTTATG 57.065 33.333 0.00 0.00 0.00 1.90
4723 4785 9.935241 CATAGGACTTAGATGTGCAATACTTAT 57.065 33.333 0.00 0.00 0.00 1.73
4724 4786 8.924303 ACATAGGACTTAGATGTGCAATACTTA 58.076 33.333 0.00 0.00 32.62 2.24
4725 4787 7.796054 ACATAGGACTTAGATGTGCAATACTT 58.204 34.615 0.00 0.00 32.62 2.24
4726 4788 7.069950 TGACATAGGACTTAGATGTGCAATACT 59.930 37.037 0.00 0.00 33.99 2.12
4727 4789 7.210174 TGACATAGGACTTAGATGTGCAATAC 58.790 38.462 0.00 0.00 33.99 1.89
4728 4790 7.360113 TGACATAGGACTTAGATGTGCAATA 57.640 36.000 0.00 0.00 33.99 1.90
4729 4791 6.239217 TGACATAGGACTTAGATGTGCAAT 57.761 37.500 0.00 0.00 33.99 3.56
4730 4792 5.675684 TGACATAGGACTTAGATGTGCAA 57.324 39.130 0.00 0.00 33.99 4.08
4731 4793 5.876651 ATGACATAGGACTTAGATGTGCA 57.123 39.130 0.00 0.00 33.99 4.57
4732 4794 6.283694 TCAATGACATAGGACTTAGATGTGC 58.716 40.000 0.00 0.00 33.99 4.57
4733 4795 8.366401 AGATCAATGACATAGGACTTAGATGTG 58.634 37.037 0.00 0.00 33.99 3.21
4734 4796 8.489676 AGATCAATGACATAGGACTTAGATGT 57.510 34.615 0.00 0.00 36.52 3.06
4739 4801 9.987272 CACATAAGATCAATGACATAGGACTTA 57.013 33.333 13.33 0.00 0.00 2.24
4740 4802 7.935755 CCACATAAGATCAATGACATAGGACTT 59.064 37.037 13.33 0.00 0.00 3.01
4741 4803 7.290948 TCCACATAAGATCAATGACATAGGACT 59.709 37.037 13.33 0.00 0.00 3.85
4742 4804 7.445121 TCCACATAAGATCAATGACATAGGAC 58.555 38.462 13.33 0.00 0.00 3.85
4743 4805 7.510343 TCTCCACATAAGATCAATGACATAGGA 59.490 37.037 13.33 10.56 0.00 2.94
4744 4806 7.674120 TCTCCACATAAGATCAATGACATAGG 58.326 38.462 13.33 7.85 0.00 2.57
4745 4807 9.722184 AATCTCCACATAAGATCAATGACATAG 57.278 33.333 13.33 6.61 32.29 2.23
4746 4808 9.716531 GAATCTCCACATAAGATCAATGACATA 57.283 33.333 13.33 0.00 32.29 2.29
4747 4809 7.387122 CGAATCTCCACATAAGATCAATGACAT 59.613 37.037 13.33 0.00 32.29 3.06
4748 4810 6.703165 CGAATCTCCACATAAGATCAATGACA 59.297 38.462 13.33 0.00 32.29 3.58
4749 4811 6.703607 ACGAATCTCCACATAAGATCAATGAC 59.296 38.462 13.33 0.00 32.29 3.06
4750 4812 6.703165 CACGAATCTCCACATAAGATCAATGA 59.297 38.462 13.33 0.00 32.29 2.57
4751 4813 6.481313 ACACGAATCTCCACATAAGATCAATG 59.519 38.462 0.00 0.75 32.29 2.82
4752 4814 6.481313 CACACGAATCTCCACATAAGATCAAT 59.519 38.462 0.00 0.00 32.29 2.57
4753 4815 5.812127 CACACGAATCTCCACATAAGATCAA 59.188 40.000 0.00 0.00 32.29 2.57
4754 4816 5.351458 CACACGAATCTCCACATAAGATCA 58.649 41.667 0.00 0.00 32.29 2.92
4755 4817 4.747108 CCACACGAATCTCCACATAAGATC 59.253 45.833 0.00 0.00 32.29 2.75
4756 4818 4.405680 TCCACACGAATCTCCACATAAGAT 59.594 41.667 0.00 0.00 34.96 2.40
4757 4819 3.767131 TCCACACGAATCTCCACATAAGA 59.233 43.478 0.00 0.00 0.00 2.10
4758 4820 4.123497 TCCACACGAATCTCCACATAAG 57.877 45.455 0.00 0.00 0.00 1.73
4759 4821 4.545208 TTCCACACGAATCTCCACATAA 57.455 40.909 0.00 0.00 0.00 1.90
4760 4822 4.545208 TTTCCACACGAATCTCCACATA 57.455 40.909 0.00 0.00 0.00 2.29
4761 4823 3.417069 TTTCCACACGAATCTCCACAT 57.583 42.857 0.00 0.00 0.00 3.21
4762 4824 2.920724 TTTCCACACGAATCTCCACA 57.079 45.000 0.00 0.00 0.00 4.17
4763 4825 4.766404 AAATTTCCACACGAATCTCCAC 57.234 40.909 0.00 0.00 0.00 4.02
4764 4826 5.070001 AGAAAATTTCCACACGAATCTCCA 58.930 37.500 1.57 0.00 0.00 3.86
4765 4827 5.629079 AGAAAATTTCCACACGAATCTCC 57.371 39.130 1.57 0.00 0.00 3.71
4766 4828 7.096065 CCAAAAGAAAATTTCCACACGAATCTC 60.096 37.037 1.57 0.00 0.00 2.75
4767 4829 6.701400 CCAAAAGAAAATTTCCACACGAATCT 59.299 34.615 1.57 0.00 0.00 2.40
4768 4830 6.073819 CCCAAAAGAAAATTTCCACACGAATC 60.074 38.462 1.57 0.00 0.00 2.52
4769 4831 5.757808 CCCAAAAGAAAATTTCCACACGAAT 59.242 36.000 1.57 0.00 0.00 3.34
4770 4832 5.112686 CCCAAAAGAAAATTTCCACACGAA 58.887 37.500 1.57 0.00 0.00 3.85
4771 4833 4.160626 ACCCAAAAGAAAATTTCCACACGA 59.839 37.500 1.57 0.00 0.00 4.35
4772 4834 4.438148 ACCCAAAAGAAAATTTCCACACG 58.562 39.130 1.57 0.00 0.00 4.49
4773 4835 6.751514 AAACCCAAAAGAAAATTTCCACAC 57.248 33.333 1.57 0.00 0.00 3.82
4774 4836 7.767250 AAAAACCCAAAAGAAAATTTCCACA 57.233 28.000 1.57 0.00 0.00 4.17
4796 4858 9.981114 GAATCAAGTATGGAAAGGAAAAGAAAA 57.019 29.630 0.00 0.00 0.00 2.29
4797 4859 9.367160 AGAATCAAGTATGGAAAGGAAAAGAAA 57.633 29.630 0.00 0.00 0.00 2.52
4798 4860 8.796475 CAGAATCAAGTATGGAAAGGAAAAGAA 58.204 33.333 0.00 0.00 0.00 2.52
4799 4861 7.944554 ACAGAATCAAGTATGGAAAGGAAAAGA 59.055 33.333 0.00 0.00 0.00 2.52
4800 4862 8.115490 ACAGAATCAAGTATGGAAAGGAAAAG 57.885 34.615 0.00 0.00 0.00 2.27
4801 4863 7.723616 TGACAGAATCAAGTATGGAAAGGAAAA 59.276 33.333 0.00 0.00 33.02 2.29
4802 4864 7.174946 GTGACAGAATCAAGTATGGAAAGGAAA 59.825 37.037 0.00 0.00 39.72 3.13
4803 4865 6.655003 GTGACAGAATCAAGTATGGAAAGGAA 59.345 38.462 0.00 0.00 39.72 3.36
4804 4866 6.013379 AGTGACAGAATCAAGTATGGAAAGGA 60.013 38.462 0.00 0.00 39.72 3.36
4805 4867 6.176183 AGTGACAGAATCAAGTATGGAAAGG 58.824 40.000 0.00 0.00 39.72 3.11
4806 4868 7.678947 AAGTGACAGAATCAAGTATGGAAAG 57.321 36.000 0.00 0.00 39.72 2.62
4807 4869 8.593679 TCTAAGTGACAGAATCAAGTATGGAAA 58.406 33.333 0.00 0.00 39.72 3.13
4808 4870 8.134202 TCTAAGTGACAGAATCAAGTATGGAA 57.866 34.615 0.00 0.00 39.72 3.53
4809 4871 7.718334 TCTAAGTGACAGAATCAAGTATGGA 57.282 36.000 0.00 0.00 39.72 3.41
4810 4872 7.984050 ACATCTAAGTGACAGAATCAAGTATGG 59.016 37.037 0.00 0.00 39.72 2.74
4811 4873 8.815189 CACATCTAAGTGACAGAATCAAGTATG 58.185 37.037 0.00 0.00 42.05 2.39
4812 4874 7.493971 GCACATCTAAGTGACAGAATCAAGTAT 59.506 37.037 0.00 0.00 42.05 2.12
4813 4875 6.813649 GCACATCTAAGTGACAGAATCAAGTA 59.186 38.462 0.00 0.00 42.05 2.24
4814 4876 5.641209 GCACATCTAAGTGACAGAATCAAGT 59.359 40.000 0.00 0.00 42.05 3.16
4815 4877 5.640783 TGCACATCTAAGTGACAGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
4816 4878 5.550290 TGCACATCTAAGTGACAGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
4817 4879 5.151297 TGCACATCTAAGTGACAGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
4818 4880 6.674694 ATTGCACATCTAAGTGACAGAATC 57.325 37.500 0.00 0.00 42.05 2.52
4819 4881 7.826252 AGTTATTGCACATCTAAGTGACAGAAT 59.174 33.333 0.00 0.00 42.05 2.40
4820 4882 7.161404 AGTTATTGCACATCTAAGTGACAGAA 58.839 34.615 0.00 0.00 42.05 3.02
4821 4883 6.701340 AGTTATTGCACATCTAAGTGACAGA 58.299 36.000 0.00 0.00 42.05 3.41
4822 4884 6.974932 AGTTATTGCACATCTAAGTGACAG 57.025 37.500 0.00 0.00 42.05 3.51
4823 4885 9.750125 CTATAGTTATTGCACATCTAAGTGACA 57.250 33.333 0.00 0.00 42.05 3.58
4824 4886 8.704234 GCTATAGTTATTGCACATCTAAGTGAC 58.296 37.037 0.84 0.00 42.05 3.67
4825 4887 8.421002 TGCTATAGTTATTGCACATCTAAGTGA 58.579 33.333 0.84 0.00 42.05 3.41
4826 4888 8.593492 TGCTATAGTTATTGCACATCTAAGTG 57.407 34.615 0.84 0.00 38.99 3.16
4836 4898 8.992835 CATCTAGATGTGCTATAGTTATTGCA 57.007 34.615 22.42 4.52 40.96 4.08
4852 4914 4.944619 TTGTCTAGGGCACATCTAGATG 57.055 45.455 27.63 27.63 43.25 2.90
4853 4915 4.101741 GGTTTGTCTAGGGCACATCTAGAT 59.898 45.833 0.00 0.00 43.25 1.98
4854 4916 3.451178 GGTTTGTCTAGGGCACATCTAGA 59.549 47.826 0.00 0.00 40.38 2.43
4855 4917 3.432326 GGGTTTGTCTAGGGCACATCTAG 60.432 52.174 0.00 0.00 36.46 2.43
4856 4918 2.504175 GGGTTTGTCTAGGGCACATCTA 59.496 50.000 0.00 0.00 0.00 1.98
4857 4919 1.282157 GGGTTTGTCTAGGGCACATCT 59.718 52.381 0.00 0.00 0.00 2.90
4858 4920 1.682087 GGGGTTTGTCTAGGGCACATC 60.682 57.143 0.00 0.00 0.00 3.06
4859 4921 0.331616 GGGGTTTGTCTAGGGCACAT 59.668 55.000 0.00 0.00 0.00 3.21
4860 4922 0.770557 AGGGGTTTGTCTAGGGCACA 60.771 55.000 0.00 0.00 0.00 4.57
4861 4923 0.404426 AAGGGGTTTGTCTAGGGCAC 59.596 55.000 0.00 0.00 0.00 5.01
4862 4924 1.154430 AAAGGGGTTTGTCTAGGGCA 58.846 50.000 0.00 0.00 0.00 5.36
4863 4925 2.168496 GAAAAGGGGTTTGTCTAGGGC 58.832 52.381 0.00 0.00 0.00 5.19
4864 4926 3.518992 TGAAAAGGGGTTTGTCTAGGG 57.481 47.619 0.00 0.00 0.00 3.53
4865 4927 6.663734 AGATATGAAAAGGGGTTTGTCTAGG 58.336 40.000 0.00 0.00 0.00 3.02
4868 4930 8.778059 TGTATAGATATGAAAAGGGGTTTGTCT 58.222 33.333 0.00 0.00 0.00 3.41
4869 4931 8.974060 TGTATAGATATGAAAAGGGGTTTGTC 57.026 34.615 0.00 0.00 0.00 3.18
4870 4932 9.762381 TTTGTATAGATATGAAAAGGGGTTTGT 57.238 29.630 0.00 0.00 0.00 2.83
4872 4934 9.990868 ACTTTGTATAGATATGAAAAGGGGTTT 57.009 29.630 10.98 0.00 0.00 3.27
4875 4937 9.726438 CCTACTTTGTATAGATATGAAAAGGGG 57.274 37.037 10.98 9.26 0.00 4.79
4948 5010 0.824109 CTCCTGACTCCGCCATGTAA 59.176 55.000 0.00 0.00 0.00 2.41
5029 5098 8.807667 ATTTATTTTTGAGCTCTTGTTGAGTG 57.192 30.769 16.19 0.00 44.41 3.51
5059 5132 5.630121 TCATTGTACAGTCAGGTTTGGAAT 58.370 37.500 0.00 0.00 0.00 3.01
5216 5292 2.833582 GGGAGGATCGTCGAGGCA 60.834 66.667 9.20 0.00 34.37 4.75


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

AutoCloner maintained by Alex Coulton.