Multiple sequence alignment - TraesCS3D01G471400

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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 TraesCS3D01G471400 chr3D 100.000 5187 0 0 1 5187 573769664 573764478 0.000000e+00 9579.0
1 TraesCS3D01G471400 chr3D 89.259 270 27 2 709 977 573815215 573814947 2.310000e-88 337.0
2 TraesCS3D01G471400 chr3A 95.881 4613 148 28 18 4600 708823900 708819300 0.000000e+00 7428.0
3 TraesCS3D01G471400 chr3A 84.615 338 24 10 2309 2645 708653556 708653866 1.400000e-80 311.0
4 TraesCS3D01G471400 chr3A 86.131 137 10 7 3858 3994 6702611 6702738 7.000000e-29 139.0
5 TraesCS3D01G471400 chr3A 85.437 103 10 3 4756 4858 708819207 708819110 9.190000e-18 102.0
6 TraesCS3D01G471400 chr3B 95.045 3653 150 20 973 4602 763341662 763345306 0.000000e+00 5714.0
7 TraesCS3D01G471400 chr3B 85.189 898 99 21 3638 4527 763457175 763458046 0.000000e+00 891.0
8 TraesCS3D01G471400 chr3B 83.187 571 49 16 417 982 763341109 763341637 3.630000e-131 479.0
9 TraesCS3D01G471400 chr3B 91.085 258 19 1 4931 5184 763460393 763460650 3.840000e-91 346.0
10 TraesCS3D01G471400 chr3B 83.077 325 26 8 2322 2645 763611977 763611681 8.560000e-68 268.0
11 TraesCS3D01G471400 chr3B 82.319 345 26 9 18 361 763340782 763341092 3.080000e-67 267.0
12 TraesCS3D01G471400 chr3B 86.228 167 18 4 4609 4772 704132912 704132748 5.340000e-40 176.0
13 TraesCS3D01G471400 chr3B 85.119 168 20 3 4605 4769 483571042 483571207 3.210000e-37 167.0
14 TraesCS3D01G471400 chr2A 85.842 1010 128 13 1893 2901 218212971 218211976 0.000000e+00 1059.0
15 TraesCS3D01G471400 chr2A 90.184 163 13 2 4609 4769 249754619 249754458 5.260000e-50 209.0
16 TraesCS3D01G471400 chr2A 86.310 168 21 2 4609 4776 526066616 526066781 1.150000e-41 182.0
17 TraesCS3D01G471400 chr1D 84.105 950 91 32 3086 3994 386378331 386377401 0.000000e+00 863.0
18 TraesCS3D01G471400 chr6D 83.824 952 92 38 3086 3994 86934415 86935347 0.000000e+00 848.0
19 TraesCS3D01G471400 chr6A 83.775 943 96 34 3090 3994 369412481 369411558 0.000000e+00 841.0
20 TraesCS3D01G471400 chr6A 86.061 165 20 2 4609 4771 366035502 366035339 1.920000e-39 174.0
21 TraesCS3D01G471400 chr5B 81.914 951 107 34 3086 3994 195738451 195739378 0.000000e+00 743.0
22 TraesCS3D01G471400 chr7A 82.486 708 79 24 3086 3755 53973821 53974521 3.480000e-161 579.0
23 TraesCS3D01G471400 chr6B 84.091 572 56 21 3036 3576 675196474 675195907 2.140000e-143 520.0
24 TraesCS3D01G471400 chr6B 85.890 163 20 2 4609 4769 36133664 36133503 2.480000e-38 171.0
25 TraesCS3D01G471400 chr5A 87.037 162 18 2 4609 4768 680074832 680074992 4.130000e-41 180.0
26 TraesCS3D01G471400 chr5A 87.591 137 8 7 3858 3994 617937855 617937982 3.240000e-32 150.0
27 TraesCS3D01G471400 chr4D 86.667 165 18 2 4609 4771 42146450 42146288 4.130000e-41 180.0
28 TraesCS3D01G471400 chr4D 85.802 162 20 2 4609 4768 479687261 479687421 8.930000e-38 169.0
29 TraesCS3D01G471400 chr4A 96.296 54 2 0 1717 1770 225329238 225329185 7.150000e-14 89.8


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 TraesCS3D01G471400 chr3D 573764478 573769664 5186 True 9579.000000 9579 100.000000 1 5187 1 chr3D.!!$R1 5186
1 TraesCS3D01G471400 chr3A 708819110 708823900 4790 True 3765.000000 7428 90.659000 18 4858 2 chr3A.!!$R1 4840
2 TraesCS3D01G471400 chr3B 763340782 763345306 4524 False 2153.333333 5714 86.850333 18 4602 3 chr3B.!!$F2 4584
3 TraesCS3D01G471400 chr3B 763457175 763460650 3475 False 618.500000 891 88.137000 3638 5184 2 chr3B.!!$F3 1546
4 TraesCS3D01G471400 chr2A 218211976 218212971 995 True 1059.000000 1059 85.842000 1893 2901 1 chr2A.!!$R1 1008
5 TraesCS3D01G471400 chr1D 386377401 386378331 930 True 863.000000 863 84.105000 3086 3994 1 chr1D.!!$R1 908
6 TraesCS3D01G471400 chr6D 86934415 86935347 932 False 848.000000 848 83.824000 3086 3994 1 chr6D.!!$F1 908
7 TraesCS3D01G471400 chr6A 369411558 369412481 923 True 841.000000 841 83.775000 3090 3994 1 chr6A.!!$R2 904
8 TraesCS3D01G471400 chr5B 195738451 195739378 927 False 743.000000 743 81.914000 3086 3994 1 chr5B.!!$F1 908
9 TraesCS3D01G471400 chr7A 53973821 53974521 700 False 579.000000 579 82.486000 3086 3755 1 chr7A.!!$F1 669
10 TraesCS3D01G471400 chr6B 675195907 675196474 567 True 520.000000 520 84.091000 3036 3576 1 chr6B.!!$R2 540

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
208 209 0.179134 CGATCTCTGGGTTCGTGGTC 60.179 60.000 0.00 0.0 33.83 4.02 F
648 652 0.239347 CTGCTTGCAGTTGCCTGTAC 59.761 55.000 13.89 0.0 41.02 2.90 F
653 657 0.758734 TGCAGTTGCCTGTACTGTCT 59.241 50.000 1.06 0.0 43.81 3.41 F
1686 1728 1.017387 GGGGAATGACATCGCAACTC 58.983 55.000 0.00 0.0 34.19 3.01 F
2490 2532 1.001487 CAAAGCATGGACAGCGAAACA 60.001 47.619 0.00 0.0 37.01 2.83 F
3263 3315 0.397941 TCAGTTGGCTTCTCCACTGG 59.602 55.000 11.02 0.0 46.55 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1685 0.251634 GCTCTGAGGTAAGCAGGCTT 59.748 55.000 11.70 11.70 38.42 4.35 R
1879 1921 1.840635 GGGACTATTTGAGCCCTCTGT 59.159 52.381 0.00 0.00 38.08 3.41 R
2373 2415 2.416893 CCGAAAAAGACTAGCAAGCTCC 59.583 50.000 0.00 0.00 0.00 4.70 R
2834 2876 1.526575 TTGCAGGCTTGGCTTAGTGC 61.527 55.000 0.00 0.00 41.94 4.40 R
3388 3469 2.511659 AGTCTGCATTGCAATCACAGT 58.488 42.857 26.64 13.95 38.41 3.55 R
4929 5354 0.389817 CGTCCAACTGCTCCAATCGA 60.390 55.000 0.00 0.00 0.00 3.59 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
69 70 4.087892 ATCGCGTTCCCTGCTGCT 62.088 61.111 5.77 0.00 0.00 4.24
204 205 0.663688 CGATCGATCTCTGGGTTCGT 59.336 55.000 22.43 0.00 38.07 3.85
208 209 0.179134 CGATCTCTGGGTTCGTGGTC 60.179 60.000 0.00 0.00 33.83 4.02
291 292 4.115516 CTCATCACTGTCCGATTCGAATT 58.884 43.478 12.81 0.00 0.00 2.17
300 301 4.243270 GTCCGATTCGAATTCGGGAATAT 58.757 43.478 30.77 12.61 46.03 1.28
342 343 1.115930 ACGCTCCGGATGCCTAATCT 61.116 55.000 3.57 0.00 35.43 2.40
361 362 2.707849 GCGCCGTGGAGAAGGACTA 61.708 63.158 0.00 0.00 0.00 2.59
362 363 1.888018 CGCCGTGGAGAAGGACTAA 59.112 57.895 0.00 0.00 0.00 2.24
363 364 0.460311 CGCCGTGGAGAAGGACTAAT 59.540 55.000 0.00 0.00 0.00 1.73
393 394 2.303163 TTTAGAGGAAATAGCGCGCA 57.697 45.000 35.10 19.76 0.00 6.09
461 464 6.175471 AGTCACTGTGATGCATATCTGAAAA 58.825 36.000 14.37 0.00 34.31 2.29
484 487 2.781681 TCTTAGTGGCAGCCTAAACC 57.218 50.000 14.15 0.00 0.00 3.27
530 534 6.327154 TGCAAATTCTGATATGCACTTTCTG 58.673 36.000 8.01 0.00 43.32 3.02
536 540 5.308014 TCTGATATGCACTTTCTGTTGTGT 58.692 37.500 0.00 0.00 36.63 3.72
559 563 6.266786 TGTGAACACTGTCTAATCTGAACCTA 59.733 38.462 6.51 0.00 0.00 3.08
565 569 8.157476 ACACTGTCTAATCTGAACCTAACATTT 58.843 33.333 0.00 0.00 0.00 2.32
596 600 3.627395 TGATAGTGTCCATCAACCACC 57.373 47.619 0.00 0.00 29.55 4.61
611 615 1.165270 CCACCGGTCACCTCAAAATC 58.835 55.000 2.59 0.00 0.00 2.17
648 652 0.239347 CTGCTTGCAGTTGCCTGTAC 59.761 55.000 13.89 0.00 41.02 2.90
653 657 0.758734 TGCAGTTGCCTGTACTGTCT 59.241 50.000 1.06 0.00 43.81 3.41
655 659 2.367241 TGCAGTTGCCTGTACTGTCTTA 59.633 45.455 1.06 0.00 43.81 2.10
657 661 3.186613 GCAGTTGCCTGTACTGTCTTAAC 59.813 47.826 0.00 0.00 43.81 2.01
658 662 3.428870 CAGTTGCCTGTACTGTCTTAACG 59.571 47.826 0.00 0.00 38.51 3.18
662 666 2.877335 CCTGTACTGTCTTAACGCTCC 58.123 52.381 0.00 0.00 0.00 4.70
680 684 1.829222 TCCGTATCCCTGAACAACTCC 59.171 52.381 0.00 0.00 0.00 3.85
737 741 7.334421 TGTTCCTACATTCTCTTTAAGTGCATC 59.666 37.037 0.00 0.00 0.00 3.91
740 744 5.557891 ACATTCTCTTTAAGTGCATCTGC 57.442 39.130 0.00 0.00 42.50 4.26
1065 1107 1.301558 GGAGCCAGGAGATGCATCG 60.302 63.158 20.67 7.56 0.00 3.84
1643 1685 3.213506 TGCTAGTTCAAGAGCAAAAGCA 58.786 40.909 0.00 0.00 45.47 3.91
1686 1728 1.017387 GGGGAATGACATCGCAACTC 58.983 55.000 0.00 0.00 34.19 3.01
1879 1921 4.280929 CAGACGTAATCATGGGATCTGGTA 59.719 45.833 0.00 0.00 31.88 3.25
2373 2415 2.089980 CTGAAATCACCAGCTTCCAGG 58.910 52.381 0.00 0.00 0.00 4.45
2490 2532 1.001487 CAAAGCATGGACAGCGAAACA 60.001 47.619 0.00 0.00 37.01 2.83
2522 2564 9.918630 AGATCAAACAAAGGTATTTCATTTCAG 57.081 29.630 0.00 0.00 0.00 3.02
2682 2724 4.142578 TGCTGAAAAGTTTGCTCGTACAAA 60.143 37.500 0.00 2.23 37.20 2.83
2834 2876 3.869272 GCTTCAGCATGCCCGTCG 61.869 66.667 15.66 0.37 41.59 5.12
2883 2925 7.259161 CCACTGTTAGAGGTTAGTGTCTAATC 58.741 42.308 0.00 0.00 37.55 1.75
3122 3171 6.210784 TGGTTATCCTACATCCTTATCTTCCG 59.789 42.308 0.00 0.00 34.23 4.30
3140 3189 5.880332 TCTTCCGAAGAAATTGGTTATCCTG 59.120 40.000 8.45 0.00 33.83 3.86
3263 3315 0.397941 TCAGTTGGCTTCTCCACTGG 59.602 55.000 11.02 0.00 46.55 4.00
3352 3407 8.671384 AGTGACTAATTTTGTAGCAGTTTGTA 57.329 30.769 0.00 0.00 0.00 2.41
3361 3442 5.856126 TGTAGCAGTTTGTAGCATGTTAC 57.144 39.130 12.39 12.39 32.11 2.50
3388 3469 4.998671 TTGCACCAAAAATTCTGAGACA 57.001 36.364 0.00 0.00 0.00 3.41
3389 3470 4.305989 TGCACCAAAAATTCTGAGACAC 57.694 40.909 0.00 0.00 0.00 3.67
3400 3481 3.473923 TCTGAGACACTGTGATTGCAA 57.526 42.857 15.86 0.00 0.00 4.08
3496 3578 5.705609 TGGAAGATTTTCTTGTTACCTGC 57.294 39.130 0.00 0.00 36.73 4.85
3506 3588 1.598882 TGTTACCTGCGTTGCATTCA 58.401 45.000 0.00 0.00 38.13 2.57
3507 3589 2.158559 TGTTACCTGCGTTGCATTCAT 58.841 42.857 0.00 0.00 38.13 2.57
4183 4282 4.651503 CCTGTAGTTACTGATGTGATCCCT 59.348 45.833 0.00 0.00 0.00 4.20
4327 4426 8.068380 GCTTGGATCGTGTAAGGATTTAATTAC 58.932 37.037 0.00 0.00 42.28 1.89
4538 4933 6.369065 GGGGTTATCTCTTATATGCTTTCACG 59.631 42.308 0.00 0.00 0.00 4.35
4573 4983 7.658179 CACACTAGTGTTCTAACATGATTGT 57.342 36.000 25.89 0.00 42.83 2.71
4596 5006 6.883756 TGTGAGTGCATGTATGGATCTTAAAA 59.116 34.615 0.00 0.00 0.00 1.52
4598 5008 6.543465 TGAGTGCATGTATGGATCTTAAAAGG 59.457 38.462 0.00 0.00 0.00 3.11
4599 5009 5.300286 AGTGCATGTATGGATCTTAAAAGGC 59.700 40.000 0.00 0.00 0.00 4.35
4600 5010 5.067674 GTGCATGTATGGATCTTAAAAGGCA 59.932 40.000 0.00 0.00 0.00 4.75
4607 5028 9.249053 TGTATGGATCTTAAAAGGCATTTTACA 57.751 29.630 15.35 10.33 39.89 2.41
4612 5033 8.523658 GGATCTTAAAAGGCATTTTACAACTCT 58.476 33.333 15.35 0.00 39.89 3.24
4622 5043 4.950205 TTTTACAACTCTCTCCGTTCCT 57.050 40.909 0.00 0.00 0.00 3.36
4624 5045 6.409524 TTTTACAACTCTCTCCGTTCCTAA 57.590 37.500 0.00 0.00 0.00 2.69
4625 5046 6.409524 TTTACAACTCTCTCCGTTCCTAAA 57.590 37.500 0.00 0.00 0.00 1.85
4628 5049 6.793505 ACAACTCTCTCCGTTCCTAAATAT 57.206 37.500 0.00 0.00 0.00 1.28
4629 5050 7.893124 ACAACTCTCTCCGTTCCTAAATATA 57.107 36.000 0.00 0.00 0.00 0.86
4630 5051 8.302515 ACAACTCTCTCCGTTCCTAAATATAA 57.697 34.615 0.00 0.00 0.00 0.98
4631 5052 8.196103 ACAACTCTCTCCGTTCCTAAATATAAC 58.804 37.037 0.00 0.00 0.00 1.89
4632 5053 7.893124 ACTCTCTCCGTTCCTAAATATAACA 57.107 36.000 0.00 0.00 0.00 2.41
4634 5055 7.341256 ACTCTCTCCGTTCCTAAATATAACACA 59.659 37.037 0.00 0.00 0.00 3.72
4636 5057 8.701895 TCTCTCCGTTCCTAAATATAACACATT 58.298 33.333 0.00 0.00 0.00 2.71
4637 5058 9.326413 CTCTCCGTTCCTAAATATAACACATTT 57.674 33.333 0.00 0.00 0.00 2.32
4675 5096 8.833231 ATATGGACTACATACGAAGGAAAATG 57.167 34.615 0.00 0.00 44.41 2.32
4676 5097 6.288941 TGGACTACATACGAAGGAAAATGA 57.711 37.500 0.00 0.00 0.00 2.57
4677 5098 6.338146 TGGACTACATACGAAGGAAAATGAG 58.662 40.000 0.00 0.00 0.00 2.90
4678 5099 6.070995 TGGACTACATACGAAGGAAAATGAGT 60.071 38.462 0.00 0.00 0.00 3.41
4682 5103 8.041323 ACTACATACGAAGGAAAATGAGTGAAT 58.959 33.333 0.00 0.00 0.00 2.57
4683 5104 7.308782 ACATACGAAGGAAAATGAGTGAATC 57.691 36.000 0.00 0.00 0.00 2.52
4684 5105 7.106239 ACATACGAAGGAAAATGAGTGAATCT 58.894 34.615 0.00 0.00 0.00 2.40
4686 5107 6.969828 ACGAAGGAAAATGAGTGAATCTAC 57.030 37.500 0.00 0.00 0.00 2.59
4687 5108 6.464222 ACGAAGGAAAATGAGTGAATCTACA 58.536 36.000 0.00 0.00 0.00 2.74
4688 5109 6.369065 ACGAAGGAAAATGAGTGAATCTACAC 59.631 38.462 0.00 0.00 40.60 2.90
4702 5123 9.860650 AGTGAATCTACACTCTAGAATACATCT 57.139 33.333 0.00 0.00 46.36 2.90
4722 5143 8.389779 ACATCTATACATCTGTCTGTAGTCTG 57.610 38.462 0.00 0.00 35.21 3.51
4723 5144 7.996066 ACATCTATACATCTGTCTGTAGTCTGT 59.004 37.037 0.00 0.00 35.21 3.41
4724 5145 9.495572 CATCTATACATCTGTCTGTAGTCTGTA 57.504 37.037 0.00 0.00 35.21 2.74
4728 5149 8.753497 ATACATCTGTCTGTAGTCTGTATTGA 57.247 34.615 0.00 0.00 35.21 2.57
4729 5150 7.468141 ACATCTGTCTGTAGTCTGTATTGAA 57.532 36.000 0.00 0.00 0.00 2.69
4730 5151 7.896811 ACATCTGTCTGTAGTCTGTATTGAAA 58.103 34.615 0.00 0.00 0.00 2.69
4731 5152 8.535335 ACATCTGTCTGTAGTCTGTATTGAAAT 58.465 33.333 0.00 0.00 0.00 2.17
4792 5214 5.286267 AGGTAAGGTATGGTCGTATTTGG 57.714 43.478 0.00 0.00 0.00 3.28
4799 5221 4.696402 GGTATGGTCGTATTTGGTGTTGAA 59.304 41.667 0.00 0.00 0.00 2.69
4804 5226 4.756135 GGTCGTATTTGGTGTTGAAAGGTA 59.244 41.667 0.00 0.00 0.00 3.08
4811 5233 9.880157 GTATTTGGTGTTGAAAGGTACTCTATA 57.120 33.333 0.00 0.00 38.49 1.31
4815 5237 6.212791 TGGTGTTGAAAGGTACTCTATAGCTT 59.787 38.462 0.00 0.00 38.49 3.74
4822 5244 6.527057 AAGGTACTCTATAGCTTGTTCGTT 57.473 37.500 0.00 0.00 38.49 3.85
4831 5253 1.021968 GCTTGTTCGTTCACCAACCT 58.978 50.000 0.00 0.00 0.00 3.50
4861 5283 0.107459 GGCCTGGCCTCTCTTACAAG 60.107 60.000 30.42 0.00 46.69 3.16
4862 5284 0.107459 GCCTGGCCTCTCTTACAAGG 60.107 60.000 7.66 0.00 35.65 3.61
4863 5285 0.543749 CCTGGCCTCTCTTACAAGGG 59.456 60.000 3.32 0.00 32.98 3.95
4886 5310 1.306226 ACTCCCTAGTGCCTCCACC 60.306 63.158 0.00 0.00 43.09 4.61
4889 5313 0.909610 TCCCTAGTGCCTCCACCTTG 60.910 60.000 0.00 0.00 43.09 3.61
4892 5316 1.339151 CCTAGTGCCTCCACCTTGAAC 60.339 57.143 0.00 0.00 43.09 3.18
4912 5337 5.181811 TGAACAAGGTAGCATTGAGAATGTG 59.818 40.000 9.94 0.00 41.01 3.21
4914 5339 5.804639 ACAAGGTAGCATTGAGAATGTGTA 58.195 37.500 9.94 0.00 41.01 2.90
4923 5348 6.148480 AGCATTGAGAATGTGTAGAGAACAAC 59.852 38.462 0.00 0.00 40.63 3.32
4927 5352 4.569943 AGAATGTGTAGAGAACAACGCAT 58.430 39.130 0.00 0.00 46.01 4.73
4928 5353 4.389992 AGAATGTGTAGAGAACAACGCATG 59.610 41.667 2.60 0.00 43.95 4.06
4929 5354 3.106242 TGTGTAGAGAACAACGCATGT 57.894 42.857 0.00 0.00 46.82 3.21
4931 5356 2.090658 GTGTAGAGAACAACGCATGTCG 59.909 50.000 7.79 7.79 42.99 4.35
4932 5357 2.030628 TGTAGAGAACAACGCATGTCGA 60.031 45.455 14.88 0.00 42.99 4.20
4933 5358 2.370281 AGAGAACAACGCATGTCGAT 57.630 45.000 14.88 2.05 42.99 3.59
4935 5360 2.413112 AGAGAACAACGCATGTCGATTG 59.587 45.455 14.88 15.30 42.99 2.67
4944 7152 1.202110 GCATGTCGATTGGAGCAGTTG 60.202 52.381 0.00 0.00 0.00 3.16
4961 7169 1.263217 GTTGGACGTTGCAACCTACTG 59.737 52.381 23.42 11.57 41.94 2.74
5016 7224 2.132762 GTCACCAACATCGACGTTTCT 58.867 47.619 0.00 0.00 0.00 2.52
5048 7256 4.583073 TGCATTGCATAGCATGAGAGAATT 59.417 37.500 7.38 0.00 38.76 2.17
5072 7284 3.618690 TGGGAAAGGTTGTTTTGGTTG 57.381 42.857 0.00 0.00 0.00 3.77
5075 7287 3.687212 GGGAAAGGTTGTTTTGGTTGTTG 59.313 43.478 0.00 0.00 0.00 3.33
5085 7297 2.359975 GGTTGTTGGAGGAGGCCG 60.360 66.667 0.00 0.00 0.00 6.13
5125 7337 2.673523 CAGGGGTGGAGCAAGGAG 59.326 66.667 0.00 0.00 0.00 3.69
5176 7388 4.220821 ACACACGTCATGGATCTAGACTTT 59.779 41.667 0.00 0.00 0.00 2.66
5178 7390 6.071560 ACACACGTCATGGATCTAGACTTTAA 60.072 38.462 0.00 0.00 0.00 1.52
5184 7396 6.271159 GTCATGGATCTAGACTTTAAGGGGAT 59.729 42.308 0.00 0.00 0.00 3.85
5185 7397 7.455008 GTCATGGATCTAGACTTTAAGGGGATA 59.545 40.741 0.00 0.00 0.00 2.59
5186 7398 8.016652 TCATGGATCTAGACTTTAAGGGGATAA 58.983 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.439701 CTCGTACCTCGGAGCCCA 60.440 66.667 0.00 0.00 40.32 5.36
193 194 0.244994 CAGAGACCACGAACCCAGAG 59.755 60.000 0.00 0.00 0.00 3.35
204 205 3.680786 CGACGGCACCAGAGACCA 61.681 66.667 0.00 0.00 0.00 4.02
208 209 0.108615 ATTTCTCGACGGCACCAGAG 60.109 55.000 0.00 0.00 0.00 3.35
291 292 9.431887 GTAAATCAAACTAGCATATATTCCCGA 57.568 33.333 0.00 0.00 0.00 5.14
300 301 7.861372 GCGTAGAGAGTAAATCAAACTAGCATA 59.139 37.037 0.00 0.00 0.00 3.14
323 324 1.115930 AGATTAGGCATCCGGAGCGT 61.116 55.000 11.34 16.90 31.20 5.07
342 343 4.373116 GTCCTTCTCCACGGCGCA 62.373 66.667 10.83 0.00 0.00 6.09
361 362 6.463995 TTTCCTCTAAAACACAGCAACATT 57.536 33.333 0.00 0.00 0.00 2.71
362 363 6.655078 ATTTCCTCTAAAACACAGCAACAT 57.345 33.333 0.00 0.00 0.00 2.71
363 364 6.293955 GCTATTTCCTCTAAAACACAGCAACA 60.294 38.462 0.00 0.00 0.00 3.33
461 464 4.455606 GTTTAGGCTGCCACTAAGATCAT 58.544 43.478 22.65 0.00 32.52 2.45
484 487 6.372381 TGCATCTATAATGTGGATTTCGGATG 59.628 38.462 0.00 0.00 0.00 3.51
536 540 5.808366 AGGTTCAGATTAGACAGTGTTCA 57.192 39.130 0.00 0.00 0.00 3.18
565 569 8.554835 TGATGGACACTATCAACGATTAAAAA 57.445 30.769 0.00 0.00 31.98 1.94
586 590 0.673644 GAGGTGACCGGTGGTTGATG 60.674 60.000 14.63 0.00 35.25 3.07
596 600 2.076863 GACAGGATTTTGAGGTGACCG 58.923 52.381 0.00 0.00 0.00 4.79
611 615 2.286872 CAGAGCTTGCCAATAGACAGG 58.713 52.381 0.00 0.00 0.00 4.00
648 652 2.543238 GGGATACGGAGCGTTAAGACAG 60.543 54.545 0.00 0.00 41.54 3.51
653 657 1.766494 TCAGGGATACGGAGCGTTAA 58.234 50.000 0.00 0.00 41.54 2.01
655 659 0.175073 GTTCAGGGATACGGAGCGTT 59.825 55.000 0.00 0.00 41.54 4.84
657 661 0.174845 TTGTTCAGGGATACGGAGCG 59.825 55.000 0.00 0.00 37.60 5.03
658 662 1.207329 AGTTGTTCAGGGATACGGAGC 59.793 52.381 0.00 0.00 37.60 4.70
662 666 1.922570 CGGAGTTGTTCAGGGATACG 58.077 55.000 0.00 0.00 37.60 3.06
680 684 0.870393 AATGAGTTGTGCTGACTGCG 59.130 50.000 0.00 0.00 46.63 5.18
737 741 2.090400 ATCAGTATAGGCATGCGCAG 57.910 50.000 18.32 9.45 41.24 5.18
740 744 3.044235 TCCAATCAGTATAGGCATGCG 57.956 47.619 12.44 0.00 0.00 4.73
743 747 7.170965 CCAAAGTATCCAATCAGTATAGGCAT 58.829 38.462 0.00 0.00 0.00 4.40
788 795 2.559668 AGCAACACAGAATGAATGGTGG 59.440 45.455 0.00 0.00 39.69 4.61
908 916 0.822121 AACAAGGGAACGGAACTGGC 60.822 55.000 0.00 0.00 0.00 4.85
1065 1107 1.176527 TATCAAAAGCACTGGCCTGC 58.823 50.000 9.95 9.41 42.56 4.85
1643 1685 0.251634 GCTCTGAGGTAAGCAGGCTT 59.748 55.000 11.70 11.70 38.42 4.35
1686 1728 2.808543 GTGGTCTACCTTGAGTTGCTTG 59.191 50.000 0.02 0.00 36.82 4.01
1879 1921 1.840635 GGGACTATTTGAGCCCTCTGT 59.159 52.381 0.00 0.00 38.08 3.41
2373 2415 2.416893 CCGAAAAAGACTAGCAAGCTCC 59.583 50.000 0.00 0.00 0.00 4.70
2512 2554 7.812690 AGTATATGCAGATGCTGAAATGAAA 57.187 32.000 11.32 0.00 42.66 2.69
2540 2582 8.531982 ACATCAAGCTATCTTCAGTTACTTGTA 58.468 33.333 0.00 0.00 35.64 2.41
2834 2876 1.526575 TTGCAGGCTTGGCTTAGTGC 61.527 55.000 0.00 0.00 41.94 4.40
2916 2964 9.860898 ATTGTCCTCTGCAACTATTTATTTTTC 57.139 29.630 0.00 0.00 0.00 2.29
2930 2978 9.797642 ATTATGATTATACAATTGTCCTCTGCA 57.202 29.630 15.85 8.23 0.00 4.41
3122 3171 8.738645 ATAGTCACAGGATAACCAATTTCTTC 57.261 34.615 0.00 0.00 38.94 2.87
3140 3189 4.130118 GGGACATTGTCATGGATAGTCAC 58.870 47.826 18.09 0.00 34.27 3.67
3263 3315 5.239525 AGAACATTAAACTCACACTGGAAGC 59.760 40.000 0.00 0.00 37.60 3.86
3352 3407 3.504134 TGGTGCAATTTACGTAACATGCT 59.496 39.130 29.69 6.91 34.59 3.79
3361 3442 6.640499 TCTCAGAATTTTTGGTGCAATTTACG 59.360 34.615 0.00 0.00 0.00 3.18
3388 3469 2.511659 AGTCTGCATTGCAATCACAGT 58.488 42.857 26.64 13.95 38.41 3.55
3389 3470 4.690184 TTAGTCTGCATTGCAATCACAG 57.310 40.909 23.97 23.97 38.41 3.66
3400 3481 7.094463 CCTCACAGATTTCTTTTTAGTCTGCAT 60.094 37.037 0.00 0.00 39.83 3.96
3496 3578 6.515043 AAGTCAAGAAAAATGAATGCAACG 57.485 33.333 0.00 0.00 0.00 4.10
3506 3588 9.634021 AGAGGAAAGAACTAAGTCAAGAAAAAT 57.366 29.630 0.00 0.00 0.00 1.82
3507 3589 9.462606 AAGAGGAAAGAACTAAGTCAAGAAAAA 57.537 29.630 0.00 0.00 0.00 1.94
3722 3809 5.221925 ACAAGAGATTACAAAGGCTCCTTCA 60.222 40.000 1.05 0.00 34.84 3.02
4183 4282 6.509418 ACTAGCAAAAAGAAGTGTGTTCAA 57.491 33.333 0.00 0.00 0.00 2.69
4517 4622 7.497595 ACCACGTGAAAGCATATAAGAGATAA 58.502 34.615 19.30 0.00 0.00 1.75
4538 4933 1.873591 CACTAGTGTGCTCCAAACCAC 59.126 52.381 15.06 0.00 37.38 4.16
4554 4964 6.368791 GCACTCACAATCATGTTAGAACACTA 59.631 38.462 0.00 0.00 42.51 2.74
4556 4966 5.049474 TGCACTCACAATCATGTTAGAACAC 60.049 40.000 0.00 0.00 42.51 3.32
4573 4983 6.543465 CCTTTTAAGATCCATACATGCACTCA 59.457 38.462 0.00 0.00 0.00 3.41
4596 5006 3.008049 ACGGAGAGAGTTGTAAAATGCCT 59.992 43.478 0.00 0.00 0.00 4.75
4598 5008 4.142881 GGAACGGAGAGAGTTGTAAAATGC 60.143 45.833 0.00 0.00 31.14 3.56
4599 5009 5.238583 AGGAACGGAGAGAGTTGTAAAATG 58.761 41.667 0.00 0.00 31.14 2.32
4600 5010 5.485209 AGGAACGGAGAGAGTTGTAAAAT 57.515 39.130 0.00 0.00 31.14 1.82
4607 5028 8.196103 GTGTTATATTTAGGAACGGAGAGAGTT 58.804 37.037 0.00 0.00 34.07 3.01
4612 5033 9.675464 AAAATGTGTTATATTTAGGAACGGAGA 57.325 29.630 0.00 0.00 0.00 3.71
4650 5071 8.647796 TCATTTTCCTTCGTATGTAGTCCATAT 58.352 33.333 0.00 0.00 38.29 1.78
4652 5073 6.884832 TCATTTTCCTTCGTATGTAGTCCAT 58.115 36.000 0.00 0.00 37.58 3.41
4653 5074 6.070995 ACTCATTTTCCTTCGTATGTAGTCCA 60.071 38.462 0.00 0.00 0.00 4.02
4654 5075 6.255887 CACTCATTTTCCTTCGTATGTAGTCC 59.744 42.308 0.00 0.00 0.00 3.85
4655 5076 7.033791 TCACTCATTTTCCTTCGTATGTAGTC 58.966 38.462 0.00 0.00 0.00 2.59
4656 5077 6.931838 TCACTCATTTTCCTTCGTATGTAGT 58.068 36.000 0.00 0.00 0.00 2.73
4657 5078 7.827819 TTCACTCATTTTCCTTCGTATGTAG 57.172 36.000 0.00 0.00 0.00 2.74
4658 5079 8.258007 AGATTCACTCATTTTCCTTCGTATGTA 58.742 33.333 0.00 0.00 0.00 2.29
4660 5081 7.545362 AGATTCACTCATTTTCCTTCGTATG 57.455 36.000 0.00 0.00 0.00 2.39
4662 5083 7.544566 GTGTAGATTCACTCATTTTCCTTCGTA 59.455 37.037 0.00 0.00 35.68 3.43
4663 5084 6.369065 GTGTAGATTCACTCATTTTCCTTCGT 59.631 38.462 0.00 0.00 35.68 3.85
4664 5085 6.591834 AGTGTAGATTCACTCATTTTCCTTCG 59.408 38.462 0.00 0.00 44.07 3.79
4665 5086 7.913674 AGTGTAGATTCACTCATTTTCCTTC 57.086 36.000 0.00 0.00 44.07 3.46
4676 5097 9.860650 AGATGTATTCTAGAGTGTAGATTCACT 57.139 33.333 0.00 0.00 41.03 3.41
4696 5117 9.495572 CAGACTACAGACAGATGTATAGATGTA 57.504 37.037 0.00 0.00 35.21 2.29
4697 5118 7.996066 ACAGACTACAGACAGATGTATAGATGT 59.004 37.037 0.00 6.72 35.21 3.06
4698 5119 8.389779 ACAGACTACAGACAGATGTATAGATG 57.610 38.462 0.00 6.31 35.21 2.90
4702 5123 9.847224 TCAATACAGACTACAGACAGATGTATA 57.153 33.333 0.00 0.00 35.21 1.47
4703 5124 8.753497 TCAATACAGACTACAGACAGATGTAT 57.247 34.615 0.00 0.00 35.21 2.29
4704 5125 8.575649 TTCAATACAGACTACAGACAGATGTA 57.424 34.615 0.00 0.00 34.56 2.29
4705 5126 7.468141 TTCAATACAGACTACAGACAGATGT 57.532 36.000 0.00 0.00 37.19 3.06
4706 5127 8.939201 ATTTCAATACAGACTACAGACAGATG 57.061 34.615 0.00 0.00 0.00 2.90
4736 5157 8.248253 CCACCGTTTCTAAATATAAGGCTTTTT 58.752 33.333 4.45 2.60 0.00 1.94
4737 5158 7.147966 CCCACCGTTTCTAAATATAAGGCTTTT 60.148 37.037 4.45 0.00 0.00 2.27
4738 5159 6.320418 CCCACCGTTTCTAAATATAAGGCTTT 59.680 38.462 4.45 0.00 0.00 3.51
4739 5160 5.826208 CCCACCGTTTCTAAATATAAGGCTT 59.174 40.000 4.58 4.58 0.00 4.35
4740 5161 5.131475 TCCCACCGTTTCTAAATATAAGGCT 59.869 40.000 0.00 0.00 0.00 4.58
4741 5162 5.370679 TCCCACCGTTTCTAAATATAAGGC 58.629 41.667 0.00 0.00 0.00 4.35
4742 5163 6.589135 ACTCCCACCGTTTCTAAATATAAGG 58.411 40.000 0.00 0.00 0.00 2.69
4743 5164 8.636213 TCTACTCCCACCGTTTCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
4744 5165 8.537728 TCTACTCCCACCGTTTCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
4745 5166 8.537728 TTCTACTCCCACCGTTTCTAAATATA 57.462 34.615 0.00 0.00 0.00 0.86
4746 5167 7.418712 CCTTCTACTCCCACCGTTTCTAAATAT 60.419 40.741 0.00 0.00 0.00 1.28
4747 5168 6.127253 CCTTCTACTCCCACCGTTTCTAAATA 60.127 42.308 0.00 0.00 0.00 1.40
4748 5169 5.338137 CCTTCTACTCCCACCGTTTCTAAAT 60.338 44.000 0.00 0.00 0.00 1.40
4749 5170 4.020839 CCTTCTACTCCCACCGTTTCTAAA 60.021 45.833 0.00 0.00 0.00 1.85
4750 5171 3.512724 CCTTCTACTCCCACCGTTTCTAA 59.487 47.826 0.00 0.00 0.00 2.10
4751 5172 3.094572 CCTTCTACTCCCACCGTTTCTA 58.905 50.000 0.00 0.00 0.00 2.10
4752 5173 1.900486 CCTTCTACTCCCACCGTTTCT 59.100 52.381 0.00 0.00 0.00 2.52
4753 5174 1.622312 ACCTTCTACTCCCACCGTTTC 59.378 52.381 0.00 0.00 0.00 2.78
4754 5175 1.725803 ACCTTCTACTCCCACCGTTT 58.274 50.000 0.00 0.00 0.00 3.60
4755 5176 2.610438 TACCTTCTACTCCCACCGTT 57.390 50.000 0.00 0.00 0.00 4.44
4756 5177 2.454538 CTTACCTTCTACTCCCACCGT 58.545 52.381 0.00 0.00 0.00 4.83
4757 5178 1.755380 CCTTACCTTCTACTCCCACCG 59.245 57.143 0.00 0.00 0.00 4.94
4758 5179 2.830293 ACCTTACCTTCTACTCCCACC 58.170 52.381 0.00 0.00 0.00 4.61
4759 5180 4.344390 CCATACCTTACCTTCTACTCCCAC 59.656 50.000 0.00 0.00 0.00 4.61
4760 5181 4.015918 ACCATACCTTACCTTCTACTCCCA 60.016 45.833 0.00 0.00 0.00 4.37
4761 5182 4.554683 ACCATACCTTACCTTCTACTCCC 58.445 47.826 0.00 0.00 0.00 4.30
4792 5214 7.097834 ACAAGCTATAGAGTACCTTTCAACAC 58.902 38.462 3.21 0.00 0.00 3.32
4799 5221 6.152323 TGAACGAACAAGCTATAGAGTACCTT 59.848 38.462 3.21 0.00 0.00 3.50
4804 5226 4.219944 TGGTGAACGAACAAGCTATAGAGT 59.780 41.667 3.21 0.00 0.00 3.24
4811 5233 1.021968 GGTTGGTGAACGAACAAGCT 58.978 50.000 9.99 0.00 38.97 3.74
4815 5237 2.171027 AGGTAAGGTTGGTGAACGAACA 59.829 45.455 9.99 0.00 36.47 3.18
4822 5244 3.560453 GCCAATGTAGGTAAGGTTGGTGA 60.560 47.826 4.58 0.00 41.01 4.02
4831 5253 3.894742 GCCAGGCCAATGTAGGTAA 57.105 52.632 5.01 0.00 0.00 2.85
4850 5272 2.167487 GAGTGCCTCCCTTGTAAGAGAG 59.833 54.545 0.00 0.00 31.37 3.20
4868 5290 1.306226 GGTGGAGGCACTAGGGAGT 60.306 63.158 0.00 0.00 41.55 3.85
4869 5291 0.618968 AAGGTGGAGGCACTAGGGAG 60.619 60.000 0.00 0.00 41.55 4.30
4870 5292 0.909610 CAAGGTGGAGGCACTAGGGA 60.910 60.000 0.00 0.00 41.55 4.20
4872 5296 0.984230 TTCAAGGTGGAGGCACTAGG 59.016 55.000 0.00 0.00 41.55 3.02
4886 5310 5.947228 TTCTCAATGCTACCTTGTTCAAG 57.053 39.130 5.66 5.66 0.00 3.02
4889 5313 5.182001 ACACATTCTCAATGCTACCTTGTTC 59.818 40.000 0.00 0.00 42.69 3.18
4892 5316 6.108687 TCTACACATTCTCAATGCTACCTTG 58.891 40.000 0.00 0.00 42.69 3.61
4897 5321 6.935167 TGTTCTCTACACATTCTCAATGCTA 58.065 36.000 0.00 0.00 42.69 3.49
4898 5322 5.798132 TGTTCTCTACACATTCTCAATGCT 58.202 37.500 0.00 0.00 42.69 3.79
4899 5323 6.310197 GTTGTTCTCTACACATTCTCAATGC 58.690 40.000 0.00 0.00 42.69 3.56
4900 5324 6.528826 CGTTGTTCTCTACACATTCTCAATG 58.471 40.000 0.00 0.00 44.48 2.82
4912 5337 2.592194 TCGACATGCGTTGTTCTCTAC 58.408 47.619 8.91 0.00 39.18 2.59
4914 5339 2.370281 ATCGACATGCGTTGTTCTCT 57.630 45.000 8.91 0.00 39.18 3.10
4923 5348 1.086067 ACTGCTCCAATCGACATGCG 61.086 55.000 0.00 0.00 42.69 4.73
4927 5352 0.684535 TCCAACTGCTCCAATCGACA 59.315 50.000 0.00 0.00 0.00 4.35
4928 5353 1.079503 GTCCAACTGCTCCAATCGAC 58.920 55.000 0.00 0.00 0.00 4.20
4929 5354 0.389817 CGTCCAACTGCTCCAATCGA 60.390 55.000 0.00 0.00 0.00 3.59
4931 5356 1.197721 CAACGTCCAACTGCTCCAATC 59.802 52.381 0.00 0.00 0.00 2.67
4932 5357 1.238439 CAACGTCCAACTGCTCCAAT 58.762 50.000 0.00 0.00 0.00 3.16
4933 5358 1.444119 GCAACGTCCAACTGCTCCAA 61.444 55.000 1.95 0.00 33.20 3.53
4935 5360 1.444119 TTGCAACGTCCAACTGCTCC 61.444 55.000 10.27 0.00 37.00 4.70
4944 7152 0.953960 CCCAGTAGGTTGCAACGTCC 60.954 60.000 26.63 16.75 0.00 4.79
4961 7169 2.435938 TCAACGCCTCGCATTCCC 60.436 61.111 0.00 0.00 0.00 3.97
4997 7205 2.035449 AGAGAAACGTCGATGTTGGTGA 59.965 45.455 23.05 0.00 31.10 4.02
4998 7206 2.155732 CAGAGAAACGTCGATGTTGGTG 59.844 50.000 23.05 13.73 31.10 4.17
5000 7208 1.726791 CCAGAGAAACGTCGATGTTGG 59.273 52.381 23.05 16.19 31.10 3.77
5011 7219 4.808558 TGCAATGCATTAACCAGAGAAAC 58.191 39.130 12.53 0.00 31.71 2.78
5048 7256 3.777522 ACCAAAACAACCTTTCCCATTCA 59.222 39.130 0.00 0.00 0.00 2.57
5085 7297 1.364626 CCATGAAGTCACAGCTCGCC 61.365 60.000 0.00 0.00 0.00 5.54
5088 7300 0.393537 CCCCCATGAAGTCACAGCTC 60.394 60.000 0.00 0.00 0.00 4.09
5125 7337 3.188460 TCTTTGTCTCCATTAAGCGCAAC 59.812 43.478 11.47 0.00 0.00 4.17
5130 7342 6.017109 TGTTGTCTTCTTTGTCTCCATTAAGC 60.017 38.462 0.00 0.00 0.00 3.09
5144 7356 2.872245 CCATGACGTGTGTTGTCTTCTT 59.128 45.455 0.00 0.00 37.26 2.52


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

AutoCloner maintained by Alex Coulton.