Multiple sequence alignment - TraesCS3B01G243600

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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 TraesCS3B01G243600 chr3B 100.000 2631 0 0 1 2631 385144555 385141925 0.000000e+00 4859
1 TraesCS3B01G243600 chr3B 84.674 783 90 19 1871 2630 625214118 625214893 0.000000e+00 754
2 TraesCS3B01G243600 chr3B 83.495 206 24 9 110 311 562779899 562779700 1.610000e-42 183
3 TraesCS3B01G243600 chr3B 96.330 109 2 2 467 574 542736177 542736284 7.480000e-41 178
4 TraesCS3B01G243600 chr3A 92.241 1147 60 7 1505 2631 384685067 384683930 0.000000e+00 1598
5 TraesCS3B01G243600 chr3A 95.091 713 23 5 831 1537 384685807 384685101 0.000000e+00 1112
6 TraesCS3B01G243600 chr3A 87.739 261 23 4 89 349 384686658 384686407 1.980000e-76 296
7 TraesCS3B01G243600 chr3A 95.495 111 4 1 720 829 384685952 384685842 2.690000e-40 176
8 TraesCS3B01G243600 chr3D 96.729 642 18 2 899 1537 291963974 291963333 0.000000e+00 1066
9 TraesCS3B01G243600 chr3D 94.737 570 28 2 2063 2631 291954986 291954418 0.000000e+00 885
10 TraesCS3B01G243600 chr3D 92.466 584 25 8 1505 2073 291963299 291962720 0.000000e+00 817
11 TraesCS3B01G243600 chr3D 85.932 263 29 3 89 351 291965040 291964786 9.280000e-70 274
12 TraesCS3B01G243600 chr3D 96.330 109 2 2 467 574 158938953 158939060 7.480000e-41 178
13 TraesCS3B01G243600 chr3D 94.643 112 5 1 720 830 291964395 291964284 3.480000e-39 172
14 TraesCS3B01G243600 chr3D 83.133 166 19 8 110 273 338297286 338297128 2.730000e-30 143
15 TraesCS3B01G243600 chr3D 97.222 72 0 2 827 896 291964094 291964023 1.280000e-23 121
16 TraesCS3B01G243600 chr2B 85.696 783 82 9 1871 2630 239884113 239883338 0.000000e+00 798
17 TraesCS3B01G243600 chr2B 85.441 783 84 11 1871 2630 592470242 592469467 0.000000e+00 787
18 TraesCS3B01G243600 chr2B 85.313 783 85 10 1871 2630 93788479 93789254 0.000000e+00 782
19 TraesCS3B01G243600 chr2B 78.173 197 36 5 118 312 628946854 628947045 4.600000e-23 119
20 TraesCS3B01G243600 chr7A 85.298 789 86 12 1871 2630 512592754 512591967 0.000000e+00 787
21 TraesCS3B01G243600 chr7B 85.044 789 80 19 1871 2630 745364874 745364095 0.000000e+00 769
22 TraesCS3B01G243600 chr7B 84.177 158 16 7 125 281 713634153 713634004 7.590000e-31 145
23 TraesCS3B01G243600 chr4A 84.949 784 86 10 1871 2630 243639850 243639075 0.000000e+00 765
24 TraesCS3B01G243600 chr4B 84.821 784 87 15 1871 2630 42274453 42273678 0.000000e+00 760
25 TraesCS3B01G243600 chr2D 84.674 783 89 18 1871 2630 100360334 100361108 0.000000e+00 752
26 TraesCS3B01G243600 chr2D 84.419 783 92 11 1871 2630 507300776 507301551 0.000000e+00 743
27 TraesCS3B01G243600 chr1A 84.419 783 92 8 1871 2630 485483306 485482531 0.000000e+00 743
28 TraesCS3B01G243600 chr4D 84.291 783 93 8 1871 2630 368916578 368915803 0.000000e+00 737
29 TraesCS3B01G243600 chr5B 84.224 786 91 18 1871 2630 391662681 391661903 0.000000e+00 734
30 TraesCS3B01G243600 chr5B 96.330 109 2 2 467 574 429064994 429065101 7.480000e-41 178
31 TraesCS3B01G243600 chr5B 96.330 109 2 2 467 574 429065322 429065429 7.480000e-41 178
32 TraesCS3B01G243600 chr5B 87.069 116 10 5 110 222 234087751 234087864 2.750000e-25 126
33 TraesCS3B01G243600 chrUn 96.330 109 2 2 467 574 341019498 341019391 7.480000e-41 178
34 TraesCS3B01G243600 chrUn 96.330 109 2 2 467 574 355920707 355920600 7.480000e-41 178
35 TraesCS3B01G243600 chrUn 96.296 108 3 1 467 573 362351142 362351035 2.690000e-40 176
36 TraesCS3B01G243600 chr5D 96.330 109 2 2 467 574 503254493 503254600 7.480000e-41 178
37 TraesCS3B01G243600 chr5A 96.330 109 2 2 467 574 482022295 482022188 7.480000e-41 178
38 TraesCS3B01G243600 chr2A 82.639 144 19 6 133 275 766474216 766474078 3.560000e-24 122
39 TraesCS3B01G243600 chr1D 78.090 178 32 7 136 311 211490923 211490751 3.580000e-19 106


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 TraesCS3B01G243600 chr3B 385141925 385144555 2630 True 4859.0 4859 100.0000 1 2631 1 chr3B.!!$R1 2630
1 TraesCS3B01G243600 chr3B 625214118 625214893 775 False 754.0 754 84.6740 1871 2630 1 chr3B.!!$F2 759
2 TraesCS3B01G243600 chr3A 384683930 384686658 2728 True 795.5 1598 92.6415 89 2631 4 chr3A.!!$R1 2542
3 TraesCS3B01G243600 chr3D 291954418 291954986 568 True 885.0 885 94.7370 2063 2631 1 chr3D.!!$R1 568
4 TraesCS3B01G243600 chr3D 291962720 291965040 2320 True 490.0 1066 93.3984 89 2073 5 chr3D.!!$R3 1984
5 TraesCS3B01G243600 chr2B 239883338 239884113 775 True 798.0 798 85.6960 1871 2630 1 chr2B.!!$R1 759
6 TraesCS3B01G243600 chr2B 592469467 592470242 775 True 787.0 787 85.4410 1871 2630 1 chr2B.!!$R2 759
7 TraesCS3B01G243600 chr2B 93788479 93789254 775 False 782.0 782 85.3130 1871 2630 1 chr2B.!!$F1 759
8 TraesCS3B01G243600 chr7A 512591967 512592754 787 True 787.0 787 85.2980 1871 2630 1 chr7A.!!$R1 759
9 TraesCS3B01G243600 chr7B 745364095 745364874 779 True 769.0 769 85.0440 1871 2630 1 chr7B.!!$R2 759
10 TraesCS3B01G243600 chr4A 243639075 243639850 775 True 765.0 765 84.9490 1871 2630 1 chr4A.!!$R1 759
11 TraesCS3B01G243600 chr4B 42273678 42274453 775 True 760.0 760 84.8210 1871 2630 1 chr4B.!!$R1 759
12 TraesCS3B01G243600 chr2D 100360334 100361108 774 False 752.0 752 84.6740 1871 2630 1 chr2D.!!$F1 759
13 TraesCS3B01G243600 chr2D 507300776 507301551 775 False 743.0 743 84.4190 1871 2630 1 chr2D.!!$F2 759
14 TraesCS3B01G243600 chr1A 485482531 485483306 775 True 743.0 743 84.4190 1871 2630 1 chr1A.!!$R1 759
15 TraesCS3B01G243600 chr4D 368915803 368916578 775 True 737.0 737 84.2910 1871 2630 1 chr4D.!!$R1 759
16 TraesCS3B01G243600 chr5B 391661903 391662681 778 True 734.0 734 84.2240 1871 2630 1 chr5B.!!$R1 759

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
75 76 0.618458 TGTTCATGAGGTGTAGGGGC 59.382 55.0 0.0 0.0 0.0 5.80 F
1174 1725 0.038251 CTGCGACAAGACCTGCTACA 60.038 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1927 0.164647 CTCGCGGTCTGCAAAAAGAG 59.835 55.0 6.13 0.0 46.97 2.85 R
2523 3212 0.311790 AACTTGCATCACTTGGTGCG 59.688 50.0 9.84 0.0 44.11 5.34 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
24 25 7.591006 CATGTTTGATCCCTGAAATTTTCTG 57.409 36.000 10.33 9.41 0.00 3.02
25 26 6.975196 TGTTTGATCCCTGAAATTTTCTGA 57.025 33.333 15.29 7.90 0.00 3.27
26 27 6.748132 TGTTTGATCCCTGAAATTTTCTGAC 58.252 36.000 15.29 6.32 0.00 3.51
27 28 6.550854 TGTTTGATCCCTGAAATTTTCTGACT 59.449 34.615 15.29 2.46 0.00 3.41
28 29 7.069826 TGTTTGATCCCTGAAATTTTCTGACTT 59.930 33.333 15.29 2.32 0.00 3.01
29 30 7.601705 TTGATCCCTGAAATTTTCTGACTTT 57.398 32.000 15.29 0.90 0.00 2.66
30 31 7.601705 TGATCCCTGAAATTTTCTGACTTTT 57.398 32.000 15.29 0.00 0.00 2.27
31 32 8.021898 TGATCCCTGAAATTTTCTGACTTTTT 57.978 30.769 15.29 0.00 0.00 1.94
55 56 9.695884 TTTTCTTGCAATTTTGTTCGAATTTAC 57.304 25.926 0.00 0.00 0.00 2.01
56 57 8.641499 TTCTTGCAATTTTGTTCGAATTTACT 57.359 26.923 0.00 0.00 0.00 2.24
57 58 8.060020 TCTTGCAATTTTGTTCGAATTTACTG 57.940 30.769 0.00 0.00 0.00 2.74
58 59 7.704472 TCTTGCAATTTTGTTCGAATTTACTGT 59.296 29.630 0.00 0.00 0.00 3.55
59 60 7.763172 TGCAATTTTGTTCGAATTTACTGTT 57.237 28.000 0.00 0.00 0.00 3.16
60 61 7.836512 TGCAATTTTGTTCGAATTTACTGTTC 58.163 30.769 0.00 0.00 0.00 3.18
61 62 7.489435 TGCAATTTTGTTCGAATTTACTGTTCA 59.511 29.630 0.00 0.00 0.00 3.18
62 63 8.487176 GCAATTTTGTTCGAATTTACTGTTCAT 58.513 29.630 0.00 0.00 0.00 2.57
63 64 9.782028 CAATTTTGTTCGAATTTACTGTTCATG 57.218 29.630 0.00 0.00 0.00 3.07
64 65 9.743057 AATTTTGTTCGAATTTACTGTTCATGA 57.257 25.926 0.00 0.00 0.00 3.07
65 66 8.781067 TTTTGTTCGAATTTACTGTTCATGAG 57.219 30.769 0.00 0.00 0.00 2.90
66 67 6.480524 TGTTCGAATTTACTGTTCATGAGG 57.519 37.500 0.00 0.00 0.00 3.86
67 68 5.995282 TGTTCGAATTTACTGTTCATGAGGT 59.005 36.000 0.00 0.00 0.00 3.85
68 69 6.073276 TGTTCGAATTTACTGTTCATGAGGTG 60.073 38.462 0.00 0.00 0.00 4.00
69 70 5.547465 TCGAATTTACTGTTCATGAGGTGT 58.453 37.500 0.00 0.00 0.00 4.16
70 71 6.693466 TCGAATTTACTGTTCATGAGGTGTA 58.307 36.000 0.00 0.00 0.00 2.90
71 72 6.811665 TCGAATTTACTGTTCATGAGGTGTAG 59.188 38.462 0.00 0.00 0.00 2.74
72 73 6.036083 CGAATTTACTGTTCATGAGGTGTAGG 59.964 42.308 0.00 0.00 0.00 3.18
73 74 4.819105 TTACTGTTCATGAGGTGTAGGG 57.181 45.455 0.00 0.00 0.00 3.53
74 75 1.909302 ACTGTTCATGAGGTGTAGGGG 59.091 52.381 0.00 0.00 0.00 4.79
75 76 0.618458 TGTTCATGAGGTGTAGGGGC 59.382 55.000 0.00 0.00 0.00 5.80
76 77 0.618458 GTTCATGAGGTGTAGGGGCA 59.382 55.000 0.00 0.00 0.00 5.36
77 78 0.618458 TTCATGAGGTGTAGGGGCAC 59.382 55.000 0.00 0.00 38.56 5.01
120 121 7.029563 GCAACTGAGTCGGATATTTTCAAAAT 58.970 34.615 5.81 0.02 0.00 1.82
223 224 8.862325 TTAGGCTTGTTCTTCAAAAGATATGA 57.138 30.769 0.00 0.00 37.38 2.15
224 225 7.765695 AGGCTTGTTCTTCAAAAGATATGAA 57.234 32.000 0.00 0.00 37.38 2.57
288 289 4.969196 ACTCACTGCCCACGCACG 62.969 66.667 0.00 0.00 41.12 5.34
321 322 7.996758 ACGAATCCTCTCCCCATAATAATAT 57.003 36.000 0.00 0.00 0.00 1.28
328 329 8.100791 TCCTCTCCCCATAATAATATTGAAACG 58.899 37.037 0.00 0.00 0.00 3.60
348 642 2.729882 CGGTCAGGTAAGAAAGACAACG 59.270 50.000 0.00 0.00 32.79 4.10
400 695 1.354506 GCGCTAGCCTGCATGAAAG 59.645 57.895 9.66 0.00 37.42 2.62
413 708 3.005684 TGCATGAAAGCAAACCGAATCTT 59.994 39.130 0.00 0.00 42.46 2.40
414 709 4.217334 TGCATGAAAGCAAACCGAATCTTA 59.783 37.500 0.00 0.00 42.46 2.10
415 710 5.160641 GCATGAAAGCAAACCGAATCTTAA 58.839 37.500 0.00 0.00 0.00 1.85
416 711 5.633182 GCATGAAAGCAAACCGAATCTTAAA 59.367 36.000 0.00 0.00 0.00 1.52
417 712 6.183360 GCATGAAAGCAAACCGAATCTTAAAG 60.183 38.462 0.00 0.00 0.00 1.85
418 713 6.385649 TGAAAGCAAACCGAATCTTAAAGT 57.614 33.333 0.00 0.00 0.00 2.66
419 714 7.499321 TGAAAGCAAACCGAATCTTAAAGTA 57.501 32.000 0.00 0.00 0.00 2.24
420 715 8.106247 TGAAAGCAAACCGAATCTTAAAGTAT 57.894 30.769 0.00 0.00 0.00 2.12
421 716 8.573035 TGAAAGCAAACCGAATCTTAAAGTATT 58.427 29.630 0.00 0.00 0.00 1.89
422 717 9.406828 GAAAGCAAACCGAATCTTAAAGTATTT 57.593 29.630 0.00 0.00 43.42 1.40
423 718 9.758651 AAAGCAAACCGAATCTTAAAGTATTTT 57.241 25.926 0.00 0.00 40.09 1.82
424 719 9.758651 AAGCAAACCGAATCTTAAAGTATTTTT 57.241 25.926 0.00 0.00 40.09 1.94
429 724 9.524496 AACCGAATCTTAAAGTATTTTTACCCT 57.476 29.630 0.00 0.00 40.09 4.34
430 725 9.524496 ACCGAATCTTAAAGTATTTTTACCCTT 57.476 29.630 0.00 0.00 40.09 3.95
439 734 7.940178 AAGTATTTTTACCCTTTCTTTTGCG 57.060 32.000 0.00 0.00 0.00 4.85
440 735 6.452242 AGTATTTTTACCCTTTCTTTTGCGG 58.548 36.000 0.00 0.00 0.00 5.69
441 736 3.737032 TTTTACCCTTTCTTTTGCGGG 57.263 42.857 0.00 0.00 42.53 6.13
442 737 2.660670 TTACCCTTTCTTTTGCGGGA 57.339 45.000 0.00 0.00 39.08 5.14
447 742 3.898741 ACCCTTTCTTTTGCGGGATAAAA 59.101 39.130 0.00 0.00 39.08 1.52
448 743 4.530553 ACCCTTTCTTTTGCGGGATAAAAT 59.469 37.500 0.00 0.00 39.08 1.82
450 745 6.040247 CCCTTTCTTTTGCGGGATAAAATAC 58.960 40.000 0.00 0.00 39.08 1.89
483 778 9.985730 CCTACGGTATATAAACATAGGTTTTCA 57.014 33.333 11.18 0.00 44.63 2.69
495 790 9.696917 AAACATAGGTTTTCATTGAATTCACTC 57.303 29.630 7.89 0.00 44.63 3.51
496 791 8.408043 ACATAGGTTTTCATTGAATTCACTCA 57.592 30.769 7.89 0.00 0.00 3.41
497 792 8.859090 ACATAGGTTTTCATTGAATTCACTCAA 58.141 29.630 7.89 0.00 39.56 3.02
498 793 9.865321 CATAGGTTTTCATTGAATTCACTCAAT 57.135 29.630 7.89 0.00 44.98 2.57
500 795 7.954835 AGGTTTTCATTGAATTCACTCAATCA 58.045 30.769 7.89 0.00 42.79 2.57
501 796 8.423349 AGGTTTTCATTGAATTCACTCAATCAA 58.577 29.630 7.89 0.00 42.79 2.57
502 797 9.211485 GGTTTTCATTGAATTCACTCAATCAAT 57.789 29.630 7.89 0.00 42.79 2.57
532 827 5.938438 GAAACAAGAGAGCTGTTTCATCT 57.062 39.130 18.47 0.00 46.10 2.90
533 828 6.311055 GAAACAAGAGAGCTGTTTCATCTT 57.689 37.500 18.47 0.71 46.10 2.40
534 829 6.705863 AAACAAGAGAGCTGTTTCATCTTT 57.294 33.333 0.00 0.00 30.99 2.52
535 830 5.686159 ACAAGAGAGCTGTTTCATCTTTG 57.314 39.130 0.00 0.00 0.00 2.77
536 831 5.128919 ACAAGAGAGCTGTTTCATCTTTGT 58.871 37.500 0.00 0.00 0.00 2.83
537 832 5.591877 ACAAGAGAGCTGTTTCATCTTTGTT 59.408 36.000 0.00 0.00 0.00 2.83
538 833 6.096001 ACAAGAGAGCTGTTTCATCTTTGTTT 59.904 34.615 0.00 0.00 0.00 2.83
539 834 6.705863 AGAGAGCTGTTTCATCTTTGTTTT 57.294 33.333 0.00 0.00 0.00 2.43
540 835 7.807977 AGAGAGCTGTTTCATCTTTGTTTTA 57.192 32.000 0.00 0.00 0.00 1.52
541 836 8.225603 AGAGAGCTGTTTCATCTTTGTTTTAA 57.774 30.769 0.00 0.00 0.00 1.52
542 837 8.686334 AGAGAGCTGTTTCATCTTTGTTTTAAA 58.314 29.630 0.00 0.00 0.00 1.52
543 838 8.862550 AGAGCTGTTTCATCTTTGTTTTAAAG 57.137 30.769 0.00 0.00 0.00 1.85
544 839 8.686334 AGAGCTGTTTCATCTTTGTTTTAAAGA 58.314 29.630 0.00 4.75 40.17 2.52
545 840 9.301153 GAGCTGTTTCATCTTTGTTTTAAAGAA 57.699 29.630 6.23 0.00 39.43 2.52
546 841 9.651913 AGCTGTTTCATCTTTGTTTTAAAGAAA 57.348 25.926 6.23 0.31 39.43 2.52
593 888 9.555727 AGATAAGACATGACTACTTCTCTAGAC 57.444 37.037 0.00 0.00 29.72 2.59
594 889 6.671614 AAGACATGACTACTTCTCTAGACG 57.328 41.667 0.00 0.00 0.00 4.18
595 890 5.979993 AGACATGACTACTTCTCTAGACGA 58.020 41.667 0.00 0.00 0.00 4.20
596 891 6.046593 AGACATGACTACTTCTCTAGACGAG 58.953 44.000 0.00 0.00 41.30 4.18
597 892 5.979993 ACATGACTACTTCTCTAGACGAGA 58.020 41.667 0.00 0.00 46.82 4.04
610 905 5.844004 TCTAGACGAGAATTAGCAAATCCC 58.156 41.667 0.00 0.00 0.00 3.85
615 910 7.110155 AGACGAGAATTAGCAAATCCCTTTAA 58.890 34.615 0.00 0.00 0.00 1.52
618 913 8.244113 ACGAGAATTAGCAAATCCCTTTAAAAG 58.756 33.333 0.00 0.00 0.00 2.27
626 921 7.436933 AGCAAATCCCTTTAAAAGAAACTCAG 58.563 34.615 0.00 0.00 0.00 3.35
646 941 2.668280 GCTCCAACGCAACGGTCTC 61.668 63.158 0.00 0.00 0.00 3.36
672 977 3.707793 GAGACGAGAGAGAGAGAGAGAC 58.292 54.545 0.00 0.00 0.00 3.36
683 988 5.045651 AGAGAGAGAGAGACAGTCTTCATCA 60.046 44.000 4.05 0.00 34.71 3.07
685 990 3.696051 AGAGAGAGACAGTCTTCATCAGC 59.304 47.826 4.05 1.43 34.71 4.26
686 991 2.423185 AGAGAGACAGTCTTCATCAGCG 59.577 50.000 4.05 0.00 34.71 5.18
698 1003 3.355626 TCATCAGCGAGAATCCTAACG 57.644 47.619 0.00 0.00 0.00 3.18
699 1004 2.688446 TCATCAGCGAGAATCCTAACGT 59.312 45.455 0.00 0.00 0.00 3.99
700 1005 3.130516 TCATCAGCGAGAATCCTAACGTT 59.869 43.478 5.88 5.88 0.00 3.99
701 1006 3.587797 TCAGCGAGAATCCTAACGTTT 57.412 42.857 5.91 0.00 0.00 3.60
702 1007 4.707030 TCAGCGAGAATCCTAACGTTTA 57.293 40.909 5.91 0.00 0.00 2.01
703 1008 5.258456 TCAGCGAGAATCCTAACGTTTAT 57.742 39.130 5.91 0.00 0.00 1.40
704 1009 5.279384 TCAGCGAGAATCCTAACGTTTATC 58.721 41.667 5.91 0.00 0.00 1.75
705 1010 4.444720 CAGCGAGAATCCTAACGTTTATCC 59.555 45.833 5.91 0.00 0.00 2.59
706 1011 4.341520 AGCGAGAATCCTAACGTTTATCCT 59.658 41.667 5.91 0.00 0.00 3.24
707 1012 5.048507 GCGAGAATCCTAACGTTTATCCTT 58.951 41.667 5.91 0.00 0.00 3.36
708 1013 5.522824 GCGAGAATCCTAACGTTTATCCTTT 59.477 40.000 5.91 0.00 0.00 3.11
709 1014 6.292221 GCGAGAATCCTAACGTTTATCCTTTC 60.292 42.308 5.91 3.43 0.00 2.62
710 1015 6.755141 CGAGAATCCTAACGTTTATCCTTTCA 59.245 38.462 5.91 0.00 0.00 2.69
711 1016 7.277098 CGAGAATCCTAACGTTTATCCTTTCAA 59.723 37.037 5.91 0.00 0.00 2.69
712 1017 8.857694 AGAATCCTAACGTTTATCCTTTCAAA 57.142 30.769 5.91 0.00 0.00 2.69
713 1018 9.292195 AGAATCCTAACGTTTATCCTTTCAAAA 57.708 29.630 5.91 0.00 0.00 2.44
714 1019 9.902196 GAATCCTAACGTTTATCCTTTCAAAAA 57.098 29.630 5.91 0.00 0.00 1.94
789 1095 2.358615 CGCCCTGCACAACTGCTA 60.359 61.111 0.00 0.00 44.57 3.49
807 1113 1.958902 TACCGGCGCCTATCCGTTTT 61.959 55.000 26.68 0.00 45.09 2.43
892 1392 1.518572 CGTACACGCACCCATCTCC 60.519 63.158 0.00 0.00 0.00 3.71
949 1497 2.307768 CCTCTCTATAAGACACCGCCA 58.692 52.381 0.00 0.00 0.00 5.69
950 1498 2.693591 CCTCTCTATAAGACACCGCCAA 59.306 50.000 0.00 0.00 0.00 4.52
1174 1725 0.038251 CTGCGACAAGACCTGCTACA 60.038 55.000 0.00 0.00 0.00 2.74
1266 1817 1.371558 GACTTCCTGCCACCGTCTT 59.628 57.895 0.00 0.00 0.00 3.01
1371 1927 1.787012 ACGACGATGTGGTGGTAAAC 58.213 50.000 0.00 0.00 0.00 2.01
1694 2316 3.057019 GACCAATCGATATGTAAGCGCA 58.943 45.455 11.47 0.00 0.00 6.09
1765 2392 7.011576 TGCTAATGGGTGTACACGTATTATTTG 59.988 37.037 22.87 17.20 0.00 2.32
1815 2443 4.321824 GCTACTTGTAACGGGAAGTTCTCT 60.322 45.833 0.31 0.00 43.06 3.10
1850 2478 4.024641 GTGTACGGGTTTGTTAAACTCAGG 60.025 45.833 5.30 0.00 42.06 3.86
1879 2523 4.218312 AGATTAAATTCAGTGGGCCATCC 58.782 43.478 10.70 0.00 0.00 3.51
1943 2588 2.157738 ACAAGGCTGCATTCTTGAGTC 58.842 47.619 25.98 0.28 41.94 3.36
1972 2617 2.892374 TGCACTAGATGGAATGTCACG 58.108 47.619 0.00 0.00 0.00 4.35
1978 2623 6.507900 CACTAGATGGAATGTCACGTATCTT 58.492 40.000 0.00 0.00 0.00 2.40
2003 2648 4.602995 GTTGAAAACCGCAATCAACTACA 58.397 39.130 9.86 0.00 45.86 2.74
2061 2707 7.497909 CCCACTCTATACGTTGGATTTAAACAT 59.502 37.037 3.23 0.00 0.00 2.71
2220 2887 1.686052 GTTGGAAATGTGGGCTGACAA 59.314 47.619 0.00 0.00 0.00 3.18
2323 3003 3.019564 GTGAATGAGAATGACAAGGGGG 58.980 50.000 0.00 0.00 0.00 5.40
2343 3023 4.065088 GGGATGGGAAAGCAAAGAAAAAC 58.935 43.478 0.00 0.00 0.00 2.43
2354 3039 4.513318 AGCAAAGAAAAACGAAGAGGAGAG 59.487 41.667 0.00 0.00 0.00 3.20
2395 3080 1.817357 TGCAGCTGTTCTTGATCCAG 58.183 50.000 16.64 0.00 0.00 3.86
2522 3211 5.179368 TGTTTGCAGAGTACAAAGCTATGTC 59.821 40.000 0.00 0.00 37.67 3.06
2523 3212 3.861840 TGCAGAGTACAAAGCTATGTCC 58.138 45.455 0.00 0.00 34.75 4.02
2601 3291 1.186200 GGGCAGGAAGGAAATTGGTC 58.814 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.330208 GTCAGAAAATTTCAGGGATCAAACATG 59.670 37.037 8.55 0.00 0.00 3.21
1 2 7.234166 AGTCAGAAAATTTCAGGGATCAAACAT 59.766 33.333 8.55 0.00 0.00 2.71
2 3 6.550854 AGTCAGAAAATTTCAGGGATCAAACA 59.449 34.615 8.55 0.00 0.00 2.83
3 4 6.986250 AGTCAGAAAATTTCAGGGATCAAAC 58.014 36.000 8.55 0.00 0.00 2.93
4 5 7.601705 AAGTCAGAAAATTTCAGGGATCAAA 57.398 32.000 8.55 0.00 0.00 2.69
5 6 7.601705 AAAGTCAGAAAATTTCAGGGATCAA 57.398 32.000 8.55 0.00 0.00 2.57
6 7 7.601705 AAAAGTCAGAAAATTTCAGGGATCA 57.398 32.000 8.55 0.00 0.00 2.92
29 30 9.695884 GTAAATTCGAACAAAATTGCAAGAAAA 57.304 25.926 4.94 0.00 0.00 2.29
30 31 9.092876 AGTAAATTCGAACAAAATTGCAAGAAA 57.907 25.926 4.94 0.00 0.00 2.52
31 32 8.538856 CAGTAAATTCGAACAAAATTGCAAGAA 58.461 29.630 4.94 0.35 0.00 2.52
32 33 7.704472 ACAGTAAATTCGAACAAAATTGCAAGA 59.296 29.630 4.94 0.00 0.00 3.02
33 34 7.840489 ACAGTAAATTCGAACAAAATTGCAAG 58.160 30.769 4.94 0.00 0.00 4.01
34 35 7.763172 ACAGTAAATTCGAACAAAATTGCAA 57.237 28.000 0.00 0.00 0.00 4.08
35 36 7.489435 TGAACAGTAAATTCGAACAAAATTGCA 59.511 29.630 0.00 0.00 0.00 4.08
36 37 7.836512 TGAACAGTAAATTCGAACAAAATTGC 58.163 30.769 0.00 0.00 0.00 3.56
37 38 9.782028 CATGAACAGTAAATTCGAACAAAATTG 57.218 29.630 0.00 0.00 0.00 2.32
38 39 9.743057 TCATGAACAGTAAATTCGAACAAAATT 57.257 25.926 0.00 0.00 0.00 1.82
39 40 9.398170 CTCATGAACAGTAAATTCGAACAAAAT 57.602 29.630 0.00 0.00 0.00 1.82
40 41 7.860373 CCTCATGAACAGTAAATTCGAACAAAA 59.140 33.333 0.00 0.00 0.00 2.44
41 42 7.012894 ACCTCATGAACAGTAAATTCGAACAAA 59.987 33.333 0.00 0.00 0.00 2.83
42 43 6.485313 ACCTCATGAACAGTAAATTCGAACAA 59.515 34.615 0.00 0.00 0.00 2.83
43 44 5.995282 ACCTCATGAACAGTAAATTCGAACA 59.005 36.000 0.00 0.00 0.00 3.18
44 45 6.073222 ACACCTCATGAACAGTAAATTCGAAC 60.073 38.462 0.00 0.00 0.00 3.95
45 46 5.995282 ACACCTCATGAACAGTAAATTCGAA 59.005 36.000 0.00 0.00 0.00 3.71
46 47 5.547465 ACACCTCATGAACAGTAAATTCGA 58.453 37.500 0.00 0.00 0.00 3.71
47 48 5.862924 ACACCTCATGAACAGTAAATTCG 57.137 39.130 0.00 0.00 0.00 3.34
48 49 6.316390 CCCTACACCTCATGAACAGTAAATTC 59.684 42.308 0.00 0.00 0.00 2.17
49 50 6.180472 CCCTACACCTCATGAACAGTAAATT 58.820 40.000 0.00 0.00 0.00 1.82
50 51 5.339200 CCCCTACACCTCATGAACAGTAAAT 60.339 44.000 0.00 0.00 0.00 1.40
51 52 4.019681 CCCCTACACCTCATGAACAGTAAA 60.020 45.833 0.00 0.00 0.00 2.01
52 53 3.517901 CCCCTACACCTCATGAACAGTAA 59.482 47.826 0.00 0.00 0.00 2.24
53 54 3.104512 CCCCTACACCTCATGAACAGTA 58.895 50.000 0.00 0.00 0.00 2.74
54 55 1.909302 CCCCTACACCTCATGAACAGT 59.091 52.381 0.00 0.00 0.00 3.55
55 56 1.407437 GCCCCTACACCTCATGAACAG 60.407 57.143 0.00 0.00 0.00 3.16
56 57 0.618458 GCCCCTACACCTCATGAACA 59.382 55.000 0.00 0.00 0.00 3.18
57 58 0.618458 TGCCCCTACACCTCATGAAC 59.382 55.000 0.00 0.00 0.00 3.18
58 59 0.618458 GTGCCCCTACACCTCATGAA 59.382 55.000 0.00 0.00 34.35 2.57
59 60 2.296920 GTGCCCCTACACCTCATGA 58.703 57.895 0.00 0.00 34.35 3.07
60 61 4.963878 GTGCCCCTACACCTCATG 57.036 61.111 0.00 0.00 34.35 3.07
72 73 4.256180 CATAGCTCCCGGGTGCCC 62.256 72.222 37.33 16.78 35.48 5.36
73 74 4.256180 CCATAGCTCCCGGGTGCC 62.256 72.222 37.33 22.60 35.48 5.01
74 75 3.161450 TCCATAGCTCCCGGGTGC 61.161 66.667 35.10 35.10 35.16 5.01
75 76 1.410850 ATGTCCATAGCTCCCGGGTG 61.411 60.000 22.86 20.53 0.00 4.61
76 77 1.074471 ATGTCCATAGCTCCCGGGT 60.074 57.895 22.86 3.24 0.00 5.28
77 78 1.372683 CATGTCCATAGCTCCCGGG 59.627 63.158 16.85 16.85 0.00 5.73
78 79 1.302033 GCATGTCCATAGCTCCCGG 60.302 63.158 0.00 0.00 0.00 5.73
79 80 0.179048 TTGCATGTCCATAGCTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
80 81 1.133976 AGTTGCATGTCCATAGCTCCC 60.134 52.381 0.00 0.00 0.00 4.30
81 82 1.945394 CAGTTGCATGTCCATAGCTCC 59.055 52.381 0.00 0.00 0.00 4.70
82 83 2.871022 CTCAGTTGCATGTCCATAGCTC 59.129 50.000 0.00 0.00 0.00 4.09
83 84 2.238144 ACTCAGTTGCATGTCCATAGCT 59.762 45.455 0.00 0.00 0.00 3.32
84 85 2.611292 GACTCAGTTGCATGTCCATAGC 59.389 50.000 0.00 0.00 0.00 2.97
85 86 2.862536 CGACTCAGTTGCATGTCCATAG 59.137 50.000 0.00 0.00 0.00 2.23
86 87 2.418609 CCGACTCAGTTGCATGTCCATA 60.419 50.000 0.00 0.00 0.00 2.74
87 88 1.676916 CCGACTCAGTTGCATGTCCAT 60.677 52.381 0.00 0.00 0.00 3.41
157 158 2.831526 TCGTGTTTCTCATGATGAGGGA 59.168 45.455 21.27 8.70 44.39 4.20
163 164 8.267620 TGTTTCATATTCGTGTTTCTCATGAT 57.732 30.769 0.00 0.00 41.08 2.45
167 168 8.402472 AGTTTTGTTTCATATTCGTGTTTCTCA 58.598 29.630 0.00 0.00 0.00 3.27
253 254 0.947180 GTCCCTCGTGCGTGCTTTTA 60.947 55.000 0.00 0.00 0.00 1.52
254 255 2.110213 TCCCTCGTGCGTGCTTTT 59.890 55.556 0.00 0.00 0.00 2.27
255 256 2.665185 GTCCCTCGTGCGTGCTTT 60.665 61.111 0.00 0.00 0.00 3.51
256 257 3.575351 GAGTCCCTCGTGCGTGCTT 62.575 63.158 0.00 0.00 0.00 3.91
288 289 0.179134 AGAGGATTCGTAGCACGCAC 60.179 55.000 4.15 0.00 42.21 5.34
292 293 0.389757 GGGGAGAGGATTCGTAGCAC 59.610 60.000 0.00 0.00 0.00 4.40
321 322 4.812626 GTCTTTCTTACCTGACCGTTTCAA 59.187 41.667 0.00 0.00 32.21 2.69
328 329 2.479275 GCGTTGTCTTTCTTACCTGACC 59.521 50.000 0.00 0.00 0.00 4.02
363 657 1.223187 CGGCGTGTTTACTCTTTGGT 58.777 50.000 0.00 0.00 0.00 3.67
393 688 6.863126 ACTTTAAGATTCGGTTTGCTTTCATG 59.137 34.615 0.00 0.00 0.00 3.07
413 708 9.465985 CGCAAAAGAAAGGGTAAAAATACTTTA 57.534 29.630 0.00 0.00 33.66 1.85
414 709 7.439955 CCGCAAAAGAAAGGGTAAAAATACTTT 59.560 33.333 0.00 0.00 35.99 2.66
415 710 6.926826 CCGCAAAAGAAAGGGTAAAAATACTT 59.073 34.615 0.00 0.00 0.00 2.24
416 711 6.452242 CCGCAAAAGAAAGGGTAAAAATACT 58.548 36.000 0.00 0.00 0.00 2.12
417 712 5.636121 CCCGCAAAAGAAAGGGTAAAAATAC 59.364 40.000 0.00 0.00 39.05 1.89
418 713 5.539193 TCCCGCAAAAGAAAGGGTAAAAATA 59.461 36.000 0.00 0.00 44.13 1.40
419 714 4.345547 TCCCGCAAAAGAAAGGGTAAAAAT 59.654 37.500 0.00 0.00 44.13 1.82
420 715 3.705072 TCCCGCAAAAGAAAGGGTAAAAA 59.295 39.130 0.00 0.00 44.13 1.94
421 716 3.297736 TCCCGCAAAAGAAAGGGTAAAA 58.702 40.909 0.00 0.00 44.13 1.52
422 717 2.946785 TCCCGCAAAAGAAAGGGTAAA 58.053 42.857 0.00 0.00 44.13 2.01
423 718 2.660670 TCCCGCAAAAGAAAGGGTAA 57.339 45.000 0.00 0.00 44.13 2.85
424 719 2.891191 ATCCCGCAAAAGAAAGGGTA 57.109 45.000 0.00 0.00 44.13 3.69
425 720 2.891191 TATCCCGCAAAAGAAAGGGT 57.109 45.000 0.00 0.00 44.13 4.34
426 721 4.529109 TTTTATCCCGCAAAAGAAAGGG 57.471 40.909 0.00 0.00 45.10 3.95
427 722 6.863275 AGTATTTTATCCCGCAAAAGAAAGG 58.137 36.000 0.00 0.00 0.00 3.11
428 723 8.757164 AAAGTATTTTATCCCGCAAAAGAAAG 57.243 30.769 0.00 0.00 31.62 2.62
469 764 9.696917 GAGTGAATTCAATGAAAACCTATGTTT 57.303 29.630 14.00 0.00 46.50 2.83
470 765 8.859090 TGAGTGAATTCAATGAAAACCTATGTT 58.141 29.630 14.00 0.00 35.82 2.71
471 766 8.408043 TGAGTGAATTCAATGAAAACCTATGT 57.592 30.769 14.00 0.00 0.00 2.29
472 767 9.865321 ATTGAGTGAATTCAATGAAAACCTATG 57.135 29.630 14.00 0.00 44.04 2.23
474 769 9.076781 TGATTGAGTGAATTCAATGAAAACCTA 57.923 29.630 14.00 0.00 45.30 3.08
475 770 7.954835 TGATTGAGTGAATTCAATGAAAACCT 58.045 30.769 14.00 1.71 45.30 3.50
476 771 8.592105 TTGATTGAGTGAATTCAATGAAAACC 57.408 30.769 14.00 5.95 45.30 3.27
510 805 5.938438 AGATGAAACAGCTCTCTTGTTTC 57.062 39.130 18.80 18.80 46.65 2.78
511 806 6.096001 ACAAAGATGAAACAGCTCTCTTGTTT 59.904 34.615 3.27 3.27 38.31 2.83
512 807 5.591877 ACAAAGATGAAACAGCTCTCTTGTT 59.408 36.000 0.00 0.00 0.00 2.83
513 808 5.128919 ACAAAGATGAAACAGCTCTCTTGT 58.871 37.500 0.00 0.00 0.00 3.16
514 809 5.686159 ACAAAGATGAAACAGCTCTCTTG 57.314 39.130 0.00 0.00 0.00 3.02
515 810 6.705863 AAACAAAGATGAAACAGCTCTCTT 57.294 33.333 0.00 0.00 0.00 2.85
516 811 6.705863 AAAACAAAGATGAAACAGCTCTCT 57.294 33.333 0.00 0.00 0.00 3.10
517 812 8.856490 TTTAAAACAAAGATGAAACAGCTCTC 57.144 30.769 0.00 0.00 0.00 3.20
518 813 8.686334 TCTTTAAAACAAAGATGAAACAGCTCT 58.314 29.630 0.00 0.00 31.86 4.09
519 814 8.856490 TCTTTAAAACAAAGATGAAACAGCTC 57.144 30.769 0.00 0.00 31.86 4.09
520 815 9.651913 TTTCTTTAAAACAAAGATGAAACAGCT 57.348 25.926 0.62 0.00 36.30 4.24
567 862 9.555727 GTCTAGAGAAGTAGTCATGTCTTATCT 57.444 37.037 16.60 16.60 40.91 1.98
568 863 8.492748 CGTCTAGAGAAGTAGTCATGTCTTATC 58.507 40.741 0.00 4.08 32.00 1.75
569 864 8.205512 TCGTCTAGAGAAGTAGTCATGTCTTAT 58.794 37.037 0.00 0.00 0.00 1.73
570 865 7.554211 TCGTCTAGAGAAGTAGTCATGTCTTA 58.446 38.462 0.00 0.00 0.00 2.10
571 866 6.408035 TCGTCTAGAGAAGTAGTCATGTCTT 58.592 40.000 0.00 0.00 0.00 3.01
572 867 5.979993 TCGTCTAGAGAAGTAGTCATGTCT 58.020 41.667 0.00 0.00 0.00 3.41
587 882 5.598830 AGGGATTTGCTAATTCTCGTCTAGA 59.401 40.000 0.00 0.00 0.00 2.43
588 883 5.848406 AGGGATTTGCTAATTCTCGTCTAG 58.152 41.667 0.00 0.00 0.00 2.43
589 884 5.871396 AGGGATTTGCTAATTCTCGTCTA 57.129 39.130 0.00 0.00 0.00 2.59
590 885 4.762289 AGGGATTTGCTAATTCTCGTCT 57.238 40.909 0.00 0.00 0.00 4.18
591 886 5.819825 AAAGGGATTTGCTAATTCTCGTC 57.180 39.130 0.00 0.00 0.00 4.20
592 887 7.696992 TTTAAAGGGATTTGCTAATTCTCGT 57.303 32.000 0.00 0.00 0.00 4.18
593 888 8.458843 TCTTTTAAAGGGATTTGCTAATTCTCG 58.541 33.333 4.77 0.00 0.00 4.04
598 893 9.929180 GAGTTTCTTTTAAAGGGATTTGCTAAT 57.071 29.630 4.77 0.00 0.00 1.73
610 905 4.024048 TGGAGCGCTGAGTTTCTTTTAAAG 60.024 41.667 18.48 0.00 0.00 1.85
615 910 1.604278 GTTGGAGCGCTGAGTTTCTTT 59.396 47.619 18.48 0.00 0.00 2.52
618 913 1.493311 CGTTGGAGCGCTGAGTTTC 59.507 57.895 18.48 0.00 0.00 2.78
672 977 3.122297 GGATTCTCGCTGATGAAGACTG 58.878 50.000 0.00 0.00 0.00 3.51
683 988 4.341520 AGGATAAACGTTAGGATTCTCGCT 59.658 41.667 0.00 0.00 0.00 4.93
685 990 6.755141 TGAAAGGATAAACGTTAGGATTCTCG 59.245 38.462 0.00 0.00 0.00 4.04
686 991 8.488651 TTGAAAGGATAAACGTTAGGATTCTC 57.511 34.615 0.00 0.00 0.00 2.87
797 1103 1.202031 GCGCACAAGGAAAACGGATAG 60.202 52.381 0.30 0.00 0.00 2.08
892 1392 1.405821 GACTCATGAGTGTCTACGGGG 59.594 57.143 32.50 0.54 42.66 5.73
1266 1817 3.459227 TGCCAATCTGATTACCTGGATCA 59.541 43.478 9.70 0.00 32.87 2.92
1371 1927 0.164647 CTCGCGGTCTGCAAAAAGAG 59.835 55.000 6.13 0.00 46.97 2.85
1471 2027 2.112815 GCCTAACGTGGTGGGCATC 61.113 63.158 7.48 0.00 43.59 3.91
1528 2084 3.272334 GCACGGACCGCATCATCC 61.272 66.667 15.39 0.00 0.00 3.51
1629 2251 2.733227 CGTACGCCGAGGTATTCTTGTT 60.733 50.000 0.52 0.00 39.56 2.83
1694 2316 2.671070 CCTCCGCACCTGGTGATT 59.329 61.111 30.23 0.00 35.23 2.57
1815 2443 7.784037 ACAAACCCGTACACTATATTGATACA 58.216 34.615 0.00 0.00 0.00 2.29
1850 2478 5.220796 GCCCACTGAATTTAATCTCCGTTAC 60.221 44.000 0.00 0.00 0.00 2.50
1903 2548 2.737252 GTCCACCTTTTCTAACTCAGCG 59.263 50.000 0.00 0.00 0.00 5.18
1943 2588 7.563020 ACATTCCATCTAGTGCATATATCCAG 58.437 38.462 0.00 0.00 0.00 3.86
1972 2617 7.247728 TGATTGCGGTTTTCAACATAAGATAC 58.752 34.615 0.00 0.00 0.00 2.24
2061 2707 4.835615 AGAGAGTACCAAGAGCTTTCTCAA 59.164 41.667 10.02 0.00 41.81 3.02
2220 2887 7.970061 GCCATGTATTACGCAAAATATCATCAT 59.030 33.333 0.00 0.00 0.00 2.45
2323 3003 4.616953 TCGTTTTTCTTTGCTTTCCCATC 58.383 39.130 0.00 0.00 0.00 3.51
2343 3023 3.249091 CATGTTCACACTCTCCTCTTCG 58.751 50.000 0.00 0.00 0.00 3.79
2354 3039 6.035435 TGCAACAAATACAAACATGTTCACAC 59.965 34.615 12.39 0.00 33.97 3.82
2438 3123 5.109210 TGTCTCCATTTAACTCAGCATACG 58.891 41.667 0.00 0.00 0.00 3.06
2522 3211 1.210931 CTTGCATCACTTGGTGCGG 59.789 57.895 9.84 1.94 44.11 5.69
2523 3212 0.311790 AACTTGCATCACTTGGTGCG 59.688 50.000 9.84 0.00 44.11 5.34
2601 3291 7.340487 ACTCTCAGCTTTTTATTTATCCAAGGG 59.660 37.037 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.