Multiple sequence alignment - TraesCS4B01G230600

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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 TraesCS4B01G230600 chr4B 100.000 2735 0 0 1 2735 481642187 481639453 0.000000e+00 5051.0
1 TraesCS4B01G230600 chr4D 93.047 1841 85 23 753 2580 391729492 391727682 0.000000e+00 2651.0
2 TraesCS4B01G230600 chr4D 88.406 621 58 9 1 611 414053783 414054399 0.000000e+00 736.0
3 TraesCS4B01G230600 chr4D 97.674 43 1 0 2580 2622 391727420 391727378 1.050000e-09 75.0
4 TraesCS4B01G230600 chr4A 94.526 1023 45 7 786 1800 73461670 73460651 0.000000e+00 1568.0
5 TraesCS4B01G230600 chr4A 94.928 690 24 4 1801 2482 73460607 73459921 0.000000e+00 1070.0
6 TraesCS4B01G230600 chr4A 94.444 144 8 0 2479 2622 73459810 73459667 3.540000e-54 222.0
7 TraesCS4B01G230600 chr4A 94.017 117 6 1 2620 2735 662882050 662881934 2.800000e-40 176.0
8 TraesCS4B01G230600 chr5B 91.100 618 44 7 1 617 451159646 451160253 0.000000e+00 826.0
9 TraesCS4B01G230600 chr5B 92.437 119 8 1 2618 2735 567933210 567933092 4.680000e-38 169.0
10 TraesCS4B01G230600 chr7D 88.710 620 56 11 1 607 475502809 475503427 0.000000e+00 745.0
11 TraesCS4B01G230600 chr7D 92.437 119 8 1 2612 2729 150359293 150359411 4.680000e-38 169.0
12 TraesCS4B01G230600 chr2B 85.106 611 74 15 1 601 474540887 474541490 2.330000e-170 608.0
13 TraesCS4B01G230600 chr2B 86.111 72 10 0 648 719 334438301 334438230 8.120000e-11 78.7
14 TraesCS4B01G230600 chr7B 91.344 439 36 2 1 439 222989103 222989539 1.400000e-167 599.0
15 TraesCS4B01G230600 chr7B 89.764 127 11 2 2611 2735 40703574 40703448 7.840000e-36 161.0
16 TraesCS4B01G230600 chr7B 81.308 107 13 2 619 718 89779144 89779250 2.260000e-11 80.5
17 TraesCS4B01G230600 chr7B 84.615 78 12 0 642 719 38968001 38967924 8.120000e-11 78.7
18 TraesCS4B01G230600 chr3A 84.491 619 65 24 2 607 50601393 50601993 1.410000e-162 582.0
19 TraesCS4B01G230600 chr3A 94.017 117 6 1 2620 2735 227483721 227483605 2.800000e-40 176.0
20 TraesCS4B01G230600 chr3A 81.553 103 17 2 619 719 400411260 400411362 1.750000e-12 84.2
21 TraesCS4B01G230600 chr3A 100.000 28 0 0 693 720 7716850 7716877 5.000000e-03 52.8
22 TraesCS4B01G230600 chr1B 84.279 617 74 18 2 607 173147928 173147324 5.080000e-162 580.0
23 TraesCS4B01G230600 chr1B 85.185 81 12 0 641 721 664809637 664809717 1.750000e-12 84.2
24 TraesCS4B01G230600 chr3D 84.117 617 75 21 2 607 126371414 126370810 2.360000e-160 575.0
25 TraesCS4B01G230600 chr3D 91.200 125 10 1 2612 2735 67437199 67437075 4.680000e-38 169.0
26 TraesCS4B01G230600 chr2A 82.759 609 92 13 2 607 212996180 212996778 5.190000e-147 531.0
27 TraesCS4B01G230600 chr2A 85.577 104 12 2 619 719 504067903 504067800 3.720000e-19 106.0
28 TraesCS4B01G230600 chr5D 93.220 118 8 0 2612 2729 76160215 76160332 1.010000e-39 174.0
29 TraesCS4B01G230600 chr7A 90.076 131 11 2 2607 2735 736384104 736383974 4.680000e-38 169.0
30 TraesCS4B01G230600 chr3B 90.076 131 7 6 2599 2729 93250653 93250777 6.060000e-37 165.0
31 TraesCS4B01G230600 chr1D 85.897 78 11 0 641 718 480382254 480382177 1.750000e-12 84.2
32 TraesCS4B01G230600 chr6B 81.250 80 13 1 641 718 132142494 132142573 2.270000e-06 63.9


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 TraesCS4B01G230600 chr4B 481639453 481642187 2734 True 5051.000000 5051 100.000000 1 2735 1 chr4B.!!$R1 2734
1 TraesCS4B01G230600 chr4D 391727378 391729492 2114 True 1363.000000 2651 95.360500 753 2622 2 chr4D.!!$R1 1869
2 TraesCS4B01G230600 chr4D 414053783 414054399 616 False 736.000000 736 88.406000 1 611 1 chr4D.!!$F1 610
3 TraesCS4B01G230600 chr4A 73459667 73461670 2003 True 953.333333 1568 94.632667 786 2622 3 chr4A.!!$R2 1836
4 TraesCS4B01G230600 chr5B 451159646 451160253 607 False 826.000000 826 91.100000 1 617 1 chr5B.!!$F1 616
5 TraesCS4B01G230600 chr7D 475502809 475503427 618 False 745.000000 745 88.710000 1 607 1 chr7D.!!$F2 606
6 TraesCS4B01G230600 chr2B 474540887 474541490 603 False 608.000000 608 85.106000 1 601 1 chr2B.!!$F1 600
7 TraesCS4B01G230600 chr3A 50601393 50601993 600 False 582.000000 582 84.491000 2 607 1 chr3A.!!$F2 605
8 TraesCS4B01G230600 chr1B 173147324 173147928 604 True 580.000000 580 84.279000 2 607 1 chr1B.!!$R1 605
9 TraesCS4B01G230600 chr3D 126370810 126371414 604 True 575.000000 575 84.117000 2 607 1 chr3D.!!$R2 605
10 TraesCS4B01G230600 chr2A 212996180 212996778 598 False 531.000000 531 82.759000 2 607 1 chr2A.!!$F1 605

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
523 561 0.033208 GCCTCCCCATCAACCATTGA 60.033 55.0 0.0 0.0 45.01 2.57 F
845 900 0.108567 GGCTCCGTGACTTTCTCCTC 60.109 60.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1600 0.469917 CCAGAATATCCGTGGGCACT 59.530 55.000 0.00 0.00 0.00 4.40 R
2495 2731 2.163815 AGTTACGCTTGCGTGTCTATCT 59.836 45.455 27.59 11.15 35.15 1.98 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
49 50 7.537715 TGCTTAATGACAGAATAAACACATGG 58.462 34.615 0.00 0.00 0.00 3.66
62 63 9.125026 GAATAAACACATGGGATCTATTGAACT 57.875 33.333 0.00 0.00 0.00 3.01
306 311 6.434965 TGGAGCATCTGAAATCAAAGAAATGA 59.565 34.615 0.00 0.00 33.73 2.57
395 400 9.897744 TCAAGTTAATCATGTTGAAAGCTAAAG 57.102 29.630 0.00 0.00 0.00 1.85
523 561 0.033208 GCCTCCCCATCAACCATTGA 60.033 55.000 0.00 0.00 45.01 2.57
526 564 3.377573 CCTCCCCATCAACCATTGAAAT 58.622 45.455 0.00 0.00 43.95 2.17
607 659 6.238648 ACCCTACTGTTCTATGGTCAAAAAG 58.761 40.000 0.00 0.00 0.00 2.27
611 663 8.454106 CCTACTGTTCTATGGTCAAAAAGATTG 58.546 37.037 0.00 0.00 0.00 2.67
612 664 7.823745 ACTGTTCTATGGTCAAAAAGATTGT 57.176 32.000 0.00 0.00 0.00 2.71
614 666 6.980593 TGTTCTATGGTCAAAAAGATTGTGG 58.019 36.000 0.00 0.00 0.00 4.17
616 668 7.286546 TGTTCTATGGTCAAAAAGATTGTGGAA 59.713 33.333 0.00 0.00 0.00 3.53
617 669 7.214467 TCTATGGTCAAAAAGATTGTGGAAC 57.786 36.000 0.00 0.00 37.35 3.62
618 670 4.664150 TGGTCAAAAAGATTGTGGAACC 57.336 40.909 0.00 0.00 34.36 3.62
619 671 3.067461 TGGTCAAAAAGATTGTGGAACCG 59.933 43.478 0.00 0.00 34.36 4.44
620 672 3.552068 GGTCAAAAAGATTGTGGAACCGG 60.552 47.826 0.00 0.00 34.36 5.28
621 673 2.035321 TCAAAAAGATTGTGGAACCGGC 59.965 45.455 0.00 0.00 34.36 6.13
622 674 0.966179 AAAAGATTGTGGAACCGGCC 59.034 50.000 0.00 0.00 34.36 6.13
623 675 0.112412 AAAGATTGTGGAACCGGCCT 59.888 50.000 0.00 0.00 34.36 5.19
624 676 0.988832 AAGATTGTGGAACCGGCCTA 59.011 50.000 0.00 0.00 34.36 3.93
625 677 0.252197 AGATTGTGGAACCGGCCTAC 59.748 55.000 0.00 2.15 34.36 3.18
626 678 0.746923 GATTGTGGAACCGGCCTACC 60.747 60.000 0.00 0.00 34.36 3.18
627 679 2.206182 ATTGTGGAACCGGCCTACCC 62.206 60.000 0.00 0.00 34.36 3.69
628 680 4.105553 GTGGAACCGGCCTACCCC 62.106 72.222 0.00 0.00 0.00 4.95
629 681 4.342086 TGGAACCGGCCTACCCCT 62.342 66.667 0.00 0.00 0.00 4.79
630 682 3.013327 GGAACCGGCCTACCCCTT 61.013 66.667 0.00 0.00 0.00 3.95
631 683 1.690283 GGAACCGGCCTACCCCTTA 60.690 63.158 0.00 0.00 0.00 2.69
632 684 1.273986 GGAACCGGCCTACCCCTTAA 61.274 60.000 0.00 0.00 0.00 1.85
633 685 0.620030 GAACCGGCCTACCCCTTAAA 59.380 55.000 0.00 0.00 0.00 1.52
634 686 1.004628 GAACCGGCCTACCCCTTAAAA 59.995 52.381 0.00 0.00 0.00 1.52
635 687 1.074766 ACCGGCCTACCCCTTAAAAA 58.925 50.000 0.00 0.00 0.00 1.94
636 688 1.642238 ACCGGCCTACCCCTTAAAAAT 59.358 47.619 0.00 0.00 0.00 1.82
637 689 2.304092 CCGGCCTACCCCTTAAAAATC 58.696 52.381 0.00 0.00 0.00 2.17
638 690 2.357361 CCGGCCTACCCCTTAAAAATCA 60.357 50.000 0.00 0.00 0.00 2.57
639 691 3.358118 CGGCCTACCCCTTAAAAATCAA 58.642 45.455 0.00 0.00 0.00 2.57
640 692 3.764972 CGGCCTACCCCTTAAAAATCAAA 59.235 43.478 0.00 0.00 0.00 2.69
641 693 4.142249 CGGCCTACCCCTTAAAAATCAAAG 60.142 45.833 0.00 0.00 0.00 2.77
642 694 4.161565 GGCCTACCCCTTAAAAATCAAAGG 59.838 45.833 0.00 0.00 41.69 3.11
650 702 6.928348 CCTTAAAAATCAAAGGGGGTAAGT 57.072 37.500 0.00 0.00 38.91 2.24
651 703 7.311092 CCTTAAAAATCAAAGGGGGTAAGTT 57.689 36.000 0.00 0.00 38.91 2.66
652 704 7.741785 CCTTAAAAATCAAAGGGGGTAAGTTT 58.258 34.615 0.00 0.00 38.91 2.66
653 705 7.659799 CCTTAAAAATCAAAGGGGGTAAGTTTG 59.340 37.037 0.00 0.00 38.91 2.93
654 706 6.569127 AAAAATCAAAGGGGGTAAGTTTGT 57.431 33.333 0.00 0.00 33.69 2.83
655 707 5.545063 AAATCAAAGGGGGTAAGTTTGTG 57.455 39.130 0.00 0.00 33.69 3.33
656 708 3.955524 TCAAAGGGGGTAAGTTTGTGA 57.044 42.857 0.00 0.00 33.69 3.58
657 709 4.463050 TCAAAGGGGGTAAGTTTGTGAT 57.537 40.909 0.00 0.00 33.69 3.06
658 710 4.810345 TCAAAGGGGGTAAGTTTGTGATT 58.190 39.130 0.00 0.00 33.69 2.57
659 711 4.586841 TCAAAGGGGGTAAGTTTGTGATTG 59.413 41.667 0.00 0.00 33.69 2.67
660 712 3.169512 AGGGGGTAAGTTTGTGATTGG 57.830 47.619 0.00 0.00 0.00 3.16
661 713 2.449345 AGGGGGTAAGTTTGTGATTGGT 59.551 45.455 0.00 0.00 0.00 3.67
662 714 2.823747 GGGGGTAAGTTTGTGATTGGTC 59.176 50.000 0.00 0.00 0.00 4.02
663 715 3.492337 GGGGTAAGTTTGTGATTGGTCA 58.508 45.455 0.00 0.00 0.00 4.02
664 716 3.892588 GGGGTAAGTTTGTGATTGGTCAA 59.107 43.478 0.00 0.00 35.80 3.18
665 717 4.526650 GGGGTAAGTTTGTGATTGGTCAAT 59.473 41.667 0.00 0.00 35.80 2.57
666 718 5.712917 GGGGTAAGTTTGTGATTGGTCAATA 59.287 40.000 0.00 0.00 35.80 1.90
667 719 6.127730 GGGGTAAGTTTGTGATTGGTCAATAG 60.128 42.308 0.00 0.00 35.80 1.73
668 720 6.657541 GGGTAAGTTTGTGATTGGTCAATAGA 59.342 38.462 0.00 0.00 35.80 1.98
669 721 7.339466 GGGTAAGTTTGTGATTGGTCAATAGAT 59.661 37.037 0.00 0.00 35.80 1.98
670 722 8.184192 GGTAAGTTTGTGATTGGTCAATAGATG 58.816 37.037 0.00 0.00 35.80 2.90
671 723 8.946085 GTAAGTTTGTGATTGGTCAATAGATGA 58.054 33.333 0.00 0.00 35.80 2.92
672 724 8.408043 AAGTTTGTGATTGGTCAATAGATGAA 57.592 30.769 0.00 0.00 40.50 2.57
673 725 8.408043 AGTTTGTGATTGGTCAATAGATGAAA 57.592 30.769 0.00 0.00 40.50 2.69
674 726 8.859090 AGTTTGTGATTGGTCAATAGATGAAAA 58.141 29.630 0.00 0.00 40.50 2.29
675 727 9.474920 GTTTGTGATTGGTCAATAGATGAAAAA 57.525 29.630 0.00 0.00 40.50 1.94
698 750 7.891498 AAAGTCTGTAAAACCCTGTATTTGT 57.109 32.000 0.00 0.00 0.00 2.83
699 751 7.891498 AAGTCTGTAAAACCCTGTATTTGTT 57.109 32.000 0.00 0.00 0.00 2.83
700 752 7.891498 AGTCTGTAAAACCCTGTATTTGTTT 57.109 32.000 0.00 0.00 33.86 2.83
701 753 7.712797 AGTCTGTAAAACCCTGTATTTGTTTG 58.287 34.615 0.00 0.00 32.85 2.93
702 754 7.340999 AGTCTGTAAAACCCTGTATTTGTTTGT 59.659 33.333 0.00 0.00 32.85 2.83
703 755 8.623030 GTCTGTAAAACCCTGTATTTGTTTGTA 58.377 33.333 0.00 0.00 32.85 2.41
704 756 9.357161 TCTGTAAAACCCTGTATTTGTTTGTAT 57.643 29.630 0.00 0.00 32.85 2.29
705 757 9.405587 CTGTAAAACCCTGTATTTGTTTGTATG 57.594 33.333 0.00 0.00 32.85 2.39
706 758 8.915036 TGTAAAACCCTGTATTTGTTTGTATGT 58.085 29.630 0.00 0.00 32.85 2.29
707 759 9.401873 GTAAAACCCTGTATTTGTTTGTATGTC 57.598 33.333 0.00 0.00 32.85 3.06
708 760 7.833285 AAACCCTGTATTTGTTTGTATGTCT 57.167 32.000 0.00 0.00 31.41 3.41
709 761 8.927675 AAACCCTGTATTTGTTTGTATGTCTA 57.072 30.769 0.00 0.00 31.41 2.59
710 762 8.561738 AACCCTGTATTTGTTTGTATGTCTAG 57.438 34.615 0.00 0.00 0.00 2.43
711 763 6.598064 ACCCTGTATTTGTTTGTATGTCTAGC 59.402 38.462 0.00 0.00 0.00 3.42
712 764 6.597672 CCCTGTATTTGTTTGTATGTCTAGCA 59.402 38.462 0.00 0.00 0.00 3.49
713 765 7.283127 CCCTGTATTTGTTTGTATGTCTAGCAT 59.717 37.037 5.25 5.25 41.42 3.79
714 766 8.677300 CCTGTATTTGTTTGTATGTCTAGCATT 58.323 33.333 5.22 0.00 38.94 3.56
719 771 9.979578 ATTTGTTTGTATGTCTAGCATTTTTGA 57.020 25.926 5.22 0.00 38.94 2.69
720 772 9.979578 TTTGTTTGTATGTCTAGCATTTTTGAT 57.020 25.926 5.22 0.00 38.94 2.57
731 783 9.278734 GTCTAGCATTTTTGATAAAAGTAGTGC 57.721 33.333 0.00 0.00 36.73 4.40
732 784 9.008965 TCTAGCATTTTTGATAAAAGTAGTGCA 57.991 29.630 0.00 0.00 37.70 4.57
733 785 7.873739 AGCATTTTTGATAAAAGTAGTGCAC 57.126 32.000 9.40 9.40 37.70 4.57
734 786 7.661040 AGCATTTTTGATAAAAGTAGTGCACT 58.339 30.769 25.12 25.12 37.70 4.40
735 787 7.809806 AGCATTTTTGATAAAAGTAGTGCACTC 59.190 33.333 25.56 15.02 37.70 3.51
736 788 7.201266 GCATTTTTGATAAAAGTAGTGCACTCG 60.201 37.037 25.56 0.00 36.36 4.18
737 789 4.921470 TTGATAAAAGTAGTGCACTCGC 57.079 40.909 25.56 17.49 36.04 5.03
738 790 7.521423 ATTTTTGATAAAAGTAGTGCACTCGCA 60.521 33.333 25.56 2.37 40.19 5.10
747 799 3.202923 TGCACTCGCACGTATTTGA 57.797 47.368 0.00 0.00 45.36 2.69
748 800 1.067693 TGCACTCGCACGTATTTGAG 58.932 50.000 0.00 0.00 45.36 3.02
749 801 1.336424 TGCACTCGCACGTATTTGAGA 60.336 47.619 11.11 0.00 45.36 3.27
750 802 1.724623 GCACTCGCACGTATTTGAGAA 59.275 47.619 11.11 0.00 38.36 2.87
751 803 2.222596 GCACTCGCACGTATTTGAGAAG 60.223 50.000 11.11 5.82 38.36 2.85
752 804 3.242518 CACTCGCACGTATTTGAGAAGA 58.757 45.455 11.11 0.00 32.81 2.87
753 805 3.673338 CACTCGCACGTATTTGAGAAGAA 59.327 43.478 11.11 0.00 32.81 2.52
754 806 4.149922 CACTCGCACGTATTTGAGAAGAAA 59.850 41.667 11.11 0.00 32.81 2.52
755 807 4.748102 ACTCGCACGTATTTGAGAAGAAAA 59.252 37.500 11.11 0.00 32.81 2.29
756 808 5.235616 ACTCGCACGTATTTGAGAAGAAAAA 59.764 36.000 11.11 0.00 32.81 1.94
784 836 0.803768 CTTGTGCACCGGATCTCTCG 60.804 60.000 15.69 0.00 0.00 4.04
832 887 1.165907 TTGTGCTTCACTTGGCTCCG 61.166 55.000 0.00 0.00 35.11 4.63
844 899 0.832135 TGGCTCCGTGACTTTCTCCT 60.832 55.000 0.00 0.00 0.00 3.69
845 900 0.108567 GGCTCCGTGACTTTCTCCTC 60.109 60.000 0.00 0.00 0.00 3.71
907 973 1.749634 GCTCTACGGCCTTCTAGAACA 59.250 52.381 0.00 0.00 0.00 3.18
935 1001 2.101582 CCCCTTCCATAACAGAGTCGAG 59.898 54.545 0.00 0.00 0.00 4.04
991 1057 1.461559 CCTCCGATCTATACCCCGAC 58.538 60.000 0.00 0.00 0.00 4.79
1048 1114 1.300233 CCTAGCGGCGTCAATCTCC 60.300 63.158 9.37 0.00 0.00 3.71
1059 1125 0.698238 TCAATCTCCCCAACCCACAG 59.302 55.000 0.00 0.00 0.00 3.66
1113 1183 4.029809 CCGGACCACACCTTCCCC 62.030 72.222 0.00 0.00 0.00 4.81
1116 1186 2.603652 GGACCACACCTTCCCCCTC 61.604 68.421 0.00 0.00 0.00 4.30
1302 1372 3.467226 CGCCCCTTCGCCTTCCTA 61.467 66.667 0.00 0.00 0.00 2.94
1500 1570 3.438087 ACCTCTTCAATTTCATGCAGTCG 59.562 43.478 0.00 0.00 0.00 4.18
1621 1691 5.998454 TCTGAAAAGCTTTGACTTCTGAG 57.002 39.130 13.54 0.00 0.00 3.35
1642 1712 4.856509 AGACCAAAGCTTTAGGTATTCCC 58.143 43.478 24.25 15.58 35.36 3.97
1650 1720 5.983608 AGCTTTAGGTATTCCCTCTCCTAT 58.016 41.667 0.00 0.00 44.81 2.57
1693 1763 1.742308 TCTTAGGTTCCTTGGGTGCT 58.258 50.000 0.00 0.00 0.00 4.40
1726 1797 5.293814 CAGGAATGCTTAGTCTCATTGAGTG 59.706 44.000 13.23 0.00 33.49 3.51
1776 1847 1.823169 TACAAGGGCGACACCACCTC 61.823 60.000 0.00 0.00 42.05 3.85
1829 1943 4.017808 ACCTCTTAGTTCGTCAGCTATGT 58.982 43.478 0.00 0.00 0.00 2.29
1849 1963 7.912250 GCTATGTGATCTGGTGTTAATTTTCAG 59.088 37.037 0.00 0.00 0.00 3.02
1911 2025 1.695114 TATGCCCCGGTGAGATGTGG 61.695 60.000 0.00 0.00 0.00 4.17
1915 2029 1.517832 CCCGGTGAGATGTGGACTC 59.482 63.158 0.00 0.00 35.26 3.36
2181 2295 2.105821 TGCAAATATAACGCCCTAGCCT 59.894 45.455 0.00 0.00 34.57 4.58
2423 2545 1.782752 CCACCATGACCCCTCCATATT 59.217 52.381 0.00 0.00 0.00 1.28
2495 2731 3.256631 GGACTTACTAACGGAGAACCACA 59.743 47.826 0.00 0.00 35.59 4.17
2625 3123 9.841295 TTCCAACATAAATTATACAGTACTCCC 57.159 33.333 0.00 0.00 0.00 4.30
2626 3124 9.220906 TCCAACATAAATTATACAGTACTCCCT 57.779 33.333 0.00 0.00 0.00 4.20
2627 3125 9.490379 CCAACATAAATTATACAGTACTCCCTC 57.510 37.037 0.00 0.00 0.00 4.30
2630 3128 9.435570 ACATAAATTATACAGTACTCCCTCTGT 57.564 33.333 0.00 0.00 45.21 3.41
2631 3129 9.915629 CATAAATTATACAGTACTCCCTCTGTC 57.084 37.037 0.00 0.00 42.77 3.51
2632 3130 6.980416 AATTATACAGTACTCCCTCTGTCC 57.020 41.667 0.00 0.00 42.77 4.02
2633 3131 2.414994 TACAGTACTCCCTCTGTCCG 57.585 55.000 0.00 0.00 42.77 4.79
2634 3132 0.697079 ACAGTACTCCCTCTGTCCGA 59.303 55.000 0.00 0.00 40.28 4.55
2635 3133 1.075050 ACAGTACTCCCTCTGTCCGAA 59.925 52.381 0.00 0.00 40.28 4.30
2636 3134 2.168496 CAGTACTCCCTCTGTCCGAAA 58.832 52.381 0.00 0.00 0.00 3.46
2637 3135 2.561419 CAGTACTCCCTCTGTCCGAAAA 59.439 50.000 0.00 0.00 0.00 2.29
2638 3136 3.195825 CAGTACTCCCTCTGTCCGAAAAT 59.804 47.826 0.00 0.00 0.00 1.82
2639 3137 4.401519 CAGTACTCCCTCTGTCCGAAAATA 59.598 45.833 0.00 0.00 0.00 1.40
2640 3138 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
2641 3139 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
2642 3140 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
2643 3141 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2644 3142 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2645 3143 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2646 3144 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2647 3145 5.178797 CCTCTGTCCGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
2648 3146 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
2649 3147 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
2650 3148 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
2651 3149 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
2652 3150 7.227711 TCTGTCCGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
2653 3151 7.881142 TGTCCGAAAATACTTGTCATCAAAAT 58.119 30.769 0.00 0.00 32.87 1.82
2654 3152 7.807433 TGTCCGAAAATACTTGTCATCAAAATG 59.193 33.333 0.00 0.00 32.87 2.32
2655 3153 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2656 3154 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2657 3155 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2670 3168 9.814899 TCATCAAAATGGATAAAAATTATGCGT 57.185 25.926 0.00 0.00 33.42 5.24
2678 3176 8.958119 TGGATAAAAATTATGCGTCTAGAACT 57.042 30.769 0.00 0.00 0.00 3.01
2691 3189 9.900710 ATGCGTCTAGAACTAAAATACATCTAG 57.099 33.333 0.00 0.00 40.46 2.43
2692 3190 9.117183 TGCGTCTAGAACTAAAATACATCTAGA 57.883 33.333 6.70 6.70 43.71 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 6.513066 GCATGCTCTTTCAGTTCAATAGATCC 60.513 42.308 11.37 0.00 0.00 3.36
62 63 3.682696 AGTCAAGATGCATGCTCTTTCA 58.317 40.909 22.06 13.28 30.60 2.69
306 311 6.888632 GCAAGGTATCCCATCAAATATCATCT 59.111 38.462 0.00 0.00 0.00 2.90
378 383 5.942236 AGAGATGCTTTAGCTTTCAACATGA 59.058 36.000 0.00 0.00 42.66 3.07
387 392 4.383989 CCTCCTTCAGAGATGCTTTAGCTT 60.384 45.833 0.00 0.00 46.50 3.74
395 400 0.473326 ATGCCCTCCTTCAGAGATGC 59.527 55.000 0.00 0.00 46.50 3.91
607 659 0.746923 GGTAGGCCGGTTCCACAATC 60.747 60.000 1.90 0.00 0.00 2.67
611 663 4.105553 GGGGTAGGCCGGTTCCAC 62.106 72.222 1.90 0.00 34.97 4.02
612 664 2.474133 TAAGGGGTAGGCCGGTTCCA 62.474 60.000 1.90 0.00 34.97 3.53
614 666 0.620030 TTTAAGGGGTAGGCCGGTTC 59.380 55.000 1.90 0.00 34.97 3.62
616 668 1.074766 TTTTTAAGGGGTAGGCCGGT 58.925 50.000 1.90 0.00 34.97 5.28
617 669 2.304092 GATTTTTAAGGGGTAGGCCGG 58.696 52.381 0.00 0.00 34.97 6.13
618 670 3.007473 TGATTTTTAAGGGGTAGGCCG 57.993 47.619 0.00 0.00 34.97 6.13
619 671 4.161565 CCTTTGATTTTTAAGGGGTAGGCC 59.838 45.833 0.00 0.00 37.78 5.19
620 672 5.339008 CCTTTGATTTTTAAGGGGTAGGC 57.661 43.478 0.00 0.00 37.78 3.93
627 679 6.928348 ACTTACCCCCTTTGATTTTTAAGG 57.072 37.500 0.00 0.00 40.50 2.69
628 680 8.208224 ACAAACTTACCCCCTTTGATTTTTAAG 58.792 33.333 0.00 0.00 0.00 1.85
629 681 7.988028 CACAAACTTACCCCCTTTGATTTTTAA 59.012 33.333 0.00 0.00 0.00 1.52
630 682 7.344871 TCACAAACTTACCCCCTTTGATTTTTA 59.655 33.333 0.00 0.00 0.00 1.52
631 683 6.157123 TCACAAACTTACCCCCTTTGATTTTT 59.843 34.615 0.00 0.00 0.00 1.94
632 684 5.663556 TCACAAACTTACCCCCTTTGATTTT 59.336 36.000 0.00 0.00 0.00 1.82
633 685 5.212745 TCACAAACTTACCCCCTTTGATTT 58.787 37.500 0.00 0.00 0.00 2.17
634 686 4.810345 TCACAAACTTACCCCCTTTGATT 58.190 39.130 0.00 0.00 0.00 2.57
635 687 4.463050 TCACAAACTTACCCCCTTTGAT 57.537 40.909 0.00 0.00 0.00 2.57
636 688 3.955524 TCACAAACTTACCCCCTTTGA 57.044 42.857 0.00 0.00 0.00 2.69
637 689 4.262420 CCAATCACAAACTTACCCCCTTTG 60.262 45.833 0.00 0.00 0.00 2.77
638 690 3.901222 CCAATCACAAACTTACCCCCTTT 59.099 43.478 0.00 0.00 0.00 3.11
639 691 3.116900 ACCAATCACAAACTTACCCCCTT 60.117 43.478 0.00 0.00 0.00 3.95
640 692 2.449345 ACCAATCACAAACTTACCCCCT 59.551 45.455 0.00 0.00 0.00 4.79
641 693 2.823747 GACCAATCACAAACTTACCCCC 59.176 50.000 0.00 0.00 0.00 5.40
642 694 3.492337 TGACCAATCACAAACTTACCCC 58.508 45.455 0.00 0.00 0.00 4.95
643 695 5.722021 ATTGACCAATCACAAACTTACCC 57.278 39.130 0.00 0.00 33.38 3.69
644 696 7.681939 TCTATTGACCAATCACAAACTTACC 57.318 36.000 0.00 0.00 33.38 2.85
645 697 8.946085 TCATCTATTGACCAATCACAAACTTAC 58.054 33.333 0.00 0.00 33.38 2.34
646 698 9.513906 TTCATCTATTGACCAATCACAAACTTA 57.486 29.630 0.00 0.00 33.38 2.24
647 699 8.408043 TTCATCTATTGACCAATCACAAACTT 57.592 30.769 0.00 0.00 33.38 2.66
648 700 8.408043 TTTCATCTATTGACCAATCACAAACT 57.592 30.769 0.00 0.00 33.38 2.66
649 701 9.474920 TTTTTCATCTATTGACCAATCACAAAC 57.525 29.630 0.00 0.00 33.38 2.93
672 724 8.755028 ACAAATACAGGGTTTTACAGACTTTTT 58.245 29.630 0.00 0.00 0.00 1.94
673 725 8.301252 ACAAATACAGGGTTTTACAGACTTTT 57.699 30.769 0.00 0.00 0.00 2.27
674 726 7.891498 ACAAATACAGGGTTTTACAGACTTT 57.109 32.000 0.00 0.00 0.00 2.66
675 727 7.891498 AACAAATACAGGGTTTTACAGACTT 57.109 32.000 0.00 0.00 0.00 3.01
676 728 7.340999 ACAAACAAATACAGGGTTTTACAGACT 59.659 33.333 0.00 0.00 32.79 3.24
677 729 7.485810 ACAAACAAATACAGGGTTTTACAGAC 58.514 34.615 0.00 0.00 32.79 3.51
678 730 7.648039 ACAAACAAATACAGGGTTTTACAGA 57.352 32.000 0.00 0.00 32.79 3.41
679 731 9.405587 CATACAAACAAATACAGGGTTTTACAG 57.594 33.333 0.00 0.00 32.79 2.74
680 732 8.915036 ACATACAAACAAATACAGGGTTTTACA 58.085 29.630 0.00 0.00 32.79 2.41
681 733 9.401873 GACATACAAACAAATACAGGGTTTTAC 57.598 33.333 0.00 0.00 32.79 2.01
682 734 9.357161 AGACATACAAACAAATACAGGGTTTTA 57.643 29.630 0.00 0.00 32.79 1.52
683 735 8.245195 AGACATACAAACAAATACAGGGTTTT 57.755 30.769 0.00 0.00 32.79 2.43
684 736 7.833285 AGACATACAAACAAATACAGGGTTT 57.167 32.000 0.00 0.00 35.27 3.27
685 737 7.120726 GCTAGACATACAAACAAATACAGGGTT 59.879 37.037 0.00 0.00 0.00 4.11
686 738 6.598064 GCTAGACATACAAACAAATACAGGGT 59.402 38.462 0.00 0.00 0.00 4.34
687 739 6.597672 TGCTAGACATACAAACAAATACAGGG 59.402 38.462 0.00 0.00 0.00 4.45
688 740 7.609760 TGCTAGACATACAAACAAATACAGG 57.390 36.000 0.00 0.00 0.00 4.00
693 745 9.979578 TCAAAAATGCTAGACATACAAACAAAT 57.020 25.926 0.00 0.00 38.34 2.32
694 746 9.979578 ATCAAAAATGCTAGACATACAAACAAA 57.020 25.926 0.00 0.00 38.34 2.83
705 757 9.278734 GCACTACTTTTATCAAAAATGCTAGAC 57.721 33.333 0.00 0.00 35.47 2.59
706 758 9.008965 TGCACTACTTTTATCAAAAATGCTAGA 57.991 29.630 0.00 0.00 37.58 2.43
707 759 9.065871 GTGCACTACTTTTATCAAAAATGCTAG 57.934 33.333 10.32 0.00 37.58 3.42
708 760 8.792633 AGTGCACTACTTTTATCAAAAATGCTA 58.207 29.630 20.16 0.00 37.58 3.49
709 761 7.661040 AGTGCACTACTTTTATCAAAAATGCT 58.339 30.769 20.16 0.00 37.58 3.79
710 762 7.201266 CGAGTGCACTACTTTTATCAAAAATGC 60.201 37.037 21.73 0.00 40.53 3.56
711 763 7.201266 GCGAGTGCACTACTTTTATCAAAAATG 60.201 37.037 21.73 0.00 40.53 2.32
712 764 6.801862 GCGAGTGCACTACTTTTATCAAAAAT 59.198 34.615 21.73 0.00 40.53 1.82
713 765 6.140110 GCGAGTGCACTACTTTTATCAAAAA 58.860 36.000 21.73 0.00 40.53 1.94
714 766 5.685841 GCGAGTGCACTACTTTTATCAAAA 58.314 37.500 21.73 0.00 40.53 2.44
715 767 5.277601 GCGAGTGCACTACTTTTATCAAA 57.722 39.130 21.73 0.00 40.53 2.69
716 768 4.921470 GCGAGTGCACTACTTTTATCAA 57.079 40.909 21.73 0.00 40.53 2.57
730 782 1.346365 TCTCAAATACGTGCGAGTGC 58.654 50.000 0.00 0.00 43.20 4.40
731 783 3.242518 TCTTCTCAAATACGTGCGAGTG 58.757 45.455 0.00 0.00 0.00 3.51
732 784 3.570926 TCTTCTCAAATACGTGCGAGT 57.429 42.857 0.00 0.00 0.00 4.18
733 785 4.903638 TTTCTTCTCAAATACGTGCGAG 57.096 40.909 0.00 0.00 0.00 5.03
734 786 5.660629 TTTTTCTTCTCAAATACGTGCGA 57.339 34.783 0.00 0.00 0.00 5.10
754 806 2.415357 CGGTGCACAAGTGACAGTTTTT 60.415 45.455 20.43 0.00 0.00 1.94
755 807 1.132262 CGGTGCACAAGTGACAGTTTT 59.868 47.619 20.43 0.00 0.00 2.43
756 808 0.732571 CGGTGCACAAGTGACAGTTT 59.267 50.000 20.43 0.00 0.00 2.66
757 809 1.095228 CCGGTGCACAAGTGACAGTT 61.095 55.000 20.43 0.00 0.00 3.16
758 810 1.523711 CCGGTGCACAAGTGACAGT 60.524 57.895 20.43 0.00 0.00 3.55
759 811 0.603707 ATCCGGTGCACAAGTGACAG 60.604 55.000 20.43 0.00 0.00 3.51
760 812 0.602638 GATCCGGTGCACAAGTGACA 60.603 55.000 20.43 0.00 0.00 3.58
761 813 0.320771 AGATCCGGTGCACAAGTGAC 60.321 55.000 20.43 5.19 0.00 3.67
762 814 0.037326 GAGATCCGGTGCACAAGTGA 60.037 55.000 20.43 9.14 0.00 3.41
763 815 0.036952 AGAGATCCGGTGCACAAGTG 60.037 55.000 20.43 4.90 0.00 3.16
764 816 0.247736 GAGAGATCCGGTGCACAAGT 59.752 55.000 20.43 0.60 0.00 3.16
784 836 2.109126 GTGCCAGCTTCGTGGATCC 61.109 63.158 4.20 4.20 40.44 3.36
812 864 1.032014 GGAGCCAAGTGAAGCACAAA 58.968 50.000 0.00 0.00 36.74 2.83
814 866 1.597854 CGGAGCCAAGTGAAGCACA 60.598 57.895 0.00 0.00 36.74 4.57
877 943 3.812019 CGTAGAGCGTGCCCGTCT 61.812 66.667 0.00 0.00 36.15 4.18
907 973 1.082194 TGTTATGGAAGGGGGAGGAGT 59.918 52.381 0.00 0.00 0.00 3.85
935 1001 0.179000 AAGGAGGTGATGGCGATGTC 59.821 55.000 0.00 0.00 0.00 3.06
1530 1600 0.469917 CCAGAATATCCGTGGGCACT 59.530 55.000 0.00 0.00 0.00 4.40
1642 1712 6.723298 ACCAATACACTGAGAATAGGAGAG 57.277 41.667 0.00 0.00 0.00 3.20
1693 1763 7.093068 TGAGACTAAGCATTCCTGTACCAATTA 60.093 37.037 0.00 0.00 0.00 1.40
1776 1847 3.449737 TCACGATCTTAAACTACCAGGGG 59.550 47.826 0.00 0.00 0.00 4.79
1829 1943 7.581213 AACACTGAAAATTAACACCAGATCA 57.419 32.000 0.00 0.00 0.00 2.92
1849 1963 2.639751 GTCATGAACTCGCACAAACAC 58.360 47.619 0.00 0.00 0.00 3.32
2111 2225 8.651589 ATCTAATAGGTCCTCGAATCATACAA 57.348 34.615 0.00 0.00 0.00 2.41
2121 2235 5.692613 ACGAAGAATCTAATAGGTCCTCG 57.307 43.478 0.00 9.67 0.00 4.63
2181 2295 9.899661 ATACACACTAGGCACTAATCAAATTTA 57.100 29.630 0.00 0.00 42.17 1.40
2340 2462 4.746309 TCTGCATGGGCCACCTGC 62.746 66.667 22.31 22.31 39.69 4.85
2423 2545 7.873719 TGTTTCTTGAATGGTTTAGTTCAGA 57.126 32.000 0.00 0.00 35.91 3.27
2495 2731 2.163815 AGTTACGCTTGCGTGTCTATCT 59.836 45.455 27.59 11.15 35.15 1.98
2622 3120 3.581332 ACAAGTATTTTCGGACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2623 3121 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2624 3122 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
2625 3123 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
2626 3124 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
2627 3125 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
2628 3126 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
2629 3127 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2630 3128 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2631 3129 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
2632 3130 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
2644 3142 9.814899 ACGCATAATTTTTATCCATTTTGATGA 57.185 25.926 0.00 0.00 0.00 2.92
2652 3150 9.561069 AGTTCTAGACGCATAATTTTTATCCAT 57.439 29.630 0.00 0.00 0.00 3.41
2653 3151 8.958119 AGTTCTAGACGCATAATTTTTATCCA 57.042 30.769 0.00 0.00 0.00 3.41
2665 3163 9.900710 CTAGATGTATTTTAGTTCTAGACGCAT 57.099 33.333 0.00 0.00 38.66 4.73
2666 3164 9.117183 TCTAGATGTATTTTAGTTCTAGACGCA 57.883 33.333 0.00 0.00 39.75 5.24


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

AutoCloner maintained by Alex Coulton.