Multiple sequence alignment - TraesCS3B01G129300

Loading Multiple Alignment...

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 TraesCS3B01G129300 chr3B 100.000 3026 0 0 1 3026 109948435 109945410 0 5589
1 TraesCS3B01G129300 chr3B 91.420 676 49 4 4 670 101251948 101251273 0 918
2 TraesCS3B01G129300 chr3B 90.639 673 54 4 7 670 39602740 39603412 0 885
3 TraesCS3B01G129300 chr3A 92.575 2101 97 26 820 2895 77476316 77474250 0 2961
4 TraesCS3B01G129300 chr3D 90.413 2274 114 41 786 3025 66344920 66342717 0 2896
5 TraesCS3B01G129300 chr4D 92.899 676 40 3 1 670 297210122 297209449 0 976
6 TraesCS3B01G129300 chr5B 91.272 676 49 5 4 670 125264806 125264132 0 913
7 TraesCS3B01G129300 chr5B 90.801 674 47 7 7 670 692442112 692442780 0 887
8 TraesCS3B01G129300 chr5A 91.233 673 45 7 7 670 196311636 196312303 0 904
9 TraesCS3B01G129300 chr5A 90.923 672 53 3 7 670 617223398 617222727 0 896
10 TraesCS3B01G129300 chr5D 89.816 707 49 9 1 692 275204862 275204164 0 885
11 TraesCS3B01G129300 chr7D 91.465 621 43 5 1 612 549660134 549660753 0 845


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 TraesCS3B01G129300 chr3B 109945410 109948435 3025 True 5589 5589 100.000 1 3026 1 chr3B.!!$R2 3025
1 TraesCS3B01G129300 chr3B 101251273 101251948 675 True 918 918 91.420 4 670 1 chr3B.!!$R1 666
2 TraesCS3B01G129300 chr3B 39602740 39603412 672 False 885 885 90.639 7 670 1 chr3B.!!$F1 663
3 TraesCS3B01G129300 chr3A 77474250 77476316 2066 True 2961 2961 92.575 820 2895 1 chr3A.!!$R1 2075
4 TraesCS3B01G129300 chr3D 66342717 66344920 2203 True 2896 2896 90.413 786 3025 1 chr3D.!!$R1 2239
5 TraesCS3B01G129300 chr4D 297209449 297210122 673 True 976 976 92.899 1 670 1 chr4D.!!$R1 669
6 TraesCS3B01G129300 chr5B 125264132 125264806 674 True 913 913 91.272 4 670 1 chr5B.!!$R1 666
7 TraesCS3B01G129300 chr5B 692442112 692442780 668 False 887 887 90.801 7 670 1 chr5B.!!$F1 663
8 TraesCS3B01G129300 chr5A 196311636 196312303 667 False 904 904 91.233 7 670 1 chr5A.!!$F1 663
9 TraesCS3B01G129300 chr5A 617222727 617223398 671 True 896 896 90.923 7 670 1 chr5A.!!$R1 663
10 TraesCS3B01G129300 chr5D 275204164 275204862 698 True 885 885 89.816 1 692 1 chr5D.!!$R1 691
11 TraesCS3B01G129300 chr7D 549660134 549660753 619 False 845 845 91.465 1 612 1 chr7D.!!$F1 611

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
707 733 0.037046 TAGTCCGACGAAAAAGCCCC 60.037 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2633 2682 0.324614 AATGCAGGTCGACATGTCCA 59.675 50.0 28.62 20.03 0.0 4.02 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
53 58 3.425713 CACATCCACGCGCTGCTT 61.426 61.111 5.73 0.00 0.00 3.91
56 61 4.704833 ATCCACGCGCTGCTTGGT 62.705 61.111 19.75 9.31 46.17 3.67
91 97 1.296392 CACAATCCTCACGCCCAGA 59.704 57.895 0.00 0.00 0.00 3.86
132 140 2.979813 GCTTTTGGTGCGTCACATTTAG 59.020 45.455 11.20 5.25 35.86 1.85
133 141 3.304391 GCTTTTGGTGCGTCACATTTAGA 60.304 43.478 11.20 0.00 35.86 2.10
166 174 3.305676 CCCATTTTACCGTGTTTGCATGA 60.306 43.478 0.00 0.00 33.58 3.07
254 264 8.435931 AAATTAGAACTGAGGGCCTTTTAAAT 57.564 30.769 7.89 3.12 0.00 1.40
256 266 7.849322 TTAGAACTGAGGGCCTTTTAAATTT 57.151 32.000 7.89 0.00 0.00 1.82
312 322 5.914635 GCAGAATTTTTGTTTGTCTGATCGA 59.085 36.000 3.25 0.00 38.37 3.59
341 352 3.845178 TGGTGCTGATTTACGTACTGAG 58.155 45.455 0.00 0.00 0.00 3.35
408 419 6.589830 ATTACTAACTGCTGATACTTTGCG 57.410 37.500 0.00 0.00 0.00 4.85
431 442 5.277974 CGTCAGTGATTTCAATTCTGTTGGT 60.278 40.000 0.00 0.00 0.00 3.67
441 452 6.139679 TCAATTCTGTTGGTCCTCCTTAAT 57.860 37.500 0.00 0.00 34.23 1.40
453 464 5.458215 GGTCCTCCTTAATATTGCTTGGGAT 60.458 44.000 0.00 0.00 0.00 3.85
524 539 7.013464 TGTGGATTTGTGACTAATTAACGGTTT 59.987 33.333 0.00 0.00 0.00 3.27
582 597 6.425721 GGGTATTGCATCGCTTGTACTTATAA 59.574 38.462 0.00 0.00 0.00 0.98
589 604 9.051679 TGCATCGCTTGTACTTATAATAAATGT 57.948 29.630 0.00 0.00 0.00 2.71
624 641 8.354426 TCATATGTTTCAATATGTGCCTGAATG 58.646 33.333 1.90 0.00 40.15 2.67
672 698 5.071115 ACATGGCTTACTTTTGGCCTTTTTA 59.929 36.000 3.32 0.00 45.45 1.52
681 707 1.898902 TGGCCTTTTTAGCGCAACTA 58.101 45.000 11.47 0.00 0.00 2.24
692 718 7.464830 TTTTAGCGCAACTAATCATCTAGTC 57.535 36.000 11.47 0.00 40.55 2.59
693 719 3.983741 AGCGCAACTAATCATCTAGTCC 58.016 45.455 11.47 0.00 30.67 3.85
694 720 2.726760 GCGCAACTAATCATCTAGTCCG 59.273 50.000 0.30 0.00 30.67 4.79
695 721 3.550233 GCGCAACTAATCATCTAGTCCGA 60.550 47.826 0.30 0.00 32.59 4.55
696 722 3.975670 CGCAACTAATCATCTAGTCCGAC 59.024 47.826 0.00 0.00 32.59 4.79
697 723 3.975670 GCAACTAATCATCTAGTCCGACG 59.024 47.826 0.00 0.00 30.67 5.12
698 724 4.261072 GCAACTAATCATCTAGTCCGACGA 60.261 45.833 0.00 0.00 30.67 4.20
699 725 5.732528 GCAACTAATCATCTAGTCCGACGAA 60.733 44.000 0.00 0.00 30.67 3.85
700 726 6.263344 CAACTAATCATCTAGTCCGACGAAA 58.737 40.000 0.00 0.00 30.67 3.46
701 727 6.446781 ACTAATCATCTAGTCCGACGAAAA 57.553 37.500 0.00 0.00 0.00 2.29
702 728 6.860080 ACTAATCATCTAGTCCGACGAAAAA 58.140 36.000 0.00 0.00 0.00 1.94
703 729 6.973474 ACTAATCATCTAGTCCGACGAAAAAG 59.027 38.462 0.00 0.00 0.00 2.27
704 730 3.508762 TCATCTAGTCCGACGAAAAAGC 58.491 45.455 0.00 0.00 0.00 3.51
705 731 2.358939 TCTAGTCCGACGAAAAAGCC 57.641 50.000 0.00 0.00 0.00 4.35
706 732 1.067354 TCTAGTCCGACGAAAAAGCCC 60.067 52.381 0.00 0.00 0.00 5.19
707 733 0.037046 TAGTCCGACGAAAAAGCCCC 60.037 55.000 0.00 0.00 0.00 5.80
708 734 1.598685 GTCCGACGAAAAAGCCCCA 60.599 57.895 0.00 0.00 0.00 4.96
709 735 1.598685 TCCGACGAAAAAGCCCCAC 60.599 57.895 0.00 0.00 0.00 4.61
710 736 2.622962 CCGACGAAAAAGCCCCACC 61.623 63.158 0.00 0.00 0.00 4.61
711 737 2.951458 GACGAAAAAGCCCCACCG 59.049 61.111 0.00 0.00 0.00 4.94
712 738 1.895231 GACGAAAAAGCCCCACCGT 60.895 57.895 0.00 0.00 0.00 4.83
713 739 2.125202 GACGAAAAAGCCCCACCGTG 62.125 60.000 0.00 0.00 0.00 4.94
714 740 1.894756 CGAAAAAGCCCCACCGTGA 60.895 57.895 0.00 0.00 0.00 4.35
715 741 1.852067 CGAAAAAGCCCCACCGTGAG 61.852 60.000 0.00 0.00 0.00 3.51
716 742 2.142357 GAAAAAGCCCCACCGTGAGC 62.142 60.000 0.00 2.70 0.00 4.26
733 759 4.735132 CGGCCGTCAGCGAGGAAA 62.735 66.667 19.50 0.00 45.17 3.13
734 760 2.815647 GGCCGTCAGCGAGGAAAG 60.816 66.667 0.00 0.00 45.17 2.62
735 761 2.261671 GCCGTCAGCGAGGAAAGA 59.738 61.111 0.00 0.00 41.33 2.52
736 762 1.807573 GCCGTCAGCGAGGAAAGAG 60.808 63.158 0.00 0.00 41.33 2.85
737 763 1.883732 CCGTCAGCGAGGAAAGAGA 59.116 57.895 0.00 0.00 41.33 3.10
738 764 0.243907 CCGTCAGCGAGGAAAGAGAA 59.756 55.000 0.00 0.00 41.33 2.87
739 765 1.336887 CCGTCAGCGAGGAAAGAGAAA 60.337 52.381 0.00 0.00 41.33 2.52
740 766 1.721926 CGTCAGCGAGGAAAGAGAAAC 59.278 52.381 0.00 0.00 41.33 2.78
741 767 2.608261 CGTCAGCGAGGAAAGAGAAACT 60.608 50.000 0.00 0.00 41.33 2.66
742 768 2.734079 GTCAGCGAGGAAAGAGAAACTG 59.266 50.000 0.00 0.00 0.00 3.16
743 769 2.365617 TCAGCGAGGAAAGAGAAACTGT 59.634 45.455 0.00 0.00 0.00 3.55
744 770 2.734079 CAGCGAGGAAAGAGAAACTGTC 59.266 50.000 0.00 0.00 32.34 3.51
745 771 1.721926 GCGAGGAAAGAGAAACTGTCG 59.278 52.381 0.00 0.00 33.85 4.35
746 772 2.862921 GCGAGGAAAGAGAAACTGTCGT 60.863 50.000 0.00 0.00 33.85 4.34
747 773 3.381949 CGAGGAAAGAGAAACTGTCGTT 58.618 45.455 0.00 0.00 33.85 3.85
748 774 3.182572 CGAGGAAAGAGAAACTGTCGTTG 59.817 47.826 0.00 0.00 33.85 4.10
749 775 4.369182 GAGGAAAGAGAAACTGTCGTTGA 58.631 43.478 0.00 0.00 33.85 3.18
750 776 4.766375 AGGAAAGAGAAACTGTCGTTGAA 58.234 39.130 0.00 0.00 33.85 2.69
751 777 5.183228 AGGAAAGAGAAACTGTCGTTGAAA 58.817 37.500 0.00 0.00 33.85 2.69
752 778 5.064834 AGGAAAGAGAAACTGTCGTTGAAAC 59.935 40.000 0.00 0.00 33.85 2.78
753 779 5.064834 GGAAAGAGAAACTGTCGTTGAAACT 59.935 40.000 0.00 0.00 33.85 2.66
754 780 5.720261 AAGAGAAACTGTCGTTGAAACTC 57.280 39.130 0.00 0.00 32.65 3.01
755 781 3.797256 AGAGAAACTGTCGTTGAAACTCG 59.203 43.478 0.00 0.00 32.65 4.18
756 782 3.518590 AGAAACTGTCGTTGAAACTCGT 58.481 40.909 0.00 0.00 32.65 4.18
757 783 3.550678 AGAAACTGTCGTTGAAACTCGTC 59.449 43.478 0.00 0.00 32.65 4.20
758 784 1.474017 ACTGTCGTTGAAACTCGTCG 58.526 50.000 0.00 0.00 0.00 5.12
759 785 1.202222 ACTGTCGTTGAAACTCGTCGT 60.202 47.619 0.00 0.00 0.00 4.34
760 786 1.850441 CTGTCGTTGAAACTCGTCGTT 59.150 47.619 0.00 0.00 37.47 3.85
761 787 1.847999 TGTCGTTGAAACTCGTCGTTC 59.152 47.619 0.00 0.00 33.90 3.95
762 788 1.188791 GTCGTTGAAACTCGTCGTTCC 59.811 52.381 0.00 0.00 33.90 3.62
763 789 1.066002 TCGTTGAAACTCGTCGTTCCT 59.934 47.619 0.00 0.00 33.90 3.36
764 790 1.856597 CGTTGAAACTCGTCGTTCCTT 59.143 47.619 0.00 0.00 33.90 3.36
765 791 2.097541 CGTTGAAACTCGTCGTTCCTTC 60.098 50.000 0.00 0.00 33.90 3.46
766 792 3.121544 GTTGAAACTCGTCGTTCCTTCT 58.878 45.455 0.00 0.00 33.90 2.85
767 793 4.293415 GTTGAAACTCGTCGTTCCTTCTA 58.707 43.478 0.00 0.00 33.90 2.10
768 794 3.893720 TGAAACTCGTCGTTCCTTCTAC 58.106 45.455 0.00 0.00 33.90 2.59
769 795 2.608467 AACTCGTCGTTCCTTCTACG 57.392 50.000 0.00 0.00 40.23 3.51
770 796 0.167689 ACTCGTCGTTCCTTCTACGC 59.832 55.000 0.00 0.00 38.81 4.42
771 797 0.447011 CTCGTCGTTCCTTCTACGCT 59.553 55.000 0.00 0.00 38.81 5.07
772 798 1.662629 CTCGTCGTTCCTTCTACGCTA 59.337 52.381 0.00 0.00 38.81 4.26
773 799 1.394917 TCGTCGTTCCTTCTACGCTAC 59.605 52.381 0.00 0.00 38.81 3.58
774 800 1.396301 CGTCGTTCCTTCTACGCTACT 59.604 52.381 0.00 0.00 38.81 2.57
775 801 2.536529 CGTCGTTCCTTCTACGCTACTC 60.537 54.545 0.00 0.00 38.81 2.59
776 802 2.677337 GTCGTTCCTTCTACGCTACTCT 59.323 50.000 0.00 0.00 38.81 3.24
777 803 3.126686 GTCGTTCCTTCTACGCTACTCTT 59.873 47.826 0.00 0.00 38.81 2.85
778 804 4.331168 GTCGTTCCTTCTACGCTACTCTTA 59.669 45.833 0.00 0.00 38.81 2.10
779 805 5.007528 GTCGTTCCTTCTACGCTACTCTTAT 59.992 44.000 0.00 0.00 38.81 1.73
780 806 6.201806 GTCGTTCCTTCTACGCTACTCTTATA 59.798 42.308 0.00 0.00 38.81 0.98
781 807 6.763135 TCGTTCCTTCTACGCTACTCTTATAA 59.237 38.462 0.00 0.00 38.81 0.98
782 808 7.280876 TCGTTCCTTCTACGCTACTCTTATAAA 59.719 37.037 0.00 0.00 38.81 1.40
783 809 7.912250 CGTTCCTTCTACGCTACTCTTATAAAA 59.088 37.037 0.00 0.00 31.73 1.52
784 810 9.747293 GTTCCTTCTACGCTACTCTTATAAAAT 57.253 33.333 0.00 0.00 0.00 1.82
860 886 2.040606 TCCTCTACACCCAGCCCC 59.959 66.667 0.00 0.00 0.00 5.80
882 908 0.685660 GGACGTTTCTTCCTCCCAGT 59.314 55.000 0.00 0.00 0.00 4.00
894 920 1.517242 CTCCCAGTGTTGTTCAGAGC 58.483 55.000 0.00 0.00 0.00 4.09
942 969 4.688413 GTCAACTCAGTCACTTTCTCCATC 59.312 45.833 0.00 0.00 0.00 3.51
986 1015 2.936498 CAATCTCCATTAACGCGAGGTT 59.064 45.455 15.93 0.00 42.75 3.50
1552 1590 3.549900 TTCAGCAGCGTGGCCATCA 62.550 57.895 9.72 0.00 0.00 3.07
1557 1595 1.947013 CAGCGTGGCCATCATGATC 59.053 57.895 9.72 0.00 34.35 2.92
1641 1679 4.431131 ATGCCCAGGGACGCCAAG 62.431 66.667 10.89 0.00 0.00 3.61
1698 1736 4.123506 TCAAGTCAAAGCACGTTGATGTA 58.876 39.130 2.43 0.00 39.61 2.29
1830 1868 2.028020 GTCGTTCTTGGATGAGAAGGGT 60.028 50.000 7.28 0.00 40.27 4.34
1842 1880 5.414144 GGATGAGAAGGGTTTTCTGAAGAAG 59.586 44.000 0.00 0.00 35.21 2.85
1854 1892 2.316067 TCTGAAGAAGGATGGGAGGAGA 59.684 50.000 0.00 0.00 0.00 3.71
1864 1902 2.047179 GGAGGAGAACACCGTGGC 60.047 66.667 3.03 0.00 34.73 5.01
2034 2072 5.357878 GGATCACAAGATTTGAAGGCACATA 59.642 40.000 0.00 0.00 33.72 2.29
2043 2081 7.710896 AGATTTGAAGGCACATAATTTCTAGC 58.289 34.615 0.00 0.00 0.00 3.42
2098 2136 1.144708 TGGTTTTGAGAGGATGCACCA 59.855 47.619 7.86 0.00 42.04 4.17
2234 2272 1.993956 TTGCCATTGTGGTTACTGCT 58.006 45.000 0.00 0.00 40.46 4.24
2257 2295 5.781210 TTATTGGTGTCACAAGCAAATGA 57.219 34.783 5.12 0.00 40.62 2.57
2266 2304 4.035558 GTCACAAGCAAATGAGTGAACTGA 59.964 41.667 0.00 0.00 42.03 3.41
2362 2405 9.685276 TTGATAAATTTATCCTCTCTGAGCAAA 57.315 29.630 27.53 12.88 38.98 3.68
2365 2408 9.692325 ATAAATTTATCCTCTCTGAGCAAAGTT 57.308 29.630 4.81 3.88 0.00 2.66
2391 2434 1.117994 TGTGCAGCCACATTTTTCCA 58.882 45.000 0.00 0.00 46.51 3.53
2420 2463 6.703607 CCACTTGGATATCTTGTCATAGTGTC 59.296 42.308 2.05 0.00 37.39 3.67
2451 2494 9.332502 TCTGACTAACTGACAGTATATCTCTTC 57.667 37.037 8.91 0.00 39.03 2.87
2525 2570 4.506271 CCATGCTTAATCAGTAGGGATGCT 60.506 45.833 0.00 0.00 41.35 3.79
2533 2578 0.252696 AGTAGGGATGCTGGTGGACA 60.253 55.000 0.00 0.00 0.00 4.02
2535 2580 0.839277 TAGGGATGCTGGTGGACATG 59.161 55.000 0.00 0.00 0.00 3.21
2538 2583 2.043652 ATGCTGGTGGACATGCCC 60.044 61.111 0.00 0.00 34.97 5.36
2540 2585 4.722700 GCTGGTGGACATGCCCGT 62.723 66.667 0.00 0.00 34.97 5.28
2544 2589 3.118454 GTGGACATGCCCGTCGTG 61.118 66.667 0.00 0.00 36.73 4.35
2557 2602 1.653115 GTCGTGTCCGTGTCTGTCT 59.347 57.895 0.00 0.00 35.01 3.41
2562 2607 3.295273 TCCGTGTCTGTCTGCGCT 61.295 61.111 9.73 0.00 0.00 5.92
2586 2635 5.163405 TGGACCAAGATGTACTAATCTCTGC 60.163 44.000 0.00 0.00 35.83 4.26
2596 2645 6.878317 TGTACTAATCTCTGCTGCTGTAATT 58.122 36.000 0.00 7.59 0.00 1.40
2619 2668 4.801147 TCGTGCTAATGCTGAAATGATC 57.199 40.909 0.00 0.00 40.48 2.92
2623 2672 5.643664 GTGCTAATGCTGAAATGATCAACA 58.356 37.500 0.00 0.00 38.44 3.33
2628 2677 2.483877 TGCTGAAATGATCAACACGGAC 59.516 45.455 0.00 0.00 37.67 4.79
2629 2678 2.744202 GCTGAAATGATCAACACGGACT 59.256 45.455 0.00 0.00 37.67 3.85
2630 2679 3.181516 GCTGAAATGATCAACACGGACTC 60.182 47.826 0.00 0.00 37.67 3.36
2631 2680 2.993220 TGAAATGATCAACACGGACTCG 59.007 45.455 0.00 0.00 37.50 4.18
2632 2681 2.010145 AATGATCAACACGGACTCGG 57.990 50.000 0.00 0.00 41.39 4.63
2633 2682 0.895530 ATGATCAACACGGACTCGGT 59.104 50.000 0.00 0.00 41.39 4.69
2634 2683 0.038618 TGATCAACACGGACTCGGTG 60.039 55.000 13.68 13.68 41.39 4.94
2635 2684 0.736325 GATCAACACGGACTCGGTGG 60.736 60.000 18.13 4.70 41.39 4.61
2636 2685 1.183030 ATCAACACGGACTCGGTGGA 61.183 55.000 18.13 9.10 41.39 4.02
2637 2686 1.663702 CAACACGGACTCGGTGGAC 60.664 63.158 18.13 0.00 41.39 4.02
2638 2687 2.129146 AACACGGACTCGGTGGACA 61.129 57.895 18.13 0.00 41.39 4.02
2639 2688 1.469335 AACACGGACTCGGTGGACAT 61.469 55.000 18.13 2.51 41.39 3.06
2640 2689 1.446099 CACGGACTCGGTGGACATG 60.446 63.158 8.53 0.00 41.39 3.21
2641 2690 1.906824 ACGGACTCGGTGGACATGT 60.907 57.895 0.00 0.00 41.39 3.21
2642 2691 1.153823 CGGACTCGGTGGACATGTC 60.154 63.158 17.91 17.91 0.00 3.06
2643 2692 1.153823 GGACTCGGTGGACATGTCG 60.154 63.158 19.33 8.98 0.00 4.35
2644 2693 1.592400 GGACTCGGTGGACATGTCGA 61.592 60.000 19.33 13.33 0.00 4.20
2645 2694 0.456312 GACTCGGTGGACATGTCGAC 60.456 60.000 27.34 27.34 37.55 4.20
2649 2698 3.876300 GTGGACATGTCGACCTGC 58.124 61.111 25.61 12.27 33.05 4.85
2650 2699 1.005037 GTGGACATGTCGACCTGCA 60.005 57.895 25.61 12.08 33.05 4.41
2651 2700 0.391661 GTGGACATGTCGACCTGCAT 60.392 55.000 25.61 2.38 33.05 3.96
2652 2701 0.324614 TGGACATGTCGACCTGCATT 59.675 50.000 19.33 1.67 0.00 3.56
2658 2707 2.890808 TGTCGACCTGCATTCCTATC 57.109 50.000 14.12 0.00 0.00 2.08
2677 2726 7.603651 TCCTATCAGTCAGTCACTAGAAAAAC 58.396 38.462 0.00 0.00 32.21 2.43
2715 2764 9.796120 TTTCTTACAACTATTTGGTGTTCAAAG 57.204 29.630 0.00 0.00 45.79 2.77
2717 2766 9.616156 TCTTACAACTATTTGGTGTTCAAAGTA 57.384 29.630 0.00 0.00 45.79 2.24
2718 2767 9.878599 CTTACAACTATTTGGTGTTCAAAGTAG 57.121 33.333 0.00 0.00 45.79 2.57
2719 2768 7.272037 ACAACTATTTGGTGTTCAAAGTAGG 57.728 36.000 0.00 0.00 45.79 3.18
2726 2782 3.392947 TGGTGTTCAAAGTAGGACATCCA 59.607 43.478 0.00 0.00 38.89 3.41
2745 2801 4.204799 TCCAGAGAAATGATCATTGCAGG 58.795 43.478 25.32 21.92 0.00 4.85
2747 2803 4.036498 CCAGAGAAATGATCATTGCAGGTC 59.964 45.833 25.32 16.60 0.00 3.85
2781 2842 3.424703 AGGTACTCCGTTACTTGCAGTA 58.575 45.455 0.00 0.00 39.05 2.74
2845 2906 2.259266 TCAATCAGCAGTTGAGCACA 57.741 45.000 0.00 0.00 39.68 4.57
2848 2909 2.096220 ATCAGCAGTTGAGCACAGAG 57.904 50.000 0.00 0.00 39.68 3.35
2849 2910 0.602106 TCAGCAGTTGAGCACAGAGC 60.602 55.000 0.00 0.00 46.19 4.09
2864 2925 1.129998 CAGAGCACCGAATCTGCAAAG 59.870 52.381 0.00 0.00 36.80 2.77
2867 2928 1.808945 AGCACCGAATCTGCAAAGAAG 59.191 47.619 0.00 0.00 37.08 2.85
3018 3079 4.237018 TCTCACCCAACCTTACCTTTACT 58.763 43.478 0.00 0.00 0.00 2.24
3025 3086 6.171213 CCCAACCTTACCTTTACTCAAGTAG 58.829 44.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.592993 CCAGGATGACGGTGGTGGT 61.593 63.158 0.00 0.00 39.69 4.16
56 61 1.532078 TGCCGGTGACCTAGTGACA 60.532 57.895 1.90 0.00 0.00 3.58
91 97 3.502211 AGCGGAAGAAAATGTTGAACGAT 59.498 39.130 0.00 0.00 0.00 3.73
132 140 5.472478 ACGGTAAAATGGGAAAGAAAGACTC 59.528 40.000 0.00 0.00 0.00 3.36
133 141 5.240844 CACGGTAAAATGGGAAAGAAAGACT 59.759 40.000 0.00 0.00 0.00 3.24
166 174 7.235399 ACCTTCAAATCCAACCAAACATCTTAT 59.765 33.333 0.00 0.00 0.00 1.73
256 266 9.502091 ACTGAAAAACACTATTATGCAAGACTA 57.498 29.630 0.00 0.00 0.00 2.59
312 322 4.081087 ACGTAAATCAGCACCAAGGATAGT 60.081 41.667 0.00 0.00 0.00 2.12
408 419 6.076981 ACCAACAGAATTGAAATCACTGAC 57.923 37.500 13.39 0.00 33.53 3.51
431 442 5.930209 ATCCCAAGCAATATTAAGGAGGA 57.070 39.130 0.00 0.00 0.00 3.71
441 452 2.025037 AGCCTCACAATCCCAAGCAATA 60.025 45.455 0.00 0.00 0.00 1.90
453 464 5.394773 GGGTTGAAACTTTTAAGCCTCACAA 60.395 40.000 16.28 0.00 38.56 3.33
594 611 9.027129 CAGGCACATATTGAAACATATGAAAAG 57.973 33.333 10.38 0.00 35.38 2.27
672 698 3.551046 CGGACTAGATGATTAGTTGCGCT 60.551 47.826 9.73 0.00 34.13 5.92
681 707 4.567159 GCTTTTTCGTCGGACTAGATGATT 59.433 41.667 6.57 0.00 36.21 2.57
692 718 2.622962 GGTGGGGCTTTTTCGTCGG 61.623 63.158 0.00 0.00 0.00 4.79
693 719 2.951458 GGTGGGGCTTTTTCGTCG 59.049 61.111 0.00 0.00 0.00 5.12
694 720 1.895231 ACGGTGGGGCTTTTTCGTC 60.895 57.895 0.00 0.00 0.00 4.20
695 721 2.190841 CACGGTGGGGCTTTTTCGT 61.191 57.895 0.00 0.00 0.00 3.85
696 722 1.852067 CTCACGGTGGGGCTTTTTCG 61.852 60.000 8.50 0.00 0.00 3.46
697 723 1.956802 CTCACGGTGGGGCTTTTTC 59.043 57.895 8.50 0.00 0.00 2.29
698 724 2.200337 GCTCACGGTGGGGCTTTTT 61.200 57.895 10.52 0.00 0.00 1.94
699 725 2.597510 GCTCACGGTGGGGCTTTT 60.598 61.111 10.52 0.00 0.00 2.27
716 742 4.735132 TTTCCTCGCTGACGGCCG 62.735 66.667 26.86 26.86 40.63 6.13
717 743 2.815647 CTTTCCTCGCTGACGGCC 60.816 66.667 0.00 0.00 40.63 6.13
718 744 1.807573 CTCTTTCCTCGCTGACGGC 60.808 63.158 0.00 0.00 40.63 5.68
719 745 0.243907 TTCTCTTTCCTCGCTGACGG 59.756 55.000 0.00 0.00 40.63 4.79
720 746 1.721926 GTTTCTCTTTCCTCGCTGACG 59.278 52.381 0.00 0.00 42.01 4.35
721 747 2.734079 CAGTTTCTCTTTCCTCGCTGAC 59.266 50.000 0.00 0.00 0.00 3.51
722 748 2.365617 ACAGTTTCTCTTTCCTCGCTGA 59.634 45.455 0.00 0.00 0.00 4.26
723 749 2.734079 GACAGTTTCTCTTTCCTCGCTG 59.266 50.000 0.00 0.00 0.00 5.18
724 750 2.608261 CGACAGTTTCTCTTTCCTCGCT 60.608 50.000 0.00 0.00 0.00 4.93
725 751 1.721926 CGACAGTTTCTCTTTCCTCGC 59.278 52.381 0.00 0.00 0.00 5.03
726 752 3.014604 ACGACAGTTTCTCTTTCCTCG 57.985 47.619 0.00 0.00 0.00 4.63
727 753 4.369182 TCAACGACAGTTTCTCTTTCCTC 58.631 43.478 0.00 0.00 38.79 3.71
728 754 4.402056 TCAACGACAGTTTCTCTTTCCT 57.598 40.909 0.00 0.00 38.79 3.36
729 755 5.064834 AGTTTCAACGACAGTTTCTCTTTCC 59.935 40.000 0.00 0.00 38.79 3.13
730 756 6.108097 AGTTTCAACGACAGTTTCTCTTTC 57.892 37.500 0.00 0.00 38.79 2.62
731 757 5.220416 CGAGTTTCAACGACAGTTTCTCTTT 60.220 40.000 0.00 0.00 38.79 2.52
732 758 4.267928 CGAGTTTCAACGACAGTTTCTCTT 59.732 41.667 0.00 0.00 38.79 2.85
733 759 3.797256 CGAGTTTCAACGACAGTTTCTCT 59.203 43.478 0.00 0.00 38.79 3.10
734 760 3.550678 ACGAGTTTCAACGACAGTTTCTC 59.449 43.478 0.00 0.00 38.79 2.87
735 761 3.518590 ACGAGTTTCAACGACAGTTTCT 58.481 40.909 0.00 0.00 38.79 2.52
736 762 3.598670 CGACGAGTTTCAACGACAGTTTC 60.599 47.826 0.00 0.00 38.79 2.78
737 763 2.280708 CGACGAGTTTCAACGACAGTTT 59.719 45.455 0.00 0.00 38.79 2.66
738 764 1.850441 CGACGAGTTTCAACGACAGTT 59.150 47.619 0.00 0.00 42.15 3.16
739 765 1.202222 ACGACGAGTTTCAACGACAGT 60.202 47.619 0.00 0.00 0.00 3.55
740 766 1.474017 ACGACGAGTTTCAACGACAG 58.526 50.000 0.00 0.00 0.00 3.51
741 767 1.847999 GAACGACGAGTTTCAACGACA 59.152 47.619 0.00 0.00 44.35 4.35
742 768 1.188791 GGAACGACGAGTTTCAACGAC 59.811 52.381 0.00 0.00 44.35 4.34
743 769 1.066002 AGGAACGACGAGTTTCAACGA 59.934 47.619 0.00 0.00 44.35 3.85
744 770 1.484356 AGGAACGACGAGTTTCAACG 58.516 50.000 0.00 0.00 44.35 4.10
745 771 3.121544 AGAAGGAACGACGAGTTTCAAC 58.878 45.455 0.00 3.62 44.35 3.18
746 772 3.447918 AGAAGGAACGACGAGTTTCAA 57.552 42.857 0.00 0.00 44.35 2.69
747 773 3.607775 CGTAGAAGGAACGACGAGTTTCA 60.608 47.826 0.00 0.00 44.35 2.69
748 774 2.907392 CGTAGAAGGAACGACGAGTTTC 59.093 50.000 0.00 0.00 44.35 2.78
749 775 2.919807 GCGTAGAAGGAACGACGAGTTT 60.920 50.000 0.00 0.00 44.35 2.66
751 777 0.167689 GCGTAGAAGGAACGACGAGT 59.832 55.000 0.00 0.00 42.90 4.18
752 778 0.447011 AGCGTAGAAGGAACGACGAG 59.553 55.000 0.00 0.00 42.90 4.18
753 779 1.394917 GTAGCGTAGAAGGAACGACGA 59.605 52.381 0.00 0.00 42.90 4.20
754 780 1.396301 AGTAGCGTAGAAGGAACGACG 59.604 52.381 0.00 0.00 42.90 5.12
755 781 2.677337 AGAGTAGCGTAGAAGGAACGAC 59.323 50.000 0.00 0.00 42.90 4.34
756 782 2.983229 AGAGTAGCGTAGAAGGAACGA 58.017 47.619 0.00 0.00 42.90 3.85
757 783 3.761311 AAGAGTAGCGTAGAAGGAACG 57.239 47.619 0.00 0.00 43.12 3.95
758 784 9.747293 ATTTTATAAGAGTAGCGTAGAAGGAAC 57.253 33.333 0.00 0.00 0.00 3.62
860 886 0.669625 GGGAGGAAGAAACGTCCGTG 60.670 60.000 0.00 0.00 43.23 4.94
882 908 2.210116 GGAACGAAGCTCTGAACAACA 58.790 47.619 0.00 0.00 0.00 3.33
894 920 1.071699 TCTGGACAAAGGGGAACGAAG 59.928 52.381 0.00 0.00 0.00 3.79
942 969 2.050442 GTTTGGGGCTTCGCGTTG 60.050 61.111 5.77 0.75 0.00 4.10
1216 1248 3.488569 GATGGTGCATCCGGGGGA 61.489 66.667 0.00 0.00 39.52 4.81
1650 1688 0.659427 CTATGCTTGACGCCACCATG 59.341 55.000 0.00 0.00 38.05 3.66
1660 1698 4.248859 GACTTGAGCTTGTCTATGCTTGA 58.751 43.478 7.81 0.00 37.43 3.02
1698 1736 1.758514 ATCGCACTGGATCTCCCGT 60.759 57.895 0.00 0.00 37.93 5.28
1830 1868 3.916349 TCCTCCCATCCTTCTTCAGAAAA 59.084 43.478 0.00 0.00 33.07 2.29
1842 1880 1.265454 ACGGTGTTCTCCTCCCATCC 61.265 60.000 0.00 0.00 0.00 3.51
1854 1892 4.643387 GCCTCCTGCCACGGTGTT 62.643 66.667 7.45 0.00 0.00 3.32
2034 2072 3.766545 TCAAGTTGGCCAGCTAGAAATT 58.233 40.909 23.61 2.57 0.00 1.82
2043 2081 2.174334 CCGACATCAAGTTGGCCAG 58.826 57.895 5.11 0.00 44.72 4.85
2098 2136 5.668135 TTCCACCTCCCATGAATCATAAT 57.332 39.130 0.00 0.00 0.00 1.28
2234 2272 6.154203 TCATTTGCTTGTGACACCAATAAA 57.846 33.333 2.45 0.89 0.00 1.40
2257 2295 4.156455 ACAACAATGAGGTCAGTTCACT 57.844 40.909 0.00 0.00 0.00 3.41
2266 2304 6.826741 AGTTACAACAGTAACAACAATGAGGT 59.173 34.615 17.63 0.00 46.32 3.85
2420 2463 4.592485 ACTGTCAGTTAGTCAGAACCTG 57.408 45.455 0.00 0.00 36.94 4.00
2451 2494 8.553459 AAGAAATGTTATCCTACTCAACACAG 57.447 34.615 0.00 0.00 35.17 3.66
2499 2543 6.533730 CATCCCTACTGATTAAGCATGGTTA 58.466 40.000 13.22 13.22 0.00 2.85
2511 2556 1.135094 CCACCAGCATCCCTACTGAT 58.865 55.000 0.00 0.00 35.90 2.90
2525 2570 4.386951 CGACGGGCATGTCCACCA 62.387 66.667 18.31 0.00 35.40 4.17
2533 2578 4.735132 CACGGACACGACGGGCAT 62.735 66.667 0.00 0.00 44.60 4.40
2538 2583 1.724929 GACAGACACGGACACGACG 60.725 63.158 0.00 0.00 44.60 5.12
2540 2585 1.652563 CAGACAGACACGGACACGA 59.347 57.895 0.00 0.00 44.60 4.35
2544 2589 3.106407 GCGCAGACAGACACGGAC 61.106 66.667 0.30 0.00 0.00 4.79
2557 2602 0.391130 GTACATCTTGGTCCAGCGCA 60.391 55.000 11.47 0.00 0.00 6.09
2562 2607 5.163405 GCAGAGATTAGTACATCTTGGTCCA 60.163 44.000 0.00 0.00 33.36 4.02
2586 2635 4.496895 GCATTAGCACGAAAATTACAGCAG 59.503 41.667 0.00 0.00 41.58 4.24
2596 2645 5.123661 TGATCATTTCAGCATTAGCACGAAA 59.876 36.000 0.00 7.29 43.73 3.46
2619 2668 1.663702 GTCCACCGAGTCCGTGTTG 60.664 63.158 10.18 0.00 0.00 3.33
2623 2672 1.874345 GACATGTCCACCGAGTCCGT 61.874 60.000 15.31 0.00 0.00 4.69
2628 2677 1.153823 GGTCGACATGTCCACCGAG 60.154 63.158 24.22 8.20 31.50 4.63
2629 2678 1.605451 AGGTCGACATGTCCACCGA 60.605 57.895 29.55 17.92 44.18 4.69
2630 2679 1.446099 CAGGTCGACATGTCCACCG 60.446 63.158 29.55 22.16 44.18 4.94
2631 2680 1.741770 GCAGGTCGACATGTCCACC 60.742 63.158 29.20 29.20 40.55 4.61
2632 2681 0.391661 ATGCAGGTCGACATGTCCAC 60.392 55.000 28.62 17.20 0.00 4.02
2633 2682 0.324614 AATGCAGGTCGACATGTCCA 59.675 50.000 28.62 20.03 0.00 4.02
2634 2683 1.009829 GAATGCAGGTCGACATGTCC 58.990 55.000 28.62 15.25 0.00 4.02
2635 2684 1.009829 GGAATGCAGGTCGACATGTC 58.990 55.000 28.62 21.10 0.00 3.06
2636 2685 0.615331 AGGAATGCAGGTCGACATGT 59.385 50.000 28.62 11.62 0.00 3.21
2637 2686 2.602257 TAGGAATGCAGGTCGACATG 57.398 50.000 25.00 25.00 0.00 3.21
2638 2687 2.700371 TGATAGGAATGCAGGTCGACAT 59.300 45.455 18.91 7.60 0.00 3.06
2639 2688 2.101415 CTGATAGGAATGCAGGTCGACA 59.899 50.000 18.91 0.00 0.00 4.35
2640 2689 2.101582 ACTGATAGGAATGCAGGTCGAC 59.898 50.000 7.13 7.13 34.05 4.20
2641 2690 2.362397 GACTGATAGGAATGCAGGTCGA 59.638 50.000 0.00 0.00 34.05 4.20
2642 2691 2.101415 TGACTGATAGGAATGCAGGTCG 59.899 50.000 0.00 0.00 34.05 4.79
2643 2692 3.133721 ACTGACTGATAGGAATGCAGGTC 59.866 47.826 0.00 0.00 34.05 3.85
2644 2693 3.110705 ACTGACTGATAGGAATGCAGGT 58.889 45.455 0.00 0.00 34.05 4.00
2645 2694 3.133542 TGACTGACTGATAGGAATGCAGG 59.866 47.826 0.00 0.00 34.05 4.85
2646 2695 4.118410 GTGACTGACTGATAGGAATGCAG 58.882 47.826 0.00 0.00 35.81 4.41
2647 2696 3.771479 AGTGACTGACTGATAGGAATGCA 59.229 43.478 0.00 0.00 31.75 3.96
2648 2697 4.399004 AGTGACTGACTGATAGGAATGC 57.601 45.455 0.00 0.00 31.75 3.56
2649 2698 6.951062 TCTAGTGACTGACTGATAGGAATG 57.049 41.667 0.00 0.00 35.96 2.67
2650 2699 7.962995 TTTCTAGTGACTGACTGATAGGAAT 57.037 36.000 0.00 0.00 35.96 3.01
2651 2700 7.776618 TTTTCTAGTGACTGACTGATAGGAA 57.223 36.000 0.00 0.00 35.96 3.36
2652 2701 7.451877 AGTTTTTCTAGTGACTGACTGATAGGA 59.548 37.037 0.00 0.00 35.96 2.94
2692 2741 9.878599 CTACTTTGAACACCAAATAGTTGTAAG 57.121 33.333 1.80 0.00 43.19 2.34
2715 2764 6.166984 TGATCATTTCTCTGGATGTCCTAC 57.833 41.667 0.00 0.00 36.82 3.18
2717 2766 5.908562 ATGATCATTTCTCTGGATGTCCT 57.091 39.130 1.18 0.00 36.82 3.85
2718 2767 5.278364 GCAATGATCATTTCTCTGGATGTCC 60.278 44.000 18.41 0.00 0.00 4.02
2719 2768 5.298527 TGCAATGATCATTTCTCTGGATGTC 59.701 40.000 18.41 2.82 0.00 3.06
2726 2782 5.113446 AGACCTGCAATGATCATTTCTCT 57.887 39.130 18.41 9.84 0.00 3.10
2754 2810 6.066690 TGCAAGTAACGGAGTACCTAGATAT 58.933 40.000 0.00 0.00 45.00 1.63
2758 2814 4.030134 CTGCAAGTAACGGAGTACCTAG 57.970 50.000 0.00 0.00 45.00 3.02
2823 2884 4.325972 TGTGCTCAACTGCTGATTGATTA 58.674 39.130 0.00 0.00 35.57 1.75
2829 2890 1.944892 GCTCTGTGCTCAACTGCTGAT 60.945 52.381 0.00 0.00 38.95 2.90
2845 2906 1.002430 TCTTTGCAGATTCGGTGCTCT 59.998 47.619 0.00 0.00 41.78 4.09
2848 2909 1.537202 ACTTCTTTGCAGATTCGGTGC 59.463 47.619 0.00 0.00 41.59 5.01
2849 2910 2.549754 ACACTTCTTTGCAGATTCGGTG 59.450 45.455 0.00 0.00 0.00 4.94
2850 2911 2.851195 ACACTTCTTTGCAGATTCGGT 58.149 42.857 0.00 0.00 0.00 4.69
2851 2912 3.904136 AACACTTCTTTGCAGATTCGG 57.096 42.857 0.00 0.00 0.00 4.30
2852 2913 4.847633 TCAAACACTTCTTTGCAGATTCG 58.152 39.130 0.00 0.00 32.10 3.34
2853 2914 7.436080 TGATTTCAAACACTTCTTTGCAGATTC 59.564 33.333 0.00 0.00 32.10 2.52
2854 2915 7.223387 GTGATTTCAAACACTTCTTTGCAGATT 59.777 33.333 0.00 0.00 34.65 2.40
2931 2992 9.851686 AATGGATGAATTTAGTAGTAGCATTCA 57.148 29.630 13.02 13.02 38.04 2.57
2951 3012 9.784531 AATATCTGAATGTCGAGTTAAATGGAT 57.215 29.630 0.00 0.00 0.00 3.41
2982 3043 1.478916 GGTGAGAGCCTGAGAGGTAAC 59.521 57.143 0.00 0.00 37.80 2.50
2987 3048 0.248843 GTTGGGTGAGAGCCTGAGAG 59.751 60.000 0.00 0.00 36.53 3.20
2988 3049 1.194781 GGTTGGGTGAGAGCCTGAGA 61.195 60.000 0.00 0.00 36.53 3.27
2989 3050 1.197430 AGGTTGGGTGAGAGCCTGAG 61.197 60.000 0.00 0.00 36.53 3.35
2990 3051 0.768221 AAGGTTGGGTGAGAGCCTGA 60.768 55.000 0.00 0.00 36.53 3.86
2991 3052 0.984230 TAAGGTTGGGTGAGAGCCTG 59.016 55.000 0.00 0.00 36.53 4.85
2992 3053 0.984995 GTAAGGTTGGGTGAGAGCCT 59.015 55.000 0.00 0.00 36.53 4.58
2993 3054 0.035343 GGTAAGGTTGGGTGAGAGCC 60.035 60.000 0.00 0.00 36.00 4.70
2994 3055 0.984995 AGGTAAGGTTGGGTGAGAGC 59.015 55.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.