Multiple sequence alignment - TraesCS2A01G261700

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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 TraesCS2A01G261700 chr2A 100.000 5604 0 0 1 5604 412506390 412511993 0.000000e+00 10349.0
1 TraesCS2A01G261700 chr2B 96.516 4133 115 12 1485 5604 387081003 387076887 0.000000e+00 6807.0
2 TraesCS2A01G261700 chr2B 94.086 558 26 4 831 1387 387081739 387081188 0.000000e+00 841.0
3 TraesCS2A01G261700 chr2B 96.939 98 3 0 1388 1485 387081140 387081043 1.250000e-36 165.0
4 TraesCS2A01G261700 chr2D 95.477 3228 106 22 2396 5604 318557226 318554020 0.000000e+00 5116.0
5 TraesCS2A01G261700 chr2D 89.482 599 61 2 1 598 484129879 484129282 0.000000e+00 756.0
6 TraesCS2A01G261700 chr2D 87.823 657 36 18 896 1543 318558570 318557949 0.000000e+00 730.0
7 TraesCS2A01G261700 chr2D 89.136 405 32 7 1769 2164 318557729 318557328 1.400000e-135 494.0
8 TraesCS2A01G261700 chr2D 98.182 55 1 0 831 885 318560664 318560610 4.620000e-16 97.1
9 TraesCS2A01G261700 chr1D 83.179 862 93 26 1 829 143440435 143439593 0.000000e+00 741.0
10 TraesCS2A01G261700 chr1D 82.517 858 104 20 1 827 140108810 140109652 0.000000e+00 712.0
11 TraesCS2A01G261700 chr4D 83.159 861 93 27 1 829 477919891 477919051 0.000000e+00 739.0
12 TraesCS2A01G261700 chr4D 87.346 648 75 7 1 645 70672261 70671618 0.000000e+00 736.0
13 TraesCS2A01G261700 chr3D 87.481 647 72 8 1 645 579032768 579032129 0.000000e+00 737.0
14 TraesCS2A01G261700 chr6B 87.017 647 77 6 1 645 227835182 227834541 0.000000e+00 723.0
15 TraesCS2A01G261700 chrUn 85.759 646 80 6 1 645 53430358 53430992 0.000000e+00 673.0
16 TraesCS2A01G261700 chr5B 85.893 638 81 6 1 636 620309819 620309189 0.000000e+00 671.0
17 TraesCS2A01G261700 chr5B 96.875 32 1 0 1219 1250 426586144 426586175 3.000000e-03 54.7
18 TraesCS2A01G261700 chr5A 76.705 176 30 9 658 829 476999292 476999460 2.780000e-13 87.9
19 TraesCS2A01G261700 chr7B 80.645 93 12 4 742 829 695318400 695318309 3.620000e-07 67.6


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 TraesCS2A01G261700 chr2A 412506390 412511993 5603 False 10349.000000 10349 100.0000 1 5604 1 chr2A.!!$F1 5603
1 TraesCS2A01G261700 chr2B 387076887 387081739 4852 True 2604.333333 6807 95.8470 831 5604 3 chr2B.!!$R1 4773
2 TraesCS2A01G261700 chr2D 318554020 318560664 6644 True 1609.275000 5116 92.6545 831 5604 4 chr2D.!!$R2 4773
3 TraesCS2A01G261700 chr2D 484129282 484129879 597 True 756.000000 756 89.4820 1 598 1 chr2D.!!$R1 597
4 TraesCS2A01G261700 chr1D 143439593 143440435 842 True 741.000000 741 83.1790 1 829 1 chr1D.!!$R1 828
5 TraesCS2A01G261700 chr1D 140108810 140109652 842 False 712.000000 712 82.5170 1 827 1 chr1D.!!$F1 826
6 TraesCS2A01G261700 chr4D 477919051 477919891 840 True 739.000000 739 83.1590 1 829 1 chr4D.!!$R2 828
7 TraesCS2A01G261700 chr4D 70671618 70672261 643 True 736.000000 736 87.3460 1 645 1 chr4D.!!$R1 644
8 TraesCS2A01G261700 chr3D 579032129 579032768 639 True 737.000000 737 87.4810 1 645 1 chr3D.!!$R1 644
9 TraesCS2A01G261700 chr6B 227834541 227835182 641 True 723.000000 723 87.0170 1 645 1 chr6B.!!$R1 644
10 TraesCS2A01G261700 chrUn 53430358 53430992 634 False 673.000000 673 85.7590 1 645 1 chrUn.!!$F1 644
11 TraesCS2A01G261700 chr5B 620309189 620309819 630 True 671.000000 671 85.8930 1 636 1 chr5B.!!$R1 635

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
772 780 0.108138 ACTGAGGGATTTTCTCGGCG 60.108 55.0 0.00 0.0 40.35 6.46 F
774 782 0.108329 TGAGGGATTTTCTCGGCGTC 60.108 55.0 6.85 0.0 34.19 5.19 F
828 836 0.382158 CGCGAGTGGAGATGCTCTTA 59.618 55.0 0.00 0.0 0.00 2.10 F
1371 3413 0.396278 CTGATTCCAAGGGAAGGGGC 60.396 60.0 3.85 0.0 45.48 5.80 F
2727 4991 2.416547 GGTAGTGCAGTATGTTGCTGTG 59.583 50.0 4.19 0.0 44.38 3.66 F
3370 5645 0.034670 AGATTCAAGCAGACCTGGGC 60.035 55.0 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 4795 0.595095 GGCGATGAAAGATCCATGGC 59.405 55.000 6.96 8.31 42.50 4.40 R
2548 4796 1.971481 TGGCGATGAAAGATCCATGG 58.029 50.000 4.97 4.97 0.00 3.66 R
2727 4991 3.942115 GTCTAACCAGGGCTGAAGAAATC 59.058 47.826 0.00 0.00 0.00 2.17 R
3023 5297 0.898326 TGTAGAGCCACAGGAGCGAA 60.898 55.000 0.00 0.00 34.64 4.70 R
4480 6759 1.280133 CCGCATATCTGACCCATCCAT 59.720 52.381 0.00 0.00 0.00 3.41 R
4751 7030 0.515127 TATCACACAAAACTGGCGCG 59.485 50.000 0.00 0.00 0.00 6.86 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
23 24 4.366267 ACTTATGGAGTGAGGGTGAATCT 58.634 43.478 0.00 0.00 37.17 2.40
66 67 4.765273 TCTTGCACTTGAAGTAGTTGTCA 58.235 39.130 0.00 0.00 0.00 3.58
77 78 6.403049 TGAAGTAGTTGTCAAACTCACAGAA 58.597 36.000 0.00 0.00 43.34 3.02
99 100 5.261040 AGGAATTCACAATCCTGAGGAAA 57.739 39.130 4.76 0.00 44.38 3.13
108 109 3.703001 ATCCTGAGGAAAAGCTTTCGA 57.297 42.857 13.10 0.53 34.34 3.71
111 112 3.576982 TCCTGAGGAAAAGCTTTCGACTA 59.423 43.478 13.10 0.00 0.00 2.59
141 142 1.365699 GGCGCCGAAATACTTTCTCA 58.634 50.000 12.58 0.00 37.52 3.27
322 323 2.232298 CTCTTCCTCCTGGGTGTCGC 62.232 65.000 0.00 0.00 36.25 5.19
329 330 3.770040 CTGGGTGTCGCCATCGGA 61.770 66.667 4.48 0.00 39.65 4.55
378 379 2.232452 CTCCTCGTTGTCTGAGTCCATT 59.768 50.000 0.00 0.00 0.00 3.16
521 524 1.166129 GAACCTTCTCTTTTCCGGGC 58.834 55.000 0.00 0.00 0.00 6.13
523 526 1.295423 CCTTCTCTTTTCCGGGCGA 59.705 57.895 0.00 0.00 0.00 5.54
646 654 0.109597 AAGATGCTTTTTCGCCTGCG 60.110 50.000 4.92 4.92 41.35 5.18
647 655 1.514873 GATGCTTTTTCGCCTGCGG 60.515 57.895 12.06 0.00 40.25 5.69
648 656 2.872337 GATGCTTTTTCGCCTGCGGG 62.872 60.000 7.41 7.41 40.25 6.13
649 657 3.670377 GCTTTTTCGCCTGCGGGT 61.670 61.111 14.55 0.00 40.25 5.28
650 658 3.039134 CTTTTTCGCCTGCGGGTT 58.961 55.556 14.55 0.00 40.25 4.11
651 659 1.362355 CTTTTTCGCCTGCGGGTTT 59.638 52.632 14.55 0.00 40.25 3.27
652 660 0.249280 CTTTTTCGCCTGCGGGTTTT 60.249 50.000 14.55 0.00 40.25 2.43
653 661 0.249114 TTTTTCGCCTGCGGGTTTTC 60.249 50.000 14.55 0.00 40.25 2.29
654 662 2.077821 TTTTCGCCTGCGGGTTTTCC 62.078 55.000 14.55 0.00 40.25 3.13
655 663 2.969300 TTTCGCCTGCGGGTTTTCCT 62.969 55.000 14.55 0.00 40.46 3.36
656 664 2.969300 TTCGCCTGCGGGTTTTCCTT 62.969 55.000 14.55 0.00 40.46 3.36
657 665 2.962569 GCCTGCGGGTTTTCCTTC 59.037 61.111 14.55 0.00 40.46 3.46
658 666 2.636412 GCCTGCGGGTTTTCCTTCC 61.636 63.158 14.55 0.00 40.46 3.46
659 667 1.977009 CCTGCGGGTTTTCCTTCCC 60.977 63.158 2.29 0.00 40.46 3.97
660 668 1.977009 CTGCGGGTTTTCCTTCCCC 60.977 63.158 0.00 0.00 40.54 4.81
663 671 3.173323 GGGTTTTCCTTCCCCGGA 58.827 61.111 0.73 0.00 40.46 5.14
664 672 1.001269 GGGTTTTCCTTCCCCGGAG 60.001 63.158 0.73 0.00 40.46 4.63
665 673 1.677966 GGTTTTCCTTCCCCGGAGC 60.678 63.158 0.73 0.00 36.94 4.70
666 674 2.038837 GTTTTCCTTCCCCGGAGCG 61.039 63.158 0.73 0.00 33.89 5.03
667 675 3.912745 TTTTCCTTCCCCGGAGCGC 62.913 63.158 0.73 0.00 33.89 5.92
685 693 3.717294 CCCCTAGTGCGCTGGGTT 61.717 66.667 25.91 0.00 41.28 4.11
686 694 2.125106 CCCTAGTGCGCTGGGTTC 60.125 66.667 25.91 0.00 41.28 3.62
687 695 2.509336 CCTAGTGCGCTGGGTTCG 60.509 66.667 20.81 0.00 38.42 3.95
688 696 2.509336 CTAGTGCGCTGGGTTCGG 60.509 66.667 10.80 0.00 0.00 4.30
689 697 3.296709 CTAGTGCGCTGGGTTCGGT 62.297 63.158 10.80 0.00 0.00 4.69
690 698 3.583276 TAGTGCGCTGGGTTCGGTG 62.583 63.158 10.80 0.00 0.00 4.94
696 704 4.760047 CTGGGTTCGGTGGCCTCG 62.760 72.222 3.32 8.65 0.00 4.63
699 707 3.782443 GGTTCGGTGGCCTCGGAT 61.782 66.667 14.88 0.00 0.00 4.18
700 708 2.202892 GTTCGGTGGCCTCGGATC 60.203 66.667 14.88 10.89 0.00 3.36
701 709 3.833645 TTCGGTGGCCTCGGATCG 61.834 66.667 14.88 1.34 0.00 3.69
713 721 3.065567 GGATCGCCGGCCCAAAAA 61.066 61.111 23.46 0.00 0.00 1.94
729 737 2.267045 AAAAATGGGTCGAGCCAGC 58.733 52.632 36.55 12.13 39.65 4.85
730 738 1.586154 AAAAATGGGTCGAGCCAGCG 61.586 55.000 36.55 0.00 39.65 5.18
731 739 3.976701 AAATGGGTCGAGCCAGCGG 62.977 63.158 36.55 0.00 39.65 5.52
734 742 4.162690 GGGTCGAGCCAGCGGATT 62.163 66.667 28.27 0.00 39.65 3.01
735 743 2.125106 GGTCGAGCCAGCGGATTT 60.125 61.111 2.39 0.00 37.17 2.17
736 744 2.174319 GGTCGAGCCAGCGGATTTC 61.174 63.158 2.39 0.00 37.17 2.17
737 745 2.202743 TCGAGCCAGCGGATTTCG 60.203 61.111 0.00 4.97 42.76 3.46
738 746 2.509336 CGAGCCAGCGGATTTCGT 60.509 61.111 0.00 0.00 41.72 3.85
739 747 2.517450 CGAGCCAGCGGATTTCGTC 61.517 63.158 0.00 0.00 41.72 4.20
740 748 2.509336 AGCCAGCGGATTTCGTCG 60.509 61.111 0.00 0.00 41.72 5.12
741 749 2.813908 GCCAGCGGATTTCGTCGT 60.814 61.111 0.00 0.00 41.72 4.34
742 750 2.388232 GCCAGCGGATTTCGTCGTT 61.388 57.895 0.00 0.00 41.72 3.85
743 751 1.708027 CCAGCGGATTTCGTCGTTC 59.292 57.895 0.00 0.00 41.72 3.95
744 752 0.736325 CCAGCGGATTTCGTCGTTCT 60.736 55.000 0.00 0.00 41.72 3.01
745 753 0.366871 CAGCGGATTTCGTCGTTCTG 59.633 55.000 0.00 0.00 41.72 3.02
746 754 0.736325 AGCGGATTTCGTCGTTCTGG 60.736 55.000 0.00 0.00 41.72 3.86
747 755 1.693083 GCGGATTTCGTCGTTCTGGG 61.693 60.000 0.00 0.00 41.72 4.45
748 756 0.108992 CGGATTTCGTCGTTCTGGGA 60.109 55.000 0.00 0.00 0.00 4.37
749 757 1.470979 CGGATTTCGTCGTTCTGGGAT 60.471 52.381 0.00 0.00 0.00 3.85
750 758 1.933853 GGATTTCGTCGTTCTGGGATG 59.066 52.381 0.00 0.00 0.00 3.51
751 759 1.327764 GATTTCGTCGTTCTGGGATGC 59.672 52.381 0.00 0.00 0.00 3.91
752 760 1.011968 TTTCGTCGTTCTGGGATGCG 61.012 55.000 0.00 0.00 0.00 4.73
753 761 1.868987 TTCGTCGTTCTGGGATGCGA 61.869 55.000 0.00 0.00 0.00 5.10
754 762 2.158959 CGTCGTTCTGGGATGCGAC 61.159 63.158 5.95 5.95 46.78 5.19
755 763 1.215647 GTCGTTCTGGGATGCGACT 59.784 57.895 8.41 0.00 46.74 4.18
756 764 1.078759 GTCGTTCTGGGATGCGACTG 61.079 60.000 8.41 0.00 46.74 3.51
757 765 1.215382 CGTTCTGGGATGCGACTGA 59.785 57.895 0.00 0.00 0.00 3.41
758 766 0.803768 CGTTCTGGGATGCGACTGAG 60.804 60.000 0.00 0.00 0.00 3.35
759 767 0.460987 GTTCTGGGATGCGACTGAGG 60.461 60.000 0.00 0.00 0.00 3.86
760 768 1.617018 TTCTGGGATGCGACTGAGGG 61.617 60.000 0.00 0.00 0.00 4.30
761 769 2.038813 TGGGATGCGACTGAGGGA 59.961 61.111 0.00 0.00 0.00 4.20
762 770 1.383109 TGGGATGCGACTGAGGGAT 60.383 57.895 0.00 0.00 0.00 3.85
763 771 0.982852 TGGGATGCGACTGAGGGATT 60.983 55.000 0.00 0.00 0.00 3.01
764 772 0.181350 GGGATGCGACTGAGGGATTT 59.819 55.000 0.00 0.00 0.00 2.17
765 773 1.408822 GGGATGCGACTGAGGGATTTT 60.409 52.381 0.00 0.00 0.00 1.82
766 774 1.943340 GGATGCGACTGAGGGATTTTC 59.057 52.381 0.00 0.00 0.00 2.29
767 775 2.420687 GGATGCGACTGAGGGATTTTCT 60.421 50.000 0.00 0.00 0.00 2.52
768 776 2.386661 TGCGACTGAGGGATTTTCTC 57.613 50.000 0.00 0.00 0.00 2.87
769 777 1.281899 GCGACTGAGGGATTTTCTCG 58.718 55.000 0.00 0.00 34.19 4.04
770 778 1.927895 CGACTGAGGGATTTTCTCGG 58.072 55.000 0.00 0.00 41.91 4.63
771 779 1.657822 GACTGAGGGATTTTCTCGGC 58.342 55.000 0.00 0.00 40.35 5.54
772 780 0.108138 ACTGAGGGATTTTCTCGGCG 60.108 55.000 0.00 0.00 40.35 6.46
773 781 0.108138 CTGAGGGATTTTCTCGGCGT 60.108 55.000 6.85 0.00 34.19 5.68
774 782 0.108329 TGAGGGATTTTCTCGGCGTC 60.108 55.000 6.85 0.00 34.19 5.19
775 783 1.146358 GAGGGATTTTCTCGGCGTCG 61.146 60.000 1.15 1.15 37.82 5.12
776 784 2.171725 GGGATTTTCTCGGCGTCGG 61.172 63.158 10.62 0.00 36.95 4.79
777 785 2.701606 GATTTTCTCGGCGTCGGC 59.298 61.111 10.62 9.07 36.95 5.54
778 786 2.047655 ATTTTCTCGGCGTCGGCA 60.048 55.556 19.59 5.26 42.47 5.69
779 787 2.292802 GATTTTCTCGGCGTCGGCAC 62.293 60.000 19.59 0.00 42.47 5.01
808 816 4.052518 CCCTGGGGCTGTTGAGGG 62.053 72.222 4.27 0.00 39.42 4.30
809 817 4.748144 CCTGGGGCTGTTGAGGGC 62.748 72.222 0.00 0.00 0.00 5.19
816 824 3.114616 CTGTTGAGGGCGCGAGTG 61.115 66.667 12.10 0.00 0.00 3.51
817 825 4.680237 TGTTGAGGGCGCGAGTGG 62.680 66.667 12.10 0.00 0.00 4.00
818 826 4.373116 GTTGAGGGCGCGAGTGGA 62.373 66.667 12.10 0.00 0.00 4.02
819 827 4.069232 TTGAGGGCGCGAGTGGAG 62.069 66.667 12.10 0.00 0.00 3.86
821 829 3.532155 GAGGGCGCGAGTGGAGAT 61.532 66.667 12.10 0.00 0.00 2.75
822 830 3.781770 GAGGGCGCGAGTGGAGATG 62.782 68.421 12.10 0.00 0.00 2.90
824 832 4.521062 GGCGCGAGTGGAGATGCT 62.521 66.667 12.10 0.00 0.00 3.79
825 833 2.959071 GCGCGAGTGGAGATGCTC 60.959 66.667 12.10 0.00 0.00 4.26
826 834 2.804167 CGCGAGTGGAGATGCTCT 59.196 61.111 0.00 0.00 0.00 4.09
827 835 1.140589 CGCGAGTGGAGATGCTCTT 59.859 57.895 0.00 0.00 0.00 2.85
828 836 0.382158 CGCGAGTGGAGATGCTCTTA 59.618 55.000 0.00 0.00 0.00 2.10
829 837 1.599171 CGCGAGTGGAGATGCTCTTAG 60.599 57.143 0.00 0.00 0.00 2.18
939 2980 3.130160 CCTCCCTGCGCTTGCTTC 61.130 66.667 9.73 0.00 40.12 3.86
980 3022 2.228103 CACATCACAGAGCACAAGCAAT 59.772 45.455 0.00 0.00 45.49 3.56
1044 3086 0.962356 CGTTGCTGGATGGGAAGCTT 60.962 55.000 0.00 0.00 40.21 3.74
1047 3089 2.128771 TGCTGGATGGGAAGCTTAAC 57.871 50.000 0.00 0.00 40.21 2.01
1309 3351 1.137282 TCGCGCTCATGGTACCAATTA 59.863 47.619 20.76 6.35 0.00 1.40
1313 3355 5.105675 TCGCGCTCATGGTACCAATTATATA 60.106 40.000 20.76 0.00 0.00 0.86
1314 3356 5.005394 CGCGCTCATGGTACCAATTATATAC 59.995 44.000 20.76 4.01 0.00 1.47
1315 3357 5.293569 GCGCTCATGGTACCAATTATATACC 59.706 44.000 20.76 0.00 39.12 2.73
1361 3403 7.120716 TCTCCATTGATTTGATCTGATTCCAA 58.879 34.615 0.00 0.00 0.00 3.53
1369 3411 2.511218 TGATCTGATTCCAAGGGAAGGG 59.489 50.000 3.85 0.00 45.48 3.95
1371 3413 0.396278 CTGATTCCAAGGGAAGGGGC 60.396 60.000 3.85 0.00 45.48 5.80
1373 3415 2.911221 GATTCCAAGGGAAGGGGCCG 62.911 65.000 0.00 0.00 45.48 6.13
1638 3794 7.123397 TCTGTCTGCAGATTAATTACTCAGACT 59.877 37.037 21.47 3.99 45.94 3.24
1696 3852 9.477484 AGTTGTATCAGTTAATATCCTAAAGCG 57.523 33.333 0.00 0.00 0.00 4.68
1724 3880 5.335261 TGGTTAGGTCCTTGACATGTACTA 58.665 41.667 0.00 0.00 33.68 1.82
2107 4355 4.278419 CCCTATTATGCTGGCACCTAAAAC 59.722 45.833 0.00 0.00 0.00 2.43
2138 4386 9.309516 CGCTTTAGTCCTTACACATTTATTCTA 57.690 33.333 0.00 0.00 0.00 2.10
2164 4412 2.438868 GGAAAAGTCCTTGCGCATTT 57.561 45.000 12.75 7.66 41.24 2.32
2259 4507 5.347012 CCATTTGGCTTCAAATTCAACAC 57.653 39.130 2.05 0.00 45.71 3.32
2271 4519 6.871844 TCAAATTCAACACAAGGAAACATCA 58.128 32.000 0.00 0.00 0.00 3.07
2384 4632 2.957006 CAGTTGTCTAGCCGGTAGGTAT 59.043 50.000 1.90 0.00 40.50 2.73
2400 4648 7.368833 CGGTAGGTATTATAAGACTGGTCAAG 58.631 42.308 9.93 0.00 0.00 3.02
2457 4705 4.400884 AGTGTGTTGTGGTTGCAAAGATAA 59.599 37.500 0.00 0.00 0.00 1.75
2508 4756 9.900710 ACTCTCAAGTATGCTTCGTTATAATAG 57.099 33.333 0.00 0.00 32.59 1.73
2547 4795 5.066505 GGCTAGGACCATTGTTGTAAGATTG 59.933 44.000 0.00 0.00 0.00 2.67
2548 4796 5.449177 GCTAGGACCATTGTTGTAAGATTGC 60.449 44.000 0.00 0.00 0.00 3.56
2727 4991 2.416547 GGTAGTGCAGTATGTTGCTGTG 59.583 50.000 4.19 0.00 44.38 3.66
2835 5103 3.316283 CACAAAACCTTACGCAATGCAT 58.684 40.909 5.91 0.00 0.00 3.96
3023 5297 2.289133 GGCTCTCTTTTCAGTCCTCGTT 60.289 50.000 0.00 0.00 0.00 3.85
3370 5645 0.034670 AGATTCAAGCAGACCTGGGC 60.035 55.000 0.00 0.00 0.00 5.36
3460 5735 5.304871 TGATGGTGTGGTTAGTACACTTACA 59.695 40.000 8.01 0.00 45.82 2.41
3467 5742 6.016024 TGTGGTTAGTACACTTACAACGATCT 60.016 38.462 0.00 0.00 39.52 2.75
3547 5822 3.230134 ACCTACAAATGGCAGCTTTGAA 58.770 40.909 17.84 0.00 37.12 2.69
4181 6460 9.471702 AATGGATCTCTCTAAATGTGTTTCAAT 57.528 29.630 0.00 0.00 0.00 2.57
4385 6664 6.433404 ACATGTCTTTCTGAAATTCAGCATCT 59.567 34.615 17.58 1.13 43.95 2.90
4588 6867 1.308998 CGACAAACAGCAAAGAGGGT 58.691 50.000 0.00 0.00 0.00 4.34
4641 6920 6.642707 TGTTAGGTTTAACTTGAACATGGG 57.357 37.500 0.00 0.00 39.90 4.00
4642 6921 5.536916 TGTTAGGTTTAACTTGAACATGGGG 59.463 40.000 0.00 0.00 39.90 4.96
4660 6939 2.637947 GGGCTGGAAGTTTGAGAGATC 58.362 52.381 0.00 0.00 35.30 2.75
4666 6945 5.296151 TGGAAGTTTGAGAGATCAAGTGT 57.704 39.130 0.00 0.00 0.00 3.55
4751 7030 8.394121 CAAGTAGGAAGAGCTGAATAAAATGTC 58.606 37.037 0.00 0.00 0.00 3.06
4754 7033 3.933155 AGAGCTGAATAAAATGTCGCG 57.067 42.857 0.00 0.00 0.00 5.87
4794 7073 3.543680 AAGATCTGGAATGGTGTACCG 57.456 47.619 0.00 0.00 39.43 4.02
5093 7373 2.028385 ACCAACAGGATCAACTACGACC 60.028 50.000 0.00 0.00 0.00 4.79
5103 7383 0.739561 AACTACGACCGCTGAGATCC 59.260 55.000 0.00 0.00 0.00 3.36
5144 7424 1.133407 GCACACTTTTCGGTGAACCAA 59.867 47.619 0.00 0.00 40.13 3.67
5145 7425 2.792749 CACACTTTTCGGTGAACCAAC 58.207 47.619 0.00 0.00 40.13 3.77
5146 7426 1.746787 ACACTTTTCGGTGAACCAACC 59.253 47.619 0.00 0.00 40.13 3.77
5147 7427 1.746220 CACTTTTCGGTGAACCAACCA 59.254 47.619 0.00 0.00 40.53 3.67
5520 7805 3.365832 CCATGCACGTTCATAAAGATGC 58.634 45.455 0.00 0.00 32.62 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.163078 CACTTAGATTCACCCTCACTCCAT 59.837 45.833 0.00 0.00 0.00 3.41
14 15 1.369625 CGGCACACTTAGATTCACCC 58.630 55.000 0.00 0.00 0.00 4.61
23 24 1.903860 AGGATTGTACCGGCACACTTA 59.096 47.619 7.11 0.00 34.73 2.24
66 67 6.015940 GGATTGTGAATTCCTTCTGTGAGTTT 60.016 38.462 2.27 0.00 32.29 2.66
77 78 4.934797 TTCCTCAGGATTGTGAATTCCT 57.065 40.909 0.00 0.00 0.00 3.36
99 100 4.738740 CGTTATCGGATTAGTCGAAAGCTT 59.261 41.667 0.00 0.00 40.15 3.74
141 142 4.664677 GACGCTCCACTGCACGGT 62.665 66.667 0.00 0.00 0.00 4.83
162 163 3.119424 GCTTGCTCTACTCCGACTACTTT 60.119 47.826 0.00 0.00 0.00 2.66
286 287 2.907703 AGCATCTCATGGTCCTCGT 58.092 52.632 0.00 0.00 35.90 4.18
322 323 0.683973 CTGGAGGAGGAATCCGATGG 59.316 60.000 0.00 0.00 39.91 3.51
329 330 2.906458 CGCTGCTGGAGGAGGAAT 59.094 61.111 0.00 0.00 33.79 3.01
461 462 0.036952 CTCTTGGGCGAGCTTTCTGA 60.037 55.000 0.00 0.00 0.00 3.27
646 654 1.001269 CTCCGGGGAAGGAAAACCC 60.001 63.158 0.00 0.00 44.89 4.11
647 655 1.677966 GCTCCGGGGAAGGAAAACC 60.678 63.158 4.80 0.00 40.25 3.27
648 656 2.038837 CGCTCCGGGGAAGGAAAAC 61.039 63.158 4.80 0.00 40.25 2.43
649 657 2.349755 CGCTCCGGGGAAGGAAAA 59.650 61.111 4.80 0.00 40.25 2.29
650 658 4.404098 GCGCTCCGGGGAAGGAAA 62.404 66.667 4.80 0.00 40.25 3.13
670 678 2.509336 CGAACCCAGCGCACTAGG 60.509 66.667 11.47 6.84 0.00 3.02
671 679 2.509336 CCGAACCCAGCGCACTAG 60.509 66.667 11.47 0.00 0.00 2.57
672 680 3.307906 ACCGAACCCAGCGCACTA 61.308 61.111 11.47 0.00 0.00 2.74
673 681 4.988598 CACCGAACCCAGCGCACT 62.989 66.667 11.47 0.00 0.00 4.40
679 687 4.760047 CGAGGCCACCGAACCCAG 62.760 72.222 5.01 0.00 0.00 4.45
682 690 3.735037 GATCCGAGGCCACCGAACC 62.735 68.421 17.57 3.89 0.00 3.62
683 691 2.202892 GATCCGAGGCCACCGAAC 60.203 66.667 17.57 1.40 0.00 3.95
684 692 3.833645 CGATCCGAGGCCACCGAA 61.834 66.667 17.57 0.00 0.00 4.30
696 704 3.065567 TTTTTGGGCCGGCGATCC 61.066 61.111 22.54 17.20 0.00 3.36
711 719 1.586154 CGCTGGCTCGACCCATTTTT 61.586 55.000 0.00 0.00 37.83 1.94
712 720 2.040544 CGCTGGCTCGACCCATTTT 61.041 57.895 0.00 0.00 37.83 1.82
713 721 2.436646 CGCTGGCTCGACCCATTT 60.437 61.111 0.00 0.00 37.83 2.32
714 722 4.473520 CCGCTGGCTCGACCCATT 62.474 66.667 0.00 0.00 37.83 3.16
717 725 3.682292 AAATCCGCTGGCTCGACCC 62.682 63.158 1.55 0.00 37.83 4.46
718 726 2.125106 AAATCCGCTGGCTCGACC 60.125 61.111 1.55 0.00 39.84 4.79
719 727 2.517450 CGAAATCCGCTGGCTCGAC 61.517 63.158 1.55 0.00 0.00 4.20
720 728 2.202743 CGAAATCCGCTGGCTCGA 60.203 61.111 1.55 0.00 0.00 4.04
721 729 2.509336 ACGAAATCCGCTGGCTCG 60.509 61.111 0.00 9.89 43.32 5.03
722 730 2.517450 CGACGAAATCCGCTGGCTC 61.517 63.158 0.00 0.00 43.32 4.70
723 731 2.509336 CGACGAAATCCGCTGGCT 60.509 61.111 0.00 0.00 43.32 4.75
724 732 2.292802 GAACGACGAAATCCGCTGGC 62.293 60.000 0.00 0.00 43.32 4.85
725 733 0.736325 AGAACGACGAAATCCGCTGG 60.736 55.000 0.00 0.00 43.32 4.85
726 734 0.366871 CAGAACGACGAAATCCGCTG 59.633 55.000 0.00 0.00 43.32 5.18
727 735 0.736325 CCAGAACGACGAAATCCGCT 60.736 55.000 0.00 0.00 43.32 5.52
728 736 1.693083 CCCAGAACGACGAAATCCGC 61.693 60.000 0.00 0.00 43.32 5.54
729 737 0.108992 TCCCAGAACGACGAAATCCG 60.109 55.000 0.00 0.00 45.44 4.18
730 738 1.933853 CATCCCAGAACGACGAAATCC 59.066 52.381 0.00 0.00 0.00 3.01
731 739 1.327764 GCATCCCAGAACGACGAAATC 59.672 52.381 0.00 0.00 0.00 2.17
732 740 1.369625 GCATCCCAGAACGACGAAAT 58.630 50.000 0.00 0.00 0.00 2.17
733 741 1.011968 CGCATCCCAGAACGACGAAA 61.012 55.000 0.00 0.00 0.00 3.46
734 742 1.445410 CGCATCCCAGAACGACGAA 60.445 57.895 0.00 0.00 0.00 3.85
735 743 2.180769 CGCATCCCAGAACGACGA 59.819 61.111 0.00 0.00 0.00 4.20
736 744 2.158959 GTCGCATCCCAGAACGACG 61.159 63.158 7.48 0.00 44.42 5.12
737 745 3.782042 GTCGCATCCCAGAACGAC 58.218 61.111 7.48 7.48 46.64 4.34
738 746 1.215382 CAGTCGCATCCCAGAACGA 59.785 57.895 0.00 0.00 0.00 3.85
739 747 0.803768 CTCAGTCGCATCCCAGAACG 60.804 60.000 0.00 0.00 0.00 3.95
740 748 0.460987 CCTCAGTCGCATCCCAGAAC 60.461 60.000 0.00 0.00 0.00 3.01
741 749 1.617018 CCCTCAGTCGCATCCCAGAA 61.617 60.000 0.00 0.00 0.00 3.02
742 750 2.060383 CCCTCAGTCGCATCCCAGA 61.060 63.158 0.00 0.00 0.00 3.86
743 751 1.406065 ATCCCTCAGTCGCATCCCAG 61.406 60.000 0.00 0.00 0.00 4.45
744 752 0.982852 AATCCCTCAGTCGCATCCCA 60.983 55.000 0.00 0.00 0.00 4.37
745 753 0.181350 AAATCCCTCAGTCGCATCCC 59.819 55.000 0.00 0.00 0.00 3.85
746 754 1.943340 GAAAATCCCTCAGTCGCATCC 59.057 52.381 0.00 0.00 0.00 3.51
747 755 2.869192 GAGAAAATCCCTCAGTCGCATC 59.131 50.000 0.00 0.00 0.00 3.91
748 756 2.739932 CGAGAAAATCCCTCAGTCGCAT 60.740 50.000 0.00 0.00 0.00 4.73
749 757 1.404181 CGAGAAAATCCCTCAGTCGCA 60.404 52.381 0.00 0.00 0.00 5.10
750 758 1.281899 CGAGAAAATCCCTCAGTCGC 58.718 55.000 0.00 0.00 0.00 5.19
751 759 1.927895 CCGAGAAAATCCCTCAGTCG 58.072 55.000 0.00 0.00 0.00 4.18
752 760 1.657822 GCCGAGAAAATCCCTCAGTC 58.342 55.000 0.00 0.00 0.00 3.51
753 761 0.108138 CGCCGAGAAAATCCCTCAGT 60.108 55.000 0.00 0.00 0.00 3.41
754 762 0.108138 ACGCCGAGAAAATCCCTCAG 60.108 55.000 0.00 0.00 0.00 3.35
755 763 0.108329 GACGCCGAGAAAATCCCTCA 60.108 55.000 0.00 0.00 0.00 3.86
756 764 1.146358 CGACGCCGAGAAAATCCCTC 61.146 60.000 0.00 0.00 38.22 4.30
757 765 1.153628 CGACGCCGAGAAAATCCCT 60.154 57.895 0.00 0.00 38.22 4.20
758 766 2.171725 CCGACGCCGAGAAAATCCC 61.172 63.158 0.00 0.00 38.22 3.85
759 767 2.810012 GCCGACGCCGAGAAAATCC 61.810 63.158 0.00 0.00 38.22 3.01
760 768 2.098233 TGCCGACGCCGAGAAAATC 61.098 57.895 0.00 0.00 38.22 2.17
761 769 2.047655 TGCCGACGCCGAGAAAAT 60.048 55.556 0.00 0.00 38.22 1.82
762 770 3.039588 GTGCCGACGCCGAGAAAA 61.040 61.111 0.00 0.00 38.22 2.29
767 775 4.946266 TTTTCGTGCCGACGCCGA 62.946 61.111 0.00 0.00 45.68 5.54
768 776 4.003011 TTTTTCGTGCCGACGCCG 62.003 61.111 0.00 0.00 45.68 6.46
791 799 4.052518 CCCTCAACAGCCCCAGGG 62.053 72.222 0.00 0.00 39.90 4.45
792 800 4.748144 GCCCTCAACAGCCCCAGG 62.748 72.222 0.00 0.00 0.00 4.45
799 807 3.114616 CACTCGCGCCCTCAACAG 61.115 66.667 0.00 0.00 0.00 3.16
800 808 4.680237 CCACTCGCGCCCTCAACA 62.680 66.667 0.00 0.00 0.00 3.33
801 809 4.373116 TCCACTCGCGCCCTCAAC 62.373 66.667 0.00 0.00 0.00 3.18
802 810 4.069232 CTCCACTCGCGCCCTCAA 62.069 66.667 0.00 0.00 0.00 3.02
804 812 3.532155 ATCTCCACTCGCGCCCTC 61.532 66.667 0.00 0.00 0.00 4.30
805 813 3.842923 CATCTCCACTCGCGCCCT 61.843 66.667 0.00 0.00 0.00 5.19
807 815 4.521062 AGCATCTCCACTCGCGCC 62.521 66.667 0.00 0.00 0.00 6.53
808 816 2.959071 GAGCATCTCCACTCGCGC 60.959 66.667 0.00 0.00 0.00 6.86
939 2980 1.738099 GTGTACGGAGCAGCAGGTG 60.738 63.158 0.00 0.00 0.00 4.00
980 3022 0.336392 TCCCTCTCTCTGCAGGCTTA 59.664 55.000 15.13 0.00 0.00 3.09
1062 3104 2.125106 GCCTCTCCGTCGCCATTT 60.125 61.111 0.00 0.00 0.00 2.32
1309 3351 6.814954 AGGATGAGGCGAAATATGGTATAT 57.185 37.500 0.00 0.00 0.00 0.86
1313 3355 3.392616 AGAAGGATGAGGCGAAATATGGT 59.607 43.478 0.00 0.00 0.00 3.55
1314 3356 4.013267 AGAAGGATGAGGCGAAATATGG 57.987 45.455 0.00 0.00 0.00 2.74
1315 3357 5.303971 AGAAGAAGGATGAGGCGAAATATG 58.696 41.667 0.00 0.00 0.00 1.78
1322 3364 0.826715 TGGAGAAGAAGGATGAGGCG 59.173 55.000 0.00 0.00 0.00 5.52
1369 3411 3.855853 GAGGAGGAGAAGCCGGCC 61.856 72.222 26.15 9.10 43.43 6.13
1371 3413 1.076339 AGAGAGGAGGAGAAGCCGG 60.076 63.158 0.00 0.00 43.43 6.13
1373 3415 1.111277 GACAGAGAGGAGGAGAAGCC 58.889 60.000 0.00 0.00 0.00 4.35
1374 3416 1.111277 GGACAGAGAGGAGGAGAAGC 58.889 60.000 0.00 0.00 0.00 3.86
1377 3419 1.388174 AAGGGACAGAGAGGAGGAGA 58.612 55.000 0.00 0.00 0.00 3.71
1670 3826 9.477484 CGCTTTAGGATATTAACTGATACAACT 57.523 33.333 0.00 0.00 0.00 3.16
1671 3827 9.257651 ACGCTTTAGGATATTAACTGATACAAC 57.742 33.333 0.00 0.00 0.00 3.32
1678 3834 9.052759 ACCAAATACGCTTTAGGATATTAACTG 57.947 33.333 0.00 0.00 0.00 3.16
1696 3852 5.944007 ACATGTCAAGGACCTAACCAAATAC 59.056 40.000 0.00 0.00 0.00 1.89
1791 4030 5.451520 CCAATCCAAGATTGAGAAGCCATTC 60.452 44.000 16.89 0.00 35.52 2.67
1934 4173 7.633789 ACCCAACACTGAAAGAATATCATACT 58.366 34.615 0.00 0.00 37.43 2.12
1935 4174 7.865706 ACCCAACACTGAAAGAATATCATAC 57.134 36.000 0.00 0.00 37.43 2.39
2107 4355 3.251571 GTGTAAGGACTAAAGCGACAGG 58.748 50.000 0.00 0.00 0.00 4.00
2145 4393 2.061028 CAAATGCGCAAGGACTTTTCC 58.939 47.619 17.11 0.00 44.26 3.13
2259 4507 3.054878 GCTGCACTTTGATGTTTCCTTG 58.945 45.455 0.00 0.00 0.00 3.61
2271 4519 4.885413 TGCATAAATTTCTGCTGCACTTT 58.115 34.783 23.88 0.00 37.88 2.66
2339 4587 6.932960 TGATCATAGCTCATGTACTGAAATGG 59.067 38.462 0.00 0.00 35.96 3.16
2457 4705 3.276857 CTCTATGCTTCACAGCCAACAT 58.723 45.455 0.00 0.00 46.74 2.71
2494 4742 7.753580 ACAAACTTTTGCCTATTATAACGAAGC 59.246 33.333 1.49 0.00 41.79 3.86
2508 4756 2.029918 CCTAGCCTGACAAACTTTTGCC 60.030 50.000 1.49 0.00 41.79 4.52
2547 4795 0.595095 GGCGATGAAAGATCCATGGC 59.405 55.000 6.96 8.31 42.50 4.40
2548 4796 1.971481 TGGCGATGAAAGATCCATGG 58.029 50.000 4.97 4.97 0.00 3.66
2727 4991 3.942115 GTCTAACCAGGGCTGAAGAAATC 59.058 47.826 0.00 0.00 0.00 2.17
2835 5103 9.939802 GTTCCTCTTGGTTTCTCTACTAAAATA 57.060 33.333 0.00 0.00 34.23 1.40
3023 5297 0.898326 TGTAGAGCCACAGGAGCGAA 60.898 55.000 0.00 0.00 34.64 4.70
3370 5645 1.535462 ACGCTTCTGTTGAAAATCCCG 59.465 47.619 0.00 0.00 0.00 5.14
3460 5735 5.922053 TCAATGAATGGATCTGAGATCGTT 58.078 37.500 15.64 12.70 0.00 3.85
3467 5742 3.072038 AGGCGATCAATGAATGGATCTGA 59.928 43.478 6.19 0.00 38.18 3.27
3522 5797 3.433306 AGCTGCCATTTGTAGGTAACA 57.567 42.857 0.00 0.00 35.52 2.41
3547 5822 4.141482 ACCAATATCTCAAACGCCCAGTAT 60.141 41.667 0.00 0.00 0.00 2.12
3850 6125 8.296713 GCATTGTCAACTTAATCTTAAAGGACA 58.703 33.333 0.00 0.00 31.29 4.02
3851 6126 8.515414 AGCATTGTCAACTTAATCTTAAAGGAC 58.485 33.333 0.00 0.00 0.00 3.85
4181 6460 4.079253 GGCCTTCACCTGAAACAATAAGA 58.921 43.478 0.00 0.00 33.07 2.10
4385 6664 3.191162 GCACAACAAACATGCCTGAGATA 59.809 43.478 0.00 0.00 33.06 1.98
4477 6756 4.384537 CCGCATATCTGACCCATCCATAAT 60.385 45.833 0.00 0.00 0.00 1.28
4480 6759 1.280133 CCGCATATCTGACCCATCCAT 59.720 52.381 0.00 0.00 0.00 3.41
4618 6897 5.536916 CCCCATGTTCAAGTTAAACCTAACA 59.463 40.000 0.00 0.00 40.03 2.41
4641 6920 3.340814 TGATCTCTCAAACTTCCAGCC 57.659 47.619 0.00 0.00 0.00 4.85
4642 6921 4.153835 CACTTGATCTCTCAAACTTCCAGC 59.846 45.833 0.00 0.00 40.78 4.85
4660 6939 7.439955 TGGTACTGTCTACATTTACAACACTTG 59.560 37.037 0.00 0.00 0.00 3.16
4666 6945 6.526526 TGCTTGGTACTGTCTACATTTACAA 58.473 36.000 0.00 0.00 0.00 2.41
4751 7030 0.515127 TATCACACAAAACTGGCGCG 59.485 50.000 0.00 0.00 0.00 6.86
4794 7073 2.673368 CAAACACTGCTTCGGAGGTATC 59.327 50.000 0.00 0.00 0.00 2.24
4876 7155 7.916977 GTCAGCAATGTGATATTTTCTGCAATA 59.083 33.333 0.00 0.00 0.00 1.90
4939 7219 4.591498 TGAGTTACCTTAGGAAAGCAGACA 59.409 41.667 4.77 0.00 0.00 3.41
5033 7313 5.022227 AGTTATATGGGATCTGCTCCTCT 57.978 43.478 0.00 0.00 44.28 3.69
5093 7373 2.420890 GCTGGAGGGATCTCAGCG 59.579 66.667 12.35 0.00 41.69 5.18
5103 7383 3.245668 AAGCTGGTGTCGCTGGAGG 62.246 63.158 0.00 0.00 37.87 4.30
5144 7424 3.600388 GAAGACGATTGATCCTGTTGGT 58.400 45.455 0.00 0.00 34.23 3.67
5145 7425 2.604914 CGAAGACGATTGATCCTGTTGG 59.395 50.000 0.00 0.00 42.66 3.77
5146 7426 3.511699 TCGAAGACGATTGATCCTGTTG 58.488 45.455 0.00 0.00 43.81 3.33
5147 7427 3.868757 TCGAAGACGATTGATCCTGTT 57.131 42.857 0.00 0.00 43.81 3.16
5171 7451 3.756117 ACTGCTTTTTCTTCGGGAAGAT 58.244 40.909 11.60 0.00 45.78 2.40
5520 7805 4.761739 ACAGGACAATGAACAACATAGTGG 59.238 41.667 0.00 0.00 38.38 4.00


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

AutoCloner maintained by Alex Coulton.