Multiple sequence alignment - TraesCS3D01G083800

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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 TraesCS3D01G083800 chr3D 100.000 5801 0 0 1 5801 42499056 42493256 0.000000e+00 10713.0
1 TraesCS3D01G083800 chr3A 97.068 3684 87 9 873 4541 53842150 53838473 0.000000e+00 6185.0
2 TraesCS3D01G083800 chr3A 96.833 1263 23 7 4539 5801 53838448 53837203 0.000000e+00 2095.0
3 TraesCS3D01G083800 chr3A 96.970 33 1 0 850 882 53842208 53842176 8.120000e-04 56.5
4 TraesCS3D01G083800 chr3B 96.903 3681 89 10 873 4541 66190120 66186453 0.000000e+00 6143.0
5 TraesCS3D01G083800 chr3B 97.319 1268 26 3 4539 5801 66186428 66185164 0.000000e+00 2146.0
6 TraesCS3D01G083800 chr3B 84.141 227 30 5 4296 4518 170804708 170804932 1.270000e-51 215.0
7 TraesCS3D01G083800 chr3B 78.261 253 47 6 4271 4518 126652954 126653203 7.780000e-34 156.0
8 TraesCS3D01G083800 chr3B 97.368 38 1 0 850 887 66190179 66190142 1.350000e-06 65.8
9 TraesCS3D01G083800 chr7D 87.727 717 67 15 1 705 637148802 637149509 0.000000e+00 817.0
10 TraesCS3D01G083800 chr7D 86.869 693 66 17 29 705 595647102 595646419 0.000000e+00 752.0
11 TraesCS3D01G083800 chr5A 86.740 724 65 21 4 705 296306679 296305965 0.000000e+00 776.0
12 TraesCS3D01G083800 chr6D 86.283 729 63 21 1 705 347714022 347714737 0.000000e+00 758.0
13 TraesCS3D01G083800 chr6D 85.950 726 69 17 4 705 422220913 422220197 0.000000e+00 745.0
14 TraesCS3D01G083800 chr4D 86.389 720 66 19 4 705 500549227 500549932 0.000000e+00 758.0
15 TraesCS3D01G083800 chr4D 88.764 89 4 2 2269 2357 132962133 132962215 2.860000e-18 104.0
16 TraesCS3D01G083800 chr1D 86.069 725 71 18 4 705 470919736 470919019 0.000000e+00 752.0
17 TraesCS3D01G083800 chr2A 85.908 738 62 26 1 705 749965466 749966194 0.000000e+00 749.0
18 TraesCS3D01G083800 chr2A 84.615 104 10 3 2266 2368 86440630 86440532 1.330000e-16 99.0
19 TraesCS3D01G083800 chr2D 85.576 721 74 22 1 705 489573435 489574141 0.000000e+00 728.0
20 TraesCS3D01G083800 chr2D 85.870 460 50 7 4539 4990 612521106 612520654 5.260000e-130 475.0
21 TraesCS3D01G083800 chr2D 84.426 244 30 7 4281 4518 612521397 612521156 3.500000e-57 233.0
22 TraesCS3D01G083800 chr2D 85.577 104 9 3 2266 2368 86081000 86080902 2.860000e-18 104.0
23 TraesCS3D01G083800 chr2D 82.979 94 9 4 2272 2364 494729739 494729652 1.730000e-10 78.7
24 TraesCS3D01G083800 chr1A 86.214 457 51 6 4539 4990 308302279 308301830 8.740000e-133 484.0
25 TraesCS3D01G083800 chr1A 84.016 244 31 7 4281 4518 308302570 308302329 1.630000e-55 228.0
26 TraesCS3D01G083800 chr4A 81.779 461 52 10 4539 4993 619158797 619158363 1.990000e-94 357.0
27 TraesCS3D01G083800 chr4A 82.018 228 33 6 4296 4518 619159071 619158847 2.760000e-43 187.0
28 TraesCS3D01G083800 chr2B 86.538 104 8 3 2266 2368 139072918 139072820 6.150000e-20 110.0
29 TraesCS3D01G083800 chr5D 82.796 93 11 3 2269 2361 527571291 527571378 1.730000e-10 78.7
30 TraesCS3D01G083800 chr5D 82.796 93 11 3 2269 2361 527600854 527600941 1.730000e-10 78.7


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 TraesCS3D01G083800 chr3D 42493256 42499056 5800 True 10713.000000 10713 100.000000 1 5801 1 chr3D.!!$R1 5800
1 TraesCS3D01G083800 chr3A 53837203 53842208 5005 True 2778.833333 6185 96.957000 850 5801 3 chr3A.!!$R1 4951
2 TraesCS3D01G083800 chr3B 66185164 66190179 5015 True 2784.933333 6143 97.196667 850 5801 3 chr3B.!!$R1 4951
3 TraesCS3D01G083800 chr7D 637148802 637149509 707 False 817.000000 817 87.727000 1 705 1 chr7D.!!$F1 704
4 TraesCS3D01G083800 chr7D 595646419 595647102 683 True 752.000000 752 86.869000 29 705 1 chr7D.!!$R1 676
5 TraesCS3D01G083800 chr5A 296305965 296306679 714 True 776.000000 776 86.740000 4 705 1 chr5A.!!$R1 701
6 TraesCS3D01G083800 chr6D 347714022 347714737 715 False 758.000000 758 86.283000 1 705 1 chr6D.!!$F1 704
7 TraesCS3D01G083800 chr6D 422220197 422220913 716 True 745.000000 745 85.950000 4 705 1 chr6D.!!$R1 701
8 TraesCS3D01G083800 chr4D 500549227 500549932 705 False 758.000000 758 86.389000 4 705 1 chr4D.!!$F2 701
9 TraesCS3D01G083800 chr1D 470919019 470919736 717 True 752.000000 752 86.069000 4 705 1 chr1D.!!$R1 701
10 TraesCS3D01G083800 chr2A 749965466 749966194 728 False 749.000000 749 85.908000 1 705 1 chr2A.!!$F1 704
11 TraesCS3D01G083800 chr2D 489573435 489574141 706 False 728.000000 728 85.576000 1 705 1 chr2D.!!$F1 704
12 TraesCS3D01G083800 chr2D 612520654 612521397 743 True 354.000000 475 85.148000 4281 4990 2 chr2D.!!$R3 709
13 TraesCS3D01G083800 chr1A 308301830 308302570 740 True 356.000000 484 85.115000 4281 4990 2 chr1A.!!$R1 709
14 TraesCS3D01G083800 chr4A 619158363 619159071 708 True 272.000000 357 81.898500 4296 4993 2 chr4A.!!$R1 697

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
844 899 0.106519 CCCATGTAGGCCCAAGAAGG 60.107 60.000 0.0 0.0 35.39 3.46 F
1689 1788 0.109319 CCAACATGCCAAACTACGCC 60.109 55.000 0.0 0.0 0.00 5.68 F
2546 2656 1.017387 CTGAGCCCAATTCTTACGGC 58.983 55.000 0.0 0.0 41.96 5.68 F
2877 2987 1.338389 GCAGCCACCATGAAAAATGCT 60.338 47.619 0.0 0.0 0.00 3.79 F
3991 4101 1.203287 GAGGTGGCAAAGATGAAAGGC 59.797 52.381 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2658 2768 0.676466 CGTTACTGAGGGCCAATGCA 60.676 55.000 6.18 0.0 40.13 3.96 R
3434 3544 3.515502 TGATCTTGACCGAGACTTGGATT 59.484 43.478 16.24 0.0 0.00 3.01 R
3991 4101 0.320374 TCCACTGCGTCCTTTACAGG 59.680 55.000 0.00 0.0 42.50 4.00 R
4701 4849 0.394565 AGCACATATCTTCCTCGGCC 59.605 55.000 0.00 0.0 0.00 6.13 R
5778 5944 0.036022 GCAGAGGACAGGTGCTTCTT 59.964 55.000 0.00 0.0 34.23 2.52 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
321 340 0.304705 ACTCTCGCAAAAGCACAACG 59.695 50.000 0.00 0.00 0.00 4.10
352 371 0.234884 GGAAGCAAAACCGTGACTCG 59.765 55.000 0.00 0.00 39.52 4.18
353 372 0.935196 GAAGCAAAACCGTGACTCGT 59.065 50.000 0.00 0.00 37.94 4.18
357 379 1.062880 GCAAAACCGTGACTCGTGAAA 59.937 47.619 0.00 0.00 37.94 2.69
551 598 1.483004 CTGGGGGAAAACCAAAACGTT 59.517 47.619 0.00 0.00 42.91 3.99
705 760 2.959275 CGAAGGAGCGCTCGTTAAT 58.041 52.632 36.96 21.62 37.75 1.40
706 761 1.278238 CGAAGGAGCGCTCGTTAATT 58.722 50.000 36.96 21.28 37.75 1.40
707 762 1.659098 CGAAGGAGCGCTCGTTAATTT 59.341 47.619 36.96 20.92 37.75 1.82
708 763 2.534939 CGAAGGAGCGCTCGTTAATTTG 60.535 50.000 36.96 22.86 37.75 2.32
709 764 0.727398 AGGAGCGCTCGTTAATTTGC 59.273 50.000 29.81 13.35 0.00 3.68
713 768 3.668641 CGCTCGTTAATTTGCGGTT 57.331 47.368 9.87 0.00 43.97 4.44
714 769 1.958417 CGCTCGTTAATTTGCGGTTT 58.042 45.000 9.87 0.00 43.97 3.27
715 770 1.902504 CGCTCGTTAATTTGCGGTTTC 59.097 47.619 9.87 0.00 43.97 2.78
716 771 2.412325 CGCTCGTTAATTTGCGGTTTCT 60.412 45.455 9.87 0.00 43.97 2.52
717 772 3.161306 GCTCGTTAATTTGCGGTTTCTC 58.839 45.455 0.00 0.00 0.00 2.87
718 773 3.364565 GCTCGTTAATTTGCGGTTTCTCA 60.365 43.478 0.00 0.00 0.00 3.27
719 774 4.394795 CTCGTTAATTTGCGGTTTCTCAG 58.605 43.478 0.00 0.00 0.00 3.35
720 775 4.059511 TCGTTAATTTGCGGTTTCTCAGA 58.940 39.130 0.00 0.00 0.00 3.27
721 776 4.084223 TCGTTAATTTGCGGTTTCTCAGAC 60.084 41.667 0.00 0.00 0.00 3.51
722 777 4.319190 CGTTAATTTGCGGTTTCTCAGACA 60.319 41.667 0.00 0.00 0.00 3.41
723 778 3.626028 AATTTGCGGTTTCTCAGACAC 57.374 42.857 0.00 0.00 0.00 3.67
724 779 2.031258 TTTGCGGTTTCTCAGACACA 57.969 45.000 0.00 0.00 0.00 3.72
725 780 2.031258 TTGCGGTTTCTCAGACACAA 57.969 45.000 0.00 0.00 0.00 3.33
726 781 2.031258 TGCGGTTTCTCAGACACAAA 57.969 45.000 0.00 0.00 0.00 2.83
727 782 1.939934 TGCGGTTTCTCAGACACAAAG 59.060 47.619 0.00 0.00 0.00 2.77
728 783 1.334149 GCGGTTTCTCAGACACAAAGC 60.334 52.381 0.00 0.00 0.00 3.51
729 784 1.264288 CGGTTTCTCAGACACAAAGCC 59.736 52.381 0.00 0.00 0.00 4.35
730 785 2.297701 GGTTTCTCAGACACAAAGCCA 58.702 47.619 0.00 0.00 0.00 4.75
731 786 2.291741 GGTTTCTCAGACACAAAGCCAG 59.708 50.000 0.00 0.00 0.00 4.85
732 787 3.206150 GTTTCTCAGACACAAAGCCAGA 58.794 45.455 0.00 0.00 0.00 3.86
733 788 3.777106 TTCTCAGACACAAAGCCAGAT 57.223 42.857 0.00 0.00 0.00 2.90
734 789 3.777106 TCTCAGACACAAAGCCAGATT 57.223 42.857 0.00 0.00 0.00 2.40
735 790 4.090761 TCTCAGACACAAAGCCAGATTT 57.909 40.909 0.00 0.00 0.00 2.17
736 791 5.227569 TCTCAGACACAAAGCCAGATTTA 57.772 39.130 0.00 0.00 0.00 1.40
737 792 4.997395 TCTCAGACACAAAGCCAGATTTAC 59.003 41.667 0.00 0.00 0.00 2.01
738 793 4.713553 TCAGACACAAAGCCAGATTTACA 58.286 39.130 0.00 0.00 0.00 2.41
739 794 5.129634 TCAGACACAAAGCCAGATTTACAA 58.870 37.500 0.00 0.00 0.00 2.41
740 795 5.592282 TCAGACACAAAGCCAGATTTACAAA 59.408 36.000 0.00 0.00 0.00 2.83
741 796 6.096141 TCAGACACAAAGCCAGATTTACAAAA 59.904 34.615 0.00 0.00 0.00 2.44
742 797 6.418819 CAGACACAAAGCCAGATTTACAAAAG 59.581 38.462 0.00 0.00 0.00 2.27
743 798 6.321181 AGACACAAAGCCAGATTTACAAAAGA 59.679 34.615 0.00 0.00 0.00 2.52
744 799 6.872920 ACACAAAGCCAGATTTACAAAAGAA 58.127 32.000 0.00 0.00 0.00 2.52
745 800 7.327214 ACACAAAGCCAGATTTACAAAAGAAA 58.673 30.769 0.00 0.00 0.00 2.52
746 801 7.986889 ACACAAAGCCAGATTTACAAAAGAAAT 59.013 29.630 0.00 0.00 0.00 2.17
747 802 8.829612 CACAAAGCCAGATTTACAAAAGAAATT 58.170 29.630 0.00 0.00 0.00 1.82
748 803 9.394767 ACAAAGCCAGATTTACAAAAGAAATTT 57.605 25.926 0.00 0.00 0.00 1.82
761 816 7.742556 CAAAAGAAATTTGGGCCTTATGAAA 57.257 32.000 4.53 0.00 43.85 2.69
762 817 8.164058 CAAAAGAAATTTGGGCCTTATGAAAA 57.836 30.769 4.53 0.00 43.85 2.29
763 818 8.628280 CAAAAGAAATTTGGGCCTTATGAAAAA 58.372 29.630 4.53 0.00 43.85 1.94
764 819 8.938801 AAAGAAATTTGGGCCTTATGAAAAAT 57.061 26.923 4.53 0.00 0.00 1.82
770 825 9.806448 AATTTGGGCCTTATGAAAAATAAAAGT 57.194 25.926 4.53 0.00 0.00 2.66
771 826 9.806448 ATTTGGGCCTTATGAAAAATAAAAGTT 57.194 25.926 4.53 0.00 0.00 2.66
791 846 8.797266 AAAGTTAAACGAATAGCAAGGAAAAG 57.203 30.769 0.00 0.00 0.00 2.27
792 847 6.909909 AGTTAAACGAATAGCAAGGAAAAGG 58.090 36.000 0.00 0.00 0.00 3.11
793 848 3.850122 AACGAATAGCAAGGAAAAGGC 57.150 42.857 0.00 0.00 0.00 4.35
794 849 2.092323 ACGAATAGCAAGGAAAAGGCC 58.908 47.619 0.00 0.00 0.00 5.19
795 850 1.064060 CGAATAGCAAGGAAAAGGCCG 59.936 52.381 0.00 0.00 0.00 6.13
796 851 2.365582 GAATAGCAAGGAAAAGGCCGA 58.634 47.619 0.00 0.00 0.00 5.54
797 852 2.736670 ATAGCAAGGAAAAGGCCGAT 57.263 45.000 0.00 0.00 0.00 4.18
798 853 1.750193 TAGCAAGGAAAAGGCCGATG 58.250 50.000 0.00 0.00 0.00 3.84
799 854 0.251341 AGCAAGGAAAAGGCCGATGT 60.251 50.000 0.00 0.00 0.00 3.06
800 855 1.004277 AGCAAGGAAAAGGCCGATGTA 59.996 47.619 0.00 0.00 0.00 2.29
801 856 1.816224 GCAAGGAAAAGGCCGATGTAA 59.184 47.619 0.00 0.00 0.00 2.41
802 857 2.159379 GCAAGGAAAAGGCCGATGTAAG 60.159 50.000 0.00 0.00 0.00 2.34
803 858 1.751437 AGGAAAAGGCCGATGTAAGC 58.249 50.000 0.00 0.00 0.00 3.09
808 863 3.827634 GGCCGATGTAAGCCCAAG 58.172 61.111 0.00 0.00 43.76 3.61
809 864 1.223487 GGCCGATGTAAGCCCAAGA 59.777 57.895 0.00 0.00 43.76 3.02
810 865 0.393808 GGCCGATGTAAGCCCAAGAA 60.394 55.000 0.00 0.00 43.76 2.52
811 866 1.017387 GCCGATGTAAGCCCAAGAAG 58.983 55.000 0.00 0.00 0.00 2.85
812 867 1.406887 GCCGATGTAAGCCCAAGAAGA 60.407 52.381 0.00 0.00 0.00 2.87
813 868 2.280628 CCGATGTAAGCCCAAGAAGAC 58.719 52.381 0.00 0.00 0.00 3.01
814 869 1.927174 CGATGTAAGCCCAAGAAGACG 59.073 52.381 0.00 0.00 0.00 4.18
815 870 1.666189 GATGTAAGCCCAAGAAGACGC 59.334 52.381 0.00 0.00 0.00 5.19
816 871 0.394938 TGTAAGCCCAAGAAGACGCA 59.605 50.000 0.00 0.00 0.00 5.24
817 872 1.202710 TGTAAGCCCAAGAAGACGCAA 60.203 47.619 0.00 0.00 0.00 4.85
819 874 0.890996 AAGCCCAAGAAGACGCAAGG 60.891 55.000 0.00 0.00 46.39 3.61
820 875 1.302511 GCCCAAGAAGACGCAAGGA 60.303 57.895 0.00 0.00 46.39 3.36
821 876 0.889186 GCCCAAGAAGACGCAAGGAA 60.889 55.000 0.00 0.00 46.39 3.36
822 877 1.604604 CCCAAGAAGACGCAAGGAAA 58.395 50.000 0.00 0.00 46.39 3.13
823 878 1.953686 CCCAAGAAGACGCAAGGAAAA 59.046 47.619 0.00 0.00 46.39 2.29
824 879 2.030805 CCCAAGAAGACGCAAGGAAAAG 60.031 50.000 0.00 0.00 46.39 2.27
825 880 2.605580 CCAAGAAGACGCAAGGAAAAGC 60.606 50.000 0.00 0.00 46.39 3.51
826 881 1.239347 AGAAGACGCAAGGAAAAGCC 58.761 50.000 0.00 0.00 46.39 4.35
827 882 0.241213 GAAGACGCAAGGAAAAGCCC 59.759 55.000 0.00 0.00 46.39 5.19
828 883 0.467290 AAGACGCAAGGAAAAGCCCA 60.467 50.000 0.00 0.00 46.39 5.36
829 884 0.251341 AGACGCAAGGAAAAGCCCAT 60.251 50.000 0.00 0.00 46.39 4.00
830 885 0.109132 GACGCAAGGAAAAGCCCATG 60.109 55.000 0.00 0.00 46.39 3.66
831 886 0.827507 ACGCAAGGAAAAGCCCATGT 60.828 50.000 0.00 0.00 46.39 3.21
832 887 1.173043 CGCAAGGAAAAGCCCATGTA 58.827 50.000 0.00 0.00 37.37 2.29
833 888 1.133025 CGCAAGGAAAAGCCCATGTAG 59.867 52.381 0.00 0.00 37.37 2.74
834 889 1.478105 GCAAGGAAAAGCCCATGTAGG 59.522 52.381 0.00 0.00 37.37 3.18
843 898 3.502164 CCCATGTAGGCCCAAGAAG 57.498 57.895 0.00 0.00 35.39 2.85
844 899 0.106519 CCCATGTAGGCCCAAGAAGG 60.107 60.000 0.00 0.00 35.39 3.46
928 1024 2.042520 CTCGTCTTCTCCTCTCCGCG 62.043 65.000 0.00 0.00 0.00 6.46
955 1051 4.079253 CAAAGCCAAACCCTAGAAAGCTA 58.921 43.478 0.00 0.00 0.00 3.32
956 1052 3.351794 AGCCAAACCCTAGAAAGCTAC 57.648 47.619 0.00 0.00 0.00 3.58
957 1053 2.026169 AGCCAAACCCTAGAAAGCTACC 60.026 50.000 0.00 0.00 0.00 3.18
958 1054 2.944542 GCCAAACCCTAGAAAGCTACCC 60.945 54.545 0.00 0.00 0.00 3.69
1572 1671 1.188219 TCCCTGTCTTCTTCAGCGCT 61.188 55.000 2.64 2.64 0.00 5.92
1689 1788 0.109319 CCAACATGCCAAACTACGCC 60.109 55.000 0.00 0.00 0.00 5.68
2050 2149 3.137533 GAGCAGGCTTCATCAGGTAATC 58.862 50.000 0.00 0.00 0.00 1.75
2106 2207 5.749109 GTGCGCTCTATTGTTGAACTAGTAT 59.251 40.000 9.73 0.00 0.00 2.12
2107 2208 6.916387 GTGCGCTCTATTGTTGAACTAGTATA 59.084 38.462 9.73 0.00 0.00 1.47
2109 2210 7.648112 TGCGCTCTATTGTTGAACTAGTATAAG 59.352 37.037 9.73 0.00 0.00 1.73
2165 2268 7.851228 TCCTCAGTATGCCGAATCAATAATAT 58.149 34.615 0.00 0.00 34.76 1.28
2184 2287 8.758633 ATAATATAGACATGTTAGGTCGCAAC 57.241 34.615 0.00 0.00 40.20 4.17
2313 2423 6.749923 AAGATGTTTCTTTAGGCTAGCTTG 57.250 37.500 15.72 0.00 39.18 4.01
2330 2440 2.223618 GCTTGGCCTACAAAAACGAACA 60.224 45.455 3.32 0.00 38.91 3.18
2462 2572 1.505353 GCTCACCTGCATGTTGAGC 59.495 57.895 21.66 21.66 43.83 4.26
2546 2656 1.017387 CTGAGCCCAATTCTTACGGC 58.983 55.000 0.00 0.00 41.96 5.68
2877 2987 1.338389 GCAGCCACCATGAAAAATGCT 60.338 47.619 0.00 0.00 0.00 3.79
3076 3186 5.947228 TGTTCCTGATTTTGCTCTACTTG 57.053 39.130 0.00 0.00 0.00 3.16
3090 3200 5.860182 TGCTCTACTTGTACATTACAACGTC 59.140 40.000 0.00 0.00 43.23 4.34
3233 3343 6.016276 TGTTTGTTTTCAAGAGATAGCTTCCC 60.016 38.462 0.00 0.00 41.09 3.97
3434 3544 1.682451 CCATCGCCCCCTTCTCGTAA 61.682 60.000 0.00 0.00 0.00 3.18
3991 4101 1.203287 GAGGTGGCAAAGATGAAAGGC 59.797 52.381 0.00 0.00 0.00 4.35
4044 4154 8.032952 CAGATACTTCTGTTGTTGCTCATAAA 57.967 34.615 0.00 0.00 43.73 1.40
4257 4367 6.267928 AGAAACATGACACAAGTAGGAGTACT 59.732 38.462 0.00 0.00 41.61 2.73
4401 4512 4.228210 TCCCATAGAAGTTCAAGGCATTCT 59.772 41.667 5.50 0.00 36.11 2.40
4639 4787 2.795329 TCCAGGAAGACCAGCAATTTC 58.205 47.619 0.00 0.00 38.94 2.17
4958 5111 0.473755 TTTGGAGAGCTTCAGTGCCA 59.526 50.000 0.00 0.00 0.00 4.92
5419 5572 4.752101 AGCAGCTTAATTGATCCGTATGTC 59.248 41.667 0.00 0.00 0.00 3.06
5438 5592 8.425491 CGTATGTCAAGTTCAGTAGTTGTTTAG 58.575 37.037 0.00 0.00 38.19 1.85
5777 5943 1.778591 GCACATGTTTGTTCGTTTCGG 59.221 47.619 0.00 0.00 32.34 4.30
5778 5944 2.539953 GCACATGTTTGTTCGTTTCGGA 60.540 45.455 0.00 0.00 32.34 4.55
5779 5945 3.686128 CACATGTTTGTTCGTTTCGGAA 58.314 40.909 0.00 0.00 32.34 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.163818 TCGCGAGAGTCATGGTTTTT 57.836 45.000 3.71 0.00 34.84 1.94
102 113 1.070786 TTTTGCTTCCGCGAGAGGT 59.929 52.632 8.23 0.00 39.65 3.85
169 182 2.970639 CGTGCCTCTCCGGAAAGA 59.029 61.111 6.29 0.00 33.16 2.52
190 203 0.038251 TGTGCTTTCGCGAGAGTCAT 60.038 50.000 25.34 0.00 43.69 3.06
271 284 3.009695 TGCCTCTCGGAAAGGGAAAAATA 59.990 43.478 0.00 0.00 34.26 1.40
321 340 2.435059 GCTTCCGTGAGAGGCACC 60.435 66.667 0.00 0.00 46.54 5.01
387 412 2.391389 GGCCGTGCCTCTCGAAAAG 61.391 63.158 7.58 0.00 46.69 2.27
511 557 5.478332 CCCAGTCTTCCTTAGCTTTTTGATT 59.522 40.000 0.00 0.00 0.00 2.57
646 701 1.301244 CACTTGGCGTGCTCTCAGT 60.301 57.895 0.00 0.00 36.72 3.41
673 728 3.302347 CTTCGGGAGCCTCGCAACT 62.302 63.158 9.61 0.00 0.00 3.16
705 760 2.031258 TGTGTCTGAGAAACCGCAAA 57.969 45.000 0.00 0.00 0.00 3.68
706 761 2.031258 TTGTGTCTGAGAAACCGCAA 57.969 45.000 0.00 0.00 0.00 4.85
707 762 1.939934 CTTTGTGTCTGAGAAACCGCA 59.060 47.619 0.00 0.00 0.00 5.69
708 763 1.334149 GCTTTGTGTCTGAGAAACCGC 60.334 52.381 0.00 0.00 0.00 5.68
709 764 1.264288 GGCTTTGTGTCTGAGAAACCG 59.736 52.381 0.00 0.00 0.00 4.44
710 765 2.291741 CTGGCTTTGTGTCTGAGAAACC 59.708 50.000 0.00 0.00 0.00 3.27
711 766 3.206150 TCTGGCTTTGTGTCTGAGAAAC 58.794 45.455 0.00 0.00 0.00 2.78
712 767 3.558931 TCTGGCTTTGTGTCTGAGAAA 57.441 42.857 0.00 0.00 0.00 2.52
713 768 3.777106 ATCTGGCTTTGTGTCTGAGAA 57.223 42.857 0.00 0.00 31.94 2.87
714 769 3.777106 AATCTGGCTTTGTGTCTGAGA 57.223 42.857 0.00 0.00 31.94 3.27
715 770 4.756642 TGTAAATCTGGCTTTGTGTCTGAG 59.243 41.667 0.00 0.00 31.94 3.35
716 771 4.713553 TGTAAATCTGGCTTTGTGTCTGA 58.286 39.130 0.00 0.00 32.93 3.27
717 772 5.437289 TTGTAAATCTGGCTTTGTGTCTG 57.563 39.130 0.00 0.00 0.00 3.51
718 773 6.321181 TCTTTTGTAAATCTGGCTTTGTGTCT 59.679 34.615 0.00 0.00 0.00 3.41
719 774 6.503524 TCTTTTGTAAATCTGGCTTTGTGTC 58.496 36.000 0.00 0.00 0.00 3.67
720 775 6.463995 TCTTTTGTAAATCTGGCTTTGTGT 57.536 33.333 0.00 0.00 0.00 3.72
721 776 7.769272 TTTCTTTTGTAAATCTGGCTTTGTG 57.231 32.000 0.00 0.00 0.00 3.33
722 777 8.962884 AATTTCTTTTGTAAATCTGGCTTTGT 57.037 26.923 0.00 0.00 0.00 2.83
723 778 9.654417 CAAATTTCTTTTGTAAATCTGGCTTTG 57.346 29.630 0.00 0.00 39.93 2.77
724 779 8.839343 CCAAATTTCTTTTGTAAATCTGGCTTT 58.161 29.630 0.00 0.00 42.68 3.51
725 780 7.445096 CCCAAATTTCTTTTGTAAATCTGGCTT 59.555 33.333 0.00 0.00 42.68 4.35
726 781 6.936335 CCCAAATTTCTTTTGTAAATCTGGCT 59.064 34.615 0.00 0.00 42.68 4.75
727 782 6.348458 GCCCAAATTTCTTTTGTAAATCTGGC 60.348 38.462 0.00 0.00 42.68 4.85
728 783 6.149308 GGCCCAAATTTCTTTTGTAAATCTGG 59.851 38.462 0.00 0.00 42.68 3.86
729 784 6.936335 AGGCCCAAATTTCTTTTGTAAATCTG 59.064 34.615 0.00 0.00 42.68 2.90
730 785 7.078249 AGGCCCAAATTTCTTTTGTAAATCT 57.922 32.000 0.00 0.00 42.68 2.40
731 786 7.744087 AAGGCCCAAATTTCTTTTGTAAATC 57.256 32.000 0.00 0.00 42.68 2.17
732 787 9.230122 CATAAGGCCCAAATTTCTTTTGTAAAT 57.770 29.630 0.00 0.00 42.68 1.40
733 788 8.432805 TCATAAGGCCCAAATTTCTTTTGTAAA 58.567 29.630 0.00 0.00 42.68 2.01
734 789 7.967908 TCATAAGGCCCAAATTTCTTTTGTAA 58.032 30.769 0.00 0.00 42.68 2.41
735 790 7.546250 TCATAAGGCCCAAATTTCTTTTGTA 57.454 32.000 0.00 0.00 42.68 2.41
736 791 6.432403 TCATAAGGCCCAAATTTCTTTTGT 57.568 33.333 0.00 0.00 42.68 2.83
737 792 7.742556 TTTCATAAGGCCCAAATTTCTTTTG 57.257 32.000 0.00 0.00 43.64 2.44
738 793 8.759481 TTTTTCATAAGGCCCAAATTTCTTTT 57.241 26.923 0.00 0.00 0.00 2.27
739 794 8.938801 ATTTTTCATAAGGCCCAAATTTCTTT 57.061 26.923 0.00 0.00 0.00 2.52
744 799 9.806448 ACTTTTATTTTTCATAAGGCCCAAATT 57.194 25.926 0.00 0.00 0.00 1.82
745 800 9.806448 AACTTTTATTTTTCATAAGGCCCAAAT 57.194 25.926 0.00 0.00 0.00 2.32
765 820 9.244799 CTTTTCCTTGCTATTCGTTTAACTTTT 57.755 29.630 0.00 0.00 0.00 2.27
766 821 7.865889 CCTTTTCCTTGCTATTCGTTTAACTTT 59.134 33.333 0.00 0.00 0.00 2.66
767 822 7.368059 CCTTTTCCTTGCTATTCGTTTAACTT 58.632 34.615 0.00 0.00 0.00 2.66
768 823 6.569801 GCCTTTTCCTTGCTATTCGTTTAACT 60.570 38.462 0.00 0.00 0.00 2.24
769 824 5.571741 GCCTTTTCCTTGCTATTCGTTTAAC 59.428 40.000 0.00 0.00 0.00 2.01
770 825 5.336134 GGCCTTTTCCTTGCTATTCGTTTAA 60.336 40.000 0.00 0.00 0.00 1.52
771 826 4.157105 GGCCTTTTCCTTGCTATTCGTTTA 59.843 41.667 0.00 0.00 0.00 2.01
772 827 3.056821 GGCCTTTTCCTTGCTATTCGTTT 60.057 43.478 0.00 0.00 0.00 3.60
773 828 2.492088 GGCCTTTTCCTTGCTATTCGTT 59.508 45.455 0.00 0.00 0.00 3.85
774 829 2.092323 GGCCTTTTCCTTGCTATTCGT 58.908 47.619 0.00 0.00 0.00 3.85
775 830 1.064060 CGGCCTTTTCCTTGCTATTCG 59.936 52.381 0.00 0.00 0.00 3.34
776 831 2.365582 TCGGCCTTTTCCTTGCTATTC 58.634 47.619 0.00 0.00 0.00 1.75
777 832 2.507407 TCGGCCTTTTCCTTGCTATT 57.493 45.000 0.00 0.00 0.00 1.73
778 833 2.301346 CATCGGCCTTTTCCTTGCTAT 58.699 47.619 0.00 0.00 0.00 2.97
779 834 1.004277 ACATCGGCCTTTTCCTTGCTA 59.996 47.619 0.00 0.00 0.00 3.49
780 835 0.251341 ACATCGGCCTTTTCCTTGCT 60.251 50.000 0.00 0.00 0.00 3.91
781 836 1.459450 TACATCGGCCTTTTCCTTGC 58.541 50.000 0.00 0.00 0.00 4.01
782 837 2.159379 GCTTACATCGGCCTTTTCCTTG 60.159 50.000 0.00 0.00 0.00 3.61
783 838 2.092323 GCTTACATCGGCCTTTTCCTT 58.908 47.619 0.00 0.00 0.00 3.36
784 839 1.682087 GGCTTACATCGGCCTTTTCCT 60.682 52.381 0.00 0.00 44.48 3.36
785 840 0.738975 GGCTTACATCGGCCTTTTCC 59.261 55.000 0.00 0.00 44.48 3.13
786 841 0.738975 GGGCTTACATCGGCCTTTTC 59.261 55.000 0.00 0.00 46.80 2.29
787 842 0.039035 TGGGCTTACATCGGCCTTTT 59.961 50.000 0.00 0.00 46.80 2.27
788 843 0.039035 TTGGGCTTACATCGGCCTTT 59.961 50.000 0.00 0.00 46.80 3.11
789 844 0.394352 CTTGGGCTTACATCGGCCTT 60.394 55.000 0.00 0.00 46.80 4.35
790 845 1.224592 CTTGGGCTTACATCGGCCT 59.775 57.895 0.00 0.00 46.80 5.19
791 846 0.393808 TTCTTGGGCTTACATCGGCC 60.394 55.000 0.00 0.00 46.89 6.13
792 847 1.017387 CTTCTTGGGCTTACATCGGC 58.983 55.000 0.00 0.00 0.00 5.54
793 848 2.280628 GTCTTCTTGGGCTTACATCGG 58.719 52.381 0.00 0.00 0.00 4.18
794 849 1.927174 CGTCTTCTTGGGCTTACATCG 59.073 52.381 0.00 0.00 0.00 3.84
795 850 1.666189 GCGTCTTCTTGGGCTTACATC 59.334 52.381 0.00 0.00 0.00 3.06
796 851 1.003118 TGCGTCTTCTTGGGCTTACAT 59.997 47.619 0.00 0.00 0.00 2.29
797 852 0.394938 TGCGTCTTCTTGGGCTTACA 59.605 50.000 0.00 0.00 0.00 2.41
798 853 1.464997 CTTGCGTCTTCTTGGGCTTAC 59.535 52.381 0.00 0.00 0.00 2.34
799 854 1.610624 CCTTGCGTCTTCTTGGGCTTA 60.611 52.381 0.00 0.00 0.00 3.09
800 855 0.890996 CCTTGCGTCTTCTTGGGCTT 60.891 55.000 0.00 0.00 0.00 4.35
801 856 1.302832 CCTTGCGTCTTCTTGGGCT 60.303 57.895 0.00 0.00 0.00 5.19
802 857 0.889186 TTCCTTGCGTCTTCTTGGGC 60.889 55.000 0.00 0.00 0.00 5.36
803 858 1.604604 TTTCCTTGCGTCTTCTTGGG 58.395 50.000 0.00 0.00 0.00 4.12
804 859 2.605580 GCTTTTCCTTGCGTCTTCTTGG 60.606 50.000 0.00 0.00 0.00 3.61
805 860 2.605580 GGCTTTTCCTTGCGTCTTCTTG 60.606 50.000 0.00 0.00 0.00 3.02
806 861 1.609072 GGCTTTTCCTTGCGTCTTCTT 59.391 47.619 0.00 0.00 0.00 2.52
807 862 1.239347 GGCTTTTCCTTGCGTCTTCT 58.761 50.000 0.00 0.00 0.00 2.85
808 863 0.241213 GGGCTTTTCCTTGCGTCTTC 59.759 55.000 0.00 0.00 34.39 2.87
809 864 0.467290 TGGGCTTTTCCTTGCGTCTT 60.467 50.000 0.00 0.00 34.39 3.01
810 865 0.251341 ATGGGCTTTTCCTTGCGTCT 60.251 50.000 0.00 0.00 34.39 4.18
811 866 0.109132 CATGGGCTTTTCCTTGCGTC 60.109 55.000 0.00 0.00 34.39 5.19
812 867 0.827507 ACATGGGCTTTTCCTTGCGT 60.828 50.000 0.00 0.00 35.94 5.24
813 868 1.133025 CTACATGGGCTTTTCCTTGCG 59.867 52.381 0.00 0.00 35.94 4.85
814 869 1.478105 CCTACATGGGCTTTTCCTTGC 59.522 52.381 0.00 0.00 35.94 4.01
825 880 0.106519 CCTTCTTGGGCCTACATGGG 60.107 60.000 4.53 0.00 36.00 4.00
826 881 0.753111 GCCTTCTTGGGCCTACATGG 60.753 60.000 4.53 2.98 45.92 3.66
827 882 2.799176 GCCTTCTTGGGCCTACATG 58.201 57.895 4.53 0.00 45.92 3.21
835 890 4.659172 TGCCACCGCCTTCTTGGG 62.659 66.667 0.00 0.00 36.00 4.12
836 891 2.463589 TACTGCCACCGCCTTCTTGG 62.464 60.000 0.00 0.00 39.35 3.61
837 892 0.392998 ATACTGCCACCGCCTTCTTG 60.393 55.000 0.00 0.00 0.00 3.02
838 893 0.107654 GATACTGCCACCGCCTTCTT 60.108 55.000 0.00 0.00 0.00 2.52
839 894 1.264749 TGATACTGCCACCGCCTTCT 61.265 55.000 0.00 0.00 0.00 2.85
840 895 1.090052 GTGATACTGCCACCGCCTTC 61.090 60.000 0.00 0.00 0.00 3.46
841 896 1.078426 GTGATACTGCCACCGCCTT 60.078 57.895 0.00 0.00 0.00 4.35
842 897 2.584608 GTGATACTGCCACCGCCT 59.415 61.111 0.00 0.00 0.00 5.52
843 898 2.513897 GGTGATACTGCCACCGCC 60.514 66.667 0.00 0.00 43.80 6.13
847 902 0.801067 GACGACGGTGATACTGCCAC 60.801 60.000 0.00 0.00 0.00 5.01
848 903 1.509463 GACGACGGTGATACTGCCA 59.491 57.895 0.00 0.00 0.00 4.92
928 1024 1.546029 CTAGGGTTTGGCTTTGGCTTC 59.454 52.381 0.00 0.00 38.73 3.86
955 1051 2.689034 GGCAGAGCTAGGGTGGGT 60.689 66.667 0.00 0.00 0.00 4.51
956 1052 3.854669 CGGCAGAGCTAGGGTGGG 61.855 72.222 0.00 0.00 0.00 4.61
957 1053 3.077556 ACGGCAGAGCTAGGGTGG 61.078 66.667 0.00 0.00 0.00 4.61
958 1054 2.496817 GACGGCAGAGCTAGGGTG 59.503 66.667 0.00 0.00 0.00 4.61
1323 1422 4.657824 ACGACGGTGAAGGTGGCG 62.658 66.667 0.00 0.00 0.00 5.69
1557 1656 1.669115 GGCAGCGCTGAAGAAGACA 60.669 57.895 40.21 0.00 0.00 3.41
1620 1719 3.766691 GACGAGGCGGCAGGGTAA 61.767 66.667 13.08 0.00 33.63 2.85
2078 2179 1.398041 TCAACAATAGAGCGCACATGC 59.602 47.619 11.47 0.00 37.78 4.06
2106 2207 7.619302 AGGGTCATCAGGCAAATTTTAATCTTA 59.381 33.333 0.00 0.00 0.00 2.10
2107 2208 6.441604 AGGGTCATCAGGCAAATTTTAATCTT 59.558 34.615 0.00 0.00 0.00 2.40
2109 2210 6.044682 CAGGGTCATCAGGCAAATTTTAATC 58.955 40.000 0.00 0.00 0.00 1.75
2128 2231 1.807814 ACTGAGGAAGAACACAGGGT 58.192 50.000 0.00 0.00 35.08 4.34
2129 2232 3.866651 CATACTGAGGAAGAACACAGGG 58.133 50.000 0.00 0.00 35.08 4.45
2165 2268 2.093869 GGGTTGCGACCTAACATGTCTA 60.094 50.000 22.72 0.00 45.75 2.59
2231 2334 5.376625 AGATTTTGTAACTGGACTTGCTCA 58.623 37.500 0.00 0.00 0.00 4.26
2310 2420 3.701532 TGTTCGTTTTTGTAGGCCAAG 57.298 42.857 5.01 0.00 33.75 3.61
2313 2423 4.499037 AAGATGTTCGTTTTTGTAGGCC 57.501 40.909 0.00 0.00 0.00 5.19
2462 2572 1.687123 CTTCCGTCATACCTACAGGGG 59.313 57.143 0.00 0.00 40.27 4.79
2546 2656 2.890808 TAGCTGCTTAATGGTCTCCG 57.109 50.000 7.79 0.00 0.00 4.63
2658 2768 0.676466 CGTTACTGAGGGCCAATGCA 60.676 55.000 6.18 0.00 40.13 3.96
3076 3186 7.274904 TGCTTCTAATCTGACGTTGTAATGTAC 59.725 37.037 0.00 0.00 0.00 2.90
3090 3200 6.870965 AGTAAAGACAGTGTGCTTCTAATCTG 59.129 38.462 0.00 0.00 0.00 2.90
3434 3544 3.515502 TGATCTTGACCGAGACTTGGATT 59.484 43.478 16.24 0.00 0.00 3.01
3991 4101 0.320374 TCCACTGCGTCCTTTACAGG 59.680 55.000 0.00 0.00 42.50 4.00
4044 4154 7.499292 CATCTTCAGATACAGATGAACTCCTT 58.501 38.462 5.01 0.00 46.52 3.36
4257 4367 5.682234 TCTTGCCATCTGTCTTCATCTTA 57.318 39.130 0.00 0.00 0.00 2.10
4401 4512 6.287359 ACCATCCCTATGATATTTATCCCCA 58.713 40.000 0.00 0.00 34.84 4.96
4639 4787 7.467811 GCATTTATCTGTACCAGTTTCATCAGG 60.468 40.741 0.00 0.00 32.61 3.86
4700 4848 0.603975 GCACATATCTTCCTCGGCCC 60.604 60.000 0.00 0.00 0.00 5.80
4701 4849 0.394565 AGCACATATCTTCCTCGGCC 59.605 55.000 0.00 0.00 0.00 6.13
4958 5111 6.805016 ATAGATCAGATGAACACTCTGGTT 57.195 37.500 0.00 0.00 40.44 3.67
5419 5572 7.306632 CGAAGGACTAAACAACTACTGAACTTG 60.307 40.741 0.00 0.00 0.00 3.16
5564 5730 6.884472 AGGAAAAGGAAAAAGGAAAGGAAA 57.116 33.333 0.00 0.00 0.00 3.13
5565 5731 6.884472 AAGGAAAAGGAAAAAGGAAAGGAA 57.116 33.333 0.00 0.00 0.00 3.36
5566 5732 6.884472 AAAGGAAAAGGAAAAAGGAAAGGA 57.116 33.333 0.00 0.00 0.00 3.36
5567 5733 6.542370 GGAAAAGGAAAAGGAAAAAGGAAAGG 59.458 38.462 0.00 0.00 0.00 3.11
5568 5734 6.542370 GGGAAAAGGAAAAGGAAAAAGGAAAG 59.458 38.462 0.00 0.00 0.00 2.62
5569 5735 6.419791 GGGAAAAGGAAAAGGAAAAAGGAAA 58.580 36.000 0.00 0.00 0.00 3.13
5570 5736 5.104277 GGGGAAAAGGAAAAGGAAAAAGGAA 60.104 40.000 0.00 0.00 0.00 3.36
5571 5737 4.410883 GGGGAAAAGGAAAAGGAAAAAGGA 59.589 41.667 0.00 0.00 0.00 3.36
5578 5744 3.583228 GAAAGGGGGAAAAGGAAAAGGA 58.417 45.455 0.00 0.00 0.00 3.36
5580 5746 3.324846 CAGGAAAGGGGGAAAAGGAAAAG 59.675 47.826 0.00 0.00 0.00 2.27
5732 5898 7.651808 CAAGAGCAAAAAGAAGACAAGGAATA 58.348 34.615 0.00 0.00 0.00 1.75
5777 5943 1.943507 GCAGAGGACAGGTGCTTCTTC 60.944 57.143 0.00 0.00 34.23 2.87
5778 5944 0.036022 GCAGAGGACAGGTGCTTCTT 59.964 55.000 0.00 0.00 34.23 2.52
5779 5945 1.123861 TGCAGAGGACAGGTGCTTCT 61.124 55.000 0.00 0.00 38.09 2.85


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

AutoCloner maintained by Alex Coulton.