Multiple sequence alignment - TraesCS2D01G096100

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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 TraesCS2D01G096100 chr2D 100.000 2477 0 0 1 2477 48224671 48222195 0.000000e+00 4575
1 TraesCS2D01G096100 chr2D 99.278 554 4 0 1924 2477 547558886 547558333 0.000000e+00 1002
2 TraesCS2D01G096100 chr2D 98.741 556 5 1 1924 2477 5255651 5256206 0.000000e+00 987
3 TraesCS2D01G096100 chr2D 98.566 558 6 1 1922 2477 610640767 610640210 0.000000e+00 985
4 TraesCS2D01G096100 chr2B 90.311 1094 73 18 856 1920 75696397 75697486 0.000000e+00 1402
5 TraesCS2D01G096100 chr3D 98.723 705 5 3 1 703 516420457 516419755 0.000000e+00 1249
6 TraesCS2D01G096100 chr3D 96.738 705 18 4 1 702 113999807 113999105 0.000000e+00 1170
7 TraesCS2D01G096100 chr3D 98.750 560 5 2 1919 2477 564884067 564883509 0.000000e+00 994
8 TraesCS2D01G096100 chr3D 78.363 171 33 3 1753 1922 605064179 605064346 9.370000e-20 108
9 TraesCS2D01G096100 chr5D 98.435 703 7 3 1 701 6981544 6980844 0.000000e+00 1234
10 TraesCS2D01G096100 chr5D 97.743 709 11 4 1 704 80295552 80294844 0.000000e+00 1216
11 TraesCS2D01G096100 chr5D 97.297 703 12 4 1 700 438936907 438937605 0.000000e+00 1186
12 TraesCS2D01G096100 chr5D 98.741 556 5 1 1924 2477 460112557 460113112 0.000000e+00 987
13 TraesCS2D01G096100 chr5D 83.284 676 87 17 815 1484 104113315 104112660 1.270000e-167 599
14 TraesCS2D01G096100 chr5D 83.333 600 86 9 883 1478 104143064 104142475 2.170000e-150 542
15 TraesCS2D01G096100 chr1D 97.500 720 14 3 1 718 303063650 303062933 0.000000e+00 1227
16 TraesCS2D01G096100 chr7D 97.571 700 7 3 1 699 111109879 111109189 0.000000e+00 1190
17 TraesCS2D01G096100 chr7D 97.171 707 12 5 1 704 564166055 564165354 0.000000e+00 1188
18 TraesCS2D01G096100 chr7D 98.919 555 5 1 1924 2477 583399521 583400075 0.000000e+00 990
19 TraesCS2D01G096100 chr7D 98.743 557 5 1 1923 2477 605132640 605132084 0.000000e+00 989
20 TraesCS2D01G096100 chr7D 98.399 562 5 1 1920 2477 290559897 290559336 0.000000e+00 985
21 TraesCS2D01G096100 chr7D 79.394 165 27 5 1764 1923 595934215 595934377 2.600000e-20 110
22 TraesCS2D01G096100 chr6D 97.297 703 12 4 1 701 450251338 450250641 0.000000e+00 1186
23 TraesCS2D01G096100 chr6D 83.603 494 59 15 1001 1477 9195541 9195053 6.290000e-121 444
24 TraesCS2D01G096100 chr6D 83.333 492 67 9 998 1477 9147175 9147663 8.130000e-120 440
25 TraesCS2D01G096100 chr4D 98.923 557 3 1 1924 2477 314619177 314618621 0.000000e+00 992
26 TraesCS2D01G096100 chr5B 82.544 739 95 23 815 1538 113328146 113327427 9.730000e-174 619
27 TraesCS2D01G096100 chr5B 81.833 600 88 13 883 1478 113456956 113456374 3.700000e-133 484
28 TraesCS2D01G096100 chr6B 80.193 621 89 21 883 1477 17091780 17091168 3.780000e-118 435
29 TraesCS2D01G096100 chr6B 83.096 491 67 12 998 1477 16970590 16971075 1.360000e-117 433
30 TraesCS2D01G096100 chr6B 85.030 167 20 5 1756 1922 659947009 659946848 5.480000e-37 165
31 TraesCS2D01G096100 chrUn 82.840 169 24 4 1756 1920 87057092 87057259 1.990000e-31 147
32 TraesCS2D01G096100 chr1A 81.761 159 22 6 1769 1922 348698430 348698274 2.590000e-25 126
33 TraesCS2D01G096100 chr1B 80.864 162 23 7 1764 1921 550289163 550289006 1.200000e-23 121
34 TraesCS2D01G096100 chr2A 79.412 170 29 4 1756 1922 603782390 603782556 5.600000e-22 115
35 TraesCS2D01G096100 chr4B 80.120 166 22 10 1764 1922 7877537 7877698 2.010000e-21 113


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 TraesCS2D01G096100 chr2D 48222195 48224671 2476 True 4575 4575 100.000 1 2477 1 chr2D.!!$R1 2476
1 TraesCS2D01G096100 chr2D 547558333 547558886 553 True 1002 1002 99.278 1924 2477 1 chr2D.!!$R2 553
2 TraesCS2D01G096100 chr2D 5255651 5256206 555 False 987 987 98.741 1924 2477 1 chr2D.!!$F1 553
3 TraesCS2D01G096100 chr2D 610640210 610640767 557 True 985 985 98.566 1922 2477 1 chr2D.!!$R3 555
4 TraesCS2D01G096100 chr2B 75696397 75697486 1089 False 1402 1402 90.311 856 1920 1 chr2B.!!$F1 1064
5 TraesCS2D01G096100 chr3D 516419755 516420457 702 True 1249 1249 98.723 1 703 1 chr3D.!!$R2 702
6 TraesCS2D01G096100 chr3D 113999105 113999807 702 True 1170 1170 96.738 1 702 1 chr3D.!!$R1 701
7 TraesCS2D01G096100 chr3D 564883509 564884067 558 True 994 994 98.750 1919 2477 1 chr3D.!!$R3 558
8 TraesCS2D01G096100 chr5D 6980844 6981544 700 True 1234 1234 98.435 1 701 1 chr5D.!!$R1 700
9 TraesCS2D01G096100 chr5D 80294844 80295552 708 True 1216 1216 97.743 1 704 1 chr5D.!!$R2 703
10 TraesCS2D01G096100 chr5D 438936907 438937605 698 False 1186 1186 97.297 1 700 1 chr5D.!!$F1 699
11 TraesCS2D01G096100 chr5D 460112557 460113112 555 False 987 987 98.741 1924 2477 1 chr5D.!!$F2 553
12 TraesCS2D01G096100 chr5D 104112660 104113315 655 True 599 599 83.284 815 1484 1 chr5D.!!$R3 669
13 TraesCS2D01G096100 chr5D 104142475 104143064 589 True 542 542 83.333 883 1478 1 chr5D.!!$R4 595
14 TraesCS2D01G096100 chr1D 303062933 303063650 717 True 1227 1227 97.500 1 718 1 chr1D.!!$R1 717
15 TraesCS2D01G096100 chr7D 111109189 111109879 690 True 1190 1190 97.571 1 699 1 chr7D.!!$R1 698
16 TraesCS2D01G096100 chr7D 564165354 564166055 701 True 1188 1188 97.171 1 704 1 chr7D.!!$R3 703
17 TraesCS2D01G096100 chr7D 583399521 583400075 554 False 990 990 98.919 1924 2477 1 chr7D.!!$F1 553
18 TraesCS2D01G096100 chr7D 605132084 605132640 556 True 989 989 98.743 1923 2477 1 chr7D.!!$R4 554
19 TraesCS2D01G096100 chr7D 290559336 290559897 561 True 985 985 98.399 1920 2477 1 chr7D.!!$R2 557
20 TraesCS2D01G096100 chr6D 450250641 450251338 697 True 1186 1186 97.297 1 701 1 chr6D.!!$R2 700
21 TraesCS2D01G096100 chr4D 314618621 314619177 556 True 992 992 98.923 1924 2477 1 chr4D.!!$R1 553
22 TraesCS2D01G096100 chr5B 113327427 113328146 719 True 619 619 82.544 815 1538 1 chr5B.!!$R1 723
23 TraesCS2D01G096100 chr5B 113456374 113456956 582 True 484 484 81.833 883 1478 1 chr5B.!!$R2 595
24 TraesCS2D01G096100 chr6B 17091168 17091780 612 True 435 435 80.193 883 1477 1 chr6B.!!$R1 594

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
796 809 0.035458 GACTTGTGGTGTAGCAGCCT 59.965 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1787 0.241213 ACATCTGTGTCCGACTCACG 59.759 55.0 0.0 0.0 38.48 4.35 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
318 319 7.163441 ACTGCAGAAATGATTTGGCTTTTAAT 58.837 30.769 23.35 0.00 0.00 1.40
722 735 3.268034 AAAACCATAAAGGGCCCAAGA 57.732 42.857 27.56 8.50 43.89 3.02
723 736 3.268034 AAACCATAAAGGGCCCAAGAA 57.732 42.857 27.56 6.57 43.89 2.52
724 737 2.532250 ACCATAAAGGGCCCAAGAAG 57.468 50.000 27.56 10.74 43.89 2.85
725 738 2.000048 ACCATAAAGGGCCCAAGAAGA 59.000 47.619 27.56 2.49 43.89 2.87
726 739 2.291605 ACCATAAAGGGCCCAAGAAGAC 60.292 50.000 27.56 0.00 43.89 3.01
727 740 2.291540 CCATAAAGGGCCCAAGAAGACA 60.292 50.000 27.56 0.00 0.00 3.41
728 741 3.628257 CCATAAAGGGCCCAAGAAGACAT 60.628 47.826 27.56 0.00 0.00 3.06
729 742 1.928868 AAAGGGCCCAAGAAGACATG 58.071 50.000 27.56 0.00 0.00 3.21
730 743 0.613012 AAGGGCCCAAGAAGACATGC 60.613 55.000 27.56 0.00 0.00 4.06
731 744 1.304381 GGGCCCAAGAAGACATGCA 60.304 57.895 19.95 0.00 0.00 3.96
732 745 1.598701 GGGCCCAAGAAGACATGCAC 61.599 60.000 19.95 0.00 0.00 4.57
733 746 0.895100 GGCCCAAGAAGACATGCACA 60.895 55.000 0.00 0.00 0.00 4.57
734 747 1.180029 GCCCAAGAAGACATGCACAT 58.820 50.000 0.00 0.00 0.00 3.21
735 748 2.368439 GCCCAAGAAGACATGCACATA 58.632 47.619 0.00 0.00 0.00 2.29
736 749 2.098117 GCCCAAGAAGACATGCACATAC 59.902 50.000 0.00 0.00 0.00 2.39
737 750 2.684881 CCCAAGAAGACATGCACATACC 59.315 50.000 0.00 0.00 0.00 2.73
738 751 3.346315 CCAAGAAGACATGCACATACCA 58.654 45.455 0.00 0.00 0.00 3.25
739 752 3.758023 CCAAGAAGACATGCACATACCAA 59.242 43.478 0.00 0.00 0.00 3.67
740 753 4.142534 CCAAGAAGACATGCACATACCAAG 60.143 45.833 0.00 0.00 0.00 3.61
741 754 3.614092 AGAAGACATGCACATACCAAGG 58.386 45.455 0.00 0.00 0.00 3.61
742 755 1.755179 AGACATGCACATACCAAGGC 58.245 50.000 0.00 0.00 0.00 4.35
743 756 0.740737 GACATGCACATACCAAGGCC 59.259 55.000 0.00 0.00 0.00 5.19
744 757 0.684153 ACATGCACATACCAAGGCCC 60.684 55.000 0.00 0.00 0.00 5.80
745 758 1.453745 ATGCACATACCAAGGCCCG 60.454 57.895 0.00 0.00 0.00 6.13
746 759 2.828549 GCACATACCAAGGCCCGG 60.829 66.667 7.28 7.28 0.00 5.73
747 760 2.674754 CACATACCAAGGCCCGGT 59.325 61.111 18.08 18.08 40.73 5.28
748 761 1.748879 CACATACCAAGGCCCGGTG 60.749 63.158 22.07 10.55 37.33 4.94
749 762 1.921346 ACATACCAAGGCCCGGTGA 60.921 57.895 22.07 8.63 37.33 4.02
750 763 1.301623 CATACCAAGGCCCGGTGAA 59.698 57.895 22.07 5.86 37.33 3.18
751 764 0.748005 CATACCAAGGCCCGGTGAAG 60.748 60.000 22.07 9.49 37.33 3.02
752 765 1.205460 ATACCAAGGCCCGGTGAAGT 61.205 55.000 22.07 5.50 37.33 3.01
753 766 2.119484 TACCAAGGCCCGGTGAAGTG 62.119 60.000 22.07 0.00 37.33 3.16
754 767 2.672996 CAAGGCCCGGTGAAGTGG 60.673 66.667 0.00 0.00 0.00 4.00
755 768 3.175710 AAGGCCCGGTGAAGTGGT 61.176 61.111 0.00 0.00 0.00 4.16
756 769 3.491598 AAGGCCCGGTGAAGTGGTG 62.492 63.158 0.00 0.00 0.00 4.17
757 770 3.948719 GGCCCGGTGAAGTGGTGA 61.949 66.667 0.00 0.00 0.00 4.02
758 771 2.112297 GCCCGGTGAAGTGGTGAA 59.888 61.111 0.00 0.00 0.00 3.18
759 772 2.258726 GCCCGGTGAAGTGGTGAAC 61.259 63.158 0.00 0.00 0.00 3.18
760 773 1.959226 CCCGGTGAAGTGGTGAACG 60.959 63.158 0.00 0.00 0.00 3.95
761 774 1.959226 CCGGTGAAGTGGTGAACGG 60.959 63.158 0.00 0.00 0.00 4.44
762 775 1.959226 CGGTGAAGTGGTGAACGGG 60.959 63.158 0.00 0.00 0.00 5.28
763 776 1.448497 GGTGAAGTGGTGAACGGGA 59.552 57.895 0.00 0.00 0.00 5.14
764 777 0.602905 GGTGAAGTGGTGAACGGGAG 60.603 60.000 0.00 0.00 0.00 4.30
765 778 0.602905 GTGAAGTGGTGAACGGGAGG 60.603 60.000 0.00 0.00 0.00 4.30
766 779 1.003718 GAAGTGGTGAACGGGAGGG 60.004 63.158 0.00 0.00 0.00 4.30
767 780 3.192103 AAGTGGTGAACGGGAGGGC 62.192 63.158 0.00 0.00 0.00 5.19
768 781 3.948719 GTGGTGAACGGGAGGGCA 61.949 66.667 0.00 0.00 0.00 5.36
769 782 3.948719 TGGTGAACGGGAGGGCAC 61.949 66.667 0.00 0.00 37.31 5.01
771 784 3.998672 GTGAACGGGAGGGCACGA 61.999 66.667 0.00 0.00 45.89 4.35
772 785 3.691342 TGAACGGGAGGGCACGAG 61.691 66.667 0.00 0.00 45.89 4.18
773 786 3.379445 GAACGGGAGGGCACGAGA 61.379 66.667 0.00 0.00 45.89 4.04
774 787 3.644399 GAACGGGAGGGCACGAGAC 62.644 68.421 0.00 0.00 45.89 3.36
775 788 4.680537 ACGGGAGGGCACGAGACT 62.681 66.667 0.00 0.00 45.89 3.24
776 789 4.135153 CGGGAGGGCACGAGACTG 62.135 72.222 0.00 0.00 45.89 3.51
777 790 3.775654 GGGAGGGCACGAGACTGG 61.776 72.222 0.00 0.00 0.00 4.00
778 791 2.680352 GGAGGGCACGAGACTGGA 60.680 66.667 0.00 0.00 0.00 3.86
779 792 2.574399 GAGGGCACGAGACTGGAC 59.426 66.667 0.00 0.00 0.00 4.02
780 793 1.979693 GAGGGCACGAGACTGGACT 60.980 63.158 0.00 0.00 0.00 3.85
781 794 1.534235 AGGGCACGAGACTGGACTT 60.534 57.895 0.00 0.00 0.00 3.01
782 795 1.374758 GGGCACGAGACTGGACTTG 60.375 63.158 0.00 0.00 0.00 3.16
783 796 1.367840 GGCACGAGACTGGACTTGT 59.632 57.895 0.00 0.00 35.17 3.16
785 798 0.946221 GCACGAGACTGGACTTGTGG 60.946 60.000 17.26 4.91 46.49 4.17
786 799 0.389391 CACGAGACTGGACTTGTGGT 59.611 55.000 10.91 0.00 44.18 4.16
787 800 0.389391 ACGAGACTGGACTTGTGGTG 59.611 55.000 0.00 0.00 33.77 4.17
788 801 0.389391 CGAGACTGGACTTGTGGTGT 59.611 55.000 0.00 0.00 0.00 4.16
789 802 1.611977 CGAGACTGGACTTGTGGTGTA 59.388 52.381 0.00 0.00 0.00 2.90
790 803 2.351835 CGAGACTGGACTTGTGGTGTAG 60.352 54.545 0.00 0.00 0.00 2.74
791 804 1.344763 AGACTGGACTTGTGGTGTAGC 59.655 52.381 0.00 0.00 0.00 3.58
792 805 1.070134 GACTGGACTTGTGGTGTAGCA 59.930 52.381 0.00 0.00 0.00 3.49
793 806 1.070758 ACTGGACTTGTGGTGTAGCAG 59.929 52.381 0.00 0.00 0.00 4.24
794 807 0.250295 TGGACTTGTGGTGTAGCAGC 60.250 55.000 0.00 0.00 0.00 5.25
795 808 0.955919 GGACTTGTGGTGTAGCAGCC 60.956 60.000 0.00 0.00 0.00 4.85
796 809 0.035458 GACTTGTGGTGTAGCAGCCT 59.965 55.000 0.00 0.00 0.00 4.58
797 810 0.250467 ACTTGTGGTGTAGCAGCCTG 60.250 55.000 0.00 0.00 0.00 4.85
798 811 1.580845 CTTGTGGTGTAGCAGCCTGC 61.581 60.000 9.13 9.13 45.46 4.85
807 820 2.360350 GCAGCCTGCAGCCTTGTA 60.360 61.111 12.82 0.00 44.26 2.41
808 821 2.694760 GCAGCCTGCAGCCTTGTAC 61.695 63.158 12.82 0.00 44.26 2.90
809 822 1.002868 CAGCCTGCAGCCTTGTACT 60.003 57.895 8.66 0.00 45.47 2.73
810 823 1.002868 AGCCTGCAGCCTTGTACTG 60.003 57.895 8.66 0.00 45.47 2.74
811 824 2.042831 GCCTGCAGCCTTGTACTGG 61.043 63.158 8.66 0.00 35.62 4.00
812 825 1.679311 CCTGCAGCCTTGTACTGGA 59.321 57.895 8.66 0.00 35.62 3.86
813 826 0.036732 CCTGCAGCCTTGTACTGGAA 59.963 55.000 8.66 0.00 34.90 3.53
814 827 1.545428 CCTGCAGCCTTGTACTGGAAA 60.545 52.381 8.66 0.00 34.90 3.13
815 828 1.808945 CTGCAGCCTTGTACTGGAAAG 59.191 52.381 0.00 0.00 34.90 2.62
816 829 0.523519 GCAGCCTTGTACTGGAAAGC 59.476 55.000 9.20 5.85 35.62 3.51
817 830 0.798776 CAGCCTTGTACTGGAAAGCG 59.201 55.000 9.20 0.00 0.00 4.68
818 831 0.321653 AGCCTTGTACTGGAAAGCGG 60.322 55.000 9.20 0.00 0.00 5.52
819 832 0.321298 GCCTTGTACTGGAAAGCGGA 60.321 55.000 9.20 0.00 0.00 5.54
823 836 3.621715 CCTTGTACTGGAAAGCGGAATAC 59.378 47.826 0.00 0.00 0.00 1.89
825 838 2.835764 TGTACTGGAAAGCGGAATACCT 59.164 45.455 0.00 0.00 0.00 3.08
836 849 0.103572 GGAATACCTGACGCGGCTAA 59.896 55.000 15.80 0.00 0.00 3.09
841 854 0.249398 ACCTGACGCGGCTAAAATCT 59.751 50.000 15.80 0.00 0.00 2.40
855 868 4.443598 GCTAAAATCTCGAACCATCCTCCT 60.444 45.833 0.00 0.00 0.00 3.69
856 869 3.828875 AAATCTCGAACCATCCTCCTC 57.171 47.619 0.00 0.00 0.00 3.71
857 870 1.710816 ATCTCGAACCATCCTCCTCC 58.289 55.000 0.00 0.00 0.00 4.30
858 871 0.397254 TCTCGAACCATCCTCCTCCC 60.397 60.000 0.00 0.00 0.00 4.30
859 872 0.397816 CTCGAACCATCCTCCTCCCT 60.398 60.000 0.00 0.00 0.00 4.20
860 873 0.687757 TCGAACCATCCTCCTCCCTG 60.688 60.000 0.00 0.00 0.00 4.45
942 959 2.838467 AAGCCAGTGCCAGCCTCTT 61.838 57.895 0.00 0.00 38.69 2.85
943 960 1.492133 AAGCCAGTGCCAGCCTCTTA 61.492 55.000 0.00 0.00 38.69 2.10
945 962 0.817229 GCCAGTGCCAGCCTCTTATC 60.817 60.000 0.00 0.00 0.00 1.75
948 967 2.559440 CAGTGCCAGCCTCTTATCTTC 58.441 52.381 0.00 0.00 0.00 2.87
950 969 1.488393 GTGCCAGCCTCTTATCTTCCT 59.512 52.381 0.00 0.00 0.00 3.36
981 1001 2.363683 AGTCCTTCCTAGTTCGTACCG 58.636 52.381 0.00 0.00 0.00 4.02
1143 1188 0.837691 TGAAGCTGAGCCTGGAGGAA 60.838 55.000 0.00 0.00 37.39 3.36
1470 1521 5.502706 CGAGGTGAAGATCGTCTACTACAAG 60.503 48.000 10.08 0.00 34.30 3.16
1506 1568 3.271014 GCTTTGCTAGCTGCTGCA 58.729 55.556 17.23 16.46 46.77 4.41
1523 1585 0.727398 GCATACCTGCGAGTGGTTTC 59.273 55.000 0.05 0.00 38.92 2.78
1524 1586 1.369625 CATACCTGCGAGTGGTTTCC 58.630 55.000 0.05 0.00 38.88 3.13
1533 1595 3.438781 TGCGAGTGGTTTCCAATAATGTC 59.561 43.478 0.00 0.00 34.18 3.06
1546 1612 1.926561 TAATGTCGCAGTGCAGCTAG 58.073 50.000 16.83 0.00 0.00 3.42
1556 1622 0.932585 GTGCAGCTAGCTCGATCGTC 60.933 60.000 16.15 8.44 45.94 4.20
1559 1625 0.660488 CAGCTAGCTCGATCGTCAGT 59.340 55.000 16.15 1.25 0.00 3.41
1560 1626 0.941542 AGCTAGCTCGATCGTCAGTC 59.058 55.000 12.68 2.96 0.00 3.51
1561 1627 0.383737 GCTAGCTCGATCGTCAGTCG 60.384 60.000 15.94 2.16 40.30 4.18
1562 1628 0.233590 CTAGCTCGATCGTCAGTCGG 59.766 60.000 15.94 0.00 39.45 4.79
1563 1629 0.461516 TAGCTCGATCGTCAGTCGGT 60.462 55.000 15.94 6.19 39.45 4.69
1564 1630 0.461516 AGCTCGATCGTCAGTCGGTA 60.462 55.000 15.94 0.00 39.45 4.02
1581 1647 0.661020 GTACGGTGTTGCAGCTGTTT 59.339 50.000 16.64 0.00 0.00 2.83
1584 1650 1.723608 CGGTGTTGCAGCTGTTTCCA 61.724 55.000 16.64 1.04 0.00 3.53
1585 1651 0.459489 GGTGTTGCAGCTGTTTCCAA 59.541 50.000 16.64 8.00 0.00 3.53
1586 1652 1.069049 GGTGTTGCAGCTGTTTCCAAT 59.931 47.619 16.64 0.00 0.00 3.16
1587 1653 2.129607 GTGTTGCAGCTGTTTCCAATG 58.870 47.619 16.64 0.00 0.00 2.82
1588 1654 2.030371 TGTTGCAGCTGTTTCCAATGA 58.970 42.857 16.64 0.00 0.00 2.57
1592 1658 2.629137 TGCAGCTGTTTCCAATGATTGT 59.371 40.909 16.64 0.00 0.00 2.71
1594 1660 2.991190 CAGCTGTTTCCAATGATTGTGC 59.009 45.455 5.25 0.00 0.00 4.57
1596 1662 2.607771 GCTGTTTCCAATGATTGTGCGT 60.608 45.455 4.27 0.00 0.00 5.24
1597 1663 3.641648 CTGTTTCCAATGATTGTGCGTT 58.358 40.909 4.27 0.00 0.00 4.84
1598 1664 3.379240 TGTTTCCAATGATTGTGCGTTG 58.621 40.909 4.27 0.00 35.15 4.10
1600 1666 2.740668 CCAATGATTGTGCGTTGGC 58.259 52.632 4.27 0.00 45.09 4.52
1621 1697 4.447365 CGGTCACCGTCGTTAGTC 57.553 61.111 8.54 0.00 42.73 2.59
1632 1708 3.291585 CGTCGTTAGTCGTGTAGTGTTT 58.708 45.455 0.00 0.00 40.80 2.83
1640 1716 3.874543 AGTCGTGTAGTGTTTGATTTGCA 59.125 39.130 0.00 0.00 0.00 4.08
1652 1728 7.064490 AGTGTTTGATTTGCAGTTTAACTTTGG 59.936 33.333 0.00 0.00 0.00 3.28
1654 1730 7.064016 TGTTTGATTTGCAGTTTAACTTTGGAC 59.936 33.333 0.00 0.00 0.00 4.02
1669 1745 1.746470 TGGACTTGCAGAGATGCATG 58.254 50.000 2.46 12.83 44.94 4.06
1682 1758 0.469331 ATGCATGCATGGGCTTAGCT 60.469 50.000 31.74 4.69 41.91 3.32
1697 1773 3.190118 GCTTAGCTCAGATGCAAGTGTTT 59.810 43.478 0.00 0.00 34.99 2.83
1698 1774 4.720090 CTTAGCTCAGATGCAAGTGTTTG 58.280 43.478 0.00 0.00 37.36 2.93
1711 1787 0.598065 GTGTTTGGGTGTCATGGCTC 59.402 55.000 0.00 0.00 0.00 4.70
1733 1809 1.816835 TGAGTCGGACACAGATGTACC 59.183 52.381 11.27 0.00 39.95 3.34
1749 1825 7.093289 ACAGATGTACCAGCTACTGTTATTTCT 60.093 37.037 0.00 0.00 35.52 2.52
1835 1911 0.621609 TTAAGCACATACCCGGCCTT 59.378 50.000 0.00 0.00 0.00 4.35
1847 1923 1.609208 CCGGCCTTTGCATAGCTATT 58.391 50.000 2.64 0.00 40.13 1.73
1863 1939 4.053983 AGCTATTATGCACACATCTCACG 58.946 43.478 0.00 0.00 37.74 4.35
1887 1963 4.090729 CAACACATACAATAAGCACGCTG 58.909 43.478 0.00 0.00 0.00 5.18
1902 1978 3.853307 GCACGCTGACAATTAGCAAAGTT 60.853 43.478 0.00 0.00 41.18 2.66
2039 2121 0.172803 AATCGCGCCTCTTACGAACT 59.827 50.000 0.00 0.00 39.56 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
513 514 1.004277 ACCGGCTGGCAGAAAAATAGA 59.996 47.619 20.86 0.00 39.70 1.98
598 608 7.504922 TCAACAATGTCGAAAAGTTGAAAAG 57.495 32.000 19.03 0.43 43.71 2.27
603 613 5.339990 AGGTTCAACAATGTCGAAAAGTTG 58.660 37.500 14.77 14.77 40.53 3.16
706 719 2.291540 TGTCTTCTTGGGCCCTTTATGG 60.292 50.000 25.70 9.05 0.00 2.74
707 720 3.085952 TGTCTTCTTGGGCCCTTTATG 57.914 47.619 25.70 10.78 0.00 1.90
711 724 0.613012 GCATGTCTTCTTGGGCCCTT 60.613 55.000 25.70 0.00 0.00 3.95
718 731 4.142534 CCTTGGTATGTGCATGTCTTCTTG 60.143 45.833 0.00 0.00 0.00 3.02
719 732 4.012374 CCTTGGTATGTGCATGTCTTCTT 58.988 43.478 0.00 0.00 0.00 2.52
720 733 3.614092 CCTTGGTATGTGCATGTCTTCT 58.386 45.455 0.00 0.00 0.00 2.85
721 734 2.098117 GCCTTGGTATGTGCATGTCTTC 59.902 50.000 0.00 0.00 0.00 2.87
722 735 2.094675 GCCTTGGTATGTGCATGTCTT 58.905 47.619 0.00 0.00 0.00 3.01
723 736 1.683011 GGCCTTGGTATGTGCATGTCT 60.683 52.381 0.00 0.00 0.00 3.41
724 737 0.740737 GGCCTTGGTATGTGCATGTC 59.259 55.000 0.00 0.00 0.00 3.06
725 738 0.684153 GGGCCTTGGTATGTGCATGT 60.684 55.000 0.84 0.00 0.00 3.21
726 739 1.727511 CGGGCCTTGGTATGTGCATG 61.728 60.000 0.84 0.00 0.00 4.06
727 740 1.453745 CGGGCCTTGGTATGTGCAT 60.454 57.895 0.84 0.00 0.00 3.96
728 741 2.045438 CGGGCCTTGGTATGTGCA 60.045 61.111 0.84 0.00 0.00 4.57
729 742 2.828549 CCGGGCCTTGGTATGTGC 60.829 66.667 0.84 0.00 0.00 4.57
730 743 1.748879 CACCGGGCCTTGGTATGTG 60.749 63.158 18.11 4.56 37.72 3.21
731 744 1.493854 TTCACCGGGCCTTGGTATGT 61.494 55.000 18.11 0.00 37.72 2.29
732 745 0.748005 CTTCACCGGGCCTTGGTATG 60.748 60.000 18.11 8.87 37.72 2.39
733 746 1.205460 ACTTCACCGGGCCTTGGTAT 61.205 55.000 18.11 4.11 37.72 2.73
734 747 1.844289 ACTTCACCGGGCCTTGGTA 60.844 57.895 18.11 5.19 37.72 3.25
735 748 3.175710 ACTTCACCGGGCCTTGGT 61.176 61.111 13.65 13.65 41.47 3.67
736 749 2.672996 CACTTCACCGGGCCTTGG 60.673 66.667 6.32 12.37 0.00 3.61
737 750 2.672996 CCACTTCACCGGGCCTTG 60.673 66.667 6.32 0.00 0.00 3.61
738 751 3.175710 ACCACTTCACCGGGCCTT 61.176 61.111 6.32 0.00 0.00 4.35
739 752 3.953775 CACCACTTCACCGGGCCT 61.954 66.667 6.32 0.00 0.00 5.19
740 753 3.485346 TTCACCACTTCACCGGGCC 62.485 63.158 6.32 0.00 0.00 5.80
741 754 2.112297 TTCACCACTTCACCGGGC 59.888 61.111 6.32 0.00 0.00 6.13
742 755 1.959226 CGTTCACCACTTCACCGGG 60.959 63.158 6.32 0.00 0.00 5.73
743 756 1.959226 CCGTTCACCACTTCACCGG 60.959 63.158 0.00 0.00 0.00 5.28
744 757 1.959226 CCCGTTCACCACTTCACCG 60.959 63.158 0.00 0.00 0.00 4.94
745 758 0.602905 CTCCCGTTCACCACTTCACC 60.603 60.000 0.00 0.00 0.00 4.02
746 759 0.602905 CCTCCCGTTCACCACTTCAC 60.603 60.000 0.00 0.00 0.00 3.18
747 760 1.752198 CCTCCCGTTCACCACTTCA 59.248 57.895 0.00 0.00 0.00 3.02
748 761 1.003718 CCCTCCCGTTCACCACTTC 60.004 63.158 0.00 0.00 0.00 3.01
749 762 3.157680 CCCTCCCGTTCACCACTT 58.842 61.111 0.00 0.00 0.00 3.16
750 763 3.637273 GCCCTCCCGTTCACCACT 61.637 66.667 0.00 0.00 0.00 4.00
751 764 3.948719 TGCCCTCCCGTTCACCAC 61.949 66.667 0.00 0.00 0.00 4.16
752 765 3.948719 GTGCCCTCCCGTTCACCA 61.949 66.667 0.00 0.00 0.00 4.17
754 767 3.934391 CTCGTGCCCTCCCGTTCAC 62.934 68.421 0.00 0.00 0.00 3.18
755 768 3.691342 CTCGTGCCCTCCCGTTCA 61.691 66.667 0.00 0.00 0.00 3.18
756 769 3.379445 TCTCGTGCCCTCCCGTTC 61.379 66.667 0.00 0.00 0.00 3.95
757 770 3.692406 GTCTCGTGCCCTCCCGTT 61.692 66.667 0.00 0.00 0.00 4.44
758 771 4.680537 AGTCTCGTGCCCTCCCGT 62.681 66.667 0.00 0.00 0.00 5.28
759 772 4.135153 CAGTCTCGTGCCCTCCCG 62.135 72.222 0.00 0.00 0.00 5.14
760 773 3.775654 CCAGTCTCGTGCCCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
761 774 2.680352 TCCAGTCTCGTGCCCTCC 60.680 66.667 0.00 0.00 0.00 4.30
762 775 1.536943 AAGTCCAGTCTCGTGCCCTC 61.537 60.000 0.00 0.00 0.00 4.30
763 776 1.534235 AAGTCCAGTCTCGTGCCCT 60.534 57.895 0.00 0.00 0.00 5.19
764 777 1.374758 CAAGTCCAGTCTCGTGCCC 60.375 63.158 0.00 0.00 0.00 5.36
765 778 0.946221 CACAAGTCCAGTCTCGTGCC 60.946 60.000 0.00 0.00 0.00 5.01
766 779 0.946221 CCACAAGTCCAGTCTCGTGC 60.946 60.000 0.00 0.00 0.00 5.34
767 780 0.389391 ACCACAAGTCCAGTCTCGTG 59.611 55.000 0.00 0.00 0.00 4.35
768 781 0.389391 CACCACAAGTCCAGTCTCGT 59.611 55.000 0.00 0.00 0.00 4.18
769 782 0.389391 ACACCACAAGTCCAGTCTCG 59.611 55.000 0.00 0.00 0.00 4.04
770 783 2.610727 GCTACACCACAAGTCCAGTCTC 60.611 54.545 0.00 0.00 0.00 3.36
771 784 1.344763 GCTACACCACAAGTCCAGTCT 59.655 52.381 0.00 0.00 0.00 3.24
772 785 1.070134 TGCTACACCACAAGTCCAGTC 59.930 52.381 0.00 0.00 0.00 3.51
773 786 1.070758 CTGCTACACCACAAGTCCAGT 59.929 52.381 0.00 0.00 0.00 4.00
774 787 1.800805 CTGCTACACCACAAGTCCAG 58.199 55.000 0.00 0.00 0.00 3.86
775 788 0.250295 GCTGCTACACCACAAGTCCA 60.250 55.000 0.00 0.00 0.00 4.02
776 789 0.955919 GGCTGCTACACCACAAGTCC 60.956 60.000 0.00 0.00 0.00 3.85
777 790 0.035458 AGGCTGCTACACCACAAGTC 59.965 55.000 0.00 0.00 0.00 3.01
778 791 0.250467 CAGGCTGCTACACCACAAGT 60.250 55.000 0.00 0.00 0.00 3.16
779 792 1.580845 GCAGGCTGCTACACCACAAG 61.581 60.000 31.37 0.00 40.96 3.16
780 793 1.600636 GCAGGCTGCTACACCACAA 60.601 57.895 31.37 0.00 40.96 3.33
781 794 2.032528 GCAGGCTGCTACACCACA 59.967 61.111 31.37 0.00 40.96 4.17
782 795 2.032528 TGCAGGCTGCTACACCAC 59.967 61.111 36.50 9.19 45.31 4.16
783 796 2.348620 CTGCAGGCTGCTACACCA 59.651 61.111 36.50 17.10 45.31 4.17
784 797 3.130160 GCTGCAGGCTGCTACACC 61.130 66.667 36.50 17.83 45.31 4.16
785 798 3.130160 GGCTGCAGGCTGCTACAC 61.130 66.667 36.50 22.98 45.31 2.90
793 806 2.042831 CCAGTACAAGGCTGCAGGC 61.043 63.158 31.58 31.58 41.43 4.85
794 807 0.036732 TTCCAGTACAAGGCTGCAGG 59.963 55.000 17.12 0.31 32.93 4.85
795 808 1.808945 CTTTCCAGTACAAGGCTGCAG 59.191 52.381 10.11 10.11 32.93 4.41
796 809 1.896220 CTTTCCAGTACAAGGCTGCA 58.104 50.000 0.50 0.00 32.93 4.41
797 810 0.523519 GCTTTCCAGTACAAGGCTGC 59.476 55.000 0.00 0.00 32.93 5.25
798 811 0.798776 CGCTTTCCAGTACAAGGCTG 59.201 55.000 0.00 0.00 0.00 4.85
799 812 0.321653 CCGCTTTCCAGTACAAGGCT 60.322 55.000 0.00 0.00 0.00 4.58
800 813 0.321298 TCCGCTTTCCAGTACAAGGC 60.321 55.000 0.00 0.00 0.00 4.35
801 814 2.178912 TTCCGCTTTCCAGTACAAGG 57.821 50.000 0.00 0.00 0.00 3.61
802 815 3.621715 GGTATTCCGCTTTCCAGTACAAG 59.378 47.826 0.00 0.00 0.00 3.16
803 816 3.262405 AGGTATTCCGCTTTCCAGTACAA 59.738 43.478 0.00 0.00 39.05 2.41
804 817 2.835764 AGGTATTCCGCTTTCCAGTACA 59.164 45.455 0.00 0.00 39.05 2.90
805 818 3.118884 TCAGGTATTCCGCTTTCCAGTAC 60.119 47.826 0.00 0.00 39.05 2.73
806 819 3.101437 TCAGGTATTCCGCTTTCCAGTA 58.899 45.455 0.00 0.00 39.05 2.74
807 820 1.906574 TCAGGTATTCCGCTTTCCAGT 59.093 47.619 0.00 0.00 39.05 4.00
808 821 2.280628 GTCAGGTATTCCGCTTTCCAG 58.719 52.381 0.00 0.00 39.05 3.86
809 822 1.404986 CGTCAGGTATTCCGCTTTCCA 60.405 52.381 0.00 0.00 39.05 3.53
810 823 1.287425 CGTCAGGTATTCCGCTTTCC 58.713 55.000 0.00 0.00 39.05 3.13
811 824 0.651031 GCGTCAGGTATTCCGCTTTC 59.349 55.000 0.00 0.00 42.66 2.62
812 825 1.082117 CGCGTCAGGTATTCCGCTTT 61.082 55.000 0.00 0.00 43.70 3.51
813 826 1.518572 CGCGTCAGGTATTCCGCTT 60.519 57.895 0.00 0.00 43.70 4.68
814 827 2.104331 CGCGTCAGGTATTCCGCT 59.896 61.111 0.00 0.00 43.70 5.52
815 828 2.960129 CCGCGTCAGGTATTCCGC 60.960 66.667 4.92 0.00 42.53 5.54
816 829 2.067091 TAGCCGCGTCAGGTATTCCG 62.067 60.000 4.92 0.00 39.05 4.30
817 830 0.103572 TTAGCCGCGTCAGGTATTCC 59.896 55.000 4.92 0.00 0.00 3.01
818 831 1.930567 TTTAGCCGCGTCAGGTATTC 58.069 50.000 4.92 0.00 0.00 1.75
819 832 2.389962 TTTTAGCCGCGTCAGGTATT 57.610 45.000 4.92 0.00 0.00 1.89
823 836 0.931005 GAGATTTTAGCCGCGTCAGG 59.069 55.000 4.92 0.00 0.00 3.86
825 838 0.171679 TCGAGATTTTAGCCGCGTCA 59.828 50.000 4.92 0.00 0.00 4.35
836 849 2.436173 GGAGGAGGATGGTTCGAGATTT 59.564 50.000 0.00 0.00 0.00 2.17
841 854 0.687757 CAGGGAGGAGGATGGTTCGA 60.688 60.000 0.00 0.00 0.00 3.71
855 868 0.978146 GCTTCACTAGGGCTCAGGGA 60.978 60.000 0.00 0.00 0.00 4.20
856 869 0.980231 AGCTTCACTAGGGCTCAGGG 60.980 60.000 0.00 0.00 0.00 4.45
857 870 0.908198 AAGCTTCACTAGGGCTCAGG 59.092 55.000 0.00 0.00 35.06 3.86
858 871 1.830477 AGAAGCTTCACTAGGGCTCAG 59.170 52.381 27.57 0.00 35.06 3.35
859 872 1.827969 GAGAAGCTTCACTAGGGCTCA 59.172 52.381 27.57 0.00 35.06 4.26
860 873 2.107366 AGAGAAGCTTCACTAGGGCTC 58.893 52.381 27.57 13.66 35.06 4.70
942 959 3.700038 GACTTGGGAGTCGAAGGAAGATA 59.300 47.826 0.00 0.00 42.60 1.98
943 960 2.498078 GACTTGGGAGTCGAAGGAAGAT 59.502 50.000 0.00 0.00 42.60 2.40
945 962 2.371910 GACTTGGGAGTCGAAGGAAG 57.628 55.000 0.00 0.00 42.60 3.46
1195 1243 3.103911 GTCGAACGACCCGTGCTG 61.104 66.667 15.16 0.00 39.99 4.41
1202 1250 3.749373 CGCACACGTCGAACGACC 61.749 66.667 19.15 6.21 46.05 4.79
1315 1363 4.506255 GACAAGGATGGGGCCCGG 62.506 72.222 19.83 5.35 0.00 5.73
1470 1521 3.089117 GATTCGATCGGTCTACGGC 57.911 57.895 16.41 0.00 44.45 5.68
1506 1568 0.981183 TGGAAACCACTCGCAGGTAT 59.019 50.000 0.00 0.00 38.76 2.73
1523 1585 1.532505 GCTGCACTGCGACATTATTGG 60.533 52.381 0.00 0.00 0.00 3.16
1524 1586 1.399440 AGCTGCACTGCGACATTATTG 59.601 47.619 1.02 0.00 38.13 1.90
1533 1595 2.950565 ATCGAGCTAGCTGCACTGCG 62.951 60.000 24.99 18.12 45.94 5.18
1546 1612 0.316032 GTACCGACTGACGATCGAGC 60.316 60.000 24.34 13.69 45.77 5.03
1556 1622 1.282248 CTGCAACACCGTACCGACTG 61.282 60.000 0.00 0.00 0.00 3.51
1559 1625 2.356553 GCTGCAACACCGTACCGA 60.357 61.111 0.00 0.00 0.00 4.69
1560 1626 2.357034 AGCTGCAACACCGTACCG 60.357 61.111 1.02 0.00 0.00 4.02
1561 1627 1.164041 AACAGCTGCAACACCGTACC 61.164 55.000 15.27 0.00 0.00 3.34
1562 1628 0.661020 AAACAGCTGCAACACCGTAC 59.339 50.000 15.27 0.00 0.00 3.67
1563 1629 0.941542 GAAACAGCTGCAACACCGTA 59.058 50.000 15.27 0.00 0.00 4.02
1564 1630 1.724582 GGAAACAGCTGCAACACCGT 61.725 55.000 15.27 0.00 0.00 4.83
1570 1636 3.069872 ACAATCATTGGAAACAGCTGCAA 59.930 39.130 15.27 10.35 44.54 4.08
1581 1647 0.243365 GCCAACGCACAATCATTGGA 59.757 50.000 1.58 0.00 43.66 3.53
1584 1650 4.866088 CGCCAACGCACAATCATT 57.134 50.000 0.00 0.00 34.03 2.57
1616 1691 5.524281 TGCAAATCAAACACTACACGACTAA 59.476 36.000 0.00 0.00 0.00 2.24
1617 1692 5.051153 TGCAAATCAAACACTACACGACTA 58.949 37.500 0.00 0.00 0.00 2.59
1621 1697 4.209452 ACTGCAAATCAAACACTACACG 57.791 40.909 0.00 0.00 0.00 4.49
1632 1708 6.463995 AGTCCAAAGTTAAACTGCAAATCA 57.536 33.333 0.00 0.00 0.00 2.57
1640 1716 5.437060 TCTCTGCAAGTCCAAAGTTAAACT 58.563 37.500 0.00 0.00 33.76 2.66
1669 1745 1.236628 CATCTGAGCTAAGCCCATGC 58.763 55.000 0.00 0.00 37.95 4.06
1682 1758 1.955778 CACCCAAACACTTGCATCTGA 59.044 47.619 0.00 0.00 0.00 3.27
1697 1773 2.171209 CTCACGAGCCATGACACCCA 62.171 60.000 0.00 0.00 0.00 4.51
1698 1774 1.448540 CTCACGAGCCATGACACCC 60.449 63.158 0.00 0.00 0.00 4.61
1711 1787 0.241213 ACATCTGTGTCCGACTCACG 59.759 55.000 0.00 0.00 38.48 4.35
1733 1809 7.813852 AAAGACGTAGAAATAACAGTAGCTG 57.186 36.000 0.00 0.00 37.52 4.24
1814 1890 2.051692 AGGCCGGGTATGTGCTTAATA 58.948 47.619 2.18 0.00 0.00 0.98
1825 1901 1.153046 GCTATGCAAAGGCCGGGTA 60.153 57.895 2.18 0.00 40.13 3.69
1847 1923 2.993220 GTTGACGTGAGATGTGTGCATA 59.007 45.455 0.00 0.00 35.07 3.14
1863 1939 4.088648 GCGTGCTTATTGTATGTGTTGAC 58.911 43.478 0.00 0.00 0.00 3.18
1902 1978 7.161404 CAGTGGCATAGCTTTGGTCTTATATA 58.839 38.462 6.29 0.00 0.00 0.86
2039 2121 2.263540 GACGGGCCTTTAGTCGCA 59.736 61.111 0.84 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.