Multiple sequence alignment - TraesCS4D01G171900

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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 TraesCS4D01G171900 chr4D 100.000 3620 0 0 1 3620 298903125 298899506 0.000000e+00 6685
1 TraesCS4D01G171900 chr4D 90.827 556 35 12 51 600 477406839 477407384 0.000000e+00 730
2 TraesCS4D01G171900 chr4D 79.384 422 49 20 51 440 477406660 477407075 2.770000e-66 263
3 TraesCS4D01G171900 chr4D 93.846 130 7 1 592 721 477407411 477407539 1.030000e-45 195
4 TraesCS4D01G171900 chr4B 94.944 1958 47 17 872 2792 370916930 370914988 0.000000e+00 3020
5 TraesCS4D01G171900 chr4B 79.045 377 71 8 2955 3328 168936528 168936157 6.000000e-63 252
6 TraesCS4D01G171900 chr4B 97.581 124 3 0 594 717 664532600 664532477 2.830000e-51 213
7 TraesCS4D01G171900 chr4A 96.763 1761 41 5 840 2592 186689360 186691112 0.000000e+00 2922
8 TraesCS4D01G171900 chr4A 78.150 1016 152 37 2648 3610 186691393 186692391 1.870000e-162 582
9 TraesCS4D01G171900 chr4A 77.560 459 71 25 31 469 697938020 697937574 7.760000e-62 248
10 TraesCS4D01G171900 chr5D 81.882 712 114 5 2913 3611 9126581 9127290 1.450000e-163 586
11 TraesCS4D01G171900 chr5D 80.280 715 109 17 2925 3610 384883437 384882726 8.970000e-141 510
12 TraesCS4D01G171900 chr1A 80.959 772 120 19 2859 3610 573384075 573383311 1.450000e-163 586
13 TraesCS4D01G171900 chr1A 78.734 790 128 23 2859 3616 592469786 592469005 3.250000e-135 492
14 TraesCS4D01G171900 chr1A 77.121 778 126 33 2858 3617 79117360 79118103 1.570000e-108 403
15 TraesCS4D01G171900 chr1D 81.767 713 116 12 2913 3617 280042664 280043370 5.210000e-163 584
16 TraesCS4D01G171900 chr1D 96.825 126 4 0 592 717 344209575 344209700 1.020000e-50 211
17 TraesCS4D01G171900 chr6A 81.197 702 118 14 2918 3613 70968538 70969231 1.470000e-153 553
18 TraesCS4D01G171900 chr6A 80.000 370 59 14 11 369 35324536 35324171 3.590000e-65 259
19 TraesCS4D01G171900 chr5B 80.449 757 114 14 2863 3616 419769551 419768826 6.830000e-152 547
20 TraesCS4D01G171900 chr5B 97.638 127 3 0 592 718 447129880 447129754 6.090000e-53 219
21 TraesCS4D01G171900 chr7B 78.817 845 149 23 2793 3616 700626865 700626030 3.180000e-150 542
22 TraesCS4D01G171900 chr2D 80.867 669 108 13 2855 3518 378899326 378899979 3.220000e-140 508
23 TraesCS4D01G171900 chr2D 80.041 491 87 7 3127 3610 536516983 536517469 1.600000e-93 353
24 TraesCS4D01G171900 chr6B 79.205 755 138 16 2864 3603 145373675 145372925 1.160000e-139 507
25 TraesCS4D01G171900 chr6B 78.475 446 55 32 72 483 351858222 351858660 1.670000e-63 254
26 TraesCS4D01G171900 chr6B 95.312 128 6 0 592 719 5599325 5599452 1.700000e-48 204
27 TraesCS4D01G171900 chr6B 95.312 128 6 0 592 719 5617176 5617303 1.700000e-48 204
28 TraesCS4D01G171900 chr6B 97.500 120 2 1 592 710 68011745 68011864 1.700000e-48 204
29 TraesCS4D01G171900 chr6B 95.238 126 5 1 592 716 569025233 569025108 7.930000e-47 198
30 TraesCS4D01G171900 chr7D 80.148 675 110 16 2946 3612 478369708 478369050 1.950000e-132 483
31 TraesCS4D01G171900 chr7D 76.025 805 146 30 2829 3613 580174188 580174965 1.230000e-99 374
32 TraesCS4D01G171900 chr7D 79.116 498 93 11 3127 3617 258191275 258190782 2.080000e-87 333
33 TraesCS4D01G171900 chr6D 82.441 467 63 17 3147 3598 346270638 346270176 1.220000e-104 390
34 TraesCS4D01G171900 chr6D 79.941 339 51 16 43 369 125393706 125393373 2.170000e-57 233
35 TraesCS4D01G171900 chr5A 79.287 449 68 19 1 436 351997939 351998375 1.270000e-74 291
36 TraesCS4D01G171900 chr2B 80.879 387 58 10 2957 3329 450184930 450185314 1.270000e-74 291
37 TraesCS4D01G171900 chr2B 83.922 255 39 2 3360 3613 449222133 449222386 3.610000e-60 243
38 TraesCS4D01G171900 chr7A 79.688 384 47 21 125 484 689235426 689235050 7.760000e-62 248
39 TraesCS4D01G171900 chr3D 77.412 425 67 24 26 430 70241310 70241725 3.640000e-55 226
40 TraesCS4D01G171900 chr3B 95.935 123 3 1 595 717 7316550 7316430 7.930000e-47 198


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 TraesCS4D01G171900 chr4D 298899506 298903125 3619 True 6685 6685 100.0000 1 3620 1 chr4D.!!$R1 3619
1 TraesCS4D01G171900 chr4D 477406660 477407539 879 False 396 730 88.0190 51 721 3 chr4D.!!$F1 670
2 TraesCS4D01G171900 chr4B 370914988 370916930 1942 True 3020 3020 94.9440 872 2792 1 chr4B.!!$R2 1920
3 TraesCS4D01G171900 chr4A 186689360 186692391 3031 False 1752 2922 87.4565 840 3610 2 chr4A.!!$F1 2770
4 TraesCS4D01G171900 chr5D 9126581 9127290 709 False 586 586 81.8820 2913 3611 1 chr5D.!!$F1 698
5 TraesCS4D01G171900 chr5D 384882726 384883437 711 True 510 510 80.2800 2925 3610 1 chr5D.!!$R1 685
6 TraesCS4D01G171900 chr1A 573383311 573384075 764 True 586 586 80.9590 2859 3610 1 chr1A.!!$R1 751
7 TraesCS4D01G171900 chr1A 592469005 592469786 781 True 492 492 78.7340 2859 3616 1 chr1A.!!$R2 757
8 TraesCS4D01G171900 chr1A 79117360 79118103 743 False 403 403 77.1210 2858 3617 1 chr1A.!!$F1 759
9 TraesCS4D01G171900 chr1D 280042664 280043370 706 False 584 584 81.7670 2913 3617 1 chr1D.!!$F1 704
10 TraesCS4D01G171900 chr6A 70968538 70969231 693 False 553 553 81.1970 2918 3613 1 chr6A.!!$F1 695
11 TraesCS4D01G171900 chr5B 419768826 419769551 725 True 547 547 80.4490 2863 3616 1 chr5B.!!$R1 753
12 TraesCS4D01G171900 chr7B 700626030 700626865 835 True 542 542 78.8170 2793 3616 1 chr7B.!!$R1 823
13 TraesCS4D01G171900 chr2D 378899326 378899979 653 False 508 508 80.8670 2855 3518 1 chr2D.!!$F1 663
14 TraesCS4D01G171900 chr6B 145372925 145373675 750 True 507 507 79.2050 2864 3603 1 chr6B.!!$R1 739
15 TraesCS4D01G171900 chr7D 478369050 478369708 658 True 483 483 80.1480 2946 3612 1 chr7D.!!$R2 666
16 TraesCS4D01G171900 chr7D 580174188 580174965 777 False 374 374 76.0250 2829 3613 1 chr7D.!!$F1 784

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
737 869 0.035820 ATACGACGGCCCAACATTGT 60.036 50.0 0.00 0.0 0.00 2.71 F
785 917 0.179468 TGTTAATACAGGGCCTCCGC 59.821 55.0 0.95 0.0 38.33 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1936 1.217244 GGTGTAGATGTCCGCCGTT 59.783 57.895 0.0 0.0 0.00 4.44 R
2784 3157 2.151202 GAGGATTTTTGCGTGTCCTGA 58.849 47.619 0.0 0.0 41.03 3.86 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
32 33 8.766000 AACTTTTGTTAAAATCGGTGAACTTT 57.234 26.923 0.00 0.00 41.50 2.66
33 34 8.766000 ACTTTTGTTAAAATCGGTGAACTTTT 57.234 26.923 0.00 0.00 0.00 2.27
89 118 9.918630 ATGAACTCTTTTTCAAAATCGATGAAT 57.081 25.926 0.00 0.00 38.95 2.57
592 724 2.455674 TCAACACTTGACCGATCCAG 57.544 50.000 0.00 0.00 34.08 3.86
593 725 1.001974 TCAACACTTGACCGATCCAGG 59.998 52.381 0.00 0.00 34.08 4.45
594 726 0.324943 AACACTTGACCGATCCAGGG 59.675 55.000 0.00 0.00 35.02 4.45
595 727 0.544357 ACACTTGACCGATCCAGGGA 60.544 55.000 0.00 0.00 35.02 4.20
596 728 0.176680 CACTTGACCGATCCAGGGAG 59.823 60.000 0.00 0.00 35.02 4.30
597 729 1.144936 CTTGACCGATCCAGGGAGC 59.855 63.158 0.00 0.00 35.02 4.70
603 735 3.237741 GATCCAGGGAGCGAGGGG 61.238 72.222 0.00 0.00 0.00 4.79
604 736 3.758133 GATCCAGGGAGCGAGGGGA 62.758 68.421 0.00 0.00 0.00 4.81
605 737 3.765257 ATCCAGGGAGCGAGGGGAG 62.765 68.421 0.00 0.00 0.00 4.30
610 742 4.516195 GGAGCGAGGGGAGCGAAC 62.516 72.222 0.00 0.00 40.04 3.95
611 743 4.856607 GAGCGAGGGGAGCGAACG 62.857 72.222 0.00 0.00 40.04 3.95
613 745 4.856607 GCGAGGGGAGCGAACGAG 62.857 72.222 0.00 0.00 0.00 4.18
614 746 4.856607 CGAGGGGAGCGAACGAGC 62.857 72.222 0.00 0.00 37.41 5.03
615 747 3.760035 GAGGGGAGCGAACGAGCA 61.760 66.667 0.00 0.00 40.15 4.26
616 748 3.708220 GAGGGGAGCGAACGAGCAG 62.708 68.421 0.00 0.00 40.15 4.24
617 749 3.760035 GGGGAGCGAACGAGCAGA 61.760 66.667 0.00 0.00 40.15 4.26
618 750 2.261671 GGGAGCGAACGAGCAGAA 59.738 61.111 0.00 0.00 40.15 3.02
619 751 1.807573 GGGAGCGAACGAGCAGAAG 60.808 63.158 0.00 0.00 40.15 2.85
620 752 1.080434 GGAGCGAACGAGCAGAAGT 60.080 57.895 0.00 0.00 40.15 3.01
621 753 1.347817 GGAGCGAACGAGCAGAAGTG 61.348 60.000 0.00 0.00 40.15 3.16
622 754 1.347817 GAGCGAACGAGCAGAAGTGG 61.348 60.000 0.00 0.00 40.15 4.00
623 755 1.372997 GCGAACGAGCAGAAGTGGA 60.373 57.895 0.00 0.00 37.05 4.02
624 756 0.944311 GCGAACGAGCAGAAGTGGAA 60.944 55.000 0.00 0.00 37.05 3.53
625 757 0.784778 CGAACGAGCAGAAGTGGAAC 59.215 55.000 0.00 0.00 0.00 3.62
626 758 1.865865 GAACGAGCAGAAGTGGAACA 58.134 50.000 0.00 0.00 41.43 3.18
627 759 2.210116 GAACGAGCAGAAGTGGAACAA 58.790 47.619 0.00 0.00 44.16 2.83
628 760 1.871080 ACGAGCAGAAGTGGAACAAG 58.129 50.000 0.00 0.00 44.16 3.16
629 761 0.514691 CGAGCAGAAGTGGAACAAGC 59.485 55.000 0.00 0.00 44.16 4.01
630 762 0.514691 GAGCAGAAGTGGAACAAGCG 59.485 55.000 0.00 0.00 44.16 4.68
631 763 0.106708 AGCAGAAGTGGAACAAGCGA 59.893 50.000 0.00 0.00 44.16 4.93
632 764 0.944386 GCAGAAGTGGAACAAGCGAA 59.056 50.000 0.00 0.00 44.16 4.70
633 765 1.334149 GCAGAAGTGGAACAAGCGAAC 60.334 52.381 0.00 0.00 44.16 3.95
634 766 1.070577 CAGAAGTGGAACAAGCGAACG 60.071 52.381 0.00 0.00 44.16 3.95
635 767 1.202486 AGAAGTGGAACAAGCGAACGA 60.202 47.619 0.00 0.00 44.16 3.85
636 768 1.192534 GAAGTGGAACAAGCGAACGAG 59.807 52.381 0.00 0.00 44.16 4.18
637 769 0.600255 AGTGGAACAAGCGAACGAGG 60.600 55.000 0.00 0.00 44.16 4.63
638 770 1.959226 TGGAACAAGCGAACGAGGC 60.959 57.895 0.00 0.00 31.92 4.70
639 771 1.959226 GGAACAAGCGAACGAGGCA 60.959 57.895 0.00 0.00 0.00 4.75
640 772 1.503818 GGAACAAGCGAACGAGGCAA 61.504 55.000 0.00 0.00 0.00 4.52
641 773 0.110644 GAACAAGCGAACGAGGCAAG 60.111 55.000 0.00 0.00 0.00 4.01
642 774 2.117941 AACAAGCGAACGAGGCAAGC 62.118 55.000 0.00 0.00 0.00 4.01
643 775 2.031163 AAGCGAACGAGGCAAGCT 59.969 55.556 0.00 0.00 40.20 3.74
644 776 2.320587 AAGCGAACGAGGCAAGCTG 61.321 57.895 0.00 0.00 38.28 4.24
645 777 3.793144 GCGAACGAGGCAAGCTGG 61.793 66.667 0.00 0.00 0.00 4.85
646 778 3.121030 CGAACGAGGCAAGCTGGG 61.121 66.667 0.00 0.00 0.00 4.45
647 779 3.435186 GAACGAGGCAAGCTGGGC 61.435 66.667 6.54 6.54 0.00 5.36
708 840 3.195698 GCTGAAGGCGCCCGTTAG 61.196 66.667 26.15 18.58 0.00 2.34
709 841 2.511600 CTGAAGGCGCCCGTTAGG 60.512 66.667 26.15 4.98 39.47 2.69
731 863 3.788145 CCCCATACGACGGCCCAA 61.788 66.667 0.00 0.00 0.00 4.12
732 864 2.512974 CCCATACGACGGCCCAAC 60.513 66.667 0.00 0.00 0.00 3.77
733 865 2.266372 CCATACGACGGCCCAACA 59.734 61.111 0.00 0.00 0.00 3.33
734 866 1.153249 CCATACGACGGCCCAACAT 60.153 57.895 0.00 0.00 0.00 2.71
735 867 0.746563 CCATACGACGGCCCAACATT 60.747 55.000 0.00 0.00 0.00 2.71
736 868 0.376852 CATACGACGGCCCAACATTG 59.623 55.000 0.00 0.00 0.00 2.82
737 869 0.035820 ATACGACGGCCCAACATTGT 60.036 50.000 0.00 0.00 0.00 2.71
738 870 0.951525 TACGACGGCCCAACATTGTG 60.952 55.000 0.00 0.00 0.00 3.33
739 871 2.258013 CGACGGCCCAACATTGTGT 61.258 57.895 0.00 0.00 0.00 3.72
740 872 1.791103 CGACGGCCCAACATTGTGTT 61.791 55.000 0.00 0.00 42.08 3.32
741 873 1.240256 GACGGCCCAACATTGTGTTA 58.760 50.000 0.00 0.00 38.77 2.41
742 874 1.609555 GACGGCCCAACATTGTGTTAA 59.390 47.619 0.00 0.00 38.77 2.01
743 875 2.230266 GACGGCCCAACATTGTGTTAAT 59.770 45.455 0.00 0.00 38.77 1.40
744 876 3.422796 ACGGCCCAACATTGTGTTAATA 58.577 40.909 0.00 0.00 38.77 0.98
745 877 3.191791 ACGGCCCAACATTGTGTTAATAC 59.808 43.478 0.00 0.00 38.77 1.89
746 878 3.442273 CGGCCCAACATTGTGTTAATACT 59.558 43.478 0.00 0.00 38.77 2.12
747 879 4.082463 CGGCCCAACATTGTGTTAATACTT 60.082 41.667 0.00 0.00 38.77 2.24
748 880 5.565834 CGGCCCAACATTGTGTTAATACTTT 60.566 40.000 0.00 0.00 38.77 2.66
749 881 5.867174 GGCCCAACATTGTGTTAATACTTTC 59.133 40.000 3.89 0.00 38.77 2.62
750 882 6.295067 GGCCCAACATTGTGTTAATACTTTCT 60.295 38.462 3.89 0.00 38.77 2.52
751 883 7.151976 GCCCAACATTGTGTTAATACTTTCTT 58.848 34.615 3.89 0.00 38.77 2.52
752 884 7.655732 GCCCAACATTGTGTTAATACTTTCTTT 59.344 33.333 3.89 0.00 38.77 2.52
753 885 9.541143 CCCAACATTGTGTTAATACTTTCTTTT 57.459 29.630 3.89 0.00 38.77 2.27
778 910 7.214467 AGAACAACATTGTGTTAATACAGGG 57.786 36.000 5.15 4.79 41.78 4.45
779 911 5.385509 ACAACATTGTGTTAATACAGGGC 57.614 39.130 5.15 0.00 38.77 5.19
780 912 4.219725 ACAACATTGTGTTAATACAGGGCC 59.780 41.667 5.15 0.00 38.77 5.80
781 913 4.316025 ACATTGTGTTAATACAGGGCCT 57.684 40.909 0.00 0.00 34.24 5.19
782 914 4.270008 ACATTGTGTTAATACAGGGCCTC 58.730 43.478 0.95 0.00 34.24 4.70
783 915 3.359695 TTGTGTTAATACAGGGCCTCC 57.640 47.619 0.95 0.00 34.24 4.30
784 916 1.208535 TGTGTTAATACAGGGCCTCCG 59.791 52.381 0.95 0.00 38.33 4.63
785 917 0.179468 TGTTAATACAGGGCCTCCGC 59.821 55.000 0.95 0.00 38.33 5.54
786 918 0.468648 GTTAATACAGGGCCTCCGCT 59.531 55.000 0.95 0.00 38.33 5.52
787 919 0.756903 TTAATACAGGGCCTCCGCTC 59.243 55.000 0.95 0.00 38.33 5.03
793 925 4.459089 GGGCCTCCGCTCTGTGTC 62.459 72.222 0.84 0.00 34.44 3.67
794 926 3.386237 GGCCTCCGCTCTGTGTCT 61.386 66.667 0.00 0.00 34.44 3.41
795 927 2.183046 GCCTCCGCTCTGTGTCTC 59.817 66.667 0.00 0.00 0.00 3.36
796 928 2.640302 GCCTCCGCTCTGTGTCTCA 61.640 63.158 0.00 0.00 0.00 3.27
797 929 1.967535 CCTCCGCTCTGTGTCTCAA 59.032 57.895 0.00 0.00 0.00 3.02
798 930 0.318441 CCTCCGCTCTGTGTCTCAAA 59.682 55.000 0.00 0.00 0.00 2.69
799 931 1.270305 CCTCCGCTCTGTGTCTCAAAA 60.270 52.381 0.00 0.00 0.00 2.44
800 932 2.483876 CTCCGCTCTGTGTCTCAAAAA 58.516 47.619 0.00 0.00 0.00 1.94
835 967 2.809601 GCTCTCTCGCGGCGAAAA 60.810 61.111 26.28 15.78 34.74 2.29
836 968 2.167861 GCTCTCTCGCGGCGAAAAT 61.168 57.895 26.28 0.00 34.74 1.82
837 969 1.633171 CTCTCTCGCGGCGAAAATG 59.367 57.895 26.28 14.42 34.74 2.32
838 970 1.756375 CTCTCTCGCGGCGAAAATGG 61.756 60.000 26.28 14.03 34.74 3.16
856 988 1.312815 GGGAAAATGAGATGCCCGAG 58.687 55.000 0.00 0.00 0.00 4.63
1557 1699 1.807573 CGAGGCAAAGGAGACGCTC 60.808 63.158 0.00 0.00 0.00 5.03
1590 1732 3.387947 CGCGGTTACCTCCCCAGT 61.388 66.667 0.00 0.00 0.00 4.00
1593 1735 1.295423 CGGTTACCTCCCCAGTGTG 59.705 63.158 0.00 0.00 0.00 3.82
1656 1798 3.010144 GTCACCAGGGCCATGGAT 58.990 61.111 41.60 23.14 43.57 3.41
1794 1936 1.600636 CAAGGACTCGCCCAAGCAA 60.601 57.895 0.00 0.00 39.83 3.91
1849 1991 1.378762 GGGTTCTGCAAGGTAGGCA 59.621 57.895 0.00 0.00 39.32 4.75
2586 2728 4.704833 GTCAAGGAGGCGCTGGCA 62.705 66.667 7.64 0.00 42.47 4.92
2631 2797 0.817654 TCCCATAGTGAGCGAGTGTG 59.182 55.000 0.00 0.00 0.00 3.82
2731 3099 3.594603 TGGGTTCTCGTGAAAGAGATC 57.405 47.619 0.74 0.00 45.55 2.75
2784 3157 2.567615 ACAGAAAGGCGGTAGAACAGAT 59.432 45.455 0.00 0.00 0.00 2.90
2785 3158 3.190874 CAGAAAGGCGGTAGAACAGATC 58.809 50.000 0.00 0.00 0.00 2.75
2786 3159 2.832129 AGAAAGGCGGTAGAACAGATCA 59.168 45.455 0.00 0.00 0.00 2.92
2787 3160 2.969628 AAGGCGGTAGAACAGATCAG 57.030 50.000 0.00 0.00 0.00 2.90
2788 3161 1.115467 AGGCGGTAGAACAGATCAGG 58.885 55.000 0.00 0.00 0.00 3.86
2791 3181 1.476891 GCGGTAGAACAGATCAGGACA 59.523 52.381 0.00 0.00 0.00 4.02
2810 3200 1.154035 CGCAAAAATCCTCCCGCAC 60.154 57.895 0.00 0.00 0.00 5.34
2824 3214 1.079543 CGCACCTGTCCCTGAAGAG 60.080 63.158 0.00 0.00 0.00 2.85
2844 3234 3.385115 AGAGGGGGATAAGTTCACGAAT 58.615 45.455 0.00 0.00 0.00 3.34
2853 3243 7.148018 GGGGATAAGTTCACGAATACGGATATA 60.148 40.741 0.00 0.00 44.46 0.86
2870 3260 5.003804 GGATATAAGACGCAACCATCCAAT 58.996 41.667 0.00 0.00 32.47 3.16
2933 3330 3.919804 ACGAAATTCATTCAAACATGGCG 59.080 39.130 0.00 0.00 37.96 5.69
2940 3337 3.260380 TCATTCAAACATGGCGGGATTTT 59.740 39.130 0.00 0.00 0.00 1.82
2978 3416 7.115236 CCGAATTTCATATAAACACGACGGATA 59.885 37.037 0.00 0.00 36.91 2.59
3133 3599 4.140599 CTCGGCGCTCTCCAGCTT 62.141 66.667 7.64 0.00 44.40 3.74
3137 3618 4.810661 GCGCTCTCCAGCTTCGCT 62.811 66.667 0.00 0.00 44.40 4.93
3139 3620 1.739562 CGCTCTCCAGCTTCGCTTT 60.740 57.895 0.00 0.00 44.40 3.51
3224 3707 1.073722 CTCAGCCCACCAAGCTTGA 59.926 57.895 28.05 4.04 38.95 3.02
3234 3719 1.202758 ACCAAGCTTGACATTGACGGA 60.203 47.619 28.05 0.00 0.00 4.69
3273 3758 3.349927 CTTTCTGGGACATGAGCAATGA 58.650 45.455 0.00 0.00 38.72 2.57
3325 3810 4.758251 CGGTGCCTGCGGACATGA 62.758 66.667 0.00 0.00 0.00 3.07
3386 3897 1.734388 GCCGGTCTTGCCAAACAACT 61.734 55.000 1.90 0.00 36.97 3.16
3390 3901 2.031870 GGTCTTGCCAAACAACTCCTT 58.968 47.619 0.00 0.00 37.17 3.36
3480 3992 1.597302 CTAGACGGATCTCGCGGGA 60.597 63.158 13.04 13.04 43.89 5.14
3572 4084 1.687146 AATCTGCTCCTCCGCCTGA 60.687 57.895 0.00 0.00 0.00 3.86
3578 4090 1.965754 GCTCCTCCGCCTGAAGATGT 61.966 60.000 0.00 0.00 0.00 3.06
3588 4100 1.211457 CCTGAAGATGTTCCTGGAGGG 59.789 57.143 0.00 0.00 35.41 4.30
3617 4130 1.268066 TGTAGTTGGGTCGGCATGTA 58.732 50.000 0.00 0.00 0.00 2.29
3618 4131 1.834896 TGTAGTTGGGTCGGCATGTAT 59.165 47.619 0.00 0.00 0.00 2.29
3619 4132 3.032459 TGTAGTTGGGTCGGCATGTATA 58.968 45.455 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.857957 AAGTTCACCGATTTTAACAAAAGTTAA 57.142 25.926 0.00 0.00 33.22 2.01
6 7 9.857957 AAAGTTCACCGATTTTAACAAAAGTTA 57.142 25.926 0.00 0.00 33.22 2.24
8 9 8.766000 AAAAGTTCACCGATTTTAACAAAAGT 57.234 26.923 0.00 0.00 33.22 2.66
61 72 8.567104 TCATCGATTTTGAAAAAGAGTTCATCA 58.433 29.630 0.00 0.00 37.36 3.07
143 252 8.925161 AGTTCATCGATTTTGAAAAACTTTCA 57.075 26.923 0.00 0.00 35.03 2.69
257 388 9.541724 CGAATTTGAAAAAGAGTTCATCGATTA 57.458 29.630 0.00 0.00 38.73 1.75
361 492 8.733857 AAAGTTTCATCGAATTTGAGTTCATC 57.266 30.769 1.10 0.00 0.00 2.92
484 616 5.237236 TGAAAGAAAGTCCGGGAACTTAT 57.763 39.130 8.83 0.00 38.52 1.73
493 625 8.850454 TTTCATAAAACTTGAAAGAAAGTCCG 57.150 30.769 0.00 0.00 39.48 4.79
577 709 0.176680 CTCCCTGGATCGGTCAAGTG 59.823 60.000 0.00 0.00 0.00 3.16
585 717 3.610669 CCCTCGCTCCCTGGATCG 61.611 72.222 3.12 3.12 35.41 3.69
593 725 4.516195 GTTCGCTCCCCTCGCTCC 62.516 72.222 0.00 0.00 0.00 4.70
594 726 4.856607 CGTTCGCTCCCCTCGCTC 62.857 72.222 0.00 0.00 0.00 5.03
596 728 4.856607 CTCGTTCGCTCCCCTCGC 62.857 72.222 0.00 0.00 0.00 5.03
597 729 4.856607 GCTCGTTCGCTCCCCTCG 62.857 72.222 0.00 0.00 0.00 4.63
598 730 3.708220 CTGCTCGTTCGCTCCCCTC 62.708 68.421 0.00 0.00 0.00 4.30
599 731 3.764466 CTGCTCGTTCGCTCCCCT 61.764 66.667 0.00 0.00 0.00 4.79
600 732 3.296709 TTCTGCTCGTTCGCTCCCC 62.297 63.158 0.00 0.00 0.00 4.81
601 733 1.807573 CTTCTGCTCGTTCGCTCCC 60.808 63.158 0.00 0.00 0.00 4.30
602 734 1.080434 ACTTCTGCTCGTTCGCTCC 60.080 57.895 0.00 0.00 0.00 4.70
603 735 1.347817 CCACTTCTGCTCGTTCGCTC 61.348 60.000 0.00 0.00 0.00 5.03
604 736 1.373497 CCACTTCTGCTCGTTCGCT 60.373 57.895 0.00 0.00 0.00 4.93
605 737 0.944311 TTCCACTTCTGCTCGTTCGC 60.944 55.000 0.00 0.00 0.00 4.70
606 738 0.784778 GTTCCACTTCTGCTCGTTCG 59.215 55.000 0.00 0.00 0.00 3.95
607 739 1.865865 TGTTCCACTTCTGCTCGTTC 58.134 50.000 0.00 0.00 0.00 3.95
608 740 2.213499 CTTGTTCCACTTCTGCTCGTT 58.787 47.619 0.00 0.00 0.00 3.85
609 741 1.871080 CTTGTTCCACTTCTGCTCGT 58.129 50.000 0.00 0.00 0.00 4.18
610 742 0.514691 GCTTGTTCCACTTCTGCTCG 59.485 55.000 0.00 0.00 0.00 5.03
611 743 0.514691 CGCTTGTTCCACTTCTGCTC 59.485 55.000 0.00 0.00 0.00 4.26
612 744 0.106708 TCGCTTGTTCCACTTCTGCT 59.893 50.000 0.00 0.00 0.00 4.24
613 745 0.944386 TTCGCTTGTTCCACTTCTGC 59.056 50.000 0.00 0.00 0.00 4.26
614 746 1.070577 CGTTCGCTTGTTCCACTTCTG 60.071 52.381 0.00 0.00 0.00 3.02
615 747 1.202486 TCGTTCGCTTGTTCCACTTCT 60.202 47.619 0.00 0.00 0.00 2.85
616 748 1.192534 CTCGTTCGCTTGTTCCACTTC 59.807 52.381 0.00 0.00 0.00 3.01
617 749 1.217882 CTCGTTCGCTTGTTCCACTT 58.782 50.000 0.00 0.00 0.00 3.16
618 750 0.600255 CCTCGTTCGCTTGTTCCACT 60.600 55.000 0.00 0.00 0.00 4.00
619 751 1.860078 CCTCGTTCGCTTGTTCCAC 59.140 57.895 0.00 0.00 0.00 4.02
620 752 1.959226 GCCTCGTTCGCTTGTTCCA 60.959 57.895 0.00 0.00 0.00 3.53
621 753 1.503818 TTGCCTCGTTCGCTTGTTCC 61.504 55.000 0.00 0.00 0.00 3.62
622 754 0.110644 CTTGCCTCGTTCGCTTGTTC 60.111 55.000 0.00 0.00 0.00 3.18
623 755 1.941812 CTTGCCTCGTTCGCTTGTT 59.058 52.632 0.00 0.00 0.00 2.83
624 756 2.607892 GCTTGCCTCGTTCGCTTGT 61.608 57.895 0.00 0.00 0.00 3.16
625 757 2.174349 GCTTGCCTCGTTCGCTTG 59.826 61.111 0.00 0.00 0.00 4.01
626 758 2.031163 AGCTTGCCTCGTTCGCTT 59.969 55.556 0.00 0.00 0.00 4.68
627 759 2.740055 CAGCTTGCCTCGTTCGCT 60.740 61.111 0.00 0.00 0.00 4.93
628 760 3.793144 CCAGCTTGCCTCGTTCGC 61.793 66.667 0.00 0.00 0.00 4.70
629 761 3.121030 CCCAGCTTGCCTCGTTCG 61.121 66.667 0.00 0.00 0.00 3.95
630 762 3.435186 GCCCAGCTTGCCTCGTTC 61.435 66.667 0.00 0.00 0.00 3.95
691 823 3.195698 CTAACGGGCGCCTTCAGC 61.196 66.667 28.56 8.15 38.52 4.26
692 824 2.511600 CCTAACGGGCGCCTTCAG 60.512 66.667 28.56 17.45 0.00 3.02
714 846 3.788145 TTGGGCCGTCGTATGGGG 61.788 66.667 0.00 0.00 0.00 4.96
715 847 2.512974 GTTGGGCCGTCGTATGGG 60.513 66.667 0.00 0.00 0.00 4.00
716 848 0.746563 AATGTTGGGCCGTCGTATGG 60.747 55.000 0.00 0.00 0.00 2.74
717 849 0.376852 CAATGTTGGGCCGTCGTATG 59.623 55.000 0.00 0.00 0.00 2.39
718 850 0.035820 ACAATGTTGGGCCGTCGTAT 60.036 50.000 0.00 0.00 0.00 3.06
719 851 0.951525 CACAATGTTGGGCCGTCGTA 60.952 55.000 0.00 0.00 0.00 3.43
720 852 2.112297 ACAATGTTGGGCCGTCGT 59.888 55.556 0.00 0.00 0.00 4.34
721 853 1.791103 AACACAATGTTGGGCCGTCG 61.791 55.000 0.00 0.00 39.45 5.12
722 854 1.240256 TAACACAATGTTGGGCCGTC 58.760 50.000 0.00 0.00 41.30 4.79
723 855 1.693627 TTAACACAATGTTGGGCCGT 58.306 45.000 0.00 0.00 41.30 5.68
724 856 3.442273 AGTATTAACACAATGTTGGGCCG 59.558 43.478 0.00 0.00 41.30 6.13
725 857 5.400066 AAGTATTAACACAATGTTGGGCC 57.600 39.130 0.00 0.00 41.30 5.80
726 858 6.687604 AGAAAGTATTAACACAATGTTGGGC 58.312 36.000 4.46 0.00 41.30 5.36
727 859 9.541143 AAAAGAAAGTATTAACACAATGTTGGG 57.459 29.630 4.46 0.00 41.30 4.12
752 884 8.788806 CCCTGTATTAACACAATGTTGTTCTAA 58.211 33.333 4.46 0.00 41.30 2.10
753 885 7.094549 GCCCTGTATTAACACAATGTTGTTCTA 60.095 37.037 4.46 0.00 41.30 2.10
754 886 6.294508 GCCCTGTATTAACACAATGTTGTTCT 60.295 38.462 4.46 0.00 41.30 3.01
755 887 5.861787 GCCCTGTATTAACACAATGTTGTTC 59.138 40.000 4.46 0.00 41.30 3.18
756 888 5.279256 GGCCCTGTATTAACACAATGTTGTT 60.279 40.000 4.46 5.14 41.30 2.83
757 889 4.219725 GGCCCTGTATTAACACAATGTTGT 59.780 41.667 4.46 0.00 41.30 3.32
758 890 4.462483 AGGCCCTGTATTAACACAATGTTG 59.538 41.667 0.00 0.00 41.30 3.33
759 891 4.672899 AGGCCCTGTATTAACACAATGTT 58.327 39.130 0.00 0.00 43.88 2.71
760 892 4.270008 GAGGCCCTGTATTAACACAATGT 58.730 43.478 0.00 0.00 0.00 2.71
761 893 3.632145 GGAGGCCCTGTATTAACACAATG 59.368 47.826 0.00 0.00 0.00 2.82
762 894 3.684413 CGGAGGCCCTGTATTAACACAAT 60.684 47.826 0.00 0.00 0.00 2.71
763 895 2.355310 CGGAGGCCCTGTATTAACACAA 60.355 50.000 0.00 0.00 0.00 3.33
764 896 1.208535 CGGAGGCCCTGTATTAACACA 59.791 52.381 0.00 0.00 0.00 3.72
765 897 1.949465 CGGAGGCCCTGTATTAACAC 58.051 55.000 0.00 0.00 0.00 3.32
766 898 0.179468 GCGGAGGCCCTGTATTAACA 59.821 55.000 0.00 0.00 0.00 2.41
767 899 0.468648 AGCGGAGGCCCTGTATTAAC 59.531 55.000 0.00 0.00 41.24 2.01
768 900 0.756903 GAGCGGAGGCCCTGTATTAA 59.243 55.000 0.00 0.00 41.24 1.40
769 901 0.105658 AGAGCGGAGGCCCTGTATTA 60.106 55.000 0.00 0.00 41.24 0.98
770 902 1.383248 AGAGCGGAGGCCCTGTATT 60.383 57.895 0.00 0.00 41.24 1.89
771 903 2.136878 CAGAGCGGAGGCCCTGTAT 61.137 63.158 0.00 0.00 39.89 2.29
772 904 2.759973 CAGAGCGGAGGCCCTGTA 60.760 66.667 0.00 0.00 39.89 2.74
776 908 4.459089 GACACAGAGCGGAGGCCC 62.459 72.222 0.00 0.00 41.24 5.80
777 909 3.363844 GAGACACAGAGCGGAGGCC 62.364 68.421 0.00 0.00 41.24 5.19
778 910 2.159819 TTGAGACACAGAGCGGAGGC 62.160 60.000 0.00 0.00 40.37 4.70
779 911 0.318441 TTTGAGACACAGAGCGGAGG 59.682 55.000 0.00 0.00 0.00 4.30
780 912 2.154854 TTTTGAGACACAGAGCGGAG 57.845 50.000 0.00 0.00 0.00 4.63
781 913 2.613026 TTTTTGAGACACAGAGCGGA 57.387 45.000 0.00 0.00 0.00 5.54
818 950 2.167861 ATTTTCGCCGCGAGAGAGC 61.168 57.895 16.14 0.00 37.14 4.09
819 951 1.633171 CATTTTCGCCGCGAGAGAG 59.367 57.895 16.14 4.28 37.14 3.20
820 952 1.809619 CCATTTTCGCCGCGAGAGA 60.810 57.895 16.14 6.43 37.14 3.10
821 953 2.703409 CCATTTTCGCCGCGAGAG 59.297 61.111 16.14 7.15 37.14 3.20
822 954 2.789845 TTCCCATTTTCGCCGCGAGA 62.790 55.000 16.14 8.97 37.14 4.04
823 955 1.917782 TTTCCCATTTTCGCCGCGAG 61.918 55.000 16.14 4.13 37.14 5.03
824 956 1.516365 TTTTCCCATTTTCGCCGCGA 61.516 50.000 12.39 12.39 0.00 5.87
825 957 0.457681 ATTTTCCCATTTTCGCCGCG 60.458 50.000 6.39 6.39 0.00 6.46
826 958 0.998669 CATTTTCCCATTTTCGCCGC 59.001 50.000 0.00 0.00 0.00 6.53
827 959 2.163412 TCTCATTTTCCCATTTTCGCCG 59.837 45.455 0.00 0.00 0.00 6.46
828 960 3.866883 TCTCATTTTCCCATTTTCGCC 57.133 42.857 0.00 0.00 0.00 5.54
829 961 3.553105 GCATCTCATTTTCCCATTTTCGC 59.447 43.478 0.00 0.00 0.00 4.70
830 962 4.114794 GGCATCTCATTTTCCCATTTTCG 58.885 43.478 0.00 0.00 0.00 3.46
831 963 4.445453 GGGCATCTCATTTTCCCATTTTC 58.555 43.478 0.00 0.00 36.96 2.29
832 964 3.118665 CGGGCATCTCATTTTCCCATTTT 60.119 43.478 0.00 0.00 36.79 1.82
833 965 2.431782 CGGGCATCTCATTTTCCCATTT 59.568 45.455 0.00 0.00 36.79 2.32
834 966 2.034124 CGGGCATCTCATTTTCCCATT 58.966 47.619 0.00 0.00 36.79 3.16
835 967 1.215173 TCGGGCATCTCATTTTCCCAT 59.785 47.619 0.00 0.00 36.79 4.00
836 968 0.623194 TCGGGCATCTCATTTTCCCA 59.377 50.000 0.00 0.00 36.79 4.37
837 969 1.312815 CTCGGGCATCTCATTTTCCC 58.687 55.000 0.00 0.00 0.00 3.97
838 970 2.044123 ACTCGGGCATCTCATTTTCC 57.956 50.000 0.00 0.00 0.00 3.13
856 988 0.110373 CGCGAGCTACAAAACCCAAC 60.110 55.000 0.00 0.00 0.00 3.77
1366 1508 4.148825 GGAGATGGTGAGCGCCGT 62.149 66.667 2.29 0.00 0.00 5.68
1557 1699 2.278206 CGAGCCACCATCTCGTCG 60.278 66.667 4.44 0.00 45.86 5.12
1794 1936 1.217244 GGTGTAGATGTCCGCCGTT 59.783 57.895 0.00 0.00 0.00 4.44
1849 1991 3.461773 CATGGCGTCCTCCGTCCT 61.462 66.667 0.00 0.00 41.60 3.85
2784 3157 2.151202 GAGGATTTTTGCGTGTCCTGA 58.849 47.619 0.00 0.00 41.03 3.86
2785 3158 1.200020 GGAGGATTTTTGCGTGTCCTG 59.800 52.381 0.00 0.00 41.03 3.86
2786 3159 1.534729 GGAGGATTTTTGCGTGTCCT 58.465 50.000 0.00 0.00 43.54 3.85
2787 3160 0.526211 GGGAGGATTTTTGCGTGTCC 59.474 55.000 0.00 0.00 0.00 4.02
2788 3161 0.168128 CGGGAGGATTTTTGCGTGTC 59.832 55.000 0.00 0.00 0.00 3.67
2791 3181 1.602323 TGCGGGAGGATTTTTGCGT 60.602 52.632 0.00 0.00 0.00 5.24
2817 3207 4.033709 TGAACTTATCCCCCTCTCTTCAG 58.966 47.826 0.00 0.00 0.00 3.02
2824 3214 3.840124 ATTCGTGAACTTATCCCCCTC 57.160 47.619 0.00 0.00 0.00 4.30
2844 3234 4.321452 GGATGGTTGCGTCTTATATCCGTA 60.321 45.833 0.00 0.00 0.00 4.02
2853 3243 2.198827 TGATTGGATGGTTGCGTCTT 57.801 45.000 0.00 0.00 0.00 3.01
2870 3260 8.744568 TGTTGTGAAAATATATGTGGCTATGA 57.255 30.769 0.00 0.00 0.00 2.15
3002 3443 0.749649 CTTCAGAGTCCGCCTAGCAT 59.250 55.000 0.00 0.00 0.00 3.79
3044 3494 1.043673 AGGACCAGACCCAGCGATAC 61.044 60.000 0.00 0.00 0.00 2.24
3045 3495 0.755698 GAGGACCAGACCCAGCGATA 60.756 60.000 0.00 0.00 0.00 2.92
3133 3599 2.260434 CCGGGACTTCGAAAGCGA 59.740 61.111 0.00 0.00 46.33 4.93
3137 3618 0.034337 CAGTTCCCGGGACTTCGAAA 59.966 55.000 26.87 2.87 0.00 3.46
3139 3620 0.828762 TTCAGTTCCCGGGACTTCGA 60.829 55.000 26.87 14.96 0.00 3.71
3187 3670 1.139058 AGCATCTTCGGCCGATTAGTT 59.861 47.619 31.56 16.47 0.00 2.24
3224 3707 0.546747 TCCTCCCCTTCCGTCAATGT 60.547 55.000 0.00 0.00 0.00 2.71
3264 3749 0.172578 CGGTAGGTCGTCATTGCTCA 59.827 55.000 0.00 0.00 0.00 4.26
3273 3758 0.607489 AGTAGTGCACGGTAGGTCGT 60.607 55.000 12.01 0.00 44.91 4.34
3315 3800 1.958715 CACAACCGTCATGTCCGCA 60.959 57.895 0.00 0.00 0.00 5.69
3368 3879 0.310854 GAGTTGTTTGGCAAGACCGG 59.689 55.000 0.00 0.00 43.94 5.28
3480 3992 2.124236 CGAGTCCTACCCGCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
3486 3998 1.139095 CGTTGCTCGAGTCCTACCC 59.861 63.158 15.13 0.00 42.86 3.69
3554 4066 1.267574 TTCAGGCGGAGGAGCAGATT 61.268 55.000 0.00 0.00 39.27 2.40
3556 4068 2.283894 TTCAGGCGGAGGAGCAGA 60.284 61.111 0.00 0.00 39.27 4.26
3572 4084 0.178831 ACCCCCTCCAGGAACATCTT 60.179 55.000 0.00 0.00 38.24 2.40
3578 4090 2.160171 CCACAACCCCCTCCAGGAA 61.160 63.158 0.00 0.00 38.24 3.36
3588 4100 1.324383 CCCAACTACAACCACAACCC 58.676 55.000 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.