Multiple sequence alignment - TraesCS3D01G115400

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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 TraesCS3D01G115400 chr3D 100.000 2447 0 0 1 2447 68841967 68844413 0.000000e+00 4519
1 TraesCS3D01G115400 chr3D 94.051 790 33 4 1 780 579165461 579166246 0.000000e+00 1186
2 TraesCS3D01G115400 chr3D 93.671 790 35 5 1 780 252331887 252331103 0.000000e+00 1168
3 TraesCS3D01G115400 chr3D 92.061 781 55 4 1 780 567667168 567667942 0.000000e+00 1092
4 TraesCS3D01G115400 chr3D 85.868 927 59 32 779 1642 68430342 68431259 0.000000e+00 920
5 TraesCS3D01G115400 chr3D 87.453 805 51 27 878 1642 68389074 68389868 0.000000e+00 881
6 TraesCS3D01G115400 chr3D 87.421 787 41 21 782 1520 68336010 68335234 0.000000e+00 852
7 TraesCS3D01G115400 chr3D 88.066 729 39 17 836 1521 68833105 68833828 0.000000e+00 821
8 TraesCS3D01G115400 chr3D 95.455 66 3 0 812 877 68388985 68389050 3.330000e-19 106
9 TraesCS3D01G115400 chr3A 84.637 1764 124 57 779 2447 80412893 80414604 0.000000e+00 1620
10 TraesCS3D01G115400 chr4A 93.598 781 45 2 1 780 572219870 572220646 0.000000e+00 1160
11 TraesCS3D01G115400 chr2D 93.214 781 48 2 1 780 562465962 562466738 0.000000e+00 1144
12 TraesCS3D01G115400 chr3B 86.890 1045 71 28 779 1766 112465857 112464822 0.000000e+00 1110
13 TraesCS3D01G115400 chr3B 85.948 918 66 33 779 1642 112948599 112947691 0.000000e+00 922
14 TraesCS3D01G115400 chr3B 88.183 787 45 24 779 1521 112497355 112496573 0.000000e+00 894
15 TraesCS3D01G115400 chr3B 85.054 930 73 30 779 1642 112836248 112835319 0.000000e+00 887
16 TraesCS3D01G115400 chr3B 89.143 700 29 7 782 1438 113483296 113483991 0.000000e+00 828
17 TraesCS3D01G115400 chr3B 84.152 896 69 25 817 1642 113299437 113298545 0.000000e+00 800
18 TraesCS3D01G115400 chr3B 89.700 466 40 4 1984 2447 112464533 112464074 2.710000e-164 588
19 TraesCS3D01G115400 chr3B 79.945 728 84 26 782 1461 113304368 113303655 1.700000e-131 479
20 TraesCS3D01G115400 chr5B 92.031 778 56 3 4 780 648758665 648757893 0.000000e+00 1088
21 TraesCS3D01G115400 chr5B 91.409 745 54 6 1 743 530259956 530260692 0.000000e+00 1013
22 TraesCS3D01G115400 chr5B 83.835 798 97 16 4 785 635461531 635462312 0.000000e+00 730
23 TraesCS3D01G115400 chr4B 91.013 790 57 6 4 783 134418861 134418076 0.000000e+00 1053
24 TraesCS3D01G115400 chr4D 90.967 786 53 7 4 787 65096919 65096150 0.000000e+00 1042
25 TraesCS3D01G115400 chr4D 85.876 793 54 29 779 1515 134550598 134549808 0.000000e+00 791
26 TraesCS3D01G115400 chr1B 87.347 735 64 14 8 736 535941296 535940585 0.000000e+00 815
27 TraesCS3D01G115400 chr7B 85.422 782 67 25 782 1521 603657035 603657811 0.000000e+00 769


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 TraesCS3D01G115400 chr3D 68841967 68844413 2446 False 4519.0 4519 100.000 1 2447 1 chr3D.!!$F3 2446
1 TraesCS3D01G115400 chr3D 579165461 579166246 785 False 1186.0 1186 94.051 1 780 1 chr3D.!!$F5 779
2 TraesCS3D01G115400 chr3D 252331103 252331887 784 True 1168.0 1168 93.671 1 780 1 chr3D.!!$R2 779
3 TraesCS3D01G115400 chr3D 567667168 567667942 774 False 1092.0 1092 92.061 1 780 1 chr3D.!!$F4 779
4 TraesCS3D01G115400 chr3D 68430342 68431259 917 False 920.0 920 85.868 779 1642 1 chr3D.!!$F1 863
5 TraesCS3D01G115400 chr3D 68335234 68336010 776 True 852.0 852 87.421 782 1520 1 chr3D.!!$R1 738
6 TraesCS3D01G115400 chr3D 68833105 68833828 723 False 821.0 821 88.066 836 1521 1 chr3D.!!$F2 685
7 TraesCS3D01G115400 chr3D 68388985 68389868 883 False 493.5 881 91.454 812 1642 2 chr3D.!!$F6 830
8 TraesCS3D01G115400 chr3A 80412893 80414604 1711 False 1620.0 1620 84.637 779 2447 1 chr3A.!!$F1 1668
9 TraesCS3D01G115400 chr4A 572219870 572220646 776 False 1160.0 1160 93.598 1 780 1 chr4A.!!$F1 779
10 TraesCS3D01G115400 chr2D 562465962 562466738 776 False 1144.0 1144 93.214 1 780 1 chr2D.!!$F1 779
11 TraesCS3D01G115400 chr3B 112947691 112948599 908 True 922.0 922 85.948 779 1642 1 chr3B.!!$R3 863
12 TraesCS3D01G115400 chr3B 112496573 112497355 782 True 894.0 894 88.183 779 1521 1 chr3B.!!$R1 742
13 TraesCS3D01G115400 chr3B 112835319 112836248 929 True 887.0 887 85.054 779 1642 1 chr3B.!!$R2 863
14 TraesCS3D01G115400 chr3B 112464074 112465857 1783 True 849.0 1110 88.295 779 2447 2 chr3B.!!$R6 1668
15 TraesCS3D01G115400 chr3B 113483296 113483991 695 False 828.0 828 89.143 782 1438 1 chr3B.!!$F1 656
16 TraesCS3D01G115400 chr3B 113298545 113299437 892 True 800.0 800 84.152 817 1642 1 chr3B.!!$R4 825
17 TraesCS3D01G115400 chr3B 113303655 113304368 713 True 479.0 479 79.945 782 1461 1 chr3B.!!$R5 679
18 TraesCS3D01G115400 chr5B 648757893 648758665 772 True 1088.0 1088 92.031 4 780 1 chr5B.!!$R1 776
19 TraesCS3D01G115400 chr5B 530259956 530260692 736 False 1013.0 1013 91.409 1 743 1 chr5B.!!$F1 742
20 TraesCS3D01G115400 chr5B 635461531 635462312 781 False 730.0 730 83.835 4 785 1 chr5B.!!$F2 781
21 TraesCS3D01G115400 chr4B 134418076 134418861 785 True 1053.0 1053 91.013 4 783 1 chr4B.!!$R1 779
22 TraesCS3D01G115400 chr4D 65096150 65096919 769 True 1042.0 1042 90.967 4 787 1 chr4D.!!$R1 783
23 TraesCS3D01G115400 chr4D 134549808 134550598 790 True 791.0 791 85.876 779 1515 1 chr4D.!!$R2 736
24 TraesCS3D01G115400 chr1B 535940585 535941296 711 True 815.0 815 87.347 8 736 1 chr1B.!!$R1 728
25 TraesCS3D01G115400 chr7B 603657035 603657811 776 False 769.0 769 85.422 782 1521 1 chr7B.!!$F1 739

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
677 696 0.036164 ACTAGGATGCACGCAACCAA 59.964 50.0 19.07 0.0 40.76 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2408 0.882042 GCTGTGCGCTGCCATACTAT 60.882 55.0 17.42 0.0 34.09 2.12 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
70 71 3.143728 GTGGTAGGTTAACACCAAGGTG 58.856 50.000 16.97 17.35 46.11 4.00
111 112 0.876399 GCCGTATGATCATGCATGCA 59.124 50.000 25.04 25.04 31.39 3.96
112 113 1.471287 GCCGTATGATCATGCATGCAT 59.529 47.619 27.46 27.46 37.08 3.96
200 209 0.949397 TGCTGCTTCAACTCTTGCTG 59.051 50.000 0.00 0.00 0.00 4.41
245 254 0.107643 TGCCGTGTTCATTGGTGAGA 59.892 50.000 0.00 0.00 35.39 3.27
494 504 0.390603 CGCCCAGTTCGTCACCATTA 60.391 55.000 0.00 0.00 0.00 1.90
522 532 1.294138 GGCGTTGGTGTGCTAGGTA 59.706 57.895 0.00 0.00 0.00 3.08
544 563 2.185387 GGGTAAGCTCACCAACTAGGA 58.815 52.381 8.72 0.00 40.65 2.94
624 643 2.263540 GCCAATGCAGCCAACCAG 59.736 61.111 0.00 0.00 37.47 4.00
666 685 3.692257 CCTAATGCAGGGACTAGGATG 57.308 52.381 0.00 0.00 41.26 3.51
667 686 2.289945 CCTAATGCAGGGACTAGGATGC 60.290 54.545 0.00 0.00 41.26 3.91
668 687 4.478531 TGCAGGGACTAGGATGCA 57.521 55.556 8.71 8.71 45.82 3.96
669 688 1.907739 TGCAGGGACTAGGATGCAC 59.092 57.895 8.71 0.00 43.34 4.57
670 689 1.227380 GCAGGGACTAGGATGCACG 60.227 63.158 0.00 0.00 36.02 5.34
671 690 1.227380 CAGGGACTAGGATGCACGC 60.227 63.158 0.00 0.00 36.02 5.34
672 691 1.685765 AGGGACTAGGATGCACGCA 60.686 57.895 0.00 0.00 36.02 5.24
673 692 1.220749 GGGACTAGGATGCACGCAA 59.779 57.895 0.00 0.00 0.00 4.85
674 693 1.090052 GGGACTAGGATGCACGCAAC 61.090 60.000 0.00 0.00 0.00 4.17
675 694 1.090052 GGACTAGGATGCACGCAACC 61.090 60.000 10.13 10.13 38.91 3.77
676 695 0.391130 GACTAGGATGCACGCAACCA 60.391 55.000 19.07 5.86 40.76 3.67
677 696 0.036164 ACTAGGATGCACGCAACCAA 59.964 50.000 19.07 0.00 40.76 3.67
678 697 1.340017 ACTAGGATGCACGCAACCAAT 60.340 47.619 19.07 3.57 40.76 3.16
679 698 1.331756 CTAGGATGCACGCAACCAATC 59.668 52.381 19.07 1.37 40.76 2.67
680 699 0.608856 AGGATGCACGCAACCAATCA 60.609 50.000 19.07 0.00 40.76 2.57
681 700 0.243365 GGATGCACGCAACCAATCAA 59.757 50.000 12.95 0.00 38.55 2.57
682 701 1.336702 GGATGCACGCAACCAATCAAA 60.337 47.619 12.95 0.00 38.55 2.69
683 702 2.609350 GATGCACGCAACCAATCAAAT 58.391 42.857 0.00 0.00 0.00 2.32
684 703 2.522836 TGCACGCAACCAATCAAATT 57.477 40.000 0.00 0.00 0.00 1.82
685 704 2.133553 TGCACGCAACCAATCAAATTG 58.866 42.857 0.00 0.00 39.94 2.32
686 705 2.134346 GCACGCAACCAATCAAATTGT 58.866 42.857 0.00 0.00 38.59 2.71
687 706 3.243535 TGCACGCAACCAATCAAATTGTA 60.244 39.130 0.00 0.00 38.59 2.41
688 707 3.925913 GCACGCAACCAATCAAATTGTAT 59.074 39.130 0.00 0.00 38.59 2.29
689 708 5.098893 GCACGCAACCAATCAAATTGTATA 58.901 37.500 0.00 0.00 38.59 1.47
690 709 5.748152 GCACGCAACCAATCAAATTGTATAT 59.252 36.000 0.00 0.00 38.59 0.86
691 710 6.291743 GCACGCAACCAATCAAATTGTATATG 60.292 38.462 0.00 0.00 38.59 1.78
692 711 6.198778 CACGCAACCAATCAAATTGTATATGG 59.801 38.462 0.00 0.86 38.59 2.74
693 712 5.175491 CGCAACCAATCAAATTGTATATGGC 59.825 40.000 8.25 0.00 38.59 4.40
694 713 5.175491 GCAACCAATCAAATTGTATATGGCG 59.825 40.000 8.25 0.00 38.59 5.69
695 714 6.272318 CAACCAATCAAATTGTATATGGCGT 58.728 36.000 8.25 0.00 38.59 5.68
696 715 7.421599 CAACCAATCAAATTGTATATGGCGTA 58.578 34.615 8.25 0.00 38.59 4.42
697 716 7.759489 ACCAATCAAATTGTATATGGCGTAT 57.241 32.000 4.38 4.38 38.59 3.06
698 717 8.177119 ACCAATCAAATTGTATATGGCGTATT 57.823 30.769 4.25 0.00 38.59 1.89
699 718 9.290988 ACCAATCAAATTGTATATGGCGTATTA 57.709 29.630 4.25 0.00 38.59 0.98
700 719 9.773328 CCAATCAAATTGTATATGGCGTATTAG 57.227 33.333 4.25 0.00 38.59 1.73
701 720 9.773328 CAATCAAATTGTATATGGCGTATTAGG 57.227 33.333 4.25 0.00 35.57 2.69
702 721 9.733556 AATCAAATTGTATATGGCGTATTAGGA 57.266 29.630 4.25 0.00 0.00 2.94
703 722 8.542497 TCAAATTGTATATGGCGTATTAGGAC 57.458 34.615 4.25 0.00 0.00 3.85
704 723 7.604927 TCAAATTGTATATGGCGTATTAGGACC 59.395 37.037 4.25 0.00 0.00 4.46
705 724 6.869206 ATTGTATATGGCGTATTAGGACCT 57.131 37.500 4.25 0.00 0.00 3.85
706 725 5.654603 TGTATATGGCGTATTAGGACCTG 57.345 43.478 3.53 0.00 0.00 4.00
707 726 5.081728 TGTATATGGCGTATTAGGACCTGT 58.918 41.667 3.53 0.00 0.00 4.00
708 727 5.541101 TGTATATGGCGTATTAGGACCTGTT 59.459 40.000 3.53 0.00 0.00 3.16
709 728 3.926058 ATGGCGTATTAGGACCTGTTT 57.074 42.857 3.53 0.00 0.00 2.83
710 729 3.706600 TGGCGTATTAGGACCTGTTTT 57.293 42.857 3.53 0.00 0.00 2.43
711 730 4.023726 TGGCGTATTAGGACCTGTTTTT 57.976 40.909 3.53 0.00 0.00 1.94
733 752 8.704849 TTTTTCTTAACCAGATTGGATTGAGA 57.295 30.769 1.40 2.37 40.96 3.27
734 753 8.704849 TTTTCTTAACCAGATTGGATTGAGAA 57.295 30.769 1.40 7.54 40.96 2.87
735 754 7.928307 TTCTTAACCAGATTGGATTGAGAAG 57.072 36.000 1.40 0.00 40.96 2.85
736 755 6.418101 TCTTAACCAGATTGGATTGAGAAGG 58.582 40.000 1.40 0.00 40.96 3.46
737 756 3.659183 ACCAGATTGGATTGAGAAGGG 57.341 47.619 1.40 0.00 40.96 3.95
738 757 2.305009 CCAGATTGGATTGAGAAGGGC 58.695 52.381 0.00 0.00 40.96 5.19
739 758 2.357465 CCAGATTGGATTGAGAAGGGCA 60.357 50.000 0.00 0.00 40.96 5.36
740 759 3.563223 CAGATTGGATTGAGAAGGGCAT 58.437 45.455 0.00 0.00 0.00 4.40
741 760 3.318275 CAGATTGGATTGAGAAGGGCATG 59.682 47.826 0.00 0.00 0.00 4.06
742 761 1.477553 TTGGATTGAGAAGGGCATGC 58.522 50.000 9.90 9.90 0.00 4.06
743 762 0.332293 TGGATTGAGAAGGGCATGCA 59.668 50.000 21.36 0.00 0.00 3.96
744 763 1.272592 TGGATTGAGAAGGGCATGCAA 60.273 47.619 21.36 3.14 0.00 4.08
745 764 1.135721 GGATTGAGAAGGGCATGCAAC 59.864 52.381 21.36 11.90 0.00 4.17
746 765 1.820519 GATTGAGAAGGGCATGCAACA 59.179 47.619 21.36 6.80 0.00 3.33
747 766 0.961019 TTGAGAAGGGCATGCAACAC 59.039 50.000 21.36 7.99 0.00 3.32
748 767 1.236616 TGAGAAGGGCATGCAACACG 61.237 55.000 21.36 0.00 0.00 4.49
749 768 0.955428 GAGAAGGGCATGCAACACGA 60.955 55.000 21.36 0.00 0.00 4.35
750 769 1.210155 GAAGGGCATGCAACACGAC 59.790 57.895 21.36 0.00 0.00 4.34
751 770 1.228245 AAGGGCATGCAACACGACT 60.228 52.632 21.36 2.48 0.00 4.18
752 771 1.518056 AAGGGCATGCAACACGACTG 61.518 55.000 21.36 0.00 0.00 3.51
753 772 2.126734 GGCATGCAACACGACTGC 60.127 61.111 21.36 0.00 40.35 4.40
754 773 2.620112 GGCATGCAACACGACTGCT 61.620 57.895 21.36 0.00 40.59 4.24
755 774 1.298157 GGCATGCAACACGACTGCTA 61.298 55.000 21.36 0.00 40.59 3.49
756 775 0.729116 GCATGCAACACGACTGCTAT 59.271 50.000 14.21 0.75 40.59 2.97
757 776 1.131126 GCATGCAACACGACTGCTATT 59.869 47.619 14.21 0.00 40.59 1.73
758 777 2.789092 GCATGCAACACGACTGCTATTC 60.789 50.000 14.21 0.00 40.59 1.75
759 778 1.438651 TGCAACACGACTGCTATTCC 58.561 50.000 8.99 0.00 40.59 3.01
760 779 1.270571 TGCAACACGACTGCTATTCCA 60.271 47.619 8.99 0.00 40.59 3.53
761 780 1.804151 GCAACACGACTGCTATTCCAA 59.196 47.619 0.00 0.00 36.84 3.53
762 781 2.225491 GCAACACGACTGCTATTCCAAA 59.775 45.455 0.00 0.00 36.84 3.28
763 782 3.810373 CAACACGACTGCTATTCCAAAC 58.190 45.455 0.00 0.00 0.00 2.93
764 783 3.402628 ACACGACTGCTATTCCAAACT 57.597 42.857 0.00 0.00 0.00 2.66
765 784 3.067106 ACACGACTGCTATTCCAAACTG 58.933 45.455 0.00 0.00 0.00 3.16
766 785 2.416547 CACGACTGCTATTCCAAACTGG 59.583 50.000 0.00 0.00 39.43 4.00
767 786 2.301870 ACGACTGCTATTCCAAACTGGA 59.698 45.455 0.00 0.00 46.61 3.86
777 796 1.746220 TCCAAACTGGAACCAAACACG 59.254 47.619 0.00 0.00 45.00 4.49
778 797 1.555477 CAAACTGGAACCAAACACGC 58.445 50.000 0.00 0.00 0.00 5.34
779 798 0.458260 AAACTGGAACCAAACACGCC 59.542 50.000 0.00 0.00 0.00 5.68
780 799 0.395173 AACTGGAACCAAACACGCCT 60.395 50.000 0.00 0.00 0.00 5.52
975 1076 0.531974 GAACGAGAATGGCGGGCATA 60.532 55.000 17.99 0.00 0.00 3.14
1203 1322 2.359850 GGCGACATCCAGGTGCAA 60.360 61.111 0.00 0.00 0.00 4.08
1329 1448 0.322975 AGTTCGTGCTGCCAGAGAAT 59.677 50.000 0.00 0.00 0.00 2.40
1332 1451 1.744368 CGTGCTGCCAGAGAATGCT 60.744 57.895 0.00 0.00 0.00 3.79
1361 1480 4.451150 GATCTCCGCCGTGTGCCA 62.451 66.667 0.00 0.00 36.24 4.92
1480 1612 1.594760 CGCGTCGAATCGAATCAGAGA 60.595 52.381 7.01 0.00 37.72 3.10
1481 1613 1.776333 GCGTCGAATCGAATCAGAGAC 59.224 52.381 7.01 0.00 37.72 3.36
1482 1614 2.030523 CGTCGAATCGAATCAGAGACG 58.969 52.381 7.01 12.72 42.65 4.18
1483 1615 3.320733 GTCGAATCGAATCAGAGACGA 57.679 47.619 7.01 4.58 37.72 4.20
1484 1616 3.284914 GTCGAATCGAATCAGAGACGAG 58.715 50.000 7.01 0.00 37.72 4.18
1485 1617 3.001431 GTCGAATCGAATCAGAGACGAGA 59.999 47.826 7.01 0.00 37.72 4.04
1505 1648 3.158676 GAGTGAGTGGGTAGTGAGTTCT 58.841 50.000 0.00 0.00 0.00 3.01
1548 1738 2.432510 GGTTATCTGAGAGAGGGTGTGG 59.567 54.545 0.00 0.00 0.00 4.17
1598 1788 5.698832 TGTTTGATGCTTCGTTAATGGAAG 58.301 37.500 12.45 12.45 42.93 3.46
1646 1836 7.219535 CCTGAATAAAACATGCGAATCTTGAAG 59.780 37.037 0.00 0.00 0.00 3.02
1669 1865 4.746836 TTTGAAGCGCGTTTTTAAGTTG 57.253 36.364 10.23 0.00 0.00 3.16
1670 1866 3.677190 TGAAGCGCGTTTTTAAGTTGA 57.323 38.095 10.23 0.00 0.00 3.18
1677 1873 2.223852 GCGTTTTTAAGTTGAAGGCCCA 60.224 45.455 0.00 0.00 0.00 5.36
1679 1875 4.627058 CGTTTTTAAGTTGAAGGCCCATT 58.373 39.130 0.00 0.00 0.00 3.16
1680 1876 4.447389 CGTTTTTAAGTTGAAGGCCCATTG 59.553 41.667 0.00 0.00 0.00 2.82
1681 1877 4.615588 TTTTAAGTTGAAGGCCCATTGG 57.384 40.909 0.00 0.00 0.00 3.16
1684 1880 2.101640 AGTTGAAGGCCCATTGGTTT 57.898 45.000 0.00 0.00 0.00 3.27
1685 1881 1.693606 AGTTGAAGGCCCATTGGTTTG 59.306 47.619 0.00 0.00 0.00 2.93
1704 1901 6.128063 TGGTTTGGAAATTTTGAAAACTGCAG 60.128 34.615 13.48 13.48 32.60 4.41
1716 1913 6.126568 TGAAAACTGCAGTTGTACCTAAAC 57.873 37.500 31.73 13.37 38.44 2.01
1730 1927 2.224917 ACCTAAACGGGAAATTGGAGCA 60.225 45.455 0.00 0.00 36.97 4.26
1761 1958 7.918643 TGTCAAATTTTGGAGAAATTTTCAGC 58.081 30.769 11.53 3.22 37.64 4.26
1762 1959 7.551974 TGTCAAATTTTGGAGAAATTTTCAGCA 59.448 29.630 11.53 2.85 37.64 4.41
1763 1960 8.066000 GTCAAATTTTGGAGAAATTTTCAGCAG 58.934 33.333 11.53 0.00 37.64 4.24
1764 1961 6.549912 AATTTTGGAGAAATTTTCAGCAGC 57.450 33.333 11.53 0.00 0.00 5.25
1765 1962 4.942761 TTTGGAGAAATTTTCAGCAGCT 57.057 36.364 11.53 0.00 0.00 4.24
1788 1999 4.081752 TGTGTTTTGATGTCTGGCTTTTGT 60.082 37.500 0.00 0.00 0.00 2.83
1795 2006 3.228188 TGTCTGGCTTTTGTGAAGGAT 57.772 42.857 0.00 0.00 0.00 3.24
1826 2038 1.831580 AGTTTCCTCCTGCAATCTGC 58.168 50.000 0.00 0.00 45.29 4.26
1829 2042 1.210204 TTCCTCCTGCAATCTGCCCT 61.210 55.000 0.00 0.00 44.23 5.19
1831 2044 0.750911 CCTCCTGCAATCTGCCCTTC 60.751 60.000 0.00 0.00 44.23 3.46
1832 2045 0.034767 CTCCTGCAATCTGCCCTTCA 60.035 55.000 0.00 0.00 44.23 3.02
1837 2050 2.557056 CTGCAATCTGCCCTTCATATGG 59.443 50.000 2.13 0.00 44.23 2.74
1841 2054 4.505566 GCAATCTGCCCTTCATATGGTAGA 60.506 45.833 2.13 1.47 45.57 2.59
1848 2061 6.252995 TGCCCTTCATATGGTAGAAAAACTT 58.747 36.000 2.13 0.00 0.00 2.66
1871 2094 9.342308 ACTTCCAAATTCGATTACACATATGAT 57.658 29.630 10.38 0.00 0.00 2.45
1874 2097 9.996554 TCCAAATTCGATTACACATATGATACT 57.003 29.630 10.38 0.00 0.00 2.12
1882 2105 7.692705 CGATTACACATATGATACTGAGGTACG 59.307 40.741 10.38 0.34 0.00 3.67
1892 2115 7.649533 TGATACTGAGGTACGAGGAAATTTA 57.350 36.000 0.00 0.00 0.00 1.40
1893 2116 8.070034 TGATACTGAGGTACGAGGAAATTTAA 57.930 34.615 0.00 0.00 0.00 1.52
1895 2118 6.600882 ACTGAGGTACGAGGAAATTTAAGA 57.399 37.500 0.00 0.00 0.00 2.10
1896 2119 7.184067 ACTGAGGTACGAGGAAATTTAAGAT 57.816 36.000 0.00 0.00 0.00 2.40
1897 2120 8.302515 ACTGAGGTACGAGGAAATTTAAGATA 57.697 34.615 0.00 0.00 0.00 1.98
1898 2121 8.196103 ACTGAGGTACGAGGAAATTTAAGATAC 58.804 37.037 0.00 0.00 0.00 2.24
1899 2122 7.198390 TGAGGTACGAGGAAATTTAAGATACG 58.802 38.462 0.00 0.00 0.00 3.06
1901 2124 5.176406 GGTACGAGGAAATTTAAGATACGCC 59.824 44.000 0.00 0.00 0.00 5.68
1902 2125 4.124970 ACGAGGAAATTTAAGATACGCCC 58.875 43.478 0.00 0.00 0.00 6.13
1903 2126 4.141779 ACGAGGAAATTTAAGATACGCCCT 60.142 41.667 0.00 0.00 0.00 5.19
1904 2127 5.069516 ACGAGGAAATTTAAGATACGCCCTA 59.930 40.000 0.00 0.00 0.00 3.53
1905 2128 6.164176 CGAGGAAATTTAAGATACGCCCTAT 58.836 40.000 0.00 0.00 0.00 2.57
1906 2129 6.649557 CGAGGAAATTTAAGATACGCCCTATT 59.350 38.462 0.00 0.00 0.00 1.73
1907 2130 7.172703 CGAGGAAATTTAAGATACGCCCTATTT 59.827 37.037 0.00 0.00 0.00 1.40
1908 2131 8.392372 AGGAAATTTAAGATACGCCCTATTTC 57.608 34.615 0.00 0.00 32.67 2.17
1909 2132 7.447545 AGGAAATTTAAGATACGCCCTATTTCC 59.552 37.037 12.88 12.88 44.99 3.13
1925 2177 9.259832 GCCCTATTTCCCAGAAATTTGATATAT 57.740 33.333 7.79 0.00 0.00 0.86
1997 2285 9.737427 TTTATTTCGACACAGAGCAAAATAAAA 57.263 25.926 7.84 0.00 36.44 1.52
2008 2296 6.309737 CAGAGCAAAATAAAACTGCCTGATTC 59.690 38.462 0.00 0.00 36.93 2.52
2009 2297 6.015180 AGAGCAAAATAAAACTGCCTGATTCA 60.015 34.615 0.00 0.00 36.73 2.57
2026 2314 0.326595 TCACGCAGGGCCTTATTTCA 59.673 50.000 1.32 0.00 0.00 2.69
2034 2326 4.081476 GCAGGGCCTTATTTCAACAGAAAT 60.081 41.667 1.32 8.33 42.78 2.17
2038 2330 8.093927 CAGGGCCTTATTTCAACAGAAATAAAA 58.906 33.333 18.48 5.77 45.91 1.52
2039 2331 8.655901 AGGGCCTTATTTCAACAGAAATAAAAA 58.344 29.630 18.48 5.24 45.91 1.94
2069 2361 8.311109 ACACAACTAAACCTGATTTCAGTTTTT 58.689 29.630 8.16 8.40 39.01 1.94
2112 2408 1.053424 ACCCCGAGCTCTGTTACAAA 58.947 50.000 12.85 0.00 0.00 2.83
2113 2409 1.628846 ACCCCGAGCTCTGTTACAAAT 59.371 47.619 12.85 0.00 0.00 2.32
2124 2420 5.277538 GCTCTGTTACAAATAGTATGGCAGC 60.278 44.000 0.00 0.00 32.35 5.25
2158 2454 4.202151 ACCACAAGGCAGAAAAATCAGTTC 60.202 41.667 0.00 0.00 39.06 3.01
2159 2455 4.202141 CCACAAGGCAGAAAAATCAGTTCA 60.202 41.667 0.00 0.00 0.00 3.18
2160 2456 5.350633 CACAAGGCAGAAAAATCAGTTCAA 58.649 37.500 0.00 0.00 0.00 2.69
2161 2457 5.987347 CACAAGGCAGAAAAATCAGTTCAAT 59.013 36.000 0.00 0.00 0.00 2.57
2162 2458 6.145048 CACAAGGCAGAAAAATCAGTTCAATC 59.855 38.462 0.00 0.00 0.00 2.67
2163 2459 6.041296 ACAAGGCAGAAAAATCAGTTCAATCT 59.959 34.615 0.00 0.00 0.00 2.40
2164 2460 6.661304 AGGCAGAAAAATCAGTTCAATCTT 57.339 33.333 0.00 0.00 0.00 2.40
2165 2461 6.685657 AGGCAGAAAAATCAGTTCAATCTTC 58.314 36.000 0.00 0.00 0.00 2.87
2166 2462 6.266103 AGGCAGAAAAATCAGTTCAATCTTCA 59.734 34.615 0.00 0.00 0.00 3.02
2167 2463 6.925165 GGCAGAAAAATCAGTTCAATCTTCAA 59.075 34.615 0.00 0.00 0.00 2.69
2168 2464 7.115947 GGCAGAAAAATCAGTTCAATCTTCAAG 59.884 37.037 0.00 0.00 0.00 3.02
2169 2465 7.115947 GCAGAAAAATCAGTTCAATCTTCAAGG 59.884 37.037 0.00 0.00 0.00 3.61
2170 2466 8.139989 CAGAAAAATCAGTTCAATCTTCAAGGT 58.860 33.333 0.00 0.00 0.00 3.50
2171 2467 8.139989 AGAAAAATCAGTTCAATCTTCAAGGTG 58.860 33.333 0.00 0.00 0.00 4.00
2172 2468 7.587037 AAAATCAGTTCAATCTTCAAGGTGA 57.413 32.000 0.00 0.00 0.00 4.02
2173 2469 6.814506 AATCAGTTCAATCTTCAAGGTGAG 57.185 37.500 0.00 0.00 0.00 3.51
2227 2539 9.699410 ATAAGATGGTCCACTATCAAAATTTCA 57.301 29.630 0.00 0.00 36.45 2.69
2238 2550 9.467258 CACTATCAAAATTTCATGTTGTGTCTT 57.533 29.630 0.00 0.00 0.00 3.01
2240 2552 9.681692 CTATCAAAATTTCATGTTGTGTCTTCA 57.318 29.630 0.00 0.00 0.00 3.02
2252 2564 2.104622 TGTGTCTTCAAGATGTCAGGCA 59.895 45.455 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 2.481289 AGCAAGTTCTTCCTAGCACC 57.519 50.000 0.00 0.00 0.00 5.01
111 112 4.019860 TGGAGCAGAAGAGAAGTAAAGCAT 60.020 41.667 0.00 0.00 0.00 3.79
112 113 3.324846 TGGAGCAGAAGAGAAGTAAAGCA 59.675 43.478 0.00 0.00 0.00 3.91
113 114 3.931578 TGGAGCAGAAGAGAAGTAAAGC 58.068 45.455 0.00 0.00 0.00 3.51
114 115 5.936956 ACAATGGAGCAGAAGAGAAGTAAAG 59.063 40.000 0.00 0.00 0.00 1.85
245 254 5.400189 CCCATGAACTATAAACCCCTGGAAT 60.400 44.000 0.00 0.00 0.00 3.01
290 300 4.818534 AATTGCTGTTGCTATACGATGG 57.181 40.909 0.00 0.00 40.48 3.51
371 381 2.433318 GACACTGCTGCCTCCGTC 60.433 66.667 0.00 0.00 0.00 4.79
494 504 1.377987 ACCAACGCCACAACACAGT 60.378 52.632 0.00 0.00 0.00 3.55
522 532 2.505819 CCTAGTTGGTGAGCTTACCCAT 59.494 50.000 23.81 12.43 40.09 4.00
544 563 6.202188 GCGTATATGTTGTGCTTACCTTGTAT 59.798 38.462 0.00 0.00 0.00 2.29
664 683 2.737783 CAATTTGATTGGTTGCGTGCAT 59.262 40.909 0.00 0.00 36.63 3.96
665 684 2.133553 CAATTTGATTGGTTGCGTGCA 58.866 42.857 0.00 0.00 36.63 4.57
666 685 2.134346 ACAATTTGATTGGTTGCGTGC 58.866 42.857 2.79 0.00 44.42 5.34
667 686 6.198778 CCATATACAATTTGATTGGTTGCGTG 59.801 38.462 2.79 0.00 44.42 5.34
668 687 6.272318 CCATATACAATTTGATTGGTTGCGT 58.728 36.000 2.79 0.00 44.42 5.24
669 688 5.175491 GCCATATACAATTTGATTGGTTGCG 59.825 40.000 2.79 0.00 44.42 4.85
670 689 5.175491 CGCCATATACAATTTGATTGGTTGC 59.825 40.000 2.79 0.00 44.42 4.17
671 690 6.272318 ACGCCATATACAATTTGATTGGTTG 58.728 36.000 2.79 4.66 44.42 3.77
672 691 6.463995 ACGCCATATACAATTTGATTGGTT 57.536 33.333 2.79 0.00 44.42 3.67
673 692 7.759489 ATACGCCATATACAATTTGATTGGT 57.241 32.000 2.79 0.00 44.42 3.67
674 693 9.773328 CTAATACGCCATATACAATTTGATTGG 57.227 33.333 2.79 5.55 44.42 3.16
675 694 9.773328 CCTAATACGCCATATACAATTTGATTG 57.227 33.333 2.79 0.00 45.59 2.67
676 695 9.733556 TCCTAATACGCCATATACAATTTGATT 57.266 29.630 2.79 0.00 0.00 2.57
677 696 9.162764 GTCCTAATACGCCATATACAATTTGAT 57.837 33.333 2.79 0.00 0.00 2.57
678 697 7.604927 GGTCCTAATACGCCATATACAATTTGA 59.395 37.037 2.79 0.00 0.00 2.69
679 698 7.606456 AGGTCCTAATACGCCATATACAATTTG 59.394 37.037 0.00 0.00 0.00 2.32
680 699 7.606456 CAGGTCCTAATACGCCATATACAATTT 59.394 37.037 0.00 0.00 0.00 1.82
681 700 7.103641 CAGGTCCTAATACGCCATATACAATT 58.896 38.462 0.00 0.00 0.00 2.32
682 701 6.212791 ACAGGTCCTAATACGCCATATACAAT 59.787 38.462 0.00 0.00 0.00 2.71
683 702 5.541101 ACAGGTCCTAATACGCCATATACAA 59.459 40.000 0.00 0.00 0.00 2.41
684 703 5.081728 ACAGGTCCTAATACGCCATATACA 58.918 41.667 0.00 0.00 0.00 2.29
685 704 5.656213 ACAGGTCCTAATACGCCATATAC 57.344 43.478 0.00 0.00 0.00 1.47
686 705 6.675413 AAACAGGTCCTAATACGCCATATA 57.325 37.500 0.00 0.00 0.00 0.86
687 706 5.562298 AAACAGGTCCTAATACGCCATAT 57.438 39.130 0.00 0.00 0.00 1.78
688 707 5.362105 AAAACAGGTCCTAATACGCCATA 57.638 39.130 0.00 0.00 0.00 2.74
689 708 3.926058 AAACAGGTCCTAATACGCCAT 57.074 42.857 0.00 0.00 0.00 4.40
690 709 3.706600 AAAACAGGTCCTAATACGCCA 57.293 42.857 0.00 0.00 0.00 5.69
708 727 8.704849 TCTCAATCCAATCTGGTTAAGAAAAA 57.295 30.769 0.00 0.00 38.79 1.94
709 728 8.704849 TTCTCAATCCAATCTGGTTAAGAAAA 57.295 30.769 0.00 0.00 38.79 2.29
710 729 7.394359 CCTTCTCAATCCAATCTGGTTAAGAAA 59.606 37.037 0.00 0.00 38.79 2.52
711 730 6.886459 CCTTCTCAATCCAATCTGGTTAAGAA 59.114 38.462 0.00 0.00 38.79 2.52
712 731 6.418101 CCTTCTCAATCCAATCTGGTTAAGA 58.582 40.000 0.00 0.00 39.03 2.10
713 732 5.591877 CCCTTCTCAATCCAATCTGGTTAAG 59.408 44.000 0.00 0.00 39.03 1.85
714 733 5.509498 CCCTTCTCAATCCAATCTGGTTAA 58.491 41.667 0.00 0.00 39.03 2.01
715 734 4.628715 GCCCTTCTCAATCCAATCTGGTTA 60.629 45.833 0.00 0.00 39.03 2.85
716 735 3.879321 GCCCTTCTCAATCCAATCTGGTT 60.879 47.826 0.00 0.00 39.03 3.67
717 736 2.357569 GCCCTTCTCAATCCAATCTGGT 60.358 50.000 0.00 0.00 39.03 4.00
718 737 2.305009 GCCCTTCTCAATCCAATCTGG 58.695 52.381 0.00 0.00 39.43 3.86
719 738 3.008835 TGCCCTTCTCAATCCAATCTG 57.991 47.619 0.00 0.00 0.00 2.90
720 739 3.563223 CATGCCCTTCTCAATCCAATCT 58.437 45.455 0.00 0.00 0.00 2.40
721 740 2.035576 GCATGCCCTTCTCAATCCAATC 59.964 50.000 6.36 0.00 0.00 2.67
722 741 2.037144 GCATGCCCTTCTCAATCCAAT 58.963 47.619 6.36 0.00 0.00 3.16
723 742 1.272592 TGCATGCCCTTCTCAATCCAA 60.273 47.619 16.68 0.00 0.00 3.53
724 743 0.332293 TGCATGCCCTTCTCAATCCA 59.668 50.000 16.68 0.00 0.00 3.41
725 744 1.135721 GTTGCATGCCCTTCTCAATCC 59.864 52.381 16.68 0.00 0.00 3.01
726 745 1.820519 TGTTGCATGCCCTTCTCAATC 59.179 47.619 16.68 0.00 0.00 2.67
727 746 1.547372 GTGTTGCATGCCCTTCTCAAT 59.453 47.619 16.68 0.00 0.00 2.57
728 747 0.961019 GTGTTGCATGCCCTTCTCAA 59.039 50.000 16.68 0.00 0.00 3.02
729 748 1.236616 CGTGTTGCATGCCCTTCTCA 61.237 55.000 16.68 2.53 0.00 3.27
730 749 0.955428 TCGTGTTGCATGCCCTTCTC 60.955 55.000 16.68 3.26 0.00 2.87
731 750 1.073025 TCGTGTTGCATGCCCTTCT 59.927 52.632 16.68 0.00 0.00 2.85
732 751 1.210155 GTCGTGTTGCATGCCCTTC 59.790 57.895 16.68 3.46 0.00 3.46
733 752 1.228245 AGTCGTGTTGCATGCCCTT 60.228 52.632 16.68 0.00 0.00 3.95
734 753 1.968017 CAGTCGTGTTGCATGCCCT 60.968 57.895 16.68 0.00 0.00 5.19
735 754 2.562912 CAGTCGTGTTGCATGCCC 59.437 61.111 16.68 6.36 0.00 5.36
736 755 1.298157 TAGCAGTCGTGTTGCATGCC 61.298 55.000 16.68 0.28 43.92 4.40
737 756 0.729116 ATAGCAGTCGTGTTGCATGC 59.271 50.000 11.82 11.82 43.92 4.06
738 757 2.223112 GGAATAGCAGTCGTGTTGCATG 60.223 50.000 10.21 0.00 43.92 4.06
739 758 2.009774 GGAATAGCAGTCGTGTTGCAT 58.990 47.619 10.21 1.55 43.92 3.96
740 759 1.270571 TGGAATAGCAGTCGTGTTGCA 60.271 47.619 10.21 0.00 43.92 4.08
741 760 1.438651 TGGAATAGCAGTCGTGTTGC 58.561 50.000 0.00 1.32 41.83 4.17
742 761 3.498397 AGTTTGGAATAGCAGTCGTGTTG 59.502 43.478 0.00 0.00 0.00 3.33
743 762 3.498397 CAGTTTGGAATAGCAGTCGTGTT 59.502 43.478 0.00 0.00 0.00 3.32
744 763 3.067106 CAGTTTGGAATAGCAGTCGTGT 58.933 45.455 0.00 0.00 0.00 4.49
745 764 2.416547 CCAGTTTGGAATAGCAGTCGTG 59.583 50.000 0.00 0.00 40.96 4.35
746 765 2.301870 TCCAGTTTGGAATAGCAGTCGT 59.698 45.455 0.00 0.00 45.00 4.34
747 766 2.972625 TCCAGTTTGGAATAGCAGTCG 58.027 47.619 0.00 0.00 45.00 4.18
757 776 1.746220 CGTGTTTGGTTCCAGTTTGGA 59.254 47.619 0.00 0.00 46.61 3.53
758 777 1.801025 GCGTGTTTGGTTCCAGTTTGG 60.801 52.381 0.00 0.00 39.43 3.28
759 778 1.555477 GCGTGTTTGGTTCCAGTTTG 58.445 50.000 0.00 0.00 0.00 2.93
760 779 0.458260 GGCGTGTTTGGTTCCAGTTT 59.542 50.000 0.00 0.00 0.00 2.66
761 780 0.395173 AGGCGTGTTTGGTTCCAGTT 60.395 50.000 0.00 0.00 0.00 3.16
762 781 0.395173 AAGGCGTGTTTGGTTCCAGT 60.395 50.000 0.00 0.00 0.00 4.00
763 782 1.535462 CTAAGGCGTGTTTGGTTCCAG 59.465 52.381 0.00 0.00 0.00 3.86
764 783 1.141254 TCTAAGGCGTGTTTGGTTCCA 59.859 47.619 0.00 0.00 0.00 3.53
765 784 1.886886 TCTAAGGCGTGTTTGGTTCC 58.113 50.000 0.00 0.00 0.00 3.62
766 785 2.876550 AGTTCTAAGGCGTGTTTGGTTC 59.123 45.455 0.00 0.00 0.00 3.62
767 786 2.927028 AGTTCTAAGGCGTGTTTGGTT 58.073 42.857 0.00 0.00 0.00 3.67
768 787 2.632987 AGTTCTAAGGCGTGTTTGGT 57.367 45.000 0.00 0.00 0.00 3.67
769 788 3.564225 AGAAAGTTCTAAGGCGTGTTTGG 59.436 43.478 0.00 0.00 35.34 3.28
770 789 4.319549 GGAGAAAGTTCTAAGGCGTGTTTG 60.320 45.833 0.00 0.00 37.73 2.93
771 790 3.813724 GGAGAAAGTTCTAAGGCGTGTTT 59.186 43.478 0.00 0.00 37.73 2.83
772 791 3.181458 TGGAGAAAGTTCTAAGGCGTGTT 60.181 43.478 0.00 0.00 37.73 3.32
773 792 2.367567 TGGAGAAAGTTCTAAGGCGTGT 59.632 45.455 0.00 0.00 37.73 4.49
774 793 3.040147 TGGAGAAAGTTCTAAGGCGTG 57.960 47.619 0.00 0.00 37.73 5.34
775 794 3.676324 CGATGGAGAAAGTTCTAAGGCGT 60.676 47.826 0.00 0.00 37.73 5.68
776 795 2.860735 CGATGGAGAAAGTTCTAAGGCG 59.139 50.000 0.00 0.00 37.73 5.52
777 796 3.198872 CCGATGGAGAAAGTTCTAAGGC 58.801 50.000 0.00 0.00 37.73 4.35
778 797 4.184629 CACCGATGGAGAAAGTTCTAAGG 58.815 47.826 0.00 0.00 37.73 2.69
779 798 3.619038 GCACCGATGGAGAAAGTTCTAAG 59.381 47.826 0.00 0.00 37.73 2.18
780 799 3.596214 GCACCGATGGAGAAAGTTCTAA 58.404 45.455 0.00 0.00 37.73 2.10
958 1044 1.069765 CTATGCCCGCCATTCTCGT 59.930 57.895 0.00 0.00 35.34 4.18
975 1076 0.250338 GGTTCTCCAAGCCGAACACT 60.250 55.000 0.00 0.00 40.88 3.55
1203 1322 4.680537 ACCCGCTCGTCCTCCACT 62.681 66.667 0.00 0.00 0.00 4.00
1297 1416 1.059994 CGAACTTGCGCATCAGCTC 59.940 57.895 12.75 6.68 39.10 4.09
1329 1448 3.815856 GAGATCTTCTCCATGTCAGCA 57.184 47.619 0.00 0.00 37.55 4.41
1480 1612 1.073444 TCACTACCCACTCACTCTCGT 59.927 52.381 0.00 0.00 0.00 4.18
1481 1613 1.740585 CTCACTACCCACTCACTCTCG 59.259 57.143 0.00 0.00 0.00 4.04
1482 1614 2.797786 ACTCACTACCCACTCACTCTC 58.202 52.381 0.00 0.00 0.00 3.20
1483 1615 2.982339 ACTCACTACCCACTCACTCT 57.018 50.000 0.00 0.00 0.00 3.24
1484 1616 3.158676 AGAACTCACTACCCACTCACTC 58.841 50.000 0.00 0.00 0.00 3.51
1485 1617 3.158676 GAGAACTCACTACCCACTCACT 58.841 50.000 0.00 0.00 0.00 3.41
1505 1648 4.835056 CCATACTCCCATCACTCATACAGA 59.165 45.833 0.00 0.00 0.00 3.41
1548 1738 1.050767 GTACGCACGAACAGACAGTC 58.949 55.000 0.00 0.00 0.00 3.51
1646 1836 4.748503 ACTTAAAAACGCGCTTCAAAAC 57.251 36.364 5.73 0.00 0.00 2.43
1669 1865 1.347062 TTCCAAACCAATGGGCCTTC 58.653 50.000 4.53 0.00 41.05 3.46
1670 1866 1.813102 TTTCCAAACCAATGGGCCTT 58.187 45.000 4.53 0.00 41.05 4.35
1677 1873 7.094032 TGCAGTTTTCAAAATTTCCAAACCAAT 60.094 29.630 12.69 0.00 0.00 3.16
1679 1875 5.707298 TGCAGTTTTCAAAATTTCCAAACCA 59.293 32.000 12.69 5.89 0.00 3.67
1680 1876 6.128035 ACTGCAGTTTTCAAAATTTCCAAACC 60.128 34.615 15.25 0.91 0.00 3.27
1681 1877 6.841119 ACTGCAGTTTTCAAAATTTCCAAAC 58.159 32.000 15.25 9.98 0.00 2.93
1684 1880 5.936956 ACAACTGCAGTTTTCAAAATTTCCA 59.063 32.000 29.23 0.00 35.83 3.53
1685 1881 6.421377 ACAACTGCAGTTTTCAAAATTTCC 57.579 33.333 29.23 0.00 35.83 3.13
1704 1901 4.761227 TCCAATTTCCCGTTTAGGTACAAC 59.239 41.667 0.00 0.00 38.74 3.32
1716 1913 3.056607 ACAATTCTTGCTCCAATTTCCCG 60.057 43.478 0.00 0.00 0.00 5.14
1738 1935 7.254863 GCTGCTGAAAATTTCTCCAAAATTTGA 60.255 33.333 7.37 0.00 39.13 2.69
1746 1943 3.005050 CACAGCTGCTGAAAATTTCTCCA 59.995 43.478 34.28 3.50 35.18 3.86
1749 1946 4.660789 AACACAGCTGCTGAAAATTTCT 57.339 36.364 34.28 7.99 35.18 2.52
1758 1955 2.292569 AGACATCAAAACACAGCTGCTG 59.707 45.455 27.02 27.02 37.52 4.41
1760 1957 2.606308 CCAGACATCAAAACACAGCTGC 60.606 50.000 15.27 0.00 0.00 5.25
1761 1958 2.606308 GCCAGACATCAAAACACAGCTG 60.606 50.000 13.48 13.48 0.00 4.24
1762 1959 1.610522 GCCAGACATCAAAACACAGCT 59.389 47.619 0.00 0.00 0.00 4.24
1763 1960 1.610522 AGCCAGACATCAAAACACAGC 59.389 47.619 0.00 0.00 0.00 4.40
1764 1961 3.996150 AAGCCAGACATCAAAACACAG 57.004 42.857 0.00 0.00 0.00 3.66
1765 1962 4.081752 ACAAAAGCCAGACATCAAAACACA 60.082 37.500 0.00 0.00 0.00 3.72
1795 2006 7.345691 TGCAGGAGGAAACTTAATATGATTCA 58.654 34.615 0.00 0.00 44.43 2.57
1826 2038 6.889722 TGGAAGTTTTTCTACCATATGAAGGG 59.110 38.462 3.65 0.00 33.68 3.95
1831 2044 9.289303 CGAATTTGGAAGTTTTTCTACCATATG 57.711 33.333 0.00 0.00 33.68 1.78
1832 2045 9.238368 TCGAATTTGGAAGTTTTTCTACCATAT 57.762 29.630 0.00 0.00 33.68 1.78
1837 2050 9.887406 TGTAATCGAATTTGGAAGTTTTTCTAC 57.113 29.630 0.00 0.00 33.68 2.59
1848 2061 9.996554 AGTATCATATGTGTAATCGAATTTGGA 57.003 29.630 1.90 0.00 0.00 3.53
1871 2094 7.707624 TCTTAAATTTCCTCGTACCTCAGTA 57.292 36.000 0.00 0.00 0.00 2.74
1873 2096 7.378995 CGTATCTTAAATTTCCTCGTACCTCAG 59.621 40.741 0.00 0.00 0.00 3.35
1874 2097 7.198390 CGTATCTTAAATTTCCTCGTACCTCA 58.802 38.462 0.00 0.00 0.00 3.86
1877 2100 5.176406 GGCGTATCTTAAATTTCCTCGTACC 59.824 44.000 0.00 0.00 0.00 3.34
1882 2105 7.981102 AATAGGGCGTATCTTAAATTTCCTC 57.019 36.000 0.00 0.00 0.00 3.71
1892 2115 3.314693 TCTGGGAAATAGGGCGTATCTT 58.685 45.455 0.00 0.00 0.00 2.40
1893 2116 2.972348 TCTGGGAAATAGGGCGTATCT 58.028 47.619 0.00 0.00 0.00 1.98
1895 2118 4.724279 ATTTCTGGGAAATAGGGCGTAT 57.276 40.909 4.00 0.00 0.00 3.06
1896 2119 4.513406 AATTTCTGGGAAATAGGGCGTA 57.487 40.909 6.02 0.00 0.00 4.42
1897 2120 3.382083 AATTTCTGGGAAATAGGGCGT 57.618 42.857 6.02 0.00 0.00 5.68
1898 2121 3.699038 TCAAATTTCTGGGAAATAGGGCG 59.301 43.478 6.02 0.00 0.00 6.13
1899 2122 5.876651 ATCAAATTTCTGGGAAATAGGGC 57.123 39.130 6.02 0.00 0.00 5.19
1904 2127 9.370930 TCAGCATATATCAAATTTCTGGGAAAT 57.629 29.630 0.31 0.31 0.00 2.17
1905 2128 8.765488 TCAGCATATATCAAATTTCTGGGAAA 57.235 30.769 0.00 0.00 0.00 3.13
1906 2129 8.945195 ATCAGCATATATCAAATTTCTGGGAA 57.055 30.769 0.00 0.00 0.00 3.97
1907 2130 8.945195 AATCAGCATATATCAAATTTCTGGGA 57.055 30.769 0.00 0.00 0.00 4.37
1908 2131 9.419297 CAAATCAGCATATATCAAATTTCTGGG 57.581 33.333 0.00 0.00 0.00 4.45
1909 2132 9.419297 CCAAATCAGCATATATCAAATTTCTGG 57.581 33.333 0.00 0.00 0.00 3.86
1925 2177 2.089201 CAGCACATCTCCAAATCAGCA 58.911 47.619 0.00 0.00 0.00 4.41
2008 2296 1.135402 GTTGAAATAAGGCCCTGCGTG 60.135 52.381 0.00 0.00 0.00 5.34
2009 2297 1.173913 GTTGAAATAAGGCCCTGCGT 58.826 50.000 0.00 0.00 0.00 5.24
2038 2330 6.153680 TGAAATCAGGTTTAGTTGTGTGGTTT 59.846 34.615 0.00 0.00 0.00 3.27
2039 2331 5.654650 TGAAATCAGGTTTAGTTGTGTGGTT 59.345 36.000 0.00 0.00 0.00 3.67
2040 2332 5.197451 TGAAATCAGGTTTAGTTGTGTGGT 58.803 37.500 0.00 0.00 0.00 4.16
2041 2333 5.762045 CTGAAATCAGGTTTAGTTGTGTGG 58.238 41.667 2.38 0.00 40.20 4.17
2042 2334 6.795399 AACTGAAATCAGGTTTAGTTGTGTG 58.205 36.000 14.50 0.00 42.10 3.82
2112 2408 0.882042 GCTGTGCGCTGCCATACTAT 60.882 55.000 17.42 0.00 34.09 2.12
2113 2409 1.521457 GCTGTGCGCTGCCATACTA 60.521 57.895 17.42 0.00 34.09 1.82
2124 2420 1.647545 CCTTGTGGTATGGCTGTGCG 61.648 60.000 0.00 0.00 0.00 5.34
2158 2454 7.225145 TGAAATTTTTGCTCACCTTGAAGATTG 59.775 33.333 0.00 0.00 0.00 2.67
2159 2455 7.225341 GTGAAATTTTTGCTCACCTTGAAGATT 59.775 33.333 0.00 0.00 34.63 2.40
2160 2456 6.703165 GTGAAATTTTTGCTCACCTTGAAGAT 59.297 34.615 0.00 0.00 34.63 2.40
2161 2457 6.042143 GTGAAATTTTTGCTCACCTTGAAGA 58.958 36.000 0.00 0.00 34.63 2.87
2162 2458 6.044682 AGTGAAATTTTTGCTCACCTTGAAG 58.955 36.000 4.04 0.00 40.29 3.02
2163 2459 5.976458 AGTGAAATTTTTGCTCACCTTGAA 58.024 33.333 4.04 0.00 40.29 2.69
2164 2460 5.596836 AGTGAAATTTTTGCTCACCTTGA 57.403 34.783 4.04 0.00 40.29 3.02
2165 2461 6.418819 CAGTAGTGAAATTTTTGCTCACCTTG 59.581 38.462 4.04 0.00 40.29 3.61
2166 2462 6.461509 CCAGTAGTGAAATTTTTGCTCACCTT 60.462 38.462 0.00 0.00 40.29 3.50
2167 2463 5.010012 CCAGTAGTGAAATTTTTGCTCACCT 59.990 40.000 0.00 0.00 40.29 4.00
2168 2464 5.222631 CCAGTAGTGAAATTTTTGCTCACC 58.777 41.667 0.00 0.00 40.29 4.02
2169 2465 5.221244 ACCCAGTAGTGAAATTTTTGCTCAC 60.221 40.000 0.00 0.00 39.83 3.51
2170 2466 4.892934 ACCCAGTAGTGAAATTTTTGCTCA 59.107 37.500 0.00 0.00 0.00 4.26
2171 2467 5.453567 ACCCAGTAGTGAAATTTTTGCTC 57.546 39.130 0.00 0.00 0.00 4.26
2172 2468 5.830991 TGTACCCAGTAGTGAAATTTTTGCT 59.169 36.000 0.00 0.00 0.00 3.91
2173 2469 5.918576 GTGTACCCAGTAGTGAAATTTTTGC 59.081 40.000 0.00 0.00 0.00 3.68
2227 2539 4.758674 CCTGACATCTTGAAGACACAACAT 59.241 41.667 0.00 0.00 0.00 2.71
2238 2550 1.618343 TCGTTCTGCCTGACATCTTGA 59.382 47.619 0.00 0.00 0.00 3.02
2240 2552 2.417719 GTTCGTTCTGCCTGACATCTT 58.582 47.619 0.00 0.00 0.00 2.40
2252 2564 2.481449 GGAGATGTATGGCGTTCGTTCT 60.481 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.