Multiple sequence alignment - TraesCS7A01G044000

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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 TraesCS7A01G044000 chr7A 100.000 2531 0 0 1 2531 20393805 20391275 0.000000e+00 4674.0
1 TraesCS7A01G044000 chr7A 93.029 1750 119 3 784 2531 705595631 705597379 0.000000e+00 2553.0
2 TraesCS7A01G044000 chr7A 92.971 1750 120 3 784 2531 639765248 639766996 0.000000e+00 2547.0
3 TraesCS7A01G044000 chr7A 94.864 623 30 1 1 623 575740972 575740352 0.000000e+00 972.0
4 TraesCS7A01G044000 chr6A 93.143 1750 117 3 784 2531 328977219 328978967 0.000000e+00 2564.0
5 TraesCS7A01G044000 chr5B 93.086 1750 117 4 784 2531 580378873 580380620 0.000000e+00 2558.0
6 TraesCS7A01G044000 chr3B 92.971 1750 120 3 784 2531 54309595 54311343 0.000000e+00 2547.0
7 TraesCS7A01G044000 chr3B 92.955 1746 120 3 788 2531 769392737 769390993 0.000000e+00 2540.0
8 TraesCS7A01G044000 chr3A 92.914 1750 120 4 784 2531 508181245 508179498 0.000000e+00 2542.0
9 TraesCS7A01G044000 chr2B 92.922 1752 117 6 784 2531 384098892 384100640 0.000000e+00 2542.0
10 TraesCS7A01G044000 chr7B 92.955 1746 120 3 788 2531 622494956 622496700 0.000000e+00 2540.0
11 TraesCS7A01G044000 chr6B 95.432 613 27 1 1 613 356803315 356803926 0.000000e+00 976.0
12 TraesCS7A01G044000 chr1A 94.652 617 32 1 1 617 253908441 253909056 0.000000e+00 955.0
13 TraesCS7A01G044000 chr3D 92.857 84 6 0 619 702 126293117 126293034 3.420000e-24 122.0
14 TraesCS7A01G044000 chr4D 82.645 121 13 6 626 743 440384598 440384483 1.600000e-17 100.0
15 TraesCS7A01G044000 chr2D 92.537 67 5 0 626 692 56317812 56317878 2.070000e-16 97.1
16 TraesCS7A01G044000 chr4A 96.078 51 2 0 626 676 674910349 674910299 1.610000e-12 84.2


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 TraesCS7A01G044000 chr7A 20391275 20393805 2530 True 4674 4674 100.000 1 2531 1 chr7A.!!$R1 2530
1 TraesCS7A01G044000 chr7A 705595631 705597379 1748 False 2553 2553 93.029 784 2531 1 chr7A.!!$F2 1747
2 TraesCS7A01G044000 chr7A 639765248 639766996 1748 False 2547 2547 92.971 784 2531 1 chr7A.!!$F1 1747
3 TraesCS7A01G044000 chr7A 575740352 575740972 620 True 972 972 94.864 1 623 1 chr7A.!!$R2 622
4 TraesCS7A01G044000 chr6A 328977219 328978967 1748 False 2564 2564 93.143 784 2531 1 chr6A.!!$F1 1747
5 TraesCS7A01G044000 chr5B 580378873 580380620 1747 False 2558 2558 93.086 784 2531 1 chr5B.!!$F1 1747
6 TraesCS7A01G044000 chr3B 54309595 54311343 1748 False 2547 2547 92.971 784 2531 1 chr3B.!!$F1 1747
7 TraesCS7A01G044000 chr3B 769390993 769392737 1744 True 2540 2540 92.955 788 2531 1 chr3B.!!$R1 1743
8 TraesCS7A01G044000 chr3A 508179498 508181245 1747 True 2542 2542 92.914 784 2531 1 chr3A.!!$R1 1747
9 TraesCS7A01G044000 chr2B 384098892 384100640 1748 False 2542 2542 92.922 784 2531 1 chr2B.!!$F1 1747
10 TraesCS7A01G044000 chr7B 622494956 622496700 1744 False 2540 2540 92.955 788 2531 1 chr7B.!!$F1 1743
11 TraesCS7A01G044000 chr6B 356803315 356803926 611 False 976 976 95.432 1 613 1 chr6B.!!$F1 612
12 TraesCS7A01G044000 chr1A 253908441 253909056 615 False 955 955 94.652 1 617 1 chr1A.!!$F1 616

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
552 554 0.10412 TGTGGCGATTTCGATCGGAT 59.896 50.0 16.41 9.89 43.66 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1868 0.110056 GATATGCATTGAAGCGCCGG 60.11 55.0 3.54 0.0 37.31 6.13 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
57 58 1.046472 AGGTCCACGAGTCCACAACA 61.046 55.000 0.00 0.00 0.00 3.33
60 61 1.116308 TCCACGAGTCCACAACAAGA 58.884 50.000 0.00 0.00 0.00 3.02
97 98 2.091640 TTGGAATCTGCAGGGGCCAA 62.092 55.000 22.57 22.57 40.13 4.52
100 101 2.786512 GAATCTGCAGGGGCCAACCA 62.787 60.000 15.13 0.00 42.91 3.67
151 152 3.635510 GGATCGAAGGTCCCAGCT 58.364 61.111 0.00 0.00 0.00 4.24
212 213 1.818131 CGTAGGATGATGACGGGAGGA 60.818 57.143 0.00 0.00 33.01 3.71
449 450 0.465460 GGAAGGTGTCAGGTGTGCAA 60.465 55.000 0.00 0.00 0.00 4.08
453 454 0.381801 GGTGTCAGGTGTGCAAAGTG 59.618 55.000 0.00 0.00 0.00 3.16
454 455 0.381801 GTGTCAGGTGTGCAAAGTGG 59.618 55.000 0.00 0.00 0.00 4.00
509 511 1.815817 AATTGGTCTTTGGGCGGCAC 61.816 55.000 12.47 0.00 0.00 5.01
535 537 2.129555 GACCACCCAGCACCTGATGT 62.130 60.000 0.00 0.00 32.44 3.06
552 554 0.104120 TGTGGCGATTTCGATCGGAT 59.896 50.000 16.41 9.89 43.66 4.18
555 557 1.000843 TGGCGATTTCGATCGGATGAT 59.999 47.619 16.41 0.00 43.66 2.45
564 566 1.000171 CGATCGGATGATGCAGAAGGA 60.000 52.381 7.38 0.00 34.09 3.36
613 615 8.143835 AGCACAACTGCACTTTTTAGAATTTAT 58.856 29.630 0.00 0.00 46.97 1.40
614 616 8.216453 GCACAACTGCACTTTTTAGAATTTATG 58.784 33.333 0.00 0.00 43.62 1.90
615 617 9.248291 CACAACTGCACTTTTTAGAATTTATGT 57.752 29.630 0.00 0.00 0.00 2.29
616 618 9.816354 ACAACTGCACTTTTTAGAATTTATGTT 57.184 25.926 0.00 0.00 0.00 2.71
618 620 9.816354 AACTGCACTTTTTAGAATTTATGTTGT 57.184 25.926 0.00 0.00 0.00 3.32
619 621 9.816354 ACTGCACTTTTTAGAATTTATGTTGTT 57.184 25.926 0.00 0.00 0.00 2.83
638 640 8.445275 TGTTGTTTTTAAGCTAATCACAGAGA 57.555 30.769 0.00 0.00 0.00 3.10
639 641 9.066892 TGTTGTTTTTAAGCTAATCACAGAGAT 57.933 29.630 0.00 0.00 39.09 2.75
645 647 7.969536 TTAAGCTAATCACAGAGATAATGCC 57.030 36.000 0.00 0.00 35.39 4.40
646 648 4.904241 AGCTAATCACAGAGATAATGCCC 58.096 43.478 0.00 0.00 35.39 5.36
647 649 4.349048 AGCTAATCACAGAGATAATGCCCA 59.651 41.667 0.00 0.00 35.39 5.36
648 650 4.453819 GCTAATCACAGAGATAATGCCCAC 59.546 45.833 0.00 0.00 35.39 4.61
649 651 3.498774 ATCACAGAGATAATGCCCACC 57.501 47.619 0.00 0.00 34.43 4.61
650 652 1.138859 TCACAGAGATAATGCCCACCG 59.861 52.381 0.00 0.00 0.00 4.94
651 653 0.179045 ACAGAGATAATGCCCACCGC 60.179 55.000 0.00 0.00 38.31 5.68
652 654 0.886490 CAGAGATAATGCCCACCGCC 60.886 60.000 0.00 0.00 36.24 6.13
653 655 1.148273 GAGATAATGCCCACCGCCA 59.852 57.895 0.00 0.00 36.24 5.69
654 656 0.886490 GAGATAATGCCCACCGCCAG 60.886 60.000 0.00 0.00 36.24 4.85
655 657 1.898574 GATAATGCCCACCGCCAGG 60.899 63.158 0.00 0.00 45.13 4.45
656 658 2.337879 GATAATGCCCACCGCCAGGA 62.338 60.000 0.00 0.00 41.02 3.86
657 659 2.343475 ATAATGCCCACCGCCAGGAG 62.343 60.000 0.00 0.00 41.02 3.69
660 662 4.115199 GCCCACCGCCAGGAGATT 62.115 66.667 0.00 0.00 41.02 2.40
661 663 2.677228 CCCACCGCCAGGAGATTT 59.323 61.111 0.00 0.00 41.02 2.17
662 664 1.912220 CCCACCGCCAGGAGATTTA 59.088 57.895 0.00 0.00 41.02 1.40
663 665 0.179045 CCCACCGCCAGGAGATTTAG 60.179 60.000 0.00 0.00 41.02 1.85
664 666 0.815615 CCACCGCCAGGAGATTTAGC 60.816 60.000 0.00 0.00 41.02 3.09
665 667 1.144057 ACCGCCAGGAGATTTAGCG 59.856 57.895 0.00 0.00 46.04 4.26
666 668 4.033894 CGCCAGGAGATTTAGCGG 57.966 61.111 0.00 0.00 42.93 5.52
667 669 1.595382 CGCCAGGAGATTTAGCGGG 60.595 63.158 0.00 0.00 42.93 6.13
668 670 1.227973 GCCAGGAGATTTAGCGGGG 60.228 63.158 0.00 0.00 0.00 5.73
669 671 1.451936 CCAGGAGATTTAGCGGGGG 59.548 63.158 0.00 0.00 0.00 5.40
670 672 1.227973 CAGGAGATTTAGCGGGGGC 60.228 63.158 0.00 0.00 0.00 5.80
671 673 2.113351 GGAGATTTAGCGGGGGCC 59.887 66.667 0.00 0.00 0.00 5.80
672 674 2.113351 GAGATTTAGCGGGGGCCC 59.887 66.667 15.76 15.76 0.00 5.80
673 675 2.694616 AGATTTAGCGGGGGCCCA 60.695 61.111 26.86 1.73 35.37 5.36
674 676 2.069165 GAGATTTAGCGGGGGCCCAT 62.069 60.000 26.86 12.39 35.37 4.00
675 677 1.903404 GATTTAGCGGGGGCCCATG 60.903 63.158 26.86 17.65 35.37 3.66
676 678 2.640581 GATTTAGCGGGGGCCCATGT 62.641 60.000 26.86 10.15 35.37 3.21
677 679 2.236959 ATTTAGCGGGGGCCCATGTT 62.237 55.000 26.86 16.62 35.37 2.71
678 680 3.653664 TTAGCGGGGGCCCATGTTG 62.654 63.158 26.86 8.94 35.37 3.33
682 684 2.688299 GGGGGCCCATGTTGCAAT 60.688 61.111 26.86 0.00 35.81 3.56
683 685 2.734720 GGGGGCCCATGTTGCAATC 61.735 63.158 26.86 0.59 35.81 2.67
684 686 2.734720 GGGGCCCATGTTGCAATCC 61.735 63.158 26.86 0.00 0.00 3.01
685 687 2.495866 GGCCCATGTTGCAATCCG 59.504 61.111 0.59 0.00 0.00 4.18
686 688 2.350458 GGCCCATGTTGCAATCCGT 61.350 57.895 0.59 0.00 0.00 4.69
687 689 1.139520 GCCCATGTTGCAATCCGTC 59.860 57.895 0.59 0.00 0.00 4.79
688 690 1.315257 GCCCATGTTGCAATCCGTCT 61.315 55.000 0.59 0.00 0.00 4.18
689 691 1.176527 CCCATGTTGCAATCCGTCTT 58.823 50.000 0.59 0.00 0.00 3.01
690 692 1.135315 CCCATGTTGCAATCCGTCTTG 60.135 52.381 0.59 0.00 0.00 3.02
691 693 1.135315 CCATGTTGCAATCCGTCTTGG 60.135 52.381 0.59 3.49 40.09 3.61
692 694 1.541147 CATGTTGCAATCCGTCTTGGT 59.459 47.619 0.59 0.00 39.52 3.67
693 695 2.552599 TGTTGCAATCCGTCTTGGTA 57.447 45.000 0.59 0.00 39.52 3.25
694 696 2.147958 TGTTGCAATCCGTCTTGGTAC 58.852 47.619 0.59 0.00 39.52 3.34
695 697 1.127951 GTTGCAATCCGTCTTGGTACG 59.872 52.381 0.59 0.00 42.49 3.67
696 698 0.604073 TGCAATCCGTCTTGGTACGA 59.396 50.000 0.00 0.00 45.68 3.43
697 699 1.206132 TGCAATCCGTCTTGGTACGAT 59.794 47.619 0.00 0.00 45.68 3.73
698 700 2.427812 TGCAATCCGTCTTGGTACGATA 59.572 45.455 0.00 0.00 45.68 2.92
699 701 3.050619 GCAATCCGTCTTGGTACGATAG 58.949 50.000 0.00 0.00 45.68 2.08
700 702 3.243301 GCAATCCGTCTTGGTACGATAGA 60.243 47.826 0.00 0.00 45.68 1.98
701 703 4.735578 GCAATCCGTCTTGGTACGATAGAA 60.736 45.833 0.00 0.00 45.68 2.10
702 704 4.564940 ATCCGTCTTGGTACGATAGAAC 57.435 45.455 0.00 0.00 45.68 3.01
703 705 2.684881 TCCGTCTTGGTACGATAGAACC 59.315 50.000 0.00 0.00 45.68 3.62
704 706 2.424601 CCGTCTTGGTACGATAGAACCA 59.575 50.000 0.00 0.00 45.68 3.67
705 707 3.067742 CCGTCTTGGTACGATAGAACCAT 59.932 47.826 0.00 0.00 44.98 3.55
706 708 4.441079 CCGTCTTGGTACGATAGAACCATT 60.441 45.833 0.00 0.00 44.98 3.16
707 709 5.107133 CGTCTTGGTACGATAGAACCATTT 58.893 41.667 0.00 0.00 44.98 2.32
708 710 5.579511 CGTCTTGGTACGATAGAACCATTTT 59.420 40.000 0.00 0.00 44.98 1.82
709 711 6.091713 CGTCTTGGTACGATAGAACCATTTTT 59.908 38.462 0.00 0.00 44.98 1.94
710 712 7.461918 GTCTTGGTACGATAGAACCATTTTTC 58.538 38.462 0.00 0.00 44.98 2.29
711 713 7.333672 GTCTTGGTACGATAGAACCATTTTTCT 59.666 37.037 0.00 0.00 44.98 2.52
712 714 7.881232 TCTTGGTACGATAGAACCATTTTTCTT 59.119 33.333 0.00 0.00 44.98 2.52
713 715 7.989416 TGGTACGATAGAACCATTTTTCTTT 57.011 32.000 0.00 0.00 40.84 2.52
714 716 8.398878 TGGTACGATAGAACCATTTTTCTTTT 57.601 30.769 0.00 0.00 40.84 2.27
715 717 8.508875 TGGTACGATAGAACCATTTTTCTTTTC 58.491 33.333 0.00 0.00 40.84 2.29
716 718 8.727910 GGTACGATAGAACCATTTTTCTTTTCT 58.272 33.333 0.00 0.00 37.09 2.52
719 721 8.297426 ACGATAGAACCATTTTTCTTTTCTTCC 58.703 33.333 0.00 0.00 37.09 3.46
720 722 8.296713 CGATAGAACCATTTTTCTTTTCTTCCA 58.703 33.333 0.00 0.00 37.09 3.53
721 723 9.631452 GATAGAACCATTTTTCTTTTCTTCCAG 57.369 33.333 0.00 0.00 37.09 3.86
722 724 7.423844 AGAACCATTTTTCTTTTCTTCCAGT 57.576 32.000 0.00 0.00 31.39 4.00
723 725 8.533569 AGAACCATTTTTCTTTTCTTCCAGTA 57.466 30.769 0.00 0.00 31.39 2.74
724 726 9.147732 AGAACCATTTTTCTTTTCTTCCAGTAT 57.852 29.630 0.00 0.00 31.39 2.12
725 727 9.764363 GAACCATTTTTCTTTTCTTCCAGTATT 57.236 29.630 0.00 0.00 0.00 1.89
726 728 9.764363 AACCATTTTTCTTTTCTTCCAGTATTC 57.236 29.630 0.00 0.00 0.00 1.75
727 729 8.923270 ACCATTTTTCTTTTCTTCCAGTATTCA 58.077 29.630 0.00 0.00 0.00 2.57
728 730 9.196552 CCATTTTTCTTTTCTTCCAGTATTCAC 57.803 33.333 0.00 0.00 0.00 3.18
729 731 8.905702 CATTTTTCTTTTCTTCCAGTATTCACG 58.094 33.333 0.00 0.00 0.00 4.35
730 732 5.607119 TTCTTTTCTTCCAGTATTCACGC 57.393 39.130 0.00 0.00 0.00 5.34
731 733 4.637276 TCTTTTCTTCCAGTATTCACGCA 58.363 39.130 0.00 0.00 0.00 5.24
732 734 5.060506 TCTTTTCTTCCAGTATTCACGCAA 58.939 37.500 0.00 0.00 0.00 4.85
734 736 2.972625 TCTTCCAGTATTCACGCAAGG 58.027 47.619 0.00 0.00 46.39 3.61
735 737 2.565391 TCTTCCAGTATTCACGCAAGGA 59.435 45.455 0.00 0.00 46.39 3.36
736 738 3.197766 TCTTCCAGTATTCACGCAAGGAT 59.802 43.478 0.00 0.00 46.39 3.24
737 739 4.404394 TCTTCCAGTATTCACGCAAGGATA 59.596 41.667 0.00 0.00 46.39 2.59
738 740 4.322080 TCCAGTATTCACGCAAGGATAG 57.678 45.455 0.00 0.00 46.39 2.08
739 741 3.069586 TCCAGTATTCACGCAAGGATAGG 59.930 47.826 0.00 0.00 46.39 2.57
740 742 3.393800 CAGTATTCACGCAAGGATAGGG 58.606 50.000 0.00 0.00 46.39 3.53
741 743 2.368875 AGTATTCACGCAAGGATAGGGG 59.631 50.000 0.00 0.00 46.39 4.79
742 744 0.474184 ATTCACGCAAGGATAGGGGG 59.526 55.000 0.00 0.00 46.39 5.40
762 764 5.811796 GGGGGTTAACCTGTGTTAATTTT 57.188 39.130 23.69 0.00 45.84 1.82
763 765 5.786311 GGGGGTTAACCTGTGTTAATTTTC 58.214 41.667 23.69 2.59 45.84 2.29
764 766 5.304871 GGGGGTTAACCTGTGTTAATTTTCA 59.695 40.000 23.69 0.00 45.84 2.69
765 767 6.452242 GGGGTTAACCTGTGTTAATTTTCAG 58.548 40.000 23.69 0.00 45.84 3.02
766 768 6.265876 GGGGTTAACCTGTGTTAATTTTCAGA 59.734 38.462 23.69 0.00 45.84 3.27
767 769 7.039293 GGGGTTAACCTGTGTTAATTTTCAGAT 60.039 37.037 23.69 0.00 45.84 2.90
768 770 9.016438 GGGTTAACCTGTGTTAATTTTCAGATA 57.984 33.333 23.69 0.00 45.84 1.98
769 771 9.836076 GGTTAACCTGTGTTAATTTTCAGATAC 57.164 33.333 17.83 0.00 45.84 2.24
773 775 8.691661 ACCTGTGTTAATTTTCAGATACAAGT 57.308 30.769 0.00 0.00 0.00 3.16
774 776 9.787435 ACCTGTGTTAATTTTCAGATACAAGTA 57.213 29.630 0.00 0.00 0.00 2.24
780 782 9.968743 GTTAATTTTCAGATACAAGTAAGACCG 57.031 33.333 0.00 0.00 0.00 4.79
781 783 6.663944 ATTTTCAGATACAAGTAAGACCGC 57.336 37.500 0.00 0.00 0.00 5.68
782 784 4.794278 TTCAGATACAAGTAAGACCGCA 57.206 40.909 0.00 0.00 0.00 5.69
786 788 3.380637 AGATACAAGTAAGACCGCACGAT 59.619 43.478 0.00 0.00 0.00 3.73
855 857 1.087771 CGCGGCCGGATCTTACTTTT 61.088 55.000 29.38 0.00 0.00 2.27
871 873 3.083386 TTTTTCCCCCGGCGATCT 58.917 55.556 9.30 0.00 0.00 2.75
937 941 1.378119 CCTTACCCGGCCTTGGTTC 60.378 63.158 17.90 0.00 37.31 3.62
939 943 0.392595 CTTACCCGGCCTTGGTTCTC 60.393 60.000 17.90 0.00 37.31 2.87
956 960 2.742372 CGTGGTTTCTCCGGCAGG 60.742 66.667 0.00 0.00 39.52 4.85
965 969 0.110678 TCTCCGGCAGGTCGATCTAT 59.889 55.000 0.00 0.00 39.05 1.98
978 982 3.930848 GTCGATCTATGGTTTTCGTTGGT 59.069 43.478 0.00 0.00 33.52 3.67
979 983 5.104374 GTCGATCTATGGTTTTCGTTGGTA 58.896 41.667 0.00 0.00 33.52 3.25
980 984 5.577945 GTCGATCTATGGTTTTCGTTGGTAA 59.422 40.000 0.00 0.00 33.52 2.85
995 999 3.069079 TGGTAACGACTAGACTGCTCT 57.931 47.619 0.00 0.00 42.51 4.09
996 1000 4.212143 TGGTAACGACTAGACTGCTCTA 57.788 45.455 0.00 0.00 42.51 2.43
998 1002 4.815308 TGGTAACGACTAGACTGCTCTATC 59.185 45.833 0.00 0.00 42.51 2.08
1072 1076 1.020437 GCTGCTAGCCAGGTTGAATC 58.980 55.000 13.29 0.00 42.03 2.52
1107 1111 4.220693 AGATGATGATTTCGTGTGGGAA 57.779 40.909 0.00 0.00 0.00 3.97
1113 1117 2.370519 TGATTTCGTGTGGGAAGAGGAA 59.629 45.455 0.00 0.00 0.00 3.36
1118 1122 1.611673 CGTGTGGGAAGAGGAATTGCT 60.612 52.381 0.00 0.00 0.00 3.91
1119 1123 2.354704 CGTGTGGGAAGAGGAATTGCTA 60.355 50.000 0.00 0.00 0.00 3.49
1135 1139 4.533124 TAGATCTGGGGGCGCCGA 62.533 66.667 22.54 12.79 0.00 5.54
1272 1276 2.717639 AGGACAACTTGTTCACAGCT 57.282 45.000 2.94 0.00 0.00 4.24
1288 1292 4.067896 CACAGCTCAGTTTGGTTGTCTAT 58.932 43.478 0.00 0.00 0.00 1.98
1399 1403 5.180868 CCTGATAGCATCAAGTTGGATAAGC 59.819 44.000 2.34 0.90 39.11 3.09
1423 1427 0.975887 AGTTTGGGCGCAAATCCATT 59.024 45.000 28.69 11.84 32.48 3.16
1434 1438 4.677779 GCGCAAATCCATTGTTTACCTGAT 60.678 41.667 0.30 0.00 41.32 2.90
1449 1453 9.058174 TGTTTACCTGATAACTTTTTGATCGAA 57.942 29.630 0.00 0.00 0.00 3.71
1481 1485 1.370900 GGATGGCATCGCGAATTGC 60.371 57.895 23.11 23.11 41.47 3.56
1494 1498 1.743772 CGAATTGCGGAGGTGGAAGAT 60.744 52.381 0.00 0.00 36.03 2.40
1565 1569 5.584649 GTGAGGGTGAAAATCGATATCAACA 59.415 40.000 23.09 14.42 32.38 3.33
1607 1611 2.929043 ACTGGAAAGAAGGGGGATGAAT 59.071 45.455 0.00 0.00 0.00 2.57
1612 1616 3.941704 AAGAAGGGGGATGAATGAGTC 57.058 47.619 0.00 0.00 0.00 3.36
1618 1622 3.906846 AGGGGGATGAATGAGTCAGATAC 59.093 47.826 0.00 0.00 40.43 2.24
1717 1721 5.769162 TGATGGTGTTCATGATGAGACAAAA 59.231 36.000 10.49 4.91 35.97 2.44
1741 1745 3.042682 TGAGTGGGGTGACTTTGTTCTA 58.957 45.455 0.00 0.00 0.00 2.10
1759 1763 5.874810 TGTTCTAGCTGACAATATTCGCTTT 59.125 36.000 0.00 0.00 32.49 3.51
1768 1772 4.013728 ACAATATTCGCTTTAGGCAACCA 58.986 39.130 0.00 0.00 41.91 3.67
1837 1841 0.637195 CAGGAGGAAGAGGTAGGGGA 59.363 60.000 0.00 0.00 0.00 4.81
1846 1850 0.683504 GAGGTAGGGGACGAGAGCAA 60.684 60.000 0.00 0.00 0.00 3.91
1864 1868 5.302823 AGAGCAATATAACCCCAATCAAAGC 59.697 40.000 0.00 0.00 0.00 3.51
1865 1869 4.344968 AGCAATATAACCCCAATCAAAGCC 59.655 41.667 0.00 0.00 0.00 4.35
1920 1924 1.306825 AGGCTGAGAGGCAGGATGT 60.307 57.895 0.00 0.00 44.19 3.06
1922 1926 0.833287 GGCTGAGAGGCAGGATGTAA 59.167 55.000 0.00 0.00 45.03 2.41
1926 1930 1.759445 TGAGAGGCAGGATGTAAGAGC 59.241 52.381 0.00 0.00 39.31 4.09
1948 1952 2.756760 GGACAATGCAATGACCACAGAT 59.243 45.455 16.93 0.00 35.57 2.90
1975 1979 4.785453 CCAAGCGAGCCCCAGGTC 62.785 72.222 0.00 0.00 37.15 3.85
1986 1990 1.070445 CCCAGGTCATGATCGAGGC 59.930 63.158 13.30 0.00 0.00 4.70
1990 1994 0.977627 AGGTCATGATCGAGGCACCA 60.978 55.000 0.00 0.00 0.00 4.17
1991 1995 0.531532 GGTCATGATCGAGGCACCAG 60.532 60.000 0.00 0.00 0.00 4.00
1992 1996 0.531532 GTCATGATCGAGGCACCAGG 60.532 60.000 0.00 0.00 0.00 4.45
2023 2027 1.559065 TAGGGGTAGTGGTGGCAAGC 61.559 60.000 0.00 0.00 0.00 4.01
2041 2045 3.151912 AGCAACAAGAGGCAATCTTCT 57.848 42.857 0.68 0.00 45.50 2.85
2053 2057 3.057946 GGCAATCTTCTGACAAGAACCAC 60.058 47.826 0.00 0.00 37.51 4.16
2056 2060 1.070134 TCTTCTGACAAGAACCACCCG 59.930 52.381 0.00 0.00 37.51 5.28
2063 2067 0.107831 CAAGAACCACCCGGAGACAA 59.892 55.000 0.73 0.00 35.59 3.18
2064 2068 0.108019 AAGAACCACCCGGAGACAAC 59.892 55.000 0.73 0.00 35.59 3.32
2079 2083 0.109086 ACAACTCAGTCGAGCGATGG 60.109 55.000 0.00 0.00 43.66 3.51
2080 2084 1.153745 AACTCAGTCGAGCGATGGC 60.154 57.895 0.00 0.00 43.66 4.40
2081 2085 1.877576 AACTCAGTCGAGCGATGGCA 61.878 55.000 1.50 0.00 43.66 4.92
2091 2095 3.036429 GCGATGGCAGAGAAGGGGT 62.036 63.158 0.00 0.00 39.62 4.95
2097 2101 1.973812 GCAGAGAAGGGGTTGTGGC 60.974 63.158 0.00 0.00 0.00 5.01
2114 2118 1.553690 GGCCCCAGTGAGCTCTACAA 61.554 60.000 16.19 0.00 0.00 2.41
2129 2133 7.829706 TGAGCTCTACAACTCTTGTAATCTCTA 59.170 37.037 16.19 0.00 44.80 2.43
2139 2143 4.710375 TCTTGTAATCTCTAGAAAGCCGGT 59.290 41.667 1.90 0.00 0.00 5.28
2170 2174 1.203758 CCGATGCCGCCTGTATATGTA 59.796 52.381 0.00 0.00 0.00 2.29
2191 2195 5.309543 TGTATCTCCAAGGAAAGAGGTGAAA 59.690 40.000 0.00 0.00 0.00 2.69
2193 2197 3.458118 TCTCCAAGGAAAGAGGTGAAACA 59.542 43.478 0.00 0.00 39.98 2.83
2196 2200 3.068165 CCAAGGAAAGAGGTGAAACAACC 59.932 47.826 0.00 0.00 39.98 3.77
2215 2219 2.955660 ACCGAAGAAAGATGTTGGCAAA 59.044 40.909 0.00 0.00 0.00 3.68
2218 2222 4.990426 CCGAAGAAAGATGTTGGCAAAAAT 59.010 37.500 0.00 0.00 0.00 1.82
2265 2269 1.823295 CAGGGACACCGAGTATGGG 59.177 63.158 0.00 0.00 43.47 4.00
2282 2286 0.543749 GGGGACAGATGGAGTGGAAG 59.456 60.000 0.00 0.00 0.00 3.46
2283 2287 1.573108 GGGACAGATGGAGTGGAAGA 58.427 55.000 0.00 0.00 0.00 2.87
2284 2288 1.909302 GGGACAGATGGAGTGGAAGAA 59.091 52.381 0.00 0.00 0.00 2.52
2297 2301 1.202927 TGGAAGAAGGCAAGGACCAAG 60.203 52.381 0.00 0.00 0.00 3.61
2310 2314 1.417890 GGACCAAGATGATGGATCGGT 59.582 52.381 0.00 0.00 43.54 4.69
2319 2323 1.694169 ATGGATCGGTGGGCTCCTT 60.694 57.895 0.00 0.00 0.00 3.36
2370 2374 0.745128 TTTGTTGGAACTGTCGCGGT 60.745 50.000 6.13 0.00 0.00 5.68
2403 2407 0.660595 CGACAGTTCGTGAGCTTCGT 60.661 55.000 10.97 0.00 40.61 3.85
2408 2412 1.878088 AGTTCGTGAGCTTCGTGACTA 59.122 47.619 15.51 0.00 0.00 2.59
2411 2415 1.810755 TCGTGAGCTTCGTGACTATGT 59.189 47.619 10.97 0.00 0.00 2.29
2434 2438 2.995283 AGAAATTTACCCCTACCGTGC 58.005 47.619 0.00 0.00 0.00 5.34
2451 2455 3.242903 CCGTGCTGTGTATTGTTGAAACA 60.243 43.478 0.00 0.00 37.08 2.83
2496 2500 3.351794 GCTTTAGCTAACTCCTTGGGT 57.648 47.619 5.45 0.00 38.21 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.348888 ATCGACGACGCCCCTTCTT 61.349 57.895 0.00 0.00 39.58 2.52
60 61 4.143333 CCATCGACGACGCCCCTT 62.143 66.667 0.00 0.00 39.58 3.95
100 101 3.368571 GAAGGCTGCGGCTGCTTT 61.369 61.111 24.86 24.86 43.34 3.51
199 200 1.938585 ACTTCTTCCTCCCGTCATCA 58.061 50.000 0.00 0.00 0.00 3.07
346 347 4.641645 CACCGAGCCAACCCTGCA 62.642 66.667 0.00 0.00 0.00 4.41
520 522 2.759114 CCACATCAGGTGCTGGGT 59.241 61.111 0.00 0.00 46.50 4.51
552 554 1.003928 AGCACACATCCTTCTGCATCA 59.996 47.619 0.00 0.00 31.71 3.07
555 557 0.671472 CGAGCACACATCCTTCTGCA 60.671 55.000 0.00 0.00 31.71 4.41
613 615 8.445275 TCTCTGTGATTAGCTTAAAAACAACA 57.555 30.769 0.00 0.00 0.00 3.33
619 621 8.840321 GGCATTATCTCTGTGATTAGCTTAAAA 58.160 33.333 0.00 0.00 36.65 1.52
620 622 7.445402 GGGCATTATCTCTGTGATTAGCTTAAA 59.555 37.037 0.00 0.00 36.65 1.52
621 623 6.936900 GGGCATTATCTCTGTGATTAGCTTAA 59.063 38.462 0.00 0.00 36.65 1.85
622 624 6.043127 TGGGCATTATCTCTGTGATTAGCTTA 59.957 38.462 0.00 0.00 36.65 3.09
623 625 5.163163 TGGGCATTATCTCTGTGATTAGCTT 60.163 40.000 0.00 0.00 36.65 3.74
624 626 4.349048 TGGGCATTATCTCTGTGATTAGCT 59.651 41.667 0.00 0.00 36.65 3.32
625 627 4.453819 GTGGGCATTATCTCTGTGATTAGC 59.546 45.833 0.00 1.01 36.65 3.09
626 628 4.999950 GGTGGGCATTATCTCTGTGATTAG 59.000 45.833 0.00 0.00 36.65 1.73
627 629 4.503123 CGGTGGGCATTATCTCTGTGATTA 60.503 45.833 0.00 0.00 36.65 1.75
628 630 3.745480 CGGTGGGCATTATCTCTGTGATT 60.745 47.826 0.00 0.00 36.65 2.57
629 631 2.224378 CGGTGGGCATTATCTCTGTGAT 60.224 50.000 0.00 0.00 39.11 3.06
630 632 1.138859 CGGTGGGCATTATCTCTGTGA 59.861 52.381 0.00 0.00 0.00 3.58
631 633 1.586422 CGGTGGGCATTATCTCTGTG 58.414 55.000 0.00 0.00 0.00 3.66
632 634 0.179045 GCGGTGGGCATTATCTCTGT 60.179 55.000 0.00 0.00 42.87 3.41
633 635 0.886490 GGCGGTGGGCATTATCTCTG 60.886 60.000 0.00 0.00 46.16 3.35
634 636 1.344953 TGGCGGTGGGCATTATCTCT 61.345 55.000 0.00 0.00 44.78 3.10
635 637 1.148273 TGGCGGTGGGCATTATCTC 59.852 57.895 0.00 0.00 44.78 2.75
636 638 3.330192 TGGCGGTGGGCATTATCT 58.670 55.556 0.00 0.00 44.78 1.98
643 645 2.265467 TAAATCTCCTGGCGGTGGGC 62.265 60.000 0.00 0.00 42.51 5.36
644 646 0.179045 CTAAATCTCCTGGCGGTGGG 60.179 60.000 0.00 0.00 0.00 4.61
645 647 0.815615 GCTAAATCTCCTGGCGGTGG 60.816 60.000 0.00 0.00 0.00 4.61
646 648 1.154205 CGCTAAATCTCCTGGCGGTG 61.154 60.000 0.00 0.00 41.77 4.94
647 649 1.144057 CGCTAAATCTCCTGGCGGT 59.856 57.895 0.00 0.00 41.77 5.68
648 650 4.033894 CGCTAAATCTCCTGGCGG 57.966 61.111 0.00 0.00 41.77 6.13
649 651 1.595382 CCCGCTAAATCTCCTGGCG 60.595 63.158 0.00 0.00 44.48 5.69
650 652 1.227973 CCCCGCTAAATCTCCTGGC 60.228 63.158 0.00 0.00 0.00 4.85
651 653 1.451936 CCCCCGCTAAATCTCCTGG 59.548 63.158 0.00 0.00 0.00 4.45
652 654 1.227973 GCCCCCGCTAAATCTCCTG 60.228 63.158 0.00 0.00 0.00 3.86
653 655 2.452937 GGCCCCCGCTAAATCTCCT 61.453 63.158 0.00 0.00 34.44 3.69
654 656 2.113351 GGCCCCCGCTAAATCTCC 59.887 66.667 0.00 0.00 34.44 3.71
655 657 2.069165 ATGGGCCCCCGCTAAATCTC 62.069 60.000 22.27 0.00 39.42 2.75
656 658 2.084930 ATGGGCCCCCGCTAAATCT 61.085 57.895 22.27 0.00 39.42 2.40
657 659 1.903404 CATGGGCCCCCGCTAAATC 60.903 63.158 22.27 0.00 39.42 2.17
658 660 2.198426 CATGGGCCCCCGCTAAAT 59.802 61.111 22.27 0.00 39.42 1.40
659 661 2.925117 AACATGGGCCCCCGCTAAA 61.925 57.895 22.27 0.00 39.42 1.85
660 662 3.343326 AACATGGGCCCCCGCTAA 61.343 61.111 22.27 0.00 39.42 3.09
661 663 4.122149 CAACATGGGCCCCCGCTA 62.122 66.667 22.27 0.00 39.42 4.26
665 667 2.688299 ATTGCAACATGGGCCCCC 60.688 61.111 22.27 0.00 0.00 5.40
666 668 2.734720 GGATTGCAACATGGGCCCC 61.735 63.158 22.27 2.17 0.00 5.80
667 669 2.902584 GGATTGCAACATGGGCCC 59.097 61.111 17.59 17.59 0.00 5.80
668 670 2.283472 GACGGATTGCAACATGGGCC 62.283 60.000 0.00 0.00 0.00 5.80
669 671 1.139520 GACGGATTGCAACATGGGC 59.860 57.895 0.00 0.49 0.00 5.36
670 672 1.135315 CAAGACGGATTGCAACATGGG 60.135 52.381 0.00 0.00 0.00 4.00
671 673 1.135315 CCAAGACGGATTGCAACATGG 60.135 52.381 0.00 0.00 36.56 3.66
672 674 1.541147 ACCAAGACGGATTGCAACATG 59.459 47.619 0.00 0.00 38.63 3.21
673 675 1.909700 ACCAAGACGGATTGCAACAT 58.090 45.000 0.00 0.00 38.63 2.71
674 676 2.147958 GTACCAAGACGGATTGCAACA 58.852 47.619 0.00 0.00 38.63 3.33
675 677 1.127951 CGTACCAAGACGGATTGCAAC 59.872 52.381 0.00 0.00 39.19 4.17
676 678 1.001068 TCGTACCAAGACGGATTGCAA 59.999 47.619 0.00 0.00 43.12 4.08
677 679 0.604073 TCGTACCAAGACGGATTGCA 59.396 50.000 0.00 0.00 43.12 4.08
678 680 1.935933 ATCGTACCAAGACGGATTGC 58.064 50.000 0.00 0.00 43.12 3.56
679 681 4.563337 TCTATCGTACCAAGACGGATTG 57.437 45.455 0.00 0.00 43.12 2.67
680 682 4.202090 GGTTCTATCGTACCAAGACGGATT 60.202 45.833 0.00 0.00 43.12 3.01
681 683 3.317430 GGTTCTATCGTACCAAGACGGAT 59.683 47.826 0.00 0.00 43.12 4.18
682 684 2.684881 GGTTCTATCGTACCAAGACGGA 59.315 50.000 0.00 0.00 43.12 4.69
683 685 2.424601 TGGTTCTATCGTACCAAGACGG 59.575 50.000 0.00 0.00 41.30 4.79
684 686 3.770263 TGGTTCTATCGTACCAAGACG 57.230 47.619 0.00 0.00 41.30 4.18
685 687 6.980051 AAAATGGTTCTATCGTACCAAGAC 57.020 37.500 0.00 0.00 46.74 3.01
686 688 7.391620 AGAAAAATGGTTCTATCGTACCAAGA 58.608 34.615 0.00 0.00 46.74 3.02
687 689 7.611213 AGAAAAATGGTTCTATCGTACCAAG 57.389 36.000 0.00 0.00 46.74 3.61
688 690 7.989416 AAGAAAAATGGTTCTATCGTACCAA 57.011 32.000 0.00 0.00 46.74 3.67
690 692 8.727910 AGAAAAGAAAAATGGTTCTATCGTACC 58.272 33.333 0.00 0.00 36.84 3.34
693 695 8.297426 GGAAGAAAAGAAAAATGGTTCTATCGT 58.703 33.333 0.00 0.00 36.84 3.73
694 696 8.296713 TGGAAGAAAAGAAAAATGGTTCTATCG 58.703 33.333 0.00 0.00 36.84 2.92
695 697 9.631452 CTGGAAGAAAAGAAAAATGGTTCTATC 57.369 33.333 0.00 0.00 34.11 2.08
696 698 9.147732 ACTGGAAGAAAAGAAAAATGGTTCTAT 57.852 29.630 0.00 0.00 35.32 1.98
697 699 8.533569 ACTGGAAGAAAAGAAAAATGGTTCTA 57.466 30.769 0.00 0.00 35.32 2.10
698 700 7.423844 ACTGGAAGAAAAGAAAAATGGTTCT 57.576 32.000 0.00 0.00 37.05 3.01
699 701 9.764363 AATACTGGAAGAAAAGAAAAATGGTTC 57.236 29.630 0.00 0.00 37.43 3.62
700 702 9.764363 GAATACTGGAAGAAAAGAAAAATGGTT 57.236 29.630 0.00 0.00 37.43 3.67
701 703 8.923270 TGAATACTGGAAGAAAAGAAAAATGGT 58.077 29.630 0.00 0.00 37.43 3.55
702 704 9.196552 GTGAATACTGGAAGAAAAGAAAAATGG 57.803 33.333 0.00 0.00 37.43 3.16
703 705 8.905702 CGTGAATACTGGAAGAAAAGAAAAATG 58.094 33.333 0.00 0.00 37.43 2.32
704 706 7.595130 GCGTGAATACTGGAAGAAAAGAAAAAT 59.405 33.333 0.00 0.00 37.43 1.82
705 707 6.915843 GCGTGAATACTGGAAGAAAAGAAAAA 59.084 34.615 0.00 0.00 37.43 1.94
706 708 6.038825 TGCGTGAATACTGGAAGAAAAGAAAA 59.961 34.615 0.00 0.00 37.43 2.29
707 709 5.529430 TGCGTGAATACTGGAAGAAAAGAAA 59.471 36.000 0.00 0.00 37.43 2.52
708 710 5.060506 TGCGTGAATACTGGAAGAAAAGAA 58.939 37.500 0.00 0.00 37.43 2.52
709 711 4.637276 TGCGTGAATACTGGAAGAAAAGA 58.363 39.130 0.00 0.00 37.43 2.52
710 712 5.356882 TTGCGTGAATACTGGAAGAAAAG 57.643 39.130 0.00 0.00 37.43 2.27
711 713 4.215399 CCTTGCGTGAATACTGGAAGAAAA 59.785 41.667 0.00 0.00 37.43 2.29
712 714 3.751175 CCTTGCGTGAATACTGGAAGAAA 59.249 43.478 0.00 0.00 37.43 2.52
713 715 3.007506 TCCTTGCGTGAATACTGGAAGAA 59.992 43.478 0.00 0.00 37.43 2.52
714 716 2.565391 TCCTTGCGTGAATACTGGAAGA 59.435 45.455 0.00 0.00 37.43 2.87
715 717 2.972625 TCCTTGCGTGAATACTGGAAG 58.027 47.619 0.00 0.00 42.29 3.46
716 718 3.627395 ATCCTTGCGTGAATACTGGAA 57.373 42.857 0.00 0.00 0.00 3.53
717 719 3.069586 CCTATCCTTGCGTGAATACTGGA 59.930 47.826 0.00 0.00 0.00 3.86
718 720 3.393800 CCTATCCTTGCGTGAATACTGG 58.606 50.000 0.00 0.00 0.00 4.00
719 721 3.393800 CCCTATCCTTGCGTGAATACTG 58.606 50.000 0.00 0.00 0.00 2.74
720 722 2.368875 CCCCTATCCTTGCGTGAATACT 59.631 50.000 0.00 0.00 0.00 2.12
721 723 2.550208 CCCCCTATCCTTGCGTGAATAC 60.550 54.545 0.00 0.00 0.00 1.89
722 724 1.697432 CCCCCTATCCTTGCGTGAATA 59.303 52.381 0.00 0.00 0.00 1.75
723 725 0.474184 CCCCCTATCCTTGCGTGAAT 59.526 55.000 0.00 0.00 0.00 2.57
724 726 1.912220 CCCCCTATCCTTGCGTGAA 59.088 57.895 0.00 0.00 0.00 3.18
725 727 3.642078 CCCCCTATCCTTGCGTGA 58.358 61.111 0.00 0.00 0.00 4.35
747 749 9.131791 ACTTGTATCTGAAAATTAACACAGGTT 57.868 29.630 0.00 0.00 41.06 3.50
748 750 8.691661 ACTTGTATCTGAAAATTAACACAGGT 57.308 30.769 0.00 0.00 0.00 4.00
754 756 9.968743 CGGTCTTACTTGTATCTGAAAATTAAC 57.031 33.333 0.00 0.00 0.00 2.01
755 757 8.662141 GCGGTCTTACTTGTATCTGAAAATTAA 58.338 33.333 0.00 0.00 0.00 1.40
756 758 7.820386 TGCGGTCTTACTTGTATCTGAAAATTA 59.180 33.333 0.00 0.00 0.00 1.40
757 759 6.653320 TGCGGTCTTACTTGTATCTGAAAATT 59.347 34.615 0.00 0.00 0.00 1.82
758 760 6.092259 GTGCGGTCTTACTTGTATCTGAAAAT 59.908 38.462 0.00 0.00 0.00 1.82
759 761 5.407387 GTGCGGTCTTACTTGTATCTGAAAA 59.593 40.000 0.00 0.00 0.00 2.29
760 762 4.927425 GTGCGGTCTTACTTGTATCTGAAA 59.073 41.667 0.00 0.00 0.00 2.69
761 763 4.491676 GTGCGGTCTTACTTGTATCTGAA 58.508 43.478 0.00 0.00 0.00 3.02
762 764 3.427098 CGTGCGGTCTTACTTGTATCTGA 60.427 47.826 0.00 0.00 0.00 3.27
763 765 2.852413 CGTGCGGTCTTACTTGTATCTG 59.148 50.000 0.00 0.00 0.00 2.90
764 766 2.751259 TCGTGCGGTCTTACTTGTATCT 59.249 45.455 0.00 0.00 0.00 1.98
765 767 3.141002 TCGTGCGGTCTTACTTGTATC 57.859 47.619 0.00 0.00 0.00 2.24
766 768 3.795623 ATCGTGCGGTCTTACTTGTAT 57.204 42.857 0.00 0.00 0.00 2.29
767 769 3.581024 AATCGTGCGGTCTTACTTGTA 57.419 42.857 0.00 0.00 0.00 2.41
768 770 2.450609 AATCGTGCGGTCTTACTTGT 57.549 45.000 0.00 0.00 0.00 3.16
769 771 3.806316 AAAATCGTGCGGTCTTACTTG 57.194 42.857 0.00 0.00 0.00 3.16
770 772 4.062991 AGAAAAATCGTGCGGTCTTACTT 58.937 39.130 0.00 0.00 0.00 2.24
771 773 3.660865 AGAAAAATCGTGCGGTCTTACT 58.339 40.909 0.00 0.00 0.00 2.24
772 774 3.678548 AGAGAAAAATCGTGCGGTCTTAC 59.321 43.478 0.00 0.00 0.00 2.34
773 775 3.921677 AGAGAAAAATCGTGCGGTCTTA 58.078 40.909 0.00 0.00 0.00 2.10
774 776 2.737252 GAGAGAAAAATCGTGCGGTCTT 59.263 45.455 0.00 0.00 0.00 3.01
775 777 2.338500 GAGAGAAAAATCGTGCGGTCT 58.662 47.619 0.00 0.00 0.00 3.85
776 778 1.393883 GGAGAGAAAAATCGTGCGGTC 59.606 52.381 0.00 0.00 0.00 4.79
777 779 1.439679 GGAGAGAAAAATCGTGCGGT 58.560 50.000 0.00 0.00 0.00 5.68
778 780 0.727398 GGGAGAGAAAAATCGTGCGG 59.273 55.000 0.00 0.00 0.00 5.69
779 781 0.727398 GGGGAGAGAAAAATCGTGCG 59.273 55.000 0.00 0.00 0.00 5.34
780 782 0.727398 CGGGGAGAGAAAAATCGTGC 59.273 55.000 0.00 0.00 0.00 5.34
781 783 2.000447 GTCGGGGAGAGAAAAATCGTG 59.000 52.381 0.00 0.00 0.00 4.35
782 784 1.403780 CGTCGGGGAGAGAAAAATCGT 60.404 52.381 0.00 0.00 0.00 3.73
786 788 1.004200 GCCGTCGGGGAGAGAAAAA 60.004 57.895 14.38 0.00 38.47 1.94
855 857 1.377987 CAAGATCGCCGGGGGAAAA 60.378 57.895 19.63 0.00 0.00 2.29
865 867 1.162800 GGGATCACCAGCAAGATCGC 61.163 60.000 0.00 0.00 43.70 4.58
866 868 0.533755 GGGGATCACCAGCAAGATCG 60.534 60.000 9.87 0.00 41.16 3.69
867 869 0.842635 AGGGGATCACCAGCAAGATC 59.157 55.000 18.46 0.00 42.91 2.75
868 870 0.549950 CAGGGGATCACCAGCAAGAT 59.450 55.000 18.46 0.00 42.91 2.40
869 871 1.565390 CCAGGGGATCACCAGCAAGA 61.565 60.000 18.46 0.00 42.91 3.02
870 872 1.077212 CCAGGGGATCACCAGCAAG 60.077 63.158 18.46 0.00 42.91 4.01
871 873 1.541118 TCCAGGGGATCACCAGCAA 60.541 57.895 18.46 0.00 42.91 3.91
937 941 1.738099 CTGCCGGAGAAACCACGAG 60.738 63.158 5.05 0.00 38.90 4.18
939 943 2.742372 CCTGCCGGAGAAACCACG 60.742 66.667 5.05 0.00 38.90 4.94
956 960 3.930848 ACCAACGAAAACCATAGATCGAC 59.069 43.478 0.64 0.00 38.59 4.20
978 982 5.032327 TGGATAGAGCAGTCTAGTCGTTA 57.968 43.478 0.00 0.00 38.73 3.18
979 983 3.887352 TGGATAGAGCAGTCTAGTCGTT 58.113 45.455 0.00 0.00 38.73 3.85
980 984 3.562343 TGGATAGAGCAGTCTAGTCGT 57.438 47.619 0.00 0.00 38.73 4.34
995 999 0.830023 TGATCCCGACGCCATGGATA 60.830 55.000 18.40 0.00 38.98 2.59
996 1000 1.695114 TTGATCCCGACGCCATGGAT 61.695 55.000 18.40 1.25 41.54 3.41
998 1002 1.889105 CTTGATCCCGACGCCATGG 60.889 63.158 7.63 7.63 0.00 3.66
1032 1036 3.358076 CTCCGTCGTCTCCTTGCCC 62.358 68.421 0.00 0.00 0.00 5.36
1072 1076 1.493861 TCATCTTCCTCCTCCTGCAG 58.506 55.000 6.78 6.78 0.00 4.41
1107 1111 2.978278 CCCCAGATCTAGCAATTCCTCT 59.022 50.000 0.00 0.00 0.00 3.69
1113 1117 1.757306 CGCCCCCAGATCTAGCAAT 59.243 57.895 0.00 0.00 0.00 3.56
1118 1122 4.533124 TCGGCGCCCCCAGATCTA 62.533 66.667 23.46 0.00 0.00 1.98
1161 1165 2.224314 GCTGAAAGTCCTTGTAGTGTGC 59.776 50.000 0.00 0.00 35.30 4.57
1230 1234 1.592223 CTTCCTCCAGACCACCGTC 59.408 63.158 0.00 0.00 39.50 4.79
1272 1276 4.927267 ATCCCATAGACAACCAAACTGA 57.073 40.909 0.00 0.00 0.00 3.41
1288 1292 2.961510 CATGGCCTTATTCCAATCCCA 58.038 47.619 3.32 0.00 37.13 4.37
1399 1403 2.438951 ATTTGCGCCCAAACTGCCAG 62.439 55.000 4.18 0.00 43.20 4.85
1423 1427 8.610248 TCGATCAAAAAGTTATCAGGTAAACA 57.390 30.769 0.00 0.00 0.00 2.83
1434 1438 4.819630 ACTGCAGGTTCGATCAAAAAGTTA 59.180 37.500 19.93 0.00 0.00 2.24
1481 1485 0.742281 CTGCACATCTTCCACCTCCG 60.742 60.000 0.00 0.00 0.00 4.63
1482 1486 1.028868 GCTGCACATCTTCCACCTCC 61.029 60.000 0.00 0.00 0.00 4.30
1565 1569 7.123547 TCCAGTGACAAACCTCTTAATTTTTGT 59.876 33.333 3.87 3.87 43.22 2.83
1630 1634 6.959639 AAGCAAAAGACAGGTAATTTCTCA 57.040 33.333 0.00 0.00 0.00 3.27
1717 1721 3.312736 ACAAAGTCACCCCACTCAAAT 57.687 42.857 0.00 0.00 0.00 2.32
1741 1745 3.561725 GCCTAAAGCGAATATTGTCAGCT 59.438 43.478 0.00 0.00 40.20 4.24
1759 1763 1.538876 ACCTCTGCCTGGTTGCCTA 60.539 57.895 0.00 0.00 33.34 3.93
1768 1772 1.145571 TACCAAAACCACCTCTGCCT 58.854 50.000 0.00 0.00 0.00 4.75
1837 1841 4.102524 TGATTGGGGTTATATTGCTCTCGT 59.897 41.667 0.00 0.00 0.00 4.18
1846 1850 3.496331 CCGGCTTTGATTGGGGTTATAT 58.504 45.455 0.00 0.00 0.00 0.86
1864 1868 0.110056 GATATGCATTGAAGCGCCGG 60.110 55.000 3.54 0.00 37.31 6.13
1865 1869 0.587768 TGATATGCATTGAAGCGCCG 59.412 50.000 3.54 0.00 37.31 6.46
1906 1910 1.759445 GCTCTTACATCCTGCCTCTCA 59.241 52.381 0.00 0.00 0.00 3.27
1908 1912 0.749649 CGCTCTTACATCCTGCCTCT 59.250 55.000 0.00 0.00 0.00 3.69
1920 1924 2.677836 GTCATTGCATTGTCCGCTCTTA 59.322 45.455 8.36 0.00 0.00 2.10
1922 1926 1.089920 GTCATTGCATTGTCCGCTCT 58.910 50.000 8.36 0.00 0.00 4.09
1926 1930 0.880441 TGTGGTCATTGCATTGTCCG 59.120 50.000 16.48 0.00 0.00 4.79
1970 1974 0.531532 GGTGCCTCGATCATGACCTG 60.532 60.000 0.00 0.00 0.00 4.00
1974 1978 0.977627 ACCTGGTGCCTCGATCATGA 60.978 55.000 0.00 0.00 0.00 3.07
1975 1979 0.812811 CACCTGGTGCCTCGATCATG 60.813 60.000 14.87 0.00 0.00 3.07
1990 1994 4.463879 CCTAGCGCTGCAGCACCT 62.464 66.667 36.03 30.47 42.21 4.00
2000 2004 2.499685 CACCACTACCCCTAGCGC 59.500 66.667 0.00 0.00 0.00 5.92
2005 2009 2.907179 GCTTGCCACCACTACCCCT 61.907 63.158 0.00 0.00 0.00 4.79
2023 2027 3.817084 TGTCAGAAGATTGCCTCTTGTTG 59.183 43.478 3.56 3.20 44.42 3.33
2041 2045 0.761323 TCTCCGGGTGGTTCTTGTCA 60.761 55.000 0.00 0.00 36.30 3.58
2053 2057 1.213013 CGACTGAGTTGTCTCCGGG 59.787 63.158 0.00 0.00 39.75 5.73
2056 2060 0.455295 CGCTCGACTGAGTTGTCTCC 60.455 60.000 0.00 0.00 44.48 3.71
2063 2067 2.276863 CTGCCATCGCTCGACTGAGT 62.277 60.000 0.00 0.00 44.48 3.41
2064 2068 1.588403 CTGCCATCGCTCGACTGAG 60.588 63.158 0.00 0.00 45.49 3.35
2079 2083 1.973812 GCCACAACCCCTTCTCTGC 60.974 63.158 0.00 0.00 0.00 4.26
2080 2084 1.303643 GGCCACAACCCCTTCTCTG 60.304 63.158 0.00 0.00 0.00 3.35
2081 2085 2.539081 GGGCCACAACCCCTTCTCT 61.539 63.158 4.39 0.00 45.00 3.10
2091 2095 3.177884 AGCTCACTGGGGCCACAA 61.178 61.111 10.16 0.00 0.00 3.33
2097 2101 1.205893 GAGTTGTAGAGCTCACTGGGG 59.794 57.143 17.77 0.00 0.00 4.96
2114 2118 5.163499 CCGGCTTTCTAGAGATTACAAGAGT 60.163 44.000 4.18 0.00 0.00 3.24
2129 2133 3.246880 AACCCCGACCGGCTTTCT 61.247 61.111 0.00 0.00 0.00 2.52
2170 2174 4.104738 TGTTTCACCTCTTTCCTTGGAGAT 59.895 41.667 0.00 0.00 0.00 2.75
2191 2195 2.293399 GCCAACATCTTTCTTCGGTTGT 59.707 45.455 0.00 0.00 37.67 3.32
2193 2197 2.582052 TGCCAACATCTTTCTTCGGTT 58.418 42.857 0.00 0.00 0.00 4.44
2196 2200 5.107375 CCATTTTTGCCAACATCTTTCTTCG 60.107 40.000 0.00 0.00 0.00 3.79
2215 2219 3.431415 GTCCTTAAACAGGGCTCCATTT 58.569 45.455 0.00 0.00 45.12 2.32
2240 2244 0.179073 CTCGGTGTCCCTGCATAAGG 60.179 60.000 0.00 0.00 46.94 2.69
2243 2247 1.686587 CATACTCGGTGTCCCTGCATA 59.313 52.381 0.00 0.00 0.00 3.14
2265 2269 2.093235 CCTTCTTCCACTCCATCTGTCC 60.093 54.545 0.00 0.00 0.00 4.02
2282 2286 2.496899 TCATCTTGGTCCTTGCCTTC 57.503 50.000 0.00 0.00 0.00 3.46
2283 2287 2.622452 CCATCATCTTGGTCCTTGCCTT 60.622 50.000 0.00 0.00 31.74 4.35
2284 2288 1.064166 CCATCATCTTGGTCCTTGCCT 60.064 52.381 0.00 0.00 31.74 4.75
2297 2301 0.321122 GAGCCCACCGATCCATCATC 60.321 60.000 0.00 0.00 0.00 2.92
2403 2407 7.027874 AGGGGTAAATTTCTTCACATAGTCA 57.972 36.000 0.00 0.00 0.00 3.41
2408 2412 5.190677 CGGTAGGGGTAAATTTCTTCACAT 58.809 41.667 0.00 0.00 0.00 3.21
2411 2415 4.581868 CACGGTAGGGGTAAATTTCTTCA 58.418 43.478 0.00 0.00 0.00 3.02
2451 2455 4.817464 TCTACACGTGCACCTTTTAATTGT 59.183 37.500 17.22 4.54 0.00 2.71
2455 2459 3.249080 GCTTCTACACGTGCACCTTTTAA 59.751 43.478 17.22 0.00 0.00 1.52
2460 2464 0.393077 AAGCTTCTACACGTGCACCT 59.607 50.000 17.22 0.00 0.00 4.00
2488 2492 6.484288 CATAGGCATTATCATAACCCAAGGA 58.516 40.000 0.00 0.00 0.00 3.36
2490 2494 5.163723 CGCATAGGCATTATCATAACCCAAG 60.164 44.000 0.00 0.00 41.24 3.61


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

AutoCloner maintained by Alex Coulton.