Multiple sequence alignment - TraesCS3A01G509000

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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 TraesCS3A01G509000 chr3A 100.000 3874 0 0 1 3874 729947054 729950927 0.000000e+00 7155.0
1 TraesCS3A01G509000 chr3A 95.029 684 26 5 1 678 338339022 338338341 0.000000e+00 1068.0
2 TraesCS3A01G509000 chr3A 96.774 31 1 0 1567 1597 9825614 9825584 7.000000e-03 52.8
3 TraesCS3A01G509000 chr3D 95.479 1460 56 6 2418 3874 600420114 600421566 0.000000e+00 2322.0
4 TraesCS3A01G509000 chr3D 90.992 655 51 4 1774 2421 600419426 600420079 0.000000e+00 876.0
5 TraesCS3A01G509000 chr3D 88.593 675 53 10 848 1511 600418605 600419266 0.000000e+00 798.0
6 TraesCS3A01G509000 chr3D 89.831 177 16 2 1584 1759 600419265 600419440 3.890000e-55 226.0
7 TraesCS3A01G509000 chr3D 92.308 39 1 2 1556 1594 573122440 573122476 2.000000e-03 54.7
8 TraesCS3A01G509000 chr3B 95.686 1414 54 4 2418 3830 807434425 807435832 0.000000e+00 2266.0
9 TraesCS3A01G509000 chr3B 93.073 563 35 3 1859 2418 807433827 807434388 0.000000e+00 821.0
10 TraesCS3A01G509000 chr3B 88.532 654 43 14 862 1499 807432900 807433537 0.000000e+00 763.0
11 TraesCS3A01G509000 chr3B 89.773 176 17 1 1584 1758 807433548 807433723 1.400000e-54 224.0
12 TraesCS3A01G509000 chr6A 96.677 662 22 0 1 662 429726865 429727526 0.000000e+00 1101.0
13 TraesCS3A01G509000 chr6A 96.102 667 20 2 1 661 466536391 466537057 0.000000e+00 1083.0
14 TraesCS3A01G509000 chr5A 95.970 670 21 2 1 665 568534424 568533756 0.000000e+00 1083.0
15 TraesCS3A01G509000 chr5A 95.815 669 21 4 4 667 536835471 536834805 0.000000e+00 1074.0
16 TraesCS3A01G509000 chr2A 96.102 667 21 1 1 662 35044761 35045427 0.000000e+00 1083.0
17 TraesCS3A01G509000 chr2A 92.199 141 11 0 657 797 626838743 626838883 2.360000e-47 200.0
18 TraesCS3A01G509000 chr2A 87.324 142 15 3 657 796 681510529 681510669 4.010000e-35 159.0
19 TraesCS3A01G509000 chr1A 96.102 667 21 2 1 662 84634800 84635466 0.000000e+00 1083.0
20 TraesCS3A01G509000 chr4A 95.833 672 23 2 1 667 623912989 623912318 0.000000e+00 1081.0
21 TraesCS3A01G509000 chr4A 95.833 672 23 2 1 667 623922955 623922284 0.000000e+00 1081.0
22 TraesCS3A01G509000 chr1B 89.333 150 15 1 657 806 92554853 92555001 1.840000e-43 187.0
23 TraesCS3A01G509000 chr7B 90.000 130 13 0 666 795 584088995 584088866 6.660000e-38 169.0
24 TraesCS3A01G509000 chr7B 94.286 35 1 1 1560 1594 418204601 418204568 7.000000e-03 52.8
25 TraesCS3A01G509000 chr6D 87.143 140 17 1 657 795 305171308 305171447 1.440000e-34 158.0
26 TraesCS3A01G509000 chr6D 86.331 139 19 0 657 795 394727863 394728001 6.700000e-33 152.0
27 TraesCS3A01G509000 chr6D 85.714 140 19 1 657 795 463214602 463214741 3.120000e-31 147.0
28 TraesCS3A01G509000 chr7A 87.313 134 16 1 666 798 194358318 194358185 6.700000e-33 152.0
29 TraesCS3A01G509000 chr7D 84.286 140 21 1 657 795 70107553 70107692 6.750000e-28 135.0
30 TraesCS3A01G509000 chr6B 100.000 30 0 0 1566 1595 143434757 143434728 5.410000e-04 56.5
31 TraesCS3A01G509000 chr6B 100.000 28 0 0 1567 1594 177796553 177796526 7.000000e-03 52.8


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 TraesCS3A01G509000 chr3A 729947054 729950927 3873 False 7155.0 7155 100.00000 1 3874 1 chr3A.!!$F1 3873
1 TraesCS3A01G509000 chr3A 338338341 338339022 681 True 1068.0 1068 95.02900 1 678 1 chr3A.!!$R2 677
2 TraesCS3A01G509000 chr3D 600418605 600421566 2961 False 1055.5 2322 91.22375 848 3874 4 chr3D.!!$F2 3026
3 TraesCS3A01G509000 chr3B 807432900 807435832 2932 False 1018.5 2266 91.76600 862 3830 4 chr3B.!!$F1 2968
4 TraesCS3A01G509000 chr6A 429726865 429727526 661 False 1101.0 1101 96.67700 1 662 1 chr6A.!!$F1 661
5 TraesCS3A01G509000 chr6A 466536391 466537057 666 False 1083.0 1083 96.10200 1 661 1 chr6A.!!$F2 660
6 TraesCS3A01G509000 chr5A 568533756 568534424 668 True 1083.0 1083 95.97000 1 665 1 chr5A.!!$R2 664
7 TraesCS3A01G509000 chr5A 536834805 536835471 666 True 1074.0 1074 95.81500 4 667 1 chr5A.!!$R1 663
8 TraesCS3A01G509000 chr2A 35044761 35045427 666 False 1083.0 1083 96.10200 1 662 1 chr2A.!!$F1 661
9 TraesCS3A01G509000 chr1A 84634800 84635466 666 False 1083.0 1083 96.10200 1 662 1 chr1A.!!$F1 661
10 TraesCS3A01G509000 chr4A 623912318 623912989 671 True 1081.0 1081 95.83300 1 667 1 chr4A.!!$R1 666
11 TraesCS3A01G509000 chr4A 623922284 623922955 671 True 1081.0 1081 95.83300 1 667 1 chr4A.!!$R2 666

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
828 835 0.742505 ACACTGAGTCGACCAAACGA 59.257 50.0 13.01 0.0 40.00 3.85 F
1403 1426 0.103208 CTATGACAGTGGCGGACCTC 59.897 60.0 0.00 0.0 36.63 3.85 F
1420 1443 0.104304 CTCGGATGTTAGTTCGGGGG 59.896 60.0 0.00 0.0 0.00 5.40 F
2060 2120 0.650512 CTATGCAACTTGGTACGCGG 59.349 55.0 12.47 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2120 0.387750 GCACTAGCTTTGCAAGTGGC 60.388 55.0 15.4 13.37 39.93 5.01 R
2673 2770 0.988832 AGCGATAACAAGGTTCCCCA 59.011 50.0 0.0 0.00 0.00 4.96 R
2794 2891 1.048724 TCCCTCCTGAATACCGGCAG 61.049 60.0 0.0 0.00 0.00 4.85 R
3486 3584 1.986882 GCATAGCTGCCTAATGGGTT 58.013 50.0 0.0 0.00 42.88 4.11 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
125 126 0.894835 TGCATAGTTCCGCTCTCACA 59.105 50.000 0.00 0.00 0.00 3.58
258 259 7.833682 ACCACTTTGTGTTGGATGATGATTATA 59.166 33.333 0.00 0.00 0.00 0.98
367 368 9.114952 GTGCTAAAGATTCTTCTATAAAGCCTT 57.885 33.333 0.00 0.00 0.00 4.35
442 449 3.815401 GAGTGGAGAAAAGTTAGCAGCAA 59.185 43.478 0.00 0.00 0.00 3.91
447 454 0.941542 AAAAGTTAGCAGCAACGCGA 59.058 45.000 15.93 0.00 36.85 5.87
629 636 2.740447 CGCTACTAAAAGGCCGAAAACT 59.260 45.455 0.00 0.00 0.00 2.66
631 638 3.749609 GCTACTAAAAGGCCGAAAACTCA 59.250 43.478 0.00 0.00 0.00 3.41
639 646 1.289109 GCCGAAAACTCACGCTGCTA 61.289 55.000 0.00 0.00 0.00 3.49
662 669 5.265350 CTAGGCTTTTCCCTAGTAGTGTC 57.735 47.826 0.00 0.00 46.16 3.67
670 677 7.363968 GCTTTTCCCTAGTAGTGTCTAACTGAT 60.364 40.741 0.00 0.00 40.26 2.90
671 678 9.186837 CTTTTCCCTAGTAGTGTCTAACTGATA 57.813 37.037 0.00 0.00 40.26 2.15
672 679 9.710818 TTTTCCCTAGTAGTGTCTAACTGATAT 57.289 33.333 0.00 0.00 40.26 1.63
673 680 8.693120 TTCCCTAGTAGTGTCTAACTGATATG 57.307 38.462 0.00 0.00 40.26 1.78
675 682 6.490381 CCCTAGTAGTGTCTAACTGATATGCA 59.510 42.308 0.00 0.00 40.26 3.96
676 683 7.364200 CCTAGTAGTGTCTAACTGATATGCAC 58.636 42.308 0.00 0.00 40.26 4.57
677 684 7.229707 CCTAGTAGTGTCTAACTGATATGCACT 59.770 40.741 0.00 0.00 40.26 4.40
678 685 7.033530 AGTAGTGTCTAACTGATATGCACTC 57.966 40.000 0.00 0.00 40.26 3.51
679 686 6.831353 AGTAGTGTCTAACTGATATGCACTCT 59.169 38.462 0.00 0.00 40.26 3.24
680 687 6.537453 AGTGTCTAACTGATATGCACTCTT 57.463 37.500 0.00 0.00 37.88 2.85
681 688 6.940739 AGTGTCTAACTGATATGCACTCTTT 58.059 36.000 0.00 0.00 37.88 2.52
682 689 7.390027 AGTGTCTAACTGATATGCACTCTTTT 58.610 34.615 0.00 0.00 37.88 2.27
683 690 8.531982 AGTGTCTAACTGATATGCACTCTTTTA 58.468 33.333 0.00 0.00 37.88 1.52
684 691 8.812329 GTGTCTAACTGATATGCACTCTTTTAG 58.188 37.037 0.00 1.37 0.00 1.85
685 692 8.749354 TGTCTAACTGATATGCACTCTTTTAGA 58.251 33.333 12.81 12.81 0.00 2.10
687 694 6.917217 AACTGATATGCACTCTTTTAGAGC 57.083 37.500 3.68 0.00 46.12 4.09
688 695 6.232581 ACTGATATGCACTCTTTTAGAGCT 57.767 37.500 3.68 0.00 46.12 4.09
689 696 6.648192 ACTGATATGCACTCTTTTAGAGCTT 58.352 36.000 3.68 0.00 46.12 3.74
690 697 6.538021 ACTGATATGCACTCTTTTAGAGCTTG 59.462 38.462 3.68 0.00 46.12 4.01
691 698 6.643388 TGATATGCACTCTTTTAGAGCTTGA 58.357 36.000 3.68 0.00 46.12 3.02
692 699 7.278135 TGATATGCACTCTTTTAGAGCTTGAT 58.722 34.615 3.68 0.00 46.12 2.57
693 700 5.814764 ATGCACTCTTTTAGAGCTTGATG 57.185 39.130 3.68 0.00 46.12 3.07
694 701 4.645535 TGCACTCTTTTAGAGCTTGATGT 58.354 39.130 3.68 0.00 46.12 3.06
695 702 4.453478 TGCACTCTTTTAGAGCTTGATGTG 59.547 41.667 3.68 0.00 46.12 3.21
696 703 4.453819 GCACTCTTTTAGAGCTTGATGTGT 59.546 41.667 3.68 0.00 46.12 3.72
697 704 5.616424 GCACTCTTTTAGAGCTTGATGTGTG 60.616 44.000 3.68 0.00 46.12 3.82
698 705 5.468072 CACTCTTTTAGAGCTTGATGTGTGT 59.532 40.000 3.68 0.00 46.12 3.72
699 706 5.698545 ACTCTTTTAGAGCTTGATGTGTGTC 59.301 40.000 3.68 0.00 46.12 3.67
700 707 5.858381 TCTTTTAGAGCTTGATGTGTGTCT 58.142 37.500 0.00 0.00 0.00 3.41
701 708 6.291377 TCTTTTAGAGCTTGATGTGTGTCTT 58.709 36.000 0.00 0.00 0.00 3.01
702 709 6.425114 TCTTTTAGAGCTTGATGTGTGTCTTC 59.575 38.462 0.00 0.00 0.00 2.87
703 710 3.051081 AGAGCTTGATGTGTGTCTTCC 57.949 47.619 0.00 0.00 0.00 3.46
704 711 2.636893 AGAGCTTGATGTGTGTCTTCCT 59.363 45.455 0.00 0.00 0.00 3.36
705 712 2.740981 GAGCTTGATGTGTGTCTTCCTG 59.259 50.000 0.00 0.00 0.00 3.86
706 713 2.105477 AGCTTGATGTGTGTCTTCCTGT 59.895 45.455 0.00 0.00 0.00 4.00
707 714 2.880890 GCTTGATGTGTGTCTTCCTGTT 59.119 45.455 0.00 0.00 0.00 3.16
708 715 4.065088 GCTTGATGTGTGTCTTCCTGTTA 58.935 43.478 0.00 0.00 0.00 2.41
709 716 4.697352 GCTTGATGTGTGTCTTCCTGTTAT 59.303 41.667 0.00 0.00 0.00 1.89
710 717 5.391310 GCTTGATGTGTGTCTTCCTGTTATG 60.391 44.000 0.00 0.00 0.00 1.90
711 718 5.227569 TGATGTGTGTCTTCCTGTTATGT 57.772 39.130 0.00 0.00 0.00 2.29
712 719 4.996758 TGATGTGTGTCTTCCTGTTATGTG 59.003 41.667 0.00 0.00 0.00 3.21
713 720 4.681074 TGTGTGTCTTCCTGTTATGTGA 57.319 40.909 0.00 0.00 0.00 3.58
714 721 5.227569 TGTGTGTCTTCCTGTTATGTGAT 57.772 39.130 0.00 0.00 0.00 3.06
715 722 6.353404 TGTGTGTCTTCCTGTTATGTGATA 57.647 37.500 0.00 0.00 0.00 2.15
716 723 6.163476 TGTGTGTCTTCCTGTTATGTGATAC 58.837 40.000 0.00 0.00 0.00 2.24
717 724 5.581085 GTGTGTCTTCCTGTTATGTGATACC 59.419 44.000 0.00 0.00 0.00 2.73
718 725 5.483937 TGTGTCTTCCTGTTATGTGATACCT 59.516 40.000 0.00 0.00 0.00 3.08
719 726 6.013725 TGTGTCTTCCTGTTATGTGATACCTT 60.014 38.462 0.00 0.00 0.00 3.50
720 727 6.879458 GTGTCTTCCTGTTATGTGATACCTTT 59.121 38.462 0.00 0.00 0.00 3.11
721 728 7.390718 GTGTCTTCCTGTTATGTGATACCTTTT 59.609 37.037 0.00 0.00 0.00 2.27
722 729 7.390440 TGTCTTCCTGTTATGTGATACCTTTTG 59.610 37.037 0.00 0.00 0.00 2.44
724 731 6.381498 TCCTGTTATGTGATACCTTTTGGA 57.619 37.500 0.00 0.00 44.07 3.53
725 732 6.177610 TCCTGTTATGTGATACCTTTTGGAC 58.822 40.000 0.00 0.00 44.07 4.02
726 733 5.064707 CCTGTTATGTGATACCTTTTGGACG 59.935 44.000 0.00 0.00 44.07 4.79
727 734 5.553123 TGTTATGTGATACCTTTTGGACGT 58.447 37.500 0.00 0.00 44.07 4.34
728 735 5.998981 TGTTATGTGATACCTTTTGGACGTT 59.001 36.000 0.00 0.00 44.07 3.99
729 736 7.160049 TGTTATGTGATACCTTTTGGACGTTA 58.840 34.615 0.00 0.00 44.07 3.18
730 737 7.825270 TGTTATGTGATACCTTTTGGACGTTAT 59.175 33.333 0.00 0.00 44.07 1.89
731 738 8.671028 GTTATGTGATACCTTTTGGACGTTATT 58.329 33.333 0.00 0.00 44.07 1.40
732 739 9.887629 TTATGTGATACCTTTTGGACGTTATTA 57.112 29.630 0.00 0.00 44.07 0.98
733 740 8.974060 ATGTGATACCTTTTGGACGTTATTAT 57.026 30.769 0.00 0.00 44.07 1.28
734 741 8.203937 TGTGATACCTTTTGGACGTTATTATG 57.796 34.615 0.00 0.00 44.07 1.90
735 742 7.130269 GTGATACCTTTTGGACGTTATTATGC 58.870 38.462 0.00 0.00 44.07 3.14
736 743 4.976224 ACCTTTTGGACGTTATTATGCC 57.024 40.909 0.00 0.00 44.07 4.40
737 744 4.337145 ACCTTTTGGACGTTATTATGCCA 58.663 39.130 0.00 0.00 44.07 4.92
738 745 4.157105 ACCTTTTGGACGTTATTATGCCAC 59.843 41.667 0.00 0.00 44.07 5.01
739 746 4.156922 CCTTTTGGACGTTATTATGCCACA 59.843 41.667 0.00 0.00 44.07 4.17
740 747 4.688511 TTTGGACGTTATTATGCCACAC 57.311 40.909 0.00 0.00 0.00 3.82
741 748 3.620427 TGGACGTTATTATGCCACACT 57.380 42.857 0.00 0.00 0.00 3.55
742 749 3.266636 TGGACGTTATTATGCCACACTG 58.733 45.455 0.00 0.00 0.00 3.66
743 750 3.055747 TGGACGTTATTATGCCACACTGA 60.056 43.478 0.00 0.00 0.00 3.41
744 751 4.127171 GGACGTTATTATGCCACACTGAT 58.873 43.478 0.00 0.00 0.00 2.90
745 752 4.024893 GGACGTTATTATGCCACACTGATG 60.025 45.833 0.00 0.00 0.00 3.07
746 753 4.765273 ACGTTATTATGCCACACTGATGA 58.235 39.130 0.00 0.00 0.00 2.92
747 754 5.182487 ACGTTATTATGCCACACTGATGAA 58.818 37.500 0.00 0.00 0.00 2.57
748 755 5.064707 ACGTTATTATGCCACACTGATGAAC 59.935 40.000 0.00 0.00 0.00 3.18
749 756 5.064579 CGTTATTATGCCACACTGATGAACA 59.935 40.000 0.00 0.00 0.00 3.18
750 757 6.238456 CGTTATTATGCCACACTGATGAACAT 60.238 38.462 0.00 0.00 0.00 2.71
751 758 4.968812 TTATGCCACACTGATGAACATG 57.031 40.909 0.00 0.00 0.00 3.21
752 759 0.883153 TGCCACACTGATGAACATGC 59.117 50.000 0.00 0.00 0.00 4.06
753 760 1.171308 GCCACACTGATGAACATGCT 58.829 50.000 0.00 0.00 0.00 3.79
754 761 2.290197 TGCCACACTGATGAACATGCTA 60.290 45.455 0.00 0.00 0.00 3.49
755 762 2.749076 GCCACACTGATGAACATGCTAA 59.251 45.455 0.00 0.00 0.00 3.09
756 763 3.379372 GCCACACTGATGAACATGCTAAT 59.621 43.478 0.00 0.00 0.00 1.73
757 764 4.576053 GCCACACTGATGAACATGCTAATA 59.424 41.667 0.00 0.00 0.00 0.98
758 765 5.240183 GCCACACTGATGAACATGCTAATAT 59.760 40.000 0.00 0.00 0.00 1.28
759 766 6.238842 GCCACACTGATGAACATGCTAATATT 60.239 38.462 0.00 0.00 0.00 1.28
760 767 7.682741 GCCACACTGATGAACATGCTAATATTT 60.683 37.037 0.00 0.00 0.00 1.40
761 768 8.839343 CCACACTGATGAACATGCTAATATTTA 58.161 33.333 0.00 0.00 0.00 1.40
762 769 9.655769 CACACTGATGAACATGCTAATATTTAC 57.344 33.333 0.00 0.00 0.00 2.01
763 770 9.618890 ACACTGATGAACATGCTAATATTTACT 57.381 29.630 0.00 0.00 0.00 2.24
765 772 9.277783 ACTGATGAACATGCTAATATTTACTCC 57.722 33.333 0.00 0.00 0.00 3.85
766 773 8.621532 TGATGAACATGCTAATATTTACTCCC 57.378 34.615 0.00 0.00 0.00 4.30
767 774 7.387673 TGATGAACATGCTAATATTTACTCCCG 59.612 37.037 0.00 0.00 0.00 5.14
768 775 6.588204 TGAACATGCTAATATTTACTCCCGT 58.412 36.000 0.00 0.00 0.00 5.28
769 776 7.051623 TGAACATGCTAATATTTACTCCCGTT 58.948 34.615 0.00 0.00 0.00 4.44
770 777 6.861065 ACATGCTAATATTTACTCCCGTTG 57.139 37.500 0.00 0.00 0.00 4.10
771 778 5.238650 ACATGCTAATATTTACTCCCGTTGC 59.761 40.000 0.00 0.00 0.00 4.17
772 779 4.771903 TGCTAATATTTACTCCCGTTGCA 58.228 39.130 0.00 0.00 0.00 4.08
773 780 5.186942 TGCTAATATTTACTCCCGTTGCAA 58.813 37.500 0.00 0.00 0.00 4.08
774 781 5.065474 TGCTAATATTTACTCCCGTTGCAAC 59.935 40.000 19.89 19.89 0.00 4.17
784 791 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
785 792 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
786 793 2.043405 TTGCAACGCACGGGCATAT 61.043 52.632 11.77 0.00 38.71 1.78
787 794 2.024588 GCAACGCACGGGCATATG 59.975 61.111 11.77 6.17 41.24 1.78
788 795 2.760159 GCAACGCACGGGCATATGT 61.760 57.895 11.77 0.00 41.24 2.29
789 796 1.062365 CAACGCACGGGCATATGTG 59.938 57.895 11.77 0.00 41.24 3.21
812 819 9.777575 TGTGCTAGTAAAAAGTAAAAGAAACAC 57.222 29.630 0.00 0.00 0.00 3.32
813 820 9.999009 GTGCTAGTAAAAAGTAAAAGAAACACT 57.001 29.630 0.00 0.00 0.00 3.55
814 821 9.997482 TGCTAGTAAAAAGTAAAAGAAACACTG 57.003 29.630 0.00 0.00 0.00 3.66
819 826 9.207042 GTAAAAAGTAAAAGAAACACTGAGTCG 57.793 33.333 0.00 0.00 0.00 4.18
820 827 7.605410 AAAAGTAAAAGAAACACTGAGTCGA 57.395 32.000 0.00 0.00 0.00 4.20
821 828 6.585389 AAGTAAAAGAAACACTGAGTCGAC 57.415 37.500 7.70 7.70 0.00 4.20
822 829 5.048507 AGTAAAAGAAACACTGAGTCGACC 58.951 41.667 13.01 4.42 0.00 4.79
823 830 3.536956 AAAGAAACACTGAGTCGACCA 57.463 42.857 13.01 9.18 0.00 4.02
824 831 3.536956 AAGAAACACTGAGTCGACCAA 57.463 42.857 13.01 0.00 0.00 3.67
825 832 3.536956 AGAAACACTGAGTCGACCAAA 57.463 42.857 13.01 0.00 0.00 3.28
826 833 3.195661 AGAAACACTGAGTCGACCAAAC 58.804 45.455 13.01 2.35 0.00 2.93
827 834 1.567504 AACACTGAGTCGACCAAACG 58.432 50.000 13.01 0.86 0.00 3.60
828 835 0.742505 ACACTGAGTCGACCAAACGA 59.257 50.000 13.01 0.00 40.00 3.85
829 836 1.135527 ACACTGAGTCGACCAAACGAA 59.864 47.619 13.01 0.00 43.75 3.85
830 837 2.223971 ACACTGAGTCGACCAAACGAAT 60.224 45.455 13.01 0.00 43.75 3.34
835 842 2.828877 AGTCGACCAAACGAATCAACA 58.171 42.857 13.01 0.00 43.75 3.33
836 843 2.542595 AGTCGACCAAACGAATCAACAC 59.457 45.455 13.01 0.00 43.75 3.32
837 844 1.868498 TCGACCAAACGAATCAACACC 59.132 47.619 0.00 0.00 39.34 4.16
838 845 1.397945 CGACCAAACGAATCAACACCG 60.398 52.381 0.00 0.00 35.09 4.94
839 846 1.868498 GACCAAACGAATCAACACCGA 59.132 47.619 0.00 0.00 0.00 4.69
840 847 2.482721 GACCAAACGAATCAACACCGAT 59.517 45.455 0.00 0.00 0.00 4.18
841 848 2.225491 ACCAAACGAATCAACACCGATG 59.775 45.455 0.00 0.00 0.00 3.84
842 849 2.414029 CCAAACGAATCAACACCGATGG 60.414 50.000 0.00 0.00 0.00 3.51
843 850 2.465860 AACGAATCAACACCGATGGA 57.534 45.000 0.00 0.00 0.00 3.41
844 851 2.010145 ACGAATCAACACCGATGGAG 57.990 50.000 0.00 0.00 0.00 3.86
845 852 1.275291 ACGAATCAACACCGATGGAGT 59.725 47.619 0.00 0.00 0.00 3.85
846 853 2.494471 ACGAATCAACACCGATGGAGTA 59.506 45.455 0.00 0.00 0.00 2.59
860 867 4.098044 CGATGGAGTAGGTAAGATGTGTGT 59.902 45.833 0.00 0.00 0.00 3.72
876 883 3.351416 GTTCCACGTGGCGAACCC 61.351 66.667 30.25 9.22 33.71 4.11
891 898 3.702048 CCCGGTCCACCACGTCAT 61.702 66.667 0.00 0.00 35.14 3.06
917 924 2.494059 CTCTTCTTCCCTGCGAACAAA 58.506 47.619 0.00 0.00 0.00 2.83
1191 1204 4.067913 CGGTGCATTTGGGCCACC 62.068 66.667 5.23 1.17 34.04 4.61
1196 1209 2.755469 CATTTGGGCCACCTCCGG 60.755 66.667 5.23 0.00 37.76 5.14
1209 1222 4.972733 TCCGGTCGGTCGTGGGAA 62.973 66.667 9.36 0.00 36.47 3.97
1210 1223 4.729856 CCGGTCGGTCGTGGGAAC 62.730 72.222 0.55 0.00 0.00 3.62
1318 1332 5.401531 TTGTGTACTATGTTCAGAGGTCC 57.598 43.478 0.00 0.00 0.00 4.46
1321 1335 4.705507 GTGTACTATGTTCAGAGGTCCAGA 59.294 45.833 0.00 0.00 0.00 3.86
1322 1336 4.705507 TGTACTATGTTCAGAGGTCCAGAC 59.294 45.833 0.00 0.00 0.00 3.51
1354 1368 7.063934 AGTAATAGTAGAATTGGGTGTAGCC 57.936 40.000 0.00 0.00 0.00 3.93
1366 1388 2.355412 GGGTGTAGCCGGACATAGTTTT 60.355 50.000 5.05 0.00 38.44 2.43
1375 1397 5.475564 AGCCGGACATAGTTTTGTGTTAAAT 59.524 36.000 5.05 0.00 0.00 1.40
1403 1426 0.103208 CTATGACAGTGGCGGACCTC 59.897 60.000 0.00 0.00 36.63 3.85
1416 1439 1.533338 CGGACCTCGGATGTTAGTTCG 60.533 57.143 0.00 0.00 34.75 3.95
1420 1443 0.104304 CTCGGATGTTAGTTCGGGGG 59.896 60.000 0.00 0.00 0.00 5.40
1531 1555 7.957992 ATAGCACTACCTCTGTAAACTAAGT 57.042 36.000 0.00 0.00 0.00 2.24
1533 1557 7.771927 AGCACTACCTCTGTAAACTAAGTAA 57.228 36.000 0.00 0.00 0.00 2.24
1534 1558 8.363761 AGCACTACCTCTGTAAACTAAGTAAT 57.636 34.615 0.00 0.00 0.00 1.89
1535 1559 9.471702 AGCACTACCTCTGTAAACTAAGTAATA 57.528 33.333 0.00 0.00 0.00 0.98
1563 1587 6.833342 ACGTTTTAAATCACTACGTCTTGT 57.167 33.333 8.75 0.00 41.04 3.16
1564 1588 7.928908 ACGTTTTAAATCACTACGTCTTGTA 57.071 32.000 8.75 0.00 41.04 2.41
1565 1589 7.777425 ACGTTTTAAATCACTACGTCTTGTAC 58.223 34.615 8.75 0.00 41.04 2.90
1566 1590 7.649306 ACGTTTTAAATCACTACGTCTTGTACT 59.351 33.333 8.75 0.00 41.04 2.73
1567 1591 9.117145 CGTTTTAAATCACTACGTCTTGTACTA 57.883 33.333 0.00 0.00 0.00 1.82
1577 1601 9.203668 CACTACGTCTTGTACTATTAGTTTACG 57.796 37.037 0.85 7.78 0.00 3.18
1578 1602 8.391106 ACTACGTCTTGTACTATTAGTTTACGG 58.609 37.037 0.85 0.00 0.00 4.02
1579 1603 7.377766 ACGTCTTGTACTATTAGTTTACGGA 57.622 36.000 0.85 0.00 0.00 4.69
1580 1604 7.467623 ACGTCTTGTACTATTAGTTTACGGAG 58.532 38.462 0.85 0.00 0.00 4.63
1581 1605 6.909357 CGTCTTGTACTATTAGTTTACGGAGG 59.091 42.308 0.85 1.34 0.00 4.30
1582 1606 7.199078 GTCTTGTACTATTAGTTTACGGAGGG 58.801 42.308 0.85 0.00 0.00 4.30
1692 1717 9.899661 TGTATAATATAAACTCTTGTGCCACTT 57.100 29.630 0.00 0.00 0.00 3.16
1749 1774 3.491792 GGTGAAGAGCCATCAGTAGCTAC 60.492 52.174 16.43 16.43 40.11 3.58
1753 1778 2.761208 AGAGCCATCAGTAGCTACGTTT 59.239 45.455 17.99 4.11 40.11 3.60
1754 1779 3.195825 AGAGCCATCAGTAGCTACGTTTT 59.804 43.478 17.99 0.00 40.11 2.43
1755 1780 3.933332 GAGCCATCAGTAGCTACGTTTTT 59.067 43.478 17.99 0.00 40.11 1.94
1792 1817 5.989551 AAAAGCTATGTTGTTTTTGGCTG 57.010 34.783 0.00 0.00 31.09 4.85
1798 1823 2.175202 TGTTGTTTTTGGCTGGTCACT 58.825 42.857 0.00 0.00 0.00 3.41
1801 1826 2.175202 TGTTTTTGGCTGGTCACTTGT 58.825 42.857 0.00 0.00 0.00 3.16
1833 1865 2.211250 ACCCTCTTACGCAGTAGTCA 57.789 50.000 0.00 0.00 46.93 3.41
1881 1939 8.519799 TGAAAAAGAACCATTCTACTCTGTTT 57.480 30.769 0.00 0.00 39.61 2.83
1999 2059 7.379098 GAAGGAAACATTTTCTACCTTCGAT 57.621 36.000 0.00 0.00 42.06 3.59
2023 2083 8.924511 ATGAGTTATTGGAGAAGTCTGAAAAA 57.075 30.769 0.00 0.00 0.00 1.94
2032 2092 6.766467 TGGAGAAGTCTGAAAAACCTTTACTC 59.234 38.462 0.00 0.00 0.00 2.59
2056 2116 4.326548 GTCGACTTCTATGCAACTTGGTAC 59.673 45.833 8.70 0.00 0.00 3.34
2060 2120 0.650512 CTATGCAACTTGGTACGCGG 59.349 55.000 12.47 0.00 0.00 6.46
2109 2169 5.134202 TGTACATATGGCCTAGAACATCG 57.866 43.478 3.32 0.00 0.00 3.84
2112 2172 2.820059 TATGGCCTAGAACATCGCTG 57.180 50.000 3.32 0.00 0.00 5.18
2204 2264 1.985159 TGGCATGTCCTGTTCCTACTT 59.015 47.619 0.00 0.00 35.26 2.24
2256 2316 8.352942 GTTTTCTTTAGTGTTCATCTTGTGGAT 58.647 33.333 0.00 0.00 34.51 3.41
2306 2366 4.583871 CTTTAGTCCAAAGATGACTGCCT 58.416 43.478 3.30 0.00 45.62 4.75
2308 2368 3.515602 AGTCCAAAGATGACTGCCTTT 57.484 42.857 0.00 0.00 41.40 3.11
2317 2377 4.973168 AGATGACTGCCTTTTGAACACTA 58.027 39.130 0.00 0.00 0.00 2.74
2396 2456 6.656270 ACATACTTTGATGAAGAAGTGCATCA 59.344 34.615 0.00 0.00 46.50 3.07
2463 2560 4.227300 TGGCTATGTTGTAGGAAGATTGGT 59.773 41.667 0.00 0.00 0.00 3.67
2662 2759 7.894376 ATTGAAGCATTACCAACTTTCATTG 57.106 32.000 0.00 0.00 0.00 2.82
2673 2770 5.835280 ACCAACTTTCATTGTCTTCAAGGAT 59.165 36.000 0.00 0.00 42.51 3.24
2750 2847 1.102154 TGGTGTTTTGACTGGTGCTG 58.898 50.000 0.00 0.00 0.00 4.41
2760 2857 3.489355 TGACTGGTGCTGATGAAATTGT 58.511 40.909 0.00 0.00 0.00 2.71
2780 2877 3.749088 TGTTATAACGTGGCTTTGGTCTG 59.251 43.478 10.92 0.00 0.00 3.51
2794 2891 7.870445 TGGCTTTGGTCTGTATTTTTGTTTATC 59.130 33.333 0.00 0.00 0.00 1.75
2798 2895 6.919721 TGGTCTGTATTTTTGTTTATCTGCC 58.080 36.000 0.00 0.00 0.00 4.85
2906 3003 1.896220 TGTCAGCAAGGAATTTCGCT 58.104 45.000 0.00 0.00 34.29 4.93
2991 3088 7.178097 TGGATCATCCATTGTTGATTGTTGTTA 59.822 33.333 0.66 0.00 42.67 2.41
2992 3089 7.489113 GGATCATCCATTGTTGATTGTTGTTAC 59.511 37.037 0.00 0.00 36.28 2.50
3125 3222 8.352201 TGGTTACTGATTTTGTCAAAATGAGAG 58.648 33.333 31.62 22.47 42.40 3.20
3129 3226 7.869800 ACTGATTTTGTCAAAATGAGAGACTC 58.130 34.615 31.62 16.55 42.40 3.36
3132 3229 8.853126 TGATTTTGTCAAAATGAGAGACTCAAT 58.147 29.630 24.74 0.54 40.97 2.57
3188 3285 5.064441 AGCAGAACTTTGTTTGGCATATC 57.936 39.130 0.00 0.00 0.00 1.63
3316 3413 7.748847 AGTTAGTTATGCAAAAGTCCATTACG 58.251 34.615 0.00 0.00 0.00 3.18
3334 3432 2.985896 ACGTATTCTGGTTCACCATGG 58.014 47.619 11.19 11.19 46.46 3.66
3341 3439 2.955660 TCTGGTTCACCATGGTTTTGTC 59.044 45.455 16.84 4.88 46.46 3.18
3390 3488 2.489971 CCTTTCGGCAACTGTAGTTCA 58.510 47.619 0.00 0.00 35.83 3.18
3397 3495 4.159693 TCGGCAACTGTAGTTCACTATGAT 59.840 41.667 0.00 0.00 35.83 2.45
3486 3584 3.782523 AGGATTCTAAGCCAGTTGATCCA 59.217 43.478 0.00 0.00 36.79 3.41
3646 3748 2.107950 TTACTGGGAAATCTGGCACG 57.892 50.000 0.00 0.00 0.00 5.34
3680 3782 4.201656 GGAGTCGATTAAAAACAGGCGTAC 60.202 45.833 0.00 0.00 0.00 3.67
3684 3786 3.836348 CGATTAAAAACAGGCGTACGTTG 59.164 43.478 17.90 17.22 0.00 4.10
3695 3797 2.248487 GCGTACGTTGGACTTCACTAG 58.752 52.381 17.90 0.00 0.00 2.57
3830 3932 4.428615 TCATTGTCAACATGCTGATGTG 57.571 40.909 1.44 2.64 42.30 3.21
3845 3947 6.288294 TGCTGATGTGTACTCACTTAGTTTT 58.712 36.000 0.00 0.00 44.14 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 5.221521 GGAACTATGCAGTACATGAGATGGA 60.222 44.000 0.00 0.00 40.06 3.41
125 126 3.058570 CGCGAGAAGAGCTATCACTATGT 60.059 47.826 0.00 0.00 0.00 2.29
301 302 5.942826 TGATACACATACAAATGCCTGTGAA 59.057 36.000 17.65 3.72 41.11 3.18
403 410 5.726397 TCCACTCGCTACTGCTAATTTTAA 58.274 37.500 0.00 0.00 36.97 1.52
442 449 0.866061 CGCTACTGCTACAATCGCGT 60.866 55.000 5.77 0.00 36.97 6.01
447 454 1.153647 TGCGCGCTACTGCTACAAT 60.154 52.632 33.29 0.00 36.97 2.71
629 636 0.895530 AAAGCCTAGTAGCAGCGTGA 59.104 50.000 0.00 0.00 34.23 4.35
631 638 1.405661 GGAAAAGCCTAGTAGCAGCGT 60.406 52.381 0.00 0.00 34.23 5.07
662 669 7.925483 AGCTCTAAAAGAGTGCATATCAGTTAG 59.075 37.037 5.86 4.31 45.38 2.34
670 677 6.314648 CACATCAAGCTCTAAAAGAGTGCATA 59.685 38.462 5.86 0.00 45.38 3.14
671 678 5.123502 CACATCAAGCTCTAAAAGAGTGCAT 59.876 40.000 5.86 0.00 45.38 3.96
672 679 4.453478 CACATCAAGCTCTAAAAGAGTGCA 59.547 41.667 5.86 0.00 45.38 4.57
673 680 4.453819 ACACATCAAGCTCTAAAAGAGTGC 59.546 41.667 5.86 0.00 44.12 4.40
675 682 5.615289 ACACACATCAAGCTCTAAAAGAGT 58.385 37.500 5.86 0.00 44.12 3.24
676 683 5.931146 AGACACACATCAAGCTCTAAAAGAG 59.069 40.000 0.00 0.00 45.04 2.85
677 684 5.858381 AGACACACATCAAGCTCTAAAAGA 58.142 37.500 0.00 0.00 0.00 2.52
678 685 6.348050 GGAAGACACACATCAAGCTCTAAAAG 60.348 42.308 0.00 0.00 0.00 2.27
679 686 5.470098 GGAAGACACACATCAAGCTCTAAAA 59.530 40.000 0.00 0.00 0.00 1.52
680 687 4.997395 GGAAGACACACATCAAGCTCTAAA 59.003 41.667 0.00 0.00 0.00 1.85
681 688 4.284490 AGGAAGACACACATCAAGCTCTAA 59.716 41.667 0.00 0.00 0.00 2.10
682 689 3.834813 AGGAAGACACACATCAAGCTCTA 59.165 43.478 0.00 0.00 0.00 2.43
683 690 2.636893 AGGAAGACACACATCAAGCTCT 59.363 45.455 0.00 0.00 0.00 4.09
684 691 2.740981 CAGGAAGACACACATCAAGCTC 59.259 50.000 0.00 0.00 0.00 4.09
685 692 2.105477 ACAGGAAGACACACATCAAGCT 59.895 45.455 0.00 0.00 0.00 3.74
686 693 2.498167 ACAGGAAGACACACATCAAGC 58.502 47.619 0.00 0.00 0.00 4.01
687 694 5.702670 ACATAACAGGAAGACACACATCAAG 59.297 40.000 0.00 0.00 0.00 3.02
688 695 5.469760 CACATAACAGGAAGACACACATCAA 59.530 40.000 0.00 0.00 0.00 2.57
689 696 4.996758 CACATAACAGGAAGACACACATCA 59.003 41.667 0.00 0.00 0.00 3.07
690 697 5.237815 TCACATAACAGGAAGACACACATC 58.762 41.667 0.00 0.00 0.00 3.06
691 698 5.227569 TCACATAACAGGAAGACACACAT 57.772 39.130 0.00 0.00 0.00 3.21
692 699 4.681074 TCACATAACAGGAAGACACACA 57.319 40.909 0.00 0.00 0.00 3.72
693 700 5.581085 GGTATCACATAACAGGAAGACACAC 59.419 44.000 0.00 0.00 0.00 3.82
694 701 5.483937 AGGTATCACATAACAGGAAGACACA 59.516 40.000 0.00 0.00 0.00 3.72
695 702 5.978814 AGGTATCACATAACAGGAAGACAC 58.021 41.667 0.00 0.00 0.00 3.67
696 703 6.620877 AAGGTATCACATAACAGGAAGACA 57.379 37.500 0.00 0.00 0.00 3.41
697 704 7.148239 CCAAAAGGTATCACATAACAGGAAGAC 60.148 40.741 0.00 0.00 0.00 3.01
698 705 6.884295 CCAAAAGGTATCACATAACAGGAAGA 59.116 38.462 0.00 0.00 0.00 2.87
699 706 6.884295 TCCAAAAGGTATCACATAACAGGAAG 59.116 38.462 0.00 0.00 0.00 3.46
700 707 6.657541 GTCCAAAAGGTATCACATAACAGGAA 59.342 38.462 0.00 0.00 0.00 3.36
701 708 6.177610 GTCCAAAAGGTATCACATAACAGGA 58.822 40.000 0.00 0.00 0.00 3.86
702 709 5.064707 CGTCCAAAAGGTATCACATAACAGG 59.935 44.000 0.00 0.00 0.00 4.00
703 710 5.642063 ACGTCCAAAAGGTATCACATAACAG 59.358 40.000 0.00 0.00 0.00 3.16
704 711 5.553123 ACGTCCAAAAGGTATCACATAACA 58.447 37.500 0.00 0.00 0.00 2.41
705 712 6.490566 AACGTCCAAAAGGTATCACATAAC 57.509 37.500 0.00 0.00 0.00 1.89
706 713 8.795842 AATAACGTCCAAAAGGTATCACATAA 57.204 30.769 0.00 0.00 0.00 1.90
708 715 8.836413 CATAATAACGTCCAAAAGGTATCACAT 58.164 33.333 0.00 0.00 0.00 3.21
709 716 7.201661 GCATAATAACGTCCAAAAGGTATCACA 60.202 37.037 0.00 0.00 0.00 3.58
710 717 7.130269 GCATAATAACGTCCAAAAGGTATCAC 58.870 38.462 0.00 0.00 0.00 3.06
711 718 6.261381 GGCATAATAACGTCCAAAAGGTATCA 59.739 38.462 0.00 0.00 0.00 2.15
712 719 6.261381 TGGCATAATAACGTCCAAAAGGTATC 59.739 38.462 0.00 0.00 0.00 2.24
713 720 6.038936 GTGGCATAATAACGTCCAAAAGGTAT 59.961 38.462 0.00 0.00 0.00 2.73
714 721 5.354792 GTGGCATAATAACGTCCAAAAGGTA 59.645 40.000 0.00 0.00 0.00 3.08
715 722 4.157105 GTGGCATAATAACGTCCAAAAGGT 59.843 41.667 0.00 0.00 0.00 3.50
716 723 4.156922 TGTGGCATAATAACGTCCAAAAGG 59.843 41.667 0.00 0.00 0.00 3.11
717 724 5.092781 GTGTGGCATAATAACGTCCAAAAG 58.907 41.667 0.00 0.00 0.00 2.27
718 725 4.762765 AGTGTGGCATAATAACGTCCAAAA 59.237 37.500 0.00 0.00 0.00 2.44
719 726 4.155099 CAGTGTGGCATAATAACGTCCAAA 59.845 41.667 0.00 0.00 0.00 3.28
720 727 3.687212 CAGTGTGGCATAATAACGTCCAA 59.313 43.478 0.00 0.00 0.00 3.53
721 728 3.055747 TCAGTGTGGCATAATAACGTCCA 60.056 43.478 0.00 0.00 0.00 4.02
722 729 3.527533 TCAGTGTGGCATAATAACGTCC 58.472 45.455 0.00 0.00 0.00 4.79
723 730 4.808895 TCATCAGTGTGGCATAATAACGTC 59.191 41.667 0.00 0.00 0.00 4.34
724 731 4.765273 TCATCAGTGTGGCATAATAACGT 58.235 39.130 0.00 0.00 0.00 3.99
725 732 5.064579 TGTTCATCAGTGTGGCATAATAACG 59.935 40.000 0.00 0.00 0.00 3.18
726 733 6.435430 TGTTCATCAGTGTGGCATAATAAC 57.565 37.500 0.00 0.00 0.00 1.89
727 734 6.459985 GCATGTTCATCAGTGTGGCATAATAA 60.460 38.462 0.00 0.00 0.00 1.40
728 735 5.008911 GCATGTTCATCAGTGTGGCATAATA 59.991 40.000 0.00 0.00 0.00 0.98
729 736 4.202080 GCATGTTCATCAGTGTGGCATAAT 60.202 41.667 0.00 0.00 0.00 1.28
730 737 3.129113 GCATGTTCATCAGTGTGGCATAA 59.871 43.478 0.00 0.00 0.00 1.90
731 738 2.684374 GCATGTTCATCAGTGTGGCATA 59.316 45.455 0.00 0.00 0.00 3.14
732 739 1.475280 GCATGTTCATCAGTGTGGCAT 59.525 47.619 0.00 0.00 0.00 4.40
733 740 0.883153 GCATGTTCATCAGTGTGGCA 59.117 50.000 0.00 0.00 0.00 4.92
734 741 1.171308 AGCATGTTCATCAGTGTGGC 58.829 50.000 0.00 0.00 0.00 5.01
735 742 6.872628 ATATTAGCATGTTCATCAGTGTGG 57.127 37.500 0.00 0.00 0.00 4.17
736 743 9.655769 GTAAATATTAGCATGTTCATCAGTGTG 57.344 33.333 0.00 0.00 0.00 3.82
737 744 9.618890 AGTAAATATTAGCATGTTCATCAGTGT 57.381 29.630 0.00 0.00 0.00 3.55
739 746 9.277783 GGAGTAAATATTAGCATGTTCATCAGT 57.722 33.333 0.00 0.00 0.00 3.41
740 747 8.725148 GGGAGTAAATATTAGCATGTTCATCAG 58.275 37.037 0.00 0.00 0.00 2.90
741 748 7.387673 CGGGAGTAAATATTAGCATGTTCATCA 59.612 37.037 0.00 0.00 0.00 3.07
742 749 7.387948 ACGGGAGTAAATATTAGCATGTTCATC 59.612 37.037 0.00 0.00 44.60 2.92
743 750 7.224297 ACGGGAGTAAATATTAGCATGTTCAT 58.776 34.615 0.00 0.00 44.60 2.57
744 751 6.588204 ACGGGAGTAAATATTAGCATGTTCA 58.412 36.000 0.00 0.00 44.60 3.18
745 752 7.352739 CAACGGGAGTAAATATTAGCATGTTC 58.647 38.462 0.00 0.00 46.69 3.18
746 753 6.238648 GCAACGGGAGTAAATATTAGCATGTT 60.239 38.462 0.00 0.00 46.69 2.71
747 754 5.238650 GCAACGGGAGTAAATATTAGCATGT 59.761 40.000 0.00 0.00 46.69 3.21
748 755 5.238432 TGCAACGGGAGTAAATATTAGCATG 59.762 40.000 0.00 0.00 46.69 4.06
749 756 5.373222 TGCAACGGGAGTAAATATTAGCAT 58.627 37.500 0.00 0.00 46.69 3.79
750 757 4.771903 TGCAACGGGAGTAAATATTAGCA 58.228 39.130 0.00 0.00 46.69 3.49
751 758 5.507974 GTTGCAACGGGAGTAAATATTAGC 58.492 41.667 14.90 0.00 46.69 3.09
767 774 2.265073 ATATGCCCGTGCGTTGCAAC 62.265 55.000 19.89 19.89 41.47 4.17
768 775 2.043405 ATATGCCCGTGCGTTGCAA 61.043 52.632 0.00 0.00 41.47 4.08
769 776 2.437537 ATATGCCCGTGCGTTGCA 60.438 55.556 8.11 8.11 41.78 4.08
770 777 2.024588 CATATGCCCGTGCGTTGC 59.975 61.111 0.00 0.00 41.78 4.17
771 778 1.062365 CACATATGCCCGTGCGTTG 59.938 57.895 1.58 0.00 41.78 4.10
772 779 3.496711 CACATATGCCCGTGCGTT 58.503 55.556 1.58 0.00 41.78 4.84
786 793 9.777575 GTGTTTCTTTTACTTTTTACTAGCACA 57.222 29.630 0.00 0.00 0.00 4.57
787 794 9.999009 AGTGTTTCTTTTACTTTTTACTAGCAC 57.001 29.630 0.00 0.00 0.00 4.40
788 795 9.997482 CAGTGTTTCTTTTACTTTTTACTAGCA 57.003 29.630 0.00 0.00 0.00 3.49
793 800 9.207042 CGACTCAGTGTTTCTTTTACTTTTTAC 57.793 33.333 0.00 0.00 0.00 2.01
794 801 9.153721 TCGACTCAGTGTTTCTTTTACTTTTTA 57.846 29.630 0.00 0.00 0.00 1.52
795 802 7.961283 GTCGACTCAGTGTTTCTTTTACTTTTT 59.039 33.333 8.70 0.00 0.00 1.94
796 803 7.413767 GGTCGACTCAGTGTTTCTTTTACTTTT 60.414 37.037 16.46 0.00 0.00 2.27
797 804 6.036844 GGTCGACTCAGTGTTTCTTTTACTTT 59.963 38.462 16.46 0.00 0.00 2.66
798 805 5.522824 GGTCGACTCAGTGTTTCTTTTACTT 59.477 40.000 16.46 0.00 0.00 2.24
799 806 5.048507 GGTCGACTCAGTGTTTCTTTTACT 58.951 41.667 16.46 0.00 0.00 2.24
800 807 4.807304 TGGTCGACTCAGTGTTTCTTTTAC 59.193 41.667 16.46 0.00 0.00 2.01
801 808 5.013568 TGGTCGACTCAGTGTTTCTTTTA 57.986 39.130 16.46 0.00 0.00 1.52
802 809 3.869065 TGGTCGACTCAGTGTTTCTTTT 58.131 40.909 16.46 0.00 0.00 2.27
803 810 3.536956 TGGTCGACTCAGTGTTTCTTT 57.463 42.857 16.46 0.00 0.00 2.52
804 811 3.536956 TTGGTCGACTCAGTGTTTCTT 57.463 42.857 16.46 0.00 0.00 2.52
805 812 3.195661 GTTTGGTCGACTCAGTGTTTCT 58.804 45.455 16.46 0.00 0.00 2.52
806 813 2.034001 CGTTTGGTCGACTCAGTGTTTC 60.034 50.000 16.46 0.00 0.00 2.78
807 814 1.931172 CGTTTGGTCGACTCAGTGTTT 59.069 47.619 16.46 0.00 0.00 2.83
808 815 1.135527 TCGTTTGGTCGACTCAGTGTT 59.864 47.619 16.46 0.00 34.85 3.32
809 816 0.742505 TCGTTTGGTCGACTCAGTGT 59.257 50.000 16.46 0.00 34.85 3.55
810 817 1.847818 TTCGTTTGGTCGACTCAGTG 58.152 50.000 16.46 3.50 39.58 3.66
811 818 2.035449 TGATTCGTTTGGTCGACTCAGT 59.965 45.455 16.46 0.00 41.79 3.41
812 819 2.672714 TGATTCGTTTGGTCGACTCAG 58.327 47.619 16.46 3.32 41.79 3.35
813 820 2.798283 GTTGATTCGTTTGGTCGACTCA 59.202 45.455 16.46 9.06 43.72 3.41
814 821 2.798283 TGTTGATTCGTTTGGTCGACTC 59.202 45.455 16.46 6.30 39.58 3.36
815 822 2.542595 GTGTTGATTCGTTTGGTCGACT 59.457 45.455 16.46 0.00 39.58 4.18
816 823 2.349155 GGTGTTGATTCGTTTGGTCGAC 60.349 50.000 7.13 7.13 39.58 4.20
817 824 1.868498 GGTGTTGATTCGTTTGGTCGA 59.132 47.619 0.00 0.00 38.08 4.20
818 825 1.397945 CGGTGTTGATTCGTTTGGTCG 60.398 52.381 0.00 0.00 0.00 4.79
819 826 1.868498 TCGGTGTTGATTCGTTTGGTC 59.132 47.619 0.00 0.00 0.00 4.02
820 827 1.956297 TCGGTGTTGATTCGTTTGGT 58.044 45.000 0.00 0.00 0.00 3.67
821 828 2.414029 CCATCGGTGTTGATTCGTTTGG 60.414 50.000 0.00 0.00 0.00 3.28
822 829 2.482336 TCCATCGGTGTTGATTCGTTTG 59.518 45.455 0.00 0.00 0.00 2.93
823 830 2.742053 CTCCATCGGTGTTGATTCGTTT 59.258 45.455 0.00 0.00 0.00 3.60
824 831 2.289444 ACTCCATCGGTGTTGATTCGTT 60.289 45.455 0.00 0.00 0.00 3.85
825 832 1.275291 ACTCCATCGGTGTTGATTCGT 59.725 47.619 0.00 0.00 0.00 3.85
826 833 2.010145 ACTCCATCGGTGTTGATTCG 57.990 50.000 0.00 0.00 0.00 3.34
827 834 3.118738 ACCTACTCCATCGGTGTTGATTC 60.119 47.826 0.00 0.00 31.55 2.52
828 835 2.838202 ACCTACTCCATCGGTGTTGATT 59.162 45.455 0.00 0.00 31.55 2.57
829 836 2.467880 ACCTACTCCATCGGTGTTGAT 58.532 47.619 0.00 0.00 31.55 2.57
830 837 1.933021 ACCTACTCCATCGGTGTTGA 58.067 50.000 0.00 0.00 31.55 3.18
831 838 3.446161 TCTTACCTACTCCATCGGTGTTG 59.554 47.826 0.00 0.00 31.55 3.33
832 839 3.705051 TCTTACCTACTCCATCGGTGTT 58.295 45.455 0.00 0.00 31.55 3.32
833 840 3.377253 TCTTACCTACTCCATCGGTGT 57.623 47.619 0.00 0.00 33.75 4.16
834 841 3.637229 ACATCTTACCTACTCCATCGGTG 59.363 47.826 0.00 0.00 32.36 4.94
835 842 3.637229 CACATCTTACCTACTCCATCGGT 59.363 47.826 0.00 0.00 34.86 4.69
836 843 3.637229 ACACATCTTACCTACTCCATCGG 59.363 47.826 0.00 0.00 0.00 4.18
837 844 4.098044 ACACACATCTTACCTACTCCATCG 59.902 45.833 0.00 0.00 0.00 3.84
838 845 5.599999 ACACACATCTTACCTACTCCATC 57.400 43.478 0.00 0.00 0.00 3.51
839 846 5.104900 GGAACACACATCTTACCTACTCCAT 60.105 44.000 0.00 0.00 0.00 3.41
840 847 4.222145 GGAACACACATCTTACCTACTCCA 59.778 45.833 0.00 0.00 0.00 3.86
841 848 4.222145 TGGAACACACATCTTACCTACTCC 59.778 45.833 0.00 0.00 0.00 3.85
842 849 5.401531 TGGAACACACATCTTACCTACTC 57.598 43.478 0.00 0.00 0.00 2.59
860 867 4.973055 CGGGTTCGCCACGTGGAA 62.973 66.667 38.30 21.40 39.65 3.53
876 883 2.125673 GGATGACGTGGTGGACCG 60.126 66.667 0.00 0.00 39.43 4.79
891 898 0.618968 GCAGGGAAGAAGAGGGAGGA 60.619 60.000 0.00 0.00 0.00 3.71
1147 1160 2.443016 CAGTAGAGCGGCTCCCCT 60.443 66.667 25.49 18.11 0.00 4.79
1158 1171 2.708051 CACCGAGTACTCACCAGTAGA 58.292 52.381 22.37 0.00 35.67 2.59
1161 1174 0.826256 TGCACCGAGTACTCACCAGT 60.826 55.000 22.37 10.73 36.55 4.00
1206 1219 0.247537 CTAAAATCCGTGCGCGTTCC 60.248 55.000 19.61 0.00 36.15 3.62
1207 1220 0.441145 ACTAAAATCCGTGCGCGTTC 59.559 50.000 19.61 0.00 36.15 3.95
1208 1221 0.165079 CACTAAAATCCGTGCGCGTT 59.835 50.000 19.61 8.68 36.15 4.84
1209 1222 1.632046 CCACTAAAATCCGTGCGCGT 61.632 55.000 19.61 1.48 36.15 6.01
1210 1223 1.060308 CCACTAAAATCCGTGCGCG 59.940 57.895 13.88 13.88 37.95 6.86
1211 1224 1.427819 CCCACTAAAATCCGTGCGC 59.572 57.895 0.00 0.00 0.00 6.09
1212 1225 0.391927 TCCCCACTAAAATCCGTGCG 60.392 55.000 0.00 0.00 0.00 5.34
1213 1226 1.828979 TTCCCCACTAAAATCCGTGC 58.171 50.000 0.00 0.00 0.00 5.34
1214 1227 5.400066 AAAATTCCCCACTAAAATCCGTG 57.600 39.130 0.00 0.00 0.00 4.94
1215 1228 6.250711 ACTAAAATTCCCCACTAAAATCCGT 58.749 36.000 0.00 0.00 0.00 4.69
1216 1229 6.769134 ACTAAAATTCCCCACTAAAATCCG 57.231 37.500 0.00 0.00 0.00 4.18
1321 1335 8.881262 CCCAATTCTACTATTACTAGGATTGGT 58.119 37.037 18.29 0.00 35.80 3.67
1322 1336 8.881262 ACCCAATTCTACTATTACTAGGATTGG 58.119 37.037 14.87 14.87 36.42 3.16
1335 1349 2.696707 CCGGCTACACCCAATTCTACTA 59.303 50.000 0.00 0.00 33.26 1.82
1354 1368 9.834628 ATTACATTTAACACAAAACTATGTCCG 57.165 29.630 0.00 0.00 0.00 4.79
1375 1397 4.180817 CGCCACTGTCATAGACAATTACA 58.819 43.478 1.19 0.00 42.26 2.41
1382 1405 0.179108 GGTCCGCCACTGTCATAGAC 60.179 60.000 0.00 0.00 34.09 2.59
1403 1426 4.848685 CCCCCGAACTAACATCCG 57.151 61.111 0.00 0.00 0.00 4.18
1509 1533 7.771927 TTACTTAGTTTACAGAGGTAGTGCT 57.228 36.000 0.00 0.00 0.00 4.40
1553 1577 8.604035 TCCGTAAACTAATAGTACAAGACGTAG 58.396 37.037 0.00 0.00 0.00 3.51
1554 1578 8.487313 TCCGTAAACTAATAGTACAAGACGTA 57.513 34.615 0.00 0.00 0.00 3.57
1555 1579 7.377766 TCCGTAAACTAATAGTACAAGACGT 57.622 36.000 0.00 0.00 0.00 4.34
1556 1580 6.909357 CCTCCGTAAACTAATAGTACAAGACG 59.091 42.308 0.00 0.21 0.00 4.18
1557 1581 7.067494 TCCCTCCGTAAACTAATAGTACAAGAC 59.933 40.741 0.00 0.00 0.00 3.01
1558 1582 7.118723 TCCCTCCGTAAACTAATAGTACAAGA 58.881 38.462 0.00 0.00 0.00 3.02
1559 1583 7.067981 ACTCCCTCCGTAAACTAATAGTACAAG 59.932 40.741 0.00 0.00 0.00 3.16
1560 1584 6.891908 ACTCCCTCCGTAAACTAATAGTACAA 59.108 38.462 0.00 0.00 0.00 2.41
1561 1585 6.426587 ACTCCCTCCGTAAACTAATAGTACA 58.573 40.000 0.00 0.00 0.00 2.90
1562 1586 6.951062 ACTCCCTCCGTAAACTAATAGTAC 57.049 41.667 0.00 0.00 0.00 2.73
1564 1588 9.819754 ATAATACTCCCTCCGTAAACTAATAGT 57.180 33.333 0.00 0.00 0.00 2.12
1568 1592 9.603921 CAAAATAATACTCCCTCCGTAAACTAA 57.396 33.333 0.00 0.00 0.00 2.24
1569 1593 8.761689 ACAAAATAATACTCCCTCCGTAAACTA 58.238 33.333 0.00 0.00 0.00 2.24
1570 1594 7.627311 ACAAAATAATACTCCCTCCGTAAACT 58.373 34.615 0.00 0.00 0.00 2.66
1571 1595 7.011763 GGACAAAATAATACTCCCTCCGTAAAC 59.988 40.741 0.00 0.00 0.00 2.01
1572 1596 7.049754 GGACAAAATAATACTCCCTCCGTAAA 58.950 38.462 0.00 0.00 0.00 2.01
1573 1597 6.156602 TGGACAAAATAATACTCCCTCCGTAA 59.843 38.462 0.00 0.00 0.00 3.18
1574 1598 5.662208 TGGACAAAATAATACTCCCTCCGTA 59.338 40.000 0.00 0.00 0.00 4.02
1575 1599 4.472108 TGGACAAAATAATACTCCCTCCGT 59.528 41.667 0.00 0.00 0.00 4.69
1576 1600 5.031066 TGGACAAAATAATACTCCCTCCG 57.969 43.478 0.00 0.00 0.00 4.63
1577 1601 7.342026 ACATTTGGACAAAATAATACTCCCTCC 59.658 37.037 1.17 0.00 36.28 4.30
1578 1602 8.293699 ACATTTGGACAAAATAATACTCCCTC 57.706 34.615 1.17 0.00 36.28 4.30
1579 1603 8.116026 AGACATTTGGACAAAATAATACTCCCT 58.884 33.333 1.17 0.00 36.28 4.20
1580 1604 8.293699 AGACATTTGGACAAAATAATACTCCC 57.706 34.615 1.17 0.00 36.28 4.30
1581 1605 9.788960 GAAGACATTTGGACAAAATAATACTCC 57.211 33.333 1.17 0.00 36.28 3.85
1684 1709 3.489229 GGAAGAAAACAGACAAGTGGCAC 60.489 47.826 10.29 10.29 0.00 5.01
1692 1717 3.391296 ACAGCCTAGGAAGAAAACAGACA 59.609 43.478 14.75 0.00 0.00 3.41
1769 1794 5.296531 CCAGCCAAAAACAACATAGCTTTTT 59.703 36.000 0.00 0.00 0.00 1.94
1770 1795 4.815846 CCAGCCAAAAACAACATAGCTTTT 59.184 37.500 0.00 0.00 0.00 2.27
1771 1796 4.141733 ACCAGCCAAAAACAACATAGCTTT 60.142 37.500 0.00 0.00 0.00 3.51
1772 1797 3.387699 ACCAGCCAAAAACAACATAGCTT 59.612 39.130 0.00 0.00 0.00 3.74
1773 1798 2.965147 ACCAGCCAAAAACAACATAGCT 59.035 40.909 0.00 0.00 0.00 3.32
1774 1799 3.243704 TGACCAGCCAAAAACAACATAGC 60.244 43.478 0.00 0.00 0.00 2.97
1775 1800 4.037923 AGTGACCAGCCAAAAACAACATAG 59.962 41.667 0.00 0.00 0.00 2.23
1776 1801 3.957497 AGTGACCAGCCAAAAACAACATA 59.043 39.130 0.00 0.00 0.00 2.29
1782 1807 2.959507 ACAAGTGACCAGCCAAAAAC 57.040 45.000 0.00 0.00 0.00 2.43
1792 1817 2.100584 TGCACCATTGAAACAAGTGACC 59.899 45.455 0.00 0.00 0.00 4.02
1798 1823 2.102252 GAGGGTTGCACCATTGAAACAA 59.898 45.455 7.49 0.00 42.61 2.83
1801 1826 2.380064 AGAGGGTTGCACCATTGAAA 57.620 45.000 7.49 0.00 41.02 2.69
1823 1855 4.560136 ATGTCTGTAGATGACTACTGCG 57.440 45.455 0.00 0.00 46.33 5.18
1824 1856 7.652727 TGATAATGTCTGTAGATGACTACTGC 58.347 38.462 0.00 0.00 46.33 4.40
1881 1939 7.870509 AAGCAGCAGATCATTAAGTCATTAA 57.129 32.000 0.00 0.00 35.41 1.40
1886 1944 8.970691 TTTTAAAAGCAGCAGATCATTAAGTC 57.029 30.769 0.00 0.00 0.00 3.01
1999 2059 7.228706 GGTTTTTCAGACTTCTCCAATAACTCA 59.771 37.037 0.00 0.00 0.00 3.41
2023 2083 4.438472 GCATAGAAGTCGACGAGTAAAGGT 60.438 45.833 10.46 0.00 0.00 3.50
2032 2092 2.345641 CCAAGTTGCATAGAAGTCGACG 59.654 50.000 10.46 0.00 0.00 5.12
2060 2120 0.387750 GCACTAGCTTTGCAAGTGGC 60.388 55.000 15.40 13.37 39.93 5.01
2091 2151 2.998670 CAGCGATGTTCTAGGCCATATG 59.001 50.000 5.01 0.00 0.00 1.78
2138 2198 4.717233 TTAACACAATGATGATGGGCAC 57.283 40.909 0.00 0.00 0.00 5.01
2141 2201 5.920193 AGGTTTAACACAATGATGATGGG 57.080 39.130 0.00 0.00 0.00 4.00
2204 2264 2.176889 AGAGCTTGGCGGTACTTTCTA 58.823 47.619 0.00 0.00 0.00 2.10
2256 2316 8.685838 AAACTAACATGGTAGCACTTTAAGAA 57.314 30.769 17.94 0.00 0.00 2.52
2346 2406 8.798153 GTGAAAGAAATTAGTCACAAAACACAG 58.202 33.333 0.00 0.00 40.10 3.66
2430 2490 3.264104 ACAACATAGCCATGCAATTTGC 58.736 40.909 14.49 14.49 45.29 3.68
2662 2759 1.636003 AGGTTCCCCATCCTTGAAGAC 59.364 52.381 0.00 0.00 0.00 3.01
2673 2770 0.988832 AGCGATAACAAGGTTCCCCA 59.011 50.000 0.00 0.00 0.00 4.96
2732 2829 1.388547 TCAGCACCAGTCAAAACACC 58.611 50.000 0.00 0.00 0.00 4.16
2739 2836 3.489355 ACAATTTCATCAGCACCAGTCA 58.511 40.909 0.00 0.00 0.00 3.41
2750 2847 7.009174 CCAAAGCCACGTTATAACAATTTCATC 59.991 37.037 15.67 0.00 0.00 2.92
2760 2857 4.010667 ACAGACCAAAGCCACGTTATAA 57.989 40.909 0.00 0.00 0.00 0.98
2780 2877 8.185505 TGAATACCGGCAGATAAACAAAAATAC 58.814 33.333 0.00 0.00 0.00 1.89
2794 2891 1.048724 TCCCTCCTGAATACCGGCAG 61.049 60.000 0.00 0.00 0.00 4.85
2798 2895 1.364171 CGCTCCCTCCTGAATACCG 59.636 63.158 0.00 0.00 0.00 4.02
2906 3003 4.523083 GGTAGCAACATACATTTCAGGGA 58.477 43.478 0.00 0.00 0.00 4.20
3019 3116 8.189119 TGTAGCTTTGAAGGGAATGTTTATTT 57.811 30.769 0.00 0.00 0.00 1.40
3020 3117 7.451566 ACTGTAGCTTTGAAGGGAATGTTTATT 59.548 33.333 0.00 0.00 0.00 1.40
3125 3222 8.830580 ACATACTGCACAATATGTAATTGAGTC 58.169 33.333 3.09 0.00 39.65 3.36
3278 3375 2.981859 ACTAACTTCGCCGATTCCAT 57.018 45.000 0.00 0.00 0.00 3.41
3341 3439 2.317040 TCTAGATTCGGCTAGTTGGGG 58.683 52.381 0.00 0.00 39.10 4.96
3397 3495 9.880157 GAGATGGTAAAAGTAACTGTGGTAATA 57.120 33.333 0.00 0.00 0.00 0.98
3486 3584 1.986882 GCATAGCTGCCTAATGGGTT 58.013 50.000 0.00 0.00 42.88 4.11
3523 3622 4.708177 AGAAAGAAAGAGCACAGTAGCAA 58.292 39.130 0.00 0.00 36.85 3.91
3524 3623 4.342862 AGAAAGAAAGAGCACAGTAGCA 57.657 40.909 0.00 0.00 36.85 3.49
3525 3624 6.976636 AATAGAAAGAAAGAGCACAGTAGC 57.023 37.500 0.00 0.00 0.00 3.58
3646 3748 2.086054 ATCGACTCCAAACAGCAGTC 57.914 50.000 0.00 0.00 31.34 3.51
3680 3782 6.645415 ACAATTTACTCTAGTGAAGTCCAACG 59.355 38.462 0.00 0.00 0.00 4.10
3812 3914 4.388485 AGTACACATCAGCATGTTGACAA 58.612 39.130 14.96 0.00 40.66 3.18
3830 3932 7.664758 TCCCTTACAGAAAACTAAGTGAGTAC 58.335 38.462 0.00 0.00 37.44 2.73
3845 3947 8.063153 TCTGTAATGTAACCTATCCCTTACAGA 58.937 37.037 14.78 14.78 45.33 3.41


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

AutoCloner maintained by Alex Coulton.