Multiple sequence alignment - TraesCS6A01G078900

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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 TraesCS6A01G078900 chr6A 100.000 5806 0 0 1 5806 48562002 48556197 0.000000e+00 10722.0
1 TraesCS6A01G078900 chr6B 95.201 2042 92 4 903 2944 85791773 85789738 0.000000e+00 3223.0
2 TraesCS6A01G078900 chr6B 93.282 1563 68 21 3547 5097 85788875 85787338 0.000000e+00 2270.0
3 TraesCS6A01G078900 chr6B 89.597 596 49 9 2955 3542 85789652 85789062 0.000000e+00 745.0
4 TraesCS6A01G078900 chr6B 92.520 508 29 5 5308 5806 85786583 85786076 0.000000e+00 719.0
5 TraesCS6A01G078900 chr6B 84.158 101 4 3 5089 5189 85787064 85786976 2.880000e-13 87.9
6 TraesCS6A01G078900 chr6D 91.681 2260 139 23 3556 5806 36820481 36818262 0.000000e+00 3086.0
7 TraesCS6A01G078900 chr6D 93.345 1713 91 11 1683 3384 36822450 36820750 0.000000e+00 2510.0
8 TraesCS6A01G078900 chr6D 95.397 630 26 2 1 630 464214321 464213695 0.000000e+00 1000.0
9 TraesCS6A01G078900 chr6D 94.497 636 31 3 1 635 232765303 232765935 0.000000e+00 977.0
10 TraesCS6A01G078900 chr6D 89.911 783 44 18 738 1515 36823200 36822448 0.000000e+00 976.0
11 TraesCS6A01G078900 chr6D 90.164 61 5 1 669 728 36884440 36884380 1.730000e-10 78.7
12 TraesCS6A01G078900 chr3A 96.172 627 21 2 1 627 660861406 660860783 0.000000e+00 1022.0
13 TraesCS6A01G078900 chr7D 95.707 629 24 3 1 629 114467716 114468341 0.000000e+00 1009.0
14 TraesCS6A01G078900 chr3D 95.541 628 23 5 1 627 214959107 214959730 0.000000e+00 1000.0
15 TraesCS6A01G078900 chr2D 94.836 639 27 5 1 638 70391323 70391956 0.000000e+00 992.0
16 TraesCS6A01G078900 chr2D 94.795 634 28 4 1 633 101660260 101660889 0.000000e+00 983.0
17 TraesCS6A01G078900 chr2D 94.646 635 28 4 1 635 542526479 542525851 0.000000e+00 979.0
18 TraesCS6A01G078900 chr1A 94.828 638 28 4 1 636 579858794 579858160 0.000000e+00 990.0
19 TraesCS6A01G078900 chr5A 76.540 341 47 15 3086 3412 115247274 115246953 7.790000e-34 156.0
20 TraesCS6A01G078900 chr1D 82.716 81 12 1 3557 3635 432811309 432811229 2.900000e-08 71.3
21 TraesCS6A01G078900 chr5B 83.099 71 8 3 3574 3642 313116510 313116442 1.750000e-05 62.1


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 TraesCS6A01G078900 chr6A 48556197 48562002 5805 True 10722.000000 10722 100.000000 1 5806 1 chr6A.!!$R1 5805
1 TraesCS6A01G078900 chr6B 85786076 85791773 5697 True 1408.980000 3223 90.951600 903 5806 5 chr6B.!!$R1 4903
2 TraesCS6A01G078900 chr6D 36818262 36823200 4938 True 2190.666667 3086 91.645667 738 5806 3 chr6D.!!$R3 5068
3 TraesCS6A01G078900 chr6D 464213695 464214321 626 True 1000.000000 1000 95.397000 1 630 1 chr6D.!!$R2 629
4 TraesCS6A01G078900 chr6D 232765303 232765935 632 False 977.000000 977 94.497000 1 635 1 chr6D.!!$F1 634
5 TraesCS6A01G078900 chr3A 660860783 660861406 623 True 1022.000000 1022 96.172000 1 627 1 chr3A.!!$R1 626
6 TraesCS6A01G078900 chr7D 114467716 114468341 625 False 1009.000000 1009 95.707000 1 629 1 chr7D.!!$F1 628
7 TraesCS6A01G078900 chr3D 214959107 214959730 623 False 1000.000000 1000 95.541000 1 627 1 chr3D.!!$F1 626
8 TraesCS6A01G078900 chr2D 70391323 70391956 633 False 992.000000 992 94.836000 1 638 1 chr2D.!!$F1 637
9 TraesCS6A01G078900 chr2D 101660260 101660889 629 False 983.000000 983 94.795000 1 633 1 chr2D.!!$F2 632
10 TraesCS6A01G078900 chr2D 542525851 542526479 628 True 979.000000 979 94.646000 1 635 1 chr2D.!!$R1 634
11 TraesCS6A01G078900 chr1A 579858160 579858794 634 True 990.000000 990 94.828000 1 636 1 chr1A.!!$R1 635

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
731 736 0.038892 GAGCTGTGGCACCAAACATG 60.039 55.0 16.26 0.0 41.70 3.21 F
1458 1468 0.175989 GGAATCTCGGGAGTGACCAC 59.824 60.0 0.00 0.0 41.20 4.16 F
1655 1665 0.180406 ATCGGGGATGTAGGTGTTGC 59.820 55.0 0.00 0.0 0.00 4.17 F
2983 3077 0.258774 GCTTCCCTATTTGGCCCTGA 59.741 55.0 0.00 0.0 0.00 3.86 F
3595 3902 0.253630 TCAGGGCCAAATAGGGAGGT 60.254 55.0 6.18 0.0 38.09 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2142 0.250234 GACACTATCCTGGTGCTGCA 59.750 55.0 0.00 0.00 38.14 4.41 R
3064 3160 0.322008 GGAGTGGAGCAGTCCCAAAG 60.322 60.0 0.00 0.00 45.46 2.77 R
3303 3405 1.002857 AAGCTCATTAGGGGGTGCTT 58.997 50.0 0.00 0.00 36.16 3.91 R
4285 4593 0.179111 TGTGTCCTCGCGGATTGATC 60.179 55.0 6.13 0.00 42.43 2.92 R
5528 6404 0.968405 TGCTGGTTCCTGGATTTTGC 59.032 50.0 0.00 1.34 0.00 3.68 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
157 161 4.020485 CCTAGTGTTAGTAGGTGGCAACTT 60.020 45.833 11.85 0.00 36.69 2.66
163 167 6.484308 GTGTTAGTAGGTGGCAACTTCTAAAA 59.516 38.462 26.68 21.25 37.61 1.52
195 199 0.674895 GGCAACTGCAGTAGACCAGG 60.675 60.000 22.01 5.19 44.36 4.45
307 311 2.290008 TGTAGTTGTCCGACATGGCAAT 60.290 45.455 1.09 0.00 36.56 3.56
325 329 3.179048 CAATCGTAGTTCAGCGACATGA 58.821 45.455 0.00 0.00 40.03 3.07
396 400 2.736682 GCGCGCGGTAAAGTGTCAT 61.737 57.895 33.06 0.00 0.00 3.06
430 434 0.106167 AGCATGAGGTACGAGGCCTA 60.106 55.000 4.42 0.00 36.29 3.93
539 544 2.888834 ATTCTTTTGCCCACACACAC 57.111 45.000 0.00 0.00 0.00 3.82
540 545 1.550327 TTCTTTTGCCCACACACACA 58.450 45.000 0.00 0.00 0.00 3.72
541 546 1.550327 TCTTTTGCCCACACACACAA 58.450 45.000 0.00 0.00 0.00 3.33
546 551 0.392595 TGCCCACACACACAAACGTA 60.393 50.000 0.00 0.00 0.00 3.57
591 596 0.518636 CAGAACGTGTGGGCAGATTG 59.481 55.000 0.00 0.00 0.00 2.67
621 626 0.315886 ACACGTGTGGCAGTTATCGA 59.684 50.000 22.71 0.00 34.19 3.59
659 664 8.764524 TTTGTAATTTCAAATCCAATAACCCG 57.235 30.769 6.17 0.00 33.23 5.28
660 665 7.704578 TGTAATTTCAAATCCAATAACCCGA 57.295 32.000 0.00 0.00 0.00 5.14
661 666 8.123639 TGTAATTTCAAATCCAATAACCCGAA 57.876 30.769 0.00 0.00 0.00 4.30
662 667 8.754080 TGTAATTTCAAATCCAATAACCCGAAT 58.246 29.630 0.00 0.00 0.00 3.34
663 668 9.030301 GTAATTTCAAATCCAATAACCCGAATG 57.970 33.333 0.00 0.00 0.00 2.67
664 669 6.597832 TTTCAAATCCAATAACCCGAATGT 57.402 33.333 0.00 0.00 0.00 2.71
665 670 5.574891 TCAAATCCAATAACCCGAATGTG 57.425 39.130 0.00 0.00 0.00 3.21
666 671 4.111916 CAAATCCAATAACCCGAATGTGC 58.888 43.478 0.00 0.00 0.00 4.57
667 672 1.757682 TCCAATAACCCGAATGTGCC 58.242 50.000 0.00 0.00 0.00 5.01
668 673 1.004862 TCCAATAACCCGAATGTGCCA 59.995 47.619 0.00 0.00 0.00 4.92
669 674 1.821753 CCAATAACCCGAATGTGCCAA 59.178 47.619 0.00 0.00 0.00 4.52
670 675 2.232452 CCAATAACCCGAATGTGCCAAA 59.768 45.455 0.00 0.00 0.00 3.28
671 676 3.118811 CCAATAACCCGAATGTGCCAAAT 60.119 43.478 0.00 0.00 0.00 2.32
672 677 4.111916 CAATAACCCGAATGTGCCAAATC 58.888 43.478 0.00 0.00 0.00 2.17
673 678 0.894835 AACCCGAATGTGCCAAATCC 59.105 50.000 0.00 0.00 0.00 3.01
674 679 0.251564 ACCCGAATGTGCCAAATCCA 60.252 50.000 0.00 0.00 0.00 3.41
675 680 0.894141 CCCGAATGTGCCAAATCCAA 59.106 50.000 0.00 0.00 0.00 3.53
676 681 1.481772 CCCGAATGTGCCAAATCCAAT 59.518 47.619 0.00 0.00 0.00 3.16
677 682 2.692557 CCCGAATGTGCCAAATCCAATA 59.307 45.455 0.00 0.00 0.00 1.90
678 683 3.131933 CCCGAATGTGCCAAATCCAATAA 59.868 43.478 0.00 0.00 0.00 1.40
679 684 4.382470 CCCGAATGTGCCAAATCCAATAAA 60.382 41.667 0.00 0.00 0.00 1.40
680 685 5.174395 CCGAATGTGCCAAATCCAATAAAA 58.826 37.500 0.00 0.00 0.00 1.52
681 686 5.816777 CCGAATGTGCCAAATCCAATAAAAT 59.183 36.000 0.00 0.00 0.00 1.82
682 687 6.018832 CCGAATGTGCCAAATCCAATAAAATC 60.019 38.462 0.00 0.00 0.00 2.17
683 688 6.018832 CGAATGTGCCAAATCCAATAAAATCC 60.019 38.462 0.00 0.00 0.00 3.01
684 689 5.752036 TGTGCCAAATCCAATAAAATCCA 57.248 34.783 0.00 0.00 0.00 3.41
685 690 6.310764 TGTGCCAAATCCAATAAAATCCAT 57.689 33.333 0.00 0.00 0.00 3.41
686 691 6.114089 TGTGCCAAATCCAATAAAATCCATG 58.886 36.000 0.00 0.00 0.00 3.66
687 692 5.007921 GTGCCAAATCCAATAAAATCCATGC 59.992 40.000 0.00 0.00 0.00 4.06
688 693 5.124645 GCCAAATCCAATAAAATCCATGCA 58.875 37.500 0.00 0.00 0.00 3.96
689 694 5.589452 GCCAAATCCAATAAAATCCATGCAA 59.411 36.000 0.00 0.00 0.00 4.08
690 695 6.458615 GCCAAATCCAATAAAATCCATGCAAC 60.459 38.462 0.00 0.00 0.00 4.17
691 696 6.038492 CCAAATCCAATAAAATCCATGCAACC 59.962 38.462 0.00 0.00 0.00 3.77
692 697 6.564557 AATCCAATAAAATCCATGCAACCT 57.435 33.333 0.00 0.00 0.00 3.50
693 698 7.673641 AATCCAATAAAATCCATGCAACCTA 57.326 32.000 0.00 0.00 0.00 3.08
694 699 7.673641 ATCCAATAAAATCCATGCAACCTAA 57.326 32.000 0.00 0.00 0.00 2.69
695 700 7.487822 TCCAATAAAATCCATGCAACCTAAA 57.512 32.000 0.00 0.00 0.00 1.85
696 701 7.555087 TCCAATAAAATCCATGCAACCTAAAG 58.445 34.615 0.00 0.00 0.00 1.85
697 702 7.398618 TCCAATAAAATCCATGCAACCTAAAGA 59.601 33.333 0.00 0.00 0.00 2.52
698 703 8.206189 CCAATAAAATCCATGCAACCTAAAGAT 58.794 33.333 0.00 0.00 0.00 2.40
701 706 6.396829 AAATCCATGCAACCTAAAGATAGC 57.603 37.500 0.00 0.00 0.00 2.97
702 707 3.820557 TCCATGCAACCTAAAGATAGCC 58.179 45.455 0.00 0.00 0.00 3.93
703 708 3.201930 TCCATGCAACCTAAAGATAGCCA 59.798 43.478 0.00 0.00 0.00 4.75
704 709 3.953612 CCATGCAACCTAAAGATAGCCAA 59.046 43.478 0.00 0.00 0.00 4.52
705 710 4.037208 CCATGCAACCTAAAGATAGCCAAG 59.963 45.833 0.00 0.00 0.00 3.61
706 711 4.301072 TGCAACCTAAAGATAGCCAAGT 57.699 40.909 0.00 0.00 0.00 3.16
707 712 4.662278 TGCAACCTAAAGATAGCCAAGTT 58.338 39.130 0.00 0.00 0.00 2.66
708 713 5.076873 TGCAACCTAAAGATAGCCAAGTTT 58.923 37.500 0.00 0.00 0.00 2.66
709 714 5.538433 TGCAACCTAAAGATAGCCAAGTTTT 59.462 36.000 0.00 0.00 0.00 2.43
710 715 5.863935 GCAACCTAAAGATAGCCAAGTTTTG 59.136 40.000 0.00 0.00 0.00 2.44
711 716 6.516693 GCAACCTAAAGATAGCCAAGTTTTGT 60.517 38.462 0.00 0.00 0.00 2.83
712 717 6.575162 ACCTAAAGATAGCCAAGTTTTGTG 57.425 37.500 0.00 0.00 0.00 3.33
713 718 6.303839 ACCTAAAGATAGCCAAGTTTTGTGA 58.696 36.000 0.00 0.00 0.00 3.58
714 719 6.431234 ACCTAAAGATAGCCAAGTTTTGTGAG 59.569 38.462 0.00 0.00 0.00 3.51
715 720 4.773323 AAGATAGCCAAGTTTTGTGAGC 57.227 40.909 0.00 0.00 0.00 4.26
716 721 4.026356 AGATAGCCAAGTTTTGTGAGCT 57.974 40.909 0.00 0.00 0.00 4.09
717 722 3.755378 AGATAGCCAAGTTTTGTGAGCTG 59.245 43.478 0.00 0.00 0.00 4.24
718 723 1.767759 AGCCAAGTTTTGTGAGCTGT 58.232 45.000 0.00 0.00 0.00 4.40
719 724 1.406539 AGCCAAGTTTTGTGAGCTGTG 59.593 47.619 0.00 0.00 0.00 3.66
720 725 1.536709 GCCAAGTTTTGTGAGCTGTGG 60.537 52.381 0.00 0.00 0.00 4.17
721 726 1.536709 CCAAGTTTTGTGAGCTGTGGC 60.537 52.381 0.00 0.00 39.06 5.01
722 727 1.134753 CAAGTTTTGTGAGCTGTGGCA 59.865 47.619 0.00 0.00 41.70 4.92
723 728 0.740737 AGTTTTGTGAGCTGTGGCAC 59.259 50.000 11.55 11.55 41.70 5.01
724 729 0.249031 GTTTTGTGAGCTGTGGCACC 60.249 55.000 16.26 0.00 41.70 5.01
725 730 0.682532 TTTTGTGAGCTGTGGCACCA 60.683 50.000 16.26 2.32 41.70 4.17
726 731 0.682532 TTTGTGAGCTGTGGCACCAA 60.683 50.000 16.26 7.89 41.70 3.67
727 732 0.682532 TTGTGAGCTGTGGCACCAAA 60.683 50.000 16.26 0.00 41.70 3.28
728 733 1.360192 GTGAGCTGTGGCACCAAAC 59.640 57.895 16.26 5.18 41.70 2.93
729 734 1.077140 TGAGCTGTGGCACCAAACA 60.077 52.632 16.26 7.80 41.70 2.83
730 735 0.467844 TGAGCTGTGGCACCAAACAT 60.468 50.000 16.26 0.00 41.70 2.71
731 736 0.038892 GAGCTGTGGCACCAAACATG 60.039 55.000 16.26 0.00 41.70 3.21
732 737 0.467844 AGCTGTGGCACCAAACATGA 60.468 50.000 16.26 0.00 41.70 3.07
733 738 0.604578 GCTGTGGCACCAAACATGAT 59.395 50.000 16.26 0.00 38.54 2.45
734 739 1.403249 GCTGTGGCACCAAACATGATC 60.403 52.381 16.26 0.00 38.54 2.92
735 740 1.887854 CTGTGGCACCAAACATGATCA 59.112 47.619 16.26 0.00 0.00 2.92
736 741 2.296752 CTGTGGCACCAAACATGATCAA 59.703 45.455 16.26 0.00 0.00 2.57
743 748 6.817641 TGGCACCAAACATGATCAATAAAATC 59.182 34.615 0.00 0.00 0.00 2.17
766 771 4.800784 TGCCACCGCTAAGTTTTATTTTC 58.199 39.130 0.00 0.00 35.36 2.29
767 772 4.521256 TGCCACCGCTAAGTTTTATTTTCT 59.479 37.500 0.00 0.00 35.36 2.52
769 774 6.207025 TGCCACCGCTAAGTTTTATTTTCTAA 59.793 34.615 0.00 0.00 35.36 2.10
770 775 7.094118 TGCCACCGCTAAGTTTTATTTTCTAAT 60.094 33.333 0.00 0.00 35.36 1.73
771 776 7.431376 GCCACCGCTAAGTTTTATTTTCTAATC 59.569 37.037 0.00 0.00 0.00 1.75
773 778 8.455682 CACCGCTAAGTTTTATTTTCTAATCCA 58.544 33.333 0.00 0.00 0.00 3.41
844 853 4.868450 TGGCCGAAATTTATACACGAAG 57.132 40.909 0.00 0.00 0.00 3.79
875 884 3.111442 GCGGGCGCATTTGTTTGG 61.111 61.111 10.83 0.00 41.49 3.28
876 885 2.338257 CGGGCGCATTTGTTTGGT 59.662 55.556 10.83 0.00 0.00 3.67
877 886 1.732683 CGGGCGCATTTGTTTGGTC 60.733 57.895 10.83 0.00 0.00 4.02
878 887 1.365633 GGGCGCATTTGTTTGGTCA 59.634 52.632 10.83 0.00 0.00 4.02
879 888 0.667184 GGGCGCATTTGTTTGGTCAG 60.667 55.000 10.83 0.00 0.00 3.51
880 889 0.313672 GGCGCATTTGTTTGGTCAGA 59.686 50.000 10.83 0.00 0.00 3.27
881 890 1.269517 GGCGCATTTGTTTGGTCAGAA 60.270 47.619 10.83 0.00 0.00 3.02
882 891 2.610232 GGCGCATTTGTTTGGTCAGAAT 60.610 45.455 10.83 0.00 0.00 2.40
883 892 3.366883 GGCGCATTTGTTTGGTCAGAATA 60.367 43.478 10.83 0.00 0.00 1.75
884 893 3.608073 GCGCATTTGTTTGGTCAGAATAC 59.392 43.478 0.30 0.00 0.00 1.89
886 895 3.608073 GCATTTGTTTGGTCAGAATACGC 59.392 43.478 0.00 0.00 0.00 4.42
888 897 1.816074 TGTTTGGTCAGAATACGCCC 58.184 50.000 0.00 0.00 0.00 6.13
890 899 0.322322 TTTGGTCAGAATACGCCCGT 59.678 50.000 0.00 0.00 0.00 5.28
892 901 0.968901 TGGTCAGAATACGCCCGTCT 60.969 55.000 0.00 0.00 0.00 4.18
893 902 0.527817 GGTCAGAATACGCCCGTCTG 60.528 60.000 0.00 0.00 40.15 3.51
896 905 0.384309 CAGAATACGCCCGTCTGCTA 59.616 55.000 0.00 0.00 32.96 3.49
897 906 0.669077 AGAATACGCCCGTCTGCTAG 59.331 55.000 0.00 0.00 0.00 3.42
898 907 0.318784 GAATACGCCCGTCTGCTAGG 60.319 60.000 0.00 0.00 0.00 3.02
899 908 2.365095 AATACGCCCGTCTGCTAGGC 62.365 60.000 0.00 0.00 43.53 3.93
903 912 3.217017 CCCGTCTGCTAGGCGCTA 61.217 66.667 7.64 0.00 42.90 4.26
904 913 2.333225 CCGTCTGCTAGGCGCTAG 59.667 66.667 7.64 8.43 42.90 3.42
920 930 3.659089 TAGCCGCTCCGTTGCCTTC 62.659 63.158 0.00 0.00 0.00 3.46
925 935 1.743252 GCTCCGTTGCCTTCCTCTG 60.743 63.158 0.00 0.00 0.00 3.35
996 1006 1.157870 CGATTCCAATCCGAACCCCG 61.158 60.000 0.00 0.00 38.18 5.73
1070 1080 3.203412 CGACCTCCTCGAGTCCGG 61.203 72.222 12.31 10.68 46.14 5.14
1269 1279 3.787001 CTTCTCCCGCTCCACCCC 61.787 72.222 0.00 0.00 0.00 4.95
1332 1342 1.475213 CCCAACTATTCGCTCCCCTTC 60.475 57.143 0.00 0.00 0.00 3.46
1418 1428 0.899720 AATTCCACCAGCAATGGCAG 59.100 50.000 0.00 0.00 44.61 4.85
1458 1468 0.175989 GGAATCTCGGGAGTGACCAC 59.824 60.000 0.00 0.00 41.20 4.16
1461 1471 4.436998 CTCGGGAGTGACCACGGC 62.437 72.222 0.00 0.00 41.20 5.68
1505 1515 6.641169 TGTGAGTCGCATTCTAGAGAATAT 57.359 37.500 1.22 0.00 42.41 1.28
1514 1524 4.881019 TTCTAGAGAATATGGAGCAGGC 57.119 45.455 0.00 0.00 0.00 4.85
1532 1542 1.153489 CCAGTGAGACCAGCGATGG 60.153 63.158 20.26 20.26 0.00 3.51
1557 1567 4.047059 CACCTTGCGCTTGCTGGG 62.047 66.667 9.73 4.20 40.12 4.45
1561 1571 1.588082 CTTGCGCTTGCTGGGATTT 59.412 52.632 9.73 0.00 40.12 2.17
1599 1609 0.809385 CAGATGAGCTGCACTTTGGG 59.191 55.000 1.02 0.00 37.90 4.12
1655 1665 0.180406 ATCGGGGATGTAGGTGTTGC 59.820 55.000 0.00 0.00 0.00 4.17
1659 1669 1.679032 GGGGATGTAGGTGTTGCTGTC 60.679 57.143 0.00 0.00 0.00 3.51
1860 1870 1.072331 AGACATCGGTTGGACTTTGCT 59.928 47.619 0.00 0.00 0.00 3.91
1915 1925 3.907260 TTTGCAGCTCGGAGGGCAG 62.907 63.158 7.20 0.00 37.59 4.85
1931 1941 1.524482 CAGCTGTAGAAGGGAGGCC 59.476 63.158 5.25 0.00 0.00 5.19
1947 1957 2.593134 GCCTGACGATGATCAGCGC 61.593 63.158 31.44 23.37 45.05 5.92
2001 2011 4.015406 CAGTGTGGGCCGGTAGCA 62.015 66.667 1.90 0.00 46.50 3.49
2064 2074 0.686112 AGGAGCTCCTTCCTCTTCCG 60.686 60.000 30.40 0.00 46.09 4.30
2067 2077 2.202810 CTCCTTCCTCTTCCGCGC 60.203 66.667 0.00 0.00 0.00 6.86
2118 2128 1.542915 GGAAATTCAGCTGAGCTTGCA 59.457 47.619 17.43 0.54 36.40 4.08
2136 2146 2.490509 TGCAAAGAATCAGGTCATGCAG 59.509 45.455 0.00 0.00 37.56 4.41
2179 2189 1.073897 GAAGCAGGGCCAGTGACTT 59.926 57.895 6.18 9.15 0.00 3.01
2232 2242 8.763356 GCTGATGAGAAGACTAAAGATTATGTG 58.237 37.037 0.00 0.00 0.00 3.21
2263 2273 4.271049 GTGTATGTGAATATGCGCAAGAGT 59.729 41.667 17.11 4.34 43.02 3.24
2532 2542 2.052237 CGGCGTGCTGTTGTTGTC 60.052 61.111 0.00 0.00 0.00 3.18
2707 2717 6.202570 GCTTGCAACTGTTGATTAAAATGGAA 59.797 34.615 23.81 1.22 0.00 3.53
2773 2784 3.802948 ATCTGTTACACGGATGAGGTC 57.197 47.619 0.00 0.00 42.31 3.85
2823 2834 5.058490 GCGGGTTATGCCTACTTGTATTAA 58.942 41.667 0.00 0.00 37.43 1.40
2827 2838 6.709397 GGGTTATGCCTACTTGTATTAACCTC 59.291 42.308 8.39 0.00 35.89 3.85
2872 2883 7.769044 CGGGATAAATTATCTCCGGTCATATTT 59.231 37.037 23.26 5.56 41.32 1.40
2873 2884 9.462606 GGGATAAATTATCTCCGGTCATATTTT 57.537 33.333 12.19 10.08 35.52 1.82
2983 3077 0.258774 GCTTCCCTATTTGGCCCTGA 59.741 55.000 0.00 0.00 0.00 3.86
3037 3133 8.008332 TCTAAATTTCTTCCTGGGGTAAAACTT 58.992 33.333 0.00 0.00 0.00 2.66
3046 3142 5.958987 TCCTGGGGTAAAACTTTCTTTTCAA 59.041 36.000 0.00 0.00 0.00 2.69
3064 3160 4.222124 TCAATTCTCACTTAAGGGCCTC 57.778 45.455 6.46 0.00 0.00 4.70
3118 3215 3.274288 GGAGCAAATTCACCTAGGAGTG 58.726 50.000 17.98 4.10 39.20 3.51
3180 3281 7.729116 TCCAGCTTCAAGAATGAGAAAATTTT 58.271 30.769 2.28 2.28 36.78 1.82
3186 3287 7.123355 TCAAGAATGAGAAAATTTTGTGGGT 57.877 32.000 8.47 0.00 0.00 4.51
3247 3348 1.479323 GGCGTATCCACTTACTGGTGA 59.521 52.381 0.00 0.00 41.52 4.02
3283 3385 2.663196 CCCAACTCCACGAGGACC 59.337 66.667 0.00 0.00 39.61 4.46
3284 3386 1.913762 CCCAACTCCACGAGGACCT 60.914 63.158 0.00 0.00 39.61 3.85
3291 3393 2.372172 ACTCCACGAGGACCTTTTGAAT 59.628 45.455 0.00 0.00 39.61 2.57
3303 3405 8.533569 AGGACCTTTTGAATTAGAGTTTTTGA 57.466 30.769 0.00 0.00 0.00 2.69
3312 3414 1.704641 AGAGTTTTTGAAGCACCCCC 58.295 50.000 0.00 0.00 0.00 5.40
3314 3416 2.445525 AGAGTTTTTGAAGCACCCCCTA 59.554 45.455 0.00 0.00 0.00 3.53
3316 3418 3.832490 GAGTTTTTGAAGCACCCCCTAAT 59.168 43.478 0.00 0.00 0.00 1.73
3441 3547 2.158519 CCCAAACGGGCCCTTAATATCT 60.159 50.000 22.43 0.00 36.72 1.98
3448 3554 6.752285 ACGGGCCCTTAATATCTTTAGTAA 57.248 37.500 22.43 0.00 0.00 2.24
3451 3557 6.464749 CGGGCCCTTAATATCTTTAGTAACCA 60.465 42.308 22.43 0.00 0.00 3.67
3452 3558 7.467650 GGGCCCTTAATATCTTTAGTAACCAT 58.532 38.462 17.04 0.00 0.00 3.55
3453 3559 8.608598 GGGCCCTTAATATCTTTAGTAACCATA 58.391 37.037 17.04 0.00 0.00 2.74
3480 3586 6.971726 ATTGACGGTAGTATCACATTAGGA 57.028 37.500 0.00 0.00 0.00 2.94
3481 3587 6.778834 TTGACGGTAGTATCACATTAGGAA 57.221 37.500 0.00 0.00 0.00 3.36
3482 3588 6.778834 TGACGGTAGTATCACATTAGGAAA 57.221 37.500 0.00 0.00 0.00 3.13
3542 3648 2.050918 GGGTTAGGATTGAGAGAGGGG 58.949 57.143 0.00 0.00 0.00 4.79
3569 3876 2.295349 GTCCGAGCGTCAAATAGGGATA 59.705 50.000 0.00 0.00 0.00 2.59
3595 3902 0.253630 TCAGGGCCAAATAGGGAGGT 60.254 55.000 6.18 0.00 38.09 3.85
3648 3955 7.880160 TTCTCTCTTTGTTTTTCTCATTGGA 57.120 32.000 0.00 0.00 0.00 3.53
3711 4018 9.787532 ATGCAATTTGTTAGATACATACAACAC 57.212 29.630 0.00 0.00 36.44 3.32
3840 4147 9.956640 CTTGCCTTTGATTATATTAGGAGATCT 57.043 33.333 0.00 0.00 0.00 2.75
3869 4176 7.050970 AGGTAGTTCATTCAAAACCCTTTTC 57.949 36.000 0.00 0.00 0.00 2.29
3870 4177 6.609616 AGGTAGTTCATTCAAAACCCTTTTCA 59.390 34.615 0.00 0.00 0.00 2.69
3871 4178 7.290014 AGGTAGTTCATTCAAAACCCTTTTCAT 59.710 33.333 0.00 0.00 0.00 2.57
3872 4179 8.581578 GGTAGTTCATTCAAAACCCTTTTCATA 58.418 33.333 0.00 0.00 0.00 2.15
3976 4283 1.291132 GGATTAGCGTCAGGAGTTGC 58.709 55.000 0.00 0.00 0.00 4.17
4165 4472 1.712977 CTGCGGCTCATCTTCCTTGC 61.713 60.000 0.00 0.00 0.00 4.01
4195 4502 5.674525 TCAGGTAAGCTAAGATCACAATGG 58.325 41.667 0.00 0.00 0.00 3.16
4285 4593 7.446319 TCCTTTATGACATTCAGAATATGGCTG 59.554 37.037 0.00 0.00 32.07 4.85
4339 4648 3.635373 CCCAATAGCAGAGACATTGCAAT 59.365 43.478 5.99 5.99 43.92 3.56
4352 4661 7.068348 AGAGACATTGCAATCATCATTAGCTTT 59.932 33.333 9.53 0.00 0.00 3.51
4378 4687 3.270027 CCCTGTCGAGTATTTTCATGCA 58.730 45.455 0.00 0.00 0.00 3.96
4404 4717 8.263640 ACTGACTTGATTGCTATAAAGATGAGT 58.736 33.333 11.71 7.27 0.00 3.41
4420 4733 2.619931 TGAGTCTTGGACCATTGGAGA 58.380 47.619 10.37 0.00 32.18 3.71
4426 4739 4.337555 GTCTTGGACCATTGGAGATTGATG 59.662 45.833 10.37 0.00 0.00 3.07
4430 4743 5.085920 TGGACCATTGGAGATTGATGTTTT 58.914 37.500 10.37 0.00 0.00 2.43
4457 4771 5.842328 AGCCCAAATCACATTATTCCATGAT 59.158 36.000 0.00 0.00 33.18 2.45
4496 4810 2.096248 GCACTGCTACCTGTAGAGACT 58.904 52.381 8.48 0.00 35.21 3.24
4587 4901 0.953960 GGCGGAATTTGTCACCTCGT 60.954 55.000 0.00 0.00 0.00 4.18
4646 4960 2.807622 GCCCATGTTGCGGAATCC 59.192 61.111 0.00 0.00 0.00 3.01
4804 5118 3.659786 ACAGAACTATTGCACGCTTGTA 58.340 40.909 0.00 0.00 0.00 2.41
4828 5142 3.937079 CACTATCTTGCTCATGCTTGTCA 59.063 43.478 0.00 0.00 40.48 3.58
4902 5220 4.332543 GCATGTTGCAAGTATAGTACTGCA 59.667 41.667 5.39 3.12 44.26 4.41
4914 5233 9.672673 AAGTATAGTACTGCATTTTCATCTTGT 57.327 29.630 5.39 0.00 39.39 3.16
4918 5237 7.458409 AGTACTGCATTTTCATCTTGTCATT 57.542 32.000 0.00 0.00 0.00 2.57
4922 5241 7.833786 ACTGCATTTTCATCTTGTCATTATGT 58.166 30.769 0.00 0.00 0.00 2.29
4924 5243 8.058667 TGCATTTTCATCTTGTCATTATGTCT 57.941 30.769 0.00 0.00 0.00 3.41
4929 5248 9.500785 TTTTCATCTTGTCATTATGTCTGTACA 57.499 29.630 0.00 0.00 40.69 2.90
5009 5328 8.922058 AGATTTAATGATTCATGTTGCTTGAC 57.078 30.769 0.00 0.00 0.00 3.18
5044 5363 0.620556 GGACATCTCCAGCCAAAGGA 59.379 55.000 0.00 0.00 36.42 3.36
5062 5381 3.947868 AGGATGATCCATGCTAAATCCG 58.052 45.455 14.90 0.00 40.60 4.18
5087 5406 7.518211 CGAACACAAATCAAGTTGAGATACACA 60.518 37.037 11.91 0.00 32.59 3.72
5141 5742 7.595819 AGGAAGATTCAGTTATCTCCAGTAG 57.404 40.000 0.00 0.00 33.81 2.57
5142 5743 7.129425 AGGAAGATTCAGTTATCTCCAGTAGT 58.871 38.462 0.00 0.00 33.81 2.73
5227 5828 8.921205 AGAGGGGATAAAAATCAATGATCAAAG 58.079 33.333 0.00 0.00 0.00 2.77
5230 5831 8.699130 GGGGATAAAAATCAATGATCAAAGACT 58.301 33.333 0.00 0.00 0.00 3.24
5277 5878 1.590238 GAGAAATGCCAGATCACGTCG 59.410 52.381 0.00 0.00 0.00 5.12
5283 5884 1.920051 CCAGATCACGTCGCAATCG 59.080 57.895 0.00 0.00 0.00 3.34
5346 6221 6.808829 TCATTTCTGGTAAATACGACGGTAT 58.191 36.000 0.00 0.00 41.09 2.73
5376 6252 5.368145 GTGCCTATTCATGACATTAGACCA 58.632 41.667 0.00 0.00 0.00 4.02
5427 6303 0.255890 CCAGGGGTGAGGTTATGTGG 59.744 60.000 0.00 0.00 0.00 4.17
5435 6311 0.447801 GAGGTTATGTGGCTGCAACG 59.552 55.000 2.19 0.00 0.00 4.10
5492 6368 1.067915 GGCTACGAAATGGCAAAGCAA 60.068 47.619 0.00 0.00 36.24 3.91
5528 6404 5.233902 CGCTCAAATCCTCATCTACTGAAAG 59.766 44.000 0.00 0.00 42.29 2.62
5615 6494 5.804771 GCAGGTAAATCTATCCCAATCCTCC 60.805 48.000 0.00 0.00 0.00 4.30
5623 6502 2.068834 TCCCAATCCTCCTCTACGAC 57.931 55.000 0.00 0.00 0.00 4.34
5702 6581 3.181521 TGCAATAAATCGAGCGTGTCAAG 60.182 43.478 0.00 0.00 0.00 3.02
5708 6587 5.643339 AAATCGAGCGTGTCAAGAATATC 57.357 39.130 0.00 0.00 0.00 1.63
5724 6603 5.128919 AGAATATCGCAAAATGCTTCCTCT 58.871 37.500 0.43 0.00 42.25 3.69
5737 6616 3.118542 GCTTCCTCTGCAAGTTTTTGTG 58.881 45.455 0.00 0.00 36.65 3.33
5752 6631 3.342377 TTTGTGGGAACGAGATGCATA 57.658 42.857 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 161 8.991026 CAGTTGCCATGATTTCAAAATTTTAGA 58.009 29.630 2.44 1.38 0.00 2.10
163 167 4.643463 TGCAGTTGCCATGATTTCAAAAT 58.357 34.783 1.06 0.00 41.18 1.82
307 311 1.538075 TGTCATGTCGCTGAACTACGA 59.462 47.619 0.00 0.00 35.62 3.43
325 329 4.497340 CCATGTTCGTTTAAGTGCAGTTGT 60.497 41.667 17.21 0.00 0.00 3.32
376 380 4.675029 ACACTTTACCGCGCGCCT 62.675 61.111 27.36 14.24 0.00 5.52
415 419 0.322816 ACGTTAGGCCTCGTACCTCA 60.323 55.000 17.20 0.00 38.81 3.86
512 517 0.817654 GGGCAAAAGAATTAGCGCCT 59.182 50.000 2.29 0.00 39.53 5.52
523 528 1.999024 GTTTGTGTGTGTGGGCAAAAG 59.001 47.619 0.00 0.00 33.43 2.27
539 544 0.035439 AGGACCAGCCCATACGTTTG 60.035 55.000 0.00 0.00 37.37 2.93
540 545 0.252197 GAGGACCAGCCCATACGTTT 59.748 55.000 0.00 0.00 37.37 3.60
541 546 0.617820 AGAGGACCAGCCCATACGTT 60.618 55.000 0.00 0.00 37.37 3.99
546 551 1.348775 GCCTAAGAGGACCAGCCCAT 61.349 60.000 0.00 0.00 37.67 4.00
591 596 2.248835 ACACGTGTGGGCGTTAAGC 61.249 57.895 22.71 0.00 43.83 3.09
636 641 7.704578 TCGGGTTATTGGATTTGAAATTACA 57.295 32.000 0.00 0.00 0.00 2.41
637 642 9.030301 CATTCGGGTTATTGGATTTGAAATTAC 57.970 33.333 0.00 0.00 0.00 1.89
638 643 8.754080 ACATTCGGGTTATTGGATTTGAAATTA 58.246 29.630 0.00 0.00 0.00 1.40
639 644 7.548780 CACATTCGGGTTATTGGATTTGAAATT 59.451 33.333 0.00 0.00 0.00 1.82
640 645 7.041107 CACATTCGGGTTATTGGATTTGAAAT 58.959 34.615 0.00 0.00 0.00 2.17
641 646 6.393990 CACATTCGGGTTATTGGATTTGAAA 58.606 36.000 0.00 0.00 0.00 2.69
642 647 5.623368 GCACATTCGGGTTATTGGATTTGAA 60.623 40.000 0.00 0.00 0.00 2.69
643 648 4.142271 GCACATTCGGGTTATTGGATTTGA 60.142 41.667 0.00 0.00 0.00 2.69
644 649 4.111916 GCACATTCGGGTTATTGGATTTG 58.888 43.478 0.00 0.00 0.00 2.32
645 650 3.132111 GGCACATTCGGGTTATTGGATTT 59.868 43.478 0.00 0.00 0.00 2.17
646 651 2.693074 GGCACATTCGGGTTATTGGATT 59.307 45.455 0.00 0.00 0.00 3.01
647 652 2.306847 GGCACATTCGGGTTATTGGAT 58.693 47.619 0.00 0.00 0.00 3.41
648 653 1.004862 TGGCACATTCGGGTTATTGGA 59.995 47.619 0.00 0.00 0.00 3.53
649 654 1.468985 TGGCACATTCGGGTTATTGG 58.531 50.000 0.00 0.00 0.00 3.16
650 655 3.584406 TTTGGCACATTCGGGTTATTG 57.416 42.857 0.00 0.00 39.30 1.90
651 656 3.132111 GGATTTGGCACATTCGGGTTATT 59.868 43.478 0.00 0.00 39.30 1.40
652 657 2.693074 GGATTTGGCACATTCGGGTTAT 59.307 45.455 0.00 0.00 39.30 1.89
653 658 2.096248 GGATTTGGCACATTCGGGTTA 58.904 47.619 0.00 0.00 39.30 2.85
654 659 0.894835 GGATTTGGCACATTCGGGTT 59.105 50.000 0.00 0.00 39.30 4.11
655 660 0.251564 TGGATTTGGCACATTCGGGT 60.252 50.000 0.00 0.00 39.30 5.28
656 661 0.894141 TTGGATTTGGCACATTCGGG 59.106 50.000 0.00 0.00 39.30 5.14
657 662 2.965572 ATTGGATTTGGCACATTCGG 57.034 45.000 0.00 0.00 39.30 4.30
658 663 6.018832 GGATTTTATTGGATTTGGCACATTCG 60.019 38.462 0.00 0.00 39.30 3.34
659 664 6.822676 TGGATTTTATTGGATTTGGCACATTC 59.177 34.615 0.00 0.00 39.30 2.67
660 665 6.719301 TGGATTTTATTGGATTTGGCACATT 58.281 32.000 0.00 0.00 39.30 2.71
661 666 6.310764 TGGATTTTATTGGATTTGGCACAT 57.689 33.333 0.00 0.00 39.30 3.21
662 667 5.752036 TGGATTTTATTGGATTTGGCACA 57.248 34.783 0.00 0.00 0.00 4.57
663 668 5.007921 GCATGGATTTTATTGGATTTGGCAC 59.992 40.000 0.00 0.00 0.00 5.01
664 669 5.124645 GCATGGATTTTATTGGATTTGGCA 58.875 37.500 0.00 0.00 0.00 4.92
665 670 5.124645 TGCATGGATTTTATTGGATTTGGC 58.875 37.500 0.00 0.00 0.00 4.52
666 671 6.038492 GGTTGCATGGATTTTATTGGATTTGG 59.962 38.462 0.00 0.00 0.00 3.28
667 672 6.824704 AGGTTGCATGGATTTTATTGGATTTG 59.175 34.615 0.00 0.00 0.00 2.32
668 673 6.961042 AGGTTGCATGGATTTTATTGGATTT 58.039 32.000 0.00 0.00 0.00 2.17
669 674 6.564557 AGGTTGCATGGATTTTATTGGATT 57.435 33.333 0.00 0.00 0.00 3.01
670 675 7.673641 TTAGGTTGCATGGATTTTATTGGAT 57.326 32.000 0.00 0.00 0.00 3.41
671 676 7.398618 TCTTTAGGTTGCATGGATTTTATTGGA 59.601 33.333 0.00 0.00 0.00 3.53
672 677 7.555087 TCTTTAGGTTGCATGGATTTTATTGG 58.445 34.615 0.00 0.00 0.00 3.16
675 680 8.579863 GCTATCTTTAGGTTGCATGGATTTTAT 58.420 33.333 0.00 0.00 0.00 1.40
676 681 7.014230 GGCTATCTTTAGGTTGCATGGATTTTA 59.986 37.037 0.00 0.00 0.00 1.52
677 682 6.183360 GGCTATCTTTAGGTTGCATGGATTTT 60.183 38.462 0.00 0.00 0.00 1.82
678 683 5.302823 GGCTATCTTTAGGTTGCATGGATTT 59.697 40.000 0.00 0.00 0.00 2.17
679 684 4.829492 GGCTATCTTTAGGTTGCATGGATT 59.171 41.667 0.00 0.00 0.00 3.01
680 685 4.141181 TGGCTATCTTTAGGTTGCATGGAT 60.141 41.667 0.00 0.00 0.00 3.41
681 686 3.201930 TGGCTATCTTTAGGTTGCATGGA 59.798 43.478 0.00 0.00 0.00 3.41
682 687 3.554934 TGGCTATCTTTAGGTTGCATGG 58.445 45.455 0.00 0.00 0.00 3.66
683 688 4.641989 ACTTGGCTATCTTTAGGTTGCATG 59.358 41.667 0.00 0.00 0.00 4.06
684 689 4.860022 ACTTGGCTATCTTTAGGTTGCAT 58.140 39.130 0.00 0.00 0.00 3.96
685 690 4.301072 ACTTGGCTATCTTTAGGTTGCA 57.699 40.909 0.00 0.00 0.00 4.08
686 691 5.644977 AAACTTGGCTATCTTTAGGTTGC 57.355 39.130 0.00 0.00 0.00 4.17
687 692 6.863126 CACAAAACTTGGCTATCTTTAGGTTG 59.137 38.462 0.00 0.00 34.12 3.77
688 693 6.775629 TCACAAAACTTGGCTATCTTTAGGTT 59.224 34.615 0.00 0.00 34.12 3.50
689 694 6.303839 TCACAAAACTTGGCTATCTTTAGGT 58.696 36.000 0.00 0.00 34.12 3.08
690 695 6.623767 GCTCACAAAACTTGGCTATCTTTAGG 60.624 42.308 0.00 0.00 34.12 2.69
691 696 6.150140 AGCTCACAAAACTTGGCTATCTTTAG 59.850 38.462 0.00 0.00 34.12 1.85
692 697 6.003950 AGCTCACAAAACTTGGCTATCTTTA 58.996 36.000 0.00 0.00 34.12 1.85
693 698 4.829492 AGCTCACAAAACTTGGCTATCTTT 59.171 37.500 0.00 0.00 34.12 2.52
694 699 4.217118 CAGCTCACAAAACTTGGCTATCTT 59.783 41.667 0.00 0.00 34.12 2.40
695 700 3.755378 CAGCTCACAAAACTTGGCTATCT 59.245 43.478 0.00 0.00 34.12 1.98
696 701 3.503748 ACAGCTCACAAAACTTGGCTATC 59.496 43.478 0.00 0.00 34.12 2.08
697 702 3.254166 CACAGCTCACAAAACTTGGCTAT 59.746 43.478 0.00 0.00 34.12 2.97
698 703 2.618241 CACAGCTCACAAAACTTGGCTA 59.382 45.455 0.00 0.00 34.12 3.93
699 704 1.406539 CACAGCTCACAAAACTTGGCT 59.593 47.619 0.00 0.00 34.12 4.75
700 705 1.536709 CCACAGCTCACAAAACTTGGC 60.537 52.381 0.00 0.00 34.12 4.52
701 706 1.536709 GCCACAGCTCACAAAACTTGG 60.537 52.381 0.00 0.00 35.50 3.61
702 707 1.134753 TGCCACAGCTCACAAAACTTG 59.865 47.619 0.00 0.00 40.80 3.16
703 708 1.134946 GTGCCACAGCTCACAAAACTT 59.865 47.619 0.00 0.00 40.80 2.66
704 709 0.740737 GTGCCACAGCTCACAAAACT 59.259 50.000 0.00 0.00 40.80 2.66
705 710 0.249031 GGTGCCACAGCTCACAAAAC 60.249 55.000 0.00 0.00 40.80 2.43
706 711 0.682532 TGGTGCCACAGCTCACAAAA 60.683 50.000 0.00 0.00 40.80 2.44
707 712 0.682532 TTGGTGCCACAGCTCACAAA 60.683 50.000 0.00 0.00 40.80 2.83
708 713 0.682532 TTTGGTGCCACAGCTCACAA 60.683 50.000 0.00 0.00 40.80 3.33
709 714 1.077140 TTTGGTGCCACAGCTCACA 60.077 52.632 0.00 0.00 40.80 3.58
710 715 1.360192 GTTTGGTGCCACAGCTCAC 59.640 57.895 0.00 0.00 40.80 3.51
711 716 0.467844 ATGTTTGGTGCCACAGCTCA 60.468 50.000 0.00 0.00 40.80 4.26
712 717 0.038892 CATGTTTGGTGCCACAGCTC 60.039 55.000 0.00 0.00 40.80 4.09
713 718 0.467844 TCATGTTTGGTGCCACAGCT 60.468 50.000 0.00 0.00 40.80 4.24
714 719 0.604578 ATCATGTTTGGTGCCACAGC 59.395 50.000 0.00 0.00 40.48 4.40
715 720 1.887854 TGATCATGTTTGGTGCCACAG 59.112 47.619 0.00 0.00 0.00 3.66
716 721 1.992538 TGATCATGTTTGGTGCCACA 58.007 45.000 0.00 0.00 0.00 4.17
717 722 3.598019 ATTGATCATGTTTGGTGCCAC 57.402 42.857 0.00 0.00 0.00 5.01
718 723 5.735285 TTTATTGATCATGTTTGGTGCCA 57.265 34.783 0.00 0.00 0.00 4.92
719 724 7.010738 CAGATTTTATTGATCATGTTTGGTGCC 59.989 37.037 0.00 0.00 0.00 5.01
720 725 7.464977 GCAGATTTTATTGATCATGTTTGGTGC 60.465 37.037 0.00 0.00 0.00 5.01
721 726 7.010738 GGCAGATTTTATTGATCATGTTTGGTG 59.989 37.037 0.00 0.00 0.00 4.17
722 727 7.043565 GGCAGATTTTATTGATCATGTTTGGT 58.956 34.615 0.00 0.00 0.00 3.67
723 728 7.010738 GTGGCAGATTTTATTGATCATGTTTGG 59.989 37.037 0.00 0.00 0.00 3.28
724 729 7.010738 GGTGGCAGATTTTATTGATCATGTTTG 59.989 37.037 0.00 0.00 0.00 2.93
725 730 7.043565 GGTGGCAGATTTTATTGATCATGTTT 58.956 34.615 0.00 0.00 0.00 2.83
726 731 6.576185 GGTGGCAGATTTTATTGATCATGTT 58.424 36.000 0.00 0.00 0.00 2.71
727 732 5.221106 CGGTGGCAGATTTTATTGATCATGT 60.221 40.000 0.00 0.00 0.00 3.21
728 733 5.217393 CGGTGGCAGATTTTATTGATCATG 58.783 41.667 0.00 0.00 0.00 3.07
729 734 4.261741 GCGGTGGCAGATTTTATTGATCAT 60.262 41.667 0.00 0.00 39.62 2.45
730 735 3.066621 GCGGTGGCAGATTTTATTGATCA 59.933 43.478 0.00 0.00 39.62 2.92
731 736 3.316308 AGCGGTGGCAGATTTTATTGATC 59.684 43.478 0.00 0.00 43.41 2.92
732 737 3.290710 AGCGGTGGCAGATTTTATTGAT 58.709 40.909 0.00 0.00 43.41 2.57
733 738 2.722094 AGCGGTGGCAGATTTTATTGA 58.278 42.857 0.00 0.00 43.41 2.57
734 739 4.096382 ACTTAGCGGTGGCAGATTTTATTG 59.904 41.667 0.00 0.00 43.41 1.90
735 740 4.270008 ACTTAGCGGTGGCAGATTTTATT 58.730 39.130 0.00 0.00 43.41 1.40
736 741 3.886123 ACTTAGCGGTGGCAGATTTTAT 58.114 40.909 0.00 0.00 43.41 1.40
743 748 4.434713 AAATAAAACTTAGCGGTGGCAG 57.565 40.909 0.00 0.00 43.41 4.85
805 814 5.043248 CGGCCAAATTTTGAACTCCATATC 58.957 41.667 10.72 0.00 0.00 1.63
810 819 3.378911 TTCGGCCAAATTTTGAACTCC 57.621 42.857 10.72 5.45 0.00 3.85
840 849 3.548587 CCGCTTGCATTTCATATCTTCG 58.451 45.455 0.00 0.00 0.00 3.79
844 853 1.664016 CGCCCGCTTGCATTTCATATC 60.664 52.381 0.00 0.00 0.00 1.63
875 884 1.146358 GCAGACGGGCGTATTCTGAC 61.146 60.000 2.02 0.00 39.36 3.51
876 885 1.141019 GCAGACGGGCGTATTCTGA 59.859 57.895 2.02 0.00 39.36 3.27
877 886 0.384309 TAGCAGACGGGCGTATTCTG 59.616 55.000 0.00 0.00 39.89 3.02
878 887 0.669077 CTAGCAGACGGGCGTATTCT 59.331 55.000 0.00 0.00 39.27 2.40
879 888 0.318784 CCTAGCAGACGGGCGTATTC 60.319 60.000 0.00 0.00 39.27 1.75
880 889 1.740285 CCTAGCAGACGGGCGTATT 59.260 57.895 0.00 0.00 39.27 1.89
881 890 2.857744 GCCTAGCAGACGGGCGTAT 61.858 63.158 0.00 0.00 39.27 3.06
882 891 3.524606 GCCTAGCAGACGGGCGTA 61.525 66.667 0.00 0.00 39.27 4.42
901 910 3.665675 AAGGCAACGGAGCGGCTAG 62.666 63.158 0.60 2.56 46.39 3.42
902 911 3.659089 GAAGGCAACGGAGCGGCTA 62.659 63.158 0.60 0.00 46.39 3.93
905 914 4.394712 AGGAAGGCAACGGAGCGG 62.395 66.667 0.00 0.00 46.39 5.52
906 915 2.815647 GAGGAAGGCAACGGAGCG 60.816 66.667 0.00 0.00 46.39 5.03
920 930 2.099405 GACTTGAGAGGACTCCAGAGG 58.901 57.143 0.00 0.00 41.99 3.69
1391 1401 1.272092 TGCTGGTGGAATTCTTGGAGG 60.272 52.381 5.23 0.00 0.00 4.30
1505 1515 2.203832 TCTCACTGGCCTGCTCCA 60.204 61.111 9.95 0.00 34.42 3.86
1514 1524 1.153489 CCATCGCTGGTCTCACTGG 60.153 63.158 0.00 0.00 37.79 4.00
1599 1609 0.543749 CCAGGGACACAAGGATCCTC 59.456 60.000 16.52 1.49 35.15 3.71
1655 1665 1.446907 CAGCTTAAGCACCCTGACAG 58.553 55.000 28.39 0.00 45.16 3.51
1659 1669 0.962356 CCACCAGCTTAAGCACCCTG 60.962 60.000 28.39 17.32 45.16 4.45
1860 1870 0.693049 GAGCCTCCTTCAACCTTGGA 59.307 55.000 0.00 0.00 0.00 3.53
1865 1875 0.693049 TTCAGGAGCCTCCTTCAACC 59.307 55.000 11.57 0.00 46.91 3.77
1866 1876 1.814793 GTTCAGGAGCCTCCTTCAAC 58.185 55.000 11.57 13.10 46.91 3.18
1915 1925 0.978146 TCAGGCCTCCCTTCTACAGC 60.978 60.000 0.00 0.00 40.33 4.40
1931 1941 2.298629 CGGCGCTGATCATCGTCAG 61.299 63.158 21.79 11.58 46.59 3.51
1947 1957 1.202533 ACACACTGAAGAAGGACACGG 60.203 52.381 0.00 0.00 0.00 4.94
2001 2011 6.535150 CACACCGTAACACTGAATCATTAGAT 59.465 38.462 0.00 0.00 35.53 1.98
2064 2074 0.599728 CTGAGATCCTAAGCAGGCGC 60.600 60.000 0.00 0.00 42.30 6.53
2067 2077 5.362430 ACTCTTAACTGAGATCCTAAGCAGG 59.638 44.000 0.00 0.00 39.09 4.85
2118 2128 2.490903 GTGCTGCATGACCTGATTCTTT 59.509 45.455 5.27 0.00 0.00 2.52
2132 2142 0.250234 GACACTATCCTGGTGCTGCA 59.750 55.000 0.00 0.00 38.14 4.41
2179 2189 3.719268 ATACTGATTGCACAGAACCCA 57.281 42.857 11.03 0.00 40.63 4.51
2232 2242 5.556382 CGCATATTCACATACACGAGTTTCC 60.556 44.000 0.00 0.00 0.00 3.13
2263 2273 3.557185 GCTGCACGAAGATGATGATACAA 59.443 43.478 0.00 0.00 0.00 2.41
2532 2542 1.068748 GCTGCCGCATTATCCTGATTG 60.069 52.381 0.00 0.00 35.78 2.67
2613 2623 6.158695 AGGAGATTAGGAGAGTGGCATTAAAA 59.841 38.462 0.00 0.00 0.00 1.52
2773 2784 1.640428 ACAATATGCGTGACGTCTGG 58.360 50.000 17.92 9.50 0.00 3.86
2823 2834 6.051717 CGAATTAGATGAGTTGGAATGAGGT 58.948 40.000 0.00 0.00 0.00 3.85
2827 2838 5.368145 TCCCGAATTAGATGAGTTGGAATG 58.632 41.667 0.00 0.00 0.00 2.67
2858 2869 6.494666 AGGATACAAAAATATGACCGGAGA 57.505 37.500 9.46 0.00 41.41 3.71
2872 2883 9.263446 AGTAGTGGTGTCTATAAAGGATACAAA 57.737 33.333 0.00 0.00 41.41 2.83
2873 2884 8.834004 AGTAGTGGTGTCTATAAAGGATACAA 57.166 34.615 0.00 0.00 41.41 2.41
2950 3044 9.603921 CAAATAGGGAAGCACATTTTTATGATT 57.396 29.630 0.00 0.00 0.00 2.57
2951 3045 8.206189 CCAAATAGGGAAGCACATTTTTATGAT 58.794 33.333 0.00 0.00 0.00 2.45
2952 3046 7.555087 CCAAATAGGGAAGCACATTTTTATGA 58.445 34.615 0.00 0.00 0.00 2.15
2953 3047 6.258507 GCCAAATAGGGAAGCACATTTTTATG 59.741 38.462 0.00 0.00 38.09 1.90
2990 3084 3.882888 GACCGAATGCCAAATAAGGATGA 59.117 43.478 0.00 0.00 0.00 2.92
2991 3085 3.885297 AGACCGAATGCCAAATAAGGATG 59.115 43.478 0.00 0.00 0.00 3.51
2992 3086 4.170468 AGACCGAATGCCAAATAAGGAT 57.830 40.909 0.00 0.00 0.00 3.24
3006 3102 4.566907 CCCCAGGAAGAAATTTAGACCGAA 60.567 45.833 0.00 0.00 0.00 4.30
3037 3133 6.015434 GGCCCTTAAGTGAGAATTGAAAAGAA 60.015 38.462 0.97 0.00 0.00 2.52
3046 3142 4.568592 CCAAAGAGGCCCTTAAGTGAGAAT 60.569 45.833 0.00 0.00 34.00 2.40
3064 3160 0.322008 GGAGTGGAGCAGTCCCAAAG 60.322 60.000 0.00 0.00 45.46 2.77
3118 3215 1.174712 TGCTCTTTGGTGAAGCTGCC 61.175 55.000 0.00 0.00 35.30 4.85
3180 3281 2.916934 AGCCAAATAGACCTTACCCACA 59.083 45.455 0.00 0.00 0.00 4.17
3186 3287 3.054655 GTCACCCAGCCAAATAGACCTTA 60.055 47.826 0.00 0.00 0.00 2.69
3247 3348 3.236047 GGGGAAAATTAACCACCACTGT 58.764 45.455 3.77 0.00 0.00 3.55
3257 3358 4.076394 CTCGTGGAGTTGGGGAAAATTAA 58.924 43.478 0.00 0.00 0.00 1.40
3283 3385 8.542953 GGTGCTTCAAAAACTCTAATTCAAAAG 58.457 33.333 0.00 0.00 0.00 2.27
3284 3386 7.494298 GGGTGCTTCAAAAACTCTAATTCAAAA 59.506 33.333 0.00 0.00 0.00 2.44
3291 3393 3.117284 AGGGGGTGCTTCAAAAACTCTAA 60.117 43.478 0.00 0.00 0.00 2.10
3303 3405 1.002857 AAGCTCATTAGGGGGTGCTT 58.997 50.000 0.00 0.00 36.16 3.91
3427 3533 6.844829 TGGTTACTAAAGATATTAAGGGCCC 58.155 40.000 16.46 16.46 0.00 5.80
3448 3554 8.644216 TGTGATACTACCGTCAATTATTATGGT 58.356 33.333 0.00 0.00 38.54 3.55
3453 3559 9.706691 CCTAATGTGATACTACCGTCAATTATT 57.293 33.333 0.00 0.00 0.00 1.40
3481 3587 6.498304 CAGCGGCAGATGTCTATTTATTTTT 58.502 36.000 1.45 0.00 0.00 1.94
3482 3588 5.506317 GCAGCGGCAGATGTCTATTTATTTT 60.506 40.000 3.18 0.00 40.72 1.82
3486 3592 2.483876 GCAGCGGCAGATGTCTATTTA 58.516 47.619 3.18 0.00 40.72 1.40
3487 3593 1.303309 GCAGCGGCAGATGTCTATTT 58.697 50.000 3.18 0.00 40.72 1.40
3489 3595 1.070445 GGCAGCGGCAGATGTCTAT 59.930 57.895 11.88 0.00 43.71 1.98
3490 3596 2.501128 GGCAGCGGCAGATGTCTA 59.499 61.111 11.88 0.00 43.71 2.59
3491 3597 4.827087 CGGCAGCGGCAGATGTCT 62.827 66.667 11.88 0.00 43.71 3.41
3542 3648 1.880819 TTTGACGCTCGGACTACCCC 61.881 60.000 0.00 0.00 0.00 4.95
3735 4042 3.628008 TGATACCATCACCGAGTGTACT 58.372 45.455 0.00 0.00 33.59 2.73
3840 4147 5.303333 GGGTTTTGAATGAACTACCTCCAAA 59.697 40.000 0.00 0.00 0.00 3.28
3871 4178 9.918630 GTCGCCTAGTTAGGAACAAAATATATA 57.081 33.333 9.39 0.00 46.63 0.86
3872 4179 8.648693 AGTCGCCTAGTTAGGAACAAAATATAT 58.351 33.333 9.39 0.00 46.63 0.86
3873 4180 7.924412 CAGTCGCCTAGTTAGGAACAAAATATA 59.076 37.037 9.39 0.00 46.63 0.86
3874 4181 6.761714 CAGTCGCCTAGTTAGGAACAAAATAT 59.238 38.462 9.39 0.00 46.63 1.28
3876 4183 4.935808 CAGTCGCCTAGTTAGGAACAAAAT 59.064 41.667 9.39 0.00 46.63 1.82
3976 4283 1.447317 AAGGTGCCGAACAAGTGCAG 61.447 55.000 0.00 0.00 35.33 4.41
4076 4383 4.302067 ACCTCCATAATGATCTGTCCTGT 58.698 43.478 0.00 0.00 0.00 4.00
4131 4438 1.745087 CCGCAGCAACAAGTCCAATAT 59.255 47.619 0.00 0.00 0.00 1.28
4165 4472 6.809196 GTGATCTTAGCTTACCTGAATATCGG 59.191 42.308 0.00 0.00 0.00 4.18
4195 4502 7.222999 GCTCTACACACCATCAGAAAGTAATAC 59.777 40.741 0.00 0.00 0.00 1.89
4285 4593 0.179111 TGTGTCCTCGCGGATTGATC 60.179 55.000 6.13 0.00 42.43 2.92
4339 4648 5.324409 ACAGGGTTTCAAAGCTAATGATGA 58.676 37.500 0.00 0.00 0.00 2.92
4352 4661 4.963373 TGAAAATACTCGACAGGGTTTCA 58.037 39.130 0.00 0.00 30.72 2.69
4378 4687 8.263640 ACTCATCTTTATAGCAATCAAGTCAGT 58.736 33.333 0.00 0.00 0.00 3.41
4404 4717 4.018141 ACATCAATCTCCAATGGTCCAAGA 60.018 41.667 0.00 0.00 0.00 3.02
4420 4733 8.076910 TGTGATTTGGGCTATAAAACATCAAT 57.923 30.769 0.00 0.00 0.00 2.57
4426 4739 9.476202 GGAATAATGTGATTTGGGCTATAAAAC 57.524 33.333 0.00 0.00 0.00 2.43
4430 4743 8.169393 TCATGGAATAATGTGATTTGGGCTATA 58.831 33.333 0.00 0.00 0.00 1.31
4457 4771 2.006888 GCTGCATGCGTAGTAGGAAAA 58.993 47.619 14.09 0.00 0.00 2.29
4496 4810 5.415701 GTGTTGAGGGAATAAAATCTGCAGA 59.584 40.000 20.79 20.79 0.00 4.26
4646 4960 1.593006 GGCTTCCGTACAACATCATCG 59.407 52.381 0.00 0.00 0.00 3.84
4649 4963 1.346395 ACAGGCTTCCGTACAACATCA 59.654 47.619 0.00 0.00 0.00 3.07
4676 4990 1.139058 GATAGGGACTGCAACCACGAT 59.861 52.381 10.99 0.00 41.52 3.73
4804 5118 4.330250 ACAAGCATGAGCAAGATAGTGTT 58.670 39.130 0.00 0.00 45.49 3.32
4828 5142 8.109705 TGTTAATGTACAACATGATCAAGCTT 57.890 30.769 0.00 0.00 37.97 3.74
5003 5322 4.413087 CATGAAGCATTTCAGAGTCAAGC 58.587 43.478 0.00 0.00 45.89 4.01
5009 5328 4.882427 AGATGTCCATGAAGCATTTCAGAG 59.118 41.667 0.00 0.00 45.89 3.35
5044 5363 4.516698 GTGTTCGGATTTAGCATGGATCAT 59.483 41.667 0.00 0.00 0.00 2.45
5062 5381 7.639039 TGTGTATCTCAACTTGATTTGTGTTC 58.361 34.615 0.00 0.00 0.00 3.18
5087 5406 4.277672 GGTGATGCATCTTGATAATGTGCT 59.722 41.667 26.32 0.00 36.78 4.40
5141 5742 2.096496 CCCTCGTTTGCTCATTGATCAC 59.904 50.000 0.00 0.00 0.00 3.06
5142 5743 2.358957 CCCTCGTTTGCTCATTGATCA 58.641 47.619 0.00 0.00 0.00 2.92
5197 5798 9.799106 GATCATTGATTTTTATCCCCTCTAGAA 57.201 33.333 0.00 0.00 0.00 2.10
5198 5799 8.948362 TGATCATTGATTTTTATCCCCTCTAGA 58.052 33.333 0.00 0.00 0.00 2.43
5199 5800 9.578576 TTGATCATTGATTTTTATCCCCTCTAG 57.421 33.333 0.00 0.00 0.00 2.43
5200 5801 9.934784 TTTGATCATTGATTTTTATCCCCTCTA 57.065 29.630 0.00 0.00 0.00 2.43
5201 5802 8.843308 TTTGATCATTGATTTTTATCCCCTCT 57.157 30.769 0.00 0.00 0.00 3.69
5202 5803 8.917088 TCTTTGATCATTGATTTTTATCCCCTC 58.083 33.333 0.00 0.00 0.00 4.30
5203 5804 8.699130 GTCTTTGATCATTGATTTTTATCCCCT 58.301 33.333 0.00 0.00 0.00 4.79
5204 5805 8.699130 AGTCTTTGATCATTGATTTTTATCCCC 58.301 33.333 0.00 0.00 0.00 4.81
5205 5806 9.525409 CAGTCTTTGATCATTGATTTTTATCCC 57.475 33.333 0.00 0.00 0.00 3.85
5227 5828 9.729023 CTATGCTATGCTACTATATTGTCAGTC 57.271 37.037 0.00 0.00 0.00 3.51
5248 5849 6.313411 GTGATCTGGCATTTCTCTATCTATGC 59.687 42.308 0.00 0.00 41.94 3.14
5277 5878 3.626028 AACTGTGAAGTTTCCGATTGC 57.374 42.857 0.00 0.00 0.00 3.56
5283 5884 6.445357 TGTTCCTTAAACTGTGAAGTTTCC 57.555 37.500 7.10 0.00 41.58 3.13
5339 6214 2.399611 GCACGCAGCAATACCGTC 59.600 61.111 0.00 0.00 44.79 4.79
5376 6252 9.284968 GCTGGGAATGTAATTATACAGTACATT 57.715 33.333 14.72 14.72 46.18 2.71
5435 6311 2.025155 TCTCGAGACCTTGGCTGATAC 58.975 52.381 12.08 0.00 0.00 2.24
5492 6368 2.341846 TTTGAGCGAAACCCTGTCTT 57.658 45.000 0.00 0.00 0.00 3.01
5528 6404 0.968405 TGCTGGTTCCTGGATTTTGC 59.032 50.000 0.00 1.34 0.00 3.68
5588 6467 5.707764 GGATTGGGATAGATTTACCTGCTTC 59.292 44.000 0.00 0.00 0.00 3.86
5589 6468 5.373854 AGGATTGGGATAGATTTACCTGCTT 59.626 40.000 0.00 0.00 0.00 3.91
5590 6469 4.916424 AGGATTGGGATAGATTTACCTGCT 59.084 41.667 0.00 0.00 0.00 4.24
5615 6494 7.867305 ATACATATACATCAGGGTCGTAGAG 57.133 40.000 0.00 0.00 36.95 2.43
5623 6502 4.337274 TCGCGGTATACATATACATCAGGG 59.663 45.833 6.13 7.27 40.16 4.45
5724 6603 1.819288 TCGTTCCCACAAAAACTTGCA 59.181 42.857 0.00 0.00 0.00 4.08
5737 6616 4.792521 ATCTACTATGCATCTCGTTCCC 57.207 45.455 0.19 0.00 0.00 3.97
5752 6631 4.081807 GTGTGAACTTTCCCCGTATCTACT 60.082 45.833 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.