Multiple sequence alignment - TraesCS6A01G170600

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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 TraesCS6A01G170600 chr6A 100.000 2898 0 0 1 2898 181012045 181014942 0.000000e+00 5352.0
1 TraesCS6A01G170600 chr6D 89.166 1486 93 30 701 2139 138383919 138385383 0.000000e+00 1790.0
2 TraesCS6A01G170600 chr6D 89.749 517 22 10 2220 2719 138385484 138385986 1.470000e-177 632.0
3 TraesCS6A01G170600 chr6D 93.990 416 17 5 1 408 138383230 138383645 8.820000e-175 623.0
4 TraesCS6A01G170600 chr6D 96.341 164 5 1 2724 2886 138386189 138386352 4.760000e-68 268.0
5 TraesCS6A01G170600 chr6D 89.583 96 10 0 460 555 138383808 138383903 3.920000e-24 122.0
6 TraesCS6A01G170600 chr6D 95.556 45 1 1 2160 2204 138385382 138385425 1.440000e-08 71.3
7 TraesCS6A01G170600 chr6B 90.137 1389 80 25 701 2053 237730609 237731976 0.000000e+00 1753.0
8 TraesCS6A01G170600 chr6B 93.699 492 27 4 2408 2898 237731986 237732474 0.000000e+00 734.0
9 TraesCS6A01G170600 chr6B 92.124 419 31 2 1 418 237730096 237730513 8.940000e-165 590.0
10 TraesCS6A01G170600 chr6B 87.261 157 17 2 544 700 566830689 566830842 2.970000e-40 176.0
11 TraesCS6A01G170600 chr6B 86.139 101 14 0 455 555 237730499 237730599 3.050000e-20 110.0
12 TraesCS6A01G170600 chr7B 82.661 248 36 7 1331 1574 530590632 530590388 2.260000e-51 213.0
13 TraesCS6A01G170600 chr7B 82.258 248 37 7 1331 1574 530434725 530434481 1.050000e-49 207.0
14 TraesCS6A01G170600 chr7A 82.906 234 34 6 1344 1574 567591240 567591010 3.790000e-49 206.0
15 TraesCS6A01G170600 chr7D 82.051 234 36 6 1344 1574 501108284 501108054 8.190000e-46 195.0
16 TraesCS6A01G170600 chr7D 88.889 144 16 0 558 701 176959585 176959442 8.250000e-41 178.0
17 TraesCS6A01G170600 chr7D 88.889 144 16 0 558 701 428501610 428501753 8.250000e-41 178.0
18 TraesCS6A01G170600 chr1D 89.189 148 16 0 558 705 492370348 492370495 4.930000e-43 185.0
19 TraesCS6A01G170600 chr1D 88.889 144 16 0 558 701 10673232 10673375 8.250000e-41 178.0
20 TraesCS6A01G170600 chr1D 88.889 144 16 0 558 701 322624910 322624767 8.250000e-41 178.0
21 TraesCS6A01G170600 chr2D 89.510 143 15 0 558 700 150887163 150887021 6.380000e-42 182.0
22 TraesCS6A01G170600 chrUn 88.966 145 16 0 558 702 112557286 112557430 2.290000e-41 180.0
23 TraesCS6A01G170600 chr4D 88.889 144 16 0 558 701 323113044 323113187 8.250000e-41 178.0


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 TraesCS6A01G170600 chr6A 181012045 181014942 2897 False 5352.000000 5352 100.00000 1 2898 1 chr6A.!!$F1 2897
1 TraesCS6A01G170600 chr6D 138383230 138386352 3122 False 584.383333 1790 92.39750 1 2886 6 chr6D.!!$F1 2885
2 TraesCS6A01G170600 chr6B 237730096 237732474 2378 False 796.750000 1753 90.52475 1 2898 4 chr6B.!!$F2 2897

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
691 811 0.028505 GCGCTTGCATCCATACTGTG 59.971 55.0 0.0 0.0 38.92 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2350 0.034059 CGCCCTCTCTGAAAGTGTGT 59.966 55.0 0.0 0.0 33.76 3.72 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
45 46 2.868583 CGTAGGATCCATTTGCACTCAG 59.131 50.000 15.82 0.00 0.00 3.35
191 194 0.108019 ACTCGACCCTGTGTTTTCCC 59.892 55.000 0.00 0.00 0.00 3.97
270 273 7.344093 TGAATTTATCTATTGGGCAATTGGTCA 59.656 33.333 7.72 0.00 32.50 4.02
359 364 5.705902 AGTAATCGGCCATTGTAAAACAAC 58.294 37.500 2.24 0.00 41.40 3.32
363 368 3.752222 TCGGCCATTGTAAAACAACGTAT 59.248 39.130 2.24 0.00 41.40 3.06
377 386 1.989706 ACGTATTTGGTGGTGGCTTT 58.010 45.000 0.00 0.00 0.00 3.51
383 392 1.529226 TTGGTGGTGGCTTTCATACG 58.471 50.000 0.00 0.00 0.00 3.06
470 590 4.347000 AGGGGTAATACGCATGTCTTATGT 59.653 41.667 9.65 0.00 32.03 2.29
483 603 8.269424 CGCATGTCTTATGTGTATTCTAGAAAC 58.731 37.037 9.71 9.59 0.00 2.78
508 628 9.259832 ACATATATTAGGTAGCATCTGTCATGA 57.740 33.333 0.00 0.00 0.00 3.07
514 634 1.498264 AGCATCTGTCATGAGAGCCT 58.502 50.000 14.89 8.08 0.00 4.58
555 675 2.155155 GGACGTTGAACGAAGTGATCAC 59.845 50.000 25.62 18.47 45.00 3.06
556 676 2.792674 GACGTTGAACGAAGTGATCACA 59.207 45.455 27.02 2.05 45.00 3.58
559 679 4.143835 CGTTGAACGAAGTGATCACAATG 58.856 43.478 27.02 17.19 45.00 2.82
576 696 5.622770 ACAATGGTGACCTCGTAAATTTC 57.377 39.130 2.11 0.00 0.00 2.17
577 697 5.067273 ACAATGGTGACCTCGTAAATTTCA 58.933 37.500 2.11 0.00 0.00 2.69
578 698 5.533154 ACAATGGTGACCTCGTAAATTTCAA 59.467 36.000 2.11 0.00 0.00 2.69
579 699 5.880054 ATGGTGACCTCGTAAATTTCAAG 57.120 39.130 2.11 0.00 0.00 3.02
580 700 4.963373 TGGTGACCTCGTAAATTTCAAGA 58.037 39.130 2.11 0.00 0.00 3.02
581 701 5.556915 TGGTGACCTCGTAAATTTCAAGAT 58.443 37.500 2.11 0.00 0.00 2.40
582 702 5.411361 TGGTGACCTCGTAAATTTCAAGATG 59.589 40.000 2.11 0.00 0.00 2.90
583 703 5.163754 GGTGACCTCGTAAATTTCAAGATGG 60.164 44.000 0.00 0.44 0.00 3.51
584 704 5.411669 GTGACCTCGTAAATTTCAAGATGGT 59.588 40.000 0.00 3.31 0.00 3.55
585 705 6.592607 GTGACCTCGTAAATTTCAAGATGGTA 59.407 38.462 0.00 0.00 0.00 3.25
586 706 7.280205 GTGACCTCGTAAATTTCAAGATGGTAT 59.720 37.037 0.00 0.00 0.00 2.73
587 707 7.279981 TGACCTCGTAAATTTCAAGATGGTATG 59.720 37.037 0.00 0.00 0.00 2.39
588 708 6.038271 ACCTCGTAAATTTCAAGATGGTATGC 59.962 38.462 0.00 0.00 0.00 3.14
589 709 6.371809 TCGTAAATTTCAAGATGGTATGCC 57.628 37.500 0.00 0.00 0.00 4.40
590 710 5.007234 TCGTAAATTTCAAGATGGTATGCCG 59.993 40.000 0.00 0.00 37.67 5.69
591 711 4.654091 AAATTTCAAGATGGTATGCCGG 57.346 40.909 0.00 0.00 37.67 6.13
592 712 1.388547 TTTCAAGATGGTATGCCGGC 58.611 50.000 22.73 22.73 37.67 6.13
593 713 0.546122 TTCAAGATGGTATGCCGGCT 59.454 50.000 29.70 15.76 37.67 5.52
594 714 0.106708 TCAAGATGGTATGCCGGCTC 59.893 55.000 29.70 15.82 37.67 4.70
595 715 0.179048 CAAGATGGTATGCCGGCTCA 60.179 55.000 29.70 19.88 37.67 4.26
596 716 0.107456 AAGATGGTATGCCGGCTCAG 59.893 55.000 29.70 0.00 37.67 3.35
597 717 1.050988 AGATGGTATGCCGGCTCAGT 61.051 55.000 29.70 13.44 37.67 3.41
598 718 0.601311 GATGGTATGCCGGCTCAGTC 60.601 60.000 29.70 14.01 37.67 3.51
599 719 1.050988 ATGGTATGCCGGCTCAGTCT 61.051 55.000 29.70 5.58 37.67 3.24
600 720 1.264749 TGGTATGCCGGCTCAGTCTT 61.265 55.000 29.70 6.03 37.67 3.01
601 721 0.107654 GGTATGCCGGCTCAGTCTTT 60.108 55.000 29.70 4.59 0.00 2.52
602 722 1.138266 GGTATGCCGGCTCAGTCTTTA 59.862 52.381 29.70 3.35 0.00 1.85
603 723 2.474816 GTATGCCGGCTCAGTCTTTAG 58.525 52.381 29.70 0.00 0.00 1.85
604 724 0.179000 ATGCCGGCTCAGTCTTTAGG 59.821 55.000 29.70 0.00 0.00 2.69
605 725 0.902984 TGCCGGCTCAGTCTTTAGGA 60.903 55.000 29.70 0.00 0.00 2.94
606 726 0.179097 GCCGGCTCAGTCTTTAGGAG 60.179 60.000 22.15 0.00 0.00 3.69
607 727 1.475403 CCGGCTCAGTCTTTAGGAGA 58.525 55.000 0.00 0.00 0.00 3.71
608 728 2.035632 CCGGCTCAGTCTTTAGGAGAT 58.964 52.381 0.00 0.00 36.61 2.75
609 729 2.223923 CCGGCTCAGTCTTTAGGAGATG 60.224 54.545 0.00 0.00 36.61 2.90
610 730 2.801342 CGGCTCAGTCTTTAGGAGATGC 60.801 54.545 0.00 0.00 36.61 3.91
611 731 2.433970 GGCTCAGTCTTTAGGAGATGCT 59.566 50.000 0.00 0.00 36.61 3.79
612 732 3.492482 GGCTCAGTCTTTAGGAGATGCTC 60.492 52.174 0.00 0.00 36.61 4.26
613 733 3.131933 GCTCAGTCTTTAGGAGATGCTCA 59.868 47.826 0.00 0.00 36.61 4.26
614 734 4.202243 GCTCAGTCTTTAGGAGATGCTCAT 60.202 45.833 0.00 0.00 36.61 2.90
615 735 5.010516 GCTCAGTCTTTAGGAGATGCTCATA 59.989 44.000 0.00 0.00 36.61 2.15
616 736 6.647334 TCAGTCTTTAGGAGATGCTCATAG 57.353 41.667 0.00 0.00 36.61 2.23
617 737 6.368805 TCAGTCTTTAGGAGATGCTCATAGA 58.631 40.000 0.00 0.00 36.61 1.98
618 738 6.489700 TCAGTCTTTAGGAGATGCTCATAGAG 59.510 42.308 0.00 0.00 36.61 2.43
619 739 5.774690 AGTCTTTAGGAGATGCTCATAGAGG 59.225 44.000 6.77 0.00 36.61 3.69
620 740 5.538433 GTCTTTAGGAGATGCTCATAGAGGT 59.462 44.000 6.77 0.00 36.61 3.85
621 741 6.717540 GTCTTTAGGAGATGCTCATAGAGGTA 59.282 42.308 6.77 0.00 36.61 3.08
622 742 7.231722 GTCTTTAGGAGATGCTCATAGAGGTAA 59.768 40.741 6.77 0.00 36.61 2.85
623 743 7.450014 TCTTTAGGAGATGCTCATAGAGGTAAG 59.550 40.741 6.77 1.06 32.40 2.34
624 744 4.415596 AGGAGATGCTCATAGAGGTAAGG 58.584 47.826 0.00 0.00 31.08 2.69
625 745 4.140805 AGGAGATGCTCATAGAGGTAAGGT 60.141 45.833 0.00 0.00 31.08 3.50
626 746 4.021544 GGAGATGCTCATAGAGGTAAGGTG 60.022 50.000 0.00 0.00 31.08 4.00
627 747 4.551671 AGATGCTCATAGAGGTAAGGTGT 58.448 43.478 0.00 0.00 0.00 4.16
628 748 4.343526 AGATGCTCATAGAGGTAAGGTGTG 59.656 45.833 0.00 0.00 0.00 3.82
629 749 3.441101 TGCTCATAGAGGTAAGGTGTGT 58.559 45.455 0.00 0.00 0.00 3.72
630 750 4.606210 TGCTCATAGAGGTAAGGTGTGTA 58.394 43.478 0.00 0.00 0.00 2.90
631 751 5.208890 TGCTCATAGAGGTAAGGTGTGTAT 58.791 41.667 0.00 0.00 0.00 2.29
632 752 5.069119 TGCTCATAGAGGTAAGGTGTGTATG 59.931 44.000 0.00 0.00 0.00 2.39
633 753 5.069251 GCTCATAGAGGTAAGGTGTGTATGT 59.931 44.000 0.00 0.00 0.00 2.29
634 754 6.407074 GCTCATAGAGGTAAGGTGTGTATGTT 60.407 42.308 0.00 0.00 0.00 2.71
635 755 7.490657 TCATAGAGGTAAGGTGTGTATGTTT 57.509 36.000 0.00 0.00 0.00 2.83
636 756 7.327975 TCATAGAGGTAAGGTGTGTATGTTTG 58.672 38.462 0.00 0.00 0.00 2.93
637 757 4.324267 AGAGGTAAGGTGTGTATGTTTGC 58.676 43.478 0.00 0.00 0.00 3.68
638 758 3.071479 AGGTAAGGTGTGTATGTTTGCG 58.929 45.455 0.00 0.00 0.00 4.85
639 759 2.809696 GGTAAGGTGTGTATGTTTGCGT 59.190 45.455 0.00 0.00 0.00 5.24
640 760 3.251487 GGTAAGGTGTGTATGTTTGCGTT 59.749 43.478 0.00 0.00 0.00 4.84
641 761 3.619233 AAGGTGTGTATGTTTGCGTTC 57.381 42.857 0.00 0.00 0.00 3.95
642 762 2.566913 AGGTGTGTATGTTTGCGTTCA 58.433 42.857 0.00 0.00 0.00 3.18
643 763 3.146066 AGGTGTGTATGTTTGCGTTCAT 58.854 40.909 0.00 0.00 0.00 2.57
644 764 4.320023 AGGTGTGTATGTTTGCGTTCATA 58.680 39.130 0.00 0.00 0.00 2.15
645 765 4.757657 AGGTGTGTATGTTTGCGTTCATAA 59.242 37.500 0.00 0.00 0.00 1.90
646 766 5.414454 AGGTGTGTATGTTTGCGTTCATAAT 59.586 36.000 0.00 0.00 0.00 1.28
647 767 6.072175 AGGTGTGTATGTTTGCGTTCATAATT 60.072 34.615 0.00 0.00 0.00 1.40
648 768 6.033407 GGTGTGTATGTTTGCGTTCATAATTG 59.967 38.462 0.00 0.00 0.00 2.32
649 769 6.580791 GTGTGTATGTTTGCGTTCATAATTGT 59.419 34.615 0.00 0.00 0.00 2.71
650 770 6.580416 TGTGTATGTTTGCGTTCATAATTGTG 59.420 34.615 0.00 0.00 0.00 3.33
651 771 6.799441 GTGTATGTTTGCGTTCATAATTGTGA 59.201 34.615 0.03 0.03 0.00 3.58
652 772 7.007367 GTGTATGTTTGCGTTCATAATTGTGAG 59.993 37.037 4.99 0.00 0.00 3.51
653 773 5.431420 TGTTTGCGTTCATAATTGTGAGT 57.569 34.783 4.99 0.00 0.00 3.41
654 774 5.211454 TGTTTGCGTTCATAATTGTGAGTG 58.789 37.500 4.99 3.65 0.00 3.51
655 775 5.212194 GTTTGCGTTCATAATTGTGAGTGT 58.788 37.500 4.99 0.00 0.00 3.55
656 776 6.017852 TGTTTGCGTTCATAATTGTGAGTGTA 60.018 34.615 4.99 0.00 0.00 2.90
657 777 6.735678 TTGCGTTCATAATTGTGAGTGTAT 57.264 33.333 4.99 0.00 0.00 2.29
658 778 6.105657 TGCGTTCATAATTGTGAGTGTATG 57.894 37.500 4.99 0.00 0.00 2.39
659 779 4.963953 GCGTTCATAATTGTGAGTGTATGC 59.036 41.667 4.99 4.36 0.00 3.14
660 780 5.190342 CGTTCATAATTGTGAGTGTATGCG 58.810 41.667 4.99 0.75 0.00 4.73
661 781 4.794248 TCATAATTGTGAGTGTATGCGC 57.206 40.909 0.00 0.00 0.00 6.09
662 782 3.245048 TCATAATTGTGAGTGTATGCGCG 59.755 43.478 0.00 0.00 0.00 6.86
663 783 1.438651 AATTGTGAGTGTATGCGCGT 58.561 45.000 8.43 7.55 0.00 6.01
664 784 0.721154 ATTGTGAGTGTATGCGCGTG 59.279 50.000 13.61 0.00 0.00 5.34
665 785 0.598942 TTGTGAGTGTATGCGCGTGT 60.599 50.000 13.61 0.00 0.00 4.49
666 786 0.241481 TGTGAGTGTATGCGCGTGTA 59.759 50.000 13.61 0.00 0.00 2.90
667 787 1.135228 TGTGAGTGTATGCGCGTGTAT 60.135 47.619 13.61 4.63 0.00 2.29
668 788 2.097791 TGTGAGTGTATGCGCGTGTATA 59.902 45.455 13.61 2.40 0.00 1.47
669 789 3.243267 TGTGAGTGTATGCGCGTGTATAT 60.243 43.478 13.61 0.00 0.00 0.86
670 790 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
671 791 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
672 792 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
673 793 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
676 796 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
677 797 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
678 798 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
679 799 0.111089 GCGTGTATATGAGCGCTTGC 60.111 55.000 13.26 0.00 45.48 4.01
680 800 1.208259 CGTGTATATGAGCGCTTGCA 58.792 50.000 13.26 6.25 42.66 4.08
681 801 1.794701 CGTGTATATGAGCGCTTGCAT 59.205 47.619 13.26 14.41 42.66 3.96
682 802 2.159920 CGTGTATATGAGCGCTTGCATC 60.160 50.000 13.26 0.00 42.66 3.91
683 803 2.158449 GTGTATATGAGCGCTTGCATCC 59.842 50.000 13.26 0.00 42.66 3.51
684 804 2.224257 TGTATATGAGCGCTTGCATCCA 60.224 45.455 13.26 3.49 42.66 3.41
685 805 2.195741 ATATGAGCGCTTGCATCCAT 57.804 45.000 13.26 11.98 42.66 3.41
686 806 2.837532 TATGAGCGCTTGCATCCATA 57.162 45.000 13.26 10.85 42.66 2.74
687 807 1.233019 ATGAGCGCTTGCATCCATAC 58.767 50.000 13.26 0.00 42.66 2.39
688 808 0.178767 TGAGCGCTTGCATCCATACT 59.821 50.000 13.26 0.00 42.66 2.12
689 809 0.585357 GAGCGCTTGCATCCATACTG 59.415 55.000 13.26 0.00 42.66 2.74
690 810 0.107508 AGCGCTTGCATCCATACTGT 60.108 50.000 2.64 0.00 42.66 3.55
691 811 0.028505 GCGCTTGCATCCATACTGTG 59.971 55.000 0.00 0.00 38.92 3.66
692 812 1.372582 CGCTTGCATCCATACTGTGT 58.627 50.000 0.00 0.00 0.00 3.72
693 813 1.739466 CGCTTGCATCCATACTGTGTT 59.261 47.619 0.00 0.00 0.00 3.32
694 814 2.935849 CGCTTGCATCCATACTGTGTTA 59.064 45.455 0.00 0.00 0.00 2.41
695 815 3.373748 CGCTTGCATCCATACTGTGTTAA 59.626 43.478 0.00 0.00 0.00 2.01
696 816 4.142708 CGCTTGCATCCATACTGTGTTAAA 60.143 41.667 0.00 0.00 0.00 1.52
697 817 5.618863 CGCTTGCATCCATACTGTGTTAAAA 60.619 40.000 0.00 0.00 0.00 1.52
698 818 6.155827 GCTTGCATCCATACTGTGTTAAAAA 58.844 36.000 0.00 0.00 0.00 1.94
719 839 0.108992 AACTCTGCAATGCAATGCCG 60.109 50.000 23.47 17.49 45.83 5.69
733 855 1.459450 ATGCCGTTCCACATGTAACC 58.541 50.000 0.00 0.00 0.00 2.85
740 862 1.803334 TCCACATGTAACCAACGAGC 58.197 50.000 0.00 0.00 0.00 5.03
745 867 4.155099 CCACATGTAACCAACGAGCATTTA 59.845 41.667 0.00 0.00 0.00 1.40
785 907 3.015516 TGGAACAGAAAGAACCGCC 57.984 52.632 0.00 0.00 0.00 6.13
799 921 0.249405 ACCGCCGTTACTTTCGACAA 60.249 50.000 0.00 0.00 0.00 3.18
807 929 5.684184 GCCGTTACTTTCGACAAAATTTCTT 59.316 36.000 0.00 0.00 0.00 2.52
820 942 5.519927 ACAAAATTTCTTCACGCAGAAAAGG 59.480 36.000 8.59 3.31 44.18 3.11
843 965 5.390991 GGAAGGCGTTTCTTTCTATCAACAG 60.391 44.000 0.00 0.00 36.03 3.16
893 1015 3.034562 GTCGACGACAGATTACGAATCC 58.965 50.000 22.66 0.00 38.71 3.01
909 1031 5.902681 ACGAATCCAGACGATAATTCTCAA 58.097 37.500 0.00 0.00 0.00 3.02
910 1032 6.338146 ACGAATCCAGACGATAATTCTCAAA 58.662 36.000 0.00 0.00 0.00 2.69
911 1033 6.255887 ACGAATCCAGACGATAATTCTCAAAC 59.744 38.462 0.00 0.00 0.00 2.93
974 1096 4.624364 TCACCACGCCAGCCACAG 62.624 66.667 0.00 0.00 0.00 3.66
1073 1195 4.623595 GGCAAGAAACACACGAAAGAAAAA 59.376 37.500 0.00 0.00 0.00 1.94
1074 1196 5.220209 GGCAAGAAACACACGAAAGAAAAAG 60.220 40.000 0.00 0.00 0.00 2.27
1075 1197 5.571357 GCAAGAAACACACGAAAGAAAAAGA 59.429 36.000 0.00 0.00 0.00 2.52
1076 1198 6.088883 GCAAGAAACACACGAAAGAAAAAGAA 59.911 34.615 0.00 0.00 0.00 2.52
1077 1199 7.358848 GCAAGAAACACACGAAAGAAAAAGAAA 60.359 33.333 0.00 0.00 0.00 2.52
1078 1200 8.484008 CAAGAAACACACGAAAGAAAAAGAAAA 58.516 29.630 0.00 0.00 0.00 2.29
1079 1201 8.227731 AGAAACACACGAAAGAAAAAGAAAAG 57.772 30.769 0.00 0.00 0.00 2.27
1253 1399 2.189521 GGTGGCTCCATACACCGG 59.810 66.667 0.00 0.00 46.61 5.28
1256 1402 2.203070 GGCTCCATACACCGGCTG 60.203 66.667 0.00 1.20 0.00 4.85
1645 1791 1.498865 CGGCAATACGGCTTAGCTGG 61.499 60.000 17.98 6.15 39.57 4.85
1647 1793 1.221414 GCAATACGGCTTAGCTGGAG 58.779 55.000 17.98 0.00 39.57 3.86
1661 1807 7.308951 GGCTTAGCTGGAGTACTAATAAGAGAG 60.309 44.444 3.59 0.00 0.00 3.20
1662 1808 7.446013 GCTTAGCTGGAGTACTAATAAGAGAGA 59.554 40.741 0.00 0.00 0.00 3.10
1663 1809 8.911918 TTAGCTGGAGTACTAATAAGAGAGAG 57.088 38.462 0.00 0.00 0.00 3.20
1775 1927 1.881925 CGGTGAGGAAATGGAACTGCA 60.882 52.381 0.00 0.00 0.00 4.41
1808 1986 2.169352 CAGTTGGAATCGGGTGAGAGAT 59.831 50.000 0.00 0.00 0.00 2.75
1816 1994 0.460311 CGGGTGAGAGATGGGTGTAC 59.540 60.000 0.00 0.00 0.00 2.90
1820 1998 2.832129 GGTGAGAGATGGGTGTACAGAA 59.168 50.000 0.00 0.00 0.00 3.02
1821 1999 3.118956 GGTGAGAGATGGGTGTACAGAAG 60.119 52.174 0.00 0.00 0.00 2.85
1824 2002 4.020543 GAGAGATGGGTGTACAGAAGAGT 58.979 47.826 0.00 0.00 0.00 3.24
1826 2004 5.772004 AGAGATGGGTGTACAGAAGAGTAT 58.228 41.667 0.00 0.00 0.00 2.12
1833 2011 4.036971 GGTGTACAGAAGAGTATGAGCGAT 59.963 45.833 0.00 0.00 0.00 4.58
1847 2025 2.283298 GAGCGATTTCAGCCATTGAGA 58.717 47.619 0.00 0.00 37.07 3.27
1886 2073 7.915397 GGCATATCGACTATCACAAACAAAATT 59.085 33.333 0.00 0.00 0.00 1.82
1894 2081 9.677567 GACTATCACAAACAAAATTAGCAAGAA 57.322 29.630 0.00 0.00 0.00 2.52
1931 2118 0.886490 GATCGGCCAGAATTCCGCAT 60.886 55.000 14.99 3.38 44.91 4.73
2004 2191 2.231721 GCCGAGTACTCTTTCTTCACCT 59.768 50.000 20.34 0.00 0.00 4.00
2036 2223 1.142965 CTGGACACGGTCACACACA 59.857 57.895 6.41 0.00 33.68 3.72
2038 2225 2.235016 GGACACGGTCACACACACG 61.235 63.158 6.41 0.00 33.68 4.49
2054 2241 4.988598 CGGCCGTTCTGCACCAGT 62.989 66.667 19.50 0.00 32.61 4.00
2056 2243 3.414700 GCCGTTCTGCACCAGTCG 61.415 66.667 0.00 0.00 32.61 4.18
2057 2244 2.738521 CCGTTCTGCACCAGTCGG 60.739 66.667 13.31 13.31 40.57 4.79
2102 2299 6.403200 CCCACCTCAAATTACAAACGAGTATG 60.403 42.308 0.00 0.00 0.00 2.39
2126 2323 0.877071 CAACTTACTGCTGGGTGCTG 59.123 55.000 0.00 0.00 44.70 4.41
2133 2330 4.357279 GCTGGGTGCTGAAGCCCT 62.357 66.667 0.42 0.00 46.70 5.19
2139 2336 1.454201 GGTGCTGAAGCCCTACTTTC 58.546 55.000 0.00 0.00 39.29 2.62
2140 2337 1.079503 GTGCTGAAGCCCTACTTTCG 58.920 55.000 0.00 0.00 39.29 3.46
2142 2339 1.066858 TGCTGAAGCCCTACTTTCGAG 60.067 52.381 0.00 0.00 39.29 4.04
2143 2340 1.740718 GCTGAAGCCCTACTTTCGAGG 60.741 57.143 0.00 0.00 39.29 4.63
2150 2347 1.941325 CCTACTTTCGAGGGCACATC 58.059 55.000 0.00 0.00 0.00 3.06
2151 2348 1.473434 CCTACTTTCGAGGGCACATCC 60.473 57.143 0.00 0.00 0.00 3.51
2152 2349 1.482593 CTACTTTCGAGGGCACATCCT 59.517 52.381 0.00 0.00 40.43 3.24
2153 2350 1.568504 ACTTTCGAGGGCACATCCTA 58.431 50.000 0.00 0.00 37.25 2.94
2154 2351 1.207329 ACTTTCGAGGGCACATCCTAC 59.793 52.381 0.00 0.00 37.25 3.18
2155 2352 1.207089 CTTTCGAGGGCACATCCTACA 59.793 52.381 0.00 0.00 37.25 2.74
2156 2353 0.535335 TTCGAGGGCACATCCTACAC 59.465 55.000 0.00 0.00 37.25 2.90
2157 2354 0.613572 TCGAGGGCACATCCTACACA 60.614 55.000 0.00 0.00 37.25 3.72
2158 2355 0.460284 CGAGGGCACATCCTACACAC 60.460 60.000 0.00 0.00 37.25 3.82
2159 2356 0.905357 GAGGGCACATCCTACACACT 59.095 55.000 0.00 0.00 37.25 3.55
2160 2357 1.279271 GAGGGCACATCCTACACACTT 59.721 52.381 0.00 0.00 37.25 3.16
2161 2358 1.705186 AGGGCACATCCTACACACTTT 59.295 47.619 0.00 0.00 34.92 2.66
2162 2359 2.084546 GGGCACATCCTACACACTTTC 58.915 52.381 0.00 0.00 34.39 2.62
2163 2360 2.552155 GGGCACATCCTACACACTTTCA 60.552 50.000 0.00 0.00 34.39 2.69
2164 2361 2.744202 GGCACATCCTACACACTTTCAG 59.256 50.000 0.00 0.00 0.00 3.02
2165 2362 3.557054 GGCACATCCTACACACTTTCAGA 60.557 47.826 0.00 0.00 0.00 3.27
2166 2363 3.681897 GCACATCCTACACACTTTCAGAG 59.318 47.826 0.00 0.00 0.00 3.35
2167 2364 4.561530 GCACATCCTACACACTTTCAGAGA 60.562 45.833 0.00 0.00 0.00 3.10
2168 2365 5.167121 CACATCCTACACACTTTCAGAGAG 58.833 45.833 0.00 0.00 0.00 3.20
2204 2401 4.080687 TGTTGATTGAATGATGGTGCTCA 58.919 39.130 0.00 0.00 0.00 4.26
2206 2403 5.010820 TGTTGATTGAATGATGGTGCTCAAA 59.989 36.000 0.00 0.00 31.94 2.69
2207 2404 5.319140 TGATTGAATGATGGTGCTCAAAG 57.681 39.130 0.00 0.00 31.94 2.77
2208 2405 3.581024 TTGAATGATGGTGCTCAAAGC 57.419 42.857 0.00 0.00 42.82 3.51
2210 2407 2.751259 TGAATGATGGTGCTCAAAGCTC 59.249 45.455 0.11 0.00 42.97 4.09
2211 2408 2.502142 ATGATGGTGCTCAAAGCTCA 57.498 45.000 0.11 0.00 42.97 4.26
2212 2409 2.275134 TGATGGTGCTCAAAGCTCAA 57.725 45.000 0.11 0.00 42.97 3.02
2213 2410 2.799017 TGATGGTGCTCAAAGCTCAAT 58.201 42.857 0.11 0.00 42.97 2.57
2214 2411 3.159472 TGATGGTGCTCAAAGCTCAATT 58.841 40.909 0.11 0.00 42.97 2.32
2216 2413 1.888512 TGGTGCTCAAAGCTCAATTCC 59.111 47.619 0.11 0.00 42.97 3.01
2217 2414 1.203287 GGTGCTCAAAGCTCAATTCCC 59.797 52.381 0.11 0.00 42.97 3.97
2236 2476 3.777925 CACCTTGACGCGCCTTCG 61.778 66.667 5.73 0.00 39.07 3.79
2266 2506 1.048601 TTTCCTGCCGAGACTTCAGT 58.951 50.000 0.00 0.00 0.00 3.41
2284 2524 2.743928 CGCTTCCTGTGGTGGCTC 60.744 66.667 0.00 0.00 0.00 4.70
2354 2594 1.203052 CATGCAACAGGTTGACCATCC 59.797 52.381 15.88 0.00 42.93 3.51
2355 2595 0.184692 TGCAACAGGTTGACCATCCA 59.815 50.000 15.88 0.63 42.93 3.41
2356 2596 1.327303 GCAACAGGTTGACCATCCAA 58.673 50.000 15.88 0.00 42.93 3.53
2357 2597 1.270550 GCAACAGGTTGACCATCCAAG 59.729 52.381 15.88 0.00 42.93 3.61
2358 2598 1.888512 CAACAGGTTGACCATCCAAGG 59.111 52.381 6.29 0.00 42.93 3.61
2359 2599 1.444933 ACAGGTTGACCATCCAAGGA 58.555 50.000 2.56 0.00 38.89 3.36
2360 2600 1.352352 ACAGGTTGACCATCCAAGGAG 59.648 52.381 2.56 0.00 38.89 3.69
2361 2601 0.995024 AGGTTGACCATCCAAGGAGG 59.005 55.000 2.56 0.00 38.89 4.30
2362 2602 0.698818 GGTTGACCATCCAAGGAGGT 59.301 55.000 9.17 9.17 38.63 3.85
2363 2603 1.075536 GGTTGACCATCCAAGGAGGTT 59.924 52.381 10.31 0.00 35.36 3.50
2364 2604 2.490902 GGTTGACCATCCAAGGAGGTTT 60.491 50.000 10.31 0.00 35.36 3.27
2365 2605 2.820197 GTTGACCATCCAAGGAGGTTTC 59.180 50.000 10.31 3.21 39.02 2.78
2413 2665 1.758280 ACCGGTACAGACAGACAAACA 59.242 47.619 4.49 0.00 0.00 2.83
2420 2672 3.016736 ACAGACAGACAAACAAACAGGG 58.983 45.455 0.00 0.00 0.00 4.45
2471 2723 3.189080 TCTGAAACATCTTCGGCAACATG 59.811 43.478 0.00 0.00 0.00 3.21
2479 2732 3.210227 TCTTCGGCAACATGTTTTCTGA 58.790 40.909 8.77 11.24 0.00 3.27
2518 2771 2.046411 TGGGCTGCCACATGTACG 60.046 61.111 22.05 0.00 0.00 3.67
2598 2855 2.945668 GTGGATGGTAGATGGAAAGTGC 59.054 50.000 0.00 0.00 0.00 4.40
2625 2882 9.639601 CAAGTCTACTTACTGACAATATGACAA 57.360 33.333 0.00 0.00 35.81 3.18
2635 2892 7.243487 ACTGACAATATGACAATTAGCAAACG 58.757 34.615 0.00 0.00 0.00 3.60
2646 2903 1.795768 TAGCAAACGAAGCCACAGAG 58.204 50.000 0.00 0.00 0.00 3.35
2650 2907 0.663153 AAACGAAGCCACAGAGCAAC 59.337 50.000 0.00 0.00 34.23 4.17
2658 2915 1.959042 CCACAGAGCAACACTGAAGT 58.041 50.000 0.00 0.00 38.55 3.01
2719 2976 2.006888 CGTATGCCCACGATTTTGTCT 58.993 47.619 1.18 0.00 44.69 3.41
2720 2977 3.119065 TCGTATGCCCACGATTTTGTCTA 60.119 43.478 5.84 0.00 45.45 2.59
2724 2981 3.857052 TGCCCACGATTTTGTCTAGTAG 58.143 45.455 0.00 0.00 0.00 2.57
2725 2982 3.195661 GCCCACGATTTTGTCTAGTAGG 58.804 50.000 0.00 0.00 0.00 3.18
2815 3271 1.739608 AAATGCCCAACCCTGACCCT 61.740 55.000 0.00 0.00 0.00 4.34
2852 3308 5.046014 GGTCCATTCATCATAGGTATGCTCT 60.046 44.000 0.00 0.00 33.76 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.878778 ACTGAGTGCAAATGGATCCTAC 58.121 45.455 14.23 2.88 0.00 3.18
241 244 7.658575 CCAATTGCCCAATAGATAAATTCAAGG 59.341 37.037 0.00 0.00 0.00 3.61
270 273 1.270550 CCAGTCTTGGCGCAAAATTCT 59.729 47.619 10.83 0.00 37.73 2.40
359 364 1.883275 TGAAAGCCACCACCAAATACG 59.117 47.619 0.00 0.00 0.00 3.06
363 368 1.883275 CGTATGAAAGCCACCACCAAA 59.117 47.619 0.00 0.00 0.00 3.28
442 451 5.747342 AGACATGCGTATTACCCCTAAAAA 58.253 37.500 0.00 0.00 0.00 1.94
443 452 5.362105 AGACATGCGTATTACCCCTAAAA 57.638 39.130 0.00 0.00 0.00 1.52
447 456 4.347000 ACATAAGACATGCGTATTACCCCT 59.653 41.667 0.00 0.00 31.92 4.79
448 457 4.451096 CACATAAGACATGCGTATTACCCC 59.549 45.833 0.00 0.00 31.92 4.95
449 458 5.054477 ACACATAAGACATGCGTATTACCC 58.946 41.667 0.00 0.00 31.92 3.69
450 459 7.884816 ATACACATAAGACATGCGTATTACC 57.115 36.000 0.00 0.00 31.92 2.85
451 460 9.193133 AGAATACACATAAGACATGCGTATTAC 57.807 33.333 9.45 5.65 37.37 1.89
454 463 8.793592 TCTAGAATACACATAAGACATGCGTAT 58.206 33.333 0.00 0.00 31.03 3.06
455 464 8.161699 TCTAGAATACACATAAGACATGCGTA 57.838 34.615 0.00 0.00 0.00 4.42
483 603 9.747293 CTCATGACAGATGCTACCTAATATATG 57.253 37.037 0.00 0.00 0.00 1.78
486 606 7.363705 GCTCTCATGACAGATGCTACCTAATAT 60.364 40.741 1.66 0.00 0.00 1.28
491 611 2.364970 GCTCTCATGACAGATGCTACCT 59.635 50.000 1.66 0.00 0.00 3.08
494 614 2.627221 GAGGCTCTCATGACAGATGCTA 59.373 50.000 7.40 0.00 0.00 3.49
508 628 1.484444 GGGGGCGATTATGAGGCTCT 61.484 60.000 16.72 3.93 33.50 4.09
514 634 2.035237 GACCGTGGGGGCGATTATGA 62.035 60.000 0.00 0.00 40.62 2.15
555 675 5.621197 TGAAATTTACGAGGTCACCATTG 57.379 39.130 0.00 0.00 0.00 2.82
556 676 6.001460 TCTTGAAATTTACGAGGTCACCATT 58.999 36.000 0.00 0.00 0.00 3.16
559 679 5.163754 CCATCTTGAAATTTACGAGGTCACC 60.164 44.000 0.00 0.00 0.00 4.02
564 684 6.430451 GCATACCATCTTGAAATTTACGAGG 58.570 40.000 0.00 0.00 0.00 4.63
566 686 5.007234 CGGCATACCATCTTGAAATTTACGA 59.993 40.000 0.00 0.00 34.57 3.43
567 687 5.204833 CGGCATACCATCTTGAAATTTACG 58.795 41.667 0.00 0.00 34.57 3.18
569 689 4.037446 GCCGGCATACCATCTTGAAATTTA 59.963 41.667 24.80 0.00 34.57 1.40
570 690 3.181476 GCCGGCATACCATCTTGAAATTT 60.181 43.478 24.80 0.00 34.57 1.82
571 691 2.362077 GCCGGCATACCATCTTGAAATT 59.638 45.455 24.80 0.00 34.57 1.82
572 692 1.956477 GCCGGCATACCATCTTGAAAT 59.044 47.619 24.80 0.00 34.57 2.17
573 693 1.064758 AGCCGGCATACCATCTTGAAA 60.065 47.619 31.54 0.00 34.57 2.69
574 694 0.546122 AGCCGGCATACCATCTTGAA 59.454 50.000 31.54 0.00 34.57 2.69
575 695 0.106708 GAGCCGGCATACCATCTTGA 59.893 55.000 31.54 0.00 34.57 3.02
576 696 0.179048 TGAGCCGGCATACCATCTTG 60.179 55.000 31.54 0.00 34.57 3.02
577 697 0.107456 CTGAGCCGGCATACCATCTT 59.893 55.000 31.54 3.33 34.57 2.40
578 698 1.050988 ACTGAGCCGGCATACCATCT 61.051 55.000 31.54 4.27 34.57 2.90
579 699 0.601311 GACTGAGCCGGCATACCATC 60.601 60.000 31.54 16.99 34.57 3.51
580 700 1.050988 AGACTGAGCCGGCATACCAT 61.051 55.000 31.54 6.18 34.57 3.55
581 701 1.264749 AAGACTGAGCCGGCATACCA 61.265 55.000 31.54 18.81 34.57 3.25
582 702 0.107654 AAAGACTGAGCCGGCATACC 60.108 55.000 31.54 14.98 0.00 2.73
583 703 2.474816 CTAAAGACTGAGCCGGCATAC 58.525 52.381 31.54 19.58 0.00 2.39
584 704 1.412710 CCTAAAGACTGAGCCGGCATA 59.587 52.381 31.54 16.21 0.00 3.14
585 705 0.179000 CCTAAAGACTGAGCCGGCAT 59.821 55.000 31.54 14.28 0.00 4.40
586 706 0.902984 TCCTAAAGACTGAGCCGGCA 60.903 55.000 31.54 7.98 0.00 5.69
587 707 0.179097 CTCCTAAAGACTGAGCCGGC 60.179 60.000 21.89 21.89 0.00 6.13
588 708 1.475403 TCTCCTAAAGACTGAGCCGG 58.525 55.000 0.00 0.00 0.00 6.13
589 709 2.801342 GCATCTCCTAAAGACTGAGCCG 60.801 54.545 0.00 0.00 36.65 5.52
590 710 2.433970 AGCATCTCCTAAAGACTGAGCC 59.566 50.000 0.00 0.00 36.65 4.70
591 711 3.131933 TGAGCATCTCCTAAAGACTGAGC 59.868 47.826 0.00 0.00 36.65 4.26
592 712 4.998671 TGAGCATCTCCTAAAGACTGAG 57.001 45.455 0.00 0.00 36.65 3.35
593 713 6.368805 TCTATGAGCATCTCCTAAAGACTGA 58.631 40.000 0.00 0.00 36.65 3.41
594 714 6.294675 CCTCTATGAGCATCTCCTAAAGACTG 60.295 46.154 0.00 0.00 36.65 3.51
595 715 5.774690 CCTCTATGAGCATCTCCTAAAGACT 59.225 44.000 0.00 0.00 36.65 3.24
596 716 5.538433 ACCTCTATGAGCATCTCCTAAAGAC 59.462 44.000 0.00 0.00 36.65 3.01
597 717 5.710646 ACCTCTATGAGCATCTCCTAAAGA 58.289 41.667 0.00 0.00 38.72 2.52
598 718 7.309744 CCTTACCTCTATGAGCATCTCCTAAAG 60.310 44.444 0.00 0.00 34.92 1.85
599 719 6.495181 CCTTACCTCTATGAGCATCTCCTAAA 59.505 42.308 0.00 0.00 34.92 1.85
600 720 6.013379 CCTTACCTCTATGAGCATCTCCTAA 58.987 44.000 0.00 0.00 34.92 2.69
601 721 5.075205 ACCTTACCTCTATGAGCATCTCCTA 59.925 44.000 0.00 0.00 34.92 2.94
602 722 4.140805 ACCTTACCTCTATGAGCATCTCCT 60.141 45.833 0.00 0.00 34.92 3.69
603 723 4.021544 CACCTTACCTCTATGAGCATCTCC 60.022 50.000 0.00 0.00 34.92 3.71
604 724 4.586841 ACACCTTACCTCTATGAGCATCTC 59.413 45.833 0.00 0.00 34.92 2.75
605 725 4.343526 CACACCTTACCTCTATGAGCATCT 59.656 45.833 0.00 0.00 34.92 2.90
606 726 4.100189 ACACACCTTACCTCTATGAGCATC 59.900 45.833 0.00 0.00 0.00 3.91
607 727 4.033709 ACACACCTTACCTCTATGAGCAT 58.966 43.478 0.00 0.00 0.00 3.79
608 728 3.441101 ACACACCTTACCTCTATGAGCA 58.559 45.455 0.00 0.00 0.00 4.26
609 729 5.069251 ACATACACACCTTACCTCTATGAGC 59.931 44.000 0.00 0.00 0.00 4.26
610 730 6.716934 ACATACACACCTTACCTCTATGAG 57.283 41.667 0.00 0.00 0.00 2.90
611 731 7.327975 CAAACATACACACCTTACCTCTATGA 58.672 38.462 0.00 0.00 0.00 2.15
612 732 6.037172 GCAAACATACACACCTTACCTCTATG 59.963 42.308 0.00 0.00 0.00 2.23
613 733 6.113411 GCAAACATACACACCTTACCTCTAT 58.887 40.000 0.00 0.00 0.00 1.98
614 734 5.484715 GCAAACATACACACCTTACCTCTA 58.515 41.667 0.00 0.00 0.00 2.43
615 735 4.324267 GCAAACATACACACCTTACCTCT 58.676 43.478 0.00 0.00 0.00 3.69
616 736 3.124636 CGCAAACATACACACCTTACCTC 59.875 47.826 0.00 0.00 0.00 3.85
617 737 3.071479 CGCAAACATACACACCTTACCT 58.929 45.455 0.00 0.00 0.00 3.08
618 738 2.809696 ACGCAAACATACACACCTTACC 59.190 45.455 0.00 0.00 0.00 2.85
619 739 4.024725 TGAACGCAAACATACACACCTTAC 60.025 41.667 0.00 0.00 0.00 2.34
620 740 4.127907 TGAACGCAAACATACACACCTTA 58.872 39.130 0.00 0.00 0.00 2.69
621 741 2.946329 TGAACGCAAACATACACACCTT 59.054 40.909 0.00 0.00 0.00 3.50
622 742 2.566913 TGAACGCAAACATACACACCT 58.433 42.857 0.00 0.00 0.00 4.00
623 743 3.552604 ATGAACGCAAACATACACACC 57.447 42.857 0.00 0.00 0.00 4.16
624 744 6.580791 ACAATTATGAACGCAAACATACACAC 59.419 34.615 0.00 0.00 0.00 3.82
625 745 6.580416 CACAATTATGAACGCAAACATACACA 59.420 34.615 0.00 0.00 0.00 3.72
626 746 6.799441 TCACAATTATGAACGCAAACATACAC 59.201 34.615 0.00 0.00 0.00 2.90
627 747 6.903419 TCACAATTATGAACGCAAACATACA 58.097 32.000 0.00 0.00 0.00 2.29
628 748 7.007367 CACTCACAATTATGAACGCAAACATAC 59.993 37.037 0.00 0.00 0.00 2.39
629 749 7.020602 CACTCACAATTATGAACGCAAACATA 58.979 34.615 0.00 0.00 0.00 2.29
630 750 5.858049 CACTCACAATTATGAACGCAAACAT 59.142 36.000 0.00 0.00 0.00 2.71
631 751 5.211454 CACTCACAATTATGAACGCAAACA 58.789 37.500 0.00 0.00 0.00 2.83
632 752 5.212194 ACACTCACAATTATGAACGCAAAC 58.788 37.500 0.00 0.00 0.00 2.93
633 753 5.431420 ACACTCACAATTATGAACGCAAA 57.569 34.783 0.00 0.00 0.00 3.68
634 754 6.541969 CATACACTCACAATTATGAACGCAA 58.458 36.000 0.00 0.00 0.00 4.85
635 755 5.447144 GCATACACTCACAATTATGAACGCA 60.447 40.000 0.00 0.00 0.00 5.24
636 756 4.963953 GCATACACTCACAATTATGAACGC 59.036 41.667 0.00 0.00 0.00 4.84
637 757 5.190342 CGCATACACTCACAATTATGAACG 58.810 41.667 0.00 0.00 0.00 3.95
638 758 4.963953 GCGCATACACTCACAATTATGAAC 59.036 41.667 0.30 0.00 0.00 3.18
639 759 4.260172 CGCGCATACACTCACAATTATGAA 60.260 41.667 8.75 0.00 0.00 2.57
640 760 3.245048 CGCGCATACACTCACAATTATGA 59.755 43.478 8.75 0.00 0.00 2.15
641 761 3.001228 ACGCGCATACACTCACAATTATG 59.999 43.478 5.73 0.00 0.00 1.90
642 762 3.001228 CACGCGCATACACTCACAATTAT 59.999 43.478 5.73 0.00 0.00 1.28
643 763 2.347150 CACGCGCATACACTCACAATTA 59.653 45.455 5.73 0.00 0.00 1.40
644 764 1.128507 CACGCGCATACACTCACAATT 59.871 47.619 5.73 0.00 0.00 2.32
645 765 0.721154 CACGCGCATACACTCACAAT 59.279 50.000 5.73 0.00 0.00 2.71
646 766 0.598942 ACACGCGCATACACTCACAA 60.599 50.000 5.73 0.00 0.00 3.33
647 767 0.241481 TACACGCGCATACACTCACA 59.759 50.000 5.73 0.00 0.00 3.58
648 768 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
649 769 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
650 770 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
651 771 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
652 772 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
653 773 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
654 774 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
655 775 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
656 776 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
657 777 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
661 781 1.208259 TGCAAGCGCTCATATACACG 58.792 50.000 12.06 0.00 39.64 4.49
662 782 2.158449 GGATGCAAGCGCTCATATACAC 59.842 50.000 12.06 0.00 39.64 2.90
663 783 2.224257 TGGATGCAAGCGCTCATATACA 60.224 45.455 12.06 9.54 39.64 2.29
664 784 2.416747 TGGATGCAAGCGCTCATATAC 58.583 47.619 12.06 6.70 39.64 1.47
665 785 2.837532 TGGATGCAAGCGCTCATATA 57.162 45.000 12.06 0.40 39.64 0.86
666 786 2.195741 ATGGATGCAAGCGCTCATAT 57.804 45.000 12.06 4.99 39.64 1.78
667 787 2.037641 AGTATGGATGCAAGCGCTCATA 59.962 45.455 12.06 10.39 39.64 2.15
668 788 1.202734 AGTATGGATGCAAGCGCTCAT 60.203 47.619 12.06 11.47 39.64 2.90
669 789 0.178767 AGTATGGATGCAAGCGCTCA 59.821 50.000 12.06 5.63 39.64 4.26
670 790 0.585357 CAGTATGGATGCAAGCGCTC 59.415 55.000 12.06 0.00 39.64 5.03
671 791 0.107508 ACAGTATGGATGCAAGCGCT 60.108 50.000 2.64 2.64 43.62 5.92
672 792 0.028505 CACAGTATGGATGCAAGCGC 59.971 55.000 0.00 0.00 43.62 5.92
673 793 1.372582 ACACAGTATGGATGCAAGCG 58.627 50.000 0.00 0.00 43.62 4.68
674 794 4.963276 TTAACACAGTATGGATGCAAGC 57.037 40.909 0.00 0.00 43.62 4.01
697 817 2.809696 GGCATTGCATTGCAGAGTTTTT 59.190 40.909 28.93 0.00 44.59 1.94
698 818 2.419667 GGCATTGCATTGCAGAGTTTT 58.580 42.857 28.93 0.00 44.59 2.43
699 819 1.670674 CGGCATTGCATTGCAGAGTTT 60.671 47.619 28.93 0.00 44.59 2.66
707 827 0.038435 TGTGGAACGGCATTGCATTG 60.038 50.000 11.39 4.20 41.17 2.82
719 839 2.095919 GCTCGTTGGTTACATGTGGAAC 60.096 50.000 9.11 5.74 37.35 3.62
733 855 4.846137 GCACAGTAAACTAAATGCTCGTTG 59.154 41.667 6.13 0.00 0.00 4.10
740 862 4.472286 CAACCCGCACAGTAAACTAAATG 58.528 43.478 0.00 0.00 0.00 2.32
745 867 2.327228 GCAACCCGCACAGTAAACT 58.673 52.632 0.00 0.00 41.79 2.66
785 907 7.355354 CGTGAAGAAATTTTGTCGAAAGTAACG 60.355 37.037 0.00 0.00 0.00 3.18
799 921 5.514274 TCCTTTTCTGCGTGAAGAAATTT 57.486 34.783 3.91 0.00 43.75 1.82
807 929 1.227999 CGCCTTCCTTTTCTGCGTGA 61.228 55.000 0.00 0.00 40.33 4.35
820 942 5.408604 TCTGTTGATAGAAAGAAACGCCTTC 59.591 40.000 0.00 0.00 0.00 3.46
893 1015 6.153212 ACGTTGTTTGAGAATTATCGTCTG 57.847 37.500 0.00 0.00 0.00 3.51
1032 1154 4.891727 CGGACGAATGGAGCGGGG 62.892 72.222 0.00 0.00 0.00 5.73
1073 1195 6.418057 TTGCAATTATTGGTGGACTTTTCT 57.582 33.333 7.08 0.00 0.00 2.52
1074 1196 6.073276 GGTTTGCAATTATTGGTGGACTTTTC 60.073 38.462 0.00 0.00 0.00 2.29
1075 1197 5.762711 GGTTTGCAATTATTGGTGGACTTTT 59.237 36.000 0.00 0.00 0.00 2.27
1076 1198 5.071653 AGGTTTGCAATTATTGGTGGACTTT 59.928 36.000 0.00 0.00 0.00 2.66
1077 1199 4.592778 AGGTTTGCAATTATTGGTGGACTT 59.407 37.500 0.00 0.00 0.00 3.01
1078 1200 4.159557 AGGTTTGCAATTATTGGTGGACT 58.840 39.130 0.00 0.00 0.00 3.85
1079 1201 4.494484 GAGGTTTGCAATTATTGGTGGAC 58.506 43.478 0.00 0.00 0.00 4.02
1295 1441 4.065281 CGTCCACCGAGTCACCCC 62.065 72.222 0.00 0.00 39.56 4.95
1562 1708 4.271816 CCATCCCGTCGAGCCTCG 62.272 72.222 8.05 8.05 42.10 4.63
1645 1791 7.373966 CGCGTTTTCTCTCTCTTATTAGTACTC 59.626 40.741 0.00 0.00 0.00 2.59
1647 1793 6.075467 GCGCGTTTTCTCTCTCTTATTAGTAC 60.075 42.308 8.43 0.00 0.00 2.73
1661 1807 1.134694 GTCCCATGCGCGTTTTCTC 59.865 57.895 8.43 0.00 0.00 2.87
1662 1808 1.302511 AGTCCCATGCGCGTTTTCT 60.303 52.632 8.43 0.00 0.00 2.52
1663 1809 1.154225 CAGTCCCATGCGCGTTTTC 60.154 57.895 8.43 0.00 0.00 2.29
1668 1816 1.162181 ATGAATCAGTCCCATGCGCG 61.162 55.000 0.00 0.00 0.00 6.86
1808 1986 3.447586 GCTCATACTCTTCTGTACACCCA 59.552 47.826 0.00 0.00 0.00 4.51
1816 1994 4.208873 GCTGAAATCGCTCATACTCTTCTG 59.791 45.833 0.00 0.00 0.00 3.02
1820 1998 2.432146 TGGCTGAAATCGCTCATACTCT 59.568 45.455 0.00 0.00 0.00 3.24
1821 1999 2.826428 TGGCTGAAATCGCTCATACTC 58.174 47.619 0.00 0.00 0.00 2.59
1824 2002 3.807553 TCAATGGCTGAAATCGCTCATA 58.192 40.909 0.00 0.00 0.00 2.15
1826 2004 2.011947 CTCAATGGCTGAAATCGCTCA 58.988 47.619 0.00 0.00 32.17 4.26
1833 2011 3.119743 CGCAGATTTCTCAATGGCTGAAA 60.120 43.478 0.00 0.00 32.17 2.69
1847 2025 0.250467 ATATGCCTCGGCGCAGATTT 60.250 50.000 11.52 0.00 43.26 2.17
1886 2073 1.225855 CTGTGCAACCGTTCTTGCTA 58.774 50.000 10.09 1.31 45.79 3.49
1894 2081 3.832237 CTGGAGGCTGTGCAACCGT 62.832 63.158 0.00 0.00 34.36 4.83
1931 2118 3.364441 GTGGACGCCATGCTTGCA 61.364 61.111 0.00 0.00 35.28 4.08
1989 2176 3.366679 CCGCGTTAGGTGAAGAAAGAGTA 60.367 47.826 4.92 0.00 0.00 2.59
2036 2223 4.988598 CTGGTGCAGAACGGCCGT 62.989 66.667 28.70 28.70 32.44 5.68
2038 2225 3.050275 GACTGGTGCAGAACGGCC 61.050 66.667 0.00 0.00 35.18 6.13
2102 2299 2.744202 CACCCAGCAGTAAGTTGATGAC 59.256 50.000 0.00 0.00 36.61 3.06
2133 2330 1.568504 AGGATGTGCCCTCGAAAGTA 58.431 50.000 0.00 0.00 37.37 2.24
2139 2336 0.460284 GTGTGTAGGATGTGCCCTCG 60.460 60.000 0.00 0.00 37.74 4.63
2140 2337 0.905357 AGTGTGTAGGATGTGCCCTC 59.095 55.000 0.00 0.00 37.74 4.30
2142 2339 2.084546 GAAAGTGTGTAGGATGTGCCC 58.915 52.381 0.00 0.00 37.37 5.36
2143 2340 2.744202 CTGAAAGTGTGTAGGATGTGCC 59.256 50.000 0.00 0.00 0.00 5.01
2145 2342 5.139435 TCTCTGAAAGTGTGTAGGATGTG 57.861 43.478 0.00 0.00 33.76 3.21
2146 2343 4.221703 CCTCTCTGAAAGTGTGTAGGATGT 59.778 45.833 0.00 0.00 33.76 3.06
2147 2344 4.382470 CCCTCTCTGAAAGTGTGTAGGATG 60.382 50.000 0.00 0.00 33.76 3.51
2148 2345 3.772025 CCCTCTCTGAAAGTGTGTAGGAT 59.228 47.826 0.00 0.00 33.76 3.24
2149 2346 3.165875 CCCTCTCTGAAAGTGTGTAGGA 58.834 50.000 0.00 0.00 33.76 2.94
2150 2347 2.354203 GCCCTCTCTGAAAGTGTGTAGG 60.354 54.545 0.00 0.00 33.76 3.18
2151 2348 2.672478 CGCCCTCTCTGAAAGTGTGTAG 60.672 54.545 0.00 0.00 33.76 2.74
2152 2349 1.272490 CGCCCTCTCTGAAAGTGTGTA 59.728 52.381 0.00 0.00 33.76 2.90
2153 2350 0.034059 CGCCCTCTCTGAAAGTGTGT 59.966 55.000 0.00 0.00 33.76 3.72
2154 2351 0.318441 TCGCCCTCTCTGAAAGTGTG 59.682 55.000 0.00 0.00 33.76 3.82
2155 2352 1.066573 CATCGCCCTCTCTGAAAGTGT 60.067 52.381 0.00 0.00 33.76 3.55
2156 2353 1.205655 TCATCGCCCTCTCTGAAAGTG 59.794 52.381 0.00 0.00 33.76 3.16
2157 2354 1.561643 TCATCGCCCTCTCTGAAAGT 58.438 50.000 0.00 0.00 33.76 2.66
2158 2355 2.158986 ACATCATCGCCCTCTCTGAAAG 60.159 50.000 0.00 0.00 0.00 2.62
2159 2356 1.833630 ACATCATCGCCCTCTCTGAAA 59.166 47.619 0.00 0.00 0.00 2.69
2160 2357 1.489481 ACATCATCGCCCTCTCTGAA 58.511 50.000 0.00 0.00 0.00 3.02
2161 2358 2.364972 TACATCATCGCCCTCTCTGA 57.635 50.000 0.00 0.00 0.00 3.27
2162 2359 3.244009 ACAATACATCATCGCCCTCTCTG 60.244 47.826 0.00 0.00 0.00 3.35
2163 2360 2.968574 ACAATACATCATCGCCCTCTCT 59.031 45.455 0.00 0.00 0.00 3.10
2164 2361 3.393089 ACAATACATCATCGCCCTCTC 57.607 47.619 0.00 0.00 0.00 3.20
2165 2362 3.134623 TCAACAATACATCATCGCCCTCT 59.865 43.478 0.00 0.00 0.00 3.69
2166 2363 3.466836 TCAACAATACATCATCGCCCTC 58.533 45.455 0.00 0.00 0.00 4.30
2167 2364 3.558931 TCAACAATACATCATCGCCCT 57.441 42.857 0.00 0.00 0.00 5.19
2168 2365 4.275689 TCAATCAACAATACATCATCGCCC 59.724 41.667 0.00 0.00 0.00 6.13
2204 2401 0.251341 AGGTGCGGGAATTGAGCTTT 60.251 50.000 0.00 0.00 0.00 3.51
2206 2403 0.962356 CAAGGTGCGGGAATTGAGCT 60.962 55.000 0.00 0.00 0.00 4.09
2207 2404 0.960364 TCAAGGTGCGGGAATTGAGC 60.960 55.000 0.00 0.00 0.00 4.26
2208 2405 0.804989 GTCAAGGTGCGGGAATTGAG 59.195 55.000 0.00 0.00 32.64 3.02
2210 2407 1.501741 CGTCAAGGTGCGGGAATTG 59.498 57.895 0.00 0.00 0.00 2.32
2211 2408 2.332654 GCGTCAAGGTGCGGGAATT 61.333 57.895 0.00 0.00 0.00 2.17
2212 2409 2.746277 GCGTCAAGGTGCGGGAAT 60.746 61.111 0.00 0.00 0.00 3.01
2236 2476 0.521735 GGCAGGAAAATGGACACGAC 59.478 55.000 0.00 0.00 0.00 4.34
2266 2506 3.240134 GAGCCACCACAGGAAGCGA 62.240 63.158 0.00 0.00 31.68 4.93
2284 2524 2.849120 CTTGCACAGAGAGGAGGCGG 62.849 65.000 0.00 0.00 0.00 6.13
2314 2554 6.096564 TGCATGTGTAAAATGATGCTTGGATA 59.903 34.615 0.00 0.00 31.34 2.59
2330 2570 2.226330 GGTCAACCTGTTGCATGTGTA 58.774 47.619 5.14 0.00 40.24 2.90
2334 2574 1.203052 GGATGGTCAACCTGTTGCATG 59.797 52.381 5.14 0.00 40.24 4.06
2354 2594 1.419374 CGTCAGACGAAACCTCCTTG 58.581 55.000 18.63 0.00 46.05 3.61
2355 2595 3.888093 CGTCAGACGAAACCTCCTT 57.112 52.632 18.63 0.00 46.05 3.36
2380 2620 2.562298 TGTACCGGTGGTTCGTAATCTT 59.438 45.455 19.93 0.00 37.09 2.40
2413 2665 3.625649 TTTTCTTTTGCTGCCCTGTTT 57.374 38.095 0.00 0.00 0.00 2.83
2420 2672 3.068560 TGATGCCATTTTCTTTTGCTGC 58.931 40.909 0.00 0.00 0.00 5.25
2518 2771 7.970614 CACATTTTCAGGAAGGCTTAATAGTTC 59.029 37.037 0.00 0.00 0.00 3.01
2566 2823 6.295011 CCATCTACCATCCACTCTACATCTTC 60.295 46.154 0.00 0.00 0.00 2.87
2574 2831 4.163078 CACTTTCCATCTACCATCCACTCT 59.837 45.833 0.00 0.00 0.00 3.24
2598 2855 8.251026 TGTCATATTGTCAGTAAGTAGACTTGG 58.749 37.037 5.15 0.00 37.40 3.61
2625 2882 2.744202 CTCTGTGGCTTCGTTTGCTAAT 59.256 45.455 0.00 0.00 0.00 1.73
2635 2892 0.590195 CAGTGTTGCTCTGTGGCTTC 59.410 55.000 0.00 0.00 0.00 3.86
2646 2903 3.929610 GAGATGAGGTACTTCAGTGTTGC 59.070 47.826 13.55 0.00 41.55 4.17
2650 2907 4.082733 TGTTCGAGATGAGGTACTTCAGTG 60.083 45.833 13.55 3.52 41.55 3.66
2658 2915 4.202172 TGTGTTTGTGTTCGAGATGAGGTA 60.202 41.667 0.00 0.00 0.00 3.08
2719 2976 7.397476 CCTTGATGCTCCAATATACTCCTACTA 59.603 40.741 0.00 0.00 0.00 1.82
2720 2977 6.212388 CCTTGATGCTCCAATATACTCCTACT 59.788 42.308 0.00 0.00 0.00 2.57
2724 2981 5.489792 TCCTTGATGCTCCAATATACTCC 57.510 43.478 0.00 0.00 0.00 3.85
2725 2982 8.481314 TGATATCCTTGATGCTCCAATATACTC 58.519 37.037 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.