Multiple sequence alignment - TraesCS4D01G330000

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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 TraesCS4D01G330000 chr4D 100.000 2426 0 0 1 2426 488494368 488496793 0.000000e+00 4481.0
1 TraesCS4D01G330000 chr4D 94.137 597 27 5 1 591 471814716 471815310 0.000000e+00 902.0
2 TraesCS4D01G330000 chr4D 95.402 87 3 1 521 607 301506863 301506778 1.170000e-28 137.0
3 TraesCS4D01G330000 chr4B 90.136 811 28 21 1665 2426 625118679 625119486 0.000000e+00 1007.0
4 TraesCS4D01G330000 chr4B 86.239 763 50 19 898 1637 624871108 624871838 0.000000e+00 776.0
5 TraesCS4D01G330000 chr5A 89.617 809 26 22 1658 2423 670250906 670251699 0.000000e+00 976.0
6 TraesCS4D01G330000 chr5A 93.960 596 30 2 1 590 584710081 584710676 0.000000e+00 896.0
7 TraesCS4D01G330000 chr5A 93.635 597 27 8 940 1530 670250145 670250736 0.000000e+00 881.0
8 TraesCS4D01G330000 chr5A 86.957 46 6 0 592 637 46624582 46624537 4.000000e-03 52.8
9 TraesCS4D01G330000 chr2D 95.537 605 20 3 1 600 429202375 429202977 0.000000e+00 961.0
10 TraesCS4D01G330000 chr2D 94.966 596 20 5 1 591 201456025 201456615 0.000000e+00 926.0
11 TraesCS4D01G330000 chr2D 94.781 594 26 1 1 589 511531776 511532369 0.000000e+00 920.0
12 TraesCS4D01G330000 chr2A 94.932 592 23 4 1 587 446012668 446012079 0.000000e+00 920.0
13 TraesCS4D01G330000 chr2A 84.043 94 14 1 521 613 723536495 723536402 3.320000e-14 89.8
14 TraesCS4D01G330000 chr5D 94.640 597 23 5 1 592 493829880 493829288 0.000000e+00 917.0
15 TraesCS4D01G330000 chr5D 88.636 88 8 2 521 607 464610608 464610522 3.300000e-19 106.0
16 TraesCS4D01G330000 chr5D 85.417 96 12 2 521 614 386143944 386143849 5.520000e-17 99.0
17 TraesCS4D01G330000 chr7D 94.157 599 26 4 1 593 602028196 602028791 0.000000e+00 904.0
18 TraesCS4D01G330000 chr7D 87.156 109 5 7 521 627 593670710 593670609 5.480000e-22 115.0
19 TraesCS4D01G330000 chr7A 93.792 596 31 2 1 591 563873049 563873643 0.000000e+00 891.0
20 TraesCS4D01G330000 chr7B 78.484 409 70 14 217 608 25633950 25634357 4.000000e-63 252.0
21 TraesCS4D01G330000 chr1D 77.156 429 69 23 198 606 291082701 291083120 3.140000e-54 222.0
22 TraesCS4D01G330000 chr3D 92.222 90 2 2 522 607 471961567 471961479 3.280000e-24 122.0
23 TraesCS4D01G330000 chrUn 97.222 36 1 0 589 624 62656171 62656206 7.240000e-06 62.1
24 TraesCS4D01G330000 chr2B 94.595 37 2 0 592 628 748490274 748490238 9.370000e-05 58.4
25 TraesCS4D01G330000 chr6B 90.698 43 3 1 592 634 62005090 62005049 3.370000e-04 56.5
26 TraesCS4D01G330000 chr4A 92.308 39 3 0 589 627 266932822 266932860 3.370000e-04 56.5
27 TraesCS4D01G330000 chr1B 87.500 48 4 2 592 637 345500269 345500222 1.000000e-03 54.7


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 TraesCS4D01G330000 chr4D 488494368 488496793 2425 False 4481.0 4481 100.000 1 2426 1 chr4D.!!$F2 2425
1 TraesCS4D01G330000 chr4D 471814716 471815310 594 False 902.0 902 94.137 1 591 1 chr4D.!!$F1 590
2 TraesCS4D01G330000 chr4B 625118679 625119486 807 False 1007.0 1007 90.136 1665 2426 1 chr4B.!!$F2 761
3 TraesCS4D01G330000 chr4B 624871108 624871838 730 False 776.0 776 86.239 898 1637 1 chr4B.!!$F1 739
4 TraesCS4D01G330000 chr5A 670250145 670251699 1554 False 928.5 976 91.626 940 2423 2 chr5A.!!$F2 1483
5 TraesCS4D01G330000 chr5A 584710081 584710676 595 False 896.0 896 93.960 1 590 1 chr5A.!!$F1 589
6 TraesCS4D01G330000 chr2D 429202375 429202977 602 False 961.0 961 95.537 1 600 1 chr2D.!!$F2 599
7 TraesCS4D01G330000 chr2D 201456025 201456615 590 False 926.0 926 94.966 1 591 1 chr2D.!!$F1 590
8 TraesCS4D01G330000 chr2D 511531776 511532369 593 False 920.0 920 94.781 1 589 1 chr2D.!!$F3 588
9 TraesCS4D01G330000 chr2A 446012079 446012668 589 True 920.0 920 94.932 1 587 1 chr2A.!!$R1 586
10 TraesCS4D01G330000 chr5D 493829288 493829880 592 True 917.0 917 94.640 1 592 1 chr5D.!!$R3 591
11 TraesCS4D01G330000 chr7D 602028196 602028791 595 False 904.0 904 94.157 1 593 1 chr7D.!!$F1 592
12 TraesCS4D01G330000 chr7A 563873049 563873643 594 False 891.0 891 93.792 1 591 1 chr7A.!!$F1 590

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
851 861 0.249741 CACGTTCTCCCGGTTGACTT 60.25 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1890 1.141881 ATTGAGGTGCGTCGCTAGG 59.858 57.895 19.5 0.0 0.0 3.02 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
38 39 2.348104 TAGTGCGCGAGTGGGTCAT 61.348 57.895 12.10 0.00 0.00 3.06
158 159 2.500165 CCTGCAGATGCTCGAGCT 59.500 61.111 35.27 22.01 42.66 4.09
592 602 2.076863 CCCGTTGGAGTTGCTCTTAAG 58.923 52.381 0.00 0.00 0.00 1.85
593 603 2.550208 CCCGTTGGAGTTGCTCTTAAGT 60.550 50.000 1.63 0.00 0.00 2.24
594 604 2.737252 CCGTTGGAGTTGCTCTTAAGTC 59.263 50.000 1.63 0.00 0.00 3.01
595 605 3.390135 CGTTGGAGTTGCTCTTAAGTCA 58.610 45.455 1.63 0.00 32.78 3.41
597 607 4.092091 CGTTGGAGTTGCTCTTAAGTCATC 59.908 45.833 1.63 2.17 32.78 2.92
598 608 5.241662 GTTGGAGTTGCTCTTAAGTCATCT 58.758 41.667 1.63 6.58 32.78 2.90
599 609 6.398918 GTTGGAGTTGCTCTTAAGTCATCTA 58.601 40.000 1.63 0.00 32.78 1.98
600 610 6.798427 TGGAGTTGCTCTTAAGTCATCTAT 57.202 37.500 1.63 0.00 32.78 1.98
601 611 7.187824 TGGAGTTGCTCTTAAGTCATCTATT 57.812 36.000 1.63 0.00 32.78 1.73
602 612 7.624549 TGGAGTTGCTCTTAAGTCATCTATTT 58.375 34.615 1.63 0.00 32.78 1.40
603 613 8.103305 TGGAGTTGCTCTTAAGTCATCTATTTT 58.897 33.333 1.63 0.00 32.78 1.82
604 614 8.394121 GGAGTTGCTCTTAAGTCATCTATTTTG 58.606 37.037 1.63 0.00 32.78 2.44
605 615 9.155975 GAGTTGCTCTTAAGTCATCTATTTTGA 57.844 33.333 1.63 0.00 31.73 2.69
606 616 9.507329 AGTTGCTCTTAAGTCATCTATTTTGAA 57.493 29.630 1.63 0.00 0.00 2.69
609 619 8.443160 TGCTCTTAAGTCATCTATTTTGAAACG 58.557 33.333 1.63 0.00 0.00 3.60
610 620 7.905493 GCTCTTAAGTCATCTATTTTGAAACGG 59.095 37.037 1.63 0.00 0.00 4.44
611 621 9.151471 CTCTTAAGTCATCTATTTTGAAACGGA 57.849 33.333 1.63 0.00 0.00 4.69
612 622 9.151471 TCTTAAGTCATCTATTTTGAAACGGAG 57.849 33.333 1.63 0.00 0.00 4.63
613 623 6.743575 AAGTCATCTATTTTGAAACGGAGG 57.256 37.500 0.00 0.00 0.00 4.30
614 624 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
615 625 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
616 626 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
617 627 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
618 628 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
619 629 5.727434 TCTATTTTGAAACGGAGGGAGTAC 58.273 41.667 0.00 0.00 0.00 2.73
620 630 3.842007 TTTTGAAACGGAGGGAGTACA 57.158 42.857 0.00 0.00 0.00 2.90
621 631 4.360951 TTTTGAAACGGAGGGAGTACAT 57.639 40.909 0.00 0.00 0.00 2.29
622 632 3.328382 TTGAAACGGAGGGAGTACATG 57.672 47.619 0.00 0.00 0.00 3.21
623 633 1.553248 TGAAACGGAGGGAGTACATGG 59.447 52.381 0.00 0.00 0.00 3.66
624 634 1.553704 GAAACGGAGGGAGTACATGGT 59.446 52.381 0.00 0.00 0.00 3.55
625 635 2.537633 AACGGAGGGAGTACATGGTA 57.462 50.000 0.00 0.00 0.00 3.25
626 636 2.537633 ACGGAGGGAGTACATGGTAA 57.462 50.000 0.00 0.00 0.00 2.85
627 637 2.823959 ACGGAGGGAGTACATGGTAAA 58.176 47.619 0.00 0.00 0.00 2.01
628 638 3.175594 ACGGAGGGAGTACATGGTAAAA 58.824 45.455 0.00 0.00 0.00 1.52
629 639 3.583966 ACGGAGGGAGTACATGGTAAAAA 59.416 43.478 0.00 0.00 0.00 1.94
630 640 4.226620 ACGGAGGGAGTACATGGTAAAAAT 59.773 41.667 0.00 0.00 0.00 1.82
631 641 4.574828 CGGAGGGAGTACATGGTAAAAATG 59.425 45.833 0.00 0.00 0.00 2.32
632 642 5.506708 GGAGGGAGTACATGGTAAAAATGT 58.493 41.667 0.00 0.00 41.14 2.71
633 643 5.949952 GGAGGGAGTACATGGTAAAAATGTT 59.050 40.000 0.00 0.00 39.05 2.71
634 644 6.436218 GGAGGGAGTACATGGTAAAAATGTTT 59.564 38.462 0.00 0.00 39.05 2.83
635 645 7.227049 AGGGAGTACATGGTAAAAATGTTTG 57.773 36.000 0.00 0.00 39.05 2.93
636 646 7.007723 AGGGAGTACATGGTAAAAATGTTTGA 58.992 34.615 0.00 0.00 39.05 2.69
637 647 7.507616 AGGGAGTACATGGTAAAAATGTTTGAA 59.492 33.333 0.00 0.00 39.05 2.69
638 648 7.597369 GGGAGTACATGGTAAAAATGTTTGAAC 59.403 37.037 0.00 0.00 39.05 3.18
639 649 7.325097 GGAGTACATGGTAAAAATGTTTGAACG 59.675 37.037 0.00 0.00 39.05 3.95
640 650 5.898630 ACATGGTAAAAATGTTTGAACGC 57.101 34.783 0.00 0.00 34.60 4.84
641 651 5.352284 ACATGGTAAAAATGTTTGAACGCA 58.648 33.333 0.00 0.00 34.60 5.24
642 652 5.988561 ACATGGTAAAAATGTTTGAACGCAT 59.011 32.000 0.00 0.00 34.60 4.73
643 653 6.481644 ACATGGTAAAAATGTTTGAACGCATT 59.518 30.769 0.00 0.00 34.60 3.56
644 654 6.910536 TGGTAAAAATGTTTGAACGCATTT 57.089 29.167 0.00 0.00 44.29 2.32
681 691 8.547894 TCATGTCAAACATACTATAAATGTCGC 58.452 33.333 0.00 0.00 36.53 5.19
682 692 6.928820 TGTCAAACATACTATAAATGTCGCG 58.071 36.000 0.00 0.00 36.56 5.87
683 693 6.532302 TGTCAAACATACTATAAATGTCGCGT 59.468 34.615 5.77 0.00 36.56 6.01
684 694 6.839301 GTCAAACATACTATAAATGTCGCGTG 59.161 38.462 5.77 0.00 36.56 5.34
685 695 5.900339 AACATACTATAAATGTCGCGTGG 57.100 39.130 5.77 0.00 36.56 4.94
686 696 4.304110 ACATACTATAAATGTCGCGTGGG 58.696 43.478 5.77 0.00 32.02 4.61
687 697 2.973694 ACTATAAATGTCGCGTGGGT 57.026 45.000 5.77 0.00 0.00 4.51
688 698 2.817901 ACTATAAATGTCGCGTGGGTC 58.182 47.619 5.77 0.00 0.00 4.46
689 699 1.784856 CTATAAATGTCGCGTGGGTCG 59.215 52.381 5.77 0.00 43.12 4.79
690 700 0.808453 ATAAATGTCGCGTGGGTCGG 60.808 55.000 5.77 0.00 40.26 4.79
702 712 4.368543 GGTCGGGTCGGGTGTGTC 62.369 72.222 0.00 0.00 0.00 3.67
703 713 4.712425 GTCGGGTCGGGTGTGTCG 62.712 72.222 0.00 0.00 0.00 4.35
727 737 4.368543 GTGTGGTCGGGTCGGGTC 62.369 72.222 0.00 0.00 0.00 4.46
741 751 2.755469 GGTCGGGCGGGTACTGTA 60.755 66.667 0.00 0.00 36.83 2.74
742 752 2.491621 GTCGGGCGGGTACTGTAC 59.508 66.667 9.46 9.46 36.83 2.90
743 753 2.048603 GTCGGGCGGGTACTGTACT 61.049 63.158 16.79 0.00 36.83 2.73
744 754 1.750399 TCGGGCGGGTACTGTACTC 60.750 63.158 16.79 12.58 36.83 2.59
745 755 2.779033 CGGGCGGGTACTGTACTCC 61.779 68.421 16.79 14.46 36.83 3.85
746 756 2.429767 GGGCGGGTACTGTACTCCC 61.430 68.421 16.79 18.43 36.83 4.30
747 757 2.429767 GGCGGGTACTGTACTCCCC 61.430 68.421 16.79 11.47 38.09 4.81
749 759 3.214253 GGGTACTGTACTCCCCGC 58.786 66.667 16.79 0.14 35.52 6.13
750 760 1.683365 GGGTACTGTACTCCCCGCA 60.683 63.158 16.79 0.00 35.52 5.69
751 761 1.047034 GGGTACTGTACTCCCCGCAT 61.047 60.000 16.79 0.00 35.52 4.73
752 762 0.828677 GGTACTGTACTCCCCGCATT 59.171 55.000 16.79 0.00 0.00 3.56
753 763 1.208776 GGTACTGTACTCCCCGCATTT 59.791 52.381 16.79 0.00 0.00 2.32
754 764 2.547826 GTACTGTACTCCCCGCATTTC 58.452 52.381 10.64 0.00 0.00 2.17
755 765 0.981183 ACTGTACTCCCCGCATTTCA 59.019 50.000 0.00 0.00 0.00 2.69
756 766 1.559682 ACTGTACTCCCCGCATTTCAT 59.440 47.619 0.00 0.00 0.00 2.57
757 767 2.769663 ACTGTACTCCCCGCATTTCATA 59.230 45.455 0.00 0.00 0.00 2.15
758 768 3.199071 ACTGTACTCCCCGCATTTCATAA 59.801 43.478 0.00 0.00 0.00 1.90
759 769 4.141482 ACTGTACTCCCCGCATTTCATAAT 60.141 41.667 0.00 0.00 0.00 1.28
760 770 4.787551 TGTACTCCCCGCATTTCATAATT 58.212 39.130 0.00 0.00 0.00 1.40
761 771 4.819630 TGTACTCCCCGCATTTCATAATTC 59.180 41.667 0.00 0.00 0.00 2.17
762 772 4.170468 ACTCCCCGCATTTCATAATTCT 57.830 40.909 0.00 0.00 0.00 2.40
763 773 4.536765 ACTCCCCGCATTTCATAATTCTT 58.463 39.130 0.00 0.00 0.00 2.52
764 774 4.580580 ACTCCCCGCATTTCATAATTCTTC 59.419 41.667 0.00 0.00 0.00 2.87
765 775 3.563808 TCCCCGCATTTCATAATTCTTCG 59.436 43.478 0.00 0.00 0.00 3.79
766 776 3.563808 CCCCGCATTTCATAATTCTTCGA 59.436 43.478 0.00 0.00 0.00 3.71
767 777 4.216257 CCCCGCATTTCATAATTCTTCGAT 59.784 41.667 0.00 0.00 0.00 3.59
768 778 5.385617 CCCGCATTTCATAATTCTTCGATC 58.614 41.667 0.00 0.00 0.00 3.69
769 779 5.075448 CCGCATTTCATAATTCTTCGATCG 58.925 41.667 9.36 9.36 0.00 3.69
770 780 5.107491 CCGCATTTCATAATTCTTCGATCGA 60.107 40.000 15.15 15.15 0.00 3.59
771 781 6.401474 CCGCATTTCATAATTCTTCGATCGAT 60.401 38.462 20.18 5.98 0.00 3.59
772 782 6.676163 CGCATTTCATAATTCTTCGATCGATC 59.324 38.462 20.18 15.68 0.00 3.69
773 783 7.513132 GCATTTCATAATTCTTCGATCGATCA 58.487 34.615 24.40 5.47 0.00 2.92
774 784 7.687347 GCATTTCATAATTCTTCGATCGATCAG 59.313 37.037 24.40 14.48 0.00 2.90
775 785 8.919661 CATTTCATAATTCTTCGATCGATCAGA 58.080 33.333 24.40 16.71 0.00 3.27
776 786 7.859613 TTCATAATTCTTCGATCGATCAGAC 57.140 36.000 24.40 0.00 0.00 3.51
777 787 6.080406 TCATAATTCTTCGATCGATCAGACG 58.920 40.000 24.40 18.08 0.00 4.18
778 788 3.972950 ATTCTTCGATCGATCAGACGT 57.027 42.857 24.40 8.16 34.70 4.34
779 789 3.320733 TTCTTCGATCGATCAGACGTC 57.679 47.619 24.40 7.70 34.70 4.34
780 790 2.552031 TCTTCGATCGATCAGACGTCT 58.448 47.619 24.40 13.58 34.70 4.18
781 791 2.285488 TCTTCGATCGATCAGACGTCTG 59.715 50.000 34.76 34.76 45.08 3.51
782 792 1.653151 TCGATCGATCAGACGTCTGT 58.347 50.000 37.21 26.87 44.12 3.41
783 793 1.327764 TCGATCGATCAGACGTCTGTG 59.672 52.381 37.21 28.40 44.12 3.66
784 794 1.595732 CGATCGATCAGACGTCTGTGG 60.596 57.143 37.21 27.66 44.12 4.17
785 795 1.402259 GATCGATCAGACGTCTGTGGT 59.598 52.381 37.21 26.54 44.12 4.16
786 796 1.244816 TCGATCAGACGTCTGTGGTT 58.755 50.000 37.21 23.50 44.12 3.67
787 797 1.611977 TCGATCAGACGTCTGTGGTTT 59.388 47.619 37.21 21.39 44.12 3.27
788 798 2.035449 TCGATCAGACGTCTGTGGTTTT 59.965 45.455 37.21 19.89 44.12 2.43
789 799 3.253921 TCGATCAGACGTCTGTGGTTTTA 59.746 43.478 37.21 21.49 44.12 1.52
790 800 3.364023 CGATCAGACGTCTGTGGTTTTAC 59.636 47.826 37.21 21.04 44.12 2.01
791 801 2.734670 TCAGACGTCTGTGGTTTTACG 58.265 47.619 37.21 14.50 44.12 3.18
792 802 2.358582 TCAGACGTCTGTGGTTTTACGA 59.641 45.455 37.21 17.03 44.12 3.43
793 803 2.724690 CAGACGTCTGTGGTTTTACGAG 59.275 50.000 32.77 6.84 39.09 4.18
794 804 2.360165 AGACGTCTGTGGTTTTACGAGT 59.640 45.455 19.30 0.00 38.64 4.18
795 805 2.723143 GACGTCTGTGGTTTTACGAGTC 59.277 50.000 8.70 0.00 38.64 3.36
796 806 2.360165 ACGTCTGTGGTTTTACGAGTCT 59.640 45.455 0.00 0.00 38.64 3.24
797 807 2.978489 CGTCTGTGGTTTTACGAGTCTC 59.022 50.000 0.00 0.00 37.53 3.36
798 808 2.978489 GTCTGTGGTTTTACGAGTCTCG 59.022 50.000 20.57 20.57 46.93 4.04
807 817 3.351450 CGAGTCTCGTGGTGTGGA 58.649 61.111 14.27 0.00 34.72 4.02
808 818 1.081376 CGAGTCTCGTGGTGTGGAC 60.081 63.158 14.27 0.00 34.72 4.02
809 819 1.516365 CGAGTCTCGTGGTGTGGACT 61.516 60.000 14.27 0.00 41.05 3.85
810 820 0.674534 GAGTCTCGTGGTGTGGACTT 59.325 55.000 0.00 0.00 38.87 3.01
811 821 0.674534 AGTCTCGTGGTGTGGACTTC 59.325 55.000 0.00 0.00 35.82 3.01
812 822 0.674534 GTCTCGTGGTGTGGACTTCT 59.325 55.000 0.00 0.00 0.00 2.85
813 823 0.673985 TCTCGTGGTGTGGACTTCTG 59.326 55.000 0.00 0.00 0.00 3.02
814 824 0.673985 CTCGTGGTGTGGACTTCTGA 59.326 55.000 0.00 0.00 0.00 3.27
815 825 0.673985 TCGTGGTGTGGACTTCTGAG 59.326 55.000 0.00 0.00 0.00 3.35
816 826 0.389391 CGTGGTGTGGACTTCTGAGT 59.611 55.000 0.00 0.00 39.32 3.41
826 836 1.527311 GACTTCTGAGTCGGTGTTTGC 59.473 52.381 0.00 0.00 42.60 3.68
827 837 0.508641 CTTCTGAGTCGGTGTTTGCG 59.491 55.000 0.00 0.00 0.00 4.85
828 838 1.495584 TTCTGAGTCGGTGTTTGCGC 61.496 55.000 0.00 0.00 0.00 6.09
829 839 3.281751 CTGAGTCGGTGTTTGCGCG 62.282 63.158 0.00 0.00 0.00 6.86
830 840 4.719616 GAGTCGGTGTTTGCGCGC 62.720 66.667 27.26 27.26 0.00 6.86
846 856 4.324991 GCCCACGTTCTCCCGGTT 62.325 66.667 0.00 0.00 0.00 4.44
847 857 2.358247 CCCACGTTCTCCCGGTTG 60.358 66.667 0.00 0.00 0.00 3.77
848 858 2.738480 CCACGTTCTCCCGGTTGA 59.262 61.111 0.00 0.00 0.00 3.18
849 859 1.666872 CCACGTTCTCCCGGTTGAC 60.667 63.158 0.00 0.00 0.00 3.18
850 860 1.366366 CACGTTCTCCCGGTTGACT 59.634 57.895 0.00 0.00 0.00 3.41
851 861 0.249741 CACGTTCTCCCGGTTGACTT 60.250 55.000 0.00 0.00 0.00 3.01
852 862 0.466963 ACGTTCTCCCGGTTGACTTT 59.533 50.000 0.00 0.00 0.00 2.66
853 863 1.688197 ACGTTCTCCCGGTTGACTTTA 59.312 47.619 0.00 0.00 0.00 1.85
854 864 2.102925 ACGTTCTCCCGGTTGACTTTAA 59.897 45.455 0.00 0.00 0.00 1.52
855 865 2.477754 CGTTCTCCCGGTTGACTTTAAC 59.522 50.000 0.00 0.00 0.00 2.01
856 866 2.810274 GTTCTCCCGGTTGACTTTAACC 59.190 50.000 0.00 0.00 45.28 2.85
866 876 5.488645 GTTGACTTTAACCAAAGACCGAA 57.511 39.130 4.23 0.00 43.32 4.30
867 877 5.268544 GTTGACTTTAACCAAAGACCGAAC 58.731 41.667 4.23 0.00 43.32 3.95
868 878 4.515361 TGACTTTAACCAAAGACCGAACA 58.485 39.130 4.23 0.00 43.32 3.18
869 879 4.573201 TGACTTTAACCAAAGACCGAACAG 59.427 41.667 4.23 0.00 43.32 3.16
870 880 4.773013 ACTTTAACCAAAGACCGAACAGA 58.227 39.130 4.23 0.00 43.32 3.41
871 881 5.187687 ACTTTAACCAAAGACCGAACAGAA 58.812 37.500 4.23 0.00 43.32 3.02
872 882 5.296035 ACTTTAACCAAAGACCGAACAGAAG 59.704 40.000 4.23 0.00 43.32 2.85
873 883 1.594331 ACCAAAGACCGAACAGAAGC 58.406 50.000 0.00 0.00 0.00 3.86
874 884 1.141053 ACCAAAGACCGAACAGAAGCT 59.859 47.619 0.00 0.00 0.00 3.74
875 885 2.222027 CCAAAGACCGAACAGAAGCTT 58.778 47.619 0.00 0.00 0.00 3.74
876 886 2.224314 CCAAAGACCGAACAGAAGCTTC 59.776 50.000 19.11 19.11 0.00 3.86
877 887 3.134458 CAAAGACCGAACAGAAGCTTCT 58.866 45.455 23.49 23.49 38.25 2.85
878 888 2.734276 AGACCGAACAGAAGCTTCTC 57.266 50.000 26.18 14.39 34.74 2.87
879 889 1.964223 AGACCGAACAGAAGCTTCTCA 59.036 47.619 26.18 0.00 34.74 3.27
880 890 2.365617 AGACCGAACAGAAGCTTCTCAA 59.634 45.455 26.18 0.00 34.74 3.02
881 891 3.131396 GACCGAACAGAAGCTTCTCAAA 58.869 45.455 26.18 0.00 34.74 2.69
882 892 2.872858 ACCGAACAGAAGCTTCTCAAAC 59.127 45.455 26.18 15.59 34.74 2.93
883 893 2.096713 CCGAACAGAAGCTTCTCAAACG 60.097 50.000 26.18 24.18 34.74 3.60
884 894 2.660362 CGAACAGAAGCTTCTCAAACGC 60.660 50.000 26.18 11.19 34.74 4.84
885 895 1.230324 ACAGAAGCTTCTCAAACGCC 58.770 50.000 26.18 0.00 34.74 5.68
886 896 0.519077 CAGAAGCTTCTCAAACGCCC 59.481 55.000 26.18 0.00 34.74 6.13
887 897 0.951040 AGAAGCTTCTCAAACGCCCG 60.951 55.000 23.49 0.00 29.94 6.13
888 898 1.912371 GAAGCTTCTCAAACGCCCGG 61.912 60.000 19.44 0.00 0.00 5.73
889 899 2.668550 GCTTCTCAAACGCCCGGT 60.669 61.111 0.00 0.00 0.00 5.28
890 900 2.677979 GCTTCTCAAACGCCCGGTC 61.678 63.158 0.00 0.00 0.00 4.79
891 901 2.356553 TTCTCAAACGCCCGGTCG 60.357 61.111 1.92 1.92 0.00 4.79
892 902 3.154584 TTCTCAAACGCCCGGTCGT 62.155 57.895 3.85 3.85 45.58 4.34
893 903 3.110178 CTCAAACGCCCGGTCGTC 61.110 66.667 12.48 0.00 42.46 4.20
894 904 4.668118 TCAAACGCCCGGTCGTCC 62.668 66.667 12.48 0.00 42.46 4.79
895 905 4.675029 CAAACGCCCGGTCGTCCT 62.675 66.667 12.48 0.00 42.46 3.85
896 906 3.932483 AAACGCCCGGTCGTCCTT 61.932 61.111 12.48 0.00 42.46 3.36
935 949 4.783155 TCCTTCACCCCCAAGGAA 57.217 55.556 0.00 0.00 45.40 3.36
968 992 1.418334 CAAATCCCCCACACCAAACA 58.582 50.000 0.00 0.00 0.00 2.83
969 993 1.765314 CAAATCCCCCACACCAAACAA 59.235 47.619 0.00 0.00 0.00 2.83
970 994 1.419381 AATCCCCCACACCAAACAAC 58.581 50.000 0.00 0.00 0.00 3.32
980 1004 2.834549 ACACCAAACAACCATCCAAACA 59.165 40.909 0.00 0.00 0.00 2.83
993 1017 1.652012 CAAACAACACGGCCACGAT 59.348 52.632 2.24 0.00 44.60 3.73
1084 1111 2.525629 TGAACCTGTCGGCCTCCA 60.526 61.111 0.00 0.00 0.00 3.86
1296 1323 4.527157 GTCTACGACGACGGGCCG 62.527 72.222 27.06 27.06 44.46 6.13
1445 1478 1.507141 CCGCCGAGTTGTGAAGCTTT 61.507 55.000 0.00 0.00 0.00 3.51
1457 1490 1.745087 TGAAGCTTTGATTCATCCCGC 59.255 47.619 0.00 0.00 31.86 6.13
1503 1536 3.126001 TGTGTTTCCTTCCTGCTGTAG 57.874 47.619 0.00 0.00 0.00 2.74
1532 1568 8.959058 CAGCACTACTACTAGATGTAAAAATCG 58.041 37.037 0.00 0.00 0.00 3.34
1537 1573 9.798994 CTACTACTAGATGTAAAAATCGTTGGT 57.201 33.333 0.00 0.00 0.00 3.67
1541 1577 4.472286 AGATGTAAAAATCGTTGGTTGCG 58.528 39.130 0.00 0.00 0.00 4.85
1546 1582 4.707210 AAAAATCGTTGGTTGCGAAATG 57.293 36.364 0.00 0.00 41.84 2.32
1553 1589 3.443976 GTTGGTTGCGAAATGAACTTGT 58.556 40.909 0.00 0.00 0.00 3.16
1557 1593 3.059461 GGTTGCGAAATGAACTTGTACGA 60.059 43.478 0.00 0.00 0.00 3.43
1561 1597 3.427528 GCGAAATGAACTTGTACGAGTGA 59.572 43.478 16.68 7.07 0.00 3.41
1572 1608 5.756347 ACTTGTACGAGTGAAATTTGCTGTA 59.244 36.000 15.25 0.00 0.00 2.74
1584 1621 8.057742 GTGAAATTTGCTGTAAATTGTGTGAAG 58.942 33.333 15.53 0.00 45.74 3.02
1595 1632 2.347697 TGTGTGAAGATCGAAGACGG 57.652 50.000 0.00 0.00 42.51 4.79
1608 1645 2.673893 CGAAGACGGTGTGATCCATCAA 60.674 50.000 0.00 0.00 35.74 2.57
1611 1648 0.984230 ACGGTGTGATCCATCAACCT 59.016 50.000 14.05 4.62 38.75 3.50
1618 1655 4.023193 GTGTGATCCATCAACCTTCGTTTT 60.023 41.667 0.00 0.00 38.75 2.43
1620 1657 5.765677 TGTGATCCATCAACCTTCGTTTTAA 59.234 36.000 0.00 0.00 38.75 1.52
1621 1658 6.084277 GTGATCCATCAACCTTCGTTTTAAC 58.916 40.000 0.00 0.00 38.75 2.01
1622 1659 6.001460 TGATCCATCAACCTTCGTTTTAACT 58.999 36.000 0.00 0.00 33.08 2.24
1623 1660 5.682943 TCCATCAACCTTCGTTTTAACTG 57.317 39.130 0.00 0.00 0.00 3.16
1624 1661 5.127491 TCCATCAACCTTCGTTTTAACTGT 58.873 37.500 0.00 0.00 0.00 3.55
1625 1662 5.591067 TCCATCAACCTTCGTTTTAACTGTT 59.409 36.000 0.00 0.00 0.00 3.16
1626 1663 5.912955 CCATCAACCTTCGTTTTAACTGTTC 59.087 40.000 0.00 0.00 0.00 3.18
1627 1664 6.238648 CCATCAACCTTCGTTTTAACTGTTCT 60.239 38.462 0.00 0.00 0.00 3.01
1628 1665 6.114221 TCAACCTTCGTTTTAACTGTTCTG 57.886 37.500 0.00 0.00 0.00 3.02
1629 1666 5.875910 TCAACCTTCGTTTTAACTGTTCTGA 59.124 36.000 0.00 0.00 0.00 3.27
1630 1667 6.372103 TCAACCTTCGTTTTAACTGTTCTGAA 59.628 34.615 0.00 0.00 0.00 3.02
1631 1668 6.937436 ACCTTCGTTTTAACTGTTCTGAAT 57.063 33.333 0.00 0.00 0.00 2.57
1657 1694 7.926674 TCTGATCTGATTTGCTGTGAAAATA 57.073 32.000 0.00 0.00 0.00 1.40
1659 1696 6.558009 TGATCTGATTTGCTGTGAAAATAGC 58.442 36.000 0.00 0.00 40.29 2.97
1735 1877 3.162858 AACCCAACCGACGACCCA 61.163 61.111 0.00 0.00 0.00 4.51
1740 1882 4.303993 AACCGACGACCCAACCCG 62.304 66.667 0.00 0.00 0.00 5.28
1742 1884 4.729856 CCGACGACCCAACCCGAC 62.730 72.222 0.00 0.00 0.00 4.79
1743 1885 4.729856 CGACGACCCAACCCGACC 62.730 72.222 0.00 0.00 0.00 4.79
1744 1886 4.383861 GACGACCCAACCCGACCC 62.384 72.222 0.00 0.00 0.00 4.46
1747 1889 4.383861 GACCCAACCCGACCCGAC 62.384 72.222 0.00 0.00 0.00 4.79
1751 1893 2.681064 CAACCCGACCCGACCCTA 60.681 66.667 0.00 0.00 0.00 3.53
1752 1894 2.363406 AACCCGACCCGACCCTAG 60.363 66.667 0.00 0.00 0.00 3.02
1762 1904 3.450115 GACCCTAGCGACGCACCT 61.450 66.667 23.70 3.65 0.00 4.00
1764 1906 3.449227 CCCTAGCGACGCACCTCA 61.449 66.667 23.70 0.26 0.00 3.86
1771 1913 2.359850 GACGCACCTCAATGGCCA 60.360 61.111 8.56 8.56 40.22 5.36
2319 2482 6.705381 TGCTGCTGCTTATGTTTGTTAATTTT 59.295 30.769 17.00 0.00 40.48 1.82
2320 2483 7.226325 TGCTGCTGCTTATGTTTGTTAATTTTT 59.774 29.630 17.00 0.00 40.48 1.94
2382 2575 2.494870 GCATTTCTTCCTTGTCATGCCT 59.505 45.455 0.00 0.00 32.53 4.75
2423 2616 7.352079 AGAAATGTGACAGGAAATCAACTTT 57.648 32.000 0.00 0.00 0.00 2.66
2424 2617 7.428826 AGAAATGTGACAGGAAATCAACTTTC 58.571 34.615 0.00 0.00 42.18 2.62
2425 2618 6.713762 AATGTGACAGGAAATCAACTTTCA 57.286 33.333 0.00 0.00 44.29 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 2.440430 CCTCCTCTTCGGCCTCGA 60.440 66.667 0.00 0.00 44.44 4.04
358 360 3.268103 AAGGCCGGCGAAAGTCCAT 62.268 57.895 22.54 0.00 0.00 3.41
592 602 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
593 603 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
594 604 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
595 605 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
597 607 5.484715 TGTACTCCCTCCGTTTCAAAATAG 58.515 41.667 0.00 0.00 0.00 1.73
598 608 5.486735 TGTACTCCCTCCGTTTCAAAATA 57.513 39.130 0.00 0.00 0.00 1.40
599 609 4.360951 TGTACTCCCTCCGTTTCAAAAT 57.639 40.909 0.00 0.00 0.00 1.82
600 610 3.842007 TGTACTCCCTCCGTTTCAAAA 57.158 42.857 0.00 0.00 0.00 2.44
601 611 3.558321 CCATGTACTCCCTCCGTTTCAAA 60.558 47.826 0.00 0.00 0.00 2.69
602 612 2.027561 CCATGTACTCCCTCCGTTTCAA 60.028 50.000 0.00 0.00 0.00 2.69
603 613 1.553248 CCATGTACTCCCTCCGTTTCA 59.447 52.381 0.00 0.00 0.00 2.69
604 614 1.553704 ACCATGTACTCCCTCCGTTTC 59.446 52.381 0.00 0.00 0.00 2.78
605 615 1.652947 ACCATGTACTCCCTCCGTTT 58.347 50.000 0.00 0.00 0.00 3.60
606 616 2.537633 TACCATGTACTCCCTCCGTT 57.462 50.000 0.00 0.00 0.00 4.44
607 617 2.537633 TTACCATGTACTCCCTCCGT 57.462 50.000 0.00 0.00 0.00 4.69
608 618 3.899052 TTTTACCATGTACTCCCTCCG 57.101 47.619 0.00 0.00 0.00 4.63
609 619 5.506708 ACATTTTTACCATGTACTCCCTCC 58.493 41.667 0.00 0.00 32.88 4.30
610 620 7.175990 TCAAACATTTTTACCATGTACTCCCTC 59.824 37.037 0.00 0.00 33.54 4.30
611 621 7.007723 TCAAACATTTTTACCATGTACTCCCT 58.992 34.615 0.00 0.00 33.54 4.20
612 622 7.222000 TCAAACATTTTTACCATGTACTCCC 57.778 36.000 0.00 0.00 33.54 4.30
613 623 7.325097 CGTTCAAACATTTTTACCATGTACTCC 59.675 37.037 0.00 0.00 33.54 3.85
614 624 7.149031 GCGTTCAAACATTTTTACCATGTACTC 60.149 37.037 0.00 0.00 33.54 2.59
615 625 6.639279 GCGTTCAAACATTTTTACCATGTACT 59.361 34.615 0.00 0.00 33.54 2.73
616 626 6.418226 TGCGTTCAAACATTTTTACCATGTAC 59.582 34.615 0.00 0.00 33.54 2.90
617 627 6.504398 TGCGTTCAAACATTTTTACCATGTA 58.496 32.000 0.00 0.00 33.54 2.29
618 628 5.352284 TGCGTTCAAACATTTTTACCATGT 58.648 33.333 0.00 0.00 36.36 3.21
619 629 5.896922 TGCGTTCAAACATTTTTACCATG 57.103 34.783 0.00 0.00 0.00 3.66
620 630 7.489574 AAATGCGTTCAAACATTTTTACCAT 57.510 28.000 0.00 0.00 42.34 3.55
621 631 6.910536 AAATGCGTTCAAACATTTTTACCA 57.089 29.167 0.00 0.00 42.34 3.25
655 665 8.547894 GCGACATTTATAGTATGTTTGACATGA 58.452 33.333 0.00 0.00 39.53 3.07
656 666 7.527183 CGCGACATTTATAGTATGTTTGACATG 59.473 37.037 0.00 0.00 39.53 3.21
657 667 7.223971 ACGCGACATTTATAGTATGTTTGACAT 59.776 33.333 15.93 0.00 42.35 3.06
658 668 6.532302 ACGCGACATTTATAGTATGTTTGACA 59.468 34.615 15.93 0.00 36.41 3.58
659 669 6.839301 CACGCGACATTTATAGTATGTTTGAC 59.161 38.462 15.93 0.00 36.41 3.18
660 670 6.019398 CCACGCGACATTTATAGTATGTTTGA 60.019 38.462 15.93 0.00 36.41 2.69
661 671 6.126741 CCACGCGACATTTATAGTATGTTTG 58.873 40.000 15.93 0.00 36.41 2.93
662 672 5.235616 CCCACGCGACATTTATAGTATGTTT 59.764 40.000 15.93 0.00 36.41 2.83
663 673 4.748102 CCCACGCGACATTTATAGTATGTT 59.252 41.667 15.93 0.00 36.41 2.71
664 674 4.202182 ACCCACGCGACATTTATAGTATGT 60.202 41.667 15.93 3.08 38.86 2.29
665 675 4.304110 ACCCACGCGACATTTATAGTATG 58.696 43.478 15.93 0.00 0.00 2.39
666 676 4.553323 GACCCACGCGACATTTATAGTAT 58.447 43.478 15.93 0.00 0.00 2.12
667 677 3.548616 CGACCCACGCGACATTTATAGTA 60.549 47.826 15.93 0.00 34.51 1.82
668 678 2.797087 CGACCCACGCGACATTTATAGT 60.797 50.000 15.93 0.00 34.51 2.12
669 679 1.784856 CGACCCACGCGACATTTATAG 59.215 52.381 15.93 0.00 34.51 1.31
670 680 1.536496 CCGACCCACGCGACATTTATA 60.536 52.381 15.93 0.00 41.07 0.98
671 681 0.808453 CCGACCCACGCGACATTTAT 60.808 55.000 15.93 0.00 41.07 1.40
672 682 1.446445 CCGACCCACGCGACATTTA 60.446 57.895 15.93 0.00 41.07 1.40
673 683 2.740826 CCGACCCACGCGACATTT 60.741 61.111 15.93 0.00 41.07 2.32
674 684 4.752879 CCCGACCCACGCGACATT 62.753 66.667 15.93 0.00 41.07 2.71
685 695 4.368543 GACACACCCGACCCGACC 62.369 72.222 0.00 0.00 0.00 4.79
686 696 4.712425 CGACACACCCGACCCGAC 62.712 72.222 0.00 0.00 0.00 4.79
710 720 4.368543 GACCCGACCCGACCACAC 62.369 72.222 0.00 0.00 0.00 3.82
724 734 2.755469 TACAGTACCCGCCCGACC 60.755 66.667 0.00 0.00 0.00 4.79
725 735 1.997928 GAGTACAGTACCCGCCCGAC 61.998 65.000 7.13 0.00 0.00 4.79
726 736 1.750399 GAGTACAGTACCCGCCCGA 60.750 63.158 7.13 0.00 0.00 5.14
727 737 2.779033 GGAGTACAGTACCCGCCCG 61.779 68.421 7.13 0.00 0.00 6.13
728 738 2.429767 GGGAGTACAGTACCCGCCC 61.430 68.421 14.81 14.81 34.03 6.13
729 739 2.429767 GGGGAGTACAGTACCCGCC 61.430 68.421 11.90 11.90 44.09 6.13
730 740 3.214253 GGGGAGTACAGTACCCGC 58.786 66.667 15.12 15.12 44.09 6.13
732 742 1.047034 ATGCGGGGAGTACAGTACCC 61.047 60.000 7.13 8.17 42.58 3.69
733 743 0.828677 AATGCGGGGAGTACAGTACC 59.171 55.000 7.13 0.00 0.00 3.34
734 744 2.093869 TGAAATGCGGGGAGTACAGTAC 60.094 50.000 2.05 2.05 0.00 2.73
735 745 2.181125 TGAAATGCGGGGAGTACAGTA 58.819 47.619 0.00 0.00 0.00 2.74
736 746 0.981183 TGAAATGCGGGGAGTACAGT 59.019 50.000 0.00 0.00 0.00 3.55
737 747 2.332063 ATGAAATGCGGGGAGTACAG 57.668 50.000 0.00 0.00 0.00 2.74
738 748 3.916359 TTATGAAATGCGGGGAGTACA 57.084 42.857 0.00 0.00 0.00 2.90
739 749 5.063880 AGAATTATGAAATGCGGGGAGTAC 58.936 41.667 0.00 0.00 0.00 2.73
740 750 5.304686 AGAATTATGAAATGCGGGGAGTA 57.695 39.130 0.00 0.00 0.00 2.59
741 751 4.170468 AGAATTATGAAATGCGGGGAGT 57.830 40.909 0.00 0.00 0.00 3.85
742 752 4.319766 CGAAGAATTATGAAATGCGGGGAG 60.320 45.833 0.00 0.00 0.00 4.30
743 753 3.563808 CGAAGAATTATGAAATGCGGGGA 59.436 43.478 0.00 0.00 0.00 4.81
744 754 3.563808 TCGAAGAATTATGAAATGCGGGG 59.436 43.478 0.00 0.00 0.00 5.73
745 755 4.811555 TCGAAGAATTATGAAATGCGGG 57.188 40.909 0.00 0.00 0.00 6.13
746 756 5.075448 CGATCGAAGAATTATGAAATGCGG 58.925 41.667 10.26 0.00 43.58 5.69
747 757 5.904802 TCGATCGAAGAATTATGAAATGCG 58.095 37.500 16.99 0.00 43.58 4.73
748 758 7.513132 TGATCGATCGAAGAATTATGAAATGC 58.487 34.615 23.50 0.00 43.58 3.56
749 759 8.919661 TCTGATCGATCGAAGAATTATGAAATG 58.080 33.333 23.50 0.00 43.58 2.32
750 760 8.920665 GTCTGATCGATCGAAGAATTATGAAAT 58.079 33.333 23.50 0.00 43.58 2.17
751 761 7.113544 CGTCTGATCGATCGAAGAATTATGAAA 59.886 37.037 23.50 0.00 43.58 2.69
752 762 6.578919 CGTCTGATCGATCGAAGAATTATGAA 59.421 38.462 23.50 0.00 43.58 2.57
753 763 6.080406 CGTCTGATCGATCGAAGAATTATGA 58.920 40.000 23.50 8.97 43.58 2.15
754 764 5.853810 ACGTCTGATCGATCGAAGAATTATG 59.146 40.000 23.50 12.84 43.58 1.90
755 765 6.003234 ACGTCTGATCGATCGAAGAATTAT 57.997 37.500 23.50 2.89 43.58 1.28
756 766 5.236695 AGACGTCTGATCGATCGAAGAATTA 59.763 40.000 23.50 1.01 43.58 1.40
757 767 4.035792 AGACGTCTGATCGATCGAAGAATT 59.964 41.667 23.50 10.97 43.58 2.17
758 768 3.562141 AGACGTCTGATCGATCGAAGAAT 59.438 43.478 23.50 12.45 43.58 2.40
759 769 2.937149 AGACGTCTGATCGATCGAAGAA 59.063 45.455 23.50 9.61 43.58 2.52
760 770 2.285488 CAGACGTCTGATCGATCGAAGA 59.715 50.000 36.73 18.18 46.59 2.87
761 771 2.031068 ACAGACGTCTGATCGATCGAAG 59.969 50.000 43.55 19.05 46.59 3.79
762 772 2.007608 ACAGACGTCTGATCGATCGAA 58.992 47.619 43.55 5.51 46.59 3.71
763 773 1.327764 CACAGACGTCTGATCGATCGA 59.672 52.381 43.55 21.86 46.59 3.59
764 774 1.595732 CCACAGACGTCTGATCGATCG 60.596 57.143 43.55 23.64 46.59 3.69
765 775 1.402259 ACCACAGACGTCTGATCGATC 59.598 52.381 43.55 18.72 46.59 3.69
766 776 1.464734 ACCACAGACGTCTGATCGAT 58.535 50.000 43.55 23.71 46.59 3.59
767 777 1.244816 AACCACAGACGTCTGATCGA 58.755 50.000 43.55 0.00 46.59 3.59
768 778 2.065993 AAACCACAGACGTCTGATCG 57.934 50.000 43.55 31.18 46.59 3.69
769 779 3.364023 CGTAAAACCACAGACGTCTGATC 59.636 47.826 43.55 23.56 46.59 2.92
770 780 3.005050 TCGTAAAACCACAGACGTCTGAT 59.995 43.478 43.55 27.80 46.59 2.90
771 781 2.358582 TCGTAAAACCACAGACGTCTGA 59.641 45.455 43.55 22.31 46.59 3.27
773 783 2.360165 ACTCGTAAAACCACAGACGTCT 59.640 45.455 13.58 13.58 36.69 4.18
774 784 2.723143 GACTCGTAAAACCACAGACGTC 59.277 50.000 7.70 7.70 36.69 4.34
775 785 2.360165 AGACTCGTAAAACCACAGACGT 59.640 45.455 0.00 0.00 36.69 4.34
776 786 2.978489 GAGACTCGTAAAACCACAGACG 59.022 50.000 0.00 0.00 36.66 4.18
777 787 2.978489 CGAGACTCGTAAAACCACAGAC 59.022 50.000 16.83 0.00 34.72 3.51
778 788 3.278367 CGAGACTCGTAAAACCACAGA 57.722 47.619 16.83 0.00 34.72 3.41
790 800 1.081376 GTCCACACCACGAGACTCG 60.081 63.158 22.97 22.97 46.93 4.18
791 801 0.674534 AAGTCCACACCACGAGACTC 59.325 55.000 0.00 0.00 38.61 3.36
792 802 0.674534 GAAGTCCACACCACGAGACT 59.325 55.000 0.00 0.00 41.25 3.24
793 803 0.674534 AGAAGTCCACACCACGAGAC 59.325 55.000 0.00 0.00 0.00 3.36
794 804 0.673985 CAGAAGTCCACACCACGAGA 59.326 55.000 0.00 0.00 0.00 4.04
795 805 0.673985 TCAGAAGTCCACACCACGAG 59.326 55.000 0.00 0.00 0.00 4.18
796 806 0.673985 CTCAGAAGTCCACACCACGA 59.326 55.000 0.00 0.00 0.00 4.35
797 807 0.389391 ACTCAGAAGTCCACACCACG 59.611 55.000 0.00 0.00 0.00 4.94
798 808 2.156343 GACTCAGAAGTCCACACCAC 57.844 55.000 0.00 0.00 45.26 4.16
807 817 1.583054 GCAAACACCGACTCAGAAGT 58.417 50.000 0.00 0.00 38.88 3.01
808 818 0.508641 CGCAAACACCGACTCAGAAG 59.491 55.000 0.00 0.00 0.00 2.85
809 819 1.495584 GCGCAAACACCGACTCAGAA 61.496 55.000 0.30 0.00 0.00 3.02
810 820 1.954146 GCGCAAACACCGACTCAGA 60.954 57.895 0.30 0.00 0.00 3.27
811 821 2.551270 GCGCAAACACCGACTCAG 59.449 61.111 0.30 0.00 0.00 3.35
812 822 3.334751 CGCGCAAACACCGACTCA 61.335 61.111 8.75 0.00 0.00 3.41
813 823 4.719616 GCGCGCAAACACCGACTC 62.720 66.667 29.10 0.00 0.00 3.36
829 839 4.324991 AACCGGGAGAACGTGGGC 62.325 66.667 6.32 0.00 0.00 5.36
830 840 2.358247 CAACCGGGAGAACGTGGG 60.358 66.667 6.32 0.00 0.00 4.61
831 841 1.666872 GTCAACCGGGAGAACGTGG 60.667 63.158 6.32 0.00 0.00 4.94
832 842 0.249741 AAGTCAACCGGGAGAACGTG 60.250 55.000 6.32 0.00 0.00 4.49
833 843 0.466963 AAAGTCAACCGGGAGAACGT 59.533 50.000 6.32 0.00 0.00 3.99
834 844 2.443887 TAAAGTCAACCGGGAGAACG 57.556 50.000 6.32 0.00 0.00 3.95
835 845 2.810274 GGTTAAAGTCAACCGGGAGAAC 59.190 50.000 6.32 0.00 38.74 3.01
836 846 3.130280 GGTTAAAGTCAACCGGGAGAA 57.870 47.619 6.32 0.00 38.74 2.87
837 847 2.845363 GGTTAAAGTCAACCGGGAGA 57.155 50.000 6.32 0.00 38.74 3.71
843 853 3.878699 TCGGTCTTTGGTTAAAGTCAACC 59.121 43.478 0.00 0.00 46.90 3.77
844 854 5.163733 TGTTCGGTCTTTGGTTAAAGTCAAC 60.164 40.000 0.00 0.00 43.04 3.18
845 855 4.942483 TGTTCGGTCTTTGGTTAAAGTCAA 59.058 37.500 0.00 0.00 43.04 3.18
846 856 4.515361 TGTTCGGTCTTTGGTTAAAGTCA 58.485 39.130 0.00 0.00 43.04 3.41
847 857 4.812626 TCTGTTCGGTCTTTGGTTAAAGTC 59.187 41.667 0.00 0.00 43.04 3.01
848 858 4.773013 TCTGTTCGGTCTTTGGTTAAAGT 58.227 39.130 0.00 0.00 43.04 2.66
849 859 5.744666 TTCTGTTCGGTCTTTGGTTAAAG 57.255 39.130 0.00 0.00 43.72 1.85
850 860 4.035909 GCTTCTGTTCGGTCTTTGGTTAAA 59.964 41.667 0.00 0.00 0.00 1.52
851 861 3.562557 GCTTCTGTTCGGTCTTTGGTTAA 59.437 43.478 0.00 0.00 0.00 2.01
852 862 3.135994 GCTTCTGTTCGGTCTTTGGTTA 58.864 45.455 0.00 0.00 0.00 2.85
853 863 1.947456 GCTTCTGTTCGGTCTTTGGTT 59.053 47.619 0.00 0.00 0.00 3.67
854 864 1.141053 AGCTTCTGTTCGGTCTTTGGT 59.859 47.619 0.00 0.00 0.00 3.67
855 865 1.884235 AGCTTCTGTTCGGTCTTTGG 58.116 50.000 0.00 0.00 0.00 3.28
856 866 3.134458 AGAAGCTTCTGTTCGGTCTTTG 58.866 45.455 27.96 0.00 35.89 2.77
857 867 3.181465 TGAGAAGCTTCTGTTCGGTCTTT 60.181 43.478 33.07 4.83 37.73 2.52
858 868 2.365617 TGAGAAGCTTCTGTTCGGTCTT 59.634 45.455 33.07 5.41 37.73 3.01
859 869 1.964223 TGAGAAGCTTCTGTTCGGTCT 59.036 47.619 33.07 6.04 37.73 3.85
860 870 2.440539 TGAGAAGCTTCTGTTCGGTC 57.559 50.000 33.07 16.96 37.73 4.79
861 871 2.872858 GTTTGAGAAGCTTCTGTTCGGT 59.127 45.455 33.07 7.84 37.73 4.69
862 872 2.096713 CGTTTGAGAAGCTTCTGTTCGG 60.097 50.000 33.07 15.08 37.73 4.30
863 873 2.660362 GCGTTTGAGAAGCTTCTGTTCG 60.660 50.000 33.07 26.93 37.73 3.95
864 874 2.349912 GGCGTTTGAGAAGCTTCTGTTC 60.350 50.000 33.07 19.10 37.73 3.18
865 875 1.604278 GGCGTTTGAGAAGCTTCTGTT 59.396 47.619 33.07 10.30 37.73 3.16
866 876 1.230324 GGCGTTTGAGAAGCTTCTGT 58.770 50.000 33.07 11.13 37.73 3.41
867 877 0.519077 GGGCGTTTGAGAAGCTTCTG 59.481 55.000 33.07 18.72 37.73 3.02
868 878 0.951040 CGGGCGTTTGAGAAGCTTCT 60.951 55.000 28.83 28.83 41.00 2.85
869 879 1.497722 CGGGCGTTTGAGAAGCTTC 59.502 57.895 19.11 19.11 0.00 3.86
870 880 1.966451 CCGGGCGTTTGAGAAGCTT 60.966 57.895 0.00 0.00 0.00 3.74
871 881 2.358737 CCGGGCGTTTGAGAAGCT 60.359 61.111 0.00 0.00 0.00 3.74
872 882 2.668550 ACCGGGCGTTTGAGAAGC 60.669 61.111 6.32 0.00 0.00 3.86
873 883 2.380410 CGACCGGGCGTTTGAGAAG 61.380 63.158 25.18 0.00 0.00 2.85
874 884 2.356553 CGACCGGGCGTTTGAGAA 60.357 61.111 25.18 0.00 0.00 2.87
875 885 3.562779 GACGACCGGGCGTTTGAGA 62.563 63.158 39.68 0.00 45.72 3.27
876 886 3.110178 GACGACCGGGCGTTTGAG 61.110 66.667 39.68 6.39 45.72 3.02
877 887 4.668118 GGACGACCGGGCGTTTGA 62.668 66.667 39.68 0.00 45.72 2.69
878 888 4.675029 AGGACGACCGGGCGTTTG 62.675 66.667 39.68 7.82 45.72 2.93
879 889 3.871248 GAAGGACGACCGGGCGTTT 62.871 63.158 39.68 29.06 45.72 3.60
880 890 4.368543 GAAGGACGACCGGGCGTT 62.369 66.667 39.68 23.26 45.72 4.84
882 892 3.869473 TTTGAAGGACGACCGGGCG 62.869 63.158 32.33 32.33 41.83 6.13
883 893 2.031465 TTTGAAGGACGACCGGGC 59.969 61.111 6.32 0.00 41.83 6.13
884 894 2.033194 GCTTTGAAGGACGACCGGG 61.033 63.158 6.32 0.00 41.83 5.73
885 895 1.004918 AGCTTTGAAGGACGACCGG 60.005 57.895 0.00 0.00 41.83 5.28
886 896 1.901650 GCAGCTTTGAAGGACGACCG 61.902 60.000 0.00 0.00 41.83 4.79
887 897 1.578206 GGCAGCTTTGAAGGACGACC 61.578 60.000 0.00 0.00 0.00 4.79
888 898 1.869690 GGCAGCTTTGAAGGACGAC 59.130 57.895 0.00 0.00 0.00 4.34
889 899 1.667830 CGGCAGCTTTGAAGGACGA 60.668 57.895 0.00 0.00 0.00 4.20
890 900 1.961277 ACGGCAGCTTTGAAGGACG 60.961 57.895 0.00 0.00 0.00 4.79
891 901 1.576421 CACGGCAGCTTTGAAGGAC 59.424 57.895 0.00 0.00 0.00 3.85
892 902 2.260869 GCACGGCAGCTTTGAAGGA 61.261 57.895 0.00 0.00 0.00 3.36
893 903 2.256461 GCACGGCAGCTTTGAAGG 59.744 61.111 0.00 0.00 0.00 3.46
894 904 2.256461 GGCACGGCAGCTTTGAAG 59.744 61.111 0.00 0.00 34.17 3.02
915 925 2.221299 CCTTGGGGGTGAAGGACGA 61.221 63.158 0.00 0.00 42.44 4.20
935 949 0.037734 GATTTGGAGGGGTGGTTCGT 59.962 55.000 0.00 0.00 0.00 3.85
968 992 0.387565 GCCGTGTTGTTTGGATGGTT 59.612 50.000 0.00 0.00 0.00 3.67
969 993 1.460273 GGCCGTGTTGTTTGGATGGT 61.460 55.000 0.00 0.00 0.00 3.55
970 994 1.288752 GGCCGTGTTGTTTGGATGG 59.711 57.895 0.00 0.00 0.00 3.51
980 1004 2.431942 GTCGATCGTGGCCGTGTT 60.432 61.111 15.94 0.00 35.01 3.32
1191 1218 1.517475 GAGCGTCTCGAAGAAGGGC 60.517 63.158 0.00 0.00 34.09 5.19
1430 1463 4.472691 TGAATCAAAGCTTCACAACTCG 57.527 40.909 0.00 0.00 0.00 4.18
1437 1470 1.745087 GCGGGATGAATCAAAGCTTCA 59.255 47.619 0.00 0.00 37.06 3.02
1445 1478 3.163832 ATCGCCGCGGGATGAATCA 62.164 57.895 29.38 0.00 33.98 2.57
1472 1505 2.423577 AGGAAACACATCTGTAACCGC 58.576 47.619 0.00 0.00 33.48 5.68
1474 1507 4.455877 CAGGAAGGAAACACATCTGTAACC 59.544 45.833 0.00 0.00 0.00 2.85
1532 1568 3.443976 ACAAGTTCATTTCGCAACCAAC 58.556 40.909 0.00 0.00 0.00 3.77
1537 1573 3.805422 ACTCGTACAAGTTCATTTCGCAA 59.195 39.130 0.00 0.00 0.00 4.85
1541 1577 8.682016 CAAATTTCACTCGTACAAGTTCATTTC 58.318 33.333 0.00 0.00 0.00 2.17
1546 1582 5.621228 CAGCAAATTTCACTCGTACAAGTTC 59.379 40.000 0.00 0.00 0.00 3.01
1553 1589 7.589587 CACAATTTACAGCAAATTTCACTCGTA 59.410 33.333 0.00 0.00 42.93 3.43
1557 1593 7.264221 TCACACAATTTACAGCAAATTTCACT 58.736 30.769 0.00 0.00 42.93 3.41
1561 1597 8.891671 ATCTTCACACAATTTACAGCAAATTT 57.108 26.923 0.00 0.00 42.93 1.82
1572 1608 4.152402 CCGTCTTCGATCTTCACACAATTT 59.848 41.667 0.00 0.00 39.71 1.82
1584 1621 1.134367 TGGATCACACCGTCTTCGATC 59.866 52.381 0.00 0.00 39.71 3.69
1595 1632 2.699954 ACGAAGGTTGATGGATCACAC 58.300 47.619 0.00 0.00 36.36 3.82
1608 1645 6.937436 ATTCAGAACAGTTAAAACGAAGGT 57.063 33.333 0.00 0.00 0.00 3.50
1611 1648 8.670135 TCAGAAATTCAGAACAGTTAAAACGAA 58.330 29.630 0.00 0.00 0.00 3.85
1618 1655 9.730705 AATCAGATCAGAAATTCAGAACAGTTA 57.269 29.630 0.00 0.00 0.00 2.24
1620 1657 8.512956 CAAATCAGATCAGAAATTCAGAACAGT 58.487 33.333 0.00 0.00 0.00 3.55
1621 1658 7.485277 GCAAATCAGATCAGAAATTCAGAACAG 59.515 37.037 0.00 0.00 0.00 3.16
1622 1659 7.176165 AGCAAATCAGATCAGAAATTCAGAACA 59.824 33.333 0.00 0.00 0.00 3.18
1623 1660 7.485277 CAGCAAATCAGATCAGAAATTCAGAAC 59.515 37.037 0.00 0.00 0.00 3.01
1624 1661 7.176165 ACAGCAAATCAGATCAGAAATTCAGAA 59.824 33.333 0.00 0.00 0.00 3.02
1625 1662 6.657966 ACAGCAAATCAGATCAGAAATTCAGA 59.342 34.615 0.00 0.00 0.00 3.27
1626 1663 6.747739 CACAGCAAATCAGATCAGAAATTCAG 59.252 38.462 0.00 0.00 0.00 3.02
1627 1664 6.431852 TCACAGCAAATCAGATCAGAAATTCA 59.568 34.615 0.00 0.00 0.00 2.57
1628 1665 6.849502 TCACAGCAAATCAGATCAGAAATTC 58.150 36.000 0.00 0.00 0.00 2.17
1629 1666 6.829229 TCACAGCAAATCAGATCAGAAATT 57.171 33.333 0.00 0.00 0.00 1.82
1630 1667 6.829229 TTCACAGCAAATCAGATCAGAAAT 57.171 33.333 0.00 0.00 0.00 2.17
1631 1668 6.638096 TTTCACAGCAAATCAGATCAGAAA 57.362 33.333 0.00 0.00 0.00 2.52
1657 1694 4.974721 CCTGGTTGGGTTGCGGCT 62.975 66.667 0.00 0.00 0.00 5.52
1659 1696 2.983592 GACCTGGTTGGGTTGCGG 60.984 66.667 0.00 0.00 40.06 5.69
1735 1877 2.363406 CTAGGGTCGGGTCGGGTT 60.363 66.667 0.00 0.00 0.00 4.11
1740 1882 3.885521 CGTCGCTAGGGTCGGGTC 61.886 72.222 16.54 0.00 0.00 4.46
1743 1885 4.849329 GTGCGTCGCTAGGGTCGG 62.849 72.222 23.24 8.77 0.00 4.79
1744 1886 4.849329 GGTGCGTCGCTAGGGTCG 62.849 72.222 19.50 19.23 0.00 4.79
1745 1887 3.412879 GAGGTGCGTCGCTAGGGTC 62.413 68.421 19.50 4.49 0.00 4.46
1746 1888 3.450115 GAGGTGCGTCGCTAGGGT 61.450 66.667 19.50 0.00 0.00 4.34
1747 1889 2.298158 ATTGAGGTGCGTCGCTAGGG 62.298 60.000 19.50 0.00 0.00 3.53
1748 1890 1.141881 ATTGAGGTGCGTCGCTAGG 59.858 57.895 19.50 0.00 0.00 3.02
1749 1891 1.148157 CCATTGAGGTGCGTCGCTAG 61.148 60.000 19.50 0.00 0.00 3.42
1750 1892 1.153647 CCATTGAGGTGCGTCGCTA 60.154 57.895 19.50 1.76 0.00 4.26
1751 1893 2.434884 CCATTGAGGTGCGTCGCT 60.435 61.111 19.50 0.00 0.00 4.93
1752 1894 4.166011 GCCATTGAGGTGCGTCGC 62.166 66.667 11.10 11.10 40.61 5.19
2382 2575 7.882791 TCACATTTCTTGGCAAAGATAGAACTA 59.117 33.333 3.86 0.00 42.04 2.24


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

AutoCloner maintained by Alex Coulton.