Multiple sequence alignment - TraesCS5D01G105400

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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 TraesCS5D01G105400 chr5D 100.000 4532 0 0 1 4532 119480825 119485356 0.000000e+00 8370.0
1 TraesCS5D01G105400 chr5A 95.880 2476 63 18 2060 4532 129597816 129600255 0.000000e+00 3971.0
2 TraesCS5D01G105400 chr5A 95.478 1150 47 5 824 1970 129596671 129597818 0.000000e+00 1831.0
3 TraesCS5D01G105400 chr5A 87.778 540 30 22 1 504 426932024 426932563 2.330000e-167 599.0
4 TraesCS5D01G105400 chr5A 88.023 526 36 17 1 499 78266242 78266767 8.390000e-167 597.0
5 TraesCS5D01G105400 chr5A 87.867 511 47 13 1 504 78325074 78325576 1.820000e-163 586.0
6 TraesCS5D01G105400 chr5A 97.403 77 2 0 750 826 129595242 129595318 1.020000e-26 132.0
7 TraesCS5D01G105400 chr5B 94.054 1934 56 28 2018 3948 132284211 132286088 0.000000e+00 2880.0
8 TraesCS5D01G105400 chr5B 95.130 1273 54 6 753 2021 132282186 132283454 0.000000e+00 2001.0
9 TraesCS5D01G105400 chr5B 97.372 761 19 1 753 1513 132280782 132281541 0.000000e+00 1293.0
10 TraesCS5D01G105400 chr5B 97.240 761 20 1 753 1513 132279393 132280152 0.000000e+00 1288.0
11 TraesCS5D01G105400 chr5B 98.430 637 8 2 3896 4532 132286091 132286725 0.000000e+00 1120.0
12 TraesCS5D01G105400 chr5B 97.778 45 1 0 523 567 592838397 592838353 1.350000e-10 78.7
13 TraesCS5D01G105400 chr3D 93.003 586 12 5 1 557 187407 187992 0.000000e+00 828.0
14 TraesCS5D01G105400 chr3D 93.678 522 10 2 1 499 281330637 281331158 0.000000e+00 760.0
15 TraesCS5D01G105400 chr3D 90.256 195 16 2 561 753 502903 502710 7.530000e-63 252.0
16 TraesCS5D01G105400 chr3D 88.325 197 14 4 561 751 571605130 571605323 1.270000e-55 228.0
17 TraesCS5D01G105400 chr3D 87.952 83 1 4 492 566 497712570 497712651 6.240000e-14 89.8
18 TraesCS5D01G105400 chr7D 91.003 578 13 15 1 568 403215648 403216196 0.000000e+00 743.0
19 TraesCS5D01G105400 chr7D 95.960 198 8 0 561 758 14627500 14627303 5.660000e-84 322.0
20 TraesCS5D01G105400 chr7D 89.552 201 12 3 562 754 629559130 629558931 3.500000e-61 246.0
21 TraesCS5D01G105400 chr7D 87.245 196 17 2 562 749 634273044 634272849 2.750000e-52 217.0
22 TraesCS5D01G105400 chr7D 90.000 50 3 2 523 571 510411077 510411125 3.780000e-06 63.9
23 TraesCS5D01G105400 chr7D 90.698 43 4 0 521 563 240521555 240521597 1.760000e-04 58.4
24 TraesCS5D01G105400 chr2A 90.019 531 24 15 1 504 734549198 734548670 0.000000e+00 660.0
25 TraesCS5D01G105400 chr2A 95.767 189 7 1 561 749 768478068 768478255 2.050000e-78 303.0
26 TraesCS5D01G105400 chr4A 89.484 523 31 4 1 499 599904438 599904960 1.370000e-179 640.0
27 TraesCS5D01G105400 chr7A 89.245 530 27 17 1 504 193577693 193577168 1.780000e-178 636.0
28 TraesCS5D01G105400 chr1A 88.425 527 32 17 1 499 244510650 244511175 3.880000e-170 608.0
29 TraesCS5D01G105400 chr1A 86.304 533 44 20 1 504 97646786 97647318 1.840000e-153 553.0
30 TraesCS5D01G105400 chr1A 93.750 48 2 1 521 568 398111114 398111068 2.260000e-08 71.3
31 TraesCS5D01G105400 chrUn 92.208 308 20 3 1 305 480582112 480582418 2.500000e-117 433.0
32 TraesCS5D01G105400 chrUn 95.556 45 0 1 523 565 479100343 479100387 2.260000e-08 71.3
33 TraesCS5D01G105400 chr6D 91.542 201 13 4 561 760 307533649 307533846 1.610000e-69 274.0
34 TraesCS5D01G105400 chr6B 90.640 203 14 4 561 760 474828577 474828777 9.670000e-67 265.0
35 TraesCS5D01G105400 chr6A 91.304 184 15 1 561 744 444708192 444708374 2.710000e-62 250.0
36 TraesCS5D01G105400 chr6A 86.567 67 7 2 498 563 562265169 562265234 6.290000e-09 73.1
37 TraesCS5D01G105400 chr2D 87.624 202 21 2 2947 3148 500811956 500811759 9.800000e-57 231.0
38 TraesCS5D01G105400 chr2D 95.556 45 0 1 523 565 427532484 427532440 2.260000e-08 71.3
39 TraesCS5D01G105400 chr3A 85.922 206 23 5 2947 3148 25031940 25032143 9.870000e-52 215.0
40 TraesCS5D01G105400 chr1D 90.278 72 0 2 500 564 113846532 113846603 2.250000e-13 87.9
41 TraesCS5D01G105400 chr3B 97.619 42 0 1 523 563 778669712 778669671 2.260000e-08 71.3
42 TraesCS5D01G105400 chr3B 90.566 53 2 3 527 579 23989281 23989232 2.930000e-07 67.6
43 TraesCS5D01G105400 chr7B 89.583 48 5 0 521 568 417648717 417648670 1.360000e-05 62.1
44 TraesCS5D01G105400 chr7B 97.143 35 1 0 536 570 704640859 704640893 4.900000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G105400 chr5D 119480825 119485356 4531 False 8370.0 8370 100.000000 1 4532 1 chr5D.!!$F1 4531
1 TraesCS5D01G105400 chr5A 129595242 129600255 5013 False 1978.0 3971 96.253667 750 4532 3 chr5A.!!$F4 3782
2 TraesCS5D01G105400 chr5A 426932024 426932563 539 False 599.0 599 87.778000 1 504 1 chr5A.!!$F3 503
3 TraesCS5D01G105400 chr5A 78266242 78266767 525 False 597.0 597 88.023000 1 499 1 chr5A.!!$F1 498
4 TraesCS5D01G105400 chr5A 78325074 78325576 502 False 586.0 586 87.867000 1 504 1 chr5A.!!$F2 503
5 TraesCS5D01G105400 chr5B 132279393 132286725 7332 False 1716.4 2880 96.445200 753 4532 5 chr5B.!!$F1 3779
6 TraesCS5D01G105400 chr3D 187407 187992 585 False 828.0 828 93.003000 1 557 1 chr3D.!!$F1 556
7 TraesCS5D01G105400 chr3D 281330637 281331158 521 False 760.0 760 93.678000 1 499 1 chr3D.!!$F2 498
8 TraesCS5D01G105400 chr7D 403215648 403216196 548 False 743.0 743 91.003000 1 568 1 chr7D.!!$F2 567
9 TraesCS5D01G105400 chr2A 734548670 734549198 528 True 660.0 660 90.019000 1 504 1 chr2A.!!$R1 503
10 TraesCS5D01G105400 chr4A 599904438 599904960 522 False 640.0 640 89.484000 1 499 1 chr4A.!!$F1 498
11 TraesCS5D01G105400 chr7A 193577168 193577693 525 True 636.0 636 89.245000 1 504 1 chr7A.!!$R1 503
12 TraesCS5D01G105400 chr1A 244510650 244511175 525 False 608.0 608 88.425000 1 499 1 chr1A.!!$F2 498
13 TraesCS5D01G105400 chr1A 97646786 97647318 532 False 553.0 553 86.304000 1 504 1 chr1A.!!$F1 503

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
589 637 0.034574 TGTGTGTTTGGGCACTGAGT 60.035 50.0 0.0 0.0 39.89 3.41 F
1973 6176 0.394216 ATGCCTGCGTTTGGATAGCA 60.394 50.0 0.0 0.0 39.25 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 6192 1.216990 AAACATCTCCTGGGCCCTAG 58.783 55.0 25.70 18.18 0.0 3.02 R
3574 8543 0.099968 CCACATCCAGCGCAATTCAG 59.900 55.0 11.47 0.00 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
446 487 5.860941 TTTTTGGATGCCACTAAAACAGA 57.139 34.783 0.00 0.00 31.93 3.41
521 562 2.102925 AGGAGGTTGGACGAAACGTAAA 59.897 45.455 0.00 0.00 41.37 2.01
558 606 9.678260 ACGTTTCTTTTAGGTAGTAGAGATAGA 57.322 33.333 0.00 0.00 0.00 1.98
581 629 8.511604 AGAGATAATAGAAATGTGTGTTTGGG 57.488 34.615 0.00 0.00 0.00 4.12
582 630 7.067494 AGAGATAATAGAAATGTGTGTTTGGGC 59.933 37.037 0.00 0.00 0.00 5.36
583 631 6.663093 AGATAATAGAAATGTGTGTTTGGGCA 59.337 34.615 0.00 0.00 0.00 5.36
584 632 2.888834 AGAAATGTGTGTTTGGGCAC 57.111 45.000 0.00 0.00 39.65 5.01
585 633 2.387757 AGAAATGTGTGTTTGGGCACT 58.612 42.857 0.00 0.00 39.89 4.40
586 634 2.101249 AGAAATGTGTGTTTGGGCACTG 59.899 45.455 0.00 0.00 39.89 3.66
587 635 1.774110 AATGTGTGTTTGGGCACTGA 58.226 45.000 0.00 0.00 39.89 3.41
588 636 1.321474 ATGTGTGTTTGGGCACTGAG 58.679 50.000 0.00 0.00 39.89 3.35
589 637 0.034574 TGTGTGTTTGGGCACTGAGT 60.035 50.000 0.00 0.00 39.89 3.41
590 638 0.663153 GTGTGTTTGGGCACTGAGTC 59.337 55.000 0.00 0.00 39.89 3.36
591 639 0.546122 TGTGTTTGGGCACTGAGTCT 59.454 50.000 0.00 0.00 39.89 3.24
592 640 1.230324 GTGTTTGGGCACTGAGTCTC 58.770 55.000 0.00 0.00 36.51 3.36
593 641 1.131638 TGTTTGGGCACTGAGTCTCT 58.868 50.000 0.65 0.00 0.00 3.10
594 642 1.070758 TGTTTGGGCACTGAGTCTCTC 59.929 52.381 0.65 0.00 0.00 3.20
595 643 1.346068 GTTTGGGCACTGAGTCTCTCT 59.654 52.381 0.65 0.00 0.00 3.10
596 644 0.972134 TTGGGCACTGAGTCTCTCTG 59.028 55.000 0.65 1.61 35.91 3.35
597 645 0.902048 TGGGCACTGAGTCTCTCTGG 60.902 60.000 0.65 0.00 34.46 3.86
598 646 1.612395 GGGCACTGAGTCTCTCTGGG 61.612 65.000 0.65 5.37 36.21 4.45
599 647 1.612395 GGCACTGAGTCTCTCTGGGG 61.612 65.000 0.65 2.26 34.19 4.96
600 648 0.902516 GCACTGAGTCTCTCTGGGGT 60.903 60.000 0.65 0.00 34.19 4.95
601 649 1.617263 GCACTGAGTCTCTCTGGGGTA 60.617 57.143 0.65 0.00 34.19 3.69
602 650 2.808919 CACTGAGTCTCTCTGGGGTAA 58.191 52.381 0.65 0.00 34.46 2.85
603 651 3.165875 CACTGAGTCTCTCTGGGGTAAA 58.834 50.000 0.65 0.00 34.46 2.01
604 652 3.578716 CACTGAGTCTCTCTGGGGTAAAA 59.421 47.826 0.65 0.00 34.46 1.52
605 653 3.579151 ACTGAGTCTCTCTGGGGTAAAAC 59.421 47.826 0.65 0.00 34.46 2.43
606 654 3.578716 CTGAGTCTCTCTGGGGTAAAACA 59.421 47.826 0.65 0.00 0.00 2.83
607 655 3.323979 TGAGTCTCTCTGGGGTAAAACAC 59.676 47.826 0.65 0.00 0.00 3.32
608 656 2.299297 AGTCTCTCTGGGGTAAAACACG 59.701 50.000 0.00 0.00 0.00 4.49
609 657 2.298163 GTCTCTCTGGGGTAAAACACGA 59.702 50.000 0.00 0.00 0.00 4.35
610 658 3.056035 GTCTCTCTGGGGTAAAACACGAT 60.056 47.826 0.00 0.00 0.00 3.73
611 659 3.194968 TCTCTCTGGGGTAAAACACGATC 59.805 47.826 0.00 0.00 0.00 3.69
612 660 3.170717 TCTCTGGGGTAAAACACGATCT 58.829 45.455 0.00 0.00 0.00 2.75
613 661 4.346730 TCTCTGGGGTAAAACACGATCTA 58.653 43.478 0.00 0.00 0.00 1.98
614 662 4.401519 TCTCTGGGGTAAAACACGATCTAG 59.598 45.833 0.00 0.00 0.00 2.43
615 663 4.346730 TCTGGGGTAAAACACGATCTAGA 58.653 43.478 0.00 0.00 0.00 2.43
616 664 4.773674 TCTGGGGTAAAACACGATCTAGAA 59.226 41.667 0.00 0.00 0.00 2.10
617 665 5.080969 TGGGGTAAAACACGATCTAGAAG 57.919 43.478 0.00 0.00 0.00 2.85
618 666 4.081309 TGGGGTAAAACACGATCTAGAAGG 60.081 45.833 0.00 0.00 0.00 3.46
619 667 3.869832 GGGTAAAACACGATCTAGAAGGC 59.130 47.826 0.00 0.00 0.00 4.35
620 668 4.382793 GGGTAAAACACGATCTAGAAGGCT 60.383 45.833 0.00 0.00 0.00 4.58
621 669 4.804665 GGTAAAACACGATCTAGAAGGCTC 59.195 45.833 0.00 0.00 0.00 4.70
622 670 3.528597 AAACACGATCTAGAAGGCTCC 57.471 47.619 0.00 0.00 0.00 4.70
623 671 2.445682 ACACGATCTAGAAGGCTCCT 57.554 50.000 0.00 0.00 0.00 3.69
624 672 3.579534 ACACGATCTAGAAGGCTCCTA 57.420 47.619 0.00 0.00 0.00 2.94
625 673 3.899726 ACACGATCTAGAAGGCTCCTAA 58.100 45.455 0.00 0.00 0.00 2.69
626 674 4.279145 ACACGATCTAGAAGGCTCCTAAA 58.721 43.478 0.00 0.00 0.00 1.85
627 675 4.710375 ACACGATCTAGAAGGCTCCTAAAA 59.290 41.667 0.00 0.00 0.00 1.52
628 676 5.187186 ACACGATCTAGAAGGCTCCTAAAAA 59.813 40.000 0.00 0.00 0.00 1.94
629 677 6.127026 ACACGATCTAGAAGGCTCCTAAAAAT 60.127 38.462 0.00 0.00 0.00 1.82
630 678 6.763610 CACGATCTAGAAGGCTCCTAAAAATT 59.236 38.462 0.00 0.00 0.00 1.82
631 679 7.926555 CACGATCTAGAAGGCTCCTAAAAATTA 59.073 37.037 0.00 0.00 0.00 1.40
632 680 8.483758 ACGATCTAGAAGGCTCCTAAAAATTAA 58.516 33.333 0.00 0.00 0.00 1.40
633 681 9.326413 CGATCTAGAAGGCTCCTAAAAATTAAA 57.674 33.333 0.00 0.00 0.00 1.52
636 684 9.462606 TCTAGAAGGCTCCTAAAAATTAAAAGG 57.537 33.333 0.00 0.00 0.00 3.11
637 685 7.482169 AGAAGGCTCCTAAAAATTAAAAGGG 57.518 36.000 0.00 0.00 0.00 3.95
638 686 6.440647 AGAAGGCTCCTAAAAATTAAAAGGGG 59.559 38.462 0.00 0.00 32.34 4.79
639 687 5.661565 AGGCTCCTAAAAATTAAAAGGGGT 58.338 37.500 2.67 0.00 31.76 4.95
640 688 6.807286 AGGCTCCTAAAAATTAAAAGGGGTA 58.193 36.000 2.67 0.00 31.76 3.69
641 689 7.250454 AGGCTCCTAAAAATTAAAAGGGGTAA 58.750 34.615 2.67 0.00 31.76 2.85
642 690 7.735777 AGGCTCCTAAAAATTAAAAGGGGTAAA 59.264 33.333 2.67 0.00 31.76 2.01
643 691 8.377034 GGCTCCTAAAAATTAAAAGGGGTAAAA 58.623 33.333 2.67 0.00 31.76 1.52
644 692 9.781633 GCTCCTAAAAATTAAAAGGGGTAAAAA 57.218 29.630 2.67 0.00 31.76 1.94
650 698 9.961264 AAAAATTAAAAGGGGTAAAAACAGACA 57.039 25.926 0.00 0.00 0.00 3.41
651 699 9.961264 AAAATTAAAAGGGGTAAAAACAGACAA 57.039 25.926 0.00 0.00 0.00 3.18
657 705 7.849322 AAGGGGTAAAAACAGACAATATTGT 57.151 32.000 20.93 20.93 45.65 2.71
674 722 9.131791 ACAATATTGTCACTAAATGGGGTAATC 57.868 33.333 15.47 0.00 36.50 1.75
675 723 9.354673 CAATATTGTCACTAAATGGGGTAATCT 57.645 33.333 7.32 0.00 0.00 2.40
676 724 8.924511 ATATTGTCACTAAATGGGGTAATCTG 57.075 34.615 0.00 0.00 0.00 2.90
677 725 5.110814 TGTCACTAAATGGGGTAATCTGG 57.889 43.478 0.00 0.00 0.00 3.86
678 726 4.785914 TGTCACTAAATGGGGTAATCTGGA 59.214 41.667 0.00 0.00 0.00 3.86
679 727 5.431731 TGTCACTAAATGGGGTAATCTGGAT 59.568 40.000 0.00 0.00 0.00 3.41
680 728 5.765182 GTCACTAAATGGGGTAATCTGGATG 59.235 44.000 0.00 0.00 0.00 3.51
681 729 5.669904 TCACTAAATGGGGTAATCTGGATGA 59.330 40.000 0.00 0.00 0.00 2.92
682 730 6.159575 TCACTAAATGGGGTAATCTGGATGAA 59.840 38.462 0.00 0.00 0.00 2.57
683 731 6.833416 CACTAAATGGGGTAATCTGGATGAAA 59.167 38.462 0.00 0.00 0.00 2.69
684 732 7.341769 CACTAAATGGGGTAATCTGGATGAAAA 59.658 37.037 0.00 0.00 0.00 2.29
685 733 8.067488 ACTAAATGGGGTAATCTGGATGAAAAT 58.933 33.333 0.00 0.00 0.00 1.82
686 734 7.754091 AAATGGGGTAATCTGGATGAAAATT 57.246 32.000 0.00 0.00 0.00 1.82
687 735 7.754091 AATGGGGTAATCTGGATGAAAATTT 57.246 32.000 0.00 0.00 0.00 1.82
688 736 6.543430 TGGGGTAATCTGGATGAAAATTTG 57.457 37.500 0.00 0.00 0.00 2.32
689 737 6.022315 TGGGGTAATCTGGATGAAAATTTGT 58.978 36.000 0.00 0.00 0.00 2.83
690 738 6.500049 TGGGGTAATCTGGATGAAAATTTGTT 59.500 34.615 0.00 0.00 0.00 2.83
691 739 7.676043 TGGGGTAATCTGGATGAAAATTTGTTA 59.324 33.333 0.00 0.00 0.00 2.41
692 740 8.536175 GGGGTAATCTGGATGAAAATTTGTTAA 58.464 33.333 0.00 0.00 0.00 2.01
693 741 9.936759 GGGTAATCTGGATGAAAATTTGTTAAA 57.063 29.630 0.00 0.00 0.00 1.52
697 745 9.452287 AATCTGGATGAAAATTTGTTAAATGGG 57.548 29.630 0.00 0.00 0.00 4.00
698 746 7.393216 TCTGGATGAAAATTTGTTAAATGGGG 58.607 34.615 0.00 0.00 0.00 4.96
699 747 7.017056 TCTGGATGAAAATTTGTTAAATGGGGT 59.983 33.333 0.00 0.00 0.00 4.95
700 748 8.207350 TGGATGAAAATTTGTTAAATGGGGTA 57.793 30.769 0.00 0.00 0.00 3.69
701 749 8.660435 TGGATGAAAATTTGTTAAATGGGGTAA 58.340 29.630 0.00 0.00 0.00 2.85
702 750 8.941977 GGATGAAAATTTGTTAAATGGGGTAAC 58.058 33.333 0.00 0.00 33.00 2.50
703 751 9.719355 GATGAAAATTTGTTAAATGGGGTAACT 57.281 29.630 0.00 0.00 33.46 2.24
710 758 8.707796 TTTGTTAAATGGGGTAACTAATGTCA 57.292 30.769 0.00 0.00 33.46 3.58
711 759 8.707796 TTGTTAAATGGGGTAACTAATGTCAA 57.292 30.769 0.00 0.00 33.46 3.18
712 760 8.707796 TGTTAAATGGGGTAACTAATGTCAAA 57.292 30.769 0.00 0.00 33.46 2.69
713 761 9.144298 TGTTAAATGGGGTAACTAATGTCAAAA 57.856 29.630 0.00 0.00 33.46 2.44
714 762 9.984190 GTTAAATGGGGTAACTAATGTCAAAAA 57.016 29.630 0.00 0.00 0.00 1.94
717 765 6.031751 TGGGGTAACTAATGTCAAAAATGC 57.968 37.500 0.00 0.00 0.00 3.56
718 766 5.777732 TGGGGTAACTAATGTCAAAAATGCT 59.222 36.000 0.00 0.00 0.00 3.79
719 767 6.948886 TGGGGTAACTAATGTCAAAAATGCTA 59.051 34.615 0.00 0.00 0.00 3.49
720 768 7.451877 TGGGGTAACTAATGTCAAAAATGCTAA 59.548 33.333 0.00 0.00 0.00 3.09
721 769 8.308207 GGGGTAACTAATGTCAAAAATGCTAAA 58.692 33.333 0.00 0.00 0.00 1.85
722 770 9.869757 GGGTAACTAATGTCAAAAATGCTAAAT 57.130 29.630 0.00 0.00 0.00 1.40
728 776 9.533253 CTAATGTCAAAAATGCTAAATTAGGGG 57.467 33.333 1.88 0.00 0.00 4.79
729 777 6.293004 TGTCAAAAATGCTAAATTAGGGGG 57.707 37.500 1.88 0.00 0.00 5.40
730 778 5.782845 TGTCAAAAATGCTAAATTAGGGGGT 59.217 36.000 1.88 0.00 0.00 4.95
731 779 6.954684 TGTCAAAAATGCTAAATTAGGGGGTA 59.045 34.615 1.88 0.00 0.00 3.69
732 780 7.455008 TGTCAAAAATGCTAAATTAGGGGGTAA 59.545 33.333 1.88 0.00 0.00 2.85
733 781 8.315482 GTCAAAAATGCTAAATTAGGGGGTAAA 58.685 33.333 1.88 0.00 0.00 2.01
734 782 8.881262 TCAAAAATGCTAAATTAGGGGGTAAAA 58.119 29.630 1.88 0.00 0.00 1.52
735 783 9.508642 CAAAAATGCTAAATTAGGGGGTAAAAA 57.491 29.630 1.88 0.00 0.00 1.94
736 784 9.509956 AAAAATGCTAAATTAGGGGGTAAAAAC 57.490 29.630 1.88 0.00 0.00 2.43
737 785 8.444010 AAATGCTAAATTAGGGGGTAAAAACT 57.556 30.769 1.88 0.00 0.00 2.66
738 786 6.844097 TGCTAAATTAGGGGGTAAAAACTG 57.156 37.500 1.88 0.00 0.00 3.16
739 787 5.717654 TGCTAAATTAGGGGGTAAAAACTGG 59.282 40.000 1.88 0.00 0.00 4.00
740 788 5.953548 GCTAAATTAGGGGGTAAAAACTGGA 59.046 40.000 1.88 0.00 0.00 3.86
741 789 6.438108 GCTAAATTAGGGGGTAAAAACTGGAA 59.562 38.462 1.88 0.00 0.00 3.53
742 790 7.125204 GCTAAATTAGGGGGTAAAAACTGGAAT 59.875 37.037 1.88 0.00 0.00 3.01
743 791 7.881912 AAATTAGGGGGTAAAAACTGGAATT 57.118 32.000 0.00 0.00 0.00 2.17
744 792 7.490657 AATTAGGGGGTAAAAACTGGAATTC 57.509 36.000 0.00 0.00 0.00 2.17
745 793 4.479156 AGGGGGTAAAAACTGGAATTCA 57.521 40.909 7.93 0.00 0.00 2.57
746 794 4.157246 AGGGGGTAAAAACTGGAATTCAC 58.843 43.478 7.93 0.00 0.00 3.18
747 795 4.140782 AGGGGGTAAAAACTGGAATTCACT 60.141 41.667 7.93 0.00 0.00 3.41
748 796 4.219944 GGGGGTAAAAACTGGAATTCACTC 59.780 45.833 7.93 0.00 0.00 3.51
754 802 9.406828 GGTAAAAACTGGAATTCACTCATAAAC 57.593 33.333 7.93 0.00 0.00 2.01
907 3699 8.201242 ACACCCTCCAAATTTGTTACATTTAT 57.799 30.769 16.73 0.00 0.00 1.40
1343 5539 4.509970 TCGATCTCTCTTCTCTCGTGAATC 59.490 45.833 0.00 0.00 0.00 2.52
1355 5551 2.106683 GTGAATCCCTGTTCGCCCG 61.107 63.158 0.00 0.00 33.58 6.13
1378 5574 5.228427 CGTCGATTCGTATGTCACACAATTA 59.772 40.000 5.89 0.00 0.00 1.40
1520 5718 7.279615 ACGTTTATCATGATGGGATTCTGTTA 58.720 34.615 18.72 0.00 0.00 2.41
1550 5748 3.963129 TGATTTGGTTAGGCGATTTCCT 58.037 40.909 0.00 0.00 40.21 3.36
1679 5880 1.342496 TCTGGCTCTTATCCTGCATCG 59.658 52.381 0.00 0.00 0.00 3.84
1712 5913 4.626042 TGTTTTCCACAAATATTGCGCTT 58.374 34.783 9.73 0.00 29.87 4.68
1756 5958 0.911769 TGGCATCTTTCATCGGTCCT 59.088 50.000 0.00 0.00 0.00 3.85
1852 6054 5.991606 TCAGTGTCCTCATTTCTGTAACTTG 59.008 40.000 0.00 0.00 0.00 3.16
1895 6097 4.556942 TTGTCAGTTCATTCTGCAAGTG 57.443 40.909 0.00 0.00 35.63 3.16
1973 6176 0.394216 ATGCCTGCGTTTGGATAGCA 60.394 50.000 0.00 0.00 39.25 3.49
2035 6998 6.441093 TCTTGCTATTAATGAGCTTGGTTG 57.559 37.500 14.13 3.81 40.76 3.77
2205 7168 8.267894 AGTGTGGATAATTAGCAAATAGACTGT 58.732 33.333 2.72 0.00 0.00 3.55
2312 7275 4.286813 TGGGGAGGAACTTATCAGAGAT 57.713 45.455 0.00 0.00 41.55 2.75
2497 7460 2.443255 AGTGGTGTTCCTGTCATCCTTT 59.557 45.455 0.00 0.00 34.23 3.11
2498 7461 2.814336 GTGGTGTTCCTGTCATCCTTTC 59.186 50.000 0.00 0.00 34.23 2.62
2499 7462 2.711009 TGGTGTTCCTGTCATCCTTTCT 59.289 45.455 0.00 0.00 34.23 2.52
2500 7463 3.138283 TGGTGTTCCTGTCATCCTTTCTT 59.862 43.478 0.00 0.00 34.23 2.52
2501 7464 4.349636 TGGTGTTCCTGTCATCCTTTCTTA 59.650 41.667 0.00 0.00 34.23 2.10
2517 7480 8.108378 TCCTTTCTTACCCATTAATATGACCA 57.892 34.615 0.00 0.00 33.37 4.02
2519 7482 9.367160 CCTTTCTTACCCATTAATATGACCAAT 57.633 33.333 0.00 0.00 33.37 3.16
2533 7496 7.765695 ATATGACCAATGGCCTTAACTAATG 57.234 36.000 3.32 0.00 0.00 1.90
2733 7696 5.535029 AGTTGTAACCCACCTGATATCCTA 58.465 41.667 0.00 0.00 0.00 2.94
2734 7697 6.151049 AGTTGTAACCCACCTGATATCCTAT 58.849 40.000 0.00 0.00 0.00 2.57
2735 7698 7.310634 AGTTGTAACCCACCTGATATCCTATA 58.689 38.462 0.00 0.00 0.00 1.31
2754 7717 8.792830 TCCTATAGTGATTAGCAAATAATGGC 57.207 34.615 0.00 0.00 34.10 4.40
2890 7854 4.565652 GGCAACAGTAATTCTCTGGAGGAA 60.566 45.833 12.90 0.00 37.25 3.36
2895 7859 9.231297 CAACAGTAATTCTCTGGAGGAAAAATA 57.769 33.333 12.90 0.00 37.25 1.40
2898 7862 6.763610 AGTAATTCTCTGGAGGAAAAATAGCG 59.236 38.462 0.00 0.00 0.00 4.26
2933 7897 7.828508 ATGGATGTTAAATATGCACAGATGT 57.171 32.000 0.00 0.00 0.00 3.06
2934 7898 7.643569 TGGATGTTAAATATGCACAGATGTT 57.356 32.000 0.00 0.00 0.00 2.71
2935 7899 8.744568 TGGATGTTAAATATGCACAGATGTTA 57.255 30.769 0.00 0.00 0.00 2.41
2936 7900 8.620416 TGGATGTTAAATATGCACAGATGTTAC 58.380 33.333 0.00 0.00 0.00 2.50
2937 7901 8.840321 GGATGTTAAATATGCACAGATGTTACT 58.160 33.333 0.00 0.00 0.00 2.24
2938 7902 9.869844 GATGTTAAATATGCACAGATGTTACTC 57.130 33.333 0.00 0.00 0.00 2.59
2939 7903 9.618890 ATGTTAAATATGCACAGATGTTACTCT 57.381 29.630 0.00 0.00 0.00 3.24
2940 7904 9.098355 TGTTAAATATGCACAGATGTTACTCTC 57.902 33.333 0.00 0.00 0.00 3.20
2941 7905 6.834959 AAATATGCACAGATGTTACTCTCG 57.165 37.500 0.00 0.00 0.00 4.04
2942 7906 5.774498 ATATGCACAGATGTTACTCTCGA 57.226 39.130 0.00 0.00 0.00 4.04
2943 7907 3.934457 TGCACAGATGTTACTCTCGAA 57.066 42.857 0.00 0.00 0.00 3.71
2944 7908 4.251543 TGCACAGATGTTACTCTCGAAA 57.748 40.909 0.00 0.00 0.00 3.46
2945 7909 4.627058 TGCACAGATGTTACTCTCGAAAA 58.373 39.130 0.00 0.00 0.00 2.29
2946 7910 5.053811 TGCACAGATGTTACTCTCGAAAAA 58.946 37.500 0.00 0.00 0.00 1.94
2990 7954 8.958119 TGTCATCATTTTACTATGACCTAACC 57.042 34.615 11.07 0.00 45.74 2.85
2991 7955 8.544622 TGTCATCATTTTACTATGACCTAACCA 58.455 33.333 11.07 0.00 45.74 3.67
2992 7956 9.046296 GTCATCATTTTACTATGACCTAACCAG 57.954 37.037 0.00 0.00 42.30 4.00
2993 7957 8.768397 TCATCATTTTACTATGACCTAACCAGT 58.232 33.333 0.00 0.00 37.36 4.00
3040 8009 5.877012 CACTATCATTAGCTGGTCACACTTT 59.123 40.000 0.00 0.00 0.00 2.66
3439 8408 3.994165 AGCAAATGGAGGCTCATGT 57.006 47.368 17.69 0.33 34.76 3.21
3477 8446 2.699846 GAGAGTCTGGGCATCATCTCTT 59.300 50.000 0.00 2.49 37.01 2.85
3534 8503 4.639334 GAGCTGCTAGATTGGATTGATGA 58.361 43.478 0.15 0.00 0.00 2.92
3574 8543 2.894387 GAGAGCATGCGGGCTGTC 60.894 66.667 13.01 8.62 45.99 3.51
3600 8569 1.220206 CGCTGGATGTGGAAGCTCT 59.780 57.895 0.00 0.00 34.72 4.09
3702 8672 7.065085 AGACACACTGTAACATTAATCATGAGC 59.935 37.037 0.09 0.00 36.24 4.26
3971 8995 8.756927 TCATGGACAATATATTGATCTCTCCTC 58.243 37.037 28.13 14.07 40.14 3.71
4320 9344 1.208706 TTGATATCCGCCCTTCCACA 58.791 50.000 0.00 0.00 0.00 4.17
4503 9527 0.729116 ATTTCTCATTGCGAGCCACG 59.271 50.000 0.00 0.00 41.98 4.94
4509 9533 1.005037 ATTGCGAGCCACGAAGTCA 60.005 52.632 5.11 0.00 41.61 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
277 291 4.227134 CAGGAGGATGGACGGCGG 62.227 72.222 13.24 0.00 0.00 6.13
446 487 0.693049 AGGAAATCAACCCGCAGTCT 59.307 50.000 0.00 0.00 0.00 3.24
557 605 7.148086 TGCCCAAACACACATTTCTATTATCTC 60.148 37.037 0.00 0.00 0.00 2.75
558 606 6.663093 TGCCCAAACACACATTTCTATTATCT 59.337 34.615 0.00 0.00 0.00 1.98
559 607 6.751888 GTGCCCAAACACACATTTCTATTATC 59.248 38.462 0.00 0.00 40.40 1.75
561 609 5.772672 AGTGCCCAAACACACATTTCTATTA 59.227 36.000 0.00 0.00 43.23 0.98
563 611 4.022068 CAGTGCCCAAACACACATTTCTAT 60.022 41.667 0.00 0.00 43.23 1.98
564 612 3.317711 CAGTGCCCAAACACACATTTCTA 59.682 43.478 0.00 0.00 43.23 2.10
565 613 2.101249 CAGTGCCCAAACACACATTTCT 59.899 45.455 0.00 0.00 43.23 2.52
566 614 2.100584 TCAGTGCCCAAACACACATTTC 59.899 45.455 0.00 0.00 43.23 2.17
567 615 2.101249 CTCAGTGCCCAAACACACATTT 59.899 45.455 0.00 0.00 43.23 2.32
569 617 1.321474 CTCAGTGCCCAAACACACAT 58.679 50.000 0.00 0.00 43.23 3.21
570 618 0.034574 ACTCAGTGCCCAAACACACA 60.035 50.000 0.00 0.00 43.23 3.72
571 619 0.663153 GACTCAGTGCCCAAACACAC 59.337 55.000 0.00 0.00 43.23 3.82
572 620 0.546122 AGACTCAGTGCCCAAACACA 59.454 50.000 0.00 0.00 43.23 3.72
573 621 1.202698 AGAGACTCAGTGCCCAAACAC 60.203 52.381 5.02 0.00 41.02 3.32
574 622 1.070758 GAGAGACTCAGTGCCCAAACA 59.929 52.381 5.02 0.00 0.00 2.83
575 623 1.346068 AGAGAGACTCAGTGCCCAAAC 59.654 52.381 5.02 0.00 32.06 2.93
576 624 1.345741 CAGAGAGACTCAGTGCCCAAA 59.654 52.381 5.02 0.00 32.06 3.28
577 625 0.972134 CAGAGAGACTCAGTGCCCAA 59.028 55.000 5.02 0.00 32.06 4.12
578 626 0.902048 CCAGAGAGACTCAGTGCCCA 60.902 60.000 5.02 0.00 32.06 5.36
579 627 1.612395 CCCAGAGAGACTCAGTGCCC 61.612 65.000 5.02 0.00 32.06 5.36
580 628 1.612395 CCCCAGAGAGACTCAGTGCC 61.612 65.000 5.02 0.00 32.06 5.01
581 629 0.902516 ACCCCAGAGAGACTCAGTGC 60.903 60.000 5.02 0.00 32.06 4.40
582 630 2.516227 TACCCCAGAGAGACTCAGTG 57.484 55.000 5.02 1.23 32.06 3.66
583 631 3.544698 TTTACCCCAGAGAGACTCAGT 57.455 47.619 5.02 0.00 32.06 3.41
584 632 3.578716 TGTTTTACCCCAGAGAGACTCAG 59.421 47.826 5.02 0.00 32.06 3.35
585 633 3.323979 GTGTTTTACCCCAGAGAGACTCA 59.676 47.826 5.02 0.00 32.06 3.41
586 634 3.614390 CGTGTTTTACCCCAGAGAGACTC 60.614 52.174 0.00 0.00 0.00 3.36
587 635 2.299297 CGTGTTTTACCCCAGAGAGACT 59.701 50.000 0.00 0.00 0.00 3.24
588 636 2.298163 TCGTGTTTTACCCCAGAGAGAC 59.702 50.000 0.00 0.00 0.00 3.36
589 637 2.600790 TCGTGTTTTACCCCAGAGAGA 58.399 47.619 0.00 0.00 0.00 3.10
590 638 3.195825 AGATCGTGTTTTACCCCAGAGAG 59.804 47.826 0.00 0.00 0.00 3.20
591 639 3.170717 AGATCGTGTTTTACCCCAGAGA 58.829 45.455 0.00 0.00 0.00 3.10
592 640 3.611766 AGATCGTGTTTTACCCCAGAG 57.388 47.619 0.00 0.00 0.00 3.35
593 641 4.346730 TCTAGATCGTGTTTTACCCCAGA 58.653 43.478 0.00 0.00 0.00 3.86
594 642 4.730949 TCTAGATCGTGTTTTACCCCAG 57.269 45.455 0.00 0.00 0.00 4.45
595 643 4.081309 CCTTCTAGATCGTGTTTTACCCCA 60.081 45.833 0.00 0.00 0.00 4.96
596 644 4.439968 CCTTCTAGATCGTGTTTTACCCC 58.560 47.826 0.00 0.00 0.00 4.95
597 645 3.869832 GCCTTCTAGATCGTGTTTTACCC 59.130 47.826 0.00 0.00 0.00 3.69
598 646 4.756502 AGCCTTCTAGATCGTGTTTTACC 58.243 43.478 0.00 0.00 0.00 2.85
599 647 4.804665 GGAGCCTTCTAGATCGTGTTTTAC 59.195 45.833 0.00 0.00 0.00 2.01
600 648 4.710375 AGGAGCCTTCTAGATCGTGTTTTA 59.290 41.667 0.00 0.00 0.00 1.52
601 649 3.515901 AGGAGCCTTCTAGATCGTGTTTT 59.484 43.478 0.00 0.00 0.00 2.43
602 650 3.100671 AGGAGCCTTCTAGATCGTGTTT 58.899 45.455 0.00 0.00 0.00 2.83
603 651 2.741145 AGGAGCCTTCTAGATCGTGTT 58.259 47.619 0.00 0.00 0.00 3.32
604 652 2.445682 AGGAGCCTTCTAGATCGTGT 57.554 50.000 0.00 0.00 0.00 4.49
605 653 4.920640 TTTAGGAGCCTTCTAGATCGTG 57.079 45.455 0.00 0.00 0.00 4.35
606 654 5.934402 TTTTTAGGAGCCTTCTAGATCGT 57.066 39.130 0.00 0.00 0.00 3.73
607 655 8.888579 TTAATTTTTAGGAGCCTTCTAGATCG 57.111 34.615 0.00 0.00 0.00 3.69
610 658 9.462606 CCTTTTAATTTTTAGGAGCCTTCTAGA 57.537 33.333 0.00 0.00 0.00 2.43
611 659 8.687242 CCCTTTTAATTTTTAGGAGCCTTCTAG 58.313 37.037 0.00 0.00 0.00 2.43
612 660 7.618117 CCCCTTTTAATTTTTAGGAGCCTTCTA 59.382 37.037 0.00 0.00 0.00 2.10
613 661 6.440647 CCCCTTTTAATTTTTAGGAGCCTTCT 59.559 38.462 0.00 0.00 0.00 2.85
614 662 6.212791 ACCCCTTTTAATTTTTAGGAGCCTTC 59.787 38.462 0.00 0.00 0.00 3.46
615 663 6.088819 ACCCCTTTTAATTTTTAGGAGCCTT 58.911 36.000 0.00 0.00 0.00 4.35
616 664 5.661565 ACCCCTTTTAATTTTTAGGAGCCT 58.338 37.500 0.00 0.00 0.00 4.58
617 665 7.484993 TTACCCCTTTTAATTTTTAGGAGCC 57.515 36.000 0.00 0.00 0.00 4.70
618 666 9.781633 TTTTTACCCCTTTTAATTTTTAGGAGC 57.218 29.630 0.00 0.00 0.00 4.70
624 672 9.961264 TGTCTGTTTTTACCCCTTTTAATTTTT 57.039 25.926 0.00 0.00 0.00 1.94
625 673 9.961264 TTGTCTGTTTTTACCCCTTTTAATTTT 57.039 25.926 0.00 0.00 0.00 1.82
631 679 8.710239 ACAATATTGTCTGTTTTTACCCCTTTT 58.290 29.630 15.47 0.00 36.50 2.27
632 680 8.257602 ACAATATTGTCTGTTTTTACCCCTTT 57.742 30.769 15.47 0.00 36.50 3.11
633 681 7.849322 ACAATATTGTCTGTTTTTACCCCTT 57.151 32.000 15.47 0.00 36.50 3.95
648 696 9.131791 GATTACCCCATTTAGTGACAATATTGT 57.868 33.333 20.93 20.93 45.65 2.71
649 697 9.354673 AGATTACCCCATTTAGTGACAATATTG 57.645 33.333 14.01 14.01 0.00 1.90
650 698 9.354673 CAGATTACCCCATTTAGTGACAATATT 57.645 33.333 0.00 0.00 0.00 1.28
651 699 7.944554 CCAGATTACCCCATTTAGTGACAATAT 59.055 37.037 0.00 0.00 0.00 1.28
652 700 7.128109 TCCAGATTACCCCATTTAGTGACAATA 59.872 37.037 0.00 0.00 0.00 1.90
653 701 6.069088 TCCAGATTACCCCATTTAGTGACAAT 60.069 38.462 0.00 0.00 0.00 2.71
654 702 5.251932 TCCAGATTACCCCATTTAGTGACAA 59.748 40.000 0.00 0.00 0.00 3.18
655 703 4.785914 TCCAGATTACCCCATTTAGTGACA 59.214 41.667 0.00 0.00 0.00 3.58
656 704 5.367945 TCCAGATTACCCCATTTAGTGAC 57.632 43.478 0.00 0.00 0.00 3.67
657 705 5.669904 TCATCCAGATTACCCCATTTAGTGA 59.330 40.000 0.00 0.00 0.00 3.41
658 706 5.940617 TCATCCAGATTACCCCATTTAGTG 58.059 41.667 0.00 0.00 0.00 2.74
659 707 6.590656 TTCATCCAGATTACCCCATTTAGT 57.409 37.500 0.00 0.00 0.00 2.24
660 708 7.896383 TTTTCATCCAGATTACCCCATTTAG 57.104 36.000 0.00 0.00 0.00 1.85
661 709 8.852671 AATTTTCATCCAGATTACCCCATTTA 57.147 30.769 0.00 0.00 0.00 1.40
662 710 7.754091 AATTTTCATCCAGATTACCCCATTT 57.246 32.000 0.00 0.00 0.00 2.32
663 711 7.182568 ACAAATTTTCATCCAGATTACCCCATT 59.817 33.333 0.00 0.00 0.00 3.16
664 712 6.673537 ACAAATTTTCATCCAGATTACCCCAT 59.326 34.615 0.00 0.00 0.00 4.00
665 713 6.022315 ACAAATTTTCATCCAGATTACCCCA 58.978 36.000 0.00 0.00 0.00 4.96
666 714 6.544928 ACAAATTTTCATCCAGATTACCCC 57.455 37.500 0.00 0.00 0.00 4.95
667 715 9.936759 TTTAACAAATTTTCATCCAGATTACCC 57.063 29.630 0.00 0.00 0.00 3.69
671 719 9.452287 CCCATTTAACAAATTTTCATCCAGATT 57.548 29.630 0.00 0.00 0.00 2.40
672 720 8.048514 CCCCATTTAACAAATTTTCATCCAGAT 58.951 33.333 0.00 0.00 0.00 2.90
673 721 7.017056 ACCCCATTTAACAAATTTTCATCCAGA 59.983 33.333 0.00 0.00 0.00 3.86
674 722 7.167535 ACCCCATTTAACAAATTTTCATCCAG 58.832 34.615 0.00 0.00 0.00 3.86
675 723 7.084268 ACCCCATTTAACAAATTTTCATCCA 57.916 32.000 0.00 0.00 0.00 3.41
676 724 8.941977 GTTACCCCATTTAACAAATTTTCATCC 58.058 33.333 0.00 0.00 30.95 3.51
677 725 9.719355 AGTTACCCCATTTAACAAATTTTCATC 57.281 29.630 0.00 0.00 32.70 2.92
684 732 9.315363 TGACATTAGTTACCCCATTTAACAAAT 57.685 29.630 0.00 0.00 32.70 2.32
685 733 8.707796 TGACATTAGTTACCCCATTTAACAAA 57.292 30.769 0.00 0.00 32.70 2.83
686 734 8.707796 TTGACATTAGTTACCCCATTTAACAA 57.292 30.769 0.00 0.00 32.70 2.83
687 735 8.707796 TTTGACATTAGTTACCCCATTTAACA 57.292 30.769 0.00 0.00 32.70 2.41
688 736 9.984190 TTTTTGACATTAGTTACCCCATTTAAC 57.016 29.630 0.00 0.00 0.00 2.01
691 739 7.606073 GCATTTTTGACATTAGTTACCCCATTT 59.394 33.333 0.00 0.00 0.00 2.32
692 740 7.038373 AGCATTTTTGACATTAGTTACCCCATT 60.038 33.333 0.00 0.00 0.00 3.16
693 741 6.440328 AGCATTTTTGACATTAGTTACCCCAT 59.560 34.615 0.00 0.00 0.00 4.00
694 742 5.777732 AGCATTTTTGACATTAGTTACCCCA 59.222 36.000 0.00 0.00 0.00 4.96
695 743 6.280855 AGCATTTTTGACATTAGTTACCCC 57.719 37.500 0.00 0.00 0.00 4.95
696 744 9.869757 ATTTAGCATTTTTGACATTAGTTACCC 57.130 29.630 0.00 0.00 0.00 3.69
702 750 9.533253 CCCCTAATTTAGCATTTTTGACATTAG 57.467 33.333 0.00 0.00 0.00 1.73
703 751 8.482128 CCCCCTAATTTAGCATTTTTGACATTA 58.518 33.333 0.00 0.00 0.00 1.90
704 752 7.037658 ACCCCCTAATTTAGCATTTTTGACATT 60.038 33.333 0.00 0.00 0.00 2.71
705 753 6.443527 ACCCCCTAATTTAGCATTTTTGACAT 59.556 34.615 0.00 0.00 0.00 3.06
706 754 5.782845 ACCCCCTAATTTAGCATTTTTGACA 59.217 36.000 0.00 0.00 0.00 3.58
707 755 6.294361 ACCCCCTAATTTAGCATTTTTGAC 57.706 37.500 0.00 0.00 0.00 3.18
708 756 8.437274 TTTACCCCCTAATTTAGCATTTTTGA 57.563 30.769 0.00 0.00 0.00 2.69
709 757 9.508642 TTTTTACCCCCTAATTTAGCATTTTTG 57.491 29.630 0.00 0.00 0.00 2.44
710 758 9.509956 GTTTTTACCCCCTAATTTAGCATTTTT 57.490 29.630 0.00 0.00 0.00 1.94
711 759 8.886369 AGTTTTTACCCCCTAATTTAGCATTTT 58.114 29.630 0.00 0.00 0.00 1.82
712 760 8.318412 CAGTTTTTACCCCCTAATTTAGCATTT 58.682 33.333 0.00 0.00 0.00 2.32
713 761 7.093068 CCAGTTTTTACCCCCTAATTTAGCATT 60.093 37.037 0.00 0.00 0.00 3.56
714 762 6.382859 CCAGTTTTTACCCCCTAATTTAGCAT 59.617 38.462 0.00 0.00 0.00 3.79
715 763 5.717654 CCAGTTTTTACCCCCTAATTTAGCA 59.282 40.000 0.00 0.00 0.00 3.49
716 764 5.953548 TCCAGTTTTTACCCCCTAATTTAGC 59.046 40.000 0.00 0.00 0.00 3.09
717 765 8.603898 ATTCCAGTTTTTACCCCCTAATTTAG 57.396 34.615 0.00 0.00 0.00 1.85
718 766 8.975925 AATTCCAGTTTTTACCCCCTAATTTA 57.024 30.769 0.00 0.00 0.00 1.40
719 767 7.514473 TGAATTCCAGTTTTTACCCCCTAATTT 59.486 33.333 2.27 0.00 0.00 1.82
720 768 7.020009 TGAATTCCAGTTTTTACCCCCTAATT 58.980 34.615 2.27 0.00 0.00 1.40
721 769 6.439375 GTGAATTCCAGTTTTTACCCCCTAAT 59.561 38.462 2.27 0.00 0.00 1.73
722 770 5.776208 GTGAATTCCAGTTTTTACCCCCTAA 59.224 40.000 2.27 0.00 0.00 2.69
723 771 5.075344 AGTGAATTCCAGTTTTTACCCCCTA 59.925 40.000 2.27 0.00 0.00 3.53
724 772 4.140782 AGTGAATTCCAGTTTTTACCCCCT 60.141 41.667 2.27 0.00 0.00 4.79
725 773 4.157246 AGTGAATTCCAGTTTTTACCCCC 58.843 43.478 2.27 0.00 0.00 5.40
726 774 4.830600 TGAGTGAATTCCAGTTTTTACCCC 59.169 41.667 2.27 0.00 0.00 4.95
727 775 6.590234 ATGAGTGAATTCCAGTTTTTACCC 57.410 37.500 2.27 0.00 0.00 3.69
728 776 9.406828 GTTTATGAGTGAATTCCAGTTTTTACC 57.593 33.333 2.27 0.00 0.00 2.85
729 777 9.959749 TGTTTATGAGTGAATTCCAGTTTTTAC 57.040 29.630 2.27 0.00 0.00 2.01
731 779 9.883142 TTTGTTTATGAGTGAATTCCAGTTTTT 57.117 25.926 2.27 0.00 0.00 1.94
732 780 9.313118 GTTTGTTTATGAGTGAATTCCAGTTTT 57.687 29.630 2.27 0.00 0.00 2.43
733 781 8.474025 TGTTTGTTTATGAGTGAATTCCAGTTT 58.526 29.630 2.27 0.00 0.00 2.66
734 782 8.006298 TGTTTGTTTATGAGTGAATTCCAGTT 57.994 30.769 2.27 0.00 0.00 3.16
735 783 7.581213 TGTTTGTTTATGAGTGAATTCCAGT 57.419 32.000 2.27 0.00 0.00 4.00
736 784 7.920151 TGTTGTTTGTTTATGAGTGAATTCCAG 59.080 33.333 2.27 0.00 0.00 3.86
737 785 7.776107 TGTTGTTTGTTTATGAGTGAATTCCA 58.224 30.769 2.27 0.00 0.00 3.53
738 786 8.539674 GTTGTTGTTTGTTTATGAGTGAATTCC 58.460 33.333 2.27 0.00 0.00 3.01
739 787 9.081997 TGTTGTTGTTTGTTTATGAGTGAATTC 57.918 29.630 0.00 0.00 0.00 2.17
740 788 8.994429 TGTTGTTGTTTGTTTATGAGTGAATT 57.006 26.923 0.00 0.00 0.00 2.17
741 789 8.868916 GTTGTTGTTGTTTGTTTATGAGTGAAT 58.131 29.630 0.00 0.00 0.00 2.57
742 790 7.867909 TGTTGTTGTTGTTTGTTTATGAGTGAA 59.132 29.630 0.00 0.00 0.00 3.18
743 791 7.327275 GTGTTGTTGTTGTTTGTTTATGAGTGA 59.673 33.333 0.00 0.00 0.00 3.41
744 792 7.444245 GTGTTGTTGTTGTTTGTTTATGAGTG 58.556 34.615 0.00 0.00 0.00 3.51
745 793 6.306837 CGTGTTGTTGTTGTTTGTTTATGAGT 59.693 34.615 0.00 0.00 0.00 3.41
746 794 6.524933 TCGTGTTGTTGTTGTTTGTTTATGAG 59.475 34.615 0.00 0.00 0.00 2.90
747 795 6.379386 TCGTGTTGTTGTTGTTTGTTTATGA 58.621 32.000 0.00 0.00 0.00 2.15
748 796 6.306837 ACTCGTGTTGTTGTTGTTTGTTTATG 59.693 34.615 0.00 0.00 0.00 1.90
754 802 6.677027 TTTAACTCGTGTTGTTGTTGTTTG 57.323 33.333 12.89 0.00 37.59 2.93
907 3699 4.748102 AGCTTTGTCACGAGAACGAAAATA 59.252 37.500 0.00 0.00 42.66 1.40
914 3706 1.527311 GGTCAGCTTTGTCACGAGAAC 59.473 52.381 0.00 0.00 0.00 3.01
1026 5222 1.621672 GGAGCACAAGGAGGAGGAGG 61.622 65.000 0.00 0.00 0.00 4.30
1355 5551 5.450376 AATTGTGTGACATACGAATCGAC 57.550 39.130 10.55 0.00 0.00 4.20
1378 5574 7.363268 GCATCAAGATTTAGGAACTGGACATTT 60.363 37.037 0.00 0.00 41.52 2.32
1525 5723 6.070824 AGGAAATCGCCTAACCAAATCAAAAT 60.071 34.615 0.00 0.00 36.22 1.82
1550 5748 4.342862 TTCGCCCCAAATGAAATTGAAA 57.657 36.364 0.00 0.00 36.10 2.69
1756 5958 6.127366 CCCTAAATTGGCATCTTGAAAAGCTA 60.127 38.462 0.00 0.00 45.70 3.32
1873 6075 4.639755 TCACTTGCAGAATGAACTGACAAA 59.360 37.500 0.00 0.00 39.69 2.83
1989 6192 1.216990 AAACATCTCCTGGGCCCTAG 58.783 55.000 25.70 18.18 0.00 3.02
1990 6193 2.579624 TAAACATCTCCTGGGCCCTA 57.420 50.000 25.70 8.68 0.00 3.53
2090 7053 1.340248 CTCATTGGCAGGCAATCCATC 59.660 52.381 19.08 0.00 33.74 3.51
2205 7168 7.391275 TCACACTTCATAAGCAGATGATTTTCA 59.609 33.333 1.79 0.00 35.77 2.69
2312 7275 2.781174 AGTGTACTCCTTTCCACCCAAA 59.219 45.455 0.00 0.00 0.00 3.28
2497 7460 6.719370 GCCATTGGTCATATTAATGGGTAAGA 59.281 38.462 14.83 0.00 46.88 2.10
2498 7461 6.071391 GGCCATTGGTCATATTAATGGGTAAG 60.071 42.308 14.83 0.00 46.88 2.34
2499 7462 5.777732 GGCCATTGGTCATATTAATGGGTAA 59.222 40.000 14.83 0.00 46.88 2.85
2500 7463 5.075761 AGGCCATTGGTCATATTAATGGGTA 59.924 40.000 10.50 0.00 46.88 3.69
2501 7464 4.140710 AGGCCATTGGTCATATTAATGGGT 60.141 41.667 10.50 0.00 46.88 4.51
2533 7496 3.549794 ACTCTGCAAATCATAAGGAGGC 58.450 45.455 0.00 0.00 0.00 4.70
2708 7671 2.762535 ATCAGGTGGGTTACAACTCG 57.237 50.000 0.00 0.00 46.59 4.18
2733 7696 9.224267 CAGTAGCCATTATTTGCTAATCACTAT 57.776 33.333 0.00 0.00 41.42 2.12
2734 7697 8.210946 ACAGTAGCCATTATTTGCTAATCACTA 58.789 33.333 0.00 0.00 41.42 2.74
2735 7698 7.012704 CACAGTAGCCATTATTTGCTAATCACT 59.987 37.037 0.00 0.00 41.42 3.41
2945 7909 9.740239 GATGACAATTACATCTGTGCATATTTT 57.260 29.630 13.91 0.00 40.36 1.82
2946 7910 8.905850 TGATGACAATTACATCTGTGCATATTT 58.094 29.630 18.83 0.00 42.89 1.40
2947 7911 8.454570 TGATGACAATTACATCTGTGCATATT 57.545 30.769 18.83 0.00 42.89 1.28
2948 7912 8.631480 ATGATGACAATTACATCTGTGCATAT 57.369 30.769 18.83 6.25 42.89 1.78
2949 7913 8.454570 AATGATGACAATTACATCTGTGCATA 57.545 30.769 18.83 0.00 42.89 3.14
2950 7914 6.954487 ATGATGACAATTACATCTGTGCAT 57.046 33.333 18.83 7.64 42.89 3.96
2951 7915 6.762702 AATGATGACAATTACATCTGTGCA 57.237 33.333 18.83 0.00 42.89 4.57
2952 7916 9.013490 GTAAAATGATGACAATTACATCTGTGC 57.987 33.333 18.83 7.50 42.89 4.57
2967 7931 8.768397 ACTGGTTAGGTCATAGTAAAATGATGA 58.232 33.333 0.00 0.00 38.13 2.92
2982 7946 8.421784 TGATCTAACAATCATACTGGTTAGGTC 58.578 37.037 13.83 13.83 46.59 3.85
2988 7952 9.373450 AGTATCTGATCTAACAATCATACTGGT 57.627 33.333 0.00 0.00 33.39 4.00
2989 7953 9.636879 CAGTATCTGATCTAACAATCATACTGG 57.363 37.037 14.31 3.47 40.93 4.00
2990 7954 9.138062 GCAGTATCTGATCTAACAATCATACTG 57.862 37.037 16.24 16.24 43.77 2.74
2991 7955 8.864087 TGCAGTATCTGATCTAACAATCATACT 58.136 33.333 0.00 0.00 34.25 2.12
2992 7956 8.920665 GTGCAGTATCTGATCTAACAATCATAC 58.079 37.037 0.00 0.00 35.21 2.39
2993 7957 8.864087 AGTGCAGTATCTGATCTAACAATCATA 58.136 33.333 0.00 0.00 35.21 2.15
3266 8235 7.014422 GGAAGAAGAACGAGAATATCCTTAGGA 59.986 40.741 2.37 2.37 35.55 2.94
3327 8296 1.448893 GGCGTGCCGGAAGTATTGA 60.449 57.895 5.05 0.00 0.00 2.57
3439 8408 4.922206 ACTCTCATGTTTATGGCTCCAAA 58.078 39.130 0.00 0.00 34.97 3.28
3477 8446 0.249868 CACCAAGAGACACGGAAGCA 60.250 55.000 0.00 0.00 0.00 3.91
3534 8503 2.159490 CGCCCGACGTTAAAATCCAAAT 60.159 45.455 0.00 0.00 36.87 2.32
3574 8543 0.099968 CCACATCCAGCGCAATTCAG 59.900 55.000 11.47 0.00 0.00 3.02
3600 8569 6.426633 CCACTACATGTTCATGTGAGTTACAA 59.573 38.462 23.33 5.06 43.77 2.41
3625 8594 8.970691 ATTTACATGCTACAAACAAGATGTTC 57.029 30.769 0.00 0.00 40.14 3.18
3702 8672 6.215121 TGCTCAAAAACTATGACAATTGGTG 58.785 36.000 10.83 0.00 0.00 4.17
3971 8995 4.256110 TGCACACCTTCAATGTAGATGAG 58.744 43.478 0.00 0.00 0.00 2.90
4293 9317 1.202818 GGGCGGATATCAAAGAGGCTT 60.203 52.381 4.83 0.00 0.00 4.35
4320 9344 4.265073 CCGAAAACATCAGGGAGAAGATT 58.735 43.478 0.00 0.00 0.00 2.40
4503 9527 6.219473 TGAAATCAACTCTGAGACTGACTTC 58.781 40.000 19.23 19.23 34.23 3.01


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

AutoCloner maintained by Alex Coulton.