Multiple sequence alignment - TraesCS4B01G015800

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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 TraesCS4B01G015800 chr4B 100.000 2429 0 0 1 2429 11733989 11736417 0.000000e+00 4486.0
1 TraesCS4B01G015800 chr4B 90.070 574 45 7 1 566 55751171 55751740 0.000000e+00 734.0
2 TraesCS4B01G015800 chr4D 88.084 1670 91 53 818 2429 6573162 6574781 0.000000e+00 1882.0
3 TraesCS4B01G015800 chr4A 85.812 881 53 33 785 1617 596828579 596827723 0.000000e+00 869.0
4 TraesCS4B01G015800 chr4A 87.240 721 68 14 1723 2429 596827531 596826821 0.000000e+00 800.0
5 TraesCS4B01G015800 chr7D 91.463 574 38 2 1 566 486170705 486170135 0.000000e+00 778.0
6 TraesCS4B01G015800 chr2D 90.909 572 38 5 1 564 627644361 627644926 0.000000e+00 756.0
7 TraesCS4B01G015800 chr2A 90.893 571 39 9 1 564 758256123 758255559 0.000000e+00 754.0
8 TraesCS4B01G015800 chr2A 88.696 575 44 4 1 566 763633795 763634357 0.000000e+00 682.0
9 TraesCS4B01G015800 chr2A 85.965 114 14 2 639 750 16079856 16079743 1.180000e-23 121.0
10 TraesCS4B01G015800 chr2A 85.841 113 14 2 639 749 70275733 70275845 4.240000e-23 119.0
11 TraesCS4B01G015800 chr5D 90.592 574 42 5 1 566 311767382 311767951 0.000000e+00 750.0
12 TraesCS4B01G015800 chr7B 87.831 567 37 20 1 566 513959853 513959318 9.470000e-179 636.0
13 TraesCS4B01G015800 chr6A 87.050 556 51 11 12 566 376485585 376486120 2.070000e-170 608.0
14 TraesCS4B01G015800 chr6A 89.189 74 8 0 617 690 184667805 184667878 2.570000e-15 93.5
15 TraesCS4B01G015800 chrUn 90.349 373 29 5 1 371 324091861 324092228 1.310000e-132 483.0
16 TraesCS4B01G015800 chr1D 81.129 567 86 12 1 558 487442567 487442013 3.710000e-118 435.0
17 TraesCS4B01G015800 chr1D 89.014 355 31 1 220 566 372459644 372459290 1.330000e-117 433.0
18 TraesCS4B01G015800 chr2B 86.192 239 23 6 337 566 170766192 170766429 1.440000e-62 250.0
19 TraesCS4B01G015800 chr2B 82.439 205 14 8 363 567 451341541 451341723 2.500000e-35 159.0
20 TraesCS4B01G015800 chr1A 87.156 109 10 4 612 716 471956806 471956698 1.180000e-23 121.0
21 TraesCS4B01G015800 chr5B 80.909 110 18 3 640 747 641108239 641108131 1.550000e-12 84.2


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 TraesCS4B01G015800 chr4B 11733989 11736417 2428 False 4486.0 4486 100.000 1 2429 1 chr4B.!!$F1 2428
1 TraesCS4B01G015800 chr4B 55751171 55751740 569 False 734.0 734 90.070 1 566 1 chr4B.!!$F2 565
2 TraesCS4B01G015800 chr4D 6573162 6574781 1619 False 1882.0 1882 88.084 818 2429 1 chr4D.!!$F1 1611
3 TraesCS4B01G015800 chr4A 596826821 596828579 1758 True 834.5 869 86.526 785 2429 2 chr4A.!!$R1 1644
4 TraesCS4B01G015800 chr7D 486170135 486170705 570 True 778.0 778 91.463 1 566 1 chr7D.!!$R1 565
5 TraesCS4B01G015800 chr2D 627644361 627644926 565 False 756.0 756 90.909 1 564 1 chr2D.!!$F1 563
6 TraesCS4B01G015800 chr2A 758255559 758256123 564 True 754.0 754 90.893 1 564 1 chr2A.!!$R2 563
7 TraesCS4B01G015800 chr2A 763633795 763634357 562 False 682.0 682 88.696 1 566 1 chr2A.!!$F2 565
8 TraesCS4B01G015800 chr5D 311767382 311767951 569 False 750.0 750 90.592 1 566 1 chr5D.!!$F1 565
9 TraesCS4B01G015800 chr7B 513959318 513959853 535 True 636.0 636 87.831 1 566 1 chr7B.!!$R1 565
10 TraesCS4B01G015800 chr6A 376485585 376486120 535 False 608.0 608 87.050 12 566 1 chr6A.!!$F2 554
11 TraesCS4B01G015800 chr1D 487442013 487442567 554 True 435.0 435 81.129 1 558 1 chr1D.!!$R2 557

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
579 595 0.036306 GAGGAGTTTGAGGGGCGAAA 59.964 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1720 0.37337 CGATTCGCCTTCGCATGAAA 59.627 50.0 0.0 0.0 32.66 2.69 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
173 177 4.519350 CCACCAAGATGGATGATGATGAAG 59.481 45.833 2.85 0.00 43.02 3.02
277 281 2.694760 GGCTTCAAGCTTGCGGGAG 61.695 63.158 21.99 15.90 41.99 4.30
301 305 4.029520 AGCTAGATCACATGGTCAAGTCT 58.970 43.478 0.00 0.00 0.00 3.24
307 311 7.134362 AGATCACATGGTCAAGTCTAATGAT 57.866 36.000 0.00 0.00 0.00 2.45
395 410 2.563179 GCAACTACTCAAGGAGGAGACA 59.437 50.000 12.29 0.00 42.94 3.41
477 493 1.355066 GCTTCTTGCCGAGGAGAACG 61.355 60.000 0.00 0.00 32.05 3.95
482 498 0.895530 TTGCCGAGGAGAACGAGATT 59.104 50.000 0.00 0.00 0.00 2.40
546 562 1.273048 GGCATGACATTGCAAGGTTGA 59.727 47.619 18.94 8.71 44.59 3.18
559 575 5.132502 TGCAAGGTTGAAGATCTTGAAGAA 58.867 37.500 14.00 0.00 39.97 2.52
566 582 6.463360 GTTGAAGATCTTGAAGAAGAGGAGT 58.537 40.000 14.00 0.00 41.62 3.85
567 583 6.678568 TGAAGATCTTGAAGAAGAGGAGTT 57.321 37.500 14.00 0.00 41.62 3.01
568 584 7.072263 TGAAGATCTTGAAGAAGAGGAGTTT 57.928 36.000 14.00 0.00 41.62 2.66
569 585 6.933521 TGAAGATCTTGAAGAAGAGGAGTTTG 59.066 38.462 14.00 0.00 41.62 2.93
570 586 6.678568 AGATCTTGAAGAAGAGGAGTTTGA 57.321 37.500 0.00 0.00 41.62 2.69
571 587 6.700352 AGATCTTGAAGAAGAGGAGTTTGAG 58.300 40.000 0.00 0.00 41.62 3.02
572 588 5.220710 TCTTGAAGAAGAGGAGTTTGAGG 57.779 43.478 0.00 0.00 32.98 3.86
573 589 4.040952 TCTTGAAGAAGAGGAGTTTGAGGG 59.959 45.833 0.00 0.00 32.98 4.30
574 590 2.639839 TGAAGAAGAGGAGTTTGAGGGG 59.360 50.000 0.00 0.00 0.00 4.79
575 591 0.988063 AGAAGAGGAGTTTGAGGGGC 59.012 55.000 0.00 0.00 0.00 5.80
576 592 0.391793 GAAGAGGAGTTTGAGGGGCG 60.392 60.000 0.00 0.00 0.00 6.13
577 593 0.836400 AAGAGGAGTTTGAGGGGCGA 60.836 55.000 0.00 0.00 0.00 5.54
578 594 0.836400 AGAGGAGTTTGAGGGGCGAA 60.836 55.000 0.00 0.00 0.00 4.70
579 595 0.036306 GAGGAGTTTGAGGGGCGAAA 59.964 55.000 0.00 0.00 0.00 3.46
580 596 0.250770 AGGAGTTTGAGGGGCGAAAC 60.251 55.000 0.00 0.00 33.11 2.78
581 597 1.241990 GGAGTTTGAGGGGCGAAACC 61.242 60.000 0.00 0.00 33.34 3.27
582 598 1.574702 GAGTTTGAGGGGCGAAACCG 61.575 60.000 0.00 0.00 40.62 4.44
583 599 2.281900 TTTGAGGGGCGAAACCGG 60.282 61.111 0.00 0.00 40.62 5.28
584 600 2.820400 TTTGAGGGGCGAAACCGGA 61.820 57.895 9.46 0.00 40.62 5.14
585 601 2.340673 TTTGAGGGGCGAAACCGGAA 62.341 55.000 9.46 0.00 40.62 4.30
586 602 2.436115 GAGGGGCGAAACCGGAAG 60.436 66.667 9.46 0.00 40.62 3.46
587 603 4.717313 AGGGGCGAAACCGGAAGC 62.717 66.667 9.46 7.62 40.62 3.86
593 609 4.445545 GAAACCGGAAGCGCGCAG 62.446 66.667 35.10 20.31 0.00 5.18
594 610 4.980805 AAACCGGAAGCGCGCAGA 62.981 61.111 35.10 0.00 0.00 4.26
595 611 4.980805 AACCGGAAGCGCGCAGAA 62.981 61.111 35.10 0.00 0.00 3.02
598 614 3.711842 CGGAAGCGCGCAGAACAA 61.712 61.111 35.10 0.00 0.00 2.83
599 615 2.637025 GGAAGCGCGCAGAACAAA 59.363 55.556 35.10 0.00 0.00 2.83
600 616 1.441016 GGAAGCGCGCAGAACAAAG 60.441 57.895 35.10 0.00 0.00 2.77
601 617 2.050985 AAGCGCGCAGAACAAAGC 60.051 55.556 35.10 0.00 0.00 3.51
602 618 3.542629 AAGCGCGCAGAACAAAGCC 62.543 57.895 35.10 0.00 0.00 4.35
604 620 4.741781 CGCGCAGAACAAAGCCCG 62.742 66.667 8.75 0.00 0.00 6.13
606 622 3.659092 CGCAGAACAAAGCCCGCA 61.659 61.111 0.00 0.00 0.00 5.69
607 623 2.727544 GCAGAACAAAGCCCGCAA 59.272 55.556 0.00 0.00 0.00 4.85
608 624 1.067250 GCAGAACAAAGCCCGCAAA 59.933 52.632 0.00 0.00 0.00 3.68
609 625 1.215014 GCAGAACAAAGCCCGCAAAC 61.215 55.000 0.00 0.00 0.00 2.93
610 626 0.597377 CAGAACAAAGCCCGCAAACC 60.597 55.000 0.00 0.00 0.00 3.27
611 627 1.300620 GAACAAAGCCCGCAAACCC 60.301 57.895 0.00 0.00 0.00 4.11
612 628 3.145422 AACAAAGCCCGCAAACCCG 62.145 57.895 0.00 0.00 0.00 5.28
619 635 2.513895 CCGCAAACCCGGGGATAT 59.486 61.111 27.92 4.78 44.46 1.63
620 636 1.152839 CCGCAAACCCGGGGATATT 60.153 57.895 27.92 11.44 44.46 1.28
621 637 1.170290 CCGCAAACCCGGGGATATTC 61.170 60.000 27.92 7.55 44.46 1.75
622 638 0.179029 CGCAAACCCGGGGATATTCT 60.179 55.000 27.92 0.00 0.00 2.40
623 639 1.605753 GCAAACCCGGGGATATTCTC 58.394 55.000 27.92 1.44 0.00 2.87
624 640 1.143073 GCAAACCCGGGGATATTCTCT 59.857 52.381 27.92 0.00 0.00 3.10
625 641 2.422945 GCAAACCCGGGGATATTCTCTT 60.423 50.000 27.92 2.89 0.00 2.85
626 642 3.898482 CAAACCCGGGGATATTCTCTTT 58.102 45.455 27.92 9.91 0.00 2.52
627 643 4.278310 CAAACCCGGGGATATTCTCTTTT 58.722 43.478 27.92 9.10 0.00 2.27
628 644 5.442391 CAAACCCGGGGATATTCTCTTTTA 58.558 41.667 27.92 0.00 0.00 1.52
629 645 5.924769 AACCCGGGGATATTCTCTTTTAT 57.075 39.130 27.92 0.00 0.00 1.40
630 646 5.500546 ACCCGGGGATATTCTCTTTTATC 57.499 43.478 27.92 0.00 0.00 1.75
631 647 4.020485 ACCCGGGGATATTCTCTTTTATCG 60.020 45.833 27.92 0.00 0.00 2.92
632 648 3.933332 CCGGGGATATTCTCTTTTATCGC 59.067 47.826 0.00 0.00 37.16 4.58
633 649 4.322801 CCGGGGATATTCTCTTTTATCGCT 60.323 45.833 0.00 0.00 37.70 4.93
634 650 4.865365 CGGGGATATTCTCTTTTATCGCTC 59.135 45.833 0.00 0.00 37.70 5.03
635 651 4.865365 GGGGATATTCTCTTTTATCGCTCG 59.135 45.833 0.00 0.00 37.70 5.03
636 652 4.865365 GGGATATTCTCTTTTATCGCTCGG 59.135 45.833 0.00 0.00 35.82 4.63
637 653 5.471257 GGATATTCTCTTTTATCGCTCGGT 58.529 41.667 0.00 0.00 0.00 4.69
638 654 5.927115 GGATATTCTCTTTTATCGCTCGGTT 59.073 40.000 0.00 0.00 0.00 4.44
639 655 6.424207 GGATATTCTCTTTTATCGCTCGGTTT 59.576 38.462 0.00 0.00 0.00 3.27
640 656 7.041984 GGATATTCTCTTTTATCGCTCGGTTTT 60.042 37.037 0.00 0.00 0.00 2.43
641 657 4.921470 TCTCTTTTATCGCTCGGTTTTG 57.079 40.909 0.00 0.00 0.00 2.44
642 658 3.124636 TCTCTTTTATCGCTCGGTTTTGC 59.875 43.478 0.00 0.00 0.00 3.68
648 664 4.103103 GCTCGGTTTTGCGGGCTC 62.103 66.667 0.00 0.00 0.00 4.70
649 665 2.358737 CTCGGTTTTGCGGGCTCT 60.359 61.111 0.00 0.00 0.00 4.09
650 666 2.668212 TCGGTTTTGCGGGCTCTG 60.668 61.111 0.00 0.00 0.00 3.35
651 667 2.978010 CGGTTTTGCGGGCTCTGT 60.978 61.111 0.00 0.00 0.00 3.41
652 668 2.551912 CGGTTTTGCGGGCTCTGTT 61.552 57.895 0.00 0.00 0.00 3.16
653 669 1.285950 GGTTTTGCGGGCTCTGTTC 59.714 57.895 0.00 0.00 0.00 3.18
654 670 1.082104 GTTTTGCGGGCTCTGTTCG 60.082 57.895 0.00 0.00 0.00 3.95
655 671 2.258013 TTTTGCGGGCTCTGTTCGG 61.258 57.895 0.00 0.00 0.00 4.30
682 698 2.168201 CGATTTCGGCCCTTAAAACG 57.832 50.000 0.00 2.64 35.37 3.60
683 699 1.792632 CGATTTCGGCCCTTAAAACGC 60.793 52.381 0.00 0.00 35.37 4.84
684 700 0.169451 ATTTCGGCCCTTAAAACGCG 59.831 50.000 3.53 3.53 0.00 6.01
685 701 1.165284 TTTCGGCCCTTAAAACGCGT 61.165 50.000 5.58 5.58 0.00 6.01
686 702 1.165284 TTCGGCCCTTAAAACGCGTT 61.165 50.000 20.79 20.79 0.00 4.84
687 703 1.165284 TCGGCCCTTAAAACGCGTTT 61.165 50.000 30.36 30.36 0.00 3.60
688 704 0.318022 CGGCCCTTAAAACGCGTTTT 60.318 50.000 41.13 41.13 44.16 2.43
689 705 1.855513 GGCCCTTAAAACGCGTTTTT 58.144 45.000 43.50 30.13 42.22 1.94
711 727 4.993705 TTGGCCCTTATCTGGTTATAGG 57.006 45.455 0.00 0.00 0.00 2.57
712 728 3.256704 TGGCCCTTATCTGGTTATAGGG 58.743 50.000 0.00 0.00 38.11 3.53
713 729 2.576648 GGCCCTTATCTGGTTATAGGGG 59.423 54.545 7.54 6.68 46.65 4.79
714 730 3.257578 GCCCTTATCTGGTTATAGGGGT 58.742 50.000 11.42 0.00 45.99 4.95
715 731 3.263681 GCCCTTATCTGGTTATAGGGGTC 59.736 52.174 11.42 2.72 45.99 4.46
716 732 3.514309 CCCTTATCTGGTTATAGGGGTCG 59.486 52.174 0.00 0.00 41.62 4.79
717 733 3.056035 CCTTATCTGGTTATAGGGGTCGC 60.056 52.174 0.00 0.00 0.00 5.19
718 734 0.966920 ATCTGGTTATAGGGGTCGCG 59.033 55.000 0.00 0.00 0.00 5.87
719 735 1.111116 TCTGGTTATAGGGGTCGCGG 61.111 60.000 6.13 0.00 0.00 6.46
720 736 2.095978 CTGGTTATAGGGGTCGCGGG 62.096 65.000 6.13 0.00 0.00 6.13
721 737 2.136229 GGTTATAGGGGTCGCGGGT 61.136 63.158 6.13 0.00 0.00 5.28
722 738 1.689243 GGTTATAGGGGTCGCGGGTT 61.689 60.000 6.13 0.00 0.00 4.11
723 739 0.249615 GTTATAGGGGTCGCGGGTTC 60.250 60.000 6.13 0.00 0.00 3.62
724 740 0.687098 TTATAGGGGTCGCGGGTTCA 60.687 55.000 6.13 0.00 0.00 3.18
725 741 0.687098 TATAGGGGTCGCGGGTTCAA 60.687 55.000 6.13 0.00 0.00 2.69
726 742 1.968050 ATAGGGGTCGCGGGTTCAAG 61.968 60.000 6.13 0.00 0.00 3.02
730 746 4.324991 GTCGCGGGTTCAAGGGGT 62.325 66.667 6.13 0.00 0.00 4.95
731 747 3.562232 TCGCGGGTTCAAGGGGTT 61.562 61.111 6.13 0.00 0.00 4.11
732 748 2.596338 CGCGGGTTCAAGGGGTTT 60.596 61.111 0.00 0.00 0.00 3.27
733 749 2.914908 CGCGGGTTCAAGGGGTTTG 61.915 63.158 0.00 0.00 38.17 2.93
734 750 3.047735 CGGGTTCAAGGGGTTTGC 58.952 61.111 0.00 0.00 36.70 3.68
735 751 1.530655 CGGGTTCAAGGGGTTTGCT 60.531 57.895 0.00 0.00 36.70 3.91
736 752 0.250989 CGGGTTCAAGGGGTTTGCTA 60.251 55.000 0.00 0.00 36.70 3.49
737 753 1.545841 GGGTTCAAGGGGTTTGCTAG 58.454 55.000 0.00 0.00 36.70 3.42
738 754 1.074889 GGGTTCAAGGGGTTTGCTAGA 59.925 52.381 0.00 0.00 36.70 2.43
739 755 2.437413 GGTTCAAGGGGTTTGCTAGAG 58.563 52.381 0.00 0.00 36.70 2.43
740 756 2.224793 GGTTCAAGGGGTTTGCTAGAGT 60.225 50.000 0.00 0.00 36.70 3.24
741 757 3.487372 GTTCAAGGGGTTTGCTAGAGTT 58.513 45.455 0.00 0.00 36.70 3.01
742 758 3.140325 TCAAGGGGTTTGCTAGAGTTG 57.860 47.619 0.00 0.00 36.70 3.16
743 759 1.541588 CAAGGGGTTTGCTAGAGTTGC 59.458 52.381 0.00 0.00 0.00 4.17
744 760 1.068121 AGGGGTTTGCTAGAGTTGCT 58.932 50.000 0.00 0.00 0.00 3.91
745 761 1.003696 AGGGGTTTGCTAGAGTTGCTC 59.996 52.381 0.00 0.00 0.00 4.26
746 762 1.003696 GGGGTTTGCTAGAGTTGCTCT 59.996 52.381 4.02 4.02 43.83 4.09
747 763 2.236395 GGGGTTTGCTAGAGTTGCTCTA 59.764 50.000 0.00 5.84 41.50 2.43
748 764 3.307480 GGGGTTTGCTAGAGTTGCTCTAA 60.307 47.826 7.22 0.00 41.74 2.10
749 765 4.324267 GGGTTTGCTAGAGTTGCTCTAAA 58.676 43.478 7.22 0.00 41.74 1.85
750 766 4.393371 GGGTTTGCTAGAGTTGCTCTAAAG 59.607 45.833 7.22 0.62 41.74 1.85
751 767 4.393371 GGTTTGCTAGAGTTGCTCTAAAGG 59.607 45.833 7.22 0.00 41.74 3.11
752 768 3.895232 TGCTAGAGTTGCTCTAAAGGG 57.105 47.619 7.22 0.00 41.74 3.95
753 769 2.501723 TGCTAGAGTTGCTCTAAAGGGG 59.498 50.000 7.22 0.00 41.74 4.79
754 770 2.743510 GCTAGAGTTGCTCTAAAGGGGC 60.744 54.545 7.22 3.76 41.74 5.80
755 771 0.250513 AGAGTTGCTCTAAAGGGGCG 59.749 55.000 0.00 0.00 39.28 6.13
756 772 0.744771 GAGTTGCTCTAAAGGGGCGG 60.745 60.000 0.00 0.00 0.00 6.13
757 773 1.749258 GTTGCTCTAAAGGGGCGGG 60.749 63.158 0.00 0.00 0.00 6.13
758 774 1.921346 TTGCTCTAAAGGGGCGGGA 60.921 57.895 0.00 0.00 0.00 5.14
759 775 2.189784 GCTCTAAAGGGGCGGGAC 59.810 66.667 0.00 0.00 0.00 4.46
760 776 2.908796 CTCTAAAGGGGCGGGACC 59.091 66.667 0.00 0.00 37.93 4.46
761 777 3.078836 TCTAAAGGGGCGGGACCG 61.079 66.667 6.35 6.35 40.62 4.79
778 794 4.722700 GCGGGAGGCAGCCAAAGA 62.723 66.667 15.80 0.00 42.87 2.52
779 795 2.273449 CGGGAGGCAGCCAAAGAT 59.727 61.111 15.80 0.00 0.00 2.40
780 796 1.379044 CGGGAGGCAGCCAAAGATT 60.379 57.895 15.80 0.00 0.00 2.40
781 797 1.660560 CGGGAGGCAGCCAAAGATTG 61.661 60.000 15.80 0.00 0.00 2.67
795 811 4.379394 CCAAAGATTGGTGTTCGGTACATG 60.379 45.833 0.87 0.00 45.93 3.21
800 816 5.354234 AGATTGGTGTTCGGTACATGAAATC 59.646 40.000 0.00 9.74 39.39 2.17
813 829 7.119262 CGGTACATGAAATCTATGTATTTCCCC 59.881 40.741 0.00 0.00 42.63 4.81
830 846 1.153745 CCTATGGCGGATCTAGCGC 60.154 63.158 0.00 0.00 35.00 5.92
838 854 1.396644 CGGATCTAGCGCGTAAGAAC 58.603 55.000 14.92 12.45 43.02 3.01
875 891 1.078426 AGCGGCTGTGATTACACCC 60.078 57.895 0.00 0.00 45.40 4.61
891 907 2.037136 CCCAGGCAAAGCGAGACAG 61.037 63.158 0.00 0.00 0.00 3.51
922 941 1.000283 CACAGCGCCTTATCCTCTAGG 60.000 57.143 2.29 0.00 34.54 3.02
931 950 4.244326 TCCTCTAGGAGAGCACGC 57.756 61.111 0.00 0.00 40.98 5.34
932 951 1.454111 TCCTCTAGGAGAGCACGCC 60.454 63.158 0.00 0.00 40.98 5.68
934 953 1.040339 CCTCTAGGAGAGCACGCCTT 61.040 60.000 12.23 0.00 43.53 4.35
935 954 0.102120 CTCTAGGAGAGCACGCCTTG 59.898 60.000 12.23 10.30 43.53 3.61
936 955 0.323451 TCTAGGAGAGCACGCCTTGA 60.323 55.000 12.23 12.58 43.53 3.02
937 956 0.179124 CTAGGAGAGCACGCCTTGAC 60.179 60.000 12.23 0.00 43.53 3.18
938 957 1.934220 TAGGAGAGCACGCCTTGACG 61.934 60.000 12.23 0.00 43.53 4.35
939 958 3.482783 GAGAGCACGCCTTGACGC 61.483 66.667 0.00 0.00 36.19 5.19
940 959 3.923563 GAGAGCACGCCTTGACGCT 62.924 63.158 0.00 0.00 37.44 5.07
941 960 3.482783 GAGCACGCCTTGACGCTC 61.483 66.667 0.00 0.00 43.60 5.03
1176 1219 0.031716 TGGTGGAGATGGAGGAGGAG 60.032 60.000 0.00 0.00 0.00 3.69
1317 1360 2.502080 CTCAGCGACGACGTGGTC 60.502 66.667 19.53 19.53 41.98 4.02
1400 1443 4.544689 CGAGGACGAGCTGCTCCG 62.545 72.222 22.97 19.13 42.66 4.63
1431 1474 4.309950 ACCGCCAACGACTGACCC 62.310 66.667 0.00 0.00 43.93 4.46
1434 1477 3.948719 GCCAACGACTGACCCCCA 61.949 66.667 0.00 0.00 0.00 4.96
1473 1553 2.741985 CGGCGTTCATGTGCTCCA 60.742 61.111 0.00 0.00 0.00 3.86
1492 1572 5.449177 GCTCCAAGGCTTTGTACAATGTATC 60.449 44.000 19.31 11.34 32.21 2.24
1497 1577 5.804639 AGGCTTTGTACAATGTATCTCACA 58.195 37.500 19.31 0.00 42.69 3.58
1514 1594 4.397103 TCTCACAAGCCATTGCAATAAGAG 59.603 41.667 12.53 11.01 40.27 2.85
1515 1595 4.334552 TCACAAGCCATTGCAATAAGAGA 58.665 39.130 12.53 1.65 40.27 3.10
1517 1597 5.041287 CACAAGCCATTGCAATAAGAGATG 58.959 41.667 12.53 9.19 40.27 2.90
1617 1697 0.661020 CATTGGTTCGGCGATAACCC 59.339 55.000 23.81 15.82 44.86 4.11
1631 1711 2.459060 TAACCCGAACATCAGCGAAA 57.541 45.000 0.00 0.00 0.00 3.46
1632 1712 1.821216 AACCCGAACATCAGCGAAAT 58.179 45.000 0.00 0.00 0.00 2.17
1633 1713 1.369625 ACCCGAACATCAGCGAAATC 58.630 50.000 0.00 0.00 0.00 2.17
1634 1714 0.301687 CCCGAACATCAGCGAAATCG 59.698 55.000 0.00 0.00 43.27 3.34
1635 1715 1.277326 CCGAACATCAGCGAAATCGA 58.723 50.000 7.06 0.00 43.02 3.59
1636 1716 1.658596 CCGAACATCAGCGAAATCGAA 59.341 47.619 7.06 0.00 43.02 3.71
1637 1717 2.093625 CCGAACATCAGCGAAATCGAAA 59.906 45.455 7.06 0.00 43.02 3.46
1638 1718 3.337130 CGAACATCAGCGAAATCGAAAG 58.663 45.455 7.06 0.00 43.02 2.62
1653 1733 2.095853 TCGAAAGATTTCATGCGAAGGC 59.904 45.455 6.16 0.00 37.01 4.35
1654 1734 2.444351 GAAAGATTTCATGCGAAGGCG 58.556 47.619 0.44 0.00 38.38 5.52
1655 1735 1.737838 AAGATTTCATGCGAAGGCGA 58.262 45.000 0.00 0.00 44.10 5.54
1656 1736 1.737838 AGATTTCATGCGAAGGCGAA 58.262 45.000 0.00 0.00 44.10 4.70
1661 1741 1.145759 TCATGCGAAGGCGAATCGAC 61.146 55.000 6.91 2.37 42.76 4.20
1668 1748 2.285256 CGAAGGCGAATCGACAGATTTG 60.285 50.000 12.38 0.00 46.30 2.32
1765 1960 0.459899 ACACACAGCACGAGTTCAGA 59.540 50.000 0.00 0.00 0.00 3.27
1766 1961 1.069204 ACACACAGCACGAGTTCAGAT 59.931 47.619 0.00 0.00 0.00 2.90
1768 1963 2.156504 CACACAGCACGAGTTCAGATTC 59.843 50.000 0.00 0.00 0.00 2.52
1810 2007 0.855598 ATTACAGGCATGGGGAGCAT 59.144 50.000 2.31 0.00 0.00 3.79
1811 2008 1.517238 TTACAGGCATGGGGAGCATA 58.483 50.000 2.31 0.00 0.00 3.14
1812 2009 1.746157 TACAGGCATGGGGAGCATAT 58.254 50.000 2.31 0.00 0.00 1.78
1813 2010 1.746157 ACAGGCATGGGGAGCATATA 58.254 50.000 2.31 0.00 0.00 0.86
1854 2051 8.352942 GCAAGGTCATTATTTATTTGGGAGTAG 58.647 37.037 0.00 0.00 0.00 2.57
1855 2052 9.627123 CAAGGTCATTATTTATTTGGGAGTAGA 57.373 33.333 0.00 0.00 0.00 2.59
1884 2081 5.423015 GCACTGGATGTTTTCTCTCAGATA 58.577 41.667 0.00 0.00 0.00 1.98
1918 2116 2.203788 TTCAGCCTCGAGGTGGGT 60.204 61.111 31.43 10.84 44.42 4.51
1919 2117 0.970937 CTTCAGCCTCGAGGTGGGTA 60.971 60.000 31.43 14.26 44.42 3.69
1967 2169 6.073819 GCAAAATTTGTTGGATCAGTGTAACC 60.074 38.462 7.60 0.00 37.80 2.85
1977 2179 4.381718 GGATCAGTGTAACCCAGTACTCAC 60.382 50.000 0.00 0.00 37.80 3.51
2022 2230 2.910199 CTTCAGCATAACAGCCTAGCA 58.090 47.619 0.00 0.00 34.23 3.49
2083 2291 0.455815 GGTGCAATTTAAGCTCGGGG 59.544 55.000 0.00 0.00 0.00 5.73
2099 2307 2.750712 TCGGGGAATTCATTTCGGAAAC 59.249 45.455 7.93 0.00 34.98 2.78
2187 2395 2.408704 CGCAGAAGTAGAAGGTGTTTCG 59.591 50.000 0.00 0.00 40.86 3.46
2193 2401 1.719780 GTAGAAGGTGTTTCGTGCTCG 59.280 52.381 0.81 0.81 40.86 5.03
2195 2403 2.480426 GAAGGTGTTTCGTGCTCGCG 62.480 60.000 0.00 0.00 36.96 5.87
2274 2482 3.067833 GAGGTAGAACCAAGCTGTCAAC 58.932 50.000 0.00 0.00 41.95 3.18
2294 2502 1.098050 GATGGTTGAGGTGTGGATGC 58.902 55.000 0.00 0.00 0.00 3.91
2311 2519 1.236616 TGCTGTTGGAATGGACTGCG 61.237 55.000 0.00 0.00 41.74 5.18
2323 2531 2.422597 TGGACTGCGGTACAAAGATTG 58.577 47.619 8.57 0.00 32.59 2.67
2337 2546 9.072294 GGTACAAAGATTGTATGCAATAAACAC 57.928 33.333 9.16 3.61 46.73 3.32
2353 2562 7.059945 GCAATAAACACGAAAAGACAGATGAAG 59.940 37.037 0.00 0.00 0.00 3.02
2407 2617 9.519191 TTGTTTCAGATATCAGAATTCCAAAGA 57.481 29.630 10.94 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 4.094830 TCATCATCATCCATCTTGGTGG 57.905 45.455 0.00 0.00 39.03 4.61
173 177 2.805099 GGCCATCGTCATCTTCATCTTC 59.195 50.000 0.00 0.00 0.00 2.87
230 234 3.909995 TCCTTCTTGATCTTGTCCTTGGA 59.090 43.478 0.00 0.00 0.00 3.53
277 281 4.764172 ACTTGACCATGTGATCTAGCTTC 58.236 43.478 0.00 0.00 0.00 3.86
307 311 6.312141 TCCAATGTCTTGATCACCAATAGA 57.688 37.500 0.00 0.00 34.04 1.98
339 343 1.002544 CCTTCTTCTCGGCCAACTCTT 59.997 52.381 2.24 0.00 0.00 2.85
340 344 0.610687 CCTTCTTCTCGGCCAACTCT 59.389 55.000 2.24 0.00 0.00 3.24
341 345 1.021920 GCCTTCTTCTCGGCCAACTC 61.022 60.000 2.24 0.00 40.43 3.01
395 410 2.342650 AATGACGGCCTTGCGCATT 61.343 52.632 12.75 0.00 40.31 3.56
482 498 8.316214 TCCATCTCATTTCGATTCATCATCATA 58.684 33.333 0.00 0.00 0.00 2.15
546 562 7.072263 TCAAACTCCTCTTCTTCAAGATCTT 57.928 36.000 0.88 0.88 38.02 2.40
559 575 0.836400 TTCGCCCCTCAAACTCCTCT 60.836 55.000 0.00 0.00 0.00 3.69
566 582 2.281900 CCGGTTTCGCCCCTCAAA 60.282 61.111 0.00 0.00 34.56 2.69
567 583 2.741486 CTTCCGGTTTCGCCCCTCAA 62.741 60.000 0.00 0.00 34.56 3.02
568 584 3.243053 TTCCGGTTTCGCCCCTCA 61.243 61.111 0.00 0.00 34.56 3.86
569 585 2.436115 CTTCCGGTTTCGCCCCTC 60.436 66.667 0.00 0.00 34.56 4.30
570 586 4.717313 GCTTCCGGTTTCGCCCCT 62.717 66.667 0.00 0.00 34.56 4.79
576 592 4.445545 CTGCGCGCTTCCGGTTTC 62.446 66.667 33.29 0.00 34.32 2.78
577 593 4.980805 TCTGCGCGCTTCCGGTTT 62.981 61.111 33.29 0.00 34.32 3.27
578 594 4.980805 TTCTGCGCGCTTCCGGTT 62.981 61.111 33.29 0.00 34.32 4.44
581 597 3.235292 TTTGTTCTGCGCGCTTCCG 62.235 57.895 33.29 17.36 37.57 4.30
582 598 1.441016 CTTTGTTCTGCGCGCTTCC 60.441 57.895 33.29 17.24 0.00 3.46
583 599 2.077198 GCTTTGTTCTGCGCGCTTC 61.077 57.895 33.29 18.78 0.00 3.86
584 600 2.050985 GCTTTGTTCTGCGCGCTT 60.051 55.556 33.29 0.00 0.00 4.68
585 601 4.030452 GGCTTTGTTCTGCGCGCT 62.030 61.111 33.29 0.00 0.00 5.92
589 605 2.676016 TTTGCGGGCTTTGTTCTGCG 62.676 55.000 0.00 0.00 38.05 5.18
590 606 1.067250 TTTGCGGGCTTTGTTCTGC 59.933 52.632 0.00 0.00 35.93 4.26
591 607 0.597377 GGTTTGCGGGCTTTGTTCTG 60.597 55.000 0.00 0.00 0.00 3.02
592 608 1.739667 GGTTTGCGGGCTTTGTTCT 59.260 52.632 0.00 0.00 0.00 3.01
593 609 1.300620 GGGTTTGCGGGCTTTGTTC 60.301 57.895 0.00 0.00 0.00 3.18
594 610 2.818841 GGGTTTGCGGGCTTTGTT 59.181 55.556 0.00 0.00 0.00 2.83
595 611 3.601685 CGGGTTTGCGGGCTTTGT 61.602 61.111 0.00 0.00 0.00 2.83
596 612 4.356442 CCGGGTTTGCGGGCTTTG 62.356 66.667 0.00 0.00 0.00 2.77
601 617 2.634193 AATATCCCCGGGTTTGCGGG 62.634 60.000 21.85 0.00 44.62 6.13
602 618 1.152839 AATATCCCCGGGTTTGCGG 60.153 57.895 21.85 2.11 0.00 5.69
603 619 0.179029 AGAATATCCCCGGGTTTGCG 60.179 55.000 21.85 2.99 0.00 4.85
604 620 1.143073 AGAGAATATCCCCGGGTTTGC 59.857 52.381 21.85 3.32 0.00 3.68
605 621 3.577805 AAGAGAATATCCCCGGGTTTG 57.422 47.619 21.85 3.89 0.00 2.93
606 622 4.603094 AAAAGAGAATATCCCCGGGTTT 57.397 40.909 21.85 8.88 0.00 3.27
607 623 5.512576 CGATAAAAGAGAATATCCCCGGGTT 60.513 44.000 21.85 6.79 0.00 4.11
608 624 4.020485 CGATAAAAGAGAATATCCCCGGGT 60.020 45.833 21.85 3.79 0.00 5.28
609 625 4.504858 CGATAAAAGAGAATATCCCCGGG 58.495 47.826 15.80 15.80 0.00 5.73
610 626 3.933332 GCGATAAAAGAGAATATCCCCGG 59.067 47.826 0.00 0.00 0.00 5.73
611 627 4.822026 AGCGATAAAAGAGAATATCCCCG 58.178 43.478 0.00 0.00 0.00 5.73
612 628 4.865365 CGAGCGATAAAAGAGAATATCCCC 59.135 45.833 0.00 0.00 0.00 4.81
613 629 4.865365 CCGAGCGATAAAAGAGAATATCCC 59.135 45.833 0.00 0.00 0.00 3.85
614 630 5.471257 ACCGAGCGATAAAAGAGAATATCC 58.529 41.667 0.00 0.00 0.00 2.59
615 631 7.409465 AAACCGAGCGATAAAAGAGAATATC 57.591 36.000 0.00 0.00 0.00 1.63
616 632 7.630924 CAAAACCGAGCGATAAAAGAGAATAT 58.369 34.615 0.00 0.00 0.00 1.28
617 633 6.456449 GCAAAACCGAGCGATAAAAGAGAATA 60.456 38.462 0.00 0.00 0.00 1.75
618 634 5.673818 GCAAAACCGAGCGATAAAAGAGAAT 60.674 40.000 0.00 0.00 0.00 2.40
619 635 4.378046 GCAAAACCGAGCGATAAAAGAGAA 60.378 41.667 0.00 0.00 0.00 2.87
620 636 3.124636 GCAAAACCGAGCGATAAAAGAGA 59.875 43.478 0.00 0.00 0.00 3.10
621 637 3.417185 GCAAAACCGAGCGATAAAAGAG 58.583 45.455 0.00 0.00 0.00 2.85
622 638 3.465122 GCAAAACCGAGCGATAAAAGA 57.535 42.857 0.00 0.00 0.00 2.52
631 647 4.103103 GAGCCCGCAAAACCGAGC 62.103 66.667 0.00 0.00 31.71 5.03
632 648 2.358737 AGAGCCCGCAAAACCGAG 60.359 61.111 0.00 0.00 0.00 4.63
633 649 2.668212 CAGAGCCCGCAAAACCGA 60.668 61.111 0.00 0.00 0.00 4.69
634 650 2.458006 GAACAGAGCCCGCAAAACCG 62.458 60.000 0.00 0.00 0.00 4.44
635 651 1.285950 GAACAGAGCCCGCAAAACC 59.714 57.895 0.00 0.00 0.00 3.27
636 652 1.082104 CGAACAGAGCCCGCAAAAC 60.082 57.895 0.00 0.00 0.00 2.43
637 653 2.258013 CCGAACAGAGCCCGCAAAA 61.258 57.895 0.00 0.00 0.00 2.44
638 654 2.668212 CCGAACAGAGCCCGCAAA 60.668 61.111 0.00 0.00 0.00 3.68
663 679 1.792632 GCGTTTTAAGGGCCGAAATCG 60.793 52.381 22.44 22.44 39.44 3.34
664 680 1.792632 CGCGTTTTAAGGGCCGAAATC 60.793 52.381 0.00 6.31 0.00 2.17
665 681 0.169451 CGCGTTTTAAGGGCCGAAAT 59.831 50.000 0.00 0.00 0.00 2.17
666 682 1.165284 ACGCGTTTTAAGGGCCGAAA 61.165 50.000 5.58 0.00 0.00 3.46
667 683 1.165284 AACGCGTTTTAAGGGCCGAA 61.165 50.000 20.79 0.00 0.00 4.30
668 684 1.165284 AAACGCGTTTTAAGGGCCGA 61.165 50.000 30.36 0.00 0.00 5.54
669 685 0.318022 AAAACGCGTTTTAAGGGCCG 60.318 50.000 40.00 0.00 40.61 6.13
670 686 1.855513 AAAAACGCGTTTTAAGGGCC 58.144 45.000 40.51 0.00 41.45 5.80
687 703 6.133356 CCTATAACCAGATAAGGGCCAAAAA 58.867 40.000 6.18 0.00 0.00 1.94
688 704 5.399727 CCCTATAACCAGATAAGGGCCAAAA 60.400 44.000 6.18 0.00 0.00 2.44
689 705 4.105697 CCCTATAACCAGATAAGGGCCAAA 59.894 45.833 6.18 0.00 0.00 3.28
690 706 3.655777 CCCTATAACCAGATAAGGGCCAA 59.344 47.826 6.18 0.00 0.00 4.52
691 707 3.256704 CCCTATAACCAGATAAGGGCCA 58.743 50.000 6.18 0.00 0.00 5.36
692 708 2.576648 CCCCTATAACCAGATAAGGGCC 59.423 54.545 0.00 0.00 33.97 5.80
693 709 3.257578 ACCCCTATAACCAGATAAGGGC 58.742 50.000 0.00 0.00 36.75 5.19
694 710 3.514309 CGACCCCTATAACCAGATAAGGG 59.486 52.174 0.00 0.00 38.55 3.95
695 711 3.056035 GCGACCCCTATAACCAGATAAGG 60.056 52.174 0.00 0.00 0.00 2.69
696 712 3.367087 CGCGACCCCTATAACCAGATAAG 60.367 52.174 0.00 0.00 0.00 1.73
697 713 2.559668 CGCGACCCCTATAACCAGATAA 59.440 50.000 0.00 0.00 0.00 1.75
698 714 2.165167 CGCGACCCCTATAACCAGATA 58.835 52.381 0.00 0.00 0.00 1.98
699 715 0.966920 CGCGACCCCTATAACCAGAT 59.033 55.000 0.00 0.00 0.00 2.90
700 716 1.111116 CCGCGACCCCTATAACCAGA 61.111 60.000 8.23 0.00 0.00 3.86
701 717 1.366366 CCGCGACCCCTATAACCAG 59.634 63.158 8.23 0.00 0.00 4.00
702 718 2.135581 CCCGCGACCCCTATAACCA 61.136 63.158 8.23 0.00 0.00 3.67
703 719 1.689243 AACCCGCGACCCCTATAACC 61.689 60.000 8.23 0.00 0.00 2.85
704 720 0.249615 GAACCCGCGACCCCTATAAC 60.250 60.000 8.23 0.00 0.00 1.89
705 721 0.687098 TGAACCCGCGACCCCTATAA 60.687 55.000 8.23 0.00 0.00 0.98
706 722 0.687098 TTGAACCCGCGACCCCTATA 60.687 55.000 8.23 0.00 0.00 1.31
707 723 1.968050 CTTGAACCCGCGACCCCTAT 61.968 60.000 8.23 0.00 0.00 2.57
708 724 2.604079 TTGAACCCGCGACCCCTA 60.604 61.111 8.23 0.00 0.00 3.53
709 725 4.016706 CTTGAACCCGCGACCCCT 62.017 66.667 8.23 0.00 0.00 4.79
713 729 3.837570 AACCCCTTGAACCCGCGAC 62.838 63.158 8.23 0.00 0.00 5.19
714 730 3.122727 AAACCCCTTGAACCCGCGA 62.123 57.895 8.23 0.00 0.00 5.87
715 731 2.596338 AAACCCCTTGAACCCGCG 60.596 61.111 0.00 0.00 0.00 6.46
716 732 3.047735 CAAACCCCTTGAACCCGC 58.952 61.111 0.00 0.00 37.17 6.13
717 733 0.250989 TAGCAAACCCCTTGAACCCG 60.251 55.000 0.00 0.00 37.17 5.28
718 734 1.074889 TCTAGCAAACCCCTTGAACCC 59.925 52.381 0.00 0.00 37.17 4.11
719 735 2.224793 ACTCTAGCAAACCCCTTGAACC 60.225 50.000 0.00 0.00 37.17 3.62
720 736 3.141767 ACTCTAGCAAACCCCTTGAAC 57.858 47.619 0.00 0.00 37.17 3.18
721 737 3.486383 CAACTCTAGCAAACCCCTTGAA 58.514 45.455 0.00 0.00 37.17 2.69
722 738 2.814097 GCAACTCTAGCAAACCCCTTGA 60.814 50.000 0.00 0.00 37.17 3.02
723 739 1.541588 GCAACTCTAGCAAACCCCTTG 59.458 52.381 0.00 0.00 38.15 3.61
724 740 1.425448 AGCAACTCTAGCAAACCCCTT 59.575 47.619 0.00 0.00 0.00 3.95
725 741 1.003696 GAGCAACTCTAGCAAACCCCT 59.996 52.381 0.00 0.00 0.00 4.79
726 742 1.003696 AGAGCAACTCTAGCAAACCCC 59.996 52.381 0.00 0.00 39.28 4.95
727 743 2.481289 AGAGCAACTCTAGCAAACCC 57.519 50.000 0.00 0.00 39.28 4.11
728 744 4.393371 CCTTTAGAGCAACTCTAGCAAACC 59.607 45.833 4.64 0.00 42.92 3.27
729 745 4.393371 CCCTTTAGAGCAACTCTAGCAAAC 59.607 45.833 4.64 0.00 42.92 2.93
730 746 4.565652 CCCCTTTAGAGCAACTCTAGCAAA 60.566 45.833 4.64 0.00 42.92 3.68
731 747 3.055094 CCCCTTTAGAGCAACTCTAGCAA 60.055 47.826 4.64 0.00 42.92 3.91
732 748 2.501723 CCCCTTTAGAGCAACTCTAGCA 59.498 50.000 4.64 0.00 42.92 3.49
733 749 2.743510 GCCCCTTTAGAGCAACTCTAGC 60.744 54.545 4.64 1.72 42.92 3.42
734 750 2.482142 CGCCCCTTTAGAGCAACTCTAG 60.482 54.545 4.64 0.00 42.92 2.43
735 751 1.480954 CGCCCCTTTAGAGCAACTCTA 59.519 52.381 0.16 0.16 41.50 2.43
736 752 0.250513 CGCCCCTTTAGAGCAACTCT 59.749 55.000 2.23 2.23 43.83 3.24
737 753 0.744771 CCGCCCCTTTAGAGCAACTC 60.745 60.000 0.00 0.00 0.00 3.01
738 754 1.299976 CCGCCCCTTTAGAGCAACT 59.700 57.895 0.00 0.00 0.00 3.16
739 755 1.749258 CCCGCCCCTTTAGAGCAAC 60.749 63.158 0.00 0.00 0.00 4.17
740 756 1.921346 TCCCGCCCCTTTAGAGCAA 60.921 57.895 0.00 0.00 0.00 3.91
741 757 2.285069 TCCCGCCCCTTTAGAGCA 60.285 61.111 0.00 0.00 0.00 4.26
742 758 2.189784 GTCCCGCCCCTTTAGAGC 59.810 66.667 0.00 0.00 0.00 4.09
743 759 2.908796 GGTCCCGCCCCTTTAGAG 59.091 66.667 0.00 0.00 0.00 2.43
744 760 3.078836 CGGTCCCGCCCCTTTAGA 61.079 66.667 0.00 0.00 0.00 2.10
761 777 4.722700 TCTTTGGCTGCCTCCCGC 62.723 66.667 21.03 0.00 38.31 6.13
762 778 1.379044 AATCTTTGGCTGCCTCCCG 60.379 57.895 21.03 5.91 0.00 5.14
763 779 1.325476 CCAATCTTTGGCTGCCTCCC 61.325 60.000 21.03 0.00 45.17 4.30
764 780 2.196319 CCAATCTTTGGCTGCCTCC 58.804 57.895 21.03 0.00 45.17 4.30
773 789 4.454161 TCATGTACCGAACACCAATCTTTG 59.546 41.667 0.00 0.00 42.09 2.77
774 790 4.647611 TCATGTACCGAACACCAATCTTT 58.352 39.130 0.00 0.00 42.09 2.52
775 791 4.280436 TCATGTACCGAACACCAATCTT 57.720 40.909 0.00 0.00 42.09 2.40
776 792 3.973206 TCATGTACCGAACACCAATCT 57.027 42.857 0.00 0.00 42.09 2.40
777 793 5.354234 AGATTTCATGTACCGAACACCAATC 59.646 40.000 0.00 0.00 42.09 2.67
778 794 5.253330 AGATTTCATGTACCGAACACCAAT 58.747 37.500 0.00 0.00 42.09 3.16
779 795 4.647611 AGATTTCATGTACCGAACACCAA 58.352 39.130 0.00 0.00 42.09 3.67
780 796 4.280436 AGATTTCATGTACCGAACACCA 57.720 40.909 0.00 0.00 42.09 4.17
781 797 5.815740 ACATAGATTTCATGTACCGAACACC 59.184 40.000 0.00 0.00 42.09 4.16
782 798 6.903883 ACATAGATTTCATGTACCGAACAC 57.096 37.500 0.00 0.00 42.09 3.32
783 799 9.607988 AAATACATAGATTTCATGTACCGAACA 57.392 29.630 0.00 0.00 40.64 3.18
795 811 6.316390 CGCCATAGGGGAAATACATAGATTTC 59.684 42.308 0.00 1.11 42.63 2.17
813 829 4.485554 GCGCTAGATCCGCCATAG 57.514 61.111 0.00 0.00 45.30 2.23
838 854 2.740981 GCTCATTATCTTCCTGCATCCG 59.259 50.000 0.00 0.00 0.00 4.18
843 859 0.871057 GCCGCTCATTATCTTCCTGC 59.129 55.000 0.00 0.00 0.00 4.85
875 891 1.962822 TGCTGTCTCGCTTTGCCTG 60.963 57.895 0.00 0.00 0.00 4.85
891 907 4.678269 CGCTGTGCTGTGCTGTGC 62.678 66.667 0.00 0.00 0.00 4.57
922 941 3.482783 GCGTCAAGGCGTGCTCTC 61.483 66.667 0.00 0.00 0.00 3.20
923 942 3.996124 AGCGTCAAGGCGTGCTCT 61.996 61.111 0.00 0.00 38.18 4.09
924 943 3.482783 GAGCGTCAAGGCGTGCTC 61.483 66.667 0.00 1.36 45.95 4.26
932 951 4.680237 TGGTGCCGGAGCGTCAAG 62.680 66.667 5.05 0.00 44.31 3.02
933 952 4.980805 GTGGTGCCGGAGCGTCAA 62.981 66.667 5.05 0.00 44.31 3.18
939 958 4.394712 GGTCAGGTGGTGCCGGAG 62.395 72.222 5.05 0.00 42.04 4.63
1029 1048 2.448736 GGGGAGGAGATGGGGGTC 60.449 72.222 0.00 0.00 0.00 4.46
1176 1219 1.522580 GCGCTCCAGGATGTTCTCC 60.523 63.158 0.00 0.00 45.33 3.71
1455 1509 3.499737 GGAGCACATGAACGCCGG 61.500 66.667 0.00 0.00 0.00 6.13
1473 1553 6.237901 TGTGAGATACATTGTACAAAGCCTT 58.762 36.000 13.23 0.00 33.42 4.35
1492 1572 4.397103 TCTCTTATTGCAATGGCTTGTGAG 59.603 41.667 22.27 15.67 41.91 3.51
1497 1577 3.958798 AGCATCTCTTATTGCAATGGCTT 59.041 39.130 22.27 0.00 41.35 4.35
1527 1607 5.936956 ACTGAAGCAGCTGATTATATTAGGC 59.063 40.000 18.72 2.89 34.37 3.93
1528 1608 7.443575 ACAACTGAAGCAGCTGATTATATTAGG 59.556 37.037 18.72 6.93 34.37 2.69
1530 1610 8.615211 CAACAACTGAAGCAGCTGATTATATTA 58.385 33.333 18.72 1.33 34.37 0.98
1531 1611 7.478322 CAACAACTGAAGCAGCTGATTATATT 58.522 34.615 18.72 8.97 34.37 1.28
1533 1613 5.163723 GCAACAACTGAAGCAGCTGATTATA 60.164 40.000 18.72 9.02 34.37 0.98
1542 1622 1.311859 TCAGGCAACAACTGAAGCAG 58.688 50.000 0.00 0.00 41.66 4.24
1569 1649 3.829948 CATGACAAGCAGGAATGTTCAC 58.170 45.455 0.00 0.00 0.00 3.18
1617 1697 3.060761 TCTTTCGATTTCGCTGATGTTCG 59.939 43.478 0.00 0.00 39.60 3.95
1631 1711 3.242870 GCCTTCGCATGAAATCTTTCGAT 60.243 43.478 0.00 0.00 36.00 3.59
1632 1712 2.095853 GCCTTCGCATGAAATCTTTCGA 59.904 45.455 0.00 0.00 36.00 3.71
1633 1713 2.444351 GCCTTCGCATGAAATCTTTCG 58.556 47.619 0.00 0.00 36.00 3.46
1634 1714 2.095853 TCGCCTTCGCATGAAATCTTTC 59.904 45.455 0.00 0.00 35.24 2.62
1635 1715 2.083774 TCGCCTTCGCATGAAATCTTT 58.916 42.857 0.00 0.00 32.66 2.52
1636 1716 1.737838 TCGCCTTCGCATGAAATCTT 58.262 45.000 0.00 0.00 32.66 2.40
1637 1717 1.737838 TTCGCCTTCGCATGAAATCT 58.262 45.000 0.00 0.00 32.66 2.40
1638 1718 2.644078 GATTCGCCTTCGCATGAAATC 58.356 47.619 0.00 0.00 32.66 2.17
1639 1719 1.003545 CGATTCGCCTTCGCATGAAAT 60.004 47.619 0.00 0.00 32.66 2.17
1640 1720 0.373370 CGATTCGCCTTCGCATGAAA 59.627 50.000 0.00 0.00 32.66 2.69
1641 1721 0.459411 TCGATTCGCCTTCGCATGAA 60.459 50.000 0.00 0.00 36.56 2.57
1642 1722 1.140804 TCGATTCGCCTTCGCATGA 59.859 52.632 0.00 0.00 36.56 3.07
1643 1723 1.273887 GTCGATTCGCCTTCGCATG 59.726 57.895 0.00 0.00 36.56 4.06
1644 1724 1.148157 CTGTCGATTCGCCTTCGCAT 61.148 55.000 0.00 0.00 36.56 4.73
1645 1725 1.805539 CTGTCGATTCGCCTTCGCA 60.806 57.895 0.00 0.00 36.56 5.10
1646 1726 0.872021 ATCTGTCGATTCGCCTTCGC 60.872 55.000 0.00 0.00 36.56 4.70
1647 1727 1.560923 AATCTGTCGATTCGCCTTCG 58.439 50.000 0.00 0.00 34.88 3.79
1648 1728 2.930040 TCAAATCTGTCGATTCGCCTTC 59.070 45.455 0.00 0.00 38.89 3.46
1649 1729 2.972625 TCAAATCTGTCGATTCGCCTT 58.027 42.857 0.00 0.00 38.89 4.35
1650 1730 2.672961 TCAAATCTGTCGATTCGCCT 57.327 45.000 0.00 0.00 38.89 5.52
1651 1731 2.609459 ACATCAAATCTGTCGATTCGCC 59.391 45.455 0.00 0.00 38.89 5.54
1652 1732 3.306973 TCACATCAAATCTGTCGATTCGC 59.693 43.478 0.00 0.00 38.89 4.70
1653 1733 5.454736 TTCACATCAAATCTGTCGATTCG 57.545 39.130 0.00 0.00 38.89 3.34
1654 1734 5.728898 GCCTTCACATCAAATCTGTCGATTC 60.729 44.000 0.00 0.00 38.89 2.52
1655 1735 4.095483 GCCTTCACATCAAATCTGTCGATT 59.905 41.667 0.00 0.00 41.53 3.34
1656 1736 3.624861 GCCTTCACATCAAATCTGTCGAT 59.375 43.478 0.00 0.00 0.00 3.59
1661 1741 4.595116 GATTCGCCTTCACATCAAATCTG 58.405 43.478 0.00 0.00 0.00 2.90
1668 1748 2.930040 TCTTTCGATTCGCCTTCACATC 59.070 45.455 0.00 0.00 0.00 3.06
1743 1938 2.198406 TGAACTCGTGCTGTGTGTTAC 58.802 47.619 0.00 0.00 0.00 2.50
1757 1952 5.384063 TGTCTGAGACTGAATCTGAACTC 57.616 43.478 14.42 3.75 38.00 3.01
1765 1960 5.071384 TGGATATGCATGTCTGAGACTGAAT 59.929 40.000 21.04 11.44 33.15 2.57
1766 1961 4.406649 TGGATATGCATGTCTGAGACTGAA 59.593 41.667 21.04 4.79 33.15 3.02
1768 1963 4.038883 TCTGGATATGCATGTCTGAGACTG 59.961 45.833 21.04 10.36 33.15 3.51
1854 2051 1.180029 AAACATCCAGTGCCATGCTC 58.820 50.000 0.00 0.00 0.00 4.26
1855 2052 1.547372 GAAAACATCCAGTGCCATGCT 59.453 47.619 0.00 0.00 0.00 3.79
1884 2081 3.215151 CTGAAGATGATGGAAGCTGCAT 58.785 45.455 1.02 0.00 0.00 3.96
1918 2116 3.244735 TGCTTGGTTGCAGGTAGTGATTA 60.245 43.478 0.00 0.00 38.12 1.75
1919 2117 2.162681 GCTTGGTTGCAGGTAGTGATT 58.837 47.619 0.00 0.00 0.00 2.57
1967 2169 3.930336 TCTTTCTGCATGTGAGTACTGG 58.070 45.455 0.00 0.00 0.00 4.00
1977 2179 5.457799 CACTGTCAGTTTTTCTTTCTGCATG 59.542 40.000 1.67 0.00 0.00 4.06
2012 2220 2.040278 AGGGAGCTGCTAGGCTGT 59.960 61.111 0.15 0.00 43.20 4.40
2083 2291 4.729746 GCCTACCGTTTCCGAAATGAATTC 60.730 45.833 13.68 0.00 35.63 2.17
2149 2357 1.287425 GCGACACCCATGTAAGTAGC 58.713 55.000 0.00 0.00 39.95 3.58
2193 2401 2.468532 CGACAAGTAACGTGCCGC 59.531 61.111 0.00 0.00 0.00 6.53
2195 2403 1.666872 AGGCGACAAGTAACGTGCC 60.667 57.895 0.00 1.25 42.76 5.01
2199 2407 2.388232 GCCCAGGCGACAAGTAACG 61.388 63.158 0.00 0.00 0.00 3.18
2274 2482 1.372582 CATCCACACCTCAACCATCG 58.627 55.000 0.00 0.00 0.00 3.84
2294 2502 0.606401 ACCGCAGTCCATTCCAACAG 60.606 55.000 0.00 0.00 0.00 3.16
2323 2531 7.295201 TCTGTCTTTTCGTGTTTATTGCATAC 58.705 34.615 0.00 0.00 0.00 2.39
2337 2546 4.391216 ACTGCATCTTCATCTGTCTTTTCG 59.609 41.667 0.00 0.00 0.00 3.46
2353 2562 4.082625 TGTGAATGACAAATGGACTGCATC 60.083 41.667 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.