Multiple sequence alignment - TraesCS5D01G260100

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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 TraesCS5D01G260100 chr5D 100.000 3212 0 0 1 3212 366673161 366676372 0.000000e+00 5932
1 TraesCS5D01G260100 chr5D 97.753 89 2 0 2374 2462 381563830 381563918 1.540000e-33 154
2 TraesCS5D01G260100 chr5A 96.027 1485 45 5 842 2317 468859619 468861098 0.000000e+00 2403
3 TraesCS5D01G260100 chr5A 91.348 497 22 12 2723 3212 468861411 468861893 0.000000e+00 660
4 TraesCS5D01G260100 chr5A 84.640 625 89 7 1 621 675653525 675654146 1.640000e-172 616
5 TraesCS5D01G260100 chr5A 97.333 225 5 1 2460 2683 468861193 468861417 6.500000e-102 381
6 TraesCS5D01G260100 chr5A 96.512 86 3 0 2376 2461 362170894 362170809 3.340000e-30 143
7 TraesCS5D01G260100 chr5A 87.500 112 11 3 2354 2464 504574384 504574275 3.360000e-25 126
8 TraesCS5D01G260100 chr5A 81.879 149 17 7 3027 3172 13387288 13387429 2.020000e-22 117
9 TraesCS5D01G260100 chr5B 95.487 1418 45 7 919 2317 433869318 433870735 0.000000e+00 2246
10 TraesCS5D01G260100 chr5B 92.459 305 19 4 2894 3197 433883225 433883526 1.770000e-117 433
11 TraesCS5D01G260100 chr5B 95.045 222 10 1 2463 2683 433870834 433871055 6.590000e-92 348
12 TraesCS5D01G260100 chr5B 94.074 135 8 0 2723 2857 433871049 433871183 4.200000e-49 206
13 TraesCS5D01G260100 chr5B 96.970 66 2 0 2313 2378 433870770 433870835 9.420000e-21 111
14 TraesCS5D01G260100 chr1A 87.898 628 66 9 1 621 545477627 545478251 0.000000e+00 730
15 TraesCS5D01G260100 chr7D 86.386 617 80 4 1 615 494973886 494974500 0.000000e+00 671
16 TraesCS5D01G260100 chr7D 83.108 148 16 6 3028 3172 605162810 605162951 3.360000e-25 126
17 TraesCS5D01G260100 chr7B 86.408 618 77 7 3 615 522819689 522820304 0.000000e+00 669
18 TraesCS5D01G260100 chr7B 83.784 629 88 13 1 621 295076310 295075688 4.620000e-163 584
19 TraesCS5D01G260100 chr7B 82.993 147 25 0 3026 3172 10943724 10943870 2.010000e-27 134
20 TraesCS5D01G260100 chrUn 84.824 626 81 12 1 620 56349858 56349241 4.550000e-173 617
21 TraesCS5D01G260100 chrUn 84.824 626 81 12 1 620 282825808 282825191 4.550000e-173 617
22 TraesCS5D01G260100 chrUn 83.673 147 24 0 3026 3172 84535227 84535373 4.320000e-29 139
23 TraesCS5D01G260100 chr7A 84.084 622 87 10 1 616 356363511 356362896 9.920000e-165 590
24 TraesCS5D01G260100 chr7A 83.108 148 25 0 3025 3172 70769661 70769514 5.590000e-28 135
25 TraesCS5D01G260100 chr7A 81.325 166 19 9 3030 3193 137830760 137830605 1.210000e-24 124
26 TraesCS5D01G260100 chr2D 83.784 629 93 6 1 621 322977771 322978398 3.570000e-164 588
27 TraesCS5D01G260100 chr3B 94.681 94 4 1 2369 2461 476038631 476038724 9.290000e-31 145
28 TraesCS5D01G260100 chr6D 95.556 90 3 1 2376 2464 381355497 381355408 3.340000e-30 143
29 TraesCS5D01G260100 chr4A 94.565 92 5 0 2376 2467 744188295 744188204 3.340000e-30 143
30 TraesCS5D01G260100 chr4A 79.781 183 28 6 3026 3206 132062703 132062878 1.210000e-24 124
31 TraesCS5D01G260100 chr6A 93.617 94 4 2 2372 2464 548412699 548412791 4.320000e-29 139
32 TraesCS5D01G260100 chr1D 91.000 100 7 2 2373 2471 471923464 471923562 2.010000e-27 134
33 TraesCS5D01G260100 chr1D 91.489 94 6 2 2372 2464 492948134 492948042 9.350000e-26 128


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 TraesCS5D01G260100 chr5D 366673161 366676372 3211 False 5932.00 5932 100.000000 1 3212 1 chr5D.!!$F1 3211
1 TraesCS5D01G260100 chr5A 468859619 468861893 2274 False 1148.00 2403 94.902667 842 3212 3 chr5A.!!$F3 2370
2 TraesCS5D01G260100 chr5A 675653525 675654146 621 False 616.00 616 84.640000 1 621 1 chr5A.!!$F2 620
3 TraesCS5D01G260100 chr5B 433869318 433871183 1865 False 727.75 2246 95.394000 919 2857 4 chr5B.!!$F2 1938
4 TraesCS5D01G260100 chr1A 545477627 545478251 624 False 730.00 730 87.898000 1 621 1 chr1A.!!$F1 620
5 TraesCS5D01G260100 chr7D 494973886 494974500 614 False 671.00 671 86.386000 1 615 1 chr7D.!!$F1 614
6 TraesCS5D01G260100 chr7B 522819689 522820304 615 False 669.00 669 86.408000 3 615 1 chr7B.!!$F2 612
7 TraesCS5D01G260100 chr7B 295075688 295076310 622 True 584.00 584 83.784000 1 621 1 chr7B.!!$R1 620
8 TraesCS5D01G260100 chrUn 56349241 56349858 617 True 617.00 617 84.824000 1 620 1 chrUn.!!$R1 619
9 TraesCS5D01G260100 chrUn 282825191 282825808 617 True 617.00 617 84.824000 1 620 1 chrUn.!!$R2 619
10 TraesCS5D01G260100 chr7A 356362896 356363511 615 True 590.00 590 84.084000 1 616 1 chr7A.!!$R3 615
11 TraesCS5D01G260100 chr2D 322977771 322978398 627 False 588.00 588 83.784000 1 621 1 chr2D.!!$F1 620

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
624 648 0.034896 GGAGTGGAGACGGCAGAAAA 59.965 55.0 0.0 0.0 0.0 2.29 F
737 761 0.107165 GTCCGCAAAGGGCTAATCCT 60.107 55.0 0.0 0.0 42.7 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2130 1.604278 GTCTCCAGGTTGAGCACAAAC 59.396 52.381 3.44 3.44 43.31 2.93 R
2442 2563 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44 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
138 143 4.707105 TGCACAATCGATTAGGATCATGT 58.293 39.130 10.97 0.00 32.33 3.21
148 153 7.782049 TCGATTAGGATCATGTGTTACTCTTT 58.218 34.615 0.00 0.00 32.33 2.52
156 161 7.119699 GGATCATGTGTTACTCTTTCATGTCAA 59.880 37.037 0.00 0.00 37.64 3.18
221 236 7.741027 ATAATTAGCACTCATCACCAATCAG 57.259 36.000 0.00 0.00 0.00 2.90
231 246 5.375773 TCATCACCAATCAGACAAGTGAAA 58.624 37.500 0.00 0.00 40.56 2.69
232 247 6.005823 TCATCACCAATCAGACAAGTGAAAT 58.994 36.000 0.00 0.00 40.56 2.17
239 254 9.334947 ACCAATCAGACAAGTGAAATATCATAG 57.665 33.333 0.00 0.00 38.01 2.23
286 301 6.183360 CCAAGCAAGCATATCATCAAAGTACA 60.183 38.462 0.00 0.00 0.00 2.90
293 308 8.824159 AGCATATCATCAAAGTACAGTATGAC 57.176 34.615 0.00 0.00 39.69 3.06
305 320 6.106673 AGTACAGTATGACCAAGCACATAAC 58.893 40.000 0.00 0.00 39.69 1.89
312 327 7.775093 AGTATGACCAAGCACATAACAACATAT 59.225 33.333 0.00 0.00 32.07 1.78
322 337 9.394767 AGCACATAACAACATATTCTCATACAA 57.605 29.630 0.00 0.00 0.00 2.41
330 345 8.959548 ACAACATATTCTCATACAAGCATCAAA 58.040 29.630 0.00 0.00 0.00 2.69
384 401 6.683715 TCAAAGAAACCAAACGAGAAAAAGT 58.316 32.000 0.00 0.00 0.00 2.66
459 480 6.672118 GCAACAAGTACCAAAAAGTTCAAAGC 60.672 38.462 0.00 0.00 0.00 3.51
494 515 2.092103 ACGTCTCTCTAGGCCTGATCTT 60.092 50.000 17.99 0.00 0.00 2.40
496 517 3.561143 GTCTCTCTAGGCCTGATCTTCA 58.439 50.000 17.99 0.00 0.00 3.02
504 525 1.519246 CCTGATCTTCAGCGGCTCA 59.481 57.895 0.00 0.00 42.98 4.26
511 532 1.078918 TTCAGCGGCTCATGGTGAG 60.079 57.895 0.00 2.65 46.90 3.51
552 576 1.424403 CCAGTGTGCATAAACGTCGA 58.576 50.000 0.00 0.00 0.00 4.20
577 601 2.201732 GAGATAAGTGCATCCGCGAAA 58.798 47.619 8.23 0.00 42.97 3.46
578 602 2.802816 GAGATAAGTGCATCCGCGAAAT 59.197 45.455 8.23 0.00 42.97 2.17
601 625 3.793465 GCTTTGACAAAGTCTTCTGTGCC 60.793 47.826 24.98 4.82 40.64 5.01
621 645 1.679305 GAGGAGTGGAGACGGCAGA 60.679 63.158 0.00 0.00 0.00 4.26
622 646 1.228894 AGGAGTGGAGACGGCAGAA 60.229 57.895 0.00 0.00 0.00 3.02
623 647 0.832135 AGGAGTGGAGACGGCAGAAA 60.832 55.000 0.00 0.00 0.00 2.52
624 648 0.034896 GGAGTGGAGACGGCAGAAAA 59.965 55.000 0.00 0.00 0.00 2.29
625 649 1.339151 GGAGTGGAGACGGCAGAAAAT 60.339 52.381 0.00 0.00 0.00 1.82
626 650 2.427506 GAGTGGAGACGGCAGAAAATT 58.572 47.619 0.00 0.00 0.00 1.82
627 651 2.416893 GAGTGGAGACGGCAGAAAATTC 59.583 50.000 0.00 0.00 0.00 2.17
628 652 1.128692 GTGGAGACGGCAGAAAATTCG 59.871 52.381 0.00 0.00 0.00 3.34
629 653 1.001520 TGGAGACGGCAGAAAATTCGA 59.998 47.619 0.00 0.00 0.00 3.71
630 654 2.073816 GGAGACGGCAGAAAATTCGAA 58.926 47.619 0.00 0.00 0.00 3.71
631 655 2.094417 GGAGACGGCAGAAAATTCGAAG 59.906 50.000 3.35 0.00 0.00 3.79
632 656 2.993899 GAGACGGCAGAAAATTCGAAGA 59.006 45.455 3.35 0.00 0.00 2.87
633 657 3.399330 AGACGGCAGAAAATTCGAAGAA 58.601 40.909 3.35 0.00 45.90 2.52
634 658 3.433615 AGACGGCAGAAAATTCGAAGAAG 59.566 43.478 3.35 0.00 45.90 2.85
635 659 2.484264 ACGGCAGAAAATTCGAAGAAGG 59.516 45.455 3.35 0.00 45.90 3.46
636 660 2.729156 CGGCAGAAAATTCGAAGAAGGC 60.729 50.000 3.35 2.53 45.90 4.35
637 661 2.509870 GCAGAAAATTCGAAGAAGGCG 58.490 47.619 3.35 0.00 45.90 5.52
638 662 2.159627 GCAGAAAATTCGAAGAAGGCGA 59.840 45.455 3.35 0.00 45.90 5.54
639 663 3.737305 CAGAAAATTCGAAGAAGGCGAC 58.263 45.455 3.35 0.00 45.90 5.19
640 664 2.412089 AGAAAATTCGAAGAAGGCGACG 59.588 45.455 3.35 0.00 45.90 5.12
641 665 1.792006 AAATTCGAAGAAGGCGACGT 58.208 45.000 3.35 0.00 45.90 4.34
642 666 1.347320 AATTCGAAGAAGGCGACGTC 58.653 50.000 5.18 5.18 45.90 4.34
650 674 2.342910 GAAGGCGACGTCTAAACAGA 57.657 50.000 14.70 0.00 35.80 3.41
651 675 2.877335 GAAGGCGACGTCTAAACAGAT 58.123 47.619 14.70 0.00 35.80 2.90
652 676 2.279582 AGGCGACGTCTAAACAGATG 57.720 50.000 14.70 0.00 0.00 2.90
653 677 1.816835 AGGCGACGTCTAAACAGATGA 59.183 47.619 14.70 0.00 0.00 2.92
654 678 2.159366 AGGCGACGTCTAAACAGATGAG 60.159 50.000 14.70 0.00 0.00 2.90
655 679 2.159421 GGCGACGTCTAAACAGATGAGA 60.159 50.000 14.70 0.00 0.00 3.27
656 680 3.102276 GCGACGTCTAAACAGATGAGAG 58.898 50.000 14.70 0.00 0.00 3.20
657 681 3.181509 GCGACGTCTAAACAGATGAGAGA 60.182 47.826 14.70 0.00 0.00 3.10
658 682 4.672024 GCGACGTCTAAACAGATGAGAGAA 60.672 45.833 14.70 0.00 0.00 2.87
659 683 5.391449 CGACGTCTAAACAGATGAGAGAAA 58.609 41.667 14.70 0.00 0.00 2.52
660 684 5.856986 CGACGTCTAAACAGATGAGAGAAAA 59.143 40.000 14.70 0.00 0.00 2.29
661 685 6.032985 CGACGTCTAAACAGATGAGAGAAAAG 59.967 42.308 14.70 0.00 0.00 2.27
662 686 6.982852 ACGTCTAAACAGATGAGAGAAAAGA 58.017 36.000 1.01 0.00 0.00 2.52
663 687 6.864165 ACGTCTAAACAGATGAGAGAAAAGAC 59.136 38.462 1.01 0.00 0.00 3.01
664 688 6.863645 CGTCTAAACAGATGAGAGAAAAGACA 59.136 38.462 0.00 0.00 32.03 3.41
665 689 7.061673 CGTCTAAACAGATGAGAGAAAAGACAG 59.938 40.741 0.00 0.00 32.03 3.51
666 690 7.330700 GTCTAAACAGATGAGAGAAAAGACAGG 59.669 40.741 0.00 0.00 32.03 4.00
667 691 4.550076 ACAGATGAGAGAAAAGACAGGG 57.450 45.455 0.00 0.00 0.00 4.45
668 692 3.906846 ACAGATGAGAGAAAAGACAGGGT 59.093 43.478 0.00 0.00 0.00 4.34
669 693 4.020662 ACAGATGAGAGAAAAGACAGGGTC 60.021 45.833 0.00 0.00 0.00 4.46
670 694 4.222588 CAGATGAGAGAAAAGACAGGGTCT 59.777 45.833 0.00 0.00 45.64 3.85
671 695 4.466015 AGATGAGAGAAAAGACAGGGTCTC 59.534 45.833 0.00 0.00 42.59 3.36
672 696 3.576861 TGAGAGAAAAGACAGGGTCTCA 58.423 45.455 0.00 0.00 42.59 3.27
673 697 4.163427 TGAGAGAAAAGACAGGGTCTCAT 58.837 43.478 0.00 0.00 42.59 2.90
674 698 4.020751 TGAGAGAAAAGACAGGGTCTCATG 60.021 45.833 0.00 0.00 42.59 3.07
675 699 3.906846 AGAGAAAAGACAGGGTCTCATGT 59.093 43.478 0.00 0.00 42.59 3.21
676 700 4.349342 AGAGAAAAGACAGGGTCTCATGTT 59.651 41.667 0.00 0.00 42.59 2.71
677 701 5.053978 AGAAAAGACAGGGTCTCATGTTT 57.946 39.130 0.00 0.00 42.59 2.83
678 702 5.449553 AGAAAAGACAGGGTCTCATGTTTT 58.550 37.500 0.00 0.00 42.59 2.43
679 703 5.893824 AGAAAAGACAGGGTCTCATGTTTTT 59.106 36.000 0.00 0.00 42.59 1.94
702 726 6.849588 TTTTTCTCACCTTCTACCGTAAAC 57.150 37.500 0.00 0.00 0.00 2.01
703 727 5.796424 TTTCTCACCTTCTACCGTAAACT 57.204 39.130 0.00 0.00 0.00 2.66
704 728 6.899393 TTTCTCACCTTCTACCGTAAACTA 57.101 37.500 0.00 0.00 0.00 2.24
705 729 6.899393 TTCTCACCTTCTACCGTAAACTAA 57.101 37.500 0.00 0.00 0.00 2.24
706 730 6.259550 TCTCACCTTCTACCGTAAACTAAC 57.740 41.667 0.00 0.00 0.00 2.34
707 731 5.769662 TCTCACCTTCTACCGTAAACTAACA 59.230 40.000 0.00 0.00 0.00 2.41
708 732 6.017400 TCACCTTCTACCGTAAACTAACAG 57.983 41.667 0.00 0.00 0.00 3.16
709 733 5.536161 TCACCTTCTACCGTAAACTAACAGT 59.464 40.000 0.00 0.00 0.00 3.55
710 734 6.714810 TCACCTTCTACCGTAAACTAACAGTA 59.285 38.462 0.00 0.00 0.00 2.74
711 735 7.025963 CACCTTCTACCGTAAACTAACAGTAG 58.974 42.308 0.00 0.00 33.48 2.57
712 736 6.942576 ACCTTCTACCGTAAACTAACAGTAGA 59.057 38.462 0.00 0.00 37.51 2.59
713 737 7.448469 ACCTTCTACCGTAAACTAACAGTAGAA 59.552 37.037 10.68 10.68 42.71 2.10
714 738 8.299570 CCTTCTACCGTAAACTAACAGTAGAAA 58.700 37.037 11.75 1.15 43.56 2.52
715 739 9.683069 CTTCTACCGTAAACTAACAGTAGAAAA 57.317 33.333 11.75 0.00 43.56 2.29
716 740 9.463443 TTCTACCGTAAACTAACAGTAGAAAAC 57.537 33.333 9.32 0.00 42.32 2.43
717 741 8.629158 TCTACCGTAAACTAACAGTAGAAAACA 58.371 33.333 0.00 0.00 36.76 2.83
718 742 7.704789 ACCGTAAACTAACAGTAGAAAACAG 57.295 36.000 0.00 0.00 0.00 3.16
719 743 7.267857 ACCGTAAACTAACAGTAGAAAACAGT 58.732 34.615 0.00 0.00 0.00 3.55
720 744 7.436376 ACCGTAAACTAACAGTAGAAAACAGTC 59.564 37.037 0.00 0.00 0.00 3.51
721 745 7.095899 CCGTAAACTAACAGTAGAAAACAGTCC 60.096 40.741 0.00 0.00 0.00 3.85
722 746 6.839820 AAACTAACAGTAGAAAACAGTCCG 57.160 37.500 0.00 0.00 0.00 4.79
723 747 4.304939 ACTAACAGTAGAAAACAGTCCGC 58.695 43.478 0.00 0.00 0.00 5.54
724 748 2.902705 ACAGTAGAAAACAGTCCGCA 57.097 45.000 0.00 0.00 0.00 5.69
725 749 3.188159 ACAGTAGAAAACAGTCCGCAA 57.812 42.857 0.00 0.00 0.00 4.85
726 750 3.537580 ACAGTAGAAAACAGTCCGCAAA 58.462 40.909 0.00 0.00 0.00 3.68
727 751 3.560068 ACAGTAGAAAACAGTCCGCAAAG 59.440 43.478 0.00 0.00 0.00 2.77
728 752 3.058914 CAGTAGAAAACAGTCCGCAAAGG 60.059 47.826 0.00 0.00 42.97 3.11
729 753 1.318576 AGAAAACAGTCCGCAAAGGG 58.681 50.000 0.00 0.00 41.52 3.95
736 760 2.405143 GTCCGCAAAGGGCTAATCC 58.595 57.895 0.00 0.00 42.70 3.01
737 761 0.107165 GTCCGCAAAGGGCTAATCCT 60.107 55.000 0.00 0.00 42.70 3.24
797 821 4.359475 GCGCAAAGCCAAATGGTT 57.641 50.000 0.30 0.00 40.81 3.67
798 822 1.861440 GCGCAAAGCCAAATGGTTG 59.139 52.632 0.30 0.20 40.81 3.77
799 823 0.599728 GCGCAAAGCCAAATGGTTGA 60.600 50.000 0.30 0.00 40.81 3.18
800 824 1.863267 CGCAAAGCCAAATGGTTGAA 58.137 45.000 6.91 0.00 36.83 2.69
801 825 1.526464 CGCAAAGCCAAATGGTTGAAC 59.474 47.619 6.91 0.00 36.83 3.18
802 826 2.559440 GCAAAGCCAAATGGTTGAACA 58.441 42.857 6.91 0.00 36.83 3.18
803 827 2.287644 GCAAAGCCAAATGGTTGAACAC 59.712 45.455 6.91 0.00 36.83 3.32
804 828 3.529533 CAAAGCCAAATGGTTGAACACA 58.470 40.909 0.00 0.00 36.83 3.72
805 829 3.902881 AAGCCAAATGGTTGAACACAA 57.097 38.095 0.00 0.00 36.83 3.33
806 830 3.177997 AGCCAAATGGTTGAACACAAC 57.822 42.857 0.00 0.00 41.91 3.32
814 838 1.318576 GTTGAACACAACCCCTCAGG 58.681 55.000 0.00 0.00 38.23 3.86
815 839 1.133915 GTTGAACACAACCCCTCAGGA 60.134 52.381 0.00 0.00 38.23 3.86
816 840 1.217916 TGAACACAACCCCTCAGGAA 58.782 50.000 0.00 0.00 39.89 3.36
817 841 1.566703 TGAACACAACCCCTCAGGAAA 59.433 47.619 0.00 0.00 39.89 3.13
818 842 2.024846 TGAACACAACCCCTCAGGAAAA 60.025 45.455 0.00 0.00 39.89 2.29
819 843 2.838637 ACACAACCCCTCAGGAAAAA 57.161 45.000 0.00 0.00 39.89 1.94
870 897 2.044946 AGGATGGACCCAAAGCGC 60.045 61.111 0.00 0.00 40.05 5.92
872 899 2.435938 GATGGACCCAAAGCGCGA 60.436 61.111 12.10 0.00 0.00 5.87
877 904 1.373748 GACCCAAAGCGCGAGTGTA 60.374 57.895 12.10 0.00 0.00 2.90
891 918 2.350522 GAGTGTATGTGTTGAGGCCTG 58.649 52.381 12.00 0.00 0.00 4.85
892 919 1.003580 AGTGTATGTGTTGAGGCCTGG 59.996 52.381 12.00 0.00 0.00 4.45
893 920 1.064003 TGTATGTGTTGAGGCCTGGT 58.936 50.000 12.00 0.00 0.00 4.00
894 921 1.003118 TGTATGTGTTGAGGCCTGGTC 59.997 52.381 12.00 0.00 0.00 4.02
895 922 0.618458 TATGTGTTGAGGCCTGGTCC 59.382 55.000 12.00 0.00 0.00 4.46
903 930 3.948719 GGCCTGGTCCGGTTCACA 61.949 66.667 0.00 0.00 0.00 3.58
912 939 2.551912 CCGGTTCACACCTGGCAAC 61.552 63.158 0.00 0.00 41.64 4.17
924 951 2.037847 GGCAACTTGGGGCTCCAT 59.962 61.111 5.88 0.00 43.63 3.41
936 963 1.307097 GGCTCCATTGCATCTGACTC 58.693 55.000 0.00 0.00 34.04 3.36
937 964 0.935898 GCTCCATTGCATCTGACTCG 59.064 55.000 0.00 0.00 0.00 4.18
1554 1587 4.516195 GGCTCCTCGTTCCGCCTC 62.516 72.222 0.00 0.00 39.42 4.70
1976 2015 4.748892 CTTCACAAGACGGTACATCTGAT 58.251 43.478 0.00 0.00 23.53 2.90
2013 2052 3.242220 CGACAATCTTTGATCCTTCTGCG 60.242 47.826 0.00 0.00 0.00 5.18
2015 2054 3.273434 CAATCTTTGATCCTTCTGCGGA 58.727 45.455 0.00 0.00 37.50 5.54
2064 2103 0.846693 ACCAGAGTGGCTCCTTGTTT 59.153 50.000 0.00 0.00 42.67 2.83
2079 2118 1.140804 GTTTTTGCGTGCTGTGGGT 59.859 52.632 0.00 0.00 0.00 4.51
2291 2337 4.693283 AGTGTTCAGTTCTGTTTCGATGA 58.307 39.130 0.00 0.00 0.00 2.92
2362 2483 9.528018 GCTTATTGTATTTGGCTTTGCTTATTA 57.472 29.630 0.00 0.00 0.00 0.98
2385 2506 9.890915 ATTATAGTCTTCATTTCTACTCCCTCT 57.109 33.333 0.00 0.00 0.00 3.69
2386 2507 5.930837 AGTCTTCATTTCTACTCCCTCTG 57.069 43.478 0.00 0.00 0.00 3.35
2387 2508 5.337788 AGTCTTCATTTCTACTCCCTCTGT 58.662 41.667 0.00 0.00 0.00 3.41
2388 2509 5.420739 AGTCTTCATTTCTACTCCCTCTGTC 59.579 44.000 0.00 0.00 0.00 3.51
2389 2510 4.712337 TCTTCATTTCTACTCCCTCTGTCC 59.288 45.833 0.00 0.00 0.00 4.02
2390 2511 3.375699 TCATTTCTACTCCCTCTGTCCC 58.624 50.000 0.00 0.00 0.00 4.46
2391 2512 3.107601 CATTTCTACTCCCTCTGTCCCA 58.892 50.000 0.00 0.00 0.00 4.37
2392 2513 2.534042 TTCTACTCCCTCTGTCCCAG 57.466 55.000 0.00 0.00 0.00 4.45
2393 2514 1.682478 TCTACTCCCTCTGTCCCAGA 58.318 55.000 0.00 0.00 38.25 3.86
2394 2515 2.000803 TCTACTCCCTCTGTCCCAGAA 58.999 52.381 0.00 0.00 40.18 3.02
2395 2516 2.587777 TCTACTCCCTCTGTCCCAGAAT 59.412 50.000 0.00 0.00 40.18 2.40
2396 2517 3.792114 TCTACTCCCTCTGTCCCAGAATA 59.208 47.826 0.00 0.00 40.18 1.75
2397 2518 3.715648 ACTCCCTCTGTCCCAGAATAT 57.284 47.619 0.00 0.00 40.18 1.28
2398 2519 4.834406 ACTCCCTCTGTCCCAGAATATA 57.166 45.455 0.00 0.00 40.18 0.86
2399 2520 5.157770 ACTCCCTCTGTCCCAGAATATAA 57.842 43.478 0.00 0.00 40.18 0.98
2400 2521 5.151454 ACTCCCTCTGTCCCAGAATATAAG 58.849 45.833 0.00 0.00 40.18 1.73
2401 2522 5.103043 ACTCCCTCTGTCCCAGAATATAAGA 60.103 44.000 0.00 0.00 40.18 2.10
2402 2523 5.788430 TCCCTCTGTCCCAGAATATAAGAA 58.212 41.667 0.00 0.00 40.18 2.52
2403 2524 5.602978 TCCCTCTGTCCCAGAATATAAGAAC 59.397 44.000 0.00 0.00 40.18 3.01
2404 2525 5.509840 CCCTCTGTCCCAGAATATAAGAACG 60.510 48.000 0.00 0.00 40.18 3.95
2405 2526 5.069251 CCTCTGTCCCAGAATATAAGAACGT 59.931 44.000 0.00 0.00 40.18 3.99
2406 2527 6.407074 CCTCTGTCCCAGAATATAAGAACGTT 60.407 42.308 0.00 0.00 40.18 3.99
2407 2528 6.942976 TCTGTCCCAGAATATAAGAACGTTT 58.057 36.000 0.46 0.00 37.57 3.60
2408 2529 7.391620 TCTGTCCCAGAATATAAGAACGTTTT 58.608 34.615 0.46 0.00 37.57 2.43
2409 2530 7.881232 TCTGTCCCAGAATATAAGAACGTTTTT 59.119 33.333 9.22 9.22 37.57 1.94
2452 2573 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
2453 2574 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
2454 2575 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
2455 2576 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
2456 2577 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
2457 2578 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
2458 2579 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
2568 2689 6.928492 TGAAAGAAACAGGATTAAATTGTGCC 59.072 34.615 0.00 0.00 0.00 5.01
2637 2758 7.339466 TCTTGGAAGGCAAGATTTTAGTTATCC 59.661 37.037 0.00 0.00 34.16 2.59
2678 2799 9.895138 AATAGGAGAAATTTTATTGCTTTGCAT 57.105 25.926 0.00 0.00 38.76 3.96
2679 2800 9.895138 ATAGGAGAAATTTTATTGCTTTGCATT 57.105 25.926 0.00 0.00 38.76 3.56
2680 2801 8.625786 AGGAGAAATTTTATTGCTTTGCATTT 57.374 26.923 0.00 0.00 38.76 2.32
2681 2802 8.508875 AGGAGAAATTTTATTGCTTTGCATTTG 58.491 29.630 0.00 0.00 38.76 2.32
2682 2803 8.505625 GGAGAAATTTTATTGCTTTGCATTTGA 58.494 29.630 0.00 0.00 38.76 2.69
2683 2804 9.321590 GAGAAATTTTATTGCTTTGCATTTGAC 57.678 29.630 0.00 0.00 38.76 3.18
2684 2805 8.291740 AGAAATTTTATTGCTTTGCATTTGACC 58.708 29.630 0.00 0.00 38.76 4.02
2685 2806 7.507733 AATTTTATTGCTTTGCATTTGACCA 57.492 28.000 0.00 0.00 38.76 4.02
2686 2807 5.921004 TTTATTGCTTTGCATTTGACCAC 57.079 34.783 0.00 0.00 38.76 4.16
2687 2808 2.975732 TTGCTTTGCATTTGACCACA 57.024 40.000 0.00 0.00 38.76 4.17
2688 2809 3.472283 TTGCTTTGCATTTGACCACAT 57.528 38.095 0.00 0.00 38.76 3.21
2689 2810 4.597404 TTGCTTTGCATTTGACCACATA 57.403 36.364 0.00 0.00 38.76 2.29
2690 2811 4.804868 TGCTTTGCATTTGACCACATAT 57.195 36.364 0.00 0.00 31.71 1.78
2691 2812 5.149973 TGCTTTGCATTTGACCACATATT 57.850 34.783 0.00 0.00 31.71 1.28
2692 2813 5.170021 TGCTTTGCATTTGACCACATATTC 58.830 37.500 0.00 0.00 31.71 1.75
2693 2814 5.170021 GCTTTGCATTTGACCACATATTCA 58.830 37.500 0.00 0.00 0.00 2.57
2694 2815 5.638657 GCTTTGCATTTGACCACATATTCAA 59.361 36.000 0.00 0.00 0.00 2.69
2695 2816 6.314400 GCTTTGCATTTGACCACATATTCAAT 59.686 34.615 0.00 0.00 31.87 2.57
2696 2817 7.492020 GCTTTGCATTTGACCACATATTCAATA 59.508 33.333 0.00 0.00 31.87 1.90
2697 2818 8.700722 TTTGCATTTGACCACATATTCAATAC 57.299 30.769 0.00 0.00 31.87 1.89
2698 2819 6.493978 TGCATTTGACCACATATTCAATACG 58.506 36.000 0.00 0.00 31.87 3.06
2699 2820 6.317391 TGCATTTGACCACATATTCAATACGA 59.683 34.615 0.00 0.00 31.87 3.43
2700 2821 7.148171 TGCATTTGACCACATATTCAATACGAA 60.148 33.333 0.00 0.00 38.22 3.85
2701 2822 7.165812 GCATTTGACCACATATTCAATACGAAC 59.834 37.037 0.00 0.00 36.12 3.95
2702 2823 7.915293 TTTGACCACATATTCAATACGAACT 57.085 32.000 0.00 0.00 36.12 3.01
2703 2824 6.902224 TGACCACATATTCAATACGAACTG 57.098 37.500 0.00 0.00 36.12 3.16
2704 2825 5.815222 TGACCACATATTCAATACGAACTGG 59.185 40.000 0.00 0.00 36.12 4.00
2705 2826 4.574828 ACCACATATTCAATACGAACTGGC 59.425 41.667 0.00 0.00 36.12 4.85
2706 2827 4.816385 CCACATATTCAATACGAACTGGCT 59.184 41.667 0.00 0.00 36.12 4.75
2707 2828 5.989168 CCACATATTCAATACGAACTGGCTA 59.011 40.000 0.00 0.00 36.12 3.93
2708 2829 6.073765 CCACATATTCAATACGAACTGGCTAC 60.074 42.308 0.00 0.00 36.12 3.58
2709 2830 5.989777 ACATATTCAATACGAACTGGCTACC 59.010 40.000 0.00 0.00 36.12 3.18
2710 2831 4.755266 ATTCAATACGAACTGGCTACCT 57.245 40.909 0.00 0.00 36.12 3.08
2711 2832 3.520290 TCAATACGAACTGGCTACCTG 57.480 47.619 0.00 0.00 0.00 4.00
2712 2833 3.093814 TCAATACGAACTGGCTACCTGA 58.906 45.455 0.00 0.00 0.00 3.86
2713 2834 3.704566 TCAATACGAACTGGCTACCTGAT 59.295 43.478 0.00 0.00 0.00 2.90
2714 2835 4.161565 TCAATACGAACTGGCTACCTGATT 59.838 41.667 0.00 0.00 0.00 2.57
2715 2836 4.755266 ATACGAACTGGCTACCTGATTT 57.245 40.909 0.00 0.00 0.00 2.17
2716 2837 3.418684 ACGAACTGGCTACCTGATTTT 57.581 42.857 0.00 0.00 0.00 1.82
2717 2838 3.751518 ACGAACTGGCTACCTGATTTTT 58.248 40.909 0.00 0.00 0.00 1.94
2718 2839 4.901868 ACGAACTGGCTACCTGATTTTTA 58.098 39.130 0.00 0.00 0.00 1.52
2719 2840 5.310451 ACGAACTGGCTACCTGATTTTTAA 58.690 37.500 0.00 0.00 0.00 1.52
2720 2841 5.766174 ACGAACTGGCTACCTGATTTTTAAA 59.234 36.000 0.00 0.00 0.00 1.52
2721 2842 6.263617 ACGAACTGGCTACCTGATTTTTAAAA 59.736 34.615 0.00 0.00 0.00 1.52
2722 2843 7.142680 CGAACTGGCTACCTGATTTTTAAAAA 58.857 34.615 15.38 15.38 0.00 1.94
2742 2863 7.410120 AAAAATTCTGAGGTGACAACTCTTT 57.590 32.000 20.91 10.32 35.98 2.52
2757 2878 6.164176 ACAACTCTTTTGATCGGGTAGTAAG 58.836 40.000 0.00 0.00 0.00 2.34
2818 2941 9.405587 GATTATGATTACTAGAGCTGACAGTTC 57.594 37.037 11.09 11.09 0.00 3.01
2825 2948 5.204292 ACTAGAGCTGACAGTTCCATCATA 58.796 41.667 14.95 1.19 0.00 2.15
2868 2991 6.701400 CACAATATACGTTCCATCATGTCTGA 59.299 38.462 0.00 0.00 35.41 3.27
2871 2994 3.961480 ACGTTCCATCATGTCTGAGAA 57.039 42.857 0.00 0.00 34.12 2.87
2873 2996 5.598416 ACGTTCCATCATGTCTGAGAATA 57.402 39.130 0.00 0.00 34.12 1.75
2874 2997 6.166984 ACGTTCCATCATGTCTGAGAATAT 57.833 37.500 0.00 0.00 34.12 1.28
2875 2998 7.290110 ACGTTCCATCATGTCTGAGAATATA 57.710 36.000 0.00 0.00 34.12 0.86
2877 3000 7.816513 ACGTTCCATCATGTCTGAGAATATATG 59.183 37.037 0.00 0.00 34.12 1.78
2878 3001 8.031277 CGTTCCATCATGTCTGAGAATATATGA 58.969 37.037 0.00 0.00 34.12 2.15
2879 3002 9.149225 GTTCCATCATGTCTGAGAATATATGAC 57.851 37.037 0.00 0.00 34.12 3.06
2880 3003 8.426569 TCCATCATGTCTGAGAATATATGACA 57.573 34.615 5.56 5.56 41.07 3.58
2881 3004 8.309656 TCCATCATGTCTGAGAATATATGACAC 58.690 37.037 5.28 0.00 39.90 3.67
2883 3006 9.485206 CATCATGTCTGAGAATATATGACACAA 57.515 33.333 5.28 0.00 39.90 3.33
2986 3114 4.417506 CACATGTGTGCTTCCATATTGTG 58.582 43.478 18.03 0.00 39.39 3.33
3040 3168 7.615403 ACGTCATGCAGTAGATATTTCCATAT 58.385 34.615 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 0.975887 AATGCGCAAATTTGGAGGGT 59.024 45.000 17.11 0.00 0.00 4.34
72 73 6.900568 TTTAATAATGCGCAAATTTGGAGG 57.099 33.333 17.11 0.00 0.00 4.30
156 161 0.249489 GCGCTCCACCGAGATGTATT 60.249 55.000 0.00 0.00 38.52 1.89
165 172 1.135315 CATTTTGAGCGCTCCACCG 59.865 57.895 33.23 14.87 0.00 4.94
221 236 9.102757 TGCTCTTTCTATGATATTTCACTTGTC 57.897 33.333 0.00 0.00 33.85 3.18
286 301 5.312895 TGTTGTTATGTGCTTGGTCATACT 58.687 37.500 0.00 0.00 0.00 2.12
293 308 7.087409 TGAGAATATGTTGTTATGTGCTTGG 57.913 36.000 0.00 0.00 0.00 3.61
305 320 9.229784 GTTTGATGCTTGTATGAGAATATGTTG 57.770 33.333 0.00 0.00 0.00 3.33
312 327 7.715657 ACTTTTGTTTGATGCTTGTATGAGAA 58.284 30.769 0.00 0.00 0.00 2.87
322 337 7.547227 ACTTTGAGTTACTTTTGTTTGATGCT 58.453 30.769 0.00 0.00 0.00 3.79
330 345 7.859325 TCTTGCTACTTTGAGTTACTTTTGT 57.141 32.000 0.00 0.00 0.00 2.83
459 480 6.854496 AGAGAGACGTTTAGCTCTATACTG 57.146 41.667 4.62 0.00 41.33 2.74
494 515 2.580815 CTCACCATGAGCCGCTGA 59.419 61.111 0.00 0.00 37.72 4.26
496 517 2.249413 CTTCCTCACCATGAGCCGCT 62.249 60.000 0.00 0.00 42.98 5.52
545 569 3.834610 CACTTATCTCCACTTCGACGTT 58.165 45.455 0.00 0.00 0.00 3.99
552 576 2.743183 GCGGATGCACTTATCTCCACTT 60.743 50.000 2.86 0.00 42.15 3.16
577 601 4.498682 GCACAGAAGACTTTGTCAAAGCAT 60.499 41.667 22.58 10.48 42.27 3.79
578 602 3.181497 GCACAGAAGACTTTGTCAAAGCA 60.181 43.478 22.58 0.00 42.27 3.91
601 625 3.827898 GCCGTCTCCACTCCTCCG 61.828 72.222 0.00 0.00 0.00 4.63
621 645 2.140717 ACGTCGCCTTCTTCGAATTTT 58.859 42.857 0.00 0.00 37.73 1.82
622 646 1.725164 GACGTCGCCTTCTTCGAATTT 59.275 47.619 0.00 0.00 37.73 1.82
623 647 1.067776 AGACGTCGCCTTCTTCGAATT 60.068 47.619 10.46 0.00 37.73 2.17
624 648 0.526662 AGACGTCGCCTTCTTCGAAT 59.473 50.000 10.46 0.00 37.73 3.34
625 649 1.159285 TAGACGTCGCCTTCTTCGAA 58.841 50.000 10.46 0.00 37.73 3.71
626 650 1.159285 TTAGACGTCGCCTTCTTCGA 58.841 50.000 10.46 0.00 0.00 3.71
627 651 1.647702 GTTTAGACGTCGCCTTCTTCG 59.352 52.381 10.46 0.00 0.00 3.79
628 652 2.662156 CTGTTTAGACGTCGCCTTCTTC 59.338 50.000 10.46 0.00 0.00 2.87
629 653 2.295349 TCTGTTTAGACGTCGCCTTCTT 59.705 45.455 10.46 0.00 0.00 2.52
630 654 1.884579 TCTGTTTAGACGTCGCCTTCT 59.115 47.619 10.46 0.00 0.00 2.85
631 655 2.342910 TCTGTTTAGACGTCGCCTTC 57.657 50.000 10.46 2.15 0.00 3.46
632 656 2.230508 TCATCTGTTTAGACGTCGCCTT 59.769 45.455 10.46 0.00 35.34 4.35
633 657 1.816835 TCATCTGTTTAGACGTCGCCT 59.183 47.619 10.46 0.00 35.34 5.52
634 658 2.159421 TCTCATCTGTTTAGACGTCGCC 60.159 50.000 10.46 0.00 35.34 5.54
635 659 3.102276 CTCTCATCTGTTTAGACGTCGC 58.898 50.000 10.46 2.84 35.34 5.19
636 660 4.601621 TCTCTCATCTGTTTAGACGTCG 57.398 45.455 10.46 0.00 35.34 5.12
637 661 7.061326 GTCTTTTCTCTCATCTGTTTAGACGTC 59.939 40.741 7.70 7.70 35.34 4.34
638 662 6.864165 GTCTTTTCTCTCATCTGTTTAGACGT 59.136 38.462 0.00 0.00 35.34 4.34
639 663 6.863645 TGTCTTTTCTCTCATCTGTTTAGACG 59.136 38.462 0.00 0.00 35.34 4.18
640 664 7.330700 CCTGTCTTTTCTCTCATCTGTTTAGAC 59.669 40.741 0.00 0.00 35.34 2.59
641 665 7.382110 CCTGTCTTTTCTCTCATCTGTTTAGA 58.618 38.462 0.00 0.00 37.35 2.10
642 666 6.593382 CCCTGTCTTTTCTCTCATCTGTTTAG 59.407 42.308 0.00 0.00 0.00 1.85
643 667 6.043243 ACCCTGTCTTTTCTCTCATCTGTTTA 59.957 38.462 0.00 0.00 0.00 2.01
644 668 5.163152 ACCCTGTCTTTTCTCTCATCTGTTT 60.163 40.000 0.00 0.00 0.00 2.83
645 669 4.349342 ACCCTGTCTTTTCTCTCATCTGTT 59.651 41.667 0.00 0.00 0.00 3.16
646 670 3.906846 ACCCTGTCTTTTCTCTCATCTGT 59.093 43.478 0.00 0.00 0.00 3.41
647 671 4.222588 AGACCCTGTCTTTTCTCTCATCTG 59.777 45.833 0.00 0.00 40.28 2.90
648 672 4.424842 AGACCCTGTCTTTTCTCTCATCT 58.575 43.478 0.00 0.00 40.28 2.90
649 673 4.221703 TGAGACCCTGTCTTTTCTCTCATC 59.778 45.833 0.00 0.00 43.53 2.92
650 674 4.163427 TGAGACCCTGTCTTTTCTCTCAT 58.837 43.478 0.00 0.00 43.53 2.90
651 675 3.576861 TGAGACCCTGTCTTTTCTCTCA 58.423 45.455 0.00 0.00 43.53 3.27
652 676 4.020662 ACATGAGACCCTGTCTTTTCTCTC 60.021 45.833 0.00 0.00 43.53 3.20
653 677 3.906846 ACATGAGACCCTGTCTTTTCTCT 59.093 43.478 0.00 0.00 43.53 3.10
654 678 4.278975 ACATGAGACCCTGTCTTTTCTC 57.721 45.455 0.00 0.00 43.53 2.87
655 679 4.713792 AACATGAGACCCTGTCTTTTCT 57.286 40.909 0.00 0.00 43.53 2.52
656 680 5.774498 AAAACATGAGACCCTGTCTTTTC 57.226 39.130 0.00 0.00 43.53 2.29
679 703 6.585416 AGTTTACGGTAGAAGGTGAGAAAAA 58.415 36.000 0.00 0.00 0.00 1.94
680 704 6.165700 AGTTTACGGTAGAAGGTGAGAAAA 57.834 37.500 0.00 0.00 0.00 2.29
681 705 5.796424 AGTTTACGGTAGAAGGTGAGAAA 57.204 39.130 0.00 0.00 0.00 2.52
682 706 6.265196 TGTTAGTTTACGGTAGAAGGTGAGAA 59.735 38.462 0.00 0.00 0.00 2.87
683 707 5.769662 TGTTAGTTTACGGTAGAAGGTGAGA 59.230 40.000 0.00 0.00 0.00 3.27
684 708 6.017400 TGTTAGTTTACGGTAGAAGGTGAG 57.983 41.667 0.00 0.00 0.00 3.51
685 709 5.536161 ACTGTTAGTTTACGGTAGAAGGTGA 59.464 40.000 0.00 0.00 35.90 4.02
686 710 5.776744 ACTGTTAGTTTACGGTAGAAGGTG 58.223 41.667 0.00 0.00 35.90 4.00
693 717 8.413229 ACTGTTTTCTACTGTTAGTTTACGGTA 58.587 33.333 0.00 0.00 38.53 4.02
694 718 7.267857 ACTGTTTTCTACTGTTAGTTTACGGT 58.732 34.615 0.00 0.00 40.59 4.83
695 719 7.095899 GGACTGTTTTCTACTGTTAGTTTACGG 60.096 40.741 0.00 0.00 38.82 4.02
696 720 7.357859 CGGACTGTTTTCTACTGTTAGTTTACG 60.358 40.741 0.00 0.00 38.82 3.18
697 721 7.568315 GCGGACTGTTTTCTACTGTTAGTTTAC 60.568 40.741 0.00 0.00 38.82 2.01
698 722 6.421801 GCGGACTGTTTTCTACTGTTAGTTTA 59.578 38.462 0.00 0.00 38.82 2.01
699 723 5.235831 GCGGACTGTTTTCTACTGTTAGTTT 59.764 40.000 0.00 0.00 38.82 2.66
700 724 4.748600 GCGGACTGTTTTCTACTGTTAGTT 59.251 41.667 0.00 0.00 38.82 2.24
701 725 4.202182 TGCGGACTGTTTTCTACTGTTAGT 60.202 41.667 0.00 0.00 38.82 2.24
702 726 4.304110 TGCGGACTGTTTTCTACTGTTAG 58.696 43.478 0.00 0.00 38.82 2.34
703 727 4.325028 TGCGGACTGTTTTCTACTGTTA 57.675 40.909 0.00 0.00 38.82 2.41
704 728 3.188159 TGCGGACTGTTTTCTACTGTT 57.812 42.857 0.00 0.00 38.82 3.16
705 729 2.902705 TGCGGACTGTTTTCTACTGT 57.097 45.000 0.00 0.00 41.08 3.55
706 730 3.058914 CCTTTGCGGACTGTTTTCTACTG 60.059 47.826 0.00 0.00 33.16 2.74
707 731 3.139077 CCTTTGCGGACTGTTTTCTACT 58.861 45.455 0.00 0.00 33.16 2.57
708 732 2.225727 CCCTTTGCGGACTGTTTTCTAC 59.774 50.000 0.00 0.00 33.16 2.59
709 733 2.500229 CCCTTTGCGGACTGTTTTCTA 58.500 47.619 0.00 0.00 33.16 2.10
710 734 1.318576 CCCTTTGCGGACTGTTTTCT 58.681 50.000 0.00 0.00 33.16 2.52
711 735 0.318699 GCCCTTTGCGGACTGTTTTC 60.319 55.000 0.00 0.00 33.16 2.29
712 736 1.739667 GCCCTTTGCGGACTGTTTT 59.260 52.632 0.00 0.00 33.16 2.43
713 737 3.443588 GCCCTTTGCGGACTGTTT 58.556 55.556 0.00 0.00 33.16 2.83
717 741 4.019474 AAGGATTAGCCCTTTGCGGACT 62.019 50.000 0.00 0.00 43.68 3.85
718 742 1.682087 AAGGATTAGCCCTTTGCGGAC 60.682 52.381 0.00 0.00 43.68 4.79
719 743 0.623723 AAGGATTAGCCCTTTGCGGA 59.376 50.000 0.00 0.00 43.68 5.54
720 744 3.191182 AAGGATTAGCCCTTTGCGG 57.809 52.632 0.00 0.00 43.68 5.69
762 786 8.334632 GCTTTGCGCAATAATATGGTTTTAATT 58.665 29.630 25.64 0.00 38.92 1.40
763 787 7.042119 GGCTTTGCGCAATAATATGGTTTTAAT 60.042 33.333 25.64 0.00 41.67 1.40
764 788 6.256757 GGCTTTGCGCAATAATATGGTTTTAA 59.743 34.615 25.64 2.13 41.67 1.52
765 789 5.751028 GGCTTTGCGCAATAATATGGTTTTA 59.249 36.000 25.64 2.62 41.67 1.52
766 790 4.570369 GGCTTTGCGCAATAATATGGTTTT 59.430 37.500 25.64 0.00 41.67 2.43
767 791 4.119136 GGCTTTGCGCAATAATATGGTTT 58.881 39.130 25.64 0.00 41.67 3.27
768 792 3.131933 TGGCTTTGCGCAATAATATGGTT 59.868 39.130 25.64 0.00 41.67 3.67
769 793 2.692557 TGGCTTTGCGCAATAATATGGT 59.307 40.909 25.64 0.00 41.67 3.55
770 794 3.367992 TGGCTTTGCGCAATAATATGG 57.632 42.857 25.64 9.20 41.67 2.74
771 795 5.333492 CCATTTGGCTTTGCGCAATAATATG 60.333 40.000 25.64 19.84 41.67 1.78
772 796 4.751098 CCATTTGGCTTTGCGCAATAATAT 59.249 37.500 25.64 10.06 41.67 1.28
773 797 4.118410 CCATTTGGCTTTGCGCAATAATA 58.882 39.130 25.64 7.99 41.67 0.98
774 798 2.937799 CCATTTGGCTTTGCGCAATAAT 59.062 40.909 25.64 14.77 41.67 1.28
775 799 2.289320 ACCATTTGGCTTTGCGCAATAA 60.289 40.909 25.64 13.83 41.67 1.40
776 800 1.274728 ACCATTTGGCTTTGCGCAATA 59.725 42.857 25.64 13.72 41.67 1.90
777 801 0.035176 ACCATTTGGCTTTGCGCAAT 59.965 45.000 25.64 3.58 41.67 3.56
778 802 0.179062 AACCATTTGGCTTTGCGCAA 60.179 45.000 21.02 21.02 41.67 4.85
779 803 0.879400 CAACCATTTGGCTTTGCGCA 60.879 50.000 5.66 5.66 41.67 6.09
780 804 0.599728 TCAACCATTTGGCTTTGCGC 60.600 50.000 0.00 0.00 39.32 6.09
781 805 1.526464 GTTCAACCATTTGGCTTTGCG 59.474 47.619 0.00 0.00 39.32 4.85
782 806 2.287644 GTGTTCAACCATTTGGCTTTGC 59.712 45.455 0.00 0.00 39.32 3.68
783 807 3.529533 TGTGTTCAACCATTTGGCTTTG 58.470 40.909 0.00 0.00 39.32 2.77
784 808 3.902881 TGTGTTCAACCATTTGGCTTT 57.097 38.095 0.00 0.00 39.32 3.51
785 809 3.530535 GTTGTGTTCAACCATTTGGCTT 58.469 40.909 0.00 0.00 45.60 4.35
786 810 3.177997 GTTGTGTTCAACCATTTGGCT 57.822 42.857 0.00 0.00 45.60 4.75
796 820 1.217916 TCCTGAGGGGTTGTGTTCAA 58.782 50.000 0.00 0.00 36.25 2.69
797 821 1.217916 TTCCTGAGGGGTTGTGTTCA 58.782 50.000 0.00 0.00 36.25 3.18
798 822 2.358322 TTTCCTGAGGGGTTGTGTTC 57.642 50.000 0.00 0.00 36.25 3.18
799 823 2.838637 TTTTCCTGAGGGGTTGTGTT 57.161 45.000 0.00 0.00 36.25 3.32
800 824 2.838637 TTTTTCCTGAGGGGTTGTGT 57.161 45.000 0.00 0.00 36.25 3.72
847 871 2.291217 GCTTTGGGTCCATCCTCTCTTT 60.291 50.000 0.00 0.00 36.25 2.52
859 883 0.739813 ATACACTCGCGCTTTGGGTC 60.740 55.000 5.56 0.00 0.00 4.46
870 897 1.066858 AGGCCTCAACACATACACTCG 60.067 52.381 0.00 0.00 0.00 4.18
872 899 1.003580 CCAGGCCTCAACACATACACT 59.996 52.381 0.00 0.00 0.00 3.55
877 904 1.380302 GGACCAGGCCTCAACACAT 59.620 57.895 0.00 0.00 0.00 3.21
891 918 2.032071 CCAGGTGTGAACCGGACC 59.968 66.667 9.46 4.37 34.28 4.46
892 919 2.668550 GCCAGGTGTGAACCGGAC 60.669 66.667 9.46 1.77 34.28 4.79
893 920 2.747443 TTGCCAGGTGTGAACCGGA 61.747 57.895 9.46 0.00 34.28 5.14
894 921 2.203280 TTGCCAGGTGTGAACCGG 60.203 61.111 0.00 0.00 34.28 5.28
895 922 1.101049 AAGTTGCCAGGTGTGAACCG 61.101 55.000 0.00 0.00 34.28 4.44
903 930 3.511610 AGCCCCAAGTTGCCAGGT 61.512 61.111 0.00 0.00 0.00 4.00
924 951 1.596934 GACCCCGAGTCAGATGCAA 59.403 57.895 0.00 0.00 45.55 4.08
1900 1933 2.897326 TGAAGTTCCAGACGGAGATCAA 59.103 45.455 0.00 0.00 44.10 2.57
2013 2052 2.284995 ACAGAGAGCCCCCACTCC 60.285 66.667 0.00 0.00 37.39 3.85
2015 2054 2.151307 TACGACAGAGAGCCCCCACT 62.151 60.000 0.00 0.00 0.00 4.00
2064 2103 2.124529 TCACCCACAGCACGCAAA 60.125 55.556 0.00 0.00 0.00 3.68
2079 2118 3.884774 ACAAACAGGCCGCCCTCA 61.885 61.111 5.55 0.00 40.33 3.86
2091 2130 1.604278 GTCTCCAGGTTGAGCACAAAC 59.396 52.381 3.44 3.44 43.31 2.93
2362 2483 7.129425 ACAGAGGGAGTAGAAATGAAGACTAT 58.871 38.462 0.00 0.00 0.00 2.12
2385 2506 7.989416 AAAAACGTTCTTATATTCTGGGACA 57.011 32.000 0.00 0.00 0.00 4.02
2427 2548 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
2428 2549 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
2429 2550 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
2430 2551 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
2431 2552 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
2432 2553 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
2433 2554 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
2434 2555 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
2435 2556 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
2436 2557 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
2437 2558 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
2438 2559 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
2439 2560 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
2440 2561 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2441 2562 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2442 2563 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
2443 2564 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2444 2565 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2445 2566 2.852714 TTATTACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
2446 2567 3.236896 TGATTATTACTCCCTCCGTCCC 58.763 50.000 0.00 0.00 0.00 4.46
2447 2568 3.896272 ACTGATTATTACTCCCTCCGTCC 59.104 47.826 0.00 0.00 0.00 4.79
2448 2569 4.341520 ACACTGATTATTACTCCCTCCGTC 59.658 45.833 0.00 0.00 0.00 4.79
2449 2570 4.287552 ACACTGATTATTACTCCCTCCGT 58.712 43.478 0.00 0.00 0.00 4.69
2450 2571 4.262079 GGACACTGATTATTACTCCCTCCG 60.262 50.000 0.00 0.00 0.00 4.63
2451 2572 4.902448 AGGACACTGATTATTACTCCCTCC 59.098 45.833 0.00 0.00 0.00 4.30
2452 2573 5.836358 AGAGGACACTGATTATTACTCCCTC 59.164 44.000 0.00 0.00 37.36 4.30
2453 2574 5.782925 AGAGGACACTGATTATTACTCCCT 58.217 41.667 0.00 0.00 0.00 4.20
2454 2575 6.778559 AGTAGAGGACACTGATTATTACTCCC 59.221 42.308 0.00 0.00 0.00 4.30
2455 2576 7.653647 CAGTAGAGGACACTGATTATTACTCC 58.346 42.308 0.00 0.00 45.10 3.85
2456 2577 7.013846 AGCAGTAGAGGACACTGATTATTACTC 59.986 40.741 6.67 0.00 45.10 2.59
2457 2578 6.836527 AGCAGTAGAGGACACTGATTATTACT 59.163 38.462 6.67 0.00 45.10 2.24
2458 2579 7.045126 AGCAGTAGAGGACACTGATTATTAC 57.955 40.000 6.67 0.00 45.10 1.89
2565 2686 6.017934 GCATAGTGAATCGAAGAAAATAGGCA 60.018 38.462 0.00 0.00 43.58 4.75
2568 2689 7.482654 TGGCATAGTGAATCGAAGAAAATAG 57.517 36.000 0.00 0.00 43.58 1.73
2637 2758 4.701651 TCTCCTATTGTTCACATTGGCTTG 59.298 41.667 0.00 0.00 0.00 4.01
2678 2799 7.148323 CCAGTTCGTATTGAATATGTGGTCAAA 60.148 37.037 4.48 0.00 39.21 2.69
2679 2800 6.315144 CCAGTTCGTATTGAATATGTGGTCAA 59.685 38.462 4.48 0.00 39.21 3.18
2680 2801 5.815222 CCAGTTCGTATTGAATATGTGGTCA 59.185 40.000 4.48 0.00 39.21 4.02
2681 2802 5.277345 GCCAGTTCGTATTGAATATGTGGTC 60.277 44.000 11.74 4.17 39.21 4.02
2682 2803 4.574828 GCCAGTTCGTATTGAATATGTGGT 59.425 41.667 11.74 0.00 39.21 4.16
2683 2804 4.816385 AGCCAGTTCGTATTGAATATGTGG 59.184 41.667 4.48 6.31 39.21 4.17
2684 2805 5.991328 AGCCAGTTCGTATTGAATATGTG 57.009 39.130 4.48 0.00 39.21 3.21
2685 2806 5.989777 GGTAGCCAGTTCGTATTGAATATGT 59.010 40.000 4.48 0.00 39.21 2.29
2686 2807 6.146184 CAGGTAGCCAGTTCGTATTGAATATG 59.854 42.308 0.00 0.00 39.21 1.78
2687 2808 6.041637 TCAGGTAGCCAGTTCGTATTGAATAT 59.958 38.462 0.00 0.00 39.21 1.28
2688 2809 5.361571 TCAGGTAGCCAGTTCGTATTGAATA 59.638 40.000 0.00 0.00 39.21 1.75
2689 2810 4.161565 TCAGGTAGCCAGTTCGTATTGAAT 59.838 41.667 0.00 0.00 39.21 2.57
2690 2811 3.512329 TCAGGTAGCCAGTTCGTATTGAA 59.488 43.478 0.00 0.00 0.00 2.69
2691 2812 3.093814 TCAGGTAGCCAGTTCGTATTGA 58.906 45.455 0.00 0.00 0.00 2.57
2692 2813 3.520290 TCAGGTAGCCAGTTCGTATTG 57.480 47.619 0.00 0.00 0.00 1.90
2693 2814 4.755266 AATCAGGTAGCCAGTTCGTATT 57.245 40.909 0.00 0.00 0.00 1.89
2694 2815 4.755266 AAATCAGGTAGCCAGTTCGTAT 57.245 40.909 0.00 0.00 0.00 3.06
2695 2816 4.546829 AAAATCAGGTAGCCAGTTCGTA 57.453 40.909 0.00 0.00 0.00 3.43
2696 2817 3.418684 AAAATCAGGTAGCCAGTTCGT 57.581 42.857 0.00 0.00 0.00 3.85
2697 2818 5.873179 TTAAAAATCAGGTAGCCAGTTCG 57.127 39.130 0.00 0.00 0.00 3.95
2698 2819 9.489084 AATTTTTAAAAATCAGGTAGCCAGTTC 57.511 29.630 22.96 0.00 37.62 3.01
2699 2820 9.489084 GAATTTTTAAAAATCAGGTAGCCAGTT 57.511 29.630 22.96 6.79 37.62 3.16
2700 2821 8.870116 AGAATTTTTAAAAATCAGGTAGCCAGT 58.130 29.630 22.96 6.28 37.62 4.00
2701 2822 9.143631 CAGAATTTTTAAAAATCAGGTAGCCAG 57.856 33.333 22.96 4.87 37.62 4.85
2702 2823 8.865090 TCAGAATTTTTAAAAATCAGGTAGCCA 58.135 29.630 22.96 0.00 37.62 4.75
2703 2824 9.358872 CTCAGAATTTTTAAAAATCAGGTAGCC 57.641 33.333 22.96 8.18 37.62 3.93
2704 2825 9.358872 CCTCAGAATTTTTAAAAATCAGGTAGC 57.641 33.333 22.96 9.43 37.62 3.58
2707 2828 8.923270 TCACCTCAGAATTTTTAAAAATCAGGT 58.077 29.630 22.96 23.78 37.62 4.00
2708 2829 9.196552 GTCACCTCAGAATTTTTAAAAATCAGG 57.803 33.333 22.96 23.31 37.62 3.86
2709 2830 9.748708 TGTCACCTCAGAATTTTTAAAAATCAG 57.251 29.630 22.96 16.21 37.62 2.90
2713 2834 9.581099 GAGTTGTCACCTCAGAATTTTTAAAAA 57.419 29.630 15.38 15.38 0.00 1.94
2714 2835 8.966868 AGAGTTGTCACCTCAGAATTTTTAAAA 58.033 29.630 0.00 0.00 0.00 1.52
2715 2836 8.519799 AGAGTTGTCACCTCAGAATTTTTAAA 57.480 30.769 0.00 0.00 0.00 1.52
2716 2837 8.519799 AAGAGTTGTCACCTCAGAATTTTTAA 57.480 30.769 0.00 0.00 0.00 1.52
2717 2838 8.519799 AAAGAGTTGTCACCTCAGAATTTTTA 57.480 30.769 0.00 0.00 0.00 1.52
2718 2839 7.410120 AAAGAGTTGTCACCTCAGAATTTTT 57.590 32.000 0.00 0.00 0.00 1.94
2719 2840 7.122650 TCAAAAGAGTTGTCACCTCAGAATTTT 59.877 33.333 0.00 0.00 0.00 1.82
2720 2841 6.603201 TCAAAAGAGTTGTCACCTCAGAATTT 59.397 34.615 0.00 0.00 0.00 1.82
2721 2842 6.122277 TCAAAAGAGTTGTCACCTCAGAATT 58.878 36.000 0.00 0.00 0.00 2.17
2722 2843 5.684704 TCAAAAGAGTTGTCACCTCAGAAT 58.315 37.500 0.00 0.00 0.00 2.40
2818 2941 9.018582 TGTCATACTAACTCTCAGATATGATGG 57.981 37.037 0.00 0.00 33.07 3.51
2921 3044 9.601810 TGAGGACAGGCTATTTAGATATTAGAA 57.398 33.333 0.00 0.00 0.00 2.10
2926 3049 8.174085 AGTAGTGAGGACAGGCTATTTAGATAT 58.826 37.037 0.00 0.00 0.00 1.63
2928 3051 6.377912 AGTAGTGAGGACAGGCTATTTAGAT 58.622 40.000 0.00 0.00 0.00 1.98
2930 3053 6.999272 TCTAGTAGTGAGGACAGGCTATTTAG 59.001 42.308 0.00 0.00 0.00 1.85
2933 3056 5.390087 TCTAGTAGTGAGGACAGGCTATT 57.610 43.478 0.00 0.00 0.00 1.73
2934 3057 5.592587 ATCTAGTAGTGAGGACAGGCTAT 57.407 43.478 0.00 0.00 0.00 2.97
2937 3060 4.647399 AGAAATCTAGTAGTGAGGACAGGC 59.353 45.833 0.00 0.00 0.00 4.85
2938 3061 6.039270 CAGAGAAATCTAGTAGTGAGGACAGG 59.961 46.154 0.00 0.00 0.00 4.00
2939 3062 6.459573 GCAGAGAAATCTAGTAGTGAGGACAG 60.460 46.154 0.00 0.00 0.00 3.51
2940 3063 5.358442 GCAGAGAAATCTAGTAGTGAGGACA 59.642 44.000 0.00 0.00 0.00 4.02
2986 3114 3.982475 TCACGATGATGTCTGGCTATTC 58.018 45.455 0.00 0.00 0.00 1.75
3061 3189 6.064060 AGAGACATCAAAATCAACTCCACAA 58.936 36.000 0.00 0.00 0.00 3.33
3125 3253 6.183360 CCTCAGCTTCACAATCATACTTTGAG 60.183 42.308 0.00 0.00 37.89 3.02
3126 3254 5.645067 CCTCAGCTTCACAATCATACTTTGA 59.355 40.000 0.00 0.00 39.12 2.69


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

AutoCloner maintained by Alex Coulton.