Multiple sequence alignment - TraesCS1B01G121300

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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 TraesCS1B01G121300 chr1B 100.000 2507 0 0 1 2507 143452456 143449950 0.000000e+00 4630.0
1 TraesCS1B01G121300 chr1B 86.316 570 71 6 1009 1575 145360292 145360857 4.580000e-172 614.0
2 TraesCS1B01G121300 chr1B 80.247 486 95 1 1010 1494 145349607 145350092 5.100000e-97 364.0
3 TraesCS1B01G121300 chr1B 93.220 118 8 0 1604 1721 143111299 143111182 9.220000e-40 174.0
4 TraesCS1B01G121300 chr1B 97.619 42 1 0 633 674 143451786 143451745 3.460000e-09 73.1
5 TraesCS1B01G121300 chr1B 97.619 42 1 0 671 712 143451824 143451783 3.460000e-09 73.1
6 TraesCS1B01G121300 chr1A 88.556 900 99 4 702 1599 85905122 85906019 0.000000e+00 1088.0
7 TraesCS1B01G121300 chr1A 81.277 705 118 11 1784 2476 15328628 15327926 2.180000e-155 558.0
8 TraesCS1B01G121300 chr1A 81.575 597 101 8 1009 1602 85841190 85841780 3.750000e-133 484.0
9 TraesCS1B01G121300 chr1A 80.935 556 100 4 1009 1559 85826820 85827374 3.830000e-118 435.0
10 TraesCS1B01G121300 chr1A 78.392 597 103 16 1009 1601 86608009 86608583 5.100000e-97 364.0
11 TraesCS1B01G121300 chr2D 94.885 567 22 4 1 560 245602959 245602393 0.000000e+00 880.0
12 TraesCS1B01G121300 chr2D 94.014 568 31 2 1 568 222616204 222616768 0.000000e+00 857.0
13 TraesCS1B01G121300 chr7D 93.870 571 30 5 1 568 279723905 279724473 0.000000e+00 856.0
14 TraesCS1B01G121300 chrUn 93.870 571 26 4 1 568 67765801 67765237 0.000000e+00 852.0
15 TraesCS1B01G121300 chrUn 79.134 762 137 18 1755 2504 51444671 51445422 8.000000e-140 507.0
16 TraesCS1B01G121300 chr3A 93.728 574 26 7 1 568 630256892 630256323 0.000000e+00 852.0
17 TraesCS1B01G121300 chr7B 93.576 576 27 8 1 568 275767321 275766748 0.000000e+00 850.0
18 TraesCS1B01G121300 chr5D 93.543 573 32 3 1 568 309911895 309911323 0.000000e+00 848.0
19 TraesCS1B01G121300 chr3D 93.520 571 34 2 1 568 534701158 534701728 0.000000e+00 846.0
20 TraesCS1B01G121300 chr6D 93.357 572 33 4 1 568 295201833 295201263 0.000000e+00 841.0
21 TraesCS1B01G121300 chr6D 82.893 795 122 10 1726 2507 266323386 266322593 0.000000e+00 702.0
22 TraesCS1B01G121300 chr5A 83.615 769 111 12 1721 2478 144390590 144391354 0.000000e+00 708.0
23 TraesCS1B01G121300 chr6A 82.368 794 129 9 1724 2507 377484117 377483325 0.000000e+00 680.0
24 TraesCS1B01G121300 chr5B 82.637 766 122 10 1723 2478 141459488 141460252 0.000000e+00 667.0
25 TraesCS1B01G121300 chr5B 84.069 634 90 9 1851 2478 545814829 545815457 3.570000e-168 601.0
26 TraesCS1B01G121300 chr1D 90.215 511 48 2 702 1211 89601678 89602187 0.000000e+00 665.0
27 TraesCS1B01G121300 chr1D 82.137 599 95 9 1009 1602 89560929 89561520 1.040000e-138 503.0
28 TraesCS1B01G121300 chr1D 83.119 545 90 2 1009 1552 89990826 89991369 1.730000e-136 496.0
29 TraesCS1B01G121300 chr1D 78.297 599 99 19 1009 1601 90581788 90582361 8.530000e-95 357.0
30 TraesCS1B01G121300 chr7A 81.159 759 128 13 1732 2478 33498473 33499228 1.660000e-166 595.0
31 TraesCS1B01G121300 chr3B 79.497 795 143 16 1724 2504 414823607 414824395 4.710000e-152 547.0
32 TraesCS1B01G121300 chr2B 93.333 75 5 0 819 893 655631116 655631042 7.330000e-21 111.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G121300 chr1B 143449950 143452456 2506 True 1592.066667 4630 98.412667 1 2507 3 chr1B.!!$R2 2506
1 TraesCS1B01G121300 chr1B 145360292 145360857 565 False 614.000000 614 86.316000 1009 1575 1 chr1B.!!$F2 566
2 TraesCS1B01G121300 chr1A 85905122 85906019 897 False 1088.000000 1088 88.556000 702 1599 1 chr1A.!!$F3 897
3 TraesCS1B01G121300 chr1A 15327926 15328628 702 True 558.000000 558 81.277000 1784 2476 1 chr1A.!!$R1 692
4 TraesCS1B01G121300 chr1A 85841190 85841780 590 False 484.000000 484 81.575000 1009 1602 1 chr1A.!!$F2 593
5 TraesCS1B01G121300 chr1A 85826820 85827374 554 False 435.000000 435 80.935000 1009 1559 1 chr1A.!!$F1 550
6 TraesCS1B01G121300 chr1A 86608009 86608583 574 False 364.000000 364 78.392000 1009 1601 1 chr1A.!!$F4 592
7 TraesCS1B01G121300 chr2D 245602393 245602959 566 True 880.000000 880 94.885000 1 560 1 chr2D.!!$R1 559
8 TraesCS1B01G121300 chr2D 222616204 222616768 564 False 857.000000 857 94.014000 1 568 1 chr2D.!!$F1 567
9 TraesCS1B01G121300 chr7D 279723905 279724473 568 False 856.000000 856 93.870000 1 568 1 chr7D.!!$F1 567
10 TraesCS1B01G121300 chrUn 67765237 67765801 564 True 852.000000 852 93.870000 1 568 1 chrUn.!!$R1 567
11 TraesCS1B01G121300 chrUn 51444671 51445422 751 False 507.000000 507 79.134000 1755 2504 1 chrUn.!!$F1 749
12 TraesCS1B01G121300 chr3A 630256323 630256892 569 True 852.000000 852 93.728000 1 568 1 chr3A.!!$R1 567
13 TraesCS1B01G121300 chr7B 275766748 275767321 573 True 850.000000 850 93.576000 1 568 1 chr7B.!!$R1 567
14 TraesCS1B01G121300 chr5D 309911323 309911895 572 True 848.000000 848 93.543000 1 568 1 chr5D.!!$R1 567
15 TraesCS1B01G121300 chr3D 534701158 534701728 570 False 846.000000 846 93.520000 1 568 1 chr3D.!!$F1 567
16 TraesCS1B01G121300 chr6D 295201263 295201833 570 True 841.000000 841 93.357000 1 568 1 chr6D.!!$R2 567
17 TraesCS1B01G121300 chr6D 266322593 266323386 793 True 702.000000 702 82.893000 1726 2507 1 chr6D.!!$R1 781
18 TraesCS1B01G121300 chr5A 144390590 144391354 764 False 708.000000 708 83.615000 1721 2478 1 chr5A.!!$F1 757
19 TraesCS1B01G121300 chr6A 377483325 377484117 792 True 680.000000 680 82.368000 1724 2507 1 chr6A.!!$R1 783
20 TraesCS1B01G121300 chr5B 141459488 141460252 764 False 667.000000 667 82.637000 1723 2478 1 chr5B.!!$F1 755
21 TraesCS1B01G121300 chr5B 545814829 545815457 628 False 601.000000 601 84.069000 1851 2478 1 chr5B.!!$F2 627
22 TraesCS1B01G121300 chr1D 89601678 89602187 509 False 665.000000 665 90.215000 702 1211 1 chr1D.!!$F2 509
23 TraesCS1B01G121300 chr1D 89560929 89561520 591 False 503.000000 503 82.137000 1009 1602 1 chr1D.!!$F1 593
24 TraesCS1B01G121300 chr1D 89990826 89991369 543 False 496.000000 496 83.119000 1009 1552 1 chr1D.!!$F3 543
25 TraesCS1B01G121300 chr1D 90581788 90582361 573 False 357.000000 357 78.297000 1009 1601 1 chr1D.!!$F4 592
26 TraesCS1B01G121300 chr7A 33498473 33499228 755 False 595.000000 595 81.159000 1732 2478 1 chr7A.!!$F1 746
27 TraesCS1B01G121300 chr3B 414823607 414824395 788 False 547.000000 547 79.497000 1724 2504 1 chr3B.!!$F1 780

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
930 945 0.03467 AGCCCTCTCAATCTTGTGCC 60.035 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2207 2.094182 CGTGGCTAAAAGGAGTAGAGCA 60.094 50.0 0.0 0.0 34.76 4.26 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
134 135 5.593909 CCAATGCATAACCTTCCAATCACTA 59.406 40.000 0.00 0.00 0.00 2.74
177 180 7.568199 TTAGGCATAAGAGGCAAGTATTTTC 57.432 36.000 0.00 0.00 36.37 2.29
179 182 5.591877 AGGCATAAGAGGCAAGTATTTTCTG 59.408 40.000 0.00 0.00 36.37 3.02
226 236 6.287589 TGTTTGTTTCACCCACAACTAAAT 57.712 33.333 0.00 0.00 33.81 1.40
405 419 7.569111 AGGTGGAAGTGATAAGTATGGAGTATT 59.431 37.037 0.00 0.00 0.00 1.89
438 452 7.988028 ACAAGGAGCTAAAGGTAAGATCAATAC 59.012 37.037 0.00 0.00 30.94 1.89
523 537 9.334693 TCTAGAAACGAGAAATAAAACTACGTC 57.665 33.333 0.00 0.00 0.00 4.34
532 546 7.771183 AGAAATAAAACTACGTCGTGGGTATA 58.229 34.615 13.62 3.32 0.00 1.47
561 575 5.585445 GGATAGCTTTGCATGATATCAGAGG 59.415 44.000 19.83 4.67 35.30 3.69
568 582 7.307870 GCTTTGCATGATATCAGAGGACTAAAG 60.308 40.741 11.78 13.52 0.00 1.85
569 583 6.983906 TGCATGATATCAGAGGACTAAAGA 57.016 37.500 11.78 0.00 0.00 2.52
570 584 6.990798 TGCATGATATCAGAGGACTAAAGAG 58.009 40.000 11.78 0.00 0.00 2.85
571 585 6.779539 TGCATGATATCAGAGGACTAAAGAGA 59.220 38.462 11.78 0.00 0.00 3.10
572 586 7.454066 TGCATGATATCAGAGGACTAAAGAGAT 59.546 37.037 11.78 0.00 0.00 2.75
573 587 7.760794 GCATGATATCAGAGGACTAAAGAGATG 59.239 40.741 11.78 0.00 0.00 2.90
574 588 8.805175 CATGATATCAGAGGACTAAAGAGATGT 58.195 37.037 11.78 0.00 0.00 3.06
575 589 8.175925 TGATATCAGAGGACTAAAGAGATGTG 57.824 38.462 0.00 0.00 0.00 3.21
576 590 4.727507 TCAGAGGACTAAAGAGATGTGC 57.272 45.455 0.00 0.00 0.00 4.57
577 591 4.089361 TCAGAGGACTAAAGAGATGTGCA 58.911 43.478 0.00 0.00 0.00 4.57
578 592 4.713814 TCAGAGGACTAAAGAGATGTGCAT 59.286 41.667 0.00 0.00 0.00 3.96
579 593 4.809958 CAGAGGACTAAAGAGATGTGCATG 59.190 45.833 0.00 0.00 0.00 4.06
580 594 3.539604 AGGACTAAAGAGATGTGCATGC 58.460 45.455 11.82 11.82 0.00 4.06
581 595 2.286294 GGACTAAAGAGATGTGCATGCG 59.714 50.000 14.09 0.00 0.00 4.73
582 596 3.190079 GACTAAAGAGATGTGCATGCGA 58.810 45.455 14.09 1.89 0.00 5.10
583 597 3.193263 ACTAAAGAGATGTGCATGCGAG 58.807 45.455 14.09 0.04 0.00 5.03
584 598 2.391616 AAAGAGATGTGCATGCGAGA 57.608 45.000 14.09 1.12 0.00 4.04
585 599 2.616634 AAGAGATGTGCATGCGAGAT 57.383 45.000 14.09 6.35 0.00 2.75
586 600 2.616634 AGAGATGTGCATGCGAGATT 57.383 45.000 14.09 0.00 0.00 2.40
587 601 2.210961 AGAGATGTGCATGCGAGATTG 58.789 47.619 14.09 0.00 0.00 2.67
588 602 0.661552 AGATGTGCATGCGAGATTGC 59.338 50.000 14.09 0.00 39.33 3.56
596 610 3.556817 TGCGAGATTGCACCAAGAT 57.443 47.368 0.00 0.00 40.62 2.40
597 611 1.089112 TGCGAGATTGCACCAAGATG 58.911 50.000 0.00 0.00 40.62 2.90
598 612 1.089920 GCGAGATTGCACCAAGATGT 58.910 50.000 0.00 0.00 34.15 3.06
599 613 1.202110 GCGAGATTGCACCAAGATGTG 60.202 52.381 0.00 0.00 39.29 3.21
600 614 2.079158 CGAGATTGCACCAAGATGTGT 58.921 47.619 0.00 0.00 38.52 3.72
601 615 2.485426 CGAGATTGCACCAAGATGTGTT 59.515 45.455 0.00 0.00 38.52 3.32
602 616 3.058016 CGAGATTGCACCAAGATGTGTTT 60.058 43.478 0.00 0.00 38.52 2.83
603 617 4.232221 GAGATTGCACCAAGATGTGTTTG 58.768 43.478 0.00 0.00 38.52 2.93
604 618 2.222007 TTGCACCAAGATGTGTTTGC 57.778 45.000 0.00 0.00 38.52 3.68
605 619 1.109609 TGCACCAAGATGTGTTTGCA 58.890 45.000 0.00 0.00 40.36 4.08
606 620 1.202394 TGCACCAAGATGTGTTTGCAC 60.202 47.619 0.00 0.00 45.44 4.57
607 621 1.869342 GCACCAAGATGTGTTTGCACC 60.869 52.381 0.00 0.00 44.65 5.01
608 622 0.667993 ACCAAGATGTGTTTGCACCG 59.332 50.000 0.00 0.00 44.65 4.94
609 623 0.950836 CCAAGATGTGTTTGCACCGA 59.049 50.000 0.00 0.00 44.65 4.69
610 624 1.069022 CCAAGATGTGTTTGCACCGAG 60.069 52.381 0.00 0.00 44.65 4.63
611 625 1.872952 CAAGATGTGTTTGCACCGAGA 59.127 47.619 0.00 0.00 44.65 4.04
612 626 1.800805 AGATGTGTTTGCACCGAGAG 58.199 50.000 0.00 0.00 44.65 3.20
630 644 5.764131 CGAGAGGCTTTCGAATCTATTACT 58.236 41.667 21.55 0.00 40.36 2.24
631 645 6.900189 CGAGAGGCTTTCGAATCTATTACTA 58.100 40.000 21.55 0.00 40.36 1.82
632 646 7.361127 CGAGAGGCTTTCGAATCTATTACTAA 58.639 38.462 21.55 0.00 40.36 2.24
633 647 7.861372 CGAGAGGCTTTCGAATCTATTACTAAA 59.139 37.037 21.55 0.00 40.36 1.85
634 648 9.699703 GAGAGGCTTTCGAATCTATTACTAAAT 57.300 33.333 0.00 0.00 0.00 1.40
648 662 9.842775 TCTATTACTAAATTCTGACTAGTCGGA 57.157 33.333 27.20 27.20 42.78 4.55
655 669 4.698583 TTCTGACTAGTCGGAAGTTAGC 57.301 45.455 33.70 3.74 46.65 3.09
656 670 3.682696 TCTGACTAGTCGGAAGTTAGCA 58.317 45.455 28.44 6.65 41.64 3.49
657 671 3.439476 TCTGACTAGTCGGAAGTTAGCAC 59.561 47.826 28.44 0.00 41.64 4.40
658 672 3.151554 TGACTAGTCGGAAGTTAGCACA 58.848 45.455 17.85 0.00 0.00 4.57
659 673 3.762288 TGACTAGTCGGAAGTTAGCACAT 59.238 43.478 17.85 0.00 0.00 3.21
660 674 4.142447 TGACTAGTCGGAAGTTAGCACATC 60.142 45.833 17.85 0.00 0.00 3.06
661 675 2.674796 AGTCGGAAGTTAGCACATCC 57.325 50.000 0.00 0.00 37.42 3.51
662 676 1.207329 AGTCGGAAGTTAGCACATCCC 59.793 52.381 0.00 0.00 37.48 3.85
663 677 1.207329 GTCGGAAGTTAGCACATCCCT 59.793 52.381 0.00 0.00 37.48 4.20
664 678 2.429610 GTCGGAAGTTAGCACATCCCTA 59.570 50.000 0.00 0.00 37.48 3.53
665 679 3.069729 GTCGGAAGTTAGCACATCCCTAT 59.930 47.826 0.00 0.00 37.48 2.57
666 680 4.280174 GTCGGAAGTTAGCACATCCCTATA 59.720 45.833 0.00 0.00 37.48 1.31
667 681 5.047235 GTCGGAAGTTAGCACATCCCTATAT 60.047 44.000 0.00 0.00 37.48 0.86
668 682 6.152323 GTCGGAAGTTAGCACATCCCTATATA 59.848 42.308 0.00 0.00 37.48 0.86
669 683 6.895756 TCGGAAGTTAGCACATCCCTATATAT 59.104 38.462 0.00 0.00 37.48 0.86
670 684 8.057011 TCGGAAGTTAGCACATCCCTATATATA 58.943 37.037 0.00 0.00 37.48 0.86
671 685 8.692710 CGGAAGTTAGCACATCCCTATATATAA 58.307 37.037 0.00 0.00 37.48 0.98
679 693 9.499369 AGCACATCCCTATATATAATTCTGACT 57.501 33.333 0.00 0.00 0.00 3.41
685 699 9.848710 TCCCTATATATAATTCTGACTAGTCGG 57.151 37.037 23.54 23.54 37.32 4.79
686 700 9.848710 CCCTATATATAATTCTGACTAGTCGGA 57.151 37.037 27.20 27.20 42.78 4.55
693 707 4.698583 TTCTGACTAGTCGGAAGTTAGC 57.301 45.455 33.70 3.74 46.65 3.09
694 708 3.682696 TCTGACTAGTCGGAAGTTAGCA 58.317 45.455 28.44 6.65 41.64 3.49
695 709 3.439476 TCTGACTAGTCGGAAGTTAGCAC 59.561 47.826 28.44 0.00 41.64 4.40
696 710 3.151554 TGACTAGTCGGAAGTTAGCACA 58.848 45.455 17.85 0.00 0.00 4.57
697 711 3.762288 TGACTAGTCGGAAGTTAGCACAT 59.238 43.478 17.85 0.00 0.00 3.21
698 712 4.142447 TGACTAGTCGGAAGTTAGCACATC 60.142 45.833 17.85 0.00 0.00 3.06
699 713 2.674796 AGTCGGAAGTTAGCACATCC 57.325 50.000 0.00 0.00 37.42 3.51
700 714 1.207329 AGTCGGAAGTTAGCACATCCC 59.793 52.381 0.00 0.00 37.48 3.85
778 792 4.821805 ACAACTTTGGTACAGATCACTTGG 59.178 41.667 0.00 0.00 42.39 3.61
780 794 3.181445 ACTTTGGTACAGATCACTTGGCA 60.181 43.478 0.00 0.00 42.39 4.92
803 817 3.060602 GCTCATATTCTCCTTGTACGCC 58.939 50.000 0.00 0.00 0.00 5.68
807 821 4.343814 TCATATTCTCCTTGTACGCCATCA 59.656 41.667 0.00 0.00 0.00 3.07
817 831 0.393673 TACGCCATCATGTGTTGGGG 60.394 55.000 19.62 19.62 46.85 4.96
854 869 2.951458 CGGTGGGGAAAAAGTCGC 59.049 61.111 0.00 0.00 38.47 5.19
861 876 1.743394 GGGGAAAAAGTCGCATCGAAT 59.257 47.619 0.00 0.00 40.96 3.34
885 900 0.320771 GAGGCAAAGAGAACGGAGCA 60.321 55.000 0.00 0.00 0.00 4.26
906 921 5.603596 GCAATATGCAAATTTCCCATGAGA 58.396 37.500 9.89 0.00 44.26 3.27
930 945 0.034670 AGCCCTCTCAATCTTGTGCC 60.035 55.000 0.00 0.00 0.00 5.01
933 948 1.280133 CCCTCTCAATCTTGTGCCTCA 59.720 52.381 0.00 0.00 0.00 3.86
938 953 3.262660 TCTCAATCTTGTGCCTCATGTCT 59.737 43.478 0.00 0.00 0.00 3.41
944 959 4.285020 TCTTGTGCCTCATGTCTAGATCT 58.715 43.478 0.00 0.00 0.00 2.75
951 966 4.614993 GCCTCATGTCTAGATCTAACGAGC 60.615 50.000 3.57 2.75 0.00 5.03
1104 1119 3.070018 AGAGCTCTTTGGTTCAATGTCG 58.930 45.455 11.45 0.00 0.00 4.35
1116 1131 3.627395 TCAATGTCGGAGGCTACAATT 57.373 42.857 0.00 0.00 0.00 2.32
1127 1142 4.130118 GAGGCTACAATTTCGTCCATCAT 58.870 43.478 0.00 0.00 0.00 2.45
1129 1144 3.876914 GGCTACAATTTCGTCCATCATGA 59.123 43.478 0.00 0.00 0.00 3.07
1134 1149 4.340097 ACAATTTCGTCCATCATGATGCAT 59.660 37.500 27.24 0.00 37.49 3.96
1159 1174 6.072112 ACATCACACCTACAACATTCAAAC 57.928 37.500 0.00 0.00 0.00 2.93
1179 1194 7.450074 TCAAACTTATGCTCCGGTTCATATAT 58.550 34.615 15.46 7.42 0.00 0.86
1180 1195 7.387673 TCAAACTTATGCTCCGGTTCATATATG 59.612 37.037 15.46 6.36 0.00 1.78
1201 1216 2.367567 GCAGATGAATTGCCCATGGAAT 59.632 45.455 15.22 2.60 35.54 3.01
1203 1218 4.222145 GCAGATGAATTGCCCATGGAATAT 59.778 41.667 15.22 0.00 35.54 1.28
1229 1244 4.400884 GCATGAGGACTCTTCTACTGAGAA 59.599 45.833 0.00 0.00 39.47 2.87
1268 1283 1.502163 GCAGCTGATCGGTATGCACC 61.502 60.000 20.43 0.00 41.93 5.01
1327 1342 5.778241 TGGGAGAAAGTGTCTGTAGATACAA 59.222 40.000 10.70 0.00 38.44 2.41
1328 1343 6.100668 GGGAGAAAGTGTCTGTAGATACAAC 58.899 44.000 10.70 2.91 38.44 3.32
1346 1361 8.043710 AGATACAACTGCAACTATCTTAGCTTT 58.956 33.333 0.00 0.00 0.00 3.51
1366 1381 2.335316 TGCCGAAACCTACAACTGTT 57.665 45.000 0.00 0.00 0.00 3.16
1367 1382 1.944024 TGCCGAAACCTACAACTGTTG 59.056 47.619 18.44 18.44 0.00 3.33
1384 1399 4.142160 ACTGTTGGGAGTTGAAGAAAAAGC 60.142 41.667 0.00 0.00 0.00 3.51
1407 1422 4.377431 CGCATTGACTTCTTTGTAGTGGAC 60.377 45.833 0.00 0.00 0.00 4.02
1421 1436 6.539649 TGTAGTGGACGAAAATTTCAAGAG 57.460 37.500 6.53 0.00 0.00 2.85
1446 1461 4.576053 GCTATGTTCACTGATGGTTATGCA 59.424 41.667 0.00 0.00 0.00 3.96
1471 1486 5.678583 TGATGCTTCTGAAATTCCTAGAGG 58.321 41.667 0.88 0.00 0.00 3.69
1474 1489 5.248640 TGCTTCTGAAATTCCTAGAGGTTG 58.751 41.667 0.00 0.00 36.34 3.77
1499 1516 7.394359 TGTTGCTGAGCTAAAAAGAGGATTTAT 59.606 33.333 5.83 0.00 0.00 1.40
1582 1603 3.258123 GCATGGTGTTTTGGAGTATGGTT 59.742 43.478 0.00 0.00 0.00 3.67
1602 1623 5.954752 TGGTTGATGGTATTTGGCATCTTTA 59.045 36.000 0.00 0.00 0.00 1.85
1603 1624 6.610830 TGGTTGATGGTATTTGGCATCTTTAT 59.389 34.615 0.00 0.00 0.00 1.40
1604 1625 7.147976 GGTTGATGGTATTTGGCATCTTTATC 58.852 38.462 0.00 0.00 0.00 1.75
1605 1626 7.201902 GGTTGATGGTATTTGGCATCTTTATCA 60.202 37.037 0.00 0.00 0.00 2.15
1606 1627 7.894753 TGATGGTATTTGGCATCTTTATCAA 57.105 32.000 0.00 0.00 0.00 2.57
1607 1628 7.944061 TGATGGTATTTGGCATCTTTATCAAG 58.056 34.615 0.00 0.00 0.00 3.02
1608 1629 6.147864 TGGTATTTGGCATCTTTATCAAGC 57.852 37.500 0.00 0.00 0.00 4.01
1609 1630 5.655974 TGGTATTTGGCATCTTTATCAAGCA 59.344 36.000 0.00 0.00 0.00 3.91
1610 1631 6.183360 TGGTATTTGGCATCTTTATCAAGCAG 60.183 38.462 0.00 0.00 0.00 4.24
1611 1632 6.039717 GGTATTTGGCATCTTTATCAAGCAGA 59.960 38.462 0.00 0.00 0.00 4.26
1612 1633 5.571784 TTTGGCATCTTTATCAAGCAGAG 57.428 39.130 0.00 0.00 0.00 3.35
1613 1634 2.947652 TGGCATCTTTATCAAGCAGAGC 59.052 45.455 0.00 0.00 0.00 4.09
1614 1635 3.212685 GGCATCTTTATCAAGCAGAGCT 58.787 45.455 0.00 0.00 42.56 4.09
1615 1636 3.250521 GGCATCTTTATCAAGCAGAGCTC 59.749 47.826 5.27 5.27 38.25 4.09
1616 1637 3.059733 GCATCTTTATCAAGCAGAGCTCG 60.060 47.826 8.37 4.60 38.25 5.03
1617 1638 3.170791 TCTTTATCAAGCAGAGCTCGG 57.829 47.619 9.76 9.76 38.25 4.63
1618 1639 2.760650 TCTTTATCAAGCAGAGCTCGGA 59.239 45.455 18.66 7.70 38.25 4.55
1619 1640 2.879002 TTATCAAGCAGAGCTCGGAG 57.121 50.000 18.66 8.70 38.25 4.63
1620 1641 0.387202 TATCAAGCAGAGCTCGGAGC 59.613 55.000 22.13 22.13 38.25 4.70
1621 1642 2.308968 ATCAAGCAGAGCTCGGAGCC 62.309 60.000 25.49 16.77 43.77 4.70
1622 1643 2.683212 AAGCAGAGCTCGGAGCCT 60.683 61.111 25.49 18.64 43.77 4.58
1623 1644 3.016541 AAGCAGAGCTCGGAGCCTG 62.017 63.158 28.89 28.89 43.77 4.85
1624 1645 3.456365 GCAGAGCTCGGAGCCTGA 61.456 66.667 33.44 0.00 43.77 3.86
1625 1646 2.806929 CAGAGCTCGGAGCCTGAG 59.193 66.667 29.16 15.38 43.77 3.35
1626 1647 1.752310 CAGAGCTCGGAGCCTGAGA 60.752 63.158 29.16 0.00 43.77 3.27
1627 1648 1.108727 CAGAGCTCGGAGCCTGAGAT 61.109 60.000 29.16 13.14 43.77 2.75
1628 1649 0.396974 AGAGCTCGGAGCCTGAGATT 60.397 55.000 25.49 5.85 43.77 2.40
1629 1650 0.249405 GAGCTCGGAGCCTGAGATTG 60.249 60.000 25.49 0.00 43.77 2.67
1630 1651 1.886777 GCTCGGAGCCTGAGATTGC 60.887 63.158 19.20 0.00 34.48 3.56
1631 1652 1.519246 CTCGGAGCCTGAGATTGCA 59.481 57.895 5.37 0.00 35.43 4.08
1632 1653 0.106335 CTCGGAGCCTGAGATTGCAT 59.894 55.000 5.37 0.00 35.43 3.96
1633 1654 1.342496 CTCGGAGCCTGAGATTGCATA 59.658 52.381 5.37 0.00 35.43 3.14
1634 1655 1.762370 TCGGAGCCTGAGATTGCATAA 59.238 47.619 0.00 0.00 0.00 1.90
1635 1656 2.369860 TCGGAGCCTGAGATTGCATAAT 59.630 45.455 0.00 0.00 0.00 1.28
1636 1657 2.740981 CGGAGCCTGAGATTGCATAATC 59.259 50.000 0.00 0.00 42.44 1.75
1648 1669 6.530913 GATTGCATAATCTTCTTCGTAGCA 57.469 37.500 0.00 0.00 39.66 3.49
1649 1670 5.973651 TTGCATAATCTTCTTCGTAGCAG 57.026 39.130 0.00 0.00 0.00 4.24
1650 1671 5.011090 TGCATAATCTTCTTCGTAGCAGT 57.989 39.130 0.00 0.00 0.00 4.40
1651 1672 6.144078 TGCATAATCTTCTTCGTAGCAGTA 57.856 37.500 0.00 0.00 0.00 2.74
1652 1673 6.749139 TGCATAATCTTCTTCGTAGCAGTAT 58.251 36.000 0.00 0.00 0.00 2.12
1653 1674 7.210174 TGCATAATCTTCTTCGTAGCAGTATT 58.790 34.615 0.00 0.00 0.00 1.89
1654 1675 7.169813 TGCATAATCTTCTTCGTAGCAGTATTG 59.830 37.037 0.00 0.00 0.00 1.90
1655 1676 7.359598 GCATAATCTTCTTCGTAGCAGTATTGG 60.360 40.741 0.00 0.00 0.00 3.16
1656 1677 4.386867 TCTTCTTCGTAGCAGTATTGGG 57.613 45.455 0.00 0.00 0.00 4.12
1657 1678 2.596904 TCTTCGTAGCAGTATTGGGC 57.403 50.000 0.00 0.00 0.00 5.36
1658 1679 2.108168 TCTTCGTAGCAGTATTGGGCT 58.892 47.619 0.00 0.00 43.94 5.19
1659 1680 2.500098 TCTTCGTAGCAGTATTGGGCTT 59.500 45.455 0.00 0.00 41.41 4.35
1660 1681 3.702548 TCTTCGTAGCAGTATTGGGCTTA 59.297 43.478 0.00 0.00 41.41 3.09
1661 1682 3.728076 TCGTAGCAGTATTGGGCTTAG 57.272 47.619 0.00 0.00 41.41 2.18
1662 1683 3.028850 TCGTAGCAGTATTGGGCTTAGT 58.971 45.455 0.00 0.00 41.41 2.24
1663 1684 3.449737 TCGTAGCAGTATTGGGCTTAGTT 59.550 43.478 0.00 0.00 41.41 2.24
1664 1685 3.555956 CGTAGCAGTATTGGGCTTAGTTG 59.444 47.826 0.00 0.00 41.41 3.16
1665 1686 2.369394 AGCAGTATTGGGCTTAGTTGC 58.631 47.619 0.00 0.00 36.92 4.17
1666 1687 2.025887 AGCAGTATTGGGCTTAGTTGCT 60.026 45.455 0.00 0.00 36.92 3.91
1667 1688 3.199946 AGCAGTATTGGGCTTAGTTGCTA 59.800 43.478 0.00 0.00 36.92 3.49
1668 1689 3.312697 GCAGTATTGGGCTTAGTTGCTAC 59.687 47.826 0.00 0.00 0.00 3.58
1669 1690 4.770795 CAGTATTGGGCTTAGTTGCTACT 58.229 43.478 6.00 6.00 38.44 2.57
1670 1691 5.684030 GCAGTATTGGGCTTAGTTGCTACTA 60.684 44.000 3.76 3.76 35.78 1.82
1671 1692 6.346096 CAGTATTGGGCTTAGTTGCTACTAA 58.654 40.000 17.82 17.82 42.97 2.24
1683 1704 6.458232 AGTTGCTACTAAGGACTGATAGTG 57.542 41.667 0.00 0.00 34.37 2.74
1684 1705 6.188407 AGTTGCTACTAAGGACTGATAGTGA 58.812 40.000 0.00 0.00 34.37 3.41
1685 1706 6.836527 AGTTGCTACTAAGGACTGATAGTGAT 59.163 38.462 0.00 0.00 34.37 3.06
1686 1707 7.999545 AGTTGCTACTAAGGACTGATAGTGATA 59.000 37.037 0.00 0.00 34.37 2.15
1687 1708 8.630917 GTTGCTACTAAGGACTGATAGTGATAA 58.369 37.037 0.00 0.00 34.37 1.75
1688 1709 8.397575 TGCTACTAAGGACTGATAGTGATAAG 57.602 38.462 0.00 0.00 34.37 1.73
1689 1710 7.999545 TGCTACTAAGGACTGATAGTGATAAGT 59.000 37.037 0.00 0.00 34.37 2.24
1690 1711 8.293867 GCTACTAAGGACTGATAGTGATAAGTG 58.706 40.741 0.00 0.00 34.37 3.16
1691 1712 9.562408 CTACTAAGGACTGATAGTGATAAGTGA 57.438 37.037 0.00 0.00 34.37 3.41
1692 1713 8.458573 ACTAAGGACTGATAGTGATAAGTGAG 57.541 38.462 0.00 0.00 31.35 3.51
1693 1714 6.723298 AAGGACTGATAGTGATAAGTGAGG 57.277 41.667 0.00 0.00 25.22 3.86
1694 1715 5.772004 AGGACTGATAGTGATAAGTGAGGT 58.228 41.667 0.00 0.00 25.22 3.85
1695 1716 5.596361 AGGACTGATAGTGATAAGTGAGGTG 59.404 44.000 0.00 0.00 25.22 4.00
1696 1717 5.594725 GGACTGATAGTGATAAGTGAGGTGA 59.405 44.000 0.00 0.00 25.22 4.02
1697 1718 6.238897 GGACTGATAGTGATAAGTGAGGTGAG 60.239 46.154 0.00 0.00 25.22 3.51
1698 1719 5.596361 ACTGATAGTGATAAGTGAGGTGAGG 59.404 44.000 0.00 0.00 0.00 3.86
1699 1720 5.519808 TGATAGTGATAAGTGAGGTGAGGT 58.480 41.667 0.00 0.00 0.00 3.85
1700 1721 5.360999 TGATAGTGATAAGTGAGGTGAGGTG 59.639 44.000 0.00 0.00 0.00 4.00
1701 1722 2.834549 AGTGATAAGTGAGGTGAGGTGG 59.165 50.000 0.00 0.00 0.00 4.61
1702 1723 2.832129 GTGATAAGTGAGGTGAGGTGGA 59.168 50.000 0.00 0.00 0.00 4.02
1703 1724 3.099905 TGATAAGTGAGGTGAGGTGGAG 58.900 50.000 0.00 0.00 0.00 3.86
1704 1725 1.938585 TAAGTGAGGTGAGGTGGAGG 58.061 55.000 0.00 0.00 0.00 4.30
1705 1726 0.191064 AAGTGAGGTGAGGTGGAGGA 59.809 55.000 0.00 0.00 0.00 3.71
1706 1727 0.415429 AGTGAGGTGAGGTGGAGGAT 59.585 55.000 0.00 0.00 0.00 3.24
1707 1728 0.539051 GTGAGGTGAGGTGGAGGATG 59.461 60.000 0.00 0.00 0.00 3.51
1708 1729 0.117140 TGAGGTGAGGTGGAGGATGT 59.883 55.000 0.00 0.00 0.00 3.06
1709 1730 1.280457 GAGGTGAGGTGGAGGATGTT 58.720 55.000 0.00 0.00 0.00 2.71
1710 1731 2.225522 TGAGGTGAGGTGGAGGATGTTA 60.226 50.000 0.00 0.00 0.00 2.41
1711 1732 3.041946 GAGGTGAGGTGGAGGATGTTAT 58.958 50.000 0.00 0.00 0.00 1.89
1712 1733 3.041946 AGGTGAGGTGGAGGATGTTATC 58.958 50.000 0.00 0.00 0.00 1.75
1713 1734 2.771943 GGTGAGGTGGAGGATGTTATCA 59.228 50.000 0.00 0.00 0.00 2.15
1714 1735 3.181461 GGTGAGGTGGAGGATGTTATCAG 60.181 52.174 0.00 0.00 0.00 2.90
1715 1736 3.706594 GTGAGGTGGAGGATGTTATCAGA 59.293 47.826 0.00 0.00 0.00 3.27
1716 1737 4.346418 GTGAGGTGGAGGATGTTATCAGAT 59.654 45.833 0.00 0.00 0.00 2.90
1717 1738 5.540337 GTGAGGTGGAGGATGTTATCAGATA 59.460 44.000 0.00 0.00 0.00 1.98
1718 1739 6.042093 GTGAGGTGGAGGATGTTATCAGATAA 59.958 42.308 0.00 0.00 0.00 1.75
1719 1740 6.042093 TGAGGTGGAGGATGTTATCAGATAAC 59.958 42.308 22.03 22.03 44.13 1.89
1720 1741 6.146760 AGGTGGAGGATGTTATCAGATAACT 58.853 40.000 26.68 16.05 44.17 2.24
1721 1742 6.617371 AGGTGGAGGATGTTATCAGATAACTT 59.383 38.462 26.68 22.22 44.17 2.66
1722 1743 6.931840 GGTGGAGGATGTTATCAGATAACTTC 59.068 42.308 26.86 26.86 44.17 3.01
1816 1842 4.946160 ATCCAAAAGGTCTATGGTCCAA 57.054 40.909 0.00 0.00 35.66 3.53
1827 1853 5.304614 GGTCTATGGTCCAATACAAGCTCTA 59.695 44.000 0.00 0.00 0.00 2.43
1918 1959 5.855045 ACACCTAGCCTATTATTGTACTGC 58.145 41.667 0.00 0.00 0.00 4.40
1931 1973 1.377987 TACTGCCATCCAAACCGGC 60.378 57.895 0.00 0.00 46.43 6.13
1952 1994 3.127895 GCTGTAGATATCCTGAGCTACCG 59.872 52.174 0.00 0.00 33.92 4.02
1986 2028 2.627933 AGACCCAGTAACCAAAGGCTA 58.372 47.619 0.00 0.00 0.00 3.93
1991 2033 2.304761 CCAGTAACCAAAGGCTACCTGA 59.695 50.000 0.00 0.00 32.13 3.86
2043 2089 0.254178 AAGCAGTGGCCCTGTAGATG 59.746 55.000 18.80 1.83 43.55 2.90
2048 2094 1.291033 AGTGGCCCTGTAGATGACCTA 59.709 52.381 0.00 0.00 0.00 3.08
2105 2153 9.561069 AACCATATCATTTCTGTAGTTCCATAC 57.439 33.333 0.00 0.00 0.00 2.39
2166 2218 5.070714 TCTCGTAGTATTCTGCTCTACTCCT 59.929 44.000 0.00 0.00 33.94 3.69
2177 2229 2.738964 GCTCTACTCCTTTTAGCCACGG 60.739 54.545 0.00 0.00 0.00 4.94
2228 2280 7.184570 TGGAGGGCTGATATTAAAGGCTATATT 59.815 37.037 0.00 0.00 38.91 1.28
2239 2292 7.979444 TTAAAGGCTATATTAATTGAGCGCT 57.021 32.000 11.27 11.27 35.71 5.92
2263 2317 7.769044 GCTATAATAGTTTGACCAGAGGACAAA 59.231 37.037 9.08 9.08 42.75 2.83
2324 2378 4.373156 AGCAACATCTTTGACTACCCTT 57.627 40.909 0.00 0.00 0.00 3.95
2362 2417 6.483307 TGCCAAATTATCCTTAGTCAGAATCG 59.517 38.462 0.00 0.00 0.00 3.34
2370 2425 3.491792 CCTTAGTCAGAATCGCCTCCTTC 60.492 52.174 0.00 0.00 0.00 3.46
2379 2434 5.934781 AGAATCGCCTCCTTCTGAATAAAT 58.065 37.500 0.00 0.00 30.68 1.40
2464 2520 4.036971 CGGACCAGAGTCAATTAGGTCTAG 59.963 50.000 9.47 1.77 46.13 2.43
2483 2539 9.607333 AGGTCTAGATACATAGATTTCCATGAA 57.393 33.333 0.00 0.00 34.41 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 8.840833 TGCCTAAAAACTTTTTCAAAAAGAGT 57.159 26.923 26.15 12.39 0.00 3.24
405 419 2.224769 CCTTTAGCTCCTTGTGGGTTCA 60.225 50.000 0.00 0.00 36.25 3.18
438 452 3.068024 GTGGCAGATAGGACTTGAGAGAG 59.932 52.174 0.00 0.00 0.00 3.20
523 537 5.470047 AAGCTATCCTCTTTATACCCACG 57.530 43.478 0.00 0.00 0.00 4.94
532 546 7.229308 TGATATCATGCAAAGCTATCCTCTTT 58.771 34.615 0.00 0.00 34.37 2.52
561 575 3.190079 TCGCATGCACATCTCTTTAGTC 58.810 45.455 19.57 0.00 0.00 2.59
568 582 1.333881 GCAATCTCGCATGCACATCTC 60.334 52.381 19.57 0.00 42.12 2.75
569 583 0.661552 GCAATCTCGCATGCACATCT 59.338 50.000 19.57 0.00 42.12 2.90
570 584 0.379316 TGCAATCTCGCATGCACATC 59.621 50.000 19.57 0.05 46.87 3.06
571 585 2.484558 TGCAATCTCGCATGCACAT 58.515 47.368 19.57 2.65 46.87 3.21
572 586 3.984352 TGCAATCTCGCATGCACA 58.016 50.000 19.57 1.88 46.87 4.57
575 589 0.524816 CTTGGTGCAATCTCGCATGC 60.525 55.000 7.91 7.91 45.26 4.06
576 590 1.089112 TCTTGGTGCAATCTCGCATG 58.911 50.000 0.00 0.00 45.26 4.06
577 591 1.674441 CATCTTGGTGCAATCTCGCAT 59.326 47.619 0.00 0.00 45.26 4.73
578 592 1.089112 CATCTTGGTGCAATCTCGCA 58.911 50.000 0.00 0.00 40.32 5.10
579 593 1.089920 ACATCTTGGTGCAATCTCGC 58.910 50.000 0.00 0.00 0.00 5.03
580 594 2.079158 ACACATCTTGGTGCAATCTCG 58.921 47.619 0.00 0.00 42.55 4.04
581 595 4.232221 CAAACACATCTTGGTGCAATCTC 58.768 43.478 0.00 0.00 42.55 2.75
582 596 3.553508 GCAAACACATCTTGGTGCAATCT 60.554 43.478 0.00 0.00 42.55 2.40
583 597 2.733026 GCAAACACATCTTGGTGCAATC 59.267 45.455 0.00 0.00 42.55 2.67
584 598 2.102757 TGCAAACACATCTTGGTGCAAT 59.897 40.909 0.00 0.00 43.59 3.56
585 599 1.479730 TGCAAACACATCTTGGTGCAA 59.520 42.857 0.00 0.00 43.59 4.08
586 600 1.109609 TGCAAACACATCTTGGTGCA 58.890 45.000 0.00 0.00 44.05 4.57
587 601 1.490621 GTGCAAACACATCTTGGTGC 58.509 50.000 0.00 0.00 46.61 5.01
597 611 1.166531 AAGCCTCTCGGTGCAAACAC 61.167 55.000 0.00 0.00 46.66 3.32
598 612 0.465460 AAAGCCTCTCGGTGCAAACA 60.465 50.000 0.00 0.00 0.00 2.83
599 613 0.238553 GAAAGCCTCTCGGTGCAAAC 59.761 55.000 0.00 0.00 0.00 2.93
600 614 1.227999 CGAAAGCCTCTCGGTGCAAA 61.228 55.000 0.00 0.00 32.62 3.68
601 615 1.667830 CGAAAGCCTCTCGGTGCAA 60.668 57.895 0.00 0.00 32.62 4.08
602 616 2.048222 CGAAAGCCTCTCGGTGCA 60.048 61.111 0.00 0.00 32.62 4.57
603 617 0.741221 ATTCGAAAGCCTCTCGGTGC 60.741 55.000 0.00 0.00 36.93 5.01
604 618 1.134965 AGATTCGAAAGCCTCTCGGTG 60.135 52.381 0.00 0.00 36.93 4.94
605 619 1.187087 AGATTCGAAAGCCTCTCGGT 58.813 50.000 0.00 0.00 36.93 4.69
606 620 3.651803 ATAGATTCGAAAGCCTCTCGG 57.348 47.619 0.00 0.00 36.93 4.63
607 621 5.764131 AGTAATAGATTCGAAAGCCTCTCG 58.236 41.667 0.00 0.00 37.66 4.04
608 622 9.699703 ATTTAGTAATAGATTCGAAAGCCTCTC 57.300 33.333 0.00 0.00 0.00 3.20
622 636 9.842775 TCCGACTAGTCAGAATTTAGTAATAGA 57.157 33.333 22.37 1.82 0.00 1.98
625 639 8.968969 ACTTCCGACTAGTCAGAATTTAGTAAT 58.031 33.333 22.37 0.12 0.00 1.89
626 640 8.345724 ACTTCCGACTAGTCAGAATTTAGTAA 57.654 34.615 22.37 0.00 0.00 2.24
627 641 7.934855 ACTTCCGACTAGTCAGAATTTAGTA 57.065 36.000 22.37 0.00 0.00 1.82
628 642 6.837471 ACTTCCGACTAGTCAGAATTTAGT 57.163 37.500 22.37 13.21 0.00 2.24
629 643 7.432838 GCTAACTTCCGACTAGTCAGAATTTAG 59.567 40.741 31.24 31.24 39.56 1.85
630 644 7.094075 TGCTAACTTCCGACTAGTCAGAATTTA 60.094 37.037 22.37 21.69 0.00 1.40
631 645 6.100668 GCTAACTTCCGACTAGTCAGAATTT 58.899 40.000 22.37 21.73 0.00 1.82
632 646 5.185249 TGCTAACTTCCGACTAGTCAGAATT 59.815 40.000 22.37 13.74 0.00 2.17
633 647 4.705507 TGCTAACTTCCGACTAGTCAGAAT 59.294 41.667 22.37 11.10 0.00 2.40
634 648 4.077108 TGCTAACTTCCGACTAGTCAGAA 58.923 43.478 22.37 20.18 0.00 3.02
635 649 3.439476 GTGCTAACTTCCGACTAGTCAGA 59.561 47.826 22.37 14.04 0.00 3.27
636 650 3.190744 TGTGCTAACTTCCGACTAGTCAG 59.809 47.826 22.37 14.32 0.00 3.51
637 651 3.151554 TGTGCTAACTTCCGACTAGTCA 58.848 45.455 22.37 0.95 0.00 3.41
638 652 3.844577 TGTGCTAACTTCCGACTAGTC 57.155 47.619 13.18 13.18 0.00 2.59
639 653 3.130693 GGATGTGCTAACTTCCGACTAGT 59.869 47.826 0.00 0.00 39.91 2.57
640 654 3.491104 GGGATGTGCTAACTTCCGACTAG 60.491 52.174 5.11 0.00 46.77 2.57
641 655 2.429610 GGGATGTGCTAACTTCCGACTA 59.570 50.000 5.11 0.00 46.77 2.59
642 656 1.207329 GGGATGTGCTAACTTCCGACT 59.793 52.381 5.11 0.00 46.77 4.18
643 657 1.207329 AGGGATGTGCTAACTTCCGAC 59.793 52.381 5.11 0.00 46.77 4.79
644 658 1.568504 AGGGATGTGCTAACTTCCGA 58.431 50.000 5.11 0.00 46.77 4.55
645 659 3.753294 ATAGGGATGTGCTAACTTCCG 57.247 47.619 5.11 0.00 46.77 4.30
653 667 9.499369 AGTCAGAATTATATATAGGGATGTGCT 57.501 33.333 0.00 0.00 0.00 4.40
659 673 9.848710 CCGACTAGTCAGAATTATATATAGGGA 57.151 37.037 22.37 0.00 0.00 4.20
660 674 9.848710 TCCGACTAGTCAGAATTATATATAGGG 57.151 37.037 22.37 9.37 0.00 3.53
667 681 8.566260 GCTAACTTCCGACTAGTCAGAATTATA 58.434 37.037 22.37 13.34 0.00 0.98
668 682 7.068348 TGCTAACTTCCGACTAGTCAGAATTAT 59.932 37.037 22.37 12.98 0.00 1.28
669 683 6.376299 TGCTAACTTCCGACTAGTCAGAATTA 59.624 38.462 22.37 17.90 0.00 1.40
670 684 5.185249 TGCTAACTTCCGACTAGTCAGAATT 59.815 40.000 22.37 13.74 0.00 2.17
671 685 4.705507 TGCTAACTTCCGACTAGTCAGAAT 59.294 41.667 22.37 11.10 0.00 2.40
672 686 4.077108 TGCTAACTTCCGACTAGTCAGAA 58.923 43.478 22.37 20.18 0.00 3.02
673 687 3.439476 GTGCTAACTTCCGACTAGTCAGA 59.561 47.826 22.37 14.04 0.00 3.27
674 688 3.190744 TGTGCTAACTTCCGACTAGTCAG 59.809 47.826 22.37 14.32 0.00 3.51
675 689 3.151554 TGTGCTAACTTCCGACTAGTCA 58.848 45.455 22.37 0.95 0.00 3.41
676 690 3.844577 TGTGCTAACTTCCGACTAGTC 57.155 47.619 13.18 13.18 0.00 2.59
677 691 3.130693 GGATGTGCTAACTTCCGACTAGT 59.869 47.826 0.00 0.00 39.91 2.57
678 692 3.491104 GGGATGTGCTAACTTCCGACTAG 60.491 52.174 5.11 0.00 46.77 2.57
679 693 2.429610 GGGATGTGCTAACTTCCGACTA 59.570 50.000 5.11 0.00 46.77 2.59
680 694 1.207329 GGGATGTGCTAACTTCCGACT 59.793 52.381 5.11 0.00 46.77 4.18
681 695 1.207329 AGGGATGTGCTAACTTCCGAC 59.793 52.381 5.11 0.00 46.77 4.79
682 696 1.568504 AGGGATGTGCTAACTTCCGA 58.431 50.000 5.11 0.00 46.77 4.55
683 697 3.753294 ATAGGGATGTGCTAACTTCCG 57.247 47.619 5.11 0.00 46.77 4.30
692 706 9.197694 CGCTTCTAAATATATATAGGGATGTGC 57.802 37.037 0.00 0.00 0.00 4.57
713 727 8.463456 AATTAGTGAACTAAAGAGTACGCTTC 57.537 34.615 12.50 0.42 41.27 3.86
778 792 4.210120 CGTACAAGGAGAATATGAGCTTGC 59.790 45.833 0.00 0.00 0.00 4.01
780 794 4.372656 GCGTACAAGGAGAATATGAGCTT 58.627 43.478 0.00 0.00 0.00 3.74
817 831 2.109181 GCCGCTAGGTCATGTCCC 59.891 66.667 5.28 0.73 40.50 4.46
854 869 5.595885 TCTCTTTGCCTCTCTTATTCGATG 58.404 41.667 0.00 0.00 0.00 3.84
861 876 3.162666 TCCGTTCTCTTTGCCTCTCTTA 58.837 45.455 0.00 0.00 0.00 2.10
885 900 7.507956 TCAGATCTCATGGGAAATTTGCATATT 59.492 33.333 12.05 0.00 0.00 1.28
895 910 1.492176 GGGCTCAGATCTCATGGGAAA 59.508 52.381 0.00 0.00 0.00 3.13
924 939 5.450550 CGTTAGATCTAGACATGAGGCACAA 60.451 44.000 0.00 0.00 0.00 3.33
930 945 4.377943 CGGCTCGTTAGATCTAGACATGAG 60.378 50.000 14.18 14.18 0.00 2.90
933 948 2.226912 GCGGCTCGTTAGATCTAGACAT 59.773 50.000 2.02 0.00 0.00 3.06
938 953 1.337071 CCAAGCGGCTCGTTAGATCTA 59.663 52.381 1.45 0.00 0.00 1.98
944 959 2.740826 GCACCAAGCGGCTCGTTA 60.741 61.111 1.45 0.00 34.57 3.18
982 997 2.829720 GCATATCTGGTGATACGGGGTA 59.170 50.000 0.00 0.00 37.92 3.69
1092 1107 1.066430 GTAGCCTCCGACATTGAACCA 60.066 52.381 0.00 0.00 0.00 3.67
1104 1119 2.396590 TGGACGAAATTGTAGCCTCC 57.603 50.000 0.00 0.00 0.00 4.30
1116 1131 3.196939 TCATGCATCATGATGGACGAA 57.803 42.857 31.62 17.80 44.60 3.85
1129 1144 3.632643 TGTAGGTGTGATGTCATGCAT 57.367 42.857 0.00 0.00 41.24 3.96
1134 1149 4.967036 TGAATGTTGTAGGTGTGATGTCA 58.033 39.130 0.00 0.00 0.00 3.58
1147 1162 4.082787 CCGGAGCATAAGTTTGAATGTTGT 60.083 41.667 0.00 0.00 0.00 3.32
1159 1174 5.178061 TGCATATATGAACCGGAGCATAAG 58.822 41.667 17.10 10.53 31.43 1.73
1179 1194 1.116308 CCATGGGCAATTCATCTGCA 58.884 50.000 2.85 0.00 41.78 4.41
1180 1195 1.405872 TCCATGGGCAATTCATCTGC 58.594 50.000 13.02 0.00 39.16 4.26
1201 1216 5.534278 CAGTAGAAGAGTCCTCATGCTCATA 59.466 44.000 0.00 0.00 34.39 2.15
1203 1218 3.698539 CAGTAGAAGAGTCCTCATGCTCA 59.301 47.826 0.00 0.00 34.39 4.26
1229 1244 1.073897 GCAAGCAGGTCCTGGAACT 59.926 57.895 20.72 8.88 31.21 3.01
1268 1283 5.188194 CGCAAATAATCTTTAGTCGGTTCG 58.812 41.667 0.00 0.00 0.00 3.95
1270 1285 4.201881 GGCGCAAATAATCTTTAGTCGGTT 60.202 41.667 10.83 0.00 0.00 4.44
1327 1342 4.156739 GGCAAAAGCTAAGATAGTTGCAGT 59.843 41.667 8.29 0.00 42.38 4.40
1328 1343 4.666237 GGCAAAAGCTAAGATAGTTGCAG 58.334 43.478 8.29 0.00 42.38 4.41
1346 1361 2.335316 ACAGTTGTAGGTTTCGGCAA 57.665 45.000 0.00 0.00 0.00 4.52
1366 1381 1.336755 GCGCTTTTTCTTCAACTCCCA 59.663 47.619 0.00 0.00 0.00 4.37
1367 1382 1.336755 TGCGCTTTTTCTTCAACTCCC 59.663 47.619 9.73 0.00 0.00 4.30
1380 1395 3.715628 ACAAAGAAGTCAATGCGCTTT 57.284 38.095 9.73 5.65 0.00 3.51
1384 1399 3.745975 TCCACTACAAAGAAGTCAATGCG 59.254 43.478 0.00 0.00 0.00 4.73
1407 1422 5.567138 ACATAGCCCTCTTGAAATTTTCG 57.433 39.130 4.76 0.00 0.00 3.46
1421 1436 2.717639 ACCATCAGTGAACATAGCCC 57.282 50.000 0.00 0.00 0.00 5.19
1446 1461 6.771749 CCTCTAGGAATTTCAGAAGCATCAAT 59.228 38.462 0.00 0.00 37.39 2.57
1471 1486 4.275936 TCCTCTTTTTAGCTCAGCAACAAC 59.724 41.667 0.00 0.00 0.00 3.32
1474 1489 5.635417 AATCCTCTTTTTAGCTCAGCAAC 57.365 39.130 0.00 0.00 0.00 4.17
1582 1603 7.470424 GCTTGATAAAGATGCCAAATACCATCA 60.470 37.037 0.00 0.00 40.15 3.07
1602 1623 1.143620 GCTCCGAGCTCTGCTTGAT 59.856 57.895 13.42 0.00 42.27 2.57
1603 1624 2.575993 GCTCCGAGCTCTGCTTGA 59.424 61.111 13.42 0.00 42.27 3.02
1604 1625 2.511145 GGCTCCGAGCTCTGCTTG 60.511 66.667 19.68 0.06 41.99 4.01
1605 1626 2.683212 AGGCTCCGAGCTCTGCTT 60.683 61.111 19.68 7.06 41.99 3.91
1606 1627 3.459965 CAGGCTCCGAGCTCTGCT 61.460 66.667 19.68 5.75 41.99 4.24
1607 1628 3.429080 CTCAGGCTCCGAGCTCTGC 62.429 68.421 23.62 12.78 41.99 4.26
1608 1629 1.108727 ATCTCAGGCTCCGAGCTCTG 61.109 60.000 22.93 22.93 41.99 3.35
1609 1630 0.396974 AATCTCAGGCTCCGAGCTCT 60.397 55.000 19.68 12.15 41.99 4.09
1610 1631 0.249405 CAATCTCAGGCTCCGAGCTC 60.249 60.000 19.68 2.73 41.99 4.09
1611 1632 1.821936 CAATCTCAGGCTCCGAGCT 59.178 57.895 19.68 3.61 41.99 4.09
1612 1633 1.886777 GCAATCTCAGGCTCCGAGC 60.887 63.158 12.27 12.27 41.46 5.03
1613 1634 0.106335 ATGCAATCTCAGGCTCCGAG 59.894 55.000 0.00 0.00 0.00 4.63
1614 1635 1.413118 TATGCAATCTCAGGCTCCGA 58.587 50.000 0.00 0.00 0.00 4.55
1615 1636 2.245159 TTATGCAATCTCAGGCTCCG 57.755 50.000 0.00 0.00 0.00 4.63
1616 1637 4.018484 AGATTATGCAATCTCAGGCTCC 57.982 45.455 0.00 0.00 46.50 4.70
1625 1646 6.201806 ACTGCTACGAAGAAGATTATGCAATC 59.798 38.462 0.00 0.00 40.85 2.67
1626 1647 6.051717 ACTGCTACGAAGAAGATTATGCAAT 58.948 36.000 0.00 0.00 31.96 3.56
1627 1648 5.419542 ACTGCTACGAAGAAGATTATGCAA 58.580 37.500 0.00 0.00 31.96 4.08
1628 1649 5.011090 ACTGCTACGAAGAAGATTATGCA 57.989 39.130 0.00 0.00 31.96 3.96
1629 1650 7.359598 CCAATACTGCTACGAAGAAGATTATGC 60.360 40.741 0.00 0.00 31.96 3.14
1630 1651 7.116948 CCCAATACTGCTACGAAGAAGATTATG 59.883 40.741 0.00 0.00 31.96 1.90
1631 1652 7.155328 CCCAATACTGCTACGAAGAAGATTAT 58.845 38.462 0.00 0.00 31.96 1.28
1632 1653 6.513180 CCCAATACTGCTACGAAGAAGATTA 58.487 40.000 0.00 0.00 31.96 1.75
1633 1654 5.360591 CCCAATACTGCTACGAAGAAGATT 58.639 41.667 0.00 0.00 31.96 2.40
1634 1655 4.740934 GCCCAATACTGCTACGAAGAAGAT 60.741 45.833 0.00 0.00 31.96 2.40
1635 1656 3.430374 GCCCAATACTGCTACGAAGAAGA 60.430 47.826 0.00 0.00 31.96 2.87
1636 1657 2.866762 GCCCAATACTGCTACGAAGAAG 59.133 50.000 0.00 0.00 34.06 2.85
1637 1658 2.500098 AGCCCAATACTGCTACGAAGAA 59.500 45.455 0.00 0.00 35.69 2.52
1638 1659 2.108168 AGCCCAATACTGCTACGAAGA 58.892 47.619 0.00 0.00 35.69 2.87
1639 1660 2.604046 AGCCCAATACTGCTACGAAG 57.396 50.000 0.00 0.00 35.69 3.79
1640 1661 3.449737 ACTAAGCCCAATACTGCTACGAA 59.550 43.478 0.00 0.00 36.66 3.85
1641 1662 3.028850 ACTAAGCCCAATACTGCTACGA 58.971 45.455 0.00 0.00 36.66 3.43
1642 1663 3.454371 ACTAAGCCCAATACTGCTACG 57.546 47.619 0.00 0.00 36.66 3.51
1643 1664 3.312697 GCAACTAAGCCCAATACTGCTAC 59.687 47.826 0.00 0.00 36.66 3.58
1644 1665 3.199946 AGCAACTAAGCCCAATACTGCTA 59.800 43.478 0.00 0.00 37.14 3.49
1645 1666 2.025887 AGCAACTAAGCCCAATACTGCT 60.026 45.455 0.00 0.00 40.17 4.24
1646 1667 2.369394 AGCAACTAAGCCCAATACTGC 58.631 47.619 0.00 0.00 34.23 4.40
1647 1668 4.770795 AGTAGCAACTAAGCCCAATACTG 58.229 43.478 0.00 0.00 32.84 2.74
1648 1669 6.555463 TTAGTAGCAACTAAGCCCAATACT 57.445 37.500 0.00 0.00 42.09 2.12
1658 1679 7.832685 TCACTATCAGTCCTTAGTAGCAACTAA 59.167 37.037 0.00 0.00 44.19 2.24
1659 1680 7.344134 TCACTATCAGTCCTTAGTAGCAACTA 58.656 38.462 0.00 0.00 37.15 2.24
1660 1681 6.188407 TCACTATCAGTCCTTAGTAGCAACT 58.812 40.000 0.00 0.00 39.91 3.16
1661 1682 6.452494 TCACTATCAGTCCTTAGTAGCAAC 57.548 41.667 0.00 0.00 0.00 4.17
1662 1683 8.762481 TTATCACTATCAGTCCTTAGTAGCAA 57.238 34.615 0.00 0.00 0.00 3.91
1663 1684 7.999545 ACTTATCACTATCAGTCCTTAGTAGCA 59.000 37.037 0.00 0.00 0.00 3.49
1664 1685 8.293867 CACTTATCACTATCAGTCCTTAGTAGC 58.706 40.741 0.00 0.00 0.00 3.58
1665 1686 9.562408 TCACTTATCACTATCAGTCCTTAGTAG 57.438 37.037 0.00 0.00 0.00 2.57
1666 1687 9.562408 CTCACTTATCACTATCAGTCCTTAGTA 57.438 37.037 0.00 0.00 0.00 1.82
1667 1688 7.504238 CCTCACTTATCACTATCAGTCCTTAGT 59.496 40.741 0.00 0.00 0.00 2.24
1668 1689 7.504238 ACCTCACTTATCACTATCAGTCCTTAG 59.496 40.741 0.00 0.00 0.00 2.18
1669 1690 7.285629 CACCTCACTTATCACTATCAGTCCTTA 59.714 40.741 0.00 0.00 0.00 2.69
1670 1691 6.097554 CACCTCACTTATCACTATCAGTCCTT 59.902 42.308 0.00 0.00 0.00 3.36
1671 1692 5.596361 CACCTCACTTATCACTATCAGTCCT 59.404 44.000 0.00 0.00 0.00 3.85
1672 1693 5.594725 TCACCTCACTTATCACTATCAGTCC 59.405 44.000 0.00 0.00 0.00 3.85
1673 1694 6.238897 CCTCACCTCACTTATCACTATCAGTC 60.239 46.154 0.00 0.00 0.00 3.51
1674 1695 5.596361 CCTCACCTCACTTATCACTATCAGT 59.404 44.000 0.00 0.00 0.00 3.41
1675 1696 5.596361 ACCTCACCTCACTTATCACTATCAG 59.404 44.000 0.00 0.00 0.00 2.90
1676 1697 5.360999 CACCTCACCTCACTTATCACTATCA 59.639 44.000 0.00 0.00 0.00 2.15
1677 1698 5.221342 CCACCTCACCTCACTTATCACTATC 60.221 48.000 0.00 0.00 0.00 2.08
1678 1699 4.651503 CCACCTCACCTCACTTATCACTAT 59.348 45.833 0.00 0.00 0.00 2.12
1679 1700 4.023980 CCACCTCACCTCACTTATCACTA 58.976 47.826 0.00 0.00 0.00 2.74
1680 1701 2.834549 CCACCTCACCTCACTTATCACT 59.165 50.000 0.00 0.00 0.00 3.41
1681 1702 2.832129 TCCACCTCACCTCACTTATCAC 59.168 50.000 0.00 0.00 0.00 3.06
1682 1703 3.099905 CTCCACCTCACCTCACTTATCA 58.900 50.000 0.00 0.00 0.00 2.15
1683 1704 2.432510 CCTCCACCTCACCTCACTTATC 59.567 54.545 0.00 0.00 0.00 1.75
1684 1705 2.044492 TCCTCCACCTCACCTCACTTAT 59.956 50.000 0.00 0.00 0.00 1.73
1685 1706 1.431633 TCCTCCACCTCACCTCACTTA 59.568 52.381 0.00 0.00 0.00 2.24
1686 1707 0.191064 TCCTCCACCTCACCTCACTT 59.809 55.000 0.00 0.00 0.00 3.16
1687 1708 0.415429 ATCCTCCACCTCACCTCACT 59.585 55.000 0.00 0.00 0.00 3.41
1688 1709 0.539051 CATCCTCCACCTCACCTCAC 59.461 60.000 0.00 0.00 0.00 3.51
1689 1710 0.117140 ACATCCTCCACCTCACCTCA 59.883 55.000 0.00 0.00 0.00 3.86
1690 1711 1.280457 AACATCCTCCACCTCACCTC 58.720 55.000 0.00 0.00 0.00 3.85
1691 1712 2.642171 TAACATCCTCCACCTCACCT 57.358 50.000 0.00 0.00 0.00 4.00
1692 1713 2.771943 TGATAACATCCTCCACCTCACC 59.228 50.000 0.00 0.00 0.00 4.02
1693 1714 3.706594 TCTGATAACATCCTCCACCTCAC 59.293 47.826 0.00 0.00 0.00 3.51
1694 1715 3.994317 TCTGATAACATCCTCCACCTCA 58.006 45.455 0.00 0.00 0.00 3.86
1695 1716 6.268847 AGTTATCTGATAACATCCTCCACCTC 59.731 42.308 31.31 9.49 45.80 3.85
1696 1717 6.146760 AGTTATCTGATAACATCCTCCACCT 58.853 40.000 31.31 12.38 45.80 4.00
1697 1718 6.426646 AGTTATCTGATAACATCCTCCACC 57.573 41.667 31.31 10.06 45.80 4.61
1698 1719 7.731054 AGAAGTTATCTGATAACATCCTCCAC 58.269 38.462 31.31 14.15 45.80 4.02
1699 1720 7.921041 AGAAGTTATCTGATAACATCCTCCA 57.079 36.000 31.31 0.49 45.80 3.86
1700 1721 9.620259 AAAAGAAGTTATCTGATAACATCCTCC 57.380 33.333 31.31 17.78 45.80 4.30
1711 1732 9.726438 CTCCTTTCCTAAAAAGAAGTTATCTGA 57.274 33.333 0.00 0.00 38.79 3.27
1712 1733 8.951243 CCTCCTTTCCTAAAAAGAAGTTATCTG 58.049 37.037 0.00 0.00 38.79 2.90
1713 1734 8.891501 TCCTCCTTTCCTAAAAAGAAGTTATCT 58.108 33.333 0.00 0.00 41.32 1.98
1714 1735 9.688091 ATCCTCCTTTCCTAAAAAGAAGTTATC 57.312 33.333 0.00 0.00 0.00 1.75
1717 1738 9.298250 GTAATCCTCCTTTCCTAAAAAGAAGTT 57.702 33.333 0.00 0.00 0.00 2.66
1718 1739 7.889073 GGTAATCCTCCTTTCCTAAAAAGAAGT 59.111 37.037 0.00 0.00 0.00 3.01
1719 1740 8.110271 AGGTAATCCTCCTTTCCTAAAAAGAAG 58.890 37.037 0.00 0.00 40.58 2.85
1720 1741 7.996788 AGGTAATCCTCCTTTCCTAAAAAGAA 58.003 34.615 0.00 0.00 40.58 2.52
1721 1742 7.584396 AGGTAATCCTCCTTTCCTAAAAAGA 57.416 36.000 0.00 0.00 40.58 2.52
1772 1797 3.769300 ACTTTGCTTAATAAAGGGGCTGG 59.231 43.478 13.65 0.00 38.99 4.85
1931 1973 4.328536 ACGGTAGCTCAGGATATCTACAG 58.671 47.826 2.05 0.10 34.61 2.74
1986 2028 4.737578 TGTTACTCCTACAGAAGTCAGGT 58.262 43.478 0.00 0.00 0.00 4.00
1991 2033 5.307196 ACATGGTTGTTACTCCTACAGAAGT 59.693 40.000 0.00 0.00 29.55 3.01
2064 2112 9.840427 AATGATATGGTTTTTAAGAGACAAACG 57.160 29.630 0.00 0.00 32.18 3.60
2105 2153 3.696051 AGTATGCACATTACTTTGGGCTG 59.304 43.478 0.00 0.00 46.43 4.85
2155 2207 2.094182 CGTGGCTAAAAGGAGTAGAGCA 60.094 50.000 0.00 0.00 34.76 4.26
2166 2218 2.217510 TATTTGGGCCGTGGCTAAAA 57.782 45.000 11.25 11.63 41.60 1.52
2177 2229 9.248291 CAAATAGTATTCACATGTTATTTGGGC 57.752 33.333 20.78 1.38 36.00 5.36
2228 2280 7.929245 TGGTCAAACTATTATAGCGCTCAATTA 59.071 33.333 16.34 0.00 0.00 1.40
2239 2292 9.613428 CATTTGTCCTCTGGTCAAACTATTATA 57.387 33.333 10.21 0.00 41.66 0.98
2251 2305 4.263243 CCTCTTTCTCATTTGTCCTCTGGT 60.263 45.833 0.00 0.00 0.00 4.00
2263 2317 9.793259 TGAAACTATTAAACACCTCTTTCTCAT 57.207 29.630 0.00 0.00 0.00 2.90
2299 2353 5.598417 AGGGTAGTCAAAGATGTTGCTTTTT 59.402 36.000 0.00 0.00 36.01 1.94
2324 2378 3.951775 ATTTGGCAAAGCGTAATTGGA 57.048 38.095 18.61 0.00 0.00 3.53
2362 2417 5.824624 TCATGTGATTTATTCAGAAGGAGGC 59.175 40.000 0.00 0.00 34.17 4.70
2379 2434 5.578336 CGCTAAGAATCAAGTCTTCATGTGA 59.422 40.000 0.00 0.00 38.75 3.58
2437 2493 4.960469 ACCTAATTGACTCTGGTCCGATTA 59.040 41.667 0.00 0.00 41.47 1.75


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

AutoCloner maintained by Alex Coulton.