Multiple sequence alignment - TraesCS2A01G213900

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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 TraesCS2A01G213900 chr2A 100.000 6036 0 0 1 6036 199587660 199581625 0.000000e+00 11147
1 TraesCS2A01G213900 chr2D 95.302 2618 89 13 719 3320 186964590 186961991 0.000000e+00 4122
2 TraesCS2A01G213900 chr2D 95.299 1489 46 4 4513 5978 186960861 186959374 0.000000e+00 2340
3 TraesCS2A01G213900 chr2D 95.280 1144 33 11 3348 4480 186961992 186960859 0.000000e+00 1794
4 TraesCS2A01G213900 chr2D 85.812 585 68 7 1 581 569414485 569415058 1.860000e-169 606
5 TraesCS2A01G213900 chr2D 85.940 569 66 8 8 572 333832845 333832287 4.030000e-166 595
6 TraesCS2A01G213900 chr2B 94.309 1599 50 19 4295 5868 240309867 240308285 0.000000e+00 2410
7 TraesCS2A01G213900 chr2B 97.063 1362 38 1 729 2090 240319422 240318063 0.000000e+00 2292
8 TraesCS2A01G213900 chr2B 95.752 1224 30 6 2083 3292 240317303 240316088 0.000000e+00 1953
9 TraesCS2A01G213900 chr2B 95.951 494 11 5 3350 3834 240315921 240315428 0.000000e+00 793
10 TraesCS2A01G213900 chr2B 96.008 476 18 1 3827 4302 240310537 240310063 0.000000e+00 773
11 TraesCS2A01G213900 chr2B 91.065 582 37 9 1 580 240320742 240320174 0.000000e+00 773
12 TraesCS2A01G213900 chr2B 93.789 161 4 3 5832 5991 240308268 240308113 2.810000e-58 237
13 TraesCS2A01G213900 chr2B 85.047 107 16 0 622 728 72500395 72500289 6.400000e-20 110
14 TraesCS2A01G213900 chr3B 86.426 582 63 10 1 577 547483189 547483759 1.850000e-174 623
15 TraesCS2A01G213900 chr3B 84.854 581 66 13 8 577 392632448 392631879 3.160000e-157 566
16 TraesCS2A01G213900 chr1D 86.632 576 62 11 1 572 269015637 269016201 1.850000e-174 623
17 TraesCS2A01G213900 chr1D 89.320 103 11 0 622 724 781044 781146 4.910000e-26 130
18 TraesCS2A01G213900 chr1A 85.788 584 70 7 1 580 412210878 412210304 1.860000e-169 606
19 TraesCS2A01G213900 chr1B 85.864 573 67 8 2 570 376115014 376115576 1.120000e-166 597
20 TraesCS2A01G213900 chr3D 84.734 583 65 18 8 577 297590149 297589578 4.080000e-156 562
21 TraesCS2A01G213900 chr7A 83.030 165 17 2 580 733 5749750 5749586 8.160000e-29 139
22 TraesCS2A01G213900 chr4A 82.317 164 17 6 573 725 165057371 165057533 1.370000e-26 132
23 TraesCS2A01G213900 chrUn 89.320 103 11 0 622 724 283087131 283087233 4.910000e-26 130
24 TraesCS2A01G213900 chr6D 88.679 106 10 2 622 726 427618375 427618479 1.770000e-25 128
25 TraesCS2A01G213900 chr5A 88.350 103 12 0 622 724 521761105 521761003 2.280000e-24 124
26 TraesCS2A01G213900 chr7D 87.379 103 9 4 622 723 62641948 62642047 1.370000e-21 115
27 TraesCS2A01G213900 chr3A 87.629 97 12 0 622 718 45563660 45563564 4.940000e-21 113


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 TraesCS2A01G213900 chr2A 199581625 199587660 6035 True 11147.00 11147 100.000000 1 6036 1 chr2A.!!$R1 6035
1 TraesCS2A01G213900 chr2D 186959374 186964590 5216 True 2752.00 4122 95.293667 719 5978 3 chr2D.!!$R2 5259
2 TraesCS2A01G213900 chr2D 569414485 569415058 573 False 606.00 606 85.812000 1 581 1 chr2D.!!$F1 580
3 TraesCS2A01G213900 chr2D 333832287 333832845 558 True 595.00 595 85.940000 8 572 1 chr2D.!!$R1 564
4 TraesCS2A01G213900 chr2B 240315428 240320742 5314 True 1452.75 2292 94.957750 1 3834 4 chr2B.!!$R3 3833
5 TraesCS2A01G213900 chr2B 240308113 240310537 2424 True 1140.00 2410 94.702000 3827 5991 3 chr2B.!!$R2 2164
6 TraesCS2A01G213900 chr3B 547483189 547483759 570 False 623.00 623 86.426000 1 577 1 chr3B.!!$F1 576
7 TraesCS2A01G213900 chr3B 392631879 392632448 569 True 566.00 566 84.854000 8 577 1 chr3B.!!$R1 569
8 TraesCS2A01G213900 chr1D 269015637 269016201 564 False 623.00 623 86.632000 1 572 1 chr1D.!!$F2 571
9 TraesCS2A01G213900 chr1A 412210304 412210878 574 True 606.00 606 85.788000 1 580 1 chr1A.!!$R1 579
10 TraesCS2A01G213900 chr1B 376115014 376115576 562 False 597.00 597 85.864000 2 570 1 chr1B.!!$F1 568
11 TraesCS2A01G213900 chr3D 297589578 297590149 571 True 562.00 562 84.734000 8 577 1 chr3D.!!$R1 569

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
592 611 1.053048 CGTGACGATCGATGTATGCC 58.947 55.000 24.34 0.00 0.00 4.40 F
716 799 1.061033 AGAGGGAGGTGGGCAATATCT 60.061 52.381 0.00 0.00 0.00 1.98 F
1300 1924 1.064825 TCCCTTCCTTCCTCACCAAC 58.935 55.000 0.00 0.00 0.00 3.77 F
2464 3860 0.181114 AGTCTGGTGAAAGTGCTGCA 59.819 50.000 0.00 0.00 0.00 4.41 F
2940 4339 0.312102 TCATCAGCTAGTGCCGATCG 59.688 55.000 8.51 8.51 34.39 3.69 F
3878 5401 1.547372 CTGCCAATTTAGCTGTTGCCT 59.453 47.619 0.00 0.00 40.80 4.75 F
4719 6453 0.316278 CCTACACGACGCGATGAGAG 60.316 60.000 15.93 10.55 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 2041 0.554305 TACCCGGTCCAGATCTAGCA 59.446 55.000 0.00 0.00 0.00 3.49 R
1786 2410 1.228552 CACTGGTTCCACCCCCTTG 60.229 63.158 0.00 0.00 37.50 3.61 R
2742 4141 1.063912 TGCAAACAAACAGAGCAGACG 59.936 47.619 0.00 0.00 0.00 4.18 R
4102 5626 1.025113 CCGTCTAGCAGTCCTCACGA 61.025 60.000 0.00 0.00 33.81 4.35 R
4103 5627 1.429825 CCGTCTAGCAGTCCTCACG 59.570 63.158 0.00 0.00 32.48 4.35 R
4982 6716 0.951558 GAGTGCAATGTCCCGTTGTT 59.048 50.000 0.00 0.00 33.39 2.83 R
5980 7806 1.133253 CGACTGTGCTGCATTTCGG 59.867 57.895 17.52 8.74 32.20 4.30 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
35 38 5.612925 CGTCAAAATGTGCATGGTTGATTTG 60.613 40.000 11.96 6.62 32.08 2.32
131 138 2.705658 TGGGACTTCACATTCTCACAGT 59.294 45.455 0.00 0.00 0.00 3.55
159 166 9.926751 GTGATCCATATATTAAAATGAGCATCG 57.073 33.333 0.00 0.00 38.61 3.84
169 176 7.974243 TTAAAATGAGCATCGAAATGACATG 57.026 32.000 0.00 0.00 38.61 3.21
280 287 3.062763 CTGTGAAGACAGCGATGACTTT 58.937 45.455 18.63 4.48 43.24 2.66
334 343 3.177997 TGTTGCTTCTTTTCAAAGCCC 57.822 42.857 5.48 0.00 46.81 5.19
339 348 2.548707 GCTTCTTTTCAAAGCCCTTGGG 60.549 50.000 0.32 0.32 42.63 4.12
353 363 1.539157 CTTGGGTTTTCTCTCCTGGC 58.461 55.000 0.00 0.00 0.00 4.85
560 579 5.419471 TGAATCATGTGATGAGATGCCAAAA 59.581 36.000 0.00 0.00 43.53 2.44
565 584 4.334552 TGTGATGAGATGCCAAAAGCTTA 58.665 39.130 0.00 0.00 44.23 3.09
577 596 5.163642 TGCCAAAAGCTTAAAAGTAACGTGA 60.164 36.000 0.00 0.00 44.23 4.35
581 600 6.535274 AAAGCTTAAAAGTAACGTGACGAT 57.465 33.333 13.70 1.21 0.00 3.73
582 601 5.758570 AGCTTAAAAGTAACGTGACGATC 57.241 39.130 13.70 1.13 0.00 3.69
585 604 5.004156 GCTTAAAAGTAACGTGACGATCGAT 59.996 40.000 24.34 5.96 0.00 3.59
586 605 4.817987 AAAAGTAACGTGACGATCGATG 57.182 40.909 24.34 8.37 0.00 3.84
588 607 4.604843 AAGTAACGTGACGATCGATGTA 57.395 40.909 24.34 1.52 0.00 2.29
590 609 4.524749 AGTAACGTGACGATCGATGTATG 58.475 43.478 24.34 11.90 0.00 2.39
591 610 1.755161 ACGTGACGATCGATGTATGC 58.245 50.000 24.34 3.57 0.00 3.14
592 611 1.053048 CGTGACGATCGATGTATGCC 58.947 55.000 24.34 0.00 0.00 4.40
593 612 1.599419 CGTGACGATCGATGTATGCCA 60.599 52.381 24.34 3.46 0.00 4.92
595 614 1.407258 TGACGATCGATGTATGCCACA 59.593 47.619 24.34 3.19 42.69 4.17
596 615 2.054363 GACGATCGATGTATGCCACAG 58.946 52.381 24.34 0.00 41.51 3.66
600 619 3.366121 CGATCGATGTATGCCACAGAATC 59.634 47.826 10.26 0.00 41.51 2.52
601 620 2.742774 TCGATGTATGCCACAGAATCG 58.257 47.619 0.00 0.00 41.51 3.34
603 622 2.866156 CGATGTATGCCACAGAATCGTT 59.134 45.455 0.00 0.00 41.51 3.85
605 624 4.201812 CGATGTATGCCACAGAATCGTTTT 60.202 41.667 0.00 0.00 41.51 2.43
606 625 5.006261 CGATGTATGCCACAGAATCGTTTTA 59.994 40.000 0.00 0.00 41.51 1.52
607 626 6.292865 CGATGTATGCCACAGAATCGTTTTAT 60.293 38.462 0.00 0.00 41.51 1.40
608 627 6.751514 TGTATGCCACAGAATCGTTTTATT 57.248 33.333 0.00 0.00 31.89 1.40
609 628 7.851387 TGTATGCCACAGAATCGTTTTATTA 57.149 32.000 0.00 0.00 31.89 0.98
610 629 8.270080 TGTATGCCACAGAATCGTTTTATTAA 57.730 30.769 0.00 0.00 31.89 1.40
611 630 8.898761 TGTATGCCACAGAATCGTTTTATTAAT 58.101 29.630 0.00 0.00 31.89 1.40
614 633 8.500753 TGCCACAGAATCGTTTTATTAATACT 57.499 30.769 0.00 0.00 0.00 2.12
615 634 8.394877 TGCCACAGAATCGTTTTATTAATACTG 58.605 33.333 0.00 0.00 0.00 2.74
616 635 7.376072 GCCACAGAATCGTTTTATTAATACTGC 59.624 37.037 0.00 0.00 0.00 4.40
617 636 7.582679 CCACAGAATCGTTTTATTAATACTGCG 59.417 37.037 0.00 0.69 0.00 5.18
621 640 8.120465 AGAATCGTTTTATTAATACTGCGTTGG 58.880 33.333 0.00 0.00 0.00 3.77
622 641 6.964741 TCGTTTTATTAATACTGCGTTGGA 57.035 33.333 0.00 0.00 0.00 3.53
623 642 7.361889 TCGTTTTATTAATACTGCGTTGGAA 57.638 32.000 0.00 0.00 0.00 3.53
625 644 7.118101 TCGTTTTATTAATACTGCGTTGGAACT 59.882 33.333 0.00 0.00 0.00 3.01
626 645 7.747357 CGTTTTATTAATACTGCGTTGGAACTT 59.253 33.333 0.00 0.00 0.00 2.66
630 649 9.656040 TTATTAATACTGCGTTGGAACTTAAGA 57.344 29.630 10.09 0.00 0.00 2.10
631 650 5.857822 AATACTGCGTTGGAACTTAAGAC 57.142 39.130 10.09 2.77 0.00 3.01
632 651 3.470645 ACTGCGTTGGAACTTAAGACT 57.529 42.857 10.09 0.00 0.00 3.24
634 653 3.808174 ACTGCGTTGGAACTTAAGACTTC 59.192 43.478 10.09 3.35 0.00 3.01
635 654 4.058817 CTGCGTTGGAACTTAAGACTTCT 58.941 43.478 10.09 0.00 0.00 2.85
637 656 4.272504 TGCGTTGGAACTTAAGACTTCTTG 59.727 41.667 10.09 0.00 37.40 3.02
638 657 4.319549 GCGTTGGAACTTAAGACTTCTTGG 60.320 45.833 10.09 0.00 37.40 3.61
639 658 4.319549 CGTTGGAACTTAAGACTTCTTGGC 60.320 45.833 10.09 0.00 37.40 4.52
640 659 4.706842 TGGAACTTAAGACTTCTTGGCT 57.293 40.909 10.09 0.00 37.40 4.75
641 660 4.642429 TGGAACTTAAGACTTCTTGGCTC 58.358 43.478 10.09 0.00 37.40 4.70
642 661 4.102524 TGGAACTTAAGACTTCTTGGCTCA 59.897 41.667 10.09 0.00 37.40 4.26
644 663 5.511545 GGAACTTAAGACTTCTTGGCTCAGA 60.512 44.000 10.09 0.00 37.40 3.27
645 664 5.753721 ACTTAAGACTTCTTGGCTCAGAT 57.246 39.130 10.09 0.00 37.40 2.90
646 665 6.859112 ACTTAAGACTTCTTGGCTCAGATA 57.141 37.500 10.09 0.00 37.40 1.98
648 667 4.479786 AAGACTTCTTGGCTCAGATACC 57.520 45.455 0.00 0.00 34.38 2.73
649 668 3.445008 AGACTTCTTGGCTCAGATACCA 58.555 45.455 0.00 0.00 0.00 3.25
651 670 5.211973 AGACTTCTTGGCTCAGATACCATA 58.788 41.667 0.00 0.00 35.42 2.74
652 671 5.843421 AGACTTCTTGGCTCAGATACCATAT 59.157 40.000 0.00 0.00 35.42 1.78
655 674 6.100279 ACTTCTTGGCTCAGATACCATATTGA 59.900 38.462 0.00 0.00 35.42 2.57
657 740 7.083062 TCTTGGCTCAGATACCATATTGAAT 57.917 36.000 0.00 0.00 35.42 2.57
659 742 7.663081 TCTTGGCTCAGATACCATATTGAATTC 59.337 37.037 0.00 0.00 35.42 2.17
662 745 7.392393 TGGCTCAGATACCATATTGAATTCATG 59.608 37.037 9.40 4.74 0.00 3.07
666 749 8.570488 TCAGATACCATATTGAATTCATGTTGC 58.430 33.333 9.40 0.00 0.00 4.17
668 751 9.085645 AGATACCATATTGAATTCATGTTGCAT 57.914 29.630 9.40 1.06 0.00 3.96
684 767 5.834239 GTTGCATCCAACTCATTCAAAAG 57.166 39.130 0.00 0.00 46.13 2.27
686 769 5.125100 TGCATCCAACTCATTCAAAAGTC 57.875 39.130 0.00 0.00 0.00 3.01
688 771 4.726416 CATCCAACTCATTCAAAAGTCCG 58.274 43.478 0.00 0.00 0.00 4.79
689 772 4.079980 TCCAACTCATTCAAAAGTCCGA 57.920 40.909 0.00 0.00 0.00 4.55
692 775 4.275936 CCAACTCATTCAAAAGTCCGAACT 59.724 41.667 0.00 0.00 37.32 3.01
693 776 5.468746 CCAACTCATTCAAAAGTCCGAACTA 59.531 40.000 0.00 0.00 33.48 2.24
694 777 6.149474 CCAACTCATTCAAAAGTCCGAACTAT 59.851 38.462 0.00 0.00 33.48 2.12
696 779 8.717821 CAACTCATTCAAAAGTCCGAACTATTA 58.282 33.333 0.00 0.00 33.48 0.98
697 780 8.480643 ACTCATTCAAAAGTCCGAACTATTAG 57.519 34.615 0.00 0.00 33.48 1.73
698 781 8.311836 ACTCATTCAAAAGTCCGAACTATTAGA 58.688 33.333 0.00 0.00 33.48 2.10
699 782 8.703604 TCATTCAAAAGTCCGAACTATTAGAG 57.296 34.615 0.00 0.00 33.48 2.43
700 783 7.764443 TCATTCAAAAGTCCGAACTATTAGAGG 59.236 37.037 0.00 0.00 33.48 3.69
701 784 5.974108 TCAAAAGTCCGAACTATTAGAGGG 58.026 41.667 0.00 0.00 33.48 4.30
702 785 5.718130 TCAAAAGTCCGAACTATTAGAGGGA 59.282 40.000 0.00 0.00 33.48 4.20
703 786 5.855740 AAAGTCCGAACTATTAGAGGGAG 57.144 43.478 0.00 0.00 33.48 4.30
704 787 3.834938 AGTCCGAACTATTAGAGGGAGG 58.165 50.000 0.00 0.00 32.59 4.30
705 788 3.204831 AGTCCGAACTATTAGAGGGAGGT 59.795 47.826 0.00 0.00 32.59 3.85
706 789 3.318557 GTCCGAACTATTAGAGGGAGGTG 59.681 52.174 0.00 0.00 0.00 4.00
708 791 2.628657 CGAACTATTAGAGGGAGGTGGG 59.371 54.545 0.00 0.00 0.00 4.61
709 792 2.104669 ACTATTAGAGGGAGGTGGGC 57.895 55.000 0.00 0.00 0.00 5.36
710 793 1.294068 ACTATTAGAGGGAGGTGGGCA 59.706 52.381 0.00 0.00 0.00 5.36
711 794 2.293586 ACTATTAGAGGGAGGTGGGCAA 60.294 50.000 0.00 0.00 0.00 4.52
712 795 1.912862 ATTAGAGGGAGGTGGGCAAT 58.087 50.000 0.00 0.00 0.00 3.56
713 796 2.579624 TTAGAGGGAGGTGGGCAATA 57.420 50.000 0.00 0.00 0.00 1.90
714 797 2.815357 TAGAGGGAGGTGGGCAATAT 57.185 50.000 0.00 0.00 0.00 1.28
715 798 1.439543 AGAGGGAGGTGGGCAATATC 58.560 55.000 0.00 0.00 0.00 1.63
716 799 1.061033 AGAGGGAGGTGGGCAATATCT 60.061 52.381 0.00 0.00 0.00 1.98
717 800 1.777272 GAGGGAGGTGGGCAATATCTT 59.223 52.381 0.00 0.00 0.00 2.40
719 802 2.175715 AGGGAGGTGGGCAATATCTTTC 59.824 50.000 0.00 0.00 0.00 2.62
720 803 2.091885 GGGAGGTGGGCAATATCTTTCA 60.092 50.000 0.00 0.00 0.00 2.69
721 804 3.627237 GGGAGGTGGGCAATATCTTTCAA 60.627 47.826 0.00 0.00 0.00 2.69
722 805 3.381590 GGAGGTGGGCAATATCTTTCAAC 59.618 47.826 0.00 0.00 0.00 3.18
723 806 4.016444 GAGGTGGGCAATATCTTTCAACA 58.984 43.478 0.00 0.00 0.00 3.33
724 807 3.763897 AGGTGGGCAATATCTTTCAACAC 59.236 43.478 0.00 0.00 0.00 3.32
726 809 4.021544 GGTGGGCAATATCTTTCAACACAA 60.022 41.667 0.00 0.00 0.00 3.33
727 810 5.163513 GTGGGCAATATCTTTCAACACAAG 58.836 41.667 0.00 0.00 0.00 3.16
779 1401 6.884280 AAACAACCCTCAGTTATCTTTCTG 57.116 37.500 0.00 0.00 36.18 3.02
780 1402 4.327680 ACAACCCTCAGTTATCTTTCTGC 58.672 43.478 0.00 0.00 36.18 4.26
812 1434 2.231964 ACGATGCGAGTTACCCAAAGTA 59.768 45.455 0.00 0.00 0.00 2.24
1120 1744 1.077805 CCCCAAACCCTAACCCCAC 59.922 63.158 0.00 0.00 0.00 4.61
1150 1774 2.088763 CACCGTGCTGTAGCTGACG 61.089 63.158 5.38 7.49 42.66 4.35
1300 1924 1.064825 TCCCTTCCTTCCTCACCAAC 58.935 55.000 0.00 0.00 0.00 3.77
1686 2310 1.202604 TGGAACGAGAGGGTTTGACAC 60.203 52.381 0.00 0.00 0.00 3.67
1786 2410 2.690778 GCTGGACGTTGCCATGGAC 61.691 63.158 18.40 7.64 37.30 4.02
1792 2416 2.342650 CGTTGCCATGGACAAGGGG 61.343 63.158 18.40 7.82 31.09 4.79
1930 2554 4.323028 CCTGCACCATCACCTACCTATATG 60.323 50.000 0.00 0.00 0.00 1.78
1950 2574 3.445008 TGGAAGAGAAGCAGGTGACTAT 58.555 45.455 0.00 0.00 40.21 2.12
1959 2583 5.896678 AGAAGCAGGTGACTATATCTGTTCT 59.103 40.000 0.00 0.00 40.21 3.01
1960 2584 6.382570 AGAAGCAGGTGACTATATCTGTTCTT 59.617 38.462 0.00 0.00 40.21 2.52
1961 2585 6.552445 AGCAGGTGACTATATCTGTTCTTT 57.448 37.500 0.00 0.00 40.21 2.52
2015 2639 1.359130 AGATGGCCCTTTAACCTTGCT 59.641 47.619 0.00 0.00 0.00 3.91
2021 2645 2.593026 CCCTTTAACCTTGCTTGGTGA 58.407 47.619 2.12 0.00 40.73 4.02
2038 2662 2.303311 GGTGACACCTTTCTTCCTAGCT 59.697 50.000 17.84 0.00 34.73 3.32
2272 3668 3.066900 TCCGTGGTGGTTTAACAATTGTG 59.933 43.478 12.82 0.00 39.52 3.33
2350 3746 1.723870 GCGCCAGAATGTGATGGTC 59.276 57.895 0.00 0.00 38.91 4.02
2464 3860 0.181114 AGTCTGGTGAAAGTGCTGCA 59.819 50.000 0.00 0.00 0.00 4.41
2507 3903 4.500603 AGCTTCTCATTTTGCTCTTGTG 57.499 40.909 0.00 0.00 0.00 3.33
2739 4138 0.667453 TGCGCAACTTTGATGCAGAA 59.333 45.000 8.16 0.00 44.01 3.02
2742 4141 2.343544 GCGCAACTTTGATGCAGAATTC 59.656 45.455 0.30 0.00 44.01 2.17
2766 4165 4.023707 GTCTGCTCTGTTTGTTTGCACTAT 60.024 41.667 0.00 0.00 0.00 2.12
2820 4219 8.082242 GGCAGATCAAAATAACACCCAATATAC 58.918 37.037 0.00 0.00 0.00 1.47
2821 4220 8.850156 GCAGATCAAAATAACACCCAATATACT 58.150 33.333 0.00 0.00 0.00 2.12
2908 4307 2.358898 ACACACCTGTCTTGCATTTCAC 59.641 45.455 0.00 0.00 0.00 3.18
2909 4308 2.358582 CACACCTGTCTTGCATTTCACA 59.641 45.455 0.00 0.00 0.00 3.58
2940 4339 0.312102 TCATCAGCTAGTGCCGATCG 59.688 55.000 8.51 8.51 34.39 3.69
3037 4443 8.918961 TTTAAACATTTTAATACCATGCGGAG 57.081 30.769 0.00 0.00 35.59 4.63
3049 4455 3.131396 CCATGCGGAGGAGTTTATGTAC 58.869 50.000 0.00 0.00 0.00 2.90
3190 4596 7.432059 GGTGTCTGTAATAGTAGAATGGTACC 58.568 42.308 4.43 4.43 0.00 3.34
3234 4640 3.288092 GTTTACAACATCCCCATCCCTC 58.712 50.000 0.00 0.00 0.00 4.30
3292 4698 6.876257 CCCTATATACTGGTGCTGAATTTCTC 59.124 42.308 0.00 0.00 0.00 2.87
3334 4740 7.775397 GCAATATGCATTTAACTGGTTTGAT 57.225 32.000 3.54 0.00 44.26 2.57
3335 4741 8.870160 GCAATATGCATTTAACTGGTTTGATA 57.130 30.769 3.54 0.00 44.26 2.15
3336 4742 9.311916 GCAATATGCATTTAACTGGTTTGATAA 57.688 29.630 3.54 0.00 44.26 1.75
3342 4748 7.967854 TGCATTTAACTGGTTTGATAAGAATCG 59.032 33.333 0.00 0.00 34.60 3.34
3347 4862 6.969828 ACTGGTTTGATAAGAATCGTCTTC 57.030 37.500 0.00 0.00 43.30 2.87
3348 4863 6.464222 ACTGGTTTGATAAGAATCGTCTTCA 58.536 36.000 0.00 0.00 43.30 3.02
3429 4951 6.816640 TGCAATCACTGTTACTGTTACTATCC 59.183 38.462 0.00 0.00 0.00 2.59
3697 5220 4.081862 TGGCAGGTAGTTACATGTAGACAC 60.082 45.833 5.56 1.87 39.90 3.67
3792 5315 9.985730 ATTATTGTTGTTCATCTTGAATGTGTT 57.014 25.926 0.00 0.00 38.79 3.32
3855 5378 8.430801 TGTGTAATTTTGATTTGTTTTCTGGG 57.569 30.769 0.00 0.00 0.00 4.45
3877 5400 2.000429 CTGCCAATTTAGCTGTTGCC 58.000 50.000 0.00 0.00 40.80 4.52
3878 5401 1.547372 CTGCCAATTTAGCTGTTGCCT 59.453 47.619 0.00 0.00 40.80 4.75
4100 5624 5.541101 TCTTGGTAGCCTACAGTTACAGAAA 59.459 40.000 3.95 0.00 0.00 2.52
4102 5626 6.368779 TGGTAGCCTACAGTTACAGAAATT 57.631 37.500 3.95 0.00 0.00 1.82
4103 5627 6.403878 TGGTAGCCTACAGTTACAGAAATTC 58.596 40.000 3.95 0.00 0.00 2.17
4139 5666 1.587547 GGGCCTTCGCTCTTAAGATG 58.412 55.000 5.44 2.08 34.44 2.90
4177 5704 3.494626 CGTATGCTGTTGACAACACTTCT 59.505 43.478 17.02 5.27 36.25 2.85
4335 6065 6.609616 AGGTTTATTTTGGAGTGTCAAGGAAA 59.390 34.615 0.00 0.00 0.00 3.13
4526 6260 9.093970 TGAAGATGTCACATTTACTAATAACCG 57.906 33.333 0.00 0.00 0.00 4.44
4581 6315 1.433534 GTCGAGCAGAAGGTTGAAGG 58.566 55.000 0.00 0.00 37.40 3.46
4719 6453 0.316278 CCTACACGACGCGATGAGAG 60.316 60.000 15.93 10.55 0.00 3.20
4991 6725 1.053424 AAGGCTCACTAACAACGGGA 58.947 50.000 0.00 0.00 0.00 5.14
5105 6839 0.682209 ATGGCCATCCTGAAGCACAC 60.682 55.000 14.09 0.00 0.00 3.82
5189 6923 1.834822 GGAGGGGCGCTAGTCTCAT 60.835 63.158 7.64 0.00 0.00 2.90
5235 6969 1.201414 GTAAGTTGGTGGCCCATTTCG 59.799 52.381 0.00 0.00 41.49 3.46
5382 7116 1.539388 TCTGGCGTGCTTGTTTTATGG 59.461 47.619 0.00 0.00 0.00 2.74
5432 7166 6.536224 CCCTCTTACCAAAATGATTTCATTGC 59.464 38.462 6.56 0.00 45.06 3.56
5445 7179 2.742954 TCATTGCGATTTCATCAGCG 57.257 45.000 0.00 0.00 33.59 5.18
5505 7261 5.862845 TGATTTGCTTCTTTTATTTGCCCA 58.137 33.333 0.00 0.00 0.00 5.36
5512 7268 6.036470 GCTTCTTTTATTTGCCCACTGTATC 58.964 40.000 0.00 0.00 0.00 2.24
5554 7310 3.930336 TGACCTGAATGTTGCAGAGTAG 58.070 45.455 0.00 0.00 35.39 2.57
5570 7329 4.158764 CAGAGTAGAGTTGGATTTCTCCGT 59.841 45.833 0.00 0.00 45.37 4.69
5571 7330 4.399934 AGAGTAGAGTTGGATTTCTCCGTC 59.600 45.833 0.00 0.00 45.37 4.79
5572 7331 2.656560 AGAGTTGGATTTCTCCGTCG 57.343 50.000 0.00 0.00 45.37 5.12
5590 7360 0.110823 CGTTTTCCGAAACTGGCTCG 60.111 55.000 0.00 0.00 42.35 5.03
5612 7382 4.473199 GAAGTATTGCTTTTGTCGAACCC 58.527 43.478 0.00 0.00 37.59 4.11
5744 7523 2.093235 AGCCAGCACTAGAAGGAATCAC 60.093 50.000 0.00 0.00 0.00 3.06
5786 7565 3.674138 GCTCATATTGGGCACACAAACAG 60.674 47.826 0.00 0.00 45.01 3.16
5949 7775 2.482839 GCCTGCAGGTAGAGAGACAATC 60.483 54.545 32.81 8.48 37.57 2.67
5967 7793 5.880901 ACAATCATCTGGGTCAGTTTTAGT 58.119 37.500 0.00 0.00 32.61 2.24
5969 7795 5.762179 ATCATCTGGGTCAGTTTTAGTGA 57.238 39.130 0.00 0.00 32.61 3.41
5980 7806 7.118422 GTCAGTTTTAGTGACACAAGGATAC 57.882 40.000 8.59 0.00 45.49 2.24
5982 7808 5.120208 CAGTTTTAGTGACACAAGGATACCG 59.880 44.000 8.59 0.00 37.17 4.02
5983 7809 5.011329 AGTTTTAGTGACACAAGGATACCGA 59.989 40.000 8.59 0.00 37.17 4.69
5986 7812 4.553330 AGTGACACAAGGATACCGAAAT 57.447 40.909 8.59 0.00 37.17 2.17
5991 7817 2.017049 ACAAGGATACCGAAATGCAGC 58.983 47.619 0.00 0.00 37.17 5.25
5992 7818 2.016318 CAAGGATACCGAAATGCAGCA 58.984 47.619 0.00 0.00 37.17 4.41
5993 7819 1.668419 AGGATACCGAAATGCAGCAC 58.332 50.000 0.00 0.00 37.17 4.40
5994 7820 1.065491 AGGATACCGAAATGCAGCACA 60.065 47.619 0.00 0.00 37.17 4.57
5995 7821 1.331756 GGATACCGAAATGCAGCACAG 59.668 52.381 0.00 0.00 0.00 3.66
5996 7822 2.009774 GATACCGAAATGCAGCACAGT 58.990 47.619 0.00 0.00 0.00 3.55
5997 7823 1.438651 TACCGAAATGCAGCACAGTC 58.561 50.000 0.00 0.00 0.00 3.51
5998 7824 1.133253 CCGAAATGCAGCACAGTCG 59.867 57.895 14.44 14.44 38.72 4.18
5999 7825 1.568612 CCGAAATGCAGCACAGTCGT 61.569 55.000 18.10 0.00 37.81 4.34
6000 7826 1.067693 CGAAATGCAGCACAGTCGTA 58.932 50.000 13.54 0.00 35.86 3.43
6001 7827 1.459209 CGAAATGCAGCACAGTCGTAA 59.541 47.619 13.54 0.00 35.86 3.18
6002 7828 2.721797 CGAAATGCAGCACAGTCGTAAC 60.722 50.000 13.54 0.00 35.86 2.50
6003 7829 2.169832 AATGCAGCACAGTCGTAACT 57.830 45.000 0.00 0.00 35.60 2.24
6004 7830 2.169832 ATGCAGCACAGTCGTAACTT 57.830 45.000 0.00 0.00 31.71 2.66
6005 7831 1.948104 TGCAGCACAGTCGTAACTTT 58.052 45.000 0.00 0.00 31.71 2.66
6006 7832 3.100658 TGCAGCACAGTCGTAACTTTA 57.899 42.857 0.00 0.00 31.71 1.85
6007 7833 2.798283 TGCAGCACAGTCGTAACTTTAC 59.202 45.455 0.00 0.00 31.71 2.01
6008 7834 2.798283 GCAGCACAGTCGTAACTTTACA 59.202 45.455 0.32 0.00 31.71 2.41
6009 7835 3.432252 GCAGCACAGTCGTAACTTTACAT 59.568 43.478 0.32 0.00 31.71 2.29
6010 7836 4.666655 GCAGCACAGTCGTAACTTTACATG 60.667 45.833 0.00 0.00 31.71 3.21
6011 7837 4.684242 CAGCACAGTCGTAACTTTACATGA 59.316 41.667 0.00 0.00 31.71 3.07
6012 7838 5.176774 CAGCACAGTCGTAACTTTACATGAA 59.823 40.000 0.00 0.00 31.71 2.57
6013 7839 5.405571 AGCACAGTCGTAACTTTACATGAAG 59.594 40.000 0.00 0.00 31.71 3.02
6014 7840 5.609088 CACAGTCGTAACTTTACATGAAGC 58.391 41.667 0.00 0.00 31.71 3.86
6015 7841 5.176774 CACAGTCGTAACTTTACATGAAGCA 59.823 40.000 0.00 0.00 31.71 3.91
6016 7842 5.932303 ACAGTCGTAACTTTACATGAAGCAT 59.068 36.000 0.00 0.00 31.71 3.79
6017 7843 6.426937 ACAGTCGTAACTTTACATGAAGCATT 59.573 34.615 0.00 0.00 31.71 3.56
6018 7844 6.955963 CAGTCGTAACTTTACATGAAGCATTC 59.044 38.462 0.00 0.00 38.70 2.67
6020 7846 7.172532 AGTCGTAACTTTACATGAAGCATTCAA 59.827 33.333 0.00 0.00 46.51 2.69
6033 7859 6.710692 GAAGCATTCAATTTCCGTGATTTT 57.289 33.333 0.00 0.00 46.62 1.82
6034 7860 7.120789 GAAGCATTCAATTTCCGTGATTTTT 57.879 32.000 0.00 0.00 46.62 1.94
6035 7861 6.470557 AGCATTCAATTTCCGTGATTTTTG 57.529 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 38 5.405935 ACTCAAATTCAAATTGGCCTACC 57.594 39.130 3.32 0.00 0.00 3.18
269 276 6.039616 GTCATCTCTTAAGAAAGTCATCGCT 58.960 40.000 6.63 0.00 34.49 4.93
307 314 7.466805 GCTTTGAAAAGAAGCAACAAGAAATT 58.533 30.769 6.98 0.00 46.67 1.82
334 343 1.539157 GCCAGGAGAGAAAACCCAAG 58.461 55.000 0.00 0.00 0.00 3.61
339 348 1.283321 AGATGGGCCAGGAGAGAAAAC 59.717 52.381 13.78 0.00 0.00 2.43
388 398 6.429692 TGTTGGAAATCGAAGAGCTCAAAATA 59.570 34.615 17.77 0.00 43.63 1.40
529 548 7.612677 CATCTCATCACATGATTCATCCTCTA 58.387 38.462 0.00 0.00 38.85 2.43
560 579 4.322804 CGATCGTCACGTTACTTTTAAGCT 59.677 41.667 7.03 0.00 0.00 3.74
565 584 4.232221 ACATCGATCGTCACGTTACTTTT 58.768 39.130 15.94 0.00 0.00 2.27
577 596 1.681264 TCTGTGGCATACATCGATCGT 59.319 47.619 15.94 0.01 38.92 3.73
581 600 2.100749 ACGATTCTGTGGCATACATCGA 59.899 45.455 20.88 0.00 40.14 3.59
582 601 2.473816 ACGATTCTGTGGCATACATCG 58.526 47.619 15.39 15.39 42.22 3.84
585 604 6.751514 AATAAAACGATTCTGTGGCATACA 57.248 33.333 0.00 0.00 37.78 2.29
588 607 9.120538 AGTATTAATAAAACGATTCTGTGGCAT 57.879 29.630 0.00 0.00 0.00 4.40
590 609 7.376072 GCAGTATTAATAAAACGATTCTGTGGC 59.624 37.037 0.00 0.00 0.00 5.01
591 610 7.582679 CGCAGTATTAATAAAACGATTCTGTGG 59.417 37.037 0.00 0.00 0.00 4.17
592 611 8.114290 ACGCAGTATTAATAAAACGATTCTGTG 58.886 33.333 15.25 14.24 41.94 3.66
593 612 8.193250 ACGCAGTATTAATAAAACGATTCTGT 57.807 30.769 15.25 0.00 41.94 3.41
595 614 8.120465 CCAACGCAGTATTAATAAAACGATTCT 58.880 33.333 15.25 0.00 45.00 2.40
596 615 8.117988 TCCAACGCAGTATTAATAAAACGATTC 58.882 33.333 15.25 0.00 45.00 2.52
600 619 7.238571 AGTTCCAACGCAGTATTAATAAAACG 58.761 34.615 0.00 4.05 45.00 3.60
601 620 8.959734 AAGTTCCAACGCAGTATTAATAAAAC 57.040 30.769 0.00 0.00 45.00 2.43
605 624 9.090692 GTCTTAAGTTCCAACGCAGTATTAATA 57.909 33.333 1.63 0.00 45.00 0.98
606 625 7.822822 AGTCTTAAGTTCCAACGCAGTATTAAT 59.177 33.333 1.63 0.00 45.00 1.40
607 626 7.156673 AGTCTTAAGTTCCAACGCAGTATTAA 58.843 34.615 1.63 0.00 45.00 1.40
608 627 6.694447 AGTCTTAAGTTCCAACGCAGTATTA 58.306 36.000 1.63 0.00 45.00 0.98
609 628 5.548406 AGTCTTAAGTTCCAACGCAGTATT 58.452 37.500 1.63 0.00 45.00 1.89
610 629 5.148651 AGTCTTAAGTTCCAACGCAGTAT 57.851 39.130 1.63 0.00 45.00 2.12
611 630 4.595762 AGTCTTAAGTTCCAACGCAGTA 57.404 40.909 1.63 0.00 45.00 2.74
612 631 4.443034 AGAAGTCTTAAGTTCCAACGCAGT 60.443 41.667 1.63 0.00 37.76 4.40
613 632 4.058817 AGAAGTCTTAAGTTCCAACGCAG 58.941 43.478 1.63 0.00 35.74 5.18
614 633 4.067972 AGAAGTCTTAAGTTCCAACGCA 57.932 40.909 1.63 0.00 35.74 5.24
615 634 4.319549 CCAAGAAGTCTTAAGTTCCAACGC 60.320 45.833 1.63 0.00 35.74 4.84
616 635 4.319549 GCCAAGAAGTCTTAAGTTCCAACG 60.320 45.833 1.63 0.00 35.74 4.10
617 636 4.822350 AGCCAAGAAGTCTTAAGTTCCAAC 59.178 41.667 1.63 0.00 35.74 3.77
621 640 5.542779 TCTGAGCCAAGAAGTCTTAAGTTC 58.457 41.667 1.63 0.04 34.28 3.01
622 641 5.552870 TCTGAGCCAAGAAGTCTTAAGTT 57.447 39.130 1.63 0.00 34.28 2.66
623 642 5.753721 ATCTGAGCCAAGAAGTCTTAAGT 57.246 39.130 1.63 0.00 34.28 2.24
625 644 5.483937 TGGTATCTGAGCCAAGAAGTCTTAA 59.516 40.000 1.84 0.00 34.28 1.85
626 645 5.023452 TGGTATCTGAGCCAAGAAGTCTTA 58.977 41.667 1.84 0.00 34.28 2.10
629 648 3.895232 TGGTATCTGAGCCAAGAAGTC 57.105 47.619 1.84 0.00 0.00 3.01
630 649 6.100279 TCAATATGGTATCTGAGCCAAGAAGT 59.900 38.462 7.64 0.00 38.38 3.01
631 650 6.528321 TCAATATGGTATCTGAGCCAAGAAG 58.472 40.000 7.64 1.20 38.38 2.85
632 651 6.499106 TCAATATGGTATCTGAGCCAAGAA 57.501 37.500 7.64 0.00 38.38 2.52
634 653 7.446319 TGAATTCAATATGGTATCTGAGCCAAG 59.554 37.037 5.45 0.93 38.38 3.61
635 654 7.289310 TGAATTCAATATGGTATCTGAGCCAA 58.711 34.615 5.45 0.22 38.38 4.52
637 656 7.392673 ACATGAATTCAATATGGTATCTGAGCC 59.607 37.037 13.09 0.00 0.00 4.70
638 657 8.332996 ACATGAATTCAATATGGTATCTGAGC 57.667 34.615 13.09 0.00 0.00 4.26
640 659 8.570488 GCAACATGAATTCAATATGGTATCTGA 58.430 33.333 13.09 0.00 0.00 3.27
641 660 8.354426 TGCAACATGAATTCAATATGGTATCTG 58.646 33.333 13.09 4.59 0.00 2.90
642 661 8.467963 TGCAACATGAATTCAATATGGTATCT 57.532 30.769 13.09 0.00 0.00 1.98
644 663 8.308931 GGATGCAACATGAATTCAATATGGTAT 58.691 33.333 13.09 6.52 0.00 2.73
645 664 7.287235 TGGATGCAACATGAATTCAATATGGTA 59.713 33.333 13.09 1.83 0.00 3.25
646 665 6.098552 TGGATGCAACATGAATTCAATATGGT 59.901 34.615 13.09 1.84 0.00 3.55
648 667 7.709182 AGTTGGATGCAACATGAATTCAATATG 59.291 33.333 28.72 9.06 33.58 1.78
649 668 7.788026 AGTTGGATGCAACATGAATTCAATAT 58.212 30.769 28.72 3.58 33.58 1.28
651 670 6.045072 AGTTGGATGCAACATGAATTCAAT 57.955 33.333 28.72 4.28 33.58 2.57
652 671 5.010820 TGAGTTGGATGCAACATGAATTCAA 59.989 36.000 28.72 7.54 37.52 2.69
655 674 5.670792 ATGAGTTGGATGCAACATGAATT 57.329 34.783 28.72 9.69 37.52 2.17
657 740 4.523558 TGAATGAGTTGGATGCAACATGAA 59.476 37.500 28.72 13.23 37.52 2.57
659 742 4.443913 TGAATGAGTTGGATGCAACATG 57.556 40.909 28.72 0.00 37.52 3.21
662 745 5.291971 ACTTTTGAATGAGTTGGATGCAAC 58.708 37.500 21.29 21.29 35.43 4.17
666 749 4.455533 TCGGACTTTTGAATGAGTTGGATG 59.544 41.667 0.00 0.00 0.00 3.51
668 751 4.079980 TCGGACTTTTGAATGAGTTGGA 57.920 40.909 0.00 0.00 0.00 3.53
673 756 8.703604 TCTAATAGTTCGGACTTTTGAATGAG 57.296 34.615 0.00 0.00 37.33 2.90
674 757 7.764443 CCTCTAATAGTTCGGACTTTTGAATGA 59.236 37.037 0.00 0.00 37.33 2.57
679 762 5.974108 TCCCTCTAATAGTTCGGACTTTTG 58.026 41.667 0.00 0.00 37.33 2.44
680 763 5.128991 CCTCCCTCTAATAGTTCGGACTTTT 59.871 44.000 0.00 2.66 37.33 2.27
684 767 3.318557 CACCTCCCTCTAATAGTTCGGAC 59.681 52.174 0.00 0.00 0.00 4.79
686 769 2.628657 CCACCTCCCTCTAATAGTTCGG 59.371 54.545 0.00 0.00 0.00 4.30
688 771 2.369203 GCCCACCTCCCTCTAATAGTTC 59.631 54.545 0.00 0.00 0.00 3.01
689 772 2.293586 TGCCCACCTCCCTCTAATAGTT 60.294 50.000 0.00 0.00 0.00 2.24
692 775 2.579624 TTGCCCACCTCCCTCTAATA 57.420 50.000 0.00 0.00 0.00 0.98
693 776 1.912862 ATTGCCCACCTCCCTCTAAT 58.087 50.000 0.00 0.00 0.00 1.73
694 777 2.579624 TATTGCCCACCTCCCTCTAA 57.420 50.000 0.00 0.00 0.00 2.10
696 779 1.061033 AGATATTGCCCACCTCCCTCT 60.061 52.381 0.00 0.00 0.00 3.69
697 780 1.439543 AGATATTGCCCACCTCCCTC 58.560 55.000 0.00 0.00 0.00 4.30
698 781 1.912862 AAGATATTGCCCACCTCCCT 58.087 50.000 0.00 0.00 0.00 4.20
699 782 2.091885 TGAAAGATATTGCCCACCTCCC 60.092 50.000 0.00 0.00 0.00 4.30
700 783 3.297134 TGAAAGATATTGCCCACCTCC 57.703 47.619 0.00 0.00 0.00 4.30
701 784 4.016444 TGTTGAAAGATATTGCCCACCTC 58.984 43.478 0.00 0.00 0.00 3.85
702 785 3.763897 GTGTTGAAAGATATTGCCCACCT 59.236 43.478 0.00 0.00 0.00 4.00
703 786 3.509575 TGTGTTGAAAGATATTGCCCACC 59.490 43.478 0.00 0.00 0.00 4.61
704 787 4.782019 TGTGTTGAAAGATATTGCCCAC 57.218 40.909 0.00 0.00 0.00 4.61
705 788 5.076182 TCTTGTGTTGAAAGATATTGCCCA 58.924 37.500 0.00 0.00 0.00 5.36
706 789 5.415701 TCTCTTGTGTTGAAAGATATTGCCC 59.584 40.000 0.00 0.00 33.34 5.36
708 791 7.138692 ACTCTCTTGTGTTGAAAGATATTGC 57.861 36.000 0.00 0.00 33.34 3.56
709 792 7.536622 GCAACTCTCTTGTGTTGAAAGATATTG 59.463 37.037 13.00 1.46 45.28 1.90
710 793 7.446625 AGCAACTCTCTTGTGTTGAAAGATATT 59.553 33.333 13.00 0.00 45.28 1.28
711 794 6.939163 AGCAACTCTCTTGTGTTGAAAGATAT 59.061 34.615 13.00 0.00 45.28 1.63
712 795 6.291377 AGCAACTCTCTTGTGTTGAAAGATA 58.709 36.000 13.00 0.00 45.28 1.98
713 796 5.128919 AGCAACTCTCTTGTGTTGAAAGAT 58.871 37.500 13.00 0.00 45.28 2.40
714 797 4.517285 AGCAACTCTCTTGTGTTGAAAGA 58.483 39.130 13.00 0.00 45.28 2.52
715 798 4.842029 GAGCAACTCTCTTGTGTTGAAAG 58.158 43.478 13.00 0.00 45.28 2.62
716 799 4.882671 GAGCAACTCTCTTGTGTTGAAA 57.117 40.909 13.00 0.00 45.28 2.69
727 810 3.690628 ACGACTAGGTAAGAGCAACTCTC 59.309 47.826 0.00 0.00 40.28 3.20
779 1401 1.067846 TCGCATCGTATGTATCCAGGC 60.068 52.381 0.00 0.00 0.00 4.85
780 1402 2.229062 ACTCGCATCGTATGTATCCAGG 59.771 50.000 0.00 0.00 0.00 4.45
795 1417 2.568062 TCCATACTTTGGGTAACTCGCA 59.432 45.455 0.00 0.00 46.45 5.10
812 1434 1.462731 TTTGCACTTTGGCGCTCCAT 61.463 50.000 7.64 0.00 43.05 3.41
1150 1774 2.677979 GCGAAAACGGGAGCAGTCC 61.678 63.158 0.00 0.00 43.05 3.85
1151 1775 1.959226 TGCGAAAACGGGAGCAGTC 60.959 57.895 0.00 0.00 34.39 3.51
1202 1826 4.194720 CGAAGAGGCGGACGGAGG 62.195 72.222 0.00 0.00 0.00 4.30
1417 2041 0.554305 TACCCGGTCCAGATCTAGCA 59.446 55.000 0.00 0.00 0.00 3.49
1786 2410 1.228552 CACTGGTTCCACCCCCTTG 60.229 63.158 0.00 0.00 37.50 3.61
1792 2416 2.034221 GGCCTCACTGGTTCCACC 59.966 66.667 0.00 0.00 39.22 4.61
1930 2554 5.538433 AGATATAGTCACCTGCTTCTCTTCC 59.462 44.000 0.00 0.00 0.00 3.46
1993 2617 2.094026 GCAAGGTTAAAGGGCCATCTTG 60.094 50.000 6.18 8.34 34.86 3.02
2015 2639 3.496160 GCTAGGAAGAAAGGTGTCACCAA 60.496 47.826 24.02 0.00 41.95 3.67
2021 2645 4.081198 CAGATCAGCTAGGAAGAAAGGTGT 60.081 45.833 0.00 0.00 41.03 4.16
2038 2662 6.651225 TGCAATTTCAATTTGCAATCAGATCA 59.349 30.769 15.63 0.00 33.09 2.92
2109 3500 5.230726 GCAAACTCCGCTTGAATAATCAATG 59.769 40.000 0.00 0.00 44.29 2.82
2114 3505 4.782019 TTGCAAACTCCGCTTGAATAAT 57.218 36.364 0.00 0.00 0.00 1.28
2137 3528 6.548993 TCGCATGAAGATATCTCCTATATGCT 59.451 38.462 22.75 3.79 37.00 3.79
2138 3529 6.743110 TCGCATGAAGATATCTCCTATATGC 58.257 40.000 19.21 19.21 36.11 3.14
2350 3746 4.038080 GCCACTCCCGTTTTGGCG 62.038 66.667 0.00 0.00 46.11 5.69
2464 3860 4.772886 AAACACTGTGTACCTCTCCTTT 57.227 40.909 14.69 0.00 0.00 3.11
2712 4111 4.422840 CATCAAAGTTGCGCATATTGGAA 58.577 39.130 12.75 2.70 0.00 3.53
2739 4138 3.548818 GCAAACAAACAGAGCAGACGAAT 60.549 43.478 0.00 0.00 0.00 3.34
2742 4141 1.063912 TGCAAACAAACAGAGCAGACG 59.936 47.619 0.00 0.00 0.00 4.18
2766 4165 6.597672 CCAGCCATTTGTAGTTAGAATACACA 59.402 38.462 0.00 0.00 33.01 3.72
2820 4219 3.902881 AAAGAGAGACATGGCCTACAG 57.097 47.619 3.32 0.00 0.00 2.74
2821 4220 4.640771 AAAAAGAGAGACATGGCCTACA 57.359 40.909 3.32 0.00 0.00 2.74
2822 4221 5.488341 TGTAAAAAGAGAGACATGGCCTAC 58.512 41.667 3.32 0.00 0.00 3.18
2887 4286 2.358898 GTGAAATGCAAGACAGGTGTGT 59.641 45.455 0.00 0.00 40.71 3.72
2908 4307 7.541783 GCACTAGCTGATGATATTAACTCTCTG 59.458 40.741 0.00 0.00 37.91 3.35
2909 4308 7.309744 GGCACTAGCTGATGATATTAACTCTCT 60.310 40.741 0.00 0.00 41.70 3.10
2940 4339 2.427095 AGAAAAACAGTGACACCAAGGC 59.573 45.455 0.84 0.00 0.00 4.35
3078 4484 9.607333 ATCCAAATCAGAACTATGATACTCCTA 57.393 33.333 0.00 0.00 39.00 2.94
3079 4485 7.921041 TCCAAATCAGAACTATGATACTCCT 57.079 36.000 0.00 0.00 39.00 3.69
3080 4486 9.868277 CTATCCAAATCAGAACTATGATACTCC 57.132 37.037 0.00 0.00 39.00 3.85
3165 4571 7.287235 AGGTACCATTCTACTATTACAGACACC 59.713 40.741 15.94 0.00 0.00 4.16
3190 4596 6.042143 ACAAATAACAGAAAACAGCACCAAG 58.958 36.000 0.00 0.00 0.00 3.61
3256 4662 6.323739 CACCAGTATATAGGGCCAAAACAATT 59.676 38.462 6.18 0.00 0.00 2.32
3320 4726 8.842358 AGACGATTCTTATCAAACCAGTTAAA 57.158 30.769 0.00 0.00 0.00 1.52
3323 4729 6.934645 TGAAGACGATTCTTATCAAACCAGTT 59.065 34.615 0.00 0.00 42.53 3.16
3324 4730 6.464222 TGAAGACGATTCTTATCAAACCAGT 58.536 36.000 0.00 0.00 42.53 4.00
3325 4731 6.968131 TGAAGACGATTCTTATCAAACCAG 57.032 37.500 0.00 0.00 42.53 4.00
3326 4732 7.626240 GCATTGAAGACGATTCTTATCAAACCA 60.626 37.037 0.00 0.00 42.53 3.67
3327 4733 6.688813 GCATTGAAGACGATTCTTATCAAACC 59.311 38.462 0.00 0.00 42.53 3.27
3328 4734 6.688813 GGCATTGAAGACGATTCTTATCAAAC 59.311 38.462 0.00 0.00 42.53 2.93
3329 4735 6.599244 AGGCATTGAAGACGATTCTTATCAAA 59.401 34.615 0.00 0.00 42.53 2.69
3332 4738 6.926272 ACTAGGCATTGAAGACGATTCTTATC 59.074 38.462 0.00 0.00 42.53 1.75
3333 4739 6.821388 ACTAGGCATTGAAGACGATTCTTAT 58.179 36.000 0.00 0.00 42.53 1.73
3334 4740 6.222038 ACTAGGCATTGAAGACGATTCTTA 57.778 37.500 0.00 0.00 42.53 2.10
3335 4741 5.091261 ACTAGGCATTGAAGACGATTCTT 57.909 39.130 0.00 0.00 45.35 2.52
3336 4742 4.744795 ACTAGGCATTGAAGACGATTCT 57.255 40.909 0.00 0.00 0.00 2.40
3337 4743 4.870426 TGAACTAGGCATTGAAGACGATTC 59.130 41.667 0.00 0.00 0.00 2.52
3339 4745 4.471904 TGAACTAGGCATTGAAGACGAT 57.528 40.909 0.00 0.00 0.00 3.73
3340 4746 3.953712 TGAACTAGGCATTGAAGACGA 57.046 42.857 0.00 0.00 0.00 4.20
3342 4748 6.456988 CGGTAAATGAACTAGGCATTGAAGAC 60.457 42.308 12.16 8.93 36.20 3.01
3347 4862 3.945285 ACCGGTAAATGAACTAGGCATTG 59.055 43.478 4.49 4.46 36.20 2.82
3348 4863 4.230745 ACCGGTAAATGAACTAGGCATT 57.769 40.909 4.49 7.14 37.56 3.56
3724 5247 7.435192 GCAAAATGCTAGTAATAATGTCAACCC 59.565 37.037 0.00 0.00 40.96 4.11
3792 5315 8.449625 AGCAAGGTAGTAGGAAGAATCTAGATA 58.550 37.037 5.46 0.00 0.00 1.98
3855 5378 2.872370 CAACAGCTAAATTGGCAGCTC 58.128 47.619 3.77 0.00 44.83 4.09
3877 5400 4.929808 CAGCACAAGGTTAACTAGGTACAG 59.070 45.833 5.42 0.00 0.00 2.74
3878 5401 4.801581 GCAGCACAAGGTTAACTAGGTACA 60.802 45.833 5.42 0.00 0.00 2.90
3928 5451 7.834181 AGTTTTACTGGCATAATACACTGGAAT 59.166 33.333 0.00 0.00 0.00 3.01
4100 5624 1.402259 CGTCTAGCAGTCCTCACGAAT 59.598 52.381 0.00 0.00 33.81 3.34
4102 5626 1.025113 CCGTCTAGCAGTCCTCACGA 61.025 60.000 0.00 0.00 33.81 4.35
4103 5627 1.429825 CCGTCTAGCAGTCCTCACG 59.570 63.158 0.00 0.00 32.48 4.35
4139 5666 7.524065 ACAGCATACGATTTGTAACTTTTACC 58.476 34.615 0.00 0.00 36.44 2.85
4177 5704 3.849911 CCTGATAGAAACAGCGTCAAGA 58.150 45.455 0.00 0.00 34.47 3.02
4491 6225 6.889301 AATGTGACATCTTCAACTTGACAT 57.111 33.333 0.00 0.00 35.39 3.06
4526 6260 3.695830 TTTGGACCTAGATGACACACC 57.304 47.619 0.00 0.00 0.00 4.16
4581 6315 3.883489 GCCTGAAGGGTTAATGGTCATAC 59.117 47.826 0.00 0.00 37.43 2.39
4719 6453 2.093235 ACATCTCTAGCAACCTTCCTGC 60.093 50.000 0.00 0.00 40.24 4.85
4982 6716 0.951558 GAGTGCAATGTCCCGTTGTT 59.048 50.000 0.00 0.00 33.39 2.83
4991 6725 3.244665 TGTGAAGATCCAGAGTGCAATGT 60.245 43.478 0.00 0.00 0.00 2.71
5105 6839 4.256920 AGGCTGTAATGTAAAGCAGTGAG 58.743 43.478 0.00 0.00 38.73 3.51
5235 6969 6.707440 TCTCATCTCCTGTTATCAAGAGAC 57.293 41.667 4.57 0.00 41.90 3.36
5382 7116 2.200373 ACACCCTAATCTGGCAACAC 57.800 50.000 0.00 0.00 46.17 3.32
5505 7261 3.118482 CCCTGTGATCAGCAAGATACAGT 60.118 47.826 0.00 0.00 40.09 3.55
5512 7268 2.704464 TCATCCCTGTGATCAGCAAG 57.296 50.000 0.00 0.00 40.09 4.01
5554 7310 2.365408 ACGACGGAGAAATCCAACTC 57.635 50.000 0.00 0.00 0.00 3.01
5572 7331 1.223187 TCGAGCCAGTTTCGGAAAAC 58.777 50.000 4.46 0.32 44.24 2.43
5590 7360 4.473199 GGGTTCGACAAAAGCAATACTTC 58.527 43.478 0.00 0.00 37.75 3.01
5612 7382 2.408835 GCATGATTTGGTCGGCCG 59.591 61.111 22.12 22.12 37.67 6.13
5786 7565 2.167487 GTCTGACCATGAACCCTCTCTC 59.833 54.545 0.00 0.00 0.00 3.20
5949 7775 4.452455 GTGTCACTAAAACTGACCCAGATG 59.548 45.833 0.45 0.00 37.79 2.90
5967 7793 3.006940 GCATTTCGGTATCCTTGTGTCA 58.993 45.455 0.00 0.00 0.00 3.58
5969 7795 3.009723 CTGCATTTCGGTATCCTTGTGT 58.990 45.455 0.00 0.00 0.00 3.72
5978 7804 1.438651 GACTGTGCTGCATTTCGGTA 58.561 50.000 5.27 0.00 0.00 4.02
5979 7805 1.568612 CGACTGTGCTGCATTTCGGT 61.569 55.000 17.52 11.44 32.20 4.69
5980 7806 1.133253 CGACTGTGCTGCATTTCGG 59.867 57.895 17.52 8.74 32.20 4.30
5982 7808 2.480419 AGTTACGACTGTGCTGCATTTC 59.520 45.455 5.27 1.78 33.99 2.17
5983 7809 2.494059 AGTTACGACTGTGCTGCATTT 58.506 42.857 5.27 0.00 33.99 2.32
5986 7812 1.948104 AAAGTTACGACTGTGCTGCA 58.052 45.000 0.00 0.00 35.91 4.41
5991 7817 5.176774 TGCTTCATGTAAAGTTACGACTGTG 59.823 40.000 0.00 0.00 35.91 3.66
5992 7818 5.294356 TGCTTCATGTAAAGTTACGACTGT 58.706 37.500 0.00 0.00 35.91 3.55
5993 7819 5.839262 TGCTTCATGTAAAGTTACGACTG 57.161 39.130 0.00 0.00 35.91 3.51
5994 7820 6.649141 TGAATGCTTCATGTAAAGTTACGACT 59.351 34.615 0.00 0.00 33.95 4.18
5995 7821 6.827641 TGAATGCTTCATGTAAAGTTACGAC 58.172 36.000 0.00 0.00 33.95 4.34
5996 7822 7.428282 TTGAATGCTTCATGTAAAGTTACGA 57.572 32.000 0.00 0.00 39.84 3.43
5997 7823 8.673626 AATTGAATGCTTCATGTAAAGTTACG 57.326 30.769 0.00 0.00 39.84 3.18
5999 7825 9.638239 GGAAATTGAATGCTTCATGTAAAGTTA 57.362 29.630 0.00 0.00 39.84 2.24
6000 7826 7.329226 CGGAAATTGAATGCTTCATGTAAAGTT 59.671 33.333 0.00 0.00 39.84 2.66
6001 7827 6.808212 CGGAAATTGAATGCTTCATGTAAAGT 59.192 34.615 0.00 0.00 39.84 2.66
6002 7828 6.808212 ACGGAAATTGAATGCTTCATGTAAAG 59.192 34.615 0.00 0.00 39.84 1.85
6003 7829 6.585702 CACGGAAATTGAATGCTTCATGTAAA 59.414 34.615 0.00 0.00 39.84 2.01
6004 7830 6.072230 TCACGGAAATTGAATGCTTCATGTAA 60.072 34.615 0.00 0.00 39.84 2.41
6005 7831 5.414144 TCACGGAAATTGAATGCTTCATGTA 59.586 36.000 0.00 0.00 39.84 2.29
6006 7832 4.218200 TCACGGAAATTGAATGCTTCATGT 59.782 37.500 0.00 0.00 39.84 3.21
6007 7833 4.735985 TCACGGAAATTGAATGCTTCATG 58.264 39.130 0.41 0.00 39.84 3.07
6008 7834 5.587388 ATCACGGAAATTGAATGCTTCAT 57.413 34.783 0.41 0.00 39.84 2.57
6009 7835 5.389859 AATCACGGAAATTGAATGCTTCA 57.610 34.783 0.00 0.00 38.04 3.02
6010 7836 6.710692 AAAATCACGGAAATTGAATGCTTC 57.289 33.333 0.00 0.00 0.00 3.86
6011 7837 6.890558 CAAAAATCACGGAAATTGAATGCTT 58.109 32.000 0.00 0.00 0.00 3.91
6012 7838 6.470557 CAAAAATCACGGAAATTGAATGCT 57.529 33.333 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.