Multiple sequence alignment - TraesCS1B01G245800

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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 TraesCS1B01G245800 chr1B 100.000 2851 0 0 1 2851 435041705 435044555 0.000000e+00 5265.0
1 TraesCS1B01G245800 chr1B 89.189 74 5 3 1311 1381 434835518 434835591 3.910000e-14 89.8
2 TraesCS1B01G245800 chr1D 88.456 1412 104 28 884 2274 322262404 322263777 0.000000e+00 1650.0
3 TraesCS1B01G245800 chr1D 89.350 554 54 5 2301 2851 322263777 322264328 0.000000e+00 691.0
4 TraesCS1B01G245800 chr1D 89.157 415 26 6 40 437 322261597 322262009 1.530000e-137 499.0
5 TraesCS1B01G245800 chr1D 89.189 74 5 3 1311 1381 322165246 322165319 3.910000e-14 89.8
6 TraesCS1B01G245800 chr1A 89.313 917 46 22 912 1809 406142920 406143803 0.000000e+00 1103.0
7 TraesCS1B01G245800 chr1A 85.470 1053 103 24 1817 2851 406144116 406145136 0.000000e+00 1051.0
8 TraesCS1B01G245800 chr1A 86.181 398 28 12 40 437 406142157 406142527 3.420000e-109 405.0
9 TraesCS1B01G245800 chr1A 92.424 66 5 0 1316 1381 405869121 405869186 8.410000e-16 95.3


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 TraesCS1B01G245800 chr1B 435041705 435044555 2850 False 5265.000000 5265 100.000000 1 2851 1 chr1B.!!$F2 2850
1 TraesCS1B01G245800 chr1D 322261597 322264328 2731 False 946.666667 1650 88.987667 40 2851 3 chr1D.!!$F2 2811
2 TraesCS1B01G245800 chr1A 406142157 406145136 2979 False 853.000000 1103 86.988000 40 2851 3 chr1A.!!$F2 2811

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
471 539 0.033405 TTCGCTACTACCTCTGCCCT 60.033 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2908 0.031449 CGTTTGGGCGTCCATTTTGT 59.969 50.0 10.94 0.0 43.63 2.83 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
54 55 2.338577 ACTGTAGTATAGGACGGCGT 57.661 50.000 14.65 14.65 0.00 5.68
58 59 0.670162 TAGTATAGGACGGCGTTGCC 59.330 55.000 16.19 12.40 46.75 4.52
111 112 3.560068 CCTCCATTATTTCCGGAAGAACG 59.440 47.826 17.97 8.38 32.95 3.95
114 115 3.002348 CCATTATTTCCGGAAGAACGAGC 59.998 47.826 17.97 0.00 32.95 5.03
124 125 2.837371 AAGAACGAGCGCTACCTGGC 62.837 60.000 11.50 0.00 0.00 4.85
178 187 1.202336 CCACGGTTACTCGGTATCCAC 60.202 57.143 10.08 0.00 30.62 4.02
212 221 3.142951 CACCACAGTGGACCGAATTTTA 58.857 45.455 27.39 0.00 40.96 1.52
239 256 4.142026 TGCCTAGATAGAAAACTTGCGCTA 60.142 41.667 9.73 0.00 0.00 4.26
287 304 5.837437 TGTTTATTCTGATGGTGCGTTTTT 58.163 33.333 0.00 0.00 0.00 1.94
364 381 4.853196 CAGTGCAACGAATCATAAAAGGTG 59.147 41.667 0.00 0.00 45.86 4.00
368 385 4.857037 GCAACGAATCATAAAAGGTGGAAC 59.143 41.667 0.00 0.00 0.00 3.62
428 445 2.350192 TCTAACATAAATGCCACGCGTG 59.650 45.455 31.77 31.77 0.00 5.34
451 519 6.249035 GGTATTGAACCTTTCGTCATTCAA 57.751 37.500 1.14 1.14 45.75 2.69
456 524 3.471495 ACCTTTCGTCATTCAATTCGC 57.529 42.857 0.00 0.00 0.00 4.70
459 527 4.092968 ACCTTTCGTCATTCAATTCGCTAC 59.907 41.667 0.00 0.00 0.00 3.58
461 529 5.518847 CCTTTCGTCATTCAATTCGCTACTA 59.481 40.000 0.00 0.00 0.00 1.82
463 531 4.357142 TCGTCATTCAATTCGCTACTACC 58.643 43.478 0.00 0.00 0.00 3.18
464 532 4.097437 TCGTCATTCAATTCGCTACTACCT 59.903 41.667 0.00 0.00 0.00 3.08
465 533 4.441415 CGTCATTCAATTCGCTACTACCTC 59.559 45.833 0.00 0.00 0.00 3.85
466 534 5.593010 GTCATTCAATTCGCTACTACCTCT 58.407 41.667 0.00 0.00 0.00 3.69
467 535 5.460419 GTCATTCAATTCGCTACTACCTCTG 59.540 44.000 0.00 0.00 0.00 3.35
468 536 3.438297 TCAATTCGCTACTACCTCTGC 57.562 47.619 0.00 0.00 0.00 4.26
469 537 2.100916 TCAATTCGCTACTACCTCTGCC 59.899 50.000 0.00 0.00 0.00 4.85
470 538 1.041437 ATTCGCTACTACCTCTGCCC 58.959 55.000 0.00 0.00 0.00 5.36
471 539 0.033405 TTCGCTACTACCTCTGCCCT 60.033 55.000 0.00 0.00 0.00 5.19
472 540 0.752009 TCGCTACTACCTCTGCCCTG 60.752 60.000 0.00 0.00 0.00 4.45
473 541 0.752009 CGCTACTACCTCTGCCCTGA 60.752 60.000 0.00 0.00 0.00 3.86
474 542 1.710816 GCTACTACCTCTGCCCTGAT 58.289 55.000 0.00 0.00 0.00 2.90
475 543 2.043227 GCTACTACCTCTGCCCTGATT 58.957 52.381 0.00 0.00 0.00 2.57
476 544 2.436173 GCTACTACCTCTGCCCTGATTT 59.564 50.000 0.00 0.00 0.00 2.17
477 545 3.641906 GCTACTACCTCTGCCCTGATTTA 59.358 47.826 0.00 0.00 0.00 1.40
479 547 5.221742 GCTACTACCTCTGCCCTGATTTATT 60.222 44.000 0.00 0.00 0.00 1.40
480 548 5.041191 ACTACCTCTGCCCTGATTTATTG 57.959 43.478 0.00 0.00 0.00 1.90
483 551 4.723309 ACCTCTGCCCTGATTTATTGATC 58.277 43.478 0.00 0.00 0.00 2.92
484 552 4.414846 ACCTCTGCCCTGATTTATTGATCT 59.585 41.667 0.00 0.00 0.00 2.75
485 553 5.103771 ACCTCTGCCCTGATTTATTGATCTT 60.104 40.000 0.00 0.00 0.00 2.40
486 554 5.832060 CCTCTGCCCTGATTTATTGATCTTT 59.168 40.000 0.00 0.00 0.00 2.52
487 555 6.323225 CCTCTGCCCTGATTTATTGATCTTTT 59.677 38.462 0.00 0.00 0.00 2.27
489 557 6.664816 TCTGCCCTGATTTATTGATCTTTTGT 59.335 34.615 0.00 0.00 0.00 2.83
490 558 7.833682 TCTGCCCTGATTTATTGATCTTTTGTA 59.166 33.333 0.00 0.00 0.00 2.41
491 559 8.537728 TGCCCTGATTTATTGATCTTTTGTAT 57.462 30.769 0.00 0.00 0.00 2.29
493 561 9.822185 GCCCTGATTTATTGATCTTTTGTATTT 57.178 29.630 0.00 0.00 0.00 1.40
545 613 9.840427 AACTGATAAAGTGTTAATGCATGTTAC 57.160 29.630 0.00 0.00 39.81 2.50
546 614 9.231297 ACTGATAAAGTGTTAATGCATGTTACT 57.769 29.630 0.00 0.00 37.88 2.24
547 615 9.494479 CTGATAAAGTGTTAATGCATGTTACTG 57.506 33.333 0.00 0.00 0.00 2.74
548 616 9.225436 TGATAAAGTGTTAATGCATGTTACTGA 57.775 29.630 0.00 0.00 0.00 3.41
551 619 8.801715 AAAGTGTTAATGCATGTTACTGAAAG 57.198 30.769 0.00 0.00 42.29 2.62
585 653 9.661563 TTGTTAAATTCGTACTTGATCATACCT 57.338 29.630 0.00 0.00 0.00 3.08
586 654 9.661563 TGTTAAATTCGTACTTGATCATACCTT 57.338 29.630 0.00 0.00 0.00 3.50
590 658 8.786826 AATTCGTACTTGATCATACCTTTTGA 57.213 30.769 0.00 0.00 0.00 2.69
591 659 8.964476 ATTCGTACTTGATCATACCTTTTGAT 57.036 30.769 0.00 0.00 36.54 2.57
592 660 7.770801 TCGTACTTGATCATACCTTTTGATG 57.229 36.000 0.00 0.00 34.03 3.07
593 661 7.552459 TCGTACTTGATCATACCTTTTGATGA 58.448 34.615 0.00 0.00 34.03 2.92
594 662 8.204160 TCGTACTTGATCATACCTTTTGATGAT 58.796 33.333 0.00 0.00 43.82 2.45
595 663 9.476202 CGTACTTGATCATACCTTTTGATGATA 57.524 33.333 0.00 0.00 41.74 2.15
612 680 9.558648 TTTGATGATATTTTCTTTGATGACGTG 57.441 29.630 0.00 0.00 0.00 4.49
613 681 8.491331 TGATGATATTTTCTTTGATGACGTGA 57.509 30.769 0.00 0.00 0.00 4.35
614 682 8.945057 TGATGATATTTTCTTTGATGACGTGAA 58.055 29.630 0.00 0.00 0.00 3.18
615 683 9.941664 GATGATATTTTCTTTGATGACGTGAAT 57.058 29.630 0.00 0.00 0.00 2.57
616 684 9.941664 ATGATATTTTCTTTGATGACGTGAATC 57.058 29.630 0.00 0.00 0.00 2.52
617 685 8.945057 TGATATTTTCTTTGATGACGTGAATCA 58.055 29.630 0.00 0.00 32.24 2.57
618 686 9.773328 GATATTTTCTTTGATGACGTGAATCAA 57.227 29.630 15.77 15.77 41.19 2.57
625 693 9.558648 TCTTTGATGACGTGAATCAATATTTTG 57.441 29.630 18.88 9.24 42.15 2.44
626 694 9.345517 CTTTGATGACGTGAATCAATATTTTGT 57.654 29.630 18.88 0.00 42.15 2.83
627 695 9.689976 TTTGATGACGTGAATCAATATTTTGTT 57.310 25.926 18.88 0.00 42.15 2.83
629 697 9.986833 TGATGACGTGAATCAATATTTTGTTAG 57.013 29.630 7.83 0.00 34.32 2.34
630 698 8.841444 ATGACGTGAATCAATATTTTGTTAGC 57.159 30.769 0.00 0.00 34.32 3.09
631 699 8.039603 TGACGTGAATCAATATTTTGTTAGCT 57.960 30.769 0.00 0.00 34.32 3.32
632 700 8.175069 TGACGTGAATCAATATTTTGTTAGCTC 58.825 33.333 0.00 0.00 34.32 4.09
633 701 8.039603 ACGTGAATCAATATTTTGTTAGCTCA 57.960 30.769 0.00 0.00 34.32 4.26
634 702 8.511321 ACGTGAATCAATATTTTGTTAGCTCAA 58.489 29.630 0.00 0.00 34.32 3.02
635 703 9.003112 CGTGAATCAATATTTTGTTAGCTCAAG 57.997 33.333 0.00 0.00 34.32 3.02
636 704 8.801913 GTGAATCAATATTTTGTTAGCTCAAGC 58.198 33.333 0.00 0.00 36.35 4.01
637 705 8.522003 TGAATCAATATTTTGTTAGCTCAAGCA 58.478 29.630 4.59 0.00 37.54 3.91
638 706 9.357652 GAATCAATATTTTGTTAGCTCAAGCAA 57.642 29.630 4.59 0.00 37.54 3.91
639 707 9.709495 AATCAATATTTTGTTAGCTCAAGCAAA 57.291 25.926 4.59 0.00 37.54 3.68
640 708 8.746922 TCAATATTTTGTTAGCTCAAGCAAAG 57.253 30.769 4.59 0.00 37.54 2.77
641 709 7.814107 TCAATATTTTGTTAGCTCAAGCAAAGG 59.186 33.333 4.59 0.00 37.54 3.11
642 710 5.535753 ATTTTGTTAGCTCAAGCAAAGGT 57.464 34.783 4.59 0.00 45.16 3.50
643 711 5.337578 TTTTGTTAGCTCAAGCAAAGGTT 57.662 34.783 4.59 0.00 45.16 3.50
644 712 6.458232 TTTTGTTAGCTCAAGCAAAGGTTA 57.542 33.333 4.59 0.00 45.16 2.85
645 713 6.458232 TTTGTTAGCTCAAGCAAAGGTTAA 57.542 33.333 4.59 0.00 45.16 2.01
646 714 6.458232 TTGTTAGCTCAAGCAAAGGTTAAA 57.542 33.333 4.59 0.00 45.16 1.52
647 715 6.072112 TGTTAGCTCAAGCAAAGGTTAAAG 57.928 37.500 4.59 0.00 45.16 1.85
648 716 5.592688 TGTTAGCTCAAGCAAAGGTTAAAGT 59.407 36.000 4.59 0.00 45.16 2.66
649 717 6.096282 TGTTAGCTCAAGCAAAGGTTAAAGTT 59.904 34.615 4.59 0.00 45.16 2.66
650 718 5.598416 AGCTCAAGCAAAGGTTAAAGTTT 57.402 34.783 4.59 0.00 45.16 2.66
651 719 5.351458 AGCTCAAGCAAAGGTTAAAGTTTG 58.649 37.500 4.59 6.47 45.16 2.93
652 720 5.127031 AGCTCAAGCAAAGGTTAAAGTTTGA 59.873 36.000 12.76 0.00 45.16 2.69
653 721 5.985530 GCTCAAGCAAAGGTTAAAGTTTGAT 59.014 36.000 12.76 5.62 41.59 2.57
654 722 7.014230 AGCTCAAGCAAAGGTTAAAGTTTGATA 59.986 33.333 12.76 0.00 45.16 2.15
655 723 7.114953 GCTCAAGCAAAGGTTAAAGTTTGATAC 59.885 37.037 12.76 0.00 41.59 2.24
656 724 8.001881 TCAAGCAAAGGTTAAAGTTTGATACA 57.998 30.769 12.76 0.00 35.99 2.29
657 725 8.134895 TCAAGCAAAGGTTAAAGTTTGATACAG 58.865 33.333 12.76 3.73 35.99 2.74
658 726 7.582667 AGCAAAGGTTAAAGTTTGATACAGT 57.417 32.000 12.76 0.00 35.99 3.55
659 727 8.685838 AGCAAAGGTTAAAGTTTGATACAGTA 57.314 30.769 12.76 0.00 35.99 2.74
660 728 9.297037 AGCAAAGGTTAAAGTTTGATACAGTAT 57.703 29.630 12.76 0.00 35.99 2.12
676 744 9.127277 TGATACAGTATAAAATACAAAAGGGGC 57.873 33.333 0.00 0.00 0.00 5.80
677 745 9.127277 GATACAGTATAAAATACAAAAGGGGCA 57.873 33.333 0.00 0.00 0.00 5.36
678 746 7.784470 ACAGTATAAAATACAAAAGGGGCAA 57.216 32.000 0.33 0.00 0.00 4.52
679 747 8.374184 ACAGTATAAAATACAAAAGGGGCAAT 57.626 30.769 0.33 0.00 0.00 3.56
680 748 9.482175 ACAGTATAAAATACAAAAGGGGCAATA 57.518 29.630 0.33 0.00 0.00 1.90
684 752 8.731275 ATAAAATACAAAAGGGGCAATAAAGC 57.269 30.769 0.00 0.00 0.00 3.51
685 753 5.753721 AATACAAAAGGGGCAATAAAGCA 57.246 34.783 0.00 0.00 35.83 3.91
686 754 3.683365 ACAAAAGGGGCAATAAAGCAG 57.317 42.857 0.00 0.00 35.83 4.24
687 755 2.302733 ACAAAAGGGGCAATAAAGCAGG 59.697 45.455 0.00 0.00 35.83 4.85
688 756 2.566724 CAAAAGGGGCAATAAAGCAGGA 59.433 45.455 0.00 0.00 35.83 3.86
689 757 1.852633 AAGGGGCAATAAAGCAGGAC 58.147 50.000 0.00 0.00 35.83 3.85
690 758 0.394352 AGGGGCAATAAAGCAGGACG 60.394 55.000 0.00 0.00 35.83 4.79
691 759 1.384222 GGGGCAATAAAGCAGGACGG 61.384 60.000 0.00 0.00 35.83 4.79
692 760 0.393808 GGGCAATAAAGCAGGACGGA 60.394 55.000 0.00 0.00 35.83 4.69
693 761 1.459450 GGCAATAAAGCAGGACGGAA 58.541 50.000 0.00 0.00 35.83 4.30
694 762 1.401905 GGCAATAAAGCAGGACGGAAG 59.598 52.381 0.00 0.00 35.83 3.46
695 763 1.401905 GCAATAAAGCAGGACGGAAGG 59.598 52.381 0.00 0.00 0.00 3.46
696 764 2.711542 CAATAAAGCAGGACGGAAGGT 58.288 47.619 0.00 0.00 0.00 3.50
697 765 3.869065 CAATAAAGCAGGACGGAAGGTA 58.131 45.455 0.00 0.00 0.00 3.08
698 766 3.821421 ATAAAGCAGGACGGAAGGTAG 57.179 47.619 0.00 0.00 0.00 3.18
699 767 1.349067 AAAGCAGGACGGAAGGTAGT 58.651 50.000 0.00 0.00 0.00 2.73
700 768 0.608640 AAGCAGGACGGAAGGTAGTG 59.391 55.000 0.00 0.00 0.00 2.74
701 769 1.218316 GCAGGACGGAAGGTAGTGG 59.782 63.158 0.00 0.00 0.00 4.00
702 770 1.542187 GCAGGACGGAAGGTAGTGGT 61.542 60.000 0.00 0.00 0.00 4.16
703 771 0.974383 CAGGACGGAAGGTAGTGGTT 59.026 55.000 0.00 0.00 0.00 3.67
704 772 2.173519 CAGGACGGAAGGTAGTGGTTA 58.826 52.381 0.00 0.00 0.00 2.85
705 773 2.764572 CAGGACGGAAGGTAGTGGTTAT 59.235 50.000 0.00 0.00 0.00 1.89
706 774 2.764572 AGGACGGAAGGTAGTGGTTATG 59.235 50.000 0.00 0.00 0.00 1.90
707 775 2.159000 GGACGGAAGGTAGTGGTTATGG 60.159 54.545 0.00 0.00 0.00 2.74
708 776 1.835531 ACGGAAGGTAGTGGTTATGGG 59.164 52.381 0.00 0.00 0.00 4.00
709 777 1.835531 CGGAAGGTAGTGGTTATGGGT 59.164 52.381 0.00 0.00 0.00 4.51
722 790 6.321181 AGTGGTTATGGGTATAAAATGTGCAG 59.679 38.462 0.00 0.00 30.92 4.41
727 799 9.430623 GTTATGGGTATAAAATGTGCAGTTTTT 57.569 29.630 13.19 11.77 30.92 1.94
774 852 8.991783 TTAGCAGGTACAGTACAGTATATCTT 57.008 34.615 12.89 0.00 0.00 2.40
775 853 7.278461 AGCAGGTACAGTACAGTATATCTTG 57.722 40.000 12.89 0.00 0.00 3.02
789 869 7.234782 ACAGTATATCTTGGTCATCCCGAATTA 59.765 37.037 0.00 0.00 35.15 1.40
790 870 7.545965 CAGTATATCTTGGTCATCCCGAATTAC 59.454 40.741 0.00 0.00 35.15 1.89
802 882 1.467875 CGAATTACCTGACGAGCTCG 58.532 55.000 33.45 33.45 46.33 5.03
807 887 3.893763 CCTGACGAGCTCGCGGAT 61.894 66.667 34.83 16.71 44.43 4.18
809 889 4.854784 TGACGAGCTCGCGGATGC 62.855 66.667 34.83 17.33 44.43 3.91
820 900 1.136147 GCGGATGCAGCAAACAGAG 59.864 57.895 3.51 0.00 42.15 3.35
823 904 1.662629 CGGATGCAGCAAACAGAGTAG 59.337 52.381 3.51 0.00 0.00 2.57
824 905 2.704572 GGATGCAGCAAACAGAGTAGT 58.295 47.619 3.51 0.00 0.00 2.73
825 906 3.676049 CGGATGCAGCAAACAGAGTAGTA 60.676 47.826 3.51 0.00 0.00 1.82
826 907 3.619038 GGATGCAGCAAACAGAGTAGTAC 59.381 47.826 3.51 0.00 0.00 2.73
827 908 4.499183 GATGCAGCAAACAGAGTAGTACT 58.501 43.478 1.37 1.37 0.00 2.73
828 909 5.394224 GGATGCAGCAAACAGAGTAGTACTA 60.394 44.000 3.51 0.00 0.00 1.82
829 910 4.806330 TGCAGCAAACAGAGTAGTACTAC 58.194 43.478 23.03 23.03 36.35 2.73
832 913 6.208007 TGCAGCAAACAGAGTAGTACTACTTA 59.792 38.462 31.14 0.00 45.63 2.24
833 914 6.748198 GCAGCAAACAGAGTAGTACTACTTAG 59.252 42.308 31.14 26.75 45.63 2.18
843 990 9.245481 AGAGTAGTACTACTTAGCTTTGAATGT 57.755 33.333 31.14 8.85 45.63 2.71
857 1004 5.722263 CTTTGAATGTTTATGGCCATGTGA 58.278 37.500 29.04 11.24 0.00 3.58
880 1027 0.519999 GAATCTGAACGCTTGCGCTG 60.520 55.000 15.21 2.28 0.00 5.18
881 1028 1.230635 AATCTGAACGCTTGCGCTGT 61.231 50.000 15.21 0.00 0.00 4.40
882 1029 1.904852 ATCTGAACGCTTGCGCTGTG 61.905 55.000 15.21 10.97 0.00 3.66
988 1168 5.070446 ACCTCTATAAATTCACTCGCCATGA 59.930 40.000 0.00 0.00 0.00 3.07
1011 1209 0.747644 TCATGCAACCAGCCATACCG 60.748 55.000 0.00 0.00 44.83 4.02
1012 1210 1.031571 CATGCAACCAGCCATACCGT 61.032 55.000 0.00 0.00 44.83 4.83
1030 1228 2.752354 CCGTGTCTCTCTCATCTCACTT 59.248 50.000 0.00 0.00 0.00 3.16
1032 1230 3.181501 CGTGTCTCTCTCATCTCACTTCC 60.182 52.174 0.00 0.00 0.00 3.46
1033 1231 4.016444 GTGTCTCTCTCATCTCACTTCCT 58.984 47.826 0.00 0.00 0.00 3.36
1034 1232 4.096382 GTGTCTCTCTCATCTCACTTCCTC 59.904 50.000 0.00 0.00 0.00 3.71
1035 1233 4.018506 TGTCTCTCTCATCTCACTTCCTCT 60.019 45.833 0.00 0.00 0.00 3.69
1036 1234 4.336433 GTCTCTCTCATCTCACTTCCTCTG 59.664 50.000 0.00 0.00 0.00 3.35
1037 1235 4.018506 TCTCTCTCATCTCACTTCCTCTGT 60.019 45.833 0.00 0.00 0.00 3.41
1038 1236 4.269183 TCTCTCATCTCACTTCCTCTGTC 58.731 47.826 0.00 0.00 0.00 3.51
1039 1237 3.360867 TCTCATCTCACTTCCTCTGTCC 58.639 50.000 0.00 0.00 0.00 4.02
1040 1238 3.011144 TCTCATCTCACTTCCTCTGTCCT 59.989 47.826 0.00 0.00 0.00 3.85
1041 1239 3.360867 TCATCTCACTTCCTCTGTCCTC 58.639 50.000 0.00 0.00 0.00 3.71
1042 1240 3.011144 TCATCTCACTTCCTCTGTCCTCT 59.989 47.826 0.00 0.00 0.00 3.69
1043 1241 3.080300 TCTCACTTCCTCTGTCCTCTC 57.920 52.381 0.00 0.00 0.00 3.20
1048 1246 2.650322 ACTTCCTCTGTCCTCTCCTGTA 59.350 50.000 0.00 0.00 0.00 2.74
1055 1253 5.199982 TCTGTCCTCTCCTGTATCTTTCT 57.800 43.478 0.00 0.00 0.00 2.52
1058 1256 2.952978 TCCTCTCCTGTATCTTTCTCGC 59.047 50.000 0.00 0.00 0.00 5.03
1060 1258 2.690497 CTCTCCTGTATCTTTCTCGCCA 59.310 50.000 0.00 0.00 0.00 5.69
1082 1280 2.007360 CACAGAGTGGCACTGAGATC 57.993 55.000 27.45 10.49 38.55 2.75
1094 1292 1.218763 CTGAGATCGCAATCCAGCTG 58.781 55.000 6.78 6.78 31.78 4.24
1253 1451 2.347490 GAACCGCTGGCAGGAGAA 59.653 61.111 17.64 0.00 0.00 2.87
1255 1453 3.259633 AACCGCTGGCAGGAGAAGG 62.260 63.158 17.64 1.39 0.00 3.46
1356 1554 1.507174 GAGAGGTTCTACGCGCTGT 59.493 57.895 5.73 8.05 0.00 4.40
1512 1710 0.693049 TTTCAGGCTGGAGGACTTCC 59.307 55.000 15.73 0.00 46.98 3.46
1598 1796 1.446272 GGAGACCAAGGACGAAGCG 60.446 63.158 0.00 0.00 0.00 4.68
1599 1797 1.446272 GAGACCAAGGACGAAGCGG 60.446 63.158 0.00 0.00 0.00 5.52
1600 1798 3.119096 GACCAAGGACGAAGCGGC 61.119 66.667 0.00 0.00 0.00 6.53
1692 1890 2.505118 GACTCTCTGTCGCCGTGC 60.505 66.667 0.00 0.00 35.81 5.34
1861 2370 2.143876 AAGTGTTTTGAGCCCACAGT 57.856 45.000 0.00 0.00 0.00 3.55
1862 2371 3.290948 AAGTGTTTTGAGCCCACAGTA 57.709 42.857 0.00 0.00 0.00 2.74
2065 2581 0.599060 TGCGTGTACCTGACGAATCA 59.401 50.000 8.27 0.00 39.21 2.57
2084 2604 7.613022 ACGAATCATATGAATATCATGGGCTTT 59.387 33.333 9.99 0.00 37.70 3.51
2101 2621 3.181496 GGCTTTGGCAACTTAGATGCTAC 60.181 47.826 13.85 0.00 43.34 3.58
2108 2628 3.491267 GCAACTTAGATGCTACGGTGATC 59.509 47.826 7.23 0.00 40.64 2.92
2126 2646 0.680618 TCCGAGCTTTTGGACGGTTA 59.319 50.000 8.89 0.00 44.72 2.85
2155 2675 2.627515 TCCTATGGCATCTGAGCAAC 57.372 50.000 1.65 0.00 35.83 4.17
2163 2683 3.253188 TGGCATCTGAGCAACTTTTGTAC 59.747 43.478 0.00 0.00 35.83 2.90
2191 2717 3.744660 TCCAAACTCTCTGAAGGCTTTC 58.255 45.455 0.00 0.77 0.00 2.62
2193 2719 3.480470 CAAACTCTCTGAAGGCTTTCCA 58.520 45.455 6.06 0.00 32.09 3.53
2222 2748 1.588239 ATCAGACATTCTGGGAGCCA 58.412 50.000 3.40 0.00 44.39 4.75
2229 2755 1.961394 CATTCTGGGAGCCATTGGATG 59.039 52.381 6.95 0.00 30.82 3.51
2235 2761 2.092429 TGGGAGCCATTGGATGTAAGAC 60.092 50.000 6.95 0.00 0.00 3.01
2238 2764 1.134098 AGCCATTGGATGTAAGACCCG 60.134 52.381 6.95 0.00 0.00 5.28
2270 2796 3.402628 AACCGTATCATCTATGGTGCC 57.597 47.619 0.00 0.00 36.95 5.01
2274 2826 2.416027 CGTATCATCTATGGTGCCGGAG 60.416 54.545 5.05 0.00 0.00 4.63
2275 2827 0.322975 ATCATCTATGGTGCCGGAGC 59.677 55.000 5.05 0.00 40.48 4.70
2284 2836 3.970332 TGCCGGAGCACCTGATAT 58.030 55.556 5.05 0.00 46.52 1.63
2285 2837 2.220953 TGCCGGAGCACCTGATATT 58.779 52.632 5.05 0.00 46.52 1.28
2286 2838 0.106708 TGCCGGAGCACCTGATATTC 59.893 55.000 5.05 0.00 46.52 1.75
2287 2839 0.394565 GCCGGAGCACCTGATATTCT 59.605 55.000 5.05 0.00 39.53 2.40
2288 2840 1.202698 GCCGGAGCACCTGATATTCTT 60.203 52.381 5.05 0.00 39.53 2.52
2289 2841 2.760374 CCGGAGCACCTGATATTCTTC 58.240 52.381 0.00 0.00 0.00 2.87
2290 2842 2.548920 CCGGAGCACCTGATATTCTTCC 60.549 54.545 0.00 0.00 0.00 3.46
2291 2843 2.366916 CGGAGCACCTGATATTCTTCCT 59.633 50.000 0.00 0.00 0.00 3.36
2292 2844 3.737850 GGAGCACCTGATATTCTTCCTG 58.262 50.000 0.00 0.00 0.00 3.86
2293 2845 3.137533 GAGCACCTGATATTCTTCCTGC 58.862 50.000 0.00 0.00 0.00 4.85
2294 2846 2.507058 AGCACCTGATATTCTTCCTGCA 59.493 45.455 0.00 0.00 0.00 4.41
2295 2847 3.137913 AGCACCTGATATTCTTCCTGCAT 59.862 43.478 0.00 0.00 0.00 3.96
2296 2848 4.349048 AGCACCTGATATTCTTCCTGCATA 59.651 41.667 0.00 0.00 0.00 3.14
2297 2849 4.453819 GCACCTGATATTCTTCCTGCATAC 59.546 45.833 0.00 0.00 0.00 2.39
2298 2850 4.999950 CACCTGATATTCTTCCTGCATACC 59.000 45.833 0.00 0.00 0.00 2.73
2299 2851 4.660303 ACCTGATATTCTTCCTGCATACCA 59.340 41.667 0.00 0.00 0.00 3.25
2300 2852 5.132648 ACCTGATATTCTTCCTGCATACCAA 59.867 40.000 0.00 0.00 0.00 3.67
2353 2905 1.107114 ACACCATGTCCAAACGCAAA 58.893 45.000 0.00 0.00 0.00 3.68
2355 2907 2.288152 ACACCATGTCCAAACGCAAATC 60.288 45.455 0.00 0.00 0.00 2.17
2356 2908 1.959985 ACCATGTCCAAACGCAAATCA 59.040 42.857 0.00 0.00 0.00 2.57
2361 2913 3.849911 TGTCCAAACGCAAATCACAAAA 58.150 36.364 0.00 0.00 0.00 2.44
2362 2914 4.437239 TGTCCAAACGCAAATCACAAAAT 58.563 34.783 0.00 0.00 0.00 1.82
2364 2916 3.806521 TCCAAACGCAAATCACAAAATGG 59.193 39.130 0.00 0.00 0.00 3.16
2365 2917 3.806521 CCAAACGCAAATCACAAAATGGA 59.193 39.130 0.00 0.00 0.00 3.41
2366 2918 4.318689 CCAAACGCAAATCACAAAATGGAC 60.319 41.667 0.00 0.00 0.00 4.02
2367 2919 2.660490 ACGCAAATCACAAAATGGACG 58.340 42.857 0.00 0.00 0.00 4.79
2419 2972 3.515562 AGGCCATCCAACCATGTTTTTA 58.484 40.909 5.01 0.00 33.74 1.52
2430 2983 7.550906 TCCAACCATGTTTTTAAAACTTTCCTG 59.449 33.333 19.39 11.77 0.00 3.86
2596 3152 7.633361 TGAAACTAAGTAGAAAGCAGTAACG 57.367 36.000 0.00 0.00 0.00 3.18
2617 3173 1.059098 ATTAGGCATGGCATCCGAGA 58.941 50.000 22.64 0.00 0.00 4.04
2630 3186 2.509336 CGAGACCACATGGACCGC 60.509 66.667 4.53 0.00 38.94 5.68
2659 3216 0.847670 CGTCGTTGTCGTTGTTGCTA 59.152 50.000 0.00 0.00 38.33 3.49
2665 3222 3.302805 CGTTGTCGTTGTTGCTATTGACA 60.303 43.478 0.00 0.00 34.80 3.58
2674 3231 1.796017 TGCTATTGACACCCGGGATA 58.204 50.000 32.02 13.35 0.00 2.59
2754 3312 1.290009 GCCTTGCGCAACCTTGATT 59.710 52.632 21.02 0.00 37.47 2.57
2780 3338 0.817634 AGCTCGCGCTCTGACTAGAT 60.818 55.000 5.56 0.00 45.15 1.98
2782 3340 0.940833 CTCGCGCTCTGACTAGATGA 59.059 55.000 5.56 0.00 31.21 2.92
2798 3356 2.754658 GACGCCGAGGAGGAGGAA 60.755 66.667 0.00 0.00 44.78 3.36
2840 3398 1.751351 CGAGCATCAGTCTCCTTGGTA 59.249 52.381 0.00 0.00 33.17 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.060347 CCGTCCTATACTACAGTACTTTATTCA 57.940 37.037 0.00 0.00 32.72 2.57
26 27 8.020244 GCCGTCCTATACTACAGTACTTTATTC 58.980 40.741 0.00 0.00 32.72 1.75
27 28 7.308229 CGCCGTCCTATACTACAGTACTTTATT 60.308 40.741 0.00 0.00 32.72 1.40
28 29 6.148480 CGCCGTCCTATACTACAGTACTTTAT 59.852 42.308 0.00 0.00 32.72 1.40
29 30 5.466728 CGCCGTCCTATACTACAGTACTTTA 59.533 44.000 0.00 0.00 32.72 1.85
30 31 4.274459 CGCCGTCCTATACTACAGTACTTT 59.726 45.833 0.00 0.00 32.72 2.66
31 32 3.812053 CGCCGTCCTATACTACAGTACTT 59.188 47.826 0.00 0.00 32.72 2.24
32 33 3.181461 ACGCCGTCCTATACTACAGTACT 60.181 47.826 0.00 0.00 32.72 2.73
33 34 3.134458 ACGCCGTCCTATACTACAGTAC 58.866 50.000 0.00 0.00 32.72 2.73
34 35 3.475566 ACGCCGTCCTATACTACAGTA 57.524 47.619 0.00 0.00 34.67 2.74
35 36 2.338577 ACGCCGTCCTATACTACAGT 57.661 50.000 0.00 0.00 0.00 3.55
36 37 2.857489 GCAACGCCGTCCTATACTACAG 60.857 54.545 0.00 0.00 0.00 2.74
37 38 1.066002 GCAACGCCGTCCTATACTACA 59.934 52.381 0.00 0.00 0.00 2.74
38 39 1.601412 GGCAACGCCGTCCTATACTAC 60.601 57.143 0.00 0.00 39.62 2.73
111 112 4.537433 CCTGGCCAGGTAGCGCTC 62.537 72.222 39.52 5.63 43.61 5.03
124 125 1.819632 GTATGCGTTGAGGCCCTGG 60.820 63.158 0.00 0.00 0.00 4.45
149 158 1.529865 GAGTAACCGTGGTCAAAGTGC 59.470 52.381 0.00 0.00 0.00 4.40
178 187 0.179048 TGTGGTGTCTGACAGGCTTG 60.179 55.000 11.41 0.00 0.00 4.01
203 212 7.962964 TCTATCTAGGCAATGTAAAATTCGG 57.037 36.000 0.00 0.00 0.00 4.30
212 221 5.065218 CGCAAGTTTTCTATCTAGGCAATGT 59.935 40.000 0.00 0.00 0.00 2.71
239 256 0.034616 GGAATAGAGCAGAGCCGCAT 59.965 55.000 0.00 0.00 0.00 4.73
287 304 4.002982 CCTCACAAATCATGGACGAAGAA 58.997 43.478 0.00 0.00 0.00 2.52
306 323 1.160137 AAAGCATCAGCAACGTCCTC 58.840 50.000 0.00 0.00 45.49 3.71
349 366 4.155826 TGCAGTTCCACCTTTTATGATTCG 59.844 41.667 0.00 0.00 0.00 3.34
402 419 4.733230 GCGTGGCATTTATGTTAGATTGCA 60.733 41.667 0.00 0.00 0.00 4.08
428 445 7.312899 AATTGAATGACGAAAGGTTCAATACC 58.687 34.615 11.25 0.00 43.86 2.73
438 506 5.456192 AGTAGCGAATTGAATGACGAAAG 57.544 39.130 8.69 0.00 0.00 2.62
445 513 4.210120 GCAGAGGTAGTAGCGAATTGAATG 59.790 45.833 0.00 0.00 0.00 2.67
447 515 3.430374 GGCAGAGGTAGTAGCGAATTGAA 60.430 47.826 0.00 0.00 0.00 2.69
451 519 1.041437 GGGCAGAGGTAGTAGCGAAT 58.959 55.000 0.00 0.00 0.00 3.34
456 524 6.042093 TCAATAAATCAGGGCAGAGGTAGTAG 59.958 42.308 0.00 0.00 0.00 2.57
459 527 5.296151 TCAATAAATCAGGGCAGAGGTAG 57.704 43.478 0.00 0.00 0.00 3.18
461 529 4.414846 AGATCAATAAATCAGGGCAGAGGT 59.585 41.667 0.00 0.00 0.00 3.85
463 531 6.956202 AAAGATCAATAAATCAGGGCAGAG 57.044 37.500 0.00 0.00 0.00 3.35
464 532 6.664816 ACAAAAGATCAATAAATCAGGGCAGA 59.335 34.615 0.00 0.00 0.00 4.26
465 533 6.870769 ACAAAAGATCAATAAATCAGGGCAG 58.129 36.000 0.00 0.00 0.00 4.85
466 534 6.855763 ACAAAAGATCAATAAATCAGGGCA 57.144 33.333 0.00 0.00 0.00 5.36
467 535 9.822185 AAATACAAAAGATCAATAAATCAGGGC 57.178 29.630 0.00 0.00 0.00 5.19
519 587 9.840427 GTAACATGCATTAACACTTTATCAGTT 57.160 29.630 0.00 0.00 30.92 3.16
520 588 9.231297 AGTAACATGCATTAACACTTTATCAGT 57.769 29.630 0.00 0.00 35.35 3.41
521 589 9.494479 CAGTAACATGCATTAACACTTTATCAG 57.506 33.333 0.00 0.00 0.00 2.90
522 590 9.225436 TCAGTAACATGCATTAACACTTTATCA 57.775 29.630 0.00 0.00 0.00 2.15
525 593 9.891828 CTTTCAGTAACATGCATTAACACTTTA 57.108 29.630 0.00 0.00 0.00 1.85
526 594 8.413229 ACTTTCAGTAACATGCATTAACACTTT 58.587 29.630 0.00 0.00 0.00 2.66
527 595 7.940850 ACTTTCAGTAACATGCATTAACACTT 58.059 30.769 0.00 0.00 0.00 3.16
528 596 7.510549 ACTTTCAGTAACATGCATTAACACT 57.489 32.000 0.00 0.00 0.00 3.55
529 597 7.647715 ACAACTTTCAGTAACATGCATTAACAC 59.352 33.333 0.00 0.00 0.00 3.32
530 598 7.711846 ACAACTTTCAGTAACATGCATTAACA 58.288 30.769 0.00 0.00 0.00 2.41
531 599 9.840427 ATACAACTTTCAGTAACATGCATTAAC 57.160 29.630 0.00 0.00 0.00 2.01
536 604 9.008965 ACAATATACAACTTTCAGTAACATGCA 57.991 29.630 0.00 0.00 0.00 3.96
537 605 9.840427 AACAATATACAACTTTCAGTAACATGC 57.160 29.630 0.00 0.00 0.00 4.06
559 627 9.661563 AGGTATGATCAAGTACGAATTTAACAA 57.338 29.630 0.00 0.00 0.00 2.83
560 628 9.661563 AAGGTATGATCAAGTACGAATTTAACA 57.338 29.630 0.00 0.00 0.00 2.41
564 632 9.226606 TCAAAAGGTATGATCAAGTACGAATTT 57.773 29.630 0.00 0.00 0.00 1.82
565 633 8.786826 TCAAAAGGTATGATCAAGTACGAATT 57.213 30.769 0.00 0.00 0.00 2.17
566 634 8.830580 CATCAAAAGGTATGATCAAGTACGAAT 58.169 33.333 0.00 0.00 35.38 3.34
567 635 8.038351 TCATCAAAAGGTATGATCAAGTACGAA 58.962 33.333 0.00 0.00 35.38 3.85
568 636 7.552459 TCATCAAAAGGTATGATCAAGTACGA 58.448 34.615 0.00 0.00 35.38 3.43
569 637 7.770801 TCATCAAAAGGTATGATCAAGTACG 57.229 36.000 0.00 0.00 35.38 3.67
586 654 9.558648 CACGTCATCAAAGAAAATATCATCAAA 57.441 29.630 0.00 0.00 0.00 2.69
587 655 8.945057 TCACGTCATCAAAGAAAATATCATCAA 58.055 29.630 0.00 0.00 0.00 2.57
588 656 8.491331 TCACGTCATCAAAGAAAATATCATCA 57.509 30.769 0.00 0.00 0.00 3.07
589 657 9.941664 ATTCACGTCATCAAAGAAAATATCATC 57.058 29.630 0.00 0.00 0.00 2.92
590 658 9.941664 GATTCACGTCATCAAAGAAAATATCAT 57.058 29.630 0.00 0.00 0.00 2.45
591 659 8.945057 TGATTCACGTCATCAAAGAAAATATCA 58.055 29.630 4.73 0.00 0.00 2.15
592 660 9.773328 TTGATTCACGTCATCAAAGAAAATATC 57.227 29.630 14.60 0.00 37.64 1.63
599 667 9.558648 CAAAATATTGATTCACGTCATCAAAGA 57.441 29.630 18.94 12.63 42.53 2.52
600 668 9.345517 ACAAAATATTGATTCACGTCATCAAAG 57.654 29.630 18.94 10.29 42.53 2.77
601 669 9.689976 AACAAAATATTGATTCACGTCATCAAA 57.310 25.926 18.94 11.44 42.53 2.69
603 671 9.986833 CTAACAAAATATTGATTCACGTCATCA 57.013 29.630 3.27 3.27 38.94 3.07
604 672 8.947940 GCTAACAAAATATTGATTCACGTCATC 58.052 33.333 0.00 0.00 38.94 2.92
605 673 8.677300 AGCTAACAAAATATTGATTCACGTCAT 58.323 29.630 0.00 0.00 38.94 3.06
606 674 8.039603 AGCTAACAAAATATTGATTCACGTCA 57.960 30.769 0.00 0.00 38.94 4.35
607 675 8.175069 TGAGCTAACAAAATATTGATTCACGTC 58.825 33.333 0.00 0.00 38.94 4.34
608 676 8.039603 TGAGCTAACAAAATATTGATTCACGT 57.960 30.769 0.00 0.00 38.94 4.49
609 677 8.894409 TTGAGCTAACAAAATATTGATTCACG 57.106 30.769 0.00 0.00 38.94 4.35
610 678 8.801913 GCTTGAGCTAACAAAATATTGATTCAC 58.198 33.333 0.00 0.00 37.77 3.18
611 679 8.522003 TGCTTGAGCTAACAAAATATTGATTCA 58.478 29.630 4.44 0.00 42.66 2.57
612 680 8.915871 TGCTTGAGCTAACAAAATATTGATTC 57.084 30.769 4.44 0.00 42.66 2.52
613 681 9.709495 TTTGCTTGAGCTAACAAAATATTGATT 57.291 25.926 4.44 0.00 42.66 2.57
614 682 9.362539 CTTTGCTTGAGCTAACAAAATATTGAT 57.637 29.630 4.44 0.00 42.66 2.57
615 683 7.814107 CCTTTGCTTGAGCTAACAAAATATTGA 59.186 33.333 4.44 0.00 42.66 2.57
616 684 7.599998 ACCTTTGCTTGAGCTAACAAAATATTG 59.400 33.333 4.44 0.00 42.66 1.90
617 685 7.670364 ACCTTTGCTTGAGCTAACAAAATATT 58.330 30.769 4.44 0.00 42.66 1.28
618 686 7.232118 ACCTTTGCTTGAGCTAACAAAATAT 57.768 32.000 4.44 0.00 42.66 1.28
619 687 6.648879 ACCTTTGCTTGAGCTAACAAAATA 57.351 33.333 4.44 0.00 42.66 1.40
620 688 5.535753 ACCTTTGCTTGAGCTAACAAAAT 57.464 34.783 4.44 0.00 42.66 1.82
621 689 5.337578 AACCTTTGCTTGAGCTAACAAAA 57.662 34.783 4.44 0.00 42.66 2.44
622 690 6.458232 TTAACCTTTGCTTGAGCTAACAAA 57.542 33.333 4.44 0.00 42.66 2.83
623 691 6.096282 ACTTTAACCTTTGCTTGAGCTAACAA 59.904 34.615 4.44 0.00 42.66 2.83
624 692 5.592688 ACTTTAACCTTTGCTTGAGCTAACA 59.407 36.000 4.44 0.00 42.66 2.41
625 693 6.073327 ACTTTAACCTTTGCTTGAGCTAAC 57.927 37.500 4.44 0.00 42.66 2.34
626 694 6.709018 AACTTTAACCTTTGCTTGAGCTAA 57.291 33.333 4.44 2.25 42.66 3.09
627 695 6.320164 TCAAACTTTAACCTTTGCTTGAGCTA 59.680 34.615 4.44 0.00 42.66 3.32
628 696 5.127031 TCAAACTTTAACCTTTGCTTGAGCT 59.873 36.000 4.44 0.00 42.66 4.09
629 697 5.348164 TCAAACTTTAACCTTTGCTTGAGC 58.652 37.500 0.00 0.00 42.50 4.26
630 698 8.134895 TGTATCAAACTTTAACCTTTGCTTGAG 58.865 33.333 0.00 0.00 0.00 3.02
631 699 8.001881 TGTATCAAACTTTAACCTTTGCTTGA 57.998 30.769 0.00 0.00 0.00 3.02
632 700 7.920682 ACTGTATCAAACTTTAACCTTTGCTTG 59.079 33.333 0.00 0.00 0.00 4.01
633 701 8.007405 ACTGTATCAAACTTTAACCTTTGCTT 57.993 30.769 0.00 0.00 0.00 3.91
634 702 7.582667 ACTGTATCAAACTTTAACCTTTGCT 57.417 32.000 0.00 0.00 0.00 3.91
650 718 9.127277 GCCCCTTTTGTATTTTATACTGTATCA 57.873 33.333 3.09 0.00 0.00 2.15
651 719 9.127277 TGCCCCTTTTGTATTTTATACTGTATC 57.873 33.333 3.09 0.00 0.00 2.24
652 720 9.482175 TTGCCCCTTTTGTATTTTATACTGTAT 57.518 29.630 5.53 5.53 0.00 2.29
653 721 8.880991 TTGCCCCTTTTGTATTTTATACTGTA 57.119 30.769 0.00 0.00 0.00 2.74
654 722 7.784470 TTGCCCCTTTTGTATTTTATACTGT 57.216 32.000 0.00 0.00 0.00 3.55
658 726 9.825109 GCTTTATTGCCCCTTTTGTATTTTATA 57.175 29.630 0.00 0.00 0.00 0.98
659 727 8.325046 TGCTTTATTGCCCCTTTTGTATTTTAT 58.675 29.630 0.00 0.00 0.00 1.40
660 728 7.680730 TGCTTTATTGCCCCTTTTGTATTTTA 58.319 30.769 0.00 0.00 0.00 1.52
661 729 6.538263 TGCTTTATTGCCCCTTTTGTATTTT 58.462 32.000 0.00 0.00 0.00 1.82
662 730 6.120507 TGCTTTATTGCCCCTTTTGTATTT 57.879 33.333 0.00 0.00 0.00 1.40
663 731 5.338300 CCTGCTTTATTGCCCCTTTTGTATT 60.338 40.000 0.00 0.00 0.00 1.89
664 732 4.162131 CCTGCTTTATTGCCCCTTTTGTAT 59.838 41.667 0.00 0.00 0.00 2.29
665 733 3.513515 CCTGCTTTATTGCCCCTTTTGTA 59.486 43.478 0.00 0.00 0.00 2.41
666 734 2.302733 CCTGCTTTATTGCCCCTTTTGT 59.697 45.455 0.00 0.00 0.00 2.83
667 735 2.566724 TCCTGCTTTATTGCCCCTTTTG 59.433 45.455 0.00 0.00 0.00 2.44
668 736 2.567169 GTCCTGCTTTATTGCCCCTTTT 59.433 45.455 0.00 0.00 0.00 2.27
669 737 2.179427 GTCCTGCTTTATTGCCCCTTT 58.821 47.619 0.00 0.00 0.00 3.11
670 738 1.852633 GTCCTGCTTTATTGCCCCTT 58.147 50.000 0.00 0.00 0.00 3.95
671 739 0.394352 CGTCCTGCTTTATTGCCCCT 60.394 55.000 0.00 0.00 0.00 4.79
672 740 1.384222 CCGTCCTGCTTTATTGCCCC 61.384 60.000 0.00 0.00 0.00 5.80
673 741 0.393808 TCCGTCCTGCTTTATTGCCC 60.394 55.000 0.00 0.00 0.00 5.36
674 742 1.401905 CTTCCGTCCTGCTTTATTGCC 59.598 52.381 0.00 0.00 0.00 4.52
675 743 1.401905 CCTTCCGTCCTGCTTTATTGC 59.598 52.381 0.00 0.00 0.00 3.56
676 744 2.711542 ACCTTCCGTCCTGCTTTATTG 58.288 47.619 0.00 0.00 0.00 1.90
677 745 3.518303 ACTACCTTCCGTCCTGCTTTATT 59.482 43.478 0.00 0.00 0.00 1.40
678 746 3.105283 ACTACCTTCCGTCCTGCTTTAT 58.895 45.455 0.00 0.00 0.00 1.40
679 747 2.232941 CACTACCTTCCGTCCTGCTTTA 59.767 50.000 0.00 0.00 0.00 1.85
680 748 1.002087 CACTACCTTCCGTCCTGCTTT 59.998 52.381 0.00 0.00 0.00 3.51
681 749 0.608640 CACTACCTTCCGTCCTGCTT 59.391 55.000 0.00 0.00 0.00 3.91
682 750 1.258445 CCACTACCTTCCGTCCTGCT 61.258 60.000 0.00 0.00 0.00 4.24
683 751 1.218316 CCACTACCTTCCGTCCTGC 59.782 63.158 0.00 0.00 0.00 4.85
684 752 0.974383 AACCACTACCTTCCGTCCTG 59.026 55.000 0.00 0.00 0.00 3.86
685 753 2.610438 TAACCACTACCTTCCGTCCT 57.390 50.000 0.00 0.00 0.00 3.85
686 754 2.159000 CCATAACCACTACCTTCCGTCC 60.159 54.545 0.00 0.00 0.00 4.79
687 755 2.159000 CCCATAACCACTACCTTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
688 756 1.835531 CCCATAACCACTACCTTCCGT 59.164 52.381 0.00 0.00 0.00 4.69
689 757 1.835531 ACCCATAACCACTACCTTCCG 59.164 52.381 0.00 0.00 0.00 4.30
690 758 6.752285 TTATACCCATAACCACTACCTTCC 57.248 41.667 0.00 0.00 0.00 3.46
691 759 9.063615 CATTTTATACCCATAACCACTACCTTC 57.936 37.037 0.00 0.00 0.00 3.46
692 760 8.562635 ACATTTTATACCCATAACCACTACCTT 58.437 33.333 0.00 0.00 0.00 3.50
693 761 7.996644 CACATTTTATACCCATAACCACTACCT 59.003 37.037 0.00 0.00 0.00 3.08
694 762 7.255346 GCACATTTTATACCCATAACCACTACC 60.255 40.741 0.00 0.00 0.00 3.18
695 763 7.283580 TGCACATTTTATACCCATAACCACTAC 59.716 37.037 0.00 0.00 0.00 2.73
696 764 7.347252 TGCACATTTTATACCCATAACCACTA 58.653 34.615 0.00 0.00 0.00 2.74
697 765 6.191315 TGCACATTTTATACCCATAACCACT 58.809 36.000 0.00 0.00 0.00 4.00
698 766 6.096282 ACTGCACATTTTATACCCATAACCAC 59.904 38.462 0.00 0.00 0.00 4.16
699 767 6.191315 ACTGCACATTTTATACCCATAACCA 58.809 36.000 0.00 0.00 0.00 3.67
700 768 6.709018 ACTGCACATTTTATACCCATAACC 57.291 37.500 0.00 0.00 0.00 2.85
701 769 8.996024 AAAACTGCACATTTTATACCCATAAC 57.004 30.769 2.72 0.00 0.00 1.89
755 827 7.578310 TGACCAAGATATACTGTACTGTACC 57.422 40.000 14.05 7.47 0.00 3.34
774 852 2.169769 GTCAGGTAATTCGGGATGACCA 59.830 50.000 5.56 0.00 41.32 4.02
775 853 2.802057 CGTCAGGTAATTCGGGATGACC 60.802 54.545 0.00 0.00 39.36 4.02
790 870 3.893763 ATCCGCGAGCTCGTCAGG 61.894 66.667 34.46 31.20 42.22 3.86
802 882 1.136147 CTCTGTTTGCTGCATCCGC 59.864 57.895 1.84 0.00 39.24 5.54
807 887 4.523173 AGTAGTACTACTCTGTTTGCTGCA 59.477 41.667 26.61 0.00 42.30 4.41
809 889 6.748198 GCTAAGTAGTACTACTCTGTTTGCTG 59.252 42.308 30.81 15.61 44.96 4.41
824 905 8.889717 GCCATAAACATTCAAAGCTAAGTAGTA 58.110 33.333 0.00 0.00 0.00 1.82
825 906 7.148069 GGCCATAAACATTCAAAGCTAAGTAGT 60.148 37.037 0.00 0.00 0.00 2.73
826 907 7.148086 TGGCCATAAACATTCAAAGCTAAGTAG 60.148 37.037 0.00 0.00 0.00 2.57
827 908 6.661377 TGGCCATAAACATTCAAAGCTAAGTA 59.339 34.615 0.00 0.00 0.00 2.24
828 909 5.480073 TGGCCATAAACATTCAAAGCTAAGT 59.520 36.000 0.00 0.00 0.00 2.24
829 910 5.964758 TGGCCATAAACATTCAAAGCTAAG 58.035 37.500 0.00 0.00 0.00 2.18
832 913 4.223477 ACATGGCCATAAACATTCAAAGCT 59.777 37.500 20.30 0.00 0.00 3.74
833 914 4.330620 CACATGGCCATAAACATTCAAAGC 59.669 41.667 20.30 0.00 0.00 3.51
843 990 5.533528 CAGATTCTGATCACATGGCCATAAA 59.466 40.000 20.30 7.15 34.60 1.40
847 994 2.506644 TCAGATTCTGATCACATGGCCA 59.493 45.455 8.56 8.56 35.39 5.36
849 996 3.002042 CGTTCAGATTCTGATCACATGGC 59.998 47.826 16.82 1.13 40.39 4.40
857 1004 1.662629 CGCAAGCGTTCAGATTCTGAT 59.337 47.619 16.82 0.00 40.39 2.90
880 1027 9.827411 GCTTATATCTAAATTCCGGAATTTCAC 57.173 33.333 43.42 24.79 44.98 3.18
881 1028 9.567776 TGCTTATATCTAAATTCCGGAATTTCA 57.432 29.630 43.42 33.88 44.98 2.69
927 1107 5.178623 TGCTAGAAATTGTTAACACTCCGTG 59.821 40.000 8.07 0.00 39.75 4.94
929 1109 5.618561 GTGCTAGAAATTGTTAACACTCCG 58.381 41.667 8.07 1.86 0.00 4.63
935 1115 6.461698 CGTGATTCGTGCTAGAAATTGTTAAC 59.538 38.462 0.00 0.00 33.43 2.01
946 1126 0.370273 GTTGCCGTGATTCGTGCTAG 59.630 55.000 0.00 0.00 36.93 3.42
967 1147 4.991056 GCTCATGGCGAGTGAATTTATAGA 59.009 41.667 0.00 0.00 44.33 1.98
988 1168 3.058160 GGCTGGTTGCATGACGCT 61.058 61.111 0.00 0.00 45.15 5.07
989 1169 1.375853 TATGGCTGGTTGCATGACGC 61.376 55.000 0.00 0.00 45.15 5.19
990 1170 0.378257 GTATGGCTGGTTGCATGACG 59.622 55.000 0.00 0.00 45.15 4.35
991 1171 0.740737 GGTATGGCTGGTTGCATGAC 59.259 55.000 0.00 0.00 45.15 3.06
995 1193 1.673993 CACGGTATGGCTGGTTGCA 60.674 57.895 0.00 0.00 45.15 4.08
1011 1209 4.016444 AGGAAGTGAGATGAGAGAGACAC 58.984 47.826 0.00 0.00 0.00 3.67
1012 1210 4.018506 AGAGGAAGTGAGATGAGAGAGACA 60.019 45.833 0.00 0.00 0.00 3.41
1030 1228 3.127250 AGATACAGGAGAGGACAGAGGA 58.873 50.000 0.00 0.00 0.00 3.71
1032 1230 5.200483 AGAAAGATACAGGAGAGGACAGAG 58.800 45.833 0.00 0.00 0.00 3.35
1033 1231 5.197451 GAGAAAGATACAGGAGAGGACAGA 58.803 45.833 0.00 0.00 0.00 3.41
1034 1232 4.036262 CGAGAAAGATACAGGAGAGGACAG 59.964 50.000 0.00 0.00 0.00 3.51
1035 1233 3.948473 CGAGAAAGATACAGGAGAGGACA 59.052 47.826 0.00 0.00 0.00 4.02
1036 1234 3.243267 GCGAGAAAGATACAGGAGAGGAC 60.243 52.174 0.00 0.00 0.00 3.85
1037 1235 2.952978 GCGAGAAAGATACAGGAGAGGA 59.047 50.000 0.00 0.00 0.00 3.71
1038 1236 2.035321 GGCGAGAAAGATACAGGAGAGG 59.965 54.545 0.00 0.00 0.00 3.69
1039 1237 2.690497 TGGCGAGAAAGATACAGGAGAG 59.310 50.000 0.00 0.00 0.00 3.20
1040 1238 2.735151 TGGCGAGAAAGATACAGGAGA 58.265 47.619 0.00 0.00 0.00 3.71
1041 1239 3.190874 GTTGGCGAGAAAGATACAGGAG 58.809 50.000 0.00 0.00 0.00 3.69
1042 1240 2.093658 GGTTGGCGAGAAAGATACAGGA 60.094 50.000 0.00 0.00 0.00 3.86
1043 1241 2.280628 GGTTGGCGAGAAAGATACAGG 58.719 52.381 0.00 0.00 0.00 4.00
1048 1246 1.347707 TCTGTGGTTGGCGAGAAAGAT 59.652 47.619 0.00 0.00 0.00 2.40
1072 1270 0.935898 CTGGATTGCGATCTCAGTGC 59.064 55.000 13.72 0.00 31.45 4.40
1075 1273 1.218763 CAGCTGGATTGCGATCTCAG 58.781 55.000 20.11 20.11 38.13 3.35
1080 1278 0.543277 TCTTCCAGCTGGATTGCGAT 59.457 50.000 35.42 0.00 44.98 4.58
1082 1280 1.372087 GGTCTTCCAGCTGGATTGCG 61.372 60.000 35.42 22.43 44.98 4.85
1094 1292 2.159028 GCAGACTGTAGGATGGTCTTCC 60.159 54.545 3.99 0.00 38.12 3.46
1099 1297 0.539051 GCTGCAGACTGTAGGATGGT 59.461 55.000 20.43 0.00 30.40 3.55
1235 1433 3.589654 TTCTCCTGCCAGCGGTTCG 62.590 63.158 0.00 0.00 0.00 3.95
1238 1436 3.710722 CCTTCTCCTGCCAGCGGT 61.711 66.667 0.00 0.00 0.00 5.68
1493 1691 0.693049 GGAAGTCCTCCAGCCTGAAA 59.307 55.000 0.00 0.00 44.67 2.69
1599 1797 4.918201 CTCCTTCCCGCCATCCGC 62.918 72.222 0.00 0.00 35.03 5.54
1600 1798 4.241555 CCTCCTTCCCGCCATCCG 62.242 72.222 0.00 0.00 0.00 4.18
1692 1890 2.963854 CGCAGCCAGTATCAGCGG 60.964 66.667 0.00 0.00 44.20 5.52
1778 1982 3.349006 GGACATGGCATAGGCGCG 61.349 66.667 0.00 0.00 42.47 6.86
1783 1987 2.609825 GTCGCTGGACATGGCATAG 58.390 57.895 0.00 0.00 42.91 2.23
1844 2353 2.685897 TGTTACTGTGGGCTCAAAACAC 59.314 45.455 0.00 0.00 35.75 3.32
1850 2359 1.003118 GTCCATGTTACTGTGGGCTCA 59.997 52.381 5.07 0.00 37.15 4.26
1851 2360 1.739067 GTCCATGTTACTGTGGGCTC 58.261 55.000 5.07 0.00 37.15 4.70
1932 2441 4.691860 ACATCTTTTCTGCATGCAGTAC 57.308 40.909 39.08 3.87 43.96 2.73
1940 2449 2.422597 CGTGGGTACATCTTTTCTGCA 58.577 47.619 0.00 0.00 0.00 4.41
2065 2581 5.335261 TGCCAAAGCCCATGATATTCATAT 58.665 37.500 0.00 0.00 34.77 1.78
2084 2604 1.553248 ACCGTAGCATCTAAGTTGCCA 59.447 47.619 0.00 0.00 41.06 4.92
2108 2628 1.076332 CTAACCGTCCAAAAGCTCGG 58.924 55.000 7.66 7.66 46.98 4.63
2126 2646 4.712829 CAGATGCCATAGGATCAGAGATCT 59.287 45.833 0.00 0.00 0.00 2.75
2155 2675 9.057089 AGAGAGTTTGGAACATAAGTACAAAAG 57.943 33.333 0.00 0.00 39.30 2.27
2163 2683 5.123027 GCCTTCAGAGAGTTTGGAACATAAG 59.877 44.000 0.00 0.00 39.30 1.73
2222 2748 1.768870 CTCCCGGGTCTTACATCCAAT 59.231 52.381 22.86 0.00 0.00 3.16
2235 2761 0.606604 CGGTTATATGACCTCCCGGG 59.393 60.000 16.85 16.85 37.56 5.73
2238 2764 5.657302 AGATGATACGGTTATATGACCTCCC 59.343 44.000 14.25 2.60 37.56 4.30
2250 2776 2.288825 CGGCACCATAGATGATACGGTT 60.289 50.000 0.00 0.00 0.00 4.44
2270 2796 2.366916 AGGAAGAATATCAGGTGCTCCG 59.633 50.000 0.00 0.00 39.05 4.63
2274 2826 2.923121 TGCAGGAAGAATATCAGGTGC 58.077 47.619 0.00 0.00 0.00 5.01
2275 2827 4.999950 GGTATGCAGGAAGAATATCAGGTG 59.000 45.833 0.00 0.00 0.00 4.00
2276 2828 4.660303 TGGTATGCAGGAAGAATATCAGGT 59.340 41.667 0.00 0.00 25.35 4.00
2277 2829 5.233083 TGGTATGCAGGAAGAATATCAGG 57.767 43.478 0.00 0.00 25.35 3.86
2278 2830 6.769822 ACTTTGGTATGCAGGAAGAATATCAG 59.230 38.462 0.00 0.00 30.36 2.90
2279 2831 6.662755 ACTTTGGTATGCAGGAAGAATATCA 58.337 36.000 0.00 0.00 26.16 2.15
2280 2832 8.560374 GTTACTTTGGTATGCAGGAAGAATATC 58.440 37.037 0.00 0.00 0.00 1.63
2281 2833 8.052748 TGTTACTTTGGTATGCAGGAAGAATAT 58.947 33.333 0.00 0.00 0.00 1.28
2282 2834 7.398829 TGTTACTTTGGTATGCAGGAAGAATA 58.601 34.615 0.00 0.00 0.00 1.75
2283 2835 6.245408 TGTTACTTTGGTATGCAGGAAGAAT 58.755 36.000 0.00 0.00 0.00 2.40
2284 2836 5.626142 TGTTACTTTGGTATGCAGGAAGAA 58.374 37.500 0.00 0.00 0.00 2.52
2285 2837 5.012664 TCTGTTACTTTGGTATGCAGGAAGA 59.987 40.000 0.00 0.00 34.79 2.87
2286 2838 5.245531 TCTGTTACTTTGGTATGCAGGAAG 58.754 41.667 0.00 0.00 34.79 3.46
2287 2839 5.235850 TCTGTTACTTTGGTATGCAGGAA 57.764 39.130 0.00 0.00 34.79 3.36
2288 2840 4.901197 TCTGTTACTTTGGTATGCAGGA 57.099 40.909 0.00 0.00 34.79 3.86
2289 2841 5.185454 TGATCTGTTACTTTGGTATGCAGG 58.815 41.667 0.00 0.00 34.79 4.85
2290 2842 6.292542 CGATGATCTGTTACTTTGGTATGCAG 60.293 42.308 0.00 0.00 35.07 4.41
2291 2843 5.523552 CGATGATCTGTTACTTTGGTATGCA 59.476 40.000 0.00 0.00 0.00 3.96
2292 2844 5.559035 GCGATGATCTGTTACTTTGGTATGC 60.559 44.000 0.00 0.00 0.00 3.14
2293 2845 5.523552 TGCGATGATCTGTTACTTTGGTATG 59.476 40.000 0.00 0.00 0.00 2.39
2294 2846 5.670485 TGCGATGATCTGTTACTTTGGTAT 58.330 37.500 0.00 0.00 0.00 2.73
2295 2847 5.079689 TGCGATGATCTGTTACTTTGGTA 57.920 39.130 0.00 0.00 0.00 3.25
2296 2848 3.937814 TGCGATGATCTGTTACTTTGGT 58.062 40.909 0.00 0.00 0.00 3.67
2297 2849 4.393062 ACTTGCGATGATCTGTTACTTTGG 59.607 41.667 0.00 0.00 0.00 3.28
2298 2850 5.319139 CACTTGCGATGATCTGTTACTTTG 58.681 41.667 0.00 0.00 0.00 2.77
2299 2851 4.393062 CCACTTGCGATGATCTGTTACTTT 59.607 41.667 0.00 0.00 0.00 2.66
2300 2852 3.935203 CCACTTGCGATGATCTGTTACTT 59.065 43.478 0.00 0.00 0.00 2.24
2337 2889 2.288091 TGTGATTTGCGTTTGGACATGG 60.288 45.455 0.00 0.00 0.00 3.66
2341 2893 4.318689 CCATTTTGTGATTTGCGTTTGGAC 60.319 41.667 0.00 0.00 0.00 4.02
2353 2905 1.626686 TTGGGCGTCCATTTTGTGAT 58.373 45.000 10.94 0.00 43.63 3.06
2355 2907 1.496934 GTTTGGGCGTCCATTTTGTG 58.503 50.000 10.94 0.00 43.63 3.33
2356 2908 0.031449 CGTTTGGGCGTCCATTTTGT 59.969 50.000 10.94 0.00 43.63 2.83
2380 2932 0.462581 CTTCGCTTGCTAGATGCCCA 60.463 55.000 0.00 0.00 42.00 5.36
2383 2935 1.645997 GCCTTCGCTTGCTAGATGC 59.354 57.895 0.00 0.00 43.25 3.91
2419 2972 7.274447 TCATCATTTGAAAGCAGGAAAGTTTT 58.726 30.769 0.00 0.00 0.00 2.43
2585 3141 4.574828 CCATGCCTAATACGTTACTGCTTT 59.425 41.667 0.00 0.00 0.00 3.51
2586 3142 4.127171 CCATGCCTAATACGTTACTGCTT 58.873 43.478 0.00 0.00 0.00 3.91
2587 3143 3.728845 CCATGCCTAATACGTTACTGCT 58.271 45.455 0.00 0.00 0.00 4.24
2593 3149 2.504367 GGATGCCATGCCTAATACGTT 58.496 47.619 0.00 0.00 0.00 3.99
2596 3152 2.028112 TCTCGGATGCCATGCCTAATAC 60.028 50.000 0.00 0.00 0.00 1.89
2659 3216 0.544697 GTGGTATCCCGGGTGTCAAT 59.455 55.000 22.86 8.82 0.00 2.57
2665 3222 1.613035 TTTCCGTGGTATCCCGGGT 60.613 57.895 22.86 10.79 44.32 5.28
2746 3303 1.134965 CGAGCTCCGAAGAATCAAGGT 60.135 52.381 8.47 0.00 41.76 3.50
2749 3307 0.802222 CGCGAGCTCCGAAGAATCAA 60.802 55.000 16.62 0.00 41.76 2.57
2780 3338 3.578968 TTCCTCCTCCTCGGCGTCA 62.579 63.158 6.85 0.00 0.00 4.35
2782 3340 2.756283 CTTCCTCCTCCTCGGCGT 60.756 66.667 6.85 0.00 0.00 5.68
2822 3380 2.763448 GACTACCAAGGAGACTGATGCT 59.237 50.000 0.00 0.00 42.68 3.79
2828 3386 4.072698 GGTCCAAGACTACCAAGGAGACT 61.073 52.174 0.00 0.00 35.70 3.24


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

AutoCloner maintained by Alex Coulton.