Multiple sequence alignment - TraesCS3D01G259800

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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 TraesCS3D01G259800 chr3D 100.000 2536 0 0 1512 4047 361737255 361739790 0.000000e+00 4684.0
1 TraesCS3D01G259800 chr3D 100.000 1069 0 0 1 1069 361735744 361736812 0.000000e+00 1975.0
2 TraesCS3D01G259800 chr3D 78.957 556 70 21 1 516 277063499 277062951 6.480000e-88 335.0
3 TraesCS3D01G259800 chr3D 78.598 542 82 16 1 516 317091437 317090904 1.080000e-85 327.0
4 TraesCS3D01G259800 chr3D 88.889 72 5 2 512 580 286743214 286743143 7.210000e-13 86.1
5 TraesCS3D01G259800 chr3A 96.887 2538 75 2 1512 4047 482060507 482063042 0.000000e+00 4246.0
6 TraesCS3D01G259800 chr3A 88.115 244 17 8 703 944 482059921 482060154 3.080000e-71 279.0
7 TraesCS3D01G259800 chr3B 97.514 1931 48 0 1512 3442 471474965 471476895 0.000000e+00 3301.0
8 TraesCS3D01G259800 chr3B 96.141 622 17 3 3433 4047 471477079 471477700 0.000000e+00 1009.0
9 TraesCS3D01G259800 chr3B 87.240 384 23 17 701 1069 471474601 471474973 8.090000e-112 414.0
10 TraesCS3D01G259800 chr3B 79.279 555 72 21 1 516 24697771 24698321 8.320000e-92 348.0
11 TraesCS3D01G259800 chr3B 96.250 80 0 2 2 80 169703096 169703173 1.180000e-25 128.0
12 TraesCS3D01G259800 chr1B 83.148 1436 237 4 1618 3049 624885360 624886794 0.000000e+00 1306.0
13 TraesCS3D01G259800 chr1A 82.310 1498 254 10 1560 3048 548674290 548675785 0.000000e+00 1288.0
14 TraesCS3D01G259800 chr1A 78.571 840 179 1 2217 3055 548682958 548683797 1.640000e-153 553.0
15 TraesCS3D01G259800 chr1A 97.436 39 1 0 2187 2225 549593027 549593065 2.610000e-07 67.6
16 TraesCS3D01G259800 chr1D 82.916 1399 229 6 1659 3049 454564970 454563574 0.000000e+00 1251.0
17 TraesCS3D01G259800 chr1D 83.738 412 52 12 113 516 52738957 52738553 3.820000e-100 375.0
18 TraesCS3D01G259800 chr4D 84.108 409 58 7 113 515 348293395 348292988 4.910000e-104 388.0
19 TraesCS3D01G259800 chr4D 95.062 81 1 2 1 80 301956772 301956694 1.530000e-24 124.0
20 TraesCS3D01G259800 chr4B 80.037 536 69 25 1 514 387898913 387898394 2.970000e-96 363.0
21 TraesCS3D01G259800 chr4B 95.946 74 1 1 2 75 369268592 369268663 7.110000e-23 119.0
22 TraesCS3D01G259800 chr5B 82.609 414 61 7 110 514 48723460 48723871 4.980000e-94 355.0
23 TraesCS3D01G259800 chr5B 78.928 541 80 20 2 516 605628677 605628145 1.800000e-88 337.0
24 TraesCS3D01G259800 chr5B 96.078 51 2 0 522 572 591585555 591585505 2.590000e-12 84.2
25 TraesCS3D01G259800 chr5B 90.164 61 6 0 512 572 580731379 580731439 3.350000e-11 80.5
26 TraesCS3D01G259800 chr7A 80.610 459 59 17 72 504 823372 823826 1.080000e-85 327.0
27 TraesCS3D01G259800 chr7A 79.783 460 74 14 68 516 94802540 94802991 2.350000e-82 316.0
28 TraesCS3D01G259800 chr7D 75.881 539 77 24 1 496 629822029 629822557 4.070000e-55 226.0
29 TraesCS3D01G259800 chr2B 88.636 132 14 1 1 131 572441725 572441594 4.190000e-35 159.0
30 TraesCS3D01G259800 chr2A 72.760 558 89 42 2 515 194468103 194467565 3.280000e-26 130.0
31 TraesCS3D01G259800 chr2A 96.296 81 0 2 1 80 771480478 771480400 3.280000e-26 130.0
32 TraesCS3D01G259800 chr6D 95.062 81 1 2 1 80 368734018 368734096 1.530000e-24 124.0
33 TraesCS3D01G259800 chr2D 94.595 74 2 1 2 75 557171109 557171180 3.310000e-21 113.0
34 TraesCS3D01G259800 chr5D 91.803 61 5 0 512 572 316805860 316805920 7.210000e-13 86.1


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 TraesCS3D01G259800 chr3D 361735744 361739790 4046 False 3329.500000 4684 100.000000 1 4047 2 chr3D.!!$F1 4046
1 TraesCS3D01G259800 chr3D 277062951 277063499 548 True 335.000000 335 78.957000 1 516 1 chr3D.!!$R1 515
2 TraesCS3D01G259800 chr3D 317090904 317091437 533 True 327.000000 327 78.598000 1 516 1 chr3D.!!$R3 515
3 TraesCS3D01G259800 chr3A 482059921 482063042 3121 False 2262.500000 4246 92.501000 703 4047 2 chr3A.!!$F1 3344
4 TraesCS3D01G259800 chr3B 471474601 471477700 3099 False 1574.666667 3301 93.631667 701 4047 3 chr3B.!!$F3 3346
5 TraesCS3D01G259800 chr3B 24697771 24698321 550 False 348.000000 348 79.279000 1 516 1 chr3B.!!$F1 515
6 TraesCS3D01G259800 chr1B 624885360 624886794 1434 False 1306.000000 1306 83.148000 1618 3049 1 chr1B.!!$F1 1431
7 TraesCS3D01G259800 chr1A 548674290 548675785 1495 False 1288.000000 1288 82.310000 1560 3048 1 chr1A.!!$F1 1488
8 TraesCS3D01G259800 chr1A 548682958 548683797 839 False 553.000000 553 78.571000 2217 3055 1 chr1A.!!$F2 838
9 TraesCS3D01G259800 chr1D 454563574 454564970 1396 True 1251.000000 1251 82.916000 1659 3049 1 chr1D.!!$R2 1390
10 TraesCS3D01G259800 chr4B 387898394 387898913 519 True 363.000000 363 80.037000 1 514 1 chr4B.!!$R1 513
11 TraesCS3D01G259800 chr5B 605628145 605628677 532 True 337.000000 337 78.928000 2 516 1 chr5B.!!$R2 514
12 TraesCS3D01G259800 chr7D 629822029 629822557 528 False 226.000000 226 75.881000 1 496 1 chr7D.!!$F1 495

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
776 858 0.175760 GCTCCATTCTACTGCCACGA 59.824 55.000 0.0 0.0 0.0 4.35 F
792 874 0.176219 ACGACCACAACCGAAACTGA 59.824 50.000 0.0 0.0 0.0 3.41 F
945 1027 0.178888 CTCCTCCCTAATCCCCCTCC 60.179 65.000 0.0 0.0 0.0 4.30 F
951 1033 1.151788 CTAATCCCCCTCCCTCCCC 60.152 68.421 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2749 3082 1.067084 CGTCGCATCCATGAGCTCT 59.933 57.895 16.19 0.0 0.00 4.09 R
2896 3229 3.826524 TGATTGTGTGAACTTTAGCCCA 58.173 40.909 0.00 0.0 0.00 5.36 R
2977 3310 4.318332 CAAAGTCAGGCTTCACACTGATA 58.682 43.478 0.00 0.0 44.65 2.15 R
3343 3676 0.997196 GGCAACTTACGTCATCCGAC 59.003 55.000 0.00 0.0 40.70 4.79 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
366 444 0.907704 TTGCTGTCGATAGGGGTGGT 60.908 55.000 11.42 0.00 0.00 4.16
415 495 1.001760 GGCCAGGGAGGAGTAGACA 59.998 63.158 0.00 0.00 41.22 3.41
416 496 0.617820 GGCCAGGGAGGAGTAGACAA 60.618 60.000 0.00 0.00 41.22 3.18
456 537 3.115892 TCCACGCCGACGCAAATC 61.116 61.111 0.00 0.00 45.53 2.17
481 562 2.233431 CTCAAAATTGGGCCGGAAATGA 59.767 45.455 5.05 0.00 0.00 2.57
504 585 2.736995 CAGGCGGACGAAAAGCGA 60.737 61.111 0.00 0.00 44.57 4.93
532 613 4.379143 GCGCCGACCCAAACGAAC 62.379 66.667 0.00 0.00 0.00 3.95
533 614 4.067016 CGCCGACCCAAACGAACG 62.067 66.667 0.00 0.00 0.00 3.95
534 615 4.379143 GCCGACCCAAACGAACGC 62.379 66.667 0.00 0.00 0.00 4.84
535 616 4.067016 CCGACCCAAACGAACGCG 62.067 66.667 3.53 3.53 44.79 6.01
536 617 4.712873 CGACCCAAACGAACGCGC 62.713 66.667 5.73 0.00 42.48 6.86
537 618 4.712873 GACCCAAACGAACGCGCG 62.713 66.667 30.96 30.96 42.48 6.86
552 633 3.861263 GCGCGGACGAAATGGGTC 61.861 66.667 8.83 0.00 43.93 4.46
556 637 3.192922 GGACGAAATGGGTCCGCG 61.193 66.667 0.00 0.00 44.04 6.46
557 638 3.861263 GACGAAATGGGTCCGCGC 61.861 66.667 0.00 0.00 0.00 6.86
560 641 3.428282 GAAATGGGTCCGCGCGTT 61.428 61.111 29.95 14.55 38.23 4.84
561 642 3.661025 GAAATGGGTCCGCGCGTTG 62.661 63.158 29.95 14.87 36.96 4.10
567 648 4.072088 GTCCGCGCGTTGGAGTTG 62.072 66.667 29.95 10.76 35.82 3.16
570 651 4.430423 CGCGCGTTGGAGTTGCTC 62.430 66.667 24.19 0.00 0.00 4.26
571 652 3.044305 GCGCGTTGGAGTTGCTCT 61.044 61.111 8.43 0.00 0.00 4.09
572 653 3.016474 GCGCGTTGGAGTTGCTCTC 62.016 63.158 8.43 1.79 42.07 3.20
573 654 1.664649 CGCGTTGGAGTTGCTCTCA 60.665 57.895 0.00 0.00 44.40 3.27
574 655 1.016130 CGCGTTGGAGTTGCTCTCAT 61.016 55.000 0.00 0.00 44.40 2.90
575 656 1.160137 GCGTTGGAGTTGCTCTCATT 58.840 50.000 10.56 0.00 44.40 2.57
576 657 1.135859 GCGTTGGAGTTGCTCTCATTG 60.136 52.381 10.56 1.10 44.40 2.82
577 658 2.416747 CGTTGGAGTTGCTCTCATTGA 58.583 47.619 10.56 0.00 44.40 2.57
578 659 3.005554 CGTTGGAGTTGCTCTCATTGAT 58.994 45.455 10.56 0.00 44.40 2.57
579 660 3.438087 CGTTGGAGTTGCTCTCATTGATT 59.562 43.478 10.56 0.00 44.40 2.57
580 661 4.631377 CGTTGGAGTTGCTCTCATTGATTA 59.369 41.667 10.56 0.00 44.40 1.75
581 662 5.295292 CGTTGGAGTTGCTCTCATTGATTAT 59.705 40.000 10.56 0.00 44.40 1.28
582 663 6.183360 CGTTGGAGTTGCTCTCATTGATTATT 60.183 38.462 10.56 0.00 44.40 1.40
583 664 6.688637 TGGAGTTGCTCTCATTGATTATTG 57.311 37.500 10.56 0.00 44.40 1.90
584 665 6.182627 TGGAGTTGCTCTCATTGATTATTGT 58.817 36.000 10.56 0.00 44.40 2.71
585 666 6.317140 TGGAGTTGCTCTCATTGATTATTGTC 59.683 38.462 10.56 0.00 44.40 3.18
586 667 6.238593 GGAGTTGCTCTCATTGATTATTGTCC 60.239 42.308 10.56 0.00 44.40 4.02
587 668 6.182627 AGTTGCTCTCATTGATTATTGTCCA 58.817 36.000 0.00 0.00 0.00 4.02
588 669 6.832384 AGTTGCTCTCATTGATTATTGTCCAT 59.168 34.615 0.00 0.00 0.00 3.41
589 670 6.628919 TGCTCTCATTGATTATTGTCCATG 57.371 37.500 0.00 0.00 0.00 3.66
590 671 5.009310 TGCTCTCATTGATTATTGTCCATGC 59.991 40.000 0.00 0.00 0.00 4.06
591 672 5.241064 GCTCTCATTGATTATTGTCCATGCT 59.759 40.000 0.00 0.00 0.00 3.79
592 673 6.238953 GCTCTCATTGATTATTGTCCATGCTT 60.239 38.462 0.00 0.00 0.00 3.91
593 674 7.649533 TCTCATTGATTATTGTCCATGCTTT 57.350 32.000 0.00 0.00 0.00 3.51
594 675 8.070034 TCTCATTGATTATTGTCCATGCTTTT 57.930 30.769 0.00 0.00 0.00 2.27
595 676 8.192774 TCTCATTGATTATTGTCCATGCTTTTC 58.807 33.333 0.00 0.00 0.00 2.29
596 677 8.070034 TCATTGATTATTGTCCATGCTTTTCT 57.930 30.769 0.00 0.00 0.00 2.52
597 678 8.533657 TCATTGATTATTGTCCATGCTTTTCTT 58.466 29.630 0.00 0.00 0.00 2.52
598 679 9.806203 CATTGATTATTGTCCATGCTTTTCTTA 57.194 29.630 0.00 0.00 0.00 2.10
600 681 9.806203 TTGATTATTGTCCATGCTTTTCTTATG 57.194 29.630 0.00 0.00 0.00 1.90
601 682 8.415553 TGATTATTGTCCATGCTTTTCTTATGG 58.584 33.333 0.00 0.00 42.12 2.74
602 683 5.603170 ATTGTCCATGCTTTTCTTATGGG 57.397 39.130 0.00 0.00 41.31 4.00
603 684 4.046286 TGTCCATGCTTTTCTTATGGGT 57.954 40.909 0.00 0.00 41.31 4.51
604 685 5.186256 TGTCCATGCTTTTCTTATGGGTA 57.814 39.130 0.00 0.00 41.31 3.69
605 686 4.947388 TGTCCATGCTTTTCTTATGGGTAC 59.053 41.667 0.00 0.00 41.31 3.34
606 687 5.193679 GTCCATGCTTTTCTTATGGGTACT 58.806 41.667 0.00 0.00 41.31 2.73
607 688 5.652452 GTCCATGCTTTTCTTATGGGTACTT 59.348 40.000 0.00 0.00 41.31 2.24
608 689 5.652014 TCCATGCTTTTCTTATGGGTACTTG 59.348 40.000 0.00 0.00 41.31 3.16
609 690 5.343249 CATGCTTTTCTTATGGGTACTTGC 58.657 41.667 0.00 0.00 0.00 4.01
610 691 4.402829 TGCTTTTCTTATGGGTACTTGCA 58.597 39.130 0.00 0.00 0.00 4.08
611 692 5.016173 TGCTTTTCTTATGGGTACTTGCAT 58.984 37.500 0.00 0.00 0.00 3.96
612 693 5.480073 TGCTTTTCTTATGGGTACTTGCATT 59.520 36.000 0.00 0.00 0.00 3.56
613 694 6.036470 GCTTTTCTTATGGGTACTTGCATTC 58.964 40.000 0.00 0.00 0.00 2.67
614 695 6.350110 GCTTTTCTTATGGGTACTTGCATTCA 60.350 38.462 0.00 0.00 0.00 2.57
615 696 7.631377 GCTTTTCTTATGGGTACTTGCATTCAT 60.631 37.037 0.00 0.00 0.00 2.57
616 697 7.716799 TTTCTTATGGGTACTTGCATTCATT 57.283 32.000 0.00 0.00 0.00 2.57
617 698 7.716799 TTCTTATGGGTACTTGCATTCATTT 57.283 32.000 0.00 0.00 0.00 2.32
618 699 7.333528 TCTTATGGGTACTTGCATTCATTTC 57.666 36.000 0.00 0.00 0.00 2.17
619 700 7.118723 TCTTATGGGTACTTGCATTCATTTCT 58.881 34.615 0.00 0.00 0.00 2.52
620 701 8.271458 TCTTATGGGTACTTGCATTCATTTCTA 58.729 33.333 0.00 0.00 0.00 2.10
621 702 6.699575 ATGGGTACTTGCATTCATTTCTAC 57.300 37.500 0.00 0.00 0.00 2.59
622 703 4.634004 TGGGTACTTGCATTCATTTCTACG 59.366 41.667 0.00 0.00 0.00 3.51
623 704 4.634443 GGGTACTTGCATTCATTTCTACGT 59.366 41.667 0.00 0.00 0.00 3.57
624 705 5.447279 GGGTACTTGCATTCATTTCTACGTG 60.447 44.000 0.00 0.00 0.00 4.49
625 706 5.121768 GGTACTTGCATTCATTTCTACGTGT 59.878 40.000 0.00 0.00 0.00 4.49
626 707 5.283060 ACTTGCATTCATTTCTACGTGTC 57.717 39.130 0.00 0.00 0.00 3.67
627 708 3.989705 TGCATTCATTTCTACGTGTCG 57.010 42.857 0.00 0.00 0.00 4.35
628 709 2.670905 TGCATTCATTTCTACGTGTCGG 59.329 45.455 0.00 0.00 0.00 4.79
629 710 2.671396 GCATTCATTTCTACGTGTCGGT 59.329 45.455 0.00 0.00 0.00 4.69
630 711 3.241995 GCATTCATTTCTACGTGTCGGTC 60.242 47.826 0.00 0.00 0.00 4.79
631 712 3.928727 TTCATTTCTACGTGTCGGTCT 57.071 42.857 0.00 0.00 0.00 3.85
632 713 3.211803 TCATTTCTACGTGTCGGTCTG 57.788 47.619 0.00 0.00 0.00 3.51
633 714 1.654105 CATTTCTACGTGTCGGTCTGC 59.346 52.381 0.00 0.00 0.00 4.26
634 715 0.956633 TTTCTACGTGTCGGTCTGCT 59.043 50.000 0.00 0.00 0.00 4.24
635 716 1.812235 TTCTACGTGTCGGTCTGCTA 58.188 50.000 0.00 0.00 0.00 3.49
636 717 1.366679 TCTACGTGTCGGTCTGCTAG 58.633 55.000 0.00 0.00 0.00 3.42
637 718 1.066645 TCTACGTGTCGGTCTGCTAGA 60.067 52.381 0.00 0.00 0.00 2.43
638 719 1.941294 CTACGTGTCGGTCTGCTAGAT 59.059 52.381 0.00 0.00 0.00 1.98
639 720 2.034104 ACGTGTCGGTCTGCTAGATA 57.966 50.000 0.00 0.00 0.00 1.98
640 721 1.941294 ACGTGTCGGTCTGCTAGATAG 59.059 52.381 0.00 0.00 0.00 2.08
657 738 5.837770 AGATAGCATGAATGGAATCCAGA 57.162 39.130 8.40 0.00 36.75 3.86
658 739 5.806818 AGATAGCATGAATGGAATCCAGAG 58.193 41.667 8.40 0.00 36.75 3.35
659 740 3.225177 AGCATGAATGGAATCCAGAGG 57.775 47.619 8.40 0.00 36.75 3.69
660 741 2.781757 AGCATGAATGGAATCCAGAGGA 59.218 45.455 8.40 0.00 36.75 3.71
661 742 2.883386 GCATGAATGGAATCCAGAGGAC 59.117 50.000 8.40 0.00 36.75 3.85
662 743 2.988010 TGAATGGAATCCAGAGGACG 57.012 50.000 8.40 0.00 36.75 4.79
663 744 2.187958 TGAATGGAATCCAGAGGACGT 58.812 47.619 8.40 0.00 36.75 4.34
664 745 2.571653 TGAATGGAATCCAGAGGACGTT 59.428 45.455 8.40 0.00 36.75 3.99
665 746 3.009033 TGAATGGAATCCAGAGGACGTTT 59.991 43.478 8.40 0.00 36.75 3.60
666 747 3.721087 ATGGAATCCAGAGGACGTTTT 57.279 42.857 8.40 0.00 36.75 2.43
667 748 3.053831 TGGAATCCAGAGGACGTTTTC 57.946 47.619 0.00 0.00 32.98 2.29
668 749 2.370519 TGGAATCCAGAGGACGTTTTCA 59.629 45.455 0.00 0.00 32.98 2.69
669 750 3.181449 TGGAATCCAGAGGACGTTTTCAA 60.181 43.478 0.00 0.00 32.98 2.69
670 751 4.010349 GGAATCCAGAGGACGTTTTCAAT 58.990 43.478 0.00 0.00 32.98 2.57
671 752 4.459337 GGAATCCAGAGGACGTTTTCAATT 59.541 41.667 0.00 0.00 32.98 2.32
672 753 5.376854 AATCCAGAGGACGTTTTCAATTG 57.623 39.130 0.00 0.00 32.98 2.32
673 754 4.079980 TCCAGAGGACGTTTTCAATTGA 57.920 40.909 3.38 3.38 0.00 2.57
674 755 4.456535 TCCAGAGGACGTTTTCAATTGAA 58.543 39.130 16.91 16.91 0.00 2.69
675 756 4.884744 TCCAGAGGACGTTTTCAATTGAAA 59.115 37.500 26.01 26.01 41.77 2.69
676 757 5.008613 TCCAGAGGACGTTTTCAATTGAAAG 59.991 40.000 27.52 21.06 43.90 2.62
677 758 5.008613 CCAGAGGACGTTTTCAATTGAAAGA 59.991 40.000 27.52 18.19 43.90 2.52
678 759 6.459573 CCAGAGGACGTTTTCAATTGAAAGAA 60.460 38.462 27.52 15.48 43.90 2.52
679 760 6.414987 CAGAGGACGTTTTCAATTGAAAGAAC 59.585 38.462 27.52 23.10 43.90 3.01
680 761 6.318900 AGAGGACGTTTTCAATTGAAAGAACT 59.681 34.615 27.52 21.92 43.90 3.01
681 762 6.495706 AGGACGTTTTCAATTGAAAGAACTC 58.504 36.000 27.52 20.99 43.90 3.01
682 763 6.318900 AGGACGTTTTCAATTGAAAGAACTCT 59.681 34.615 27.52 20.85 43.90 3.24
683 764 7.497909 AGGACGTTTTCAATTGAAAGAACTCTA 59.502 33.333 27.52 12.94 43.90 2.43
684 765 7.586664 GGACGTTTTCAATTGAAAGAACTCTAC 59.413 37.037 27.52 20.81 43.90 2.59
685 766 8.209917 ACGTTTTCAATTGAAAGAACTCTACT 57.790 30.769 27.52 12.12 43.90 2.57
686 767 8.122952 ACGTTTTCAATTGAAAGAACTCTACTG 58.877 33.333 27.52 19.20 43.90 2.74
687 768 8.122952 CGTTTTCAATTGAAAGAACTCTACTGT 58.877 33.333 27.52 0.00 43.90 3.55
694 775 9.442047 AATTGAAAGAACTCTACTGTATCTTGG 57.558 33.333 3.01 0.00 31.14 3.61
695 776 6.936279 TGAAAGAACTCTACTGTATCTTGGG 58.064 40.000 3.01 0.00 31.14 4.12
696 777 6.724441 TGAAAGAACTCTACTGTATCTTGGGA 59.276 38.462 3.01 0.00 31.14 4.37
697 778 6.783708 AAGAACTCTACTGTATCTTGGGAG 57.216 41.667 1.67 0.69 0.00 4.30
698 779 5.205056 AGAACTCTACTGTATCTTGGGAGG 58.795 45.833 5.02 0.00 0.00 4.30
699 780 3.301274 ACTCTACTGTATCTTGGGAGGC 58.699 50.000 5.02 0.00 0.00 4.70
700 781 3.300388 CTCTACTGTATCTTGGGAGGCA 58.700 50.000 0.00 0.00 0.00 4.75
701 782 3.300388 TCTACTGTATCTTGGGAGGCAG 58.700 50.000 0.00 0.00 35.11 4.85
706 787 3.944015 CTGTATCTTGGGAGGCAGAAAAG 59.056 47.826 0.00 0.00 32.64 2.27
708 789 2.568623 TCTTGGGAGGCAGAAAAGAC 57.431 50.000 0.00 0.00 0.00 3.01
716 797 2.675348 GAGGCAGAAAAGACCAAGATCG 59.325 50.000 0.00 0.00 0.00 3.69
722 803 3.259374 AGAAAAGACCAAGATCGCAGAGA 59.741 43.478 0.00 0.00 43.63 3.10
726 807 1.260538 ACCAAGATCGCAGAGAGGCA 61.261 55.000 0.00 0.00 43.63 4.75
755 837 3.376918 GCAAGCTGGCCCTTGGAC 61.377 66.667 19.58 4.35 41.88 4.02
776 858 0.175760 GCTCCATTCTACTGCCACGA 59.824 55.000 0.00 0.00 0.00 4.35
777 859 1.927895 CTCCATTCTACTGCCACGAC 58.072 55.000 0.00 0.00 0.00 4.34
779 861 0.249120 CCATTCTACTGCCACGACCA 59.751 55.000 0.00 0.00 0.00 4.02
780 862 1.359848 CATTCTACTGCCACGACCAC 58.640 55.000 0.00 0.00 0.00 4.16
781 863 0.973632 ATTCTACTGCCACGACCACA 59.026 50.000 0.00 0.00 0.00 4.17
782 864 0.753867 TTCTACTGCCACGACCACAA 59.246 50.000 0.00 0.00 0.00 3.33
784 866 0.949105 CTACTGCCACGACCACAACC 60.949 60.000 0.00 0.00 0.00 3.77
785 867 2.702751 TACTGCCACGACCACAACCG 62.703 60.000 0.00 0.00 0.00 4.44
787 869 2.589442 GCCACGACCACAACCGAA 60.589 61.111 0.00 0.00 0.00 4.30
788 870 2.181521 GCCACGACCACAACCGAAA 61.182 57.895 0.00 0.00 0.00 3.46
789 871 1.644913 CCACGACCACAACCGAAAC 59.355 57.895 0.00 0.00 0.00 2.78
790 872 0.812412 CCACGACCACAACCGAAACT 60.812 55.000 0.00 0.00 0.00 2.66
791 873 0.303493 CACGACCACAACCGAAACTG 59.697 55.000 0.00 0.00 0.00 3.16
792 874 0.176219 ACGACCACAACCGAAACTGA 59.824 50.000 0.00 0.00 0.00 3.41
793 875 1.292061 CGACCACAACCGAAACTGAA 58.708 50.000 0.00 0.00 0.00 3.02
794 876 1.666700 CGACCACAACCGAAACTGAAA 59.333 47.619 0.00 0.00 0.00 2.69
795 877 2.538132 CGACCACAACCGAAACTGAAAC 60.538 50.000 0.00 0.00 0.00 2.78
796 878 1.746787 ACCACAACCGAAACTGAAACC 59.253 47.619 0.00 0.00 0.00 3.27
797 879 1.746220 CCACAACCGAAACTGAAACCA 59.254 47.619 0.00 0.00 0.00 3.67
801 883 4.867608 CACAACCGAAACTGAAACCAAAAT 59.132 37.500 0.00 0.00 0.00 1.82
813 895 6.593770 ACTGAAACCAAAATCAAAACCAGAAC 59.406 34.615 0.00 0.00 0.00 3.01
814 896 5.578727 TGAAACCAAAATCAAAACCAGAACG 59.421 36.000 0.00 0.00 0.00 3.95
815 897 4.729227 ACCAAAATCAAAACCAGAACGT 57.271 36.364 0.00 0.00 0.00 3.99
945 1027 0.178888 CTCCTCCCTAATCCCCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
951 1033 1.151788 CTAATCCCCCTCCCTCCCC 60.152 68.421 0.00 0.00 0.00 4.81
952 1034 2.714809 CTAATCCCCCTCCCTCCCCC 62.715 70.000 0.00 0.00 0.00 5.40
976 1064 3.610669 CATCTCCTCCTCCGCCCG 61.611 72.222 0.00 0.00 0.00 6.13
1029 1356 4.640690 ACCGCCACCACCTCCTCT 62.641 66.667 0.00 0.00 0.00 3.69
1058 1385 4.410400 CTTCGCCCACCCCCACTC 62.410 72.222 0.00 0.00 0.00 3.51
1065 1392 2.941025 CACCCCCACTCCCACCAT 60.941 66.667 0.00 0.00 0.00 3.55
1066 1393 2.614013 ACCCCCACTCCCACCATC 60.614 66.667 0.00 0.00 0.00 3.51
1067 1394 3.420482 CCCCCACTCCCACCATCC 61.420 72.222 0.00 0.00 0.00 3.51
1068 1395 3.420482 CCCCACTCCCACCATCCC 61.420 72.222 0.00 0.00 0.00 3.85
1528 1855 2.438434 CACCATCCCTCCGCCAAC 60.438 66.667 0.00 0.00 0.00 3.77
2416 2749 3.394836 GAGGGGCAGAAGACGGCT 61.395 66.667 0.00 0.00 37.38 5.52
2604 2937 3.692593 GCAAATCCACTGTACCGGTATTT 59.307 43.478 19.19 10.44 0.00 1.40
2605 2938 4.157105 GCAAATCCACTGTACCGGTATTTT 59.843 41.667 19.19 1.50 0.00 1.82
2616 2949 5.719085 TGTACCGGTATTTTAAGTCTGGGTA 59.281 40.000 19.19 0.00 0.00 3.69
2617 2950 5.963214 ACCGGTATTTTAAGTCTGGGTAT 57.037 39.130 4.49 0.00 0.00 2.73
2683 3016 4.132336 CCATACAGATTGGTGATCCAGTG 58.868 47.826 0.00 0.00 45.22 3.66
2749 3082 2.093106 GTCGAGGAAGCTACAGAGGAA 58.907 52.381 0.00 0.00 0.00 3.36
2896 3229 3.408634 GGTGGTTGTTAGTACAGCACAT 58.591 45.455 12.69 0.00 37.24 3.21
2977 3310 0.106519 GCCAGTATGCCAATCCACCT 60.107 55.000 0.00 0.00 31.97 4.00
3326 3659 1.334869 CCTGTTTCCTGTTCTGTGTGC 59.665 52.381 0.00 0.00 0.00 4.57
3327 3660 2.016318 CTGTTTCCTGTTCTGTGTGCA 58.984 47.619 0.00 0.00 0.00 4.57
3343 3676 3.306703 GTGTGCATTGTTCACTTTTGGTG 59.693 43.478 0.00 0.00 46.60 4.17
3344 3677 3.056250 TGTGCATTGTTCACTTTTGGTGT 60.056 39.130 0.00 0.00 45.50 4.16
3346 3679 2.788786 GCATTGTTCACTTTTGGTGTCG 59.211 45.455 0.00 0.00 45.50 4.35
3400 3733 9.601217 GATTGACCTAACAAGATGTATTACACT 57.399 33.333 0.00 0.00 33.22 3.55
3528 4056 9.685828 TTGTGGTTAGTGTTAATTTTCATTAGC 57.314 29.630 0.00 0.00 0.00 3.09
3621 4149 3.584848 AGCAGCTTAAGTATCTATGGGGG 59.415 47.826 4.02 0.00 0.00 5.40
3641 4169 2.288886 GGTAGTGTGGACTGTCAGAACC 60.289 54.545 6.91 10.00 33.21 3.62
3716 4244 2.221981 GCTCGACCTGTCACTTTTTGAG 59.778 50.000 0.00 0.00 33.71 3.02
4004 4537 7.954788 TTGGTTGGATAACTTTTATTTGTGC 57.045 32.000 0.00 0.00 36.99 4.57
4022 4555 1.607178 CATCCCTGCAACTGCCCAA 60.607 57.895 0.00 0.00 41.18 4.12
4024 4557 2.370459 ATCCCTGCAACTGCCCAACA 62.370 55.000 0.00 0.00 41.18 3.33
4025 4558 1.909781 CCCTGCAACTGCCCAACAT 60.910 57.895 0.00 0.00 41.18 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 124 4.457496 CTGACGCCGCCAGTCCAT 62.457 66.667 0.00 0.00 37.80 3.41
122 162 1.227380 GTCCGATACTGCCTGCTGG 60.227 63.158 5.03 5.03 0.00 4.85
127 167 0.395311 TCCTTCGTCCGATACTGCCT 60.395 55.000 0.00 0.00 0.00 4.75
131 171 1.025812 CAGCTCCTTCGTCCGATACT 58.974 55.000 0.00 0.00 0.00 2.12
134 174 3.082579 GCCAGCTCCTTCGTCCGAT 62.083 63.158 0.00 0.00 0.00 4.18
161 218 2.185608 GAGCAGGAAGTCGCCTCC 59.814 66.667 0.00 0.00 35.66 4.30
335 406 4.335647 CAGCAAGCCCTCACCCGT 62.336 66.667 0.00 0.00 0.00 5.28
340 412 0.461548 CTATCGACAGCAAGCCCTCA 59.538 55.000 0.00 0.00 0.00 3.86
366 444 3.806941 GCACATTGGCCATCCTCTA 57.193 52.632 6.09 0.00 0.00 2.43
456 537 0.527565 CCGGCCCAATTTTGAGTCTG 59.472 55.000 0.00 0.00 0.00 3.51
516 597 4.067016 CGTTCGTTTGGGTCGGCG 62.067 66.667 0.00 0.00 0.00 6.46
517 598 4.379143 GCGTTCGTTTGGGTCGGC 62.379 66.667 0.00 0.00 0.00 5.54
518 599 4.067016 CGCGTTCGTTTGGGTCGG 62.067 66.667 0.00 0.00 0.00 4.79
519 600 4.712873 GCGCGTTCGTTTGGGTCG 62.713 66.667 8.43 0.00 38.14 4.79
520 601 4.712873 CGCGCGTTCGTTTGGGTC 62.713 66.667 24.19 0.00 38.14 4.46
535 616 3.861263 GACCCATTTCGTCCGCGC 61.861 66.667 0.00 0.00 38.14 6.86
536 617 3.192922 GGACCCATTTCGTCCGCG 61.193 66.667 0.00 0.00 40.46 6.46
539 620 3.192922 CGCGGACCCATTTCGTCC 61.193 66.667 0.00 0.00 45.41 4.79
540 621 3.861263 GCGCGGACCCATTTCGTC 61.861 66.667 8.83 0.00 0.00 4.20
543 624 3.428282 AACGCGCGGACCCATTTC 61.428 61.111 35.22 0.00 0.00 2.17
544 625 3.732892 CAACGCGCGGACCCATTT 61.733 61.111 35.22 14.60 0.00 2.32
550 631 4.072088 CAACTCCAACGCGCGGAC 62.072 66.667 35.22 0.00 0.00 4.79
553 634 4.430423 GAGCAACTCCAACGCGCG 62.430 66.667 30.96 30.96 0.00 6.86
554 635 3.016474 GAGAGCAACTCCAACGCGC 62.016 63.158 5.73 0.00 39.53 6.86
555 636 1.016130 ATGAGAGCAACTCCAACGCG 61.016 55.000 3.53 3.53 44.34 6.01
556 637 1.135859 CAATGAGAGCAACTCCAACGC 60.136 52.381 8.13 0.00 44.34 4.84
557 638 2.416747 TCAATGAGAGCAACTCCAACG 58.583 47.619 8.13 0.00 44.34 4.10
558 639 6.690194 ATAATCAATGAGAGCAACTCCAAC 57.310 37.500 8.13 0.00 44.34 3.77
559 640 6.660521 ACAATAATCAATGAGAGCAACTCCAA 59.339 34.615 8.13 0.00 44.34 3.53
560 641 6.182627 ACAATAATCAATGAGAGCAACTCCA 58.817 36.000 8.13 0.00 44.34 3.86
561 642 6.238593 GGACAATAATCAATGAGAGCAACTCC 60.239 42.308 8.13 0.00 44.34 3.85
562 643 6.317140 TGGACAATAATCAATGAGAGCAACTC 59.683 38.462 4.35 4.35 45.11 3.01
563 644 6.182627 TGGACAATAATCAATGAGAGCAACT 58.817 36.000 0.00 0.00 0.00 3.16
564 645 6.441093 TGGACAATAATCAATGAGAGCAAC 57.559 37.500 0.00 0.00 0.00 4.17
565 646 6.460537 GCATGGACAATAATCAATGAGAGCAA 60.461 38.462 0.00 0.00 32.41 3.91
566 647 5.009310 GCATGGACAATAATCAATGAGAGCA 59.991 40.000 0.00 0.00 32.41 4.26
567 648 5.241064 AGCATGGACAATAATCAATGAGAGC 59.759 40.000 0.00 0.00 32.41 4.09
568 649 6.879276 AGCATGGACAATAATCAATGAGAG 57.121 37.500 0.00 0.00 32.41 3.20
569 650 7.649533 AAAGCATGGACAATAATCAATGAGA 57.350 32.000 0.00 0.00 32.41 3.27
570 651 8.195436 AGAAAAGCATGGACAATAATCAATGAG 58.805 33.333 0.00 0.00 32.41 2.90
571 652 8.070034 AGAAAAGCATGGACAATAATCAATGA 57.930 30.769 0.00 0.00 32.41 2.57
572 653 8.712285 AAGAAAAGCATGGACAATAATCAATG 57.288 30.769 0.00 0.00 33.67 2.82
574 655 9.806203 CATAAGAAAAGCATGGACAATAATCAA 57.194 29.630 0.00 0.00 0.00 2.57
575 656 8.415553 CCATAAGAAAAGCATGGACAATAATCA 58.584 33.333 0.00 0.00 41.53 2.57
576 657 7.869429 CCCATAAGAAAAGCATGGACAATAATC 59.131 37.037 1.40 0.00 41.53 1.75
577 658 7.345392 ACCCATAAGAAAAGCATGGACAATAAT 59.655 33.333 1.40 0.00 41.53 1.28
578 659 6.667414 ACCCATAAGAAAAGCATGGACAATAA 59.333 34.615 1.40 0.00 41.53 1.40
579 660 6.194235 ACCCATAAGAAAAGCATGGACAATA 58.806 36.000 1.40 0.00 41.53 1.90
580 661 5.025453 ACCCATAAGAAAAGCATGGACAAT 58.975 37.500 1.40 0.00 41.53 2.71
581 662 4.415596 ACCCATAAGAAAAGCATGGACAA 58.584 39.130 1.40 0.00 41.53 3.18
582 663 4.046286 ACCCATAAGAAAAGCATGGACA 57.954 40.909 1.40 0.00 41.53 4.02
583 664 5.193679 AGTACCCATAAGAAAAGCATGGAC 58.806 41.667 1.40 0.00 41.53 4.02
584 665 5.450818 AGTACCCATAAGAAAAGCATGGA 57.549 39.130 1.40 0.00 41.53 3.41
585 666 5.679638 GCAAGTACCCATAAGAAAAGCATGG 60.680 44.000 0.00 0.00 39.19 3.66
586 667 5.105797 TGCAAGTACCCATAAGAAAAGCATG 60.106 40.000 0.00 0.00 0.00 4.06
587 668 5.016173 TGCAAGTACCCATAAGAAAAGCAT 58.984 37.500 0.00 0.00 0.00 3.79
588 669 4.402829 TGCAAGTACCCATAAGAAAAGCA 58.597 39.130 0.00 0.00 0.00 3.91
589 670 5.582689 ATGCAAGTACCCATAAGAAAAGC 57.417 39.130 0.00 0.00 0.00 3.51
590 671 7.156876 TGAATGCAAGTACCCATAAGAAAAG 57.843 36.000 0.00 0.00 0.00 2.27
591 672 7.716799 ATGAATGCAAGTACCCATAAGAAAA 57.283 32.000 0.00 0.00 0.00 2.29
592 673 7.716799 AATGAATGCAAGTACCCATAAGAAA 57.283 32.000 0.00 0.00 0.00 2.52
593 674 7.615365 AGAAATGAATGCAAGTACCCATAAGAA 59.385 33.333 0.00 0.00 0.00 2.52
594 675 7.118723 AGAAATGAATGCAAGTACCCATAAGA 58.881 34.615 0.00 0.00 0.00 2.10
595 676 7.338800 AGAAATGAATGCAAGTACCCATAAG 57.661 36.000 0.00 0.00 0.00 1.73
596 677 7.011950 CGTAGAAATGAATGCAAGTACCCATAA 59.988 37.037 0.00 0.00 0.00 1.90
597 678 6.481976 CGTAGAAATGAATGCAAGTACCCATA 59.518 38.462 0.00 0.00 0.00 2.74
598 679 5.296780 CGTAGAAATGAATGCAAGTACCCAT 59.703 40.000 0.00 0.00 0.00 4.00
599 680 4.634004 CGTAGAAATGAATGCAAGTACCCA 59.366 41.667 0.00 0.00 0.00 4.51
600 681 4.634443 ACGTAGAAATGAATGCAAGTACCC 59.366 41.667 0.00 0.00 0.00 3.69
601 682 5.121768 ACACGTAGAAATGAATGCAAGTACC 59.878 40.000 0.00 0.00 0.00 3.34
602 683 6.165659 ACACGTAGAAATGAATGCAAGTAC 57.834 37.500 0.00 0.00 0.00 2.73
603 684 5.061684 CGACACGTAGAAATGAATGCAAGTA 59.938 40.000 0.00 0.00 0.00 2.24
604 685 4.143115 CGACACGTAGAAATGAATGCAAGT 60.143 41.667 0.00 0.00 0.00 3.16
605 686 4.326205 CGACACGTAGAAATGAATGCAAG 58.674 43.478 0.00 0.00 0.00 4.01
606 687 3.124466 CCGACACGTAGAAATGAATGCAA 59.876 43.478 0.00 0.00 0.00 4.08
607 688 2.670905 CCGACACGTAGAAATGAATGCA 59.329 45.455 0.00 0.00 0.00 3.96
608 689 2.671396 ACCGACACGTAGAAATGAATGC 59.329 45.455 0.00 0.00 0.00 3.56
609 690 4.031765 CAGACCGACACGTAGAAATGAATG 59.968 45.833 0.00 0.00 0.00 2.67
610 691 4.174009 CAGACCGACACGTAGAAATGAAT 58.826 43.478 0.00 0.00 0.00 2.57
611 692 3.571571 CAGACCGACACGTAGAAATGAA 58.428 45.455 0.00 0.00 0.00 2.57
612 693 2.670229 GCAGACCGACACGTAGAAATGA 60.670 50.000 0.00 0.00 0.00 2.57
613 694 1.654105 GCAGACCGACACGTAGAAATG 59.346 52.381 0.00 0.00 0.00 2.32
614 695 1.544691 AGCAGACCGACACGTAGAAAT 59.455 47.619 0.00 0.00 0.00 2.17
615 696 0.956633 AGCAGACCGACACGTAGAAA 59.043 50.000 0.00 0.00 0.00 2.52
616 697 1.736126 CTAGCAGACCGACACGTAGAA 59.264 52.381 0.00 0.00 0.00 2.10
617 698 1.066645 TCTAGCAGACCGACACGTAGA 60.067 52.381 0.00 0.00 0.00 2.59
618 699 1.366679 TCTAGCAGACCGACACGTAG 58.633 55.000 0.00 0.00 0.00 3.51
619 700 2.034104 ATCTAGCAGACCGACACGTA 57.966 50.000 0.00 0.00 0.00 3.57
620 701 1.941294 CTATCTAGCAGACCGACACGT 59.059 52.381 0.00 0.00 0.00 4.49
621 702 2.672188 CTATCTAGCAGACCGACACG 57.328 55.000 0.00 0.00 0.00 4.49
632 713 5.585445 CTGGATTCCATTCATGCTATCTAGC 59.415 44.000 5.70 2.18 40.46 3.42
633 714 6.944096 TCTGGATTCCATTCATGCTATCTAG 58.056 40.000 5.70 0.00 30.82 2.43
634 715 6.070366 CCTCTGGATTCCATTCATGCTATCTA 60.070 42.308 5.70 0.00 30.82 1.98
635 716 5.280573 CCTCTGGATTCCATTCATGCTATCT 60.281 44.000 5.70 0.00 30.82 1.98
636 717 4.942483 CCTCTGGATTCCATTCATGCTATC 59.058 45.833 5.70 0.00 30.82 2.08
637 718 4.600547 TCCTCTGGATTCCATTCATGCTAT 59.399 41.667 5.70 0.00 30.82 2.97
638 719 3.975982 TCCTCTGGATTCCATTCATGCTA 59.024 43.478 5.70 0.00 30.82 3.49
639 720 2.781757 TCCTCTGGATTCCATTCATGCT 59.218 45.455 5.70 0.00 30.82 3.79
640 721 2.883386 GTCCTCTGGATTCCATTCATGC 59.117 50.000 5.70 0.00 32.73 4.06
641 722 3.136763 CGTCCTCTGGATTCCATTCATG 58.863 50.000 5.70 0.00 32.73 3.07
642 723 2.774234 ACGTCCTCTGGATTCCATTCAT 59.226 45.455 5.70 0.00 32.73 2.57
643 724 2.187958 ACGTCCTCTGGATTCCATTCA 58.812 47.619 5.70 0.00 32.73 2.57
644 725 2.990066 ACGTCCTCTGGATTCCATTC 57.010 50.000 5.70 0.00 32.73 2.67
645 726 3.721087 AAACGTCCTCTGGATTCCATT 57.279 42.857 5.70 0.00 32.73 3.16
646 727 3.009033 TGAAAACGTCCTCTGGATTCCAT 59.991 43.478 5.70 0.00 32.73 3.41
647 728 2.370519 TGAAAACGTCCTCTGGATTCCA 59.629 45.455 5.05 5.05 32.73 3.53
648 729 3.053831 TGAAAACGTCCTCTGGATTCC 57.946 47.619 0.00 0.00 32.73 3.01
649 730 5.181245 TCAATTGAAAACGTCCTCTGGATTC 59.819 40.000 5.45 0.00 32.73 2.52
650 731 5.070001 TCAATTGAAAACGTCCTCTGGATT 58.930 37.500 5.45 0.00 32.73 3.01
651 732 4.651778 TCAATTGAAAACGTCCTCTGGAT 58.348 39.130 5.45 0.00 32.73 3.41
652 733 4.079980 TCAATTGAAAACGTCCTCTGGA 57.920 40.909 5.45 0.00 0.00 3.86
653 734 4.829064 TTCAATTGAAAACGTCCTCTGG 57.171 40.909 18.45 0.00 0.00 3.86
654 735 6.060028 TCTTTCAATTGAAAACGTCCTCTG 57.940 37.500 28.49 16.47 42.72 3.35
655 736 6.318900 AGTTCTTTCAATTGAAAACGTCCTCT 59.681 34.615 28.49 17.90 42.72 3.69
656 737 6.495706 AGTTCTTTCAATTGAAAACGTCCTC 58.504 36.000 28.49 16.46 42.72 3.71
657 738 6.318900 AGAGTTCTTTCAATTGAAAACGTCCT 59.681 34.615 28.49 20.42 42.72 3.85
658 739 6.495706 AGAGTTCTTTCAATTGAAAACGTCC 58.504 36.000 28.49 18.97 42.72 4.79
659 740 8.336080 AGTAGAGTTCTTTCAATTGAAAACGTC 58.664 33.333 28.49 21.88 42.72 4.34
660 741 8.122952 CAGTAGAGTTCTTTCAATTGAAAACGT 58.877 33.333 28.49 19.90 42.72 3.99
661 742 8.122952 ACAGTAGAGTTCTTTCAATTGAAAACG 58.877 33.333 28.49 20.03 42.72 3.60
668 749 9.442047 CCAAGATACAGTAGAGTTCTTTCAATT 57.558 33.333 0.00 0.00 0.00 2.32
669 750 8.043710 CCCAAGATACAGTAGAGTTCTTTCAAT 58.956 37.037 0.00 0.00 0.00 2.57
670 751 7.234782 TCCCAAGATACAGTAGAGTTCTTTCAA 59.765 37.037 0.00 0.00 0.00 2.69
671 752 6.724441 TCCCAAGATACAGTAGAGTTCTTTCA 59.276 38.462 0.00 0.00 0.00 2.69
672 753 7.171630 TCCCAAGATACAGTAGAGTTCTTTC 57.828 40.000 0.00 0.00 0.00 2.62
673 754 6.155393 CCTCCCAAGATACAGTAGAGTTCTTT 59.845 42.308 0.00 0.00 0.00 2.52
674 755 5.659079 CCTCCCAAGATACAGTAGAGTTCTT 59.341 44.000 0.00 0.00 0.00 2.52
675 756 5.205056 CCTCCCAAGATACAGTAGAGTTCT 58.795 45.833 0.00 0.00 0.00 3.01
676 757 4.202172 GCCTCCCAAGATACAGTAGAGTTC 60.202 50.000 0.00 0.00 0.00 3.01
677 758 3.707102 GCCTCCCAAGATACAGTAGAGTT 59.293 47.826 0.00 0.00 0.00 3.01
678 759 3.301274 GCCTCCCAAGATACAGTAGAGT 58.699 50.000 0.00 0.00 0.00 3.24
679 760 3.300388 TGCCTCCCAAGATACAGTAGAG 58.700 50.000 0.00 0.00 0.00 2.43
680 761 3.052869 TCTGCCTCCCAAGATACAGTAGA 60.053 47.826 0.00 0.00 0.00 2.59
681 762 3.300388 TCTGCCTCCCAAGATACAGTAG 58.700 50.000 0.00 0.00 0.00 2.57
682 763 3.398318 TCTGCCTCCCAAGATACAGTA 57.602 47.619 0.00 0.00 0.00 2.74
683 764 2.254152 TCTGCCTCCCAAGATACAGT 57.746 50.000 0.00 0.00 0.00 3.55
684 765 3.634397 TTTCTGCCTCCCAAGATACAG 57.366 47.619 0.00 0.00 0.00 2.74
685 766 3.587061 TCTTTTCTGCCTCCCAAGATACA 59.413 43.478 0.00 0.00 0.00 2.29
686 767 3.942115 GTCTTTTCTGCCTCCCAAGATAC 59.058 47.826 0.00 0.00 0.00 2.24
687 768 3.054361 GGTCTTTTCTGCCTCCCAAGATA 60.054 47.826 0.00 0.00 0.00 1.98
688 769 2.291217 GGTCTTTTCTGCCTCCCAAGAT 60.291 50.000 0.00 0.00 0.00 2.40
689 770 1.073923 GGTCTTTTCTGCCTCCCAAGA 59.926 52.381 0.00 0.00 0.00 3.02
690 771 1.202927 TGGTCTTTTCTGCCTCCCAAG 60.203 52.381 0.00 0.00 0.00 3.61
691 772 0.850100 TGGTCTTTTCTGCCTCCCAA 59.150 50.000 0.00 0.00 0.00 4.12
692 773 0.850100 TTGGTCTTTTCTGCCTCCCA 59.150 50.000 0.00 0.00 0.00 4.37
693 774 1.073923 TCTTGGTCTTTTCTGCCTCCC 59.926 52.381 0.00 0.00 0.00 4.30
694 775 2.568623 TCTTGGTCTTTTCTGCCTCC 57.431 50.000 0.00 0.00 0.00 4.30
695 776 2.675348 CGATCTTGGTCTTTTCTGCCTC 59.325 50.000 0.00 0.00 0.00 4.70
696 777 2.704572 CGATCTTGGTCTTTTCTGCCT 58.295 47.619 0.00 0.00 0.00 4.75
697 778 1.131315 GCGATCTTGGTCTTTTCTGCC 59.869 52.381 0.00 0.00 0.00 4.85
698 779 1.806542 TGCGATCTTGGTCTTTTCTGC 59.193 47.619 0.00 0.00 0.00 4.26
699 780 3.329386 TCTGCGATCTTGGTCTTTTCTG 58.671 45.455 0.00 0.00 0.00 3.02
700 781 3.259374 TCTCTGCGATCTTGGTCTTTTCT 59.741 43.478 0.00 0.00 0.00 2.52
701 782 3.589988 TCTCTGCGATCTTGGTCTTTTC 58.410 45.455 0.00 0.00 0.00 2.29
706 787 0.529555 GCCTCTCTGCGATCTTGGTC 60.530 60.000 0.00 0.00 0.00 4.02
708 789 0.530211 CTGCCTCTCTGCGATCTTGG 60.530 60.000 0.00 0.00 0.00 3.61
716 797 2.813042 GACGTGCTGCCTCTCTGC 60.813 66.667 0.00 0.00 39.73 4.26
740 821 4.351054 CCGTCCAAGGGCCAGCTT 62.351 66.667 6.18 0.00 0.00 3.74
755 837 4.445699 GGCAGTAGAATGGAGCCG 57.554 61.111 0.00 0.00 35.42 5.52
776 858 1.746787 GGTTTCAGTTTCGGTTGTGGT 59.253 47.619 0.00 0.00 0.00 4.16
777 859 1.746220 TGGTTTCAGTTTCGGTTGTGG 59.254 47.619 0.00 0.00 0.00 4.17
779 861 4.522722 TTTTGGTTTCAGTTTCGGTTGT 57.477 36.364 0.00 0.00 0.00 3.32
780 862 5.105752 TGATTTTGGTTTCAGTTTCGGTTG 58.894 37.500 0.00 0.00 0.00 3.77
781 863 5.331876 TGATTTTGGTTTCAGTTTCGGTT 57.668 34.783 0.00 0.00 0.00 4.44
782 864 4.993029 TGATTTTGGTTTCAGTTTCGGT 57.007 36.364 0.00 0.00 0.00 4.69
784 866 6.091441 TGGTTTTGATTTTGGTTTCAGTTTCG 59.909 34.615 0.00 0.00 0.00 3.46
785 867 7.333174 TCTGGTTTTGATTTTGGTTTCAGTTTC 59.667 33.333 0.00 0.00 0.00 2.78
787 869 6.706295 TCTGGTTTTGATTTTGGTTTCAGTT 58.294 32.000 0.00 0.00 0.00 3.16
788 870 6.293004 TCTGGTTTTGATTTTGGTTTCAGT 57.707 33.333 0.00 0.00 0.00 3.41
789 871 6.237808 CGTTCTGGTTTTGATTTTGGTTTCAG 60.238 38.462 0.00 0.00 0.00 3.02
790 872 5.578727 CGTTCTGGTTTTGATTTTGGTTTCA 59.421 36.000 0.00 0.00 0.00 2.69
791 873 5.579119 ACGTTCTGGTTTTGATTTTGGTTTC 59.421 36.000 0.00 0.00 0.00 2.78
792 874 5.350091 CACGTTCTGGTTTTGATTTTGGTTT 59.650 36.000 0.00 0.00 0.00 3.27
793 875 4.867608 CACGTTCTGGTTTTGATTTTGGTT 59.132 37.500 0.00 0.00 0.00 3.67
794 876 4.429108 CACGTTCTGGTTTTGATTTTGGT 58.571 39.130 0.00 0.00 0.00 3.67
795 877 3.801594 CCACGTTCTGGTTTTGATTTTGG 59.198 43.478 0.00 0.00 34.90 3.28
796 878 4.502645 GTCCACGTTCTGGTTTTGATTTTG 59.497 41.667 0.00 0.00 41.52 2.44
797 879 4.678622 GTCCACGTTCTGGTTTTGATTTT 58.321 39.130 0.00 0.00 41.52 1.82
801 883 1.292061 CGTCCACGTTCTGGTTTTGA 58.708 50.000 0.00 0.00 41.52 2.69
957 1039 3.237741 GGCGGAGGAGGAGATGGG 61.238 72.222 0.00 0.00 0.00 4.00
1012 1107 4.640690 AGAGGAGGTGGTGGCGGT 62.641 66.667 0.00 0.00 0.00 5.68
1029 1356 1.076632 GGCGAAGAGGAGGGAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
1523 1850 4.090057 GTCGAAGCGCTGGTTGGC 62.090 66.667 12.58 0.00 0.00 4.52
1528 1855 2.811317 GACCTGTCGAAGCGCTGG 60.811 66.667 12.58 9.56 0.00 4.85
1702 2029 2.070650 GGGGAAGGGCTCGTACCAT 61.071 63.158 2.15 0.00 0.00 3.55
2416 2749 2.874086 CTGTTGCAATATCTCGATGGCA 59.126 45.455 0.59 0.00 0.00 4.92
2749 3082 1.067084 CGTCGCATCCATGAGCTCT 59.933 57.895 16.19 0.00 0.00 4.09
2896 3229 3.826524 TGATTGTGTGAACTTTAGCCCA 58.173 40.909 0.00 0.00 0.00 5.36
2977 3310 4.318332 CAAAGTCAGGCTTCACACTGATA 58.682 43.478 0.00 0.00 44.65 2.15
3343 3676 0.997196 GGCAACTTACGTCATCCGAC 59.003 55.000 0.00 0.00 40.70 4.79
3344 3677 3.429043 GGCAACTTACGTCATCCGA 57.571 52.632 0.00 0.00 40.70 4.55
3400 3733 6.169094 CACCAATAATGCAATAACCCAACAA 58.831 36.000 0.00 0.00 0.00 2.83
3464 3992 5.947228 AATACATCATGTTGGGCTAATCG 57.053 39.130 0.00 0.00 0.00 3.34
3621 4149 2.364324 TGGTTCTGACAGTCCACACTAC 59.636 50.000 14.66 0.00 0.00 2.73
3641 4169 5.651172 TCGAACACTGACACTATTTTGTG 57.349 39.130 0.00 0.00 43.07 3.33
3716 4244 0.674895 AGTGCTGGGACAATCGCTTC 60.675 55.000 0.00 0.00 38.70 3.86
3864 4392 3.408634 AGTTGGTTATTTGACCTGTCCG 58.591 45.455 0.00 0.00 40.47 4.79
4004 4537 1.607178 TTGGGCAGTTGCAGGGATG 60.607 57.895 6.43 0.00 44.36 3.51


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

AutoCloner maintained by Alex Coulton.