Multiple sequence alignment - TraesCS2A01G503700

Loading Multiple Alignment...

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 TraesCS2A01G503700 chr2A 100.000 3477 0 0 1 3477 733030801 733027325 0.000000e+00 6421
1 TraesCS2A01G503700 chr2A 87.738 1419 124 32 1091 2495 733041081 733039699 0.000000e+00 1611
2 TraesCS2A01G503700 chr2A 83.263 472 63 13 272 736 772884391 772883929 1.490000e-113 420
3 TraesCS2A01G503700 chr2D 93.205 1928 96 12 748 2660 598747304 598745397 0.000000e+00 2802
4 TraesCS2A01G503700 chr2D 88.407 1475 127 22 1091 2552 598803288 598801845 0.000000e+00 1736
5 TraesCS2A01G503700 chr2D 93.860 114 7 0 2881 2994 598744870 598744757 4.610000e-39 172
6 TraesCS2A01G503700 chr2D 80.478 251 25 3 1579 1829 621875577 621875803 1.660000e-38 171
7 TraesCS2A01G503700 chr2B 91.182 1962 116 30 735 2665 727654734 727652799 0.000000e+00 2612
8 TraesCS2A01G503700 chr2B 88.020 1394 126 21 1114 2495 727681300 727679936 0.000000e+00 1611
9 TraesCS2A01G503700 chr2B 87.584 596 58 4 2879 3474 727646634 727646055 0.000000e+00 676
10 TraesCS2A01G503700 chr2B 79.437 924 140 23 921 1829 763805001 763805889 2.970000e-170 608
11 TraesCS2A01G503700 chr2B 86.139 202 6 10 2657 2838 727652196 727651997 7.610000e-47 198
12 TraesCS2A01G503700 chr7D 89.431 738 65 11 3 736 470904179 470903451 0.000000e+00 918
13 TraesCS2A01G503700 chr7D 82.527 744 111 14 1 736 47112227 47112959 1.360000e-178 636
14 TraesCS2A01G503700 chr5A 87.821 739 61 15 1 736 94115936 94116648 0.000000e+00 839
15 TraesCS2A01G503700 chr7B 84.636 742 93 12 1 736 62964155 62964881 0.000000e+00 719
16 TraesCS2A01G503700 chr7B 81.193 436 65 11 309 736 79952965 79952539 5.560000e-88 335
17 TraesCS2A01G503700 chr4A 85.903 454 56 6 2994 3443 705703446 705702997 8.730000e-131 477
18 TraesCS2A01G503700 chr6B 84.265 483 67 8 2990 3467 165508037 165507559 2.440000e-126 462
19 TraesCS2A01G503700 chr6B 81.879 447 74 6 2994 3437 646255671 646255229 1.520000e-98 370
20 TraesCS2A01G503700 chr1A 84.310 478 69 5 2994 3467 29296210 29296685 2.440000e-126 462
21 TraesCS2A01G503700 chr1A 89.189 111 12 0 2879 2989 558946924 558947034 4.680000e-29 139
22 TraesCS2A01G503700 chr5B 83.437 483 71 7 2990 3467 596683401 596682923 1.150000e-119 440
23 TraesCS2A01G503700 chr5B 82.816 483 74 7 2990 3467 596639275 596638797 1.150000e-114 424
24 TraesCS2A01G503700 chr3A 83.885 453 60 10 2990 3430 57706226 57706677 1.490000e-113 420
25 TraesCS2A01G503700 chr3A 83.081 396 49 15 322 713 251371667 251372048 9.240000e-91 344
26 TraesCS2A01G503700 chr3A 79.418 481 77 19 266 736 707908577 707909045 1.560000e-83 320
27 TraesCS2A01G503700 chr6D 82.947 475 65 15 272 739 354360090 354359625 6.940000e-112 414
28 TraesCS2A01G503700 chr3B 80.519 539 77 21 1 528 641711850 641711329 4.210000e-104 388
29 TraesCS2A01G503700 chr4D 85.013 387 50 6 2990 3370 109924948 109924564 1.510000e-103 387
30 TraesCS2A01G503700 chr5D 80.851 470 75 11 273 738 8588368 8587910 4.270000e-94 355
31 TraesCS2A01G503700 chr5D 90.566 106 10 0 2879 2984 489191503 489191608 1.300000e-29 141
32 TraesCS2A01G503700 chr1B 80.496 282 29 14 2619 2880 643581853 643581578 3.540000e-45 193
33 TraesCS2A01G503700 chr6A 77.075 253 48 10 1416 1660 565108810 565109060 1.680000e-28 137
34 TraesCS2A01G503700 chr6A 76.680 253 49 10 1416 1660 565057759 565058009 7.830000e-27 132
35 TraesCS2A01G503700 chr1D 88.288 111 13 0 2879 2989 466994983 466995093 2.180000e-27 134
36 TraesCS2A01G503700 chr3D 89.024 82 7 2 2889 2969 597966807 597966727 2.210000e-17 100


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 TraesCS2A01G503700 chr2A 733027325 733030801 3476 True 6421 6421 100.0000 1 3477 1 chr2A.!!$R1 3476
1 TraesCS2A01G503700 chr2A 733039699 733041081 1382 True 1611 1611 87.7380 1091 2495 1 chr2A.!!$R2 1404
2 TraesCS2A01G503700 chr2D 598801845 598803288 1443 True 1736 1736 88.4070 1091 2552 1 chr2D.!!$R1 1461
3 TraesCS2A01G503700 chr2D 598744757 598747304 2547 True 1487 2802 93.5325 748 2994 2 chr2D.!!$R2 2246
4 TraesCS2A01G503700 chr2B 727679936 727681300 1364 True 1611 1611 88.0200 1114 2495 1 chr2B.!!$R2 1381
5 TraesCS2A01G503700 chr2B 727651997 727654734 2737 True 1405 2612 88.6605 735 2838 2 chr2B.!!$R3 2103
6 TraesCS2A01G503700 chr2B 727646055 727646634 579 True 676 676 87.5840 2879 3474 1 chr2B.!!$R1 595
7 TraesCS2A01G503700 chr2B 763805001 763805889 888 False 608 608 79.4370 921 1829 1 chr2B.!!$F1 908
8 TraesCS2A01G503700 chr7D 470903451 470904179 728 True 918 918 89.4310 3 736 1 chr7D.!!$R1 733
9 TraesCS2A01G503700 chr7D 47112227 47112959 732 False 636 636 82.5270 1 736 1 chr7D.!!$F1 735
10 TraesCS2A01G503700 chr5A 94115936 94116648 712 False 839 839 87.8210 1 736 1 chr5A.!!$F1 735
11 TraesCS2A01G503700 chr7B 62964155 62964881 726 False 719 719 84.6360 1 736 1 chr7B.!!$F1 735
12 TraesCS2A01G503700 chr3B 641711329 641711850 521 True 388 388 80.5190 1 528 1 chr3B.!!$R1 527

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
635 652 0.036483 TGTATTGCTTGAGCCTCGCA 60.036 50.0 0.0 0.0 41.18 5.10 F
896 922 0.038166 TCTTCCCGCTGAGCCATTTT 59.962 50.0 0.0 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2049 1.305219 GCACCATGCCGAAGCTGTAA 61.305 55.0 0.00 0.0 37.42 2.41 R
2875 3633 0.846870 AAGCTTCCTAAGGGTGGCCT 60.847 55.0 3.32 0.0 34.08 5.19 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
53 54 3.652274 CAAAGCCCACATGAAACGAAAT 58.348 40.909 0.00 0.00 0.00 2.17
56 57 3.950397 AGCCCACATGAAACGAAATAGA 58.050 40.909 0.00 0.00 0.00 1.98
71 80 4.201391 CGAAATAGATGCAAACAAACGCAC 60.201 41.667 0.00 0.00 41.79 5.34
402 418 4.757149 CGGTGAGAGAGAAAAACCTCAATT 59.243 41.667 0.00 0.00 37.40 2.32
423 440 9.231297 TCAATTAATGGATCGAGAAAAAGACTT 57.769 29.630 0.00 0.00 0.00 3.01
476 493 4.169271 CCCTAGATACGGGTCGCA 57.831 61.111 0.00 0.00 36.91 5.10
545 562 3.341043 CGGAAGCGGCATCGATGG 61.341 66.667 26.00 12.02 39.00 3.51
554 571 3.403936 GCATCGATGGCTAGGGTTT 57.596 52.632 26.00 0.00 0.00 3.27
555 572 1.680338 GCATCGATGGCTAGGGTTTT 58.320 50.000 26.00 0.00 0.00 2.43
556 573 1.334869 GCATCGATGGCTAGGGTTTTG 59.665 52.381 26.00 0.00 0.00 2.44
557 574 1.949525 CATCGATGGCTAGGGTTTTGG 59.050 52.381 17.96 0.00 0.00 3.28
558 575 1.281419 TCGATGGCTAGGGTTTTGGA 58.719 50.000 0.00 0.00 0.00 3.53
559 576 1.843851 TCGATGGCTAGGGTTTTGGAT 59.156 47.619 0.00 0.00 0.00 3.41
560 577 2.158813 TCGATGGCTAGGGTTTTGGATC 60.159 50.000 0.00 0.00 0.00 3.36
561 578 2.222027 GATGGCTAGGGTTTTGGATCG 58.778 52.381 0.00 0.00 0.00 3.69
562 579 1.281419 TGGCTAGGGTTTTGGATCGA 58.719 50.000 0.00 0.00 0.00 3.59
563 580 1.209504 TGGCTAGGGTTTTGGATCGAG 59.790 52.381 0.00 0.00 0.00 4.04
564 581 1.485066 GGCTAGGGTTTTGGATCGAGA 59.515 52.381 0.00 0.00 0.00 4.04
565 582 2.104963 GGCTAGGGTTTTGGATCGAGAT 59.895 50.000 0.00 0.00 0.00 2.75
566 583 3.433740 GGCTAGGGTTTTGGATCGAGATT 60.434 47.826 0.00 0.00 0.00 2.40
567 584 4.202326 GGCTAGGGTTTTGGATCGAGATTA 60.202 45.833 0.00 0.00 0.00 1.75
568 585 4.991687 GCTAGGGTTTTGGATCGAGATTAG 59.008 45.833 0.00 0.00 0.00 1.73
569 586 4.423625 AGGGTTTTGGATCGAGATTAGG 57.576 45.455 0.00 0.00 0.00 2.69
570 587 2.879026 GGGTTTTGGATCGAGATTAGGC 59.121 50.000 0.00 0.00 0.00 3.93
571 588 3.433740 GGGTTTTGGATCGAGATTAGGCT 60.434 47.826 0.00 0.00 0.00 4.58
572 589 3.561725 GGTTTTGGATCGAGATTAGGCTG 59.438 47.826 0.00 0.00 0.00 4.85
573 590 4.442706 GTTTTGGATCGAGATTAGGCTGA 58.557 43.478 0.00 0.00 0.00 4.26
574 591 4.963318 TTTGGATCGAGATTAGGCTGAT 57.037 40.909 0.00 0.00 0.00 2.90
575 592 6.223852 GTTTTGGATCGAGATTAGGCTGATA 58.776 40.000 0.00 0.00 0.00 2.15
576 593 5.392767 TTGGATCGAGATTAGGCTGATAC 57.607 43.478 0.00 0.00 0.00 2.24
577 594 3.764434 TGGATCGAGATTAGGCTGATACC 59.236 47.826 0.00 0.00 0.00 2.73
578 595 3.764434 GGATCGAGATTAGGCTGATACCA 59.236 47.826 0.00 0.00 0.00 3.25
579 596 4.404073 GGATCGAGATTAGGCTGATACCAT 59.596 45.833 0.00 0.00 0.00 3.55
580 597 4.790765 TCGAGATTAGGCTGATACCATG 57.209 45.455 0.00 0.00 0.00 3.66
581 598 3.056536 TCGAGATTAGGCTGATACCATGC 60.057 47.826 0.00 0.00 0.00 4.06
582 599 3.056250 CGAGATTAGGCTGATACCATGCT 60.056 47.826 0.00 0.00 0.00 3.79
583 600 4.158579 CGAGATTAGGCTGATACCATGCTA 59.841 45.833 0.00 0.00 0.00 3.49
584 601 5.659463 GAGATTAGGCTGATACCATGCTAG 58.341 45.833 0.00 0.00 0.00 3.42
585 602 5.336945 AGATTAGGCTGATACCATGCTAGA 58.663 41.667 0.00 0.00 0.00 2.43
586 603 5.782331 AGATTAGGCTGATACCATGCTAGAA 59.218 40.000 0.00 0.00 0.00 2.10
587 604 5.474578 TTAGGCTGATACCATGCTAGAAG 57.525 43.478 0.00 0.00 0.00 2.85
588 605 2.636893 AGGCTGATACCATGCTAGAAGG 59.363 50.000 0.00 0.00 0.00 3.46
589 606 2.289945 GGCTGATACCATGCTAGAAGGG 60.290 54.545 0.00 0.00 0.00 3.95
590 607 2.634940 GCTGATACCATGCTAGAAGGGA 59.365 50.000 8.86 0.00 0.00 4.20
591 608 3.306641 GCTGATACCATGCTAGAAGGGAG 60.307 52.174 8.86 0.00 0.00 4.30
592 609 4.155709 CTGATACCATGCTAGAAGGGAGA 58.844 47.826 8.86 0.00 0.00 3.71
593 610 4.556697 TGATACCATGCTAGAAGGGAGAA 58.443 43.478 8.86 0.00 0.00 2.87
594 611 4.968719 TGATACCATGCTAGAAGGGAGAAA 59.031 41.667 8.86 0.00 0.00 2.52
595 612 3.922171 ACCATGCTAGAAGGGAGAAAG 57.078 47.619 8.86 0.00 0.00 2.62
596 613 2.507471 ACCATGCTAGAAGGGAGAAAGG 59.493 50.000 8.86 0.00 0.00 3.11
597 614 2.774234 CCATGCTAGAAGGGAGAAAGGA 59.226 50.000 0.00 0.00 0.00 3.36
598 615 3.200825 CCATGCTAGAAGGGAGAAAGGAA 59.799 47.826 0.00 0.00 0.00 3.36
599 616 4.141298 CCATGCTAGAAGGGAGAAAGGAAT 60.141 45.833 0.00 0.00 0.00 3.01
600 617 5.444176 CATGCTAGAAGGGAGAAAGGAATT 58.556 41.667 0.00 0.00 0.00 2.17
601 618 4.848357 TGCTAGAAGGGAGAAAGGAATTG 58.152 43.478 0.00 0.00 0.00 2.32
602 619 4.203226 GCTAGAAGGGAGAAAGGAATTGG 58.797 47.826 0.00 0.00 0.00 3.16
603 620 4.324641 GCTAGAAGGGAGAAAGGAATTGGT 60.325 45.833 0.00 0.00 0.00 3.67
604 621 4.039603 AGAAGGGAGAAAGGAATTGGTG 57.960 45.455 0.00 0.00 0.00 4.17
605 622 3.657727 AGAAGGGAGAAAGGAATTGGTGA 59.342 43.478 0.00 0.00 0.00 4.02
606 623 4.106341 AGAAGGGAGAAAGGAATTGGTGAA 59.894 41.667 0.00 0.00 0.00 3.18
607 624 4.469469 AGGGAGAAAGGAATTGGTGAAA 57.531 40.909 0.00 0.00 0.00 2.69
608 625 5.015813 AGGGAGAAAGGAATTGGTGAAAT 57.984 39.130 0.00 0.00 0.00 2.17
609 626 6.152638 AGGGAGAAAGGAATTGGTGAAATA 57.847 37.500 0.00 0.00 0.00 1.40
610 627 6.190587 AGGGAGAAAGGAATTGGTGAAATAG 58.809 40.000 0.00 0.00 0.00 1.73
611 628 5.952347 GGGAGAAAGGAATTGGTGAAATAGT 59.048 40.000 0.00 0.00 0.00 2.12
612 629 6.437477 GGGAGAAAGGAATTGGTGAAATAGTT 59.563 38.462 0.00 0.00 0.00 2.24
613 630 7.039011 GGGAGAAAGGAATTGGTGAAATAGTTT 60.039 37.037 0.00 0.00 0.00 2.66
614 631 7.814587 GGAGAAAGGAATTGGTGAAATAGTTTG 59.185 37.037 0.00 0.00 0.00 2.93
615 632 8.477419 AGAAAGGAATTGGTGAAATAGTTTGA 57.523 30.769 0.00 0.00 0.00 2.69
616 633 9.093458 AGAAAGGAATTGGTGAAATAGTTTGAT 57.907 29.630 0.00 0.00 0.00 2.57
617 634 9.143631 GAAAGGAATTGGTGAAATAGTTTGATG 57.856 33.333 0.00 0.00 0.00 3.07
618 635 7.781324 AGGAATTGGTGAAATAGTTTGATGT 57.219 32.000 0.00 0.00 0.00 3.06
619 636 8.877864 AGGAATTGGTGAAATAGTTTGATGTA 57.122 30.769 0.00 0.00 0.00 2.29
620 637 9.479549 AGGAATTGGTGAAATAGTTTGATGTAT 57.520 29.630 0.00 0.00 0.00 2.29
623 640 8.931385 ATTGGTGAAATAGTTTGATGTATTGC 57.069 30.769 0.00 0.00 0.00 3.56
624 641 7.701539 TGGTGAAATAGTTTGATGTATTGCT 57.298 32.000 0.00 0.00 0.00 3.91
625 642 8.121305 TGGTGAAATAGTTTGATGTATTGCTT 57.879 30.769 0.00 0.00 0.00 3.91
626 643 8.028354 TGGTGAAATAGTTTGATGTATTGCTTG 58.972 33.333 0.00 0.00 0.00 4.01
627 644 8.243426 GGTGAAATAGTTTGATGTATTGCTTGA 58.757 33.333 0.00 0.00 0.00 3.02
628 645 9.282247 GTGAAATAGTTTGATGTATTGCTTGAG 57.718 33.333 0.00 0.00 0.00 3.02
629 646 7.970061 TGAAATAGTTTGATGTATTGCTTGAGC 59.030 33.333 0.00 0.00 42.50 4.26
630 647 4.708726 AGTTTGATGTATTGCTTGAGCC 57.291 40.909 0.00 0.00 41.18 4.70
631 648 4.338879 AGTTTGATGTATTGCTTGAGCCT 58.661 39.130 0.00 0.00 41.18 4.58
632 649 4.397417 AGTTTGATGTATTGCTTGAGCCTC 59.603 41.667 0.00 0.00 41.18 4.70
633 650 2.554142 TGATGTATTGCTTGAGCCTCG 58.446 47.619 0.00 0.00 41.18 4.63
634 651 1.262683 GATGTATTGCTTGAGCCTCGC 59.737 52.381 0.00 0.00 41.18 5.03
635 652 0.036483 TGTATTGCTTGAGCCTCGCA 60.036 50.000 0.00 0.00 41.18 5.10
636 653 0.654683 GTATTGCTTGAGCCTCGCAG 59.345 55.000 0.00 0.00 41.18 5.18
637 654 0.462581 TATTGCTTGAGCCTCGCAGG 60.463 55.000 0.00 0.00 41.18 4.85
652 669 6.398234 CCTCGCAGGCATATATATAAGAGT 57.602 41.667 0.00 0.00 0.00 3.24
653 670 7.511959 CCTCGCAGGCATATATATAAGAGTA 57.488 40.000 0.00 0.00 0.00 2.59
654 671 7.364200 CCTCGCAGGCATATATATAAGAGTAC 58.636 42.308 0.00 0.00 0.00 2.73
655 672 7.013369 CCTCGCAGGCATATATATAAGAGTACA 59.987 40.741 0.00 0.00 0.00 2.90
656 673 8.288689 TCGCAGGCATATATATAAGAGTACAA 57.711 34.615 0.00 0.00 0.00 2.41
657 674 8.914011 TCGCAGGCATATATATAAGAGTACAAT 58.086 33.333 0.00 0.00 0.00 2.71
658 675 8.972349 CGCAGGCATATATATAAGAGTACAATG 58.028 37.037 0.00 0.00 0.00 2.82
674 691 9.244292 AGAGTACAATGATCTACTTGAAGTACA 57.756 33.333 0.00 0.00 33.62 2.90
675 692 9.856488 GAGTACAATGATCTACTTGAAGTACAA 57.144 33.333 0.00 0.00 33.62 2.41
684 701 2.356665 TTGAAGTACAAGGCAAGGCA 57.643 45.000 0.00 0.00 34.20 4.75
685 702 1.896220 TGAAGTACAAGGCAAGGCAG 58.104 50.000 0.00 0.00 0.00 4.85
686 703 1.419762 TGAAGTACAAGGCAAGGCAGA 59.580 47.619 0.00 0.00 0.00 4.26
687 704 2.158682 TGAAGTACAAGGCAAGGCAGAA 60.159 45.455 0.00 0.00 0.00 3.02
688 705 2.887151 AGTACAAGGCAAGGCAGAAT 57.113 45.000 0.00 0.00 0.00 2.40
689 706 4.261801 GAAGTACAAGGCAAGGCAGAATA 58.738 43.478 0.00 0.00 0.00 1.75
690 707 4.301072 AGTACAAGGCAAGGCAGAATAA 57.699 40.909 0.00 0.00 0.00 1.40
691 708 4.860022 AGTACAAGGCAAGGCAGAATAAT 58.140 39.130 0.00 0.00 0.00 1.28
692 709 6.001449 AGTACAAGGCAAGGCAGAATAATA 57.999 37.500 0.00 0.00 0.00 0.98
693 710 6.605119 AGTACAAGGCAAGGCAGAATAATAT 58.395 36.000 0.00 0.00 0.00 1.28
694 711 6.712547 AGTACAAGGCAAGGCAGAATAATATC 59.287 38.462 0.00 0.00 0.00 1.63
695 712 4.829492 ACAAGGCAAGGCAGAATAATATCC 59.171 41.667 0.00 0.00 0.00 2.59
696 713 5.075493 CAAGGCAAGGCAGAATAATATCCT 58.925 41.667 0.00 0.00 0.00 3.24
697 714 6.183361 ACAAGGCAAGGCAGAATAATATCCTA 60.183 38.462 0.00 0.00 0.00 2.94
698 715 5.810095 AGGCAAGGCAGAATAATATCCTAC 58.190 41.667 0.00 0.00 0.00 3.18
699 716 4.631813 GGCAAGGCAGAATAATATCCTACG 59.368 45.833 0.00 0.00 0.00 3.51
700 717 4.093556 GCAAGGCAGAATAATATCCTACGC 59.906 45.833 0.00 0.00 0.00 4.42
701 718 5.482908 CAAGGCAGAATAATATCCTACGCT 58.517 41.667 0.00 0.00 0.00 5.07
702 719 6.631016 CAAGGCAGAATAATATCCTACGCTA 58.369 40.000 0.00 0.00 0.00 4.26
703 720 7.268586 CAAGGCAGAATAATATCCTACGCTAT 58.731 38.462 0.00 0.00 0.00 2.97
704 721 7.045126 AGGCAGAATAATATCCTACGCTATC 57.955 40.000 0.00 0.00 0.00 2.08
705 722 6.041069 AGGCAGAATAATATCCTACGCTATCC 59.959 42.308 0.00 0.00 0.00 2.59
706 723 6.041069 GGCAGAATAATATCCTACGCTATCCT 59.959 42.308 0.00 0.00 0.00 3.24
707 724 7.230913 GGCAGAATAATATCCTACGCTATCCTA 59.769 40.741 0.00 0.00 0.00 2.94
708 725 8.798402 GCAGAATAATATCCTACGCTATCCTAT 58.202 37.037 0.00 0.00 0.00 2.57
714 731 7.826918 ATATCCTACGCTATCCTATCTTTCC 57.173 40.000 0.00 0.00 0.00 3.13
715 732 5.258216 TCCTACGCTATCCTATCTTTCCT 57.742 43.478 0.00 0.00 0.00 3.36
716 733 5.642165 TCCTACGCTATCCTATCTTTCCTT 58.358 41.667 0.00 0.00 0.00 3.36
717 734 6.787170 TCCTACGCTATCCTATCTTTCCTTA 58.213 40.000 0.00 0.00 0.00 2.69
718 735 6.885376 TCCTACGCTATCCTATCTTTCCTTAG 59.115 42.308 0.00 0.00 0.00 2.18
719 736 6.885376 CCTACGCTATCCTATCTTTCCTTAGA 59.115 42.308 0.00 0.00 0.00 2.10
720 737 7.393796 CCTACGCTATCCTATCTTTCCTTAGAA 59.606 40.741 0.00 0.00 0.00 2.10
721 738 7.784470 ACGCTATCCTATCTTTCCTTAGAAT 57.216 36.000 0.00 0.00 0.00 2.40
722 739 7.832769 ACGCTATCCTATCTTTCCTTAGAATC 58.167 38.462 0.00 0.00 0.00 2.52
723 740 7.451877 ACGCTATCCTATCTTTCCTTAGAATCA 59.548 37.037 0.00 0.00 0.00 2.57
724 741 8.307483 CGCTATCCTATCTTTCCTTAGAATCAA 58.693 37.037 0.00 0.00 0.00 2.57
767 784 1.543358 GCCCTGCCTTCTTCTTTCTTG 59.457 52.381 0.00 0.00 0.00 3.02
857 883 3.252974 ACCTGTCGAATCAATCAGTCC 57.747 47.619 0.00 0.00 0.00 3.85
896 922 0.038166 TCTTCCCGCTGAGCCATTTT 59.962 50.000 0.00 0.00 0.00 1.82
900 926 3.569194 TCCCGCTGAGCCATTTTATTA 57.431 42.857 0.00 0.00 0.00 0.98
901 927 3.476552 TCCCGCTGAGCCATTTTATTAG 58.523 45.455 0.00 0.00 0.00 1.73
902 928 2.554032 CCCGCTGAGCCATTTTATTAGG 59.446 50.000 0.00 0.00 0.00 2.69
911 937 6.183361 TGAGCCATTTTATTAGGGAGGAGTAC 60.183 42.308 0.00 0.00 0.00 2.73
913 939 7.080353 AGCCATTTTATTAGGGAGGAGTACTA 58.920 38.462 0.00 0.00 0.00 1.82
996 1022 1.916697 GAAGGCGTTGAGAGCTTGGC 61.917 60.000 0.00 0.00 34.52 4.52
997 1023 3.793144 GGCGTTGAGAGCTTGGCG 61.793 66.667 0.00 0.00 34.52 5.69
1038 1064 2.154462 GCTGTCACTGCAACTGGTAAT 58.846 47.619 1.02 0.00 0.00 1.89
1039 1065 2.554032 GCTGTCACTGCAACTGGTAATT 59.446 45.455 1.02 0.00 0.00 1.40
1040 1066 3.751175 GCTGTCACTGCAACTGGTAATTA 59.249 43.478 1.02 0.00 0.00 1.40
1041 1067 4.215399 GCTGTCACTGCAACTGGTAATTAA 59.785 41.667 1.02 0.00 0.00 1.40
1042 1068 5.682943 TGTCACTGCAACTGGTAATTAAC 57.317 39.130 0.00 0.00 0.00 2.01
1045 1071 6.086222 GTCACTGCAACTGGTAATTAACATG 58.914 40.000 3.09 1.62 0.00 3.21
1053 1079 7.534282 CAACTGGTAATTAACATGCATACACA 58.466 34.615 3.09 0.00 0.00 3.72
1107 1133 6.601332 TGTCTGGTCCTTAATCAGTTTTTCT 58.399 36.000 0.00 0.00 0.00 2.52
1110 1136 6.426937 TCTGGTCCTTAATCAGTTTTTCTTCG 59.573 38.462 0.00 0.00 0.00 3.79
1128 1154 0.438830 CGGCTAACTCGTGTTCTTGC 59.561 55.000 6.07 9.65 37.59 4.01
1150 1176 1.272490 TCGATTCATCCAGTATCGGCC 59.728 52.381 0.00 0.00 44.57 6.13
1258 1289 4.590647 GTGACCAAGATCATGGAGGAGATA 59.409 45.833 23.35 0.00 43.54 1.98
1261 1292 5.222870 ACCAAGATCATGGAGGAGATAAGT 58.777 41.667 23.35 0.00 43.54 2.24
1264 1295 6.070881 CCAAGATCATGGAGGAGATAAGTAGG 60.071 46.154 11.68 0.00 43.54 3.18
1330 1361 0.809385 ACGACGTGGTCATCGAGATT 59.191 50.000 0.00 0.00 40.86 2.40
1333 1364 0.895530 ACGTGGTCATCGAGATTGGT 59.104 50.000 0.00 0.00 0.00 3.67
1361 1392 4.712122 GAGAAGTTTCTCCACGAGATCT 57.288 45.455 10.15 0.00 46.20 2.75
1363 1394 4.815269 AGAAGTTTCTCCACGAGATCTTG 58.185 43.478 8.54 8.54 38.56 3.02
1381 1412 1.516386 GAACGAGAAGCCGATGCGA 60.516 57.895 0.00 0.00 44.33 5.10
1392 1423 2.305853 CGATGCGATTCAGCTCCGG 61.306 63.158 0.00 0.00 38.13 5.14
1471 1509 0.178873 TGGTCTACAAGGGGGAGCTT 60.179 55.000 0.00 0.00 0.00 3.74
1501 1539 4.636435 CCCGTGGCGGTGAAGGTT 62.636 66.667 6.82 0.00 46.80 3.50
1530 1568 1.197721 GTCCATGAACAAGAAGGTGCG 59.802 52.381 0.00 0.00 0.00 5.34
1786 1824 2.154074 GGCCAAGGGGATCCGGTAT 61.154 63.158 5.45 0.00 38.33 2.73
1864 1902 2.432628 CTCACCGCCGACTTCACC 60.433 66.667 0.00 0.00 0.00 4.02
2011 2049 0.660595 CGACAGAGAAGTGCGACGTT 60.661 55.000 0.00 0.00 0.00 3.99
2044 2082 3.877559 CATGGTGCTGTTTGAGATCCTA 58.122 45.455 0.00 0.00 0.00 2.94
2049 2087 1.210478 GCTGTTTGAGATCCTAGGGCA 59.790 52.381 9.46 0.00 0.00 5.36
2152 2190 0.610174 ACATGGAGTGCATCGTGTCT 59.390 50.000 0.00 0.00 0.00 3.41
2215 2253 0.107897 CCATGTGTAAGGTGGCGCTA 60.108 55.000 7.64 0.00 0.00 4.26
2617 2686 5.976458 TGACTTATGATTTTTGGGGAATGC 58.024 37.500 0.00 0.00 0.00 3.56
2697 3374 2.072298 GAGCTACAAGCAGAACCACAG 58.928 52.381 1.22 0.00 45.56 3.66
2705 3382 0.312102 GCAGAACCACAGCCAAACTC 59.688 55.000 0.00 0.00 0.00 3.01
2711 3388 0.389025 CCACAGCCAAACTCCCAAAC 59.611 55.000 0.00 0.00 0.00 2.93
2712 3389 1.402787 CACAGCCAAACTCCCAAACT 58.597 50.000 0.00 0.00 0.00 2.66
2713 3390 1.338020 CACAGCCAAACTCCCAAACTC 59.662 52.381 0.00 0.00 0.00 3.01
2714 3391 1.215423 ACAGCCAAACTCCCAAACTCT 59.785 47.619 0.00 0.00 0.00 3.24
2715 3392 1.610522 CAGCCAAACTCCCAAACTCTG 59.389 52.381 0.00 0.00 0.00 3.35
2716 3393 1.494721 AGCCAAACTCCCAAACTCTGA 59.505 47.619 0.00 0.00 0.00 3.27
2717 3394 1.882623 GCCAAACTCCCAAACTCTGAG 59.117 52.381 2.45 2.45 0.00 3.35
2718 3395 2.487265 GCCAAACTCCCAAACTCTGAGA 60.487 50.000 12.44 0.00 0.00 3.27
2799 3496 4.277476 ACAGGAACATGACCAAACAAAGA 58.723 39.130 0.00 0.00 0.00 2.52
2851 3609 4.924625 ACTACTAGAGAAGAAGCACTCCA 58.075 43.478 0.00 0.00 34.13 3.86
2864 3622 1.612726 GCACTCCATCTCCAACAGCTT 60.613 52.381 0.00 0.00 0.00 3.74
2886 3685 1.271840 ATCAAGCGAGGCCACCCTTA 61.272 55.000 5.01 0.00 43.12 2.69
2887 3686 1.450312 CAAGCGAGGCCACCCTTAG 60.450 63.158 5.01 0.00 43.12 2.18
2946 3745 2.302733 GCCTTGTTCCCAAATCCAACAT 59.697 45.455 0.00 0.00 30.28 2.71
2960 3759 7.408910 CAAATCCAACATCCTTTTGTTTTGTC 58.591 34.615 0.00 0.00 37.73 3.18
2967 3766 3.867857 TCCTTTTGTTTTGTCCCTTTGC 58.132 40.909 0.00 0.00 0.00 3.68
3000 3799 1.536709 CCAAGCCATTATTCCGCAAGC 60.537 52.381 0.00 0.00 0.00 4.01
3011 3810 0.884704 TCCGCAAGCCAAGTCTGAAC 60.885 55.000 0.00 0.00 0.00 3.18
3016 3815 2.542411 GCAAGCCAAGTCTGAACAACTG 60.542 50.000 0.00 0.00 0.00 3.16
3039 3838 2.416747 TGTGAAGCAAAGTCTCCATCG 58.583 47.619 0.00 0.00 0.00 3.84
3040 3839 1.129437 GTGAAGCAAAGTCTCCATCGC 59.871 52.381 0.00 0.00 0.00 4.58
3047 3846 2.749076 CAAAGTCTCCATCGCATCCAAA 59.251 45.455 0.00 0.00 0.00 3.28
3051 3850 1.281867 TCTCCATCGCATCCAAAACCT 59.718 47.619 0.00 0.00 0.00 3.50
3053 3852 1.818060 TCCATCGCATCCAAAACCTTG 59.182 47.619 0.00 0.00 0.00 3.61
3055 3854 2.415893 CCATCGCATCCAAAACCTTGAC 60.416 50.000 0.00 0.00 34.14 3.18
3063 3862 3.904717 TCCAAAACCTTGACTTTGCCTA 58.095 40.909 0.00 0.00 34.14 3.93
3082 3881 2.134789 ATTGCAGGTCCTCCAATCAC 57.865 50.000 1.80 0.00 35.89 3.06
3089 3888 1.541233 GGTCCTCCAATCACGCTATGG 60.541 57.143 0.00 0.00 35.49 2.74
3092 3891 1.544093 CCTCCAATCACGCTATGGCAT 60.544 52.381 4.88 4.88 38.60 4.40
3093 3892 2.224606 CTCCAATCACGCTATGGCATT 58.775 47.619 4.78 0.00 38.60 3.56
3094 3893 2.221169 TCCAATCACGCTATGGCATTC 58.779 47.619 4.78 0.00 38.60 2.67
3095 3894 2.158769 TCCAATCACGCTATGGCATTCT 60.159 45.455 4.78 0.00 38.60 2.40
3096 3895 2.225019 CCAATCACGCTATGGCATTCTC 59.775 50.000 4.78 0.00 38.60 2.87
3097 3896 2.175878 ATCACGCTATGGCATTCTCC 57.824 50.000 4.78 0.00 38.60 3.71
3098 3897 0.829990 TCACGCTATGGCATTCTCCA 59.170 50.000 4.78 0.00 40.97 3.86
3099 3898 0.940126 CACGCTATGGCATTCTCCAC 59.060 55.000 4.78 0.00 39.25 4.02
3100 3899 0.541392 ACGCTATGGCATTCTCCACA 59.459 50.000 4.78 0.00 39.25 4.17
3101 3900 1.141657 ACGCTATGGCATTCTCCACAT 59.858 47.619 4.78 0.00 39.25 3.21
3102 3901 1.534163 CGCTATGGCATTCTCCACATG 59.466 52.381 4.78 0.00 39.25 3.21
3103 3902 2.807837 CGCTATGGCATTCTCCACATGA 60.808 50.000 4.78 0.00 39.25 3.07
3104 3903 2.812591 GCTATGGCATTCTCCACATGAG 59.187 50.000 4.78 0.00 39.25 2.90
3105 3904 3.746751 GCTATGGCATTCTCCACATGAGT 60.747 47.826 4.78 0.00 39.25 3.41
3106 3905 2.885135 TGGCATTCTCCACATGAGTT 57.115 45.000 0.00 0.00 42.12 3.01
3107 3906 2.439409 TGGCATTCTCCACATGAGTTG 58.561 47.619 0.00 0.00 42.12 3.16
3155 3954 5.186021 ACATGTACCAAGGTGTCAACAAAAA 59.814 36.000 0.00 0.00 0.00 1.94
3156 3955 5.061920 TGTACCAAGGTGTCAACAAAAAC 57.938 39.130 1.07 0.00 0.00 2.43
3159 3958 3.056179 ACCAAGGTGTCAACAAAAACAGG 60.056 43.478 0.00 0.00 0.00 4.00
3165 3964 2.828520 TGTCAACAAAAACAGGGCTTCA 59.171 40.909 0.00 0.00 0.00 3.02
3167 3966 2.159310 TCAACAAAAACAGGGCTTCACG 60.159 45.455 0.00 0.00 0.00 4.35
3170 3969 2.293399 ACAAAAACAGGGCTTCACGATC 59.707 45.455 0.00 0.00 0.00 3.69
3171 3970 2.270352 AAAACAGGGCTTCACGATCA 57.730 45.000 0.00 0.00 0.00 2.92
3231 4030 0.991355 ACCGGCCCCTATCCAATCAA 60.991 55.000 0.00 0.00 0.00 2.57
3245 4044 2.095567 CCAATCAAGGTGTCAAAGAGCG 60.096 50.000 0.00 0.00 0.00 5.03
3267 4066 2.625790 TCATACGCCAGCCTTTGTTTTT 59.374 40.909 0.00 0.00 0.00 1.94
3271 4070 2.093711 ACGCCAGCCTTTGTTTTTCTTT 60.094 40.909 0.00 0.00 0.00 2.52
3284 4083 7.703058 TTGTTTTTCTTTGAAGGAGAAGTCT 57.297 32.000 0.00 0.00 34.84 3.24
3293 4092 2.296073 AGGAGAAGTCTGGAACTCGT 57.704 50.000 0.00 0.00 37.17 4.18
3310 4109 2.353889 CTCGTTGATGGCCAGATCAAAG 59.646 50.000 20.70 21.38 42.58 2.77
3333 4132 3.191581 AGGACTGATCACACGTAGAACAG 59.808 47.826 19.25 19.25 40.48 3.16
3340 4139 3.961182 TCACACGTAGAACAGTGACTTC 58.039 45.455 0.00 0.00 40.56 3.01
3343 4142 1.335810 ACGTAGAACAGTGACTTCGCA 59.664 47.619 15.64 0.00 32.00 5.10
3365 4164 3.851128 GACCACTAGGGCCTCCGC 61.851 72.222 10.74 0.00 42.05 5.54
3388 4187 1.668751 GGCCGATTATTTTGCGAGACA 59.331 47.619 0.00 0.00 0.00 3.41
3390 4189 2.845764 GCCGATTATTTTGCGAGACACG 60.846 50.000 0.00 0.00 45.66 4.49
3419 4218 4.391216 CCAAGATCAACCATATCTCGATGC 59.609 45.833 0.00 0.00 32.48 3.91
3425 4224 0.036010 CCATATCTCGATGCCCACCC 60.036 60.000 0.00 0.00 0.00 4.61
3439 4238 2.448931 ACCCCCGGTGAAAGGTGA 60.449 61.111 0.00 0.00 32.98 4.02
3444 4243 0.605589 CCCGGTGAAAGGTGAAGGTC 60.606 60.000 0.00 0.00 0.00 3.85
3459 4258 1.561643 AGGTCGTCACCATCATGTCT 58.438 50.000 0.00 0.00 46.68 3.41
3468 4267 1.453235 CATCATGTCTGGGGCCGAT 59.547 57.895 0.00 0.00 0.00 4.18
3471 4270 3.092511 ATGTCTGGGGCCGATGCT 61.093 61.111 0.00 0.00 37.74 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.505324 GCTTTGCAGGATACATGAAGATCAC 60.505 44.000 0.00 0.00 41.41 3.06
53 54 1.661743 GCGTGCGTTTGTTTGCATCTA 60.662 47.619 0.00 0.00 43.96 1.98
56 57 1.226802 TGCGTGCGTTTGTTTGCAT 60.227 47.368 0.00 0.00 43.96 3.96
423 440 2.030540 CGGTCGATCGGCTATCCTAAAA 60.031 50.000 20.54 0.00 0.00 1.52
538 555 1.843851 TCCAAAACCCTAGCCATCGAT 59.156 47.619 0.00 0.00 0.00 3.59
539 556 1.281419 TCCAAAACCCTAGCCATCGA 58.719 50.000 0.00 0.00 0.00 3.59
541 558 2.158813 TCGATCCAAAACCCTAGCCATC 60.159 50.000 0.00 0.00 0.00 3.51
542 559 1.843851 TCGATCCAAAACCCTAGCCAT 59.156 47.619 0.00 0.00 0.00 4.40
543 560 1.209504 CTCGATCCAAAACCCTAGCCA 59.790 52.381 0.00 0.00 0.00 4.75
544 561 1.485066 TCTCGATCCAAAACCCTAGCC 59.515 52.381 0.00 0.00 0.00 3.93
545 562 2.981859 TCTCGATCCAAAACCCTAGC 57.018 50.000 0.00 0.00 0.00 3.42
546 563 5.542779 CCTAATCTCGATCCAAAACCCTAG 58.457 45.833 0.00 0.00 0.00 3.02
547 564 4.202326 GCCTAATCTCGATCCAAAACCCTA 60.202 45.833 0.00 0.00 0.00 3.53
548 565 3.433740 GCCTAATCTCGATCCAAAACCCT 60.434 47.826 0.00 0.00 0.00 4.34
549 566 2.879026 GCCTAATCTCGATCCAAAACCC 59.121 50.000 0.00 0.00 0.00 4.11
550 567 3.561725 CAGCCTAATCTCGATCCAAAACC 59.438 47.826 0.00 0.00 0.00 3.27
551 568 4.442706 TCAGCCTAATCTCGATCCAAAAC 58.557 43.478 0.00 0.00 0.00 2.43
552 569 4.753516 TCAGCCTAATCTCGATCCAAAA 57.246 40.909 0.00 0.00 0.00 2.44
553 570 4.963318 ATCAGCCTAATCTCGATCCAAA 57.037 40.909 0.00 0.00 0.00 3.28
554 571 4.220821 GGTATCAGCCTAATCTCGATCCAA 59.779 45.833 0.00 0.00 0.00 3.53
555 572 3.764434 GGTATCAGCCTAATCTCGATCCA 59.236 47.826 0.00 0.00 0.00 3.41
556 573 3.764434 TGGTATCAGCCTAATCTCGATCC 59.236 47.826 0.00 0.00 0.00 3.36
557 574 5.347342 CATGGTATCAGCCTAATCTCGATC 58.653 45.833 0.00 0.00 0.00 3.69
558 575 4.382470 GCATGGTATCAGCCTAATCTCGAT 60.382 45.833 0.00 0.00 0.00 3.59
559 576 3.056536 GCATGGTATCAGCCTAATCTCGA 60.057 47.826 0.00 0.00 0.00 4.04
560 577 3.056250 AGCATGGTATCAGCCTAATCTCG 60.056 47.826 0.00 0.00 0.00 4.04
561 578 4.550076 AGCATGGTATCAGCCTAATCTC 57.450 45.455 0.00 0.00 0.00 2.75
562 579 5.336945 TCTAGCATGGTATCAGCCTAATCT 58.663 41.667 4.84 0.00 0.00 2.40
563 580 5.667539 TCTAGCATGGTATCAGCCTAATC 57.332 43.478 4.84 0.00 0.00 1.75
564 581 5.046014 CCTTCTAGCATGGTATCAGCCTAAT 60.046 44.000 4.84 0.00 0.00 1.73
565 582 4.284490 CCTTCTAGCATGGTATCAGCCTAA 59.716 45.833 4.84 0.00 0.00 2.69
566 583 3.834813 CCTTCTAGCATGGTATCAGCCTA 59.165 47.826 4.84 0.00 0.00 3.93
567 584 2.636893 CCTTCTAGCATGGTATCAGCCT 59.363 50.000 4.84 0.00 0.00 4.58
568 585 2.289945 CCCTTCTAGCATGGTATCAGCC 60.290 54.545 4.84 0.00 0.00 4.85
569 586 2.634940 TCCCTTCTAGCATGGTATCAGC 59.365 50.000 4.84 0.00 0.00 4.26
570 587 4.155709 TCTCCCTTCTAGCATGGTATCAG 58.844 47.826 4.84 4.51 0.00 2.90
571 588 4.199002 TCTCCCTTCTAGCATGGTATCA 57.801 45.455 4.84 0.00 0.00 2.15
572 589 5.512232 CCTTTCTCCCTTCTAGCATGGTATC 60.512 48.000 4.84 0.00 0.00 2.24
573 590 4.349342 CCTTTCTCCCTTCTAGCATGGTAT 59.651 45.833 4.84 0.00 0.00 2.73
574 591 3.711704 CCTTTCTCCCTTCTAGCATGGTA 59.288 47.826 4.27 4.27 0.00 3.25
575 592 2.507471 CCTTTCTCCCTTCTAGCATGGT 59.493 50.000 1.62 1.62 0.00 3.55
576 593 2.774234 TCCTTTCTCCCTTCTAGCATGG 59.226 50.000 0.00 0.00 0.00 3.66
577 594 4.494091 TTCCTTTCTCCCTTCTAGCATG 57.506 45.455 0.00 0.00 0.00 4.06
578 595 5.444176 CAATTCCTTTCTCCCTTCTAGCAT 58.556 41.667 0.00 0.00 0.00 3.79
579 596 4.324563 CCAATTCCTTTCTCCCTTCTAGCA 60.325 45.833 0.00 0.00 0.00 3.49
580 597 4.203226 CCAATTCCTTTCTCCCTTCTAGC 58.797 47.826 0.00 0.00 0.00 3.42
581 598 5.045578 TCACCAATTCCTTTCTCCCTTCTAG 60.046 44.000 0.00 0.00 0.00 2.43
582 599 4.849810 TCACCAATTCCTTTCTCCCTTCTA 59.150 41.667 0.00 0.00 0.00 2.10
583 600 3.657727 TCACCAATTCCTTTCTCCCTTCT 59.342 43.478 0.00 0.00 0.00 2.85
584 601 4.034285 TCACCAATTCCTTTCTCCCTTC 57.966 45.455 0.00 0.00 0.00 3.46
585 602 4.469469 TTCACCAATTCCTTTCTCCCTT 57.531 40.909 0.00 0.00 0.00 3.95
586 603 4.469469 TTTCACCAATTCCTTTCTCCCT 57.531 40.909 0.00 0.00 0.00 4.20
587 604 5.952347 ACTATTTCACCAATTCCTTTCTCCC 59.048 40.000 0.00 0.00 0.00 4.30
588 605 7.468141 AACTATTTCACCAATTCCTTTCTCC 57.532 36.000 0.00 0.00 0.00 3.71
589 606 8.576442 TCAAACTATTTCACCAATTCCTTTCTC 58.424 33.333 0.00 0.00 0.00 2.87
590 607 8.477419 TCAAACTATTTCACCAATTCCTTTCT 57.523 30.769 0.00 0.00 0.00 2.52
591 608 9.143631 CATCAAACTATTTCACCAATTCCTTTC 57.856 33.333 0.00 0.00 0.00 2.62
592 609 8.650490 ACATCAAACTATTTCACCAATTCCTTT 58.350 29.630 0.00 0.00 0.00 3.11
593 610 8.193953 ACATCAAACTATTTCACCAATTCCTT 57.806 30.769 0.00 0.00 0.00 3.36
594 611 7.781324 ACATCAAACTATTTCACCAATTCCT 57.219 32.000 0.00 0.00 0.00 3.36
597 614 9.369904 GCAATACATCAAACTATTTCACCAATT 57.630 29.630 0.00 0.00 0.00 2.32
598 615 8.752187 AGCAATACATCAAACTATTTCACCAAT 58.248 29.630 0.00 0.00 0.00 3.16
599 616 8.121305 AGCAATACATCAAACTATTTCACCAA 57.879 30.769 0.00 0.00 0.00 3.67
600 617 7.701539 AGCAATACATCAAACTATTTCACCA 57.298 32.000 0.00 0.00 0.00 4.17
601 618 8.243426 TCAAGCAATACATCAAACTATTTCACC 58.757 33.333 0.00 0.00 0.00 4.02
602 619 9.282247 CTCAAGCAATACATCAAACTATTTCAC 57.718 33.333 0.00 0.00 0.00 3.18
603 620 7.970061 GCTCAAGCAATACATCAAACTATTTCA 59.030 33.333 0.00 0.00 41.59 2.69
604 621 7.433425 GGCTCAAGCAATACATCAAACTATTTC 59.567 37.037 4.13 0.00 44.36 2.17
605 622 7.123247 AGGCTCAAGCAATACATCAAACTATTT 59.877 33.333 4.13 0.00 44.36 1.40
606 623 6.604795 AGGCTCAAGCAATACATCAAACTATT 59.395 34.615 4.13 0.00 44.36 1.73
607 624 6.125029 AGGCTCAAGCAATACATCAAACTAT 58.875 36.000 4.13 0.00 44.36 2.12
608 625 5.500234 AGGCTCAAGCAATACATCAAACTA 58.500 37.500 4.13 0.00 44.36 2.24
609 626 4.338879 AGGCTCAAGCAATACATCAAACT 58.661 39.130 4.13 0.00 44.36 2.66
610 627 4.666237 GAGGCTCAAGCAATACATCAAAC 58.334 43.478 10.25 0.00 44.36 2.93
611 628 3.374988 CGAGGCTCAAGCAATACATCAAA 59.625 43.478 15.95 0.00 44.36 2.69
612 629 2.938451 CGAGGCTCAAGCAATACATCAA 59.062 45.455 15.95 0.00 44.36 2.57
613 630 2.554142 CGAGGCTCAAGCAATACATCA 58.446 47.619 15.95 0.00 44.36 3.07
614 631 1.262683 GCGAGGCTCAAGCAATACATC 59.737 52.381 15.95 0.00 44.36 3.06
615 632 1.303309 GCGAGGCTCAAGCAATACAT 58.697 50.000 15.95 0.00 44.36 2.29
616 633 0.036483 TGCGAGGCTCAAGCAATACA 60.036 50.000 15.95 0.00 44.36 2.29
617 634 0.654683 CTGCGAGGCTCAAGCAATAC 59.345 55.000 15.95 0.00 44.36 1.89
618 635 0.462581 CCTGCGAGGCTCAAGCAATA 60.463 55.000 15.95 0.00 44.36 1.90
619 636 1.748122 CCTGCGAGGCTCAAGCAAT 60.748 57.895 15.95 0.00 44.36 3.56
620 637 2.359107 CCTGCGAGGCTCAAGCAA 60.359 61.111 15.95 1.54 44.36 3.91
629 646 6.398234 ACTCTTATATATATGCCTGCGAGG 57.602 41.667 5.44 0.00 38.80 4.63
630 647 7.931275 TGTACTCTTATATATATGCCTGCGAG 58.069 38.462 5.44 4.90 0.00 5.03
631 648 7.875327 TGTACTCTTATATATATGCCTGCGA 57.125 36.000 5.44 0.00 0.00 5.10
632 649 8.972349 CATTGTACTCTTATATATATGCCTGCG 58.028 37.037 5.44 0.00 0.00 5.18
648 665 9.244292 TGTACTTCAAGTAGATCATTGTACTCT 57.756 33.333 0.00 0.00 31.09 3.24
649 666 9.856488 TTGTACTTCAAGTAGATCATTGTACTC 57.144 33.333 0.00 0.00 31.09 2.59
650 667 9.862371 CTTGTACTTCAAGTAGATCATTGTACT 57.138 33.333 0.00 0.00 45.89 2.73
665 682 2.158682 TCTGCCTTGCCTTGTACTTCAA 60.159 45.455 0.00 0.00 34.61 2.69
666 683 1.419762 TCTGCCTTGCCTTGTACTTCA 59.580 47.619 0.00 0.00 0.00 3.02
667 684 2.185004 TCTGCCTTGCCTTGTACTTC 57.815 50.000 0.00 0.00 0.00 3.01
668 685 2.656947 TTCTGCCTTGCCTTGTACTT 57.343 45.000 0.00 0.00 0.00 2.24
669 686 2.887151 ATTCTGCCTTGCCTTGTACT 57.113 45.000 0.00 0.00 0.00 2.73
670 687 6.072452 GGATATTATTCTGCCTTGCCTTGTAC 60.072 42.308 0.00 0.00 0.00 2.90
671 688 6.003950 GGATATTATTCTGCCTTGCCTTGTA 58.996 40.000 0.00 0.00 0.00 2.41
672 689 4.829492 GGATATTATTCTGCCTTGCCTTGT 59.171 41.667 0.00 0.00 0.00 3.16
673 690 5.075493 AGGATATTATTCTGCCTTGCCTTG 58.925 41.667 0.00 0.00 0.00 3.61
674 691 5.330648 AGGATATTATTCTGCCTTGCCTT 57.669 39.130 0.00 0.00 0.00 4.35
675 692 5.569630 CGTAGGATATTATTCTGCCTTGCCT 60.570 44.000 0.00 0.00 0.00 4.75
676 693 4.631813 CGTAGGATATTATTCTGCCTTGCC 59.368 45.833 0.00 0.00 0.00 4.52
677 694 4.093556 GCGTAGGATATTATTCTGCCTTGC 59.906 45.833 0.00 0.00 0.00 4.01
678 695 5.482908 AGCGTAGGATATTATTCTGCCTTG 58.517 41.667 0.00 0.00 0.00 3.61
679 696 5.746990 AGCGTAGGATATTATTCTGCCTT 57.253 39.130 0.00 0.00 0.00 4.35
680 697 6.041069 GGATAGCGTAGGATATTATTCTGCCT 59.959 42.308 0.00 0.00 0.00 4.75
681 698 6.041069 AGGATAGCGTAGGATATTATTCTGCC 59.959 42.308 0.00 0.00 0.00 4.85
682 699 7.045126 AGGATAGCGTAGGATATTATTCTGC 57.955 40.000 0.00 0.00 0.00 4.26
688 705 9.352191 GGAAAGATAGGATAGCGTAGGATATTA 57.648 37.037 0.00 0.00 28.09 0.98
689 706 8.062536 AGGAAAGATAGGATAGCGTAGGATATT 58.937 37.037 0.00 0.00 28.09 1.28
690 707 7.588169 AGGAAAGATAGGATAGCGTAGGATAT 58.412 38.462 0.00 0.00 28.09 1.63
691 708 6.971340 AGGAAAGATAGGATAGCGTAGGATA 58.029 40.000 0.00 0.00 28.09 2.59
692 709 5.833340 AGGAAAGATAGGATAGCGTAGGAT 58.167 41.667 0.00 0.00 28.09 3.24
693 710 5.258216 AGGAAAGATAGGATAGCGTAGGA 57.742 43.478 0.00 0.00 28.09 2.94
694 711 5.986501 AAGGAAAGATAGGATAGCGTAGG 57.013 43.478 0.00 0.00 28.09 3.18
695 712 7.925043 TCTAAGGAAAGATAGGATAGCGTAG 57.075 40.000 0.00 0.00 28.09 3.51
696 713 8.880991 ATTCTAAGGAAAGATAGGATAGCGTA 57.119 34.615 0.00 0.00 34.90 4.42
697 714 7.451877 TGATTCTAAGGAAAGATAGGATAGCGT 59.548 37.037 0.00 0.00 34.90 5.07
698 715 7.831753 TGATTCTAAGGAAAGATAGGATAGCG 58.168 38.462 0.00 0.00 34.90 4.26
721 738 9.143631 CGCTGATTGATATGTTGAGTATATTGA 57.856 33.333 0.00 0.00 0.00 2.57
722 739 7.901889 GCGCTGATTGATATGTTGAGTATATTG 59.098 37.037 0.00 0.00 0.00 1.90
723 740 7.065085 GGCGCTGATTGATATGTTGAGTATATT 59.935 37.037 7.64 0.00 0.00 1.28
724 741 6.536582 GGCGCTGATTGATATGTTGAGTATAT 59.463 38.462 7.64 0.00 0.00 0.86
725 742 5.869344 GGCGCTGATTGATATGTTGAGTATA 59.131 40.000 7.64 0.00 0.00 1.47
726 743 4.692625 GGCGCTGATTGATATGTTGAGTAT 59.307 41.667 7.64 0.00 0.00 2.12
727 744 4.058124 GGCGCTGATTGATATGTTGAGTA 58.942 43.478 7.64 0.00 0.00 2.59
728 745 2.874701 GGCGCTGATTGATATGTTGAGT 59.125 45.455 7.64 0.00 0.00 3.41
729 746 2.225019 GGGCGCTGATTGATATGTTGAG 59.775 50.000 7.64 0.00 0.00 3.02
730 747 2.158769 AGGGCGCTGATTGATATGTTGA 60.159 45.455 7.64 0.00 0.00 3.18
731 748 2.031420 CAGGGCGCTGATTGATATGTTG 60.031 50.000 25.55 0.00 0.00 3.33
732 749 2.224606 CAGGGCGCTGATTGATATGTT 58.775 47.619 25.55 0.00 0.00 2.71
733 750 1.888215 CAGGGCGCTGATTGATATGT 58.112 50.000 25.55 0.00 0.00 2.29
746 763 0.322008 AGAAAGAAGAAGGCAGGGCG 60.322 55.000 0.00 0.00 0.00 6.13
754 771 5.923114 TGTCAGACGATCAAGAAAGAAGAAG 59.077 40.000 0.00 0.00 0.00 2.85
755 772 5.842907 TGTCAGACGATCAAGAAAGAAGAA 58.157 37.500 0.00 0.00 0.00 2.52
756 773 5.453567 TGTCAGACGATCAAGAAAGAAGA 57.546 39.130 0.00 0.00 0.00 2.87
767 784 3.677121 GTCATGGCATATGTCAGACGATC 59.323 47.826 16.31 4.25 30.80 3.69
857 883 4.649692 AGATAGTGATAATGCTGGCAAGG 58.350 43.478 0.00 0.00 0.00 3.61
896 922 8.463499 TCTACTCTCTAGTACTCCTCCCTAATA 58.537 40.741 0.00 0.00 37.15 0.98
900 926 5.160511 TCTACTCTCTAGTACTCCTCCCT 57.839 47.826 0.00 0.00 37.15 4.20
901 927 5.892524 TTCTACTCTCTAGTACTCCTCCC 57.107 47.826 0.00 0.00 37.15 4.30
902 928 7.069877 TCATTCTACTCTCTAGTACTCCTCC 57.930 44.000 0.00 0.00 37.15 4.30
911 937 9.308000 AGGGTTGATAATCATTCTACTCTCTAG 57.692 37.037 0.00 0.00 25.38 2.43
913 939 8.428063 CAAGGGTTGATAATCATTCTACTCTCT 58.572 37.037 0.00 0.00 30.01 3.10
931 957 2.554032 GACATTGGTCAGACAAGGGTTG 59.446 50.000 2.17 0.00 43.73 3.77
1053 1079 3.771479 TCTACTCATTCTGTCAGGTGCAT 59.229 43.478 0.00 0.00 0.00 3.96
1107 1133 2.400399 CAAGAACACGAGTTAGCCGAA 58.600 47.619 0.00 0.00 38.30 4.30
1110 1136 0.796927 GGCAAGAACACGAGTTAGCC 59.203 55.000 16.26 16.26 40.58 3.93
1128 1154 2.672478 GCCGATACTGGATGAATCGAGG 60.672 54.545 5.58 0.00 43.96 4.63
1258 1289 0.616964 GGTCCCGGTTCCTCCTACTT 60.617 60.000 0.00 0.00 0.00 2.24
1261 1292 2.043652 CGGTCCCGGTTCCTCCTA 60.044 66.667 0.00 0.00 35.56 2.94
1330 1361 0.395312 GAAACTTCTCCACCGGACCA 59.605 55.000 9.46 0.00 0.00 4.02
1361 1392 1.351430 CGCATCGGCTTCTCGTTCAA 61.351 55.000 0.00 0.00 38.10 2.69
1363 1394 0.872021 ATCGCATCGGCTTCTCGTTC 60.872 55.000 0.00 0.00 38.10 3.95
1501 1539 3.390967 TCTTGTTCATGGACACCTTGAGA 59.609 43.478 6.25 3.70 38.58 3.27
1530 1568 4.506255 CCGCCATGAACCCCTCCC 62.506 72.222 0.00 0.00 0.00 4.30
1864 1902 3.920093 GAAGTCGGCCACCTTGGGG 62.920 68.421 2.24 0.00 38.19 4.96
1996 2034 2.662700 CTGTAAACGTCGCACTTCTCT 58.337 47.619 0.00 0.00 0.00 3.10
2011 2049 1.305219 GCACCATGCCGAAGCTGTAA 61.305 55.000 0.00 0.00 37.42 2.41
2035 2073 2.502492 GCGCTGCCCTAGGATCTCA 61.502 63.158 11.48 1.62 0.00 3.27
2263 2301 3.790437 CCCTCCAGCATCCGCACT 61.790 66.667 0.00 0.00 42.27 4.40
2697 3374 1.882623 CTCAGAGTTTGGGAGTTTGGC 59.117 52.381 0.00 0.00 0.00 4.52
2705 3382 1.202687 TGTGCTGTCTCAGAGTTTGGG 60.203 52.381 0.00 0.00 32.44 4.12
2711 3388 2.806577 CACGTGTGCTGTCTCAGAG 58.193 57.895 7.58 0.00 32.44 3.35
2799 3496 1.612463 GGTCTAAGTGGTGTCGAGTGT 59.388 52.381 0.00 0.00 0.00 3.55
2851 3609 2.502142 TGATGCAAGCTGTTGGAGAT 57.498 45.000 0.00 0.00 37.44 2.75
2864 3622 2.747460 GTGGCCTCGCTTGATGCA 60.747 61.111 3.32 0.00 43.06 3.96
2873 3631 1.522569 CTTCCTAAGGGTGGCCTCG 59.477 63.158 3.32 0.00 0.00 4.63
2874 3632 1.224870 GCTTCCTAAGGGTGGCCTC 59.775 63.158 3.32 0.00 0.00 4.70
2875 3633 0.846870 AAGCTTCCTAAGGGTGGCCT 60.847 55.000 3.32 0.00 34.08 5.19
2877 3635 2.801077 TAAAGCTTCCTAAGGGTGGC 57.199 50.000 0.00 0.00 0.00 5.01
2886 3685 5.355350 GCAAGTGATGTGTATAAAGCTTCCT 59.645 40.000 0.00 0.00 0.00 3.36
2887 3686 5.355350 AGCAAGTGATGTGTATAAAGCTTCC 59.645 40.000 0.00 0.00 0.00 3.46
2946 3745 3.369997 GGCAAAGGGACAAAACAAAAGGA 60.370 43.478 0.00 0.00 0.00 3.36
2960 3759 2.094026 GGTCTATTTTGCAGGCAAAGGG 60.094 50.000 17.70 12.36 45.15 3.95
2967 3766 2.170166 TGGCTTGGTCTATTTTGCAGG 58.830 47.619 0.00 0.00 0.00 4.85
3000 3799 2.620115 ACATGCAGTTGTTCAGACTTGG 59.380 45.455 0.00 0.00 0.00 3.61
3011 3810 3.047796 GACTTTGCTTCACATGCAGTTG 58.952 45.455 0.00 0.00 41.71 3.16
3016 3815 1.881973 TGGAGACTTTGCTTCACATGC 59.118 47.619 0.00 0.00 0.00 4.06
3039 3838 2.802247 GCAAAGTCAAGGTTTTGGATGC 59.198 45.455 0.00 0.00 35.40 3.91
3040 3839 3.070015 AGGCAAAGTCAAGGTTTTGGATG 59.930 43.478 0.00 0.00 35.40 3.51
3047 3846 3.942130 GCAATAGGCAAAGTCAAGGTT 57.058 42.857 0.00 0.00 43.97 3.50
3082 3881 1.534163 CATGTGGAGAATGCCATAGCG 59.466 52.381 0.00 0.00 44.31 4.26
3095 3894 6.867519 TTCTAAGGTATCAACTCATGTGGA 57.132 37.500 0.00 0.00 0.00 4.02
3096 3895 7.989741 AGATTTCTAAGGTATCAACTCATGTGG 59.010 37.037 0.00 0.00 0.00 4.17
3097 3896 8.954950 AGATTTCTAAGGTATCAACTCATGTG 57.045 34.615 0.00 0.00 0.00 3.21
3098 3897 9.388506 CAAGATTTCTAAGGTATCAACTCATGT 57.611 33.333 0.00 0.00 0.00 3.21
3099 3898 8.834465 CCAAGATTTCTAAGGTATCAACTCATG 58.166 37.037 0.00 0.00 0.00 3.07
3100 3899 8.552296 ACCAAGATTTCTAAGGTATCAACTCAT 58.448 33.333 3.53 0.00 34.16 2.90
3101 3900 7.824289 CACCAAGATTTCTAAGGTATCAACTCA 59.176 37.037 4.80 0.00 34.16 3.41
3102 3901 7.201652 GCACCAAGATTTCTAAGGTATCAACTC 60.202 40.741 4.80 0.00 34.16 3.01
3103 3902 6.599638 GCACCAAGATTTCTAAGGTATCAACT 59.400 38.462 4.80 0.00 34.16 3.16
3104 3903 6.374333 TGCACCAAGATTTCTAAGGTATCAAC 59.626 38.462 4.80 0.00 34.16 3.18
3105 3904 6.480763 TGCACCAAGATTTCTAAGGTATCAA 58.519 36.000 4.80 0.00 34.16 2.57
3106 3905 6.061022 TGCACCAAGATTTCTAAGGTATCA 57.939 37.500 4.80 4.32 34.16 2.15
3107 3906 6.258947 GTCTGCACCAAGATTTCTAAGGTATC 59.741 42.308 4.80 0.00 34.16 2.24
3139 3938 3.520569 CCCTGTTTTTGTTGACACCTTG 58.479 45.455 0.00 0.00 0.00 3.61
3155 3954 1.296715 GGTGATCGTGAAGCCCTGT 59.703 57.895 0.00 0.00 0.00 4.00
3156 3955 1.450312 GGGTGATCGTGAAGCCCTG 60.450 63.158 0.00 0.00 36.49 4.45
3159 3958 2.511600 CCGGGTGATCGTGAAGCC 60.512 66.667 0.00 0.00 0.00 4.35
3165 3964 0.968901 TAGCTTCACCGGGTGATCGT 60.969 55.000 29.17 18.20 42.40 3.73
3167 3966 0.824759 ACTAGCTTCACCGGGTGATC 59.175 55.000 29.17 22.37 42.40 2.92
3170 3969 2.093658 ACATAACTAGCTTCACCGGGTG 60.094 50.000 21.27 21.27 34.45 4.61
3171 3970 2.185387 ACATAACTAGCTTCACCGGGT 58.815 47.619 6.32 0.00 0.00 5.28
3216 4015 1.215423 ACACCTTGATTGGATAGGGGC 59.785 52.381 0.00 0.00 35.83 5.80
3218 4017 3.931907 TGACACCTTGATTGGATAGGG 57.068 47.619 0.00 0.00 33.22 3.53
3231 4030 2.671351 CGTATGACGCTCTTTGACACCT 60.671 50.000 0.00 0.00 33.65 4.00
3245 4044 1.165270 AACAAAGGCTGGCGTATGAC 58.835 50.000 9.98 0.00 0.00 3.06
3254 4053 5.418676 TCCTTCAAAGAAAAACAAAGGCTG 58.581 37.500 0.00 0.00 34.57 4.85
3257 4056 7.323420 ACTTCTCCTTCAAAGAAAAACAAAGG 58.677 34.615 0.00 0.00 32.60 3.11
3267 4066 4.656112 AGTTCCAGACTTCTCCTTCAAAGA 59.344 41.667 0.00 0.00 33.92 2.52
3271 4070 2.558795 CGAGTTCCAGACTTCTCCTTCA 59.441 50.000 0.00 0.00 39.19 3.02
3284 4083 0.321564 CTGGCCATCAACGAGTTCCA 60.322 55.000 5.51 0.00 0.00 3.53
3293 4092 2.577563 TCCTCTTTGATCTGGCCATCAA 59.422 45.455 16.23 16.23 40.36 2.57
3310 4109 3.190744 TGTTCTACGTGTGATCAGTCCTC 59.809 47.826 0.00 0.00 0.00 3.71
3340 4139 1.153823 CCCTAGTGGTCTTCGTGCG 60.154 63.158 0.00 0.00 0.00 5.34
3343 4142 3.709567 GGCCCTAGTGGTCTTCGT 58.290 61.111 0.00 0.00 35.10 3.85
3361 4160 0.106918 AAAATAATCGGCCAGGCGGA 60.107 50.000 23.05 23.05 41.73 5.54
3365 4164 1.002468 CTCGCAAAATAATCGGCCAGG 60.002 52.381 2.24 0.00 0.00 4.45
3388 4187 2.187958 TGGTTGATCTTGGGATCTCGT 58.812 47.619 7.39 0.00 46.18 4.18
3390 4189 6.371595 AGATATGGTTGATCTTGGGATCTC 57.628 41.667 7.39 0.00 46.18 2.75
3425 4224 0.605589 GACCTTCACCTTTCACCGGG 60.606 60.000 6.32 0.00 0.00 5.73
3430 4229 2.234300 GTGACGACCTTCACCTTTCA 57.766 50.000 0.00 0.00 40.15 2.69
3439 4238 1.902508 AGACATGATGGTGACGACCTT 59.097 47.619 0.00 0.00 43.58 3.50
3444 4243 0.462581 CCCCAGACATGATGGTGACG 60.463 60.000 16.89 5.34 35.96 4.35
3452 4251 2.910360 CATCGGCCCCAGACATGA 59.090 61.111 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.