Multiple sequence alignment - TraesCS3D01G177000

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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 TraesCS3D01G177000 chr3D 100.000 3035 0 0 1 3035 158448943 158451977 0.000000e+00 5605.0
1 TraesCS3D01G177000 chr3B 94.141 2304 81 23 766 3035 235878587 235880870 0.000000e+00 3458.0
2 TraesCS3D01G177000 chr3B 92.000 325 25 1 3 327 235878063 235878386 3.570000e-124 455.0
3 TraesCS3D01G177000 chr3A 92.713 1441 64 13 781 2193 169291517 169290090 0.000000e+00 2041.0
4 TraesCS3D01G177000 chr3A 90.836 742 45 8 2200 2935 169254226 169253502 0.000000e+00 972.0
5 TraesCS3D01G177000 chr3A 90.508 748 48 8 2194 2935 169234195 169233465 0.000000e+00 966.0
6 TraesCS3D01G177000 chr3A 90.508 748 48 8 2194 2935 169273795 169273065 0.000000e+00 966.0
7 TraesCS3D01G177000 chr3A 92.283 311 24 0 20 330 169293511 169293201 2.780000e-120 442.0
8 TraesCS3D01G177000 chr3A 95.146 103 5 0 2933 3035 169272984 169272882 2.420000e-36 163.0
9 TraesCS3D01G177000 chr3A 95.050 101 5 0 2933 3033 169233384 169233284 3.130000e-35 159.0
10 TraesCS3D01G177000 chr3A 94.175 103 6 0 2933 3035 169253421 169253319 1.130000e-34 158.0
11 TraesCS3D01G177000 chr3A 87.611 113 10 4 340 449 169293153 169293042 8.830000e-26 128.0
12 TraesCS3D01G177000 chr3A 84.615 91 12 2 497 586 720694562 720694473 4.170000e-14 89.8
13 TraesCS3D01G177000 chr3A 76.301 173 31 8 450 620 693489460 693489296 1.940000e-12 84.2
14 TraesCS3D01G177000 chr1D 79.592 245 48 1 446 688 109122204 109122448 1.120000e-39 174.0
15 TraesCS3D01G177000 chr4B 95.745 47 1 1 451 497 139572869 139572914 1.170000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G177000 chr3D 158448943 158451977 3034 False 5605.000000 5605 100.0000 1 3035 1 chr3D.!!$F1 3034
1 TraesCS3D01G177000 chr3B 235878063 235880870 2807 False 1956.500000 3458 93.0705 3 3035 2 chr3B.!!$F1 3032
2 TraesCS3D01G177000 chr3A 169290090 169293511 3421 True 870.333333 2041 90.8690 20 2193 3 chr3A.!!$R6 2173
3 TraesCS3D01G177000 chr3A 169253319 169254226 907 True 565.000000 972 92.5055 2200 3035 2 chr3A.!!$R4 835
4 TraesCS3D01G177000 chr3A 169272882 169273795 913 True 564.500000 966 92.8270 2194 3035 2 chr3A.!!$R5 841
5 TraesCS3D01G177000 chr3A 169233284 169234195 911 True 562.500000 966 92.7790 2194 3033 2 chr3A.!!$R3 839

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
548 652 0.039256 CAACCAAATGTGTCGGCCAG 60.039 55.0 2.24 0.0 0.00 4.85 F
689 793 0.321653 GCCGTGTTCTCCACCAGATT 60.322 55.0 0.00 0.0 41.26 2.40 F
1424 3079 0.462759 ACTATCTGCAAGGAAGCGCC 60.463 55.0 2.29 0.0 37.31 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 3078 0.455633 AACGATTTCGACGAGACCGG 60.456 55.000 7.11 0.0 43.02 5.28 R
1594 3255 1.079127 CCCTCAAGGCACCGTACAG 60.079 63.158 0.00 0.0 0.00 2.74 R
2308 3970 2.061773 CGGCAGATATCACCATCGAAC 58.938 52.381 13.48 0.0 0.00 3.95 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
66 67 4.253685 TGAAATCTCTTTAGGAGGCAACG 58.746 43.478 0.00 0.00 42.10 4.10
78 79 3.886505 AGGAGGCAACGTTGACAAAATTA 59.113 39.130 34.30 0.00 39.18 1.40
98 99 0.606130 TGCACATCACATCCTGCGTT 60.606 50.000 0.00 0.00 31.96 4.84
116 117 4.921515 TGCGTTAACGGAATATAGATGCTC 59.078 41.667 27.82 7.70 36.59 4.26
117 118 4.921515 GCGTTAACGGAATATAGATGCTCA 59.078 41.667 27.82 0.00 40.23 4.26
162 163 7.406031 ACTCGACTGTATATCAGAAAAAGGA 57.594 36.000 8.56 0.00 46.27 3.36
173 174 6.866010 ATCAGAAAAAGGAAAATTTGGCAC 57.134 33.333 0.00 0.00 0.00 5.01
181 182 5.033589 AGGAAAATTTGGCACACATTTGA 57.966 34.783 0.00 0.00 46.39 2.69
199 200 9.492973 CACATTTGAAAGGTCTTCCAATTTAAT 57.507 29.630 0.00 0.00 35.89 1.40
211 212 4.900684 TCCAATTTAATGTGTGACCTCGA 58.099 39.130 0.00 0.00 0.00 4.04
253 254 4.362470 CATGGGTATGGTCTGATGATGT 57.638 45.455 0.00 0.00 0.00 3.06
272 274 2.544686 TGTTGCTTTGCACATTTGATGC 59.455 40.909 0.00 0.00 38.71 3.91
290 292 2.252714 TGCCTCCCCATTTGTAAAACC 58.747 47.619 0.00 0.00 0.00 3.27
390 445 5.562298 AGTAGGCATTACCGTGGATAATT 57.438 39.130 0.00 0.00 46.52 1.40
473 577 3.455990 TTTTTAAGAAAACCCGCCCAC 57.544 42.857 0.00 0.00 30.07 4.61
474 578 2.368311 TTTAAGAAAACCCGCCCACT 57.632 45.000 0.00 0.00 0.00 4.00
475 579 2.368311 TTAAGAAAACCCGCCCACTT 57.632 45.000 0.00 0.00 0.00 3.16
476 580 2.368311 TAAGAAAACCCGCCCACTTT 57.632 45.000 0.00 0.00 0.00 2.66
477 581 2.368311 AAGAAAACCCGCCCACTTTA 57.632 45.000 0.00 0.00 0.00 1.85
478 582 2.597578 AGAAAACCCGCCCACTTTAT 57.402 45.000 0.00 0.00 0.00 1.40
479 583 2.884320 AGAAAACCCGCCCACTTTATT 58.116 42.857 0.00 0.00 0.00 1.40
480 584 2.560981 AGAAAACCCGCCCACTTTATTG 59.439 45.455 0.00 0.00 0.00 1.90
481 585 2.296073 AAACCCGCCCACTTTATTGA 57.704 45.000 0.00 0.00 0.00 2.57
482 586 2.525105 AACCCGCCCACTTTATTGAT 57.475 45.000 0.00 0.00 0.00 2.57
483 587 2.525105 ACCCGCCCACTTTATTGATT 57.475 45.000 0.00 0.00 0.00 2.57
484 588 2.375146 ACCCGCCCACTTTATTGATTC 58.625 47.619 0.00 0.00 0.00 2.52
485 589 2.291282 ACCCGCCCACTTTATTGATTCA 60.291 45.455 0.00 0.00 0.00 2.57
486 590 2.958355 CCCGCCCACTTTATTGATTCAT 59.042 45.455 0.00 0.00 0.00 2.57
487 591 3.004734 CCCGCCCACTTTATTGATTCATC 59.995 47.826 0.00 0.00 0.00 2.92
488 592 3.885297 CCGCCCACTTTATTGATTCATCT 59.115 43.478 0.00 0.00 0.00 2.90
489 593 4.023707 CCGCCCACTTTATTGATTCATCTC 60.024 45.833 0.00 0.00 0.00 2.75
490 594 4.576053 CGCCCACTTTATTGATTCATCTCA 59.424 41.667 0.00 0.00 0.00 3.27
491 595 5.066375 CGCCCACTTTATTGATTCATCTCAA 59.934 40.000 0.00 0.00 39.35 3.02
492 596 6.238842 CGCCCACTTTATTGATTCATCTCAAT 60.239 38.462 4.85 4.85 45.44 2.57
493 597 6.921857 GCCCACTTTATTGATTCATCTCAATG 59.078 38.462 9.05 0.00 43.80 2.82
494 598 7.201848 GCCCACTTTATTGATTCATCTCAATGA 60.202 37.037 9.05 0.00 43.80 2.57
495 599 8.857098 CCCACTTTATTGATTCATCTCAATGAT 58.143 33.333 9.05 0.00 43.80 2.45
496 600 9.894783 CCACTTTATTGATTCATCTCAATGATC 57.105 33.333 9.05 0.00 43.80 2.92
504 608 9.716531 TTGATTCATCTCAATGATCATAGGTAC 57.283 33.333 9.04 0.00 41.49 3.34
505 609 8.873144 TGATTCATCTCAATGATCATAGGTACA 58.127 33.333 9.04 0.00 41.49 2.90
506 610 9.716531 GATTCATCTCAATGATCATAGGTACAA 57.283 33.333 9.04 0.00 41.49 2.41
507 611 9.722184 ATTCATCTCAATGATCATAGGTACAAG 57.278 33.333 9.04 0.00 41.49 3.16
508 612 7.674120 TCATCTCAATGATCATAGGTACAAGG 58.326 38.462 9.04 0.00 36.98 3.61
509 613 7.290948 TCATCTCAATGATCATAGGTACAAGGT 59.709 37.037 9.04 0.00 36.98 3.50
510 614 7.437713 TCTCAATGATCATAGGTACAAGGTT 57.562 36.000 9.04 0.00 0.00 3.50
511 615 7.861629 TCTCAATGATCATAGGTACAAGGTTT 58.138 34.615 9.04 0.00 0.00 3.27
512 616 8.328758 TCTCAATGATCATAGGTACAAGGTTTT 58.671 33.333 9.04 0.00 0.00 2.43
513 617 8.279970 TCAATGATCATAGGTACAAGGTTTTG 57.720 34.615 9.04 0.00 40.24 2.44
515 619 8.522830 CAATGATCATAGGTACAAGGTTTTGTT 58.477 33.333 9.04 0.00 45.01 2.83
516 620 7.681939 TGATCATAGGTACAAGGTTTTGTTC 57.318 36.000 0.00 0.00 45.01 3.18
517 621 7.227873 TGATCATAGGTACAAGGTTTTGTTCA 58.772 34.615 0.00 0.00 45.01 3.18
518 622 7.888021 TGATCATAGGTACAAGGTTTTGTTCAT 59.112 33.333 0.00 0.00 45.01 2.57
519 623 7.447374 TCATAGGTACAAGGTTTTGTTCATG 57.553 36.000 0.00 0.00 45.01 3.07
520 624 6.432783 TCATAGGTACAAGGTTTTGTTCATGG 59.567 38.462 0.00 0.00 45.01 3.66
521 625 3.895041 AGGTACAAGGTTTTGTTCATGGG 59.105 43.478 0.00 0.00 45.01 4.00
522 626 3.006430 GGTACAAGGTTTTGTTCATGGGG 59.994 47.826 0.00 0.00 45.01 4.96
523 627 2.758130 ACAAGGTTTTGTTCATGGGGT 58.242 42.857 0.00 0.00 45.01 4.95
524 628 3.917300 ACAAGGTTTTGTTCATGGGGTA 58.083 40.909 0.00 0.00 45.01 3.69
525 629 3.895041 ACAAGGTTTTGTTCATGGGGTAG 59.105 43.478 0.00 0.00 45.01 3.18
526 630 3.895041 CAAGGTTTTGTTCATGGGGTAGT 59.105 43.478 0.00 0.00 0.00 2.73
527 631 3.763057 AGGTTTTGTTCATGGGGTAGTC 58.237 45.455 0.00 0.00 0.00 2.59
528 632 2.823747 GGTTTTGTTCATGGGGTAGTCC 59.176 50.000 0.00 0.00 0.00 3.85
541 645 2.871453 GGTAGTCCCAACCAAATGTGT 58.129 47.619 0.00 0.00 36.96 3.72
542 646 2.817844 GGTAGTCCCAACCAAATGTGTC 59.182 50.000 0.00 0.00 36.96 3.67
543 647 1.604604 AGTCCCAACCAAATGTGTCG 58.395 50.000 0.00 0.00 0.00 4.35
544 648 0.596082 GTCCCAACCAAATGTGTCGG 59.404 55.000 0.00 0.00 0.00 4.79
545 649 1.175983 TCCCAACCAAATGTGTCGGC 61.176 55.000 0.00 0.00 0.00 5.54
546 650 1.288752 CCAACCAAATGTGTCGGCC 59.711 57.895 0.00 0.00 0.00 6.13
547 651 1.459455 CCAACCAAATGTGTCGGCCA 61.459 55.000 2.24 0.00 0.00 5.36
548 652 0.039256 CAACCAAATGTGTCGGCCAG 60.039 55.000 2.24 0.00 0.00 4.85
549 653 1.178534 AACCAAATGTGTCGGCCAGG 61.179 55.000 2.24 0.00 0.00 4.45
550 654 2.568090 CAAATGTGTCGGCCAGGC 59.432 61.111 1.26 1.26 0.00 4.85
551 655 2.676471 AAATGTGTCGGCCAGGCC 60.676 61.111 22.33 22.33 46.75 5.19
560 664 4.259952 GGCCAGGCCCAAGATTAC 57.740 61.111 21.62 0.00 44.06 1.89
561 665 1.306296 GGCCAGGCCCAAGATTACA 59.694 57.895 21.62 0.00 44.06 2.41
562 666 0.324275 GGCCAGGCCCAAGATTACAA 60.324 55.000 21.62 0.00 44.06 2.41
563 667 1.689258 GGCCAGGCCCAAGATTACAAT 60.689 52.381 21.62 0.00 44.06 2.71
564 668 1.683385 GCCAGGCCCAAGATTACAATC 59.317 52.381 0.00 0.00 35.64 2.67
565 669 2.949963 GCCAGGCCCAAGATTACAATCA 60.950 50.000 0.00 0.00 37.89 2.57
566 670 3.364549 CCAGGCCCAAGATTACAATCAA 58.635 45.455 0.00 0.00 37.89 2.57
567 671 3.768757 CCAGGCCCAAGATTACAATCAAA 59.231 43.478 0.00 0.00 37.89 2.69
568 672 4.381932 CCAGGCCCAAGATTACAATCAAAC 60.382 45.833 0.00 0.00 37.89 2.93
569 673 4.463891 CAGGCCCAAGATTACAATCAAACT 59.536 41.667 0.00 0.00 37.89 2.66
570 674 5.047092 CAGGCCCAAGATTACAATCAAACTT 60.047 40.000 0.00 0.00 37.89 2.66
571 675 5.047092 AGGCCCAAGATTACAATCAAACTTG 60.047 40.000 0.00 0.00 37.89 3.16
574 678 4.858692 CCAAGATTACAATCAAACTTGGCG 59.141 41.667 10.66 0.00 44.50 5.69
575 679 5.335583 CCAAGATTACAATCAAACTTGGCGA 60.336 40.000 10.66 0.00 44.50 5.54
576 680 5.551760 AGATTACAATCAAACTTGGCGAG 57.448 39.130 0.00 0.00 37.89 5.03
577 681 5.245531 AGATTACAATCAAACTTGGCGAGA 58.754 37.500 9.20 0.00 37.89 4.04
578 682 5.882557 AGATTACAATCAAACTTGGCGAGAT 59.117 36.000 9.20 0.00 37.89 2.75
579 683 5.957842 TTACAATCAAACTTGGCGAGATT 57.042 34.783 9.20 0.00 0.00 2.40
580 684 7.552687 AGATTACAATCAAACTTGGCGAGATTA 59.447 33.333 9.20 0.00 37.89 1.75
581 685 7.624360 TTACAATCAAACTTGGCGAGATTAT 57.376 32.000 9.20 0.00 0.00 1.28
582 686 5.883661 ACAATCAAACTTGGCGAGATTATG 58.116 37.500 9.20 5.90 0.00 1.90
583 687 5.647658 ACAATCAAACTTGGCGAGATTATGA 59.352 36.000 9.20 7.28 0.00 2.15
584 688 5.998454 ATCAAACTTGGCGAGATTATGAG 57.002 39.130 9.20 0.00 0.00 2.90
585 689 3.623060 TCAAACTTGGCGAGATTATGAGC 59.377 43.478 9.20 0.00 0.00 4.26
586 690 3.550437 AACTTGGCGAGATTATGAGCT 57.450 42.857 9.20 0.00 0.00 4.09
587 691 3.550437 ACTTGGCGAGATTATGAGCTT 57.450 42.857 9.20 0.00 0.00 3.74
588 692 3.878778 ACTTGGCGAGATTATGAGCTTT 58.121 40.909 9.20 0.00 0.00 3.51
589 693 4.265073 ACTTGGCGAGATTATGAGCTTTT 58.735 39.130 9.20 0.00 0.00 2.27
590 694 5.428253 ACTTGGCGAGATTATGAGCTTTTA 58.572 37.500 9.20 0.00 0.00 1.52
591 695 5.880332 ACTTGGCGAGATTATGAGCTTTTAA 59.120 36.000 9.20 0.00 0.00 1.52
592 696 6.374333 ACTTGGCGAGATTATGAGCTTTTAAA 59.626 34.615 9.20 0.00 0.00 1.52
593 697 6.942532 TGGCGAGATTATGAGCTTTTAAAT 57.057 33.333 0.00 0.00 0.00 1.40
594 698 7.333528 TGGCGAGATTATGAGCTTTTAAATT 57.666 32.000 0.00 0.00 0.00 1.82
595 699 8.445275 TGGCGAGATTATGAGCTTTTAAATTA 57.555 30.769 0.00 0.00 0.00 1.40
596 700 8.898761 TGGCGAGATTATGAGCTTTTAAATTAA 58.101 29.630 0.00 0.00 0.00 1.40
597 701 9.730420 GGCGAGATTATGAGCTTTTAAATTAAA 57.270 29.630 0.00 0.00 0.00 1.52
607 711 8.960075 TGAGCTTTTAAATTAAACAAACTACGC 58.040 29.630 0.00 0.00 0.00 4.42
608 712 9.177304 GAGCTTTTAAATTAAACAAACTACGCT 57.823 29.630 0.00 0.00 0.00 5.07
609 713 9.177304 AGCTTTTAAATTAAACAAACTACGCTC 57.823 29.630 0.00 0.00 0.00 5.03
610 714 8.960075 GCTTTTAAATTAAACAAACTACGCTCA 58.040 29.630 0.00 0.00 0.00 4.26
614 718 9.601971 TTAAATTAAACAAACTACGCTCATGAC 57.398 29.630 0.00 0.00 0.00 3.06
615 719 7.435068 AATTAAACAAACTACGCTCATGACT 57.565 32.000 0.00 0.00 0.00 3.41
616 720 8.542497 AATTAAACAAACTACGCTCATGACTA 57.458 30.769 0.00 0.00 0.00 2.59
617 721 7.949903 TTAAACAAACTACGCTCATGACTAA 57.050 32.000 0.00 0.00 0.00 2.24
618 722 6.854496 AAACAAACTACGCTCATGACTAAA 57.146 33.333 0.00 0.00 0.00 1.85
619 723 6.854496 AACAAACTACGCTCATGACTAAAA 57.146 33.333 0.00 0.00 0.00 1.52
620 724 6.224420 ACAAACTACGCTCATGACTAAAAC 57.776 37.500 0.00 0.00 0.00 2.43
621 725 5.756347 ACAAACTACGCTCATGACTAAAACA 59.244 36.000 0.00 0.00 0.00 2.83
622 726 6.073765 ACAAACTACGCTCATGACTAAAACAG 60.074 38.462 0.00 0.00 0.00 3.16
623 727 3.927142 ACTACGCTCATGACTAAAACAGC 59.073 43.478 0.00 0.00 0.00 4.40
624 728 2.766313 ACGCTCATGACTAAAACAGCA 58.234 42.857 0.00 0.00 0.00 4.41
625 729 3.138304 ACGCTCATGACTAAAACAGCAA 58.862 40.909 0.00 0.00 0.00 3.91
626 730 3.563808 ACGCTCATGACTAAAACAGCAAA 59.436 39.130 0.00 0.00 0.00 3.68
627 731 4.036262 ACGCTCATGACTAAAACAGCAAAA 59.964 37.500 0.00 0.00 0.00 2.44
628 732 4.975502 CGCTCATGACTAAAACAGCAAAAA 59.024 37.500 0.00 0.00 0.00 1.94
629 733 5.116074 CGCTCATGACTAAAACAGCAAAAAG 59.884 40.000 0.00 0.00 0.00 2.27
630 734 5.107722 GCTCATGACTAAAACAGCAAAAAGC 60.108 40.000 0.00 0.00 46.19 3.51
647 751 8.574196 GCAAAAAGCAAAAGTATTTCTAGTGA 57.426 30.769 0.00 0.00 44.79 3.41
648 752 9.030301 GCAAAAAGCAAAAGTATTTCTAGTGAA 57.970 29.630 0.00 0.00 44.79 3.18
670 774 9.612620 GTGAAATTAATCTCCTTTATTATGGCG 57.387 33.333 0.00 0.00 0.00 5.69
671 775 8.296713 TGAAATTAATCTCCTTTATTATGGCGC 58.703 33.333 0.00 0.00 0.00 6.53
672 776 6.759497 ATTAATCTCCTTTATTATGGCGCC 57.241 37.500 22.73 22.73 0.00 6.53
673 777 2.163818 TCTCCTTTATTATGGCGCCG 57.836 50.000 23.90 4.07 0.00 6.46
674 778 1.414919 TCTCCTTTATTATGGCGCCGT 59.585 47.619 27.04 27.04 0.00 5.68
675 779 1.531149 CTCCTTTATTATGGCGCCGTG 59.469 52.381 31.45 12.91 0.00 4.94
676 780 1.134340 TCCTTTATTATGGCGCCGTGT 60.134 47.619 31.45 20.83 0.00 4.49
677 781 1.673920 CCTTTATTATGGCGCCGTGTT 59.326 47.619 31.45 19.52 0.00 3.32
678 782 2.286772 CCTTTATTATGGCGCCGTGTTC 60.287 50.000 31.45 1.00 0.00 3.18
679 783 2.319136 TTATTATGGCGCCGTGTTCT 57.681 45.000 31.45 14.39 0.00 3.01
680 784 1.860676 TATTATGGCGCCGTGTTCTC 58.139 50.000 31.45 0.00 0.00 2.87
681 785 0.814010 ATTATGGCGCCGTGTTCTCC 60.814 55.000 31.45 0.00 0.00 3.71
682 786 2.173758 TTATGGCGCCGTGTTCTCCA 62.174 55.000 31.45 6.12 0.00 3.86
683 787 2.845752 TATGGCGCCGTGTTCTCCAC 62.846 60.000 31.45 0.00 40.89 4.02
685 789 4.980805 GCGCCGTGTTCTCCACCA 62.981 66.667 0.00 0.00 41.26 4.17
686 790 2.738521 CGCCGTGTTCTCCACCAG 60.739 66.667 0.00 0.00 41.26 4.00
687 791 2.741092 GCCGTGTTCTCCACCAGA 59.259 61.111 0.00 0.00 41.26 3.86
688 792 1.296715 GCCGTGTTCTCCACCAGAT 59.703 57.895 0.00 0.00 41.26 2.90
689 793 0.321653 GCCGTGTTCTCCACCAGATT 60.322 55.000 0.00 0.00 41.26 2.40
690 794 1.726853 CCGTGTTCTCCACCAGATTC 58.273 55.000 0.00 0.00 41.26 2.52
691 795 1.276421 CCGTGTTCTCCACCAGATTCT 59.724 52.381 0.00 0.00 41.26 2.40
692 796 2.289694 CCGTGTTCTCCACCAGATTCTT 60.290 50.000 0.00 0.00 41.26 2.52
693 797 3.403038 CGTGTTCTCCACCAGATTCTTT 58.597 45.455 0.00 0.00 41.26 2.52
694 798 3.815401 CGTGTTCTCCACCAGATTCTTTT 59.185 43.478 0.00 0.00 41.26 2.27
695 799 4.275936 CGTGTTCTCCACCAGATTCTTTTT 59.724 41.667 0.00 0.00 41.26 1.94
715 819 3.569194 TTTTAGCACTGTTCTCCACCA 57.431 42.857 0.00 0.00 0.00 4.17
716 820 2.839486 TTAGCACTGTTCTCCACCAG 57.161 50.000 0.00 0.00 34.82 4.00
717 821 2.009681 TAGCACTGTTCTCCACCAGA 57.990 50.000 0.00 0.00 32.93 3.86
718 822 1.356124 AGCACTGTTCTCCACCAGAT 58.644 50.000 0.00 0.00 32.93 2.90
719 823 1.701847 AGCACTGTTCTCCACCAGATT 59.298 47.619 0.00 0.00 32.93 2.40
720 824 2.079925 GCACTGTTCTCCACCAGATTC 58.920 52.381 0.00 0.00 32.93 2.52
721 825 2.550855 GCACTGTTCTCCACCAGATTCA 60.551 50.000 0.00 0.00 32.93 2.57
722 826 3.871463 GCACTGTTCTCCACCAGATTCAT 60.871 47.826 0.00 0.00 32.93 2.57
723 827 4.330250 CACTGTTCTCCACCAGATTCATT 58.670 43.478 0.00 0.00 32.93 2.57
724 828 4.394300 CACTGTTCTCCACCAGATTCATTC 59.606 45.833 0.00 0.00 32.93 2.67
725 829 3.944015 CTGTTCTCCACCAGATTCATTCC 59.056 47.826 0.00 0.00 0.00 3.01
726 830 3.282885 GTTCTCCACCAGATTCATTCCC 58.717 50.000 0.00 0.00 0.00 3.97
727 831 2.561187 TCTCCACCAGATTCATTCCCA 58.439 47.619 0.00 0.00 0.00 4.37
728 832 2.918934 TCTCCACCAGATTCATTCCCAA 59.081 45.455 0.00 0.00 0.00 4.12
729 833 3.528905 TCTCCACCAGATTCATTCCCAAT 59.471 43.478 0.00 0.00 0.00 3.16
730 834 4.726317 TCTCCACCAGATTCATTCCCAATA 59.274 41.667 0.00 0.00 0.00 1.90
731 835 5.373555 TCTCCACCAGATTCATTCCCAATAT 59.626 40.000 0.00 0.00 0.00 1.28
732 836 5.634118 TCCACCAGATTCATTCCCAATATC 58.366 41.667 0.00 0.00 0.00 1.63
733 837 5.373555 TCCACCAGATTCATTCCCAATATCT 59.626 40.000 0.00 0.00 0.00 1.98
734 838 6.073314 CCACCAGATTCATTCCCAATATCTT 58.927 40.000 0.00 0.00 0.00 2.40
735 839 6.552350 CCACCAGATTCATTCCCAATATCTTT 59.448 38.462 0.00 0.00 0.00 2.52
736 840 7.431249 CACCAGATTCATTCCCAATATCTTTG 58.569 38.462 0.00 0.00 0.00 2.77
737 841 7.286087 CACCAGATTCATTCCCAATATCTTTGA 59.714 37.037 0.00 0.00 0.00 2.69
738 842 8.008922 ACCAGATTCATTCCCAATATCTTTGAT 58.991 33.333 0.00 0.00 0.00 2.57
739 843 8.521176 CCAGATTCATTCCCAATATCTTTGATC 58.479 37.037 0.00 0.00 0.00 2.92
740 844 9.074576 CAGATTCATTCCCAATATCTTTGATCA 57.925 33.333 0.00 0.00 0.00 2.92
741 845 9.075678 AGATTCATTCCCAATATCTTTGATCAC 57.924 33.333 0.00 0.00 0.00 3.06
742 846 7.587037 TTCATTCCCAATATCTTTGATCACC 57.413 36.000 0.00 0.00 0.00 4.02
743 847 6.070656 TCATTCCCAATATCTTTGATCACCC 58.929 40.000 0.00 0.00 0.00 4.61
744 848 4.453480 TCCCAATATCTTTGATCACCCC 57.547 45.455 0.00 0.00 0.00 4.95
745 849 3.140144 TCCCAATATCTTTGATCACCCCC 59.860 47.826 0.00 0.00 0.00 5.40
746 850 3.140895 CCCAATATCTTTGATCACCCCCT 59.859 47.826 0.00 0.00 0.00 4.79
747 851 4.401925 CCAATATCTTTGATCACCCCCTC 58.598 47.826 0.00 0.00 0.00 4.30
748 852 4.141181 CCAATATCTTTGATCACCCCCTCA 60.141 45.833 0.00 0.00 0.00 3.86
749 853 4.713792 ATATCTTTGATCACCCCCTCAC 57.286 45.455 0.00 0.00 0.00 3.51
750 854 1.741028 TCTTTGATCACCCCCTCACA 58.259 50.000 0.00 0.00 0.00 3.58
751 855 2.061848 TCTTTGATCACCCCCTCACAA 58.938 47.619 0.00 0.00 0.00 3.33
752 856 2.649312 TCTTTGATCACCCCCTCACAAT 59.351 45.455 0.00 0.00 0.00 2.71
753 857 2.806945 TTGATCACCCCCTCACAATC 57.193 50.000 0.00 0.00 0.00 2.67
754 858 1.667595 TGATCACCCCCTCACAATCA 58.332 50.000 0.00 0.00 0.00 2.57
755 859 1.561076 TGATCACCCCCTCACAATCAG 59.439 52.381 0.00 0.00 0.00 2.90
756 860 1.839994 GATCACCCCCTCACAATCAGA 59.160 52.381 0.00 0.00 0.00 3.27
757 861 1.741028 TCACCCCCTCACAATCAGAA 58.259 50.000 0.00 0.00 0.00 3.02
758 862 2.061848 TCACCCCCTCACAATCAGAAA 58.938 47.619 0.00 0.00 0.00 2.52
759 863 2.040278 TCACCCCCTCACAATCAGAAAG 59.960 50.000 0.00 0.00 0.00 2.62
760 864 2.040278 CACCCCCTCACAATCAGAAAGA 59.960 50.000 0.00 0.00 0.00 2.52
761 865 2.716424 ACCCCCTCACAATCAGAAAGAA 59.284 45.455 0.00 0.00 0.00 2.52
762 866 3.245052 ACCCCCTCACAATCAGAAAGAAG 60.245 47.826 0.00 0.00 0.00 2.85
763 867 2.751806 CCCCTCACAATCAGAAAGAAGC 59.248 50.000 0.00 0.00 0.00 3.86
764 868 3.415212 CCCTCACAATCAGAAAGAAGCA 58.585 45.455 0.00 0.00 0.00 3.91
793 897 2.712057 TTTAACAGGACGTCGAGACC 57.288 50.000 9.92 0.00 34.82 3.85
854 2466 1.489230 GGGCCCGATTTTAGAGAGGAA 59.511 52.381 5.69 0.00 0.00 3.36
855 2467 2.485657 GGGCCCGATTTTAGAGAGGAAG 60.486 54.545 5.69 0.00 0.00 3.46
1053 2705 2.202623 GGCTCGCTCGTGTTCGAT 60.203 61.111 0.00 0.00 45.21 3.59
1095 2747 1.749063 AGCCTCGACGTACAATCATCA 59.251 47.619 0.00 0.00 0.00 3.07
1286 2938 2.387309 GTACGATGAGGACGGTCGA 58.613 57.895 1.43 0.00 38.63 4.20
1415 3070 2.026915 AGTGTGCCATCACTATCTGCAA 60.027 45.455 4.83 0.00 45.31 4.08
1421 3076 2.877168 CCATCACTATCTGCAAGGAAGC 59.123 50.000 0.00 0.00 0.00 3.86
1422 3077 2.299993 TCACTATCTGCAAGGAAGCG 57.700 50.000 0.00 0.00 37.31 4.68
1423 3078 0.654683 CACTATCTGCAAGGAAGCGC 59.345 55.000 0.00 0.00 37.31 5.92
1424 3079 0.462759 ACTATCTGCAAGGAAGCGCC 60.463 55.000 2.29 0.00 37.31 6.53
1425 3080 1.493950 CTATCTGCAAGGAAGCGCCG 61.494 60.000 2.29 0.00 43.43 6.46
1426 3081 2.923426 TATCTGCAAGGAAGCGCCGG 62.923 60.000 2.29 0.00 43.43 6.13
1557 3218 0.593128 CTTTTCCTGCCCACAAGACG 59.407 55.000 0.00 0.00 0.00 4.18
1594 3255 2.171635 CCGGTGTTTAAGGCAGAGC 58.828 57.895 0.00 0.00 0.00 4.09
1638 3299 4.265904 TGATATGGGTCGCGTTATCATT 57.734 40.909 5.77 0.00 0.00 2.57
1695 3356 7.220740 TGCTCCATTTTATATACACCGATTCA 58.779 34.615 0.00 0.00 0.00 2.57
2067 3728 0.515127 TTGGCATGCGTGTTAAGTCG 59.485 50.000 12.44 0.00 0.00 4.18
2143 3804 3.059120 GGAGCTTCGGTGAAAAACAGTAC 60.059 47.826 0.00 0.00 0.00 2.73
2163 3824 8.148351 ACAGTACTACTCTGCTAATGTTTTTCA 58.852 33.333 0.00 0.00 36.50 2.69
2308 3970 3.551863 GCAGGCTAGTGTATGCTACTCAG 60.552 52.174 0.00 0.00 35.78 3.35
2312 3974 4.283678 GCTAGTGTATGCTACTCAGTTCG 58.716 47.826 0.00 0.00 0.00 3.95
2316 3978 4.045104 GTGTATGCTACTCAGTTCGATGG 58.955 47.826 0.00 0.00 0.00 3.51
2388 4050 7.282224 GCCAGGAGTGTGTTAATGTGATTATAA 59.718 37.037 0.00 0.00 0.00 0.98
2404 4066 9.473007 TGTGATTATAAGGGAACATTTCATCAA 57.527 29.630 0.00 0.00 0.00 2.57
2429 4091 4.680171 ATGAAATTCGAAACGGGAGAAC 57.320 40.909 0.00 0.00 0.00 3.01
2470 4132 7.164171 CGAACTCTTGAGTGTTGTAAAACAATG 59.836 37.037 2.91 0.00 40.59 2.82
2625 4290 1.204146 AGCAGTTGACCCATCGGTAT 58.796 50.000 0.00 0.00 44.88 2.73
2695 4361 6.770286 ACCTATGGAATGATTGAGTACCAT 57.230 37.500 0.00 0.00 40.50 3.55
2707 4373 5.434182 TTGAGTACCATCACATCATCCAA 57.566 39.130 0.00 0.00 0.00 3.53
2907 4577 5.591067 TGAAAGTACCCCTTGTGTTGTAAAG 59.409 40.000 0.00 0.00 32.32 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.291024 ACTGGAGACCTATCCGCGATAT 60.291 50.000 8.23 2.94 42.77 1.63
1 2 1.073444 ACTGGAGACCTATCCGCGATA 59.927 52.381 8.23 2.69 42.77 2.92
13 14 3.938963 TGTTTTGTCAAGTCACTGGAGAC 59.061 43.478 0.00 0.00 38.81 3.36
66 67 7.201461 GGATGTGATGTGCATAATTTTGTCAAC 60.201 37.037 0.00 0.00 0.00 3.18
98 99 9.856488 GTAATCTTGAGCATCTATATTCCGTTA 57.144 33.333 0.00 0.00 34.92 3.18
162 163 5.651576 ACCTTTCAAATGTGTGCCAAATTTT 59.348 32.000 1.78 0.00 29.82 1.82
173 174 8.885494 TTAAATTGGAAGACCTTTCAAATGTG 57.115 30.769 7.49 0.00 41.02 3.21
181 182 7.433680 GTCACACATTAAATTGGAAGACCTTT 58.566 34.615 0.00 0.00 37.04 3.11
199 200 5.250982 TCTATAAGAAGTCGAGGTCACACA 58.749 41.667 0.00 0.00 0.00 3.72
211 212 7.946776 CCCATGGGAATTCAATCTATAAGAAGT 59.053 37.037 28.27 0.00 37.50 3.01
253 254 2.144730 GGCATCAAATGTGCAAAGCAA 58.855 42.857 0.00 0.00 44.25 3.91
272 274 2.797786 TCGGTTTTACAAATGGGGAGG 58.202 47.619 0.00 0.00 0.00 4.30
290 292 6.142818 AGGAACTCTGACTTCTCATATTCG 57.857 41.667 0.00 0.00 0.00 3.34
362 417 3.887716 CCACGGTAATGCCTACTACTACT 59.112 47.826 0.00 0.00 34.25 2.57
363 418 3.885297 TCCACGGTAATGCCTACTACTAC 59.115 47.826 0.00 0.00 34.25 2.73
390 445 4.067896 ACGACAAACTACTAGTTCCTCGA 58.932 43.478 22.95 0.00 37.47 4.04
453 557 3.032459 AGTGGGCGGGTTTTCTTAAAAA 58.968 40.909 0.00 0.00 31.13 1.94
454 558 2.668625 AGTGGGCGGGTTTTCTTAAAA 58.331 42.857 0.00 0.00 0.00 1.52
455 559 2.368311 AGTGGGCGGGTTTTCTTAAA 57.632 45.000 0.00 0.00 0.00 1.52
456 560 2.368311 AAGTGGGCGGGTTTTCTTAA 57.632 45.000 0.00 0.00 0.00 1.85
457 561 2.368311 AAAGTGGGCGGGTTTTCTTA 57.632 45.000 0.00 0.00 0.00 2.10
458 562 2.368311 TAAAGTGGGCGGGTTTTCTT 57.632 45.000 0.00 0.00 0.00 2.52
459 563 2.560981 CAATAAAGTGGGCGGGTTTTCT 59.439 45.455 0.00 0.00 0.00 2.52
460 564 2.559231 TCAATAAAGTGGGCGGGTTTTC 59.441 45.455 0.00 0.00 0.00 2.29
461 565 2.599677 TCAATAAAGTGGGCGGGTTTT 58.400 42.857 0.00 0.00 0.00 2.43
462 566 2.296073 TCAATAAAGTGGGCGGGTTT 57.704 45.000 0.00 0.00 0.00 3.27
463 567 2.525105 ATCAATAAAGTGGGCGGGTT 57.475 45.000 0.00 0.00 0.00 4.11
464 568 2.291282 TGAATCAATAAAGTGGGCGGGT 60.291 45.455 0.00 0.00 0.00 5.28
465 569 2.374184 TGAATCAATAAAGTGGGCGGG 58.626 47.619 0.00 0.00 0.00 6.13
466 570 3.885297 AGATGAATCAATAAAGTGGGCGG 59.115 43.478 0.00 0.00 0.00 6.13
467 571 4.576053 TGAGATGAATCAATAAAGTGGGCG 59.424 41.667 0.00 0.00 0.00 6.13
468 572 6.455360 TTGAGATGAATCAATAAAGTGGGC 57.545 37.500 0.00 0.00 34.31 5.36
469 573 8.229253 TCATTGAGATGAATCAATAAAGTGGG 57.771 34.615 1.90 0.00 45.83 4.61
470 574 9.894783 GATCATTGAGATGAATCAATAAAGTGG 57.105 33.333 1.90 0.00 45.83 4.00
478 582 9.716531 GTACCTATGATCATTGAGATGAATCAA 57.283 33.333 14.65 0.00 44.96 2.57
479 583 8.873144 TGTACCTATGATCATTGAGATGAATCA 58.127 33.333 14.65 0.00 44.96 2.57
480 584 9.716531 TTGTACCTATGATCATTGAGATGAATC 57.283 33.333 14.65 0.00 44.96 2.52
481 585 9.722184 CTTGTACCTATGATCATTGAGATGAAT 57.278 33.333 14.65 0.00 44.96 2.57
482 586 8.152898 CCTTGTACCTATGATCATTGAGATGAA 58.847 37.037 14.65 1.86 44.96 2.57
483 587 7.290948 ACCTTGTACCTATGATCATTGAGATGA 59.709 37.037 14.65 0.00 45.81 2.92
484 588 7.448420 ACCTTGTACCTATGATCATTGAGATG 58.552 38.462 14.65 1.76 37.00 2.90
485 589 7.623999 ACCTTGTACCTATGATCATTGAGAT 57.376 36.000 14.65 0.00 40.48 2.75
486 590 7.437713 AACCTTGTACCTATGATCATTGAGA 57.562 36.000 14.65 0.34 0.00 3.27
487 591 8.400947 CAAAACCTTGTACCTATGATCATTGAG 58.599 37.037 14.65 6.00 0.00 3.02
488 592 7.888021 ACAAAACCTTGTACCTATGATCATTGA 59.112 33.333 14.65 0.00 44.14 2.57
489 593 8.055279 ACAAAACCTTGTACCTATGATCATTG 57.945 34.615 14.65 11.96 44.14 2.82
490 594 8.650143 AACAAAACCTTGTACCTATGATCATT 57.350 30.769 14.65 0.00 45.25 2.57
491 595 7.888021 TGAACAAAACCTTGTACCTATGATCAT 59.112 33.333 13.81 13.81 45.25 2.45
492 596 7.227873 TGAACAAAACCTTGTACCTATGATCA 58.772 34.615 0.00 0.00 45.25 2.92
493 597 7.681939 TGAACAAAACCTTGTACCTATGATC 57.318 36.000 0.00 0.00 45.25 2.92
494 598 7.122650 CCATGAACAAAACCTTGTACCTATGAT 59.877 37.037 0.00 0.00 45.25 2.45
495 599 6.432783 CCATGAACAAAACCTTGTACCTATGA 59.567 38.462 0.00 0.00 45.25 2.15
496 600 6.350110 CCCATGAACAAAACCTTGTACCTATG 60.350 42.308 0.00 0.00 45.25 2.23
497 601 5.714806 CCCATGAACAAAACCTTGTACCTAT 59.285 40.000 0.00 0.00 45.25 2.57
498 602 5.074115 CCCATGAACAAAACCTTGTACCTA 58.926 41.667 0.00 0.00 45.25 3.08
499 603 3.895041 CCCATGAACAAAACCTTGTACCT 59.105 43.478 0.00 0.00 45.25 3.08
500 604 3.006430 CCCCATGAACAAAACCTTGTACC 59.994 47.826 0.00 0.00 45.25 3.34
501 605 3.639561 ACCCCATGAACAAAACCTTGTAC 59.360 43.478 0.00 0.00 45.25 2.90
502 606 3.917300 ACCCCATGAACAAAACCTTGTA 58.083 40.909 0.00 0.00 45.25 2.41
504 608 3.895041 ACTACCCCATGAACAAAACCTTG 59.105 43.478 0.00 0.00 38.61 3.61
505 609 4.149598 GACTACCCCATGAACAAAACCTT 58.850 43.478 0.00 0.00 0.00 3.50
506 610 3.499745 GGACTACCCCATGAACAAAACCT 60.500 47.826 0.00 0.00 0.00 3.50
507 611 2.823747 GGACTACCCCATGAACAAAACC 59.176 50.000 0.00 0.00 0.00 3.27
521 625 2.817844 GACACATTTGGTTGGGACTACC 59.182 50.000 0.00 0.00 40.81 3.18
522 626 2.482721 CGACACATTTGGTTGGGACTAC 59.517 50.000 0.00 0.00 0.00 2.73
523 627 2.551287 CCGACACATTTGGTTGGGACTA 60.551 50.000 0.00 0.00 36.35 2.59
524 628 1.604604 CGACACATTTGGTTGGGACT 58.395 50.000 0.00 0.00 0.00 3.85
525 629 0.596082 CCGACACATTTGGTTGGGAC 59.404 55.000 0.00 0.00 36.35 4.46
526 630 1.175983 GCCGACACATTTGGTTGGGA 61.176 55.000 0.00 0.00 39.74 4.37
527 631 1.288752 GCCGACACATTTGGTTGGG 59.711 57.895 0.00 0.00 39.74 4.12
528 632 1.288752 GGCCGACACATTTGGTTGG 59.711 57.895 0.00 0.00 41.87 3.77
529 633 0.039256 CTGGCCGACACATTTGGTTG 60.039 55.000 0.00 0.00 0.00 3.77
530 634 1.178534 CCTGGCCGACACATTTGGTT 61.179 55.000 0.00 0.00 0.00 3.67
531 635 1.603455 CCTGGCCGACACATTTGGT 60.603 57.895 0.00 0.00 0.00 3.67
532 636 2.993471 GCCTGGCCGACACATTTGG 61.993 63.158 7.66 0.00 0.00 3.28
533 637 2.568090 GCCTGGCCGACACATTTG 59.432 61.111 7.66 0.00 0.00 2.32
534 638 2.676471 GGCCTGGCCGACACATTT 60.676 61.111 24.16 0.00 39.62 2.32
543 647 3.597855 GATTGTAATCTTGGGCCTGGCC 61.598 54.545 29.93 29.93 39.01 5.36
544 648 1.683385 GATTGTAATCTTGGGCCTGGC 59.317 52.381 11.05 11.05 32.66 4.85
545 649 3.017048 TGATTGTAATCTTGGGCCTGG 57.983 47.619 4.53 0.00 36.39 4.45
546 650 4.463891 AGTTTGATTGTAATCTTGGGCCTG 59.536 41.667 4.53 0.00 36.39 4.85
547 651 4.677182 AGTTTGATTGTAATCTTGGGCCT 58.323 39.130 4.53 0.00 36.39 5.19
548 652 5.170748 CAAGTTTGATTGTAATCTTGGGCC 58.829 41.667 0.00 0.00 35.35 5.80
549 653 5.170748 CCAAGTTTGATTGTAATCTTGGGC 58.829 41.667 15.56 0.00 45.34 5.36
552 656 5.698832 TCGCCAAGTTTGATTGTAATCTTG 58.301 37.500 6.21 0.00 37.22 3.02
553 657 5.705441 TCTCGCCAAGTTTGATTGTAATCTT 59.295 36.000 6.21 0.00 36.39 2.40
554 658 5.245531 TCTCGCCAAGTTTGATTGTAATCT 58.754 37.500 6.21 0.00 36.39 2.40
555 659 5.545658 TCTCGCCAAGTTTGATTGTAATC 57.454 39.130 0.00 0.00 35.97 1.75
556 660 6.515272 AATCTCGCCAAGTTTGATTGTAAT 57.485 33.333 0.00 0.00 0.00 1.89
557 661 5.957842 AATCTCGCCAAGTTTGATTGTAA 57.042 34.783 0.00 0.00 0.00 2.41
558 662 6.821160 TCATAATCTCGCCAAGTTTGATTGTA 59.179 34.615 0.00 0.00 0.00 2.41
559 663 5.647658 TCATAATCTCGCCAAGTTTGATTGT 59.352 36.000 0.00 0.00 0.00 2.71
560 664 6.122850 TCATAATCTCGCCAAGTTTGATTG 57.877 37.500 0.00 0.00 0.00 2.67
561 665 5.220931 GCTCATAATCTCGCCAAGTTTGATT 60.221 40.000 0.00 0.00 0.00 2.57
562 666 4.274459 GCTCATAATCTCGCCAAGTTTGAT 59.726 41.667 0.00 0.00 0.00 2.57
563 667 3.623060 GCTCATAATCTCGCCAAGTTTGA 59.377 43.478 0.00 0.00 0.00 2.69
564 668 3.624861 AGCTCATAATCTCGCCAAGTTTG 59.375 43.478 0.00 0.00 0.00 2.93
565 669 3.878778 AGCTCATAATCTCGCCAAGTTT 58.121 40.909 0.00 0.00 0.00 2.66
566 670 3.550437 AGCTCATAATCTCGCCAAGTT 57.450 42.857 0.00 0.00 0.00 2.66
567 671 3.550437 AAGCTCATAATCTCGCCAAGT 57.450 42.857 0.00 0.00 0.00 3.16
568 672 4.889832 AAAAGCTCATAATCTCGCCAAG 57.110 40.909 0.00 0.00 0.00 3.61
569 673 6.751514 TTTAAAAGCTCATAATCTCGCCAA 57.248 33.333 0.00 0.00 0.00 4.52
570 674 6.942532 ATTTAAAAGCTCATAATCTCGCCA 57.057 33.333 0.00 0.00 0.00 5.69
571 675 9.730420 TTTAATTTAAAAGCTCATAATCTCGCC 57.270 29.630 0.00 0.00 0.00 5.54
581 685 8.960075 GCGTAGTTTGTTTAATTTAAAAGCTCA 58.040 29.630 3.23 0.00 0.00 4.26
582 686 9.177304 AGCGTAGTTTGTTTAATTTAAAAGCTC 57.823 29.630 3.23 0.00 0.00 4.09
583 687 9.177304 GAGCGTAGTTTGTTTAATTTAAAAGCT 57.823 29.630 3.23 0.13 0.00 3.74
584 688 8.960075 TGAGCGTAGTTTGTTTAATTTAAAAGC 58.040 29.630 3.23 0.00 0.00 3.51
588 692 9.601971 GTCATGAGCGTAGTTTGTTTAATTTAA 57.398 29.630 0.00 0.00 0.00 1.52
589 693 8.995220 AGTCATGAGCGTAGTTTGTTTAATTTA 58.005 29.630 0.00 0.00 0.00 1.40
590 694 7.871853 AGTCATGAGCGTAGTTTGTTTAATTT 58.128 30.769 0.00 0.00 0.00 1.82
591 695 7.435068 AGTCATGAGCGTAGTTTGTTTAATT 57.565 32.000 0.00 0.00 0.00 1.40
592 696 8.542497 TTAGTCATGAGCGTAGTTTGTTTAAT 57.458 30.769 0.00 0.00 0.00 1.40
593 697 7.949903 TTAGTCATGAGCGTAGTTTGTTTAA 57.050 32.000 0.00 0.00 0.00 1.52
594 698 7.949903 TTTAGTCATGAGCGTAGTTTGTTTA 57.050 32.000 0.00 0.00 0.00 2.01
595 699 6.854496 TTTAGTCATGAGCGTAGTTTGTTT 57.146 33.333 0.00 0.00 0.00 2.83
596 700 6.259167 TGTTTTAGTCATGAGCGTAGTTTGTT 59.741 34.615 0.00 0.00 0.00 2.83
597 701 5.756347 TGTTTTAGTCATGAGCGTAGTTTGT 59.244 36.000 0.00 0.00 0.00 2.83
598 702 6.223138 TGTTTTAGTCATGAGCGTAGTTTG 57.777 37.500 0.00 0.00 0.00 2.93
599 703 5.107065 GCTGTTTTAGTCATGAGCGTAGTTT 60.107 40.000 0.00 0.00 0.00 2.66
600 704 4.389077 GCTGTTTTAGTCATGAGCGTAGTT 59.611 41.667 0.00 0.00 0.00 2.24
601 705 3.927142 GCTGTTTTAGTCATGAGCGTAGT 59.073 43.478 0.00 0.00 0.00 2.73
602 706 3.926527 TGCTGTTTTAGTCATGAGCGTAG 59.073 43.478 0.00 0.00 0.00 3.51
603 707 3.920446 TGCTGTTTTAGTCATGAGCGTA 58.080 40.909 0.00 0.00 0.00 4.42
604 708 2.766313 TGCTGTTTTAGTCATGAGCGT 58.234 42.857 0.00 0.00 0.00 5.07
605 709 3.811722 TTGCTGTTTTAGTCATGAGCG 57.188 42.857 0.00 0.00 0.00 5.03
606 710 5.107722 GCTTTTTGCTGTTTTAGTCATGAGC 60.108 40.000 0.00 0.00 38.95 4.26
607 711 5.978919 TGCTTTTTGCTGTTTTAGTCATGAG 59.021 36.000 0.00 0.00 43.37 2.90
608 712 5.900425 TGCTTTTTGCTGTTTTAGTCATGA 58.100 33.333 0.00 0.00 43.37 3.07
609 713 6.586868 TTGCTTTTTGCTGTTTTAGTCATG 57.413 33.333 0.00 0.00 43.37 3.07
610 714 7.334171 ACTTTTGCTTTTTGCTGTTTTAGTCAT 59.666 29.630 0.00 0.00 43.37 3.06
611 715 6.648725 ACTTTTGCTTTTTGCTGTTTTAGTCA 59.351 30.769 0.00 0.00 43.37 3.41
612 716 7.060600 ACTTTTGCTTTTTGCTGTTTTAGTC 57.939 32.000 0.00 0.00 43.37 2.59
613 717 8.716646 ATACTTTTGCTTTTTGCTGTTTTAGT 57.283 26.923 0.00 0.00 43.37 2.24
614 718 9.986833 AAATACTTTTGCTTTTTGCTGTTTTAG 57.013 25.926 0.00 0.00 43.37 1.85
615 719 9.980780 GAAATACTTTTGCTTTTTGCTGTTTTA 57.019 25.926 0.00 0.00 43.37 1.52
616 720 8.729756 AGAAATACTTTTGCTTTTTGCTGTTTT 58.270 25.926 0.00 0.00 43.37 2.43
617 721 8.267620 AGAAATACTTTTGCTTTTTGCTGTTT 57.732 26.923 0.00 0.00 43.37 2.83
618 722 7.848223 AGAAATACTTTTGCTTTTTGCTGTT 57.152 28.000 0.00 0.00 43.37 3.16
619 723 8.197439 ACTAGAAATACTTTTGCTTTTTGCTGT 58.803 29.630 0.00 0.00 43.37 4.40
620 724 8.482429 CACTAGAAATACTTTTGCTTTTTGCTG 58.518 33.333 0.00 0.00 43.37 4.41
621 725 8.413229 TCACTAGAAATACTTTTGCTTTTTGCT 58.587 29.630 0.00 0.00 43.37 3.91
622 726 8.574196 TCACTAGAAATACTTTTGCTTTTTGC 57.426 30.769 0.00 0.00 43.25 3.68
644 748 9.612620 CGCCATAATAAAGGAGATTAATTTCAC 57.387 33.333 8.15 0.00 0.00 3.18
645 749 8.296713 GCGCCATAATAAAGGAGATTAATTTCA 58.703 33.333 8.15 0.00 0.00 2.69
646 750 7.755373 GGCGCCATAATAAAGGAGATTAATTTC 59.245 37.037 24.80 0.00 0.00 2.17
647 751 7.574967 CGGCGCCATAATAAAGGAGATTAATTT 60.575 37.037 28.98 0.00 0.00 1.82
648 752 6.128007 CGGCGCCATAATAAAGGAGATTAATT 60.128 38.462 28.98 0.00 0.00 1.40
649 753 5.354234 CGGCGCCATAATAAAGGAGATTAAT 59.646 40.000 28.98 0.00 0.00 1.40
650 754 4.693566 CGGCGCCATAATAAAGGAGATTAA 59.306 41.667 28.98 0.00 0.00 1.40
651 755 4.250464 CGGCGCCATAATAAAGGAGATTA 58.750 43.478 28.98 0.00 0.00 1.75
652 756 3.074412 CGGCGCCATAATAAAGGAGATT 58.926 45.455 28.98 0.00 0.00 2.40
653 757 2.038557 ACGGCGCCATAATAAAGGAGAT 59.961 45.455 28.98 0.00 0.00 2.75
654 758 1.414919 ACGGCGCCATAATAAAGGAGA 59.585 47.619 28.98 0.00 0.00 3.71
655 759 1.531149 CACGGCGCCATAATAAAGGAG 59.469 52.381 28.98 7.69 0.00 3.69
656 760 1.134340 ACACGGCGCCATAATAAAGGA 60.134 47.619 28.98 0.00 0.00 3.36
657 761 1.305201 ACACGGCGCCATAATAAAGG 58.695 50.000 28.98 9.11 0.00 3.11
658 762 2.612212 AGAACACGGCGCCATAATAAAG 59.388 45.455 28.98 9.93 0.00 1.85
659 763 2.610374 GAGAACACGGCGCCATAATAAA 59.390 45.455 28.98 0.00 0.00 1.40
660 764 2.206750 GAGAACACGGCGCCATAATAA 58.793 47.619 28.98 0.00 0.00 1.40
661 765 1.539496 GGAGAACACGGCGCCATAATA 60.539 52.381 28.98 0.00 0.00 0.98
662 766 0.814010 GGAGAACACGGCGCCATAAT 60.814 55.000 28.98 9.66 0.00 1.28
663 767 1.448893 GGAGAACACGGCGCCATAA 60.449 57.895 28.98 0.00 0.00 1.90
664 768 2.185867 GGAGAACACGGCGCCATA 59.814 61.111 28.98 0.00 0.00 2.74
665 769 4.015406 TGGAGAACACGGCGCCAT 62.015 61.111 28.98 8.91 29.97 4.40
666 770 4.980805 GTGGAGAACACGGCGCCA 62.981 66.667 28.98 1.29 40.85 5.69
694 798 3.882888 CTGGTGGAGAACAGTGCTAAAAA 59.117 43.478 0.00 0.00 0.00 1.94
695 799 3.135712 TCTGGTGGAGAACAGTGCTAAAA 59.864 43.478 0.00 0.00 36.17 1.52
696 800 2.703536 TCTGGTGGAGAACAGTGCTAAA 59.296 45.455 0.00 0.00 36.17 1.85
697 801 2.325484 TCTGGTGGAGAACAGTGCTAA 58.675 47.619 0.00 0.00 36.17 3.09
698 802 2.009681 TCTGGTGGAGAACAGTGCTA 57.990 50.000 0.00 0.00 36.17 3.49
699 803 1.356124 ATCTGGTGGAGAACAGTGCT 58.644 50.000 0.00 0.00 36.17 4.40
700 804 2.079925 GAATCTGGTGGAGAACAGTGC 58.920 52.381 0.00 0.00 36.17 4.40
701 805 3.407424 TGAATCTGGTGGAGAACAGTG 57.593 47.619 0.00 0.00 36.17 3.66
702 806 4.566488 GGAATGAATCTGGTGGAGAACAGT 60.566 45.833 0.00 0.00 36.17 3.55
703 807 3.944015 GGAATGAATCTGGTGGAGAACAG 59.056 47.826 0.00 0.00 33.12 3.16
704 808 3.308402 GGGAATGAATCTGGTGGAGAACA 60.308 47.826 0.00 0.00 33.12 3.18
705 809 3.282885 GGGAATGAATCTGGTGGAGAAC 58.717 50.000 0.00 0.00 33.12 3.01
706 810 2.918934 TGGGAATGAATCTGGTGGAGAA 59.081 45.455 0.00 0.00 33.12 2.87
707 811 2.561187 TGGGAATGAATCTGGTGGAGA 58.439 47.619 0.00 0.00 34.25 3.71
708 812 3.370840 TTGGGAATGAATCTGGTGGAG 57.629 47.619 0.00 0.00 0.00 3.86
709 813 5.373555 AGATATTGGGAATGAATCTGGTGGA 59.626 40.000 0.00 0.00 0.00 4.02
710 814 5.638133 AGATATTGGGAATGAATCTGGTGG 58.362 41.667 0.00 0.00 0.00 4.61
711 815 7.286087 TCAAAGATATTGGGAATGAATCTGGTG 59.714 37.037 0.00 0.00 0.00 4.17
712 816 7.356680 TCAAAGATATTGGGAATGAATCTGGT 58.643 34.615 0.00 0.00 0.00 4.00
713 817 7.828508 TCAAAGATATTGGGAATGAATCTGG 57.171 36.000 0.00 0.00 0.00 3.86
714 818 9.074576 TGATCAAAGATATTGGGAATGAATCTG 57.925 33.333 0.00 0.00 0.00 2.90
715 819 9.075678 GTGATCAAAGATATTGGGAATGAATCT 57.924 33.333 0.00 0.00 0.00 2.40
716 820 8.302438 GGTGATCAAAGATATTGGGAATGAATC 58.698 37.037 0.00 0.00 0.00 2.52
717 821 7.234166 GGGTGATCAAAGATATTGGGAATGAAT 59.766 37.037 0.00 0.00 0.00 2.57
718 822 6.550854 GGGTGATCAAAGATATTGGGAATGAA 59.449 38.462 0.00 0.00 0.00 2.57
719 823 6.070656 GGGTGATCAAAGATATTGGGAATGA 58.929 40.000 0.00 0.00 0.00 2.57
720 824 5.244626 GGGGTGATCAAAGATATTGGGAATG 59.755 44.000 0.00 0.00 0.00 2.67
721 825 5.397360 GGGGTGATCAAAGATATTGGGAAT 58.603 41.667 0.00 0.00 0.00 3.01
722 826 4.387437 GGGGGTGATCAAAGATATTGGGAA 60.387 45.833 0.00 0.00 0.00 3.97
723 827 3.140144 GGGGGTGATCAAAGATATTGGGA 59.860 47.826 0.00 0.00 0.00 4.37
724 828 3.140895 AGGGGGTGATCAAAGATATTGGG 59.859 47.826 0.00 0.00 0.00 4.12
725 829 4.141181 TGAGGGGGTGATCAAAGATATTGG 60.141 45.833 0.00 0.00 0.00 3.16
726 830 4.823989 GTGAGGGGGTGATCAAAGATATTG 59.176 45.833 0.00 0.00 0.00 1.90
727 831 4.478317 TGTGAGGGGGTGATCAAAGATATT 59.522 41.667 0.00 0.00 0.00 1.28
728 832 4.047166 TGTGAGGGGGTGATCAAAGATAT 58.953 43.478 0.00 0.00 0.00 1.63
729 833 3.459828 TGTGAGGGGGTGATCAAAGATA 58.540 45.455 0.00 0.00 0.00 1.98
730 834 2.278245 TGTGAGGGGGTGATCAAAGAT 58.722 47.619 0.00 0.00 0.00 2.40
731 835 1.741028 TGTGAGGGGGTGATCAAAGA 58.259 50.000 0.00 0.00 0.00 2.52
732 836 2.584835 TTGTGAGGGGGTGATCAAAG 57.415 50.000 0.00 0.00 0.00 2.77
733 837 2.378208 TGATTGTGAGGGGGTGATCAAA 59.622 45.455 0.00 0.00 0.00 2.69
734 838 1.991813 TGATTGTGAGGGGGTGATCAA 59.008 47.619 0.00 0.00 0.00 2.57
735 839 1.561076 CTGATTGTGAGGGGGTGATCA 59.439 52.381 0.00 0.00 0.00 2.92
736 840 1.839994 TCTGATTGTGAGGGGGTGATC 59.160 52.381 0.00 0.00 0.00 2.92
737 841 1.971149 TCTGATTGTGAGGGGGTGAT 58.029 50.000 0.00 0.00 0.00 3.06
738 842 1.741028 TTCTGATTGTGAGGGGGTGA 58.259 50.000 0.00 0.00 0.00 4.02
739 843 2.040278 TCTTTCTGATTGTGAGGGGGTG 59.960 50.000 0.00 0.00 0.00 4.61
740 844 2.348472 TCTTTCTGATTGTGAGGGGGT 58.652 47.619 0.00 0.00 0.00 4.95
741 845 3.350833 CTTCTTTCTGATTGTGAGGGGG 58.649 50.000 0.00 0.00 0.00 5.40
742 846 2.751806 GCTTCTTTCTGATTGTGAGGGG 59.248 50.000 0.00 0.00 0.00 4.79
743 847 3.415212 TGCTTCTTTCTGATTGTGAGGG 58.585 45.455 0.00 0.00 0.00 4.30
744 848 5.048224 ACATTGCTTCTTTCTGATTGTGAGG 60.048 40.000 0.00 0.00 0.00 3.86
745 849 6.010294 ACATTGCTTCTTTCTGATTGTGAG 57.990 37.500 0.00 0.00 0.00 3.51
746 850 6.210796 CAACATTGCTTCTTTCTGATTGTGA 58.789 36.000 0.00 0.00 0.00 3.58
747 851 5.404366 CCAACATTGCTTCTTTCTGATTGTG 59.596 40.000 0.00 0.00 0.00 3.33
748 852 5.535333 CCAACATTGCTTCTTTCTGATTGT 58.465 37.500 0.00 0.00 0.00 2.71
749 853 4.387862 GCCAACATTGCTTCTTTCTGATTG 59.612 41.667 0.00 0.00 0.00 2.67
750 854 4.282703 AGCCAACATTGCTTCTTTCTGATT 59.717 37.500 0.00 0.00 34.87 2.57
751 855 3.830755 AGCCAACATTGCTTCTTTCTGAT 59.169 39.130 0.00 0.00 34.87 2.90
752 856 3.225104 AGCCAACATTGCTTCTTTCTGA 58.775 40.909 0.00 0.00 34.87 3.27
753 857 3.655276 AGCCAACATTGCTTCTTTCTG 57.345 42.857 0.00 0.00 34.87 3.02
761 865 3.640967 TCCTGTTAAAAGCCAACATTGCT 59.359 39.130 0.00 0.00 41.89 3.91
762 866 3.740832 GTCCTGTTAAAAGCCAACATTGC 59.259 43.478 0.00 0.00 35.46 3.56
763 867 3.980775 CGTCCTGTTAAAAGCCAACATTG 59.019 43.478 0.00 0.00 35.46 2.82
764 868 3.634910 ACGTCCTGTTAAAAGCCAACATT 59.365 39.130 0.00 0.00 35.46 2.71
780 884 1.254026 TCAAATGGTCTCGACGTCCT 58.746 50.000 10.58 0.00 0.00 3.85
793 897 3.201290 CTCCTCCTGGACGAATCAAATG 58.799 50.000 0.00 0.00 37.46 2.32
905 2519 1.756538 GCATTTGTATGGAGGGTTGGG 59.243 52.381 0.00 0.00 32.15 4.12
1033 2685 4.373116 GAACACGAGCGAGCCCCA 62.373 66.667 0.00 0.00 0.00 4.96
1053 2705 3.066190 CCGCCGTACCCTGAGACA 61.066 66.667 0.00 0.00 0.00 3.41
1095 2747 0.179145 CGCCGACGGTGAATACTTCT 60.179 55.000 22.98 0.00 34.74 2.85
1224 2876 1.347707 TCCACCAAACTGAGCTCGAAT 59.652 47.619 9.64 0.00 0.00 3.34
1286 2938 1.160137 GCCAGAGTCAAATTCTGCGT 58.840 50.000 0.00 0.00 40.54 5.24
1296 2948 2.649034 GTTCGGTCGCCAGAGTCA 59.351 61.111 0.00 0.00 0.00 3.41
1422 3077 2.222217 CGATTTCGACGAGACCGGC 61.222 63.158 0.00 0.00 43.02 6.13
1423 3078 0.455633 AACGATTTCGACGAGACCGG 60.456 55.000 7.11 0.00 43.02 5.28
1424 3079 1.057285 CAAACGATTTCGACGAGACCG 59.943 52.381 7.01 0.00 43.02 4.79
1425 3080 1.201780 GCAAACGATTTCGACGAGACC 60.202 52.381 7.01 0.00 43.02 3.85
1426 3081 1.719780 AGCAAACGATTTCGACGAGAC 59.280 47.619 7.01 0.00 43.02 3.36
1427 3082 1.719246 CAGCAAACGATTTCGACGAGA 59.281 47.619 7.01 0.00 43.02 4.04
1428 3083 1.719246 TCAGCAAACGATTTCGACGAG 59.281 47.619 7.01 0.00 43.02 4.18
1429 3084 1.719246 CTCAGCAAACGATTTCGACGA 59.281 47.619 7.01 0.00 43.02 4.20
1432 3087 1.798223 CACCTCAGCAAACGATTTCGA 59.202 47.619 7.01 0.00 43.02 3.71
1434 3089 1.401539 GGCACCTCAGCAAACGATTTC 60.402 52.381 0.00 0.00 35.83 2.17
1594 3255 1.079127 CCCTCAAGGCACCGTACAG 60.079 63.158 0.00 0.00 0.00 2.74
1638 3299 3.364441 GCAGGTTGCATGTCGCCA 61.364 61.111 0.00 0.00 44.26 5.69
1695 3356 1.502039 AGATCATCCATGGTGGGCAAT 59.498 47.619 12.58 0.00 38.32 3.56
1734 3395 9.193806 AGCAAATGTCCAATAATCTCTTTGTAT 57.806 29.630 0.00 0.00 0.00 2.29
2067 3728 7.919690 TCAAACAAGTAGCAAGATATGTATGC 58.080 34.615 0.00 0.00 40.34 3.14
2119 3780 2.554032 CTGTTTTTCACCGAAGCTCCAT 59.446 45.455 0.00 0.00 0.00 3.41
2122 3783 3.808174 AGTACTGTTTTTCACCGAAGCTC 59.192 43.478 0.00 0.00 0.00 4.09
2143 3804 7.274250 GGCAAATGAAAAACATTAGCAGAGTAG 59.726 37.037 0.00 0.00 46.90 2.57
2163 3824 5.410355 AAGTATGCAACATCTTGGCAAAT 57.590 34.783 0.00 0.00 41.43 2.32
2168 3829 6.949352 AAGGATAAGTATGCAACATCTTGG 57.051 37.500 0.00 0.00 0.00 3.61
2255 3916 9.662947 GTAGTGTGGTAATTAAAACCTATGACT 57.337 33.333 10.69 9.17 37.91 3.41
2308 3970 2.061773 CGGCAGATATCACCATCGAAC 58.938 52.381 13.48 0.00 0.00 3.95
2312 3974 2.987149 CGTTACGGCAGATATCACCATC 59.013 50.000 13.48 2.34 0.00 3.51
2316 3978 5.164080 GCTTATTCGTTACGGCAGATATCAC 60.164 44.000 4.53 0.00 0.00 3.06
2404 4066 6.995511 TCTCCCGTTTCGAATTTCATATTT 57.004 33.333 0.00 0.00 0.00 1.40
2429 4091 3.120199 AGAGTTCGAAAATGTGGCATTCG 60.120 43.478 13.26 13.26 45.32 3.34
2470 4132 2.857186 ATTGTTTCAAATGCACCCCC 57.143 45.000 0.00 0.00 0.00 5.40
2907 4577 8.665685 ACGTTCCTTCTGTATCAAAATGATTAC 58.334 33.333 0.00 0.00 38.26 1.89


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

AutoCloner maintained by Alex Coulton.