Multiple sequence alignment - TraesCS1A01G333100

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 TraesCS1A01G333100 chr1A 100.000 3459 0 0 1 3459 521288412 521284954 0.000000e+00 6388
1 TraesCS1A01G333100 chr1A 99.305 2735 16 3 727 3459 500074427 500071694 0.000000e+00 4942
2 TraesCS1A01G333100 chr4A 98.867 2737 15 2 724 3459 644772685 644769964 0.000000e+00 4868
3 TraesCS1A01G333100 chr3A 98.760 2743 12 3 724 3459 23447067 23449794 0.000000e+00 4857
4 TraesCS1A01G333100 chr3A 98.064 2737 22 16 724 3459 57277797 57275091 0.000000e+00 4732
5 TraesCS1A01G333100 chr5A 98.758 2738 18 2 723 3459 69232549 69229827 0.000000e+00 4854
6 TraesCS1A01G333100 chr5A 78.231 735 138 19 2 721 657272439 657271712 5.260000e-123 451
7 TraesCS1A01G333100 chr7B 98.210 2737 18 2 724 3459 122624256 122626962 0.000000e+00 4754
8 TraesCS1A01G333100 chr7B 98.096 2468 16 2 723 3189 476795153 476792716 0.000000e+00 4268
9 TraesCS1A01G333100 chr7B 81.609 609 101 8 9 614 163488657 163489257 8.620000e-136 494
10 TraesCS1A01G333100 chr7B 78.446 682 120 24 9 678 225408055 225408721 1.480000e-113 420
11 TraesCS1A01G333100 chr5B 98.064 2737 22 6 724 3459 339081373 339084079 0.000000e+00 4732
12 TraesCS1A01G333100 chr5B 79.372 732 134 14 2 721 666799550 666798824 1.850000e-137 499
13 TraesCS1A01G333100 chr5B 79.235 732 135 14 2 721 666824638 666823912 8.620000e-136 494
14 TraesCS1A01G333100 chr5B 78.367 735 134 21 2 718 666859435 666858708 1.460000e-123 453
15 TraesCS1A01G333100 chr2B 97.991 2737 20 6 724 3459 165276629 165279331 0.000000e+00 4717
16 TraesCS1A01G333100 chr6B 97.417 2749 20 6 724 3459 536839746 536837036 0.000000e+00 4636
17 TraesCS1A01G333100 chr3B 96.945 2750 18 6 724 3459 344147567 344144870 0.000000e+00 4553
18 TraesCS1A01G333100 chr6A 98.629 2407 17 2 724 3129 97398564 97396173 0.000000e+00 4248
19 TraesCS1A01G333100 chr4B 97.053 2002 11 2 1476 3459 451450953 451448982 0.000000e+00 3326
20 TraesCS1A01G333100 chr1D 90.041 723 65 6 1 721 426173657 426172940 0.000000e+00 929
21 TraesCS1A01G333100 chr7D 80.417 720 119 18 2 715 199355926 199356629 2.360000e-146 529
22 TraesCS1A01G333100 chrUn 80.552 689 109 18 8 691 137886558 137887226 1.110000e-139 507


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 TraesCS1A01G333100 chr1A 521284954 521288412 3458 True 6388 6388 100.000 1 3459 1 chr1A.!!$R2 3458
1 TraesCS1A01G333100 chr1A 500071694 500074427 2733 True 4942 4942 99.305 727 3459 1 chr1A.!!$R1 2732
2 TraesCS1A01G333100 chr4A 644769964 644772685 2721 True 4868 4868 98.867 724 3459 1 chr4A.!!$R1 2735
3 TraesCS1A01G333100 chr3A 23447067 23449794 2727 False 4857 4857 98.760 724 3459 1 chr3A.!!$F1 2735
4 TraesCS1A01G333100 chr3A 57275091 57277797 2706 True 4732 4732 98.064 724 3459 1 chr3A.!!$R1 2735
5 TraesCS1A01G333100 chr5A 69229827 69232549 2722 True 4854 4854 98.758 723 3459 1 chr5A.!!$R1 2736
6 TraesCS1A01G333100 chr5A 657271712 657272439 727 True 451 451 78.231 2 721 1 chr5A.!!$R2 719
7 TraesCS1A01G333100 chr7B 122624256 122626962 2706 False 4754 4754 98.210 724 3459 1 chr7B.!!$F1 2735
8 TraesCS1A01G333100 chr7B 476792716 476795153 2437 True 4268 4268 98.096 723 3189 1 chr7B.!!$R1 2466
9 TraesCS1A01G333100 chr7B 163488657 163489257 600 False 494 494 81.609 9 614 1 chr7B.!!$F2 605
10 TraesCS1A01G333100 chr7B 225408055 225408721 666 False 420 420 78.446 9 678 1 chr7B.!!$F3 669
11 TraesCS1A01G333100 chr5B 339081373 339084079 2706 False 4732 4732 98.064 724 3459 1 chr5B.!!$F1 2735
12 TraesCS1A01G333100 chr5B 666798824 666799550 726 True 499 499 79.372 2 721 1 chr5B.!!$R1 719
13 TraesCS1A01G333100 chr5B 666823912 666824638 726 True 494 494 79.235 2 721 1 chr5B.!!$R2 719
14 TraesCS1A01G333100 chr5B 666858708 666859435 727 True 453 453 78.367 2 718 1 chr5B.!!$R3 716
15 TraesCS1A01G333100 chr2B 165276629 165279331 2702 False 4717 4717 97.991 724 3459 1 chr2B.!!$F1 2735
16 TraesCS1A01G333100 chr6B 536837036 536839746 2710 True 4636 4636 97.417 724 3459 1 chr6B.!!$R1 2735
17 TraesCS1A01G333100 chr3B 344144870 344147567 2697 True 4553 4553 96.945 724 3459 1 chr3B.!!$R1 2735
18 TraesCS1A01G333100 chr6A 97396173 97398564 2391 True 4248 4248 98.629 724 3129 1 chr6A.!!$R1 2405
19 TraesCS1A01G333100 chr4B 451448982 451450953 1971 True 3326 3326 97.053 1476 3459 1 chr4B.!!$R1 1983
20 TraesCS1A01G333100 chr1D 426172940 426173657 717 True 929 929 90.041 1 721 1 chr1D.!!$R1 720
21 TraesCS1A01G333100 chr7D 199355926 199356629 703 False 529 529 80.417 2 715 1 chr7D.!!$F1 713
22 TraesCS1A01G333100 chrUn 137886558 137887226 668 False 507 507 80.552 8 691 1 chrUn.!!$F1 683

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
660 671 0.037303 TGAAAGCAAGGGAGAGCAGG 59.963 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2808 3079 7.888021 AGTTGTAATGGATCAAGTTGTAATGGA 59.112 33.333 2.11 0.0 0.0 3.41 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
48 49 4.556942 TCAAGTTGCAACATTGAGTGAG 57.443 40.909 30.11 6.07 0.00 3.51
94 101 5.582689 AGCAACAAGAAGCAAAACTTACT 57.417 34.783 0.00 0.00 39.29 2.24
168 177 3.305950 GCACCACAAAACTTCATATGGCA 60.306 43.478 2.13 0.00 0.00 4.92
181 190 1.985473 TATGGCATTGGAGATGGTGC 58.015 50.000 4.78 0.00 36.88 5.01
340 351 1.813753 CAGATACGGCCAACCACGG 60.814 63.158 2.24 0.00 34.57 4.94
373 384 4.116747 ACTCATTCTCAATCACCGAGTC 57.883 45.455 0.00 0.00 0.00 3.36
387 398 2.203938 AGTCCCCCACCATCGTGT 60.204 61.111 0.00 0.00 38.41 4.49
392 403 0.678684 CCCCCACCATCGTGTTTACC 60.679 60.000 0.00 0.00 38.41 2.85
419 430 7.637709 AGAAAACAACAAGAAGTTCAACAAC 57.362 32.000 5.50 0.00 38.74 3.32
420 431 7.206687 AGAAAACAACAAGAAGTTCAACAACA 58.793 30.769 5.50 0.00 38.74 3.33
421 432 7.708752 AGAAAACAACAAGAAGTTCAACAACAA 59.291 29.630 5.50 0.00 38.74 2.83
422 433 7.778470 AAACAACAAGAAGTTCAACAACAAA 57.222 28.000 5.50 0.00 38.74 2.83
423 434 7.778470 AACAACAAGAAGTTCAACAACAAAA 57.222 28.000 5.50 0.00 38.74 2.44
424 435 7.778470 ACAACAAGAAGTTCAACAACAAAAA 57.222 28.000 5.50 0.00 38.74 1.94
448 459 9.804758 AAAAACTCAATAACATTTAACCGAACA 57.195 25.926 0.00 0.00 0.00 3.18
449 460 8.791355 AAACTCAATAACATTTAACCGAACAC 57.209 30.769 0.00 0.00 0.00 3.32
450 461 7.499321 ACTCAATAACATTTAACCGAACACA 57.501 32.000 0.00 0.00 0.00 3.72
451 462 8.106247 ACTCAATAACATTTAACCGAACACAT 57.894 30.769 0.00 0.00 0.00 3.21
452 463 8.020819 ACTCAATAACATTTAACCGAACACATG 58.979 33.333 0.00 0.00 0.00 3.21
453 464 8.100508 TCAATAACATTTAACCGAACACATGA 57.899 30.769 0.00 0.00 0.00 3.07
454 465 8.018520 TCAATAACATTTAACCGAACACATGAC 58.981 33.333 0.00 0.00 0.00 3.06
455 466 4.398549 ACATTTAACCGAACACATGACG 57.601 40.909 0.00 0.00 0.00 4.35
456 467 4.059511 ACATTTAACCGAACACATGACGA 58.940 39.130 0.00 0.00 0.00 4.20
457 468 4.151689 ACATTTAACCGAACACATGACGAG 59.848 41.667 0.00 0.00 0.00 4.18
458 469 1.705256 TAACCGAACACATGACGAGC 58.295 50.000 0.00 0.00 0.00 5.03
459 470 1.282248 AACCGAACACATGACGAGCG 61.282 55.000 0.00 0.00 0.00 5.03
460 471 1.733041 CCGAACACATGACGAGCGT 60.733 57.895 0.00 0.00 0.00 5.07
461 472 1.412226 CGAACACATGACGAGCGTG 59.588 57.895 0.00 0.00 39.48 5.34
462 473 1.781555 GAACACATGACGAGCGTGG 59.218 57.895 0.00 0.00 37.85 4.94
463 474 0.944311 GAACACATGACGAGCGTGGT 60.944 55.000 0.00 0.00 37.85 4.16
464 475 1.221466 AACACATGACGAGCGTGGTG 61.221 55.000 0.00 8.63 37.85 4.17
465 476 1.664649 CACATGACGAGCGTGGTGT 60.665 57.895 0.00 2.24 37.85 4.16
466 477 1.372997 ACATGACGAGCGTGGTGTC 60.373 57.895 0.00 0.00 37.85 3.67
467 478 2.094659 CATGACGAGCGTGGTGTCC 61.095 63.158 0.00 0.00 0.00 4.02
468 479 2.570284 ATGACGAGCGTGGTGTCCA 61.570 57.895 0.00 0.00 0.00 4.02
493 504 2.432628 CGGTGTCGTCAAGGGAGC 60.433 66.667 0.00 0.00 0.00 4.70
494 505 2.432628 GGTGTCGTCAAGGGAGCG 60.433 66.667 0.00 0.00 0.00 5.03
495 506 2.432628 GTGTCGTCAAGGGAGCGG 60.433 66.667 0.00 0.00 0.00 5.52
496 507 2.599281 TGTCGTCAAGGGAGCGGA 60.599 61.111 0.00 0.00 0.00 5.54
497 508 2.182030 GTCGTCAAGGGAGCGGAG 59.818 66.667 0.00 0.00 0.00 4.63
498 509 3.068691 TCGTCAAGGGAGCGGAGG 61.069 66.667 0.00 0.00 0.00 4.30
499 510 4.148825 CGTCAAGGGAGCGGAGGG 62.149 72.222 0.00 0.00 0.00 4.30
500 511 3.003763 GTCAAGGGAGCGGAGGGT 61.004 66.667 0.00 0.00 0.00 4.34
501 512 1.684734 GTCAAGGGAGCGGAGGGTA 60.685 63.158 0.00 0.00 0.00 3.69
502 513 1.684734 TCAAGGGAGCGGAGGGTAC 60.685 63.158 0.00 0.00 0.00 3.34
516 527 3.249687 GGTACCTGGTTGCAGAAGG 57.750 57.895 3.84 9.25 37.11 3.46
517 528 0.690762 GGTACCTGGTTGCAGAAGGA 59.309 55.000 15.95 0.69 34.97 3.36
518 529 1.282157 GGTACCTGGTTGCAGAAGGAT 59.718 52.381 15.95 5.49 34.97 3.24
519 530 2.633488 GTACCTGGTTGCAGAAGGATC 58.367 52.381 15.95 6.62 34.97 3.36
520 531 0.329596 ACCTGGTTGCAGAAGGATCC 59.670 55.000 15.95 2.48 34.97 3.36
521 532 0.622665 CCTGGTTGCAGAAGGATCCT 59.377 55.000 9.02 9.02 32.43 3.24
522 533 1.839994 CCTGGTTGCAGAAGGATCCTA 59.160 52.381 16.55 0.00 32.43 2.94
523 534 2.158842 CCTGGTTGCAGAAGGATCCTAG 60.159 54.545 16.55 9.53 32.43 3.02
524 535 1.839994 TGGTTGCAGAAGGATCCTAGG 59.160 52.381 16.55 8.77 0.00 3.02
525 536 1.840635 GGTTGCAGAAGGATCCTAGGT 59.159 52.381 16.55 0.00 0.00 3.08
526 537 2.420687 GGTTGCAGAAGGATCCTAGGTG 60.421 54.545 16.55 13.63 0.00 4.00
527 538 1.500474 TGCAGAAGGATCCTAGGTGG 58.500 55.000 16.55 4.61 37.10 4.61
535 546 3.384348 TCCTAGGTGGACGGCAAC 58.616 61.111 9.08 0.00 40.56 4.17
547 558 3.574780 GGCAACGTAGTCCAAGGC 58.425 61.111 0.00 0.00 45.00 4.35
548 559 2.388232 GGCAACGTAGTCCAAGGCG 61.388 63.158 0.00 0.00 45.00 5.52
549 560 2.388232 GCAACGTAGTCCAAGGCGG 61.388 63.158 0.00 0.00 45.00 6.13
550 561 1.740296 CAACGTAGTCCAAGGCGGG 60.740 63.158 0.00 0.00 45.00 6.13
551 562 3.600898 AACGTAGTCCAAGGCGGGC 62.601 63.158 0.00 0.00 45.00 6.13
552 563 4.077184 CGTAGTCCAAGGCGGGCA 62.077 66.667 3.78 0.00 44.49 5.36
553 564 2.125106 GTAGTCCAAGGCGGGCAG 60.125 66.667 3.78 0.00 44.49 4.85
554 565 3.399181 TAGTCCAAGGCGGGCAGG 61.399 66.667 3.78 5.49 44.49 4.85
574 585 2.039299 CATGGGTGGGGGTTGCAT 59.961 61.111 0.00 0.00 0.00 3.96
575 586 1.309347 CATGGGTGGGGGTTGCATA 59.691 57.895 0.00 0.00 0.00 3.14
576 587 0.105555 CATGGGTGGGGGTTGCATAT 60.106 55.000 0.00 0.00 0.00 1.78
577 588 0.105555 ATGGGTGGGGGTTGCATATG 60.106 55.000 0.00 0.00 0.00 1.78
578 589 1.309688 GGGTGGGGGTTGCATATGT 59.690 57.895 4.29 0.00 0.00 2.29
579 590 0.755327 GGGTGGGGGTTGCATATGTC 60.755 60.000 4.29 0.00 0.00 3.06
580 591 0.258774 GGTGGGGGTTGCATATGTCT 59.741 55.000 4.29 0.00 0.00 3.41
581 592 1.392589 GTGGGGGTTGCATATGTCTG 58.607 55.000 4.29 0.00 0.00 3.51
582 593 1.064758 GTGGGGGTTGCATATGTCTGA 60.065 52.381 4.29 0.00 0.00 3.27
583 594 1.212688 TGGGGGTTGCATATGTCTGAG 59.787 52.381 4.29 0.00 0.00 3.35
584 595 1.477558 GGGGGTTGCATATGTCTGAGG 60.478 57.143 4.29 0.00 0.00 3.86
585 596 1.490490 GGGGTTGCATATGTCTGAGGA 59.510 52.381 4.29 0.00 0.00 3.71
586 597 2.107204 GGGGTTGCATATGTCTGAGGAT 59.893 50.000 4.29 0.00 0.00 3.24
587 598 3.144506 GGGTTGCATATGTCTGAGGATG 58.855 50.000 4.29 0.00 0.00 3.51
588 599 3.144506 GGTTGCATATGTCTGAGGATGG 58.855 50.000 4.29 0.00 0.00 3.51
589 600 2.551459 GTTGCATATGTCTGAGGATGGC 59.449 50.000 4.29 0.00 0.00 4.40
590 601 2.052468 TGCATATGTCTGAGGATGGCT 58.948 47.619 4.29 0.00 0.00 4.75
591 602 2.224450 TGCATATGTCTGAGGATGGCTG 60.224 50.000 4.29 0.00 0.00 4.85
592 603 2.874861 GCATATGTCTGAGGATGGCTGG 60.875 54.545 4.29 0.00 0.00 4.85
593 604 1.427809 TATGTCTGAGGATGGCTGGG 58.572 55.000 0.00 0.00 0.00 4.45
594 605 0.622738 ATGTCTGAGGATGGCTGGGT 60.623 55.000 0.00 0.00 0.00 4.51
595 606 1.222936 GTCTGAGGATGGCTGGGTG 59.777 63.158 0.00 0.00 0.00 4.61
596 607 1.997311 TCTGAGGATGGCTGGGTGG 60.997 63.158 0.00 0.00 0.00 4.61
597 608 3.711059 CTGAGGATGGCTGGGTGGC 62.711 68.421 0.00 0.00 42.18 5.01
598 609 4.864334 GAGGATGGCTGGGTGGCG 62.864 72.222 0.00 0.00 45.14 5.69
600 611 4.424711 GGATGGCTGGGTGGCGAA 62.425 66.667 0.00 0.00 45.14 4.70
601 612 3.134127 GATGGCTGGGTGGCGAAC 61.134 66.667 0.00 0.00 45.14 3.95
605 616 3.423154 GCTGGGTGGCGAACGAAG 61.423 66.667 0.00 0.00 0.00 3.79
606 617 2.342279 CTGGGTGGCGAACGAAGA 59.658 61.111 0.00 0.00 0.00 2.87
607 618 1.738099 CTGGGTGGCGAACGAAGAG 60.738 63.158 0.00 0.00 0.00 2.85
608 619 2.434359 GGGTGGCGAACGAAGAGG 60.434 66.667 0.00 0.00 0.00 3.69
609 620 2.342648 GGTGGCGAACGAAGAGGT 59.657 61.111 0.00 0.00 0.00 3.85
610 621 1.588082 GGTGGCGAACGAAGAGGTA 59.412 57.895 0.00 0.00 0.00 3.08
611 622 0.735287 GGTGGCGAACGAAGAGGTAC 60.735 60.000 0.00 0.00 0.00 3.34
612 623 0.038892 GTGGCGAACGAAGAGGTACA 60.039 55.000 0.00 0.00 0.00 2.90
613 624 0.675083 TGGCGAACGAAGAGGTACAA 59.325 50.000 0.00 0.00 0.00 2.41
614 625 1.068895 TGGCGAACGAAGAGGTACAAA 59.931 47.619 0.00 0.00 0.00 2.83
615 626 1.725164 GGCGAACGAAGAGGTACAAAG 59.275 52.381 0.00 0.00 0.00 2.77
616 627 1.725164 GCGAACGAAGAGGTACAAAGG 59.275 52.381 0.00 0.00 0.00 3.11
617 628 2.865276 GCGAACGAAGAGGTACAAAGGT 60.865 50.000 0.00 0.00 0.00 3.50
618 629 2.729882 CGAACGAAGAGGTACAAAGGTG 59.270 50.000 0.00 0.00 0.00 4.00
619 630 2.833631 ACGAAGAGGTACAAAGGTGG 57.166 50.000 0.00 0.00 0.00 4.61
620 631 1.270678 ACGAAGAGGTACAAAGGTGGC 60.271 52.381 0.00 0.00 0.00 5.01
621 632 1.439679 GAAGAGGTACAAAGGTGGCG 58.560 55.000 0.00 0.00 0.00 5.69
622 633 0.605589 AAGAGGTACAAAGGTGGCGC 60.606 55.000 0.00 0.00 0.00 6.53
623 634 2.358247 AGGTACAAAGGTGGCGCG 60.358 61.111 0.00 0.00 0.00 6.86
624 635 3.428282 GGTACAAAGGTGGCGCGG 61.428 66.667 8.83 0.00 0.00 6.46
625 636 2.357760 GTACAAAGGTGGCGCGGA 60.358 61.111 8.83 0.00 0.00 5.54
626 637 2.357760 TACAAAGGTGGCGCGGAC 60.358 61.111 8.83 0.00 0.00 4.79
637 648 4.052229 CGCGGACGAGGAAGGTGT 62.052 66.667 0.00 0.00 43.93 4.16
638 649 2.432628 GCGGACGAGGAAGGTGTG 60.433 66.667 0.00 0.00 0.00 3.82
639 650 2.261671 CGGACGAGGAAGGTGTGG 59.738 66.667 0.00 0.00 0.00 4.17
640 651 2.273179 CGGACGAGGAAGGTGTGGA 61.273 63.158 0.00 0.00 0.00 4.02
641 652 1.605058 CGGACGAGGAAGGTGTGGAT 61.605 60.000 0.00 0.00 0.00 3.41
642 653 0.108138 GGACGAGGAAGGTGTGGATG 60.108 60.000 0.00 0.00 0.00 3.51
643 654 0.895530 GACGAGGAAGGTGTGGATGA 59.104 55.000 0.00 0.00 0.00 2.92
644 655 1.275291 GACGAGGAAGGTGTGGATGAA 59.725 52.381 0.00 0.00 0.00 2.57
645 656 1.697432 ACGAGGAAGGTGTGGATGAAA 59.303 47.619 0.00 0.00 0.00 2.69
646 657 2.289694 ACGAGGAAGGTGTGGATGAAAG 60.290 50.000 0.00 0.00 0.00 2.62
647 658 2.087646 GAGGAAGGTGTGGATGAAAGC 58.912 52.381 0.00 0.00 0.00 3.51
648 659 1.425066 AGGAAGGTGTGGATGAAAGCA 59.575 47.619 0.00 0.00 0.00 3.91
649 660 2.158475 AGGAAGGTGTGGATGAAAGCAA 60.158 45.455 0.00 0.00 0.00 3.91
650 661 2.229784 GGAAGGTGTGGATGAAAGCAAG 59.770 50.000 0.00 0.00 0.00 4.01
651 662 1.915141 AGGTGTGGATGAAAGCAAGG 58.085 50.000 0.00 0.00 0.00 3.61
652 663 0.890683 GGTGTGGATGAAAGCAAGGG 59.109 55.000 0.00 0.00 0.00 3.95
653 664 1.547675 GGTGTGGATGAAAGCAAGGGA 60.548 52.381 0.00 0.00 0.00 4.20
654 665 1.815003 GTGTGGATGAAAGCAAGGGAG 59.185 52.381 0.00 0.00 0.00 4.30
655 666 1.704628 TGTGGATGAAAGCAAGGGAGA 59.295 47.619 0.00 0.00 0.00 3.71
656 667 2.290514 TGTGGATGAAAGCAAGGGAGAG 60.291 50.000 0.00 0.00 0.00 3.20
657 668 1.340405 TGGATGAAAGCAAGGGAGAGC 60.340 52.381 0.00 0.00 0.00 4.09
658 669 1.340405 GGATGAAAGCAAGGGAGAGCA 60.340 52.381 0.00 0.00 0.00 4.26
659 670 2.015587 GATGAAAGCAAGGGAGAGCAG 58.984 52.381 0.00 0.00 0.00 4.24
660 671 0.037303 TGAAAGCAAGGGAGAGCAGG 59.963 55.000 0.00 0.00 0.00 4.85
661 672 0.679321 GAAAGCAAGGGAGAGCAGGG 60.679 60.000 0.00 0.00 0.00 4.45
662 673 1.136329 AAAGCAAGGGAGAGCAGGGA 61.136 55.000 0.00 0.00 0.00 4.20
663 674 1.136329 AAGCAAGGGAGAGCAGGGAA 61.136 55.000 0.00 0.00 0.00 3.97
664 675 1.077858 GCAAGGGAGAGCAGGGAAG 60.078 63.158 0.00 0.00 0.00 3.46
665 676 1.557269 GCAAGGGAGAGCAGGGAAGA 61.557 60.000 0.00 0.00 0.00 2.87
666 677 0.540923 CAAGGGAGAGCAGGGAAGAG 59.459 60.000 0.00 0.00 0.00 2.85
667 678 0.118144 AAGGGAGAGCAGGGAAGAGT 59.882 55.000 0.00 0.00 0.00 3.24
668 679 0.617249 AGGGAGAGCAGGGAAGAGTG 60.617 60.000 0.00 0.00 0.00 3.51
669 680 1.220477 GGAGAGCAGGGAAGAGTGC 59.780 63.158 0.00 0.00 40.17 4.40
670 681 1.548357 GGAGAGCAGGGAAGAGTGCA 61.548 60.000 0.00 0.00 42.47 4.57
671 682 0.322975 GAGAGCAGGGAAGAGTGCAA 59.677 55.000 0.00 0.00 42.47 4.08
672 683 0.324285 AGAGCAGGGAAGAGTGCAAG 59.676 55.000 0.00 0.00 42.47 4.01
673 684 0.322975 GAGCAGGGAAGAGTGCAAGA 59.677 55.000 0.00 0.00 42.47 3.02
674 685 0.767375 AGCAGGGAAGAGTGCAAGAA 59.233 50.000 0.00 0.00 42.47 2.52
675 686 1.143684 AGCAGGGAAGAGTGCAAGAAA 59.856 47.619 0.00 0.00 42.47 2.52
676 687 1.956477 GCAGGGAAGAGTGCAAGAAAA 59.044 47.619 0.00 0.00 39.62 2.29
677 688 2.030451 GCAGGGAAGAGTGCAAGAAAAG 60.030 50.000 0.00 0.00 39.62 2.27
678 689 2.030451 CAGGGAAGAGTGCAAGAAAAGC 60.030 50.000 0.00 0.00 0.00 3.51
679 690 1.068954 GGGAAGAGTGCAAGAAAAGCG 60.069 52.381 0.00 0.00 33.85 4.68
680 691 1.873591 GGAAGAGTGCAAGAAAAGCGA 59.126 47.619 0.00 0.00 33.85 4.93
681 692 2.290641 GGAAGAGTGCAAGAAAAGCGAA 59.709 45.455 0.00 0.00 33.85 4.70
682 693 3.292423 GAAGAGTGCAAGAAAAGCGAAC 58.708 45.455 0.00 0.00 33.85 3.95
683 694 1.604278 AGAGTGCAAGAAAAGCGAACC 59.396 47.619 0.00 0.00 33.85 3.62
684 695 1.333619 GAGTGCAAGAAAAGCGAACCA 59.666 47.619 0.00 0.00 33.85 3.67
685 696 1.334869 AGTGCAAGAAAAGCGAACCAG 59.665 47.619 0.00 0.00 33.85 4.00
686 697 1.333619 GTGCAAGAAAAGCGAACCAGA 59.666 47.619 0.00 0.00 33.85 3.86
687 698 2.020720 TGCAAGAAAAGCGAACCAGAA 58.979 42.857 0.00 0.00 33.85 3.02
688 699 2.033299 TGCAAGAAAAGCGAACCAGAAG 59.967 45.455 0.00 0.00 33.85 2.85
689 700 2.605580 GCAAGAAAAGCGAACCAGAAGG 60.606 50.000 0.00 0.00 42.21 3.46
690 701 2.878406 CAAGAAAAGCGAACCAGAAGGA 59.122 45.455 0.00 0.00 38.69 3.36
691 702 2.772287 AGAAAAGCGAACCAGAAGGAG 58.228 47.619 0.00 0.00 38.69 3.69
692 703 1.807142 GAAAAGCGAACCAGAAGGAGG 59.193 52.381 0.00 0.00 38.69 4.30
693 704 1.056660 AAAGCGAACCAGAAGGAGGA 58.943 50.000 0.00 0.00 38.69 3.71
694 705 1.280457 AAGCGAACCAGAAGGAGGAT 58.720 50.000 0.00 0.00 38.69 3.24
695 706 1.280457 AGCGAACCAGAAGGAGGATT 58.720 50.000 0.00 0.00 38.69 3.01
696 707 1.630878 AGCGAACCAGAAGGAGGATTT 59.369 47.619 0.00 0.00 38.69 2.17
697 708 2.838202 AGCGAACCAGAAGGAGGATTTA 59.162 45.455 0.00 0.00 38.69 1.40
698 709 3.263425 AGCGAACCAGAAGGAGGATTTAA 59.737 43.478 0.00 0.00 38.69 1.52
699 710 3.623510 GCGAACCAGAAGGAGGATTTAAG 59.376 47.826 0.00 0.00 38.69 1.85
700 711 4.833390 CGAACCAGAAGGAGGATTTAAGT 58.167 43.478 0.00 0.00 38.69 2.24
701 712 5.626116 GCGAACCAGAAGGAGGATTTAAGTA 60.626 44.000 0.00 0.00 38.69 2.24
702 713 6.043411 CGAACCAGAAGGAGGATTTAAGTAG 58.957 44.000 0.00 0.00 38.69 2.57
703 714 5.959583 ACCAGAAGGAGGATTTAAGTAGG 57.040 43.478 0.00 0.00 38.69 3.18
704 715 4.164413 ACCAGAAGGAGGATTTAAGTAGGC 59.836 45.833 0.00 0.00 38.69 3.93
705 716 4.164221 CCAGAAGGAGGATTTAAGTAGGCA 59.836 45.833 0.00 0.00 36.89 4.75
706 717 5.339200 CCAGAAGGAGGATTTAAGTAGGCAA 60.339 44.000 0.00 0.00 36.89 4.52
707 718 5.819901 CAGAAGGAGGATTTAAGTAGGCAAG 59.180 44.000 0.00 0.00 0.00 4.01
708 719 4.779993 AGGAGGATTTAAGTAGGCAAGG 57.220 45.455 0.00 0.00 0.00 3.61
709 720 3.459969 AGGAGGATTTAAGTAGGCAAGGG 59.540 47.826 0.00 0.00 0.00 3.95
710 721 3.435169 GGAGGATTTAAGTAGGCAAGGGG 60.435 52.174 0.00 0.00 0.00 4.79
711 722 3.198827 AGGATTTAAGTAGGCAAGGGGT 58.801 45.455 0.00 0.00 0.00 4.95
712 723 3.053619 AGGATTTAAGTAGGCAAGGGGTG 60.054 47.826 0.00 0.00 0.00 4.61
713 724 3.308904 GGATTTAAGTAGGCAAGGGGTGT 60.309 47.826 0.00 0.00 0.00 4.16
714 725 3.428413 TTTAAGTAGGCAAGGGGTGTC 57.572 47.619 0.00 0.00 0.00 3.67
715 726 2.032965 TAAGTAGGCAAGGGGTGTCA 57.967 50.000 0.00 0.00 32.63 3.58
716 727 0.693049 AAGTAGGCAAGGGGTGTCAG 59.307 55.000 0.00 0.00 32.63 3.51
717 728 0.178903 AGTAGGCAAGGGGTGTCAGA 60.179 55.000 0.00 0.00 32.63 3.27
718 729 0.250513 GTAGGCAAGGGGTGTCAGAG 59.749 60.000 0.00 0.00 32.63 3.35
719 730 0.178903 TAGGCAAGGGGTGTCAGAGT 60.179 55.000 0.00 0.00 32.63 3.24
720 731 1.003233 GGCAAGGGGTGTCAGAGTC 60.003 63.158 0.00 0.00 0.00 3.36
721 732 1.374758 GCAAGGGGTGTCAGAGTCG 60.375 63.158 0.00 0.00 0.00 4.18
1334 1353 1.209019 AGCTGGATGTGATGTCTCCAC 59.791 52.381 0.00 0.00 35.29 4.02
1448 1467 7.368198 TGTATTGTAGGATTGTAGGCATACA 57.632 36.000 7.21 7.21 40.18 2.29
1449 1468 7.973402 TGTATTGTAGGATTGTAGGCATACAT 58.027 34.615 12.63 2.72 41.49 2.29
1644 1681 6.775629 TGCTCCTCTTGTTAAATTTAGTGGTT 59.224 34.615 0.00 0.00 0.00 3.67
2805 3076 9.167311 GATAACTTCACTGATCCATTACAACTT 57.833 33.333 0.00 0.00 0.00 2.66
2806 3077 6.808008 ACTTCACTGATCCATTACAACTTG 57.192 37.500 0.00 0.00 0.00 3.16
2807 3078 6.533730 ACTTCACTGATCCATTACAACTTGA 58.466 36.000 0.00 0.00 0.00 3.02
2808 3079 7.170965 ACTTCACTGATCCATTACAACTTGAT 58.829 34.615 0.00 0.00 0.00 2.57
2809 3080 7.335422 ACTTCACTGATCCATTACAACTTGATC 59.665 37.037 0.00 0.00 33.96 2.92
2810 3081 6.115446 TCACTGATCCATTACAACTTGATCC 58.885 40.000 0.00 0.00 32.70 3.36
2811 3082 5.882000 CACTGATCCATTACAACTTGATCCA 59.118 40.000 0.00 0.00 32.70 3.41
2812 3083 6.544931 CACTGATCCATTACAACTTGATCCAT 59.455 38.462 0.00 0.00 32.70 3.41
2813 3084 7.067859 CACTGATCCATTACAACTTGATCCATT 59.932 37.037 0.00 0.00 32.70 3.16
2814 3085 8.274322 ACTGATCCATTACAACTTGATCCATTA 58.726 33.333 0.00 0.00 32.70 1.90
2815 3086 8.450578 TGATCCATTACAACTTGATCCATTAC 57.549 34.615 0.00 0.00 32.70 1.89
2816 3087 8.052141 TGATCCATTACAACTTGATCCATTACA 58.948 33.333 0.00 0.00 32.70 2.41
2817 3088 8.821686 ATCCATTACAACTTGATCCATTACAA 57.178 30.769 0.00 0.00 0.00 2.41
2818 3089 8.050778 TCCATTACAACTTGATCCATTACAAC 57.949 34.615 0.00 0.00 0.00 3.32
2819 3090 7.888021 TCCATTACAACTTGATCCATTACAACT 59.112 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 101 0.832135 GCCCCTCGACCATGGAGATA 60.832 60.000 21.47 0.00 33.27 1.98
181 190 1.134487 CGCTAACGCATTGGTGGTG 59.866 57.895 0.00 0.00 35.30 4.17
340 351 1.532868 AGAATGAGTTGTTGTGCGAGC 59.467 47.619 0.00 0.00 0.00 5.03
387 398 8.584063 AACTTCTTGTTGTTTTCTAGGGTAAA 57.416 30.769 0.00 0.00 37.52 2.01
392 403 7.535139 TGTTGAACTTCTTGTTGTTTTCTAGG 58.465 34.615 0.00 0.00 39.30 3.02
422 433 9.804758 TGTTCGGTTAAATGTTATTGAGTTTTT 57.195 25.926 0.00 0.00 0.00 1.94
423 434 9.240159 GTGTTCGGTTAAATGTTATTGAGTTTT 57.760 29.630 0.00 0.00 0.00 2.43
424 435 8.407064 TGTGTTCGGTTAAATGTTATTGAGTTT 58.593 29.630 0.00 0.00 0.00 2.66
425 436 7.932335 TGTGTTCGGTTAAATGTTATTGAGTT 58.068 30.769 0.00 0.00 0.00 3.01
426 437 7.499321 TGTGTTCGGTTAAATGTTATTGAGT 57.501 32.000 0.00 0.00 0.00 3.41
427 438 8.233868 TCATGTGTTCGGTTAAATGTTATTGAG 58.766 33.333 0.00 0.00 0.00 3.02
428 439 8.018520 GTCATGTGTTCGGTTAAATGTTATTGA 58.981 33.333 0.00 0.00 0.00 2.57
429 440 7.007009 CGTCATGTGTTCGGTTAAATGTTATTG 59.993 37.037 0.00 0.00 0.00 1.90
430 441 7.018826 CGTCATGTGTTCGGTTAAATGTTATT 58.981 34.615 0.00 0.00 0.00 1.40
431 442 6.369340 TCGTCATGTGTTCGGTTAAATGTTAT 59.631 34.615 0.00 0.00 0.00 1.89
432 443 5.695363 TCGTCATGTGTTCGGTTAAATGTTA 59.305 36.000 0.00 0.00 0.00 2.41
433 444 4.512198 TCGTCATGTGTTCGGTTAAATGTT 59.488 37.500 0.00 0.00 0.00 2.71
434 445 4.059511 TCGTCATGTGTTCGGTTAAATGT 58.940 39.130 0.00 0.00 0.00 2.71
435 446 4.637968 CTCGTCATGTGTTCGGTTAAATG 58.362 43.478 0.00 0.00 0.00 2.32
436 447 3.124636 GCTCGTCATGTGTTCGGTTAAAT 59.875 43.478 0.00 0.00 0.00 1.40
437 448 2.477375 GCTCGTCATGTGTTCGGTTAAA 59.523 45.455 0.00 0.00 0.00 1.52
438 449 2.063266 GCTCGTCATGTGTTCGGTTAA 58.937 47.619 0.00 0.00 0.00 2.01
439 450 1.705256 GCTCGTCATGTGTTCGGTTA 58.295 50.000 0.00 0.00 0.00 2.85
440 451 1.282248 CGCTCGTCATGTGTTCGGTT 61.282 55.000 0.00 0.00 0.00 4.44
441 452 1.733041 CGCTCGTCATGTGTTCGGT 60.733 57.895 0.00 0.00 0.00 4.69
442 453 1.733041 ACGCTCGTCATGTGTTCGG 60.733 57.895 0.00 0.00 0.00 4.30
443 454 1.412226 CACGCTCGTCATGTGTTCG 59.588 57.895 0.00 0.00 0.00 3.95
444 455 0.944311 ACCACGCTCGTCATGTGTTC 60.944 55.000 0.00 0.00 31.75 3.18
445 456 1.069090 ACCACGCTCGTCATGTGTT 59.931 52.632 0.00 0.00 31.75 3.32
446 457 1.664649 CACCACGCTCGTCATGTGT 60.665 57.895 0.00 0.00 31.75 3.72
447 458 1.617755 GACACCACGCTCGTCATGTG 61.618 60.000 11.37 11.69 0.00 3.21
448 459 1.372997 GACACCACGCTCGTCATGT 60.373 57.895 7.53 7.53 0.00 3.21
449 460 2.094659 GGACACCACGCTCGTCATG 61.095 63.158 0.00 0.00 0.00 3.07
450 461 2.261671 GGACACCACGCTCGTCAT 59.738 61.111 0.00 0.00 0.00 3.06
451 462 3.220658 TGGACACCACGCTCGTCA 61.221 61.111 0.00 0.00 0.00 4.35
452 463 2.733593 GTGGACACCACGCTCGTC 60.734 66.667 5.17 0.00 44.95 4.20
476 487 2.432628 GCTCCCTTGACGACACCG 60.433 66.667 0.00 0.00 42.50 4.94
477 488 2.432628 CGCTCCCTTGACGACACC 60.433 66.667 0.00 0.00 0.00 4.16
478 489 2.432628 CCGCTCCCTTGACGACAC 60.433 66.667 0.00 0.00 0.00 3.67
479 490 2.599281 TCCGCTCCCTTGACGACA 60.599 61.111 0.00 0.00 0.00 4.35
480 491 2.182030 CTCCGCTCCCTTGACGAC 59.818 66.667 0.00 0.00 0.00 4.34
481 492 3.068691 CCTCCGCTCCCTTGACGA 61.069 66.667 0.00 0.00 0.00 4.20
482 493 4.148825 CCCTCCGCTCCCTTGACG 62.149 72.222 0.00 0.00 0.00 4.35
483 494 1.684734 TACCCTCCGCTCCCTTGAC 60.685 63.158 0.00 0.00 0.00 3.18
484 495 1.684734 GTACCCTCCGCTCCCTTGA 60.685 63.158 0.00 0.00 0.00 3.02
485 496 2.732619 GGTACCCTCCGCTCCCTTG 61.733 68.421 0.00 0.00 0.00 3.61
486 497 2.365237 GGTACCCTCCGCTCCCTT 60.365 66.667 0.00 0.00 0.00 3.95
487 498 3.357082 AGGTACCCTCCGCTCCCT 61.357 66.667 8.74 0.00 0.00 4.20
488 499 3.155167 CAGGTACCCTCCGCTCCC 61.155 72.222 8.74 0.00 0.00 4.30
489 500 3.155167 CCAGGTACCCTCCGCTCC 61.155 72.222 8.74 0.00 0.00 4.70
490 501 1.988406 AACCAGGTACCCTCCGCTC 60.988 63.158 8.74 0.00 0.00 5.03
491 502 2.122056 AACCAGGTACCCTCCGCT 59.878 61.111 8.74 0.00 0.00 5.52
492 503 2.267961 CAACCAGGTACCCTCCGC 59.732 66.667 8.74 0.00 0.00 5.54
493 504 2.267961 GCAACCAGGTACCCTCCG 59.732 66.667 8.74 0.00 0.00 4.63
494 505 1.198759 TCTGCAACCAGGTACCCTCC 61.199 60.000 8.74 0.00 39.61 4.30
495 506 0.690762 TTCTGCAACCAGGTACCCTC 59.309 55.000 8.74 0.00 39.61 4.30
496 507 0.693049 CTTCTGCAACCAGGTACCCT 59.307 55.000 8.74 0.00 39.61 4.34
497 508 0.322546 CCTTCTGCAACCAGGTACCC 60.323 60.000 8.74 0.00 39.61 3.69
498 509 0.690762 TCCTTCTGCAACCAGGTACC 59.309 55.000 2.73 2.73 39.61 3.34
499 510 2.633488 GATCCTTCTGCAACCAGGTAC 58.367 52.381 0.00 0.00 39.61 3.34
500 511 1.559682 GGATCCTTCTGCAACCAGGTA 59.440 52.381 3.84 0.00 39.61 3.08
501 512 0.329596 GGATCCTTCTGCAACCAGGT 59.670 55.000 3.84 0.00 39.61 4.00
502 513 0.622665 AGGATCCTTCTGCAACCAGG 59.377 55.000 9.02 0.00 39.61 4.45
503 514 2.158842 CCTAGGATCCTTCTGCAACCAG 60.159 54.545 22.03 7.52 40.54 4.00
504 515 1.839994 CCTAGGATCCTTCTGCAACCA 59.160 52.381 22.03 0.00 0.00 3.67
505 516 1.840635 ACCTAGGATCCTTCTGCAACC 59.159 52.381 22.03 0.00 0.00 3.77
506 517 2.420687 CCACCTAGGATCCTTCTGCAAC 60.421 54.545 22.03 0.00 41.22 4.17
507 518 1.839994 CCACCTAGGATCCTTCTGCAA 59.160 52.381 22.03 0.00 41.22 4.08
508 519 1.008327 TCCACCTAGGATCCTTCTGCA 59.992 52.381 22.03 0.00 43.07 4.41
509 520 1.794714 TCCACCTAGGATCCTTCTGC 58.205 55.000 22.03 0.00 43.07 4.26
518 529 2.642254 CGTTGCCGTCCACCTAGGA 61.642 63.158 17.98 0.00 46.75 2.94
519 530 1.597797 TACGTTGCCGTCCACCTAGG 61.598 60.000 7.41 7.41 46.28 3.02
520 531 0.179145 CTACGTTGCCGTCCACCTAG 60.179 60.000 0.00 0.00 46.28 3.02
521 532 0.895100 ACTACGTTGCCGTCCACCTA 60.895 55.000 0.00 0.00 46.28 3.08
522 533 2.151049 GACTACGTTGCCGTCCACCT 62.151 60.000 0.00 0.00 46.28 4.00
523 534 1.735559 GACTACGTTGCCGTCCACC 60.736 63.158 0.00 0.00 46.28 4.61
524 535 1.735559 GGACTACGTTGCCGTCCAC 60.736 63.158 16.31 0.00 46.28 4.02
525 536 2.652530 GGACTACGTTGCCGTCCA 59.347 61.111 16.31 0.00 46.28 4.02
526 537 1.005867 TTGGACTACGTTGCCGTCC 60.006 57.895 15.05 15.05 46.28 4.79
527 538 1.012486 CCTTGGACTACGTTGCCGTC 61.012 60.000 0.00 0.00 46.28 4.79
529 540 2.388232 GCCTTGGACTACGTTGCCG 61.388 63.158 0.00 0.00 40.83 5.69
530 541 2.388232 CGCCTTGGACTACGTTGCC 61.388 63.158 0.00 0.00 0.00 4.52
531 542 2.388232 CCGCCTTGGACTACGTTGC 61.388 63.158 0.00 0.00 42.00 4.17
532 543 1.740296 CCCGCCTTGGACTACGTTG 60.740 63.158 0.00 0.00 42.00 4.10
533 544 2.660802 CCCGCCTTGGACTACGTT 59.339 61.111 0.00 0.00 42.00 3.99
534 545 4.078516 GCCCGCCTTGGACTACGT 62.079 66.667 0.00 0.00 42.00 3.57
535 546 4.077184 TGCCCGCCTTGGACTACG 62.077 66.667 0.00 0.00 42.00 3.51
536 547 2.125106 CTGCCCGCCTTGGACTAC 60.125 66.667 0.00 0.00 42.00 2.73
537 548 3.399181 CCTGCCCGCCTTGGACTA 61.399 66.667 0.00 0.00 42.00 2.59
556 567 2.870035 TATGCAACCCCCACCCATGC 62.870 60.000 0.00 0.00 37.52 4.06
557 568 0.105555 ATATGCAACCCCCACCCATG 60.106 55.000 0.00 0.00 0.00 3.66
558 569 0.105555 CATATGCAACCCCCACCCAT 60.106 55.000 0.00 0.00 0.00 4.00
559 570 1.309347 CATATGCAACCCCCACCCA 59.691 57.895 0.00 0.00 0.00 4.51
560 571 0.755327 GACATATGCAACCCCCACCC 60.755 60.000 1.58 0.00 0.00 4.61
561 572 0.258774 AGACATATGCAACCCCCACC 59.741 55.000 1.58 0.00 0.00 4.61
562 573 1.064758 TCAGACATATGCAACCCCCAC 60.065 52.381 1.58 0.00 0.00 4.61
563 574 1.212688 CTCAGACATATGCAACCCCCA 59.787 52.381 1.58 0.00 0.00 4.96
564 575 1.477558 CCTCAGACATATGCAACCCCC 60.478 57.143 1.58 0.00 0.00 5.40
565 576 1.490490 TCCTCAGACATATGCAACCCC 59.510 52.381 1.58 0.00 0.00 4.95
566 577 3.144506 CATCCTCAGACATATGCAACCC 58.855 50.000 1.58 0.00 0.00 4.11
567 578 3.144506 CCATCCTCAGACATATGCAACC 58.855 50.000 1.58 0.00 0.00 3.77
568 579 2.551459 GCCATCCTCAGACATATGCAAC 59.449 50.000 1.58 0.00 0.00 4.17
569 580 2.440627 AGCCATCCTCAGACATATGCAA 59.559 45.455 1.58 0.00 0.00 4.08
570 581 2.052468 AGCCATCCTCAGACATATGCA 58.948 47.619 1.58 0.00 0.00 3.96
571 582 2.424557 CAGCCATCCTCAGACATATGC 58.575 52.381 1.58 0.00 0.00 3.14
572 583 2.290134 CCCAGCCATCCTCAGACATATG 60.290 54.545 0.00 0.00 0.00 1.78
573 584 1.983691 CCCAGCCATCCTCAGACATAT 59.016 52.381 0.00 0.00 0.00 1.78
574 585 1.344393 ACCCAGCCATCCTCAGACATA 60.344 52.381 0.00 0.00 0.00 2.29
575 586 0.622738 ACCCAGCCATCCTCAGACAT 60.623 55.000 0.00 0.00 0.00 3.06
576 587 1.229625 ACCCAGCCATCCTCAGACA 60.230 57.895 0.00 0.00 0.00 3.41
577 588 1.222936 CACCCAGCCATCCTCAGAC 59.777 63.158 0.00 0.00 0.00 3.51
578 589 1.997311 CCACCCAGCCATCCTCAGA 60.997 63.158 0.00 0.00 0.00 3.27
579 590 2.593978 CCACCCAGCCATCCTCAG 59.406 66.667 0.00 0.00 0.00 3.35
580 591 3.731728 GCCACCCAGCCATCCTCA 61.732 66.667 0.00 0.00 0.00 3.86
581 592 4.864334 CGCCACCCAGCCATCCTC 62.864 72.222 0.00 0.00 0.00 3.71
583 594 4.424711 TTCGCCACCCAGCCATCC 62.425 66.667 0.00 0.00 0.00 3.51
584 595 3.134127 GTTCGCCACCCAGCCATC 61.134 66.667 0.00 0.00 0.00 3.51
588 599 3.423154 CTTCGTTCGCCACCCAGC 61.423 66.667 0.00 0.00 0.00 4.85
589 600 1.738099 CTCTTCGTTCGCCACCCAG 60.738 63.158 0.00 0.00 0.00 4.45
590 601 2.342279 CTCTTCGTTCGCCACCCA 59.658 61.111 0.00 0.00 0.00 4.51
591 602 1.880819 TACCTCTTCGTTCGCCACCC 61.881 60.000 0.00 0.00 0.00 4.61
592 603 0.735287 GTACCTCTTCGTTCGCCACC 60.735 60.000 0.00 0.00 0.00 4.61
593 604 0.038892 TGTACCTCTTCGTTCGCCAC 60.039 55.000 0.00 0.00 0.00 5.01
594 605 0.675083 TTGTACCTCTTCGTTCGCCA 59.325 50.000 0.00 0.00 0.00 5.69
595 606 1.725164 CTTTGTACCTCTTCGTTCGCC 59.275 52.381 0.00 0.00 0.00 5.54
596 607 1.725164 CCTTTGTACCTCTTCGTTCGC 59.275 52.381 0.00 0.00 0.00 4.70
597 608 2.729882 CACCTTTGTACCTCTTCGTTCG 59.270 50.000 0.00 0.00 0.00 3.95
598 609 3.064931 CCACCTTTGTACCTCTTCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
599 610 2.809299 GCCACCTTTGTACCTCTTCGTT 60.809 50.000 0.00 0.00 0.00 3.85
600 611 1.270678 GCCACCTTTGTACCTCTTCGT 60.271 52.381 0.00 0.00 0.00 3.85
601 612 1.439679 GCCACCTTTGTACCTCTTCG 58.560 55.000 0.00 0.00 0.00 3.79
602 613 1.439679 CGCCACCTTTGTACCTCTTC 58.560 55.000 0.00 0.00 0.00 2.87
603 614 0.605589 GCGCCACCTTTGTACCTCTT 60.606 55.000 0.00 0.00 0.00 2.85
604 615 1.003718 GCGCCACCTTTGTACCTCT 60.004 57.895 0.00 0.00 0.00 3.69
605 616 2.388232 CGCGCCACCTTTGTACCTC 61.388 63.158 0.00 0.00 0.00 3.85
606 617 2.358247 CGCGCCACCTTTGTACCT 60.358 61.111 0.00 0.00 0.00 3.08
607 618 3.428282 CCGCGCCACCTTTGTACC 61.428 66.667 0.00 0.00 0.00 3.34
608 619 2.357760 TCCGCGCCACCTTTGTAC 60.358 61.111 0.00 0.00 0.00 2.90
609 620 2.357760 GTCCGCGCCACCTTTGTA 60.358 61.111 0.00 0.00 0.00 2.41
620 631 4.052229 ACACCTTCCTCGTCCGCG 62.052 66.667 0.00 0.00 39.92 6.46
621 632 2.432628 CACACCTTCCTCGTCCGC 60.433 66.667 0.00 0.00 0.00 5.54
622 633 1.605058 ATCCACACCTTCCTCGTCCG 61.605 60.000 0.00 0.00 0.00 4.79
623 634 0.108138 CATCCACACCTTCCTCGTCC 60.108 60.000 0.00 0.00 0.00 4.79
624 635 0.895530 TCATCCACACCTTCCTCGTC 59.104 55.000 0.00 0.00 0.00 4.20
625 636 1.348064 TTCATCCACACCTTCCTCGT 58.652 50.000 0.00 0.00 0.00 4.18
626 637 2.350522 CTTTCATCCACACCTTCCTCG 58.649 52.381 0.00 0.00 0.00 4.63
627 638 2.087646 GCTTTCATCCACACCTTCCTC 58.912 52.381 0.00 0.00 0.00 3.71
628 639 1.425066 TGCTTTCATCCACACCTTCCT 59.575 47.619 0.00 0.00 0.00 3.36
629 640 1.909700 TGCTTTCATCCACACCTTCC 58.090 50.000 0.00 0.00 0.00 3.46
630 641 2.229784 CCTTGCTTTCATCCACACCTTC 59.770 50.000 0.00 0.00 0.00 3.46
631 642 2.242043 CCTTGCTTTCATCCACACCTT 58.758 47.619 0.00 0.00 0.00 3.50
632 643 1.548582 CCCTTGCTTTCATCCACACCT 60.549 52.381 0.00 0.00 0.00 4.00
633 644 0.890683 CCCTTGCTTTCATCCACACC 59.109 55.000 0.00 0.00 0.00 4.16
634 645 1.815003 CTCCCTTGCTTTCATCCACAC 59.185 52.381 0.00 0.00 0.00 3.82
635 646 1.704628 TCTCCCTTGCTTTCATCCACA 59.295 47.619 0.00 0.00 0.00 4.17
636 647 2.363683 CTCTCCCTTGCTTTCATCCAC 58.636 52.381 0.00 0.00 0.00 4.02
637 648 1.340405 GCTCTCCCTTGCTTTCATCCA 60.340 52.381 0.00 0.00 0.00 3.41
638 649 1.340405 TGCTCTCCCTTGCTTTCATCC 60.340 52.381 0.00 0.00 0.00 3.51
639 650 2.015587 CTGCTCTCCCTTGCTTTCATC 58.984 52.381 0.00 0.00 0.00 2.92
640 651 1.340795 CCTGCTCTCCCTTGCTTTCAT 60.341 52.381 0.00 0.00 0.00 2.57
641 652 0.037303 CCTGCTCTCCCTTGCTTTCA 59.963 55.000 0.00 0.00 0.00 2.69
642 653 0.679321 CCCTGCTCTCCCTTGCTTTC 60.679 60.000 0.00 0.00 0.00 2.62
643 654 1.136329 TCCCTGCTCTCCCTTGCTTT 61.136 55.000 0.00 0.00 0.00 3.51
644 655 1.136329 TTCCCTGCTCTCCCTTGCTT 61.136 55.000 0.00 0.00 0.00 3.91
645 656 1.539869 TTCCCTGCTCTCCCTTGCT 60.540 57.895 0.00 0.00 0.00 3.91
646 657 1.077858 CTTCCCTGCTCTCCCTTGC 60.078 63.158 0.00 0.00 0.00 4.01
647 658 0.540923 CTCTTCCCTGCTCTCCCTTG 59.459 60.000 0.00 0.00 0.00 3.61
648 659 0.118144 ACTCTTCCCTGCTCTCCCTT 59.882 55.000 0.00 0.00 0.00 3.95
649 660 0.617249 CACTCTTCCCTGCTCTCCCT 60.617 60.000 0.00 0.00 0.00 4.20
650 661 1.904032 CACTCTTCCCTGCTCTCCC 59.096 63.158 0.00 0.00 0.00 4.30
651 662 1.220477 GCACTCTTCCCTGCTCTCC 59.780 63.158 0.00 0.00 0.00 3.71
652 663 0.322975 TTGCACTCTTCCCTGCTCTC 59.677 55.000 0.00 0.00 34.29 3.20
653 664 0.324285 CTTGCACTCTTCCCTGCTCT 59.676 55.000 0.00 0.00 34.29 4.09
654 665 0.322975 TCTTGCACTCTTCCCTGCTC 59.677 55.000 0.00 0.00 34.29 4.26
655 666 0.767375 TTCTTGCACTCTTCCCTGCT 59.233 50.000 0.00 0.00 34.29 4.24
656 667 1.609208 TTTCTTGCACTCTTCCCTGC 58.391 50.000 0.00 0.00 0.00 4.85
657 668 2.030451 GCTTTTCTTGCACTCTTCCCTG 60.030 50.000 0.00 0.00 0.00 4.45
658 669 2.234143 GCTTTTCTTGCACTCTTCCCT 58.766 47.619 0.00 0.00 0.00 4.20
659 670 1.068954 CGCTTTTCTTGCACTCTTCCC 60.069 52.381 0.00 0.00 0.00 3.97
660 671 1.873591 TCGCTTTTCTTGCACTCTTCC 59.126 47.619 0.00 0.00 0.00 3.46
661 672 3.292423 GTTCGCTTTTCTTGCACTCTTC 58.708 45.455 0.00 0.00 0.00 2.87
662 673 2.033424 GGTTCGCTTTTCTTGCACTCTT 59.967 45.455 0.00 0.00 0.00 2.85
663 674 1.604278 GGTTCGCTTTTCTTGCACTCT 59.396 47.619 0.00 0.00 0.00 3.24
664 675 1.333619 TGGTTCGCTTTTCTTGCACTC 59.666 47.619 0.00 0.00 0.00 3.51
665 676 1.334869 CTGGTTCGCTTTTCTTGCACT 59.665 47.619 0.00 0.00 0.00 4.40
666 677 1.333619 TCTGGTTCGCTTTTCTTGCAC 59.666 47.619 0.00 0.00 0.00 4.57
667 678 1.674359 TCTGGTTCGCTTTTCTTGCA 58.326 45.000 0.00 0.00 0.00 4.08
668 679 2.605580 CCTTCTGGTTCGCTTTTCTTGC 60.606 50.000 0.00 0.00 0.00 4.01
669 680 2.878406 TCCTTCTGGTTCGCTTTTCTTG 59.122 45.455 0.00 0.00 34.23 3.02
670 681 3.142174 CTCCTTCTGGTTCGCTTTTCTT 58.858 45.455 0.00 0.00 34.23 2.52
671 682 2.551071 CCTCCTTCTGGTTCGCTTTTCT 60.551 50.000 0.00 0.00 34.23 2.52
672 683 1.807142 CCTCCTTCTGGTTCGCTTTTC 59.193 52.381 0.00 0.00 34.23 2.29
673 684 1.420138 TCCTCCTTCTGGTTCGCTTTT 59.580 47.619 0.00 0.00 34.23 2.27
674 685 1.056660 TCCTCCTTCTGGTTCGCTTT 58.943 50.000 0.00 0.00 34.23 3.51
675 686 1.280457 ATCCTCCTTCTGGTTCGCTT 58.720 50.000 0.00 0.00 34.23 4.68
676 687 1.280457 AATCCTCCTTCTGGTTCGCT 58.720 50.000 0.00 0.00 34.23 4.93
677 688 2.115343 AAATCCTCCTTCTGGTTCGC 57.885 50.000 0.00 0.00 34.23 4.70
678 689 4.833390 ACTTAAATCCTCCTTCTGGTTCG 58.167 43.478 0.00 0.00 34.23 3.95
679 690 6.350103 CCTACTTAAATCCTCCTTCTGGTTC 58.650 44.000 0.00 0.00 34.23 3.62
680 691 5.339282 GCCTACTTAAATCCTCCTTCTGGTT 60.339 44.000 0.00 0.00 34.23 3.67
681 692 4.164413 GCCTACTTAAATCCTCCTTCTGGT 59.836 45.833 0.00 0.00 34.23 4.00
682 693 4.164221 TGCCTACTTAAATCCTCCTTCTGG 59.836 45.833 0.00 0.00 0.00 3.86
683 694 5.359194 TGCCTACTTAAATCCTCCTTCTG 57.641 43.478 0.00 0.00 0.00 3.02
684 695 5.104318 CCTTGCCTACTTAAATCCTCCTTCT 60.104 44.000 0.00 0.00 0.00 2.85
685 696 5.126779 CCTTGCCTACTTAAATCCTCCTTC 58.873 45.833 0.00 0.00 0.00 3.46
686 697 4.079730 CCCTTGCCTACTTAAATCCTCCTT 60.080 45.833 0.00 0.00 0.00 3.36
687 698 3.459969 CCCTTGCCTACTTAAATCCTCCT 59.540 47.826 0.00 0.00 0.00 3.69
688 699 3.435169 CCCCTTGCCTACTTAAATCCTCC 60.435 52.174 0.00 0.00 0.00 4.30
689 700 3.202373 ACCCCTTGCCTACTTAAATCCTC 59.798 47.826 0.00 0.00 0.00 3.71
690 701 3.053619 CACCCCTTGCCTACTTAAATCCT 60.054 47.826 0.00 0.00 0.00 3.24
691 702 3.288092 CACCCCTTGCCTACTTAAATCC 58.712 50.000 0.00 0.00 0.00 3.01
692 703 3.945921 GACACCCCTTGCCTACTTAAATC 59.054 47.826 0.00 0.00 0.00 2.17
693 704 3.332485 TGACACCCCTTGCCTACTTAAAT 59.668 43.478 0.00 0.00 0.00 1.40
694 705 2.712087 TGACACCCCTTGCCTACTTAAA 59.288 45.455 0.00 0.00 0.00 1.52
695 706 2.304761 CTGACACCCCTTGCCTACTTAA 59.695 50.000 0.00 0.00 0.00 1.85
696 707 1.906574 CTGACACCCCTTGCCTACTTA 59.093 52.381 0.00 0.00 0.00 2.24
697 708 0.693049 CTGACACCCCTTGCCTACTT 59.307 55.000 0.00 0.00 0.00 2.24
698 709 0.178903 TCTGACACCCCTTGCCTACT 60.179 55.000 0.00 0.00 0.00 2.57
699 710 0.250513 CTCTGACACCCCTTGCCTAC 59.749 60.000 0.00 0.00 0.00 3.18
700 711 0.178903 ACTCTGACACCCCTTGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
701 712 1.462238 ACTCTGACACCCCTTGCCT 60.462 57.895 0.00 0.00 0.00 4.75
702 713 1.003233 GACTCTGACACCCCTTGCC 60.003 63.158 0.00 0.00 0.00 4.52
703 714 1.374758 CGACTCTGACACCCCTTGC 60.375 63.158 0.00 0.00 0.00 4.01
704 715 0.319900 CACGACTCTGACACCCCTTG 60.320 60.000 0.00 0.00 0.00 3.61
705 716 0.469331 TCACGACTCTGACACCCCTT 60.469 55.000 0.00 0.00 0.00 3.95
706 717 0.896019 CTCACGACTCTGACACCCCT 60.896 60.000 0.00 0.00 0.00 4.79
707 718 1.179814 ACTCACGACTCTGACACCCC 61.180 60.000 0.00 0.00 0.00 4.95
708 719 0.674534 AACTCACGACTCTGACACCC 59.325 55.000 0.00 0.00 0.00 4.61
709 720 3.637998 TTAACTCACGACTCTGACACC 57.362 47.619 0.00 0.00 0.00 4.16
710 721 4.143305 GCAATTAACTCACGACTCTGACAC 60.143 45.833 0.00 0.00 0.00 3.67
711 722 3.987868 GCAATTAACTCACGACTCTGACA 59.012 43.478 0.00 0.00 0.00 3.58
712 723 3.987868 TGCAATTAACTCACGACTCTGAC 59.012 43.478 0.00 0.00 0.00 3.51
713 724 3.987868 GTGCAATTAACTCACGACTCTGA 59.012 43.478 0.00 0.00 0.00 3.27
714 725 3.740832 TGTGCAATTAACTCACGACTCTG 59.259 43.478 0.00 0.00 33.69 3.35
715 726 3.990092 TGTGCAATTAACTCACGACTCT 58.010 40.909 0.00 0.00 33.69 3.24
716 727 3.987868 TCTGTGCAATTAACTCACGACTC 59.012 43.478 0.00 0.00 33.69 3.36
717 728 3.990092 TCTGTGCAATTAACTCACGACT 58.010 40.909 0.00 0.00 33.69 4.18
718 729 4.211374 ACTTCTGTGCAATTAACTCACGAC 59.789 41.667 0.00 0.00 33.69 4.34
719 730 4.377021 ACTTCTGTGCAATTAACTCACGA 58.623 39.130 0.00 0.00 33.69 4.35
720 731 4.732285 ACTTCTGTGCAATTAACTCACG 57.268 40.909 0.00 0.00 33.69 4.35
721 732 5.468746 TGGTACTTCTGTGCAATTAACTCAC 59.531 40.000 0.00 0.00 0.00 3.51
2805 3076 8.052141 TGTAATGGATCAAGTTGTAATGGATCA 58.948 33.333 2.11 0.00 36.86 2.92
2806 3077 8.450578 TGTAATGGATCAAGTTGTAATGGATC 57.549 34.615 2.11 0.00 34.93 3.36
2807 3078 8.686334 GTTGTAATGGATCAAGTTGTAATGGAT 58.314 33.333 2.11 0.00 0.00 3.41
2808 3079 7.888021 AGTTGTAATGGATCAAGTTGTAATGGA 59.112 33.333 2.11 0.00 0.00 3.41
2809 3080 8.055279 AGTTGTAATGGATCAAGTTGTAATGG 57.945 34.615 2.11 0.00 0.00 3.16
2810 3081 9.345517 CAAGTTGTAATGGATCAAGTTGTAATG 57.654 33.333 13.75 0.00 43.78 1.90
2811 3082 9.295825 TCAAGTTGTAATGGATCAAGTTGTAAT 57.704 29.630 18.40 0.00 46.35 1.89
2812 3083 8.684386 TCAAGTTGTAATGGATCAAGTTGTAA 57.316 30.769 18.40 4.88 46.35 2.41
2813 3084 8.862325 ATCAAGTTGTAATGGATCAAGTTGTA 57.138 30.769 18.40 10.32 46.35 2.41
2814 3085 7.094205 GGATCAAGTTGTAATGGATCAAGTTGT 60.094 37.037 18.40 10.44 46.35 3.32
2816 3087 6.947733 TGGATCAAGTTGTAATGGATCAAGTT 59.052 34.615 2.11 0.00 37.59 2.66
2817 3088 6.484288 TGGATCAAGTTGTAATGGATCAAGT 58.516 36.000 2.11 0.00 36.86 3.16
2818 3089 7.578310 ATGGATCAAGTTGTAATGGATCAAG 57.422 36.000 2.11 0.00 36.86 3.02
2819 3090 7.959658 AATGGATCAAGTTGTAATGGATCAA 57.040 32.000 2.11 0.00 36.86 2.57


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

AutoCloner maintained by Alex Coulton.