Multiple sequence alignment - TraesCS3B01G451800

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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 TraesCS3B01G451800 chr3B 100.000 2276 0 0 1 2276 692129300 692127025 0.000000e+00 4204
1 TraesCS3B01G451800 chr3B 84.515 536 76 6 1 534 141709607 141709077 7.200000e-145 523
2 TraesCS3B01G451800 chr3B 85.135 370 40 10 4 365 235887017 235887379 4.620000e-97 364
3 TraesCS3B01G451800 chr3A 91.134 767 34 16 719 1467 659040795 659040045 0.000000e+00 1009
4 TraesCS3B01G451800 chr3A 80.682 792 67 35 1554 2276 659039294 659038520 9.250000e-149 536
5 TraesCS3B01G451800 chr3A 92.647 68 5 0 2209 2276 659038515 659038448 5.170000e-17 99
6 TraesCS3B01G451800 chr3D 91.016 768 29 17 719 1472 524775294 524774553 0.000000e+00 1000
7 TraesCS3B01G451800 chr3D 81.693 508 69 15 1 491 593048649 593048149 3.520000e-108 401
8 TraesCS3B01G451800 chr3D 87.336 229 18 6 2057 2276 524772492 524772266 3.750000e-63 252
9 TraesCS3B01G451800 chr3D 92.638 163 7 4 1712 1874 524773188 524773031 1.760000e-56 230
10 TraesCS3B01G451800 chr3D 93.662 142 7 2 1873 2014 524772973 524772834 6.370000e-51 211
11 TraesCS3B01G451800 chr5D 84.810 553 52 8 1 528 283103278 283103823 5.570000e-146 527
12 TraesCS3B01G451800 chr5D 89.646 367 29 7 1 365 556237775 556237416 2.060000e-125 459
13 TraesCS3B01G451800 chr5D 94.007 267 15 1 1 267 437449687 437449422 9.790000e-109 403
14 TraesCS3B01G451800 chr5D 81.522 276 37 10 255 528 521145783 521146046 4.920000e-52 215
15 TraesCS3B01G451800 chr2A 84.877 529 67 11 1 528 713368113 713368629 2.590000e-144 521
16 TraesCS3B01G451800 chr1D 85.283 530 49 11 20 524 294746801 294746276 9.320000e-144 520
17 TraesCS3B01G451800 chr1D 82.523 555 51 11 1 528 458392848 458393383 1.600000e-121 446
18 TraesCS3B01G451800 chr5B 82.585 557 65 14 1 530 526192128 526191577 1.590000e-126 462
19 TraesCS3B01G451800 chr4B 82.491 554 68 16 1 528 167340417 167340967 2.060000e-125 459
20 TraesCS3B01G451800 chr6A 82.321 560 65 17 1 532 176566686 176567239 2.670000e-124 455
21 TraesCS3B01G451800 chr7D 85.088 456 34 8 1 431 401784437 401783991 3.470000e-118 435
22 TraesCS3B01G451800 chr4D 92.727 275 18 2 1 275 461466901 461466629 1.640000e-106 396
23 TraesCS3B01G451800 chr7A 86.631 374 29 12 1 361 680808267 680808632 5.890000e-106 394
24 TraesCS3B01G451800 chr2B 82.310 277 43 4 255 530 52528516 52528245 3.780000e-58 235
25 TraesCS3B01G451800 chr4A 82.079 279 40 9 255 530 179137792 179138063 1.760000e-56 230


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 TraesCS3B01G451800 chr3B 692127025 692129300 2275 True 4204.00 4204 100.000000 1 2276 1 chr3B.!!$R2 2275
1 TraesCS3B01G451800 chr3B 141709077 141709607 530 True 523.00 523 84.515000 1 534 1 chr3B.!!$R1 533
2 TraesCS3B01G451800 chr3A 659038448 659040795 2347 True 548.00 1009 88.154333 719 2276 3 chr3A.!!$R1 1557
3 TraesCS3B01G451800 chr3D 524772266 524775294 3028 True 423.25 1000 91.163000 719 2276 4 chr3D.!!$R2 1557
4 TraesCS3B01G451800 chr3D 593048149 593048649 500 True 401.00 401 81.693000 1 491 1 chr3D.!!$R1 490
5 TraesCS3B01G451800 chr5D 283103278 283103823 545 False 527.00 527 84.810000 1 528 1 chr5D.!!$F1 527
6 TraesCS3B01G451800 chr2A 713368113 713368629 516 False 521.00 521 84.877000 1 528 1 chr2A.!!$F1 527
7 TraesCS3B01G451800 chr1D 294746276 294746801 525 True 520.00 520 85.283000 20 524 1 chr1D.!!$R1 504
8 TraesCS3B01G451800 chr1D 458392848 458393383 535 False 446.00 446 82.523000 1 528 1 chr1D.!!$F1 527
9 TraesCS3B01G451800 chr5B 526191577 526192128 551 True 462.00 462 82.585000 1 530 1 chr5B.!!$R1 529
10 TraesCS3B01G451800 chr4B 167340417 167340967 550 False 459.00 459 82.491000 1 528 1 chr4B.!!$F1 527
11 TraesCS3B01G451800 chr6A 176566686 176567239 553 False 455.00 455 82.321000 1 532 1 chr6A.!!$F1 531

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
952 1004 0.038892 TCTTCGTCCTACAACGCACC 60.039 55.0 0.0 0.0 42.31 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 3434 0.447801 GGCACGAACCTTGCATGTAG 59.552 55.0 0.0 0.0 42.12 2.74 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
84 88 0.904865 ATGAGCTCTTGGGACGTCCA 60.905 55.000 34.40 18.59 45.43 4.02
132 136 1.678970 GGCCCGATTTGTTGCCTCT 60.679 57.895 0.00 0.00 40.77 3.69
137 141 3.278574 CCCGATTTGTTGCCTCTTATCA 58.721 45.455 0.00 0.00 0.00 2.15
340 372 9.965824 GTTTGATCTTCTTGGTTCTATTTTGAA 57.034 29.630 0.00 0.00 0.00 2.69
365 397 3.323115 TGAAATATTGTTTGTGCTGGGCA 59.677 39.130 0.00 0.00 35.60 5.36
366 398 4.020396 TGAAATATTGTTTGTGCTGGGCAT 60.020 37.500 0.00 0.00 41.91 4.40
370 402 0.467844 TGTTTGTGCTGGGCATGAGT 60.468 50.000 0.00 0.00 41.91 3.41
403 435 1.743252 GCGCCTGCTGAAGCTACTT 60.743 57.895 0.00 0.00 42.66 2.24
492 526 9.881529 ATTTCGACGCTGTAAAAGTTATTTTAA 57.118 25.926 0.00 0.00 41.36 1.52
494 528 7.849496 TCGACGCTGTAAAAGTTATTTTAACA 58.151 30.769 0.00 0.00 41.36 2.41
498 532 6.448879 CGCTGTAAAAGTTATTTTAACACGCG 60.449 38.462 3.53 3.53 41.36 6.01
534 569 3.056107 CCGTTGGAGATGGTCTTAGTTGA 60.056 47.826 0.00 0.00 0.00 3.18
535 570 4.383118 CCGTTGGAGATGGTCTTAGTTGAT 60.383 45.833 0.00 0.00 0.00 2.57
536 571 5.178797 CGTTGGAGATGGTCTTAGTTGATT 58.821 41.667 0.00 0.00 0.00 2.57
537 572 6.338146 CGTTGGAGATGGTCTTAGTTGATTA 58.662 40.000 0.00 0.00 0.00 1.75
538 573 6.986817 CGTTGGAGATGGTCTTAGTTGATTAT 59.013 38.462 0.00 0.00 0.00 1.28
539 574 7.042456 CGTTGGAGATGGTCTTAGTTGATTATG 60.042 40.741 0.00 0.00 0.00 1.90
540 575 7.675161 TGGAGATGGTCTTAGTTGATTATGA 57.325 36.000 0.00 0.00 0.00 2.15
541 576 8.267620 TGGAGATGGTCTTAGTTGATTATGAT 57.732 34.615 0.00 0.00 0.00 2.45
542 577 9.379770 TGGAGATGGTCTTAGTTGATTATGATA 57.620 33.333 0.00 0.00 0.00 2.15
543 578 9.868277 GGAGATGGTCTTAGTTGATTATGATAG 57.132 37.037 0.00 0.00 0.00 2.08
546 581 9.646427 GATGGTCTTAGTTGATTATGATAGACC 57.354 37.037 0.00 0.00 46.66 3.85
548 583 7.091443 GGTCTTAGTTGATTATGATAGACCGG 58.909 42.308 0.00 0.00 40.50 5.28
549 584 7.255871 GGTCTTAGTTGATTATGATAGACCGGT 60.256 40.741 6.92 6.92 40.50 5.28
550 585 7.595502 GTCTTAGTTGATTATGATAGACCGGTG 59.404 40.741 14.63 0.00 0.00 4.94
551 586 4.632153 AGTTGATTATGATAGACCGGTGC 58.368 43.478 14.63 3.40 0.00 5.01
552 587 4.345257 AGTTGATTATGATAGACCGGTGCT 59.655 41.667 14.63 12.04 0.00 4.40
553 588 4.955811 TGATTATGATAGACCGGTGCTT 57.044 40.909 14.63 0.00 0.00 3.91
554 589 4.631131 TGATTATGATAGACCGGTGCTTG 58.369 43.478 14.63 0.00 0.00 4.01
555 590 2.526304 TATGATAGACCGGTGCTTGC 57.474 50.000 14.63 0.00 0.00 4.01
556 591 0.179045 ATGATAGACCGGTGCTTGCC 60.179 55.000 14.63 0.00 0.00 4.52
571 606 2.835605 TGCCGCTGCAAACTAGTAC 58.164 52.632 0.00 0.00 46.66 2.73
572 607 1.011968 TGCCGCTGCAAACTAGTACG 61.012 55.000 0.00 0.00 46.66 3.67
573 608 1.012486 GCCGCTGCAAACTAGTACGT 61.012 55.000 0.00 0.00 37.47 3.57
574 609 1.425412 CCGCTGCAAACTAGTACGTT 58.575 50.000 0.00 0.00 0.00 3.99
575 610 1.126113 CCGCTGCAAACTAGTACGTTG 59.874 52.381 0.00 0.00 0.00 4.10
576 611 2.055838 CGCTGCAAACTAGTACGTTGA 58.944 47.619 9.49 0.00 0.00 3.18
577 612 2.666508 CGCTGCAAACTAGTACGTTGAT 59.333 45.455 9.49 0.00 0.00 2.57
578 613 3.241678 CGCTGCAAACTAGTACGTTGATC 60.242 47.826 9.49 0.00 0.00 2.92
579 614 3.241678 GCTGCAAACTAGTACGTTGATCG 60.242 47.826 9.49 0.00 46.00 3.69
580 615 4.163458 TGCAAACTAGTACGTTGATCGA 57.837 40.909 9.49 0.00 42.86 3.59
581 616 4.740268 TGCAAACTAGTACGTTGATCGAT 58.260 39.130 9.49 0.00 42.86 3.59
582 617 4.796830 TGCAAACTAGTACGTTGATCGATC 59.203 41.667 18.72 18.72 42.86 3.69
583 618 4.796830 GCAAACTAGTACGTTGATCGATCA 59.203 41.667 23.99 23.99 42.86 2.92
584 619 5.052304 GCAAACTAGTACGTTGATCGATCAG 60.052 44.000 25.95 18.58 42.86 2.90
585 620 6.255950 CAAACTAGTACGTTGATCGATCAGA 58.744 40.000 25.95 15.36 42.86 3.27
586 621 6.432607 AACTAGTACGTTGATCGATCAGAA 57.567 37.500 25.95 11.73 42.86 3.02
587 622 6.050454 ACTAGTACGTTGATCGATCAGAAG 57.950 41.667 25.95 21.82 42.86 2.85
588 623 3.696898 AGTACGTTGATCGATCAGAAGC 58.303 45.455 25.95 16.61 42.86 3.86
589 624 2.654749 ACGTTGATCGATCAGAAGCA 57.345 45.000 25.95 10.24 42.86 3.91
590 625 2.959516 ACGTTGATCGATCAGAAGCAA 58.040 42.857 25.95 9.51 42.86 3.91
591 626 2.668457 ACGTTGATCGATCAGAAGCAAC 59.332 45.455 25.95 19.06 41.10 4.17
592 627 2.667969 CGTTGATCGATCAGAAGCAACA 59.332 45.455 25.95 8.05 42.89 3.33
593 628 3.308053 CGTTGATCGATCAGAAGCAACAT 59.692 43.478 25.95 0.00 42.89 2.71
594 629 4.549680 CGTTGATCGATCAGAAGCAACATC 60.550 45.833 25.95 8.48 42.89 3.06
595 630 4.127566 TGATCGATCAGAAGCAACATCA 57.872 40.909 23.99 0.00 32.11 3.07
596 631 4.117685 TGATCGATCAGAAGCAACATCAG 58.882 43.478 23.99 0.00 32.11 2.90
597 632 3.874392 TCGATCAGAAGCAACATCAGA 57.126 42.857 0.00 0.00 0.00 3.27
598 633 3.778618 TCGATCAGAAGCAACATCAGAG 58.221 45.455 0.00 0.00 0.00 3.35
599 634 3.445096 TCGATCAGAAGCAACATCAGAGA 59.555 43.478 0.00 0.00 0.00 3.10
600 635 3.797796 CGATCAGAAGCAACATCAGAGAG 59.202 47.826 0.00 0.00 0.00 3.20
601 636 3.606595 TCAGAAGCAACATCAGAGAGG 57.393 47.619 0.00 0.00 0.00 3.69
602 637 2.902486 TCAGAAGCAACATCAGAGAGGT 59.098 45.455 0.00 0.00 0.00 3.85
603 638 4.089361 TCAGAAGCAACATCAGAGAGGTA 58.911 43.478 0.00 0.00 0.00 3.08
604 639 4.528206 TCAGAAGCAACATCAGAGAGGTAA 59.472 41.667 0.00 0.00 0.00 2.85
605 640 4.629200 CAGAAGCAACATCAGAGAGGTAAC 59.371 45.833 0.00 0.00 0.00 2.50
606 641 3.238108 AGCAACATCAGAGAGGTAACG 57.762 47.619 0.00 0.00 46.39 3.18
607 642 2.093973 AGCAACATCAGAGAGGTAACGG 60.094 50.000 0.00 0.00 46.39 4.44
608 643 2.353803 GCAACATCAGAGAGGTAACGGT 60.354 50.000 0.00 0.00 46.39 4.83
609 644 3.119245 GCAACATCAGAGAGGTAACGGTA 60.119 47.826 0.00 0.00 46.39 4.02
610 645 4.619863 GCAACATCAGAGAGGTAACGGTAA 60.620 45.833 0.00 0.00 46.39 2.85
611 646 4.985538 ACATCAGAGAGGTAACGGTAAG 57.014 45.455 0.00 0.00 46.39 2.34
612 647 3.130693 ACATCAGAGAGGTAACGGTAAGC 59.869 47.826 0.00 0.00 46.39 3.09
613 648 3.083122 TCAGAGAGGTAACGGTAAGCT 57.917 47.619 0.00 0.00 46.39 3.74
614 649 4.226427 TCAGAGAGGTAACGGTAAGCTA 57.774 45.455 0.00 0.00 46.39 3.32
615 650 3.944015 TCAGAGAGGTAACGGTAAGCTAC 59.056 47.826 0.00 0.00 46.39 3.58
616 651 3.946558 CAGAGAGGTAACGGTAAGCTACT 59.053 47.826 0.00 0.00 46.39 2.57
617 652 3.946558 AGAGAGGTAACGGTAAGCTACTG 59.053 47.826 0.00 0.00 46.39 2.74
618 653 2.426381 AGAGGTAACGGTAAGCTACTGC 59.574 50.000 0.00 0.00 46.39 4.40
633 668 6.478512 AGCTACTGCTAAAATAGCTCTCTT 57.521 37.500 10.42 0.00 46.90 2.85
634 669 6.512297 AGCTACTGCTAAAATAGCTCTCTTC 58.488 40.000 10.42 0.00 46.90 2.87
635 670 6.734597 AGCTACTGCTAAAATAGCTCTCTTCG 60.735 42.308 10.42 0.00 46.90 3.79
642 677 7.561237 CTAAAATAGCTCTCTTCGCAGTATC 57.439 40.000 0.00 0.00 0.00 2.24
643 678 4.513198 AATAGCTCTCTTCGCAGTATCC 57.487 45.455 0.00 0.00 0.00 2.59
644 679 2.065899 AGCTCTCTTCGCAGTATCCT 57.934 50.000 0.00 0.00 0.00 3.24
645 680 1.953686 AGCTCTCTTCGCAGTATCCTC 59.046 52.381 0.00 0.00 0.00 3.71
646 681 1.334599 GCTCTCTTCGCAGTATCCTCG 60.335 57.143 0.00 0.00 0.00 4.63
647 682 1.944024 CTCTCTTCGCAGTATCCTCGT 59.056 52.381 0.00 0.00 0.00 4.18
648 683 1.941294 TCTCTTCGCAGTATCCTCGTC 59.059 52.381 0.00 0.00 0.00 4.20
649 684 1.671328 CTCTTCGCAGTATCCTCGTCA 59.329 52.381 0.00 0.00 0.00 4.35
650 685 1.671328 TCTTCGCAGTATCCTCGTCAG 59.329 52.381 0.00 0.00 0.00 3.51
651 686 1.671328 CTTCGCAGTATCCTCGTCAGA 59.329 52.381 0.00 0.00 0.00 3.27
652 687 1.746470 TCGCAGTATCCTCGTCAGAA 58.254 50.000 0.00 0.00 0.00 3.02
653 688 1.671328 TCGCAGTATCCTCGTCAGAAG 59.329 52.381 0.00 0.00 0.00 2.85
654 689 1.268794 CGCAGTATCCTCGTCAGAAGG 60.269 57.143 0.00 0.00 0.00 3.46
655 690 1.067821 GCAGTATCCTCGTCAGAAGGG 59.932 57.143 0.00 0.00 0.00 3.95
656 691 1.683917 CAGTATCCTCGTCAGAAGGGG 59.316 57.143 0.00 0.00 0.00 4.79
657 692 1.041437 GTATCCTCGTCAGAAGGGGG 58.959 60.000 1.92 0.00 31.75 5.40
658 693 0.931468 TATCCTCGTCAGAAGGGGGA 59.069 55.000 1.92 0.00 43.89 4.81
659 694 0.397816 ATCCTCGTCAGAAGGGGGAG 60.398 60.000 1.92 0.00 43.04 4.30
660 695 2.726351 CCTCGTCAGAAGGGGGAGC 61.726 68.421 0.00 0.00 32.22 4.70
661 696 1.984570 CTCGTCAGAAGGGGGAGCA 60.985 63.158 0.00 0.00 0.00 4.26
662 697 1.535444 TCGTCAGAAGGGGGAGCAA 60.535 57.895 0.00 0.00 0.00 3.91
663 698 1.125093 TCGTCAGAAGGGGGAGCAAA 61.125 55.000 0.00 0.00 0.00 3.68
664 699 0.955919 CGTCAGAAGGGGGAGCAAAC 60.956 60.000 0.00 0.00 0.00 2.93
665 700 0.110486 GTCAGAAGGGGGAGCAAACA 59.890 55.000 0.00 0.00 0.00 2.83
666 701 0.850100 TCAGAAGGGGGAGCAAACAA 59.150 50.000 0.00 0.00 0.00 2.83
667 702 0.961753 CAGAAGGGGGAGCAAACAAC 59.038 55.000 0.00 0.00 0.00 3.32
668 703 0.555769 AGAAGGGGGAGCAAACAACA 59.444 50.000 0.00 0.00 0.00 3.33
669 704 0.961753 GAAGGGGGAGCAAACAACAG 59.038 55.000 0.00 0.00 0.00 3.16
670 705 0.555769 AAGGGGGAGCAAACAACAGA 59.444 50.000 0.00 0.00 0.00 3.41
671 706 0.779997 AGGGGGAGCAAACAACAGAT 59.220 50.000 0.00 0.00 0.00 2.90
672 707 1.177401 GGGGGAGCAAACAACAGATC 58.823 55.000 0.00 0.00 0.00 2.75
673 708 1.547675 GGGGGAGCAAACAACAGATCA 60.548 52.381 0.00 0.00 0.00 2.92
674 709 1.815003 GGGGAGCAAACAACAGATCAG 59.185 52.381 0.00 0.00 0.00 2.90
675 710 1.200948 GGGAGCAAACAACAGATCAGC 59.799 52.381 0.00 0.00 0.00 4.26
676 711 1.135859 GGAGCAAACAACAGATCAGCG 60.136 52.381 0.00 0.00 0.00 5.18
677 712 1.532868 GAGCAAACAACAGATCAGCGT 59.467 47.619 0.00 0.00 0.00 5.07
678 713 1.265095 AGCAAACAACAGATCAGCGTG 59.735 47.619 0.00 0.00 0.00 5.34
679 714 1.264020 GCAAACAACAGATCAGCGTGA 59.736 47.619 0.00 0.00 0.00 4.35
680 715 2.663879 GCAAACAACAGATCAGCGTGAG 60.664 50.000 0.00 0.00 0.00 3.51
697 732 5.127371 CGTGAGCCGTTAATTAGTTCTTC 57.873 43.478 0.00 0.00 0.00 2.87
698 733 4.863131 CGTGAGCCGTTAATTAGTTCTTCT 59.137 41.667 0.00 0.00 0.00 2.85
699 734 5.347907 CGTGAGCCGTTAATTAGTTCTTCTT 59.652 40.000 0.00 0.00 0.00 2.52
700 735 6.128634 CGTGAGCCGTTAATTAGTTCTTCTTT 60.129 38.462 0.00 0.00 0.00 2.52
701 736 7.235080 GTGAGCCGTTAATTAGTTCTTCTTTC 58.765 38.462 0.00 0.00 0.00 2.62
702 737 6.370718 TGAGCCGTTAATTAGTTCTTCTTTCC 59.629 38.462 0.00 0.00 0.00 3.13
703 738 6.473758 AGCCGTTAATTAGTTCTTCTTTCCT 58.526 36.000 0.00 0.00 0.00 3.36
704 739 6.940867 AGCCGTTAATTAGTTCTTCTTTCCTT 59.059 34.615 0.00 0.00 0.00 3.36
705 740 7.447545 AGCCGTTAATTAGTTCTTCTTTCCTTT 59.552 33.333 0.00 0.00 0.00 3.11
706 741 8.080417 GCCGTTAATTAGTTCTTCTTTCCTTTT 58.920 33.333 0.00 0.00 0.00 2.27
707 742 9.961265 CCGTTAATTAGTTCTTCTTTCCTTTTT 57.039 29.630 0.00 0.00 0.00 1.94
734 769 4.457949 GCGGGAGAATTAGTTCTTTTTCCA 59.542 41.667 1.61 0.00 44.57 3.53
740 775 9.764363 GGAGAATTAGTTCTTTTTCCAAATGTT 57.236 29.630 1.61 0.00 44.57 2.71
745 780 9.883142 ATTAGTTCTTTTTCCAAATGTTCAACA 57.117 25.926 0.00 0.00 0.00 3.33
746 781 9.883142 TTAGTTCTTTTTCCAAATGTTCAACAT 57.117 25.926 0.00 0.00 41.31 2.71
751 794 9.103861 TCTTTTTCCAAATGTTCAACATAAACC 57.896 29.630 2.67 0.00 37.97 3.27
918 961 3.053831 ACCACACTATAAAAGCGCACT 57.946 42.857 11.47 0.00 0.00 4.40
921 964 3.483574 CCACACTATAAAAGCGCACTTCG 60.484 47.826 11.47 0.00 42.12 3.79
936 979 2.878406 CACTTCGTCCCACAACATTCTT 59.122 45.455 0.00 0.00 0.00 2.52
952 1004 0.038892 TCTTCGTCCTACAACGCACC 60.039 55.000 0.00 0.00 42.31 5.01
970 1022 1.273886 ACCAACACACACAAACCCAAC 59.726 47.619 0.00 0.00 0.00 3.77
973 1025 1.633774 ACACACACAAACCCAACCAA 58.366 45.000 0.00 0.00 0.00 3.67
974 1026 1.548269 ACACACACAAACCCAACCAAG 59.452 47.619 0.00 0.00 0.00 3.61
975 1027 0.534873 ACACACAAACCCAACCAAGC 59.465 50.000 0.00 0.00 0.00 4.01
976 1028 0.534412 CACACAAACCCAACCAAGCA 59.466 50.000 0.00 0.00 0.00 3.91
989 1041 4.201812 CCAACCAAGCACATAGTAACATCG 60.202 45.833 0.00 0.00 0.00 3.84
990 1042 4.465632 ACCAAGCACATAGTAACATCGA 57.534 40.909 0.00 0.00 0.00 3.59
991 1043 4.181578 ACCAAGCACATAGTAACATCGAC 58.818 43.478 0.00 0.00 0.00 4.20
992 1044 3.555956 CCAAGCACATAGTAACATCGACC 59.444 47.826 0.00 0.00 0.00 4.79
1126 1181 1.367840 GTGCAGGAGTTCGACACCT 59.632 57.895 0.00 0.00 39.87 4.00
1210 1265 2.757917 GCAGGCTCGAGGAGGACT 60.758 66.667 15.58 0.00 0.00 3.85
1322 1377 6.710692 ACGATGTGTGTATATGTATGCATG 57.289 37.500 10.16 0.00 36.58 4.06
1469 1526 6.758886 ACCAGAATAAAGCTTCTCGTGATTAG 59.241 38.462 0.00 0.00 33.18 1.73
1472 1529 8.963130 CAGAATAAAGCTTCTCGTGATTAGTAG 58.037 37.037 0.00 0.00 33.18 2.57
1473 1530 8.688151 AGAATAAAGCTTCTCGTGATTAGTAGT 58.312 33.333 0.00 0.00 29.38 2.73
1474 1531 9.947669 GAATAAAGCTTCTCGTGATTAGTAGTA 57.052 33.333 0.00 0.00 0.00 1.82
1478 1535 9.733219 AAAGCTTCTCGTGATTAGTAGTATTAC 57.267 33.333 0.00 0.00 0.00 1.89
1479 1536 8.680039 AGCTTCTCGTGATTAGTAGTATTACT 57.320 34.615 3.20 3.20 42.66 2.24
1480 1537 8.776470 AGCTTCTCGTGATTAGTAGTATTACTC 58.224 37.037 0.51 0.00 40.55 2.59
1481 1538 8.776470 GCTTCTCGTGATTAGTAGTATTACTCT 58.224 37.037 0.51 1.04 40.55 3.24
1483 1540 8.085720 TCTCGTGATTAGTAGTATTACTCTGC 57.914 38.462 0.51 0.00 40.55 4.26
1496 1553 5.753721 ATTACTCTGCTTCCAGTCTCTTT 57.246 39.130 0.00 0.00 40.09 2.52
1499 1556 2.483491 CTCTGCTTCCAGTCTCTTTTGC 59.517 50.000 0.00 0.00 40.09 3.68
1500 1557 1.538950 CTGCTTCCAGTCTCTTTTGCC 59.461 52.381 0.00 0.00 34.31 4.52
1501 1558 1.133823 TGCTTCCAGTCTCTTTTGCCA 60.134 47.619 0.00 0.00 0.00 4.92
1502 1559 1.538950 GCTTCCAGTCTCTTTTGCCAG 59.461 52.381 0.00 0.00 0.00 4.85
1507 1564 3.840666 TCCAGTCTCTTTTGCCAGACTAT 59.159 43.478 1.36 0.00 46.31 2.12
1508 1565 4.287067 TCCAGTCTCTTTTGCCAGACTATT 59.713 41.667 1.36 0.00 46.31 1.73
1509 1566 5.006386 CCAGTCTCTTTTGCCAGACTATTT 58.994 41.667 1.36 0.00 46.31 1.40
1510 1567 5.474876 CCAGTCTCTTTTGCCAGACTATTTT 59.525 40.000 1.36 0.00 46.31 1.82
1511 1568 6.348868 CCAGTCTCTTTTGCCAGACTATTTTC 60.349 42.308 1.36 0.00 46.31 2.29
1512 1569 5.707764 AGTCTCTTTTGCCAGACTATTTTCC 59.292 40.000 0.00 0.00 46.21 3.13
1514 1571 5.473504 TCTCTTTTGCCAGACTATTTTCCAC 59.526 40.000 0.00 0.00 0.00 4.02
1515 1572 4.522789 TCTTTTGCCAGACTATTTTCCACC 59.477 41.667 0.00 0.00 0.00 4.61
1517 1574 3.517296 TGCCAGACTATTTTCCACCAA 57.483 42.857 0.00 0.00 0.00 3.67
1518 1575 3.838565 TGCCAGACTATTTTCCACCAAA 58.161 40.909 0.00 0.00 0.00 3.28
1519 1576 3.572255 TGCCAGACTATTTTCCACCAAAC 59.428 43.478 0.00 0.00 0.00 2.93
1521 1578 4.069304 CCAGACTATTTTCCACCAAACGA 58.931 43.478 0.00 0.00 0.00 3.85
1522 1579 4.700213 CCAGACTATTTTCCACCAAACGAT 59.300 41.667 0.00 0.00 0.00 3.73
1523 1580 5.391950 CCAGACTATTTTCCACCAAACGATG 60.392 44.000 0.00 0.00 0.00 3.84
1524 1581 4.156008 AGACTATTTTCCACCAAACGATGC 59.844 41.667 0.00 0.00 0.00 3.91
1527 1584 0.313672 TTTCCACCAAACGATGCTGC 59.686 50.000 0.00 0.00 0.00 5.25
1528 1585 0.821301 TTCCACCAAACGATGCTGCA 60.821 50.000 4.13 4.13 0.00 4.41
1529 1586 1.081242 CCACCAAACGATGCTGCAC 60.081 57.895 3.57 0.00 0.00 4.57
1546 1603 1.420378 CACGCATGCAAGCAAAATGA 58.580 45.000 19.57 0.00 0.00 2.57
1547 1604 1.996898 CACGCATGCAAGCAAAATGAT 59.003 42.857 19.57 0.00 0.00 2.45
1548 1605 2.413796 CACGCATGCAAGCAAAATGATT 59.586 40.909 19.57 0.00 0.00 2.57
1549 1606 3.613299 CACGCATGCAAGCAAAATGATTA 59.387 39.130 19.57 0.00 0.00 1.75
1552 2407 4.570935 GCATGCAAGCAAAATGATTAACG 58.429 39.130 14.21 0.00 0.00 3.18
1556 2411 4.217334 TGCAAGCAAAATGATTAACGGAGA 59.783 37.500 0.00 0.00 0.00 3.71
1566 2421 3.007506 TGATTAACGGAGAAGCAGTTCCA 59.992 43.478 0.00 0.00 36.33 3.53
1594 2449 1.003580 GACATGGGAGCAAGACCTTCA 59.996 52.381 0.00 0.00 0.00 3.02
1607 2462 5.917447 GCAAGACCTTCAAGATTTCTTTGAC 59.083 40.000 0.00 0.00 33.11 3.18
1608 2463 6.460123 GCAAGACCTTCAAGATTTCTTTGACA 60.460 38.462 0.00 0.00 33.11 3.58
1609 2464 6.874288 AGACCTTCAAGATTTCTTTGACAG 57.126 37.500 0.00 0.00 33.11 3.51
1610 2465 5.240403 AGACCTTCAAGATTTCTTTGACAGC 59.760 40.000 0.00 0.00 33.11 4.40
1612 2467 4.023707 CCTTCAAGATTTCTTTGACAGCGT 60.024 41.667 0.00 0.00 33.11 5.07
1614 2469 3.184379 TCAAGATTTCTTTGACAGCGTCG 59.816 43.478 4.65 0.00 32.48 5.12
1618 2473 0.944311 TTCTTTGACAGCGTCGCCTC 60.944 55.000 14.86 9.56 34.95 4.70
1634 2530 1.264749 CCTCACGGGATGGAGACCAA 61.265 60.000 0.00 0.00 36.95 3.67
1643 2539 2.554032 GGATGGAGACCAACAACAACAG 59.446 50.000 0.00 0.00 36.95 3.16
1644 2540 2.799126 TGGAGACCAACAACAACAGT 57.201 45.000 0.00 0.00 0.00 3.55
1645 2541 2.639065 TGGAGACCAACAACAACAGTC 58.361 47.619 0.00 0.00 0.00 3.51
1706 2967 2.605607 CCCAGGTGCATGGTCAGGA 61.606 63.158 5.63 0.00 38.81 3.86
1707 2968 1.379916 CCAGGTGCATGGTCAGGAA 59.620 57.895 0.00 0.00 35.47 3.36
1772 3033 7.440523 ACTGAACCTACTTGATCAATGAAAC 57.559 36.000 8.96 0.00 0.00 2.78
1813 3086 9.574516 AAACAAAATTCTAATGACCTCACTAGT 57.425 29.630 0.00 0.00 28.78 2.57
1815 3088 9.654663 ACAAAATTCTAATGACCTCACTAGTAC 57.345 33.333 0.00 0.00 28.78 2.73
1881 3213 1.473677 TCAACCAGTCCGTATGTACCG 59.526 52.381 0.00 0.00 0.00 4.02
1899 3231 1.740025 CCGTGATTTTCTCTTGGGCTC 59.260 52.381 0.00 0.00 0.00 4.70
1900 3232 2.616510 CCGTGATTTTCTCTTGGGCTCT 60.617 50.000 0.00 0.00 0.00 4.09
1901 3233 2.675348 CGTGATTTTCTCTTGGGCTCTC 59.325 50.000 0.00 0.00 0.00 3.20
1965 3297 8.103948 ACTAGATCCAAAACAGAAAATCACAG 57.896 34.615 0.00 0.00 0.00 3.66
1983 3318 2.808543 ACAGATCGACCAAAACAGAAGC 59.191 45.455 0.00 0.00 0.00 3.86
1997 3332 3.151554 ACAGAAGCACAAGAATCATGCA 58.848 40.909 6.87 0.00 41.97 3.96
2000 3335 3.762288 AGAAGCACAAGAATCATGCACAT 59.238 39.130 0.00 0.00 41.97 3.21
2017 3396 2.171237 CACATAAGGGATGCTGAGGTCA 59.829 50.000 0.00 0.00 39.39 4.02
2055 3434 4.142534 GCCCATCCCGTTTAAAAAGTACTC 60.143 45.833 0.00 0.00 0.00 2.59
2070 3705 4.111375 AGTACTCTACATGCAAGGTTCG 57.889 45.455 0.00 0.00 28.09 3.95
2072 3707 2.688507 ACTCTACATGCAAGGTTCGTG 58.311 47.619 0.00 0.00 28.09 4.35
2084 3722 1.026718 GGTTCGTGCCATCCCAAGAG 61.027 60.000 0.00 0.00 0.00 2.85
2124 3768 4.595762 AGCAGCAATCAACAACAGAAAT 57.404 36.364 0.00 0.00 0.00 2.17
2159 3803 9.401058 CCTTGTCATCCAAAAACTTATAGATCT 57.599 33.333 0.00 0.00 31.20 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 29 2.125512 GCCCACGCTCATTCTCGT 60.126 61.111 0.00 0.00 39.79 4.18
84 88 3.812019 CTCCGCCGTACTCGCACT 61.812 66.667 3.14 0.00 35.54 4.40
108 112 0.322997 CAACAAATCGGGCCACCCTA 60.323 55.000 4.39 0.00 42.67 3.53
132 136 2.031560 GCACGTCGAATGGCATTGATAA 59.968 45.455 19.07 0.00 0.00 1.75
137 141 3.187058 GGCACGTCGAATGGCATT 58.813 55.556 13.54 13.54 42.03 3.56
311 343 6.727824 ATAGAACCAAGAAGATCAAACACG 57.272 37.500 0.00 0.00 0.00 4.49
340 372 5.481105 CCCAGCACAAACAATATTTCACAT 58.519 37.500 0.00 0.00 0.00 3.21
377 409 0.958382 TTCAGCAGGCGCGGTAAATT 60.958 50.000 8.83 0.00 45.49 1.82
403 435 2.597971 GCTGTAAAATATAACGCGCGCA 60.598 45.455 32.58 19.39 0.00 6.09
437 469 2.307934 TTGCGTGCAGTATGATGCTA 57.692 45.000 5.68 0.00 46.63 3.49
513 548 4.188247 TCAACTAAGACCATCTCCAACG 57.812 45.455 0.00 0.00 0.00 4.10
524 559 7.595502 CACCGGTCTATCATAATCAACTAAGAC 59.404 40.741 2.59 0.00 33.10 3.01
534 569 3.403038 GCAAGCACCGGTCTATCATAAT 58.597 45.455 2.59 0.00 0.00 1.28
535 570 2.484770 GGCAAGCACCGGTCTATCATAA 60.485 50.000 2.59 0.00 0.00 1.90
536 571 1.070134 GGCAAGCACCGGTCTATCATA 59.930 52.381 2.59 0.00 0.00 2.15
537 572 0.179045 GGCAAGCACCGGTCTATCAT 60.179 55.000 2.59 0.00 0.00 2.45
538 573 1.220749 GGCAAGCACCGGTCTATCA 59.779 57.895 2.59 0.00 0.00 2.15
539 574 4.126524 GGCAAGCACCGGTCTATC 57.873 61.111 2.59 0.90 0.00 2.08
554 589 1.012486 ACGTACTAGTTTGCAGCGGC 61.012 55.000 0.00 0.31 41.68 6.53
555 590 1.126113 CAACGTACTAGTTTGCAGCGG 59.874 52.381 0.00 0.00 30.96 5.52
556 591 2.055838 TCAACGTACTAGTTTGCAGCG 58.944 47.619 0.00 0.00 30.96 5.18
557 592 3.241678 CGATCAACGTACTAGTTTGCAGC 60.242 47.826 0.00 0.00 37.22 5.25
558 593 4.163552 TCGATCAACGTACTAGTTTGCAG 58.836 43.478 0.00 0.00 43.13 4.41
559 594 4.163458 TCGATCAACGTACTAGTTTGCA 57.837 40.909 0.00 0.00 43.13 4.08
560 595 4.796830 TGATCGATCAACGTACTAGTTTGC 59.203 41.667 25.44 0.00 43.13 3.68
561 596 6.255950 TCTGATCGATCAACGTACTAGTTTG 58.744 40.000 27.09 11.92 43.13 2.93
562 597 6.432607 TCTGATCGATCAACGTACTAGTTT 57.567 37.500 27.09 0.00 43.13 2.66
563 598 6.432607 TTCTGATCGATCAACGTACTAGTT 57.567 37.500 27.09 0.00 43.13 2.24
564 599 5.504337 GCTTCTGATCGATCAACGTACTAGT 60.504 44.000 27.09 0.00 43.13 2.57
565 600 4.907010 GCTTCTGATCGATCAACGTACTAG 59.093 45.833 27.09 13.93 43.13 2.57
566 601 4.334481 TGCTTCTGATCGATCAACGTACTA 59.666 41.667 27.09 9.38 43.13 1.82
567 602 3.128764 TGCTTCTGATCGATCAACGTACT 59.871 43.478 27.09 0.00 43.13 2.73
568 603 3.435566 TGCTTCTGATCGATCAACGTAC 58.564 45.455 27.09 16.26 43.13 3.67
569 604 3.775661 TGCTTCTGATCGATCAACGTA 57.224 42.857 27.09 15.15 43.13 3.57
570 605 2.654749 TGCTTCTGATCGATCAACGT 57.345 45.000 27.09 0.00 43.13 3.99
571 606 2.667969 TGTTGCTTCTGATCGATCAACG 59.332 45.455 27.09 17.34 37.84 4.10
572 607 4.330894 TGATGTTGCTTCTGATCGATCAAC 59.669 41.667 27.09 20.76 36.18 3.18
573 608 4.506758 TGATGTTGCTTCTGATCGATCAA 58.493 39.130 27.09 13.86 36.18 2.57
574 609 4.117685 CTGATGTTGCTTCTGATCGATCA 58.882 43.478 25.80 25.80 35.16 2.92
575 610 4.366586 TCTGATGTTGCTTCTGATCGATC 58.633 43.478 18.72 18.72 0.00 3.69
576 611 4.099113 TCTCTGATGTTGCTTCTGATCGAT 59.901 41.667 0.00 0.00 0.00 3.59
577 612 3.445096 TCTCTGATGTTGCTTCTGATCGA 59.555 43.478 0.00 0.00 0.00 3.59
578 613 3.778618 TCTCTGATGTTGCTTCTGATCG 58.221 45.455 0.00 0.00 0.00 3.69
579 614 4.121317 CCTCTCTGATGTTGCTTCTGATC 58.879 47.826 0.00 0.00 0.00 2.92
580 615 3.518705 ACCTCTCTGATGTTGCTTCTGAT 59.481 43.478 0.00 0.00 0.00 2.90
581 616 2.902486 ACCTCTCTGATGTTGCTTCTGA 59.098 45.455 0.00 0.00 0.00 3.27
582 617 3.331478 ACCTCTCTGATGTTGCTTCTG 57.669 47.619 0.00 0.00 0.00 3.02
583 618 4.619394 CGTTACCTCTCTGATGTTGCTTCT 60.619 45.833 0.00 0.00 0.00 2.85
584 619 3.614616 CGTTACCTCTCTGATGTTGCTTC 59.385 47.826 0.00 0.00 0.00 3.86
585 620 3.589988 CGTTACCTCTCTGATGTTGCTT 58.410 45.455 0.00 0.00 0.00 3.91
586 621 2.093973 CCGTTACCTCTCTGATGTTGCT 60.094 50.000 0.00 0.00 0.00 3.91
587 622 2.271800 CCGTTACCTCTCTGATGTTGC 58.728 52.381 0.00 0.00 0.00 4.17
588 623 3.594603 ACCGTTACCTCTCTGATGTTG 57.405 47.619 0.00 0.00 0.00 3.33
589 624 4.381718 GCTTACCGTTACCTCTCTGATGTT 60.382 45.833 0.00 0.00 0.00 2.71
590 625 3.130693 GCTTACCGTTACCTCTCTGATGT 59.869 47.826 0.00 0.00 0.00 3.06
591 626 3.381908 AGCTTACCGTTACCTCTCTGATG 59.618 47.826 0.00 0.00 0.00 3.07
592 627 3.633418 AGCTTACCGTTACCTCTCTGAT 58.367 45.455 0.00 0.00 0.00 2.90
593 628 3.083122 AGCTTACCGTTACCTCTCTGA 57.917 47.619 0.00 0.00 0.00 3.27
594 629 3.946558 AGTAGCTTACCGTTACCTCTCTG 59.053 47.826 0.00 0.00 30.39 3.35
595 630 3.946558 CAGTAGCTTACCGTTACCTCTCT 59.053 47.826 0.00 0.00 30.39 3.10
596 631 3.488890 GCAGTAGCTTACCGTTACCTCTC 60.489 52.174 0.00 0.00 37.91 3.20
597 632 2.426381 GCAGTAGCTTACCGTTACCTCT 59.574 50.000 0.00 0.00 37.91 3.69
598 633 2.807044 GCAGTAGCTTACCGTTACCTC 58.193 52.381 0.00 0.00 37.91 3.85
599 634 2.955477 GCAGTAGCTTACCGTTACCT 57.045 50.000 0.00 0.00 37.91 3.08
618 653 6.584563 GGATACTGCGAAGAGAGCTATTTTAG 59.415 42.308 0.00 0.00 35.28 1.85
619 654 6.448006 GGATACTGCGAAGAGAGCTATTTTA 58.552 40.000 0.00 0.00 35.28 1.52
620 655 5.293560 GGATACTGCGAAGAGAGCTATTTT 58.706 41.667 0.00 0.00 35.28 1.82
621 656 4.877282 GGATACTGCGAAGAGAGCTATTT 58.123 43.478 0.00 0.00 35.28 1.40
622 657 4.513198 GGATACTGCGAAGAGAGCTATT 57.487 45.455 0.00 0.00 35.28 1.73
638 673 1.041437 CCCCCTTCTGACGAGGATAC 58.959 60.000 0.00 0.00 36.33 2.24
639 674 0.931468 TCCCCCTTCTGACGAGGATA 59.069 55.000 0.00 0.00 36.33 2.59
640 675 0.397816 CTCCCCCTTCTGACGAGGAT 60.398 60.000 0.00 0.00 36.33 3.24
641 676 1.000486 CTCCCCCTTCTGACGAGGA 60.000 63.158 0.00 0.00 36.33 3.71
642 677 2.726351 GCTCCCCCTTCTGACGAGG 61.726 68.421 0.00 0.00 0.00 4.63
643 678 1.544825 TTGCTCCCCCTTCTGACGAG 61.545 60.000 0.00 0.00 0.00 4.18
644 679 1.125093 TTTGCTCCCCCTTCTGACGA 61.125 55.000 0.00 0.00 0.00 4.20
645 680 0.955919 GTTTGCTCCCCCTTCTGACG 60.956 60.000 0.00 0.00 0.00 4.35
646 681 0.110486 TGTTTGCTCCCCCTTCTGAC 59.890 55.000 0.00 0.00 0.00 3.51
647 682 0.850100 TTGTTTGCTCCCCCTTCTGA 59.150 50.000 0.00 0.00 0.00 3.27
648 683 0.961753 GTTGTTTGCTCCCCCTTCTG 59.038 55.000 0.00 0.00 0.00 3.02
649 684 0.555769 TGTTGTTTGCTCCCCCTTCT 59.444 50.000 0.00 0.00 0.00 2.85
650 685 0.961753 CTGTTGTTTGCTCCCCCTTC 59.038 55.000 0.00 0.00 0.00 3.46
651 686 0.555769 TCTGTTGTTTGCTCCCCCTT 59.444 50.000 0.00 0.00 0.00 3.95
652 687 0.779997 ATCTGTTGTTTGCTCCCCCT 59.220 50.000 0.00 0.00 0.00 4.79
653 688 1.177401 GATCTGTTGTTTGCTCCCCC 58.823 55.000 0.00 0.00 0.00 5.40
654 689 1.815003 CTGATCTGTTGTTTGCTCCCC 59.185 52.381 0.00 0.00 0.00 4.81
655 690 1.200948 GCTGATCTGTTGTTTGCTCCC 59.799 52.381 1.27 0.00 0.00 4.30
656 691 1.135859 CGCTGATCTGTTGTTTGCTCC 60.136 52.381 1.27 0.00 0.00 4.70
657 692 1.532868 ACGCTGATCTGTTGTTTGCTC 59.467 47.619 1.27 0.00 0.00 4.26
658 693 1.265095 CACGCTGATCTGTTGTTTGCT 59.735 47.619 1.27 0.00 0.00 3.91
659 694 1.264020 TCACGCTGATCTGTTGTTTGC 59.736 47.619 1.27 0.00 0.00 3.68
660 695 2.663879 GCTCACGCTGATCTGTTGTTTG 60.664 50.000 1.27 0.00 0.00 2.93
661 696 1.532868 GCTCACGCTGATCTGTTGTTT 59.467 47.619 1.27 0.00 0.00 2.83
662 697 1.151668 GCTCACGCTGATCTGTTGTT 58.848 50.000 1.27 0.00 0.00 2.83
663 698 0.671781 GGCTCACGCTGATCTGTTGT 60.672 55.000 1.27 0.00 36.09 3.32
664 699 1.690283 CGGCTCACGCTGATCTGTTG 61.690 60.000 1.27 0.03 45.62 3.33
665 700 1.446792 CGGCTCACGCTGATCTGTT 60.447 57.895 1.27 0.00 45.62 3.16
666 701 2.182791 CGGCTCACGCTGATCTGT 59.817 61.111 1.27 0.00 45.62 3.41
676 711 6.723131 AAGAAGAACTAATTAACGGCTCAC 57.277 37.500 0.00 0.00 0.00 3.51
677 712 6.370718 GGAAAGAAGAACTAATTAACGGCTCA 59.629 38.462 0.00 0.00 0.00 4.26
678 713 6.594547 AGGAAAGAAGAACTAATTAACGGCTC 59.405 38.462 0.00 0.00 0.00 4.70
679 714 6.473758 AGGAAAGAAGAACTAATTAACGGCT 58.526 36.000 0.00 0.00 0.00 5.52
680 715 6.738832 AGGAAAGAAGAACTAATTAACGGC 57.261 37.500 0.00 0.00 0.00 5.68
681 716 9.961265 AAAAAGGAAAGAAGAACTAATTAACGG 57.039 29.630 0.00 0.00 0.00 4.44
706 741 6.399639 AAAGAACTAATTCTCCCGCAAAAA 57.600 33.333 0.00 0.00 44.82 1.94
707 742 6.399639 AAAAGAACTAATTCTCCCGCAAAA 57.600 33.333 0.00 0.00 44.82 2.44
708 743 6.399639 AAAAAGAACTAATTCTCCCGCAAA 57.600 33.333 0.00 0.00 44.82 3.68
709 744 5.048294 GGAAAAAGAACTAATTCTCCCGCAA 60.048 40.000 0.00 0.00 44.82 4.85
710 745 4.457949 GGAAAAAGAACTAATTCTCCCGCA 59.542 41.667 0.00 0.00 44.82 5.69
711 746 4.457949 TGGAAAAAGAACTAATTCTCCCGC 59.542 41.667 0.00 0.00 44.82 6.13
712 747 6.569179 TTGGAAAAAGAACTAATTCTCCCG 57.431 37.500 0.00 0.00 44.82 5.14
713 748 8.367911 ACATTTGGAAAAAGAACTAATTCTCCC 58.632 33.333 0.00 0.00 44.82 4.30
714 749 9.764363 AACATTTGGAAAAAGAACTAATTCTCC 57.236 29.630 0.00 0.00 44.82 3.71
734 769 9.500785 CCCATTTTAGGTTTATGTTGAACATTT 57.499 29.630 16.75 0.00 39.88 2.32
740 775 5.046950 GGTGCCCATTTTAGGTTTATGTTGA 60.047 40.000 0.00 0.00 0.00 3.18
745 780 5.570641 GCTTTGGTGCCCATTTTAGGTTTAT 60.571 40.000 0.00 0.00 31.53 1.40
746 781 4.262678 GCTTTGGTGCCCATTTTAGGTTTA 60.263 41.667 0.00 0.00 31.53 2.01
751 794 2.385013 GGCTTTGGTGCCCATTTTAG 57.615 50.000 0.00 0.00 46.82 1.85
918 961 2.139917 CGAAGAATGTTGTGGGACGAA 58.860 47.619 0.00 0.00 0.00 3.85
921 964 1.804748 GGACGAAGAATGTTGTGGGAC 59.195 52.381 0.00 0.00 0.00 4.46
936 979 0.598158 GTTGGTGCGTTGTAGGACGA 60.598 55.000 1.15 0.00 45.47 4.20
952 1004 1.273606 TGGTTGGGTTTGTGTGTGTTG 59.726 47.619 0.00 0.00 0.00 3.33
970 1022 3.555956 GGTCGATGTTACTATGTGCTTGG 59.444 47.826 0.00 0.00 0.00 3.61
973 1025 2.686405 TCGGTCGATGTTACTATGTGCT 59.314 45.455 0.00 0.00 0.00 4.40
974 1026 3.074504 TCGGTCGATGTTACTATGTGC 57.925 47.619 0.00 0.00 0.00 4.57
1170 1225 2.338620 CGCACCTCGAAGTGACCA 59.661 61.111 18.28 0.00 40.34 4.02
1173 1228 3.610791 CTCGCGCACCTCGAAGTGA 62.611 63.158 18.28 3.40 40.34 3.41
1227 1282 2.357034 TTGCGCTCGTGGAACTCC 60.357 61.111 9.73 0.00 31.75 3.85
1316 1371 6.370718 CACATACATATACTGCTGACATGCAT 59.629 38.462 0.00 0.00 42.48 3.96
1317 1372 5.697633 CACATACATATACTGCTGACATGCA 59.302 40.000 0.00 0.00 41.05 3.96
1322 1377 6.925718 ACATCACACATACATATACTGCTGAC 59.074 38.462 0.00 0.00 0.00 3.51
1412 1467 2.091152 CTTATTTAAGCGCTGCACGG 57.909 50.000 12.58 0.00 43.93 4.94
1469 1526 6.544564 AGAGACTGGAAGCAGAGTAATACTAC 59.455 42.308 0.00 0.00 37.60 2.73
1472 1529 5.845391 AGAGACTGGAAGCAGAGTAATAC 57.155 43.478 0.00 0.00 37.60 1.89
1473 1530 6.859112 AAAGAGACTGGAAGCAGAGTAATA 57.141 37.500 0.00 0.00 37.60 0.98
1474 1531 5.753721 AAAGAGACTGGAAGCAGAGTAAT 57.246 39.130 0.00 0.00 37.60 1.89
1475 1532 5.300752 CAAAAGAGACTGGAAGCAGAGTAA 58.699 41.667 0.00 0.00 37.60 2.24
1476 1533 4.800914 GCAAAAGAGACTGGAAGCAGAGTA 60.801 45.833 0.00 0.00 37.60 2.59
1477 1534 3.737850 CAAAAGAGACTGGAAGCAGAGT 58.262 45.455 0.00 0.00 37.60 3.24
1478 1535 2.483491 GCAAAAGAGACTGGAAGCAGAG 59.517 50.000 0.00 0.00 37.60 3.35
1479 1536 2.498167 GCAAAAGAGACTGGAAGCAGA 58.502 47.619 0.00 0.00 37.60 4.26
1480 1537 1.538950 GGCAAAAGAGACTGGAAGCAG 59.461 52.381 0.00 0.00 37.60 4.24
1481 1538 1.133823 TGGCAAAAGAGACTGGAAGCA 60.134 47.619 0.00 0.00 37.60 3.91
1482 1539 1.538950 CTGGCAAAAGAGACTGGAAGC 59.461 52.381 0.00 0.00 37.60 3.86
1483 1540 2.810852 GTCTGGCAAAAGAGACTGGAAG 59.189 50.000 0.00 0.00 36.46 3.46
1496 1553 3.517296 TGGTGGAAAATAGTCTGGCAA 57.483 42.857 0.00 0.00 0.00 4.52
1499 1556 4.069304 TCGTTTGGTGGAAAATAGTCTGG 58.931 43.478 0.00 0.00 0.00 3.86
1500 1557 5.631026 CATCGTTTGGTGGAAAATAGTCTG 58.369 41.667 0.00 0.00 0.00 3.51
1501 1558 4.156008 GCATCGTTTGGTGGAAAATAGTCT 59.844 41.667 0.00 0.00 0.00 3.24
1502 1559 4.156008 AGCATCGTTTGGTGGAAAATAGTC 59.844 41.667 0.00 0.00 33.95 2.59
1527 1584 1.420378 TCATTTTGCTTGCATGCGTG 58.580 45.000 18.54 14.04 35.36 5.34
1528 1585 2.373540 ATCATTTTGCTTGCATGCGT 57.626 40.000 18.54 3.40 35.36 5.24
1529 1586 4.570935 GTTAATCATTTTGCTTGCATGCG 58.429 39.130 18.54 0.00 35.36 4.73
1533 1590 4.217334 TCTCCGTTAATCATTTTGCTTGCA 59.783 37.500 0.00 0.00 0.00 4.08
1534 1591 4.732784 TCTCCGTTAATCATTTTGCTTGC 58.267 39.130 0.00 0.00 0.00 4.01
1535 1592 5.287035 GCTTCTCCGTTAATCATTTTGCTTG 59.713 40.000 0.00 0.00 0.00 4.01
1538 1595 4.732784 TGCTTCTCCGTTAATCATTTTGC 58.267 39.130 0.00 0.00 0.00 3.68
1541 1598 5.123979 GGAACTGCTTCTCCGTTAATCATTT 59.876 40.000 0.00 0.00 0.00 2.32
1544 1601 3.007506 TGGAACTGCTTCTCCGTTAATCA 59.992 43.478 0.00 0.00 34.14 2.57
1546 1603 3.695830 TGGAACTGCTTCTCCGTTAAT 57.304 42.857 0.00 0.00 34.14 1.40
1547 1604 3.135994 GTTGGAACTGCTTCTCCGTTAA 58.864 45.455 0.00 0.00 34.14 2.01
1548 1605 2.549349 GGTTGGAACTGCTTCTCCGTTA 60.549 50.000 0.00 0.00 34.14 3.18
1549 1606 1.594331 GTTGGAACTGCTTCTCCGTT 58.406 50.000 0.00 0.00 34.14 4.44
1552 2407 0.110486 TGGGTTGGAACTGCTTCTCC 59.890 55.000 0.00 0.00 0.00 3.71
1556 2411 2.031870 GTCTTTGGGTTGGAACTGCTT 58.968 47.619 0.00 0.00 0.00 3.91
1594 2449 2.096218 GCGACGCTGTCAAAGAAATCTT 60.096 45.455 13.73 0.00 37.91 2.40
1618 2473 0.036164 TTGTTGGTCTCCATCCCGTG 59.964 55.000 0.00 0.00 31.53 4.94
1634 2530 3.322254 CCTCTACTCTGGACTGTTGTTGT 59.678 47.826 0.00 0.00 0.00 3.32
1643 2539 1.076923 TCCGGCCTCTACTCTGGAC 60.077 63.158 0.00 0.00 33.06 4.02
1644 2540 1.076923 GTCCGGCCTCTACTCTGGA 60.077 63.158 0.00 0.00 35.49 3.86
1645 2541 0.684805 AAGTCCGGCCTCTACTCTGG 60.685 60.000 0.00 0.00 0.00 3.86
1739 3000 6.445357 TCAAGTAGGTTCAGTTTGGTTTTC 57.555 37.500 0.00 0.00 0.00 2.29
1772 3033 7.712205 AGAATTTTGTTTTTGGTGAATGGAGAG 59.288 33.333 0.00 0.00 0.00 3.20
1881 3213 3.438434 GTGAGAGCCCAAGAGAAAATCAC 59.562 47.826 0.00 0.00 0.00 3.06
1899 3231 5.692204 AGTCGTGTCTTTGTTCTATTGTGAG 59.308 40.000 0.00 0.00 0.00 3.51
1900 3232 5.597806 AGTCGTGTCTTTGTTCTATTGTGA 58.402 37.500 0.00 0.00 0.00 3.58
1901 3233 5.907197 AGTCGTGTCTTTGTTCTATTGTG 57.093 39.130 0.00 0.00 0.00 3.33
1965 3297 2.548057 TGTGCTTCTGTTTTGGTCGATC 59.452 45.455 0.00 0.00 0.00 3.69
1983 3318 4.641541 TCCCTTATGTGCATGATTCTTGTG 59.358 41.667 0.00 0.00 0.00 3.33
1997 3332 2.481441 TGACCTCAGCATCCCTTATGT 58.519 47.619 0.00 0.00 37.93 2.29
2000 3335 3.114606 TGAATGACCTCAGCATCCCTTA 58.885 45.455 0.00 0.00 0.00 2.69
2017 3396 4.448347 GGGATGGGCTCCTAGAAAATGAAT 60.448 45.833 0.00 0.00 44.28 2.57
2040 3419 7.744715 CCTTGCATGTAGAGTACTTTTTAAACG 59.255 37.037 0.00 0.00 0.00 3.60
2055 3434 0.447801 GGCACGAACCTTGCATGTAG 59.552 55.000 0.00 0.00 42.12 2.74
2070 3705 0.615331 TGAGACTCTTGGGATGGCAC 59.385 55.000 3.68 0.00 0.00 5.01
2072 3707 0.908198 AGTGAGACTCTTGGGATGGC 59.092 55.000 3.68 0.00 0.00 4.40
2103 3741 4.595762 ATTTCTGTTGTTGATTGCTGCT 57.404 36.364 0.00 0.00 0.00 4.24
2107 3751 8.841444 AATCGTATATTTCTGTTGTTGATTGC 57.159 30.769 0.00 0.00 0.00 3.56
2116 3760 8.964476 ATGACAAGGAATCGTATATTTCTGTT 57.036 30.769 0.00 0.00 0.00 3.16
2124 3768 7.827236 AGTTTTTGGATGACAAGGAATCGTATA 59.173 33.333 0.00 0.00 40.82 1.47
2179 3823 3.632145 ACATGGTTCGGGAATATTTGAGC 59.368 43.478 0.00 0.00 0.00 4.26
2182 3826 6.765989 TCTTAGACATGGTTCGGGAATATTTG 59.234 38.462 0.00 0.00 0.00 2.32
2230 3874 7.989416 ATGGACCGATAACTTTGAAGTTTTA 57.011 32.000 13.71 0.00 46.52 1.52
2240 3956 5.187967 AGTCAGAAGAATGGACCGATAACTT 59.812 40.000 0.00 0.00 31.99 2.66


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

AutoCloner maintained by Alex Coulton.