Multiple sequence alignment - TraesCS3B01G379600

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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 TraesCS3B01G379600 chr3B 100.000 2492 0 0 1 2492 597462883 597460392 0.000000e+00 4602
1 TraesCS3B01G379600 chr3B 85.000 180 21 4 490 667 444679866 444679691 7.080000e-41 178
2 TraesCS3B01G379600 chr3D 94.934 1816 56 15 710 2492 454677863 454676051 0.000000e+00 2811
3 TraesCS3B01G379600 chr3D 90.702 527 46 2 2 525 454686334 454685808 0.000000e+00 699
4 TraesCS3B01G379600 chr3D 85.475 179 22 2 490 667 612275521 612275346 1.520000e-42 183
5 TraesCS3B01G379600 chr3A 93.307 1270 47 12 711 1947 596752955 596751691 0.000000e+00 1840
6 TraesCS3B01G379600 chr3A 93.573 529 21 4 1975 2492 596751692 596751166 0.000000e+00 776
7 TraesCS3B01G379600 chr3A 86.472 377 46 4 28 402 596753542 596753169 2.310000e-110 409
8 TraesCS3B01G379600 chr7B 86.413 184 21 2 485 667 339236087 339236267 5.440000e-47 198
9 TraesCS3B01G379600 chr7B 84.831 178 21 5 492 667 137560103 137560276 9.160000e-40 174
10 TraesCS3B01G379600 chr1B 80.934 257 37 7 1001 1257 530610290 530610534 2.530000e-45 193
11 TraesCS3B01G379600 chr1D 86.034 179 21 3 490 667 377012361 377012536 3.270000e-44 189
12 TraesCS3B01G379600 chr1A 85.475 179 21 4 490 667 11790005 11790179 5.480000e-42 182
13 TraesCS3B01G379600 chr6B 84.916 179 23 3 490 667 470631260 470631085 7.080000e-41 178
14 TraesCS3B01G379600 chr5B 85.000 180 21 4 490 667 649412577 649412752 7.080000e-41 178
15 TraesCS3B01G379600 chr5A 84.916 179 23 3 490 667 18779887 18780062 7.080000e-41 178
16 TraesCS3B01G379600 chr4A 84.667 150 19 3 1000 1147 139613127 139613274 2.000000e-31 147
17 TraesCS3B01G379600 chr4D 82.432 148 26 0 1000 1147 334110129 334109982 2.010000e-26 130
18 TraesCS3B01G379600 chr4B 82.432 148 26 0 1000 1147 412084720 412084573 2.010000e-26 130


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 TraesCS3B01G379600 chr3B 597460392 597462883 2491 True 4602.000000 4602 100.000000 1 2492 1 chr3B.!!$R2 2491
1 TraesCS3B01G379600 chr3D 454676051 454677863 1812 True 2811.000000 2811 94.934000 710 2492 1 chr3D.!!$R1 1782
2 TraesCS3B01G379600 chr3D 454685808 454686334 526 True 699.000000 699 90.702000 2 525 1 chr3D.!!$R2 523
3 TraesCS3B01G379600 chr3A 596751166 596753542 2376 True 1008.333333 1840 91.117333 28 2492 3 chr3A.!!$R1 2464

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
608 697 0.172803 ATCTCACCGACGTAACTGGC 59.827 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
1494 1603 0.450184 GCGAGAGAACTCTTCGAGCT 59.55 55.0 19.32 0.0 40.61 4.09 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
37 38 6.109359 GTGCACTCCTTTGAAGATATGTACT 58.891 40.000 10.32 0.00 0.00 2.73
39 40 5.460419 GCACTCCTTTGAAGATATGTACTCG 59.540 44.000 0.00 0.00 0.00 4.18
49 50 4.480115 AGATATGTACTCGGTCCCATTCA 58.520 43.478 0.00 0.00 0.00 2.57
81 82 5.541845 GCTCCACAATGCATATAGTAGACA 58.458 41.667 0.00 0.00 0.00 3.41
154 155 0.677288 ACCTCGTGTTGACCGATTGA 59.323 50.000 0.00 0.00 33.27 2.57
156 157 1.336887 CCTCGTGTTGACCGATTGACT 60.337 52.381 0.00 0.00 33.27 3.41
198 199 0.994050 GGATCCCCTAGCCAACCCTT 60.994 60.000 0.00 0.00 32.17 3.95
231 233 1.338484 ACTGCGAGACTGCAATGACAT 60.338 47.619 0.00 0.00 45.74 3.06
238 240 4.267214 CGAGACTGCAATGACATTCTACTG 59.733 45.833 0.00 0.00 30.48 2.74
283 286 4.164988 AGGTTGTTGAGGCAGAGCTAATAT 59.835 41.667 0.00 0.00 0.00 1.28
289 292 5.316327 TGAGGCAGAGCTAATATATGACG 57.684 43.478 0.00 0.00 0.00 4.35
302 307 7.863375 GCTAATATATGACGTTATGAGGCTAGG 59.137 40.741 2.58 0.00 0.00 3.02
310 315 3.532542 GTTATGAGGCTAGGAACACACC 58.467 50.000 0.00 0.00 0.00 4.16
311 316 1.656587 ATGAGGCTAGGAACACACCA 58.343 50.000 0.00 0.00 0.00 4.17
344 349 2.811873 GCCGGGAGAATTGTGCTATGAT 60.812 50.000 2.18 0.00 0.00 2.45
417 506 8.511604 TCAAATTTTGTTGGCCTCAAATTTAA 57.488 26.923 20.88 14.33 35.25 1.52
419 508 7.872113 AATTTTGTTGGCCTCAAATTTAACA 57.128 28.000 20.88 11.08 35.25 2.41
441 530 4.025360 AGCATCCATGAAACTAAATGCCA 58.975 39.130 0.00 0.00 40.18 4.92
446 535 7.663827 CATCCATGAAACTAAATGCCATATGT 58.336 34.615 1.24 0.00 0.00 2.29
447 536 7.041635 TCCATGAAACTAAATGCCATATGTG 57.958 36.000 1.24 0.00 0.00 3.21
469 558 4.041567 TGGAACTTGCAAGAGTATTCTCCA 59.958 41.667 32.50 23.48 41.26 3.86
473 562 6.360370 ACTTGCAAGAGTATTCTCCACTTA 57.640 37.500 32.50 0.00 41.26 2.24
480 569 6.798427 AGAGTATTCTCCACTTATGAGCAA 57.202 37.500 0.00 0.00 41.26 3.91
522 611 3.452755 AAAAGTTTTGGAAAGCGGAGG 57.547 42.857 0.00 0.00 0.00 4.30
525 614 8.091237 CAAAAAGTTTTGGAAAGCGGAGGTTC 62.091 42.308 0.61 0.00 44.75 3.62
534 623 2.226962 AGCGGAGGTTCCACTTACTA 57.773 50.000 0.00 0.00 35.91 1.82
537 626 2.998670 GCGGAGGTTCCACTTACTAAAC 59.001 50.000 0.00 0.00 35.91 2.01
540 629 5.567423 GCGGAGGTTCCACTTACTAAACTTA 60.567 44.000 0.00 0.00 35.91 2.24
542 631 6.930722 CGGAGGTTCCACTTACTAAACTTAAA 59.069 38.462 0.00 0.00 35.91 1.52
566 655 9.696917 AAAATTTTCAAGCAGTATCTTTGTAGG 57.303 29.630 0.00 0.00 0.00 3.18
568 657 4.487714 TCAAGCAGTATCTTTGTAGGGG 57.512 45.455 0.00 0.00 0.00 4.79
569 658 4.101114 TCAAGCAGTATCTTTGTAGGGGA 58.899 43.478 0.00 0.00 0.00 4.81
570 659 4.162320 TCAAGCAGTATCTTTGTAGGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
571 660 3.725634 AGCAGTATCTTTGTAGGGGAGT 58.274 45.455 0.00 0.00 0.00 3.85
572 661 4.104831 AGCAGTATCTTTGTAGGGGAGTT 58.895 43.478 0.00 0.00 0.00 3.01
573 662 4.080863 AGCAGTATCTTTGTAGGGGAGTTG 60.081 45.833 0.00 0.00 0.00 3.16
574 663 4.323562 GCAGTATCTTTGTAGGGGAGTTGT 60.324 45.833 0.00 0.00 0.00 3.32
575 664 5.178797 CAGTATCTTTGTAGGGGAGTTGTG 58.821 45.833 0.00 0.00 0.00 3.33
576 665 2.561478 TCTTTGTAGGGGAGTTGTGC 57.439 50.000 0.00 0.00 0.00 4.57
577 666 2.054799 TCTTTGTAGGGGAGTTGTGCT 58.945 47.619 0.00 0.00 0.00 4.40
578 667 3.244582 TCTTTGTAGGGGAGTTGTGCTA 58.755 45.455 0.00 0.00 0.00 3.49
579 668 3.649023 TCTTTGTAGGGGAGTTGTGCTAA 59.351 43.478 0.00 0.00 0.00 3.09
580 669 3.412237 TTGTAGGGGAGTTGTGCTAAC 57.588 47.619 0.00 0.00 0.00 2.34
581 670 1.626825 TGTAGGGGAGTTGTGCTAACC 59.373 52.381 1.57 0.00 0.00 2.85
582 671 1.626825 GTAGGGGAGTTGTGCTAACCA 59.373 52.381 0.00 0.00 0.00 3.67
583 672 1.145571 AGGGGAGTTGTGCTAACCAA 58.854 50.000 0.00 0.00 0.00 3.67
584 673 1.497286 AGGGGAGTTGTGCTAACCAAA 59.503 47.619 0.00 0.00 0.00 3.28
585 674 1.886542 GGGGAGTTGTGCTAACCAAAG 59.113 52.381 0.00 0.00 0.00 2.77
586 675 2.488347 GGGGAGTTGTGCTAACCAAAGA 60.488 50.000 0.00 0.00 0.00 2.52
587 676 2.552743 GGGAGTTGTGCTAACCAAAGAC 59.447 50.000 0.00 0.00 0.00 3.01
588 677 3.211045 GGAGTTGTGCTAACCAAAGACA 58.789 45.455 1.57 0.00 0.00 3.41
589 678 3.630312 GGAGTTGTGCTAACCAAAGACAA 59.370 43.478 1.57 0.00 0.00 3.18
590 679 4.278419 GGAGTTGTGCTAACCAAAGACAAT 59.722 41.667 0.00 0.00 0.00 2.71
591 680 5.438761 AGTTGTGCTAACCAAAGACAATC 57.561 39.130 0.00 0.00 0.00 2.67
592 681 5.133221 AGTTGTGCTAACCAAAGACAATCT 58.867 37.500 0.00 0.00 0.00 2.40
593 682 5.239525 AGTTGTGCTAACCAAAGACAATCTC 59.760 40.000 0.00 0.00 0.00 2.75
594 683 4.713553 TGTGCTAACCAAAGACAATCTCA 58.286 39.130 0.00 0.00 0.00 3.27
595 684 4.515191 TGTGCTAACCAAAGACAATCTCAC 59.485 41.667 0.00 0.00 0.00 3.51
596 685 4.072131 TGCTAACCAAAGACAATCTCACC 58.928 43.478 0.00 0.00 0.00 4.02
597 686 3.125316 GCTAACCAAAGACAATCTCACCG 59.875 47.826 0.00 0.00 0.00 4.94
598 687 3.485463 AACCAAAGACAATCTCACCGA 57.515 42.857 0.00 0.00 0.00 4.69
599 688 2.767505 ACCAAAGACAATCTCACCGAC 58.232 47.619 0.00 0.00 0.00 4.79
600 689 1.726791 CCAAAGACAATCTCACCGACG 59.273 52.381 0.00 0.00 0.00 5.12
601 690 2.404215 CAAAGACAATCTCACCGACGT 58.596 47.619 0.00 0.00 0.00 4.34
602 691 3.571571 CAAAGACAATCTCACCGACGTA 58.428 45.455 0.00 0.00 0.00 3.57
603 692 3.928727 AAGACAATCTCACCGACGTAA 57.071 42.857 0.00 0.00 0.00 3.18
604 693 3.213249 AGACAATCTCACCGACGTAAC 57.787 47.619 0.00 0.00 0.00 2.50
605 694 2.818432 AGACAATCTCACCGACGTAACT 59.182 45.455 0.00 0.00 0.00 2.24
606 695 2.915463 GACAATCTCACCGACGTAACTG 59.085 50.000 0.00 0.00 0.00 3.16
607 696 2.259618 CAATCTCACCGACGTAACTGG 58.740 52.381 0.00 0.00 0.00 4.00
608 697 0.172803 ATCTCACCGACGTAACTGGC 59.827 55.000 0.00 0.00 0.00 4.85
609 698 1.445582 CTCACCGACGTAACTGGCC 60.446 63.158 0.00 0.00 0.00 5.36
610 699 2.149803 CTCACCGACGTAACTGGCCA 62.150 60.000 4.71 4.71 0.00 5.36
611 700 1.736645 CACCGACGTAACTGGCCAG 60.737 63.158 31.60 31.60 0.00 4.85
612 701 2.125673 CCGACGTAACTGGCCAGG 60.126 66.667 35.42 20.37 0.00 4.45
613 702 2.642254 CCGACGTAACTGGCCAGGA 61.642 63.158 35.42 20.91 0.00 3.86
614 703 1.290955 CGACGTAACTGGCCAGGAA 59.709 57.895 35.42 20.65 0.00 3.36
615 704 0.736325 CGACGTAACTGGCCAGGAAG 60.736 60.000 35.42 25.39 0.00 3.46
616 705 0.320697 GACGTAACTGGCCAGGAAGT 59.679 55.000 35.42 28.17 0.00 3.01
617 706 1.547372 GACGTAACTGGCCAGGAAGTA 59.453 52.381 35.42 18.73 0.00 2.24
618 707 1.972795 ACGTAACTGGCCAGGAAGTAA 59.027 47.619 35.42 11.81 0.00 2.24
619 708 2.028385 ACGTAACTGGCCAGGAAGTAAG 60.028 50.000 35.42 23.11 0.00 2.34
620 709 2.232941 CGTAACTGGCCAGGAAGTAAGA 59.767 50.000 35.42 9.15 0.00 2.10
621 710 3.306502 CGTAACTGGCCAGGAAGTAAGAA 60.307 47.826 35.42 7.78 0.00 2.52
622 711 3.425162 AACTGGCCAGGAAGTAAGAAG 57.575 47.619 35.42 8.23 0.00 2.85
623 712 2.339769 ACTGGCCAGGAAGTAAGAAGT 58.660 47.619 35.42 8.94 0.00 3.01
624 713 2.039084 ACTGGCCAGGAAGTAAGAAGTG 59.961 50.000 35.42 7.53 0.00 3.16
625 714 2.039084 CTGGCCAGGAAGTAAGAAGTGT 59.961 50.000 26.14 0.00 0.00 3.55
626 715 2.038557 TGGCCAGGAAGTAAGAAGTGTC 59.961 50.000 0.00 0.00 0.00 3.67
627 716 2.338500 GCCAGGAAGTAAGAAGTGTCG 58.662 52.381 0.00 0.00 0.00 4.35
628 717 2.288886 GCCAGGAAGTAAGAAGTGTCGT 60.289 50.000 0.00 0.00 0.00 4.34
629 718 3.802675 GCCAGGAAGTAAGAAGTGTCGTT 60.803 47.826 0.00 0.00 0.00 3.85
630 719 4.377897 CCAGGAAGTAAGAAGTGTCGTTT 58.622 43.478 0.00 0.00 0.00 3.60
631 720 4.814771 CCAGGAAGTAAGAAGTGTCGTTTT 59.185 41.667 0.00 0.00 0.00 2.43
632 721 5.296035 CCAGGAAGTAAGAAGTGTCGTTTTT 59.704 40.000 0.00 0.00 0.00 1.94
633 722 6.192360 CAGGAAGTAAGAAGTGTCGTTTTTG 58.808 40.000 0.00 0.00 0.00 2.44
634 723 5.878669 AGGAAGTAAGAAGTGTCGTTTTTGT 59.121 36.000 0.00 0.00 0.00 2.83
635 724 7.010738 CAGGAAGTAAGAAGTGTCGTTTTTGTA 59.989 37.037 0.00 0.00 0.00 2.41
636 725 7.010830 AGGAAGTAAGAAGTGTCGTTTTTGTAC 59.989 37.037 0.00 0.00 0.00 2.90
637 726 7.010830 GGAAGTAAGAAGTGTCGTTTTTGTACT 59.989 37.037 0.00 0.00 0.00 2.73
638 727 7.460751 AGTAAGAAGTGTCGTTTTTGTACTC 57.539 36.000 0.00 0.00 0.00 2.59
639 728 7.037438 AGTAAGAAGTGTCGTTTTTGTACTCA 58.963 34.615 0.00 0.00 0.00 3.41
640 729 6.920569 AAGAAGTGTCGTTTTTGTACTCAT 57.079 33.333 0.00 0.00 0.00 2.90
641 730 6.287107 AGAAGTGTCGTTTTTGTACTCATG 57.713 37.500 0.00 0.00 0.00 3.07
642 731 6.046593 AGAAGTGTCGTTTTTGTACTCATGA 58.953 36.000 0.00 0.00 0.00 3.07
643 732 6.706270 AGAAGTGTCGTTTTTGTACTCATGAT 59.294 34.615 0.00 0.00 0.00 2.45
644 733 6.228273 AGTGTCGTTTTTGTACTCATGATG 57.772 37.500 0.00 0.00 0.00 3.07
645 734 5.989168 AGTGTCGTTTTTGTACTCATGATGA 59.011 36.000 0.00 0.00 0.00 2.92
659 748 5.885230 TCATGATGAGACAATCAAACACC 57.115 39.130 0.00 0.00 42.53 4.16
660 749 5.563592 TCATGATGAGACAATCAAACACCT 58.436 37.500 0.00 0.00 42.53 4.00
661 750 5.645067 TCATGATGAGACAATCAAACACCTC 59.355 40.000 0.00 0.00 42.53 3.85
662 751 5.233083 TGATGAGACAATCAAACACCTCT 57.767 39.130 0.00 0.00 42.53 3.69
663 752 5.624159 TGATGAGACAATCAAACACCTCTT 58.376 37.500 0.00 0.00 42.53 2.85
664 753 6.064060 TGATGAGACAATCAAACACCTCTTT 58.936 36.000 0.00 0.00 42.53 2.52
665 754 6.547141 TGATGAGACAATCAAACACCTCTTTT 59.453 34.615 0.00 0.00 42.53 2.27
666 755 6.773976 TGAGACAATCAAACACCTCTTTTT 57.226 33.333 0.00 0.00 34.02 1.94
685 774 4.875544 TTTTTCAGGTTGTCAAGTCTCG 57.124 40.909 0.00 0.00 0.00 4.04
686 775 2.526304 TTCAGGTTGTCAAGTCTCGG 57.474 50.000 0.00 0.00 0.00 4.63
687 776 1.410004 TCAGGTTGTCAAGTCTCGGT 58.590 50.000 0.00 0.00 0.00 4.69
688 777 1.340248 TCAGGTTGTCAAGTCTCGGTC 59.660 52.381 0.00 0.00 0.00 4.79
689 778 0.314302 AGGTTGTCAAGTCTCGGTCG 59.686 55.000 0.00 0.00 0.00 4.79
690 779 0.313043 GGTTGTCAAGTCTCGGTCGA 59.687 55.000 0.00 0.00 0.00 4.20
691 780 1.406447 GTTGTCAAGTCTCGGTCGAC 58.594 55.000 7.13 7.13 0.00 4.20
692 781 1.001597 GTTGTCAAGTCTCGGTCGACT 60.002 52.381 16.46 0.00 45.73 4.18
698 787 2.766345 AGTCTCGGTCGACTTAGACT 57.234 50.000 30.71 30.71 41.27 3.24
699 788 3.883830 AGTCTCGGTCGACTTAGACTA 57.116 47.619 32.98 13.33 45.19 2.59
700 789 3.784338 AGTCTCGGTCGACTTAGACTAG 58.216 50.000 32.98 14.54 45.19 2.57
701 790 2.284952 GTCTCGGTCGACTTAGACTAGC 59.715 54.545 28.36 13.24 40.76 3.42
702 791 2.093816 TCTCGGTCGACTTAGACTAGCA 60.094 50.000 16.46 0.00 40.76 3.49
703 792 2.676839 CTCGGTCGACTTAGACTAGCAA 59.323 50.000 16.46 0.00 40.76 3.91
704 793 2.676839 TCGGTCGACTTAGACTAGCAAG 59.323 50.000 16.46 0.00 40.76 4.01
705 794 2.676839 CGGTCGACTTAGACTAGCAAGA 59.323 50.000 16.46 0.00 40.76 3.02
706 795 3.312973 CGGTCGACTTAGACTAGCAAGAT 59.687 47.826 16.46 0.00 40.76 2.40
707 796 4.201930 CGGTCGACTTAGACTAGCAAGATT 60.202 45.833 16.46 0.00 40.76 2.40
708 797 5.038033 GGTCGACTTAGACTAGCAAGATTG 58.962 45.833 16.46 0.00 40.76 2.67
759 849 3.774216 TGGCCTAAAAAGGAAATGGATGG 59.226 43.478 3.32 0.00 0.00 3.51
768 858 6.355588 AAAGGAAATGGATGGGGTAATACT 57.644 37.500 0.00 0.00 0.00 2.12
779 869 2.775960 GGGGTAATACTTAGGTGTGGCT 59.224 50.000 0.00 0.00 0.00 4.75
780 870 3.201487 GGGGTAATACTTAGGTGTGGCTT 59.799 47.826 0.00 0.00 0.00 4.35
786 876 3.059352 ACTTAGGTGTGGCTTTAGCTG 57.941 47.619 0.00 0.00 41.70 4.24
941 1032 0.392461 TAAACAAGCCAGGCTAGCGG 60.392 55.000 16.56 7.59 38.25 5.52
1494 1603 0.989212 AGGAGGCCTCGGAGTAGAGA 60.989 60.000 26.36 0.00 40.57 3.10
1527 1636 0.616891 TCTCGCCTTTCTTTACCCCC 59.383 55.000 0.00 0.00 0.00 5.40
1528 1637 0.618981 CTCGCCTTTCTTTACCCCCT 59.381 55.000 0.00 0.00 0.00 4.79
1626 1735 7.290014 TCTCAATACCCTGACACATGTATGTAT 59.710 37.037 0.00 0.00 39.39 2.29
1632 1741 6.183360 ACCCTGACACATGTATGTATAGTGAC 60.183 42.308 0.00 0.00 39.39 3.67
1666 1775 5.769484 TTAGTGGTTCATAGATCGGAGAC 57.231 43.478 0.00 0.00 42.51 3.36
1687 1797 8.388853 GGAGACGAGAGGAAAAATTATTGTAAC 58.611 37.037 0.00 0.00 0.00 2.50
1688 1798 9.152595 GAGACGAGAGGAAAAATTATTGTAACT 57.847 33.333 0.00 0.00 0.00 2.24
1697 1807 6.614694 AAAATTATTGTAACTCCCCCAACC 57.385 37.500 0.00 0.00 0.00 3.77
1729 1839 7.656948 AGAGATATTTAGCTGAGCTGATTGAAC 59.343 37.037 18.79 3.38 40.10 3.18
1749 1859 6.503524 TGAACTTTTCTGGGAAAATCTTTCG 58.496 36.000 6.00 0.00 0.00 3.46
1759 1869 4.753107 GGGAAAATCTTTCGTAGTGTGTGA 59.247 41.667 0.00 0.00 0.00 3.58
1764 1874 7.451281 AAATCTTTCGTAGTGTGTGATATCG 57.549 36.000 0.00 0.00 0.00 2.92
1834 1953 8.824159 ATCTTTCATAACATGGAGTATTCTCG 57.176 34.615 0.00 0.00 41.26 4.04
1860 1979 6.064846 ACAGAAGACAATGTGTGATTCAAC 57.935 37.500 0.00 0.00 32.37 3.18
1924 2052 5.043248 GGCACATTTAATTCAGTGTATGCC 58.957 41.667 0.00 0.00 34.59 4.40
1955 2083 5.425539 TCGACAAAATCCCTAGGAGAATCTT 59.574 40.000 11.48 0.00 34.05 2.40
1971 2099 5.982356 AGAATCTTACAAGCACTGCTCATA 58.018 37.500 3.40 0.00 38.25 2.15
1981 2109 7.488322 ACAAGCACTGCTCATAAAAGTAAAAA 58.512 30.769 3.40 0.00 38.25 1.94
2013 2141 4.047125 TGGCAGGGCAAGGTAGGC 62.047 66.667 0.00 0.00 0.00 3.93
2043 2171 7.417683 CCATTTGGATTACAATGCCTATTGTCA 60.418 37.037 8.75 0.00 44.66 3.58
2112 2248 9.479549 AGGAAATGATAAGTACCAACATGAATT 57.520 29.630 0.00 0.00 0.00 2.17
2183 2320 7.416213 CCCAATTATTGTCCGAAATGCTTAGAA 60.416 37.037 4.15 0.00 0.00 2.10
2432 2572 9.255029 ACAAGCTAATCTAATTTGGGTTGTTAT 57.745 29.630 10.87 0.00 39.71 1.89
2481 2624 8.686334 ACACTGTGATTTATTTTGTTCTTGAGT 58.314 29.630 15.86 0.00 0.00 3.41
2482 2625 9.173939 CACTGTGATTTATTTTGTTCTTGAGTC 57.826 33.333 0.32 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.432146 GGAGTGCACCTCAGATACATGA 59.568 50.000 14.63 0.00 42.40 3.07
37 38 1.340600 GGGTGAAATGAATGGGACCGA 60.341 52.381 0.00 0.00 0.00 4.69
39 40 1.102978 CGGGTGAAATGAATGGGACC 58.897 55.000 0.00 0.00 0.00 4.46
49 50 1.176527 CATTGTGGAGCGGGTGAAAT 58.823 50.000 0.00 0.00 0.00 2.17
81 82 4.612264 ACCCACACAATTCGTAGTAGTT 57.388 40.909 0.00 0.00 0.00 2.24
165 166 0.107654 GGATCCTTCCAACACCCTCG 60.108 60.000 3.84 0.00 42.12 4.63
198 199 0.398696 TCGCAGTTTGGGCCTTCTTA 59.601 50.000 4.53 0.00 0.00 2.10
213 215 1.733912 GAATGTCATTGCAGTCTCGCA 59.266 47.619 1.88 0.00 41.03 5.10
231 233 1.592400 CGTCCACCTCCGCAGTAGAA 61.592 60.000 0.00 0.00 0.00 2.10
238 240 0.391263 AGAATTTCGTCCACCTCCGC 60.391 55.000 0.00 0.00 0.00 5.54
283 286 4.891168 TGTTCCTAGCCTCATAACGTCATA 59.109 41.667 0.00 0.00 0.00 2.15
289 292 3.055385 TGGTGTGTTCCTAGCCTCATAAC 60.055 47.826 0.00 0.00 0.00 1.89
302 307 2.554032 CAGACCTTCCAATGGTGTGTTC 59.446 50.000 0.00 0.00 41.96 3.18
310 315 1.750399 CCCGGCAGACCTTCCAATG 60.750 63.158 0.00 0.00 0.00 2.82
311 316 1.915078 CTCCCGGCAGACCTTCCAAT 61.915 60.000 0.00 0.00 0.00 3.16
417 506 4.142093 GGCATTTAGTTTCATGGATGCTGT 60.142 41.667 6.15 0.00 39.69 4.40
419 508 4.025360 TGGCATTTAGTTTCATGGATGCT 58.975 39.130 6.15 0.00 39.69 3.79
441 530 7.341805 AGAATACTCTTGCAAGTTCCACATAT 58.658 34.615 25.19 10.86 0.00 1.78
446 535 4.041567 TGGAGAATACTCTTGCAAGTTCCA 59.958 41.667 25.19 20.83 42.28 3.53
447 536 4.393371 GTGGAGAATACTCTTGCAAGTTCC 59.607 45.833 25.19 18.99 42.28 3.62
506 595 1.000607 GGAACCTCCGCTTTCCAAAAC 60.001 52.381 0.00 0.00 41.01 2.43
507 596 1.324383 GGAACCTCCGCTTTCCAAAA 58.676 50.000 0.00 0.00 41.01 2.44
508 597 0.183971 TGGAACCTCCGCTTTCCAAA 59.816 50.000 0.48 0.00 46.70 3.28
511 600 3.982829 GTGGAACCTCCGCTTTCC 58.017 61.111 0.00 0.00 43.50 3.13
540 629 9.696917 CCTACAAAGATACTGCTTGAAAATTTT 57.303 29.630 2.28 2.28 0.00 1.82
542 631 7.093771 CCCCTACAAAGATACTGCTTGAAAATT 60.094 37.037 0.00 0.00 0.00 1.82
548 637 4.080863 ACTCCCCTACAAAGATACTGCTTG 60.081 45.833 0.00 0.00 0.00 4.01
552 641 5.178797 CACAACTCCCCTACAAAGATACTG 58.821 45.833 0.00 0.00 0.00 2.74
554 643 3.939592 GCACAACTCCCCTACAAAGATAC 59.060 47.826 0.00 0.00 0.00 2.24
555 644 3.844211 AGCACAACTCCCCTACAAAGATA 59.156 43.478 0.00 0.00 0.00 1.98
559 648 3.497227 GGTTAGCACAACTCCCCTACAAA 60.497 47.826 1.81 0.00 0.00 2.83
560 649 2.039348 GGTTAGCACAACTCCCCTACAA 59.961 50.000 1.81 0.00 0.00 2.41
562 651 1.626825 TGGTTAGCACAACTCCCCTAC 59.373 52.381 1.81 0.00 0.00 3.18
563 652 2.032965 TGGTTAGCACAACTCCCCTA 57.967 50.000 1.81 0.00 0.00 3.53
564 653 1.145571 TTGGTTAGCACAACTCCCCT 58.854 50.000 1.81 0.00 0.00 4.79
565 654 1.886542 CTTTGGTTAGCACAACTCCCC 59.113 52.381 1.81 0.00 0.00 4.81
566 655 2.552743 GTCTTTGGTTAGCACAACTCCC 59.447 50.000 1.81 0.00 0.00 4.30
568 657 4.893424 TTGTCTTTGGTTAGCACAACTC 57.107 40.909 1.81 0.00 0.00 3.01
569 658 5.133221 AGATTGTCTTTGGTTAGCACAACT 58.867 37.500 1.81 0.00 30.04 3.16
570 659 5.008613 TGAGATTGTCTTTGGTTAGCACAAC 59.991 40.000 0.00 0.00 30.04 3.32
571 660 5.008613 GTGAGATTGTCTTTGGTTAGCACAA 59.991 40.000 0.00 0.00 0.00 3.33
572 661 4.515191 GTGAGATTGTCTTTGGTTAGCACA 59.485 41.667 0.00 0.00 0.00 4.57
573 662 4.083271 GGTGAGATTGTCTTTGGTTAGCAC 60.083 45.833 0.00 0.00 0.00 4.40
574 663 4.072131 GGTGAGATTGTCTTTGGTTAGCA 58.928 43.478 0.00 0.00 0.00 3.49
575 664 3.125316 CGGTGAGATTGTCTTTGGTTAGC 59.875 47.826 0.00 0.00 0.00 3.09
576 665 4.389077 GTCGGTGAGATTGTCTTTGGTTAG 59.611 45.833 0.00 0.00 0.00 2.34
577 666 4.312443 GTCGGTGAGATTGTCTTTGGTTA 58.688 43.478 0.00 0.00 0.00 2.85
578 667 3.139077 GTCGGTGAGATTGTCTTTGGTT 58.861 45.455 0.00 0.00 0.00 3.67
579 668 2.767505 GTCGGTGAGATTGTCTTTGGT 58.232 47.619 0.00 0.00 0.00 3.67
580 669 1.726791 CGTCGGTGAGATTGTCTTTGG 59.273 52.381 0.00 0.00 0.00 3.28
581 670 2.404215 ACGTCGGTGAGATTGTCTTTG 58.596 47.619 0.00 0.00 0.00 2.77
582 671 2.814280 ACGTCGGTGAGATTGTCTTT 57.186 45.000 0.00 0.00 0.00 2.52
583 672 3.255149 AGTTACGTCGGTGAGATTGTCTT 59.745 43.478 0.00 0.00 0.00 3.01
584 673 2.818432 AGTTACGTCGGTGAGATTGTCT 59.182 45.455 0.00 0.00 0.00 3.41
585 674 2.915463 CAGTTACGTCGGTGAGATTGTC 59.085 50.000 0.00 0.00 0.00 3.18
586 675 2.352421 CCAGTTACGTCGGTGAGATTGT 60.352 50.000 0.00 0.00 0.00 2.71
587 676 2.259618 CCAGTTACGTCGGTGAGATTG 58.740 52.381 0.00 0.00 0.00 2.67
588 677 1.403780 GCCAGTTACGTCGGTGAGATT 60.404 52.381 0.00 0.00 0.00 2.40
589 678 0.172803 GCCAGTTACGTCGGTGAGAT 59.827 55.000 0.00 0.00 0.00 2.75
590 679 1.582968 GCCAGTTACGTCGGTGAGA 59.417 57.895 0.00 0.00 0.00 3.27
591 680 1.445582 GGCCAGTTACGTCGGTGAG 60.446 63.158 0.00 0.00 0.00 3.51
592 681 2.149803 CTGGCCAGTTACGTCGGTGA 62.150 60.000 25.53 0.00 0.00 4.02
593 682 1.736645 CTGGCCAGTTACGTCGGTG 60.737 63.158 25.53 0.00 0.00 4.94
594 683 2.654877 CTGGCCAGTTACGTCGGT 59.345 61.111 25.53 0.00 0.00 4.69
595 684 2.125673 CCTGGCCAGTTACGTCGG 60.126 66.667 30.63 10.62 0.00 4.79
596 685 0.736325 CTTCCTGGCCAGTTACGTCG 60.736 60.000 30.63 13.94 0.00 5.12
597 686 0.320697 ACTTCCTGGCCAGTTACGTC 59.679 55.000 30.63 0.00 0.00 4.34
598 687 1.636148 TACTTCCTGGCCAGTTACGT 58.364 50.000 30.63 22.14 0.00 3.57
599 688 2.232941 TCTTACTTCCTGGCCAGTTACG 59.767 50.000 30.63 17.86 0.00 3.18
600 689 3.975168 TCTTACTTCCTGGCCAGTTAC 57.025 47.619 30.63 0.00 0.00 2.50
601 690 3.908103 ACTTCTTACTTCCTGGCCAGTTA 59.092 43.478 30.63 16.19 0.00 2.24
602 691 2.711547 ACTTCTTACTTCCTGGCCAGTT 59.288 45.455 30.63 14.43 0.00 3.16
603 692 2.039084 CACTTCTTACTTCCTGGCCAGT 59.961 50.000 30.63 16.04 0.00 4.00
604 693 2.039084 ACACTTCTTACTTCCTGGCCAG 59.961 50.000 26.87 26.87 0.00 4.85
605 694 2.038557 GACACTTCTTACTTCCTGGCCA 59.961 50.000 4.71 4.71 0.00 5.36
606 695 2.701107 GACACTTCTTACTTCCTGGCC 58.299 52.381 0.00 0.00 0.00 5.36
607 696 2.288886 ACGACACTTCTTACTTCCTGGC 60.289 50.000 0.00 0.00 0.00 4.85
608 697 3.662247 ACGACACTTCTTACTTCCTGG 57.338 47.619 0.00 0.00 0.00 4.45
609 698 5.986004 AAAACGACACTTCTTACTTCCTG 57.014 39.130 0.00 0.00 0.00 3.86
610 699 5.878669 ACAAAAACGACACTTCTTACTTCCT 59.121 36.000 0.00 0.00 0.00 3.36
611 700 6.115450 ACAAAAACGACACTTCTTACTTCC 57.885 37.500 0.00 0.00 0.00 3.46
612 701 7.903062 AGTACAAAAACGACACTTCTTACTTC 58.097 34.615 0.00 0.00 0.00 3.01
613 702 7.546667 TGAGTACAAAAACGACACTTCTTACTT 59.453 33.333 0.00 0.00 0.00 2.24
614 703 7.037438 TGAGTACAAAAACGACACTTCTTACT 58.963 34.615 0.00 0.00 0.00 2.24
615 704 7.225523 TGAGTACAAAAACGACACTTCTTAC 57.774 36.000 0.00 0.00 0.00 2.34
616 705 7.707464 TCATGAGTACAAAAACGACACTTCTTA 59.293 33.333 0.00 0.00 0.00 2.10
617 706 6.537301 TCATGAGTACAAAAACGACACTTCTT 59.463 34.615 0.00 0.00 0.00 2.52
618 707 6.046593 TCATGAGTACAAAAACGACACTTCT 58.953 36.000 0.00 0.00 0.00 2.85
619 708 6.281848 TCATGAGTACAAAAACGACACTTC 57.718 37.500 0.00 0.00 0.00 3.01
620 709 6.481976 TCATCATGAGTACAAAAACGACACTT 59.518 34.615 0.09 0.00 0.00 3.16
621 710 5.989168 TCATCATGAGTACAAAAACGACACT 59.011 36.000 0.09 0.00 0.00 3.55
622 711 6.145534 TCTCATCATGAGTACAAAAACGACAC 59.854 38.462 14.56 0.00 44.58 3.67
623 712 6.145534 GTCTCATCATGAGTACAAAAACGACA 59.854 38.462 14.56 0.00 44.58 4.35
624 713 6.145534 TGTCTCATCATGAGTACAAAAACGAC 59.854 38.462 14.56 2.36 44.58 4.34
625 714 6.220201 TGTCTCATCATGAGTACAAAAACGA 58.780 36.000 14.56 0.00 44.58 3.85
626 715 6.466308 TGTCTCATCATGAGTACAAAAACG 57.534 37.500 14.56 0.00 44.58 3.60
627 716 8.506437 TGATTGTCTCATCATGAGTACAAAAAC 58.494 33.333 24.34 19.95 44.58 2.43
628 717 8.620116 TGATTGTCTCATCATGAGTACAAAAA 57.380 30.769 24.34 17.16 44.58 1.94
629 718 8.620116 TTGATTGTCTCATCATGAGTACAAAA 57.380 30.769 24.34 17.08 44.58 2.44
630 719 8.506437 GTTTGATTGTCTCATCATGAGTACAAA 58.494 33.333 24.34 19.83 44.58 2.83
631 720 7.661027 TGTTTGATTGTCTCATCATGAGTACAA 59.339 33.333 23.47 23.47 44.58 2.41
632 721 7.118245 GTGTTTGATTGTCTCATCATGAGTACA 59.882 37.037 14.56 13.67 44.58 2.90
633 722 7.413438 GGTGTTTGATTGTCTCATCATGAGTAC 60.413 40.741 14.56 11.43 44.58 2.73
634 723 6.595326 GGTGTTTGATTGTCTCATCATGAGTA 59.405 38.462 14.56 2.62 44.58 2.59
635 724 5.413833 GGTGTTTGATTGTCTCATCATGAGT 59.586 40.000 14.56 0.00 44.58 3.41
636 725 5.646793 AGGTGTTTGATTGTCTCATCATGAG 59.353 40.000 8.54 8.54 45.59 2.90
637 726 5.563592 AGGTGTTTGATTGTCTCATCATGA 58.436 37.500 0.00 0.00 32.72 3.07
638 727 5.646793 AGAGGTGTTTGATTGTCTCATCATG 59.353 40.000 0.00 0.00 32.72 3.07
639 728 5.813383 AGAGGTGTTTGATTGTCTCATCAT 58.187 37.500 0.00 0.00 32.72 2.45
640 729 5.233083 AGAGGTGTTTGATTGTCTCATCA 57.767 39.130 0.00 0.00 32.72 3.07
641 730 6.566197 AAAGAGGTGTTTGATTGTCTCATC 57.434 37.500 0.00 0.00 32.72 2.92
642 731 6.966534 AAAAGAGGTGTTTGATTGTCTCAT 57.033 33.333 0.00 0.00 32.72 2.90
643 732 6.773976 AAAAAGAGGTGTTTGATTGTCTCA 57.226 33.333 0.00 0.00 0.00 3.27
664 753 3.625764 CCGAGACTTGACAACCTGAAAAA 59.374 43.478 0.00 0.00 0.00 1.94
665 754 3.202906 CCGAGACTTGACAACCTGAAAA 58.797 45.455 0.00 0.00 0.00 2.29
666 755 2.169769 ACCGAGACTTGACAACCTGAAA 59.830 45.455 0.00 0.00 0.00 2.69
667 756 1.760613 ACCGAGACTTGACAACCTGAA 59.239 47.619 0.00 0.00 0.00 3.02
668 757 1.340248 GACCGAGACTTGACAACCTGA 59.660 52.381 0.00 0.00 0.00 3.86
669 758 1.784525 GACCGAGACTTGACAACCTG 58.215 55.000 0.00 0.00 0.00 4.00
670 759 0.314302 CGACCGAGACTTGACAACCT 59.686 55.000 0.00 0.00 0.00 3.50
671 760 0.313043 TCGACCGAGACTTGACAACC 59.687 55.000 0.00 0.00 0.00 3.77
672 761 1.406447 GTCGACCGAGACTTGACAAC 58.594 55.000 3.51 0.00 38.09 3.32
673 762 3.859650 GTCGACCGAGACTTGACAA 57.140 52.632 3.51 0.00 38.09 3.18
680 769 2.284952 GCTAGTCTAAGTCGACCGAGAC 59.715 54.545 27.91 27.91 41.23 3.36
681 770 2.093816 TGCTAGTCTAAGTCGACCGAGA 60.094 50.000 13.01 12.34 34.46 4.04
682 771 2.277969 TGCTAGTCTAAGTCGACCGAG 58.722 52.381 13.01 9.98 34.46 4.63
683 772 2.391616 TGCTAGTCTAAGTCGACCGA 57.608 50.000 13.01 3.70 34.46 4.69
684 773 2.676839 TCTTGCTAGTCTAAGTCGACCG 59.323 50.000 13.01 0.99 34.46 4.79
685 774 4.904253 ATCTTGCTAGTCTAAGTCGACC 57.096 45.455 13.01 0.00 34.46 4.79
686 775 5.642686 ACAATCTTGCTAGTCTAAGTCGAC 58.357 41.667 7.70 7.70 0.00 4.20
687 776 5.899120 ACAATCTTGCTAGTCTAAGTCGA 57.101 39.130 0.00 0.00 0.00 4.20
688 777 8.635877 ATTTACAATCTTGCTAGTCTAAGTCG 57.364 34.615 0.00 0.00 0.00 4.18
717 806 6.608808 AGGCCATATTTGATTGCTTTAAGACT 59.391 34.615 5.01 0.00 0.00 3.24
718 807 6.809869 AGGCCATATTTGATTGCTTTAAGAC 58.190 36.000 5.01 0.00 0.00 3.01
759 849 4.498894 AAGCCACACCTAAGTATTACCC 57.501 45.455 0.00 0.00 0.00 3.69
768 858 3.325425 TGTACAGCTAAAGCCACACCTAA 59.675 43.478 0.00 0.00 43.38 2.69
779 869 8.455682 GTGGCTATTAAAATGTGTACAGCTAAA 58.544 33.333 0.00 0.00 0.00 1.85
780 870 7.066525 GGTGGCTATTAAAATGTGTACAGCTAA 59.933 37.037 0.00 0.00 0.00 3.09
786 876 7.822658 TCTTTGGTGGCTATTAAAATGTGTAC 58.177 34.615 0.00 0.00 0.00 2.90
1277 1371 0.174617 GCTCTTCTTCCTCCTGTCGG 59.825 60.000 0.00 0.00 0.00 4.79
1494 1603 0.450184 GCGAGAGAACTCTTCGAGCT 59.550 55.000 19.32 0.00 40.61 4.09
1512 1621 1.000496 AGGAGGGGGTAAAGAAAGGC 59.000 55.000 0.00 0.00 0.00 4.35
1513 1622 1.564818 GGAGGAGGGGGTAAAGAAAGG 59.435 57.143 0.00 0.00 0.00 3.11
1527 1636 6.432403 AAGCAAGAATAATAGGAGGAGGAG 57.568 41.667 0.00 0.00 0.00 3.69
1528 1637 5.308237 GGAAGCAAGAATAATAGGAGGAGGA 59.692 44.000 0.00 0.00 0.00 3.71
1607 1716 5.897250 TCACTATACATACATGTGTCAGGGT 59.103 40.000 9.11 0.00 41.89 4.34
1626 1735 4.456911 CACTAAACCCTCTGTACGTCACTA 59.543 45.833 0.00 0.00 0.00 2.74
1632 1741 3.006110 TGAACCACTAAACCCTCTGTACG 59.994 47.826 0.00 0.00 0.00 3.67
1666 1775 7.201705 GGGGAGTTACAATAATTTTTCCTCTCG 60.202 40.741 0.00 0.00 0.00 4.04
1687 1797 0.905357 CTCTGTACAGGTTGGGGGAG 59.095 60.000 22.48 6.57 0.00 4.30
1688 1798 0.490017 TCTCTGTACAGGTTGGGGGA 59.510 55.000 22.48 0.00 0.00 4.81
1697 1807 6.862608 CAGCTCAGCTAAATATCTCTGTACAG 59.137 42.308 17.17 17.17 36.40 2.74
1729 1839 7.078228 CACTACGAAAGATTTTCCCAGAAAAG 58.922 38.462 8.34 0.00 0.00 2.27
1749 1859 5.350365 TCTTTTTGGCGATATCACACACTAC 59.650 40.000 3.12 0.00 0.00 2.73
1759 1869 7.823745 ACCATATCTTTCTTTTTGGCGATAT 57.176 32.000 0.00 0.00 0.00 1.63
1764 1874 6.691508 ACTCAACCATATCTTTCTTTTTGGC 58.308 36.000 0.00 0.00 0.00 4.52
1831 1942 4.507756 TCACACATTGTCTTCTGTTTCGAG 59.492 41.667 0.00 0.00 0.00 4.04
1834 1953 6.728200 TGAATCACACATTGTCTTCTGTTTC 58.272 36.000 0.00 0.00 0.00 2.78
1924 2052 2.341318 GGGATTTTGTCGAAAACCCG 57.659 50.000 13.65 0.00 46.49 5.28
1955 2083 7.737972 TTTACTTTTATGAGCAGTGCTTGTA 57.262 32.000 20.80 12.33 39.88 2.41
1971 2099 8.769891 CACTTTGGTTGTGTTCTTTTTACTTTT 58.230 29.630 0.00 0.00 0.00 2.27
1981 2109 1.750778 CTGCCACTTTGGTTGTGTTCT 59.249 47.619 0.00 0.00 40.46 3.01
2043 2171 4.443598 GGGGAGATCTTAAGTCGATTTGCT 60.444 45.833 3.04 0.00 0.00 3.91
2112 2248 4.081309 CCCTTTCCTTTCGTGTAGTATCCA 60.081 45.833 0.00 0.00 0.00 3.41
2432 2572 7.068348 GTGTAGATAATTGACACTAGGACCAGA 59.932 40.741 0.00 0.00 40.26 3.86


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

AutoCloner maintained by Alex Coulton.