Multiple sequence alignment - TraesCS3D01G214300

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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 TraesCS3D01G214300 chr3D 100.000 3447 0 0 1 3447 289186457 289183011 0.000000e+00 6366.0
1 TraesCS3D01G214300 chr3D 82.022 267 36 8 3186 3443 148592506 148592243 2.080000e-52 217.0
2 TraesCS3D01G214300 chr3B 97.591 2325 28 7 772 3070 381843707 381841385 0.000000e+00 3958.0
3 TraesCS3D01G214300 chr3B 88.629 598 61 4 1 596 255695206 255694614 0.000000e+00 721.0
4 TraesCS3D01G214300 chr3B 97.878 377 8 0 3071 3447 381841351 381840975 0.000000e+00 652.0
5 TraesCS3D01G214300 chr3A 95.831 2207 49 14 822 2993 380068489 380066291 0.000000e+00 3526.0
6 TraesCS3D01G214300 chr3A 88.777 597 59 5 1 596 391505024 391504435 0.000000e+00 725.0
7 TraesCS3D01G214300 chr3A 92.573 377 17 1 3071 3447 380066222 380065857 6.550000e-147 531.0
8 TraesCS3D01G214300 chr3A 97.674 43 1 0 3028 3070 380066298 380066256 1.330000e-09 75.0
9 TraesCS3D01G214300 chr1D 90.620 597 50 3 1 596 269734999 269734408 0.000000e+00 787.0
10 TraesCS3D01G214300 chr1D 88.796 598 59 5 1 596 277768981 277768390 0.000000e+00 726.0
11 TraesCS3D01G214300 chr1D 83.945 218 28 7 3229 3442 263794005 263793791 5.830000e-48 202.0
12 TraesCS3D01G214300 chr1D 83.945 218 28 7 3229 3442 263802375 263802161 5.830000e-48 202.0
13 TraesCS3D01G214300 chr4D 89.850 601 52 3 1 596 105831035 105831631 0.000000e+00 763.0
14 TraesCS3D01G214300 chr2D 89.632 598 56 3 1 596 111667245 111666652 0.000000e+00 756.0
15 TraesCS3D01G214300 chr2D 88.777 597 57 7 1 596 11729942 11729355 0.000000e+00 723.0
16 TraesCS3D01G214300 chr7D 89.500 600 57 4 1 599 437034394 437033800 0.000000e+00 754.0
17 TraesCS3D01G214300 chr5D 88.945 597 59 4 1 596 273220227 273219637 0.000000e+00 730.0
18 TraesCS3D01G214300 chr6D 84.404 218 27 6 3229 3442 352300669 352300883 1.250000e-49 207.0
19 TraesCS3D01G214300 chrUn 83.945 218 28 7 3229 3442 313152353 313152567 5.830000e-48 202.0
20 TraesCS3D01G214300 chr4A 83.871 217 30 5 3229 3442 445238598 445238384 5.830000e-48 202.0
21 TraesCS3D01G214300 chr4A 97.059 34 0 1 3033 3065 649540330 649540297 4.810000e-04 56.5
22 TraesCS3D01G214300 chr4A 96.875 32 0 1 3031 3062 549130999 549131029 6.000000e-03 52.8
23 TraesCS3D01G214300 chr1A 84.018 219 26 8 3229 3442 228947813 228947599 5.830000e-48 202.0
24 TraesCS3D01G214300 chr7B 94.595 37 2 0 3034 3070 219044097 219044133 1.340000e-04 58.4
25 TraesCS3D01G214300 chr7B 86.207 58 2 3 3013 3070 350783787 350783736 1.340000e-04 58.4
26 TraesCS3D01G214300 chr6B 92.500 40 2 1 3031 3070 493785274 493785312 4.810000e-04 56.5


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 TraesCS3D01G214300 chr3D 289183011 289186457 3446 True 6366.000000 6366 100.000000 1 3447 1 chr3D.!!$R2 3446
1 TraesCS3D01G214300 chr3B 381840975 381843707 2732 True 2305.000000 3958 97.734500 772 3447 2 chr3B.!!$R2 2675
2 TraesCS3D01G214300 chr3B 255694614 255695206 592 True 721.000000 721 88.629000 1 596 1 chr3B.!!$R1 595
3 TraesCS3D01G214300 chr3A 380065857 380068489 2632 True 1377.333333 3526 95.359333 822 3447 3 chr3A.!!$R2 2625
4 TraesCS3D01G214300 chr3A 391504435 391505024 589 True 725.000000 725 88.777000 1 596 1 chr3A.!!$R1 595
5 TraesCS3D01G214300 chr1D 269734408 269734999 591 True 787.000000 787 90.620000 1 596 1 chr1D.!!$R3 595
6 TraesCS3D01G214300 chr1D 277768390 277768981 591 True 726.000000 726 88.796000 1 596 1 chr1D.!!$R4 595
7 TraesCS3D01G214300 chr4D 105831035 105831631 596 False 763.000000 763 89.850000 1 596 1 chr4D.!!$F1 595
8 TraesCS3D01G214300 chr2D 111666652 111667245 593 True 756.000000 756 89.632000 1 596 1 chr2D.!!$R2 595
9 TraesCS3D01G214300 chr2D 11729355 11729942 587 True 723.000000 723 88.777000 1 596 1 chr2D.!!$R1 595
10 TraesCS3D01G214300 chr7D 437033800 437034394 594 True 754.000000 754 89.500000 1 599 1 chr7D.!!$R1 598
11 TraesCS3D01G214300 chr5D 273219637 273220227 590 True 730.000000 730 88.945000 1 596 1 chr5D.!!$R1 595

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
673 681 0.035439 ATCGGAAGGCACGGTCATTT 60.035 50.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2456 2498 1.062258 GTGCATGCAACATGTTTCCG 58.938 50.0 24.58 0.0 0.0 4.3 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
23 24 2.225091 ACAAAGCACCTCATCCCATTGA 60.225 45.455 0.00 0.00 0.00 2.57
47 48 3.629398 AGAAAAATCAATCTAGCTGGCCG 59.371 43.478 0.00 0.00 0.00 6.13
66 67 3.812609 GCCGAACCAAACCAAAATTTCAT 59.187 39.130 0.00 0.00 0.00 2.57
121 123 6.670077 AAAAGAGTTCACAGAAGACTCAAC 57.330 37.500 5.64 0.00 0.00 3.18
128 130 9.296400 GAGTTCACAGAAGACTCAACTAATATC 57.704 37.037 0.00 0.00 0.00 1.63
168 170 6.551385 AGATCATAAACTCGCAATTCATCC 57.449 37.500 0.00 0.00 0.00 3.51
186 188 1.134068 TCCGATCCCAACAAACACACA 60.134 47.619 0.00 0.00 0.00 3.72
246 248 7.382110 ACATCGAGGAGAATATTGTATTGAGG 58.618 38.462 3.06 0.00 0.00 3.86
280 283 4.478203 AGAAGATGCCATCTAGCTACTGA 58.522 43.478 7.81 0.00 39.08 3.41
344 351 0.549950 AGGAGCACCAATGAGGATGG 59.450 55.000 2.07 0.00 43.84 3.51
403 410 5.365619 GTGCCGAAAAAGGGATCTAGATTA 58.634 41.667 6.70 0.00 33.12 1.75
420 427 4.770795 AGATTAGATCTCGTGGTTTTGGG 58.229 43.478 0.00 0.00 33.42 4.12
456 464 4.154195 CGGAATTGTTTTTCATCGACTCCT 59.846 41.667 0.00 0.00 0.00 3.69
468 476 5.266788 TCATCGACTCCTTTAGGGTTTCTA 58.733 41.667 0.00 0.00 36.25 2.10
475 483 8.083462 CGACTCCTTTAGGGTTTCTAGAATATC 58.917 40.741 5.89 0.53 36.25 1.63
477 485 9.508721 ACTCCTTTAGGGTTTCTAGAATATCTT 57.491 33.333 5.89 0.00 36.25 2.40
501 509 4.459685 GGTATTTATAGAGCTGAGAGGCGA 59.540 45.833 0.00 0.00 37.29 5.54
619 627 4.820744 GGGCGTGCCATGGTGGAT 62.821 66.667 14.67 0.00 40.96 3.41
620 628 3.520862 GGCGTGCCATGGTGGATG 61.521 66.667 14.67 4.59 40.96 3.51
641 649 4.329545 GCGGGTGGAGGTGCAGAA 62.330 66.667 0.00 0.00 0.00 3.02
642 650 2.429930 CGGGTGGAGGTGCAGAAA 59.570 61.111 0.00 0.00 0.00 2.52
643 651 1.966451 CGGGTGGAGGTGCAGAAAC 60.966 63.158 0.00 0.00 0.00 2.78
644 652 1.150536 GGGTGGAGGTGCAGAAACA 59.849 57.895 0.00 0.00 0.00 2.83
645 653 0.467290 GGGTGGAGGTGCAGAAACAA 60.467 55.000 0.00 0.00 0.00 2.83
646 654 0.954452 GGTGGAGGTGCAGAAACAAG 59.046 55.000 0.00 0.00 0.00 3.16
647 655 1.476833 GGTGGAGGTGCAGAAACAAGA 60.477 52.381 0.00 0.00 0.00 3.02
648 656 1.876156 GTGGAGGTGCAGAAACAAGAG 59.124 52.381 0.00 0.00 0.00 2.85
649 657 1.768275 TGGAGGTGCAGAAACAAGAGA 59.232 47.619 0.00 0.00 0.00 3.10
650 658 2.373169 TGGAGGTGCAGAAACAAGAGAT 59.627 45.455 0.00 0.00 0.00 2.75
651 659 2.746362 GGAGGTGCAGAAACAAGAGATG 59.254 50.000 0.00 0.00 0.00 2.90
652 660 2.746362 GAGGTGCAGAAACAAGAGATGG 59.254 50.000 0.00 0.00 0.00 3.51
653 661 1.815003 GGTGCAGAAACAAGAGATGGG 59.185 52.381 0.00 0.00 0.00 4.00
654 662 2.553028 GGTGCAGAAACAAGAGATGGGA 60.553 50.000 0.00 0.00 0.00 4.37
655 663 3.350833 GTGCAGAAACAAGAGATGGGAT 58.649 45.455 0.00 0.00 0.00 3.85
656 664 3.376546 GTGCAGAAACAAGAGATGGGATC 59.623 47.826 0.00 0.00 0.00 3.36
657 665 2.611292 GCAGAAACAAGAGATGGGATCG 59.389 50.000 0.00 0.00 0.00 3.69
658 666 3.201290 CAGAAACAAGAGATGGGATCGG 58.799 50.000 0.00 0.00 0.00 4.18
659 667 3.107601 AGAAACAAGAGATGGGATCGGA 58.892 45.455 0.00 0.00 0.00 4.55
660 668 3.519510 AGAAACAAGAGATGGGATCGGAA 59.480 43.478 0.00 0.00 0.00 4.30
661 669 3.550437 AACAAGAGATGGGATCGGAAG 57.450 47.619 0.00 0.00 0.00 3.46
662 670 1.765314 ACAAGAGATGGGATCGGAAGG 59.235 52.381 0.00 0.00 0.00 3.46
663 671 0.761802 AAGAGATGGGATCGGAAGGC 59.238 55.000 0.00 0.00 0.00 4.35
664 672 0.399091 AGAGATGGGATCGGAAGGCA 60.399 55.000 0.00 0.00 0.00 4.75
665 673 0.250081 GAGATGGGATCGGAAGGCAC 60.250 60.000 0.00 0.00 0.00 5.01
666 674 1.595382 GATGGGATCGGAAGGCACG 60.595 63.158 0.00 0.00 0.00 5.34
667 675 2.996168 GATGGGATCGGAAGGCACGG 62.996 65.000 0.00 0.00 0.00 4.94
668 676 3.782443 GGGATCGGAAGGCACGGT 61.782 66.667 0.00 0.00 0.00 4.83
669 677 2.202892 GGATCGGAAGGCACGGTC 60.203 66.667 1.63 1.63 40.57 4.79
670 678 2.577059 GATCGGAAGGCACGGTCA 59.423 61.111 4.94 0.00 40.94 4.02
671 679 1.144057 GATCGGAAGGCACGGTCAT 59.856 57.895 4.94 0.00 40.94 3.06
672 680 0.462047 GATCGGAAGGCACGGTCATT 60.462 55.000 4.94 0.00 40.94 2.57
673 681 0.035439 ATCGGAAGGCACGGTCATTT 60.035 50.000 0.00 0.00 0.00 2.32
674 682 0.609151 TCGGAAGGCACGGTCATTTA 59.391 50.000 0.00 0.00 0.00 1.40
675 683 1.208535 TCGGAAGGCACGGTCATTTAT 59.791 47.619 0.00 0.00 0.00 1.40
676 684 2.014128 CGGAAGGCACGGTCATTTATT 58.986 47.619 0.00 0.00 0.00 1.40
677 685 2.422127 CGGAAGGCACGGTCATTTATTT 59.578 45.455 0.00 0.00 0.00 1.40
678 686 3.119637 CGGAAGGCACGGTCATTTATTTT 60.120 43.478 0.00 0.00 0.00 1.82
679 687 4.617298 CGGAAGGCACGGTCATTTATTTTT 60.617 41.667 0.00 0.00 0.00 1.94
680 688 4.862574 GGAAGGCACGGTCATTTATTTTTC 59.137 41.667 0.00 0.00 0.00 2.29
681 689 5.336451 GGAAGGCACGGTCATTTATTTTTCT 60.336 40.000 0.00 0.00 0.00 2.52
682 690 5.722021 AGGCACGGTCATTTATTTTTCTT 57.278 34.783 0.00 0.00 0.00 2.52
683 691 6.096673 AGGCACGGTCATTTATTTTTCTTT 57.903 33.333 0.00 0.00 0.00 2.52
684 692 6.521162 AGGCACGGTCATTTATTTTTCTTTT 58.479 32.000 0.00 0.00 0.00 2.27
685 693 6.645003 AGGCACGGTCATTTATTTTTCTTTTC 59.355 34.615 0.00 0.00 0.00 2.29
686 694 6.645003 GGCACGGTCATTTATTTTTCTTTTCT 59.355 34.615 0.00 0.00 0.00 2.52
687 695 7.148804 GGCACGGTCATTTATTTTTCTTTTCTC 60.149 37.037 0.00 0.00 0.00 2.87
688 696 7.595130 GCACGGTCATTTATTTTTCTTTTCTCT 59.405 33.333 0.00 0.00 0.00 3.10
689 697 9.118236 CACGGTCATTTATTTTTCTTTTCTCTC 57.882 33.333 0.00 0.00 0.00 3.20
690 698 8.846211 ACGGTCATTTATTTTTCTTTTCTCTCA 58.154 29.630 0.00 0.00 0.00 3.27
691 699 9.118236 CGGTCATTTATTTTTCTTTTCTCTCAC 57.882 33.333 0.00 0.00 0.00 3.51
692 700 9.965824 GGTCATTTATTTTTCTTTTCTCTCACA 57.034 29.630 0.00 0.00 0.00 3.58
699 707 6.598753 TTTTCTTTTCTCTCACACTTACCG 57.401 37.500 0.00 0.00 0.00 4.02
700 708 4.252971 TCTTTTCTCTCACACTTACCGG 57.747 45.455 0.00 0.00 0.00 5.28
701 709 3.640029 TCTTTTCTCTCACACTTACCGGT 59.360 43.478 13.98 13.98 0.00 5.28
702 710 4.100498 TCTTTTCTCTCACACTTACCGGTT 59.900 41.667 15.04 0.00 0.00 4.44
703 711 3.655276 TTCTCTCACACTTACCGGTTC 57.345 47.619 15.04 0.00 0.00 3.62
704 712 1.538512 TCTCTCACACTTACCGGTTCG 59.461 52.381 15.04 6.87 0.00 3.95
705 713 1.268899 CTCTCACACTTACCGGTTCGT 59.731 52.381 15.04 7.65 0.00 3.85
706 714 1.001048 TCTCACACTTACCGGTTCGTG 60.001 52.381 25.48 25.48 0.00 4.35
707 715 0.746063 TCACACTTACCGGTTCGTGT 59.254 50.000 26.52 26.52 40.91 4.49
708 716 1.136695 TCACACTTACCGGTTCGTGTT 59.863 47.619 28.47 16.73 38.44 3.32
709 717 1.259507 CACACTTACCGGTTCGTGTTG 59.740 52.381 28.47 21.67 38.44 3.33
710 718 1.136695 ACACTTACCGGTTCGTGTTGA 59.863 47.619 26.52 0.75 37.31 3.18
711 719 1.523934 CACTTACCGGTTCGTGTTGAC 59.476 52.381 15.04 0.00 0.00 3.18
712 720 1.410153 ACTTACCGGTTCGTGTTGACT 59.590 47.619 15.04 0.00 0.00 3.41
713 721 2.159057 ACTTACCGGTTCGTGTTGACTT 60.159 45.455 15.04 0.00 0.00 3.01
714 722 2.600470 TACCGGTTCGTGTTGACTTT 57.400 45.000 15.04 0.00 0.00 2.66
715 723 1.741528 ACCGGTTCGTGTTGACTTTT 58.258 45.000 0.00 0.00 0.00 2.27
716 724 2.086094 ACCGGTTCGTGTTGACTTTTT 58.914 42.857 0.00 0.00 0.00 1.94
717 725 3.269178 ACCGGTTCGTGTTGACTTTTTA 58.731 40.909 0.00 0.00 0.00 1.52
718 726 3.878699 ACCGGTTCGTGTTGACTTTTTAT 59.121 39.130 0.00 0.00 0.00 1.40
719 727 5.055812 ACCGGTTCGTGTTGACTTTTTATA 58.944 37.500 0.00 0.00 0.00 0.98
720 728 5.526846 ACCGGTTCGTGTTGACTTTTTATAA 59.473 36.000 0.00 0.00 0.00 0.98
721 729 6.075280 CCGGTTCGTGTTGACTTTTTATAAG 58.925 40.000 0.00 0.00 0.00 1.73
722 730 6.075280 CGGTTCGTGTTGACTTTTTATAAGG 58.925 40.000 0.00 0.00 0.00 2.69
723 731 6.073657 CGGTTCGTGTTGACTTTTTATAAGGA 60.074 38.462 0.00 0.00 0.00 3.36
724 732 7.295930 GGTTCGTGTTGACTTTTTATAAGGAG 58.704 38.462 0.00 0.00 0.00 3.69
725 733 7.041576 GGTTCGTGTTGACTTTTTATAAGGAGT 60.042 37.037 3.32 3.32 0.00 3.85
726 734 7.416154 TCGTGTTGACTTTTTATAAGGAGTG 57.584 36.000 7.34 0.00 0.00 3.51
727 735 6.073440 TCGTGTTGACTTTTTATAAGGAGTGC 60.073 38.462 7.34 0.00 0.00 4.40
728 736 6.077838 GTGTTGACTTTTTATAAGGAGTGCG 58.922 40.000 7.34 0.00 0.00 5.34
729 737 5.180492 TGTTGACTTTTTATAAGGAGTGCGG 59.820 40.000 7.34 0.00 0.00 5.69
730 738 4.258543 TGACTTTTTATAAGGAGTGCGGG 58.741 43.478 7.34 0.00 0.00 6.13
731 739 4.259356 GACTTTTTATAAGGAGTGCGGGT 58.741 43.478 7.34 0.00 0.00 5.28
732 740 4.659115 ACTTTTTATAAGGAGTGCGGGTT 58.341 39.130 2.96 0.00 0.00 4.11
733 741 4.457949 ACTTTTTATAAGGAGTGCGGGTTG 59.542 41.667 2.96 0.00 0.00 3.77
734 742 3.985019 TTTATAAGGAGTGCGGGTTGA 57.015 42.857 0.00 0.00 0.00 3.18
735 743 3.985019 TTATAAGGAGTGCGGGTTGAA 57.015 42.857 0.00 0.00 0.00 2.69
736 744 4.497291 TTATAAGGAGTGCGGGTTGAAT 57.503 40.909 0.00 0.00 0.00 2.57
737 745 5.617528 TTATAAGGAGTGCGGGTTGAATA 57.382 39.130 0.00 0.00 0.00 1.75
738 746 2.109425 AAGGAGTGCGGGTTGAATAC 57.891 50.000 0.00 0.00 0.00 1.89
739 747 1.276622 AGGAGTGCGGGTTGAATACT 58.723 50.000 0.00 0.00 0.00 2.12
740 748 1.628846 AGGAGTGCGGGTTGAATACTT 59.371 47.619 0.00 0.00 0.00 2.24
741 749 2.835764 AGGAGTGCGGGTTGAATACTTA 59.164 45.455 0.00 0.00 0.00 2.24
742 750 3.118738 AGGAGTGCGGGTTGAATACTTAG 60.119 47.826 0.00 0.00 0.00 2.18
743 751 3.118884 GGAGTGCGGGTTGAATACTTAGA 60.119 47.826 0.00 0.00 0.00 2.10
744 752 4.501071 GAGTGCGGGTTGAATACTTAGAA 58.499 43.478 0.00 0.00 0.00 2.10
745 753 4.251268 AGTGCGGGTTGAATACTTAGAAC 58.749 43.478 0.00 0.00 0.00 3.01
746 754 3.373130 GTGCGGGTTGAATACTTAGAACC 59.627 47.826 0.00 0.00 37.69 3.62
747 755 3.262405 TGCGGGTTGAATACTTAGAACCT 59.738 43.478 0.00 0.00 38.36 3.50
748 756 3.869832 GCGGGTTGAATACTTAGAACCTC 59.130 47.826 0.00 0.00 38.36 3.85
749 757 4.622220 GCGGGTTGAATACTTAGAACCTCA 60.622 45.833 0.00 0.00 38.36 3.86
750 758 5.109903 CGGGTTGAATACTTAGAACCTCAG 58.890 45.833 0.00 0.00 38.36 3.35
751 759 5.429130 GGGTTGAATACTTAGAACCTCAGG 58.571 45.833 0.00 0.00 38.36 3.86
752 760 5.429130 GGTTGAATACTTAGAACCTCAGGG 58.571 45.833 0.00 0.00 35.86 4.45
753 761 4.755266 TGAATACTTAGAACCTCAGGGC 57.245 45.455 0.00 0.00 35.63 5.19
754 762 3.454812 TGAATACTTAGAACCTCAGGGCC 59.545 47.826 0.00 0.00 35.63 5.80
755 763 2.942604 TACTTAGAACCTCAGGGCCT 57.057 50.000 0.00 0.00 35.63 5.19
756 764 2.046280 ACTTAGAACCTCAGGGCCTT 57.954 50.000 1.32 0.00 35.63 4.35
757 765 2.349445 ACTTAGAACCTCAGGGCCTTT 58.651 47.619 1.32 0.00 35.63 3.11
758 766 2.716969 ACTTAGAACCTCAGGGCCTTTT 59.283 45.455 1.32 0.00 35.63 2.27
759 767 3.140332 ACTTAGAACCTCAGGGCCTTTTT 59.860 43.478 1.32 0.00 35.63 1.94
790 798 4.814771 ACGCCGATCTTTTATTAGGGAAAG 59.185 41.667 0.00 0.00 34.87 2.62
810 818 4.826274 AGATATAATGTCCACCCCATCG 57.174 45.455 0.00 0.00 0.00 3.84
811 819 3.519510 AGATATAATGTCCACCCCATCGG 59.480 47.826 0.00 0.00 37.81 4.18
907 915 1.296056 CGCCCACCCGTAGAACAAAG 61.296 60.000 0.00 0.00 0.00 2.77
1272 1293 2.370189 AGCTATAGATTGGTCTGGTGGC 59.630 50.000 3.21 0.00 35.87 5.01
2456 2498 5.143376 TGGGTACTACTAAGTCAGTTTGC 57.857 43.478 0.00 0.00 38.80 3.68
2860 2911 4.619160 GCCATCTTCGAATTCTTTTGGCTT 60.619 41.667 19.17 0.00 43.86 4.35
3005 3064 1.155424 TCTTGTTTCCGTCACGCACC 61.155 55.000 0.00 0.00 0.00 5.01
3161 3253 2.192664 TTGCTTCTGCGTTGGGATAA 57.807 45.000 0.00 0.00 43.34 1.75
3184 3276 9.833917 ATAACCTACTATTTGGTTCTTCTTAGC 57.166 33.333 2.33 0.00 44.47 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.393461 CGGCCAGCTAGATTGATTTTTCTTT 60.393 40.000 2.24 0.00 0.00 2.52
47 48 9.541143 TTCTTCTATGAAATTTTGGTTTGGTTC 57.459 29.630 0.00 0.00 0.00 3.62
142 144 6.122850 TGAATTGCGAGTTTATGATCTTGG 57.877 37.500 0.00 0.00 0.00 3.61
143 145 6.854892 GGATGAATTGCGAGTTTATGATCTTG 59.145 38.462 0.00 0.00 0.00 3.02
144 146 6.293081 CGGATGAATTGCGAGTTTATGATCTT 60.293 38.462 0.00 0.00 42.53 2.40
145 147 5.178252 CGGATGAATTGCGAGTTTATGATCT 59.822 40.000 0.00 0.00 42.53 2.75
168 170 1.334960 GCTGTGTGTTTGTTGGGATCG 60.335 52.381 0.00 0.00 0.00 3.69
219 221 9.265901 CTCAATACAATATTCTCCTCGATGTTT 57.734 33.333 0.00 0.00 0.00 2.83
234 236 9.426534 TCTCTCTCTTTGATCCTCAATACAATA 57.573 33.333 0.00 0.00 36.11 1.90
246 248 5.021033 TGGCATCTTCTCTCTCTTTGATC 57.979 43.478 0.00 0.00 0.00 2.92
253 255 3.828451 AGCTAGATGGCATCTTCTCTCTC 59.172 47.826 32.93 14.75 40.76 3.20
302 309 5.670485 TCCAATGATGCGTGAGTAGTTTAT 58.330 37.500 0.00 0.00 0.00 1.40
344 351 0.038526 ACGATCACGGAGGTGTTCAC 60.039 55.000 0.00 0.00 44.68 3.18
350 357 1.595357 GGGAAACGATCACGGAGGT 59.405 57.895 0.00 0.00 44.46 3.85
403 410 1.978580 AGTCCCAAAACCACGAGATCT 59.021 47.619 0.00 0.00 0.00 2.75
433 440 4.154195 AGGAGTCGATGAAAAACAATTCCG 59.846 41.667 0.00 0.00 0.00 4.30
475 483 6.162777 GCCTCTCAGCTCTATAAATACCAAG 58.837 44.000 0.00 0.00 0.00 3.61
477 485 4.218635 CGCCTCTCAGCTCTATAAATACCA 59.781 45.833 0.00 0.00 0.00 3.25
501 509 1.990060 CCACGGGTGTCCTCTCCAT 60.990 63.158 0.00 0.00 0.00 3.41
602 610 4.820744 ATCCACCATGGCACGCCC 62.821 66.667 13.04 0.00 37.47 6.13
603 611 3.520862 CATCCACCATGGCACGCC 61.521 66.667 13.04 0.00 37.47 5.68
604 612 3.520862 CCATCCACCATGGCACGC 61.521 66.667 13.04 0.00 46.18 5.34
624 632 3.842925 TTTCTGCACCTCCACCCGC 62.843 63.158 0.00 0.00 0.00 6.13
625 633 1.966451 GTTTCTGCACCTCCACCCG 60.966 63.158 0.00 0.00 0.00 5.28
626 634 0.467290 TTGTTTCTGCACCTCCACCC 60.467 55.000 0.00 0.00 0.00 4.61
627 635 0.954452 CTTGTTTCTGCACCTCCACC 59.046 55.000 0.00 0.00 0.00 4.61
628 636 1.876156 CTCTTGTTTCTGCACCTCCAC 59.124 52.381 0.00 0.00 0.00 4.02
629 637 1.768275 TCTCTTGTTTCTGCACCTCCA 59.232 47.619 0.00 0.00 0.00 3.86
630 638 2.550830 TCTCTTGTTTCTGCACCTCC 57.449 50.000 0.00 0.00 0.00 4.30
631 639 2.746362 CCATCTCTTGTTTCTGCACCTC 59.254 50.000 0.00 0.00 0.00 3.85
632 640 2.553904 CCCATCTCTTGTTTCTGCACCT 60.554 50.000 0.00 0.00 0.00 4.00
633 641 1.815003 CCCATCTCTTGTTTCTGCACC 59.185 52.381 0.00 0.00 0.00 5.01
634 642 2.783135 TCCCATCTCTTGTTTCTGCAC 58.217 47.619 0.00 0.00 0.00 4.57
635 643 3.614092 GATCCCATCTCTTGTTTCTGCA 58.386 45.455 0.00 0.00 0.00 4.41
636 644 2.611292 CGATCCCATCTCTTGTTTCTGC 59.389 50.000 0.00 0.00 0.00 4.26
637 645 3.118629 TCCGATCCCATCTCTTGTTTCTG 60.119 47.826 0.00 0.00 0.00 3.02
638 646 3.107601 TCCGATCCCATCTCTTGTTTCT 58.892 45.455 0.00 0.00 0.00 2.52
639 647 3.543680 TCCGATCCCATCTCTTGTTTC 57.456 47.619 0.00 0.00 0.00 2.78
640 648 3.370953 CCTTCCGATCCCATCTCTTGTTT 60.371 47.826 0.00 0.00 0.00 2.83
641 649 2.171448 CCTTCCGATCCCATCTCTTGTT 59.829 50.000 0.00 0.00 0.00 2.83
642 650 1.765314 CCTTCCGATCCCATCTCTTGT 59.235 52.381 0.00 0.00 0.00 3.16
643 651 1.542108 GCCTTCCGATCCCATCTCTTG 60.542 57.143 0.00 0.00 0.00 3.02
644 652 0.761802 GCCTTCCGATCCCATCTCTT 59.238 55.000 0.00 0.00 0.00 2.85
645 653 0.399091 TGCCTTCCGATCCCATCTCT 60.399 55.000 0.00 0.00 0.00 3.10
646 654 0.250081 GTGCCTTCCGATCCCATCTC 60.250 60.000 0.00 0.00 0.00 2.75
647 655 1.832912 GTGCCTTCCGATCCCATCT 59.167 57.895 0.00 0.00 0.00 2.90
648 656 1.595382 CGTGCCTTCCGATCCCATC 60.595 63.158 0.00 0.00 0.00 3.51
649 657 2.505982 CGTGCCTTCCGATCCCAT 59.494 61.111 0.00 0.00 0.00 4.00
650 658 3.781307 CCGTGCCTTCCGATCCCA 61.781 66.667 0.00 0.00 0.00 4.37
651 659 3.735037 GACCGTGCCTTCCGATCCC 62.735 68.421 0.00 0.00 0.00 3.85
652 660 2.202892 GACCGTGCCTTCCGATCC 60.203 66.667 0.00 0.00 0.00 3.36
653 661 0.462047 AATGACCGTGCCTTCCGATC 60.462 55.000 0.00 0.00 0.00 3.69
654 662 0.035439 AAATGACCGTGCCTTCCGAT 60.035 50.000 0.00 0.00 0.00 4.18
655 663 0.609151 TAAATGACCGTGCCTTCCGA 59.391 50.000 0.00 0.00 0.00 4.55
656 664 1.663695 ATAAATGACCGTGCCTTCCG 58.336 50.000 0.00 0.00 0.00 4.30
657 665 4.450082 AAAATAAATGACCGTGCCTTCC 57.550 40.909 0.00 0.00 0.00 3.46
658 666 5.709966 AGAAAAATAAATGACCGTGCCTTC 58.290 37.500 0.00 0.00 0.00 3.46
659 667 5.722021 AGAAAAATAAATGACCGTGCCTT 57.278 34.783 0.00 0.00 0.00 4.35
660 668 5.722021 AAGAAAAATAAATGACCGTGCCT 57.278 34.783 0.00 0.00 0.00 4.75
661 669 6.645003 AGAAAAGAAAAATAAATGACCGTGCC 59.355 34.615 0.00 0.00 0.00 5.01
662 670 7.595130 AGAGAAAAGAAAAATAAATGACCGTGC 59.405 33.333 0.00 0.00 0.00 5.34
663 671 9.118236 GAGAGAAAAGAAAAATAAATGACCGTG 57.882 33.333 0.00 0.00 0.00 4.94
664 672 8.846211 TGAGAGAAAAGAAAAATAAATGACCGT 58.154 29.630 0.00 0.00 0.00 4.83
665 673 9.118236 GTGAGAGAAAAGAAAAATAAATGACCG 57.882 33.333 0.00 0.00 0.00 4.79
666 674 9.965824 TGTGAGAGAAAAGAAAAATAAATGACC 57.034 29.630 0.00 0.00 0.00 4.02
673 681 8.770828 CGGTAAGTGTGAGAGAAAAGAAAAATA 58.229 33.333 0.00 0.00 0.00 1.40
674 682 7.255139 CCGGTAAGTGTGAGAGAAAAGAAAAAT 60.255 37.037 0.00 0.00 0.00 1.82
675 683 6.037830 CCGGTAAGTGTGAGAGAAAAGAAAAA 59.962 38.462 0.00 0.00 0.00 1.94
676 684 5.526111 CCGGTAAGTGTGAGAGAAAAGAAAA 59.474 40.000 0.00 0.00 0.00 2.29
677 685 5.054477 CCGGTAAGTGTGAGAGAAAAGAAA 58.946 41.667 0.00 0.00 0.00 2.52
678 686 4.100498 ACCGGTAAGTGTGAGAGAAAAGAA 59.900 41.667 4.49 0.00 0.00 2.52
679 687 3.640029 ACCGGTAAGTGTGAGAGAAAAGA 59.360 43.478 4.49 0.00 0.00 2.52
680 688 3.991367 ACCGGTAAGTGTGAGAGAAAAG 58.009 45.455 4.49 0.00 0.00 2.27
681 689 4.374399 GAACCGGTAAGTGTGAGAGAAAA 58.626 43.478 8.00 0.00 0.00 2.29
682 690 3.551454 CGAACCGGTAAGTGTGAGAGAAA 60.551 47.826 8.00 0.00 0.00 2.52
683 691 2.030540 CGAACCGGTAAGTGTGAGAGAA 60.031 50.000 8.00 0.00 0.00 2.87
684 692 1.538512 CGAACCGGTAAGTGTGAGAGA 59.461 52.381 8.00 0.00 0.00 3.10
685 693 1.268899 ACGAACCGGTAAGTGTGAGAG 59.731 52.381 8.00 0.00 0.00 3.20
686 694 1.001048 CACGAACCGGTAAGTGTGAGA 60.001 52.381 25.53 0.00 0.00 3.27
687 695 1.269413 ACACGAACCGGTAAGTGTGAG 60.269 52.381 33.41 17.11 44.90 3.51
688 696 0.746063 ACACGAACCGGTAAGTGTGA 59.254 50.000 33.41 0.00 44.90 3.58
689 697 1.259507 CAACACGAACCGGTAAGTGTG 59.740 52.381 34.10 27.36 45.74 3.82
691 699 1.523934 GTCAACACGAACCGGTAAGTG 59.476 52.381 29.53 29.53 40.17 3.16
692 700 1.410153 AGTCAACACGAACCGGTAAGT 59.590 47.619 8.00 8.52 0.00 2.24
693 701 2.144482 AGTCAACACGAACCGGTAAG 57.856 50.000 8.00 7.74 0.00 2.34
694 702 2.600470 AAGTCAACACGAACCGGTAA 57.400 45.000 8.00 0.00 0.00 2.85
695 703 2.600470 AAAGTCAACACGAACCGGTA 57.400 45.000 8.00 0.00 0.00 4.02
696 704 1.741528 AAAAGTCAACACGAACCGGT 58.258 45.000 0.00 0.00 0.00 5.28
697 705 2.836479 AAAAAGTCAACACGAACCGG 57.164 45.000 0.00 0.00 0.00 5.28
698 706 6.073657 TCCTTATAAAAAGTCAACACGAACCG 60.074 38.462 0.00 0.00 0.00 4.44
699 707 7.041576 ACTCCTTATAAAAAGTCAACACGAACC 60.042 37.037 0.00 0.00 0.00 3.62
700 708 7.797123 CACTCCTTATAAAAAGTCAACACGAAC 59.203 37.037 0.00 0.00 0.00 3.95
701 709 7.519328 GCACTCCTTATAAAAAGTCAACACGAA 60.519 37.037 0.00 0.00 0.00 3.85
702 710 6.073440 GCACTCCTTATAAAAAGTCAACACGA 60.073 38.462 0.00 0.00 0.00 4.35
703 711 6.077838 GCACTCCTTATAAAAAGTCAACACG 58.922 40.000 0.00 0.00 0.00 4.49
704 712 6.077838 CGCACTCCTTATAAAAAGTCAACAC 58.922 40.000 0.00 0.00 0.00 3.32
705 713 5.180492 CCGCACTCCTTATAAAAAGTCAACA 59.820 40.000 0.00 0.00 0.00 3.33
706 714 5.391629 CCCGCACTCCTTATAAAAAGTCAAC 60.392 44.000 0.00 0.00 0.00 3.18
707 715 4.698304 CCCGCACTCCTTATAAAAAGTCAA 59.302 41.667 0.00 0.00 0.00 3.18
708 716 4.258543 CCCGCACTCCTTATAAAAAGTCA 58.741 43.478 0.00 0.00 0.00 3.41
709 717 4.259356 ACCCGCACTCCTTATAAAAAGTC 58.741 43.478 0.00 0.00 0.00 3.01
710 718 4.296621 ACCCGCACTCCTTATAAAAAGT 57.703 40.909 0.00 0.00 0.00 2.66
711 719 4.698304 TCAACCCGCACTCCTTATAAAAAG 59.302 41.667 0.00 0.00 0.00 2.27
712 720 4.653868 TCAACCCGCACTCCTTATAAAAA 58.346 39.130 0.00 0.00 0.00 1.94
713 721 4.289238 TCAACCCGCACTCCTTATAAAA 57.711 40.909 0.00 0.00 0.00 1.52
714 722 3.985019 TCAACCCGCACTCCTTATAAA 57.015 42.857 0.00 0.00 0.00 1.40
715 723 3.985019 TTCAACCCGCACTCCTTATAA 57.015 42.857 0.00 0.00 0.00 0.98
716 724 4.652421 AGTATTCAACCCGCACTCCTTATA 59.348 41.667 0.00 0.00 0.00 0.98
717 725 3.454812 AGTATTCAACCCGCACTCCTTAT 59.545 43.478 0.00 0.00 0.00 1.73
718 726 2.835764 AGTATTCAACCCGCACTCCTTA 59.164 45.455 0.00 0.00 0.00 2.69
719 727 1.628846 AGTATTCAACCCGCACTCCTT 59.371 47.619 0.00 0.00 0.00 3.36
720 728 1.276622 AGTATTCAACCCGCACTCCT 58.723 50.000 0.00 0.00 0.00 3.69
721 729 2.109425 AAGTATTCAACCCGCACTCC 57.891 50.000 0.00 0.00 0.00 3.85
722 730 4.119442 TCTAAGTATTCAACCCGCACTC 57.881 45.455 0.00 0.00 0.00 3.51
723 731 4.251268 GTTCTAAGTATTCAACCCGCACT 58.749 43.478 0.00 0.00 0.00 4.40
724 732 3.373130 GGTTCTAAGTATTCAACCCGCAC 59.627 47.826 0.00 0.00 35.92 5.34
725 733 3.262405 AGGTTCTAAGTATTCAACCCGCA 59.738 43.478 0.00 0.00 40.38 5.69
726 734 3.869832 GAGGTTCTAAGTATTCAACCCGC 59.130 47.826 0.00 0.00 40.38 6.13
727 735 5.080969 TGAGGTTCTAAGTATTCAACCCG 57.919 43.478 0.00 0.00 40.38 5.28
728 736 5.429130 CCTGAGGTTCTAAGTATTCAACCC 58.571 45.833 0.00 0.00 40.38 4.11
729 737 5.429130 CCCTGAGGTTCTAAGTATTCAACC 58.571 45.833 0.00 0.00 40.01 3.77
730 738 4.876679 GCCCTGAGGTTCTAAGTATTCAAC 59.123 45.833 0.00 0.00 34.57 3.18
731 739 4.080526 GGCCCTGAGGTTCTAAGTATTCAA 60.081 45.833 0.00 0.00 34.57 2.69
732 740 3.454812 GGCCCTGAGGTTCTAAGTATTCA 59.545 47.826 0.00 0.00 34.57 2.57
733 741 3.712218 AGGCCCTGAGGTTCTAAGTATTC 59.288 47.826 0.00 0.00 34.57 1.75
734 742 3.737263 AGGCCCTGAGGTTCTAAGTATT 58.263 45.455 0.00 0.00 34.57 1.89
735 743 3.423058 AGGCCCTGAGGTTCTAAGTAT 57.577 47.619 0.00 0.00 34.57 2.12
736 744 2.942604 AGGCCCTGAGGTTCTAAGTA 57.057 50.000 0.00 0.00 34.57 2.24
737 745 2.046280 AAGGCCCTGAGGTTCTAAGT 57.954 50.000 0.00 0.00 34.57 2.24
738 746 3.441500 AAAAGGCCCTGAGGTTCTAAG 57.558 47.619 0.00 0.00 34.57 2.18
739 747 3.895704 AAAAAGGCCCTGAGGTTCTAA 57.104 42.857 0.00 0.00 34.57 2.10
756 764 2.815478 AGATCGGCGTTTTTGCAAAAA 58.185 38.095 28.85 28.85 35.67 1.94
757 765 2.500509 AGATCGGCGTTTTTGCAAAA 57.499 40.000 20.46 20.46 36.28 2.44
758 766 2.500509 AAGATCGGCGTTTTTGCAAA 57.499 40.000 8.05 8.05 36.28 3.68
759 767 2.500509 AAAGATCGGCGTTTTTGCAA 57.499 40.000 6.85 0.00 36.28 4.08
760 768 2.500509 AAAAGATCGGCGTTTTTGCA 57.499 40.000 6.85 0.00 36.28 4.08
761 769 5.229260 CCTAATAAAAGATCGGCGTTTTTGC 59.771 40.000 20.69 0.00 30.77 3.68
762 770 5.741982 CCCTAATAAAAGATCGGCGTTTTTG 59.258 40.000 20.69 10.15 30.77 2.44
763 771 5.648960 TCCCTAATAAAAGATCGGCGTTTTT 59.351 36.000 6.85 14.35 30.77 1.94
764 772 5.187687 TCCCTAATAAAAGATCGGCGTTTT 58.812 37.500 6.85 9.33 30.77 2.43
765 773 4.773013 TCCCTAATAAAAGATCGGCGTTT 58.227 39.130 6.85 2.26 32.87 3.60
766 774 4.411256 TCCCTAATAAAAGATCGGCGTT 57.589 40.909 6.85 0.00 0.00 4.84
767 775 4.411256 TTCCCTAATAAAAGATCGGCGT 57.589 40.909 6.85 0.00 0.00 5.68
768 776 5.054477 TCTTTCCCTAATAAAAGATCGGCG 58.946 41.667 0.00 0.00 36.76 6.46
769 777 8.794335 ATATCTTTCCCTAATAAAAGATCGGC 57.206 34.615 12.24 0.00 44.82 5.54
790 798 3.873910 CCGATGGGGTGGACATTATATC 58.126 50.000 0.00 0.00 0.00 1.63
811 819 4.576879 TGGTTTTGGTTTTGGTTTGGTAC 58.423 39.130 0.00 0.00 0.00 3.34
1272 1293 1.813753 CAACGTATGCCCTCACCGG 60.814 63.158 0.00 0.00 0.00 5.28
2456 2498 1.062258 GTGCATGCAACATGTTTCCG 58.938 50.000 24.58 0.00 0.00 4.30
2614 2658 2.276732 TTCTCTCCAAACAGGCTTGG 57.723 50.000 0.00 0.00 46.27 3.61
2977 3036 0.954452 CGGAAACAAGAAGCCTGCTT 59.046 50.000 3.62 3.62 39.23 3.91
3005 3064 1.746615 CGACCCTGGCACCTTCATG 60.747 63.158 0.00 0.00 0.00 3.07
3161 3253 7.038231 ACAGCTAAGAAGAACCAAATAGTAGGT 60.038 37.037 0.00 0.00 40.61 3.08
3184 3276 8.393366 CACTCAATTATTCTATGGTTGTGACAG 58.607 37.037 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.