Multiple sequence alignment - TraesCS6D01G176600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G176600 chr6D 100.000 2305 0 0 1 2305 172745023 172742719 0.000000e+00 4257
1 TraesCS6D01G176600 chr6D 96.498 1656 54 2 652 2303 389246624 389244969 0.000000e+00 2734
2 TraesCS6D01G176600 chr6D 95.327 107 5 0 536 642 108502045 108501939 1.100000e-38 171
3 TraesCS6D01G176600 chr6D 95.327 107 5 0 536 642 430486439 430486333 1.100000e-38 171
4 TraesCS6D01G176600 chr3D 96.735 1654 52 2 652 2303 589264326 589262673 0.000000e+00 2754
5 TraesCS6D01G176600 chr3D 98.868 530 6 0 1 530 21163581 21163052 0.000000e+00 946
6 TraesCS6D01G176600 chr3D 98.868 530 4 1 1 530 86924434 86924961 0.000000e+00 944
7 TraesCS6D01G176600 chr3D 98.679 530 7 0 1 530 21155476 21154947 0.000000e+00 941
8 TraesCS6D01G176600 chr3D 98.682 531 6 1 1 530 207898023 207898553 0.000000e+00 941
9 TraesCS6D01G176600 chr3D 91.534 189 15 1 652 840 453124771 453124584 2.270000e-65 259
10 TraesCS6D01G176600 chr3D 97.500 120 3 0 652 771 80426291 80426410 3.000000e-49 206
11 TraesCS6D01G176600 chr3D 92.437 119 9 0 849 967 4114612 4114494 1.100000e-38 171
12 TraesCS6D01G176600 chr2D 96.437 1656 55 2 652 2303 591983807 591985462 0.000000e+00 2728
13 TraesCS6D01G176600 chr2D 98.679 530 7 0 1 530 528717156 528716627 0.000000e+00 941
14 TraesCS6D01G176600 chr2D 98.491 530 8 0 1 530 528709278 528708749 0.000000e+00 935
15 TraesCS6D01G176600 chr2D 98.302 530 9 0 1 530 498735195 498735724 0.000000e+00 929
16 TraesCS6D01G176600 chr7B 96.377 1656 56 2 652 2303 662725602 662727257 0.000000e+00 2723
17 TraesCS6D01G176600 chr7B 96.377 1656 56 2 652 2303 663100227 663098572 0.000000e+00 2723
18 TraesCS6D01G176600 chr7D 96.375 1655 57 2 652 2303 231555227 231553573 0.000000e+00 2721
19 TraesCS6D01G176600 chr7D 92.788 1664 105 7 652 2303 88622220 88620560 0.000000e+00 2394
20 TraesCS6D01G176600 chr7D 94.545 110 6 0 533 642 243934784 243934893 1.100000e-38 171
21 TraesCS6D01G176600 chr7D 95.327 107 5 0 536 642 381936691 381936585 1.100000e-38 171
22 TraesCS6D01G176600 chr3A 96.375 1655 57 2 652 2303 66005934 66004280 0.000000e+00 2721
23 TraesCS6D01G176600 chr5D 96.316 1656 57 2 652 2303 503244470 503246125 0.000000e+00 2717
24 TraesCS6D01G176600 chr2A 96.256 1656 58 2 652 2303 726907257 726905602 0.000000e+00 2712
25 TraesCS6D01G176600 chrUn 98.305 531 8 1 1 530 148088590 148088060 0.000000e+00 929
26 TraesCS6D01G176600 chrUn 95.327 107 5 0 536 642 182457147 182457041 1.100000e-38 171
27 TraesCS6D01G176600 chrUn 94.545 110 6 0 533 642 231549347 231549456 1.100000e-38 171
28 TraesCS6D01G176600 chrUn 94.545 110 6 0 533 642 333498427 333498536 1.100000e-38 171
29 TraesCS6D01G176600 chrUn 95.327 107 5 0 536 642 358548120 358548014 1.100000e-38 171
30 TraesCS6D01G176600 chr1D 98.117 531 9 1 1 530 477838493 477839023 0.000000e+00 924
31 TraesCS6D01G176600 chr4A 94.545 110 6 0 533 642 432427417 432427526 1.100000e-38 171


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 TraesCS6D01G176600 chr6D 172742719 172745023 2304 True 4257 4257 100.000 1 2305 1 chr6D.!!$R2 2304
1 TraesCS6D01G176600 chr6D 389244969 389246624 1655 True 2734 2734 96.498 652 2303 1 chr6D.!!$R3 1651
2 TraesCS6D01G176600 chr3D 589262673 589264326 1653 True 2754 2754 96.735 652 2303 1 chr3D.!!$R5 1651
3 TraesCS6D01G176600 chr3D 21163052 21163581 529 True 946 946 98.868 1 530 1 chr3D.!!$R3 529
4 TraesCS6D01G176600 chr3D 86924434 86924961 527 False 944 944 98.868 1 530 1 chr3D.!!$F2 529
5 TraesCS6D01G176600 chr3D 21154947 21155476 529 True 941 941 98.679 1 530 1 chr3D.!!$R2 529
6 TraesCS6D01G176600 chr3D 207898023 207898553 530 False 941 941 98.682 1 530 1 chr3D.!!$F3 529
7 TraesCS6D01G176600 chr2D 591983807 591985462 1655 False 2728 2728 96.437 652 2303 1 chr2D.!!$F2 1651
8 TraesCS6D01G176600 chr2D 528716627 528717156 529 True 941 941 98.679 1 530 1 chr2D.!!$R2 529
9 TraesCS6D01G176600 chr2D 528708749 528709278 529 True 935 935 98.491 1 530 1 chr2D.!!$R1 529
10 TraesCS6D01G176600 chr2D 498735195 498735724 529 False 929 929 98.302 1 530 1 chr2D.!!$F1 529
11 TraesCS6D01G176600 chr7B 662725602 662727257 1655 False 2723 2723 96.377 652 2303 1 chr7B.!!$F1 1651
12 TraesCS6D01G176600 chr7B 663098572 663100227 1655 True 2723 2723 96.377 652 2303 1 chr7B.!!$R1 1651
13 TraesCS6D01G176600 chr7D 231553573 231555227 1654 True 2721 2721 96.375 652 2303 1 chr7D.!!$R2 1651
14 TraesCS6D01G176600 chr7D 88620560 88622220 1660 True 2394 2394 92.788 652 2303 1 chr7D.!!$R1 1651
15 TraesCS6D01G176600 chr3A 66004280 66005934 1654 True 2721 2721 96.375 652 2303 1 chr3A.!!$R1 1651
16 TraesCS6D01G176600 chr5D 503244470 503246125 1655 False 2717 2717 96.316 652 2303 1 chr5D.!!$F1 1651
17 TraesCS6D01G176600 chr2A 726905602 726907257 1655 True 2712 2712 96.256 652 2303 1 chr2A.!!$R1 1651
18 TraesCS6D01G176600 chrUn 148088060 148088590 530 True 929 929 98.305 1 530 1 chrUn.!!$R1 529
19 TraesCS6D01G176600 chr1D 477838493 477839023 530 False 924 924 98.117 1 530 1 chr1D.!!$F1 529

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
572 574 0.036952 TCAGGAGGAAAGCTCGCTTG 60.037 55.0 4.73 0.0 36.26 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1853 0.094046 CGTAATCGCAACGACCCAAC 59.906 55.0 0.0 0.0 42.9 3.77 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
530 532 2.359478 AAATCGGGGGCGTCACAC 60.359 61.111 0.00 0.00 0.00 3.82
531 533 3.912745 AAATCGGGGGCGTCACACC 62.913 63.158 0.00 0.00 0.00 4.16
535 537 3.717294 GGGGGCGTCACACCAGAT 61.717 66.667 0.00 0.00 0.00 2.90
536 538 2.125106 GGGGCGTCACACCAGATC 60.125 66.667 0.00 0.00 0.00 2.75
537 539 2.662596 GGGCGTCACACCAGATCA 59.337 61.111 0.00 0.00 0.00 2.92
538 540 1.741770 GGGCGTCACACCAGATCAC 60.742 63.158 0.00 0.00 0.00 3.06
539 541 1.741770 GGCGTCACACCAGATCACC 60.742 63.158 0.00 0.00 0.00 4.02
540 542 1.741770 GCGTCACACCAGATCACCC 60.742 63.158 0.00 0.00 0.00 4.61
541 543 1.446099 CGTCACACCAGATCACCCG 60.446 63.158 0.00 0.00 0.00 5.28
542 544 1.873270 CGTCACACCAGATCACCCGA 61.873 60.000 0.00 0.00 0.00 5.14
543 545 0.320374 GTCACACCAGATCACCCGAA 59.680 55.000 0.00 0.00 0.00 4.30
544 546 1.052617 TCACACCAGATCACCCGAAA 58.947 50.000 0.00 0.00 0.00 3.46
545 547 1.156736 CACACCAGATCACCCGAAAC 58.843 55.000 0.00 0.00 0.00 2.78
546 548 1.056660 ACACCAGATCACCCGAAACT 58.943 50.000 0.00 0.00 0.00 2.66
547 549 1.002087 ACACCAGATCACCCGAAACTC 59.998 52.381 0.00 0.00 0.00 3.01
548 550 1.276421 CACCAGATCACCCGAAACTCT 59.724 52.381 0.00 0.00 0.00 3.24
549 551 1.276421 ACCAGATCACCCGAAACTCTG 59.724 52.381 0.00 0.00 34.48 3.35
550 552 1.276421 CCAGATCACCCGAAACTCTGT 59.724 52.381 0.00 0.00 33.16 3.41
551 553 2.496070 CCAGATCACCCGAAACTCTGTA 59.504 50.000 0.00 0.00 33.16 2.74
552 554 3.133003 CCAGATCACCCGAAACTCTGTAT 59.867 47.826 0.00 0.00 33.16 2.29
553 555 4.383118 CCAGATCACCCGAAACTCTGTATT 60.383 45.833 0.00 0.00 33.16 1.89
554 556 4.806247 CAGATCACCCGAAACTCTGTATTC 59.194 45.833 0.00 0.00 30.98 1.75
555 557 4.466370 AGATCACCCGAAACTCTGTATTCA 59.534 41.667 0.00 0.00 0.00 2.57
556 558 4.188247 TCACCCGAAACTCTGTATTCAG 57.812 45.455 0.00 0.00 42.54 3.02
557 559 3.056107 TCACCCGAAACTCTGTATTCAGG 60.056 47.826 0.00 0.00 41.59 3.86
558 560 3.056107 CACCCGAAACTCTGTATTCAGGA 60.056 47.826 0.00 0.00 41.59 3.86
559 561 3.195825 ACCCGAAACTCTGTATTCAGGAG 59.804 47.826 0.00 0.00 41.59 3.69
560 562 3.430929 CCCGAAACTCTGTATTCAGGAGG 60.431 52.174 0.00 0.00 41.59 4.30
561 563 3.447586 CCGAAACTCTGTATTCAGGAGGA 59.552 47.826 0.00 0.00 41.59 3.71
562 564 4.081642 CCGAAACTCTGTATTCAGGAGGAA 60.082 45.833 0.00 0.00 41.59 3.36
563 565 5.479306 CGAAACTCTGTATTCAGGAGGAAA 58.521 41.667 0.00 0.00 41.59 3.13
564 566 5.578727 CGAAACTCTGTATTCAGGAGGAAAG 59.421 44.000 0.00 0.00 41.59 2.62
565 567 4.479786 ACTCTGTATTCAGGAGGAAAGC 57.520 45.455 0.00 0.00 41.59 3.51
566 568 4.100373 ACTCTGTATTCAGGAGGAAAGCT 58.900 43.478 0.00 0.00 41.59 3.74
567 569 4.161377 ACTCTGTATTCAGGAGGAAAGCTC 59.839 45.833 0.00 0.00 41.59 4.09
568 570 3.131223 TCTGTATTCAGGAGGAAAGCTCG 59.869 47.826 0.00 0.00 41.59 5.03
569 571 2.205911 GTATTCAGGAGGAAAGCTCGC 58.794 52.381 0.00 0.00 39.39 5.03
570 572 0.908198 ATTCAGGAGGAAAGCTCGCT 59.092 50.000 0.00 0.00 39.39 4.93
571 573 0.687354 TTCAGGAGGAAAGCTCGCTT 59.313 50.000 0.00 0.00 37.98 4.68
572 574 0.036952 TCAGGAGGAAAGCTCGCTTG 60.037 55.000 4.73 0.00 36.26 4.01
573 575 0.036952 CAGGAGGAAAGCTCGCTTGA 60.037 55.000 4.73 0.00 36.26 3.02
574 576 0.687354 AGGAGGAAAGCTCGCTTGAA 59.313 50.000 4.73 0.00 36.26 2.69
575 577 1.280421 AGGAGGAAAGCTCGCTTGAAT 59.720 47.619 4.73 0.00 36.26 2.57
576 578 2.501723 AGGAGGAAAGCTCGCTTGAATA 59.498 45.455 4.73 0.00 36.26 1.75
577 579 2.609916 GGAGGAAAGCTCGCTTGAATAC 59.390 50.000 4.73 0.00 36.26 1.89
578 580 2.609916 GAGGAAAGCTCGCTTGAATACC 59.390 50.000 4.73 4.85 36.26 2.73
579 581 2.237392 AGGAAAGCTCGCTTGAATACCT 59.763 45.455 4.73 6.80 36.26 3.08
580 582 3.010420 GGAAAGCTCGCTTGAATACCTT 58.990 45.455 4.73 0.00 36.26 3.50
581 583 4.081087 AGGAAAGCTCGCTTGAATACCTTA 60.081 41.667 4.73 0.00 36.26 2.69
582 584 4.034163 GGAAAGCTCGCTTGAATACCTTAC 59.966 45.833 4.73 0.00 36.26 2.34
583 585 4.473477 AAGCTCGCTTGAATACCTTACT 57.527 40.909 2.92 0.00 34.60 2.24
584 586 4.473477 AGCTCGCTTGAATACCTTACTT 57.527 40.909 0.00 0.00 0.00 2.24
585 587 4.184629 AGCTCGCTTGAATACCTTACTTG 58.815 43.478 0.00 0.00 0.00 3.16
586 588 4.081642 AGCTCGCTTGAATACCTTACTTGA 60.082 41.667 0.00 0.00 0.00 3.02
587 589 4.630069 GCTCGCTTGAATACCTTACTTGAA 59.370 41.667 0.00 0.00 0.00 2.69
588 590 5.121768 GCTCGCTTGAATACCTTACTTGAAA 59.878 40.000 0.00 0.00 0.00 2.69
589 591 6.348213 GCTCGCTTGAATACCTTACTTGAAAA 60.348 38.462 0.00 0.00 0.00 2.29
590 592 6.894828 TCGCTTGAATACCTTACTTGAAAAC 58.105 36.000 0.00 0.00 0.00 2.43
591 593 6.483974 TCGCTTGAATACCTTACTTGAAAACA 59.516 34.615 0.00 0.00 0.00 2.83
592 594 7.012515 TCGCTTGAATACCTTACTTGAAAACAA 59.987 33.333 0.00 0.00 0.00 2.83
593 595 7.646130 CGCTTGAATACCTTACTTGAAAACAAA 59.354 33.333 0.00 0.00 0.00 2.83
594 596 8.752254 GCTTGAATACCTTACTTGAAAACAAAC 58.248 33.333 0.00 0.00 0.00 2.93
595 597 9.244799 CTTGAATACCTTACTTGAAAACAAACC 57.755 33.333 0.00 0.00 0.00 3.27
596 598 7.419204 TGAATACCTTACTTGAAAACAAACCG 58.581 34.615 0.00 0.00 0.00 4.44
597 599 4.036567 ACCTTACTTGAAAACAAACCGC 57.963 40.909 0.00 0.00 0.00 5.68
598 600 3.697542 ACCTTACTTGAAAACAAACCGCT 59.302 39.130 0.00 0.00 0.00 5.52
599 601 4.158949 ACCTTACTTGAAAACAAACCGCTT 59.841 37.500 0.00 0.00 0.00 4.68
600 602 4.502645 CCTTACTTGAAAACAAACCGCTTG 59.497 41.667 0.00 0.00 41.19 4.01
601 603 3.859411 ACTTGAAAACAAACCGCTTGA 57.141 38.095 2.82 0.00 38.50 3.02
602 604 3.769536 ACTTGAAAACAAACCGCTTGAG 58.230 40.909 2.82 0.00 38.50 3.02
603 605 2.202295 TGAAAACAAACCGCTTGAGC 57.798 45.000 2.82 0.00 38.50 4.26
604 606 1.748493 TGAAAACAAACCGCTTGAGCT 59.252 42.857 1.07 0.00 38.50 4.09
605 607 2.119457 GAAAACAAACCGCTTGAGCTG 58.881 47.619 0.00 0.00 38.50 4.24
606 608 1.102978 AAACAAACCGCTTGAGCTGT 58.897 45.000 0.00 0.00 40.20 4.40
607 609 0.381801 AACAAACCGCTTGAGCTGTG 59.618 50.000 0.00 0.00 38.49 3.66
608 610 0.463654 ACAAACCGCTTGAGCTGTGA 60.464 50.000 0.00 0.00 38.49 3.58
609 611 0.040958 CAAACCGCTTGAGCTGTGAC 60.041 55.000 0.00 0.00 38.49 3.67
610 612 1.166531 AAACCGCTTGAGCTGTGACC 61.167 55.000 0.00 0.00 38.49 4.02
611 613 3.114616 CCGCTTGAGCTGTGACCG 61.115 66.667 0.00 0.00 39.32 4.79
612 614 2.049156 CGCTTGAGCTGTGACCGA 60.049 61.111 0.00 0.00 39.32 4.69
613 615 1.664649 CGCTTGAGCTGTGACCGAA 60.665 57.895 0.00 0.00 39.32 4.30
614 616 1.221466 CGCTTGAGCTGTGACCGAAA 61.221 55.000 0.00 0.00 39.32 3.46
615 617 1.160137 GCTTGAGCTGTGACCGAAAT 58.840 50.000 0.00 0.00 38.21 2.17
616 618 2.346803 GCTTGAGCTGTGACCGAAATA 58.653 47.619 0.00 0.00 38.21 1.40
617 619 2.349886 GCTTGAGCTGTGACCGAAATAG 59.650 50.000 0.00 0.00 38.21 1.73
618 620 3.849911 CTTGAGCTGTGACCGAAATAGA 58.150 45.455 0.00 0.00 0.00 1.98
619 621 3.953712 TGAGCTGTGACCGAAATAGAA 57.046 42.857 0.00 0.00 0.00 2.10
620 622 4.265904 TGAGCTGTGACCGAAATAGAAA 57.734 40.909 0.00 0.00 0.00 2.52
621 623 4.245660 TGAGCTGTGACCGAAATAGAAAG 58.754 43.478 0.00 0.00 0.00 2.62
622 624 3.600388 AGCTGTGACCGAAATAGAAAGG 58.400 45.455 0.00 0.00 0.00 3.11
623 625 3.008049 AGCTGTGACCGAAATAGAAAGGT 59.992 43.478 0.00 0.00 40.11 3.50
624 626 3.751698 GCTGTGACCGAAATAGAAAGGTT 59.248 43.478 0.00 0.00 37.07 3.50
625 627 4.215613 GCTGTGACCGAAATAGAAAGGTTT 59.784 41.667 0.00 0.00 37.07 3.27
626 628 5.682943 TGTGACCGAAATAGAAAGGTTTG 57.317 39.130 0.00 0.00 37.07 2.93
627 629 5.369833 TGTGACCGAAATAGAAAGGTTTGA 58.630 37.500 0.00 0.00 37.07 2.69
628 630 6.001460 TGTGACCGAAATAGAAAGGTTTGAT 58.999 36.000 0.00 0.00 37.07 2.57
629 631 6.072728 TGTGACCGAAATAGAAAGGTTTGATG 60.073 38.462 0.00 0.00 37.07 3.07
630 632 6.148811 GTGACCGAAATAGAAAGGTTTGATGA 59.851 38.462 0.00 0.00 37.07 2.92
631 633 6.371548 TGACCGAAATAGAAAGGTTTGATGAG 59.628 38.462 0.00 0.00 37.07 2.90
632 634 5.123979 ACCGAAATAGAAAGGTTTGATGAGC 59.876 40.000 0.00 0.00 32.17 4.26
633 635 5.449177 CCGAAATAGAAAGGTTTGATGAGCC 60.449 44.000 0.00 0.00 0.00 4.70
634 636 5.567138 AAATAGAAAGGTTTGATGAGCCG 57.433 39.130 0.00 0.00 33.10 5.52
635 637 1.168714 AGAAAGGTTTGATGAGCCGC 58.831 50.000 0.00 0.00 33.10 6.53
636 638 1.168714 GAAAGGTTTGATGAGCCGCT 58.831 50.000 0.00 0.00 33.10 5.52
637 639 0.883833 AAAGGTTTGATGAGCCGCTG 59.116 50.000 0.00 0.00 33.10 5.18
638 640 1.589716 AAGGTTTGATGAGCCGCTGC 61.590 55.000 0.00 0.00 33.10 5.25
648 650 4.540153 GCCGCTGCTTGAGGATAA 57.460 55.556 0.00 0.00 37.90 1.75
649 651 2.780595 GCCGCTGCTTGAGGATAAA 58.219 52.632 0.00 0.00 37.90 1.40
650 652 0.378610 GCCGCTGCTTGAGGATAAAC 59.621 55.000 0.00 0.00 37.90 2.01
662 664 7.285401 TGCTTGAGGATAAACAAGTCTTCTTTT 59.715 33.333 0.00 0.00 0.00 2.27
712 714 5.961396 TGAGCTTATTATCCTAGGTCGTC 57.039 43.478 9.08 0.00 38.81 4.20
806 809 4.344104 GGATGTCAAAAGGAAAGGGATGA 58.656 43.478 0.00 0.00 0.00 2.92
897 900 1.185618 AGAGCGCGCCCCTGATAATA 61.186 55.000 30.33 0.00 0.00 0.98
898 901 0.108138 GAGCGCGCCCCTGATAATAT 60.108 55.000 30.33 3.57 0.00 1.28
952 955 3.595173 CCACACGGATAGTTCAATGTGA 58.405 45.455 3.82 0.00 39.69 3.58
1161 1176 2.411290 CGGCTCCTCTCTTCTCGC 59.589 66.667 0.00 0.00 0.00 5.03
1253 1268 3.769300 GGGAAAATGGAGCACCTAACAAT 59.231 43.478 0.71 0.00 37.04 2.71
1305 1320 2.834638 CCCTTTCATTCTGGGGTGAT 57.165 50.000 0.00 0.00 37.37 3.06
1401 1417 7.344599 ACTTTCCTAATACTCCCTTCCTTTT 57.655 36.000 0.00 0.00 0.00 2.27
1421 1437 8.726988 TCCTTTTAGGAAGAACGTGAAATTATG 58.273 33.333 0.00 0.00 42.51 1.90
1457 1473 3.290710 AGCAGAGCAGGTTTGAAAAAGA 58.709 40.909 0.00 0.00 0.00 2.52
1486 1502 1.923909 GTCTAGGGTTGGGCCAGGT 60.924 63.158 6.23 0.00 39.65 4.00
1528 1544 4.764050 TTTTCTGCCCATCGGAGTTATA 57.236 40.909 0.00 0.00 0.00 0.98
1615 1633 1.165270 GGGAGTTGTATGCTGCGTTT 58.835 50.000 0.00 0.00 0.00 3.60
1661 1679 7.502060 AAAAGGAGTCTATTGATTCTCTCCA 57.498 36.000 12.02 0.00 42.45 3.86
1795 1813 0.983467 TGCATACTCCACTTGGCTCA 59.017 50.000 0.00 0.00 34.44 4.26
1800 1818 1.920325 CTCCACTTGGCTCAGGGGA 60.920 63.158 7.87 7.87 44.84 4.81
1810 1828 2.158097 TGGCTCAGGGGAGATATAGCTT 60.158 50.000 0.00 0.00 44.26 3.74
1855 1873 0.038435 TTGGGTCGTTGCGATTACGA 60.038 50.000 0.00 3.48 44.88 3.43
1870 1888 4.207224 CGATTACGAGTTGGCTGTCTAATG 59.793 45.833 0.00 0.00 42.66 1.90
1871 1889 4.794278 TTACGAGTTGGCTGTCTAATGA 57.206 40.909 0.00 0.00 0.00 2.57
1874 1892 2.791560 CGAGTTGGCTGTCTAATGATCG 59.208 50.000 0.00 0.00 0.00 3.69
1889 1907 4.801330 ATGATCGAGGCGGTAATGATAA 57.199 40.909 0.00 0.00 0.00 1.75
1910 1928 7.506599 TGATAATATCTTGTACCTGAACCGGTA 59.493 37.037 8.00 0.00 38.49 4.02
1916 1934 1.134560 GTACCTGAACCGGTAGCTCAG 59.865 57.143 22.65 22.65 40.07 3.35
1926 1944 5.161943 ACCGGTAGCTCAGTTTTTCTAAT 57.838 39.130 4.49 0.00 0.00 1.73
1962 1980 2.624838 ACTGAAACATGCCACTGAAAGG 59.375 45.455 0.00 0.00 39.30 3.11
2183 2201 3.436704 TGAGCGAAATGTAGCAAAAGGAG 59.563 43.478 0.00 0.00 35.48 3.69
2214 2232 1.265454 GGACCGACCCCATTGTCTCT 61.265 60.000 0.00 0.00 32.97 3.10
2245 2263 2.526888 ACTACGAGATCACCCCAAGA 57.473 50.000 0.00 0.00 0.00 3.02
2246 2264 2.100989 ACTACGAGATCACCCCAAGAC 58.899 52.381 0.00 0.00 0.00 3.01
2287 2305 2.496291 CGGACCGACCATAGACCCC 61.496 68.421 8.64 0.00 38.90 4.95
2303 2321 3.007635 GACCCCGTTCAATAAGTGGAAG 58.992 50.000 0.00 0.00 0.00 3.46
2304 2322 2.640826 ACCCCGTTCAATAAGTGGAAGA 59.359 45.455 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 189 4.340617 AGAATCATCCTCGGGATCTCTAC 58.659 47.826 2.76 0.00 40.98 2.59
530 532 1.276421 ACAGAGTTTCGGGTGATCTGG 59.724 52.381 5.59 0.00 41.32 3.86
531 533 2.751166 ACAGAGTTTCGGGTGATCTG 57.249 50.000 0.00 0.00 42.43 2.90
532 534 4.466370 TGAATACAGAGTTTCGGGTGATCT 59.534 41.667 0.00 0.00 0.00 2.75
533 535 4.755411 TGAATACAGAGTTTCGGGTGATC 58.245 43.478 0.00 0.00 0.00 2.92
534 536 4.383118 CCTGAATACAGAGTTTCGGGTGAT 60.383 45.833 0.00 0.00 46.03 3.06
535 537 3.056107 CCTGAATACAGAGTTTCGGGTGA 60.056 47.826 0.00 0.00 46.03 4.02
536 538 3.056107 TCCTGAATACAGAGTTTCGGGTG 60.056 47.826 9.65 0.00 45.05 4.61
537 539 3.170717 TCCTGAATACAGAGTTTCGGGT 58.829 45.455 9.65 0.00 45.05 5.28
538 540 3.430929 CCTCCTGAATACAGAGTTTCGGG 60.431 52.174 4.48 4.48 45.81 5.14
539 541 3.447586 TCCTCCTGAATACAGAGTTTCGG 59.552 47.826 0.00 0.00 46.03 4.30
540 542 4.720649 TCCTCCTGAATACAGAGTTTCG 57.279 45.455 0.00 0.00 46.03 3.46
541 543 5.352846 GCTTTCCTCCTGAATACAGAGTTTC 59.647 44.000 0.00 0.00 46.03 2.78
542 544 5.013599 AGCTTTCCTCCTGAATACAGAGTTT 59.986 40.000 0.00 0.00 46.03 2.66
543 545 4.534103 AGCTTTCCTCCTGAATACAGAGTT 59.466 41.667 0.00 0.00 46.03 3.01
544 546 4.100373 AGCTTTCCTCCTGAATACAGAGT 58.900 43.478 0.00 0.00 46.03 3.24
545 547 4.692228 GAGCTTTCCTCCTGAATACAGAG 58.308 47.826 0.00 0.00 46.03 3.35
546 548 3.131223 CGAGCTTTCCTCCTGAATACAGA 59.869 47.826 0.00 0.00 43.23 3.41
547 549 3.452474 CGAGCTTTCCTCCTGAATACAG 58.548 50.000 0.00 0.00 43.12 2.74
548 550 2.418746 GCGAGCTTTCCTCCTGAATACA 60.419 50.000 0.00 0.00 37.27 2.29
549 551 2.159028 AGCGAGCTTTCCTCCTGAATAC 60.159 50.000 0.00 0.00 37.27 1.89
550 552 2.111384 AGCGAGCTTTCCTCCTGAATA 58.889 47.619 0.00 0.00 37.27 1.75
551 553 0.908198 AGCGAGCTTTCCTCCTGAAT 59.092 50.000 0.00 0.00 37.27 2.57
552 554 0.687354 AAGCGAGCTTTCCTCCTGAA 59.313 50.000 4.26 0.00 37.27 3.02
553 555 0.036952 CAAGCGAGCTTTCCTCCTGA 60.037 55.000 7.70 0.00 37.27 3.86
554 556 0.036952 TCAAGCGAGCTTTCCTCCTG 60.037 55.000 7.70 0.00 37.27 3.86
555 557 0.687354 TTCAAGCGAGCTTTCCTCCT 59.313 50.000 7.70 0.00 37.27 3.69
556 558 1.743996 ATTCAAGCGAGCTTTCCTCC 58.256 50.000 7.70 0.00 37.27 4.30
557 559 2.609916 GGTATTCAAGCGAGCTTTCCTC 59.390 50.000 7.70 0.00 37.22 3.71
558 560 2.237392 AGGTATTCAAGCGAGCTTTCCT 59.763 45.455 7.70 8.14 33.42 3.36
559 561 2.633488 AGGTATTCAAGCGAGCTTTCC 58.367 47.619 7.70 6.21 33.42 3.13
560 562 4.870991 AGTAAGGTATTCAAGCGAGCTTTC 59.129 41.667 7.70 0.00 33.42 2.62
561 563 4.833390 AGTAAGGTATTCAAGCGAGCTTT 58.167 39.130 7.70 0.00 33.42 3.51
562 564 4.473477 AGTAAGGTATTCAAGCGAGCTT 57.527 40.909 4.26 4.26 36.60 3.74
563 565 4.081642 TCAAGTAAGGTATTCAAGCGAGCT 60.082 41.667 0.00 0.00 0.00 4.09
564 566 4.181578 TCAAGTAAGGTATTCAAGCGAGC 58.818 43.478 0.00 0.00 0.00 5.03
565 567 6.721571 TTTCAAGTAAGGTATTCAAGCGAG 57.278 37.500 0.00 0.00 0.00 5.03
566 568 6.483974 TGTTTTCAAGTAAGGTATTCAAGCGA 59.516 34.615 0.00 0.00 0.00 4.93
567 569 6.664515 TGTTTTCAAGTAAGGTATTCAAGCG 58.335 36.000 0.00 0.00 0.00 4.68
568 570 8.752254 GTTTGTTTTCAAGTAAGGTATTCAAGC 58.248 33.333 0.00 0.00 41.09 4.01
569 571 9.244799 GGTTTGTTTTCAAGTAAGGTATTCAAG 57.755 33.333 0.00 0.00 41.09 3.02
570 572 7.916450 CGGTTTGTTTTCAAGTAAGGTATTCAA 59.084 33.333 0.00 0.00 41.09 2.69
571 573 7.419204 CGGTTTGTTTTCAAGTAAGGTATTCA 58.581 34.615 0.00 0.00 41.09 2.57
572 574 6.361481 GCGGTTTGTTTTCAAGTAAGGTATTC 59.639 38.462 0.00 0.00 41.09 1.75
573 575 6.040054 AGCGGTTTGTTTTCAAGTAAGGTATT 59.960 34.615 0.00 0.00 41.09 1.89
574 576 5.533528 AGCGGTTTGTTTTCAAGTAAGGTAT 59.466 36.000 0.00 0.00 41.09 2.73
575 577 4.883006 AGCGGTTTGTTTTCAAGTAAGGTA 59.117 37.500 0.00 0.00 41.09 3.08
576 578 3.697542 AGCGGTTTGTTTTCAAGTAAGGT 59.302 39.130 0.00 0.00 41.09 3.50
577 579 4.301637 AGCGGTTTGTTTTCAAGTAAGG 57.698 40.909 0.00 0.00 41.09 2.69
578 580 5.336744 TCAAGCGGTTTGTTTTCAAGTAAG 58.663 37.500 0.00 0.00 41.09 2.34
579 581 5.312120 TCAAGCGGTTTGTTTTCAAGTAA 57.688 34.783 0.00 0.00 41.09 2.24
580 582 4.732355 GCTCAAGCGGTTTGTTTTCAAGTA 60.732 41.667 0.00 0.00 41.09 2.24
581 583 3.769536 CTCAAGCGGTTTGTTTTCAAGT 58.230 40.909 0.00 0.00 41.09 3.16
582 584 2.535574 GCTCAAGCGGTTTGTTTTCAAG 59.464 45.455 0.00 0.00 41.09 3.02
583 585 2.535331 GCTCAAGCGGTTTGTTTTCAA 58.465 42.857 0.00 0.00 38.01 2.69
584 586 2.202295 GCTCAAGCGGTTTGTTTTCA 57.798 45.000 0.00 0.00 38.01 2.69
585 587 2.479560 ACAGCTCAAGCGGTTTGTTTTC 60.480 45.455 0.00 0.00 46.84 2.29
586 588 1.476488 ACAGCTCAAGCGGTTTGTTTT 59.524 42.857 0.00 0.00 46.84 2.43
587 589 1.102978 ACAGCTCAAGCGGTTTGTTT 58.897 45.000 0.00 0.00 46.84 2.83
588 590 0.381801 CACAGCTCAAGCGGTTTGTT 59.618 50.000 5.00 0.00 46.84 2.83
589 591 0.463654 TCACAGCTCAAGCGGTTTGT 60.464 50.000 5.00 0.00 46.84 2.83
590 592 0.040958 GTCACAGCTCAAGCGGTTTG 60.041 55.000 5.00 0.00 46.84 2.93
591 593 1.166531 GGTCACAGCTCAAGCGGTTT 61.167 55.000 5.00 0.00 46.84 3.27
592 594 1.598130 GGTCACAGCTCAAGCGGTT 60.598 57.895 5.00 0.00 46.84 4.44
596 598 1.160137 ATTTCGGTCACAGCTCAAGC 58.840 50.000 0.00 0.00 42.49 4.01
597 599 3.849911 TCTATTTCGGTCACAGCTCAAG 58.150 45.455 0.00 0.00 0.00 3.02
598 600 3.953712 TCTATTTCGGTCACAGCTCAA 57.046 42.857 0.00 0.00 0.00 3.02
599 601 3.953712 TTCTATTTCGGTCACAGCTCA 57.046 42.857 0.00 0.00 0.00 4.26
600 602 3.619038 CCTTTCTATTTCGGTCACAGCTC 59.381 47.826 0.00 0.00 0.00 4.09
601 603 3.008049 ACCTTTCTATTTCGGTCACAGCT 59.992 43.478 0.00 0.00 0.00 4.24
602 604 3.335579 ACCTTTCTATTTCGGTCACAGC 58.664 45.455 0.00 0.00 0.00 4.40
603 605 5.468746 TCAAACCTTTCTATTTCGGTCACAG 59.531 40.000 0.00 0.00 0.00 3.66
604 606 5.369833 TCAAACCTTTCTATTTCGGTCACA 58.630 37.500 0.00 0.00 0.00 3.58
605 607 5.934935 TCAAACCTTTCTATTTCGGTCAC 57.065 39.130 0.00 0.00 0.00 3.67
606 608 6.234920 TCATCAAACCTTTCTATTTCGGTCA 58.765 36.000 0.00 0.00 0.00 4.02
607 609 6.675728 GCTCATCAAACCTTTCTATTTCGGTC 60.676 42.308 0.00 0.00 0.00 4.79
608 610 5.123979 GCTCATCAAACCTTTCTATTTCGGT 59.876 40.000 0.00 0.00 0.00 4.69
609 611 5.449177 GGCTCATCAAACCTTTCTATTTCGG 60.449 44.000 0.00 0.00 0.00 4.30
610 612 5.573146 GGCTCATCAAACCTTTCTATTTCG 58.427 41.667 0.00 0.00 0.00 3.46
611 613 5.573146 CGGCTCATCAAACCTTTCTATTTC 58.427 41.667 0.00 0.00 0.00 2.17
612 614 4.142381 GCGGCTCATCAAACCTTTCTATTT 60.142 41.667 0.00 0.00 0.00 1.40
613 615 3.378427 GCGGCTCATCAAACCTTTCTATT 59.622 43.478 0.00 0.00 0.00 1.73
614 616 2.945668 GCGGCTCATCAAACCTTTCTAT 59.054 45.455 0.00 0.00 0.00 1.98
615 617 2.027192 AGCGGCTCATCAAACCTTTCTA 60.027 45.455 0.00 0.00 0.00 2.10
616 618 1.168714 GCGGCTCATCAAACCTTTCT 58.831 50.000 0.00 0.00 0.00 2.52
617 619 1.135575 CAGCGGCTCATCAAACCTTTC 60.136 52.381 0.00 0.00 0.00 2.62
618 620 0.883833 CAGCGGCTCATCAAACCTTT 59.116 50.000 0.00 0.00 0.00 3.11
619 621 1.589716 GCAGCGGCTCATCAAACCTT 61.590 55.000 0.00 0.00 36.96 3.50
620 622 2.042831 GCAGCGGCTCATCAAACCT 61.043 57.895 0.00 0.00 36.96 3.50
621 623 2.486966 GCAGCGGCTCATCAAACC 59.513 61.111 0.00 0.00 36.96 3.27
631 633 0.378610 GTTTATCCTCAAGCAGCGGC 59.621 55.000 0.00 0.00 41.61 6.53
632 634 1.737838 TGTTTATCCTCAAGCAGCGG 58.262 50.000 0.00 0.00 0.00 5.52
633 635 2.744202 ACTTGTTTATCCTCAAGCAGCG 59.256 45.455 5.06 0.00 43.05 5.18
634 636 4.006319 AGACTTGTTTATCCTCAAGCAGC 58.994 43.478 5.06 0.00 43.05 5.25
635 637 5.936956 AGAAGACTTGTTTATCCTCAAGCAG 59.063 40.000 0.00 0.00 43.05 4.24
636 638 5.869579 AGAAGACTTGTTTATCCTCAAGCA 58.130 37.500 0.00 0.00 43.05 3.91
637 639 6.809630 AAGAAGACTTGTTTATCCTCAAGC 57.190 37.500 0.00 0.00 43.05 4.01
638 640 8.624776 ACAAAAGAAGACTTGTTTATCCTCAAG 58.375 33.333 10.45 0.00 44.29 3.02
639 641 8.519799 ACAAAAGAAGACTTGTTTATCCTCAA 57.480 30.769 10.45 0.00 36.39 3.02
640 642 8.405531 CAACAAAAGAAGACTTGTTTATCCTCA 58.594 33.333 10.45 0.00 41.77 3.86
641 643 8.621286 TCAACAAAAGAAGACTTGTTTATCCTC 58.379 33.333 10.45 0.00 41.77 3.71
642 644 8.519799 TCAACAAAAGAAGACTTGTTTATCCT 57.480 30.769 10.45 0.00 41.77 3.24
643 645 7.862873 CCTCAACAAAAGAAGACTTGTTTATCC 59.137 37.037 10.45 0.00 41.77 2.59
644 646 7.862873 CCCTCAACAAAAGAAGACTTGTTTATC 59.137 37.037 10.45 0.00 41.77 1.75
645 647 7.342026 ACCCTCAACAAAAGAAGACTTGTTTAT 59.658 33.333 10.45 0.59 41.77 1.40
646 648 6.661805 ACCCTCAACAAAAGAAGACTTGTTTA 59.338 34.615 10.45 0.00 41.77 2.01
647 649 5.480422 ACCCTCAACAAAAGAAGACTTGTTT 59.520 36.000 4.55 4.55 41.77 2.83
648 650 5.016831 ACCCTCAACAAAAGAAGACTTGTT 58.983 37.500 0.00 0.00 44.53 2.83
649 651 4.399303 CACCCTCAACAAAAGAAGACTTGT 59.601 41.667 0.00 0.00 37.36 3.16
650 652 4.640201 TCACCCTCAACAAAAGAAGACTTG 59.360 41.667 0.00 0.00 36.39 3.16
662 664 3.042682 TGGTCTTACTTCACCCTCAACA 58.957 45.455 0.00 0.00 0.00 3.33
776 779 1.559368 CTTTTGACATCCCCATGCCA 58.441 50.000 0.00 0.00 32.57 4.92
851 854 2.893449 GCTAATAGCCCAACGCGCC 61.893 63.158 5.73 0.00 44.76 6.53
857 860 2.196595 ACCACTGAGCTAATAGCCCAA 58.803 47.619 8.88 0.00 43.77 4.12
897 900 2.047274 CCCAGGCACAACGACGAT 60.047 61.111 0.00 0.00 0.00 3.73
898 901 4.980805 GCCCAGGCACAACGACGA 62.981 66.667 0.00 0.00 41.49 4.20
936 939 5.107182 GCTGATGATCACATTGAACTATCCG 60.107 44.000 0.00 0.00 36.82 4.18
952 955 1.145598 CAGGTCAGGCGCTGATGAT 59.854 57.895 7.64 0.00 42.73 2.45
1063 1066 0.758734 CTCACCTGAATCGCCCCATA 59.241 55.000 0.00 0.00 0.00 2.74
1161 1176 5.871524 CACTGATAAGGGATGTATGGATTCG 59.128 44.000 0.00 0.00 0.00 3.34
1253 1268 3.141398 GTTCTTGGTCTGTGAAGATGCA 58.859 45.455 0.00 0.00 0.00 3.96
1305 1320 1.037493 CGAATGGTACGATCCCTCCA 58.963 55.000 0.00 0.93 0.00 3.86
1335 1350 1.402968 CAGACCGCTGGGAAAATCATG 59.597 52.381 0.00 0.00 38.51 3.07
1336 1351 1.755179 CAGACCGCTGGGAAAATCAT 58.245 50.000 0.00 0.00 38.51 2.45
1337 1352 3.248043 CAGACCGCTGGGAAAATCA 57.752 52.632 0.00 0.00 38.51 2.57
1347 1363 1.294780 CTGCTTTCTCCAGACCGCT 59.705 57.895 0.00 0.00 32.03 5.52
1401 1417 7.881232 AGGAAACATAATTTCACGTTCTTCCTA 59.119 33.333 0.00 0.00 30.44 2.94
1419 1435 4.934356 TCTGCTCCCATTTAAGGAAACAT 58.066 39.130 0.00 0.00 31.49 2.71
1421 1437 3.129462 GCTCTGCTCCCATTTAAGGAAAC 59.871 47.826 0.00 0.00 31.49 2.78
1457 1473 4.717280 CCCAACCCTAGACACTCTAAGATT 59.283 45.833 0.00 0.00 0.00 2.40
1486 1502 0.611714 GGAAGGCGTTAAGAGACCCA 59.388 55.000 0.00 0.00 0.00 4.51
1528 1544 3.602104 CATGGCAAGTCCTTGGGAT 57.398 52.632 8.97 0.00 40.74 3.85
1615 1633 0.469917 GGAGCGATTCATCCTTCCCA 59.530 55.000 0.00 0.00 32.51 4.37
1661 1679 3.308401 GCCCCTATGATCCAACCAATTT 58.692 45.455 0.00 0.00 0.00 1.82
1675 1693 4.642429 GTGAAGTAAATCATCGCCCCTAT 58.358 43.478 0.00 0.00 0.00 2.57
1795 1813 5.094569 ACCAACTAAGCTATATCTCCCCT 57.905 43.478 0.00 0.00 0.00 4.79
1800 1818 6.661805 GGAGCTCTACCAACTAAGCTATATCT 59.338 42.308 14.64 0.00 44.77 1.98
1835 1853 0.094046 CGTAATCGCAACGACCCAAC 59.906 55.000 0.00 0.00 42.90 3.77
1855 1873 3.181471 CCTCGATCATTAGACAGCCAACT 60.181 47.826 0.00 0.00 0.00 3.16
1870 1888 6.740110 AGATATTATCATTACCGCCTCGATC 58.260 40.000 6.46 0.00 0.00 3.69
1871 1889 6.716934 AGATATTATCATTACCGCCTCGAT 57.283 37.500 6.46 0.00 0.00 3.59
1874 1892 7.491696 GGTACAAGATATTATCATTACCGCCTC 59.508 40.741 6.46 0.00 0.00 4.70
1889 1907 4.038883 GCTACCGGTTCAGGTACAAGATAT 59.961 45.833 15.04 0.00 43.89 1.63
1910 1928 7.182060 TCCCCATTAATTAGAAAAACTGAGCT 58.818 34.615 0.00 0.00 0.00 4.09
1916 1934 8.467598 GTCCTCTTCCCCATTAATTAGAAAAAC 58.532 37.037 0.00 0.00 0.00 2.43
1926 1944 4.352595 TGTTTCAGTCCTCTTCCCCATTAA 59.647 41.667 0.00 0.00 0.00 1.40
1962 1980 5.008118 GCCCATATTTTTGTCTCAGTAGAGC 59.992 44.000 0.00 0.00 41.81 4.09
2064 2082 2.042435 AAGCCTAGGAGAGCCGCT 60.042 61.111 14.75 0.00 39.96 5.52
2111 2129 1.535204 ATTCGCAAGGGCCAACTTGG 61.535 55.000 19.58 3.10 46.10 3.61
2183 2201 1.389555 GTCGGTCCATGGATTTTCCC 58.610 55.000 19.62 13.00 35.03 3.97


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

AutoCloner maintained by Alex Coulton.