Multiple sequence alignment - TraesCS5D01G340100

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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 TraesCS5D01G340100 chr5D 100.000 3557 0 0 1 3557 428698917 428702473 0.000000e+00 6569
1 TraesCS5D01G340100 chr5D 84.690 1032 137 16 1541 2559 388872658 388871635 0.000000e+00 1011
2 TraesCS5D01G340100 chr5D 94.281 612 25 9 1 606 399962370 399961763 0.000000e+00 928
3 TraesCS5D01G340100 chr5D 88.128 438 40 4 1040 1477 388873172 388872747 8.810000e-141 510
4 TraesCS5D01G340100 chr5D 83.203 256 28 8 2744 2987 428704286 428704034 1.660000e-53 220
5 TraesCS5D01G340100 chr5D 91.608 143 12 0 2738 2880 410380201 410380343 7.790000e-47 198
6 TraesCS5D01G340100 chr5B 95.010 2024 68 14 740 2743 517852171 517854181 0.000000e+00 3147
7 TraesCS5D01G340100 chr5B 84.884 1032 135 14 1541 2559 467371101 467370078 0.000000e+00 1022
8 TraesCS5D01G340100 chr5A 94.409 1878 77 10 715 2580 544533553 544535414 0.000000e+00 2861
9 TraesCS5D01G340100 chr2D 98.526 814 12 0 2744 3557 405871205 405870392 0.000000e+00 1437
10 TraesCS5D01G340100 chr2D 94.281 612 25 9 1 607 19211007 19211613 0.000000e+00 928
11 TraesCS5D01G340100 chr7D 83.138 1536 178 44 1046 2552 634920418 634918935 0.000000e+00 1327
12 TraesCS5D01G340100 chr7D 94.300 614 23 9 1 608 501000466 501001073 0.000000e+00 929
13 TraesCS5D01G340100 chr7D 98.410 503 4 4 3058 3557 557431180 557431681 0.000000e+00 881
14 TraesCS5D01G340100 chr7D 97.846 325 7 0 2742 3066 557417512 557417836 2.400000e-156 562
15 TraesCS5D01G340100 chr7A 81.551 1534 187 48 1046 2547 730723137 730721668 0.000000e+00 1177
16 TraesCS5D01G340100 chr7A 84.071 339 52 2 3217 3554 709978694 709979031 3.420000e-85 326
17 TraesCS5D01G340100 chr6D 94.156 616 24 11 1 607 60514873 60514261 0.000000e+00 928
18 TraesCS5D01G340100 chr7B 83.781 1005 133 24 1539 2526 741226991 741227982 0.000000e+00 926
19 TraesCS5D01G340100 chr7B 82.827 757 109 15 1773 2520 741261807 741261063 0.000000e+00 658
20 TraesCS5D01G340100 chr1D 94.127 613 28 7 1 607 452266797 452266187 0.000000e+00 926
21 TraesCS5D01G340100 chr3D 94.118 612 24 11 1 606 594499440 594498835 0.000000e+00 920
22 TraesCS5D01G340100 chr3D 93.954 612 28 7 1 604 361386189 361385579 0.000000e+00 917
23 TraesCS5D01G340100 chr4D 93.607 610 29 8 1 607 472212380 472211778 0.000000e+00 902
24 TraesCS5D01G340100 chr4D 93.607 610 24 10 1 607 366316098 366315501 0.000000e+00 896
25 TraesCS5D01G340100 chr3A 89.919 248 22 3 3186 3431 487452785 487453031 2.060000e-82 316
26 TraesCS5D01G340100 chr3A 83.333 258 33 4 2739 2987 487452332 487452588 2.760000e-56 230
27 TraesCS5D01G340100 chr4A 89.431 246 23 3 3188 3431 368126625 368126869 1.240000e-79 307
28 TraesCS5D01G340100 chr4A 84.615 247 28 4 2750 2987 368126183 368126428 1.650000e-58 237
29 TraesCS5D01G340100 chr4A 83.607 244 29 6 2744 2978 368127670 368127429 5.980000e-53 219
30 TraesCS5D01G340100 chr2B 83.534 249 30 4 2741 2980 559129423 559129669 4.620000e-54 222
31 TraesCS5D01G340100 chr2A 91.034 145 13 0 2739 2883 10990125 10989981 2.800000e-46 196


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 TraesCS5D01G340100 chr5D 428698917 428702473 3556 False 6569.0 6569 100.000 1 3557 1 chr5D.!!$F2 3556
1 TraesCS5D01G340100 chr5D 399961763 399962370 607 True 928.0 928 94.281 1 606 1 chr5D.!!$R1 605
2 TraesCS5D01G340100 chr5D 388871635 388873172 1537 True 760.5 1011 86.409 1040 2559 2 chr5D.!!$R3 1519
3 TraesCS5D01G340100 chr5B 517852171 517854181 2010 False 3147.0 3147 95.010 740 2743 1 chr5B.!!$F1 2003
4 TraesCS5D01G340100 chr5B 467370078 467371101 1023 True 1022.0 1022 84.884 1541 2559 1 chr5B.!!$R1 1018
5 TraesCS5D01G340100 chr5A 544533553 544535414 1861 False 2861.0 2861 94.409 715 2580 1 chr5A.!!$F1 1865
6 TraesCS5D01G340100 chr2D 405870392 405871205 813 True 1437.0 1437 98.526 2744 3557 1 chr2D.!!$R1 813
7 TraesCS5D01G340100 chr2D 19211007 19211613 606 False 928.0 928 94.281 1 607 1 chr2D.!!$F1 606
8 TraesCS5D01G340100 chr7D 634918935 634920418 1483 True 1327.0 1327 83.138 1046 2552 1 chr7D.!!$R1 1506
9 TraesCS5D01G340100 chr7D 501000466 501001073 607 False 929.0 929 94.300 1 608 1 chr7D.!!$F1 607
10 TraesCS5D01G340100 chr7D 557431180 557431681 501 False 881.0 881 98.410 3058 3557 1 chr7D.!!$F3 499
11 TraesCS5D01G340100 chr7A 730721668 730723137 1469 True 1177.0 1177 81.551 1046 2547 1 chr7A.!!$R1 1501
12 TraesCS5D01G340100 chr6D 60514261 60514873 612 True 928.0 928 94.156 1 607 1 chr6D.!!$R1 606
13 TraesCS5D01G340100 chr7B 741226991 741227982 991 False 926.0 926 83.781 1539 2526 1 chr7B.!!$F1 987
14 TraesCS5D01G340100 chr7B 741261063 741261807 744 True 658.0 658 82.827 1773 2520 1 chr7B.!!$R1 747
15 TraesCS5D01G340100 chr1D 452266187 452266797 610 True 926.0 926 94.127 1 607 1 chr1D.!!$R1 606
16 TraesCS5D01G340100 chr3D 594498835 594499440 605 True 920.0 920 94.118 1 606 1 chr3D.!!$R2 605
17 TraesCS5D01G340100 chr3D 361385579 361386189 610 True 917.0 917 93.954 1 604 1 chr3D.!!$R1 603
18 TraesCS5D01G340100 chr4D 472211778 472212380 602 True 902.0 902 93.607 1 607 1 chr4D.!!$R2 606
19 TraesCS5D01G340100 chr4D 366315501 366316098 597 True 896.0 896 93.607 1 607 1 chr4D.!!$R1 606
20 TraesCS5D01G340100 chr3A 487452332 487453031 699 False 273.0 316 86.626 2739 3431 2 chr3A.!!$F1 692
21 TraesCS5D01G340100 chr4A 368126183 368126869 686 False 272.0 307 87.023 2750 3431 2 chr4A.!!$F1 681

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
689 698 0.037160 GGAAAAGGGTTCGCCTACCA 59.963 55.0 4.46 0.0 40.09 3.25 F
701 710 0.240145 GCCTACCAAGAAAACGGCAC 59.760 55.0 0.00 0.0 37.48 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1519 0.383231 CATGACCGGACGTACTACCC 59.617 60.0 9.46 0.0 0.00 3.69 R
2623 2783 0.989890 AAATACGCGAAGACACGAGC 59.010 50.0 15.93 0.0 36.63 5.03 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
409 417 6.919662 ACTCGACTTAAATCCGCGAATATAAA 59.080 34.615 8.23 0.00 0.00 1.40
466 474 6.145371 CCAAACTTTGCGTAAATTTGCTACAT 59.855 34.615 18.77 0.00 30.99 2.29
490 499 4.079446 TTTTTCTCTGCGCCTGGG 57.921 55.556 4.18 0.00 0.00 4.45
491 500 1.603455 TTTTTCTCTGCGCCTGGGG 60.603 57.895 4.18 6.36 0.00 4.96
492 501 4.722700 TTTCTCTGCGCCTGGGGC 62.723 66.667 27.02 27.02 46.75 5.80
527 536 2.272471 GCTAGGGGCCAACTCACC 59.728 66.667 4.39 0.00 34.27 4.02
528 537 2.998949 CTAGGGGCCAACTCACCC 59.001 66.667 4.39 0.00 46.24 4.61
531 540 2.998949 GGGGCCAACTCACCCTAG 59.001 66.667 4.39 0.00 46.19 3.02
532 541 2.680370 GGGGCCAACTCACCCTAGG 61.680 68.421 4.39 0.06 46.19 3.02
533 542 2.272471 GGCCAACTCACCCTAGGC 59.728 66.667 2.05 0.00 44.48 3.93
534 543 2.272471 GCCAACTCACCCTAGGCC 59.728 66.667 2.05 0.00 39.42 5.19
535 544 2.998949 CCAACTCACCCTAGGCCC 59.001 66.667 2.05 0.00 0.00 5.80
536 545 1.616628 CCAACTCACCCTAGGCCCT 60.617 63.158 2.05 0.00 0.00 5.19
537 546 1.208165 CCAACTCACCCTAGGCCCTT 61.208 60.000 2.05 0.00 0.00 3.95
538 547 0.698818 CAACTCACCCTAGGCCCTTT 59.301 55.000 2.05 0.00 0.00 3.11
539 548 1.075536 CAACTCACCCTAGGCCCTTTT 59.924 52.381 2.05 0.00 0.00 2.27
540 549 1.456919 ACTCACCCTAGGCCCTTTTT 58.543 50.000 2.05 0.00 0.00 1.94
555 564 3.990466 TTTTTCGCCGGATCACCC 58.010 55.556 5.05 0.00 0.00 4.61
556 565 1.676303 TTTTTCGCCGGATCACCCC 60.676 57.895 5.05 0.00 0.00 4.95
557 566 2.413211 TTTTTCGCCGGATCACCCCA 62.413 55.000 5.05 0.00 0.00 4.96
558 567 2.813226 TTTTCGCCGGATCACCCCAG 62.813 60.000 5.05 0.00 0.00 4.45
559 568 4.770362 TCGCCGGATCACCCCAGA 62.770 66.667 5.05 0.00 0.00 3.86
560 569 4.530857 CGCCGGATCACCCCAGAC 62.531 72.222 5.05 0.00 0.00 3.51
561 570 4.530857 GCCGGATCACCCCAGACG 62.531 72.222 5.05 0.00 0.00 4.18
562 571 3.849951 CCGGATCACCCCAGACGG 61.850 72.222 0.00 0.00 35.01 4.79
563 572 4.530857 CGGATCACCCCAGACGGC 62.531 72.222 0.00 0.00 0.00 5.68
564 573 4.530857 GGATCACCCCAGACGGCG 62.531 72.222 4.80 4.80 0.00 6.46
565 574 3.458163 GATCACCCCAGACGGCGA 61.458 66.667 16.62 0.00 0.00 5.54
566 575 2.764128 ATCACCCCAGACGGCGAT 60.764 61.111 16.62 0.00 0.00 4.58
567 576 2.311688 GATCACCCCAGACGGCGATT 62.312 60.000 16.62 0.00 0.00 3.34
568 577 1.910580 ATCACCCCAGACGGCGATTT 61.911 55.000 16.62 0.00 0.00 2.17
569 578 1.674322 CACCCCAGACGGCGATTTT 60.674 57.895 16.62 0.00 0.00 1.82
570 579 0.391927 CACCCCAGACGGCGATTTTA 60.392 55.000 16.62 0.00 0.00 1.52
571 580 0.107848 ACCCCAGACGGCGATTTTAG 60.108 55.000 16.62 0.00 0.00 1.85
572 581 0.814010 CCCCAGACGGCGATTTTAGG 60.814 60.000 16.62 6.17 0.00 2.69
573 582 1.436983 CCCAGACGGCGATTTTAGGC 61.437 60.000 16.62 0.00 0.00 3.93
579 588 2.516225 GCGATTTTAGGCGCCCCT 60.516 61.111 26.15 8.44 46.93 4.79
580 589 2.834618 GCGATTTTAGGCGCCCCTG 61.835 63.158 26.15 7.46 46.93 4.45
581 590 2.186826 CGATTTTAGGCGCCCCTGG 61.187 63.158 26.15 1.98 42.90 4.45
582 591 1.828224 GATTTTAGGCGCCCCTGGG 60.828 63.158 26.15 5.50 42.90 4.45
601 610 4.473520 CCAACGGCGGGAGATGCT 62.474 66.667 13.24 0.00 0.00 3.79
602 611 2.892425 CAACGGCGGGAGATGCTC 60.892 66.667 13.24 0.00 0.00 4.26
603 612 3.077556 AACGGCGGGAGATGCTCT 61.078 61.111 13.24 0.00 0.00 4.09
604 613 1.756950 AACGGCGGGAGATGCTCTA 60.757 57.895 13.24 0.00 0.00 2.43
605 614 1.327690 AACGGCGGGAGATGCTCTAA 61.328 55.000 13.24 0.00 0.00 2.10
606 615 1.006805 CGGCGGGAGATGCTCTAAG 60.007 63.158 0.00 0.00 0.00 2.18
607 616 1.369321 GGCGGGAGATGCTCTAAGG 59.631 63.158 0.00 0.00 0.00 2.69
608 617 1.369321 GCGGGAGATGCTCTAAGGG 59.631 63.158 0.00 0.00 0.00 3.95
609 618 1.403687 GCGGGAGATGCTCTAAGGGT 61.404 60.000 0.00 0.00 0.00 4.34
610 619 0.390860 CGGGAGATGCTCTAAGGGTG 59.609 60.000 0.00 0.00 0.00 4.61
611 620 1.501582 GGGAGATGCTCTAAGGGTGT 58.498 55.000 0.00 0.00 0.00 4.16
612 621 1.840635 GGGAGATGCTCTAAGGGTGTT 59.159 52.381 0.00 0.00 0.00 3.32
613 622 2.158885 GGGAGATGCTCTAAGGGTGTTC 60.159 54.545 0.00 0.00 0.00 3.18
614 623 2.482142 GGAGATGCTCTAAGGGTGTTCG 60.482 54.545 0.00 0.00 0.00 3.95
615 624 1.134670 AGATGCTCTAAGGGTGTTCGC 60.135 52.381 0.00 0.00 0.00 4.70
616 625 0.905357 ATGCTCTAAGGGTGTTCGCT 59.095 50.000 0.00 0.00 38.50 4.93
617 626 0.037326 TGCTCTAAGGGTGTTCGCTG 60.037 55.000 0.00 0.00 36.95 5.18
618 627 0.741221 GCTCTAAGGGTGTTCGCTGG 60.741 60.000 0.00 0.00 36.95 4.85
619 628 0.108138 CTCTAAGGGTGTTCGCTGGG 60.108 60.000 0.00 0.00 36.95 4.45
620 629 0.543410 TCTAAGGGTGTTCGCTGGGA 60.543 55.000 0.00 0.00 36.95 4.37
621 630 0.541863 CTAAGGGTGTTCGCTGGGAT 59.458 55.000 0.00 0.00 36.95 3.85
622 631 0.988832 TAAGGGTGTTCGCTGGGATT 59.011 50.000 0.00 0.00 36.95 3.01
623 632 0.609131 AAGGGTGTTCGCTGGGATTG 60.609 55.000 0.00 0.00 36.95 2.67
624 633 2.700773 GGGTGTTCGCTGGGATTGC 61.701 63.158 0.00 0.00 0.00 3.56
625 634 1.675641 GGTGTTCGCTGGGATTGCT 60.676 57.895 0.00 0.00 0.00 3.91
626 635 1.244019 GGTGTTCGCTGGGATTGCTT 61.244 55.000 0.00 0.00 0.00 3.91
627 636 1.448985 GTGTTCGCTGGGATTGCTTA 58.551 50.000 0.00 0.00 0.00 3.09
628 637 1.810151 GTGTTCGCTGGGATTGCTTAA 59.190 47.619 0.00 0.00 0.00 1.85
629 638 2.227865 GTGTTCGCTGGGATTGCTTAAA 59.772 45.455 0.00 0.00 0.00 1.52
630 639 2.887783 TGTTCGCTGGGATTGCTTAAAA 59.112 40.909 0.00 0.00 0.00 1.52
631 640 3.319405 TGTTCGCTGGGATTGCTTAAAAA 59.681 39.130 0.00 0.00 0.00 1.94
632 641 3.848272 TCGCTGGGATTGCTTAAAAAG 57.152 42.857 0.00 0.00 0.00 2.27
646 655 2.712057 AAAAAGCTGATGTTCGCTGG 57.288 45.000 0.00 0.00 36.45 4.85
647 656 1.609208 AAAAGCTGATGTTCGCTGGT 58.391 45.000 0.00 0.00 36.45 4.00
648 657 1.609208 AAAGCTGATGTTCGCTGGTT 58.391 45.000 0.00 0.00 36.45 3.67
649 658 2.472695 AAGCTGATGTTCGCTGGTTA 57.527 45.000 0.00 0.00 36.45 2.85
650 659 2.015736 AGCTGATGTTCGCTGGTTAG 57.984 50.000 0.00 0.00 34.69 2.34
651 660 1.276421 AGCTGATGTTCGCTGGTTAGT 59.724 47.619 0.00 0.00 34.69 2.24
652 661 1.394917 GCTGATGTTCGCTGGTTAGTG 59.605 52.381 0.00 0.00 35.74 2.74
653 662 2.002586 CTGATGTTCGCTGGTTAGTGG 58.997 52.381 0.00 0.00 35.14 4.00
654 663 0.727398 GATGTTCGCTGGTTAGTGGC 59.273 55.000 0.00 0.00 35.14 5.01
655 664 0.324943 ATGTTCGCTGGTTAGTGGCT 59.675 50.000 0.00 0.00 35.14 4.75
656 665 0.107831 TGTTCGCTGGTTAGTGGCTT 59.892 50.000 0.00 0.00 35.14 4.35
657 666 1.345089 TGTTCGCTGGTTAGTGGCTTA 59.655 47.619 0.00 0.00 35.14 3.09
658 667 1.730612 GTTCGCTGGTTAGTGGCTTAC 59.269 52.381 0.00 0.00 35.14 2.34
659 668 1.263356 TCGCTGGTTAGTGGCTTACT 58.737 50.000 0.19 0.19 43.56 2.24
660 669 2.449464 TCGCTGGTTAGTGGCTTACTA 58.551 47.619 0.00 0.00 40.89 1.82
661 670 3.028850 TCGCTGGTTAGTGGCTTACTAT 58.971 45.455 2.92 0.00 41.36 2.12
662 671 4.209538 TCGCTGGTTAGTGGCTTACTATA 58.790 43.478 2.92 0.00 41.36 1.31
663 672 4.831155 TCGCTGGTTAGTGGCTTACTATAT 59.169 41.667 2.92 0.00 41.36 0.86
664 673 5.303589 TCGCTGGTTAGTGGCTTACTATATT 59.696 40.000 2.92 0.00 41.36 1.28
665 674 5.989777 CGCTGGTTAGTGGCTTACTATATTT 59.010 40.000 2.92 0.00 41.36 1.40
666 675 6.482308 CGCTGGTTAGTGGCTTACTATATTTT 59.518 38.462 2.92 0.00 41.36 1.82
667 676 7.654520 CGCTGGTTAGTGGCTTACTATATTTTA 59.345 37.037 2.92 0.00 41.36 1.52
668 677 9.333724 GCTGGTTAGTGGCTTACTATATTTTAA 57.666 33.333 2.92 0.00 41.36 1.52
683 692 8.464404 ACTATATTTTAAAGGAAAAGGGTTCGC 58.536 33.333 0.00 0.00 40.34 4.70
684 693 4.325028 TTTTAAAGGAAAAGGGTTCGCC 57.675 40.909 0.00 0.00 31.90 5.54
685 694 2.963599 TAAAGGAAAAGGGTTCGCCT 57.036 45.000 0.00 0.00 37.45 5.52
686 695 2.963599 AAAGGAAAAGGGTTCGCCTA 57.036 45.000 0.00 0.00 37.45 3.93
687 696 2.195741 AAGGAAAAGGGTTCGCCTAC 57.804 50.000 0.00 0.00 37.45 3.18
688 697 0.327259 AGGAAAAGGGTTCGCCTACC 59.673 55.000 0.00 0.00 37.45 3.18
689 698 0.037160 GGAAAAGGGTTCGCCTACCA 59.963 55.000 4.46 0.00 40.09 3.25
690 699 1.546099 GGAAAAGGGTTCGCCTACCAA 60.546 52.381 4.46 0.00 40.09 3.67
691 700 1.810755 GAAAAGGGTTCGCCTACCAAG 59.189 52.381 4.46 0.00 40.09 3.61
692 701 1.061546 AAAGGGTTCGCCTACCAAGA 58.938 50.000 4.46 0.00 40.09 3.02
693 702 1.061546 AAGGGTTCGCCTACCAAGAA 58.938 50.000 4.46 0.00 40.09 2.52
694 703 1.061546 AGGGTTCGCCTACCAAGAAA 58.938 50.000 4.46 0.00 40.09 2.52
695 704 1.422402 AGGGTTCGCCTACCAAGAAAA 59.578 47.619 4.46 0.00 40.09 2.29
696 705 1.538512 GGGTTCGCCTACCAAGAAAAC 59.461 52.381 4.46 0.00 40.09 2.43
697 706 1.196127 GGTTCGCCTACCAAGAAAACG 59.804 52.381 0.00 0.00 38.12 3.60
698 707 1.196127 GTTCGCCTACCAAGAAAACGG 59.804 52.381 0.00 0.00 0.00 4.44
699 708 0.952010 TCGCCTACCAAGAAAACGGC 60.952 55.000 0.00 0.00 0.00 5.68
700 709 1.231958 CGCCTACCAAGAAAACGGCA 61.232 55.000 0.00 0.00 37.39 5.69
701 710 0.240145 GCCTACCAAGAAAACGGCAC 59.760 55.000 0.00 0.00 37.48 5.01
720 729 3.195610 GCACGATCATACTCCCCATATCA 59.804 47.826 0.00 0.00 0.00 2.15
723 732 3.181486 CGATCATACTCCCCATATCACGG 60.181 52.174 0.00 0.00 0.00 4.94
727 736 0.763223 ACTCCCCATATCACGGGTCC 60.763 60.000 0.00 0.00 42.77 4.46
753 762 4.832608 GCCGGACACGTCCCATCC 62.833 72.222 5.05 0.33 46.96 3.51
857 866 2.028930 AGCAGGACTACCGACTTTCTTG 60.029 50.000 0.00 0.00 41.83 3.02
861 870 2.353505 GGACTACCGACTTTCTTGGTCC 60.354 54.545 0.00 0.00 37.83 4.46
887 898 1.068954 GGTGCGAGGAAGCTCTTTTTG 60.069 52.381 0.00 0.00 38.13 2.44
912 923 6.725246 CCAAATATGGTATGTTTTCCGTCTC 58.275 40.000 0.00 0.00 42.18 3.36
917 928 3.071479 GGTATGTTTTCCGTCTCTGCAA 58.929 45.455 0.00 0.00 0.00 4.08
942 953 1.291877 ATTCACTCCACGCTTGCGAC 61.292 55.000 22.03 0.00 0.00 5.19
990 1002 2.247790 TTGCTTCCAAGAAGCGAGC 58.752 52.632 20.86 2.47 45.80 5.03
991 1003 0.250467 TTGCTTCCAAGAAGCGAGCT 60.250 50.000 20.86 0.00 45.80 4.09
1461 1481 2.106938 CTCCCGCGCATAGCTGAA 59.893 61.111 8.75 0.00 45.59 3.02
1497 1519 2.202919 TGCCATGGCGATCGAGTG 60.203 61.111 30.87 13.10 45.51 3.51
1517 1539 0.248784 GGTAGTACGTCCGGTCATGC 60.249 60.000 0.00 0.00 0.00 4.06
2621 2781 8.876275 CATAAAACCATGGAATAATTCACTGG 57.124 34.615 21.47 0.00 38.20 4.00
2623 2783 2.951642 ACCATGGAATAATTCACTGGCG 59.048 45.455 21.47 0.00 36.67 5.69
2635 2795 3.175240 CTGGCGCTCGTGTCTTCG 61.175 66.667 7.64 0.00 0.00 3.79
2903 3074 1.818221 GCTACCGTATTTCGCTGGCG 61.818 60.000 8.80 8.80 41.35 5.69
2972 3143 8.296713 TGAAAATCAGGTTTTTATGACTAGTGC 58.703 33.333 0.00 0.00 40.04 4.40
2997 3232 3.189910 CCCGCTGTCAGTACGCTAATATA 59.810 47.826 0.93 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
409 417 2.484594 CCAAATTTCGGCAAACTTGGGT 60.485 45.455 11.98 0.00 42.71 4.51
510 519 2.272471 GGTGAGTTGGCCCCTAGC 59.728 66.667 0.00 0.00 42.60 3.42
511 520 2.998949 GGGTGAGTTGGCCCCTAG 59.001 66.667 0.00 0.00 38.99 3.02
514 523 2.680370 CCTAGGGTGAGTTGGCCCC 61.680 68.421 0.00 0.00 45.95 5.80
515 524 2.998949 CCTAGGGTGAGTTGGCCC 59.001 66.667 0.00 0.00 45.16 5.80
516 525 2.272471 GCCTAGGGTGAGTTGGCC 59.728 66.667 11.72 0.00 37.81 5.36
517 526 2.272471 GGCCTAGGGTGAGTTGGC 59.728 66.667 11.72 0.00 42.56 4.52
518 527 1.208165 AAGGGCCTAGGGTGAGTTGG 61.208 60.000 6.41 0.00 0.00 3.77
519 528 0.698818 AAAGGGCCTAGGGTGAGTTG 59.301 55.000 6.41 0.00 0.00 3.16
520 529 1.456919 AAAAGGGCCTAGGGTGAGTT 58.543 50.000 6.41 0.00 0.00 3.01
521 530 1.456919 AAAAAGGGCCTAGGGTGAGT 58.543 50.000 6.41 0.00 0.00 3.41
538 547 1.676303 GGGGTGATCCGGCGAAAAA 60.676 57.895 9.30 0.00 36.01 1.94
539 548 2.045731 GGGGTGATCCGGCGAAAA 60.046 61.111 9.30 0.00 36.01 2.29
540 549 3.323286 TGGGGTGATCCGGCGAAA 61.323 61.111 9.30 0.00 36.01 3.46
541 550 3.781307 CTGGGGTGATCCGGCGAA 61.781 66.667 9.30 0.00 36.01 4.70
542 551 4.770362 TCTGGGGTGATCCGGCGA 62.770 66.667 9.30 0.00 36.01 5.54
543 552 4.530857 GTCTGGGGTGATCCGGCG 62.531 72.222 0.00 0.00 36.01 6.46
544 553 4.530857 CGTCTGGGGTGATCCGGC 62.531 72.222 0.00 0.00 36.01 6.13
545 554 3.849951 CCGTCTGGGGTGATCCGG 61.850 72.222 0.00 0.00 36.01 5.14
546 555 4.530857 GCCGTCTGGGGTGATCCG 62.531 72.222 0.00 0.00 36.01 4.18
547 556 4.530857 CGCCGTCTGGGGTGATCC 62.531 72.222 0.00 0.00 43.03 3.36
554 563 1.436983 GCCTAAAATCGCCGTCTGGG 61.437 60.000 0.00 0.00 39.58 4.45
555 564 1.762222 CGCCTAAAATCGCCGTCTGG 61.762 60.000 0.00 0.00 38.77 3.86
556 565 1.636340 CGCCTAAAATCGCCGTCTG 59.364 57.895 0.00 0.00 0.00 3.51
557 566 2.171725 GCGCCTAAAATCGCCGTCT 61.172 57.895 0.00 0.00 45.01 4.18
558 567 2.323447 GCGCCTAAAATCGCCGTC 59.677 61.111 0.00 0.00 45.01 4.79
563 572 2.186826 CCAGGGGCGCCTAAAATCG 61.187 63.158 28.56 8.84 0.00 3.34
564 573 1.828224 CCCAGGGGCGCCTAAAATC 60.828 63.158 28.56 8.16 0.00 2.17
565 574 2.278738 CCCAGGGGCGCCTAAAAT 59.721 61.111 28.56 4.89 0.00 1.82
566 575 4.055227 CCCCAGGGGCGCCTAAAA 62.055 66.667 28.56 0.00 35.35 1.52
584 593 4.473520 AGCATCTCCCGCCGTTGG 62.474 66.667 0.00 0.00 0.00 3.77
585 594 2.892425 GAGCATCTCCCGCCGTTG 60.892 66.667 0.00 0.00 0.00 4.10
596 605 1.134670 AGCGAACACCCTTAGAGCATC 60.135 52.381 0.00 0.00 0.00 3.91
597 606 0.905357 AGCGAACACCCTTAGAGCAT 59.095 50.000 0.00 0.00 0.00 3.79
598 607 0.037326 CAGCGAACACCCTTAGAGCA 60.037 55.000 0.00 0.00 0.00 4.26
599 608 0.741221 CCAGCGAACACCCTTAGAGC 60.741 60.000 0.00 0.00 0.00 4.09
600 609 0.108138 CCCAGCGAACACCCTTAGAG 60.108 60.000 0.00 0.00 0.00 2.43
601 610 0.543410 TCCCAGCGAACACCCTTAGA 60.543 55.000 0.00 0.00 0.00 2.10
602 611 0.541863 ATCCCAGCGAACACCCTTAG 59.458 55.000 0.00 0.00 0.00 2.18
603 612 0.988832 AATCCCAGCGAACACCCTTA 59.011 50.000 0.00 0.00 0.00 2.69
604 613 0.609131 CAATCCCAGCGAACACCCTT 60.609 55.000 0.00 0.00 0.00 3.95
605 614 1.002134 CAATCCCAGCGAACACCCT 60.002 57.895 0.00 0.00 0.00 4.34
606 615 2.700773 GCAATCCCAGCGAACACCC 61.701 63.158 0.00 0.00 0.00 4.61
607 616 1.244019 AAGCAATCCCAGCGAACACC 61.244 55.000 0.00 0.00 37.01 4.16
608 617 1.448985 TAAGCAATCCCAGCGAACAC 58.551 50.000 0.00 0.00 37.01 3.32
609 618 2.192664 TTAAGCAATCCCAGCGAACA 57.807 45.000 0.00 0.00 37.01 3.18
610 619 3.569250 TTTTAAGCAATCCCAGCGAAC 57.431 42.857 0.00 0.00 37.01 3.95
611 620 4.173036 CTTTTTAAGCAATCCCAGCGAA 57.827 40.909 0.00 0.00 37.01 4.70
612 621 3.848272 CTTTTTAAGCAATCCCAGCGA 57.152 42.857 0.00 0.00 37.01 4.93
624 633 4.161333 CCAGCGAACATCAGCTTTTTAAG 58.839 43.478 0.00 0.00 42.52 1.85
625 634 3.568007 ACCAGCGAACATCAGCTTTTTAA 59.432 39.130 0.00 0.00 42.52 1.52
626 635 3.146066 ACCAGCGAACATCAGCTTTTTA 58.854 40.909 0.00 0.00 42.52 1.52
627 636 1.956477 ACCAGCGAACATCAGCTTTTT 59.044 42.857 0.00 0.00 42.52 1.94
628 637 1.609208 ACCAGCGAACATCAGCTTTT 58.391 45.000 0.00 0.00 42.52 2.27
629 638 1.609208 AACCAGCGAACATCAGCTTT 58.391 45.000 0.00 0.00 42.52 3.51
630 639 2.289694 ACTAACCAGCGAACATCAGCTT 60.290 45.455 0.00 0.00 42.52 3.74
631 640 1.276421 ACTAACCAGCGAACATCAGCT 59.724 47.619 0.00 0.00 45.74 4.24
632 641 1.394917 CACTAACCAGCGAACATCAGC 59.605 52.381 0.00 0.00 0.00 4.26
633 642 2.002586 CCACTAACCAGCGAACATCAG 58.997 52.381 0.00 0.00 0.00 2.90
634 643 1.943968 GCCACTAACCAGCGAACATCA 60.944 52.381 0.00 0.00 0.00 3.07
635 644 0.727398 GCCACTAACCAGCGAACATC 59.273 55.000 0.00 0.00 0.00 3.06
636 645 0.324943 AGCCACTAACCAGCGAACAT 59.675 50.000 0.00 0.00 0.00 2.71
637 646 0.107831 AAGCCACTAACCAGCGAACA 59.892 50.000 0.00 0.00 0.00 3.18
638 647 1.730612 GTAAGCCACTAACCAGCGAAC 59.269 52.381 0.00 0.00 0.00 3.95
639 648 1.621814 AGTAAGCCACTAACCAGCGAA 59.378 47.619 0.00 0.00 34.98 4.70
640 649 1.263356 AGTAAGCCACTAACCAGCGA 58.737 50.000 0.00 0.00 34.98 4.93
641 650 2.953466 TAGTAAGCCACTAACCAGCG 57.047 50.000 0.00 0.00 36.78 5.18
642 651 7.803279 AAAATATAGTAAGCCACTAACCAGC 57.197 36.000 0.29 0.00 43.00 4.85
657 666 8.464404 GCGAACCCTTTTCCTTTAAAATATAGT 58.536 33.333 0.00 0.00 36.49 2.12
658 667 7.919091 GGCGAACCCTTTTCCTTTAAAATATAG 59.081 37.037 0.00 0.00 36.49 1.31
659 668 7.616542 AGGCGAACCCTTTTCCTTTAAAATATA 59.383 33.333 0.00 0.00 43.06 0.86
660 669 6.439375 AGGCGAACCCTTTTCCTTTAAAATAT 59.561 34.615 0.00 0.00 43.06 1.28
661 670 5.776208 AGGCGAACCCTTTTCCTTTAAAATA 59.224 36.000 0.00 0.00 43.06 1.40
662 671 4.591498 AGGCGAACCCTTTTCCTTTAAAAT 59.409 37.500 0.00 0.00 43.06 1.82
663 672 3.962063 AGGCGAACCCTTTTCCTTTAAAA 59.038 39.130 0.00 0.00 43.06 1.52
664 673 3.568443 AGGCGAACCCTTTTCCTTTAAA 58.432 40.909 0.00 0.00 43.06 1.52
665 674 3.232720 AGGCGAACCCTTTTCCTTTAA 57.767 42.857 0.00 0.00 43.06 1.52
666 675 2.963599 AGGCGAACCCTTTTCCTTTA 57.036 45.000 0.00 0.00 43.06 1.85
667 676 2.511659 GTAGGCGAACCCTTTTCCTTT 58.488 47.619 0.00 0.00 43.06 3.11
668 677 1.271762 GGTAGGCGAACCCTTTTCCTT 60.272 52.381 0.98 0.00 43.06 3.36
669 678 0.327259 GGTAGGCGAACCCTTTTCCT 59.673 55.000 0.98 0.00 43.06 3.36
670 679 0.037160 TGGTAGGCGAACCCTTTTCC 59.963 55.000 9.22 0.00 43.06 3.13
671 680 1.810755 CTTGGTAGGCGAACCCTTTTC 59.189 52.381 9.22 0.00 43.06 2.29
672 681 1.422402 TCTTGGTAGGCGAACCCTTTT 59.578 47.619 9.22 0.00 43.06 2.27
673 682 1.061546 TCTTGGTAGGCGAACCCTTT 58.938 50.000 9.22 0.00 43.06 3.11
674 683 1.061546 TTCTTGGTAGGCGAACCCTT 58.938 50.000 9.22 0.00 43.06 3.95
676 685 1.538512 GTTTTCTTGGTAGGCGAACCC 59.461 52.381 9.22 0.00 38.90 4.11
677 686 1.196127 CGTTTTCTTGGTAGGCGAACC 59.804 52.381 5.24 5.24 40.19 3.62
678 687 1.196127 CCGTTTTCTTGGTAGGCGAAC 59.804 52.381 0.00 0.00 0.00 3.95
679 688 1.515081 CCGTTTTCTTGGTAGGCGAA 58.485 50.000 0.00 0.00 0.00 4.70
680 689 0.952010 GCCGTTTTCTTGGTAGGCGA 60.952 55.000 0.00 0.00 34.94 5.54
681 690 1.231958 TGCCGTTTTCTTGGTAGGCG 61.232 55.000 0.00 0.00 46.85 5.52
682 691 0.240145 GTGCCGTTTTCTTGGTAGGC 59.760 55.000 0.00 0.00 44.38 3.93
683 692 0.515564 CGTGCCGTTTTCTTGGTAGG 59.484 55.000 0.00 0.00 0.00 3.18
684 693 1.504359 TCGTGCCGTTTTCTTGGTAG 58.496 50.000 0.00 0.00 0.00 3.18
685 694 2.070783 GATCGTGCCGTTTTCTTGGTA 58.929 47.619 0.00 0.00 0.00 3.25
686 695 0.872388 GATCGTGCCGTTTTCTTGGT 59.128 50.000 0.00 0.00 0.00 3.67
687 696 0.871722 TGATCGTGCCGTTTTCTTGG 59.128 50.000 0.00 0.00 0.00 3.61
688 697 2.900122 ATGATCGTGCCGTTTTCTTG 57.100 45.000 0.00 0.00 0.00 3.02
689 698 3.596214 AGTATGATCGTGCCGTTTTCTT 58.404 40.909 0.00 0.00 0.00 2.52
690 699 3.187700 GAGTATGATCGTGCCGTTTTCT 58.812 45.455 0.00 0.00 0.00 2.52
691 700 2.284417 GGAGTATGATCGTGCCGTTTTC 59.716 50.000 0.00 0.00 0.00 2.29
692 701 2.277084 GGAGTATGATCGTGCCGTTTT 58.723 47.619 0.00 0.00 0.00 2.43
693 702 1.472728 GGGAGTATGATCGTGCCGTTT 60.473 52.381 0.00 0.00 0.00 3.60
694 703 0.104304 GGGAGTATGATCGTGCCGTT 59.896 55.000 0.00 0.00 0.00 4.44
695 704 1.740285 GGGAGTATGATCGTGCCGT 59.260 57.895 0.00 0.00 0.00 5.68
696 705 1.006102 GGGGAGTATGATCGTGCCG 60.006 63.158 0.00 0.00 0.00 5.69
697 706 0.687354 ATGGGGAGTATGATCGTGCC 59.313 55.000 0.00 0.00 0.00 5.01
698 707 3.195610 TGATATGGGGAGTATGATCGTGC 59.804 47.826 0.00 0.00 0.00 5.34
699 708 4.675408 CGTGATATGGGGAGTATGATCGTG 60.675 50.000 0.00 0.00 0.00 4.35
700 709 3.444034 CGTGATATGGGGAGTATGATCGT 59.556 47.826 0.00 0.00 0.00 3.73
701 710 3.181486 CCGTGATATGGGGAGTATGATCG 60.181 52.174 0.00 0.00 0.00 3.69
702 711 4.392921 CCGTGATATGGGGAGTATGATC 57.607 50.000 0.00 0.00 0.00 2.92
713 722 2.095978 GACCGGGACCCGTGATATGG 62.096 65.000 30.60 16.08 46.80 2.74
753 762 1.729586 TAGGAATGGAATCGGGGAGG 58.270 55.000 0.00 0.00 0.00 4.30
796 805 3.256136 AGACGAGACGGAGAAGAAATGTT 59.744 43.478 0.00 0.00 0.00 2.71
861 870 3.114616 CTTCCTCGCACCTGCACG 61.115 66.667 0.00 0.00 42.21 5.34
912 923 1.396653 GGAGTGAATCCCCATTGCAG 58.603 55.000 0.00 0.00 43.01 4.41
942 953 2.112522 CGCTACAACTGAGCTACATCG 58.887 52.381 0.00 0.00 37.81 3.84
990 1002 2.541547 TTTCCGCCATGGCCTCTGAG 62.542 60.000 30.79 15.29 37.80 3.35
991 1003 2.601702 TTTCCGCCATGGCCTCTGA 61.602 57.895 30.79 18.48 37.80 3.27
1146 1158 3.228017 TTCCTCGGCGTGGACACA 61.228 61.111 28.35 13.07 32.65 3.72
1451 1471 1.131883 CCTTGTGCTGTTCAGCTATGC 59.868 52.381 22.44 12.15 35.49 3.14
1461 1481 1.000163 CAGAGACGTACCTTGTGCTGT 60.000 52.381 0.00 0.00 0.00 4.40
1497 1519 0.383231 CATGACCGGACGTACTACCC 59.617 60.000 9.46 0.00 0.00 3.69
1517 1539 2.807895 CGTTGGAGCCACGTACGG 60.808 66.667 21.06 8.46 0.00 4.02
1608 1691 3.119096 GCCTCGTTCACCGCCTTC 61.119 66.667 0.00 0.00 36.19 3.46
2132 2263 3.692406 GCTCCTGGAACCCGTCGT 61.692 66.667 0.00 0.00 0.00 4.34
2589 2748 3.168035 TCCATGGTTTTATGGCACTGT 57.832 42.857 12.58 0.00 45.83 3.55
2614 2773 2.355837 GACACGAGCGCCAGTGAA 60.356 61.111 30.96 0.00 40.56 3.18
2623 2783 0.989890 AAATACGCGAAGACACGAGC 59.010 50.000 15.93 0.00 36.63 5.03
2635 2795 3.947626 ACGATATTGGTTGCAAATACGC 58.052 40.909 0.00 0.00 0.00 4.42
2637 2797 7.892445 CAACTACGATATTGGTTGCAAATAC 57.108 36.000 0.00 0.00 33.86 1.89
2903 3074 5.128827 TCTCTACAAATGGACCCTATGTCAC 59.871 44.000 0.00 0.00 46.38 3.67
2955 3126 3.373130 GGGACGCACTAGTCATAAAAACC 59.627 47.826 0.00 0.00 42.62 3.27
2997 3232 0.035056 GGTGGAGTGGCTAGCACAAT 60.035 55.000 18.24 11.35 0.00 2.71


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

AutoCloner maintained by Alex Coulton.