Multiple sequence alignment - TraesCS6D01G089700

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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 TraesCS6D01G089700 chr6D 100.000 2491 0 0 1 2491 55880016 55877526 0.000000e+00 4601
1 TraesCS6D01G089700 chr6D 98.599 571 7 1 1921 2490 55874751 55875321 0.000000e+00 1009
2 TraesCS6D01G089700 chr6D 89.109 404 36 6 3 400 38873913 38874314 1.720000e-136 496
3 TraesCS6D01G089700 chr3D 98.985 1281 13 0 575 1855 599328961 599330241 0.000000e+00 2294
4 TraesCS6D01G089700 chr3D 98.985 788 6 1 1705 2490 406139369 406140156 0.000000e+00 1410
5 TraesCS6D01G089700 chr3D 98.756 643 6 1 1850 2490 599330351 599330993 0.000000e+00 1142
6 TraesCS6D01G089700 chr3D 98.885 538 6 0 1217 1754 406138833 406139370 0.000000e+00 961
7 TraesCS6D01G089700 chr3D 84.013 957 130 14 575 1527 105899732 105898795 0.000000e+00 898
8 TraesCS6D01G089700 chr7D 98.898 1180 12 1 575 1754 549946252 549947430 0.000000e+00 2106
9 TraesCS6D01G089700 chr7D 99.111 787 6 1 1705 2490 549947429 549948215 0.000000e+00 1413
10 TraesCS6D01G089700 chr7B 94.062 640 34 3 1852 2490 40012871 40013507 0.000000e+00 968
11 TraesCS6D01G089700 chr7B 89.788 754 39 16 1032 1750 40011791 40012541 0.000000e+00 931
12 TraesCS6D01G089700 chr7B 94.156 462 25 2 574 1034 39987225 39987685 0.000000e+00 702
13 TraesCS6D01G089700 chr7B 84.834 211 10 10 1666 1855 40012541 40012750 2.530000e-45 193
14 TraesCS6D01G089700 chr3A 84.864 958 130 11 575 1527 23147973 23148920 0.000000e+00 952
15 TraesCS6D01G089700 chr3A 84.368 435 53 4 2056 2490 23149688 23150107 1.780000e-111 412
16 TraesCS6D01G089700 chr2B 84.807 961 130 10 572 1527 717883112 717884061 0.000000e+00 952
17 TraesCS6D01G089700 chr1B 84.134 958 136 12 575 1527 448411159 448412105 0.000000e+00 913
18 TraesCS6D01G089700 chr1D 85.871 821 89 15 575 1372 474361499 474362315 0.000000e+00 848
19 TraesCS6D01G089700 chr1D 88.525 610 60 6 1886 2490 474362993 474363597 0.000000e+00 730
20 TraesCS6D01G089700 chr1D 81.988 322 31 16 1413 1732 474362320 474362616 5.320000e-62 248
21 TraesCS6D01G089700 chr4D 85.437 824 89 18 574 1372 81317970 81318787 0.000000e+00 828
22 TraesCS6D01G089700 chr4D 87.993 608 66 4 1886 2490 81319406 81320009 0.000000e+00 712
23 TraesCS6D01G089700 chr4D 80.435 322 36 15 1413 1732 81318792 81319088 1.160000e-53 220
24 TraesCS6D01G089700 chr4A 89.907 535 44 7 4 531 501478863 501478332 0.000000e+00 680
25 TraesCS6D01G089700 chr6A 89.239 539 41 9 1 531 76818670 76819199 0.000000e+00 658
26 TraesCS6D01G089700 chr3B 89.239 539 41 9 1 531 486823764 486824293 0.000000e+00 658
27 TraesCS6D01G089700 chr6B 89.219 538 41 9 1 531 207921700 207922227 0.000000e+00 656
28 TraesCS6D01G089700 chr2D 89.054 539 44 7 1 531 578885357 578884826 0.000000e+00 654
29 TraesCS6D01G089700 chr4B 89.033 538 40 11 1 531 258744577 258744052 0.000000e+00 649
30 TraesCS6D01G089700 chr7A 88.868 539 43 9 1 531 333964316 333964845 0.000000e+00 647
31 TraesCS6D01G089700 chrUn 86.034 537 42 16 1 531 1899874 1899365 1.680000e-151 545
32 TraesCS6D01G089700 chr5A 89.245 437 46 1 2055 2490 650780224 650779788 1.680000e-151 545


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 TraesCS6D01G089700 chr6D 55877526 55880016 2490 True 4601.000000 4601 100.000000 1 2491 1 chr6D.!!$R1 2490
1 TraesCS6D01G089700 chr6D 55874751 55875321 570 False 1009.000000 1009 98.599000 1921 2490 1 chr6D.!!$F2 569
2 TraesCS6D01G089700 chr3D 599328961 599330993 2032 False 1718.000000 2294 98.870500 575 2490 2 chr3D.!!$F2 1915
3 TraesCS6D01G089700 chr3D 406138833 406140156 1323 False 1185.500000 1410 98.935000 1217 2490 2 chr3D.!!$F1 1273
4 TraesCS6D01G089700 chr3D 105898795 105899732 937 True 898.000000 898 84.013000 575 1527 1 chr3D.!!$R1 952
5 TraesCS6D01G089700 chr7D 549946252 549948215 1963 False 1759.500000 2106 99.004500 575 2490 2 chr7D.!!$F1 1915
6 TraesCS6D01G089700 chr7B 40011791 40013507 1716 False 697.333333 968 89.561333 1032 2490 3 chr7B.!!$F2 1458
7 TraesCS6D01G089700 chr3A 23147973 23150107 2134 False 682.000000 952 84.616000 575 2490 2 chr3A.!!$F1 1915
8 TraesCS6D01G089700 chr2B 717883112 717884061 949 False 952.000000 952 84.807000 572 1527 1 chr2B.!!$F1 955
9 TraesCS6D01G089700 chr1B 448411159 448412105 946 False 913.000000 913 84.134000 575 1527 1 chr1B.!!$F1 952
10 TraesCS6D01G089700 chr1D 474361499 474363597 2098 False 608.666667 848 85.461333 575 2490 3 chr1D.!!$F1 1915
11 TraesCS6D01G089700 chr4D 81317970 81320009 2039 False 586.666667 828 84.621667 574 2490 3 chr4D.!!$F1 1916
12 TraesCS6D01G089700 chr4A 501478332 501478863 531 True 680.000000 680 89.907000 4 531 1 chr4A.!!$R1 527
13 TraesCS6D01G089700 chr6A 76818670 76819199 529 False 658.000000 658 89.239000 1 531 1 chr6A.!!$F1 530
14 TraesCS6D01G089700 chr3B 486823764 486824293 529 False 658.000000 658 89.239000 1 531 1 chr3B.!!$F1 530
15 TraesCS6D01G089700 chr6B 207921700 207922227 527 False 656.000000 656 89.219000 1 531 1 chr6B.!!$F1 530
16 TraesCS6D01G089700 chr2D 578884826 578885357 531 True 654.000000 654 89.054000 1 531 1 chr2D.!!$R1 530
17 TraesCS6D01G089700 chr4B 258744052 258744577 525 True 649.000000 649 89.033000 1 531 1 chr4B.!!$R1 530
18 TraesCS6D01G089700 chr7A 333964316 333964845 529 False 647.000000 647 88.868000 1 531 1 chr7A.!!$F1 530
19 TraesCS6D01G089700 chrUn 1899365 1899874 509 True 545.000000 545 86.034000 1 531 1 chrUn.!!$R1 530

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
568 587 0.039708 GCAGCAGCAGAAAAGACCAC 60.04 55.0 0.0 0.0 41.58 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2847 2.158623 TCAGCACCAACTGGAAATGAGT 60.159 45.455 1.86 0.0 38.26 3.41 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
93 97 5.935789 TGTGTTTGTAGGTAAGTTATCAGGC 59.064 40.000 0.00 0.00 0.00 4.85
97 101 1.875488 AGGTAAGTTATCAGGCCCGT 58.125 50.000 0.00 0.00 0.00 5.28
137 141 8.431593 CCATGTTGTTTACACAAAATTTATCGG 58.568 33.333 0.00 0.00 44.72 4.18
203 208 4.637387 TTCCGGGTCAAAATTACTACCA 57.363 40.909 0.00 0.00 33.46 3.25
234 239 5.756195 TTGAAGTTGTCTGGATCAAAGTG 57.244 39.130 0.00 0.00 0.00 3.16
235 240 5.034852 TGAAGTTGTCTGGATCAAAGTGA 57.965 39.130 0.00 0.00 0.00 3.41
236 241 5.436175 TGAAGTTGTCTGGATCAAAGTGAA 58.564 37.500 0.00 0.00 0.00 3.18
293 298 8.037382 AGAGATGTGTATCTGACAAAAACATG 57.963 34.615 0.00 0.00 43.63 3.21
350 359 7.718753 ACCACAAAAATGGAAGAAAATGCATAA 59.281 29.630 0.00 0.00 43.02 1.90
376 385 1.065701 AGTAGAACGCATCGGCTACTG 59.934 52.381 16.98 0.00 42.64 2.74
391 400 3.209410 GCTACTGGCATGAAATAGCAGT 58.791 45.455 0.00 0.00 38.49 4.40
475 493 5.626116 GCCTAACCTAGCTAGTAAACAGCAA 60.626 44.000 19.31 0.00 41.66 3.91
479 497 3.619038 CCTAGCTAGTAAACAGCAACAGC 59.381 47.826 19.31 0.00 41.66 4.40
480 498 3.126001 AGCTAGTAAACAGCAACAGCA 57.874 42.857 0.00 0.00 41.66 4.41
492 510 0.726827 CAACAGCACGCGTATGGAAT 59.273 50.000 22.84 9.73 0.00 3.01
514 532 3.157087 AGTGGCAGGAACAACAAATAGG 58.843 45.455 0.00 0.00 0.00 2.57
519 537 3.119708 GCAGGAACAACAAATAGGAGCAG 60.120 47.826 0.00 0.00 0.00 4.24
522 541 2.584835 ACAACAAATAGGAGCAGGCA 57.415 45.000 0.00 0.00 0.00 4.75
549 568 3.620428 CACGCGCGTATGGAGCAG 61.620 66.667 37.24 17.08 42.14 4.24
552 571 3.634072 GCGCGTATGGAGCAGCAG 61.634 66.667 8.43 0.00 41.59 4.24
553 572 3.634072 CGCGTATGGAGCAGCAGC 61.634 66.667 0.00 0.00 42.56 5.25
554 573 2.512286 GCGTATGGAGCAGCAGCA 60.512 61.111 3.17 0.00 45.49 4.41
555 574 2.532256 GCGTATGGAGCAGCAGCAG 61.532 63.158 3.17 0.00 45.49 4.24
556 575 2.532256 CGTATGGAGCAGCAGCAGC 61.532 63.158 3.17 0.46 45.49 5.25
557 576 1.450848 GTATGGAGCAGCAGCAGCA 60.451 57.895 12.92 0.00 45.49 4.41
558 577 1.153229 TATGGAGCAGCAGCAGCAG 60.153 57.895 12.92 0.00 45.49 4.24
559 578 1.619807 TATGGAGCAGCAGCAGCAGA 61.620 55.000 12.92 0.00 45.49 4.26
560 579 2.359602 GGAGCAGCAGCAGCAGAA 60.360 61.111 12.92 0.00 45.49 3.02
561 580 1.970114 GGAGCAGCAGCAGCAGAAA 60.970 57.895 12.92 0.00 45.49 2.52
562 581 1.521450 GGAGCAGCAGCAGCAGAAAA 61.521 55.000 12.92 0.00 45.49 2.29
563 582 0.109689 GAGCAGCAGCAGCAGAAAAG 60.110 55.000 12.92 0.00 45.49 2.27
564 583 0.536687 AGCAGCAGCAGCAGAAAAGA 60.537 50.000 12.92 0.00 45.49 2.52
565 584 0.386985 GCAGCAGCAGCAGAAAAGAC 60.387 55.000 4.63 0.00 45.49 3.01
566 585 0.240411 CAGCAGCAGCAGAAAAGACC 59.760 55.000 3.17 0.00 45.49 3.85
567 586 0.179009 AGCAGCAGCAGAAAAGACCA 60.179 50.000 3.17 0.00 45.49 4.02
568 587 0.039708 GCAGCAGCAGAAAAGACCAC 60.040 55.000 0.00 0.00 41.58 4.16
569 588 1.311859 CAGCAGCAGAAAAGACCACA 58.688 50.000 0.00 0.00 0.00 4.17
570 589 1.002033 CAGCAGCAGAAAAGACCACAC 60.002 52.381 0.00 0.00 0.00 3.82
1355 1403 5.126067 GGTGCATTCTGTATGGAAGTACAT 58.874 41.667 0.00 0.00 36.25 2.29
2016 2716 8.547967 AACAACCACATTTCAGTAGTACATAG 57.452 34.615 2.52 0.00 0.00 2.23
2098 2846 3.031736 GCAGATGTACTTCCTCCAGGTA 58.968 50.000 5.19 0.00 36.34 3.08
2099 2847 3.451178 GCAGATGTACTTCCTCCAGGTAA 59.549 47.826 5.19 0.00 36.34 2.85
2490 3242 7.614974 TGATCCACAAGTGATTTGAATTCCATA 59.385 33.333 2.27 0.00 39.21 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 97 2.438411 TGGTATTTTAAGCACCACGGG 58.562 47.619 1.85 0.00 37.42 5.28
97 101 6.412362 AACAACATGGTATTTTAAGCACCA 57.588 33.333 0.00 7.19 45.96 4.17
203 208 6.065976 TCCAGACAACTTCAATACCATCAT 57.934 37.500 0.00 0.00 0.00 2.45
241 246 4.627467 GCAGTAAACTGTCTGTCGATGATT 59.373 41.667 11.54 0.00 45.45 2.57
245 250 2.228103 TCGCAGTAAACTGTCTGTCGAT 59.772 45.455 11.54 0.00 45.45 3.59
250 255 3.189495 TCTCTCTCGCAGTAAACTGTCTG 59.811 47.826 11.54 3.06 45.45 3.51
334 341 7.466746 ACTAGCTTTTATGCATTTTCTTCCA 57.533 32.000 3.54 0.00 34.99 3.53
335 342 8.893727 TCTACTAGCTTTTATGCATTTTCTTCC 58.106 33.333 3.54 0.00 34.99 3.46
339 346 7.164335 GCGTTCTACTAGCTTTTATGCATTTTC 59.836 37.037 3.54 0.00 34.99 2.29
343 352 5.116180 TGCGTTCTACTAGCTTTTATGCAT 58.884 37.500 3.79 3.79 34.99 3.96
350 359 2.810650 CCGATGCGTTCTACTAGCTTT 58.189 47.619 0.00 0.00 0.00 3.51
363 372 2.280389 ATGCCAGTAGCCGATGCG 60.280 61.111 0.00 0.00 44.33 4.73
376 385 3.209410 AGTGCTACTGCTATTTCATGCC 58.791 45.455 0.00 0.00 40.48 4.40
475 493 1.136305 ACTATTCCATACGCGTGCTGT 59.864 47.619 24.59 6.27 0.00 4.40
479 497 0.859232 GCCACTATTCCATACGCGTG 59.141 55.000 24.59 5.75 0.00 5.34
480 498 0.462375 TGCCACTATTCCATACGCGT 59.538 50.000 19.17 19.17 0.00 6.01
492 510 4.042311 TCCTATTTGTTGTTCCTGCCACTA 59.958 41.667 0.00 0.00 0.00 2.74
514 532 2.827642 GGCTCCATGTGCCTGCTC 60.828 66.667 16.78 0.00 46.38 4.26
532 551 3.620428 CTGCTCCATACGCGCGTG 61.620 66.667 42.78 27.91 0.00 5.34
535 554 3.634072 CTGCTGCTCCATACGCGC 61.634 66.667 5.73 0.00 0.00 6.86
536 555 3.634072 GCTGCTGCTCCATACGCG 61.634 66.667 3.53 3.53 36.03 6.01
537 556 2.512286 TGCTGCTGCTCCATACGC 60.512 61.111 17.00 0.00 40.48 4.42
538 557 2.532256 GCTGCTGCTGCTCCATACG 61.532 63.158 22.10 0.00 40.48 3.06
539 558 1.437772 CTGCTGCTGCTGCTCCATAC 61.438 60.000 27.67 2.64 40.48 2.39
540 559 1.153229 CTGCTGCTGCTGCTCCATA 60.153 57.895 27.67 10.07 40.48 2.74
541 560 2.438614 CTGCTGCTGCTGCTCCAT 60.439 61.111 27.67 0.00 40.48 3.41
542 561 2.685804 TTTCTGCTGCTGCTGCTCCA 62.686 55.000 27.67 11.88 40.48 3.86
543 562 1.521450 TTTTCTGCTGCTGCTGCTCC 61.521 55.000 27.67 7.96 40.48 4.70
544 563 0.109689 CTTTTCTGCTGCTGCTGCTC 60.110 55.000 27.67 8.99 40.48 4.26
545 564 0.536687 TCTTTTCTGCTGCTGCTGCT 60.537 50.000 27.67 0.00 40.48 4.24
546 565 0.386985 GTCTTTTCTGCTGCTGCTGC 60.387 55.000 22.51 22.51 40.48 5.25
547 566 0.240411 GGTCTTTTCTGCTGCTGCTG 59.760 55.000 17.00 15.94 40.48 4.41
548 567 0.179009 TGGTCTTTTCTGCTGCTGCT 60.179 50.000 17.00 0.00 40.48 4.24
549 568 0.039708 GTGGTCTTTTCTGCTGCTGC 60.040 55.000 8.89 8.89 40.20 5.25
550 569 1.002033 GTGTGGTCTTTTCTGCTGCTG 60.002 52.381 0.00 0.00 0.00 4.41
551 570 1.133976 AGTGTGGTCTTTTCTGCTGCT 60.134 47.619 0.00 0.00 0.00 4.24
552 571 1.002033 CAGTGTGGTCTTTTCTGCTGC 60.002 52.381 0.00 0.00 0.00 5.25
553 572 1.605710 CCAGTGTGGTCTTTTCTGCTG 59.394 52.381 0.00 0.00 31.35 4.41
554 573 1.477558 CCCAGTGTGGTCTTTTCTGCT 60.478 52.381 0.00 0.00 35.17 4.24
555 574 0.954452 CCCAGTGTGGTCTTTTCTGC 59.046 55.000 0.00 0.00 35.17 4.26
556 575 2.158755 ACTCCCAGTGTGGTCTTTTCTG 60.159 50.000 0.00 0.00 35.17 3.02
557 576 2.127708 ACTCCCAGTGTGGTCTTTTCT 58.872 47.619 0.00 0.00 35.17 2.52
558 577 2.158813 TCACTCCCAGTGTGGTCTTTTC 60.159 50.000 3.64 0.00 46.03 2.29
559 578 1.843851 TCACTCCCAGTGTGGTCTTTT 59.156 47.619 3.64 0.00 46.03 2.27
560 579 1.507140 TCACTCCCAGTGTGGTCTTT 58.493 50.000 3.64 0.00 46.03 2.52
561 580 1.417890 CTTCACTCCCAGTGTGGTCTT 59.582 52.381 3.64 0.00 46.03 3.01
562 581 1.051812 CTTCACTCCCAGTGTGGTCT 58.948 55.000 3.64 0.00 46.03 3.85
563 582 0.759346 ACTTCACTCCCAGTGTGGTC 59.241 55.000 3.64 0.00 46.03 4.02
564 583 0.759346 GACTTCACTCCCAGTGTGGT 59.241 55.000 3.64 4.29 46.03 4.16
565 584 1.051812 AGACTTCACTCCCAGTGTGG 58.948 55.000 3.64 1.47 46.03 4.17
566 585 1.688735 TCAGACTTCACTCCCAGTGTG 59.311 52.381 3.64 0.00 46.03 3.82
567 586 2.088104 TCAGACTTCACTCCCAGTGT 57.912 50.000 3.64 0.00 46.03 3.55
569 588 3.648067 TCATTTCAGACTTCACTCCCAGT 59.352 43.478 0.00 0.00 0.00 4.00
570 589 4.277515 TCATTTCAGACTTCACTCCCAG 57.722 45.455 0.00 0.00 0.00 4.45
1355 1403 4.456911 CCTGCACTTTGCTCATTTCTCTTA 59.543 41.667 0.00 0.00 45.31 2.10
2098 2846 2.624838 CAGCACCAACTGGAAATGAGTT 59.375 45.455 1.86 0.00 38.94 3.01
2099 2847 2.158623 TCAGCACCAACTGGAAATGAGT 60.159 45.455 1.86 0.00 38.26 3.41


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

AutoCloner maintained by Alex Coulton.