Multiple sequence alignment - TraesCS6B01G024600

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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 TraesCS6B01G024600 chr6B 100.000 2716 0 0 1 2716 14878269 14880984 0.000000e+00 5016.0
1 TraesCS6B01G024600 chr6B 96.068 2721 89 14 1 2716 14868803 14866096 0.000000e+00 4416.0
2 TraesCS6B01G024600 chrUn 100.000 426 0 0 935 1360 476523088 476523513 0.000000e+00 787.0
3 TraesCS6B01G024600 chr5D 78.125 128 23 4 548 673 294349973 294349849 2.900000e-10 76.8
4 TraesCS6B01G024600 chr3A 74.302 179 35 10 592 762 727269935 727270110 6.280000e-07 65.8
5 TraesCS6B01G024600 chr7D 74.691 162 32 8 611 765 622126409 622126250 2.260000e-06 63.9
6 TraesCS6B01G024600 chr4A 100.000 29 0 0 620 648 699889509 699889537 1.000000e-03 54.7
7 TraesCS6B01G024600 chr4A 100.000 28 0 0 618 645 608602146 608602173 5.000000e-03 52.8


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 TraesCS6B01G024600 chr6B 14878269 14880984 2715 False 5016 5016 100.000 1 2716 1 chr6B.!!$F1 2715
1 TraesCS6B01G024600 chr6B 14866096 14868803 2707 True 4416 4416 96.068 1 2716 1 chr6B.!!$R1 2715

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
26 27 0.386113 GGCCCGTTGCAAGTTTAACA 59.614 50.000 0.0 0.0 43.89 2.41 F
1536 1539 1.080366 CGCCGTGCAAGTAGTGGTA 60.080 57.895 0.0 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 1580 0.248843 GTGAAGAGCTGAGTCCAGGG 59.751 60.0 0.00 0.00 40.72 4.45 R
2367 2371 0.251354 TCAGAGTCTCATGCCAAGGC 59.749 55.0 3.61 3.61 42.35 4.35 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
26 27 0.386113 GGCCCGTTGCAAGTTTAACA 59.614 50.000 0.00 0.00 43.89 2.41
40 41 7.231722 TGCAAGTTTAACACCACCACTATTATT 59.768 33.333 0.00 0.00 0.00 1.40
43 44 8.797350 AGTTTAACACCACCACTATTATTACC 57.203 34.615 0.00 0.00 0.00 2.85
44 45 8.608598 AGTTTAACACCACCACTATTATTACCT 58.391 33.333 0.00 0.00 0.00 3.08
57 58 8.988934 CACTATTATTACCTTATGACGTTGCAT 58.011 33.333 0.00 0.00 0.00 3.96
70 71 2.117137 CGTTGCATAGTACTGTAGCCG 58.883 52.381 5.39 3.41 0.00 5.52
122 123 1.542915 ACAACTTCACATGCATGGCTC 59.457 47.619 29.41 0.00 0.00 4.70
128 129 2.411701 CATGCATGGCTCGGCTTG 59.588 61.111 19.40 2.56 0.00 4.01
194 195 4.222588 TGCTTTAGATGGACCCCAAATTTG 59.777 41.667 11.40 11.40 36.95 2.32
328 330 3.426159 GCATGTAAGTTTCACCCATCACG 60.426 47.826 0.00 0.00 0.00 4.35
334 336 2.878406 AGTTTCACCCATCACGTCAAAG 59.122 45.455 0.00 0.00 0.00 2.77
347 349 6.280855 TCACGTCAAAGGAGAATCTAATGA 57.719 37.500 0.00 0.00 33.73 2.57
468 470 5.991328 TGTGAGTTTCTCTTTGATGTGAC 57.009 39.130 0.00 0.00 0.00 3.67
486 488 7.605691 TGATGTGACATTTTGGTGAAAACTTTT 59.394 29.630 0.00 0.00 33.86 2.27
488 490 6.148480 TGTGACATTTTGGTGAAAACTTTTGG 59.852 34.615 0.00 0.00 33.86 3.28
489 491 6.148645 GTGACATTTTGGTGAAAACTTTTGGT 59.851 34.615 0.00 0.00 33.86 3.67
513 515 2.917713 ATGAACACCCCTTGCCATTA 57.082 45.000 0.00 0.00 0.00 1.90
515 517 1.427368 TGAACACCCCTTGCCATTAGT 59.573 47.619 0.00 0.00 0.00 2.24
527 529 7.202029 CCCCTTGCCATTAGTATTCAAATGAAT 60.202 37.037 12.82 12.82 45.77 2.57
552 554 3.206964 TCCAATGTGTGAACAAAGCGTA 58.793 40.909 0.00 0.00 0.00 4.42
570 572 3.251571 CGTAGCTCAACTGGTAAGGTTC 58.748 50.000 0.00 0.00 0.00 3.62
595 597 2.317230 GTGAAACCTGACCACCACG 58.683 57.895 0.00 0.00 0.00 4.94
596 598 1.147376 TGAAACCTGACCACCACGG 59.853 57.895 0.00 0.00 42.50 4.94
608 610 2.841215 CCACCACGGTTTAAGTTCTCA 58.159 47.619 0.00 0.00 0.00 3.27
612 614 3.139077 CCACGGTTTAAGTTCTCAGCTT 58.861 45.455 0.00 0.00 0.00 3.74
630 632 2.511600 GGCGCTGGTGCTCGTATT 60.512 61.111 7.64 0.00 36.97 1.89
636 638 2.474526 CGCTGGTGCTCGTATTTTTCTG 60.475 50.000 0.00 0.00 36.97 3.02
680 683 4.155280 CGGTGTTATTTTTCAGGTAGGTGG 59.845 45.833 0.00 0.00 0.00 4.61
681 684 4.082408 GGTGTTATTTTTCAGGTAGGTGGC 60.082 45.833 0.00 0.00 0.00 5.01
682 685 4.765339 GTGTTATTTTTCAGGTAGGTGGCT 59.235 41.667 0.00 0.00 0.00 4.75
684 687 5.475564 TGTTATTTTTCAGGTAGGTGGCTTC 59.524 40.000 0.00 0.00 0.00 3.86
690 693 2.599757 GGTAGGTGGCTTCCCCGTT 61.600 63.158 0.00 0.00 35.87 4.44
697 700 1.223487 GGCTTCCCCGTTGATAGCA 59.777 57.895 0.00 0.00 33.60 3.49
704 707 1.299541 CCCGTTGATAGCAAAGCGAT 58.700 50.000 5.42 0.00 35.42 4.58
709 712 4.508971 CGTTGATAGCAAAGCGATAGTTG 58.491 43.478 0.00 0.00 35.42 3.16
716 719 3.433615 AGCAAAGCGATAGTTGTGACTTC 59.566 43.478 0.00 0.00 37.33 3.01
728 731 6.771188 AGTTGTGACTTCGTCAATCTAAAG 57.229 37.500 0.00 0.00 44.49 1.85
737 740 5.813080 TCGTCAATCTAAAGATCTGTCGA 57.187 39.130 0.00 14.02 34.60 4.20
748 751 6.827586 AAAGATCTGTCGACTTAGTCTCTT 57.172 37.500 17.92 14.68 0.00 2.85
762 765 3.652055 AGTCTCTTGGAGGTGCTCATAT 58.348 45.455 0.00 0.00 31.08 1.78
766 769 2.171237 TCTTGGAGGTGCTCATATGGTG 59.829 50.000 2.13 0.00 31.08 4.17
782 785 2.726821 TGGTGGAGGTAAGGTACGTAG 58.273 52.381 0.00 0.00 0.00 3.51
783 786 2.027385 GGTGGAGGTAAGGTACGTAGG 58.973 57.143 0.00 0.00 0.00 3.18
791 794 4.019321 AGGTAAGGTACGTAGGTGTGTCTA 60.019 45.833 0.00 0.00 0.00 2.59
793 796 2.363683 AGGTACGTAGGTGTGTCTAGC 58.636 52.381 0.00 0.00 0.00 3.42
800 803 4.037684 ACGTAGGTGTGTCTAGCCATATTC 59.962 45.833 0.00 0.00 0.00 1.75
802 805 5.451381 CGTAGGTGTGTCTAGCCATATTCAA 60.451 44.000 0.00 0.00 0.00 2.69
933 936 5.818336 TCTTCATTTTGTTTACTCCACGACA 59.182 36.000 0.00 0.00 0.00 4.35
1360 1363 5.163972 TGCACGTACGTGTCCATTTTATTAC 60.164 40.000 39.56 23.08 46.90 1.89
1384 1387 2.868583 GCTTATCACGCATCTGTGTCAT 59.131 45.455 0.00 0.00 40.74 3.06
1394 1397 5.753438 ACGCATCTGTGTCATAATAAATCGT 59.247 36.000 0.00 0.00 32.60 3.73
1536 1539 1.080366 CGCCGTGCAAGTAGTGGTA 60.080 57.895 0.00 0.00 0.00 3.25
1577 1580 1.099879 TACCGAGTCTAGCTTCCGGC 61.100 60.000 0.00 0.00 43.56 6.13
1579 1582 2.816012 GAGTCTAGCTTCCGGCCC 59.184 66.667 0.00 0.00 43.05 5.80
1587 1590 3.003173 CTTCCGGCCCTGGACTCA 61.003 66.667 0.00 0.00 37.89 3.41
1664 1667 2.444895 GGATCGAGCTCCCAGGGT 60.445 66.667 8.47 0.00 0.00 4.34
1760 1763 6.198966 GTGTGTGTCAAATTCATTTCTGAACC 59.801 38.462 0.00 0.00 43.92 3.62
1777 1780 3.885901 TGAACCCACGATTTCATTCACAA 59.114 39.130 0.00 0.00 0.00 3.33
1800 1803 8.460428 ACAAATTTACTTGTGGAAAACGAACTA 58.540 29.630 0.00 0.00 38.12 2.24
2076 2080 8.900983 ATGCTTTGGCTTGTATTCTTTAAAAA 57.099 26.923 0.00 0.00 39.59 1.94
2215 2219 4.561105 GCCATCATTGCCTAGAGTACTAC 58.439 47.826 0.00 0.00 0.00 2.73
2245 2249 9.627395 CGTTCTTAGATATATGTGGTTTAGGAG 57.373 37.037 0.00 0.00 0.00 3.69
2290 2294 6.821665 TGGACTGGCTTACTTGTCATAAATAC 59.178 38.462 0.00 0.00 0.00 1.89
2310 2314 8.913487 AAATACCCTATATTTAAGAACGGTGG 57.087 34.615 0.00 0.00 0.00 4.61
2376 2380 5.680594 TTATCAAAGAAATGCCTTGGCAT 57.319 34.783 20.26 20.26 0.00 4.40
2382 2386 2.097825 GAAATGCCTTGGCATGAGACT 58.902 47.619 25.51 8.73 0.00 3.24
2416 2420 5.178061 CCCTTTGTTTTCATCTATTTGGCC 58.822 41.667 0.00 0.00 0.00 5.36
2447 2452 5.889289 ACAAACCCAACTTAGCTTCTAACAA 59.111 36.000 0.00 0.00 0.00 2.83
2517 2522 8.717717 AGGGTTCTGATCAGTTCATTAATGATA 58.282 33.333 21.92 7.47 36.56 2.15
2537 2542 6.207928 TGATAATTGTGCCATTGCTAAATCG 58.792 36.000 0.00 0.00 38.71 3.34
2574 2579 8.322091 AGCAAGGTTAATAATAGAGACAAGTGT 58.678 33.333 0.00 0.00 0.00 3.55
2698 2704 6.691818 ACTTGTTAGTTATTATCAGAGACGCG 59.308 38.462 3.53 3.53 0.00 6.01
2700 2706 2.651701 AGTTATTATCAGAGACGCGCG 58.348 47.619 30.96 30.96 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.405821 TGGTGTTAAACTTGCAACGGG 59.594 47.619 0.00 0.00 0.00 5.28
12 13 3.119280 AGTGGTGGTGTTAAACTTGCAAC 60.119 43.478 0.00 0.00 0.00 4.17
26 27 7.070322 ACGTCATAAGGTAATAATAGTGGTGGT 59.930 37.037 0.00 0.00 0.00 4.16
40 41 6.095860 ACAGTACTATGCAACGTCATAAGGTA 59.904 38.462 0.00 0.00 0.00 3.08
43 44 6.142480 GCTACAGTACTATGCAACGTCATAAG 59.858 42.308 0.00 0.00 0.00 1.73
44 45 5.975344 GCTACAGTACTATGCAACGTCATAA 59.025 40.000 0.00 0.00 0.00 1.90
46 47 4.360563 GCTACAGTACTATGCAACGTCAT 58.639 43.478 0.00 0.00 0.00 3.06
57 58 0.466922 GCTCCCCGGCTACAGTACTA 60.467 60.000 0.00 0.00 0.00 1.82
58 59 1.757340 GCTCCCCGGCTACAGTACT 60.757 63.158 0.00 0.00 0.00 2.73
59 60 2.017559 CTGCTCCCCGGCTACAGTAC 62.018 65.000 0.00 0.00 0.00 2.73
70 71 2.046507 CACACTGCTCTGCTCCCC 60.047 66.667 0.00 0.00 0.00 4.81
90 91 4.098155 TGTGAAGTTGTACCCTATAGCCA 58.902 43.478 0.00 0.00 0.00 4.75
128 129 6.014669 TGAATATAATTATTGGTGCCAAGGCC 60.015 38.462 8.89 0.00 39.47 5.19
134 135 8.121305 TGTGGATGAATATAATTATTGGTGCC 57.879 34.615 2.68 0.51 0.00 5.01
170 171 3.756082 TTTGGGGTCCATCTAAAGCAT 57.244 42.857 0.00 0.00 31.53 3.79
194 195 4.280677 TCCTTTGATGTGATGGGTGAAAAC 59.719 41.667 0.00 0.00 0.00 2.43
328 330 5.679601 AGCCTCATTAGATTCTCCTTTGAC 58.320 41.667 0.00 0.00 0.00 3.18
347 349 7.023120 TGACCCTAAATCCATATAAGTAGCCT 58.977 38.462 0.00 0.00 0.00 4.58
419 421 8.446599 TCATGTAGTATGAATGTAGACGAGAA 57.553 34.615 0.00 0.00 0.00 2.87
420 422 8.446599 TTCATGTAGTATGAATGTAGACGAGA 57.553 34.615 0.00 0.00 33.55 4.04
468 470 5.645497 TCCACCAAAAGTTTTCACCAAAATG 59.355 36.000 0.00 0.00 33.98 2.32
488 490 1.000843 GCAAGGGGTGTTCATTTCCAC 59.999 52.381 0.00 0.00 0.00 4.02
489 491 1.337118 GCAAGGGGTGTTCATTTCCA 58.663 50.000 0.00 0.00 0.00 3.53
527 529 4.619973 GCTTTGTTCACACATTGGATCAA 58.380 39.130 0.00 0.00 31.06 2.57
536 538 1.864711 GAGCTACGCTTTGTTCACACA 59.135 47.619 0.00 0.00 39.88 3.72
552 554 4.137543 CAAAGAACCTTACCAGTTGAGCT 58.862 43.478 0.00 0.00 0.00 4.09
570 572 2.374184 TGGTCAGGTTTCACCACAAAG 58.626 47.619 0.00 0.00 41.95 2.77
595 597 2.095718 CGCCAAGCTGAGAACTTAAACC 60.096 50.000 0.00 0.00 0.00 3.27
596 598 2.665794 GCGCCAAGCTGAGAACTTAAAC 60.666 50.000 0.00 0.00 44.04 2.01
680 683 1.401905 CTTTGCTATCAACGGGGAAGC 59.598 52.381 0.00 0.00 30.75 3.86
681 684 1.401905 GCTTTGCTATCAACGGGGAAG 59.598 52.381 0.00 0.00 30.75 3.46
682 685 1.459450 GCTTTGCTATCAACGGGGAA 58.541 50.000 0.00 0.00 30.75 3.97
684 687 0.742990 TCGCTTTGCTATCAACGGGG 60.743 55.000 1.05 0.00 35.85 5.73
690 693 4.566759 GTCACAACTATCGCTTTGCTATCA 59.433 41.667 0.00 0.00 0.00 2.15
697 700 3.650139 ACGAAGTCACAACTATCGCTTT 58.350 40.909 0.00 0.00 29.74 3.51
716 719 5.574082 AGTCGACAGATCTTTAGATTGACG 58.426 41.667 19.50 14.04 34.37 4.35
728 731 4.636648 TCCAAGAGACTAAGTCGACAGATC 59.363 45.833 19.50 9.48 37.67 2.75
737 740 2.829120 GAGCACCTCCAAGAGACTAAGT 59.171 50.000 0.00 0.00 0.00 2.24
748 751 0.839277 CCACCATATGAGCACCTCCA 59.161 55.000 3.65 0.00 0.00 3.86
762 765 2.621407 CCTACGTACCTTACCTCCACCA 60.621 54.545 0.00 0.00 0.00 4.17
766 769 2.424956 CACACCTACGTACCTTACCTCC 59.575 54.545 0.00 0.00 0.00 4.30
782 785 4.516698 CCATTGAATATGGCTAGACACACC 59.483 45.833 0.00 0.00 31.75 4.16
783 786 5.368145 TCCATTGAATATGGCTAGACACAC 58.632 41.667 0.00 0.00 39.01 3.82
791 794 5.647230 TCATTCCATCCATTGAATATGGCT 58.353 37.500 2.70 0.00 40.05 4.75
933 936 2.982130 AGCGGTCTTTGCTCGGAT 59.018 55.556 0.00 0.00 38.62 4.18
1360 1363 3.711086 ACACAGATGCGTGATAAGCTAG 58.289 45.455 0.00 0.00 39.34 3.42
1384 1387 4.031991 CCGAACGCAGAACACGATTTATTA 59.968 41.667 0.00 0.00 0.00 0.98
1394 1397 1.180456 TAGGGACCGAACGCAGAACA 61.180 55.000 0.00 0.00 0.00 3.18
1577 1580 0.248843 GTGAAGAGCTGAGTCCAGGG 59.751 60.000 0.00 0.00 40.72 4.45
1579 1582 0.600557 ACGTGAAGAGCTGAGTCCAG 59.399 55.000 0.00 0.00 43.22 3.86
1587 1590 2.259818 CGCAGGACGTGAAGAGCT 59.740 61.111 0.00 0.00 36.87 4.09
1631 1634 2.032860 ATCCTTCTCACATCCCGCCG 62.033 60.000 0.00 0.00 0.00 6.46
1664 1667 5.637810 GTGATTACATGACTCAAAGGAACGA 59.362 40.000 0.00 0.00 0.00 3.85
1760 1763 8.427012 CAAGTAAATTTGTGAATGAAATCGTGG 58.573 33.333 0.00 0.00 0.00 4.94
1777 1780 8.126700 CACTAGTTCGTTTTCCACAAGTAAATT 58.873 33.333 0.00 0.00 0.00 1.82
1800 1803 1.661463 AGACCCACATGTCATCCACT 58.339 50.000 0.00 0.00 37.73 4.00
2076 2080 6.980978 CACTCGTATCTCCATTACTTCAACAT 59.019 38.462 0.00 0.00 0.00 2.71
2215 2219 6.591750 ACCACATATATCTAAGAACGGAGG 57.408 41.667 0.00 0.00 0.00 4.30
2290 2294 9.734984 AATATTCCACCGTTCTTAAATATAGGG 57.265 33.333 0.00 0.00 0.00 3.53
2349 2353 7.909267 GCCAAGGCATTTCTTTGATAAATAAC 58.091 34.615 6.14 0.00 41.49 1.89
2367 2371 0.251354 TCAGAGTCTCATGCCAAGGC 59.749 55.000 3.61 3.61 42.35 4.35
2371 2375 1.973515 ACAACTCAGAGTCTCATGCCA 59.026 47.619 2.72 0.00 0.00 4.92
2376 2380 3.527507 AGGGTACAACTCAGAGTCTCA 57.472 47.619 2.72 0.00 0.00 3.27
2382 2386 5.502079 TGAAAACAAAGGGTACAACTCAGA 58.498 37.500 0.00 0.00 0.00 3.27
2416 2420 3.191371 GCTAAGTTGGGTTTGTCAGGATG 59.809 47.826 0.00 0.00 37.54 3.51
2673 2679 6.691818 CGCGTCTCTGATAATAACTAACAAGT 59.308 38.462 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.