Multiple sequence alignment - TraesCS6B01G024500

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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 TraesCS6B01G024500 chr6B 100.000 2420 0 0 1 2420 14868842 14866423 0.000000e+00 4470.0
1 TraesCS6B01G024500 chr6B 96.129 2428 81 10 3 2420 14878232 14880656 0.000000e+00 3951.0
2 TraesCS6B01G024500 chrUn 100.000 426 0 0 969 1394 476523088 476523513 0.000000e+00 787.0
3 TraesCS6B01G024500 chr3A 89.552 67 2 5 745 807 434070723 434070788 1.990000e-11 80.5
4 TraesCS6B01G024500 chr3A 78.846 104 14 8 710 807 176136681 176136580 2.010000e-06 63.9
5 TraesCS6B01G024500 chr5D 83.750 80 5 7 745 821 547048788 547048714 4.320000e-08 69.4
6 TraesCS6B01G024500 chr5D 88.136 59 3 3 745 799 238910794 238910736 1.550000e-07 67.6
7 TraesCS6B01G024500 chr3B 74.850 167 31 8 647 806 808101001 808100839 5.580000e-07 65.8
8 TraesCS6B01G024500 chr4D 84.848 66 5 5 745 806 352524428 352524364 7.220000e-06 62.1
9 TraesCS6B01G024500 chr2D 84.848 66 5 5 745 806 22771080 22771016 7.220000e-06 62.1
10 TraesCS6B01G024500 chr5A 74.691 162 27 12 651 802 561125308 561125465 2.600000e-05 60.2


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 TraesCS6B01G024500 chr6B 14866423 14868842 2419 True 4470 4470 100.000 1 2420 1 chr6B.!!$R1 2419
1 TraesCS6B01G024500 chr6B 14878232 14880656 2424 False 3951 3951 96.129 3 2420 1 chr6B.!!$F1 2417

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
800 808 0.554305 TCGGAGGTGCTCATAGGGTA 59.446 55.0 0.0 0.0 31.08 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1621 0.039437 GACGTGAAGAGCGAGTCCAA 60.039 55.0 0.0 0.0 0.0 3.53 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
48 49 8.024865 GCCGTTGTAAAAATATTTTGACTAGGT 58.975 33.333 23.22 7.01 33.52 3.08
65 66 3.915437 AGGTCCATTGCAAGTTTAACG 57.085 42.857 4.94 0.00 0.00 3.18
79 80 6.483687 CAAGTTTAACGCCACCACTATTATC 58.516 40.000 0.00 0.00 0.00 1.75
82 83 3.906720 AACGCCACCACTATTATCACT 57.093 42.857 0.00 0.00 0.00 3.41
83 84 3.179443 ACGCCACCACTATTATCACTG 57.821 47.619 0.00 0.00 0.00 3.66
85 86 2.866156 CGCCACCACTATTATCACTGTG 59.134 50.000 0.17 0.17 0.00 3.66
106 110 1.273886 TGACGTTGCATACTGTAGCCA 59.726 47.619 0.00 0.00 0.00 4.75
126 130 2.745492 GAGCAGAGCAGTGTGGCC 60.745 66.667 0.00 0.00 0.00 5.36
158 162 1.271379 ACAACTTCACATGCATGGCTG 59.729 47.619 29.41 19.54 0.00 4.85
164 168 2.056223 ACATGCATGGCTGGGCTTC 61.056 57.895 29.41 0.00 0.00 3.86
230 234 4.843516 TGCTTTAGATGGACCCCAAATTTT 59.156 37.500 0.00 0.00 36.95 1.82
365 369 3.505680 GCATGTAAGTTTCACCCATCACA 59.494 43.478 0.00 0.00 0.00 3.58
371 375 5.867903 AAGTTTCACCCATCACATCAAAA 57.132 34.783 0.00 0.00 0.00 2.44
502 509 6.798315 ATGTGAGTTTCTCTTTGATGTGAG 57.202 37.500 0.00 0.00 0.00 3.51
520 527 7.492020 TGATGTGAGATTTTGGTGAAAACTTTG 59.508 33.333 0.00 0.00 33.86 2.77
522 529 5.006649 GTGAGATTTTGGTGAAAACTTTGGC 59.993 40.000 0.00 0.00 33.86 4.52
546 554 2.028561 ATGAACACCCCTTGCCATTT 57.971 45.000 0.00 0.00 0.00 2.32
548 556 1.337118 GAACACCCCTTGCCATTTGA 58.663 50.000 0.00 0.00 0.00 2.69
569 577 8.592105 TTTGAATTCAAATGAACTGATCCAAC 57.408 30.769 26.01 0.00 40.55 3.77
585 593 1.452717 CAACGTGTGAACAAAGCGTC 58.547 50.000 0.00 0.00 34.56 5.19
603 611 2.352030 CGTCGCTCAACTGGTAAGGTTA 60.352 50.000 0.00 0.00 0.00 2.85
628 636 2.197324 TGAAACCTGGCCACCACC 59.803 61.111 0.00 0.00 0.00 4.61
629 637 2.197324 GAAACCTGGCCACCACCA 59.803 61.111 0.00 0.00 38.29 4.17
637 645 2.291282 CCTGGCCACCACCATTTAAGTA 60.291 50.000 0.00 0.00 39.54 2.24
641 649 2.676342 GCCACCACCATTTAAGTACTCG 59.324 50.000 0.00 0.00 0.00 4.18
645 653 2.936498 CCACCATTTAAGTACTCGGCTG 59.064 50.000 0.00 0.00 0.00 4.85
663 671 2.415843 GGCGCTGGTGCTCGTATA 59.584 61.111 7.64 0.00 36.97 1.47
669 677 3.855895 GCGCTGGTGCTCGTATATTTCTA 60.856 47.826 0.00 0.00 36.97 2.10
731 739 0.589708 TGATGTACCCGTCGATAGCG 59.410 55.000 0.00 0.00 39.35 4.26
771 779 7.584987 ACTTTGTCAATCTAAAAATCTGTCGG 58.415 34.615 0.00 0.00 0.00 4.79
782 790 4.379339 AAATCTGTCGGCTTAGTCTCTC 57.621 45.455 0.00 0.00 0.00 3.20
796 804 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
800 808 0.554305 TCGGAGGTGCTCATAGGGTA 59.446 55.000 0.00 0.00 31.08 3.69
816 824 6.273260 TCATAGGGTAGAGGTAAGGTACGTAT 59.727 42.308 0.00 0.00 0.00 3.06
817 825 7.457852 TCATAGGGTAGAGGTAAGGTACGTATA 59.542 40.741 0.00 0.00 0.00 1.47
825 833 6.485984 AGAGGTAAGGTACGTATATGTGTCTG 59.514 42.308 7.89 0.00 0.00 3.51
827 835 5.300286 GGTAAGGTACGTATATGTGTCTGGT 59.700 44.000 7.89 0.00 0.00 4.00
834 842 8.086522 GGTACGTATATGTGTCTGGTCATATTT 58.913 37.037 7.89 0.00 38.01 1.40
967 975 6.053005 TCTTCATTTTGTTTACTCCACGACT 58.947 36.000 0.00 0.00 0.00 4.18
1394 1402 5.581479 TGCACGTACGTGTCCATTTTATTAT 59.419 36.000 39.56 4.22 46.90 1.28
1418 1426 2.029728 GCTTATCACGCATCTGTGTCAC 59.970 50.000 0.00 0.00 40.74 3.67
1428 1436 4.031028 GCATCTGTGTCACAATAAATCGC 58.969 43.478 7.18 0.00 0.00 4.58
1570 1578 2.667318 CGCCGTGCAAGTAGTGGTG 61.667 63.158 0.00 0.00 0.00 4.17
1611 1619 3.921521 CCGAGTCTAGCTTCCGGT 58.078 61.111 0.00 0.00 35.83 5.28
1613 1621 0.748729 CCGAGTCTAGCTTCCGGTCT 60.749 60.000 0.00 0.00 35.83 3.85
1697 1706 3.934962 GGATCGAGCTCCCAGGGC 61.935 72.222 8.47 0.00 0.00 5.19
1793 1802 5.970612 TGTGTGTCAAATTCATTTCTGAACG 59.029 36.000 0.00 0.00 43.92 3.95
1810 1819 2.880822 ACGCACGATTTCATTCACAG 57.119 45.000 0.00 0.00 0.00 3.66
1833 1842 7.148137 ACAGATTTACTTGTGGAAAACGAACTT 60.148 33.333 0.00 0.00 0.00 2.66
2086 2095 6.306987 GGTCACAACATCCATATAAGGGATT 58.693 40.000 6.57 0.00 42.47 3.01
2110 2119 8.900983 TTGCTTTGGCTTGTATTCTTTAAAAT 57.099 26.923 0.00 0.00 39.59 1.82
2249 2258 4.223923 GGCCATCATTGCCTAGAGTACTAT 59.776 45.833 0.00 0.00 45.70 2.12
2279 2288 9.408069 CGTTCTTAGATATATGTGGTTTAGGAC 57.592 37.037 0.00 0.00 0.00 3.85
2408 2419 7.732222 ATTTATCAAAGAAATACCTGGGCAA 57.268 32.000 0.00 0.00 0.00 4.52
2414 2425 2.239907 AGAAATACCTGGGCAAGAGACC 59.760 50.000 0.00 0.00 46.36 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.551883 GAAGCAGAACCAATGGGCATT 59.448 47.619 3.55 0.00 37.90 3.56
1 2 1.188863 GAAGCAGAACCAATGGGCAT 58.811 50.000 3.55 0.00 37.90 4.40
10 11 1.166531 ACAACGGCAGAAGCAGAACC 61.167 55.000 0.00 0.00 44.61 3.62
48 49 1.957177 TGGCGTTAAACTTGCAATGGA 59.043 42.857 0.00 0.00 0.00 3.41
51 52 1.683917 TGGTGGCGTTAAACTTGCAAT 59.316 42.857 0.00 0.00 0.00 3.56
65 66 3.623060 CACACAGTGATAATAGTGGTGGC 59.377 47.826 7.81 0.00 35.23 5.01
79 80 2.096762 CAGTATGCAACGTCACACAGTG 60.097 50.000 0.00 0.00 34.45 3.66
82 83 2.232756 ACAGTATGCAACGTCACACA 57.767 45.000 0.00 0.00 42.53 3.72
83 84 2.092211 GCTACAGTATGCAACGTCACAC 59.908 50.000 0.00 0.00 42.53 3.82
85 86 1.659098 GGCTACAGTATGCAACGTCAC 59.341 52.381 0.00 0.00 42.53 3.67
106 110 2.591072 CCACACTGCTCTGCTCCCT 61.591 63.158 0.00 0.00 0.00 4.20
126 130 3.131577 TGTGAAGTTGTACCCTATAGCCG 59.868 47.826 0.00 0.00 0.00 5.52
164 168 7.144661 TGAATATAATTATTGGTGCAAAGGCG 58.855 34.615 2.68 0.00 45.35 5.52
170 174 8.703378 TGTGGATGAATATAATTATTGGTGCA 57.297 30.769 2.68 0.00 0.00 4.57
206 210 2.507407 TTGGGGTCCATCTAAAGCAC 57.493 50.000 0.00 0.00 31.53 4.40
230 234 4.898265 TCCTTTGATGTGATGGGTGAAAAA 59.102 37.500 0.00 0.00 0.00 1.94
365 369 6.023334 AGCCCCATTAGATTCTCTTTTGAT 57.977 37.500 0.00 0.00 0.00 2.57
371 375 8.986991 CATATAAGTAGCCCCATTAGATTCTCT 58.013 37.037 0.00 0.00 0.00 3.10
384 388 6.214819 TGACCCTAAATCCATATAAGTAGCCC 59.785 42.308 0.00 0.00 0.00 5.19
502 509 3.247411 CCGCCAAAGTTTTCACCAAAATC 59.753 43.478 0.00 0.00 33.98 2.17
520 527 0.898326 AAGGGGTGTTCATTTCCGCC 60.898 55.000 0.00 0.00 35.26 6.13
522 529 0.243636 GCAAGGGGTGTTCATTTCCG 59.756 55.000 0.00 0.00 0.00 4.30
546 554 6.016360 ACGTTGGATCAGTTCATTTGAATTCA 60.016 34.615 3.38 3.38 36.33 2.57
548 556 6.151691 CACGTTGGATCAGTTCATTTGAATT 58.848 36.000 0.00 0.00 36.33 2.17
560 568 3.849645 GCTTTGTTCACACGTTGGATCAG 60.850 47.826 0.00 0.00 0.00 2.90
569 577 1.717728 GCGACGCTTTGTTCACACG 60.718 57.895 13.73 0.00 0.00 4.49
585 593 4.454504 ACAAATAACCTTACCAGTTGAGCG 59.545 41.667 0.00 0.00 0.00 5.03
603 611 1.047801 GGCCAGGTTTCACCACAAAT 58.952 50.000 0.00 0.00 41.95 2.32
620 628 2.676342 CGAGTACTTAAATGGTGGTGGC 59.324 50.000 0.00 0.00 0.00 5.01
628 636 1.940613 GCCCAGCCGAGTACTTAAATG 59.059 52.381 0.00 0.00 0.00 2.32
629 637 1.472728 CGCCCAGCCGAGTACTTAAAT 60.473 52.381 0.00 0.00 0.00 1.40
714 722 1.266175 CTTCGCTATCGACGGGTACAT 59.734 52.381 0.00 0.00 45.43 2.29
715 723 0.659427 CTTCGCTATCGACGGGTACA 59.341 55.000 0.00 0.00 45.43 2.90
716 724 0.659711 GCTTCGCTATCGACGGGTAC 60.660 60.000 0.00 0.00 45.43 3.34
718 726 2.412112 GCTTCGCTATCGACGGGT 59.588 61.111 0.00 0.00 45.43 5.28
724 732 2.101053 TAACTGTCGCTTCGCTATCG 57.899 50.000 0.00 0.00 0.00 2.92
731 739 4.447724 TGACAAAGTCATAACTGTCGCTTC 59.552 41.667 0.00 0.00 37.67 3.86
750 758 5.245531 AGCCGACAGATTTTTAGATTGACA 58.754 37.500 0.00 0.00 0.00 3.58
762 770 2.356382 CGAGAGACTAAGCCGACAGATT 59.644 50.000 0.00 0.00 0.00 2.40
771 779 0.101579 GCACCTCCGAGAGACTAAGC 59.898 60.000 0.00 0.00 0.00 3.09
782 790 0.962489 CTACCCTATGAGCACCTCCG 59.038 60.000 0.00 0.00 0.00 4.63
796 804 6.150140 CACATATACGTACCTTACCTCTACCC 59.850 46.154 0.00 0.00 0.00 3.69
800 808 6.485984 CAGACACATATACGTACCTTACCTCT 59.514 42.308 0.00 0.00 0.00 3.69
816 824 7.669089 TCCACTAAATATGACCAGACACATA 57.331 36.000 0.00 0.00 34.27 2.29
817 825 6.560003 TCCACTAAATATGACCAGACACAT 57.440 37.500 0.00 0.00 0.00 3.21
825 833 8.463930 TTTCATTCCATCCACTAAATATGACC 57.536 34.615 0.00 0.00 0.00 4.02
967 975 2.741092 AGCGGTCTTTGCTCGGAA 59.259 55.556 0.00 0.00 38.62 4.30
1394 1402 4.112634 GACACAGATGCGTGATAAGCTAA 58.887 43.478 0.00 0.00 39.34 3.09
1570 1578 3.777016 CGAGCTACCTATTCTCGCC 57.223 57.895 0.00 0.00 42.28 5.54
1611 1619 0.241213 CGTGAAGAGCGAGTCCAAGA 59.759 55.000 0.00 0.00 0.00 3.02
1613 1621 0.039437 GACGTGAAGAGCGAGTCCAA 60.039 55.000 0.00 0.00 0.00 3.53
1664 1673 0.982852 ATCCTTCTCACATCCCGCCA 60.983 55.000 0.00 0.00 0.00 5.69
1697 1706 4.935205 TGATTACATGACTCAAAGGAACGG 59.065 41.667 0.00 0.00 0.00 4.44
1793 1802 6.546395 AGTAAATCTGTGAATGAAATCGTGC 58.454 36.000 0.00 0.00 0.00 5.34
1810 1819 6.970613 ACAAGTTCGTTTTCCACAAGTAAATC 59.029 34.615 0.00 0.00 0.00 2.17
1833 1842 1.361204 AGACCCACATGTCATCCACA 58.639 50.000 0.00 0.00 40.18 4.17
2086 2095 8.772705 CAATTTTAAAGAATACAAGCCAAAGCA 58.227 29.630 0.00 0.00 43.56 3.91
2110 2119 6.811665 CACTCGTATCTCCATTACTTCAACAA 59.188 38.462 0.00 0.00 0.00 2.83
2249 2258 7.834881 AACCACATATATCTAAGAACGGAGA 57.165 36.000 0.00 0.00 0.00 3.71
2324 2333 9.787435 AATATTGCACCGTTCTTAAATATAGGA 57.213 29.630 0.00 0.00 0.00 2.94
2381 2392 9.261035 TGCCCAGGTATTTCTTTGATAAATAAA 57.739 29.630 0.00 0.00 32.21 1.40


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

AutoCloner maintained by Alex Coulton.