Multiple sequence alignment - TraesCS6B01G091200

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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 TraesCS6B01G091200 chr6B 100.000 2836 0 0 1 2836 66920731 66917896 0 5238
1 TraesCS6B01G091200 chr6B 96.499 2856 71 8 1 2836 66945332 66942486 0 4693
2 TraesCS6B01G091200 chr6B 96.318 2852 74 9 1 2836 66862860 66860024 0 4656
3 TraesCS6B01G091200 chr6B 86.432 2189 224 40 231 2388 66755831 66753685 0 2329
4 TraesCS6B01G091200 chr6B 91.494 482 35 5 2359 2836 66784240 66783761 0 658
5 TraesCS6B01G091200 chrUn 94.009 2871 126 14 1 2836 100490026 100492885 0 4307
6 TraesCS6B01G091200 chrUn 92.868 2047 94 16 839 2836 100620877 100622920 0 2924
7 TraesCS6B01G091200 chrUn 92.871 2020 113 17 1 1995 100637432 100639445 0 2904
8 TraesCS6B01G091200 chrUn 95.156 1569 62 7 1 1560 323636416 323637979 0 2464
9 TraesCS6B01G091200 chrUn 95.156 1569 61 8 1 1560 323668273 323669835 0 2462
10 TraesCS6B01G091200 chrUn 93.374 1298 61 5 1562 2836 344891260 344892555 0 1897
11 TraesCS6B01G091200 chrUn 93.357 843 44 1 2006 2836 100660342 100661184 0 1236
12 TraesCS6B01G091200 chr6A 93.935 2869 131 15 1 2836 35990809 35987951 0 4294
13 TraesCS6B01G091200 chr6A 93.933 2868 133 13 1 2836 36056202 36053344 0 4294
14 TraesCS6B01G091200 chr7A 94.817 1582 75 4 317 1893 255897065 255895486 0 2460


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 TraesCS6B01G091200 chr6B 66917896 66920731 2835 True 5238 5238 100.000 1 2836 1 chr6B.!!$R4 2835
1 TraesCS6B01G091200 chr6B 66942486 66945332 2846 True 4693 4693 96.499 1 2836 1 chr6B.!!$R5 2835
2 TraesCS6B01G091200 chr6B 66860024 66862860 2836 True 4656 4656 96.318 1 2836 1 chr6B.!!$R3 2835
3 TraesCS6B01G091200 chr6B 66753685 66755831 2146 True 2329 2329 86.432 231 2388 1 chr6B.!!$R1 2157
4 TraesCS6B01G091200 chrUn 100490026 100492885 2859 False 4307 4307 94.009 1 2836 1 chrUn.!!$F1 2835
5 TraesCS6B01G091200 chrUn 100620877 100622920 2043 False 2924 2924 92.868 839 2836 1 chrUn.!!$F2 1997
6 TraesCS6B01G091200 chrUn 100637432 100639445 2013 False 2904 2904 92.871 1 1995 1 chrUn.!!$F3 1994
7 TraesCS6B01G091200 chrUn 323636416 323637979 1563 False 2464 2464 95.156 1 1560 1 chrUn.!!$F5 1559
8 TraesCS6B01G091200 chrUn 323668273 323669835 1562 False 2462 2462 95.156 1 1560 1 chrUn.!!$F6 1559
9 TraesCS6B01G091200 chrUn 344891260 344892555 1295 False 1897 1897 93.374 1562 2836 1 chrUn.!!$F7 1274
10 TraesCS6B01G091200 chrUn 100660342 100661184 842 False 1236 1236 93.357 2006 2836 1 chrUn.!!$F4 830
11 TraesCS6B01G091200 chr6A 35987951 35990809 2858 True 4294 4294 93.935 1 2836 1 chr6A.!!$R1 2835
12 TraesCS6B01G091200 chr6A 36053344 36056202 2858 True 4294 4294 93.933 1 2836 1 chr6A.!!$R2 2835
13 TraesCS6B01G091200 chr7A 255895486 255897065 1579 True 2460 2460 94.817 317 1893 1 chr7A.!!$R1 1576

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
189 194 0.108424 CTCTTCAGGAACCAGCGAGG 60.108 60.000 0.0 0.0 45.67 4.63 F
893 913 1.633432 CCCCTTCTTGTGGTGTATGGA 59.367 52.381 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1492 0.620556 ATCCACCCACCATCTGTGTC 59.379 55.000 0.0 0.0 43.85 3.67 R
2593 2676 1.002134 CCTTCGCACTCCCCATGTT 60.002 57.895 0.0 0.0 0.00 2.71 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
32 37 2.287644 GCATGTTTGTGTGCCTTTTTCC 59.712 45.455 0.00 0.00 35.35 3.13
33 38 3.529533 CATGTTTGTGTGCCTTTTTCCA 58.470 40.909 0.00 0.00 0.00 3.53
189 194 0.108424 CTCTTCAGGAACCAGCGAGG 60.108 60.000 0.00 0.00 45.67 4.63
729 745 5.051816 ACTTGAGTGCAATTTTGTCAATGG 58.948 37.500 0.00 0.00 32.68 3.16
830 849 3.515502 TGTGTAGCATAGAAGCACCTCTT 59.484 43.478 0.00 0.00 37.83 2.85
893 913 1.633432 CCCCTTCTTGTGGTGTATGGA 59.367 52.381 0.00 0.00 0.00 3.41
921 941 6.260936 ACGATGTTCTTCAGAAGTTCACAAAT 59.739 34.615 10.09 0.00 34.27 2.32
1250 1274 4.311816 AGAAGTTGCAACATCAAAGTGG 57.688 40.909 30.15 0.00 0.00 4.00
1353 1399 7.785033 TGCATATTGATAAGAGAGAACTCACA 58.215 34.615 4.64 0.00 44.79 3.58
1567 1619 4.901849 TCCTTCTCAAGATATCGGGTTGAT 59.098 41.667 6.39 0.00 41.30 2.57
1637 1689 3.695606 TCGCCACACAGGAGGAGC 61.696 66.667 0.00 0.00 41.22 4.70
1638 1690 3.699894 CGCCACACAGGAGGAGCT 61.700 66.667 0.00 0.00 41.22 4.09
1774 1831 9.265901 ACATCTTAGATATGTCTAATTGCACAC 57.734 33.333 11.82 0.00 43.91 3.82
1847 1904 5.417580 TGGTTTGACATAAACATTAGGCCTC 59.582 40.000 9.68 0.00 32.04 4.70
1986 2054 5.547465 TCAAACTCATTGGTTAGTCACGAT 58.453 37.500 0.00 0.00 39.62 3.73
2149 2229 4.143242 CGCTGATATGGTCATAAAAGAGCG 60.143 45.833 15.15 15.15 38.81 5.03
2472 2555 5.063944 CCTAAGAAATGGTGTCATCACTTCG 59.936 44.000 1.82 0.00 43.41 3.79
2593 2676 3.556862 AGATCATGAGGCTCTGGGATA 57.443 47.619 16.72 0.00 0.00 2.59
2607 2690 0.535102 GGGATAACATGGGGAGTGCG 60.535 60.000 0.00 0.00 0.00 5.34
2629 2712 1.760613 AGGTCAGAACACACCGAGAAA 59.239 47.619 0.00 0.00 37.79 2.52
2696 2781 8.671921 CATGAGTTATTTCATACCATATCCTGC 58.328 37.037 0.00 0.00 36.08 4.85
2726 2811 5.693104 GTGCATTCAAGTTGACATTGACAAT 59.307 36.000 4.68 0.00 36.44 2.71
2741 2826 9.440773 GACATTGACAATATTAGGCATGATCTA 57.559 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 37 5.462405 GGACGGAGACAGTATAATTAGCTG 58.538 45.833 14.60 14.6 36.41 4.24
33 38 4.523558 GGGACGGAGACAGTATAATTAGCT 59.476 45.833 0.00 0.0 0.00 3.32
220 225 5.499313 TGTGCTCATTCCAGAAACATCATA 58.501 37.500 0.00 0.0 0.00 2.15
424 438 5.654497 CTTGAACATTCAATAGGCTTTCCC 58.346 41.667 7.48 0.0 45.26 3.97
582 596 3.165058 TGCGTCAAGTAGATCATCACC 57.835 47.619 0.00 0.0 0.00 4.02
807 826 3.118956 AGAGGTGCTTCTATGCTACACAC 60.119 47.826 0.00 0.0 32.89 3.82
893 913 5.463724 GTGAACTTCTGAAGAACATCGTCTT 59.536 40.000 23.36 4.3 40.62 3.01
921 941 6.321181 GCCTAAGGTTGAAATCACCATTATCA 59.679 38.462 0.00 0.0 0.00 2.15
1250 1274 6.349300 TCATACCTCTTAACCTCTTGCATTC 58.651 40.000 0.00 0.0 0.00 2.67
1440 1492 0.620556 ATCCACCCACCATCTGTGTC 59.379 55.000 0.00 0.0 43.85 3.67
1567 1619 3.763360 CCATTGAGATAACCTTTGTGGCA 59.237 43.478 0.00 0.0 40.22 4.92
1637 1689 5.850557 TGCCTCATTAAAGAGAGAGAGAG 57.149 43.478 9.26 0.0 37.87 3.20
1638 1690 6.382282 TGATTGCCTCATTAAAGAGAGAGAGA 59.618 38.462 9.26 0.0 37.87 3.10
1905 1973 2.019249 GCAGCCTTGAGTATGCAATGA 58.981 47.619 0.00 0.0 38.54 2.57
2014 2082 5.915758 TGCGCGTGAAACTTTTGTAATAATT 59.084 32.000 8.43 0.0 31.75 1.40
2253 2334 6.103997 CACATAAATACGTGAGGTGGTACTT 58.896 40.000 0.00 0.0 35.02 2.24
2472 2555 4.159506 TGCATAAATAAAAGTGGTGCTCCC 59.840 41.667 1.59 0.0 32.67 4.30
2593 2676 1.002134 CCTTCGCACTCCCCATGTT 60.002 57.895 0.00 0.0 0.00 2.71
2607 2690 1.340248 TCTCGGTGTGTTCTGACCTTC 59.660 52.381 0.00 0.0 0.00 3.46
2629 2712 7.145985 ACTAATCACATAGTCGTGCGATAAAT 58.854 34.615 0.00 0.0 36.80 1.40
2683 2768 2.373169 CACACCCAGCAGGATATGGTAT 59.627 50.000 0.00 0.0 37.60 2.73
2696 2781 1.955778 TCAACTTGAATGCACACCCAG 59.044 47.619 0.00 0.0 0.00 4.45


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

AutoCloner maintained by Alex Coulton.