Multiple sequence alignment - TraesCS5A01G390100

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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 TraesCS5A01G390100 chr5A 100.000 2468 0 0 1 2468 585486565 585489032 0.000000e+00 4558
1 TraesCS5A01G390100 chr5A 96.285 673 23 2 1 672 653659837 653659166 0.000000e+00 1103
2 TraesCS5A01G390100 chr5A 100.000 62 0 0 2383 2444 585488886 585488947 5.580000e-22 115
3 TraesCS5A01G390100 chr5A 100.000 62 0 0 2322 2383 585488947 585489008 5.580000e-22 115
4 TraesCS5A01G390100 chr5D 85.860 1570 97 69 666 2156 465198374 465199897 0.000000e+00 1554
5 TraesCS5A01G390100 chr5B 89.782 1057 40 27 708 1739 572544547 572545560 0.000000e+00 1291
6 TraesCS5A01G390100 chr5B 96.847 666 18 3 1 666 686832093 686832755 0.000000e+00 1110
7 TraesCS5A01G390100 chr5B 96.702 667 19 3 1 665 63252263 63251598 0.000000e+00 1107
8 TraesCS5A01G390100 chr5B 80.583 412 44 18 1789 2182 572545578 572545971 4.020000e-73 285
9 TraesCS5A01G390100 chr2B 96.313 678 23 2 1 676 699182261 699181584 0.000000e+00 1112
10 TraesCS5A01G390100 chr2B 96.572 671 20 3 1 670 640687805 640687137 0.000000e+00 1109
11 TraesCS5A01G390100 chr3A 96.577 672 20 3 1 670 378337648 378336978 0.000000e+00 1110
12 TraesCS5A01G390100 chr3B 96.285 673 21 1 1 669 171120244 171120916 0.000000e+00 1101
13 TraesCS5A01G390100 chr3B 96.280 672 23 2 1 670 247809139 247809810 0.000000e+00 1101
14 TraesCS5A01G390100 chr6B 95.620 685 28 2 1 683 646915863 646915179 0.000000e+00 1098


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 TraesCS5A01G390100 chr5A 585486565 585489032 2467 False 1596 4558 100.0000 1 2468 3 chr5A.!!$F1 2467
1 TraesCS5A01G390100 chr5A 653659166 653659837 671 True 1103 1103 96.2850 1 672 1 chr5A.!!$R1 671
2 TraesCS5A01G390100 chr5D 465198374 465199897 1523 False 1554 1554 85.8600 666 2156 1 chr5D.!!$F1 1490
3 TraesCS5A01G390100 chr5B 686832093 686832755 662 False 1110 1110 96.8470 1 666 1 chr5B.!!$F1 665
4 TraesCS5A01G390100 chr5B 63251598 63252263 665 True 1107 1107 96.7020 1 665 1 chr5B.!!$R1 664
5 TraesCS5A01G390100 chr5B 572544547 572545971 1424 False 788 1291 85.1825 708 2182 2 chr5B.!!$F2 1474
6 TraesCS5A01G390100 chr2B 699181584 699182261 677 True 1112 1112 96.3130 1 676 1 chr2B.!!$R2 675
7 TraesCS5A01G390100 chr2B 640687137 640687805 668 True 1109 1109 96.5720 1 670 1 chr2B.!!$R1 669
8 TraesCS5A01G390100 chr3A 378336978 378337648 670 True 1110 1110 96.5770 1 670 1 chr3A.!!$R1 669
9 TraesCS5A01G390100 chr3B 171120244 171120916 672 False 1101 1101 96.2850 1 669 1 chr3B.!!$F1 668
10 TraesCS5A01G390100 chr3B 247809139 247809810 671 False 1101 1101 96.2800 1 670 1 chr3B.!!$F2 669
11 TraesCS5A01G390100 chr6B 646915179 646915863 684 True 1098 1098 95.6200 1 683 1 chr6B.!!$R1 682


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
918 942 1.597797 TAACCGATCCGACAACCGCT 61.598 55.0 0.0 0.0 36.84 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2570 0.106149 AGCGTGTTCCTCTTTTCCGT 59.894 50.0 0.0 0.0 0.0 4.69 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)



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AutoCloner maintained by Alex Coulton.