Multiple sequence alignment - TraesCS5A01G004700

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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 TraesCS5A01G004700 chr5A 100.000 4084 0 0 1 4084 3198026 3193943 0.000000e+00 7542
1 TraesCS5A01G004700 chr5D 96.762 4077 105 7 1 4076 6454631 6458681 0.000000e+00 6772
2 TraesCS5A01G004700 chr5D 89.451 1166 100 17 2071 3218 5424520 5425680 0.000000e+00 1450
3 TraesCS5A01G004700 chr5D 86.380 558 65 6 979 1528 5423585 5424139 2.100000e-167 599


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 TraesCS5A01G004700 chr5A 3193943 3198026 4083 True 7542.0 7542 100.0000 1 4084 1 chr5A.!!$R1 4083
1 TraesCS5A01G004700 chr5D 6454631 6458681 4050 False 6772.0 6772 96.7620 1 4076 1 chr5D.!!$F1 4075
2 TraesCS5A01G004700 chr5D 5423585 5425680 2095 False 1024.5 1450 87.9155 979 3218 2 chr5D.!!$F2 2239


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
727 728 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
1869 1910 0.776451 CGCCGTTAATAGCACGCTAG 59.224 55.000 4.87 0.0 36.27 3.42 F
2531 2616 1.153549 CGGAGCTTGCCTACTCACC 60.154 63.158 0.00 0.0 34.48 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1966 0.953471 AGCGCACGCCTCAAAATACA 60.953 50.0 11.47 0.0 43.17 2.29 R
2861 2946 0.104120 AAGAAAACTTGCCGCCAACC 59.896 50.0 0.00 0.0 0.00 3.77 R
3949 4047 0.179070 TGACAACGTAGTGCTTGCCA 60.179 50.0 0.00 0.0 45.00 4.92 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.