Multiple sequence alignment - TraesCS5B01G112000

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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 TraesCS5B01G112000 chr5B 100.000 2729 0 0 1 2729 170658537 170661265 0 5040
1 TraesCS5B01G112000 chr5B 92.693 2737 186 11 1 2729 197849213 197851943 0 3934
2 TraesCS5B01G112000 chr5D 93.114 2730 172 10 4 2729 248977055 248974338 0 3986
3 TraesCS5B01G112000 chr5D 92.988 2738 174 10 1 2729 49712723 49715451 0 3976
4 TraesCS5B01G112000 chr7B 92.975 2733 177 10 1 2729 107284669 107287390 0 3969
5 TraesCS5B01G112000 chr7B 92.865 2733 178 8 1 2729 478025061 478027780 0 3951
6 TraesCS5B01G112000 chr3B 92.959 2727 181 9 7 2729 244462980 244460261 0 3962
7 TraesCS5B01G112000 chr3D 92.944 2721 180 9 1 2716 169270245 169272958 0 3951
8 TraesCS5B01G112000 chr6B 92.815 2728 180 11 4 2729 289634295 289631582 0 3938
9 TraesCS5B01G112000 chr6D 92.787 2731 179 14 1 2725 294362562 294365280 0 3936


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 TraesCS5B01G112000 chr5B 170658537 170661265 2728 False 5040 5040 100.000 1 2729 1 chr5B.!!$F1 2728
1 TraesCS5B01G112000 chr5B 197849213 197851943 2730 False 3934 3934 92.693 1 2729 1 chr5B.!!$F2 2728
2 TraesCS5B01G112000 chr5D 248974338 248977055 2717 True 3986 3986 93.114 4 2729 1 chr5D.!!$R1 2725
3 TraesCS5B01G112000 chr5D 49712723 49715451 2728 False 3976 3976 92.988 1 2729 1 chr5D.!!$F1 2728
4 TraesCS5B01G112000 chr7B 107284669 107287390 2721 False 3969 3969 92.975 1 2729 1 chr7B.!!$F1 2728
5 TraesCS5B01G112000 chr7B 478025061 478027780 2719 False 3951 3951 92.865 1 2729 1 chr7B.!!$F2 2728
6 TraesCS5B01G112000 chr3B 244460261 244462980 2719 True 3962 3962 92.959 7 2729 1 chr3B.!!$R1 2722
7 TraesCS5B01G112000 chr3D 169270245 169272958 2713 False 3951 3951 92.944 1 2716 1 chr3D.!!$F1 2715
8 TraesCS5B01G112000 chr6B 289631582 289634295 2713 True 3938 3938 92.815 4 2729 1 chr6B.!!$R1 2725
9 TraesCS5B01G112000 chr6D 294362562 294365280 2718 False 3936 3936 92.787 1 2725 1 chr6D.!!$F1 2724


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
939 949 0.038526 CGGACACGACCACTAAGCTT 60.039 55.0 3.48 3.48 44.6 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1834 0.527565 CACAAGGGCATACAAGTGGC 59.472 55.0 0.0 0.0 43.34 5.01 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.