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
TraesCS3B01G188100
chr3B
100.000
2255
0
0
1
2255
201537588
201535334
0
4165
1
TraesCS3B01G188100
chr6D
98.848
2256
25
1
1
2255
389255237
389252982
0
4021
2
TraesCS3B01G188100
chr6D
98.715
2256
28
1
1
2255
389250442
389248187
0
4004
3
TraesCS3B01G188100
chr3A
98.670
2256
28
2
1
2255
66007064
66009318
0
3999
4
TraesCS3B01G188100
chr3D
98.582
2256
30
2
1
2255
589265455
589267709
0
3988
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
TraesCS3B01G188100
chr3B
201535334
201537588
2254
True
4165.0
4165
100.0000
1
2255
1
chr3B.!!$R1
2254
1
TraesCS3B01G188100
chr6D
389248187
389255237
7050
True
4012.5
4021
98.7815
1
2255
2
chr6D.!!$R1
2254
2
TraesCS3B01G188100
chr3A
66007064
66009318
2254
False
3999.0
3999
98.6700
1
2255
1
chr3A.!!$F1
2254
3
TraesCS3B01G188100
chr3D
589265455
589267709
2254
False
3988.0
3988
98.5820
1
2255
1
chr3D.!!$F1
2254
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.
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.