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
TraesCS6B01G093800
chr6B
100.000
4723
0
0
1
4723
69705566
69700844
0
8722
1
TraesCS6B01G093800
chr3A
98.583
4729
58
9
1
4723
212717365
212712640
0
8353
2
TraesCS6B01G093800
chr2A
98.498
4728
65
6
1
4723
306631056
306626330
0
8333
3
TraesCS6B01G093800
chr2A
98.287
4728
74
7
1
4723
740477620
740472895
0
8275
4
TraesCS6B01G093800
chr3B
98.435
4727
68
6
1
4723
193965014
193969738
0
8314
5
TraesCS6B01G093800
chr3B
98.308
4728
73
7
1
4723
542902183
542906908
0
8281
6
TraesCS6B01G093800
chr3B
98.287
4728
73
8
1
4723
798434504
798429780
0
8275
7
TraesCS6B01G093800
chr7B
98.371
4728
70
7
1
4723
147718769
147714044
0
8298
8
TraesCS6B01G093800
chr7A
98.287
4729
73
8
1
4723
457566305
457561579
0
8277
9
TraesCS6B01G093800
chr5B
98.267
4732
71
11
1
4723
158895547
158890818
0
8274
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
TraesCS6B01G093800
chr6B
69700844
69705566
4722
True
8722
8722
100.000
1
4723
1
chr6B.!!$R1
4722
1
TraesCS6B01G093800
chr3A
212712640
212717365
4725
True
8353
8353
98.583
1
4723
1
chr3A.!!$R1
4722
2
TraesCS6B01G093800
chr2A
306626330
306631056
4726
True
8333
8333
98.498
1
4723
1
chr2A.!!$R1
4722
3
TraesCS6B01G093800
chr2A
740472895
740477620
4725
True
8275
8275
98.287
1
4723
1
chr2A.!!$R2
4722
4
TraesCS6B01G093800
chr3B
193965014
193969738
4724
False
8314
8314
98.435
1
4723
1
chr3B.!!$F1
4722
5
TraesCS6B01G093800
chr3B
542902183
542906908
4725
False
8281
8281
98.308
1
4723
1
chr3B.!!$F2
4722
6
TraesCS6B01G093800
chr3B
798429780
798434504
4724
True
8275
8275
98.287
1
4723
1
chr3B.!!$R1
4722
7
TraesCS6B01G093800
chr7B
147714044
147718769
4725
True
8298
8298
98.371
1
4723
1
chr7B.!!$R1
4722
8
TraesCS6B01G093800
chr7A
457561579
457566305
4726
True
8277
8277
98.287
1
4723
1
chr7A.!!$R1
4722
9
TraesCS6B01G093800
chr5B
158890818
158895547
4729
True
8274
8274
98.267
1
4723
1
chr5B.!!$R1
4722
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.