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
TraesCS3B01G188000
chr3B
100.000
2177
0
0
1
2177
201537274
201535098
0
4021
1
TraesCS3B01G188000
chr6D
98.852
2178
24
1
1
2177
389254923
389252746
0
3882
2
TraesCS3B01G188000
chr3A
98.760
2178
25
2
1
2177
66007378
66009554
0
3871
3
TraesCS3B01G188000
chr3A
98.026
2178
42
1
1
2177
672899767
672901944
0
3783
4
TraesCS3B01G188000
chr5D
98.714
2178
26
2
1
2177
503238780
503236604
0
3866
5
TraesCS3B01G188000
chr5D
98.801
2168
24
2
11
2177
503243019
503240853
0
3858
6
TraesCS3B01G188000
chrUn
98.531
2179
27
3
1
2177
216508364
216510539
0
3842
7
TraesCS3B01G188000
chr2A
97.888
2178
45
1
1
2177
335845066
335842889
0
3766
8
TraesCS3B01G188000
chr2B
97.750
2178
48
1
1
2177
474918684
474916507
0
3749
9
TraesCS3B01G188000
chr1B
97.612
2178
45
2
1
2177
633743659
633745830
0
3727
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
TraesCS3B01G188000
chr3B
201535098
201537274
2176
True
4021
4021
100.0000
1
2177
1
chr3B.!!$R1
2176
1
TraesCS3B01G188000
chr6D
389252746
389254923
2177
True
3882
3882
98.8520
1
2177
1
chr6D.!!$R1
2176
2
TraesCS3B01G188000
chr3A
66007378
66009554
2176
False
3871
3871
98.7600
1
2177
1
chr3A.!!$F1
2176
3
TraesCS3B01G188000
chr3A
672899767
672901944
2177
False
3783
3783
98.0260
1
2177
1
chr3A.!!$F2
2176
4
TraesCS3B01G188000
chr5D
503236604
503243019
6415
True
3862
3866
98.7575
1
2177
2
chr5D.!!$R1
2176
5
TraesCS3B01G188000
chrUn
216508364
216510539
2175
False
3842
3842
98.5310
1
2177
1
chrUn.!!$F1
2176
6
TraesCS3B01G188000
chr2A
335842889
335845066
2177
True
3766
3766
97.8880
1
2177
1
chr2A.!!$R1
2176
7
TraesCS3B01G188000
chr2B
474916507
474918684
2177
True
3749
3749
97.7500
1
2177
1
chr2B.!!$R1
2176
8
TraesCS3B01G188000
chr1B
633743659
633745830
2171
False
3727
3727
97.6120
1
2177
1
chr1B.!!$F1
2176
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.