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
TraesCS3A01G502600
chr3A
100.000
2594
0
0
1
2594
725796715
725799308
0
4791
1
TraesCS3A01G502600
chr5A
98.305
2596
42
2
1
2594
19248878
19246283
0
4549
2
TraesCS3A01G502600
chr7D
98.304
2595
43
1
1
2594
381923967
381926561
0
4547
3
TraesCS3A01G502600
chr7D
98.151
2596
46
2
1
2594
382050044
382052639
0
4527
4
TraesCS3A01G502600
chr7D
98.150
2595
47
1
1
2594
203499965
203502559
0
4525
5
TraesCS3A01G502600
chr7D
97.962
2600
44
3
1
2594
381973801
381971205
0
4499
6
TraesCS3A01G502600
chr7B
97.996
2595
45
3
1
2594
716878814
716876226
0
4497
7
TraesCS3A01G502600
chr7B
97.612
2596
54
4
1
2594
742989412
742992001
0
4444
8
TraesCS3A01G502600
chr7A
97.803
2595
51
2
1
2594
60279279
60281868
0
4471
9
TraesCS3A01G502600
chr3B
96.495
2596
81
5
1
2594
797592968
797590381
0
4281
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
TraesCS3A01G502600
chr3A
725796715
725799308
2593
False
4791
4791
100.000
1
2594
1
chr3A.!!$F1
2593
1
TraesCS3A01G502600
chr5A
19246283
19248878
2595
True
4549
4549
98.305
1
2594
1
chr5A.!!$R1
2593
2
TraesCS3A01G502600
chr7D
381923967
381926561
2594
False
4547
4547
98.304
1
2594
1
chr7D.!!$F2
2593
3
TraesCS3A01G502600
chr7D
382050044
382052639
2595
False
4527
4527
98.151
1
2594
1
chr7D.!!$F3
2593
4
TraesCS3A01G502600
chr7D
203499965
203502559
2594
False
4525
4525
98.150
1
2594
1
chr7D.!!$F1
2593
5
TraesCS3A01G502600
chr7D
381971205
381973801
2596
True
4499
4499
97.962
1
2594
1
chr7D.!!$R1
2593
6
TraesCS3A01G502600
chr7B
716876226
716878814
2588
True
4497
4497
97.996
1
2594
1
chr7B.!!$R1
2593
7
TraesCS3A01G502600
chr7B
742989412
742992001
2589
False
4444
4444
97.612
1
2594
1
chr7B.!!$F1
2593
8
TraesCS3A01G502600
chr7A
60279279
60281868
2589
False
4471
4471
97.803
1
2594
1
chr7A.!!$F1
2593
9
TraesCS3A01G502600
chr3B
797590381
797592968
2587
True
4281
4281
96.495
1
2594
1
chr3B.!!$R1
2593
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.