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
TraesCS3B01G343700
chr3B
100.000
2504
0
0
1
2504
552490508
552488005
0
4625
1
TraesCS3B01G343700
chr5B
99.042
2504
19
5
1
2502
179239832
179237332
0
4486
2
TraesCS3B01G343700
chr5B
98.840
2500
25
4
1
2500
420729577
420727082
0
4453
3
TraesCS3B01G343700
chr5B
98.642
2504
27
7
1
2501
406858243
406860742
0
4429
4
TraesCS3B01G343700
chr2A
99.041
2503
19
5
1
2500
719466166
719463666
0
4484
5
TraesCS3B01G343700
chr7B
98.761
2503
25
6
1
2500
68109801
68107302
0
4446
6
TraesCS3B01G343700
chr7B
98.722
2504
27
5
1
2500
528912472
528909970
0
4442
7
TraesCS3B01G343700
chr6B
98.722
2504
24
7
1
2500
408674337
408671838
0
4440
8
TraesCS3B01G343700
chr6B
98.682
2504
27
6
1
2501
704838302
704840802
0
4436
9
TraesCS3B01G343700
chr7A
98.602
2504
30
5
1
2501
171431011
171428510
0
4425
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
TraesCS3B01G343700
chr3B
552488005
552490508
2503
True
4625
4625
100.000
1
2504
1
chr3B.!!$R1
2503
1
TraesCS3B01G343700
chr5B
179237332
179239832
2500
True
4486
4486
99.042
1
2502
1
chr5B.!!$R1
2501
2
TraesCS3B01G343700
chr5B
420727082
420729577
2495
True
4453
4453
98.840
1
2500
1
chr5B.!!$R2
2499
3
TraesCS3B01G343700
chr5B
406858243
406860742
2499
False
4429
4429
98.642
1
2501
1
chr5B.!!$F1
2500
4
TraesCS3B01G343700
chr2A
719463666
719466166
2500
True
4484
4484
99.041
1
2500
1
chr2A.!!$R1
2499
5
TraesCS3B01G343700
chr7B
68107302
68109801
2499
True
4446
4446
98.761
1
2500
1
chr7B.!!$R1
2499
6
TraesCS3B01G343700
chr7B
528909970
528912472
2502
True
4442
4442
98.722
1
2500
1
chr7B.!!$R2
2499
7
TraesCS3B01G343700
chr6B
408671838
408674337
2499
True
4440
4440
98.722
1
2500
1
chr6B.!!$R1
2499
8
TraesCS3B01G343700
chr6B
704838302
704840802
2500
False
4436
4436
98.682
1
2501
1
chr6B.!!$F1
2500
9
TraesCS3B01G343700
chr7A
171428510
171431011
2501
True
4425
4425
98.602
1
2501
1
chr7A.!!$R1
2500
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.