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
TraesCS1D01G128200
chr1D
100.000
2483
0
0
1
2483
141316693
141319175
0
4586
1
TraesCS1D01G128200
chr7D
99.517
2484
11
1
1
2483
381958719
381961202
0
4519
2
TraesCS1D01G128200
chr7D
99.436
2484
13
1
1
2483
382065120
382062637
0
4508
3
TraesCS1D01G128200
chr7D
99.155
2485
18
3
1
2483
626682793
626685276
0
4470
4
TraesCS1D01G128200
chr7D
98.954
2485
22
3
1
2483
203515035
203512553
0
4442
5
TraesCS1D01G128200
chr7D
97.143
420
12
0
1
420
306895788
306895369
0
710
6
TraesCS1D01G128200
chr6D
99.517
2484
11
1
1
2483
124532564
124530081
0
4519
7
TraesCS1D01G128200
chr7B
99.276
2485
16
1
1
2483
644463886
644461402
0
4488
8
TraesCS1D01G128200
chrUn
99.236
2487
15
3
1
2483
189407526
189405040
0
4484
9
TraesCS1D01G128200
chr6B
98.431
2485
27
6
1
2483
306999548
307002022
0
4362
10
TraesCS1D01G128200
chr5A
98.137
2147
39
1
338
2483
157783623
157781477
0
3742
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
TraesCS1D01G128200
chr1D
141316693
141319175
2482
False
4586
4586
100.000
1
2483
1
chr1D.!!$F1
2482
1
TraesCS1D01G128200
chr7D
381958719
381961202
2483
False
4519
4519
99.517
1
2483
1
chr7D.!!$F1
2482
2
TraesCS1D01G128200
chr7D
382062637
382065120
2483
True
4508
4508
99.436
1
2483
1
chr7D.!!$R3
2482
3
TraesCS1D01G128200
chr7D
626682793
626685276
2483
False
4470
4470
99.155
1
2483
1
chr7D.!!$F2
2482
4
TraesCS1D01G128200
chr7D
203512553
203515035
2482
True
4442
4442
98.954
1
2483
1
chr7D.!!$R1
2482
5
TraesCS1D01G128200
chr6D
124530081
124532564
2483
True
4519
4519
99.517
1
2483
1
chr6D.!!$R1
2482
6
TraesCS1D01G128200
chr7B
644461402
644463886
2484
True
4488
4488
99.276
1
2483
1
chr7B.!!$R1
2482
7
TraesCS1D01G128200
chrUn
189405040
189407526
2486
True
4484
4484
99.236
1
2483
1
chrUn.!!$R1
2482
8
TraesCS1D01G128200
chr6B
306999548
307002022
2474
False
4362
4362
98.431
1
2483
1
chr6B.!!$F1
2482
9
TraesCS1D01G128200
chr5A
157781477
157783623
2146
True
3742
3742
98.137
338
2483
1
chr5A.!!$R1
2145
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.