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
TraesCS7D01G238700
chr7D
100.000
2483
0
0
1
2483
203515035
203512553
0
4586
1
TraesCS7D01G238700
chr7D
99.034
2485
21
2
1
2483
381958719
381961202
0
4453
2
TraesCS7D01G238700
chr7D
98.954
2485
23
2
1
2483
382065120
382062637
0
4442
3
TraesCS7D01G238700
chr7D
98.833
2486
24
4
1
2483
626682793
626685276
0
4425
4
TraesCS7D01G238700
chr6D
99.034
2485
21
2
1
2483
124532564
124530081
0
4453
5
TraesCS7D01G238700
chr1D
98.954
2485
22
3
1
2483
141316693
141319175
0
4442
6
TraesCS7D01G238700
chrUn
98.834
2488
23
5
1
2483
189407526
189405040
0
4429
7
TraesCS7D01G238700
chr7B
98.833
2486
25
3
1
2483
644463886
644461402
0
4427
8
TraesCS7D01G238700
chr3A
98.551
2485
33
2
1
2483
633107698
633105215
0
4386
9
TraesCS7D01G238700
chr1B
98.513
2489
30
4
1
2483
668808717
668811204
0
4385
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
TraesCS7D01G238700
chr7D
203512553
203515035
2482
True
4586
4586
100.000
1
2483
1
chr7D.!!$R1
2482
1
TraesCS7D01G238700
chr7D
381958719
381961202
2483
False
4453
4453
99.034
1
2483
1
chr7D.!!$F1
2482
2
TraesCS7D01G238700
chr7D
382062637
382065120
2483
True
4442
4442
98.954
1
2483
1
chr7D.!!$R2
2482
3
TraesCS7D01G238700
chr7D
626682793
626685276
2483
False
4425
4425
98.833
1
2483
1
chr7D.!!$F2
2482
4
TraesCS7D01G238700
chr6D
124530081
124532564
2483
True
4453
4453
99.034
1
2483
1
chr6D.!!$R1
2482
5
TraesCS7D01G238700
chr1D
141316693
141319175
2482
False
4442
4442
98.954
1
2483
1
chr1D.!!$F1
2482
6
TraesCS7D01G238700
chrUn
189405040
189407526
2486
True
4429
4429
98.834
1
2483
1
chrUn.!!$R1
2482
7
TraesCS7D01G238700
chr7B
644461402
644463886
2484
True
4427
4427
98.833
1
2483
1
chr7B.!!$R1
2482
8
TraesCS7D01G238700
chr3A
633105215
633107698
2483
True
4386
4386
98.551
1
2483
1
chr3A.!!$R1
2482
9
TraesCS7D01G238700
chr1B
668808717
668811204
2487
False
4385
4385
98.513
1
2483
1
chr1B.!!$F1
2482
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.