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
TraesCS4D01G152200
chr4D
100.000
3063
0
0
467
3529
180194385
180191323
0.000000e+00
5657.0
1
TraesCS4D01G152200
chr4D
100.000
40
0
0
1
40
180194851
180194812
1.360000e-09
75.0
2
TraesCS4D01G152200
chrUn
97.554
3066
47
11
467
3529
56132558
56129518
0.000000e+00
5221.0
3
TraesCS4D01G152200
chrUn
100.000
29
0
0
12
40
56132673
56132645
2.000000e-03
54.7
4
TraesCS4D01G152200
chr4A
96.395
3079
76
7
467
3528
296906211
296903151
0.000000e+00
5038.0
5
TraesCS4D01G152200
chr7B
100.000
28
0
0
873
900
231094248
231094221
6.000000e-03
52.8
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
TraesCS4D01G152200
chr4D
180191323
180194851
3528
True
2866.00
5657
100.000
1
3529
2
chr4D.!!$R1
3528
1
TraesCS4D01G152200
chrUn
56129518
56132673
3155
True
2637.85
5221
98.777
12
3529
2
chrUn.!!$R1
3517
2
TraesCS4D01G152200
chr4A
296903151
296906211
3060
True
5038.00
5038
96.395
467
3528
1
chr4A.!!$R1
3061
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.