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
TraesCS4B01G081300
chr4B
100.000
2450
0
0
1
2450
78829610
78827161
0
4525
1
TraesCS4B01G081300
chr1B
94.237
2464
107
23
1
2450
106887645
106890087
0
3731
2
TraesCS4B01G081300
chr6B
92.110
2446
176
12
1
2440
459691961
459694395
0
3432
3
TraesCS4B01G081300
chr5B
90.269
2456
211
20
1
2450
547746192
547748625
0
3186
4
TraesCS4B01G081300
chr5B
90.269
2456
211
19
1
2450
547767243
547769676
0
3186
5
TraesCS4B01G081300
chr5B
90.228
2456
212
19
1
2450
547751734
547754167
0
3181
6
TraesCS4B01G081300
chr5B
90.187
2456
212
18
1
2450
547756796
547759228
0
3173
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
TraesCS4B01G081300
chr4B
78827161
78829610
2449
True
4525
4525
100.000
1
2450
1
chr4B.!!$R1
2449
1
TraesCS4B01G081300
chr1B
106887645
106890087
2442
False
3731
3731
94.237
1
2450
1
chr1B.!!$F1
2449
2
TraesCS4B01G081300
chr6B
459691961
459694395
2434
False
3432
3432
92.110
1
2440
1
chr6B.!!$F1
2439
3
TraesCS4B01G081300
chr5B
547767243
547769676
2433
False
3186
3186
90.269
1
2450
1
chr5B.!!$F1
2449
4
TraesCS4B01G081300
chr5B
547746192
547759228
13036
False
3180
3186
90.228
1
2450
3
chr5B.!!$F2
2449
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.