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
TraesCS1B01G430300
chr1B
100.000
2449
0
0
1
2449
654687360
654684912
0
4523
1
TraesCS1B01G430300
chr5B
97.553
2452
57
2
1
2449
494655852
494658303
0
4193
2
TraesCS1B01G430300
chr5B
97.269
2453
63
3
1
2449
41406868
41404416
0
4156
3
TraesCS1B01G430300
chr5B
97.188
2454
63
5
1
2449
660354748
660352296
0
4145
4
TraesCS1B01G430300
chr5B
97.146
2453
64
5
1
2449
494664111
494661661
0
4137
5
TraesCS1B01G430300
chr2B
97.391
2453
60
3
1
2449
50469407
50471859
0
4172
6
TraesCS1B01G430300
chr2B
97.268
2452
63
4
1
2449
66032270
66029820
0
4154
7
TraesCS1B01G430300
chr6B
96.983
2453
70
3
1
2449
663151559
663149107
0
4117
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
TraesCS1B01G430300
chr1B
654684912
654687360
2448
True
4523
4523
100.000
1
2449
1
chr1B.!!$R1
2448
1
TraesCS1B01G430300
chr5B
494655852
494658303
2451
False
4193
4193
97.553
1
2449
1
chr5B.!!$F1
2448
2
TraesCS1B01G430300
chr5B
41404416
41406868
2452
True
4156
4156
97.269
1
2449
1
chr5B.!!$R1
2448
3
TraesCS1B01G430300
chr5B
660352296
660354748
2452
True
4145
4145
97.188
1
2449
1
chr5B.!!$R3
2448
4
TraesCS1B01G430300
chr5B
494661661
494664111
2450
True
4137
4137
97.146
1
2449
1
chr5B.!!$R2
2448
5
TraesCS1B01G430300
chr2B
50469407
50471859
2452
False
4172
4172
97.391
1
2449
1
chr2B.!!$F1
2448
6
TraesCS1B01G430300
chr2B
66029820
66032270
2450
True
4154
4154
97.268
1
2449
1
chr2B.!!$R1
2448
7
TraesCS1B01G430300
chr6B
663149107
663151559
2452
True
4117
4117
96.983
1
2449
1
chr6B.!!$R1
2448
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.