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
TraesCS1D01G138900
chr1D
100.000
2574
0
0
1
2574
190762425
190764998
0.000000e+00
4754.0
1
TraesCS1D01G138900
chr1B
96.785
2582
44
11
1
2574
264341030
264343580
0.000000e+00
4272.0
2
TraesCS1D01G138900
chr1A
91.565
1316
59
16
252
1567
168553184
168554447
0.000000e+00
1768.0
3
TraesCS1D01G138900
chr1A
95.030
825
31
3
1595
2414
168554507
168555326
0.000000e+00
1288.0
4
TraesCS1D01G138900
chr1A
89.474
152
15
1
1
151
168547454
168547605
9.400000e-45
191.0
5
TraesCS1D01G138900
chr1A
94.915
59
3
0
2414
2472
168567459
168567517
2.730000e-15
93.5
6
TraesCS1D01G138900
chr7B
93.333
45
2
1
170
214
285360215
285360258
5.940000e-07
65.8
7
TraesCS1D01G138900
chr7A
95.122
41
2
0
174
214
367010832
367010872
5.940000e-07
65.8
8
TraesCS1D01G138900
chr7D
90.698
43
3
1
177
219
303313591
303313550
3.580000e-04
56.5
9
TraesCS1D01G138900
chrUn
100.000
28
0
0
187
214
284606602
284606575
5.000000e-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
TraesCS1D01G138900
chr1D
190762425
190764998
2573
False
4754
4754
100.0000
1
2574
1
chr1D.!!$F1
2573
1
TraesCS1D01G138900
chr1B
264341030
264343580
2550
False
4272
4272
96.7850
1
2574
1
chr1B.!!$F1
2573
2
TraesCS1D01G138900
chr1A
168553184
168555326
2142
False
1528
1768
93.2975
252
2414
2
chr1A.!!$F3
2162
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.