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
TraesCS7D01G054100
chr7D
100.000
2548
0
0
1
2548
28674016
28676563
0.000000e+00
4706
1
TraesCS7D01G054100
chr7D
87.093
2394
246
37
1
2359
28695993
28698358
0.000000e+00
2651
2
TraesCS7D01G054100
chr4A
88.516
2203
201
26
292
2466
702398791
702400969
0.000000e+00
2619
3
TraesCS7D01G054100
chr4A
86.174
2394
263
39
74
2428
701313074
701310710
0.000000e+00
2525
4
TraesCS7D01G054100
chr4A
91.673
1369
74
19
795
2142
702380993
702382342
0.000000e+00
1860
5
TraesCS7D01G054100
chr4A
93.293
820
45
6
1
819
702380163
702380973
0.000000e+00
1201
6
TraesCS7D01G054100
chr4A
85.753
1116
131
16
853
1949
702339892
702340998
0.000000e+00
1155
7
TraesCS7D01G054100
chr4A
85.884
843
99
6
853
1678
702505160
702505999
0.000000e+00
880
8
TraesCS7D01G054100
chr4A
83.079
656
98
11
1
652
702504403
702505049
3.650000e-163
584
9
TraesCS7D01G054100
chr4A
94.595
333
16
2
2217
2548
702382348
702382679
4.860000e-142
514
10
TraesCS7D01G054100
chr7A
86.683
2403
249
38
1
2374
29109736
29112096
0.000000e+00
2599
11
TraesCS7D01G054100
chr7A
90.350
1627
128
18
1
1611
29032424
29034037
0.000000e+00
2108
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
TraesCS7D01G054100
chr7D
28674016
28676563
2547
False
4706.000000
4706
100.0000
1
2548
1
chr7D.!!$F1
2547
1
TraesCS7D01G054100
chr7D
28695993
28698358
2365
False
2651.000000
2651
87.0930
1
2359
1
chr7D.!!$F2
2358
2
TraesCS7D01G054100
chr4A
702398791
702400969
2178
False
2619.000000
2619
88.5160
292
2466
1
chr4A.!!$F2
2174
3
TraesCS7D01G054100
chr4A
701310710
701313074
2364
True
2525.000000
2525
86.1740
74
2428
1
chr4A.!!$R1
2354
4
TraesCS7D01G054100
chr4A
702380163
702382679
2516
False
1191.666667
1860
93.1870
1
2548
3
chr4A.!!$F3
2547
5
TraesCS7D01G054100
chr4A
702339892
702340998
1106
False
1155.000000
1155
85.7530
853
1949
1
chr4A.!!$F1
1096
6
TraesCS7D01G054100
chr4A
702504403
702505999
1596
False
732.000000
880
84.4815
1
1678
2
chr4A.!!$F4
1677
7
TraesCS7D01G054100
chr7A
29109736
29112096
2360
False
2599.000000
2599
86.6830
1
2374
1
chr7A.!!$F2
2373
8
TraesCS7D01G054100
chr7A
29032424
29034037
1613
False
2108.000000
2108
90.3500
1
1611
1
chr7A.!!$F1
1610
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.