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
TraesCS5D01G056500
chr5D
100.000
2459
0
0
1
2459
52374407
52371949
0
4542
1
TraesCS5D01G056500
chr5D
97.929
2462
28
3
1
2459
422770488
422772929
0
4242
2
TraesCS5D01G056500
chr5D
97.323
2465
31
7
1
2459
282366386
282368821
0
4154
3
TraesCS5D01G056500
chr5D
97.153
2459
30
4
1
2459
356119376
356116958
0
4117
4
TraesCS5D01G056500
chr3D
97.926
2459
28
3
1
2459
52842562
52844997
0
4237
5
TraesCS5D01G056500
chr3D
98.345
1269
17
2
199
1467
534219379
534218115
0
2224
6
TraesCS5D01G056500
chr3D
96.695
938
14
1
1522
2459
534218112
534217192
0
1544
7
TraesCS5D01G056500
chr7D
97.888
2462
26
3
1
2459
634767962
634770400
0
4235
8
TraesCS5D01G056500
chr7D
97.235
2459
25
6
1
2459
426837116
426834701
0
4124
9
TraesCS5D01G056500
chr7D
96.921
2468
44
6
1
2459
538836171
538838615
0
4108
10
TraesCS5D01G056500
chr7D
96.764
2472
50
4
1
2459
112191189
112188735
0
4095
11
TraesCS5D01G056500
chr7D
97.050
1593
32
6
1
1579
445229045
445230636
0
2667
12
TraesCS5D01G056500
chr4D
97.693
2471
26
5
1
2459
392724726
392722275
0
4218
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
TraesCS5D01G056500
chr5D
52371949
52374407
2458
True
4542
4542
100.000
1
2459
1
chr5D.!!$R1
2458
1
TraesCS5D01G056500
chr5D
422770488
422772929
2441
False
4242
4242
97.929
1
2459
1
chr5D.!!$F2
2458
2
TraesCS5D01G056500
chr5D
282366386
282368821
2435
False
4154
4154
97.323
1
2459
1
chr5D.!!$F1
2458
3
TraesCS5D01G056500
chr5D
356116958
356119376
2418
True
4117
4117
97.153
1
2459
1
chr5D.!!$R2
2458
4
TraesCS5D01G056500
chr3D
52842562
52844997
2435
False
4237
4237
97.926
1
2459
1
chr3D.!!$F1
2458
5
TraesCS5D01G056500
chr3D
534217192
534219379
2187
True
1884
2224
97.520
199
2459
2
chr3D.!!$R1
2260
6
TraesCS5D01G056500
chr7D
634767962
634770400
2438
False
4235
4235
97.888
1
2459
1
chr7D.!!$F3
2458
7
TraesCS5D01G056500
chr7D
426834701
426837116
2415
True
4124
4124
97.235
1
2459
1
chr7D.!!$R2
2458
8
TraesCS5D01G056500
chr7D
538836171
538838615
2444
False
4108
4108
96.921
1
2459
1
chr7D.!!$F2
2458
9
TraesCS5D01G056500
chr7D
112188735
112191189
2454
True
4095
4095
96.764
1
2459
1
chr7D.!!$R1
2458
10
TraesCS5D01G056500
chr7D
445229045
445230636
1591
False
2667
2667
97.050
1
1579
1
chr7D.!!$F1
1578
11
TraesCS5D01G056500
chr4D
392722275
392724726
2451
True
4218
4218
97.693
1
2459
1
chr4D.!!$R1
2458
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.