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
TraesCS1A01G184200
chr1A
100.000
3536
0
0
1
3536
334076924
334073389
0.000000e+00
6530
1
TraesCS1A01G184200
chr2D
97.715
3239
69
4
1
3235
635037258
635040495
0.000000e+00
5566
2
TraesCS1A01G184200
chr7B
97.684
3239
69
2
1
3233
743066303
743069541
0.000000e+00
5561
3
TraesCS1A01G184200
chr7B
96.382
304
8
2
3234
3536
743073145
743073446
6.820000e-137
497
4
TraesCS1A01G184200
chr3D
97.654
3239
72
3
1
3235
202611944
202615182
0.000000e+00
5557
5
TraesCS1A01G184200
chr5A
97.595
3243
70
3
1
3235
16623277
16620035
0.000000e+00
5550
6
TraesCS1A01G184200
chr7A
97.593
3240
72
3
1
3235
671960570
671957332
0.000000e+00
5546
7
TraesCS1A01G184200
chr7A
97.529
3238
74
4
1
3235
120828850
120825616
0.000000e+00
5531
8
TraesCS1A01G184200
chr7A
96.040
303
10
1
3234
3536
120918865
120918565
3.170000e-135
492
9
TraesCS1A01G184200
chr4D
97.532
3242
71
4
1
3235
123367640
123370879
0.000000e+00
5535
10
TraesCS1A01G184200
chr4D
95.395
304
11
2
3234
3536
123374638
123374939
6.870000e-132
481
11
TraesCS1A01G184200
chr4D
95.395
304
8
2
3234
3536
123585429
123585727
2.470000e-131
479
12
TraesCS1A01G184200
chr2A
97.502
3242
72
4
1
3235
735172797
735176036
0.000000e+00
5529
13
TraesCS1A01G184200
chr4A
97.467
3237
78
4
1
3235
432419669
432422903
0.000000e+00
5520
14
TraesCS1A01G184200
chr4A
97.039
304
8
1
3234
3536
552102096
552101793
8.760000e-141
510
15
TraesCS1A01G184200
chr7D
96.382
304
8
2
3234
3536
382004502
382004201
6.820000e-137
497
16
TraesCS1A01G184200
chr7D
95.380
303
10
1
3234
3536
297148473
297148771
2.470000e-131
479
17
TraesCS1A01G184200
chr6B
96.370
303
9
2
3234
3535
525685045
525685346
6.820000e-137
497
18
TraesCS1A01G184200
chr3B
95.425
306
9
3
3234
3536
201628681
201628378
1.910000e-132
483
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
TraesCS1A01G184200
chr1A
334073389
334076924
3535
True
6530
6530
100.0000
1
3536
1
chr1A.!!$R1
3535
1
TraesCS1A01G184200
chr2D
635037258
635040495
3237
False
5566
5566
97.7150
1
3235
1
chr2D.!!$F1
3234
2
TraesCS1A01G184200
chr7B
743066303
743073446
7143
False
3029
5561
97.0330
1
3536
2
chr7B.!!$F1
3535
3
TraesCS1A01G184200
chr3D
202611944
202615182
3238
False
5557
5557
97.6540
1
3235
1
chr3D.!!$F1
3234
4
TraesCS1A01G184200
chr5A
16620035
16623277
3242
True
5550
5550
97.5950
1
3235
1
chr5A.!!$R1
3234
5
TraesCS1A01G184200
chr7A
671957332
671960570
3238
True
5546
5546
97.5930
1
3235
1
chr7A.!!$R3
3234
6
TraesCS1A01G184200
chr7A
120825616
120828850
3234
True
5531
5531
97.5290
1
3235
1
chr7A.!!$R1
3234
7
TraesCS1A01G184200
chr4D
123367640
123374939
7299
False
3008
5535
96.4635
1
3536
2
chr4D.!!$F2
3535
8
TraesCS1A01G184200
chr2A
735172797
735176036
3239
False
5529
5529
97.5020
1
3235
1
chr2A.!!$F1
3234
9
TraesCS1A01G184200
chr4A
432419669
432422903
3234
False
5520
5520
97.4670
1
3235
1
chr4A.!!$F1
3234
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.