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
TraesCS6D01G186100
chr6D
100.000
3068
0
0
1
3068
243425648
243422581
0.000000e+00
5666.0
1
TraesCS6D01G186100
chr6D
96.016
2485
74
8
590
3068
243450502
243448037
0.000000e+00
4017.0
2
TraesCS6D01G186100
chr6A
95.276
868
36
3
590
1455
333958976
333959840
0.000000e+00
1371.0
3
TraesCS6D01G186100
chr6A
94.034
771
40
4
1745
2511
333960323
333961091
0.000000e+00
1164.0
4
TraesCS6D01G186100
chr6A
98.635
293
4
0
1457
1749
333959874
333960166
1.260000e-143
520.0
5
TraesCS6D01G186100
chr6B
94.816
868
36
3
590
1455
334453353
334452493
0.000000e+00
1345.0
6
TraesCS6D01G186100
chr6B
93.759
689
20
6
1457
2143
334452334
334451667
0.000000e+00
1013.0
7
TraesCS6D01G186100
chr6B
90.365
384
24
6
2196
2578
334451547
334451176
2.750000e-135
492.0
8
TraesCS6D01G186100
chr6B
87.192
203
24
1
2594
2796
334444536
334444336
2.380000e-56
230.0
9
TraesCS6D01G186100
chr1D
92.712
590
42
1
1
589
195845841
195846430
0.000000e+00
850.0
10
TraesCS6D01G186100
chr1D
89.262
596
58
6
1
591
50669367
50668773
0.000000e+00
741.0
11
TraesCS6D01G186100
chr5D
89.769
606
53
8
1
600
355731639
355732241
0.000000e+00
767.0
12
TraesCS6D01G186100
chr7D
89.580
595
53
8
1
589
492164925
492164334
0.000000e+00
747.0
13
TraesCS6D01G186100
chr7D
89.262
596
54
7
1
589
244492137
244491545
0.000000e+00
737.0
14
TraesCS6D01G186100
chr2D
89.412
595
56
5
1
589
150731239
150731832
0.000000e+00
743.0
15
TraesCS6D01G186100
chr2D
89.376
593
57
6
1
589
540010470
540009880
0.000000e+00
741.0
16
TraesCS6D01G186100
chr2D
89.226
594
53
9
4
589
531564280
531563690
0.000000e+00
732.0
17
TraesCS6D01G186100
chr2D
93.617
47
3
0
590
636
605107471
605107425
1.530000e-08
71.3
18
TraesCS6D01G186100
chr4D
89.112
597
53
10
1
589
114024325
114024917
0.000000e+00
732.0
19
TraesCS6D01G186100
chr4A
96.970
33
1
0
645
677
681713068
681713100
4.270000e-04
56.5
20
TraesCS6D01G186100
chr3D
100.000
29
0
0
645
673
254114671
254114643
2.000000e-03
54.7
21
TraesCS6D01G186100
chr2A
100.000
28
0
0
645
672
130809850
130809823
6.000000e-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
TraesCS6D01G186100
chr6D
243422581
243425648
3067
True
5666.000000
5666
100.000000
1
3068
1
chr6D.!!$R1
3067
1
TraesCS6D01G186100
chr6D
243448037
243450502
2465
True
4017.000000
4017
96.016000
590
3068
1
chr6D.!!$R2
2478
2
TraesCS6D01G186100
chr6A
333958976
333961091
2115
False
1018.333333
1371
95.981667
590
2511
3
chr6A.!!$F1
1921
3
TraesCS6D01G186100
chr6B
334451176
334453353
2177
True
950.000000
1345
92.980000
590
2578
3
chr6B.!!$R2
1988
4
TraesCS6D01G186100
chr1D
195845841
195846430
589
False
850.000000
850
92.712000
1
589
1
chr1D.!!$F1
588
5
TraesCS6D01G186100
chr1D
50668773
50669367
594
True
741.000000
741
89.262000
1
591
1
chr1D.!!$R1
590
6
TraesCS6D01G186100
chr5D
355731639
355732241
602
False
767.000000
767
89.769000
1
600
1
chr5D.!!$F1
599
7
TraesCS6D01G186100
chr7D
492164334
492164925
591
True
747.000000
747
89.580000
1
589
1
chr7D.!!$R2
588
8
TraesCS6D01G186100
chr7D
244491545
244492137
592
True
737.000000
737
89.262000
1
589
1
chr7D.!!$R1
588
9
TraesCS6D01G186100
chr2D
150731239
150731832
593
False
743.000000
743
89.412000
1
589
1
chr2D.!!$F1
588
10
TraesCS6D01G186100
chr2D
540009880
540010470
590
True
741.000000
741
89.376000
1
589
1
chr2D.!!$R2
588
11
TraesCS6D01G186100
chr2D
531563690
531564280
590
True
732.000000
732
89.226000
4
589
1
chr2D.!!$R1
585
12
TraesCS6D01G186100
chr4D
114024325
114024917
592
False
732.000000
732
89.112000
1
589
1
chr4D.!!$F1
588
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.