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
TraesCS5D01G313300
chr5D
100.000
3205
0
0
1
3205
408555956
408552752
0.000000e+00
5919
1
TraesCS5D01G313300
chr5D
95.137
987
39
4
610
1595
545533140
545534118
0.000000e+00
1548
2
TraesCS5D01G313300
chr7D
97.769
2600
50
6
612
3205
92234553
92231956
0.000000e+00
4473
3
TraesCS5D01G313300
chr7D
97.499
2599
43
12
613
3205
631818589
631816007
0.000000e+00
4420
4
TraesCS5D01G313300
chr3D
97.306
2598
48
12
613
3205
45063224
45060644
0.000000e+00
4390
5
TraesCS5D01G313300
chr3D
85.924
2657
201
73
615
3180
502048028
502045454
0.000000e+00
2675
6
TraesCS5D01G313300
chr1D
96.964
2602
53
8
613
3205
414451242
414448658
0.000000e+00
4344
7
TraesCS5D01G313300
chr1D
93.110
987
41
8
612
1595
444898363
444899325
0.000000e+00
1421
8
TraesCS5D01G313300
chr4B
91.622
2614
154
38
613
3184
657805507
657802917
0.000000e+00
3554
9
TraesCS5D01G313300
chr5A
91.742
2555
152
32
614
3140
650150479
650153002
0.000000e+00
3494
10
TraesCS5D01G313300
chr5A
91.000
200
11
2
408
606
514453674
514453481
2.450000e-66
263
11
TraesCS5D01G313300
chr2A
91.751
2558
146
33
614
3140
769227587
769230110
0.000000e+00
3494
12
TraesCS5D01G313300
chr2A
91.393
2556
154
41
614
3140
115129965
115132483
0.000000e+00
3441
13
TraesCS5D01G313300
chr4A
91.585
2555
152
35
614
3140
604389451
604386932
0.000000e+00
3469
14
TraesCS5D01G313300
chr7B
87.377
1014
99
18
614
1606
591160032
591161037
0.000000e+00
1136
15
TraesCS5D01G313300
chrUn
88.069
922
69
19
616
1513
97254877
97255781
0.000000e+00
1055
16
TraesCS5D01G313300
chrUn
87.608
928
71
22
611
1513
97174529
97175437
0.000000e+00
1037
17
TraesCS5D01G313300
chr6B
85.516
1008
111
20
614
1606
238144255
238145242
0.000000e+00
1020
18
TraesCS5D01G313300
chr5B
85.443
632
26
21
6
606
490103705
490103109
5.920000e-167
597
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
TraesCS5D01G313300
chr5D
408552752
408555956
3204
True
5919
5919
100.000
1
3205
1
chr5D.!!$R1
3204
1
TraesCS5D01G313300
chr5D
545533140
545534118
978
False
1548
1548
95.137
610
1595
1
chr5D.!!$F1
985
2
TraesCS5D01G313300
chr7D
92231956
92234553
2597
True
4473
4473
97.769
612
3205
1
chr7D.!!$R1
2593
3
TraesCS5D01G313300
chr7D
631816007
631818589
2582
True
4420
4420
97.499
613
3205
1
chr7D.!!$R2
2592
4
TraesCS5D01G313300
chr3D
45060644
45063224
2580
True
4390
4390
97.306
613
3205
1
chr3D.!!$R1
2592
5
TraesCS5D01G313300
chr3D
502045454
502048028
2574
True
2675
2675
85.924
615
3180
1
chr3D.!!$R2
2565
6
TraesCS5D01G313300
chr1D
414448658
414451242
2584
True
4344
4344
96.964
613
3205
1
chr1D.!!$R1
2592
7
TraesCS5D01G313300
chr1D
444898363
444899325
962
False
1421
1421
93.110
612
1595
1
chr1D.!!$F1
983
8
TraesCS5D01G313300
chr4B
657802917
657805507
2590
True
3554
3554
91.622
613
3184
1
chr4B.!!$R1
2571
9
TraesCS5D01G313300
chr5A
650150479
650153002
2523
False
3494
3494
91.742
614
3140
1
chr5A.!!$F1
2526
10
TraesCS5D01G313300
chr2A
769227587
769230110
2523
False
3494
3494
91.751
614
3140
1
chr2A.!!$F2
2526
11
TraesCS5D01G313300
chr2A
115129965
115132483
2518
False
3441
3441
91.393
614
3140
1
chr2A.!!$F1
2526
12
TraesCS5D01G313300
chr4A
604386932
604389451
2519
True
3469
3469
91.585
614
3140
1
chr4A.!!$R1
2526
13
TraesCS5D01G313300
chr7B
591160032
591161037
1005
False
1136
1136
87.377
614
1606
1
chr7B.!!$F1
992
14
TraesCS5D01G313300
chrUn
97254877
97255781
904
False
1055
1055
88.069
616
1513
1
chrUn.!!$F2
897
15
TraesCS5D01G313300
chrUn
97174529
97175437
908
False
1037
1037
87.608
611
1513
1
chrUn.!!$F1
902
16
TraesCS5D01G313300
chr6B
238144255
238145242
987
False
1020
1020
85.516
614
1606
1
chr6B.!!$F1
992
17
TraesCS5D01G313300
chr5B
490103109
490103705
596
True
597
597
85.443
6
606
1
chr5B.!!$R1
600
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.