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
TraesCS4D01G053300
chr4D
100.000
7143
0
0
1
7143
29322479
29329621
0.000000e+00
13191.0
1
TraesCS4D01G053300
chr4D
96.007
551
22
0
6588
7138
29346814
29347364
0.000000e+00
896.0
2
TraesCS4D01G053300
chr4D
93.182
44
3
0
5933
5976
259053329
259053286
1.660000e-06
65.8
3
TraesCS4D01G053300
chr4A
97.352
5930
92
15
3
5881
573892931
573887016
0.000000e+00
10021.0
4
TraesCS4D01G053300
chr4A
95.007
761
22
7
5847
6600
573886949
573886198
0.000000e+00
1181.0
5
TraesCS4D01G053300
chr4B
97.015
4623
97
19
941
5545
41778037
41782636
0.000000e+00
7734.0
6
TraesCS4D01G053300
chr4B
93.039
747
34
12
5852
6589
41783066
41783803
0.000000e+00
1075.0
7
TraesCS4D01G053300
chr4B
96.620
355
12
0
5524
5878
41782711
41783065
2.220000e-164
590.0
8
TraesCS4D01G053300
chr4B
91.899
395
27
4
4888
5280
42141373
42141764
1.350000e-151
547.0
9
TraesCS4D01G053300
chr4B
82.055
613
50
22
326
915
41777464
41778039
1.080000e-127
468.0
10
TraesCS4D01G053300
chr4B
91.343
335
19
3
1
325
41776174
41776508
3.930000e-122
449.0
11
TraesCS4D01G053300
chr4B
92.308
299
21
1
5272
5568
42144186
42144484
2.380000e-114
424.0
12
TraesCS4D01G053300
chr4B
86.207
87
10
2
4818
4904
42141272
42141356
7.630000e-15
93.5
13
TraesCS4D01G053300
chr3D
95.100
551
27
0
6588
7138
118502844
118503394
0.000000e+00
869.0
14
TraesCS4D01G053300
chr3D
94.918
551
28
0
6588
7138
75548104
75548654
0.000000e+00
863.0
15
TraesCS4D01G053300
chrUn
94.918
551
28
0
6588
7138
143842946
143843496
0.000000e+00
863.0
16
TraesCS4D01G053300
chr5D
94.918
551
28
0
6588
7138
435979781
435980331
0.000000e+00
863.0
17
TraesCS4D01G053300
chr5D
94.434
557
29
2
6585
7141
255513597
255513043
0.000000e+00
856.0
18
TraesCS4D01G053300
chr3A
94.604
556
30
0
6588
7143
469793034
469793589
0.000000e+00
861.0
19
TraesCS4D01G053300
chr3A
91.566
83
7
0
5892
5974
705926309
705926227
1.630000e-21
115.0
20
TraesCS4D01G053300
chr1D
94.909
550
28
0
6588
7137
164482554
164482005
0.000000e+00
861.0
21
TraesCS4D01G053300
chr1D
91.860
86
2
1
843
928
469030402
469030482
1.630000e-21
115.0
22
TraesCS4D01G053300
chr1D
97.872
47
1
0
5892
5938
481042121
481042075
1.650000e-11
82.4
23
TraesCS4D01G053300
chr6D
94.585
554
30
0
6588
7141
121672816
121672263
0.000000e+00
857.0
24
TraesCS4D01G053300
chr6D
95.238
42
2
0
5933
5974
423818549
423818508
4.620000e-07
67.6
25
TraesCS4D01G053300
chr7A
84.167
360
46
7
5424
5777
610205449
610205803
8.880000e-89
339.0
26
TraesCS4D01G053300
chr2A
83.708
356
46
8
5424
5773
238530331
238530680
6.910000e-85
326.0
27
TraesCS4D01G053300
chr1A
91.333
150
6
3
801
948
562004818
562004962
1.570000e-46
198.0
28
TraesCS4D01G053300
chr1A
92.308
143
4
3
805
945
562001592
562001729
5.650000e-46
196.0
29
TraesCS4D01G053300
chr1A
93.548
93
1
1
836
928
561981076
561981163
4.500000e-27
134.0
30
TraesCS4D01G053300
chr6B
95.238
42
2
0
5933
5974
15269085
15269044
4.620000e-07
67.6
31
TraesCS4D01G053300
chr6A
95.238
42
2
0
5933
5974
142074852
142074893
4.620000e-07
67.6
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
TraesCS4D01G053300
chr4D
29322479
29329621
7142
False
13191.000000
13191
100.0000
1
7143
1
chr4D.!!$F1
7142
1
TraesCS4D01G053300
chr4D
29346814
29347364
550
False
896.000000
896
96.0070
6588
7138
1
chr4D.!!$F2
550
2
TraesCS4D01G053300
chr4A
573886198
573892931
6733
True
5601.000000
10021
96.1795
3
6600
2
chr4A.!!$R1
6597
3
TraesCS4D01G053300
chr4B
41776174
41783803
7629
False
2063.200000
7734
92.0144
1
6589
5
chr4B.!!$F1
6588
4
TraesCS4D01G053300
chr4B
42141272
42144484
3212
False
354.833333
547
90.1380
4818
5568
3
chr4B.!!$F2
750
5
TraesCS4D01G053300
chr3D
118502844
118503394
550
False
869.000000
869
95.1000
6588
7138
1
chr3D.!!$F2
550
6
TraesCS4D01G053300
chr3D
75548104
75548654
550
False
863.000000
863
94.9180
6588
7138
1
chr3D.!!$F1
550
7
TraesCS4D01G053300
chrUn
143842946
143843496
550
False
863.000000
863
94.9180
6588
7138
1
chrUn.!!$F1
550
8
TraesCS4D01G053300
chr5D
435979781
435980331
550
False
863.000000
863
94.9180
6588
7138
1
chr5D.!!$F1
550
9
TraesCS4D01G053300
chr5D
255513043
255513597
554
True
856.000000
856
94.4340
6585
7141
1
chr5D.!!$R1
556
10
TraesCS4D01G053300
chr3A
469793034
469793589
555
False
861.000000
861
94.6040
6588
7143
1
chr3A.!!$F1
555
11
TraesCS4D01G053300
chr1D
164482005
164482554
549
True
861.000000
861
94.9090
6588
7137
1
chr1D.!!$R1
549
12
TraesCS4D01G053300
chr6D
121672263
121672816
553
True
857.000000
857
94.5850
6588
7141
1
chr6D.!!$R1
553
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.