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
TraesCS5D01G084800
chr5D
100.000
5366
0
0
1
5366
88880265
88874900
0.000000e+00
9910.0
1
TraesCS5D01G084800
chr5D
87.379
103
13
0
1548
1650
6108593
6108491
9.440000e-23
119.0
2
TraesCS5D01G084800
chr5A
95.244
4479
129
26
701
5127
82872455
82868009
0.000000e+00
7014.0
3
TraesCS5D01G084800
chr5A
92.537
67
3
1
5165
5231
82868018
82867954
1.590000e-15
95.3
4
TraesCS5D01G084800
chr5B
96.270
3190
60
10
1807
4971
95513170
95516325
0.000000e+00
5177.0
5
TraesCS5D01G084800
chr5B
96.506
1202
32
2
698
1889
95511977
95513178
0.000000e+00
1978.0
6
TraesCS5D01G084800
chr5B
88.356
584
43
12
2537
3107
53664967
53665538
0.000000e+00
678.0
7
TraesCS5D01G084800
chr5B
91.268
355
22
7
5001
5350
95516326
95516676
4.860000e-130
475.0
8
TraesCS5D01G084800
chr5B
88.350
103
12
0
1548
1650
690647367
690647265
2.030000e-24
124.0
9
TraesCS5D01G084800
chr7D
86.339
549
71
4
3
549
478799469
478798923
3.580000e-166
595.0
10
TraesCS5D01G084800
chr7D
81.304
690
98
22
24
698
636717084
636717757
1.020000e-146
531.0
11
TraesCS5D01G084800
chr7D
87.805
123
12
2
5224
5346
596440156
596440037
2.010000e-29
141.0
12
TraesCS5D01G084800
chr7D
87.603
121
13
2
5226
5345
351907074
351906955
7.250000e-29
139.0
13
TraesCS5D01G084800
chr3B
86.472
547
69
5
3
546
708392116
708392660
3.580000e-166
595.0
14
TraesCS5D01G084800
chr3B
93.333
135
7
2
3177
3311
117589430
117589298
1.180000e-46
198.0
15
TraesCS5D01G084800
chr3B
91.912
136
11
0
3177
3312
42630984
42630849
1.970000e-44
191.0
16
TraesCS5D01G084800
chr3B
88.136
118
12
2
5229
5345
10717871
10717987
7.250000e-29
139.0
17
TraesCS5D01G084800
chr7B
86.182
550
71
5
3
549
739379942
739379395
1.660000e-164
590.0
18
TraesCS5D01G084800
chr7B
80.392
714
118
19
3
698
707963846
707963137
1.710000e-144
523.0
19
TraesCS5D01G084800
chr7B
91.971
137
11
0
3176
3312
522721480
522721344
5.480000e-45
193.0
20
TraesCS5D01G084800
chr4A
87.170
530
48
9
2590
3110
58720871
58720353
7.740000e-163
584.0
21
TraesCS5D01G084800
chr4A
87.603
121
11
4
5227
5345
594278520
594278638
2.610000e-28
137.0
22
TraesCS5D01G084800
chr4A
94.118
51
2
1
2537
2586
58786705
58786655
5.760000e-10
76.8
23
TraesCS5D01G084800
chr1B
85.818
550
73
5
3
549
94009779
94009232
3.600000e-161
579.0
24
TraesCS5D01G084800
chr6B
80.699
715
114
21
3
699
706517237
706516529
7.910000e-148
534.0
25
TraesCS5D01G084800
chr3D
81.124
694
96
26
24
698
489527699
489528376
1.710000e-144
523.0
26
TraesCS5D01G084800
chr3D
80.456
701
119
18
3
691
614469664
614468970
2.220000e-143
520.0
27
TraesCS5D01G084800
chr3D
89.732
224
23
0
1548
1771
382002131
382002354
2.450000e-73
287.0
28
TraesCS5D01G084800
chr3D
91.912
136
11
0
3177
3312
71517844
71517709
1.970000e-44
191.0
29
TraesCS5D01G084800
chr3D
87.903
124
13
2
5224
5346
557470733
557470855
1.560000e-30
145.0
30
TraesCS5D01G084800
chr2B
87.901
405
29
5
2540
2925
10728516
10728919
4.900000e-125
459.0
31
TraesCS5D01G084800
chr2B
86.096
187
17
4
2921
3107
10741579
10741756
5.480000e-45
193.0
32
TraesCS5D01G084800
chr2B
92.373
118
8
1
1654
1771
574708122
574708238
3.320000e-37
167.0
33
TraesCS5D01G084800
chr2B
88.430
121
12
2
5226
5345
575828172
575828053
1.560000e-30
145.0
34
TraesCS5D01G084800
chr7A
74.291
564
114
19
115
668
504226056
504225514
5.450000e-50
209.0
35
TraesCS5D01G084800
chr3A
92.647
136
10
0
3177
3312
34532615
34532480
4.240000e-46
196.0
36
TraesCS5D01G084800
chr1D
93.846
130
8
0
3177
3306
175820002
175819873
4.240000e-46
196.0
37
TraesCS5D01G084800
chr6D
91.912
136
11
0
3177
3312
304099286
304099421
1.970000e-44
191.0
38
TraesCS5D01G084800
chr2A
89.831
118
11
1
1654
1771
634598169
634598285
3.350000e-32
150.0
39
TraesCS5D01G084800
chr4D
89.076
119
10
3
5229
5345
311274756
311274873
1.560000e-30
145.0
40
TraesCS5D01G084800
chr1A
88.235
119
12
2
5228
5345
82355200
82355083
2.010000e-29
141.0
41
TraesCS5D01G084800
chr1A
90.291
103
10
0
1548
1650
590838825
590838723
9.370000e-28
135.0
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
TraesCS5D01G084800
chr5D
88874900
88880265
5365
True
9910.000000
9910
100.000000
1
5366
1
chr5D.!!$R2
5365
1
TraesCS5D01G084800
chr5A
82867954
82872455
4501
True
3554.650000
7014
93.890500
701
5231
2
chr5A.!!$R1
4530
2
TraesCS5D01G084800
chr5B
95511977
95516676
4699
False
2543.333333
5177
94.681333
698
5350
3
chr5B.!!$F2
4652
3
TraesCS5D01G084800
chr5B
53664967
53665538
571
False
678.000000
678
88.356000
2537
3107
1
chr5B.!!$F1
570
4
TraesCS5D01G084800
chr7D
478798923
478799469
546
True
595.000000
595
86.339000
3
549
1
chr7D.!!$R2
546
5
TraesCS5D01G084800
chr7D
636717084
636717757
673
False
531.000000
531
81.304000
24
698
1
chr7D.!!$F1
674
6
TraesCS5D01G084800
chr3B
708392116
708392660
544
False
595.000000
595
86.472000
3
546
1
chr3B.!!$F2
543
7
TraesCS5D01G084800
chr7B
739379395
739379942
547
True
590.000000
590
86.182000
3
549
1
chr7B.!!$R3
546
8
TraesCS5D01G084800
chr7B
707963137
707963846
709
True
523.000000
523
80.392000
3
698
1
chr7B.!!$R2
695
9
TraesCS5D01G084800
chr4A
58720353
58720871
518
True
584.000000
584
87.170000
2590
3110
1
chr4A.!!$R1
520
10
TraesCS5D01G084800
chr1B
94009232
94009779
547
True
579.000000
579
85.818000
3
549
1
chr1B.!!$R1
546
11
TraesCS5D01G084800
chr6B
706516529
706517237
708
True
534.000000
534
80.699000
3
699
1
chr6B.!!$R1
696
12
TraesCS5D01G084800
chr3D
489527699
489528376
677
False
523.000000
523
81.124000
24
698
1
chr3D.!!$F2
674
13
TraesCS5D01G084800
chr3D
614468970
614469664
694
True
520.000000
520
80.456000
3
691
1
chr3D.!!$R2
688
14
TraesCS5D01G084800
chr7A
504225514
504226056
542
True
209.000000
209
74.291000
115
668
1
chr7A.!!$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.