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
TraesCS6D01G115400
chr6D
100.000
5177
0
0
1
5177
81936379
81931203
0.000000e+00
9561.0
1
TraesCS6D01G115400
chr6D
88.063
3795
400
30
482
4268
82139624
82135875
0.000000e+00
4449.0
2
TraesCS6D01G115400
chr6D
87.013
77
6
3
195
271
82139704
82139632
3.320000e-12
84.2
3
TraesCS6D01G115400
chr6B
94.914
5210
185
28
1
5177
156741984
156736822
0.000000e+00
8080.0
4
TraesCS6D01G115400
chr6B
87.609
3793
424
27
482
4267
157027897
157024144
0.000000e+00
4359.0
5
TraesCS6D01G115400
chr6B
81.308
3900
631
52
480
4353
157489764
157485937
0.000000e+00
3073.0
6
TraesCS6D01G115400
chr6B
80.825
3708
619
70
708
4371
157109667
157106008
0.000000e+00
2824.0
7
TraesCS6D01G115400
chr6B
82.314
3302
534
39
981
4255
156550964
156547686
0.000000e+00
2817.0
8
TraesCS6D01G115400
chr6B
85.189
2093
292
14
934
3018
157900247
157902329
0.000000e+00
2132.0
9
TraesCS6D01G115400
chr6B
87.893
1462
110
28
3755
5177
156686243
156684810
0.000000e+00
1657.0
10
TraesCS6D01G115400
chr6B
82.692
208
23
5
264
466
130964701
130964900
6.890000e-39
172.0
11
TraesCS6D01G115400
chr6A
96.817
4524
121
13
2
4518
98324839
98320332
0.000000e+00
7535.0
12
TraesCS6D01G115400
chr6A
89.335
3807
360
30
482
4281
98814098
98810331
0.000000e+00
4739.0
13
TraesCS6D01G115400
chr6A
84.345
3181
469
21
982
4146
98250013
98246846
0.000000e+00
3088.0
14
TraesCS6D01G115400
chr6A
82.647
3325
521
43
981
4282
98309991
98306700
0.000000e+00
2892.0
15
TraesCS6D01G115400
chr6A
85.062
2671
362
27
1825
4471
98916398
98913741
0.000000e+00
2687.0
16
TraesCS6D01G115400
chr6A
79.290
3718
678
58
480
4174
98982844
98979196
0.000000e+00
2516.0
17
TraesCS6D01G115400
chr6A
93.224
428
29
0
4538
4965
98320077
98319650
9.460000e-177
630.0
18
TraesCS6D01G115400
chr6A
90.135
223
10
3
4961
5177
98319162
98318946
3.950000e-71
279.0
19
TraesCS6D01G115400
chr6A
86.826
167
11
3
283
445
595488651
595488492
5.330000e-40
176.0
20
TraesCS6D01G115400
chr7D
82.674
2528
358
46
525
3019
560999783
561002263
0.000000e+00
2169.0
21
TraesCS6D01G115400
chr7A
83.049
2289
350
24
757
3019
645087615
645089891
0.000000e+00
2043.0
22
TraesCS6D01G115400
chr4D
87.222
180
18
5
291
466
509822275
509822453
3.160000e-47
200.0
23
TraesCS6D01G115400
chr2D
86.243
189
16
3
282
466
30487805
30487623
4.090000e-46
196.0
24
TraesCS6D01G115400
chr7B
85.714
189
20
4
282
464
15031621
15031434
5.290000e-45
193.0
25
TraesCS6D01G115400
chr7B
85.638
188
16
4
283
466
680910914
680911094
2.460000e-43
187.0
26
TraesCS6D01G115400
chr2A
82.192
219
27
4
252
466
569281635
569281845
1.480000e-40
178.0
27
TraesCS6D01G115400
chr4B
83.684
190
25
4
282
466
643784363
643784551
1.920000e-39
174.0
28
TraesCS6D01G115400
chr1D
83.246
191
22
5
283
467
394464362
394464548
3.210000e-37
167.0
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
TraesCS6D01G115400
chr6D
81931203
81936379
5176
True
9561.000000
9561
100.000
1
5177
1
chr6D.!!$R1
5176
1
TraesCS6D01G115400
chr6D
82135875
82139704
3829
True
2266.600000
4449
87.538
195
4268
2
chr6D.!!$R2
4073
2
TraesCS6D01G115400
chr6B
156736822
156741984
5162
True
8080.000000
8080
94.914
1
5177
1
chr6B.!!$R3
5176
3
TraesCS6D01G115400
chr6B
157024144
157027897
3753
True
4359.000000
4359
87.609
482
4267
1
chr6B.!!$R4
3785
4
TraesCS6D01G115400
chr6B
157485937
157489764
3827
True
3073.000000
3073
81.308
480
4353
1
chr6B.!!$R6
3873
5
TraesCS6D01G115400
chr6B
157106008
157109667
3659
True
2824.000000
2824
80.825
708
4371
1
chr6B.!!$R5
3663
6
TraesCS6D01G115400
chr6B
156547686
156550964
3278
True
2817.000000
2817
82.314
981
4255
1
chr6B.!!$R1
3274
7
TraesCS6D01G115400
chr6B
157900247
157902329
2082
False
2132.000000
2132
85.189
934
3018
1
chr6B.!!$F2
2084
8
TraesCS6D01G115400
chr6B
156684810
156686243
1433
True
1657.000000
1657
87.893
3755
5177
1
chr6B.!!$R2
1422
9
TraesCS6D01G115400
chr6A
98810331
98814098
3767
True
4739.000000
4739
89.335
482
4281
1
chr6A.!!$R3
3799
10
TraesCS6D01G115400
chr6A
98246846
98250013
3167
True
3088.000000
3088
84.345
982
4146
1
chr6A.!!$R1
3164
11
TraesCS6D01G115400
chr6A
98306700
98309991
3291
True
2892.000000
2892
82.647
981
4282
1
chr6A.!!$R2
3301
12
TraesCS6D01G115400
chr6A
98318946
98324839
5893
True
2814.666667
7535
93.392
2
5177
3
chr6A.!!$R7
5175
13
TraesCS6D01G115400
chr6A
98913741
98916398
2657
True
2687.000000
2687
85.062
1825
4471
1
chr6A.!!$R4
2646
14
TraesCS6D01G115400
chr6A
98979196
98982844
3648
True
2516.000000
2516
79.290
480
4174
1
chr6A.!!$R5
3694
15
TraesCS6D01G115400
chr7D
560999783
561002263
2480
False
2169.000000
2169
82.674
525
3019
1
chr7D.!!$F1
2494
16
TraesCS6D01G115400
chr7A
645087615
645089891
2276
False
2043.000000
2043
83.049
757
3019
1
chr7A.!!$F1
2262
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.