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
TraesCS4A01G478600
chr4A
100.000
5045
0
0
1
5045
735732884
735737928
0.000000e+00
9317
1
TraesCS4A01G478600
chr4A
99.102
4786
41
2
250
5035
736434588
736429805
0.000000e+00
8599
2
TraesCS4A01G478600
chr4A
98.085
2663
48
1
2383
5045
736816021
736818680
0.000000e+00
4632
3
TraesCS4A01G478600
chr4A
83.470
3902
603
35
1030
4912
735316355
735320233
0.000000e+00
3594
4
TraesCS4A01G478600
chr4A
82.801
3942
623
44
1030
4940
735562665
735558748
0.000000e+00
3472
5
TraesCS4A01G478600
chr4A
82.397
3971
621
54
1030
4981
735487908
735483997
0.000000e+00
3389
6
TraesCS4A01G478600
chr4A
82.143
3920
643
43
1030
4930
736756369
736760250
0.000000e+00
3308
7
TraesCS4A01G478600
chr4A
81.353
4065
681
54
937
4980
736119676
736123684
0.000000e+00
3236
8
TraesCS4A01G478600
chr4A
81.515
3933
662
43
1030
4938
736147331
736151222
0.000000e+00
3175
9
TraesCS4A01G478600
chr4A
81.317
3522
621
29
1436
4940
735689506
735693007
0.000000e+00
2824
10
TraesCS4A01G478600
chr4A
97.319
1343
29
4
272
1609
736810677
736812017
0.000000e+00
2274
11
TraesCS4A01G478600
chr4A
83.064
2409
383
13
937
3343
734876163
734878548
0.000000e+00
2165
12
TraesCS4A01G478600
chr4A
84.116
2216
342
10
1001
3212
734480156
734482365
0.000000e+00
2134
13
TraesCS4A01G478600
chr4A
84.550
2013
298
11
993
3000
735020295
735022299
0.000000e+00
1982
14
TraesCS4A01G478600
chr4A
80.310
2448
447
28
2519
4940
735777962
735780400
0.000000e+00
1818
15
TraesCS4A01G478600
chr4A
79.630
2489
455
40
2347
4817
735652463
735650009
0.000000e+00
1740
16
TraesCS4A01G478600
chr4A
81.651
1744
292
20
3207
4938
734482990
734484717
0.000000e+00
1423
17
TraesCS4A01G478600
chr4A
100.000
526
0
0
5336
5861
735738219
735738744
0.000000e+00
972
18
TraesCS4A01G478600
chr4A
98.384
495
5
1
5367
5861
736429440
736428949
0.000000e+00
867
19
TraesCS4A01G478600
chr4A
93.097
536
17
4
5342
5861
736818759
736819290
0.000000e+00
767
20
TraesCS4A01G478600
chr4A
89.062
192
0
1
1
192
736434753
736434583
9.890000e-53
219
21
TraesCS4A01G478600
chr7D
98.040
4796
67
3
250
5045
5788863
5784095
0.000000e+00
8311
22
TraesCS4A01G478600
chr7D
79.349
2794
506
54
2245
5014
5665585
5662839
0.000000e+00
1897
23
TraesCS4A01G478600
chr7D
92.379
538
19
5
5342
5861
5783791
5783258
0.000000e+00
747
24
TraesCS4A01G478600
chr7D
94.872
195
4
2
4
192
5789052
5788858
3.430000e-77
300
25
TraesCS4A01G478600
chr7A
81.440
3944
663
42
1030
4940
7045455
7041548
0.000000e+00
3164
26
TraesCS4A01G478600
chr2B
100.000
57
0
0
190
246
503219867
503219923
8.030000e-19
106
27
TraesCS4A01G478600
chr2B
96.774
62
2
0
187
248
492777760
492777821
2.890000e-18
104
28
TraesCS4A01G478600
chrUn
95.385
65
2
1
185
248
390137195
390137131
1.040000e-17
102
29
TraesCS4A01G478600
chr6A
95.385
65
1
2
184
248
135929010
135929072
1.040000e-17
102
30
TraesCS4A01G478600
chr5B
96.721
61
2
0
188
248
409549118
409549058
1.040000e-17
102
31
TraesCS4A01G478600
chr7B
91.667
72
6
0
177
248
38563922
38563851
3.740000e-17
100
32
TraesCS4A01G478600
chr4B
95.238
63
3
0
190
252
403253326
403253264
3.740000e-17
100
33
TraesCS4A01G478600
chr5A
92.647
68
5
0
185
252
564703213
564703146
1.340000e-16
99
34
TraesCS4A01G478600
chr1B
92.647
68
5
0
181
248
678865143
678865210
1.340000e-16
99
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
TraesCS4A01G478600
chr4A
735732884
735738744
5860
False
5144.500000
9317
100.0000
1
5861
2
chr4A.!!$F11
5860
1
TraesCS4A01G478600
chr4A
735316355
735320233
3878
False
3594.000000
3594
83.4700
1030
4912
1
chr4A.!!$F3
3882
2
TraesCS4A01G478600
chr4A
735558748
735562665
3917
True
3472.000000
3472
82.8010
1030
4940
1
chr4A.!!$R2
3910
3
TraesCS4A01G478600
chr4A
735483997
735487908
3911
True
3389.000000
3389
82.3970
1030
4981
1
chr4A.!!$R1
3951
4
TraesCS4A01G478600
chr4A
736756369
736760250
3881
False
3308.000000
3308
82.1430
1030
4930
1
chr4A.!!$F8
3900
5
TraesCS4A01G478600
chr4A
736119676
736123684
4008
False
3236.000000
3236
81.3530
937
4980
1
chr4A.!!$F6
4043
6
TraesCS4A01G478600
chr4A
736428949
736434753
5804
True
3228.333333
8599
95.5160
1
5861
3
chr4A.!!$R4
5860
7
TraesCS4A01G478600
chr4A
736147331
736151222
3891
False
3175.000000
3175
81.5150
1030
4938
1
chr4A.!!$F7
3908
8
TraesCS4A01G478600
chr4A
735689506
735693007
3501
False
2824.000000
2824
81.3170
1436
4940
1
chr4A.!!$F4
3504
9
TraesCS4A01G478600
chr4A
736816021
736819290
3269
False
2699.500000
4632
95.5910
2383
5861
2
chr4A.!!$F12
3478
10
TraesCS4A01G478600
chr4A
736810677
736812017
1340
False
2274.000000
2274
97.3190
272
1609
1
chr4A.!!$F9
1337
11
TraesCS4A01G478600
chr4A
734876163
734878548
2385
False
2165.000000
2165
83.0640
937
3343
1
chr4A.!!$F1
2406
12
TraesCS4A01G478600
chr4A
735020295
735022299
2004
False
1982.000000
1982
84.5500
993
3000
1
chr4A.!!$F2
2007
13
TraesCS4A01G478600
chr4A
735777962
735780400
2438
False
1818.000000
1818
80.3100
2519
4940
1
chr4A.!!$F5
2421
14
TraesCS4A01G478600
chr4A
734480156
734484717
4561
False
1778.500000
2134
82.8835
1001
4938
2
chr4A.!!$F10
3937
15
TraesCS4A01G478600
chr4A
735650009
735652463
2454
True
1740.000000
1740
79.6300
2347
4817
1
chr4A.!!$R3
2470
16
TraesCS4A01G478600
chr7D
5783258
5789052
5794
True
3119.333333
8311
95.0970
4
5861
3
chr7D.!!$R2
5857
17
TraesCS4A01G478600
chr7D
5662839
5665585
2746
True
1897.000000
1897
79.3490
2245
5014
1
chr7D.!!$R1
2769
18
TraesCS4A01G478600
chr7A
7041548
7045455
3907
True
3164.000000
3164
81.4400
1030
4940
1
chr7A.!!$R1
3910
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.