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
TraesCS7D01G314200
chr7D
100.000
4178
0
0
1
4178
399831947
399836124
0.000000e+00
7716.0
1
TraesCS7D01G314200
chr7D
81.256
1067
192
8
2063
3125
400184826
400183764
0.000000e+00
856.0
2
TraesCS7D01G314200
chr7D
80.486
1071
189
16
2068
3125
193935685
193936748
0.000000e+00
802.0
3
TraesCS7D01G314200
chr7D
86.391
654
88
1
1029
1681
400185879
400185226
0.000000e+00
713.0
4
TraesCS7D01G314200
chr7D
80.843
522
60
18
1
505
333709310
333709808
1.420000e-99
374.0
5
TraesCS7D01G314200
chr7A
93.224
3778
134
32
1
3726
457682092
457685799
0.000000e+00
5446.0
6
TraesCS7D01G314200
chr7A
78.622
987
193
17
2063
3045
457921584
457920612
4.560000e-179
638.0
7
TraesCS7D01G314200
chr7A
92.926
311
20
1
3718
4028
457692395
457692703
6.370000e-123
451.0
8
TraesCS7D01G314200
chr7A
87.500
168
18
3
4013
4177
457692715
457692882
1.530000e-44
191.0
9
TraesCS7D01G314200
chr7A
100.000
28
0
0
3750
3777
20214983
20214956
8.000000e-03
52.8
10
TraesCS7D01G314200
chr7B
93.968
3017
99
32
529
3518
409219398
409222358
0.000000e+00
4486.0
11
TraesCS7D01G314200
chr7B
95.294
680
12
3
3517
4178
409222519
409223196
0.000000e+00
1061.0
12
TraesCS7D01G314200
chr7B
81.614
1066
190
6
2063
3125
409749079
409748017
0.000000e+00
878.0
13
TraesCS7D01G314200
chr7B
87.768
654
79
1
1029
1681
409750121
409749468
0.000000e+00
763.0
14
TraesCS7D01G314200
chr7B
89.286
84
7
2
4095
4178
329900426
329900345
2.050000e-18
104.0
15
TraesCS7D01G314200
chr1D
84.472
1230
169
8
2063
3286
416681
417894
0.000000e+00
1194.0
16
TraesCS7D01G314200
chr1D
91.556
675
55
2
999
1672
415434
416107
0.000000e+00
929.0
17
TraesCS7D01G314200
chr1D
79.473
1062
190
18
2085
3125
80843133
80844187
0.000000e+00
728.0
18
TraesCS7D01G314200
chr1D
80.192
520
64
17
4
505
468306597
468307095
1.850000e-93
353.0
19
TraesCS7D01G314200
chr1A
80.654
1070
190
13
2069
3125
99319309
99320374
0.000000e+00
813.0
20
TraesCS7D01G314200
chrUn
87.762
621
76
0
1053
1673
100315253
100314633
0.000000e+00
726.0
21
TraesCS7D01G314200
chrUn
80.137
438
51
14
84
505
476709669
476709252
1.140000e-75
294.0
22
TraesCS7D01G314200
chr4D
85.756
681
91
3
996
1673
503920983
503920306
0.000000e+00
715.0
23
TraesCS7D01G314200
chr4B
86.482
651
88
0
1021
1671
667572889
667572239
0.000000e+00
715.0
24
TraesCS7D01G314200
chr4B
84.581
681
99
3
996
1673
649837059
649836382
0.000000e+00
671.0
25
TraesCS7D01G314200
chr4B
85.321
109
13
2
4073
4178
268077055
268077163
4.420000e-20
110.0
26
TraesCS7D01G314200
chr5A
75.585
1069
244
14
2064
3125
688613327
688612269
2.880000e-141
512.0
27
TraesCS7D01G314200
chr5A
87.437
199
21
4
1
198
693612219
693612414
4.200000e-55
226.0
28
TraesCS7D01G314200
chr2D
80.769
520
62
16
4
505
525499410
525499909
5.100000e-99
372.0
29
TraesCS7D01G314200
chr3D
80.664
512
61
16
11
505
118511847
118512337
3.070000e-96
363.0
30
TraesCS7D01G314200
chr3B
80.271
517
65
16
4
505
610478632
610479126
5.140000e-94
355.0
31
TraesCS7D01G314200
chr3B
80.273
512
62
17
11
505
164471235
164470746
2.390000e-92
350.0
32
TraesCS7D01G314200
chr3B
78.748
527
64
24
4
505
4749498
4748995
4.060000e-80
309.0
33
TraesCS7D01G314200
chr3B
78.203
523
72
24
4
505
738918814
738918313
3.160000e-76
296.0
34
TraesCS7D01G314200
chr2B
80.000
365
47
19
1
357
800967797
800968143
3.230000e-61
246.0
35
TraesCS7D01G314200
chr2B
86.735
98
11
1
4070
4165
428778420
428778323
1.590000e-19
108.0
36
TraesCS7D01G314200
chr1B
76.636
535
70
34
2
504
357536290
357536801
1.160000e-60
244.0
37
TraesCS7D01G314200
chr5B
86.190
210
27
2
11
219
571524681
571524889
4.200000e-55
226.0
38
TraesCS7D01G314200
chr5B
87.113
194
19
5
1
190
308568709
308568518
9.100000e-52
215.0
39
TraesCS7D01G314200
chr6A
86.598
194
20
5
1
190
108080954
108080763
4.230000e-50
209.0
40
TraesCS7D01G314200
chr3A
96.970
33
1
0
3750
3782
375814996
375814964
5.840000e-04
56.5
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
TraesCS7D01G314200
chr7D
399831947
399836124
4177
False
7716.0
7716
100.0000
1
4178
1
chr7D.!!$F3
4177
1
TraesCS7D01G314200
chr7D
193935685
193936748
1063
False
802.0
802
80.4860
2068
3125
1
chr7D.!!$F1
1057
2
TraesCS7D01G314200
chr7D
400183764
400185879
2115
True
784.5
856
83.8235
1029
3125
2
chr7D.!!$R1
2096
3
TraesCS7D01G314200
chr7A
457682092
457685799
3707
False
5446.0
5446
93.2240
1
3726
1
chr7A.!!$F1
3725
4
TraesCS7D01G314200
chr7A
457920612
457921584
972
True
638.0
638
78.6220
2063
3045
1
chr7A.!!$R2
982
5
TraesCS7D01G314200
chr7B
409219398
409223196
3798
False
2773.5
4486
94.6310
529
4178
2
chr7B.!!$F1
3649
6
TraesCS7D01G314200
chr7B
409748017
409750121
2104
True
820.5
878
84.6910
1029
3125
2
chr7B.!!$R2
2096
7
TraesCS7D01G314200
chr1D
415434
417894
2460
False
1061.5
1194
88.0140
999
3286
2
chr1D.!!$F3
2287
8
TraesCS7D01G314200
chr1D
80843133
80844187
1054
False
728.0
728
79.4730
2085
3125
1
chr1D.!!$F1
1040
9
TraesCS7D01G314200
chr1A
99319309
99320374
1065
False
813.0
813
80.6540
2069
3125
1
chr1A.!!$F1
1056
10
TraesCS7D01G314200
chrUn
100314633
100315253
620
True
726.0
726
87.7620
1053
1673
1
chrUn.!!$R1
620
11
TraesCS7D01G314200
chr4D
503920306
503920983
677
True
715.0
715
85.7560
996
1673
1
chr4D.!!$R1
677
12
TraesCS7D01G314200
chr4B
667572239
667572889
650
True
715.0
715
86.4820
1021
1671
1
chr4B.!!$R2
650
13
TraesCS7D01G314200
chr4B
649836382
649837059
677
True
671.0
671
84.5810
996
1673
1
chr4B.!!$R1
677
14
TraesCS7D01G314200
chr5A
688612269
688613327
1058
True
512.0
512
75.5850
2064
3125
1
chr5A.!!$R1
1061
15
TraesCS7D01G314200
chr3B
4748995
4749498
503
True
309.0
309
78.7480
4
505
1
chr3B.!!$R1
501
16
TraesCS7D01G314200
chr3B
738918313
738918814
501
True
296.0
296
78.2030
4
505
1
chr3B.!!$R3
501
17
TraesCS7D01G314200
chr1B
357536290
357536801
511
False
244.0
244
76.6360
2
504
1
chr1B.!!$F1
502
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.