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
TraesCS7B01G307500
chr7B
100.000
4799
0
0
1
4799
551468075
551463277
0.000000e+00
8863.0
1
TraesCS7B01G307500
chr7A
95.776
3906
126
18
901
4799
592931385
592927512
0.000000e+00
6263.0
2
TraesCS7B01G307500
chr7A
88.800
375
16
8
908
1282
593017054
593016706
2.050000e-118
436.0
3
TraesCS7B01G307500
chr7A
97.512
201
5
0
1310
1510
593016712
593016512
1.280000e-90
344.0
4
TraesCS7B01G307500
chr7A
95.122
41
2
0
4081
4121
542967837
542967877
1.110000e-06
65.8
5
TraesCS7B01G307500
chr7D
95.050
3899
140
31
908
4799
518060270
518056418
0.000000e+00
6082.0
6
TraesCS7B01G307500
chr2B
92.552
913
59
7
1
907
74410632
74411541
0.000000e+00
1301.0
7
TraesCS7B01G307500
chr2B
92.308
52
3
1
4034
4085
644610185
644610235
6.660000e-09
73.1
8
TraesCS7B01G307500
chr6B
91.557
912
61
10
4
907
261663172
261662269
0.000000e+00
1243.0
9
TraesCS7B01G307500
chr3B
91.128
913
68
11
4
907
650827736
650826828
0.000000e+00
1225.0
10
TraesCS7B01G307500
chr3B
91.251
903
70
8
4
900
752096143
752095244
0.000000e+00
1221.0
11
TraesCS7B01G307500
chr3B
97.436
39
1
0
4084
4122
448777377
448777339
3.100000e-07
67.6
12
TraesCS7B01G307500
chr3D
90.576
902
80
4
5
902
555149237
555150137
0.000000e+00
1190.0
13
TraesCS7B01G307500
chr3D
81.250
256
29
7
2668
2905
30940775
30941029
6.340000e-44
189.0
14
TraesCS7B01G307500
chr3D
86.667
60
6
2
4024
4081
553626328
553626387
1.110000e-06
65.8
15
TraesCS7B01G307500
chr2D
90.365
903
78
6
5
900
50658090
50658990
0.000000e+00
1177.0
16
TraesCS7B01G307500
chr2D
97.674
43
1
0
4045
4087
354327312
354327270
1.850000e-09
75.0
17
TraesCS7B01G307500
chr5D
89.838
866
75
11
5
859
297575287
297574424
0.000000e+00
1099.0
18
TraesCS7B01G307500
chr5D
89.831
59
1
2
4027
4085
3563149
3563096
2.400000e-08
71.3
19
TraesCS7B01G307500
chr1A
88.996
827
79
8
5
824
521713736
521714557
0.000000e+00
1013.0
20
TraesCS7B01G307500
chr1A
91.837
49
3
1
4073
4121
52453661
52453614
3.100000e-07
67.6
21
TraesCS7B01G307500
chr4A
84.118
913
118
21
4
901
14251169
14252069
0.000000e+00
857.0
22
TraesCS7B01G307500
chr4A
97.368
38
1
0
4085
4122
93977295
93977258
1.110000e-06
65.8
23
TraesCS7B01G307500
chr5B
92.453
53
4
0
4029
4081
6417690
6417742
5.150000e-10
76.8
24
TraesCS7B01G307500
chr1B
89.231
65
2
3
4017
4081
638674641
638674700
5.150000e-10
76.8
25
TraesCS7B01G307500
chr1B
89.655
58
5
1
4036
4092
297337086
297337143
6.660000e-09
73.1
26
TraesCS7B01G307500
chr3A
97.500
40
0
1
4084
4122
11690308
11690269
3.100000e-07
67.6
27
TraesCS7B01G307500
chr3A
97.500
40
0
1
4084
4122
11715643
11715604
3.100000e-07
67.6
28
TraesCS7B01G307500
chr3A
95.122
41
1
1
4082
4121
616953719
616953679
4.010000e-06
63.9
29
TraesCS7B01G307500
chr2A
91.489
47
1
3
4075
4121
194551843
194551886
1.440000e-05
62.1
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
TraesCS7B01G307500
chr7B
551463277
551468075
4798
True
8863
8863
100.000
1
4799
1
chr7B.!!$R1
4798
1
TraesCS7B01G307500
chr7A
592927512
592931385
3873
True
6263
6263
95.776
901
4799
1
chr7A.!!$R1
3898
2
TraesCS7B01G307500
chr7A
593016512
593017054
542
True
390
436
93.156
908
1510
2
chr7A.!!$R2
602
3
TraesCS7B01G307500
chr7D
518056418
518060270
3852
True
6082
6082
95.050
908
4799
1
chr7D.!!$R1
3891
4
TraesCS7B01G307500
chr2B
74410632
74411541
909
False
1301
1301
92.552
1
907
1
chr2B.!!$F1
906
5
TraesCS7B01G307500
chr6B
261662269
261663172
903
True
1243
1243
91.557
4
907
1
chr6B.!!$R1
903
6
TraesCS7B01G307500
chr3B
650826828
650827736
908
True
1225
1225
91.128
4
907
1
chr3B.!!$R2
903
7
TraesCS7B01G307500
chr3B
752095244
752096143
899
True
1221
1221
91.251
4
900
1
chr3B.!!$R3
896
8
TraesCS7B01G307500
chr3D
555149237
555150137
900
False
1190
1190
90.576
5
902
1
chr3D.!!$F3
897
9
TraesCS7B01G307500
chr2D
50658090
50658990
900
False
1177
1177
90.365
5
900
1
chr2D.!!$F1
895
10
TraesCS7B01G307500
chr5D
297574424
297575287
863
True
1099
1099
89.838
5
859
1
chr5D.!!$R2
854
11
TraesCS7B01G307500
chr1A
521713736
521714557
821
False
1013
1013
88.996
5
824
1
chr1A.!!$F1
819
12
TraesCS7B01G307500
chr4A
14251169
14252069
900
False
857
857
84.118
4
901
1
chr4A.!!$F1
897
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.