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
TraesCS7B01G315600
chr7B
100.000
3317
0
0
1
3317
564171347
564174663
0.000000e+00
6126.0
1
TraesCS7B01G315600
chr7D
96.941
2550
65
5
778
3317
527706468
527709014
0.000000e+00
4265.0
2
TraesCS7B01G315600
chr7D
88.263
213
13
6
1955
2163
527709845
527710049
9.190000e-61
244.0
3
TraesCS7B01G315600
chr7A
97.062
1906
48
2
800
2698
607543737
607545641
0.000000e+00
3203.0
4
TraesCS7B01G315600
chr7A
96.986
564
17
0
2754
3317
607545640
607546203
0.000000e+00
948.0
5
TraesCS7B01G315600
chr7A
86.346
791
95
7
3
782
607523104
607523892
0.000000e+00
850.0
6
TraesCS7B01G315600
chr7A
86.425
221
11
9
1955
2170
607547043
607547249
1.200000e-54
224.0
7
TraesCS7B01G315600
chr7A
83.133
166
14
8
2714
2867
640674933
640674770
4.460000e-29
139.0
8
TraesCS7B01G315600
chr7A
94.545
55
2
1
2242
2295
607549863
607549917
2.120000e-12
84.2
9
TraesCS7B01G315600
chr2A
89.580
643
58
7
1
638
199711745
199712383
0.000000e+00
808.0
10
TraesCS7B01G315600
chr2A
81.818
165
18
8
2705
2859
57704778
57704940
9.660000e-26
128.0
11
TraesCS7B01G315600
chr2A
84.536
97
12
3
2766
2861
43659108
43659202
3.520000e-15
93.5
12
TraesCS7B01G315600
chr3D
89.392
641
62
6
1
638
398412791
398412154
0.000000e+00
802.0
13
TraesCS7B01G315600
chr3D
89.097
642
64
5
1
638
98610364
98611003
0.000000e+00
793.0
14
TraesCS7B01G315600
chr5D
89.236
641
61
7
1
638
407009906
407009271
0.000000e+00
795.0
15
TraesCS7B01G315600
chr3B
89.342
638
59
6
3
638
373287607
373286977
0.000000e+00
793.0
16
TraesCS7B01G315600
chr2D
89.028
638
63
6
3
638
364972518
364971886
0.000000e+00
784.0
17
TraesCS7B01G315600
chr2D
83.505
97
13
3
2766
2861
41905632
41905726
1.640000e-13
87.9
18
TraesCS7B01G315600
chr5B
88.768
641
58
11
1
638
488118567
488119196
0.000000e+00
773.0
19
TraesCS7B01G315600
chr4D
87.297
677
75
9
3
674
348294260
348294930
0.000000e+00
763.0
20
TraesCS7B01G315600
chr1A
87.912
182
21
1
1086
1267
78316097
78316277
2.590000e-51
213.0
21
TraesCS7B01G315600
chr1A
87.363
182
22
1
1086
1267
536801829
536802009
1.210000e-49
207.0
22
TraesCS7B01G315600
chr6A
86.813
182
23
1
1086
1267
88364802
88364982
5.610000e-48
202.0
23
TraesCS7B01G315600
chr1D
85.455
165
12
5
2705
2859
239336096
239335934
9.520000e-36
161.0
24
TraesCS7B01G315600
chr6B
82.609
184
15
8
2701
2867
133364234
133364051
2.670000e-31
147.0
25
TraesCS7B01G315600
chr4B
83.636
165
15
8
2705
2859
223394154
223394316
9.590000e-31
145.0
26
TraesCS7B01G315600
chr5A
82.677
127
10
8
2743
2859
529786688
529786812
5.850000e-18
102.0
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
TraesCS7B01G315600
chr7B
564171347
564174663
3316
False
6126.0
6126
100.0000
1
3317
1
chr7B.!!$F1
3316
1
TraesCS7B01G315600
chr7D
527706468
527710049
3581
False
2254.5
4265
92.6020
778
3317
2
chr7D.!!$F1
2539
2
TraesCS7B01G315600
chr7A
607543737
607549917
6180
False
1114.8
3203
93.7545
800
3317
4
chr7A.!!$F2
2517
3
TraesCS7B01G315600
chr7A
607523104
607523892
788
False
850.0
850
86.3460
3
782
1
chr7A.!!$F1
779
4
TraesCS7B01G315600
chr2A
199711745
199712383
638
False
808.0
808
89.5800
1
638
1
chr2A.!!$F3
637
5
TraesCS7B01G315600
chr3D
398412154
398412791
637
True
802.0
802
89.3920
1
638
1
chr3D.!!$R1
637
6
TraesCS7B01G315600
chr3D
98610364
98611003
639
False
793.0
793
89.0970
1
638
1
chr3D.!!$F1
637
7
TraesCS7B01G315600
chr5D
407009271
407009906
635
True
795.0
795
89.2360
1
638
1
chr5D.!!$R1
637
8
TraesCS7B01G315600
chr3B
373286977
373287607
630
True
793.0
793
89.3420
3
638
1
chr3B.!!$R1
635
9
TraesCS7B01G315600
chr2D
364971886
364972518
632
True
784.0
784
89.0280
3
638
1
chr2D.!!$R1
635
10
TraesCS7B01G315600
chr5B
488118567
488119196
629
False
773.0
773
88.7680
1
638
1
chr5B.!!$F1
637
11
TraesCS7B01G315600
chr4D
348294260
348294930
670
False
763.0
763
87.2970
3
674
1
chr4D.!!$F1
671
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.