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
TraesCS5B01G572900
chr5B
100.000
5345
0
0
4635
9979
713041576
713036232
0
9871
1
TraesCS5B01G572900
chr5B
100.000
4055
0
0
1
4055
713046210
713042156
0
7489
2
TraesCS5B01G572900
chr5A
98.223
5346
89
6
4635
9979
300053212
300058552
0
9341
3
TraesCS5B01G572900
chr5A
98.545
4056
54
4
5
4055
16623270
16619215
0
7158
4
TraesCS5B01G572900
chr5A
98.348
4055
65
2
3
4055
300048568
300052622
0
7116
5
TraesCS5B01G572900
chr7A
98.017
5346
101
4
4635
9979
671956321
671950980
0
9280
6
TraesCS5B01G572900
chr7A
97.871
5354
102
6
4635
9979
120921486
120916136
0
9245
7
TraesCS5B01G572900
chr7A
98.397
4056
60
4
3
4055
671960565
671956512
0
7125
8
TraesCS5B01G572900
chr7A
98.273
4053
67
2
3
4055
120828845
120824796
0
7094
9
TraesCS5B01G572900
chr6B
97.965
5356
94
8
4635
9979
525682425
525687776
0
9273
10
TraesCS5B01G572900
chr6B
98.195
997
17
1
8984
9979
394498524
394499520
0
1740
11
TraesCS5B01G572900
chr4B
97.476
5348
126
8
4635
9979
209145365
209140024
0
9119
12
TraesCS5B01G572900
chr7D
98.501
4403
55
5
4635
9034
382009925
382005531
0
7755
13
TraesCS5B01G572900
chr4D
97.979
4403
77
6
4635
9034
123582819
123587212
0
7627
14
TraesCS5B01G572900
chr4D
97.979
4404
74
7
4635
9031
123372027
123376422
0
7625
15
TraesCS5B01G572900
chr2D
97.637
4402
92
6
4635
9034
17962982
17958591
0
7542
16
TraesCS5B01G572900
chr2D
98.274
4056
64
3
3
4055
635037263
635041315
0
7097
17
TraesCS5B01G572900
chr7B
98.545
4056
54
4
3
4055
743066308
743070361
0
7158
18
TraesCS5B01G572900
chr2A
98.250
4056
67
4
3
4055
735172802
735176856
0
7094
19
TraesCS5B01G572900
chr3D
98.225
4056
67
3
3
4055
202611949
202616002
0
7086
20
TraesCS5B01G572900
chr3B
98.224
4054
68
3
3
4055
201635800
201631750
0
7084
21
TraesCS5B01G572900
chr3B
97.635
1015
22
2
8966
9979
775449268
775450281
0
1740
22
TraesCS5B01G572900
chr6A
98.269
1213
20
1
8768
9979
289117145
289118357
0
2122
23
TraesCS5B01G572900
chr2B
97.122
1251
34
2
8680
9930
357723273
357722025
0
2109
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
TraesCS5B01G572900
chr5B
713036232
713046210
9978
True
8680.0
9871
100.0000
1
9979
2
chr5B.!!$R1
9978
1
TraesCS5B01G572900
chr5A
300048568
300058552
9984
False
8228.5
9341
98.2855
3
9979
2
chr5A.!!$F1
9976
2
TraesCS5B01G572900
chr5A
16619215
16623270
4055
True
7158.0
7158
98.5450
5
4055
1
chr5A.!!$R1
4050
3
TraesCS5B01G572900
chr7A
120916136
120921486
5350
True
9245.0
9245
97.8710
4635
9979
1
chr7A.!!$R2
5344
4
TraesCS5B01G572900
chr7A
671950980
671960565
9585
True
8202.5
9280
98.2070
3
9979
2
chr7A.!!$R3
9976
5
TraesCS5B01G572900
chr7A
120824796
120828845
4049
True
7094.0
7094
98.2730
3
4055
1
chr7A.!!$R1
4052
6
TraesCS5B01G572900
chr6B
525682425
525687776
5351
False
9273.0
9273
97.9650
4635
9979
1
chr6B.!!$F2
5344
7
TraesCS5B01G572900
chr6B
394498524
394499520
996
False
1740.0
1740
98.1950
8984
9979
1
chr6B.!!$F1
995
8
TraesCS5B01G572900
chr4B
209140024
209145365
5341
True
9119.0
9119
97.4760
4635
9979
1
chr4B.!!$R1
5344
9
TraesCS5B01G572900
chr7D
382005531
382009925
4394
True
7755.0
7755
98.5010
4635
9034
1
chr7D.!!$R1
4399
10
TraesCS5B01G572900
chr4D
123582819
123587212
4393
False
7627.0
7627
97.9790
4635
9034
1
chr4D.!!$F2
4399
11
TraesCS5B01G572900
chr4D
123372027
123376422
4395
False
7625.0
7625
97.9790
4635
9031
1
chr4D.!!$F1
4396
12
TraesCS5B01G572900
chr2D
17958591
17962982
4391
True
7542.0
7542
97.6370
4635
9034
1
chr2D.!!$R1
4399
13
TraesCS5B01G572900
chr2D
635037263
635041315
4052
False
7097.0
7097
98.2740
3
4055
1
chr2D.!!$F1
4052
14
TraesCS5B01G572900
chr7B
743066308
743070361
4053
False
7158.0
7158
98.5450
3
4055
1
chr7B.!!$F1
4052
15
TraesCS5B01G572900
chr2A
735172802
735176856
4054
False
7094.0
7094
98.2500
3
4055
1
chr2A.!!$F1
4052
16
TraesCS5B01G572900
chr3D
202611949
202616002
4053
False
7086.0
7086
98.2250
3
4055
1
chr3D.!!$F1
4052
17
TraesCS5B01G572900
chr3B
201631750
201635800
4050
True
7084.0
7084
98.2240
3
4055
1
chr3B.!!$R1
4052
18
TraesCS5B01G572900
chr3B
775449268
775450281
1013
False
1740.0
1740
97.6350
8966
9979
1
chr3B.!!$F1
1013
19
TraesCS5B01G572900
chr6A
289117145
289118357
1212
False
2122.0
2122
98.2690
8768
9979
1
chr6A.!!$F1
1211
20
TraesCS5B01G572900
chr2B
357722025
357723273
1248
True
2109.0
2109
97.1220
8680
9930
1
chr2B.!!$R1
1250
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.