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
TraesCS2B01G462000
chr2B
100.000
2516
0
0
1
2516
655676970
655674455
0.000000e+00
4647
1
TraesCS2B01G462000
chr2B
96.343
2516
77
11
1
2513
655681889
655684392
0.000000e+00
4122
2
TraesCS2B01G462000
chr2B
96.268
2519
85
9
2
2516
670339415
670336902
0.000000e+00
4122
3
TraesCS2B01G462000
chr2B
95.390
2516
81
16
1
2513
717661922
717664405
0.000000e+00
3971
4
TraesCS2B01G462000
chr2B
95.181
249
11
1
1
249
741199249
741199002
2.350000e-105
392
5
TraesCS2B01G462000
chr2B
94.779
249
12
1
1
249
741228996
741228749
1.090000e-103
387
6
TraesCS2B01G462000
chr4B
95.557
2521
98
12
1
2516
15528754
15526243
0.000000e+00
4023
7
TraesCS2B01G462000
chr5A
93.245
2502
124
32
38
2516
693855035
693852556
0.000000e+00
3642
8
TraesCS2B01G462000
chr5D
93.229
2496
121
22
38
2516
36575294
36572830
0.000000e+00
3629
9
TraesCS2B01G462000
chr6B
95.775
2201
80
13
325
2516
319483081
319480885
0.000000e+00
3537
10
TraesCS2B01G462000
chr6A
92.375
2505
143
30
38
2513
602785383
602787868
0.000000e+00
3524
11
TraesCS2B01G462000
chr1D
92.422
2494
129
27
38
2513
383338813
383341264
0.000000e+00
3504
12
TraesCS2B01G462000
chr2D
93.111
2395
116
23
139
2516
87968479
87966117
0.000000e+00
3463
13
TraesCS2B01G462000
chr7A
92.732
1775
98
16
38
1796
204218202
204216443
0.000000e+00
2534
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
TraesCS2B01G462000
chr2B
655674455
655676970
2515
True
4647
4647
100.000
1
2516
1
chr2B.!!$R1
2515
1
TraesCS2B01G462000
chr2B
655681889
655684392
2503
False
4122
4122
96.343
1
2513
1
chr2B.!!$F1
2512
2
TraesCS2B01G462000
chr2B
670336902
670339415
2513
True
4122
4122
96.268
2
2516
1
chr2B.!!$R2
2514
3
TraesCS2B01G462000
chr2B
717661922
717664405
2483
False
3971
3971
95.390
1
2513
1
chr2B.!!$F2
2512
4
TraesCS2B01G462000
chr4B
15526243
15528754
2511
True
4023
4023
95.557
1
2516
1
chr4B.!!$R1
2515
5
TraesCS2B01G462000
chr5A
693852556
693855035
2479
True
3642
3642
93.245
38
2516
1
chr5A.!!$R1
2478
6
TraesCS2B01G462000
chr5D
36572830
36575294
2464
True
3629
3629
93.229
38
2516
1
chr5D.!!$R1
2478
7
TraesCS2B01G462000
chr6B
319480885
319483081
2196
True
3537
3537
95.775
325
2516
1
chr6B.!!$R1
2191
8
TraesCS2B01G462000
chr6A
602785383
602787868
2485
False
3524
3524
92.375
38
2513
1
chr6A.!!$F1
2475
9
TraesCS2B01G462000
chr1D
383338813
383341264
2451
False
3504
3504
92.422
38
2513
1
chr1D.!!$F1
2475
10
TraesCS2B01G462000
chr2D
87966117
87968479
2362
True
3463
3463
93.111
139
2516
1
chr2D.!!$R1
2377
11
TraesCS2B01G462000
chr7A
204216443
204218202
1759
True
2534
2534
92.732
38
1796
1
chr7A.!!$R1
1758
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.