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
TraesCS5D01G009500
chr5D
100.000
2201
0
0
1
2201
6206665
6204465
0.000000e+00
4065
1
TraesCS5D01G009500
chr5D
98.442
2054
28
4
152
2201
240132461
240134514
0.000000e+00
3613
2
TraesCS5D01G009500
chr5D
98.240
1591
24
4
614
2201
449153933
449152344
0.000000e+00
2780
3
TraesCS5D01G009500
chr3B
97.686
2204
46
5
1
2201
201507736
201509937
0.000000e+00
3783
4
TraesCS5D01G009500
chr3D
97.731
2204
29
5
1
2201
21898714
21900899
0.000000e+00
3773
5
TraesCS5D01G009500
chr2D
96.150
2234
50
8
1
2201
334227074
334229304
0.000000e+00
3616
6
TraesCS5D01G009500
chr2D
98.662
299
4
0
103
401
141098400
141098102
4.160000e-147
531
7
TraesCS5D01G009500
chr2D
90.556
180
3
6
427
604
565514811
565514978
2.200000e-55
226
8
TraesCS5D01G009500
chr1D
98.608
1796
19
6
123
1914
254490942
254492735
0.000000e+00
3173
9
TraesCS5D01G009500
chr1D
98.641
1692
20
3
1
1689
483921800
483920109
0.000000e+00
2994
10
TraesCS5D01G009500
chr1D
98.160
1413
21
4
794
2201
483919206
483917794
0.000000e+00
2460
11
TraesCS5D01G009500
chr1D
98.610
1151
12
4
1054
2201
254493672
254494821
0.000000e+00
2034
12
TraesCS5D01G009500
chr1D
98.113
954
15
3
1220
2170
254493682
254492729
0.000000e+00
1659
13
TraesCS5D01G009500
chrUn
98.905
1553
17
0
1
1553
317472028
317470476
0.000000e+00
2774
14
TraesCS5D01G009500
chr7A
96.809
376
10
2
442
816
694550350
694550724
5.160000e-176
627
15
TraesCS5D01G009500
chr7A
98.208
279
5
0
196
474
167574529
167574807
2.540000e-134
488
16
TraesCS5D01G009500
chr6B
97.143
175
5
0
1
175
276897523
276897349
1.650000e-76
296
17
TraesCS5D01G009500
chr7B
98.182
165
2
1
1
165
262233605
262233442
9.940000e-74
287
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
TraesCS5D01G009500
chr5D
6204465
6206665
2200
True
4065.0
4065
100.0000
1
2201
1
chr5D.!!$R1
2200
1
TraesCS5D01G009500
chr5D
240132461
240134514
2053
False
3613.0
3613
98.4420
152
2201
1
chr5D.!!$F1
2049
2
TraesCS5D01G009500
chr5D
449152344
449153933
1589
True
2780.0
2780
98.2400
614
2201
1
chr5D.!!$R2
1587
3
TraesCS5D01G009500
chr3B
201507736
201509937
2201
False
3783.0
3783
97.6860
1
2201
1
chr3B.!!$F1
2200
4
TraesCS5D01G009500
chr3D
21898714
21900899
2185
False
3773.0
3773
97.7310
1
2201
1
chr3D.!!$F1
2200
5
TraesCS5D01G009500
chr2D
334227074
334229304
2230
False
3616.0
3616
96.1500
1
2201
1
chr2D.!!$F1
2200
6
TraesCS5D01G009500
chr1D
483917794
483921800
4006
True
2727.0
2994
98.4005
1
2201
2
chr1D.!!$R2
2200
7
TraesCS5D01G009500
chr1D
254490942
254494821
3879
False
2603.5
3173
98.6090
123
2201
2
chr1D.!!$F1
2078
8
TraesCS5D01G009500
chr1D
254492729
254493682
953
True
1659.0
1659
98.1130
1220
2170
1
chr1D.!!$R1
950
9
TraesCS5D01G009500
chrUn
317470476
317472028
1552
True
2774.0
2774
98.9050
1
1553
1
chrUn.!!$R1
1552
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.