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
TraesCS7A01G289200
chr7A
100.000
2141
0
0
1
2141
352181629
352179489
0
3954
1
TraesCS7A01G289200
chr2D
95.026
2151
93
7
1
2141
272793671
272791525
0
3367
2
TraesCS7A01G289200
chr2D
94.103
2001
87
12
169
2141
272564345
272566342
0
3013
3
TraesCS7A01G289200
chr3D
94.421
2169
87
16
1
2141
589279320
589277158
0
3304
4
TraesCS7A01G289200
chr5D
94.191
2169
95
12
1
2141
503218440
503220605
0
3278
5
TraesCS7A01G289200
chr5D
93.868
2169
102
14
1
2141
503278004
503275839
0
3240
6
TraesCS7A01G289200
chr5D
93.638
2169
107
14
1
2141
6189162
6191327
0
3212
7
TraesCS7A01G289200
chr5D
94.051
1933
84
12
237
2141
446174242
446176171
0
2904
8
TraesCS7A01G289200
chr1A
94.191
2169
95
12
1
2141
554512470
554514635
0
3278
9
TraesCS7A01G289200
chr3B
94.099
2169
97
14
1
2141
201527246
201529411
0
3267
10
TraesCS7A01G289200
chr3B
94.349
1681
65
11
488
2141
101911885
101913562
0
2551
11
TraesCS7A01G289200
chr3A
94.050
2168
98
14
1
2141
672909785
672907622
0
3260
12
TraesCS7A01G289200
chr3A
93.865
2168
103
14
1
2141
594899402
594897238
0
3240
13
TraesCS7A01G289200
chrUn
94.004
2168
100
11
1
2141
216518380
216516216
0
3256
14
TraesCS7A01G289200
chrUn
93.816
1714
83
11
1
1692
346596272
346594560
0
2556
15
TraesCS7A01G289200
chr6D
93.963
2170
98
16
1
2141
168255148
168257313
0
3251
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
TraesCS7A01G289200
chr7A
352179489
352181629
2140
True
3954
3954
100.000
1
2141
1
chr7A.!!$R1
2140
1
TraesCS7A01G289200
chr2D
272791525
272793671
2146
True
3367
3367
95.026
1
2141
1
chr2D.!!$R1
2140
2
TraesCS7A01G289200
chr2D
272564345
272566342
1997
False
3013
3013
94.103
169
2141
1
chr2D.!!$F1
1972
3
TraesCS7A01G289200
chr3D
589277158
589279320
2162
True
3304
3304
94.421
1
2141
1
chr3D.!!$R1
2140
4
TraesCS7A01G289200
chr5D
503218440
503220605
2165
False
3278
3278
94.191
1
2141
1
chr5D.!!$F3
2140
5
TraesCS7A01G289200
chr5D
503275839
503278004
2165
True
3240
3240
93.868
1
2141
1
chr5D.!!$R1
2140
6
TraesCS7A01G289200
chr5D
6189162
6191327
2165
False
3212
3212
93.638
1
2141
1
chr5D.!!$F1
2140
7
TraesCS7A01G289200
chr5D
446174242
446176171
1929
False
2904
2904
94.051
237
2141
1
chr5D.!!$F2
1904
8
TraesCS7A01G289200
chr1A
554512470
554514635
2165
False
3278
3278
94.191
1
2141
1
chr1A.!!$F1
2140
9
TraesCS7A01G289200
chr3B
201527246
201529411
2165
False
3267
3267
94.099
1
2141
1
chr3B.!!$F2
2140
10
TraesCS7A01G289200
chr3B
101911885
101913562
1677
False
2551
2551
94.349
488
2141
1
chr3B.!!$F1
1653
11
TraesCS7A01G289200
chr3A
672907622
672909785
2163
True
3260
3260
94.050
1
2141
1
chr3A.!!$R2
2140
12
TraesCS7A01G289200
chr3A
594897238
594899402
2164
True
3240
3240
93.865
1
2141
1
chr3A.!!$R1
2140
13
TraesCS7A01G289200
chrUn
216516216
216518380
2164
True
3256
3256
94.004
1
2141
1
chrUn.!!$R1
2140
14
TraesCS7A01G289200
chrUn
346594560
346596272
1712
True
2556
2556
93.816
1
1692
1
chrUn.!!$R2
1691
15
TraesCS7A01G289200
chr6D
168255148
168257313
2165
False
3251
3251
93.963
1
2141
1
chr6D.!!$F1
2140
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.