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
TraesCS7B01G120200
chr7B
100.000
2277
0
0
1
2277
139619347
139617071
0
4205
1
TraesCS7B01G120200
chr7B
96.004
2277
84
3
1
2277
698126662
698124393
0
3694
2
TraesCS7B01G120200
chr7B
95.608
2277
94
2
1
2277
716795567
716793297
0
3646
3
TraesCS7B01G120200
chr1D
96.355
2277
82
1
1
2277
212429140
212431415
0
3744
4
TraesCS7B01G120200
chrUn
96.311
2277
83
1
1
2277
257944383
257946658
0
3738
5
TraesCS7B01G120200
chrUn
96.047
2277
84
2
1
2277
233524997
233522727
0
3701
6
TraesCS7B01G120200
chr7A
95.872
2277
88
2
1
2277
60095927
60093657
0
3679
7
TraesCS7B01G120200
chr7A
95.608
2277
99
1
1
2277
211237863
211235588
0
3650
8
TraesCS7B01G120200
chr2D
95.784
2277
93
3
1
2277
637308434
637306161
0
3670
9
TraesCS7B01G120200
chr4D
95.740
2277
96
1
1
2277
123689233
123691508
0
3666
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
TraesCS7B01G120200
chr7B
139617071
139619347
2276
True
4205
4205
100.000
1
2277
1
chr7B.!!$R1
2276
1
TraesCS7B01G120200
chr7B
698124393
698126662
2269
True
3694
3694
96.004
1
2277
1
chr7B.!!$R2
2276
2
TraesCS7B01G120200
chr7B
716793297
716795567
2270
True
3646
3646
95.608
1
2277
1
chr7B.!!$R3
2276
3
TraesCS7B01G120200
chr1D
212429140
212431415
2275
False
3744
3744
96.355
1
2277
1
chr1D.!!$F1
2276
4
TraesCS7B01G120200
chrUn
257944383
257946658
2275
False
3738
3738
96.311
1
2277
1
chrUn.!!$F1
2276
5
TraesCS7B01G120200
chrUn
233522727
233524997
2270
True
3701
3701
96.047
1
2277
1
chrUn.!!$R1
2276
6
TraesCS7B01G120200
chr7A
60093657
60095927
2270
True
3679
3679
95.872
1
2277
1
chr7A.!!$R1
2276
7
TraesCS7B01G120200
chr7A
211235588
211237863
2275
True
3650
3650
95.608
1
2277
1
chr7A.!!$R2
2276
8
TraesCS7B01G120200
chr2D
637306161
637308434
2273
True
3670
3670
95.784
1
2277
1
chr2D.!!$R1
2276
9
TraesCS7B01G120200
chr4D
123689233
123691508
2275
False
3666
3666
95.740
1
2277
1
chr4D.!!$F1
2276
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.