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
TraesCS1B01G016200
chr1B
100.000
4497
0
0
1
4497
7902813
7898317
0.000000e+00
8305
1
TraesCS1B01G016200
chr1B
97.244
4499
120
4
1
4497
567735587
567731091
0.000000e+00
7618
2
TraesCS1B01G016200
chr1B
97.088
4499
124
7
1
4497
676864401
676859908
0.000000e+00
7576
3
TraesCS1B01G016200
chr6B
97.399
4498
112
5
1
4497
572516290
572511797
0.000000e+00
7653
4
TraesCS1B01G016200
chr4A
97.065
4498
128
4
2
4497
673171281
673166786
0.000000e+00
7572
5
TraesCS1B01G016200
chr2B
96.821
4498
137
5
1
4497
785300765
785296273
0.000000e+00
7509
6
TraesCS1B01G016200
chr2B
96.333
4499
124
11
1
4497
662568065
662572524
0.000000e+00
7356
7
TraesCS1B01G016200
chr5B
96.777
4499
136
5
1
4497
18261522
18257031
0.000000e+00
7496
8
TraesCS1B01G016200
chr5B
96.503
2002
55
3
2497
4497
568809872
568811859
0.000000e+00
3295
9
TraesCS1B01G016200
chr3B
96.577
4499
143
7
1
4497
667633189
667637678
0.000000e+00
7444
10
TraesCS1B01G016200
chr3B
91.617
167
12
2
3964
4129
13141464
13141629
3.500000e-56
230
11
TraesCS1B01G016200
chr7B
96.087
4498
149
6
1
4497
629987599
629992070
0.000000e+00
7306
12
TraesCS1B01G016200
chr2A
94.520
3960
213
4
1
3958
773697694
773693737
0.000000e+00
6107
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
TraesCS1B01G016200
chr1B
7898317
7902813
4496
True
8305
8305
100.000
1
4497
1
chr1B.!!$R1
4496
1
TraesCS1B01G016200
chr1B
567731091
567735587
4496
True
7618
7618
97.244
1
4497
1
chr1B.!!$R2
4496
2
TraesCS1B01G016200
chr1B
676859908
676864401
4493
True
7576
7576
97.088
1
4497
1
chr1B.!!$R3
4496
3
TraesCS1B01G016200
chr6B
572511797
572516290
4493
True
7653
7653
97.399
1
4497
1
chr6B.!!$R1
4496
4
TraesCS1B01G016200
chr4A
673166786
673171281
4495
True
7572
7572
97.065
2
4497
1
chr4A.!!$R1
4495
5
TraesCS1B01G016200
chr2B
785296273
785300765
4492
True
7509
7509
96.821
1
4497
1
chr2B.!!$R1
4496
6
TraesCS1B01G016200
chr2B
662568065
662572524
4459
False
7356
7356
96.333
1
4497
1
chr2B.!!$F1
4496
7
TraesCS1B01G016200
chr5B
18257031
18261522
4491
True
7496
7496
96.777
1
4497
1
chr5B.!!$R1
4496
8
TraesCS1B01G016200
chr5B
568809872
568811859
1987
False
3295
3295
96.503
2497
4497
1
chr5B.!!$F1
2000
9
TraesCS1B01G016200
chr3B
667633189
667637678
4489
False
7444
7444
96.577
1
4497
1
chr3B.!!$F2
4496
10
TraesCS1B01G016200
chr7B
629987599
629992070
4471
False
7306
7306
96.087
1
4497
1
chr7B.!!$F1
4496
11
TraesCS1B01G016200
chr2A
773693737
773697694
3957
True
6107
6107
94.520
1
3958
1
chr2A.!!$R1
3957
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.