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
TraesCS6A01G252200
chr6A
100.000
2264
0
0
1
2264
466678913
466681176
0.000000e+00
4181
1
TraesCS6A01G252200
chr5A
98.455
2266
31
4
1
2264
591473726
591475989
0.000000e+00
3988
2
TraesCS6A01G252200
chr1B
98.453
2262
31
4
1
2260
649301320
649299061
0.000000e+00
3980
3
TraesCS6A01G252200
chr7A
98.276
2262
35
4
1
2260
497719530
497717271
0.000000e+00
3958
4
TraesCS6A01G252200
chr5B
98.258
2182
34
4
1
2180
297110492
297112671
0.000000e+00
3816
5
TraesCS6A01G252200
chr5B
99.126
1946
16
1
1
1945
351469616
351467671
0.000000e+00
3498
6
TraesCS6A01G252200
chr5B
99.126
1946
16
1
1
1945
433002513
433000568
0.000000e+00
3498
7
TraesCS6A01G252200
chr5B
99.126
1945
17
0
1
1945
471294933
471292989
0.000000e+00
3498
8
TraesCS6A01G252200
chr5B
98.028
355
7
0
1910
2264
433000567
433000213
3.190000e-173
617
9
TraesCS6A01G252200
chr5B
97.183
355
10
0
1910
2264
471292988
471292634
3.220000e-168
601
10
TraesCS6A01G252200
chr2A
99.177
1945
16
0
1
1945
148615284
148613340
0.000000e+00
3504
11
TraesCS6A01G252200
chr2A
99.228
1942
15
0
1
1942
728933672
728935613
0.000000e+00
3504
12
TraesCS6A01G252200
chr2A
97.746
355
8
0
1910
2264
728935735
728936089
1.490000e-171
612
13
TraesCS6A01G252200
chr3B
87.311
528
55
10
1738
2262
16122670
16122152
5.380000e-166
593
14
TraesCS6A01G252200
chr2B
86.338
527
58
11
1738
2262
563915374
563914860
1.520000e-156
562
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
TraesCS6A01G252200
chr6A
466678913
466681176
2263
False
4181.0
4181
100.0000
1
2264
1
chr6A.!!$F1
2263
1
TraesCS6A01G252200
chr5A
591473726
591475989
2263
False
3988.0
3988
98.4550
1
2264
1
chr5A.!!$F1
2263
2
TraesCS6A01G252200
chr1B
649299061
649301320
2259
True
3980.0
3980
98.4530
1
2260
1
chr1B.!!$R1
2259
3
TraesCS6A01G252200
chr7A
497717271
497719530
2259
True
3958.0
3958
98.2760
1
2260
1
chr7A.!!$R1
2259
4
TraesCS6A01G252200
chr5B
297110492
297112671
2179
False
3816.0
3816
98.2580
1
2180
1
chr5B.!!$F1
2179
5
TraesCS6A01G252200
chr5B
351467671
351469616
1945
True
3498.0
3498
99.1260
1
1945
1
chr5B.!!$R1
1944
6
TraesCS6A01G252200
chr5B
433000213
433002513
2300
True
2057.5
3498
98.5770
1
2264
2
chr5B.!!$R2
2263
7
TraesCS6A01G252200
chr5B
471292634
471294933
2299
True
2049.5
3498
98.1545
1
2264
2
chr5B.!!$R3
2263
8
TraesCS6A01G252200
chr2A
148613340
148615284
1944
True
3504.0
3504
99.1770
1
1945
1
chr2A.!!$R1
1944
9
TraesCS6A01G252200
chr2A
728933672
728936089
2417
False
2058.0
3504
98.4870
1
2264
2
chr2A.!!$F1
2263
10
TraesCS6A01G252200
chr3B
16122152
16122670
518
True
593.0
593
87.3110
1738
2262
1
chr3B.!!$R1
524
11
TraesCS6A01G252200
chr2B
563914860
563915374
514
True
562.0
562
86.3380
1738
2262
1
chr2B.!!$R1
524
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.