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
TraesCS2D01G564600
chr2D
100.000
2528
0
0
1
2528
635037259
635039786
0
4669
1
TraesCS2D01G564600
chr7B
98.775
2531
27
3
1
2528
743066304
743068833
0
4499
2
TraesCS2D01G564600
chr2A
98.696
2530
27
3
1
2526
735172798
735175325
0
4484
3
TraesCS2D01G564600
chr7A
98.655
2528
31
1
1
2528
120828849
120826325
0
4477
4
TraesCS2D01G564600
chr7A
98.538
2530
33
4
1
2528
671960569
671958042
0
4464
5
TraesCS2D01G564600
chr3D
98.616
2529
33
2
1
2528
202611945
202614472
0
4475
6
TraesCS2D01G564600
chr5A
98.579
2533
30
4
1
2528
16623276
16620745
0
4473
7
TraesCS2D01G564600
chr3B
98.616
2528
32
2
1
2528
201635804
201633280
0
4471
8
TraesCS2D01G564600
chr5B
98.458
2530
34
2
1
2528
713046212
713043686
0
4451
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
TraesCS2D01G564600
chr2D
635037259
635039786
2527
False
4669
4669
100.000
1
2528
1
chr2D.!!$F1
2527
1
TraesCS2D01G564600
chr7B
743066304
743068833
2529
False
4499
4499
98.775
1
2528
1
chr7B.!!$F1
2527
2
TraesCS2D01G564600
chr2A
735172798
735175325
2527
False
4484
4484
98.696
1
2526
1
chr2A.!!$F1
2525
3
TraesCS2D01G564600
chr7A
120826325
120828849
2524
True
4477
4477
98.655
1
2528
1
chr7A.!!$R1
2527
4
TraesCS2D01G564600
chr7A
671958042
671960569
2527
True
4464
4464
98.538
1
2528
1
chr7A.!!$R2
2527
5
TraesCS2D01G564600
chr3D
202611945
202614472
2527
False
4475
4475
98.616
1
2528
1
chr3D.!!$F1
2527
6
TraesCS2D01G564600
chr5A
16620745
16623276
2531
True
4473
4473
98.579
1
2528
1
chr5A.!!$R1
2527
7
TraesCS2D01G564600
chr3B
201633280
201635804
2524
True
4471
4471
98.616
1
2528
1
chr3B.!!$R1
2527
8
TraesCS2D01G564600
chr5B
713043686
713046212
2526
True
4451
4451
98.458
1
2528
1
chr5B.!!$R1
2527
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.