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
TraesCS1D01G128100
chr1D
100.000
2636
0
0
1
2636
141317645
141315010
0
4868
1
TraesCS1D01G128100
chrUn
99.242
2638
15
4
1
2636
189406574
189409208
0
4756
2
TraesCS1D01G128100
chrUn
98.939
2638
22
4
1
2636
251410021
251407388
0
4711
3
TraesCS1D01G128100
chr6D
99.052
2637
20
3
1
2636
124531612
124534244
0
4726
4
TraesCS1D01G128100
chr7D
98.862
2637
24
4
1
2636
626683745
626681114
0
4698
5
TraesCS1D01G128100
chr7B
98.749
2638
28
4
1
2636
644462934
644465568
0
4684
6
TraesCS1D01G128100
chr1B
98.560
2638
32
4
1
2636
668809669
668807036
0
4656
7
TraesCS1D01G128100
chr1B
98.522
2638
33
5
1
2636
638705174
638702541
0
4650
8
TraesCS1D01G128100
chr1B
98.218
2638
42
4
1
2636
672474652
672477286
0
4606
9
TraesCS1D01G128100
chr3A
98.446
2638
35
5
1
2636
633106746
633109379
0
4639
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
TraesCS1D01G128100
chr1D
141315010
141317645
2635
True
4868
4868
100.000
1
2636
1
chr1D.!!$R1
2635
1
TraesCS1D01G128100
chrUn
189406574
189409208
2634
False
4756
4756
99.242
1
2636
1
chrUn.!!$F1
2635
2
TraesCS1D01G128100
chrUn
251407388
251410021
2633
True
4711
4711
98.939
1
2636
1
chrUn.!!$R1
2635
3
TraesCS1D01G128100
chr6D
124531612
124534244
2632
False
4726
4726
99.052
1
2636
1
chr6D.!!$F1
2635
4
TraesCS1D01G128100
chr7D
626681114
626683745
2631
True
4698
4698
98.862
1
2636
1
chr7D.!!$R1
2635
5
TraesCS1D01G128100
chr7B
644462934
644465568
2634
False
4684
4684
98.749
1
2636
1
chr7B.!!$F1
2635
6
TraesCS1D01G128100
chr1B
668807036
668809669
2633
True
4656
4656
98.560
1
2636
1
chr1B.!!$R2
2635
7
TraesCS1D01G128100
chr1B
638702541
638705174
2633
True
4650
4650
98.522
1
2636
1
chr1B.!!$R1
2635
8
TraesCS1D01G128100
chr1B
672474652
672477286
2634
False
4606
4606
98.218
1
2636
1
chr1B.!!$F1
2635
9
TraesCS1D01G128100
chr3A
633106746
633109379
2633
False
4639
4639
98.446
1
2636
1
chr3A.!!$F1
2635
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.