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
TraesCS2B01G283400
chr2B
100.000
2609
0
0
1
2609
391143792
391146400
0
4819
1
TraesCS2B01G283400
chr2B
97.359
2613
63
3
1
2609
391226256
391223646
0
4438
2
TraesCS2B01G283400
chr6B
98.200
2611
45
1
1
2609
596602871
596600261
0
4560
3
TraesCS2B01G283400
chr7A
98.047
2612
47
2
1
2609
638508678
638506068
0
4538
4
TraesCS2B01G283400
chr7A
97.894
2611
50
3
1
2609
708244614
708247221
0
4512
5
TraesCS2B01G283400
chrUn
98.047
2612
46
4
1
2609
171007273
171009882
0
4536
6
TraesCS2B01G283400
chr5B
97.742
2613
55
2
1
2609
567278982
567281594
0
4495
7
TraesCS2B01G283400
chr1B
97.664
2611
58
3
1
2609
672540211
672542820
0
4481
8
TraesCS2B01G283400
chr4B
97.317
2609
66
4
1
2609
495566953
495569557
0
4427
9
TraesCS2B01G283400
chr3B
96.180
2618
87
9
1
2609
39876066
39878679
0
4268
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
TraesCS2B01G283400
chr2B
391143792
391146400
2608
False
4819
4819
100.000
1
2609
1
chr2B.!!$F1
2608
1
TraesCS2B01G283400
chr2B
391223646
391226256
2610
True
4438
4438
97.359
1
2609
1
chr2B.!!$R1
2608
2
TraesCS2B01G283400
chr6B
596600261
596602871
2610
True
4560
4560
98.200
1
2609
1
chr6B.!!$R1
2608
3
TraesCS2B01G283400
chr7A
638506068
638508678
2610
True
4538
4538
98.047
1
2609
1
chr7A.!!$R1
2608
4
TraesCS2B01G283400
chr7A
708244614
708247221
2607
False
4512
4512
97.894
1
2609
1
chr7A.!!$F1
2608
5
TraesCS2B01G283400
chrUn
171007273
171009882
2609
False
4536
4536
98.047
1
2609
1
chrUn.!!$F1
2608
6
TraesCS2B01G283400
chr5B
567278982
567281594
2612
False
4495
4495
97.742
1
2609
1
chr5B.!!$F1
2608
7
TraesCS2B01G283400
chr1B
672540211
672542820
2609
False
4481
4481
97.664
1
2609
1
chr1B.!!$F1
2608
8
TraesCS2B01G283400
chr4B
495566953
495569557
2604
False
4427
4427
97.317
1
2609
1
chr4B.!!$F1
2608
9
TraesCS2B01G283400
chr3B
39876066
39878679
2613
False
4268
4268
96.180
1
2609
1
chr3B.!!$F1
2608
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.