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
TraesCS2D01G089700
chr2D
100.000
2297
0
0
1
2297
39589461
39591757
0
4242
1
TraesCS2D01G089700
chr2D
96.875
2304
65
5
1
2297
644701523
644703826
0
3849
2
TraesCS2D01G089700
chrUn
97.004
2303
62
5
1
2297
261514803
261512502
0
3864
3
TraesCS2D01G089700
chrUn
96.874
2303
63
5
1
2297
45099055
45101354
0
3845
4
TraesCS2D01G089700
chr5B
96.874
2303
63
5
1
2297
130613164
130615463
0
3845
5
TraesCS2D01G089700
chr5B
96.658
2304
70
5
1
2297
130570496
130568193
0
3821
6
TraesCS2D01G089700
chr5B
96.613
2303
69
5
1
2297
130608140
130610439
0
3812
7
TraesCS2D01G089700
chr3A
96.743
2303
67
5
1
2297
66032051
66029751
0
3831
8
TraesCS2D01G089700
chr7B
96.439
2303
74
5
1
2297
743035438
743033138
0
3792
9
TraesCS2D01G089700
chr2B
96.353
2303
75
6
1
2297
112867376
112869675
0
3779
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
TraesCS2D01G089700
chr2D
39589461
39591757
2296
False
4242.0
4242
100.0000
1
2297
1
chr2D.!!$F1
2296
1
TraesCS2D01G089700
chr2D
644701523
644703826
2303
False
3849.0
3849
96.8750
1
2297
1
chr2D.!!$F2
2296
2
TraesCS2D01G089700
chrUn
261512502
261514803
2301
True
3864.0
3864
97.0040
1
2297
1
chrUn.!!$R1
2296
3
TraesCS2D01G089700
chrUn
45099055
45101354
2299
False
3845.0
3845
96.8740
1
2297
1
chrUn.!!$F1
2296
4
TraesCS2D01G089700
chr5B
130608140
130615463
7323
False
3828.5
3845
96.7435
1
2297
2
chr5B.!!$F1
2296
5
TraesCS2D01G089700
chr5B
130568193
130570496
2303
True
3821.0
3821
96.6580
1
2297
1
chr5B.!!$R1
2296
6
TraesCS2D01G089700
chr3A
66029751
66032051
2300
True
3831.0
3831
96.7430
1
2297
1
chr3A.!!$R1
2296
7
TraesCS2D01G089700
chr7B
743033138
743035438
2300
True
3792.0
3792
96.4390
1
2297
1
chr7B.!!$R1
2296
8
TraesCS2D01G089700
chr2B
112867376
112869675
2299
False
3779.0
3779
96.3530
1
2297
1
chr2B.!!$F1
2296
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.