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
TraesCS4B01G158900
chr4B
100.000
2189
0
0
1
2189
308679727
308677539
0
4043
1
TraesCS4B01G158900
chr2D
97.258
2188
54
6
3
2189
638424548
638426730
0
3703
2
TraesCS4B01G158900
chr5D
96.986
2190
59
7
3
2189
503291914
503294099
0
3672
3
TraesCS4B01G158900
chr5D
96.300
2189
58
9
3
2189
6176873
6174706
0
3572
4
TraesCS4B01G158900
chr5D
97.682
1855
38
5
3
1855
512410228
512412079
0
3182
5
TraesCS4B01G158900
chr5D
97.682
1855
37
6
3
1855
512417165
512419015
0
3182
6
TraesCS4B01G158900
chr5D
92.418
488
34
3
1702
2189
12935856
12936340
0
693
7
TraesCS4B01G158900
chr1D
96.758
2190
61
8
3
2189
254435077
254437259
0
3642
8
TraesCS4B01G158900
chr1D
95.477
2189
84
10
3
2189
51871894
51869719
0
3480
9
TraesCS4B01G158900
chr4D
93.656
2191
120
10
3
2189
207068182
207066007
0
3258
10
TraesCS4B01G158900
chr1B
96.930
1889
51
6
303
2189
633708037
633709920
0
3160
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
TraesCS4B01G158900
chr4B
308677539
308679727
2188
True
4043
4043
100.000
1
2189
1
chr4B.!!$R1
2188
1
TraesCS4B01G158900
chr2D
638424548
638426730
2182
False
3703
3703
97.258
3
2189
1
chr2D.!!$F1
2186
2
TraesCS4B01G158900
chr5D
503291914
503294099
2185
False
3672
3672
96.986
3
2189
1
chr5D.!!$F2
2186
3
TraesCS4B01G158900
chr5D
6174706
6176873
2167
True
3572
3572
96.300
3
2189
1
chr5D.!!$R1
2186
4
TraesCS4B01G158900
chr5D
512410228
512412079
1851
False
3182
3182
97.682
3
1855
1
chr5D.!!$F3
1852
5
TraesCS4B01G158900
chr5D
512417165
512419015
1850
False
3182
3182
97.682
3
1855
1
chr5D.!!$F4
1852
6
TraesCS4B01G158900
chr1D
254435077
254437259
2182
False
3642
3642
96.758
3
2189
1
chr1D.!!$F1
2186
7
TraesCS4B01G158900
chr1D
51869719
51871894
2175
True
3480
3480
95.477
3
2189
1
chr1D.!!$R1
2186
8
TraesCS4B01G158900
chr4D
207066007
207068182
2175
True
3258
3258
93.656
3
2189
1
chr4D.!!$R1
2186
9
TraesCS4B01G158900
chr1B
633708037
633709920
1883
False
3160
3160
96.930
303
2189
1
chr1B.!!$F1
1886
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.