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
TraesCS5D01G183800
chr5D
100.000
2123
0
0
1
2123
285464577
285466699
0.000000e+00
3921
1
TraesCS5D01G183800
chr5D
91.736
121
9
1
1
121
285300703
285300822
1.300000e-37
167
2
TraesCS5D01G183800
chr5A
94.111
1715
68
14
1
1692
377181744
377183448
0.000000e+00
2577
3
TraesCS5D01G183800
chr5A
97.895
285
6
0
1839
2123
377184148
377184432
5.260000e-136
494
4
TraesCS5D01G183800
chr5A
95.726
117
4
1
1681
1797
377183618
377183733
1.000000e-43
187
5
TraesCS5D01G183800
chr5B
89.695
2067
128
45
5
2016
322912959
322914995
0.000000e+00
2558
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
TraesCS5D01G183800
chr5D
285464577
285466699
2122
False
3921
3921
100.000000
1
2123
1
chr5D.!!$F2
2122
1
TraesCS5D01G183800
chr5A
377181744
377184432
2688
False
1086
2577
95.910667
1
2123
3
chr5A.!!$F1
2122
2
TraesCS5D01G183800
chr5B
322912959
322914995
2036
False
2558
2558
89.695000
5
2016
1
chr5B.!!$F1
2011
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.