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
TraesCS7A01G307500
chr7A
100.000
2995
0
0
1
2995
434741319
434738325
0.000000e+00
5531
1
TraesCS7A01G307500
chr7D
96.272
3031
73
8
1
2995
386360423
386357397
0.000000e+00
4935
2
TraesCS7A01G307500
chr7B
93.225
1963
83
11
402
2331
380538653
380536708
0.000000e+00
2843
3
TraesCS7A01G307500
chr7B
94.141
495
23
3
2500
2994
380511800
380511312
0.000000e+00
749
4
TraesCS7A01G307500
chr7B
95.238
357
12
3
1
354
380538996
380538642
7.250000e-156
560
5
TraesCS7A01G307500
chr7B
85.965
171
16
4
2335
2504
380511991
380511828
3.070000e-40
176
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
TraesCS7A01G307500
chr7A
434738325
434741319
2994
True
5531.0
5531
100.0000
1
2995
1
chr7A.!!$R1
2994
1
TraesCS7A01G307500
chr7D
386357397
386360423
3026
True
4935.0
4935
96.2720
1
2995
1
chr7D.!!$R1
2994
2
TraesCS7A01G307500
chr7B
380536708
380538996
2288
True
1701.5
2843
94.2315
1
2331
2
chr7B.!!$R2
2330
3
TraesCS7A01G307500
chr7B
380511312
380511991
679
True
462.5
749
90.0530
2335
2994
2
chr7B.!!$R1
659
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.