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
TraesCS5D01G345800
chr5D
100.000
2388
0
0
1
2388
432433806
432436193
0
4410
1
TraesCS5D01G345800
chr5D
98.079
2395
37
6
1
2388
503243819
503246211
0
4159
2
TraesCS5D01G345800
chr6D
98.246
2395
33
6
1
2388
389247275
389244883
0
4181
3
TraesCS5D01G345800
chr7B
98.121
2395
36
6
1
2388
663100878
663098486
0
4165
4
TraesCS5D01G345800
chr7B
97.912
2395
41
6
1
2388
662724951
662727343
0
4137
5
TraesCS5D01G345800
chr3A
98.079
2394
38
6
1
2388
66006585
66004194
0
4159
6
TraesCS5D01G345800
chr3A
97.368
2394
53
7
1
2388
650015965
650013576
0
4063
7
TraesCS5D01G345800
chr3D
98.078
2393
38
6
1
2388
589264976
589262587
0
4157
8
TraesCS5D01G345800
chr2A
97.912
2395
41
6
1
2388
726907908
726905516
0
4137
9
TraesCS5D01G345800
chr3B
97.663
2396
46
6
1
2388
201538068
201540461
0
4106
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
TraesCS5D01G345800
chr5D
432433806
432436193
2387
False
4410
4410
100.000
1
2388
1
chr5D.!!$F1
2387
1
TraesCS5D01G345800
chr5D
503243819
503246211
2392
False
4159
4159
98.079
1
2388
1
chr5D.!!$F2
2387
2
TraesCS5D01G345800
chr6D
389244883
389247275
2392
True
4181
4181
98.246
1
2388
1
chr6D.!!$R1
2387
3
TraesCS5D01G345800
chr7B
663098486
663100878
2392
True
4165
4165
98.121
1
2388
1
chr7B.!!$R1
2387
4
TraesCS5D01G345800
chr7B
662724951
662727343
2392
False
4137
4137
97.912
1
2388
1
chr7B.!!$F1
2387
5
TraesCS5D01G345800
chr3A
66004194
66006585
2391
True
4159
4159
98.079
1
2388
1
chr3A.!!$R1
2387
6
TraesCS5D01G345800
chr3A
650013576
650015965
2389
True
4063
4063
97.368
1
2388
1
chr3A.!!$R2
2387
7
TraesCS5D01G345800
chr3D
589262587
589264976
2389
True
4157
4157
98.078
1
2388
1
chr3D.!!$R1
2387
8
TraesCS5D01G345800
chr2A
726905516
726907908
2392
True
4137
4137
97.912
1
2388
1
chr2A.!!$R1
2387
9
TraesCS5D01G345800
chr3B
201538068
201540461
2393
False
4106
4106
97.663
1
2388
1
chr3B.!!$F1
2387
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.