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
TraesCS3A01G456800
chr3A
100.000
2815
0
0
1
2815
694367026
694364212
0
5199
1
TraesCS3A01G456800
chr5B
98.652
2819
34
3
1
2815
533066664
533069482
0
4992
2
TraesCS3A01G456800
chrUn
98.652
2818
34
4
1
2815
86455117
86457933
0
4990
3
TraesCS3A01G456800
chrUn
98.617
2819
35
3
1
2815
222680160
222677342
0
4987
4
TraesCS3A01G456800
chrUn
98.546
2819
36
4
1
2815
86449117
86451934
0
4974
5
TraesCS3A01G456800
chr1A
98.546
2820
36
3
1
2815
238117485
238120304
0
4975
6
TraesCS3A01G456800
chr1A
98.439
2819
39
4
1
2815
238121408
238124225
0
4957
7
TraesCS3A01G456800
chr6B
98.510
2818
38
4
1
2815
596628844
596631660
0
4968
8
TraesCS3A01G456800
chr3B
98.085
2820
49
3
1
2815
92326382
92329201
0
4903
9
TraesCS3A01G456800
chr2A
96.345
2818
89
12
1
2815
444294984
444292178
0
4621
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
TraesCS3A01G456800
chr3A
694364212
694367026
2814
True
5199
5199
100.0000
1
2815
1
chr3A.!!$R1
2814
1
TraesCS3A01G456800
chr5B
533066664
533069482
2818
False
4992
4992
98.6520
1
2815
1
chr5B.!!$F1
2814
2
TraesCS3A01G456800
chrUn
222677342
222680160
2818
True
4987
4987
98.6170
1
2815
1
chrUn.!!$R1
2814
3
TraesCS3A01G456800
chrUn
86449117
86457933
8816
False
4982
4990
98.5990
1
2815
2
chrUn.!!$F1
2814
4
TraesCS3A01G456800
chr1A
238117485
238124225
6740
False
4966
4975
98.4925
1
2815
2
chr1A.!!$F1
2814
5
TraesCS3A01G456800
chr6B
596628844
596631660
2816
False
4968
4968
98.5100
1
2815
1
chr6B.!!$F1
2814
6
TraesCS3A01G456800
chr3B
92326382
92329201
2819
False
4903
4903
98.0850
1
2815
1
chr3B.!!$F1
2814
7
TraesCS3A01G456800
chr2A
444292178
444294984
2806
True
4621
4621
96.3450
1
2815
1
chr2A.!!$R1
2814
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.