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
TraesCS3B01G363900
chr3B
100.000
2585
0
0
1
2585
575756190
575753606
0
4774
1
TraesCS3B01G363900
chr7A
97.895
1995
41
1
592
2585
60107873
60105879
0
3450
2
TraesCS3B01G363900
chr7A
97.980
594
12
0
1
594
60108502
60107909
0
1031
3
TraesCS3B01G363900
chr5A
97.895
1995
41
1
592
2585
73030715
73032709
0
3450
4
TraesCS3B01G363900
chr5A
97.811
594
13
0
1
594
73030086
73030679
0
1026
5
TraesCS3B01G363900
chr1B
97.644
1995
46
1
592
2585
638750886
638748892
0
3422
6
TraesCS3B01G363900
chr1B
97.980
594
12
0
1
594
638751515
638750922
0
1031
7
TraesCS3B01G363900
chr2D
97.494
1995
48
2
592
2585
637322006
637320013
0
3406
8
TraesCS3B01G363900
chr2D
96.540
1994
66
2
592
2582
189854086
189856079
0
3297
9
TraesCS3B01G363900
chr2D
97.663
599
9
1
1
594
635050985
635051583
0
1024
10
TraesCS3B01G363900
chr3D
97.093
1995
56
2
592
2585
523758739
523760732
0
3362
11
TraesCS3B01G363900
chr2B
96.842
1995
62
1
592
2585
500713242
500715236
0
3334
12
TraesCS3B01G363900
chr2B
98.316
594
10
0
1
594
500712613
500713206
0
1042
13
TraesCS3B01G363900
chr6B
96.591
1995
66
2
592
2585
388368508
388366515
0
3306
14
TraesCS3B01G363900
chr6B
95.984
1992
78
2
592
2581
588838077
588840068
0
3234
15
TraesCS3B01G363900
chr6B
97.980
594
12
0
1
594
388177394
388176801
0
1031
16
TraesCS3B01G363900
chrUn
98.485
594
9
0
1
594
273321806
273321213
0
1048
17
TraesCS3B01G363900
chrUn
98.485
594
9
0
1
594
404560500
404561093
0
1048
18
TraesCS3B01G363900
chr6A
97.997
599
7
1
1
594
608885504
608886102
0
1035
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
TraesCS3B01G363900
chr3B
575753606
575756190
2584
True
4774.0
4774
100.0000
1
2585
1
chr3B.!!$R1
2584
1
TraesCS3B01G363900
chr7A
60105879
60108502
2623
True
2240.5
3450
97.9375
1
2585
2
chr7A.!!$R1
2584
2
TraesCS3B01G363900
chr5A
73030086
73032709
2623
False
2238.0
3450
97.8530
1
2585
2
chr5A.!!$F1
2584
3
TraesCS3B01G363900
chr1B
638748892
638751515
2623
True
2226.5
3422
97.8120
1
2585
2
chr1B.!!$R1
2584
4
TraesCS3B01G363900
chr2D
637320013
637322006
1993
True
3406.0
3406
97.4940
592
2585
1
chr2D.!!$R1
1993
5
TraesCS3B01G363900
chr2D
189854086
189856079
1993
False
3297.0
3297
96.5400
592
2582
1
chr2D.!!$F1
1990
6
TraesCS3B01G363900
chr2D
635050985
635051583
598
False
1024.0
1024
97.6630
1
594
1
chr2D.!!$F2
593
7
TraesCS3B01G363900
chr3D
523758739
523760732
1993
False
3362.0
3362
97.0930
592
2585
1
chr3D.!!$F1
1993
8
TraesCS3B01G363900
chr2B
500712613
500715236
2623
False
2188.0
3334
97.5790
1
2585
2
chr2B.!!$F1
2584
9
TraesCS3B01G363900
chr6B
388366515
388368508
1993
True
3306.0
3306
96.5910
592
2585
1
chr6B.!!$R2
1993
10
TraesCS3B01G363900
chr6B
588838077
588840068
1991
False
3234.0
3234
95.9840
592
2581
1
chr6B.!!$F1
1989
11
TraesCS3B01G363900
chr6B
388176801
388177394
593
True
1031.0
1031
97.9800
1
594
1
chr6B.!!$R1
593
12
TraesCS3B01G363900
chrUn
273321213
273321806
593
True
1048.0
1048
98.4850
1
594
1
chrUn.!!$R1
593
13
TraesCS3B01G363900
chrUn
404560500
404561093
593
False
1048.0
1048
98.4850
1
594
1
chrUn.!!$F1
593
14
TraesCS3B01G363900
chr6A
608885504
608886102
598
False
1035.0
1035
97.9970
1
594
1
chr6A.!!$F1
593
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.