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
TraesCS1D01G153000
chr1D
100.000
2577
0
0
1
2577
212468996
212466420
0
4759
1
TraesCS1D01G153000
chr7D
98.689
2593
16
6
1
2577
579028591
579031181
0
4584
2
TraesCS1D01G153000
chr4D
98.650
2592
20
6
1
2577
123655989
123653398
0
4578
3
TraesCS1D01G153000
chr4D
98.611
2592
21
6
1
2577
123509290
123506699
0
4573
4
TraesCS1D01G153000
chr4D
98.497
2595
19
9
1
2577
123738787
123736195
0
4558
5
TraesCS1D01G153000
chr6D
97.879
2593
38
7
1
2577
108466575
108469166
0
4468
6
TraesCS1D01G153000
chrUn
95.625
2606
66
25
1
2577
221549555
221546969
0
4137
7
TraesCS1D01G153000
chrUn
95.463
2601
80
22
1
2577
186192553
186189967
0
4115
8
TraesCS1D01G153000
chr7B
95.238
2604
81
25
1
2577
743004925
743007512
0
4082
9
TraesCS1D01G153000
chr7B
96.664
1439
35
4
1
1427
139543318
139541881
0
2379
10
TraesCS1D01G153000
chr4B
97.377
1563
20
7
1035
2577
209271422
209269861
0
2639
11
TraesCS1D01G153000
chr5A
96.949
1442
29
3
1
1427
534932661
534934102
0
2405
12
TraesCS1D01G153000
chr7A
96.736
1440
33
4
1
1427
211291172
211292610
0
2386
13
TraesCS1D01G153000
chr2B
97.220
1403
28
6
1
1392
357246177
357244775
0
2364
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
TraesCS1D01G153000
chr1D
212466420
212468996
2576
True
4759
4759
100.000
1
2577
1
chr1D.!!$R1
2576
1
TraesCS1D01G153000
chr7D
579028591
579031181
2590
False
4584
4584
98.689
1
2577
1
chr7D.!!$F1
2576
2
TraesCS1D01G153000
chr4D
123653398
123655989
2591
True
4578
4578
98.650
1
2577
1
chr4D.!!$R2
2576
3
TraesCS1D01G153000
chr4D
123506699
123509290
2591
True
4573
4573
98.611
1
2577
1
chr4D.!!$R1
2576
4
TraesCS1D01G153000
chr4D
123736195
123738787
2592
True
4558
4558
98.497
1
2577
1
chr4D.!!$R3
2576
5
TraesCS1D01G153000
chr6D
108466575
108469166
2591
False
4468
4468
97.879
1
2577
1
chr6D.!!$F1
2576
6
TraesCS1D01G153000
chrUn
221546969
221549555
2586
True
4137
4137
95.625
1
2577
1
chrUn.!!$R2
2576
7
TraesCS1D01G153000
chrUn
186189967
186192553
2586
True
4115
4115
95.463
1
2577
1
chrUn.!!$R1
2576
8
TraesCS1D01G153000
chr7B
743004925
743007512
2587
False
4082
4082
95.238
1
2577
1
chr7B.!!$F1
2576
9
TraesCS1D01G153000
chr7B
139541881
139543318
1437
True
2379
2379
96.664
1
1427
1
chr7B.!!$R1
1426
10
TraesCS1D01G153000
chr4B
209269861
209271422
1561
True
2639
2639
97.377
1035
2577
1
chr4B.!!$R1
1542
11
TraesCS1D01G153000
chr5A
534932661
534934102
1441
False
2405
2405
96.949
1
1427
1
chr5A.!!$F1
1426
12
TraesCS1D01G153000
chr7A
211291172
211292610
1438
False
2386
2386
96.736
1
1427
1
chr7A.!!$F1
1426
13
TraesCS1D01G153000
chr2B
357244775
357246177
1402
True
2364
2364
97.220
1
1392
1
chr2B.!!$R1
1391
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.