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
TraesCS5A01G116600
chr5A
100.000
2319
0
0
1
2319
238791595
238789277
0
4283
1
TraesCS5A01G116600
chr5A
98.264
1786
25
2
1
1785
300072979
300074759
0
3121
2
TraesCS5A01G116600
chr5A
97.353
529
14
0
1791
2319
169395371
169395899
0
900
3
TraesCS5A01G116600
chr5A
97.358
530
13
1
1791
2319
610021121
610021650
0
900
4
TraesCS5A01G116600
chr7A
98.487
1785
27
0
1
1785
4959838
4961622
0
3147
5
TraesCS5A01G116600
chr7A
97.736
530
11
1
1791
2319
443009303
443009832
0
911
6
TraesCS5A01G116600
chr7A
97.358
530
13
1
1791
2319
344568306
344568835
0
900
7
TraesCS5A01G116600
chrUn
98.264
1786
25
2
1
1785
189392539
189394319
0
3121
8
TraesCS5A01G116600
chr2A
98.155
1789
27
2
1
1788
618279956
618278173
0
3116
9
TraesCS5A01G116600
chr7D
98.099
1789
28
2
1
1788
626698490
626696707
0
3110
10
TraesCS5A01G116600
chr7D
97.987
1788
31
1
1
1788
203556345
203554563
0
3097
11
TraesCS5A01G116600
chr7B
98.152
1786
27
2
1
1785
743086199
743087979
0
3110
12
TraesCS5A01G116600
chr6A
98.151
1785
27
3
1
1785
289128632
289130410
0
3109
13
TraesCS5A01G116600
chr6A
97.363
531
12
2
1791
2319
356065621
356066151
0
902
14
TraesCS5A01G116600
chr4A
97.931
1788
34
3
1
1788
67587531
67585747
0
3094
15
TraesCS5A01G116600
chr3A
97.732
529
12
0
1791
2319
309311555
309311027
0
911
16
TraesCS5A01G116600
chr3A
97.547
530
12
1
1791
2319
370183848
370184377
0
905
17
TraesCS5A01G116600
chr1A
97.547
530
12
1
1791
2319
372508644
372509173
0
905
18
TraesCS5A01G116600
chr1A
97.363
531
12
2
1791
2319
88423709
88424239
0
902
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
TraesCS5A01G116600
chr5A
238789277
238791595
2318
True
4283
4283
100.000
1
2319
1
chr5A.!!$R1
2318
1
TraesCS5A01G116600
chr5A
300072979
300074759
1780
False
3121
3121
98.264
1
1785
1
chr5A.!!$F2
1784
2
TraesCS5A01G116600
chr5A
169395371
169395899
528
False
900
900
97.353
1791
2319
1
chr5A.!!$F1
528
3
TraesCS5A01G116600
chr5A
610021121
610021650
529
False
900
900
97.358
1791
2319
1
chr5A.!!$F3
528
4
TraesCS5A01G116600
chr7A
4959838
4961622
1784
False
3147
3147
98.487
1
1785
1
chr7A.!!$F1
1784
5
TraesCS5A01G116600
chr7A
443009303
443009832
529
False
911
911
97.736
1791
2319
1
chr7A.!!$F3
528
6
TraesCS5A01G116600
chr7A
344568306
344568835
529
False
900
900
97.358
1791
2319
1
chr7A.!!$F2
528
7
TraesCS5A01G116600
chrUn
189392539
189394319
1780
False
3121
3121
98.264
1
1785
1
chrUn.!!$F1
1784
8
TraesCS5A01G116600
chr2A
618278173
618279956
1783
True
3116
3116
98.155
1
1788
1
chr2A.!!$R1
1787
9
TraesCS5A01G116600
chr7D
626696707
626698490
1783
True
3110
3110
98.099
1
1788
1
chr7D.!!$R2
1787
10
TraesCS5A01G116600
chr7D
203554563
203556345
1782
True
3097
3097
97.987
1
1788
1
chr7D.!!$R1
1787
11
TraesCS5A01G116600
chr7B
743086199
743087979
1780
False
3110
3110
98.152
1
1785
1
chr7B.!!$F1
1784
12
TraesCS5A01G116600
chr6A
289128632
289130410
1778
False
3109
3109
98.151
1
1785
1
chr6A.!!$F1
1784
13
TraesCS5A01G116600
chr6A
356065621
356066151
530
False
902
902
97.363
1791
2319
1
chr6A.!!$F2
528
14
TraesCS5A01G116600
chr4A
67585747
67587531
1784
True
3094
3094
97.931
1
1788
1
chr4A.!!$R1
1787
15
TraesCS5A01G116600
chr3A
309311027
309311555
528
True
911
911
97.732
1791
2319
1
chr3A.!!$R1
528
16
TraesCS5A01G116600
chr3A
370183848
370184377
529
False
905
905
97.547
1791
2319
1
chr3A.!!$F1
528
17
TraesCS5A01G116600
chr1A
372508644
372509173
529
False
905
905
97.547
1791
2319
1
chr1A.!!$F2
528
18
TraesCS5A01G116600
chr1A
88423709
88424239
530
False
902
902
97.363
1791
2319
1
chr1A.!!$F1
528
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.