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
TraesCS3B01G423900
chr3B
100.000
2549
0
0
1
2549
661407227
661409775
0
4708
1
TraesCS3B01G423900
chr3B
97.980
1980
36
3
570
2549
702857655
702855680
0
3432
2
TraesCS3B01G423900
chr6A
98.131
1980
33
3
571
2549
617222869
617220893
0
3448
3
TraesCS3B01G423900
chr6A
98.031
1981
35
3
570
2549
533982323
533980346
0
3439
4
TraesCS3B01G423900
chr6B
98.031
1981
38
1
569
2549
8435751
8437730
0
3441
5
TraesCS3B01G423900
chr6B
96.120
567
22
0
4
570
685255419
685254853
0
926
6
TraesCS3B01G423900
chr4A
98.032
1982
36
2
569
2549
36562911
36564890
0
3441
7
TraesCS3B01G423900
chr1B
97.938
1988
37
3
563
2549
42162347
42160363
0
3441
8
TraesCS3B01G423900
chr3A
98.031
1981
35
3
569
2549
54951916
54953892
0
3439
9
TraesCS3B01G423900
chr3A
95.246
568
27
0
3
570
455473367
455473934
0
900
10
TraesCS3B01G423900
chr2B
97.981
1981
35
4
570
2549
776222961
776224937
0
3432
11
TraesCS3B01G423900
chr2B
97.981
1981
35
4
570
2549
781094240
781096216
0
3432
12
TraesCS3B01G423900
chr5D
96.303
568
21
0
3
570
54996993
54996426
0
933
13
TraesCS3B01G423900
chr5D
96.303
568
21
0
3
570
427018407
427017840
0
933
14
TraesCS3B01G423900
chr5D
96.303
568
21
0
3
570
427086105
427085538
0
933
15
TraesCS3B01G423900
chr3D
96.303
568
21
0
3
570
103339663
103339096
0
933
16
TraesCS3B01G423900
chr3D
94.718
568
30
0
3
570
158513086
158513653
0
883
17
TraesCS3B01G423900
chr1D
96.303
568
21
0
3
570
237452043
237452610
0
933
18
TraesCS3B01G423900
chr1A
95.567
564
25
0
3
566
570884330
570883767
0
904
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
TraesCS3B01G423900
chr3B
661407227
661409775
2548
False
4708
4708
100.000
1
2549
1
chr3B.!!$F1
2548
1
TraesCS3B01G423900
chr3B
702855680
702857655
1975
True
3432
3432
97.980
570
2549
1
chr3B.!!$R1
1979
2
TraesCS3B01G423900
chr6A
617220893
617222869
1976
True
3448
3448
98.131
571
2549
1
chr6A.!!$R2
1978
3
TraesCS3B01G423900
chr6A
533980346
533982323
1977
True
3439
3439
98.031
570
2549
1
chr6A.!!$R1
1979
4
TraesCS3B01G423900
chr6B
8435751
8437730
1979
False
3441
3441
98.031
569
2549
1
chr6B.!!$F1
1980
5
TraesCS3B01G423900
chr6B
685254853
685255419
566
True
926
926
96.120
4
570
1
chr6B.!!$R1
566
6
TraesCS3B01G423900
chr4A
36562911
36564890
1979
False
3441
3441
98.032
569
2549
1
chr4A.!!$F1
1980
7
TraesCS3B01G423900
chr1B
42160363
42162347
1984
True
3441
3441
97.938
563
2549
1
chr1B.!!$R1
1986
8
TraesCS3B01G423900
chr3A
54951916
54953892
1976
False
3439
3439
98.031
569
2549
1
chr3A.!!$F1
1980
9
TraesCS3B01G423900
chr3A
455473367
455473934
567
False
900
900
95.246
3
570
1
chr3A.!!$F2
567
10
TraesCS3B01G423900
chr2B
776222961
776224937
1976
False
3432
3432
97.981
570
2549
1
chr2B.!!$F1
1979
11
TraesCS3B01G423900
chr2B
781094240
781096216
1976
False
3432
3432
97.981
570
2549
1
chr2B.!!$F2
1979
12
TraesCS3B01G423900
chr5D
54996426
54996993
567
True
933
933
96.303
3
570
1
chr5D.!!$R1
567
13
TraesCS3B01G423900
chr5D
427017840
427018407
567
True
933
933
96.303
3
570
1
chr5D.!!$R2
567
14
TraesCS3B01G423900
chr5D
427085538
427086105
567
True
933
933
96.303
3
570
1
chr5D.!!$R3
567
15
TraesCS3B01G423900
chr3D
103339096
103339663
567
True
933
933
96.303
3
570
1
chr3D.!!$R1
567
16
TraesCS3B01G423900
chr3D
158513086
158513653
567
False
883
883
94.718
3
570
1
chr3D.!!$F1
567
17
TraesCS3B01G423900
chr1D
237452043
237452610
567
False
933
933
96.303
3
570
1
chr1D.!!$F1
567
18
TraesCS3B01G423900
chr1A
570883767
570884330
563
True
904
904
95.567
3
566
1
chr1A.!!$R1
563
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.