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
TraesCS1B01G281900
chr1B
100.000
2549
0
0
1
2549
490564128
490561580
0
4708
1
TraesCS1B01G281900
chr1B
96.177
1988
69
7
566
2549
232740733
232742717
0
3243
2
TraesCS1B01G281900
chr1B
96.133
1991
70
7
564
2549
663786492
663788480
0
3243
3
TraesCS1B01G281900
chr7B
96.427
1987
63
7
567
2549
718488474
718486492
0
3269
4
TraesCS1B01G281900
chr3B
96.278
1988
65
7
565
2549
129332739
129330758
0
3253
5
TraesCS1B01G281900
chr2B
96.276
1987
64
8
567
2549
543889470
543887490
0
3251
6
TraesCS1B01G281900
chr2B
96.225
1987
65
8
567
2549
544319641
544317661
0
3245
7
TraesCS1B01G281900
chr2B
95.894
1997
71
9
562
2549
602077190
602075196
0
3223
8
TraesCS1B01G281900
chr2B
92.945
567
39
1
1
566
526963320
526962754
0
824
9
TraesCS1B01G281900
chr2B
91.901
568
44
1
1
566
589714179
589713612
0
793
10
TraesCS1B01G281900
chr2B
91.740
569
43
3
1
566
100407022
100406455
0
787
11
TraesCS1B01G281900
chr2B
91.373
568
47
1
1
566
387999780
387999213
0
776
12
TraesCS1B01G281900
chr5B
96.179
1989
68
7
567
2549
269389473
269391459
0
3245
13
TraesCS1B01G281900
chr5B
96.086
1993
68
9
562
2547
446193260
446191271
0
3240
14
TraesCS1B01G281900
chr5B
93.463
566
37
0
1
566
474025108
474024543
0
841
15
TraesCS1B01G281900
chr5B
90.845
568
50
1
1
566
407955585
407955018
0
760
16
TraesCS1B01G281900
chr6B
93.110
566
38
1
1
566
623250596
623250032
0
828
17
TraesCS1B01G281900
chr4B
92.430
568
41
1
1
566
540222311
540222878
0
809
18
TraesCS1B01G281900
chr4B
92.430
568
41
1
1
566
563461445
563462012
0
809
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
TraesCS1B01G281900
chr1B
490561580
490564128
2548
True
4708
4708
100.000
1
2549
1
chr1B.!!$R1
2548
1
TraesCS1B01G281900
chr1B
232740733
232742717
1984
False
3243
3243
96.177
566
2549
1
chr1B.!!$F1
1983
2
TraesCS1B01G281900
chr1B
663786492
663788480
1988
False
3243
3243
96.133
564
2549
1
chr1B.!!$F2
1985
3
TraesCS1B01G281900
chr7B
718486492
718488474
1982
True
3269
3269
96.427
567
2549
1
chr7B.!!$R1
1982
4
TraesCS1B01G281900
chr3B
129330758
129332739
1981
True
3253
3253
96.278
565
2549
1
chr3B.!!$R1
1984
5
TraesCS1B01G281900
chr2B
543887490
543889470
1980
True
3251
3251
96.276
567
2549
1
chr2B.!!$R4
1982
6
TraesCS1B01G281900
chr2B
544317661
544319641
1980
True
3245
3245
96.225
567
2549
1
chr2B.!!$R5
1982
7
TraesCS1B01G281900
chr2B
602075196
602077190
1994
True
3223
3223
95.894
562
2549
1
chr2B.!!$R7
1987
8
TraesCS1B01G281900
chr2B
526962754
526963320
566
True
824
824
92.945
1
566
1
chr2B.!!$R3
565
9
TraesCS1B01G281900
chr2B
589713612
589714179
567
True
793
793
91.901
1
566
1
chr2B.!!$R6
565
10
TraesCS1B01G281900
chr2B
100406455
100407022
567
True
787
787
91.740
1
566
1
chr2B.!!$R1
565
11
TraesCS1B01G281900
chr2B
387999213
387999780
567
True
776
776
91.373
1
566
1
chr2B.!!$R2
565
12
TraesCS1B01G281900
chr5B
269389473
269391459
1986
False
3245
3245
96.179
567
2549
1
chr5B.!!$F1
1982
13
TraesCS1B01G281900
chr5B
446191271
446193260
1989
True
3240
3240
96.086
562
2547
1
chr5B.!!$R2
1985
14
TraesCS1B01G281900
chr5B
474024543
474025108
565
True
841
841
93.463
1
566
1
chr5B.!!$R3
565
15
TraesCS1B01G281900
chr5B
407955018
407955585
567
True
760
760
90.845
1
566
1
chr5B.!!$R1
565
16
TraesCS1B01G281900
chr6B
623250032
623250596
564
True
828
828
93.110
1
566
1
chr6B.!!$R1
565
17
TraesCS1B01G281900
chr4B
540222311
540222878
567
False
809
809
92.430
1
566
1
chr4B.!!$F1
565
18
TraesCS1B01G281900
chr4B
563461445
563462012
567
False
809
809
92.430
1
566
1
chr4B.!!$F2
565
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.