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
TraesCS2A01G365200
chr2A
100.000
2870
0
0
1
2870
608937200
608940069
0.000000e+00
5301.0
1
TraesCS2A01G365200
chr2A
89.512
553
52
4
2321
2868
705811152
705811703
0.000000e+00
695.0
2
TraesCS2A01G365200
chr2A
90.164
61
4
1
647
705
81468197
81468257
8.530000e-11
78.7
3
TraesCS2A01G365200
chr2D
93.936
1781
67
12
737
2501
469167939
469169694
0.000000e+00
2652.0
4
TraesCS2A01G365200
chr2B
92.956
1519
64
16
737
2255
547836343
547837818
0.000000e+00
2172.0
5
TraesCS2A01G365200
chr5B
98.310
710
12
0
1
710
239324992
239325701
0.000000e+00
1245.0
6
TraesCS2A01G365200
chr5B
87.477
551
60
7
2323
2868
532534208
532534754
6.750000e-176
627.0
7
TraesCS2A01G365200
chr7B
98.036
713
14
0
1
713
516450819
516450107
0.000000e+00
1240.0
8
TraesCS2A01G365200
chr5A
98.036
713
14
0
1
713
320269823
320269111
0.000000e+00
1240.0
9
TraesCS2A01G365200
chr5A
87.862
552
59
7
2321
2868
622993810
622994357
2.410000e-180
641.0
10
TraesCS2A01G365200
chr4B
98.036
713
14
0
1
713
92550342
92549630
0.000000e+00
1240.0
11
TraesCS2A01G365200
chr6B
98.028
710
14
0
1
710
346416226
346416935
0.000000e+00
1234.0
12
TraesCS2A01G365200
chr3D
88.225
552
56
8
2321
2868
562355628
562355082
0.000000e+00
651.0
13
TraesCS2A01G365200
chr6A
86.874
579
75
1
1
579
106071539
106072116
0.000000e+00
647.0
14
TraesCS2A01G365200
chr6D
87.703
553
61
6
2321
2868
397352675
397352125
3.120000e-179
638.0
15
TraesCS2A01G365200
chr6D
86.140
570
69
7
142
705
88091127
88091692
8.790000e-170
606.0
16
TraesCS2A01G365200
chr1A
87.751
547
62
4
2326
2870
547419400
547418857
4.030000e-178
634.0
17
TraesCS2A01G365200
chr5D
87.636
550
60
6
2321
2868
557652621
557653164
1.450000e-177
632.0
18
TraesCS2A01G365200
chr1D
87.161
553
63
7
2321
2870
203875906
203875359
3.140000e-174
621.0
19
TraesCS2A01G365200
chr7A
86.918
558
64
7
2315
2868
693483715
693484267
4.060000e-173
617.0
20
TraesCS2A01G365200
chr7D
92.492
333
25
0
1
333
580113212
580113544
7.190000e-131
477.0
21
TraesCS2A01G365200
chr3B
77.616
688
131
18
2
678
478095651
478094976
2.070000e-106
396.0
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
TraesCS2A01G365200
chr2A
608937200
608940069
2869
False
5301
5301
100.000
1
2870
1
chr2A.!!$F2
2869
1
TraesCS2A01G365200
chr2A
705811152
705811703
551
False
695
695
89.512
2321
2868
1
chr2A.!!$F3
547
2
TraesCS2A01G365200
chr2D
469167939
469169694
1755
False
2652
2652
93.936
737
2501
1
chr2D.!!$F1
1764
3
TraesCS2A01G365200
chr2B
547836343
547837818
1475
False
2172
2172
92.956
737
2255
1
chr2B.!!$F1
1518
4
TraesCS2A01G365200
chr5B
239324992
239325701
709
False
1245
1245
98.310
1
710
1
chr5B.!!$F1
709
5
TraesCS2A01G365200
chr5B
532534208
532534754
546
False
627
627
87.477
2323
2868
1
chr5B.!!$F2
545
6
TraesCS2A01G365200
chr7B
516450107
516450819
712
True
1240
1240
98.036
1
713
1
chr7B.!!$R1
712
7
TraesCS2A01G365200
chr5A
320269111
320269823
712
True
1240
1240
98.036
1
713
1
chr5A.!!$R1
712
8
TraesCS2A01G365200
chr5A
622993810
622994357
547
False
641
641
87.862
2321
2868
1
chr5A.!!$F1
547
9
TraesCS2A01G365200
chr4B
92549630
92550342
712
True
1240
1240
98.036
1
713
1
chr4B.!!$R1
712
10
TraesCS2A01G365200
chr6B
346416226
346416935
709
False
1234
1234
98.028
1
710
1
chr6B.!!$F1
709
11
TraesCS2A01G365200
chr3D
562355082
562355628
546
True
651
651
88.225
2321
2868
1
chr3D.!!$R1
547
12
TraesCS2A01G365200
chr6A
106071539
106072116
577
False
647
647
86.874
1
579
1
chr6A.!!$F1
578
13
TraesCS2A01G365200
chr6D
397352125
397352675
550
True
638
638
87.703
2321
2868
1
chr6D.!!$R1
547
14
TraesCS2A01G365200
chr6D
88091127
88091692
565
False
606
606
86.140
142
705
1
chr6D.!!$F1
563
15
TraesCS2A01G365200
chr1A
547418857
547419400
543
True
634
634
87.751
2326
2870
1
chr1A.!!$R1
544
16
TraesCS2A01G365200
chr5D
557652621
557653164
543
False
632
632
87.636
2321
2868
1
chr5D.!!$F1
547
17
TraesCS2A01G365200
chr1D
203875359
203875906
547
True
621
621
87.161
2321
2870
1
chr1D.!!$R1
549
18
TraesCS2A01G365200
chr7A
693483715
693484267
552
False
617
617
86.918
2315
2868
1
chr7A.!!$F1
553
19
TraesCS2A01G365200
chr3B
478094976
478095651
675
True
396
396
77.616
2
678
1
chr3B.!!$R1
676
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.