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
TraesCS3B01G331800
chr3B
100.000
3742
0
0
1
3742
537311186
537307445
0.000000e+00
6911
1
TraesCS3B01G331800
chr3B
98.139
591
11
0
3150
3740
537302570
537301980
0.000000e+00
1031
2
TraesCS3B01G331800
chr3A
96.904
2261
62
6
897
3152
540683192
540685449
0.000000e+00
3781
3
TraesCS3B01G331800
chr3A
86.333
439
50
6
1
435
540671461
540671893
1.570000e-128
470
4
TraesCS3B01G331800
chr3D
96.326
2259
68
4
897
3152
410973279
410971033
0.000000e+00
3698
5
TraesCS3B01G331800
chr3D
88.533
811
80
8
1
799
410981543
410980734
0.000000e+00
970
6
TraesCS3B01G331800
chr1B
97.808
593
13
0
3150
3742
678578635
678578043
0.000000e+00
1024
7
TraesCS3B01G331800
chr1B
97.470
593
15
0
3150
3742
678595104
678594512
0.000000e+00
1013
8
TraesCS3B01G331800
chr1B
97.293
591
16
0
3150
3740
630281263
630280673
0.000000e+00
1003
9
TraesCS3B01G331800
chr1B
96.812
596
16
1
3150
3742
640810533
640809938
0.000000e+00
992
10
TraesCS3B01G331800
chr1B
83.681
766
107
12
77
827
598846457
598845695
0.000000e+00
706
11
TraesCS3B01G331800
chr1B
82.496
617
87
13
84
689
540444361
540443755
4.280000e-144
521
12
TraesCS3B01G331800
chr1B
78.464
729
123
19
109
824
102671580
102670873
2.650000e-121
446
13
TraesCS3B01G331800
chr1B
79.563
641
107
16
193
829
65556324
65555704
1.600000e-118
436
14
TraesCS3B01G331800
chr1B
81.296
540
85
12
87
612
624996263
624996800
1.240000e-114
424
15
TraesCS3B01G331800
chr2B
97.470
593
15
0
3150
3742
598592489
598593081
0.000000e+00
1013
16
TraesCS3B01G331800
chr2B
97.302
593
16
0
3150
3742
598618811
598619403
0.000000e+00
1007
17
TraesCS3B01G331800
chr2B
97.302
593
16
0
3150
3742
786565567
786564975
0.000000e+00
1007
18
TraesCS3B01G331800
chr2B
83.831
402
48
9
443
828
160906879
160907279
2.120000e-97
366
19
TraesCS3B01G331800
chr4A
97.133
593
17
0
3150
3742
742526133
742526725
0.000000e+00
1002
20
TraesCS3B01G331800
chr4D
81.984
766
109
19
86
829
6922951
6923709
1.140000e-174
623
21
TraesCS3B01G331800
chr4D
81.420
479
79
10
77
549
12415844
12416318
2.110000e-102
383
22
TraesCS3B01G331800
chr5D
84.235
647
85
13
154
790
520788642
520789281
6.870000e-172
614
23
TraesCS3B01G331800
chr5D
80.395
760
129
13
89
832
497835558
497834803
9.080000e-156
560
24
TraesCS3B01G331800
chr5D
80.218
733
103
21
86
806
402948721
402948019
2.580000e-141
512
25
TraesCS3B01G331800
chr1D
83.179
648
96
7
193
829
347783045
347782400
6.970000e-162
580
26
TraesCS3B01G331800
chr1D
82.189
539
79
12
87
612
454484577
454484043
7.370000e-122
448
27
TraesCS3B01G331800
chr7A
80.901
644
110
10
194
828
573447016
573447655
2.600000e-136
496
28
TraesCS3B01G331800
chr5A
81.838
457
72
4
384
829
574944260
574944716
1.270000e-99
374
29
TraesCS3B01G331800
chr1A
81.797
423
57
13
422
829
45788764
45789181
1.670000e-88
337
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
TraesCS3B01G331800
chr3B
537307445
537311186
3741
True
6911
6911
100.000
1
3742
1
chr3B.!!$R2
3741
1
TraesCS3B01G331800
chr3B
537301980
537302570
590
True
1031
1031
98.139
3150
3740
1
chr3B.!!$R1
590
2
TraesCS3B01G331800
chr3A
540683192
540685449
2257
False
3781
3781
96.904
897
3152
1
chr3A.!!$F2
2255
3
TraesCS3B01G331800
chr3D
410971033
410973279
2246
True
3698
3698
96.326
897
3152
1
chr3D.!!$R1
2255
4
TraesCS3B01G331800
chr3D
410980734
410981543
809
True
970
970
88.533
1
799
1
chr3D.!!$R2
798
5
TraesCS3B01G331800
chr1B
678578043
678578635
592
True
1024
1024
97.808
3150
3742
1
chr1B.!!$R7
592
6
TraesCS3B01G331800
chr1B
678594512
678595104
592
True
1013
1013
97.470
3150
3742
1
chr1B.!!$R8
592
7
TraesCS3B01G331800
chr1B
630280673
630281263
590
True
1003
1003
97.293
3150
3740
1
chr1B.!!$R5
590
8
TraesCS3B01G331800
chr1B
640809938
640810533
595
True
992
992
96.812
3150
3742
1
chr1B.!!$R6
592
9
TraesCS3B01G331800
chr1B
598845695
598846457
762
True
706
706
83.681
77
827
1
chr1B.!!$R4
750
10
TraesCS3B01G331800
chr1B
540443755
540444361
606
True
521
521
82.496
84
689
1
chr1B.!!$R3
605
11
TraesCS3B01G331800
chr1B
102670873
102671580
707
True
446
446
78.464
109
824
1
chr1B.!!$R2
715
12
TraesCS3B01G331800
chr1B
65555704
65556324
620
True
436
436
79.563
193
829
1
chr1B.!!$R1
636
13
TraesCS3B01G331800
chr1B
624996263
624996800
537
False
424
424
81.296
87
612
1
chr1B.!!$F1
525
14
TraesCS3B01G331800
chr2B
598592489
598593081
592
False
1013
1013
97.470
3150
3742
1
chr2B.!!$F2
592
15
TraesCS3B01G331800
chr2B
598618811
598619403
592
False
1007
1007
97.302
3150
3742
1
chr2B.!!$F3
592
16
TraesCS3B01G331800
chr2B
786564975
786565567
592
True
1007
1007
97.302
3150
3742
1
chr2B.!!$R1
592
17
TraesCS3B01G331800
chr4A
742526133
742526725
592
False
1002
1002
97.133
3150
3742
1
chr4A.!!$F1
592
18
TraesCS3B01G331800
chr4D
6922951
6923709
758
False
623
623
81.984
86
829
1
chr4D.!!$F1
743
19
TraesCS3B01G331800
chr5D
520788642
520789281
639
False
614
614
84.235
154
790
1
chr5D.!!$F1
636
20
TraesCS3B01G331800
chr5D
497834803
497835558
755
True
560
560
80.395
89
832
1
chr5D.!!$R2
743
21
TraesCS3B01G331800
chr5D
402948019
402948721
702
True
512
512
80.218
86
806
1
chr5D.!!$R1
720
22
TraesCS3B01G331800
chr1D
347782400
347783045
645
True
580
580
83.179
193
829
1
chr1D.!!$R1
636
23
TraesCS3B01G331800
chr1D
454484043
454484577
534
True
448
448
82.189
87
612
1
chr1D.!!$R2
525
24
TraesCS3B01G331800
chr7A
573447016
573447655
639
False
496
496
80.901
194
828
1
chr7A.!!$F1
634
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.