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
TraesCS3B01G466300
chr3B
100.000
3296
0
0
1
3296
708912775
708909480
0.000000e+00
6087
1
TraesCS3B01G466300
chr3B
86.787
1945
133
62
605
2498
708502833
708504704
0.000000e+00
2054
2
TraesCS3B01G466300
chr3B
83.025
1514
150
58
193
1667
708496434
708497879
0.000000e+00
1273
3
TraesCS3B01G466300
chr3B
88.048
661
55
10
2603
3262
2122010
2122647
0.000000e+00
761
4
TraesCS3B01G466300
chr3B
87.083
689
61
10
2574
3262
188235425
188234765
0.000000e+00
754
5
TraesCS3B01G466300
chr3B
84.384
365
30
15
193
553
708499579
708499920
1.900000e-87
333
6
TraesCS3B01G466300
chr3B
77.285
383
82
5
1287
1666
708367622
708367242
1.540000e-53
220
7
TraesCS3B01G466300
chr3A
90.597
2446
112
56
229
2592
671766647
671764238
0.000000e+00
3134
8
TraesCS3B01G466300
chr3A
77.487
382
77
6
1287
1663
671697913
671697536
1.540000e-53
220
9
TraesCS3B01G466300
chr3A
89.062
128
10
2
2
125
671766830
671766703
4.400000e-34
156
10
TraesCS3B01G466300
chr3D
90.798
2369
97
55
164
2462
536339321
536337004
0.000000e+00
3055
11
TraesCS3B01G466300
chr3D
78.068
383
76
7
1287
1663
536027765
536028145
5.500000e-58
235
12
TraesCS3B01G466300
chr3D
98.230
113
2
0
1
113
536369192
536369080
7.210000e-47
198
13
TraesCS3B01G466300
chr5B
88.267
733
58
6
2576
3296
659735938
659735222
0.000000e+00
852
14
TraesCS3B01G466300
chr5B
80.670
388
58
11
2849
3229
559396890
559397267
5.380000e-73
285
15
TraesCS3B01G466300
chr7B
87.534
730
54
14
2578
3296
664321563
664320860
0.000000e+00
809
16
TraesCS3B01G466300
chr7B
87.994
708
53
12
2578
3262
126843907
126843209
0.000000e+00
808
17
TraesCS3B01G466300
chr7B
87.123
730
56
13
2578
3296
664349757
664349055
0.000000e+00
793
18
TraesCS3B01G466300
chr7B
82.114
492
47
16
2578
3057
615737379
615736917
1.860000e-102
383
19
TraesCS3B01G466300
chr5D
88.338
686
60
8
2578
3262
249086260
249085594
0.000000e+00
806
20
TraesCS3B01G466300
chr5D
80.172
696
85
32
2610
3296
442671713
442671062
3.850000e-129
472
21
TraesCS3B01G466300
chr6B
86.498
711
58
10
2576
3262
476733043
476733739
0.000000e+00
747
22
TraesCS3B01G466300
chr6B
87.168
678
60
10
2578
3242
95441039
95441702
0.000000e+00
745
23
TraesCS3B01G466300
chr2B
84.104
692
72
16
2573
3241
705151442
705152118
4.640000e-178
634
24
TraesCS3B01G466300
chr6D
82.345
742
93
13
2573
3293
25369911
25370635
7.820000e-171
610
25
TraesCS3B01G466300
chr4B
83.550
693
70
15
2576
3241
631062077
631062752
2.810000e-170
608
26
TraesCS3B01G466300
chr2A
82.192
730
98
20
2576
3296
47363679
47362973
1.690000e-167
599
27
TraesCS3B01G466300
chr4A
84.877
529
47
10
2792
3296
720075955
720076474
1.370000e-138
503
28
TraesCS3B01G466300
chr1B
80.315
381
52
15
2855
3231
670875932
670876293
1.950000e-67
267
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
TraesCS3B01G466300
chr3B
708909480
708912775
3295
True
6087
6087
100.0000
1
3296
1
chr3B.!!$R3
3295
1
TraesCS3B01G466300
chr3B
708496434
708504704
8270
False
1220
2054
84.7320
193
2498
3
chr3B.!!$F2
2305
2
TraesCS3B01G466300
chr3B
2122010
2122647
637
False
761
761
88.0480
2603
3262
1
chr3B.!!$F1
659
3
TraesCS3B01G466300
chr3B
188234765
188235425
660
True
754
754
87.0830
2574
3262
1
chr3B.!!$R1
688
4
TraesCS3B01G466300
chr3A
671764238
671766830
2592
True
1645
3134
89.8295
2
2592
2
chr3A.!!$R2
2590
5
TraesCS3B01G466300
chr3D
536337004
536339321
2317
True
3055
3055
90.7980
164
2462
1
chr3D.!!$R1
2298
6
TraesCS3B01G466300
chr5B
659735222
659735938
716
True
852
852
88.2670
2576
3296
1
chr5B.!!$R1
720
7
TraesCS3B01G466300
chr7B
664320860
664321563
703
True
809
809
87.5340
2578
3296
1
chr7B.!!$R3
718
8
TraesCS3B01G466300
chr7B
126843209
126843907
698
True
808
808
87.9940
2578
3262
1
chr7B.!!$R1
684
9
TraesCS3B01G466300
chr7B
664349055
664349757
702
True
793
793
87.1230
2578
3296
1
chr7B.!!$R4
718
10
TraesCS3B01G466300
chr5D
249085594
249086260
666
True
806
806
88.3380
2578
3262
1
chr5D.!!$R1
684
11
TraesCS3B01G466300
chr5D
442671062
442671713
651
True
472
472
80.1720
2610
3296
1
chr5D.!!$R2
686
12
TraesCS3B01G466300
chr6B
476733043
476733739
696
False
747
747
86.4980
2576
3262
1
chr6B.!!$F2
686
13
TraesCS3B01G466300
chr6B
95441039
95441702
663
False
745
745
87.1680
2578
3242
1
chr6B.!!$F1
664
14
TraesCS3B01G466300
chr2B
705151442
705152118
676
False
634
634
84.1040
2573
3241
1
chr2B.!!$F1
668
15
TraesCS3B01G466300
chr6D
25369911
25370635
724
False
610
610
82.3450
2573
3293
1
chr6D.!!$F1
720
16
TraesCS3B01G466300
chr4B
631062077
631062752
675
False
608
608
83.5500
2576
3241
1
chr4B.!!$F1
665
17
TraesCS3B01G466300
chr2A
47362973
47363679
706
True
599
599
82.1920
2576
3296
1
chr2A.!!$R1
720
18
TraesCS3B01G466300
chr4A
720075955
720076474
519
False
503
503
84.8770
2792
3296
1
chr4A.!!$F1
504
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.