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
TraesCS6D01G354400
chr6D
100.000
3719
0
0
1
3719
449845556
449841838
0.000000e+00
6868.0
1
TraesCS6D01G354400
chr6D
88.935
2178
195
23
870
3033
449818499
449816354
0.000000e+00
2645.0
2
TraesCS6D01G354400
chr6D
78.333
1080
177
34
1057
2118
452082762
452081722
0.000000e+00
645.0
3
TraesCS6D01G354400
chr6D
75.345
941
169
41
1867
2789
450168337
450167442
9.680000e-106
394.0
4
TraesCS6D01G354400
chr6D
82.479
468
62
14
1655
2118
462409647
462409196
3.480000e-105
392.0
5
TraesCS6D01G354400
chr6D
72.637
1312
283
54
1441
2709
450212096
450210818
7.590000e-97
364.0
6
TraesCS6D01G354400
chr6D
92.308
52
4
0
3029
3080
449815548
449815497
1.430000e-09
75.0
7
TraesCS6D01G354400
chr6D
93.182
44
2
1
1064
1107
380495624
380495666
3.100000e-06
63.9
8
TraesCS6D01G354400
chr6D
93.182
44
2
1
1064
1107
380565618
380565660
3.100000e-06
63.9
9
TraesCS6D01G354400
chr6B
94.504
3639
152
16
111
3719
682417004
682420624
0.000000e+00
5568.0
10
TraesCS6D01G354400
chr6B
89.918
1220
89
22
1863
3080
681929816
681928629
0.000000e+00
1541.0
11
TraesCS6D01G354400
chr6B
92.694
1054
77
0
902
1955
681930869
681929816
0.000000e+00
1520.0
12
TraesCS6D01G354400
chr6B
73.770
1971
395
82
870
2783
682662256
682660351
0.000000e+00
664.0
13
TraesCS6D01G354400
chr6B
87.821
312
13
6
111
416
681931191
681930899
3.560000e-90
342.0
14
TraesCS6D01G354400
chr6B
78.373
541
100
8
2173
2709
682707636
682707109
5.950000e-88
335.0
15
TraesCS6D01G354400
chr6B
93.182
44
2
1
1064
1107
567764986
567765028
3.100000e-06
63.9
16
TraesCS6D01G354400
chr6B
93.182
44
2
1
1064
1107
567844261
567844303
3.100000e-06
63.9
17
TraesCS6D01G354400
chr6A
94.646
1158
60
2
815
1970
595490133
595488976
0.000000e+00
1794.0
18
TraesCS6D01G354400
chr6A
86.704
1617
103
41
2122
3650
595488471
595486879
0.000000e+00
1692.0
19
TraesCS6D01G354400
chr6A
93.459
688
30
6
111
787
595490813
595490130
0.000000e+00
1007.0
20
TraesCS6D01G354400
chr6A
73.806
1779
351
77
1062
2783
595664810
595663090
6.870000e-167
597.0
21
TraesCS6D01G354400
chr6A
77.332
1072
171
31
1071
2127
609163391
609162377
5.390000e-158
568.0
22
TraesCS6D01G354400
chr6A
95.556
135
4
2
2007
2139
595488786
595488652
8.090000e-52
215.0
23
TraesCS6D01G354400
chr6A
93.182
44
2
1
1064
1107
522044537
522044579
3.100000e-06
63.9
24
TraesCS6D01G354400
chr3B
82.326
877
89
38
33
871
653623372
653622524
0.000000e+00
701.0
25
TraesCS6D01G354400
chr1A
93.277
119
8
0
109
227
583526054
583526172
3.820000e-40
176.0
26
TraesCS6D01G354400
chr1A
82.143
196
28
6
676
868
16760004
16760195
1.070000e-35
161.0
27
TraesCS6D01G354400
chr2B
78.061
196
25
10
676
868
32053338
32053518
1.410000e-19
108.0
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
TraesCS6D01G354400
chr6D
449841838
449845556
3718
True
6868.000000
6868
100.000000
1
3719
1
chr6D.!!$R1
3718
1
TraesCS6D01G354400
chr6D
449815497
449818499
3002
True
1360.000000
2645
90.621500
870
3080
2
chr6D.!!$R6
2210
2
TraesCS6D01G354400
chr6D
452081722
452082762
1040
True
645.000000
645
78.333000
1057
2118
1
chr6D.!!$R4
1061
3
TraesCS6D01G354400
chr6D
450167442
450168337
895
True
394.000000
394
75.345000
1867
2789
1
chr6D.!!$R2
922
4
TraesCS6D01G354400
chr6D
450210818
450212096
1278
True
364.000000
364
72.637000
1441
2709
1
chr6D.!!$R3
1268
5
TraesCS6D01G354400
chr6B
682417004
682420624
3620
False
5568.000000
5568
94.504000
111
3719
1
chr6B.!!$F3
3608
6
TraesCS6D01G354400
chr6B
681928629
681931191
2562
True
1134.333333
1541
90.144333
111
3080
3
chr6B.!!$R3
2969
7
TraesCS6D01G354400
chr6B
682660351
682662256
1905
True
664.000000
664
73.770000
870
2783
1
chr6B.!!$R1
1913
8
TraesCS6D01G354400
chr6B
682707109
682707636
527
True
335.000000
335
78.373000
2173
2709
1
chr6B.!!$R2
536
9
TraesCS6D01G354400
chr6A
595486879
595490813
3934
True
1177.000000
1794
92.591250
111
3650
4
chr6A.!!$R3
3539
10
TraesCS6D01G354400
chr6A
595663090
595664810
1720
True
597.000000
597
73.806000
1062
2783
1
chr6A.!!$R1
1721
11
TraesCS6D01G354400
chr6A
609162377
609163391
1014
True
568.000000
568
77.332000
1071
2127
1
chr6A.!!$R2
1056
12
TraesCS6D01G354400
chr3B
653622524
653623372
848
True
701.000000
701
82.326000
33
871
1
chr3B.!!$R1
838
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.