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
TraesCS5D01G079700
chr5D
100.000
4311
0
0
1
4311
80034550
80030240
0.000000e+00
7962
1
TraesCS5D01G079700
chr7D
97.698
3215
72
2
897
4110
579030867
579034080
0.000000e+00
5526
2
TraesCS5D01G079700
chr7D
94.972
537
26
1
364
900
182071362
182070827
0.000000e+00
841
3
TraesCS5D01G079700
chr7D
96.552
203
6
1
4109
4311
579034124
579034325
6.910000e-88
335
4
TraesCS5D01G079700
chr1A
97.418
3215
80
3
897
4110
112003773
112000561
0.000000e+00
5474
5
TraesCS5D01G079700
chr1A
96.552
203
6
1
4109
4311
112000517
112000316
6.910000e-88
335
6
TraesCS5D01G079700
chrUn
97.387
3215
80
4
897
4110
86479188
86482399
0.000000e+00
5469
7
TraesCS5D01G079700
chrUn
97.263
3215
86
2
897
4110
186190281
186187068
0.000000e+00
5448
8
TraesCS5D01G079700
chrUn
86.374
433
46
9
478
899
476309608
476310038
1.090000e-125
460
9
TraesCS5D01G079700
chrUn
97.044
203
5
1
4109
4311
349950244
349950043
1.480000e-89
340
10
TraesCS5D01G079700
chrUn
96.552
203
6
1
4109
4311
221556476
221556677
6.910000e-88
335
11
TraesCS5D01G079700
chrUn
96.552
203
6
1
4109
4311
229484120
229483919
6.910000e-88
335
12
TraesCS5D01G079700
chrUn
96.059
203
7
1
4109
4311
86482443
86482644
3.210000e-86
329
13
TraesCS5D01G079700
chrUn
96.059
203
7
1
4109
4311
186187024
186186823
3.210000e-86
329
14
TraesCS5D01G079700
chr2D
97.263
3215
85
3
897
4110
200915400
200918612
0.000000e+00
5446
15
TraesCS5D01G079700
chr2D
96.569
204
6
1
4108
4311
200918655
200918857
1.920000e-88
337
16
TraesCS5D01G079700
chr7B
97.201
3215
86
4
897
4110
743007198
743010409
0.000000e+00
5435
17
TraesCS5D01G079700
chr1D
97.201
3216
85
5
897
4110
212466734
212463522
0.000000e+00
5435
18
TraesCS5D01G079700
chr1D
87.259
934
89
17
1
909
422063015
422063943
0.000000e+00
1038
19
TraesCS5D01G079700
chr7A
97.107
3215
90
3
897
4110
120881581
120884793
0.000000e+00
5419
20
TraesCS5D01G079700
chr7A
93.187
910
42
13
1
898
194333633
194332732
0.000000e+00
1319
21
TraesCS5D01G079700
chr6D
96.858
3215
95
6
897
4110
369999238
369996029
0.000000e+00
5373
22
TraesCS5D01G079700
chr6D
96.985
199
6
0
4113
4311
369913616
369913418
6.910000e-88
335
23
TraesCS5D01G079700
chr2B
94.157
907
38
9
1
898
156324226
156323326
0.000000e+00
1367
24
TraesCS5D01G079700
chr2A
92.181
908
34
8
1
900
115498466
115499344
0.000000e+00
1249
25
TraesCS5D01G079700
chr5A
88.973
925
80
13
1
905
584942841
584943763
0.000000e+00
1123
26
TraesCS5D01G079700
chr5A
88.986
917
81
11
1
899
17143526
17144440
0.000000e+00
1116
27
TraesCS5D01G079700
chr1B
89.107
918
78
13
1
899
14132137
14131223
0.000000e+00
1122
28
TraesCS5D01G079700
chr3D
88.530
898
78
14
24
898
279698011
279698906
0.000000e+00
1064
29
TraesCS5D01G079700
chr3D
87.757
923
84
16
1
899
103669992
103670909
0.000000e+00
1051
30
TraesCS5D01G079700
chr3A
94.671
563
21
4
1
557
410105231
410104672
0.000000e+00
865
31
TraesCS5D01G079700
chr3A
92.903
310
17
4
589
897
410104399
410104094
3.060000e-121
446
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
TraesCS5D01G079700
chr5D
80030240
80034550
4310
True
7962.0
7962
100.000
1
4311
1
chr5D.!!$R1
4310
1
TraesCS5D01G079700
chr7D
579030867
579034325
3458
False
2930.5
5526
97.125
897
4311
2
chr7D.!!$F1
3414
2
TraesCS5D01G079700
chr7D
182070827
182071362
535
True
841.0
841
94.972
364
900
1
chr7D.!!$R1
536
3
TraesCS5D01G079700
chr1A
112000316
112003773
3457
True
2904.5
5474
96.985
897
4311
2
chr1A.!!$R1
3414
4
TraesCS5D01G079700
chrUn
86479188
86482644
3456
False
2899.0
5469
96.723
897
4311
2
chrUn.!!$F3
3414
5
TraesCS5D01G079700
chrUn
186186823
186190281
3458
True
2888.5
5448
96.661
897
4311
2
chrUn.!!$R3
3414
6
TraesCS5D01G079700
chr2D
200915400
200918857
3457
False
2891.5
5446
96.916
897
4311
2
chr2D.!!$F1
3414
7
TraesCS5D01G079700
chr7B
743007198
743010409
3211
False
5435.0
5435
97.201
897
4110
1
chr7B.!!$F1
3213
8
TraesCS5D01G079700
chr1D
212463522
212466734
3212
True
5435.0
5435
97.201
897
4110
1
chr1D.!!$R1
3213
9
TraesCS5D01G079700
chr1D
422063015
422063943
928
False
1038.0
1038
87.259
1
909
1
chr1D.!!$F1
908
10
TraesCS5D01G079700
chr7A
120881581
120884793
3212
False
5419.0
5419
97.107
897
4110
1
chr7A.!!$F1
3213
11
TraesCS5D01G079700
chr7A
194332732
194333633
901
True
1319.0
1319
93.187
1
898
1
chr7A.!!$R1
897
12
TraesCS5D01G079700
chr6D
369996029
369999238
3209
True
5373.0
5373
96.858
897
4110
1
chr6D.!!$R2
3213
13
TraesCS5D01G079700
chr2B
156323326
156324226
900
True
1367.0
1367
94.157
1
898
1
chr2B.!!$R1
897
14
TraesCS5D01G079700
chr2A
115498466
115499344
878
False
1249.0
1249
92.181
1
900
1
chr2A.!!$F1
899
15
TraesCS5D01G079700
chr5A
584942841
584943763
922
False
1123.0
1123
88.973
1
905
1
chr5A.!!$F2
904
16
TraesCS5D01G079700
chr5A
17143526
17144440
914
False
1116.0
1116
88.986
1
899
1
chr5A.!!$F1
898
17
TraesCS5D01G079700
chr1B
14131223
14132137
914
True
1122.0
1122
89.107
1
899
1
chr1B.!!$R1
898
18
TraesCS5D01G079700
chr3D
279698011
279698906
895
False
1064.0
1064
88.530
24
898
1
chr3D.!!$F2
874
19
TraesCS5D01G079700
chr3D
103669992
103670909
917
False
1051.0
1051
87.757
1
899
1
chr3D.!!$F1
898
20
TraesCS5D01G079700
chr3A
410104094
410105231
1137
True
655.5
865
93.787
1
897
2
chr3A.!!$R1
896
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.