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
TraesCS7D01G304100
chr7D
100.000
3080
0
0
1
3080
385716975
385720054
0.000000e+00
5688
1
TraesCS7D01G304100
chr7A
93.570
2053
80
24
1
2040
433742219
433744232
0.000000e+00
3013
2
TraesCS7D01G304100
chr7A
88.722
133
14
1
2140
2271
433744938
433745070
8.840000e-36
161
3
TraesCS7D01G304100
chr7B
93.975
1776
66
14
500
2270
380079197
380080936
0.000000e+00
2649
4
TraesCS7D01G304100
chr7B
90.113
354
27
8
1
348
380076287
380076638
1.300000e-123
453
5
TraesCS7D01G304100
chr7B
89.796
147
14
1
336
482
380076657
380076802
1.460000e-43
187
6
TraesCS7D01G304100
chr1D
95.466
816
33
3
2267
3080
297519113
297519926
0.000000e+00
1299
7
TraesCS7D01G304100
chr6D
94.377
818
39
6
2267
3080
23775102
23775916
0.000000e+00
1249
8
TraesCS7D01G304100
chr6D
94.010
818
39
6
2266
3080
276128266
276127456
0.000000e+00
1230
9
TraesCS7D01G304100
chr5A
94.363
816
39
5
2269
3080
602360821
602360009
0.000000e+00
1245
10
TraesCS7D01G304100
chr3D
94.125
817
44
3
2267
3080
110280478
110279663
0.000000e+00
1240
11
TraesCS7D01G304100
chr3D
93.325
824
44
7
2264
3080
537304561
537305380
0.000000e+00
1206
12
TraesCS7D01G304100
chr5D
93.390
817
47
4
2267
3080
51856348
51855536
0.000000e+00
1203
13
TraesCS7D01G304100
chr5D
93.293
820
48
5
2264
3080
238112719
238113534
0.000000e+00
1203
14
TraesCS7D01G304100
chr2D
93.382
816
48
4
2269
3080
86069495
86068682
0.000000e+00
1203
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
TraesCS7D01G304100
chr7D
385716975
385720054
3079
False
5688.000000
5688
100.000000
1
3080
1
chr7D.!!$F1
3079
1
TraesCS7D01G304100
chr7A
433742219
433745070
2851
False
1587.000000
3013
91.146000
1
2271
2
chr7A.!!$F1
2270
2
TraesCS7D01G304100
chr7B
380076287
380080936
4649
False
1096.333333
2649
91.294667
1
2270
3
chr7B.!!$F1
2269
3
TraesCS7D01G304100
chr1D
297519113
297519926
813
False
1299.000000
1299
95.466000
2267
3080
1
chr1D.!!$F1
813
4
TraesCS7D01G304100
chr6D
23775102
23775916
814
False
1249.000000
1249
94.377000
2267
3080
1
chr6D.!!$F1
813
5
TraesCS7D01G304100
chr6D
276127456
276128266
810
True
1230.000000
1230
94.010000
2266
3080
1
chr6D.!!$R1
814
6
TraesCS7D01G304100
chr5A
602360009
602360821
812
True
1245.000000
1245
94.363000
2269
3080
1
chr5A.!!$R1
811
7
TraesCS7D01G304100
chr3D
110279663
110280478
815
True
1240.000000
1240
94.125000
2267
3080
1
chr3D.!!$R1
813
8
TraesCS7D01G304100
chr3D
537304561
537305380
819
False
1206.000000
1206
93.325000
2264
3080
1
chr3D.!!$F1
816
9
TraesCS7D01G304100
chr5D
51855536
51856348
812
True
1203.000000
1203
93.390000
2267
3080
1
chr5D.!!$R1
813
10
TraesCS7D01G304100
chr5D
238112719
238113534
815
False
1203.000000
1203
93.293000
2264
3080
1
chr5D.!!$F1
816
11
TraesCS7D01G304100
chr2D
86068682
86069495
813
True
1203.000000
1203
93.382000
2269
3080
1
chr2D.!!$R1
811
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.