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
TraesCS4A01G134900
chr4A
100.000
4045
0
0
2279
6323
183983652
183979608
0.000000e+00
7470.0
1
TraesCS4A01G134900
chr4A
100.000
1862
0
0
1
1862
183985930
183984069
0.000000e+00
3439.0
2
TraesCS4A01G134900
chr4A
92.941
170
10
2
4808
4975
137967148
137966979
4.900000e-61
246.0
3
TraesCS4A01G134900
chr4A
92.941
170
10
2
4808
4975
137972661
137972830
4.900000e-61
246.0
4
TraesCS4A01G134900
chr4A
90.323
62
1
4
5152
5212
493268146
493268089
6.800000e-10
76.8
5
TraesCS4A01G134900
chr4D
92.744
1888
90
16
1
1862
299762571
299764437
0.000000e+00
2684.0
6
TraesCS4A01G134900
chr4D
95.883
1603
46
10
4726
6323
299766977
299768564
0.000000e+00
2577.0
7
TraesCS4A01G134900
chr4D
98.210
1397
23
2
2279
3675
299764457
299765851
0.000000e+00
2440.0
8
TraesCS4A01G134900
chr4D
96.715
1096
27
5
3658
4745
299765865
299766959
0.000000e+00
1816.0
9
TraesCS4A01G134900
chr4D
93.333
45
1
2
4486
4529
299766794
299766837
1.470000e-06
65.8
10
TraesCS4A01G134900
chr4B
90.531
1922
110
38
1
1862
372818441
372820350
0.000000e+00
2475.0
11
TraesCS4A01G134900
chr4B
97.639
1398
25
4
2279
3675
372820369
372821759
0.000000e+00
2392.0
12
TraesCS4A01G134900
chr4B
95.007
1502
47
9
4834
6323
372823052
372824537
0.000000e+00
2333.0
13
TraesCS4A01G134900
chr4B
96.365
1183
33
5
3658
4836
372821773
372822949
0.000000e+00
1938.0
14
TraesCS4A01G134900
chr4B
93.333
45
1
2
4486
4529
372822694
372822737
1.470000e-06
65.8
15
TraesCS4A01G134900
chr5D
92.683
164
11
1
4815
4977
529218327
529218164
1.060000e-57
235.0
16
TraesCS4A01G134900
chr1D
91.279
172
11
3
4812
4982
451226903
451226735
1.370000e-56
231.0
17
TraesCS4A01G134900
chr1D
90.323
62
1
4
5152
5212
5660357
5660414
6.800000e-10
76.8
18
TraesCS4A01G134900
chr1D
90.323
62
1
4
5152
5212
64303544
64303487
6.800000e-10
76.8
19
TraesCS4A01G134900
chr6B
90.805
174
10
3
4810
4982
377935530
377935698
1.770000e-55
228.0
20
TraesCS4A01G134900
chr6B
79.310
87
18
0
513
599
651986726
651986812
1.900000e-05
62.1
21
TraesCS4A01G134900
chrUn
91.515
165
11
2
4815
4978
96478384
96478222
2.290000e-54
224.0
22
TraesCS4A01G134900
chr2D
88.333
180
19
2
4806
4983
571079129
571078950
1.380000e-51
215.0
23
TraesCS4A01G134900
chr7A
90.323
62
1
4
5152
5212
12211275
12211332
6.800000e-10
76.8
24
TraesCS4A01G134900
chr5A
90.323
62
1
4
5152
5212
671856180
671856237
6.800000e-10
76.8
25
TraesCS4A01G134900
chr2A
97.222
36
1
0
6101
6136
12976362
12976327
1.900000e-05
62.1
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
TraesCS4A01G134900
chr4A
183979608
183985930
6322
True
5454.50
7470
100.000
1
6323
2
chr4A.!!$R3
6322
1
TraesCS4A01G134900
chr4D
299762571
299768564
5993
False
1916.56
2684
95.377
1
6323
5
chr4D.!!$F1
6322
2
TraesCS4A01G134900
chr4B
372818441
372824537
6096
False
1840.76
2475
94.575
1
6323
5
chr4B.!!$F1
6322
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.