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
TraesCS5A01G072900
chr5A
100.000
2951
0
0
1
2951
84389689
84386739
0.000000e+00
5450
1
TraesCS5A01G072900
chr5B
96.326
2967
86
14
6
2951
96140483
96137519
0.000000e+00
4854
2
TraesCS5A01G072900
chr5D
95.895
2972
96
13
1
2951
90925844
90922878
0.000000e+00
4789
3
TraesCS5A01G072900
chr5D
90.132
152
15
0
1
152
411155737
411155888
6.450000e-47
198
4
TraesCS5A01G072900
chr2A
91.447
152
13
0
1
152
766144396
766144547
2.980000e-50
209
5
TraesCS5A01G072900
chr3D
90.850
153
14
0
1
153
104097520
104097368
3.860000e-49
206
6
TraesCS5A01G072900
chr7D
90.789
152
14
0
1
152
116602311
116602462
1.390000e-48
204
7
TraesCS5A01G072900
chr6A
90.667
150
14
0
3
152
5126737
5126886
1.790000e-47
200
8
TraesCS5A01G072900
chr6A
90.667
150
14
0
1
150
592431710
592431859
1.790000e-47
200
9
TraesCS5A01G072900
chr3A
90.667
150
14
0
1
150
64085408
64085259
1.790000e-47
200
10
TraesCS5A01G072900
chr2D
90.667
150
14
0
1
150
624783098
624783247
1.790000e-47
200
11
TraesCS5A01G072900
chr7B
90.000
150
15
0
1
150
339619392
339619541
8.350000e-46
195
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
TraesCS5A01G072900
chr5A
84386739
84389689
2950
True
5450
5450
100.000
1
2951
1
chr5A.!!$R1
2950
1
TraesCS5A01G072900
chr5B
96137519
96140483
2964
True
4854
4854
96.326
6
2951
1
chr5B.!!$R1
2945
2
TraesCS5A01G072900
chr5D
90922878
90925844
2966
True
4789
4789
95.895
1
2951
1
chr5D.!!$R1
2950
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.