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
TraesCS3A01G004900
chr3A
100.000
2371
0
0
1
2371
4461302
4463672
0
4379
1
TraesCS3A01G004900
chr3A
98.988
2371
23
1
1
2371
3409936
3412305
0
4244
2
TraesCS3A01G004900
chr3A
98.819
2371
28
0
1
2371
5470069
5472439
0
4224
3
TraesCS3A01G004900
chr3A
98.524
2371
33
2
1
2371
2897579
2899947
0
4183
4
TraesCS3A01G004900
chr3A
98.314
2372
38
2
1
2371
5486750
5489120
0
4157
5
TraesCS3A01G004900
chr3A
98.313
2371
38
2
2
2371
2914401
2916770
0
4156
6
TraesCS3A01G004900
chr3A
98.272
2372
39
2
1
2371
3434237
3436607
0
4152
7
TraesCS3A01G004900
chr3A
98.272
2372
39
2
1
2371
4484518
4486888
0
4152
8
TraesCS3A01G004900
chr3A
98.229
2372
38
4
1
2371
2434786
2437154
0
4145
9
TraesCS3A01G004900
chr3A
98.229
2372
39
3
1
2371
4478124
4480493
0
4145
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
TraesCS3A01G004900
chr3A
4461302
4463672
2370
False
4379
4379
100.000
1
2371
1
chr3A.!!$F6
2370
1
TraesCS3A01G004900
chr3A
3409936
3412305
2369
False
4244
4244
98.988
1
2371
1
chr3A.!!$F4
2370
2
TraesCS3A01G004900
chr3A
5470069
5472439
2370
False
4224
4224
98.819
1
2371
1
chr3A.!!$F9
2370
3
TraesCS3A01G004900
chr3A
2897579
2899947
2368
False
4183
4183
98.524
1
2371
1
chr3A.!!$F2
2370
4
TraesCS3A01G004900
chr3A
5486750
5489120
2370
False
4157
4157
98.314
1
2371
1
chr3A.!!$F10
2370
5
TraesCS3A01G004900
chr3A
2914401
2916770
2369
False
4156
4156
98.313
2
2371
1
chr3A.!!$F3
2369
6
TraesCS3A01G004900
chr3A
3434237
3436607
2370
False
4152
4152
98.272
1
2371
1
chr3A.!!$F5
2370
7
TraesCS3A01G004900
chr3A
4484518
4486888
2370
False
4152
4152
98.272
1
2371
1
chr3A.!!$F8
2370
8
TraesCS3A01G004900
chr3A
2434786
2437154
2368
False
4145
4145
98.229
1
2371
1
chr3A.!!$F1
2370
9
TraesCS3A01G004900
chr3A
4478124
4480493
2369
False
4145
4145
98.229
1
2371
1
chr3A.!!$F7
2370
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.