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
TraesCS3B01G442500
chr3B
100.000
2450
0
0
1
2450
682015432
682012983
0.000000e+00
4525
1
TraesCS3B01G442500
chr3B
91.304
138
10
2
2314
2450
321733783
321733647
1.160000e-43
187
2
TraesCS3B01G442500
chr3B
90.580
138
11
2
2314
2450
393195360
393195496
5.380000e-42
182
3
TraesCS3B01G442500
chr2B
93.040
2457
152
13
1
2450
550079267
550076823
0.000000e+00
3572
4
TraesCS3B01G442500
chr1B
92.342
2455
146
32
2
2440
346594896
346597324
0.000000e+00
3454
5
TraesCS3B01G442500
chr1B
93.475
2314
129
15
1
2303
106887645
106889947
0.000000e+00
3417
6
TraesCS3B01G442500
chr4B
91.182
2495
165
35
1
2450
78829610
78827126
0.000000e+00
3338
7
TraesCS3B01G442500
chr4A
91.203
2478
164
36
2
2440
721639036
721641498
0.000000e+00
3319
8
TraesCS3B01G442500
chr4A
90.024
2456
223
14
2
2450
500274898
500272458
0.000000e+00
3158
9
TraesCS3B01G442500
chr6D
91.046
2457
198
12
1
2450
283635549
283633108
0.000000e+00
3299
10
TraesCS3B01G442500
chr5B
90.854
2471
183
26
1
2440
547746192
547748650
0.000000e+00
3271
11
TraesCS3B01G442500
chr5B
90.692
2471
187
26
1
2440
547767243
547769701
0.000000e+00
3249
12
TraesCS3B01G442500
chr5B
88.128
219
16
7
2241
2450
4634660
4634443
4.040000e-63
252
13
TraesCS3B01G442500
chr7B
89.855
138
12
2
2314
2450
368858040
368858176
2.500000e-40
176
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
TraesCS3B01G442500
chr3B
682012983
682015432
2449
True
4525
4525
100.000
1
2450
1
chr3B.!!$R2
2449
1
TraesCS3B01G442500
chr2B
550076823
550079267
2444
True
3572
3572
93.040
1
2450
1
chr2B.!!$R1
2449
2
TraesCS3B01G442500
chr1B
346594896
346597324
2428
False
3454
3454
92.342
2
2440
1
chr1B.!!$F2
2438
3
TraesCS3B01G442500
chr1B
106887645
106889947
2302
False
3417
3417
93.475
1
2303
1
chr1B.!!$F1
2302
4
TraesCS3B01G442500
chr4B
78827126
78829610
2484
True
3338
3338
91.182
1
2450
1
chr4B.!!$R1
2449
5
TraesCS3B01G442500
chr4A
721639036
721641498
2462
False
3319
3319
91.203
2
2440
1
chr4A.!!$F1
2438
6
TraesCS3B01G442500
chr4A
500272458
500274898
2440
True
3158
3158
90.024
2
2450
1
chr4A.!!$R1
2448
7
TraesCS3B01G442500
chr6D
283633108
283635549
2441
True
3299
3299
91.046
1
2450
1
chr6D.!!$R1
2449
8
TraesCS3B01G442500
chr5B
547746192
547748650
2458
False
3271
3271
90.854
1
2440
1
chr5B.!!$F1
2439
9
TraesCS3B01G442500
chr5B
547767243
547769701
2458
False
3249
3249
90.692
1
2440
1
chr5B.!!$F2
2439
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.