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
TraesCS3B01G183900
chr3B
100.000
2450
0
0
1
2450
195665361
195667810
0.000000e+00
4525
1
TraesCS3B01G183900
chr3B
94.483
2284
112
7
1
2273
288475200
288477480
0.000000e+00
3507
2
TraesCS3B01G183900
chr3B
89.593
2460
212
31
1
2433
331024944
331027386
0.000000e+00
3085
3
TraesCS3B01G183900
chr1B
98.203
2449
40
3
1
2448
287516454
287518899
0.000000e+00
4276
4
TraesCS3B01G183900
chr1B
90.443
2459
198
25
1
2433
200995202
200997649
0.000000e+00
3205
5
TraesCS3B01G183900
chr1B
89.724
2462
211
22
1
2433
387430129
387427681
0.000000e+00
3107
6
TraesCS3B01G183900
chr2B
95.311
2282
96
6
1
2273
762706218
762708497
0.000000e+00
3611
7
TraesCS3B01G183900
chr2B
95.238
294
13
1
2158
2450
545609926
545609633
4.770000e-127
464
8
TraesCS3B01G183900
chr2B
89.121
239
24
2
2212
2450
465449102
465448866
1.840000e-76
296
9
TraesCS3B01G183900
chr2A
91.038
2466
196
16
2
2450
267980584
267983041
0.000000e+00
3306
10
TraesCS3B01G183900
chr4B
92.128
2312
153
16
11
2302
534533200
534535502
0.000000e+00
3234
11
TraesCS3B01G183900
chr1D
90.049
2462
200
30
1
2433
246373124
246375569
0.000000e+00
3147
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
TraesCS3B01G183900
chr3B
195665361
195667810
2449
False
4525
4525
100.000
1
2450
1
chr3B.!!$F1
2449
1
TraesCS3B01G183900
chr3B
288475200
288477480
2280
False
3507
3507
94.483
1
2273
1
chr3B.!!$F2
2272
2
TraesCS3B01G183900
chr3B
331024944
331027386
2442
False
3085
3085
89.593
1
2433
1
chr3B.!!$F3
2432
3
TraesCS3B01G183900
chr1B
287516454
287518899
2445
False
4276
4276
98.203
1
2448
1
chr1B.!!$F2
2447
4
TraesCS3B01G183900
chr1B
200995202
200997649
2447
False
3205
3205
90.443
1
2433
1
chr1B.!!$F1
2432
5
TraesCS3B01G183900
chr1B
387427681
387430129
2448
True
3107
3107
89.724
1
2433
1
chr1B.!!$R1
2432
6
TraesCS3B01G183900
chr2B
762706218
762708497
2279
False
3611
3611
95.311
1
2273
1
chr2B.!!$F1
2272
7
TraesCS3B01G183900
chr2A
267980584
267983041
2457
False
3306
3306
91.038
2
2450
1
chr2A.!!$F1
2448
8
TraesCS3B01G183900
chr4B
534533200
534535502
2302
False
3234
3234
92.128
11
2302
1
chr4B.!!$F1
2291
9
TraesCS3B01G183900
chr1D
246373124
246375569
2445
False
3147
3147
90.049
1
2433
1
chr1D.!!$F1
2432
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.