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
TraesCS4B01G394100
chr4B
100.000
2303
0
0
1
2303
668228749
668231051
0
4253
1
TraesCS4B01G394100
chr4B
97.225
2306
57
6
1
2303
669484884
669487185
0
3897
2
TraesCS4B01G394100
chr4B
97.182
2307
56
7
1
2303
668906604
668908905
0
3892
3
TraesCS4B01G394100
chr4B
97.102
2312
52
7
1
2303
668464701
668467006
0
3884
4
TraesCS4B01G394100
chr4B
96.921
2306
58
9
1
2303
668525822
668528117
0
3853
5
TraesCS4B01G394100
chr4B
95.776
2320
49
18
1
2303
668623665
668625952
0
3696
6
TraesCS4B01G394100
chr4B
95.521
2322
52
21
1
2303
669588520
669590808
0
3664
7
TraesCS4B01G394100
chr4B
97.914
1534
28
4
772
2303
669142067
669140536
0
2652
8
TraesCS4B01G394100
chr4B
97.715
1532
32
3
772
2302
668992011
668993540
0
2632
9
TraesCS4B01G394100
chr4B
97.262
1534
36
5
772
2303
669303507
669301978
0
2595
10
TraesCS4B01G394100
chr4B
96.917
1200
29
6
1107
2303
668398706
668399900
0
2004
11
TraesCS4B01G394100
chr4B
98.361
549
9
0
1
549
668374318
668374866
0
965
12
TraesCS4B01G394100
chr5A
97.752
1468
30
2
1
1468
707877713
707879177
0
2525
13
TraesCS4B01G394100
chr5A
96.791
779
17
7
1529
2303
707879177
707879951
0
1293
14
TraesCS4B01G394100
chr7B
95.286
594
28
0
1
594
336367701
336368294
0
942
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
TraesCS4B01G394100
chr4B
668228749
668231051
2302
False
4253
4253
100.0000
1
2303
1
chr4B.!!$F1
2302
1
TraesCS4B01G394100
chr4B
669484884
669487185
2301
False
3897
3897
97.2250
1
2303
1
chr4B.!!$F9
2302
2
TraesCS4B01G394100
chr4B
668906604
668908905
2301
False
3892
3892
97.1820
1
2303
1
chr4B.!!$F7
2302
3
TraesCS4B01G394100
chr4B
668464701
668467006
2305
False
3884
3884
97.1020
1
2303
1
chr4B.!!$F4
2302
4
TraesCS4B01G394100
chr4B
668525822
668528117
2295
False
3853
3853
96.9210
1
2303
1
chr4B.!!$F5
2302
5
TraesCS4B01G394100
chr4B
668623665
668625952
2287
False
3696
3696
95.7760
1
2303
1
chr4B.!!$F6
2302
6
TraesCS4B01G394100
chr4B
669588520
669590808
2288
False
3664
3664
95.5210
1
2303
1
chr4B.!!$F10
2302
7
TraesCS4B01G394100
chr4B
669140536
669142067
1531
True
2652
2652
97.9140
772
2303
1
chr4B.!!$R1
1531
8
TraesCS4B01G394100
chr4B
668992011
668993540
1529
False
2632
2632
97.7150
772
2302
1
chr4B.!!$F8
1530
9
TraesCS4B01G394100
chr4B
669301978
669303507
1529
True
2595
2595
97.2620
772
2303
1
chr4B.!!$R2
1531
10
TraesCS4B01G394100
chr4B
668398706
668399900
1194
False
2004
2004
96.9170
1107
2303
1
chr4B.!!$F3
1196
11
TraesCS4B01G394100
chr4B
668374318
668374866
548
False
965
965
98.3610
1
549
1
chr4B.!!$F2
548
12
TraesCS4B01G394100
chr5A
707877713
707879951
2238
False
1909
2525
97.2715
1
2303
2
chr5A.!!$F1
2302
13
TraesCS4B01G394100
chr7B
336367701
336368294
593
False
942
942
95.2860
1
594
1
chr7B.!!$F1
593
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.