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
TraesCS4A01G153300
chr4A
100.000
2366
0
0
1
2366
309510057
309512422
0.000000e+00
4370
1
TraesCS4A01G153300
chr5D
96.633
2376
60
10
1
2360
483806512
483808883
0.000000e+00
3927
2
TraesCS4A01G153300
chr5D
96.346
2381
67
10
1
2366
503284372
503281997
0.000000e+00
3897
3
TraesCS4A01G153300
chr5D
96.301
2379
70
10
1
2366
6183870
6186243
0.000000e+00
3890
4
TraesCS4A01G153300
chr5D
93.493
584
24
5
2
575
167069012
167068433
0.000000e+00
856
5
TraesCS4A01G153300
chr6D
96.299
2378
71
10
1
2366
45514498
45516870
0.000000e+00
3888
6
TraesCS4A01G153300
chr1D
96.175
2379
65
13
1
2366
254403176
254400811
0.000000e+00
3866
7
TraesCS4A01G153300
chr1D
95.244
2376
91
13
1
2366
51880998
51883361
0.000000e+00
3742
8
TraesCS4A01G153300
chr2A
95.965
2379
77
12
1
2366
335833575
335835947
0.000000e+00
3843
9
TraesCS4A01G153300
chr3D
96.378
2319
56
11
1
2304
598875876
598873571
0.000000e+00
3792
10
TraesCS4A01G153300
chr4B
94.613
2376
96
17
3
2366
308691426
308693781
0.000000e+00
3650
11
TraesCS4A01G153300
chrUn
95.805
2241
75
12
1
2230
261572040
261574272
0.000000e+00
3600
12
TraesCS4A01G153300
chrUn
98.571
70
1
0
1
70
442414360
442414429
8.880000e-25
124
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
TraesCS4A01G153300
chr4A
309510057
309512422
2365
False
4370
4370
100.000
1
2366
1
chr4A.!!$F1
2365
1
TraesCS4A01G153300
chr5D
483806512
483808883
2371
False
3927
3927
96.633
1
2360
1
chr5D.!!$F2
2359
2
TraesCS4A01G153300
chr5D
503281997
503284372
2375
True
3897
3897
96.346
1
2366
1
chr5D.!!$R2
2365
3
TraesCS4A01G153300
chr5D
6183870
6186243
2373
False
3890
3890
96.301
1
2366
1
chr5D.!!$F1
2365
4
TraesCS4A01G153300
chr5D
167068433
167069012
579
True
856
856
93.493
2
575
1
chr5D.!!$R1
573
5
TraesCS4A01G153300
chr6D
45514498
45516870
2372
False
3888
3888
96.299
1
2366
1
chr6D.!!$F1
2365
6
TraesCS4A01G153300
chr1D
254400811
254403176
2365
True
3866
3866
96.175
1
2366
1
chr1D.!!$R1
2365
7
TraesCS4A01G153300
chr1D
51880998
51883361
2363
False
3742
3742
95.244
1
2366
1
chr1D.!!$F1
2365
8
TraesCS4A01G153300
chr2A
335833575
335835947
2372
False
3843
3843
95.965
1
2366
1
chr2A.!!$F1
2365
9
TraesCS4A01G153300
chr3D
598873571
598875876
2305
True
3792
3792
96.378
1
2304
1
chr3D.!!$R1
2303
10
TraesCS4A01G153300
chr4B
308691426
308693781
2355
False
3650
3650
94.613
3
2366
1
chr4B.!!$F1
2363
11
TraesCS4A01G153300
chrUn
261572040
261574272
2232
False
3600
3600
95.805
1
2230
1
chrUn.!!$F1
2229
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.