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
TraesCS5A01G337200
chr5A
100.000
2498
0
0
1
2498
545646412
545643915
0.000000e+00
4614
1
TraesCS5A01G337200
chr5A
72.900
369
83
13
705
1062
445499519
445499881
7.300000e-21
111
2
TraesCS5A01G337200
chr6D
91.766
2514
172
13
12
2498
377187403
377189908
0.000000e+00
3463
3
TraesCS5A01G337200
chr6D
86.207
2059
243
27
468
2498
312812413
312810368
0.000000e+00
2191
4
TraesCS5A01G337200
chr1A
86.624
2026
244
19
12
2018
592546648
592548665
0.000000e+00
2215
5
TraesCS5A01G337200
chr1A
81.890
2529
388
36
1
2498
515117322
515119811
0.000000e+00
2069
6
TraesCS5A01G337200
chr1A
81.811
2529
390
36
1
2498
514861077
514863566
0.000000e+00
2058
7
TraesCS5A01G337200
chr1A
87.082
1556
192
6
12
1567
265638973
265637427
0.000000e+00
1751
8
TraesCS5A01G337200
chr1A
85.348
935
122
11
1573
2498
265628882
265627954
0.000000e+00
953
9
TraesCS5A01G337200
chr5D
82.857
2520
375
30
1
2498
88531849
88529365
0.000000e+00
2207
10
TraesCS5A01G337200
chr3A
82.153
2527
395
27
1
2498
32907266
32904767
0.000000e+00
2117
11
TraesCS5A01G337200
chr4A
80.330
2542
439
38
1
2498
547206118
547208642
0.000000e+00
1868
12
TraesCS5A01G337200
chr2D
80.245
2526
440
33
6
2498
250625308
250622809
0.000000e+00
1845
13
TraesCS5A01G337200
chr2D
93.320
1003
43
9
1505
2498
633446221
633445234
0.000000e+00
1459
14
TraesCS5A01G337200
chr2D
93.260
549
33
2
1949
2497
31903967
31903423
0.000000e+00
806
15
TraesCS5A01G337200
chr7D
89.857
1262
96
11
1264
2498
3718696
3719952
0.000000e+00
1592
16
TraesCS5A01G337200
chr3D
80.280
1785
320
20
6
1766
581411751
581409975
0.000000e+00
1317
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
TraesCS5A01G337200
chr5A
545643915
545646412
2497
True
4614
4614
100.000
1
2498
1
chr5A.!!$R1
2497
1
TraesCS5A01G337200
chr6D
377187403
377189908
2505
False
3463
3463
91.766
12
2498
1
chr6D.!!$F1
2486
2
TraesCS5A01G337200
chr6D
312810368
312812413
2045
True
2191
2191
86.207
468
2498
1
chr6D.!!$R1
2030
3
TraesCS5A01G337200
chr1A
592546648
592548665
2017
False
2215
2215
86.624
12
2018
1
chr1A.!!$F3
2006
4
TraesCS5A01G337200
chr1A
515117322
515119811
2489
False
2069
2069
81.890
1
2498
1
chr1A.!!$F2
2497
5
TraesCS5A01G337200
chr1A
514861077
514863566
2489
False
2058
2058
81.811
1
2498
1
chr1A.!!$F1
2497
6
TraesCS5A01G337200
chr1A
265637427
265638973
1546
True
1751
1751
87.082
12
1567
1
chr1A.!!$R2
1555
7
TraesCS5A01G337200
chr1A
265627954
265628882
928
True
953
953
85.348
1573
2498
1
chr1A.!!$R1
925
8
TraesCS5A01G337200
chr5D
88529365
88531849
2484
True
2207
2207
82.857
1
2498
1
chr5D.!!$R1
2497
9
TraesCS5A01G337200
chr3A
32904767
32907266
2499
True
2117
2117
82.153
1
2498
1
chr3A.!!$R1
2497
10
TraesCS5A01G337200
chr4A
547206118
547208642
2524
False
1868
1868
80.330
1
2498
1
chr4A.!!$F1
2497
11
TraesCS5A01G337200
chr2D
250622809
250625308
2499
True
1845
1845
80.245
6
2498
1
chr2D.!!$R2
2492
12
TraesCS5A01G337200
chr2D
633445234
633446221
987
True
1459
1459
93.320
1505
2498
1
chr2D.!!$R3
993
13
TraesCS5A01G337200
chr2D
31903423
31903967
544
True
806
806
93.260
1949
2497
1
chr2D.!!$R1
548
14
TraesCS5A01G337200
chr7D
3718696
3719952
1256
False
1592
1592
89.857
1264
2498
1
chr7D.!!$F1
1234
15
TraesCS5A01G337200
chr3D
581409975
581411751
1776
True
1317
1317
80.280
6
1766
1
chr3D.!!$R1
1760
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.