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
TraesCS5A01G322000
chr5A
100.000
2477
0
0
1
2477
534624071
534621595
0
4575
1
TraesCS5A01G322000
chr5A
89.050
1169
106
15
1
1154
107748853
107750014
0
1430
2
TraesCS5A01G322000
chr5A
79.614
1501
282
19
2
1485
81479727
81481220
0
1055
3
TraesCS5A01G322000
chr3D
89.870
1382
112
15
1
1367
11552120
11553488
0
1751
4
TraesCS5A01G322000
chr3D
87.450
996
104
10
517
1503
452411137
452410154
0
1127
5
TraesCS5A01G322000
chr2A
82.577
1521
231
22
1
1506
728563699
728565200
0
1310
6
TraesCS5A01G322000
chr5D
90.564
975
68
16
1506
2477
421213131
421212178
0
1269
7
TraesCS5A01G322000
chr4B
82.866
1354
198
20
53
1390
560005196
560003861
0
1184
8
TraesCS5A01G322000
chr5B
80.146
1511
283
14
8
1505
8879672
8878166
0
1112
9
TraesCS5A01G322000
chr5B
81.951
892
139
14
1506
2384
507569407
507568525
0
736
10
TraesCS5A01G322000
chr1D
87.022
994
111
14
1
982
55395550
55394563
0
1105
11
TraesCS5A01G322000
chr1B
85.141
996
124
19
1
982
90872596
90871611
0
998
12
TraesCS5A01G322000
chr2D
79.119
1475
278
26
30
1485
49897319
49895856
0
990
13
TraesCS5A01G322000
chr2B
79.914
1389
245
30
137
1503
625421391
625420015
0
989
14
TraesCS5A01G322000
chr1A
78.861
1457
280
23
1
1438
521871667
521870220
0
959
15
TraesCS5A01G322000
chr4D
77.279
1514
307
29
12
1506
312917233
312918728
0
856
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
TraesCS5A01G322000
chr5A
534621595
534624071
2476
True
4575
4575
100.000
1
2477
1
chr5A.!!$R1
2476
1
TraesCS5A01G322000
chr5A
107748853
107750014
1161
False
1430
1430
89.050
1
1154
1
chr5A.!!$F2
1153
2
TraesCS5A01G322000
chr5A
81479727
81481220
1493
False
1055
1055
79.614
2
1485
1
chr5A.!!$F1
1483
3
TraesCS5A01G322000
chr3D
11552120
11553488
1368
False
1751
1751
89.870
1
1367
1
chr3D.!!$F1
1366
4
TraesCS5A01G322000
chr3D
452410154
452411137
983
True
1127
1127
87.450
517
1503
1
chr3D.!!$R1
986
5
TraesCS5A01G322000
chr2A
728563699
728565200
1501
False
1310
1310
82.577
1
1506
1
chr2A.!!$F1
1505
6
TraesCS5A01G322000
chr5D
421212178
421213131
953
True
1269
1269
90.564
1506
2477
1
chr5D.!!$R1
971
7
TraesCS5A01G322000
chr4B
560003861
560005196
1335
True
1184
1184
82.866
53
1390
1
chr4B.!!$R1
1337
8
TraesCS5A01G322000
chr5B
8878166
8879672
1506
True
1112
1112
80.146
8
1505
1
chr5B.!!$R1
1497
9
TraesCS5A01G322000
chr5B
507568525
507569407
882
True
736
736
81.951
1506
2384
1
chr5B.!!$R2
878
10
TraesCS5A01G322000
chr1D
55394563
55395550
987
True
1105
1105
87.022
1
982
1
chr1D.!!$R1
981
11
TraesCS5A01G322000
chr1B
90871611
90872596
985
True
998
998
85.141
1
982
1
chr1B.!!$R1
981
12
TraesCS5A01G322000
chr2D
49895856
49897319
1463
True
990
990
79.119
30
1485
1
chr2D.!!$R1
1455
13
TraesCS5A01G322000
chr2B
625420015
625421391
1376
True
989
989
79.914
137
1503
1
chr2B.!!$R1
1366
14
TraesCS5A01G322000
chr1A
521870220
521871667
1447
True
959
959
78.861
1
1438
1
chr1A.!!$R1
1437
15
TraesCS5A01G322000
chr4D
312917233
312918728
1495
False
856
856
77.279
12
1506
1
chr4D.!!$F1
1494
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.