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
TraesCS1B01G158400
chr1B
100.000
2360
0
0
1
2360
268900420
268898061
0.000000e+00
4359.0
1
TraesCS1B01G158400
chr1B
81.915
376
55
10
225
599
667612269
667612632
2.950000e-79
305.0
2
TraesCS1B01G158400
chr1A
87.256
1436
142
19
1
1428
241378535
241377133
0.000000e+00
1600.0
3
TraesCS1B01G158400
chr1A
91.611
906
35
11
1483
2355
241377117
241376220
0.000000e+00
1214.0
4
TraesCS1B01G158400
chr1A
82.305
486
80
6
118
599
38586783
38586300
1.300000e-112
416.0
5
TraesCS1B01G158400
chr1A
82.863
461
74
4
143
599
38639820
38639361
2.180000e-110
409.0
6
TraesCS1B01G158400
chr1D
93.234
872
30
6
1510
2360
194201683
194200820
0.000000e+00
1256.0
7
TraesCS1B01G158400
chr1D
91.783
791
42
9
641
1429
194202467
194201698
0.000000e+00
1079.0
8
TraesCS1B01G158400
chr1D
87.246
345
43
1
1
344
194218890
194218546
2.200000e-105
392.0
9
TraesCS1B01G158400
chr2A
80.602
598
104
6
1
594
695185544
695186133
3.580000e-123
451.0
10
TraesCS1B01G158400
chr2A
81.649
485
86
3
116
599
692210759
692211241
1.310000e-107
399.0
11
TraesCS1B01G158400
chr3B
79.225
645
112
14
1
625
807153147
807153789
1.680000e-116
429.0
12
TraesCS1B01G158400
chr3B
92.857
42
3
0
619
660
10634078
10634119
7.040000e-06
62.1
13
TraesCS1B01G158400
chr7D
79.534
601
86
21
1
599
172265280
172264715
6.110000e-106
394.0
14
TraesCS1B01G158400
chr2D
81.432
377
63
5
196
566
612978619
612978244
3.810000e-78
302.0
15
TraesCS1B01G158400
chr6A
84.568
162
16
5
669
829
64321666
64321513
4.060000e-33
152.0
16
TraesCS1B01G158400
chr7B
83.871
155
18
5
668
821
613151216
613151364
8.790000e-30
141.0
17
TraesCS1B01G158400
chr7B
91.837
49
4
0
1434
1482
594046380
594046428
4.210000e-08
69.4
18
TraesCS1B01G158400
chr7B
90.476
42
2
2
1441
1482
32435203
32435164
1.000000e-03
54.7
19
TraesCS1B01G158400
chr4A
82.278
158
21
5
666
822
683889124
683889275
1.900000e-26
130.0
20
TraesCS1B01G158400
chr5B
81.707
164
20
6
666
828
36481766
36481920
6.850000e-26
128.0
21
TraesCS1B01G158400
chr3D
82.667
150
18
6
666
813
545176707
545176564
2.460000e-25
126.0
22
TraesCS1B01G158400
chr5D
81.212
165
19
6
666
828
101809912
101809758
3.190000e-24
122.0
23
TraesCS1B01G158400
chr2B
81.212
165
20
8
666
829
793277925
793278079
3.190000e-24
122.0
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
TraesCS1B01G158400
chr1B
268898061
268900420
2359
True
4359.0
4359
100.0000
1
2360
1
chr1B.!!$R1
2359
1
TraesCS1B01G158400
chr1A
241376220
241378535
2315
True
1407.0
1600
89.4335
1
2355
2
chr1A.!!$R3
2354
2
TraesCS1B01G158400
chr1D
194200820
194202467
1647
True
1167.5
1256
92.5085
641
2360
2
chr1D.!!$R2
1719
3
TraesCS1B01G158400
chr2A
695185544
695186133
589
False
451.0
451
80.6020
1
594
1
chr2A.!!$F2
593
4
TraesCS1B01G158400
chr3B
807153147
807153789
642
False
429.0
429
79.2250
1
625
1
chr3B.!!$F2
624
5
TraesCS1B01G158400
chr7D
172264715
172265280
565
True
394.0
394
79.5340
1
599
1
chr7D.!!$R1
598
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.