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
TraesCS6A01G306500
chr6A
100.000
2415
0
0
801
3215
540146045
540143631
0.000000e+00
4460.0
1
TraesCS6A01G306500
chr6A
100.000
483
0
0
1
483
540146845
540146363
0.000000e+00
893.0
2
TraesCS6A01G306500
chr6D
95.017
2388
81
15
848
3215
393936546
393934177
0.000000e+00
3716.0
3
TraesCS6A01G306500
chr6D
86.270
488
18
28
1
483
393937329
393936886
4.820000e-133
484.0
4
TraesCS6A01G306500
chr6B
93.388
2208
85
21
827
3032
589129603
589127455
0.000000e+00
3212.0
5
TraesCS6A01G306500
chr6B
92.578
256
6
8
3
255
589130730
589130485
3.940000e-94
355.0
6
TraesCS6A01G306500
chr6B
93.301
209
4
1
275
483
589130497
589130299
1.870000e-77
300.0
7
TraesCS6A01G306500
chr6B
90.909
44
3
1
3033
3075
217157830
217157787
1.250000e-04
58.4
8
TraesCS6A01G306500
chr7D
78.133
1157
137
72
972
2085
140232496
140233579
2.110000e-176
628.0
9
TraesCS6A01G306500
chr7D
100.000
32
0
0
3103
3134
562029388
562029419
3.460000e-05
60.2
10
TraesCS6A01G306500
chr7D
86.538
52
4
2
3027
3075
269039019
269038968
2.000000e-03
54.7
11
TraesCS6A01G306500
chr7A
77.498
1151
150
63
973
2085
140536530
140537609
9.930000e-165
590.0
12
TraesCS6A01G306500
chr7B
77.178
1148
143
71
972
2085
105323152
105324214
2.800000e-155
558.0
13
TraesCS6A01G306500
chr7B
91.111
45
3
1
3032
3075
641326219
641326263
3.460000e-05
60.2
14
TraesCS6A01G306500
chr7B
94.595
37
1
1
3103
3138
380502482
380502518
4.480000e-04
56.5
15
TraesCS6A01G306500
chr5D
89.474
209
22
0
1197
1405
205995773
205995981
6.840000e-67
265.0
16
TraesCS6A01G306500
chr5A
89.474
209
22
0
1197
1405
264421493
264421701
6.840000e-67
265.0
17
TraesCS6A01G306500
chr5B
88.995
209
23
0
1197
1405
206102407
206102199
3.180000e-65
259.0
18
TraesCS6A01G306500
chr4D
84.937
239
31
4
1177
1414
65577854
65577620
1.490000e-58
237.0
19
TraesCS6A01G306500
chr4D
96.875
32
1
0
3103
3134
499105485
499105454
2.000000e-03
54.7
20
TraesCS6A01G306500
chr2D
93.478
46
2
1
3026
3070
628933054
628933099
2.070000e-07
67.6
21
TraesCS6A01G306500
chr3A
93.182
44
2
1
3032
3075
23192118
23192160
2.680000e-06
63.9
22
TraesCS6A01G306500
chr3A
94.595
37
1
1
3103
3138
734523182
734523146
4.480000e-04
56.5
23
TraesCS6A01G306500
chr1B
81.707
82
7
5
3002
3075
662552779
662552698
9.630000e-06
62.1
24
TraesCS6A01G306500
chr1B
88.000
50
5
1
3027
3075
29408987
29408938
1.250000e-04
58.4
25
TraesCS6A01G306500
chr1B
96.875
32
1
0
3103
3134
120399849
120399818
2.000000e-03
54.7
26
TraesCS6A01G306500
chr3D
92.500
40
3
0
3036
3075
507041043
507041082
1.250000e-04
58.4
27
TraesCS6A01G306500
chr3D
92.500
40
3
0
3036
3075
550996804
550996843
1.250000e-04
58.4
28
TraesCS6A01G306500
chr1A
94.595
37
1
1
3103
3138
22251324
22251288
4.480000e-04
56.5
29
TraesCS6A01G306500
chr2B
94.286
35
2
0
3103
3137
756567547
756567513
2.000000e-03
54.7
30
TraesCS6A01G306500
chr2A
96.875
32
1
0
3103
3134
749913487
749913456
2.000000e-03
54.7
31
TraesCS6A01G306500
chr1D
100.000
29
0
0
3103
3131
486886604
486886632
2.000000e-03
54.7
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
TraesCS6A01G306500
chr6A
540143631
540146845
3214
True
2676.5
4460
100.0000
1
3215
2
chr6A.!!$R1
3214
1
TraesCS6A01G306500
chr6D
393934177
393937329
3152
True
2100.0
3716
90.6435
1
3215
2
chr6D.!!$R1
3214
2
TraesCS6A01G306500
chr6B
589127455
589130730
3275
True
1289.0
3212
93.0890
3
3032
3
chr6B.!!$R2
3029
3
TraesCS6A01G306500
chr7D
140232496
140233579
1083
False
628.0
628
78.1330
972
2085
1
chr7D.!!$F1
1113
4
TraesCS6A01G306500
chr7A
140536530
140537609
1079
False
590.0
590
77.4980
973
2085
1
chr7A.!!$F1
1112
5
TraesCS6A01G306500
chr7B
105323152
105324214
1062
False
558.0
558
77.1780
972
2085
1
chr7B.!!$F1
1113
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.