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
TraesCS2D01G047000
chr2D
100.000
2246
0
0
1
2246
17238191
17235946
0.000000e+00
4148
1
TraesCS2D01G047000
chr2D
86.425
663
59
13
928
1578
17182299
17181656
0.000000e+00
697
2
TraesCS2D01G047000
chr2D
86.233
661
64
15
928
1578
17326632
17325989
0.000000e+00
691
3
TraesCS2D01G047000
chr2D
91.094
393
32
3
535
926
17327054
17326664
1.530000e-146
529
4
TraesCS2D01G047000
chr2D
90.840
393
33
3
535
926
17182721
17182331
7.110000e-145
523
5
TraesCS2D01G047000
chr2D
86.620
284
34
4
14
294
17183052
17182770
6.020000e-81
311
6
TraesCS2D01G047000
chr2D
86.620
284
35
3
14
295
17327384
17327102
6.020000e-81
311
7
TraesCS2D01G047000
chr2B
91.641
2285
135
36
1
2246
29871429
29873696
0.000000e+00
3110
8
TraesCS2D01G047000
chr2B
85.396
1212
123
26
464
1644
29055311
29054123
0.000000e+00
1208
9
TraesCS2D01G047000
chr2B
86.416
1119
100
21
464
1540
29980320
29981428
0.000000e+00
1177
10
TraesCS2D01G047000
chr2B
86.207
696
63
21
487
1151
28995786
28995093
0.000000e+00
723
11
TraesCS2D01G047000
chr2B
86.004
493
46
14
1153
1641
28993416
28992943
7.160000e-140
507
12
TraesCS2D01G047000
chr2B
86.786
280
34
3
14
291
28996075
28995797
2.170000e-80
309
13
TraesCS2D01G047000
chr2A
92.136
1793
101
20
251
2007
18675381
18673593
0.000000e+00
2494
14
TraesCS2D01G047000
chr2A
85.689
1146
91
31
464
1567
18646890
18645776
0.000000e+00
1140
15
TraesCS2D01G047000
chr2A
90.086
464
44
1
464
927
18614222
18613761
3.190000e-168
601
16
TraesCS2D01G047000
chr2A
91.774
389
32
0
928
1316
18613730
18613342
1.960000e-150
542
17
TraesCS2D01G047000
chr2A
91.639
299
18
6
1
295
18676061
18675766
7.470000e-110
407
18
TraesCS2D01G047000
chr2A
83.281
317
33
13
1314
1626
18613219
18612919
7.900000e-70
274
19
TraesCS2D01G047000
chr2A
89.506
162
17
0
295
456
680277628
680277467
2.920000e-49
206
20
TraesCS2D01G047000
chr2A
86.624
157
20
1
299
455
11897878
11897723
2.970000e-39
172
21
TraesCS2D01G047000
chr2A
86.420
162
17
4
296
455
267885449
267885291
2.970000e-39
172
22
TraesCS2D01G047000
chr3D
89.506
162
13
4
296
456
374360465
374360307
3.780000e-48
202
23
TraesCS2D01G047000
chr3D
88.485
165
18
1
294
457
597295668
597295504
4.890000e-47
198
24
TraesCS2D01G047000
chr3B
87.898
157
18
1
299
455
177086365
177086520
1.370000e-42
183
25
TraesCS2D01G047000
chr1D
86.335
161
20
2
295
455
231021204
231021046
8.250000e-40
174
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
TraesCS2D01G047000
chr2D
17235946
17238191
2245
True
4148.000000
4148
100.000000
1
2246
1
chr2D.!!$R1
2245
1
TraesCS2D01G047000
chr2D
17181656
17183052
1396
True
510.333333
697
87.961667
14
1578
3
chr2D.!!$R2
1564
2
TraesCS2D01G047000
chr2D
17325989
17327384
1395
True
510.333333
691
87.982333
14
1578
3
chr2D.!!$R3
1564
3
TraesCS2D01G047000
chr2B
29871429
29873696
2267
False
3110.000000
3110
91.641000
1
2246
1
chr2B.!!$F1
2245
4
TraesCS2D01G047000
chr2B
29054123
29055311
1188
True
1208.000000
1208
85.396000
464
1644
1
chr2B.!!$R1
1180
5
TraesCS2D01G047000
chr2B
29980320
29981428
1108
False
1177.000000
1177
86.416000
464
1540
1
chr2B.!!$F2
1076
6
TraesCS2D01G047000
chr2B
28992943
28996075
3132
True
513.000000
723
86.332333
14
1641
3
chr2B.!!$R2
1627
7
TraesCS2D01G047000
chr2A
18673593
18676061
2468
True
1450.500000
2494
91.887500
1
2007
2
chr2A.!!$R6
2006
8
TraesCS2D01G047000
chr2A
18645776
18646890
1114
True
1140.000000
1140
85.689000
464
1567
1
chr2A.!!$R2
1103
9
TraesCS2D01G047000
chr2A
18612919
18614222
1303
True
472.333333
601
88.380333
464
1626
3
chr2A.!!$R5
1162
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.