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
TraesCS2D01G138900
chr2D
100.000
4761
0
0
1
4761
81944662
81939902
0.000000e+00
8793.0
1
TraesCS2D01G138900
chr2D
97.297
37
1
0
4670
4706
540811449
540811485
3.980000e-06
63.9
2
TraesCS2D01G138900
chr2B
92.973
4113
183
31
710
4760
133809265
133805197
0.000000e+00
5897.0
3
TraesCS2D01G138900
chr2B
92.457
3513
215
20
1283
4760
133704763
133701266
0.000000e+00
4974.0
4
TraesCS2D01G138900
chr2B
78.945
2484
436
57
1312
3764
134242907
134240480
0.000000e+00
1609.0
5
TraesCS2D01G138900
chr2B
78.369
2501
442
60
1294
3764
134350226
134347795
0.000000e+00
1530.0
6
TraesCS2D01G138900
chr2B
78.891
1947
311
51
1294
3175
134366318
134364407
0.000000e+00
1227.0
7
TraesCS2D01G138900
chr2B
82.506
423
51
16
783
1204
133705203
133704803
2.730000e-92
350.0
8
TraesCS2D01G138900
chr2B
97.059
34
1
0
4673
4706
497850212
497850179
1.850000e-04
58.4
9
TraesCS2D01G138900
chr2A
83.985
3734
440
72
712
4379
82202171
82198530
0.000000e+00
3437.0
10
TraesCS2D01G138900
chr2A
92.256
2079
96
17
2596
4640
82131399
82129352
0.000000e+00
2887.0
11
TraesCS2D01G138900
chr2A
95.659
1290
52
3
711
2000
82132684
82131399
0.000000e+00
2069.0
12
TraesCS2D01G138900
chr2A
78.489
2501
434
62
1294
3764
82538612
82536186
0.000000e+00
1543.0
13
TraesCS2D01G138900
chr2A
80.918
1939
299
52
1283
3202
82069793
82067907
0.000000e+00
1465.0
14
TraesCS2D01G138900
chr2A
82.195
966
154
9
1283
2245
82157801
82156851
0.000000e+00
815.0
15
TraesCS2D01G138900
chr2A
79.472
341
35
19
4114
4428
82064184
82063853
4.830000e-50
209.0
16
TraesCS2D01G138900
chr3B
90.069
725
40
12
1
712
127307293
127306588
0.000000e+00
911.0
17
TraesCS2D01G138900
chr3B
84.958
472
24
12
267
708
44769509
44769963
7.320000e-118
435.0
18
TraesCS2D01G138900
chr3B
82.759
348
43
12
371
703
157663110
157663455
1.300000e-75
294.0
19
TraesCS2D01G138900
chr3B
91.121
214
9
7
3
208
157662846
157663057
1.010000e-71
281.0
20
TraesCS2D01G138900
chr3B
81.944
216
29
7
4
209
796516038
796516253
1.760000e-39
174.0
21
TraesCS2D01G138900
chr3B
86.184
152
21
0
557
708
127308217
127308368
1.060000e-36
165.0
22
TraesCS2D01G138900
chr1A
88.740
746
44
14
1
723
57966134
57966862
0.000000e+00
876.0
23
TraesCS2D01G138900
chr5B
90.616
341
23
3
371
710
95510803
95511135
1.220000e-120
444.0
24
TraesCS2D01G138900
chr5B
94.521
146
8
0
1
146
95509337
95509482
4.790000e-55
226.0
25
TraesCS2D01G138900
chr5B
94.737
57
3
0
4650
4706
21588518
21588462
6.560000e-14
89.8
26
TraesCS2D01G138900
chr5B
94.828
58
2
1
233
289
95510712
95510769
6.560000e-14
89.8
27
TraesCS2D01G138900
chr7A
88.076
369
32
5
1
359
650554095
650553729
1.220000e-115
427.0
28
TraesCS2D01G138900
chr7A
80.634
284
37
11
426
708
646689371
646689637
2.250000e-48
204.0
29
TraesCS2D01G138900
chr6B
93.333
210
14
0
1
210
607328550
607328759
1.290000e-80
311.0
30
TraesCS2D01G138900
chr3D
82.111
341
53
7
371
710
606908513
606908846
7.800000e-73
285.0
31
TraesCS2D01G138900
chr6A
84.524
252
31
4
457
708
162983909
162984152
4.760000e-60
243.0
32
TraesCS2D01G138900
chr5D
90.000
60
6
0
4650
4709
494472312
494472253
1.420000e-10
78.7
33
TraesCS2D01G138900
chr5D
100.000
34
0
0
4673
4706
238386563
238386596
3.980000e-06
63.9
34
TraesCS2D01G138900
chr7D
88.333
60
7
0
4650
4709
63453563
63453504
6.610000e-09
73.1
35
TraesCS2D01G138900
chr6D
92.308
52
2
2
4649
4699
4725093
4725043
6.610000e-09
73.1
36
TraesCS2D01G138900
chr7B
100.000
34
0
0
4673
4706
190259942
190259909
3.980000e-06
63.9
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
TraesCS2D01G138900
chr2D
81939902
81944662
4760
True
8793.000000
8793
100.000000
1
4761
1
chr2D.!!$R1
4760
1
TraesCS2D01G138900
chr2B
133805197
133809265
4068
True
5897.000000
5897
92.973000
710
4760
1
chr2B.!!$R1
4050
2
TraesCS2D01G138900
chr2B
133701266
133705203
3937
True
2662.000000
4974
87.481500
783
4760
2
chr2B.!!$R6
3977
3
TraesCS2D01G138900
chr2B
134240480
134242907
2427
True
1609.000000
1609
78.945000
1312
3764
1
chr2B.!!$R2
2452
4
TraesCS2D01G138900
chr2B
134347795
134350226
2431
True
1530.000000
1530
78.369000
1294
3764
1
chr2B.!!$R3
2470
5
TraesCS2D01G138900
chr2B
134364407
134366318
1911
True
1227.000000
1227
78.891000
1294
3175
1
chr2B.!!$R4
1881
6
TraesCS2D01G138900
chr2A
82198530
82202171
3641
True
3437.000000
3437
83.985000
712
4379
1
chr2A.!!$R2
3667
7
TraesCS2D01G138900
chr2A
82129352
82132684
3332
True
2478.000000
2887
93.957500
711
4640
2
chr2A.!!$R5
3929
8
TraesCS2D01G138900
chr2A
82536186
82538612
2426
True
1543.000000
1543
78.489000
1294
3764
1
chr2A.!!$R3
2470
9
TraesCS2D01G138900
chr2A
82063853
82069793
5940
True
837.000000
1465
80.195000
1283
4428
2
chr2A.!!$R4
3145
10
TraesCS2D01G138900
chr2A
82156851
82157801
950
True
815.000000
815
82.195000
1283
2245
1
chr2A.!!$R1
962
11
TraesCS2D01G138900
chr3B
127306588
127307293
705
True
911.000000
911
90.069000
1
712
1
chr3B.!!$R1
711
12
TraesCS2D01G138900
chr3B
157662846
157663455
609
False
287.500000
294
86.940000
3
703
2
chr3B.!!$F4
700
13
TraesCS2D01G138900
chr1A
57966134
57966862
728
False
876.000000
876
88.740000
1
723
1
chr1A.!!$F1
722
14
TraesCS2D01G138900
chr5B
95509337
95511135
1798
False
253.266667
444
93.321667
1
710
3
chr5B.!!$F1
709
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.