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
TraesCS5B01G286800
chr5B
100.000
5921
0
0
1
5921
473119530
473113610
0.000000e+00
10935.0
1
TraesCS5B01G286800
chr5B
93.589
4274
165
35
694
4914
471021027
471025244
0.000000e+00
6274.0
2
TraesCS5B01G286800
chr5B
85.354
396
45
9
2486
2872
693677346
693677737
1.200000e-106
398.0
3
TraesCS5B01G286800
chr5B
85.714
56
5
1
5387
5439
697279651
697279596
8.290000e-04
56.5
4
TraesCS5B01G286800
chr5D
93.082
4134
191
26
819
4908
390692389
390696471
0.000000e+00
5962.0
5
TraesCS5B01G286800
chr5D
97.216
3305
75
8
1164
4455
393059711
393056411
0.000000e+00
5578.0
6
TraesCS5B01G286800
chr5D
98.178
933
16
1
4459
5390
393056278
393055346
0.000000e+00
1628.0
7
TraesCS5B01G286800
chr5D
98.881
536
6
0
5386
5921
393041052
393040517
0.000000e+00
957.0
8
TraesCS5B01G286800
chr5D
97.059
510
8
2
675
1178
393060388
393059880
0.000000e+00
852.0
9
TraesCS5B01G286800
chr5D
93.478
138
9
0
680
817
390692207
390692344
7.780000e-49
206.0
10
TraesCS5B01G286800
chr5D
72.163
564
123
29
3896
4444
387682656
387682112
2.220000e-29
141.0
11
TraesCS5B01G286800
chr5A
93.710
2687
115
21
1138
3803
494229557
494232210
0.000000e+00
3976.0
12
TraesCS5B01G286800
chr5A
94.194
1085
48
4
3840
4909
494232209
494233293
0.000000e+00
1640.0
13
TraesCS5B01G286800
chr5A
94.955
674
34
0
1
674
491696997
491696324
0.000000e+00
1057.0
14
TraesCS5B01G286800
chr5A
89.189
444
32
6
675
1108
494229121
494229558
1.880000e-149
540.0
15
TraesCS5B01G286800
chr5A
73.934
633
125
32
4094
4710
490594003
490593395
9.990000e-53
219.0
16
TraesCS5B01G286800
chr5A
80.986
142
27
0
4573
4714
512621102
512620961
4.850000e-21
113.0
17
TraesCS5B01G286800
chr2D
97.774
674
15
0
1
674
89210456
89209783
0.000000e+00
1162.0
18
TraesCS5B01G286800
chr2D
97.626
674
16
0
1
674
104907068
104907741
0.000000e+00
1157.0
19
TraesCS5B01G286800
chr2D
87.348
411
44
5
2486
2892
87754474
87754068
1.160000e-126
464.0
20
TraesCS5B01G286800
chr3B
97.173
672
19
0
3
674
663177657
663178328
0.000000e+00
1136.0
21
TraesCS5B01G286800
chr3A
97.168
671
19
0
3
673
681395037
681394367
0.000000e+00
1134.0
22
TraesCS5B01G286800
chr3A
84.483
58
7
1
5385
5440
170234691
170234634
8.290000e-04
56.5
23
TraesCS5B01G286800
chr1D
97.006
668
20
0
1
668
474236517
474237184
0.000000e+00
1123.0
24
TraesCS5B01G286800
chr1D
96.439
674
24
0
1
674
282721235
282720562
0.000000e+00
1112.0
25
TraesCS5B01G286800
chr2A
96.588
674
23
0
1
674
322827061
322827734
0.000000e+00
1118.0
26
TraesCS5B01G286800
chr2A
93.023
43
1
2
5377
5418
705877094
705877135
1.780000e-05
62.1
27
TraesCS5B01G286800
chr3D
94.792
672
34
1
3
674
286899930
286899260
0.000000e+00
1046.0
28
TraesCS5B01G286800
chr3D
87.037
54
4
1
5370
5420
438949650
438949597
2.300000e-04
58.4
29
TraesCS5B01G286800
chr3D
85.965
57
5
3
5365
5418
515964536
515964480
2.300000e-04
58.4
30
TraesCS5B01G286800
chr4A
86.340
388
40
8
2515
2895
572842860
572843241
1.540000e-110
411.0
31
TraesCS5B01G286800
chr7A
89.247
279
21
5
2498
2767
667232296
667232018
2.040000e-89
340.0
32
TraesCS5B01G286800
chr7A
83.607
366
39
15
2538
2893
400068711
400069065
2.060000e-84
324.0
33
TraesCS5B01G286800
chr6B
93.023
43
3
0
5386
5428
282987528
282987570
4.950000e-06
63.9
34
TraesCS5B01G286800
chr2B
88.679
53
4
1
5389
5439
713548788
713548736
4.950000e-06
63.9
35
TraesCS5B01G286800
chr7D
93.023
43
1
2
5377
5418
104216520
104216479
1.780000e-05
62.1
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
TraesCS5B01G286800
chr5B
473113610
473119530
5920
True
10935
10935
100.000000
1
5921
1
chr5B.!!$R1
5920
1
TraesCS5B01G286800
chr5B
471021027
471025244
4217
False
6274
6274
93.589000
694
4914
1
chr5B.!!$F1
4220
2
TraesCS5B01G286800
chr5D
390692207
390696471
4264
False
3084
5962
93.280000
680
4908
2
chr5D.!!$F1
4228
3
TraesCS5B01G286800
chr5D
393055346
393060388
5042
True
2686
5578
97.484333
675
5390
3
chr5D.!!$R3
4715
4
TraesCS5B01G286800
chr5D
393040517
393041052
535
True
957
957
98.881000
5386
5921
1
chr5D.!!$R2
535
5
TraesCS5B01G286800
chr5A
494229121
494233293
4172
False
2052
3976
92.364333
675
4909
3
chr5A.!!$F1
4234
6
TraesCS5B01G286800
chr5A
491696324
491696997
673
True
1057
1057
94.955000
1
674
1
chr5A.!!$R2
673
7
TraesCS5B01G286800
chr5A
490593395
490594003
608
True
219
219
73.934000
4094
4710
1
chr5A.!!$R1
616
8
TraesCS5B01G286800
chr2D
89209783
89210456
673
True
1162
1162
97.774000
1
674
1
chr2D.!!$R2
673
9
TraesCS5B01G286800
chr2D
104907068
104907741
673
False
1157
1157
97.626000
1
674
1
chr2D.!!$F1
673
10
TraesCS5B01G286800
chr3B
663177657
663178328
671
False
1136
1136
97.173000
3
674
1
chr3B.!!$F1
671
11
TraesCS5B01G286800
chr3A
681394367
681395037
670
True
1134
1134
97.168000
3
673
1
chr3A.!!$R2
670
12
TraesCS5B01G286800
chr1D
474236517
474237184
667
False
1123
1123
97.006000
1
668
1
chr1D.!!$F1
667
13
TraesCS5B01G286800
chr1D
282720562
282721235
673
True
1112
1112
96.439000
1
674
1
chr1D.!!$R1
673
14
TraesCS5B01G286800
chr2A
322827061
322827734
673
False
1118
1118
96.588000
1
674
1
chr2A.!!$F1
673
15
TraesCS5B01G286800
chr3D
286899260
286899930
670
True
1046
1046
94.792000
3
674
1
chr3D.!!$R1
671
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.