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
TraesCS2D01G180900
chr2D
100.000
3236
0
0
1
3236
125345950
125342715
0.000000e+00
5976.0
1
TraesCS2D01G180900
chr2D
77.946
331
52
18
1691
2012
37245727
37245409
1.530000e-43
187.0
2
TraesCS2D01G180900
chr2B
91.234
1791
101
32
1172
2954
178731949
178730207
0.000000e+00
2386.0
3
TraesCS2D01G180900
chr2B
82.463
536
77
9
434
957
583108266
583107736
1.370000e-123
453.0
4
TraesCS2D01G180900
chr2B
78.443
334
48
16
1691
2012
64863763
64864084
2.550000e-46
196.0
5
TraesCS2D01G180900
chr2A
94.461
1372
46
13
968
2334
131712460
131711114
0.000000e+00
2085.0
6
TraesCS2D01G180900
chr2A
86.976
906
73
22
2341
3236
131711003
131710133
0.000000e+00
977.0
7
TraesCS2D01G180900
chr2A
74.651
860
171
37
1219
2059
24003220
24002389
1.440000e-88
337.0
8
TraesCS2D01G180900
chr2A
80.147
272
49
4
1744
2011
679971485
679971755
7.080000e-47
198.0
9
TraesCS2D01G180900
chr2A
80.000
275
42
10
1746
2012
42027189
42027458
1.180000e-44
191.0
10
TraesCS2D01G180900
chr2A
83.962
106
15
2
3131
3235
718839856
718839960
2.050000e-17
100.0
11
TraesCS2D01G180900
chr7B
93.548
558
24
7
418
964
363231831
363232387
0.000000e+00
821.0
12
TraesCS2D01G180900
chr7B
97.381
420
9
1
1
420
363231374
363231791
0.000000e+00
713.0
13
TraesCS2D01G180900
chr3D
93.548
558
24
7
418
964
570538470
570537914
0.000000e+00
821.0
14
TraesCS2D01G180900
chr3D
92.832
558
28
7
418
964
478426410
478426966
0.000000e+00
798.0
15
TraesCS2D01G180900
chr3D
95.952
420
15
1
1
420
478425953
478426370
0.000000e+00
680.0
16
TraesCS2D01G180900
chr3D
95.952
420
15
1
1
420
570538927
570538510
0.000000e+00
680.0
17
TraesCS2D01G180900
chr3D
83.240
537
74
11
434
957
584682701
584682168
2.260000e-131
479.0
18
TraesCS2D01G180900
chr5D
91.039
558
38
7
418
964
564237719
564237163
0.000000e+00
743.0
19
TraesCS2D01G180900
chr5D
97.143
420
10
1
1
420
564238176
564237759
0.000000e+00
708.0
20
TraesCS2D01G180900
chr5D
95.952
420
14
2
1
420
399974009
399974425
0.000000e+00
678.0
21
TraesCS2D01G180900
chr7A
96.190
420
14
1
1
420
640368696
640368279
0.000000e+00
686.0
22
TraesCS2D01G180900
chr7A
90.952
420
36
1
1
420
418712570
418712153
6.060000e-157
564.0
23
TraesCS2D01G180900
chr7A
81.495
535
85
10
434
957
380509718
380509187
8.300000e-116
427.0
24
TraesCS2D01G180900
chr7A
75.121
824
161
32
1213
2019
46911803
46911007
2.390000e-91
346.0
25
TraesCS2D01G180900
chr7A
74.142
379
87
9
1205
1579
163916284
163915913
2.600000e-31
147.0
26
TraesCS2D01G180900
chr3B
95.000
420
17
3
1
420
664535688
664535273
0.000000e+00
656.0
27
TraesCS2D01G180900
chr6B
91.727
411
32
1
1
411
705858713
705859121
1.300000e-158
569.0
28
TraesCS2D01G180900
chr4D
82.276
536
78
11
434
957
297376489
297375959
6.370000e-122
448.0
29
TraesCS2D01G180900
chr6A
83.298
467
68
8
418
875
23217770
23218235
3.860000e-114
422.0
30
TraesCS2D01G180900
chr6A
82.075
106
18
1
3131
3235
455318981
455318876
4.450000e-14
89.8
31
TraesCS2D01G180900
chr1A
79.852
541
93
7
425
954
27317456
27317991
6.550000e-102
381.0
32
TraesCS2D01G180900
chr1A
77.152
639
122
20
1380
2009
11531069
11530446
1.850000e-92
350.0
33
TraesCS2D01G180900
chr7D
74.858
879
180
29
1205
2070
163011470
163010620
8.530000e-96
361.0
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
TraesCS2D01G180900
chr2D
125342715
125345950
3235
True
5976.0
5976
100.0000
1
3236
1
chr2D.!!$R2
3235
1
TraesCS2D01G180900
chr2B
178730207
178731949
1742
True
2386.0
2386
91.2340
1172
2954
1
chr2B.!!$R1
1782
2
TraesCS2D01G180900
chr2B
583107736
583108266
530
True
453.0
453
82.4630
434
957
1
chr2B.!!$R2
523
3
TraesCS2D01G180900
chr2A
131710133
131712460
2327
True
1531.0
2085
90.7185
968
3236
2
chr2A.!!$R2
2268
4
TraesCS2D01G180900
chr2A
24002389
24003220
831
True
337.0
337
74.6510
1219
2059
1
chr2A.!!$R1
840
5
TraesCS2D01G180900
chr7B
363231374
363232387
1013
False
767.0
821
95.4645
1
964
2
chr7B.!!$F1
963
6
TraesCS2D01G180900
chr3D
570537914
570538927
1013
True
750.5
821
94.7500
1
964
2
chr3D.!!$R2
963
7
TraesCS2D01G180900
chr3D
478425953
478426966
1013
False
739.0
798
94.3920
1
964
2
chr3D.!!$F1
963
8
TraesCS2D01G180900
chr3D
584682168
584682701
533
True
479.0
479
83.2400
434
957
1
chr3D.!!$R1
523
9
TraesCS2D01G180900
chr5D
564237163
564238176
1013
True
725.5
743
94.0910
1
964
2
chr5D.!!$R1
963
10
TraesCS2D01G180900
chr7A
380509187
380509718
531
True
427.0
427
81.4950
434
957
1
chr7A.!!$R3
523
11
TraesCS2D01G180900
chr7A
46911007
46911803
796
True
346.0
346
75.1210
1213
2019
1
chr7A.!!$R1
806
12
TraesCS2D01G180900
chr4D
297375959
297376489
530
True
448.0
448
82.2760
434
957
1
chr4D.!!$R1
523
13
TraesCS2D01G180900
chr1A
27317456
27317991
535
False
381.0
381
79.8520
425
954
1
chr1A.!!$F1
529
14
TraesCS2D01G180900
chr1A
11530446
11531069
623
True
350.0
350
77.1520
1380
2009
1
chr1A.!!$R1
629
15
TraesCS2D01G180900
chr7D
163010620
163011470
850
True
361.0
361
74.8580
1205
2070
1
chr7D.!!$R1
865
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.