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
TraesCS5D01G478000
chr5D
100.000
2597
0
0
1
2597
517035674
517038270
0.000000e+00
4796
1
TraesCS5D01G478000
chr5D
93.404
1986
96
24
635
2597
84221159
84219186
0.000000e+00
2909
2
TraesCS5D01G478000
chr5D
91.031
2018
90
39
639
2597
6910282
6908297
0.000000e+00
2639
3
TraesCS5D01G478000
chr5D
92.321
1719
89
16
639
2326
514514291
514512585
0.000000e+00
2403
4
TraesCS5D01G478000
chr5D
94.186
1376
50
14
640
1991
539819769
539818400
0.000000e+00
2071
5
TraesCS5D01G478000
chr5D
93.372
1373
55
19
975
2322
482331808
482330447
0.000000e+00
1999
6
TraesCS5D01G478000
chr5D
81.579
532
83
7
121
639
539457096
539456567
2.390000e-115
425
7
TraesCS5D01G478000
chr5D
81.676
513
80
9
130
631
504194456
504194965
5.170000e-112
414
8
TraesCS5D01G478000
chr5D
80.469
256
36
7
123
367
396081215
396081467
1.590000e-42
183
9
TraesCS5D01G478000
chr5D
83.425
181
30
0
115
295
277499674
277499854
4.440000e-38
169
10
TraesCS5D01G478000
chr3D
94.393
1962
78
7
639
2597
527509676
527511608
0.000000e+00
2985
11
TraesCS5D01G478000
chr3D
92.660
1703
81
22
638
2317
475106679
475108360
0.000000e+00
2412
12
TraesCS5D01G478000
chr3D
90.909
561
43
5
62
614
31743804
31744364
0.000000e+00
747
13
TraesCS5D01G478000
chr3D
86.548
394
38
4
254
639
45689201
45688815
1.110000e-113
420
14
TraesCS5D01G478000
chr3D
86.863
373
26
8
14
376
529507789
529508148
1.870000e-106
396
15
TraesCS5D01G478000
chr3D
80.297
269
41
10
37
295
393469406
393469672
2.640000e-45
193
16
TraesCS5D01G478000
chr3D
79.775
267
40
8
121
376
157708790
157708527
5.710000e-42
182
17
TraesCS5D01G478000
chr3D
80.000
255
37
10
124
367
482307839
482307588
2.660000e-40
176
18
TraesCS5D01G478000
chr3D
76.504
349
62
16
37
367
331537899
331537553
3.440000e-39
172
19
TraesCS5D01G478000
chr1D
92.718
2005
87
25
640
2597
25464319
25466311
0.000000e+00
2839
20
TraesCS5D01G478000
chr1D
96.284
296
11
0
2302
2597
17039004
17038709
1.080000e-133
486
21
TraesCS5D01G478000
chr1D
80.318
503
83
10
90
580
204801845
204801347
1.470000e-97
366
22
TraesCS5D01G478000
chr1D
80.078
256
37
8
123
367
303397884
303397632
7.390000e-41
178
23
TraesCS5D01G478000
chr6D
92.090
2010
87
24
630
2597
28981292
28979313
0.000000e+00
2765
24
TraesCS5D01G478000
chr6D
92.731
1637
62
9
966
2597
448517888
448519472
0.000000e+00
2311
25
TraesCS5D01G478000
chr6D
85.400
637
73
5
12
639
219790860
219790235
0.000000e+00
643
26
TraesCS5D01G478000
chr6D
78.916
498
84
12
95
578
407210141
407209651
4.170000e-83
318
27
TraesCS5D01G478000
chr6D
79.437
462
82
7
126
578
293800316
293800773
5.390000e-82
315
28
TraesCS5D01G478000
chr6D
81.108
397
65
6
193
580
106705684
106706079
2.510000e-80
309
29
TraesCS5D01G478000
chr6D
78.587
467
90
4
121
578
28267350
28266885
1.510000e-77
300
30
TraesCS5D01G478000
chr6D
77.154
499
91
7
88
578
468259374
468259857
4.260000e-68
268
31
TraesCS5D01G478000
chr7D
91.687
2021
94
29
638
2597
22901540
22899533
0.000000e+00
2734
32
TraesCS5D01G478000
chr7D
90.744
2042
86
37
639
2597
574727119
574725098
0.000000e+00
2628
33
TraesCS5D01G478000
chr7D
92.415
1714
82
25
629
2317
63995381
63997071
0.000000e+00
2401
34
TraesCS5D01G478000
chr1A
90.688
2019
106
35
638
2597
462529531
462531526
0.000000e+00
2612
35
TraesCS5D01G478000
chr1A
91.882
1897
104
20
737
2597
514041853
514043735
0.000000e+00
2604
36
TraesCS5D01G478000
chr1A
90.789
1737
92
29
640
2322
547456220
547457942
0.000000e+00
2259
37
TraesCS5D01G478000
chr1A
95.946
296
11
1
2302
2597
543261164
543261458
1.810000e-131
479
38
TraesCS5D01G478000
chr2A
90.495
2020
95
36
640
2597
613866458
613868442
0.000000e+00
2577
39
TraesCS5D01G478000
chr2A
92.679
1721
78
28
630
2322
744582020
744583720
0.000000e+00
2436
40
TraesCS5D01G478000
chr2A
92.569
1709
86
21
640
2322
677958469
677956776
0.000000e+00
2414
41
TraesCS5D01G478000
chr7B
90.035
2007
117
32
642
2597
75356804
75354830
0.000000e+00
2521
42
TraesCS5D01G478000
chr7B
85.290
639
79
11
12
639
558751085
558751719
0.000000e+00
645
43
TraesCS5D01G478000
chrUn
91.850
1546
58
21
1090
2597
302374319
302375834
0.000000e+00
2095
44
TraesCS5D01G478000
chrUn
79.468
526
92
12
118
634
28622902
28622384
2.460000e-95
359
45
TraesCS5D01G478000
chrUn
77.143
490
94
9
99
577
377802683
377802201
4.260000e-68
268
46
TraesCS5D01G478000
chrUn
77.215
474
94
8
115
577
272849784
272850254
5.510000e-67
265
47
TraesCS5D01G478000
chrUn
76.793
474
96
9
115
577
245559651
245560121
1.190000e-63
254
48
TraesCS5D01G478000
chrUn
88.024
167
20
0
411
577
235714991
235715157
5.670000e-47
198
49
TraesCS5D01G478000
chrUn
88.024
167
20
0
411
577
316936388
316936222
5.670000e-47
198
50
TraesCS5D01G478000
chrUn
73.684
532
112
21
61
577
130102665
130102147
5.710000e-42
182
51
TraesCS5D01G478000
chr4D
88.125
640
59
11
12
639
401352642
401352008
0.000000e+00
745
52
TraesCS5D01G478000
chr4D
90.093
535
44
5
113
639
417804272
417804805
0.000000e+00
686
53
TraesCS5D01G478000
chr4D
84.074
653
84
11
6
639
426212869
426212218
1.710000e-171
612
54
TraesCS5D01G478000
chr4D
79.356
528
83
12
64
578
488180614
488180100
5.320000e-92
348
55
TraesCS5D01G478000
chr4D
81.008
258
35
9
121
367
139242586
139242332
2.640000e-45
193
56
TraesCS5D01G478000
chr4D
85.326
184
27
0
113
296
86395081
86394898
9.490000e-45
191
57
TraesCS5D01G478000
chr4D
80.620
258
36
8
121
367
408867830
408868084
1.230000e-43
187
58
TraesCS5D01G478000
chr4D
85.393
178
26
0
118
295
61647894
61647717
4.410000e-43
185
59
TraesCS5D01G478000
chr4D
82.857
175
29
1
121
295
413961604
413961431
3.460000e-34
156
60
TraesCS5D01G478000
chr4D
85.714
119
6
2
12
119
417795761
417795879
5.870000e-22
115
61
TraesCS5D01G478000
chr6B
85.317
647
75
10
12
639
500221760
500221115
0.000000e+00
651
62
TraesCS5D01G478000
chr6B
79.095
464
87
6
125
580
221399796
221399335
6.980000e-81
311
63
TraesCS5D01G478000
chr4B
84.748
636
76
13
13
636
82507621
82508247
3.670000e-173
617
64
TraesCS5D01G478000
chr4B
81.376
596
85
19
6
580
468002982
468003572
1.820000e-126
462
65
TraesCS5D01G478000
chr4B
90.301
299
15
8
2302
2597
546329996
546329709
1.890000e-101
379
66
TraesCS5D01G478000
chr5A
94.054
370
18
2
2232
2597
548401337
548401706
2.260000e-155
558
67
TraesCS5D01G478000
chr5B
88.453
459
45
2
189
639
50522820
50522362
4.890000e-152
547
68
TraesCS5D01G478000
chr5B
84.818
303
33
4
3
294
664725537
664725837
2.530000e-75
292
69
TraesCS5D01G478000
chr4A
82.942
639
75
20
12
639
713511100
713510485
1.760000e-151
545
70
TraesCS5D01G478000
chr4A
82.555
642
78
20
9
639
713882152
713882770
3.800000e-148
534
71
TraesCS5D01G478000
chr4A
80.769
468
82
3
121
580
690667371
690667838
2.460000e-95
359
72
TraesCS5D01G478000
chr1B
83.119
622
75
9
26
639
138853448
138852849
8.180000e-150
540
73
TraesCS5D01G478000
chr1B
85.339
457
58
3
191
639
389226126
389225671
5.060000e-127
464
74
TraesCS5D01G478000
chr2D
85.049
515
67
3
133
639
539014601
539015113
1.380000e-142
516
75
TraesCS5D01G478000
chr2D
80.678
590
85
18
3
580
112553598
112554170
5.130000e-117
431
76
TraesCS5D01G478000
chr2D
86.424
302
28
7
6
295
25326104
25325804
4.170000e-83
318
77
TraesCS5D01G478000
chr6A
86.288
423
50
2
225
639
587966068
587966490
1.100000e-123
453
78
TraesCS5D01G478000
chr6A
74.538
487
94
19
118
580
217773225
217773705
4.410000e-43
185
79
TraesCS5D01G478000
chr3A
77.222
540
108
10
49
578
670927906
670928440
4.200000e-78
302
80
TraesCS5D01G478000
chr3B
91.371
197
17
0
12
208
757288363
757288167
1.180000e-68
270
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
TraesCS5D01G478000
chr5D
517035674
517038270
2596
False
4796
4796
100.000
1
2597
1
chr5D.!!$F4
2596
1
TraesCS5D01G478000
chr5D
84219186
84221159
1973
True
2909
2909
93.404
635
2597
1
chr5D.!!$R2
1962
2
TraesCS5D01G478000
chr5D
6908297
6910282
1985
True
2639
2639
91.031
639
2597
1
chr5D.!!$R1
1958
3
TraesCS5D01G478000
chr5D
514512585
514514291
1706
True
2403
2403
92.321
639
2326
1
chr5D.!!$R4
1687
4
TraesCS5D01G478000
chr5D
539818400
539819769
1369
True
2071
2071
94.186
640
1991
1
chr5D.!!$R6
1351
5
TraesCS5D01G478000
chr5D
482330447
482331808
1361
True
1999
1999
93.372
975
2322
1
chr5D.!!$R3
1347
6
TraesCS5D01G478000
chr5D
539456567
539457096
529
True
425
425
81.579
121
639
1
chr5D.!!$R5
518
7
TraesCS5D01G478000
chr5D
504194456
504194965
509
False
414
414
81.676
130
631
1
chr5D.!!$F3
501
8
TraesCS5D01G478000
chr3D
527509676
527511608
1932
False
2985
2985
94.393
639
2597
1
chr3D.!!$F4
1958
9
TraesCS5D01G478000
chr3D
475106679
475108360
1681
False
2412
2412
92.660
638
2317
1
chr3D.!!$F3
1679
10
TraesCS5D01G478000
chr3D
31743804
31744364
560
False
747
747
90.909
62
614
1
chr3D.!!$F1
552
11
TraesCS5D01G478000
chr1D
25464319
25466311
1992
False
2839
2839
92.718
640
2597
1
chr1D.!!$F1
1957
12
TraesCS5D01G478000
chr6D
28979313
28981292
1979
True
2765
2765
92.090
630
2597
1
chr6D.!!$R2
1967
13
TraesCS5D01G478000
chr6D
448517888
448519472
1584
False
2311
2311
92.731
966
2597
1
chr6D.!!$F3
1631
14
TraesCS5D01G478000
chr6D
219790235
219790860
625
True
643
643
85.400
12
639
1
chr6D.!!$R3
627
15
TraesCS5D01G478000
chr7D
22899533
22901540
2007
True
2734
2734
91.687
638
2597
1
chr7D.!!$R1
1959
16
TraesCS5D01G478000
chr7D
574725098
574727119
2021
True
2628
2628
90.744
639
2597
1
chr7D.!!$R2
1958
17
TraesCS5D01G478000
chr7D
63995381
63997071
1690
False
2401
2401
92.415
629
2317
1
chr7D.!!$F1
1688
18
TraesCS5D01G478000
chr1A
462529531
462531526
1995
False
2612
2612
90.688
638
2597
1
chr1A.!!$F1
1959
19
TraesCS5D01G478000
chr1A
514041853
514043735
1882
False
2604
2604
91.882
737
2597
1
chr1A.!!$F2
1860
20
TraesCS5D01G478000
chr1A
547456220
547457942
1722
False
2259
2259
90.789
640
2322
1
chr1A.!!$F4
1682
21
TraesCS5D01G478000
chr2A
613866458
613868442
1984
False
2577
2577
90.495
640
2597
1
chr2A.!!$F1
1957
22
TraesCS5D01G478000
chr2A
744582020
744583720
1700
False
2436
2436
92.679
630
2322
1
chr2A.!!$F2
1692
23
TraesCS5D01G478000
chr2A
677956776
677958469
1693
True
2414
2414
92.569
640
2322
1
chr2A.!!$R1
1682
24
TraesCS5D01G478000
chr7B
75354830
75356804
1974
True
2521
2521
90.035
642
2597
1
chr7B.!!$R1
1955
25
TraesCS5D01G478000
chr7B
558751085
558751719
634
False
645
645
85.290
12
639
1
chr7B.!!$F1
627
26
TraesCS5D01G478000
chrUn
302374319
302375834
1515
False
2095
2095
91.850
1090
2597
1
chrUn.!!$F4
1507
27
TraesCS5D01G478000
chrUn
28622384
28622902
518
True
359
359
79.468
118
634
1
chrUn.!!$R1
516
28
TraesCS5D01G478000
chr4D
401352008
401352642
634
True
745
745
88.125
12
639
1
chr4D.!!$R4
627
29
TraesCS5D01G478000
chr4D
417804272
417804805
533
False
686
686
90.093
113
639
1
chr4D.!!$F3
526
30
TraesCS5D01G478000
chr4D
426212218
426212869
651
True
612
612
84.074
6
639
1
chr4D.!!$R6
633
31
TraesCS5D01G478000
chr4D
488180100
488180614
514
True
348
348
79.356
64
578
1
chr4D.!!$R7
514
32
TraesCS5D01G478000
chr6B
500221115
500221760
645
True
651
651
85.317
12
639
1
chr6B.!!$R2
627
33
TraesCS5D01G478000
chr4B
82507621
82508247
626
False
617
617
84.748
13
636
1
chr4B.!!$F1
623
34
TraesCS5D01G478000
chr4B
468002982
468003572
590
False
462
462
81.376
6
580
1
chr4B.!!$F2
574
35
TraesCS5D01G478000
chr4A
713510485
713511100
615
True
545
545
82.942
12
639
1
chr4A.!!$R1
627
36
TraesCS5D01G478000
chr4A
713882152
713882770
618
False
534
534
82.555
9
639
1
chr4A.!!$F2
630
37
TraesCS5D01G478000
chr1B
138852849
138853448
599
True
540
540
83.119
26
639
1
chr1B.!!$R1
613
38
TraesCS5D01G478000
chr2D
539014601
539015113
512
False
516
516
85.049
133
639
1
chr2D.!!$F2
506
39
TraesCS5D01G478000
chr2D
112553598
112554170
572
False
431
431
80.678
3
580
1
chr2D.!!$F1
577
40
TraesCS5D01G478000
chr3A
670927906
670928440
534
False
302
302
77.222
49
578
1
chr3A.!!$F1
529
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.