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
TraesCS5A01G077800
chr5A
100.000
2375
0
0
1
2375
94783467
94781093
0.000000e+00
4386.0
1
TraesCS5A01G077800
chr5A
95.947
1357
54
1
423
1778
94795504
94794148
0.000000e+00
2200.0
2
TraesCS5A01G077800
chr5A
93.610
1158
68
5
420
1572
433069204
433068048
0.000000e+00
1724.0
3
TraesCS5A01G077800
chr5A
93.980
598
33
1
1778
2375
94764587
94763993
0.000000e+00
902.0
4
TraesCS5A01G077800
chr5A
84.587
545
74
10
1
541
502877190
502877728
1.250000e-147
532.0
5
TraesCS5A01G077800
chr5A
80.696
632
104
13
13
633
36725063
36725687
2.140000e-130
475.0
6
TraesCS5A01G077800
chr5A
88.579
394
41
4
1778
2169
146435793
146435402
2.140000e-130
475.0
7
TraesCS5A01G077800
chr5A
80.573
628
107
13
12
630
218845274
218844653
9.940000e-129
470.0
8
TraesCS5A01G077800
chr5A
88.710
372
42
0
1037
1408
295687381
295687752
2.780000e-124
455.0
9
TraesCS5A01G077800
chr5A
85.151
431
59
5
1778
2205
146298200
146297772
1.010000e-118
436.0
10
TraesCS5A01G077800
chr3A
93.010
1359
90
5
423
1778
195156760
195155404
0.000000e+00
1978.0
11
TraesCS5A01G077800
chr3A
95.297
893
41
1
11
902
195148918
195148026
0.000000e+00
1415.0
12
TraesCS5A01G077800
chr3A
92.382
827
62
1
942
1767
195148028
195147202
0.000000e+00
1177.0
13
TraesCS5A01G077800
chr3A
83.158
570
86
9
21
585
623011447
623010883
1.630000e-141
512.0
14
TraesCS5A01G077800
chr3A
85.401
137
14
4
2234
2367
119912145
119912012
1.140000e-28
137.0
15
TraesCS5A01G077800
chr1A
86.510
682
74
16
259
934
340353277
340353946
0.000000e+00
734.0
16
TraesCS5A01G077800
chr1A
80.485
907
144
23
23
916
446742979
446743865
0.000000e+00
664.0
17
TraesCS5A01G077800
chr1A
79.017
834
152
17
36
857
196741494
196740672
1.240000e-152
549.0
18
TraesCS5A01G077800
chr2A
89.980
489
35
11
1778
2256
310856679
310857163
9.330000e-174
619.0
19
TraesCS5A01G077800
chr2A
89.300
486
34
13
1778
2254
310848207
310848683
5.650000e-166
593.0
20
TraesCS5A01G077800
chr2A
83.019
583
86
13
11
585
150660021
150660598
1.260000e-142
516.0
21
TraesCS5A01G077800
chr2A
75.718
383
59
26
1972
2334
323973943
323974311
6.790000e-36
161.0
22
TraesCS5A01G077800
chr4A
91.549
426
29
7
512
934
309517403
309517824
4.400000e-162
580.0
23
TraesCS5A01G077800
chr7D
82.753
632
91
16
12
633
406002203
406001580
4.460000e-152
547.0
24
TraesCS5A01G077800
chr2D
83.306
605
88
12
11
606
252161700
252162300
1.610000e-151
545.0
25
TraesCS5A01G077800
chr2D
82.537
607
94
11
1
603
570175762
570176360
7.520000e-145
523.0
26
TraesCS5A01G077800
chr2D
93.220
59
4
0
1076
1134
414415780
414415838
1.170000e-13
87.9
27
TraesCS5A01G077800
chr2D
82.418
91
8
7
2287
2375
264318402
264318318
3.270000e-09
73.1
28
TraesCS5A01G077800
chr2D
81.818
88
8
7
2287
2372
144954067
144954148
1.520000e-07
67.6
29
TraesCS5A01G077800
chr2D
80.952
84
7
6
2234
2316
344575449
344575374
9.170000e-05
58.4
30
TraesCS5A01G077800
chr5D
85.150
532
62
17
411
934
82880142
82879620
1.620000e-146
529.0
31
TraesCS5A01G077800
chr5D
90.588
85
8
0
1481
1565
78427039
78426955
1.930000e-21
113.0
32
TraesCS5A01G077800
chr1B
81.150
626
107
9
12
631
211259735
211259115
2.120000e-135
492.0
33
TraesCS5A01G077800
chr1B
86.131
411
52
3
1778
2186
248440701
248441108
2.800000e-119
438.0
34
TraesCS5A01G077800
chr1B
83.885
453
63
9
1779
2226
248424872
248425319
7.850000e-115
424.0
35
TraesCS5A01G077800
chr1B
85.330
409
56
3
1778
2186
446984171
446983767
1.020000e-113
420.0
36
TraesCS5A01G077800
chr1B
92.784
97
6
1
2237
2333
169315637
169315542
3.180000e-29
139.0
37
TraesCS5A01G077800
chr3D
85.649
439
47
12
1779
2205
168370515
168370949
4.660000e-122
448.0
38
TraesCS5A01G077800
chr3D
85.577
416
51
9
1817
2226
164998287
164998699
6.070000e-116
427.0
39
TraesCS5A01G077800
chr3D
81.818
88
8
7
2287
2372
197958631
197958712
1.520000e-07
67.6
40
TraesCS5A01G077800
chr3D
97.059
34
1
0
2342
2375
405201385
405201352
9.170000e-05
58.4
41
TraesCS5A01G077800
chr6D
89.683
126
9
4
2231
2354
325429162
325429039
8.790000e-35
158.0
42
TraesCS5A01G077800
chr4B
85.714
126
13
5
2231
2354
353832136
353832014
6.890000e-26
128.0
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
TraesCS5A01G077800
chr5A
94781093
94783467
2374
True
4386
4386
100.0000
1
2375
1
chr5A.!!$R2
2374
1
TraesCS5A01G077800
chr5A
94794148
94795504
1356
True
2200
2200
95.9470
423
1778
1
chr5A.!!$R3
1355
2
TraesCS5A01G077800
chr5A
433068048
433069204
1156
True
1724
1724
93.6100
420
1572
1
chr5A.!!$R7
1152
3
TraesCS5A01G077800
chr5A
94763993
94764587
594
True
902
902
93.9800
1778
2375
1
chr5A.!!$R1
597
4
TraesCS5A01G077800
chr5A
502877190
502877728
538
False
532
532
84.5870
1
541
1
chr5A.!!$F3
540
5
TraesCS5A01G077800
chr5A
36725063
36725687
624
False
475
475
80.6960
13
633
1
chr5A.!!$F1
620
6
TraesCS5A01G077800
chr5A
218844653
218845274
621
True
470
470
80.5730
12
630
1
chr5A.!!$R6
618
7
TraesCS5A01G077800
chr3A
195155404
195156760
1356
True
1978
1978
93.0100
423
1778
1
chr3A.!!$R2
1355
8
TraesCS5A01G077800
chr3A
195147202
195148918
1716
True
1296
1415
93.8395
11
1767
2
chr3A.!!$R4
1756
9
TraesCS5A01G077800
chr3A
623010883
623011447
564
True
512
512
83.1580
21
585
1
chr3A.!!$R3
564
10
TraesCS5A01G077800
chr1A
340353277
340353946
669
False
734
734
86.5100
259
934
1
chr1A.!!$F1
675
11
TraesCS5A01G077800
chr1A
446742979
446743865
886
False
664
664
80.4850
23
916
1
chr1A.!!$F2
893
12
TraesCS5A01G077800
chr1A
196740672
196741494
822
True
549
549
79.0170
36
857
1
chr1A.!!$R1
821
13
TraesCS5A01G077800
chr2A
150660021
150660598
577
False
516
516
83.0190
11
585
1
chr2A.!!$F1
574
14
TraesCS5A01G077800
chr7D
406001580
406002203
623
True
547
547
82.7530
12
633
1
chr7D.!!$R1
621
15
TraesCS5A01G077800
chr2D
252161700
252162300
600
False
545
545
83.3060
11
606
1
chr2D.!!$F2
595
16
TraesCS5A01G077800
chr2D
570175762
570176360
598
False
523
523
82.5370
1
603
1
chr2D.!!$F4
602
17
TraesCS5A01G077800
chr5D
82879620
82880142
522
True
529
529
85.1500
411
934
1
chr5D.!!$R2
523
18
TraesCS5A01G077800
chr1B
211259115
211259735
620
True
492
492
81.1500
12
631
1
chr1B.!!$R2
619
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.