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
TraesCS3D01G031800
chr3D
100.000
3109
0
0
1
3109
11730964
11734072
0.000000e+00
5742.0
1
TraesCS3D01G031800
chr3D
82.097
391
63
7
2722
3108
464341606
464341219
8.310000e-86
327.0
2
TraesCS3D01G031800
chr3D
90.868
219
11
5
581
795
11704208
11704421
5.070000e-73
285.0
3
TraesCS3D01G031800
chr3B
92.480
1915
88
17
1230
3109
16404113
16406006
0.000000e+00
2687.0
4
TraesCS3D01G031800
chr3B
95.833
672
17
5
583
1244
16403382
16404052
0.000000e+00
1075.0
5
TraesCS3D01G031800
chr3B
90.411
219
12
3
581
795
16400608
16400821
2.360000e-71
279.0
6
TraesCS3D01G031800
chr3B
90.909
55
3
2
1265
1319
598447516
598447464
4.300000e-09
73.1
7
TraesCS3D01G031800
chr3B
89.091
55
4
2
1265
1319
474402086
474402034
2.000000e-07
67.6
8
TraesCS3D01G031800
chr2D
95.034
584
27
2
1
583
24573488
24574070
0.000000e+00
917.0
9
TraesCS3D01G031800
chr2D
93.299
582
36
2
1
582
606736048
606735470
0.000000e+00
856.0
10
TraesCS3D01G031800
chr2D
87.671
146
16
2
2574
2718
543823620
543823764
5.330000e-38
169.0
11
TraesCS3D01G031800
chr2D
88.043
92
7
4
509
598
255810698
255810787
4.240000e-19
106.0
12
TraesCS3D01G031800
chr2D
91.667
48
4
0
1654
1701
643954197
643954244
2.000000e-07
67.6
13
TraesCS3D01G031800
chr6D
91.910
581
46
1
1
581
397624960
397625539
0.000000e+00
811.0
14
TraesCS3D01G031800
chr6D
82.051
390
67
3
2722
3109
223731169
223730781
2.310000e-86
329.0
15
TraesCS3D01G031800
chr6D
81.980
394
65
6
2719
3108
238029589
238029980
2.310000e-86
329.0
16
TraesCS3D01G031800
chr2B
93.726
526
31
2
57
582
190057970
190058493
0.000000e+00
787.0
17
TraesCS3D01G031800
chr1B
87.458
598
70
5
1
596
149530845
149531439
0.000000e+00
684.0
18
TraesCS3D01G031800
chr1B
84.354
147
21
2
2574
2718
599336068
599335922
3.230000e-30
143.0
19
TraesCS3D01G031800
chr1B
89.655
58
4
2
1262
1319
125755099
125755154
4.300000e-09
73.1
20
TraesCS3D01G031800
chr1B
82.667
75
8
5
1244
1317
572646590
572646660
9.310000e-06
62.1
21
TraesCS3D01G031800
chr4A
91.958
286
21
2
83
367
616272765
616272481
1.740000e-107
399.0
22
TraesCS3D01G031800
chr2A
84.062
389
61
1
2722
3109
683625605
683625217
1.050000e-99
374.0
23
TraesCS3D01G031800
chr2A
87.273
55
5
1
894
946
769020260
769020314
9.310000e-06
62.1
24
TraesCS3D01G031800
chr3A
78.173
591
116
11
1
584
476290802
476290218
6.340000e-97
364.0
25
TraesCS3D01G031800
chr3A
87.597
129
15
1
2574
2702
79392889
79392762
6.950000e-32
148.0
26
TraesCS3D01G031800
chr7A
83.290
389
64
1
2722
3109
85972597
85972209
1.060000e-94
357.0
27
TraesCS3D01G031800
chr4D
82.776
389
63
4
2722
3107
85431915
85431528
8.250000e-91
344.0
28
TraesCS3D01G031800
chr4B
82.474
388
64
4
2722
3107
589753918
589753533
1.380000e-88
337.0
29
TraesCS3D01G031800
chr5D
81.888
392
67
4
2719
3107
253171243
253171633
8.310000e-86
327.0
30
TraesCS3D01G031800
chr5D
89.286
56
4
2
1264
1319
188826620
188826567
5.560000e-08
69.4
31
TraesCS3D01G031800
chr7D
90.698
129
12
0
2574
2702
543335980
543336108
4.120000e-39
172.0
32
TraesCS3D01G031800
chr7D
85.906
149
20
1
433
581
271501836
271501689
1.150000e-34
158.0
33
TraesCS3D01G031800
chr7D
82.639
144
25
0
2575
2718
631320485
631320342
9.050000e-26
128.0
34
TraesCS3D01G031800
chr5B
87.597
129
16
0
2574
2702
110129157
110129285
1.930000e-32
150.0
35
TraesCS3D01G031800
chr5B
89.286
56
4
2
1264
1319
217907768
217907715
5.560000e-08
69.4
36
TraesCS3D01G031800
chr6B
95.522
67
3
0
517
583
629461492
629461558
1.180000e-19
108.0
37
TraesCS3D01G031800
chr6B
95.238
42
2
0
1259
1300
439065967
439066008
2.000000e-07
67.6
38
TraesCS3D01G031800
chr5A
93.750
48
0
2
1250
1297
453762841
453762797
5.560000e-08
69.4
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
TraesCS3D01G031800
chr3D
11730964
11734072
3108
False
5742
5742
100.000
1
3109
1
chr3D.!!$F2
3108
1
TraesCS3D01G031800
chr3B
16400608
16406006
5398
False
1347
2687
92.908
581
3109
3
chr3B.!!$F1
2528
2
TraesCS3D01G031800
chr2D
24573488
24574070
582
False
917
917
95.034
1
583
1
chr2D.!!$F1
582
3
TraesCS3D01G031800
chr2D
606735470
606736048
578
True
856
856
93.299
1
582
1
chr2D.!!$R1
581
4
TraesCS3D01G031800
chr6D
397624960
397625539
579
False
811
811
91.910
1
581
1
chr6D.!!$F2
580
5
TraesCS3D01G031800
chr2B
190057970
190058493
523
False
787
787
93.726
57
582
1
chr2B.!!$F1
525
6
TraesCS3D01G031800
chr1B
149530845
149531439
594
False
684
684
87.458
1
596
1
chr1B.!!$F2
595
7
TraesCS3D01G031800
chr3A
476290218
476290802
584
True
364
364
78.173
1
584
1
chr3A.!!$R2
583
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.