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
TraesCS5D01G259900
chr5D
100.000
2621
0
0
1486
4106
366054192
366051572
0.000000e+00
4841.0
1
TraesCS5D01G259900
chr5D
100.000
1130
0
0
1
1130
366055677
366054548
0.000000e+00
2087.0
2
TraesCS5D01G259900
chr5D
88.156
591
32
11
38
591
390366227
390366816
0.000000e+00
669.0
3
TraesCS5D01G259900
chr5D
88.889
486
28
6
128
589
519338737
519339220
3.560000e-160
575.0
4
TraesCS5D01G259900
chr5D
98.182
55
0
1
592
646
309044323
309044376
1.220000e-15
95.3
5
TraesCS5D01G259900
chr5B
99.352
2623
15
2
1486
4106
433534517
433531895
0.000000e+00
4748.0
6
TraesCS5D01G259900
chr5B
94.118
425
6
6
722
1130
433534954
433534533
2.690000e-176
628.0
7
TraesCS5D01G259900
chr5A
97.414
2514
54
6
1488
3993
468468677
468466167
0.000000e+00
4272.0
8
TraesCS5D01G259900
chr5A
85.647
641
38
21
10
600
296306421
296307057
3.480000e-175
625.0
9
TraesCS5D01G259900
chr5A
92.135
445
11
8
707
1130
468469426
468468985
1.260000e-169
606.0
10
TraesCS5D01G259900
chr6D
89.499
619
27
16
10
591
147647102
147646485
0.000000e+00
749.0
11
TraesCS5D01G259900
chr6D
88.301
624
34
15
13
599
402808342
402807721
0.000000e+00
712.0
12
TraesCS5D01G259900
chr6D
84.843
607
54
19
10
591
13005244
13005837
9.900000e-161
577.0
13
TraesCS5D01G259900
chr7D
87.025
632
31
15
10
592
92297634
92297005
0.000000e+00
665.0
14
TraesCS5D01G259900
chr7D
84.020
607
62
17
12
590
69244068
69244667
6.000000e-153
551.0
15
TraesCS5D01G259900
chr7D
98.000
50
1
0
592
641
546051365
546051316
2.030000e-13
87.9
16
TraesCS5D01G259900
chr3D
88.612
562
26
15
67
591
587320474
587319914
0.000000e+00
649.0
17
TraesCS5D01G259900
chr3D
86.190
630
39
25
13
606
285767729
285767112
4.480000e-179
638.0
18
TraesCS5D01G259900
chr3D
95.918
49
1
1
592
639
552581139
552581187
1.220000e-10
78.7
19
TraesCS5D01G259900
chr2D
88.704
540
22
11
88
592
55411816
55412351
1.250000e-174
623.0
20
TraesCS5D01G259900
chr2D
96.000
50
2
0
592
641
24988204
24988155
9.460000e-12
82.4
21
TraesCS5D01G259900
chr6A
83.819
618
57
16
12
589
532029119
532029733
7.760000e-152
547.0
22
TraesCS5D01G259900
chr3B
83.887
602
64
17
14
591
760316506
760315914
1.000000e-150
544.0
23
TraesCS5D01G259900
chr7B
82.792
616
67
21
12
597
331008533
331009139
7.870000e-142
514.0
24
TraesCS5D01G259900
chr2B
82.219
613
72
18
10
591
645487000
645486394
1.030000e-135
494.0
25
TraesCS5D01G259900
chr2B
82.383
596
60
19
38
591
170084604
170084012
1.030000e-130
477.0
26
TraesCS5D01G259900
chr2B
95.918
49
2
0
592
640
748068022
748068070
3.400000e-11
80.5
27
TraesCS5D01G259900
chr4B
86.313
453
44
14
3
446
589813714
589813271
1.030000e-130
477.0
28
TraesCS5D01G259900
chr4B
90.196
51
3
2
592
641
83146339
83146290
9.530000e-07
65.8
29
TraesCS5D01G259900
chr7A
79.888
358
64
8
237
591
22952590
22952942
5.270000e-64
255.0
30
TraesCS5D01G259900
chr6B
97.917
48
1
0
592
639
234662466
234662513
2.630000e-12
84.2
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
TraesCS5D01G259900
chr5D
366051572
366055677
4105
True
3464
4841
100.0000
1
4106
2
chr5D.!!$R1
4105
1
TraesCS5D01G259900
chr5D
390366227
390366816
589
False
669
669
88.1560
38
591
1
chr5D.!!$F2
553
2
TraesCS5D01G259900
chr5B
433531895
433534954
3059
True
2688
4748
96.7350
722
4106
2
chr5B.!!$R1
3384
3
TraesCS5D01G259900
chr5A
468466167
468469426
3259
True
2439
4272
94.7745
707
3993
2
chr5A.!!$R1
3286
4
TraesCS5D01G259900
chr5A
296306421
296307057
636
False
625
625
85.6470
10
600
1
chr5A.!!$F1
590
5
TraesCS5D01G259900
chr6D
147646485
147647102
617
True
749
749
89.4990
10
591
1
chr6D.!!$R1
581
6
TraesCS5D01G259900
chr6D
402807721
402808342
621
True
712
712
88.3010
13
599
1
chr6D.!!$R2
586
7
TraesCS5D01G259900
chr6D
13005244
13005837
593
False
577
577
84.8430
10
591
1
chr6D.!!$F1
581
8
TraesCS5D01G259900
chr7D
92297005
92297634
629
True
665
665
87.0250
10
592
1
chr7D.!!$R1
582
9
TraesCS5D01G259900
chr7D
69244068
69244667
599
False
551
551
84.0200
12
590
1
chr7D.!!$F1
578
10
TraesCS5D01G259900
chr3D
587319914
587320474
560
True
649
649
88.6120
67
591
1
chr3D.!!$R2
524
11
TraesCS5D01G259900
chr3D
285767112
285767729
617
True
638
638
86.1900
13
606
1
chr3D.!!$R1
593
12
TraesCS5D01G259900
chr2D
55411816
55412351
535
False
623
623
88.7040
88
592
1
chr2D.!!$F1
504
13
TraesCS5D01G259900
chr6A
532029119
532029733
614
False
547
547
83.8190
12
589
1
chr6A.!!$F1
577
14
TraesCS5D01G259900
chr3B
760315914
760316506
592
True
544
544
83.8870
14
591
1
chr3B.!!$R1
577
15
TraesCS5D01G259900
chr7B
331008533
331009139
606
False
514
514
82.7920
12
597
1
chr7B.!!$F1
585
16
TraesCS5D01G259900
chr2B
645486394
645487000
606
True
494
494
82.2190
10
591
1
chr2B.!!$R2
581
17
TraesCS5D01G259900
chr2B
170084012
170084604
592
True
477
477
82.3830
38
591
1
chr2B.!!$R1
553
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.