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
TraesCS3B01G342900
chr3B
100.000
4863
0
0
1
4863
550728817
550733679
0.000000e+00
8981.0
1
TraesCS3B01G342900
chr3B
95.065
851
36
3
1
850
460338442
460339287
0.000000e+00
1334.0
2
TraesCS3B01G342900
chr3B
94.947
851
37
3
1
850
460325745
460326590
0.000000e+00
1328.0
3
TraesCS3B01G342900
chr3B
94.947
851
37
3
1
850
460331545
460332390
0.000000e+00
1328.0
4
TraesCS3B01G342900
chr3B
94.947
851
37
3
1
850
460344428
460345273
0.000000e+00
1328.0
5
TraesCS3B01G342900
chr3B
87.500
640
69
8
4199
4834
639434142
639434774
0.000000e+00
728.0
6
TraesCS3B01G342900
chr3A
91.743
2931
154
34
1287
4152
566327637
566324730
0.000000e+00
3991.0
7
TraesCS3B01G342900
chr3A
99.049
841
8
0
1
841
723143346
723142506
0.000000e+00
1509.0
8
TraesCS3B01G342900
chr3A
96.269
402
14
1
840
1241
566328038
566327638
0.000000e+00
658.0
9
TraesCS3B01G342900
chr3D
92.693
2258
85
33
1996
4198
422648396
422650628
0.000000e+00
3182.0
10
TraesCS3B01G342900
chr3D
97.506
401
8
2
841
1241
422647187
422647585
0.000000e+00
684.0
11
TraesCS3B01G342900
chr3D
89.358
545
41
8
1287
1821
422647586
422648123
0.000000e+00
669.0
12
TraesCS3B01G342900
chr3D
94.771
153
8
0
1815
1967
422648146
422648298
6.290000e-59
239.0
13
TraesCS3B01G342900
chr4A
95.193
853
39
2
1
852
271087203
271088054
0.000000e+00
1347.0
14
TraesCS3B01G342900
chr2D
94.656
842
41
3
1
840
295576574
295575735
0.000000e+00
1303.0
15
TraesCS3B01G342900
chr2D
86.917
665
78
9
4198
4858
313845875
313845216
0.000000e+00
737.0
16
TraesCS3B01G342900
chrUn
96.311
759
24
2
1
756
96416066
96415309
0.000000e+00
1243.0
17
TraesCS3B01G342900
chrUn
100.000
179
0
0
1
179
479358356
479358534
1.010000e-86
331.0
18
TraesCS3B01G342900
chrUn
92.857
98
7
0
746
843
96414581
96414484
5.070000e-30
143.0
19
TraesCS3B01G342900
chr6B
91.445
678
42
6
4201
4863
292823713
292824389
0.000000e+00
917.0
20
TraesCS3B01G342900
chr6B
91.189
681
46
3
4197
4863
537721430
537720750
0.000000e+00
913.0
21
TraesCS3B01G342900
chr6B
91.176
680
46
3
4198
4863
382921713
382921034
0.000000e+00
911.0
22
TraesCS3B01G342900
chr6B
90.105
667
62
4
4199
4863
199044003
199043339
0.000000e+00
863.0
23
TraesCS3B01G342900
chr4D
91.228
684
45
4
4195
4863
15122132
15122815
0.000000e+00
917.0
24
TraesCS3B01G342900
chr4D
86.826
668
77
9
4199
4863
403547638
403546979
0.000000e+00
736.0
25
TraesCS3B01G342900
chr2B
91.189
681
43
6
4198
4863
195951382
195950704
0.000000e+00
909.0
26
TraesCS3B01G342900
chr2B
91.029
680
47
4
4198
4863
595364267
595363588
0.000000e+00
905.0
27
TraesCS3B01G342900
chr2B
85.859
99
11
3
744
840
601390163
601390260
8.610000e-18
102.0
28
TraesCS3B01G342900
chr5B
94.128
596
35
0
4268
4863
499007793
499007198
0.000000e+00
907.0
29
TraesCS3B01G342900
chr5B
87.779
671
65
12
4199
4863
121938587
121939246
0.000000e+00
769.0
30
TraesCS3B01G342900
chr7B
90.776
683
49
4
4195
4863
389227824
389228506
0.000000e+00
900.0
31
TraesCS3B01G342900
chr4B
87.592
677
74
8
4195
4863
602048253
602048927
0.000000e+00
776.0
32
TraesCS3B01G342900
chr4B
88.346
635
63
9
4234
4863
548566071
548566699
0.000000e+00
752.0
33
TraesCS3B01G342900
chr5D
87.500
664
72
11
4199
4858
112941165
112940509
0.000000e+00
756.0
34
TraesCS3B01G342900
chr7A
86.154
650
78
10
4199
4846
217884178
217883539
0.000000e+00
691.0
35
TraesCS3B01G342900
chr7A
85.562
658
67
14
1094
1738
95652068
95652710
0.000000e+00
664.0
36
TraesCS3B01G342900
chr7A
87.261
157
17
3
944
1098
95644837
95644992
5.000000e-40
176.0
37
TraesCS3B01G342900
chr1A
84.211
133
20
1
3344
3476
516786899
516786768
1.420000e-25
128.0
38
TraesCS3B01G342900
chr1A
73.789
351
68
20
2893
3231
516787546
516787208
3.080000e-22
117.0
39
TraesCS3B01G342900
chr1A
78.899
109
23
0
2893
3001
516850148
516850040
1.880000e-09
75.0
40
TraesCS3B01G342900
chr1B
83.459
133
21
1
3344
3476
568569130
568568999
6.610000e-24
122.0
41
TraesCS3B01G342900
chr1B
73.219
351
73
18
2893
3231
568569750
568569409
1.850000e-19
108.0
42
TraesCS3B01G342900
chr1B
79.817
109
22
0
2893
3001
568644106
568643998
4.030000e-11
80.5
43
TraesCS3B01G342900
chr1D
82.707
133
22
1
3344
3476
420554311
420554180
3.080000e-22
117.0
44
TraesCS3B01G342900
chr1D
85.714
91
11
2
2893
2982
420555042
420554953
1.440000e-15
95.3
45
TraesCS3B01G342900
chr1D
79.245
106
22
0
2893
2998
420565690
420565585
1.880000e-09
75.0
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
TraesCS3B01G342900
chr3B
550728817
550733679
4862
False
8981.0
8981
100.000
1
4863
1
chr3B.!!$F5
4862
1
TraesCS3B01G342900
chr3B
460338442
460339287
845
False
1334.0
1334
95.065
1
850
1
chr3B.!!$F3
849
2
TraesCS3B01G342900
chr3B
460325745
460326590
845
False
1328.0
1328
94.947
1
850
1
chr3B.!!$F1
849
3
TraesCS3B01G342900
chr3B
460331545
460332390
845
False
1328.0
1328
94.947
1
850
1
chr3B.!!$F2
849
4
TraesCS3B01G342900
chr3B
460344428
460345273
845
False
1328.0
1328
94.947
1
850
1
chr3B.!!$F4
849
5
TraesCS3B01G342900
chr3B
639434142
639434774
632
False
728.0
728
87.500
4199
4834
1
chr3B.!!$F6
635
6
TraesCS3B01G342900
chr3A
566324730
566328038
3308
True
2324.5
3991
94.006
840
4152
2
chr3A.!!$R2
3312
7
TraesCS3B01G342900
chr3A
723142506
723143346
840
True
1509.0
1509
99.049
1
841
1
chr3A.!!$R1
840
8
TraesCS3B01G342900
chr3D
422647187
422650628
3441
False
1193.5
3182
93.582
841
4198
4
chr3D.!!$F1
3357
9
TraesCS3B01G342900
chr4A
271087203
271088054
851
False
1347.0
1347
95.193
1
852
1
chr4A.!!$F1
851
10
TraesCS3B01G342900
chr2D
295575735
295576574
839
True
1303.0
1303
94.656
1
840
1
chr2D.!!$R1
839
11
TraesCS3B01G342900
chr2D
313845216
313845875
659
True
737.0
737
86.917
4198
4858
1
chr2D.!!$R2
660
12
TraesCS3B01G342900
chrUn
96414484
96416066
1582
True
693.0
1243
94.584
1
843
2
chrUn.!!$R1
842
13
TraesCS3B01G342900
chr6B
292823713
292824389
676
False
917.0
917
91.445
4201
4863
1
chr6B.!!$F1
662
14
TraesCS3B01G342900
chr6B
537720750
537721430
680
True
913.0
913
91.189
4197
4863
1
chr6B.!!$R3
666
15
TraesCS3B01G342900
chr6B
382921034
382921713
679
True
911.0
911
91.176
4198
4863
1
chr6B.!!$R2
665
16
TraesCS3B01G342900
chr6B
199043339
199044003
664
True
863.0
863
90.105
4199
4863
1
chr6B.!!$R1
664
17
TraesCS3B01G342900
chr4D
15122132
15122815
683
False
917.0
917
91.228
4195
4863
1
chr4D.!!$F1
668
18
TraesCS3B01G342900
chr4D
403546979
403547638
659
True
736.0
736
86.826
4199
4863
1
chr4D.!!$R1
664
19
TraesCS3B01G342900
chr2B
195950704
195951382
678
True
909.0
909
91.189
4198
4863
1
chr2B.!!$R1
665
20
TraesCS3B01G342900
chr2B
595363588
595364267
679
True
905.0
905
91.029
4198
4863
1
chr2B.!!$R2
665
21
TraesCS3B01G342900
chr5B
499007198
499007793
595
True
907.0
907
94.128
4268
4863
1
chr5B.!!$R1
595
22
TraesCS3B01G342900
chr5B
121938587
121939246
659
False
769.0
769
87.779
4199
4863
1
chr5B.!!$F1
664
23
TraesCS3B01G342900
chr7B
389227824
389228506
682
False
900.0
900
90.776
4195
4863
1
chr7B.!!$F1
668
24
TraesCS3B01G342900
chr4B
602048253
602048927
674
False
776.0
776
87.592
4195
4863
1
chr4B.!!$F2
668
25
TraesCS3B01G342900
chr4B
548566071
548566699
628
False
752.0
752
88.346
4234
4863
1
chr4B.!!$F1
629
26
TraesCS3B01G342900
chr5D
112940509
112941165
656
True
756.0
756
87.500
4199
4858
1
chr5D.!!$R1
659
27
TraesCS3B01G342900
chr7A
217883539
217884178
639
True
691.0
691
86.154
4199
4846
1
chr7A.!!$R1
647
28
TraesCS3B01G342900
chr7A
95652068
95652710
642
False
664.0
664
85.562
1094
1738
1
chr7A.!!$F2
644
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.