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
TraesCS3B01G371900
chr3B
100.000
4886
0
0
1
4886
584699017
584694132
0.000000e+00
9023
1
TraesCS3B01G371900
chr3B
90.464
1573
115
19
1368
2914
588439840
588441403
0.000000e+00
2041
2
TraesCS3B01G371900
chr3B
92.753
1435
68
20
2923
4350
588441451
588442856
0.000000e+00
2041
3
TraesCS3B01G371900
chr3B
97.584
538
12
1
4349
4886
620821796
620821260
0.000000e+00
920
4
TraesCS3B01G371900
chr3B
79.437
355
36
23
2733
3065
588441590
588441929
2.960000e-52
217
5
TraesCS3B01G371900
chr3B
78.736
348
35
21
2748
3065
584695941
584695603
3.860000e-46
196
6
TraesCS3B01G371900
chr3B
78.736
348
35
21
3077
3415
584696270
584695953
3.860000e-46
196
7
TraesCS3B01G371900
chr3A
93.888
3027
122
32
1012
3985
587564629
587561613
0.000000e+00
4506
8
TraesCS3B01G371900
chr3A
85.522
967
63
26
1
939
587565820
587564903
0.000000e+00
939
9
TraesCS3B01G371900
chr3A
93.473
383
16
5
3977
4350
587559074
587558692
1.190000e-155
560
10
TraesCS3B01G371900
chr3A
81.098
492
69
19
4
480
587571474
587570992
5.970000e-99
372
11
TraesCS3B01G371900
chr3A
83.846
390
43
16
4
390
587568928
587568556
2.160000e-93
353
12
TraesCS3B01G371900
chr3A
79.472
492
73
23
1
473
587574162
587573680
1.700000e-84
324
13
TraesCS3B01G371900
chr3A
78.337
517
60
33
1
479
587567429
587566927
2.230000e-73
287
14
TraesCS3B01G371900
chr3A
78.571
322
35
17
2768
3065
587562494
587562183
1.080000e-41
182
15
TraesCS3B01G371900
chr3D
91.925
2514
111
45
527
2970
445811325
445808834
0.000000e+00
3434
16
TraesCS3B01G371900
chr3D
96.739
1196
30
4
3160
4350
445808482
445807291
0.000000e+00
1984
17
TraesCS3B01G371900
chr3D
83.398
512
37
23
1
480
445814019
445813524
9.720000e-117
431
18
TraesCS3B01G371900
chr3D
83.200
500
51
14
1
480
445814800
445814314
1.260000e-115
427
19
TraesCS3B01G371900
chr3D
82.635
501
58
17
1
480
445815597
445815105
2.720000e-112
416
20
TraesCS3B01G371900
chr3D
93.214
280
18
1
3
282
445812352
445812074
1.270000e-110
411
21
TraesCS3B01G371900
chr3D
85.979
378
41
9
16
390
445817219
445816851
1.270000e-105
394
22
TraesCS3B01G371900
chr3D
97.423
194
5
0
2966
3159
445808755
445808562
1.010000e-86
331
23
TraesCS3B01G371900
chr3D
80.144
277
28
17
221
480
445812934
445812668
1.080000e-41
182
24
TraesCS3B01G371900
chr3D
91.057
123
9
2
405
525
445811612
445811490
1.090000e-36
165
25
TraesCS3B01G371900
chr3D
87.500
144
15
2
2925
3065
445808373
445808230
3.910000e-36
163
26
TraesCS3B01G371900
chr3D
91.000
100
9
0
3316
3415
445808755
445808656
8.530000e-28
135
27
TraesCS3B01G371900
chr2B
97.207
537
14
1
4349
4885
627322009
627321474
0.000000e+00
907
28
TraesCS3B01G371900
chr6B
97.026
538
15
1
4349
4886
602490441
602490977
0.000000e+00
904
29
TraesCS3B01G371900
chr4A
97.026
538
15
1
4349
4886
661308656
661308120
0.000000e+00
904
30
TraesCS3B01G371900
chr1B
97.026
538
15
1
4349
4886
161398729
161398193
0.000000e+00
904
31
TraesCS3B01G371900
chr1B
96.840
538
16
1
4349
4886
638818676
638818140
0.000000e+00
898
32
TraesCS3B01G371900
chr7B
96.654
538
17
1
4349
4886
110319299
110318763
0.000000e+00
893
33
TraesCS3B01G371900
chr5B
96.468
538
18
1
4349
4886
78311271
78311807
0.000000e+00
887
34
TraesCS3B01G371900
chr5B
96.468
538
18
1
4349
4886
495529520
495528984
0.000000e+00
887
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
TraesCS3B01G371900
chr3B
584694132
584699017
4885
True
3138.333333
9023
85.824000
1
4886
3
chr3B.!!$R2
4885
1
TraesCS3B01G371900
chr3B
588439840
588442856
3016
False
1433.000000
2041
87.551333
1368
4350
3
chr3B.!!$F1
2982
2
TraesCS3B01G371900
chr3B
620821260
620821796
536
True
920.000000
920
97.584000
4349
4886
1
chr3B.!!$R1
537
3
TraesCS3B01G371900
chr3A
587558692
587574162
15470
True
940.375000
4506
84.275875
1
4350
8
chr3A.!!$R1
4349
4
TraesCS3B01G371900
chr3D
445807291
445817219
9928
True
706.083333
3434
88.684500
1
4350
12
chr3D.!!$R1
4349
5
TraesCS3B01G371900
chr2B
627321474
627322009
535
True
907.000000
907
97.207000
4349
4885
1
chr2B.!!$R1
536
6
TraesCS3B01G371900
chr6B
602490441
602490977
536
False
904.000000
904
97.026000
4349
4886
1
chr6B.!!$F1
537
7
TraesCS3B01G371900
chr4A
661308120
661308656
536
True
904.000000
904
97.026000
4349
4886
1
chr4A.!!$R1
537
8
TraesCS3B01G371900
chr1B
161398193
161398729
536
True
904.000000
904
97.026000
4349
4886
1
chr1B.!!$R1
537
9
TraesCS3B01G371900
chr1B
638818140
638818676
536
True
898.000000
898
96.840000
4349
4886
1
chr1B.!!$R2
537
10
TraesCS3B01G371900
chr7B
110318763
110319299
536
True
893.000000
893
96.654000
4349
4886
1
chr7B.!!$R1
537
11
TraesCS3B01G371900
chr5B
78311271
78311807
536
False
887.000000
887
96.468000
4349
4886
1
chr5B.!!$F1
537
12
TraesCS3B01G371900
chr5B
495528984
495529520
536
True
887.000000
887
96.468000
4349
4886
1
chr5B.!!$R1
537
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.