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
TraesCS3D01G519500
chr3D
100.000
3218
0
0
1
3218
602262555
602259338
0.000000e+00
5943.0
1
TraesCS3D01G519500
chr3D
78.888
1241
210
37
1019
2236
602235180
602236391
0.000000e+00
793.0
2
TraesCS3D01G519500
chr3D
79.942
1027
163
26
1238
2241
602210864
602211870
0.000000e+00
715.0
3
TraesCS3D01G519500
chr3D
81.106
434
75
4
1835
2268
597300787
597300361
1.110000e-89
340.0
4
TraesCS3D01G519500
chr3A
89.661
2215
139
33
948
3096
731844357
731842167
0.000000e+00
2739.0
5
TraesCS3D01G519500
chr3A
94.891
1468
57
9
909
2362
731894475
731893012
0.000000e+00
2279.0
6
TraesCS3D01G519500
chr3A
94.138
853
33
6
2369
3218
731892848
731892010
0.000000e+00
1282.0
7
TraesCS3D01G519500
chr3A
79.864
1326
215
34
1019
2332
730851579
730850294
0.000000e+00
922.0
8
TraesCS3D01G519500
chr3A
79.171
989
157
32
1325
2277
730905275
730904300
9.730000e-180
640.0
9
TraesCS3D01G519500
chr3A
87.228
368
43
3
966
1333
730908439
730908076
1.790000e-112
416.0
10
TraesCS3D01G519500
chr3A
85.612
139
20
0
2415
2553
730850129
730849991
2.590000e-31
147.0
11
TraesCS3D01G519500
chr5B
92.076
896
58
3
9
892
496987148
496988042
0.000000e+00
1249.0
12
TraesCS3D01G519500
chr5B
73.579
598
114
26
1720
2298
672823195
672822623
4.240000e-44
189.0
13
TraesCS3D01G519500
chr6D
88.098
899
93
5
9
893
455463640
455464538
0.000000e+00
1055.0
14
TraesCS3D01G519500
chr6A
87.248
894
93
6
9
890
466845486
466846370
0.000000e+00
1000.0
15
TraesCS3D01G519500
chr6A
84.770
893
123
6
9
890
583767866
583768756
0.000000e+00
883.0
16
TraesCS3D01G519500
chr7A
78.723
1316
228
36
1022
2298
11230329
11229027
0.000000e+00
832.0
17
TraesCS3D01G519500
chr7A
76.061
848
146
32
1428
2242
11311820
11310997
3.890000e-104
388.0
18
TraesCS3D01G519500
chr7A
79.130
575
110
7
1731
2298
11345583
11345012
3.890000e-104
388.0
19
TraesCS3D01G519500
chr7A
84.739
249
36
2
1418
1665
11346089
11345842
6.890000e-62
248.0
20
TraesCS3D01G519500
chr3B
90.476
609
55
3
1755
2362
809464312
809463706
0.000000e+00
800.0
21
TraesCS3D01G519500
chr3B
87.183
671
72
10
966
1626
809237463
809236797
0.000000e+00
750.0
22
TraesCS3D01G519500
chr3B
84.098
654
60
22
2586
3218
809463252
809462622
2.760000e-165
592.0
23
TraesCS3D01G519500
chr3B
86.626
486
58
6
948
1431
809510265
809509785
6.110000e-147
531.0
24
TraesCS3D01G519500
chr3B
93.750
336
21
0
968
1303
809347754
809348089
3.700000e-139
505.0
25
TraesCS3D01G519500
chr3B
86.854
426
36
6
1929
2351
809509777
809509369
2.930000e-125
459.0
26
TraesCS3D01G519500
chr3B
97.026
269
8
0
2948
3216
809503028
809502760
1.360000e-123
453.0
27
TraesCS3D01G519500
chr3B
87.037
378
36
7
2611
2977
809503409
809503034
6.420000e-112
414.0
28
TraesCS3D01G519500
chr3B
74.611
772
176
15
111
874
20478782
20478023
4.000000e-84
322.0
29
TraesCS3D01G519500
chr3B
79.027
329
58
5
1957
2277
809348090
809348415
6.990000e-52
215.0
30
TraesCS3D01G519500
chr3B
93.706
143
8
1
2416
2558
809463466
809463325
2.510000e-51
213.0
31
TraesCS3D01G519500
chr3B
86.224
196
16
6
2369
2553
809509192
809508997
5.440000e-48
202.0
32
TraesCS3D01G519500
chr3B
94.286
35
2
0
224
258
11063584
11063618
2.000000e-03
54.7
33
TraesCS3D01G519500
chr7B
76.726
1289
236
46
1052
2299
750116588
750115323
0.000000e+00
660.0
34
TraesCS3D01G519500
chr7D
77.129
1198
223
35
1070
2242
11928845
11927674
0.000000e+00
647.0
35
TraesCS3D01G519500
chr7D
75.671
1266
240
37
1016
2227
26760017
26758766
1.300000e-158
569.0
36
TraesCS3D01G519500
chr7D
79.716
493
78
13
1022
1497
11727506
11727019
1.430000e-88
337.0
37
TraesCS3D01G519500
chr7D
91.026
78
7
0
2571
2648
12045547
12045470
4.390000e-19
106.0
38
TraesCS3D01G519500
chr4A
76.553
853
139
39
1422
2242
726073342
726074165
8.310000e-111
411.0
39
TraesCS3D01G519500
chr4A
76.371
529
103
17
1720
2237
725864869
725865386
6.850000e-67
265.0
40
TraesCS3D01G519500
chr4A
79.926
269
47
5
2025
2286
726064720
726064988
1.180000e-44
191.0
41
TraesCS3D01G519500
chr4D
74.622
859
178
25
42
874
307265147
307265991
3.070000e-90
342.0
42
TraesCS3D01G519500
chr1A
90.984
244
22
0
631
874
17829362
17829605
2.390000e-86
329.0
43
TraesCS3D01G519500
chr5D
73.508
687
154
24
206
874
485163537
485164213
5.370000e-58
235.0
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
TraesCS3D01G519500
chr3D
602259338
602262555
3217
True
5943.000000
5943
100.000000
1
3218
1
chr3D.!!$R2
3217
1
TraesCS3D01G519500
chr3D
602235180
602236391
1211
False
793.000000
793
78.888000
1019
2236
1
chr3D.!!$F2
1217
2
TraesCS3D01G519500
chr3D
602210864
602211870
1006
False
715.000000
715
79.942000
1238
2241
1
chr3D.!!$F1
1003
3
TraesCS3D01G519500
chr3A
731842167
731844357
2190
True
2739.000000
2739
89.661000
948
3096
1
chr3A.!!$R1
2148
4
TraesCS3D01G519500
chr3A
731892010
731894475
2465
True
1780.500000
2279
94.514500
909
3218
2
chr3A.!!$R4
2309
5
TraesCS3D01G519500
chr3A
730849991
730851579
1588
True
534.500000
922
82.738000
1019
2553
2
chr3A.!!$R2
1534
6
TraesCS3D01G519500
chr3A
730904300
730908439
4139
True
528.000000
640
83.199500
966
2277
2
chr3A.!!$R3
1311
7
TraesCS3D01G519500
chr5B
496987148
496988042
894
False
1249.000000
1249
92.076000
9
892
1
chr5B.!!$F1
883
8
TraesCS3D01G519500
chr6D
455463640
455464538
898
False
1055.000000
1055
88.098000
9
893
1
chr6D.!!$F1
884
9
TraesCS3D01G519500
chr6A
466845486
466846370
884
False
1000.000000
1000
87.248000
9
890
1
chr6A.!!$F1
881
10
TraesCS3D01G519500
chr6A
583767866
583768756
890
False
883.000000
883
84.770000
9
890
1
chr6A.!!$F2
881
11
TraesCS3D01G519500
chr7A
11229027
11230329
1302
True
832.000000
832
78.723000
1022
2298
1
chr7A.!!$R1
1276
12
TraesCS3D01G519500
chr7A
11310997
11311820
823
True
388.000000
388
76.061000
1428
2242
1
chr7A.!!$R2
814
13
TraesCS3D01G519500
chr7A
11345012
11346089
1077
True
318.000000
388
81.934500
1418
2298
2
chr7A.!!$R3
880
14
TraesCS3D01G519500
chr3B
809236797
809237463
666
True
750.000000
750
87.183000
966
1626
1
chr3B.!!$R2
660
15
TraesCS3D01G519500
chr3B
809462622
809464312
1690
True
535.000000
800
89.426667
1755
3218
3
chr3B.!!$R3
1463
16
TraesCS3D01G519500
chr3B
809502760
809503409
649
True
433.500000
453
92.031500
2611
3216
2
chr3B.!!$R4
605
17
TraesCS3D01G519500
chr3B
809508997
809510265
1268
True
397.333333
531
86.568000
948
2553
3
chr3B.!!$R5
1605
18
TraesCS3D01G519500
chr3B
809347754
809348415
661
False
360.000000
505
86.388500
968
2277
2
chr3B.!!$F2
1309
19
TraesCS3D01G519500
chr3B
20478023
20478782
759
True
322.000000
322
74.611000
111
874
1
chr3B.!!$R1
763
20
TraesCS3D01G519500
chr7B
750115323
750116588
1265
True
660.000000
660
76.726000
1052
2299
1
chr7B.!!$R1
1247
21
TraesCS3D01G519500
chr7D
11927674
11928845
1171
True
647.000000
647
77.129000
1070
2242
1
chr7D.!!$R2
1172
22
TraesCS3D01G519500
chr7D
26758766
26760017
1251
True
569.000000
569
75.671000
1016
2227
1
chr7D.!!$R4
1211
23
TraesCS3D01G519500
chr4A
726073342
726074165
823
False
411.000000
411
76.553000
1422
2242
1
chr4A.!!$F3
820
24
TraesCS3D01G519500
chr4A
725864869
725865386
517
False
265.000000
265
76.371000
1720
2237
1
chr4A.!!$F1
517
25
TraesCS3D01G519500
chr4D
307265147
307265991
844
False
342.000000
342
74.622000
42
874
1
chr4D.!!$F1
832
26
TraesCS3D01G519500
chr5D
485163537
485164213
676
False
235.000000
235
73.508000
206
874
1
chr5D.!!$F1
668
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.