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
TraesCS2A01G328400
chr2A
100.000
4223
0
0
1
4223
559837574
559833352
0.000000e+00
7799.0
1
TraesCS2A01G328400
chr2A
93.673
980
61
1
2933
3912
559778046
559777068
0.000000e+00
1465.0
2
TraesCS2A01G328400
chr2A
86.801
1341
137
20
1
1332
559779351
559778042
0.000000e+00
1459.0
3
TraesCS2A01G328400
chr2A
86.080
1056
100
21
2977
4016
559704427
559703403
0.000000e+00
1092.0
4
TraesCS2A01G328400
chr2A
92.695
616
41
1
720
1331
559741263
559740648
0.000000e+00
885.0
5
TraesCS2A01G328400
chr2A
84.974
772
83
13
1
742
559742823
559742055
0.000000e+00
752.0
6
TraesCS2A01G328400
chr2A
94.357
443
15
3
1333
1773
559835077
559834643
0.000000e+00
671.0
7
TraesCS2A01G328400
chr2A
94.357
443
15
3
2498
2932
559836242
559835802
0.000000e+00
671.0
8
TraesCS2A01G328400
chr2A
84.457
682
75
17
1807
2462
564075702
564075026
0.000000e+00
643.0
9
TraesCS2A01G328400
chr2A
95.349
301
10
2
3923
4223
559776783
559776487
3.820000e-130
475.0
10
TraesCS2A01G328400
chr2D
90.889
1339
90
8
1
1332
427924619
427925932
0.000000e+00
1768.0
11
TraesCS2A01G328400
chr2D
90.957
1338
83
10
1
1332
427943847
427945152
0.000000e+00
1766.0
12
TraesCS2A01G328400
chr2D
91.475
1220
85
15
2933
4144
427910179
427911387
0.000000e+00
1659.0
13
TraesCS2A01G328400
chr2D
90.519
1234
105
9
1
1222
427905287
427906520
0.000000e+00
1620.0
14
TraesCS2A01G328400
chr2D
90.339
1180
106
5
159
1332
427909006
427910183
0.000000e+00
1541.0
15
TraesCS2A01G328400
chr2D
86.519
1350
131
23
1
1331
427783722
427785039
0.000000e+00
1437.0
16
TraesCS2A01G328400
chr2D
90.153
914
73
12
3238
4144
427927958
427928861
0.000000e+00
1173.0
17
TraesCS2A01G328400
chr2D
89.655
841
59
13
2934
3747
427945149
427945988
0.000000e+00
1046.0
18
TraesCS2A01G328400
chr2D
94.855
311
16
0
2933
3243
427925928
427926238
1.770000e-133
486.0
19
TraesCS2A01G328400
chr2D
88.038
418
37
6
2938
3343
427785041
427785457
2.280000e-132
483.0
20
TraesCS2A01G328400
chr2D
79.147
211
22
9
3806
4016
427785622
427785810
4.430000e-25
126.0
21
TraesCS2A01G328400
chr2D
97.222
72
2
0
4152
4223
427911557
427911628
5.730000e-24
122.0
22
TraesCS2A01G328400
chr2D
97.222
72
2
0
4152
4223
427929031
427929102
5.730000e-24
122.0
23
TraesCS2A01G328400
chr2B
87.803
1361
119
13
1
1332
504769247
504770589
0.000000e+00
1550.0
24
TraesCS2A01G328400
chr2B
86.852
1369
111
23
1
1332
512358783
512357447
0.000000e+00
1467.0
25
TraesCS2A01G328400
chr2B
88.586
1139
83
13
2933
4062
512357451
512356351
0.000000e+00
1339.0
26
TraesCS2A01G328400
chr2B
91.489
846
62
5
2933
3771
504770585
504771427
0.000000e+00
1155.0
27
TraesCS2A01G328400
chr2B
86.765
884
100
10
3
876
512365135
512364259
0.000000e+00
968.0
28
TraesCS2A01G328400
chr2B
88.220
747
60
9
1730
2462
773559861
773560593
0.000000e+00
867.0
29
TraesCS2A01G328400
chr2B
87.586
290
28
4
3774
4062
504771981
504772263
3.150000e-86
329.0
30
TraesCS2A01G328400
chr7A
88.221
798
62
9
1732
2506
78567652
78566864
0.000000e+00
924.0
31
TraesCS2A01G328400
chr7A
84.178
651
59
16
1821
2456
643774716
643775337
3.640000e-165
592.0
32
TraesCS2A01G328400
chr7A
83.634
666
63
16
1807
2456
643775967
643776602
6.080000e-163
584.0
33
TraesCS2A01G328400
chr6A
89.243
753
61
6
1730
2468
448648254
448647508
0.000000e+00
924.0
34
TraesCS2A01G328400
chr6A
80.592
608
61
28
2112
2668
317156623
317156022
2.350000e-112
416.0
35
TraesCS2A01G328400
chr6A
85.608
403
39
9
1978
2362
187728917
187729318
5.080000e-109
405.0
36
TraesCS2A01G328400
chr4A
88.331
737
64
14
1730
2452
22533725
22534453
0.000000e+00
865.0
37
TraesCS2A01G328400
chr4A
86.486
555
55
7
1734
2284
441825533
441824995
3.640000e-165
592.0
38
TraesCS2A01G328400
chr4A
86.444
450
53
8
1727
2171
244914321
244914767
1.770000e-133
486.0
39
TraesCS2A01G328400
chr4A
87.407
135
6
10
2567
2694
625092833
625092703
1.220000e-30
145.0
40
TraesCS2A01G328400
chr1A
87.370
768
57
13
1730
2476
31815926
31815178
0.000000e+00
845.0
41
TraesCS2A01G328400
chr7B
87.635
647
51
10
1828
2451
658023537
658024177
0.000000e+00
725.0
42
TraesCS2A01G328400
chr5B
89.251
521
41
6
1730
2241
592748076
592747562
4.600000e-179
638.0
43
TraesCS2A01G328400
chr5B
86.712
444
37
11
1978
2406
319312857
319312421
1.370000e-129
473.0
44
TraesCS2A01G328400
chr5B
85.654
237
19
4
2230
2452
592741528
592741293
7.060000e-58
235.0
45
TraesCS2A01G328400
chr6B
93.824
421
17
3
1333
1745
151910802
151911221
3.580000e-175
625.0
46
TraesCS2A01G328400
chr6B
90.150
467
36
5
1333
1792
151909580
151910043
2.170000e-167
599.0
47
TraesCS2A01G328400
chr6B
92.027
439
14
8
2483
2904
151910787
151911221
7.820000e-167
597.0
48
TraesCS2A01G328400
chr6B
89.882
425
25
7
2497
2906
151909579
151910000
8.040000e-147
531.0
49
TraesCS2A01G328400
chr6D
85.769
527
59
10
1978
2502
343477182
343477694
1.030000e-150
544.0
50
TraesCS2A01G328400
chr6D
96.610
59
2
0
2448
2506
367105434
367105376
9.660000e-17
99.0
51
TraesCS2A01G328400
chr5A
87.257
463
37
14
1730
2179
133508110
133507657
3.770000e-140
508.0
52
TraesCS2A01G328400
chr7D
84.162
543
56
15
1978
2506
627818042
627818568
2.270000e-137
499.0
53
TraesCS2A01G328400
chr5D
87.359
443
36
6
1978
2406
18158608
18159044
1.360000e-134
490.0
54
TraesCS2A01G328400
chr5D
85.981
214
12
10
2449
2658
23109727
23109926
3.310000e-51
213.0
55
TraesCS2A01G328400
chr5D
86.957
138
8
7
2527
2658
23108660
23108793
3.400000e-31
147.0
56
TraesCS2A01G328400
chr4D
82.993
588
47
18
2102
2650
351689235
351688662
2.280000e-132
483.0
57
TraesCS2A01G328400
chr4D
93.141
277
13
3
1333
1604
238023996
238024271
6.580000e-108
401.0
58
TraesCS2A01G328400
chr4D
92.419
277
12
4
2498
2768
238023996
238024269
1.840000e-103
387.0
59
TraesCS2A01G328400
chr1D
86.456
443
40
6
1978
2406
14314454
14314018
6.390000e-128
468.0
60
TraesCS2A01G328400
chr1D
80.000
285
37
17
2448
2721
395094621
395094896
4.310000e-45
193.0
61
TraesCS2A01G328400
chr3B
88.852
305
29
4
2165
2468
94484220
94483920
1.850000e-98
370.0
62
TraesCS2A01G328400
chr3B
95.161
62
3
0
2447
2508
36434285
36434346
9.660000e-17
99.0
63
TraesCS2A01G328400
chr3D
82.036
167
16
11
2448
2606
390047465
390047305
3.430000e-26
130.0
64
TraesCS2A01G328400
chr3D
80.838
167
18
11
2448
2606
390045632
390045472
7.420000e-23
119.0
65
TraesCS2A01G328400
chr3D
77.647
170
23
15
2454
2609
69914210
69914042
5.820000e-14
89.8
66
TraesCS2A01G328400
chrUn
80.272
147
21
8
2448
2590
126797668
126797810
2.080000e-18
104.0
67
TraesCS2A01G328400
chrUn
93.846
65
4
0
1422
1486
146408994
146408930
9.660000e-17
99.0
68
TraesCS2A01G328400
chrUn
93.333
60
4
0
1427
1486
146421475
146421416
5.820000e-14
89.8
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
TraesCS2A01G328400
chr2A
559833352
559837574
4222
True
3047.000000
7799
96.238000
1
4223
3
chr2A.!!$R5
4222
1
TraesCS2A01G328400
chr2A
559776487
559779351
2864
True
1133.000000
1465
91.941000
1
4223
3
chr2A.!!$R4
4222
2
TraesCS2A01G328400
chr2A
559703403
559704427
1024
True
1092.000000
1092
86.080000
2977
4016
1
chr2A.!!$R1
1039
3
TraesCS2A01G328400
chr2A
559740648
559742823
2175
True
818.500000
885
88.834500
1
1331
2
chr2A.!!$R3
1330
4
TraesCS2A01G328400
chr2A
564075026
564075702
676
True
643.000000
643
84.457000
1807
2462
1
chr2A.!!$R2
655
5
TraesCS2A01G328400
chr2D
427943847
427945988
2141
False
1406.000000
1766
90.306000
1
3747
2
chr2D.!!$F4
3746
6
TraesCS2A01G328400
chr2D
427905287
427911628
6341
False
1235.500000
1659
92.388750
1
4223
4
chr2D.!!$F2
4222
7
TraesCS2A01G328400
chr2D
427924619
427929102
4483
False
887.250000
1768
93.279750
1
4223
4
chr2D.!!$F3
4222
8
TraesCS2A01G328400
chr2D
427783722
427785810
2088
False
682.000000
1437
84.568000
1
4016
3
chr2D.!!$F1
4015
9
TraesCS2A01G328400
chr2B
512356351
512358783
2432
True
1403.000000
1467
87.719000
1
4062
2
chr2B.!!$R2
4061
10
TraesCS2A01G328400
chr2B
504769247
504772263
3016
False
1011.333333
1550
88.959333
1
4062
3
chr2B.!!$F2
4061
11
TraesCS2A01G328400
chr2B
512364259
512365135
876
True
968.000000
968
86.765000
3
876
1
chr2B.!!$R1
873
12
TraesCS2A01G328400
chr2B
773559861
773560593
732
False
867.000000
867
88.220000
1730
2462
1
chr2B.!!$F1
732
13
TraesCS2A01G328400
chr7A
78566864
78567652
788
True
924.000000
924
88.221000
1732
2506
1
chr7A.!!$R1
774
14
TraesCS2A01G328400
chr7A
643774716
643776602
1886
False
588.000000
592
83.906000
1807
2456
2
chr7A.!!$F1
649
15
TraesCS2A01G328400
chr6A
448647508
448648254
746
True
924.000000
924
89.243000
1730
2468
1
chr6A.!!$R2
738
16
TraesCS2A01G328400
chr6A
317156022
317156623
601
True
416.000000
416
80.592000
2112
2668
1
chr6A.!!$R1
556
17
TraesCS2A01G328400
chr4A
22533725
22534453
728
False
865.000000
865
88.331000
1730
2452
1
chr4A.!!$F1
722
18
TraesCS2A01G328400
chr4A
441824995
441825533
538
True
592.000000
592
86.486000
1734
2284
1
chr4A.!!$R1
550
19
TraesCS2A01G328400
chr1A
31815178
31815926
748
True
845.000000
845
87.370000
1730
2476
1
chr1A.!!$R1
746
20
TraesCS2A01G328400
chr7B
658023537
658024177
640
False
725.000000
725
87.635000
1828
2451
1
chr7B.!!$F1
623
21
TraesCS2A01G328400
chr5B
592747562
592748076
514
True
638.000000
638
89.251000
1730
2241
1
chr5B.!!$R3
511
22
TraesCS2A01G328400
chr6B
151909579
151911221
1642
False
588.000000
625
91.470750
1333
2906
4
chr6B.!!$F1
1573
23
TraesCS2A01G328400
chr6D
343477182
343477694
512
False
544.000000
544
85.769000
1978
2502
1
chr6D.!!$F1
524
24
TraesCS2A01G328400
chr7D
627818042
627818568
526
False
499.000000
499
84.162000
1978
2506
1
chr7D.!!$F1
528
25
TraesCS2A01G328400
chr4D
351688662
351689235
573
True
483.000000
483
82.993000
2102
2650
1
chr4D.!!$R1
548
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.