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
TraesCS1D01G341000
chr1D
100.000
8961
0
0
1
8961
430573413
430564453
0.000000e+00
16548.0
1
TraesCS1D01G341000
chr1D
86.158
773
92
12
788
1558
376058133
376057374
0.000000e+00
821.0
2
TraesCS1D01G341000
chr1D
84.407
776
106
12
787
1558
376066358
376065594
0.000000e+00
749.0
3
TraesCS1D01G341000
chr1D
84.884
258
33
2
5895
6152
430569589
430569338
1.150000e-63
255.0
4
TraesCS1D01G341000
chr1D
73.313
652
139
29
4580
5212
430566492
430565857
3.280000e-49
207.0
5
TraesCS1D01G341000
chr1D
73.313
652
139
29
6922
7557
430568834
430568202
3.280000e-49
207.0
6
TraesCS1D01G341000
chr1D
82.946
129
22
0
5563
5691
430569627
430569499
5.680000e-22
117.0
7
TraesCS1D01G341000
chr1A
94.468
8460
283
53
545
8961
528673284
528664967
0.000000e+00
12859.0
8
TraesCS1D01G341000
chr1A
95.513
468
20
1
1
468
528673750
528673284
0.000000e+00
747.0
9
TraesCS1D01G341000
chr1A
87.108
574
67
5
788
1361
475305167
475304601
2.110000e-180
643.0
10
TraesCS1D01G341000
chr1A
85.837
233
30
1
5896
6128
528670045
528669816
2.500000e-60
244.0
11
TraesCS1D01G341000
chr1A
74.423
563
107
27
5002
5548
528666554
528666013
3.280000e-49
207.0
12
TraesCS1D01G341000
chr1A
82.171
129
23
0
5563
5691
528670084
528669956
2.640000e-20
111.0
13
TraesCS1D01G341000
chr1A
86.667
75
7
2
6461
6534
350162571
350162499
7.460000e-11
80.5
14
TraesCS1D01G341000
chr1B
97.778
7245
128
18
1
7238
581699394
581692176
0.000000e+00
12456.0
15
TraesCS1D01G341000
chr1B
94.114
1699
76
11
7265
8961
581692180
581690504
0.000000e+00
2562.0
16
TraesCS1D01G341000
chr1B
86.435
575
69
7
788
1361
502631982
502631416
9.880000e-174
621.0
17
TraesCS1D01G341000
chr1B
84.884
258
33
2
5895
6152
581695572
581695321
1.150000e-63
255.0
18
TraesCS1D01G341000
chr1B
84.977
213
26
5
5002
5212
581692096
581691888
2.530000e-50
211.0
19
TraesCS1D01G341000
chr1B
72.471
603
102
43
7261
7840
581694476
581693915
1.570000e-27
135.0
20
TraesCS1D01G341000
chr1B
82.946
129
22
0
5563
5691
581695610
581695482
5.680000e-22
117.0
21
TraesCS1D01G341000
chr3B
82.767
2356
316
44
2299
4615
679517
677213
0.000000e+00
2019.0
22
TraesCS1D01G341000
chr3B
86.595
1201
137
11
2873
4063
921195
922381
0.000000e+00
1304.0
23
TraesCS1D01G341000
chr3B
82.166
1071
135
28
638
1669
919041
920094
0.000000e+00
869.0
24
TraesCS1D01G341000
chr3B
81.869
1070
145
22
2928
3986
611879
612910
0.000000e+00
856.0
25
TraesCS1D01G341000
chr3B
87.483
743
87
4
2873
3613
904748
905486
0.000000e+00
852.0
26
TraesCS1D01G341000
chr3B
82.659
692
91
14
7318
7987
676296
675612
3.600000e-163
586.0
27
TraesCS1D01G341000
chr3B
81.268
694
85
23
4110
4791
906565
907225
3.710000e-143
520.0
28
TraesCS1D01G341000
chr3B
81.268
694
85
23
4110
4791
922380
923040
3.710000e-143
520.0
29
TraesCS1D01G341000
chr3B
75.983
916
147
49
7623
8506
571895
572769
1.080000e-108
405.0
30
TraesCS1D01G341000
chr3B
79.275
579
53
35
2165
2706
920366
920914
8.620000e-90
342.0
31
TraesCS1D01G341000
chr3B
80.429
373
47
16
100
464
110455264
110454910
2.480000e-65
261.0
32
TraesCS1D01G341000
chr3B
89.205
176
19
0
7097
7272
676467
676292
4.210000e-53
220.0
33
TraesCS1D01G341000
chr3B
85.000
200
28
2
5890
6087
906321
906520
1.530000e-47
202.0
34
TraesCS1D01G341000
chr3B
85.000
200
28
2
5890
6087
922136
922335
1.530000e-47
202.0
35
TraesCS1D01G341000
chr3B
82.158
241
36
4
7645
7880
907447
907685
5.490000e-47
200.0
36
TraesCS1D01G341000
chr3B
81.743
241
37
4
7645
7880
923262
923500
2.550000e-45
195.0
37
TraesCS1D01G341000
chr3B
86.188
181
23
2
6536
6715
544928724
544928545
2.550000e-45
195.0
38
TraesCS1D01G341000
chr3B
80.224
268
39
8
6460
6715
250139395
250139130
1.190000e-43
189.0
39
TraesCS1D01G341000
chr3B
85.083
181
25
2
6536
6715
544836353
544836174
5.530000e-42
183.0
40
TraesCS1D01G341000
chr3B
85.065
154
21
2
6895
7047
676621
676469
1.200000e-33
156.0
41
TraesCS1D01G341000
chr3B
83.908
87
4
1
2796
2882
920970
921046
3.470000e-09
75.0
42
TraesCS1D01G341000
chr3A
86.279
1873
196
25
2165
4017
1209555
1211386
0.000000e+00
1978.0
43
TraesCS1D01G341000
chr3A
83.103
870
119
12
813
1669
1200567
1201421
0.000000e+00
767.0
44
TraesCS1D01G341000
chr3A
76.471
1513
235
74
7042
8507
1067426
1068864
0.000000e+00
710.0
45
TraesCS1D01G341000
chr3A
79.368
475
69
16
1
466
77545462
77545008
3.140000e-79
307.0
46
TraesCS1D01G341000
chr3A
85.354
198
28
1
5890
6087
1211190
1211386
4.240000e-48
204.0
47
TraesCS1D01G341000
chrUn
86.203
1725
199
20
2508
4220
31955838
31954141
0.000000e+00
1831.0
48
TraesCS1D01G341000
chrUn
86.872
1135
124
12
2850
3983
31996338
31997448
0.000000e+00
1247.0
49
TraesCS1D01G341000
chrUn
86.696
1135
123
15
2850
3983
269076889
269075782
0.000000e+00
1234.0
50
TraesCS1D01G341000
chrUn
82.260
1071
134
28
638
1669
321410780
321409727
0.000000e+00
874.0
51
TraesCS1D01G341000
chrUn
82.770
621
69
22
2200
2806
31995740
31996336
3.710000e-143
520.0
52
TraesCS1D01G341000
chrUn
82.126
621
73
22
2200
2806
269077487
269076891
1.740000e-136
497.0
53
TraesCS1D01G341000
chrUn
80.923
650
71
21
7314
7934
31870652
31871277
1.760000e-126
464.0
54
TraesCS1D01G341000
chrUn
87.622
307
29
4
7318
7617
31948343
31948039
1.850000e-91
348.0
55
TraesCS1D01G341000
chrUn
79.275
579
53
35
2165
2706
321409455
321408907
8.620000e-90
342.0
56
TraesCS1D01G341000
chrUn
83.110
373
41
14
2437
2806
401018626
401018979
4.040000e-83
320.0
57
TraesCS1D01G341000
chrUn
80.605
397
68
3
6585
6980
31953284
31952896
1.890000e-76
298.0
58
TraesCS1D01G341000
chrUn
81.395
129
24
0
5563
5691
31997252
31997380
1.230000e-18
106.0
59
TraesCS1D01G341000
chrUn
81.395
129
24
0
5563
5691
269075978
269075850
1.230000e-18
106.0
60
TraesCS1D01G341000
chrUn
81.395
129
24
0
5563
5691
401019892
401020020
1.230000e-18
106.0
61
TraesCS1D01G341000
chrUn
83.908
87
4
1
2796
2882
321408851
321408775
3.470000e-09
75.0
62
TraesCS1D01G341000
chr3D
88.286
1400
144
12
2832
4220
3780198
3781588
0.000000e+00
1659.0
63
TraesCS1D01G341000
chr3D
77.152
1313
179
67
7036
8312
3856721
3855494
0.000000e+00
651.0
64
TraesCS1D01G341000
chr3D
80.739
758
90
29
7042
7780
3908225
3907505
2.850000e-149
540.0
65
TraesCS1D01G341000
chr3D
83.125
480
62
10
4300
4774
3781586
3782051
3.870000e-113
420.0
66
TraesCS1D01G341000
chr3D
79.138
580
85
18
7436
7987
3902878
3902307
1.420000e-97
368.0
67
TraesCS1D01G341000
chr3D
80.083
482
65
14
7532
7987
3891481
3891005
6.710000e-86
329.0
68
TraesCS1D01G341000
chr3D
84.918
305
34
7
7318
7617
3782963
3783260
1.890000e-76
298.0
69
TraesCS1D01G341000
chr3D
79.095
464
70
16
1
455
66526529
66526084
2.450000e-75
294.0
70
TraesCS1D01G341000
chr3D
83.083
266
31
9
6460
6715
171148373
171148112
7.000000e-56
230.0
71
TraesCS1D01G341000
chr3D
82.625
259
32
7
2141
2397
3779698
3779945
5.450000e-52
217.0
72
TraesCS1D01G341000
chr3D
83.871
186
27
3
6536
6719
418561632
418561448
3.330000e-39
174.0
73
TraesCS1D01G341000
chr3D
92.553
94
4
2
459
549
545547789
545547882
2.030000e-26
132.0
74
TraesCS1D01G341000
chr3D
84.615
130
18
2
5563
5691
3781150
3781278
2.630000e-25
128.0
75
TraesCS1D01G341000
chr3D
94.030
67
3
1
7909
7975
3783247
3783312
5.720000e-17
100.0
76
TraesCS1D01G341000
chr2B
82.938
211
25
6
6535
6743
728387545
728387746
7.150000e-41
180.0
77
TraesCS1D01G341000
chr7D
83.871
186
27
3
6531
6715
449232611
449232794
3.330000e-39
174.0
78
TraesCS1D01G341000
chr7D
92.632
95
3
2
462
553
485090875
485090968
5.640000e-27
134.0
79
TraesCS1D01G341000
chr7D
90.099
101
7
1
459
556
24045715
24045615
2.630000e-25
128.0
80
TraesCS1D01G341000
chr7D
86.842
76
7
2
6461
6535
72952271
72952344
2.070000e-11
82.4
81
TraesCS1D01G341000
chr7D
86.667
75
7
2
6461
6534
202244299
202244227
7.460000e-11
80.5
82
TraesCS1D01G341000
chr7D
85.897
78
8
2
6458
6534
436142518
436142593
7.460000e-11
80.5
83
TraesCS1D01G341000
chr7D
86.667
75
7
2
6461
6534
449593615
449593543
7.460000e-11
80.5
84
TraesCS1D01G341000
chr5D
94.565
92
2
1
461
549
373214568
373214659
1.210000e-28
139.0
85
TraesCS1D01G341000
chr4B
92.632
95
4
3
458
549
180553962
180553868
5.640000e-27
134.0
86
TraesCS1D01G341000
chr7A
91.667
96
5
1
460
552
136806195
136806100
7.300000e-26
130.0
87
TraesCS1D01G341000
chr4D
91.667
96
4
3
454
546
225215515
225215609
7.300000e-26
130.0
88
TraesCS1D01G341000
chr4D
89.320
103
6
3
465
563
403409531
403409632
3.400000e-24
124.0
89
TraesCS1D01G341000
chr2D
88.158
76
6
2
6461
6535
518263458
518263531
4.460000e-13
87.9
90
TraesCS1D01G341000
chr6D
86.667
75
6
2
6461
6535
125088537
125088467
7.460000e-11
80.5
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
TraesCS1D01G341000
chr1D
430564453
430573413
8960
True
16548.000000
16548
100.000000
1
8961
1
chr1D.!!$R3
8960
1
TraesCS1D01G341000
chr1D
376057374
376058133
759
True
821.000000
821
86.158000
788
1558
1
chr1D.!!$R1
770
2
TraesCS1D01G341000
chr1D
376065594
376066358
764
True
749.000000
749
84.407000
787
1558
1
chr1D.!!$R2
771
3
TraesCS1D01G341000
chr1A
528664967
528673284
8317
True
12859.000000
12859
94.468000
545
8961
1
chr1A.!!$R3
8416
4
TraesCS1D01G341000
chr1A
475304601
475305167
566
True
643.000000
643
87.108000
788
1361
1
chr1A.!!$R2
573
5
TraesCS1D01G341000
chr1A
528666013
528673750
7737
True
327.250000
747
84.486000
1
6128
4
chr1A.!!$R4
6127
6
TraesCS1D01G341000
chr1B
581690504
581699394
8890
True
5076.333333
12456
92.289667
1
8961
3
chr1B.!!$R2
8960
7
TraesCS1D01G341000
chr1B
502631416
502631982
566
True
621.000000
621
86.435000
788
1361
1
chr1B.!!$R1
573
8
TraesCS1D01G341000
chr3B
611879
612910
1031
False
856.000000
856
81.869000
2928
3986
1
chr3B.!!$F2
1058
9
TraesCS1D01G341000
chr3B
675612
679517
3905
True
745.250000
2019
84.924000
2299
7987
4
chr3B.!!$R5
5688
10
TraesCS1D01G341000
chr3B
919041
923500
4459
False
501.000000
1304
82.850714
638
7880
7
chr3B.!!$F4
7242
11
TraesCS1D01G341000
chr3B
904748
907685
2937
False
443.500000
852
83.977250
2873
7880
4
chr3B.!!$F3
5007
12
TraesCS1D01G341000
chr3B
571895
572769
874
False
405.000000
405
75.983000
7623
8506
1
chr3B.!!$F1
883
13
TraesCS1D01G341000
chr3A
1209555
1211386
1831
False
1091.000000
1978
85.816500
2165
6087
2
chr3A.!!$F3
3922
14
TraesCS1D01G341000
chr3A
1200567
1201421
854
False
767.000000
767
83.103000
813
1669
1
chr3A.!!$F2
856
15
TraesCS1D01G341000
chr3A
1067426
1068864
1438
False
710.000000
710
76.471000
7042
8507
1
chr3A.!!$F1
1465
16
TraesCS1D01G341000
chrUn
31952896
31955838
2942
True
1064.500000
1831
83.404000
2508
6980
2
chrUn.!!$R2
4472
17
TraesCS1D01G341000
chrUn
31995740
31997448
1708
False
624.333333
1247
83.679000
2200
5691
3
chrUn.!!$F2
3491
18
TraesCS1D01G341000
chrUn
269075782
269077487
1705
True
612.333333
1234
83.405667
2200
5691
3
chrUn.!!$R3
3491
19
TraesCS1D01G341000
chrUn
31870652
31871277
625
False
464.000000
464
80.923000
7314
7934
1
chrUn.!!$F1
620
20
TraesCS1D01G341000
chrUn
321408775
321410780
2005
True
430.333333
874
81.814333
638
2882
3
chrUn.!!$R4
2244
21
TraesCS1D01G341000
chrUn
401018626
401020020
1394
False
213.000000
320
82.252500
2437
5691
2
chrUn.!!$F3
3254
22
TraesCS1D01G341000
chr3D
3855494
3856721
1227
True
651.000000
651
77.152000
7036
8312
1
chr3D.!!$R1
1276
23
TraesCS1D01G341000
chr3D
3907505
3908225
720
True
540.000000
540
80.739000
7042
7780
1
chr3D.!!$R4
738
24
TraesCS1D01G341000
chr3D
3779698
3783312
3614
False
470.333333
1659
86.266500
2141
7975
6
chr3D.!!$F2
5834
25
TraesCS1D01G341000
chr3D
3902307
3902878
571
True
368.000000
368
79.138000
7436
7987
1
chr3D.!!$R3
551
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.