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
TraesCS4D01G166200
chr4D
100.000
7996
0
0
1
7996
280175022
280183017
0.000000e+00
14766.0
1
TraesCS4D01G166200
chr4D
94.668
4782
168
43
2893
7643
108630465
108625740
0.000000e+00
7337.0
2
TraesCS4D01G166200
chr4D
94.340
848
24
12
1
827
302347474
302346630
0.000000e+00
1279.0
3
TraesCS4D01G166200
chr4D
96.255
721
26
1
990
1709
108631178
108630458
0.000000e+00
1181.0
4
TraesCS4D01G166200
chr4D
94.554
202
11
0
7795
7996
108610301
108610100
6.020000e-81
313.0
5
TraesCS4D01G166200
chr4D
81.271
299
37
13
7524
7814
256642437
256642724
2.900000e-54
224.0
6
TraesCS4D01G166200
chr4D
93.458
107
7
0
4685
4791
259497365
259497259
8.310000e-35
159.0
7
TraesCS4D01G166200
chr4D
91.667
60
5
0
938
997
108632464
108632405
5.140000e-12
84.2
8
TraesCS4D01G166200
chr4D
100.000
35
0
0
7291
7325
280182277
280182311
1.860000e-06
65.8
9
TraesCS4D01G166200
chr4D
100.000
35
0
0
7256
7290
280182312
280182346
1.860000e-06
65.8
10
TraesCS4D01G166200
chr4A
96.447
4222
124
18
3050
7259
467682575
467686782
0.000000e+00
6942.0
11
TraesCS4D01G166200
chr4A
96.489
712
20
4
999
1706
467681554
467682264
0.000000e+00
1171.0
12
TraesCS4D01G166200
chr4A
88.105
765
78
8
1706
2467
405552457
405551703
0.000000e+00
896.0
13
TraesCS4D01G166200
chr4A
84.830
501
57
8
7319
7813
467749005
467749492
3.350000e-133
486.0
14
TraesCS4D01G166200
chr4A
92.195
205
16
0
7792
7996
467749502
467749706
2.820000e-74
291.0
15
TraesCS4D01G166200
chr4A
98.561
139
2
0
2893
3031
467682260
467682398
6.200000e-61
246.0
16
TraesCS4D01G166200
chr4A
90.000
120
11
1
4676
4795
590945700
590945818
3.860000e-33
154.0
17
TraesCS4D01G166200
chr6B
95.135
2631
87
21
4800
7416
69444500
69441897
0.000000e+00
4111.0
18
TraesCS4D01G166200
chr6B
92.435
846
39
13
1
827
79274491
79273652
0.000000e+00
1184.0
19
TraesCS4D01G166200
chr6B
92.737
716
18
10
1017
1709
69446910
69446206
0.000000e+00
1003.0
20
TraesCS4D01G166200
chr6B
96.769
588
10
4
3387
3967
69445529
69444944
0.000000e+00
972.0
21
TraesCS4D01G166200
chr6B
98.618
434
6
0
4019
4452
69444944
69444511
0.000000e+00
769.0
22
TraesCS4D01G166200
chr6B
90.019
531
18
11
2893
3390
69446213
69445685
0.000000e+00
654.0
23
TraesCS4D01G166200
chr6B
88.685
327
34
3
4789
5114
377933308
377933632
5.820000e-106
396.0
24
TraesCS4D01G166200
chr6B
83.108
444
26
10
7481
7883
69441895
69441460
7.630000e-95
359.0
25
TraesCS4D01G166200
chr6B
92.222
90
7
0
938
1027
69448371
69448282
2.340000e-25
128.0
26
TraesCS4D01G166200
chr3A
92.137
1170
74
9
1740
2893
662416780
662417947
0.000000e+00
1635.0
27
TraesCS4D01G166200
chr3A
87.234
329
36
4
4788
5114
264032029
264031705
3.520000e-98
370.0
28
TraesCS4D01G166200
chr3A
92.045
264
18
3
4332
4594
664692847
664693108
1.270000e-97
368.0
29
TraesCS4D01G166200
chr3A
92.661
109
8
0
4685
4793
503822393
503822285
2.990000e-34
158.0
30
TraesCS4D01G166200
chr5D
88.411
1208
116
12
1702
2891
216018749
216019950
0.000000e+00
1434.0
31
TraesCS4D01G166200
chr5D
93.839
844
31
11
1
827
391047116
391047955
0.000000e+00
1251.0
32
TraesCS4D01G166200
chr5D
81.601
1212
186
24
1707
2893
543654193
543655392
0.000000e+00
968.0
33
TraesCS4D01G166200
chr5D
89.535
258
25
2
5130
5386
201664577
201664321
7.740000e-85
326.0
34
TraesCS4D01G166200
chr5D
89.375
160
14
2
5622
5779
215301982
215302140
1.760000e-46
198.0
35
TraesCS4D01G166200
chr5D
93.519
108
7
0
4684
4791
371860609
371860716
2.310000e-35
161.0
36
TraesCS4D01G166200
chr6D
87.262
1209
128
10
1702
2893
83206710
83207909
0.000000e+00
1356.0
37
TraesCS4D01G166200
chr6D
88.450
329
33
5
4788
5114
276144719
276144394
7.520000e-105
392.0
38
TraesCS4D01G166200
chr6D
91.288
264
20
3
4332
4594
423215391
423215652
2.740000e-94
357.0
39
TraesCS4D01G166200
chr6D
87.938
257
29
2
5128
5383
175718544
175718289
1.300000e-77
302.0
40
TraesCS4D01G166200
chr6D
90.777
206
18
1
7792
7996
361546319
361546524
2.840000e-69
274.0
41
TraesCS4D01G166200
chr6D
90.476
147
14
0
5630
5776
386931496
386931642
2.280000e-45
195.0
42
TraesCS4D01G166200
chr6D
92.661
109
8
0
4683
4791
302113642
302113750
2.990000e-34
158.0
43
TraesCS4D01G166200
chr4B
87.292
1204
132
10
1706
2893
562551031
562549833
0.000000e+00
1356.0
44
TraesCS4D01G166200
chr4B
93.197
441
19
6
396
827
45203464
45203026
8.750000e-179
638.0
45
TraesCS4D01G166200
chr7D
94.681
846
21
9
1
827
635162657
635161817
0.000000e+00
1291.0
46
TraesCS4D01G166200
chr7D
93.288
730
26
11
119
827
633938101
633938828
0.000000e+00
1055.0
47
TraesCS4D01G166200
chr7D
85.747
884
106
10
2027
2893
500158832
500159712
0.000000e+00
917.0
48
TraesCS4D01G166200
chr7D
90.132
152
15
0
5626
5777
156796841
156796992
1.760000e-46
198.0
49
TraesCS4D01G166200
chr7D
89.103
156
16
1
5627
5781
379326469
379326314
8.190000e-45
193.0
50
TraesCS4D01G166200
chr3D
94.543
843
22
10
1
827
457396009
457395175
0.000000e+00
1280.0
51
TraesCS4D01G166200
chr3D
93.118
465
14
7
1
451
896359
895899
0.000000e+00
665.0
52
TraesCS4D01G166200
chr3D
92.661
109
8
0
4685
4793
379826241
379826349
2.990000e-34
158.0
53
TraesCS4D01G166200
chr5B
85.866
1224
132
15
1704
2893
659093238
659092022
0.000000e+00
1264.0
54
TraesCS4D01G166200
chr7A
85.112
1209
155
10
1701
2893
183842924
183844123
0.000000e+00
1212.0
55
TraesCS4D01G166200
chr7A
93.026
846
30
12
1
829
24423815
24422982
0.000000e+00
1208.0
56
TraesCS4D01G166200
chr7A
89.449
853
54
21
1
827
16929983
16929141
0.000000e+00
1044.0
57
TraesCS4D01G166200
chr7A
91.698
265
17
4
4331
4594
515737512
515737772
5.900000e-96
363.0
58
TraesCS4D01G166200
chr7A
89.542
153
16
0
5624
5776
462978739
462978587
2.280000e-45
195.0
59
TraesCS4D01G166200
chr6A
83.951
1215
166
14
1705
2893
30205106
30203895
0.000000e+00
1136.0
60
TraesCS4D01G166200
chr6A
88.073
327
34
5
4789
5114
294645366
294645688
4.530000e-102
383.0
61
TraesCS4D01G166200
chr6A
88.350
206
23
1
7792
7996
502737135
502737340
6.200000e-61
246.0
62
TraesCS4D01G166200
chrUn
92.032
753
44
3
2042
2778
108750267
108749515
0.000000e+00
1044.0
63
TraesCS4D01G166200
chr2B
94.178
584
24
5
1
579
594259794
594260372
0.000000e+00
881.0
64
TraesCS4D01G166200
chr2B
87.156
327
36
4
4790
5114
333042515
333042837
4.560000e-97
366.0
65
TraesCS4D01G166200
chr2B
90.272
257
22
3
5128
5383
234367961
234367707
4.620000e-87
333.0
66
TraesCS4D01G166200
chr7B
92.105
266
18
3
4331
4595
173229520
173229783
9.800000e-99
372.0
67
TraesCS4D01G166200
chr7B
88.119
202
24
0
7795
7996
592178257
592178056
2.880000e-59
241.0
68
TraesCS4D01G166200
chr7B
80.198
303
39
12
7523
7813
478729999
478729706
2.920000e-49
207.0
69
TraesCS4D01G166200
chr7B
77.586
290
52
10
7524
7809
177877080
177877360
6.420000e-36
163.0
70
TraesCS4D01G166200
chr7B
91.304
115
10
0
4677
4791
357651476
357651590
2.990000e-34
158.0
71
TraesCS4D01G166200
chr3B
86.930
329
35
6
4788
5114
299132981
299133303
5.900000e-96
363.0
72
TraesCS4D01G166200
chr3B
80.872
298
41
7
7523
7813
472664095
472664383
3.760000e-53
220.0
73
TraesCS4D01G166200
chr1D
91.635
263
19
3
4332
4593
100462103
100461843
2.120000e-95
361.0
74
TraesCS4D01G166200
chr1D
75.594
463
92
13
7536
7988
286193883
286193432
8.130000e-50
209.0
75
TraesCS4D01G166200
chr1D
84.848
198
29
1
7791
7988
288080388
288080584
1.760000e-46
198.0
76
TraesCS4D01G166200
chr2D
91.603
262
17
5
4331
4590
74146852
74147110
2.740000e-94
357.0
77
TraesCS4D01G166200
chr2D
88.417
259
22
6
5128
5383
633320460
633320713
1.010000e-78
305.0
78
TraesCS4D01G166200
chr2D
87.938
257
29
2
5128
5383
177460083
177459828
1.300000e-77
302.0
79
TraesCS4D01G166200
chr2D
88.235
153
16
2
7791
7942
379295631
379295782
1.770000e-41
182.0
80
TraesCS4D01G166200
chr2D
83.696
184
29
1
7524
7706
345514134
345513951
1.070000e-38
172.0
81
TraesCS4D01G166200
chr5A
90.977
266
21
3
4331
4595
535518763
535518500
9.870000e-94
355.0
82
TraesCS4D01G166200
chr5A
91.667
60
4
1
3696
3755
642914198
642914140
1.850000e-11
82.4
83
TraesCS4D01G166200
chr2A
88.372
258
27
3
5128
5383
190317508
190317252
2.800000e-79
307.0
84
TraesCS4D01G166200
chr2A
89.655
203
21
0
7792
7994
381506526
381506728
7.960000e-65
259.0
85
TraesCS4D01G166200
chr2A
89.542
153
14
1
5624
5776
329688022
329688172
8.190000e-45
193.0
86
TraesCS4D01G166200
chr1A
77.413
487
57
24
7524
7972
13900713
13901184
2.880000e-59
241.0
87
TraesCS4D01G166200
chr1B
78.947
304
43
12
7520
7813
616137287
616137579
3.810000e-43
187.0
88
TraesCS4D01G166200
chr1B
76.589
299
50
11
7524
7813
242238112
242237825
6.470000e-31
147.0
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
TraesCS4D01G166200
chr4D
280175022
280183017
7995
False
4965.866667
14766
100.000000
1
7996
3
chr4D.!!$F2
7995
1
TraesCS4D01G166200
chr4D
108625740
108632464
6724
True
2867.400000
7337
94.196667
938
7643
3
chr4D.!!$R4
6705
2
TraesCS4D01G166200
chr4D
302346630
302347474
844
True
1279.000000
1279
94.340000
1
827
1
chr4D.!!$R3
826
3
TraesCS4D01G166200
chr4A
467681554
467686782
5228
False
2786.333333
6942
97.165667
999
7259
3
chr4A.!!$F2
6260
4
TraesCS4D01G166200
chr4A
405551703
405552457
754
True
896.000000
896
88.105000
1706
2467
1
chr4A.!!$R1
761
5
TraesCS4D01G166200
chr4A
467749005
467749706
701
False
388.500000
486
88.512500
7319
7996
2
chr4A.!!$F3
677
6
TraesCS4D01G166200
chr6B
79273652
79274491
839
True
1184.000000
1184
92.435000
1
827
1
chr6B.!!$R1
826
7
TraesCS4D01G166200
chr6B
69441460
69448371
6911
True
1142.285714
4111
92.658286
938
7883
7
chr6B.!!$R2
6945
8
TraesCS4D01G166200
chr3A
662416780
662417947
1167
False
1635.000000
1635
92.137000
1740
2893
1
chr3A.!!$F1
1153
9
TraesCS4D01G166200
chr5D
216018749
216019950
1201
False
1434.000000
1434
88.411000
1702
2891
1
chr5D.!!$F2
1189
10
TraesCS4D01G166200
chr5D
391047116
391047955
839
False
1251.000000
1251
93.839000
1
827
1
chr5D.!!$F4
826
11
TraesCS4D01G166200
chr5D
543654193
543655392
1199
False
968.000000
968
81.601000
1707
2893
1
chr5D.!!$F5
1186
12
TraesCS4D01G166200
chr6D
83206710
83207909
1199
False
1356.000000
1356
87.262000
1702
2893
1
chr6D.!!$F1
1191
13
TraesCS4D01G166200
chr4B
562549833
562551031
1198
True
1356.000000
1356
87.292000
1706
2893
1
chr4B.!!$R2
1187
14
TraesCS4D01G166200
chr7D
635161817
635162657
840
True
1291.000000
1291
94.681000
1
827
1
chr7D.!!$R2
826
15
TraesCS4D01G166200
chr7D
633938101
633938828
727
False
1055.000000
1055
93.288000
119
827
1
chr7D.!!$F3
708
16
TraesCS4D01G166200
chr7D
500158832
500159712
880
False
917.000000
917
85.747000
2027
2893
1
chr7D.!!$F2
866
17
TraesCS4D01G166200
chr3D
457395175
457396009
834
True
1280.000000
1280
94.543000
1
827
1
chr3D.!!$R2
826
18
TraesCS4D01G166200
chr5B
659092022
659093238
1216
True
1264.000000
1264
85.866000
1704
2893
1
chr5B.!!$R1
1189
19
TraesCS4D01G166200
chr7A
183842924
183844123
1199
False
1212.000000
1212
85.112000
1701
2893
1
chr7A.!!$F1
1192
20
TraesCS4D01G166200
chr7A
24422982
24423815
833
True
1208.000000
1208
93.026000
1
829
1
chr7A.!!$R2
828
21
TraesCS4D01G166200
chr7A
16929141
16929983
842
True
1044.000000
1044
89.449000
1
827
1
chr7A.!!$R1
826
22
TraesCS4D01G166200
chr6A
30203895
30205106
1211
True
1136.000000
1136
83.951000
1705
2893
1
chr6A.!!$R1
1188
23
TraesCS4D01G166200
chrUn
108749515
108750267
752
True
1044.000000
1044
92.032000
2042
2778
1
chrUn.!!$R1
736
24
TraesCS4D01G166200
chr2B
594259794
594260372
578
False
881.000000
881
94.178000
1
579
1
chr2B.!!$F2
578
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.