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
TraesCS6D01G156200
chr6D
100.000
6222
0
0
1
6222
132314569
132308348
0.000000e+00
11490.0
1
TraesCS6D01G156200
chr6D
98.169
2950
31
5
2358
5285
132413291
132410343
0.000000e+00
5127.0
2
TraesCS6D01G156200
chr6D
98.108
2061
29
3
1
2061
132415343
132413293
0.000000e+00
3581.0
3
TraesCS6D01G156200
chr6D
86.905
336
30
9
5644
5973
87083312
87083639
1.270000e-96
364.0
4
TraesCS6D01G156200
chr6D
87.227
321
34
4
5317
5634
87082946
87083262
5.930000e-95
359.0
5
TraesCS6D01G156200
chr6A
97.458
5310
98
12
1
5285
171461696
171456399
0.000000e+00
9023.0
6
TraesCS6D01G156200
chr6B
94.785
3030
115
14
606
3611
229729812
229726802
0.000000e+00
4680.0
7
TraesCS6D01G156200
chr6B
90.248
1610
99
26
3701
5272
229726803
229725214
0.000000e+00
2050.0
8
TraesCS6D01G156200
chr6B
93.475
613
27
7
1
608
229730438
229729834
0.000000e+00
898.0
9
TraesCS6D01G156200
chr2A
94.073
793
21
2
5285
6051
734964136
734964928
0.000000e+00
1181.0
10
TraesCS6D01G156200
chr2A
95.954
173
7
0
6047
6219
734966534
734966706
1.320000e-71
281.0
11
TraesCS6D01G156200
chr2A
81.273
267
30
14
2167
2423
386294347
386294603
1.370000e-46
198.0
12
TraesCS6D01G156200
chr5D
81.888
519
53
16
5644
6127
548285101
548284589
3.490000e-107
399.0
13
TraesCS6D01G156200
chr5D
85.890
326
32
6
5320
5634
548285473
548285151
9.990000e-88
335.0
14
TraesCS6D01G156200
chr5D
78.058
515
96
15
1156
1658
74090878
74090369
6.060000e-80
309.0
15
TraesCS6D01G156200
chr5D
80.385
260
44
7
2167
2420
315936231
315935973
2.290000e-44
191.0
16
TraesCS6D01G156200
chr5D
87.500
64
5
1
5660
5720
444310011
444309948
3.110000e-08
71.3
17
TraesCS6D01G156200
chr5B
81.801
522
49
20
5644
6127
594278964
594279477
4.520000e-106
396.0
18
TraesCS6D01G156200
chr5B
86.018
329
33
5
5317
5634
594278588
594278914
2.150000e-89
340.0
19
TraesCS6D01G156200
chr5B
78.860
421
79
8
1154
1571
78420696
78421109
6.140000e-70
276.0
20
TraesCS6D01G156200
chr1B
88.024
334
32
6
5645
5973
470894632
470894302
7.560000e-104
388.0
21
TraesCS6D01G156200
chr1B
86.025
322
39
5
5317
5634
470895008
470894689
2.150000e-89
340.0
22
TraesCS6D01G156200
chr1B
80.303
264
43
7
2169
2426
104349882
104349622
2.290000e-44
191.0
23
TraesCS6D01G156200
chr7A
87.574
338
31
8
5645
5973
672011539
672011874
1.270000e-101
381.0
24
TraesCS6D01G156200
chr7A
84.161
322
45
4
5317
5634
672011163
672011482
2.180000e-79
307.0
25
TraesCS6D01G156200
chr7A
84.112
107
15
2
2167
2271
700824169
700824063
1.100000e-17
102.0
26
TraesCS6D01G156200
chr4A
85.119
336
40
7
5644
5973
352129989
352129658
9.990000e-88
335.0
27
TraesCS6D01G156200
chr4A
89.205
176
16
2
5462
5634
352130214
352130039
3.780000e-52
217.0
28
TraesCS6D01G156200
chr4A
77.703
296
55
11
213
505
516487625
516487912
2.980000e-38
171.0
29
TraesCS6D01G156200
chr5A
76.693
502
104
11
1154
1648
69103998
69103503
3.700000e-67
267.0
30
TraesCS6D01G156200
chr4D
84.351
262
35
4
2167
2422
301756303
301756564
1.040000e-62
252.0
31
TraesCS6D01G156200
chr4D
75.974
308
58
15
212
512
67358128
67357830
1.810000e-30
145.0
32
TraesCS6D01G156200
chr4B
82.061
262
41
4
2167
2422
376157709
376157970
1.050000e-52
219.0
33
TraesCS6D01G156200
chr4B
77.104
297
53
14
213
501
99430382
99430671
2.320000e-34
158.0
34
TraesCS6D01G156200
chr4B
84.892
139
13
6
2168
2301
93286449
93286314
3.910000e-27
134.0
35
TraesCS6D01G156200
chr7B
91.262
103
9
0
5524
5626
641101276
641101174
2.340000e-29
141.0
36
TraesCS6D01G156200
chr7B
91.398
93
7
1
6130
6222
503117734
503117825
6.550000e-25
126.0
37
TraesCS6D01G156200
chr2D
92.000
100
8
0
5524
5623
191027678
191027777
2.340000e-29
141.0
38
TraesCS6D01G156200
chr2D
85.000
120
11
4
4877
4995
166197115
166197228
1.420000e-21
115.0
39
TraesCS6D01G156200
chr3D
84.286
140
20
2
2284
2422
159794640
159794502
1.090000e-27
135.0
40
TraesCS6D01G156200
chr1D
80.645
155
25
4
2258
2408
404253054
404253207
1.420000e-21
115.0
41
TraesCS6D01G156200
chr1D
76.437
174
33
7
2255
2422
478140149
478140320
3.090000e-13
87.9
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
TraesCS6D01G156200
chr6D
132308348
132314569
6221
True
11490.000000
11490
100.0000
1
6222
1
chr6D.!!$R1
6221
1
TraesCS6D01G156200
chr6D
132410343
132415343
5000
True
4354.000000
5127
98.1385
1
5285
2
chr6D.!!$R2
5284
2
TraesCS6D01G156200
chr6D
87082946
87083639
693
False
361.500000
364
87.0660
5317
5973
2
chr6D.!!$F1
656
3
TraesCS6D01G156200
chr6A
171456399
171461696
5297
True
9023.000000
9023
97.4580
1
5285
1
chr6A.!!$R1
5284
4
TraesCS6D01G156200
chr6B
229725214
229730438
5224
True
2542.666667
4680
92.8360
1
5272
3
chr6B.!!$R1
5271
5
TraesCS6D01G156200
chr2A
734964136
734966706
2570
False
731.000000
1181
95.0135
5285
6219
2
chr2A.!!$F2
934
6
TraesCS6D01G156200
chr5D
548284589
548285473
884
True
367.000000
399
83.8890
5320
6127
2
chr5D.!!$R4
807
7
TraesCS6D01G156200
chr5D
74090369
74090878
509
True
309.000000
309
78.0580
1156
1658
1
chr5D.!!$R1
502
8
TraesCS6D01G156200
chr5B
594278588
594279477
889
False
368.000000
396
83.9095
5317
6127
2
chr5B.!!$F2
810
9
TraesCS6D01G156200
chr1B
470894302
470895008
706
True
364.000000
388
87.0245
5317
5973
2
chr1B.!!$R2
656
10
TraesCS6D01G156200
chr7A
672011163
672011874
711
False
344.000000
381
85.8675
5317
5973
2
chr7A.!!$F1
656
11
TraesCS6D01G156200
chr4A
352129658
352130214
556
True
276.000000
335
87.1620
5462
5973
2
chr4A.!!$R1
511
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.