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
TraesCS5B01G160400
chr5B
100.000
3455
0
0
1361
4815
295383144
295379690
0.000000e+00
6381.0
1
TraesCS5B01G160400
chr5B
100.000
733
0
0
409
1141
295384096
295383364
0.000000e+00
1354.0
2
TraesCS5B01G160400
chr5B
100.000
126
0
0
1
126
295384504
295384379
2.900000e-57
233.0
3
TraesCS5B01G160400
chr5B
89.091
55
3
3
4609
4662
611866288
611866236
1.120000e-06
65.8
4
TraesCS5B01G160400
chr5A
93.816
3509
110
42
1361
4813
348720309
348716852
0.000000e+00
5179.0
5
TraesCS5B01G160400
chr5A
93.658
473
25
2
669
1141
348720830
348720363
0.000000e+00
702.0
6
TraesCS5B01G160400
chr5A
96.617
266
4
1
409
674
512393673
512393933
2.060000e-118
436.0
7
TraesCS5B01G160400
chr5A
94.515
237
12
1
434
669
512393265
512393029
9.850000e-97
364.0
8
TraesCS5B01G160400
chr5A
96.032
126
5
0
1
126
512393172
512393297
6.320000e-49
206.0
9
TraesCS5B01G160400
chr5A
77.833
203
37
8
4613
4813
350525984
350526180
8.470000e-23
119.0
10
TraesCS5B01G160400
chr5A
100.000
31
0
0
4611
4641
537248308
537248278
1.870000e-04
58.4
11
TraesCS5B01G160400
chr5D
93.005
1644
32
35
2585
4190
262840388
262838790
0.000000e+00
2322.0
12
TraesCS5B01G160400
chr5D
95.543
875
17
6
1361
2220
262841956
262841089
0.000000e+00
1380.0
13
TraesCS5B01G160400
chr5D
96.535
635
12
3
4189
4813
262838696
262838062
0.000000e+00
1042.0
14
TraesCS5B01G160400
chr5D
93.263
475
23
6
669
1141
262842477
262842010
0.000000e+00
691.0
15
TraesCS5B01G160400
chr5D
96.035
227
7
1
2286
2512
262840912
262840688
7.610000e-98
368.0
16
TraesCS5B01G160400
chr5D
88.172
93
1
4
2517
2599
262840629
262840537
8.530000e-18
102.0
17
TraesCS5B01G160400
chr5D
100.000
43
0
0
2232
2274
262841098
262841056
3.990000e-11
80.5
18
TraesCS5B01G160400
chr4B
96.923
260
5
1
409
668
633291467
633291211
2.660000e-117
433.0
19
TraesCS5B01G160400
chr4B
98.413
126
2
0
1
126
633292204
633292079
6.270000e-54
222.0
20
TraesCS5B01G160400
chr2A
96.124
258
4
2
412
669
283303974
283303723
2.680000e-112
416.0
21
TraesCS5B01G160400
chr2A
98.413
126
2
0
1
126
283304526
283304401
6.270000e-54
222.0
22
TraesCS5B01G160400
chr2A
88.889
54
3
3
4610
4662
725890649
725890598
4.020000e-06
63.9
23
TraesCS5B01G160400
chr4A
96.639
238
7
1
432
668
672516011
672516248
1.260000e-105
394.0
24
TraesCS5B01G160400
chr4A
94.561
239
11
2
432
668
32641326
32641088
7.610000e-98
368.0
25
TraesCS5B01G160400
chr7A
95.397
239
10
1
432
669
209404407
209404169
3.520000e-101
379.0
26
TraesCS5B01G160400
chr7A
94.262
244
8
3
430
669
209405243
209405484
7.610000e-98
368.0
27
TraesCS5B01G160400
chr7A
93.023
43
2
1
4770
4811
512257966
512258008
1.450000e-05
62.1
28
TraesCS5B01G160400
chr1A
93.416
243
10
3
430
668
45841523
45841283
5.930000e-94
355.0
29
TraesCS5B01G160400
chr1A
97.619
126
3
0
1
126
125159109
125158984
2.920000e-52
217.0
30
TraesCS5B01G160400
chr1A
95.745
94
4
0
1
94
97805191
97805098
8.350000e-33
152.0
31
TraesCS5B01G160400
chr7B
94.215
121
2
2
1
118
481845943
481845825
3.830000e-41
180.0
32
TraesCS5B01G160400
chr7B
94.949
99
2
1
1
96
284939492
284939590
8.350000e-33
152.0
33
TraesCS5B01G160400
chr2B
94.175
103
4
2
1
102
78000394
78000293
6.450000e-34
156.0
34
TraesCS5B01G160400
chr2B
76.961
204
37
5
4614
4810
717496139
717496339
1.830000e-19
108.0
35
TraesCS5B01G160400
chr1D
91.743
109
5
1
1
109
419029130
419029026
1.080000e-31
148.0
36
TraesCS5B01G160400
chr3D
81.159
138
18
7
4682
4812
73456087
73456223
2.370000e-18
104.0
37
TraesCS5B01G160400
chr3D
92.683
41
0
2
4611
4651
535506217
535506254
6.730000e-04
56.5
38
TraesCS5B01G160400
chr6B
89.583
48
4
1
4611
4658
211810942
211810896
5.200000e-05
60.2
39
TraesCS5B01G160400
chr6D
88.000
50
3
3
4610
4658
59026466
59026513
6.730000e-04
56.5
40
TraesCS5B01G160400
chr1B
86.538
52
6
1
4611
4662
553454121
553454071
6.730000e-04
56.5
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
TraesCS5B01G160400
chr5B
295379690
295384504
4814
True
2656.000000
6381
100.000000
1
4815
3
chr5B.!!$R2
4814
1
TraesCS5B01G160400
chr5A
348716852
348720830
3978
True
2940.500000
5179
93.737000
669
4813
2
chr5A.!!$R3
4144
2
TraesCS5B01G160400
chr5A
512393172
512393933
761
False
321.000000
436
96.324500
1
674
2
chr5A.!!$F2
673
3
TraesCS5B01G160400
chr5D
262838062
262842477
4415
True
855.071429
2322
94.650429
669
4813
7
chr5D.!!$R1
4144
4
TraesCS5B01G160400
chr4B
633291211
633292204
993
True
327.500000
433
97.668000
1
668
2
chr4B.!!$R1
667
5
TraesCS5B01G160400
chr2A
283303723
283304526
803
True
319.000000
416
97.268500
1
669
2
chr2A.!!$R2
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.