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
TraesCS6A01G128300
chr6A
100.000
9901
0
0
1
9901
100743486
100753386
0.000000e+00
18284
1
TraesCS6A01G128300
chr6A
90.732
1230
112
2
1
1229
100356952
100355724
0.000000e+00
1639
2
TraesCS6A01G128300
chr6A
86.642
1325
123
20
8278
9594
100361919
100360641
0.000000e+00
1417
3
TraesCS6A01G128300
chr6A
86.526
1232
160
6
1
1229
100363135
100361907
0.000000e+00
1351
4
TraesCS6A01G128300
chr6A
81.833
1211
212
7
21
1227
98813267
98812061
0.000000e+00
1011
5
TraesCS6A01G128300
chr6A
86.061
782
97
8
8278
9049
100355736
100354957
0.000000e+00
830
6
TraesCS6A01G128300
chr6A
81.304
813
119
21
8426
9226
100366492
100365701
6.530000e-176
628
7
TraesCS6A01G128300
chr6A
78.336
637
129
8
8346
8979
99785322
99784692
4.310000e-108
403
8
TraesCS6A01G128300
chr6D
92.519
7098
433
35
1231
8275
111601122
111608174
0.000000e+00
10076
9
TraesCS6A01G128300
chr6D
93.381
6421
328
23
1238
7613
29207013
29213381
0.000000e+00
9413
10
TraesCS6A01G128300
chr6D
89.358
1231
127
4
1
1229
83204938
83203710
0.000000e+00
1544
11
TraesCS6A01G128300
chr6D
82.125
1214
207
10
21
1229
82138794
82137586
0.000000e+00
1031
12
TraesCS6A01G128300
chr6D
82.005
1217
200
16
22
1227
81935041
81933833
0.000000e+00
1016
13
TraesCS6A01G128300
chr6D
85.016
961
131
9
8278
9236
83203722
83202773
0.000000e+00
965
14
TraesCS6A01G128300
chr6D
82.370
692
105
13
8426
9113
83209472
83208794
3.980000e-163
586
15
TraesCS6A01G128300
chr6D
85.338
532
75
3
8408
8938
46903091
46903620
1.880000e-151
547
16
TraesCS6A01G128300
chr6D
81.120
625
112
3
8278
8902
83019303
83018685
6.910000e-136
496
17
TraesCS6A01G128300
chr6D
84.836
488
74
0
8278
8765
81762397
81761910
8.940000e-135
492
18
TraesCS6A01G128300
chr6D
84.568
486
75
0
8278
8763
81933843
81933358
5.380000e-132
483
19
TraesCS6A01G128300
chr6D
78.912
588
115
8
8346
8929
82963035
82962453
3.350000e-104
390
20
TraesCS6A01G128300
chr6D
81.352
429
68
10
8346
8768
81758101
81757679
1.230000e-88
339
21
TraesCS6A01G128300
chr6D
76.359
423
65
19
8566
8983
82972385
82971993
2.820000e-45
195
22
TraesCS6A01G128300
chr3D
92.648
6991
447
23
1318
8274
24336950
24343907
0.000000e+00
10000
23
TraesCS6A01G128300
chr3D
92.199
7102
466
28
1227
8274
24290561
24297628
0.000000e+00
9965
24
TraesCS6A01G128300
chr3D
93.546
6182
384
12
2101
8274
24444853
24451027
0.000000e+00
9191
25
TraesCS6A01G128300
chr3D
86.107
1965
202
31
1275
3215
587278079
587276162
0.000000e+00
2050
26
TraesCS6A01G128300
chr3D
86.067
890
57
29
1229
2072
24443990
24444858
0.000000e+00
894
27
TraesCS6A01G128300
chr2D
91.766
7068
507
32
1250
8275
323122255
323115221
0.000000e+00
9758
28
TraesCS6A01G128300
chr2D
91.331
6979
521
40
1335
8278
591593107
591586178
0.000000e+00
9459
29
TraesCS6A01G128300
chr2D
92.487
6229
387
24
1233
7410
311561861
311568059
0.000000e+00
8835
30
TraesCS6A01G128300
chr2D
88.745
6948
704
46
1360
8275
44922087
44928988
0.000000e+00
8427
31
TraesCS6A01G128300
chr5D
91.229
6955
530
31
1356
8275
255574563
255567654
0.000000e+00
9391
32
TraesCS6A01G128300
chr5D
88.831
1155
73
11
1330
2461
26847319
26848440
0.000000e+00
1367
33
TraesCS6A01G128300
chr1D
90.781
6975
563
33
1337
8275
68897108
68890178
0.000000e+00
9245
34
TraesCS6A01G128300
chr4D
92.236
6041
431
16
2251
8275
420154489
420148471
0.000000e+00
8523
35
TraesCS6A01G128300
chr4D
92.117
4326
267
18
1223
5496
16932874
16937177
0.000000e+00
6032
36
TraesCS6A01G128300
chr4A
90.409
3399
265
26
1232
4592
248810683
248814058
0.000000e+00
4414
37
TraesCS6A01G128300
chr7A
89.842
2087
129
27
1233
3273
336386556
336384507
0.000000e+00
2603
38
TraesCS6A01G128300
chr6B
94.182
1633
60
15
8275
9901
159391928
159393531
0.000000e+00
2457
39
TraesCS6A01G128300
chr6B
94.897
1215
38
3
10
1224
159390748
159391938
0.000000e+00
1879
40
TraesCS6A01G128300
chr6B
89.439
1231
126
4
1
1229
158189607
158188379
0.000000e+00
1550
41
TraesCS6A01G128300
chr6B
82.164
1211
209
5
21
1229
157027066
157025861
0.000000e+00
1033
42
TraesCS6A01G128300
chr6B
84.576
966
132
11
8278
9236
158188391
158187436
0.000000e+00
942
43
TraesCS6A01G128300
chr6B
82.016
734
116
9
8275
9005
157901851
157902571
2.360000e-170
610
44
TraesCS6A01G128300
chrUn
88.526
1621
123
17
1231
2808
26517083
26515483
0.000000e+00
1905
45
TraesCS6A01G128300
chr7D
77.435
811
162
19
8278
9086
561001781
561002572
1.950000e-126
464
46
TraesCS6A01G128300
chr7B
77.628
742
154
9
8278
9017
608901833
608902564
3.280000e-119
440
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
TraesCS6A01G128300
chr6A
100743486
100753386
9900
False
18284.000000
18284
100.000000
1
9901
1
chr6A.!!$F1
9900
1
TraesCS6A01G128300
chr6A
100354957
100366492
11535
True
1173.000000
1639
86.253000
1
9594
5
chr6A.!!$R3
9593
2
TraesCS6A01G128300
chr6A
98812061
98813267
1206
True
1011.000000
1011
81.833000
21
1227
1
chr6A.!!$R1
1206
3
TraesCS6A01G128300
chr6A
99784692
99785322
630
True
403.000000
403
78.336000
8346
8979
1
chr6A.!!$R2
633
4
TraesCS6A01G128300
chr6D
111601122
111608174
7052
False
10076.000000
10076
92.519000
1231
8275
1
chr6D.!!$F3
7044
5
TraesCS6A01G128300
chr6D
29207013
29213381
6368
False
9413.000000
9413
93.381000
1238
7613
1
chr6D.!!$F1
6375
6
TraesCS6A01G128300
chr6D
83202773
83209472
6699
True
1031.666667
1544
85.581333
1
9236
3
chr6D.!!$R7
9235
7
TraesCS6A01G128300
chr6D
82137586
82138794
1208
True
1031.000000
1031
82.125000
21
1229
1
chr6D.!!$R1
1208
8
TraesCS6A01G128300
chr6D
81933358
81935041
1683
True
749.500000
1016
83.286500
22
8763
2
chr6D.!!$R6
8741
9
TraesCS6A01G128300
chr6D
46903091
46903620
529
False
547.000000
547
85.338000
8408
8938
1
chr6D.!!$F2
530
10
TraesCS6A01G128300
chr6D
83018685
83019303
618
True
496.000000
496
81.120000
8278
8902
1
chr6D.!!$R4
624
11
TraesCS6A01G128300
chr6D
81757679
81762397
4718
True
415.500000
492
83.094000
8278
8768
2
chr6D.!!$R5
490
12
TraesCS6A01G128300
chr6D
82962453
82963035
582
True
390.000000
390
78.912000
8346
8929
1
chr6D.!!$R2
583
13
TraesCS6A01G128300
chr3D
24336950
24343907
6957
False
10000.000000
10000
92.648000
1318
8274
1
chr3D.!!$F2
6956
14
TraesCS6A01G128300
chr3D
24290561
24297628
7067
False
9965.000000
9965
92.199000
1227
8274
1
chr3D.!!$F1
7047
15
TraesCS6A01G128300
chr3D
24443990
24451027
7037
False
5042.500000
9191
89.806500
1229
8274
2
chr3D.!!$F3
7045
16
TraesCS6A01G128300
chr3D
587276162
587278079
1917
True
2050.000000
2050
86.107000
1275
3215
1
chr3D.!!$R1
1940
17
TraesCS6A01G128300
chr2D
323115221
323122255
7034
True
9758.000000
9758
91.766000
1250
8275
1
chr2D.!!$R1
7025
18
TraesCS6A01G128300
chr2D
591586178
591593107
6929
True
9459.000000
9459
91.331000
1335
8278
1
chr2D.!!$R2
6943
19
TraesCS6A01G128300
chr2D
311561861
311568059
6198
False
8835.000000
8835
92.487000
1233
7410
1
chr2D.!!$F2
6177
20
TraesCS6A01G128300
chr2D
44922087
44928988
6901
False
8427.000000
8427
88.745000
1360
8275
1
chr2D.!!$F1
6915
21
TraesCS6A01G128300
chr5D
255567654
255574563
6909
True
9391.000000
9391
91.229000
1356
8275
1
chr5D.!!$R1
6919
22
TraesCS6A01G128300
chr5D
26847319
26848440
1121
False
1367.000000
1367
88.831000
1330
2461
1
chr5D.!!$F1
1131
23
TraesCS6A01G128300
chr1D
68890178
68897108
6930
True
9245.000000
9245
90.781000
1337
8275
1
chr1D.!!$R1
6938
24
TraesCS6A01G128300
chr4D
420148471
420154489
6018
True
8523.000000
8523
92.236000
2251
8275
1
chr4D.!!$R1
6024
25
TraesCS6A01G128300
chr4D
16932874
16937177
4303
False
6032.000000
6032
92.117000
1223
5496
1
chr4D.!!$F1
4273
26
TraesCS6A01G128300
chr4A
248810683
248814058
3375
False
4414.000000
4414
90.409000
1232
4592
1
chr4A.!!$F1
3360
27
TraesCS6A01G128300
chr7A
336384507
336386556
2049
True
2603.000000
2603
89.842000
1233
3273
1
chr7A.!!$R1
2040
28
TraesCS6A01G128300
chr6B
159390748
159393531
2783
False
2168.000000
2457
94.539500
10
9901
2
chr6B.!!$F2
9891
29
TraesCS6A01G128300
chr6B
158187436
158189607
2171
True
1246.000000
1550
87.007500
1
9236
2
chr6B.!!$R2
9235
30
TraesCS6A01G128300
chr6B
157025861
157027066
1205
True
1033.000000
1033
82.164000
21
1229
1
chr6B.!!$R1
1208
31
TraesCS6A01G128300
chr6B
157901851
157902571
720
False
610.000000
610
82.016000
8275
9005
1
chr6B.!!$F1
730
32
TraesCS6A01G128300
chrUn
26515483
26517083
1600
True
1905.000000
1905
88.526000
1231
2808
1
chrUn.!!$R1
1577
33
TraesCS6A01G128300
chr7D
561001781
561002572
791
False
464.000000
464
77.435000
8278
9086
1
chr7D.!!$F1
808
34
TraesCS6A01G128300
chr7B
608901833
608902564
731
False
440.000000
440
77.628000
8278
9017
1
chr7B.!!$F1
739
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.