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
TraesCS1B01G111000
chr1B
100.000
3256
0
0
1
3256
127026844
127023589
0.000000e+00
6013
1
TraesCS1B01G111000
chr4D
93.253
2505
137
12
1
2483
459190867
459193361
0.000000e+00
3661
2
TraesCS1B01G111000
chr4D
82.172
976
152
13
1189
2160
145379889
145378932
0.000000e+00
819
3
TraesCS1B01G111000
chr4D
79.472
1213
197
33
937
2119
348041285
348040095
0.000000e+00
813
4
TraesCS1B01G111000
chr4D
92.282
298
18
3
2187
2480
101391974
101392270
5.020000e-113
418
5
TraesCS1B01G111000
chr2D
92.763
2501
117
22
1
2481
631750041
631747585
0.000000e+00
3557
6
TraesCS1B01G111000
chr2D
92.308
2184
148
10
1
2174
469108412
469106239
0.000000e+00
3085
7
TraesCS1B01G111000
chr2D
88.043
1313
104
19
890
2174
330864576
330863289
0.000000e+00
1506
8
TraesCS1B01G111000
chr2D
86.269
772
76
13
2484
3254
561401886
561402628
0.000000e+00
811
9
TraesCS1B01G111000
chr2D
85.917
774
88
11
2484
3256
342654332
342655085
0.000000e+00
806
10
TraesCS1B01G111000
chr2D
85.788
774
89
10
2484
3256
488167064
488166311
0.000000e+00
800
11
TraesCS1B01G111000
chr2D
91.536
319
21
4
2166
2482
469106165
469105851
4.990000e-118
435
12
TraesCS1B01G111000
chr1A
92.156
2180
154
12
1
2174
461967264
461965096
0.000000e+00
3062
13
TraesCS1B01G111000
chr1A
92.667
1541
96
12
1
1535
35564479
35562950
0.000000e+00
2204
14
TraesCS1B01G111000
chr1A
80.127
1419
239
28
1086
2485
80283703
80282309
0.000000e+00
1018
15
TraesCS1B01G111000
chr1A
90.373
644
48
7
1531
2174
35559048
35558419
0.000000e+00
833
16
TraesCS1B01G111000
chr1A
91.463
328
19
5
2166
2486
385892639
385892314
2.980000e-120
442
17
TraesCS1B01G111000
chr1A
91.185
329
21
5
2159
2486
461965054
461964733
1.070000e-119
440
18
TraesCS1B01G111000
chr1A
90.184
326
25
4
2159
2483
35558377
35558058
5.020000e-113
418
19
TraesCS1B01G111000
chr3B
91.743
2180
157
17
1
2170
597426312
597428478
0.000000e+00
3007
20
TraesCS1B01G111000
chr3B
92.920
1695
83
16
812
2483
8505203
8506883
0.000000e+00
2431
21
TraesCS1B01G111000
chr3B
86.070
201
21
5
890
1087
597427123
597427319
3.290000e-50
209
22
TraesCS1B01G111000
chr3B
95.312
128
6
0
960
1087
8505193
8505320
1.530000e-48
204
23
TraesCS1B01G111000
chr7B
91.621
2184
156
19
1
2175
551485194
551483029
0.000000e+00
2994
24
TraesCS1B01G111000
chr2B
92.432
1546
80
20
969
2485
677292341
677293878
0.000000e+00
2172
25
TraesCS1B01G111000
chr2B
94.807
982
47
4
1
979
677291529
677292509
0.000000e+00
1528
26
TraesCS1B01G111000
chr3D
94.745
1313
48
4
1189
2483
6991411
6992720
0.000000e+00
2023
27
TraesCS1B01G111000
chr3D
92.366
655
32
3
1848
2485
5544737
5545390
0.000000e+00
917
28
TraesCS1B01G111000
chr3D
86.211
776
78
13
2480
3253
462375070
462374322
0.000000e+00
813
29
TraesCS1B01G111000
chr7A
93.521
1281
65
13
969
2236
48781641
48782916
0.000000e+00
1890
30
TraesCS1B01G111000
chr7A
95.510
980
42
2
1
978
48780829
48781808
0.000000e+00
1565
31
TraesCS1B01G111000
chrUn
91.879
1293
87
8
890
2174
96553413
96554695
0.000000e+00
1790
32
TraesCS1B01G111000
chrUn
92.236
322
19
4
2166
2485
96554769
96555086
4.950000e-123
451
33
TraesCS1B01G111000
chr7D
89.148
986
73
7
1517
2484
422343534
422344503
0.000000e+00
1197
34
TraesCS1B01G111000
chr7D
87.855
774
73
10
2484
3256
469140344
469141097
0.000000e+00
889
35
TraesCS1B01G111000
chr7D
86.658
772
76
12
2484
3254
54861135
54860390
0.000000e+00
830
36
TraesCS1B01G111000
chr7D
86.658
772
76
12
2484
3254
452809811
452810556
0.000000e+00
830
37
TraesCS1B01G111000
chr7D
86.305
774
84
12
2484
3256
368587906
368588658
0.000000e+00
822
38
TraesCS1B01G111000
chr7D
86.340
776
79
16
2484
3256
277245815
277245064
0.000000e+00
821
39
TraesCS1B01G111000
chr7D
92.236
322
19
3
2166
2485
69948616
69948933
4.950000e-123
451
40
TraesCS1B01G111000
chr5D
80.948
1202
198
20
969
2157
538687093
538688276
0.000000e+00
922
41
TraesCS1B01G111000
chr5D
86.805
773
74
13
2484
3254
330341757
330341011
0.000000e+00
837
42
TraesCS1B01G111000
chr5D
86.788
772
75
12
2484
3254
412700713
412701458
0.000000e+00
835
43
TraesCS1B01G111000
chr5D
85.548
775
81
17
2484
3256
217197947
217198692
0.000000e+00
782
44
TraesCS1B01G111000
chr5D
77.717
1288
219
37
890
2141
420019256
420020511
0.000000e+00
726
45
TraesCS1B01G111000
chr5D
84.326
772
80
18
2484
3254
301958574
301959305
0.000000e+00
717
46
TraesCS1B01G111000
chr1D
86.693
774
82
10
2484
3256
339170363
339169610
0.000000e+00
839
47
TraesCS1B01G111000
chr1D
86.528
772
77
12
2484
3254
154363968
154363223
0.000000e+00
824
48
TraesCS1B01G111000
chr6D
86.136
779
86
12
2480
3256
358893668
358894426
0.000000e+00
821
49
TraesCS1B01G111000
chr3A
85.714
770
89
11
2484
3252
518834453
518835202
0.000000e+00
793
50
TraesCS1B01G111000
chr6B
84.685
777
94
15
2483
3256
449334319
449335073
0.000000e+00
752
51
TraesCS1B01G111000
chr6B
89.908
327
25
5
2166
2488
658405706
658405384
6.500000e-112
414
52
TraesCS1B01G111000
chr4A
91.049
324
22
4
2166
2483
445298243
445297921
6.450000e-117
431
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
TraesCS1B01G111000
chr1B
127023589
127026844
3255
True
6013.000000
6013
100.000000
1
3256
1
chr1B.!!$R1
3255
1
TraesCS1B01G111000
chr4D
459190867
459193361
2494
False
3661.000000
3661
93.253000
1
2483
1
chr4D.!!$F2
2482
2
TraesCS1B01G111000
chr4D
145378932
145379889
957
True
819.000000
819
82.172000
1189
2160
1
chr4D.!!$R1
971
3
TraesCS1B01G111000
chr4D
348040095
348041285
1190
True
813.000000
813
79.472000
937
2119
1
chr4D.!!$R2
1182
4
TraesCS1B01G111000
chr2D
631747585
631750041
2456
True
3557.000000
3557
92.763000
1
2481
1
chr2D.!!$R3
2480
5
TraesCS1B01G111000
chr2D
469105851
469108412
2561
True
1760.000000
3085
91.922000
1
2482
2
chr2D.!!$R4
2481
6
TraesCS1B01G111000
chr2D
330863289
330864576
1287
True
1506.000000
1506
88.043000
890
2174
1
chr2D.!!$R1
1284
7
TraesCS1B01G111000
chr2D
561401886
561402628
742
False
811.000000
811
86.269000
2484
3254
1
chr2D.!!$F2
770
8
TraesCS1B01G111000
chr2D
342654332
342655085
753
False
806.000000
806
85.917000
2484
3256
1
chr2D.!!$F1
772
9
TraesCS1B01G111000
chr2D
488166311
488167064
753
True
800.000000
800
85.788000
2484
3256
1
chr2D.!!$R2
772
10
TraesCS1B01G111000
chr1A
461964733
461967264
2531
True
1751.000000
3062
91.670500
1
2486
2
chr1A.!!$R4
2485
11
TraesCS1B01G111000
chr1A
35558058
35564479
6421
True
1151.666667
2204
91.074667
1
2483
3
chr1A.!!$R3
2482
12
TraesCS1B01G111000
chr1A
80282309
80283703
1394
True
1018.000000
1018
80.127000
1086
2485
1
chr1A.!!$R1
1399
13
TraesCS1B01G111000
chr3B
597426312
597428478
2166
False
1608.000000
3007
88.906500
1
2170
2
chr3B.!!$F2
2169
14
TraesCS1B01G111000
chr3B
8505193
8506883
1690
False
1317.500000
2431
94.116000
812
2483
2
chr3B.!!$F1
1671
15
TraesCS1B01G111000
chr7B
551483029
551485194
2165
True
2994.000000
2994
91.621000
1
2175
1
chr7B.!!$R1
2174
16
TraesCS1B01G111000
chr2B
677291529
677293878
2349
False
1850.000000
2172
93.619500
1
2485
2
chr2B.!!$F1
2484
17
TraesCS1B01G111000
chr3D
6991411
6992720
1309
False
2023.000000
2023
94.745000
1189
2483
1
chr3D.!!$F2
1294
18
TraesCS1B01G111000
chr3D
5544737
5545390
653
False
917.000000
917
92.366000
1848
2485
1
chr3D.!!$F1
637
19
TraesCS1B01G111000
chr3D
462374322
462375070
748
True
813.000000
813
86.211000
2480
3253
1
chr3D.!!$R1
773
20
TraesCS1B01G111000
chr7A
48780829
48782916
2087
False
1727.500000
1890
94.515500
1
2236
2
chr7A.!!$F1
2235
21
TraesCS1B01G111000
chrUn
96553413
96555086
1673
False
1120.500000
1790
92.057500
890
2485
2
chrUn.!!$F1
1595
22
TraesCS1B01G111000
chr7D
422343534
422344503
969
False
1197.000000
1197
89.148000
1517
2484
1
chr7D.!!$F3
967
23
TraesCS1B01G111000
chr7D
469140344
469141097
753
False
889.000000
889
87.855000
2484
3256
1
chr7D.!!$F5
772
24
TraesCS1B01G111000
chr7D
54860390
54861135
745
True
830.000000
830
86.658000
2484
3254
1
chr7D.!!$R1
770
25
TraesCS1B01G111000
chr7D
452809811
452810556
745
False
830.000000
830
86.658000
2484
3254
1
chr7D.!!$F4
770
26
TraesCS1B01G111000
chr7D
368587906
368588658
752
False
822.000000
822
86.305000
2484
3256
1
chr7D.!!$F2
772
27
TraesCS1B01G111000
chr7D
277245064
277245815
751
True
821.000000
821
86.340000
2484
3256
1
chr7D.!!$R2
772
28
TraesCS1B01G111000
chr5D
538687093
538688276
1183
False
922.000000
922
80.948000
969
2157
1
chr5D.!!$F5
1188
29
TraesCS1B01G111000
chr5D
330341011
330341757
746
True
837.000000
837
86.805000
2484
3254
1
chr5D.!!$R1
770
30
TraesCS1B01G111000
chr5D
412700713
412701458
745
False
835.000000
835
86.788000
2484
3254
1
chr5D.!!$F3
770
31
TraesCS1B01G111000
chr5D
217197947
217198692
745
False
782.000000
782
85.548000
2484
3256
1
chr5D.!!$F1
772
32
TraesCS1B01G111000
chr5D
420019256
420020511
1255
False
726.000000
726
77.717000
890
2141
1
chr5D.!!$F4
1251
33
TraesCS1B01G111000
chr5D
301958574
301959305
731
False
717.000000
717
84.326000
2484
3254
1
chr5D.!!$F2
770
34
TraesCS1B01G111000
chr1D
339169610
339170363
753
True
839.000000
839
86.693000
2484
3256
1
chr1D.!!$R2
772
35
TraesCS1B01G111000
chr1D
154363223
154363968
745
True
824.000000
824
86.528000
2484
3254
1
chr1D.!!$R1
770
36
TraesCS1B01G111000
chr6D
358893668
358894426
758
False
821.000000
821
86.136000
2480
3256
1
chr6D.!!$F1
776
37
TraesCS1B01G111000
chr3A
518834453
518835202
749
False
793.000000
793
85.714000
2484
3252
1
chr3A.!!$F1
768
38
TraesCS1B01G111000
chr6B
449334319
449335073
754
False
752.000000
752
84.685000
2483
3256
1
chr6B.!!$F1
773
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.