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
TraesCS6D01G157900
chr6D
100.000
4046
0
0
1
4046
134589404
134585359
0.000000e+00
7472.0
1
TraesCS6D01G157900
chr6D
98.836
3607
32
3
3
3609
135042849
135039253
0.000000e+00
6420.0
2
TraesCS6D01G157900
chr6D
90.219
1963
163
19
1096
3048
134742432
134740489
0.000000e+00
2534.0
3
TraesCS6D01G157900
chr6D
89.898
1970
161
24
1096
3048
134337497
134335549
0.000000e+00
2501.0
4
TraesCS6D01G157900
chr6D
94.305
439
23
1
3608
4046
135039296
135038860
0.000000e+00
671.0
5
TraesCS6D01G157900
chr6D
91.753
97
8
0
3922
4018
448698031
448698127
7.050000e-28
135.0
6
TraesCS6D01G157900
chr6D
96.154
78
3
0
3532
3609
287510366
287510443
1.180000e-25
128.0
7
TraesCS6D01G157900
chr6D
96.154
78
3
0
3532
3609
361663294
361663371
1.180000e-25
128.0
8
TraesCS6D01G157900
chr6D
93.590
78
5
0
1710
1787
33243212
33243135
2.560000e-22
117.0
9
TraesCS6D01G157900
chr6D
93.333
45
3
0
3874
3918
462081379
462081423
2.610000e-07
67.6
10
TraesCS6D01G157900
chr6D
97.222
36
1
0
639
674
388207871
388207836
1.210000e-05
62.1
11
TraesCS6D01G157900
chr6D
92.308
39
3
0
3879
3917
206632653
206632615
5.650000e-04
56.5
12
TraesCS6D01G157900
chr6B
91.755
3311
134
53
73
3314
233675048
233671808
0.000000e+00
4473.0
13
TraesCS6D01G157900
chr6B
90.367
1962
162
18
1096
3048
233088913
233086970
0.000000e+00
2551.0
14
TraesCS6D01G157900
chr6B
94.215
121
6
1
3336
3456
233671822
233671703
2.480000e-42
183.0
15
TraesCS6D01G157900
chr6B
82.927
123
18
1
3923
4045
617458476
617458357
1.540000e-19
108.0
16
TraesCS6D01G157900
chr6B
79.675
123
21
4
2441
2561
479079564
479079444
7.210000e-13
86.1
17
TraesCS6D01G157900
chr6A
95.814
2556
67
18
689
3213
176294386
176291840
0.000000e+00
4091.0
18
TraesCS6D01G157900
chr6A
90.973
1573
126
11
1477
3048
175997191
175995634
0.000000e+00
2104.0
19
TraesCS6D01G157900
chr6A
87.545
554
47
17
146
683
176295025
176294478
4.440000e-174
621.0
20
TraesCS6D01G157900
chr6A
91.703
229
17
1
3608
3836
183778019
183778245
2.350000e-82
316.0
21
TraesCS6D01G157900
chr6A
90.987
233
17
2
3605
3836
170779665
170779894
1.090000e-80
311.0
22
TraesCS6D01G157900
chr6A
90.968
155
12
2
1096
1249
176002955
176002802
1.470000e-49
207.0
23
TraesCS6D01G157900
chr6A
92.481
133
8
2
3335
3467
176285155
176285025
5.340000e-44
189.0
24
TraesCS6D01G157900
chr6A
87.179
117
12
3
3198
3314
176285253
176285140
3.280000e-26
130.0
25
TraesCS6D01G157900
chr6A
96.154
78
3
0
3532
3609
183777985
183778062
1.180000e-25
128.0
26
TraesCS6D01G157900
chr6A
89.474
95
10
0
3949
4043
283930156
283930250
1.980000e-23
121.0
27
TraesCS6D01G157900
chr6A
95.000
40
1
1
633
672
16101015
16100977
1.210000e-05
62.1
28
TraesCS6D01G157900
chr2D
74.334
939
199
32
2101
3008
565090943
565091870
1.070000e-95
361.0
29
TraesCS6D01G157900
chr2D
76.471
663
128
21
2101
2740
565052904
565053561
6.480000e-88
335.0
30
TraesCS6D01G157900
chr2D
93.023
43
3
0
629
671
38220625
38220583
3.380000e-06
63.9
31
TraesCS6D01G157900
chr2A
76.783
659
130
14
2101
2740
705532001
705532655
8.320000e-92
348.0
32
TraesCS6D01G157900
chr2A
88.776
98
7
4
3534
3627
209730556
209730653
2.560000e-22
117.0
33
TraesCS6D01G157900
chr2A
86.792
53
7
0
3869
3921
619856918
619856866
4.370000e-05
60.2
34
TraesCS6D01G157900
chr4D
91.139
237
19
2
3608
3842
338071278
338071042
1.810000e-83
320.0
35
TraesCS6D01G157900
chr4D
96.154
78
3
0
3532
3609
226345487
226345564
1.180000e-25
128.0
36
TraesCS6D01G157900
chr4D
82.540
126
18
2
3922
4043
11905628
11905753
1.540000e-19
108.0
37
TraesCS6D01G157900
chr4D
92.683
41
2
1
630
669
251431732
251431692
1.570000e-04
58.4
38
TraesCS6D01G157900
chr5B
91.064
235
19
1
3608
3842
228385272
228385040
2.350000e-82
316.0
39
TraesCS6D01G157900
chr5B
97.059
34
1
0
3880
3913
582790746
582790713
1.570000e-04
58.4
40
TraesCS6D01G157900
chr5B
89.130
46
4
1
3868
3912
658521605
658521650
5.650000e-04
56.5
41
TraesCS6D01G157900
chr7D
91.266
229
18
1
3608
3836
158534960
158535186
1.090000e-80
311.0
42
TraesCS6D01G157900
chr7D
76.354
554
107
21
1093
1633
30264392
30264934
3.980000e-70
276.0
43
TraesCS6D01G157900
chr7D
97.436
78
2
0
3532
3609
312415922
312415999
2.540000e-27
134.0
44
TraesCS6D01G157900
chr7D
95.349
43
2
0
631
673
26445382
26445340
7.260000e-08
69.4
45
TraesCS6D01G157900
chr7D
95.122
41
2
0
631
671
272666267
272666307
9.390000e-07
65.8
46
TraesCS6D01G157900
chr1D
90.638
235
20
1
3608
3842
132791102
132790870
1.090000e-80
311.0
47
TraesCS6D01G157900
chr1D
91.266
229
19
1
3608
3836
155403858
155404085
1.090000e-80
311.0
48
TraesCS6D01G157900
chr1D
86.066
122
17
0
3922
4043
364093168
364093289
9.120000e-27
132.0
49
TraesCS6D01G157900
chr1D
93.182
44
3
0
628
671
72629634
72629677
9.390000e-07
65.8
50
TraesCS6D01G157900
chr3D
90.213
235
21
1
3608
3842
251145958
251145726
5.080000e-79
305.0
51
TraesCS6D01G157900
chr3D
96.154
78
3
0
3532
3609
283129592
283129669
1.180000e-25
128.0
52
TraesCS6D01G157900
chr3D
91.139
79
7
0
3922
4000
592913042
592912964
1.540000e-19
108.0
53
TraesCS6D01G157900
chr3D
97.674
43
1
0
631
673
313713541
313713583
1.560000e-09
75.0
54
TraesCS6D01G157900
chr3D
92.683
41
2
1
630
669
168088331
168088371
1.570000e-04
58.4
55
TraesCS6D01G157900
chr4A
74.601
689
139
23
1093
1762
698171061
698170390
1.850000e-68
270.0
56
TraesCS6D01G157900
chr4A
89.381
113
12
0
3934
4046
520130034
520130146
4.220000e-30
143.0
57
TraesCS6D01G157900
chr2B
88.112
143
10
4
2410
2545
138547272
138547130
3.240000e-36
163.0
58
TraesCS6D01G157900
chr4B
89.344
122
13
0
3922
4043
548766089
548765968
1.950000e-33
154.0
59
TraesCS6D01G157900
chr5D
96.154
78
3
0
3532
3609
223052991
223052914
1.180000e-25
128.0
60
TraesCS6D01G157900
chr7A
97.561
41
1
0
631
671
306434112
306434152
2.020000e-08
71.3
61
TraesCS6D01G157900
chr3B
90.385
52
4
1
631
682
662015439
662015389
2.610000e-07
67.6
62
TraesCS6D01G157900
chr1B
93.333
45
3
0
627
671
15379574
15379618
2.610000e-07
67.6
63
TraesCS6D01G157900
chr7B
93.333
45
2
1
3874
3918
437208453
437208410
9.390000e-07
65.8
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
TraesCS6D01G157900
chr6D
134585359
134589404
4045
True
7472.0
7472
100.0000
1
4046
1
chr6D.!!$R3
4045
1
TraesCS6D01G157900
chr6D
135038860
135042849
3989
True
3545.5
6420
96.5705
3
4046
2
chr6D.!!$R7
4043
2
TraesCS6D01G157900
chr6D
134740489
134742432
1943
True
2534.0
2534
90.2190
1096
3048
1
chr6D.!!$R4
1952
3
TraesCS6D01G157900
chr6D
134335549
134337497
1948
True
2501.0
2501
89.8980
1096
3048
1
chr6D.!!$R2
1952
4
TraesCS6D01G157900
chr6B
233086970
233088913
1943
True
2551.0
2551
90.3670
1096
3048
1
chr6B.!!$R1
1952
5
TraesCS6D01G157900
chr6B
233671703
233675048
3345
True
2328.0
4473
92.9850
73
3456
2
chr6B.!!$R4
3383
6
TraesCS6D01G157900
chr6A
176291840
176295025
3185
True
2356.0
4091
91.6795
146
3213
2
chr6A.!!$R5
3067
7
TraesCS6D01G157900
chr6A
175995634
175997191
1557
True
2104.0
2104
90.9730
1477
3048
1
chr6A.!!$R2
1571
8
TraesCS6D01G157900
chr2D
565090943
565091870
927
False
361.0
361
74.3340
2101
3008
1
chr2D.!!$F2
907
9
TraesCS6D01G157900
chr2D
565052904
565053561
657
False
335.0
335
76.4710
2101
2740
1
chr2D.!!$F1
639
10
TraesCS6D01G157900
chr2A
705532001
705532655
654
False
348.0
348
76.7830
2101
2740
1
chr2A.!!$F2
639
11
TraesCS6D01G157900
chr7D
30264392
30264934
542
False
276.0
276
76.3540
1093
1633
1
chr7D.!!$F1
540
12
TraesCS6D01G157900
chr4A
698170390
698171061
671
True
270.0
270
74.6010
1093
1762
1
chr4A.!!$R1
669
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.