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
TraesCS7D01G169900
chr7D
100.000
2339
0
0
1
2339
122681612
122683950
0.000000e+00
4320
1
TraesCS7D01G169900
chr7D
98.864
88
1
0
76
163
94261224
94261311
8.650000e-35
158
2
TraesCS7D01G169900
chr7B
87.979
1539
58
42
855
2338
83922204
83920738
0.000000e+00
1700
3
TraesCS7D01G169900
chr7A
87.628
978
47
27
792
1718
125676597
125677551
0.000000e+00
1068
4
TraesCS7D01G169900
chr7A
97.959
392
5
1
1948
2339
125677923
125678311
0.000000e+00
676
5
TraesCS7D01G169900
chr7A
92.375
459
31
3
346
800
299294908
299294450
0.000000e+00
651
6
TraesCS7D01G169900
chr7A
94.798
173
6
2
165
337
299295366
299295197
1.380000e-67
267
7
TraesCS7D01G169900
chr7A
81.439
264
18
8
792
1038
125915462
125915213
1.100000e-43
187
8
TraesCS7D01G169900
chr7A
83.673
196
11
2
1124
1319
125913744
125913570
5.170000e-37
165
9
TraesCS7D01G169900
chr7A
98.750
80
1
0
1
80
299295447
299295368
2.420000e-30
143
10
TraesCS7D01G169900
chr4D
94.311
457
24
1
338
792
325887479
325887935
0.000000e+00
699
11
TraesCS7D01G169900
chr4D
96.591
176
3
2
162
337
325887045
325887217
2.940000e-74
289
12
TraesCS7D01G169900
chr4D
93.750
80
2
1
1
80
325886970
325887046
1.470000e-22
117
13
TraesCS7D01G169900
chr2A
92.688
465
26
7
341
800
28335053
28334592
0.000000e+00
664
14
TraesCS7D01G169900
chr5A
92.544
456
30
2
339
792
564710568
564710115
0.000000e+00
651
15
TraesCS7D01G169900
chr5A
92.634
448
29
2
346
791
396369159
396369604
1.960000e-180
641
16
TraesCS7D01G169900
chr5A
94.886
176
6
2
162
337
396368698
396368870
2.960000e-69
272
17
TraesCS7D01G169900
chr5A
97.163
141
4
0
165
305
564710775
564710635
3.000000e-59
239
18
TraesCS7D01G169900
chr5A
93.333
105
3
4
75
176
428189442
428189339
4.030000e-33
152
19
TraesCS7D01G169900
chr5A
98.750
80
1
0
1
80
396368620
396368699
2.420000e-30
143
20
TraesCS7D01G169900
chr1A
91.775
462
33
4
339
797
66702738
66703197
2.530000e-179
638
21
TraesCS7D01G169900
chr1A
92.878
337
21
2
460
793
100365057
100364721
9.720000e-134
486
22
TraesCS7D01G169900
chr1A
94.798
173
6
2
165
337
100365469
100365300
1.380000e-67
267
23
TraesCS7D01G169900
chr1A
93.750
176
4
4
162
337
66702307
66702475
8.290000e-65
257
24
TraesCS7D01G169900
chr1A
96.739
92
3
0
72
163
575557264
575557355
1.120000e-33
154
25
TraesCS7D01G169900
chr1A
98.750
80
1
0
1
80
100365550
100365471
2.420000e-30
143
26
TraesCS7D01G169900
chr4B
89.869
306
23
3
495
792
157954524
157954829
1.010000e-103
387
27
TraesCS7D01G169900
chr4B
94.318
176
8
1
162
337
157953904
157954077
3.830000e-68
268
28
TraesCS7D01G169900
chr4B
90.683
161
13
2
338
498
157954337
157954495
1.820000e-51
213
29
TraesCS7D01G169900
chr4B
96.250
80
3
0
1
80
157953826
157953905
5.240000e-27
132
30
TraesCS7D01G169900
chr1B
94.891
137
5
1
201
337
631793726
631793860
1.820000e-51
213
31
TraesCS7D01G169900
chr1B
88.462
130
12
2
665
791
631805847
631805976
1.120000e-33
154
32
TraesCS7D01G169900
chr1B
96.250
80
3
0
3
82
631776362
631776441
5.240000e-27
132
33
TraesCS7D01G169900
chr2B
98.864
88
1
0
76
163
546125979
546125892
8.650000e-35
158
34
TraesCS7D01G169900
chr2B
93.939
99
5
1
66
163
554296026
554296124
5.210000e-32
148
35
TraesCS7D01G169900
chr6D
95.789
95
3
1
79
173
58042761
58042854
4.030000e-33
152
36
TraesCS7D01G169900
chr6D
94.845
97
5
0
79
175
417354786
417354690
4.030000e-33
152
37
TraesCS7D01G169900
chr3A
90.991
111
7
3
56
163
330699692
330699582
1.870000e-31
147
38
TraesCS7D01G169900
chr2D
89.565
115
8
3
52
163
572049239
572049126
2.420000e-30
143
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
TraesCS7D01G169900
chr7D
122681612
122683950
2338
False
4320.000000
4320
100.000000
1
2339
1
chr7D.!!$F2
2338
1
TraesCS7D01G169900
chr7B
83920738
83922204
1466
True
1700.000000
1700
87.979000
855
2338
1
chr7B.!!$R1
1483
2
TraesCS7D01G169900
chr7A
125676597
125678311
1714
False
872.000000
1068
92.793500
792
2339
2
chr7A.!!$F1
1547
3
TraesCS7D01G169900
chr7A
299294450
299295447
997
True
353.666667
651
95.307667
1
800
3
chr7A.!!$R2
799
4
TraesCS7D01G169900
chr4D
325886970
325887935
965
False
368.333333
699
94.884000
1
792
3
chr4D.!!$F1
791
5
TraesCS7D01G169900
chr5A
564710115
564710775
660
True
445.000000
651
94.853500
165
792
2
chr5A.!!$R2
627
6
TraesCS7D01G169900
chr5A
396368620
396369604
984
False
352.000000
641
95.423333
1
791
3
chr5A.!!$F1
790
7
TraesCS7D01G169900
chr1A
66702307
66703197
890
False
447.500000
638
92.762500
162
797
2
chr1A.!!$F2
635
8
TraesCS7D01G169900
chr1A
100364721
100365550
829
True
298.666667
486
95.475333
1
793
3
chr1A.!!$R1
792
9
TraesCS7D01G169900
chr4B
157953826
157954829
1003
False
250.000000
387
92.780000
1
792
4
chr4B.!!$F1
791
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.