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
TraesCS3B01G186700
chr3B
100.000
2252
0
0
1
2252
201506849
201504598
0.000000e+00
4159
1
TraesCS3B01G186700
chr3B
97.500
120
3
0
1
120
386605388
386605269
2.930000e-49
206
2
TraesCS3B01G186700
chr2D
96.992
2261
37
8
1
2252
628285940
628283702
0.000000e+00
3770
3
TraesCS3B01G186700
chr2D
96.647
2237
52
10
1
2229
334226193
334223972
0.000000e+00
3694
4
TraesCS3B01G186700
chr6D
96.903
2260
46
8
1
2252
431400298
431398055
0.000000e+00
3764
5
TraesCS3B01G186700
chr1D
96.813
2259
52
6
1
2252
254489973
254487728
0.000000e+00
3755
6
TraesCS3B01G186700
chr2A
96.459
2259
66
4
1
2252
276440803
276443054
0.000000e+00
3716
7
TraesCS3B01G186700
chr2A
96.016
2259
61
9
1
2252
335826551
335824315
0.000000e+00
3646
8
TraesCS3B01G186700
chr2A
96.377
138
5
0
1
138
703347076
703347213
6.260000e-56
228
9
TraesCS3B01G186700
chr3D
96.459
2259
53
9
1
2252
21897827
21895589
0.000000e+00
3703
10
TraesCS3B01G186700
chr5D
96.071
2265
63
10
1
2250
329131434
329133687
0.000000e+00
3666
11
TraesCS3B01G186700
chr1A
97.191
2136
36
7
1
2129
256025895
256028013
0.000000e+00
3591
12
TraesCS3B01G186700
chr1A
98.717
1403
17
1
850
2252
554465601
554467002
0.000000e+00
2490
13
TraesCS3B01G186700
chr5A
95.531
2260
59
9
1
2252
684325859
684323634
0.000000e+00
3576
14
TraesCS3B01G186700
chr7D
95.265
887
38
2
1
884
88605858
88604973
0.000000e+00
1402
15
TraesCS3B01G186700
chrUn
98.573
771
7
2
1
767
404958508
404957738
0.000000e+00
1360
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
TraesCS3B01G186700
chr3B
201504598
201506849
2251
True
4159
4159
100.000
1
2252
1
chr3B.!!$R1
2251
1
TraesCS3B01G186700
chr2D
628283702
628285940
2238
True
3770
3770
96.992
1
2252
1
chr2D.!!$R2
2251
2
TraesCS3B01G186700
chr2D
334223972
334226193
2221
True
3694
3694
96.647
1
2229
1
chr2D.!!$R1
2228
3
TraesCS3B01G186700
chr6D
431398055
431400298
2243
True
3764
3764
96.903
1
2252
1
chr6D.!!$R1
2251
4
TraesCS3B01G186700
chr1D
254487728
254489973
2245
True
3755
3755
96.813
1
2252
1
chr1D.!!$R1
2251
5
TraesCS3B01G186700
chr2A
276440803
276443054
2251
False
3716
3716
96.459
1
2252
1
chr2A.!!$F1
2251
6
TraesCS3B01G186700
chr2A
335824315
335826551
2236
True
3646
3646
96.016
1
2252
1
chr2A.!!$R1
2251
7
TraesCS3B01G186700
chr3D
21895589
21897827
2238
True
3703
3703
96.459
1
2252
1
chr3D.!!$R1
2251
8
TraesCS3B01G186700
chr5D
329131434
329133687
2253
False
3666
3666
96.071
1
2250
1
chr5D.!!$F1
2249
9
TraesCS3B01G186700
chr1A
256025895
256028013
2118
False
3591
3591
97.191
1
2129
1
chr1A.!!$F1
2128
10
TraesCS3B01G186700
chr1A
554465601
554467002
1401
False
2490
2490
98.717
850
2252
1
chr1A.!!$F2
1402
11
TraesCS3B01G186700
chr5A
684323634
684325859
2225
True
3576
3576
95.531
1
2252
1
chr5A.!!$R1
2251
12
TraesCS3B01G186700
chr7D
88604973
88605858
885
True
1402
1402
95.265
1
884
1
chr7D.!!$R1
883
13
TraesCS3B01G186700
chrUn
404957738
404958508
770
True
1360
1360
98.573
1
767
1
chrUn.!!$R1
766
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.