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
TraesCS7D01G118000
chr7D
100.000
3335
0
0
1
3335
72968214
72964880
0.000000e+00
6159.0
1
TraesCS7D01G118000
chr7B
93.490
2719
148
14
1
2714
15504786
15507480
0.000000e+00
4013.0
2
TraesCS7D01G118000
chr7B
100.000
38
0
0
2706
2743
15507773
15507810
1.660000e-08
71.3
3
TraesCS7D01G118000
chr7A
89.131
2659
183
49
1
2615
77417915
77420511
0.000000e+00
3212.0
4
TraesCS7D01G118000
chr7A
90.244
123
9
3
2626
2746
77429146
77429267
1.240000e-34
158.0
5
TraesCS7D01G118000
chr7A
79.630
108
22
0
1417
1524
135689638
135689531
9.920000e-11
78.7
6
TraesCS7D01G118000
chr4D
99.492
590
3
0
2746
3335
488441821
488441232
0.000000e+00
1074.0
7
TraesCS7D01G118000
chr3D
99.492
591
1
1
2745
3335
79454268
79454856
0.000000e+00
1074.0
8
TraesCS7D01G118000
chr3D
99.322
590
4
0
2746
3335
512523174
512522585
0.000000e+00
1068.0
9
TraesCS7D01G118000
chr2D
99.323
591
4
0
2745
3335
612512755
612513345
0.000000e+00
1070.0
10
TraesCS7D01G118000
chr2D
99.322
590
4
0
2746
3335
107554309
107554898
0.000000e+00
1068.0
11
TraesCS7D01G118000
chr6D
99.322
590
4
0
2746
3335
301812115
301811526
0.000000e+00
1068.0
12
TraesCS7D01G118000
chr6D
99.322
590
4
0
2746
3335
473257617
473257028
0.000000e+00
1068.0
13
TraesCS7D01G118000
chr6D
75.694
144
35
0
1417
1560
388951394
388951251
4.620000e-09
73.1
14
TraesCS7D01G118000
chr5D
99.157
593
5
0
2743
3335
482203405
482203997
0.000000e+00
1068.0
15
TraesCS7D01G118000
chr5D
84.685
111
17
0
1415
1525
488900975
488900865
9.780000e-21
111.0
16
TraesCS7D01G118000
chr1D
99.322
590
4
0
2746
3335
484820906
484820317
0.000000e+00
1068.0
17
TraesCS7D01G118000
chr5B
83.784
111
18
0
1415
1525
602341196
602341086
4.550000e-19
106.0
18
TraesCS7D01G118000
chr5A
82.883
111
19
0
1415
1525
609956113
609956003
2.120000e-17
100.0
19
TraesCS7D01G118000
chr6B
75.862
145
35
0
1417
1561
581867810
581867666
1.280000e-09
75.0
20
TraesCS7D01G118000
chr6A
75.694
144
35
0
1417
1560
535403361
535403218
4.620000e-09
73.1
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
TraesCS7D01G118000
chr7D
72964880
72968214
3334
True
6159.00
6159
100.000
1
3335
1
chr7D.!!$R1
3334
1
TraesCS7D01G118000
chr7B
15504786
15507810
3024
False
2042.15
4013
96.745
1
2743
2
chr7B.!!$F1
2742
2
TraesCS7D01G118000
chr7A
77417915
77420511
2596
False
3212.00
3212
89.131
1
2615
1
chr7A.!!$F1
2614
3
TraesCS7D01G118000
chr4D
488441232
488441821
589
True
1074.00
1074
99.492
2746
3335
1
chr4D.!!$R1
589
4
TraesCS7D01G118000
chr3D
79454268
79454856
588
False
1074.00
1074
99.492
2745
3335
1
chr3D.!!$F1
590
5
TraesCS7D01G118000
chr3D
512522585
512523174
589
True
1068.00
1068
99.322
2746
3335
1
chr3D.!!$R1
589
6
TraesCS7D01G118000
chr2D
612512755
612513345
590
False
1070.00
1070
99.323
2745
3335
1
chr2D.!!$F2
590
7
TraesCS7D01G118000
chr2D
107554309
107554898
589
False
1068.00
1068
99.322
2746
3335
1
chr2D.!!$F1
589
8
TraesCS7D01G118000
chr6D
301811526
301812115
589
True
1068.00
1068
99.322
2746
3335
1
chr6D.!!$R1
589
9
TraesCS7D01G118000
chr6D
473257028
473257617
589
True
1068.00
1068
99.322
2746
3335
1
chr6D.!!$R3
589
10
TraesCS7D01G118000
chr5D
482203405
482203997
592
False
1068.00
1068
99.157
2743
3335
1
chr5D.!!$F1
592
11
TraesCS7D01G118000
chr1D
484820317
484820906
589
True
1068.00
1068
99.322
2746
3335
1
chr1D.!!$R1
589
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.