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
TraesCS5A01G124400
chr5A
100.000
2514
0
0
1
2514
272196020
272198533
0
4643
1
TraesCS5A01G124400
chr3D
94.988
2534
98
16
1
2513
360444228
360441703
0
3949
2
TraesCS5A01G124400
chr3D
94.907
2533
95
15
1
2513
543133975
543131457
0
3932
3
TraesCS5A01G124400
chr3D
94.758
2537
105
13
1
2513
551735223
551732691
0
3923
4
TraesCS5A01G124400
chr3D
94.567
2540
102
19
1
2513
384995243
384997773
0
3893
5
TraesCS5A01G124400
chr3D
92.616
948
39
8
1
930
434077741
434078675
0
1334
6
TraesCS5A01G124400
chr2D
94.907
2533
100
15
1
2513
46525239
46527762
0
3936
7
TraesCS5A01G124400
chr2D
93.016
945
38
7
1
930
304671611
304672542
0
1354
8
TraesCS5A01G124400
chr7D
94.868
2533
103
16
1
2513
510254720
510257245
0
3932
9
TraesCS5A01G124400
chr7D
93.031
947
35
10
1
930
207213986
207213054
0
1354
10
TraesCS5A01G124400
chr7D
93.661
631
22
6
1
615
591992522
591991894
0
928
11
TraesCS5A01G124400
chr6B
94.793
2535
107
12
1
2513
151617793
151620324
0
3927
12
TraesCS5A01G124400
chr5D
94.799
2538
99
21
1
2513
306886184
306883655
0
3925
13
TraesCS5A01G124400
chr7B
94.512
2533
115
10
1
2513
432966832
432969360
0
3886
14
TraesCS5A01G124400
chr6D
94.353
2072
81
15
1
2054
451600149
451598096
0
3145
15
TraesCS5A01G124400
chr6D
94.316
2076
79
15
1
2054
397854472
397852414
0
3144
16
TraesCS5A01G124400
chr1D
93.822
2072
86
17
1
2054
374127036
374129083
0
3079
17
TraesCS5A01G124400
chr1D
91.719
954
38
13
1
934
466981907
466980975
0
1286
18
TraesCS5A01G124400
chr4D
91.209
728
34
12
1
711
90542456
90541742
0
963
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
TraesCS5A01G124400
chr5A
272196020
272198533
2513
False
4643
4643
100.000
1
2514
1
chr5A.!!$F1
2513
1
TraesCS5A01G124400
chr3D
360441703
360444228
2525
True
3949
3949
94.988
1
2513
1
chr3D.!!$R1
2512
2
TraesCS5A01G124400
chr3D
543131457
543133975
2518
True
3932
3932
94.907
1
2513
1
chr3D.!!$R2
2512
3
TraesCS5A01G124400
chr3D
551732691
551735223
2532
True
3923
3923
94.758
1
2513
1
chr3D.!!$R3
2512
4
TraesCS5A01G124400
chr3D
384995243
384997773
2530
False
3893
3893
94.567
1
2513
1
chr3D.!!$F1
2512
5
TraesCS5A01G124400
chr3D
434077741
434078675
934
False
1334
1334
92.616
1
930
1
chr3D.!!$F2
929
6
TraesCS5A01G124400
chr2D
46525239
46527762
2523
False
3936
3936
94.907
1
2513
1
chr2D.!!$F1
2512
7
TraesCS5A01G124400
chr2D
304671611
304672542
931
False
1354
1354
93.016
1
930
1
chr2D.!!$F2
929
8
TraesCS5A01G124400
chr7D
510254720
510257245
2525
False
3932
3932
94.868
1
2513
1
chr7D.!!$F1
2512
9
TraesCS5A01G124400
chr7D
207213054
207213986
932
True
1354
1354
93.031
1
930
1
chr7D.!!$R1
929
10
TraesCS5A01G124400
chr7D
591991894
591992522
628
True
928
928
93.661
1
615
1
chr7D.!!$R2
614
11
TraesCS5A01G124400
chr6B
151617793
151620324
2531
False
3927
3927
94.793
1
2513
1
chr6B.!!$F1
2512
12
TraesCS5A01G124400
chr5D
306883655
306886184
2529
True
3925
3925
94.799
1
2513
1
chr5D.!!$R1
2512
13
TraesCS5A01G124400
chr7B
432966832
432969360
2528
False
3886
3886
94.512
1
2513
1
chr7B.!!$F1
2512
14
TraesCS5A01G124400
chr6D
451598096
451600149
2053
True
3145
3145
94.353
1
2054
1
chr6D.!!$R2
2053
15
TraesCS5A01G124400
chr6D
397852414
397854472
2058
True
3144
3144
94.316
1
2054
1
chr6D.!!$R1
2053
16
TraesCS5A01G124400
chr1D
374127036
374129083
2047
False
3079
3079
93.822
1
2054
1
chr1D.!!$F1
2053
17
TraesCS5A01G124400
chr1D
466980975
466981907
932
True
1286
1286
91.719
1
934
1
chr1D.!!$R1
933
18
TraesCS5A01G124400
chr4D
90541742
90542456
714
True
963
963
91.209
1
711
1
chr4D.!!$R1
710
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.