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
TraesCS7B01G395800
chr7B
100.000
3287
0
0
1
3287
662754028
662750742
0
6071
1
TraesCS7B01G395800
chr1A
98.986
2366
21
2
925
3287
554483987
554486352
0
4233
2
TraesCS7B01G395800
chr2B
98.943
2365
23
1
925
3287
683729407
683731771
0
4228
3
TraesCS7B01G395800
chr3A
98.604
2364
32
1
925
3287
105554994
105552631
0
4181
4
TraesCS7B01G395800
chr3A
97.859
934
16
3
1
931
105555952
105555020
0
1611
5
TraesCS7B01G395800
chr5D
98.308
2364
37
3
925
3287
6251310
6248949
0
4141
6
TraesCS7B01G395800
chr5D
98.223
2364
38
4
925
3287
503315468
503317828
0
4130
7
TraesCS7B01G395800
chr5D
97.122
2363
62
4
925
3287
432268317
432265961
0
3982
8
TraesCS7B01G395800
chr5D
98.075
935
13
3
1
931
299970983
299970050
0
1622
9
TraesCS7B01G395800
chr5D
97.540
935
16
5
1
931
503340450
503341381
0
1592
10
TraesCS7B01G395800
chr1D
97.805
2369
44
5
925
3287
254461367
254463733
0
4080
11
TraesCS7B01G395800
chr1D
97.294
2365
54
6
925
3287
51830000
51827644
0
4004
12
TraesCS7B01G395800
chr1D
97.216
934
17
5
1
931
254460414
254461341
0
1572
13
TraesCS7B01G395800
chr7A
96.743
2364
65
6
925
3287
537839447
537837095
0
3928
14
TraesCS7B01G395800
chr5A
98.077
936
11
4
1
931
559030943
559030010
0
1622
15
TraesCS7B01G395800
chrUn
97.968
935
14
3
1
931
386224624
386225557
0
1616
16
TraesCS7B01G395800
chrUn
97.433
935
18
4
1
931
261567685
261566753
0
1589
17
TraesCS7B01G395800
chr5B
97.968
935
14
3
1
931
57514118
57513185
0
1616
18
TraesCS7B01G395800
chr1B
97.953
928
15
2
1
924
633717976
633718903
0
1605
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
TraesCS7B01G395800
chr7B
662750742
662754028
3286
True
6071
6071
100.0000
1
3287
1
chr7B.!!$R1
3286
1
TraesCS7B01G395800
chr1A
554483987
554486352
2365
False
4233
4233
98.9860
925
3287
1
chr1A.!!$F1
2362
2
TraesCS7B01G395800
chr2B
683729407
683731771
2364
False
4228
4228
98.9430
925
3287
1
chr2B.!!$F1
2362
3
TraesCS7B01G395800
chr3A
105552631
105555952
3321
True
2896
4181
98.2315
1
3287
2
chr3A.!!$R1
3286
4
TraesCS7B01G395800
chr5D
6248949
6251310
2361
True
4141
4141
98.3080
925
3287
1
chr5D.!!$R1
2362
5
TraesCS7B01G395800
chr5D
503315468
503317828
2360
False
4130
4130
98.2230
925
3287
1
chr5D.!!$F1
2362
6
TraesCS7B01G395800
chr5D
432265961
432268317
2356
True
3982
3982
97.1220
925
3287
1
chr5D.!!$R3
2362
7
TraesCS7B01G395800
chr5D
299970050
299970983
933
True
1622
1622
98.0750
1
931
1
chr5D.!!$R2
930
8
TraesCS7B01G395800
chr5D
503340450
503341381
931
False
1592
1592
97.5400
1
931
1
chr5D.!!$F2
930
9
TraesCS7B01G395800
chr1D
51827644
51830000
2356
True
4004
4004
97.2940
925
3287
1
chr1D.!!$R1
2362
10
TraesCS7B01G395800
chr1D
254460414
254463733
3319
False
2826
4080
97.5105
1
3287
2
chr1D.!!$F1
3286
11
TraesCS7B01G395800
chr7A
537837095
537839447
2352
True
3928
3928
96.7430
925
3287
1
chr7A.!!$R1
2362
12
TraesCS7B01G395800
chr5A
559030010
559030943
933
True
1622
1622
98.0770
1
931
1
chr5A.!!$R1
930
13
TraesCS7B01G395800
chrUn
386224624
386225557
933
False
1616
1616
97.9680
1
931
1
chrUn.!!$F1
930
14
TraesCS7B01G395800
chrUn
261566753
261567685
932
True
1589
1589
97.4330
1
931
1
chrUn.!!$R1
930
15
TraesCS7B01G395800
chr5B
57513185
57514118
933
True
1616
1616
97.9680
1
931
1
chr5B.!!$R1
930
16
TraesCS7B01G395800
chr1B
633717976
633718903
927
False
1605
1605
97.9530
1
924
1
chr1B.!!$F1
923
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.