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
TraesCS7A01G230700
chr7A
100.000
2432
0
0
1
2432
201367144
201369575
0.000000e+00
4492
1
TraesCS7A01G230700
chrUn
97.375
1600
31
6
841
2432
93418001
93419597
0.000000e+00
2712
2
TraesCS7A01G230700
chrUn
98.588
850
8
2
1
846
327660628
327661477
0.000000e+00
1500
3
TraesCS7A01G230700
chrUn
98.239
852
9
4
1
846
93417096
93417947
0.000000e+00
1485
4
TraesCS7A01G230700
chr1D
97.312
1600
31
7
841
2432
144237051
144235456
0.000000e+00
2706
5
TraesCS7A01G230700
chr1D
97.892
854
10
5
1
846
144237958
144237105
0.000000e+00
1471
6
TraesCS7A01G230700
chr5D
97.250
1600
32
7
841
2432
560878815
560877220
0.000000e+00
2700
7
TraesCS7A01G230700
chr5D
97.188
1600
32
8
841
2432
503212254
503210660
0.000000e+00
2693
8
TraesCS7A01G230700
chr5D
97.070
1331
36
2
1099
2427
329196036
329194707
0.000000e+00
2239
9
TraesCS7A01G230700
chr5D
98.474
852
7
3
1
846
560879720
560878869
0.000000e+00
1496
10
TraesCS7A01G230700
chr5D
97.535
852
10
6
1
846
503213154
503212308
0.000000e+00
1447
11
TraesCS7A01G230700
chr3B
97.188
1600
33
7
841
2432
201521022
201519427
0.000000e+00
2695
12
TraesCS7A01G230700
chr3B
97.186
853
16
6
1
846
201521926
201521075
0.000000e+00
1435
13
TraesCS7A01G230700
chr3B
94.964
139
2
2
891
1024
804586607
804586469
1.890000e-51
213
14
TraesCS7A01G230700
chr6A
96.289
1590
49
5
850
2432
271183789
271182203
0.000000e+00
2601
15
TraesCS7A01G230700
chr6A
95.810
1599
56
6
841
2432
260126433
260128027
0.000000e+00
2571
16
TraesCS7A01G230700
chr6A
98.233
849
12
1
1
846
271184698
271183850
0.000000e+00
1482
17
TraesCS7A01G230700
chr1A
95.812
1600
52
9
841
2432
168444269
168445861
0.000000e+00
2569
18
TraesCS7A01G230700
chr2D
98.588
850
8
2
1
846
272798982
272799831
0.000000e+00
1500
19
TraesCS7A01G230700
chr4A
97.532
851
13
5
1
846
722779640
722780487
0.000000e+00
1448
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
TraesCS7A01G230700
chr7A
201367144
201369575
2431
False
4492.0
4492
100.0000
1
2432
1
chr7A.!!$F1
2431
1
TraesCS7A01G230700
chrUn
93417096
93419597
2501
False
2098.5
2712
97.8070
1
2432
2
chrUn.!!$F2
2431
2
TraesCS7A01G230700
chrUn
327660628
327661477
849
False
1500.0
1500
98.5880
1
846
1
chrUn.!!$F1
845
3
TraesCS7A01G230700
chr1D
144235456
144237958
2502
True
2088.5
2706
97.6020
1
2432
2
chr1D.!!$R1
2431
4
TraesCS7A01G230700
chr5D
329194707
329196036
1329
True
2239.0
2239
97.0700
1099
2427
1
chr5D.!!$R1
1328
5
TraesCS7A01G230700
chr5D
560877220
560879720
2500
True
2098.0
2700
97.8620
1
2432
2
chr5D.!!$R3
2431
6
TraesCS7A01G230700
chr5D
503210660
503213154
2494
True
2070.0
2693
97.3615
1
2432
2
chr5D.!!$R2
2431
7
TraesCS7A01G230700
chr3B
201519427
201521926
2499
True
2065.0
2695
97.1870
1
2432
2
chr3B.!!$R2
2431
8
TraesCS7A01G230700
chr6A
260126433
260128027
1594
False
2571.0
2571
95.8100
841
2432
1
chr6A.!!$F1
1591
9
TraesCS7A01G230700
chr6A
271182203
271184698
2495
True
2041.5
2601
97.2610
1
2432
2
chr6A.!!$R1
2431
10
TraesCS7A01G230700
chr1A
168444269
168445861
1592
False
2569.0
2569
95.8120
841
2432
1
chr1A.!!$F1
1591
11
TraesCS7A01G230700
chr2D
272798982
272799831
849
False
1500.0
1500
98.5880
1
846
1
chr2D.!!$F1
845
12
TraesCS7A01G230700
chr4A
722779640
722780487
847
False
1448.0
1448
97.5320
1
846
1
chr4A.!!$F1
845
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.