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
TraesCS7D01G455600
chr7D
100.000
2348
0
0
1
2348
574721142
574723489
0
4337
1
TraesCS7D01G455600
chr7D
96.913
907
22
5
1443
2348
113995923
113995022
0
1515
2
TraesCS7D01G455600
chr5D
97.095
2375
42
11
1
2348
336342354
336344728
0
3978
3
TraesCS7D01G455600
chr5D
96.509
2349
45
5
1
2348
213965274
213962962
0
3849
4
TraesCS7D01G455600
chr5D
96.424
2349
47
5
1
2348
559988282
559990594
0
3838
5
TraesCS7D01G455600
chr5D
96.343
1832
42
8
1
1808
482324764
482326594
0
2988
6
TraesCS7D01G455600
chr6D
96.797
2373
49
4
1
2348
109969253
109966883
0
3936
7
TraesCS7D01G455600
chr6D
96.514
2352
45
4
1
2348
52515771
52518089
0
3855
8
TraesCS7D01G455600
chr6D
96.214
2351
42
5
1
2348
277561450
277563756
0
3805
9
TraesCS7D01G455600
chr2D
96.674
2375
50
4
1
2348
547205943
547208315
0
3921
10
TraesCS7D01G455600
chr2D
96.346
2381
47
6
1
2348
435218591
435216218
0
3879
11
TraesCS7D01G455600
chr2D
96.207
2373
61
5
1
2348
299997995
299995627
0
3856
12
TraesCS7D01G455600
chr2D
96.128
2350
50
6
1
2348
498465676
498467986
0
3797
13
TraesCS7D01G455600
chrUn
95.597
2385
64
16
1
2348
93720440
93722820
0
3784
14
TraesCS7D01G455600
chr2A
95.447
2350
67
10
1
2348
50268185
50270496
0
3711
15
TraesCS7D01G455600
chr2B
95.396
2346
72
4
6
2348
757368695
757366383
0
3701
16
TraesCS7D01G455600
chr3D
95.928
1940
38
7
1
1906
475112748
475110816
0
3107
17
TraesCS7D01G455600
chr7B
95.861
1788
68
2
1
1783
223460029
223461815
0
2887
18
TraesCS7D01G455600
chr3A
95.634
962
35
5
1390
2348
120658453
120657496
0
1537
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
TraesCS7D01G455600
chr7D
574721142
574723489
2347
False
4337
4337
100.000
1
2348
1
chr7D.!!$F1
2347
1
TraesCS7D01G455600
chr7D
113995022
113995923
901
True
1515
1515
96.913
1443
2348
1
chr7D.!!$R1
905
2
TraesCS7D01G455600
chr5D
336342354
336344728
2374
False
3978
3978
97.095
1
2348
1
chr5D.!!$F1
2347
3
TraesCS7D01G455600
chr5D
213962962
213965274
2312
True
3849
3849
96.509
1
2348
1
chr5D.!!$R1
2347
4
TraesCS7D01G455600
chr5D
559988282
559990594
2312
False
3838
3838
96.424
1
2348
1
chr5D.!!$F3
2347
5
TraesCS7D01G455600
chr5D
482324764
482326594
1830
False
2988
2988
96.343
1
1808
1
chr5D.!!$F2
1807
6
TraesCS7D01G455600
chr6D
109966883
109969253
2370
True
3936
3936
96.797
1
2348
1
chr6D.!!$R1
2347
7
TraesCS7D01G455600
chr6D
52515771
52518089
2318
False
3855
3855
96.514
1
2348
1
chr6D.!!$F1
2347
8
TraesCS7D01G455600
chr6D
277561450
277563756
2306
False
3805
3805
96.214
1
2348
1
chr6D.!!$F2
2347
9
TraesCS7D01G455600
chr2D
547205943
547208315
2372
False
3921
3921
96.674
1
2348
1
chr2D.!!$F2
2347
10
TraesCS7D01G455600
chr2D
435216218
435218591
2373
True
3879
3879
96.346
1
2348
1
chr2D.!!$R2
2347
11
TraesCS7D01G455600
chr2D
299995627
299997995
2368
True
3856
3856
96.207
1
2348
1
chr2D.!!$R1
2347
12
TraesCS7D01G455600
chr2D
498465676
498467986
2310
False
3797
3797
96.128
1
2348
1
chr2D.!!$F1
2347
13
TraesCS7D01G455600
chrUn
93720440
93722820
2380
False
3784
3784
95.597
1
2348
1
chrUn.!!$F1
2347
14
TraesCS7D01G455600
chr2A
50268185
50270496
2311
False
3711
3711
95.447
1
2348
1
chr2A.!!$F1
2347
15
TraesCS7D01G455600
chr2B
757366383
757368695
2312
True
3701
3701
95.396
6
2348
1
chr2B.!!$R1
2342
16
TraesCS7D01G455600
chr3D
475110816
475112748
1932
True
3107
3107
95.928
1
1906
1
chr3D.!!$R1
1905
17
TraesCS7D01G455600
chr7B
223460029
223461815
1786
False
2887
2887
95.861
1
1783
1
chr7B.!!$F1
1782
18
TraesCS7D01G455600
chr3A
120657496
120658453
957
True
1537
1537
95.634
1390
2348
1
chr3A.!!$R1
958
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.