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
TraesCS7B01G284000
chr7B
100.000
2369
0
0
1
2369
518289908
518287540
0
4375
1
TraesCS7B01G284000
chr7B
99.620
2369
9
0
1
2369
518305917
518303549
0
4325
2
TraesCS7B01G284000
chr4B
96.380
2376
76
6
3
2369
485379952
485382326
0
3903
3
TraesCS7B01G284000
chr4B
93.924
2370
135
8
3
2369
165971548
165969185
0
3570
4
TraesCS7B01G284000
chr3A
88.791
2382
239
22
1
2369
46666767
46664401
0
2894
5
TraesCS7B01G284000
chr3A
88.146
2379
242
22
1
2369
167683344
167680996
0
2795
6
TraesCS7B01G284000
chr2A
88.445
2380
232
25
1
2369
82414415
82412068
0
2832
7
TraesCS7B01G284000
chr2A
86.993
2391
258
36
1
2369
266908213
266905854
0
2643
8
TraesCS7B01G284000
chr2A
84.719
1996
262
32
1
1983
140707849
140709814
0
1956
9
TraesCS7B01G284000
chr2A
87.163
1223
148
8
1
1219
100908406
100907189
0
1380
10
TraesCS7B01G284000
chr1A
87.516
2275
255
25
1
2265
313569434
313567179
0
2601
11
TraesCS7B01G284000
chr7A
86.783
2285
265
25
1
2261
592894921
592897192
0
2512
12
TraesCS7B01G284000
chr1B
88.927
2023
188
31
364
2369
260841935
260839932
0
2462
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
TraesCS7B01G284000
chr7B
518287540
518289908
2368
True
4375
4375
100.000
1
2369
1
chr7B.!!$R1
2368
1
TraesCS7B01G284000
chr7B
518303549
518305917
2368
True
4325
4325
99.620
1
2369
1
chr7B.!!$R2
2368
2
TraesCS7B01G284000
chr4B
485379952
485382326
2374
False
3903
3903
96.380
3
2369
1
chr4B.!!$F1
2366
3
TraesCS7B01G284000
chr4B
165969185
165971548
2363
True
3570
3570
93.924
3
2369
1
chr4B.!!$R1
2366
4
TraesCS7B01G284000
chr3A
46664401
46666767
2366
True
2894
2894
88.791
1
2369
1
chr3A.!!$R1
2368
5
TraesCS7B01G284000
chr3A
167680996
167683344
2348
True
2795
2795
88.146
1
2369
1
chr3A.!!$R2
2368
6
TraesCS7B01G284000
chr2A
82412068
82414415
2347
True
2832
2832
88.445
1
2369
1
chr2A.!!$R1
2368
7
TraesCS7B01G284000
chr2A
266905854
266908213
2359
True
2643
2643
86.993
1
2369
1
chr2A.!!$R3
2368
8
TraesCS7B01G284000
chr2A
140707849
140709814
1965
False
1956
1956
84.719
1
1983
1
chr2A.!!$F1
1982
9
TraesCS7B01G284000
chr2A
100907189
100908406
1217
True
1380
1380
87.163
1
1219
1
chr2A.!!$R2
1218
10
TraesCS7B01G284000
chr1A
313567179
313569434
2255
True
2601
2601
87.516
1
2265
1
chr1A.!!$R1
2264
11
TraesCS7B01G284000
chr7A
592894921
592897192
2271
False
2512
2512
86.783
1
2261
1
chr7A.!!$F1
2260
12
TraesCS7B01G284000
chr1B
260839932
260841935
2003
True
2462
2462
88.927
364
2369
1
chr1B.!!$R1
2005
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.