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
TraesCS2B01G478600
chr2B
100.000
3691
0
0
1
3691
675968200
675964510
0
6817
1
TraesCS2B01G478600
chr2B
92.608
3720
231
21
1
3691
260628256
260631960
0
5306
2
TraesCS2B01G478600
chr2B
90.254
2760
229
22
6
2739
249627562
249630307
0
3570
3
TraesCS2B01G478600
chr2B
92.408
2384
140
13
1
2353
67196764
67194391
0
3362
4
TraesCS2B01G478600
chr2B
90.901
2385
170
16
1
2353
687305090
687302721
0
3158
5
TraesCS2B01G478600
chr2B
91.730
1983
136
19
1710
3691
504863211
504865166
0
2728
6
TraesCS2B01G478600
chr6B
90.929
3737
252
49
1
3691
169045528
169049223
0
4942
7
TraesCS2B01G478600
chr6B
91.334
2631
180
27
1
2602
677467986
677470597
0
3552
8
TraesCS2B01G478600
chr6B
91.643
1783
117
24
1913
3691
593274840
593273086
0
2438
9
TraesCS2B01G478600
chr7B
90.342
3717
311
36
1
3691
54291686
54287992
0
4831
10
TraesCS2B01G478600
chr7B
91.044
3506
264
32
211
3691
331002081
330998601
0
4689
11
TraesCS2B01G478600
chr7B
91.522
2595
156
30
1
2542
655035987
655033404
0
3515
12
TraesCS2B01G478600
chr7B
92.653
2382
136
11
1
2353
16171985
16169614
0
3393
13
TraesCS2B01G478600
chr1B
89.510
3718
324
37
1
3691
117925548
117929226
0
4645
14
TraesCS2B01G478600
chr1B
92.614
2383
133
19
1
2353
547571325
547568956
0
3386
15
TraesCS2B01G478600
chr3B
88.606
3730
340
56
1
3691
543862331
543858648
0
4455
16
TraesCS2B01G478600
chr3B
89.522
2806
242
32
1
2778
725450344
725447563
0
3506
17
TraesCS2B01G478600
chr3B
92.401
2382
139
12
1
2353
46768146
46770514
0
3358
18
TraesCS2B01G478600
chr5B
92.065
2382
148
15
1
2351
541106378
541108749
0
3314
19
TraesCS2B01G478600
chr4B
93.700
1857
108
9
1838
3691
409315886
409317736
0
2772
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
TraesCS2B01G478600
chr2B
675964510
675968200
3690
True
6817
6817
100.000
1
3691
1
chr2B.!!$R2
3690
1
TraesCS2B01G478600
chr2B
260628256
260631960
3704
False
5306
5306
92.608
1
3691
1
chr2B.!!$F2
3690
2
TraesCS2B01G478600
chr2B
249627562
249630307
2745
False
3570
3570
90.254
6
2739
1
chr2B.!!$F1
2733
3
TraesCS2B01G478600
chr2B
67194391
67196764
2373
True
3362
3362
92.408
1
2353
1
chr2B.!!$R1
2352
4
TraesCS2B01G478600
chr2B
687302721
687305090
2369
True
3158
3158
90.901
1
2353
1
chr2B.!!$R3
2352
5
TraesCS2B01G478600
chr2B
504863211
504865166
1955
False
2728
2728
91.730
1710
3691
1
chr2B.!!$F3
1981
6
TraesCS2B01G478600
chr6B
169045528
169049223
3695
False
4942
4942
90.929
1
3691
1
chr6B.!!$F1
3690
7
TraesCS2B01G478600
chr6B
677467986
677470597
2611
False
3552
3552
91.334
1
2602
1
chr6B.!!$F2
2601
8
TraesCS2B01G478600
chr6B
593273086
593274840
1754
True
2438
2438
91.643
1913
3691
1
chr6B.!!$R1
1778
9
TraesCS2B01G478600
chr7B
54287992
54291686
3694
True
4831
4831
90.342
1
3691
1
chr7B.!!$R2
3690
10
TraesCS2B01G478600
chr7B
330998601
331002081
3480
True
4689
4689
91.044
211
3691
1
chr7B.!!$R3
3480
11
TraesCS2B01G478600
chr7B
655033404
655035987
2583
True
3515
3515
91.522
1
2542
1
chr7B.!!$R4
2541
12
TraesCS2B01G478600
chr7B
16169614
16171985
2371
True
3393
3393
92.653
1
2353
1
chr7B.!!$R1
2352
13
TraesCS2B01G478600
chr1B
117925548
117929226
3678
False
4645
4645
89.510
1
3691
1
chr1B.!!$F1
3690
14
TraesCS2B01G478600
chr1B
547568956
547571325
2369
True
3386
3386
92.614
1
2353
1
chr1B.!!$R1
2352
15
TraesCS2B01G478600
chr3B
543858648
543862331
3683
True
4455
4455
88.606
1
3691
1
chr3B.!!$R1
3690
16
TraesCS2B01G478600
chr3B
725447563
725450344
2781
True
3506
3506
89.522
1
2778
1
chr3B.!!$R2
2777
17
TraesCS2B01G478600
chr3B
46768146
46770514
2368
False
3358
3358
92.401
1
2353
1
chr3B.!!$F1
2352
18
TraesCS2B01G478600
chr5B
541106378
541108749
2371
False
3314
3314
92.065
1
2351
1
chr5B.!!$F1
2350
19
TraesCS2B01G478600
chr4B
409315886
409317736
1850
False
2772
2772
93.700
1838
3691
1
chr4B.!!$F1
1853
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.