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
TraesCS3B01G381700
chr3B
100.000
2438
0
0
1
2438
600724395
600721958
0
4503
1
TraesCS3B01G381700
chr3B
95.263
2449
97
8
4
2438
600811011
600808568
0
3862
2
TraesCS3B01G381700
chr3B
94.120
2449
122
10
4
2438
600686155
600683715
0
3705
3
TraesCS3B01G381700
chr3B
89.202
2445
230
18
10
2438
136864985
136862559
0
3022
4
TraesCS3B01G381700
chr3B
91.098
2112
158
15
352
2438
543790839
543788733
0
2832
5
TraesCS3B01G381700
chr3B
89.251
1442
128
15
1012
2438
119553431
119552002
0
1779
6
TraesCS3B01G381700
chr7B
89.833
2449
215
15
15
2437
600951683
600949243
0
3112
7
TraesCS3B01G381700
chr6B
89.743
2447
219
15
15
2436
590255078
590252639
0
3099
8
TraesCS3B01G381700
chr6B
88.979
2459
238
15
6
2438
122918168
122920619
0
3009
9
TraesCS3B01G381700
chr6B
88.336
2452
252
21
5
2438
190437241
190439676
0
2913
10
TraesCS3B01G381700
chr6B
89.395
2131
203
11
1
2116
169614690
169616812
0
2662
11
TraesCS3B01G381700
chr2B
89.678
2451
217
19
15
2438
170716046
170713605
0
3092
12
TraesCS3B01G381700
chr2B
88.780
2451
238
22
5
2438
246192273
246189843
0
2968
13
TraesCS3B01G381700
chr2B
92.457
875
51
5
1578
2438
696571205
696572078
0
1236
14
TraesCS3B01G381700
chr5B
89.510
2450
222
21
5
2438
430441439
430443869
0
3068
15
TraesCS3B01G381700
chr4B
88.610
2432
242
25
4
2417
155993890
155991476
0
2924
16
TraesCS3B01G381700
chr4B
87.796
2450
261
25
4
2438
377199850
377197424
0
2833
17
TraesCS3B01G381700
chr4B
86.765
2448
283
24
11
2438
339692376
339689950
0
2687
18
TraesCS3B01G381700
chr1B
81.714
2450
403
34
4
2438
685068101
685070520
0
2001
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
TraesCS3B01G381700
chr3B
600721958
600724395
2437
True
4503
4503
100.000
1
2438
1
chr3B.!!$R5
2437
1
TraesCS3B01G381700
chr3B
600808568
600811011
2443
True
3862
3862
95.263
4
2438
1
chr3B.!!$R6
2434
2
TraesCS3B01G381700
chr3B
600683715
600686155
2440
True
3705
3705
94.120
4
2438
1
chr3B.!!$R4
2434
3
TraesCS3B01G381700
chr3B
136862559
136864985
2426
True
3022
3022
89.202
10
2438
1
chr3B.!!$R2
2428
4
TraesCS3B01G381700
chr3B
543788733
543790839
2106
True
2832
2832
91.098
352
2438
1
chr3B.!!$R3
2086
5
TraesCS3B01G381700
chr3B
119552002
119553431
1429
True
1779
1779
89.251
1012
2438
1
chr3B.!!$R1
1426
6
TraesCS3B01G381700
chr7B
600949243
600951683
2440
True
3112
3112
89.833
15
2437
1
chr7B.!!$R1
2422
7
TraesCS3B01G381700
chr6B
590252639
590255078
2439
True
3099
3099
89.743
15
2436
1
chr6B.!!$R1
2421
8
TraesCS3B01G381700
chr6B
122918168
122920619
2451
False
3009
3009
88.979
6
2438
1
chr6B.!!$F1
2432
9
TraesCS3B01G381700
chr6B
190437241
190439676
2435
False
2913
2913
88.336
5
2438
1
chr6B.!!$F3
2433
10
TraesCS3B01G381700
chr6B
169614690
169616812
2122
False
2662
2662
89.395
1
2116
1
chr6B.!!$F2
2115
11
TraesCS3B01G381700
chr2B
170713605
170716046
2441
True
3092
3092
89.678
15
2438
1
chr2B.!!$R1
2423
12
TraesCS3B01G381700
chr2B
246189843
246192273
2430
True
2968
2968
88.780
5
2438
1
chr2B.!!$R2
2433
13
TraesCS3B01G381700
chr2B
696571205
696572078
873
False
1236
1236
92.457
1578
2438
1
chr2B.!!$F1
860
14
TraesCS3B01G381700
chr5B
430441439
430443869
2430
False
3068
3068
89.510
5
2438
1
chr5B.!!$F1
2433
15
TraesCS3B01G381700
chr4B
155991476
155993890
2414
True
2924
2924
88.610
4
2417
1
chr4B.!!$R1
2413
16
TraesCS3B01G381700
chr4B
377197424
377199850
2426
True
2833
2833
87.796
4
2438
1
chr4B.!!$R3
2434
17
TraesCS3B01G381700
chr4B
339689950
339692376
2426
True
2687
2687
86.765
11
2438
1
chr4B.!!$R2
2427
18
TraesCS3B01G381700
chr1B
685068101
685070520
2419
False
2001
2001
81.714
4
2438
1
chr1B.!!$F1
2434
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.