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
TraesCS4A01G444700
chr4A
100.000
3146
0
0
1
3146
713013959
713017104
0.000000e+00
5810
1
TraesCS4A01G444700
chr4A
87.484
2317
253
17
848
3140
713032310
713034613
0.000000e+00
2638
2
TraesCS4A01G444700
chr4A
87.942
821
65
15
3
818
713031524
713032315
0.000000e+00
937
3
TraesCS4A01G444700
chr4A
90.682
601
42
9
3
590
494467550
494468149
0.000000e+00
787
4
TraesCS4A01G444700
chr4A
92.222
360
28
0
3
362
617108919
617109278
7.780000e-141
510
5
TraesCS4A01G444700
chr7D
87.744
3182
339
31
1
3146
20484762
20487928
0.000000e+00
3668
6
TraesCS4A01G444700
chr7D
89.062
2377
240
16
3
2371
20520398
20522762
0.000000e+00
2931
7
TraesCS4A01G444700
chr7D
86.719
2402
282
26
770
3146
20310770
20313159
0.000000e+00
2634
8
TraesCS4A01G444700
chr7D
84.891
2429
315
28
742
3144
20598269
20600671
0.000000e+00
2405
9
TraesCS4A01G444700
chr7D
83.682
2341
344
23
833
3146
20404284
20406613
0.000000e+00
2172
10
TraesCS4A01G444700
chr7D
82.581
2394
373
32
783
3146
20947076
20949455
0.000000e+00
2071
11
TraesCS4A01G444700
chr7A
88.337
2375
252
20
783
3146
20588683
20591043
0.000000e+00
2828
12
TraesCS4A01G444700
chr7A
87.238
2390
272
9
779
3146
20650734
20653112
0.000000e+00
2693
13
TraesCS4A01G444700
chr7A
85.599
2604
330
27
561
3146
20910419
20912995
0.000000e+00
2689
14
TraesCS4A01G444700
chr7A
86.373
2407
288
26
770
3146
20482718
20485114
0.000000e+00
2591
15
TraesCS4A01G444700
chr7A
86.029
2405
295
32
770
3146
20966196
20968587
0.000000e+00
2542
16
TraesCS4A01G444700
chr7A
87.586
2175
260
7
975
3146
20457865
20460032
0.000000e+00
2512
17
TraesCS4A01G444700
chr7A
83.675
2389
348
27
787
3146
20659584
20661959
0.000000e+00
2213
18
TraesCS4A01G444700
chr7A
87.250
549
58
9
13
555
20909752
20910294
1.600000e-172
616
19
TraesCS4A01G444700
chr7A
80.569
211
30
7
314
518
20697595
20697800
5.430000e-33
152
20
TraesCS4A01G444700
chr6B
91.892
333
27
0
3
335
534958038
534958370
1.710000e-127
466
21
TraesCS4A01G444700
chr6B
91.156
147
11
2
329
473
534977438
534977584
6.880000e-47
198
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
TraesCS4A01G444700
chr4A
713013959
713017104
3145
False
5810.0
5810
100.0000
1
3146
1
chr4A.!!$F3
3145
1
TraesCS4A01G444700
chr4A
713031524
713034613
3089
False
1787.5
2638
87.7130
3
3140
2
chr4A.!!$F4
3137
2
TraesCS4A01G444700
chr4A
494467550
494468149
599
False
787.0
787
90.6820
3
590
1
chr4A.!!$F1
587
3
TraesCS4A01G444700
chr7D
20484762
20487928
3166
False
3668.0
3668
87.7440
1
3146
1
chr7D.!!$F3
3145
4
TraesCS4A01G444700
chr7D
20520398
20522762
2364
False
2931.0
2931
89.0620
3
2371
1
chr7D.!!$F4
2368
5
TraesCS4A01G444700
chr7D
20310770
20313159
2389
False
2634.0
2634
86.7190
770
3146
1
chr7D.!!$F1
2376
6
TraesCS4A01G444700
chr7D
20598269
20600671
2402
False
2405.0
2405
84.8910
742
3144
1
chr7D.!!$F5
2402
7
TraesCS4A01G444700
chr7D
20404284
20406613
2329
False
2172.0
2172
83.6820
833
3146
1
chr7D.!!$F2
2313
8
TraesCS4A01G444700
chr7D
20947076
20949455
2379
False
2071.0
2071
82.5810
783
3146
1
chr7D.!!$F6
2363
9
TraesCS4A01G444700
chr7A
20588683
20591043
2360
False
2828.0
2828
88.3370
783
3146
1
chr7A.!!$F3
2363
10
TraesCS4A01G444700
chr7A
20650734
20653112
2378
False
2693.0
2693
87.2380
779
3146
1
chr7A.!!$F4
2367
11
TraesCS4A01G444700
chr7A
20482718
20485114
2396
False
2591.0
2591
86.3730
770
3146
1
chr7A.!!$F2
2376
12
TraesCS4A01G444700
chr7A
20966196
20968587
2391
False
2542.0
2542
86.0290
770
3146
1
chr7A.!!$F7
2376
13
TraesCS4A01G444700
chr7A
20457865
20460032
2167
False
2512.0
2512
87.5860
975
3146
1
chr7A.!!$F1
2171
14
TraesCS4A01G444700
chr7A
20659584
20661959
2375
False
2213.0
2213
83.6750
787
3146
1
chr7A.!!$F5
2359
15
TraesCS4A01G444700
chr7A
20909752
20912995
3243
False
1652.5
2689
86.4245
13
3146
2
chr7A.!!$F8
3133
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.