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
TraesCS2A01G347800
chr2A
100.000
5702
0
0
1
5702
586445202
586450903
0.000000e+00
10530.0
1
TraesCS2A01G347800
chr2A
85.256
156
22
1
1287
1442
18322541
18322387
5.910000e-35
159.0
2
TraesCS2A01G347800
chr2D
97.093
4884
89
17
3
4861
442975840
442980695
0.000000e+00
8183.0
3
TraesCS2A01G347800
chr2D
88.864
880
44
19
4869
5702
442982363
442983234
0.000000e+00
1033.0
4
TraesCS2A01G347800
chr2B
96.638
2915
76
6
788
3697
522079226
522082123
0.000000e+00
4820.0
5
TraesCS2A01G347800
chr2B
92.582
2076
70
26
3684
5702
522082140
522084188
0.000000e+00
2904.0
6
TraesCS2A01G347800
chr2B
87.985
799
52
18
3
778
522078145
522078922
0.000000e+00
904.0
7
TraesCS2A01G347800
chr2B
83.373
415
41
15
1541
1927
182254422
182254008
5.430000e-95
359.0
8
TraesCS2A01G347800
chr2B
90.000
280
24
3
1538
1815
283295414
283295691
5.430000e-95
359.0
9
TraesCS2A01G347800
chr2B
85.397
315
33
3
3252
3554
283295962
283296275
1.190000e-81
315.0
10
TraesCS2A01G347800
chr2B
81.108
397
54
17
379
761
283294174
283294563
1.200000e-76
298.0
11
TraesCS2A01G347800
chr2B
83.067
313
31
10
3252
3552
182253879
182253577
1.220000e-66
265.0
12
TraesCS2A01G347800
chr1B
85.103
584
64
16
1442
2013
357238307
357238879
4.950000e-160
575.0
13
TraesCS2A01G347800
chr1B
79.716
705
82
31
379
1046
357237425
357238105
2.420000e-123
453.0
14
TraesCS2A01G347800
chr1B
83.636
220
21
8
1070
1289
357238101
357238305
5.830000e-45
193.0
15
TraesCS2A01G347800
chr4B
83.493
418
39
17
1538
1927
195450940
195451355
4.200000e-96
363.0
16
TraesCS2A01G347800
chr4B
84.494
316
34
5
3252
3554
195451484
195451797
1.200000e-76
298.0
17
TraesCS2A01G347800
chr3B
83.513
279
38
8
2403
2676
479852440
479852165
2.640000e-63
254.0
18
TraesCS2A01G347800
chr3D
88.462
156
18
0
1289
1444
441388819
441388664
7.540000e-44
189.0
19
TraesCS2A01G347800
chr3D
85.065
154
22
1
1288
1441
375193911
375193759
7.650000e-34
156.0
20
TraesCS2A01G347800
chr3A
87.821
156
19
0
1289
1444
582283367
582283212
3.510000e-42
183.0
21
TraesCS2A01G347800
chr3A
86.364
154
20
1
1288
1441
498230087
498229935
3.530000e-37
167.0
22
TraesCS2A01G347800
chr6B
87.179
156
19
1
1289
1444
468734617
468734463
5.870000e-40
176.0
23
TraesCS2A01G347800
chr6B
86.538
52
7
0
2559
2610
554033901
554033850
2.220000e-04
58.4
24
TraesCS2A01G347800
chr7A
84.615
169
24
2
1286
1452
511930528
511930696
3.530000e-37
167.0
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
TraesCS2A01G347800
chr2A
586445202
586450903
5701
False
10530.0
10530
100.000000
1
5702
1
chr2A.!!$F1
5701
1
TraesCS2A01G347800
chr2D
442975840
442983234
7394
False
4608.0
8183
92.978500
3
5702
2
chr2D.!!$F1
5699
2
TraesCS2A01G347800
chr2B
522078145
522084188
6043
False
2876.0
4820
92.401667
3
5702
3
chr2B.!!$F2
5699
3
TraesCS2A01G347800
chr2B
283294174
283296275
2101
False
324.0
359
85.501667
379
3554
3
chr2B.!!$F1
3175
4
TraesCS2A01G347800
chr2B
182253577
182254422
845
True
312.0
359
83.220000
1541
3552
2
chr2B.!!$R1
2011
5
TraesCS2A01G347800
chr1B
357237425
357238879
1454
False
407.0
575
82.818333
379
2013
3
chr1B.!!$F1
1634
6
TraesCS2A01G347800
chr4B
195450940
195451797
857
False
330.5
363
83.993500
1538
3554
2
chr4B.!!$F1
2016
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.