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
TraesCS6A01G025400
chr6A
100.000
3397
0
0
1
3397
12588695
12592091
0.000000e+00
6274.0
1
TraesCS6A01G025400
chr6A
93.910
2496
85
26
759
3192
12892927
12890437
0.000000e+00
3705.0
2
TraesCS6A01G025400
chr6A
79.497
2507
323
103
354
2716
12628078
12625619
0.000000e+00
1605.0
3
TraesCS6A01G025400
chr6A
81.634
1824
222
58
977
2716
12857341
12859135
0.000000e+00
1408.0
4
TraesCS6A01G025400
chr6A
79.851
536
91
9
1731
2259
12863535
12864060
3.200000e-100
375.0
5
TraesCS6A01G025400
chr6A
85.149
202
28
1
3195
3396
12861497
12861696
4.440000e-49
206.0
6
TraesCS6A01G025400
chr6A
86.047
172
24
0
3192
3363
12622140
12621969
5.790000e-43
185.0
7
TraesCS6A01G025400
chr6A
83.410
217
19
5
2977
3192
12864091
12864291
5.790000e-43
185.0
8
TraesCS6A01G025400
chr6A
85.882
85
12
0
1731
1815
12623030
12622946
1.300000e-14
91.6
9
TraesCS6A01G025400
chr6B
91.670
2209
132
24
810
2976
21143682
21145880
0.000000e+00
3013.0
10
TraesCS6A01G025400
chr6B
79.363
1914
256
72
332
2137
21210898
21209016
0.000000e+00
1218.0
11
TraesCS6A01G025400
chr6B
85.055
823
83
23
2174
2976
21208853
21208051
0.000000e+00
802.0
12
TraesCS6A01G025400
chr6B
91.688
385
25
4
437
821
21143286
21143663
8.350000e-146
527.0
13
TraesCS6A01G025400
chr6B
93.839
211
13
0
3187
3397
21149009
21149219
5.470000e-83
318.0
14
TraesCS6A01G025400
chr6B
87.791
172
21
0
3187
3358
21207637
21207466
5.750000e-48
202.0
15
TraesCS6A01G025400
chr6B
82.273
220
21
12
2977
3192
21208000
21207795
1.250000e-39
174.0
16
TraesCS6A01G025400
chr6D
94.269
1745
55
11
1217
2933
11569344
11567617
0.000000e+00
2627.0
17
TraesCS6A01G025400
chr6D
78.842
2505
346
99
332
2716
11359653
11357213
0.000000e+00
1520.0
18
TraesCS6A01G025400
chr6D
81.065
1991
225
78
837
2716
11430174
11432123
0.000000e+00
1448.0
19
TraesCS6A01G025400
chr6D
95.588
816
34
2
2583
3397
11335913
11336727
0.000000e+00
1306.0
20
TraesCS6A01G025400
chr6D
90.671
954
43
15
1641
2593
11333607
11334515
0.000000e+00
1227.0
21
TraesCS6A01G025400
chr6D
94.394
767
43
0
1
767
11322287
11323053
0.000000e+00
1179.0
22
TraesCS6A01G025400
chr6D
90.909
792
47
12
873
1647
11324612
11325395
0.000000e+00
1040.0
23
TraesCS6A01G025400
chr6D
80.990
505
79
10
1733
2230
11434553
11435047
5.320000e-103
385.0
24
TraesCS6A01G025400
chr6D
93.511
262
12
1
2931
3192
11565902
11565646
5.320000e-103
385.0
25
TraesCS6A01G025400
chr6D
93.583
187
12
0
3210
3396
11492444
11492258
2.580000e-71
279.0
26
TraesCS6A01G025400
chr6D
83.871
217
19
5
2977
3192
11354099
11353898
3.460000e-45
193.0
27
TraesCS6A01G025400
chr6D
84.971
173
20
2
3192
3363
11353735
11353568
1.620000e-38
171.0
28
TraesCS6A01G025400
chr6D
74.359
429
92
13
333
756
11406245
11405830
2.100000e-37
167.0
29
TraesCS6A01G025400
chr6D
100.000
38
0
0
770
807
11323219
11323256
1.690000e-08
71.3
30
TraesCS6A01G025400
chr1D
74.473
1187
217
50
991
2108
485737461
485736292
5.210000e-118
435.0
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
TraesCS6A01G025400
chr6A
12588695
12592091
3396
False
6274.000000
6274
100.000000
1
3397
1
chr6A.!!$F1
3396
1
TraesCS6A01G025400
chr6A
12890437
12892927
2490
True
3705.000000
3705
93.910000
759
3192
1
chr6A.!!$R1
2433
2
TraesCS6A01G025400
chr6A
12621969
12628078
6109
True
627.200000
1605
83.808667
354
3363
3
chr6A.!!$R2
3009
3
TraesCS6A01G025400
chr6A
12857341
12864291
6950
False
543.500000
1408
82.511000
977
3396
4
chr6A.!!$F2
2419
4
TraesCS6A01G025400
chr6B
21143286
21149219
5933
False
1286.000000
3013
92.399000
437
3397
3
chr6B.!!$F1
2960
5
TraesCS6A01G025400
chr6B
21207466
21210898
3432
True
599.000000
1218
83.620500
332
3358
4
chr6B.!!$R1
3026
6
TraesCS6A01G025400
chr6D
11565646
11569344
3698
True
1506.000000
2627
93.890000
1217
3192
2
chr6D.!!$R4
1975
7
TraesCS6A01G025400
chr6D
11333607
11336727
3120
False
1266.500000
1306
93.129500
1641
3397
2
chr6D.!!$F2
1756
8
TraesCS6A01G025400
chr6D
11430174
11435047
4873
False
916.500000
1448
81.027500
837
2716
2
chr6D.!!$F3
1879
9
TraesCS6A01G025400
chr6D
11322287
11325395
3108
False
763.433333
1179
95.101000
1
1647
3
chr6D.!!$F1
1646
10
TraesCS6A01G025400
chr6D
11353568
11359653
6085
True
628.000000
1520
82.561333
332
3363
3
chr6D.!!$R3
3031
11
TraesCS6A01G025400
chr1D
485736292
485737461
1169
True
435.000000
435
74.473000
991
2108
1
chr1D.!!$R1
1117
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.