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
TraesCS6B01G018000
chr6B
100.000
4007
0
0
1
4007
11410227
11406221
0.000000e+00
7400.0
1
TraesCS6B01G018000
chr6B
88.777
1595
138
12
175
1730
11515353
11513761
0.000000e+00
1916.0
2
TraesCS6B01G018000
chr6B
87.713
1172
95
20
2397
3550
11512743
11511603
0.000000e+00
1321.0
3
TraesCS6B01G018000
chr6B
98.292
527
8
1
2463
2989
31996567
31997092
0.000000e+00
922.0
4
TraesCS6B01G018000
chr6B
89.823
226
16
5
3785
4007
11341041
11340820
2.360000e-72
283.0
5
TraesCS6B01G018000
chr6B
89.823
226
16
5
3785
4007
11357170
11356949
2.360000e-72
283.0
6
TraesCS6B01G018000
chr6B
88.546
227
17
7
3785
4007
11380343
11380122
2.370000e-67
267.0
7
TraesCS6B01G018000
chr6B
88.957
163
18
0
2235
2397
11512955
11512793
6.790000e-48
202.0
8
TraesCS6B01G018000
chr6D
93.626
2275
86
15
1
2239
6110790
6108539
0.000000e+00
3343.0
9
TraesCS6B01G018000
chr6D
94.295
1788
68
7
2235
4007
6108502
6106734
0.000000e+00
2706.0
10
TraesCS6B01G018000
chr6D
86.552
2268
223
36
26
2241
6250224
6247987
0.000000e+00
2423.0
11
TraesCS6B01G018000
chr6D
89.140
1197
100
20
2397
3580
6247704
6246525
0.000000e+00
1463.0
12
TraesCS6B01G018000
chr6D
88.957
163
18
0
2235
2397
6247916
6247754
6.790000e-48
202.0
13
TraesCS6B01G018000
chr6D
78.689
244
47
3
1441
1684
12643005
12642767
1.490000e-34
158.0
14
TraesCS6B01G018000
chr6D
89.109
101
9
2
3688
3786
6246535
6246435
1.510000e-24
124.0
15
TraesCS6B01G018000
chr6A
92.619
2276
122
12
1
2239
5468332
5466066
0.000000e+00
3230.0
16
TraesCS6B01G018000
chr6A
90.211
2278
106
32
1
2239
5494640
5492441
0.000000e+00
2863.0
17
TraesCS6B01G018000
chr6A
94.482
1486
67
4
2235
3707
5466029
5464546
0.000000e+00
2276.0
18
TraesCS6B01G018000
chr6A
88.115
1767
126
32
4
1726
5544342
5542616
0.000000e+00
2023.0
19
TraesCS6B01G018000
chr6A
93.460
948
46
3
2567
3502
5492129
5491186
0.000000e+00
1393.0
20
TraesCS6B01G018000
chr6A
89.194
1055
86
13
2447
3482
5542148
5541103
0.000000e+00
1291.0
21
TraesCS6B01G018000
chr6A
90.643
513
43
3
3499
4007
5489425
5488914
0.000000e+00
676.0
22
TraesCS6B01G018000
chr6A
90.287
453
39
4
1775
2224
5542602
5542152
4.460000e-164
588.0
23
TraesCS6B01G018000
chr6A
95.730
281
12
0
2235
2515
5492404
5492124
1.700000e-123
453.0
24
TraesCS6B01G018000
chr6A
90.879
307
25
2
3704
4007
5445293
5444987
3.730000e-110
409.0
25
TraesCS6B01G018000
chr6A
77.007
274
55
6
1441
1711
13983797
13983529
2.490000e-32
150.0
26
TraesCS6B01G018000
chr6A
89.899
99
8
2
3687
3784
5541054
5540957
4.200000e-25
126.0
27
TraesCS6B01G018000
chr3B
88.202
178
11
7
3835
4004
508219893
508219718
1.890000e-48
204.0
28
TraesCS6B01G018000
chr2A
87.845
181
12
7
3835
4007
27534162
27533984
1.890000e-48
204.0
29
TraesCS6B01G018000
chr1D
86.224
196
17
7
3817
4004
30289121
30289314
1.890000e-48
204.0
30
TraesCS6B01G018000
chrUn
81.818
132
24
0
1441
1572
410434832
410434963
1.180000e-20
111.0
31
TraesCS6B01G018000
chrUn
81.818
132
24
0
1441
1572
451882298
451882429
1.180000e-20
111.0
32
TraesCS6B01G018000
chr7D
94.737
38
2
0
482
519
42685800
42685837
4.320000e-05
60.2
33
TraesCS6B01G018000
chr7B
94.444
36
2
0
482
517
725520332
725520367
5.590000e-04
56.5
34
TraesCS6B01G018000
chr4B
96.970
33
1
0
482
514
3866742
3866774
5.590000e-04
56.5
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
TraesCS6B01G018000
chr6B
11406221
11410227
4006
True
7400.000000
7400
100.000000
1
4007
1
chr6B.!!$R4
4006
1
TraesCS6B01G018000
chr6B
11511603
11515353
3750
True
1146.333333
1916
88.482333
175
3550
3
chr6B.!!$R5
3375
2
TraesCS6B01G018000
chr6B
31996567
31997092
525
False
922.000000
922
98.292000
2463
2989
1
chr6B.!!$F1
526
3
TraesCS6B01G018000
chr6D
6106734
6110790
4056
True
3024.500000
3343
93.960500
1
4007
2
chr6D.!!$R2
4006
4
TraesCS6B01G018000
chr6D
6246435
6250224
3789
True
1053.000000
2423
88.439500
26
3786
4
chr6D.!!$R3
3760
5
TraesCS6B01G018000
chr6A
5464546
5468332
3786
True
2753.000000
3230
93.550500
1
3707
2
chr6A.!!$R3
3706
6
TraesCS6B01G018000
chr6A
5488914
5494640
5726
True
1346.250000
2863
92.511000
1
4007
4
chr6A.!!$R4
4006
7
TraesCS6B01G018000
chr6A
5540957
5544342
3385
True
1007.000000
2023
89.373750
4
3784
4
chr6A.!!$R5
3780
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.