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
TraesCS6A01G328400
chr6A
100.000
2596
0
0
1
2596
561652013
561649418
0.000000e+00
4795
1
TraesCS6A01G328400
chr6A
99.158
831
6
1
1
830
561425944
561426774
0.000000e+00
1495
2
TraesCS6A01G328400
chr4B
95.086
2605
103
12
1
2596
22465474
22462886
0.000000e+00
4078
3
TraesCS6A01G328400
chr2B
94.998
2599
100
13
1
2596
601695283
601697854
0.000000e+00
4052
4
TraesCS6A01G328400
chr2B
92.331
1995
110
16
45
2022
663367625
663365657
0.000000e+00
2796
5
TraesCS6A01G328400
chr2B
93.310
583
39
0
2014
2596
663362354
663361772
0.000000e+00
861
6
TraesCS6A01G328400
chr3D
95.330
2441
85
10
164
2596
482857972
482855553
0.000000e+00
3849
7
TraesCS6A01G328400
chr4A
93.908
2446
105
22
164
2596
30742179
30744593
0.000000e+00
3651
8
TraesCS6A01G328400
chr2D
94.433
1940
67
20
1
1928
564584029
564585939
0.000000e+00
2946
9
TraesCS6A01G328400
chr2D
95.856
1641
62
5
960
2596
564448144
564449782
0.000000e+00
2649
10
TraesCS6A01G328400
chr2D
93.474
1471
85
8
1132
2596
556200845
556202310
0.000000e+00
2174
11
TraesCS6A01G328400
chr2D
92.479
1077
47
9
1
1071
556199799
556200847
0.000000e+00
1509
12
TraesCS6A01G328400
chr2A
92.648
2081
95
22
1
2067
695775792
695777828
0.000000e+00
2942
13
TraesCS6A01G328400
chr2A
92.610
2084
91
18
1
2067
695951508
695953545
0.000000e+00
2937
14
TraesCS6A01G328400
chr2A
97.452
157
4
0
2440
2596
695956773
695956929
4.260000e-68
268
15
TraesCS6A01G328400
chr2A
95.541
157
7
0
2440
2596
695781102
695781258
4.290000e-63
252
16
TraesCS6A01G328400
chr3A
81.055
417
68
8
1898
2310
679498678
679498269
3.220000e-84
322
17
TraesCS6A01G328400
chr6D
90.795
239
8
5
1
239
428238206
428238430
9.020000e-80
307
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
TraesCS6A01G328400
chr6A
561649418
561652013
2595
True
4795.0
4795
100.0000
1
2596
1
chr6A.!!$R1
2595
1
TraesCS6A01G328400
chr6A
561425944
561426774
830
False
1495.0
1495
99.1580
1
830
1
chr6A.!!$F1
829
2
TraesCS6A01G328400
chr4B
22462886
22465474
2588
True
4078.0
4078
95.0860
1
2596
1
chr4B.!!$R1
2595
3
TraesCS6A01G328400
chr2B
601695283
601697854
2571
False
4052.0
4052
94.9980
1
2596
1
chr2B.!!$F1
2595
4
TraesCS6A01G328400
chr2B
663361772
663367625
5853
True
1828.5
2796
92.8205
45
2596
2
chr2B.!!$R1
2551
5
TraesCS6A01G328400
chr3D
482855553
482857972
2419
True
3849.0
3849
95.3300
164
2596
1
chr3D.!!$R1
2432
6
TraesCS6A01G328400
chr4A
30742179
30744593
2414
False
3651.0
3651
93.9080
164
2596
1
chr4A.!!$F1
2432
7
TraesCS6A01G328400
chr2D
564584029
564585939
1910
False
2946.0
2946
94.4330
1
1928
1
chr2D.!!$F2
1927
8
TraesCS6A01G328400
chr2D
564448144
564449782
1638
False
2649.0
2649
95.8560
960
2596
1
chr2D.!!$F1
1636
9
TraesCS6A01G328400
chr2D
556199799
556202310
2511
False
1841.5
2174
92.9765
1
2596
2
chr2D.!!$F3
2595
10
TraesCS6A01G328400
chr2A
695951508
695956929
5421
False
1602.5
2937
95.0310
1
2596
2
chr2A.!!$F2
2595
11
TraesCS6A01G328400
chr2A
695775792
695781258
5466
False
1597.0
2942
94.0945
1
2596
2
chr2A.!!$F1
2595
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.