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
TraesCS3D01G232200
chr3D
100.000
2978
0
0
1
2978
318772111
318769134
0.000000e+00
5500.0
1
TraesCS3D01G232200
chr3D
98.077
1768
26
5
1217
2978
607244397
607242632
0.000000e+00
3070.0
2
TraesCS3D01G232200
chr7A
94.605
2984
151
7
1
2978
735719081
735716102
0.000000e+00
4610.0
3
TraesCS3D01G232200
chr6B
96.681
2139
63
5
846
2978
158172865
158175001
0.000000e+00
3550.0
4
TraesCS3D01G232200
chr6B
97.481
794
19
1
1
793
158172077
158172870
0.000000e+00
1354.0
5
TraesCS3D01G232200
chr4A
91.959
1480
115
4
12
1490
681887954
681886478
0.000000e+00
2071.0
6
TraesCS3D01G232200
chr4A
90.934
1489
126
6
1496
2978
681838642
681837157
0.000000e+00
1993.0
7
TraesCS3D01G232200
chr1B
85.779
1097
142
11
1855
2947
572324439
572325525
0.000000e+00
1149.0
8
TraesCS3D01G232200
chr1B
88.496
452
46
5
2526
2973
572388366
572388815
2.610000e-150
542.0
9
TraesCS3D01G232200
chr1B
87.154
397
49
2
2135
2530
572358919
572359314
1.630000e-122
449.0
10
TraesCS3D01G232200
chr4D
79.097
598
117
7
890
1483
461386760
461386167
3.570000e-109
405.0
11
TraesCS3D01G232200
chr7B
73.927
606
133
18
887
1486
272759028
272759614
1.390000e-53
220.0
12
TraesCS3D01G232200
chr7D
97.143
35
0
1
536
569
274872014
274871980
1.150000e-04
58.4
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
TraesCS3D01G232200
chr3D
318769134
318772111
2977
True
5500
5500
100.000
1
2978
1
chr3D.!!$R1
2977
1
TraesCS3D01G232200
chr3D
607242632
607244397
1765
True
3070
3070
98.077
1217
2978
1
chr3D.!!$R2
1761
2
TraesCS3D01G232200
chr7A
735716102
735719081
2979
True
4610
4610
94.605
1
2978
1
chr7A.!!$R1
2977
3
TraesCS3D01G232200
chr6B
158172077
158175001
2924
False
2452
3550
97.081
1
2978
2
chr6B.!!$F1
2977
4
TraesCS3D01G232200
chr4A
681886478
681887954
1476
True
2071
2071
91.959
12
1490
1
chr4A.!!$R2
1478
5
TraesCS3D01G232200
chr4A
681837157
681838642
1485
True
1993
1993
90.934
1496
2978
1
chr4A.!!$R1
1482
6
TraesCS3D01G232200
chr1B
572324439
572325525
1086
False
1149
1149
85.779
1855
2947
1
chr1B.!!$F1
1092
7
TraesCS3D01G232200
chr4D
461386167
461386760
593
True
405
405
79.097
890
1483
1
chr4D.!!$R1
593
8
TraesCS3D01G232200
chr7B
272759028
272759614
586
False
220
220
73.927
887
1486
1
chr7B.!!$F1
599
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.