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
TraesCS7D01G177100
chr7D
100.000
1604
0
0
536
2139
129799145
129797542
0.000000e+00
2963.0
1
TraesCS7D01G177100
chr7D
100.000
324
0
0
2547
2870
129797134
129796811
1.470000e-167
599.0
2
TraesCS7D01G177100
chr7D
100.000
44
0
0
1
44
129799680
129799637
6.590000e-12
82.4
3
TraesCS7D01G177100
chr7B
97.387
1569
38
2
537
2103
91212764
91211197
0.000000e+00
2667.0
4
TraesCS7D01G177100
chr7B
95.608
296
11
2
2574
2868
91210540
91210246
9.310000e-130
473.0
5
TraesCS7D01G177100
chr7B
93.182
44
0
2
1
44
91213270
91213230
8.590000e-06
62.1
6
TraesCS7D01G177100
chr7A
97.334
1463
39
0
536
1998
128914807
128913345
0.000000e+00
2486.0
7
TraesCS7D01G177100
chr7A
93.189
323
19
3
2548
2867
128913163
128912841
3.350000e-129
472.0
8
TraesCS7D01G177100
chr7A
97.778
90
1
1
2014
2103
128913354
128913266
1.380000e-33
154.0
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
TraesCS7D01G177100
chr7D
129796811
129799680
2869
True
1214.800000
2963
100.000000
1
2870
3
chr7D.!!$R1
2869
1
TraesCS7D01G177100
chr7B
91210246
91213270
3024
True
1067.366667
2667
95.392333
1
2868
3
chr7B.!!$R1
2867
2
TraesCS7D01G177100
chr7A
128912841
128914807
1966
True
1037.333333
2486
96.100333
536
2867
3
chr7A.!!$R1
2331
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.