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
TraesCS6A01G233400
chr6A
100.000
1095
0
0
551
1645
441435435
441434341
0.000000e+00
2023
1
TraesCS6A01G233400
chr6A
95.687
997
26
6
551
1532
410894928
410895922
0.000000e+00
1587
2
TraesCS6A01G233400
chr6A
100.000
429
0
0
1914
2342
441434072
441433644
0.000000e+00
793
3
TraesCS6A01G233400
chr6A
94.911
393
19
1
1951
2342
410895975
410896367
4.280000e-172
614
4
TraesCS6A01G233400
chr6A
100.000
225
0
0
1
225
441435985
441435761
1.290000e-112
416
5
TraesCS6A01G233400
chr6A
98.667
225
3
0
1
225
410894635
410894859
1.300000e-107
399
6
TraesCS6A01G233400
chr6B
97.536
1096
21
4
551
1645
470132075
470130985
0.000000e+00
1869
7
TraesCS6A01G233400
chr6B
98.724
392
5
0
1951
2342
470130544
470130153
0.000000e+00
697
8
TraesCS6A01G233400
chr6B
99.111
225
2
0
1
225
470132368
470132144
2.800000e-109
405
9
TraesCS6A01G233400
chr6D
95.562
1104
32
8
551
1645
304287942
304286847
0.000000e+00
1751
10
TraesCS6A01G233400
chr6D
95.641
390
17
0
1953
2342
304286434
304286045
5.490000e-176
627
11
TraesCS6A01G233400
chr6D
99.556
225
1
0
1
225
304288235
304288011
6.020000e-111
411
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
TraesCS6A01G233400
chr6A
441433644
441435985
2341
True
1077.333333
2023
100.000000
1
2342
3
chr6A.!!$R1
2341
1
TraesCS6A01G233400
chr6A
410894635
410896367
1732
False
866.666667
1587
96.421667
1
2342
3
chr6A.!!$F1
2341
2
TraesCS6A01G233400
chr6B
470130153
470132368
2215
True
990.333333
1869
98.457000
1
2342
3
chr6B.!!$R1
2341
3
TraesCS6A01G233400
chr6D
304286045
304288235
2190
True
929.666667
1751
96.919667
1
2342
3
chr6D.!!$R1
2341
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.