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
TraesCS1B01G065300
chr1B
100.000
3155
0
0
1
3155
49787123
49783969
0
5827
1
TraesCS1B01G065300
chr1B
96.777
3165
81
8
1
3155
583548107
583551260
0
5260
2
TraesCS1B01G065300
chr1B
96.531
3171
90
9
1
3155
49815632
49818798
0
5228
3
TraesCS1B01G065300
chr7B
97.126
3166
70
8
1
3155
716798042
716794887
0
5323
4
TraesCS1B01G065300
chr7B
96.712
3163
73
13
3
3155
742935290
742938431
0
5236
5
TraesCS1B01G065300
chr7B
95.839
3172
114
10
1
3155
47217234
47220404
0
5110
6
TraesCS1B01G065300
chr7B
95.515
3166
110
10
1
3155
139621806
139618662
0
5031
7
TraesCS1B01G065300
chr6B
97.093
3165
67
8
1
3155
128892181
128889032
0
5312
8
TraesCS1B01G065300
chr5B
96.997
3164
75
7
1
3155
713115164
713112012
0
5299
9
TraesCS1B01G065300
chr5B
96.747
3166
80
10
1
3155
713093563
713096716
0
5254
10
TraesCS1B01G065300
chr5B
96.656
2273
55
7
1
2264
127821197
127818937
0
3757
11
TraesCS1B01G065300
chr7A
96.723
2258
53
10
908
3155
60097493
60095247
0
3740
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
TraesCS1B01G065300
chr1B
49783969
49787123
3154
True
5827
5827
100.000
1
3155
1
chr1B.!!$R1
3154
1
TraesCS1B01G065300
chr1B
583548107
583551260
3153
False
5260
5260
96.777
1
3155
1
chr1B.!!$F2
3154
2
TraesCS1B01G065300
chr1B
49815632
49818798
3166
False
5228
5228
96.531
1
3155
1
chr1B.!!$F1
3154
3
TraesCS1B01G065300
chr7B
716794887
716798042
3155
True
5323
5323
97.126
1
3155
1
chr7B.!!$R2
3154
4
TraesCS1B01G065300
chr7B
742935290
742938431
3141
False
5236
5236
96.712
3
3155
1
chr7B.!!$F2
3152
5
TraesCS1B01G065300
chr7B
47217234
47220404
3170
False
5110
5110
95.839
1
3155
1
chr7B.!!$F1
3154
6
TraesCS1B01G065300
chr7B
139618662
139621806
3144
True
5031
5031
95.515
1
3155
1
chr7B.!!$R1
3154
7
TraesCS1B01G065300
chr6B
128889032
128892181
3149
True
5312
5312
97.093
1
3155
1
chr6B.!!$R1
3154
8
TraesCS1B01G065300
chr5B
713112012
713115164
3152
True
5299
5299
96.997
1
3155
1
chr5B.!!$R2
3154
9
TraesCS1B01G065300
chr5B
713093563
713096716
3153
False
5254
5254
96.747
1
3155
1
chr5B.!!$F1
3154
10
TraesCS1B01G065300
chr5B
127818937
127821197
2260
True
3757
3757
96.656
1
2264
1
chr5B.!!$R1
2263
11
TraesCS1B01G065300
chr7A
60095247
60097493
2246
True
3740
3740
96.723
908
3155
1
chr7A.!!$R1
2247
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.