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
TraesCS7D01G552000
chr7D
100.000
3319
0
0
1
3319
634979597
634982915
0.000000e+00
6130
1
TraesCS7D01G552000
chr7D
92.545
3340
214
23
1
3319
634881872
634878547
0.000000e+00
4756
2
TraesCS7D01G552000
chr7D
96.373
2785
94
7
1
2781
634987009
634989790
0.000000e+00
4577
3
TraesCS7D01G552000
chr7D
94.417
2651
125
8
678
3319
635434665
635437301
0.000000e+00
4054
4
TraesCS7D01G552000
chr7D
91.243
2969
216
26
1
2938
634958707
634961662
0.000000e+00
4002
5
TraesCS7D01G552000
chr7D
92.013
2692
183
15
271
2938
635417423
635420106
0.000000e+00
3751
6
TraesCS7D01G552000
chr7D
93.236
1508
80
9
1815
3319
634868206
634866718
0.000000e+00
2200
7
TraesCS7D01G552000
chr7B
94.217
3320
174
12
1
3310
740849915
740846604
0.000000e+00
5051
8
TraesCS7D01G552000
chr7B
93.767
3321
161
16
1
3310
740813466
740810181
0.000000e+00
4944
9
TraesCS7D01G552000
chr7B
93.746
3326
156
19
1
3310
740887705
740884416
0.000000e+00
4942
10
TraesCS7D01G552000
chr7B
90.555
2975
221
30
1
2944
741233295
741230350
0.000000e+00
3882
11
TraesCS7D01G552000
chr7A
91.169
2763
207
23
1
2738
730702917
730700167
0.000000e+00
3716
12
TraesCS7D01G552000
chr7A
91.327
1568
120
12
1
1558
730669609
730668048
0.000000e+00
2128
13
TraesCS7D01G552000
chr7A
89.109
505
49
5
1
500
730690970
730690467
1.010000e-174
623
14
TraesCS7D01G552000
chr7A
90.000
90
6
3
58
146
730702766
730702679
2.710000e-21
113
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
TraesCS7D01G552000
chr7D
634979597
634982915
3318
False
6130.0
6130
100.0000
1
3319
1
chr7D.!!$F2
3318
1
TraesCS7D01G552000
chr7D
634878547
634881872
3325
True
4756.0
4756
92.5450
1
3319
1
chr7D.!!$R2
3318
2
TraesCS7D01G552000
chr7D
634987009
634989790
2781
False
4577.0
4577
96.3730
1
2781
1
chr7D.!!$F3
2780
3
TraesCS7D01G552000
chr7D
635434665
635437301
2636
False
4054.0
4054
94.4170
678
3319
1
chr7D.!!$F5
2641
4
TraesCS7D01G552000
chr7D
634958707
634961662
2955
False
4002.0
4002
91.2430
1
2938
1
chr7D.!!$F1
2937
5
TraesCS7D01G552000
chr7D
635417423
635420106
2683
False
3751.0
3751
92.0130
271
2938
1
chr7D.!!$F4
2667
6
TraesCS7D01G552000
chr7D
634866718
634868206
1488
True
2200.0
2200
93.2360
1815
3319
1
chr7D.!!$R1
1504
7
TraesCS7D01G552000
chr7B
740846604
740849915
3311
True
5051.0
5051
94.2170
1
3310
1
chr7B.!!$R2
3309
8
TraesCS7D01G552000
chr7B
740810181
740813466
3285
True
4944.0
4944
93.7670
1
3310
1
chr7B.!!$R1
3309
9
TraesCS7D01G552000
chr7B
740884416
740887705
3289
True
4942.0
4942
93.7460
1
3310
1
chr7B.!!$R3
3309
10
TraesCS7D01G552000
chr7B
741230350
741233295
2945
True
3882.0
3882
90.5550
1
2944
1
chr7B.!!$R4
2943
11
TraesCS7D01G552000
chr7A
730668048
730669609
1561
True
2128.0
2128
91.3270
1
1558
1
chr7A.!!$R1
1557
12
TraesCS7D01G552000
chr7A
730700167
730702917
2750
True
1914.5
3716
90.5845
1
2738
2
chr7A.!!$R3
2737
13
TraesCS7D01G552000
chr7A
730690467
730690970
503
True
623.0
623
89.1090
1
500
1
chr7A.!!$R2
499
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.