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
TraesCS4B01G309700
chr4B
100.000
2627
0
0
1
2627
600432677
600430051
0.000000e+00
4852
1
TraesCS4B01G309700
chr4B
87.507
1825
201
15
3
1812
600376921
600378733
0.000000e+00
2082
2
TraesCS4B01G309700
chr4B
92.806
278
20
0
1865
2142
600424199
600423922
1.130000e-108
403
3
TraesCS4B01G309700
chr4D
95.610
1845
71
5
1
1836
476198896
476197053
0.000000e+00
2950
4
TraesCS4B01G309700
chr4D
87.638
1715
197
9
3
1711
475954016
475952311
0.000000e+00
1978
5
TraesCS4B01G309700
chr4A
94.869
1871
76
10
1
1864
683258481
683256624
0.000000e+00
2905
6
TraesCS4B01G309700
chr4A
87.588
1853
187
27
1
1816
682991706
682989860
0.000000e+00
2108
7
TraesCS4B01G309700
chr5B
78.440
1192
236
14
3
1179
420012260
420013445
0.000000e+00
758
8
TraesCS4B01G309700
chr5A
78.072
1172
235
14
3
1158
413220731
413221896
0.000000e+00
721
9
TraesCS4B01G309700
chr1B
81.593
766
130
10
1865
2624
435753855
435754615
7.980000e-175
623
10
TraesCS4B01G309700
chr1D
79.716
774
134
22
1865
2624
231012212
231012976
2.980000e-149
538
11
TraesCS4B01G309700
chr5D
79.275
772
141
17
1863
2624
553047972
553048734
3.000000e-144
521
12
TraesCS4B01G309700
chr5D
78.506
656
125
14
1979
2624
123943874
123944523
1.450000e-112
416
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
TraesCS4B01G309700
chr4B
600430051
600432677
2626
True
4852
4852
100.000
1
2627
1
chr4B.!!$R2
2626
1
TraesCS4B01G309700
chr4B
600376921
600378733
1812
False
2082
2082
87.507
3
1812
1
chr4B.!!$F1
1809
2
TraesCS4B01G309700
chr4D
476197053
476198896
1843
True
2950
2950
95.610
1
1836
1
chr4D.!!$R2
1835
3
TraesCS4B01G309700
chr4D
475952311
475954016
1705
True
1978
1978
87.638
3
1711
1
chr4D.!!$R1
1708
4
TraesCS4B01G309700
chr4A
683256624
683258481
1857
True
2905
2905
94.869
1
1864
1
chr4A.!!$R2
1863
5
TraesCS4B01G309700
chr4A
682989860
682991706
1846
True
2108
2108
87.588
1
1816
1
chr4A.!!$R1
1815
6
TraesCS4B01G309700
chr5B
420012260
420013445
1185
False
758
758
78.440
3
1179
1
chr5B.!!$F1
1176
7
TraesCS4B01G309700
chr5A
413220731
413221896
1165
False
721
721
78.072
3
1158
1
chr5A.!!$F1
1155
8
TraesCS4B01G309700
chr1B
435753855
435754615
760
False
623
623
81.593
1865
2624
1
chr1B.!!$F1
759
9
TraesCS4B01G309700
chr1D
231012212
231012976
764
False
538
538
79.716
1865
2624
1
chr1D.!!$F1
759
10
TraesCS4B01G309700
chr5D
553047972
553048734
762
False
521
521
79.275
1863
2624
1
chr5D.!!$F2
761
11
TraesCS4B01G309700
chr5D
123943874
123944523
649
False
416
416
78.506
1979
2624
1
chr5D.!!$F1
645
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.