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
TraesCS2D01G218200
chr2D
100.000
3902
0
0
1
3902
181434198
181438099
0.000000e+00
7206
1
TraesCS2D01G218200
chr2D
91.451
889
63
10
1
879
176585314
176586199
0.000000e+00
1208
2
TraesCS2D01G218200
chr2B
98.711
2561
27
4
932
3488
238254085
238256643
0.000000e+00
4542
3
TraesCS2D01G218200
chr2B
88.773
383
22
8
3524
3902
238256638
238257003
2.140000e-122
449
4
TraesCS2D01G218200
chr2A
90.713
2132
125
34
1801
3902
197216728
197218816
0.000000e+00
2772
5
TraesCS2D01G218200
chr2A
89.034
921
48
17
899
1794
197215669
197216561
0.000000e+00
1092
6
TraesCS2D01G218200
chr2A
85.714
245
24
1
3569
3813
197222467
197222700
8.370000e-62
248
7
TraesCS2D01G218200
chrUn
92.601
892
55
5
1
883
68157664
68156775
0.000000e+00
1271
8
TraesCS2D01G218200
chrUn
92.135
890
58
6
1
880
102557054
102556167
0.000000e+00
1245
9
TraesCS2D01G218200
chr6D
92.120
901
58
7
1
890
463451787
463450889
0.000000e+00
1258
10
TraesCS2D01G218200
chr6D
89.858
917
75
16
1
905
121800410
121799500
0.000000e+00
1162
11
TraesCS2D01G218200
chr3D
92.247
890
57
7
1
880
605996932
605997819
0.000000e+00
1251
12
TraesCS2D01G218200
chr3D
91.011
890
67
11
1
880
253573783
253572897
0.000000e+00
1188
13
TraesCS2D01G218200
chr7D
90.858
897
68
11
1
886
68432606
68433499
0.000000e+00
1190
14
TraesCS2D01G218200
chr5B
90.929
893
69
6
1
883
612294314
612295204
0.000000e+00
1190
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
TraesCS2D01G218200
chr2D
181434198
181438099
3901
False
7206.000000
7206
100.000
1
3902
1
chr2D.!!$F2
3901
1
TraesCS2D01G218200
chr2D
176585314
176586199
885
False
1208.000000
1208
91.451
1
879
1
chr2D.!!$F1
878
2
TraesCS2D01G218200
chr2B
238254085
238257003
2918
False
2495.500000
4542
93.742
932
3902
2
chr2B.!!$F1
2970
3
TraesCS2D01G218200
chr2A
197215669
197222700
7031
False
1370.666667
2772
88.487
899
3902
3
chr2A.!!$F1
3003
4
TraesCS2D01G218200
chrUn
68156775
68157664
889
True
1271.000000
1271
92.601
1
883
1
chrUn.!!$R1
882
5
TraesCS2D01G218200
chrUn
102556167
102557054
887
True
1245.000000
1245
92.135
1
880
1
chrUn.!!$R2
879
6
TraesCS2D01G218200
chr6D
463450889
463451787
898
True
1258.000000
1258
92.120
1
890
1
chr6D.!!$R2
889
7
TraesCS2D01G218200
chr6D
121799500
121800410
910
True
1162.000000
1162
89.858
1
905
1
chr6D.!!$R1
904
8
TraesCS2D01G218200
chr3D
605996932
605997819
887
False
1251.000000
1251
92.247
1
880
1
chr3D.!!$F1
879
9
TraesCS2D01G218200
chr3D
253572897
253573783
886
True
1188.000000
1188
91.011
1
880
1
chr3D.!!$R1
879
10
TraesCS2D01G218200
chr7D
68432606
68433499
893
False
1190.000000
1190
90.858
1
886
1
chr7D.!!$F1
885
11
TraesCS2D01G218200
chr5B
612294314
612295204
890
False
1190.000000
1190
90.929
1
883
1
chr5B.!!$F1
882
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.