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
TraesCS4A01G124700
chr4A
100.000
2891
0
0
1
2891
157690999
157693889
0.000000e+00
5339
1
TraesCS4A01G124700
chr4B
94.737
1425
57
9
667
2081
394376840
394375424
0.000000e+00
2200
2
TraesCS4A01G124700
chr4B
91.869
578
41
6
2092
2667
394363732
394363159
0.000000e+00
802
3
TraesCS4A01G124700
chr4B
92.308
234
18
0
2656
2889
394356439
394356206
1.660000e-87
333
4
TraesCS4A01G124700
chr4D
96.194
1340
30
8
770
2090
317181719
317180382
0.000000e+00
2172
5
TraesCS4A01G124700
chr4D
92.810
612
37
2
2279
2889
317180123
317179518
0.000000e+00
880
6
TraesCS4A01G124700
chr4D
96.190
105
4
0
667
771
317182217
317182113
3.830000e-39
172
7
TraesCS4A01G124700
chr3A
92.643
666
48
1
3
667
391424768
391425433
0.000000e+00
957
8
TraesCS4A01G124700
chr3A
91.742
666
54
1
3
667
126977223
126976558
0.000000e+00
924
9
TraesCS4A01G124700
chr3A
91.867
664
50
4
4
666
384625178
384624518
0.000000e+00
924
10
TraesCS4A01G124700
chr3A
91.441
666
54
3
3
665
299909037
299909702
0.000000e+00
911
11
TraesCS4A01G124700
chr6A
91.892
666
53
1
3
667
434039631
434038966
0.000000e+00
929
12
TraesCS4A01G124700
chr2A
91.880
665
53
1
3
666
595673658
595674322
0.000000e+00
928
13
TraesCS4A01G124700
chr2A
91.429
665
55
2
3
666
344722190
344721527
0.000000e+00
911
14
TraesCS4A01G124700
chr2A
91.429
665
55
2
3
666
757383241
757382578
0.000000e+00
911
15
TraesCS4A01G124700
chr1D
91.441
666
55
2
3
666
194992761
194993426
0.000000e+00
913
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
TraesCS4A01G124700
chr4A
157690999
157693889
2890
False
5339.000000
5339
100.000000
1
2891
1
chr4A.!!$F1
2890
1
TraesCS4A01G124700
chr4B
394375424
394376840
1416
True
2200.000000
2200
94.737000
667
2081
1
chr4B.!!$R3
1414
2
TraesCS4A01G124700
chr4B
394363159
394363732
573
True
802.000000
802
91.869000
2092
2667
1
chr4B.!!$R2
575
3
TraesCS4A01G124700
chr4D
317179518
317182217
2699
True
1074.666667
2172
95.064667
667
2889
3
chr4D.!!$R1
2222
4
TraesCS4A01G124700
chr3A
391424768
391425433
665
False
957.000000
957
92.643000
3
667
1
chr3A.!!$F2
664
5
TraesCS4A01G124700
chr3A
126976558
126977223
665
True
924.000000
924
91.742000
3
667
1
chr3A.!!$R1
664
6
TraesCS4A01G124700
chr3A
384624518
384625178
660
True
924.000000
924
91.867000
4
666
1
chr3A.!!$R2
662
7
TraesCS4A01G124700
chr3A
299909037
299909702
665
False
911.000000
911
91.441000
3
665
1
chr3A.!!$F1
662
8
TraesCS4A01G124700
chr6A
434038966
434039631
665
True
929.000000
929
91.892000
3
667
1
chr6A.!!$R1
664
9
TraesCS4A01G124700
chr2A
595673658
595674322
664
False
928.000000
928
91.880000
3
666
1
chr2A.!!$F1
663
10
TraesCS4A01G124700
chr2A
344721527
344722190
663
True
911.000000
911
91.429000
3
666
1
chr2A.!!$R1
663
11
TraesCS4A01G124700
chr2A
757382578
757383241
663
True
911.000000
911
91.429000
3
666
1
chr2A.!!$R2
663
12
TraesCS4A01G124700
chr1D
194992761
194993426
665
False
913.000000
913
91.441000
3
666
1
chr1D.!!$F1
663
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.