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
TraesCS4B01G158700
chr4B
100.000
2105
0
0
1
2105
308674841
308672737
0.000000e+00
3888.0
1
TraesCS4B01G158700
chr4B
100.000
46
0
0
2060
2105
429228703
429228658
3.720000e-13
86.1
2
TraesCS4B01G158700
chr5D
96.741
2117
46
9
7
2105
503296839
503298950
0.000000e+00
3506.0
3
TraesCS4B01G158700
chr5D
96.174
2117
56
11
7
2105
6271042
6268933
0.000000e+00
3437.0
4
TraesCS4B01G158700
chr5D
95.409
2113
55
17
7
2105
6171977
6169893
0.000000e+00
3326.0
5
TraesCS4B01G158700
chr5D
96.059
1218
29
7
901
2105
329162135
329160924
0.000000e+00
1965.0
6
TraesCS4B01G158700
chr5D
96.881
481
13
2
7
485
512414207
512414687
0.000000e+00
804.0
7
TraesCS4B01G158700
chr1D
96.459
2118
49
12
7
2105
254439973
254442083
0.000000e+00
3472.0
8
TraesCS4B01G158700
chr1D
95.445
1427
36
4
9
1431
51866992
51865591
0.000000e+00
2248.0
9
TraesCS4B01G158700
chr1D
96.881
481
13
2
7
485
491423457
491422977
0.000000e+00
804.0
10
TraesCS4B01G158700
chr2D
96.268
2117
50
10
7
2105
638429369
638431474
0.000000e+00
3445.0
11
TraesCS4B01G158700
chr4D
95.784
2111
58
11
7
2105
19873448
19875539
0.000000e+00
3376.0
12
TraesCS4B01G158700
chr3D
93.920
1842
69
13
298
2105
235644625
235646457
0.000000e+00
2741.0
13
TraesCS4B01G158700
chr4A
96.126
1678
45
8
442
2105
309484656
309482985
0.000000e+00
2721.0
14
TraesCS4B01G158700
chr3B
98.505
669
10
0
475
1143
796325651
796324983
0.000000e+00
1181.0
15
TraesCS4B01G158700
chr5A
98.693
153
2
0
1953
2105
186939306
186939458
2.660000e-69
272.0
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
TraesCS4B01G158700
chr4B
308672737
308674841
2104
True
3888
3888
100.000
1
2105
1
chr4B.!!$R1
2104
1
TraesCS4B01G158700
chr5D
503296839
503298950
2111
False
3506
3506
96.741
7
2105
1
chr5D.!!$F1
2098
2
TraesCS4B01G158700
chr5D
6268933
6271042
2109
True
3437
3437
96.174
7
2105
1
chr5D.!!$R2
2098
3
TraesCS4B01G158700
chr5D
6169893
6171977
2084
True
3326
3326
95.409
7
2105
1
chr5D.!!$R1
2098
4
TraesCS4B01G158700
chr5D
329160924
329162135
1211
True
1965
1965
96.059
901
2105
1
chr5D.!!$R3
1204
5
TraesCS4B01G158700
chr1D
254439973
254442083
2110
False
3472
3472
96.459
7
2105
1
chr1D.!!$F1
2098
6
TraesCS4B01G158700
chr1D
51865591
51866992
1401
True
2248
2248
95.445
9
1431
1
chr1D.!!$R1
1422
7
TraesCS4B01G158700
chr2D
638429369
638431474
2105
False
3445
3445
96.268
7
2105
1
chr2D.!!$F1
2098
8
TraesCS4B01G158700
chr4D
19873448
19875539
2091
False
3376
3376
95.784
7
2105
1
chr4D.!!$F1
2098
9
TraesCS4B01G158700
chr3D
235644625
235646457
1832
False
2741
2741
93.920
298
2105
1
chr3D.!!$F1
1807
10
TraesCS4B01G158700
chr4A
309482985
309484656
1671
True
2721
2721
96.126
442
2105
1
chr4A.!!$R1
1663
11
TraesCS4B01G158700
chr3B
796324983
796325651
668
True
1181
1181
98.505
475
1143
1
chr3B.!!$R1
668
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.