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
TraesCS7B01G396400
chr7B
100.000
2177
0
0
1
2177
663101670
663103846
0.000000e+00
4021
1
TraesCS7B01G396400
chr7B
98.771
1953
10
2
1
1939
662724159
662722207
0.000000e+00
3461
2
TraesCS7B01G396400
chr6D
98.859
2191
11
2
1
2177
389254924
389252734
0.000000e+00
3895
3
TraesCS7B01G396400
chr6D
98.744
2070
12
2
1
2056
389250129
389248060
0.000000e+00
3666
4
TraesCS7B01G396400
chr3A
98.768
2191
12
3
1
2177
66007377
66009566
0.000000e+00
3882
5
TraesCS7B01G396400
chr5D
98.722
2191
13
3
1
2177
503238781
503236592
0.000000e+00
3877
6
TraesCS7B01G396400
chr5D
98.676
2191
11
4
1
2177
503243027
503240841
0.000000e+00
3869
7
TraesCS7B01G396400
chr5D
98.462
1951
13
3
1
1937
503229000
503227053
0.000000e+00
3421
8
TraesCS7B01G396400
chr5D
97.484
795
7
1
1396
2177
503227069
503226275
0.000000e+00
1345
9
TraesCS7B01G396400
chr5D
97.358
795
8
1
1396
2177
503269475
503270269
0.000000e+00
1339
10
TraesCS7B01G396400
chrUn
98.403
2192
17
4
1
2177
216508363
216510551
0.000000e+00
3838
11
TraesCS7B01G396400
chrUn
98.258
1435
12
1
756
2177
397077306
397078740
0.000000e+00
2499
12
TraesCS7B01G396400
chr3D
98.602
2075
14
3
1
2061
589265768
589267841
0.000000e+00
3657
13
TraesCS7B01G396400
chr4A
95.181
2179
70
8
1
2177
310786276
310788421
0.000000e+00
3410
14
TraesCS7B01G396400
chr6A
97.961
981
6
2
1210
2177
608869208
608870187
0.000000e+00
1688
15
TraesCS7B01G396400
chr7D
92.179
358
20
4
1591
1948
202053379
202053030
1.160000e-137
499
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
TraesCS7B01G396400
chr7B
663101670
663103846
2176
False
4021.0
4021
100.0000
1
2177
1
chr7B.!!$F1
2176
1
TraesCS7B01G396400
chr7B
662722207
662724159
1952
True
3461.0
3461
98.7710
1
1939
1
chr7B.!!$R1
1938
2
TraesCS7B01G396400
chr6D
389248060
389254924
6864
True
3780.5
3895
98.8015
1
2177
2
chr6D.!!$R1
2176
3
TraesCS7B01G396400
chr3A
66007377
66009566
2189
False
3882.0
3882
98.7680
1
2177
1
chr3A.!!$F1
2176
4
TraesCS7B01G396400
chr5D
503236592
503243027
6435
True
3873.0
3877
98.6990
1
2177
2
chr5D.!!$R2
2176
5
TraesCS7B01G396400
chr5D
503226275
503229000
2725
True
2383.0
3421
97.9730
1
2177
2
chr5D.!!$R1
2176
6
TraesCS7B01G396400
chr5D
503269475
503270269
794
False
1339.0
1339
97.3580
1396
2177
1
chr5D.!!$F1
781
7
TraesCS7B01G396400
chrUn
216508363
216510551
2188
False
3838.0
3838
98.4030
1
2177
1
chrUn.!!$F1
2176
8
TraesCS7B01G396400
chrUn
397077306
397078740
1434
False
2499.0
2499
98.2580
756
2177
1
chrUn.!!$F2
1421
9
TraesCS7B01G396400
chr3D
589265768
589267841
2073
False
3657.0
3657
98.6020
1
2061
1
chr3D.!!$F1
2060
10
TraesCS7B01G396400
chr4A
310786276
310788421
2145
False
3410.0
3410
95.1810
1
2177
1
chr4A.!!$F1
2176
11
TraesCS7B01G396400
chr6A
608869208
608870187
979
False
1688.0
1688
97.9610
1210
2177
1
chr6A.!!$F1
967
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.