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
TraesCS5D01G566300
chr5D
100.000
2327
0
0
1
2327
564670386
564672712
0.000000e+00
4298
1
TraesCS5D01G566300
chr6D
97.798
1680
35
2
1
1679
367879771
367878093
0.000000e+00
2896
2
TraesCS5D01G566300
chr6A
95.003
1681
73
7
1
1679
183314290
183312619
0.000000e+00
2628
3
TraesCS5D01G566300
chr6A
94.411
1682
89
5
1
1681
183929704
183931381
0.000000e+00
2580
4
TraesCS5D01G566300
chr6A
89.487
1189
102
17
500
1680
22262078
22263251
0.000000e+00
1482
5
TraesCS5D01G566300
chr7A
94.170
1681
91
7
6
1684
721643425
721641750
0.000000e+00
2555
6
TraesCS5D01G566300
chr7A
90.608
1693
142
12
1
1681
717769091
717767404
0.000000e+00
2230
7
TraesCS5D01G566300
chr1B
90.973
1695
129
20
1
1681
145446317
145444633
0.000000e+00
2261
8
TraesCS5D01G566300
chr5A
90.812
1687
141
13
1
1681
31278727
31280405
0.000000e+00
2244
9
TraesCS5D01G566300
chr2B
83.539
1622
240
22
69
1680
748211381
748212985
0.000000e+00
1491
10
TraesCS5D01G566300
chr5B
87.425
668
51
19
1683
2327
706951667
706952324
0.000000e+00
737
11
TraesCS5D01G566300
chr4A
87.571
531
51
11
1683
2204
607952037
607951513
3.310000e-168
601
12
TraesCS5D01G566300
chr3A
89.180
305
28
4
1385
1684
621497548
621497852
2.180000e-100
375
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
TraesCS5D01G566300
chr5D
564670386
564672712
2326
False
4298
4298
100.000
1
2327
1
chr5D.!!$F1
2326
1
TraesCS5D01G566300
chr6D
367878093
367879771
1678
True
2896
2896
97.798
1
1679
1
chr6D.!!$R1
1678
2
TraesCS5D01G566300
chr6A
183312619
183314290
1671
True
2628
2628
95.003
1
1679
1
chr6A.!!$R1
1678
3
TraesCS5D01G566300
chr6A
183929704
183931381
1677
False
2580
2580
94.411
1
1681
1
chr6A.!!$F2
1680
4
TraesCS5D01G566300
chr6A
22262078
22263251
1173
False
1482
1482
89.487
500
1680
1
chr6A.!!$F1
1180
5
TraesCS5D01G566300
chr7A
721641750
721643425
1675
True
2555
2555
94.170
6
1684
1
chr7A.!!$R2
1678
6
TraesCS5D01G566300
chr7A
717767404
717769091
1687
True
2230
2230
90.608
1
1681
1
chr7A.!!$R1
1680
7
TraesCS5D01G566300
chr1B
145444633
145446317
1684
True
2261
2261
90.973
1
1681
1
chr1B.!!$R1
1680
8
TraesCS5D01G566300
chr5A
31278727
31280405
1678
False
2244
2244
90.812
1
1681
1
chr5A.!!$F1
1680
9
TraesCS5D01G566300
chr2B
748211381
748212985
1604
False
1491
1491
83.539
69
1680
1
chr2B.!!$F1
1611
10
TraesCS5D01G566300
chr5B
706951667
706952324
657
False
737
737
87.425
1683
2327
1
chr5B.!!$F1
644
11
TraesCS5D01G566300
chr4A
607951513
607952037
524
True
601
601
87.571
1683
2204
1
chr4A.!!$R1
521
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.