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
TraesCS2D01G196000
chr2D
100.000
2473
0
0
1
2473
142523399
142520927
0
4567
1
TraesCS2D01G196000
chr2D
95.773
1987
59
5
1
1963
588796878
588794893
0
3181
2
TraesCS2D01G196000
chr2D
95.619
1986
61
13
1
1962
476878749
476880732
0
3162
3
TraesCS2D01G196000
chr2D
95.391
1584
55
7
387
1952
130840024
130838441
0
2505
4
TraesCS2D01G196000
chr2D
96.512
516
18
0
1958
2473
155852139
155852654
0
854
5
TraesCS2D01G196000
chr5D
95.926
1988
50
8
1
1962
365120459
365118477
0
3193
6
TraesCS2D01G196000
chr5D
95.521
1987
62
7
1
1962
304884343
304882359
0
3151
7
TraesCS2D01G196000
chr5D
96.899
516
16
0
1958
2473
340772383
340772898
0
865
8
TraesCS2D01G196000
chr1D
95.850
1976
63
7
1
1961
464935392
464937363
0
3177
9
TraesCS2D01G196000
chr1D
96.512
516
18
0
1958
2473
138638460
138638975
0
854
10
TraesCS2D01G196000
chr1D
96.686
513
17
0
1961
2473
143842185
143841673
0
854
11
TraesCS2D01G196000
chr7D
95.540
1749
60
8
1
1736
203038673
203036930
0
2782
12
TraesCS2D01G196000
chr7D
96.881
513
16
0
1961
2473
609931621
609931109
0
859
13
TraesCS2D01G196000
chr3A
93.418
1884
104
10
96
1963
658727946
658726067
0
2774
14
TraesCS2D01G196000
chr3D
95.369
1749
67
7
1
1736
365508992
365507245
0
2769
15
TraesCS2D01G196000
chr3D
96.512
516
18
0
1958
2473
140970272
140970787
0
854
16
TraesCS2D01G196000
chr3D
96.512
516
18
0
1958
2473
368326551
368327066
0
854
17
TraesCS2D01G196000
chr4B
90.519
1656
132
8
1
1633
456359503
456357850
0
2165
18
TraesCS2D01G196000
chr3B
90.235
1659
125
17
1
1633
741700720
741699073
0
2132
19
TraesCS2D01G196000
chr6B
90.012
1642
135
12
15
1633
46354155
46355790
0
2097
20
TraesCS2D01G196000
chr1A
89.640
1583
114
20
56
1633
405356358
405354821
0
1969
21
TraesCS2D01G196000
chr4D
96.881
513
15
1
1961
2473
260601863
260601352
0
857
22
TraesCS2D01G196000
chr4D
96.686
513
16
1
1961
2473
75302632
75302121
0
852
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
TraesCS2D01G196000
chr2D
142520927
142523399
2472
True
4567
4567
100.000
1
2473
1
chr2D.!!$R2
2472
1
TraesCS2D01G196000
chr2D
588794893
588796878
1985
True
3181
3181
95.773
1
1963
1
chr2D.!!$R3
1962
2
TraesCS2D01G196000
chr2D
476878749
476880732
1983
False
3162
3162
95.619
1
1962
1
chr2D.!!$F2
1961
3
TraesCS2D01G196000
chr2D
130838441
130840024
1583
True
2505
2505
95.391
387
1952
1
chr2D.!!$R1
1565
4
TraesCS2D01G196000
chr2D
155852139
155852654
515
False
854
854
96.512
1958
2473
1
chr2D.!!$F1
515
5
TraesCS2D01G196000
chr5D
365118477
365120459
1982
True
3193
3193
95.926
1
1962
1
chr5D.!!$R2
1961
6
TraesCS2D01G196000
chr5D
304882359
304884343
1984
True
3151
3151
95.521
1
1962
1
chr5D.!!$R1
1961
7
TraesCS2D01G196000
chr5D
340772383
340772898
515
False
865
865
96.899
1958
2473
1
chr5D.!!$F1
515
8
TraesCS2D01G196000
chr1D
464935392
464937363
1971
False
3177
3177
95.850
1
1961
1
chr1D.!!$F2
1960
9
TraesCS2D01G196000
chr1D
138638460
138638975
515
False
854
854
96.512
1958
2473
1
chr1D.!!$F1
515
10
TraesCS2D01G196000
chr1D
143841673
143842185
512
True
854
854
96.686
1961
2473
1
chr1D.!!$R1
512
11
TraesCS2D01G196000
chr7D
203036930
203038673
1743
True
2782
2782
95.540
1
1736
1
chr7D.!!$R1
1735
12
TraesCS2D01G196000
chr7D
609931109
609931621
512
True
859
859
96.881
1961
2473
1
chr7D.!!$R2
512
13
TraesCS2D01G196000
chr3A
658726067
658727946
1879
True
2774
2774
93.418
96
1963
1
chr3A.!!$R1
1867
14
TraesCS2D01G196000
chr3D
365507245
365508992
1747
True
2769
2769
95.369
1
1736
1
chr3D.!!$R1
1735
15
TraesCS2D01G196000
chr3D
140970272
140970787
515
False
854
854
96.512
1958
2473
1
chr3D.!!$F1
515
16
TraesCS2D01G196000
chr3D
368326551
368327066
515
False
854
854
96.512
1958
2473
1
chr3D.!!$F2
515
17
TraesCS2D01G196000
chr4B
456357850
456359503
1653
True
2165
2165
90.519
1
1633
1
chr4B.!!$R1
1632
18
TraesCS2D01G196000
chr3B
741699073
741700720
1647
True
2132
2132
90.235
1
1633
1
chr3B.!!$R1
1632
19
TraesCS2D01G196000
chr6B
46354155
46355790
1635
False
2097
2097
90.012
15
1633
1
chr6B.!!$F1
1618
20
TraesCS2D01G196000
chr1A
405354821
405356358
1537
True
1969
1969
89.640
56
1633
1
chr1A.!!$R1
1577
21
TraesCS2D01G196000
chr4D
260601352
260601863
511
True
857
857
96.881
1961
2473
1
chr4D.!!$R2
512
22
TraesCS2D01G196000
chr4D
75302121
75302632
511
True
852
852
96.686
1961
2473
1
chr4D.!!$R1
512
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.