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
TraesCS5D01G229000
chr5D
100.000
2892
0
0
1
2892
336240763
336237872
0.000000e+00
5341
1
TraesCS5D01G229000
chr5D
95.608
1890
56
11
1
1885
336337642
336339509
0.000000e+00
3005
2
TraesCS5D01G229000
chr5D
88.078
1644
111
39
295
1905
336314279
336315870
0.000000e+00
1871
3
TraesCS5D01G229000
chr5D
84.597
1636
139
61
310
1888
336382022
336380443
0.000000e+00
1520
4
TraesCS5D01G229000
chr5D
81.557
938
92
36
295
1200
336258529
336257641
0.000000e+00
699
5
TraesCS5D01G229000
chr5D
94.801
327
13
3
1580
1905
336257245
336256922
9.250000e-140
507
6
TraesCS5D01G229000
chr5B
89.667
1771
84
40
211
1905
394581881
394580134
0.000000e+00
2165
7
TraesCS5D01G229000
chr5B
88.091
1629
127
37
312
1905
394628742
394627146
0.000000e+00
1871
8
TraesCS5D01G229000
chr5B
90.674
1083
77
13
829
1905
394572568
394571504
0.000000e+00
1419
9
TraesCS5D01G229000
chr5B
87.090
914
75
23
1999
2892
394570472
394569582
0.000000e+00
994
10
TraesCS5D01G229000
chr5B
81.507
292
34
10
295
569
394573026
394572738
3.750000e-54
222
11
TraesCS5D01G229000
chr5B
88.000
150
12
5
623
768
394572738
394572591
3.830000e-39
172
12
TraesCS5D01G229000
chr5B
93.043
115
5
2
1898
2009
394571443
394571329
6.410000e-37
165
13
TraesCS5D01G229000
chr5B
82.249
169
25
4
9
175
208700696
208700861
1.080000e-29
141
14
TraesCS5D01G229000
chr5A
90.453
1613
85
33
321
1885
437400668
437399077
0.000000e+00
2061
15
TraesCS5D01G229000
chr5A
88.020
1636
106
44
295
1901
437393835
437392261
0.000000e+00
1853
16
TraesCS5D01G229000
chr5A
85.688
1607
98
56
321
1901
437413291
437411791
0.000000e+00
1572
17
TraesCS5D01G229000
chr5A
84.221
1014
50
34
1903
2892
437392189
437391262
0.000000e+00
885
18
TraesCS5D01G229000
chr5A
81.181
271
27
10
9
279
437408411
437408165
2.270000e-46
196
19
TraesCS5D01G229000
chr4B
81.548
168
29
2
4
170
163799250
163799416
1.400000e-28
137
20
TraesCS5D01G229000
chr4B
81.548
168
29
2
4
170
163799713
163799879
1.400000e-28
137
21
TraesCS5D01G229000
chr2D
85.484
124
17
1
14
137
486961286
486961408
8.410000e-26
128
22
TraesCS5D01G229000
chr2D
79.866
149
28
2
21
168
33326544
33326397
1.100000e-19
108
23
TraesCS5D01G229000
chr7D
79.878
164
31
2
6
168
115139817
115139655
5.060000e-23
119
24
TraesCS5D01G229000
chr7B
80.000
165
25
6
11
171
558915615
558915455
6.550000e-22
115
25
TraesCS5D01G229000
chr4A
79.874
159
28
4
13
170
429237142
429237297
2.360000e-21
113
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
TraesCS5D01G229000
chr5D
336237872
336240763
2891
True
5341.0
5341
100.0000
1
2892
1
chr5D.!!$R1
2891
1
TraesCS5D01G229000
chr5D
336337642
336339509
1867
False
3005.0
3005
95.6080
1
1885
1
chr5D.!!$F2
1884
2
TraesCS5D01G229000
chr5D
336314279
336315870
1591
False
1871.0
1871
88.0780
295
1905
1
chr5D.!!$F1
1610
3
TraesCS5D01G229000
chr5D
336380443
336382022
1579
True
1520.0
1520
84.5970
310
1888
1
chr5D.!!$R2
1578
4
TraesCS5D01G229000
chr5D
336256922
336258529
1607
True
603.0
699
88.1790
295
1905
2
chr5D.!!$R3
1610
5
TraesCS5D01G229000
chr5B
394580134
394581881
1747
True
2165.0
2165
89.6670
211
1905
1
chr5B.!!$R1
1694
6
TraesCS5D01G229000
chr5B
394627146
394628742
1596
True
1871.0
1871
88.0910
312
1905
1
chr5B.!!$R2
1593
7
TraesCS5D01G229000
chr5B
394569582
394573026
3444
True
594.4
1419
88.0628
295
2892
5
chr5B.!!$R3
2597
8
TraesCS5D01G229000
chr5A
437399077
437400668
1591
True
2061.0
2061
90.4530
321
1885
1
chr5A.!!$R1
1564
9
TraesCS5D01G229000
chr5A
437391262
437393835
2573
True
1369.0
1853
86.1205
295
2892
2
chr5A.!!$R2
2597
10
TraesCS5D01G229000
chr5A
437408165
437413291
5126
True
884.0
1572
83.4345
9
1901
2
chr5A.!!$R3
1892
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.