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
TraesCS1B01G261800
chr1B
100.000
3079
0
0
1
3079
460149394
460146316
0.000000e+00
5686.0
1
TraesCS1B01G261800
chr1B
97.869
704
14
1
1
704
544793926
544793224
0.000000e+00
1216.0
2
TraesCS1B01G261800
chr1B
87.805
164
14
3
1945
2107
316666512
316666670
1.460000e-43
187.0
3
TraesCS1B01G261800
chr1D
92.571
2396
113
36
705
3079
342878346
342875995
0.000000e+00
3378.0
4
TraesCS1B01G261800
chr1D
91.667
612
49
2
91
700
30064851
30064240
0.000000e+00
846.0
5
TraesCS1B01G261800
chr1A
91.441
2290
117
40
751
3008
442614938
442612696
0.000000e+00
3070.0
6
TraesCS1B01G261800
chr1A
93.827
81
4
1
2999
3079
442609760
442609681
1.500000e-23
121.0
7
TraesCS1B01G261800
chr2B
97.106
691
20
0
1
691
69358178
69358868
0.000000e+00
1166.0
8
TraesCS1B01G261800
chr2B
98.438
64
1
0
1
64
750448260
750448197
2.510000e-21
113.0
9
TraesCS1B01G261800
chr2B
90.625
64
4
2
56
118
750448083
750448021
1.970000e-12
84.2
10
TraesCS1B01G261800
chr6B
94.617
613
26
6
91
699
230757085
230756476
0.000000e+00
942.0
11
TraesCS1B01G261800
chr6B
98.438
64
1
0
1
64
230757342
230757279
2.510000e-21
113.0
12
TraesCS1B01G261800
chr6B
89.231
65
4
3
56
118
230757166
230757103
9.150000e-11
78.7
13
TraesCS1B01G261800
chr5A
94.318
616
32
3
91
704
647573242
647573856
0.000000e+00
941.0
14
TraesCS1B01G261800
chr5A
92.821
599
41
2
108
704
650157602
650158200
0.000000e+00
867.0
15
TraesCS1B01G261800
chr4A
92.727
605
42
2
108
710
604384876
604384272
0.000000e+00
872.0
16
TraesCS1B01G261800
chr4A
85.542
249
20
9
1951
2186
457450027
457449782
2.370000e-61
246.0
17
TraesCS1B01G261800
chr4A
85.259
251
21
10
1949
2186
457456710
457456957
8.530000e-61
244.0
18
TraesCS1B01G261800
chr4A
84.252
254
22
10
1949
2189
462071135
462070887
6.640000e-57
231.0
19
TraesCS1B01G261800
chr6A
91.640
622
45
3
91
705
162661025
162661646
0.000000e+00
854.0
20
TraesCS1B01G261800
chr3D
91.220
615
52
2
92
704
20295268
20295882
0.000000e+00
835.0
21
TraesCS1B01G261800
chr2A
84.109
258
25
10
1945
2189
168479150
168478896
5.130000e-58
235.0
22
TraesCS1B01G261800
chr5B
96.875
64
2
0
1
64
69037388
69037451
1.170000e-19
108.0
23
TraesCS1B01G261800
chrUn
95.312
64
3
0
1
64
347395984
347396047
5.430000e-18
102.0
24
TraesCS1B01G261800
chrUn
95.312
64
3
0
1
64
379922139
379922076
5.430000e-18
102.0
25
TraesCS1B01G261800
chrUn
95.312
64
3
0
1
64
384283279
384283216
5.430000e-18
102.0
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
TraesCS1B01G261800
chr1B
460146316
460149394
3078
True
5686.0
5686
100.000000
1
3079
1
chr1B.!!$R1
3078
1
TraesCS1B01G261800
chr1B
544793224
544793926
702
True
1216.0
1216
97.869000
1
704
1
chr1B.!!$R2
703
2
TraesCS1B01G261800
chr1D
342875995
342878346
2351
True
3378.0
3378
92.571000
705
3079
1
chr1D.!!$R2
2374
3
TraesCS1B01G261800
chr1D
30064240
30064851
611
True
846.0
846
91.667000
91
700
1
chr1D.!!$R1
609
4
TraesCS1B01G261800
chr1A
442609681
442614938
5257
True
1595.5
3070
92.634000
751
3079
2
chr1A.!!$R1
2328
5
TraesCS1B01G261800
chr2B
69358178
69358868
690
False
1166.0
1166
97.106000
1
691
1
chr2B.!!$F1
690
6
TraesCS1B01G261800
chr6B
230756476
230757342
866
True
377.9
942
94.095333
1
699
3
chr6B.!!$R1
698
7
TraesCS1B01G261800
chr5A
647573242
647573856
614
False
941.0
941
94.318000
91
704
1
chr5A.!!$F1
613
8
TraesCS1B01G261800
chr5A
650157602
650158200
598
False
867.0
867
92.821000
108
704
1
chr5A.!!$F2
596
9
TraesCS1B01G261800
chr4A
604384272
604384876
604
True
872.0
872
92.727000
108
710
1
chr4A.!!$R3
602
10
TraesCS1B01G261800
chr6A
162661025
162661646
621
False
854.0
854
91.640000
91
705
1
chr6A.!!$F1
614
11
TraesCS1B01G261800
chr3D
20295268
20295882
614
False
835.0
835
91.220000
92
704
1
chr3D.!!$F1
612
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.