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
TraesCS2B01G134800
chr2B
100.000
3912
0
0
1
3912
101410466
101414377
0.000000e+00
7225.0
1
TraesCS2B01G134800
chr2B
92.063
126
10
0
613
738
387105735
387105610
1.120000e-40
178.0
2
TraesCS2B01G134800
chr2B
80.292
137
12
6
2840
2961
101413245
101413381
5.380000e-14
89.8
3
TraesCS2B01G134800
chr2B
80.292
137
12
6
2780
2916
101413305
101413426
5.380000e-14
89.8
4
TraesCS2B01G134800
chr2D
96.143
3345
46
17
604
3912
69221135
69217838
0.000000e+00
5385.0
5
TraesCS2B01G134800
chr2D
97.862
608
10
2
1
606
65532390
65532996
0.000000e+00
1048.0
6
TraesCS2B01G134800
chr2D
91.089
101
9
0
1615
1715
290739041
290738941
1.900000e-28
137.0
7
TraesCS2B01G134800
chr2D
90.909
99
9
0
1615
1713
2476681
2476583
2.450000e-27
134.0
8
TraesCS2B01G134800
chr2D
81.884
138
10
6
2779
2916
69218924
69218802
6.920000e-18
102.0
9
TraesCS2B01G134800
chr3B
94.958
119
6
0
613
731
588418291
588418173
1.860000e-43
187.0
10
TraesCS2B01G134800
chr3B
94.286
35
2
0
3459
3493
74282517
74282551
2.000000e-03
54.7
11
TraesCS2B01G134800
chr6A
91.176
136
11
1
601
735
404985888
404986023
2.400000e-42
183.0
12
TraesCS2B01G134800
chr4B
92.248
129
8
2
602
730
664392015
664391889
8.630000e-42
182.0
13
TraesCS2B01G134800
chr4B
87.619
105
12
1
1614
1718
576192125
576192228
1.910000e-23
121.0
14
TraesCS2B01G134800
chr3D
91.603
131
10
1
607
736
525280362
525280492
3.110000e-41
180.0
15
TraesCS2B01G134800
chr3D
91.753
97
8
0
1615
1711
601221851
601221755
6.820000e-28
135.0
16
TraesCS2B01G134800
chr3D
89.796
98
10
0
1615
1712
608238805
608238708
4.100000e-25
126.0
17
TraesCS2B01G134800
chr3D
94.286
35
2
0
3459
3493
47481332
47481366
2.000000e-03
54.7
18
TraesCS2B01G134800
chr6D
88.435
147
12
5
611
753
400083086
400082941
5.200000e-39
172.0
19
TraesCS2B01G134800
chr5B
90.769
130
11
1
601
729
571230020
571230149
5.200000e-39
172.0
20
TraesCS2B01G134800
chr3A
90.769
130
11
1
610
738
1706731
1706602
5.200000e-39
172.0
21
TraesCS2B01G134800
chr3A
89.130
46
5
0
3459
3504
59519080
59519125
1.520000e-04
58.4
22
TraesCS2B01G134800
chrUn
91.919
99
8
0
1615
1713
15903921
15904019
5.270000e-29
139.0
23
TraesCS2B01G134800
chr2A
89.796
98
8
1
1615
1712
315037986
315038081
1.480000e-24
124.0
24
TraesCS2B01G134800
chr1B
85.841
113
12
3
1608
1718
560219698
560219588
2.470000e-22
117.0
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
TraesCS2B01G134800
chr2B
101410466
101414377
3911
False
2468.2
7225
86.861333
1
3912
3
chr2B.!!$F1
3911
1
TraesCS2B01G134800
chr2D
69217838
69221135
3297
True
2743.5
5385
89.013500
604
3912
2
chr2D.!!$R3
3308
2
TraesCS2B01G134800
chr2D
65532390
65532996
606
False
1048.0
1048
97.862000
1
606
1
chr2D.!!$F1
605
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.