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
TraesCS3A01G205500
chr3A
100.000
2765
0
0
1
2765
361614373
361611609
0.000000e+00
5107.0
1
TraesCS3A01G205500
chr3D
96.746
1598
35
4
674
2263
277930640
277932228
0.000000e+00
2647.0
2
TraesCS3A01G205500
chr3D
92.843
503
30
5
2264
2765
277932386
277932883
0.000000e+00
725.0
3
TraesCS3A01G205500
chr7B
96.746
676
21
1
1
675
377594886
377594211
0.000000e+00
1125.0
4
TraesCS3A01G205500
chr5B
96.450
676
23
1
1
675
585013268
585012593
0.000000e+00
1114.0
5
TraesCS3A01G205500
chr5B
95.266
676
30
1
1
674
660928735
660928060
0.000000e+00
1070.0
6
TraesCS3A01G205500
chr4B
96.000
675
26
1
1
674
177225693
177225019
0.000000e+00
1096.0
7
TraesCS3A01G205500
chr3B
94.805
693
33
3
1
692
740858800
740859490
0.000000e+00
1077.0
8
TraesCS3A01G205500
chr3B
95.238
42
1
1
637
678
194627323
194627283
6.390000e-07
65.8
9
TraesCS3A01G205500
chrUn
95.538
650
27
2
25
674
12455938
12455291
0.000000e+00
1038.0
10
TraesCS3A01G205500
chr7A
96.055
507
18
1
1
507
40833661
40833157
0.000000e+00
824.0
11
TraesCS3A01G205500
chr7A
93.007
143
10
0
532
674
40832896
40832754
2.790000e-50
209.0
12
TraesCS3A01G205500
chr2D
87.329
513
35
8
32
540
12868856
12868370
6.690000e-156
560.0
13
TraesCS3A01G205500
chr2A
83.236
513
44
16
32
540
14957221
14956747
1.520000e-117
433.0
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
TraesCS3A01G205500
chr3A
361611609
361614373
2764
True
5107.0
5107
100.0000
1
2765
1
chr3A.!!$R1
2764
1
TraesCS3A01G205500
chr3D
277930640
277932883
2243
False
1686.0
2647
94.7945
674
2765
2
chr3D.!!$F1
2091
2
TraesCS3A01G205500
chr7B
377594211
377594886
675
True
1125.0
1125
96.7460
1
675
1
chr7B.!!$R1
674
3
TraesCS3A01G205500
chr5B
585012593
585013268
675
True
1114.0
1114
96.4500
1
675
1
chr5B.!!$R1
674
4
TraesCS3A01G205500
chr5B
660928060
660928735
675
True
1070.0
1070
95.2660
1
674
1
chr5B.!!$R2
673
5
TraesCS3A01G205500
chr4B
177225019
177225693
674
True
1096.0
1096
96.0000
1
674
1
chr4B.!!$R1
673
6
TraesCS3A01G205500
chr3B
740858800
740859490
690
False
1077.0
1077
94.8050
1
692
1
chr3B.!!$F1
691
7
TraesCS3A01G205500
chrUn
12455291
12455938
647
True
1038.0
1038
95.5380
25
674
1
chrUn.!!$R1
649
8
TraesCS3A01G205500
chr7A
40832754
40833661
907
True
516.5
824
94.5310
1
674
2
chr7A.!!$R1
673
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.