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
TraesCS5D01G552300
chr5D
100.000
2480
0
0
1
2480
557793951
557796430
0
4580
1
TraesCS5D01G552300
chr5D
96.691
967
28
4
749
1713
565809433
565810397
0
1605
2
TraesCS5D01G552300
chr5D
97.250
909
24
1
1573
2480
565810202
565811110
0
1539
3
TraesCS5D01G552300
chr2D
99.114
2482
19
3
1
2480
621997766
622000246
0
4458
4
TraesCS5D01G552300
chr3D
98.353
1700
24
3
1
1700
359527468
359525773
0
2981
5
TraesCS5D01G552300
chr3D
98.460
909
13
1
1573
2480
359525955
359525047
0
1600
6
TraesCS5D01G552300
chr4D
98.076
1715
28
5
1
1713
393458506
393460217
0
2979
7
TraesCS5D01G552300
chr4D
98.350
909
14
1
1573
2480
393460022
393460930
0
1594
8
TraesCS5D01G552300
chr1D
97.608
1714
37
4
1
1713
251020562
251022272
0
2935
9
TraesCS5D01G552300
chr1D
97.690
909
20
1
1573
2480
251022077
251022985
0
1561
10
TraesCS5D01G552300
chr3B
97.116
1699
46
3
1
1699
389719858
389721553
0
2863
11
TraesCS5D01G552300
chr3B
96.791
1714
52
3
1
1713
361795829
361797540
0
2857
12
TraesCS5D01G552300
chr3B
97.250
909
24
1
1573
2480
361797345
361798253
0
1539
13
TraesCS5D01G552300
chr2B
96.674
1714
54
3
1
1713
728070272
728068561
0
2846
14
TraesCS5D01G552300
chr2B
96.429
924
29
4
1560
2480
728068770
728067848
0
1520
15
TraesCS5D01G552300
chr6B
96.558
1714
53
4
1
1713
587366781
587365073
0
2833
16
TraesCS5D01G552300
chr6B
96.320
924
30
4
1560
2480
587365282
587364360
0
1515
17
TraesCS5D01G552300
chr6A
94.248
1721
80
9
1
1713
583326533
583328242
0
2612
18
TraesCS5D01G552300
chr6A
95.055
910
43
2
1573
2480
583328046
583328955
0
1430
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
TraesCS5D01G552300
chr5D
557793951
557796430
2479
False
4580.0
4580
100.0000
1
2480
1
chr5D.!!$F1
2479
1
TraesCS5D01G552300
chr5D
565809433
565811110
1677
False
1572.0
1605
96.9705
749
2480
2
chr5D.!!$F2
1731
2
TraesCS5D01G552300
chr2D
621997766
622000246
2480
False
4458.0
4458
99.1140
1
2480
1
chr2D.!!$F1
2479
3
TraesCS5D01G552300
chr3D
359525047
359527468
2421
True
2290.5
2981
98.4065
1
2480
2
chr3D.!!$R1
2479
4
TraesCS5D01G552300
chr4D
393458506
393460930
2424
False
2286.5
2979
98.2130
1
2480
2
chr4D.!!$F1
2479
5
TraesCS5D01G552300
chr1D
251020562
251022985
2423
False
2248.0
2935
97.6490
1
2480
2
chr1D.!!$F1
2479
6
TraesCS5D01G552300
chr3B
389719858
389721553
1695
False
2863.0
2863
97.1160
1
1699
1
chr3B.!!$F1
1698
7
TraesCS5D01G552300
chr3B
361795829
361798253
2424
False
2198.0
2857
97.0205
1
2480
2
chr3B.!!$F2
2479
8
TraesCS5D01G552300
chr2B
728067848
728070272
2424
True
2183.0
2846
96.5515
1
2480
2
chr2B.!!$R1
2479
9
TraesCS5D01G552300
chr6B
587364360
587366781
2421
True
2174.0
2833
96.4390
1
2480
2
chr6B.!!$R1
2479
10
TraesCS5D01G552300
chr6A
583326533
583328955
2422
False
2021.0
2612
94.6515
1
2480
2
chr6A.!!$F1
2479
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.