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
TraesCS1D01G060200
chr1D
100.000
5573
0
0
1
5573
40236046
40230474
0.000000e+00
10292.0
1
TraesCS1D01G060200
chr1D
93.000
100
6
1
1
99
40230111
40230210
1.620000e-30
145.0
2
TraesCS1D01G060200
chr6D
98.597
3064
41
2
1
3062
262426333
262423270
0.000000e+00
5419.0
3
TraesCS1D01G060200
chr6D
98.150
2541
35
3
3044
5573
262423258
262420719
0.000000e+00
4421.0
4
TraesCS1D01G060200
chr6D
93.750
96
6
0
4
99
262420351
262420446
1.620000e-30
145.0
5
TraesCS1D01G060200
chr3D
98.597
3064
40
3
1
3062
29938595
29935533
0.000000e+00
5417.0
6
TraesCS1D01G060200
chr3D
97.088
2541
37
5
3044
5573
29935520
29933006
0.000000e+00
4248.0
7
TraesCS1D01G060200
chr3D
93.000
100
6
1
1
99
29932634
29932733
1.620000e-30
145.0
8
TraesCS1D01G060200
chr5D
95.699
2325
81
14
739
3060
479153055
479150747
0.000000e+00
3722.0
9
TraesCS1D01G060200
chr5D
89.281
737
45
10
98
823
479153629
479152916
0.000000e+00
893.0
10
TraesCS1D01G060200
chr5D
96.797
281
8
1
3356
3636
479150604
479150325
8.450000e-128
468.0
11
TraesCS1D01G060200
chr5D
92.000
100
7
1
1
99
479132800
479132899
7.530000e-29
139.0
12
TraesCS1D01G060200
chr5D
94.872
78
4
0
3048
3125
479150682
479150605
7.580000e-24
122.0
13
TraesCS1D01G060200
chr2D
79.835
2906
529
42
914
3804
560223194
560220331
0.000000e+00
2067.0
14
TraesCS1D01G060200
chr2D
83.607
305
39
6
4379
4673
560219646
560219343
5.500000e-70
276.0
15
TraesCS1D01G060200
chr4B
78.240
3079
561
69
914
3953
112963202
112966210
0.000000e+00
1873.0
16
TraesCS1D01G060200
chr5B
80.828
1497
251
25
914
2394
604859303
604860779
0.000000e+00
1142.0
17
TraesCS1D01G060200
chr5B
88.435
147
16
1
5428
5573
530257309
530257455
5.740000e-40
176.0
18
TraesCS1D01G060200
chr5B
87.692
65
5
3
6
68
530260792
530260729
7.740000e-09
73.1
19
TraesCS1D01G060200
chr7B
80.166
1447
261
20
914
2349
629503428
629504859
0.000000e+00
1059.0
20
TraesCS1D01G060200
chr7B
75.029
1718
359
59
921
2622
56911168
56909505
0.000000e+00
732.0
21
TraesCS1D01G060200
chr7B
73.913
1196
209
68
3552
4667
214997554
214998726
8.760000e-103
385.0
22
TraesCS1D01G060200
chr7B
75.664
678
157
7
1946
2619
426108282
426107609
1.160000e-86
331.0
23
TraesCS1D01G060200
chr3B
95.918
245
10
0
2025
2269
357218005
357217761
1.120000e-106
398.0
24
TraesCS1D01G060200
chr6A
73.073
1077
258
27
1559
2619
14155750
14154690
2.470000e-93
353.0
25
TraesCS1D01G060200
chr2A
74.901
761
161
21
1561
2312
545835756
545835017
2.500000e-83
320.0
26
TraesCS1D01G060200
chr7A
76.881
545
118
7
2079
2619
52223366
52222826
9.070000e-78
302.0
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
TraesCS1D01G060200
chr1D
40230474
40236046
5572
True
10292.00
10292
100.00000
1
5573
1
chr1D.!!$R1
5572
1
TraesCS1D01G060200
chr6D
262420719
262426333
5614
True
4920.00
5419
98.37350
1
5573
2
chr6D.!!$R1
5572
2
TraesCS1D01G060200
chr3D
29933006
29938595
5589
True
4832.50
5417
97.84250
1
5573
2
chr3D.!!$R1
5572
3
TraesCS1D01G060200
chr5D
479150325
479153629
3304
True
1301.25
3722
94.16225
98
3636
4
chr5D.!!$R1
3538
4
TraesCS1D01G060200
chr2D
560219343
560223194
3851
True
1171.50
2067
81.72100
914
4673
2
chr2D.!!$R1
3759
5
TraesCS1D01G060200
chr4B
112963202
112966210
3008
False
1873.00
1873
78.24000
914
3953
1
chr4B.!!$F1
3039
6
TraesCS1D01G060200
chr5B
604859303
604860779
1476
False
1142.00
1142
80.82800
914
2394
1
chr5B.!!$F2
1480
7
TraesCS1D01G060200
chr7B
629503428
629504859
1431
False
1059.00
1059
80.16600
914
2349
1
chr7B.!!$F2
1435
8
TraesCS1D01G060200
chr7B
56909505
56911168
1663
True
732.00
732
75.02900
921
2622
1
chr7B.!!$R1
1701
9
TraesCS1D01G060200
chr7B
214997554
214998726
1172
False
385.00
385
73.91300
3552
4667
1
chr7B.!!$F1
1115
10
TraesCS1D01G060200
chr7B
426107609
426108282
673
True
331.00
331
75.66400
1946
2619
1
chr7B.!!$R2
673
11
TraesCS1D01G060200
chr6A
14154690
14155750
1060
True
353.00
353
73.07300
1559
2619
1
chr6A.!!$R1
1060
12
TraesCS1D01G060200
chr2A
545835017
545835756
739
True
320.00
320
74.90100
1561
2312
1
chr2A.!!$R1
751
13
TraesCS1D01G060200
chr7A
52222826
52223366
540
True
302.00
302
76.88100
2079
2619
1
chr7A.!!$R1
540
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.