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
TraesCS4A01G359200
chr4A
100.000
2751
0
0
921
3671
632155407
632152657
0.000000e+00
5081.0
1
TraesCS4A01G359200
chr4A
100.000
637
0
0
1
637
632156327
632155691
0.000000e+00
1177.0
2
TraesCS4A01G359200
chr4A
97.917
48
1
0
3374
3421
632152908
632152861
2.350000e-12
84.2
3
TraesCS4A01G359200
chr4A
97.917
48
1
0
3420
3467
632152954
632152907
2.350000e-12
84.2
4
TraesCS4A01G359200
chr5D
97.808
2327
36
4
974
3292
537969710
537967391
0.000000e+00
4000.0
5
TraesCS4A01G359200
chr5D
90.364
467
23
5
1
467
537970666
537970222
8.780000e-166
593.0
6
TraesCS4A01G359200
chr5D
98.551
69
0
1
508
575
537970234
537970166
1.790000e-23
121.0
7
TraesCS4A01G359200
chr5B
94.975
2229
64
9
1003
3214
678622534
678620337
0.000000e+00
3452.0
8
TraesCS4A01G359200
chr5B
89.408
321
27
6
1
321
678624897
678624584
7.390000e-107
398.0
9
TraesCS4A01G359200
chr5B
88.500
200
23
0
3425
3624
373563169
373563368
3.660000e-60
243.0
10
TraesCS4A01G359200
chr5B
100.000
53
0
0
3240
3292
678620336
678620284
8.390000e-17
99.0
11
TraesCS4A01G359200
chr2D
97.758
223
5
0
3420
3642
14768926
14769148
5.750000e-103
385.0
12
TraesCS4A01G359200
chr2D
98.450
129
2
0
3293
3421
14768845
14768973
1.030000e-55
228.0
13
TraesCS4A01G359200
chr7D
91.729
266
7
7
3420
3671
238988003
238987739
4.510000e-94
355.0
14
TraesCS4A01G359200
chr7D
97.674
129
3
0
3293
3421
238988084
238987956
4.770000e-54
222.0
15
TraesCS4A01G359200
chr7D
86.842
114
1
6
3572
3671
238987085
238986972
8.330000e-22
115.0
16
TraesCS4A01G359200
chr1D
91.739
230
7
6
3454
3671
438008546
438008775
3.560000e-80
309.0
17
TraesCS4A01G359200
chr1D
95.575
113
5
0
3290
3402
438008448
438008560
8.100000e-42
182.0
18
TraesCS4A01G359200
chr1D
100.000
29
0
0
3420
3448
438008532
438008560
2.000000e-03
54.7
19
TraesCS4A01G359200
chr5A
93.659
205
13
0
3420
3624
628847816
628848020
1.280000e-79
307.0
20
TraesCS4A01G359200
chr5A
95.349
129
6
0
3293
3421
628847735
628847863
4.810000e-49
206.0
21
TraesCS4A01G359200
chr6D
93.182
132
9
0
3290
3421
17260924
17261055
1.040000e-45
195.0
22
TraesCS4A01G359200
chr3D
86.538
52
5
2
51
101
112319112
112319162
5.120000e-04
56.5
23
TraesCS4A01G359200
chr3B
96.875
32
1
0
70
101
162799088
162799119
2.000000e-03
54.7
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
TraesCS4A01G359200
chr4A
632152657
632156327
3670
True
1606.600000
5081
98.958500
1
3671
4
chr4A.!!$R1
3670
1
TraesCS4A01G359200
chr5D
537967391
537970666
3275
True
1571.333333
4000
95.574333
1
3292
3
chr5D.!!$R1
3291
2
TraesCS4A01G359200
chr5B
678620284
678624897
4613
True
1316.333333
3452
94.794333
1
3292
3
chr5B.!!$R1
3291
3
TraesCS4A01G359200
chr7D
238986972
238988084
1112
True
230.666667
355
92.081667
3293
3671
3
chr7D.!!$R1
378
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.