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
TraesCS6D01G216300
chr6D
100.000
3806
0
0
1
3806
306140643
306136838
0.000000e+00
7029.0
1
TraesCS6D01G216300
chr6D
100.000
73
0
0
3734
3806
306136419
306136491
6.630000e-28
135.0
2
TraesCS6D01G216300
chr6D
95.122
82
4
0
1199
1280
306139406
306139325
3.090000e-26
130.0
3
TraesCS6D01G216300
chr6D
95.122
82
4
0
1238
1319
306139445
306139364
3.090000e-26
130.0
4
TraesCS6D01G216300
chr6D
95.349
43
2
0
1199
1241
306139367
306139325
6.820000e-08
69.4
5
TraesCS6D01G216300
chr6D
95.349
43
2
0
1277
1319
306139445
306139403
6.820000e-08
69.4
6
TraesCS6D01G216300
chr6A
94.326
3507
167
19
1
3483
441502672
441499174
0.000000e+00
5345.0
7
TraesCS6D01G216300
chr6A
88.727
275
24
2
3539
3806
441499173
441498899
2.830000e-86
329.0
8
TraesCS6D01G216300
chr6A
95.122
82
4
0
1199
1280
441501419
441501338
3.090000e-26
130.0
9
TraesCS6D01G216300
chr6A
95.122
82
4
0
1238
1319
441501458
441501377
3.090000e-26
130.0
10
TraesCS6D01G216300
chr6A
95.349
43
2
0
1199
1241
441501380
441501338
6.820000e-08
69.4
11
TraesCS6D01G216300
chr6A
95.349
43
2
0
1277
1319
441501458
441501416
6.820000e-08
69.4
12
TraesCS6D01G216300
chr6B
95.285
3033
106
9
720
3719
473070049
473067021
0.000000e+00
4774.0
13
TraesCS6D01G216300
chr6B
89.197
361
22
11
240
592
473070762
473070411
5.840000e-118
435.0
14
TraesCS6D01G216300
chr6B
86.122
245
22
6
1
244
473074919
473074686
1.750000e-63
254.0
15
TraesCS6D01G216300
chr6B
94.792
96
5
0
3711
3806
473062926
473062831
2.370000e-32
150.0
16
TraesCS6D01G216300
chr6B
95.238
42
2
0
1200
1241
473069491
473069450
2.450000e-07
67.6
17
TraesCS6D01G216300
chr6B
93.023
43
3
0
1277
1319
473069570
473069528
3.170000e-06
63.9
18
TraesCS6D01G216300
chr7D
98.824
85
1
0
3245
3329
252062992
252063076
6.590000e-33
152.0
19
TraesCS6D01G216300
chr5A
98.810
84
1
0
3247
3330
510463984
510463901
2.370000e-32
150.0
20
TraesCS6D01G216300
chr5A
97.619
84
2
0
3247
3330
510464097
510464180
1.100000e-30
145.0
21
TraesCS6D01G216300
chr7A
97.647
85
2
0
3245
3329
269102302
269102218
3.060000e-31
147.0
22
TraesCS6D01G216300
chr5D
96.591
88
2
1
3245
3331
402976795
402976882
1.100000e-30
145.0
23
TraesCS6D01G216300
chr5D
96.552
87
2
1
3243
3329
402976701
402976616
3.960000e-30
143.0
24
TraesCS6D01G216300
chr7B
96.512
86
3
0
3245
3330
228827638
228827723
3.960000e-30
143.0
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
TraesCS6D01G216300
chr6D
306136838
306140643
3805
True
1485.560000
7029
96.188400
1
3806
5
chr6D.!!$R1
3805
1
TraesCS6D01G216300
chr6A
441498899
441502672
3773
True
1012.133333
5345
93.999167
1
3806
6
chr6A.!!$R1
3805
2
TraesCS6D01G216300
chr6B
473067021
473074919
7898
True
1118.900000
4774
91.773000
1
3719
5
chr6B.!!$R2
3718
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.