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
TraesCS6B01G046700
chr6B
100.000
3527
0
0
1
3527
27821239
27817713
0.000000e+00
6514
1
TraesCS6B01G046700
chr6B
92.692
2559
176
9
326
2881
27806939
27804389
0.000000e+00
3679
2
TraesCS6B01G046700
chr6B
89.504
343
20
6
3185
3527
27804184
27803858
1.510000e-113
420
3
TraesCS6B01G046700
chr6B
95.370
216
9
1
2907
3121
27804392
27804177
3.370000e-90
342
4
TraesCS6B01G046700
chr6D
92.031
3200
236
13
326
3520
15799938
15796753
0.000000e+00
4479
5
TraesCS6B01G046700
chr6D
91.253
2458
190
9
326
2777
15809503
15807065
0.000000e+00
3325
6
TraesCS6B01G046700
chr6D
85.915
1775
202
28
1015
2779
15783831
15782095
0.000000e+00
1849
7
TraesCS6B01G046700
chr6D
84.926
1758
251
8
778
2530
15419831
15418083
0.000000e+00
1766
8
TraesCS6B01G046700
chr6D
84.876
1739
251
8
797
2530
15385360
15383629
0.000000e+00
1744
9
TraesCS6B01G046700
chr6D
87.805
779
70
11
280
1055
15784715
15783959
0.000000e+00
889
10
TraesCS6B01G046700
chr6A
92.447
2979
208
11
326
3299
16401365
16398399
0.000000e+00
4239
11
TraesCS6B01G046700
chr6A
90.247
2635
227
13
150
2779
16410866
16408257
0.000000e+00
3415
12
TraesCS6B01G046700
chr6A
87.453
1586
192
5
953
2531
16388242
16386657
0.000000e+00
1820
13
TraesCS6B01G046700
chr6A
84.669
1735
254
7
797
2526
15953615
15951888
0.000000e+00
1720
14
TraesCS6B01G046700
chr6A
85.890
163
13
5
3
164
16412511
16412358
7.830000e-37
165
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
TraesCS6B01G046700
chr6B
27817713
27821239
3526
True
6514.000000
6514
100.0000
1
3527
1
chr6B.!!$R1
3526
1
TraesCS6B01G046700
chr6B
27803858
27806939
3081
True
1480.333333
3679
92.5220
326
3527
3
chr6B.!!$R2
3201
2
TraesCS6B01G046700
chr6D
15796753
15799938
3185
True
4479.000000
4479
92.0310
326
3520
1
chr6D.!!$R3
3194
3
TraesCS6B01G046700
chr6D
15807065
15809503
2438
True
3325.000000
3325
91.2530
326
2777
1
chr6D.!!$R4
2451
4
TraesCS6B01G046700
chr6D
15418083
15419831
1748
True
1766.000000
1766
84.9260
778
2530
1
chr6D.!!$R2
1752
5
TraesCS6B01G046700
chr6D
15383629
15385360
1731
True
1744.000000
1744
84.8760
797
2530
1
chr6D.!!$R1
1733
6
TraesCS6B01G046700
chr6D
15782095
15784715
2620
True
1369.000000
1849
86.8600
280
2779
2
chr6D.!!$R5
2499
7
TraesCS6B01G046700
chr6A
16398399
16401365
2966
True
4239.000000
4239
92.4470
326
3299
1
chr6A.!!$R3
2973
8
TraesCS6B01G046700
chr6A
16386657
16388242
1585
True
1820.000000
1820
87.4530
953
2531
1
chr6A.!!$R2
1578
9
TraesCS6B01G046700
chr6A
16408257
16412511
4254
True
1790.000000
3415
88.0685
3
2779
2
chr6A.!!$R4
2776
10
TraesCS6B01G046700
chr6A
15951888
15953615
1727
True
1720.000000
1720
84.6690
797
2526
1
chr6A.!!$R1
1729
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.