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
TraesCS2B01G363200
chr2B
100.000
6262
0
0
1
6262
517595231
517601492
0.000000e+00
11564.0
1
TraesCS2B01G363200
chr2D
97.656
4692
50
14
1616
6262
439564114
439568790
0.000000e+00
8000.0
2
TraesCS2B01G363200
chr2D
94.676
1634
47
18
1
1619
439562269
439563877
0.000000e+00
2499.0
3
TraesCS2B01G363200
chr2D
90.667
75
4
2
5722
5795
376701251
376701179
5.170000e-16
97.1
4
TraesCS2B01G363200
chr2D
93.846
65
1
3
5721
5784
8495912
8495974
1.860000e-15
95.3
5
TraesCS2B01G363200
chr2D
91.429
70
2
2
5721
5789
327614836
327614902
6.680000e-15
93.5
6
TraesCS2B01G363200
chr2A
94.269
5217
162
63
525
5647
549294798
549289625
0.000000e+00
7851.0
7
TraesCS2B01G363200
chr2A
94.059
505
9
6
5777
6262
549289433
549288931
0.000000e+00
747.0
8
TraesCS2B01G363200
chr2A
91.776
535
32
4
1
526
549295589
549295058
0.000000e+00
734.0
9
TraesCS2B01G363200
chr2A
91.503
153
12
1
4847
4998
79316158
79316006
6.360000e-50
209.0
10
TraesCS2B01G363200
chr2A
90.667
75
4
2
5721
5794
754039077
754039005
5.170000e-16
97.1
11
TraesCS2B01G363200
chr2A
97.436
39
1
0
5686
5724
549289558
549289520
4.050000e-07
67.6
12
TraesCS2B01G363200
chr3B
89.866
523
43
3
1
513
40870223
40869701
0.000000e+00
664.0
13
TraesCS2B01G363200
chr3B
94.030
67
2
2
5723
5787
445886096
445886030
3.990000e-17
100.0
14
TraesCS2B01G363200
chr4B
93.151
146
9
1
4854
4998
146469362
146469217
4.920000e-51
213.0
15
TraesCS2B01G363200
chr5B
92.105
152
9
2
4848
4998
665744619
665744470
1.770000e-50
211.0
16
TraesCS2B01G363200
chr4D
90.683
161
12
3
4845
5002
74079508
74079348
1.770000e-50
211.0
17
TraesCS2B01G363200
chr5D
90.184
163
9
5
4841
4998
233044603
233044443
8.230000e-49
206.0
18
TraesCS2B01G363200
chr7B
90.000
160
13
3
4842
4998
505937474
505937315
2.960000e-48
204.0
19
TraesCS2B01G363200
chr3D
89.937
159
13
3
4842
4998
76231151
76230994
1.060000e-47
202.0
20
TraesCS2B01G363200
chr3D
85.484
124
14
4
3205
3328
613071481
613071362
6.590000e-25
126.0
21
TraesCS2B01G363200
chr6A
94.118
68
1
3
5721
5785
611567687
611567754
3.990000e-17
100.0
22
TraesCS2B01G363200
chr6D
93.750
64
2
2
5722
5784
469492349
469492411
1.860000e-15
95.3
23
TraesCS2B01G363200
chr7D
91.304
69
4
2
5721
5788
447760444
447760511
6.680000e-15
93.5
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
TraesCS2B01G363200
chr2B
517595231
517601492
6261
False
11564.0
11564
100.000
1
6262
1
chr2B.!!$F1
6261
1
TraesCS2B01G363200
chr2D
439562269
439568790
6521
False
5249.5
8000
96.166
1
6262
2
chr2D.!!$F3
6261
2
TraesCS2B01G363200
chr2A
549288931
549295589
6658
True
2349.9
7851
94.385
1
6262
4
chr2A.!!$R3
6261
3
TraesCS2B01G363200
chr3B
40869701
40870223
522
True
664.0
664
89.866
1
513
1
chr3B.!!$R1
512
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.