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
TraesCS5D01G512500
chr5D
100.000
4590
0
0
1
4590
536759459
536754870
0.000000e+00
8477.0
1
TraesCS5D01G512500
chr5D
75.695
827
152
38
1128
1940
511941291
511942082
7.250000e-98
368.0
2
TraesCS5D01G512500
chr5D
91.111
45
1
1
4509
4550
324940518
324940474
1.780000e-04
58.4
3
TraesCS5D01G512500
chr4A
95.324
3678
113
19
902
4550
634418041
634421688
0.000000e+00
5784.0
4
TraesCS5D01G512500
chr4A
95.160
3678
119
19
902
4550
634450310
634453957
0.000000e+00
5751.0
5
TraesCS5D01G512500
chr4A
95.376
757
30
4
1
753
634414437
634415192
0.000000e+00
1199.0
6
TraesCS5D01G512500
chr4A
95.376
757
30
4
1
753
634446707
634447462
0.000000e+00
1199.0
7
TraesCS5D01G512500
chr4A
95.676
185
8
0
1
185
634414224
634414408
9.650000e-77
298.0
8
TraesCS5D01G512500
chr4A
95.676
185
8
0
1
185
634446494
634446678
9.650000e-77
298.0
9
TraesCS5D01G512500
chr4A
93.284
134
6
3
771
904
634417828
634417958
1.300000e-45
195.0
10
TraesCS5D01G512500
chr4A
92.537
134
7
3
771
904
634450093
634450223
6.060000e-44
189.0
11
TraesCS5D01G512500
chr4A
93.478
46
1
2
4547
4590
634421895
634421940
2.960000e-07
67.6
12
TraesCS5D01G512500
chr4A
93.478
46
1
2
4547
4590
634454164
634454209
2.960000e-07
67.6
13
TraesCS5D01G512500
chr5B
93.947
2478
106
14
2093
4550
677674208
677676661
0.000000e+00
3705.0
14
TraesCS5D01G512500
chr5B
93.339
1171
41
12
898
2047
677673050
677674204
0.000000e+00
1696.0
15
TraesCS5D01G512500
chr5B
90.323
186
9
5
548
732
677672390
677672567
7.680000e-58
235.0
16
TraesCS5D01G512500
chr5B
91.111
45
1
1
4509
4550
375849565
375849609
1.780000e-04
58.4
17
TraesCS5D01G512500
chr5A
76.784
827
157
28
1128
1941
640273840
640274644
9.120000e-117
431.0
18
TraesCS5D01G512500
chr2A
73.658
801
186
17
1130
1919
551721616
551722402
2.090000e-73
287.0
19
TraesCS5D01G512500
chr2A
87.603
242
26
3
2361
2598
20900062
20899821
1.260000e-70
278.0
20
TraesCS5D01G512500
chr2A
88.128
219
22
2
2361
2575
20869886
20869668
1.640000e-64
257.0
21
TraesCS5D01G512500
chr3B
81.006
358
68
0
1126
1483
704134954
704135311
7.520000e-73
285.0
22
TraesCS5D01G512500
chr3B
83.408
223
34
3
2355
2574
752042491
752042269
2.170000e-48
204.0
23
TraesCS5D01G512500
chr3A
81.006
358
68
0
1126
1483
667219122
667219479
7.520000e-73
285.0
24
TraesCS5D01G512500
chr3A
80.447
358
70
0
1126
1483
667262191
667262548
1.630000e-69
274.0
25
TraesCS5D01G512500
chr3A
88.462
52
1
3
4504
4550
167747420
167747471
1.780000e-04
58.4
26
TraesCS5D01G512500
chr1A
87.281
228
22
5
2376
2598
241361003
241360778
2.120000e-63
254.0
27
TraesCS5D01G512500
chr1A
83.471
242
35
4
2361
2598
544945076
544945316
2.150000e-53
220.0
28
TraesCS5D01G512500
chr1A
91.111
45
1
1
4509
4550
159452038
159451994
1.780000e-04
58.4
29
TraesCS5D01G512500
chr7B
73.345
574
144
8
3011
3581
704114029
704114596
2.170000e-48
204.0
30
TraesCS5D01G512500
chr6B
80.992
242
40
5
2361
2598
84759689
84759450
2.180000e-43
187.0
31
TraesCS5D01G512500
chr1D
96.154
52
2
0
4499
4550
409489163
409489214
8.180000e-13
86.1
32
TraesCS5D01G512500
chr7D
77.119
118
19
7
3965
4080
100766080
100765969
1.380000e-05
62.1
33
TraesCS5D01G512500
chr6A
91.111
45
1
1
4509
4550
443816721
443816765
1.780000e-04
58.4
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
TraesCS5D01G512500
chr5D
536754870
536759459
4589
True
8477.000000
8477
100.000000
1
4590
1
chr5D.!!$R2
4589
1
TraesCS5D01G512500
chr5D
511941291
511942082
791
False
368.000000
368
75.695000
1128
1940
1
chr5D.!!$F1
812
2
TraesCS5D01G512500
chr4A
634414224
634421940
7716
False
1508.720000
5784
94.627600
1
4590
5
chr4A.!!$F1
4589
3
TraesCS5D01G512500
chr4A
634446494
634454209
7715
False
1500.920000
5751
94.445400
1
4590
5
chr4A.!!$F2
4589
4
TraesCS5D01G512500
chr5B
677672390
677676661
4271
False
1878.666667
3705
92.536333
548
4550
3
chr5B.!!$F2
4002
5
TraesCS5D01G512500
chr5A
640273840
640274644
804
False
431.000000
431
76.784000
1128
1941
1
chr5A.!!$F1
813
6
TraesCS5D01G512500
chr2A
551721616
551722402
786
False
287.000000
287
73.658000
1130
1919
1
chr2A.!!$F1
789
7
TraesCS5D01G512500
chr7B
704114029
704114596
567
False
204.000000
204
73.345000
3011
3581
1
chr7B.!!$F1
570
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.