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
TraesCS1D01G351900
chr1D
100.000
2474
0
0
1
2474
437294007
437291534
0.000000e+00
4569.0
1
TraesCS1D01G351900
chr1D
80.533
1351
224
31
968
2295
7371994
7373328
0.000000e+00
1002.0
2
TraesCS1D01G351900
chr1B
95.038
2499
79
17
1
2474
592368237
592365759
0.000000e+00
3886.0
3
TraesCS1D01G351900
chr1B
80.710
1353
218
34
968
2295
9647338
9648672
0.000000e+00
1013.0
4
TraesCS1D01G351900
chr1A
94.602
2297
64
18
193
2474
534274452
534276703
0.000000e+00
3500.0
5
TraesCS1D01G351900
chr1A
79.874
1431
240
34
897
2295
9533173
9531759
0.000000e+00
1003.0
6
TraesCS1D01G351900
chr1A
96.154
78
3
0
2
79
534274375
534274452
7.180000e-26
128.0
7
TraesCS1D01G351900
chr5D
75.131
957
199
32
1030
1962
41878416
41877475
1.770000e-111
412.0
8
TraesCS1D01G351900
chr5D
71.984
257
61
11
1712
1961
375586275
375586527
5.710000e-07
65.8
9
TraesCS1D01G351900
chr2B
80.934
514
81
11
994
1503
785984561
785984061
8.300000e-105
390.0
10
TraesCS1D01G351900
chr2B
77.844
501
95
13
1030
1522
775385775
775386267
1.860000e-76
296.0
11
TraesCS1D01G351900
chr2B
84.351
262
28
7
465
716
93790534
93790792
6.830000e-61
244.0
12
TraesCS1D01G351900
chr2B
79.620
368
45
17
76
420
772594252
772593892
1.140000e-58
237.0
13
TraesCS1D01G351900
chr2B
88.325
197
18
2
520
716
477510765
477510574
5.320000e-57
231.0
14
TraesCS1D01G351900
chr2B
79.348
368
46
17
76
420
477511187
477510827
5.320000e-57
231.0
15
TraesCS1D01G351900
chr2B
88.083
193
21
2
524
716
239881992
239881802
6.880000e-56
228.0
16
TraesCS1D01G351900
chr2D
76.291
523
106
13
1009
1522
631983067
631983580
1.890000e-66
263.0
17
TraesCS1D01G351900
chr2D
84.030
263
27
9
466
716
100362514
100362773
3.180000e-59
239.0
18
TraesCS1D01G351900
chr4B
83.624
287
28
13
465
739
42272387
42272108
4.080000e-63
252.0
19
TraesCS1D01G351900
chr7B
84.733
262
27
7
465
716
745362801
745362543
1.470000e-62
250.0
20
TraesCS1D01G351900
chr2A
83.650
263
30
8
466
716
664977633
664977894
4.110000e-58
235.0
21
TraesCS1D01G351900
chr2A
75.551
499
106
13
1030
1520
759795198
759794708
5.320000e-57
231.0
22
TraesCS1D01G351900
chr3D
78.151
238
42
8
1730
1962
514680439
514680207
2.560000e-30
143.0
23
TraesCS1D01G351900
chr3B
91.228
57
5
0
2160
2216
676966922
676966866
7.340000e-11
78.7
24
TraesCS1D01G351900
chr5B
72.481
258
58
8
1712
1961
448314635
448314887
1.230000e-08
71.3
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
TraesCS1D01G351900
chr1D
437291534
437294007
2473
True
4569
4569
100.0000
1
2474
1
chr1D.!!$R1
2473
1
TraesCS1D01G351900
chr1D
7371994
7373328
1334
False
1002
1002
80.5330
968
2295
1
chr1D.!!$F1
1327
2
TraesCS1D01G351900
chr1B
592365759
592368237
2478
True
3886
3886
95.0380
1
2474
1
chr1B.!!$R1
2473
3
TraesCS1D01G351900
chr1B
9647338
9648672
1334
False
1013
1013
80.7100
968
2295
1
chr1B.!!$F1
1327
4
TraesCS1D01G351900
chr1A
534274375
534276703
2328
False
1814
3500
95.3780
2
2474
2
chr1A.!!$F1
2472
5
TraesCS1D01G351900
chr1A
9531759
9533173
1414
True
1003
1003
79.8740
897
2295
1
chr1A.!!$R1
1398
6
TraesCS1D01G351900
chr5D
41877475
41878416
941
True
412
412
75.1310
1030
1962
1
chr5D.!!$R1
932
7
TraesCS1D01G351900
chr2B
785984061
785984561
500
True
390
390
80.9340
994
1503
1
chr2B.!!$R3
509
8
TraesCS1D01G351900
chr2B
477510574
477511187
613
True
231
231
83.8365
76
716
2
chr2B.!!$R4
640
9
TraesCS1D01G351900
chr2D
631983067
631983580
513
False
263
263
76.2910
1009
1522
1
chr2D.!!$F2
513
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.