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
TraesCS3D01G005600
chr3D
100.000
2516
0
0
1
2516
2152273
2149758
0.000000e+00
4647.0
1
TraesCS3D01G005600
chr3D
88.710
62
5
2
299
359
452490576
452490516
9.650000e-10
75.0
2
TraesCS3D01G005600
chr3D
100.000
29
0
0
737
765
2151460
2151432
1.000000e-03
54.7
3
TraesCS3D01G005600
chr3D
100.000
29
0
0
814
842
2151537
2151509
1.000000e-03
54.7
4
TraesCS3D01G005600
chr3A
90.549
984
44
21
1569
2516
1919290
1920260
0.000000e+00
1256.0
5
TraesCS3D01G005600
chr3A
89.164
646
37
10
1
620
1904224
1904862
0.000000e+00
774.0
6
TraesCS3D01G005600
chr3A
90.722
291
24
1
1281
1568
1918739
1919029
3.930000e-103
385.0
7
TraesCS3D01G005600
chr3A
91.603
262
21
1
1019
1279
1909434
1909695
6.620000e-96
361.0
8
TraesCS3D01G005600
chr3A
92.727
110
7
1
616
725
1904888
1904996
9.320000e-35
158.0
9
TraesCS3D01G005600
chr3A
86.525
141
14
2
2341
2481
95843325
95843190
1.560000e-32
150.0
10
TraesCS3D01G005600
chr3B
86.165
1142
71
44
1440
2512
4332192
4331069
0.000000e+00
1153.0
11
TraesCS3D01G005600
chr3B
92.295
623
38
9
1
620
4334384
4333769
0.000000e+00
876.0
12
TraesCS3D01G005600
chr3B
90.728
604
48
2
765
1362
4332803
4332202
0.000000e+00
798.0
13
TraesCS3D01G005600
chr3B
91.484
411
28
6
4
413
4406791
4406387
2.190000e-155
558.0
14
TraesCS3D01G005600
chr2A
79.495
634
69
28
1745
2346
20809281
20809885
6.520000e-106
394.0
15
TraesCS3D01G005600
chr5B
87.671
292
30
6
1729
2017
670366538
670366250
4.010000e-88
335.0
16
TraesCS3D01G005600
chrUn
96.000
200
8
0
1
200
351353410
351353211
2.410000e-85
326.0
17
TraesCS3D01G005600
chrUn
90.574
244
18
4
378
620
351355343
351355104
4.040000e-83
318.0
18
TraesCS3D01G005600
chrUn
77.856
569
62
28
1740
2285
306110406
306110933
6.810000e-76
294.0
19
TraesCS3D01G005600
chrUn
93.458
107
6
1
619
725
351355075
351354970
9.320000e-35
158.0
20
TraesCS3D01G005600
chr2B
78.207
569
61
28
1740
2285
31678209
31677681
3.140000e-79
305.0
21
TraesCS3D01G005600
chr2B
77.719
570
61
30
1740
2285
31656948
31656421
3.170000e-74
289.0
22
TraesCS3D01G005600
chr5D
87.429
175
21
1
2106
2280
12872122
12871949
1.530000e-47
200.0
23
TraesCS3D01G005600
chr5D
88.276
145
10
4
2336
2478
227771908
227772047
1.550000e-37
167.0
24
TraesCS3D01G005600
chr6A
87.500
144
11
4
2336
2477
31918676
31918814
2.590000e-35
159.0
25
TraesCS3D01G005600
chr6A
93.103
58
3
1
299
355
613904904
613904961
1.600000e-12
84.2
26
TraesCS3D01G005600
chr6B
86.957
138
13
2
2344
2481
22055636
22055504
1.560000e-32
150.0
27
TraesCS3D01G005600
chr1A
86.861
137
13
2
2341
2477
80620369
80620238
5.610000e-32
148.0
28
TraesCS3D01G005600
chr4B
85.417
144
14
4
2336
2477
584687386
584687524
2.610000e-30
143.0
29
TraesCS3D01G005600
chr4A
84.459
148
17
6
2336
2478
602083668
602083814
9.380000e-30
141.0
30
TraesCS3D01G005600
chr4A
90.323
62
4
2
299
359
551127079
551127019
2.070000e-11
80.5
31
TraesCS3D01G005600
chr4D
93.939
66
3
1
2220
2285
244327047
244326983
5.730000e-17
99.0
32
TraesCS3D01G005600
chr4D
90.164
61
4
2
299
357
47343951
47344011
7.460000e-11
78.7
33
TraesCS3D01G005600
chr7B
90.625
64
5
1
299
361
708439152
708439089
1.600000e-12
84.2
34
TraesCS3D01G005600
chr1D
91.379
58
4
1
299
355
352938291
352938348
7.460000e-11
78.7
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
TraesCS3D01G005600
chr3D
2149758
2152273
2515
True
1585.466667
4647
100.000000
1
2516
3
chr3D.!!$R2
2515
1
TraesCS3D01G005600
chr3A
1918739
1920260
1521
False
820.500000
1256
90.635500
1281
2516
2
chr3A.!!$F3
1235
2
TraesCS3D01G005600
chr3A
1904224
1904996
772
False
466.000000
774
90.945500
1
725
2
chr3A.!!$F2
724
3
TraesCS3D01G005600
chr3B
4331069
4334384
3315
True
942.333333
1153
89.729333
1
2512
3
chr3B.!!$R2
2511
4
TraesCS3D01G005600
chr2A
20809281
20809885
604
False
394.000000
394
79.495000
1745
2346
1
chr2A.!!$F1
601
5
TraesCS3D01G005600
chrUn
306110406
306110933
527
False
294.000000
294
77.856000
1740
2285
1
chrUn.!!$F1
545
6
TraesCS3D01G005600
chrUn
351353211
351355343
2132
True
267.333333
326
93.344000
1
725
3
chrUn.!!$R1
724
7
TraesCS3D01G005600
chr2B
31677681
31678209
528
True
305.000000
305
78.207000
1740
2285
1
chr2B.!!$R2
545
8
TraesCS3D01G005600
chr2B
31656421
31656948
527
True
289.000000
289
77.719000
1740
2285
1
chr2B.!!$R1
545
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.