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
TraesCS3A01G012900
chr3A
100.000
4350
0
0
1
4350
9613880
9609531
0.000000e+00
8034.0
1
TraesCS3A01G012900
chr3A
97.499
2399
47
7
1154
3541
9780875
9783271
0.000000e+00
4085.0
2
TraesCS3A01G012900
chr3A
96.763
865
22
3
1
859
9779394
9780258
0.000000e+00
1437.0
3
TraesCS3A01G012900
chr3A
98.113
265
3
1
902
1164
9780253
9780517
1.100000e-125
460.0
4
TraesCS3A01G012900
chr3D
95.411
2070
79
10
1
2062
4168631
4170692
0.000000e+00
3282.0
5
TraesCS3A01G012900
chr3D
86.840
2082
179
42
1
2062
4076593
4074587
0.000000e+00
2239.0
6
TraesCS3A01G012900
chr3D
93.763
1459
78
7
2072
3524
4073806
4072355
0.000000e+00
2178.0
7
TraesCS3A01G012900
chr3D
93.442
1479
72
4
2067
3541
4171277
4172734
0.000000e+00
2170.0
8
TraesCS3A01G012900
chr3D
87.692
780
27
16
3541
4261
4072290
4071521
0.000000e+00
845.0
9
TraesCS3A01G012900
chr3D
97.959
49
1
0
4246
4294
4071506
4071458
7.750000e-13
86.1
10
TraesCS3A01G012900
chrUn
94.293
1472
80
1
2070
3541
246337618
246336151
0.000000e+00
2250.0
11
TraesCS3A01G012900
chrUn
94.317
1179
54
7
892
2062
246339297
246338124
0.000000e+00
1794.0
12
TraesCS3A01G012900
chrUn
87.112
869
43
17
3541
4350
246336113
246335255
0.000000e+00
920.0
13
TraesCS3A01G012900
chrUn
84.427
899
101
15
1
885
246340214
246339341
0.000000e+00
848.0
14
TraesCS3A01G012900
chrUn
79.151
1060
208
13
2261
3313
238779954
238778901
0.000000e+00
721.0
15
TraesCS3A01G012900
chrUn
79.186
1057
207
13
2261
3310
240356320
240357370
0.000000e+00
721.0
16
TraesCS3A01G012900
chrUn
95.968
248
10
0
1639
1886
469290951
469290704
1.880000e-108
403.0
17
TraesCS3A01G012900
chr3B
94.293
1472
80
1
2070
3541
6391718
6390251
0.000000e+00
2250.0
18
TraesCS3A01G012900
chr3B
94.317
1179
54
7
892
2062
6393397
6392224
0.000000e+00
1794.0
19
TraesCS3A01G012900
chr3B
88.028
852
82
9
2688
3523
13947142
13947989
0.000000e+00
990.0
20
TraesCS3A01G012900
chr3B
87.112
869
43
17
3541
4350
6390213
6389355
0.000000e+00
920.0
21
TraesCS3A01G012900
chr3B
92.593
621
40
4
2070
2686
13940812
13941430
0.000000e+00
887.0
22
TraesCS3A01G012900
chr3B
84.427
899
101
15
1
885
6394314
6393441
0.000000e+00
848.0
23
TraesCS3A01G012900
chr3B
94.769
497
15
2
1
486
6667174
6667670
0.000000e+00
763.0
24
TraesCS3A01G012900
chr3B
93.786
515
19
5
1557
2062
13939561
13940071
0.000000e+00
761.0
25
TraesCS3A01G012900
chr3B
96.154
234
9
0
411
644
13939283
13939516
2.450000e-102
383.0
26
TraesCS3A01G012900
chr3B
89.767
215
10
4
528
742
6667662
6667864
9.280000e-67
265.0
27
TraesCS3A01G012900
chr3B
96.721
61
1
1
783
842
6667856
6667916
2.770000e-17
100.0
28
TraesCS3A01G012900
chr3B
100.000
28
0
0
4321
4348
31785186
31785213
8.000000e-03
52.8
29
TraesCS3A01G012900
chr6A
92.019
1466
101
6
2086
3541
609884788
609883329
0.000000e+00
2045.0
30
TraesCS3A01G012900
chr6A
91.034
1015
64
15
909
1904
609886616
609885610
0.000000e+00
1345.0
31
TraesCS3A01G012900
chr6A
87.736
106
11
2
1958
2062
609885607
609885503
5.910000e-24
122.0
32
TraesCS3A01G012900
chr1B
78.195
133
27
2
376
507
9597473
9597342
2.790000e-12
84.2
33
TraesCS3A01G012900
chr2D
100.000
30
0
0
4313
4342
63756903
63756932
6.080000e-04
56.5
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
TraesCS3A01G012900
chr3A
9609531
9613880
4349
True
8034.000000
8034
100.000000
1
4350
1
chr3A.!!$R1
4349
1
TraesCS3A01G012900
chr3A
9779394
9783271
3877
False
1994.000000
4085
97.458333
1
3541
3
chr3A.!!$F1
3540
2
TraesCS3A01G012900
chr3D
4168631
4172734
4103
False
2726.000000
3282
94.426500
1
3541
2
chr3D.!!$F1
3540
3
TraesCS3A01G012900
chr3D
4071458
4076593
5135
True
1337.025000
2239
91.563500
1
4294
4
chr3D.!!$R1
4293
4
TraesCS3A01G012900
chrUn
246335255
246340214
4959
True
1453.000000
2250
90.037250
1
4350
4
chrUn.!!$R3
4349
5
TraesCS3A01G012900
chrUn
238778901
238779954
1053
True
721.000000
721
79.151000
2261
3313
1
chrUn.!!$R1
1052
6
TraesCS3A01G012900
chrUn
240356320
240357370
1050
False
721.000000
721
79.186000
2261
3310
1
chrUn.!!$F1
1049
7
TraesCS3A01G012900
chr3B
6389355
6394314
4959
True
1453.000000
2250
90.037250
1
4350
4
chr3B.!!$R1
4349
8
TraesCS3A01G012900
chr3B
13947142
13947989
847
False
990.000000
990
88.028000
2688
3523
1
chr3B.!!$F1
835
9
TraesCS3A01G012900
chr3B
13939283
13941430
2147
False
677.000000
887
94.177667
411
2686
3
chr3B.!!$F4
2275
10
TraesCS3A01G012900
chr3B
6667174
6667916
742
False
376.000000
763
93.752333
1
842
3
chr3B.!!$F3
841
11
TraesCS3A01G012900
chr6A
609883329
609886616
3287
True
1170.666667
2045
90.263000
909
3541
3
chr6A.!!$R1
2632
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.