Multiple sequence alignment - TraesCS7B01G135500
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
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
TraesCS7B01G135500
chr7B
100.000
3986
0
0
1
3986
165533291
165529306
0.000000e+00
7361
1
TraesCS7B01G135500
chr7D
95.712
3661
91
27
40
3646
202059488
202055840
0.000000e+00
5830
2
TraesCS7B01G135500
chr7D
92.537
335
15
6
3662
3986
202055856
202055522
4.660000e-129
472
3
TraesCS7B01G135500
chr7D
94.686
207
8
1
3783
3986
201979084
201978878
6.430000e-83
318
4
TraesCS7B01G135500
chr7A
96.711
3497
79
10
21
3486
214436511
214433020
0.000000e+00
5788
5
TraesCS7B01G135500
chr7A
94.833
329
13
2
3662
3986
214432929
214432601
9.880000e-141
510
6
TraesCS7B01G135500
chr7A
92.568
148
8
2
3501
3646
214433059
214432913
4.040000e-50
209
7
TraesCS7B01G135500
chr6D
76.086
1865
385
50
1138
2979
375028608
375030434
0.000000e+00
917
8
TraesCS7B01G135500
chr6B
75.417
1920
413
46
1082
2979
561701016
561702898
0.000000e+00
876
BLAST Results - HSPs grouped
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
TraesCS7B01G135500
chr7B
165529306
165533291
3985
True
7361
7361
100.0000
1
3986
1
chr7B.!!$R1
3985
1
TraesCS7B01G135500
chr7D
202055522
202059488
3966
True
3151
5830
94.1245
40
3986
2
chr7D.!!$R2
3946
2
TraesCS7B01G135500
chr7A
214432601
214436511
3910
True
2169
5788
94.7040
21
3986
3
chr7A.!!$R1
3965
3
TraesCS7B01G135500
chr6D
375028608
375030434
1826
False
917
917
76.0860
1138
2979
1
chr6D.!!$F1
1841
4
TraesCS7B01G135500
chr6B
561701016
561702898
1882
False
876
876
75.4170
1082
2979
1
chr6B.!!$F1
1897
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
298
305
0.173481
CCTTCTCGACGCTTCCATCA
59.827
55.000
0.0
0.0
0.00
3.07
F
1031
1063
1.595489
GCTGCACAGTTCTTGTTGTCG
60.595
52.381
0.0
0.0
38.16
4.35
F
2073
2105
2.092968
TGTGTTCAGAGAGCCAACTTGT
60.093
45.455
0.0
0.0
0.00
3.16
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2073
2105
5.245584
TCATGATGCATAATAGCTTGGGA
57.754
39.130
0.0
0.0
34.99
4.37
R
2499
2531
0.165944
GAATCTGGTTGGTGCGAACG
59.834
55.000
0.0
0.0
0.00
3.95
R
3759
3874
2.029844
GGTCACCAGAGCAGCGTTC
61.030
63.158
0.0
0.0
41.81
3.95
R
All possible primers
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
87
91
5.222130
GGCAGGAAATGGAAATCCTATCCTA
60.222
44.000
15.92
0.00
44.26
2.94
147
151
1.136828
CCCAAATATCTCGACCCCCA
58.863
55.000
0.00
0.00
0.00
4.96
298
305
0.173481
CCTTCTCGACGCTTCCATCA
59.827
55.000
0.00
0.00
0.00
3.07
378
385
1.930520
CCCGGATTTCATTCCCCCT
59.069
57.895
0.73
0.00
31.61
4.79
414
421
2.091555
AGATCTCCGAGTTCCTTAGGCT
60.092
50.000
0.00
0.00
0.00
4.58
422
429
4.177783
CGAGTTCCTTAGGCTCTTTTCTC
58.822
47.826
0.00
0.00
0.00
2.87
495
502
2.862536
CCTGCTCTGTAATCGATGTGTG
59.137
50.000
0.00
0.00
0.00
3.82
553
560
4.375706
CGATTTTAGGCGCGTAGGAAATAC
60.376
45.833
15.84
10.64
0.00
1.89
664
672
1.609072
GCCCTCTGTTTGTTGGAGAAC
59.391
52.381
0.00
0.00
0.00
3.01
740
753
9.339492
CGTTAGTTACTTCTTAAGGTAGTCAAG
57.661
37.037
12.53
6.22
0.00
3.02
775
788
6.585416
TCGGAGGGGAATTAATGTTTACTAC
58.415
40.000
0.00
0.00
0.00
2.73
873
904
4.526970
ACACCTTTCAGATGTTGTTGTCT
58.473
39.130
0.00
0.00
0.00
3.41
922
954
6.882610
ATGATGGATGTAATTTATGCGTGT
57.117
33.333
0.00
0.00
0.00
4.49
1024
1056
2.980233
GGGCGCTGCACAGTTCTT
60.980
61.111
7.64
0.00
0.00
2.52
1031
1063
1.595489
GCTGCACAGTTCTTGTTGTCG
60.595
52.381
0.00
0.00
38.16
4.35
2073
2105
2.092968
TGTGTTCAGAGAGCCAACTTGT
60.093
45.455
0.00
0.00
0.00
3.16
2337
2369
4.447138
TTTCCCTGGTGTCATGTTTACT
57.553
40.909
0.00
0.00
0.00
2.24
2499
2531
2.498885
AGCAGAGCAAATTGAATTCCCC
59.501
45.455
2.27
0.00
0.00
4.81
2778
2810
2.362077
GTGGAAGGCTTTCTTTGCTTCA
59.638
45.455
7.14
0.00
35.50
3.02
3119
3152
6.611381
TGTTTTTAGTAGATGTTGATGCAGC
58.389
36.000
0.00
0.00
0.00
5.25
3234
3268
5.371526
CAAGTCTGCAACCCATATCTACAT
58.628
41.667
0.00
0.00
0.00
2.29
3254
3288
6.630203
ACATAGTGTTAAGGGGTAATGACA
57.370
37.500
0.00
0.00
0.00
3.58
3413
3447
3.617284
AGTGTCGTTTTTCCTTCCAACT
58.383
40.909
0.00
0.00
0.00
3.16
3414
3448
3.377172
AGTGTCGTTTTTCCTTCCAACTG
59.623
43.478
0.00
0.00
0.00
3.16
3491
3605
4.787598
CAGAATGTCACTTTGTTAGCCAC
58.212
43.478
0.00
0.00
0.00
5.01
3492
3606
4.516698
CAGAATGTCACTTTGTTAGCCACT
59.483
41.667
0.00
0.00
0.00
4.00
3493
3607
5.009010
CAGAATGTCACTTTGTTAGCCACTT
59.991
40.000
0.00
0.00
0.00
3.16
3494
3608
5.239525
AGAATGTCACTTTGTTAGCCACTTC
59.760
40.000
0.00
0.00
0.00
3.01
3495
3609
4.150897
TGTCACTTTGTTAGCCACTTCT
57.849
40.909
0.00
0.00
0.00
2.85
3496
3610
5.284861
TGTCACTTTGTTAGCCACTTCTA
57.715
39.130
0.00
0.00
0.00
2.10
3497
3611
5.054477
TGTCACTTTGTTAGCCACTTCTAC
58.946
41.667
0.00
0.00
0.00
2.59
3498
3612
5.054477
GTCACTTTGTTAGCCACTTCTACA
58.946
41.667
0.00
0.00
0.00
2.74
3499
3613
5.526111
GTCACTTTGTTAGCCACTTCTACAA
59.474
40.000
0.00
0.00
0.00
2.41
3500
3614
5.758296
TCACTTTGTTAGCCACTTCTACAAG
59.242
40.000
0.00
0.00
35.50
3.16
3501
3615
5.758296
CACTTTGTTAGCCACTTCTACAAGA
59.242
40.000
0.00
0.00
33.34
3.02
3502
3616
6.260050
CACTTTGTTAGCCACTTCTACAAGAA
59.740
38.462
0.00
0.00
33.34
2.52
3503
3617
6.826741
ACTTTGTTAGCCACTTCTACAAGAAA
59.173
34.615
0.00
0.00
33.19
2.52
3504
3618
7.338449
ACTTTGTTAGCCACTTCTACAAGAAAA
59.662
33.333
0.00
0.00
33.19
2.29
3505
3619
7.817418
TTGTTAGCCACTTCTACAAGAAAAT
57.183
32.000
0.00
0.00
33.19
1.82
3506
3620
7.817418
TGTTAGCCACTTCTACAAGAAAATT
57.183
32.000
0.00
0.00
33.19
1.82
3507
3621
8.232913
TGTTAGCCACTTCTACAAGAAAATTT
57.767
30.769
0.00
0.00
33.19
1.82
3508
3622
8.349983
TGTTAGCCACTTCTACAAGAAAATTTC
58.650
33.333
0.00
0.00
33.19
2.17
3509
3623
8.568794
GTTAGCCACTTCTACAAGAAAATTTCT
58.431
33.333
1.80
1.80
43.15
2.52
3539
3653
9.337396
TGTTTCTTCTACATAATGTCACTTTGT
57.663
29.630
0.00
0.00
0.00
2.83
3597
3711
0.250295
CACTTCAGCGGTCCAGGAAA
60.250
55.000
0.00
0.00
0.00
3.13
3626
3740
1.073763
TGGCATGCTAGTGGTTCTGTT
59.926
47.619
18.92
0.00
0.00
3.16
3630
3744
1.882912
TGCTAGTGGTTCTGTTGCAG
58.117
50.000
0.00
0.00
0.00
4.41
3631
3745
1.140852
TGCTAGTGGTTCTGTTGCAGT
59.859
47.619
0.00
0.00
32.61
4.40
3632
3746
1.532868
GCTAGTGGTTCTGTTGCAGTG
59.467
52.381
0.00
0.00
32.61
3.66
3633
3747
2.806745
GCTAGTGGTTCTGTTGCAGTGA
60.807
50.000
0.00
0.00
32.61
3.41
3634
3748
1.668419
AGTGGTTCTGTTGCAGTGAC
58.332
50.000
0.00
0.00
32.61
3.67
3635
3749
1.065491
AGTGGTTCTGTTGCAGTGACA
60.065
47.619
0.00
0.00
32.61
3.58
3636
3750
1.949525
GTGGTTCTGTTGCAGTGACAT
59.050
47.619
0.00
0.00
32.61
3.06
3637
3751
1.948834
TGGTTCTGTTGCAGTGACATG
59.051
47.619
0.00
0.00
32.61
3.21
3638
3752
1.335324
GGTTCTGTTGCAGTGACATGC
60.335
52.381
0.00
1.00
46.68
4.06
3649
3763
5.752098
GCAGTGACATGCAAAAGTAATTC
57.248
39.130
0.00
0.00
45.77
2.17
3650
3764
4.321745
GCAGTGACATGCAAAAGTAATTCG
59.678
41.667
0.00
0.00
45.77
3.34
3651
3765
4.321745
CAGTGACATGCAAAAGTAATTCGC
59.678
41.667
0.00
0.00
0.00
4.70
3652
3766
4.023279
AGTGACATGCAAAAGTAATTCGCA
60.023
37.500
0.00
2.93
36.95
5.10
3653
3767
4.679197
GTGACATGCAAAAGTAATTCGCAA
59.321
37.500
4.38
0.00
35.98
4.85
3654
3768
5.174761
GTGACATGCAAAAGTAATTCGCAAA
59.825
36.000
4.38
0.00
35.98
3.68
3655
3769
5.750547
TGACATGCAAAAGTAATTCGCAAAA
59.249
32.000
4.38
0.00
35.98
2.44
3656
3770
6.256539
TGACATGCAAAAGTAATTCGCAAAAA
59.743
30.769
4.38
0.00
35.98
1.94
3704
3818
6.770785
AGAGTTTTTGTAGGCAGTTGAATACA
59.229
34.615
0.00
0.00
0.00
2.29
3759
3874
5.927030
TGCAGAAGCTGTTCTTTTATTACG
58.073
37.500
0.00
0.00
41.40
3.18
3812
3928
4.022589
TGAACAACAGAAGACGTAGGTAGG
60.023
45.833
0.00
0.00
0.00
3.18
3851
3975
0.379669
TCGATCTTAGTTCCGGCGAC
59.620
55.000
9.30
0.00
0.00
5.19
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
5.065474
CCCTACAAAACACGAACAAGAAAGA
59.935
40.000
0.00
0.0
0.00
2.52
1
2
5.270853
CCCTACAAAACACGAACAAGAAAG
58.729
41.667
0.00
0.0
0.00
2.62
2
3
4.096682
CCCCTACAAAACACGAACAAGAAA
59.903
41.667
0.00
0.0
0.00
2.52
3
4
3.628487
CCCCTACAAAACACGAACAAGAA
59.372
43.478
0.00
0.0
0.00
2.52
4
5
3.118334
TCCCCTACAAAACACGAACAAGA
60.118
43.478
0.00
0.0
0.00
3.02
5
6
3.207778
TCCCCTACAAAACACGAACAAG
58.792
45.455
0.00
0.0
0.00
3.16
6
7
3.207778
CTCCCCTACAAAACACGAACAA
58.792
45.455
0.00
0.0
0.00
2.83
7
8
2.171027
ACTCCCCTACAAAACACGAACA
59.829
45.455
0.00
0.0
0.00
3.18
8
9
2.842457
ACTCCCCTACAAAACACGAAC
58.158
47.619
0.00
0.0
0.00
3.95
9
10
3.564053
AACTCCCCTACAAAACACGAA
57.436
42.857
0.00
0.0
0.00
3.85
10
11
3.564053
AAACTCCCCTACAAAACACGA
57.436
42.857
0.00
0.0
0.00
4.35
11
12
4.337274
AGAAAAACTCCCCTACAAAACACG
59.663
41.667
0.00
0.0
0.00
4.49
12
13
5.847111
AGAAAAACTCCCCTACAAAACAC
57.153
39.130
0.00
0.0
0.00
3.32
13
14
6.192044
AGAAGAAAAACTCCCCTACAAAACA
58.808
36.000
0.00
0.0
0.00
2.83
14
15
6.710597
AGAAGAAAAACTCCCCTACAAAAC
57.289
37.500
0.00
0.0
0.00
2.43
15
16
6.038936
CGAAGAAGAAAAACTCCCCTACAAAA
59.961
38.462
0.00
0.0
0.00
2.44
16
17
5.529800
CGAAGAAGAAAAACTCCCCTACAAA
59.470
40.000
0.00
0.0
0.00
2.83
17
18
5.061179
CGAAGAAGAAAAACTCCCCTACAA
58.939
41.667
0.00
0.0
0.00
2.41
18
19
4.504340
CCGAAGAAGAAAAACTCCCCTACA
60.504
45.833
0.00
0.0
0.00
2.74
19
20
4.001652
CCGAAGAAGAAAAACTCCCCTAC
58.998
47.826
0.00
0.0
0.00
3.18
64
68
4.734266
AGGATAGGATTTCCATTTCCTGC
58.266
43.478
11.87
0.0
42.38
4.85
87
91
4.982701
GTTGGGCTGGGCTGCTGT
62.983
66.667
0.00
0.0
0.00
4.40
298
305
2.755103
GCGAATTGAAGGAGTGGGAATT
59.245
45.455
0.00
0.0
0.00
2.17
378
385
3.131933
GGAGATCTAGAGCAAGCAACTGA
59.868
47.826
11.20
0.0
0.00
3.41
414
421
2.695666
CCCCGCAGATCTAGAGAAAAGA
59.304
50.000
0.00
0.0
0.00
2.52
422
429
1.933853
CGAAAAACCCCGCAGATCTAG
59.066
52.381
0.00
0.0
0.00
2.43
483
490
5.405269
CACTTCACAGTTCACACATCGATTA
59.595
40.000
0.00
0.0
0.00
1.75
484
491
4.212004
CACTTCACAGTTCACACATCGATT
59.788
41.667
0.00
0.0
0.00
3.34
495
502
4.900635
ACCATGAAACACTTCACAGTTC
57.099
40.909
0.00
0.0
44.28
3.01
553
560
3.581755
TCTAACCAGACGAACAATTCCG
58.418
45.455
0.00
0.0
0.00
4.30
664
672
3.933155
ATAGAAGCGCGATGACAAAAG
57.067
42.857
12.10
0.0
0.00
2.27
740
753
6.954487
AATTCCCCTCCGATTAAACAATAC
57.046
37.500
0.00
0.0
0.00
1.89
775
788
5.512749
CCATCCATTCCCTCACAATCTAGAG
60.513
48.000
0.00
0.0
0.00
2.43
900
932
6.691754
AACACGCATAAATTACATCCATCA
57.308
33.333
0.00
0.0
0.00
3.07
1024
1056
2.224426
ACAATAACAGAGCCCGACAACA
60.224
45.455
0.00
0.0
0.00
3.33
1031
1063
1.474077
CAGCCAACAATAACAGAGCCC
59.526
52.381
0.00
0.0
0.00
5.19
2073
2105
5.245584
TCATGATGCATAATAGCTTGGGA
57.754
39.130
0.00
0.0
34.99
4.37
2337
2369
6.016610
GCACAAAGTTTAAGATGGTAAGGACA
60.017
38.462
0.00
0.0
0.00
4.02
2499
2531
0.165944
GAATCTGGTTGGTGCGAACG
59.834
55.000
0.00
0.0
0.00
3.95
2778
2810
1.216710
GTAGAGCGCAACAGAGCCT
59.783
57.895
11.47
0.0
0.00
4.58
3119
3152
6.036844
GCGGAACTACATTTACTAGGGAAAAG
59.963
42.308
0.00
0.0
0.00
2.27
3234
3268
7.260387
TCATTGTCATTACCCCTTAACACTA
57.740
36.000
0.00
0.0
0.00
2.74
3254
3288
5.220931
GCCACTCGCAGATTAGAATTTCATT
60.221
40.000
0.00
0.0
37.47
2.57
3336
3370
8.527810
AGTTTTGAAATTAGGTCAAGAAACACA
58.472
29.630
7.91
0.0
36.41
3.72
3374
3408
8.658499
ACGACACTATAAAAGAAACAGAAAGT
57.342
30.769
0.00
0.0
0.00
2.66
3391
3425
4.573201
CAGTTGGAAGGAAAAACGACACTA
59.427
41.667
0.00
0.0
0.00
2.74
3513
3627
9.337396
ACAAAGTGACATTATGTAGAAGAAACA
57.663
29.630
0.00
0.0
0.00
2.83
3516
3630
9.778741
AGAACAAAGTGACATTATGTAGAAGAA
57.221
29.630
0.00
0.0
0.00
2.52
3517
3631
9.778741
AAGAACAAAGTGACATTATGTAGAAGA
57.221
29.630
0.00
0.0
0.00
2.87
3519
3633
9.778741
AGAAGAACAAAGTGACATTATGTAGAA
57.221
29.630
0.00
0.0
0.00
2.10
3522
3636
9.990360
TGTAGAAGAACAAAGTGACATTATGTA
57.010
29.630
0.00
0.0
0.00
2.29
3523
3637
8.902540
TGTAGAAGAACAAAGTGACATTATGT
57.097
30.769
0.00
0.0
0.00
2.29
3524
3638
9.817365
CTTGTAGAAGAACAAAGTGACATTATG
57.183
33.333
0.00
0.0
38.81
1.90
3525
3639
9.778741
TCTTGTAGAAGAACAAAGTGACATTAT
57.221
29.630
0.00
0.0
38.81
1.28
3526
3640
9.607988
TTCTTGTAGAAGAACAAAGTGACATTA
57.392
29.630
10.82
0.0
42.23
1.90
3527
3641
8.506168
TTCTTGTAGAAGAACAAAGTGACATT
57.494
30.769
10.82
0.0
42.23
2.71
3540
3654
9.521503
CTGTTCGAATCATATTCTTGTAGAAGA
57.478
33.333
0.00
0.0
37.69
2.87
3630
3744
4.806056
GCGAATTACTTTTGCATGTCAC
57.194
40.909
0.00
0.0
43.26
3.67
3677
3791
3.315191
TCAACTGCCTACAAAAACTCTGC
59.685
43.478
0.00
0.0
0.00
4.26
3759
3874
2.029844
GGTCACCAGAGCAGCGTTC
61.030
63.158
0.00
0.0
41.81
3.95
3812
3928
9.426837
AGATCGATGTACTACTACTATCTGTTC
57.573
37.037
0.54
0.0
0.00
3.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.