Multiple sequence alignment - TraesCS3B01G246000
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
TraesCS3B01G246000
chr3B
100.000
3278
0
0
1
3278
390451630
390454907
0.000000e+00
6054
1
TraesCS3B01G246000
chr3A
93.772
1718
35
20
1599
3278
394026598
394028281
0.000000e+00
2514
2
TraesCS3B01G246000
chr3A
96.131
827
18
4
730
1547
394025777
394026598
0.000000e+00
1338
3
TraesCS3B01G246000
chr3A
86.450
738
65
21
5
713
394024974
394025705
0.000000e+00
776
4
TraesCS3B01G246000
chr3D
92.051
1711
58
15
1609
3278
296039965
296041638
0.000000e+00
2335
5
TraesCS3B01G246000
chr3D
96.259
1203
34
7
395
1594
296038785
296039979
0.000000e+00
1962
6
TraesCS3B01G246000
chr3D
92.701
411
24
4
3
412
296038358
296038763
3.640000e-164
588
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
TraesCS3B01G246000
chr3B
390451630
390454907
3277
False
6054.000000
6054
100.000000
1
3278
1
chr3B.!!$F1
3277
1
TraesCS3B01G246000
chr3A
394024974
394028281
3307
False
1542.666667
2514
92.117667
5
3278
3
chr3A.!!$F1
3273
2
TraesCS3B01G246000
chr3D
296038358
296041638
3280
False
1628.333333
2335
93.670333
3
3278
3
chr3D.!!$F1
3275
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
165
166
0.178958
AACACCCGTGGAGAGAGAGT
60.179
55.0
0.0
0.0
34.19
3.24
F
1290
1423
1.078759
CGGTGCTTCTGTCCATCGAC
61.079
60.0
0.0
0.0
37.76
4.20
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2130
2290
1.083015
CGCCGACAAAAGTGGAACG
60.083
57.895
0.0
0.0
45.86
3.95
R
2357
2518
0.107993
GCAGCAGACACAGCCTGATA
60.108
55.000
0.0
0.0
33.65
2.15
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
43
44
5.983118
ACAAAAACTTCAAAATCGGTCATCC
59.017
36.000
0.00
0.00
0.00
3.51
68
69
6.845302
TGTGCAAATATTCATCAGTTGAGAC
58.155
36.000
0.00
0.00
35.27
3.36
109
110
1.246294
AGGTATGGCCTCCCTAGTCT
58.754
55.000
3.32
0.00
46.96
3.24
115
116
3.596940
TGGCCTCCCTAGTCTACTAAG
57.403
52.381
3.32
0.00
0.00
2.18
123
124
6.039605
CCTCCCTAGTCTACTAAGCTAAACAC
59.960
46.154
0.00
0.00
0.00
3.32
142
143
1.759445
ACTATGTGCCACCTCTAGCTG
59.241
52.381
0.00
0.00
0.00
4.24
152
153
1.348036
ACCTCTAGCTGAACAACACCC
59.652
52.381
0.00
0.00
0.00
4.61
154
155
1.000955
CTCTAGCTGAACAACACCCGT
59.999
52.381
0.00
0.00
0.00
5.28
165
166
0.178958
AACACCCGTGGAGAGAGAGT
60.179
55.000
0.00
0.00
34.19
3.24
169
170
1.747367
CCGTGGAGAGAGAGTCGCT
60.747
63.158
0.00
0.00
0.00
4.93
235
236
3.803021
GCAAACATTGGAAGGCATGTGAA
60.803
43.478
0.00
0.00
33.76
3.18
259
260
3.624861
AGAAAGCCATATTGCGAGACTTG
59.375
43.478
0.00
0.00
36.02
3.16
276
277
3.305720
ACTTGATGTAATAGAGGGCGGA
58.694
45.455
0.00
0.00
0.00
5.54
277
278
3.904339
ACTTGATGTAATAGAGGGCGGAT
59.096
43.478
0.00
0.00
0.00
4.18
278
279
3.961480
TGATGTAATAGAGGGCGGATG
57.039
47.619
0.00
0.00
0.00
3.51
379
380
3.560636
ACGGGGAGAATGGTAAGATTG
57.439
47.619
0.00
0.00
0.00
2.67
515
583
4.219725
GGTGTTGCCCTAATAAAAGAAGCA
59.780
41.667
0.00
0.00
0.00
3.91
573
643
6.100004
AGTGTTGATTATACAACCTCGTGAG
58.900
40.000
0.00
0.00
46.32
3.51
621
692
1.377202
CAGGCCCTGCGCTCTAAAA
60.377
57.895
9.73
0.00
37.74
1.52
672
743
4.143179
GGAACATTCCTAACGAAGTTGACG
60.143
45.833
3.24
0.00
46.91
4.35
804
934
1.610379
ATCCACAGCCAAAAGGCCC
60.610
57.895
0.00
0.00
35.12
5.80
962
1092
1.528309
ACCCGCACCAAAAGACAGG
60.528
57.895
0.00
0.00
0.00
4.00
1245
1378
2.444256
GGCCCCTAGCTCCATCGTT
61.444
63.158
0.00
0.00
43.05
3.85
1290
1423
1.078759
CGGTGCTTCTGTCCATCGAC
61.079
60.000
0.00
0.00
37.76
4.20
1495
1630
5.588648
TCAGACCTTTTTGTACCTGAGTTTG
59.411
40.000
0.00
0.00
0.00
2.93
1500
1635
5.290885
CCTTTTTGTACCTGAGTTTGTTTGC
59.709
40.000
0.00
0.00
0.00
3.68
1501
1636
5.392767
TTTTGTACCTGAGTTTGTTTGCA
57.607
34.783
0.00
0.00
0.00
4.08
1555
1690
8.418597
ACTAATAAAGTCGCATTATCCCTCTA
57.581
34.615
0.00
0.00
30.33
2.43
1685
1821
2.566833
TGGTCCTTCTGTGAACATGG
57.433
50.000
0.00
0.00
0.00
3.66
2151
2311
1.161563
TTCCACTTTTGTCGGCGTCC
61.162
55.000
6.85
0.00
0.00
4.79
2491
2652
5.164254
CGTTGTTGATGTGTGTAGTACGTAC
60.164
44.000
18.10
18.10
0.00
3.67
2492
2653
4.465921
TGTTGATGTGTGTAGTACGTACG
58.534
43.478
19.49
15.01
33.87
3.67
2493
2654
4.024133
TGTTGATGTGTGTAGTACGTACGT
60.024
41.667
25.98
25.98
33.87
3.57
2494
2655
5.178438
TGTTGATGTGTGTAGTACGTACGTA
59.822
40.000
23.60
23.60
33.87
3.57
2543
2712
5.682943
TGTAAAAACCAGAATCTCCAACG
57.317
39.130
0.00
0.00
0.00
4.10
2580
2749
3.864686
CCACGCTACGCATGCACC
61.865
66.667
19.57
1.09
0.00
5.01
2590
2759
1.451207
GCATGCACCCGGATGTACA
60.451
57.895
14.21
0.00
42.60
2.90
2591
2760
1.029408
GCATGCACCCGGATGTACAA
61.029
55.000
14.21
0.00
42.60
2.41
2592
2761
1.016627
CATGCACCCGGATGTACAAG
58.983
55.000
0.73
0.00
36.29
3.16
2595
2764
1.206132
TGCACCCGGATGTACAAGTAG
59.794
52.381
0.73
0.00
0.00
2.57
2596
2765
1.206371
GCACCCGGATGTACAAGTAGT
59.794
52.381
0.73
0.00
0.00
2.73
2598
2767
3.490419
GCACCCGGATGTACAAGTAGTAG
60.490
52.174
0.73
0.00
32.19
2.57
2613
2782
7.479150
ACAAGTAGTAGTAGTAGAATTTCGGC
58.521
38.462
0.00
0.00
0.00
5.54
2821
2996
3.217743
CTACGCCTCCCTCCGGAC
61.218
72.222
0.00
0.00
33.32
4.79
2841
3016
1.048601
CTGGGATACGGTAGGTGCAT
58.951
55.000
0.00
0.00
37.60
3.96
3063
3238
1.820056
GGGAGAAAAGCTAGGCGGC
60.820
63.158
0.00
0.00
0.00
6.53
3092
3270
5.537300
CTTATCCAGCACAGTGGTACTAT
57.463
43.478
4.57
2.27
38.88
2.12
3130
3316
4.374702
CGCACCTGCAACAGACGC
62.375
66.667
0.00
0.00
42.21
5.19
3131
3317
2.974698
GCACCTGCAACAGACGCT
60.975
61.111
0.00
0.00
41.59
5.07
3198
3398
3.389329
AGAGTGTCTTCTTTGCTCCAAGA
59.611
43.478
0.00
0.00
0.00
3.02
3199
3399
3.737850
AGTGTCTTCTTTGCTCCAAGAG
58.262
45.455
0.00
0.00
0.00
2.85
3200
3400
2.810852
GTGTCTTCTTTGCTCCAAGAGG
59.189
50.000
0.00
0.00
0.00
3.69
3201
3401
1.809547
GTCTTCTTTGCTCCAAGAGGC
59.190
52.381
0.00
0.00
33.74
4.70
3202
3402
1.421268
TCTTCTTTGCTCCAAGAGGCA
59.579
47.619
0.00
0.00
36.62
4.75
3203
3403
2.158623
TCTTCTTTGCTCCAAGAGGCAA
60.159
45.455
0.00
0.00
45.06
4.52
3204
3404
1.901591
TCTTTGCTCCAAGAGGCAAG
58.098
50.000
0.00
0.00
46.75
4.01
3222
3422
4.380867
GGCAAGTGGACAATTAATCACCAG
60.381
45.833
7.98
1.28
0.00
4.00
3243
3443
1.425066
TCCATCCAACAAAGGCAGACT
59.575
47.619
0.00
0.00
0.00
3.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
8.448615
GTTTTTGTTAAATCTCGTACCAGCTAT
58.551
33.333
0.00
0.00
0.00
2.97
1
2
7.658575
AGTTTTTGTTAAATCTCGTACCAGCTA
59.341
33.333
0.00
0.00
0.00
3.32
43
44
6.965500
GTCTCAACTGATGAATATTTGCACAG
59.035
38.462
0.00
0.00
37.67
3.66
68
69
3.118629
TCATGGTCAGGATTCCTTTCTCG
60.119
47.826
1.28
0.00
0.00
4.04
109
110
6.103997
GTGGCACATAGTGTTTAGCTTAGTA
58.896
40.000
13.86
0.00
44.52
1.82
115
116
2.678336
GAGGTGGCACATAGTGTTTAGC
59.322
50.000
20.82
0.00
44.52
3.09
123
124
2.034878
TCAGCTAGAGGTGGCACATAG
58.965
52.381
20.82
17.56
44.52
2.23
142
143
0.391597
TCTCTCCACGGGTGTTGTTC
59.608
55.000
0.00
0.00
0.00
3.18
152
153
1.719117
GAGCGACTCTCTCTCCACG
59.281
63.158
0.00
0.00
38.78
4.94
154
155
0.036294
TTCGAGCGACTCTCTCTCCA
60.036
55.000
0.00
0.00
39.70
3.86
165
166
3.001533
GTGTTGGTTTTAGTTTCGAGCGA
59.998
43.478
0.00
0.00
0.00
4.93
169
170
4.033129
CGACTGTGTTGGTTTTAGTTTCGA
59.967
41.667
0.00
0.00
0.00
3.71
235
236
4.265073
AGTCTCGCAATATGGCTTTCTTT
58.735
39.130
0.00
0.00
0.00
2.52
259
260
2.832129
TCCATCCGCCCTCTATTACATC
59.168
50.000
0.00
0.00
0.00
3.06
276
277
6.923199
AAAACTCAATTCTCAACCATCCAT
57.077
33.333
0.00
0.00
0.00
3.41
277
278
6.462768
CCAAAAACTCAATTCTCAACCATCCA
60.463
38.462
0.00
0.00
0.00
3.41
278
279
5.928264
CCAAAAACTCAATTCTCAACCATCC
59.072
40.000
0.00
0.00
0.00
3.51
573
643
0.098728
CCATCGCCGTCATGTTTTCC
59.901
55.000
0.00
0.00
0.00
3.13
575
645
1.401552
CATCCATCGCCGTCATGTTTT
59.598
47.619
0.00
0.00
0.00
2.43
579
649
2.084610
ATACATCCATCGCCGTCATG
57.915
50.000
0.00
0.00
0.00
3.07
580
650
2.839486
AATACATCCATCGCCGTCAT
57.161
45.000
0.00
0.00
0.00
3.06
621
692
2.287129
GCCACCGTACACGTGAATTTTT
60.287
45.455
25.01
0.00
37.74
1.94
659
730
1.937278
TTGCACCGTCAACTTCGTTA
58.063
45.000
0.00
0.00
0.00
3.18
672
743
4.683781
TCTTTTGATGCGTAAATTTGCACC
59.316
37.500
5.42
0.00
45.07
5.01
804
934
8.642885
CACTATAAATATGCTGCTTCTACTTCG
58.357
37.037
0.00
0.00
0.00
3.79
962
1092
0.861837
CTAAATCGATCCGCACTGCC
59.138
55.000
0.00
0.00
0.00
4.85
1290
1423
4.168291
GCCCTCTCCAAGCCCTCG
62.168
72.222
0.00
0.00
0.00
4.63
1382
1515
7.960793
GTGTAACTGCGTATTTCTGTTTATCT
58.039
34.615
0.00
0.00
0.00
1.98
1500
1635
9.571810
GTCAAGATGAGATAGACTAGCATAATG
57.428
37.037
0.00
2.19
0.00
1.90
1501
1636
8.748412
GGTCAAGATGAGATAGACTAGCATAAT
58.252
37.037
0.00
0.00
0.00
1.28
1590
1725
8.923270
AGAAGAAGAAGAAGAAGAAGAAGAAGA
58.077
33.333
0.00
0.00
0.00
2.87
1591
1726
9.546428
AAGAAGAAGAAGAAGAAGAAGAAGAAG
57.454
33.333
0.00
0.00
0.00
2.85
1592
1727
9.541143
GAAGAAGAAGAAGAAGAAGAAGAAGAA
57.459
33.333
0.00
0.00
0.00
2.52
1593
1728
8.923270
AGAAGAAGAAGAAGAAGAAGAAGAAGA
58.077
33.333
0.00
0.00
0.00
2.87
1594
1729
9.546428
AAGAAGAAGAAGAAGAAGAAGAAGAAG
57.454
33.333
0.00
0.00
0.00
2.85
1595
1730
9.541143
GAAGAAGAAGAAGAAGAAGAAGAAGAA
57.459
33.333
0.00
0.00
0.00
2.52
1596
1731
8.923270
AGAAGAAGAAGAAGAAGAAGAAGAAGA
58.077
33.333
0.00
0.00
0.00
2.87
1597
1732
9.546428
AAGAAGAAGAAGAAGAAGAAGAAGAAG
57.454
33.333
0.00
0.00
0.00
2.85
1685
1821
1.474143
GCTCCATGGAACTCCTGTAGC
60.474
57.143
17.00
8.49
36.82
3.58
2130
2290
1.083015
CGCCGACAAAAGTGGAACG
60.083
57.895
0.00
0.00
45.86
3.95
2172
2332
0.540923
GAGGCTGCTCCATCAGAACT
59.459
55.000
0.00
0.00
36.19
3.01
2205
2365
2.357517
GAGCAGTGGTGACCGTGG
60.358
66.667
0.00
0.00
0.00
4.94
2352
2513
3.118956
AGCAGACACAGCCTGATAGTAAC
60.119
47.826
0.00
0.00
33.65
2.50
2353
2514
3.099905
AGCAGACACAGCCTGATAGTAA
58.900
45.455
0.00
0.00
33.65
2.24
2354
2515
2.428530
CAGCAGACACAGCCTGATAGTA
59.571
50.000
0.00
0.00
33.65
1.82
2355
2516
1.206610
CAGCAGACACAGCCTGATAGT
59.793
52.381
0.00
0.00
33.65
2.12
2356
2517
1.937278
CAGCAGACACAGCCTGATAG
58.063
55.000
0.00
0.00
33.65
2.08
2357
2518
0.107993
GCAGCAGACACAGCCTGATA
60.108
55.000
0.00
0.00
33.65
2.15
2440
2601
1.588404
CAATTAGCACTACTCGCACGG
59.412
52.381
0.00
0.00
0.00
4.94
2447
2608
5.593679
ACGTATCCACAATTAGCACTACT
57.406
39.130
0.00
0.00
0.00
2.57
2497
2658
2.749441
GGACCCAAGAGCAGCAGC
60.749
66.667
0.00
0.00
42.56
5.25
2543
2712
1.034292
GGGAACAGGAGCATGCTTCC
61.034
60.000
23.61
22.75
29.87
3.46
2580
2749
7.212976
TCTACTACTACTACTTGTACATCCGG
58.787
42.308
0.00
0.00
0.00
5.14
2590
2759
6.540189
TCGCCGAAATTCTACTACTACTACTT
59.460
38.462
0.00
0.00
0.00
2.24
2591
2760
6.051717
TCGCCGAAATTCTACTACTACTACT
58.948
40.000
0.00
0.00
0.00
2.57
2592
2761
6.292389
TCGCCGAAATTCTACTACTACTAC
57.708
41.667
0.00
0.00
0.00
2.73
2595
2764
6.142002
GTGATTCGCCGAAATTCTACTACTAC
59.858
42.308
2.60
0.00
0.00
2.73
2596
2765
6.204359
GTGATTCGCCGAAATTCTACTACTA
58.796
40.000
2.60
0.00
0.00
1.82
2598
2767
4.085721
CGTGATTCGCCGAAATTCTACTAC
60.086
45.833
2.60
0.00
0.00
2.73
2613
2782
1.209128
GTATGGACAGCCGTGATTCG
58.791
55.000
0.00
0.00
36.79
3.34
2651
2826
2.367894
TGAATGCCTGCATTTGGAACAA
59.632
40.909
17.66
0.00
45.50
2.83
2663
2838
4.149571
CGACGATAAGAATCTGAATGCCTG
59.850
45.833
0.00
0.00
0.00
4.85
2821
2996
1.046472
TGCACCTACCGTATCCCAGG
61.046
60.000
0.00
0.00
0.00
4.45
2841
3016
3.699538
AGGAATGAGCACTGTACGATACA
59.300
43.478
0.00
0.00
37.13
2.29
3088
3266
4.585162
CCGGAATCCTGAGACAGTAATAGT
59.415
45.833
0.00
0.00
0.00
2.12
3092
3270
2.758979
GACCGGAATCCTGAGACAGTAA
59.241
50.000
9.46
0.00
0.00
2.24
3130
3316
2.964464
ACATAGGCATCACTCAGAGGAG
59.036
50.000
1.53
0.00
46.96
3.69
3131
3317
2.961741
GACATAGGCATCACTCAGAGGA
59.038
50.000
1.53
0.00
0.00
3.71
3198
3398
3.763897
GGTGATTAATTGTCCACTTGCCT
59.236
43.478
5.34
0.00
0.00
4.75
3199
3399
3.509575
TGGTGATTAATTGTCCACTTGCC
59.490
43.478
5.34
0.00
0.00
4.52
3200
3400
4.218417
ACTGGTGATTAATTGTCCACTTGC
59.782
41.667
5.34
0.00
0.00
4.01
3201
3401
5.106157
GGACTGGTGATTAATTGTCCACTTG
60.106
44.000
14.72
7.71
42.32
3.16
3202
3402
5.010282
GGACTGGTGATTAATTGTCCACTT
58.990
41.667
14.72
3.81
42.32
3.16
3203
3403
4.042809
TGGACTGGTGATTAATTGTCCACT
59.957
41.667
16.73
5.75
45.86
4.00
3204
3404
4.331968
TGGACTGGTGATTAATTGTCCAC
58.668
43.478
16.73
9.15
45.86
4.02
3222
3422
1.541588
GTCTGCCTTTGTTGGATGGAC
59.458
52.381
0.00
0.00
0.00
4.02
3227
3427
2.435372
ACAAGTCTGCCTTTGTTGGA
57.565
45.000
0.00
0.00
0.00
3.53
3243
3443
5.903010
TGCTACCTTTCTCCATCCTATACAA
59.097
40.000
0.00
0.00
0.00
2.41
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.