Multiple sequence alignment - TraesCS2B01G306100
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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
TraesCS2B01G306100
chr2B
100.000
4854
0
0
1
4854
436991082
436995935
0.000000e+00
8964
1
TraesCS2B01G306100
chr2D
96.120
4871
124
24
1
4854
367989640
367994462
0.000000e+00
7888
2
TraesCS2B01G306100
chr2A
96.639
3749
93
11
932
4668
498086212
498089939
0.000000e+00
6194
3
TraesCS2B01G306100
chr2A
93.908
952
33
13
1
947
498085267
498086198
0.000000e+00
1413
4
TraesCS2B01G306100
chr2A
98.113
212
2
1
4645
4854
498090115
498090326
7.680000e-98
368
5
TraesCS2B01G306100
chr2A
90.196
102
7
2
4754
4852
762011912
762011811
3.940000e-26
130
6
TraesCS2B01G306100
chr4A
85.116
430
64
0
1673
2102
5405427
5405856
1.600000e-119
440
7
TraesCS2B01G306100
chr4B
84.651
430
66
0
1673
2102
581537724
581537295
3.470000e-116
429
8
TraesCS2B01G306100
chr4B
73.950
357
55
26
2231
2563
518872403
518872745
5.140000e-20
110
9
TraesCS2B01G306100
chr4D
93.137
102
4
2
4755
4853
289339810
289339911
3.910000e-31
147
10
TraesCS2B01G306100
chr5A
92.784
97
4
2
4756
4849
110665086
110664990
2.360000e-28
137
11
TraesCS2B01G306100
chr3A
92.708
96
5
2
4756
4849
167879890
167879795
2.360000e-28
137
12
TraesCS2B01G306100
chr6B
91.837
98
5
2
4756
4850
684940398
684940301
3.050000e-27
134
13
TraesCS2B01G306100
chr5D
91.089
101
6
2
4752
4849
134782210
134782110
3.050000e-27
134
14
TraesCS2B01G306100
chr5B
87.826
115
9
4
4741
4852
698467298
698467186
3.940000e-26
130
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
TraesCS2B01G306100
chr2B
436991082
436995935
4853
False
8964.000000
8964
100.00
1
4854
1
chr2B.!!$F1
4853
1
TraesCS2B01G306100
chr2D
367989640
367994462
4822
False
7888.000000
7888
96.12
1
4854
1
chr2D.!!$F1
4853
2
TraesCS2B01G306100
chr2A
498085267
498090326
5059
False
2658.333333
6194
96.22
1
4854
3
chr2A.!!$F1
4853
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
72
73
0.881600
TCTGGAATCATCGCATGCCG
60.882
55.000
13.15
7.68
38.61
5.69
F
366
372
1.798813
GACTCTTAGTGGTTTGTGGCG
59.201
52.381
0.00
0.00
0.00
5.69
F
1847
1892
1.141657
TGGAAGCTCAAGCAGACAAGT
59.858
47.619
4.59
0.00
45.16
3.16
F
2453
2498
3.054139
TCCATGCAATCTAACCTCTTGCT
60.054
43.478
7.85
0.00
44.29
3.91
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1847
1892
1.080093
CTTCTTAGCGTCGGTGCCA
60.080
57.895
7.30
0.0
34.65
4.92
R
2326
2371
5.906772
ACCCTAATACTAAATCCCCTGTG
57.093
43.478
0.00
0.0
0.00
3.66
R
3025
3078
1.078918
TGCATCACAGAAGGCTCGG
60.079
57.895
0.00
0.0
0.00
4.63
R
4432
4486
0.976641
TAGTGACACCTGAAGCCCTG
59.023
55.000
0.84
0.0
0.00
4.45
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
37
38
2.126502
CCACGCGACCAAAATGCC
60.127
61.111
15.93
0.00
0.00
4.40
72
73
0.881600
TCTGGAATCATCGCATGCCG
60.882
55.000
13.15
7.68
38.61
5.69
104
105
5.481473
ACATACATTTCCATTCCAACAAGCT
59.519
36.000
0.00
0.00
0.00
3.74
107
108
2.673775
TTCCATTCCAACAAGCTCCA
57.326
45.000
0.00
0.00
0.00
3.86
112
113
3.305608
CCATTCCAACAAGCTCCAAGTTC
60.306
47.826
0.00
0.00
0.00
3.01
175
176
4.696479
ATTCCGGAGCTTCTGAACATAT
57.304
40.909
3.34
0.00
0.00
1.78
353
359
6.687081
AAAACCAACGAAATGTGACTCTTA
57.313
33.333
0.00
0.00
0.00
2.10
366
372
1.798813
GACTCTTAGTGGTTTGTGGCG
59.201
52.381
0.00
0.00
0.00
5.69
464
470
6.778559
TGCCAGGTAGTTAAGTAAAACCAATT
59.221
34.615
4.01
0.00
32.43
2.32
720
731
5.217400
AGTTTATACCCTCCCAGAGTAAGG
58.783
45.833
0.00
0.00
0.00
2.69
833
845
7.079700
TCCTAATGTTAATATGACCCTCCAGA
58.920
38.462
0.00
0.00
0.00
3.86
1258
1298
5.473162
TCAGTGTTTATGAGTTCAACCCATG
59.527
40.000
0.00
0.00
0.00
3.66
1465
1505
8.458573
TGAACAATCACTTGTAAACAACCTAT
57.541
30.769
0.00
0.00
44.83
2.57
1527
1571
1.929494
TGATTCACCCCAGGGCTAATT
59.071
47.619
0.00
0.00
39.32
1.40
1528
1572
3.127250
TGATTCACCCCAGGGCTAATTA
58.873
45.455
0.00
0.00
39.32
1.40
1529
1573
3.529734
TGATTCACCCCAGGGCTAATTAA
59.470
43.478
0.00
0.00
39.32
1.40
1530
1574
4.169856
TGATTCACCCCAGGGCTAATTAAT
59.830
41.667
0.00
0.00
39.32
1.40
1847
1892
1.141657
TGGAAGCTCAAGCAGACAAGT
59.858
47.619
4.59
0.00
45.16
3.16
2165
2210
5.888724
TGGAGTTGTCTGGTATTTCAACAAA
59.111
36.000
9.04
0.00
41.43
2.83
2201
2246
8.407832
CAGCTGGATTAATTGTTGATTATGACA
58.592
33.333
5.57
0.00
30.56
3.58
2263
2308
5.423015
TGGTTTGCAGTATTCAAAAAGCAA
58.577
33.333
0.00
0.00
31.99
3.91
2264
2309
5.523188
TGGTTTGCAGTATTCAAAAAGCAAG
59.477
36.000
0.00
0.00
42.11
4.01
2326
2371
8.816640
TTTCAAATCCTACAGAAATCAAAAGC
57.183
30.769
0.00
0.00
0.00
3.51
2345
2390
7.556275
TCAAAAGCACAGGGGATTTAGTATTAG
59.444
37.037
0.00
0.00
0.00
1.73
2421
2466
7.014326
GTGGATACCATAGTTGTCATAGACTCA
59.986
40.741
0.00
0.00
35.28
3.41
2453
2498
3.054139
TCCATGCAATCTAACCTCTTGCT
60.054
43.478
7.85
0.00
44.29
3.91
2469
2514
5.072329
CCTCTTGCTAGGAATCCTATGGAAA
59.928
44.000
9.80
0.00
39.15
3.13
2606
2651
4.261031
CCTTTGACCTAAAAGAACCGTGTG
60.261
45.833
0.00
0.00
39.12
3.82
2818
2864
8.684386
TCTTTGTTTCCAAGTGTTACATGATA
57.316
30.769
0.00
0.00
0.00
2.15
2851
2897
7.396540
AGTTGTTCTTGTTTCAGAGTGAATT
57.603
32.000
0.00
0.00
36.11
2.17
2865
2911
9.515020
TTCAGAGTGAATTTCAAACACAATAAC
57.485
29.630
0.00
0.00
37.05
1.89
2870
2916
7.069331
AGTGAATTTCAAACACAATAACCTGGA
59.931
33.333
0.00
0.00
37.05
3.86
2896
2942
8.581253
AATCCTAGTAGAAAAACATTTCCCTG
57.419
34.615
0.00
0.00
0.00
4.45
2973
3026
8.725405
TCTGAAATGCCGATATTTACAAACTA
57.275
30.769
0.00
0.00
30.78
2.24
2991
3044
7.127686
ACAAACTAACATTTCTTTCCGTTACG
58.872
34.615
0.00
0.00
0.00
3.18
3025
3078
2.175878
AGGACAGCTTCATCACACAC
57.824
50.000
0.00
0.00
0.00
3.82
3044
3097
1.364626
CCGAGCCTTCTGTGATGCAC
61.365
60.000
0.00
0.00
34.56
4.57
3323
3376
2.024176
TGGGAGTGAACCAAGCTCTA
57.976
50.000
0.00
0.00
34.44
2.43
3496
3549
1.008327
TCTTCTGGCATCCTAGGGACA
59.992
52.381
9.46
0.44
32.98
4.02
3505
3558
0.178970
TCCTAGGGACACCGATAGCC
60.179
60.000
9.46
0.00
43.47
3.93
3556
3609
2.926200
CAACAGCTCCTACATGAACTCG
59.074
50.000
0.00
0.00
0.00
4.18
3607
3660
2.825836
GCAGTGCCTTGGATCGGG
60.826
66.667
2.85
0.00
0.00
5.14
4144
4198
2.680312
TGCTGGAATAGAGAGTGCAC
57.320
50.000
9.40
9.40
0.00
4.57
4166
4220
7.493645
TGCACAACATGTATTTGATTGAACAAA
59.506
29.630
0.00
0.00
42.58
2.83
4251
4305
3.498774
ACAGAGTTGCCTCTCAAATGT
57.501
42.857
7.75
1.87
45.08
2.71
4252
4306
3.825328
ACAGAGTTGCCTCTCAAATGTT
58.175
40.909
7.75
0.00
45.08
2.71
4254
4308
5.564550
ACAGAGTTGCCTCTCAAATGTTAT
58.435
37.500
7.75
0.00
45.08
1.89
4255
4309
5.645497
ACAGAGTTGCCTCTCAAATGTTATC
59.355
40.000
7.75
0.00
45.08
1.75
4256
4310
5.065731
CAGAGTTGCCTCTCAAATGTTATCC
59.934
44.000
7.75
0.00
45.08
2.59
4257
4311
5.045286
AGAGTTGCCTCTCAAATGTTATCCT
60.045
40.000
7.75
0.00
45.08
3.24
4258
4312
5.574188
AGTTGCCTCTCAAATGTTATCCTT
58.426
37.500
0.00
0.00
36.26
3.36
4259
4313
5.649831
AGTTGCCTCTCAAATGTTATCCTTC
59.350
40.000
0.00
0.00
36.26
3.46
4260
4314
5.178096
TGCCTCTCAAATGTTATCCTTCA
57.822
39.130
0.00
0.00
0.00
3.02
4261
4315
5.188434
TGCCTCTCAAATGTTATCCTTCAG
58.812
41.667
0.00
0.00
0.00
3.02
4262
4316
5.189180
GCCTCTCAAATGTTATCCTTCAGT
58.811
41.667
0.00
0.00
0.00
3.41
4263
4317
5.295540
GCCTCTCAAATGTTATCCTTCAGTC
59.704
44.000
0.00
0.00
0.00
3.51
4383
4437
1.973515
AGAGGCTCAATGTCACTCACA
59.026
47.619
18.26
0.00
40.18
3.58
4432
4486
0.179001
ACAGTTTGTGGGCCAGTACC
60.179
55.000
6.40
0.00
0.00
3.34
4444
4498
1.201429
CCAGTACCAGGGCTTCAGGT
61.201
60.000
0.00
0.00
39.41
4.00
4530
4584
5.903010
TGATCCCTATTCTTAGGCTTGTACA
59.097
40.000
0.00
0.00
43.34
2.90
4617
4674
3.243535
TGCATGCGTTTACAAAATGTGGA
60.244
39.130
14.09
0.00
0.00
4.02
4716
4972
4.058721
TGATCTTCATGTACCATCACGG
57.941
45.455
0.00
0.00
42.50
4.94
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
37
38
0.674895
CAGAGAACCGAAAGCTGGGG
60.675
60.000
0.00
0.00
0.00
4.96
72
73
9.921637
TTGGAATGGAAATGTATGTTTAAACTC
57.078
29.630
18.72
9.99
0.00
3.01
175
176
5.479027
TCACTAGTGTAGCATACTTTGTGGA
59.521
40.000
21.99
0.00
43.54
4.02
292
298
7.193595
ACTTGCATTTGTGTTAACTGAGTTAC
58.806
34.615
4.23
0.00
0.00
2.50
353
359
0.110486
AGGATTCGCCACAAACCACT
59.890
50.000
0.00
0.00
40.02
4.00
366
372
4.555262
GCTGTGTAGCTCATCTAGGATTC
58.445
47.826
0.00
0.00
46.57
2.52
439
445
5.307544
TGGTTTTACTTAACTACCTGGCA
57.692
39.130
0.00
0.00
0.00
4.92
464
470
2.615391
TGAACCCTGTGTCCTGATACA
58.385
47.619
0.00
0.00
0.00
2.29
472
478
2.232941
TCCTTCGTATGAACCCTGTGTC
59.767
50.000
0.00
0.00
0.00
3.67
720
731
1.354506
GATCAAGCGCATCAGGCAC
59.645
57.895
11.47
0.00
45.17
5.01
833
845
4.536765
AGTTTTTGAGACCACTGGAACAT
58.463
39.130
0.71
0.00
38.20
2.71
895
907
9.398170
CAGCCAAATATATATTTTGTTTCCTCG
57.602
33.333
16.47
4.29
33.88
4.63
911
923
9.850198
ATTATTTGCCATTAAACAGCCAAATAT
57.150
25.926
0.00
0.00
0.00
1.28
912
924
9.107177
CATTATTTGCCATTAAACAGCCAAATA
57.893
29.630
0.00
0.00
0.00
1.40
1150
1190
1.453235
CATGGATGATGGGGTCGCT
59.547
57.895
0.00
0.00
0.00
4.93
1231
1271
6.549364
TGGGTTGAACTCATAAACACTGAAAT
59.451
34.615
0.00
0.00
0.00
2.17
1239
1279
5.391312
AAGCATGGGTTGAACTCATAAAC
57.609
39.130
10.82
3.80
37.15
2.01
1258
1298
2.360801
TGCCTTTGTGGTAGTTGAAAGC
59.639
45.455
0.00
0.00
38.35
3.51
1465
1505
9.296400
GTAAAAACAATAGTTCAGCAGTGAAAA
57.704
29.630
0.00
0.00
44.44
2.29
1530
1574
9.841295
AGAGCTATTTATTACCCGTGAAATAAA
57.159
29.630
0.00
7.88
40.15
1.40
1847
1892
1.080093
CTTCTTAGCGTCGGTGCCA
60.080
57.895
7.30
0.00
34.65
4.92
2180
2225
8.078596
GGAGCTGTCATAATCAACAATTAATCC
58.921
37.037
0.00
0.00
33.59
3.01
2201
2246
6.491403
GGGTATTGAATATCACATTTGGAGCT
59.509
38.462
0.00
0.00
0.00
4.09
2263
2308
8.840751
CCTATTCCTATGATTTTCCTATTCCCT
58.159
37.037
0.00
0.00
0.00
4.20
2264
2309
8.836735
TCCTATTCCTATGATTTTCCTATTCCC
58.163
37.037
0.00
0.00
0.00
3.97
2326
2371
5.906772
ACCCTAATACTAAATCCCCTGTG
57.093
43.478
0.00
0.00
0.00
3.66
2402
2447
6.878317
TCCTTTGAGTCTATGACAACTATGG
58.122
40.000
0.46
3.83
34.60
2.74
2453
2498
7.931015
ACACTACATTTCCATAGGATTCCTA
57.069
36.000
14.77
14.77
40.71
2.94
2469
2514
7.283127
CCTATGGATTGCTTTTGTACACTACAT
59.717
37.037
0.00
0.00
38.68
2.29
2519
2564
6.985188
TTTTCCTTTAGGTTCATCTGATCG
57.015
37.500
0.00
0.00
36.34
3.69
2520
2565
9.794685
GAAATTTTCCTTTAGGTTCATCTGATC
57.205
33.333
0.00
0.00
36.34
2.92
2576
2621
7.169140
CGGTTCTTTTAGGTCAAAGGATTTTTG
59.831
37.037
0.00
0.00
35.03
2.44
2579
2624
5.831525
ACGGTTCTTTTAGGTCAAAGGATTT
59.168
36.000
0.00
0.00
40.26
2.17
2606
2651
7.816640
TGTAATTGAATTTCTAGCCTGTGAAC
58.183
34.615
0.00
0.00
0.00
3.18
2729
2775
3.370103
GGTGAAACGGATGGTGGATCTAA
60.370
47.826
0.00
0.00
38.12
2.10
2803
2849
7.814107
ACTTGGCAAAATATCATGTAACACTTG
59.186
33.333
0.00
0.00
0.00
3.16
2851
2897
6.553100
AGGATTTCCAGGTTATTGTGTTTGAA
59.447
34.615
0.00
0.00
38.89
2.69
2865
2911
8.581253
AATGTTTTTCTACTAGGATTTCCAGG
57.419
34.615
0.00
0.00
38.89
4.45
2870
2916
9.025041
CAGGGAAATGTTTTTCTACTAGGATTT
57.975
33.333
0.00
0.00
40.91
2.17
2973
3026
8.036273
ACAATATCGTAACGGAAAGAAATGTT
57.964
30.769
0.00
0.00
0.00
2.71
2991
3044
7.334421
TGAAGCTGTCCTTTCTGTAACAATATC
59.666
37.037
0.00
0.00
32.78
1.63
3025
3078
1.078918
TGCATCACAGAAGGCTCGG
60.079
57.895
0.00
0.00
0.00
4.63
3044
3097
9.092876
GTTGATTCTGGAGTTATCTTCAGTTAG
57.907
37.037
8.65
0.00
45.11
2.34
3323
3376
3.133721
GGAGAGCTCATGGACATGTAAGT
59.866
47.826
17.77
0.00
39.72
2.24
3496
3549
6.493802
TCTTTCTATCACTATTGGCTATCGGT
59.506
38.462
0.00
0.00
0.00
4.69
3505
3558
7.978414
TCAGCAGTCTTCTTTCTATCACTATTG
59.022
37.037
0.00
0.00
0.00
1.90
3607
3660
1.202405
CCCATTGAAAATGGCGGTAGC
60.202
52.381
12.64
0.00
44.18
3.58
3622
3675
3.033909
GCTTCTATTTTCTGCCCCCATT
58.966
45.455
0.00
0.00
0.00
3.16
3991
4045
9.631257
TTTCATGAAATCATCTTCTAGCCATAA
57.369
29.630
16.91
0.00
33.61
1.90
4254
4308
9.098355
CAGATAAAAATGTATTCGACTGAAGGA
57.902
33.333
0.00
0.00
37.57
3.36
4255
4309
7.852945
GCAGATAAAAATGTATTCGACTGAAGG
59.147
37.037
0.00
0.00
37.57
3.46
4256
4310
8.607459
AGCAGATAAAAATGTATTCGACTGAAG
58.393
33.333
0.00
0.00
37.57
3.02
4257
4311
8.492673
AGCAGATAAAAATGTATTCGACTGAA
57.507
30.769
0.00
0.00
38.76
3.02
4258
4312
8.492673
AAGCAGATAAAAATGTATTCGACTGA
57.507
30.769
0.00
0.00
0.00
3.41
4259
4313
8.390354
TGAAGCAGATAAAAATGTATTCGACTG
58.610
33.333
0.00
0.00
0.00
3.51
4260
4314
8.492673
TGAAGCAGATAAAAATGTATTCGACT
57.507
30.769
0.00
0.00
0.00
4.18
4261
4315
8.391106
ACTGAAGCAGATAAAAATGTATTCGAC
58.609
33.333
0.82
0.00
35.18
4.20
4262
4316
8.492673
ACTGAAGCAGATAAAAATGTATTCGA
57.507
30.769
0.82
0.00
35.18
3.71
4383
4437
2.616376
TGTATTGTGTCGCAACAGCTTT
59.384
40.909
0.00
0.00
40.28
3.51
4432
4486
0.976641
TAGTGACACCTGAAGCCCTG
59.023
55.000
0.84
0.00
0.00
4.45
4444
4498
1.342074
AAGCTCTGCCAGTAGTGACA
58.658
50.000
0.00
0.00
0.00
3.58
4592
4649
5.333952
CCACATTTTGTAAACGCATGCATTT
60.334
36.000
16.71
16.71
0.00
2.32
4593
4650
4.152045
CCACATTTTGTAAACGCATGCATT
59.848
37.500
19.57
14.28
0.00
3.56
4594
4651
3.679025
CCACATTTTGTAAACGCATGCAT
59.321
39.130
19.57
0.00
0.00
3.96
4602
4659
6.366061
GCCATTTCTCTCCACATTTTGTAAAC
59.634
38.462
0.00
0.00
0.00
2.01
4617
4674
3.795688
TTGAAGAGGTGCCATTTCTCT
57.204
42.857
0.00
0.00
39.31
3.10
4716
4972
1.961793
TATTTATGTCCCAGCGGCAC
58.038
50.000
1.45
0.00
0.00
5.01
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.