Multiple sequence alignment - TraesCS3D01G129000
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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
TraesCS3D01G129000
chr3D
100.000
2580
0
0
579
3158
88094111
88091532
0.000000e+00
4765
1
TraesCS3D01G129000
chr3D
100.000
269
0
0
1
269
88094689
88094421
6.080000e-137
497
2
TraesCS3D01G129000
chr3B
96.838
2024
63
1
579
2602
137604722
137602700
0.000000e+00
3382
3
TraesCS3D01G129000
chr3B
97.211
502
12
1
2619
3118
137602715
137602214
0.000000e+00
848
4
TraesCS3D01G129000
chr3B
93.023
258
15
3
1
256
137605172
137604916
1.070000e-99
374
5
TraesCS3D01G129000
chr3A
96.800
2000
54
4
607
2602
104559198
104557205
0.000000e+00
3330
6
TraesCS3D01G129000
chr3A
90.132
304
18
6
2622
2923
104557217
104556924
4.940000e-103
385
7
TraesCS3D01G129000
chr3A
93.902
246
13
2
1
244
104559441
104559196
1.380000e-98
370
8
TraesCS3D01G129000
chr3A
84.959
246
21
13
2928
3158
104556864
104556620
5.270000e-58
235
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
TraesCS3D01G129000
chr3D
88091532
88094689
3157
True
2631.000000
4765
100.000000
1
3158
2
chr3D.!!$R1
3157
1
TraesCS3D01G129000
chr3B
137602214
137605172
2958
True
1534.666667
3382
95.690667
1
3118
3
chr3B.!!$R1
3117
2
TraesCS3D01G129000
chr3A
104556620
104559441
2821
True
1080.000000
3330
91.448250
1
3158
4
chr3A.!!$R1
3157
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
639
784
0.108138
AAGTTCGAGCTTCCCATCGG
60.108
55.0
8.9
0.0
39.38
4.18
F
658
803
1.160137
GCGCAGAGTTCATGTTTCCT
58.840
50.0
0.3
0.0
0.00
3.36
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2139
2284
0.036952
CTCAGCTCCCACGTGTTGAT
60.037
55.0
15.65
0.0
0.0
2.57
R
2219
2364
0.393402
GATCACCCATCACAGCTGCA
60.393
55.0
15.27
0.0
0.0
4.41
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
33
34
2.618709
GGTCTGCACATACCCAATTAGC
59.381
50.000
0.00
0.00
0.00
3.09
113
115
6.658188
TGGACGAAAATACCCTTTTGAAAT
57.342
33.333
0.00
0.00
0.00
2.17
116
118
7.654116
TGGACGAAAATACCCTTTTGAAATTTC
59.346
33.333
11.41
11.41
0.00
2.17
201
205
6.650120
AGTTCTCTGTAAAGGAGTCAAACAA
58.350
36.000
0.00
0.00
33.06
2.83
597
742
1.967319
GAGTCACTCCTTGGTGCAAA
58.033
50.000
0.00
0.00
37.16
3.68
615
760
4.928615
TGCAAAGTTTGAGTTTCTTGTTGG
59.071
37.500
19.82
0.00
0.00
3.77
639
784
0.108138
AAGTTCGAGCTTCCCATCGG
60.108
55.000
8.90
0.00
39.38
4.18
658
803
1.160137
GCGCAGAGTTCATGTTTCCT
58.840
50.000
0.30
0.00
0.00
3.36
671
816
1.748493
TGTTTCCTGTTGGTGTGAAGC
59.252
47.619
0.00
0.00
34.23
3.86
735
880
2.056223
CGGATCCGGGTAGTGTGGT
61.056
63.158
26.95
0.00
35.56
4.16
782
927
3.100207
GGGACAAATTTCCATCCCTCA
57.900
47.619
18.60
0.00
46.43
3.86
871
1016
5.798132
ACTGAATCTGTTGCTAGAACATGA
58.202
37.500
0.00
2.67
0.00
3.07
875
1020
8.429493
TGAATCTGTTGCTAGAACATGATAAG
57.571
34.615
0.00
0.00
0.00
1.73
879
1024
8.621532
TCTGTTGCTAGAACATGATAAGTTTT
57.378
30.769
0.00
0.00
0.00
2.43
976
1121
6.696198
CAAGTATGCGTCTATAATATTGCCG
58.304
40.000
0.00
0.00
0.00
5.69
1059
1204
2.409870
GCAGTTCCCTTGCATCCCG
61.410
63.158
0.00
0.00
41.17
5.14
1401
1546
2.956964
GATTCTGCCGAGTCCGCG
60.957
66.667
0.00
0.00
0.00
6.46
1506
1651
4.569865
GGGGATGTTAAAGGATGGACTGTT
60.570
45.833
0.00
0.00
0.00
3.16
1911
2056
4.851639
AGGTAGTTTGGATGAGAGCATT
57.148
40.909
0.00
0.00
34.11
3.56
1926
2071
1.284198
AGCATTGACTTCCTGGCATCT
59.716
47.619
0.00
0.00
31.11
2.90
2051
2196
5.618236
TGATTCTTCTGATATCCAGCAAGG
58.382
41.667
0.00
0.00
42.62
3.61
2058
2203
2.846206
TGATATCCAGCAAGGTCCAGTT
59.154
45.455
0.00
0.00
39.02
3.16
2139
2284
2.092323
CCTATGGTGACTCACGTGAGA
58.908
52.381
43.55
26.03
44.74
3.27
2142
2287
1.616159
TGGTGACTCACGTGAGATCA
58.384
50.000
43.55
35.81
44.74
2.92
2179
2324
1.277842
GGTTTTAAACTGCCATGGGGG
59.722
52.381
15.13
0.00
40.85
5.40
2219
2364
3.127895
TGCGCGAGTTAGGCAAAAATAAT
59.872
39.130
12.10
0.00
33.01
1.28
2234
2379
2.742428
ATAATGCAGCTGTGATGGGT
57.258
45.000
16.64
0.00
0.00
4.51
2235
2380
1.753930
TAATGCAGCTGTGATGGGTG
58.246
50.000
16.64
0.00
35.58
4.61
2238
2383
0.393402
TGCAGCTGTGATGGGTGATC
60.393
55.000
16.64
0.00
34.56
2.92
2310
2459
1.290324
GAGACGGCAGCAACAGAGA
59.710
57.895
0.00
0.00
0.00
3.10
2502
2651
5.206587
ACTATGGACGGGTTGTTATCTAGT
58.793
41.667
0.00
0.00
0.00
2.57
2582
2731
1.595489
CCGCGAGCTTGTTATTCATGC
60.595
52.381
8.23
0.00
44.29
4.06
2602
2751
4.331968
TGCGTGGATCTTCTTTATGGTTT
58.668
39.130
0.00
0.00
0.00
3.27
2603
2752
4.764823
TGCGTGGATCTTCTTTATGGTTTT
59.235
37.500
0.00
0.00
0.00
2.43
2604
2753
5.242838
TGCGTGGATCTTCTTTATGGTTTTT
59.757
36.000
0.00
0.00
0.00
1.94
2631
2780
5.929697
TTGCGCATAGATCTTCTTTATGG
57.070
39.130
12.75
0.00
0.00
2.74
2632
2781
4.960938
TGCGCATAGATCTTCTTTATGGT
58.039
39.130
5.66
0.00
0.00
3.55
2633
2782
5.368145
TGCGCATAGATCTTCTTTATGGTT
58.632
37.500
5.66
0.00
0.00
3.67
2638
2787
9.081997
CGCATAGATCTTCTTTATGGTTCTATC
57.918
37.037
0.00
0.00
0.00
2.08
2949
3158
6.759272
ACTTGCGTATTCATACCTGACATAT
58.241
36.000
0.00
0.00
0.00
1.78
2998
3217
7.553881
ACAGCTAACACATGGTTATACATTC
57.446
36.000
0.00
0.00
41.00
2.67
3076
3298
4.494091
AGATTGGATATTAGGATGGCCG
57.506
45.455
0.00
0.00
39.96
6.13
3098
3320
6.293462
GCCGTACTTTCAATCATCTTTATCCC
60.293
42.308
0.00
0.00
0.00
3.85
3135
3357
3.018423
ACTCTGTTTGCTTTGGAGGTT
57.982
42.857
0.00
0.00
0.00
3.50
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
79
81
7.883311
AGGGTATTTTCGTCCATCCATATAAAG
59.117
37.037
0.00
0.00
0.00
1.85
113
115
0.690762
GGCACACACCCCTAGAGAAA
59.309
55.000
0.00
0.00
0.00
2.52
116
118
1.541310
TTCGGCACACACCCCTAGAG
61.541
60.000
0.00
0.00
0.00
2.43
166
169
8.881262
TCCTTTACAGAGAACTTCCTTTTAGAT
58.119
33.333
0.00
0.00
0.00
1.98
174
178
5.470047
TGACTCCTTTACAGAGAACTTCC
57.530
43.478
0.00
0.00
35.27
3.46
201
205
6.182627
TGCTCTTTACTGATGAATCATGGTT
58.817
36.000
0.00
0.00
36.02
3.67
591
736
5.163963
CCAACAAGAAACTCAAACTTTGCAC
60.164
40.000
0.00
0.00
0.00
4.57
597
742
4.764823
TCACACCAACAAGAAACTCAAACT
59.235
37.500
0.00
0.00
0.00
2.66
639
784
1.135859
CAGGAAACATGAACTCTGCGC
60.136
52.381
0.00
0.00
0.00
6.09
671
816
4.543590
ATCTCCAAGCCTTATATCCGTG
57.456
45.455
0.00
0.00
0.00
4.94
708
853
0.748005
ACCCGGATCCGATGCTTTTG
60.748
55.000
35.42
15.32
42.83
2.44
735
880
2.021723
GCAAGTGTTGGGAAGTGGTCA
61.022
52.381
0.00
0.00
0.00
4.02
875
1020
8.976986
AGCAACAGATCAAATAATCAGAAAAC
57.023
30.769
0.00
0.00
0.00
2.43
879
1024
7.012989
CCATGAGCAACAGATCAAATAATCAGA
59.987
37.037
0.00
0.00
30.64
3.27
1003
1148
4.752101
AGATAGCCAATAAGTTAAGCAGCG
59.248
41.667
5.91
0.00
0.00
5.18
1055
1200
3.090790
GCCATAACTTTAAAACCCGGGA
58.909
45.455
32.02
0.00
0.00
5.14
1059
1204
5.830000
ATCTCGCCATAACTTTAAAACCC
57.170
39.130
0.00
0.00
0.00
4.11
1401
1546
3.157087
TGGAGAAAATGGAAGGTTCAGC
58.843
45.455
0.00
0.00
0.00
4.26
1404
1549
5.163457
TGTGTTTGGAGAAAATGGAAGGTTC
60.163
40.000
0.00
0.00
0.00
3.62
1506
1651
3.289128
CTGACGAGCAGGTTCAACA
57.711
52.632
0.00
0.00
41.07
3.33
1794
1939
5.818887
TCCAAGTCAAATTCATCTCCATCA
58.181
37.500
0.00
0.00
0.00
3.07
1911
2056
4.706476
CCAAATAAAGATGCCAGGAAGTCA
59.294
41.667
0.00
0.00
0.00
3.41
1926
2071
1.882989
GCCTGCCACGGCCAAATAAA
61.883
55.000
2.24
0.00
44.41
1.40
2051
2196
3.146847
CCCCTTTGAGTGTTAACTGGAC
58.853
50.000
7.22
0.00
36.52
4.02
2058
2203
0.251165
GCTGCCCCCTTTGAGTGTTA
60.251
55.000
0.00
0.00
0.00
2.41
2139
2284
0.036952
CTCAGCTCCCACGTGTTGAT
60.037
55.000
15.65
0.00
0.00
2.57
2142
2287
2.743718
CCTCAGCTCCCACGTGTT
59.256
61.111
15.65
0.00
0.00
3.32
2179
2324
2.225019
CGCATGGATAGAATGAACAGGC
59.775
50.000
0.00
0.00
35.73
4.85
2219
2364
0.393402
GATCACCCATCACAGCTGCA
60.393
55.000
15.27
0.00
0.00
4.41
2234
2379
0.687757
CCTCGGAGAACCAGGGATCA
60.688
60.000
6.58
0.00
34.09
2.92
2235
2380
0.688087
ACCTCGGAGAACCAGGGATC
60.688
60.000
6.58
0.00
38.15
3.36
2238
2383
2.359967
GGACCTCGGAGAACCAGGG
61.360
68.421
6.58
0.00
38.15
4.45
2310
2459
1.779061
ATCCCAGTCCAACCTGCGTT
61.779
55.000
0.00
0.00
0.00
4.84
2379
2528
1.914764
ACTGCTTTGGCCCCCAATG
60.915
57.895
0.00
1.85
43.55
2.82
2502
2651
5.963176
ACAAATGACACATGTAGCAATCA
57.037
34.783
0.00
0.00
0.00
2.57
2606
2755
7.148086
ACCATAAAGAAGATCTATGCGCAAAAA
60.148
33.333
17.11
2.09
0.00
1.94
2607
2756
6.318648
ACCATAAAGAAGATCTATGCGCAAAA
59.681
34.615
17.11
4.61
0.00
2.44
2608
2757
5.822519
ACCATAAAGAAGATCTATGCGCAAA
59.177
36.000
17.11
2.99
0.00
3.68
2609
2758
5.368145
ACCATAAAGAAGATCTATGCGCAA
58.632
37.500
17.11
0.00
0.00
4.85
2610
2759
4.960938
ACCATAAAGAAGATCTATGCGCA
58.039
39.130
14.96
14.96
0.00
6.09
2611
2760
5.698545
AGAACCATAAAGAAGATCTATGCGC
59.301
40.000
0.00
0.00
0.00
6.09
2612
2761
8.994429
ATAGAACCATAAAGAAGATCTATGCG
57.006
34.615
0.00
0.00
29.90
4.73
2613
2762
9.081997
CGATAGAACCATAAAGAAGATCTATGC
57.918
37.037
0.00
0.00
39.76
3.14
2620
2769
9.909644
GCTAATACGATAGAACCATAAAGAAGA
57.090
33.333
0.00
0.00
41.38
2.87
2621
2770
9.915629
AGCTAATACGATAGAACCATAAAGAAG
57.084
33.333
0.00
0.00
41.38
2.85
2626
2775
9.582431
GCAATAGCTAATACGATAGAACCATAA
57.418
33.333
0.00
0.00
37.59
1.90
2975
3184
7.792374
AGAATGTATAACCATGTGTTAGCTG
57.208
36.000
0.00
0.00
42.50
4.24
2998
3217
4.198028
TGACTCTGGATGACATGACAAG
57.802
45.455
0.00
0.00
0.00
3.16
3098
3320
8.697067
CAAACAGAGTAAATGCAATGAAGAAAG
58.303
33.333
0.00
0.00
0.00
2.62
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.