Multiple sequence alignment - TraesCS2D01G210500
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
TraesCS2D01G210500
chr2D
100.000
3875
0
0
1
3875
166866663
166862789
0.000000e+00
7156
1
TraesCS2D01G210500
chr2A
92.661
3488
183
38
1
3459
183513096
183516539
0.000000e+00
4955
2
TraesCS2D01G210500
chr2A
93.452
168
6
2
3712
3875
183516849
183517015
1.080000e-60
244
3
TraesCS2D01G210500
chr2B
94.970
3141
103
17
1
3129
230968080
230971177
0.000000e+00
4874
4
TraesCS2D01G210500
chr2B
92.222
720
27
15
3164
3872
230971176
230971877
0.000000e+00
992
5
TraesCS2D01G210500
chr5D
81.205
415
73
3
1
414
565330025
565329615
2.890000e-86
329
6
TraesCS2D01G210500
chr4A
79.952
414
79
2
1
414
562294841
562295250
6.290000e-78
302
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
TraesCS2D01G210500
chr2D
166862789
166866663
3874
True
7156.0
7156
100.0000
1
3875
1
chr2D.!!$R1
3874
1
TraesCS2D01G210500
chr2A
183513096
183517015
3919
False
2599.5
4955
93.0565
1
3875
2
chr2A.!!$F1
3874
2
TraesCS2D01G210500
chr2B
230968080
230971877
3797
False
2933.0
4874
93.5960
1
3872
2
chr2B.!!$F1
3871
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
175
176
0.738975
TTCTCGCTACACTGATCGGG
59.261
55.0
6.47
0.0
0.00
5.14
F
1906
1935
0.668535
CATCTGCTCCGATCACCGTA
59.331
55.0
0.00
0.0
36.31
4.02
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2097
2126
0.468214
CGACCTCCCTGGATGAGCTA
60.468
60.0
0.0
0.0
39.71
3.32
R
3708
3862
0.455410
GAACAACACAGCAGCAACCA
59.545
50.0
0.0
0.0
0.00
3.67
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
172
173
4.046938
TGGAATTCTCGCTACACTGATC
57.953
45.455
5.23
0.00
0.00
2.92
173
174
3.046390
GGAATTCTCGCTACACTGATCG
58.954
50.000
5.23
0.00
0.00
3.69
174
175
2.783828
ATTCTCGCTACACTGATCGG
57.216
50.000
0.00
0.00
0.00
4.18
175
176
0.738975
TTCTCGCTACACTGATCGGG
59.261
55.000
6.47
0.00
0.00
5.14
273
275
5.845103
TGTACTAAGATCAACAAACGGTCA
58.155
37.500
0.00
0.00
0.00
4.02
293
295
6.051717
GGTCATGCACATCTCTGTACTAATT
58.948
40.000
0.00
0.00
33.14
1.40
319
321
3.300852
TGTACGCTTAATGTGACCGAA
57.699
42.857
0.00
0.00
0.00
4.30
321
323
4.056740
TGTACGCTTAATGTGACCGAAAA
58.943
39.130
0.00
0.00
0.00
2.29
367
369
1.761784
CTGATCAGTAGCTTCCTGGCT
59.238
52.381
14.95
0.00
45.29
4.75
368
370
1.483827
TGATCAGTAGCTTCCTGGCTG
59.516
52.381
11.80
3.46
43.01
4.85
369
371
0.835941
ATCAGTAGCTTCCTGGCTGG
59.164
55.000
3.65
3.65
43.01
4.85
370
372
1.451028
CAGTAGCTTCCTGGCTGGC
60.451
63.158
5.39
0.00
43.01
4.85
371
373
1.614824
AGTAGCTTCCTGGCTGGCT
60.615
57.895
5.39
11.29
43.01
4.75
418
428
3.399440
AGCTCTGTGAAGTTCCTTGAG
57.601
47.619
0.00
6.15
0.00
3.02
498
510
3.353557
ACAGTAGCATCTCCGTGAGTTA
58.646
45.455
0.00
0.00
0.00
2.24
556
571
1.096967
TAGCATTGCTGGGCATGTCG
61.097
55.000
21.31
0.00
40.10
4.35
715
741
3.190849
CATCCACAGTCCGCGCTG
61.191
66.667
5.56
11.54
41.92
5.18
1107
1136
4.202243
GCCATAAACTCTCTCATCTCTGCT
60.202
45.833
0.00
0.00
0.00
4.24
1119
1148
1.518133
CTCTGCTTCCTTCTCCGCG
60.518
63.158
0.00
0.00
0.00
6.46
1157
1186
1.300963
GGCAGCTCATCAGGGACAA
59.699
57.895
0.00
0.00
0.00
3.18
1510
1539
2.604686
ACCTCTTCGCCAGGCTCA
60.605
61.111
10.54
0.00
33.84
4.26
1899
1928
3.548745
TTGATCAACATCTGCTCCGAT
57.451
42.857
3.38
0.00
0.00
4.18
1906
1935
0.668535
CATCTGCTCCGATCACCGTA
59.331
55.000
0.00
0.00
36.31
4.02
2097
2126
3.675563
GCGATCGCCTCCGGAGAT
61.676
66.667
33.39
18.66
44.53
2.75
2115
2144
1.899142
GATAGCTCATCCAGGGAGGTC
59.101
57.143
0.00
0.00
41.78
3.85
2231
2260
2.807045
CGCGCTCTGCTTCTCGTT
60.807
61.111
5.56
0.00
43.27
3.85
2235
2264
1.669115
GCTCTGCTTCTCGTTGCCA
60.669
57.895
0.00
0.00
0.00
4.92
2277
2306
2.434359
GCCGTCTTCCTCAACCGG
60.434
66.667
0.00
0.00
41.50
5.28
2320
2349
4.854924
ACACCACGCTGCAGCACA
62.855
61.111
36.03
0.00
42.21
4.57
2434
2463
3.656280
TCCAGGCGGCCAAATCCA
61.656
61.111
23.09
0.00
0.00
3.41
2436
2465
2.492773
CCAGGCGGCCAAATCCATC
61.493
63.158
23.09
0.00
0.00
3.51
2440
2469
2.546494
GCGGCCAAATCCATCGAGG
61.546
63.158
2.24
0.00
39.47
4.63
2565
2594
2.503846
TAGGCCCCGACGAGGAGAAA
62.504
60.000
0.00
0.00
45.00
2.52
2684
2713
7.758495
AGGTAATCACAACATTAAAACGATCC
58.242
34.615
0.00
0.00
0.00
3.36
2688
2717
8.687824
AATCACAACATTAAAACGATCCAATC
57.312
30.769
0.00
0.00
0.00
2.67
2691
2720
7.807433
TCACAACATTAAAACGATCCAATCTTG
59.193
33.333
0.00
0.00
0.00
3.02
2692
2721
7.807433
CACAACATTAAAACGATCCAATCTTGA
59.193
33.333
0.00
0.00
0.00
3.02
2693
2722
8.522830
ACAACATTAAAACGATCCAATCTTGAT
58.477
29.630
0.00
0.00
0.00
2.57
2694
2723
8.800972
CAACATTAAAACGATCCAATCTTGATG
58.199
33.333
0.00
0.00
0.00
3.07
2695
2724
6.974622
ACATTAAAACGATCCAATCTTGATGC
59.025
34.615
0.00
0.00
0.00
3.91
2696
2725
6.757897
TTAAAACGATCCAATCTTGATGCT
57.242
33.333
0.00
0.00
0.00
3.79
2698
2727
6.757897
AAAACGATCCAATCTTGATGCTAA
57.242
33.333
0.00
0.00
0.00
3.09
2699
2728
5.741388
AACGATCCAATCTTGATGCTAAC
57.259
39.130
0.00
0.00
0.00
2.34
2700
2729
4.769688
ACGATCCAATCTTGATGCTAACA
58.230
39.130
0.00
0.00
0.00
2.41
2701
2730
5.185454
ACGATCCAATCTTGATGCTAACAA
58.815
37.500
0.00
0.00
0.00
2.83
2702
2731
5.065218
ACGATCCAATCTTGATGCTAACAAC
59.935
40.000
0.00
0.00
0.00
3.32
2705
2734
6.647334
TCCAATCTTGATGCTAACAACAAA
57.353
33.333
0.00
0.00
38.01
2.83
2723
2752
6.089551
ACAACAAATCTCGACTTCTGAATACG
59.910
38.462
9.09
9.09
0.00
3.06
2727
2756
4.092771
TCTCGACTTCTGAATACGTTGG
57.907
45.455
0.00
7.65
0.00
3.77
2732
2761
4.491676
GACTTCTGAATACGTTGGTGCTA
58.508
43.478
0.00
0.00
0.00
3.49
2799
2828
0.176910
TTGCAGAGACCAACGTGACA
59.823
50.000
0.00
0.00
0.00
3.58
2915
2946
3.567164
CCAGTTCTTGATTGTGCTGTCTT
59.433
43.478
0.00
0.00
0.00
3.01
2969
3000
7.484641
CCATATTTTGTTACAGTGAATGAACGG
59.515
37.037
0.00
0.00
0.00
4.44
2979
3010
4.272018
CAGTGAATGAACGGATGAATCTCC
59.728
45.833
0.00
0.00
0.00
3.71
2995
3027
3.657398
TCTCCCCAGTGTATTCGAGTA
57.343
47.619
0.00
0.00
0.00
2.59
3019
3051
0.950555
GCGATGTGTTGCTCCTGACA
60.951
55.000
0.00
0.00
0.00
3.58
3028
3060
2.047844
CTCCTGACACAGCCCACG
60.048
66.667
0.00
0.00
0.00
4.94
3036
3068
2.687200
ACAGCCCACGCCCTGATA
60.687
61.111
0.00
0.00
34.57
2.15
3041
3073
2.452064
CCCACGCCCTGATACCCAT
61.452
63.158
0.00
0.00
0.00
4.00
3060
3092
1.877576
TACGCACTGGCACTCTCCTG
61.878
60.000
0.00
0.00
41.24
3.86
3126
3158
1.338674
CCGTTCCACAATGCAGGAGTA
60.339
52.381
0.00
0.00
34.91
2.59
3129
3161
2.042686
TCCACAATGCAGGAGTATGC
57.957
50.000
0.00
0.00
46.68
3.14
3171
3203
1.409064
TCAGCGGGTCACTGTATCATC
59.591
52.381
0.00
0.00
36.50
2.92
3337
3369
2.093310
CGCCGATGAGTTATGATGATGC
59.907
50.000
0.00
0.00
0.00
3.91
3558
3634
1.995484
CGATGTAGATTATGCGCCTGG
59.005
52.381
4.18
0.00
0.00
4.45
3583
3659
3.146066
TGCAAGGACATTCTGTGGTAAC
58.854
45.455
0.00
0.00
0.00
2.50
3610
3689
6.662755
TGATGGATGTTTAGTGCTCCTTTAT
58.337
36.000
0.00
0.00
0.00
1.40
3630
3784
1.073284
TGCTGTAGGTTGGTTCCCTTC
59.927
52.381
0.00
0.00
33.35
3.46
3661
3815
2.436292
CTGCTGGTCAGGCTCTGC
60.436
66.667
0.00
0.00
39.15
4.26
3662
3816
2.926779
TGCTGGTCAGGCTCTGCT
60.927
61.111
0.00
0.00
0.00
4.24
3663
3817
2.436292
GCTGGTCAGGCTCTGCTG
60.436
66.667
0.00
0.00
0.00
4.41
3664
3818
2.436292
CTGGTCAGGCTCTGCTGC
60.436
66.667
0.00
0.00
0.00
5.25
3665
3819
3.243816
TGGTCAGGCTCTGCTGCA
61.244
61.111
0.88
0.88
34.04
4.41
3666
3820
2.436292
GGTCAGGCTCTGCTGCAG
60.436
66.667
23.31
23.31
34.04
4.41
3667
3821
2.346739
GTCAGGCTCTGCTGCAGT
59.653
61.111
27.24
7.11
32.61
4.40
3668
3822
2.033755
GTCAGGCTCTGCTGCAGTG
61.034
63.158
27.24
25.20
32.61
3.66
3669
3823
3.432588
CAGGCTCTGCTGCAGTGC
61.433
66.667
35.79
35.79
46.23
4.40
3670
3824
3.638316
AGGCTCTGCTGCAGTGCT
61.638
61.111
38.89
27.88
46.20
4.40
3671
3825
3.432588
GGCTCTGCTGCAGTGCTG
61.433
66.667
38.89
24.30
46.20
4.41
3672
3826
2.668889
GCTCTGCTGCAGTGCTGT
60.669
61.111
35.99
0.00
44.40
4.40
3684
3838
4.141287
TGCAGTGCTGTTGTACCTTAATT
58.859
39.130
17.60
0.00
0.00
1.40
3708
3862
6.735678
TGTTATTACTGATGCATTTGTCGT
57.264
33.333
0.00
0.00
0.00
4.34
3717
3871
1.277495
GCATTTGTCGTGGTTGCTGC
61.277
55.000
0.00
0.00
0.00
5.25
3731
3885
3.057315
GGTTGCTGCTGTGTTGTTCATAT
60.057
43.478
0.00
0.00
0.00
1.78
3751
3905
2.099143
TCGCTCTCGAGGCTAACTG
58.901
57.895
13.56
2.44
40.21
3.16
3808
3966
2.877097
TGGCTGCATTTCTTGGTCTA
57.123
45.000
0.50
0.00
0.00
2.59
3851
4009
1.607251
GCCAACTACACGGCTGTTACT
60.607
52.381
0.00
0.00
45.29
2.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
268
269
2.159184
AGTACAGAGATGTGCATGACCG
60.159
50.000
0.00
0.00
0.00
4.79
273
275
7.739825
ACCATAATTAGTACAGAGATGTGCAT
58.260
34.615
0.00
0.00
0.00
3.96
293
295
4.871557
GGTCACATTAAGCGTACAACCATA
59.128
41.667
0.00
0.00
0.00
2.74
319
321
7.133483
AGATAGGGATAGTGTCTAACCAGTTT
58.867
38.462
5.67
0.00
0.00
2.66
321
323
6.282568
AGATAGGGATAGTGTCTAACCAGT
57.717
41.667
5.67
0.00
0.00
4.00
367
369
0.534877
ATGCATTCGCCGAATAGCCA
60.535
50.000
22.29
16.03
37.32
4.75
368
370
0.593128
AATGCATTCGCCGAATAGCC
59.407
50.000
22.29
12.12
37.32
3.93
369
371
1.955762
GAATGCATTCGCCGAATAGC
58.044
50.000
22.90
17.30
37.32
2.97
507
519
5.585047
ACGAAAAATGTTAGGAGATGCTACC
59.415
40.000
0.00
0.00
0.00
3.18
519
534
6.709145
ATGCTACACGTACGAAAAATGTTA
57.291
33.333
24.41
6.07
0.00
2.41
556
571
0.585357
TCTACGAACTAGGATCGCGC
59.415
55.000
17.05
0.00
43.88
6.86
863
889
6.964807
TTACTAGTTATGGTATGCGGAGAA
57.035
37.500
0.00
0.00
0.00
2.87
1107
1136
2.283676
AGGGACGCGGAGAAGGAA
60.284
61.111
12.47
0.00
0.00
3.36
1119
1148
1.219393
CTTGAGCGGGAAGAGGGAC
59.781
63.158
0.00
0.00
0.00
4.46
1157
1186
2.030562
CGTGGAGCCGGTTGAACT
59.969
61.111
1.90
0.00
0.00
3.01
1657
1686
2.815647
GGCCTCTTCTTGGACGCG
60.816
66.667
3.53
3.53
0.00
6.01
1882
1911
2.484417
GGTGATCGGAGCAGATGTTGAT
60.484
50.000
0.00
0.00
0.00
2.57
2097
2126
0.468214
CGACCTCCCTGGATGAGCTA
60.468
60.000
0.00
0.00
39.71
3.32
2115
2144
3.257933
GTGCCTTCTTGGAGCACG
58.742
61.111
0.00
0.00
46.43
5.34
2178
2207
1.228124
CACCTCCCGTGCCTTTGAA
60.228
57.895
0.00
0.00
35.18
2.69
2231
2260
2.761195
CGGTCGATCGAGTCTGGCA
61.761
63.158
20.09
0.00
0.00
4.92
2235
2264
2.124653
AGCCGGTCGATCGAGTCT
60.125
61.111
21.90
10.56
0.00
3.24
2277
2306
1.448717
GCGGAGGAAGAAGAGCACC
60.449
63.158
0.00
0.00
0.00
5.01
2320
2349
2.870372
CGCTGCTTTTAAGGCGCT
59.130
55.556
7.64
0.00
41.08
5.92
2434
2463
2.427245
CCAACTCCCTCGCCTCGAT
61.427
63.158
0.00
0.00
34.61
3.59
2436
2465
4.821589
GCCAACTCCCTCGCCTCG
62.822
72.222
0.00
0.00
0.00
4.63
2684
2713
7.217636
CGAGATTTGTTGTTAGCATCAAGATTG
59.782
37.037
3.71
0.00
36.18
2.67
2688
2717
6.017933
GTCGAGATTTGTTGTTAGCATCAAG
58.982
40.000
3.71
0.00
36.18
3.02
2691
2720
5.786401
AGTCGAGATTTGTTGTTAGCATC
57.214
39.130
0.00
0.00
0.00
3.91
2692
2721
5.934625
AGAAGTCGAGATTTGTTGTTAGCAT
59.065
36.000
0.00
0.00
0.00
3.79
2693
2722
5.177511
CAGAAGTCGAGATTTGTTGTTAGCA
59.822
40.000
0.00
0.00
0.00
3.49
2694
2723
5.405571
TCAGAAGTCGAGATTTGTTGTTAGC
59.594
40.000
0.00
0.00
0.00
3.09
2695
2724
7.408132
TTCAGAAGTCGAGATTTGTTGTTAG
57.592
36.000
0.00
0.00
0.00
2.34
2696
2725
7.962964
ATTCAGAAGTCGAGATTTGTTGTTA
57.037
32.000
0.00
0.00
0.00
2.41
2698
2727
6.089551
CGTATTCAGAAGTCGAGATTTGTTGT
59.910
38.462
4.38
0.00
0.00
3.32
2699
2728
6.089551
ACGTATTCAGAAGTCGAGATTTGTTG
59.910
38.462
14.13
0.00
0.00
3.33
2700
2729
6.157211
ACGTATTCAGAAGTCGAGATTTGTT
58.843
36.000
14.13
0.00
0.00
2.83
2701
2730
5.710984
ACGTATTCAGAAGTCGAGATTTGT
58.289
37.500
14.13
0.00
0.00
2.83
2702
2731
6.454318
CCAACGTATTCAGAAGTCGAGATTTG
60.454
42.308
14.13
9.03
0.00
2.32
2705
2734
4.158025
ACCAACGTATTCAGAAGTCGAGAT
59.842
41.667
14.13
1.40
0.00
2.75
2799
2828
3.690139
TCTTCACGATCTTCTTAGCGTCT
59.310
43.478
0.00
0.00
34.37
4.18
2915
2946
5.887214
ACATATGTGTTAGCTACCCATGA
57.113
39.130
7.78
0.00
34.01
3.07
2969
3000
4.039245
TCGAATACACTGGGGAGATTCATC
59.961
45.833
0.00
0.00
0.00
2.92
2995
3027
1.738099
GAGCAACACATCGCCGAGT
60.738
57.895
0.00
0.00
0.00
4.18
3019
3051
2.687200
TATCAGGGCGTGGGCTGT
60.687
61.111
7.42
0.00
39.81
4.40
3028
3060
0.602905
GTGCGTATGGGTATCAGGGC
60.603
60.000
0.00
0.00
0.00
5.19
3036
3068
2.046314
GTGCCAGTGCGTATGGGT
60.046
61.111
4.08
0.00
41.78
4.51
3041
3073
1.606601
AGGAGAGTGCCAGTGCGTA
60.607
57.895
0.00
0.00
41.78
4.42
3060
3092
1.337823
ACAGAGACGGGCAATGTACAC
60.338
52.381
0.00
0.00
0.00
2.90
3126
3158
1.145598
CTCATCGCTGAGTGGGCAT
59.854
57.895
8.12
0.00
43.35
4.40
3171
3203
3.950087
TCGATCGATTTTGCCATTCTG
57.050
42.857
15.15
0.00
0.00
3.02
3293
3325
2.117156
TAGAGTACGTCGGCCAGGC
61.117
63.158
1.26
1.26
0.00
4.85
3583
3659
2.283298
AGCACTAAACATCCATCAGCG
58.717
47.619
0.00
0.00
0.00
5.18
3653
3807
3.638316
AGCACTGCAGCAGAGCCT
61.638
61.111
33.35
21.17
46.32
4.58
3661
3815
1.597742
AAGGTACAACAGCACTGCAG
58.402
50.000
13.48
13.48
0.00
4.41
3662
3816
2.920724
TAAGGTACAACAGCACTGCA
57.079
45.000
3.30
0.00
0.00
4.41
3663
3817
4.766404
AATTAAGGTACAACAGCACTGC
57.234
40.909
0.00
0.00
0.00
4.40
3664
3818
6.072112
ACAAATTAAGGTACAACAGCACTG
57.928
37.500
0.00
0.00
0.00
3.66
3665
3819
6.709018
AACAAATTAAGGTACAACAGCACT
57.291
33.333
0.00
0.00
0.00
4.40
3684
3838
7.020602
CACGACAAATGCATCAGTAATAACAA
58.979
34.615
0.00
0.00
0.00
2.83
3698
3852
1.277495
GCAGCAACCACGACAAATGC
61.277
55.000
0.00
0.00
37.28
3.56
3708
3862
0.455410
GAACAACACAGCAGCAACCA
59.545
50.000
0.00
0.00
0.00
3.67
3717
3871
4.428209
AGAGCGAGATATGAACAACACAG
58.572
43.478
0.00
0.00
0.00
3.66
3751
3905
6.803154
AATAAGGTTAGTGTGCTTTCAGTC
57.197
37.500
0.00
0.00
0.00
3.51
3808
3966
2.652348
TGTTTGGATTGTAGGGGGACAT
59.348
45.455
0.00
0.00
0.00
3.06
3851
4009
5.416083
CAAGTGACCAGAATACGGATACAA
58.584
41.667
0.00
0.00
0.00
2.41
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.