Multiple sequence alignment - TraesCS7D01G270100
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
TraesCS7D01G270100
chr7D
100.000
3088
0
0
1
3088
255785739
255782652
0
5703
1
TraesCS7D01G270100
chr7B
93.806
3148
79
45
1
3088
234015061
234011970
0
4626
2
TraesCS7D01G270100
chr7A
92.018
3107
103
55
36
3088
275547629
275544614
0
4229
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
TraesCS7D01G270100
chr7D
255782652
255785739
3087
True
5703
5703
100.000
1
3088
1
chr7D.!!$R1
3087
1
TraesCS7D01G270100
chr7B
234011970
234015061
3091
True
4626
4626
93.806
1
3088
1
chr7B.!!$R1
3087
2
TraesCS7D01G270100
chr7A
275544614
275547629
3015
True
4229
4229
92.018
36
3088
1
chr7A.!!$R1
3052
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
606
641
0.108186
TTACAGCCAGATCAGGTGCG
60.108
55.000
13.13
2.38
36.18
5.34
F
891
929
1.002990
TGCACAGCTGCTAGCACAT
60.003
52.632
20.88
1.64
45.56
3.21
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1824
1894
0.607762
TTATTGGCCGTTGCAGCAGA
60.608
50.0
0.0
0.0
40.13
4.26
R
2127
2197
0.948623
TCGAGCCAATGAACGTGTGG
60.949
55.0
0.0
0.0
35.39
4.17
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
51
56
2.359214
TGTAAACACCCACGTACGTACA
59.641
45.455
22.34
15.89
0.00
2.90
140
146
1.796017
TATACCGATCCTTGGTGCCA
58.204
50.000
1.35
0.00
40.73
4.92
297
312
2.892425
GGCAACGATGGCGAGGAG
60.892
66.667
2.89
0.00
42.73
3.69
298
313
2.892425
GCAACGATGGCGAGGAGG
60.892
66.667
0.00
0.00
41.64
4.30
299
314
2.892640
CAACGATGGCGAGGAGGA
59.107
61.111
0.00
0.00
41.64
3.71
490
515
1.199558
GCGGTTACTGTCTCTTCTCGT
59.800
52.381
0.00
0.00
0.00
4.18
491
516
2.417933
GCGGTTACTGTCTCTTCTCGTA
59.582
50.000
0.00
0.00
0.00
3.43
492
517
3.727376
GCGGTTACTGTCTCTTCTCGTAC
60.727
52.174
0.00
0.00
0.00
3.67
606
641
0.108186
TTACAGCCAGATCAGGTGCG
60.108
55.000
13.13
2.38
36.18
5.34
629
664
2.556534
GTGCAATCCACAGATCTTGC
57.443
50.000
7.70
7.70
44.06
4.01
669
704
4.026968
CACACCAACAGTTGTTTTATTGCG
60.027
41.667
12.42
0.00
35.83
4.85
891
929
1.002990
TGCACAGCTGCTAGCACAT
60.003
52.632
20.88
1.64
45.56
3.21
1525
1590
1.343069
ACCGCTCCTCCTCCATATTC
58.657
55.000
0.00
0.00
0.00
1.75
1819
1889
1.946768
CAAGACGGCCAAGAGAAACAA
59.053
47.619
2.24
0.00
0.00
2.83
1820
1890
1.594331
AGACGGCCAAGAGAAACAAC
58.406
50.000
2.24
0.00
0.00
3.32
1824
1894
1.608590
CGGCCAAGAGAAACAACACAT
59.391
47.619
2.24
0.00
0.00
3.21
2012
2082
2.881352
GCGCCCTCTTCTTCGTCG
60.881
66.667
0.00
0.00
0.00
5.12
2013
2083
2.567049
CGCCCTCTTCTTCGTCGT
59.433
61.111
0.00
0.00
0.00
4.34
2015
2085
1.585006
GCCCTCTTCTTCGTCGTCA
59.415
57.895
0.00
0.00
0.00
4.35
2018
2088
0.241213
CCTCTTCTTCGTCGTCAGCA
59.759
55.000
0.00
0.00
0.00
4.41
2027
2097
2.910479
TCGTCAGCACCGGTGTCT
60.910
61.111
33.92
26.98
32.43
3.41
2140
2210
4.942090
GTGGCCACACGTTCATTG
57.058
55.556
31.23
0.00
37.94
2.82
2141
2211
1.285641
GTGGCCACACGTTCATTGG
59.714
57.895
31.23
0.00
37.94
3.16
2145
2215
1.497278
CCACACGTTCATTGGCTCG
59.503
57.895
0.00
0.00
0.00
5.03
2312
2403
1.452108
CCAGCGACTCCCAAATCCC
60.452
63.158
0.00
0.00
0.00
3.85
2364
2460
1.819208
GCATGCATCGGGTGTGCTA
60.819
57.895
14.21
0.00
42.92
3.49
2400
2496
2.689983
GGTGGCCTTATGTTGATGAAGG
59.310
50.000
3.32
0.00
42.32
3.46
2418
2514
1.133869
GTTCGGAATTTCCACGGCG
59.866
57.895
15.58
4.80
35.91
6.46
2440
2536
7.278629
GGCGAATTTGTGTATAGTATTGTACG
58.721
38.462
0.00
0.00
0.00
3.67
2462
2561
7.156876
ACGGTGTACATCAAATCATCAATTT
57.843
32.000
6.97
0.00
38.11
1.82
2692
2808
4.827284
TCTCTTCAAAAGGTTCCATTCACC
59.173
41.667
0.00
0.00
34.06
4.02
2854
2974
1.035139
GGCATCATTAGCTGTTGGGG
58.965
55.000
0.00
0.00
0.00
4.96
2867
2987
1.229951
TTGGGGACTCAGGGCTGAT
60.230
57.895
0.00
0.00
39.13
2.90
2873
2993
2.603021
GGACTCAGGGCTGATGAGATA
58.397
52.381
17.57
0.00
45.80
1.98
2874
2994
3.172339
GGACTCAGGGCTGATGAGATAT
58.828
50.000
17.57
0.81
45.80
1.63
2875
2995
4.348486
GGACTCAGGGCTGATGAGATATA
58.652
47.826
17.57
0.00
45.80
0.86
2876
2996
4.159506
GGACTCAGGGCTGATGAGATATAC
59.840
50.000
17.57
6.91
45.80
1.47
2877
2997
5.009436
ACTCAGGGCTGATGAGATATACT
57.991
43.478
17.57
0.00
45.80
2.12
2878
2998
5.016173
ACTCAGGGCTGATGAGATATACTC
58.984
45.833
17.57
0.00
45.80
2.59
2905
3025
5.627499
ACATACATTTGTGTGCTTGGTAG
57.373
39.130
7.28
0.00
40.25
3.18
2963
3087
0.599991
TGCTAGGTCAGTGCGTGTTG
60.600
55.000
0.00
0.00
0.00
3.33
3004
3128
6.146898
ACGGCAAAAACAACAATACTCATAC
58.853
36.000
0.00
0.00
0.00
2.39
3005
3129
6.146216
CGGCAAAAACAACAATACTCATACA
58.854
36.000
0.00
0.00
0.00
2.29
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
5
6
6.986817
AGAAATGTGGCGTATATATATCCAGC
59.013
38.462
13.76
3.79
0.00
4.85
11
12
9.984190
TGTTTACAGAAATGTGGCGTATATATA
57.016
29.630
0.00
0.00
0.00
0.86
19
20
2.351350
GGGTGTTTACAGAAATGTGGCG
60.351
50.000
0.00
0.00
0.00
5.69
51
56
1.640917
ATCTTGGAGTGTACGTGGGT
58.359
50.000
0.00
0.00
0.00
4.51
117
123
2.549992
GCACCAAGGATCGGTATATGCA
60.550
50.000
0.00
0.00
34.02
3.96
118
124
2.076863
GCACCAAGGATCGGTATATGC
58.923
52.381
0.00
0.00
34.02
3.14
119
125
2.038426
TGGCACCAAGGATCGGTATATG
59.962
50.000
0.00
0.00
34.02
1.78
120
126
2.334977
TGGCACCAAGGATCGGTATAT
58.665
47.619
0.00
0.00
34.02
0.86
255
267
2.968206
GCCTCCAAGCAAAGCCAG
59.032
61.111
0.00
0.00
0.00
4.85
256
268
2.974692
TTCGCCTCCAAGCAAAGCCA
62.975
55.000
0.00
0.00
0.00
4.75
257
269
2.205243
CTTCGCCTCCAAGCAAAGCC
62.205
60.000
0.00
0.00
0.00
4.35
258
270
1.211190
CTTCGCCTCCAAGCAAAGC
59.789
57.895
0.00
0.00
0.00
3.51
259
271
1.878775
CCTTCGCCTCCAAGCAAAG
59.121
57.895
0.00
0.00
0.00
2.77
297
312
1.895131
GATCTCCTCATCTGCTCCTCC
59.105
57.143
0.00
0.00
0.00
4.30
298
313
1.895131
GGATCTCCTCATCTGCTCCTC
59.105
57.143
0.00
0.00
0.00
3.71
299
314
1.219980
TGGATCTCCTCATCTGCTCCT
59.780
52.381
0.00
0.00
36.82
3.69
490
515
2.171448
GACCGGACAGGAGGTAGTAGTA
59.829
54.545
9.46
0.00
45.00
1.82
491
516
0.998145
ACCGGACAGGAGGTAGTAGT
59.002
55.000
9.46
0.00
45.00
2.73
492
517
1.677942
GACCGGACAGGAGGTAGTAG
58.322
60.000
9.46
0.00
45.00
2.57
539
564
2.234661
TCACCCTGTGATCAGTGTCATC
59.765
50.000
11.34
0.00
37.67
2.92
594
629
0.376152
GCACATTCGCACCTGATCTG
59.624
55.000
0.00
0.00
0.00
2.90
606
641
4.669318
CAAGATCTGTGGATTGCACATTC
58.331
43.478
11.62
11.36
31.46
2.67
617
652
2.165167
ACACAATGGCAAGATCTGTGG
58.835
47.619
16.20
0.52
41.32
4.17
618
653
4.256110
TCTACACAATGGCAAGATCTGTG
58.744
43.478
0.00
1.41
42.43
3.66
629
664
0.394352
GTGGGGGCTCTACACAATGG
60.394
60.000
0.00
0.00
35.30
3.16
669
704
1.439365
CGAAGCAAGCGAGCAACAC
60.439
57.895
6.21
0.00
36.85
3.32
891
929
2.104963
TGCTACCGATGCTCTCTCTCTA
59.895
50.000
0.00
0.00
0.00
2.43
1525
1590
2.160219
CGGCCATCCATGAATATCAACG
59.840
50.000
2.24
0.00
0.00
4.10
1806
1876
3.854784
GCAGATGTGTTGTTTCTCTTGGC
60.855
47.826
0.00
0.00
0.00
4.52
1813
1883
2.780065
TGCAGCAGATGTGTTGTTTC
57.220
45.000
8.47
0.00
37.24
2.78
1819
1889
2.620112
GCCGTTGCAGCAGATGTGT
61.620
57.895
0.24
0.00
37.47
3.72
1820
1890
2.177531
GCCGTTGCAGCAGATGTG
59.822
61.111
0.24
0.00
37.47
3.21
1824
1894
0.607762
TTATTGGCCGTTGCAGCAGA
60.608
50.000
0.00
0.00
40.13
4.26
2012
2082
1.080025
GGTAGACACCGGTGCTGAC
60.080
63.158
34.26
25.93
34.36
3.51
2013
2083
3.373226
GGTAGACACCGGTGCTGA
58.627
61.111
34.26
16.46
34.36
4.26
2027
2097
4.830765
GTCGCCAGCGCCATGGTA
62.831
66.667
14.67
3.58
42.75
3.25
2127
2197
0.948623
TCGAGCCAATGAACGTGTGG
60.949
55.000
0.00
0.00
35.39
4.17
2129
2199
1.337728
TGATCGAGCCAATGAACGTGT
60.338
47.619
0.00
0.00
0.00
4.49
2130
2200
1.325640
CTGATCGAGCCAATGAACGTG
59.674
52.381
0.00
0.00
0.00
4.49
2131
2201
1.645034
CTGATCGAGCCAATGAACGT
58.355
50.000
0.00
0.00
0.00
3.99
2141
2211
1.008995
GAGACGAGGCTGATCGAGC
60.009
63.158
12.28
0.00
45.56
5.03
2142
2212
1.278337
CGAGACGAGGCTGATCGAG
59.722
63.158
12.28
0.00
45.56
4.04
2143
2213
2.180862
CCGAGACGAGGCTGATCGA
61.181
63.158
12.28
0.00
45.56
3.59
2145
2215
1.357334
GACCGAGACGAGGCTGATC
59.643
63.158
0.00
0.00
0.00
2.92
2312
2403
3.914312
AGTGTGTGTATCTTCTTCGTGG
58.086
45.455
0.00
0.00
0.00
4.94
2364
2460
1.205417
GCCACCACTTATTTGCAGCAT
59.795
47.619
0.00
0.00
0.00
3.79
2400
2496
1.133869
CGCCGTGGAAATTCCGAAC
59.866
57.895
7.60
0.00
40.17
3.95
2418
2514
9.090692
ACACCGTACAATACTATACACAAATTC
57.909
33.333
0.00
0.00
0.00
2.17
2440
2536
8.465999
TGGTAAATTGATGATTTGATGTACACC
58.534
33.333
0.00
0.00
38.40
4.16
2462
2561
7.817478
CGAATAAGACAGGCACATATAATGGTA
59.183
37.037
0.00
0.00
33.60
3.25
2794
2914
4.527509
ATTCAGCATATACTGGAGGACG
57.472
45.455
3.06
0.00
38.26
4.79
2801
2921
6.684131
CGACACAACAAATTCAGCATATACTG
59.316
38.462
0.00
0.00
39.12
2.74
2854
2974
5.016173
AGTATATCTCATCAGCCCTGAGTC
58.984
45.833
4.16
0.00
43.61
3.36
2874
2994
9.830975
AAGCACACAAATGTATGTATATGAGTA
57.169
29.630
0.00
0.00
36.72
2.59
2875
2995
8.615211
CAAGCACACAAATGTATGTATATGAGT
58.385
33.333
0.00
0.00
36.72
3.41
2876
2996
8.071967
CCAAGCACACAAATGTATGTATATGAG
58.928
37.037
0.00
0.00
36.72
2.90
2877
2997
7.555914
ACCAAGCACACAAATGTATGTATATGA
59.444
33.333
0.00
0.00
36.72
2.15
2878
2998
7.706159
ACCAAGCACACAAATGTATGTATATG
58.294
34.615
0.00
0.00
36.72
1.78
2888
3008
6.258160
GCTTATACTACCAAGCACACAAATG
58.742
40.000
1.62
0.00
45.20
2.32
2963
3087
1.670811
CCGTACCATTCAATCACAGCC
59.329
52.381
0.00
0.00
0.00
4.85
3004
3128
8.682936
AAGGAATCAGCCTGTAATAATAGTTG
57.317
34.615
0.00
0.00
38.58
3.16
3005
3129
9.780186
GTAAGGAATCAGCCTGTAATAATAGTT
57.220
33.333
0.00
0.00
38.58
2.24
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.