Multiple sequence alignment - TraesCS2A01G351800
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
TraesCS2A01G351800
chr2A
100.000
2231
0
0
1
2231
592097436
592095206
0.000000e+00
4120
1
TraesCS2A01G351800
chr2D
92.019
1441
86
13
469
1891
447346791
447345362
0.000000e+00
1997
2
TraesCS2A01G351800
chr2D
93.176
425
16
6
1
423
447347208
447346795
1.460000e-171
612
3
TraesCS2A01G351800
chr2D
84.545
220
23
3
2023
2231
447344809
447344590
8.070000e-50
207
4
TraesCS2A01G351800
chr2B
91.672
1453
94
12
447
1891
527000255
526998822
0.000000e+00
1988
5
TraesCS2A01G351800
chr2B
92.731
454
11
11
1
451
527001033
527000599
8.690000e-179
636
6
TraesCS2A01G351800
chr2B
84.727
275
25
9
1968
2230
526997143
526996874
2.200000e-65
259
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
TraesCS2A01G351800
chr2A
592095206
592097436
2230
True
4120.000000
4120
100.000000
1
2231
1
chr2A.!!$R1
2230
1
TraesCS2A01G351800
chr2D
447344590
447347208
2618
True
938.666667
1997
89.913333
1
2231
3
chr2D.!!$R1
2230
2
TraesCS2A01G351800
chr2B
526996874
527001033
4159
True
961.000000
1988
89.710000
1
2230
3
chr2B.!!$R1
2229
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
285
288
0.107848
CGTCCGTGGGAGGCTTAATT
60.108
55.0
0.0
0.0
30.8
1.4
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1710
2078
0.042431
AGTGAGACAGAGGGCCAGAT
59.958
55.0
6.18
0.0
0.0
2.9
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
239
240
1.871080
CCGGGTATCTAGCTTTGCTG
58.129
55.000
0.00
0.00
40.10
4.41
283
286
2.975536
CGTCCGTGGGAGGCTTAA
59.024
61.111
0.00
0.00
30.80
1.85
285
288
0.107848
CGTCCGTGGGAGGCTTAATT
60.108
55.000
0.00
0.00
30.80
1.40
286
289
1.677820
CGTCCGTGGGAGGCTTAATTT
60.678
52.381
0.00
0.00
30.80
1.82
298
301
6.405176
GGGAGGCTTAATTTGATCAACTCAAG
60.405
42.308
7.89
11.79
44.48
3.02
326
329
5.983540
AGTCAAGCTAGCTAGTATTTGCTT
58.016
37.500
19.70
14.99
40.74
3.91
331
334
5.363939
AGCTAGCTAGTATTTGCTTGAAGG
58.636
41.667
17.69
0.00
40.35
3.46
437
441
4.799564
AGTCTACTCTTTGAAGCTCAGG
57.200
45.455
0.00
0.00
0.00
3.86
554
906
1.139256
TGCCACGTGAACTTTGTCCTA
59.861
47.619
19.30
0.00
0.00
2.94
592
944
3.991242
GCCCTAGCTAGCAACCTAC
57.009
57.895
18.83
0.00
35.50
3.18
630
985
0.532862
GTGATGCATACTGTCCCCCG
60.533
60.000
0.00
0.00
0.00
5.73
668
1023
2.537730
GCGATCTGCCTCGTTTTCATTC
60.538
50.000
0.00
0.00
40.73
2.67
819
1174
2.051638
CGTCTCGTACGTGTGCAAG
58.948
57.895
16.05
4.01
46.72
4.01
825
1180
1.076533
CGTACGTGTGCAAGCTAGGG
61.077
60.000
7.22
0.00
0.00
3.53
833
1188
3.127533
CAAGCTAGGGCGGTGCAC
61.128
66.667
8.80
8.80
44.37
4.57
922
1277
3.120408
ACACGTACACTACTTAGCACGAG
60.120
47.826
10.77
6.94
33.39
4.18
980
1335
1.009389
CGCGTCTTCAACCTCCTCAC
61.009
60.000
0.00
0.00
0.00
3.51
981
1336
0.670854
GCGTCTTCAACCTCCTCACC
60.671
60.000
0.00
0.00
0.00
4.02
982
1337
0.388649
CGTCTTCAACCTCCTCACCG
60.389
60.000
0.00
0.00
0.00
4.94
1413
1779
1.741401
CACACGGCGGTCATGTGAT
60.741
57.895
19.77
0.00
45.34
3.06
1451
1817
0.814010
GCCCGGAGTAATTGCACGAT
60.814
55.000
0.73
0.00
0.00
3.73
1488
1854
6.533012
CGATTGCTTCTCAGTCTAATCTTGAA
59.467
38.462
0.00
0.00
30.09
2.69
1592
1959
1.529226
TGTTTGCCACATTCTACCCG
58.471
50.000
0.00
0.00
0.00
5.28
1613
1980
3.184986
CGACCGTCCGACAAATTTTAACT
59.815
43.478
0.00
0.00
0.00
2.24
1615
1982
5.596268
ACCGTCCGACAAATTTTAACTAC
57.404
39.130
0.00
0.00
0.00
2.73
1645
2013
7.452880
TCTGTTATCAAATTGAAGTCCTTGG
57.547
36.000
0.00
0.00
0.00
3.61
1660
2028
5.990668
AGTCCTTGGTGATATTAGAACCAC
58.009
41.667
0.00
0.00
43.55
4.16
1661
2029
5.487488
AGTCCTTGGTGATATTAGAACCACA
59.513
40.000
0.00
0.00
43.55
4.17
1667
2035
6.591935
TGGTGATATTAGAACCACATTCCTC
58.408
40.000
0.00
0.00
39.05
3.71
1669
2037
6.183361
GGTGATATTAGAACCACATTCCTCCT
60.183
42.308
0.00
0.00
38.16
3.69
1721
2089
2.609534
TTGCTGCATCTGGCCCTCT
61.610
57.895
1.84
0.00
43.89
3.69
1774
2142
1.741145
AGCTTAAACAAATACCGGCCG
59.259
47.619
21.04
21.04
0.00
6.13
1779
2147
3.729862
AAACAAATACCGGCCGAAAAA
57.270
38.095
30.73
9.13
0.00
1.94
1783
2151
0.379316
AATACCGGCCGAAAAATCGC
59.621
50.000
30.73
0.00
0.00
4.58
1784
2152
0.463116
ATACCGGCCGAAAAATCGCT
60.463
50.000
30.73
1.31
0.00
4.93
1796
2164
4.092821
CGAAAAATCGCTGATGTAGACCAA
59.907
41.667
0.00
0.00
0.00
3.67
1807
2179
3.134574
TGTAGACCAAAAGACGCCAAT
57.865
42.857
0.00
0.00
0.00
3.16
1810
2182
2.795329
AGACCAAAAGACGCCAATGAT
58.205
42.857
0.00
0.00
0.00
2.45
1820
2192
3.068165
AGACGCCAATGATAACGATCTGA
59.932
43.478
0.00
0.00
32.79
3.27
1822
2194
3.181475
ACGCCAATGATAACGATCTGAGT
60.181
43.478
0.00
0.00
32.79
3.41
1830
2202
9.004146
CAATGATAACGATCTGAGTATATCACG
57.996
37.037
0.00
0.00
33.89
4.35
1857
2230
2.035632
GGTAGCTAGCACTGAGGATGT
58.964
52.381
18.83
0.00
0.00
3.06
1858
2231
2.223923
GGTAGCTAGCACTGAGGATGTG
60.224
54.545
18.83
0.00
38.36
3.21
1891
2264
6.805016
ATCATAACTCTGGCCATATAGAGG
57.195
41.667
20.43
2.34
43.65
3.69
1907
2454
2.203153
GGCCAAGACACCACACGT
60.203
61.111
0.00
0.00
0.00
4.49
1920
2467
1.404035
CCACACGTCCTCATACGATGA
59.596
52.381
3.10
0.00
45.68
2.92
1951
2498
0.955919
GTTGGAAACGAGGCCAGGAG
60.956
60.000
5.01
0.00
36.92
3.69
2001
4041
2.186903
CATCGCCTTACCACCGCT
59.813
61.111
0.00
0.00
0.00
5.52
2011
4051
3.030652
CCACCGCTGGTCAAACAC
58.969
61.111
0.00
0.00
31.02
3.32
2025
4065
3.678548
GTCAAACACCTAGACTTAAGGCG
59.321
47.826
7.53
0.00
37.67
5.52
2030
4070
3.577415
ACACCTAGACTTAAGGCGAAACT
59.423
43.478
7.53
0.00
37.67
2.66
2052
4092
0.244994
AGCTAGTGCAACCAGAGACG
59.755
55.000
0.00
0.00
42.74
4.18
2064
4104
0.600255
CAGAGACGACACAACCACCC
60.600
60.000
0.00
0.00
0.00
4.61
2071
4111
1.308998
GACACAACCACCCTGAACTG
58.691
55.000
0.00
0.00
0.00
3.16
2091
4131
1.914764
GGTCGTCCCCACCTAACCA
60.915
63.158
0.00
0.00
0.00
3.67
2097
4137
2.355115
CCCACCTAACCAGCACCC
59.645
66.667
0.00
0.00
0.00
4.61
2098
4138
2.046314
CCACCTAACCAGCACCCG
60.046
66.667
0.00
0.00
0.00
5.28
2118
4168
1.888436
AAGGCGATGAGAACTGGCGA
61.888
55.000
0.00
0.00
0.00
5.54
2119
4169
2.167861
GGCGATGAGAACTGGCGAC
61.168
63.158
0.00
0.00
0.00
5.19
2178
4229
1.075050
CCCTAGAGGTGGAGGCGTATA
59.925
57.143
0.00
0.00
0.00
1.47
2183
4234
0.851469
AGGTGGAGGCGTATAGGAGA
59.149
55.000
0.00
0.00
0.00
3.71
2184
4235
1.202952
AGGTGGAGGCGTATAGGAGAG
60.203
57.143
0.00
0.00
0.00
3.20
2194
4245
5.012871
AGGCGTATAGGAGAGTGTCTACATA
59.987
44.000
0.00
0.00
26.62
2.29
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
239
240
3.060607
CACATTGTAAAACTTGCGCAACC
60.061
43.478
21.02
3.63
0.00
3.77
314
317
8.055279
TCCAAATTCCTTCAAGCAAATACTAG
57.945
34.615
0.00
0.00
0.00
2.57
316
319
6.721208
TCTCCAAATTCCTTCAAGCAAATACT
59.279
34.615
0.00
0.00
0.00
2.12
317
320
6.924111
TCTCCAAATTCCTTCAAGCAAATAC
58.076
36.000
0.00
0.00
0.00
1.89
318
321
7.015098
TGTTCTCCAAATTCCTTCAAGCAAATA
59.985
33.333
0.00
0.00
0.00
1.40
350
353
2.871096
TGCCGTTTGGTTCCTCTATT
57.129
45.000
0.00
0.00
37.67
1.73
425
429
7.125811
ACCTAGATGTATTACCTGAGCTTCAAA
59.874
37.037
0.00
0.00
0.00
2.69
554
906
2.480419
GCTGTAAGTTCGTTGTGCATCT
59.520
45.455
0.00
0.00
35.30
2.90
592
944
3.192844
TCACTAGGCCTCGAGTTTTAGTG
59.807
47.826
25.85
25.85
39.36
2.74
630
985
1.660607
TCGCTCGACTTTTCATGCATC
59.339
47.619
0.00
0.00
0.00
3.91
668
1023
0.894835
AGTTTGCCCTTAATTGCGGG
59.105
50.000
9.01
9.01
43.60
6.13
922
1277
2.547007
GCAGGGCTAGCTACTAGAAAGC
60.547
54.545
15.72
12.18
36.26
3.51
925
1280
1.319541
CGCAGGGCTAGCTACTAGAA
58.680
55.000
15.72
0.00
36.26
2.10
955
1310
3.335534
GTTGAAGACGCGCACGGT
61.336
61.111
5.73
0.00
46.04
4.83
1221
1576
0.824109
CTCGGTCTCATTAGTGCCCA
59.176
55.000
0.00
0.00
0.00
5.36
1230
1585
0.976641
TTCTTGCACCTCGGTCTCAT
59.023
50.000
0.00
0.00
0.00
2.90
1231
1586
0.756294
TTTCTTGCACCTCGGTCTCA
59.244
50.000
0.00
0.00
0.00
3.27
1413
1779
0.787787
CGACGTTGCGGAAAAGATCA
59.212
50.000
0.00
0.00
0.00
2.92
1438
1804
7.116376
CGACCTTATATTGATCGTGCAATTACT
59.884
37.037
9.93
1.47
39.15
2.24
1451
1817
6.816136
TGAGAAGCAATCGACCTTATATTGA
58.184
36.000
0.00
0.00
33.38
2.57
1592
1959
4.737353
AGTTAAAATTTGTCGGACGGTC
57.263
40.909
3.34
0.00
0.00
4.79
1624
1992
7.214467
TCACCAAGGACTTCAATTTGATAAC
57.786
36.000
0.00
0.00
0.00
1.89
1645
2013
6.708054
CAGGAGGAATGTGGTTCTAATATCAC
59.292
42.308
0.00
0.00
37.01
3.06
1660
2028
0.816825
CGGTGGATGCAGGAGGAATG
60.817
60.000
0.00
0.00
0.00
2.67
1661
2029
1.528824
CGGTGGATGCAGGAGGAAT
59.471
57.895
0.00
0.00
0.00
3.01
1667
2035
4.181010
CCCTCCGGTGGATGCAGG
62.181
72.222
24.22
10.17
0.00
4.85
1710
2078
0.042431
AGTGAGACAGAGGGCCAGAT
59.958
55.000
6.18
0.00
0.00
2.90
1749
2117
5.066764
GGCCGGTATTTGTTTAAGCTTATGA
59.933
40.000
7.08
0.00
0.00
2.15
1753
2121
2.162809
CGGCCGGTATTTGTTTAAGCTT
59.837
45.455
20.10
3.48
0.00
3.74
1765
2133
0.463116
AGCGATTTTTCGGCCGGTAT
60.463
50.000
27.83
13.40
0.00
2.73
1766
2134
1.078988
AGCGATTTTTCGGCCGGTA
60.079
52.632
27.83
11.46
0.00
4.02
1768
2136
1.714899
ATCAGCGATTTTTCGGCCGG
61.715
55.000
27.83
8.29
0.00
6.13
1774
2142
5.545658
TTGGTCTACATCAGCGATTTTTC
57.454
39.130
0.00
0.00
0.00
2.29
1779
2147
4.184629
GTCTTTTGGTCTACATCAGCGAT
58.815
43.478
0.00
0.00
0.00
4.58
1783
2151
2.673368
GGCGTCTTTTGGTCTACATCAG
59.327
50.000
0.00
0.00
0.00
2.90
1784
2152
2.037902
TGGCGTCTTTTGGTCTACATCA
59.962
45.455
0.00
0.00
0.00
3.07
1796
2164
4.271049
CAGATCGTTATCATTGGCGTCTTT
59.729
41.667
0.00
0.00
34.28
2.52
1807
2179
7.148457
GGACGTGATATACTCAGATCGTTATCA
60.148
40.741
0.00
0.00
35.13
2.15
1810
2182
5.410746
GGGACGTGATATACTCAGATCGTTA
59.589
44.000
0.00
0.00
35.13
3.18
1830
2202
2.443390
TGCTAGCTACCCCGGGAC
60.443
66.667
26.32
8.53
0.00
4.46
1857
2230
6.039717
GGCCAGAGTTATGATTATTTTCTGCA
59.960
38.462
0.00
0.00
31.58
4.41
1858
2231
6.039717
TGGCCAGAGTTATGATTATTTTCTGC
59.960
38.462
0.00
0.00
31.58
4.26
1891
2264
2.251642
GGACGTGTGGTGTCTTGGC
61.252
63.158
0.00
0.00
36.58
4.52
1892
2265
0.600255
GAGGACGTGTGGTGTCTTGG
60.600
60.000
0.00
0.00
36.58
3.61
1893
2266
0.104120
TGAGGACGTGTGGTGTCTTG
59.896
55.000
0.00
0.00
36.58
3.02
1894
2267
1.048601
ATGAGGACGTGTGGTGTCTT
58.951
50.000
0.00
0.00
36.58
3.01
1895
2268
1.544691
GTATGAGGACGTGTGGTGTCT
59.455
52.381
0.00
0.00
36.58
3.41
1907
2454
4.888917
TGTTGTTTGTCATCGTATGAGGA
58.111
39.130
0.00
0.00
40.53
3.71
1916
2463
4.481930
TCCAACGATGTTGTTTGTCATC
57.518
40.909
8.68
0.00
37.61
2.92
1933
2480
1.125093
TCTCCTGGCCTCGTTTCCAA
61.125
55.000
3.32
0.00
30.98
3.53
1951
2498
5.238214
GGCACTGAGAAATAAGATCACCATC
59.762
44.000
0.00
0.00
0.00
3.51
2004
4044
3.575256
TCGCCTTAAGTCTAGGTGTTTGA
59.425
43.478
0.97
0.00
42.58
2.69
2011
4051
6.016108
AGCTATAGTTTCGCCTTAAGTCTAGG
60.016
42.308
0.97
0.00
35.80
3.02
2025
4065
5.661458
TCTGGTTGCACTAGCTATAGTTTC
58.339
41.667
0.84
0.00
40.38
2.78
2030
4070
3.315470
CGTCTCTGGTTGCACTAGCTATA
59.685
47.826
0.00
0.00
42.74
1.31
2052
4092
1.308998
CAGTTCAGGGTGGTTGTGTC
58.691
55.000
0.00
0.00
0.00
3.67
2064
4104
1.004918
GGGGACGACCACAGTTCAG
60.005
63.158
6.20
0.00
42.91
3.02
2091
4131
3.376935
CTCATCGCCTTCGGGTGCT
62.377
63.158
0.00
0.00
44.74
4.40
2097
4137
1.424493
GCCAGTTCTCATCGCCTTCG
61.424
60.000
0.00
0.00
0.00
3.79
2098
4138
1.424493
CGCCAGTTCTCATCGCCTTC
61.424
60.000
0.00
0.00
0.00
3.46
2104
4144
1.203928
CATCGTCGCCAGTTCTCATC
58.796
55.000
0.00
0.00
0.00
2.92
2105
4145
0.179100
CCATCGTCGCCAGTTCTCAT
60.179
55.000
0.00
0.00
0.00
2.90
2106
4146
1.215382
CCATCGTCGCCAGTTCTCA
59.785
57.895
0.00
0.00
0.00
3.27
2113
4163
4.467084
GGGCTTCCATCGTCGCCA
62.467
66.667
0.00
0.00
44.23
5.69
2118
4168
0.760945
CCTCCTAGGGCTTCCATCGT
60.761
60.000
9.46
0.00
0.00
3.73
2119
4169
0.470080
TCCTCCTAGGGCTTCCATCG
60.470
60.000
9.46
0.00
35.59
3.84
2178
4229
9.733556
CTGAACTATATATGTAGACACTCTCCT
57.266
37.037
12.95
0.00
0.00
3.69
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.