Multiple sequence alignment - TraesCS7B01G236500
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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
TraesCS7B01G236500
chr7B
100.000
2303
0
0
1
2303
440807929
440810231
0.000000e+00
4253
1
TraesCS7B01G236500
chr7A
94.294
2331
62
18
1
2303
509474838
509472551
0.000000e+00
3502
2
TraesCS7B01G236500
chr7D
93.130
1703
77
17
1
1687
423703856
423705534
0.000000e+00
2460
3
TraesCS7B01G236500
chr7D
90.278
360
27
5
1945
2303
423705599
423705951
4.480000e-127
464
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
TraesCS7B01G236500
chr7B
440807929
440810231
2302
False
4253
4253
100.000
1
2303
1
chr7B.!!$F1
2302
1
TraesCS7B01G236500
chr7A
509472551
509474838
2287
True
3502
3502
94.294
1
2303
1
chr7A.!!$R1
2302
2
TraesCS7B01G236500
chr7D
423703856
423705951
2095
False
1462
2460
91.704
1
2303
2
chr7D.!!$F1
2302
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
891
910
0.111061
TCAGTTTCAGCCACAGCCAT
59.889
50.0
0.0
0.0
41.25
4.4
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1868
1892
1.489481
CTGGGACCTATCACTGAGCA
58.511
55.0
0.0
0.0
28.7
4.26
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
156
165
2.351455
GCTTGTAGCTCCCACTCTTTC
58.649
52.381
0.00
0.00
38.45
2.62
192
201
1.674359
CGTATGGTTATGCTTGCCCA
58.326
50.000
0.00
0.00
0.00
5.36
241
250
3.030291
AGTTGGCAAAACCTGATCAACA
58.970
40.909
0.00
0.00
40.33
3.33
272
281
7.912056
AAACTTGTCAGCATATATCGCATAT
57.088
32.000
9.01
0.00
0.00
1.78
308
318
4.931027
ACTCTGGAGTCTGGTTACTCTA
57.069
45.455
4.20
0.00
44.42
2.43
310
320
3.949113
CTCTGGAGTCTGGTTACTCTACC
59.051
52.174
4.20
0.00
44.42
3.18
341
351
5.622770
ATTTCTTGTTAACCGTGCTAAGG
57.377
39.130
2.48
0.00
0.00
2.69
342
352
3.756933
TCTTGTTAACCGTGCTAAGGT
57.243
42.857
2.48
0.00
45.29
3.50
343
353
3.395639
TCTTGTTAACCGTGCTAAGGTG
58.604
45.455
2.48
0.00
41.95
4.00
344
354
1.515081
TGTTAACCGTGCTAAGGTGC
58.485
50.000
2.48
0.00
41.95
5.01
345
355
0.800631
GTTAACCGTGCTAAGGTGCC
59.199
55.000
0.00
0.00
41.95
5.01
346
356
0.688487
TTAACCGTGCTAAGGTGCCT
59.312
50.000
0.00
0.00
41.95
4.75
347
357
1.559368
TAACCGTGCTAAGGTGCCTA
58.441
50.000
0.00
0.00
41.95
3.93
348
358
0.688487
AACCGTGCTAAGGTGCCTAA
59.312
50.000
0.00
0.00
41.95
2.69
349
359
0.249398
ACCGTGCTAAGGTGCCTAAG
59.751
55.000
0.00
0.00
41.10
2.18
382
392
3.261897
TCCCTTGAGTTGAGATCTGTTCC
59.738
47.826
0.00
0.00
0.00
3.62
392
402
1.347707
AGATCTGTTCCGAAACCTGCA
59.652
47.619
0.00
0.00
34.28
4.41
473
483
1.471684
CACAAAGCTGAGGATGCCTTC
59.528
52.381
0.00
0.00
31.76
3.46
562
573
3.129462
GGAAGAGTAAATTGGAGCTTGGC
59.871
47.826
0.00
0.00
0.00
4.52
579
590
0.391263
GGCTTCTGTTACGGTCCTGG
60.391
60.000
0.00
0.00
0.00
4.45
592
603
2.158900
CGGTCCTGGTATGAATGCTCTT
60.159
50.000
0.00
0.00
0.00
2.85
607
618
4.600692
TGCTCTTGTTTACTGCAGTCTA
57.399
40.909
25.56
10.29
0.00
2.59
675
687
6.592994
CCCAGCATCAGATATGTACATAAGTG
59.407
42.308
19.11
17.56
0.00
3.16
692
704
6.369890
ACATAAGTGCAGTATGTCAAGTCTTG
59.630
38.462
14.49
6.21
37.59
3.02
882
901
0.315251
GCCCACCTTTCAGTTTCAGC
59.685
55.000
0.00
0.00
0.00
4.26
891
910
0.111061
TCAGTTTCAGCCACAGCCAT
59.889
50.000
0.00
0.00
41.25
4.40
892
911
1.350684
TCAGTTTCAGCCACAGCCATA
59.649
47.619
0.00
0.00
41.25
2.74
893
912
2.161855
CAGTTTCAGCCACAGCCATAA
58.838
47.619
0.00
0.00
41.25
1.90
1119
1138
1.455217
CGAGTCCTACCGTCCCCAT
60.455
63.158
0.00
0.00
0.00
4.00
1158
1177
2.295602
TTTCTACCCTGGCCCGTCC
61.296
63.158
0.00
0.00
0.00
4.79
1246
1265
0.338467
TAGCTCCTTCCCTGGCACTA
59.662
55.000
0.00
0.00
0.00
2.74
1496
1520
6.472486
GTCTTTGTAAAAGACTTGTTCTTGGC
59.528
38.462
20.42
0.00
44.41
4.52
1556
1580
1.532316
TCGTGGGTTCGAAGTCCCT
60.532
57.895
21.04
0.00
41.44
4.20
1586
1610
4.292186
TCTTTGATTTGGAGAGTGAGGG
57.708
45.455
0.00
0.00
0.00
4.30
1646
1670
2.100252
TGTTCCGTGTCTCGTCTCTTTT
59.900
45.455
0.00
0.00
37.94
2.27
1657
1681
7.597743
GTGTCTCGTCTCTTTTAAGTATTTCCA
59.402
37.037
0.00
0.00
0.00
3.53
1699
1723
9.409312
TGCTTTCAGTTTATTATGTTGTTGATG
57.591
29.630
0.00
0.00
0.00
3.07
1786
1810
4.065088
GCGGCATCATCTTTAGTTATGGA
58.935
43.478
0.00
0.00
0.00
3.41
1787
1811
4.515191
GCGGCATCATCTTTAGTTATGGAA
59.485
41.667
0.00
0.00
0.00
3.53
1788
1812
5.560953
GCGGCATCATCTTTAGTTATGGAAC
60.561
44.000
0.00
0.00
35.64
3.62
1802
1826
2.198827
TGGAACACTGGGTAGCATTG
57.801
50.000
0.00
0.00
0.00
2.82
1803
1827
1.702401
TGGAACACTGGGTAGCATTGA
59.298
47.619
0.00
0.00
0.00
2.57
1804
1828
2.308570
TGGAACACTGGGTAGCATTGAT
59.691
45.455
0.00
0.00
0.00
2.57
1805
1829
3.521531
TGGAACACTGGGTAGCATTGATA
59.478
43.478
0.00
0.00
0.00
2.15
1806
1830
4.165950
TGGAACACTGGGTAGCATTGATAT
59.834
41.667
0.00
0.00
0.00
1.63
1807
1831
5.133221
GGAACACTGGGTAGCATTGATATT
58.867
41.667
0.00
0.00
0.00
1.28
1808
1832
5.009010
GGAACACTGGGTAGCATTGATATTG
59.991
44.000
0.00
0.00
0.00
1.90
1809
1833
5.116084
ACACTGGGTAGCATTGATATTGT
57.884
39.130
0.00
0.00
0.00
2.71
1810
1834
4.883585
ACACTGGGTAGCATTGATATTGTG
59.116
41.667
0.00
0.00
0.00
3.33
1811
1835
3.885297
ACTGGGTAGCATTGATATTGTGC
59.115
43.478
0.00
0.00
39.10
4.57
1894
1918
2.026822
AGTGATAGGTCCCAGCTTGTTG
60.027
50.000
0.00
0.00
0.00
3.33
2148
2179
9.649167
GTCTAAAAGTACCTCTGTAATTGCTAA
57.351
33.333
0.00
0.00
35.58
3.09
2225
2256
3.532542
ACGAAGTATAAGAAGGGCAAGC
58.467
45.455
0.00
0.00
41.94
4.01
2269
2300
8.328864
GCCGATTAGTTTTCATTACTAGTTCTG
58.671
37.037
0.00
0.00
30.36
3.02
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
98
107
8.000780
AGAACAACAAAGCTAGAAAGTTCAAT
57.999
30.769
17.80
2.42
37.25
2.57
147
156
4.214332
GCAACAAACTAGAGGAAAGAGTGG
59.786
45.833
0.00
0.00
0.00
4.00
156
165
1.878953
ACGGTGCAACAAACTAGAGG
58.121
50.000
0.98
0.00
39.98
3.69
182
191
0.681175
GTCCAAAACTGGGCAAGCAT
59.319
50.000
0.00
0.00
32.88
3.79
241
250
7.653713
CGATATATGCTGACAAGTTTTCCTAGT
59.346
37.037
0.00
0.00
0.00
2.57
272
281
7.973048
ACTCCAGAGTCCAGTATAACAAATA
57.027
36.000
0.00
0.00
36.92
1.40
341
351
4.591072
AGGGATAGAAGATGACTTAGGCAC
59.409
45.833
0.00
0.00
36.39
5.01
342
352
4.820775
AGGGATAGAAGATGACTTAGGCA
58.179
43.478
0.00
0.00
36.39
4.75
343
353
5.305644
TCAAGGGATAGAAGATGACTTAGGC
59.694
44.000
0.00
0.00
36.39
3.93
344
354
6.553100
ACTCAAGGGATAGAAGATGACTTAGG
59.447
42.308
0.00
0.00
36.39
2.69
345
355
7.595819
ACTCAAGGGATAGAAGATGACTTAG
57.404
40.000
0.00
0.00
36.39
2.18
346
356
7.619698
TCAACTCAAGGGATAGAAGATGACTTA
59.380
37.037
0.00
0.00
36.39
2.24
347
357
6.441924
TCAACTCAAGGGATAGAAGATGACTT
59.558
38.462
0.00
0.00
39.24
3.01
348
358
5.960811
TCAACTCAAGGGATAGAAGATGACT
59.039
40.000
0.00
0.00
0.00
3.41
349
359
6.097554
TCTCAACTCAAGGGATAGAAGATGAC
59.902
42.308
0.00
0.00
0.00
3.06
382
392
4.414852
CAATAAAGGACATGCAGGTTTCG
58.585
43.478
5.07
0.00
0.00
3.46
392
402
8.877864
TGTAACATTTCTCCAATAAAGGACAT
57.122
30.769
0.00
0.00
33.19
3.06
473
483
2.163010
CAGGTAGGTCTGCAGCAAATTG
59.837
50.000
9.47
0.00
0.00
2.32
562
573
3.446161
TCATACCAGGACCGTAACAGAAG
59.554
47.826
0.00
0.00
0.00
2.85
579
590
6.128172
ACTGCAGTAAACAAGAGCATTCATAC
60.128
38.462
20.16
0.00
34.35
2.39
592
603
2.637872
AGGCCTTAGACTGCAGTAAACA
59.362
45.455
21.73
3.24
0.00
2.83
607
618
2.282462
CGAGGGTTGCAAGGCCTT
60.282
61.111
13.78
13.78
0.00
4.35
675
687
2.704572
AGCCAAGACTTGACATACTGC
58.295
47.619
16.99
9.21
0.00
4.40
692
704
6.934048
AGCTTGAGTTAAGATCATAAAGCC
57.066
37.500
7.97
0.00
38.76
4.35
720
739
5.925509
ACATGTTTACTCTGTTGGTGTACT
58.074
37.500
0.00
0.00
0.00
2.73
882
901
1.518325
TCGTTGTGTTATGGCTGTGG
58.482
50.000
0.00
0.00
0.00
4.17
891
910
3.398406
ACTGTGCATGATCGTTGTGTTA
58.602
40.909
0.00
0.00
0.00
2.41
892
911
2.221169
ACTGTGCATGATCGTTGTGTT
58.779
42.857
0.00
0.00
0.00
3.32
893
912
1.882912
ACTGTGCATGATCGTTGTGT
58.117
45.000
0.00
0.00
0.00
3.72
1119
1138
1.540797
CCACCGAACCCAAAGACGTTA
60.541
52.381
0.00
0.00
0.00
3.18
1158
1177
1.503818
CCGGAAACACCCAGTTGACG
61.504
60.000
0.00
0.00
41.19
4.35
1525
1549
1.202710
ACCCACGACAGCAATACAACA
60.203
47.619
0.00
0.00
0.00
3.33
1556
1580
6.716628
ACTCTCCAAATCAAAGATACAGCAAA
59.283
34.615
0.00
0.00
0.00
3.68
1586
1610
2.424956
GATCCAGCTCATGGGTTCAAAC
59.575
50.000
0.00
0.00
45.07
2.93
1646
1670
9.605275
CACTGAGAAGAATGATGGAAATACTTA
57.395
33.333
0.00
0.00
0.00
2.24
1657
1681
5.311265
TGAAAGCACACTGAGAAGAATGAT
58.689
37.500
0.00
0.00
0.00
2.45
1699
1723
8.937634
AGAACAAAGATATGGAAATGCATTTC
57.062
30.769
34.36
34.36
44.08
2.17
1786
1810
5.357878
CACAATATCAATGCTACCCAGTGTT
59.642
40.000
0.00
0.00
40.29
3.32
1787
1811
4.883585
CACAATATCAATGCTACCCAGTGT
59.116
41.667
0.00
0.00
40.29
3.55
1788
1812
4.261322
GCACAATATCAATGCTACCCAGTG
60.261
45.833
0.00
0.00
40.73
3.66
1789
1813
3.885297
GCACAATATCAATGCTACCCAGT
59.115
43.478
0.00
0.00
36.40
4.00
1790
1814
3.884693
TGCACAATATCAATGCTACCCAG
59.115
43.478
7.17
0.00
40.13
4.45
1791
1815
3.631686
GTGCACAATATCAATGCTACCCA
59.368
43.478
13.17
0.00
40.13
4.51
1792
1816
3.631686
TGTGCACAATATCAATGCTACCC
59.368
43.478
19.28
0.00
40.13
3.69
1793
1817
4.898829
TGTGCACAATATCAATGCTACC
57.101
40.909
19.28
0.00
40.13
3.18
1794
1818
5.688621
CCAATGTGCACAATATCAATGCTAC
59.311
40.000
25.72
0.00
40.13
3.58
1795
1819
5.360429
ACCAATGTGCACAATATCAATGCTA
59.640
36.000
25.72
0.00
40.13
3.49
1796
1820
4.160814
ACCAATGTGCACAATATCAATGCT
59.839
37.500
25.72
0.00
40.13
3.79
1797
1821
4.435425
ACCAATGTGCACAATATCAATGC
58.565
39.130
25.72
0.00
39.88
3.56
1798
1822
7.254185
GCTTAACCAATGTGCACAATATCAATG
60.254
37.037
25.72
13.20
0.00
2.82
1799
1823
6.757947
GCTTAACCAATGTGCACAATATCAAT
59.242
34.615
25.72
9.63
0.00
2.57
1800
1824
6.098679
GCTTAACCAATGTGCACAATATCAA
58.901
36.000
25.72
12.48
0.00
2.57
1801
1825
5.184671
TGCTTAACCAATGTGCACAATATCA
59.815
36.000
25.72
9.28
0.00
2.15
1802
1826
5.649557
TGCTTAACCAATGTGCACAATATC
58.350
37.500
25.72
6.85
0.00
1.63
1803
1827
5.657826
TGCTTAACCAATGTGCACAATAT
57.342
34.783
25.72
10.56
0.00
1.28
1867
1891
2.045524
CTGGGACCTATCACTGAGCAT
58.954
52.381
0.00
0.00
28.70
3.79
1868
1892
1.489481
CTGGGACCTATCACTGAGCA
58.511
55.000
0.00
0.00
28.70
4.26
1912
1940
3.774766
GGGGAAAAGGCCATAAACTTGAT
59.225
43.478
5.01
0.00
0.00
2.57
2119
2150
8.657729
GCAATTACAGAGGTACTTTTAGACTTC
58.342
37.037
0.00
0.00
41.55
3.01
2148
2179
3.919834
AGAAATTAGCATCAAGGGCCAT
58.080
40.909
6.18
0.00
0.00
4.40
2225
2256
3.438360
CGGCTTAAATGCTAAAAGCTGG
58.562
45.455
7.13
0.00
44.98
4.85
2269
2300
3.915437
TCGGGAGCATTTTTCTTGAAC
57.085
42.857
0.00
0.00
0.00
3.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.