Multiple sequence alignment - TraesCS6A01G269300
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
TraesCS6A01G269300
chr6A
100.000
2126
0
0
1
2126
495683945
495686070
0.000000e+00
3927.0
1
TraesCS6A01G269300
chr6A
95.775
71
1
2
1806
1874
495685716
495685786
1.720000e-21
113.0
2
TraesCS6A01G269300
chr6A
95.775
71
1
2
1772
1842
495685750
495685818
1.720000e-21
113.0
3
TraesCS6A01G269300
chr6B
92.291
1881
87
20
2
1842
532336668
532338530
0.000000e+00
2617.0
4
TraesCS6A01G269300
chr6B
95.963
322
7
3
1806
2126
532338461
532338777
3.130000e-143
518.0
5
TraesCS6A01G269300
chr6B
97.368
38
0
1
1772
1809
532338494
532338530
1.760000e-06
63.9
6
TraesCS6A01G269300
chr6D
91.234
1369
71
17
1
1364
347689293
347687969
0.000000e+00
1818.0
7
TraesCS6A01G269300
chr6D
95.297
404
13
3
1444
1842
347687968
347687566
8.270000e-179
636.0
8
TraesCS6A01G269300
chr6D
97.516
322
6
2
1806
2126
347687635
347687315
1.110000e-152
549.0
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
TraesCS6A01G269300
chr6A
495683945
495686070
2125
False
1384.333333
3927
97.183333
1
2126
3
chr6A.!!$F1
2125
1
TraesCS6A01G269300
chr6B
532336668
532338777
2109
False
1066.300000
2617
95.207333
2
2126
3
chr6B.!!$F1
2124
2
TraesCS6A01G269300
chr6D
347687315
347689293
1978
True
1001.000000
1818
94.682333
1
2126
3
chr6D.!!$R1
2125
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
262
272
0.03759
ATGCAGGCGTTTTCCCACTA
59.962
50.0
0.0
0.0
0.0
2.74
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1562
1608
1.942776
TGAGCCTTGACCTCAGATGA
58.057
50.0
0.0
0.0
34.59
2.92
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
35
36
4.725790
AGCTTATTTTCAGGATTGTGCC
57.274
40.909
0.00
0.00
0.00
5.01
72
74
7.927629
TCTGTTTGGATTTTTCATCTTCCTTTG
59.072
33.333
0.00
0.00
0.00
2.77
203
213
3.880047
ATTGTGATTGAGGTGGCAATG
57.120
42.857
0.00
0.00
38.53
2.82
233
243
6.259829
AGTTTGAGAGAGAAGCTCAGAAAAAC
59.740
38.462
0.00
0.00
46.45
2.43
253
263
0.609131
AAGGTAGCAATGCAGGCGTT
60.609
50.000
8.35
2.09
36.08
4.84
260
270
0.667184
CAATGCAGGCGTTTTCCCAC
60.667
55.000
0.00
0.00
0.00
4.61
262
272
0.037590
ATGCAGGCGTTTTCCCACTA
59.962
50.000
0.00
0.00
0.00
2.74
263
273
0.179015
TGCAGGCGTTTTCCCACTAA
60.179
50.000
0.00
0.00
0.00
2.24
272
282
3.824443
CGTTTTCCCACTAATTCCAACCT
59.176
43.478
0.00
0.00
0.00
3.50
337
347
6.631636
GGATTTTGCTACGATAAATCCGTTTC
59.368
38.462
9.34
0.00
44.15
2.78
368
378
8.567948
AGTAATGGGATAGCAACATTATTTTCG
58.432
33.333
9.57
0.00
38.76
3.46
371
381
7.581213
TGGGATAGCAACATTATTTTCGAAT
57.419
32.000
0.00
0.00
0.00
3.34
374
384
9.313118
GGGATAGCAACATTATTTTCGAATTTT
57.687
29.630
0.00
0.00
0.00
1.82
388
398
7.531280
TTTCGAATTTTGATGTTTCAAGCAA
57.469
28.000
0.00
0.00
42.60
3.91
399
409
3.682858
TGTTTCAAGCAACGGTATAGCTC
59.317
43.478
0.00
0.00
37.70
4.09
408
418
1.607628
ACGGTATAGCTCGATCACCAC
59.392
52.381
0.00
0.00
0.00
4.16
467
477
7.227049
TGAATAGCATCATTGATAGTACCGA
57.773
36.000
0.00
0.00
0.00
4.69
468
478
7.840931
TGAATAGCATCATTGATAGTACCGAT
58.159
34.615
0.00
0.00
0.00
4.18
469
479
8.966868
TGAATAGCATCATTGATAGTACCGATA
58.033
33.333
0.00
0.00
0.00
2.92
470
480
9.239002
GAATAGCATCATTGATAGTACCGATAC
57.761
37.037
0.00
0.00
0.00
2.24
471
481
6.842437
AGCATCATTGATAGTACCGATACT
57.158
37.500
0.00
0.00
44.22
2.12
634
644
2.605837
TTGGTTCTAGCAACACGTGA
57.394
45.000
25.01
0.00
29.68
4.35
639
649
2.730672
CTAGCAACACGTGAGCCGC
61.731
63.158
25.01
17.56
41.42
6.53
649
659
3.625764
ACACGTGAGCCGCAAATTATTAT
59.374
39.130
25.01
0.00
41.42
1.28
698
708
1.276138
TGCTGTGTACAGACCTCCATG
59.724
52.381
15.78
0.00
46.59
3.66
774
784
6.563753
CGGAAATGTTGCTAAATTTGTGTTGG
60.564
38.462
0.73
0.00
0.00
3.77
796
806
5.419155
TGGTTTCTGATAGAGATCGTCAGTT
59.581
40.000
15.25
0.00
40.13
3.16
837
847
2.665649
AATGGTTCTACGTCGCATCA
57.334
45.000
0.00
0.00
0.00
3.07
851
861
2.106418
CGCATCAATGTTCATGCTTCG
58.894
47.619
0.33
0.00
42.84
3.79
943
979
7.552330
TCGACCACATCATTCTGATTCAAATAA
59.448
33.333
0.00
0.00
34.28
1.40
1246
1286
7.724061
TCCTTTCTTTTGTTCTATTGGCTAAGT
59.276
33.333
0.00
0.00
0.00
2.24
1265
1305
9.860898
GGCTAAGTTTTTATCATCTCATTTTGT
57.139
29.630
0.00
0.00
0.00
2.83
1422
1462
7.446931
TCAAACTGTTCTTTCCTGCATGTATTA
59.553
33.333
0.00
0.00
0.00
0.98
1562
1608
4.403432
AGTTGCCATTTGCTTGCTGTATAT
59.597
37.500
0.00
0.00
42.00
0.86
1659
1705
3.383761
CAAATCCAAGACAGCACAAACC
58.616
45.455
0.00
0.00
0.00
3.27
1701
1747
6.823182
TCAATTGACGGATCATACATCTGTTT
59.177
34.615
3.38
0.00
37.73
2.83
1787
1833
7.432869
TGTTGATTTTTCTTGATACCTGGTTG
58.567
34.615
3.84
0.00
0.00
3.77
1788
1834
7.069331
TGTTGATTTTTCTTGATACCTGGTTGT
59.931
33.333
3.84
0.00
0.00
3.32
1789
1835
7.214467
TGATTTTTCTTGATACCTGGTTGTC
57.786
36.000
3.84
4.77
0.00
3.18
1790
1836
6.208599
TGATTTTTCTTGATACCTGGTTGTCC
59.791
38.462
3.84
0.00
0.00
4.02
1791
1837
3.713826
TTCTTGATACCTGGTTGTCCC
57.286
47.619
3.84
0.00
0.00
4.46
1792
1838
2.626785
TCTTGATACCTGGTTGTCCCA
58.373
47.619
3.84
0.00
42.51
4.37
1793
1839
2.983192
TCTTGATACCTGGTTGTCCCAA
59.017
45.455
3.84
2.17
44.65
4.12
1794
1840
3.396276
TCTTGATACCTGGTTGTCCCAAA
59.604
43.478
3.84
0.00
44.65
3.28
1795
1841
3.433306
TGATACCTGGTTGTCCCAAAG
57.567
47.619
3.84
0.00
44.65
2.77
1796
1842
2.041081
TGATACCTGGTTGTCCCAAAGG
59.959
50.000
3.84
0.00
44.65
3.11
1797
1843
1.822425
TACCTGGTTGTCCCAAAGGA
58.178
50.000
3.84
0.00
44.65
3.36
1798
1844
0.930726
ACCTGGTTGTCCCAAAGGAA
59.069
50.000
0.00
0.00
46.38
3.36
1799
1845
1.289530
ACCTGGTTGTCCCAAAGGAAA
59.710
47.619
0.00
0.00
46.38
3.13
1800
1846
2.292587
ACCTGGTTGTCCCAAAGGAAAA
60.293
45.455
0.00
0.00
46.38
2.29
1801
1847
2.769095
CCTGGTTGTCCCAAAGGAAAAA
59.231
45.455
0.00
0.00
46.38
1.94
1802
1848
3.181466
CCTGGTTGTCCCAAAGGAAAAAG
60.181
47.826
0.00
0.00
46.38
2.27
1803
1849
2.769095
TGGTTGTCCCAAAGGAAAAAGG
59.231
45.455
0.00
0.00
46.38
3.11
1804
1850
2.484770
GGTTGTCCCAAAGGAAAAAGGC
60.485
50.000
0.00
0.00
46.38
4.35
1805
1851
2.434336
GTTGTCCCAAAGGAAAAAGGCT
59.566
45.455
0.00
0.00
46.38
4.58
1806
1852
2.758130
TGTCCCAAAGGAAAAAGGCTT
58.242
42.857
0.00
0.00
46.38
4.35
1807
1853
2.698274
TGTCCCAAAGGAAAAAGGCTTC
59.302
45.455
0.00
0.00
46.38
3.86
1808
1854
2.965831
GTCCCAAAGGAAAAAGGCTTCT
59.034
45.455
0.00
0.00
46.38
2.85
1809
1855
3.388024
GTCCCAAAGGAAAAAGGCTTCTT
59.612
43.478
0.00
0.00
46.38
2.52
1810
1856
3.387699
TCCCAAAGGAAAAAGGCTTCTTG
59.612
43.478
0.00
0.00
40.08
3.02
1811
1857
3.387699
CCCAAAGGAAAAAGGCTTCTTGA
59.612
43.478
0.00
0.00
33.47
3.02
1812
1858
4.040829
CCCAAAGGAAAAAGGCTTCTTGAT
59.959
41.667
0.00
0.00
33.47
2.57
1813
1859
5.245977
CCCAAAGGAAAAAGGCTTCTTGATA
59.754
40.000
0.00
0.00
33.47
2.15
1814
1860
6.159293
CCAAAGGAAAAAGGCTTCTTGATAC
58.841
40.000
0.00
0.00
0.00
2.24
1815
1861
5.984695
AAGGAAAAAGGCTTCTTGATACC
57.015
39.130
0.00
0.00
0.00
2.73
1816
1862
5.262455
AGGAAAAAGGCTTCTTGATACCT
57.738
39.130
0.00
0.00
0.00
3.08
1817
1863
5.012893
AGGAAAAAGGCTTCTTGATACCTG
58.987
41.667
0.00
0.00
31.32
4.00
1818
1864
4.158579
GGAAAAAGGCTTCTTGATACCTGG
59.841
45.833
0.00
0.00
31.32
4.45
1819
1865
4.388577
AAAAGGCTTCTTGATACCTGGT
57.611
40.909
4.05
4.05
31.32
4.00
1820
1866
4.388577
AAAGGCTTCTTGATACCTGGTT
57.611
40.909
3.84
0.00
31.32
3.67
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
19
20
1.185315
CCCGGCACAATCCTGAAAAT
58.815
50.000
0.00
0.00
0.00
1.82
31
32
1.244019
ACAGAAAAGCATCCCGGCAC
61.244
55.000
0.00
0.00
35.83
5.01
35
36
1.885887
TCCAAACAGAAAAGCATCCCG
59.114
47.619
0.00
0.00
0.00
5.14
72
74
4.327087
CGCAAAAATCTAAATCAGCCAACC
59.673
41.667
0.00
0.00
0.00
3.77
112
120
0.958876
AAGGCGCCTTTTAACGGGAG
60.959
55.000
35.84
0.00
31.29
4.30
166
176
4.983538
TCACAATTTACATTGCAAGCACAG
59.016
37.500
4.94
0.00
43.39
3.66
203
213
3.663025
AGCTTCTCTCTCAAACTTCTGC
58.337
45.455
0.00
0.00
0.00
4.26
233
243
1.308069
ACGCCTGCATTGCTACCTTG
61.308
55.000
10.49
0.00
0.00
3.61
253
263
4.508405
CCTCAGGTTGGAATTAGTGGGAAA
60.508
45.833
0.00
0.00
0.00
3.13
260
270
2.691409
TCGCCTCAGGTTGGAATTAG
57.309
50.000
0.00
0.00
0.00
1.73
262
272
3.864789
ATATCGCCTCAGGTTGGAATT
57.135
42.857
0.00
0.00
0.00
2.17
263
273
3.864789
AATATCGCCTCAGGTTGGAAT
57.135
42.857
0.00
0.00
0.00
3.01
272
282
3.118920
TCCGAACTCAAAATATCGCCTCA
60.119
43.478
0.00
0.00
34.13
3.86
330
340
1.339631
CCCATTACTGGCTGAAACGGA
60.340
52.381
0.00
0.00
41.64
4.69
337
347
2.880890
GTTGCTATCCCATTACTGGCTG
59.119
50.000
0.00
0.00
41.64
4.85
368
378
5.234116
ACCGTTGCTTGAAACATCAAAATTC
59.766
36.000
0.00
0.00
0.00
2.17
371
381
4.116747
ACCGTTGCTTGAAACATCAAAA
57.883
36.364
0.00
0.00
0.00
2.44
374
384
4.094294
GCTATACCGTTGCTTGAAACATCA
59.906
41.667
0.00
0.00
0.00
3.07
388
398
1.607628
GTGGTGATCGAGCTATACCGT
59.392
52.381
0.90
0.00
34.16
4.83
399
409
0.374758
CTCAATTGGCGTGGTGATCG
59.625
55.000
5.42
0.00
0.00
3.69
461
471
4.201783
GGACATTGCAAACAGTATCGGTAC
60.202
45.833
1.71
0.00
0.00
3.34
462
472
3.936453
GGACATTGCAAACAGTATCGGTA
59.064
43.478
1.71
0.00
0.00
4.02
464
474
2.746904
TGGACATTGCAAACAGTATCGG
59.253
45.455
1.71
0.00
0.00
4.18
465
475
3.728864
GCTGGACATTGCAAACAGTATCG
60.729
47.826
18.61
6.62
0.00
2.92
466
476
3.441572
AGCTGGACATTGCAAACAGTATC
59.558
43.478
18.61
9.29
0.00
2.24
467
477
3.424703
AGCTGGACATTGCAAACAGTAT
58.575
40.909
18.61
9.85
0.00
2.12
468
478
2.813754
GAGCTGGACATTGCAAACAGTA
59.186
45.455
18.61
2.14
0.00
2.74
469
479
1.610522
GAGCTGGACATTGCAAACAGT
59.389
47.619
18.61
12.07
0.00
3.55
470
480
1.068055
GGAGCTGGACATTGCAAACAG
60.068
52.381
1.71
10.97
0.00
3.16
471
481
0.961019
GGAGCTGGACATTGCAAACA
59.039
50.000
1.71
0.00
0.00
2.83
590
600
8.755696
ACATTAATGCACAAAACGAAACATAT
57.244
26.923
15.48
0.00
0.00
1.78
599
609
6.843069
AGAACCAACATTAATGCACAAAAC
57.157
33.333
15.48
2.76
0.00
2.43
634
644
6.952773
TTAAGTGGATAATAATTTGCGGCT
57.047
33.333
0.00
0.00
0.00
5.52
674
684
3.181445
TGGAGGTCTGTACACAGCAAAAT
60.181
43.478
4.43
0.00
43.46
1.82
726
736
9.681062
TCCGAATCTAGTTTAAAGAATCCATTT
57.319
29.630
0.00
0.00
0.00
2.32
734
744
8.234546
GCAACATTTCCGAATCTAGTTTAAAGA
58.765
33.333
0.00
0.00
0.00
2.52
749
759
6.354080
CAACACAAATTTAGCAACATTTCCG
58.646
36.000
0.00
0.00
0.00
4.30
774
784
6.470877
GTCAACTGACGATCTCTATCAGAAAC
59.529
42.308
15.79
9.15
42.07
2.78
796
806
9.161629
CCATTTGGATTATATATAACGCAGTCA
57.838
33.333
7.34
0.00
37.19
3.41
828
838
1.459756
GCATGAACATTGATGCGACG
58.540
50.000
0.00
0.00
37.99
5.12
837
847
4.218200
TCATTTCCACGAAGCATGAACATT
59.782
37.500
0.00
0.00
0.00
2.71
851
861
5.928264
CCAAAGGAACAAGAATCATTTCCAC
59.072
40.000
9.31
0.00
40.13
4.02
943
979
2.029649
GCTGGTGCAATCTGACACAATT
60.030
45.455
0.00
0.00
38.57
2.32
974
1014
5.473504
TCTTTGATGAACACTTTAAGCTCCC
59.526
40.000
0.00
0.00
0.00
4.30
1275
1315
3.133691
TGGAGATGATGCGCTGATAAAC
58.866
45.455
9.73
0.00
0.00
2.01
1422
1462
6.403866
TGGTTGATTTAGTTTTCACATGCT
57.596
33.333
0.00
0.00
0.00
3.79
1562
1608
1.942776
TGAGCCTTGACCTCAGATGA
58.057
50.000
0.00
0.00
34.59
2.92
1701
1747
3.934457
TCTTGTCTATCAGTTCGCACA
57.066
42.857
0.00
0.00
0.00
4.57
1787
1833
2.965831
AGAAGCCTTTTTCCTTTGGGAC
59.034
45.455
0.00
0.00
42.05
4.46
1788
1834
3.328535
AGAAGCCTTTTTCCTTTGGGA
57.671
42.857
0.00
0.00
40.36
4.37
1789
1835
3.387699
TCAAGAAGCCTTTTTCCTTTGGG
59.612
43.478
0.00
0.00
0.00
4.12
1790
1836
4.670896
TCAAGAAGCCTTTTTCCTTTGG
57.329
40.909
0.00
0.00
0.00
3.28
1791
1837
6.015095
AGGTATCAAGAAGCCTTTTTCCTTTG
60.015
38.462
0.00
0.00
0.00
2.77
1792
1838
6.015095
CAGGTATCAAGAAGCCTTTTTCCTTT
60.015
38.462
0.00
0.00
0.00
3.11
1793
1839
5.478332
CAGGTATCAAGAAGCCTTTTTCCTT
59.522
40.000
0.00
0.00
0.00
3.36
1794
1840
5.012893
CAGGTATCAAGAAGCCTTTTTCCT
58.987
41.667
0.00
0.00
0.00
3.36
1795
1841
4.158579
CCAGGTATCAAGAAGCCTTTTTCC
59.841
45.833
0.00
0.00
0.00
3.13
1796
1842
4.767409
ACCAGGTATCAAGAAGCCTTTTTC
59.233
41.667
0.00
0.00
0.00
2.29
1797
1843
4.740902
ACCAGGTATCAAGAAGCCTTTTT
58.259
39.130
0.00
0.00
0.00
1.94
1798
1844
4.388577
ACCAGGTATCAAGAAGCCTTTT
57.611
40.909
0.00
0.00
0.00
2.27
1799
1845
4.082125
CAACCAGGTATCAAGAAGCCTTT
58.918
43.478
0.00
0.00
0.00
3.11
1800
1846
3.074538
ACAACCAGGTATCAAGAAGCCTT
59.925
43.478
0.00
0.00
0.00
4.35
1801
1847
2.644798
ACAACCAGGTATCAAGAAGCCT
59.355
45.455
0.00
0.00
0.00
4.58
1802
1848
3.010420
GACAACCAGGTATCAAGAAGCC
58.990
50.000
0.00
0.00
0.00
4.35
1803
1849
3.010420
GGACAACCAGGTATCAAGAAGC
58.990
50.000
0.00
0.00
35.97
3.86
1804
1850
3.009033
TGGGACAACCAGGTATCAAGAAG
59.991
47.826
0.00
0.00
46.80
2.85
1805
1851
2.983192
TGGGACAACCAGGTATCAAGAA
59.017
45.455
0.00
0.00
46.80
2.52
1806
1852
2.626785
TGGGACAACCAGGTATCAAGA
58.373
47.619
0.00
0.00
46.80
3.02
1820
1866
2.091333
AGAAGCCTTTTCCTTTGGGACA
60.091
45.455
0.00
0.00
42.05
4.02
1927
1974
4.678256
ACAACTGTTATCCAGAGGAGAGA
58.322
43.478
0.00
0.00
44.49
3.10
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.