Multiple sequence alignment - TraesCS3B01G477300
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
TraesCS3B01G477300
chr3B
100.000
3060
0
0
1
3060
725706334
725709393
0
5651
1
TraesCS3B01G477300
chr3A
94.114
3075
129
17
1
3060
685118816
685121853
0
4628
2
TraesCS3B01G477300
chr3D
92.629
2564
121
29
545
3060
548246698
548249241
0
3626
3
TraesCS3B01G477300
chr3D
94.843
543
28
0
1
543
548246107
548246649
0
848
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
TraesCS3B01G477300
chr3B
725706334
725709393
3059
False
5651
5651
100.000
1
3060
1
chr3B.!!$F1
3059
1
TraesCS3B01G477300
chr3A
685118816
685121853
3037
False
4628
4628
94.114
1
3060
1
chr3A.!!$F1
3059
2
TraesCS3B01G477300
chr3D
548246107
548249241
3134
False
2237
3626
93.736
1
3060
2
chr3D.!!$F1
3059
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
975
1049
1.229529
GGGTGTGGAGAAGAGGGGA
60.23
63.158
0.0
0.0
0.0
4.81
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2286
2384
0.037232
GAGAGTAGCGCCAAACTGGT
60.037
55.0
11.88
0.31
40.46
4.0
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
64
65
1.477700
TGCTTCATACTTGCATTGGCC
59.522
47.619
0.00
0.00
40.13
5.36
293
294
2.505819
ACCGAGGAGCTGGTTATGAAAT
59.494
45.455
0.00
0.00
33.81
2.17
294
295
3.054361
ACCGAGGAGCTGGTTATGAAATT
60.054
43.478
0.00
0.00
33.81
1.82
346
347
6.473758
ACCAGGTAATCTTCTTGTAAACTCC
58.526
40.000
0.00
0.00
0.00
3.85
377
378
4.724399
TGTTGGCATTCTAAGGTTTCTGA
58.276
39.130
0.00
0.00
0.00
3.27
381
382
6.916360
TGGCATTCTAAGGTTTCTGAATTT
57.084
33.333
0.00
0.00
0.00
1.82
411
412
1.998315
GTGCTGACATGCTGACACTAG
59.002
52.381
0.00
0.00
0.00
2.57
434
436
4.322725
GGTCTTTTCATTTTAAGGGGGCAG
60.323
45.833
0.00
0.00
0.00
4.85
723
780
5.359860
GGTATTTTCCTTCCCCTTATGTGTG
59.640
44.000
0.00
0.00
0.00
3.82
733
790
6.134535
TCCCCTTATGTGTGAACATAAAGT
57.865
37.500
11.31
0.00
40.67
2.66
734
791
6.548321
TCCCCTTATGTGTGAACATAAAGTT
58.452
36.000
11.31
0.00
44.93
2.66
828
885
4.757149
AGTTTCTGTGAGTTGATTACTGGC
59.243
41.667
0.00
0.00
37.17
4.85
975
1049
1.229529
GGGTGTGGAGAAGAGGGGA
60.230
63.158
0.00
0.00
0.00
4.81
984
1058
2.530151
AAGAGGGGAGGCACAGCA
60.530
61.111
0.00
0.00
0.00
4.41
1053
1136
3.368571
GCCACTGCTGCTTGTCCC
61.369
66.667
0.00
0.00
33.53
4.46
1289
1378
1.672363
TCTTGTTCTTGCTGCTGTGTG
59.328
47.619
0.00
0.00
0.00
3.82
1290
1379
1.402968
CTTGTTCTTGCTGCTGTGTGT
59.597
47.619
0.00
0.00
0.00
3.72
1298
1387
1.016627
GCTGCTGTGTGTTGTCTGAA
58.983
50.000
0.00
0.00
0.00
3.02
1457
1546
4.866682
ATGCGTTTCTCTAGCTAAAAGC
57.133
40.909
15.46
15.46
42.84
3.51
1471
1560
0.524862
AAAAGCTGCGCTGATTCTGG
59.475
50.000
18.14
0.00
39.62
3.86
1595
1685
0.322975
ACACTCACTCATGGTGCCTC
59.677
55.000
8.87
0.00
44.98
4.70
1629
1720
6.653320
TGGAAACAGTATACATGTCCTTGAAC
59.347
38.462
0.00
0.00
35.01
3.18
1647
1738
6.183360
CCTTGAACCTTTCTCATTAGCATCAG
60.183
42.308
0.00
0.00
0.00
2.90
1651
1742
4.225942
ACCTTTCTCATTAGCATCAGTGGA
59.774
41.667
0.00
0.00
0.00
4.02
1868
1963
1.069204
GGGCAGCTATCTTCATCGTCA
59.931
52.381
0.00
0.00
0.00
4.35
2074
2169
3.356290
ACCATAGGTGCCATTCAGAAAC
58.644
45.455
0.00
0.00
32.98
2.78
2076
2171
3.270027
CATAGGTGCCATTCAGAAACGA
58.730
45.455
0.00
0.00
0.00
3.85
2162
2257
4.100373
AGCACTCTCTAAGGAAATCAGGT
58.900
43.478
0.00
0.00
0.00
4.00
2194
2289
5.242615
AGCTCCAAGAAAAGGATCTTCAAAC
59.757
40.000
0.00
0.00
37.56
2.93
2201
2296
6.877236
AGAAAAGGATCTTCAAACAAAGCAA
58.123
32.000
0.00
0.00
0.00
3.91
2232
2327
2.039818
ATGCAGAGCAGATTGTCAGG
57.960
50.000
0.00
0.00
43.65
3.86
2302
2400
1.346722
AGTTACCAGTTTGGCGCTACT
59.653
47.619
7.64
5.92
42.67
2.57
2309
2407
0.802607
GTTTGGCGCTACTCTCTCGG
60.803
60.000
7.64
0.00
0.00
4.63
2454
2554
0.309922
CACTTGAGTTGCACAGCTGG
59.690
55.000
19.93
8.27
0.00
4.85
2538
2638
9.549078
CTAATCTATAACCCTGAAAGAGGAAAC
57.451
37.037
0.00
0.00
46.33
2.78
2573
2673
7.223387
GCCTTTGAAATGCTATAACTTTCCATG
59.777
37.037
0.00
0.00
0.00
3.66
2665
2765
1.494960
GTCCTCCTGATCTCCTGCTT
58.505
55.000
0.00
0.00
0.00
3.91
2684
2784
1.682740
TGCGTATCCGGTGTATCTCA
58.317
50.000
0.00
0.00
33.68
3.27
2809
2909
5.604231
TGGTCATTCTCCTATCTGCTATTGT
59.396
40.000
0.00
0.00
0.00
2.71
3038
3138
4.398044
ACAAGGAACACACCAAAACTGTAG
59.602
41.667
0.00
0.00
0.00
2.74
3047
3147
5.050091
CACACCAAAACTGTAGACATCACTC
60.050
44.000
0.00
0.00
0.00
3.51
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
64
65
8.196802
TGATTGTAAGAACCTTTCATATGACG
57.803
34.615
4.48
0.00
0.00
4.35
293
294
8.677148
AATTGAGTTTACTAGCTTTGTCTGAA
57.323
30.769
0.00
0.00
0.00
3.02
294
295
8.559536
CAAATTGAGTTTACTAGCTTTGTCTGA
58.440
33.333
0.00
0.00
0.00
3.27
369
370
6.442112
CACTTCTTGGAGAAATTCAGAAACC
58.558
40.000
0.00
0.00
33.19
3.27
377
378
4.464008
TGTCAGCACTTCTTGGAGAAATT
58.536
39.130
0.00
0.00
33.19
1.82
381
382
2.873245
GCATGTCAGCACTTCTTGGAGA
60.873
50.000
0.00
0.00
0.00
3.71
411
412
3.580895
TGCCCCCTTAAAATGAAAAGACC
59.419
43.478
0.00
0.00
0.00
3.85
414
415
3.582647
ACCTGCCCCCTTAAAATGAAAAG
59.417
43.478
0.00
0.00
0.00
2.27
416
417
3.268034
ACCTGCCCCCTTAAAATGAAA
57.732
42.857
0.00
0.00
0.00
2.69
470
472
1.309499
CGCGTCTCTCCTCAACCTCT
61.309
60.000
0.00
0.00
0.00
3.69
473
475
2.182030
CCGCGTCTCTCCTCAACC
59.818
66.667
4.92
0.00
0.00
3.77
584
633
3.507233
TCCTTGAACATCTCCACATTTGC
59.493
43.478
0.00
0.00
0.00
3.68
787
844
3.222173
ACTGTTACATGGCTGGACAAA
57.778
42.857
0.00
0.00
0.00
2.83
828
885
7.764443
TCCTTTTCCTTGATATCTGTAAACTCG
59.236
37.037
3.98
0.00
0.00
4.18
975
1049
2.284112
CCCCCAAATGCTGTGCCT
60.284
61.111
0.00
0.00
0.00
4.75
984
1058
3.205056
TGCTCATTATCTCACCCCCAAAT
59.795
43.478
0.00
0.00
0.00
2.32
1021
1104
2.183555
GGCTGCTGCAGAAATGGC
59.816
61.111
32.30
16.63
41.91
4.40
1256
1345
5.063438
GCAAGAACAAGAAAACCAAGGAAAC
59.937
40.000
0.00
0.00
0.00
2.78
1289
1378
4.761739
TGTCATCCCAATTCTTCAGACAAC
59.238
41.667
0.00
0.00
32.46
3.32
1290
1379
4.761739
GTGTCATCCCAATTCTTCAGACAA
59.238
41.667
0.00
0.00
36.63
3.18
1298
1387
2.915604
ACTCCAGTGTCATCCCAATTCT
59.084
45.455
0.00
0.00
0.00
2.40
1435
1524
5.968387
GCTTTTAGCTAGAGAAACGCATA
57.032
39.130
9.64
0.00
38.45
3.14
1457
1546
0.671472
TCACACCAGAATCAGCGCAG
60.671
55.000
11.47
0.00
0.00
5.18
1460
1549
1.395954
CACATCACACCAGAATCAGCG
59.604
52.381
0.00
0.00
0.00
5.18
1595
1685
7.712639
ACATGTATACTGTTTCCAGATAGCAAG
59.287
37.037
0.00
0.00
41.50
4.01
1629
1720
4.774124
TCCACTGATGCTAATGAGAAAGG
58.226
43.478
0.00
0.00
0.00
3.11
1647
1738
2.157738
AGTGCTGCAAGAGATTTCCAC
58.842
47.619
2.77
0.00
34.07
4.02
1651
1742
3.940221
GAGATGAGTGCTGCAAGAGATTT
59.060
43.478
2.77
0.00
34.07
2.17
1755
1846
6.835174
ACAGATGATGCATGTAAATAGGAGT
58.165
36.000
2.46
0.00
0.00
3.85
1868
1963
2.467838
CATCTCGATGACGCAGAACAT
58.532
47.619
0.59
0.00
41.20
2.71
2074
2169
0.249447
TCTAGCCAATGCGACCATCG
60.249
55.000
0.00
0.00
44.33
3.84
2076
2171
2.158769
TGAATCTAGCCAATGCGACCAT
60.159
45.455
0.00
0.00
44.33
3.55
2162
2257
4.165950
TCCTTTTCTTGGAGCTATGCCATA
59.834
41.667
0.00
0.00
34.90
2.74
2223
2318
6.109359
AGTAGCATAGTGTTTCCTGACAATC
58.891
40.000
0.00
0.00
0.00
2.67
2232
2327
6.677781
TTGCCATTAGTAGCATAGTGTTTC
57.322
37.500
0.00
0.00
39.11
2.78
2286
2384
0.037232
GAGAGTAGCGCCAAACTGGT
60.037
55.000
11.88
0.31
40.46
4.00
2302
2400
4.931661
AGACTTTTGTAACACCGAGAGA
57.068
40.909
0.00
0.00
0.00
3.10
2470
2570
6.266131
TGCCCCATTAGTTTCTTCTCATAT
57.734
37.500
0.00
0.00
0.00
1.78
2538
2638
3.950395
AGCATTTCAAAGGCTAAGCTAGG
59.050
43.478
7.70
0.00
35.82
3.02
2640
2740
1.028905
GAGATCAGGAGGACGACAGG
58.971
60.000
0.00
0.00
0.00
4.00
2684
2784
1.606531
GATGAGCCTGGTGGAAGCT
59.393
57.895
0.00
0.00
40.24
3.74
2713
2813
1.006571
GTGAACCCGACAAGCGAGA
60.007
57.895
0.00
0.00
44.57
4.04
2816
2916
9.305925
GTTCAAAACTTTCAAGAATCAAGTGAT
57.694
29.630
0.00
0.00
36.07
3.06
2837
2937
4.409901
TCCATCTCTGATATGCAGGTTCAA
59.590
41.667
0.00
0.00
44.98
2.69
2838
2938
3.969312
TCCATCTCTGATATGCAGGTTCA
59.031
43.478
0.00
0.00
44.98
3.18
2927
3027
8.591072
ACTGATTCCTGATGATTGTTCAATTTT
58.409
29.630
0.00
0.00
34.96
1.82
2928
3028
8.130671
ACTGATTCCTGATGATTGTTCAATTT
57.869
30.769
0.00
0.00
34.96
1.82
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.