Multiple sequence alignment - TraesCS5A01G536300
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
TraesCS5A01G536300
chr5A
100.000
2404
0
0
1
2404
692788653
692786250
0.000000e+00
4440.0
1
TraesCS5A01G536300
chr4D
92.520
2139
139
13
278
2404
507681064
507678935
0.000000e+00
3044.0
2
TraesCS5A01G536300
chr4D
94.700
283
12
3
1
281
507683040
507682759
1.020000e-118
436.0
3
TraesCS5A01G536300
chr4B
90.133
2250
165
28
198
2404
656285835
656288070
0.000000e+00
2872.0
4
TraesCS5A01G536300
chr4B
93.085
188
7
4
1
184
656285584
656285769
1.100000e-68
270.0
5
TraesCS5A01G536300
chr7B
80.208
384
62
7
2022
2402
440179037
440179409
2.350000e-70
276.0
6
TraesCS5A01G536300
chr7B
82.186
247
38
6
2161
2404
135714888
135715131
8.710000e-50
207.0
7
TraesCS5A01G536300
chr7B
81.781
247
39
6
2161
2404
135664903
135665146
4.050000e-48
202.0
8
TraesCS5A01G536300
chr4A
81.448
221
37
4
2182
2401
717055389
717055606
6.830000e-41
178.0
9
TraesCS5A01G536300
chr2D
80.838
167
32
0
2154
2320
96824041
96824207
5.390000e-27
132.0
10
TraesCS5A01G536300
chr2A
73.994
323
59
13
2022
2320
95835333
95835654
9.090000e-20
108.0
11
TraesCS5A01G536300
chr7D
89.394
66
6
1
2337
2402
423301450
423301514
5.510000e-12
82.4
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
TraesCS5A01G536300
chr5A
692786250
692788653
2403
True
4440
4440
100.000
1
2404
1
chr5A.!!$R1
2403
1
TraesCS5A01G536300
chr4D
507678935
507683040
4105
True
1740
3044
93.610
1
2404
2
chr4D.!!$R1
2403
2
TraesCS5A01G536300
chr4B
656285584
656288070
2486
False
1571
2872
91.609
1
2404
2
chr4B.!!$F1
2403
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
782
2552
0.323302
TACAAGCATGTCTTCCCGCA
59.677
50.0
0.0
0.0
41.05
5.69
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2029
3839
0.550914
ATTGGGGTCATGCGTATGGT
59.449
50.0
13.77
0.0
34.97
3.55
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
189
194
3.943958
TCTTACGTCGATATTCGTGTGG
58.056
45.455
8.84
0.44
41.35
4.17
213
281
8.581578
TGGATTCACCCTTTTGTTTACTATTTC
58.418
33.333
0.00
0.00
38.00
2.17
268
337
7.575332
TTCGTTTTGAGAAAAACAGGAAAAG
57.425
32.000
12.91
0.00
41.43
2.27
329
2097
8.687824
ATAGAAAAATGAAACAGTAAATGCCG
57.312
30.769
0.00
0.00
0.00
5.69
363
2133
9.854668
ATGTACTACTGTTATATCTCACTCAGT
57.145
33.333
0.00
0.00
39.11
3.41
430
2200
7.475771
TGCAAAGAAACAAATTACCAATGAC
57.524
32.000
0.00
0.00
0.00
3.06
454
2224
8.600449
ACCGATTGATGCTTGAAAATTAAAAA
57.400
26.923
0.00
0.00
0.00
1.94
507
2277
0.467290
AAGATGGCGGTGTGGTGTTT
60.467
50.000
0.00
0.00
0.00
2.83
512
2282
2.551912
GCGGTGTGGTGTTTCAGGG
61.552
63.158
0.00
0.00
0.00
4.45
614
2384
9.820229
TTCAAATTATAGTTAAGTTGCTCGTTG
57.180
29.630
2.09
0.00
41.09
4.10
637
2407
6.905578
TGAAACATCTCATGTGAATCAAGTG
58.094
36.000
0.90
0.00
44.07
3.16
645
2415
1.425066
TGTGAATCAAGTGGCCTCCTT
59.575
47.619
3.32
2.98
0.00
3.36
646
2416
2.087646
GTGAATCAAGTGGCCTCCTTC
58.912
52.381
3.32
2.44
0.00
3.46
720
2490
1.348064
ACCCATTCCTCAGTGACGAA
58.652
50.000
6.97
6.97
0.00
3.85
721
2491
1.276421
ACCCATTCCTCAGTGACGAAG
59.724
52.381
9.86
1.01
0.00
3.79
749
2519
5.168569
TGTTATCTCTGTTGACGACAATCC
58.831
41.667
3.18
0.00
37.93
3.01
760
2530
3.256960
ACAATCCTGTGGGCCCGT
61.257
61.111
19.37
2.50
33.30
5.28
782
2552
0.323302
TACAAGCATGTCTTCCCGCA
59.677
50.000
0.00
0.00
41.05
5.69
830
2600
1.886222
CGGATTGCCCTTCAAGGTCAA
60.886
52.381
1.54
1.54
38.22
3.18
853
2623
4.053983
CAGATGACGCTGCTACATAACAT
58.946
43.478
0.00
0.00
0.00
2.71
934
2704
4.846940
AGGGTATCCTTTTCTCTGTGTTCT
59.153
41.667
0.00
0.00
41.56
3.01
952
2722
4.134563
GTTCTAACTCCAAAGCAACTGGA
58.865
43.478
1.96
1.96
40.77
3.86
994
2764
0.654683
GATCGAGCTGCCATCACAAC
59.345
55.000
0.00
0.00
0.00
3.32
1042
2812
3.764237
TTTACTCGGAGTTGGAAGCTT
57.236
42.857
16.95
0.00
0.00
3.74
1047
2817
2.563427
GAGTTGGAAGCTTGCGGC
59.437
61.111
13.65
8.35
42.19
6.53
1088
2858
0.988678
GACCTTGGAGGGGGCACTAT
60.989
60.000
0.00
0.00
40.58
2.12
1100
2882
3.073946
GGGGGCACTATGGTATGTATGTT
59.926
47.826
0.00
0.00
0.00
2.71
1113
2895
8.334263
TGGTATGTATGTTTGTATGCATATGG
57.666
34.615
10.16
0.00
37.74
2.74
1118
2900
8.916628
TGTATGTTTGTATGCATATGGTGTAT
57.083
30.769
10.16
4.04
36.99
2.29
1153
2943
9.687210
ACATGCATTCATTCATTCAATACATAC
57.313
29.630
0.00
0.00
0.00
2.39
1325
3117
2.939103
GAGGAAGAATGTGGTGAATCGG
59.061
50.000
0.00
0.00
0.00
4.18
1412
3204
5.765182
CACCAAGTATTTCTGACTGGTTTCT
59.235
40.000
0.00
0.00
30.64
2.52
1443
3235
7.644062
AGAATTATCGTCCTCCCATCTATCTA
58.356
38.462
0.00
0.00
0.00
1.98
1491
3283
1.095130
TTCTACCCCCTCCCTACACA
58.905
55.000
0.00
0.00
0.00
3.72
1503
3295
1.550179
CCCTACACACTCTCCCACTCA
60.550
57.143
0.00
0.00
0.00
3.41
1504
3296
2.248248
CCTACACACTCTCCCACTCAA
58.752
52.381
0.00
0.00
0.00
3.02
1555
3347
2.095372
ACGGCGTATTAAGAGCAAAAGC
59.905
45.455
12.58
0.00
0.00
3.51
1597
3389
9.872684
ATTATCCACAATCTCCTCAAATTATGT
57.127
29.630
0.00
0.00
0.00
2.29
1856
3652
5.521372
GGAAACAATTGATTAGAAGGCATGC
59.479
40.000
13.59
9.90
0.00
4.06
1896
3692
8.071967
TCAGCTGCAGATAAATATTTTCAATCG
58.928
33.333
20.43
0.00
0.00
3.34
1918
3714
4.256920
GTCGTGAGGGTTGAGTACTACTA
58.743
47.826
0.00
0.00
0.00
1.82
1919
3715
4.697352
GTCGTGAGGGTTGAGTACTACTAA
59.303
45.833
0.00
0.00
0.00
2.24
2055
3865
2.092429
ACGCATGACCCCAATGTAGATT
60.092
45.455
0.00
0.00
0.00
2.40
2084
3894
0.755686
TGCCCCTTCGTTTGCAAAAT
59.244
45.000
14.67
0.00
0.00
1.82
2107
3917
9.492973
AAATTTCAACTTTCATGATTAAGGTGG
57.507
29.630
20.12
6.76
39.11
4.61
2134
3944
7.405292
ACCCAAAGAAATGAGATAGAACATCA
58.595
34.615
0.00
0.00
0.00
3.07
2167
3977
5.399892
CAGAATCGCCGATAGTTAGAACTTC
59.600
44.000
0.00
0.00
40.37
3.01
2176
3987
6.529125
CCGATAGTTAGAACTTCGTAGCAAAA
59.471
38.462
17.56
0.00
40.37
2.44
2197
4008
2.053865
CCACCATGCCGGCAAGAAT
61.054
57.895
36.33
17.93
39.03
2.40
2206
4017
3.417101
TGCCGGCAAGAATAGAAAAGAA
58.583
40.909
30.74
0.00
0.00
2.52
2211
4022
4.853743
CGGCAAGAATAGAAAAGAAGCAAC
59.146
41.667
0.00
0.00
0.00
4.17
2356
4168
8.928270
AACAAATCTAATCTACTACGGAACAG
57.072
34.615
0.00
0.00
0.00
3.16
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
176
181
2.800544
GGGTGAATCCACACGAATATCG
59.199
50.000
0.00
0.00
44.93
2.92
313
2081
2.432444
CCTCCGGCATTTACTGTTTCA
58.568
47.619
0.00
0.00
0.00
2.69
322
2090
0.916086
TACATCACCCTCCGGCATTT
59.084
50.000
0.00
0.00
0.00
2.32
329
2097
7.670559
AGATATAACAGTAGTACATCACCCTCC
59.329
40.741
2.52
0.00
0.00
4.30
343
2111
7.201830
GCCTCAACTGAGTGAGATATAACAGTA
60.202
40.741
11.79
0.00
46.76
2.74
363
2133
1.292223
GCGTGTGTCTAGGCCTCAA
59.708
57.895
9.68
0.00
0.00
3.02
426
2196
5.587388
ATTTTCAAGCATCAATCGGTCAT
57.413
34.783
0.00
0.00
0.00
3.06
430
2200
7.689400
GCTTTTTAATTTTCAAGCATCAATCGG
59.311
33.333
9.24
0.00
41.16
4.18
454
2224
1.945394
GATCTGCGGACATTTCATGCT
59.055
47.619
0.00
0.00
0.00
3.79
475
2245
0.392193
CCATCTTCCTCAGCACGCTT
60.392
55.000
0.00
0.00
0.00
4.68
614
2384
6.320171
CCACTTGATTCACATGAGATGTTTC
58.680
40.000
0.00
0.00
42.70
2.78
645
2415
7.844009
ACATAGTTAAGATTTAAGACCACCGA
58.156
34.615
0.00
0.00
0.00
4.69
646
2416
8.388103
CAACATAGTTAAGATTTAAGACCACCG
58.612
37.037
0.00
0.00
0.00
4.94
702
2472
1.550524
TCTTCGTCACTGAGGAATGGG
59.449
52.381
13.25
4.36
36.18
4.00
720
2490
5.004448
TCGTCAACAGAGATAACAGAGTCT
58.996
41.667
0.00
0.00
0.00
3.24
721
2491
5.090083
GTCGTCAACAGAGATAACAGAGTC
58.910
45.833
0.00
0.00
0.00
3.36
749
2519
1.663695
CTTGTATAACGGGCCCACAG
58.336
55.000
24.92
8.33
0.00
3.66
760
2530
3.202906
GCGGGAAGACATGCTTGTATAA
58.797
45.455
5.05
0.00
36.83
0.98
797
2567
2.095364
GGCAATCCGATGAATGAGATGC
60.095
50.000
0.00
0.00
0.00
3.91
830
2600
3.119137
TGTTATGTAGCAGCGTCATCTGT
60.119
43.478
8.29
0.00
36.49
3.41
841
2611
9.884636
ATCTGTAAAAGTGTATGTTATGTAGCA
57.115
29.630
0.00
0.00
0.00
3.49
903
2673
7.458170
ACAGAGAAAAGGATACCCTAGAGAAAA
59.542
37.037
0.00
0.00
43.48
2.29
952
2722
3.118454
CGACAGAACGCCGGCAAT
61.118
61.111
28.98
14.87
0.00
3.56
960
2730
0.525668
CGATCCTTCCCGACAGAACG
60.526
60.000
0.00
0.00
0.00
3.95
994
2764
0.395686
ACATCCCGCATCATCTCCTG
59.604
55.000
0.00
0.00
0.00
3.86
1042
2812
2.491770
TATCTTTTGGGCCAGCCGCA
62.492
55.000
6.23
0.00
40.31
5.69
1047
2817
3.071874
TGAGTGTATCTTTTGGGCCAG
57.928
47.619
6.23
0.00
0.00
4.85
1050
2820
3.378427
GGTCATGAGTGTATCTTTTGGGC
59.622
47.826
0.00
0.00
0.00
5.36
1088
2858
7.941790
ACCATATGCATACAAACATACATACCA
59.058
33.333
8.99
0.00
31.87
3.25
1100
2882
9.348476
ACAAATACATACACCATATGCATACAA
57.652
29.630
8.99
0.00
0.00
2.41
1118
2900
9.518906
GAATGAATGAATGCATGTACAAATACA
57.481
29.630
0.00
0.00
45.37
2.29
1153
2943
6.174720
TGGCCTATTTGTCTTGGAGTATAG
57.825
41.667
3.32
0.00
0.00
1.31
1166
2956
1.881973
CCATCGACCATGGCCTATTTG
59.118
52.381
13.04
2.34
46.18
2.32
1212
3004
6.918022
TCGTCATACTCATACTAAATGCACAG
59.082
38.462
0.00
0.00
0.00
3.66
1412
3204
5.641155
TGGGAGGACGATAATTCTCTATCA
58.359
41.667
0.00
0.00
0.00
2.15
1443
3235
8.059798
AGATCTTGCAGTTTTAGCAACAATAT
57.940
30.769
0.00
0.00
46.13
1.28
1458
3250
3.495806
GGGGTAGAATGGAGATCTTGCAG
60.496
52.174
0.00
0.00
0.00
4.41
1459
3251
2.439507
GGGGTAGAATGGAGATCTTGCA
59.560
50.000
0.00
0.00
0.00
4.08
1465
3257
1.132365
GGGAGGGGGTAGAATGGAGAT
60.132
57.143
0.00
0.00
0.00
2.75
1491
3283
4.421131
ACTGACTATTTGAGTGGGAGAGT
58.579
43.478
0.00
0.00
39.06
3.24
1503
3295
7.442656
GTGGCCACTACATATACTGACTATTT
58.557
38.462
29.12
0.00
0.00
1.40
1504
3296
6.294564
CGTGGCCACTACATATACTGACTATT
60.295
42.308
32.28
0.00
0.00
1.73
1536
3328
2.538939
CCGCTTTTGCTCTTAATACGCC
60.539
50.000
0.00
0.00
44.80
5.68
1555
3347
7.719483
TGTGGATAATAGGTTTCTAGTTACCG
58.281
38.462
9.39
0.00
39.46
4.02
1597
3389
8.516811
TGCGTTAAAACACTTTTCAACTTTTA
57.483
26.923
0.00
0.00
34.19
1.52
1630
3422
7.170658
GCAACTTTAGTTTGCAACCAATCAATA
59.829
33.333
0.00
0.00
35.83
1.90
1737
3529
9.738832
TTGAATTGTTAAAAGGTTACAACTAGC
57.261
29.630
0.00
0.00
0.00
3.42
1767
3559
8.722480
TTTCAGTCATGACTTATGTTGGATAG
57.278
34.615
25.84
10.03
40.20
2.08
1856
3652
4.609947
TGCAGCTGACTAACAAATTTGTG
58.390
39.130
23.93
14.80
41.31
3.33
1896
3692
3.080319
AGTAGTACTCAACCCTCACGAC
58.920
50.000
0.00
0.00
0.00
4.34
2029
3839
0.550914
ATTGGGGTCATGCGTATGGT
59.449
50.000
13.77
0.00
34.97
3.55
2055
3865
4.497291
AACGAAGGGGCATGTAGATTTA
57.503
40.909
0.00
0.00
0.00
1.40
2070
3880
7.232994
TGAAAGTTGAAATTTTGCAAACGAAG
58.767
30.769
12.39
0.00
0.00
3.79
2084
3894
7.831691
TCCACCTTAATCATGAAAGTTGAAA
57.168
32.000
0.00
0.00
0.00
2.69
2107
3917
7.687941
TGTTCTATCTCATTTCTTTGGGTTC
57.312
36.000
0.00
0.00
0.00
3.62
2134
3944
1.344438
TCGGCGATTCTGGCTATCAAT
59.656
47.619
4.99
0.00
0.00
2.57
2167
3977
1.202290
GCATGGTGGGATTTTGCTACG
60.202
52.381
0.00
0.00
0.00
3.51
2176
3987
4.059304
TTGCCGGCATGGTGGGAT
62.059
61.111
33.25
0.00
41.21
3.85
2197
4008
6.260936
CCTCACTTGAAGTTGCTTCTTTTCTA
59.739
38.462
0.00
0.00
40.73
2.10
2206
4017
1.952296
CTTGCCTCACTTGAAGTTGCT
59.048
47.619
0.00
0.00
0.00
3.91
2211
4022
3.441496
TTTTGCTTGCCTCACTTGAAG
57.559
42.857
0.00
0.00
0.00
3.02
2330
4142
9.367444
CTGTTCCGTAGTAGATTAGATTTGTTT
57.633
33.333
0.00
0.00
0.00
2.83
2333
4145
8.928270
AACTGTTCCGTAGTAGATTAGATTTG
57.072
34.615
0.00
0.00
0.00
2.32
2356
4168
3.444703
TGTGTGGGTATTGCACAAAAC
57.555
42.857
0.00
0.00
39.76
2.43
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.