Multiple sequence alignment - TraesCS5B01G532200
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
TraesCS5B01G532200
chr5B
100.000
3844
0
0
1
3844
689901870
689898027
0.000000e+00
7099.0
1
TraesCS5B01G532200
chr5B
100.000
131
0
0
4140
4270
689897731
689897601
4.270000e-60
243.0
2
TraesCS5B01G532200
chr5B
79.237
236
18
16
972
1197
689879137
689878923
7.450000e-28
135.0
3
TraesCS5B01G532200
chr5D
94.466
3867
164
16
1
3844
546824485
546828324
0.000000e+00
5910.0
4
TraesCS5B01G532200
chr5D
77.951
449
31
25
334
779
546683017
546682634
7.190000e-53
219.0
5
TraesCS5B01G532200
chr5D
96.183
131
5
0
4140
4270
546828759
546828889
9.300000e-52
215.0
6
TraesCS5B01G532200
chr4A
93.700
3857
197
22
1
3826
622176404
622172563
0.000000e+00
5734.0
7
TraesCS5B01G532200
chr4A
93.115
305
21
0
3488
3792
53767606
53767302
8.420000e-122
448.0
8
TraesCS5B01G532200
chr4A
87.766
188
15
5
3658
3837
461675130
461674943
3.340000e-51
213.0
9
TraesCS5B01G532200
chr4A
84.579
214
18
3
235
448
622245899
622246097
9.370000e-47
198.0
10
TraesCS5B01G532200
chr4A
82.677
254
13
15
529
779
622248010
622248235
3.370000e-46
196.0
11
TraesCS5B01G532200
chr4A
90.789
76
1
2
4147
4216
622172535
622172460
3.510000e-16
97.1
12
TraesCS5B01G532200
chr3D
93.506
308
20
0
3485
3792
97984604
97984911
3.890000e-125
459.0
13
TraesCS5B01G532200
chr2D
94.314
299
17
0
3494
3792
411766120
411765822
3.890000e-125
459.0
14
TraesCS5B01G532200
chr6D
93.311
299
20
0
3494
3792
38963688
38963390
3.920000e-120
442.0
15
TraesCS5B01G532200
chr2A
88.360
189
12
7
3658
3837
574011867
574012054
7.190000e-53
219.0
16
TraesCS5B01G532200
chr2A
87.766
188
15
5
3658
3837
266791952
266791765
3.340000e-51
213.0
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
TraesCS5B01G532200
chr5B
689897601
689901870
4269
True
3671.00
7099
100.0000
1
4270
2
chr5B.!!$R2
4269
1
TraesCS5B01G532200
chr5D
546824485
546828889
4404
False
3062.50
5910
95.3245
1
4270
2
chr5D.!!$F1
4269
2
TraesCS5B01G532200
chr4A
622172460
622176404
3944
True
2915.55
5734
92.2445
1
4216
2
chr4A.!!$R3
4215
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
106
107
0.183492
TCACTTTGTGCTCCTGGCTT
59.817
50.000
0.00
0.0
42.39
4.35
F
229
233
0.532115
ATGCCCAAATGAGCCGAAAC
59.468
50.000
0.00
0.0
0.00
2.78
F
772
776
0.600518
CTCCATCTCCATCGCTGCTG
60.601
60.000
0.00
0.0
0.00
4.41
F
947
959
1.098050
ATCCATTTCCAGCTCGTTGC
58.902
50.000
0.00
0.0
43.29
4.17
F
2143
2166
1.153289
AAGGCCATAGCACTGCTCG
60.153
57.895
6.86
0.0
42.56
5.03
F
2928
2951
0.178955
TGGAGGTCAGGAACGTGGTA
60.179
55.000
0.00
0.0
0.00
3.25
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1749
1772
0.249868
TGCACTGGAGGTTGTCGAAG
60.250
55.000
0.00
0.00
0.00
3.79
R
2064
2087
0.325933
TCCAGCTGACAATGTCTGGG
59.674
55.000
17.39
13.64
44.62
4.45
R
2353
2376
0.172578
TCACGGTGATCCATGACGTC
59.827
55.000
9.11
9.11
30.56
4.34
R
2433
2456
0.249699
TCTCGCTGAACGCCTTCAAA
60.250
50.000
0.00
0.00
43.23
2.69
R
2997
3020
2.301009
TGTATCTCGCATGGCATCAGAT
59.699
45.455
14.43
14.43
0.00
2.90
R
3800
3837
3.311106
TCAGTAACTTCGTGTTTAGGCG
58.689
45.455
2.43
0.00
39.89
5.52
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
47
48
2.441164
ACACAAAACCGGCAGGCA
60.441
55.556
0.00
0.00
42.76
4.75
49
50
1.080569
CACAAAACCGGCAGGCATC
60.081
57.895
0.00
0.00
42.76
3.91
106
107
0.183492
TCACTTTGTGCTCCTGGCTT
59.817
50.000
0.00
0.00
42.39
4.35
144
145
0.611896
AGTGCCCTGCCAAACCATAC
60.612
55.000
0.00
0.00
0.00
2.39
146
147
0.611618
TGCCCTGCCAAACCATACAG
60.612
55.000
0.00
0.00
0.00
2.74
229
233
0.532115
ATGCCCAAATGAGCCGAAAC
59.468
50.000
0.00
0.00
0.00
2.78
765
769
2.356793
CGCGCCTCCATCTCCATC
60.357
66.667
0.00
0.00
0.00
3.51
772
776
0.600518
CTCCATCTCCATCGCTGCTG
60.601
60.000
0.00
0.00
0.00
4.41
773
777
2.252346
CCATCTCCATCGCTGCTGC
61.252
63.158
5.34
5.34
0.00
5.25
774
778
1.227586
CATCTCCATCGCTGCTGCT
60.228
57.895
14.03
0.00
36.97
4.24
775
779
1.227586
ATCTCCATCGCTGCTGCTG
60.228
57.895
14.03
5.96
36.97
4.41
779
783
3.574445
CATCGCTGCTGCTGCTCC
61.574
66.667
25.43
6.56
40.48
4.70
864
872
2.630580
TGTGTATTCTTTTGTTGGGCCC
59.369
45.455
17.59
17.59
0.00
5.80
866
874
2.630580
TGTATTCTTTTGTTGGGCCCAC
59.369
45.455
28.70
20.43
0.00
4.61
867
875
2.101640
ATTCTTTTGTTGGGCCCACT
57.898
45.000
28.70
0.00
0.00
4.00
947
959
1.098050
ATCCATTTCCAGCTCGTTGC
58.902
50.000
0.00
0.00
43.29
4.17
964
976
2.498726
CTTCCTCTCTGCGGCTCC
59.501
66.667
0.00
0.00
0.00
4.70
1250
1273
3.124921
GTTCGCGGACATGGTGGG
61.125
66.667
14.01
0.00
0.00
4.61
1566
1589
4.802051
CAGATGGTGGTGCGGGGG
62.802
72.222
0.00
0.00
0.00
5.40
1605
1628
2.512515
GTGACGAGCATCCTGGCC
60.513
66.667
0.00
0.00
0.00
5.36
1716
1739
1.711298
GCGCTGATCGATTTCTACTCG
59.289
52.381
0.00
0.00
41.67
4.18
1742
1765
2.508891
GCGAGTTCGACATGGCGAG
61.509
63.158
24.88
13.76
41.79
5.03
1749
1772
2.202756
GACATGGCGAGGACGGTC
60.203
66.667
0.00
0.00
40.15
4.79
1961
1984
1.202915
TCACTCTTTGGCCATCAAGCA
60.203
47.619
6.09
0.00
36.62
3.91
1989
2012
1.817209
GAGTGATCTCCGGGTGTCC
59.183
63.158
0.00
0.00
34.87
4.02
2064
2087
2.105128
CTCCGTGGCATCGAGGAC
59.895
66.667
0.00
0.00
0.00
3.85
2143
2166
1.153289
AAGGCCATAGCACTGCTCG
60.153
57.895
6.86
0.00
42.56
5.03
2181
2204
2.000447
GGTCTCATGCCAAACGACTAC
59.000
52.381
0.00
0.00
0.00
2.73
2353
2376
4.139420
CAGCGAGGCTTGCGTTCG
62.139
66.667
20.63
7.50
36.40
3.95
2433
2456
2.959484
CGGTGAGGTGGACATGGCT
61.959
63.158
0.00
0.00
0.00
4.75
2458
2481
1.704582
GCGTTCAGCGAGATGTGTC
59.295
57.895
0.00
0.00
44.77
3.67
2628
2651
4.451150
GTCGACATGCTGGGCCGA
62.451
66.667
11.55
0.00
0.00
5.54
2688
2711
2.649129
GCCTTTTGAGCCCGGCATT
61.649
57.895
13.15
0.00
42.06
3.56
2874
2897
3.606662
CGGCGGAGGATGGACGAT
61.607
66.667
0.00
0.00
0.00
3.73
2877
2900
2.029666
CGGAGGATGGACGATGCC
59.970
66.667
0.00
0.00
0.00
4.40
2924
2947
2.214920
GGGTGGAGGTCAGGAACGT
61.215
63.158
0.00
0.00
0.00
3.99
2928
2951
0.178955
TGGAGGTCAGGAACGTGGTA
60.179
55.000
0.00
0.00
0.00
3.25
2931
2954
1.549170
GAGGTCAGGAACGTGGTACAT
59.451
52.381
0.00
0.00
44.52
2.29
2940
2963
2.369870
CGTGGTACATGCCTTCGTC
58.630
57.895
0.00
0.00
44.52
4.20
2945
2968
3.709880
TACATGCCTTCGTCGCCCG
62.710
63.158
0.00
0.00
38.13
6.13
2989
3012
1.826921
TCCATCTACCGGACGCTCC
60.827
63.158
9.46
0.00
0.00
4.70
2990
3013
2.125326
CCATCTACCGGACGCTCCA
61.125
63.158
9.46
0.00
35.91
3.86
2993
3016
3.528370
CTACCGGACGCTCCAGGG
61.528
72.222
9.46
7.60
35.91
4.45
2997
3020
2.131709
CCGGACGCTCCAGGGATTA
61.132
63.158
0.00
0.00
35.91
1.75
3024
3047
1.937108
GCCATGCGAGATACAGCCTAC
60.937
57.143
0.00
0.00
0.00
3.18
3025
3048
1.341209
CCATGCGAGATACAGCCTACA
59.659
52.381
0.00
0.00
0.00
2.74
3029
3052
1.864435
GCGAGATACAGCCTACAACGG
60.864
57.143
0.00
0.00
0.00
4.44
3063
3086
9.358872
GAATTCTTCGATGTACATATGCAGATA
57.641
33.333
8.71
2.52
0.00
1.98
3127
3163
5.358725
GGTAACTGGGTCTTTGTTCTTTTCA
59.641
40.000
0.00
0.00
0.00
2.69
3298
3334
5.979517
GCTGCAGAAAGTTGATTAAAACACT
59.020
36.000
20.43
0.00
32.21
3.55
3366
3402
4.073293
ACCCTATTTGGCATTAGACTCG
57.927
45.455
6.57
0.00
0.00
4.18
3387
3423
7.263496
ACTCGCTAGTAAACTGGGTTTATAAG
58.737
38.462
6.22
7.75
39.64
1.73
3500
3537
9.371136
CACTACACTAACTAATCACATGAACAT
57.629
33.333
0.00
0.00
0.00
2.71
3510
3547
7.877612
ACTAATCACATGAACATAACAGACACA
59.122
33.333
0.00
0.00
0.00
3.72
3528
3565
6.036844
CAGACACATAGCTACGAGTTACACTA
59.963
42.308
0.00
0.00
0.00
2.74
3725
3762
3.084039
CACTATGGTGCATTGGTTCACT
58.916
45.455
0.00
0.00
36.61
3.41
4251
4442
7.817418
ATCTCTGAAGTCTCTTGGTATCTAC
57.183
40.000
0.00
0.00
0.00
2.59
4256
4447
5.123502
TGAAGTCTCTTGGTATCTACGTGAC
59.876
44.000
0.00
0.00
0.00
3.67
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
106
107
2.076100
CTGACTAACAATGCGAGGCAA
58.924
47.619
0.00
0.00
43.62
4.52
144
145
5.069648
TGTTCTTACTGATCTCCTATGCCTG
59.930
44.000
0.00
0.00
0.00
4.85
146
147
5.537188
CTGTTCTTACTGATCTCCTATGCC
58.463
45.833
0.00
0.00
0.00
4.40
229
233
2.868583
CCTTGTTCTCGTATGCCATCAG
59.131
50.000
0.00
0.00
0.00
2.90
468
472
3.379445
TTCTCCGACGTGCTCCCC
61.379
66.667
0.00
0.00
0.00
4.81
772
776
0.106519
AGAGAGAGAGAGGGAGCAGC
60.107
60.000
0.00
0.00
0.00
5.25
773
777
2.172505
TGTAGAGAGAGAGAGGGAGCAG
59.827
54.545
0.00
0.00
0.00
4.24
774
778
2.172505
CTGTAGAGAGAGAGAGGGAGCA
59.827
54.545
0.00
0.00
0.00
4.26
775
779
2.851195
CTGTAGAGAGAGAGAGGGAGC
58.149
57.143
0.00
0.00
0.00
4.70
779
783
3.632145
GGAAAGCTGTAGAGAGAGAGAGG
59.368
52.174
0.00
0.00
0.00
3.69
840
848
4.929211
GGCCCAACAAAAGAATACACATTC
59.071
41.667
0.00
0.00
40.85
2.67
913
921
0.107017
TGGATAAGCTTCAGCCCAGC
60.107
55.000
0.00
0.00
43.38
4.85
947
959
1.892819
TTGGAGCCGCAGAGAGGAAG
61.893
60.000
0.00
0.00
0.00
3.46
955
967
1.673665
AAAGAGCTTGGAGCCGCAG
60.674
57.895
0.00
0.00
43.77
5.18
956
968
1.968017
CAAAGAGCTTGGAGCCGCA
60.968
57.895
0.00
0.00
43.77
5.69
964
976
0.815734
CTCCCATGGCAAAGAGCTTG
59.184
55.000
6.09
0.00
44.79
4.01
1090
1113
2.513204
CATGAGCCCGTCCAGCTG
60.513
66.667
6.78
6.78
41.75
4.24
1091
1114
2.249413
CTTCATGAGCCCGTCCAGCT
62.249
60.000
0.00
0.00
45.23
4.24
1566
1589
4.373116
TGCTCGTTCGGCTCCACC
62.373
66.667
7.06
0.00
0.00
4.61
1716
1739
1.710013
TGTCGAACTCGCCATTTCTC
58.290
50.000
0.00
0.00
39.60
2.87
1729
1752
2.180769
CGTCCTCGCCATGTCGAA
59.819
61.111
0.00
0.00
38.08
3.71
1749
1772
0.249868
TGCACTGGAGGTTGTCGAAG
60.250
55.000
0.00
0.00
0.00
3.79
1807
1830
1.144936
CCGGCCTTCCATCTCTGAC
59.855
63.158
0.00
0.00
0.00
3.51
1961
1984
0.749649
GAGATCACTCGCCAGGTCAT
59.250
55.000
0.00
0.00
33.32
3.06
1989
2012
0.395311
ACATGGAGAGCAGGGCATTG
60.395
55.000
0.00
0.00
0.00
2.82
2064
2087
0.325933
TCCAGCTGACAATGTCTGGG
59.674
55.000
17.39
13.64
44.62
4.45
2106
2129
1.191489
TCTCACCATGGCCGTTCTGA
61.191
55.000
13.04
5.95
0.00
3.27
2143
2166
1.310933
CCTTGTGAGTGCATCTGGGC
61.311
60.000
0.00
0.00
0.00
5.36
2337
2360
4.357947
TCGAACGCAAGCCTCGCT
62.358
61.111
6.38
0.00
43.37
4.93
2353
2376
0.172578
TCACGGTGATCCATGACGTC
59.827
55.000
9.11
9.11
30.56
4.34
2433
2456
0.249699
TCTCGCTGAACGCCTTCAAA
60.250
50.000
0.00
0.00
43.23
2.69
2628
2651
1.300697
GTCGTCGAACCTGCCACTT
60.301
57.895
0.00
0.00
0.00
3.16
2686
2709
2.563179
ACAGCGTCTTCCACACTAGAAT
59.437
45.455
0.00
0.00
0.00
2.40
2688
2711
1.617322
ACAGCGTCTTCCACACTAGA
58.383
50.000
0.00
0.00
0.00
2.43
2749
2772
4.577246
GAGCTTCTCGGCGGCGAT
62.577
66.667
34.71
19.82
37.29
4.58
2778
2801
3.827898
CTCGCCGAGTCCTGGTCC
61.828
72.222
5.82
0.00
0.00
4.46
2874
2897
2.528127
TCCTTTCTCACCCCGGCA
60.528
61.111
0.00
0.00
0.00
5.69
2877
2900
2.269241
GCCTCCTTTCTCACCCCG
59.731
66.667
0.00
0.00
0.00
5.73
2924
2947
1.447140
GCGACGAAGGCATGTACCA
60.447
57.895
0.00
0.00
0.00
3.25
2951
2974
4.131088
GCGAGTCCGGGTGAGACC
62.131
72.222
0.00
0.00
37.60
3.85
2984
3007
2.934364
GCATCAGATAATCCCTGGAGCG
60.934
54.545
0.00
0.00
32.73
5.03
2989
3012
2.753452
GCATGGCATCAGATAATCCCTG
59.247
50.000
0.00
0.00
0.00
4.45
2990
3013
2.617276
CGCATGGCATCAGATAATCCCT
60.617
50.000
0.00
0.00
0.00
4.20
2993
3016
3.593096
TCTCGCATGGCATCAGATAATC
58.407
45.455
0.00
0.00
0.00
1.75
2997
3020
2.301009
TGTATCTCGCATGGCATCAGAT
59.699
45.455
14.43
14.43
0.00
2.90
3045
3068
9.178427
CACATCTATATCTGCATATGTACATCG
57.822
37.037
12.68
6.23
0.00
3.84
3090
3113
3.181454
CCCAGTTACCTTGACAGAACAGT
60.181
47.826
0.00
0.00
0.00
3.55
3091
3114
3.181454
ACCCAGTTACCTTGACAGAACAG
60.181
47.826
0.00
0.00
0.00
3.16
3092
3115
2.775384
ACCCAGTTACCTTGACAGAACA
59.225
45.455
0.00
0.00
0.00
3.18
3111
3147
5.584251
TGGCAATTTGAAAAGAACAAAGACC
59.416
36.000
0.00
0.00
39.90
3.85
3256
3292
7.377398
TCTGCAGCACATTTTAATTGTTACAT
58.623
30.769
9.47
0.00
0.00
2.29
3298
3334
3.086818
TCGTCGATGTCACACTGAAAA
57.913
42.857
4.21
0.00
0.00
2.29
3366
3402
7.825761
TGGAACTTATAAACCCAGTTTACTAGC
59.174
37.037
2.22
0.00
40.16
3.42
3500
3537
5.892160
AACTCGTAGCTATGTGTCTGTTA
57.108
39.130
18.36
0.00
0.00
2.41
3725
3762
2.821378
CAGTGGCATCAGGAAATCACAA
59.179
45.455
0.00
0.00
0.00
3.33
3800
3837
3.311106
TCAGTAACTTCGTGTTTAGGCG
58.689
45.455
2.43
0.00
39.89
5.52
4229
4420
5.587043
ACGTAGATACCAAGAGACTTCAGAG
59.413
44.000
0.00
0.00
0.00
3.35
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.