Multiple sequence alignment - TraesCS2A01G201700
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
TraesCS2A01G201700
chr2A
100.000
2823
0
0
1
2823
175436488
175439310
0.000000e+00
5214
1
TraesCS2A01G201700
chr2B
92.782
2757
102
43
32
2736
223090341
223093052
0.000000e+00
3899
2
TraesCS2A01G201700
chr2D
91.926
2663
102
49
1
2613
175299466
175302065
0.000000e+00
3622
3
TraesCS2A01G201700
chr2D
93.333
90
6
0
2733
2822
175302223
175302312
1.760000e-27
134
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
TraesCS2A01G201700
chr2A
175436488
175439310
2822
False
5214
5214
100.0000
1
2823
1
chr2A.!!$F1
2822
1
TraesCS2A01G201700
chr2B
223090341
223093052
2711
False
3899
3899
92.7820
32
2736
1
chr2B.!!$F1
2704
2
TraesCS2A01G201700
chr2D
175299466
175302312
2846
False
1878
3622
92.6295
1
2822
2
chr2D.!!$F1
2821
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
741
772
0.042013
CGTACGTGGAGAGCTCGATC
60.042
60.0
8.37
0.68
0.0
3.69
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2234
2300
0.100682
GCAGGCTGCATGATCAACAG
59.899
55.0
33.33
19.69
44.26
3.16
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
29
30
2.238898
AGGGTTAATTTGGACGAGGAGG
59.761
50.000
0.00
0.00
0.00
4.30
30
31
2.026542
GGGTTAATTTGGACGAGGAGGT
60.027
50.000
0.00
0.00
0.00
3.85
79
85
2.964438
AAAGCGAACGCAGACACGGA
62.964
55.000
20.66
0.00
44.88
4.69
80
86
3.764049
GCGAACGCAGACACGGAC
61.764
66.667
14.26
0.00
41.49
4.79
81
87
3.458579
CGAACGCAGACACGGACG
61.459
66.667
0.00
0.00
37.37
4.79
82
88
2.354305
GAACGCAGACACGGACGT
60.354
61.111
0.00
0.00
41.16
4.34
183
193
0.247460
AAACGGTAGTTCTACCCGCC
59.753
55.000
19.44
0.09
45.49
6.13
185
195
2.810403
GGTAGTTCTACCCGCCCG
59.190
66.667
15.81
0.00
34.06
6.13
187
197
3.520862
TAGTTCTACCCGCCCGCG
61.521
66.667
0.00
0.00
39.44
6.46
239
261
1.888638
CGTCCCGTCGGTTGGTTTT
60.889
57.895
11.06
0.00
0.00
2.43
269
291
6.619437
TCTCCCAATCCATCTAAAATACTCCA
59.381
38.462
0.00
0.00
0.00
3.86
270
292
6.601332
TCCCAATCCATCTAAAATACTCCAC
58.399
40.000
0.00
0.00
0.00
4.02
354
376
1.894282
GCTGCCTAGAATTCGCCCC
60.894
63.158
0.00
0.00
0.00
5.80
356
378
0.250081
CTGCCTAGAATTCGCCCCTC
60.250
60.000
0.00
0.00
0.00
4.30
358
380
0.180406
GCCTAGAATTCGCCCCTCAA
59.820
55.000
0.00
0.00
0.00
3.02
360
382
2.749800
GCCTAGAATTCGCCCCTCAATT
60.750
50.000
0.00
0.00
0.00
2.32
361
383
3.142174
CCTAGAATTCGCCCCTCAATTC
58.858
50.000
0.00
0.00
38.70
2.17
362
384
1.668419
AGAATTCGCCCCTCAATTCG
58.332
50.000
0.00
0.00
41.84
3.34
364
386
1.743394
GAATTCGCCCCTCAATTCGTT
59.257
47.619
0.00
0.00
31.17
3.85
365
387
1.379527
ATTCGCCCCTCAATTCGTTC
58.620
50.000
0.00
0.00
0.00
3.95
366
388
0.675522
TTCGCCCCTCAATTCGTTCC
60.676
55.000
0.00
0.00
0.00
3.62
380
402
1.773496
GTTCCTTCGTTCGTCGCAG
59.227
57.895
0.00
0.00
39.67
5.18
440
462
1.070175
ACGCAAACCGATGAACGAAAG
60.070
47.619
0.00
0.00
45.77
2.62
442
464
2.571206
GCAAACCGATGAACGAAAGAC
58.429
47.619
0.00
0.00
45.77
3.01
452
476
5.960683
CGATGAACGAAAGACACTAGTAGAG
59.039
44.000
3.59
0.00
45.77
2.43
453
477
6.183360
CGATGAACGAAAGACACTAGTAGAGA
60.183
42.308
3.59
0.00
45.77
3.10
528
559
1.940613
GGTCTGTCTGTGTGTTGGTTC
59.059
52.381
0.00
0.00
0.00
3.62
540
571
0.733223
GTTGGTTCCTCTCGCGTCTC
60.733
60.000
5.77
0.00
0.00
3.36
619
650
0.460109
TGCTCCGTACGCGTCTACTA
60.460
55.000
18.63
0.00
36.15
1.82
730
761
2.278596
CTCCATCGCCGTACGTGG
60.279
66.667
15.21
14.91
44.19
4.94
738
769
2.403987
CCGTACGTGGAGAGCTCG
59.596
66.667
15.21
0.00
0.00
5.03
739
770
2.104859
CCGTACGTGGAGAGCTCGA
61.105
63.158
15.21
0.00
0.00
4.04
740
771
1.437772
CCGTACGTGGAGAGCTCGAT
61.438
60.000
15.21
0.00
0.00
3.59
741
772
0.042013
CGTACGTGGAGAGCTCGATC
60.042
60.000
8.37
0.68
0.00
3.69
759
790
0.532417
TCGTAGCTCCCGCTCTCTAC
60.532
60.000
0.00
0.00
45.15
2.59
859
890
1.807573
GGCTGCTGTCGTGAGCTAC
60.808
63.158
0.00
2.62
39.90
3.58
863
894
1.292223
GCTGTCGTGAGCTACCCAA
59.708
57.895
0.00
0.00
35.95
4.12
865
896
0.603569
CTGTCGTGAGCTACCCAACT
59.396
55.000
0.00
0.00
0.00
3.16
866
897
0.317160
TGTCGTGAGCTACCCAACTG
59.683
55.000
0.00
0.00
0.00
3.16
867
898
0.317479
GTCGTGAGCTACCCAACTGT
59.683
55.000
0.00
0.00
0.00
3.55
868
899
1.542915
GTCGTGAGCTACCCAACTGTA
59.457
52.381
0.00
0.00
0.00
2.74
912
943
2.028130
CTAGCTAGCTACCTGCACACT
58.972
52.381
20.67
0.00
45.94
3.55
919
950
0.179171
CTACCTGCACACTCGTACGG
60.179
60.000
16.52
8.79
0.00
4.02
948
979
4.148838
GGTAGCAGTACAGATCTCCATCT
58.851
47.826
0.00
0.00
40.32
2.90
995
1026
1.227118
GCTTGCTCGACCTAGCTCC
60.227
63.158
6.88
0.00
43.19
4.70
1020
1051
1.674651
GGCCTCAACCGGAGTTTCC
60.675
63.158
9.46
0.00
42.40
3.13
1149
1180
3.844090
GAGGAGTCTCTGGCCGGC
61.844
72.222
21.18
21.18
37.07
6.13
1503
1534
1.153823
CTACCTCCCGCAAGACGTG
60.154
63.158
0.00
0.00
41.42
4.49
1623
1670
8.439286
GCATCATTTTCTTCCTCTTCGATATAC
58.561
37.037
0.00
0.00
0.00
1.47
1624
1671
9.703892
CATCATTTTCTTCCTCTTCGATATACT
57.296
33.333
0.00
0.00
0.00
2.12
1989
2043
7.038659
ACATTCGTTTTTCTTTGGTTGATTCA
58.961
30.769
0.00
0.00
0.00
2.57
1997
2051
4.555262
TCTTTGGTTGATTCATTTTCGGC
58.445
39.130
0.00
0.00
0.00
5.54
2020
2076
2.491152
GTTCATGGGTGCATGCCG
59.509
61.111
16.68
0.00
32.87
5.69
2036
2092
2.749865
CCGTAGCCGCCAATGTGTG
61.750
63.158
0.00
0.00
0.00
3.82
2162
2221
6.599244
AGTTCGATCACATATTCCACAATTGT
59.401
34.615
4.92
4.92
0.00
2.71
2234
2300
0.681175
AACCATGCCCAAACAGCTTC
59.319
50.000
0.00
0.00
0.00
3.86
2252
2318
1.746470
TCTGTTGATCATGCAGCCTG
58.254
50.000
17.89
0.00
0.00
4.85
2339
2405
7.154656
GCCCACTAAAAAGAAACAATTGATCT
58.845
34.615
13.59
12.10
0.00
2.75
2366
2432
4.640201
GCCATTTCTAGAGTGCCACAATTA
59.360
41.667
0.00
0.00
0.00
1.40
2373
2439
6.245408
TCTAGAGTGCCACAATTATTTTGGT
58.755
36.000
11.23
0.00
32.50
3.67
2399
2465
3.282885
AGCAGATCAGTGTCGTCATCTA
58.717
45.455
0.00
0.00
0.00
1.98
2404
2470
6.268566
CAGATCAGTGTCGTCATCTATGAAA
58.731
40.000
0.00
0.00
38.75
2.69
2406
2472
5.644977
TCAGTGTCGTCATCTATGAAAGT
57.355
39.130
0.00
0.00
38.75
2.66
2440
2506
1.760192
TACCAACTCCTCGAGCTACC
58.240
55.000
6.99
0.00
32.04
3.18
2462
2528
1.716826
GCCTCGCGTAGTACTGCTCT
61.717
60.000
5.77
0.00
0.00
4.09
2463
2529
0.305313
CCTCGCGTAGTACTGCTCTC
59.695
60.000
5.77
0.00
0.00
3.20
2618
2699
2.866762
ACGATGCTCGAAATAGGCTTTC
59.133
45.455
11.64
0.00
43.74
2.62
2638
2719
8.870375
GGCTTTCGTGCCGCTTTATAAATAAAG
61.870
40.741
15.20
15.20
45.02
1.85
2680
2761
5.356470
AGCATCCAAGTTCTGAAATAGCTTC
59.644
40.000
0.00
0.00
34.31
3.86
2775
2933
2.865079
TGTCCTTCGGTTGGCATTTTA
58.135
42.857
0.00
0.00
0.00
1.52
2822
2980
3.338249
ACATGAACCTTGAAGACGATGG
58.662
45.455
0.00
0.00
0.00
3.51
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
29
30
2.830104
ACTTTCAACACCTCGTACCAC
58.170
47.619
0.00
0.00
0.00
4.16
30
31
3.118702
TCAACTTTCAACACCTCGTACCA
60.119
43.478
0.00
0.00
0.00
3.25
79
85
1.337260
ACTCTCCGACTGTACGTACGT
60.337
52.381
25.98
25.98
0.00
3.57
80
86
1.322936
GACTCTCCGACTGTACGTACG
59.677
57.143
20.18
15.01
0.00
3.67
81
87
1.663135
GGACTCTCCGACTGTACGTAC
59.337
57.143
18.90
18.90
0.00
3.67
82
88
1.276138
TGGACTCTCCGACTGTACGTA
59.724
52.381
0.00
0.00
40.17
3.57
188
198
2.124487
AGAGACTCCGGCGAGAGG
60.124
66.667
22.97
8.15
38.52
3.69
190
200
1.303398
AACAGAGACTCCGGCGAGA
60.303
57.895
9.30
2.74
38.52
4.04
192
202
2.341101
GGAACAGAGACTCCGGCGA
61.341
63.158
9.30
0.00
0.00
5.54
195
205
0.900647
AGGTGGAACAGAGACTCCGG
60.901
60.000
0.00
0.00
41.80
5.14
196
206
0.528470
GAGGTGGAACAGAGACTCCG
59.472
60.000
0.00
0.00
41.80
4.63
239
261
6.387192
TTTTAGATGGATTGGGAGACAAGA
57.613
37.500
0.00
0.00
43.48
3.02
354
376
2.729882
ACGAACGAAGGAACGAATTGAG
59.270
45.455
0.14
0.00
37.03
3.02
356
378
2.470140
CGACGAACGAAGGAACGAATTG
60.470
50.000
0.14
0.00
45.77
2.32
358
380
1.334054
CGACGAACGAAGGAACGAAT
58.666
50.000
0.14
0.00
45.77
3.34
360
382
1.727022
GCGACGAACGAAGGAACGA
60.727
57.895
0.00
0.00
45.77
3.85
361
383
1.930816
CTGCGACGAACGAAGGAACG
61.931
60.000
0.00
0.00
43.40
3.95
362
384
0.662374
TCTGCGACGAACGAAGGAAC
60.662
55.000
12.83
0.00
46.77
3.62
364
386
0.031043
TTTCTGCGACGAACGAAGGA
59.969
50.000
12.83
3.83
46.77
3.36
365
387
0.435008
CTTTCTGCGACGAACGAAGG
59.565
55.000
12.83
0.00
46.77
3.46
380
402
1.224722
GCAGATCGATCCGGCCTTTC
61.225
60.000
21.66
0.00
0.00
2.62
408
430
4.637276
TCGGTTTGCGTGGATAATATCAT
58.363
39.130
2.41
0.00
0.00
2.45
409
431
4.061357
TCGGTTTGCGTGGATAATATCA
57.939
40.909
2.41
0.00
0.00
2.15
410
432
4.688879
TCATCGGTTTGCGTGGATAATATC
59.311
41.667
0.00
0.00
0.00
1.63
452
476
9.690434
GATCTTACGTTGATCACTTTACAATTC
57.310
33.333
19.64
0.00
39.85
2.17
453
477
9.214957
TGATCTTACGTTGATCACTTTACAATT
57.785
29.630
21.93
0.00
43.47
2.32
540
571
2.745884
TTCAATGGTGCCCTCGCG
60.746
61.111
0.00
0.00
38.08
5.87
619
650
7.067859
GGTTTGAAAAGGTGGAAAACTAGTAGT
59.932
37.037
0.00
0.00
32.60
2.73
759
790
3.055312
GGGAGCTCGGGTTTATATAAGGG
60.055
52.174
7.83
0.00
0.00
3.95
859
890
1.531264
CGATCGAGACGTACAGTTGGG
60.531
57.143
10.26
0.00
0.00
4.12
863
894
1.396301
GGAACGATCGAGACGTACAGT
59.604
52.381
24.34
5.47
43.16
3.55
902
933
1.900016
TCCGTACGAGTGTGCAGGT
60.900
57.895
18.76
0.00
0.00
4.00
919
950
2.103736
GTACTGCTACCGGCCGTC
59.896
66.667
26.12
10.61
39.11
4.79
948
979
2.807470
CGTGTGCGTGCGTGGATA
60.807
61.111
0.00
0.00
0.00
2.59
971
1002
2.271607
TAGGTCGAGCAAGCTCAGCG
62.272
60.000
20.75
8.84
42.86
5.18
995
1026
0.394216
TCCGGTTGAGGCCATTGATG
60.394
55.000
5.01
0.00
0.00
3.07
1020
1051
0.681733
CCATGATGGAGGACCTACGG
59.318
60.000
5.27
0.00
40.96
4.02
1149
1180
1.443194
CACGTCGTACTGGGGTTCG
60.443
63.158
0.00
0.00
37.53
3.95
1158
1189
2.154389
GTGGTTGATGAACACGTCGTAC
59.846
50.000
0.00
0.00
33.27
3.67
1503
1534
3.689411
GCGTACTTGTAGCGCTCC
58.311
61.111
16.34
1.51
46.55
4.70
1623
1670
6.146184
CACGGCACAGATGGAATTATACTTAG
59.854
42.308
0.00
0.00
0.00
2.18
1624
1671
5.989168
CACGGCACAGATGGAATTATACTTA
59.011
40.000
0.00
0.00
0.00
2.24
1625
1672
4.816385
CACGGCACAGATGGAATTATACTT
59.184
41.667
0.00
0.00
0.00
2.24
1714
1761
1.227380
CTCGGCTATGTCCCTGCAC
60.227
63.158
0.00
0.00
0.00
4.57
1927
1975
5.532025
AAAACGAACGAATGAATCCTCTC
57.468
39.130
0.14
0.00
0.00
3.20
1953
2007
5.128008
AGAAAAACGAATGTCCCCTCAAAAA
59.872
36.000
0.00
0.00
0.00
1.94
1989
2043
3.384467
CCCATGAACCTAATGCCGAAAAT
59.616
43.478
0.00
0.00
0.00
1.82
2020
2076
3.187058
CCACACATTGGCGGCTAC
58.813
61.111
11.43
0.00
39.07
3.58
2036
2092
4.153655
GCCAGCCGTATAGCTTATTTTACC
59.846
45.833
0.00
0.00
42.61
2.85
2162
2221
6.536941
GGCCTCACAAATTTTGTAAACAGAAA
59.463
34.615
14.13
0.00
43.23
2.52
2234
2300
0.100682
GCAGGCTGCATGATCAACAG
59.899
55.000
33.33
19.69
44.26
3.16
2252
2318
1.644786
ATTGTTTGCTCGTAGGGCGC
61.645
55.000
0.00
0.00
41.07
6.53
2339
2405
1.406887
GGCACTCTAGAAATGGCGGAA
60.407
52.381
12.72
0.00
0.00
4.30
2366
2432
4.946157
CACTGATCTGCTCCTTACCAAAAT
59.054
41.667
0.00
0.00
0.00
1.82
2373
2439
2.423892
GACGACACTGATCTGCTCCTTA
59.576
50.000
0.00
0.00
0.00
2.69
2420
2486
2.097825
GGTAGCTCGAGGAGTTGGTAA
58.902
52.381
15.58
0.00
31.39
2.85
2421
2487
1.760192
GGTAGCTCGAGGAGTTGGTA
58.240
55.000
15.58
0.00
31.39
3.25
2563
2641
5.014755
ACCATTGGTTAAGATCCAACACCTA
59.985
40.000
1.37
0.33
45.84
3.08
2639
2720
1.468127
TGCTGGTTGTATGCATCGTTG
59.532
47.619
0.19
0.00
0.00
4.10
2657
2738
5.449725
GGAAGCTATTTCAGAACTTGGATGC
60.450
44.000
0.00
0.00
37.54
3.91
2736
2818
7.630242
AGGACATCTACATTGTTTATGGTTG
57.370
36.000
12.82
0.00
38.64
3.77
2739
2821
6.948353
CGAAGGACATCTACATTGTTTATGG
58.052
40.000
12.82
0.00
38.64
2.74
2796
2954
7.362056
CCATCGTCTTCAAGGTTCATGTAAAAT
60.362
37.037
0.00
0.00
0.00
1.82
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.