Multiple sequence alignment - TraesCS2D01G215000
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
TraesCS2D01G215000
chr2D
100.000
3624
0
0
1
3624
177092539
177096162
0.000000e+00
6693
1
TraesCS2D01G215000
chr2A
94.523
3104
94
30
547
3617
189600712
189603772
0.000000e+00
4721
2
TraesCS2D01G215000
chr2A
91.395
430
37
0
1
430
189599968
189600397
1.120000e-164
590
3
TraesCS2D01G215000
chr2B
93.607
2456
67
32
497
2897
234084579
234086999
0.000000e+00
3583
4
TraesCS2D01G215000
chr2B
90.377
717
27
15
2917
3624
234086985
234087668
0.000000e+00
904
5
TraesCS2D01G215000
chr2B
92.641
462
33
1
1
462
234084133
234084593
0.000000e+00
664
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
TraesCS2D01G215000
chr2D
177092539
177096162
3623
False
6693.0
6693
100.000000
1
3624
1
chr2D.!!$F1
3623
1
TraesCS2D01G215000
chr2A
189599968
189603772
3804
False
2655.5
4721
92.959000
1
3617
2
chr2A.!!$F1
3616
2
TraesCS2D01G215000
chr2B
234084133
234087668
3535
False
1717.0
3583
92.208333
1
3624
3
chr2B.!!$F1
3623
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
472
473
0.106419
AAGGACCTCACCCGCAAAAA
60.106
50.000
0.0
0.0
0.00
1.94
F
654
853
1.513586
GCCACGGAGTAACTCGTCG
60.514
63.158
0.0
0.0
41.61
5.12
F
2246
2470
0.491823
TCCTTTGGGAGAGGAGACCA
59.508
55.000
0.0
0.0
38.37
4.02
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1952
2173
0.250234
CCATCTTCACCTCTGCGGAA
59.750
55.0
0.0
0.0
36.31
4.30
R
2334
2568
0.941542
TCCGGCGAGAAAACAACAAG
59.058
50.0
9.3
0.0
0.00
3.16
R
3208
3477
0.887387
GCGTTGACCACCCTTGCTTA
60.887
55.0
0.0
0.0
0.00
3.09
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
90
91
1.669115
ACTCGCGCATTGCAGACTT
60.669
52.632
8.75
0.00
46.97
3.01
112
113
2.125269
AGATGGGTACGTTGGCGC
60.125
61.111
0.00
0.00
42.83
6.53
136
137
3.947196
TGCTGGAAAATTGCTATGACGAT
59.053
39.130
0.00
0.00
0.00
3.73
189
190
3.320673
CCCGTTATGGCTCCTAGATTC
57.679
52.381
0.00
0.00
35.87
2.52
192
193
2.352814
CGTTATGGCTCCTAGATTCCGG
60.353
54.545
0.00
0.00
0.00
5.14
219
220
4.101585
GTGGATGGATGGATCTTGACTACA
59.898
45.833
0.00
0.00
0.00
2.74
331
332
1.604378
CTCCCTCTGAAACCGCCAT
59.396
57.895
0.00
0.00
0.00
4.40
451
452
3.944871
GGGAAATGCGCCATAGTTG
57.055
52.632
4.18
0.00
0.00
3.16
452
453
0.249031
GGGAAATGCGCCATAGTTGC
60.249
55.000
4.18
0.00
0.00
4.17
453
454
0.455410
GGAAATGCGCCATAGTTGCA
59.545
50.000
4.18
0.00
43.67
4.08
454
455
1.135141
GGAAATGCGCCATAGTTGCAA
60.135
47.619
4.18
0.00
42.65
4.08
455
456
2.187707
GAAATGCGCCATAGTTGCAAG
58.812
47.619
4.18
0.00
42.65
4.01
456
457
0.457035
AATGCGCCATAGTTGCAAGG
59.543
50.000
4.18
0.00
42.65
3.61
457
458
0.394216
ATGCGCCATAGTTGCAAGGA
60.394
50.000
4.18
0.00
42.65
3.36
458
459
1.305219
TGCGCCATAGTTGCAAGGAC
61.305
55.000
4.18
0.00
35.33
3.85
459
460
1.993369
GCGCCATAGTTGCAAGGACC
61.993
60.000
0.00
0.00
0.00
4.46
460
461
0.392998
CGCCATAGTTGCAAGGACCT
60.393
55.000
0.00
0.00
0.00
3.85
461
462
1.383523
GCCATAGTTGCAAGGACCTC
58.616
55.000
0.00
0.00
0.00
3.85
462
463
1.340017
GCCATAGTTGCAAGGACCTCA
60.340
52.381
0.00
0.00
0.00
3.86
463
464
2.359900
CCATAGTTGCAAGGACCTCAC
58.640
52.381
0.00
0.00
0.00
3.51
464
465
2.359900
CATAGTTGCAAGGACCTCACC
58.640
52.381
0.00
0.00
0.00
4.02
465
466
0.690762
TAGTTGCAAGGACCTCACCC
59.309
55.000
0.00
0.00
0.00
4.61
466
467
1.966451
GTTGCAAGGACCTCACCCG
60.966
63.158
0.00
0.00
0.00
5.28
467
468
3.842925
TTGCAAGGACCTCACCCGC
62.843
63.158
0.00
0.00
0.00
6.13
468
469
4.329545
GCAAGGACCTCACCCGCA
62.330
66.667
0.00
0.00
0.00
5.69
469
470
2.429930
CAAGGACCTCACCCGCAA
59.570
61.111
0.00
0.00
0.00
4.85
470
471
1.228124
CAAGGACCTCACCCGCAAA
60.228
57.895
0.00
0.00
0.00
3.68
471
472
0.821711
CAAGGACCTCACCCGCAAAA
60.822
55.000
0.00
0.00
0.00
2.44
472
473
0.106419
AAGGACCTCACCCGCAAAAA
60.106
50.000
0.00
0.00
0.00
1.94
521
522
8.240267
AGTTACAAGGATCTCTACTTATGTCC
57.760
38.462
0.00
0.00
0.00
4.02
529
530
7.037586
AGGATCTCTACTTATGTCCACCAAAAA
60.038
37.037
0.00
0.00
0.00
1.94
554
753
5.049060
TGTGGTGATTAGTGTTGTACAATGC
60.049
40.000
12.26
7.83
0.00
3.56
570
769
4.555262
ACAATGCCGTCAACATTTTTAGG
58.445
39.130
0.00
0.00
35.58
2.69
654
853
1.513586
GCCACGGAGTAACTCGTCG
60.514
63.158
0.00
0.00
41.61
5.12
679
878
2.591429
CAGGGTCACGCACAAGCA
60.591
61.111
0.00
0.00
42.27
3.91
681
880
4.012895
GGGTCACGCACAAGCACG
62.013
66.667
0.00
0.00
42.27
5.34
762
962
4.851252
CCTCCATGCCCTCCCCCT
62.851
72.222
0.00
0.00
0.00
4.79
828
1028
2.009681
ACCCCAAATCCACACCTTTC
57.990
50.000
0.00
0.00
0.00
2.62
1015
1215
3.807839
CCATGGACATGCCGGGGA
61.808
66.667
5.56
0.00
40.66
4.81
1398
1619
6.432472
AGATGGTGTCTTTCTTTCAAGAATCC
59.568
38.462
2.83
3.13
43.92
3.01
1574
1795
6.256321
CGATGATTATTGCCCTTTTCCTTTTG
59.744
38.462
0.00
0.00
0.00
2.44
1623
1844
5.123979
GGGGATTAGTTGTCAATCAAGTGTC
59.876
44.000
0.00
0.00
39.67
3.67
1687
1908
4.429212
CGACGCGGTGACCATCCA
62.429
66.667
12.47
0.00
0.00
3.41
1952
2173
1.536662
AACCGCTGACCTCTTCCCT
60.537
57.895
0.00
0.00
0.00
4.20
2136
2358
3.030291
ACATTTTTGTTCTCCACTGCCA
58.970
40.909
0.00
0.00
0.00
4.92
2168
2392
6.570654
CCCCCTTAATTCTCCACTACTAAA
57.429
41.667
0.00
0.00
0.00
1.85
2176
2400
7.932120
AATTCTCCACTACTAAATCGAATCG
57.068
36.000
0.00
0.00
0.00
3.34
2191
2415
0.675522
AATCGCCCAAGTAACCACCG
60.676
55.000
0.00
0.00
0.00
4.94
2208
2432
2.816360
CGCCTGTCATGTCATGCCG
61.816
63.158
8.03
6.27
0.00
5.69
2246
2470
0.491823
TCCTTTGGGAGAGGAGACCA
59.508
55.000
0.00
0.00
38.37
4.02
2326
2560
3.499737
CGATTGACCCGCACTGCC
61.500
66.667
0.00
0.00
0.00
4.85
2334
2568
3.272334
CCGCACTGCCGATAAGCC
61.272
66.667
0.00
0.00
0.00
4.35
2337
2571
1.723870
GCACTGCCGATAAGCCTTG
59.276
57.895
0.00
0.00
0.00
3.61
2700
2947
3.857157
TTACTCTTGCCCTGTTGTTCT
57.143
42.857
0.00
0.00
0.00
3.01
2774
3027
1.262683
GTAAGCAGCGATGCAGATTCC
59.737
52.381
29.24
0.08
37.25
3.01
2841
3094
3.817709
TGTTTCCCTTGGCTTTTCTTG
57.182
42.857
0.00
0.00
0.00
3.02
2911
3170
4.409187
AGGCTGGTATTTTCCCGTAAAAA
58.591
39.130
0.00
0.00
40.37
1.94
3022
3281
5.503927
ACCATGTGCTCATTACTGATCTTT
58.496
37.500
0.00
0.00
31.15
2.52
3030
3290
8.510505
GTGCTCATTACTGATCTTTTCTTTCTT
58.489
33.333
0.00
0.00
0.00
2.52
3035
3295
5.854431
ACTGATCTTTTCTTTCTTCTCGC
57.146
39.130
0.00
0.00
0.00
5.03
3059
3319
6.292008
GCTTCTGTTTTGAAAAGTCTTCATGC
60.292
38.462
0.00
0.00
0.00
4.06
3060
3320
5.273170
TCTGTTTTGAAAAGTCTTCATGCG
58.727
37.500
0.00
0.00
0.00
4.73
3194
3463
7.201574
GGCTCTGTAGATACGTATGAGTAGATG
60.202
44.444
13.97
7.03
0.00
2.90
3207
3476
9.151471
CGTATGAGTAGATGGAAAGAAAGAAAA
57.849
33.333
0.00
0.00
0.00
2.29
3227
3501
0.887387
TAAGCAAGGGTGGTCAACGC
60.887
55.000
0.00
0.00
41.96
4.84
3416
3692
5.409520
CCATGCGTACGTACTATTACTCCTA
59.590
44.000
22.55
0.00
0.00
2.94
3421
3697
6.089685
GCGTACGTACTATTACTCCTACTACC
59.910
46.154
22.55
0.00
0.00
3.18
3438
3714
2.370281
ACCACTACGAAGAGTGCATG
57.630
50.000
10.18
0.00
44.65
4.06
3617
3902
1.754234
GGCTTACATGTGGGCCCAG
60.754
63.158
29.55
17.45
38.77
4.45
3618
3903
1.754234
GCTTACATGTGGGCCCAGG
60.754
63.158
29.55
20.71
0.00
4.45
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
13
14
5.045215
TCCCACTATTTACGCGACTAAATG
58.955
41.667
15.93
10.69
30.53
2.32
17
18
4.924305
AATCCCACTATTTACGCGACTA
57.076
40.909
15.93
0.00
0.00
2.59
90
91
1.609580
GCCAACGTACCCATCTGTCAA
60.610
52.381
0.00
0.00
0.00
3.18
112
113
3.429085
GTCATAGCAATTTTCCAGCACG
58.571
45.455
0.00
0.00
0.00
5.34
136
137
2.125310
CACGCGATAACCCAGGCA
60.125
61.111
15.93
0.00
0.00
4.75
176
177
1.382557
TGCCGGAATCTAGGAGCCA
60.383
57.895
5.05
0.00
0.00
4.75
189
190
2.896854
CATCCATCCACGTGCCGG
60.897
66.667
10.91
9.89
0.00
6.13
192
193
0.107456
AGATCCATCCATCCACGTGC
59.893
55.000
10.91
0.00
0.00
5.34
196
197
3.853355
AGTCAAGATCCATCCATCCAC
57.147
47.619
0.00
0.00
0.00
4.02
277
278
2.764010
GGGAAGAGTCCTTTCTCTCTCC
59.236
54.545
12.18
12.18
43.03
3.71
350
351
2.743636
AAAAGAAGGAGATCACGCGA
57.256
45.000
15.93
0.00
0.00
5.87
439
440
1.002746
TCCTTGCAACTATGGCGCA
60.003
52.632
10.83
0.00
0.00
6.09
444
445
2.359900
GGTGAGGTCCTTGCAACTATG
58.640
52.381
0.00
0.00
0.00
2.23
447
448
1.456287
GGGTGAGGTCCTTGCAACT
59.544
57.895
0.00
0.00
0.00
3.16
448
449
1.966451
CGGGTGAGGTCCTTGCAAC
60.966
63.158
0.00
0.00
0.00
4.17
449
450
2.429930
CGGGTGAGGTCCTTGCAA
59.570
61.111
0.00
0.00
0.00
4.08
450
451
4.329545
GCGGGTGAGGTCCTTGCA
62.330
66.667
0.00
0.00
0.00
4.08
451
452
3.842925
TTGCGGGTGAGGTCCTTGC
62.843
63.158
0.00
0.00
0.00
4.01
452
453
0.821711
TTTTGCGGGTGAGGTCCTTG
60.822
55.000
0.00
0.00
0.00
3.61
453
454
0.106419
TTTTTGCGGGTGAGGTCCTT
60.106
50.000
0.00
0.00
0.00
3.36
454
455
1.534697
TTTTTGCGGGTGAGGTCCT
59.465
52.632
0.00
0.00
0.00
3.85
455
456
4.167597
TTTTTGCGGGTGAGGTCC
57.832
55.556
0.00
0.00
0.00
4.46
495
496
8.697292
GGACATAAGTAGAGATCCTTGTAACTT
58.303
37.037
0.00
0.00
0.00
2.66
529
530
6.349280
GCATTGTACAACACTAATCACCACAT
60.349
38.462
11.22
0.00
0.00
3.21
538
539
3.729966
TGACGGCATTGTACAACACTAA
58.270
40.909
11.22
0.00
0.00
2.24
554
753
8.512138
AGTAATTCTTCCTAAAAATGTTGACGG
58.488
33.333
0.00
0.00
0.00
4.79
570
769
9.362539
TGAAGAAACGTGGTATAGTAATTCTTC
57.637
33.333
18.36
18.36
45.78
2.87
648
847
2.701780
CCCTGTGAGACCCGACGAG
61.702
68.421
0.00
0.00
0.00
4.18
654
853
2.657237
CGTGACCCTGTGAGACCC
59.343
66.667
0.00
0.00
0.00
4.46
762
962
2.683933
GGCCCGAGACAGGAGGAA
60.684
66.667
0.00
0.00
0.00
3.36
828
1028
4.402528
TCCGGGGACAATGGCACG
62.403
66.667
0.00
0.00
0.00
5.34
1398
1619
5.812127
TGTCAGATCAGACCGAAATATTGTG
59.188
40.000
14.91
0.00
37.73
3.33
1574
1795
2.811317
CTCGCGACAGAGCAACCC
60.811
66.667
3.71
0.00
36.85
4.11
1884
2105
2.028733
CGGGTTTGCTTGGCATTGC
61.029
57.895
0.00
0.00
38.76
3.56
1943
2164
1.519719
CTCTGCGGAAGGGAAGAGG
59.480
63.158
0.00
0.00
33.91
3.69
1952
2173
0.250234
CCATCTTCACCTCTGCGGAA
59.750
55.000
0.00
0.00
36.31
4.30
2168
2392
1.208535
TGGTTACTTGGGCGATTCGAT
59.791
47.619
10.88
0.00
0.00
3.59
2176
2400
3.060000
GGCGGTGGTTACTTGGGC
61.060
66.667
0.00
0.00
0.00
5.36
2191
2415
3.104766
CGGCATGACATGACAGGC
58.895
61.111
23.22
23.22
45.01
4.85
2208
2432
1.237285
ATCTGGAGTGTGTTTGGCGC
61.237
55.000
0.00
0.00
0.00
6.53
2246
2470
1.228862
GAACAGTTGGGGTGGCCAT
60.229
57.895
9.72
0.00
0.00
4.40
2326
2560
4.394795
CGAGAAAACAACAAGGCTTATCG
58.605
43.478
0.00
0.00
0.00
2.92
2334
2568
0.941542
TCCGGCGAGAAAACAACAAG
59.058
50.000
9.30
0.00
0.00
3.16
2337
2571
0.942252
AACTCCGGCGAGAAAACAAC
59.058
50.000
9.30
0.00
38.52
3.32
2774
3027
0.246635
CTACCACCACCGGTTCTCTG
59.753
60.000
2.97
0.00
40.67
3.35
2841
3094
3.552890
GCAAAAATCACTCCAGGGAACAC
60.553
47.826
0.00
0.00
0.00
3.32
2926
3185
6.720748
CACATCCCAATATATTCATCCACCAA
59.279
38.462
0.00
0.00
0.00
3.67
3022
3281
5.584649
TCAAAACAGAAGCGAGAAGAAAGAA
59.415
36.000
0.00
0.00
0.00
2.52
3030
3290
4.876107
AGACTTTTCAAAACAGAAGCGAGA
59.124
37.500
0.00
0.00
0.00
4.04
3035
3295
6.075205
CGCATGAAGACTTTTCAAAACAGAAG
60.075
38.462
0.00
0.00
31.55
2.85
3059
3319
5.346551
TCAACATACAAAATCTCACGTACCG
59.653
40.000
0.00
0.00
0.00
4.02
3060
3320
6.715344
TCAACATACAAAATCTCACGTACC
57.285
37.500
0.00
0.00
0.00
3.34
3068
3331
6.040842
ACTGGCAACTTCAACATACAAAATCT
59.959
34.615
0.00
0.00
37.61
2.40
3079
3342
2.223572
CCAGAACACTGGCAACTTCAAC
60.224
50.000
3.31
0.00
43.51
3.18
3158
3426
2.211532
TCTACAGAGCCCAGTACCCTA
58.788
52.381
0.00
0.00
0.00
3.53
3194
3463
6.646653
CACCCTTGCTTATTTTCTTTCTTTCC
59.353
38.462
0.00
0.00
0.00
3.13
3207
3476
1.821216
CGTTGACCACCCTTGCTTAT
58.179
50.000
0.00
0.00
0.00
1.73
3208
3477
0.887387
GCGTTGACCACCCTTGCTTA
60.887
55.000
0.00
0.00
0.00
3.09
3211
3480
2.904866
TGCGTTGACCACCCTTGC
60.905
61.111
0.00
0.00
0.00
4.01
3279
3553
1.736126
GTCTGCCCGTAAAGGTAAAGC
59.264
52.381
0.00
0.00
38.74
3.51
3416
3692
2.511659
TGCACTCTTCGTAGTGGTAGT
58.488
47.619
14.14
0.00
45.75
2.73
3438
3714
1.009389
GCAGTGTCACGAGTAGCACC
61.009
60.000
0.00
0.00
32.75
5.01
3557
3840
1.032114
GTTCCTACAGGCATGGTGGC
61.032
60.000
2.31
0.00
44.10
5.01
3591
3874
1.474077
CCACATGTAAGCCTGCTTTCC
59.526
52.381
10.01
2.33
37.47
3.13
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.