Multiple sequence alignment - TraesCS1D01G149300
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
TraesCS1D01G149300
chr1D
100.000
3060
0
0
1
3060
205479587
205482646
0
5651
1
TraesCS1D01G149300
chr1A
94.835
1665
64
10
1
1651
262013317
262014973
0
2579
2
TraesCS1D01G149300
chr1A
93.853
1399
64
9
1674
3060
262842219
262840831
0
2087
3
TraesCS1D01G149300
chr1B
91.958
1517
73
18
597
2083
301255721
301257218
0
2080
4
TraesCS1D01G149300
chr1B
94.515
948
47
4
2114
3060
301257213
301258156
0
1458
5
TraesCS1D01G149300
chr1B
95.567
609
20
3
1
605
301253530
301254135
0
968
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
TraesCS1D01G149300
chr1D
205479587
205482646
3059
False
5651
5651
100.000000
1
3060
1
chr1D.!!$F1
3059
1
TraesCS1D01G149300
chr1A
262013317
262014973
1656
False
2579
2579
94.835000
1
1651
1
chr1A.!!$F1
1650
2
TraesCS1D01G149300
chr1A
262840831
262842219
1388
True
2087
2087
93.853000
1674
3060
1
chr1A.!!$R1
1386
3
TraesCS1D01G149300
chr1B
301253530
301258156
4626
False
1502
2080
94.013333
1
3060
3
chr1B.!!$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
940
2541
0.247736
CCAGTCCAGTACAGCACTCC
59.752
60.0
0.0
0.0
34.26
3.85
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2738
4381
0.473326
GAGGAGATTGCAGAGGCCAT
59.527
55.0
5.01
0.0
40.13
4.4
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
352
356
1.469335
GGTGGTCGTCCTCCTTGTCA
61.469
60.000
11.86
0.00
42.33
3.58
363
367
0.615331
TCCTTGTCATCTCTGTGGCC
59.385
55.000
0.00
0.00
0.00
5.36
370
374
0.323178
CATCTCTGTGGCCCAGCTTT
60.323
55.000
14.49
1.58
41.25
3.51
437
441
1.202348
GGCCAACATGTTAACTCCAGC
59.798
52.381
11.53
5.77
0.00
4.85
474
479
4.724074
TTCCTGCCAAGAAATGCTAATG
57.276
40.909
0.00
0.00
0.00
1.90
553
558
4.643387
ACTCCGTTGGGGCTGCAC
62.643
66.667
0.50
0.00
34.94
4.57
570
575
1.395608
GCACCACGCTAATTCGCTTAA
59.604
47.619
0.08
0.00
37.77
1.85
571
576
2.031683
GCACCACGCTAATTCGCTTAAT
59.968
45.455
0.08
0.00
37.77
1.40
572
577
3.246699
GCACCACGCTAATTCGCTTAATA
59.753
43.478
0.08
0.00
37.77
0.98
577
582
5.339611
CCACGCTAATTCGCTTAATAATTGC
59.660
40.000
0.08
0.00
0.00
3.56
610
2211
4.085302
GCTGCTGCGTCTGTAGAG
57.915
61.111
0.00
0.00
0.00
2.43
619
2220
5.748630
TGCTGCGTCTGTAGAGTAAAATATG
59.251
40.000
0.00
0.00
0.00
1.78
641
2242
5.076182
TGAACACATTCCTGCCAAGAAATA
58.924
37.500
0.00
0.00
33.49
1.40
652
2253
8.548880
TCCTGCCAAGAAATACTAATAGTAGT
57.451
34.615
8.10
8.10
43.27
2.73
653
2254
9.650714
TCCTGCCAAGAAATACTAATAGTAGTA
57.349
33.333
12.13
12.13
44.93
1.82
668
2269
7.527568
AATAGTAGTACTATCTTGTGCCCTC
57.472
40.000
20.61
0.00
40.32
4.30
703
2304
8.838365
GCATCAGATTGATCTCTTAAGATTTGT
58.162
33.333
5.44
0.00
42.46
2.83
815
2416
2.500229
CCTTTGGCAAGAAGACGGTAA
58.500
47.619
0.00
0.00
30.57
2.85
816
2417
3.081804
CCTTTGGCAAGAAGACGGTAAT
58.918
45.455
0.00
0.00
30.57
1.89
913
2514
2.519771
TTTGGGCGGACTCTAGTCTA
57.480
50.000
9.84
0.00
44.20
2.59
926
2527
6.462067
GGACTCTAGTCTAGTCTAGTCCAGTC
60.462
50.000
26.78
22.83
44.20
3.51
927
2528
5.364735
ACTCTAGTCTAGTCTAGTCCAGTCC
59.635
48.000
19.35
0.00
38.66
3.85
928
2529
5.278873
TCTAGTCTAGTCTAGTCCAGTCCA
58.721
45.833
19.35
0.39
38.66
4.02
929
2530
4.497291
AGTCTAGTCTAGTCCAGTCCAG
57.503
50.000
6.77
0.00
0.00
3.86
930
2531
3.847780
AGTCTAGTCTAGTCCAGTCCAGT
59.152
47.826
6.77
0.00
0.00
4.00
940
2541
0.247736
CCAGTCCAGTACAGCACTCC
59.752
60.000
0.00
0.00
34.26
3.85
1005
2611
1.615124
TTGGGGAGGCGGAATGAGA
60.615
57.895
0.00
0.00
0.00
3.27
1638
3262
0.529378
GCCCTCCATTTGCAGAGTTG
59.471
55.000
0.61
0.00
0.00
3.16
1870
3509
1.260033
CTCTCGCCGAATTCATTCTGC
59.740
52.381
6.22
6.00
41.63
4.26
1871
3510
1.009078
CTCGCCGAATTCATTCTGCA
58.991
50.000
14.10
0.00
44.11
4.41
1874
3513
1.334419
CGCCGAATTCATTCTGCATCC
60.334
52.381
14.10
0.00
44.11
3.51
1883
3522
2.677836
TCATTCTGCATCCAGTAAACGC
59.322
45.455
0.00
0.00
40.09
4.84
1884
3523
2.177394
TTCTGCATCCAGTAAACGCA
57.823
45.000
0.00
0.00
40.09
5.24
1885
3524
1.438651
TCTGCATCCAGTAAACGCAC
58.561
50.000
0.00
0.00
40.09
5.34
1886
3525
0.095245
CTGCATCCAGTAAACGCACG
59.905
55.000
0.00
0.00
34.31
5.34
1887
3526
1.295357
TGCATCCAGTAAACGCACGG
61.295
55.000
0.00
0.00
0.00
4.94
1888
3527
1.423845
CATCCAGTAAACGCACGGC
59.576
57.895
0.00
0.00
0.00
5.68
1914
3553
0.663688
CCATGAGCTGAGCTGATTGC
59.336
55.000
13.71
0.00
39.88
3.56
1924
3566
1.969862
GCTGATTGCTGCCTTTGGT
59.030
52.632
0.00
0.00
38.95
3.67
2163
3805
6.339587
TGTAAAATTCCATGAAACCAGTCC
57.660
37.500
0.00
0.00
0.00
3.85
2179
3821
7.839680
AACCAGTCCAGTTTATTCAAATTCT
57.160
32.000
0.00
0.00
0.00
2.40
2187
3829
8.092068
TCCAGTTTATTCAAATTCTAGACGACA
58.908
33.333
0.00
0.00
0.00
4.35
2224
3866
9.941325
TTAAAATGTTCCTGCAATTCATTATGT
57.059
25.926
0.00
0.00
0.00
2.29
2313
3955
9.474920
TCATGTCAAAAATTTCCAAGTACATTC
57.525
29.630
0.00
0.00
0.00
2.67
2361
4003
2.124901
TTTACGGCGCCTCATGGG
60.125
61.111
26.68
10.34
38.36
4.00
2369
4011
0.663153
GCGCCTCATGGGAAACATAC
59.337
55.000
0.00
0.00
37.84
2.39
2414
4056
4.863491
ACTGTTACAATGCTTTCTTGCTG
58.137
39.130
0.00
0.00
0.00
4.41
2486
4128
6.529220
AGCTTTACTGATGTTGAAGAGTTCT
58.471
36.000
0.00
0.00
0.00
3.01
2516
4158
2.690881
TCAGTATGCCCCGGCCTT
60.691
61.111
0.00
0.00
41.09
4.35
2517
4159
2.275418
CAGTATGCCCCGGCCTTT
59.725
61.111
0.00
0.00
41.09
3.11
2518
4160
2.120909
CAGTATGCCCCGGCCTTTG
61.121
63.158
0.00
0.00
41.09
2.77
2616
4259
4.392940
GGCATTCAGACCAGCAAGTATAT
58.607
43.478
0.00
0.00
0.00
0.86
2695
4338
2.169789
CGCATCCTGGCTTGAGTCG
61.170
63.158
0.00
0.00
0.00
4.18
2738
4381
0.719015
AGACTCAGAGGATGGGGGAA
59.281
55.000
1.53
0.00
31.46
3.97
2803
4446
0.686789
TGAAGTGCCTAGCTTCAGCA
59.313
50.000
7.07
0.00
44.90
4.41
3015
4658
3.046870
GTGGCATTTCCGCACCAA
58.953
55.556
0.00
0.00
44.77
3.67
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
117
118
3.624410
CGATGGAGAAATGAGCATTGTCA
59.376
43.478
0.00
0.00
0.00
3.58
363
367
3.760151
TCCAGATGATGAACAAAAGCTGG
59.240
43.478
14.15
14.15
38.13
4.85
437
441
3.120060
GCAGGAATGTTACAAGTGCAGAG
60.120
47.826
0.00
0.00
0.00
3.35
474
479
3.669536
AGACACTAGAAAGGAGCAAAGC
58.330
45.455
0.00
0.00
0.00
3.51
553
558
5.339611
GCAATTATTAAGCGAATTAGCGTGG
59.660
40.000
9.09
0.00
43.00
4.94
577
582
1.009675
AGCGTTGCGTGCTTTCAAG
60.010
52.632
0.00
0.00
40.48
3.02
610
2211
6.862209
TGGCAGGAATGTGTTCATATTTTAC
58.138
36.000
0.00
0.00
36.01
2.01
619
2220
4.525912
ATTTCTTGGCAGGAATGTGTTC
57.474
40.909
13.13
0.00
25.39
3.18
641
2242
8.226112
AGGGCACAAGATAGTACTACTATTAGT
58.774
37.037
4.31
1.30
41.21
2.24
651
2252
1.854227
GCGAGGGCACAAGATAGTAC
58.146
55.000
0.00
0.00
39.62
2.73
652
2253
0.384309
CGCGAGGGCACAAGATAGTA
59.616
55.000
0.00
0.00
39.92
1.82
653
2254
1.141881
CGCGAGGGCACAAGATAGT
59.858
57.895
0.00
0.00
39.92
2.12
668
2269
1.135717
TCAATCTGATGCAAAACCGCG
60.136
47.619
0.00
0.00
33.35
6.46
779
2380
2.737252
CAAAGGCCTGTTCTTACGAGTC
59.263
50.000
5.69
0.00
0.00
3.36
913
2514
3.874584
GCTGTACTGGACTGGACTAGACT
60.875
52.174
0.00
0.00
0.00
3.24
926
2527
2.729194
AGAGTAGGAGTGCTGTACTGG
58.271
52.381
2.28
0.00
40.53
4.00
927
2528
3.310227
CGTAGAGTAGGAGTGCTGTACTG
59.690
52.174
2.28
0.00
40.53
2.74
928
2529
3.197333
TCGTAGAGTAGGAGTGCTGTACT
59.803
47.826
0.00
0.00
44.02
2.73
929
2530
3.529533
TCGTAGAGTAGGAGTGCTGTAC
58.470
50.000
0.00
0.00
33.40
2.90
930
2531
3.900966
TCGTAGAGTAGGAGTGCTGTA
57.099
47.619
0.00
0.00
0.00
2.74
1005
2611
5.176592
GGGTACGTCTTCTTATTCTGCTTT
58.823
41.667
0.00
0.00
0.00
3.51
1065
2671
1.429463
GCTTGACGAGGAACGATTGT
58.571
50.000
0.00
0.00
45.77
2.71
1186
2801
2.203153
CCGGCGGGTAGGGATTTG
60.203
66.667
20.56
0.00
0.00
2.32
1290
2911
3.094572
AGAACAAGGGCAGATTGATTGG
58.905
45.455
3.73
0.00
0.00
3.16
1296
2917
1.428912
TGGGAAGAACAAGGGCAGATT
59.571
47.619
0.00
0.00
0.00
2.40
1588
3212
4.083862
GGGCTCTTCCGCTTCCGT
62.084
66.667
0.00
0.00
34.94
4.69
1638
3262
6.254589
CACAAACTAGTAGTAGCATGAAGAGC
59.745
42.308
2.50
0.00
0.00
4.09
1870
3509
1.423845
GCCGTGCGTTTACTGGATG
59.576
57.895
0.00
0.00
0.00
3.51
1871
3510
3.884900
GCCGTGCGTTTACTGGAT
58.115
55.556
0.00
0.00
0.00
3.41
1914
3553
2.341176
GCAGGCAACCAAAGGCAG
59.659
61.111
0.00
0.00
37.17
4.85
1918
3560
1.662044
GTCTGGCAGGCAACCAAAG
59.338
57.895
15.50
0.00
36.56
2.77
2108
3750
1.109323
ACTTGCAAACTGGGGTCTGC
61.109
55.000
0.00
0.00
39.64
4.26
2179
3821
5.503662
TTAACGCAGGATAATGTCGTCTA
57.496
39.130
0.00
0.00
33.80
2.59
2187
3829
6.680378
GCAGGAACATTTTAACGCAGGATAAT
60.680
38.462
0.00
0.00
0.00
1.28
2224
3866
6.403049
TCAACTCTGCGTTCCATCTTATTTA
58.597
36.000
0.00
0.00
32.27
1.40
2233
3875
2.354510
CTGTTTTCAACTCTGCGTTCCA
59.645
45.455
0.00
0.00
32.27
3.53
2253
3895
2.787994
CCATTCTCCAAAGTGACTGCT
58.212
47.619
0.00
0.00
0.00
4.24
2256
3898
2.613977
CGAGCCATTCTCCAAAGTGACT
60.614
50.000
0.00
0.00
38.62
3.41
2259
3901
1.813513
ACGAGCCATTCTCCAAAGTG
58.186
50.000
0.00
0.00
38.62
3.16
2260
3902
3.260884
TCTTACGAGCCATTCTCCAAAGT
59.739
43.478
0.00
0.00
38.62
2.66
2312
3954
4.581077
CATCTGATTGATGGTCGAGAGA
57.419
45.455
0.00
0.00
46.55
3.10
2369
4011
9.741168
CAGTCAACAATTTATGTACTTTACGAG
57.259
33.333
0.00
0.00
42.99
4.18
2414
4056
5.255916
AGGGATAGGGGGTCTAGTAATCTAC
59.744
48.000
0.00
0.00
0.00
2.59
2486
4128
1.204704
CATACTGACTGCGTCCCTGAA
59.795
52.381
6.30
0.00
0.00
3.02
2502
4144
2.833121
CCAAAGGCCGGGGCATAC
60.833
66.667
23.67
0.00
44.11
2.39
2553
4195
0.698238
AGGATAACCAAGCACAGGCA
59.302
50.000
0.00
0.00
39.87
4.75
2599
4241
7.665559
AGAACAAAAATATACTTGCTGGTCTGA
59.334
33.333
0.00
0.00
0.00
3.27
2616
4259
9.650539
TTGATCATTTTCAGAACAGAACAAAAA
57.349
25.926
0.00
0.00
0.00
1.94
2695
4338
0.883833
CACCAAAGCCTGACCATGAC
59.116
55.000
0.00
0.00
0.00
3.06
2738
4381
0.473326
GAGGAGATTGCAGAGGCCAT
59.527
55.000
5.01
0.00
40.13
4.40
2803
4446
4.387026
TCCAGAGTGGGTTGATTTTGAT
57.613
40.909
0.00
0.00
38.32
2.57
3009
4652
2.098117
GCTATGGTGTGAATCTTGGTGC
59.902
50.000
0.00
0.00
0.00
5.01
3015
4658
4.785346
AGAATGGCTATGGTGTGAATCT
57.215
40.909
0.00
0.00
0.00
2.40
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.