Multiple sequence alignment - TraesCS6D01G265400
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
TraesCS6D01G265400
chr6D
100.000
3974
0
0
1
3974
375014977
375018950
0.000000e+00
7339
1
TraesCS6D01G265400
chr6B
94.502
4056
106
50
1
3973
561691487
561695508
0.000000e+00
6146
2
TraesCS6D01G265400
chr6A
96.606
3477
72
22
1
3445
516407631
516411093
0.000000e+00
5725
3
TraesCS6D01G265400
chr6A
87.829
304
19
5
3687
3973
516411377
516411679
1.370000e-89
340
4
TraesCS6D01G265400
chr6A
87.027
185
6
7
3471
3640
516411088
516411269
4.050000e-45
193
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
TraesCS6D01G265400
chr6D
375014977
375018950
3973
False
7339
7339
100.000000
1
3974
1
chr6D.!!$F1
3973
1
TraesCS6D01G265400
chr6B
561691487
561695508
4021
False
6146
6146
94.502000
1
3973
1
chr6B.!!$F1
3972
2
TraesCS6D01G265400
chr6A
516407631
516411679
4048
False
2086
5725
90.487333
1
3973
3
chr6A.!!$F1
3972
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
211
212
0.744874
GCTGATCTAGGTGGCACGTA
59.255
55.000
18.03
18.03
0.0
3.57
F
428
429
6.983307
CCCAAATATGTTTGTTGTCTGTTTGA
59.017
34.615
13.13
0.00
42.5
2.69
F
1202
1224
1.120530
CCATACTGCCGTCCTAAGGT
58.879
55.000
0.00
0.00
0.0
3.50
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1040
1062
0.252479
AGCAGGAGCCATCACAAGAG
59.748
55.0
0.00
0.0
43.56
2.85
R
1902
1924
2.113860
TGCCAGCCAAGAACAGTATC
57.886
50.0
0.00
0.0
0.00
2.24
R
3171
3203
0.883153
AGAGCGCATTTGCATCAACA
59.117
45.0
11.47
0.0
42.21
3.33
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
26
27
1.743995
GTTTACCCGCTCGCATGGT
60.744
57.895
0.00
5.58
36.15
3.55
148
149
2.744768
AAGCAGCTCCAGTGCCACTC
62.745
60.000
0.00
0.00
42.24
3.51
211
212
0.744874
GCTGATCTAGGTGGCACGTA
59.255
55.000
18.03
18.03
0.00
3.57
428
429
6.983307
CCCAAATATGTTTGTTGTCTGTTTGA
59.017
34.615
13.13
0.00
42.50
2.69
475
479
9.673454
GTAAAAGAACGACTATGAATTGGTTTT
57.327
29.630
0.00
0.00
0.00
2.43
697
715
9.454859
CTTATTTTACTCTTTGATCCTCCTTGT
57.545
33.333
0.00
0.00
0.00
3.16
1040
1062
2.072298
CTCTGCTTTGCTAGTGGTGTC
58.928
52.381
0.00
0.00
0.00
3.67
1202
1224
1.120530
CCATACTGCCGTCCTAAGGT
58.879
55.000
0.00
0.00
0.00
3.50
1280
1302
2.118313
AATTCCCCTTACCGTTTCCG
57.882
50.000
0.00
0.00
0.00
4.30
1782
1804
2.103941
CAGGGAGAAGGAGCAGATTACC
59.896
54.545
0.00
0.00
0.00
2.85
1902
1924
6.313658
TCTCAATTATGAACTCGTTGATGGTG
59.686
38.462
0.00
0.00
34.49
4.17
2706
2728
3.182967
CGCTGAGGTATCTGTTGTTCTC
58.817
50.000
0.00
0.00
0.00
2.87
2809
2831
6.602406
TGTGTTCCTCTACTCTATCAACTACC
59.398
42.308
0.00
0.00
0.00
3.18
3136
3168
8.718102
TGTTCTAGTAGATGTGATTTTAAGCC
57.282
34.615
0.00
0.00
0.00
4.35
3171
3203
4.581824
TCTCTTCTCTTTGCTGCAACATTT
59.418
37.500
15.72
0.00
0.00
2.32
3192
3224
2.487372
TGTTGATGCAAATGCGCTCTTA
59.513
40.909
9.73
0.00
45.83
2.10
3199
3231
4.808558
TGCAAATGCGCTCTTAAAAATCT
58.191
34.783
9.73
0.00
45.83
2.40
3211
3243
7.229530
GCTCTTAAAAATCTTGAATTTTGCCG
58.770
34.615
6.65
0.00
32.23
5.69
3212
3244
7.095649
GCTCTTAAAAATCTTGAATTTTGCCGT
60.096
33.333
6.65
0.00
32.23
5.68
3215
3247
6.676237
AAAAATCTTGAATTTTGCCGTGTT
57.324
29.167
0.00
0.00
32.23
3.32
3216
3248
7.778470
AAAAATCTTGAATTTTGCCGTGTTA
57.222
28.000
0.00
0.00
32.23
2.41
3220
3252
5.837437
TCTTGAATTTTGCCGTGTTATTGT
58.163
33.333
0.00
0.00
0.00
2.71
3244
3276
1.774110
TGTGCAACTGTTGGTTCCAT
58.226
45.000
21.01
0.00
38.04
3.41
3275
3307
6.601332
TCTTTTCCAAGATAGGTTTGTCACT
58.399
36.000
0.00
0.00
33.80
3.41
3338
3398
3.186409
TGTGCTTTTCTGACTTGCGTATC
59.814
43.478
0.00
0.00
0.00
2.24
3410
3470
7.592938
TGGTAATTCATAAGTGAAGTGCTTTG
58.407
34.615
6.64
0.00
46.75
2.77
3517
3577
0.957888
GGTTTGCTCCTCTGTCCAGC
60.958
60.000
0.00
0.00
0.00
4.85
3518
3578
0.036022
GTTTGCTCCTCTGTCCAGCT
59.964
55.000
0.00
0.00
34.03
4.24
3577
3637
8.253810
TGTAAGAGACAGTTCCATTATTCTGAG
58.746
37.037
0.00
0.00
32.86
3.35
3578
3638
6.865834
AGAGACAGTTCCATTATTCTGAGT
57.134
37.500
0.00
0.00
0.00
3.41
3580
3640
7.327214
AGAGACAGTTCCATTATTCTGAGTTC
58.673
38.462
0.00
0.00
0.00
3.01
3610
3676
3.799035
CTTTCGCATATCGCACCATAAC
58.201
45.455
0.00
0.00
42.60
1.89
3630
3704
1.556911
CTTCTATGCCCATATCGCCCT
59.443
52.381
0.00
0.00
0.00
5.19
3635
3709
0.033601
TGCCCATATCGCCCTGTTTT
60.034
50.000
0.00
0.00
0.00
2.43
3662
3736
7.517614
TTTTTCTTTGCCTTTTGTTTTCCTT
57.482
28.000
0.00
0.00
0.00
3.36
3663
3737
7.517614
TTTTCTTTGCCTTTTGTTTTCCTTT
57.482
28.000
0.00
0.00
0.00
3.11
3676
3750
2.358322
TTCCTTTCCCTTTTCGCTGT
57.642
45.000
0.00
0.00
0.00
4.40
3693
3767
4.215185
TCGCTGTTGCATAATGTTCAAAGA
59.785
37.500
0.00
0.00
39.64
2.52
3697
3771
7.253422
GCTGTTGCATAATGTTCAAAGATAGT
58.747
34.615
0.00
0.00
39.41
2.12
3712
3869
7.603651
TCAAAGATAGTTCTGAGAACACTACC
58.396
38.462
25.45
10.61
30.72
3.18
3786
3955
3.554934
TCTCAGTGCAATCTTTGTTGGT
58.445
40.909
0.00
0.00
0.00
3.67
3854
4027
0.472471
ACCCGTGACAGTGAAATGGT
59.528
50.000
0.00
0.00
0.00
3.55
3866
4039
5.426509
ACAGTGAAATGGTGGATCTATCTCA
59.573
40.000
0.00
0.00
0.00
3.27
3890
4063
5.982465
TTTGCCTTACAAAAAGAACATGC
57.018
34.783
0.00
0.00
45.22
4.06
3901
4074
0.608130
AGAACATGCGAGGTGCTGTA
59.392
50.000
0.00
0.00
46.63
2.74
3967
4143
1.066143
GTGGCTCCAAGGAGATTTCGA
60.066
52.381
19.99
0.00
44.53
3.71
3973
4149
4.256920
CTCCAAGGAGATTTCGAACACAT
58.743
43.478
10.66
0.00
44.53
3.21
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
37
38
2.027314
CTCGGGCGAGCAGATCTG
59.973
66.667
18.84
18.84
35.31
2.90
148
149
6.835914
ACTAAATCAGCGACAAATCTTGAAG
58.164
36.000
0.00
0.00
0.00
3.02
211
212
4.164988
AGTTAGAAGCATGGATGGCTAAGT
59.835
41.667
0.00
0.00
41.66
2.24
475
479
7.836685
TGGCCAAAGGTGTTAGATGAAATAATA
59.163
33.333
0.61
0.00
0.00
0.98
489
493
1.145738
AGAATGTCTGGCCAAAGGTGT
59.854
47.619
7.01
0.00
0.00
4.16
697
715
0.474184
GCCCAGGATAAGCTAAGCCA
59.526
55.000
0.00
0.00
0.00
4.75
1040
1062
0.252479
AGCAGGAGCCATCACAAGAG
59.748
55.000
0.00
0.00
43.56
2.85
1202
1224
4.908601
TCAGCACTCTTCTTTATCCCAA
57.091
40.909
0.00
0.00
0.00
4.12
1280
1302
4.093998
AGAGCGATTCATTGACATTGACAC
59.906
41.667
0.00
0.00
0.00
3.67
1902
1924
2.113860
TGCCAGCCAAGAACAGTATC
57.886
50.000
0.00
0.00
0.00
2.24
2706
2728
1.325640
GCACAGAGATGCATGTACGTG
59.674
52.381
16.55
16.55
45.39
4.49
2809
2831
3.672808
AGCTTCTGAGATCAAACACCAG
58.327
45.455
0.00
0.00
0.00
4.00
3146
3178
3.947196
TGTTGCAGCAAAGAGAAGAGAAA
59.053
39.130
10.11
0.00
0.00
2.52
3171
3203
0.883153
AGAGCGCATTTGCATCAACA
59.117
45.000
11.47
0.00
42.21
3.33
3186
3218
7.095649
ACGGCAAAATTCAAGATTTTTAAGAGC
60.096
33.333
3.28
3.44
0.00
4.09
3192
3224
6.676237
AACACGGCAAAATTCAAGATTTTT
57.324
29.167
0.00
0.00
0.00
1.94
3199
3231
4.210120
GCACAATAACACGGCAAAATTCAA
59.790
37.500
0.00
0.00
0.00
2.69
3250
3282
7.013274
CAGTGACAAACCTATCTTGGAAAAGAA
59.987
37.037
0.00
0.00
31.77
2.52
3275
3307
9.851686
ACACTGCATAGATAAAATAAATCTCCA
57.148
29.630
0.00
0.00
35.36
3.86
3338
3398
3.877559
TGACATACAGAATCTTGGGCAG
58.122
45.455
0.00
0.00
0.00
4.85
3410
3470
8.094798
TGTCAGTCAACAAGGAATAATAACAC
57.905
34.615
0.00
0.00
0.00
3.32
3555
3615
6.865834
ACTCAGAATAATGGAACTGTCTCT
57.134
37.500
0.00
0.00
0.00
3.10
3556
3616
7.064016
GTGAACTCAGAATAATGGAACTGTCTC
59.936
40.741
0.00
0.00
0.00
3.36
3610
3676
1.556911
AGGGCGATATGGGCATAGAAG
59.443
52.381
13.23
0.00
0.00
2.85
3642
3716
5.182487
GGAAAGGAAAACAAAAGGCAAAGA
58.818
37.500
0.00
0.00
0.00
2.52
3643
3717
4.335315
GGGAAAGGAAAACAAAAGGCAAAG
59.665
41.667
0.00
0.00
0.00
2.77
3644
3718
4.018870
AGGGAAAGGAAAACAAAAGGCAAA
60.019
37.500
0.00
0.00
0.00
3.68
3645
3719
3.521531
AGGGAAAGGAAAACAAAAGGCAA
59.478
39.130
0.00
0.00
0.00
4.52
3646
3720
3.111484
AGGGAAAGGAAAACAAAAGGCA
58.889
40.909
0.00
0.00
0.00
4.75
3647
3721
3.838244
AGGGAAAGGAAAACAAAAGGC
57.162
42.857
0.00
0.00
0.00
4.35
3648
3722
5.293324
CGAAAAGGGAAAGGAAAACAAAAGG
59.707
40.000
0.00
0.00
0.00
3.11
3649
3723
5.220586
GCGAAAAGGGAAAGGAAAACAAAAG
60.221
40.000
0.00
0.00
0.00
2.27
3650
3724
4.632251
GCGAAAAGGGAAAGGAAAACAAAA
59.368
37.500
0.00
0.00
0.00
2.44
3651
3725
4.081365
AGCGAAAAGGGAAAGGAAAACAAA
60.081
37.500
0.00
0.00
0.00
2.83
3652
3726
3.449377
AGCGAAAAGGGAAAGGAAAACAA
59.551
39.130
0.00
0.00
0.00
2.83
3653
3727
3.028130
AGCGAAAAGGGAAAGGAAAACA
58.972
40.909
0.00
0.00
0.00
2.83
3654
3728
3.181479
ACAGCGAAAAGGGAAAGGAAAAC
60.181
43.478
0.00
0.00
0.00
2.43
3655
3729
3.028130
ACAGCGAAAAGGGAAAGGAAAA
58.972
40.909
0.00
0.00
0.00
2.29
3656
3730
2.661718
ACAGCGAAAAGGGAAAGGAAA
58.338
42.857
0.00
0.00
0.00
3.13
3657
3731
2.358322
ACAGCGAAAAGGGAAAGGAA
57.642
45.000
0.00
0.00
0.00
3.36
3658
3732
1.953686
CAACAGCGAAAAGGGAAAGGA
59.046
47.619
0.00
0.00
0.00
3.36
3659
3733
1.602920
GCAACAGCGAAAAGGGAAAGG
60.603
52.381
0.00
0.00
0.00
3.11
3660
3734
1.066908
TGCAACAGCGAAAAGGGAAAG
59.933
47.619
0.00
0.00
0.00
2.62
3661
3735
1.107114
TGCAACAGCGAAAAGGGAAA
58.893
45.000
0.00
0.00
0.00
3.13
3662
3736
1.327303
ATGCAACAGCGAAAAGGGAA
58.673
45.000
0.00
0.00
0.00
3.97
3663
3737
2.192664
TATGCAACAGCGAAAAGGGA
57.807
45.000
0.00
0.00
0.00
4.20
3676
3750
9.230122
TCAGAACTATCTTTGAACATTATGCAA
57.770
29.630
0.00
0.00
32.03
4.08
3693
3767
5.334421
ACTGGGTAGTGTTCTCAGAACTAT
58.666
41.667
18.49
9.34
35.34
2.12
3697
3771
3.830755
GGTACTGGGTAGTGTTCTCAGAA
59.169
47.826
0.00
0.00
37.78
3.02
3712
3869
5.527214
TCAGATTTCATTAATGCGGTACTGG
59.473
40.000
10.76
0.00
0.00
4.00
3807
3976
7.817962
AGCACAAATGGTTTACTAGTACTACTG
59.182
37.037
0.91
1.86
30.39
2.74
3811
3980
7.605309
GGTAAGCACAAATGGTTTACTAGTACT
59.395
37.037
0.91
0.00
44.10
2.73
3854
4027
6.899089
TGTAAGGCAAAATGAGATAGATCCA
58.101
36.000
0.00
0.00
0.00
3.41
3909
4082
8.146053
TCCCTCTATCTCAAAATGTAAAGACA
57.854
34.615
0.00
0.00
40.72
3.41
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.