Multiple sequence alignment - TraesCS6D01G196100
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
TraesCS6D01G196100
chr6D
100.000
4086
0
0
1
4086
272110690
272106605
0.000000e+00
7546.0
1
TraesCS6D01G196100
chr6B
95.237
3653
96
32
1
3620
433273915
433270308
0.000000e+00
5710.0
2
TraesCS6D01G196100
chr6A
94.681
2369
68
19
587
2924
388211473
388209132
0.000000e+00
3624.0
3
TraesCS6D01G196100
chr6A
93.531
742
39
6
2927
3664
388208873
388208137
0.000000e+00
1096.0
4
TraesCS6D01G196100
chr6A
95.691
557
17
1
1
550
388212007
388211451
0.000000e+00
889.0
5
TraesCS6D01G196100
chr6A
100.000
31
0
0
3400
3430
91906104
91906134
1.590000e-04
58.4
6
TraesCS6D01G196100
chr7B
97.010
1739
25
13
1
1727
438422426
438420703
0.000000e+00
2898.0
7
TraesCS6D01G196100
chr7B
93.166
1156
29
19
1718
2840
438399764
438398626
0.000000e+00
1652.0
8
TraesCS6D01G196100
chr7B
89.455
825
41
13
2832
3653
438396804
438396023
0.000000e+00
1000.0
9
TraesCS6D01G196100
chr2A
79.379
354
49
20
2387
2727
679993204
679992862
1.140000e-55
228.0
10
TraesCS6D01G196100
chr2A
85.124
121
16
2
1925
2043
679993950
679993830
5.550000e-24
122.0
11
TraesCS6D01G196100
chr2A
73.502
317
67
14
3777
4085
214244583
214244890
2.010000e-18
104.0
12
TraesCS6D01G196100
chr3B
80.364
275
39
12
3811
4084
766380266
766380526
1.160000e-45
195.0
13
TraesCS6D01G196100
chr2D
92.391
92
7
0
1952
2043
537459936
537459845
9.220000e-27
132.0
14
TraesCS6D01G196100
chr2B
86.179
123
13
4
1925
2043
640104695
640104573
3.310000e-26
130.0
15
TraesCS6D01G196100
chr3A
88.421
95
9
2
3987
4080
552610419
552610326
3.340000e-21
113.0
16
TraesCS6D01G196100
chr3A
89.873
79
7
1
4006
4084
711074010
711073933
2.600000e-17
100.0
17
TraesCS6D01G196100
chr4A
87.368
95
10
2
3987
4080
467156760
467156853
1.550000e-19
108.0
18
TraesCS6D01G196100
chr5A
87.778
90
9
2
3992
4080
688262962
688262874
2.010000e-18
104.0
19
TraesCS6D01G196100
chr4D
85.000
100
12
3
3987
4084
10763116
10763018
9.350000e-17
99.0
20
TraesCS6D01G196100
chr4B
85.567
97
11
3
3985
4080
643624635
643624541
9.350000e-17
99.0
21
TraesCS6D01G196100
chr1B
83.505
97
12
4
3990
4084
653789229
653789135
2.020000e-13
87.9
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
TraesCS6D01G196100
chr6D
272106605
272110690
4085
True
7546.000000
7546
100.000000
1
4086
1
chr6D.!!$R1
4085
1
TraesCS6D01G196100
chr6B
433270308
433273915
3607
True
5710.000000
5710
95.237000
1
3620
1
chr6B.!!$R1
3619
2
TraesCS6D01G196100
chr6A
388208137
388212007
3870
True
1869.666667
3624
94.634333
1
3664
3
chr6A.!!$R1
3663
3
TraesCS6D01G196100
chr7B
438420703
438422426
1723
True
2898.000000
2898
97.010000
1
1727
1
chr7B.!!$R1
1726
4
TraesCS6D01G196100
chr7B
438396023
438399764
3741
True
1326.000000
1652
91.310500
1718
3653
2
chr7B.!!$R2
1935
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
378
386
2.705658
TCGGGATTTACATCTGGCAGAT
59.294
45.455
24.01
24.01
34.74
2.90
F
1450
1460
2.222976
CGCATGTCTCAGCAATCTGTTC
60.223
50.000
0.00
0.00
41.10
3.18
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1450
1460
1.227999
ACAGAAATGGTGGTGACGCG
61.228
55.0
3.53
3.53
43.50
6.01
R
3433
5584
0.618968
ATTCTTGGTCGAGCCTCCCT
60.619
55.0
12.85
0.00
38.35
4.20
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
378
386
2.705658
TCGGGATTTACATCTGGCAGAT
59.294
45.455
24.01
24.01
34.74
2.90
1450
1460
2.222976
CGCATGTCTCAGCAATCTGTTC
60.223
50.000
0.00
0.00
41.10
3.18
1531
1546
0.598065
GCAATTGCTTCCACGGACTT
59.402
50.000
23.21
0.00
38.21
3.01
1532
1547
1.810151
GCAATTGCTTCCACGGACTTA
59.190
47.619
23.21
0.00
38.21
2.24
1533
1548
2.414161
GCAATTGCTTCCACGGACTTAC
60.414
50.000
23.21
0.00
38.21
2.34
1534
1549
3.074412
CAATTGCTTCCACGGACTTACT
58.926
45.455
0.00
0.00
0.00
2.24
1535
1550
4.250464
CAATTGCTTCCACGGACTTACTA
58.750
43.478
0.00
0.00
0.00
1.82
1536
1551
3.308438
TTGCTTCCACGGACTTACTAC
57.692
47.619
0.00
0.00
0.00
2.73
2058
2073
4.062293
TCAAGGTTAGTTTGATGACCGTG
58.938
43.478
0.00
0.00
41.18
4.94
2060
2075
3.660865
AGGTTAGTTTGATGACCGTGTC
58.339
45.455
0.00
0.00
37.26
3.67
2077
2094
5.178067
ACCGTGTCCGTTTAGTAAATCTTTG
59.822
40.000
0.00
0.00
0.00
2.77
2142
2159
4.569943
TCCAGACATCTGAAAAGTGCTAC
58.430
43.478
10.55
0.00
46.59
3.58
2187
2223
1.765314
AGTTTGTCCTGCACTGTCTCT
59.235
47.619
0.00
0.00
0.00
3.10
2288
2324
6.205464
GGCGGAATATTCTTTGATGATCTCAA
59.795
38.462
14.95
0.00
42.15
3.02
2334
2370
2.186076
GACTTCGCGACAGGTATCAAG
58.814
52.381
9.15
2.05
0.00
3.02
2356
2397
5.073428
AGAAACTCTGAATTTGGGTCCTTC
58.927
41.667
0.00
0.00
0.00
3.46
2720
2775
7.441458
GGTGGGAGTATGATCATGTAAGTTAAC
59.559
40.741
18.72
5.71
0.00
2.01
2779
2837
3.663025
ACATTTTGATCCCCGCAAAAAG
58.337
40.909
0.00
0.00
45.14
2.27
2846
4734
5.108254
GGCGCTGCAATATTTAAAATCTTCG
60.108
40.000
7.64
0.00
0.00
3.79
2913
4801
8.020819
TGGAAAGATTCATTTGACACGTTAATC
58.979
33.333
0.00
0.00
0.00
1.75
2998
5143
6.042143
CAGTGGCATTTTGTCAAGTTTACTT
58.958
36.000
0.00
0.00
31.67
2.24
3011
5156
7.066043
TGTCAAGTTTACTTACGACCATTTGTT
59.934
33.333
9.35
0.00
34.28
2.83
3150
5295
7.860872
CCGCTAACTTTATTTTGAAGTGTCTTT
59.139
33.333
0.00
0.00
37.41
2.52
3226
5371
3.299503
AGCTTGGAAATCTGTGTTTGGT
58.700
40.909
0.00
0.00
0.00
3.67
3249
5394
9.745880
TGGTTGTTTGCTTAATTTTCGTATAAA
57.254
25.926
0.00
0.00
0.00
1.40
3282
5431
6.399639
TGGTCTTGTTCCTTCCAATAAAAC
57.600
37.500
0.00
0.00
0.00
2.43
3305
5454
3.428725
CCTCCGTTCAAGTGAGATCTCTG
60.429
52.174
22.95
13.38
0.00
3.35
3309
5458
3.613671
CGTTCAAGTGAGATCTCTGCTGT
60.614
47.826
22.95
9.47
0.00
4.40
3339
5488
6.762187
ACATAGCAGATCATGACAAAGAAGAG
59.238
38.462
0.00
0.00
0.00
2.85
3340
5489
5.163281
AGCAGATCATGACAAAGAAGAGT
57.837
39.130
0.00
0.00
0.00
3.24
3341
5490
5.558818
AGCAGATCATGACAAAGAAGAGTT
58.441
37.500
0.00
0.00
0.00
3.01
3342
5491
6.705302
AGCAGATCATGACAAAGAAGAGTTA
58.295
36.000
0.00
0.00
0.00
2.24
3346
5497
9.985318
CAGATCATGACAAAGAAGAGTTATTTC
57.015
33.333
0.00
0.00
0.00
2.17
3361
5512
9.467796
AAGAGTTATTTCATCTAAAAAGAGGGG
57.532
33.333
0.00
0.00
0.00
4.79
3364
5515
9.244292
AGTTATTTCATCTAAAAAGAGGGGAAC
57.756
33.333
0.00
0.00
0.00
3.62
3381
5532
4.758251
CGTCCACCGGCATCTGCA
62.758
66.667
0.00
0.00
44.36
4.41
3433
5584
8.729805
ATTGCAAAGTTTTAAGATCCAAACAA
57.270
26.923
1.71
4.45
35.66
2.83
3451
5602
0.836400
AAGGGAGGCTCGACCAAGAA
60.836
55.000
8.69
0.00
43.14
2.52
3493
5644
0.669077
GGCGATGTCCTACTCGATGT
59.331
55.000
0.00
0.00
37.05
3.06
3498
5649
3.181500
CGATGTCCTACTCGATGTTGACA
60.181
47.826
15.38
15.38
40.74
3.58
3532
5683
1.806542
ACGGAGATGACATGTTGCAAC
59.193
47.619
22.83
22.83
0.00
4.17
3568
5719
4.019174
CCATGAAGAAGCAACCACCTATT
58.981
43.478
0.00
0.00
0.00
1.73
3635
5786
6.750148
AGATCTTCAGACTCGTACAAACTTT
58.250
36.000
0.00
0.00
0.00
2.66
3664
5815
7.869429
GGATCATTCACATATTAAAGGGCTTTG
59.131
37.037
0.00
0.00
34.23
2.77
3665
5816
7.111247
TCATTCACATATTAAAGGGCTTTGG
57.889
36.000
0.00
0.00
34.23
3.28
3666
5817
5.930837
TTCACATATTAAAGGGCTTTGGG
57.069
39.130
0.00
0.00
34.23
4.12
3667
5818
4.285863
TCACATATTAAAGGGCTTTGGGG
58.714
43.478
0.00
0.00
34.23
4.96
3668
5819
4.017037
TCACATATTAAAGGGCTTTGGGGA
60.017
41.667
0.00
0.00
34.23
4.81
3669
5820
4.714308
CACATATTAAAGGGCTTTGGGGAA
59.286
41.667
0.00
0.00
34.23
3.97
3670
5821
5.188751
CACATATTAAAGGGCTTTGGGGAAA
59.811
40.000
0.00
0.00
34.23
3.13
3671
5822
5.188948
ACATATTAAAGGGCTTTGGGGAAAC
59.811
40.000
0.00
0.00
34.23
2.78
3672
5823
2.777459
TAAAGGGCTTTGGGGAAACA
57.223
45.000
0.00
0.00
34.23
2.83
3673
5824
1.886422
AAAGGGCTTTGGGGAAACAA
58.114
45.000
0.00
0.00
0.00
2.83
3674
5825
1.886422
AAGGGCTTTGGGGAAACAAA
58.114
45.000
0.00
0.00
37.96
2.83
3675
5826
2.116869
AGGGCTTTGGGGAAACAAAT
57.883
45.000
0.00
0.00
39.39
2.32
3676
5827
1.699083
AGGGCTTTGGGGAAACAAATG
59.301
47.619
0.00
0.00
39.39
2.32
3677
5828
1.271325
GGGCTTTGGGGAAACAAATGG
60.271
52.381
0.00
0.00
39.39
3.16
3678
5829
1.696884
GGCTTTGGGGAAACAAATGGA
59.303
47.619
0.00
0.00
39.39
3.41
3679
5830
2.305635
GGCTTTGGGGAAACAAATGGAT
59.694
45.455
0.00
0.00
39.39
3.41
3680
5831
3.244875
GGCTTTGGGGAAACAAATGGATT
60.245
43.478
0.00
0.00
39.39
3.01
3681
5832
4.397420
GCTTTGGGGAAACAAATGGATTT
58.603
39.130
0.00
0.00
39.39
2.17
3682
5833
4.826733
GCTTTGGGGAAACAAATGGATTTT
59.173
37.500
0.00
0.00
39.39
1.82
3684
5835
5.636903
TTGGGGAAACAAATGGATTTTGA
57.363
34.783
5.17
0.00
46.36
2.69
3685
5836
5.636903
TGGGGAAACAAATGGATTTTGAA
57.363
34.783
5.17
0.00
46.36
2.69
3686
5837
5.372373
TGGGGAAACAAATGGATTTTGAAC
58.628
37.500
5.17
0.00
46.36
3.18
3687
5838
4.450757
GGGGAAACAAATGGATTTTGAACG
59.549
41.667
5.17
0.00
46.36
3.95
3688
5839
4.084066
GGGAAACAAATGGATTTTGAACGC
60.084
41.667
5.17
1.87
46.36
4.84
3689
5840
4.509600
GGAAACAAATGGATTTTGAACGCA
59.490
37.500
5.17
0.00
46.36
5.24
3690
5841
5.333263
GGAAACAAATGGATTTTGAACGCAG
60.333
40.000
5.17
0.00
46.36
5.18
3691
5842
3.059166
ACAAATGGATTTTGAACGCAGC
58.941
40.909
5.17
0.00
46.36
5.25
3692
5843
3.243839
ACAAATGGATTTTGAACGCAGCT
60.244
39.130
5.17
0.00
46.36
4.24
3693
5844
2.927553
ATGGATTTTGAACGCAGCTC
57.072
45.000
0.00
0.00
0.00
4.09
3694
5845
0.881118
TGGATTTTGAACGCAGCTCC
59.119
50.000
0.00
0.00
0.00
4.70
3695
5846
1.168714
GGATTTTGAACGCAGCTCCT
58.831
50.000
0.00
0.00
0.00
3.69
3696
5847
1.135575
GGATTTTGAACGCAGCTCCTG
60.136
52.381
0.00
0.00
34.12
3.86
3705
5856
4.834453
CAGCTCCTGCGCTCCTGG
62.834
72.222
9.73
5.95
45.42
4.45
3740
5891
4.473520
CGCCCCTGTCGCCAGAAT
62.474
66.667
0.00
0.00
41.50
2.40
3741
5892
2.825836
GCCCCTGTCGCCAGAATG
60.826
66.667
0.00
0.00
41.50
2.67
3742
5893
2.825836
CCCCTGTCGCCAGAATGC
60.826
66.667
0.00
0.00
41.50
3.56
3743
5894
2.825836
CCCTGTCGCCAGAATGCC
60.826
66.667
0.00
0.00
41.50
4.40
3744
5895
2.825836
CCTGTCGCCAGAATGCCC
60.826
66.667
0.00
0.00
41.50
5.36
3745
5896
2.046023
CTGTCGCCAGAATGCCCA
60.046
61.111
0.00
0.00
41.50
5.36
3746
5897
2.359850
TGTCGCCAGAATGCCCAC
60.360
61.111
0.00
0.00
31.97
4.61
3747
5898
3.134127
GTCGCCAGAATGCCCACC
61.134
66.667
0.00
0.00
31.97
4.61
3748
5899
4.424711
TCGCCAGAATGCCCACCC
62.425
66.667
0.00
0.00
31.97
4.61
3751
5902
4.738998
CCAGAATGCCCACCCGCA
62.739
66.667
0.00
0.00
44.35
5.69
3752
5903
3.136123
CAGAATGCCCACCCGCAG
61.136
66.667
0.00
0.00
43.26
5.18
3823
5974
4.935495
CAGGCCACGGTGCTGTGT
62.935
66.667
5.01
0.00
38.20
3.72
3824
5975
4.189580
AGGCCACGGTGCTGTGTT
62.190
61.111
5.01
0.00
38.20
3.32
3825
5976
3.964875
GGCCACGGTGCTGTGTTG
61.965
66.667
1.68
0.00
38.20
3.33
3826
5977
3.964875
GCCACGGTGCTGTGTTGG
61.965
66.667
1.68
0.00
38.20
3.77
3827
5978
3.286751
CCACGGTGCTGTGTTGGG
61.287
66.667
1.68
0.00
38.20
4.12
3828
5979
3.964875
CACGGTGCTGTGTTGGGC
61.965
66.667
0.00
0.00
35.12
5.36
3831
5982
4.947147
GGTGCTGTGTTGGGCCGA
62.947
66.667
0.00
0.00
0.00
5.54
3832
5983
2.672996
GTGCTGTGTTGGGCCGAT
60.673
61.111
0.00
0.00
0.00
4.18
3833
5984
2.672651
TGCTGTGTTGGGCCGATG
60.673
61.111
0.00
0.00
0.00
3.84
3834
5985
2.672996
GCTGTGTTGGGCCGATGT
60.673
61.111
0.00
0.00
0.00
3.06
3835
5986
2.690778
GCTGTGTTGGGCCGATGTC
61.691
63.158
0.00
0.00
0.00
3.06
3836
5987
2.358125
TGTGTTGGGCCGATGTCG
60.358
61.111
0.00
0.00
39.44
4.35
3837
5988
3.799755
GTGTTGGGCCGATGTCGC
61.800
66.667
0.00
0.00
38.18
5.19
3846
5997
3.209812
CGATGTCGCGGAGGAGGA
61.210
66.667
6.13
0.00
0.00
3.71
3847
5998
2.413765
GATGTCGCGGAGGAGGAC
59.586
66.667
6.13
0.00
0.00
3.85
3848
5999
3.471244
GATGTCGCGGAGGAGGACG
62.471
68.421
6.13
0.00
33.45
4.79
3849
6000
3.989838
ATGTCGCGGAGGAGGACGA
62.990
63.158
6.13
0.00
33.45
4.20
3850
6001
4.176851
GTCGCGGAGGAGGACGAC
62.177
72.222
6.13
0.00
46.64
4.34
3853
6004
4.477975
GCGGAGGAGGACGACGTG
62.478
72.222
4.58
0.00
0.00
4.49
3854
6005
3.812019
CGGAGGAGGACGACGTGG
61.812
72.222
4.58
0.00
0.00
4.94
3855
6006
4.131088
GGAGGAGGACGACGTGGC
62.131
72.222
4.58
0.00
0.00
5.01
3856
6007
4.131088
GAGGAGGACGACGTGGCC
62.131
72.222
4.58
0.36
0.00
5.36
3874
6025
4.767255
GCTGGCTGTCCCCTCGTG
62.767
72.222
0.00
0.00
0.00
4.35
3875
6026
4.767255
CTGGCTGTCCCCTCGTGC
62.767
72.222
0.00
0.00
0.00
5.34
3901
6052
4.394712
CCCTCGGCTCGCAAGGTT
62.395
66.667
8.25
0.00
38.47
3.50
3902
6053
3.121030
CCTCGGCTCGCAAGGTTG
61.121
66.667
2.42
0.00
38.47
3.77
3903
6054
2.357517
CTCGGCTCGCAAGGTTGT
60.358
61.111
0.00
0.00
38.47
3.32
3904
6055
2.664851
TCGGCTCGCAAGGTTGTG
60.665
61.111
0.00
0.00
39.93
3.33
3905
6056
2.664851
CGGCTCGCAAGGTTGTGA
60.665
61.111
5.86
5.86
44.63
3.58
3906
6057
2.946762
GGCTCGCAAGGTTGTGAC
59.053
61.111
1.79
0.81
42.25
3.67
3907
6058
2.617274
GGCTCGCAAGGTTGTGACC
61.617
63.158
1.79
5.72
46.92
4.02
3915
6066
2.280797
GGTTGTGACCAGCGCAGA
60.281
61.111
11.47
0.00
45.77
4.26
3916
6067
2.320587
GGTTGTGACCAGCGCAGAG
61.321
63.158
11.47
0.00
45.77
3.35
3917
6068
1.300931
GTTGTGACCAGCGCAGAGA
60.301
57.895
11.47
0.00
38.43
3.10
3918
6069
1.005748
TTGTGACCAGCGCAGAGAG
60.006
57.895
11.47
0.00
38.43
3.20
3919
6070
2.813042
GTGACCAGCGCAGAGAGC
60.813
66.667
11.47
0.00
40.87
4.09
3939
6090
3.414700
GCTGTCGCCTCGTTGTGG
61.415
66.667
0.00
0.00
0.00
4.17
3940
6091
3.414700
CTGTCGCCTCGTTGTGGC
61.415
66.667
0.00
0.00
46.42
5.01
3946
6097
3.052082
CCTCGTTGTGGCAGCCTG
61.052
66.667
14.15
0.00
0.00
4.85
3947
6098
3.052082
CTCGTTGTGGCAGCCTGG
61.052
66.667
14.15
0.00
0.00
4.45
3948
6099
4.641645
TCGTTGTGGCAGCCTGGG
62.642
66.667
14.15
0.00
0.00
4.45
3955
6106
4.792804
GGCAGCCTGGGCACTCTC
62.793
72.222
14.39
0.00
44.88
3.20
3956
6107
3.715097
GCAGCCTGGGCACTCTCT
61.715
66.667
14.39
0.00
44.88
3.10
3957
6108
3.076092
CAGCCTGGGCACTCTCTT
58.924
61.111
14.39
0.00
44.88
2.85
3958
6109
1.376942
CAGCCTGGGCACTCTCTTG
60.377
63.158
14.39
0.00
44.88
3.02
3959
6110
2.749441
GCCTGGGCACTCTCTTGC
60.749
66.667
6.75
0.00
42.18
4.01
3960
6111
2.435586
CCTGGGCACTCTCTTGCG
60.436
66.667
0.00
0.00
44.00
4.85
3961
6112
2.435586
CTGGGCACTCTCTTGCGG
60.436
66.667
0.00
0.00
44.00
5.69
3962
6113
3.241530
TGGGCACTCTCTTGCGGT
61.242
61.111
0.00
0.00
44.00
5.68
3963
6114
2.435059
GGGCACTCTCTTGCGGTC
60.435
66.667
0.00
0.00
44.00
4.79
3964
6115
2.811317
GGCACTCTCTTGCGGTCG
60.811
66.667
0.00
0.00
44.00
4.79
3965
6116
3.482783
GCACTCTCTTGCGGTCGC
61.483
66.667
8.54
8.54
42.35
5.19
3966
6117
3.175240
CACTCTCTTGCGGTCGCG
61.175
66.667
10.79
0.00
45.51
5.87
4025
6176
3.503099
GGGCCACCTTGGGTTCTA
58.497
61.111
4.39
0.00
38.19
2.10
4026
6177
1.303282
GGGCCACCTTGGGTTCTAG
59.697
63.158
4.39
0.00
38.19
2.43
4027
6178
1.303282
GGCCACCTTGGGTTCTAGG
59.697
63.158
0.00
0.00
38.19
3.02
4028
6179
1.205460
GGCCACCTTGGGTTCTAGGA
61.205
60.000
0.00
0.00
38.19
2.94
4029
6180
0.035343
GCCACCTTGGGTTCTAGGAC
60.035
60.000
0.00
0.00
38.19
3.85
4030
6181
0.618981
CCACCTTGGGTTCTAGGACC
59.381
60.000
12.35
12.35
38.88
4.46
4031
6182
0.249398
CACCTTGGGTTCTAGGACCG
59.751
60.000
14.38
2.68
40.75
4.79
4032
6183
1.221021
CCTTGGGTTCTAGGACCGC
59.779
63.158
14.38
7.83
40.75
5.68
4033
6184
1.265454
CCTTGGGTTCTAGGACCGCT
61.265
60.000
14.38
0.00
40.75
5.52
4034
6185
0.175989
CTTGGGTTCTAGGACCGCTC
59.824
60.000
14.38
0.94
40.75
5.03
4035
6186
1.601419
TTGGGTTCTAGGACCGCTCG
61.601
60.000
14.38
0.00
40.75
5.03
4036
6187
2.104530
GGTTCTAGGACCGCTCGC
59.895
66.667
3.86
0.00
0.00
5.03
4037
6188
2.104530
GTTCTAGGACCGCTCGCC
59.895
66.667
0.00
0.00
0.00
5.54
4038
6189
3.515286
TTCTAGGACCGCTCGCCG
61.515
66.667
0.00
0.00
0.00
6.46
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
378
386
1.338973
GCCTTACGATGGTACCGATCA
59.661
52.381
18.49
0.00
0.00
2.92
582
590
2.496871
TGGTGCCATGAACCATGATTTC
59.503
45.455
14.28
0.00
43.81
2.17
1244
1254
2.049433
CGGCCTTCTCGAACACGT
60.049
61.111
0.00
0.00
0.00
4.49
1450
1460
1.227999
ACAGAAATGGTGGTGACGCG
61.228
55.000
3.53
3.53
43.50
6.01
1531
1546
7.064134
CGCCAAAACAAGAATCATGTAGTAGTA
59.936
37.037
0.00
0.00
0.00
1.82
1532
1547
6.128282
CGCCAAAACAAGAATCATGTAGTAGT
60.128
38.462
0.00
0.00
0.00
2.73
1533
1548
6.128282
ACGCCAAAACAAGAATCATGTAGTAG
60.128
38.462
0.00
0.00
0.00
2.57
1534
1549
5.703592
ACGCCAAAACAAGAATCATGTAGTA
59.296
36.000
0.00
0.00
0.00
1.82
1535
1550
4.518970
ACGCCAAAACAAGAATCATGTAGT
59.481
37.500
0.00
0.00
0.00
2.73
1536
1551
5.046910
ACGCCAAAACAAGAATCATGTAG
57.953
39.130
0.00
0.00
0.00
2.74
1691
1706
9.559732
TCTCTGAATTTGACTTGAATTCTGTTA
57.440
29.630
7.05
0.23
41.70
2.41
1692
1707
8.455903
TCTCTGAATTTGACTTGAATTCTGTT
57.544
30.769
7.05
0.00
41.70
3.16
1693
1708
8.632906
ATCTCTGAATTTGACTTGAATTCTGT
57.367
30.769
7.05
5.73
41.70
3.41
1806
1821
9.628746
TGTCATACAGAATGAAAATGTTTGATG
57.371
29.630
0.00
0.00
46.17
3.07
1942
1957
7.087639
TGTTTTTGAACCTGAAAGTGTACAAG
58.912
34.615
0.00
0.00
0.00
3.16
2058
2073
5.005740
ACCCCAAAGATTTACTAAACGGAC
58.994
41.667
0.00
0.00
0.00
4.79
2060
2075
5.005094
TCACCCCAAAGATTTACTAAACGG
58.995
41.667
0.00
0.00
0.00
4.44
2077
2094
5.099042
ACATTGTACAGACTAATCACCCC
57.901
43.478
0.00
0.00
0.00
4.95
2142
2159
4.212847
CACATTGCGGGATATTCAGAAGAG
59.787
45.833
0.00
0.00
0.00
2.85
2202
2238
9.722184
AGACAAGTAATCATCTCCATGAATATG
57.278
33.333
0.00
0.00
42.53
1.78
2288
2324
6.719301
AGAAGAGTTTCTTGATCATGGTCAT
58.281
36.000
10.04
0.00
40.79
3.06
2334
2370
5.073428
AGAAGGACCCAAATTCAGAGTTTC
58.927
41.667
0.00
0.00
0.00
2.78
2356
2397
6.705381
CCTTAGCATTTCAGAAGATGGTAGAG
59.295
42.308
12.75
12.54
37.49
2.43
2383
2424
2.911926
GCAGGGAAGGAAGGCAGGT
61.912
63.158
0.00
0.00
0.00
4.00
2720
2775
9.973450
AGAGTTATATAACAGTAACAGAGCATG
57.027
33.333
24.05
0.00
38.62
4.06
2755
2810
6.378564
TCTTTTTGCGGGGATCAAAATGTATA
59.621
34.615
0.00
0.00
41.35
1.47
2815
2873
7.518731
TTTAAATATTGCAGCGCCTTTAAAG
57.481
32.000
2.29
8.32
0.00
1.85
2816
2874
7.891183
TTTTAAATATTGCAGCGCCTTTAAA
57.109
28.000
2.29
7.04
0.00
1.52
2817
2875
7.978975
AGATTTTAAATATTGCAGCGCCTTTAA
59.021
29.630
2.29
1.19
0.00
1.52
2818
2876
7.488322
AGATTTTAAATATTGCAGCGCCTTTA
58.512
30.769
2.29
0.00
0.00
1.85
2819
2877
6.340522
AGATTTTAAATATTGCAGCGCCTTT
58.659
32.000
2.29
0.00
0.00
3.11
2820
2878
5.906073
AGATTTTAAATATTGCAGCGCCTT
58.094
33.333
2.29
0.00
0.00
4.35
2821
2879
5.520376
AGATTTTAAATATTGCAGCGCCT
57.480
34.783
2.29
0.00
0.00
5.52
2998
5143
4.498345
GGTTTCTGCAAACAAATGGTCGTA
60.498
41.667
3.80
0.00
43.41
3.43
3150
5295
5.233902
GCAAATGCACAAAATCTACACACAA
59.766
36.000
0.00
0.00
41.59
3.33
3282
5431
1.827969
AGATCTCACTTGAACGGAGGG
59.172
52.381
0.00
0.00
0.00
4.30
3305
5454
2.421073
TGATCTGCTATGTTGCAACAGC
59.579
45.455
33.44
30.39
43.04
4.40
3309
5458
4.263435
TGTCATGATCTGCTATGTTGCAA
58.737
39.130
0.00
0.00
42.83
4.08
3339
5488
8.182227
CGTTCCCCTCTTTTTAGATGAAATAAC
58.818
37.037
0.00
0.00
0.00
1.89
3340
5489
7.886446
ACGTTCCCCTCTTTTTAGATGAAATAA
59.114
33.333
0.00
0.00
0.00
1.40
3341
5490
7.399634
ACGTTCCCCTCTTTTTAGATGAAATA
58.600
34.615
0.00
0.00
0.00
1.40
3342
5491
6.246163
ACGTTCCCCTCTTTTTAGATGAAAT
58.754
36.000
0.00
0.00
0.00
2.17
3346
5497
3.939592
GGACGTTCCCCTCTTTTTAGATG
59.060
47.826
0.00
0.00
0.00
2.90
3361
5512
2.100631
CAGATGCCGGTGGACGTTC
61.101
63.158
1.90
0.00
42.24
3.95
3364
5515
4.758251
TGCAGATGCCGGTGGACG
62.758
66.667
1.90
0.00
41.18
4.79
3433
5584
0.618968
ATTCTTGGTCGAGCCTCCCT
60.619
55.000
12.85
0.00
38.35
4.20
3451
5602
4.476628
ACTATTCGTACCACGGGAAAAT
57.523
40.909
0.00
0.00
42.81
1.82
3493
5644
2.223144
CGTGATTCGAAGCCTTTGTCAA
59.777
45.455
11.45
0.00
42.86
3.18
3498
5649
1.275291
TCTCCGTGATTCGAAGCCTTT
59.725
47.619
11.45
0.00
42.86
3.11
3520
5671
3.536158
ACATACACGTTGCAACATGTC
57.464
42.857
32.03
4.14
36.62
3.06
3523
5674
3.006940
CCCTACATACACGTTGCAACAT
58.993
45.455
28.01
11.97
0.00
2.71
3532
5683
3.383505
TCTTCATGGACCCTACATACACG
59.616
47.826
0.00
0.00
0.00
4.49
3535
5686
4.141711
TGCTTCTTCATGGACCCTACATAC
60.142
45.833
0.00
0.00
0.00
2.39
3536
5687
4.037222
TGCTTCTTCATGGACCCTACATA
58.963
43.478
0.00
0.00
0.00
2.29
3538
5689
2.265367
TGCTTCTTCATGGACCCTACA
58.735
47.619
0.00
0.00
0.00
2.74
3568
5719
1.142667
TGTGGTCAGAAGCCATTGTGA
59.857
47.619
0.00
0.00
38.40
3.58
3621
5772
6.877611
ATGATCCAAAAAGTTTGTACGAGT
57.122
33.333
0.00
0.00
0.00
4.18
3635
5786
7.564660
AGCCCTTTAATATGTGAATGATCCAAA
59.435
33.333
0.00
0.00
0.00
3.28
3664
5815
4.450757
CGTTCAAAATCCATTTGTTTCCCC
59.549
41.667
1.35
0.00
46.89
4.81
3665
5816
4.084066
GCGTTCAAAATCCATTTGTTTCCC
60.084
41.667
1.35
0.00
46.89
3.97
3666
5817
4.509600
TGCGTTCAAAATCCATTTGTTTCC
59.490
37.500
1.35
0.00
46.89
3.13
3667
5818
5.649602
TGCGTTCAAAATCCATTTGTTTC
57.350
34.783
1.35
0.00
46.89
2.78
3668
5819
4.024977
GCTGCGTTCAAAATCCATTTGTTT
60.025
37.500
1.35
0.00
46.89
2.83
3669
5820
3.494251
GCTGCGTTCAAAATCCATTTGTT
59.506
39.130
1.35
0.00
46.89
2.83
3670
5821
3.059166
GCTGCGTTCAAAATCCATTTGT
58.941
40.909
1.35
0.00
46.89
2.83
3672
5823
3.578688
GAGCTGCGTTCAAAATCCATTT
58.421
40.909
0.00
0.00
0.00
2.32
3673
5824
2.094545
GGAGCTGCGTTCAAAATCCATT
60.095
45.455
0.00
0.00
0.00
3.16
3674
5825
1.474077
GGAGCTGCGTTCAAAATCCAT
59.526
47.619
0.00
0.00
0.00
3.41
3675
5826
0.881118
GGAGCTGCGTTCAAAATCCA
59.119
50.000
0.00
0.00
0.00
3.41
3676
5827
1.135575
CAGGAGCTGCGTTCAAAATCC
60.136
52.381
0.00
0.00
0.00
3.01
3677
5828
2.253392
CAGGAGCTGCGTTCAAAATC
57.747
50.000
0.00
0.00
0.00
2.17
3731
5882
4.424711
GGGTGGGCATTCTGGCGA
62.425
66.667
0.00
0.00
44.78
5.54
3734
5885
4.738998
TGCGGGTGGGCATTCTGG
62.739
66.667
0.00
0.00
38.17
3.86
3735
5886
3.136123
CTGCGGGTGGGCATTCTG
61.136
66.667
0.00
0.00
42.99
3.02
3806
5957
4.935495
ACACAGCACCGTGGCCTG
62.935
66.667
3.32
2.81
41.38
4.85
3807
5958
4.189580
AACACAGCACCGTGGCCT
62.190
61.111
3.32
0.00
41.38
5.19
3808
5959
3.964875
CAACACAGCACCGTGGCC
61.965
66.667
0.00
0.00
41.38
5.36
3809
5960
3.964875
CCAACACAGCACCGTGGC
61.965
66.667
0.00
0.00
41.38
5.01
3810
5961
3.286751
CCCAACACAGCACCGTGG
61.287
66.667
0.00
0.00
41.38
4.94
3811
5962
3.964875
GCCCAACACAGCACCGTG
61.965
66.667
0.00
0.00
42.81
4.94
3814
5965
4.947147
TCGGCCCAACACAGCACC
62.947
66.667
0.00
0.00
0.00
5.01
3815
5966
2.672996
ATCGGCCCAACACAGCAC
60.673
61.111
0.00
0.00
0.00
4.40
3816
5967
2.672651
CATCGGCCCAACACAGCA
60.673
61.111
0.00
0.00
0.00
4.41
3817
5968
2.672996
ACATCGGCCCAACACAGC
60.673
61.111
0.00
0.00
0.00
4.40
3818
5969
2.390599
CGACATCGGCCCAACACAG
61.391
63.158
0.00
0.00
35.37
3.66
3819
5970
2.358125
CGACATCGGCCCAACACA
60.358
61.111
0.00
0.00
35.37
3.72
3820
5971
3.799755
GCGACATCGGCCCAACAC
61.800
66.667
0.00
0.00
40.23
3.32
3829
5980
3.209812
TCCTCCTCCGCGACATCG
61.210
66.667
8.23
0.00
43.27
3.84
3830
5981
2.413765
GTCCTCCTCCGCGACATC
59.586
66.667
8.23
0.00
0.00
3.06
3831
5982
3.518998
CGTCCTCCTCCGCGACAT
61.519
66.667
8.23
0.00
0.00
3.06
3832
5983
4.710167
TCGTCCTCCTCCGCGACA
62.710
66.667
8.23
0.00
0.00
4.35
3833
5984
4.176851
GTCGTCCTCCTCCGCGAC
62.177
72.222
8.23
0.00
44.93
5.19
3836
5987
4.477975
CACGTCGTCCTCCTCCGC
62.478
72.222
0.00
0.00
0.00
5.54
3837
5988
3.812019
CCACGTCGTCCTCCTCCG
61.812
72.222
0.00
0.00
0.00
4.63
3838
5989
4.131088
GCCACGTCGTCCTCCTCC
62.131
72.222
0.00
0.00
0.00
4.30
3839
5990
4.131088
GGCCACGTCGTCCTCCTC
62.131
72.222
0.00
0.00
0.00
3.71
3857
6008
4.767255
CACGAGGGGACAGCCAGC
62.767
72.222
0.00
0.00
35.15
4.85
3858
6009
4.767255
GCACGAGGGGACAGCCAG
62.767
72.222
0.00
0.00
35.15
4.85
3886
6037
2.357517
ACAACCTTGCGAGCCGAG
60.358
61.111
0.00
0.00
0.00
4.63
3887
6038
2.664851
CACAACCTTGCGAGCCGA
60.665
61.111
0.00
0.00
0.00
5.54
3888
6039
2.664851
TCACAACCTTGCGAGCCG
60.665
61.111
0.00
0.00
0.00
5.52
3889
6040
2.617274
GGTCACAACCTTGCGAGCC
61.617
63.158
0.00
0.00
42.80
4.70
3890
6041
1.845809
CTGGTCACAACCTTGCGAGC
61.846
60.000
0.00
0.00
46.60
5.03
3891
6042
1.845809
GCTGGTCACAACCTTGCGAG
61.846
60.000
0.00
0.00
46.60
5.03
3892
6043
1.891919
GCTGGTCACAACCTTGCGA
60.892
57.895
0.00
0.00
46.60
5.10
3893
6044
2.639286
GCTGGTCACAACCTTGCG
59.361
61.111
0.00
0.00
46.60
4.85
3894
6045
2.639286
CGCTGGTCACAACCTTGC
59.361
61.111
0.00
0.51
46.60
4.01
3895
6046
2.121564
CTGCGCTGGTCACAACCTTG
62.122
60.000
9.73
0.00
46.60
3.61
3896
6047
1.893808
CTGCGCTGGTCACAACCTT
60.894
57.895
9.73
0.00
46.60
3.50
3897
6048
2.281070
CTGCGCTGGTCACAACCT
60.281
61.111
9.73
0.00
46.60
3.50
3898
6049
2.280797
TCTGCGCTGGTCACAACC
60.281
61.111
14.70
0.00
46.66
3.77
3899
6050
1.287730
CTCTCTGCGCTGGTCACAAC
61.288
60.000
14.70
0.00
0.00
3.32
3900
6051
1.005748
CTCTCTGCGCTGGTCACAA
60.006
57.895
14.70
0.00
0.00
3.33
3901
6052
2.653115
CTCTCTGCGCTGGTCACA
59.347
61.111
14.70
0.00
0.00
3.58
3902
6053
2.813042
GCTCTCTGCGCTGGTCAC
60.813
66.667
14.70
0.00
0.00
3.67
3922
6073
3.414700
CCACAACGAGGCGACAGC
61.415
66.667
0.00
0.00
44.18
4.40
3923
6074
3.414700
GCCACAACGAGGCGACAG
61.415
66.667
0.00
0.00
43.15
3.51
3929
6080
3.052082
CAGGCTGCCACAACGAGG
61.052
66.667
22.65
0.00
0.00
4.63
3930
6081
3.052082
CCAGGCTGCCACAACGAG
61.052
66.667
22.65
1.23
0.00
4.18
3931
6082
4.641645
CCCAGGCTGCCACAACGA
62.642
66.667
22.65
0.00
0.00
3.85
3938
6089
4.792804
GAGAGTGCCCAGGCTGCC
62.793
72.222
11.65
11.65
42.51
4.85
3939
6090
3.265272
AAGAGAGTGCCCAGGCTGC
62.265
63.158
9.56
0.00
42.51
5.25
3940
6091
1.376942
CAAGAGAGTGCCCAGGCTG
60.377
63.158
7.75
7.75
42.51
4.85
3941
6092
3.076092
CAAGAGAGTGCCCAGGCT
58.924
61.111
10.58
0.00
42.51
4.58
3942
6093
2.749441
GCAAGAGAGTGCCCAGGC
60.749
66.667
0.38
0.38
38.66
4.85
3943
6094
2.435586
CGCAAGAGAGTGCCCAGG
60.436
66.667
0.00
0.00
41.73
4.45
3944
6095
2.435586
CCGCAAGAGAGTGCCCAG
60.436
66.667
0.00
0.00
41.73
4.45
3945
6096
3.240134
GACCGCAAGAGAGTGCCCA
62.240
63.158
0.00
0.00
41.73
5.36
3946
6097
2.435059
GACCGCAAGAGAGTGCCC
60.435
66.667
0.00
0.00
41.73
5.36
3947
6098
2.811317
CGACCGCAAGAGAGTGCC
60.811
66.667
0.00
0.00
41.73
5.01
3948
6099
3.482783
GCGACCGCAAGAGAGTGC
61.483
66.667
9.73
0.00
41.49
4.40
3949
6100
3.175240
CGCGACCGCAAGAGAGTG
61.175
66.667
14.91
0.00
42.06
3.51
4007
6158
1.151677
TAGAACCCAAGGTGGCCCT
60.152
57.895
0.00
0.00
45.63
5.19
4008
6159
1.303282
CTAGAACCCAAGGTGGCCC
59.697
63.158
0.00
0.00
35.34
5.80
4009
6160
1.205460
TCCTAGAACCCAAGGTGGCC
61.205
60.000
0.00
0.00
35.34
5.36
4010
6161
0.035343
GTCCTAGAACCCAAGGTGGC
60.035
60.000
0.00
0.00
35.34
5.01
4011
6162
0.618981
GGTCCTAGAACCCAAGGTGG
59.381
60.000
0.00
0.00
35.34
4.61
4012
6163
0.249398
CGGTCCTAGAACCCAAGGTG
59.751
60.000
0.00
0.00
35.34
4.00
4013
6164
1.551019
GCGGTCCTAGAACCCAAGGT
61.551
60.000
0.00
0.00
37.65
3.50
4014
6165
1.221021
GCGGTCCTAGAACCCAAGG
59.779
63.158
0.00
0.00
35.79
3.61
4015
6166
0.175989
GAGCGGTCCTAGAACCCAAG
59.824
60.000
2.39
0.00
35.79
3.61
4016
6167
1.601419
CGAGCGGTCCTAGAACCCAA
61.601
60.000
9.39
0.00
35.79
4.12
4017
6168
2.050350
CGAGCGGTCCTAGAACCCA
61.050
63.158
9.39
0.00
35.79
4.51
4018
6169
2.806237
CGAGCGGTCCTAGAACCC
59.194
66.667
9.39
0.00
35.79
4.11
4019
6170
2.104530
GCGAGCGGTCCTAGAACC
59.895
66.667
9.39
0.00
35.86
3.62
4020
6171
2.104530
GGCGAGCGGTCCTAGAAC
59.895
66.667
9.39
0.00
0.00
3.01
4021
6172
3.515286
CGGCGAGCGGTCCTAGAA
61.515
66.667
9.39
0.00
0.00
2.10
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.