Multiple sequence alignment - TraesCS4B01G145400
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
TraesCS4B01G145400
chr4B
100.000
6942
0
0
1
6942
203853832
203846891
0.000000e+00
12820.0
1
TraesCS4B01G145400
chr4D
97.406
6553
99
16
1
6511
172019992
172026515
0.000000e+00
11093.0
2
TraesCS4B01G145400
chr4D
85.981
107
9
4
6538
6639
14609594
14609699
7.360000e-20
110.0
3
TraesCS4B01G145400
chr4A
95.782
6922
178
48
1
6856
415677387
415684260
0.000000e+00
11060.0
4
TraesCS4B01G145400
chr1A
86.712
2506
305
23
3449
5943
208212431
208209943
0.000000e+00
2758.0
5
TraesCS4B01G145400
chr1A
86.931
857
108
3
4359
5213
207986861
207986007
0.000000e+00
959.0
6
TraesCS4B01G145400
chr1A
80.233
688
115
19
2071
2752
208213873
208213201
1.340000e-136
497.0
7
TraesCS4B01G145400
chr1A
84.127
441
63
7
5212
5647
207957766
207957328
2.990000e-113
420.0
8
TraesCS4B01G145400
chr1D
86.669
2513
303
27
3444
5943
153773314
153775807
0.000000e+00
2756.0
9
TraesCS4B01G145400
chr1D
79.798
693
114
22
2071
2752
153771932
153772609
1.350000e-131
481.0
10
TraesCS4B01G145400
chr1D
88.780
205
19
2
2460
2664
70540903
70540703
1.500000e-61
248.0
11
TraesCS4B01G145400
chr1B
86.027
2512
321
24
3444
5943
230946414
230948907
0.000000e+00
2667.0
12
TraesCS4B01G145400
chr1B
78.792
712
121
24
2071
2774
230945066
230945755
1.060000e-122
451.0
13
TraesCS4B01G145400
chr5D
81.109
1551
188
52
1038
2527
55546089
55544583
0.000000e+00
1144.0
14
TraesCS4B01G145400
chr5D
81.101
1090
132
52
1506
2541
55549413
55548344
0.000000e+00
804.0
15
TraesCS4B01G145400
chr5D
83.360
625
68
18
3088
3693
55543965
55543358
4.730000e-151
545.0
16
TraesCS4B01G145400
chr5D
87.560
418
38
7
3753
4169
55548071
55547667
8.150000e-129
472.0
17
TraesCS4B01G145400
chr5D
86.757
370
40
7
1038
1405
55549836
55549474
3.020000e-108
403.0
18
TraesCS4B01G145400
chr5D
89.268
205
18
2
2460
2664
388420538
388420338
3.210000e-63
254.0
19
TraesCS4B01G145400
chr5D
89.000
100
8
3
6540
6638
491004601
491004698
3.400000e-23
121.0
20
TraesCS4B01G145400
chr5D
87.000
100
9
4
6534
6632
423232379
423232475
7.360000e-20
110.0
21
TraesCS4B01G145400
chr5B
81.661
1096
123
43
1506
2541
57977874
57976797
0.000000e+00
839.0
22
TraesCS4B01G145400
chr5B
86.170
282
24
10
1126
1405
57978257
57977989
2.450000e-74
291.0
23
TraesCS4B01G145400
chr5B
86.641
262
27
6
3293
3548
57975868
57975609
4.100000e-72
283.0
24
TraesCS4B01G145400
chr5B
91.176
204
16
2
2551
2753
57976707
57976505
6.860000e-70
276.0
25
TraesCS4B01G145400
chr5B
94.737
38
2
0
3769
3806
57975603
57975566
7.520000e-05
60.2
26
TraesCS4B01G145400
chr5A
81.171
1025
123
40
1572
2541
44287779
44286770
0.000000e+00
760.0
27
TraesCS4B01G145400
chr5A
82.240
625
71
24
3088
3693
44286159
44285556
2.890000e-138
503.0
28
TraesCS4B01G145400
chr5A
84.792
480
55
8
2551
3015
44286681
44286205
3.790000e-127
466.0
29
TraesCS4B01G145400
chr3B
87.317
205
21
3
2460
2664
545855431
545855630
5.420000e-56
230.0
30
TraesCS4B01G145400
chr7B
92.174
115
7
1
2550
2664
742259029
742259141
2.000000e-35
161.0
31
TraesCS4B01G145400
chr7B
87.000
100
10
2
6540
6639
64413104
64413008
7.360000e-20
110.0
32
TraesCS4B01G145400
chr7B
89.130
92
3
4
6541
6632
115197
115281
2.650000e-19
108.0
33
TraesCS4B01G145400
chr2D
90.816
98
7
2
6544
6640
83966687
83966783
5.650000e-26
130.0
34
TraesCS4B01G145400
chr2D
89.130
92
6
3
6541
6632
376700734
376700821
2.050000e-20
111.0
35
TraesCS4B01G145400
chr7D
86.607
112
9
4
6534
6643
604292587
604292694
1.220000e-22
119.0
36
TraesCS4B01G145400
chr2A
87.755
98
8
3
6538
6632
746253393
746253489
2.050000e-20
111.0
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
TraesCS4B01G145400
chr4B
203846891
203853832
6941
True
12820.000000
12820
100.000000
1
6942
1
chr4B.!!$R1
6941
1
TraesCS4B01G145400
chr4D
172019992
172026515
6523
False
11093.000000
11093
97.406000
1
6511
1
chr4D.!!$F2
6510
2
TraesCS4B01G145400
chr4A
415677387
415684260
6873
False
11060.000000
11060
95.782000
1
6856
1
chr4A.!!$F1
6855
3
TraesCS4B01G145400
chr1A
208209943
208213873
3930
True
1627.500000
2758
83.472500
2071
5943
2
chr1A.!!$R3
3872
4
TraesCS4B01G145400
chr1A
207986007
207986861
854
True
959.000000
959
86.931000
4359
5213
1
chr1A.!!$R2
854
5
TraesCS4B01G145400
chr1D
153771932
153775807
3875
False
1618.500000
2756
83.233500
2071
5943
2
chr1D.!!$F1
3872
6
TraesCS4B01G145400
chr1B
230945066
230948907
3841
False
1559.000000
2667
82.409500
2071
5943
2
chr1B.!!$F1
3872
7
TraesCS4B01G145400
chr5D
55543358
55549836
6478
True
673.600000
1144
83.977400
1038
4169
5
chr5D.!!$R2
3131
8
TraesCS4B01G145400
chr5B
57975566
57978257
2691
True
349.840000
839
88.077000
1126
3806
5
chr5B.!!$R1
2680
9
TraesCS4B01G145400
chr5A
44285556
44287779
2223
True
576.333333
760
82.734333
1572
3693
3
chr5A.!!$R1
2121
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
962
998
2.773487
TGTTAAATCTGGTGTCGTGGG
58.227
47.619
0.00
0.00
0.00
4.61
F
1413
4157
1.005924
AGTAATTCTGCCACCCCAAGG
59.994
52.381
0.00
0.00
40.04
3.61
F
1633
4378
1.092345
GGCAGATCAGAAACGAGCCC
61.092
60.000
0.00
0.00
34.71
5.19
F
2950
5906
2.143122
TCTCCGATGTTGTTTGCTCAC
58.857
47.619
0.00
0.00
0.00
3.51
F
3135
6287
3.002038
TGGACATGCATGCAACATCTA
57.998
42.857
26.68
16.75
0.00
1.98
F
4817
8122
2.092158
TGTCTTGGTTGGTGATCCACAA
60.092
45.455
0.00
0.00
44.22
3.33
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2078
4864
0.605589
AGTTCCGACTCCTCTGCTTG
59.394
55.000
0.00
0.00
0.00
4.01
R
2541
5447
2.361789
TGGGTAAATAAGCGGAGTTGC
58.638
47.619
0.00
0.00
0.00
4.17
R
2960
5916
2.392821
CATGTATGACGAGAGCAGAGC
58.607
52.381
0.00
0.00
0.00
4.09
R
4817
8122
1.127567
TAACAGTGGCAGGGAGCTGT
61.128
55.000
0.00
2.18
44.79
4.40
R
5017
8322
4.710423
TCTCTATAGAATGCCTCATCGC
57.290
45.455
3.57
0.00
0.00
4.58
R
6519
9834
1.043816
TTGTTTACGGACGGGGTACA
58.956
50.000
0.00
0.00
0.00
2.90
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
58
69
3.370978
GTCGCTGATAGCTTTGCTACAAA
59.629
43.478
0.00
0.00
44.24
2.83
91
102
6.395629
CAAACTAACGACCTCTTCCAGATAA
58.604
40.000
0.00
0.00
0.00
1.75
274
285
4.578105
GGGAAATCAAGAGTCAGCTATTGG
59.422
45.833
0.00
0.00
42.43
3.16
445
456
4.871993
CGCAGCTTCTCAGTTATTGATT
57.128
40.909
0.00
0.00
34.68
2.57
446
457
5.227238
CGCAGCTTCTCAGTTATTGATTT
57.773
39.130
0.00
0.00
34.68
2.17
447
458
5.634896
CGCAGCTTCTCAGTTATTGATTTT
58.365
37.500
0.00
0.00
34.68
1.82
600
611
3.983044
AGGAAAGAGGCGAACTGTTAT
57.017
42.857
0.00
0.00
31.52
1.89
962
998
2.773487
TGTTAAATCTGGTGTCGTGGG
58.227
47.619
0.00
0.00
0.00
4.61
1034
1070
2.328819
AGAGATCCAGTGCTTCATGC
57.671
50.000
0.00
0.00
43.25
4.06
1413
4157
1.005924
AGTAATTCTGCCACCCCAAGG
59.994
52.381
0.00
0.00
40.04
3.61
1633
4378
1.092345
GGCAGATCAGAAACGAGCCC
61.092
60.000
0.00
0.00
34.71
5.19
1832
4583
7.119699
CAGTTGAATACAGTTGCTTAATCTGGA
59.880
37.037
0.00
0.00
34.02
3.86
2021
4806
8.227791
TCTTTTGCGTCTTCACTATTTCATTAC
58.772
33.333
0.00
0.00
0.00
1.89
2541
5447
6.598753
TTTACTCTCGAGAAAGTGTTTTGG
57.401
37.500
17.36
3.02
0.00
3.28
2950
5906
2.143122
TCTCCGATGTTGTTTGCTCAC
58.857
47.619
0.00
0.00
0.00
3.51
2960
5916
4.270084
TGTTGTTTGCTCACTAAGACTTCG
59.730
41.667
0.00
0.00
0.00
3.79
3135
6287
3.002038
TGGACATGCATGCAACATCTA
57.998
42.857
26.68
16.75
0.00
1.98
3309
6594
5.190677
GGGTTTTAGCTGCTAGGTTGATAA
58.809
41.667
9.62
0.00
0.00
1.75
3866
7171
5.130477
TGGAGTAGTGAAGAAACAAGAACCT
59.870
40.000
0.00
0.00
0.00
3.50
4088
7393
4.859304
AGTTTTGCAGAGCATGAATCAA
57.141
36.364
0.00
0.00
38.76
2.57
4817
8122
2.092158
TGTCTTGGTTGGTGATCCACAA
60.092
45.455
0.00
0.00
44.22
3.33
5375
8680
1.077357
TGCCTCAAACCACGGTGTT
60.077
52.632
7.45
0.00
0.00
3.32
5472
8777
7.296856
TCCATCCTCCTTCAAAAATATGCATA
58.703
34.615
9.27
9.27
0.00
3.14
6395
9708
4.456911
CCTGCATAAATTCTGTCTGTGTGT
59.543
41.667
0.00
0.00
0.00
3.72
6396
9709
5.643348
CCTGCATAAATTCTGTCTGTGTGTA
59.357
40.000
0.00
0.00
0.00
2.90
6397
9710
6.317140
CCTGCATAAATTCTGTCTGTGTGTAT
59.683
38.462
0.00
0.00
0.00
2.29
6398
9711
7.075674
TGCATAAATTCTGTCTGTGTGTATG
57.924
36.000
0.00
0.00
0.00
2.39
6444
9757
4.819105
ACAAGTCCATAATCTGGTTCGA
57.181
40.909
0.00
0.00
46.08
3.71
6445
9758
5.359194
ACAAGTCCATAATCTGGTTCGAT
57.641
39.130
0.00
0.00
46.08
3.59
6473
9786
4.424711
GGCATGGCCGACCTTGGA
62.425
66.667
8.35
0.00
39.62
3.53
6474
9787
2.124151
GCATGGCCGACCTTGGAT
60.124
61.111
5.80
0.00
40.63
3.41
6519
9834
6.016360
TGTGCTTGCACTGTCTTAATATTGTT
60.016
34.615
23.53
0.00
0.00
2.83
6520
9835
6.306356
GTGCTTGCACTGTCTTAATATTGTTG
59.694
38.462
17.36
0.00
0.00
3.33
6521
9836
6.016360
TGCTTGCACTGTCTTAATATTGTTGT
60.016
34.615
0.00
0.00
0.00
3.32
6522
9837
7.174080
TGCTTGCACTGTCTTAATATTGTTGTA
59.826
33.333
0.00
0.00
0.00
2.41
6523
9838
7.481798
GCTTGCACTGTCTTAATATTGTTGTAC
59.518
37.037
0.00
0.00
0.00
2.90
6530
9860
5.525012
GTCTTAATATTGTTGTACCCCGTCC
59.475
44.000
0.00
0.00
0.00
4.79
6542
9872
3.632643
ACCCCGTCCGTAAACAAATAT
57.367
42.857
0.00
0.00
0.00
1.28
6544
9874
3.940852
ACCCCGTCCGTAAACAAATATTC
59.059
43.478
0.00
0.00
0.00
1.75
6545
9875
3.313249
CCCCGTCCGTAAACAAATATTCC
59.687
47.826
0.00
0.00
0.00
3.01
6546
9876
3.313249
CCCGTCCGTAAACAAATATTCCC
59.687
47.826
0.00
0.00
0.00
3.97
6548
9878
4.271776
CCGTCCGTAAACAAATATTCCCTC
59.728
45.833
0.00
0.00
0.00
4.30
6549
9879
4.271776
CGTCCGTAAACAAATATTCCCTCC
59.728
45.833
0.00
0.00
0.00
4.30
6550
9880
4.271776
GTCCGTAAACAAATATTCCCTCCG
59.728
45.833
0.00
0.00
0.00
4.63
6551
9881
4.080975
TCCGTAAACAAATATTCCCTCCGT
60.081
41.667
0.00
0.00
0.00
4.69
6586
9916
4.270834
AGAGCGTTTAGATCACTACTCCA
58.729
43.478
0.00
0.00
37.82
3.86
6587
9917
4.336993
AGAGCGTTTAGATCACTACTCCAG
59.663
45.833
0.00
0.00
37.82
3.86
6588
9918
4.017808
AGCGTTTAGATCACTACTCCAGT
58.982
43.478
0.00
0.00
38.32
4.00
6600
9930
5.444744
ACTACTCCAGTGATCTGAGTAGT
57.555
43.478
25.40
25.40
46.01
2.73
6610
9940
6.909895
CAGTGATCTGAGTAGTGATCTAAACG
59.090
42.308
0.00
0.00
43.76
3.60
6633
9963
9.804758
AACGGTCTTATATTTCTTTACAGAGAG
57.195
33.333
0.00
0.00
0.00
3.20
6634
9964
8.414778
ACGGTCTTATATTTCTTTACAGAGAGG
58.585
37.037
0.00
0.00
0.00
3.69
6635
9965
7.868415
CGGTCTTATATTTCTTTACAGAGAGGG
59.132
40.741
0.00
0.00
0.00
4.30
6636
9966
8.706521
GGTCTTATATTTCTTTACAGAGAGGGT
58.293
37.037
0.00
0.00
0.00
4.34
6713
10046
4.312443
AGTACCAGTGTGTTTATCAACGG
58.688
43.478
0.00
0.00
35.40
4.44
6740
10073
1.967779
TCACAAGTGTACCTAGCTGCA
59.032
47.619
1.02
0.00
0.00
4.41
6745
10078
0.460987
GTGTACCTAGCTGCAGGCAG
60.461
60.000
17.12
16.68
46.15
4.85
6746
10079
1.144936
GTACCTAGCTGCAGGCAGG
59.855
63.158
21.63
16.97
43.77
4.85
6747
10080
1.001631
TACCTAGCTGCAGGCAGGA
59.998
57.895
21.63
5.64
43.77
3.86
6748
10081
1.045350
TACCTAGCTGCAGGCAGGAG
61.045
60.000
21.63
6.77
43.77
3.69
6749
10082
2.062777
CCTAGCTGCAGGCAGGAGA
61.063
63.158
21.63
0.00
43.77
3.71
6750
10083
1.442567
CTAGCTGCAGGCAGGAGAG
59.557
63.158
21.63
0.00
43.77
3.20
6751
10084
1.305633
TAGCTGCAGGCAGGAGAGT
60.306
57.895
21.63
0.00
43.77
3.24
6752
10085
1.326213
TAGCTGCAGGCAGGAGAGTC
61.326
60.000
21.63
4.98
43.77
3.36
6753
10086
2.583520
CTGCAGGCAGGAGAGTCC
59.416
66.667
13.39
0.00
38.04
3.85
6754
10087
3.368190
CTGCAGGCAGGAGAGTCCG
62.368
68.421
13.39
0.00
42.75
4.79
6755
10088
3.386237
GCAGGCAGGAGAGTCCGT
61.386
66.667
0.00
0.00
42.75
4.69
6756
10089
2.888863
CAGGCAGGAGAGTCCGTC
59.111
66.667
0.00
0.00
42.75
4.79
6784
10117
1.001503
CCTCTGGTGGCTCTCCTCT
59.998
63.158
0.00
0.00
0.00
3.69
6786
10119
1.958902
CTCTGGTGGCTCTCCTCTGC
61.959
65.000
0.00
0.00
0.00
4.26
6793
10126
4.200283
CTCTCCTCTGCCGGCGAC
62.200
72.222
23.90
0.00
0.00
5.19
6808
10141
2.987547
GACCCTGGTCGTCGGTGA
60.988
66.667
0.00
0.00
35.30
4.02
6809
10142
2.283676
ACCCTGGTCGTCGGTGAT
60.284
61.111
0.00
0.00
0.00
3.06
6814
10147
1.303806
TGGTCGTCGGTGATGAGGA
60.304
57.895
0.00
0.00
0.00
3.71
6821
10154
1.141881
CGGTGATGAGGAGGGTTCG
59.858
63.158
0.00
0.00
0.00
3.95
6822
10155
1.153349
GGTGATGAGGAGGGTTCGC
60.153
63.158
0.00
0.00
0.00
4.70
6825
10158
3.447025
GATGAGGAGGGTTCGCCGG
62.447
68.421
0.00
0.00
37.94
6.13
6831
10164
1.186267
GGAGGGTTCGCCGGATCTAT
61.186
60.000
5.05
0.00
38.45
1.98
6835
10168
0.731855
GGTTCGCCGGATCTATACGC
60.732
60.000
5.05
0.00
31.29
4.42
6856
10189
3.674138
GCGTGGATCGTGTAGTTTTAGGA
60.674
47.826
0.00
0.00
42.13
2.94
6857
10190
4.679662
CGTGGATCGTGTAGTTTTAGGAT
58.320
43.478
0.00
0.00
34.52
3.24
6858
10191
5.107133
CGTGGATCGTGTAGTTTTAGGATT
58.893
41.667
0.00
0.00
34.52
3.01
6859
10192
5.005394
CGTGGATCGTGTAGTTTTAGGATTG
59.995
44.000
0.00
0.00
34.52
2.67
6860
10193
5.873164
GTGGATCGTGTAGTTTTAGGATTGT
59.127
40.000
0.00
0.00
0.00
2.71
6861
10194
6.035758
GTGGATCGTGTAGTTTTAGGATTGTC
59.964
42.308
0.00
0.00
0.00
3.18
6862
10195
6.070995
TGGATCGTGTAGTTTTAGGATTGTCT
60.071
38.462
0.00
0.00
0.00
3.41
6863
10196
6.817140
GGATCGTGTAGTTTTAGGATTGTCTT
59.183
38.462
0.00
0.00
0.00
3.01
6864
10197
7.201530
GGATCGTGTAGTTTTAGGATTGTCTTG
60.202
40.741
0.00
0.00
0.00
3.02
6865
10198
5.929992
TCGTGTAGTTTTAGGATTGTCTTGG
59.070
40.000
0.00
0.00
0.00
3.61
6866
10199
5.390567
CGTGTAGTTTTAGGATTGTCTTGGC
60.391
44.000
0.00
0.00
0.00
4.52
6867
10200
5.705905
GTGTAGTTTTAGGATTGTCTTGGCT
59.294
40.000
0.00
0.00
0.00
4.75
6868
10201
6.206829
GTGTAGTTTTAGGATTGTCTTGGCTT
59.793
38.462
0.00
0.00
0.00
4.35
6869
10202
5.966742
AGTTTTAGGATTGTCTTGGCTTC
57.033
39.130
0.00
0.00
0.00
3.86
6870
10203
5.385198
AGTTTTAGGATTGTCTTGGCTTCA
58.615
37.500
0.00
0.00
0.00
3.02
6871
10204
5.833131
AGTTTTAGGATTGTCTTGGCTTCAA
59.167
36.000
0.00
0.00
0.00
2.69
6872
10205
6.323739
AGTTTTAGGATTGTCTTGGCTTCAAA
59.676
34.615
0.00
0.00
0.00
2.69
6873
10206
6.723298
TTTAGGATTGTCTTGGCTTCAAAA
57.277
33.333
0.00
0.00
0.00
2.44
6874
10207
4.861102
AGGATTGTCTTGGCTTCAAAAG
57.139
40.909
0.00
0.00
0.00
2.27
6875
10208
4.218312
AGGATTGTCTTGGCTTCAAAAGT
58.782
39.130
0.00
0.00
0.00
2.66
6876
10209
4.038402
AGGATTGTCTTGGCTTCAAAAGTG
59.962
41.667
0.00
0.00
0.00
3.16
6877
10210
3.799281
TTGTCTTGGCTTCAAAAGTGG
57.201
42.857
0.00
0.00
0.00
4.00
6878
10211
1.408702
TGTCTTGGCTTCAAAAGTGGC
59.591
47.619
0.00
0.00
0.00
5.01
6879
10212
0.667993
TCTTGGCTTCAAAAGTGGCG
59.332
50.000
0.00
0.00
0.00
5.69
6880
10213
0.667993
CTTGGCTTCAAAAGTGGCGA
59.332
50.000
0.00
0.00
0.00
5.54
6881
10214
1.270550
CTTGGCTTCAAAAGTGGCGAT
59.729
47.619
0.00
0.00
0.00
4.58
6882
10215
0.881118
TGGCTTCAAAAGTGGCGATC
59.119
50.000
0.00
0.00
0.00
3.69
6883
10216
0.179189
GGCTTCAAAAGTGGCGATCG
60.179
55.000
11.69
11.69
0.00
3.69
6884
10217
0.794605
GCTTCAAAAGTGGCGATCGC
60.795
55.000
31.52
31.52
41.06
4.58
6885
10218
0.519175
CTTCAAAAGTGGCGATCGCG
60.519
55.000
31.76
17.24
43.06
5.87
6895
10228
3.608041
CGATCGCGCCGTTGAATA
58.392
55.556
0.26
0.00
0.00
1.75
6896
10229
1.198397
CGATCGCGCCGTTGAATAC
59.802
57.895
0.26
0.00
0.00
1.89
6897
10230
1.476235
CGATCGCGCCGTTGAATACA
61.476
55.000
0.26
0.00
0.00
2.29
6898
10231
0.229753
GATCGCGCCGTTGAATACAG
59.770
55.000
0.00
0.00
0.00
2.74
6899
10232
0.179121
ATCGCGCCGTTGAATACAGA
60.179
50.000
0.00
0.00
0.00
3.41
6900
10233
0.388778
TCGCGCCGTTGAATACAGAA
60.389
50.000
0.00
0.00
0.00
3.02
6901
10234
0.025001
CGCGCCGTTGAATACAGAAG
59.975
55.000
0.00
0.00
0.00
2.85
6902
10235
1.076332
GCGCCGTTGAATACAGAAGT
58.924
50.000
0.00
0.00
0.00
3.01
6903
10236
1.463444
GCGCCGTTGAATACAGAAGTT
59.537
47.619
0.00
0.00
0.00
2.66
6904
10237
2.095919
GCGCCGTTGAATACAGAAGTTT
60.096
45.455
0.00
0.00
0.00
2.66
6905
10238
3.732943
CGCCGTTGAATACAGAAGTTTC
58.267
45.455
0.00
0.00
0.00
2.78
6906
10239
3.185594
CGCCGTTGAATACAGAAGTTTCA
59.814
43.478
0.00
0.00
0.00
2.69
6907
10240
4.666655
CGCCGTTGAATACAGAAGTTTCAG
60.667
45.833
0.00
0.00
31.40
3.02
6908
10241
4.451096
GCCGTTGAATACAGAAGTTTCAGA
59.549
41.667
0.00
0.00
31.40
3.27
6909
10242
5.122396
GCCGTTGAATACAGAAGTTTCAGAT
59.878
40.000
0.00
0.00
31.40
2.90
6910
10243
6.673316
GCCGTTGAATACAGAAGTTTCAGATC
60.673
42.308
0.00
0.00
31.40
2.75
6911
10244
6.591834
CCGTTGAATACAGAAGTTTCAGATCT
59.408
38.462
0.00
0.00
31.40
2.75
6912
10245
7.201478
CCGTTGAATACAGAAGTTTCAGATCTC
60.201
40.741
0.00
0.00
31.40
2.75
6913
10246
7.543868
CGTTGAATACAGAAGTTTCAGATCTCT
59.456
37.037
0.00
0.00
31.40
3.10
6914
10247
9.213799
GTTGAATACAGAAGTTTCAGATCTCTT
57.786
33.333
0.00
0.00
31.40
2.85
6915
10248
8.994429
TGAATACAGAAGTTTCAGATCTCTTC
57.006
34.615
11.99
11.99
37.24
2.87
6916
10249
8.037758
TGAATACAGAAGTTTCAGATCTCTTCC
58.962
37.037
14.96
3.71
37.56
3.46
6917
10250
5.159273
ACAGAAGTTTCAGATCTCTTCCC
57.841
43.478
14.96
0.00
37.56
3.97
6918
10251
4.180057
CAGAAGTTTCAGATCTCTTCCCG
58.820
47.826
14.96
6.46
37.56
5.14
6919
10252
4.081972
CAGAAGTTTCAGATCTCTTCCCGA
60.082
45.833
14.96
0.00
37.56
5.14
6920
10253
3.878160
AGTTTCAGATCTCTTCCCGAC
57.122
47.619
0.00
0.00
0.00
4.79
6921
10254
2.164624
AGTTTCAGATCTCTTCCCGACG
59.835
50.000
0.00
0.00
0.00
5.12
6922
10255
2.124277
TTCAGATCTCTTCCCGACGA
57.876
50.000
0.00
0.00
0.00
4.20
6923
10256
1.669604
TCAGATCTCTTCCCGACGAG
58.330
55.000
0.00
0.00
0.00
4.18
6924
10257
0.665835
CAGATCTCTTCCCGACGAGG
59.334
60.000
0.00
0.00
40.63
4.63
6925
10258
1.104577
AGATCTCTTCCCGACGAGGC
61.105
60.000
0.00
0.00
39.21
4.70
6926
10259
1.379977
ATCTCTTCCCGACGAGGCA
60.380
57.895
0.00
0.00
39.21
4.75
6927
10260
0.970937
ATCTCTTCCCGACGAGGCAA
60.971
55.000
0.00
0.00
39.21
4.52
6928
10261
0.970937
TCTCTTCCCGACGAGGCAAT
60.971
55.000
0.00
0.00
39.21
3.56
6929
10262
0.108138
CTCTTCCCGACGAGGCAATT
60.108
55.000
0.00
0.00
39.21
2.32
6930
10263
0.391130
TCTTCCCGACGAGGCAATTG
60.391
55.000
0.00
0.00
39.21
2.32
6931
10264
1.369091
CTTCCCGACGAGGCAATTGG
61.369
60.000
7.72
0.00
39.21
3.16
6932
10265
2.046314
CCCGACGAGGCAATTGGT
60.046
61.111
7.72
0.00
39.21
3.67
6933
10266
1.674322
CCCGACGAGGCAATTGGTT
60.674
57.895
7.72
0.00
39.21
3.67
6934
10267
1.241315
CCCGACGAGGCAATTGGTTT
61.241
55.000
7.72
0.00
39.21
3.27
6935
10268
0.596082
CCGACGAGGCAATTGGTTTT
59.404
50.000
7.72
0.00
0.00
2.43
6936
10269
1.807742
CCGACGAGGCAATTGGTTTTA
59.192
47.619
7.72
0.00
0.00
1.52
6937
10270
2.422127
CCGACGAGGCAATTGGTTTTAT
59.578
45.455
7.72
0.00
0.00
1.40
6938
10271
3.425404
CGACGAGGCAATTGGTTTTATG
58.575
45.455
7.72
0.00
0.00
1.90
6939
10272
3.126171
CGACGAGGCAATTGGTTTTATGA
59.874
43.478
7.72
0.00
0.00
2.15
6940
10273
4.201910
CGACGAGGCAATTGGTTTTATGAT
60.202
41.667
7.72
0.00
0.00
2.45
6941
10274
5.650543
GACGAGGCAATTGGTTTTATGATT
58.349
37.500
7.72
0.00
0.00
2.57
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
58
69
5.419471
AGAGGTCGTTAGTTTGCTATCTTCT
59.581
40.000
0.00
0.00
0.00
2.85
91
102
2.695147
GCATGTGCTAAGGGCCTTTAAT
59.305
45.455
26.29
8.42
40.92
1.40
274
285
0.034670
AGGAAGCTGAATGTGCTCCC
60.035
55.000
0.00
0.00
40.22
4.30
397
408
9.014297
CAAATTTTCCCTTATATAGCCTACTGG
57.986
37.037
0.00
0.00
0.00
4.00
600
611
6.122277
AGAGACACCAAAGACAAATCTTCAA
58.878
36.000
0.00
0.00
44.82
2.69
775
786
3.096489
TGAATTGCTTGTGAAACCTGC
57.904
42.857
0.00
0.00
34.36
4.85
962
998
3.002348
GTCAGCAGCAATCCCGTATTTAC
59.998
47.826
0.00
0.00
0.00
2.01
1034
1070
1.340114
GGTTTTCTAGCTCTGTGGGGG
60.340
57.143
0.00
0.00
0.00
5.40
1413
4157
5.128919
ACACTGGAATCTGCATTTCTATCC
58.871
41.667
8.83
2.85
0.00
2.59
1504
4249
2.890945
GCCTTGGTACAGATTGTTGGTT
59.109
45.455
0.00
0.00
42.39
3.67
1832
4583
9.961265
CATTCTCATCACACAGCATATAATTTT
57.039
29.630
0.00
0.00
0.00
1.82
2021
4806
5.615544
CGTGCAAAAGTAGTCTTTCCATCAG
60.616
44.000
0.00
0.00
42.26
2.90
2078
4864
0.605589
AGTTCCGACTCCTCTGCTTG
59.394
55.000
0.00
0.00
0.00
4.01
2541
5447
2.361789
TGGGTAAATAAGCGGAGTTGC
58.638
47.619
0.00
0.00
0.00
4.17
2950
5906
2.538737
CGAGAGCAGAGCGAAGTCTTAG
60.539
54.545
0.00
0.00
0.00
2.18
2960
5916
2.392821
CATGTATGACGAGAGCAGAGC
58.607
52.381
0.00
0.00
0.00
4.09
3866
7171
2.950781
TGTACCAATGTGAAAGGCCAA
58.049
42.857
5.01
0.00
0.00
4.52
4088
7393
1.947456
GGAAGAGTGCGAAACAGGTTT
59.053
47.619
0.00
0.00
35.14
3.27
4817
8122
1.127567
TAACAGTGGCAGGGAGCTGT
61.128
55.000
0.00
2.18
44.79
4.40
5017
8322
4.710423
TCTCTATAGAATGCCTCATCGC
57.290
45.455
3.57
0.00
0.00
4.58
5375
8680
3.127895
GGCGTATATCTGCAACAAAACCA
59.872
43.478
0.00
0.00
0.00
3.67
5472
8777
7.568199
AAACAACACTAGTACATTGCTCTTT
57.432
32.000
11.65
5.05
0.00
2.52
6138
9446
6.767524
TGTTCAAATATGGTCCATGTAACC
57.232
37.500
15.10
7.42
37.31
2.85
6396
9709
5.929697
CATGCGGATTTCTGTATGTACAT
57.070
39.130
13.93
13.93
39.50
2.29
6467
9780
1.519455
GACCGACGCAGATCCAAGG
60.519
63.158
0.00
0.00
0.00
3.61
6468
9781
1.874019
CGACCGACGCAGATCCAAG
60.874
63.158
0.00
0.00
34.51
3.61
6469
9782
1.663379
ATCGACCGACGCAGATCCAA
61.663
55.000
0.00
0.00
42.26
3.53
6471
9784
1.658717
CATCGACCGACGCAGATCC
60.659
63.158
0.00
0.00
42.26
3.36
6473
9786
2.278857
GCATCGACCGACGCAGAT
60.279
61.111
5.57
0.00
42.26
2.90
6474
9787
2.867333
GAAGCATCGACCGACGCAGA
62.867
60.000
12.85
0.00
42.26
4.26
6519
9834
1.043816
TTGTTTACGGACGGGGTACA
58.956
50.000
0.00
0.00
0.00
2.90
6520
9835
2.162319
TTTGTTTACGGACGGGGTAC
57.838
50.000
0.00
0.00
0.00
3.34
6521
9836
4.751767
ATATTTGTTTACGGACGGGGTA
57.248
40.909
0.00
0.00
0.00
3.69
6522
9837
3.632643
ATATTTGTTTACGGACGGGGT
57.367
42.857
0.00
0.00
0.00
4.95
6523
9838
3.313249
GGAATATTTGTTTACGGACGGGG
59.687
47.826
0.00
0.00
0.00
5.73
6530
9860
8.592105
TTATACGGAGGGAATATTTGTTTACG
57.408
34.615
0.00
0.00
0.00
3.18
6542
9872
8.529476
GCTCTTATATTTCTTATACGGAGGGAA
58.471
37.037
0.00
0.00
30.88
3.97
6544
9874
6.973474
CGCTCTTATATTTCTTATACGGAGGG
59.027
42.308
0.00
0.00
34.04
4.30
6545
9875
7.536855
ACGCTCTTATATTTCTTATACGGAGG
58.463
38.462
0.00
0.00
30.88
4.30
6546
9876
8.967552
AACGCTCTTATATTTCTTATACGGAG
57.032
34.615
0.00
0.00
32.05
4.63
6579
9909
5.432645
TCACTACTCAGATCACTGGAGTAG
58.567
45.833
25.83
25.83
45.95
2.57
6582
9912
5.132502
AGATCACTACTCAGATCACTGGAG
58.867
45.833
0.00
0.00
42.36
3.86
6586
9916
6.038825
CCGTTTAGATCACTACTCAGATCACT
59.961
42.308
0.00
0.00
42.36
3.41
6587
9917
6.183360
ACCGTTTAGATCACTACTCAGATCAC
60.183
42.308
0.00
0.00
42.36
3.06
6588
9918
5.886474
ACCGTTTAGATCACTACTCAGATCA
59.114
40.000
0.00
0.00
42.36
2.92
6589
9919
6.261381
AGACCGTTTAGATCACTACTCAGATC
59.739
42.308
0.00
0.00
40.68
2.75
6590
9920
6.123651
AGACCGTTTAGATCACTACTCAGAT
58.876
40.000
0.00
0.00
0.00
2.90
6592
9922
5.821516
AGACCGTTTAGATCACTACTCAG
57.178
43.478
0.00
0.00
0.00
3.35
6593
9923
7.876936
ATAAGACCGTTTAGATCACTACTCA
57.123
36.000
0.00
0.00
0.00
3.41
6610
9940
8.706521
ACCCTCTCTGTAAAGAAATATAAGACC
58.293
37.037
0.00
0.00
0.00
3.85
6713
10046
5.070580
AGCTAGGTACACTTGTGATTATCCC
59.929
44.000
7.83
0.00
0.00
3.85
6740
10073
2.363147
GGACGGACTCTCCTGCCT
60.363
66.667
0.00
0.00
33.30
4.75
6745
10078
4.500116
GCTGCGGACGGACTCTCC
62.500
72.222
0.00
0.00
0.00
3.71
6746
10079
4.500116
GGCTGCGGACGGACTCTC
62.500
72.222
0.00
0.00
0.00
3.20
6748
10081
3.991536
GAAGGCTGCGGACGGACTC
62.992
68.421
0.00
0.00
40.88
3.36
6749
10082
4.070552
GAAGGCTGCGGACGGACT
62.071
66.667
0.00
0.00
45.14
3.85
6752
10085
4.821589
GAGGAAGGCTGCGGACGG
62.822
72.222
0.00
0.00
0.00
4.79
6753
10086
3.764466
AGAGGAAGGCTGCGGACG
61.764
66.667
0.00
0.00
0.00
4.79
6754
10087
2.125350
CAGAGGAAGGCTGCGGAC
60.125
66.667
0.00
0.00
0.00
4.79
6755
10088
3.393970
CCAGAGGAAGGCTGCGGA
61.394
66.667
0.00
0.00
32.06
5.54
6756
10089
3.710722
ACCAGAGGAAGGCTGCGG
61.711
66.667
0.00
0.00
32.06
5.69
6793
10126
2.184322
CATCACCGACGACCAGGG
59.816
66.667
0.00
0.00
0.00
4.45
6800
10133
1.605058
AACCCTCCTCATCACCGACG
61.605
60.000
0.00
0.00
0.00
5.12
6804
10137
1.153349
GCGAACCCTCCTCATCACC
60.153
63.158
0.00
0.00
0.00
4.02
6808
10141
3.470888
CCGGCGAACCCTCCTCAT
61.471
66.667
9.30
0.00
0.00
2.90
6809
10142
3.976490
ATCCGGCGAACCCTCCTCA
62.976
63.158
9.30
0.00
0.00
3.86
6814
10147
1.254954
GTATAGATCCGGCGAACCCT
58.745
55.000
9.30
2.18
0.00
4.34
6821
10154
1.443872
CCACGCGTATAGATCCGGC
60.444
63.158
13.44
0.00
0.00
6.13
6822
10155
0.809385
ATCCACGCGTATAGATCCGG
59.191
55.000
13.44
6.53
0.00
5.14
6825
10158
2.095869
ACACGATCCACGCGTATAGATC
60.096
50.000
24.96
24.96
46.94
2.75
6831
10164
0.804364
AACTACACGATCCACGCGTA
59.196
50.000
13.44
0.00
46.94
4.42
6856
10189
3.493176
GCCACTTTTGAAGCCAAGACAAT
60.493
43.478
0.00
0.00
33.23
2.71
6857
10190
2.159114
GCCACTTTTGAAGCCAAGACAA
60.159
45.455
0.00
0.00
33.23
3.18
6858
10191
1.408702
GCCACTTTTGAAGCCAAGACA
59.591
47.619
0.00
0.00
33.23
3.41
6859
10192
1.600413
CGCCACTTTTGAAGCCAAGAC
60.600
52.381
0.00
0.00
33.23
3.01
6860
10193
0.667993
CGCCACTTTTGAAGCCAAGA
59.332
50.000
0.00
0.00
33.23
3.02
6861
10194
0.667993
TCGCCACTTTTGAAGCCAAG
59.332
50.000
0.00
0.00
33.23
3.61
6862
10195
1.269448
GATCGCCACTTTTGAAGCCAA
59.731
47.619
0.00
0.00
0.00
4.52
6863
10196
0.881118
GATCGCCACTTTTGAAGCCA
59.119
50.000
0.00
0.00
0.00
4.75
6864
10197
0.179189
CGATCGCCACTTTTGAAGCC
60.179
55.000
0.26
0.00
0.00
4.35
6865
10198
0.794605
GCGATCGCCACTTTTGAAGC
60.795
55.000
29.48
0.00
34.56
3.86
6866
10199
0.519175
CGCGATCGCCACTTTTGAAG
60.519
55.000
32.63
11.93
37.98
3.02
6867
10200
1.495509
CGCGATCGCCACTTTTGAA
59.504
52.632
32.63
0.00
37.98
2.69
6868
10201
3.164576
CGCGATCGCCACTTTTGA
58.835
55.556
32.63
0.00
37.98
2.69
6878
10211
1.198397
GTATTCAACGGCGCGATCG
59.802
57.895
12.10
15.98
39.07
3.69
6879
10212
0.229753
CTGTATTCAACGGCGCGATC
59.770
55.000
12.10
0.00
0.00
3.69
6880
10213
0.179121
TCTGTATTCAACGGCGCGAT
60.179
50.000
12.10
0.00
34.14
4.58
6881
10214
0.388778
TTCTGTATTCAACGGCGCGA
60.389
50.000
12.10
0.00
34.14
5.87
6882
10215
0.025001
CTTCTGTATTCAACGGCGCG
59.975
55.000
6.90
0.00
34.14
6.86
6883
10216
1.076332
ACTTCTGTATTCAACGGCGC
58.924
50.000
6.90
0.00
34.14
6.53
6884
10217
3.185594
TGAAACTTCTGTATTCAACGGCG
59.814
43.478
4.80
4.80
34.14
6.46
6885
10218
4.451096
TCTGAAACTTCTGTATTCAACGGC
59.549
41.667
0.00
0.00
33.08
5.68
6886
10219
6.591834
AGATCTGAAACTTCTGTATTCAACGG
59.408
38.462
0.00
0.00
33.08
4.44
6887
10220
7.543868
AGAGATCTGAAACTTCTGTATTCAACG
59.456
37.037
0.00
0.00
33.08
4.10
6888
10221
8.770438
AGAGATCTGAAACTTCTGTATTCAAC
57.230
34.615
0.00
0.00
33.08
3.18
6889
10222
9.429359
GAAGAGATCTGAAACTTCTGTATTCAA
57.571
33.333
0.00
0.00
36.72
2.69
6890
10223
8.037758
GGAAGAGATCTGAAACTTCTGTATTCA
58.962
37.037
16.98
0.00
38.78
2.57
6891
10224
7.494298
GGGAAGAGATCTGAAACTTCTGTATTC
59.506
40.741
16.98
4.43
38.78
1.75
6892
10225
7.334858
GGGAAGAGATCTGAAACTTCTGTATT
58.665
38.462
16.98
0.00
38.78
1.89
6893
10226
6.406400
CGGGAAGAGATCTGAAACTTCTGTAT
60.406
42.308
16.98
0.00
38.78
2.29
6894
10227
5.105716
CGGGAAGAGATCTGAAACTTCTGTA
60.106
44.000
16.98
0.00
38.78
2.74
6895
10228
4.322349
CGGGAAGAGATCTGAAACTTCTGT
60.322
45.833
16.98
0.00
38.78
3.41
6896
10229
4.081972
TCGGGAAGAGATCTGAAACTTCTG
60.082
45.833
16.98
12.00
38.78
3.02
6897
10230
4.081917
GTCGGGAAGAGATCTGAAACTTCT
60.082
45.833
16.98
0.00
38.78
2.85
6898
10231
4.177783
GTCGGGAAGAGATCTGAAACTTC
58.822
47.826
0.00
6.65
38.26
3.01
6899
10232
3.367498
CGTCGGGAAGAGATCTGAAACTT
60.367
47.826
0.00
0.00
0.00
2.66
6900
10233
2.164624
CGTCGGGAAGAGATCTGAAACT
59.835
50.000
0.00
0.00
0.00
2.66
6901
10234
2.163815
TCGTCGGGAAGAGATCTGAAAC
59.836
50.000
0.00
0.00
0.00
2.78
6902
10235
2.423892
CTCGTCGGGAAGAGATCTGAAA
59.576
50.000
0.00
0.00
38.88
2.69
6903
10236
2.017782
CTCGTCGGGAAGAGATCTGAA
58.982
52.381
0.00
0.00
38.88
3.02
6904
10237
1.669604
CTCGTCGGGAAGAGATCTGA
58.330
55.000
0.00
0.00
38.88
3.27
6905
10238
0.665835
CCTCGTCGGGAAGAGATCTG
59.334
60.000
12.30
0.00
38.88
2.90
6906
10239
1.104577
GCCTCGTCGGGAAGAGATCT
61.105
60.000
12.30
0.00
38.88
2.75
6907
10240
1.360911
GCCTCGTCGGGAAGAGATC
59.639
63.158
12.30
1.85
38.88
2.75
6908
10241
0.970937
TTGCCTCGTCGGGAAGAGAT
60.971
55.000
12.30
0.00
38.30
2.75
6909
10242
0.970937
ATTGCCTCGTCGGGAAGAGA
60.971
55.000
12.30
0.00
46.96
3.10
6910
10243
0.108138
AATTGCCTCGTCGGGAAGAG
60.108
55.000
0.00
4.87
46.96
2.85
6911
10244
0.391130
CAATTGCCTCGTCGGGAAGA
60.391
55.000
0.00
0.00
46.96
2.87
6912
10245
1.369091
CCAATTGCCTCGTCGGGAAG
61.369
60.000
0.00
0.00
46.96
3.46
6914
10247
2.119484
AACCAATTGCCTCGTCGGGA
62.119
55.000
0.00
0.00
0.00
5.14
6915
10248
1.241315
AAACCAATTGCCTCGTCGGG
61.241
55.000
0.00
0.00
0.00
5.14
6916
10249
0.596082
AAAACCAATTGCCTCGTCGG
59.404
50.000
0.00
0.00
0.00
4.79
6917
10250
3.126171
TCATAAAACCAATTGCCTCGTCG
59.874
43.478
0.00
0.00
0.00
5.12
6918
10251
4.695217
TCATAAAACCAATTGCCTCGTC
57.305
40.909
0.00
0.00
0.00
4.20
6919
10252
5.659440
AATCATAAAACCAATTGCCTCGT
57.341
34.783
0.00
0.00
0.00
4.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.