Multiple sequence alignment - TraesCS7A01G462100
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
TraesCS7A01G462100
chr7A
100.000
3398
0
0
1
3398
658706917
658703520
0.000000e+00
6276
1
TraesCS7A01G462100
chr7A
97.343
3237
67
4
176
3398
576403313
576406544
0.000000e+00
5483
2
TraesCS7A01G462100
chr7A
97.143
175
5
0
1
175
727192390
727192564
2.560000e-76
296
3
TraesCS7A01G462100
chr4A
97.015
2714
62
5
697
3395
628881991
628884700
0.000000e+00
4545
4
TraesCS7A01G462100
chr4A
94.769
325
13
3
697
1017
628889866
628889542
1.410000e-138
503
5
TraesCS7A01G462100
chr4A
91.608
143
12
0
470
612
715634096
715633954
7.440000e-47
198
6
TraesCS7A01G462100
chr4A
94.286
70
4
0
612
681
715621692
715621623
1.290000e-19
108
7
TraesCS7A01G462100
chr5A
96.394
2718
74
7
696
3398
697625372
697628080
0.000000e+00
4455
8
TraesCS7A01G462100
chr5A
90.255
2155
114
45
697
2795
78443874
78441760
0.000000e+00
2728
9
TraesCS7A01G462100
chr5A
93.846
325
16
3
697
1017
697642232
697641908
1.420000e-133
486
10
TraesCS7A01G462100
chr2A
96.356
2717
63
8
697
3398
752883172
752880477
0.000000e+00
4436
11
TraesCS7A01G462100
chr2A
95.385
1972
85
5
695
2664
739802159
739804126
0.000000e+00
3133
12
TraesCS7A01G462100
chr2A
96.089
179
7
0
1
179
626282691
626282513
3.320000e-75
292
13
TraesCS7A01G462100
chr2A
94.652
187
9
1
1
186
766800557
766800371
4.290000e-74
289
14
TraesCS7A01G462100
chr2A
93.651
189
12
0
1
189
131532838
131533026
2.000000e-72
283
15
TraesCS7A01G462100
chr2A
93.651
189
12
0
1
189
131553362
131553550
2.000000e-72
283
16
TraesCS7A01G462100
chr1A
96.283
2717
65
12
697
3398
13813934
13811239
0.000000e+00
4425
17
TraesCS7A01G462100
chr1A
96.102
2719
67
11
697
3398
34337446
34340142
0.000000e+00
4397
18
TraesCS7A01G462100
chr1A
95.668
2724
81
13
691
3398
566074881
566072179
0.000000e+00
4342
19
TraesCS7A01G462100
chr1A
95.082
183
8
1
1
183
274537724
274537543
1.540000e-73
287
20
TraesCS7A01G462100
chr6A
95.376
2725
77
12
697
3398
71102124
71099426
0.000000e+00
4289
21
TraesCS7A01G462100
chr6A
95.580
181
7
1
1
181
35885117
35884938
4.290000e-74
289
22
TraesCS7A01G462100
chr5D
94.950
2713
76
10
697
3398
356119496
356116834
0.000000e+00
4194
23
TraesCS7A01G462100
chr5D
94.118
2737
94
26
696
3398
52374528
52371825
0.000000e+00
4100
24
TraesCS7A01G462100
chr7D
94.652
2730
77
10
697
3398
538836051
538838739
0.000000e+00
4169
25
TraesCS7A01G462100
chr7D
92.985
2737
82
33
696
3398
426837237
426834577
0.000000e+00
3890
26
TraesCS7A01G462100
chr7D
96.179
602
23
0
2797
3398
445243613
445244214
0.000000e+00
985
27
TraesCS7A01G462100
chr7D
93.233
399
22
2
303
696
569232265
569231867
1.760000e-162
582
28
TraesCS7A01G462100
chr7D
92.473
93
7
0
219
311
569233556
569233464
2.130000e-27
134
29
TraesCS7A01G462100
chr4D
94.453
2740
72
10
696
3398
392724847
392722151
0.000000e+00
4145
30
TraesCS7A01G462100
chr4D
86.413
1288
111
31
697
1938
428621339
428622608
0.000000e+00
1351
31
TraesCS7A01G462100
chr4D
78.414
454
73
17
985
1427
108842555
108842994
4.320000e-69
272
32
TraesCS7A01G462100
chr3D
95.080
2134
53
10
696
2795
52842441
52844556
0.000000e+00
3312
33
TraesCS7A01G462100
chr2B
92.822
1226
68
4
1585
2792
629732798
629731575
0.000000e+00
1759
34
TraesCS7A01G462100
chr1B
96.571
175
6
0
1
175
322054496
322054670
1.190000e-74
291
35
TraesCS7A01G462100
chr3A
94.624
186
8
2
1
185
566863057
566862873
1.540000e-73
287
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
TraesCS7A01G462100
chr7A
658703520
658706917
3397
True
6276
6276
100.000
1
3398
1
chr7A.!!$R1
3397
1
TraesCS7A01G462100
chr7A
576403313
576406544
3231
False
5483
5483
97.343
176
3398
1
chr7A.!!$F1
3222
2
TraesCS7A01G462100
chr4A
628881991
628884700
2709
False
4545
4545
97.015
697
3395
1
chr4A.!!$F1
2698
3
TraesCS7A01G462100
chr5A
697625372
697628080
2708
False
4455
4455
96.394
696
3398
1
chr5A.!!$F1
2702
4
TraesCS7A01G462100
chr5A
78441760
78443874
2114
True
2728
2728
90.255
697
2795
1
chr5A.!!$R1
2098
5
TraesCS7A01G462100
chr2A
752880477
752883172
2695
True
4436
4436
96.356
697
3398
1
chr2A.!!$R2
2701
6
TraesCS7A01G462100
chr2A
739802159
739804126
1967
False
3133
3133
95.385
695
2664
1
chr2A.!!$F3
1969
7
TraesCS7A01G462100
chr1A
13811239
13813934
2695
True
4425
4425
96.283
697
3398
1
chr1A.!!$R1
2701
8
TraesCS7A01G462100
chr1A
34337446
34340142
2696
False
4397
4397
96.102
697
3398
1
chr1A.!!$F1
2701
9
TraesCS7A01G462100
chr1A
566072179
566074881
2702
True
4342
4342
95.668
691
3398
1
chr1A.!!$R3
2707
10
TraesCS7A01G462100
chr6A
71099426
71102124
2698
True
4289
4289
95.376
697
3398
1
chr6A.!!$R2
2701
11
TraesCS7A01G462100
chr5D
356116834
356119496
2662
True
4194
4194
94.950
697
3398
1
chr5D.!!$R2
2701
12
TraesCS7A01G462100
chr5D
52371825
52374528
2703
True
4100
4100
94.118
696
3398
1
chr5D.!!$R1
2702
13
TraesCS7A01G462100
chr7D
538836051
538838739
2688
False
4169
4169
94.652
697
3398
1
chr7D.!!$F2
2701
14
TraesCS7A01G462100
chr7D
426834577
426837237
2660
True
3890
3890
92.985
696
3398
1
chr7D.!!$R1
2702
15
TraesCS7A01G462100
chr7D
445243613
445244214
601
False
985
985
96.179
2797
3398
1
chr7D.!!$F1
601
16
TraesCS7A01G462100
chr7D
569231867
569233556
1689
True
358
582
92.853
219
696
2
chr7D.!!$R2
477
17
TraesCS7A01G462100
chr4D
392722151
392724847
2696
True
4145
4145
94.453
696
3398
1
chr4D.!!$R1
2702
18
TraesCS7A01G462100
chr4D
428621339
428622608
1269
False
1351
1351
86.413
697
1938
1
chr4D.!!$F2
1241
19
TraesCS7A01G462100
chr3D
52842441
52844556
2115
False
3312
3312
95.080
696
2795
1
chr3D.!!$F1
2099
20
TraesCS7A01G462100
chr2B
629731575
629732798
1223
True
1759
1759
92.822
1585
2792
1
chr2B.!!$R1
1207
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
125
126
0.042581
TGATCTGTGGGGCCAGTCTA
59.957
55.000
4.39
0.00
34.02
2.59
F
149
150
0.109412
CCGACAGGAGTAACGACCAC
60.109
60.000
0.00
0.00
41.02
4.16
F
153
154
0.389948
CAGGAGTAACGACCACTGGC
60.390
60.000
0.00
0.00
0.00
4.85
F
598
599
0.539986
GGGGTCGAGTTGGATGCTAA
59.460
55.000
0.00
0.00
0.00
3.09
F
638
639
1.756538
CAATTTGAGTATGGGGGCCAC
59.243
52.381
4.39
0.17
35.80
5.01
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1305
2268
1.541588
GATTCAACCACAAGCCCACTC
59.458
52.381
0.0
0.0
0.00
3.51
R
1577
2661
6.183347
AGATGTTCCCTAAATTCAGTTCCTG
58.817
40.000
0.0
0.0
0.00
3.86
R
2194
3313
6.054295
CAGCCTTCAGTAGCTTAGAAATGAT
58.946
40.000
0.0
0.0
37.18
2.45
R
2203
3322
1.352083
TGACCAGCCTTCAGTAGCTT
58.648
50.000
0.0
0.0
37.18
3.74
R
3034
4356
4.438797
GCTACATCAAATGCAAACATAGCG
59.561
41.667
0.0
0.0
34.62
4.26
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
22
23
4.351874
AGTTAAGTGTGCTTAGCTTGGA
57.648
40.909
5.60
0.00
43.24
3.53
23
24
4.319177
AGTTAAGTGTGCTTAGCTTGGAG
58.681
43.478
5.60
0.00
43.24
3.86
24
25
2.938956
AAGTGTGCTTAGCTTGGAGT
57.061
45.000
5.60
0.00
32.27
3.85
25
26
5.011738
AGTTAAGTGTGCTTAGCTTGGAGTA
59.988
40.000
5.60
0.00
43.24
2.59
26
27
3.601443
AGTGTGCTTAGCTTGGAGTAG
57.399
47.619
5.60
0.00
0.00
2.57
27
28
2.900546
AGTGTGCTTAGCTTGGAGTAGT
59.099
45.455
5.60
0.00
0.00
2.73
28
29
2.996621
GTGTGCTTAGCTTGGAGTAGTG
59.003
50.000
5.60
0.00
0.00
2.74
29
30
2.632996
TGTGCTTAGCTTGGAGTAGTGT
59.367
45.455
5.60
0.00
0.00
3.55
30
31
3.254892
GTGCTTAGCTTGGAGTAGTGTC
58.745
50.000
5.60
0.00
0.00
3.67
31
32
2.897326
TGCTTAGCTTGGAGTAGTGTCA
59.103
45.455
5.60
0.00
0.00
3.58
32
33
3.056536
TGCTTAGCTTGGAGTAGTGTCAG
60.057
47.826
5.60
0.00
0.00
3.51
33
34
3.677424
GCTTAGCTTGGAGTAGTGTCAGG
60.677
52.174
0.00
0.00
0.00
3.86
34
35
2.310779
AGCTTGGAGTAGTGTCAGGA
57.689
50.000
0.00
0.00
0.00
3.86
35
36
2.826488
AGCTTGGAGTAGTGTCAGGAT
58.174
47.619
0.00
0.00
0.00
3.24
36
37
2.499289
AGCTTGGAGTAGTGTCAGGATG
59.501
50.000
0.00
0.00
37.54
3.51
37
38
2.419297
GCTTGGAGTAGTGTCAGGATGG
60.419
54.545
0.00
0.00
36.16
3.51
38
39
1.866015
TGGAGTAGTGTCAGGATGGG
58.134
55.000
0.00
0.00
36.16
4.00
39
40
1.078823
TGGAGTAGTGTCAGGATGGGT
59.921
52.381
0.00
0.00
36.16
4.51
40
41
1.482593
GGAGTAGTGTCAGGATGGGTG
59.517
57.143
0.00
0.00
36.16
4.61
41
42
2.457598
GAGTAGTGTCAGGATGGGTGA
58.542
52.381
0.00
0.00
36.16
4.02
42
43
2.166664
GAGTAGTGTCAGGATGGGTGAC
59.833
54.545
0.00
0.00
43.97
3.67
55
56
4.324991
GTGACCGGCCGGGAAGTT
62.325
66.667
44.99
26.86
39.97
2.66
56
57
4.323477
TGACCGGCCGGGAAGTTG
62.323
66.667
44.99
21.06
39.97
3.16
65
66
3.647771
GGGAAGTTGCTCCCGGGT
61.648
66.667
22.86
0.00
45.81
5.28
66
67
2.359975
GGAAGTTGCTCCCGGGTG
60.360
66.667
22.86
20.53
0.00
4.61
67
68
3.056328
GAAGTTGCTCCCGGGTGC
61.056
66.667
35.31
35.31
35.46
5.01
80
81
4.357947
GGTGCGCACGAGTGAGGA
62.358
66.667
32.35
1.86
0.00
3.71
81
82
3.106407
GTGCGCACGAGTGAGGAC
61.106
66.667
26.77
14.42
43.08
3.85
82
83
4.700365
TGCGCACGAGTGAGGACG
62.700
66.667
5.66
2.25
0.00
4.79
83
84
4.400109
GCGCACGAGTGAGGACGA
62.400
66.667
0.30
0.00
0.00
4.20
84
85
2.254350
CGCACGAGTGAGGACGAA
59.746
61.111
7.50
0.00
0.00
3.85
85
86
1.797933
CGCACGAGTGAGGACGAAG
60.798
63.158
7.50
0.00
0.00
3.79
98
99
2.986311
ACGAAGTGCGCAGAAAAGA
58.014
47.368
12.22
0.00
46.04
2.52
99
100
0.582005
ACGAAGTGCGCAGAAAAGAC
59.418
50.000
12.22
0.00
46.04
3.01
100
101
0.861837
CGAAGTGCGCAGAAAAGACT
59.138
50.000
12.22
0.00
0.00
3.24
101
102
2.058798
CGAAGTGCGCAGAAAAGACTA
58.941
47.619
12.22
0.00
0.00
2.59
102
103
2.091277
CGAAGTGCGCAGAAAAGACTAG
59.909
50.000
12.22
0.00
0.00
2.57
103
104
2.821991
AGTGCGCAGAAAAGACTAGT
57.178
45.000
12.22
0.00
0.00
2.57
104
105
3.936372
AGTGCGCAGAAAAGACTAGTA
57.064
42.857
12.22
0.00
0.00
1.82
105
106
4.457834
AGTGCGCAGAAAAGACTAGTAT
57.542
40.909
12.22
0.00
0.00
2.12
106
107
4.822026
AGTGCGCAGAAAAGACTAGTATT
58.178
39.130
12.22
0.00
0.00
1.89
107
108
4.627467
AGTGCGCAGAAAAGACTAGTATTG
59.373
41.667
12.22
0.00
0.00
1.90
108
109
4.625742
GTGCGCAGAAAAGACTAGTATTGA
59.374
41.667
12.22
0.00
0.00
2.57
109
110
5.292101
GTGCGCAGAAAAGACTAGTATTGAT
59.708
40.000
12.22
0.00
0.00
2.57
110
111
5.520288
TGCGCAGAAAAGACTAGTATTGATC
59.480
40.000
5.66
5.93
0.00
2.92
111
112
5.751028
GCGCAGAAAAGACTAGTATTGATCT
59.249
40.000
0.30
8.07
0.00
2.75
112
113
6.292061
GCGCAGAAAAGACTAGTATTGATCTG
60.292
42.308
26.54
26.54
34.47
2.90
113
114
6.754209
CGCAGAAAAGACTAGTATTGATCTGT
59.246
38.462
28.67
6.17
34.16
3.41
114
115
7.253917
CGCAGAAAAGACTAGTATTGATCTGTG
60.254
40.741
28.67
28.07
35.17
3.66
115
116
7.010923
GCAGAAAAGACTAGTATTGATCTGTGG
59.989
40.741
28.67
15.98
34.16
4.17
116
117
7.493971
CAGAAAAGACTAGTATTGATCTGTGGG
59.506
40.741
24.47
10.26
30.53
4.61
117
118
5.878406
AAGACTAGTATTGATCTGTGGGG
57.122
43.478
1.03
0.00
0.00
4.96
118
119
3.643792
AGACTAGTATTGATCTGTGGGGC
59.356
47.826
0.00
0.00
0.00
5.80
119
120
2.706190
ACTAGTATTGATCTGTGGGGCC
59.294
50.000
0.00
0.00
0.00
5.80
120
121
1.595311
AGTATTGATCTGTGGGGCCA
58.405
50.000
4.39
0.00
0.00
5.36
121
122
1.492176
AGTATTGATCTGTGGGGCCAG
59.508
52.381
4.39
0.00
0.00
4.85
122
123
1.212935
GTATTGATCTGTGGGGCCAGT
59.787
52.381
4.39
0.00
34.02
4.00
123
124
0.257039
ATTGATCTGTGGGGCCAGTC
59.743
55.000
4.39
0.00
34.02
3.51
124
125
0.842030
TTGATCTGTGGGGCCAGTCT
60.842
55.000
4.39
0.00
34.02
3.24
125
126
0.042581
TGATCTGTGGGGCCAGTCTA
59.957
55.000
4.39
0.00
34.02
2.59
126
127
0.755686
GATCTGTGGGGCCAGTCTAG
59.244
60.000
4.39
0.00
34.02
2.43
127
128
0.339859
ATCTGTGGGGCCAGTCTAGA
59.660
55.000
4.39
1.35
34.02
2.43
128
129
0.339859
TCTGTGGGGCCAGTCTAGAT
59.660
55.000
4.39
0.00
34.02
1.98
129
130
0.755686
CTGTGGGGCCAGTCTAGATC
59.244
60.000
4.39
0.00
0.00
2.75
130
131
0.691078
TGTGGGGCCAGTCTAGATCC
60.691
60.000
4.39
0.00
0.00
3.36
131
132
1.074471
TGGGGCCAGTCTAGATCCC
60.074
63.158
4.39
11.66
36.25
3.85
132
133
2.210711
GGGGCCAGTCTAGATCCCG
61.211
68.421
4.39
0.00
37.85
5.14
133
134
1.152525
GGGCCAGTCTAGATCCCGA
60.153
63.158
4.39
0.00
0.00
5.14
134
135
1.465200
GGGCCAGTCTAGATCCCGAC
61.465
65.000
4.39
4.30
0.00
4.79
135
136
0.755698
GGCCAGTCTAGATCCCGACA
60.756
60.000
12.79
0.00
32.68
4.35
136
137
0.671251
GCCAGTCTAGATCCCGACAG
59.329
60.000
12.79
6.21
32.68
3.51
137
138
1.323412
CCAGTCTAGATCCCGACAGG
58.677
60.000
12.79
10.58
31.81
4.00
146
147
2.559785
TCCCGACAGGAGTAACGAC
58.440
57.895
0.00
0.00
40.93
4.34
147
148
0.962356
TCCCGACAGGAGTAACGACC
60.962
60.000
0.00
0.00
40.93
4.79
148
149
1.246056
CCCGACAGGAGTAACGACCA
61.246
60.000
0.00
0.00
41.02
4.02
149
150
0.109412
CCGACAGGAGTAACGACCAC
60.109
60.000
0.00
0.00
41.02
4.16
150
151
0.879765
CGACAGGAGTAACGACCACT
59.120
55.000
0.00
0.00
0.00
4.00
151
152
1.401148
CGACAGGAGTAACGACCACTG
60.401
57.143
0.00
0.00
36.43
3.66
152
153
0.966920
ACAGGAGTAACGACCACTGG
59.033
55.000
0.00
0.00
35.30
4.00
153
154
0.389948
CAGGAGTAACGACCACTGGC
60.390
60.000
0.00
0.00
0.00
4.85
154
155
1.445582
GGAGTAACGACCACTGGCG
60.446
63.158
9.51
9.51
0.00
5.69
155
156
1.445582
GAGTAACGACCACTGGCGG
60.446
63.158
13.99
0.00
0.00
6.13
156
157
2.433664
GTAACGACCACTGGCGGG
60.434
66.667
13.99
0.00
0.00
6.13
157
158
2.918802
TAACGACCACTGGCGGGT
60.919
61.111
13.99
0.00
42.61
5.28
158
159
3.229156
TAACGACCACTGGCGGGTG
62.229
63.158
13.99
0.48
39.19
4.61
161
162
4.250305
GACCACTGGCGGGTGTGT
62.250
66.667
0.00
1.76
39.19
3.72
162
163
4.250305
ACCACTGGCGGGTGTGTC
62.250
66.667
0.00
0.00
37.23
3.67
171
172
3.881104
GGGTGTGTCCGGGGTGTT
61.881
66.667
0.00
0.00
37.00
3.32
172
173
2.518709
GGGTGTGTCCGGGGTGTTA
61.519
63.158
0.00
0.00
37.00
2.41
173
174
1.301953
GGTGTGTCCGGGGTGTTAC
60.302
63.158
0.00
0.00
0.00
2.50
174
175
1.446791
GTGTGTCCGGGGTGTTACA
59.553
57.895
0.00
0.00
0.00
2.41
387
388
3.684788
AGGATTGTTTTTCGGTCAGATCG
59.315
43.478
0.00
0.00
0.00
3.69
451
452
1.404583
GCAGGCAGGCGAAATTTCATT
60.405
47.619
17.99
0.04
0.00
2.57
488
489
3.404869
TCAATCTTCTGGAGAGCCCTA
57.595
47.619
0.00
0.00
37.93
3.53
521
522
3.587840
CCTCCAAGGGTCCACCAA
58.412
61.111
0.00
0.00
43.89
3.67
556
557
1.867233
CGCACATAACAGCCATCCTAC
59.133
52.381
0.00
0.00
0.00
3.18
598
599
0.539986
GGGGTCGAGTTGGATGCTAA
59.460
55.000
0.00
0.00
0.00
3.09
616
617
2.624316
AAATGCTTGCTGTGTCATCG
57.376
45.000
0.00
0.00
0.00
3.84
627
628
2.485426
CTGTGTCATCGGCAATTTGAGT
59.515
45.455
0.00
0.00
0.00
3.41
633
634
2.051334
TCGGCAATTTGAGTATGGGG
57.949
50.000
0.00
0.00
0.00
4.96
638
639
1.756538
CAATTTGAGTATGGGGGCCAC
59.243
52.381
4.39
0.17
35.80
5.01
1237
1924
7.097192
TCTTCCATGTAGTTCTTATGTGTGAC
58.903
38.462
0.00
0.00
0.00
3.67
1305
2268
4.253685
ACACGGTGATAGATCCAAGTTTG
58.746
43.478
16.29
0.00
0.00
2.93
1429
2488
4.212716
TGGATGTGCTACTACGGTAAGAT
58.787
43.478
0.00
0.00
0.00
2.40
1513
2572
9.467258
AACATTGATATTCTTGTTGTTTCAGTG
57.533
29.630
0.00
0.00
31.45
3.66
1577
2661
7.331934
TGTTCATGTGTTAGCTAAATCTCTGAC
59.668
37.037
7.99
4.08
0.00
3.51
2194
3313
4.029520
AGAGAAGAAGAAGCTGGAGCATA
58.970
43.478
0.65
0.00
45.16
3.14
2203
3322
6.430962
AGAAGCTGGAGCATATCATTTCTA
57.569
37.500
0.65
0.00
45.16
2.10
2815
4131
8.738199
TTATACAGTTCAACTACTGACGAAAG
57.262
34.615
10.46
0.00
46.72
2.62
3034
4356
0.716108
CGTCGTCTTCATGCACCTTC
59.284
55.000
0.00
0.00
0.00
3.46
3038
4360
1.735700
CGTCTTCATGCACCTTCGCTA
60.736
52.381
0.00
0.00
0.00
4.26
3083
4405
0.613572
TGGAGTGACATAGCGGTGGA
60.614
55.000
0.00
0.00
0.00
4.02
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
4.714632
TCCAAGCTAAGCACACTTAACTT
58.285
39.130
0.00
0.00
42.71
2.66
2
3
4.065789
ACTCCAAGCTAAGCACACTTAAC
58.934
43.478
0.00
0.00
37.91
2.01
4
5
4.527038
ACTACTCCAAGCTAAGCACACTTA
59.473
41.667
0.00
0.00
37.33
2.24
5
6
2.938956
ACTCCAAGCTAAGCACACTT
57.061
45.000
0.00
0.00
40.07
3.16
6
7
2.900546
ACTACTCCAAGCTAAGCACACT
59.099
45.455
0.00
0.00
0.00
3.55
7
8
2.996621
CACTACTCCAAGCTAAGCACAC
59.003
50.000
0.00
0.00
0.00
3.82
8
9
2.632996
ACACTACTCCAAGCTAAGCACA
59.367
45.455
0.00
0.00
0.00
4.57
9
10
3.254892
GACACTACTCCAAGCTAAGCAC
58.745
50.000
0.00
0.00
0.00
4.40
10
11
2.897326
TGACACTACTCCAAGCTAAGCA
59.103
45.455
0.00
0.00
0.00
3.91
11
12
3.516615
CTGACACTACTCCAAGCTAAGC
58.483
50.000
0.00
0.00
0.00
3.09
12
13
3.764434
TCCTGACACTACTCCAAGCTAAG
59.236
47.826
0.00
0.00
0.00
2.18
13
14
3.774734
TCCTGACACTACTCCAAGCTAA
58.225
45.455
0.00
0.00
0.00
3.09
14
15
3.451402
TCCTGACACTACTCCAAGCTA
57.549
47.619
0.00
0.00
0.00
3.32
15
16
2.310779
TCCTGACACTACTCCAAGCT
57.689
50.000
0.00
0.00
0.00
3.74
16
17
2.419297
CCATCCTGACACTACTCCAAGC
60.419
54.545
0.00
0.00
0.00
4.01
17
18
2.169352
CCCATCCTGACACTACTCCAAG
59.831
54.545
0.00
0.00
0.00
3.61
18
19
2.187958
CCCATCCTGACACTACTCCAA
58.812
52.381
0.00
0.00
0.00
3.53
19
20
1.078823
ACCCATCCTGACACTACTCCA
59.921
52.381
0.00
0.00
0.00
3.86
20
21
1.482593
CACCCATCCTGACACTACTCC
59.517
57.143
0.00
0.00
0.00
3.85
21
22
2.166664
GTCACCCATCCTGACACTACTC
59.833
54.545
0.00
0.00
38.36
2.59
22
23
2.180276
GTCACCCATCCTGACACTACT
58.820
52.381
0.00
0.00
38.36
2.57
23
24
1.207329
GGTCACCCATCCTGACACTAC
59.793
57.143
1.29
0.00
39.97
2.73
24
25
1.568504
GGTCACCCATCCTGACACTA
58.431
55.000
1.29
0.00
39.97
2.74
25
26
1.544825
CGGTCACCCATCCTGACACT
61.545
60.000
0.00
0.00
39.97
3.55
26
27
1.079127
CGGTCACCCATCCTGACAC
60.079
63.158
0.00
0.00
39.97
3.67
27
28
2.290287
CCGGTCACCCATCCTGACA
61.290
63.158
0.00
0.00
39.97
3.58
28
29
2.584608
CCGGTCACCCATCCTGAC
59.415
66.667
0.00
0.00
37.84
3.51
29
30
3.399181
GCCGGTCACCCATCCTGA
61.399
66.667
1.90
0.00
0.00
3.86
30
31
4.489771
GGCCGGTCACCCATCCTG
62.490
72.222
0.00
0.00
0.00
3.86
38
39
4.324991
AACTTCCCGGCCGGTCAC
62.325
66.667
40.52
0.00
0.00
3.67
39
40
4.323477
CAACTTCCCGGCCGGTCA
62.323
66.667
40.52
25.50
0.00
4.02
49
50
2.359975
CACCCGGGAGCAACTTCC
60.360
66.667
32.02
0.00
36.46
3.46
50
51
3.056328
GCACCCGGGAGCAACTTC
61.056
66.667
34.66
6.62
0.00
3.01
63
64
4.357947
TCCTCACTCGTGCGCACC
62.358
66.667
33.23
16.56
0.00
5.01
64
65
3.106407
GTCCTCACTCGTGCGCAC
61.106
66.667
30.42
30.42
0.00
5.34
65
66
4.700365
CGTCCTCACTCGTGCGCA
62.700
66.667
5.66
5.66
0.00
6.09
66
67
3.891586
TTCGTCCTCACTCGTGCGC
62.892
63.158
0.00
0.00
0.00
6.09
67
68
1.797933
CTTCGTCCTCACTCGTGCG
60.798
63.158
0.00
0.00
0.00
5.34
68
69
1.004277
CACTTCGTCCTCACTCGTGC
61.004
60.000
0.00
0.00
0.00
5.34
69
70
1.004277
GCACTTCGTCCTCACTCGTG
61.004
60.000
0.00
0.00
0.00
4.35
70
71
1.286260
GCACTTCGTCCTCACTCGT
59.714
57.895
0.00
0.00
0.00
4.18
71
72
1.797933
CGCACTTCGTCCTCACTCG
60.798
63.158
0.00
0.00
0.00
4.18
72
73
2.089349
GCGCACTTCGTCCTCACTC
61.089
63.158
0.30
0.00
41.07
3.51
73
74
2.049063
GCGCACTTCGTCCTCACT
60.049
61.111
0.30
0.00
41.07
3.41
74
75
2.355837
TGCGCACTTCGTCCTCAC
60.356
61.111
5.66
0.00
41.07
3.51
75
76
2.049156
CTGCGCACTTCGTCCTCA
60.049
61.111
5.66
0.00
41.07
3.86
76
77
0.944311
TTTCTGCGCACTTCGTCCTC
60.944
55.000
5.66
0.00
41.07
3.71
77
78
0.531974
TTTTCTGCGCACTTCGTCCT
60.532
50.000
5.66
0.00
41.07
3.85
78
79
0.110644
CTTTTCTGCGCACTTCGTCC
60.111
55.000
5.66
0.00
41.07
4.79
79
80
0.859232
TCTTTTCTGCGCACTTCGTC
59.141
50.000
5.66
0.00
41.07
4.20
80
81
0.582005
GTCTTTTCTGCGCACTTCGT
59.418
50.000
5.66
0.00
41.07
3.85
81
82
0.861837
AGTCTTTTCTGCGCACTTCG
59.138
50.000
5.66
0.00
42.12
3.79
82
83
3.060602
ACTAGTCTTTTCTGCGCACTTC
58.939
45.455
5.66
0.00
0.00
3.01
83
84
3.113260
ACTAGTCTTTTCTGCGCACTT
57.887
42.857
5.66
0.00
0.00
3.16
84
85
2.821991
ACTAGTCTTTTCTGCGCACT
57.178
45.000
5.66
2.15
0.00
4.40
85
86
4.625742
TCAATACTAGTCTTTTCTGCGCAC
59.374
41.667
5.66
0.00
0.00
5.34
86
87
4.816392
TCAATACTAGTCTTTTCTGCGCA
58.184
39.130
10.98
10.98
0.00
6.09
87
88
5.751028
AGATCAATACTAGTCTTTTCTGCGC
59.249
40.000
0.00
0.00
0.00
6.09
88
89
6.754209
ACAGATCAATACTAGTCTTTTCTGCG
59.246
38.462
20.08
7.76
33.16
5.18
89
90
7.010923
CCACAGATCAATACTAGTCTTTTCTGC
59.989
40.741
20.08
1.61
33.16
4.26
90
91
7.493971
CCCACAGATCAATACTAGTCTTTTCTG
59.506
40.741
19.27
19.27
35.40
3.02
91
92
7.365117
CCCCACAGATCAATACTAGTCTTTTCT
60.365
40.741
0.00
0.00
0.00
2.52
92
93
6.763610
CCCCACAGATCAATACTAGTCTTTTC
59.236
42.308
0.00
0.00
0.00
2.29
93
94
6.653989
CCCCACAGATCAATACTAGTCTTTT
58.346
40.000
0.00
0.00
0.00
2.27
94
95
5.396884
GCCCCACAGATCAATACTAGTCTTT
60.397
44.000
0.00
0.00
0.00
2.52
95
96
4.101741
GCCCCACAGATCAATACTAGTCTT
59.898
45.833
0.00
0.00
0.00
3.01
96
97
3.643792
GCCCCACAGATCAATACTAGTCT
59.356
47.826
0.00
0.00
0.00
3.24
97
98
3.244249
GGCCCCACAGATCAATACTAGTC
60.244
52.174
0.00
0.00
0.00
2.59
98
99
2.706190
GGCCCCACAGATCAATACTAGT
59.294
50.000
0.00
0.00
0.00
2.57
99
100
2.705658
TGGCCCCACAGATCAATACTAG
59.294
50.000
0.00
0.00
0.00
2.57
100
101
2.705658
CTGGCCCCACAGATCAATACTA
59.294
50.000
0.00
0.00
40.97
1.82
101
102
1.492176
CTGGCCCCACAGATCAATACT
59.508
52.381
0.00
0.00
40.97
2.12
102
103
1.212935
ACTGGCCCCACAGATCAATAC
59.787
52.381
0.00
0.00
40.97
1.89
103
104
1.490490
GACTGGCCCCACAGATCAATA
59.510
52.381
0.00
0.00
40.97
1.90
104
105
0.257039
GACTGGCCCCACAGATCAAT
59.743
55.000
0.00
0.00
40.97
2.57
105
106
0.842030
AGACTGGCCCCACAGATCAA
60.842
55.000
0.00
0.00
40.97
2.57
106
107
0.042581
TAGACTGGCCCCACAGATCA
59.957
55.000
0.00
0.00
40.97
2.92
107
108
0.755686
CTAGACTGGCCCCACAGATC
59.244
60.000
0.00
0.00
40.97
2.75
108
109
0.339859
TCTAGACTGGCCCCACAGAT
59.660
55.000
0.00
0.00
40.97
2.90
109
110
0.339859
ATCTAGACTGGCCCCACAGA
59.660
55.000
0.00
0.00
40.97
3.41
110
111
0.755686
GATCTAGACTGGCCCCACAG
59.244
60.000
0.00
0.00
44.03
3.66
111
112
0.691078
GGATCTAGACTGGCCCCACA
60.691
60.000
0.00
0.00
0.00
4.17
112
113
1.411651
GGGATCTAGACTGGCCCCAC
61.412
65.000
0.00
0.00
34.10
4.61
113
114
1.074471
GGGATCTAGACTGGCCCCA
60.074
63.158
0.00
0.00
34.10
4.96
114
115
2.210711
CGGGATCTAGACTGGCCCC
61.211
68.421
0.00
9.76
35.30
5.80
115
116
1.152525
TCGGGATCTAGACTGGCCC
60.153
63.158
0.00
3.13
35.40
5.80
116
117
0.755698
TGTCGGGATCTAGACTGGCC
60.756
60.000
17.40
0.00
38.16
5.36
117
118
0.671251
CTGTCGGGATCTAGACTGGC
59.329
60.000
17.40
0.00
38.16
4.85
118
119
1.323412
CCTGTCGGGATCTAGACTGG
58.677
60.000
22.00
22.00
45.39
4.00
119
120
2.226330
CTCCTGTCGGGATCTAGACTG
58.774
57.143
17.40
16.40
44.15
3.51
120
121
1.847737
ACTCCTGTCGGGATCTAGACT
59.152
52.381
17.40
0.00
44.15
3.24
121
122
2.351706
ACTCCTGTCGGGATCTAGAC
57.648
55.000
0.00
12.16
44.15
2.59
122
123
3.743584
CGTTACTCCTGTCGGGATCTAGA
60.744
52.174
0.00
0.00
44.15
2.43
123
124
2.548904
CGTTACTCCTGTCGGGATCTAG
59.451
54.545
0.00
0.00
44.15
2.43
124
125
2.171237
TCGTTACTCCTGTCGGGATCTA
59.829
50.000
0.00
0.00
44.15
1.98
125
126
1.064906
TCGTTACTCCTGTCGGGATCT
60.065
52.381
0.00
0.00
44.15
2.75
126
127
1.065251
GTCGTTACTCCTGTCGGGATC
59.935
57.143
0.00
0.00
44.15
3.36
127
128
1.101331
GTCGTTACTCCTGTCGGGAT
58.899
55.000
0.00
0.00
44.15
3.85
128
129
0.962356
GGTCGTTACTCCTGTCGGGA
60.962
60.000
0.00
0.00
42.77
5.14
129
130
1.246056
TGGTCGTTACTCCTGTCGGG
61.246
60.000
0.00
0.00
0.00
5.14
130
131
0.109412
GTGGTCGTTACTCCTGTCGG
60.109
60.000
0.00
0.00
0.00
4.79
131
132
0.879765
AGTGGTCGTTACTCCTGTCG
59.120
55.000
0.00
0.00
0.00
4.35
132
133
1.067776
CCAGTGGTCGTTACTCCTGTC
60.068
57.143
0.00
0.00
0.00
3.51
133
134
0.966920
CCAGTGGTCGTTACTCCTGT
59.033
55.000
0.00
0.00
0.00
4.00
134
135
0.389948
GCCAGTGGTCGTTACTCCTG
60.390
60.000
11.74
0.00
0.00
3.86
135
136
1.874345
CGCCAGTGGTCGTTACTCCT
61.874
60.000
11.74
0.00
0.00
3.69
136
137
1.445582
CGCCAGTGGTCGTTACTCC
60.446
63.158
11.74
0.00
0.00
3.85
137
138
1.445582
CCGCCAGTGGTCGTTACTC
60.446
63.158
19.84
0.00
0.00
2.59
138
139
2.654877
CCGCCAGTGGTCGTTACT
59.345
61.111
19.84
0.00
0.00
2.24
139
140
2.433664
CCCGCCAGTGGTCGTTAC
60.434
66.667
19.84
0.00
0.00
2.50
140
141
2.918802
ACCCGCCAGTGGTCGTTA
60.919
61.111
19.84
0.00
0.00
3.18
141
142
4.619227
CACCCGCCAGTGGTCGTT
62.619
66.667
19.84
7.92
32.46
3.85
144
145
4.250305
ACACACCCGCCAGTGGTC
62.250
66.667
11.74
2.09
42.28
4.02
145
146
4.250305
GACACACCCGCCAGTGGT
62.250
66.667
11.74
1.28
42.28
4.16
154
155
2.518709
TAACACCCCGGACACACCC
61.519
63.158
0.73
0.00
34.64
4.61
155
156
1.301953
GTAACACCCCGGACACACC
60.302
63.158
0.73
0.00
0.00
4.16
156
157
0.601841
CTGTAACACCCCGGACACAC
60.602
60.000
0.73
0.00
0.00
3.82
157
158
0.759812
TCTGTAACACCCCGGACACA
60.760
55.000
0.73
0.00
0.00
3.72
158
159
0.320160
GTCTGTAACACCCCGGACAC
60.320
60.000
0.73
0.00
37.03
3.67
159
160
0.759812
TGTCTGTAACACCCCGGACA
60.760
55.000
0.73
0.00
42.97
4.02
160
161
2.051941
TGTCTGTAACACCCCGGAC
58.948
57.895
0.73
0.00
37.46
4.79
161
162
4.623308
TGTCTGTAACACCCCGGA
57.377
55.556
0.73
0.00
31.20
5.14
168
169
2.545113
GCGTGAGAAGGTGTCTGTAACA
60.545
50.000
0.00
0.00
36.41
2.41
169
170
2.059541
GCGTGAGAAGGTGTCTGTAAC
58.940
52.381
0.00
0.00
36.41
2.50
170
171
1.335597
CGCGTGAGAAGGTGTCTGTAA
60.336
52.381
0.00
0.00
36.41
2.41
171
172
0.240145
CGCGTGAGAAGGTGTCTGTA
59.760
55.000
0.00
0.00
36.41
2.74
172
173
1.007271
CGCGTGAGAAGGTGTCTGT
60.007
57.895
0.00
0.00
36.41
3.41
173
174
0.730834
CTCGCGTGAGAAGGTGTCTG
60.731
60.000
21.40
0.00
45.57
3.51
174
175
1.173444
ACTCGCGTGAGAAGGTGTCT
61.173
55.000
31.50
4.24
45.57
3.41
387
388
1.137479
TGCACGTACACCCTATAAGCC
59.863
52.381
0.00
0.00
0.00
4.35
451
452
7.784073
AGAAGATTGATCTATCCTCTTGTCTCA
59.216
37.037
12.72
0.00
35.76
3.27
488
489
2.225343
TGGAGGGCACTGAATTTTCCAT
60.225
45.455
0.00
0.00
0.00
3.41
556
557
6.418956
CCAATTCGTACAATATTCCTGAACG
58.581
40.000
0.00
0.00
0.00
3.95
598
599
0.806868
CCGATGACACAGCAAGCATT
59.193
50.000
0.00
0.00
0.00
3.56
616
617
0.752658
GCCCCCATACTCAAATTGCC
59.247
55.000
0.00
0.00
0.00
4.52
627
628
1.089123
AGAAAAAGGTGGCCCCCATA
58.911
50.000
7.14
0.00
35.28
2.74
633
634
2.049156
GCGCAGAAAAAGGTGGCC
60.049
61.111
0.30
0.00
0.00
5.36
638
639
0.665369
CCTTGCAGCGCAGAAAAAGG
60.665
55.000
11.47
12.20
40.61
3.11
1237
1924
4.183865
CCCATATATATCAGCCACACACG
58.816
47.826
0.00
0.00
0.00
4.49
1305
2268
1.541588
GATTCAACCACAAGCCCACTC
59.458
52.381
0.00
0.00
0.00
3.51
1429
2488
8.908903
ACATGAAAACCACTAACAATTAGTTGA
58.091
29.630
4.81
0.00
43.70
3.18
1513
2572
9.997482
TTGTACTTCAATTTTCAGTAAACAGAC
57.003
29.630
0.00
0.00
0.00
3.51
1577
2661
6.183347
AGATGTTCCCTAAATTCAGTTCCTG
58.817
40.000
0.00
0.00
0.00
3.86
2194
3313
6.054295
CAGCCTTCAGTAGCTTAGAAATGAT
58.946
40.000
0.00
0.00
37.18
2.45
2203
3322
1.352083
TGACCAGCCTTCAGTAGCTT
58.648
50.000
0.00
0.00
37.18
3.74
3034
4356
4.438797
GCTACATCAAATGCAAACATAGCG
59.561
41.667
0.00
0.00
34.62
4.26
3038
4360
5.636121
CACAAGCTACATCAAATGCAAACAT
59.364
36.000
0.00
0.00
38.49
2.71
3069
4391
1.218047
GCAGTCCACCGCTATGTCA
59.782
57.895
0.00
0.00
0.00
3.58
3094
4416
4.764771
GATGCTGGGCAGGGGCAA
62.765
66.667
0.00
0.00
43.65
4.52
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.