Multiple sequence alignment - TraesCS7A01G408300
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
TraesCS7A01G408300
chr7A
100.000
2921
0
0
1
2921
594451519
594454439
0.000000e+00
5395.0
1
TraesCS7A01G408300
chr7A
93.568
2410
130
9
461
2847
628652620
628655027
0.000000e+00
3568.0
2
TraesCS7A01G408300
chr7A
87.003
1762
218
6
1098
2850
628867155
628865396
0.000000e+00
1975.0
3
TraesCS7A01G408300
chr7A
97.107
242
7
0
1
242
13882738
13882497
2.710000e-110
409.0
4
TraesCS7A01G408300
chr7D
96.590
2317
47
8
245
2541
518776736
518779040
0.000000e+00
3812.0
5
TraesCS7A01G408300
chr7D
93.400
2409
136
7
461
2847
545654205
545656612
0.000000e+00
3546.0
6
TraesCS7A01G408300
chr7D
87.535
1797
211
8
1061
2847
545660102
545661895
0.000000e+00
2065.0
7
TraesCS7A01G408300
chr7D
87.070
1802
220
8
1059
2850
546129865
546128067
0.000000e+00
2025.0
8
TraesCS7A01G408300
chr7D
97.959
392
4
1
2534
2921
518779182
518779573
0.000000e+00
676.0
9
TraesCS7A01G408300
chr7D
97.934
242
5
0
1
242
27010003
27009762
1.250000e-113
420.0
10
TraesCS7A01G408300
chr7B
91.168
2389
152
14
243
2606
589939134
589941488
0.000000e+00
3188.0
11
TraesCS7A01G408300
chr7B
86.090
1826
243
6
1040
2856
590107498
590105675
0.000000e+00
1954.0
12
TraesCS7A01G408300
chr7B
85.516
1802
241
14
1058
2847
589899221
589901014
0.000000e+00
1864.0
13
TraesCS7A01G408300
chr7B
92.672
232
13
1
2620
2847
589942917
589943148
6.030000e-87
331.0
14
TraesCS7A01G408300
chr7B
86.567
67
6
2
2854
2920
552115284
552115347
1.450000e-08
71.3
15
TraesCS7A01G408300
chr5B
96.694
242
8
0
1
242
545884412
545884653
1.260000e-108
403.0
16
TraesCS7A01G408300
chr2B
97.071
239
7
0
1
239
25413162
25413400
1.260000e-108
403.0
17
TraesCS7A01G408300
chr2B
96.281
242
9
0
1
242
117720935
117721176
5.870000e-107
398.0
18
TraesCS7A01G408300
chr6B
96.281
242
9
0
1
242
706981406
706981647
5.870000e-107
398.0
19
TraesCS7A01G408300
chr6A
96.281
242
9
0
1
242
41483495
41483254
5.870000e-107
398.0
20
TraesCS7A01G408300
chr1A
96.281
242
9
0
1
242
366122526
366122285
5.870000e-107
398.0
21
TraesCS7A01G408300
chr1A
96.266
241
9
0
2
242
586093813
586093573
2.110000e-106
396.0
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
TraesCS7A01G408300
chr7A
594451519
594454439
2920
False
5395.0
5395
100.0000
1
2921
1
chr7A.!!$F1
2920
1
TraesCS7A01G408300
chr7A
628652620
628655027
2407
False
3568.0
3568
93.5680
461
2847
1
chr7A.!!$F2
2386
2
TraesCS7A01G408300
chr7A
628865396
628867155
1759
True
1975.0
1975
87.0030
1098
2850
1
chr7A.!!$R2
1752
3
TraesCS7A01G408300
chr7D
545654205
545661895
7690
False
2805.5
3546
90.4675
461
2847
2
chr7D.!!$F2
2386
4
TraesCS7A01G408300
chr7D
518776736
518779573
2837
False
2244.0
3812
97.2745
245
2921
2
chr7D.!!$F1
2676
5
TraesCS7A01G408300
chr7D
546128067
546129865
1798
True
2025.0
2025
87.0700
1059
2850
1
chr7D.!!$R2
1791
6
TraesCS7A01G408300
chr7B
590105675
590107498
1823
True
1954.0
1954
86.0900
1040
2856
1
chr7B.!!$R1
1816
7
TraesCS7A01G408300
chr7B
589899221
589901014
1793
False
1864.0
1864
85.5160
1058
2847
1
chr7B.!!$F2
1789
8
TraesCS7A01G408300
chr7B
589939134
589943148
4014
False
1759.5
3188
91.9200
243
2847
2
chr7B.!!$F3
2604
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
136
137
0.188587
TACCTGAGGCTCCCGATGAT
59.811
55.0
12.86
0.0
0.0
2.45
F
145
146
0.244721
CTCCCGATGATGCTGCGATA
59.755
55.0
0.00
0.0
0.0
2.92
F
1467
1493
0.113190
CAAACCCCAGCCTTCCTCTT
59.887
55.0
0.00
0.0
0.0
2.85
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1401
1427
1.131638
TGAGGTGGTTGAAGCTGACT
58.868
50.000
0.0
0.0
0.00
3.41
R
1779
1806
6.165700
AGAACTCCTTGCAAATCATTGTTT
57.834
33.333
0.0
0.0
38.85
2.83
R
2468
2502
1.918262
AGCCCAGTTCATCAATCCAGA
59.082
47.619
0.0
0.0
0.00
3.86
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
17
18
2.960129
CCCGCGATGTACCGAAGC
60.960
66.667
8.23
0.00
0.00
3.86
18
19
2.202690
CCGCGATGTACCGAAGCA
60.203
61.111
8.23
0.00
0.00
3.91
19
20
2.230940
CCGCGATGTACCGAAGCAG
61.231
63.158
8.23
0.00
0.00
4.24
20
21
2.230940
CGCGATGTACCGAAGCAGG
61.231
63.158
0.00
0.00
37.30
4.85
22
23
1.421410
GCGATGTACCGAAGCAGGTG
61.421
60.000
8.53
0.00
45.54
4.00
23
24
1.421410
CGATGTACCGAAGCAGGTGC
61.421
60.000
8.53
7.76
45.54
5.01
33
34
3.730761
GCAGGTGCTTGACGGCAG
61.731
66.667
0.00
0.00
43.25
4.85
37
38
3.782244
GTGCTTGACGGCAGCGAG
61.782
66.667
7.96
0.00
43.25
5.03
38
39
3.989787
TGCTTGACGGCAGCGAGA
61.990
61.111
7.96
0.00
37.29
4.04
39
40
2.510238
GCTTGACGGCAGCGAGAT
60.510
61.111
0.00
0.00
0.00
2.75
40
41
2.806856
GCTTGACGGCAGCGAGATG
61.807
63.158
0.00
0.00
0.00
2.90
41
42
1.153765
CTTGACGGCAGCGAGATGA
60.154
57.895
0.00
0.00
0.00
2.92
42
43
0.529337
CTTGACGGCAGCGAGATGAT
60.529
55.000
0.00
0.00
0.00
2.45
43
44
0.528466
TTGACGGCAGCGAGATGATC
60.528
55.000
0.00
0.00
0.00
2.92
51
52
3.228624
CGAGATGATCGCTTGCCG
58.771
61.111
0.00
0.00
45.98
5.69
52
53
2.305853
CGAGATGATCGCTTGCCGG
61.306
63.158
0.00
0.00
45.98
6.13
53
54
1.958205
GAGATGATCGCTTGCCGGG
60.958
63.158
2.18
0.00
37.59
5.73
54
55
2.974698
GATGATCGCTTGCCGGGG
60.975
66.667
2.18
0.00
37.59
5.73
62
63
3.142838
CTTGCCGGGGCTTCCATG
61.143
66.667
11.55
0.00
42.51
3.66
63
64
3.643595
CTTGCCGGGGCTTCCATGA
62.644
63.158
11.55
0.00
42.51
3.07
64
65
3.216985
TTGCCGGGGCTTCCATGAA
62.217
57.895
11.55
0.00
42.51
2.57
65
66
3.140814
GCCGGGGCTTCCATGAAC
61.141
66.667
2.18
0.00
38.26
3.18
66
67
2.440247
CCGGGGCTTCCATGAACC
60.440
66.667
0.00
0.00
34.36
3.62
67
68
2.677228
CGGGGCTTCCATGAACCT
59.323
61.111
0.00
0.00
34.36
3.50
68
69
1.632018
CCGGGGCTTCCATGAACCTA
61.632
60.000
0.00
0.00
34.36
3.08
69
70
0.463833
CGGGGCTTCCATGAACCTAC
60.464
60.000
0.00
0.00
34.36
3.18
70
71
0.919710
GGGGCTTCCATGAACCTACT
59.080
55.000
0.00
0.00
35.00
2.57
71
72
1.134068
GGGGCTTCCATGAACCTACTC
60.134
57.143
0.00
0.00
35.00
2.59
72
73
1.559682
GGGCTTCCATGAACCTACTCA
59.440
52.381
0.00
0.00
0.00
3.41
73
74
2.420687
GGGCTTCCATGAACCTACTCAG
60.421
54.545
0.00
0.00
0.00
3.35
83
84
3.583054
CCTACTCAGGTACCCGACA
57.417
57.895
8.74
0.00
37.15
4.35
84
85
1.843368
CCTACTCAGGTACCCGACAA
58.157
55.000
8.74
0.00
37.15
3.18
85
86
1.475682
CCTACTCAGGTACCCGACAAC
59.524
57.143
8.74
0.00
37.15
3.32
86
87
1.131883
CTACTCAGGTACCCGACAACG
59.868
57.143
8.74
0.00
39.43
4.10
87
88
0.538057
ACTCAGGTACCCGACAACGA
60.538
55.000
8.74
0.00
42.66
3.85
88
89
0.599558
CTCAGGTACCCGACAACGAA
59.400
55.000
8.74
0.00
42.66
3.85
89
90
0.314935
TCAGGTACCCGACAACGAAC
59.685
55.000
8.74
0.00
42.66
3.95
90
91
1.005294
CAGGTACCCGACAACGAACG
61.005
60.000
8.74
0.00
42.66
3.95
91
92
1.007387
GGTACCCGACAACGAACGT
60.007
57.895
0.00
0.00
42.66
3.99
92
93
1.277495
GGTACCCGACAACGAACGTG
61.277
60.000
0.00
0.00
42.66
4.49
93
94
0.317770
GTACCCGACAACGAACGTGA
60.318
55.000
0.00
0.00
42.66
4.35
94
95
0.597568
TACCCGACAACGAACGTGAT
59.402
50.000
0.00
0.00
42.66
3.06
95
96
0.942410
ACCCGACAACGAACGTGATG
60.942
55.000
0.00
0.00
42.66
3.07
96
97
0.942410
CCCGACAACGAACGTGATGT
60.942
55.000
0.00
2.52
42.66
3.06
97
98
0.433492
CCGACAACGAACGTGATGTC
59.567
55.000
16.89
16.89
42.66
3.06
98
99
0.433492
CGACAACGAACGTGATGTCC
59.567
55.000
19.34
8.15
42.66
4.02
99
100
0.433492
GACAACGAACGTGATGTCCG
59.567
55.000
16.34
0.00
36.94
4.79
100
101
0.942410
ACAACGAACGTGATGTCCGG
60.942
55.000
0.00
0.00
0.00
5.14
101
102
0.942410
CAACGAACGTGATGTCCGGT
60.942
55.000
0.00
0.00
0.00
5.28
102
103
0.665369
AACGAACGTGATGTCCGGTC
60.665
55.000
0.00
0.00
38.63
4.79
103
104
3.763319
GAACGTGATGTCCGGTCG
58.237
61.111
0.00
1.01
31.71
4.79
104
105
1.804326
GAACGTGATGTCCGGTCGG
60.804
63.158
0.00
2.52
31.71
4.79
105
106
3.291101
AACGTGATGTCCGGTCGGG
62.291
63.158
9.68
0.00
35.59
5.14
106
107
3.755628
CGTGATGTCCGGTCGGGT
61.756
66.667
9.68
0.00
37.00
5.28
107
108
2.125673
GTGATGTCCGGTCGGGTG
60.126
66.667
9.68
0.00
37.00
4.61
108
109
2.602267
TGATGTCCGGTCGGGTGT
60.602
61.111
9.68
0.00
37.00
4.16
109
110
2.125673
GATGTCCGGTCGGGTGTG
60.126
66.667
9.68
0.00
37.00
3.82
110
111
4.388499
ATGTCCGGTCGGGTGTGC
62.388
66.667
9.68
0.00
37.00
4.57
118
119
2.598099
TCGGGTGTGCACGAGGTA
60.598
61.111
13.13
0.00
46.67
3.08
119
120
2.431942
CGGGTGTGCACGAGGTAC
60.432
66.667
13.13
3.88
45.97
3.34
120
121
2.047560
GGGTGTGCACGAGGTACC
60.048
66.667
13.13
13.36
0.00
3.34
121
122
2.580601
GGGTGTGCACGAGGTACCT
61.581
63.158
16.26
16.26
0.00
3.08
122
123
1.374252
GGTGTGCACGAGGTACCTG
60.374
63.158
22.10
14.16
0.00
4.00
123
124
1.663739
GTGTGCACGAGGTACCTGA
59.336
57.895
22.10
0.00
0.00
3.86
124
125
0.388649
GTGTGCACGAGGTACCTGAG
60.389
60.000
22.10
15.64
0.00
3.35
125
126
1.215647
GTGCACGAGGTACCTGAGG
59.784
63.158
22.10
10.90
0.00
3.86
126
127
2.184579
GCACGAGGTACCTGAGGC
59.815
66.667
22.10
15.50
0.00
4.70
127
128
2.352032
GCACGAGGTACCTGAGGCT
61.352
63.158
22.10
0.00
0.00
4.58
128
129
1.810532
CACGAGGTACCTGAGGCTC
59.189
63.158
22.10
7.79
0.00
4.70
129
130
1.380112
ACGAGGTACCTGAGGCTCC
60.380
63.158
22.10
1.21
0.00
4.70
130
131
2.128507
CGAGGTACCTGAGGCTCCC
61.129
68.421
22.10
5.29
0.00
4.30
131
132
2.042843
AGGTACCTGAGGCTCCCG
60.043
66.667
15.42
4.12
0.00
5.14
132
133
2.043248
GGTACCTGAGGCTCCCGA
60.043
66.667
12.86
0.00
0.00
5.14
133
134
1.457831
GGTACCTGAGGCTCCCGAT
60.458
63.158
12.86
0.00
0.00
4.18
134
135
1.742768
GTACCTGAGGCTCCCGATG
59.257
63.158
12.86
0.00
0.00
3.84
135
136
0.755698
GTACCTGAGGCTCCCGATGA
60.756
60.000
12.86
0.00
0.00
2.92
136
137
0.188587
TACCTGAGGCTCCCGATGAT
59.811
55.000
12.86
0.00
0.00
2.45
137
138
1.370437
CCTGAGGCTCCCGATGATG
59.630
63.158
12.86
0.00
0.00
3.07
138
139
1.301558
CTGAGGCTCCCGATGATGC
60.302
63.158
12.86
0.00
0.00
3.91
139
140
1.756408
CTGAGGCTCCCGATGATGCT
61.756
60.000
12.86
0.00
0.00
3.79
140
141
1.301558
GAGGCTCCCGATGATGCTG
60.302
63.158
2.15
0.00
0.00
4.41
141
142
2.976903
GGCTCCCGATGATGCTGC
60.977
66.667
0.00
0.00
0.00
5.25
142
143
3.344215
GCTCCCGATGATGCTGCG
61.344
66.667
0.00
0.00
0.00
5.18
143
144
2.418777
CTCCCGATGATGCTGCGA
59.581
61.111
0.00
0.00
0.00
5.10
144
145
1.005275
CTCCCGATGATGCTGCGAT
60.005
57.895
0.00
0.00
0.00
4.58
145
146
0.244721
CTCCCGATGATGCTGCGATA
59.755
55.000
0.00
0.00
0.00
2.92
146
147
0.244721
TCCCGATGATGCTGCGATAG
59.755
55.000
0.00
0.00
0.00
2.08
147
148
0.244721
CCCGATGATGCTGCGATAGA
59.755
55.000
0.00
0.00
39.76
1.98
148
149
1.626747
CCGATGATGCTGCGATAGAG
58.373
55.000
0.00
0.00
39.76
2.43
149
150
1.067985
CCGATGATGCTGCGATAGAGT
60.068
52.381
0.00
0.00
39.76
3.24
150
151
1.984297
CGATGATGCTGCGATAGAGTG
59.016
52.381
0.00
0.00
39.76
3.51
151
152
2.606551
CGATGATGCTGCGATAGAGTGT
60.607
50.000
0.00
0.00
39.76
3.55
152
153
3.365364
CGATGATGCTGCGATAGAGTGTA
60.365
47.826
0.00
0.00
39.76
2.90
153
154
3.632855
TGATGCTGCGATAGAGTGTAG
57.367
47.619
0.00
0.00
39.76
2.74
154
155
2.287849
TGATGCTGCGATAGAGTGTAGC
60.288
50.000
0.00
0.00
39.76
3.58
155
156
1.102978
TGCTGCGATAGAGTGTAGCA
58.897
50.000
0.85
0.85
38.68
3.49
156
157
1.683385
TGCTGCGATAGAGTGTAGCAT
59.317
47.619
0.85
0.00
36.37
3.79
157
158
2.287849
TGCTGCGATAGAGTGTAGCATC
60.288
50.000
0.85
0.00
36.37
3.91
158
159
2.924454
GCTGCGATAGAGTGTAGCATCC
60.924
54.545
0.00
0.00
37.20
3.51
159
160
2.294512
CTGCGATAGAGTGTAGCATCCA
59.705
50.000
0.00
0.00
37.20
3.41
160
161
2.034685
TGCGATAGAGTGTAGCATCCAC
59.965
50.000
0.00
0.00
39.76
4.02
161
162
2.608261
GCGATAGAGTGTAGCATCCACC
60.608
54.545
0.00
0.00
39.76
4.61
162
163
2.350868
CGATAGAGTGTAGCATCCACCG
60.351
54.545
0.00
0.00
39.76
4.94
163
164
0.744874
TAGAGTGTAGCATCCACCGC
59.255
55.000
0.00
0.00
33.20
5.68
164
165
1.521681
GAGTGTAGCATCCACCGCC
60.522
63.158
0.00
0.00
33.20
6.13
165
166
1.961180
GAGTGTAGCATCCACCGCCT
61.961
60.000
0.00
0.00
33.20
5.52
166
167
1.078426
GTGTAGCATCCACCGCCTT
60.078
57.895
0.00
0.00
0.00
4.35
167
168
1.090052
GTGTAGCATCCACCGCCTTC
61.090
60.000
0.00
0.00
0.00
3.46
168
169
1.264749
TGTAGCATCCACCGCCTTCT
61.265
55.000
0.00
0.00
0.00
2.85
169
170
0.530870
GTAGCATCCACCGCCTTCTC
60.531
60.000
0.00
0.00
0.00
2.87
170
171
2.016393
TAGCATCCACCGCCTTCTCG
62.016
60.000
0.00
0.00
0.00
4.04
178
179
4.955089
CGCCTTCTCGGAGCTATC
57.045
61.111
0.00
0.00
33.16
2.08
179
180
1.287503
CGCCTTCTCGGAGCTATCC
59.712
63.158
0.00
0.00
42.81
2.59
180
181
1.175983
CGCCTTCTCGGAGCTATCCT
61.176
60.000
0.00
0.00
44.22
3.24
181
182
1.044611
GCCTTCTCGGAGCTATCCTT
58.955
55.000
0.00
0.00
44.22
3.36
182
183
1.270041
GCCTTCTCGGAGCTATCCTTG
60.270
57.143
0.00
0.00
44.22
3.61
183
184
1.270041
CCTTCTCGGAGCTATCCTTGC
60.270
57.143
0.00
0.00
44.22
4.01
184
185
1.686052
CTTCTCGGAGCTATCCTTGCT
59.314
52.381
0.00
0.00
44.22
3.91
185
186
1.035923
TCTCGGAGCTATCCTTGCTG
58.964
55.000
0.00
0.00
44.22
4.41
186
187
1.035923
CTCGGAGCTATCCTTGCTGA
58.964
55.000
0.00
0.00
44.22
4.26
187
188
1.000385
CTCGGAGCTATCCTTGCTGAG
60.000
57.143
0.00
0.00
44.22
3.35
188
189
0.599728
CGGAGCTATCCTTGCTGAGC
60.600
60.000
0.00
0.00
44.22
4.26
190
191
1.140652
GGAGCTATCCTTGCTGAGCTT
59.859
52.381
5.83
0.00
45.15
3.74
191
192
2.482864
GAGCTATCCTTGCTGAGCTTC
58.517
52.381
5.83
0.00
45.15
3.86
192
193
1.836166
AGCTATCCTTGCTGAGCTTCA
59.164
47.619
5.83
0.00
42.59
3.02
193
194
2.158928
AGCTATCCTTGCTGAGCTTCAG
60.159
50.000
5.83
8.34
46.90
3.02
200
201
3.123620
CTGAGCTTCAGCCGTGCC
61.124
66.667
0.00
0.00
43.38
5.01
201
202
3.602513
CTGAGCTTCAGCCGTGCCT
62.603
63.158
0.00
0.00
43.38
4.75
202
203
2.817396
GAGCTTCAGCCGTGCCTC
60.817
66.667
0.00
0.00
43.38
4.70
203
204
4.400961
AGCTTCAGCCGTGCCTCC
62.401
66.667
0.00
0.00
43.38
4.30
204
205
4.704833
GCTTCAGCCGTGCCTCCA
62.705
66.667
0.00
0.00
34.31
3.86
205
206
2.270205
CTTCAGCCGTGCCTCCAT
59.730
61.111
0.00
0.00
0.00
3.41
206
207
1.377725
CTTCAGCCGTGCCTCCATT
60.378
57.895
0.00
0.00
0.00
3.16
207
208
1.651240
CTTCAGCCGTGCCTCCATTG
61.651
60.000
0.00
0.00
0.00
2.82
208
209
3.136123
CAGCCGTGCCTCCATTGG
61.136
66.667
0.00
0.00
0.00
3.16
209
210
3.329889
AGCCGTGCCTCCATTGGA
61.330
61.111
5.05
5.05
0.00
3.53
217
218
3.181367
CTCCATTGGAGCGTGCAC
58.819
61.111
19.49
6.82
43.29
4.57
218
219
2.741985
TCCATTGGAGCGTGCACG
60.742
61.111
34.01
34.01
43.27
5.34
219
220
3.803082
CCATTGGAGCGTGCACGG
61.803
66.667
37.47
20.19
40.23
4.94
220
221
4.465512
CATTGGAGCGTGCACGGC
62.466
66.667
37.47
28.57
40.23
5.68
229
230
4.107051
GTGCACGGCATGGCAGTC
62.107
66.667
20.37
7.34
41.91
3.51
232
233
2.360350
CACGGCATGGCAGTCCTT
60.360
61.111
20.37
0.00
34.30
3.36
233
234
2.045926
ACGGCATGGCAGTCCTTC
60.046
61.111
20.37
0.00
29.95
3.46
234
235
2.046023
CGGCATGGCAGTCCTTCA
60.046
61.111
20.37
0.00
0.00
3.02
235
236
1.452651
CGGCATGGCAGTCCTTCAT
60.453
57.895
20.37
0.00
0.00
2.57
236
237
1.721664
CGGCATGGCAGTCCTTCATG
61.722
60.000
20.37
0.00
40.66
3.07
241
242
3.194719
GCAGTCCTTCATGCCTGC
58.805
61.111
0.00
0.00
42.94
4.85
344
347
3.307480
CCCCGATTCAGTCCACTTAACTT
60.307
47.826
0.00
0.00
0.00
2.66
348
351
4.559251
CGATTCAGTCCACTTAACTTCTCG
59.441
45.833
0.00
0.00
0.00
4.04
493
501
0.339859
ACCAGGGCTCTCTCCACATA
59.660
55.000
0.00
0.00
0.00
2.29
568
576
5.993106
AACAGCAGAGAAACTTGTACTTC
57.007
39.130
0.00
0.00
0.00
3.01
649
658
2.099756
ACCCGCGTATTCTTGTAGGTAC
59.900
50.000
4.92
0.00
0.00
3.34
900
912
1.480545
TGAGTACCACACCATCATCCG
59.519
52.381
0.00
0.00
0.00
4.18
945
957
4.222145
TCAGTACTAAAAATCTCAGGCGGT
59.778
41.667
0.00
0.00
0.00
5.68
1066
1092
1.538950
CTTTCCTTGGACTTGCTGCTC
59.461
52.381
0.00
0.00
0.00
4.26
1074
1100
1.949847
GACTTGCTGCTCGCCTCCTA
61.950
60.000
0.00
0.00
38.05
2.94
1100
1126
1.280421
CTTTGCCTCTCCTACCAGCTT
59.720
52.381
0.00
0.00
0.00
3.74
1401
1427
2.945008
CAGAAGCATTATTGGCCTCGAA
59.055
45.455
3.32
0.00
0.00
3.71
1467
1493
0.113190
CAAACCCCAGCCTTCCTCTT
59.887
55.000
0.00
0.00
0.00
2.85
1620
1646
0.460722
TCAATGCCCCATCATTTGCG
59.539
50.000
0.00
0.00
34.68
4.85
1779
1806
2.568956
ACTGGAGCACATCTCTTTAGCA
59.431
45.455
0.00
0.00
41.60
3.49
1787
1814
5.474532
AGCACATCTCTTTAGCAAACAATGA
59.525
36.000
0.00
0.00
0.00
2.57
2172
2199
0.770499
TTCATGGCCAGTTCTCACCA
59.230
50.000
13.05
0.00
36.43
4.17
2308
2341
3.942130
GGAACCAATTTCAAGGGTGAG
57.058
47.619
0.00
0.00
35.70
3.51
2362
2395
6.968131
TTTGAGAATCTTCAGGTATTGACG
57.032
37.500
0.00
0.00
34.94
4.35
2369
2402
9.521841
AGAATCTTCAGGTATTGACGATAGATA
57.478
33.333
0.00
0.00
42.19
1.98
2465
2499
8.684386
TTAAATCAACTCACTGGACAAATACA
57.316
30.769
0.00
0.00
0.00
2.29
2468
2502
7.765695
ATCAACTCACTGGACAAATACAATT
57.234
32.000
0.00
0.00
0.00
2.32
2900
4502
8.947055
AACTGCATTTTAAACTTCTTTGTCAT
57.053
26.923
0.00
0.00
0.00
3.06
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
1
2
2.202690
TGCTTCGGTACATCGCGG
60.203
61.111
6.13
0.00
0.00
6.46
2
3
2.230940
CCTGCTTCGGTACATCGCG
61.231
63.158
0.00
0.00
0.00
5.87
4
5
1.421410
GCACCTGCTTCGGTACATCG
61.421
60.000
0.00
0.00
34.94
3.84
6
7
4.617875
GCACCTGCTTCGGTACAT
57.382
55.556
0.00
0.00
34.94
2.29
16
17
3.730761
CTGCCGTCAAGCACCTGC
61.731
66.667
0.00
0.00
38.00
4.85
17
18
3.730761
GCTGCCGTCAAGCACCTG
61.731
66.667
0.00
0.00
38.00
4.00
20
21
3.782244
CTCGCTGCCGTCAAGCAC
61.782
66.667
0.00
0.00
38.00
4.40
21
22
3.300934
ATCTCGCTGCCGTCAAGCA
62.301
57.895
0.00
0.00
41.46
3.91
22
23
2.510238
ATCTCGCTGCCGTCAAGC
60.510
61.111
0.00
0.00
35.54
4.01
23
24
0.529337
ATCATCTCGCTGCCGTCAAG
60.529
55.000
0.00
0.00
35.54
3.02
24
25
0.528466
GATCATCTCGCTGCCGTCAA
60.528
55.000
0.00
0.00
35.54
3.18
25
26
1.066422
GATCATCTCGCTGCCGTCA
59.934
57.895
0.00
0.00
35.54
4.35
26
27
2.013483
CGATCATCTCGCTGCCGTC
61.013
63.158
0.00
0.00
41.14
4.79
27
28
2.026734
CGATCATCTCGCTGCCGT
59.973
61.111
0.00
0.00
41.14
5.68
35
36
1.958205
CCCGGCAAGCGATCATCTC
60.958
63.158
0.00
0.00
0.00
2.75
36
37
2.109799
CCCGGCAAGCGATCATCT
59.890
61.111
0.00
0.00
0.00
2.90
37
38
2.974698
CCCCGGCAAGCGATCATC
60.975
66.667
0.00
0.00
0.00
2.92
45
46
3.142838
CATGGAAGCCCCGGCAAG
61.143
66.667
8.74
0.00
44.88
4.01
46
47
3.216985
TTCATGGAAGCCCCGGCAA
62.217
57.895
8.74
0.00
44.88
4.52
47
48
3.656280
TTCATGGAAGCCCCGGCA
61.656
61.111
8.74
0.00
44.88
5.69
48
49
3.140814
GTTCATGGAAGCCCCGGC
61.141
66.667
0.00
0.00
42.33
6.13
49
50
1.632018
TAGGTTCATGGAAGCCCCGG
61.632
60.000
0.00
0.00
40.41
5.73
50
51
0.463833
GTAGGTTCATGGAAGCCCCG
60.464
60.000
4.69
0.00
40.41
5.73
51
52
0.919710
AGTAGGTTCATGGAAGCCCC
59.080
55.000
4.69
0.00
40.41
5.80
52
53
1.559682
TGAGTAGGTTCATGGAAGCCC
59.440
52.381
4.69
0.00
40.41
5.19
53
54
2.420687
CCTGAGTAGGTTCATGGAAGCC
60.421
54.545
4.69
0.00
40.41
4.35
54
55
2.911484
CCTGAGTAGGTTCATGGAAGC
58.089
52.381
0.00
0.15
39.39
3.86
74
75
0.317770
TCACGTTCGTTGTCGGGTAC
60.318
55.000
0.00
0.00
37.69
3.34
75
76
0.597568
ATCACGTTCGTTGTCGGGTA
59.402
50.000
0.00
0.00
37.69
3.69
76
77
0.942410
CATCACGTTCGTTGTCGGGT
60.942
55.000
0.00
0.00
37.69
5.28
77
78
0.942410
ACATCACGTTCGTTGTCGGG
60.942
55.000
0.00
0.00
37.69
5.14
78
79
0.433492
GACATCACGTTCGTTGTCGG
59.567
55.000
12.20
0.00
37.69
4.79
79
80
0.433492
GGACATCACGTTCGTTGTCG
59.567
55.000
17.70
0.69
39.45
4.35
80
81
0.433492
CGGACATCACGTTCGTTGTC
59.567
55.000
16.70
16.70
42.07
3.18
81
82
0.942410
CCGGACATCACGTTCGTTGT
60.942
55.000
0.00
2.96
45.89
3.32
82
83
0.942410
ACCGGACATCACGTTCGTTG
60.942
55.000
9.46
0.00
45.89
4.10
83
84
0.665369
GACCGGACATCACGTTCGTT
60.665
55.000
9.46
0.00
45.89
3.85
84
85
1.080974
GACCGGACATCACGTTCGT
60.081
57.895
9.46
0.00
45.89
3.85
85
86
2.150218
CGACCGGACATCACGTTCG
61.150
63.158
9.46
0.00
46.97
3.95
86
87
1.804326
CCGACCGGACATCACGTTC
60.804
63.158
9.46
0.00
37.50
3.95
87
88
2.260434
CCGACCGGACATCACGTT
59.740
61.111
9.46
0.00
37.50
3.99
88
89
3.755628
CCCGACCGGACATCACGT
61.756
66.667
9.46
0.00
37.50
4.49
89
90
3.755628
ACCCGACCGGACATCACG
61.756
66.667
9.46
3.72
37.50
4.35
90
91
2.125673
CACCCGACCGGACATCAC
60.126
66.667
9.46
0.00
37.50
3.06
91
92
2.602267
ACACCCGACCGGACATCA
60.602
61.111
9.46
0.00
37.50
3.07
92
93
2.125673
CACACCCGACCGGACATC
60.126
66.667
9.46
0.00
37.50
3.06
93
94
4.388499
GCACACCCGACCGGACAT
62.388
66.667
9.46
0.00
37.50
3.06
100
101
2.922950
TACCTCGTGCACACCCGAC
61.923
63.158
18.64
0.00
0.00
4.79
101
102
2.598099
TACCTCGTGCACACCCGA
60.598
61.111
18.64
7.34
0.00
5.14
102
103
2.431942
GTACCTCGTGCACACCCG
60.432
66.667
18.64
2.38
0.00
5.28
103
104
2.047560
GGTACCTCGTGCACACCC
60.048
66.667
18.64
2.77
0.00
4.61
104
105
1.374252
CAGGTACCTCGTGCACACC
60.374
63.158
18.64
16.01
0.00
4.16
105
106
0.388649
CTCAGGTACCTCGTGCACAC
60.389
60.000
18.64
6.69
32.68
3.82
106
107
1.532604
CCTCAGGTACCTCGTGCACA
61.533
60.000
18.64
3.15
32.68
4.57
107
108
1.215647
CCTCAGGTACCTCGTGCAC
59.784
63.158
12.84
6.82
32.68
4.57
108
109
2.646175
GCCTCAGGTACCTCGTGCA
61.646
63.158
12.84
0.00
32.68
4.57
109
110
2.184579
GCCTCAGGTACCTCGTGC
59.815
66.667
12.84
10.84
32.68
5.34
110
111
1.668101
GGAGCCTCAGGTACCTCGTG
61.668
65.000
12.84
8.71
0.00
4.35
111
112
1.380112
GGAGCCTCAGGTACCTCGT
60.380
63.158
12.84
0.00
0.00
4.18
112
113
2.128507
GGGAGCCTCAGGTACCTCG
61.129
68.421
12.84
8.23
41.76
4.63
113
114
2.128507
CGGGAGCCTCAGGTACCTC
61.129
68.421
12.84
0.00
42.96
3.85
114
115
1.950748
ATCGGGAGCCTCAGGTACCT
61.951
60.000
9.21
9.21
42.96
3.08
115
116
1.457831
ATCGGGAGCCTCAGGTACC
60.458
63.158
2.73
2.73
41.56
3.34
116
117
0.755698
TCATCGGGAGCCTCAGGTAC
60.756
60.000
0.00
0.00
0.00
3.34
117
118
0.188587
ATCATCGGGAGCCTCAGGTA
59.811
55.000
0.00
0.00
0.00
3.08
118
119
1.074926
ATCATCGGGAGCCTCAGGT
60.075
57.895
0.00
0.00
0.00
4.00
119
120
1.370437
CATCATCGGGAGCCTCAGG
59.630
63.158
0.00
0.00
0.00
3.86
120
121
1.301558
GCATCATCGGGAGCCTCAG
60.302
63.158
0.00
0.00
0.00
3.35
121
122
1.763655
AGCATCATCGGGAGCCTCA
60.764
57.895
0.00
0.00
0.00
3.86
122
123
1.301558
CAGCATCATCGGGAGCCTC
60.302
63.158
0.00
0.00
0.00
4.70
123
124
2.827423
CAGCATCATCGGGAGCCT
59.173
61.111
0.00
0.00
0.00
4.58
124
125
2.976903
GCAGCATCATCGGGAGCC
60.977
66.667
0.00
0.00
0.00
4.70
125
126
3.344215
CGCAGCATCATCGGGAGC
61.344
66.667
0.00
0.00
0.00
4.70
126
127
0.244721
TATCGCAGCATCATCGGGAG
59.755
55.000
0.00
0.00
0.00
4.30
127
128
0.244721
CTATCGCAGCATCATCGGGA
59.755
55.000
0.00
0.00
0.00
5.14
128
129
0.244721
TCTATCGCAGCATCATCGGG
59.755
55.000
0.00
0.00
0.00
5.14
129
130
1.067985
ACTCTATCGCAGCATCATCGG
60.068
52.381
0.00
0.00
0.00
4.18
130
131
1.984297
CACTCTATCGCAGCATCATCG
59.016
52.381
0.00
0.00
0.00
3.84
131
132
3.023946
ACACTCTATCGCAGCATCATC
57.976
47.619
0.00
0.00
0.00
2.92
132
133
3.613671
GCTACACTCTATCGCAGCATCAT
60.614
47.826
0.00
0.00
0.00
2.45
133
134
2.287849
GCTACACTCTATCGCAGCATCA
60.288
50.000
0.00
0.00
0.00
3.07
134
135
2.287849
TGCTACACTCTATCGCAGCATC
60.288
50.000
0.00
0.00
34.30
3.91
135
136
1.683385
TGCTACACTCTATCGCAGCAT
59.317
47.619
0.00
0.00
34.30
3.79
136
137
1.102978
TGCTACACTCTATCGCAGCA
58.897
50.000
0.00
0.00
36.72
4.41
137
138
2.323959
GATGCTACACTCTATCGCAGC
58.676
52.381
0.00
0.00
33.72
5.25
138
139
2.294512
TGGATGCTACACTCTATCGCAG
59.705
50.000
0.00
0.00
33.72
5.18
139
140
2.034685
GTGGATGCTACACTCTATCGCA
59.965
50.000
0.00
0.00
35.98
5.10
140
141
2.608261
GGTGGATGCTACACTCTATCGC
60.608
54.545
6.09
0.00
38.83
4.58
141
142
2.350868
CGGTGGATGCTACACTCTATCG
60.351
54.545
6.09
0.00
38.83
2.92
142
143
2.608261
GCGGTGGATGCTACACTCTATC
60.608
54.545
6.09
0.00
38.83
2.08
143
144
1.341531
GCGGTGGATGCTACACTCTAT
59.658
52.381
6.09
0.00
38.83
1.98
144
145
0.744874
GCGGTGGATGCTACACTCTA
59.255
55.000
6.09
0.00
38.83
2.43
145
146
1.517832
GCGGTGGATGCTACACTCT
59.482
57.895
6.09
0.00
38.83
3.24
146
147
1.521681
GGCGGTGGATGCTACACTC
60.522
63.158
6.09
0.46
38.83
3.51
147
148
1.553690
AAGGCGGTGGATGCTACACT
61.554
55.000
6.09
0.00
38.83
3.55
148
149
1.078426
AAGGCGGTGGATGCTACAC
60.078
57.895
0.00
0.00
38.10
2.90
149
150
1.220749
GAAGGCGGTGGATGCTACA
59.779
57.895
0.00
0.00
0.00
2.74
150
151
0.530870
GAGAAGGCGGTGGATGCTAC
60.531
60.000
0.00
0.00
0.00
3.58
151
152
1.823295
GAGAAGGCGGTGGATGCTA
59.177
57.895
0.00
0.00
0.00
3.49
152
153
2.586792
GAGAAGGCGGTGGATGCT
59.413
61.111
0.00
0.00
0.00
3.79
153
154
2.892425
CGAGAAGGCGGTGGATGC
60.892
66.667
0.00
0.00
0.00
3.91
154
155
2.202932
CCGAGAAGGCGGTGGATG
60.203
66.667
0.00
0.00
46.07
3.51
161
162
1.287503
GGATAGCTCCGAGAAGGCG
59.712
63.158
0.00
0.00
40.77
5.52
170
171
0.758123
AGCTCAGCAAGGATAGCTCC
59.242
55.000
0.00
0.00
41.35
4.70
171
172
2.158986
TGAAGCTCAGCAAGGATAGCTC
60.159
50.000
0.00
0.00
44.30
4.09
172
173
1.836166
TGAAGCTCAGCAAGGATAGCT
59.164
47.619
0.00
0.00
46.96
3.32
173
174
2.211806
CTGAAGCTCAGCAAGGATAGC
58.788
52.381
0.00
0.00
37.72
2.97
183
184
3.123620
GGCACGGCTGAAGCTCAG
61.124
66.667
0.00
8.34
46.90
3.35
184
185
3.596066
GAGGCACGGCTGAAGCTCA
62.596
63.158
0.00
0.00
41.70
4.26
185
186
2.817396
GAGGCACGGCTGAAGCTC
60.817
66.667
0.00
0.00
41.70
4.09
186
187
4.400961
GGAGGCACGGCTGAAGCT
62.401
66.667
0.00
0.00
41.70
3.74
187
188
3.984193
ATGGAGGCACGGCTGAAGC
62.984
63.158
0.00
2.39
41.14
3.86
188
189
1.377725
AATGGAGGCACGGCTGAAG
60.378
57.895
0.00
0.00
0.00
3.02
189
190
1.675310
CAATGGAGGCACGGCTGAA
60.675
57.895
0.00
0.00
0.00
3.02
190
191
2.046023
CAATGGAGGCACGGCTGA
60.046
61.111
0.00
0.00
0.00
4.26
191
192
3.136123
CCAATGGAGGCACGGCTG
61.136
66.667
0.00
0.00
0.00
4.85
192
193
3.329889
TCCAATGGAGGCACGGCT
61.330
61.111
0.00
0.00
0.00
5.52
193
194
2.825836
CTCCAATGGAGGCACGGC
60.826
66.667
21.25
0.00
45.43
5.68
201
202
2.741985
CGTGCACGCTCCAATGGA
60.742
61.111
28.16
0.48
0.00
3.41
202
203
3.803082
CCGTGCACGCTCCAATGG
61.803
66.667
33.17
13.44
38.18
3.16
203
204
4.465512
GCCGTGCACGCTCCAATG
62.466
66.667
33.17
18.44
38.18
2.82
212
213
4.107051
GACTGCCATGCCGTGCAC
62.107
66.667
6.82
6.82
43.04
4.57
215
216
2.360350
AAGGACTGCCATGCCGTG
60.360
61.111
0.00
0.00
36.29
4.94
216
217
2.045926
GAAGGACTGCCATGCCGT
60.046
61.111
0.00
0.00
36.29
5.68
217
218
1.452651
ATGAAGGACTGCCATGCCG
60.453
57.895
0.00
0.00
36.29
5.69
218
219
2.112898
CATGAAGGACTGCCATGCC
58.887
57.895
0.00
0.00
36.29
4.40
226
227
0.395311
CATGGCAGGCATGAAGGACT
60.395
55.000
28.95
0.00
32.09
3.85
227
228
0.682209
ACATGGCAGGCATGAAGGAC
60.682
55.000
36.69
0.00
34.39
3.85
228
229
0.681887
CACATGGCAGGCATGAAGGA
60.682
55.000
36.69
0.00
34.39
3.36
229
230
1.672854
CCACATGGCAGGCATGAAGG
61.673
60.000
36.69
30.91
34.39
3.46
230
231
0.968901
ACCACATGGCAGGCATGAAG
60.969
55.000
36.69
28.14
39.32
3.02
231
232
0.966875
GACCACATGGCAGGCATGAA
60.967
55.000
36.69
0.00
39.32
2.57
232
233
1.378911
GACCACATGGCAGGCATGA
60.379
57.895
36.69
0.00
39.32
3.07
233
234
2.767445
CGACCACATGGCAGGCATG
61.767
63.158
30.44
30.44
39.32
4.06
234
235
2.438975
CGACCACATGGCAGGCAT
60.439
61.111
2.93
2.93
39.32
4.40
235
236
3.610619
CTCGACCACATGGCAGGCA
62.611
63.158
0.00
0.00
39.32
4.75
236
237
2.821366
CTCGACCACATGGCAGGC
60.821
66.667
0.00
0.00
39.32
4.85
237
238
1.742880
CACTCGACCACATGGCAGG
60.743
63.158
0.00
0.00
39.32
4.85
238
239
1.742880
CCACTCGACCACATGGCAG
60.743
63.158
0.00
0.00
39.32
4.85
239
240
2.347114
CCACTCGACCACATGGCA
59.653
61.111
0.00
0.00
39.32
4.92
240
241
2.436646
CCCACTCGACCACATGGC
60.437
66.667
0.00
0.00
39.32
4.40
241
242
2.436646
GCCCACTCGACCACATGG
60.437
66.667
0.00
0.00
42.17
3.66
493
501
2.911636
TGGCCATTTTGATTGGAACCAT
59.088
40.909
0.00
0.00
36.26
3.55
568
576
9.793259
ATTTTATCCTACCACCAGTATGTATTG
57.207
33.333
0.00
0.00
0.00
1.90
649
658
4.615588
AAGTCAACTCTTGAGAGAAGGG
57.384
45.455
14.61
1.86
44.74
3.95
900
912
3.359950
AGCCATGAGGAAAACAGGAATC
58.640
45.455
0.00
0.00
36.89
2.52
945
957
8.896320
TGTACTGCTCTGAACAATACTAAAAA
57.104
30.769
2.02
0.00
0.00
1.94
1066
1092
1.646189
GCAAAGAAGAGTAGGAGGCG
58.354
55.000
0.00
0.00
0.00
5.52
1074
1100
2.835156
GGTAGGAGAGGCAAAGAAGAGT
59.165
50.000
0.00
0.00
0.00
3.24
1194
1220
1.350684
TCCCATTTGCAGCAGTCTGTA
59.649
47.619
0.93
0.00
42.29
2.74
1401
1427
1.131638
TGAGGTGGTTGAAGCTGACT
58.868
50.000
0.00
0.00
0.00
3.41
1467
1493
6.544928
TTGCTTGAGATATTCAGTACCTGA
57.455
37.500
0.00
0.00
38.87
3.86
1620
1646
8.789825
ATTGGTTATATGAGAGATCAAGCATC
57.210
34.615
0.00
0.00
0.00
3.91
1779
1806
6.165700
AGAACTCCTTGCAAATCATTGTTT
57.834
33.333
0.00
0.00
38.85
2.83
2172
2199
3.766051
GGACCTGAGATTTCCAATGCTTT
59.234
43.478
0.00
0.00
0.00
3.51
2308
2341
6.455360
AATGTTTCATCATGTGGTATGGTC
57.545
37.500
0.00
0.00
0.00
4.02
2362
2395
6.506500
CCAGTCAATGGGCAATTATCTATC
57.493
41.667
0.00
0.00
46.36
2.08
2465
2499
3.703052
GCCCAGTTCATCAATCCAGAATT
59.297
43.478
0.00
0.00
0.00
2.17
2468
2502
1.918262
AGCCCAGTTCATCAATCCAGA
59.082
47.619
0.00
0.00
0.00
3.86
2872
4474
8.196802
ACAAAGAAGTTTAAAATGCAGTTTCC
57.803
30.769
16.40
5.65
0.00
3.13
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.