Multiple sequence alignment - TraesCS3D01G083300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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 TraesCS3D01G083300 chr3D 100.000 3092 0 0 1 3092 42349356 42352447 0.000000e+00 5710
1 TraesCS3D01G083300 chr5D 98.693 2830 24 3 275 3092 565815801 565818629 0.000000e+00 5009
2 TraesCS3D01G083300 chr5D 98.692 2829 24 2 276 3092 260689962 260687135 0.000000e+00 5007
3 TraesCS3D01G083300 chr5D 97.350 2830 56 6 276 3092 480824254 480821431 0.000000e+00 4793
4 TraesCS3D01G083300 chr7D 98.445 2829 30 3 276 3092 54583766 54580940 0.000000e+00 4968
5 TraesCS3D01G083300 chr7D 98.410 2830 33 1 275 3092 245402432 245399603 0.000000e+00 4966
6 TraesCS3D01G083300 chr7D 98.162 2829 40 1 276 3092 115100272 115103100 0.000000e+00 4926
7 TraesCS3D01G083300 chr7D 97.595 2828 44 4 277 3092 10896028 10893213 0.000000e+00 4824
8 TraesCS3D01G083300 chr7D 97.721 1755 24 5 1352 3092 608523830 608522078 0.000000e+00 3005
9 TraesCS3D01G083300 chr6D 98.339 2829 34 2 276 3092 51499464 51502291 0.000000e+00 4951
10 TraesCS3D01G083300 chr6D 98.093 2831 36 5 275 3092 472510962 472513787 0.000000e+00 4913
11 TraesCS3D01G083300 chr6D 96.926 2830 64 6 276 3092 367564537 367561718 0.000000e+00 4723
12 TraesCS3D01G083300 chr4D 97.884 2836 42 4 269 3092 164897173 164900002 0.000000e+00 4889
13 TraesCS3D01G083300 chr4D 97.005 2838 59 8 275 3092 398986368 398983537 0.000000e+00 4747
14 TraesCS3D01G083300 chr1D 97.915 2830 44 4 275 3092 22577396 22574570 0.000000e+00 4885
15 TraesCS3D01G083300 chr1D 96.547 2838 73 10 270 3092 6491902 6489075 0.000000e+00 4674
16 TraesCS3D01G083300 chr3A 92.553 94 5 2 183 274 53340193 53340100 1.930000e-27 134


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 TraesCS3D01G083300 chr3D 42349356 42352447 3091 False 5710 5710 100.000 1 3092 1 chr3D.!!$F1 3091
1 TraesCS3D01G083300 chr5D 565815801 565818629 2828 False 5009 5009 98.693 275 3092 1 chr5D.!!$F1 2817
2 TraesCS3D01G083300 chr5D 260687135 260689962 2827 True 5007 5007 98.692 276 3092 1 chr5D.!!$R1 2816
3 TraesCS3D01G083300 chr5D 480821431 480824254 2823 True 4793 4793 97.350 276 3092 1 chr5D.!!$R2 2816
4 TraesCS3D01G083300 chr7D 54580940 54583766 2826 True 4968 4968 98.445 276 3092 1 chr7D.!!$R2 2816
5 TraesCS3D01G083300 chr7D 245399603 245402432 2829 True 4966 4966 98.410 275 3092 1 chr7D.!!$R3 2817
6 TraesCS3D01G083300 chr7D 115100272 115103100 2828 False 4926 4926 98.162 276 3092 1 chr7D.!!$F1 2816
7 TraesCS3D01G083300 chr7D 10893213 10896028 2815 True 4824 4824 97.595 277 3092 1 chr7D.!!$R1 2815
8 TraesCS3D01G083300 chr7D 608522078 608523830 1752 True 3005 3005 97.721 1352 3092 1 chr7D.!!$R4 1740
9 TraesCS3D01G083300 chr6D 51499464 51502291 2827 False 4951 4951 98.339 276 3092 1 chr6D.!!$F1 2816
10 TraesCS3D01G083300 chr6D 472510962 472513787 2825 False 4913 4913 98.093 275 3092 1 chr6D.!!$F2 2817
11 TraesCS3D01G083300 chr6D 367561718 367564537 2819 True 4723 4723 96.926 276 3092 1 chr6D.!!$R1 2816
12 TraesCS3D01G083300 chr4D 164897173 164900002 2829 False 4889 4889 97.884 269 3092 1 chr4D.!!$F1 2823
13 TraesCS3D01G083300 chr4D 398983537 398986368 2831 True 4747 4747 97.005 275 3092 1 chr4D.!!$R1 2817
14 TraesCS3D01G083300 chr1D 22574570 22577396 2826 True 4885 4885 97.915 275 3092 1 chr1D.!!$R2 2817
15 TraesCS3D01G083300 chr1D 6489075 6491902 2827 True 4674 4674 96.547 270 3092 1 chr1D.!!$R1 2822

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.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
140 141 0.037447 TTGCACATTCATCCGTGGGA 59.963 50.0 0.0 0.0 35.55 4.37 F
186 187 0.169009 GATGCGCACCCTTGAGTTTC 59.831 55.0 14.9 0.0 0.00 2.78 F
190 191 0.443869 CGCACCCTTGAGTTTCATCG 59.556 55.0 0.0 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1631 1.210204 ACATGTCCCACAGCCTGGAT 61.210 55.000 0.00 0.0 43.95 3.41 R
1878 1898 2.387757 TCCTTGGCAAGTTTGAGCTTT 58.612 42.857 24.57 0.0 0.00 3.51 R
2623 2645 1.673477 CACTCCACTGCCTGCACTA 59.327 57.895 0.00 0.0 0.00 2.74 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.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.987594 GAGAATGGTCCTTGGCCTT 57.012 52.632 3.32 0.00 0.00 4.35
19 20 2.222227 GAGAATGGTCCTTGGCCTTT 57.778 50.000 3.32 0.00 0.00 3.11
20 21 1.821136 GAGAATGGTCCTTGGCCTTTG 59.179 52.381 3.32 0.00 0.00 2.77
21 22 0.897621 GAATGGTCCTTGGCCTTTGG 59.102 55.000 3.32 3.34 0.00 3.28
22 23 0.190815 AATGGTCCTTGGCCTTTGGT 59.809 50.000 3.32 0.00 0.00 3.67
23 24 1.080638 ATGGTCCTTGGCCTTTGGTA 58.919 50.000 3.32 0.00 0.00 3.25
24 25 0.404040 TGGTCCTTGGCCTTTGGTAG 59.596 55.000 3.32 0.00 0.00 3.18
25 26 0.965866 GGTCCTTGGCCTTTGGTAGC 60.966 60.000 3.32 0.53 0.00 3.58
31 32 3.681473 GCCTTTGGTAGCCACACC 58.319 61.111 0.00 0.00 39.20 4.16
32 33 1.228429 GCCTTTGGTAGCCACACCA 60.228 57.895 0.00 0.00 46.97 4.17
37 38 3.905331 TGGTAGCCACACCAAACAA 57.095 47.368 0.12 0.00 45.65 2.83
38 39 2.145397 TGGTAGCCACACCAAACAAA 57.855 45.000 0.12 0.00 45.65 2.83
39 40 2.672098 TGGTAGCCACACCAAACAAAT 58.328 42.857 0.12 0.00 45.65 2.32
40 41 3.833732 TGGTAGCCACACCAAACAAATA 58.166 40.909 0.12 0.00 45.65 1.40
41 42 3.823873 TGGTAGCCACACCAAACAAATAG 59.176 43.478 0.12 0.00 45.65 1.73
42 43 4.076394 GGTAGCCACACCAAACAAATAGA 58.924 43.478 0.00 0.00 38.55 1.98
43 44 4.705023 GGTAGCCACACCAAACAAATAGAT 59.295 41.667 0.00 0.00 38.55 1.98
44 45 5.185056 GGTAGCCACACCAAACAAATAGATT 59.815 40.000 0.00 0.00 38.55 2.40
45 46 6.376018 GGTAGCCACACCAAACAAATAGATTA 59.624 38.462 0.00 0.00 38.55 1.75
46 47 6.909550 AGCCACACCAAACAAATAGATTAA 57.090 33.333 0.00 0.00 0.00 1.40
47 48 7.480760 AGCCACACCAAACAAATAGATTAAT 57.519 32.000 0.00 0.00 0.00 1.40
48 49 8.588290 AGCCACACCAAACAAATAGATTAATA 57.412 30.769 0.00 0.00 0.00 0.98
49 50 9.030452 AGCCACACCAAACAAATAGATTAATAA 57.970 29.630 0.00 0.00 0.00 1.40
50 51 9.646427 GCCACACCAAACAAATAGATTAATAAA 57.354 29.630 0.00 0.00 0.00 1.40
76 77 8.992835 ATCCTCATAAGAAAAAGAACAATTGC 57.007 30.769 5.05 0.00 0.00 3.56
77 78 7.950512 TCCTCATAAGAAAAAGAACAATTGCA 58.049 30.769 5.05 0.00 0.00 4.08
78 79 8.587608 TCCTCATAAGAAAAAGAACAATTGCAT 58.412 29.630 5.05 0.00 0.00 3.96
79 80 8.866956 CCTCATAAGAAAAAGAACAATTGCATC 58.133 33.333 5.05 4.51 0.00 3.91
80 81 8.761575 TCATAAGAAAAAGAACAATTGCATCC 57.238 30.769 5.05 0.00 0.00 3.51
81 82 8.366401 TCATAAGAAAAAGAACAATTGCATCCA 58.634 29.630 5.05 0.00 0.00 3.41
82 83 6.849588 AAGAAAAAGAACAATTGCATCCAC 57.150 33.333 5.05 0.00 0.00 4.02
83 84 5.916318 AGAAAAAGAACAATTGCATCCACA 58.084 33.333 5.05 0.00 0.00 4.17
84 85 6.347696 AGAAAAAGAACAATTGCATCCACAA 58.652 32.000 5.05 0.00 0.00 3.33
85 86 6.993902 AGAAAAAGAACAATTGCATCCACAAT 59.006 30.769 5.05 0.00 42.01 2.71
87 88 7.571080 AAAAGAACAATTGCATCCACAATTT 57.429 28.000 5.05 0.00 45.63 1.82
88 89 6.548441 AAGAACAATTGCATCCACAATTTG 57.452 33.333 5.05 0.00 45.63 2.32
89 90 5.856156 AGAACAATTGCATCCACAATTTGA 58.144 33.333 5.05 0.00 45.63 2.69
90 91 6.469410 AGAACAATTGCATCCACAATTTGAT 58.531 32.000 5.05 0.00 45.63 2.57
91 92 6.592607 AGAACAATTGCATCCACAATTTGATC 59.407 34.615 5.05 0.00 45.63 2.92
92 93 5.795972 ACAATTGCATCCACAATTTGATCA 58.204 33.333 5.05 0.00 45.63 2.92
93 94 6.411376 ACAATTGCATCCACAATTTGATCAT 58.589 32.000 5.05 0.00 45.63 2.45
94 95 6.882140 ACAATTGCATCCACAATTTGATCATT 59.118 30.769 5.05 0.00 45.63 2.57
95 96 7.065324 ACAATTGCATCCACAATTTGATCATTC 59.935 33.333 5.05 0.00 45.63 2.67
96 97 5.662674 TGCATCCACAATTTGATCATTCA 57.337 34.783 2.79 0.00 0.00 2.57
97 98 5.412640 TGCATCCACAATTTGATCATTCAC 58.587 37.500 2.79 0.00 0.00 3.18
98 99 4.807304 GCATCCACAATTTGATCATTCACC 59.193 41.667 2.79 0.00 0.00 4.02
99 100 5.624967 GCATCCACAATTTGATCATTCACCA 60.625 40.000 2.79 0.00 0.00 4.17
100 101 5.389859 TCCACAATTTGATCATTCACCAC 57.610 39.130 2.79 0.00 0.00 4.16
101 102 4.831710 TCCACAATTTGATCATTCACCACA 59.168 37.500 2.79 0.00 0.00 4.17
102 103 5.481122 TCCACAATTTGATCATTCACCACAT 59.519 36.000 2.79 0.00 0.00 3.21
103 104 5.808540 CCACAATTTGATCATTCACCACATC 59.191 40.000 2.79 0.00 0.00 3.06
104 105 5.513849 CACAATTTGATCATTCACCACATCG 59.486 40.000 2.79 0.00 0.00 3.84
105 106 5.415389 ACAATTTGATCATTCACCACATCGA 59.585 36.000 2.79 0.00 0.00 3.59
106 107 6.072008 ACAATTTGATCATTCACCACATCGAA 60.072 34.615 2.79 0.00 0.00 3.71
107 108 5.550232 TTTGATCATTCACCACATCGAAG 57.450 39.130 0.00 0.00 0.00 3.79
108 109 4.470334 TGATCATTCACCACATCGAAGA 57.530 40.909 0.00 0.00 45.75 2.87
109 110 4.831107 TGATCATTCACCACATCGAAGAA 58.169 39.130 0.00 0.00 43.58 2.52
110 111 5.244755 TGATCATTCACCACATCGAAGAAA 58.755 37.500 0.00 0.00 43.58 2.52
111 112 5.704978 TGATCATTCACCACATCGAAGAAAA 59.295 36.000 0.00 0.00 43.58 2.29
112 113 6.206438 TGATCATTCACCACATCGAAGAAAAA 59.794 34.615 0.00 0.00 43.58 1.94
113 114 5.757886 TCATTCACCACATCGAAGAAAAAC 58.242 37.500 0.00 0.00 43.58 2.43
114 115 5.298026 TCATTCACCACATCGAAGAAAAACA 59.702 36.000 0.00 0.00 43.58 2.83
115 116 4.545823 TCACCACATCGAAGAAAAACAC 57.454 40.909 0.00 0.00 43.58 3.32
116 117 3.942115 TCACCACATCGAAGAAAAACACA 59.058 39.130 0.00 0.00 43.58 3.72
117 118 4.578516 TCACCACATCGAAGAAAAACACAT 59.421 37.500 0.00 0.00 43.58 3.21
118 119 5.067153 TCACCACATCGAAGAAAAACACATT 59.933 36.000 0.00 0.00 43.58 2.71
119 120 5.173673 CACCACATCGAAGAAAAACACATTG 59.826 40.000 0.00 0.00 43.58 2.82
120 121 5.163561 ACCACATCGAAGAAAAACACATTGT 60.164 36.000 0.00 0.00 43.58 2.71
121 122 5.748152 CCACATCGAAGAAAAACACATTGTT 59.252 36.000 0.00 0.00 41.35 2.83
122 123 6.255453 CCACATCGAAGAAAAACACATTGTTT 59.745 34.615 0.00 0.00 46.03 2.83
123 124 7.112397 CACATCGAAGAAAAACACATTGTTTG 58.888 34.615 5.09 0.00 44.30 2.93
124 125 6.122125 CATCGAAGAAAAACACATTGTTTGC 58.878 36.000 5.09 1.86 44.30 3.68
125 126 5.809562 ATCGAAGAAAAACACATTGTTTGCA 59.190 32.000 5.09 0.00 44.30 4.08
126 127 6.237808 ATCGAAGAAAAACACATTGTTTGCAC 60.238 34.615 5.09 1.37 44.30 4.57
127 128 8.527127 ATCGAAGAAAAACACATTGTTTGCACA 61.527 33.333 5.09 0.00 44.30 4.57
133 134 5.910637 AACACATTGTTTGCACATTCATC 57.089 34.783 0.00 0.00 37.26 2.92
134 135 4.309099 ACACATTGTTTGCACATTCATCC 58.691 39.130 0.00 0.00 31.06 3.51
135 136 3.365520 CACATTGTTTGCACATTCATCCG 59.634 43.478 0.00 0.00 31.06 4.18
136 137 3.005684 ACATTGTTTGCACATTCATCCGT 59.994 39.130 0.00 0.00 31.06 4.69
137 138 2.702898 TGTTTGCACATTCATCCGTG 57.297 45.000 0.00 0.00 36.18 4.94
138 139 1.269174 TGTTTGCACATTCATCCGTGG 59.731 47.619 0.00 0.00 33.62 4.94
139 140 0.887247 TTTGCACATTCATCCGTGGG 59.113 50.000 0.00 0.00 33.62 4.61
140 141 0.037447 TTGCACATTCATCCGTGGGA 59.963 50.000 0.00 0.00 35.55 4.37
141 142 0.255604 TGCACATTCATCCGTGGGAT 59.744 50.000 0.00 0.00 44.21 3.85
142 143 1.340893 TGCACATTCATCCGTGGGATT 60.341 47.619 0.00 0.00 39.79 3.01
143 144 2.092699 TGCACATTCATCCGTGGGATTA 60.093 45.455 0.00 0.00 39.79 1.75
144 145 3.149196 GCACATTCATCCGTGGGATTAT 58.851 45.455 0.00 0.00 39.79 1.28
145 146 3.189287 GCACATTCATCCGTGGGATTATC 59.811 47.826 0.00 0.00 39.79 1.75
146 147 3.753272 CACATTCATCCGTGGGATTATCC 59.247 47.826 1.91 1.91 39.79 2.59
147 148 3.652869 ACATTCATCCGTGGGATTATCCT 59.347 43.478 11.40 0.00 39.79 3.24
148 149 4.104738 ACATTCATCCGTGGGATTATCCTT 59.895 41.667 11.40 0.00 39.79 3.36
149 150 4.788925 TTCATCCGTGGGATTATCCTTT 57.211 40.909 11.40 0.00 39.79 3.11
150 151 4.085357 TCATCCGTGGGATTATCCTTTG 57.915 45.455 11.40 1.14 39.79 2.77
151 152 3.714280 TCATCCGTGGGATTATCCTTTGA 59.286 43.478 11.40 3.85 39.79 2.69
152 153 3.838244 TCCGTGGGATTATCCTTTGAG 57.162 47.619 11.40 0.00 36.57 3.02
153 154 3.380393 TCCGTGGGATTATCCTTTGAGA 58.620 45.455 11.40 0.00 36.57 3.27
154 155 3.778075 TCCGTGGGATTATCCTTTGAGAA 59.222 43.478 11.40 0.00 36.57 2.87
155 156 4.130118 CCGTGGGATTATCCTTTGAGAAG 58.870 47.826 11.40 0.00 36.57 2.85
156 157 8.381906 ATCCGTGGGATTATCCTTTGAGAAGG 62.382 46.154 11.40 0.00 45.71 3.46
167 168 4.525912 CTTTGAGAAGGAACCAAATGGG 57.474 45.455 4.17 0.00 44.81 4.00
168 169 3.893753 TTGAGAAGGAACCAAATGGGA 57.106 42.857 4.17 0.00 41.15 4.37
169 170 4.402616 TTGAGAAGGAACCAAATGGGAT 57.597 40.909 4.17 0.00 41.15 3.85
170 171 3.700538 TGAGAAGGAACCAAATGGGATG 58.299 45.455 4.17 0.00 41.15 3.51
171 172 2.428530 GAGAAGGAACCAAATGGGATGC 59.571 50.000 4.17 0.00 41.15 3.91
172 173 1.134946 GAAGGAACCAAATGGGATGCG 59.865 52.381 4.17 0.00 41.15 4.73
173 174 1.141665 GGAACCAAATGGGATGCGC 59.858 57.895 0.00 0.00 41.15 6.09
174 175 1.603236 GGAACCAAATGGGATGCGCA 61.603 55.000 14.96 14.96 41.15 6.09
175 176 0.458370 GAACCAAATGGGATGCGCAC 60.458 55.000 14.90 6.86 41.15 5.34
176 177 1.887344 AACCAAATGGGATGCGCACC 61.887 55.000 14.90 16.57 41.15 5.01
177 178 2.495866 CAAATGGGATGCGCACCC 59.504 61.111 29.98 29.98 46.87 4.61
178 179 2.053865 CAAATGGGATGCGCACCCT 61.054 57.895 33.43 22.43 46.82 4.34
179 180 1.305213 AAATGGGATGCGCACCCTT 60.305 52.632 33.43 27.99 46.82 3.95
180 181 1.606885 AAATGGGATGCGCACCCTTG 61.607 55.000 33.43 0.00 46.82 3.61
181 182 2.497792 AATGGGATGCGCACCCTTGA 62.498 55.000 33.43 21.75 46.82 3.02
182 183 2.825836 GGGATGCGCACCCTTGAG 60.826 66.667 29.62 0.00 43.65 3.02
183 184 2.045926 GGATGCGCACCCTTGAGT 60.046 61.111 15.63 0.00 0.00 3.41
184 185 1.675641 GGATGCGCACCCTTGAGTT 60.676 57.895 15.63 0.00 0.00 3.01
185 186 1.244019 GGATGCGCACCCTTGAGTTT 61.244 55.000 15.63 0.00 0.00 2.66
186 187 0.169009 GATGCGCACCCTTGAGTTTC 59.831 55.000 14.90 0.00 0.00 2.78
187 188 0.537143 ATGCGCACCCTTGAGTTTCA 60.537 50.000 14.90 0.00 0.00 2.69
188 189 0.537143 TGCGCACCCTTGAGTTTCAT 60.537 50.000 5.66 0.00 0.00 2.57
189 190 0.169009 GCGCACCCTTGAGTTTCATC 59.831 55.000 0.30 0.00 0.00 2.92
190 191 0.443869 CGCACCCTTGAGTTTCATCG 59.556 55.000 0.00 0.00 0.00 3.84
191 192 1.808411 GCACCCTTGAGTTTCATCGA 58.192 50.000 0.00 0.00 0.00 3.59
192 193 2.359900 GCACCCTTGAGTTTCATCGAT 58.640 47.619 0.00 0.00 0.00 3.59
193 194 2.352960 GCACCCTTGAGTTTCATCGATC 59.647 50.000 0.00 0.00 0.00 3.69
194 195 2.939103 CACCCTTGAGTTTCATCGATCC 59.061 50.000 0.00 0.00 0.00 3.36
195 196 2.571653 ACCCTTGAGTTTCATCGATCCA 59.428 45.455 0.00 0.00 0.00 3.41
196 197 3.009033 ACCCTTGAGTTTCATCGATCCAA 59.991 43.478 0.00 0.00 0.00 3.53
197 198 3.375299 CCCTTGAGTTTCATCGATCCAAC 59.625 47.826 0.00 1.23 0.00 3.77
198 199 4.002982 CCTTGAGTTTCATCGATCCAACA 58.997 43.478 15.42 2.02 0.00 3.33
199 200 4.637534 CCTTGAGTTTCATCGATCCAACAT 59.362 41.667 15.42 4.38 0.00 2.71
200 201 5.448225 CCTTGAGTTTCATCGATCCAACATG 60.448 44.000 15.42 0.00 0.00 3.21
201 202 4.578871 TGAGTTTCATCGATCCAACATGT 58.421 39.130 15.42 0.00 0.00 3.21
202 203 5.729510 TGAGTTTCATCGATCCAACATGTA 58.270 37.500 15.42 0.00 0.00 2.29
203 204 5.812127 TGAGTTTCATCGATCCAACATGTAG 59.188 40.000 15.42 0.00 0.00 2.74
204 205 5.118990 AGTTTCATCGATCCAACATGTAGG 58.881 41.667 15.42 0.00 0.00 3.18
205 206 5.104941 AGTTTCATCGATCCAACATGTAGGA 60.105 40.000 15.42 0.00 38.50 2.94
206 207 4.590850 TCATCGATCCAACATGTAGGAG 57.409 45.455 0.00 0.00 37.34 3.69
207 208 3.321968 TCATCGATCCAACATGTAGGAGG 59.678 47.826 0.00 0.00 37.34 4.30
208 209 3.026707 TCGATCCAACATGTAGGAGGA 57.973 47.619 0.00 5.23 37.34 3.71
209 210 2.959030 TCGATCCAACATGTAGGAGGAG 59.041 50.000 0.00 0.00 37.34 3.69
210 211 2.959030 CGATCCAACATGTAGGAGGAGA 59.041 50.000 0.00 0.00 37.34 3.71
211 212 3.005261 CGATCCAACATGTAGGAGGAGAG 59.995 52.174 0.00 0.04 37.34 3.20
212 213 3.757947 TCCAACATGTAGGAGGAGAGA 57.242 47.619 0.00 0.00 0.00 3.10
213 214 4.061131 TCCAACATGTAGGAGGAGAGAA 57.939 45.455 0.00 0.00 0.00 2.87
214 215 4.425772 TCCAACATGTAGGAGGAGAGAAA 58.574 43.478 0.00 0.00 0.00 2.52
215 216 4.844085 TCCAACATGTAGGAGGAGAGAAAA 59.156 41.667 0.00 0.00 0.00 2.29
216 217 5.309543 TCCAACATGTAGGAGGAGAGAAAAA 59.690 40.000 0.00 0.00 0.00 1.94
237 238 4.900635 AAAAGGACAACTACACAAGCAG 57.099 40.909 0.00 0.00 0.00 4.24
238 239 3.560636 AAGGACAACTACACAAGCAGT 57.439 42.857 0.00 0.00 0.00 4.40
239 240 4.682778 AAGGACAACTACACAAGCAGTA 57.317 40.909 0.00 0.00 0.00 2.74
240 241 4.258702 AGGACAACTACACAAGCAGTAG 57.741 45.455 0.00 0.00 43.51 2.57
241 242 3.895656 AGGACAACTACACAAGCAGTAGA 59.104 43.478 7.30 0.00 41.07 2.59
242 243 4.528596 AGGACAACTACACAAGCAGTAGAT 59.471 41.667 7.30 0.00 41.07 1.98
243 244 5.715279 AGGACAACTACACAAGCAGTAGATA 59.285 40.000 7.30 0.00 41.07 1.98
244 245 5.805994 GGACAACTACACAAGCAGTAGATAC 59.194 44.000 7.30 0.00 41.07 2.24
245 246 6.350277 GGACAACTACACAAGCAGTAGATACT 60.350 42.308 7.30 0.00 41.07 2.12
246 247 6.622549 ACAACTACACAAGCAGTAGATACTC 58.377 40.000 7.30 0.00 41.07 2.59
247 248 6.434652 ACAACTACACAAGCAGTAGATACTCT 59.565 38.462 7.30 0.00 41.07 3.24
248 249 7.039644 ACAACTACACAAGCAGTAGATACTCTT 60.040 37.037 7.30 0.00 41.07 2.85
249 250 7.090953 ACTACACAAGCAGTAGATACTCTTC 57.909 40.000 7.30 0.00 41.07 2.87
250 251 6.887545 ACTACACAAGCAGTAGATACTCTTCT 59.112 38.462 7.30 0.00 41.07 2.85
251 252 5.960113 ACACAAGCAGTAGATACTCTTCTG 58.040 41.667 6.45 6.45 42.53 3.02
252 253 5.712446 ACACAAGCAGTAGATACTCTTCTGA 59.288 40.000 13.07 0.00 42.32 3.27
253 254 6.209589 ACACAAGCAGTAGATACTCTTCTGAA 59.790 38.462 13.07 0.00 42.32 3.02
254 255 6.751425 CACAAGCAGTAGATACTCTTCTGAAG 59.249 42.308 11.18 11.18 42.32 3.02
255 256 6.435904 ACAAGCAGTAGATACTCTTCTGAAGT 59.564 38.462 16.43 2.39 42.32 3.01
256 257 6.693315 AGCAGTAGATACTCTTCTGAAGTC 57.307 41.667 16.43 7.36 42.32 3.01
257 258 6.423182 AGCAGTAGATACTCTTCTGAAGTCT 58.577 40.000 16.43 13.65 42.32 3.24
258 259 7.570132 AGCAGTAGATACTCTTCTGAAGTCTA 58.430 38.462 16.43 12.76 42.32 2.59
259 260 8.217799 AGCAGTAGATACTCTTCTGAAGTCTAT 58.782 37.037 16.43 11.80 42.32 1.98
260 261 9.496873 GCAGTAGATACTCTTCTGAAGTCTATA 57.503 37.037 16.43 6.30 42.32 1.31
266 267 9.921637 GATACTCTTCTGAAGTCTATATTTGGG 57.078 37.037 16.43 0.00 0.00 4.12
267 268 7.741554 ACTCTTCTGAAGTCTATATTTGGGT 57.258 36.000 16.43 0.00 0.00 4.51
271 272 9.807921 TCTTCTGAAGTCTATATTTGGGTTTTT 57.192 29.630 16.43 0.00 0.00 1.94
366 367 6.260050 TGATTGATACCTACCATTTTTCTCGC 59.740 38.462 0.00 0.00 0.00 5.03
709 728 1.359475 GACGGGGATACGAGCTCAC 59.641 63.158 15.40 1.68 37.61 3.51
1878 1898 2.348472 AGGTTGGAGGTTCAGATGGAA 58.652 47.619 0.00 0.00 0.00 3.53
2943 2967 6.780031 TGAAAGAAAGTTTGGATGGTGGAATA 59.220 34.615 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.821136 CAAAGGCCAAGGACCATTCTC 59.179 52.381 5.01 0.00 0.00 2.87
1 2 1.550869 CCAAAGGCCAAGGACCATTCT 60.551 52.381 5.01 0.00 0.00 2.40
2 3 0.897621 CCAAAGGCCAAGGACCATTC 59.102 55.000 5.01 0.00 0.00 2.67
4 5 1.005924 CTACCAAAGGCCAAGGACCAT 59.994 52.381 5.01 0.00 0.00 3.55
6 7 0.965866 GCTACCAAAGGCCAAGGACC 60.966 60.000 5.01 0.00 0.00 4.46
7 8 0.965866 GGCTACCAAAGGCCAAGGAC 60.966 60.000 5.01 0.00 46.84 3.85
8 9 1.382629 GGCTACCAAAGGCCAAGGA 59.617 57.895 5.01 0.00 46.84 3.36
9 10 4.018409 GGCTACCAAAGGCCAAGG 57.982 61.111 5.01 5.98 46.84 3.61
20 21 4.076394 TCTATTTGTTTGGTGTGGCTACC 58.924 43.478 0.00 4.80 41.24 3.18
21 22 5.897377 ATCTATTTGTTTGGTGTGGCTAC 57.103 39.130 0.00 0.00 0.00 3.58
22 23 8.588290 ATTAATCTATTTGTTTGGTGTGGCTA 57.412 30.769 0.00 0.00 0.00 3.93
23 24 6.909550 TTAATCTATTTGTTTGGTGTGGCT 57.090 33.333 0.00 0.00 0.00 4.75
24 25 9.646427 TTTATTAATCTATTTGTTTGGTGTGGC 57.354 29.630 0.00 0.00 0.00 5.01
50 51 9.428097 GCAATTGTTCTTTTTCTTATGAGGATT 57.572 29.630 7.40 0.00 0.00 3.01
51 52 8.587608 TGCAATTGTTCTTTTTCTTATGAGGAT 58.412 29.630 7.40 0.00 0.00 3.24
52 53 7.950512 TGCAATTGTTCTTTTTCTTATGAGGA 58.049 30.769 7.40 0.00 0.00 3.71
53 54 8.767478 ATGCAATTGTTCTTTTTCTTATGAGG 57.233 30.769 7.40 0.00 0.00 3.86
54 55 8.866956 GGATGCAATTGTTCTTTTTCTTATGAG 58.133 33.333 7.40 0.00 0.00 2.90
55 56 8.366401 TGGATGCAATTGTTCTTTTTCTTATGA 58.634 29.630 7.40 0.00 0.00 2.15
56 57 8.437742 GTGGATGCAATTGTTCTTTTTCTTATG 58.562 33.333 7.40 0.00 0.00 1.90
57 58 8.149647 TGTGGATGCAATTGTTCTTTTTCTTAT 58.850 29.630 7.40 0.00 0.00 1.73
58 59 7.495901 TGTGGATGCAATTGTTCTTTTTCTTA 58.504 30.769 7.40 0.00 0.00 2.10
59 60 6.347696 TGTGGATGCAATTGTTCTTTTTCTT 58.652 32.000 7.40 0.00 0.00 2.52
60 61 5.916318 TGTGGATGCAATTGTTCTTTTTCT 58.084 33.333 7.40 0.00 0.00 2.52
61 62 6.601741 TTGTGGATGCAATTGTTCTTTTTC 57.398 33.333 7.40 0.00 0.00 2.29
62 63 7.571080 AATTGTGGATGCAATTGTTCTTTTT 57.429 28.000 7.40 0.00 44.49 1.94
63 64 7.282675 TCAAATTGTGGATGCAATTGTTCTTTT 59.717 29.630 7.40 0.84 45.17 2.27
64 65 6.766944 TCAAATTGTGGATGCAATTGTTCTTT 59.233 30.769 7.40 0.00 45.17 2.52
65 66 6.289834 TCAAATTGTGGATGCAATTGTTCTT 58.710 32.000 7.40 0.00 45.17 2.52
66 67 5.856156 TCAAATTGTGGATGCAATTGTTCT 58.144 33.333 7.40 0.00 45.17 3.01
67 68 6.369340 TGATCAAATTGTGGATGCAATTGTTC 59.631 34.615 7.40 4.76 45.17 3.18
68 69 6.231951 TGATCAAATTGTGGATGCAATTGTT 58.768 32.000 7.40 0.00 45.17 2.83
69 70 5.795972 TGATCAAATTGTGGATGCAATTGT 58.204 33.333 7.40 0.00 45.17 2.71
70 71 6.918892 ATGATCAAATTGTGGATGCAATTG 57.081 33.333 0.00 0.00 45.17 2.32
72 73 6.537301 GTGAATGATCAAATTGTGGATGCAAT 59.463 34.615 0.00 0.00 40.43 3.56
73 74 5.870433 GTGAATGATCAAATTGTGGATGCAA 59.130 36.000 0.00 0.00 37.30 4.08
74 75 5.412640 GTGAATGATCAAATTGTGGATGCA 58.587 37.500 0.00 0.00 37.30 3.96
75 76 4.807304 GGTGAATGATCAAATTGTGGATGC 59.193 41.667 0.00 0.00 37.30 3.91
76 77 5.808540 GTGGTGAATGATCAAATTGTGGATG 59.191 40.000 0.00 0.00 37.30 3.51
77 78 5.481122 TGTGGTGAATGATCAAATTGTGGAT 59.519 36.000 0.00 0.00 37.30 3.41
78 79 4.831710 TGTGGTGAATGATCAAATTGTGGA 59.168 37.500 0.00 0.00 37.30 4.02
79 80 5.136816 TGTGGTGAATGATCAAATTGTGG 57.863 39.130 0.00 0.00 37.30 4.17
80 81 5.513849 CGATGTGGTGAATGATCAAATTGTG 59.486 40.000 0.00 0.00 37.30 3.33
81 82 5.415389 TCGATGTGGTGAATGATCAAATTGT 59.585 36.000 0.00 0.00 37.30 2.71
82 83 5.882553 TCGATGTGGTGAATGATCAAATTG 58.117 37.500 0.00 0.00 37.30 2.32
83 84 6.375174 TCTTCGATGTGGTGAATGATCAAATT 59.625 34.615 0.00 0.00 37.30 1.82
84 85 5.882000 TCTTCGATGTGGTGAATGATCAAAT 59.118 36.000 0.00 0.00 37.30 2.32
85 86 5.244755 TCTTCGATGTGGTGAATGATCAAA 58.755 37.500 0.00 0.00 37.30 2.69
86 87 4.831107 TCTTCGATGTGGTGAATGATCAA 58.169 39.130 0.00 0.00 37.30 2.57
87 88 4.470334 TCTTCGATGTGGTGAATGATCA 57.530 40.909 0.00 0.00 0.00 2.92
88 89 5.801350 TTTCTTCGATGTGGTGAATGATC 57.199 39.130 0.00 0.00 0.00 2.92
89 90 6.016360 TGTTTTTCTTCGATGTGGTGAATGAT 60.016 34.615 0.00 0.00 0.00 2.45
90 91 5.298026 TGTTTTTCTTCGATGTGGTGAATGA 59.702 36.000 0.00 0.00 0.00 2.57
91 92 5.399301 GTGTTTTTCTTCGATGTGGTGAATG 59.601 40.000 0.00 0.00 0.00 2.67
92 93 5.067153 TGTGTTTTTCTTCGATGTGGTGAAT 59.933 36.000 0.00 0.00 0.00 2.57
93 94 4.396478 TGTGTTTTTCTTCGATGTGGTGAA 59.604 37.500 0.00 0.00 0.00 3.18
94 95 3.942115 TGTGTTTTTCTTCGATGTGGTGA 59.058 39.130 0.00 0.00 0.00 4.02
95 96 4.285807 TGTGTTTTTCTTCGATGTGGTG 57.714 40.909 0.00 0.00 0.00 4.17
96 97 5.163561 ACAATGTGTTTTTCTTCGATGTGGT 60.164 36.000 0.00 0.00 0.00 4.16
97 98 5.280945 ACAATGTGTTTTTCTTCGATGTGG 58.719 37.500 0.00 0.00 0.00 4.17
98 99 6.810888 AACAATGTGTTTTTCTTCGATGTG 57.189 33.333 0.00 0.00 37.26 3.21
111 112 4.751098 GGATGAATGTGCAAACAATGTGTT 59.249 37.500 0.00 0.00 43.41 3.32
112 113 4.309099 GGATGAATGTGCAAACAATGTGT 58.691 39.130 0.00 0.00 0.00 3.72
113 114 3.365520 CGGATGAATGTGCAAACAATGTG 59.634 43.478 0.00 0.00 0.00 3.21
114 115 3.005684 ACGGATGAATGTGCAAACAATGT 59.994 39.130 0.00 0.00 0.00 2.71
115 116 3.365520 CACGGATGAATGTGCAAACAATG 59.634 43.478 0.00 0.00 0.00 2.82
116 117 3.577667 CACGGATGAATGTGCAAACAAT 58.422 40.909 0.00 0.00 0.00 2.71
117 118 2.288091 CCACGGATGAATGTGCAAACAA 60.288 45.455 0.00 0.00 34.77 2.83
118 119 1.269174 CCACGGATGAATGTGCAAACA 59.731 47.619 0.00 0.00 34.77 2.83
119 120 1.402720 CCCACGGATGAATGTGCAAAC 60.403 52.381 0.00 0.00 34.77 2.93
120 121 0.887247 CCCACGGATGAATGTGCAAA 59.113 50.000 0.00 0.00 34.77 3.68
121 122 0.037447 TCCCACGGATGAATGTGCAA 59.963 50.000 0.00 0.00 34.77 4.08
122 123 0.255604 ATCCCACGGATGAATGTGCA 59.744 50.000 0.00 0.00 41.43 4.57
123 124 1.392589 AATCCCACGGATGAATGTGC 58.607 50.000 0.00 0.00 42.27 4.57
124 125 3.753272 GGATAATCCCACGGATGAATGTG 59.247 47.826 0.00 0.00 42.27 3.21
125 126 3.652869 AGGATAATCCCACGGATGAATGT 59.347 43.478 0.00 0.00 42.27 2.71
126 127 4.292186 AGGATAATCCCACGGATGAATG 57.708 45.455 0.00 0.00 42.27 2.67
127 128 5.072741 CAAAGGATAATCCCACGGATGAAT 58.927 41.667 0.00 0.00 42.27 2.57
128 129 4.165180 TCAAAGGATAATCCCACGGATGAA 59.835 41.667 0.00 0.00 42.27 2.57
129 130 3.714280 TCAAAGGATAATCCCACGGATGA 59.286 43.478 0.00 0.00 42.27 2.92
130 131 4.067896 CTCAAAGGATAATCCCACGGATG 58.932 47.826 0.00 0.00 42.27 3.51
131 132 3.973973 TCTCAAAGGATAATCCCACGGAT 59.026 43.478 0.00 0.00 45.46 4.18
132 133 3.380393 TCTCAAAGGATAATCCCACGGA 58.620 45.455 0.00 0.00 37.19 4.69
133 134 3.838244 TCTCAAAGGATAATCCCACGG 57.162 47.619 0.00 0.00 37.19 4.94
145 146 4.996774 TCCCATTTGGTTCCTTCTCAAAGG 60.997 45.833 0.00 0.00 43.63 3.11
146 147 4.151883 TCCCATTTGGTTCCTTCTCAAAG 58.848 43.478 0.00 0.00 34.47 2.77
147 148 4.191804 TCCCATTTGGTTCCTTCTCAAA 57.808 40.909 0.00 0.00 35.30 2.69
148 149 3.893753 TCCCATTTGGTTCCTTCTCAA 57.106 42.857 0.00 0.00 34.77 3.02
149 150 3.700538 CATCCCATTTGGTTCCTTCTCA 58.299 45.455 0.00 0.00 34.77 3.27
150 151 2.428530 GCATCCCATTTGGTTCCTTCTC 59.571 50.000 0.00 0.00 34.77 2.87
151 152 2.460669 GCATCCCATTTGGTTCCTTCT 58.539 47.619 0.00 0.00 34.77 2.85
152 153 1.134946 CGCATCCCATTTGGTTCCTTC 59.865 52.381 0.00 0.00 34.77 3.46
153 154 1.185315 CGCATCCCATTTGGTTCCTT 58.815 50.000 0.00 0.00 34.77 3.36
154 155 1.322538 GCGCATCCCATTTGGTTCCT 61.323 55.000 0.30 0.00 34.77 3.36
155 156 1.141665 GCGCATCCCATTTGGTTCC 59.858 57.895 0.30 0.00 34.77 3.62
156 157 0.458370 GTGCGCATCCCATTTGGTTC 60.458 55.000 15.91 0.00 34.77 3.62
157 158 1.591183 GTGCGCATCCCATTTGGTT 59.409 52.632 15.91 0.00 34.77 3.67
158 159 2.350458 GGTGCGCATCCCATTTGGT 61.350 57.895 15.91 0.00 34.77 3.67
159 160 2.495866 GGTGCGCATCCCATTTGG 59.504 61.111 15.91 0.00 0.00 3.28
160 161 1.606885 AAGGGTGCGCATCCCATTTG 61.607 55.000 35.63 0.00 46.82 2.32
161 162 1.305213 AAGGGTGCGCATCCCATTT 60.305 52.632 35.63 21.10 46.82 2.32
162 163 2.053865 CAAGGGTGCGCATCCCATT 61.054 57.895 35.63 22.78 46.82 3.16
163 164 2.440796 CAAGGGTGCGCATCCCAT 60.441 61.111 35.63 24.89 46.82 4.00
164 165 3.626996 CTCAAGGGTGCGCATCCCA 62.627 63.158 35.63 19.02 46.82 4.37
165 166 2.825836 CTCAAGGGTGCGCATCCC 60.826 66.667 35.63 32.15 44.90 3.85
166 167 1.244019 AAACTCAAGGGTGCGCATCC 61.244 55.000 32.83 32.83 0.00 3.51
167 168 0.169009 GAAACTCAAGGGTGCGCATC 59.831 55.000 15.91 14.71 0.00 3.91
168 169 0.537143 TGAAACTCAAGGGTGCGCAT 60.537 50.000 15.91 0.00 0.00 4.73
169 170 0.537143 ATGAAACTCAAGGGTGCGCA 60.537 50.000 5.66 5.66 0.00 6.09
170 171 0.169009 GATGAAACTCAAGGGTGCGC 59.831 55.000 0.00 0.00 0.00 6.09
171 172 0.443869 CGATGAAACTCAAGGGTGCG 59.556 55.000 0.00 0.00 0.00 5.34
172 173 1.808411 TCGATGAAACTCAAGGGTGC 58.192 50.000 0.00 0.00 0.00 5.01
173 174 2.939103 GGATCGATGAAACTCAAGGGTG 59.061 50.000 0.54 0.00 0.00 4.61
174 175 2.571653 TGGATCGATGAAACTCAAGGGT 59.428 45.455 0.54 0.00 0.00 4.34
175 176 3.266510 TGGATCGATGAAACTCAAGGG 57.733 47.619 0.54 0.00 0.00 3.95
176 177 4.002982 TGTTGGATCGATGAAACTCAAGG 58.997 43.478 0.54 0.00 0.00 3.61
177 178 5.122869 ACATGTTGGATCGATGAAACTCAAG 59.877 40.000 0.54 2.14 0.00 3.02
178 179 5.003160 ACATGTTGGATCGATGAAACTCAA 58.997 37.500 0.54 0.00 0.00 3.02
179 180 4.578871 ACATGTTGGATCGATGAAACTCA 58.421 39.130 0.54 0.00 0.00 3.41
180 181 5.235186 CCTACATGTTGGATCGATGAAACTC 59.765 44.000 20.22 0.00 0.00 3.01
181 182 5.104941 TCCTACATGTTGGATCGATGAAACT 60.105 40.000 22.94 0.00 29.74 2.66
182 183 5.116180 TCCTACATGTTGGATCGATGAAAC 58.884 41.667 22.94 7.74 29.74 2.78
183 184 5.351948 TCCTACATGTTGGATCGATGAAA 57.648 39.130 22.94 0.06 29.74 2.69
184 185 4.202253 CCTCCTACATGTTGGATCGATGAA 60.202 45.833 26.07 4.92 34.19 2.57
185 186 3.321968 CCTCCTACATGTTGGATCGATGA 59.678 47.826 26.07 5.60 34.19 2.92
186 187 3.321968 TCCTCCTACATGTTGGATCGATG 59.678 47.826 26.07 15.33 34.19 3.84
187 188 3.576118 CTCCTCCTACATGTTGGATCGAT 59.424 47.826 26.07 0.00 34.19 3.59
188 189 2.959030 CTCCTCCTACATGTTGGATCGA 59.041 50.000 26.07 21.74 34.19 3.59
189 190 2.959030 TCTCCTCCTACATGTTGGATCG 59.041 50.000 26.07 19.27 34.19 3.69
190 191 4.219115 TCTCTCCTCCTACATGTTGGATC 58.781 47.826 26.07 0.00 34.19 3.36
191 192 4.271807 TCTCTCCTCCTACATGTTGGAT 57.728 45.455 26.07 0.00 34.19 3.41
192 193 3.757947 TCTCTCCTCCTACATGTTGGA 57.242 47.619 24.67 24.67 33.61 3.53
193 194 4.826274 TTTCTCTCCTCCTACATGTTGG 57.174 45.455 19.01 19.01 0.00 3.77
215 216 4.705023 ACTGCTTGTGTAGTTGTCCTTTTT 59.295 37.500 0.00 0.00 35.63 1.94
216 217 4.270008 ACTGCTTGTGTAGTTGTCCTTTT 58.730 39.130 0.00 0.00 35.63 2.27
217 218 3.886123 ACTGCTTGTGTAGTTGTCCTTT 58.114 40.909 0.00 0.00 35.63 3.11
218 219 3.560636 ACTGCTTGTGTAGTTGTCCTT 57.439 42.857 0.00 0.00 35.63 3.36
219 220 3.895656 TCTACTGCTTGTGTAGTTGTCCT 59.104 43.478 0.00 0.00 39.73 3.85
220 221 4.252971 TCTACTGCTTGTGTAGTTGTCC 57.747 45.455 0.00 0.00 39.73 4.02
221 222 6.622549 AGTATCTACTGCTTGTGTAGTTGTC 58.377 40.000 0.00 0.00 39.73 3.18
222 223 6.591750 AGTATCTACTGCTTGTGTAGTTGT 57.408 37.500 0.00 0.00 39.73 3.32
240 241 9.921637 CCCAAATATAGACTTCAGAAGAGTATC 57.078 37.037 17.56 3.87 0.00 2.24
241 242 9.440761 ACCCAAATATAGACTTCAGAAGAGTAT 57.559 33.333 17.56 13.79 0.00 2.12
242 243 8.840200 ACCCAAATATAGACTTCAGAAGAGTA 57.160 34.615 17.56 7.79 0.00 2.59
243 244 7.741554 ACCCAAATATAGACTTCAGAAGAGT 57.258 36.000 17.56 5.79 0.00 3.24
244 245 9.454859 AAAACCCAAATATAGACTTCAGAAGAG 57.545 33.333 17.56 0.00 0.00 2.85
245 246 9.807921 AAAAACCCAAATATAGACTTCAGAAGA 57.192 29.630 17.56 0.00 0.00 2.87
250 251 9.983024 TCCATAAAAACCCAAATATAGACTTCA 57.017 29.630 0.00 0.00 0.00 3.02
252 253 9.990868 ACTCCATAAAAACCCAAATATAGACTT 57.009 29.630 0.00 0.00 0.00 3.01
260 261 9.041354 TGCTATTTACTCCATAAAAACCCAAAT 57.959 29.630 0.00 0.00 36.35 2.32
261 262 8.423906 TGCTATTTACTCCATAAAAACCCAAA 57.576 30.769 0.00 0.00 36.35 3.28
262 263 8.602472 ATGCTATTTACTCCATAAAAACCCAA 57.398 30.769 0.00 0.00 36.35 4.12
263 264 9.702253 TTATGCTATTTACTCCATAAAAACCCA 57.298 29.630 0.00 0.00 36.35 4.51
709 728 1.284657 GTGATGTCGCACTCATCCTG 58.715 55.000 9.27 0.00 40.38 3.86
1373 1392 5.412594 CCTGCTTGTACAAGTACATTCACAT 59.587 40.000 30.90 0.00 44.54 3.21
1611 1631 1.210204 ACATGTCCCACAGCCTGGAT 61.210 55.000 0.00 0.00 43.95 3.41
1878 1898 2.387757 TCCTTGGCAAGTTTGAGCTTT 58.612 42.857 24.57 0.00 0.00 3.51
2623 2645 1.673477 CACTCCACTGCCTGCACTA 59.327 57.895 0.00 0.00 0.00 2.74
2737 2759 3.036819 CACCTGATGATCTTCCCTGAGA 58.963 50.000 6.17 0.00 0.00 3.27


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.