Multiple sequence alignment - TraesCS3D01G530400

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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 TraesCS3D01G530400 chr3D 100.000 3347 0 0 1 3347 607069609 607066263 0.000000e+00 6181
1 TraesCS3D01G530400 chr3A 91.677 3184 143 62 198 3347 739522802 739519707 0.000000e+00 4300
2 TraesCS3D01G530400 chr3B 94.108 2342 92 20 437 2749 816524472 816522148 0.000000e+00 3518
3 TraesCS3D01G530400 chr3B 94.737 494 15 7 2865 3347 816522078 816521585 0.000000e+00 758
4 TraesCS3D01G530400 chr3B 75.553 859 123 43 2502 3342 820499969 820499180 3.200000e-90 342


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 TraesCS3D01G530400 chr3D 607066263 607069609 3346 True 6181 6181 100.0000 1 3347 1 chr3D.!!$R1 3346
1 TraesCS3D01G530400 chr3A 739519707 739522802 3095 True 4300 4300 91.6770 198 3347 1 chr3A.!!$R1 3149
2 TraesCS3D01G530400 chr3B 816521585 816524472 2887 True 2138 3518 94.4225 437 3347 2 chr3B.!!$R2 2910
3 TraesCS3D01G530400 chr3B 820499180 820499969 789 True 342 342 75.5530 2502 3342 1 chr3B.!!$R1 840

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
714 736 0.026803 GGCGCTTGATTTCGTAGCTG 59.973 55.000 7.64 0.0 32.80 4.24 F
1726 1781 1.139058 CCTTCCCCGACATCGATTTCT 59.861 52.381 9.72 0.0 43.02 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2015 1.146485 CAGCAGCCAGGATCTCCAG 59.854 63.158 0.0 0.0 38.89 3.86 R
2749 2810 1.538047 TCTGCTTTCTGGACATTGCC 58.462 50.000 0.0 0.0 0.00 4.52 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
21 22 2.869358 CAACATCGTCTCTGTTGCAG 57.131 50.000 3.53 0.00 44.78 4.41
22 23 2.407090 CAACATCGTCTCTGTTGCAGA 58.593 47.619 3.53 0.00 44.78 4.26
37 38 3.625745 CAGAGGTTGCCGGTACTTT 57.374 52.632 1.90 0.00 0.00 2.66
38 39 1.892209 CAGAGGTTGCCGGTACTTTT 58.108 50.000 1.90 0.00 0.00 2.27
39 40 1.535462 CAGAGGTTGCCGGTACTTTTG 59.465 52.381 1.90 0.16 0.00 2.44
40 41 0.879090 GAGGTTGCCGGTACTTTTGG 59.121 55.000 1.90 0.00 0.00 3.28
41 42 0.538746 AGGTTGCCGGTACTTTTGGG 60.539 55.000 1.90 0.00 0.00 4.12
42 43 0.537828 GGTTGCCGGTACTTTTGGGA 60.538 55.000 1.90 0.00 0.00 4.37
43 44 0.879090 GTTGCCGGTACTTTTGGGAG 59.121 55.000 1.90 0.00 0.00 4.30
44 45 0.891904 TTGCCGGTACTTTTGGGAGC 60.892 55.000 1.90 0.00 0.00 4.70
45 46 1.302993 GCCGGTACTTTTGGGAGCA 60.303 57.895 1.90 0.00 0.00 4.26
46 47 0.679960 GCCGGTACTTTTGGGAGCAT 60.680 55.000 1.90 0.00 0.00 3.79
47 48 1.379527 CCGGTACTTTTGGGAGCATC 58.620 55.000 0.00 0.00 0.00 3.91
48 49 1.339631 CCGGTACTTTTGGGAGCATCA 60.340 52.381 0.00 0.00 36.25 3.07
49 50 1.737793 CGGTACTTTTGGGAGCATCAC 59.262 52.381 0.00 0.00 40.71 3.06
50 51 2.092323 GGTACTTTTGGGAGCATCACC 58.908 52.381 0.00 0.00 38.18 4.02
51 52 1.737793 GTACTTTTGGGAGCATCACCG 59.262 52.381 0.00 0.00 38.18 4.94
52 53 0.400213 ACTTTTGGGAGCATCACCGA 59.600 50.000 0.00 0.00 38.18 4.69
53 54 1.004745 ACTTTTGGGAGCATCACCGAT 59.995 47.619 0.00 0.00 38.18 4.18
54 55 1.402968 CTTTTGGGAGCATCACCGATG 59.597 52.381 0.00 0.00 38.18 3.84
55 56 0.394216 TTTGGGAGCATCACCGATGG 60.394 55.000 6.14 0.00 38.18 3.51
56 57 2.592861 GGGAGCATCACCGATGGC 60.593 66.667 6.14 0.00 40.10 4.40
57 58 2.969238 GGAGCATCACCGATGGCG 60.969 66.667 6.14 0.00 40.10 5.69
58 59 2.202932 GAGCATCACCGATGGCGT 60.203 61.111 6.14 0.00 40.10 5.68
59 60 2.512286 AGCATCACCGATGGCGTG 60.512 61.111 6.14 0.00 40.10 5.34
60 61 3.576356 GCATCACCGATGGCGTGG 61.576 66.667 6.14 0.00 40.10 4.94
61 62 3.576356 CATCACCGATGGCGTGGC 61.576 66.667 0.00 0.00 36.51 5.01
82 83 2.279186 TGCGACGGCATATCACGG 60.279 61.111 0.00 0.00 46.21 4.94
83 84 2.279252 GCGACGGCATATCACGGT 60.279 61.111 0.00 0.00 39.62 4.83
84 85 2.585869 GCGACGGCATATCACGGTG 61.586 63.158 0.56 0.56 39.62 4.94
85 86 2.585869 CGACGGCATATCACGGTGC 61.586 63.158 2.51 0.00 40.55 5.01
86 87 1.227263 GACGGCATATCACGGTGCT 60.227 57.895 2.51 0.00 41.04 4.40
87 88 0.031585 GACGGCATATCACGGTGCTA 59.968 55.000 2.51 0.00 41.04 3.49
88 89 0.032130 ACGGCATATCACGGTGCTAG 59.968 55.000 2.51 0.00 41.04 3.42
89 90 0.667487 CGGCATATCACGGTGCTAGG 60.667 60.000 2.51 0.94 41.04 3.02
90 91 0.320771 GGCATATCACGGTGCTAGGG 60.321 60.000 2.51 0.00 41.04 3.53
91 92 0.393077 GCATATCACGGTGCTAGGGT 59.607 55.000 2.51 0.00 38.30 4.34
92 93 1.873903 GCATATCACGGTGCTAGGGTG 60.874 57.143 2.51 0.00 38.30 4.61
93 94 1.048601 ATATCACGGTGCTAGGGTGG 58.951 55.000 2.51 0.00 32.65 4.61
94 95 0.324923 TATCACGGTGCTAGGGTGGT 60.325 55.000 2.51 0.00 32.65 4.16
95 96 1.899437 ATCACGGTGCTAGGGTGGTG 61.899 60.000 2.51 0.00 32.65 4.17
96 97 4.016706 ACGGTGCTAGGGTGGTGC 62.017 66.667 0.00 0.00 0.00 5.01
97 98 4.015406 CGGTGCTAGGGTGGTGCA 62.015 66.667 0.00 0.00 0.00 4.57
99 100 2.742372 GTGCTAGGGTGGTGCACG 60.742 66.667 11.45 0.00 45.62 5.34
100 101 4.015406 TGCTAGGGTGGTGCACGG 62.015 66.667 11.45 0.00 34.83 4.94
101 102 4.778143 GCTAGGGTGGTGCACGGG 62.778 72.222 11.45 0.00 34.83 5.28
102 103 4.778143 CTAGGGTGGTGCACGGGC 62.778 72.222 11.45 0.34 41.68 6.13
117 118 2.920912 GGCCGGGGATCGTGGATA 60.921 66.667 2.18 0.00 37.11 2.59
118 119 2.291043 GGCCGGGGATCGTGGATAT 61.291 63.158 2.18 0.00 37.11 1.63
119 120 1.677552 GCCGGGGATCGTGGATATT 59.322 57.895 2.18 0.00 37.11 1.28
120 121 0.673644 GCCGGGGATCGTGGATATTG 60.674 60.000 2.18 0.00 37.11 1.90
121 122 0.036388 CCGGGGATCGTGGATATTGG 60.036 60.000 0.00 0.00 37.11 3.16
122 123 0.685097 CGGGGATCGTGGATATTGGT 59.315 55.000 0.00 0.00 0.00 3.67
123 124 1.608025 CGGGGATCGTGGATATTGGTG 60.608 57.143 0.00 0.00 0.00 4.17
124 125 1.271379 GGGGATCGTGGATATTGGTGG 60.271 57.143 0.00 0.00 0.00 4.61
125 126 1.420138 GGGATCGTGGATATTGGTGGT 59.580 52.381 0.00 0.00 0.00 4.16
126 127 2.550208 GGGATCGTGGATATTGGTGGTC 60.550 54.545 0.00 0.00 0.00 4.02
127 128 2.550208 GGATCGTGGATATTGGTGGTCC 60.550 54.545 0.00 0.00 0.00 4.46
128 129 1.574263 TCGTGGATATTGGTGGTCCA 58.426 50.000 0.00 0.00 42.66 4.02
132 133 3.080300 TGGATATTGGTGGTCCACAAC 57.920 47.619 23.48 7.79 44.22 3.32
133 134 2.647299 TGGATATTGGTGGTCCACAACT 59.353 45.455 23.48 9.41 44.22 3.16
134 135 3.279434 GGATATTGGTGGTCCACAACTC 58.721 50.000 23.48 14.05 44.22 3.01
135 136 2.465860 TATTGGTGGTCCACAACTCG 57.534 50.000 23.48 0.00 44.22 4.18
136 137 0.250727 ATTGGTGGTCCACAACTCGG 60.251 55.000 23.48 0.00 44.22 4.63
137 138 2.032071 GGTGGTCCACAACTCGGG 59.968 66.667 23.48 0.00 35.86 5.14
138 139 2.513259 GGTGGTCCACAACTCGGGA 61.513 63.158 23.48 0.00 35.86 5.14
139 140 1.448497 GTGGTCCACAACTCGGGAA 59.552 57.895 17.59 0.00 34.34 3.97
140 141 0.179040 GTGGTCCACAACTCGGGAAA 60.179 55.000 17.59 0.00 34.34 3.13
141 142 0.179040 TGGTCCACAACTCGGGAAAC 60.179 55.000 0.00 0.00 34.34 2.78
142 143 1.226030 GGTCCACAACTCGGGAAACG 61.226 60.000 0.00 0.00 46.11 3.60
143 144 1.070105 TCCACAACTCGGGAAACGG 59.930 57.895 0.00 0.00 44.45 4.44
144 145 1.070105 CCACAACTCGGGAAACGGA 59.930 57.895 0.00 0.00 44.45 4.69
145 146 0.533308 CCACAACTCGGGAAACGGAA 60.533 55.000 0.00 0.00 44.45 4.30
146 147 1.301423 CACAACTCGGGAAACGGAAA 58.699 50.000 0.00 0.00 44.45 3.13
147 148 1.263217 CACAACTCGGGAAACGGAAAG 59.737 52.381 0.00 0.00 44.45 2.62
148 149 1.134310 ACAACTCGGGAAACGGAAAGT 60.134 47.619 0.00 0.00 44.45 2.66
149 150 1.263217 CAACTCGGGAAACGGAAAGTG 59.737 52.381 0.00 0.00 44.45 3.16
150 151 0.250166 ACTCGGGAAACGGAAAGTGG 60.250 55.000 0.00 0.00 44.45 4.00
151 152 0.953960 CTCGGGAAACGGAAAGTGGG 60.954 60.000 0.00 0.00 44.45 4.61
152 153 1.071814 CGGGAAACGGAAAGTGGGA 59.928 57.895 0.00 0.00 39.42 4.37
153 154 0.535553 CGGGAAACGGAAAGTGGGAA 60.536 55.000 0.00 0.00 39.42 3.97
154 155 1.244816 GGGAAACGGAAAGTGGGAAG 58.755 55.000 0.00 0.00 0.00 3.46
155 156 1.202842 GGGAAACGGAAAGTGGGAAGA 60.203 52.381 0.00 0.00 0.00 2.87
156 157 1.878088 GGAAACGGAAAGTGGGAAGAC 59.122 52.381 0.00 0.00 0.00 3.01
157 158 2.567985 GAAACGGAAAGTGGGAAGACA 58.432 47.619 0.00 0.00 0.00 3.41
158 159 2.951229 AACGGAAAGTGGGAAGACAT 57.049 45.000 0.00 0.00 0.00 3.06
159 160 2.185004 ACGGAAAGTGGGAAGACATG 57.815 50.000 0.00 0.00 0.00 3.21
160 161 1.697432 ACGGAAAGTGGGAAGACATGA 59.303 47.619 0.00 0.00 0.00 3.07
161 162 2.105821 ACGGAAAGTGGGAAGACATGAA 59.894 45.455 0.00 0.00 0.00 2.57
162 163 2.744202 CGGAAAGTGGGAAGACATGAAG 59.256 50.000 0.00 0.00 0.00 3.02
163 164 3.756117 GGAAAGTGGGAAGACATGAAGT 58.244 45.455 0.00 0.00 0.00 3.01
173 174 2.703190 GACATGAAGTCGACGATTGC 57.297 50.000 10.46 0.00 37.53 3.56
174 175 0.992072 ACATGAAGTCGACGATTGCG 59.008 50.000 10.46 1.20 44.79 4.85
175 176 0.298707 CATGAAGTCGACGATTGCGG 59.701 55.000 10.46 0.00 43.17 5.69
176 177 0.108804 ATGAAGTCGACGATTGCGGT 60.109 50.000 10.46 0.00 43.17 5.68
177 178 0.319211 TGAAGTCGACGATTGCGGTT 60.319 50.000 10.46 0.00 43.17 4.44
178 179 0.093026 GAAGTCGACGATTGCGGTTG 59.907 55.000 10.46 0.00 43.17 3.77
179 180 0.319211 AAGTCGACGATTGCGGTTGA 60.319 50.000 10.46 0.00 43.17 3.18
180 181 0.108804 AGTCGACGATTGCGGTTGAT 60.109 50.000 10.46 0.00 43.17 2.57
181 182 0.297820 GTCGACGATTGCGGTTGATC 59.702 55.000 0.00 0.00 43.17 2.92
182 183 0.804544 TCGACGATTGCGGTTGATCC 60.805 55.000 0.00 0.00 43.17 3.36
191 192 4.732106 GGTTGATCCGACGGCTAG 57.268 61.111 9.66 0.00 0.00 3.42
192 193 1.591863 GGTTGATCCGACGGCTAGC 60.592 63.158 9.66 6.04 0.00 3.42
193 194 1.141019 GTTGATCCGACGGCTAGCA 59.859 57.895 18.24 0.00 0.00 3.49
194 195 0.872021 GTTGATCCGACGGCTAGCAG 60.872 60.000 18.24 15.90 0.00 4.24
195 196 2.355244 GATCCGACGGCTAGCAGC 60.355 66.667 18.24 8.05 41.46 5.25
208 209 0.901827 TAGCAGCCCGACTGATTTCA 59.098 50.000 9.31 0.00 44.43 2.69
209 210 0.392193 AGCAGCCCGACTGATTTCAG 60.392 55.000 9.31 6.03 44.43 3.02
210 211 4.935736 TAGCAGCCCGACTGATTTCAGC 62.936 54.545 7.48 0.58 44.43 4.26
217 218 3.566261 CTGATTTCAGCACGGCGT 58.434 55.556 6.77 6.77 37.15 5.68
218 219 1.868997 CTGATTTCAGCACGGCGTT 59.131 52.632 11.19 0.00 37.15 4.84
219 220 1.075542 CTGATTTCAGCACGGCGTTA 58.924 50.000 11.19 0.00 37.15 3.18
220 221 1.061131 CTGATTTCAGCACGGCGTTAG 59.939 52.381 11.19 0.05 37.15 2.34
231 232 6.259167 TCAGCACGGCGTTAGATTTAATTATT 59.741 34.615 11.19 0.00 0.00 1.40
232 233 6.910433 CAGCACGGCGTTAGATTTAATTATTT 59.090 34.615 11.19 0.00 0.00 1.40
233 234 7.431084 CAGCACGGCGTTAGATTTAATTATTTT 59.569 33.333 11.19 0.00 0.00 1.82
255 256 4.676849 TTGGTTTGTTTTTGCTTTCTGC 57.323 36.364 0.00 0.00 43.25 4.26
263 264 2.818130 TTTGCTTTCTGCCATGGAAC 57.182 45.000 18.40 0.00 42.00 3.62
271 272 1.076841 TCTGCCATGGAACCCAATGAA 59.923 47.619 18.40 0.00 36.95 2.57
272 273 1.205417 CTGCCATGGAACCCAATGAAC 59.795 52.381 18.40 0.00 36.95 3.18
273 274 1.265236 GCCATGGAACCCAATGAACA 58.735 50.000 18.40 0.00 36.95 3.18
274 275 1.622811 GCCATGGAACCCAATGAACAA 59.377 47.619 18.40 0.00 36.95 2.83
275 276 2.236893 GCCATGGAACCCAATGAACAAT 59.763 45.455 18.40 0.00 36.95 2.71
276 277 3.864243 CCATGGAACCCAATGAACAATG 58.136 45.455 5.56 0.00 36.95 2.82
277 278 3.514706 CCATGGAACCCAATGAACAATGA 59.485 43.478 5.56 0.00 36.95 2.57
278 279 4.162698 CCATGGAACCCAATGAACAATGAT 59.837 41.667 5.56 0.00 36.95 2.45
279 280 5.338544 CCATGGAACCCAATGAACAATGATT 60.339 40.000 5.56 0.00 36.95 2.57
280 281 5.404466 TGGAACCCAATGAACAATGATTC 57.596 39.130 0.00 0.00 0.00 2.52
281 282 4.222588 TGGAACCCAATGAACAATGATTCC 59.777 41.667 13.76 13.76 34.85 3.01
282 283 4.467438 GGAACCCAATGAACAATGATTCCT 59.533 41.667 13.54 0.00 32.15 3.36
283 284 5.656416 GGAACCCAATGAACAATGATTCCTA 59.344 40.000 13.54 0.00 32.15 2.94
284 285 6.183360 GGAACCCAATGAACAATGATTCCTAG 60.183 42.308 13.54 0.00 32.15 3.02
289 290 9.305555 CCCAATGAACAATGATTCCTAGATATT 57.694 33.333 0.00 0.00 0.00 1.28
300 301 8.400184 TGATTCCTAGATATTTCAATGGCAAG 57.600 34.615 0.00 0.00 0.00 4.01
323 324 2.519771 ATCAGTGGTGTGATGGCATT 57.480 45.000 0.00 0.00 35.76 3.56
336 337 1.515519 GGCATTGCACATGCTGACG 60.516 57.895 23.69 0.00 44.02 4.35
343 344 1.062047 CACATGCTGACGATGCTGC 59.938 57.895 0.00 0.00 0.00 5.25
344 345 1.078637 ACATGCTGACGATGCTGCT 60.079 52.632 0.00 0.00 34.32 4.24
345 346 1.352056 CATGCTGACGATGCTGCTG 59.648 57.895 0.00 0.00 34.32 4.41
351 352 3.382803 GACGATGCTGCTGCCCTCT 62.383 63.158 13.47 1.08 38.71 3.69
377 378 1.278985 TGAGATCCATTCACGTGCCTT 59.721 47.619 11.67 0.00 0.00 4.35
397 400 6.016943 TGCCTTGTTACATACCAGTACAAAAC 60.017 38.462 0.00 0.00 0.00 2.43
406 409 8.172352 ACATACCAGTACAAAACAGCAATTTA 57.828 30.769 0.00 0.00 0.00 1.40
481 489 1.834856 ATCGCATCGCCATCTGGGAT 61.835 55.000 0.00 0.00 46.72 3.85
486 494 2.362736 CATCGCCATCTGGGATAATGG 58.637 52.381 0.00 0.00 44.19 3.16
491 499 1.145531 CCATCTGGGATAATGGCACCA 59.854 52.381 0.00 0.00 40.01 4.17
569 578 1.526917 CCACCAATCCTGCCCGATC 60.527 63.158 0.00 0.00 0.00 3.69
570 579 1.526917 CACCAATCCTGCCCGATCC 60.527 63.158 0.00 0.00 0.00 3.36
571 580 2.113986 CCAATCCTGCCCGATCCC 59.886 66.667 0.00 0.00 0.00 3.85
572 581 2.281070 CAATCCTGCCCGATCCCG 60.281 66.667 0.00 0.00 0.00 5.14
573 582 2.768344 AATCCTGCCCGATCCCGT 60.768 61.111 0.00 0.00 0.00 5.28
574 583 2.808206 AATCCTGCCCGATCCCGTC 61.808 63.158 0.00 0.00 0.00 4.79
575 584 3.758133 ATCCTGCCCGATCCCGTCT 62.758 63.158 0.00 0.00 0.00 4.18
576 585 4.227134 CCTGCCCGATCCCGTCTG 62.227 72.222 0.00 0.00 0.00 3.51
577 586 4.227134 CTGCCCGATCCCGTCTGG 62.227 72.222 0.00 0.00 34.56 3.86
594 603 1.454479 GGCCCCATCACATCACCAG 60.454 63.158 0.00 0.00 0.00 4.00
615 624 2.181021 CCGAGACGAAACCCCGAG 59.819 66.667 0.00 0.00 0.00 4.63
627 636 0.250989 ACCCCGAGAGAGATCGATCC 60.251 60.000 21.66 13.02 45.56 3.36
696 718 1.153168 CAGCCACTGGTAATCCCGG 60.153 63.158 0.00 0.00 46.09 5.73
714 736 0.026803 GGCGCTTGATTTCGTAGCTG 59.973 55.000 7.64 0.00 32.80 4.24
751 786 3.370061 GGCTCAAGATTTGATTTTGCAGC 59.630 43.478 0.00 0.00 39.30 5.25
759 794 6.331061 AGATTTGATTTTGCAGCTCATCTTC 58.669 36.000 0.00 0.00 0.00 2.87
1251 1306 1.296056 GGTTCATCCCCGTCAACGTG 61.296 60.000 1.48 0.00 37.74 4.49
1726 1781 1.139058 CCTTCCCCGACATCGATTTCT 59.861 52.381 9.72 0.00 43.02 2.52
1960 2015 1.266175 TCTCGTTCTTCACCGACAGTC 59.734 52.381 0.00 0.00 0.00 3.51
2007 2062 2.571653 TCCCTCGGTGATGTTGATTCTT 59.428 45.455 0.00 0.00 0.00 2.52
2103 2158 1.622811 CTCCTGATACTCCCCTGCATC 59.377 57.143 0.00 0.00 0.00 3.91
2450 2505 0.323178 CTCAGCCATGCCTCCTTGTT 60.323 55.000 0.00 0.00 0.00 2.83
2650 2710 4.919168 CAGCACAAGTTGTCAATACATTGG 59.081 41.667 5.27 0.00 38.30 3.16
2718 2779 9.098355 TGTGATACATTTGAGTAGCATCTAAAC 57.902 33.333 0.00 0.00 41.72 2.01
2723 2784 8.485976 ACATTTGAGTAGCATCTAAACTTCTC 57.514 34.615 0.00 0.00 32.65 2.87
2749 2810 9.726232 CTTAAATCACTCAATGTAATCATGGTG 57.274 33.333 0.00 0.00 34.19 4.17
2771 2832 3.065925 GGCAATGTCCAGAAAGCAGATAC 59.934 47.826 0.00 0.00 0.00 2.24
2778 2839 6.341316 TGTCCAGAAAGCAGATACACTATTC 58.659 40.000 0.00 0.00 0.00 1.75
2816 2877 6.039717 TGAGAGAGGGTGAAAAATTCAGTTTG 59.960 38.462 0.00 0.00 41.01 2.93
2817 2878 4.948847 AGAGGGTGAAAAATTCAGTTTGC 58.051 39.130 0.00 0.00 41.01 3.68
2960 3039 2.158623 TGCCAGAGTGGTGAAAAGTGAT 60.159 45.455 0.00 0.00 40.46 3.06
2977 3056 6.575162 AAGTGATCCAATAAAGAACCACAC 57.425 37.500 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.820059 TCTGCAACAGAGACGATGTT 57.180 45.000 0.00 0.00 41.47 2.71
19 20 1.535462 CAAAAGTACCGGCAACCTCTG 59.465 52.381 0.00 0.00 0.00 3.35
20 21 1.544759 CCAAAAGTACCGGCAACCTCT 60.545 52.381 0.00 0.00 0.00 3.69
21 22 0.879090 CCAAAAGTACCGGCAACCTC 59.121 55.000 0.00 0.00 0.00 3.85
22 23 0.538746 CCCAAAAGTACCGGCAACCT 60.539 55.000 0.00 0.00 0.00 3.50
23 24 0.537828 TCCCAAAAGTACCGGCAACC 60.538 55.000 0.00 0.00 0.00 3.77
24 25 0.879090 CTCCCAAAAGTACCGGCAAC 59.121 55.000 0.00 0.00 0.00 4.17
25 26 0.891904 GCTCCCAAAAGTACCGGCAA 60.892 55.000 0.00 0.00 0.00 4.52
26 27 1.302993 GCTCCCAAAAGTACCGGCA 60.303 57.895 0.00 0.00 0.00 5.69
27 28 0.679960 ATGCTCCCAAAAGTACCGGC 60.680 55.000 0.00 0.00 0.00 6.13
28 29 1.339631 TGATGCTCCCAAAAGTACCGG 60.340 52.381 0.00 0.00 0.00 5.28
29 30 1.737793 GTGATGCTCCCAAAAGTACCG 59.262 52.381 0.00 0.00 0.00 4.02
30 31 2.092323 GGTGATGCTCCCAAAAGTACC 58.908 52.381 0.00 0.00 0.00 3.34
31 32 1.737793 CGGTGATGCTCCCAAAAGTAC 59.262 52.381 0.00 0.00 0.00 2.73
32 33 1.626321 TCGGTGATGCTCCCAAAAGTA 59.374 47.619 0.00 0.00 0.00 2.24
33 34 0.400213 TCGGTGATGCTCCCAAAAGT 59.600 50.000 0.00 0.00 0.00 2.66
34 35 1.402968 CATCGGTGATGCTCCCAAAAG 59.597 52.381 0.00 0.00 33.17 2.27
35 36 1.462616 CATCGGTGATGCTCCCAAAA 58.537 50.000 0.00 0.00 33.17 2.44
36 37 0.394216 CCATCGGTGATGCTCCCAAA 60.394 55.000 0.00 0.00 38.59 3.28
37 38 1.224315 CCATCGGTGATGCTCCCAA 59.776 57.895 0.00 0.00 38.59 4.12
38 39 2.910360 CCATCGGTGATGCTCCCA 59.090 61.111 0.00 0.00 38.59 4.37
39 40 2.592861 GCCATCGGTGATGCTCCC 60.593 66.667 0.00 0.00 38.59 4.30
40 41 2.969238 CGCCATCGGTGATGCTCC 60.969 66.667 0.00 0.00 38.59 4.70
41 42 2.202932 ACGCCATCGGTGATGCTC 60.203 61.111 0.00 0.00 38.59 4.26
42 43 2.512286 CACGCCATCGGTGATGCT 60.512 61.111 0.00 0.00 38.59 3.79
43 44 3.576356 CCACGCCATCGGTGATGC 61.576 66.667 0.00 0.00 38.59 3.91
44 45 3.576356 GCCACGCCATCGGTGATG 61.576 66.667 0.00 0.00 39.52 3.07
66 67 2.279252 ACCGTGATATGCCGTCGC 60.279 61.111 0.00 0.00 0.00 5.19
67 68 2.585869 GCACCGTGATATGCCGTCG 61.586 63.158 1.65 0.00 35.73 5.12
68 69 0.031585 TAGCACCGTGATATGCCGTC 59.968 55.000 1.65 0.00 43.12 4.79
69 70 0.032130 CTAGCACCGTGATATGCCGT 59.968 55.000 1.65 0.00 43.12 5.68
70 71 0.667487 CCTAGCACCGTGATATGCCG 60.667 60.000 1.65 0.00 43.12 5.69
71 72 0.320771 CCCTAGCACCGTGATATGCC 60.321 60.000 1.65 0.00 43.12 4.40
72 73 0.393077 ACCCTAGCACCGTGATATGC 59.607 55.000 1.65 0.00 42.39 3.14
73 74 1.270305 CCACCCTAGCACCGTGATATG 60.270 57.143 1.65 0.00 0.00 1.78
74 75 1.048601 CCACCCTAGCACCGTGATAT 58.951 55.000 1.65 0.00 0.00 1.63
75 76 0.324923 ACCACCCTAGCACCGTGATA 60.325 55.000 1.65 0.00 0.00 2.15
76 77 1.612442 ACCACCCTAGCACCGTGAT 60.612 57.895 1.65 0.00 0.00 3.06
77 78 2.203728 ACCACCCTAGCACCGTGA 60.204 61.111 1.65 0.00 0.00 4.35
78 79 2.047274 CACCACCCTAGCACCGTG 60.047 66.667 0.00 0.00 0.00 4.94
79 80 4.016706 GCACCACCCTAGCACCGT 62.017 66.667 0.00 0.00 0.00 4.83
80 81 4.015406 TGCACCACCCTAGCACCG 62.015 66.667 0.00 0.00 32.55 4.94
83 84 4.015406 CCGTGCACCACCCTAGCA 62.015 66.667 12.15 0.00 35.63 3.49
84 85 4.778143 CCCGTGCACCACCCTAGC 62.778 72.222 12.15 0.00 0.00 3.42
85 86 4.778143 GCCCGTGCACCACCCTAG 62.778 72.222 12.15 0.00 37.47 3.02
100 101 1.838073 AATATCCACGATCCCCGGCC 61.838 60.000 0.00 0.00 43.93 6.13
101 102 0.673644 CAATATCCACGATCCCCGGC 60.674 60.000 0.00 0.00 43.93 6.13
102 103 0.036388 CCAATATCCACGATCCCCGG 60.036 60.000 0.00 0.00 43.93 5.73
103 104 0.685097 ACCAATATCCACGATCCCCG 59.315 55.000 0.00 0.00 45.44 5.73
104 105 1.271379 CCACCAATATCCACGATCCCC 60.271 57.143 0.00 0.00 0.00 4.81
105 106 1.420138 ACCACCAATATCCACGATCCC 59.580 52.381 0.00 0.00 0.00 3.85
106 107 2.550208 GGACCACCAATATCCACGATCC 60.550 54.545 0.00 0.00 35.97 3.36
107 108 2.104111 TGGACCACCAATATCCACGATC 59.896 50.000 0.00 0.00 43.91 3.69
108 109 2.123589 TGGACCACCAATATCCACGAT 58.876 47.619 0.00 0.00 43.91 3.73
109 110 1.574263 TGGACCACCAATATCCACGA 58.426 50.000 0.00 0.00 43.91 4.35
119 120 2.813726 CCCGAGTTGTGGACCACCA 61.814 63.158 22.00 8.39 44.76 4.17
120 121 2.032071 CCCGAGTTGTGGACCACC 59.968 66.667 22.00 7.46 32.73 4.61
121 122 0.179040 TTTCCCGAGTTGTGGACCAC 60.179 55.000 18.28 18.28 34.56 4.16
122 123 0.179040 GTTTCCCGAGTTGTGGACCA 60.179 55.000 0.00 0.00 0.00 4.02
123 124 1.226030 CGTTTCCCGAGTTGTGGACC 61.226 60.000 0.00 0.00 39.56 4.46
124 125 1.226030 CCGTTTCCCGAGTTGTGGAC 61.226 60.000 0.00 0.00 39.56 4.02
125 126 1.070105 CCGTTTCCCGAGTTGTGGA 59.930 57.895 0.00 0.00 39.56 4.02
126 127 0.533308 TTCCGTTTCCCGAGTTGTGG 60.533 55.000 0.00 0.00 39.56 4.17
127 128 1.263217 CTTTCCGTTTCCCGAGTTGTG 59.737 52.381 0.00 0.00 39.56 3.33
128 129 1.134310 ACTTTCCGTTTCCCGAGTTGT 60.134 47.619 0.00 0.00 39.56 3.32
129 130 1.263217 CACTTTCCGTTTCCCGAGTTG 59.737 52.381 0.00 0.00 39.56 3.16
130 131 1.589803 CACTTTCCGTTTCCCGAGTT 58.410 50.000 0.00 0.00 39.56 3.01
131 132 0.250166 CCACTTTCCGTTTCCCGAGT 60.250 55.000 0.00 0.00 39.56 4.18
132 133 0.953960 CCCACTTTCCGTTTCCCGAG 60.954 60.000 0.00 0.00 39.56 4.63
133 134 1.071814 CCCACTTTCCGTTTCCCGA 59.928 57.895 0.00 0.00 39.56 5.14
134 135 0.535553 TTCCCACTTTCCGTTTCCCG 60.536 55.000 0.00 0.00 0.00 5.14
135 136 1.202842 TCTTCCCACTTTCCGTTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
136 137 1.878088 GTCTTCCCACTTTCCGTTTCC 59.122 52.381 0.00 0.00 0.00 3.13
137 138 2.567985 TGTCTTCCCACTTTCCGTTTC 58.432 47.619 0.00 0.00 0.00 2.78
138 139 2.721425 TGTCTTCCCACTTTCCGTTT 57.279 45.000 0.00 0.00 0.00 3.60
139 140 2.105821 TCATGTCTTCCCACTTTCCGTT 59.894 45.455 0.00 0.00 0.00 4.44
140 141 1.697432 TCATGTCTTCCCACTTTCCGT 59.303 47.619 0.00 0.00 0.00 4.69
141 142 2.472695 TCATGTCTTCCCACTTTCCG 57.527 50.000 0.00 0.00 0.00 4.30
142 143 3.753797 GACTTCATGTCTTCCCACTTTCC 59.246 47.826 0.00 0.00 42.21 3.13
143 144 3.433615 CGACTTCATGTCTTCCCACTTTC 59.566 47.826 0.00 0.00 43.25 2.62
144 145 3.071023 TCGACTTCATGTCTTCCCACTTT 59.929 43.478 0.00 0.00 43.25 2.66
145 146 2.632996 TCGACTTCATGTCTTCCCACTT 59.367 45.455 0.00 0.00 43.25 3.16
146 147 2.028930 GTCGACTTCATGTCTTCCCACT 60.029 50.000 8.70 0.00 43.25 4.00
147 148 2.338500 GTCGACTTCATGTCTTCCCAC 58.662 52.381 8.70 0.00 43.25 4.61
148 149 1.067846 CGTCGACTTCATGTCTTCCCA 60.068 52.381 14.70 0.00 43.25 4.37
149 150 1.201647 TCGTCGACTTCATGTCTTCCC 59.798 52.381 14.70 0.00 43.25 3.97
150 151 2.631418 TCGTCGACTTCATGTCTTCC 57.369 50.000 14.70 0.00 43.25 3.46
151 152 3.241804 GCAATCGTCGACTTCATGTCTTC 60.242 47.826 14.70 0.00 43.25 2.87
152 153 2.668457 GCAATCGTCGACTTCATGTCTT 59.332 45.455 14.70 0.00 43.25 3.01
153 154 2.263077 GCAATCGTCGACTTCATGTCT 58.737 47.619 14.70 0.00 43.25 3.41
154 155 1.007011 CGCAATCGTCGACTTCATGTC 60.007 52.381 14.70 3.68 42.06 3.06
155 156 0.992072 CGCAATCGTCGACTTCATGT 59.008 50.000 14.70 0.00 0.00 3.21
156 157 0.298707 CCGCAATCGTCGACTTCATG 59.701 55.000 14.70 8.38 0.00 3.07
157 158 0.108804 ACCGCAATCGTCGACTTCAT 60.109 50.000 14.70 0.00 0.00 2.57
158 159 0.319211 AACCGCAATCGTCGACTTCA 60.319 50.000 14.70 0.00 0.00 3.02
159 160 0.093026 CAACCGCAATCGTCGACTTC 59.907 55.000 14.70 0.00 0.00 3.01
160 161 0.319211 TCAACCGCAATCGTCGACTT 60.319 50.000 14.70 0.00 0.00 3.01
161 162 0.108804 ATCAACCGCAATCGTCGACT 60.109 50.000 14.70 0.00 0.00 4.18
162 163 0.297820 GATCAACCGCAATCGTCGAC 59.702 55.000 5.18 5.18 0.00 4.20
163 164 0.804544 GGATCAACCGCAATCGTCGA 60.805 55.000 0.00 0.00 0.00 4.20
164 165 1.636340 GGATCAACCGCAATCGTCG 59.364 57.895 0.00 0.00 0.00 5.12
174 175 1.591863 GCTAGCCGTCGGATCAACC 60.592 63.158 17.49 0.00 0.00 3.77
175 176 0.872021 CTGCTAGCCGTCGGATCAAC 60.872 60.000 17.49 2.13 0.00 3.18
176 177 1.437573 CTGCTAGCCGTCGGATCAA 59.562 57.895 17.49 0.00 0.00 2.57
177 178 3.120105 CTGCTAGCCGTCGGATCA 58.880 61.111 17.49 2.68 0.00 2.92
178 179 2.355244 GCTGCTAGCCGTCGGATC 60.355 66.667 17.49 0.00 34.48 3.36
187 188 0.462759 AAATCAGTCGGGCTGCTAGC 60.463 55.000 8.10 8.10 44.66 3.42
188 189 1.134699 TGAAATCAGTCGGGCTGCTAG 60.135 52.381 4.34 0.00 44.66 3.42
189 190 0.901827 TGAAATCAGTCGGGCTGCTA 59.098 50.000 4.34 0.00 44.66 3.49
190 191 0.392193 CTGAAATCAGTCGGGCTGCT 60.392 55.000 4.34 0.00 44.66 4.24
191 192 1.986575 GCTGAAATCAGTCGGGCTGC 61.987 60.000 4.34 0.00 45.45 5.25
192 193 0.674581 TGCTGAAATCAGTCGGGCTG 60.675 55.000 11.77 2.46 45.45 4.85
193 194 0.674895 GTGCTGAAATCAGTCGGGCT 60.675 55.000 11.77 0.00 45.45 5.19
194 195 1.796796 GTGCTGAAATCAGTCGGGC 59.203 57.895 11.77 0.00 45.45 6.13
195 196 2.081526 CGTGCTGAAATCAGTCGGG 58.918 57.895 11.77 0.00 45.45 5.14
196 197 2.081526 CCGTGCTGAAATCAGTCGG 58.918 57.895 23.21 23.21 46.77 4.79
208 209 6.613755 AATAATTAAATCTAACGCCGTGCT 57.386 33.333 0.00 0.00 0.00 4.40
209 210 7.673810 AAAATAATTAAATCTAACGCCGTGC 57.326 32.000 0.00 0.00 0.00 5.34
231 232 5.917447 GCAGAAAGCAAAAACAAACCAAAAA 59.083 32.000 0.00 0.00 44.79 1.94
232 233 5.456265 GCAGAAAGCAAAAACAAACCAAAA 58.544 33.333 0.00 0.00 44.79 2.44
233 234 5.040715 GCAGAAAGCAAAAACAAACCAAA 57.959 34.783 0.00 0.00 44.79 3.28
252 253 1.205417 GTTCATTGGGTTCCATGGCAG 59.795 52.381 6.96 0.00 31.53 4.85
255 256 3.514706 TCATTGTTCATTGGGTTCCATGG 59.485 43.478 4.97 4.97 31.53 3.66
263 264 8.874744 ATATCTAGGAATCATTGTTCATTGGG 57.125 34.615 0.00 0.00 0.00 4.12
271 272 8.800332 GCCATTGAAATATCTAGGAATCATTGT 58.200 33.333 0.00 0.00 0.00 2.71
272 273 8.799367 TGCCATTGAAATATCTAGGAATCATTG 58.201 33.333 0.00 0.00 0.00 2.82
273 274 8.945195 TGCCATTGAAATATCTAGGAATCATT 57.055 30.769 0.00 0.00 0.00 2.57
274 275 8.945195 TTGCCATTGAAATATCTAGGAATCAT 57.055 30.769 0.00 0.00 0.00 2.45
275 276 7.449395 CCTTGCCATTGAAATATCTAGGAATCA 59.551 37.037 0.00 0.00 0.00 2.57
276 277 7.667219 TCCTTGCCATTGAAATATCTAGGAATC 59.333 37.037 0.00 0.00 0.00 2.52
277 278 7.529555 TCCTTGCCATTGAAATATCTAGGAAT 58.470 34.615 0.00 0.00 0.00 3.01
278 279 6.910191 TCCTTGCCATTGAAATATCTAGGAA 58.090 36.000 0.00 0.00 0.00 3.36
279 280 6.514012 TCCTTGCCATTGAAATATCTAGGA 57.486 37.500 0.00 0.00 0.00 2.94
280 281 7.587037 TTTCCTTGCCATTGAAATATCTAGG 57.413 36.000 0.00 0.00 0.00 3.02
281 282 8.853126 TGATTTCCTTGCCATTGAAATATCTAG 58.147 33.333 2.93 0.00 38.47 2.43
282 283 8.765488 TGATTTCCTTGCCATTGAAATATCTA 57.235 30.769 2.93 0.00 38.47 1.98
283 284 7.343833 ACTGATTTCCTTGCCATTGAAATATCT 59.656 33.333 2.93 0.00 38.47 1.98
284 285 7.437267 CACTGATTTCCTTGCCATTGAAATATC 59.563 37.037 2.93 0.00 38.47 1.63
289 290 3.258872 CCACTGATTTCCTTGCCATTGAA 59.741 43.478 0.00 0.00 0.00 2.69
300 301 1.474077 GCCATCACACCACTGATTTCC 59.526 52.381 0.00 0.00 0.00 3.13
323 324 1.376295 AGCATCGTCAGCATGTGCA 60.376 52.632 7.83 0.00 45.16 4.57
336 337 0.814812 GAGAAGAGGGCAGCAGCATC 60.815 60.000 2.65 0.07 44.61 3.91
343 344 2.037511 GGATCTCATGAGAAGAGGGCAG 59.962 54.545 28.40 0.00 41.36 4.85
344 345 2.045524 GGATCTCATGAGAAGAGGGCA 58.954 52.381 28.40 4.17 41.36 5.36
345 346 2.045524 TGGATCTCATGAGAAGAGGGC 58.954 52.381 28.40 13.30 41.36 5.19
351 352 4.436332 CACGTGAATGGATCTCATGAGAA 58.564 43.478 28.40 13.55 41.36 2.87
377 378 6.056236 TGCTGTTTTGTACTGGTATGTAACA 58.944 36.000 0.00 0.00 0.00 2.41
425 428 5.242838 TGGGTTTTCTAAATTGTACTGCTGG 59.757 40.000 0.00 0.00 0.00 4.85
426 429 6.325919 TGGGTTTTCTAAATTGTACTGCTG 57.674 37.500 0.00 0.00 0.00 4.41
428 431 9.699703 TTAATTGGGTTTTCTAAATTGTACTGC 57.300 29.630 0.00 0.00 0.00 4.40
569 578 4.489771 GTGATGGGGCCAGACGGG 62.490 72.222 4.39 0.00 40.85 5.28
570 579 2.947938 GATGTGATGGGGCCAGACGG 62.948 65.000 4.39 0.00 0.00 4.79
571 580 1.524621 GATGTGATGGGGCCAGACG 60.525 63.158 4.39 0.00 0.00 4.18
572 581 0.749454 GTGATGTGATGGGGCCAGAC 60.749 60.000 4.39 0.00 0.00 3.51
573 582 1.609239 GTGATGTGATGGGGCCAGA 59.391 57.895 4.39 0.00 0.00 3.86
574 583 1.454479 GGTGATGTGATGGGGCCAG 60.454 63.158 4.39 0.00 0.00 4.85
575 584 2.214122 CTGGTGATGTGATGGGGCCA 62.214 60.000 4.39 0.00 0.00 5.36
576 585 1.454479 CTGGTGATGTGATGGGGCC 60.454 63.158 0.00 0.00 0.00 5.80
577 586 0.465097 CTCTGGTGATGTGATGGGGC 60.465 60.000 0.00 0.00 0.00 5.80
594 603 2.125633 GGGTTTCGTCTCGGGCTC 60.126 66.667 0.00 0.00 0.00 4.70
615 624 1.583986 CGGCCTGGATCGATCTCTC 59.416 63.158 23.96 9.10 0.00 3.20
696 718 0.721718 ACAGCTACGAAATCAAGCGC 59.278 50.000 0.00 0.00 41.19 5.92
714 736 1.480954 TGAGCCTACGGATCCAAGAAC 59.519 52.381 13.41 4.54 37.30 3.01
751 786 3.176552 ACAATCGAGCAGGAAGATGAG 57.823 47.619 0.00 0.00 0.00 2.90
778 816 4.941657 TCAGATTCAGATTCACGAGGATG 58.058 43.478 0.00 0.00 0.00 3.51
942 988 1.151668 CTTTTCTGGCTGACTGACGG 58.848 55.000 0.00 0.00 0.00 4.79
964 1010 1.155424 CGCCGCTAATTAAAGCCGGA 61.155 55.000 5.05 0.00 39.43 5.14
1206 1261 2.658707 GAGCACGTTGTGGAGCGTC 61.659 63.158 0.00 0.00 39.48 5.19
1518 1573 2.430248 TCTCGTAGTACTGCATGGGA 57.570 50.000 11.70 0.00 0.00 4.37
1767 1822 2.048127 AAGCACCGGAGCGACTTC 60.048 61.111 18.47 0.00 40.15 3.01
1960 2015 1.146485 CAGCAGCCAGGATCTCCAG 59.854 63.158 0.00 0.00 38.89 3.86
2007 2062 2.864378 CTTCTGCGAGCATGCCTCCA 62.864 60.000 15.66 7.82 37.27 3.86
2103 2158 2.662857 ATCACGATGCCGATGCCG 60.663 61.111 0.00 0.00 39.50 5.69
2226 2281 1.222113 GCTGTAACCCCTCAGGCTC 59.778 63.158 0.00 0.00 40.58 4.70
2650 2710 8.725148 AGACATTTCACTTCATAATCAGACAAC 58.275 33.333 0.00 0.00 0.00 3.32
2691 2752 9.665719 TTTAGATGCTACTCAAATGTATCACAA 57.334 29.630 0.00 0.00 0.00 3.33
2723 2784 9.726232 CACCATGATTACATTGAGTGATTTAAG 57.274 33.333 0.00 0.00 34.30 1.85
2740 2801 2.104967 CTGGACATTGCCACCATGATT 58.895 47.619 0.00 0.00 33.52 2.57
2749 2810 1.538047 TCTGCTTTCTGGACATTGCC 58.462 50.000 0.00 0.00 0.00 4.52
2778 2839 6.378564 TCACCCTCTCTCAAGAAAGTATACAG 59.621 42.308 5.50 0.00 0.00 2.74
2816 2877 9.774742 ATTACTTCGACTTCAATTTGATAAAGC 57.225 29.630 0.00 0.00 0.00 3.51
2896 2967 6.240321 CCAGATCTCTCCAGGAACCTACTATA 60.240 46.154 0.00 0.00 0.00 1.31
2903 2974 2.038659 CTCCAGATCTCTCCAGGAACC 58.961 57.143 0.00 0.00 0.00 3.62
2960 3039 5.505780 CCCTATGTGTGGTTCTTTATTGGA 58.494 41.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.