Multiple sequence alignment - TraesCS1B01G246900

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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 TraesCS1B01G246900 chr1B 100.000 4682 0 0 1 4682 437188283 437183602 0.000000e+00 8647.0
1 TraesCS1B01G246900 chr1A 95.827 4098 127 16 1 4068 420064204 420068287 0.000000e+00 6580.0
2 TraesCS1B01G246900 chr1A 85.545 505 57 4 4180 4682 420068402 420068892 8.980000e-142 514.0
3 TraesCS1B01G246900 chr1A 76.440 191 30 13 4180 4362 209935265 209935082 6.450000e-14 89.8
4 TraesCS1B01G246900 chr1D 95.650 4115 126 22 1 4076 324703220 324699120 0.000000e+00 6558.0
5 TraesCS1B01G246900 chr1D 86.364 506 52 6 4180 4682 324699016 324698525 1.920000e-148 536.0
6 TraesCS1B01G246900 chr2B 75.899 473 85 19 4180 4641 720886896 720887350 1.020000e-51 215.0
7 TraesCS1B01G246900 chr4D 78.738 301 43 14 4212 4509 94508628 94508910 1.030000e-41 182.0
8 TraesCS1B01G246900 chr6A 77.604 192 29 12 4180 4362 294024805 294024619 2.300000e-18 104.0
9 TraesCS1B01G246900 chr7A 77.949 195 21 19 4180 4362 249442393 249442577 8.290000e-18 102.0
10 TraesCS1B01G246900 chr6D 77.551 196 20 21 4180 4362 254940539 254940723 3.860000e-16 97.1
11 TraesCS1B01G246900 chr5A 77.841 176 24 13 4180 4345 221717011 221716841 1.390000e-15 95.3
12 TraesCS1B01G246900 chr4A 76.562 192 31 12 4180 4362 275404433 275404619 4.990000e-15 93.5
13 TraesCS1B01G246900 chr4A 76.571 175 25 13 4180 4345 207139316 207139149 1.080000e-11 82.4


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 TraesCS1B01G246900 chr1B 437183602 437188283 4681 True 8647 8647 100.000 1 4682 1 chr1B.!!$R1 4681
1 TraesCS1B01G246900 chr1A 420064204 420068892 4688 False 3547 6580 90.686 1 4682 2 chr1A.!!$F1 4681
2 TraesCS1B01G246900 chr1D 324698525 324703220 4695 True 3547 6558 91.007 1 4682 2 chr1D.!!$R1 4681

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
839 854 0.108233 CCCACCGATTTGGCCATTTG 60.108 55.000 6.09 0.71 43.94 2.32 F
1203 1232 0.323999 TGGATGGCAATCTGCTGCTT 60.324 50.000 0.00 0.00 44.28 3.91 F
1488 1518 0.593128 CACCAAGGCTGGAGTTTTCG 59.407 55.000 9.53 0.00 46.92 3.46 F
2458 2496 1.408266 GGGTCATCGCATGGGTTTAGT 60.408 52.381 9.86 0.00 0.00 2.24 F
2490 2528 1.413077 CCAGGATCCCGAGTAAGTTCC 59.587 57.143 8.55 0.00 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1752 0.740737 GGCACAATTTAGGCGATGCT 59.259 50.000 0.00 0.0 33.57 3.79 R
2742 2780 0.749818 TTCAGAAAACTGCGCCACCA 60.750 50.000 4.18 0.0 0.00 4.17 R
2946 2984 2.517959 AGGCAGTCATTTTGCTTGCTA 58.482 42.857 0.00 0.0 41.27 3.49 R
3645 3702 0.179006 GGCTCCCAAGGGTGATGATC 60.179 60.000 11.25 0.0 36.47 2.92 R
4105 4162 0.251341 AAGATCACAGGCAACCCCAC 60.251 55.000 0.00 0.0 35.39 4.61 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
25 27 4.820744 CCGGTCCATGGGCAAGGG 62.821 72.222 20.13 12.28 0.00 3.95
54 56 2.044352 GACCGGGTTTCCCATGGG 60.044 66.667 26.30 26.30 45.83 4.00
67 69 1.338107 CCATGGGCAGGTATACTCGA 58.662 55.000 2.85 0.00 0.00 4.04
80 82 7.439655 GCAGGTATACTCGATGAAAATCTTCTT 59.560 37.037 2.25 0.00 32.33 2.52
224 228 0.890683 CTTTTTGCTCCCGCTCCATT 59.109 50.000 0.00 0.00 36.97 3.16
264 268 1.806568 CTCGCTCTCCGCTTCTTCT 59.193 57.895 0.00 0.00 36.73 2.85
268 272 1.939769 GCTCTCCGCTTCTTCTCGGT 61.940 60.000 0.47 0.00 45.44 4.69
313 317 1.305213 GGCACCACCCATGTCCATT 60.305 57.895 0.00 0.00 0.00 3.16
372 387 0.798776 AGAAAGATTCCAACGCAGCG 59.201 50.000 14.82 14.82 0.00 5.18
635 650 1.005630 GCAGCTAGCACCCTATCCG 60.006 63.158 18.83 0.00 44.79 4.18
833 848 0.395173 ATACCACCCACCGATTTGGC 60.395 55.000 0.00 0.00 43.94 4.52
834 849 2.487274 TACCACCCACCGATTTGGCC 62.487 60.000 0.00 0.00 43.94 5.36
835 850 2.282816 CACCCACCGATTTGGCCA 60.283 61.111 0.00 0.00 43.94 5.36
836 851 1.682005 CACCCACCGATTTGGCCAT 60.682 57.895 6.09 0.00 43.94 4.40
837 852 1.078347 ACCCACCGATTTGGCCATT 59.922 52.632 6.09 0.00 43.94 3.16
838 853 0.544120 ACCCACCGATTTGGCCATTT 60.544 50.000 6.09 0.00 43.94 2.32
839 854 0.108233 CCCACCGATTTGGCCATTTG 60.108 55.000 6.09 0.71 43.94 2.32
840 855 0.108233 CCACCGATTTGGCCATTTGG 60.108 55.000 6.09 13.64 43.94 3.28
859 874 0.337428 GGGGTAGGTGAGGACCAGTA 59.663 60.000 0.00 0.00 45.98 2.74
862 877 3.113043 GGGTAGGTGAGGACCAGTATTT 58.887 50.000 0.00 0.00 45.98 1.40
865 880 1.066143 AGGTGAGGACCAGTATTTGCG 60.066 52.381 0.00 0.00 45.98 4.85
868 883 1.066430 TGAGGACCAGTATTTGCGTCC 60.066 52.381 0.00 0.00 42.65 4.79
879 894 3.757745 ATTTGCGTCCGGTTTAGATTG 57.242 42.857 0.00 0.00 0.00 2.67
885 900 1.134189 GTCCGGTTTAGATTGGGGAGG 60.134 57.143 0.00 0.00 0.00 4.30
906 921 1.973138 CTGCTTCGCTTGACCATTTG 58.027 50.000 0.00 0.00 0.00 2.32
916 932 3.253188 GCTTGACCATTTGTAAGTGCAGA 59.747 43.478 0.00 0.00 0.00 4.26
943 959 1.605712 GCTGCTTACTCCGACACAAGT 60.606 52.381 0.00 0.00 0.00 3.16
1167 1184 1.398390 CTAGGTGAATTGCGGTTGCTC 59.602 52.381 0.00 0.00 43.34 4.26
1170 1187 1.666888 GGTGAATTGCGGTTGCTCTTG 60.667 52.381 0.00 0.00 43.34 3.02
1171 1188 1.266718 GTGAATTGCGGTTGCTCTTGA 59.733 47.619 0.00 0.00 43.34 3.02
1203 1232 0.323999 TGGATGGCAATCTGCTGCTT 60.324 50.000 0.00 0.00 44.28 3.91
1443 1473 4.441792 GGTTGCTTTTTGATGGTTCAGTT 58.558 39.130 0.00 0.00 32.27 3.16
1488 1518 0.593128 CACCAAGGCTGGAGTTTTCG 59.407 55.000 9.53 0.00 46.92 3.46
2233 2270 7.916450 CAGCTAAAGGTAGTACAACTATGAGAC 59.084 40.741 2.06 0.00 32.65 3.36
2458 2496 1.408266 GGGTCATCGCATGGGTTTAGT 60.408 52.381 9.86 0.00 0.00 2.24
2490 2528 1.413077 CCAGGATCCCGAGTAAGTTCC 59.587 57.143 8.55 0.00 0.00 3.62
2514 2552 8.000709 TCCAGTACCGTATCCTTTTATCTTCTA 58.999 37.037 0.00 0.00 0.00 2.10
2590 2628 3.648339 ATGTTCGAAAAGCTTGTGCAT 57.352 38.095 0.00 0.00 42.74 3.96
2596 2634 5.369685 TCGAAAAGCTTGTGCATGAAATA 57.630 34.783 0.00 0.00 42.74 1.40
2601 2639 7.113965 CGAAAAGCTTGTGCATGAAATATATCC 59.886 37.037 0.00 0.00 42.74 2.59
2652 2690 7.798516 GTCATCTAGTTGTATTGTTGTTGTGTG 59.201 37.037 0.83 0.00 0.00 3.82
2673 2711 5.303845 TGTGTTTCAATTGTGGGATGATCAA 59.696 36.000 5.13 0.00 0.00 2.57
2742 2780 5.506317 GCATGTTTGTTCTTAGAGCACACTT 60.506 40.000 14.49 7.25 27.83 3.16
2837 2875 1.505353 GCTGCTAGCTTGCAACCTG 59.495 57.895 22.83 12.69 42.83 4.00
2922 2960 6.423604 GCCTAGAGAGAATGCTATGAACTTTC 59.576 42.308 0.00 0.00 0.00 2.62
2946 2984 4.102367 ACTGCCTCTCTGAAAGAAGTCTTT 59.898 41.667 6.00 6.00 46.34 2.52
3109 3155 2.864946 TGTGTGCACATTGACAAAATGC 59.135 40.909 24.69 16.34 36.21 3.56
3125 3171 6.758254 ACAAAATGCTAACTATGTTGCCTTT 58.242 32.000 0.00 0.00 0.00 3.11
3126 3172 7.216494 ACAAAATGCTAACTATGTTGCCTTTT 58.784 30.769 0.00 0.00 35.05 2.27
3151 3198 3.758554 ACAAATGGAGCGTAGATTTTGCT 59.241 39.130 0.00 0.00 42.73 3.91
3926 3983 8.377681 TCGACGAATTGTATGTAATTTTCAGAC 58.622 33.333 0.00 0.00 30.78 3.51
3938 3995 3.414549 TTTTCAGACCGTTTGCTGTTC 57.585 42.857 0.00 0.00 33.90 3.18
3944 4001 0.593128 ACCGTTTGCTGTTCTGATGC 59.407 50.000 0.00 0.00 0.00 3.91
4010 4067 7.685849 AGCTGGTACCATATTAACTTCCTAA 57.314 36.000 16.75 0.00 0.00 2.69
4053 4110 2.165030 GCCAGCAGTTGCATTACTCATT 59.835 45.455 6.90 0.00 45.16 2.57
4068 4125 7.219535 GCATTACTCATTCAATGTAGCACTTTG 59.780 37.037 0.00 7.92 35.12 2.77
4069 4126 7.744087 TTACTCATTCAATGTAGCACTTTGT 57.256 32.000 0.00 0.00 35.51 2.83
4070 4127 8.840833 TTACTCATTCAATGTAGCACTTTGTA 57.159 30.769 0.00 6.06 35.51 2.41
4072 4129 8.340618 ACTCATTCAATGTAGCACTTTGTAAT 57.659 30.769 0.00 8.90 35.51 1.89
4074 4131 9.630098 CTCATTCAATGTAGCACTTTGTAATTT 57.370 29.630 0.00 0.00 35.51 1.82
4075 4132 9.409312 TCATTCAATGTAGCACTTTGTAATTTG 57.591 29.630 0.00 0.00 35.51 2.32
4076 4133 7.636259 TTCAATGTAGCACTTTGTAATTTGC 57.364 32.000 11.69 0.00 35.51 3.68
4077 4134 6.743110 TCAATGTAGCACTTTGTAATTTGCA 58.257 32.000 11.69 0.00 37.44 4.08
4078 4135 6.640499 TCAATGTAGCACTTTGTAATTTGCAC 59.360 34.615 11.69 0.00 37.44 4.57
4079 4136 4.865776 TGTAGCACTTTGTAATTTGCACC 58.134 39.130 0.78 0.00 37.44 5.01
4080 4137 4.339530 TGTAGCACTTTGTAATTTGCACCA 59.660 37.500 0.78 0.00 37.44 4.17
4082 4139 4.119136 AGCACTTTGTAATTTGCACCAAC 58.881 39.130 0.78 0.00 37.44 3.77
4083 4140 4.119136 GCACTTTGTAATTTGCACCAACT 58.881 39.130 0.00 0.00 34.97 3.16
4084 4141 4.025813 GCACTTTGTAATTTGCACCAACTG 60.026 41.667 0.00 0.00 34.97 3.16
4085 4142 5.108517 CACTTTGTAATTTGCACCAACTGT 58.891 37.500 0.00 0.00 0.00 3.55
4086 4143 6.269315 CACTTTGTAATTTGCACCAACTGTA 58.731 36.000 0.00 0.00 0.00 2.74
4087 4144 6.754209 CACTTTGTAATTTGCACCAACTGTAA 59.246 34.615 0.00 0.00 0.00 2.41
4088 4145 7.437862 CACTTTGTAATTTGCACCAACTGTAAT 59.562 33.333 0.00 0.00 0.00 1.89
4089 4146 7.984617 ACTTTGTAATTTGCACCAACTGTAATT 59.015 29.630 0.00 0.00 0.00 1.40
4090 4147 7.706281 TTGTAATTTGCACCAACTGTAATTG 57.294 32.000 0.00 0.00 0.00 2.32
4103 4160 8.801882 CCAACTGTAATTGGGAGTCTTATTTA 57.198 34.615 0.00 0.00 44.74 1.40
4107 4164 9.396022 ACTGTAATTGGGAGTCTTATTTATGTG 57.604 33.333 0.00 0.00 0.00 3.21
4108 4165 8.746052 TGTAATTGGGAGTCTTATTTATGTGG 57.254 34.615 0.00 0.00 0.00 4.17
4109 4166 7.777910 TGTAATTGGGAGTCTTATTTATGTGGG 59.222 37.037 0.00 0.00 0.00 4.61
4111 4168 4.116113 TGGGAGTCTTATTTATGTGGGGT 58.884 43.478 0.00 0.00 0.00 4.95
4112 4169 4.542525 TGGGAGTCTTATTTATGTGGGGTT 59.457 41.667 0.00 0.00 0.00 4.11
4113 4170 4.887655 GGGAGTCTTATTTATGTGGGGTTG 59.112 45.833 0.00 0.00 0.00 3.77
4116 4173 4.017499 AGTCTTATTTATGTGGGGTTGCCT 60.017 41.667 0.00 0.00 0.00 4.75
4117 4174 4.097892 GTCTTATTTATGTGGGGTTGCCTG 59.902 45.833 0.00 0.00 0.00 4.85
4118 4175 2.621556 ATTTATGTGGGGTTGCCTGT 57.378 45.000 0.00 0.00 0.00 4.00
4119 4176 1.626686 TTTATGTGGGGTTGCCTGTG 58.373 50.000 0.00 0.00 0.00 3.66
4120 4177 0.774276 TTATGTGGGGTTGCCTGTGA 59.226 50.000 0.00 0.00 0.00 3.58
4123 4180 1.380302 GTGGGGTTGCCTGTGATCT 59.620 57.895 0.00 0.00 0.00 2.75
4124 4181 0.251341 GTGGGGTTGCCTGTGATCTT 60.251 55.000 0.00 0.00 0.00 2.40
4125 4182 0.038166 TGGGGTTGCCTGTGATCTTC 59.962 55.000 0.00 0.00 0.00 2.87
4126 4183 0.329596 GGGGTTGCCTGTGATCTTCT 59.670 55.000 0.00 0.00 0.00 2.85
4128 4185 2.420687 GGGGTTGCCTGTGATCTTCTAG 60.421 54.545 0.00 0.00 0.00 2.43
4129 4186 2.420687 GGGTTGCCTGTGATCTTCTAGG 60.421 54.545 0.00 0.00 0.00 3.02
4130 4187 2.501723 GGTTGCCTGTGATCTTCTAGGA 59.498 50.000 8.62 0.00 31.91 2.94
4131 4188 3.135530 GGTTGCCTGTGATCTTCTAGGAT 59.864 47.826 8.62 0.00 31.91 3.24
4132 4189 4.384647 GGTTGCCTGTGATCTTCTAGGATT 60.385 45.833 8.62 0.00 31.91 3.01
4135 4192 4.471025 TGCCTGTGATCTTCTAGGATTTCA 59.529 41.667 8.62 0.00 31.91 2.69
4137 4194 5.363939 CCTGTGATCTTCTAGGATTTCACC 58.636 45.833 9.78 0.00 31.91 4.02
4138 4195 5.359194 TGTGATCTTCTAGGATTTCACCC 57.641 43.478 9.78 0.00 0.00 4.61
4139 4196 4.164221 TGTGATCTTCTAGGATTTCACCCC 59.836 45.833 9.78 0.00 0.00 4.95
4140 4197 4.164221 GTGATCTTCTAGGATTTCACCCCA 59.836 45.833 0.00 0.00 0.00 4.96
4141 4198 4.977739 TGATCTTCTAGGATTTCACCCCAT 59.022 41.667 0.00 0.00 0.00 4.00
4142 4199 4.778213 TCTTCTAGGATTTCACCCCATG 57.222 45.455 0.00 0.00 0.00 3.66
4145 4202 2.777692 TCTAGGATTTCACCCCATGTCC 59.222 50.000 0.00 0.00 0.00 4.02
4146 4203 1.381867 AGGATTTCACCCCATGTCCA 58.618 50.000 0.00 0.00 0.00 4.02
4147 4204 1.285962 AGGATTTCACCCCATGTCCAG 59.714 52.381 0.00 0.00 0.00 3.86
4148 4205 1.005924 GGATTTCACCCCATGTCCAGT 59.994 52.381 0.00 0.00 0.00 4.00
4149 4206 2.241176 GGATTTCACCCCATGTCCAGTA 59.759 50.000 0.00 0.00 0.00 2.74
4150 4207 3.117512 GGATTTCACCCCATGTCCAGTAT 60.118 47.826 0.00 0.00 0.00 2.12
4151 4208 3.364460 TTTCACCCCATGTCCAGTATG 57.636 47.619 0.00 0.00 0.00 2.39
4152 4209 1.965414 TCACCCCATGTCCAGTATGT 58.035 50.000 0.00 0.00 0.00 2.29
4172 4229 1.492993 GGAGTTGTCCAGCCCCTCTT 61.493 60.000 0.00 0.00 43.31 2.85
4173 4230 1.276622 GAGTTGTCCAGCCCCTCTTA 58.723 55.000 0.00 0.00 0.00 2.10
4174 4231 1.840635 GAGTTGTCCAGCCCCTCTTAT 59.159 52.381 0.00 0.00 0.00 1.73
4176 4233 2.025887 AGTTGTCCAGCCCCTCTTATTG 60.026 50.000 0.00 0.00 0.00 1.90
4177 4234 1.668826 TGTCCAGCCCCTCTTATTGT 58.331 50.000 0.00 0.00 0.00 2.71
4178 4235 1.281867 TGTCCAGCCCCTCTTATTGTG 59.718 52.381 0.00 0.00 0.00 3.33
4184 4244 2.171003 GCCCCTCTTATTGTGTTGCTT 58.829 47.619 0.00 0.00 0.00 3.91
4197 4257 3.010138 TGTGTTGCTTAGCCCCTCTTATT 59.990 43.478 0.29 0.00 0.00 1.40
4199 4259 2.348411 TGCTTAGCCCCTCTTATTGC 57.652 50.000 0.29 0.00 0.00 3.56
4300 4361 6.821665 TGTTAAACTTGACTATATGCCTGACC 59.178 38.462 0.00 0.00 0.00 4.02
4337 4398 1.455383 GCCTATGCCCCGGTGATTTG 61.455 60.000 0.00 0.00 0.00 2.32
4345 4406 1.003812 CCCCGGTGATTTGTTCCACTA 59.996 52.381 0.00 0.00 33.99 2.74
4363 4425 5.073965 TCCACTATGGTCAACCCTAGTTTTT 59.926 40.000 12.74 0.00 42.37 1.94
4408 4470 1.154205 ATGAGCGCATCTTACCGTGC 61.154 55.000 11.47 0.00 38.93 5.34
4414 4476 1.079405 CATCTTACCGTGCGTGGGT 60.079 57.895 0.00 0.00 41.62 4.51
4422 4484 1.065998 ACCGTGCGTGGGTTATTATGT 60.066 47.619 0.00 0.00 32.70 2.29
4423 4485 2.011222 CCGTGCGTGGGTTATTATGTT 58.989 47.619 0.00 0.00 0.00 2.71
4424 4486 2.420722 CCGTGCGTGGGTTATTATGTTT 59.579 45.455 0.00 0.00 0.00 2.83
4425 4487 3.119779 CCGTGCGTGGGTTATTATGTTTT 60.120 43.478 0.00 0.00 0.00 2.43
4426 4488 4.092816 CGTGCGTGGGTTATTATGTTTTC 58.907 43.478 0.00 0.00 0.00 2.29
4427 4489 4.142773 CGTGCGTGGGTTATTATGTTTTCT 60.143 41.667 0.00 0.00 0.00 2.52
4428 4490 5.618195 CGTGCGTGGGTTATTATGTTTTCTT 60.618 40.000 0.00 0.00 0.00 2.52
4429 4491 6.153756 GTGCGTGGGTTATTATGTTTTCTTT 58.846 36.000 0.00 0.00 0.00 2.52
4430 4492 6.643360 GTGCGTGGGTTATTATGTTTTCTTTT 59.357 34.615 0.00 0.00 0.00 2.27
4431 4493 6.864165 TGCGTGGGTTATTATGTTTTCTTTTC 59.136 34.615 0.00 0.00 0.00 2.29
4438 4500 7.985184 GGTTATTATGTTTTCTTTTCATCCCCC 59.015 37.037 0.00 0.00 0.00 5.40
4468 4530 6.698380 TCCTTTATCTAGCGTTGAACTCTTT 58.302 36.000 0.00 0.00 0.00 2.52
4471 4533 6.946229 TTATCTAGCGTTGAACTCTTTCAC 57.054 37.500 0.00 0.00 41.64 3.18
4484 4546 1.962807 TCTTTCACAAGGCCCAACATG 59.037 47.619 0.00 0.00 0.00 3.21
4524 4587 3.440173 ACATAAAACTTGCATGGAGGTCG 59.560 43.478 1.62 0.00 0.00 4.79
4531 4594 4.181010 CATGGAGGTCGCCCCCTG 62.181 72.222 0.00 0.00 34.03 4.45
4550 4613 7.016563 GCCCCCTGGAGATATTTTCAAAATAAT 59.983 37.037 6.67 0.00 0.00 1.28
4559 4622 9.972106 AGATATTTTCAAAATAATTTGGGCCAA 57.028 25.926 16.66 16.66 44.88 4.52
4561 4624 9.752228 ATATTTTCAAAATAATTTGGGCCAACT 57.248 25.926 20.79 11.59 44.88 3.16
4572 4635 1.241990 GGGCCAACTCCCGAGAAAAC 61.242 60.000 4.39 0.00 36.38 2.43
4578 4641 0.250166 ACTCCCGAGAAAACCGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
4597 4660 2.591429 CCGCAACAGGCAGTGTGA 60.591 61.111 0.00 0.00 45.17 3.58
4609 4672 1.462238 AGTGTGAGGAGGCACCCTT 60.462 57.895 0.00 0.00 40.05 3.95
4617 4680 1.460699 GAGGCACCCTTGGGAAACT 59.539 57.895 13.39 6.60 31.76 2.66
4620 4683 2.574018 GCACCCTTGGGAAACTGGC 61.574 63.158 13.39 2.63 0.00 4.85
4629 4692 0.681243 GGGAAACTGGCCTTGGCTAG 60.681 60.000 20.95 20.95 0.00 3.42
4648 4711 0.393808 GCCGTAAGCTTTCCCATCCA 60.394 55.000 3.20 0.00 38.99 3.41
4649 4712 1.953311 GCCGTAAGCTTTCCCATCCAA 60.953 52.381 3.20 0.00 38.99 3.53
4652 4715 3.370103 CCGTAAGCTTTCCCATCCAACTA 60.370 47.826 3.20 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 6.926272 AGAAGATTTTCATCGAGTATACCTGC 59.074 38.462 0.00 0.00 35.70 4.85
94 96 1.128692 CTCCAATCGTTTTCACCGAGC 59.871 52.381 0.00 0.00 37.81 5.03
264 268 3.246403 TGCTGATGCATTTCACCGA 57.754 47.368 0.00 0.00 45.31 4.69
313 317 4.878968 TCTCCTACTACATGGACATGGAA 58.121 43.478 15.94 3.82 42.91 3.53
372 387 3.616219 TCTGGTGTAGAGAGAGAAGCTC 58.384 50.000 0.00 0.00 44.29 4.09
635 650 1.765904 GAAGGGGAGGAAGAGGATGAC 59.234 57.143 0.00 0.00 0.00 3.06
833 848 0.258774 CCTCACCTACCCCCAAATGG 59.741 60.000 0.00 0.00 0.00 3.16
834 849 1.064685 GTCCTCACCTACCCCCAAATG 60.065 57.143 0.00 0.00 0.00 2.32
835 850 1.296002 GTCCTCACCTACCCCCAAAT 58.704 55.000 0.00 0.00 0.00 2.32
836 851 0.843343 GGTCCTCACCTACCCCCAAA 60.843 60.000 0.00 0.00 40.00 3.28
837 852 1.229723 GGTCCTCACCTACCCCCAA 60.230 63.158 0.00 0.00 40.00 4.12
838 853 2.453054 GGTCCTCACCTACCCCCA 59.547 66.667 0.00 0.00 40.00 4.96
839 854 1.689582 CTGGTCCTCACCTACCCCC 60.690 68.421 0.00 0.00 44.17 5.40
840 855 0.337428 TACTGGTCCTCACCTACCCC 59.663 60.000 0.00 0.00 44.17 4.95
859 874 2.422127 CCAATCTAAACCGGACGCAAAT 59.578 45.455 9.46 0.00 0.00 2.32
862 877 0.391927 CCCAATCTAAACCGGACGCA 60.392 55.000 9.46 0.00 0.00 5.24
865 880 1.134189 CCTCCCCAATCTAAACCGGAC 60.134 57.143 9.46 0.00 0.00 4.79
868 883 0.465642 GCCCTCCCCAATCTAAACCG 60.466 60.000 0.00 0.00 0.00 4.44
966 983 1.394917 ACATCGAATCAGCAAAGTCGC 59.605 47.619 3.69 0.00 33.58 5.19
1167 1184 1.300971 CCATGGACGGTGCACTCAAG 61.301 60.000 17.98 8.56 0.00 3.02
1170 1187 1.091771 CATCCATGGACGGTGCACTC 61.092 60.000 18.99 7.21 0.00 3.51
1171 1188 1.078214 CATCCATGGACGGTGCACT 60.078 57.895 18.99 0.00 0.00 4.40
1195 1224 2.159234 CGGAGAAAGAAAGAAGCAGCAG 59.841 50.000 0.00 0.00 0.00 4.24
1196 1225 2.146342 CGGAGAAAGAAAGAAGCAGCA 58.854 47.619 0.00 0.00 0.00 4.41
1203 1232 5.068460 TGAAAATTTGCCGGAGAAAGAAAGA 59.932 36.000 5.05 0.00 0.00 2.52
1488 1518 4.272748 GCATCCAAATAGTTTACCTCGTCC 59.727 45.833 0.00 0.00 0.00 4.79
1562 1592 1.041447 AAGCATGGCAGAATGGAGGC 61.041 55.000 0.00 0.00 35.86 4.70
1600 1630 7.628234 ACAGTCAGACATAAAATTCAGGAGAT 58.372 34.615 2.66 0.00 0.00 2.75
1714 1744 3.603158 TTTAGGCGATGCTGTCAACTA 57.397 42.857 0.00 0.00 0.00 2.24
1719 1749 2.792542 GCACAATTTAGGCGATGCTGTC 60.793 50.000 0.00 0.00 0.00 3.51
1722 1752 0.740737 GGCACAATTTAGGCGATGCT 59.259 50.000 0.00 0.00 33.57 3.79
2458 2496 2.667470 GGATCCTGGTAGACACTGCTA 58.333 52.381 3.84 0.00 0.00 3.49
2514 2552 4.993029 TTTGTTGTCTGGTCCGAAAAAT 57.007 36.364 0.00 0.00 0.00 1.82
2521 2559 5.585047 GGTCTACATATTTGTTGTCTGGTCC 59.415 44.000 0.00 0.00 37.28 4.46
2652 2690 6.870769 AGATTGATCATCCCACAATTGAAAC 58.129 36.000 13.59 0.00 34.94 2.78
2742 2780 0.749818 TTCAGAAAACTGCGCCACCA 60.750 50.000 4.18 0.00 0.00 4.17
2922 2960 3.006752 AGACTTCTTTCAGAGAGGCAGTG 59.993 47.826 0.07 0.00 34.98 3.66
2946 2984 2.517959 AGGCAGTCATTTTGCTTGCTA 58.482 42.857 0.00 0.00 41.27 3.49
3028 3074 6.831664 AAGATTCCAGCCTTTCTCCTAATA 57.168 37.500 0.00 0.00 0.00 0.98
3029 3075 5.723860 AAGATTCCAGCCTTTCTCCTAAT 57.276 39.130 0.00 0.00 0.00 1.73
3042 3088 5.474532 TGGAACAGTGAATCAAAGATTCCAG 59.525 40.000 15.01 8.65 39.46 3.86
3125 3171 6.584563 GCAAAATCTACGCTCCATTTGTAAAA 59.415 34.615 0.00 0.00 32.03 1.52
3126 3172 6.072175 AGCAAAATCTACGCTCCATTTGTAAA 60.072 34.615 0.00 0.00 32.03 2.01
3128 3174 4.941263 AGCAAAATCTACGCTCCATTTGTA 59.059 37.500 0.00 0.00 32.03 2.41
3131 3178 5.648092 AGTTAGCAAAATCTACGCTCCATTT 59.352 36.000 0.00 0.00 37.20 2.32
3645 3702 0.179006 GGCTCCCAAGGGTGATGATC 60.179 60.000 11.25 0.00 36.47 2.92
3734 3791 0.471617 ACAACAGCTGCTGGACTCTT 59.528 50.000 31.00 14.69 35.51 2.85
3926 3983 0.877071 AGCATCAGAACAGCAAACGG 59.123 50.000 0.00 0.00 0.00 4.44
3938 3995 3.803021 GCTCTCAGGGATTACAGCATCAG 60.803 52.174 0.00 0.00 0.00 2.90
3944 4001 4.586421 TGATAGTGCTCTCAGGGATTACAG 59.414 45.833 0.00 0.00 0.00 2.74
4010 4067 5.817816 GGCAATTACAGTAGCTGTCAACTAT 59.182 40.000 4.95 0.00 41.21 2.12
4053 4110 6.640499 GTGCAAATTACAAAGTGCTACATTGA 59.360 34.615 9.97 0.00 37.87 2.57
4068 4125 5.637387 CCCAATTACAGTTGGTGCAAATTAC 59.363 40.000 5.09 0.00 45.78 1.89
4069 4126 5.540337 TCCCAATTACAGTTGGTGCAAATTA 59.460 36.000 5.09 0.00 45.78 1.40
4070 4127 4.346418 TCCCAATTACAGTTGGTGCAAATT 59.654 37.500 5.09 0.00 45.78 1.82
4072 4129 3.300388 TCCCAATTACAGTTGGTGCAAA 58.700 40.909 5.09 0.00 45.78 3.68
4074 4131 2.158534 ACTCCCAATTACAGTTGGTGCA 60.159 45.455 5.09 0.00 45.78 4.57
4075 4132 2.488153 GACTCCCAATTACAGTTGGTGC 59.512 50.000 5.09 0.00 45.78 5.01
4076 4133 4.021102 AGACTCCCAATTACAGTTGGTG 57.979 45.455 5.09 0.96 45.78 4.17
4077 4134 4.724279 AAGACTCCCAATTACAGTTGGT 57.276 40.909 5.09 0.00 45.78 3.67
4078 4135 7.703058 AAATAAGACTCCCAATTACAGTTGG 57.297 36.000 0.00 0.00 46.58 3.77
4080 4137 9.975218 ACATAAATAAGACTCCCAATTACAGTT 57.025 29.630 0.00 0.00 0.00 3.16
4082 4139 8.840321 CCACATAAATAAGACTCCCAATTACAG 58.160 37.037 0.00 0.00 0.00 2.74
4083 4140 7.777910 CCCACATAAATAAGACTCCCAATTACA 59.222 37.037 0.00 0.00 0.00 2.41
4084 4141 7.230712 CCCCACATAAATAAGACTCCCAATTAC 59.769 40.741 0.00 0.00 0.00 1.89
4085 4142 7.091720 ACCCCACATAAATAAGACTCCCAATTA 60.092 37.037 0.00 0.00 0.00 1.40
4086 4143 6.136155 CCCCACATAAATAAGACTCCCAATT 58.864 40.000 0.00 0.00 0.00 2.32
4087 4144 5.195756 ACCCCACATAAATAAGACTCCCAAT 59.804 40.000 0.00 0.00 0.00 3.16
4088 4145 4.542525 ACCCCACATAAATAAGACTCCCAA 59.457 41.667 0.00 0.00 0.00 4.12
4089 4146 4.116113 ACCCCACATAAATAAGACTCCCA 58.884 43.478 0.00 0.00 0.00 4.37
4090 4147 4.790718 ACCCCACATAAATAAGACTCCC 57.209 45.455 0.00 0.00 0.00 4.30
4091 4148 4.338400 GCAACCCCACATAAATAAGACTCC 59.662 45.833 0.00 0.00 0.00 3.85
4093 4150 4.017499 AGGCAACCCCACATAAATAAGACT 60.017 41.667 0.00 0.00 35.39 3.24
4095 4152 4.264172 ACAGGCAACCCCACATAAATAAGA 60.264 41.667 0.00 0.00 35.39 2.10
4097 4154 3.766591 CACAGGCAACCCCACATAAATAA 59.233 43.478 0.00 0.00 35.39 1.40
4098 4155 3.010696 TCACAGGCAACCCCACATAAATA 59.989 43.478 0.00 0.00 35.39 1.40
4099 4156 2.178580 CACAGGCAACCCCACATAAAT 58.821 47.619 0.00 0.00 35.39 1.40
4100 4157 1.145945 TCACAGGCAACCCCACATAAA 59.854 47.619 0.00 0.00 35.39 1.40
4103 4160 0.323725 GATCACAGGCAACCCCACAT 60.324 55.000 0.00 0.00 35.39 3.21
4105 4162 0.251341 AAGATCACAGGCAACCCCAC 60.251 55.000 0.00 0.00 35.39 4.61
4107 4164 0.329596 AGAAGATCACAGGCAACCCC 59.670 55.000 0.00 0.00 37.17 4.95
4108 4165 2.420687 CCTAGAAGATCACAGGCAACCC 60.421 54.545 0.00 0.00 37.17 4.11
4109 4166 2.501723 TCCTAGAAGATCACAGGCAACC 59.498 50.000 0.00 0.00 37.17 3.77
4111 4168 5.045651 TGAAATCCTAGAAGATCACAGGCAA 60.046 40.000 0.00 0.00 0.00 4.52
4112 4169 4.471025 TGAAATCCTAGAAGATCACAGGCA 59.529 41.667 0.00 0.00 0.00 4.75
4113 4170 4.813697 GTGAAATCCTAGAAGATCACAGGC 59.186 45.833 11.42 0.00 0.00 4.85
4116 4173 4.164221 GGGGTGAAATCCTAGAAGATCACA 59.836 45.833 15.66 3.87 0.00 3.58
4117 4174 4.164221 TGGGGTGAAATCCTAGAAGATCAC 59.836 45.833 0.00 0.87 0.00 3.06
4118 4175 4.370776 TGGGGTGAAATCCTAGAAGATCA 58.629 43.478 0.00 0.00 0.00 2.92
4119 4176 5.163152 ACATGGGGTGAAATCCTAGAAGATC 60.163 44.000 0.00 0.00 0.00 2.75
4120 4177 4.728860 ACATGGGGTGAAATCCTAGAAGAT 59.271 41.667 0.00 0.00 0.00 2.40
4123 4180 3.202151 GGACATGGGGTGAAATCCTAGAA 59.798 47.826 0.00 0.00 0.00 2.10
4124 4181 2.777692 GGACATGGGGTGAAATCCTAGA 59.222 50.000 0.00 0.00 0.00 2.43
4125 4182 2.509548 TGGACATGGGGTGAAATCCTAG 59.490 50.000 0.00 0.00 0.00 3.02
4126 4183 2.509548 CTGGACATGGGGTGAAATCCTA 59.490 50.000 0.00 0.00 0.00 2.94
4128 4185 1.005924 ACTGGACATGGGGTGAAATCC 59.994 52.381 0.00 0.00 0.00 3.01
4129 4186 2.514458 ACTGGACATGGGGTGAAATC 57.486 50.000 0.00 0.00 0.00 2.17
4130 4187 3.269381 ACATACTGGACATGGGGTGAAAT 59.731 43.478 0.00 0.00 0.00 2.17
4131 4188 2.647299 ACATACTGGACATGGGGTGAAA 59.353 45.455 0.00 0.00 0.00 2.69
4132 4189 2.026356 CACATACTGGACATGGGGTGAA 60.026 50.000 0.00 0.00 0.00 3.18
4135 4192 0.918983 CCACATACTGGACATGGGGT 59.081 55.000 0.00 0.00 43.95 4.95
4137 4194 1.839994 ACTCCACATACTGGACATGGG 59.160 52.381 0.00 0.00 44.99 4.00
4138 4195 3.273434 CAACTCCACATACTGGACATGG 58.727 50.000 0.00 0.00 44.99 3.66
4139 4196 3.935203 GACAACTCCACATACTGGACATG 59.065 47.826 0.00 0.00 44.99 3.21
4140 4197 3.055094 GGACAACTCCACATACTGGACAT 60.055 47.826 0.00 0.00 44.99 3.06
4141 4198 2.301870 GGACAACTCCACATACTGGACA 59.698 50.000 0.00 0.00 44.99 4.02
4142 4199 2.301870 TGGACAACTCCACATACTGGAC 59.698 50.000 0.00 0.00 44.99 4.02
4145 4202 2.350522 GCTGGACAACTCCACATACTG 58.649 52.381 0.00 0.00 42.15 2.74
4146 4203 1.279271 GGCTGGACAACTCCACATACT 59.721 52.381 0.00 0.00 42.15 2.12
4147 4204 1.679032 GGGCTGGACAACTCCACATAC 60.679 57.143 0.00 0.00 42.15 2.39
4148 4205 0.618458 GGGCTGGACAACTCCACATA 59.382 55.000 0.00 0.00 42.15 2.29
4149 4206 1.380302 GGGCTGGACAACTCCACAT 59.620 57.895 0.00 0.00 42.15 3.21
4150 4207 2.829384 GGGGCTGGACAACTCCACA 61.829 63.158 0.00 0.00 42.15 4.17
4151 4208 2.034221 GGGGCTGGACAACTCCAC 59.966 66.667 0.00 0.00 42.15 4.02
4152 4209 2.121963 AGGGGCTGGACAACTCCA 60.122 61.111 0.00 0.00 45.11 3.86
4154 4211 1.276622 TAAGAGGGGCTGGACAACTC 58.723 55.000 0.00 0.00 0.00 3.01
4156 4213 2.290960 ACAATAAGAGGGGCTGGACAAC 60.291 50.000 0.00 0.00 0.00 3.32
4157 4214 1.992557 ACAATAAGAGGGGCTGGACAA 59.007 47.619 0.00 0.00 0.00 3.18
4158 4215 1.281867 CACAATAAGAGGGGCTGGACA 59.718 52.381 0.00 0.00 0.00 4.02
4159 4216 1.282157 ACACAATAAGAGGGGCTGGAC 59.718 52.381 0.00 0.00 0.00 4.02
4160 4217 1.668826 ACACAATAAGAGGGGCTGGA 58.331 50.000 0.00 0.00 0.00 3.86
4161 4218 2.094675 CAACACAATAAGAGGGGCTGG 58.905 52.381 0.00 0.00 0.00 4.85
4162 4219 1.474077 GCAACACAATAAGAGGGGCTG 59.526 52.381 0.00 0.00 0.00 4.85
4163 4220 1.355720 AGCAACACAATAAGAGGGGCT 59.644 47.619 0.00 0.00 0.00 5.19
4165 4222 3.378427 GCTAAGCAACACAATAAGAGGGG 59.622 47.826 0.00 0.00 0.00 4.79
4166 4223 3.378427 GGCTAAGCAACACAATAAGAGGG 59.622 47.826 0.00 0.00 0.00 4.30
4167 4224 3.378427 GGGCTAAGCAACACAATAAGAGG 59.622 47.826 0.00 0.00 0.00 3.69
4168 4225 3.378427 GGGGCTAAGCAACACAATAAGAG 59.622 47.826 0.00 0.00 0.00 2.85
4169 4226 3.010138 AGGGGCTAAGCAACACAATAAGA 59.990 43.478 0.00 0.00 0.00 2.10
4172 4229 2.576191 AGAGGGGCTAAGCAACACAATA 59.424 45.455 0.00 0.00 0.00 1.90
4173 4230 1.355720 AGAGGGGCTAAGCAACACAAT 59.644 47.619 0.00 0.00 0.00 2.71
4174 4231 0.771127 AGAGGGGCTAAGCAACACAA 59.229 50.000 0.00 0.00 0.00 3.33
4176 4233 2.781681 TAAGAGGGGCTAAGCAACAC 57.218 50.000 0.00 0.00 0.00 3.32
4177 4234 3.620488 CAATAAGAGGGGCTAAGCAACA 58.380 45.455 0.00 0.00 0.00 3.33
4178 4235 2.359214 GCAATAAGAGGGGCTAAGCAAC 59.641 50.000 0.00 0.00 0.00 4.17
4184 4244 1.745827 GCAACGCAATAAGAGGGGCTA 60.746 52.381 0.00 0.00 0.00 3.93
4287 4348 2.224621 CCACCCTTGGTCAGGCATATAG 60.225 54.545 0.00 0.00 42.29 1.31
4293 4354 1.303643 CTTCCACCCTTGGTCAGGC 60.304 63.158 0.00 0.00 44.35 4.85
4300 4361 1.001641 CCTGAGCCTTCCACCCTTG 60.002 63.158 0.00 0.00 0.00 3.61
4328 4389 3.343617 ACCATAGTGGAACAAATCACCG 58.656 45.455 2.45 0.00 44.16 4.94
4337 4398 4.138487 CTAGGGTTGACCATAGTGGAAC 57.862 50.000 12.48 0.00 43.38 3.62
4345 4406 5.948842 ACTACAAAAACTAGGGTTGACCAT 58.051 37.500 2.12 0.00 43.89 3.55
4363 4425 8.704668 TCAATGAAGATAATAGCCAGAACTACA 58.295 33.333 0.00 0.00 0.00 2.74
4399 4461 1.729284 AATAACCCACGCACGGTAAG 58.271 50.000 0.00 0.00 31.69 2.34
4400 4462 3.196463 CATAATAACCCACGCACGGTAA 58.804 45.455 0.00 0.00 31.69 2.85
4405 4467 5.305139 AGAAAACATAATAACCCACGCAC 57.695 39.130 0.00 0.00 0.00 5.34
4408 4470 8.980143 ATGAAAAGAAAACATAATAACCCACG 57.020 30.769 0.00 0.00 0.00 4.94
4414 4476 8.757877 CAGGGGGATGAAAAGAAAACATAATAA 58.242 33.333 0.00 0.00 0.00 1.40
4422 4484 3.165071 GCTCAGGGGGATGAAAAGAAAA 58.835 45.455 0.00 0.00 0.00 2.29
4423 4485 2.379907 AGCTCAGGGGGATGAAAAGAAA 59.620 45.455 0.00 0.00 0.00 2.52
4424 4486 1.995542 AGCTCAGGGGGATGAAAAGAA 59.004 47.619 0.00 0.00 0.00 2.52
4425 4487 1.561542 GAGCTCAGGGGGATGAAAAGA 59.438 52.381 9.40 0.00 0.00 2.52
4426 4488 1.409381 GGAGCTCAGGGGGATGAAAAG 60.409 57.143 17.19 0.00 0.00 2.27
4427 4489 0.625849 GGAGCTCAGGGGGATGAAAA 59.374 55.000 17.19 0.00 0.00 2.29
4428 4490 0.253347 AGGAGCTCAGGGGGATGAAA 60.253 55.000 17.19 0.00 0.00 2.69
4429 4491 0.253347 AAGGAGCTCAGGGGGATGAA 60.253 55.000 17.19 0.00 0.00 2.57
4430 4492 0.253347 AAAGGAGCTCAGGGGGATGA 60.253 55.000 17.19 0.00 0.00 2.92
4431 4493 1.511613 TAAAGGAGCTCAGGGGGATG 58.488 55.000 17.19 0.00 0.00 3.51
4438 4500 4.047822 CAACGCTAGATAAAGGAGCTCAG 58.952 47.826 17.19 2.37 33.91 3.35
4468 4530 4.517663 CCATGTTGGGCCTTGTGA 57.482 55.556 4.53 0.00 32.67 3.58
4524 4587 3.312736 TTGAAAATATCTCCAGGGGGC 57.687 47.619 0.00 0.00 0.00 5.80
4531 4594 9.056005 GGCCCAAATTATTTTGAAAATATCTCC 57.944 33.333 10.81 3.59 44.11 3.71
4559 4622 0.250166 CCAACGGTTTTCTCGGGAGT 60.250 55.000 0.00 0.00 0.00 3.85
4561 4624 0.249996 GACCAACGGTTTTCTCGGGA 60.250 55.000 0.00 0.00 35.25 5.14
4597 4660 1.778383 TTTCCCAAGGGTGCCTCCT 60.778 57.895 4.80 0.00 39.17 3.69
4609 4672 1.431195 TAGCCAAGGCCAGTTTCCCA 61.431 55.000 5.01 0.00 43.17 4.37
4620 4683 4.126524 GCTTACGGCTAGCCAAGG 57.873 61.111 32.47 20.55 38.06 3.61
4629 4692 0.393808 TGGATGGGAAAGCTTACGGC 60.394 55.000 0.00 0.00 42.19 5.68
4631 4694 2.711542 AGTTGGATGGGAAAGCTTACG 58.288 47.619 0.00 0.00 0.00 3.18
4648 4711 5.933463 CGTATCTCTAGATTCGGTCCTAGTT 59.067 44.000 10.18 0.00 40.22 2.24
4649 4712 5.011943 ACGTATCTCTAGATTCGGTCCTAGT 59.988 44.000 18.96 0.00 45.48 2.57
4652 4715 4.354893 ACGTATCTCTAGATTCGGTCCT 57.645 45.455 18.96 0.61 45.48 3.85
4659 4722 4.391155 AGAGCCGAACGTATCTCTAGATT 58.609 43.478 0.00 0.00 34.45 2.40
4660 4723 4.010667 AGAGCCGAACGTATCTCTAGAT 57.989 45.455 0.00 0.00 34.45 1.98


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

AutoCloner maintained by Alex Coulton.