Multiple sequence alignment - TraesCS6D01G382600

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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 TraesCS6D01G382600 chr6D 100.000 2764 0 0 1 2764 462274070 462271307 0.000000e+00 5105
1 TraesCS6D01G382600 chr6A 85.615 2148 145 81 685 2764 609107876 609105825 0.000000e+00 2104
2 TraesCS6D01G382600 chr6A 80.475 589 29 28 145 686 609108551 609108002 3.360000e-99 372
3 TraesCS6D01G382600 chr6A 93.382 136 9 0 1 136 609109201 609109066 4.670000e-48 202
4 TraesCS6D01G382600 chr6B 87.515 1666 95 51 456 2063 704750765 704752375 0.000000e+00 1820
5 TraesCS6D01G382600 chr6B 81.596 614 79 23 2171 2764 704752462 704753061 6.930000e-131 477
6 TraesCS6D01G382600 chr6B 96.094 128 4 1 279 405 704743036 704743163 1.000000e-49 207
7 TraesCS6D01G382600 chr4B 87.132 272 33 2 1051 1321 605693090 605692820 9.620000e-80 307
8 TraesCS6D01G382600 chr4B 85.294 272 38 2 1050 1320 605682900 605683170 2.100000e-71 279
9 TraesCS6D01G382600 chr4B 78.409 264 44 12 1055 1313 77651297 77651552 2.850000e-35 159
10 TraesCS6D01G382600 chr4D 86.813 273 32 4 1050 1320 478992314 478992584 4.470000e-78 302
11 TraesCS6D01G382600 chr4D 84.586 266 37 4 1057 1320 382738013 382738276 7.590000e-66 261
12 TraesCS6D01G382600 chr4A 85.978 271 38 0 1050 1320 685372137 685372407 9.680000e-75 291
13 TraesCS6D01G382600 chr4A 84.962 266 36 4 1057 1320 64956723 64956986 1.630000e-67 267
14 TraesCS6D01G382600 chr1B 86.413 184 15 9 2564 2745 654917091 654916916 2.810000e-45 193


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 TraesCS6D01G382600 chr6D 462271307 462274070 2763 True 5105.000000 5105 100.000000 1 2764 1 chr6D.!!$R1 2763
1 TraesCS6D01G382600 chr6A 609105825 609109201 3376 True 892.666667 2104 86.490667 1 2764 3 chr6A.!!$R1 2763
2 TraesCS6D01G382600 chr6B 704750765 704753061 2296 False 1148.500000 1820 84.555500 456 2764 2 chr6B.!!$F2 2308

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
104 105 0.103572 AAAGCACTTTGGCACAGCTG 59.896 50.0 13.48 13.48 42.39 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2728 1.069358 GCTTGCGCCTCCTCTAATACT 59.931 52.381 4.18 0.0 0.0 2.12 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
41 42 1.151668 CTGCATAGGCGGTGCTATTC 58.848 55.000 16.03 0.00 45.35 1.75
48 49 1.134670 AGGCGGTGCTATTCTTCACTC 60.135 52.381 0.00 0.00 33.91 3.51
61 62 1.306642 TTCACTCTCTCGCCCTCGAC 61.307 60.000 0.00 0.00 40.21 4.20
102 103 2.127251 GTAAAAGCACTTTGGCACAGC 58.873 47.619 0.00 0.00 42.39 4.40
104 105 0.103572 AAAGCACTTTGGCACAGCTG 59.896 50.000 13.48 13.48 42.39 4.24
120 121 4.215827 CACAGCTGAAAAAGAAGCATCTCT 59.784 41.667 23.35 0.00 42.06 3.10
125 126 5.414144 GCTGAAAAAGAAGCATCTCTACCTT 59.586 40.000 0.00 0.00 39.31 3.50
133 134 0.537188 CATCTCTACCTTGGCACGGT 59.463 55.000 20.24 20.24 38.55 4.83
136 137 1.156736 CTCTACCTTGGCACGGTTTG 58.843 55.000 21.57 14.09 35.98 2.93
156 663 6.371548 GGTTTGCACAGTTAATATCAGTCTCA 59.628 38.462 0.00 0.00 0.00 3.27
161 668 5.521735 CACAGTTAATATCAGTCTCACTGCC 59.478 44.000 0.00 0.00 45.54 4.85
267 782 3.601586 CGTAGCAGTATTTGTATGCACGC 60.602 47.826 0.00 0.00 42.45 5.34
268 783 2.355197 AGCAGTATTTGTATGCACGCA 58.645 42.857 0.00 0.00 42.45 5.24
269 784 2.095853 AGCAGTATTTGTATGCACGCAC 59.904 45.455 0.00 0.00 42.45 5.34
270 785 2.692939 CAGTATTTGTATGCACGCACG 58.307 47.619 0.00 0.00 0.00 5.34
271 786 1.062002 AGTATTTGTATGCACGCACGC 59.938 47.619 0.00 0.00 0.00 5.34
273 788 0.454285 ATTTGTATGCACGCACGCAC 60.454 50.000 0.00 0.00 46.56 5.34
274 789 2.756374 TTTGTATGCACGCACGCACG 62.756 55.000 0.00 0.00 46.56 5.34
365 880 2.413963 CCATTCGGCGGGAAATGCA 61.414 57.895 7.21 0.00 38.36 3.96
390 905 4.907269 TCTTTATCCATCTGTCTATGCCCA 59.093 41.667 0.00 0.00 0.00 5.36
444 975 7.307694 TCTCAATTCATTCATTTTTCAGACGG 58.692 34.615 0.00 0.00 0.00 4.79
494 1041 0.308684 ACGTACGTTTCAGCGTCTCA 59.691 50.000 16.72 0.00 44.55 3.27
496 1043 1.578023 CGTACGTTTCAGCGTCTCATC 59.422 52.381 7.22 0.00 44.55 2.92
497 1044 2.728225 CGTACGTTTCAGCGTCTCATCT 60.728 50.000 7.22 0.00 44.55 2.90
545 1101 4.803613 GTGACAAACAAACAAAGATGGGAC 59.196 41.667 0.00 0.00 0.00 4.46
607 1167 0.368227 GCTTGCACTTCATCGTCGAG 59.632 55.000 0.00 0.00 0.00 4.04
732 1425 2.351738 GCCCTTGTATTCAACACAGCAC 60.352 50.000 0.00 0.00 38.00 4.40
818 1511 5.304357 CCTTCTCCTAATCTTCTTCCTCCTC 59.696 48.000 0.00 0.00 0.00 3.71
819 1512 5.742562 TCTCCTAATCTTCTTCCTCCTCT 57.257 43.478 0.00 0.00 0.00 3.69
820 1513 6.098716 TCTCCTAATCTTCTTCCTCCTCTT 57.901 41.667 0.00 0.00 0.00 2.85
821 1514 6.133356 TCTCCTAATCTTCTTCCTCCTCTTC 58.867 44.000 0.00 0.00 0.00 2.87
822 1515 5.843469 TCCTAATCTTCTTCCTCCTCTTCA 58.157 41.667 0.00 0.00 0.00 3.02
823 1516 5.659079 TCCTAATCTTCTTCCTCCTCTTCAC 59.341 44.000 0.00 0.00 0.00 3.18
824 1517 4.835284 AATCTTCTTCCTCCTCTTCACC 57.165 45.455 0.00 0.00 0.00 4.02
825 1518 3.551635 TCTTCTTCCTCCTCTTCACCT 57.448 47.619 0.00 0.00 0.00 4.00
826 1519 3.436243 TCTTCTTCCTCCTCTTCACCTC 58.564 50.000 0.00 0.00 0.00 3.85
827 1520 2.239681 TCTTCCTCCTCTTCACCTCC 57.760 55.000 0.00 0.00 0.00 4.30
828 1521 1.719378 TCTTCCTCCTCTTCACCTCCT 59.281 52.381 0.00 0.00 0.00 3.69
829 1522 1.830477 CTTCCTCCTCTTCACCTCCTG 59.170 57.143 0.00 0.00 0.00 3.86
851 1544 1.146930 CACCGTCCCATCCCATCAG 59.853 63.158 0.00 0.00 0.00 2.90
894 1587 6.401047 TCTATAAATACCAGTCCAACCTCG 57.599 41.667 0.00 0.00 0.00 4.63
897 1590 2.233305 ATACCAGTCCAACCTCGACT 57.767 50.000 0.00 0.00 41.29 4.18
929 1622 2.047655 CCGGCGAACCAAGTAGCA 60.048 61.111 9.30 0.00 34.57 3.49
930 1623 2.100631 CCGGCGAACCAAGTAGCAG 61.101 63.158 9.30 0.00 34.57 4.24
931 1624 2.740714 CGGCGAACCAAGTAGCAGC 61.741 63.158 0.00 0.00 34.57 5.25
932 1625 1.376037 GGCGAACCAAGTAGCAGCT 60.376 57.895 0.00 0.00 35.26 4.24
933 1626 0.108329 GGCGAACCAAGTAGCAGCTA 60.108 55.000 0.00 0.00 35.26 3.32
934 1627 1.281899 GCGAACCAAGTAGCAGCTAG 58.718 55.000 1.02 0.00 0.00 3.42
935 1628 1.281899 CGAACCAAGTAGCAGCTAGC 58.718 55.000 6.62 6.62 46.19 3.42
978 1671 0.656259 CGTCCTCGATCGACAAGCTA 59.344 55.000 15.15 0.00 39.71 3.32
1034 1735 3.779850 CTGCTGGTGCTGGTGGTGT 62.780 63.158 0.00 0.00 40.48 4.16
1037 1738 2.832661 TGGTGCTGGTGGTGTTGC 60.833 61.111 0.00 0.00 0.00 4.17
1038 1739 3.964875 GGTGCTGGTGGTGTTGCG 61.965 66.667 0.00 0.00 0.00 4.85
1131 1832 1.142097 GCCCTACTTCAGCTCCGAC 59.858 63.158 0.00 0.00 0.00 4.79
1326 2027 4.363990 CAGCAGCAGGTCCGTCGT 62.364 66.667 0.00 0.00 0.00 4.34
1327 2028 4.057428 AGCAGCAGGTCCGTCGTC 62.057 66.667 0.00 0.00 0.00 4.20
1328 2029 4.057428 GCAGCAGGTCCGTCGTCT 62.057 66.667 0.00 0.00 0.00 4.18
1329 2030 2.179517 CAGCAGGTCCGTCGTCTC 59.820 66.667 0.00 0.00 0.00 3.36
1330 2031 3.432588 AGCAGGTCCGTCGTCTCG 61.433 66.667 0.00 0.00 0.00 4.04
1333 2034 2.745492 AGGTCCGTCGTCTCGTCC 60.745 66.667 0.00 0.00 0.00 4.79
1334 2035 3.808656 GGTCCGTCGTCTCGTCCC 61.809 72.222 0.00 0.00 0.00 4.46
1335 2036 3.052082 GTCCGTCGTCTCGTCCCA 61.052 66.667 0.00 0.00 0.00 4.37
1337 2038 1.676635 TCCGTCGTCTCGTCCCATT 60.677 57.895 0.00 0.00 0.00 3.16
1338 2039 1.226603 CCGTCGTCTCGTCCCATTC 60.227 63.158 0.00 0.00 0.00 2.67
1339 2040 1.654954 CCGTCGTCTCGTCCCATTCT 61.655 60.000 0.00 0.00 0.00 2.40
1340 2041 0.170561 CGTCGTCTCGTCCCATTCTT 59.829 55.000 0.00 0.00 0.00 2.52
1341 2042 1.794437 CGTCGTCTCGTCCCATTCTTC 60.794 57.143 0.00 0.00 0.00 2.87
1342 2043 1.473278 GTCGTCTCGTCCCATTCTTCT 59.527 52.381 0.00 0.00 0.00 2.85
1343 2044 2.094649 GTCGTCTCGTCCCATTCTTCTT 60.095 50.000 0.00 0.00 0.00 2.52
1344 2045 2.163815 TCGTCTCGTCCCATTCTTCTTC 59.836 50.000 0.00 0.00 0.00 2.87
1345 2046 2.164624 CGTCTCGTCCCATTCTTCTTCT 59.835 50.000 0.00 0.00 0.00 2.85
1346 2047 3.367498 CGTCTCGTCCCATTCTTCTTCTT 60.367 47.826 0.00 0.00 0.00 2.52
1347 2048 4.177783 GTCTCGTCCCATTCTTCTTCTTC 58.822 47.826 0.00 0.00 0.00 2.87
1432 2144 2.758089 GCCATGGACGCAAGCTGAG 61.758 63.158 18.40 0.00 45.62 3.35
1440 2157 1.663135 GACGCAAGCTGAGGATTTCTC 59.337 52.381 0.00 0.00 45.62 2.87
1441 2158 1.277557 ACGCAAGCTGAGGATTTCTCT 59.722 47.619 0.00 0.00 41.91 3.10
1448 2165 6.294176 GCAAGCTGAGGATTTCTCTTTTGTTA 60.294 38.462 0.00 0.00 42.86 2.41
1824 2557 2.655090 TGCTTCCAACAACCTCATCA 57.345 45.000 0.00 0.00 0.00 3.07
1857 2594 5.557052 TGCTGCTAGCTGATGGAATCGTT 62.557 47.826 24.19 0.00 42.58 3.85
1859 2596 7.643225 TGCTGCTAGCTGATGGAATCGTTTA 62.643 44.000 24.19 0.00 42.58 2.01
2040 2786 6.261603 GCTCAGTTGATGAATGATGATTACCA 59.738 38.462 0.00 0.00 37.52 3.25
2121 2916 9.679661 TGAAAAAGGTATATGTAATCTTGCTGA 57.320 29.630 0.00 0.00 0.00 4.26
2124 2919 7.678947 AAGGTATATGTAATCTTGCTGATGC 57.321 36.000 0.00 0.00 35.21 3.91
2145 2940 3.624777 CATGGCTTAGTGAACCCAATCT 58.375 45.455 0.00 0.00 0.00 2.40
2148 2943 3.181434 TGGCTTAGTGAACCCAATCTTGT 60.181 43.478 0.00 0.00 0.00 3.16
2153 2948 4.118168 AGTGAACCCAATCTTGTGGAAT 57.882 40.909 0.00 0.00 41.65 3.01
2154 2949 4.082125 AGTGAACCCAATCTTGTGGAATC 58.918 43.478 0.00 0.00 41.65 2.52
2155 2950 3.826157 GTGAACCCAATCTTGTGGAATCA 59.174 43.478 0.00 0.00 41.65 2.57
2156 2951 4.463891 GTGAACCCAATCTTGTGGAATCAT 59.536 41.667 0.00 0.00 41.65 2.45
2159 2954 3.765511 ACCCAATCTTGTGGAATCATGTG 59.234 43.478 0.00 0.00 41.65 3.21
2160 2955 3.131577 CCCAATCTTGTGGAATCATGTGG 59.868 47.826 0.00 0.00 41.65 4.17
2161 2956 4.018490 CCAATCTTGTGGAATCATGTGGA 58.982 43.478 0.00 0.00 41.65 4.02
2162 2957 4.463539 CCAATCTTGTGGAATCATGTGGAA 59.536 41.667 0.00 0.00 41.65 3.53
2163 2958 5.047164 CCAATCTTGTGGAATCATGTGGAAA 60.047 40.000 0.00 0.00 41.65 3.13
2164 2959 6.457355 CAATCTTGTGGAATCATGTGGAAAA 58.543 36.000 0.00 0.00 0.00 2.29
2165 2960 6.669125 ATCTTGTGGAATCATGTGGAAAAA 57.331 33.333 0.00 0.00 0.00 1.94
2193 2988 4.016113 GGCGATTAGGCTACAACAAAAG 57.984 45.455 0.00 0.00 42.90 2.27
2194 2989 3.687698 GGCGATTAGGCTACAACAAAAGA 59.312 43.478 0.00 0.00 42.90 2.52
2202 2997 4.578928 AGGCTACAACAAAAGACACGAAAT 59.421 37.500 0.00 0.00 0.00 2.17
2260 3055 2.952245 GCAGTTGCAGACCAGCAG 59.048 61.111 0.00 0.00 46.54 4.24
2261 3056 2.623915 GCAGTTGCAGACCAGCAGG 61.624 63.158 0.00 0.00 46.54 4.85
2262 3057 1.071987 CAGTTGCAGACCAGCAGGA 59.928 57.895 0.35 0.00 46.54 3.86
2263 3058 0.322277 CAGTTGCAGACCAGCAGGAT 60.322 55.000 0.35 0.00 46.54 3.24
2264 3059 0.322277 AGTTGCAGACCAGCAGGATG 60.322 55.000 0.35 1.20 46.54 3.51
2265 3060 0.321919 GTTGCAGACCAGCAGGATGA 60.322 55.000 0.35 0.00 46.54 2.92
2266 3061 0.401356 TTGCAGACCAGCAGGATGAA 59.599 50.000 0.35 0.00 46.54 2.57
2268 3063 0.807496 GCAGACCAGCAGGATGAAAC 59.193 55.000 0.35 0.00 39.69 2.78
2269 3064 1.883638 GCAGACCAGCAGGATGAAACA 60.884 52.381 0.35 0.00 39.69 2.83
2273 3068 1.956477 ACCAGCAGGATGAAACACAAC 59.044 47.619 0.35 0.00 39.69 3.32
2274 3069 2.233271 CCAGCAGGATGAAACACAACT 58.767 47.619 0.00 0.00 39.69 3.16
2281 3076 5.788450 CAGGATGAAACACAACTCTCTACT 58.212 41.667 0.00 0.00 39.69 2.57
2288 3083 5.446143 AACACAACTCTCTACTGTCTGAG 57.554 43.478 4.88 4.88 0.00 3.35
2293 3088 4.788925 ACTCTCTACTGTCTGAGGCTAT 57.211 45.455 9.73 0.00 0.00 2.97
2295 3090 4.165180 ACTCTCTACTGTCTGAGGCTATCA 59.835 45.833 9.73 0.00 36.21 2.15
2299 3094 6.609212 TCTCTACTGTCTGAGGCTATCATTTT 59.391 38.462 9.73 0.00 37.28 1.82
2300 3095 7.780271 TCTCTACTGTCTGAGGCTATCATTTTA 59.220 37.037 9.73 0.00 37.28 1.52
2301 3096 8.484214 TCTACTGTCTGAGGCTATCATTTTAT 57.516 34.615 0.00 0.00 37.28 1.40
2348 3145 9.797642 TTTAGAAGTATGATATGATGGTGCATT 57.202 29.630 0.00 0.00 0.00 3.56
2366 3163 4.202243 TGCATTCCAAAAGTTCAAGGAAGG 60.202 41.667 9.79 9.79 42.84 3.46
2369 3166 3.562182 TCCAAAAGTTCAAGGAAGGGTC 58.438 45.455 0.00 0.00 0.00 4.46
2374 3171 3.778954 AGTTCAAGGAAGGGTCTGAAG 57.221 47.619 0.00 0.00 0.00 3.02
2376 3173 3.913163 AGTTCAAGGAAGGGTCTGAAGAT 59.087 43.478 0.00 0.00 0.00 2.40
2379 3176 3.652869 TCAAGGAAGGGTCTGAAGATTGT 59.347 43.478 0.00 0.00 0.00 2.71
2380 3177 4.104738 TCAAGGAAGGGTCTGAAGATTGTT 59.895 41.667 0.00 0.00 0.00 2.83
2389 3186 6.486993 AGGGTCTGAAGATTGTTTACAAGTTC 59.513 38.462 11.04 11.04 39.47 3.01
2393 3191 8.017946 GTCTGAAGATTGTTTACAAGTTCCATC 58.982 37.037 13.63 2.42 39.47 3.51
2400 3198 5.129634 TGTTTACAAGTTCCATCTCTGCAA 58.870 37.500 0.00 0.00 0.00 4.08
2404 3202 3.755378 ACAAGTTCCATCTCTGCAATGTC 59.245 43.478 0.00 0.00 0.00 3.06
2405 3203 2.996631 AGTTCCATCTCTGCAATGTCC 58.003 47.619 0.00 0.00 0.00 4.02
2415 3213 1.538512 CTGCAATGTCCCTCTGTTGTG 59.461 52.381 0.00 0.00 0.00 3.33
2416 3214 0.242017 GCAATGTCCCTCTGTTGTGC 59.758 55.000 0.00 0.00 0.00 4.57
2419 3217 0.037303 ATGTCCCTCTGTTGTGCCTG 59.963 55.000 0.00 0.00 0.00 4.85
2420 3218 1.344953 TGTCCCTCTGTTGTGCCTGT 61.345 55.000 0.00 0.00 0.00 4.00
2423 3221 0.687354 CCCTCTGTTGTGCCTGTACT 59.313 55.000 0.00 0.00 0.00 2.73
2424 3222 1.609061 CCCTCTGTTGTGCCTGTACTG 60.609 57.143 0.00 0.00 0.00 2.74
2425 3223 1.070758 CCTCTGTTGTGCCTGTACTGT 59.929 52.381 0.00 0.00 0.00 3.55
2426 3224 2.299013 CCTCTGTTGTGCCTGTACTGTA 59.701 50.000 0.00 0.00 0.00 2.74
2427 3225 3.318017 CTCTGTTGTGCCTGTACTGTAC 58.682 50.000 10.98 10.98 0.00 2.90
2428 3226 2.036733 TCTGTTGTGCCTGTACTGTACC 59.963 50.000 14.91 1.09 0.00 3.34
2429 3227 1.071071 TGTTGTGCCTGTACTGTACCC 59.929 52.381 14.91 4.79 0.00 3.69
2430 3228 0.688487 TTGTGCCTGTACTGTACCCC 59.312 55.000 14.91 4.46 0.00 4.95
2431 3229 0.472161 TGTGCCTGTACTGTACCCCA 60.472 55.000 14.91 6.81 0.00 4.96
2433 3231 1.221021 GCCTGTACTGTACCCCAGC 59.779 63.158 14.91 8.72 45.68 4.85
2434 3232 1.265454 GCCTGTACTGTACCCCAGCT 61.265 60.000 14.91 0.00 45.68 4.24
2440 3238 2.320681 ACTGTACCCCAGCTTGTCTA 57.679 50.000 0.00 0.00 45.68 2.59
2452 3250 5.297547 CCAGCTTGTCTAAAACTGTCAGTA 58.702 41.667 5.77 0.00 0.00 2.74
2455 3269 6.646653 CAGCTTGTCTAAAACTGTCAGTATCA 59.353 38.462 5.77 0.00 0.00 2.15
2458 3272 6.096673 TGTCTAAAACTGTCAGTATCAGCA 57.903 37.500 5.77 3.98 36.50 4.41
2463 3277 2.693069 ACTGTCAGTATCAGCACAAGC 58.307 47.619 2.87 0.00 42.56 4.01
2479 3293 2.896745 AAGCTTGAAAACTGCTTGGG 57.103 45.000 0.00 0.00 44.16 4.12
2498 3312 5.365021 TGGGTTTGATTTGTGTTGGAAAT 57.635 34.783 0.00 0.00 0.00 2.17
2518 3332 9.974980 TGGAAATAATTTACTCCAAAGTTTGAC 57.025 29.630 17.33 0.00 35.02 3.18
2525 3342 4.045636 ACTCCAAAGTTTGACAATGCAC 57.954 40.909 17.33 0.00 28.74 4.57
2526 3347 3.181476 ACTCCAAAGTTTGACAATGCACC 60.181 43.478 17.33 0.00 28.74 5.01
2527 3348 2.762887 TCCAAAGTTTGACAATGCACCA 59.237 40.909 17.33 0.00 0.00 4.17
2533 3354 4.573900 AGTTTGACAATGCACCACAAAAA 58.426 34.783 10.26 0.00 33.40 1.94
2535 3356 5.647225 AGTTTGACAATGCACCACAAAAATT 59.353 32.000 10.26 0.00 33.40 1.82
2542 3363 4.057406 TGCACCACAAAAATTCAAGGAG 57.943 40.909 0.00 0.00 0.00 3.69
2543 3364 3.703556 TGCACCACAAAAATTCAAGGAGA 59.296 39.130 0.00 0.00 0.00 3.71
2552 3373 9.884465 CACAAAAATTCAAGGAGAAGTTACTAG 57.116 33.333 0.00 0.00 43.12 2.57
2553 3374 9.628500 ACAAAAATTCAAGGAGAAGTTACTAGT 57.372 29.630 0.00 0.00 43.12 2.57
2562 3383 5.816777 AGGAGAAGTTACTAGTACTAGCACG 59.183 44.000 26.54 7.50 36.66 5.34
2590 3411 0.261696 AGTTGCCACCAAGTTTCCCT 59.738 50.000 0.00 0.00 30.50 4.20
2636 3459 9.090103 ACTTGTATACATTCATAGCTAGGCTTA 57.910 33.333 6.36 0.00 40.44 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.027255 TCGAGGGCGAGAGAGTGAAG 61.027 60.000 0.00 0.00 42.51 3.02
102 103 6.128063 CCAAGGTAGAGATGCTTCTTTTTCAG 60.128 42.308 3.29 0.00 30.30 3.02
104 105 5.392487 GCCAAGGTAGAGATGCTTCTTTTTC 60.392 44.000 3.29 0.00 30.30 2.29
133 134 7.161404 AGTGAGACTGATATTAACTGTGCAAA 58.839 34.615 0.00 0.00 0.00 3.68
156 663 4.286297 TGCAGTAAGAAATAGTGGCAGT 57.714 40.909 0.00 0.00 35.77 4.40
161 668 5.869753 AGCACTTGCAGTAAGAAATAGTG 57.130 39.130 5.10 5.26 45.16 2.74
275 790 2.101209 GATTTATCCCGGCGTGCGTG 62.101 60.000 6.01 0.00 0.00 5.34
276 791 1.885850 GATTTATCCCGGCGTGCGT 60.886 57.895 6.01 0.00 0.00 5.24
277 792 2.604174 GGATTTATCCCGGCGTGCG 61.604 63.158 6.01 0.00 41.20 5.34
278 793 1.525077 TGGATTTATCCCGGCGTGC 60.525 57.895 6.01 0.00 46.59 5.34
279 794 1.495584 CGTGGATTTATCCCGGCGTG 61.496 60.000 6.01 0.00 46.59 5.34
280 795 1.227438 CGTGGATTTATCCCGGCGT 60.227 57.895 6.01 0.00 46.59 5.68
281 796 1.959226 CCGTGGATTTATCCCGGCG 60.959 63.158 18.99 0.00 46.21 6.46
282 797 4.058797 CCGTGGATTTATCCCGGC 57.941 61.111 18.99 5.74 46.21 6.13
333 848 0.170339 GAATGGCCGCGCTTTAGTTT 59.830 50.000 5.56 0.00 0.00 2.66
365 880 6.044754 TGGGCATAGACAGATGGATAAAGAAT 59.955 38.462 0.00 0.00 0.00 2.40
390 905 1.006102 GTGAGTACGTGCACTGGCT 60.006 57.895 16.19 9.35 41.91 4.75
419 950 7.307694 CCGTCTGAAAAATGAATGAATTGAGA 58.692 34.615 0.00 0.00 0.00 3.27
420 951 6.529125 CCCGTCTGAAAAATGAATGAATTGAG 59.471 38.462 0.00 0.00 0.00 3.02
421 952 6.208402 TCCCGTCTGAAAAATGAATGAATTGA 59.792 34.615 0.00 0.00 0.00 2.57
422 953 6.389091 TCCCGTCTGAAAAATGAATGAATTG 58.611 36.000 0.00 0.00 0.00 2.32
423 954 6.588719 TCCCGTCTGAAAAATGAATGAATT 57.411 33.333 0.00 0.00 0.00 2.17
424 955 6.153340 ACATCCCGTCTGAAAAATGAATGAAT 59.847 34.615 0.00 0.00 0.00 2.57
425 956 5.476599 ACATCCCGTCTGAAAAATGAATGAA 59.523 36.000 0.00 0.00 0.00 2.57
426 957 5.009631 ACATCCCGTCTGAAAAATGAATGA 58.990 37.500 0.00 0.00 0.00 2.57
427 958 5.314923 ACATCCCGTCTGAAAAATGAATG 57.685 39.130 0.00 0.00 0.00 2.67
442 973 1.746615 CAGCCAGGTCAACATCCCG 60.747 63.158 0.00 0.00 0.00 5.14
444 975 1.747355 CAATCAGCCAGGTCAACATCC 59.253 52.381 0.00 0.00 0.00 3.51
494 1041 1.384989 CGGTACAGGTCGCAGGAGAT 61.385 60.000 0.00 0.00 0.00 2.75
496 1043 2.490217 CGGTACAGGTCGCAGGAG 59.510 66.667 0.00 0.00 0.00 3.69
497 1044 3.066190 CCGGTACAGGTCGCAGGA 61.066 66.667 3.54 0.00 0.00 3.86
589 1147 1.651138 GTCTCGACGATGAAGTGCAAG 59.349 52.381 0.00 0.00 0.00 4.01
590 1148 1.668919 GGTCTCGACGATGAAGTGCAA 60.669 52.381 0.00 0.00 0.00 4.08
597 1157 0.455815 CATGTGGGTCTCGACGATGA 59.544 55.000 0.00 0.00 0.00 2.92
683 1247 5.975344 GCCGGCTTCTTTTACCATAATTTAC 59.025 40.000 22.15 0.00 0.00 2.01
691 1383 1.673009 CGGCCGGCTTCTTTTACCA 60.673 57.895 28.56 0.00 0.00 3.25
732 1425 1.270625 TGAGGGGAGCAAACGTGTAAG 60.271 52.381 0.00 0.00 0.00 2.34
818 1511 2.743928 GTGGCGCAGGAGGTGAAG 60.744 66.667 10.83 0.00 0.00 3.02
819 1512 4.329545 GGTGGCGCAGGAGGTGAA 62.330 66.667 10.83 0.00 0.00 3.18
935 1628 0.817229 GCCTTGCCCTTGCTAGCTAG 60.817 60.000 16.84 16.84 38.77 3.42
936 1629 1.224592 GCCTTGCCCTTGCTAGCTA 59.775 57.895 17.23 7.59 38.77 3.32
937 1630 2.044551 GCCTTGCCCTTGCTAGCT 60.045 61.111 17.23 0.00 38.77 3.32
938 1631 2.361610 TGCCTTGCCCTTGCTAGC 60.362 61.111 8.10 8.10 38.77 3.42
939 1632 2.401766 CGTGCCTTGCCCTTGCTAG 61.402 63.158 0.00 0.00 39.64 3.42
940 1633 2.359850 CGTGCCTTGCCCTTGCTA 60.360 61.111 0.00 0.00 38.71 3.49
941 1634 4.586235 ACGTGCCTTGCCCTTGCT 62.586 61.111 0.00 0.00 38.71 3.91
942 1635 4.043200 GACGTGCCTTGCCCTTGC 62.043 66.667 0.00 0.00 38.26 4.01
943 1636 3.726517 CGACGTGCCTTGCCCTTG 61.727 66.667 0.00 0.00 0.00 3.61
944 1637 4.250305 ACGACGTGCCTTGCCCTT 62.250 61.111 0.00 0.00 0.00 3.95
945 1638 4.681978 GACGACGTGCCTTGCCCT 62.682 66.667 4.58 0.00 0.00 5.19
947 1640 4.681978 AGGACGACGTGCCTTGCC 62.682 66.667 16.35 4.40 0.00 4.52
972 1665 1.939785 CTAGCGCCGACGTAGCTTG 60.940 63.158 17.28 12.55 41.88 4.01
978 1671 2.221906 ATTGTTCCTAGCGCCGACGT 62.222 55.000 2.29 0.00 42.83 4.34
1016 1717 2.981909 CACCACCAGCACCAGCAG 60.982 66.667 0.00 0.00 45.49 4.24
1019 1720 2.848858 GCAACACCACCAGCACCAG 61.849 63.158 0.00 0.00 0.00 4.00
1326 2027 4.090090 AGAAGAAGAAGAATGGGACGAGA 58.910 43.478 0.00 0.00 0.00 4.04
1327 2028 4.464069 AGAAGAAGAAGAATGGGACGAG 57.536 45.455 0.00 0.00 0.00 4.18
1328 2029 4.528596 AGAAGAAGAAGAAGAATGGGACGA 59.471 41.667 0.00 0.00 0.00 4.20
1329 2030 4.826556 AGAAGAAGAAGAAGAATGGGACG 58.173 43.478 0.00 0.00 0.00 4.79
1330 2031 6.472016 AGAAGAAGAAGAAGAAGAATGGGAC 58.528 40.000 0.00 0.00 0.00 4.46
1333 2034 8.620116 AAGAAGAAGAAGAAGAAGAAGAATGG 57.380 34.615 0.00 0.00 0.00 3.16
1334 2035 8.720562 GGAAGAAGAAGAAGAAGAAGAAGAATG 58.279 37.037 0.00 0.00 0.00 2.67
1335 2036 8.435982 TGGAAGAAGAAGAAGAAGAAGAAGAAT 58.564 33.333 0.00 0.00 0.00 2.40
1337 2038 7.366847 TGGAAGAAGAAGAAGAAGAAGAAGA 57.633 36.000 0.00 0.00 0.00 2.87
1338 2039 8.096414 AGATGGAAGAAGAAGAAGAAGAAGAAG 58.904 37.037 0.00 0.00 0.00 2.85
1339 2040 7.972301 AGATGGAAGAAGAAGAAGAAGAAGAA 58.028 34.615 0.00 0.00 0.00 2.52
1340 2041 7.552050 AGATGGAAGAAGAAGAAGAAGAAGA 57.448 36.000 0.00 0.00 0.00 2.87
1341 2042 8.096414 AGAAGATGGAAGAAGAAGAAGAAGAAG 58.904 37.037 0.00 0.00 0.00 2.85
1342 2043 7.972301 AGAAGATGGAAGAAGAAGAAGAAGAA 58.028 34.615 0.00 0.00 0.00 2.52
1343 2044 7.552050 AGAAGATGGAAGAAGAAGAAGAAGA 57.448 36.000 0.00 0.00 0.00 2.87
1344 2045 7.334171 GGAAGAAGATGGAAGAAGAAGAAGAAG 59.666 40.741 0.00 0.00 0.00 2.85
1345 2046 7.017056 AGGAAGAAGATGGAAGAAGAAGAAGAA 59.983 37.037 0.00 0.00 0.00 2.52
1346 2047 6.500049 AGGAAGAAGATGGAAGAAGAAGAAGA 59.500 38.462 0.00 0.00 0.00 2.87
1347 2048 6.710278 AGGAAGAAGATGGAAGAAGAAGAAG 58.290 40.000 0.00 0.00 0.00 2.85
1432 2144 5.617087 GCGACCTGTAACAAAAGAGAAATCC 60.617 44.000 0.00 0.00 0.00 3.01
1440 2157 2.093783 GGATCGCGACCTGTAACAAAAG 59.906 50.000 12.93 0.00 0.00 2.27
1441 2158 2.070783 GGATCGCGACCTGTAACAAAA 58.929 47.619 12.93 0.00 0.00 2.44
1824 2557 1.470632 GCTAGCAGCACTCTGATCGTT 60.471 52.381 10.63 0.00 42.95 3.85
1982 2728 1.069358 GCTTGCGCCTCCTCTAATACT 59.931 52.381 4.18 0.00 0.00 2.12
1983 2729 1.503294 GCTTGCGCCTCCTCTAATAC 58.497 55.000 4.18 0.00 0.00 1.89
1984 2730 3.989104 GCTTGCGCCTCCTCTAATA 57.011 52.632 4.18 0.00 0.00 0.98
1985 2731 4.865865 GCTTGCGCCTCCTCTAAT 57.134 55.556 4.18 0.00 0.00 1.73
2065 2815 7.966812 TGTGACTATCAGGACTTGCAATATAT 58.033 34.615 0.00 0.00 0.00 0.86
2069 2847 4.558226 TGTGACTATCAGGACTTGCAAT 57.442 40.909 0.00 0.00 0.00 3.56
2079 2857 6.652481 ACCTTTTTCAGTGATGTGACTATCAG 59.348 38.462 0.00 0.00 37.72 2.90
2085 2863 8.268850 ACATATACCTTTTTCAGTGATGTGAC 57.731 34.615 0.00 0.00 0.00 3.67
2117 2912 1.671979 TCACTAAGCCATGCATCAGC 58.328 50.000 9.75 9.75 42.57 4.26
2130 2925 4.715534 TCCACAAGATTGGGTTCACTAA 57.284 40.909 0.00 0.00 37.24 2.24
2164 2959 6.376018 TGTTGTAGCCTAATCGCCTAATTTTT 59.624 34.615 0.00 0.00 0.00 1.94
2165 2960 5.883673 TGTTGTAGCCTAATCGCCTAATTTT 59.116 36.000 0.00 0.00 0.00 1.82
2166 2961 5.433526 TGTTGTAGCCTAATCGCCTAATTT 58.566 37.500 0.00 0.00 0.00 1.82
2167 2962 5.031066 TGTTGTAGCCTAATCGCCTAATT 57.969 39.130 0.00 0.00 0.00 1.40
2168 2963 4.682778 TGTTGTAGCCTAATCGCCTAAT 57.317 40.909 0.00 0.00 0.00 1.73
2169 2964 4.475051 TTGTTGTAGCCTAATCGCCTAA 57.525 40.909 0.00 0.00 0.00 2.69
2170 2965 4.475051 TTTGTTGTAGCCTAATCGCCTA 57.525 40.909 0.00 0.00 0.00 3.93
2171 2966 3.343941 TTTGTTGTAGCCTAATCGCCT 57.656 42.857 0.00 0.00 0.00 5.52
2172 2967 3.687698 TCTTTTGTTGTAGCCTAATCGCC 59.312 43.478 0.00 0.00 0.00 5.54
2182 2977 9.498307 AACTTTATTTCGTGTCTTTTGTTGTAG 57.502 29.630 0.00 0.00 0.00 2.74
2184 2979 8.024285 TGAACTTTATTTCGTGTCTTTTGTTGT 58.976 29.630 0.00 0.00 0.00 3.32
2187 2982 7.758495 ACTGAACTTTATTTCGTGTCTTTTGT 58.242 30.769 0.00 0.00 0.00 2.83
2191 2986 8.827177 TCATACTGAACTTTATTTCGTGTCTT 57.173 30.769 0.00 0.00 0.00 3.01
2193 2988 9.690434 GATTCATACTGAACTTTATTTCGTGTC 57.310 33.333 0.00 0.00 39.45 3.67
2194 2989 9.214957 TGATTCATACTGAACTTTATTTCGTGT 57.785 29.630 0.00 0.00 39.45 4.49
2253 3048 1.956477 GTTGTGTTTCATCCTGCTGGT 59.044 47.619 9.73 0.00 34.23 4.00
2255 3050 3.144506 AGAGTTGTGTTTCATCCTGCTG 58.855 45.455 0.00 0.00 0.00 4.41
2256 3051 3.072184 AGAGAGTTGTGTTTCATCCTGCT 59.928 43.478 0.00 0.00 0.00 4.24
2257 3052 3.406764 AGAGAGTTGTGTTTCATCCTGC 58.593 45.455 0.00 0.00 0.00 4.85
2258 3053 5.636965 CAGTAGAGAGTTGTGTTTCATCCTG 59.363 44.000 0.00 0.00 0.00 3.86
2259 3054 5.305644 ACAGTAGAGAGTTGTGTTTCATCCT 59.694 40.000 0.00 0.00 0.00 3.24
2260 3055 5.542779 ACAGTAGAGAGTTGTGTTTCATCC 58.457 41.667 0.00 0.00 0.00 3.51
2261 3056 6.364706 CAGACAGTAGAGAGTTGTGTTTCATC 59.635 42.308 0.00 0.00 0.00 2.92
2262 3057 6.040955 TCAGACAGTAGAGAGTTGTGTTTCAT 59.959 38.462 0.00 0.00 0.00 2.57
2263 3058 5.359860 TCAGACAGTAGAGAGTTGTGTTTCA 59.640 40.000 0.00 0.00 0.00 2.69
2264 3059 5.833082 TCAGACAGTAGAGAGTTGTGTTTC 58.167 41.667 0.00 0.00 0.00 2.78
2265 3060 5.221342 CCTCAGACAGTAGAGAGTTGTGTTT 60.221 44.000 4.42 0.00 33.74 2.83
2266 3061 4.279671 CCTCAGACAGTAGAGAGTTGTGTT 59.720 45.833 4.42 0.00 33.74 3.32
2268 3063 3.366883 GCCTCAGACAGTAGAGAGTTGTG 60.367 52.174 4.42 0.00 33.74 3.33
2269 3064 2.823154 GCCTCAGACAGTAGAGAGTTGT 59.177 50.000 4.42 0.00 33.74 3.32
2273 3068 4.713553 TGATAGCCTCAGACAGTAGAGAG 58.286 47.826 4.42 0.00 33.74 3.20
2274 3069 4.779993 TGATAGCCTCAGACAGTAGAGA 57.220 45.455 4.42 0.00 33.74 3.10
2321 3118 9.970553 ATGCACCATCATATCATACTTCTAAAT 57.029 29.630 0.00 0.00 0.00 1.40
2331 3128 6.325545 ACTTTTGGAATGCACCATCATATCAT 59.674 34.615 0.00 0.00 39.82 2.45
2337 3134 3.640498 TGAACTTTTGGAATGCACCATCA 59.360 39.130 0.00 0.00 39.82 3.07
2338 3135 4.255833 TGAACTTTTGGAATGCACCATC 57.744 40.909 0.00 0.00 39.82 3.51
2339 3136 4.503643 CCTTGAACTTTTGGAATGCACCAT 60.504 41.667 0.00 0.00 39.82 3.55
2340 3137 3.181467 CCTTGAACTTTTGGAATGCACCA 60.181 43.478 0.00 0.00 38.24 4.17
2341 3138 3.069443 TCCTTGAACTTTTGGAATGCACC 59.931 43.478 0.00 0.00 0.00 5.01
2348 3145 3.204382 AGACCCTTCCTTGAACTTTTGGA 59.796 43.478 0.00 0.00 0.00 3.53
2366 3163 6.262273 TGGAACTTGTAAACAATCTTCAGACC 59.738 38.462 12.15 0.00 35.02 3.85
2369 3166 8.103948 AGATGGAACTTGTAAACAATCTTCAG 57.896 34.615 12.15 0.00 35.02 3.02
2374 3171 6.072508 TGCAGAGATGGAACTTGTAAACAATC 60.073 38.462 0.00 0.00 35.02 2.67
2376 3173 5.129634 TGCAGAGATGGAACTTGTAAACAA 58.870 37.500 0.00 0.00 0.00 2.83
2379 3176 5.769662 ACATTGCAGAGATGGAACTTGTAAA 59.230 36.000 2.13 0.00 0.00 2.01
2380 3177 5.316167 ACATTGCAGAGATGGAACTTGTAA 58.684 37.500 2.13 0.00 0.00 2.41
2389 3186 1.489649 AGAGGGACATTGCAGAGATGG 59.510 52.381 2.13 0.00 0.00 3.51
2393 3191 2.082231 CAACAGAGGGACATTGCAGAG 58.918 52.381 0.00 0.00 0.00 3.35
2400 3198 0.037303 CAGGCACAACAGAGGGACAT 59.963 55.000 0.00 0.00 0.00 3.06
2404 3202 0.687354 AGTACAGGCACAACAGAGGG 59.313 55.000 0.00 0.00 0.00 4.30
2405 3203 1.070758 ACAGTACAGGCACAACAGAGG 59.929 52.381 0.00 0.00 0.00 3.69
2423 3221 3.393278 AGTTTTAGACAAGCTGGGGTACA 59.607 43.478 0.00 0.00 0.00 2.90
2424 3222 3.751698 CAGTTTTAGACAAGCTGGGGTAC 59.248 47.826 0.00 0.00 0.00 3.34
2425 3223 3.393278 ACAGTTTTAGACAAGCTGGGGTA 59.607 43.478 0.00 0.00 0.00 3.69
2426 3224 2.174854 ACAGTTTTAGACAAGCTGGGGT 59.825 45.455 0.00 0.00 0.00 4.95
2427 3225 2.814336 GACAGTTTTAGACAAGCTGGGG 59.186 50.000 0.00 0.00 0.00 4.96
2428 3226 3.476552 TGACAGTTTTAGACAAGCTGGG 58.523 45.455 0.00 0.00 0.00 4.45
2429 3227 4.130118 ACTGACAGTTTTAGACAAGCTGG 58.870 43.478 1.07 0.00 0.00 4.85
2430 3228 6.646653 TGATACTGACAGTTTTAGACAAGCTG 59.353 38.462 14.50 0.00 0.00 4.24
2431 3229 6.759272 TGATACTGACAGTTTTAGACAAGCT 58.241 36.000 14.50 0.00 0.00 3.74
2432 3230 6.401581 GCTGATACTGACAGTTTTAGACAAGC 60.402 42.308 14.50 8.33 37.64 4.01
2433 3231 6.646653 TGCTGATACTGACAGTTTTAGACAAG 59.353 38.462 14.50 2.52 37.64 3.16
2434 3232 6.423905 GTGCTGATACTGACAGTTTTAGACAA 59.576 38.462 14.50 0.00 37.64 3.18
2440 3238 4.023707 GCTTGTGCTGATACTGACAGTTTT 60.024 41.667 14.50 1.66 37.64 2.43
2463 3277 4.122143 TCAAACCCAAGCAGTTTTCAAG 57.878 40.909 0.00 0.00 35.28 3.02
2474 3288 4.399004 TCCAACACAAATCAAACCCAAG 57.601 40.909 0.00 0.00 0.00 3.61
2498 3312 8.417106 TGCATTGTCAAACTTTGGAGTAAATTA 58.583 29.630 1.62 0.00 34.21 1.40
2506 3320 2.762887 TGGTGCATTGTCAAACTTTGGA 59.237 40.909 1.62 0.00 0.00 3.53
2517 3331 4.575645 CCTTGAATTTTTGTGGTGCATTGT 59.424 37.500 0.00 0.00 0.00 2.71
2518 3332 4.815308 TCCTTGAATTTTTGTGGTGCATTG 59.185 37.500 0.00 0.00 0.00 2.82
2520 3337 4.344679 TCTCCTTGAATTTTTGTGGTGCAT 59.655 37.500 0.00 0.00 0.00 3.96
2525 3342 7.716612 AGTAACTTCTCCTTGAATTTTTGTGG 58.283 34.615 0.00 0.00 33.71 4.17
2526 3347 9.884465 CTAGTAACTTCTCCTTGAATTTTTGTG 57.116 33.333 0.00 0.00 33.71 3.33
2527 3348 9.628500 ACTAGTAACTTCTCCTTGAATTTTTGT 57.372 29.630 0.00 0.00 33.71 2.83
2533 3354 8.905850 GCTAGTACTAGTAACTTCTCCTTGAAT 58.094 37.037 26.76 0.00 35.65 2.57
2535 3356 7.336427 GTGCTAGTACTAGTAACTTCTCCTTGA 59.664 40.741 26.76 0.00 35.65 3.02
2542 3363 5.227238 TGCGTGCTAGTACTAGTAACTTC 57.773 43.478 26.76 18.78 35.65 3.01
2543 3364 5.182760 AGTTGCGTGCTAGTACTAGTAACTT 59.817 40.000 26.76 12.97 35.65 2.66
2552 3373 3.057734 ACTCAAAGTTGCGTGCTAGTAC 58.942 45.455 0.08 0.08 0.00 2.73
2553 3374 3.380479 ACTCAAAGTTGCGTGCTAGTA 57.620 42.857 0.00 0.00 0.00 1.82
2590 3411 6.954684 ACAAGTGATTTTAGGGTCTCTAGAGA 59.045 38.462 18.76 18.76 34.56 3.10


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

AutoCloner maintained by Alex Coulton.