Multiple sequence alignment - TraesCS3D01G358500

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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 TraesCS3D01G358500 chr3D 100.000 5145 0 0 1 5145 472113043 472118187 0.000000e+00 9502.0
1 TraesCS3D01G358500 chr3D 97.731 617 13 1 4369 4984 416426116 416425500 0.000000e+00 1061.0
2 TraesCS3D01G358500 chr3D 83.333 180 22 5 3677 3855 472197790 472197962 5.330000e-35 159.0
3 TraesCS3D01G358500 chr3B 90.790 4430 212 78 1 4314 627711309 627715658 0.000000e+00 5740.0
4 TraesCS3D01G358500 chr3B 81.667 180 25 5 3677 3855 627742081 627742253 5.370000e-30 143.0
5 TraesCS3D01G358500 chr3A 92.604 2231 104 25 2162 4352 614678379 614680588 0.000000e+00 3149.0
6 TraesCS3D01G358500 chr3A 91.037 2198 90 34 1 2165 614676214 614678337 0.000000e+00 2868.0
7 TraesCS3D01G358500 chr3A 92.169 166 8 5 4983 5145 614680582 614680745 4.010000e-56 230.0
8 TraesCS3D01G358500 chr3A 83.673 98 14 2 2986 3082 614691258 614691354 1.970000e-14 91.6
9 TraesCS3D01G358500 chr1D 98.052 616 10 2 4368 4981 8207677 8208292 0.000000e+00 1070.0
10 TraesCS3D01G358500 chr1D 96.970 627 16 3 4357 4981 19906212 19906837 0.000000e+00 1050.0
11 TraesCS3D01G358500 chr6D 97.893 617 12 1 4369 4984 37530675 37530059 0.000000e+00 1066.0
12 TraesCS3D01G358500 chr6D 97.411 618 14 2 4369 4984 4665948 4665331 0.000000e+00 1051.0
13 TraesCS3D01G358500 chr6D 97.403 616 14 1 4371 4984 145003752 145003137 0.000000e+00 1048.0
14 TraesCS3D01G358500 chr2D 98.042 613 10 2 4368 4978 644035500 644036112 0.000000e+00 1064.0
15 TraesCS3D01G358500 chr2D 97.557 614 13 2 4369 4981 555547855 555548467 0.000000e+00 1050.0
16 TraesCS3D01G358500 chr7D 97.557 614 14 1 4369 4981 596108134 596108747 0.000000e+00 1050.0


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 TraesCS3D01G358500 chr3D 472113043 472118187 5144 False 9502.000000 9502 100.000000 1 5145 1 chr3D.!!$F1 5144
1 TraesCS3D01G358500 chr3D 416425500 416426116 616 True 1061.000000 1061 97.731000 4369 4984 1 chr3D.!!$R1 615
2 TraesCS3D01G358500 chr3B 627711309 627715658 4349 False 5740.000000 5740 90.790000 1 4314 1 chr3B.!!$F1 4313
3 TraesCS3D01G358500 chr3A 614676214 614680745 4531 False 2082.333333 3149 91.936667 1 5145 3 chr3A.!!$F2 5144
4 TraesCS3D01G358500 chr1D 8207677 8208292 615 False 1070.000000 1070 98.052000 4368 4981 1 chr1D.!!$F1 613
5 TraesCS3D01G358500 chr1D 19906212 19906837 625 False 1050.000000 1050 96.970000 4357 4981 1 chr1D.!!$F2 624
6 TraesCS3D01G358500 chr6D 37530059 37530675 616 True 1066.000000 1066 97.893000 4369 4984 1 chr6D.!!$R2 615
7 TraesCS3D01G358500 chr6D 4665331 4665948 617 True 1051.000000 1051 97.411000 4369 4984 1 chr6D.!!$R1 615
8 TraesCS3D01G358500 chr6D 145003137 145003752 615 True 1048.000000 1048 97.403000 4371 4984 1 chr6D.!!$R3 613
9 TraesCS3D01G358500 chr2D 644035500 644036112 612 False 1064.000000 1064 98.042000 4368 4978 1 chr2D.!!$F2 610
10 TraesCS3D01G358500 chr2D 555547855 555548467 612 False 1050.000000 1050 97.557000 4369 4981 1 chr2D.!!$F1 612
11 TraesCS3D01G358500 chr7D 596108134 596108747 613 False 1050.000000 1050 97.557000 4369 4981 1 chr7D.!!$F1 612

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
342 347 0.178992 TTCAAACCCCTCACTGGCTG 60.179 55.0 0.00 0.0 0.00 4.85 F
717 728 0.254178 ATCAAAGCCATCCACGAGCT 59.746 50.0 0.00 0.0 38.88 4.09 F
897 910 0.257616 TAATGGGAAAAGAGGGGGCG 59.742 55.0 0.00 0.0 0.00 6.13 F
2296 2405 0.108585 AAGACAACTGTGGTCGGCAT 59.891 50.0 9.58 0.0 40.20 4.40 F
3856 4016 0.322187 GTCGCCAACAACCCAGGTAT 60.322 55.0 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2183 0.176910 TTGGTCGTCTGAACACTGCA 59.823 50.000 0.00 0.00 42.84 4.41 R
2296 2405 0.753867 TGCCGACCACTGACACTTAA 59.246 50.000 0.00 0.00 0.00 1.85 R
2865 3025 1.804151 TGCAGTTACAGAATTCACGGC 59.196 47.619 8.44 9.67 0.00 5.68 R
3904 4088 0.099968 CACCAAATCATCAGCAGCGG 59.900 55.000 0.00 0.00 0.00 5.52 R
4985 5192 0.534427 ATGCATGCACTCCGATCAGG 60.534 55.000 25.37 0.00 42.97 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 178 5.380043 CATAACTTGTGGGCATAATCCTCT 58.620 41.667 0.00 0.00 0.00 3.69
176 180 4.423625 ACTTGTGGGCATAATCCTCTAC 57.576 45.455 0.00 0.00 0.00 2.59
203 207 1.779683 GCTGTCGACGTGTTAAGCC 59.220 57.895 11.62 0.00 0.00 4.35
257 262 1.381056 TGGATTCGGCCATTTGGGG 60.381 57.895 2.24 0.00 37.04 4.96
342 347 0.178992 TTCAAACCCCTCACTGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
375 380 1.740285 GTGCGGATGGGATACTCGT 59.260 57.895 0.00 0.00 0.00 4.18
409 414 2.829741 ACACCTCAGCTTTGAGAGAC 57.170 50.000 4.59 0.00 38.13 3.36
433 438 5.170748 GCTTTTATTGACACAAATGAGGGG 58.829 41.667 0.00 0.00 0.00 4.79
523 529 9.084164 AGTTATTTAGCTATGTTGTCACGTTAG 57.916 33.333 0.00 0.00 0.00 2.34
559 565 9.476202 TCGTCAGAAAACAATATATATCCTGTG 57.524 33.333 0.00 0.00 0.00 3.66
561 567 8.507249 GTCAGAAAACAATATATATCCTGTGCC 58.493 37.037 0.00 0.00 0.00 5.01
562 568 7.387673 TCAGAAAACAATATATATCCTGTGCCG 59.612 37.037 0.00 0.00 0.00 5.69
653 659 2.223641 CGGGAAAGATGATTCGACGGTA 60.224 50.000 0.00 0.00 31.19 4.02
661 667 1.293924 GATTCGACGGTACTCCTCGA 58.706 55.000 0.00 6.13 39.57 4.04
670 676 4.322567 ACGGTACTCCTCGAATATAGACC 58.677 47.826 0.00 0.00 0.00 3.85
671 677 4.202398 ACGGTACTCCTCGAATATAGACCA 60.202 45.833 0.00 0.00 0.00 4.02
672 678 4.392445 CGGTACTCCTCGAATATAGACCAG 59.608 50.000 0.00 0.00 0.00 4.00
673 679 4.156373 GGTACTCCTCGAATATAGACCAGC 59.844 50.000 0.00 0.00 0.00 4.85
674 680 3.158676 ACTCCTCGAATATAGACCAGCC 58.841 50.000 0.00 0.00 0.00 4.85
715 726 2.733227 GCAAATCAAAGCCATCCACGAG 60.733 50.000 0.00 0.00 0.00 4.18
716 727 1.098050 AATCAAAGCCATCCACGAGC 58.902 50.000 0.00 0.00 0.00 5.03
717 728 0.254178 ATCAAAGCCATCCACGAGCT 59.746 50.000 0.00 0.00 38.88 4.09
865 877 0.731514 CCAGAAGCTTTACGTCGCGA 60.732 55.000 3.71 3.71 0.00 5.87
897 910 0.257616 TAATGGGAAAAGAGGGGGCG 59.742 55.000 0.00 0.00 0.00 6.13
898 911 3.662117 ATGGGAAAAGAGGGGGCGC 62.662 63.158 0.00 0.00 0.00 6.53
1004 1018 4.509616 TCGTGTTTCTTGGAAGACTTGAA 58.490 39.130 0.00 0.00 34.13 2.69
1063 1078 1.566211 TGCCTTTCCCTCTCTCTGAG 58.434 55.000 0.00 0.00 42.30 3.35
1064 1079 1.077828 TGCCTTTCCCTCTCTCTGAGA 59.922 52.381 7.24 7.24 45.39 3.27
1065 1080 1.480545 GCCTTTCCCTCTCTCTGAGAC 59.519 57.143 2.58 0.00 45.39 3.36
1066 1081 2.888069 GCCTTTCCCTCTCTCTGAGACT 60.888 54.545 2.58 0.00 45.39 3.24
1067 1082 3.023832 CCTTTCCCTCTCTCTGAGACTC 58.976 54.545 2.58 0.00 45.39 3.36
1068 1083 3.309121 CCTTTCCCTCTCTCTGAGACTCT 60.309 52.174 2.58 0.00 45.39 3.24
1069 1084 3.364460 TTCCCTCTCTCTGAGACTCTG 57.636 52.381 2.58 3.34 45.39 3.35
1070 1085 2.556766 TCCCTCTCTCTGAGACTCTGA 58.443 52.381 11.15 11.15 45.39 3.27
1080 1095 2.048127 GACTCTGACACCACCGCC 60.048 66.667 0.00 0.00 0.00 6.13
1103 1118 1.890489 TGAATCGTCTTCAACCTCGGA 59.110 47.619 1.55 0.00 0.00 4.55
1104 1119 2.297880 TGAATCGTCTTCAACCTCGGAA 59.702 45.455 1.55 0.00 0.00 4.30
1105 1120 3.056107 TGAATCGTCTTCAACCTCGGAAT 60.056 43.478 1.55 0.00 0.00 3.01
1106 1121 3.611766 ATCGTCTTCAACCTCGGAATT 57.388 42.857 0.00 0.00 0.00 2.17
1159 1174 2.509561 GCGCTCGGGGTTCTTCTC 60.510 66.667 0.00 0.00 0.00 2.87
1162 1177 1.889530 CGCTCGGGGTTCTTCTCCTT 61.890 60.000 0.00 0.00 33.68 3.36
1244 1259 1.069204 TCTCTCCGTCCATGCATAAGC 59.931 52.381 0.00 0.00 42.57 3.09
1256 1272 6.360681 GTCCATGCATAAGCGTTTTATTCATC 59.639 38.462 0.00 0.00 46.23 2.92
1332 1351 1.806542 CTTCGCCATGCCCATATGTAC 59.193 52.381 1.24 0.00 0.00 2.90
1367 1386 1.537348 CGGCTAGCGGCAACTTACATA 60.537 52.381 9.00 0.00 44.01 2.29
1368 1387 2.135933 GGCTAGCGGCAACTTACATAG 58.864 52.381 9.00 0.00 44.01 2.23
1369 1388 2.135933 GCTAGCGGCAACTTACATAGG 58.864 52.381 0.00 0.00 41.35 2.57
1370 1389 2.223971 GCTAGCGGCAACTTACATAGGA 60.224 50.000 0.00 0.00 41.35 2.94
1371 1390 2.604046 AGCGGCAACTTACATAGGAG 57.396 50.000 1.45 0.00 0.00 3.69
1372 1391 1.831736 AGCGGCAACTTACATAGGAGT 59.168 47.619 1.45 0.00 0.00 3.85
1373 1392 3.028850 AGCGGCAACTTACATAGGAGTA 58.971 45.455 1.45 0.00 0.00 2.59
1383 1402 9.790389 CAACTTACATAGGAGTACTTGACTTAG 57.210 37.037 0.00 0.00 39.06 2.18
1428 1447 8.926710 AGAGTCAACTTATATGTTCAGAAAACG 58.073 33.333 1.17 0.00 0.00 3.60
1436 1455 3.896648 TGTTCAGAAAACGGAGAATGC 57.103 42.857 0.00 0.00 0.00 3.56
1441 1460 5.084818 TCAGAAAACGGAGAATGCATAGA 57.915 39.130 0.00 0.00 0.00 1.98
1471 1490 8.567285 AGACCTGAAAATGTAGATAAAGTTGG 57.433 34.615 0.00 0.00 0.00 3.77
1474 1493 9.802039 ACCTGAAAATGTAGATAAAGTTGGTAA 57.198 29.630 0.00 0.00 0.00 2.85
1508 1548 9.047371 GGAGAGTTCTATACCTATTTTTCTTGC 57.953 37.037 0.00 0.00 0.00 4.01
1540 1580 8.934697 TGCCACCAAATCTATCTAGTATACTTT 58.065 33.333 11.40 0.00 0.00 2.66
1724 1764 4.787999 GAGGTGGTCGTCGATGTC 57.212 61.111 4.21 0.00 0.00 3.06
1784 1825 3.646736 AATCCTTAACCCCAGCTACAC 57.353 47.619 0.00 0.00 0.00 2.90
1793 1834 4.173290 ACCCCAGCTACACAAAACTTTA 57.827 40.909 0.00 0.00 0.00 1.85
1831 1883 5.060506 TGTTCTTCGAAAAACATAGAGCCA 58.939 37.500 12.91 0.00 30.73 4.75
1832 1884 5.529430 TGTTCTTCGAAAAACATAGAGCCAA 59.471 36.000 12.91 0.00 30.73 4.52
1833 1885 5.607119 TCTTCGAAAAACATAGAGCCAAC 57.393 39.130 0.00 0.00 0.00 3.77
1834 1886 5.060506 TCTTCGAAAAACATAGAGCCAACA 58.939 37.500 0.00 0.00 0.00 3.33
1835 1887 5.705441 TCTTCGAAAAACATAGAGCCAACAT 59.295 36.000 0.00 0.00 0.00 2.71
1836 1888 6.876789 TCTTCGAAAAACATAGAGCCAACATA 59.123 34.615 0.00 0.00 0.00 2.29
1837 1889 6.662414 TCGAAAAACATAGAGCCAACATAG 57.338 37.500 0.00 0.00 0.00 2.23
1838 1890 6.403049 TCGAAAAACATAGAGCCAACATAGA 58.597 36.000 0.00 0.00 0.00 1.98
1839 1891 6.535150 TCGAAAAACATAGAGCCAACATAGAG 59.465 38.462 0.00 0.00 0.00 2.43
1840 1892 6.442513 AAAAACATAGAGCCAACATAGAGC 57.557 37.500 0.00 0.00 0.00 4.09
1841 1893 3.760580 ACATAGAGCCAACATAGAGCC 57.239 47.619 0.00 0.00 0.00 4.70
1974 2027 3.499918 CCTGACAGGCAGTTTAGTTTCTG 59.500 47.826 8.99 0.00 43.33 3.02
2051 2107 2.544726 CGAAAGGGAAGGCTGTGAC 58.455 57.895 0.00 0.00 0.00 3.67
2215 2316 0.739813 CTACACTTACCGGCCACTGC 60.740 60.000 0.00 0.00 0.00 4.40
2219 2320 1.741770 CTTACCGGCCACTGCACTC 60.742 63.158 0.00 0.00 40.13 3.51
2240 2349 7.217070 GCACTCGAGAAACATTCAAACATATTC 59.783 37.037 21.68 0.00 0.00 1.75
2263 2372 2.140065 TCTGTCTTTCACGCTGTCTG 57.860 50.000 0.00 0.00 0.00 3.51
2287 2396 1.490490 TCCTCTGGCAAAGACAACTGT 59.510 47.619 0.00 0.00 0.00 3.55
2296 2405 0.108585 AAGACAACTGTGGTCGGCAT 59.891 50.000 9.58 0.00 40.20 4.40
2302 2411 1.808411 ACTGTGGTCGGCATTAAGTG 58.192 50.000 0.00 0.00 0.00 3.16
2622 2758 0.887933 GTCCCCGTCGTACTTGGTAA 59.112 55.000 0.00 0.00 0.00 2.85
2623 2759 1.478105 GTCCCCGTCGTACTTGGTAAT 59.522 52.381 0.00 0.00 0.00 1.89
2624 2760 1.750778 TCCCCGTCGTACTTGGTAATC 59.249 52.381 0.00 0.00 0.00 1.75
2625 2761 1.477700 CCCCGTCGTACTTGGTAATCA 59.522 52.381 0.00 0.00 0.00 2.57
2650 2802 5.687441 GCAGATACCATTCCTGTCCATTGTA 60.687 44.000 0.00 0.00 0.00 2.41
2658 2810 6.429078 CCATTCCTGTCCATTGTATGATAGTG 59.571 42.308 0.00 0.00 0.00 2.74
2661 2813 4.753610 CCTGTCCATTGTATGATAGTGCTG 59.246 45.833 0.00 0.00 0.00 4.41
2716 2876 1.614317 CCTGGTTGTGGATGAGGTTCC 60.614 57.143 0.00 0.00 36.24 3.62
2865 3025 4.982916 GCAAGTATGTATTACCGTCTCAGG 59.017 45.833 0.00 0.00 37.30 3.86
2867 3027 3.573110 AGTATGTATTACCGTCTCAGGCC 59.427 47.826 0.00 0.00 33.69 5.19
2883 3043 2.416547 CAGGCCGTGAATTCTGTAACTG 59.583 50.000 7.05 6.36 0.00 3.16
2896 3056 6.463995 TTCTGTAACTGCAGGTGAAATTTT 57.536 33.333 16.44 0.31 37.12 1.82
2897 3057 7.575414 TTCTGTAACTGCAGGTGAAATTTTA 57.425 32.000 16.44 0.00 37.12 1.52
2898 3058 7.759489 TCTGTAACTGCAGGTGAAATTTTAT 57.241 32.000 16.44 0.00 37.12 1.40
2900 3060 7.446931 TCTGTAACTGCAGGTGAAATTTTATGA 59.553 33.333 16.44 3.36 37.12 2.15
2907 3067 5.517770 GCAGGTGAAATTTTATGACTGATGC 59.482 40.000 12.97 7.63 0.00 3.91
2939 3099 5.937540 TGACATGATTCATTTGGTTCGTACT 59.062 36.000 0.00 0.00 0.00 2.73
3320 3480 1.671379 GCCCAACAACTCGGACTCC 60.671 63.158 0.00 0.00 0.00 3.85
3554 3714 3.993584 GCGTCCGGGGTGTACACA 61.994 66.667 26.51 3.50 0.00 3.72
3806 3966 4.147322 CGCAACACCATCGCCGTC 62.147 66.667 0.00 0.00 0.00 4.79
3856 4016 0.322187 GTCGCCAACAACCCAGGTAT 60.322 55.000 0.00 0.00 0.00 2.73
3857 4017 1.065998 GTCGCCAACAACCCAGGTATA 60.066 52.381 0.00 0.00 0.00 1.47
3859 4019 3.039743 TCGCCAACAACCCAGGTATATA 58.960 45.455 0.00 0.00 0.00 0.86
3860 4020 3.455177 TCGCCAACAACCCAGGTATATAA 59.545 43.478 0.00 0.00 0.00 0.98
3880 4064 0.687427 CCCTCCATTTCGGCCCAAAT 60.687 55.000 2.01 2.01 33.14 2.32
3881 4065 0.461135 CCTCCATTTCGGCCCAAATG 59.539 55.000 24.30 24.30 41.59 2.32
3897 4081 4.890088 CCAAATGATATGGGCCTTGATTG 58.110 43.478 4.53 1.28 34.15 2.67
3898 4082 4.589798 CCAAATGATATGGGCCTTGATTGA 59.410 41.667 4.53 0.00 34.15 2.57
3899 4083 5.247564 CCAAATGATATGGGCCTTGATTGAT 59.752 40.000 4.53 0.00 34.15 2.57
3900 4084 6.239772 CCAAATGATATGGGCCTTGATTGATT 60.240 38.462 4.53 0.00 34.15 2.57
3901 4085 7.221450 CAAATGATATGGGCCTTGATTGATTT 58.779 34.615 4.53 0.00 0.00 2.17
3902 4086 7.383156 AATGATATGGGCCTTGATTGATTTT 57.617 32.000 4.53 0.00 0.00 1.82
3904 4088 2.766345 TGGGCCTTGATTGATTTTGC 57.234 45.000 4.53 0.00 0.00 3.68
3905 4089 1.278699 TGGGCCTTGATTGATTTTGCC 59.721 47.619 4.53 0.00 36.68 4.52
3906 4090 1.643880 GGCCTTGATTGATTTTGCCG 58.356 50.000 0.00 0.00 0.00 5.69
3907 4091 1.001624 GCCTTGATTGATTTTGCCGC 58.998 50.000 0.00 0.00 0.00 6.53
3910 4094 1.657094 CTTGATTGATTTTGCCGCTGC 59.343 47.619 0.00 0.00 38.26 5.25
3912 4096 1.274596 GATTGATTTTGCCGCTGCTG 58.725 50.000 0.70 0.00 38.71 4.41
3950 4142 2.558359 GCTTGTAGGCATGTGGTTCTTT 59.442 45.455 0.00 0.00 0.00 2.52
4070 4262 1.680522 ATCTGCCCGTGTGCTAGAGG 61.681 60.000 0.00 0.00 0.00 3.69
4090 4282 4.326766 GCGCGCAAGTTTCCAGCA 62.327 61.111 29.10 0.00 41.68 4.41
4091 4283 2.562912 CGCGCAAGTTTCCAGCAT 59.437 55.556 8.75 0.00 41.68 3.79
4132 4324 7.504922 TGCGTGCAAATTTACAGAATTAATC 57.495 32.000 0.00 0.00 0.00 1.75
4209 4408 1.327292 CGTTGGTTGATTTGTCGCGC 61.327 55.000 0.00 0.00 0.00 6.86
4210 4409 1.082431 TTGGTTGATTTGTCGCGCG 60.082 52.632 26.76 26.76 0.00 6.86
4319 4523 4.179298 GTTCATTTCCTACCGAGGTGTAC 58.821 47.826 4.80 0.00 44.19 2.90
4325 4529 3.548770 TCCTACCGAGGTGTACATACTG 58.451 50.000 4.80 0.00 44.19 2.74
4346 4550 7.468922 ACTGTACACATGATGATTGAATACG 57.531 36.000 0.00 0.00 0.00 3.06
4347 4551 7.041721 ACTGTACACATGATGATTGAATACGT 58.958 34.615 0.00 0.00 0.00 3.57
4348 4552 8.194769 ACTGTACACATGATGATTGAATACGTA 58.805 33.333 0.00 0.00 0.00 3.57
4349 4553 8.347729 TGTACACATGATGATTGAATACGTAC 57.652 34.615 0.00 0.00 0.00 3.67
4350 4554 8.194769 TGTACACATGATGATTGAATACGTACT 58.805 33.333 0.00 0.00 0.00 2.73
4351 4555 7.468922 ACACATGATGATTGAATACGTACTG 57.531 36.000 0.00 0.00 0.00 2.74
4352 4556 7.041721 ACACATGATGATTGAATACGTACTGT 58.958 34.615 0.00 0.00 0.00 3.55
4353 4557 8.194769 ACACATGATGATTGAATACGTACTGTA 58.805 33.333 0.00 0.00 37.49 2.74
4354 4558 8.480066 CACATGATGATTGAATACGTACTGTAC 58.520 37.037 7.90 7.90 35.44 2.90
4355 4559 8.414003 ACATGATGATTGAATACGTACTGTACT 58.586 33.333 15.35 5.92 35.44 2.73
4356 4560 8.694394 CATGATGATTGAATACGTACTGTACTG 58.306 37.037 15.35 11.18 35.44 2.74
4357 4561 7.992008 TGATGATTGAATACGTACTGTACTGA 58.008 34.615 15.35 4.08 35.44 3.41
4358 4562 8.630037 TGATGATTGAATACGTACTGTACTGAT 58.370 33.333 15.35 6.11 35.44 2.90
4359 4563 9.119329 GATGATTGAATACGTACTGTACTGATC 57.881 37.037 15.35 8.95 35.44 2.92
4360 4564 7.130269 TGATTGAATACGTACTGTACTGATCG 58.870 38.462 15.35 11.92 35.44 3.69
4361 4565 6.667007 TTGAATACGTACTGTACTGATCGA 57.333 37.500 15.35 6.19 35.44 3.59
4362 4566 6.667007 TGAATACGTACTGTACTGATCGAA 57.333 37.500 15.35 0.00 35.44 3.71
4363 4567 6.712549 TGAATACGTACTGTACTGATCGAAG 58.287 40.000 15.35 0.81 35.44 3.79
4364 4568 6.314648 TGAATACGTACTGTACTGATCGAAGT 59.685 38.462 15.35 6.31 35.44 3.01
4365 4569 4.337985 ACGTACTGTACTGATCGAAGTG 57.662 45.455 15.35 0.00 0.00 3.16
4366 4570 3.099362 CGTACTGTACTGATCGAAGTGC 58.901 50.000 15.35 0.00 33.80 4.40
4458 4664 6.759356 CGAAATAAAAGGTTCCAACAAGGTTT 59.241 34.615 0.00 0.00 39.02 3.27
4529 4736 3.914984 GGCTGAGCACACAGACTAA 57.085 52.632 6.82 0.00 42.12 2.24
4562 4769 1.175983 CCACAACCGGCTGGCTAAAA 61.176 55.000 12.89 0.00 39.70 1.52
4877 5084 3.088532 GTGAGCCATGTCCCAAATAACA 58.911 45.455 0.00 0.00 0.00 2.41
4922 5129 8.007405 AGTAATATTAAAAGCAATGTGGACCC 57.993 34.615 0.00 0.00 0.00 4.46
4985 5192 2.167591 GTTTGATCGTCTCGTCTCGTC 58.832 52.381 0.00 0.00 0.00 4.20
4989 5196 0.108281 ATCGTCTCGTCTCGTCCTGA 60.108 55.000 0.00 0.00 0.00 3.86
5036 5244 8.271458 TCTCTTCTTTGGTGTAAATATATGCCA 58.729 33.333 0.00 0.00 0.00 4.92
5078 5286 4.707105 TCGTATCCTTCTGACGGTGTATA 58.293 43.478 0.00 0.00 37.20 1.47
5079 5287 5.125356 TCGTATCCTTCTGACGGTGTATAA 58.875 41.667 0.00 0.00 37.20 0.98
5080 5288 5.766670 TCGTATCCTTCTGACGGTGTATAAT 59.233 40.000 0.00 0.00 37.20 1.28
5081 5289 6.936335 TCGTATCCTTCTGACGGTGTATAATA 59.064 38.462 0.00 0.00 37.20 0.98
5082 5290 7.118825 TCGTATCCTTCTGACGGTGTATAATAG 59.881 40.741 0.00 0.00 37.20 1.73
5083 5291 7.118825 CGTATCCTTCTGACGGTGTATAATAGA 59.881 40.741 0.00 0.00 33.01 1.98
5084 5292 8.958506 GTATCCTTCTGACGGTGTATAATAGAT 58.041 37.037 0.00 0.00 0.00 1.98
5086 5294 8.332996 TCCTTCTGACGGTGTATAATAGATAC 57.667 38.462 0.00 0.00 0.00 2.24
5087 5295 7.392673 TCCTTCTGACGGTGTATAATAGATACC 59.607 40.741 0.00 0.00 0.00 2.73
5091 5299 7.503230 TCTGACGGTGTATAATAGATACCACAA 59.497 37.037 1.97 0.00 0.00 3.33
5105 5313 7.124573 AGATACCACAAGATTGCATACTGTA 57.875 36.000 0.00 0.00 0.00 2.74
5123 5331 3.346315 TGTAACTGATTGGAGTGCATGG 58.654 45.455 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 14 4.193865 CACATCCAGCATAAGATGACACA 58.806 43.478 6.98 0.00 42.04 3.72
174 178 1.774639 GTCGACAGCGGACAAAAGTA 58.225 50.000 11.55 0.00 38.28 2.24
176 180 1.213094 ACGTCGACAGCGGACAAAAG 61.213 55.000 17.16 0.00 38.28 2.27
203 207 2.124736 ACACATTCCGCCGGATGG 60.125 61.111 6.69 6.15 38.77 3.51
257 262 2.359975 CCAGGAGGCGGTTTGGTC 60.360 66.667 0.00 0.00 0.00 4.02
342 347 1.746991 GCACCTGAACTAGCAGCCC 60.747 63.158 0.00 0.00 34.56 5.19
375 380 2.163010 GAGGTGTAGTAGCGTACAAGCA 59.837 50.000 0.00 0.00 40.15 3.91
409 414 4.858692 CCCTCATTTGTGTCAATAAAAGCG 59.141 41.667 0.00 0.00 0.00 4.68
433 438 0.246086 CTCAGAGTGTCCCTGCTGAC 59.754 60.000 0.00 0.00 34.07 3.51
523 529 5.530519 TGTTTTCTGACGAACTATCATGC 57.469 39.130 0.00 0.00 0.00 4.06
552 558 4.142038 AGTTTTACTTTTCGGCACAGGAT 58.858 39.130 0.00 0.00 0.00 3.24
553 559 3.547746 AGTTTTACTTTTCGGCACAGGA 58.452 40.909 0.00 0.00 0.00 3.86
554 560 3.304458 GGAGTTTTACTTTTCGGCACAGG 60.304 47.826 0.00 0.00 0.00 4.00
555 561 3.564225 AGGAGTTTTACTTTTCGGCACAG 59.436 43.478 0.00 0.00 0.00 3.66
559 565 5.154222 CAATCAGGAGTTTTACTTTTCGGC 58.846 41.667 0.00 0.00 0.00 5.54
561 567 5.757886 TGCAATCAGGAGTTTTACTTTTCG 58.242 37.500 0.00 0.00 0.00 3.46
562 568 7.803079 GATGCAATCAGGAGTTTTACTTTTC 57.197 36.000 0.00 0.00 44.70 2.29
653 659 3.158676 GGCTGGTCTATATTCGAGGAGT 58.841 50.000 0.00 0.00 0.00 3.85
661 667 4.242811 TCAATCCTGGGCTGGTCTATATT 58.757 43.478 0.00 0.00 0.00 1.28
670 676 1.027357 CCGAAATCAATCCTGGGCTG 58.973 55.000 0.00 0.00 0.00 4.85
671 677 0.753111 GCCGAAATCAATCCTGGGCT 60.753 55.000 0.00 0.00 36.21 5.19
672 678 1.037030 TGCCGAAATCAATCCTGGGC 61.037 55.000 0.00 0.00 39.48 5.36
673 679 0.740737 GTGCCGAAATCAATCCTGGG 59.259 55.000 0.00 0.00 0.00 4.45
674 680 1.402968 CAGTGCCGAAATCAATCCTGG 59.597 52.381 0.00 0.00 0.00 4.45
865 877 1.944024 TCCCATTAAAATTCGCGCGAT 59.056 42.857 35.21 21.40 0.00 4.58
897 910 3.000067 TCAGTCCGACTGGCATATTTGC 61.000 50.000 25.03 0.00 45.94 3.68
898 911 2.868583 CTCAGTCCGACTGGCATATTTG 59.131 50.000 25.03 1.00 45.94 2.32
1063 1078 2.048127 GGCGGTGGTGTCAGAGTC 60.048 66.667 0.00 0.00 0.00 3.36
1064 1079 3.991051 CGGCGGTGGTGTCAGAGT 61.991 66.667 0.00 0.00 0.00 3.24
1065 1080 4.742201 CCGGCGGTGGTGTCAGAG 62.742 72.222 19.97 0.00 0.00 3.35
1080 1095 1.993370 GAGGTTGAAGACGATTCACCG 59.007 52.381 7.22 0.00 0.00 4.94
1103 1118 4.276642 GCCATGGAAGAAGAGGAAGAATT 58.723 43.478 18.40 0.00 0.00 2.17
1104 1119 3.683847 CGCCATGGAAGAAGAGGAAGAAT 60.684 47.826 18.40 0.00 0.00 2.40
1105 1120 2.355108 CGCCATGGAAGAAGAGGAAGAA 60.355 50.000 18.40 0.00 0.00 2.52
1106 1121 1.208052 CGCCATGGAAGAAGAGGAAGA 59.792 52.381 18.40 0.00 0.00 2.87
1244 1259 7.307493 TCAGATGAACTGGATGAATAAAACG 57.693 36.000 0.00 0.00 45.76 3.60
1256 1272 8.637099 TCTATCTATGAACTTCAGATGAACTGG 58.363 37.037 0.00 0.00 45.76 4.00
1332 1351 2.885676 GCCGGCGTATGTGAGCATG 61.886 63.158 12.58 0.00 36.58 4.06
1367 1386 3.764972 GCCACTCTAAGTCAAGTACTCCT 59.235 47.826 0.00 0.00 37.50 3.69
1368 1387 3.764972 AGCCACTCTAAGTCAAGTACTCC 59.235 47.826 0.00 0.00 37.50 3.85
1369 1388 6.319152 TGATAGCCACTCTAAGTCAAGTACTC 59.681 42.308 0.00 0.00 37.50 2.59
1370 1389 6.188407 TGATAGCCACTCTAAGTCAAGTACT 58.812 40.000 0.00 0.00 41.49 2.73
1371 1390 6.452494 TGATAGCCACTCTAAGTCAAGTAC 57.548 41.667 0.00 0.00 0.00 2.73
1372 1391 6.890268 TCTTGATAGCCACTCTAAGTCAAGTA 59.110 38.462 10.77 0.00 41.14 2.24
1373 1392 5.717178 TCTTGATAGCCACTCTAAGTCAAGT 59.283 40.000 10.77 0.00 41.14 3.16
1383 1402 5.669477 ACTCTGAATTCTTGATAGCCACTC 58.331 41.667 7.05 0.00 0.00 3.51
1428 1447 4.461081 AGGTCTATCGTCTATGCATTCTCC 59.539 45.833 3.54 0.00 0.00 3.71
1436 1455 8.568794 TCTACATTTTCAGGTCTATCGTCTATG 58.431 37.037 0.00 0.00 0.00 2.23
1441 1460 9.751542 CTTTATCTACATTTTCAGGTCTATCGT 57.248 33.333 0.00 0.00 0.00 3.73
1471 1490 9.577222 AGGTATAGAACTCTCCTACAGAATTAC 57.423 37.037 0.00 0.00 0.00 1.89
1513 1553 8.671987 AGTATACTAGATAGATTTGGTGGCAT 57.328 34.615 2.75 0.00 0.00 4.40
1514 1554 8.492415 AAGTATACTAGATAGATTTGGTGGCA 57.508 34.615 5.65 0.00 0.00 4.92
1515 1555 9.209175 CAAAGTATACTAGATAGATTTGGTGGC 57.791 37.037 5.65 0.00 0.00 5.01
1516 1556 9.209175 GCAAAGTATACTAGATAGATTTGGTGG 57.791 37.037 5.65 0.00 0.00 4.61
1523 1563 9.847706 CACGATTGCAAAGTATACTAGATAGAT 57.152 33.333 5.65 0.00 0.00 1.98
1784 1825 9.573133 ACAGAGTTTCAGACATTTAAAGTTTTG 57.427 29.630 0.00 0.00 0.00 2.44
1793 1834 6.049149 TCGAAGAACAGAGTTTCAGACATTT 58.951 36.000 0.00 0.00 0.00 2.32
1831 1883 2.989422 GTTGCAAACGGCTCTATGTT 57.011 45.000 0.00 0.00 45.15 2.71
1876 1928 1.205655 GAGGCTAGATGACACACAGCA 59.794 52.381 0.00 0.00 37.37 4.41
1974 2027 9.458374 GCTAAGATAGTCAGACAAACTAATCTC 57.542 37.037 2.66 0.00 33.19 2.75
2045 2101 1.359848 GTAGGGCGTCATTGTCACAG 58.640 55.000 0.00 0.00 0.00 3.66
2047 2103 0.249398 AGGTAGGGCGTCATTGTCAC 59.751 55.000 0.00 0.00 0.00 3.67
2051 2107 0.810031 CGGAAGGTAGGGCGTCATTG 60.810 60.000 0.00 0.00 0.00 2.82
2127 2183 0.176910 TTGGTCGTCTGAACACTGCA 59.823 50.000 0.00 0.00 42.84 4.41
2159 2215 5.531659 TGATCCTTTTGGCTACGTTTTGTAA 59.468 36.000 0.00 0.00 40.12 2.41
2199 2300 2.031919 TGCAGTGGCCGGTAAGTG 59.968 61.111 1.90 6.14 40.13 3.16
2215 2316 7.423598 CGAATATGTTTGAATGTTTCTCGAGTG 59.576 37.037 13.13 0.00 0.00 3.51
2219 2320 8.434870 AAACGAATATGTTTGAATGTTTCTCG 57.565 30.769 0.00 0.00 40.40 4.04
2222 2323 9.180678 ACAGAAACGAATATGTTTGAATGTTTC 57.819 29.630 6.43 6.43 41.89 2.78
2240 2349 1.593006 ACAGCGTGAAAGACAGAAACG 59.407 47.619 0.00 0.00 37.32 3.60
2263 2372 3.381590 AGTTGTCTTTGCCAGAGGAAAAC 59.618 43.478 0.00 0.00 29.34 2.43
2287 2396 1.346395 ACTGACACTTAATGCCGACCA 59.654 47.619 0.00 0.00 0.00 4.02
2296 2405 0.753867 TGCCGACCACTGACACTTAA 59.246 50.000 0.00 0.00 0.00 1.85
2383 2519 3.123620 GGCGTCAGCTTCTGCAGG 61.124 66.667 15.13 0.00 44.37 4.85
2543 2679 4.650377 GGGGCGGATGATGAGGGC 62.650 72.222 0.00 0.00 0.00 5.19
2622 2758 3.072184 GGACAGGAATGGTATCTGCTGAT 59.928 47.826 11.14 11.14 36.74 2.90
2623 2759 2.435805 GGACAGGAATGGTATCTGCTGA 59.564 50.000 0.00 0.00 32.19 4.26
2624 2760 2.171237 TGGACAGGAATGGTATCTGCTG 59.829 50.000 0.00 0.00 32.19 4.41
2625 2761 2.481441 TGGACAGGAATGGTATCTGCT 58.519 47.619 0.00 0.00 32.19 4.24
2650 2802 6.178324 CCATCCATCAATACAGCACTATCAT 58.822 40.000 0.00 0.00 0.00 2.45
2658 2810 2.553904 CCTCCCCATCCATCAATACAGC 60.554 54.545 0.00 0.00 0.00 4.40
2661 2813 3.884037 AACCTCCCCATCCATCAATAC 57.116 47.619 0.00 0.00 0.00 1.89
2716 2876 4.742201 CCACCACTCGCCTGTCCG 62.742 72.222 0.00 0.00 0.00 4.79
2865 3025 1.804151 TGCAGTTACAGAATTCACGGC 59.196 47.619 8.44 9.67 0.00 5.68
2867 3027 3.067106 ACCTGCAGTTACAGAATTCACG 58.933 45.455 13.81 0.54 40.25 4.35
2883 3043 5.517770 GCATCAGTCATAAAATTTCACCTGC 59.482 40.000 0.00 0.00 0.00 4.85
2896 3056 4.081531 TGTCACACATCAGCATCAGTCATA 60.082 41.667 0.00 0.00 0.00 2.15
2897 3057 3.268330 GTCACACATCAGCATCAGTCAT 58.732 45.455 0.00 0.00 0.00 3.06
2898 3058 2.037511 TGTCACACATCAGCATCAGTCA 59.962 45.455 0.00 0.00 0.00 3.41
2900 3060 2.845363 TGTCACACATCAGCATCAGT 57.155 45.000 0.00 0.00 0.00 3.41
2907 3067 6.033966 CCAAATGAATCATGTCACACATCAG 58.966 40.000 0.00 0.00 36.53 2.90
2939 3099 1.135489 GCCGTGAACGTCTCATCTACA 60.135 52.381 1.75 0.00 36.14 2.74
3320 3480 2.654912 GAAGTCGTTGGCCGTCGTG 61.655 63.158 16.68 0.00 37.94 4.35
3856 4016 1.422402 GGGCCGAAATGGAGGGTTATA 59.578 52.381 0.00 0.00 42.00 0.98
3857 4017 0.185175 GGGCCGAAATGGAGGGTTAT 59.815 55.000 0.00 0.00 42.00 1.89
3859 4019 2.087857 TTGGGCCGAAATGGAGGGTT 62.088 55.000 0.00 0.00 42.00 4.11
3860 4020 2.087857 TTTGGGCCGAAATGGAGGGT 62.088 55.000 9.10 0.00 42.00 4.34
3866 4050 3.916761 CCATATCATTTGGGCCGAAATG 58.083 45.455 34.99 34.99 42.40 2.32
3880 4064 5.453621 GCAAAATCAATCAAGGCCCATATCA 60.454 40.000 0.00 0.00 0.00 2.15
3881 4065 4.992951 GCAAAATCAATCAAGGCCCATATC 59.007 41.667 0.00 0.00 0.00 1.63
3897 4081 0.452987 TCATCAGCAGCGGCAAAATC 59.547 50.000 12.44 0.00 44.61 2.17
3898 4082 1.108776 ATCATCAGCAGCGGCAAAAT 58.891 45.000 12.44 0.00 44.61 1.82
3899 4083 0.889994 AATCATCAGCAGCGGCAAAA 59.110 45.000 12.44 0.00 44.61 2.44
3900 4084 0.889994 AAATCATCAGCAGCGGCAAA 59.110 45.000 12.44 0.00 44.61 3.68
3901 4085 0.171679 CAAATCATCAGCAGCGGCAA 59.828 50.000 12.44 0.00 44.61 4.52
3902 4086 1.659622 CCAAATCATCAGCAGCGGCA 61.660 55.000 12.44 0.00 44.61 5.69
3904 4088 0.099968 CACCAAATCATCAGCAGCGG 59.900 55.000 0.00 0.00 0.00 5.52
3905 4089 0.806868 ACACCAAATCATCAGCAGCG 59.193 50.000 0.00 0.00 0.00 5.18
3906 4090 2.991190 CAAACACCAAATCATCAGCAGC 59.009 45.455 0.00 0.00 0.00 5.25
3907 4091 3.581755 CCAAACACCAAATCATCAGCAG 58.418 45.455 0.00 0.00 0.00 4.24
3910 4094 2.564062 AGCCCAAACACCAAATCATCAG 59.436 45.455 0.00 0.00 0.00 2.90
3912 4096 3.244181 ACAAGCCCAAACACCAAATCATC 60.244 43.478 0.00 0.00 0.00 2.92
3950 4142 4.314440 GCGTCCAGGTGGCAGTGA 62.314 66.667 0.00 0.00 34.44 3.41
4070 4262 3.911155 CTGGAAACTTGCGCGCGTC 62.911 63.158 32.35 23.18 0.00 5.19
4075 4267 0.171903 ATCATGCTGGAAACTTGCGC 59.828 50.000 0.00 0.00 34.20 6.09
4325 4529 8.480066 CAGTACGTATTCAATCATCATGTGTAC 58.520 37.037 0.00 0.00 0.00 2.90
4337 4541 7.255491 TCGATCAGTACAGTACGTATTCAAT 57.745 36.000 5.02 0.00 31.20 2.57
4341 4545 6.484540 CACTTCGATCAGTACAGTACGTATT 58.515 40.000 5.02 0.00 31.20 1.89
4346 4550 4.092771 TGCACTTCGATCAGTACAGTAC 57.907 45.455 2.05 2.05 0.00 2.73
4347 4551 4.983671 ATGCACTTCGATCAGTACAGTA 57.016 40.909 0.00 0.00 0.00 2.74
4348 4552 3.876274 ATGCACTTCGATCAGTACAGT 57.124 42.857 0.00 0.00 0.00 3.55
4349 4553 5.536554 AAAATGCACTTCGATCAGTACAG 57.463 39.130 0.00 0.00 0.00 2.74
4350 4554 5.940192 AAAAATGCACTTCGATCAGTACA 57.060 34.783 0.00 0.00 0.00 2.90
4529 4736 2.423577 GTTGTGGCGTCTTATCTTGGT 58.576 47.619 0.00 0.00 0.00 3.67
4877 5084 3.769844 ACTCCACCGAATTCTGTCACTAT 59.230 43.478 3.52 0.00 0.00 2.12
4922 5129 3.442996 CCAGAGTACTTTGGCGGAG 57.557 57.895 18.72 0.00 0.00 4.63
4964 5171 1.172700 CGAGACGAGACGATCAAACG 58.827 55.000 0.00 0.00 39.31 3.60
4981 5188 1.037579 ATGCACTCCGATCAGGACGA 61.038 55.000 0.00 0.00 45.98 4.20
4985 5192 0.534427 ATGCATGCACTCCGATCAGG 60.534 55.000 25.37 0.00 42.97 3.86
4989 5196 1.156034 CGTCATGCATGCACTCCGAT 61.156 55.000 25.37 2.19 0.00 4.18
5036 5244 3.741344 CGAACCTCTGAAGTTCAATCGTT 59.259 43.478 16.85 8.62 43.07 3.85
5078 5286 8.213679 ACAGTATGCAATCTTGTGGTATCTATT 58.786 33.333 0.00 0.00 42.53 1.73
5079 5287 7.739825 ACAGTATGCAATCTTGTGGTATCTAT 58.260 34.615 0.00 0.00 42.53 1.98
5080 5288 7.124573 ACAGTATGCAATCTTGTGGTATCTA 57.875 36.000 0.00 0.00 42.53 1.98
5081 5289 5.994250 ACAGTATGCAATCTTGTGGTATCT 58.006 37.500 0.00 0.00 42.53 1.98
5082 5290 7.495934 AGTTACAGTATGCAATCTTGTGGTATC 59.504 37.037 0.00 0.00 42.53 2.24
5083 5291 7.280876 CAGTTACAGTATGCAATCTTGTGGTAT 59.719 37.037 0.00 0.00 42.53 2.73
5084 5292 6.593770 CAGTTACAGTATGCAATCTTGTGGTA 59.406 38.462 0.00 0.00 42.53 3.25
5085 5293 5.412594 CAGTTACAGTATGCAATCTTGTGGT 59.587 40.000 0.00 0.00 42.53 4.16
5086 5294 5.643348 TCAGTTACAGTATGCAATCTTGTGG 59.357 40.000 0.00 0.00 42.53 4.17
5087 5295 6.726258 TCAGTTACAGTATGCAATCTTGTG 57.274 37.500 0.00 0.00 42.53 3.33
5091 5299 6.653020 TCCAATCAGTTACAGTATGCAATCT 58.347 36.000 0.00 0.00 42.53 2.40
5101 5309 3.376234 CCATGCACTCCAATCAGTTACAG 59.624 47.826 0.00 0.00 0.00 2.74
5105 5313 1.180029 GCCATGCACTCCAATCAGTT 58.820 50.000 0.00 0.00 0.00 3.16
5123 5331 1.713932 GAAATTCAAAGACGCCAACGC 59.286 47.619 0.00 0.00 45.53 4.84


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

AutoCloner maintained by Alex Coulton.