Multiple sequence alignment - TraesCS5D01G203000

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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 TraesCS5D01G203000 chr5D 100.000 6671 0 0 1 6671 308231465 308224795 0.000000e+00 12320.0
1 TraesCS5D01G203000 chr5A 95.571 5125 158 32 629 5724 389713392 389718476 0.000000e+00 8142.0
2 TraesCS5D01G203000 chr5A 93.837 860 30 5 5815 6671 389718976 389719815 0.000000e+00 1273.0
3 TraesCS5D01G203000 chr5A 89.904 624 50 5 6 629 389712752 389713362 0.000000e+00 791.0
4 TraesCS5D01G203000 chr5A 82.857 105 14 4 3565 3666 365256974 365256871 2.560000e-14 91.6
5 TraesCS5D01G203000 chr5B 94.531 2304 70 16 883 3181 353040836 353038584 0.000000e+00 3506.0
6 TraesCS5D01G203000 chr5B 93.613 1503 68 13 3324 4814 353038586 353037100 0.000000e+00 2218.0
7 TraesCS5D01G203000 chr5B 89.474 1064 63 19 4845 5900 353037100 353036078 0.000000e+00 1299.0
8 TraesCS5D01G203000 chr5B 94.422 753 21 8 5932 6671 353021241 353020497 0.000000e+00 1138.0
9 TraesCS5D01G203000 chr6B 94.161 137 7 1 3179 3314 226361518 226361654 2.440000e-49 207.0
10 TraesCS5D01G203000 chr2B 94.161 137 7 1 3179 3314 608226725 608226861 2.440000e-49 207.0
11 TraesCS5D01G203000 chr2B 85.165 182 25 2 3556 3736 63837492 63837312 1.140000e-42 185.0
12 TraesCS5D01G203000 chr2B 89.474 76 8 0 668 743 653264913 653264838 5.510000e-16 97.1
13 TraesCS5D01G203000 chr6A 93.431 137 8 1 3179 3314 151467131 151466995 1.130000e-47 202.0
14 TraesCS5D01G203000 chr6A 84.663 163 22 3 3566 3726 77799171 77799010 6.920000e-35 159.0
15 TraesCS5D01G203000 chr4A 93.431 137 8 1 3179 3314 137966979 137967115 1.130000e-47 202.0
16 TraesCS5D01G203000 chr4A 93.431 137 8 1 3179 3314 137972830 137972694 1.130000e-47 202.0
17 TraesCS5D01G203000 chr3A 93.431 137 8 1 3179 3314 585500349 585500213 1.130000e-47 202.0
18 TraesCS5D01G203000 chr3A 85.714 105 15 0 3566 3670 25992064 25991960 1.970000e-20 111.0
19 TraesCS5D01G203000 chr2D 93.431 137 8 1 3179 3314 134301488 134301624 1.130000e-47 202.0
20 TraesCS5D01G203000 chr2D 85.714 182 24 2 3556 3736 37044390 37044570 2.460000e-44 191.0
21 TraesCS5D01G203000 chr1B 92.199 141 9 2 3174 3313 53067516 53067377 1.470000e-46 198.0
22 TraesCS5D01G203000 chr7D 85.256 156 15 8 3403 3557 387333756 387333608 3.220000e-33 154.0
23 TraesCS5D01G203000 chr7D 94.118 51 2 1 3442 3491 469530192 469530242 7.170000e-10 76.8
24 TraesCS5D01G203000 chr2A 89.474 76 8 0 668 743 448562431 448562356 5.510000e-16 97.1


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 TraesCS5D01G203000 chr5D 308224795 308231465 6670 True 12320 12320 100.000000 1 6671 1 chr5D.!!$R1 6670
1 TraesCS5D01G203000 chr5A 389712752 389719815 7063 False 3402 8142 93.104000 6 6671 3 chr5A.!!$F1 6665
2 TraesCS5D01G203000 chr5B 353036078 353040836 4758 True 2341 3506 92.539333 883 5900 3 chr5B.!!$R2 5017
3 TraesCS5D01G203000 chr5B 353020497 353021241 744 True 1138 1138 94.422000 5932 6671 1 chr5B.!!$R1 739

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
609 610 0.107643 GCCCTCCAAGTATGAGAGGC 59.892 60.000 0.00 0.00 40.18 4.70 F
970 1009 0.178973 TGACTCGTCTCACTTCCCCA 60.179 55.000 0.00 0.00 0.00 4.96 F
1959 2006 0.103572 GCCTGCCTACAATGCATTGG 59.896 55.000 35.85 23.24 41.96 3.16 F
2736 2783 0.516877 TGATGAAACAAGAAGCGCGG 59.483 50.000 8.83 0.00 0.00 6.46 F
3300 3351 1.067974 TCGTATGTAGTCCGCATTGGG 59.932 52.381 0.00 0.00 38.76 4.12 F
4218 4290 1.141053 ACCGCTGAAGAAGTCCTGTTT 59.859 47.619 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 1636 0.747255 GGAGGTCAGATAGCAGCGAA 59.253 55.000 0.0 0.0 0.00 4.70 R
2736 2783 0.606673 GGGAGTTCTTGGTCACTGCC 60.607 60.000 0.0 0.0 43.41 4.85 R
3521 3573 0.535797 GAGGTAGGGTCGGTTTGGAG 59.464 60.000 0.0 0.0 0.00 3.86 R
4218 4290 0.321671 CTCTGGTTCCTCAAAGGCGA 59.678 55.000 0.0 0.0 34.61 5.54 R
5148 5227 2.070783 CATGCAACAATCAACTTGGCC 58.929 47.619 0.0 0.0 39.30 5.36 R
5792 5881 0.036765 ACATGCTTGCCTGCCAAATG 60.037 50.000 0.0 0.0 31.94 2.32 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
22 23 2.638154 GATCCCGACTACGAGCCG 59.362 66.667 0.00 0.00 42.66 5.52
45 46 3.644399 GAGGGCGGACGAGGAACAC 62.644 68.421 0.00 0.00 0.00 3.32
62 63 1.400494 ACACAACGTTGAAGAACTGGC 59.600 47.619 33.66 0.00 0.00 4.85
63 64 1.670811 CACAACGTTGAAGAACTGGCT 59.329 47.619 33.66 5.05 0.00 4.75
65 66 1.670811 CAACGTTGAAGAACTGGCTGT 59.329 47.619 23.90 0.00 0.00 4.40
68 69 0.868406 GTTGAAGAACTGGCTGTCGG 59.132 55.000 0.00 0.00 0.00 4.79
114 115 2.544694 CGAGCTCAGCGACAAGGATATT 60.545 50.000 15.40 0.00 0.00 1.28
138 139 1.186267 CCCTAGACATACCTCGGGGC 61.186 65.000 0.00 0.00 35.98 5.80
156 157 3.681835 AGTCCGAGGCACGACCAC 61.682 66.667 5.74 0.00 45.77 4.16
206 207 0.178891 AAGGCCTCAAGGGAGAGACA 60.179 55.000 5.23 0.00 44.26 3.41
243 244 1.295423 GGCCGAGTTGGACTAAGCA 59.705 57.895 0.00 0.00 45.46 3.91
304 305 2.601367 CAACCAAGGCCACCCTGG 60.601 66.667 5.01 8.66 41.90 4.45
343 344 2.426522 TGAAGGAAGCCATGAAGAACG 58.573 47.619 0.00 0.00 0.00 3.95
344 345 2.224523 TGAAGGAAGCCATGAAGAACGT 60.225 45.455 0.00 0.00 0.00 3.99
346 347 0.721718 GGAAGCCATGAAGAACGTCG 59.278 55.000 0.00 0.00 0.00 5.12
347 348 1.429463 GAAGCCATGAAGAACGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
374 375 3.041940 GTCCCGTCGCACACCAAG 61.042 66.667 0.00 0.00 0.00 3.61
378 379 2.317609 CCGTCGCACACCAAGGAAG 61.318 63.158 0.00 0.00 0.00 3.46
393 394 1.017177 GGAAGAACGTGCATGCGGTA 61.017 55.000 14.09 0.00 35.98 4.02
423 424 1.815421 CGCCAGGATCAAGTTCCCG 60.815 63.158 0.00 0.00 36.35 5.14
443 444 2.336667 GGCCAAACACACATACAATGC 58.663 47.619 0.00 0.00 0.00 3.56
446 447 3.995705 GCCAAACACACATACAATGCAAT 59.004 39.130 0.00 0.00 0.00 3.56
473 474 2.479566 TCAAGAAGGTCATGGAGTGC 57.520 50.000 0.00 0.00 0.00 4.40
483 484 1.346395 TCATGGAGTGCCTAAACACGT 59.654 47.619 0.00 0.00 45.45 4.49
505 506 6.037098 CGTTCAAACTCTTGAGGGTATCTAG 58.963 44.000 2.55 0.00 42.48 2.43
507 508 4.962995 TCAAACTCTTGAGGGTATCTAGGG 59.037 45.833 2.55 0.00 36.62 3.53
545 546 4.491676 TGTACTTGCACCGTCTCTAATTC 58.508 43.478 0.00 0.00 0.00 2.17
546 547 3.963428 ACTTGCACCGTCTCTAATTCT 57.037 42.857 0.00 0.00 0.00 2.40
547 548 3.851098 ACTTGCACCGTCTCTAATTCTC 58.149 45.455 0.00 0.00 0.00 2.87
548 549 2.961526 TGCACCGTCTCTAATTCTCC 57.038 50.000 0.00 0.00 0.00 3.71
549 550 2.457598 TGCACCGTCTCTAATTCTCCT 58.542 47.619 0.00 0.00 0.00 3.69
550 551 2.166459 TGCACCGTCTCTAATTCTCCTG 59.834 50.000 0.00 0.00 0.00 3.86
551 552 2.427453 GCACCGTCTCTAATTCTCCTGA 59.573 50.000 0.00 0.00 0.00 3.86
552 553 3.068873 GCACCGTCTCTAATTCTCCTGAT 59.931 47.826 0.00 0.00 0.00 2.90
553 554 4.794655 GCACCGTCTCTAATTCTCCTGATC 60.795 50.000 0.00 0.00 0.00 2.92
554 555 4.339530 CACCGTCTCTAATTCTCCTGATCA 59.660 45.833 0.00 0.00 0.00 2.92
555 556 4.956700 ACCGTCTCTAATTCTCCTGATCAA 59.043 41.667 0.00 0.00 0.00 2.57
556 557 5.600484 ACCGTCTCTAATTCTCCTGATCAAT 59.400 40.000 0.00 0.00 0.00 2.57
557 558 6.155827 CCGTCTCTAATTCTCCTGATCAATC 58.844 44.000 0.00 0.00 0.00 2.67
560 561 7.083858 GTCTCTAATTCTCCTGATCAATCTCG 58.916 42.308 0.00 0.00 0.00 4.04
572 573 4.867047 TGATCAATCTCGAGTTCAAAGCTC 59.133 41.667 13.13 1.81 0.00 4.09
576 577 4.527509 ATCTCGAGTTCAAAGCTCTTCA 57.472 40.909 13.13 0.00 0.00 3.02
609 610 0.107643 GCCCTCCAAGTATGAGAGGC 59.892 60.000 0.00 0.00 40.18 4.70
621 622 7.122650 CCAAGTATGAGAGGCATTCCTTTTTAA 59.877 37.037 0.00 0.00 44.46 1.52
624 625 8.523658 AGTATGAGAGGCATTCCTTTTTAAAAC 58.476 33.333 0.00 0.00 44.46 2.43
645 676 8.607441 AAAACCAATTCCTTTCAAAATCTAGC 57.393 30.769 0.00 0.00 0.00 3.42
646 677 6.916360 ACCAATTCCTTTCAAAATCTAGCA 57.084 33.333 0.00 0.00 0.00 3.49
648 679 5.801947 CCAATTCCTTTCAAAATCTAGCACG 59.198 40.000 0.00 0.00 0.00 5.34
677 710 5.880341 ACTCCAACTTATAAAATCAAGCGC 58.120 37.500 0.00 0.00 0.00 5.92
689 722 2.985847 AAGCGCCACCCTTGCTTC 60.986 61.111 2.29 0.00 45.24 3.86
731 764 5.095145 AGAGTACGAAATCCTTAAACCCC 57.905 43.478 0.00 0.00 0.00 4.95
772 805 4.605183 TCTCTCCCTCTCTTCCTACAAAG 58.395 47.826 0.00 0.00 0.00 2.77
777 810 4.528596 TCCCTCTCTTCCTACAAAGACTTG 59.471 45.833 0.00 0.00 38.61 3.16
854 889 2.597903 GGTGGATGGAGCCCTTCC 59.402 66.667 15.25 15.25 44.98 3.46
857 892 1.213296 GTGGATGGAGCCCTTCCTTA 58.787 55.000 19.93 5.43 46.92 2.69
867 902 5.422012 TGGAGCCCTTCCTTATTCAAAATTC 59.578 40.000 0.00 0.00 46.92 2.17
926 964 1.585521 GTCTCACCGTCGCCGTATG 60.586 63.158 0.00 0.00 0.00 2.39
934 972 1.227176 GTCGCCGTATGGTCCTTCC 60.227 63.158 2.17 0.00 37.67 3.46
969 1008 0.528470 CTGACTCGTCTCACTTCCCC 59.472 60.000 0.00 0.00 0.00 4.81
970 1009 0.178973 TGACTCGTCTCACTTCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
971 1010 1.187087 GACTCGTCTCACTTCCCCAT 58.813 55.000 0.00 0.00 0.00 4.00
972 1011 1.550976 GACTCGTCTCACTTCCCCATT 59.449 52.381 0.00 0.00 0.00 3.16
973 1012 1.550976 ACTCGTCTCACTTCCCCATTC 59.449 52.381 0.00 0.00 0.00 2.67
974 1013 1.550524 CTCGTCTCACTTCCCCATTCA 59.449 52.381 0.00 0.00 0.00 2.57
975 1014 1.275291 TCGTCTCACTTCCCCATTCAC 59.725 52.381 0.00 0.00 0.00 3.18
976 1015 1.276421 CGTCTCACTTCCCCATTCACT 59.724 52.381 0.00 0.00 0.00 3.41
1056 1096 1.682684 GCGACCTCCTCTTCCTCCA 60.683 63.158 0.00 0.00 0.00 3.86
1092 1132 3.095332 GACCCTAACTTCCTCGGTAAGT 58.905 50.000 0.00 0.00 38.82 2.24
1562 1609 3.880846 CTGGCCAATTCGCTCGCC 61.881 66.667 7.01 0.00 41.99 5.54
1694 1741 4.545706 GATGATGCGGTCCGGGCA 62.546 66.667 14.38 7.49 45.71 5.36
1959 2006 0.103572 GCCTGCCTACAATGCATTGG 59.896 55.000 35.85 23.24 41.96 3.16
2007 2054 2.945984 CACGTGCGCAGGAACATT 59.054 55.556 34.34 10.72 0.00 2.71
2435 2482 1.668826 AGGCTGTTGAGGTATGGGAA 58.331 50.000 0.00 0.00 0.00 3.97
2610 2657 3.010420 GTTTTGAGGGATAGGCTGACAC 58.990 50.000 0.00 0.00 0.00 3.67
2726 2773 4.777896 AGTAGTAAGAGGGCTGATGAAACA 59.222 41.667 0.00 0.00 0.00 2.83
2736 2783 0.516877 TGATGAAACAAGAAGCGCGG 59.483 50.000 8.83 0.00 0.00 6.46
2758 2805 1.417890 CAGTGACCAAGAACTCCCAGT 59.582 52.381 0.00 0.00 0.00 4.00
2922 2969 9.933723 TTTAAGGTAGTAAAATGTCCAGTCTAC 57.066 33.333 0.00 0.00 0.00 2.59
3189 3239 4.270834 TCATACTATCATACTCCCTCCGC 58.729 47.826 0.00 0.00 0.00 5.54
3232 3283 8.893219 TTAGAGATTGCAATAAGGACTACATG 57.107 34.615 12.97 0.00 0.00 3.21
3271 3322 8.804688 ACATATTTTAGAGTGTAGATTCGCTC 57.195 34.615 0.00 0.00 42.95 5.03
3286 3337 3.656651 TCGCTCATTTTGCTTCGTATG 57.343 42.857 0.00 0.00 0.00 2.39
3300 3351 1.067974 TCGTATGTAGTCCGCATTGGG 59.932 52.381 0.00 0.00 38.76 4.12
3303 3354 2.550830 ATGTAGTCCGCATTGGGATC 57.449 50.000 1.69 0.00 38.61 3.36
3319 3370 5.636903 TGGGATCTCTAAAAAGATGGAGG 57.363 43.478 0.00 0.00 36.13 4.30
3326 3377 6.261435 TCTCTAAAAAGATGGAGGGAGTACA 58.739 40.000 0.00 0.00 0.00 2.90
3434 3485 7.654022 ATTAAAGGAGAGTTTGTTGGTTTCA 57.346 32.000 0.00 0.00 0.00 2.69
3518 3570 6.523840 ACCACGCGATAACCCTAATTAATTA 58.476 36.000 15.93 7.66 0.00 1.40
3521 3573 8.173130 CCACGCGATAACCCTAATTAATTATTC 58.827 37.037 15.93 0.30 0.00 1.75
3621 3674 3.662759 TTCCTTACCTTTGCCTATGGG 57.337 47.619 0.00 0.00 0.00 4.00
3629 3682 2.379005 CTTTGCCTATGGGTTCCCTTC 58.621 52.381 9.43 0.00 34.45 3.46
3909 3981 2.849942 CAGAACCCAACAGACATGACA 58.150 47.619 0.00 0.00 0.00 3.58
3980 4052 4.155280 AGGCACACCGTTCACATTAATAAC 59.845 41.667 0.00 0.00 42.76 1.89
4009 4081 7.405292 TCATCTGTCTTCTGGTGGAATAATTT 58.595 34.615 0.00 0.00 33.01 1.82
4056 4128 4.725556 TTGACGAGTTTGTACATTCTGC 57.274 40.909 0.00 0.00 0.00 4.26
4077 4149 3.998341 GCATGCATCAAATTGGAGTGTTT 59.002 39.130 14.21 0.00 0.00 2.83
4201 4273 7.626876 AAGTTTTGTACTAGTTGTTTCCAACCG 60.627 37.037 0.00 0.00 43.28 4.44
4215 4287 1.151668 CAACCGCTGAAGAAGTCCTG 58.848 55.000 0.00 0.00 0.00 3.86
4218 4290 1.141053 ACCGCTGAAGAAGTCCTGTTT 59.859 47.619 0.00 0.00 0.00 2.83
4262 4334 8.828751 AGGTGTATCCCTTTGTTTAACAGTATA 58.171 33.333 0.00 0.00 36.75 1.47
4263 4335 9.452287 GGTGTATCCCTTTGTTTAACAGTATAA 57.548 33.333 0.00 0.00 0.00 0.98
4340 4416 1.184970 TCGGTCAGATGGTGAGTGCA 61.185 55.000 0.00 0.00 35.13 4.57
4411 4487 9.979270 CACTTTACACTCATTAACTTGATGATC 57.021 33.333 0.00 0.00 33.39 2.92
4455 4531 3.381908 AGTCTATGTCCCAGAACATCGTC 59.618 47.826 0.00 0.00 40.32 4.20
4741 4817 8.807948 ATTAACAGAAGCACACCAAATATACT 57.192 30.769 0.00 0.00 0.00 2.12
4957 5033 6.645827 TGTTTAGCGCAACTTTATACTGTACA 59.354 34.615 11.47 0.00 0.00 2.90
4958 5034 7.332430 TGTTTAGCGCAACTTTATACTGTACAT 59.668 33.333 11.47 0.00 0.00 2.29
5018 5096 1.905215 AGTGCAAGGCTAGTGACAGAT 59.095 47.619 0.00 0.00 0.00 2.90
5026 5104 4.973168 AGGCTAGTGACAGATTTTTCACA 58.027 39.130 5.44 0.00 43.94 3.58
5034 5112 5.565259 GTGACAGATTTTTCACAAGCATACG 59.435 40.000 0.00 0.00 41.58 3.06
5092 5170 2.289945 ACATCAGAAGAACTCCCTGCAC 60.290 50.000 0.00 0.00 0.00 4.57
5351 5430 0.456221 ACCGACTCCGCATAACTCAG 59.544 55.000 0.00 0.00 0.00 3.35
5352 5431 0.738975 CCGACTCCGCATAACTCAGA 59.261 55.000 0.00 0.00 0.00 3.27
5423 5502 4.699735 AGTTTTCGGCATTCATGTGTATCA 59.300 37.500 0.00 0.00 0.00 2.15
5477 5563 2.686915 ACTACCGTGTGTGCTACCTATC 59.313 50.000 0.00 0.00 0.00 2.08
5641 5729 0.614697 GCAGTGGGCCTATTGGGTTT 60.615 55.000 13.56 0.00 37.43 3.27
5653 5742 3.845109 ATTGGGTTTGTTCCCCTATGT 57.155 42.857 0.00 0.00 46.48 2.29
5732 5821 4.097437 TGCATGCTGAATTTTCCTCAGATC 59.903 41.667 20.33 0.00 42.51 2.75
5749 5838 1.401552 GATCGCTAGCAAAACATGGCA 59.598 47.619 16.45 0.00 0.00 4.92
5750 5839 1.462616 TCGCTAGCAAAACATGGCAT 58.537 45.000 16.45 0.00 0.00 4.40
5769 5858 1.686355 TTGTTGCCTGATTCACCGTT 58.314 45.000 0.00 0.00 0.00 4.44
5772 5861 1.068541 GTTGCCTGATTCACCGTTTCC 60.069 52.381 0.00 0.00 0.00 3.13
5787 5876 0.878523 TTTCCGTTCGACTGTGCCAG 60.879 55.000 0.00 1.16 37.52 4.85
5789 5878 1.300620 CCGTTCGACTGTGCCAGAA 60.301 57.895 8.91 0.00 35.18 3.02
5790 5879 1.557443 CCGTTCGACTGTGCCAGAAC 61.557 60.000 8.91 3.43 39.46 3.01
5792 5881 1.070786 TTCGACTGTGCCAGAACCC 59.929 57.895 8.91 0.00 35.18 4.11
5794 5883 1.003355 CGACTGTGCCAGAACCCAT 60.003 57.895 8.91 0.00 35.18 4.00
5796 5885 1.620822 GACTGTGCCAGAACCCATTT 58.379 50.000 8.91 0.00 35.18 2.32
5797 5886 1.270550 GACTGTGCCAGAACCCATTTG 59.729 52.381 8.91 0.00 35.18 2.32
5798 5887 0.604578 CTGTGCCAGAACCCATTTGG 59.395 55.000 0.00 0.00 34.96 3.28
5802 5891 2.279842 CCAGAACCCATTTGGCAGG 58.720 57.895 0.00 0.00 37.83 4.85
5803 5892 1.593265 CAGAACCCATTTGGCAGGC 59.407 57.895 0.00 0.00 37.83 4.85
5804 5893 1.155859 AGAACCCATTTGGCAGGCA 59.844 52.632 0.00 0.00 37.83 4.75
5806 5895 0.037046 GAACCCATTTGGCAGGCAAG 60.037 55.000 9.70 0.81 37.83 4.01
5807 5896 2.115734 AACCCATTTGGCAGGCAAGC 62.116 55.000 9.70 0.00 37.83 4.01
5809 5898 1.600107 CCATTTGGCAGGCAAGCAT 59.400 52.632 9.70 0.00 35.83 3.79
5813 5902 0.469070 TTTGGCAGGCAAGCATGTTT 59.531 45.000 9.70 0.00 35.83 2.83
5817 6315 1.355971 GCAGGCAAGCATGTTTCATG 58.644 50.000 8.56 5.49 0.00 3.07
5848 6346 5.635280 CGTCACATTTATCTTGTGTCTCACT 59.365 40.000 3.98 0.00 43.86 3.41
5849 6347 6.183360 CGTCACATTTATCTTGTGTCTCACTC 60.183 42.308 3.98 0.00 43.86 3.51
5850 6348 6.870965 GTCACATTTATCTTGTGTCTCACTCT 59.129 38.462 3.98 0.00 43.86 3.24
5851 6349 7.062839 GTCACATTTATCTTGTGTCTCACTCTC 59.937 40.741 3.98 0.00 43.86 3.20
5852 6350 6.870439 CACATTTATCTTGTGTCTCACTCTCA 59.130 38.462 1.72 0.00 39.66 3.27
5853 6351 6.870965 ACATTTATCTTGTGTCTCACTCTCAC 59.129 38.462 1.72 0.00 35.11 3.51
5930 6430 2.820037 GCTGCCGCTGGTAGGTTC 60.820 66.667 12.81 0.00 35.94 3.62
6165 6677 4.379243 CTGCCACCTCCGCTTCGT 62.379 66.667 0.00 0.00 0.00 3.85
6311 6826 2.995258 GCGCGATATAATAAAACCCGGA 59.005 45.455 12.10 0.00 0.00 5.14
6523 7038 2.887568 CAGATCGTGGACAGCCGC 60.888 66.667 0.00 0.00 41.39 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.873312 CTCGTAGTCGGGATCGTCGA 60.873 60.000 0.00 0.00 40.39 4.20
1 2 1.563655 CTCGTAGTCGGGATCGTCG 59.436 63.158 1.31 1.31 40.39 5.12
2 3 1.279238 GCTCGTAGTCGGGATCGTC 59.721 63.158 0.00 0.00 40.39 4.20
3 4 2.185494 GGCTCGTAGTCGGGATCGT 61.185 63.158 0.00 0.00 40.39 3.73
4 5 2.638154 GGCTCGTAGTCGGGATCG 59.362 66.667 0.00 0.00 40.39 3.69
32 33 0.872881 AACGTTGTGTTCCTCGTCCG 60.873 55.000 0.00 0.00 35.27 4.79
33 34 0.580104 CAACGTTGTGTTCCTCGTCC 59.420 55.000 20.21 0.00 39.29 4.79
45 46 1.670811 ACAGCCAGTTCTTCAACGTTG 59.329 47.619 22.35 22.35 37.61 4.10
92 93 2.897641 ATCCTTGTCGCTGAGCTCGC 62.898 60.000 17.12 17.12 0.00 5.03
93 94 0.382158 TATCCTTGTCGCTGAGCTCG 59.618 55.000 9.64 5.21 0.00 5.03
94 95 2.810439 ATATCCTTGTCGCTGAGCTC 57.190 50.000 6.82 6.82 0.00 4.09
102 103 0.602905 GGGCCCGAATATCCTTGTCG 60.603 60.000 5.69 0.00 34.58 4.35
114 115 0.178970 GAGGTATGTCTAGGGCCCGA 60.179 60.000 18.44 11.19 0.00 5.14
138 139 3.680786 TGGTCGTGCCTCGGACTG 61.681 66.667 0.00 0.00 40.32 3.51
206 207 2.795110 GCTCTGCGCTCCAGGAGAT 61.795 63.158 21.89 0.00 42.05 2.75
224 225 1.810030 GCTTAGTCCAACTCGGCCG 60.810 63.158 22.12 22.12 33.14 6.13
234 235 4.273318 AGAATTGTTCCCATGCTTAGTCC 58.727 43.478 0.00 0.00 0.00 3.85
243 244 2.505819 AGCGACCTAGAATTGTTCCCAT 59.494 45.455 0.00 0.00 0.00 4.00
260 261 1.670949 GATGGTCTCCTGCTCAGCGA 61.671 60.000 0.00 0.00 0.00 4.93
262 263 1.145819 GGATGGTCTCCTGCTCAGC 59.854 63.158 0.00 0.00 41.29 4.26
317 318 1.562942 TCATGGCTTCCTTCATCTGCT 59.437 47.619 0.00 0.00 0.00 4.24
343 344 4.773117 GGACGGCGACTCCACGAC 62.773 72.222 16.62 0.00 38.00 4.34
362 363 0.586802 GTTCTTCCTTGGTGTGCGAC 59.413 55.000 0.00 0.00 0.00 5.19
365 366 0.307760 CACGTTCTTCCTTGGTGTGC 59.692 55.000 0.00 0.00 0.00 4.57
374 375 1.017177 TACCGCATGCACGTTCTTCC 61.017 55.000 19.57 0.00 0.00 3.46
378 379 1.708027 GACTACCGCATGCACGTTC 59.292 57.895 19.57 4.80 0.00 3.95
423 424 2.288702 TGCATTGTATGTGTGTTTGGCC 60.289 45.455 0.00 0.00 0.00 5.36
443 444 2.154462 ACCTTCTTGAACCGCTCATTG 58.846 47.619 0.00 0.00 32.78 2.82
446 447 0.756294 TGACCTTCTTGAACCGCTCA 59.244 50.000 0.00 0.00 0.00 4.26
456 457 1.366319 AGGCACTCCATGACCTTCTT 58.634 50.000 0.00 0.00 36.75 2.52
473 474 5.277345 CCTCAAGAGTTTGAACGTGTTTAGG 60.277 44.000 0.00 0.00 42.48 2.69
483 484 5.425539 CCCTAGATACCCTCAAGAGTTTGAA 59.574 44.000 0.00 0.00 42.48 2.69
507 508 4.828072 AGTACAAGAGTTTGGGAGGATC 57.172 45.455 0.00 0.00 38.66 3.36
545 546 4.645762 TGAACTCGAGATTGATCAGGAG 57.354 45.455 21.68 2.33 35.68 3.69
546 547 5.405935 TTTGAACTCGAGATTGATCAGGA 57.594 39.130 21.68 5.50 0.00 3.86
547 548 4.033817 GCTTTGAACTCGAGATTGATCAGG 59.966 45.833 21.68 11.58 0.00 3.86
548 549 4.869297 AGCTTTGAACTCGAGATTGATCAG 59.131 41.667 21.68 6.91 0.00 2.90
549 550 4.825422 AGCTTTGAACTCGAGATTGATCA 58.175 39.130 21.68 11.78 0.00 2.92
550 551 5.108517 AGAGCTTTGAACTCGAGATTGATC 58.891 41.667 21.68 10.46 39.23 2.92
551 552 5.083533 AGAGCTTTGAACTCGAGATTGAT 57.916 39.130 21.68 1.29 39.23 2.57
552 553 4.527509 AGAGCTTTGAACTCGAGATTGA 57.472 40.909 21.68 0.86 39.23 2.57
553 554 4.687948 TGAAGAGCTTTGAACTCGAGATTG 59.312 41.667 21.68 4.03 39.23 2.67
554 555 4.887748 TGAAGAGCTTTGAACTCGAGATT 58.112 39.130 21.68 9.73 39.23 2.40
555 556 4.527509 TGAAGAGCTTTGAACTCGAGAT 57.472 40.909 21.68 7.33 39.23 2.75
556 557 4.489810 GATGAAGAGCTTTGAACTCGAGA 58.510 43.478 21.68 0.00 39.23 4.04
557 558 3.616379 GGATGAAGAGCTTTGAACTCGAG 59.384 47.826 11.84 11.84 39.23 4.04
560 561 2.675348 CGGGATGAAGAGCTTTGAACTC 59.325 50.000 0.00 0.00 0.00 3.01
572 573 3.261897 AGGGCTATTATGTCGGGATGAAG 59.738 47.826 0.00 0.00 0.00 3.02
576 577 2.188817 GGAGGGCTATTATGTCGGGAT 58.811 52.381 0.00 0.00 0.00 3.85
621 622 7.657354 GTGCTAGATTTTGAAAGGAATTGGTTT 59.343 33.333 0.00 0.00 0.00 3.27
624 625 5.801947 CGTGCTAGATTTTGAAAGGAATTGG 59.198 40.000 0.00 0.00 0.00 3.16
639 670 2.100197 TGGAGTTGCTACGTGCTAGAT 58.900 47.619 0.00 0.00 43.37 1.98
644 675 1.226746 AAGTTGGAGTTGCTACGTGC 58.773 50.000 0.00 0.00 43.25 5.34
645 676 6.715344 TTTATAAGTTGGAGTTGCTACGTG 57.285 37.500 0.00 0.00 0.00 4.49
646 677 7.604927 TGATTTTATAAGTTGGAGTTGCTACGT 59.395 33.333 0.00 0.00 0.00 3.57
648 679 9.774742 CTTGATTTTATAAGTTGGAGTTGCTAC 57.225 33.333 0.00 0.00 0.00 3.58
653 686 6.322491 GCGCTTGATTTTATAAGTTGGAGTT 58.678 36.000 0.00 0.00 0.00 3.01
660 693 3.380320 GGGTGGCGCTTGATTTTATAAGT 59.620 43.478 7.64 0.00 0.00 2.24
703 736 7.983484 GGTTTAAGGATTTCGTACTCTTCCATA 59.017 37.037 0.00 0.00 0.00 2.74
731 764 0.806868 AGAAAGCATGTGTCGGCATG 59.193 50.000 0.00 1.88 46.50 4.06
813 846 1.241315 GCTAGTGGGCCGCTCAAAAA 61.241 55.000 25.40 4.35 0.00 1.94
837 872 2.597903 GGAAGGGCTCCATCCACC 59.402 66.667 9.75 0.00 44.67 4.61
857 892 9.264719 CTCTTTGTAAGGCTTTGAATTTTGAAT 57.735 29.630 4.45 0.00 0.00 2.57
902 937 1.300697 GCGACGGTGAGACAAGGTT 60.301 57.895 0.00 0.00 0.00 3.50
926 964 0.895559 CTTGGGCTTGTGGAAGGACC 60.896 60.000 0.00 0.00 39.54 4.46
934 972 1.338020 GTCAGGAAACTTGGGCTTGTG 59.662 52.381 0.00 0.00 40.21 3.33
969 1008 2.295885 GAGGGCCTGAATGAGTGAATG 58.704 52.381 12.95 0.00 0.00 2.67
970 1009 1.213926 GGAGGGCCTGAATGAGTGAAT 59.786 52.381 12.95 0.00 0.00 2.57
971 1010 0.620556 GGAGGGCCTGAATGAGTGAA 59.379 55.000 12.95 0.00 0.00 3.18
972 1011 0.252881 AGGAGGGCCTGAATGAGTGA 60.253 55.000 12.95 0.00 44.90 3.41
973 1012 2.305095 AGGAGGGCCTGAATGAGTG 58.695 57.895 12.95 0.00 44.90 3.51
974 1013 4.928981 AGGAGGGCCTGAATGAGT 57.071 55.556 12.95 0.00 44.90 3.41
1266 1307 4.388499 GGGCGAGGCGGTGAAGAA 62.388 66.667 0.00 0.00 0.00 2.52
1312 1359 3.827898 CTCGGTCGACCTCTGGGC 61.828 72.222 30.92 4.32 35.63 5.36
1314 1361 3.141488 CCCTCGGTCGACCTCTGG 61.141 72.222 30.92 26.05 0.00 3.86
1315 1362 3.827898 GCCCTCGGTCGACCTCTG 61.828 72.222 30.92 19.56 0.00 3.35
1316 1363 3.999297 GAGCCCTCGGTCGACCTCT 62.999 68.421 30.92 18.75 0.00 3.69
1317 1364 3.519930 GAGCCCTCGGTCGACCTC 61.520 72.222 30.92 17.30 0.00 3.85
1589 1636 0.747255 GGAGGTCAGATAGCAGCGAA 59.253 55.000 0.00 0.00 0.00 4.70
1598 1645 3.083997 GCCGGTGGGAGGTCAGAT 61.084 66.667 1.90 0.00 34.06 2.90
1667 1714 1.742146 CGCATCATCCGGGAGAAGA 59.258 57.895 0.00 0.79 0.00 2.87
1686 1733 1.700042 ATGGAGGAGAATGCCCGGAC 61.700 60.000 0.73 0.00 0.00 4.79
1694 1741 2.455565 CCCCGCCATGGAGGAGAAT 61.456 63.158 33.93 0.00 40.01 2.40
2007 2054 3.374988 CGGCTCTGTTGCATATCTTTCAA 59.625 43.478 0.00 0.00 34.04 2.69
2394 2441 5.823045 CCTTATCAATCCTTCCTACACCAAC 59.177 44.000 0.00 0.00 0.00 3.77
2435 2482 1.303317 GCCACGTGTTTCCATCCCT 60.303 57.895 15.65 0.00 0.00 4.20
2726 2773 4.314440 TCACTGCCCGCGCTTCTT 62.314 61.111 5.56 0.00 35.36 2.52
2736 2783 0.606673 GGGAGTTCTTGGTCACTGCC 60.607 60.000 0.00 0.00 43.41 4.85
2758 2805 4.595762 TCATTCTCATCGAGATCATGCA 57.404 40.909 0.00 0.00 38.56 3.96
2922 2969 6.926826 TGTATTAGTACAACTTCCATATGGCG 59.073 38.462 17.58 12.49 37.86 5.69
3115 3163 8.114331 AGTTCATATCAGCAAATGAGAAACAA 57.886 30.769 0.00 0.00 42.53 2.83
3216 3267 2.833794 TCCGCATGTAGTCCTTATTGC 58.166 47.619 0.00 0.00 0.00 3.56
3268 3319 5.470845 ACTACATACGAAGCAAAATGAGC 57.529 39.130 0.00 0.00 0.00 4.26
3271 3322 4.782195 GCGGACTACATACGAAGCAAAATG 60.782 45.833 0.00 0.00 0.00 2.32
3286 3337 1.689273 AGAGATCCCAATGCGGACTAC 59.311 52.381 0.00 0.00 36.56 2.73
3300 3351 6.493189 ACTCCCTCCATCTTTTTAGAGATC 57.507 41.667 0.00 0.00 34.20 2.75
3303 3354 6.546428 TGTACTCCCTCCATCTTTTTAGAG 57.454 41.667 0.00 0.00 0.00 2.43
3319 3370 4.959596 TCTTGACAGACGTATGTACTCC 57.040 45.455 17.01 4.23 32.25 3.85
3326 3377 4.456280 TGAAGCATCTTGACAGACGTAT 57.544 40.909 0.00 0.00 0.00 3.06
3434 3485 1.079323 AGGGGTGGAAGCAATGGAAAT 59.921 47.619 0.00 0.00 34.77 2.17
3518 3570 1.558294 GGTAGGGTCGGTTTGGAGAAT 59.442 52.381 0.00 0.00 0.00 2.40
3521 3573 0.535797 GAGGTAGGGTCGGTTTGGAG 59.464 60.000 0.00 0.00 0.00 3.86
3621 3674 4.200092 GAGATATGTTGTGGGAAGGGAAC 58.800 47.826 0.00 0.00 0.00 3.62
3629 3682 5.297776 GGTTGAGATTGAGATATGTTGTGGG 59.702 44.000 0.00 0.00 0.00 4.61
3820 3886 9.708222 CAGCAAATGAGTTAACAGTAATGATAC 57.292 33.333 8.61 0.00 0.00 2.24
3980 4052 4.582869 TCCACCAGAAGACAGATGAAATG 58.417 43.478 0.00 0.00 0.00 2.32
4009 4081 9.880157 AAGATAATTTAGGTCTTACGTTAAGCA 57.120 29.630 0.00 0.00 35.76 3.91
4056 4128 4.142988 GCAAACACTCCAATTTGATGCATG 60.143 41.667 2.46 0.00 37.91 4.06
4077 4149 3.825143 TCAGTGCTGCTAGAATATGCA 57.175 42.857 0.00 0.00 37.63 3.96
4201 4273 1.195674 GCGAAACAGGACTTCTTCAGC 59.804 52.381 0.00 0.00 0.00 4.26
4215 4287 1.266989 CTGGTTCCTCAAAGGCGAAAC 59.733 52.381 0.00 0.00 34.61 2.78
4218 4290 0.321671 CTCTGGTTCCTCAAAGGCGA 59.678 55.000 0.00 0.00 34.61 5.54
4411 4487 4.358851 TCAAACCTTGTTTGCTGAAATCG 58.641 39.130 13.44 0.00 0.00 3.34
4455 4531 6.459066 TCCGCAGATAAGGATATTCTTTGAG 58.541 40.000 0.40 0.00 0.00 3.02
4604 4680 6.972901 CAGCATCATAAATGCATATGACATCC 59.027 38.462 13.17 4.20 46.77 3.51
4643 4719 7.916552 AGAAACGCATAACATTGTAGAATACC 58.083 34.615 0.00 0.00 42.12 2.73
4726 4802 8.729756 TCATATATGCAAGTATATTTGGTGTGC 58.270 33.333 7.92 0.00 0.00 4.57
4771 4847 3.958018 TCCATGTTTATTGCCTAACGGT 58.042 40.909 0.00 0.00 0.00 4.83
4814 4890 9.730705 TTATAGCAGCAGCATAGATTTCTTAAT 57.269 29.630 3.17 0.00 45.49 1.40
4816 4892 9.159364 CATTATAGCAGCAGCATAGATTTCTTA 57.841 33.333 3.17 0.00 45.49 2.10
4817 4893 7.361885 GCATTATAGCAGCAGCATAGATTTCTT 60.362 37.037 3.17 0.00 45.49 2.52
5106 5184 9.757227 CAAACTGAGATGGGTTTTGTATTAAAA 57.243 29.630 0.00 0.00 34.01 1.52
5107 5185 9.137459 TCAAACTGAGATGGGTTTTGTATTAAA 57.863 29.630 0.00 0.00 34.01 1.52
5148 5227 2.070783 CATGCAACAATCAACTTGGCC 58.929 47.619 0.00 0.00 39.30 5.36
5331 5410 0.454600 TGAGTTATGCGGAGTCGGTC 59.545 55.000 0.00 0.00 36.79 4.79
5332 5411 0.456221 CTGAGTTATGCGGAGTCGGT 59.544 55.000 0.00 0.00 36.79 4.69
5351 5430 3.567478 ACCCAATCTCTTGCCTACATC 57.433 47.619 0.00 0.00 0.00 3.06
5352 5431 4.040755 ACTACCCAATCTCTTGCCTACAT 58.959 43.478 0.00 0.00 0.00 2.29
5423 5502 3.982730 TGGTCCATGGGAATACATCATCT 59.017 43.478 13.02 0.00 31.38 2.90
5641 5729 6.778069 TCACACAAAAATTACATAGGGGAACA 59.222 34.615 0.00 0.00 0.00 3.18
5732 5821 1.921887 CAATGCCATGTTTTGCTAGCG 59.078 47.619 10.77 0.00 0.00 4.26
5749 5838 1.909700 ACGGTGAATCAGGCAACAAT 58.090 45.000 0.00 0.00 41.41 2.71
5750 5839 1.686355 AACGGTGAATCAGGCAACAA 58.314 45.000 0.00 0.00 41.41 2.83
5769 5858 2.816012 TGGCACAGTCGAACGGAA 59.184 55.556 0.00 0.00 0.00 4.30
5787 5876 0.037046 CTTGCCTGCCAAATGGGTTC 60.037 55.000 0.90 0.00 39.65 3.62
5789 5878 2.586293 GCTTGCCTGCCAAATGGGT 61.586 57.895 0.90 0.00 39.65 4.51
5790 5879 1.906105 ATGCTTGCCTGCCAAATGGG 61.906 55.000 0.90 0.00 40.85 4.00
5792 5881 0.036765 ACATGCTTGCCTGCCAAATG 60.037 50.000 0.00 0.00 31.94 2.32
5794 5883 0.469070 AAACATGCTTGCCTGCCAAA 59.531 45.000 0.00 0.00 31.94 3.28
5796 5885 1.114119 TGAAACATGCTTGCCTGCCA 61.114 50.000 0.00 0.00 0.00 4.92
5797 5886 0.248289 ATGAAACATGCTTGCCTGCC 59.752 50.000 0.00 0.00 0.00 4.85
5798 5887 1.337447 ACATGAAACATGCTTGCCTGC 60.337 47.619 0.00 0.00 0.00 4.85
5800 5889 3.156293 TGTACATGAAACATGCTTGCCT 58.844 40.909 0.00 0.00 0.00 4.75
5801 5890 3.574284 TGTACATGAAACATGCTTGCC 57.426 42.857 0.00 0.00 0.00 4.52
5802 5891 3.365820 GCTTGTACATGAAACATGCTTGC 59.634 43.478 23.50 13.10 41.96 4.01
5803 5892 3.605056 CGCTTGTACATGAAACATGCTTG 59.395 43.478 25.63 15.86 42.63 4.01
5804 5893 3.253188 ACGCTTGTACATGAAACATGCTT 59.747 39.130 25.63 19.70 42.63 3.91
5806 5895 3.163594 GACGCTTGTACATGAAACATGC 58.836 45.455 22.14 22.14 41.86 4.06
5807 5896 4.151070 GTGACGCTTGTACATGAAACATG 58.849 43.478 12.65 9.72 0.00 3.21
5809 5898 3.198872 TGTGACGCTTGTACATGAAACA 58.801 40.909 12.65 0.00 0.00 2.83
5813 5902 6.106003 AGATAAATGTGACGCTTGTACATGA 58.894 36.000 12.65 0.00 35.39 3.07
5817 6315 6.165659 ACAAGATAAATGTGACGCTTGTAC 57.834 37.500 0.00 0.00 42.69 2.90
5848 6346 3.935828 CTCATACAGTCAGACTCGTGAGA 59.064 47.826 21.46 14.33 33.42 3.27
5849 6347 3.486708 GCTCATACAGTCAGACTCGTGAG 60.487 52.174 21.58 21.58 34.12 3.51
5850 6348 2.420372 GCTCATACAGTCAGACTCGTGA 59.580 50.000 0.00 4.68 0.00 4.35
5851 6349 2.789436 CGCTCATACAGTCAGACTCGTG 60.789 54.545 0.00 0.17 0.00 4.35
5852 6350 1.398739 CGCTCATACAGTCAGACTCGT 59.601 52.381 0.00 5.57 0.00 4.18
5853 6351 1.858000 GCGCTCATACAGTCAGACTCG 60.858 57.143 0.00 0.45 0.00 4.18
5881 6379 1.201414 CATGTTCGGGCAAGGGTTTAC 59.799 52.381 0.00 0.00 0.00 2.01
5882 6380 1.540267 CATGTTCGGGCAAGGGTTTA 58.460 50.000 0.00 0.00 0.00 2.01
5918 6416 2.202756 GAGCGGAACCTACCAGCG 60.203 66.667 0.00 0.00 35.71 5.18
5919 6417 2.202756 CGAGCGGAACCTACCAGC 60.203 66.667 0.00 0.00 0.00 4.85
5921 6419 3.766691 GGCGAGCGGAACCTACCA 61.767 66.667 0.00 0.00 0.00 3.25
6086 6598 3.365220 TCGTCTTTTGCGGTTTTGTTTTG 59.635 39.130 0.00 0.00 0.00 2.44
6087 6599 3.576648 TCGTCTTTTGCGGTTTTGTTTT 58.423 36.364 0.00 0.00 0.00 2.43
6088 6600 3.175929 CTCGTCTTTTGCGGTTTTGTTT 58.824 40.909 0.00 0.00 0.00 2.83
6089 6601 2.792749 CTCGTCTTTTGCGGTTTTGTT 58.207 42.857 0.00 0.00 0.00 2.83
6090 6602 1.533129 GCTCGTCTTTTGCGGTTTTGT 60.533 47.619 0.00 0.00 0.00 2.83
6290 6805 2.995258 TCCGGGTTTTATTATATCGCGC 59.005 45.455 0.00 0.00 34.19 6.86
6291 6806 4.240096 AGTCCGGGTTTTATTATATCGCG 58.760 43.478 0.00 0.00 0.00 5.87
6505 7020 2.202797 CGGCTGTCCACGATCTGG 60.203 66.667 0.00 5.18 42.29 3.86


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

AutoCloner maintained by Alex Coulton.