Multiple sequence alignment - TraesCS1B01G435800

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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 TraesCS1B01G435800 chr1B 100.000 2801 0 0 1 2801 659550304 659547504 0.000000e+00 5173.0
1 TraesCS1B01G435800 chr1B 83.607 305 39 4 2 299 659536674 659536374 2.750000e-70 276.0
2 TraesCS1B01G435800 chr1B 84.266 286 29 8 1 279 659391490 659391214 5.950000e-67 265.0
3 TraesCS1B01G435800 chr1B 82.667 300 44 4 1 299 659538764 659538472 2.770000e-65 259.0
4 TraesCS1B01G435800 chr1B 82.623 305 40 4 2 299 659394517 659394219 9.950000e-65 257.0
5 TraesCS1B01G435800 chr1B 81.818 319 43 10 4 320 659388816 659388511 1.290000e-63 254.0
6 TraesCS1B01G435800 chr1B 85.652 230 29 4 1 227 659529162 659528934 3.610000e-59 239.0
7 TraesCS1B01G435800 chr1A 91.041 2065 144 16 754 2800 568534255 568532214 0.000000e+00 2750.0
8 TraesCS1B01G435800 chr1A 87.402 381 33 9 1 368 568535354 568534976 9.270000e-115 424.0
9 TraesCS1B01G435800 chr1A 100.000 34 0 0 671 704 458510789 458510822 2.330000e-06 63.9
10 TraesCS1B01G435800 chr1D 90.964 985 76 8 870 1852 474032804 474031831 0.000000e+00 1314.0
11 TraesCS1B01G435800 chr1D 91.096 876 53 10 1841 2715 474031663 474030812 0.000000e+00 1162.0
12 TraesCS1B01G435800 chr1D 88.321 411 25 12 1 397 474033524 474033123 3.270000e-129 472.0
13 TraesCS1B01G435800 chr1D 83.219 292 41 5 2 290 474014886 474014600 7.700000e-66 261.0
14 TraesCS1B01G435800 chr5B 79.869 1530 223 45 849 2341 648307919 648306438 0.000000e+00 1040.0
15 TraesCS1B01G435800 chr5B 78.965 1526 234 50 849 2344 648266161 648264693 0.000000e+00 959.0
16 TraesCS1B01G435800 chr5D 80.264 1211 204 17 1147 2344 515639670 515638482 0.000000e+00 880.0


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 TraesCS1B01G435800 chr1B 659547504 659550304 2800 True 5173.000000 5173 100.000000 1 2801 1 chr1B.!!$R2 2800
1 TraesCS1B01G435800 chr1B 659536374 659538764 2390 True 267.500000 276 83.137000 1 299 2 chr1B.!!$R4 298
2 TraesCS1B01G435800 chr1B 659388511 659394517 6006 True 258.666667 265 82.902333 1 320 3 chr1B.!!$R3 319
3 TraesCS1B01G435800 chr1A 568532214 568535354 3140 True 1587.000000 2750 89.221500 1 2800 2 chr1A.!!$R1 2799
4 TraesCS1B01G435800 chr1D 474030812 474033524 2712 True 982.666667 1314 90.127000 1 2715 3 chr1D.!!$R2 2714
5 TraesCS1B01G435800 chr5B 648306438 648307919 1481 True 1040.000000 1040 79.869000 849 2341 1 chr5B.!!$R2 1492
6 TraesCS1B01G435800 chr5B 648264693 648266161 1468 True 959.000000 959 78.965000 849 2344 1 chr5B.!!$R1 1495
7 TraesCS1B01G435800 chr5D 515638482 515639670 1188 True 880.000000 880 80.264000 1147 2344 1 chr5D.!!$R1 1197

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
502 6955 0.103937 CCCTCGCCTCAGTTCATCTC 59.896 60.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 9182 0.110486 AGAAGGAAGAAAAGGCCGCA 59.89 50.0 0.0 0.0 0.0 5.69 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
31 3059 3.503227 GCTACTAAGATGGATCCTCCCCT 60.503 52.174 14.23 1.73 35.03 4.79
143 3173 3.713826 AAAGGCCGAGAAAGGTATGAA 57.286 42.857 0.00 0.00 0.00 2.57
145 3175 3.477210 AGGCCGAGAAAGGTATGAATC 57.523 47.619 0.00 0.00 0.00 2.52
159 3190 4.636206 GGTATGAATCGAAACAGAGCCTTT 59.364 41.667 0.00 0.00 0.00 3.11
176 3207 4.916424 AGCCTTTCCCCTCATCTTATACAT 59.084 41.667 0.00 0.00 0.00 2.29
180 3211 7.529560 GCCTTTCCCCTCATCTTATACATGTAT 60.530 40.741 21.57 21.57 0.00 2.29
195 3226 1.065928 GTATGACCGACTCCGCTGG 59.934 63.158 0.00 0.00 0.00 4.85
355 6175 2.600731 CCTGTGCACGAAACACAAAAA 58.399 42.857 13.13 0.00 46.71 1.94
398 6851 1.400494 GCGGCTGAAAAATATGGTCGT 59.600 47.619 0.00 0.00 0.00 4.34
399 6852 2.538939 GCGGCTGAAAAATATGGTCGTC 60.539 50.000 0.00 0.00 0.00 4.20
400 6853 2.936498 CGGCTGAAAAATATGGTCGTCT 59.064 45.455 0.00 0.00 0.00 4.18
401 6854 4.116961 CGGCTGAAAAATATGGTCGTCTA 58.883 43.478 0.00 0.00 0.00 2.59
402 6855 4.025979 CGGCTGAAAAATATGGTCGTCTAC 60.026 45.833 0.00 0.00 0.00 2.59
403 6856 4.025979 GGCTGAAAAATATGGTCGTCTACG 60.026 45.833 0.00 0.00 41.45 3.51
404 6857 4.565564 GCTGAAAAATATGGTCGTCTACGT 59.434 41.667 2.02 0.00 40.80 3.57
405 6858 5.063060 GCTGAAAAATATGGTCGTCTACGTT 59.937 40.000 0.00 0.00 40.80 3.99
406 6859 6.401796 GCTGAAAAATATGGTCGTCTACGTTT 60.402 38.462 0.00 0.00 40.80 3.60
407 6860 6.823531 TGAAAAATATGGTCGTCTACGTTTG 58.176 36.000 0.00 0.00 40.80 2.93
408 6861 6.424509 TGAAAAATATGGTCGTCTACGTTTGT 59.575 34.615 0.00 0.00 40.80 2.83
409 6862 6.399204 AAAATATGGTCGTCTACGTTTGTC 57.601 37.500 0.00 0.00 40.80 3.18
410 6863 4.978083 ATATGGTCGTCTACGTTTGTCT 57.022 40.909 0.00 0.00 40.80 3.41
411 6864 3.655276 ATGGTCGTCTACGTTTGTCTT 57.345 42.857 0.00 0.00 40.80 3.01
412 6865 2.734670 TGGTCGTCTACGTTTGTCTTG 58.265 47.619 0.00 0.00 40.80 3.02
413 6866 2.056577 GGTCGTCTACGTTTGTCTTGG 58.943 52.381 0.00 0.00 40.80 3.61
414 6867 2.287788 GGTCGTCTACGTTTGTCTTGGA 60.288 50.000 0.00 0.00 40.80 3.53
415 6868 3.374745 GTCGTCTACGTTTGTCTTGGAA 58.625 45.455 0.00 0.00 40.80 3.53
416 6869 3.798337 GTCGTCTACGTTTGTCTTGGAAA 59.202 43.478 0.00 0.00 40.80 3.13
417 6870 4.046462 TCGTCTACGTTTGTCTTGGAAAG 58.954 43.478 0.00 0.00 42.43 2.62
418 6871 3.183775 CGTCTACGTTTGTCTTGGAAAGG 59.816 47.826 0.00 0.00 38.46 3.11
419 6872 4.374399 GTCTACGTTTGTCTTGGAAAGGA 58.626 43.478 0.00 0.00 46.24 3.36
420 6873 4.995487 GTCTACGTTTGTCTTGGAAAGGAT 59.005 41.667 0.00 0.00 46.24 3.24
421 6874 4.994852 TCTACGTTTGTCTTGGAAAGGATG 59.005 41.667 0.00 0.00 46.24 3.51
422 6875 3.815809 ACGTTTGTCTTGGAAAGGATGA 58.184 40.909 0.00 0.00 46.24 2.92
423 6876 4.204012 ACGTTTGTCTTGGAAAGGATGAA 58.796 39.130 0.00 0.00 46.24 2.57
424 6877 4.827284 ACGTTTGTCTTGGAAAGGATGAAT 59.173 37.500 0.00 0.00 46.24 2.57
425 6878 6.001460 ACGTTTGTCTTGGAAAGGATGAATA 58.999 36.000 0.00 0.00 46.24 1.75
426 6879 6.149474 ACGTTTGTCTTGGAAAGGATGAATAG 59.851 38.462 0.00 0.00 46.24 1.73
427 6880 6.325596 GTTTGTCTTGGAAAGGATGAATAGC 58.674 40.000 0.00 0.00 46.24 2.97
428 6881 5.178096 TGTCTTGGAAAGGATGAATAGCA 57.822 39.130 0.00 0.00 46.24 3.49
429 6882 5.188434 TGTCTTGGAAAGGATGAATAGCAG 58.812 41.667 0.00 0.00 46.24 4.24
430 6883 4.578105 GTCTTGGAAAGGATGAATAGCAGG 59.422 45.833 0.00 0.00 46.24 4.85
431 6884 3.582998 TGGAAAGGATGAATAGCAGGG 57.417 47.619 0.00 0.00 0.00 4.45
432 6885 2.852449 TGGAAAGGATGAATAGCAGGGT 59.148 45.455 0.00 0.00 0.00 4.34
433 6886 3.117888 TGGAAAGGATGAATAGCAGGGTC 60.118 47.826 0.00 0.00 0.00 4.46
434 6887 2.918712 AAGGATGAATAGCAGGGTCG 57.081 50.000 0.00 0.00 0.00 4.79
435 6888 0.394565 AGGATGAATAGCAGGGTCGC 59.605 55.000 0.00 0.00 0.00 5.19
436 6889 0.106708 GGATGAATAGCAGGGTCGCA 59.893 55.000 0.00 0.00 0.00 5.10
437 6890 1.271054 GGATGAATAGCAGGGTCGCAT 60.271 52.381 0.00 0.00 0.00 4.73
438 6891 2.072298 GATGAATAGCAGGGTCGCATC 58.928 52.381 0.00 0.00 0.00 3.91
439 6892 0.829990 TGAATAGCAGGGTCGCATCA 59.170 50.000 0.00 0.00 0.00 3.07
440 6893 1.221414 GAATAGCAGGGTCGCATCAC 58.779 55.000 0.00 0.00 0.00 3.06
441 6894 0.833287 AATAGCAGGGTCGCATCACT 59.167 50.000 0.00 0.00 0.00 3.41
442 6895 0.105593 ATAGCAGGGTCGCATCACTG 59.894 55.000 3.39 3.39 41.31 3.66
443 6896 0.970427 TAGCAGGGTCGCATCACTGA 60.970 55.000 10.93 0.00 40.91 3.41
444 6897 1.153289 GCAGGGTCGCATCACTGAT 60.153 57.895 10.93 0.00 40.91 2.90
445 6898 1.156645 GCAGGGTCGCATCACTGATC 61.157 60.000 10.93 0.00 40.91 2.92
446 6899 0.531532 CAGGGTCGCATCACTGATCC 60.532 60.000 1.69 0.00 40.91 3.36
447 6900 1.592669 GGGTCGCATCACTGATCCG 60.593 63.158 0.00 0.00 0.00 4.18
448 6901 1.592669 GGTCGCATCACTGATCCGG 60.593 63.158 2.52 0.00 0.00 5.14
449 6902 1.141881 GTCGCATCACTGATCCGGT 59.858 57.895 0.00 0.00 0.00 5.28
450 6903 0.384309 GTCGCATCACTGATCCGGTA 59.616 55.000 0.00 0.00 0.00 4.02
451 6904 0.668535 TCGCATCACTGATCCGGTAG 59.331 55.000 0.00 1.08 0.00 3.18
452 6905 0.941463 CGCATCACTGATCCGGTAGC 60.941 60.000 0.00 0.00 0.00 3.58
453 6906 0.601311 GCATCACTGATCCGGTAGCC 60.601 60.000 0.00 0.00 0.00 3.93
455 6908 2.088674 ATCACTGATCCGGTAGCCGC 62.089 60.000 0.00 0.00 46.86 6.53
456 6909 2.758327 ACTGATCCGGTAGCCGCA 60.758 61.111 0.00 0.00 46.86 5.69
457 6910 2.028190 CTGATCCGGTAGCCGCAG 59.972 66.667 0.00 1.09 46.86 5.18
458 6911 4.221422 TGATCCGGTAGCCGCAGC 62.221 66.667 0.00 0.00 46.86 5.25
481 6934 3.081409 CGGGACCTCCACCGGATT 61.081 66.667 9.46 0.00 46.08 3.01
482 6935 2.666098 CGGGACCTCCACCGGATTT 61.666 63.158 9.46 0.00 46.08 2.17
483 6936 1.223763 GGGACCTCCACCGGATTTC 59.776 63.158 9.46 0.00 37.91 2.17
484 6937 1.223763 GGACCTCCACCGGATTTCC 59.776 63.158 9.46 0.56 35.64 3.13
485 6938 1.223763 GACCTCCACCGGATTTCCC 59.776 63.158 9.46 0.00 0.00 3.97
486 6939 1.229853 ACCTCCACCGGATTTCCCT 60.230 57.895 9.46 0.00 0.00 4.20
487 6940 1.272554 ACCTCCACCGGATTTCCCTC 61.273 60.000 9.46 0.00 0.00 4.30
488 6941 1.144057 CTCCACCGGATTTCCCTCG 59.856 63.158 9.46 0.00 0.00 4.63
489 6942 2.513897 CCACCGGATTTCCCTCGC 60.514 66.667 9.46 0.00 0.00 5.03
490 6943 2.513897 CACCGGATTTCCCTCGCC 60.514 66.667 9.46 0.00 0.00 5.54
491 6944 2.687566 ACCGGATTTCCCTCGCCT 60.688 61.111 9.46 0.00 0.00 5.52
492 6945 2.109181 CCGGATTTCCCTCGCCTC 59.891 66.667 0.00 0.00 0.00 4.70
493 6946 2.731571 CCGGATTTCCCTCGCCTCA 61.732 63.158 0.00 0.00 0.00 3.86
494 6947 1.227380 CGGATTTCCCTCGCCTCAG 60.227 63.158 0.00 0.00 0.00 3.35
495 6948 1.908483 GGATTTCCCTCGCCTCAGT 59.092 57.895 0.00 0.00 0.00 3.41
496 6949 0.253327 GGATTTCCCTCGCCTCAGTT 59.747 55.000 0.00 0.00 0.00 3.16
497 6950 1.657822 GATTTCCCTCGCCTCAGTTC 58.342 55.000 0.00 0.00 0.00 3.01
498 6951 0.984230 ATTTCCCTCGCCTCAGTTCA 59.016 50.000 0.00 0.00 0.00 3.18
499 6952 0.984230 TTTCCCTCGCCTCAGTTCAT 59.016 50.000 0.00 0.00 0.00 2.57
500 6953 0.537188 TTCCCTCGCCTCAGTTCATC 59.463 55.000 0.00 0.00 0.00 2.92
501 6954 0.324738 TCCCTCGCCTCAGTTCATCT 60.325 55.000 0.00 0.00 0.00 2.90
502 6955 0.103937 CCCTCGCCTCAGTTCATCTC 59.896 60.000 0.00 0.00 0.00 2.75
503 6956 1.110442 CCTCGCCTCAGTTCATCTCT 58.890 55.000 0.00 0.00 0.00 3.10
504 6957 1.066908 CCTCGCCTCAGTTCATCTCTC 59.933 57.143 0.00 0.00 0.00 3.20
505 6958 1.066908 CTCGCCTCAGTTCATCTCTCC 59.933 57.143 0.00 0.00 0.00 3.71
506 6959 0.248825 CGCCTCAGTTCATCTCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
507 6960 0.103937 GCCTCAGTTCATCTCTCCGG 59.896 60.000 0.00 0.00 0.00 5.14
508 6961 1.479709 CCTCAGTTCATCTCTCCGGT 58.520 55.000 0.00 0.00 0.00 5.28
509 6962 2.656002 CCTCAGTTCATCTCTCCGGTA 58.344 52.381 0.00 0.00 0.00 4.02
510 6963 2.359531 CCTCAGTTCATCTCTCCGGTAC 59.640 54.545 0.00 0.00 0.00 3.34
511 6964 3.017442 CTCAGTTCATCTCTCCGGTACA 58.983 50.000 0.00 0.00 0.00 2.90
512 6965 3.427573 TCAGTTCATCTCTCCGGTACAA 58.572 45.455 0.00 0.00 0.00 2.41
513 6966 3.444034 TCAGTTCATCTCTCCGGTACAAG 59.556 47.826 0.00 0.00 0.00 3.16
514 6967 3.444034 CAGTTCATCTCTCCGGTACAAGA 59.556 47.826 0.00 0.54 0.00 3.02
515 6968 3.444388 AGTTCATCTCTCCGGTACAAGAC 59.556 47.826 0.00 0.00 0.00 3.01
516 6969 2.376109 TCATCTCTCCGGTACAAGACC 58.624 52.381 0.00 0.00 45.91 3.85
546 6999 1.346538 GAGCAGCGATTCGTTGAGC 59.653 57.895 24.37 11.43 40.32 4.26
553 7006 0.924090 CGATTCGTTGAGCAGCCTAC 59.076 55.000 0.00 0.00 0.00 3.18
555 7008 1.929836 GATTCGTTGAGCAGCCTACAG 59.070 52.381 0.00 0.00 0.00 2.74
556 7009 0.966179 TTCGTTGAGCAGCCTACAGA 59.034 50.000 0.00 0.00 0.00 3.41
557 7010 0.528017 TCGTTGAGCAGCCTACAGAG 59.472 55.000 0.00 0.00 0.00 3.35
559 7012 0.107945 GTTGAGCAGCCTACAGAGGG 60.108 60.000 0.00 0.00 43.97 4.30
624 7077 1.635663 ATGGTCGCGTAAAGTGCAGC 61.636 55.000 5.77 0.00 0.00 5.25
669 7122 3.589881 GGTCGCATGGCATCAGGC 61.590 66.667 0.00 0.00 46.03 4.85
716 7169 3.740397 CGCCGTGGACGTGGAGTA 61.740 66.667 0.00 0.00 37.74 2.59
717 7170 2.181021 GCCGTGGACGTGGAGTAG 59.819 66.667 0.00 0.00 37.74 2.57
718 7171 2.338015 GCCGTGGACGTGGAGTAGA 61.338 63.158 0.00 0.00 37.74 2.59
719 7172 1.505353 CCGTGGACGTGGAGTAGAC 59.495 63.158 0.00 0.00 37.74 2.59
720 7173 0.959372 CCGTGGACGTGGAGTAGACT 60.959 60.000 0.00 0.00 37.74 3.24
726 7179 2.677337 GGACGTGGAGTAGACTGTAGAC 59.323 54.545 0.00 0.00 0.00 2.59
736 7189 2.879462 CTGTAGACGCCGAACCGC 60.879 66.667 0.00 0.00 0.00 5.68
794 7296 2.640346 GTCCGTCTCAAGACCTCTTC 57.360 55.000 4.63 0.00 41.86 2.87
829 7331 0.596082 CACAACGCGATCCCCTTTTT 59.404 50.000 15.93 0.00 0.00 1.94
920 7428 2.507102 CACGGCTCAGTACGGCAG 60.507 66.667 9.82 8.37 0.00 4.85
927 7435 2.125512 CAGTACGGCAGCACCTCC 60.126 66.667 0.00 0.00 35.61 4.30
940 7448 1.684734 ACCTCCTCGTTATGGCCGT 60.685 57.895 1.35 1.35 0.00 5.68
1050 7567 2.095469 GACGACGACGACGAGGAC 59.905 66.667 25.15 10.08 42.66 3.85
1051 7568 3.676924 GACGACGACGACGAGGACG 62.677 68.421 25.15 14.84 42.66 4.79
1223 7740 1.657794 GCTTCGACGGCTCGGATAC 60.658 63.158 0.00 0.00 40.58 2.24
1364 7897 2.434185 TGGTGAATCGCGGCTCAC 60.434 61.111 24.50 24.50 41.05 3.51
1413 7946 2.617274 GCTGAAACTGTGGGGCGAC 61.617 63.158 0.00 0.00 0.00 5.19
1517 8053 3.699067 CCAAGTTCTGTGTTTCAGCAAG 58.301 45.455 0.00 0.00 43.32 4.01
1536 8076 1.282157 AGGAACAGTGTTATGGGAGCC 59.718 52.381 8.88 4.00 0.00 4.70
1587 8133 1.000955 ACCGATGGCTCCGATGATAAC 59.999 52.381 0.98 0.00 0.00 1.89
1599 8145 0.179056 ATGATAACGTTGCCGAGGGG 60.179 55.000 11.99 0.00 37.88 4.79
1636 8182 2.910205 CTGCCGATCCAGCATACAG 58.090 57.895 5.60 0.00 40.04 2.74
1694 8240 1.211703 TGCCACCATCATATCCAACGT 59.788 47.619 0.00 0.00 0.00 3.99
1755 8301 2.348666 GTCGTACAAGCCATGTCATGAC 59.651 50.000 19.27 19.27 42.70 3.06
1756 8302 1.324435 CGTACAAGCCATGTCATGACG 59.676 52.381 20.54 10.70 42.70 4.35
1757 8303 2.616960 GTACAAGCCATGTCATGACGA 58.383 47.619 20.54 10.47 42.70 4.20
1788 8337 6.931838 AGAAACAAGACCACGTAGAATCATA 58.068 36.000 0.00 0.00 0.00 2.15
1789 8338 6.812160 AGAAACAAGACCACGTAGAATCATAC 59.188 38.462 0.00 0.00 0.00 2.39
1798 8347 6.183360 ACCACGTAGAATCATACATTACAGCT 60.183 38.462 0.00 0.00 0.00 4.24
1839 8388 1.961180 CTCGGGATTCCTCGCCAAGT 61.961 60.000 2.01 0.00 0.00 3.16
1936 8666 1.355971 CCGTGACGATGGTACCTTTG 58.644 55.000 14.36 13.31 0.00 2.77
2064 8794 4.517815 CGCCTAGCCGCCCGTAAA 62.518 66.667 0.00 0.00 0.00 2.01
2151 8882 0.681733 ACTTCATCGTGTGTGAGCCT 59.318 50.000 0.00 0.00 0.00 4.58
2276 9007 1.064906 AGATGCAGACATGGTTCAGGG 60.065 52.381 0.00 0.00 36.35 4.45
2283 9014 1.073923 GACATGGTTCAGGGACAGGTT 59.926 52.381 0.00 0.00 0.00 3.50
2429 9160 1.545582 TCTTGCTATTGTTGGCTTGGC 59.454 47.619 0.00 0.00 0.00 4.52
2451 9182 2.534990 ACTGAGCTAGCTTCCTCTGTT 58.465 47.619 20.42 0.00 37.06 3.16
2452 9183 2.233431 ACTGAGCTAGCTTCCTCTGTTG 59.767 50.000 20.42 4.32 37.06 3.33
2467 9198 0.467290 TGTTGCGGCCTTTTCTTCCT 60.467 50.000 0.00 0.00 0.00 3.36
2493 9224 7.305474 TCTCCATTCTAAATTTGTTTCGCTTC 58.695 34.615 0.00 0.00 0.00 3.86
2521 9252 7.255242 GCAGGTATTAGTTTGCATGTCACATAT 60.255 37.037 0.00 0.00 36.59 1.78
2522 9253 9.271828 CAGGTATTAGTTTGCATGTCACATATA 57.728 33.333 0.00 0.00 0.00 0.86
2543 9274 6.823678 ATATAATTGTGTTCGTCGACCTTC 57.176 37.500 10.58 0.77 0.00 3.46
2609 9342 1.002134 CCCTGAGGTGATTGCCGTT 60.002 57.895 0.00 0.00 0.00 4.44
2610 9343 0.251916 CCCTGAGGTGATTGCCGTTA 59.748 55.000 0.00 0.00 0.00 3.18
2611 9344 1.369625 CCTGAGGTGATTGCCGTTAC 58.630 55.000 0.00 0.00 0.00 2.50
2612 9345 0.999406 CTGAGGTGATTGCCGTTACG 59.001 55.000 0.00 0.00 0.00 3.18
2693 9426 9.403583 GGGTAAGGATGTAAGTGAATAATTTGA 57.596 33.333 0.00 0.00 0.00 2.69
2718 9451 4.859629 AAAAATCGACATCTTACCGCTC 57.140 40.909 0.00 0.00 0.00 5.03
2724 9457 1.084370 ACATCTTACCGCTCGCAAGC 61.084 55.000 0.00 0.00 45.56 4.01
2770 9503 4.573900 ACACAGGAGATTTTGCTAGTCTG 58.426 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 3173 1.340114 GGGGAAAGGCTCTGTTTCGAT 60.340 52.381 0.00 0.00 35.16 3.59
145 3175 0.036875 AGGGGAAAGGCTCTGTTTCG 59.963 55.000 0.00 0.00 35.16 3.46
159 3190 6.440647 GGTCATACATGTATAAGATGAGGGGA 59.559 42.308 17.86 4.79 0.00 4.81
176 3207 1.663379 CCAGCGGAGTCGGTCATACA 61.663 60.000 0.00 0.00 46.01 2.29
195 3226 2.431260 CACACCGCTTGCATTGCC 60.431 61.111 6.12 0.00 0.00 4.52
199 3230 1.836999 TAGTCCCACACCGCTTGCAT 61.837 55.000 0.00 0.00 0.00 3.96
355 6175 2.039418 GAACAACCCCAGAAAGGCTTT 58.961 47.619 13.25 13.25 35.39 3.51
398 6851 4.675976 TCCTTTCCAAGACAAACGTAGA 57.324 40.909 0.00 0.00 0.00 2.59
399 6852 4.994852 TCATCCTTTCCAAGACAAACGTAG 59.005 41.667 0.00 0.00 0.00 3.51
400 6853 4.963373 TCATCCTTTCCAAGACAAACGTA 58.037 39.130 0.00 0.00 0.00 3.57
401 6854 3.815809 TCATCCTTTCCAAGACAAACGT 58.184 40.909 0.00 0.00 0.00 3.99
402 6855 4.829064 TTCATCCTTTCCAAGACAAACG 57.171 40.909 0.00 0.00 0.00 3.60
403 6856 6.071952 TGCTATTCATCCTTTCCAAGACAAAC 60.072 38.462 0.00 0.00 0.00 2.93
404 6857 6.009589 TGCTATTCATCCTTTCCAAGACAAA 58.990 36.000 0.00 0.00 0.00 2.83
405 6858 5.569355 TGCTATTCATCCTTTCCAAGACAA 58.431 37.500 0.00 0.00 0.00 3.18
406 6859 5.178096 TGCTATTCATCCTTTCCAAGACA 57.822 39.130 0.00 0.00 0.00 3.41
407 6860 4.578105 CCTGCTATTCATCCTTTCCAAGAC 59.422 45.833 0.00 0.00 0.00 3.01
408 6861 4.385643 CCCTGCTATTCATCCTTTCCAAGA 60.386 45.833 0.00 0.00 0.00 3.02
409 6862 3.887716 CCCTGCTATTCATCCTTTCCAAG 59.112 47.826 0.00 0.00 0.00 3.61
410 6863 3.269381 ACCCTGCTATTCATCCTTTCCAA 59.731 43.478 0.00 0.00 0.00 3.53
411 6864 2.852449 ACCCTGCTATTCATCCTTTCCA 59.148 45.455 0.00 0.00 0.00 3.53
412 6865 3.481453 GACCCTGCTATTCATCCTTTCC 58.519 50.000 0.00 0.00 0.00 3.13
413 6866 3.134458 CGACCCTGCTATTCATCCTTTC 58.866 50.000 0.00 0.00 0.00 2.62
414 6867 2.746472 GCGACCCTGCTATTCATCCTTT 60.746 50.000 0.00 0.00 0.00 3.11
415 6868 1.202698 GCGACCCTGCTATTCATCCTT 60.203 52.381 0.00 0.00 0.00 3.36
416 6869 0.394565 GCGACCCTGCTATTCATCCT 59.605 55.000 0.00 0.00 0.00 3.24
417 6870 0.106708 TGCGACCCTGCTATTCATCC 59.893 55.000 0.00 0.00 35.36 3.51
418 6871 2.072298 GATGCGACCCTGCTATTCATC 58.928 52.381 0.00 0.00 35.36 2.92
419 6872 1.417517 TGATGCGACCCTGCTATTCAT 59.582 47.619 0.00 0.00 35.36 2.57
420 6873 0.829990 TGATGCGACCCTGCTATTCA 59.170 50.000 0.00 0.00 35.36 2.57
421 6874 1.202580 AGTGATGCGACCCTGCTATTC 60.203 52.381 0.00 0.00 35.36 1.75
422 6875 0.833287 AGTGATGCGACCCTGCTATT 59.167 50.000 0.00 0.00 35.36 1.73
423 6876 0.105593 CAGTGATGCGACCCTGCTAT 59.894 55.000 0.00 0.00 35.36 2.97
424 6877 0.970427 TCAGTGATGCGACCCTGCTA 60.970 55.000 0.00 0.00 35.36 3.49
425 6878 1.620739 ATCAGTGATGCGACCCTGCT 61.621 55.000 4.39 0.00 35.36 4.24
426 6879 1.153289 ATCAGTGATGCGACCCTGC 60.153 57.895 4.39 0.00 0.00 4.85
427 6880 0.531532 GGATCAGTGATGCGACCCTG 60.532 60.000 11.20 0.00 0.00 4.45
428 6881 1.826024 GGATCAGTGATGCGACCCT 59.174 57.895 11.20 0.00 0.00 4.34
429 6882 4.445699 GGATCAGTGATGCGACCC 57.554 61.111 11.20 0.79 0.00 4.46
434 6887 0.601311 GGCTACCGGATCAGTGATGC 60.601 60.000 11.20 12.91 0.00 3.91
435 6888 0.319040 CGGCTACCGGATCAGTGATG 60.319 60.000 11.20 0.00 44.15 3.07
436 6889 2.041976 CGGCTACCGGATCAGTGAT 58.958 57.895 9.46 4.98 44.15 3.06
437 6890 3.521605 CGGCTACCGGATCAGTGA 58.478 61.111 9.46 0.00 44.15 3.41
464 6917 2.588856 GAAATCCGGTGGAGGTCCCG 62.589 65.000 0.00 0.00 43.82 5.14
465 6918 1.223763 GAAATCCGGTGGAGGTCCC 59.776 63.158 0.00 0.00 34.05 4.46
466 6919 1.223763 GGAAATCCGGTGGAGGTCC 59.776 63.158 0.00 0.00 34.05 4.46
467 6920 1.223763 GGGAAATCCGGTGGAGGTC 59.776 63.158 0.00 0.00 34.05 3.85
468 6921 1.229853 AGGGAAATCCGGTGGAGGT 60.230 57.895 0.00 0.00 41.52 3.85
469 6922 1.527370 GAGGGAAATCCGGTGGAGG 59.473 63.158 0.00 0.00 41.52 4.30
470 6923 1.144057 CGAGGGAAATCCGGTGGAG 59.856 63.158 0.00 0.00 41.52 3.86
471 6924 3.026431 GCGAGGGAAATCCGGTGGA 62.026 63.158 0.00 0.00 41.52 4.02
472 6925 2.513897 GCGAGGGAAATCCGGTGG 60.514 66.667 0.00 0.00 41.52 4.61
473 6926 2.513897 GGCGAGGGAAATCCGGTG 60.514 66.667 0.00 0.00 41.52 4.94
474 6927 2.687566 AGGCGAGGGAAATCCGGT 60.688 61.111 0.00 0.00 41.52 5.28
475 6928 2.109181 GAGGCGAGGGAAATCCGG 59.891 66.667 0.00 0.00 41.52 5.14
476 6929 1.227380 CTGAGGCGAGGGAAATCCG 60.227 63.158 0.00 0.00 41.52 4.18
477 6930 0.253327 AACTGAGGCGAGGGAAATCC 59.747 55.000 0.00 0.00 0.00 3.01
478 6931 1.066143 TGAACTGAGGCGAGGGAAATC 60.066 52.381 0.00 0.00 0.00 2.17
479 6932 0.984230 TGAACTGAGGCGAGGGAAAT 59.016 50.000 0.00 0.00 0.00 2.17
480 6933 0.984230 ATGAACTGAGGCGAGGGAAA 59.016 50.000 0.00 0.00 0.00 3.13
481 6934 0.537188 GATGAACTGAGGCGAGGGAA 59.463 55.000 0.00 0.00 0.00 3.97
482 6935 0.324738 AGATGAACTGAGGCGAGGGA 60.325 55.000 0.00 0.00 0.00 4.20
483 6936 0.103937 GAGATGAACTGAGGCGAGGG 59.896 60.000 0.00 0.00 0.00 4.30
484 6937 1.066908 GAGAGATGAACTGAGGCGAGG 59.933 57.143 0.00 0.00 0.00 4.63
485 6938 1.066908 GGAGAGATGAACTGAGGCGAG 59.933 57.143 0.00 0.00 0.00 5.03
486 6939 1.107114 GGAGAGATGAACTGAGGCGA 58.893 55.000 0.00 0.00 0.00 5.54
487 6940 0.248825 CGGAGAGATGAACTGAGGCG 60.249 60.000 0.00 0.00 0.00 5.52
488 6941 0.103937 CCGGAGAGATGAACTGAGGC 59.896 60.000 0.00 0.00 0.00 4.70
489 6942 1.479709 ACCGGAGAGATGAACTGAGG 58.520 55.000 9.46 0.00 0.00 3.86
490 6943 3.017442 TGTACCGGAGAGATGAACTGAG 58.983 50.000 9.46 0.00 0.00 3.35
491 6944 3.081710 TGTACCGGAGAGATGAACTGA 57.918 47.619 9.46 0.00 0.00 3.41
492 6945 3.444034 TCTTGTACCGGAGAGATGAACTG 59.556 47.826 9.46 0.00 0.00 3.16
493 6946 3.444388 GTCTTGTACCGGAGAGATGAACT 59.556 47.826 9.46 0.00 0.00 3.01
494 6947 3.429135 GGTCTTGTACCGGAGAGATGAAC 60.429 52.174 9.46 0.74 38.88 3.18
495 6948 2.758979 GGTCTTGTACCGGAGAGATGAA 59.241 50.000 9.46 0.00 38.88 2.57
496 6949 2.376109 GGTCTTGTACCGGAGAGATGA 58.624 52.381 9.46 0.00 38.88 2.92
497 6950 2.873133 GGTCTTGTACCGGAGAGATG 57.127 55.000 9.46 0.00 38.88 2.90
506 6959 1.218316 CTCCCTGCGGTCTTGTACC 59.782 63.158 0.00 0.00 45.77 3.34
507 6960 1.448013 GCTCCCTGCGGTCTTGTAC 60.448 63.158 0.00 0.00 0.00 2.90
508 6961 1.888436 CTGCTCCCTGCGGTCTTGTA 61.888 60.000 0.00 0.00 46.63 2.41
509 6962 3.241530 TGCTCCCTGCGGTCTTGT 61.242 61.111 0.00 0.00 46.63 3.16
510 6963 2.435586 CTGCTCCCTGCGGTCTTG 60.436 66.667 0.00 0.00 46.63 3.02
511 6964 3.710722 CCTGCTCCCTGCGGTCTT 61.711 66.667 0.00 0.00 46.27 3.01
512 6965 4.704103 TCCTGCTCCCTGCGGTCT 62.704 66.667 0.00 0.00 46.27 3.85
513 6966 4.154347 CTCCTGCTCCCTGCGGTC 62.154 72.222 0.00 0.00 46.27 4.79
516 6969 4.834453 CTGCTCCTGCTCCCTGCG 62.834 72.222 0.00 0.00 46.63 5.18
518 6971 4.834453 CGCTGCTCCTGCTCCCTG 62.834 72.222 0.00 0.00 40.48 4.45
520 6973 3.397613 AATCGCTGCTCCTGCTCCC 62.398 63.158 0.00 0.00 40.48 4.30
521 6974 1.886777 GAATCGCTGCTCCTGCTCC 60.887 63.158 0.00 0.00 40.48 4.70
522 6975 2.236382 CGAATCGCTGCTCCTGCTC 61.236 63.158 0.00 0.00 40.48 4.26
523 6976 2.202851 CGAATCGCTGCTCCTGCT 60.203 61.111 0.00 0.00 40.48 4.24
524 6977 2.103042 AACGAATCGCTGCTCCTGC 61.103 57.895 1.15 0.00 40.20 4.85
525 6978 0.737367 TCAACGAATCGCTGCTCCTG 60.737 55.000 1.15 0.00 0.00 3.86
526 6979 0.459237 CTCAACGAATCGCTGCTCCT 60.459 55.000 1.15 0.00 0.00 3.69
536 6989 1.550524 TCTGTAGGCTGCTCAACGAAT 59.449 47.619 3.77 0.00 0.00 3.34
559 7012 2.127869 CATCATCATCACGCGCGC 60.128 61.111 32.58 23.91 0.00 6.86
560 7013 2.127869 GCATCATCATCACGCGCG 60.128 61.111 30.96 30.96 0.00 6.86
562 7015 1.568025 CCAGCATCATCATCACGCG 59.432 57.895 3.53 3.53 0.00 6.01
570 7023 2.114838 GGGAGGGCCAGCATCATC 59.885 66.667 6.18 0.00 35.15 2.92
637 7090 3.941657 GACCAGTCCGACTGCCAGC 62.942 68.421 21.26 7.51 44.63 4.85
638 7091 2.262915 GACCAGTCCGACTGCCAG 59.737 66.667 21.26 11.48 44.63 4.85
639 7092 3.680786 CGACCAGTCCGACTGCCA 61.681 66.667 21.26 0.00 44.63 4.92
641 7094 3.649277 ATGCGACCAGTCCGACTGC 62.649 63.158 21.26 11.59 44.63 4.40
642 7095 1.807165 CATGCGACCAGTCCGACTG 60.807 63.158 19.97 19.97 45.53 3.51
643 7096 2.573869 CATGCGACCAGTCCGACT 59.426 61.111 0.00 0.00 0.00 4.18
644 7097 2.509336 CCATGCGACCAGTCCGAC 60.509 66.667 0.00 0.00 0.00 4.79
645 7098 4.451150 GCCATGCGACCAGTCCGA 62.451 66.667 0.00 0.00 0.00 4.55
646 7099 4.758251 TGCCATGCGACCAGTCCG 62.758 66.667 0.00 0.00 0.00 4.79
647 7100 2.124570 ATGCCATGCGACCAGTCC 60.125 61.111 0.00 0.00 0.00 3.85
648 7101 1.434622 CTGATGCCATGCGACCAGTC 61.435 60.000 0.00 0.00 0.00 3.51
649 7102 1.450848 CTGATGCCATGCGACCAGT 60.451 57.895 0.00 0.00 0.00 4.00
650 7103 2.184830 CCTGATGCCATGCGACCAG 61.185 63.158 0.00 0.00 0.00 4.00
680 7133 4.778143 CCTCAACTTCCCGGGCCG 62.778 72.222 21.46 21.46 0.00 6.13
708 7161 1.062294 GCGTCTACAGTCTACTCCACG 59.938 57.143 0.00 0.00 0.00 4.94
709 7162 1.401199 GGCGTCTACAGTCTACTCCAC 59.599 57.143 0.00 0.00 0.00 4.02
710 7163 1.747709 GGCGTCTACAGTCTACTCCA 58.252 55.000 0.00 0.00 0.00 3.86
711 7164 0.656785 CGGCGTCTACAGTCTACTCC 59.343 60.000 0.00 0.00 0.00 3.85
712 7165 1.649664 TCGGCGTCTACAGTCTACTC 58.350 55.000 6.85 0.00 0.00 2.59
713 7166 1.736681 GTTCGGCGTCTACAGTCTACT 59.263 52.381 6.85 0.00 0.00 2.57
714 7167 1.202121 GGTTCGGCGTCTACAGTCTAC 60.202 57.143 6.85 0.00 0.00 2.59
715 7168 1.089920 GGTTCGGCGTCTACAGTCTA 58.910 55.000 6.85 0.00 0.00 2.59
716 7169 1.881602 GGTTCGGCGTCTACAGTCT 59.118 57.895 6.85 0.00 0.00 3.24
717 7170 1.513586 CGGTTCGGCGTCTACAGTC 60.514 63.158 6.85 0.00 0.00 3.51
718 7171 2.564975 CGGTTCGGCGTCTACAGT 59.435 61.111 6.85 0.00 0.00 3.55
719 7172 2.879462 GCGGTTCGGCGTCTACAG 60.879 66.667 6.85 6.10 0.00 2.74
794 7296 4.151335 GCGTTGTGGCTTATATGAGATGAG 59.849 45.833 0.00 0.00 0.00 2.90
905 7411 4.435436 TGCTGCCGTACTGAGCCG 62.435 66.667 0.00 0.00 31.31 5.52
920 7428 1.523938 GGCCATAACGAGGAGGTGC 60.524 63.158 0.00 0.00 0.00 5.01
927 7435 2.589798 TAAGGAACGGCCATAACGAG 57.410 50.000 2.24 0.00 40.02 4.18
940 7448 1.422402 GGTGGTGGACAGGTTAAGGAA 59.578 52.381 0.00 0.00 0.00 3.36
1067 7584 3.755628 CCGCTTCGTCCGGGAAGA 61.756 66.667 20.73 8.67 44.93 2.87
1154 7671 3.412408 GGGAGAAGGTGGGAGGGC 61.412 72.222 0.00 0.00 0.00 5.19
1384 7917 3.436704 CACAGTTTCAGCACAATCGGTAT 59.563 43.478 0.00 0.00 0.00 2.73
1389 7922 1.270550 CCCCACAGTTTCAGCACAATC 59.729 52.381 0.00 0.00 0.00 2.67
1413 7946 2.221749 CCAGCGATCCATTGTTGTATCG 59.778 50.000 0.00 0.00 43.05 2.92
1517 8053 1.751437 GGCTCCCATAACACTGTTCC 58.249 55.000 0.00 0.00 0.00 3.62
1599 8145 1.205893 AGCGTCAGAATCTCCCACTTC 59.794 52.381 0.00 0.00 0.00 3.01
1636 8182 0.612453 AGGTCGGTGAACTCCTCCTC 60.612 60.000 0.00 0.00 0.00 3.71
1694 8240 0.904649 ATCAACCCAGATCACGCAGA 59.095 50.000 0.00 0.00 0.00 4.26
1737 8283 2.616960 TCGTCATGACATGGCTTGTAC 58.383 47.619 24.93 9.76 39.18 2.90
1755 8301 3.123621 GTGGTCTTGTTTCTAGTGCATCG 59.876 47.826 0.00 0.00 0.00 3.84
1756 8302 3.123621 CGTGGTCTTGTTTCTAGTGCATC 59.876 47.826 0.00 0.00 0.00 3.91
1757 8303 3.067106 CGTGGTCTTGTTTCTAGTGCAT 58.933 45.455 0.00 0.00 0.00 3.96
1788 8337 3.452264 TGATAGGCAGTCAGCTGTAATGT 59.548 43.478 14.67 0.00 44.32 2.71
1789 8338 4.063998 TGATAGGCAGTCAGCTGTAATG 57.936 45.455 14.67 11.87 44.32 1.90
1798 8347 3.521560 GACGATTGTTGATAGGCAGTCA 58.478 45.455 0.00 0.00 0.00 3.41
1936 8666 0.393808 TAAGGATCAAGCGGCCCAAC 60.394 55.000 0.00 0.00 0.00 3.77
2064 8794 2.880890 ACAGTTGTACGGTAGAAGACGT 59.119 45.455 0.00 0.00 46.17 4.34
2151 8882 3.788227 AGCTTGTCAACATTGTCCCTA 57.212 42.857 0.00 0.00 0.00 3.53
2271 9002 1.343465 GAAGACGAAACCTGTCCCTGA 59.657 52.381 0.00 0.00 37.04 3.86
2276 9007 1.795286 CTGCAGAAGACGAAACCTGTC 59.205 52.381 8.42 0.00 36.60 3.51
2283 9014 2.365617 AGAAAGGACTGCAGAAGACGAA 59.634 45.455 23.35 0.00 0.00 3.85
2392 9123 6.485830 AGCAAGAGCCAGTATGAAGTAATA 57.514 37.500 0.00 0.00 43.56 0.98
2429 9160 3.287222 ACAGAGGAAGCTAGCTCAGTAG 58.713 50.000 19.65 9.39 0.00 2.57
2451 9182 0.110486 AGAAGGAAGAAAAGGCCGCA 59.890 50.000 0.00 0.00 0.00 5.69
2452 9183 0.805614 GAGAAGGAAGAAAAGGCCGC 59.194 55.000 0.00 0.00 0.00 6.53
2467 9198 7.214467 AGCGAAACAAATTTAGAATGGAGAA 57.786 32.000 0.00 0.00 0.00 2.87
2493 9224 2.682856 ACATGCAAACTAATACCTGCGG 59.317 45.455 0.00 0.00 37.62 5.69
2521 9252 5.957798 AGAAGGTCGACGAACACAATTATA 58.042 37.500 16.50 0.00 0.00 0.98
2522 9253 4.817517 AGAAGGTCGACGAACACAATTAT 58.182 39.130 16.50 0.00 0.00 1.28
2523 9254 4.232221 GAGAAGGTCGACGAACACAATTA 58.768 43.478 16.50 0.00 0.00 1.40
2524 9255 3.057734 GAGAAGGTCGACGAACACAATT 58.942 45.455 16.50 0.00 0.00 2.32
2587 9320 0.393537 GGCAATCACCTCAGGGTCAG 60.394 60.000 0.00 0.00 45.41 3.51
2601 9334 2.481185 CAGTTTGGTACGTAACGGCAAT 59.519 45.455 6.07 0.00 32.05 3.56
2603 9336 1.500108 CAGTTTGGTACGTAACGGCA 58.500 50.000 6.07 0.00 32.05 5.69
2604 9337 0.164432 GCAGTTTGGTACGTAACGGC 59.836 55.000 6.07 14.45 38.71 5.68
2606 9339 1.458064 CAGGCAGTTTGGTACGTAACG 59.542 52.381 6.07 0.00 32.05 3.18
2609 9342 0.320946 GCCAGGCAGTTTGGTACGTA 60.321 55.000 6.55 0.00 38.02 3.57
2610 9343 1.599797 GCCAGGCAGTTTGGTACGT 60.600 57.895 6.55 0.00 38.02 3.57
2611 9344 1.302511 AGCCAGGCAGTTTGGTACG 60.303 57.895 15.80 0.00 38.02 3.67
2612 9345 0.250727 TCAGCCAGGCAGTTTGGTAC 60.251 55.000 15.80 0.00 38.02 3.34
2706 9439 1.638467 GCTTGCGAGCGGTAAGATG 59.362 57.895 10.93 0.00 40.41 2.90
2738 9471 5.695851 AAATCTCCTGTGTTGCTACAAAG 57.304 39.130 11.13 11.13 39.03 2.77
2746 9479 4.999950 AGACTAGCAAAATCTCCTGTGTTG 59.000 41.667 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.