Multiple sequence alignment - TraesCS3D01G227300

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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 TraesCS3D01G227300 chr3D 100.000 5558 0 0 581 6138 309087503 309081946 0.000000e+00 10264.0
1 TraesCS3D01G227300 chr3D 100.000 249 0 0 1 249 309088083 309087835 1.560000e-125 460.0
2 TraesCS3D01G227300 chr3B 96.984 4543 93 17 584 5117 412245025 412249532 0.000000e+00 7590.0
3 TraesCS3D01G227300 chr3B 81.378 537 63 15 5223 5756 412250747 412251249 2.660000e-108 403.0
4 TraesCS3D01G227300 chr3A 94.437 4440 162 30 584 5020 428799658 428795301 0.000000e+00 6752.0
5 TraesCS3D01G227300 chr3A 90.826 763 62 7 5023 5782 428795104 428794347 0.000000e+00 1014.0
6 TraesCS3D01G227300 chr3A 89.753 283 27 2 5775 6056 428794072 428793791 1.630000e-95 361.0
7 TraesCS3D01G227300 chr3A 89.496 238 22 3 1 236 428801613 428801377 1.290000e-76 298.0
8 TraesCS3D01G227300 chrUn 100.000 420 0 0 3719 4138 476921318 476921737 0.000000e+00 776.0
9 TraesCS3D01G227300 chr6A 97.368 38 1 0 5326 5363 180925713 180925676 1.430000e-06 65.8
10 TraesCS3D01G227300 chr6B 93.023 43 3 0 5321 5363 237701952 237701910 5.140000e-06 63.9
11 TraesCS3D01G227300 chr5A 100.000 31 0 0 5327 5357 552064922 552064892 2.390000e-04 58.4
12 TraesCS3D01G227300 chr5B 100.000 30 0 0 5327 5356 530930843 530930814 8.590000e-04 56.5


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 TraesCS3D01G227300 chr3D 309081946 309088083 6137 True 5362.00 10264 100.000 1 6138 2 chr3D.!!$R1 6137
1 TraesCS3D01G227300 chr3B 412245025 412251249 6224 False 3996.50 7590 89.181 584 5756 2 chr3B.!!$F1 5172
2 TraesCS3D01G227300 chr3A 428793791 428801613 7822 True 2106.25 6752 91.128 1 6056 4 chr3A.!!$R1 6055

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
40 41 1.320344 TGAATCGAGACCCTCACCGG 61.320 60.000 0.00 0.0 0.00 5.28 F
1015 2394 2.001803 CTCCTCCCCATTTCCTGCA 58.998 57.895 0.00 0.0 0.00 4.41 F
1223 2602 1.216444 GTGCAGCGAGTGATCTCCA 59.784 57.895 0.00 0.0 37.40 3.86 F
1919 3299 3.717842 CGGGAGGTTTTGACCTTCA 57.282 52.632 6.24 0.0 40.86 3.02 F
3355 4736 1.000506 AGTACTGGTACAACTGGTGCG 59.999 52.381 12.54 0.0 38.70 5.34 F
4436 5819 1.004979 TCCGGGGTTAGGTTTTGATGG 59.995 52.381 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1205 2584 0.805322 CTGGAGATCACTCGCTGCAC 60.805 60.000 0.00 0.00 43.44 4.57 R
1880 3260 2.097825 GCCTTTGCATCCTCTGTTGAT 58.902 47.619 0.00 0.00 37.47 2.57 R
2165 3545 3.074390 TCTTCAAAGCCTTCTCCATTGGA 59.926 43.478 5.05 5.05 0.00 3.53 R
4169 5552 7.095649 GCTTCTTTGTTCATTGAAATAACCACC 60.096 37.037 0.00 0.00 0.00 4.61 R
4542 5925 0.030773 GACAGTGAGTCAGTGACGCA 59.969 55.000 30.34 23.67 46.77 5.24 R
5562 8257 0.034477 CAGCCCCCTATCCGTTGTTT 60.034 55.000 0.00 0.00 0.00 2.83 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
20 21 3.152400 GGTACCGATGGTCGCCCT 61.152 66.667 0.00 0.00 38.82 5.19
22 23 1.520787 GTACCGATGGTCGCCCTTG 60.521 63.158 0.00 0.00 38.82 3.61
40 41 1.320344 TGAATCGAGACCCTCACCGG 61.320 60.000 0.00 0.00 0.00 5.28
50 51 2.235402 GACCCTCACCGGAGTAAATGAA 59.765 50.000 9.46 0.00 39.64 2.57
58 59 7.360946 CCTCACCGGAGTAAATGAAACTAAAAG 60.361 40.741 9.46 0.00 39.64 2.27
69 70 7.449934 AATGAAACTAAAAGTCAAAGCAACG 57.550 32.000 0.00 0.00 0.00 4.10
96 97 5.860941 TGGCAAACAAAGGACAAGAATAA 57.139 34.783 0.00 0.00 0.00 1.40
103 104 6.959639 ACAAAGGACAAGAATAACACATGT 57.040 33.333 0.00 0.00 0.00 3.21
178 180 8.799367 TCTTTTATGACTAGCACAACTACTACA 58.201 33.333 0.00 0.00 0.00 2.74
181 183 5.324784 TGACTAGCACAACTACTACATGG 57.675 43.478 0.00 0.00 0.00 3.66
186 188 3.007940 AGCACAACTACTACATGGAAGCA 59.992 43.478 0.00 0.00 0.00 3.91
187 189 3.751175 GCACAACTACTACATGGAAGCAA 59.249 43.478 0.00 0.00 0.00 3.91
188 190 4.396166 GCACAACTACTACATGGAAGCAAT 59.604 41.667 0.00 0.00 0.00 3.56
202 204 4.706476 TGGAAGCAATGGGAAATGTTAGAG 59.294 41.667 0.00 0.00 0.00 2.43
208 210 5.649831 GCAATGGGAAATGTTAGAGAGAAGT 59.350 40.000 0.00 0.00 0.00 3.01
212 214 6.837312 TGGGAAATGTTAGAGAGAAGTTGAA 58.163 36.000 0.00 0.00 0.00 2.69
214 216 6.128526 GGGAAATGTTAGAGAGAAGTTGAACG 60.129 42.308 0.00 0.00 0.00 3.95
216 218 4.931661 TGTTAGAGAGAAGTTGAACGGT 57.068 40.909 0.00 0.00 0.00 4.83
243 266 2.498167 AGAAGCCATATTGACGATGCC 58.502 47.619 0.00 0.00 0.00 4.40
617 1991 9.155975 GATTATGCACCCTATTAGTTGATGTAG 57.844 37.037 0.00 0.00 0.00 2.74
622 1996 5.977725 CACCCTATTAGTTGATGTAGTCGTG 59.022 44.000 0.00 0.00 0.00 4.35
633 2007 3.719268 TGTAGTCGTGGGACCTAACTA 57.281 47.619 0.00 0.00 44.54 2.24
639 2013 4.341520 AGTCGTGGGACCTAACTATCATTC 59.658 45.833 0.00 0.00 44.54 2.67
644 2018 6.183360 CGTGGGACCTAACTATCATTCAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
646 2020 5.296035 GGGACCTAACTATCATTCAAAACCG 59.704 44.000 0.00 0.00 0.00 4.44
719 2093 3.292492 AGGGAAACGAAATCCATACCC 57.708 47.619 0.00 0.00 38.80 3.69
801 2175 4.995058 AGGTCCCCTCGCCCCAAA 62.995 66.667 0.00 0.00 0.00 3.28
803 2177 2.440247 GTCCCCTCGCCCCAAATG 60.440 66.667 0.00 0.00 0.00 2.32
903 2277 3.008049 AGTCGAAATCTAGGGTGCAAACT 59.992 43.478 0.00 0.00 0.00 2.66
1015 2394 2.001803 CTCCTCCCCATTTCCTGCA 58.998 57.895 0.00 0.00 0.00 4.41
1205 2584 3.488048 GATTCCTCGAGATCTGCGG 57.512 57.895 15.71 0.00 0.00 5.69
1223 2602 1.216444 GTGCAGCGAGTGATCTCCA 59.784 57.895 0.00 0.00 37.40 3.86
1537 2916 5.872617 TCTTGATTGTAGGACGTGTTATTGG 59.127 40.000 0.00 0.00 0.00 3.16
1553 2932 5.995282 TGTTATTGGTCTGACGTTCTGAATT 59.005 36.000 1.07 0.00 0.00 2.17
1661 3040 5.180304 ACTGTTTCGTTTTTGTTTTGGCATT 59.820 32.000 0.00 0.00 0.00 3.56
1919 3299 3.717842 CGGGAGGTTTTGACCTTCA 57.282 52.632 6.24 0.00 40.86 3.02
1939 3319 8.708378 ACCTTCATTTTCAGGAAAAGAAAATCT 58.292 29.630 12.21 0.00 46.94 2.40
1942 3322 8.876275 TCATTTTCAGGAAAAGAAAATCTGTG 57.124 30.769 12.21 3.79 46.94 3.66
2165 3545 5.606348 TGGTGCTGAAAAGTTTGGTTATT 57.394 34.783 0.00 0.00 0.00 1.40
2192 3572 3.007940 TGGAGAAGGCTTTGAAGATTCGA 59.992 43.478 0.00 0.00 32.08 3.71
2287 3667 1.278699 CCTGAGAAAGAGAAGGCAGCT 59.721 52.381 0.00 0.00 0.00 4.24
2327 3707 4.142038 AGTGGTGGTATGTTTCTTTGTCC 58.858 43.478 0.00 0.00 0.00 4.02
2366 3747 8.757982 ATATTTCTCAATGGCTCATACAAAGT 57.242 30.769 0.00 0.00 0.00 2.66
2451 3832 5.068460 ACCTCTGAACAAGAAGGAGATATCG 59.932 44.000 0.00 0.00 33.37 2.92
2623 4004 1.940883 ATTGCTTGATGCCTGGCACG 61.941 55.000 25.99 13.60 43.04 5.34
3355 4736 1.000506 AGTACTGGTACAACTGGTGCG 59.999 52.381 12.54 0.00 38.70 5.34
4169 5552 1.391485 CTGAGTTCAGTTCGGCGAATG 59.609 52.381 26.42 22.01 39.09 2.67
4329 5712 6.569179 TTCTGTTGCTTACCCAATTAGAAC 57.431 37.500 0.00 0.00 31.67 3.01
4386 5769 6.174720 CCTCCTTCAGGTGCAGTATTATTA 57.825 41.667 0.00 0.00 37.53 0.98
4401 5784 9.226345 GCAGTATTATTACTTCTGCACAATTTC 57.774 33.333 9.99 0.00 46.95 2.17
4409 5792 5.689819 ACTTCTGCACAATTTCGTTGATAC 58.310 37.500 0.00 0.00 40.37 2.24
4416 5799 7.534282 TGCACAATTTCGTTGATACAATATGT 58.466 30.769 0.00 0.00 40.37 2.29
4419 5802 7.373180 CACAATTTCGTTGATACAATATGTCCG 59.627 37.037 0.00 0.00 40.37 4.79
4436 5819 1.004979 TCCGGGGTTAGGTTTTGATGG 59.995 52.381 0.00 0.00 0.00 3.51
4540 5923 5.807909 AGGTTAGTCGCCTAAAATGGTAAA 58.192 37.500 0.00 0.00 35.00 2.01
4541 5924 6.420638 AGGTTAGTCGCCTAAAATGGTAAAT 58.579 36.000 0.00 0.00 35.00 1.40
4542 5925 6.888088 AGGTTAGTCGCCTAAAATGGTAAATT 59.112 34.615 0.00 0.00 35.00 1.82
4543 5926 6.970613 GGTTAGTCGCCTAAAATGGTAAATTG 59.029 38.462 0.00 0.00 35.00 2.32
4544 5927 4.993905 AGTCGCCTAAAATGGTAAATTGC 58.006 39.130 0.00 0.00 0.00 3.56
4545 5928 3.789224 GTCGCCTAAAATGGTAAATTGCG 59.211 43.478 0.00 0.00 40.72 4.85
4546 5929 3.440872 TCGCCTAAAATGGTAAATTGCGT 59.559 39.130 0.00 0.00 40.29 5.24
4547 5930 3.789224 CGCCTAAAATGGTAAATTGCGTC 59.211 43.478 0.00 0.00 35.22 5.19
4585 5970 6.545666 TCATTGGTCGTCATATTATTTTGCCT 59.454 34.615 0.00 0.00 0.00 4.75
4818 6203 0.876342 CAAGAGCGGCCTATTCGTCC 60.876 60.000 0.00 0.00 0.00 4.79
5164 7844 3.627577 GTGCATGAAGATTCCGGTATGTT 59.372 43.478 2.95 2.95 0.00 2.71
5213 7894 6.882678 ACACATACCTTATTTCTGTGGTTACC 59.117 38.462 0.00 0.00 41.09 2.85
5215 7896 7.280205 CACATACCTTATTTCTGTGGTTACCTC 59.720 40.741 2.07 0.00 34.88 3.85
5307 8000 6.481976 TGAACAAAAACGTGTCTCATACATCT 59.518 34.615 0.00 0.00 41.10 2.90
5319 8012 9.107177 GTGTCTCATACATCTGATTCAGAAAAT 57.893 33.333 19.73 10.75 44.04 1.82
5344 8038 7.831753 TCTCTCTCCGATCCATATTAATTGAC 58.168 38.462 0.00 0.00 0.00 3.18
5350 8044 5.122239 CCGATCCATATTAATTGACGCACAT 59.878 40.000 0.00 0.00 0.00 3.21
5369 8063 9.298774 ACGCACATTTAGTATAACTTAGAAGAC 57.701 33.333 0.00 0.00 0.00 3.01
5391 8085 6.160459 AGACCTTATATTTGTGAATGGAGGGT 59.840 38.462 0.00 0.00 30.50 4.34
5442 8136 3.888583 ACGTTAGTTTTTCTCCCAACCA 58.111 40.909 0.00 0.00 0.00 3.67
5460 8155 2.242196 ACCATTCTTTCGTCATCCCCAT 59.758 45.455 0.00 0.00 0.00 4.00
5514 8209 6.152661 TCTCCAACAGCATACATTAAAAAGGG 59.847 38.462 0.00 0.00 0.00 3.95
5519 8214 6.710278 ACAGCATACATTAAAAAGGGCAATT 58.290 32.000 0.00 0.00 0.00 2.32
5520 8215 7.846066 ACAGCATACATTAAAAAGGGCAATTA 58.154 30.769 0.00 0.00 0.00 1.40
5522 8217 7.439056 CAGCATACATTAAAAAGGGCAATTAGG 59.561 37.037 0.00 0.00 0.00 2.69
5532 8227 1.134220 GGGCAATTAGGATCGTCCACA 60.134 52.381 6.78 0.00 39.61 4.17
5534 8229 2.627945 GCAATTAGGATCGTCCACACA 58.372 47.619 6.78 0.00 39.61 3.72
5539 8234 0.537188 AGGATCGTCCACACATCCAC 59.463 55.000 6.78 0.00 39.61 4.02
5541 8236 0.172578 GATCGTCCACACATCCACGA 59.827 55.000 0.00 0.00 44.76 4.35
5545 8240 1.808411 GTCCACACATCCACGAACAT 58.192 50.000 0.00 0.00 0.00 2.71
5550 8245 0.721154 CACATCCACGAACATGTCCG 59.279 55.000 1.74 1.74 30.48 4.79
5582 8278 1.205460 AACAACGGATAGGGGGCTGT 61.205 55.000 0.00 0.00 0.00 4.40
5601 8297 1.895131 GTCATCCAATTTGGTGCACCT 59.105 47.619 34.75 14.17 39.03 4.00
5619 8315 4.383552 GCACCTAATGTCCATCTCTTGTCT 60.384 45.833 0.00 0.00 0.00 3.41
5623 8319 8.642432 CACCTAATGTCCATCTCTTGTCTAATA 58.358 37.037 0.00 0.00 0.00 0.98
5624 8320 8.865090 ACCTAATGTCCATCTCTTGTCTAATAG 58.135 37.037 0.00 0.00 0.00 1.73
5692 8389 1.383523 GTCCAAGGCTTGTCCATAGC 58.616 55.000 24.57 4.26 37.29 2.97
5707 8404 1.102222 ATAGCGTGTCCGGACTCCTC 61.102 60.000 33.39 21.87 33.68 3.71
5719 8416 1.349357 GGACTCCTCAAGCCACTTCTT 59.651 52.381 0.00 0.00 0.00 2.52
5730 8427 2.143925 GCCACTTCTTCGTTTGCTACT 58.856 47.619 0.00 0.00 0.00 2.57
5804 8783 6.627287 GCCCCATTAAATGACTAAAAGTGTCC 60.627 42.308 0.00 0.00 33.83 4.02
5810 8789 8.610248 TTAAATGACTAAAAGTGTCCGAATCA 57.390 30.769 0.00 0.00 33.83 2.57
5813 8792 6.037786 TGACTAAAAGTGTCCGAATCATCT 57.962 37.500 0.00 0.00 33.83 2.90
5817 8796 7.106239 ACTAAAAGTGTCCGAATCATCTGATT 58.894 34.615 5.13 5.13 46.54 2.57
5831 8810 8.915057 AATCATCTGATTCGGACATTTAGAAT 57.085 30.769 0.00 0.00 40.49 2.40
5848 8827 7.548196 TTTAGAATCGATTTGATGTACACCC 57.452 36.000 12.81 0.00 37.39 4.61
5885 8864 4.864334 CTGCACCGCATCCCCTCC 62.864 72.222 0.00 0.00 38.13 4.30
5904 8883 1.515521 CCCCGCCTGAAAATATCGGC 61.516 60.000 0.00 0.00 41.40 5.54
5943 8922 1.248785 GCACCACTCCTCACGACCTA 61.249 60.000 0.00 0.00 0.00 3.08
5949 8928 3.021695 CACTCCTCACGACCTACCATAA 58.978 50.000 0.00 0.00 0.00 1.90
5983 8962 2.358984 GCCCAACTCGGCCGTAAA 60.359 61.111 27.15 4.62 43.66 2.01
5990 8969 0.604578 ACTCGGCCGTAAAGCTGTTA 59.395 50.000 27.15 0.00 40.22 2.41
5991 8970 1.206371 ACTCGGCCGTAAAGCTGTTAT 59.794 47.619 27.15 0.00 40.22 1.89
5995 8974 0.935196 GCCGTAAAGCTGTTATCCCG 59.065 55.000 0.00 0.00 0.00 5.14
6031 9010 2.513204 CGATGCCTCCCAGTGCAG 60.513 66.667 0.00 0.00 41.46 4.41
6056 9035 0.671781 GGTAGCATCGCCATAGCCTG 60.672 60.000 0.00 0.00 34.57 4.85
6057 9036 0.318441 GTAGCATCGCCATAGCCTGA 59.682 55.000 0.00 0.00 34.57 3.86
6058 9037 0.605083 TAGCATCGCCATAGCCTGAG 59.395 55.000 0.00 0.00 34.57 3.35
6059 9038 1.070445 GCATCGCCATAGCCTGAGT 59.930 57.895 0.00 0.00 34.57 3.41
6060 9039 1.226686 GCATCGCCATAGCCTGAGTG 61.227 60.000 0.00 0.00 34.57 3.51
6061 9040 0.390492 CATCGCCATAGCCTGAGTGA 59.610 55.000 0.00 0.00 34.57 3.41
6062 9041 1.001746 CATCGCCATAGCCTGAGTGAT 59.998 52.381 0.00 0.00 34.57 3.06
6063 9042 0.676184 TCGCCATAGCCTGAGTGATC 59.324 55.000 0.00 0.00 34.57 2.92
6064 9043 0.678395 CGCCATAGCCTGAGTGATCT 59.322 55.000 0.00 0.00 34.57 2.75
6065 9044 1.336702 CGCCATAGCCTGAGTGATCTC 60.337 57.143 0.00 0.00 37.14 2.75
6066 9045 1.001860 GCCATAGCCTGAGTGATCTCC 59.998 57.143 0.00 0.00 39.75 3.71
6067 9046 1.622811 CCATAGCCTGAGTGATCTCCC 59.377 57.143 0.00 0.00 39.75 4.30
6068 9047 1.622811 CATAGCCTGAGTGATCTCCCC 59.377 57.143 0.00 0.00 39.75 4.81
6069 9048 0.105453 TAGCCTGAGTGATCTCCCCC 60.105 60.000 0.00 0.00 39.75 5.40
6070 9049 2.801631 GCCTGAGTGATCTCCCCCG 61.802 68.421 0.00 0.00 39.75 5.73
6071 9050 1.075970 CCTGAGTGATCTCCCCCGA 60.076 63.158 0.00 0.00 39.75 5.14
6072 9051 1.112315 CCTGAGTGATCTCCCCCGAG 61.112 65.000 0.00 0.00 39.75 4.63
6073 9052 1.075970 TGAGTGATCTCCCCCGAGG 60.076 63.158 0.00 0.00 39.75 4.63
6074 9053 1.230497 GAGTGATCTCCCCCGAGGA 59.770 63.158 0.00 0.00 44.91 3.71
6075 9054 0.397254 GAGTGATCTCCCCCGAGGAA 60.397 60.000 0.00 0.00 46.94 3.36
6076 9055 0.397816 AGTGATCTCCCCCGAGGAAG 60.398 60.000 0.00 0.00 46.94 3.46
6077 9056 1.762460 TGATCTCCCCCGAGGAAGC 60.762 63.158 0.00 0.00 46.94 3.86
6078 9057 2.446802 ATCTCCCCCGAGGAAGCC 60.447 66.667 0.00 0.00 46.94 4.35
6079 9058 4.798682 TCTCCCCCGAGGAAGCCC 62.799 72.222 0.00 0.00 46.94 5.19
6083 9062 4.195334 CCCCGAGGAAGCCCCATG 62.195 72.222 0.00 0.00 37.41 3.66
6084 9063 4.883354 CCCGAGGAAGCCCCATGC 62.883 72.222 0.00 0.00 41.71 4.06
6094 9073 2.440796 CCCCATGCTTGCCGTCAT 60.441 61.111 0.00 0.00 0.00 3.06
6095 9074 2.777972 CCCCATGCTTGCCGTCATG 61.778 63.158 0.00 0.00 39.67 3.07
6096 9075 2.048023 CCCATGCTTGCCGTCATGT 61.048 57.895 0.00 0.00 38.63 3.21
6097 9076 1.138036 CCATGCTTGCCGTCATGTG 59.862 57.895 0.00 0.00 38.63 3.21
6098 9077 1.588824 CCATGCTTGCCGTCATGTGT 61.589 55.000 0.00 0.00 38.63 3.72
6099 9078 0.179181 CATGCTTGCCGTCATGTGTC 60.179 55.000 0.00 0.00 36.30 3.67
6100 9079 0.606130 ATGCTTGCCGTCATGTGTCA 60.606 50.000 0.00 0.00 0.00 3.58
6101 9080 1.207593 GCTTGCCGTCATGTGTCAC 59.792 57.895 0.00 0.00 0.00 3.67
6102 9081 1.506309 GCTTGCCGTCATGTGTCACA 61.506 55.000 8.40 8.40 0.00 3.58
6103 9082 0.943673 CTTGCCGTCATGTGTCACAA 59.056 50.000 10.28 0.00 0.00 3.33
6104 9083 0.660488 TTGCCGTCATGTGTCACAAC 59.340 50.000 10.28 3.69 0.00 3.32
6105 9084 1.163420 TGCCGTCATGTGTCACAACC 61.163 55.000 10.28 0.00 0.00 3.77
6106 9085 0.884704 GCCGTCATGTGTCACAACCT 60.885 55.000 10.28 0.00 0.00 3.50
6107 9086 1.593196 CCGTCATGTGTCACAACCTT 58.407 50.000 10.28 0.00 0.00 3.50
6108 9087 1.946768 CCGTCATGTGTCACAACCTTT 59.053 47.619 10.28 0.00 0.00 3.11
6109 9088 2.286950 CCGTCATGTGTCACAACCTTTG 60.287 50.000 10.28 3.42 0.00 2.77
6110 9089 2.611751 CGTCATGTGTCACAACCTTTGA 59.388 45.455 10.28 5.94 0.00 2.69
6111 9090 3.250762 CGTCATGTGTCACAACCTTTGAT 59.749 43.478 10.28 0.00 0.00 2.57
6112 9091 4.450757 CGTCATGTGTCACAACCTTTGATA 59.549 41.667 10.28 0.00 0.00 2.15
6113 9092 5.614668 CGTCATGTGTCACAACCTTTGATAC 60.615 44.000 10.28 0.00 36.07 2.24
6114 9093 4.759693 TCATGTGTCACAACCTTTGATACC 59.240 41.667 10.28 0.00 34.98 2.73
6115 9094 3.482436 TGTGTCACAACCTTTGATACCC 58.518 45.455 2.31 0.00 34.98 3.69
6116 9095 2.482721 GTGTCACAACCTTTGATACCCG 59.517 50.000 0.00 0.00 30.94 5.28
6117 9096 2.105134 TGTCACAACCTTTGATACCCGT 59.895 45.455 0.00 0.00 0.00 5.28
6118 9097 2.482721 GTCACAACCTTTGATACCCGTG 59.517 50.000 0.00 0.00 0.00 4.94
6119 9098 2.105134 TCACAACCTTTGATACCCGTGT 59.895 45.455 0.00 0.00 0.00 4.49
6120 9099 2.225491 CACAACCTTTGATACCCGTGTG 59.775 50.000 0.00 0.00 0.00 3.82
6121 9100 1.199097 CAACCTTTGATACCCGTGTGC 59.801 52.381 0.00 0.00 0.00 4.57
6122 9101 0.672401 ACCTTTGATACCCGTGTGCG 60.672 55.000 0.00 0.00 37.95 5.34
6132 9111 2.053465 CGTGTGCGGTTGTTGACG 60.053 61.111 0.00 0.00 0.00 4.35
6133 9112 2.518312 CGTGTGCGGTTGTTGACGA 61.518 57.895 0.00 0.00 0.00 4.20
6134 9113 1.011574 GTGTGCGGTTGTTGACGAC 60.012 57.895 0.00 0.00 0.00 4.34
6135 9114 1.153529 TGTGCGGTTGTTGACGACT 60.154 52.632 0.00 0.00 0.00 4.18
6136 9115 1.149361 TGTGCGGTTGTTGACGACTC 61.149 55.000 0.00 0.00 0.00 3.36
6137 9116 0.874607 GTGCGGTTGTTGACGACTCT 60.875 55.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.530744 CGGTGAGGGTCTCGATTCAA 59.469 55.000 0.00 0.00 32.35 2.69
22 23 1.035932 TCCGGTGAGGGTCTCGATTC 61.036 60.000 0.00 0.00 41.52 2.52
40 41 9.730420 TGCTTTGACTTTTAGTTTCATTTACTC 57.270 29.630 0.00 0.00 0.00 2.59
50 51 3.129638 TGGCGTTGCTTTGACTTTTAGTT 59.870 39.130 0.00 0.00 0.00 2.24
58 59 1.284297 GCCAATGGCGTTGCTTTGAC 61.284 55.000 9.14 0.00 39.62 3.18
83 84 4.826733 TGCACATGTGTTATTCTTGTCCTT 59.173 37.500 26.01 0.00 0.00 3.36
86 87 5.180117 ACTCTGCACATGTGTTATTCTTGTC 59.820 40.000 26.01 6.75 0.00 3.18
96 97 2.071540 CGATTCACTCTGCACATGTGT 58.928 47.619 26.01 3.79 33.82 3.72
103 104 3.934457 TCTACAACGATTCACTCTGCA 57.066 42.857 0.00 0.00 0.00 4.41
131 132 0.932399 AGTTGCGTGTACCGTTTGAC 59.068 50.000 5.79 1.41 39.32 3.18
137 138 1.779569 AAAGAGAGTTGCGTGTACCG 58.220 50.000 0.00 0.00 40.40 4.02
145 147 5.639506 TGTGCTAGTCATAAAAGAGAGTTGC 59.360 40.000 0.00 0.00 36.77 4.17
178 180 5.271598 TCTAACATTTCCCATTGCTTCCAT 58.728 37.500 0.00 0.00 0.00 3.41
181 183 5.882557 TCTCTCTAACATTTCCCATTGCTTC 59.117 40.000 0.00 0.00 0.00 3.86
186 188 7.461749 TCAACTTCTCTCTAACATTTCCCATT 58.538 34.615 0.00 0.00 0.00 3.16
187 189 7.020827 TCAACTTCTCTCTAACATTTCCCAT 57.979 36.000 0.00 0.00 0.00 4.00
188 190 6.433847 TCAACTTCTCTCTAACATTTCCCA 57.566 37.500 0.00 0.00 0.00 4.37
202 204 1.566018 CCGCCACCGTTCAACTTCTC 61.566 60.000 0.00 0.00 0.00 2.87
208 210 0.320073 CTTCTACCGCCACCGTTCAA 60.320 55.000 0.00 0.00 0.00 2.69
212 214 4.078516 GGCTTCTACCGCCACCGT 62.079 66.667 0.00 0.00 46.77 4.83
580 603 2.538939 GGTGCATAATCGAGTTTTCGCC 60.539 50.000 0.00 0.00 46.28 5.54
617 1991 4.098960 TGAATGATAGTTAGGTCCCACGAC 59.901 45.833 0.00 0.00 38.38 4.34
622 1996 5.296035 CGGTTTTGAATGATAGTTAGGTCCC 59.704 44.000 0.00 0.00 0.00 4.46
633 2007 7.714813 AGTGAAAATTTTCCGGTTTTGAATGAT 59.285 29.630 24.51 0.00 36.36 2.45
639 2013 6.531948 TGTACAGTGAAAATTTTCCGGTTTTG 59.468 34.615 24.51 15.91 36.36 2.44
692 2066 6.911250 ATGGATTTCGTTTCCCTACTTTTT 57.089 33.333 0.00 0.00 31.87 1.94
698 2072 3.781407 TGGGTATGGATTTCGTTTCCCTA 59.219 43.478 0.00 0.00 35.20 3.53
801 2175 2.355115 GGGAAAGTGGGCCGTCAT 59.645 61.111 0.00 0.00 0.00 3.06
803 2177 3.205851 AAGGGGAAAGTGGGCCGTC 62.206 63.158 0.00 0.00 0.00 4.79
903 2277 1.691219 GGAGAGGGGTGGATTTGCA 59.309 57.895 0.00 0.00 0.00 4.08
1015 2394 0.846427 TGGACTGGGGAGCAAGGAAT 60.846 55.000 0.00 0.00 0.00 3.01
1102 2481 3.071206 GGAGCTGCTCCGAGGTGA 61.071 66.667 31.03 0.00 41.08 4.02
1205 2584 0.805322 CTGGAGATCACTCGCTGCAC 60.805 60.000 0.00 0.00 43.44 4.57
1213 2592 4.285020 TCATGAGCTAACTGGAGATCACT 58.715 43.478 0.00 0.00 44.15 3.41
1223 2602 5.826737 CCAAATCCAGATTCATGAGCTAACT 59.173 40.000 0.00 0.00 0.00 2.24
1369 2748 2.268280 CTGAGCTGGTGCCTCTGG 59.732 66.667 0.00 0.00 40.80 3.86
1527 2906 3.121279 CAGAACGTCAGACCAATAACACG 59.879 47.826 0.00 0.00 0.00 4.49
1537 2916 4.508124 ACAACTGAATTCAGAACGTCAGAC 59.492 41.667 36.15 0.00 46.59 3.51
1553 2932 1.375908 GCCATGCCTCGACAACTGA 60.376 57.895 0.00 0.00 0.00 3.41
1661 3040 6.708949 ACTGAAATTCGCCTAAAACAAGACTA 59.291 34.615 0.00 0.00 0.00 2.59
1760 3139 4.653341 TGACCAAAATGAGACCCAACAAAT 59.347 37.500 0.00 0.00 0.00 2.32
1880 3260 2.097825 GCCTTTGCATCCTCTGTTGAT 58.902 47.619 0.00 0.00 37.47 2.57
1939 3319 6.993079 AGATTATATCGAACCATACAGCACA 58.007 36.000 0.00 0.00 0.00 4.57
1942 3322 9.803315 TCAATAGATTATATCGAACCATACAGC 57.197 33.333 0.00 0.00 0.00 4.40
2063 3443 9.985730 CAGAATTTACAATGTGGGCAATATTAT 57.014 29.630 0.00 0.00 0.00 1.28
2165 3545 3.074390 TCTTCAAAGCCTTCTCCATTGGA 59.926 43.478 5.05 5.05 0.00 3.53
2192 3572 5.355350 GCTTGTCTGTACCAAAGCTCATATT 59.645 40.000 10.12 0.00 0.00 1.28
2327 3707 9.338291 CATTGAGAAATATTTAATCATGGAGCG 57.662 33.333 13.53 0.00 0.00 5.03
4169 5552 7.095649 GCTTCTTTGTTCATTGAAATAACCACC 60.096 37.037 0.00 0.00 0.00 4.61
4386 5769 4.836125 ATCAACGAAATTGTGCAGAAGT 57.164 36.364 1.68 0.00 39.54 3.01
4396 5779 6.017440 CCCGGACATATTGTATCAACGAAATT 60.017 38.462 0.73 0.00 0.00 1.82
4401 5784 3.064207 CCCCGGACATATTGTATCAACG 58.936 50.000 0.73 0.00 0.00 4.10
4409 5792 3.570912 AACCTAACCCCGGACATATTG 57.429 47.619 0.73 0.00 0.00 1.90
4416 5799 1.004979 CCATCAAAACCTAACCCCGGA 59.995 52.381 0.73 0.00 0.00 5.14
4419 5802 3.236047 ACAACCATCAAAACCTAACCCC 58.764 45.455 0.00 0.00 0.00 4.95
4436 5819 3.211045 TCTTCCTGCACCAGTTAACAAC 58.789 45.455 8.61 0.00 0.00 3.32
4540 5923 1.069204 ACAGTGAGTCAGTGACGCAAT 59.931 47.619 30.34 24.89 43.17 3.56
4541 5924 0.459899 ACAGTGAGTCAGTGACGCAA 59.540 50.000 30.34 12.13 43.17 4.85
4542 5925 0.030773 GACAGTGAGTCAGTGACGCA 59.969 55.000 30.34 23.67 46.77 5.24
4543 5926 2.802683 GACAGTGAGTCAGTGACGC 58.197 57.895 30.34 18.94 46.77 5.19
4585 5970 3.181434 ACAAGAGGCCATTCACAGGTTAA 60.181 43.478 5.01 0.00 0.00 2.01
5007 6393 4.304939 GACTCGGGTACAAATATGCTACC 58.695 47.826 0.00 0.00 34.83 3.18
5136 7813 1.089920 GAATCTTCATGCACCGCAGT 58.910 50.000 0.00 0.00 43.65 4.40
5137 7814 0.379669 GGAATCTTCATGCACCGCAG 59.620 55.000 0.00 0.00 43.65 5.18
5138 7815 1.368345 CGGAATCTTCATGCACCGCA 61.368 55.000 0.00 0.00 44.86 5.69
5139 7816 1.353103 CGGAATCTTCATGCACCGC 59.647 57.895 0.00 0.00 34.36 5.68
5307 8000 5.921962 TCGGAGAGAGATTTTCTGAATCA 57.078 39.130 0.00 0.00 35.87 2.57
5319 8012 7.362142 CGTCAATTAATATGGATCGGAGAGAGA 60.362 40.741 0.00 0.00 43.63 3.10
5344 8038 8.753175 GGTCTTCTAAGTTATACTAAATGTGCG 58.247 37.037 0.00 0.00 0.00 5.34
5369 8063 7.230712 GGTAACCCTCCATTCACAAATATAAGG 59.769 40.741 0.00 0.00 0.00 2.69
5391 8085 8.294954 TGAAACCTTTCATGTTGTTTAGGTAA 57.705 30.769 0.00 0.00 41.88 2.85
5442 8136 2.158608 GGGATGGGGATGACGAAAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
5460 8155 0.179121 CGAACAACGATCGATGGGGA 60.179 55.000 26.23 0.00 45.77 4.81
5506 8201 4.885325 GGACGATCCTAATTGCCCTTTTTA 59.115 41.667 0.00 0.00 32.53 1.52
5514 8209 2.627945 TGTGTGGACGATCCTAATTGC 58.372 47.619 0.00 0.00 37.46 3.56
5519 8214 1.754803 GTGGATGTGTGGACGATCCTA 59.245 52.381 0.00 0.00 37.46 2.94
5520 8215 0.537188 GTGGATGTGTGGACGATCCT 59.463 55.000 0.00 0.00 37.46 3.24
5522 8217 0.172578 TCGTGGATGTGTGGACGATC 59.827 55.000 0.00 0.00 35.99 3.69
5532 8227 0.391130 CCGGACATGTTCGTGGATGT 60.391 55.000 24.43 0.00 35.46 3.06
5534 8229 0.108329 GTCCGGACATGTTCGTGGAT 60.108 55.000 29.75 0.00 33.36 3.41
5539 8234 2.726691 GCACGTCCGGACATGTTCG 61.727 63.158 32.80 20.02 0.00 3.95
5541 8236 2.358247 GGCACGTCCGGACATGTT 60.358 61.111 32.80 12.01 0.00 2.71
5550 8245 3.587933 TTGTTTGCGGGCACGTCC 61.588 61.111 11.45 0.00 43.45 4.79
5559 8254 1.373590 CCCCCTATCCGTTGTTTGCG 61.374 60.000 0.00 0.00 0.00 4.85
5562 8257 0.034477 CAGCCCCCTATCCGTTGTTT 60.034 55.000 0.00 0.00 0.00 2.83
5563 8258 1.205460 ACAGCCCCCTATCCGTTGTT 61.205 55.000 0.00 0.00 0.00 2.83
5582 8278 2.307496 AGGTGCACCAAATTGGATGA 57.693 45.000 36.39 0.00 40.96 2.92
5601 8297 9.868160 TCTCTATTAGACAAGAGATGGACATTA 57.132 33.333 0.00 0.00 42.52 1.90
5619 8315 6.272324 CCCTTCTCTCTCCTCTCTCTCTATTA 59.728 46.154 0.00 0.00 0.00 0.98
5623 8319 2.780010 CCCTTCTCTCTCCTCTCTCTCT 59.220 54.545 0.00 0.00 0.00 3.10
5624 8320 2.777692 TCCCTTCTCTCTCCTCTCTCTC 59.222 54.545 0.00 0.00 0.00 3.20
5692 8389 1.213013 CTTGAGGAGTCCGGACACG 59.787 63.158 35.00 12.91 40.55 4.49
5707 8404 1.334869 AGCAAACGAAGAAGTGGCTTG 59.665 47.619 0.00 0.00 33.60 4.01
5730 8427 3.071479 GTGTCCGAATTCTGCTAAACCA 58.929 45.455 3.52 0.00 0.00 3.67
5767 8464 0.887933 AATGGGGCACATCAAACGTC 59.112 50.000 0.94 0.00 39.40 4.34
5769 8466 3.584406 TTTAATGGGGCACATCAAACG 57.416 42.857 0.94 0.00 39.40 3.60
5810 8789 6.749139 TCGATTCTAAATGTCCGAATCAGAT 58.251 36.000 10.63 0.00 41.78 2.90
5813 8792 7.494298 TCAAATCGATTCTAAATGTCCGAATCA 59.506 33.333 11.83 1.07 41.78 2.57
5817 8796 6.761242 ACATCAAATCGATTCTAAATGTCCGA 59.239 34.615 11.83 0.00 29.21 4.55
5831 8810 2.612604 CACGGGTGTACATCAAATCGA 58.387 47.619 8.70 0.00 0.00 3.59
5885 8864 1.515521 GCCGATATTTTCAGGCGGGG 61.516 60.000 0.00 0.00 42.09 5.73
5904 8883 3.126171 TGCGGTTTATTCATTCGGTTCAG 59.874 43.478 0.00 0.00 0.00 3.02
5917 8896 0.981183 TGAGGAGTGGTGCGGTTTAT 59.019 50.000 0.00 0.00 0.00 1.40
5921 8900 3.991051 CGTGAGGAGTGGTGCGGT 61.991 66.667 0.00 0.00 0.00 5.68
5971 8950 0.604578 TAACAGCTTTACGGCCGAGT 59.395 50.000 35.90 13.91 0.00 4.18
5975 8954 1.306148 GGGATAACAGCTTTACGGCC 58.694 55.000 0.00 0.00 0.00 6.13
5980 8959 2.772077 TGTGCGGGATAACAGCTTTA 57.228 45.000 0.00 0.00 0.00 1.85
5981 8960 2.017049 GATGTGCGGGATAACAGCTTT 58.983 47.619 0.00 0.00 30.18 3.51
5983 8962 0.541392 TGATGTGCGGGATAACAGCT 59.459 50.000 0.00 0.00 33.90 4.24
5990 8969 1.378514 GGTTGGTGATGTGCGGGAT 60.379 57.895 0.00 0.00 0.00 3.85
5991 8970 2.033448 GGTTGGTGATGTGCGGGA 59.967 61.111 0.00 0.00 0.00 5.14
5995 8974 1.216178 GCCATGGTTGGTGATGTGC 59.784 57.895 14.67 0.00 45.57 4.57
6013 8992 4.100084 TGCACTGGGAGGCATCGG 62.100 66.667 0.00 0.00 34.58 4.18
6016 8995 1.226542 CATCTGCACTGGGAGGCAT 59.773 57.895 0.00 0.00 39.65 4.40
6018 8997 2.124403 CCATCTGCACTGGGAGGC 60.124 66.667 3.05 0.00 32.55 4.70
6025 9004 0.990282 ATGCTACCCCCATCTGCACT 60.990 55.000 0.00 0.00 36.44 4.40
6026 9005 0.536006 GATGCTACCCCCATCTGCAC 60.536 60.000 0.00 0.00 36.89 4.57
6031 9010 2.032681 GGCGATGCTACCCCCATC 59.967 66.667 0.00 0.00 36.58 3.51
6056 9035 0.397254 TTCCTCGGGGGAGATCACTC 60.397 60.000 0.00 0.00 46.01 3.51
6057 9036 0.397816 CTTCCTCGGGGGAGATCACT 60.398 60.000 2.15 0.00 46.01 3.41
6058 9037 2.034048 GCTTCCTCGGGGGAGATCAC 62.034 65.000 16.18 0.00 46.01 3.06
6059 9038 1.762460 GCTTCCTCGGGGGAGATCA 60.762 63.158 16.18 0.00 46.01 2.92
6060 9039 2.512355 GGCTTCCTCGGGGGAGATC 61.512 68.421 16.18 0.00 46.01 2.75
6061 9040 2.446802 GGCTTCCTCGGGGGAGAT 60.447 66.667 16.18 0.00 46.01 2.75
6062 9041 4.798682 GGGCTTCCTCGGGGGAGA 62.799 72.222 16.18 0.00 46.01 3.71
6066 9045 4.195334 CATGGGGCTTCCTCGGGG 62.195 72.222 0.00 0.00 36.20 5.73
6067 9046 4.883354 GCATGGGGCTTCCTCGGG 62.883 72.222 0.00 0.00 40.25 5.14
6077 9056 2.440796 ATGACGGCAAGCATGGGG 60.441 61.111 0.00 0.00 0.00 4.96
6078 9057 2.048023 ACATGACGGCAAGCATGGG 61.048 57.895 0.00 0.00 44.64 4.00
6079 9058 1.138036 CACATGACGGCAAGCATGG 59.862 57.895 0.00 2.96 44.64 3.66
6080 9059 0.179181 GACACATGACGGCAAGCATG 60.179 55.000 0.00 9.49 45.56 4.06
6081 9060 0.606130 TGACACATGACGGCAAGCAT 60.606 50.000 0.00 0.00 0.00 3.79
6082 9061 1.227793 TGACACATGACGGCAAGCA 60.228 52.632 0.00 0.00 0.00 3.91
6083 9062 1.207593 GTGACACATGACGGCAAGC 59.792 57.895 0.00 0.00 0.00 4.01
6084 9063 0.943673 TTGTGACACATGACGGCAAG 59.056 50.000 9.55 0.00 0.00 4.01
6085 9064 0.660488 GTTGTGACACATGACGGCAA 59.340 50.000 9.55 0.00 0.00 4.52
6086 9065 1.163420 GGTTGTGACACATGACGGCA 61.163 55.000 9.55 0.00 0.00 5.69
6087 9066 0.884704 AGGTTGTGACACATGACGGC 60.885 55.000 9.55 0.00 0.00 5.68
6088 9067 1.593196 AAGGTTGTGACACATGACGG 58.407 50.000 9.55 0.00 0.00 4.79
6089 9068 2.611751 TCAAAGGTTGTGACACATGACG 59.388 45.455 9.55 0.00 0.00 4.35
6090 9069 4.836125 ATCAAAGGTTGTGACACATGAC 57.164 40.909 9.55 5.46 0.00 3.06
6091 9070 4.759693 GGTATCAAAGGTTGTGACACATGA 59.240 41.667 9.55 10.05 0.00 3.07
6092 9071 4.082787 GGGTATCAAAGGTTGTGACACATG 60.083 45.833 9.55 4.42 0.00 3.21
6093 9072 4.079253 GGGTATCAAAGGTTGTGACACAT 58.921 43.478 9.55 0.00 0.00 3.21
6094 9073 3.482436 GGGTATCAAAGGTTGTGACACA 58.518 45.455 3.56 3.56 0.00 3.72
6095 9074 2.482721 CGGGTATCAAAGGTTGTGACAC 59.517 50.000 0.00 0.00 0.00 3.67
6096 9075 2.105134 ACGGGTATCAAAGGTTGTGACA 59.895 45.455 0.00 0.00 0.00 3.58
6097 9076 2.482721 CACGGGTATCAAAGGTTGTGAC 59.517 50.000 0.00 0.00 0.00 3.67
6098 9077 2.105134 ACACGGGTATCAAAGGTTGTGA 59.895 45.455 0.00 0.00 0.00 3.58
6099 9078 2.225491 CACACGGGTATCAAAGGTTGTG 59.775 50.000 0.00 0.00 0.00 3.33
6100 9079 2.500229 CACACGGGTATCAAAGGTTGT 58.500 47.619 0.00 0.00 0.00 3.32
6101 9080 1.199097 GCACACGGGTATCAAAGGTTG 59.801 52.381 0.00 0.00 0.00 3.77
6102 9081 1.530323 GCACACGGGTATCAAAGGTT 58.470 50.000 0.00 0.00 0.00 3.50
6103 9082 0.672401 CGCACACGGGTATCAAAGGT 60.672 55.000 0.00 0.00 34.97 3.50
6104 9083 2.086510 CGCACACGGGTATCAAAGG 58.913 57.895 0.00 0.00 34.97 3.11
6115 9094 2.053465 CGTCAACAACCGCACACG 60.053 61.111 0.00 0.00 39.67 4.49
6116 9095 1.011574 GTCGTCAACAACCGCACAC 60.012 57.895 0.00 0.00 0.00 3.82
6117 9096 1.149361 GAGTCGTCAACAACCGCACA 61.149 55.000 0.00 0.00 0.00 4.57
6118 9097 0.874607 AGAGTCGTCAACAACCGCAC 60.875 55.000 0.00 0.00 0.00 5.34
6119 9098 1.440060 AGAGTCGTCAACAACCGCA 59.560 52.632 0.00 0.00 0.00 5.69
6120 9099 4.338327 AGAGTCGTCAACAACCGC 57.662 55.556 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.