Multiple sequence alignment - TraesCS1B01G300600

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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 TraesCS1B01G300600 chr1B 100.000 5103 0 0 1 5103 521003191 520998089 0.000000e+00 9424
1 TraesCS1B01G300600 chr1B 81.589 2140 250 85 1047 3114 520929143 520927076 0.000000e+00 1637
2 TraesCS1B01G300600 chr1B 77.632 760 131 22 3173 3913 520927047 520926308 4.720000e-115 425
3 TraesCS1B01G300600 chr1B 79.282 613 109 9 4491 5103 545059333 545059927 3.680000e-111 412
4 TraesCS1B01G300600 chr1B 86.007 293 36 4 4474 4764 377378097 377377808 4.960000e-80 309
5 TraesCS1B01G300600 chr1B 93.506 154 10 0 3957 4110 520926210 520926057 3.970000e-56 230
6 TraesCS1B01G300600 chr1A 92.834 2819 152 21 1645 4442 487465700 487462911 0.000000e+00 4041
7 TraesCS1B01G300600 chr1A 86.486 851 89 18 1673 2512 487332943 487332108 0.000000e+00 911
8 TraesCS1B01G300600 chr1A 90.148 609 37 15 97 688 487469924 487469322 0.000000e+00 771
9 TraesCS1B01G300600 chr1A 92.261 491 23 6 1178 1662 487466201 487465720 0.000000e+00 682
10 TraesCS1B01G300600 chr1A 89.135 451 38 5 703 1142 487466583 487466133 7.470000e-153 551
11 TraesCS1B01G300600 chr1A 82.385 545 60 17 2605 3114 487332085 487331542 4.690000e-120 442
12 TraesCS1B01G300600 chr1A 86.649 382 40 9 1171 1545 487333864 487333487 3.680000e-111 412
13 TraesCS1B01G300600 chr1A 93.506 154 10 0 3957 4110 487330777 487330624 3.970000e-56 230
14 TraesCS1B01G300600 chr1D 92.893 1801 97 16 2652 4442 387896391 387894612 0.000000e+00 2588
15 TraesCS1B01G300600 chr1D 92.067 1311 48 19 368 1662 387898775 387897505 0.000000e+00 1794
16 TraesCS1B01G300600 chr1D 94.701 1019 45 5 1645 2655 387897488 387896471 0.000000e+00 1574
17 TraesCS1B01G300600 chr1D 83.024 1726 174 52 1047 2730 387800776 387799128 0.000000e+00 1454
18 TraesCS1B01G300600 chr1D 83.099 639 106 2 4466 5103 346832657 346833294 9.520000e-162 580
19 TraesCS1B01G300600 chr1D 91.379 406 26 5 4 403 387899175 387898773 9.660000e-152 547
20 TraesCS1B01G300600 chr1D 85.479 365 39 10 2763 3114 387798726 387798363 8.070000e-98 368
21 TraesCS1B01G300600 chr1D 78.723 423 71 8 4682 5103 312730840 312730436 1.090000e-66 265
22 TraesCS1B01G300600 chr1D 94.805 154 8 0 3957 4110 387797018 387796865 1.840000e-59 241
23 TraesCS1B01G300600 chr1D 77.561 410 72 5 4694 5102 123686899 123687289 3.970000e-56 230
24 TraesCS1B01G300600 chr6D 81.789 615 89 13 4491 5103 307560194 307559601 1.280000e-135 494
25 TraesCS1B01G300600 chr6D 77.778 630 122 7 4474 5103 116733976 116734587 6.240000e-99 372
26 TraesCS1B01G300600 chr6D 82.071 396 67 4 4466 4860 311692960 311692568 8.190000e-88 335
27 TraesCS1B01G300600 chr6D 78.451 297 59 3 4472 4764 339541525 339541230 6.740000e-44 189
28 TraesCS1B01G300600 chr4B 81.123 641 83 17 4466 5103 437526976 437526371 3.570000e-131 479
29 TraesCS1B01G300600 chr7B 80.595 639 105 11 4466 5103 222517919 222518539 4.620000e-130 475
30 TraesCS1B01G300600 chr3D 79.844 640 125 4 4466 5103 82373217 82372580 1.000000e-126 464
31 TraesCS1B01G300600 chr2A 78.639 632 117 8 4472 5103 630613389 630612776 2.210000e-108 403
32 TraesCS1B01G300600 chr2A 85.211 142 21 0 4888 5029 589651243 589651384 4.120000e-31 147
33 TraesCS1B01G300600 chr3B 80.328 366 60 8 4486 4846 184514092 184514450 3.030000e-67 267
34 TraesCS1B01G300600 chr3B 74.317 183 43 3 4896 5077 320504865 320504686 1.970000e-09 75
35 TraesCS1B01G300600 chr2B 89.773 176 17 1 4928 5103 563832679 563832853 1.850000e-54 224


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 TraesCS1B01G300600 chr1B 520998089 521003191 5102 True 9424.000000 9424 100.000000 1 5103 1 chr1B.!!$R2 5102
1 TraesCS1B01G300600 chr1B 520926057 520929143 3086 True 764.000000 1637 84.242333 1047 4110 3 chr1B.!!$R3 3063
2 TraesCS1B01G300600 chr1B 545059333 545059927 594 False 412.000000 412 79.282000 4491 5103 1 chr1B.!!$F1 612
3 TraesCS1B01G300600 chr1A 487462911 487469924 7013 True 1511.250000 4041 91.094500 97 4442 4 chr1A.!!$R2 4345
4 TraesCS1B01G300600 chr1A 487330624 487333864 3240 True 498.750000 911 87.256500 1171 4110 4 chr1A.!!$R1 2939
5 TraesCS1B01G300600 chr1D 387894612 387899175 4563 True 1625.750000 2588 92.760000 4 4442 4 chr1D.!!$R3 4438
6 TraesCS1B01G300600 chr1D 387796865 387800776 3911 True 687.666667 1454 87.769333 1047 4110 3 chr1D.!!$R2 3063
7 TraesCS1B01G300600 chr1D 346832657 346833294 637 False 580.000000 580 83.099000 4466 5103 1 chr1D.!!$F2 637
8 TraesCS1B01G300600 chr6D 307559601 307560194 593 True 494.000000 494 81.789000 4491 5103 1 chr6D.!!$R1 612
9 TraesCS1B01G300600 chr6D 116733976 116734587 611 False 372.000000 372 77.778000 4474 5103 1 chr6D.!!$F1 629
10 TraesCS1B01G300600 chr4B 437526371 437526976 605 True 479.000000 479 81.123000 4466 5103 1 chr4B.!!$R1 637
11 TraesCS1B01G300600 chr7B 222517919 222518539 620 False 475.000000 475 80.595000 4466 5103 1 chr7B.!!$F1 637
12 TraesCS1B01G300600 chr3D 82372580 82373217 637 True 464.000000 464 79.844000 4466 5103 1 chr3D.!!$R1 637
13 TraesCS1B01G300600 chr2A 630612776 630613389 613 True 403.000000 403 78.639000 4472 5103 1 chr2A.!!$R1 631

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
722 3499 0.035458 GTGTACTCCTTGGTGCTGCT 59.965 55.0 0.0 0.0 0.00 4.24 F
947 3731 0.039437 CTATTCGATCCACCCCGACG 60.039 60.0 0.0 0.0 34.26 5.12 F
2548 5971 0.529119 CCGGTCCCTATGTTGTACGC 60.529 60.0 0.0 0.0 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 4541 0.032952 GTAGTGGACACGTGAAGCCA 59.967 55.0 25.01 21.91 36.20 4.75 R
2946 6850 0.324368 TGAGGAAGAGCCGCCTAAGA 60.324 55.0 0.00 0.00 43.43 2.10 R
4225 8728 0.179004 TTGTTTCGTCCAGGCCATGT 60.179 50.0 5.01 0.00 0.00 3.21 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
46 47 9.469097 TTTTATAATGGCTAAAGCTTCCTTGTA 57.531 29.630 0.00 0.00 41.70 2.41
54 55 7.027760 GGCTAAAGCTTCCTTGTATTAAACAC 58.972 38.462 0.00 0.00 38.43 3.32
77 78 8.253113 ACACAATTAATCTTGGGATCAACATTC 58.747 33.333 0.00 0.00 33.62 2.67
88 89 7.880160 TGGGATCAACATTCATTAAGGTAAG 57.120 36.000 0.00 0.00 0.00 2.34
94 95 8.918202 TCAACATTCATTAAGGTAAGTCTTGT 57.082 30.769 0.00 0.00 0.00 3.16
159 161 7.717875 ACACATTACTAGTCTTTGGTAAGCAAA 59.282 33.333 0.00 0.00 0.00 3.68
211 214 5.961272 ACCGATTTACCAAATGAAACCATC 58.039 37.500 0.00 0.00 0.00 3.51
227 230 2.290705 ACCATCCCTTCTTTGGTAACCG 60.291 50.000 0.00 0.00 41.88 4.44
243 246 5.353123 TGGTAACCGATAAGTGCTGATTTTC 59.647 40.000 0.00 0.00 0.00 2.29
281 287 2.684881 ACGGATTCAATTGGCAGCTAAG 59.315 45.455 5.42 0.00 0.00 2.18
282 288 2.684881 CGGATTCAATTGGCAGCTAAGT 59.315 45.455 5.42 0.00 0.00 2.24
283 289 3.242870 CGGATTCAATTGGCAGCTAAGTC 60.243 47.826 5.42 0.00 0.00 3.01
290 296 2.128771 TGGCAGCTAAGTCCCATTTC 57.871 50.000 0.00 0.00 0.00 2.17
291 297 1.340991 TGGCAGCTAAGTCCCATTTCC 60.341 52.381 0.00 0.00 0.00 3.13
329 335 5.219768 CGGCGATTGCGTATAAAATATTTGC 60.220 40.000 0.00 1.06 44.10 3.68
344 350 1.315981 TTTGCTGTCCCGTTGCAACA 61.316 50.000 28.01 9.17 44.81 3.33
557 599 2.423373 GGGTTCATCCAGCCACATACAT 60.423 50.000 0.00 0.00 38.11 2.29
559 601 4.507335 GGGTTCATCCAGCCACATACATAT 60.507 45.833 0.00 0.00 38.11 1.78
722 3499 0.035458 GTGTACTCCTTGGTGCTGCT 59.965 55.000 0.00 0.00 0.00 4.24
727 3504 1.841302 CTCCTTGGTGCTGCTGGGTA 61.841 60.000 0.00 0.00 0.00 3.69
793 3570 3.562779 CTGGTGGTAACGGACGCGT 62.563 63.158 13.85 13.85 42.51 6.01
895 3679 1.210413 CGGACACGGTCAGAGACAG 59.790 63.158 6.41 0.00 33.68 3.51
942 3726 0.600255 CACCGCTATTCGATCCACCC 60.600 60.000 0.00 0.00 41.67 4.61
945 3729 1.802337 CGCTATTCGATCCACCCCGA 61.802 60.000 0.00 0.00 41.67 5.14
947 3731 0.039437 CTATTCGATCCACCCCGACG 60.039 60.000 0.00 0.00 34.26 5.12
948 3732 1.457823 TATTCGATCCACCCCGACGG 61.458 60.000 6.99 6.99 34.26 4.79
968 3752 6.141560 ACGGCAGTTTCCTAATACTACTAC 57.858 41.667 0.00 0.00 0.00 2.73
978 3762 6.156089 TCCTAATACTACTACTCCTCCTCCA 58.844 44.000 0.00 0.00 0.00 3.86
996 3783 2.176889 CCAACTCCTCCTCCTCGTTTA 58.823 52.381 0.00 0.00 0.00 2.01
1005 3792 1.560923 CTCCTCGTTTACTCATGGCG 58.439 55.000 0.00 0.00 0.00 5.69
1019 3806 2.126189 GGCGACCGTACACCAGAC 60.126 66.667 0.00 0.00 0.00 3.51
1021 3808 2.922950 GCGACCGTACACCAGACCA 61.923 63.158 0.00 0.00 0.00 4.02
1053 3840 1.205064 CGTGAACGGCAAGAGCAAG 59.795 57.895 0.00 0.00 44.61 4.01
1061 3848 2.032528 CAAGAGCAAGGGCCACGA 59.967 61.111 6.18 0.00 42.56 4.35
1095 3882 1.226295 GAACGGCAATAGCAACGGC 60.226 57.895 0.00 0.00 44.61 5.68
1098 3885 2.480610 CGGCAATAGCAACGGCCAT 61.481 57.895 2.24 0.00 46.75 4.40
1099 3886 1.066257 GGCAATAGCAACGGCCATG 59.934 57.895 2.24 1.58 45.70 3.66
1100 3887 1.589727 GCAATAGCAACGGCCATGC 60.590 57.895 20.11 20.11 44.15 4.06
1101 3888 1.066257 CAATAGCAACGGCCATGCC 59.934 57.895 23.06 8.81 44.91 4.40
1130 3917 4.306471 CGCGAACGGCAACAGCAA 62.306 61.111 0.00 0.00 43.84 3.91
1131 3918 2.725815 GCGAACGGCAACAGCAAC 60.726 61.111 0.00 0.00 42.87 4.17
1132 3919 2.425124 CGAACGGCAACAGCAACG 60.425 61.111 0.00 0.00 0.00 4.10
1133 3920 2.051345 GAACGGCAACAGCAACGG 60.051 61.111 0.00 0.00 0.00 4.44
1134 3921 4.264638 AACGGCAACAGCAACGGC 62.265 61.111 0.00 0.00 41.61 5.68
1137 3924 4.645921 GGCAACAGCAACGGCCAC 62.646 66.667 2.24 0.00 45.70 5.01
1139 3926 4.326766 CAACAGCAACGGCCACGG 62.327 66.667 2.24 0.00 46.48 4.94
1579 4515 1.222766 TTTCGCGTGTTGCACCGTAT 61.223 50.000 5.77 0.00 46.97 3.06
1622 4954 1.069765 CTGGCTTCACGTGTCCACT 59.930 57.895 16.51 0.00 0.00 4.00
1640 4977 3.197766 CCACTACTGTTCTTCCCTATGCA 59.802 47.826 0.00 0.00 0.00 3.96
1780 5155 2.705658 AGCGATTGAGGTCATAATCCCA 59.294 45.455 0.00 0.00 31.24 4.37
1865 5240 2.428403 GCGCGGCGTTCAACAAAT 60.428 55.556 24.46 0.00 0.00 2.32
1882 5257 5.529581 ACAAATTGGAGGTTCGACATTTT 57.470 34.783 0.00 0.00 0.00 1.82
1888 5263 2.742589 GGAGGTTCGACATTTTGACCTC 59.257 50.000 18.02 18.02 40.94 3.85
1910 5285 3.083997 CCGAGAAGGGGTGGGAGG 61.084 72.222 0.00 0.00 35.97 4.30
2014 5389 4.158394 AGCGTTTACTCCTACGACCATTTA 59.842 41.667 0.00 0.00 40.03 1.40
2123 5517 5.301551 TGTGCTGATGTTGTTCAATTAGGTT 59.698 36.000 0.00 0.00 0.00 3.50
2187 5581 1.280998 AGGTATACGGCAAGCTGGTTT 59.719 47.619 5.79 0.00 0.00 3.27
2193 5587 2.510551 GGCAAGCTGGTTTTGGGCT 61.511 57.895 0.00 0.00 37.99 5.19
2546 5969 1.202498 GCTCCGGTCCCTATGTTGTAC 60.202 57.143 0.00 0.00 0.00 2.90
2548 5971 0.529119 CCGGTCCCTATGTTGTACGC 60.529 60.000 0.00 0.00 0.00 4.42
2736 6612 9.307121 CAGACTATTGAATACAACTAGTCCTTG 57.693 37.037 17.65 0.00 41.36 3.61
3132 7048 5.977489 AAGCCAGTAGTAAAATGTTTCCC 57.023 39.130 0.00 0.00 0.00 3.97
3318 7236 6.624352 AATCACCTTGATATCATTTGTCCG 57.376 37.500 6.17 0.00 35.76 4.79
3321 7239 5.353956 TCACCTTGATATCATTTGTCCGTTG 59.646 40.000 6.17 0.00 0.00 4.10
3339 7264 4.911610 CCGTTGTTTATTGTTTCTGCAGAG 59.088 41.667 17.43 0.00 0.00 3.35
3455 7382 6.189677 TGTAAACAGGTGAAACTGAACTTG 57.810 37.500 1.53 0.00 40.97 3.16
3654 7581 8.824781 AGAACATTCGATTCTATTTGACTGATG 58.175 33.333 0.00 0.00 34.59 3.07
3702 7629 9.559958 CATATTCTAATGTGTTTTTGGACTGTC 57.440 33.333 0.00 0.00 0.00 3.51
3758 8199 9.864034 GTACGCATATAATGATTACCATAATGC 57.136 33.333 0.00 0.00 39.77 3.56
3807 8248 8.908903 TGTTTTTATGTGAAAGACTAACATGGT 58.091 29.630 0.00 0.00 36.08 3.55
3814 8255 6.824196 TGTGAAAGACTAACATGGTTTGTACA 59.176 34.615 0.00 0.00 37.68 2.90
3836 8277 0.536460 TCCTTGTTTCTTGACCCGGC 60.536 55.000 0.00 0.00 0.00 6.13
3844 8293 2.203042 TTGACCCGGCGTCGTTTT 60.203 55.556 9.28 0.00 45.23 2.43
3851 8300 1.267832 CCCGGCGTCGTTTTTATCATG 60.268 52.381 9.28 0.00 33.95 3.07
3966 8469 8.213679 ACTAATGTATGTATGCCTCTCAAATGT 58.786 33.333 0.00 0.00 0.00 2.71
4022 8525 4.808364 GCATTACTTTTGCTTGTGTTCCAA 59.192 37.500 0.00 0.00 37.14 3.53
4032 8535 3.303395 GCTTGTGTTCCAACTTCTCTTCG 60.303 47.826 0.00 0.00 0.00 3.79
4119 8622 6.874134 GGTTGTTAGTTGTACATCTGACTGAT 59.126 38.462 22.27 0.00 35.40 2.90
4145 8648 7.147915 TGCTGTAAATCATTTTCAGTTATCCCC 60.148 37.037 15.79 1.52 0.00 4.81
4225 8728 8.274322 ACATCTCCTTGAATATGTTATGGTTGA 58.726 33.333 0.00 0.00 0.00 3.18
4254 8757 4.437390 CCTGGACGAAACAATAGTGAATGC 60.437 45.833 0.00 0.00 0.00 3.56
4276 8779 4.994852 GCTAGTGAAGTTACATTGGTGTCA 59.005 41.667 0.00 0.00 39.77 3.58
4277 8780 5.120830 GCTAGTGAAGTTACATTGGTGTCAG 59.879 44.000 0.00 0.00 39.77 3.51
4295 8798 8.621286 TGGTGTCAGAGATCTTTAAAGTTTTTC 58.379 33.333 14.74 8.67 0.00 2.29
4358 8861 4.724279 TTAGAGGAAAAGGCATATCCCC 57.276 45.455 0.00 0.00 33.55 4.81
4392 8895 3.942130 AAGCCTAACAAGCCAAATCAC 57.058 42.857 0.00 0.00 0.00 3.06
4400 8903 6.375455 CCTAACAAGCCAAATCACAGAGTAAT 59.625 38.462 0.00 0.00 0.00 1.89
4406 8909 7.944729 AGCCAAATCACAGAGTAATAAACAT 57.055 32.000 0.00 0.00 0.00 2.71
4408 8911 7.394359 AGCCAAATCACAGAGTAATAAACATGT 59.606 33.333 0.00 0.00 32.28 3.21
4411 8914 7.865706 AATCACAGAGTAATAAACATGTCCC 57.134 36.000 0.00 0.00 30.34 4.46
4417 8920 6.036083 CAGAGTAATAAACATGTCCCGTTCAG 59.964 42.308 0.00 0.00 0.00 3.02
4419 8922 6.106673 AGTAATAAACATGTCCCGTTCAGAG 58.893 40.000 0.00 0.00 0.00 3.35
4420 8923 2.930826 AAACATGTCCCGTTCAGAGT 57.069 45.000 0.00 0.00 0.00 3.24
4423 8926 1.000955 ACATGTCCCGTTCAGAGTCAC 59.999 52.381 0.00 0.00 0.00 3.67
4442 8945 8.915036 AGAGTCACAGAAAAGAAGTCTTAGTAA 58.085 33.333 0.00 0.00 34.61 2.24
4443 8946 9.699703 GAGTCACAGAAAAGAAGTCTTAGTAAT 57.300 33.333 0.00 0.00 34.61 1.89
4444 8947 9.699703 AGTCACAGAAAAGAAGTCTTAGTAATC 57.300 33.333 0.00 0.00 34.61 1.75
4445 8948 8.640291 GTCACAGAAAAGAAGTCTTAGTAATCG 58.360 37.037 0.00 0.00 34.61 3.34
4446 8949 7.328737 TCACAGAAAAGAAGTCTTAGTAATCGC 59.671 37.037 0.00 0.00 34.61 4.58
4447 8950 6.590677 ACAGAAAAGAAGTCTTAGTAATCGCC 59.409 38.462 0.00 0.00 34.61 5.54
4448 8951 6.814146 CAGAAAAGAAGTCTTAGTAATCGCCT 59.186 38.462 0.00 0.00 34.61 5.52
4449 8952 6.814146 AGAAAAGAAGTCTTAGTAATCGCCTG 59.186 38.462 0.00 0.00 34.61 4.85
4450 8953 5.916661 AAGAAGTCTTAGTAATCGCCTGA 57.083 39.130 0.00 0.00 33.79 3.86
4451 8954 5.508200 AGAAGTCTTAGTAATCGCCTGAG 57.492 43.478 0.00 0.00 0.00 3.35
4452 8955 4.951094 AGAAGTCTTAGTAATCGCCTGAGT 59.049 41.667 0.00 0.00 0.00 3.41
4453 8956 6.120905 AGAAGTCTTAGTAATCGCCTGAGTA 58.879 40.000 0.00 0.00 0.00 2.59
4454 8957 6.773685 AGAAGTCTTAGTAATCGCCTGAGTAT 59.226 38.462 0.00 0.00 0.00 2.12
4455 8958 6.963083 AGTCTTAGTAATCGCCTGAGTATT 57.037 37.500 0.00 0.00 0.00 1.89
4456 8959 8.461249 AAGTCTTAGTAATCGCCTGAGTATTA 57.539 34.615 0.00 0.00 0.00 0.98
4457 8960 8.101654 AGTCTTAGTAATCGCCTGAGTATTAG 57.898 38.462 0.00 0.00 0.00 1.73
4458 8961 7.720515 AGTCTTAGTAATCGCCTGAGTATTAGT 59.279 37.037 0.00 0.00 0.00 2.24
4459 8962 8.997323 GTCTTAGTAATCGCCTGAGTATTAGTA 58.003 37.037 0.00 0.00 0.00 1.82
4460 8963 9.565090 TCTTAGTAATCGCCTGAGTATTAGTAA 57.435 33.333 0.00 0.00 33.31 2.24
4461 8964 9.828852 CTTAGTAATCGCCTGAGTATTAGTAAG 57.171 37.037 13.62 13.62 39.87 2.34
4462 8965 7.216973 AGTAATCGCCTGAGTATTAGTAAGG 57.783 40.000 0.00 0.00 0.00 2.69
4463 8966 5.470047 AATCGCCTGAGTATTAGTAAGGG 57.530 43.478 4.35 0.00 0.00 3.95
4464 8967 3.228453 TCGCCTGAGTATTAGTAAGGGG 58.772 50.000 11.32 11.32 41.13 4.79
4480 8983 3.546543 GGATCATGACGGGGCGGA 61.547 66.667 0.00 0.00 0.00 5.54
4484 8987 0.762418 ATCATGACGGGGCGGATTAA 59.238 50.000 0.00 0.00 0.00 1.40
4513 9016 2.047061 TCACTACTGGAAACTGCTGGT 58.953 47.619 0.00 0.00 0.00 4.00
4519 9022 0.108585 TGGAAACTGCTGGTGACTCC 59.891 55.000 0.00 0.00 0.00 3.85
4555 9058 0.988832 TATGACTTTGGCGAGGGGTT 59.011 50.000 0.00 0.00 0.00 4.11
4573 9076 2.159707 GGTTGAATGAACACGATCACGG 60.160 50.000 0.00 0.00 44.46 4.94
4617 9120 3.118408 TGCACAATAGCGGTTCTAAGGAT 60.118 43.478 0.00 0.00 37.31 3.24
4647 9150 0.396695 TTCCGGGTCTCTATCGCCTT 60.397 55.000 0.00 0.00 0.00 4.35
4730 9233 2.292061 ACCGGGTTAGAGTAGTGACCAT 60.292 50.000 6.32 0.00 33.81 3.55
4826 9330 2.041922 TCCCTGGCGCCTCTACAT 60.042 61.111 29.70 0.00 0.00 2.29
4829 9333 2.136878 CCTGGCGCCTCTACATCCT 61.137 63.158 29.70 0.00 0.00 3.24
4840 9362 2.083835 CTACATCCTGGGCCGTACCG 62.084 65.000 0.00 0.00 40.62 4.02
4851 9373 3.122850 CGTACCGGGCGGATTACT 58.877 61.111 6.32 0.00 38.96 2.24
4852 9374 1.438814 CGTACCGGGCGGATTACTT 59.561 57.895 6.32 0.00 38.96 2.24
4853 9375 0.872881 CGTACCGGGCGGATTACTTG 60.873 60.000 6.32 0.00 38.96 3.16
4854 9376 0.176449 GTACCGGGCGGATTACTTGT 59.824 55.000 6.32 0.00 38.96 3.16
4855 9377 0.903942 TACCGGGCGGATTACTTGTT 59.096 50.000 6.32 0.00 38.96 2.83
4856 9378 0.392060 ACCGGGCGGATTACTTGTTC 60.392 55.000 6.32 0.00 38.96 3.18
4857 9379 1.093496 CCGGGCGGATTACTTGTTCC 61.093 60.000 0.00 0.00 37.50 3.62
4891 9413 3.762247 CCGGCCCCAAGCATGTTG 61.762 66.667 0.00 0.00 46.50 3.33
4977 9499 3.091545 TGGAAGCATTCTGATCCAAACC 58.908 45.455 0.00 0.00 46.56 3.27
5031 9553 1.001764 CAGCATCCAACTGAGCCCA 60.002 57.895 0.00 0.00 37.32 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 9.826574 AATGAATGTTGATCCCAAGATTAATTG 57.173 29.630 8.80 0.00 43.57 2.32
69 70 8.918202 ACAAGACTTACCTTAATGAATGTTGA 57.082 30.769 0.00 0.00 0.00 3.18
211 214 4.634443 CACTTATCGGTTACCAAAGAAGGG 59.366 45.833 12.97 5.78 0.00 3.95
262 268 3.067320 GGACTTAGCTGCCAATTGAATCC 59.933 47.826 7.12 0.00 0.00 3.01
281 287 5.066505 GTGATTACATGTCAGGAAATGGGAC 59.933 44.000 0.00 0.00 0.00 4.46
282 288 5.192927 GTGATTACATGTCAGGAAATGGGA 58.807 41.667 0.00 0.00 0.00 4.37
283 289 4.035558 CGTGATTACATGTCAGGAAATGGG 59.964 45.833 0.00 0.00 34.35 4.00
290 296 0.930310 CGCCGTGATTACATGTCAGG 59.070 55.000 0.00 0.00 0.00 3.86
291 297 1.921243 TCGCCGTGATTACATGTCAG 58.079 50.000 0.00 0.00 0.00 3.51
329 335 1.095228 AGTGTGTTGCAACGGGACAG 61.095 55.000 23.79 0.00 0.00 3.51
344 350 5.804639 TGTTGGACTAGATAATTGCAGTGT 58.195 37.500 0.00 0.00 0.00 3.55
528 570 1.414550 GCTGGATGAACCCTCCTACTC 59.585 57.143 0.00 0.00 38.00 2.59
557 599 2.835764 ACCCAGTTCCGCTCAAAGTATA 59.164 45.455 0.00 0.00 0.00 1.47
559 601 1.053424 ACCCAGTTCCGCTCAAAGTA 58.947 50.000 0.00 0.00 0.00 2.24
722 3499 4.277921 GTCCGTTTTGGTTTTATGTACCCA 59.722 41.667 0.00 0.00 39.52 4.51
727 3504 2.287728 GCGGTCCGTTTTGGTTTTATGT 60.288 45.455 13.94 0.00 39.52 2.29
855 3632 4.120331 GCACATGAACTGGGCGGC 62.120 66.667 0.00 0.00 46.18 6.53
882 3666 0.315568 GTTGCTCTGTCTCTGACCGT 59.684 55.000 0.00 0.00 0.00 4.83
942 3726 2.159142 AGTATTAGGAAACTGCCGTCGG 60.159 50.000 6.99 6.99 43.88 4.79
945 3729 5.890419 AGTAGTAGTATTAGGAAACTGCCGT 59.110 40.000 0.00 0.00 43.88 5.68
947 3731 6.550481 AGGAGTAGTAGTATTAGGAAACTGCC 59.450 42.308 0.00 0.00 43.88 4.85
948 3732 7.255555 GGAGGAGTAGTAGTATTAGGAAACTGC 60.256 44.444 0.00 0.00 43.88 4.40
968 3752 0.338120 AGGAGGAGTTGGAGGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
978 3762 3.090790 GAGTAAACGAGGAGGAGGAGTT 58.909 50.000 0.00 0.00 0.00 3.01
996 3783 1.214589 GTGTACGGTCGCCATGAGT 59.785 57.895 0.00 0.00 0.00 3.41
1005 3792 0.665369 CGTTGGTCTGGTGTACGGTC 60.665 60.000 0.00 0.00 0.00 4.79
1037 3824 1.600636 CCCTTGCTCTTGCCGTTCA 60.601 57.895 0.00 0.00 38.71 3.18
1113 3900 4.306471 TTGCTGTTGCCGTTCGCG 62.306 61.111 0.00 0.00 42.08 5.87
1114 3901 2.725815 GTTGCTGTTGCCGTTCGC 60.726 61.111 0.00 0.00 38.71 4.70
1115 3902 2.425124 CGTTGCTGTTGCCGTTCG 60.425 61.111 0.00 0.00 38.71 3.95
1116 3903 2.051345 CCGTTGCTGTTGCCGTTC 60.051 61.111 0.00 0.00 38.71 3.95
1117 3904 4.264638 GCCGTTGCTGTTGCCGTT 62.265 61.111 0.00 0.00 38.71 4.44
1120 3907 4.645921 GTGGCCGTTGCTGTTGCC 62.646 66.667 0.00 0.00 44.27 4.52
1121 3908 4.980903 CGTGGCCGTTGCTGTTGC 62.981 66.667 0.00 0.00 37.74 4.17
1122 3909 4.326766 CCGTGGCCGTTGCTGTTG 62.327 66.667 0.00 0.00 37.74 3.33
1534 4447 6.379988 AGGAAATTGTTGTTGTGTTACCTTCT 59.620 34.615 0.00 0.00 0.00 2.85
1602 4538 3.414700 GGACACGTGAAGCCAGCG 61.415 66.667 25.01 0.00 0.00 5.18
1603 4539 2.280797 TGGACACGTGAAGCCAGC 60.281 61.111 25.01 2.02 0.00 4.85
1604 4540 0.317160 TAGTGGACACGTGAAGCCAG 59.683 55.000 25.01 0.00 36.20 4.85
1605 4541 0.032952 GTAGTGGACACGTGAAGCCA 59.967 55.000 25.01 21.91 36.20 4.75
1606 4542 0.317479 AGTAGTGGACACGTGAAGCC 59.683 55.000 25.01 19.60 36.20 4.35
1607 4543 1.269621 ACAGTAGTGGACACGTGAAGC 60.270 52.381 25.01 10.81 36.20 3.86
1608 4544 2.795175 ACAGTAGTGGACACGTGAAG 57.205 50.000 25.01 0.00 36.20 3.02
1622 4954 5.425217 TCTGAATGCATAGGGAAGAACAGTA 59.575 40.000 0.00 0.00 0.00 2.74
1640 4977 6.015095 GGTGGAAGAAGGTCAAATTTCTGAAT 60.015 38.462 0.00 0.00 34.09 2.57
1765 5140 3.455910 CCAGAACTGGGATTATGACCTCA 59.544 47.826 12.54 0.00 46.81 3.86
1780 5155 2.597510 GCGGTTTGGGCCAGAACT 60.598 61.111 22.21 0.00 0.00 3.01
1864 5239 3.506067 GGTCAAAATGTCGAACCTCCAAT 59.494 43.478 0.00 0.00 0.00 3.16
1865 5240 2.882137 GGTCAAAATGTCGAACCTCCAA 59.118 45.455 0.00 0.00 0.00 3.53
1882 5257 0.687757 CCTTCTCGGGGATGAGGTCA 60.688 60.000 0.00 0.00 36.61 4.02
2014 5389 3.011708 AGGATGGATGTAAAACCTTGGCT 59.988 43.478 0.00 0.00 0.00 4.75
2123 5517 1.174712 GCTTTCTTGCCACCTCTGCA 61.175 55.000 0.00 0.00 36.84 4.41
2230 5624 2.170607 CCTATGGACAACACAGGGGTAG 59.829 54.545 0.00 0.00 0.00 3.18
2406 5804 8.908903 AGATCTACCAAAAGATAGTCAGTACAG 58.091 37.037 0.00 0.00 36.33 2.74
2548 5971 1.794151 TTTGACATGCACGTGGGCTG 61.794 55.000 18.88 6.72 34.04 4.85
2711 6226 8.478877 CCAAGGACTAGTTGTATTCAATAGTCT 58.521 37.037 20.52 12.11 40.07 3.24
2840 6736 3.951775 AGAGAAGCTGTTGTAGGTGAG 57.048 47.619 0.00 0.00 37.17 3.51
2933 6837 6.534634 AGCCGCCTAAGAAATTTGATAGTAT 58.465 36.000 0.00 0.00 0.00 2.12
2946 6850 0.324368 TGAGGAAGAGCCGCCTAAGA 60.324 55.000 0.00 0.00 43.43 2.10
3071 6975 0.538057 CTTCTGGCTTGTGAGGGCAA 60.538 55.000 0.00 0.00 38.72 4.52
3115 7019 6.734281 ACTCCCTAGGGAAACATTTTACTACT 59.266 38.462 30.59 0.00 44.66 2.57
3132 7048 7.275920 AGTTTATGCTTATTGACACTCCCTAG 58.724 38.462 0.00 0.00 0.00 3.02
3163 7079 9.051027 CATTGCGGTTCGAAATTAATCATATAC 57.949 33.333 0.00 0.00 32.17 1.47
3238 7156 6.775088 TCTTCGAATACATGCATCTTTGAAC 58.225 36.000 0.00 0.00 0.00 3.18
3318 7236 6.494842 TCACTCTGCAGAAACAATAAACAAC 58.505 36.000 18.85 0.00 0.00 3.32
3321 7239 7.959651 CAGTATCACTCTGCAGAAACAATAAAC 59.040 37.037 18.85 8.60 0.00 2.01
3387 7314 7.663493 TGTGGAAAAATGGTCTTTGTTTTTCTT 59.337 29.630 17.02 0.00 44.83 2.52
3395 7322 5.175491 CACGATTGTGGAAAAATGGTCTTTG 59.825 40.000 5.04 0.00 42.59 2.77
3398 7325 4.503741 CACGATTGTGGAAAAATGGTCT 57.496 40.909 5.04 0.00 42.59 3.85
3702 7629 7.817962 TCTCGGAAATTGTTAAGAACTTCCTAG 59.182 37.037 19.54 17.92 33.44 3.02
3795 8236 6.213600 AGGAGATGTACAAACCATGTTAGTCT 59.786 38.462 0.00 0.00 43.63 3.24
3807 8248 6.262273 GGTCAAGAAACAAGGAGATGTACAAA 59.738 38.462 0.00 0.00 32.02 2.83
3814 8255 2.290323 CCGGGTCAAGAAACAAGGAGAT 60.290 50.000 0.00 0.00 0.00 2.75
3836 8277 6.577055 ACAAACATGTCATGATAAAAACGACG 59.423 34.615 19.77 0.00 0.00 5.12
3844 8293 4.460034 AGCAGCACAAACATGTCATGATAA 59.540 37.500 19.77 0.00 0.00 1.75
3851 8300 2.042104 GTGAGCAGCACAAACATGTC 57.958 50.000 0.00 0.00 46.91 3.06
3937 8413 7.360113 TGAGAGGCATACATACATTAGTTCA 57.640 36.000 0.00 0.00 0.00 3.18
3943 8419 7.663081 CCTACATTTGAGAGGCATACATACATT 59.337 37.037 0.00 0.00 0.00 2.71
3966 8469 2.196595 CCATTCCCAGAACACTCCCTA 58.803 52.381 0.00 0.00 0.00 3.53
4032 8535 4.392921 TTGATCCTTTCGAGACCATCTC 57.607 45.455 0.00 0.00 40.06 2.75
4119 8622 7.147915 GGGGATAACTGAAAATGATTTACAGCA 60.148 37.037 0.00 0.00 32.03 4.41
4225 8728 0.179004 TTGTTTCGTCCAGGCCATGT 60.179 50.000 5.01 0.00 0.00 3.21
4254 8757 6.455647 TCTGACACCAATGTAACTTCACTAG 58.544 40.000 0.00 0.00 39.95 2.57
4295 8798 9.014297 ACTTGGAGTAATATCAAAGTTCCAAAG 57.986 33.333 4.80 2.74 39.93 2.77
4310 8813 9.574516 AAAAAGAGAATGTGTACTTGGAGTAAT 57.425 29.630 0.00 0.00 31.62 1.89
4311 8814 8.974060 AAAAAGAGAATGTGTACTTGGAGTAA 57.026 30.769 0.00 0.00 31.62 2.24
4343 8846 2.640316 AGTCGGGGATATGCCTTTTC 57.360 50.000 13.55 2.23 36.66 2.29
4347 8850 4.684724 TCTATAAAGTCGGGGATATGCCT 58.315 43.478 13.55 0.00 36.66 4.75
4349 8852 7.224949 GCTTTATCTATAAAGTCGGGGATATGC 59.775 40.741 18.85 0.00 46.78 3.14
4350 8853 7.711339 GGCTTTATCTATAAAGTCGGGGATATG 59.289 40.741 18.85 0.00 46.78 1.78
4351 8854 7.793036 GGCTTTATCTATAAAGTCGGGGATAT 58.207 38.462 18.85 0.00 46.78 1.63
4352 8855 7.179076 GGCTTTATCTATAAAGTCGGGGATA 57.821 40.000 18.85 0.00 46.78 2.59
4353 8856 6.051179 GGCTTTATCTATAAAGTCGGGGAT 57.949 41.667 18.85 0.00 46.78 3.85
4354 8857 5.479124 GGCTTTATCTATAAAGTCGGGGA 57.521 43.478 18.85 0.00 46.78 4.81
4377 8880 8.856153 TTATTACTCTGTGATTTGGCTTGTTA 57.144 30.769 0.00 0.00 0.00 2.41
4392 8895 5.872617 TGAACGGGACATGTTTATTACTCTG 59.127 40.000 0.00 0.00 0.00 3.35
4400 8903 3.322541 TGACTCTGAACGGGACATGTTTA 59.677 43.478 0.00 0.00 0.00 2.01
4406 8909 0.673985 CTGTGACTCTGAACGGGACA 59.326 55.000 0.00 0.00 0.00 4.02
4408 8911 1.699730 TTCTGTGACTCTGAACGGGA 58.300 50.000 0.00 0.00 0.00 5.14
4411 8914 4.806247 ACTTCTTTTCTGTGACTCTGAACG 59.194 41.667 0.00 0.00 34.58 3.95
4417 8920 9.699703 ATTACTAAGACTTCTTTTCTGTGACTC 57.300 33.333 0.00 0.00 37.40 3.36
4419 8922 8.640291 CGATTACTAAGACTTCTTTTCTGTGAC 58.360 37.037 0.00 0.00 37.40 3.67
4420 8923 7.328737 GCGATTACTAAGACTTCTTTTCTGTGA 59.671 37.037 0.00 0.00 37.40 3.58
4423 8926 6.814146 AGGCGATTACTAAGACTTCTTTTCTG 59.186 38.462 0.00 0.00 37.40 3.02
4442 8945 3.833070 CCCCTTACTAATACTCAGGCGAT 59.167 47.826 0.00 0.00 0.00 4.58
4443 8946 3.117398 TCCCCTTACTAATACTCAGGCGA 60.117 47.826 0.00 0.00 0.00 5.54
4444 8947 3.228453 TCCCCTTACTAATACTCAGGCG 58.772 50.000 0.00 0.00 0.00 5.52
4445 8948 4.838986 TGATCCCCTTACTAATACTCAGGC 59.161 45.833 0.00 0.00 0.00 4.85
4446 8949 6.726299 TCATGATCCCCTTACTAATACTCAGG 59.274 42.308 0.00 0.00 0.00 3.86
4447 8950 7.575909 CGTCATGATCCCCTTACTAATACTCAG 60.576 44.444 0.00 0.00 0.00 3.35
4448 8951 6.208797 CGTCATGATCCCCTTACTAATACTCA 59.791 42.308 0.00 0.00 0.00 3.41
4449 8952 6.350277 CCGTCATGATCCCCTTACTAATACTC 60.350 46.154 0.00 0.00 0.00 2.59
4450 8953 5.480772 CCGTCATGATCCCCTTACTAATACT 59.519 44.000 0.00 0.00 0.00 2.12
4451 8954 5.337330 CCCGTCATGATCCCCTTACTAATAC 60.337 48.000 0.00 0.00 0.00 1.89
4452 8955 4.775780 CCCGTCATGATCCCCTTACTAATA 59.224 45.833 0.00 0.00 0.00 0.98
4453 8956 3.583086 CCCGTCATGATCCCCTTACTAAT 59.417 47.826 0.00 0.00 0.00 1.73
4454 8957 2.969950 CCCGTCATGATCCCCTTACTAA 59.030 50.000 0.00 0.00 0.00 2.24
4455 8958 2.605257 CCCGTCATGATCCCCTTACTA 58.395 52.381 0.00 0.00 0.00 1.82
4456 8959 1.424638 CCCGTCATGATCCCCTTACT 58.575 55.000 0.00 0.00 0.00 2.24
4457 8960 0.396811 CCCCGTCATGATCCCCTTAC 59.603 60.000 0.00 0.00 0.00 2.34
4458 8961 1.415672 GCCCCGTCATGATCCCCTTA 61.416 60.000 0.00 0.00 0.00 2.69
4459 8962 2.757124 GCCCCGTCATGATCCCCTT 61.757 63.158 0.00 0.00 0.00 3.95
4460 8963 3.171388 GCCCCGTCATGATCCCCT 61.171 66.667 0.00 0.00 0.00 4.79
4461 8964 4.626081 CGCCCCGTCATGATCCCC 62.626 72.222 0.00 0.00 0.00 4.81
4462 8965 4.626081 CCGCCCCGTCATGATCCC 62.626 72.222 0.00 0.00 0.00 3.85
4463 8966 2.397413 AATCCGCCCCGTCATGATCC 62.397 60.000 0.00 0.00 0.00 3.36
4464 8967 0.320374 TAATCCGCCCCGTCATGATC 59.680 55.000 0.00 0.00 0.00 2.92
4480 8983 3.508762 CAGTAGTGAACGGCGTCTTAAT 58.491 45.455 15.17 4.58 0.00 1.40
4484 8987 0.892358 TCCAGTAGTGAACGGCGTCT 60.892 55.000 15.17 9.22 0.00 4.18
4513 9016 3.381983 AGCCGACGCATGGAGTCA 61.382 61.111 0.00 0.00 38.46 3.41
4519 9022 1.522676 CATAGTTACAGCCGACGCATG 59.477 52.381 0.00 0.00 37.52 4.06
4555 9058 1.075542 GCCGTGATCGTGTTCATTCA 58.924 50.000 0.00 0.00 35.01 2.57
4573 9076 1.227292 GGCGGCTTACTCCTACAGC 60.227 63.158 0.00 0.00 0.00 4.40
4617 9120 3.581332 AGAGACCCGGAACATAGTTGAAA 59.419 43.478 0.73 0.00 0.00 2.69
4647 9150 3.402095 ATCGAGGGAGAGTCGCCGA 62.402 63.158 6.84 1.60 36.84 5.54
4686 9189 2.198906 TAACATGTTGGCAGCAGCGC 62.199 55.000 21.42 0.00 43.41 5.92
4696 9199 2.122783 ACCCGGTGGATAACATGTTG 57.877 50.000 21.42 3.37 34.81 3.33
4730 9233 1.433053 CGGCAGTTTTCGACACCACA 61.433 55.000 0.00 0.00 0.00 4.17
4781 9285 2.409651 GGCTCAGCCTCGACTACG 59.590 66.667 9.09 0.00 46.69 3.51
4840 9362 1.379527 CAGGAACAAGTAATCCGCCC 58.620 55.000 0.00 0.00 40.78 6.13
4841 9363 1.339727 ACCAGGAACAAGTAATCCGCC 60.340 52.381 0.00 0.00 40.78 6.13
4842 9364 1.737793 CACCAGGAACAAGTAATCCGC 59.262 52.381 0.00 0.00 40.78 5.54
4843 9365 2.356135 CCACCAGGAACAAGTAATCCG 58.644 52.381 0.00 0.00 40.78 4.18
4844 9366 2.041216 ACCCACCAGGAACAAGTAATCC 59.959 50.000 0.00 0.00 39.89 3.01
4845 9367 3.434940 ACCCACCAGGAACAAGTAATC 57.565 47.619 0.00 0.00 39.89 1.75
4846 9368 3.895704 AACCCACCAGGAACAAGTAAT 57.104 42.857 0.00 0.00 39.89 1.89
4847 9369 3.717913 ACTAACCCACCAGGAACAAGTAA 59.282 43.478 0.00 0.00 39.89 2.24
4848 9370 3.320129 ACTAACCCACCAGGAACAAGTA 58.680 45.455 0.00 0.00 39.89 2.24
4849 9371 2.132686 ACTAACCCACCAGGAACAAGT 58.867 47.619 0.00 0.00 39.89 3.16
4850 9372 2.951229 ACTAACCCACCAGGAACAAG 57.049 50.000 0.00 0.00 39.89 3.16
4851 9373 2.640826 CCTACTAACCCACCAGGAACAA 59.359 50.000 0.00 0.00 39.89 2.83
4852 9374 2.262637 CCTACTAACCCACCAGGAACA 58.737 52.381 0.00 0.00 39.89 3.18
4853 9375 1.065636 GCCTACTAACCCACCAGGAAC 60.066 57.143 0.00 0.00 39.89 3.62
4854 9376 1.282382 GCCTACTAACCCACCAGGAA 58.718 55.000 0.00 0.00 39.89 3.36
4855 9377 0.619543 GGCCTACTAACCCACCAGGA 60.620 60.000 0.00 0.00 39.89 3.86
4856 9378 1.632965 GGGCCTACTAACCCACCAGG 61.633 65.000 0.84 0.00 46.22 4.45
4857 9379 1.912971 GGGCCTACTAACCCACCAG 59.087 63.158 0.84 0.00 46.22 4.00
4891 9413 3.873952 AGTATGAGGCGCAGAATCTTTTC 59.126 43.478 10.83 0.00 0.00 2.29
4977 9499 1.646189 GGCAGAGACTTTCCGCTTAG 58.354 55.000 0.00 0.00 29.71 2.18
5031 9553 1.144057 GTCAGGATGGCGACGGAAT 59.856 57.895 0.00 0.00 36.16 3.01


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

AutoCloner maintained by Alex Coulton.