Multiple sequence alignment - TraesCS1A01G190300

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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 TraesCS1A01G190300 chr1A 100.000 4427 0 0 1 4427 344182731 344187157 0.000000e+00 8176.0
1 TraesCS1A01G190300 chr1A 90.452 2545 209 14 894 3430 401221737 401224255 0.000000e+00 3323.0
2 TraesCS1A01G190300 chr1A 89.531 2407 240 7 1030 3435 391842574 391844969 0.000000e+00 3038.0
3 TraesCS1A01G190300 chr1A 89.485 2406 242 3 1030 3435 391694258 391696652 0.000000e+00 3031.0
4 TraesCS1A01G190300 chr1A 96.218 899 26 3 1 891 556979820 556980718 0.000000e+00 1465.0
5 TraesCS1A01G190300 chr1A 96.107 899 27 4 1 891 495773633 495772735 0.000000e+00 1459.0
6 TraesCS1A01G190300 chr1A 89.278 485 43 5 2964 3448 391735801 391736276 2.280000e-167 599.0
7 TraesCS1A01G190300 chr1A 89.278 485 43 5 2964 3448 391825993 391826468 2.280000e-167 599.0
8 TraesCS1A01G190300 chr1A 73.913 414 58 29 3570 3964 391845054 391845436 2.160000e-23 121.0
9 TraesCS1A01G190300 chr1B 94.857 2547 111 4 1106 3652 344369885 344372411 0.000000e+00 3960.0
10 TraesCS1A01G190300 chr1B 90.171 2401 225 6 1030 3429 421422565 421424955 0.000000e+00 3116.0
11 TraesCS1A01G190300 chr1B 89.900 2406 234 2 1030 3435 421531556 421533952 0.000000e+00 3088.0
12 TraesCS1A01G190300 chr1B 89.833 2400 235 4 1030 3429 421494525 421496915 0.000000e+00 3072.0
13 TraesCS1A01G190300 chr1B 80.027 746 46 30 3708 4427 344372434 344373102 1.450000e-124 457.0
14 TraesCS1A01G190300 chr1B 91.818 220 8 1 891 1110 344367212 344367421 9.310000e-77 298.0
15 TraesCS1A01G190300 chr1D 89.967 2422 234 3 1030 3451 345379381 345376969 0.000000e+00 3118.0
16 TraesCS1A01G190300 chr1D 89.942 2406 233 2 1030 3435 311685721 311688117 0.000000e+00 3094.0
17 TraesCS1A01G190300 chr1D 94.793 1594 67 3 891 2469 271818303 271819895 0.000000e+00 2470.0
18 TraesCS1A01G190300 chr1D 85.185 162 14 9 3657 3809 271821079 271821239 1.650000e-34 158.0
19 TraesCS1A01G190300 chr1D 89.091 110 3 3 3882 3982 271834870 271834979 1.290000e-25 128.0
20 TraesCS1A01G190300 chr1D 92.157 51 4 0 3919 3969 311688518 311688568 6.140000e-09 73.1
21 TraesCS1A01G190300 chrUn 89.223 2431 244 6 1030 3451 919898 917477 0.000000e+00 3025.0
22 TraesCS1A01G190300 chr3A 96.756 894 25 4 1 891 512586509 512587401 0.000000e+00 1487.0
23 TraesCS1A01G190300 chr3A 96.421 894 29 3 1 891 159885616 159884723 0.000000e+00 1471.0
24 TraesCS1A01G190300 chr6A 96.532 894 27 4 1 891 359154282 359153390 0.000000e+00 1476.0
25 TraesCS1A01G190300 chr5A 96.325 898 29 4 1 895 245456838 245457734 0.000000e+00 1472.0
26 TraesCS1A01G190300 chr7A 96.309 894 29 4 1 891 635061576 635062468 0.000000e+00 1465.0
27 TraesCS1A01G190300 chr7A 96.107 899 27 3 1 891 584169098 584168200 0.000000e+00 1459.0
28 TraesCS1A01G190300 chr2A 96.197 894 31 3 1 891 72725614 72726507 0.000000e+00 1459.0
29 TraesCS1A01G190300 chr3D 93.617 94 6 0 4243 4336 600090957 600091050 1.660000e-29 141.0


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 TraesCS1A01G190300 chr1A 344182731 344187157 4426 False 8176.000000 8176 100.000000 1 4427 1 chr1A.!!$F1 4426
1 TraesCS1A01G190300 chr1A 401221737 401224255 2518 False 3323.000000 3323 90.452000 894 3430 1 chr1A.!!$F5 2536
2 TraesCS1A01G190300 chr1A 391694258 391696652 2394 False 3031.000000 3031 89.485000 1030 3435 1 chr1A.!!$F2 2405
3 TraesCS1A01G190300 chr1A 391842574 391845436 2862 False 1579.500000 3038 81.722000 1030 3964 2 chr1A.!!$F7 2934
4 TraesCS1A01G190300 chr1A 556979820 556980718 898 False 1465.000000 1465 96.218000 1 891 1 chr1A.!!$F6 890
5 TraesCS1A01G190300 chr1A 495772735 495773633 898 True 1459.000000 1459 96.107000 1 891 1 chr1A.!!$R1 890
6 TraesCS1A01G190300 chr1B 421422565 421424955 2390 False 3116.000000 3116 90.171000 1030 3429 1 chr1B.!!$F1 2399
7 TraesCS1A01G190300 chr1B 421531556 421533952 2396 False 3088.000000 3088 89.900000 1030 3435 1 chr1B.!!$F3 2405
8 TraesCS1A01G190300 chr1B 421494525 421496915 2390 False 3072.000000 3072 89.833000 1030 3429 1 chr1B.!!$F2 2399
9 TraesCS1A01G190300 chr1B 344367212 344373102 5890 False 1571.666667 3960 88.900667 891 4427 3 chr1B.!!$F4 3536
10 TraesCS1A01G190300 chr1D 345376969 345379381 2412 True 3118.000000 3118 89.967000 1030 3451 1 chr1D.!!$R1 2421
11 TraesCS1A01G190300 chr1D 311685721 311688568 2847 False 1583.550000 3094 91.049500 1030 3969 2 chr1D.!!$F3 2939
12 TraesCS1A01G190300 chr1D 271818303 271821239 2936 False 1314.000000 2470 89.989000 891 3809 2 chr1D.!!$F2 2918
13 TraesCS1A01G190300 chrUn 917477 919898 2421 True 3025.000000 3025 89.223000 1030 3451 1 chrUn.!!$R1 2421
14 TraesCS1A01G190300 chr3A 512586509 512587401 892 False 1487.000000 1487 96.756000 1 891 1 chr3A.!!$F1 890
15 TraesCS1A01G190300 chr3A 159884723 159885616 893 True 1471.000000 1471 96.421000 1 891 1 chr3A.!!$R1 890
16 TraesCS1A01G190300 chr6A 359153390 359154282 892 True 1476.000000 1476 96.532000 1 891 1 chr6A.!!$R1 890
17 TraesCS1A01G190300 chr5A 245456838 245457734 896 False 1472.000000 1472 96.325000 1 895 1 chr5A.!!$F1 894
18 TraesCS1A01G190300 chr7A 635061576 635062468 892 False 1465.000000 1465 96.309000 1 891 1 chr7A.!!$F1 890
19 TraesCS1A01G190300 chr7A 584168200 584169098 898 True 1459.000000 1459 96.107000 1 891 1 chr7A.!!$R1 890
20 TraesCS1A01G190300 chr2A 72725614 72726507 893 False 1459.000000 1459 96.197000 1 891 1 chr2A.!!$F1 890

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
967 981 0.096454 GAAACTTAGCGCGCCGAATT 59.904 50.0 30.33 16.83 0.00 2.17 F
968 982 0.179200 AAACTTAGCGCGCCGAATTG 60.179 50.0 30.33 13.66 0.00 2.32 F
971 985 0.304705 CTTAGCGCGCCGAATTGAAT 59.695 50.0 30.33 8.40 0.00 2.57 F
1488 4002 0.322456 TTTTCCATGTGAGAGGCGGG 60.322 55.0 0.00 0.00 0.00 6.13 F
2890 5456 0.744414 CATCGGTGCTACCAACAGGG 60.744 60.0 6.21 0.00 38.47 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 4631 0.033208 TTCATCAGGGACCCCAATGC 60.033 55.000 7.00 0.0 38.92 3.56 R
2249 4763 0.036875 AGCCTCAGTACAAAGGGCAC 59.963 55.000 17.07 0.0 44.60 5.01 R
2890 5456 1.542108 GGCAGGGTCTATGATGTCTGC 60.542 57.143 0.00 0.0 44.60 4.26 R
3243 5818 1.977009 ATCACTCACACTCCGGCGA 60.977 57.895 9.30 0.0 0.00 5.54 R
4269 6902 0.764271 TGGCACACAGATTGGACTCA 59.236 50.000 0.00 0.0 0.00 3.41 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
86 87 2.703007 AGTTGAGAGAGAGTTGCACCTT 59.297 45.455 0.00 0.00 0.00 3.50
313 325 2.523015 ACGGACGCGTTAATTACTGAG 58.477 47.619 15.53 0.00 0.00 3.35
413 426 1.355916 GCAGACGTCTACCCTAGCG 59.644 63.158 19.57 4.21 0.00 4.26
492 506 1.383248 CTCCATCCCTCCTTCCGGT 60.383 63.158 0.00 0.00 0.00 5.28
630 644 0.725118 CGCGAACGACGACTTCTTCT 60.725 55.000 0.00 0.00 45.77 2.85
677 691 2.151202 GACATGGGTGACAACGTCAAT 58.849 47.619 0.00 0.00 44.49 2.57
729 743 6.566079 ATGTGATTCTATCCTTCCTGTTCA 57.434 37.500 0.00 0.00 0.00 3.18
763 777 8.144478 GGTAGAATTCATGCTTCTAGTATGTGA 58.856 37.037 8.44 0.00 39.05 3.58
820 834 7.766278 AGTTCGCATGATTAGTTTAATCTCTGT 59.234 33.333 0.00 0.00 43.79 3.41
903 917 9.778741 TCATATTTCCAACAGCTATAAAGGTAG 57.221 33.333 0.00 0.00 0.00 3.18
962 976 2.095843 CACGAAACTTAGCGCGCC 59.904 61.111 30.33 9.60 0.00 6.53
963 977 3.475774 ACGAAACTTAGCGCGCCG 61.476 61.111 30.33 23.93 0.00 6.46
964 978 3.176578 CGAAACTTAGCGCGCCGA 61.177 61.111 30.33 14.32 0.00 5.54
965 979 2.722731 CGAAACTTAGCGCGCCGAA 61.723 57.895 30.33 21.31 0.00 4.30
966 980 1.713830 GAAACTTAGCGCGCCGAAT 59.286 52.632 30.33 12.34 0.00 3.34
967 981 0.096454 GAAACTTAGCGCGCCGAATT 59.904 50.000 30.33 16.83 0.00 2.17
968 982 0.179200 AAACTTAGCGCGCCGAATTG 60.179 50.000 30.33 13.66 0.00 2.32
969 983 1.017177 AACTTAGCGCGCCGAATTGA 61.017 50.000 30.33 4.25 0.00 2.57
970 984 1.017177 ACTTAGCGCGCCGAATTGAA 61.017 50.000 30.33 9.62 0.00 2.69
971 985 0.304705 CTTAGCGCGCCGAATTGAAT 59.695 50.000 30.33 8.40 0.00 2.57
1089 1128 2.732597 CGAGAGAAAGAAGTCGCCGAAT 60.733 50.000 0.00 0.00 0.00 3.34
1092 1131 1.201647 AGAAAGAAGTCGCCGAATCGA 59.798 47.619 3.36 0.00 35.95 3.59
1328 3841 1.790838 CGACGTCGTCTCTGTTCATCC 60.791 57.143 29.08 0.00 34.11 3.51
1343 3856 3.006756 ATCCGTGCCCAGACGTCAG 62.007 63.158 19.50 10.04 37.66 3.51
1384 3897 2.958204 CTTCCCGTCGACGACACGA 61.958 63.158 37.65 22.84 43.02 4.35
1411 3925 1.202545 GGATCTCCGTTAGCCTGTTCC 60.203 57.143 0.00 0.00 0.00 3.62
1488 4002 0.322456 TTTTCCATGTGAGAGGCGGG 60.322 55.000 0.00 0.00 0.00 6.13
1848 4362 3.005897 GCCCAGAGATTATGTCGAAGCTA 59.994 47.826 0.00 0.00 0.00 3.32
2080 4594 1.672854 CCCGAACAGCATCGACCCTA 61.673 60.000 7.97 0.00 45.48 3.53
2109 4623 2.433436 AGATTTGGTAGGTTTGACCGC 58.567 47.619 0.00 0.00 44.90 5.68
2235 4749 3.056536 CGAGGGATACTCATGGGTATGTG 60.057 52.174 23.04 4.23 46.98 3.21
2351 4865 6.967279 GATGCAGAGATACTGAATTCCATGGT 60.967 42.308 12.58 0.00 44.30 3.55
2427 4942 4.593597 TCGTGAAACTGTTGTTGAAGTC 57.406 40.909 0.00 0.00 36.39 3.01
2649 5215 7.769044 GCTAACTTTATCAGTATCAAAGGACCA 59.231 37.037 0.00 0.00 32.94 4.02
2650 5216 9.667107 CTAACTTTATCAGTATCAAAGGACCAA 57.333 33.333 0.00 0.00 32.94 3.67
2652 5218 8.934023 ACTTTATCAGTATCAAAGGACCAAAA 57.066 30.769 0.00 0.00 34.32 2.44
2748 5314 1.073125 TGCGTCCCCTTCTTTGATGAA 59.927 47.619 0.00 0.00 0.00 2.57
2890 5456 0.744414 CATCGGTGCTACCAACAGGG 60.744 60.000 6.21 0.00 38.47 4.45
3030 5605 2.107378 TGTGGCCAAAGATGTTGACCTA 59.893 45.455 7.24 0.00 0.00 3.08
3348 5923 2.370445 CCGATTCCCTGACCAGCCT 61.370 63.158 0.00 0.00 0.00 4.58
3438 6013 5.356882 TGTACAGTTAAATTGTCTGCTGC 57.643 39.130 0.00 0.00 33.12 5.25
3448 6023 2.747460 TCTGCTGCGCCATGAACC 60.747 61.111 4.18 0.00 0.00 3.62
3465 6040 7.041303 GCCATGAACCTAGCCTAATTTAGTAAC 60.041 40.741 0.00 0.00 0.00 2.50
3473 6048 7.226918 CCTAGCCTAATTTAGTAACTTCCTTGC 59.773 40.741 2.88 0.00 0.00 4.01
3478 6053 9.099454 CCTAATTTAGTAACTTCCTTGCTGTAG 57.901 37.037 2.88 0.00 0.00 2.74
3515 6090 4.141869 GCTGGCATCTGTAAAAATGGGAAT 60.142 41.667 0.00 0.00 0.00 3.01
3535 6112 9.275398 TGGGAATACCATGTAATTATTTACGTC 57.725 33.333 0.00 0.00 46.80 4.34
3558 6135 9.916397 CGTCCAAGTTGTGATATATAAACTTTC 57.084 33.333 13.87 9.24 40.05 2.62
3607 6184 5.529289 ACTGAAGATTGTATCCTCCACCTA 58.471 41.667 0.00 0.00 0.00 3.08
3652 6230 1.208052 CCCGATTCCAGTCTGTGTGAT 59.792 52.381 0.00 0.00 0.00 3.06
3655 6233 3.865745 CCGATTCCAGTCTGTGTGATAAC 59.134 47.826 0.00 0.00 0.00 1.89
3657 6235 4.564372 CGATTCCAGTCTGTGTGATAACTG 59.436 45.833 0.00 0.00 39.04 3.16
3658 6236 5.622233 CGATTCCAGTCTGTGTGATAACTGA 60.622 44.000 0.00 0.00 41.26 3.41
3659 6237 4.521130 TCCAGTCTGTGTGATAACTGAC 57.479 45.455 0.00 6.32 44.75 3.51
3660 6238 3.895041 TCCAGTCTGTGTGATAACTGACA 59.105 43.478 14.22 0.00 46.02 3.58
3661 6239 4.343814 TCCAGTCTGTGTGATAACTGACAA 59.656 41.667 14.22 0.77 46.02 3.18
3662 6240 4.687948 CCAGTCTGTGTGATAACTGACAAG 59.312 45.833 14.22 7.89 46.02 3.16
3663 6241 4.687948 CAGTCTGTGTGATAACTGACAAGG 59.312 45.833 14.22 3.15 46.02 3.61
3668 6246 8.414003 GTCTGTGTGATAACTGACAAGGATATA 58.586 37.037 8.82 0.00 44.18 0.86
3711 6293 2.028658 TCTTGTTCTCTACAGGCTGCAG 60.029 50.000 15.89 11.99 38.19 4.41
3793 6391 7.324935 TCGAGTGTCATTGCTAATAAACCTTA 58.675 34.615 0.00 0.00 0.00 2.69
3813 6412 5.422012 CCTTATGTTATCTGCCCTTTGGTTT 59.578 40.000 0.00 0.00 0.00 3.27
3814 6413 4.806640 ATGTTATCTGCCCTTTGGTTTG 57.193 40.909 0.00 0.00 0.00 2.93
3816 6415 3.964031 TGTTATCTGCCCTTTGGTTTGTT 59.036 39.130 0.00 0.00 0.00 2.83
3818 6417 2.977772 TCTGCCCTTTGGTTTGTTTG 57.022 45.000 0.00 0.00 0.00 2.93
3819 6418 1.484240 TCTGCCCTTTGGTTTGTTTGG 59.516 47.619 0.00 0.00 0.00 3.28
3824 6423 3.508012 GCCCTTTGGTTTGTTTGGTTTTT 59.492 39.130 0.00 0.00 0.00 1.94
3854 6477 6.151144 GGTTGCAAATGGTTACTTCTACTGAT 59.849 38.462 0.00 0.00 0.00 2.90
3872 6495 2.842496 TGATCAATTCCACAGCCTCTCT 59.158 45.455 0.00 0.00 0.00 3.10
3899 6522 9.508567 GGAATTCTGACAAATTAGTTTAGCATC 57.491 33.333 5.23 0.00 0.00 3.91
3964 6593 6.262273 TGGATTCTCCAACAAAGTAACTGAAC 59.738 38.462 0.00 0.00 45.00 3.18
3983 6612 6.431234 ACTGAACTAATTTGCAAGGTAGAAGG 59.569 38.462 19.73 11.48 0.00 3.46
3984 6613 6.303839 TGAACTAATTTGCAAGGTAGAAGGT 58.696 36.000 19.73 4.96 0.00 3.50
3986 6615 7.940137 TGAACTAATTTGCAAGGTAGAAGGTTA 59.060 33.333 19.73 0.43 0.00 2.85
3987 6616 8.879427 AACTAATTTGCAAGGTAGAAGGTTAT 57.121 30.769 19.73 0.00 0.00 1.89
3988 6617 8.507524 ACTAATTTGCAAGGTAGAAGGTTATC 57.492 34.615 19.73 0.00 0.00 1.75
3989 6618 6.775594 AATTTGCAAGGTAGAAGGTTATCC 57.224 37.500 0.00 0.00 0.00 2.59
3992 6621 4.780815 TGCAAGGTAGAAGGTTATCCATG 58.219 43.478 0.00 0.00 35.89 3.66
3993 6622 4.227300 TGCAAGGTAGAAGGTTATCCATGT 59.773 41.667 0.00 0.00 35.89 3.21
3994 6623 5.193679 GCAAGGTAGAAGGTTATCCATGTT 58.806 41.667 0.00 0.00 35.89 2.71
3995 6624 5.066505 GCAAGGTAGAAGGTTATCCATGTTG 59.933 44.000 0.00 0.00 35.89 3.33
3996 6625 6.414732 CAAGGTAGAAGGTTATCCATGTTGA 58.585 40.000 0.00 0.00 35.89 3.18
3997 6626 6.831664 AGGTAGAAGGTTATCCATGTTGAT 57.168 37.500 0.00 0.00 35.89 2.57
3998 6627 6.595682 AGGTAGAAGGTTATCCATGTTGATG 58.404 40.000 0.00 0.00 35.89 3.07
3999 6628 6.158695 AGGTAGAAGGTTATCCATGTTGATGT 59.841 38.462 0.00 0.00 35.89 3.06
4000 6629 6.828785 GGTAGAAGGTTATCCATGTTGATGTT 59.171 38.462 0.00 0.00 35.89 2.71
4001 6630 6.764308 AGAAGGTTATCCATGTTGATGTTG 57.236 37.500 0.00 0.00 35.89 3.33
4002 6631 6.484288 AGAAGGTTATCCATGTTGATGTTGA 58.516 36.000 0.00 0.00 35.89 3.18
4003 6632 7.121382 AGAAGGTTATCCATGTTGATGTTGAT 58.879 34.615 0.00 0.00 35.89 2.57
4004 6633 7.616935 AGAAGGTTATCCATGTTGATGTTGATT 59.383 33.333 0.00 0.00 35.89 2.57
4005 6634 8.821686 AAGGTTATCCATGTTGATGTTGATTA 57.178 30.769 0.00 0.00 35.89 1.75
4006 6635 8.455903 AGGTTATCCATGTTGATGTTGATTAG 57.544 34.615 0.00 0.00 35.89 1.73
4007 6636 7.013655 AGGTTATCCATGTTGATGTTGATTAGC 59.986 37.037 0.00 0.00 35.89 3.09
4008 6637 7.013655 GGTTATCCATGTTGATGTTGATTAGCT 59.986 37.037 0.00 0.00 0.00 3.32
4013 6642 7.774625 TCCATGTTGATGTTGATTAGCTATTCA 59.225 33.333 13.10 13.10 0.00 2.57
4019 6648 5.102953 TGTTGATTAGCTATTCACTGCCT 57.897 39.130 16.04 0.00 0.00 4.75
4081 6710 9.619316 TTTATATAGTTGAATTGTGTGTTGTGC 57.381 29.630 0.00 0.00 0.00 4.57
4082 6711 3.163630 AGTTGAATTGTGTGTTGTGCC 57.836 42.857 0.00 0.00 0.00 5.01
4083 6712 2.495270 AGTTGAATTGTGTGTTGTGCCA 59.505 40.909 0.00 0.00 0.00 4.92
4084 6713 3.056250 AGTTGAATTGTGTGTTGTGCCAA 60.056 39.130 0.00 0.00 0.00 4.52
4085 6714 2.886081 TGAATTGTGTGTTGTGCCAAC 58.114 42.857 10.15 10.15 0.00 3.77
4086 6715 2.495270 TGAATTGTGTGTTGTGCCAACT 59.505 40.909 15.91 0.00 0.00 3.16
4087 6716 3.056250 TGAATTGTGTGTTGTGCCAACTT 60.056 39.130 15.91 4.45 0.00 2.66
4088 6717 2.360553 TTGTGTGTTGTGCCAACTTG 57.639 45.000 15.91 0.00 0.00 3.16
4089 6718 1.539157 TGTGTGTTGTGCCAACTTGA 58.461 45.000 15.91 0.00 0.00 3.02
4090 6719 2.098614 TGTGTGTTGTGCCAACTTGAT 58.901 42.857 15.91 0.00 0.00 2.57
4091 6720 2.159268 TGTGTGTTGTGCCAACTTGATG 60.159 45.455 15.91 0.00 0.00 3.07
4092 6721 2.098614 TGTGTTGTGCCAACTTGATGT 58.901 42.857 15.91 0.00 0.00 3.06
4093 6722 3.066064 GTGTGTTGTGCCAACTTGATGTA 59.934 43.478 15.91 0.00 0.00 2.29
4094 6723 3.696548 TGTGTTGTGCCAACTTGATGTAA 59.303 39.130 15.91 0.00 0.00 2.41
4095 6724 4.158579 TGTGTTGTGCCAACTTGATGTAAA 59.841 37.500 15.91 0.00 0.00 2.01
4096 6725 5.163468 TGTGTTGTGCCAACTTGATGTAAAT 60.163 36.000 15.91 0.00 0.00 1.40
4097 6726 5.752955 GTGTTGTGCCAACTTGATGTAAATT 59.247 36.000 15.91 0.00 0.00 1.82
4098 6727 6.257630 GTGTTGTGCCAACTTGATGTAAATTT 59.742 34.615 15.91 0.00 0.00 1.82
4106 6735 8.611757 GCCAACTTGATGTAAATTTCTTGTTTT 58.388 29.630 0.00 0.00 0.00 2.43
4133 6762 5.111989 TGCTTATGCTGTCATCTGTAAGAC 58.888 41.667 1.96 0.00 43.26 3.01
4137 6766 9.044326 GCTTATGCTGTCATCTGTAAGACACTG 62.044 44.444 0.00 0.00 40.65 3.66
4152 6781 3.073062 AGACACTGAAAGGCCATGTACTT 59.927 43.478 5.01 0.00 39.30 2.24
4154 6783 4.324267 ACACTGAAAGGCCATGTACTTAC 58.676 43.478 5.01 0.00 39.30 2.34
4156 6785 5.003804 CACTGAAAGGCCATGTACTTACTT 58.996 41.667 5.01 0.00 39.30 2.24
4195 6828 6.280643 TGATATAATGAAGACTGTTCCACCG 58.719 40.000 0.00 0.00 0.00 4.94
4202 6835 1.821753 AGACTGTTCCACCGAGATGAG 59.178 52.381 0.00 0.00 0.00 2.90
4208 6841 4.050313 CACCGAGATGAGGGGGAA 57.950 61.111 0.00 0.00 0.00 3.97
4212 6845 1.923148 ACCGAGATGAGGGGGAAAAAT 59.077 47.619 0.00 0.00 0.00 1.82
4215 6848 4.202472 ACCGAGATGAGGGGGAAAAATATC 60.202 45.833 0.00 0.00 0.00 1.63
4227 6860 4.580580 GGGAAAAATATCGCCTGTCTCAAT 59.419 41.667 0.00 0.00 0.00 2.57
4234 6867 3.904800 TCGCCTGTCTCAATTATGGAA 57.095 42.857 0.00 0.00 0.00 3.53
4261 6894 9.927668 AAAACAATATAAACCTTTGATGTCCTG 57.072 29.630 0.00 0.00 0.00 3.86
4262 6895 7.100458 ACAATATAAACCTTTGATGTCCTGC 57.900 36.000 0.00 0.00 0.00 4.85
4263 6896 6.891908 ACAATATAAACCTTTGATGTCCTGCT 59.108 34.615 0.00 0.00 0.00 4.24
4264 6897 6.949352 ATATAAACCTTTGATGTCCTGCTG 57.051 37.500 0.00 0.00 0.00 4.41
4265 6898 2.664402 AACCTTTGATGTCCTGCTGT 57.336 45.000 0.00 0.00 0.00 4.40
4266 6899 2.191128 ACCTTTGATGTCCTGCTGTC 57.809 50.000 0.00 0.00 0.00 3.51
4267 6900 1.701847 ACCTTTGATGTCCTGCTGTCT 59.298 47.619 0.00 0.00 0.00 3.41
4268 6901 2.289945 ACCTTTGATGTCCTGCTGTCTC 60.290 50.000 0.00 0.00 0.00 3.36
4269 6902 2.027377 CCTTTGATGTCCTGCTGTCTCT 60.027 50.000 0.00 0.00 0.00 3.10
4272 6905 1.823610 TGATGTCCTGCTGTCTCTGAG 59.176 52.381 0.00 0.00 0.00 3.35
4297 6930 4.379813 CCAATCTGTGTGCCAAGTATTGTC 60.380 45.833 0.00 0.00 46.99 3.18
4408 7043 2.508526 GCTGAAAGACCATTGGACAGT 58.491 47.619 10.37 0.00 34.07 3.55
4414 7049 0.729116 GACCATTGGACAGTGATGCG 59.271 55.000 10.37 0.00 0.00 4.73
4421 7056 0.654683 GGACAGTGATGCGAAGATGC 59.345 55.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.180408 AGTGGTAGAAGAGCTCACCTTATAAAA 59.820 37.037 17.77 0.00 32.04 1.52
492 506 2.594303 CCCTTCTTGCGGTGCACA 60.594 61.111 20.43 0.00 38.71 4.57
729 743 5.028549 AGCATGAATTCTACCACGATCTT 57.971 39.130 7.05 0.00 0.00 2.40
763 777 6.269538 AGCAGATGAACATATCACATCTAGGT 59.730 38.462 0.00 0.00 45.61 3.08
820 834 6.094464 CAGAAGATAAATCATGACCACAGCAA 59.906 38.462 0.00 0.00 0.00 3.91
903 917 1.443828 GAAGTCGAGGGGATCAGCC 59.556 63.158 0.00 0.00 0.00 4.85
962 976 3.841624 TGCTCGATTCGATTCAATTCG 57.158 42.857 9.54 0.00 40.46 3.34
963 977 5.588568 AGATGCTCGATTCGATTCAATTC 57.411 39.130 9.54 6.59 34.61 2.17
964 978 5.588568 GAGATGCTCGATTCGATTCAATT 57.411 39.130 9.54 4.07 34.61 2.32
1092 1131 3.681835 GCCTCGTCGACCACCAGT 61.682 66.667 10.58 0.00 0.00 4.00
1211 3724 1.790387 GCAATGCAGACCGTGTCTC 59.210 57.895 0.00 1.72 41.37 3.36
1328 3841 0.525668 GTATCTGACGTCTGGGCACG 60.526 60.000 20.57 0.00 45.65 5.34
1343 3856 0.928229 GTGCACGTGATTCCCGTATC 59.072 55.000 22.23 0.00 36.65 2.24
1355 3868 0.389426 GACGGGAAGTATGTGCACGT 60.389 55.000 17.19 17.19 35.64 4.49
1384 3897 1.614413 GCTAACGGAGATCCCTTCGAT 59.386 52.381 0.00 0.00 44.09 3.59
1411 3925 4.148128 AGTATGGTCTCAAGAAGGCATG 57.852 45.455 0.00 0.00 0.00 4.06
1475 3989 0.977627 TGTCATCCCGCCTCTCACAT 60.978 55.000 0.00 0.00 0.00 3.21
1488 4002 1.795768 TGAACTCCACGCTTGTCATC 58.204 50.000 0.00 0.00 0.00 2.92
1586 4100 1.327303 CTTCTCCTCATCCTCCCTCG 58.673 60.000 0.00 0.00 0.00 4.63
1848 4362 1.188219 TGCTCTCACTTTCTCCGGCT 61.188 55.000 0.00 0.00 0.00 5.52
2080 4594 6.043243 TCAAACCTACCAAATCTTCTGAGAGT 59.957 38.462 0.00 0.00 34.85 3.24
2109 4623 1.595382 GACCCCAATGCCGATCTCG 60.595 63.158 0.00 0.00 39.44 4.04
2117 4631 0.033208 TTCATCAGGGACCCCAATGC 60.033 55.000 7.00 0.00 38.92 3.56
2249 4763 0.036875 AGCCTCAGTACAAAGGGCAC 59.963 55.000 17.07 0.00 44.60 5.01
2351 4865 2.552031 TGAAATGGTCGTTCGTGACAA 58.448 42.857 7.33 0.00 40.72 3.18
2730 5296 3.059352 AGTTCATCAAAGAAGGGGACG 57.941 47.619 0.00 0.00 0.00 4.79
2735 5301 6.624352 TTGAGTCAAGTTCATCAAAGAAGG 57.376 37.500 0.08 0.00 0.00 3.46
2748 5314 3.144506 CTGAGTGGCAATTGAGTCAAGT 58.855 45.455 10.34 5.77 0.00 3.16
2890 5456 1.542108 GGCAGGGTCTATGATGTCTGC 60.542 57.143 0.00 0.00 44.60 4.26
3243 5818 1.977009 ATCACTCACACTCCGGCGA 60.977 57.895 9.30 0.00 0.00 5.54
3394 5969 2.510238 ATCGTCTTCAGCTGCCGC 60.510 61.111 9.47 0.00 0.00 6.53
3438 6013 2.550830 ATTAGGCTAGGTTCATGGCG 57.449 50.000 0.00 0.00 0.00 5.69
3448 6023 7.988028 AGCAAGGAAGTTACTAAATTAGGCTAG 59.012 37.037 4.92 0.00 0.00 3.42
3515 6090 9.669887 AACTTGGACGTAAATAATTACATGGTA 57.330 29.630 0.00 0.00 41.24 3.25
3607 6184 8.531982 GGGACTAGGAAATGCTTTTTATCTTTT 58.468 33.333 0.00 0.00 0.00 2.27
3652 6230 9.599866 CAGACAAATGTATATCCTTGTCAGTTA 57.400 33.333 15.33 0.00 46.51 2.24
3655 6233 7.466455 GCACAGACAAATGTATATCCTTGTCAG 60.466 40.741 15.33 11.39 46.51 3.51
3657 6235 6.540189 AGCACAGACAAATGTATATCCTTGTC 59.460 38.462 8.29 8.29 45.15 3.18
3658 6236 6.418101 AGCACAGACAAATGTATATCCTTGT 58.582 36.000 0.00 0.00 34.78 3.16
3659 6237 6.932356 AGCACAGACAAATGTATATCCTTG 57.068 37.500 0.00 0.00 0.00 3.61
3660 6238 7.564793 TGTAGCACAGACAAATGTATATCCTT 58.435 34.615 0.00 0.00 0.00 3.36
3661 6239 7.124573 TGTAGCACAGACAAATGTATATCCT 57.875 36.000 0.00 0.00 0.00 3.24
3662 6240 7.786178 TTGTAGCACAGACAAATGTATATCC 57.214 36.000 0.00 0.00 33.93 2.59
3663 6241 9.869844 GAATTGTAGCACAGACAAATGTATATC 57.130 33.333 0.00 0.00 40.07 1.63
3668 6246 6.000219 AGAGAATTGTAGCACAGACAAATGT 59.000 36.000 0.00 0.00 40.07 2.71
3673 6251 4.960938 ACAAGAGAATTGTAGCACAGACA 58.039 39.130 0.00 0.00 0.00 3.41
3675 6253 5.858381 AGAACAAGAGAATTGTAGCACAGA 58.142 37.500 0.00 0.00 31.50 3.41
3711 6293 7.592533 CACATACAATGATGCTAATAACCTTGC 59.407 37.037 0.00 0.00 0.00 4.01
3769 6367 6.422776 AAGGTTTATTAGCAATGACACTCG 57.577 37.500 0.00 0.00 0.00 4.18
3770 6368 8.893727 ACATAAGGTTTATTAGCAATGACACTC 58.106 33.333 0.00 0.00 0.00 3.51
3793 6391 4.159557 ACAAACCAAAGGGCAGATAACAT 58.840 39.130 0.00 0.00 37.90 2.71
3824 6423 6.410540 AGAAGTAACCATTTGCAACCAAAAA 58.589 32.000 0.00 0.00 43.58 1.94
3827 6426 5.830991 AGTAGAAGTAACCATTTGCAACCAA 59.169 36.000 0.00 0.00 0.00 3.67
3828 6427 5.240623 CAGTAGAAGTAACCATTTGCAACCA 59.759 40.000 0.00 0.00 0.00 3.67
3829 6428 5.472137 TCAGTAGAAGTAACCATTTGCAACC 59.528 40.000 0.00 0.00 0.00 3.77
3830 6429 6.554334 TCAGTAGAAGTAACCATTTGCAAC 57.446 37.500 0.00 0.00 0.00 4.17
3831 6430 6.939730 TGATCAGTAGAAGTAACCATTTGCAA 59.060 34.615 0.00 0.00 0.00 4.08
3832 6431 6.472016 TGATCAGTAGAAGTAACCATTTGCA 58.528 36.000 0.00 0.00 0.00 4.08
3833 6432 6.985188 TGATCAGTAGAAGTAACCATTTGC 57.015 37.500 0.00 0.00 0.00 3.68
3834 6433 9.994432 GAATTGATCAGTAGAAGTAACCATTTG 57.006 33.333 0.00 0.00 0.00 2.32
3835 6434 9.178758 GGAATTGATCAGTAGAAGTAACCATTT 57.821 33.333 0.00 0.00 0.00 2.32
3836 6435 8.328758 TGGAATTGATCAGTAGAAGTAACCATT 58.671 33.333 0.00 0.00 0.00 3.16
3840 6463 7.201565 GCTGTGGAATTGATCAGTAGAAGTAAC 60.202 40.741 0.00 0.00 0.00 2.50
3845 6468 4.225942 AGGCTGTGGAATTGATCAGTAGAA 59.774 41.667 0.00 0.00 0.00 2.10
3854 6477 1.280133 CCAGAGAGGCTGTGGAATTGA 59.720 52.381 4.73 0.00 46.28 2.57
3872 6495 8.402798 TGCTAAACTAATTTGTCAGAATTCCA 57.597 30.769 0.65 0.00 31.96 3.53
3873 6496 9.508567 GATGCTAAACTAATTTGTCAGAATTCC 57.491 33.333 0.65 0.00 31.96 3.01
3878 6501 7.076842 GCTGATGCTAAACTAATTTGTCAGA 57.923 36.000 0.00 0.00 32.24 3.27
3899 6522 6.970484 ACATTGTAACTAAAAGGTTCAGCTG 58.030 36.000 7.63 7.63 0.00 4.24
3901 6524 7.040961 TGGTACATTGTAACTAAAAGGTTCAGC 60.041 37.037 12.84 0.00 0.00 4.26
3964 6593 7.556275 TGGATAACCTTCTACCTTGCAAATTAG 59.444 37.037 0.00 4.15 37.04 1.73
3983 6612 7.934457 AGCTAATCAACATCAACATGGATAAC 58.066 34.615 0.00 0.00 33.82 1.89
3984 6613 9.797642 ATAGCTAATCAACATCAACATGGATAA 57.202 29.630 0.00 0.00 33.82 1.75
3986 6615 8.701908 AATAGCTAATCAACATCAACATGGAT 57.298 30.769 0.00 0.00 33.82 3.41
3987 6616 7.774625 TGAATAGCTAATCAACATCAACATGGA 59.225 33.333 9.10 0.00 33.82 3.41
3988 6617 7.859377 GTGAATAGCTAATCAACATCAACATGG 59.141 37.037 13.07 0.00 33.82 3.66
3989 6618 8.618677 AGTGAATAGCTAATCAACATCAACATG 58.381 33.333 13.07 0.00 35.92 3.21
3992 6621 6.909357 GCAGTGAATAGCTAATCAACATCAAC 59.091 38.462 13.07 0.00 0.00 3.18
3993 6622 6.038603 GGCAGTGAATAGCTAATCAACATCAA 59.961 38.462 13.07 0.00 0.00 2.57
3994 6623 5.528690 GGCAGTGAATAGCTAATCAACATCA 59.471 40.000 13.07 0.00 0.00 3.07
3995 6624 5.762218 AGGCAGTGAATAGCTAATCAACATC 59.238 40.000 13.07 1.42 0.00 3.06
3996 6625 5.688807 AGGCAGTGAATAGCTAATCAACAT 58.311 37.500 13.07 1.64 0.00 2.71
3997 6626 5.102953 AGGCAGTGAATAGCTAATCAACA 57.897 39.130 13.07 0.00 0.00 3.33
3998 6627 6.261118 CAAAGGCAGTGAATAGCTAATCAAC 58.739 40.000 13.07 7.91 0.00 3.18
3999 6628 5.357878 CCAAAGGCAGTGAATAGCTAATCAA 59.642 40.000 13.07 0.00 0.00 2.57
4000 6629 4.883585 CCAAAGGCAGTGAATAGCTAATCA 59.116 41.667 7.43 7.43 0.00 2.57
4001 6630 5.429957 CCAAAGGCAGTGAATAGCTAATC 57.570 43.478 0.00 0.00 0.00 1.75
4019 6648 3.372730 GCACCAGCGGATGCCAAA 61.373 61.111 0.00 0.00 44.31 3.28
4037 6666 1.089920 AATCATCGTCTGCAGTTGCC 58.910 50.000 14.67 0.00 41.18 4.52
4041 6670 8.360390 TCAACTATATAAATCATCGTCTGCAGT 58.640 33.333 14.67 0.00 0.00 4.40
4077 6706 6.403866 AGAAATTTACATCAAGTTGGCACA 57.596 33.333 2.34 0.00 0.00 4.57
4078 6707 6.701400 ACAAGAAATTTACATCAAGTTGGCAC 59.299 34.615 2.34 0.00 0.00 5.01
4079 6708 6.815089 ACAAGAAATTTACATCAAGTTGGCA 58.185 32.000 2.34 0.00 0.00 4.92
4080 6709 7.713764 AACAAGAAATTTACATCAAGTTGGC 57.286 32.000 2.34 0.00 0.00 4.52
4081 6710 9.919348 CAAAACAAGAAATTTACATCAAGTTGG 57.081 29.630 2.34 0.00 0.00 3.77
4082 6711 9.424659 GCAAAACAAGAAATTTACATCAAGTTG 57.575 29.630 0.00 0.00 0.00 3.16
4083 6712 9.382275 AGCAAAACAAGAAATTTACATCAAGTT 57.618 25.926 0.00 0.00 0.00 2.66
4084 6713 8.947055 AGCAAAACAAGAAATTTACATCAAGT 57.053 26.923 0.00 0.00 0.00 3.16
4085 6714 9.640974 CAAGCAAAACAAGAAATTTACATCAAG 57.359 29.630 0.00 0.00 0.00 3.02
4086 6715 8.121708 GCAAGCAAAACAAGAAATTTACATCAA 58.878 29.630 0.00 0.00 0.00 2.57
4087 6716 7.495279 AGCAAGCAAAACAAGAAATTTACATCA 59.505 29.630 0.00 0.00 0.00 3.07
4088 6717 7.854534 AGCAAGCAAAACAAGAAATTTACATC 58.145 30.769 0.00 0.00 0.00 3.06
4089 6718 7.790823 AGCAAGCAAAACAAGAAATTTACAT 57.209 28.000 0.00 0.00 0.00 2.29
4090 6719 7.608308 AAGCAAGCAAAACAAGAAATTTACA 57.392 28.000 0.00 0.00 0.00 2.41
4091 6720 9.584839 CATAAGCAAGCAAAACAAGAAATTTAC 57.415 29.630 0.00 0.00 0.00 2.01
4092 6721 8.281893 GCATAAGCAAGCAAAACAAGAAATTTA 58.718 29.630 0.00 0.00 41.58 1.40
4093 6722 7.012610 AGCATAAGCAAGCAAAACAAGAAATTT 59.987 29.630 0.00 0.00 45.49 1.82
4094 6723 6.484308 AGCATAAGCAAGCAAAACAAGAAATT 59.516 30.769 0.00 0.00 45.49 1.82
4095 6724 5.993441 AGCATAAGCAAGCAAAACAAGAAAT 59.007 32.000 0.00 0.00 45.49 2.17
4096 6725 5.234757 CAGCATAAGCAAGCAAAACAAGAAA 59.765 36.000 0.00 0.00 45.49 2.52
4097 6726 4.746115 CAGCATAAGCAAGCAAAACAAGAA 59.254 37.500 0.00 0.00 45.49 2.52
4098 6727 4.202141 ACAGCATAAGCAAGCAAAACAAGA 60.202 37.500 0.00 0.00 45.49 3.02
4106 6735 2.681344 CAGATGACAGCATAAGCAAGCA 59.319 45.455 0.00 0.00 45.49 3.91
4133 6762 4.579869 AGTAAGTACATGGCCTTTCAGTG 58.420 43.478 3.32 0.00 0.00 3.66
4137 6766 6.148315 ACGTAAAAGTAAGTACATGGCCTTTC 59.852 38.462 3.32 0.00 0.00 2.62
4138 6767 5.999600 ACGTAAAAGTAAGTACATGGCCTTT 59.000 36.000 3.32 0.00 0.00 3.11
4187 6816 1.522569 CCCCTCATCTCGGTGGAAC 59.477 63.158 0.00 0.00 0.00 3.62
4195 6828 3.753797 GCGATATTTTTCCCCCTCATCTC 59.246 47.826 0.00 0.00 0.00 2.75
4202 6835 1.954382 GACAGGCGATATTTTTCCCCC 59.046 52.381 0.00 0.00 0.00 5.40
4207 6840 7.502226 TCCATAATTGAGACAGGCGATATTTTT 59.498 33.333 0.00 0.00 0.00 1.94
4208 6841 6.998074 TCCATAATTGAGACAGGCGATATTTT 59.002 34.615 0.00 0.00 0.00 1.82
4212 6845 5.545063 TTCCATAATTGAGACAGGCGATA 57.455 39.130 0.00 0.00 0.00 2.92
4215 6848 4.963276 TTTTCCATAATTGAGACAGGCG 57.037 40.909 0.00 0.00 0.00 5.52
4238 6871 6.891908 AGCAGGACATCAAAGGTTTATATTGT 59.108 34.615 0.00 0.00 0.00 2.71
4239 6872 7.148018 ACAGCAGGACATCAAAGGTTTATATTG 60.148 37.037 0.00 0.00 0.00 1.90
4244 6877 4.072131 GACAGCAGGACATCAAAGGTTTA 58.928 43.478 0.00 0.00 0.00 2.01
4259 6892 2.496871 AGATTGGACTCAGAGACAGCAG 59.503 50.000 3.79 0.00 0.00 4.24
4260 6893 2.233186 CAGATTGGACTCAGAGACAGCA 59.767 50.000 3.79 0.00 0.00 4.41
4261 6894 2.233431 ACAGATTGGACTCAGAGACAGC 59.767 50.000 3.79 0.07 0.00 4.40
4262 6895 3.257873 ACACAGATTGGACTCAGAGACAG 59.742 47.826 3.79 0.00 0.00 3.51
4263 6896 3.006217 CACACAGATTGGACTCAGAGACA 59.994 47.826 3.79 0.00 0.00 3.41
4264 6897 3.583806 CACACAGATTGGACTCAGAGAC 58.416 50.000 3.79 0.00 0.00 3.36
4265 6898 2.028658 GCACACAGATTGGACTCAGAGA 60.029 50.000 3.79 0.00 0.00 3.10
4266 6899 2.344950 GCACACAGATTGGACTCAGAG 58.655 52.381 0.00 0.00 0.00 3.35
4267 6900 1.002430 GGCACACAGATTGGACTCAGA 59.998 52.381 0.00 0.00 0.00 3.27
4268 6901 1.271001 TGGCACACAGATTGGACTCAG 60.271 52.381 0.00 0.00 0.00 3.35
4269 6902 0.764271 TGGCACACAGATTGGACTCA 59.236 50.000 0.00 0.00 0.00 3.41
4272 6905 1.609208 ACTTGGCACACAGATTGGAC 58.391 50.000 0.00 0.00 39.29 4.02
4375 7010 6.373759 TGGTCTTTCAGCCTATATGTCTCTA 58.626 40.000 0.00 0.00 0.00 2.43
4382 7017 5.132648 TGTCCAATGGTCTTTCAGCCTATAT 59.867 40.000 0.00 0.00 0.00 0.86
4383 7018 4.473196 TGTCCAATGGTCTTTCAGCCTATA 59.527 41.667 0.00 0.00 0.00 1.31
4388 7023 2.227388 CACTGTCCAATGGTCTTTCAGC 59.773 50.000 0.00 0.00 0.00 4.26
4389 7024 3.743521 TCACTGTCCAATGGTCTTTCAG 58.256 45.455 0.00 4.71 0.00 3.02
4392 7027 2.821969 GCATCACTGTCCAATGGTCTTT 59.178 45.455 0.00 0.00 0.00 2.52
4394 7029 1.676916 CGCATCACTGTCCAATGGTCT 60.677 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.