Multiple sequence alignment - TraesCS5D01G211500

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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 TraesCS5D01G211500 chr5D 100.000 9020 0 0 1 9020 320316646 320307627 0.000000e+00 16657
1 TraesCS5D01G211500 chr5D 93.852 553 26 3 8356 8901 272355873 272356424 0.000000e+00 826
2 TraesCS5D01G211500 chr5D 93.405 561 29 2 8348 8901 212952399 212952958 0.000000e+00 824
3 TraesCS5D01G211500 chr5D 93.226 561 30 2 8348 8901 213006722 213007281 0.000000e+00 819
4 TraesCS5D01G211500 chr5D 93.226 561 30 2 8348 8901 213033334 213033893 0.000000e+00 819
5 TraesCS5D01G211500 chr5D 91.304 115 9 1 8902 9015 412713427 412713541 1.210000e-33 156
6 TraesCS5D01G211500 chr5A 98.338 7100 88 13 936 8027 414160757 414167834 0.000000e+00 12430
7 TraesCS5D01G211500 chr5A 89.519 935 41 23 8 921 414159898 414160796 0.000000e+00 1131
8 TraesCS5D01G211500 chr5A 82.258 372 16 17 8024 8355 414167932 414168293 8.920000e-70 276
9 TraesCS5D01G211500 chr5A 91.304 115 9 1 8902 9015 524710043 524709929 1.210000e-33 156
10 TraesCS5D01G211500 chr5B 96.123 7015 188 38 1275 8229 371193949 371186959 0.000000e+00 11370
11 TraesCS5D01G211500 chr5B 87.407 945 41 36 8 921 371194933 371194036 0.000000e+00 1014
12 TraesCS5D01G211500 chr5B 93.226 561 29 3 8348 8901 12642010 12641452 0.000000e+00 817
13 TraesCS5D01G211500 chr5B 98.450 129 2 0 934 1062 371194077 371193949 2.530000e-55 228
14 TraesCS5D01G211500 chr7D 93.761 561 26 3 8348 8901 438546146 438545588 0.000000e+00 833
15 TraesCS5D01G211500 chr7D 92.174 115 8 1 8902 9015 597703307 597703193 2.610000e-35 161
16 TraesCS5D01G211500 chr4D 93.772 562 23 6 8348 8901 468586079 468586636 0.000000e+00 833
17 TraesCS5D01G211500 chr4D 93.841 552 23 3 8357 8901 5724753 5724206 0.000000e+00 821
18 TraesCS5D01G211500 chr4D 91.667 120 9 1 8902 9020 494795883 494795764 2.010000e-36 165
19 TraesCS5D01G211500 chrUn 93.226 561 30 2 8348 8901 320692743 320692184 0.000000e+00 819
20 TraesCS5D01G211500 chrUn 100.000 411 0 0 4061 4471 477678615 477679025 0.000000e+00 760
21 TraesCS5D01G211500 chr2D 75.290 1036 202 29 5480 6485 146306152 146307163 6.430000e-121 446
22 TraesCS5D01G211500 chr2D 78.462 585 106 17 3853 4434 146304563 146305130 1.850000e-96 364
23 TraesCS5D01G211500 chr2B 75.290 1036 202 29 5480 6485 206373815 206374826 6.430000e-121 446
24 TraesCS5D01G211500 chr2B 77.949 585 109 16 3853 4434 206372226 206372793 1.860000e-91 348
25 TraesCS5D01G211500 chr2A 75.097 1032 205 28 5483 6485 155944083 155943075 1.390000e-117 435
26 TraesCS5D01G211500 chr2A 78.462 585 106 16 3853 4434 155945679 155945112 1.850000e-96 364
27 TraesCS5D01G211500 chr3D 92.500 120 8 1 8902 9020 267292518 267292399 4.330000e-38 171
28 TraesCS5D01G211500 chr3B 92.174 115 8 1 8902 9015 14712246 14712132 2.610000e-35 161
29 TraesCS5D01G211500 chr3B 90.984 122 8 3 8895 9015 807731631 807731750 2.610000e-35 161
30 TraesCS5D01G211500 chr1D 90.833 120 10 1 8902 9020 10132718 10132837 9.370000e-35 159
31 TraesCS5D01G211500 chr4A 91.379 116 9 1 8901 9015 412646807 412646692 3.370000e-34 158


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 TraesCS5D01G211500 chr5D 320307627 320316646 9019 True 16657.000000 16657 100.000000 1 9020 1 chr5D.!!$R1 9019
1 TraesCS5D01G211500 chr5D 272355873 272356424 551 False 826.000000 826 93.852000 8356 8901 1 chr5D.!!$F4 545
2 TraesCS5D01G211500 chr5D 212952399 212952958 559 False 824.000000 824 93.405000 8348 8901 1 chr5D.!!$F1 553
3 TraesCS5D01G211500 chr5D 213006722 213007281 559 False 819.000000 819 93.226000 8348 8901 1 chr5D.!!$F2 553
4 TraesCS5D01G211500 chr5D 213033334 213033893 559 False 819.000000 819 93.226000 8348 8901 1 chr5D.!!$F3 553
5 TraesCS5D01G211500 chr5A 414159898 414168293 8395 False 4612.333333 12430 90.038333 8 8355 3 chr5A.!!$F1 8347
6 TraesCS5D01G211500 chr5B 371186959 371194933 7974 True 4204.000000 11370 93.993333 8 8229 3 chr5B.!!$R2 8221
7 TraesCS5D01G211500 chr5B 12641452 12642010 558 True 817.000000 817 93.226000 8348 8901 1 chr5B.!!$R1 553
8 TraesCS5D01G211500 chr7D 438545588 438546146 558 True 833.000000 833 93.761000 8348 8901 1 chr7D.!!$R1 553
9 TraesCS5D01G211500 chr4D 468586079 468586636 557 False 833.000000 833 93.772000 8348 8901 1 chr4D.!!$F1 553
10 TraesCS5D01G211500 chr4D 5724206 5724753 547 True 821.000000 821 93.841000 8357 8901 1 chr4D.!!$R1 544
11 TraesCS5D01G211500 chrUn 320692184 320692743 559 True 819.000000 819 93.226000 8348 8901 1 chrUn.!!$R1 553
12 TraesCS5D01G211500 chr2D 146304563 146307163 2600 False 405.000000 446 76.876000 3853 6485 2 chr2D.!!$F1 2632
13 TraesCS5D01G211500 chr2B 206372226 206374826 2600 False 397.000000 446 76.619500 3853 6485 2 chr2B.!!$F1 2632
14 TraesCS5D01G211500 chr2A 155943075 155945679 2604 True 399.500000 435 76.779500 3853 6485 2 chr2A.!!$R1 2632

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
924 964 2.123077 CCCGCTCCATCTCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69 F
1769 1812 0.966875 TTTGATGCAGGCAAGCGGAT 60.967 50.000 0.00 0.00 37.31 4.18 F
1994 2049 0.179084 TAGCTGGTGTTAGCATCGCC 60.179 55.000 0.00 0.00 46.07 5.54 F
3573 3635 0.033796 AATGGCCACATACTGCTGCT 60.034 50.000 8.16 0.00 35.94 4.24 F
3777 3839 0.923358 TGGAAAACAGTGGGAGTGGT 59.077 50.000 0.00 0.00 0.00 4.16 F
4594 4657 1.089920 CCCTCGGTGCTGAATTTCAG 58.910 55.000 19.92 19.92 46.90 3.02 F
6451 6643 0.843309 TGACTTCTGGAAGCCCAACA 59.157 50.000 9.91 1.90 42.98 3.33 F
6930 7130 0.251165 TTTTACCAGCAGCACCCCTC 60.251 55.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2049 0.386478 GGCTTGCTTTGCTGTTCTCG 60.386 55.000 0.00 0.00 0.00 4.04 R
3552 3611 2.023673 GCAGCAGTATGTGGCCATTTA 58.976 47.619 9.72 0.14 39.31 1.40 R
3755 3817 2.763448 CCACTCCCACTGTTTTCCAAAA 59.237 45.455 0.00 0.00 0.00 2.44 R
5398 5566 0.803768 CCACGTCAAGATCTCCTGCG 60.804 60.000 0.00 2.98 0.00 5.18 R
6406 6598 4.623932 TTGAGTCAAGTGCCTGAAGTAT 57.376 40.909 0.08 0.00 0.00 2.12 R
6499 6699 0.964700 TGCCGGATCAAATGTGCAAA 59.035 45.000 5.05 0.00 0.00 3.68 R
7405 7615 0.462581 GCAGGAAGTCGATGATGCCA 60.463 55.000 0.00 0.00 0.00 4.92 R
8343 8711 1.243342 ATGTGCAATGGTCACGTGGG 61.243 55.000 17.00 0.04 37.26 4.61 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
52 53 5.596268 AACGTATTTTCCTTACCGTCAAC 57.404 39.130 0.00 0.00 0.00 3.18
258 263 3.679502 GCCCATTATCAACAACTGCAAAC 59.320 43.478 0.00 0.00 0.00 2.93
262 267 7.267128 CCCATTATCAACAACTGCAAACATAT 58.733 34.615 0.00 0.00 0.00 1.78
298 303 7.931578 TCATTTCATTTTAAGTACCGTCCAT 57.068 32.000 0.00 0.00 0.00 3.41
396 403 4.347096 CACGTTCACGGGCTGTTA 57.653 55.556 0.00 0.00 44.95 2.41
401 408 3.372822 CACGTTCACGGGCTGTTATTAAT 59.627 43.478 0.00 0.00 44.95 1.40
416 449 3.603158 ATTAATTTTCACAACCGGGGC 57.397 42.857 6.32 0.00 0.00 5.80
712 749 6.666113 TCTCCATATCCGTATAATAAGCACCA 59.334 38.462 0.00 0.00 0.00 4.17
871 911 4.496336 GCCTCTCCCGCATTGGCT 62.496 66.667 0.00 0.00 40.36 4.75
921 961 4.488911 AGCCCCGCTCCATCTCCT 62.489 66.667 0.00 0.00 30.62 3.69
922 962 3.934962 GCCCCGCTCCATCTCCTC 61.935 72.222 0.00 0.00 0.00 3.71
923 963 3.237741 CCCCGCTCCATCTCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
924 964 2.123077 CCCGCTCCATCTCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
925 965 2.206536 CCCGCTCCATCTCCTCCTC 61.207 68.421 0.00 0.00 0.00 3.71
926 966 2.560119 CCGCTCCATCTCCTCCTCG 61.560 68.421 0.00 0.00 0.00 4.63
927 967 2.733945 GCTCCATCTCCTCCTCGC 59.266 66.667 0.00 0.00 0.00 5.03
928 968 2.866726 GCTCCATCTCCTCCTCGCC 61.867 68.421 0.00 0.00 0.00 5.54
929 969 2.519541 TCCATCTCCTCCTCGCCG 60.520 66.667 0.00 0.00 0.00 6.46
930 970 3.610669 CCATCTCCTCCTCGCCGG 61.611 72.222 0.00 0.00 0.00 6.13
931 971 2.519541 CATCTCCTCCTCGCCGGA 60.520 66.667 5.05 0.00 40.30 5.14
1205 1245 3.430862 TGTGCTGGATTTCGCGGC 61.431 61.111 6.13 0.00 0.00 6.53
1645 1688 7.970614 GGTCAATTGACTTAGAATGGCTTTAAG 59.029 37.037 31.81 0.00 44.20 1.85
1647 1690 9.733556 TCAATTGACTTAGAATGGCTTTAAGTA 57.266 29.630 3.38 0.00 37.66 2.24
1769 1812 0.966875 TTTGATGCAGGCAAGCGGAT 60.967 50.000 0.00 0.00 37.31 4.18
1806 1849 3.141272 TGAACCCAGGGTCCAGTTTTTAT 59.859 43.478 13.17 0.00 33.12 1.40
1976 2031 5.106237 CGACTCAGATGATGCTCATGATCTA 60.106 44.000 10.65 1.79 39.26 1.98
1981 2036 3.679824 TGATGCTCATGATCTAGCTGG 57.320 47.619 13.83 0.00 39.53 4.85
1991 2046 4.327982 TGATCTAGCTGGTGTTAGCATC 57.672 45.455 0.00 0.00 46.07 3.91
1994 2049 0.179084 TAGCTGGTGTTAGCATCGCC 60.179 55.000 0.00 0.00 46.07 5.54
2044 2099 3.056107 TCCTGTATCTTCGACTTTGGTGG 60.056 47.826 0.00 0.00 0.00 4.61
2472 2527 3.384668 CCAACTGATAGGTATGTGCTCG 58.615 50.000 0.00 0.00 0.00 5.03
2856 2911 5.674052 ATGTGCTGATAGTTGAGAAGAGT 57.326 39.130 0.00 0.00 0.00 3.24
3552 3611 4.163441 TGATAGTCTCAGAGCTGCTACT 57.837 45.455 0.15 4.57 32.61 2.57
3573 3635 0.033796 AATGGCCACATACTGCTGCT 60.034 50.000 8.16 0.00 35.94 4.24
3755 3817 6.525629 CAAAGATACCCGTGGATTTATCTCT 58.474 40.000 0.00 0.00 31.40 3.10
3777 3839 0.923358 TGGAAAACAGTGGGAGTGGT 59.077 50.000 0.00 0.00 0.00 4.16
4594 4657 1.089920 CCCTCGGTGCTGAATTTCAG 58.910 55.000 19.92 19.92 46.90 3.02
4641 4801 5.179555 GTGAAAGGAGAAACAGTCATGGTAC 59.820 44.000 0.00 0.00 0.00 3.34
4689 4849 4.217118 AGTTCAGTGATTCATTTCTGTGCC 59.783 41.667 0.00 0.00 0.00 5.01
4951 5116 3.002348 AGTCTTTAGCGTCTTTTGTGTGC 59.998 43.478 0.00 0.00 0.00 4.57
4981 5146 7.865385 TGTTTTCCATTGTTTTTCTTATCCTCG 59.135 33.333 0.00 0.00 0.00 4.63
5089 5254 4.228451 CGTGTGAGACGTGGTCTG 57.772 61.111 2.51 0.00 43.53 3.51
5272 5437 1.541588 GAAACACATGAAGGACCTGCC 59.458 52.381 0.00 0.00 0.00 4.85
5398 5566 1.675641 GGTGGATGGTGTGAGTGGC 60.676 63.158 0.00 0.00 0.00 5.01
6158 6347 5.049267 GCCCACTTTAAGTATTCGTTTGACA 60.049 40.000 0.00 0.00 0.00 3.58
6406 6598 2.151502 TTGTTGGGTTTGCTCCTCAA 57.848 45.000 0.00 0.00 0.00 3.02
6451 6643 0.843309 TGACTTCTGGAAGCCCAACA 59.157 50.000 9.91 1.90 42.98 3.33
6492 6692 3.694566 GGAATTTATCAGGTTCGCCACTT 59.305 43.478 0.00 0.00 40.60 3.16
6493 6693 4.157840 GGAATTTATCAGGTTCGCCACTTT 59.842 41.667 0.00 0.00 40.60 2.66
6494 6694 4.965119 ATTTATCAGGTTCGCCACTTTC 57.035 40.909 0.00 0.00 40.60 2.62
6495 6695 3.695830 TTATCAGGTTCGCCACTTTCT 57.304 42.857 0.00 0.00 40.60 2.52
6496 6696 4.811969 TTATCAGGTTCGCCACTTTCTA 57.188 40.909 0.00 0.00 40.60 2.10
6497 6697 3.914426 ATCAGGTTCGCCACTTTCTAT 57.086 42.857 0.00 0.00 40.60 1.98
6498 6698 2.972625 TCAGGTTCGCCACTTTCTATG 58.027 47.619 0.00 0.00 40.60 2.23
6499 6699 2.301870 TCAGGTTCGCCACTTTCTATGT 59.698 45.455 0.00 0.00 40.60 2.29
6860 7060 5.622460 CGGTATGCAACTCTCTCAACTTACT 60.622 44.000 0.00 0.00 0.00 2.24
6930 7130 0.251165 TTTTACCAGCAGCACCCCTC 60.251 55.000 0.00 0.00 0.00 4.30
7021 7221 8.592105 AAACCATCATTTACATGACACAAAAG 57.408 30.769 0.00 0.00 42.46 2.27
7405 7615 5.757320 CGAGGAGAATAATGAGCTTGTGATT 59.243 40.000 0.00 0.00 0.00 2.57
7519 7729 0.180171 CCCCAACTGTCATATCGCCA 59.820 55.000 0.00 0.00 0.00 5.69
7772 7983 8.901472 ACTTAGCTGTAGGATATTCATATGGA 57.099 34.615 2.13 0.00 0.00 3.41
8030 8243 7.972832 AATAGGATCTGTCTAGTCTTAGTCG 57.027 40.000 0.00 0.00 0.00 4.18
8122 8460 2.861462 TTTCTGGTCGCTGGTTTTTG 57.139 45.000 0.00 0.00 0.00 2.44
8124 8462 1.021202 TCTGGTCGCTGGTTTTTGTG 58.979 50.000 0.00 0.00 0.00 3.33
8125 8463 1.021202 CTGGTCGCTGGTTTTTGTGA 58.979 50.000 0.00 0.00 0.00 3.58
8127 8465 1.336440 TGGTCGCTGGTTTTTGTGATG 59.664 47.619 0.00 0.00 0.00 3.07
8129 8467 2.223711 GGTCGCTGGTTTTTGTGATGTT 60.224 45.455 0.00 0.00 0.00 2.71
8131 8469 3.242712 GTCGCTGGTTTTTGTGATGTTTG 59.757 43.478 0.00 0.00 0.00 2.93
8171 8509 2.106566 TGTGATGTTTGCTTGTTGGGT 58.893 42.857 0.00 0.00 0.00 4.51
8182 8520 2.354203 GCTTGTTGGGTTTGTTTGTGGA 60.354 45.455 0.00 0.00 0.00 4.02
8314 8676 8.791327 AGGAATGACAAAAACAGAAACAAAAT 57.209 26.923 0.00 0.00 0.00 1.82
8343 8711 0.526211 GGAAAAGGGAACATGCCGTC 59.474 55.000 0.00 0.00 30.73 4.79
8485 8860 4.535781 AGACTTGCCATGCACCATAAATA 58.464 39.130 0.00 0.00 38.71 1.40
8589 8964 6.311200 GCCATCATCGAAAAACTAAAATTGCT 59.689 34.615 0.00 0.00 0.00 3.91
8618 8993 7.517614 TCTACAAACTAAAATTGCCACATGA 57.482 32.000 0.00 0.00 0.00 3.07
8622 8997 6.991531 ACAAACTAAAATTGCCACATGACAAT 59.008 30.769 0.00 3.61 38.11 2.71
8652 9027 3.961480 AGCACTATGACAACTACAGCA 57.039 42.857 0.00 0.00 0.00 4.41
8681 9056 2.496899 TGGCAACTTTTGGGCAAAAA 57.503 40.000 0.00 0.00 39.49 1.94
8827 9203 6.183360 ACCGAAAACCAAAAAGATTTCTGCTA 60.183 34.615 0.00 0.00 31.29 3.49
8905 9281 2.904866 ACGCCCACACGTGCATTT 60.905 55.556 17.22 0.00 46.28 2.32
8906 9282 2.334653 CGCCCACACGTGCATTTT 59.665 55.556 17.22 0.00 0.00 1.82
8907 9283 2.015627 CGCCCACACGTGCATTTTG 61.016 57.895 17.22 5.74 0.00 2.44
8908 9284 1.067250 GCCCACACGTGCATTTTGT 59.933 52.632 17.22 0.00 0.00 2.83
8909 9285 0.939106 GCCCACACGTGCATTTTGTC 60.939 55.000 17.22 0.00 0.00 3.18
8910 9286 0.383590 CCCACACGTGCATTTTGTCA 59.616 50.000 17.22 0.00 0.00 3.58
8911 9287 1.476074 CCACACGTGCATTTTGTCAC 58.524 50.000 17.22 0.00 0.00 3.67
8920 9296 4.532276 GTGCATTTTGTCACGTATGAACA 58.468 39.130 0.00 0.00 36.31 3.18
8921 9297 4.973051 GTGCATTTTGTCACGTATGAACAA 59.027 37.500 0.00 1.48 36.31 2.83
8922 9298 5.457148 GTGCATTTTGTCACGTATGAACAAA 59.543 36.000 12.99 12.99 36.31 2.83
8923 9299 6.143758 GTGCATTTTGTCACGTATGAACAAAT 59.856 34.615 15.89 4.25 36.56 2.32
8924 9300 6.143598 TGCATTTTGTCACGTATGAACAAATG 59.856 34.615 15.89 13.39 42.71 2.32
8925 9301 6.362016 GCATTTTGTCACGTATGAACAAATGA 59.638 34.615 18.13 7.83 42.60 2.57
8926 9302 7.617122 GCATTTTGTCACGTATGAACAAATGAC 60.617 37.037 18.13 7.40 42.60 3.06
8927 9303 5.993106 TTGTCACGTATGAACAAATGACA 57.007 34.783 0.91 0.91 39.22 3.58
8928 9304 6.552859 TTGTCACGTATGAACAAATGACAT 57.447 33.333 5.77 0.00 39.97 3.06
8929 9305 6.164408 TGTCACGTATGAACAAATGACATC 57.836 37.500 0.91 0.00 37.54 3.06
8930 9306 5.698545 TGTCACGTATGAACAAATGACATCA 59.301 36.000 0.91 0.00 37.54 3.07
8931 9307 6.128580 TGTCACGTATGAACAAATGACATCAG 60.129 38.462 0.91 0.00 37.54 2.90
8932 9308 5.023920 CACGTATGAACAAATGACATCAGC 58.976 41.667 0.00 0.00 0.00 4.26
8933 9309 4.694982 ACGTATGAACAAATGACATCAGCA 59.305 37.500 0.00 0.00 0.00 4.41
8934 9310 5.163824 ACGTATGAACAAATGACATCAGCAG 60.164 40.000 0.00 0.00 0.00 4.24
8935 9311 4.713824 ATGAACAAATGACATCAGCAGG 57.286 40.909 0.00 0.00 0.00 4.85
8936 9312 3.753815 TGAACAAATGACATCAGCAGGA 58.246 40.909 0.00 0.00 0.00 3.86
8937 9313 4.143543 TGAACAAATGACATCAGCAGGAA 58.856 39.130 0.00 0.00 0.00 3.36
8938 9314 4.768448 TGAACAAATGACATCAGCAGGAAT 59.232 37.500 0.00 0.00 0.00 3.01
8939 9315 4.978083 ACAAATGACATCAGCAGGAATC 57.022 40.909 0.00 0.00 0.00 2.52
8940 9316 4.597004 ACAAATGACATCAGCAGGAATCT 58.403 39.130 0.00 0.00 0.00 2.40
8941 9317 5.014858 ACAAATGACATCAGCAGGAATCTT 58.985 37.500 0.00 0.00 0.00 2.40
8942 9318 5.479375 ACAAATGACATCAGCAGGAATCTTT 59.521 36.000 0.00 0.00 0.00 2.52
8943 9319 5.831702 AATGACATCAGCAGGAATCTTTC 57.168 39.130 0.00 0.00 0.00 2.62
8944 9320 4.564782 TGACATCAGCAGGAATCTTTCT 57.435 40.909 0.00 0.00 0.00 2.52
8945 9321 4.259356 TGACATCAGCAGGAATCTTTCTG 58.741 43.478 0.00 0.00 0.00 3.02
8946 9322 3.618351 ACATCAGCAGGAATCTTTCTGG 58.382 45.455 0.56 0.00 0.00 3.86
8947 9323 3.009916 ACATCAGCAGGAATCTTTCTGGT 59.990 43.478 0.00 0.00 41.67 4.00
8948 9324 3.795688 TCAGCAGGAATCTTTCTGGTT 57.204 42.857 0.14 0.00 39.36 3.67
8949 9325 4.104383 TCAGCAGGAATCTTTCTGGTTT 57.896 40.909 0.14 0.00 39.36 3.27
8950 9326 4.473444 TCAGCAGGAATCTTTCTGGTTTT 58.527 39.130 0.14 0.00 39.36 2.43
8951 9327 4.895297 TCAGCAGGAATCTTTCTGGTTTTT 59.105 37.500 0.14 0.00 39.36 1.94
8952 9328 4.986659 CAGCAGGAATCTTTCTGGTTTTTG 59.013 41.667 0.14 0.00 39.36 2.44
8953 9329 3.742882 GCAGGAATCTTTCTGGTTTTTGC 59.257 43.478 0.56 0.00 0.00 3.68
8954 9330 4.502087 GCAGGAATCTTTCTGGTTTTTGCT 60.502 41.667 0.56 0.00 0.00 3.91
8955 9331 5.604565 CAGGAATCTTTCTGGTTTTTGCTT 58.395 37.500 0.00 0.00 0.00 3.91
8956 9332 6.738453 GCAGGAATCTTTCTGGTTTTTGCTTA 60.738 38.462 0.56 0.00 0.00 3.09
8957 9333 7.209475 CAGGAATCTTTCTGGTTTTTGCTTAA 58.791 34.615 0.00 0.00 0.00 1.85
8958 9334 7.710475 CAGGAATCTTTCTGGTTTTTGCTTAAA 59.290 33.333 0.00 0.00 0.00 1.52
8959 9335 8.264347 AGGAATCTTTCTGGTTTTTGCTTAAAA 58.736 29.630 0.00 0.00 33.41 1.52
8960 9336 8.551205 GGAATCTTTCTGGTTTTTGCTTAAAAG 58.449 33.333 0.00 0.00 36.44 2.27
8961 9337 9.098355 GAATCTTTCTGGTTTTTGCTTAAAAGT 57.902 29.630 0.00 0.00 36.44 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.630111 TGTTGACGGTAAGGAAAATACGT 58.370 39.130 0.00 0.00 0.00 3.57
33 34 7.136289 TGATTGTTGACGGTAAGGAAAATAC 57.864 36.000 0.00 0.00 0.00 1.89
52 53 6.206243 GGGATGTGGAGAGTAAATGATGATTG 59.794 42.308 0.00 0.00 0.00 2.67
109 110 8.523915 AAGATATGCCTTACAATTGATGACAA 57.476 30.769 13.59 0.00 40.42 3.18
140 145 7.616935 AGCTTGGGAAAGATCAATGAAAATCTA 59.383 33.333 0.00 0.00 32.01 1.98
236 241 3.591196 TTGCAGTTGTTGATAATGGGC 57.409 42.857 0.00 0.00 0.00 5.36
270 275 9.072294 GGACGGTACTTAAAATGAAATGAAATG 57.928 33.333 0.00 0.00 0.00 2.32
360 367 0.527817 GCGGAACCAGGTCGTATGAG 60.528 60.000 0.00 0.00 0.00 2.90
361 368 1.252215 TGCGGAACCAGGTCGTATGA 61.252 55.000 0.00 0.00 0.00 2.15
362 369 1.082117 GTGCGGAACCAGGTCGTATG 61.082 60.000 0.00 0.00 0.00 2.39
363 370 1.217244 GTGCGGAACCAGGTCGTAT 59.783 57.895 0.00 0.00 0.00 3.06
364 371 2.652530 GTGCGGAACCAGGTCGTA 59.347 61.111 0.00 0.00 0.00 3.43
365 372 4.657824 CGTGCGGAACCAGGTCGT 62.658 66.667 0.00 0.00 0.00 4.34
366 373 4.657824 ACGTGCGGAACCAGGTCG 62.658 66.667 0.00 0.00 0.00 4.79
389 396 5.575218 CCGGTTGTGAAAATTAATAACAGCC 59.425 40.000 12.47 12.47 38.38 4.85
390 397 5.575218 CCCGGTTGTGAAAATTAATAACAGC 59.425 40.000 0.00 0.00 0.00 4.40
393 400 4.865925 GCCCCGGTTGTGAAAATTAATAAC 59.134 41.667 0.00 0.00 0.00 1.89
396 403 3.056179 CAGCCCCGGTTGTGAAAATTAAT 60.056 43.478 0.00 0.00 0.00 1.40
401 408 0.684805 AACAGCCCCGGTTGTGAAAA 60.685 50.000 3.80 0.00 39.43 2.29
736 775 1.688884 GAGAGAGCAGGGGAAGGCT 60.689 63.158 0.00 0.00 44.48 4.58
737 776 2.741055 GGAGAGAGCAGGGGAAGGC 61.741 68.421 0.00 0.00 0.00 4.35
738 777 1.002792 AGGAGAGAGCAGGGGAAGG 59.997 63.158 0.00 0.00 0.00 3.46
739 778 1.048160 GGAGGAGAGAGCAGGGGAAG 61.048 65.000 0.00 0.00 0.00 3.46
870 910 4.883354 GGGGCGGGGATTCAGCAG 62.883 72.222 0.00 0.00 38.33 4.24
904 944 4.488911 AGGAGATGGAGCGGGGCT 62.489 66.667 0.00 0.00 43.88 5.19
905 945 3.934962 GAGGAGATGGAGCGGGGC 61.935 72.222 0.00 0.00 0.00 5.80
906 946 3.237741 GGAGGAGATGGAGCGGGG 61.238 72.222 0.00 0.00 0.00 5.73
907 947 2.123077 AGGAGGAGATGGAGCGGG 60.123 66.667 0.00 0.00 0.00 6.13
908 948 2.560119 CGAGGAGGAGATGGAGCGG 61.560 68.421 0.00 0.00 0.00 5.52
909 949 3.038280 CGAGGAGGAGATGGAGCG 58.962 66.667 0.00 0.00 0.00 5.03
910 950 2.733945 GCGAGGAGGAGATGGAGC 59.266 66.667 0.00 0.00 0.00 4.70
911 951 2.560119 CGGCGAGGAGGAGATGGAG 61.560 68.421 0.00 0.00 0.00 3.86
912 952 2.519541 CGGCGAGGAGGAGATGGA 60.520 66.667 0.00 0.00 0.00 3.41
913 953 3.610669 CCGGCGAGGAGGAGATGG 61.611 72.222 9.30 0.00 45.00 3.51
914 954 2.519541 TCCGGCGAGGAGGAGATG 60.520 66.667 9.30 0.00 45.98 2.90
935 975 4.292178 GAGGAGGCGATGGAGCGG 62.292 72.222 0.00 0.00 38.18 5.52
936 976 4.637489 CGAGGAGGCGATGGAGCG 62.637 72.222 0.00 0.00 38.18 5.03
937 977 4.959596 GCGAGGAGGCGATGGAGC 62.960 72.222 0.00 0.00 0.00 4.70
938 978 4.292178 GGCGAGGAGGCGATGGAG 62.292 72.222 0.00 0.00 35.04 3.86
1216 1256 1.045911 AGGGATCTGGTCTTCTCCGC 61.046 60.000 0.00 0.00 0.00 5.54
1645 1688 2.683362 CCAAAGAAAGAGGGGCGATTAC 59.317 50.000 0.00 0.00 0.00 1.89
1647 1690 1.354368 TCCAAAGAAAGAGGGGCGATT 59.646 47.619 0.00 0.00 0.00 3.34
1752 1795 2.116533 CATCCGCTTGCCTGCATCA 61.117 57.895 0.00 0.00 0.00 3.07
1769 1812 0.532573 GTTCATGAGCCTCCTCGTCA 59.467 55.000 0.00 0.00 41.13 4.35
1806 1849 2.735259 AAGAAGTAAGTCCCTGGGGA 57.265 50.000 14.00 3.92 42.90 4.81
1976 2031 1.450312 GGCGATGCTAACACCAGCT 60.450 57.895 0.00 0.00 42.30 4.24
1981 2036 0.645868 GTTCTCGGCGATGCTAACAC 59.354 55.000 11.27 0.00 0.00 3.32
1994 2049 0.386478 GGCTTGCTTTGCTGTTCTCG 60.386 55.000 0.00 0.00 0.00 4.04
2472 2527 0.863144 TGCGTAGAAACAACGGAAGC 59.137 50.000 0.00 0.00 37.76 3.86
2856 2911 2.702478 CTCCTGGGCATAAGATGAGACA 59.298 50.000 0.00 0.00 0.00 3.41
3378 3437 3.696051 GGGACAGATGATAAGCAGCAAAA 59.304 43.478 0.00 0.00 34.69 2.44
3550 3609 3.282021 CAGCAGTATGTGGCCATTTAGT 58.718 45.455 9.72 3.89 39.31 2.24
3551 3610 2.033801 GCAGCAGTATGTGGCCATTTAG 59.966 50.000 9.72 0.00 39.31 1.85
3552 3611 2.023673 GCAGCAGTATGTGGCCATTTA 58.976 47.619 9.72 0.14 39.31 1.40
3573 3635 6.691754 ATACCATCAAACATTTGCGTGATA 57.308 33.333 0.00 0.00 38.05 2.15
3755 3817 2.763448 CCACTCCCACTGTTTTCCAAAA 59.237 45.455 0.00 0.00 0.00 2.44
3777 3839 3.184382 TGGAAGTCATCTGGTGGTAGA 57.816 47.619 0.00 0.00 0.00 2.59
4641 4801 8.942669 TGTTTAACATAGAACATTAAACAGCG 57.057 30.769 14.37 0.00 46.27 5.18
4689 4849 7.116805 GCAAATAACCAAAGTTGAGAATGAAGG 59.883 37.037 0.00 0.00 36.68 3.46
4981 5146 4.757799 ACCCTGCAAAACAAAACAAAAC 57.242 36.364 0.00 0.00 0.00 2.43
5089 5254 2.802816 CCAAACGTATGCATCTAGGAGC 59.197 50.000 0.19 0.00 0.00 4.70
5398 5566 0.803768 CCACGTCAAGATCTCCTGCG 60.804 60.000 0.00 2.98 0.00 5.18
6406 6598 4.623932 TTGAGTCAAGTGCCTGAAGTAT 57.376 40.909 0.08 0.00 0.00 2.12
6451 6643 7.919385 AATTCCTAATATTTTGGCCAGACAT 57.081 32.000 5.11 1.75 0.00 3.06
6492 6692 5.392919 CCGGATCAAATGTGCAAACATAGAA 60.393 40.000 0.00 0.00 0.00 2.10
6493 6693 4.096231 CCGGATCAAATGTGCAAACATAGA 59.904 41.667 0.00 0.00 0.00 1.98
6494 6694 4.353737 CCGGATCAAATGTGCAAACATAG 58.646 43.478 0.00 0.00 0.00 2.23
6495 6695 3.428725 GCCGGATCAAATGTGCAAACATA 60.429 43.478 5.05 0.00 0.00 2.29
6496 6696 2.674747 GCCGGATCAAATGTGCAAACAT 60.675 45.455 5.05 0.00 0.00 2.71
6497 6697 1.336702 GCCGGATCAAATGTGCAAACA 60.337 47.619 5.05 0.00 0.00 2.83
6498 6698 1.336702 TGCCGGATCAAATGTGCAAAC 60.337 47.619 5.05 0.00 0.00 2.93
6499 6699 0.964700 TGCCGGATCAAATGTGCAAA 59.035 45.000 5.05 0.00 0.00 3.68
6563 6763 4.082125 GCCCTTGATATTAACCTGGATGG 58.918 47.826 0.00 0.00 42.93 3.51
6930 7130 8.378172 TGTGAAATTAAGGTGAACAAGACTAG 57.622 34.615 0.00 0.00 0.00 2.57
7021 7221 3.608796 AGATGCTTCTTCTTGCTCCTTC 58.391 45.455 0.00 0.00 0.00 3.46
7405 7615 0.462581 GCAGGAAGTCGATGATGCCA 60.463 55.000 0.00 0.00 0.00 4.92
7519 7729 6.494952 TCTGAACCTCTTCTTATACTGGACT 58.505 40.000 0.00 0.00 0.00 3.85
7673 7883 2.516923 GCTATCCGTATCGATTCACCG 58.483 52.381 1.71 1.31 0.00 4.94
7772 7983 3.884895 TCACCAATTTACATGGAGCGAT 58.115 40.909 0.00 0.00 40.56 4.58
8028 8241 3.058432 CCAAGTCTCAGTCGACTAAACGA 60.058 47.826 19.57 10.44 43.14 3.85
8029 8242 3.058432 TCCAAGTCTCAGTCGACTAAACG 60.058 47.826 19.57 5.98 43.14 3.60
8030 8243 4.215827 TCTCCAAGTCTCAGTCGACTAAAC 59.784 45.833 19.57 15.79 43.14 2.01
8138 8476 9.545105 AAGCAAACATCACAAAATCATCTTTAA 57.455 25.926 0.00 0.00 0.00 1.52
8139 8477 8.980610 CAAGCAAACATCACAAAATCATCTTTA 58.019 29.630 0.00 0.00 0.00 1.85
8140 8478 7.496591 ACAAGCAAACATCACAAAATCATCTTT 59.503 29.630 0.00 0.00 0.00 2.52
8141 8479 6.987992 ACAAGCAAACATCACAAAATCATCTT 59.012 30.769 0.00 0.00 0.00 2.40
8171 8509 3.573538 CCCATCACAGATCCACAAACAAA 59.426 43.478 0.00 0.00 0.00 2.83
8182 8520 1.911357 TCAGTCAAGCCCATCACAGAT 59.089 47.619 0.00 0.00 0.00 2.90
8259 8621 9.609346 TTCTTTTCCCTTTAACTATCTATTCCG 57.391 33.333 0.00 0.00 0.00 4.30
8305 8667 9.788960 CCTTTTCCATAGCTAGTATTTTGTTTC 57.211 33.333 0.00 0.00 0.00 2.78
8314 8676 6.591935 CATGTTCCCTTTTCCATAGCTAGTA 58.408 40.000 0.00 0.00 0.00 1.82
8343 8711 1.243342 ATGTGCAATGGTCACGTGGG 61.243 55.000 17.00 0.04 37.26 4.61
8485 8860 5.797051 AGTGCAAGTATCATGGCAATTTTT 58.203 33.333 0.00 0.00 38.10 1.94
8589 8964 9.237187 TGTGGCAATTTTAGTTTGTAGATCATA 57.763 29.630 0.00 0.00 0.00 2.15
8652 9027 5.490159 CCCAAAAGTTGCCATGATGTTTAT 58.510 37.500 0.00 0.00 0.00 1.40
8681 9056 7.858382 TGTTGATATGTTTCGACGAAATGTTTT 59.142 29.630 24.48 10.14 33.97 2.43
8685 9060 6.411782 CCATGTTGATATGTTTCGACGAAATG 59.588 38.462 24.48 14.37 33.97 2.32
8797 9173 9.607988 AGAAATCTTTTTGGTTTTCGGTTTAAT 57.392 25.926 0.00 0.00 34.17 1.40
8827 9203 3.623060 GCCACGTATGAACAGATGACATT 59.377 43.478 0.00 0.00 0.00 2.71
8901 9277 7.378194 TGTCATTTGTTCATACGTGACAAAATG 59.622 33.333 18.40 15.60 42.23 2.32
8902 9278 7.421599 TGTCATTTGTTCATACGTGACAAAAT 58.578 30.769 18.40 7.36 39.06 1.82
8903 9279 6.786207 TGTCATTTGTTCATACGTGACAAAA 58.214 32.000 18.40 5.76 39.06 2.44
8904 9280 6.364945 TGTCATTTGTTCATACGTGACAAA 57.635 33.333 17.44 17.44 39.06 2.83
8905 9281 5.993106 TGTCATTTGTTCATACGTGACAA 57.007 34.783 0.00 1.33 39.06 3.18
8906 9282 5.698545 TGATGTCATTTGTTCATACGTGACA 59.301 36.000 8.24 8.24 42.50 3.58
8907 9283 6.164408 TGATGTCATTTGTTCATACGTGAC 57.836 37.500 0.00 0.00 35.80 3.67
8908 9284 5.163864 GCTGATGTCATTTGTTCATACGTGA 60.164 40.000 0.00 0.00 0.00 4.35
8909 9285 5.023920 GCTGATGTCATTTGTTCATACGTG 58.976 41.667 0.00 0.00 0.00 4.49
8910 9286 4.694982 TGCTGATGTCATTTGTTCATACGT 59.305 37.500 0.00 0.00 0.00 3.57
8911 9287 5.220557 TGCTGATGTCATTTGTTCATACG 57.779 39.130 0.00 0.00 0.00 3.06
8912 9288 5.355071 TCCTGCTGATGTCATTTGTTCATAC 59.645 40.000 0.00 0.00 0.00 2.39
8913 9289 5.499313 TCCTGCTGATGTCATTTGTTCATA 58.501 37.500 0.00 0.00 0.00 2.15
8914 9290 4.338012 TCCTGCTGATGTCATTTGTTCAT 58.662 39.130 0.00 0.00 0.00 2.57
8915 9291 3.753815 TCCTGCTGATGTCATTTGTTCA 58.246 40.909 0.00 0.00 0.00 3.18
8916 9292 4.771590 TTCCTGCTGATGTCATTTGTTC 57.228 40.909 0.00 0.00 0.00 3.18
8917 9293 5.014858 AGATTCCTGCTGATGTCATTTGTT 58.985 37.500 0.00 0.00 0.00 2.83
8918 9294 4.597004 AGATTCCTGCTGATGTCATTTGT 58.403 39.130 0.00 0.00 0.00 2.83
8919 9295 5.578005 AAGATTCCTGCTGATGTCATTTG 57.422 39.130 0.00 0.00 0.00 2.32
8920 9296 5.950549 AGAAAGATTCCTGCTGATGTCATTT 59.049 36.000 0.00 0.00 0.00 2.32
8921 9297 5.357314 CAGAAAGATTCCTGCTGATGTCATT 59.643 40.000 0.00 0.00 31.22 2.57
8922 9298 4.882427 CAGAAAGATTCCTGCTGATGTCAT 59.118 41.667 0.00 0.00 31.22 3.06
8923 9299 4.259356 CAGAAAGATTCCTGCTGATGTCA 58.741 43.478 0.00 0.00 31.22 3.58
8924 9300 3.626670 CCAGAAAGATTCCTGCTGATGTC 59.373 47.826 0.00 0.00 31.22 3.06
8925 9301 3.009916 ACCAGAAAGATTCCTGCTGATGT 59.990 43.478 0.00 0.00 31.22 3.06
8926 9302 3.618351 ACCAGAAAGATTCCTGCTGATG 58.382 45.455 0.00 0.00 31.22 3.07
8927 9303 4.313020 AACCAGAAAGATTCCTGCTGAT 57.687 40.909 0.00 0.00 31.22 2.90
8928 9304 3.795688 AACCAGAAAGATTCCTGCTGA 57.204 42.857 0.00 0.00 31.22 4.26
8929 9305 4.861102 AAAACCAGAAAGATTCCTGCTG 57.139 40.909 0.00 0.00 0.00 4.41
8930 9306 4.502087 GCAAAAACCAGAAAGATTCCTGCT 60.502 41.667 0.00 0.00 0.00 4.24
8931 9307 3.742882 GCAAAAACCAGAAAGATTCCTGC 59.257 43.478 0.00 0.00 0.00 4.85
8932 9308 5.205759 AGCAAAAACCAGAAAGATTCCTG 57.794 39.130 0.00 0.00 0.00 3.86
8933 9309 5.876651 AAGCAAAAACCAGAAAGATTCCT 57.123 34.783 0.00 0.00 0.00 3.36
8934 9310 8.432110 TTTTAAGCAAAAACCAGAAAGATTCC 57.568 30.769 0.00 0.00 32.05 3.01
8935 9311 9.098355 ACTTTTAAGCAAAAACCAGAAAGATTC 57.902 29.630 0.00 0.00 33.33 2.52


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

AutoCloner maintained by Alex Coulton.