Multiple sequence alignment - TraesCS4D01G303400

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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 TraesCS4D01G303400 chr4D 100.000 2345 0 0 1 2345 471271485 471269141 0.000000e+00 4331.0
1 TraesCS4D01G303400 chr4D 77.358 371 57 22 996 1351 471153967 471153609 6.610000e-46 195.0
2 TraesCS4D01G303400 chr4B 91.187 1339 58 25 442 1731 593351974 593350647 0.000000e+00 1764.0
3 TraesCS4D01G303400 chr4B 88.065 310 16 8 14 321 593353461 593353171 4.800000e-92 348.0
4 TraesCS4D01G303400 chr4A 85.592 1638 93 63 335 1882 678419880 678418296 0.000000e+00 1585.0
5 TraesCS4D01G303400 chr4A 82.527 372 50 5 994 1353 678376578 678376210 1.750000e-81 313.0
6 TraesCS4D01G303400 chr4A 75.773 388 61 20 996 1353 678373764 678373380 5.180000e-37 165.0
7 TraesCS4D01G303400 chr4A 88.991 109 9 3 1 106 678420048 678419940 5.260000e-27 132.0
8 TraesCS4D01G303400 chr4A 92.593 54 1 2 238 291 678419959 678419909 8.990000e-10 75.0
9 TraesCS4D01G303400 chr2D 89.809 157 8 2 2196 2345 136616366 136616211 6.610000e-46 195.0
10 TraesCS4D01G303400 chr7A 95.238 63 2 1 2196 2257 585352422 585352484 5.330000e-17 99.0
11 TraesCS4D01G303400 chr3A 91.429 70 3 3 2197 2264 457468325 457468257 2.480000e-15 93.5
12 TraesCS4D01G303400 chrUn 92.308 65 2 3 2196 2258 207764844 207764907 3.210000e-14 89.8
13 TraesCS4D01G303400 chr7D 93.333 60 2 2 2197 2255 454076075 454076133 1.150000e-13 87.9
14 TraesCS4D01G303400 chr3D 90.909 66 3 3 2192 2255 484836148 484836212 4.150000e-13 86.1
15 TraesCS4D01G303400 chr6B 90.625 64 5 1 2195 2257 663561644 663561707 1.490000e-12 84.2
16 TraesCS4D01G303400 chr1B 89.231 65 5 2 2195 2257 83944201 83944265 1.930000e-11 80.5
17 TraesCS4D01G303400 chr5D 78.519 135 17 12 2194 2321 328404380 328404251 6.950000e-11 78.7


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 TraesCS4D01G303400 chr4D 471269141 471271485 2344 True 4331.000000 4331 100.000000 1 2345 1 chr4D.!!$R2 2344
1 TraesCS4D01G303400 chr4B 593350647 593353461 2814 True 1056.000000 1764 89.626000 14 1731 2 chr4B.!!$R1 1717
2 TraesCS4D01G303400 chr4A 678418296 678420048 1752 True 597.333333 1585 89.058667 1 1882 3 chr4A.!!$R2 1881
3 TraesCS4D01G303400 chr4A 678373380 678376578 3198 True 239.000000 313 79.150000 994 1353 2 chr4A.!!$R1 359

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
840 1933 0.690762 TCGGCTAAACCCTTGCTTCT 59.309 50.0 0.0 0.0 33.26 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 3854 0.029967 TCTCTCAGCGACGCATCATC 59.97 55.0 23.7 0.0 0.0 2.92 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
114 116 2.200337 GCCAGGCCGTTCCAAAGTT 61.200 57.895 0.00 0.00 37.29 2.66
124 126 3.428862 CCGTTCCAAAGTTTGTTTGCTCT 60.429 43.478 14.36 0.00 0.00 4.09
169 171 0.969894 GGCACTGTCCACTACTGTCT 59.030 55.000 0.00 0.00 38.11 3.41
181 183 3.439129 CACTACTGTCTGTCGTGGACATA 59.561 47.826 6.62 0.00 41.94 2.29
202 204 0.917939 CCAAACACCGAAACAAACGC 59.082 50.000 0.00 0.00 0.00 4.84
204 206 1.843753 CAAACACCGAAACAAACGCTC 59.156 47.619 0.00 0.00 0.00 5.03
228 230 2.834574 CCGCAACGGTAATAATGCAA 57.165 45.000 0.00 0.00 42.73 4.08
229 231 2.715268 CCGCAACGGTAATAATGCAAG 58.285 47.619 0.00 0.00 42.73 4.01
230 232 2.540769 CCGCAACGGTAATAATGCAAGG 60.541 50.000 0.00 0.00 42.73 3.61
231 233 2.353269 CGCAACGGTAATAATGCAAGGA 59.647 45.455 0.00 0.00 38.69 3.36
232 234 3.003275 CGCAACGGTAATAATGCAAGGAT 59.997 43.478 0.00 0.00 38.69 3.24
233 235 4.290155 GCAACGGTAATAATGCAAGGATG 58.710 43.478 0.00 0.00 38.63 3.51
234 236 4.036262 GCAACGGTAATAATGCAAGGATGA 59.964 41.667 0.00 0.00 38.63 2.92
235 237 5.278463 GCAACGGTAATAATGCAAGGATGAT 60.278 40.000 0.00 0.00 38.63 2.45
236 238 6.373779 CAACGGTAATAATGCAAGGATGATC 58.626 40.000 0.00 0.00 0.00 2.92
271 273 4.503314 CGTAGCCCGGTCCGGTTC 62.503 72.222 28.39 19.04 46.80 3.62
296 302 1.603326 TCGTCGTGTGCAGTACTGTAA 59.397 47.619 23.44 10.24 0.00 2.41
302 308 3.987868 CGTGTGCAGTACTGTAAATGAGT 59.012 43.478 23.44 0.00 0.00 3.41
304 310 5.631929 CGTGTGCAGTACTGTAAATGAGTTA 59.368 40.000 23.44 0.00 0.00 2.24
307 313 7.811236 GTGTGCAGTACTGTAAATGAGTTACTA 59.189 37.037 23.44 0.00 42.36 1.82
330 808 8.355913 ACTATAGTGTAGTTTATTTACTCGGCC 58.644 37.037 4.10 0.00 0.00 6.13
391 1326 1.983605 CAGTACGACCGTTCACATGAC 59.016 52.381 0.00 0.00 0.00 3.06
395 1330 0.856641 CGACCGTTCACATGACGTTT 59.143 50.000 0.00 0.00 0.00 3.60
473 1561 2.019249 CCGAGACTGGACCACGTATAA 58.981 52.381 0.00 0.00 0.00 0.98
479 1567 6.238566 CGAGACTGGACCACGTATAATTTCTA 60.239 42.308 0.00 0.00 0.00 2.10
504 1592 1.089920 ATTTCTGTCGTGCCATCTGC 58.910 50.000 0.00 0.00 41.77 4.26
506 1594 1.830587 TTCTGTCGTGCCATCTGCCT 61.831 55.000 0.00 0.00 40.16 4.75
606 1699 0.708370 CAAAGGATCACGTCACGTCG 59.292 55.000 0.00 0.00 38.32 5.12
721 1814 4.758251 CCGCTGTCGACATGGCCA 62.758 66.667 20.40 8.56 38.10 5.36
840 1933 0.690762 TCGGCTAAACCCTTGCTTCT 59.309 50.000 0.00 0.00 33.26 2.85
862 1955 3.633361 GCTATAAATGGCGGCCTCT 57.367 52.632 21.46 4.59 0.00 3.69
866 1959 2.069165 ATAAATGGCGGCCTCTCCCC 62.069 60.000 21.46 0.00 0.00 4.81
893 1986 3.008240 CTCACAACTCGCAGCGCAG 62.008 63.158 10.87 11.15 0.00 5.18
920 2013 0.827368 CTCCCTCCCACAGCTTCTAC 59.173 60.000 0.00 0.00 0.00 2.59
958 2068 4.813526 CTCCGTCCGTCGTCTGCG 62.814 72.222 0.00 0.00 37.94 5.18
982 2092 2.360475 AGCCAGCTTTCCTTCCGC 60.360 61.111 0.00 0.00 0.00 5.54
1500 2667 3.253432 TGCTACATACTGTATGCTCGAGG 59.747 47.826 23.94 11.04 39.79 4.63
1725 3846 1.335496 TCCGCGTTTCTTCCCTTTTTG 59.665 47.619 4.92 0.00 0.00 2.44
1726 3847 1.335496 CCGCGTTTCTTCCCTTTTTGA 59.665 47.619 4.92 0.00 0.00 2.69
1728 3849 2.604614 CGCGTTTCTTCCCTTTTTGAGG 60.605 50.000 0.00 0.00 45.86 3.86
1730 3851 3.181479 GCGTTTCTTCCCTTTTTGAGGTT 60.181 43.478 0.00 0.00 44.71 3.50
1733 3854 5.278315 CGTTTCTTCCCTTTTTGAGGTTAGG 60.278 44.000 0.00 0.00 44.71 2.69
1749 4561 0.312102 TAGGATGATGCGTCGCTGAG 59.688 55.000 19.50 0.00 0.00 3.35
1805 4625 1.278337 TGCTTACGCACTTTGCACG 59.722 52.632 0.00 0.00 45.36 5.34
1807 4627 0.509499 GCTTACGCACTTTGCACGTA 59.491 50.000 2.72 2.72 45.36 3.57
1808 4628 1.127951 GCTTACGCACTTTGCACGTAT 59.872 47.619 7.26 0.00 45.36 3.06
1809 4629 2.412325 GCTTACGCACTTTGCACGTATT 60.412 45.455 7.26 0.00 45.36 1.89
1810 4630 3.805823 CTTACGCACTTTGCACGTATTT 58.194 40.909 7.26 0.00 45.36 1.40
1811 4631 2.031037 ACGCACTTTGCACGTATTTG 57.969 45.000 0.00 0.00 45.36 2.32
1910 4755 6.439675 AAAAGAACAATTTTGCAAGCATGT 57.560 29.167 0.00 3.26 31.30 3.21
1911 4756 6.439675 AAAGAACAATTTTGCAAGCATGTT 57.560 29.167 19.36 19.36 34.01 2.71
1912 4757 6.439675 AAGAACAATTTTGCAAGCATGTTT 57.560 29.167 19.91 11.49 31.68 2.83
1913 4758 6.439675 AGAACAATTTTGCAAGCATGTTTT 57.560 29.167 19.91 14.62 31.68 2.43
1914 4759 6.854778 AGAACAATTTTGCAAGCATGTTTTT 58.145 28.000 19.91 12.55 31.68 1.94
1915 4760 6.748198 AGAACAATTTTGCAAGCATGTTTTTG 59.252 30.769 19.91 10.58 31.68 2.44
1916 4761 6.192234 ACAATTTTGCAAGCATGTTTTTGA 57.808 29.167 0.00 0.00 0.00 2.69
1917 4762 6.618811 ACAATTTTGCAAGCATGTTTTTGAA 58.381 28.000 0.00 0.00 0.00 2.69
1918 4763 7.259161 ACAATTTTGCAAGCATGTTTTTGAAT 58.741 26.923 0.00 0.00 0.00 2.57
1919 4764 7.760340 ACAATTTTGCAAGCATGTTTTTGAATT 59.240 25.926 0.00 0.00 0.00 2.17
1920 4765 7.687005 ATTTTGCAAGCATGTTTTTGAATTG 57.313 28.000 0.00 0.00 0.00 2.32
1921 4766 5.814764 TTGCAAGCATGTTTTTGAATTGT 57.185 30.435 0.00 0.00 0.00 2.71
1922 4767 5.158101 TGCAAGCATGTTTTTGAATTGTG 57.842 34.783 9.83 0.00 0.00 3.33
1923 4768 4.874396 TGCAAGCATGTTTTTGAATTGTGA 59.126 33.333 9.83 0.00 0.00 3.58
1925 4770 6.038382 TGCAAGCATGTTTTTGAATTGTGAAT 59.962 30.769 9.83 0.00 0.00 2.57
1927 4772 7.411274 CAAGCATGTTTTTGAATTGTGAATGT 58.589 30.769 0.00 0.00 0.00 2.71
1928 4773 7.181143 AGCATGTTTTTGAATTGTGAATGTC 57.819 32.000 0.00 0.00 0.00 3.06
1929 4774 6.066410 GCATGTTTTTGAATTGTGAATGTCG 58.934 36.000 0.00 0.00 0.00 4.35
1930 4775 6.074409 GCATGTTTTTGAATTGTGAATGTCGA 60.074 34.615 0.00 0.00 0.00 4.20
1933 4778 7.032580 TGTTTTTGAATTGTGAATGTCGAGTT 58.967 30.769 0.00 0.00 0.00 3.01
1934 4779 8.184848 TGTTTTTGAATTGTGAATGTCGAGTTA 58.815 29.630 0.00 0.00 0.00 2.24
1935 4780 9.180678 GTTTTTGAATTGTGAATGTCGAGTTAT 57.819 29.630 0.00 0.00 0.00 1.89
1936 4781 8.948853 TTTTGAATTGTGAATGTCGAGTTATC 57.051 30.769 0.00 0.00 0.00 1.75
1937 4782 7.665561 TTGAATTGTGAATGTCGAGTTATCA 57.334 32.000 0.00 0.00 0.00 2.15
1939 4784 5.702622 ATTGTGAATGTCGAGTTATCACG 57.297 39.130 12.90 0.00 42.47 4.35
1940 4785 4.168922 TGTGAATGTCGAGTTATCACGT 57.831 40.909 12.90 0.00 42.47 4.49
1941 4786 3.917985 TGTGAATGTCGAGTTATCACGTG 59.082 43.478 9.94 9.94 42.47 4.49
1942 4787 2.921121 TGAATGTCGAGTTATCACGTGC 59.079 45.455 11.67 0.00 0.00 5.34
1943 4788 1.922570 ATGTCGAGTTATCACGTGCC 58.077 50.000 11.67 0.00 0.00 5.01
1944 4789 0.885879 TGTCGAGTTATCACGTGCCT 59.114 50.000 11.67 3.55 0.00 4.75
1946 4791 1.132643 GTCGAGTTATCACGTGCCTCT 59.867 52.381 11.67 6.38 0.00 3.69
1947 4792 1.132453 TCGAGTTATCACGTGCCTCTG 59.868 52.381 11.67 9.40 0.00 3.35
1948 4793 1.135373 CGAGTTATCACGTGCCTCTGT 60.135 52.381 11.67 0.00 0.00 3.41
1950 4795 3.427098 CGAGTTATCACGTGCCTCTGTAA 60.427 47.826 11.67 0.51 0.00 2.41
1951 4796 4.491676 GAGTTATCACGTGCCTCTGTAAA 58.508 43.478 11.67 0.00 0.00 2.01
1952 4797 4.890088 AGTTATCACGTGCCTCTGTAAAA 58.110 39.130 11.67 0.00 0.00 1.52
1953 4798 5.302360 AGTTATCACGTGCCTCTGTAAAAA 58.698 37.500 11.67 0.00 0.00 1.94
1980 4825 9.872757 ATATTAACACGTTTAAATCGCTATTGG 57.127 29.630 9.20 0.00 0.00 3.16
1981 4826 4.609691 ACACGTTTAAATCGCTATTGGG 57.390 40.909 9.20 0.00 0.00 4.12
1983 4828 3.011119 ACGTTTAAATCGCTATTGGGCA 58.989 40.909 9.20 0.00 0.00 5.36
1985 4830 3.974401 CGTTTAAATCGCTATTGGGCATG 59.026 43.478 0.00 0.00 0.00 4.06
1987 4832 1.696063 AAATCGCTATTGGGCATGCT 58.304 45.000 18.92 0.00 0.00 3.79
1988 4833 1.696063 AATCGCTATTGGGCATGCTT 58.304 45.000 18.92 3.00 0.00 3.91
1989 4834 0.956633 ATCGCTATTGGGCATGCTTG 59.043 50.000 18.92 0.00 0.00 4.01
1992 4837 0.672342 GCTATTGGGCATGCTTGGAG 59.328 55.000 18.92 9.86 0.00 3.86
1993 4838 1.325355 CTATTGGGCATGCTTGGAGG 58.675 55.000 18.92 0.84 0.00 4.30
1994 4839 0.106066 TATTGGGCATGCTTGGAGGG 60.106 55.000 18.92 0.00 0.00 4.30
1995 4840 4.764771 TGGGCATGCTTGGAGGGC 62.765 66.667 18.92 0.00 0.00 5.19
1998 4843 3.064324 GCATGCTTGGAGGGCGTT 61.064 61.111 11.37 0.00 0.00 4.84
2000 4845 1.993369 GCATGCTTGGAGGGCGTTAC 61.993 60.000 11.37 0.00 0.00 2.50
2002 4847 0.392998 ATGCTTGGAGGGCGTTACTG 60.393 55.000 0.00 0.00 0.00 2.74
2004 4849 1.677552 CTTGGAGGGCGTTACTGGT 59.322 57.895 0.00 0.00 0.00 4.00
2005 4850 0.899720 CTTGGAGGGCGTTACTGGTA 59.100 55.000 0.00 0.00 0.00 3.25
2006 4851 1.276989 CTTGGAGGGCGTTACTGGTAA 59.723 52.381 0.00 0.00 0.00 2.85
2008 4853 1.910671 TGGAGGGCGTTACTGGTAAAT 59.089 47.619 0.00 0.00 0.00 1.40
2009 4854 3.106054 TGGAGGGCGTTACTGGTAAATA 58.894 45.455 0.00 0.00 0.00 1.40
2010 4855 3.712733 TGGAGGGCGTTACTGGTAAATAT 59.287 43.478 0.00 0.00 0.00 1.28
2011 4856 4.164604 TGGAGGGCGTTACTGGTAAATATT 59.835 41.667 0.00 0.00 0.00 1.28
2017 4862 7.070322 AGGGCGTTACTGGTAAATATTTCTCTA 59.930 37.037 3.39 0.00 0.00 2.43
2018 4863 7.712205 GGGCGTTACTGGTAAATATTTCTCTAA 59.288 37.037 3.39 0.00 0.00 2.10
2037 4882 7.085116 TCTCTAAAACTTAAGAGCAACTCTCG 58.915 38.462 10.09 0.00 46.44 4.04
2038 4883 4.733972 AAAACTTAAGAGCAACTCTCGC 57.266 40.909 10.09 0.00 46.44 5.03
2039 4884 3.669251 AACTTAAGAGCAACTCTCGCT 57.331 42.857 10.09 0.00 46.44 4.93
2040 4885 4.785511 AACTTAAGAGCAACTCTCGCTA 57.214 40.909 10.09 0.00 46.44 4.26
2041 4886 4.785511 ACTTAAGAGCAACTCTCGCTAA 57.214 40.909 10.09 0.00 46.44 3.09
2042 4887 5.331876 ACTTAAGAGCAACTCTCGCTAAT 57.668 39.130 10.09 0.00 46.44 1.73
2043 4888 6.452494 ACTTAAGAGCAACTCTCGCTAATA 57.548 37.500 10.09 0.00 46.44 0.98
2046 4891 2.033550 AGAGCAACTCTCGCTAATACCG 59.966 50.000 0.00 0.00 46.44 4.02
2047 4892 1.749634 AGCAACTCTCGCTAATACCGT 59.250 47.619 0.00 0.00 38.15 4.83
2048 4893 1.852895 GCAACTCTCGCTAATACCGTG 59.147 52.381 0.00 0.00 0.00 4.94
2049 4894 2.479049 GCAACTCTCGCTAATACCGTGA 60.479 50.000 0.00 0.00 0.00 4.35
2050 4895 3.766151 CAACTCTCGCTAATACCGTGAA 58.234 45.455 0.00 0.00 0.00 3.18
2051 4896 4.171005 CAACTCTCGCTAATACCGTGAAA 58.829 43.478 0.00 0.00 0.00 2.69
2052 4897 4.030134 ACTCTCGCTAATACCGTGAAAG 57.970 45.455 0.00 0.00 0.00 2.62
2053 4898 3.181489 ACTCTCGCTAATACCGTGAAAGG 60.181 47.826 0.00 0.00 37.30 3.11
2061 4906 4.180496 CCGTGAAAGGGCTCGTAC 57.820 61.111 0.00 0.00 33.71 3.67
2062 4907 1.590147 CCGTGAAAGGGCTCGTACT 59.410 57.895 0.00 0.00 33.71 2.73
2064 4909 0.242825 CGTGAAAGGGCTCGTACTCA 59.757 55.000 0.00 0.00 0.00 3.41
2065 4910 1.336517 CGTGAAAGGGCTCGTACTCAA 60.337 52.381 0.00 0.00 0.00 3.02
2066 4911 2.674177 CGTGAAAGGGCTCGTACTCAAT 60.674 50.000 0.00 0.00 0.00 2.57
2069 4914 3.767673 TGAAAGGGCTCGTACTCAATAGT 59.232 43.478 0.00 0.00 39.91 2.12
2071 4916 5.419788 TGAAAGGGCTCGTACTCAATAGTAA 59.580 40.000 0.00 0.00 39.90 2.24
2072 4917 4.915158 AGGGCTCGTACTCAATAGTAAC 57.085 45.455 0.00 0.00 39.90 2.50
2073 4918 4.534797 AGGGCTCGTACTCAATAGTAACT 58.465 43.478 0.00 0.00 39.90 2.24
2074 4919 5.688807 AGGGCTCGTACTCAATAGTAACTA 58.311 41.667 0.00 0.00 39.90 2.24
2090 4935 9.962759 AATAGTAACTATTGTTTTAGCGTTTCG 57.037 29.630 0.00 0.00 35.61 3.46
2094 4939 3.824414 ATTGTTTTAGCGTTTCGGAGG 57.176 42.857 0.00 0.00 0.00 4.30
2095 4940 2.243602 TGTTTTAGCGTTTCGGAGGT 57.756 45.000 0.00 0.00 0.00 3.85
2096 4941 3.383620 TGTTTTAGCGTTTCGGAGGTA 57.616 42.857 0.00 0.00 0.00 3.08
2098 4943 3.494251 TGTTTTAGCGTTTCGGAGGTAAC 59.506 43.478 0.00 0.00 31.20 2.50
2099 4944 3.383620 TTTAGCGTTTCGGAGGTAACA 57.616 42.857 0.00 0.00 41.41 2.41
2100 4945 3.383620 TTAGCGTTTCGGAGGTAACAA 57.616 42.857 0.00 0.00 41.41 2.83
2102 4947 2.563702 AGCGTTTCGGAGGTAACAAAA 58.436 42.857 0.00 0.00 41.41 2.44
2103 4948 2.546789 AGCGTTTCGGAGGTAACAAAAG 59.453 45.455 0.00 0.00 41.41 2.27
2104 4949 2.545106 GCGTTTCGGAGGTAACAAAAGA 59.455 45.455 0.00 0.00 41.41 2.52
2105 4950 3.605461 GCGTTTCGGAGGTAACAAAAGAC 60.605 47.826 0.00 0.00 41.41 3.01
2107 4952 2.845363 TCGGAGGTAACAAAAGACCC 57.155 50.000 0.00 0.00 36.27 4.46
2108 4953 1.001181 TCGGAGGTAACAAAAGACCCG 59.999 52.381 0.00 0.00 36.27 5.28
2109 4954 1.001181 CGGAGGTAACAAAAGACCCGA 59.999 52.381 0.00 0.00 36.27 5.14
2110 4955 2.354403 CGGAGGTAACAAAAGACCCGAT 60.354 50.000 0.00 0.00 36.27 4.18
2111 4956 3.268330 GGAGGTAACAAAAGACCCGATC 58.732 50.000 0.00 0.00 36.27 3.69
2113 4958 3.933332 GAGGTAACAAAAGACCCGATCAG 59.067 47.826 0.00 0.00 36.27 2.90
2114 4959 3.581332 AGGTAACAAAAGACCCGATCAGA 59.419 43.478 0.00 0.00 36.27 3.27
2115 4960 4.225267 AGGTAACAAAAGACCCGATCAGAT 59.775 41.667 0.00 0.00 36.27 2.90
2116 4961 5.424252 AGGTAACAAAAGACCCGATCAGATA 59.576 40.000 0.00 0.00 36.27 1.98
2118 4963 4.138487 ACAAAAGACCCGATCAGATACC 57.862 45.455 0.00 0.00 0.00 2.73
2119 4964 3.123804 CAAAAGACCCGATCAGATACCG 58.876 50.000 0.00 0.00 0.00 4.02
2120 4965 2.068834 AAGACCCGATCAGATACCGT 57.931 50.000 0.00 0.00 0.00 4.83
2121 4966 2.945080 AGACCCGATCAGATACCGTA 57.055 50.000 0.00 0.00 0.00 4.02
2122 4967 3.219176 AGACCCGATCAGATACCGTAA 57.781 47.619 0.00 0.00 0.00 3.18
2124 4969 4.150359 AGACCCGATCAGATACCGTAAAT 58.850 43.478 0.00 0.00 0.00 1.40
2125 4970 4.587684 AGACCCGATCAGATACCGTAAATT 59.412 41.667 0.00 0.00 0.00 1.82
2127 4972 5.054477 ACCCGATCAGATACCGTAAATTTG 58.946 41.667 0.00 0.00 0.00 2.32
2128 4973 4.451096 CCCGATCAGATACCGTAAATTTGG 59.549 45.833 0.00 0.00 0.00 3.28
2129 4974 5.054477 CCGATCAGATACCGTAAATTTGGT 58.946 41.667 0.00 3.12 42.34 3.67
2132 4977 6.423905 CGATCAGATACCGTAAATTTGGTCAT 59.576 38.462 3.58 0.00 39.70 3.06
2134 4979 8.603242 ATCAGATACCGTAAATTTGGTCATAC 57.397 34.615 3.58 0.00 39.70 2.39
2135 4980 7.788026 TCAGATACCGTAAATTTGGTCATACT 58.212 34.615 3.58 0.00 39.70 2.12
2136 4981 7.924412 TCAGATACCGTAAATTTGGTCATACTC 59.076 37.037 3.58 0.00 39.70 2.59
2137 4982 7.709182 CAGATACCGTAAATTTGGTCATACTCA 59.291 37.037 3.58 0.00 39.70 3.41
2138 4983 8.262227 AGATACCGTAAATTTGGTCATACTCAA 58.738 33.333 3.58 0.00 39.70 3.02
2139 4984 6.490566 ACCGTAAATTTGGTCATACTCAAC 57.509 37.500 0.00 0.00 31.16 3.18
2141 4986 6.713450 ACCGTAAATTTGGTCATACTCAACTT 59.287 34.615 0.00 0.00 31.16 2.66
2142 4987 7.229907 ACCGTAAATTTGGTCATACTCAACTTT 59.770 33.333 0.00 0.00 31.16 2.66
2143 4988 8.079809 CCGTAAATTTGGTCATACTCAACTTTT 58.920 33.333 0.00 0.00 31.47 2.27
2144 4989 9.458374 CGTAAATTTGGTCATACTCAACTTTTT 57.542 29.630 0.00 0.00 31.47 1.94
2147 4992 9.665719 AAATTTGGTCATACTCAACTTTTTGTT 57.334 25.926 0.00 0.00 39.92 2.83
2162 5007 7.897575 ACTTTTTGTTGTTGCAATAAACTGA 57.102 28.000 21.50 12.03 0.00 3.41
2163 5008 8.316640 ACTTTTTGTTGTTGCAATAAACTGAA 57.683 26.923 21.50 15.58 0.00 3.02
2164 5009 8.778358 ACTTTTTGTTGTTGCAATAAACTGAAA 58.222 25.926 21.50 18.73 0.00 2.69
2165 5010 9.604626 CTTTTTGTTGTTGCAATAAACTGAAAA 57.395 25.926 21.50 22.15 0.00 2.29
2166 5011 9.950680 TTTTTGTTGTTGCAATAAACTGAAAAA 57.049 22.222 21.50 20.91 0.00 1.94
2167 5012 9.604626 TTTTGTTGTTGCAATAAACTGAAAAAG 57.395 25.926 21.50 0.00 0.00 2.27
2168 5013 7.301068 TGTTGTTGCAATAAACTGAAAAAGG 57.699 32.000 21.50 0.00 0.00 3.11
2170 5015 6.227298 TGTTGCAATAAACTGAAAAAGGGA 57.773 33.333 0.59 0.00 0.00 4.20
2185 5108 4.101448 GGAGCCCGCACCTCACAT 62.101 66.667 0.00 0.00 0.00 3.21
2186 5109 2.731571 GGAGCCCGCACCTCACATA 61.732 63.158 0.00 0.00 0.00 2.29
2187 5110 1.447643 GAGCCCGCACCTCACATAT 59.552 57.895 0.00 0.00 0.00 1.78
2188 5111 0.679505 GAGCCCGCACCTCACATATA 59.320 55.000 0.00 0.00 0.00 0.86
2190 5113 0.679505 GCCCGCACCTCACATATAGA 59.320 55.000 0.00 0.00 0.00 1.98
2191 5114 1.337260 GCCCGCACCTCACATATAGAG 60.337 57.143 0.00 0.00 0.00 2.43
2192 5115 1.964223 CCCGCACCTCACATATAGAGT 59.036 52.381 4.27 0.00 0.00 3.24
2193 5116 3.154710 CCCGCACCTCACATATAGAGTA 58.845 50.000 4.27 0.00 0.00 2.59
2194 5117 3.764434 CCCGCACCTCACATATAGAGTAT 59.236 47.826 4.27 0.00 0.00 2.12
2195 5118 4.220821 CCCGCACCTCACATATAGAGTATT 59.779 45.833 4.27 0.00 0.00 1.89
2196 5119 5.279506 CCCGCACCTCACATATAGAGTATTT 60.280 44.000 4.27 0.00 0.00 1.40
2197 5120 6.223852 CCGCACCTCACATATAGAGTATTTT 58.776 40.000 4.27 0.00 0.00 1.82
2198 5121 6.706270 CCGCACCTCACATATAGAGTATTTTT 59.294 38.462 4.27 0.00 0.00 1.94
2219 5142 3.451141 TTTTTGAATGTCGGCAAAGCT 57.549 38.095 0.00 0.00 35.64 3.74
2220 5143 3.451141 TTTTGAATGTCGGCAAAGCTT 57.549 38.095 0.00 0.00 35.64 3.74
2221 5144 2.420628 TTGAATGTCGGCAAAGCTTG 57.579 45.000 0.00 0.00 0.00 4.01
2235 5158 5.873179 CAAAGCTTGCCAAATTCATTGAT 57.127 34.783 0.00 0.00 41.85 2.57
2237 5160 4.811969 AGCTTGCCAAATTCATTGATCA 57.188 36.364 0.00 0.00 41.85 2.92
2238 5161 4.755411 AGCTTGCCAAATTCATTGATCAG 58.245 39.130 0.00 0.00 41.85 2.90
2239 5162 4.464951 AGCTTGCCAAATTCATTGATCAGA 59.535 37.500 0.00 0.00 41.85 3.27
2241 5164 5.291128 GCTTGCCAAATTCATTGATCAGAAG 59.709 40.000 0.00 0.00 41.85 2.85
2242 5165 5.333299 TGCCAAATTCATTGATCAGAAGG 57.667 39.130 0.00 0.00 41.85 3.46
2244 5167 4.442472 GCCAAATTCATTGATCAGAAGGGG 60.442 45.833 0.00 2.32 41.85 4.79
2245 5168 4.713321 CCAAATTCATTGATCAGAAGGGGT 59.287 41.667 0.00 0.00 41.85 4.95
2246 5169 5.188359 CCAAATTCATTGATCAGAAGGGGTT 59.812 40.000 0.00 0.00 41.85 4.11
2247 5170 6.380846 CCAAATTCATTGATCAGAAGGGGTTA 59.619 38.462 0.00 0.00 41.85 2.85
2248 5171 7.093377 CCAAATTCATTGATCAGAAGGGGTTAA 60.093 37.037 0.00 0.00 41.85 2.01
2249 5172 7.410120 AATTCATTGATCAGAAGGGGTTAAC 57.590 36.000 0.00 0.00 0.00 2.01
2251 5174 5.500234 TCATTGATCAGAAGGGGTTAACAG 58.500 41.667 8.10 0.00 0.00 3.16
2252 5175 5.250543 TCATTGATCAGAAGGGGTTAACAGA 59.749 40.000 8.10 0.00 0.00 3.41
2254 5177 4.425772 TGATCAGAAGGGGTTAACAGAGA 58.574 43.478 8.10 0.00 0.00 3.10
2256 5179 3.583228 TCAGAAGGGGTTAACAGAGACA 58.417 45.455 8.10 0.00 0.00 3.41
2257 5180 3.971305 TCAGAAGGGGTTAACAGAGACAA 59.029 43.478 8.10 0.00 0.00 3.18
2258 5181 4.065789 CAGAAGGGGTTAACAGAGACAAC 58.934 47.826 8.10 0.00 0.00 3.32
2266 5189 2.348411 AACAGAGACAACCCAACTGG 57.652 50.000 0.00 0.00 41.37 4.00
2277 5200 2.721945 CCAACTGGGTTAAACGCCA 58.278 52.632 0.00 0.00 0.00 5.69
2278 5201 0.596082 CCAACTGGGTTAAACGCCAG 59.404 55.000 0.00 0.00 40.28 4.85
2280 5203 1.176619 AACTGGGTTAAACGCCAGCC 61.177 55.000 0.00 0.00 38.98 4.85
2281 5204 1.602323 CTGGGTTAAACGCCAGCCA 60.602 57.895 0.00 0.00 38.25 4.75
2282 5205 1.152735 TGGGTTAAACGCCAGCCAA 60.153 52.632 0.00 0.00 37.62 4.52
2283 5206 1.175983 TGGGTTAAACGCCAGCCAAG 61.176 55.000 0.00 0.00 37.62 3.61
2284 5207 0.891904 GGGTTAAACGCCAGCCAAGA 60.892 55.000 0.00 0.00 0.00 3.02
2286 5209 0.521735 GTTAAACGCCAGCCAAGAGG 59.478 55.000 0.00 0.00 38.23 3.69
2296 5219 2.668632 CCAAGAGGCAAGGCGGTA 59.331 61.111 0.00 0.00 0.00 4.02
2297 5220 1.002624 CCAAGAGGCAAGGCGGTAA 60.003 57.895 0.00 0.00 0.00 2.85
2298 5221 0.608035 CCAAGAGGCAAGGCGGTAAA 60.608 55.000 0.00 0.00 0.00 2.01
2299 5222 1.243902 CAAGAGGCAAGGCGGTAAAA 58.756 50.000 0.00 0.00 0.00 1.52
2300 5223 1.611491 CAAGAGGCAAGGCGGTAAAAA 59.389 47.619 0.00 0.00 0.00 1.94
2302 5225 1.073284 AGAGGCAAGGCGGTAAAAAGA 59.927 47.619 0.00 0.00 0.00 2.52
2303 5226 1.883926 GAGGCAAGGCGGTAAAAAGAA 59.116 47.619 0.00 0.00 0.00 2.52
2304 5227 1.886542 AGGCAAGGCGGTAAAAAGAAG 59.113 47.619 0.00 0.00 0.00 2.85
2305 5228 1.883926 GGCAAGGCGGTAAAAAGAAGA 59.116 47.619 0.00 0.00 0.00 2.87
2306 5229 2.492088 GGCAAGGCGGTAAAAAGAAGAT 59.508 45.455 0.00 0.00 0.00 2.40
2308 5231 4.157105 GGCAAGGCGGTAAAAAGAAGATAA 59.843 41.667 0.00 0.00 0.00 1.75
2309 5232 5.336134 GGCAAGGCGGTAAAAAGAAGATAAA 60.336 40.000 0.00 0.00 0.00 1.40
2310 5233 6.153756 GCAAGGCGGTAAAAAGAAGATAAAA 58.846 36.000 0.00 0.00 0.00 1.52
2311 5234 6.643360 GCAAGGCGGTAAAAAGAAGATAAAAA 59.357 34.615 0.00 0.00 0.00 1.94
2329 5252 1.986882 AAAAGGAACACTCAGCTGGG 58.013 50.000 13.44 13.44 0.00 4.45
2331 5254 1.366319 AAGGAACACTCAGCTGGGAT 58.634 50.000 23.49 4.70 0.00 3.85
2333 5256 0.615331 GGAACACTCAGCTGGGATCA 59.385 55.000 23.49 0.00 0.00 2.92
2334 5257 1.003580 GGAACACTCAGCTGGGATCAA 59.996 52.381 23.49 0.00 0.00 2.57
2335 5258 2.553028 GGAACACTCAGCTGGGATCAAA 60.553 50.000 23.49 0.00 0.00 2.69
2336 5259 2.957402 ACACTCAGCTGGGATCAAAA 57.043 45.000 23.49 0.00 0.00 2.44
2339 5262 1.988107 ACTCAGCTGGGATCAAAAGGA 59.012 47.619 23.49 0.00 0.00 3.36
2340 5263 2.376518 ACTCAGCTGGGATCAAAAGGAA 59.623 45.455 23.49 0.00 0.00 3.36
2341 5264 3.011032 ACTCAGCTGGGATCAAAAGGAAT 59.989 43.478 23.49 0.00 0.00 3.01
2342 5265 3.624777 TCAGCTGGGATCAAAAGGAATC 58.375 45.455 15.13 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.995257 GCAATGGGCTGTCGATACATCG 61.995 54.545 5.25 5.25 44.93 3.84
93 94 3.860930 TTTGGAACGGCCTGGCTCC 62.861 63.158 19.68 17.80 37.63 4.70
114 116 0.934496 CGAACCGTGAGAGCAAACAA 59.066 50.000 0.00 0.00 0.00 2.83
169 171 1.416772 TGTTTGGGTATGTCCACGACA 59.583 47.619 0.00 0.00 46.90 4.35
177 179 2.933573 TGTTTCGGTGTTTGGGTATGT 58.066 42.857 0.00 0.00 0.00 2.29
181 183 1.135344 CGTTTGTTTCGGTGTTTGGGT 60.135 47.619 0.00 0.00 0.00 4.51
222 224 1.700955 GCTGGGATCATCCTTGCATT 58.299 50.000 14.02 0.00 36.57 3.56
223 225 0.536687 CGCTGGGATCATCCTTGCAT 60.537 55.000 17.43 0.00 36.57 3.96
224 226 1.153107 CGCTGGGATCATCCTTGCA 60.153 57.895 17.43 2.39 36.57 4.08
225 227 1.895707 CCGCTGGGATCATCCTTGC 60.896 63.158 2.93 7.46 36.57 4.01
226 228 0.181114 TTCCGCTGGGATCATCCTTG 59.819 55.000 2.93 0.00 43.41 3.61
227 229 0.471617 CTTCCGCTGGGATCATCCTT 59.528 55.000 2.93 0.00 43.41 3.36
228 230 2.049627 GCTTCCGCTGGGATCATCCT 62.050 60.000 2.93 0.00 43.41 3.24
229 231 1.599240 GCTTCCGCTGGGATCATCC 60.599 63.158 0.00 0.00 43.41 3.51
230 232 0.883814 CTGCTTCCGCTGGGATCATC 60.884 60.000 0.00 0.00 43.41 2.92
231 233 1.147824 CTGCTTCCGCTGGGATCAT 59.852 57.895 0.00 0.00 43.41 2.45
232 234 1.964608 CTCTGCTTCCGCTGGGATCA 61.965 60.000 0.00 0.00 43.41 2.92
233 235 1.227497 CTCTGCTTCCGCTGGGATC 60.227 63.158 0.00 0.00 43.41 3.36
234 236 2.739996 CCTCTGCTTCCGCTGGGAT 61.740 63.158 0.00 0.00 43.41 3.85
235 237 3.393970 CCTCTGCTTCCGCTGGGA 61.394 66.667 0.00 0.00 37.75 4.37
271 273 1.124297 GTACTGCACACGACGATGTTG 59.876 52.381 0.00 0.00 0.00 3.33
304 310 8.355913 GGCCGAGTAAATAAACTACACTATAGT 58.644 37.037 0.00 0.00 0.00 2.12
307 313 7.116075 TGGCCGAGTAAATAAACTACACTAT 57.884 36.000 0.00 0.00 0.00 2.12
310 316 5.173664 ACTGGCCGAGTAAATAAACTACAC 58.826 41.667 0.00 0.00 30.86 2.90
366 844 4.233408 AACGGTCGTACTGTTCGC 57.767 55.556 1.70 0.00 43.77 4.70
395 1330 1.666700 CGACCGTTTGTTTGTCTGGAA 59.333 47.619 0.00 0.00 0.00 3.53
473 1561 7.498900 TGGCACGACAGAAATATGAATAGAAAT 59.501 33.333 0.00 0.00 0.00 2.17
479 1567 5.237996 CAGATGGCACGACAGAAATATGAAT 59.762 40.000 0.00 0.00 0.00 2.57
504 1592 2.664081 GGAGGAGGTGCTGTCCAGG 61.664 68.421 0.00 0.00 36.43 4.45
506 1594 2.607750 GGGAGGAGGTGCTGTCCA 60.608 66.667 2.93 0.00 36.43 4.02
593 1686 1.310216 TGGGATCGACGTGACGTGAT 61.310 55.000 18.09 18.07 41.37 3.06
630 1723 3.186047 CAACGGACGCGGTGGATC 61.186 66.667 12.47 0.00 0.00 3.36
704 1797 4.758251 TGGCCATGTCGACAGCGG 62.758 66.667 25.37 25.37 38.28 5.52
705 1798 3.190849 CTGGCCATGTCGACAGCG 61.191 66.667 24.41 16.64 39.35 5.18
707 1800 3.190849 CGCTGGCCATGTCGACAG 61.191 66.667 24.41 12.34 0.00 3.51
862 1955 3.319198 GTGAGTTGGAGCGGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
866 1959 1.284982 CGAGTTGTGAGTTGGAGCGG 61.285 60.000 0.00 0.00 0.00 5.52
893 1986 2.607750 TGGGAGGGAGAGGTGTGC 60.608 66.667 0.00 0.00 0.00 4.57
920 2013 3.368190 CTCTGGCCGGCTCTCTGTG 62.368 68.421 28.56 10.74 0.00 3.66
982 2092 1.120795 ATTTGGTTGGTGCTGGTGGG 61.121 55.000 0.00 0.00 0.00 4.61
1632 3305 4.965062 ACATTTTACATACACGGAAAGCG 58.035 39.130 0.00 0.00 0.00 4.68
1725 3846 1.772182 CGACGCATCATCCTAACCTC 58.228 55.000 0.00 0.00 0.00 3.85
1726 3847 0.249489 GCGACGCATCATCCTAACCT 60.249 55.000 16.42 0.00 0.00 3.50
1728 3849 0.855349 CAGCGACGCATCATCCTAAC 59.145 55.000 23.70 0.00 0.00 2.34
1730 3851 0.312102 CTCAGCGACGCATCATCCTA 59.688 55.000 23.70 0.00 0.00 2.94
1733 3854 0.029967 TCTCTCAGCGACGCATCATC 59.970 55.000 23.70 0.00 0.00 2.92
1749 4561 2.073816 TCATCGAACCGCCTTTTTCTC 58.926 47.619 0.00 0.00 0.00 2.87
1800 4620 5.977171 ATATTTCGCTACAAATACGTGCA 57.023 34.783 0.00 0.00 32.30 4.57
1886 4731 6.854778 ACATGCTTGCAAAATTGTTCTTTTT 58.145 28.000 0.00 0.00 0.00 1.94
1889 4734 6.439675 AAACATGCTTGCAAAATTGTTCTT 57.560 29.167 16.35 4.59 0.00 2.52
1891 4736 6.746364 TCAAAAACATGCTTGCAAAATTGTTC 59.254 30.769 16.35 0.00 0.00 3.18
1893 4738 6.192234 TCAAAAACATGCTTGCAAAATTGT 57.808 29.167 0.00 1.19 0.00 2.71
1895 4740 7.760340 ACAATTCAAAAACATGCTTGCAAAATT 59.240 25.926 0.00 0.00 0.00 1.82
1896 4741 7.221067 CACAATTCAAAAACATGCTTGCAAAAT 59.779 29.630 0.00 0.00 0.00 1.82
1897 4742 6.527023 CACAATTCAAAAACATGCTTGCAAAA 59.473 30.769 0.00 0.00 0.00 2.44
1898 4743 6.028368 CACAATTCAAAAACATGCTTGCAAA 58.972 32.000 0.00 0.00 0.00 3.68
1899 4744 5.353400 TCACAATTCAAAAACATGCTTGCAA 59.647 32.000 0.00 0.00 0.00 4.08
1900 4745 4.874396 TCACAATTCAAAAACATGCTTGCA 59.126 33.333 0.00 0.00 0.00 4.08
1901 4746 5.406767 TCACAATTCAAAAACATGCTTGC 57.593 34.783 0.00 0.00 0.00 4.01
1902 4747 7.411274 ACATTCACAATTCAAAAACATGCTTG 58.589 30.769 0.00 0.00 0.00 4.01
1903 4748 7.517101 CGACATTCACAATTCAAAAACATGCTT 60.517 33.333 0.00 0.00 0.00 3.91
1905 4750 6.066410 CGACATTCACAATTCAAAAACATGC 58.934 36.000 0.00 0.00 0.00 4.06
1907 4752 7.202526 ACTCGACATTCACAATTCAAAAACAT 58.797 30.769 0.00 0.00 0.00 2.71
1908 4753 6.559810 ACTCGACATTCACAATTCAAAAACA 58.440 32.000 0.00 0.00 0.00 2.83
1909 4754 7.449934 AACTCGACATTCACAATTCAAAAAC 57.550 32.000 0.00 0.00 0.00 2.43
1910 4755 9.393249 GATAACTCGACATTCACAATTCAAAAA 57.607 29.630 0.00 0.00 0.00 1.94
1911 4756 8.563732 TGATAACTCGACATTCACAATTCAAAA 58.436 29.630 0.00 0.00 0.00 2.44
1912 4757 8.015087 GTGATAACTCGACATTCACAATTCAAA 58.985 33.333 7.71 0.00 37.30 2.69
1913 4758 7.518161 GTGATAACTCGACATTCACAATTCAA 58.482 34.615 7.71 0.00 37.30 2.69
1914 4759 6.183360 CGTGATAACTCGACATTCACAATTCA 60.183 38.462 11.38 0.00 37.20 2.57
1915 4760 6.178507 CGTGATAACTCGACATTCACAATTC 58.821 40.000 11.38 0.00 37.20 2.17
1916 4761 5.637810 ACGTGATAACTCGACATTCACAATT 59.362 36.000 1.30 0.00 37.20 2.32
1917 4762 5.062183 CACGTGATAACTCGACATTCACAAT 59.938 40.000 10.90 0.30 37.20 2.71
1918 4763 4.384547 CACGTGATAACTCGACATTCACAA 59.615 41.667 10.90 0.00 37.20 3.33
1919 4764 3.917985 CACGTGATAACTCGACATTCACA 59.082 43.478 10.90 0.00 37.20 3.58
1920 4765 3.241678 GCACGTGATAACTCGACATTCAC 60.242 47.826 22.23 0.00 36.91 3.18
1921 4766 2.921121 GCACGTGATAACTCGACATTCA 59.079 45.455 22.23 0.00 36.91 2.57
1922 4767 2.281762 GGCACGTGATAACTCGACATTC 59.718 50.000 22.23 0.00 36.91 2.67
1923 4768 2.094182 AGGCACGTGATAACTCGACATT 60.094 45.455 22.23 0.00 36.91 2.71
1925 4770 0.885879 AGGCACGTGATAACTCGACA 59.114 50.000 22.23 0.00 36.91 4.35
1927 4772 1.132453 CAGAGGCACGTGATAACTCGA 59.868 52.381 22.23 0.00 36.91 4.04
1928 4773 1.135373 ACAGAGGCACGTGATAACTCG 60.135 52.381 22.23 16.44 38.66 4.18
1929 4774 2.656560 ACAGAGGCACGTGATAACTC 57.343 50.000 22.23 18.84 0.00 3.01
1930 4775 4.530710 TTTACAGAGGCACGTGATAACT 57.469 40.909 22.23 10.97 0.00 2.24
1954 4799 9.872757 CCAATAGCGATTTAAACGTGTTAATAT 57.127 29.630 0.00 0.00 0.00 1.28
1955 4800 8.336806 CCCAATAGCGATTTAAACGTGTTAATA 58.663 33.333 0.00 0.00 0.00 0.98
1956 4801 7.190871 CCCAATAGCGATTTAAACGTGTTAAT 58.809 34.615 0.00 0.00 0.00 1.40
1957 4802 6.544622 CCCAATAGCGATTTAAACGTGTTAA 58.455 36.000 0.00 0.00 0.00 2.01
1958 4803 5.447548 GCCCAATAGCGATTTAAACGTGTTA 60.448 40.000 0.00 0.00 0.00 2.41
1959 4804 4.673320 GCCCAATAGCGATTTAAACGTGTT 60.673 41.667 0.00 0.00 0.00 3.32
1960 4805 3.181504 GCCCAATAGCGATTTAAACGTGT 60.182 43.478 0.00 0.00 0.00 4.49
1961 4806 3.181505 TGCCCAATAGCGATTTAAACGTG 60.182 43.478 0.00 3.36 34.65 4.49
1963 4808 3.684103 TGCCCAATAGCGATTTAAACG 57.316 42.857 0.00 0.00 34.65 3.60
1964 4809 3.735746 GCATGCCCAATAGCGATTTAAAC 59.264 43.478 6.36 0.00 34.65 2.01
1965 4810 3.636300 AGCATGCCCAATAGCGATTTAAA 59.364 39.130 15.66 0.00 34.65 1.52
1969 4814 1.338973 CAAGCATGCCCAATAGCGATT 59.661 47.619 15.66 0.00 34.65 3.34
1971 4816 1.102809 CCAAGCATGCCCAATAGCGA 61.103 55.000 15.66 0.00 34.65 4.93
1973 4818 0.672342 CTCCAAGCATGCCCAATAGC 59.328 55.000 15.66 0.00 0.00 2.97
1976 4821 1.382146 CCCTCCAAGCATGCCCAAT 60.382 57.895 15.66 0.00 0.00 3.16
1977 4822 2.037687 CCCTCCAAGCATGCCCAA 59.962 61.111 15.66 0.00 0.00 4.12
1978 4823 4.764771 GCCCTCCAAGCATGCCCA 62.765 66.667 15.66 0.00 0.00 5.36
1981 4826 1.748879 TAACGCCCTCCAAGCATGC 60.749 57.895 10.51 10.51 0.00 4.06
1983 4828 0.392998 CAGTAACGCCCTCCAAGCAT 60.393 55.000 0.00 0.00 0.00 3.79
1985 4830 1.745489 CCAGTAACGCCCTCCAAGC 60.745 63.158 0.00 0.00 0.00 4.01
1987 4832 1.350071 TTACCAGTAACGCCCTCCAA 58.650 50.000 0.00 0.00 0.00 3.53
1988 4833 1.350071 TTTACCAGTAACGCCCTCCA 58.650 50.000 0.00 0.00 0.00 3.86
1989 4834 2.704464 ATTTACCAGTAACGCCCTCC 57.296 50.000 0.00 0.00 0.00 4.30
1992 4837 6.053650 AGAGAAATATTTACCAGTAACGCCC 58.946 40.000 0.00 0.00 0.00 6.13
1993 4838 8.652810 TTAGAGAAATATTTACCAGTAACGCC 57.347 34.615 0.00 0.00 0.00 5.68
2009 4854 9.785982 AGAGTTGCTCTTAAGTTTTAGAGAAAT 57.214 29.630 15.26 8.25 37.60 2.17
2010 4855 9.262358 GAGAGTTGCTCTTAAGTTTTAGAGAAA 57.738 33.333 15.26 10.10 41.35 2.52
2011 4856 7.595502 CGAGAGTTGCTCTTAAGTTTTAGAGAA 59.404 37.037 15.26 5.43 41.35 2.87
2017 4862 4.381411 AGCGAGAGTTGCTCTTAAGTTTT 58.619 39.130 1.63 0.00 41.35 2.43
2018 4863 3.996480 AGCGAGAGTTGCTCTTAAGTTT 58.004 40.909 1.63 0.00 41.35 2.66
2020 4865 4.785511 TTAGCGAGAGTTGCTCTTAAGT 57.214 40.909 1.63 0.00 41.35 2.24
2021 4866 5.688176 GGTATTAGCGAGAGTTGCTCTTAAG 59.312 44.000 0.00 0.00 41.35 1.85
2022 4867 5.589192 GGTATTAGCGAGAGTTGCTCTTAA 58.411 41.667 0.00 0.00 41.35 1.85
2023 4868 4.261072 CGGTATTAGCGAGAGTTGCTCTTA 60.261 45.833 9.60 0.00 41.35 2.10
2024 4869 3.489398 CGGTATTAGCGAGAGTTGCTCTT 60.489 47.826 9.60 0.00 41.35 2.85
2027 4872 1.749634 ACGGTATTAGCGAGAGTTGCT 59.250 47.619 20.97 0.00 42.41 3.91
2028 4873 1.852895 CACGGTATTAGCGAGAGTTGC 59.147 52.381 20.97 0.00 42.41 4.17
2029 4874 3.416119 TCACGGTATTAGCGAGAGTTG 57.584 47.619 20.97 8.99 42.41 3.16
2030 4875 4.421948 CTTTCACGGTATTAGCGAGAGTT 58.578 43.478 20.97 0.00 42.41 3.01
2031 4876 3.181489 CCTTTCACGGTATTAGCGAGAGT 60.181 47.826 20.97 0.00 42.41 3.24
2032 4877 3.372954 CCTTTCACGGTATTAGCGAGAG 58.627 50.000 20.97 10.56 42.41 3.20
2033 4878 2.100252 CCCTTTCACGGTATTAGCGAGA 59.900 50.000 20.97 15.61 42.41 4.04
2037 4882 2.210961 GAGCCCTTTCACGGTATTAGC 58.789 52.381 0.00 0.00 0.00 3.09
2038 4883 2.159142 ACGAGCCCTTTCACGGTATTAG 60.159 50.000 0.00 0.00 0.00 1.73
2039 4884 1.826720 ACGAGCCCTTTCACGGTATTA 59.173 47.619 0.00 0.00 0.00 0.98
2040 4885 0.611714 ACGAGCCCTTTCACGGTATT 59.388 50.000 0.00 0.00 0.00 1.89
2041 4886 1.135721 GTACGAGCCCTTTCACGGTAT 59.864 52.381 0.00 0.00 0.00 2.73
2042 4887 0.527565 GTACGAGCCCTTTCACGGTA 59.472 55.000 0.00 0.00 0.00 4.02
2043 4888 1.183676 AGTACGAGCCCTTTCACGGT 61.184 55.000 0.00 0.00 0.00 4.83
2046 4891 2.450609 TTGAGTACGAGCCCTTTCAC 57.549 50.000 0.00 0.00 0.00 3.18
2047 4892 3.767673 ACTATTGAGTACGAGCCCTTTCA 59.232 43.478 0.00 0.00 32.65 2.69
2048 4893 4.388378 ACTATTGAGTACGAGCCCTTTC 57.612 45.455 0.00 0.00 32.65 2.62
2049 4894 5.421374 AGTTACTATTGAGTACGAGCCCTTT 59.579 40.000 0.00 0.00 37.91 3.11
2050 4895 4.954826 AGTTACTATTGAGTACGAGCCCTT 59.045 41.667 0.00 0.00 37.91 3.95
2051 4896 4.534797 AGTTACTATTGAGTACGAGCCCT 58.465 43.478 0.00 0.00 37.91 5.19
2052 4897 4.915158 AGTTACTATTGAGTACGAGCCC 57.085 45.455 0.00 0.00 37.91 5.19
2064 4909 9.962759 CGAAACGCTAAAACAATAGTTACTATT 57.037 29.630 11.45 11.45 37.16 1.73
2065 4910 8.598075 CCGAAACGCTAAAACAATAGTTACTAT 58.402 33.333 0.00 0.00 36.84 2.12
2066 4911 7.812191 TCCGAAACGCTAAAACAATAGTTACTA 59.188 33.333 0.00 0.00 36.84 1.82
2069 4914 6.091169 CCTCCGAAACGCTAAAACAATAGTTA 59.909 38.462 0.00 0.00 36.84 2.24
2071 4916 4.390909 CCTCCGAAACGCTAAAACAATAGT 59.609 41.667 0.00 0.00 0.00 2.12
2072 4917 4.390909 ACCTCCGAAACGCTAAAACAATAG 59.609 41.667 0.00 0.00 0.00 1.73
2073 4918 4.317488 ACCTCCGAAACGCTAAAACAATA 58.683 39.130 0.00 0.00 0.00 1.90
2074 4919 3.143728 ACCTCCGAAACGCTAAAACAAT 58.856 40.909 0.00 0.00 0.00 2.71
2077 4922 3.494251 TGTTACCTCCGAAACGCTAAAAC 59.506 43.478 0.00 0.00 0.00 2.43
2079 4924 3.383620 TGTTACCTCCGAAACGCTAAA 57.616 42.857 0.00 0.00 0.00 1.85
2080 4925 3.383620 TTGTTACCTCCGAAACGCTAA 57.616 42.857 0.00 0.00 0.00 3.09
2081 4926 3.383620 TTTGTTACCTCCGAAACGCTA 57.616 42.857 0.00 0.00 0.00 4.26
2083 4928 2.545106 TCTTTTGTTACCTCCGAAACGC 59.455 45.455 0.00 0.00 0.00 4.84
2085 4930 3.251729 GGGTCTTTTGTTACCTCCGAAAC 59.748 47.826 0.00 0.00 35.97 2.78
2086 4931 3.479489 GGGTCTTTTGTTACCTCCGAAA 58.521 45.455 0.00 0.00 35.97 3.46
2087 4932 2.548493 CGGGTCTTTTGTTACCTCCGAA 60.548 50.000 0.00 0.00 35.97 4.30
2088 4933 1.001181 CGGGTCTTTTGTTACCTCCGA 59.999 52.381 0.00 0.00 35.97 4.55
2090 4935 2.845363 TCGGGTCTTTTGTTACCTCC 57.155 50.000 0.00 0.00 35.97 4.30
2094 4939 5.522824 GGTATCTGATCGGGTCTTTTGTTAC 59.477 44.000 0.62 0.00 0.00 2.50
2095 4940 5.667466 GGTATCTGATCGGGTCTTTTGTTA 58.333 41.667 0.62 0.00 0.00 2.41
2096 4941 4.514401 GGTATCTGATCGGGTCTTTTGTT 58.486 43.478 0.62 0.00 0.00 2.83
2098 4943 3.123804 CGGTATCTGATCGGGTCTTTTG 58.876 50.000 0.62 0.00 0.00 2.44
2099 4944 2.764572 ACGGTATCTGATCGGGTCTTTT 59.235 45.455 0.62 0.00 0.00 2.27
2100 4945 2.385803 ACGGTATCTGATCGGGTCTTT 58.614 47.619 0.62 0.00 0.00 2.52
2102 4947 2.945080 TACGGTATCTGATCGGGTCT 57.055 50.000 0.62 0.00 0.00 3.85
2103 4948 3.996150 TTTACGGTATCTGATCGGGTC 57.004 47.619 0.62 0.00 0.00 4.46
2104 4949 4.950205 AATTTACGGTATCTGATCGGGT 57.050 40.909 0.62 0.00 0.00 5.28
2105 4950 4.451096 CCAAATTTACGGTATCTGATCGGG 59.549 45.833 0.62 0.00 0.00 5.14
2107 4952 5.751509 TGACCAAATTTACGGTATCTGATCG 59.248 40.000 0.38 0.00 34.99 3.69
2108 4953 7.730364 ATGACCAAATTTACGGTATCTGATC 57.270 36.000 0.38 0.00 34.99 2.92
2109 4954 8.429641 AGTATGACCAAATTTACGGTATCTGAT 58.570 33.333 0.38 0.00 34.99 2.90
2110 4955 7.788026 AGTATGACCAAATTTACGGTATCTGA 58.212 34.615 0.38 0.00 34.99 3.27
2111 4956 7.709182 TGAGTATGACCAAATTTACGGTATCTG 59.291 37.037 0.38 0.00 34.99 2.90
2113 4958 8.333186 GTTGAGTATGACCAAATTTACGGTATC 58.667 37.037 0.38 0.00 34.99 2.24
2114 4959 8.044908 AGTTGAGTATGACCAAATTTACGGTAT 58.955 33.333 0.38 0.00 34.99 2.73
2115 4960 7.388437 AGTTGAGTATGACCAAATTTACGGTA 58.612 34.615 0.38 0.00 34.99 4.02
2116 4961 6.235664 AGTTGAGTATGACCAAATTTACGGT 58.764 36.000 0.00 0.00 38.56 4.83
2118 4963 9.458374 AAAAAGTTGAGTATGACCAAATTTACG 57.542 29.630 0.00 0.00 0.00 3.18
2121 4966 9.665719 AACAAAAAGTTGAGTATGACCAAATTT 57.334 25.926 0.00 0.00 39.49 1.82
2137 4982 8.316640 TCAGTTTATTGCAACAACAAAAAGTT 57.683 26.923 20.22 1.31 42.42 2.66
2138 4983 7.897575 TCAGTTTATTGCAACAACAAAAAGT 57.102 28.000 20.22 7.87 32.27 2.66
2139 4984 9.604626 TTTTCAGTTTATTGCAACAACAAAAAG 57.395 25.926 20.22 8.66 32.27 2.27
2141 4986 9.604626 CTTTTTCAGTTTATTGCAACAACAAAA 57.395 25.926 20.22 16.13 32.27 2.44
2142 4987 8.233190 CCTTTTTCAGTTTATTGCAACAACAAA 58.767 29.630 20.22 12.49 32.27 2.83
2143 4988 7.148340 CCCTTTTTCAGTTTATTGCAACAACAA 60.148 33.333 20.22 8.36 0.00 2.83
2144 4989 6.314896 CCCTTTTTCAGTTTATTGCAACAACA 59.685 34.615 20.22 3.60 0.00 3.33
2145 4990 6.536941 TCCCTTTTTCAGTTTATTGCAACAAC 59.463 34.615 0.00 8.31 0.00 3.32
2146 4991 6.644347 TCCCTTTTTCAGTTTATTGCAACAA 58.356 32.000 0.00 0.00 0.00 2.83
2147 4992 6.227298 TCCCTTTTTCAGTTTATTGCAACA 57.773 33.333 0.00 0.00 0.00 3.33
2148 4993 5.177511 GCTCCCTTTTTCAGTTTATTGCAAC 59.822 40.000 0.00 0.00 0.00 4.17
2149 4994 5.296748 GCTCCCTTTTTCAGTTTATTGCAA 58.703 37.500 0.00 0.00 0.00 4.08
2150 4995 4.262420 GGCTCCCTTTTTCAGTTTATTGCA 60.262 41.667 0.00 0.00 0.00 4.08
2151 4996 4.245660 GGCTCCCTTTTTCAGTTTATTGC 58.754 43.478 0.00 0.00 0.00 3.56
2152 4997 4.618227 CGGGCTCCCTTTTTCAGTTTATTG 60.618 45.833 3.11 0.00 0.00 1.90
2153 4998 3.509967 CGGGCTCCCTTTTTCAGTTTATT 59.490 43.478 3.11 0.00 0.00 1.40
2156 5001 1.328279 CGGGCTCCCTTTTTCAGTTT 58.672 50.000 3.11 0.00 0.00 2.66
2157 5002 1.179174 GCGGGCTCCCTTTTTCAGTT 61.179 55.000 3.11 0.00 0.00 3.16
2158 5003 1.603739 GCGGGCTCCCTTTTTCAGT 60.604 57.895 3.11 0.00 0.00 3.41
2159 5004 1.603455 TGCGGGCTCCCTTTTTCAG 60.603 57.895 3.11 0.00 0.00 3.02
2160 5005 1.901464 GTGCGGGCTCCCTTTTTCA 60.901 57.895 3.11 0.00 0.00 2.69
2162 5007 2.600470 GGTGCGGGCTCCCTTTTT 60.600 61.111 3.11 0.00 0.00 1.94
2163 5008 3.569200 GAGGTGCGGGCTCCCTTTT 62.569 63.158 8.06 0.00 0.00 2.27
2164 5009 4.035102 GAGGTGCGGGCTCCCTTT 62.035 66.667 8.06 0.00 0.00 3.11
2168 5013 2.044806 ATATGTGAGGTGCGGGCTCC 62.045 60.000 3.63 3.63 0.00 4.70
2170 5015 0.681733 CTATATGTGAGGTGCGGGCT 59.318 55.000 0.00 0.00 0.00 5.19
2199 5122 3.451141 AGCTTTGCCGACATTCAAAAA 57.549 38.095 0.00 0.00 32.55 1.94
2200 5123 3.122297 CAAGCTTTGCCGACATTCAAAA 58.878 40.909 0.00 0.00 32.55 2.44
2201 5124 2.741612 CAAGCTTTGCCGACATTCAAA 58.258 42.857 0.00 0.00 0.00 2.69
2202 5125 2.420628 CAAGCTTTGCCGACATTCAA 57.579 45.000 0.00 0.00 0.00 2.69
2213 5136 5.410132 TGATCAATGAATTTGGCAAGCTTTG 59.590 36.000 0.00 9.00 35.92 2.77
2214 5137 5.553123 TGATCAATGAATTTGGCAAGCTTT 58.447 33.333 0.00 0.00 35.92 3.51
2215 5138 5.046878 TCTGATCAATGAATTTGGCAAGCTT 60.047 36.000 0.00 0.00 35.92 3.74
2216 5139 4.464951 TCTGATCAATGAATTTGGCAAGCT 59.535 37.500 0.00 0.00 35.92 3.74
2219 5142 5.337733 CCCTTCTGATCAATGAATTTGGCAA 60.338 40.000 0.00 0.00 35.92 4.52
2220 5143 4.160814 CCCTTCTGATCAATGAATTTGGCA 59.839 41.667 0.00 0.00 35.92 4.92
2221 5144 4.442472 CCCCTTCTGATCAATGAATTTGGC 60.442 45.833 0.00 0.00 35.92 4.52
2224 5147 7.454380 TGTTAACCCCTTCTGATCAATGAATTT 59.546 33.333 2.48 0.00 0.00 1.82
2225 5148 6.953520 TGTTAACCCCTTCTGATCAATGAATT 59.046 34.615 2.48 0.00 0.00 2.17
2226 5149 6.493166 TGTTAACCCCTTCTGATCAATGAAT 58.507 36.000 2.48 0.00 0.00 2.57
2227 5150 5.886609 TGTTAACCCCTTCTGATCAATGAA 58.113 37.500 2.48 0.00 0.00 2.57
2228 5151 5.250543 TCTGTTAACCCCTTCTGATCAATGA 59.749 40.000 2.48 0.00 0.00 2.57
2229 5152 5.500234 TCTGTTAACCCCTTCTGATCAATG 58.500 41.667 2.48 0.00 0.00 2.82
2230 5153 5.488919 TCTCTGTTAACCCCTTCTGATCAAT 59.511 40.000 2.48 0.00 0.00 2.57
2231 5154 4.844085 TCTCTGTTAACCCCTTCTGATCAA 59.156 41.667 2.48 0.00 0.00 2.57
2232 5155 4.223032 GTCTCTGTTAACCCCTTCTGATCA 59.777 45.833 2.48 0.00 0.00 2.92
2233 5156 4.223032 TGTCTCTGTTAACCCCTTCTGATC 59.777 45.833 2.48 0.00 0.00 2.92
2234 5157 4.168101 TGTCTCTGTTAACCCCTTCTGAT 58.832 43.478 2.48 0.00 0.00 2.90
2235 5158 3.583228 TGTCTCTGTTAACCCCTTCTGA 58.417 45.455 2.48 0.00 0.00 3.27
2237 5160 3.072622 GGTTGTCTCTGTTAACCCCTTCT 59.927 47.826 2.48 0.00 38.29 2.85
2238 5161 3.409570 GGTTGTCTCTGTTAACCCCTTC 58.590 50.000 2.48 0.00 38.29 3.46
2239 5162 3.503800 GGTTGTCTCTGTTAACCCCTT 57.496 47.619 2.48 0.00 38.29 3.95
2244 5167 3.564225 CCAGTTGGGTTGTCTCTGTTAAC 59.436 47.826 0.00 0.00 0.00 2.01
2245 5168 3.815809 CCAGTTGGGTTGTCTCTGTTAA 58.184 45.455 0.00 0.00 0.00 2.01
2246 5169 3.485463 CCAGTTGGGTTGTCTCTGTTA 57.515 47.619 0.00 0.00 0.00 2.41
2247 5170 2.348411 CCAGTTGGGTTGTCTCTGTT 57.652 50.000 0.00 0.00 0.00 3.16
2266 5189 0.521735 CTCTTGGCTGGCGTTTAACC 59.478 55.000 0.00 0.00 0.00 2.85
2267 5190 0.521735 CCTCTTGGCTGGCGTTTAAC 59.478 55.000 0.00 0.00 0.00 2.01
2268 5191 2.941210 CCTCTTGGCTGGCGTTTAA 58.059 52.632 0.00 0.00 0.00 1.52
2269 5192 4.713946 CCTCTTGGCTGGCGTTTA 57.286 55.556 0.00 0.00 0.00 2.01
2280 5203 1.243902 TTTTACCGCCTTGCCTCTTG 58.756 50.000 0.00 0.00 0.00 3.02
2281 5204 1.886542 CTTTTTACCGCCTTGCCTCTT 59.113 47.619 0.00 0.00 0.00 2.85
2282 5205 1.073284 TCTTTTTACCGCCTTGCCTCT 59.927 47.619 0.00 0.00 0.00 3.69
2283 5206 1.530323 TCTTTTTACCGCCTTGCCTC 58.470 50.000 0.00 0.00 0.00 4.70
2284 5207 1.886542 CTTCTTTTTACCGCCTTGCCT 59.113 47.619 0.00 0.00 0.00 4.75
2286 5209 3.850122 ATCTTCTTTTTACCGCCTTGC 57.150 42.857 0.00 0.00 0.00 4.01
2309 5232 2.091885 TCCCAGCTGAGTGTTCCTTTTT 60.092 45.455 17.39 0.00 0.00 1.94
2310 5233 1.494721 TCCCAGCTGAGTGTTCCTTTT 59.505 47.619 17.39 0.00 0.00 2.27
2311 5234 1.140312 TCCCAGCTGAGTGTTCCTTT 58.860 50.000 17.39 0.00 0.00 3.11
2312 5235 1.280421 GATCCCAGCTGAGTGTTCCTT 59.720 52.381 17.39 0.00 0.00 3.36
2313 5236 0.908198 GATCCCAGCTGAGTGTTCCT 59.092 55.000 17.39 0.00 0.00 3.36
2314 5237 0.615331 TGATCCCAGCTGAGTGTTCC 59.385 55.000 17.39 0.00 0.00 3.62
2315 5238 2.479566 TTGATCCCAGCTGAGTGTTC 57.520 50.000 17.39 8.41 0.00 3.18
2316 5239 2.957402 TTTGATCCCAGCTGAGTGTT 57.043 45.000 17.39 0.00 0.00 3.32
2317 5240 2.553904 CCTTTTGATCCCAGCTGAGTGT 60.554 50.000 17.39 0.00 0.00 3.55
2318 5241 2.089980 CCTTTTGATCCCAGCTGAGTG 58.910 52.381 17.39 3.18 0.00 3.51
2319 5242 1.988107 TCCTTTTGATCCCAGCTGAGT 59.012 47.619 17.39 0.00 0.00 3.41
2320 5243 2.795231 TCCTTTTGATCCCAGCTGAG 57.205 50.000 17.39 0.39 0.00 3.35
2321 5244 3.624777 GATTCCTTTTGATCCCAGCTGA 58.375 45.455 17.39 0.00 0.00 4.26
2322 5245 2.692041 GGATTCCTTTTGATCCCAGCTG 59.308 50.000 6.78 6.78 0.00 4.24
2323 5246 3.023939 GGATTCCTTTTGATCCCAGCT 57.976 47.619 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.