Multiple sequence alignment - TraesCS5B01G094200

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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 TraesCS5B01G094200 chr5B 100.000 2192 0 0 1 2192 123757469 123759660 0.000000e+00 4048
1 TraesCS5B01G094200 chr5D 95.779 1777 62 7 1 1771 113388703 113390472 0.000000e+00 2854
2 TraesCS5B01G094200 chr5A 95.010 1483 44 5 1 1479 118667977 118669433 0.000000e+00 2302
3 TraesCS5B01G094200 chr5A 95.753 259 11 0 1512 1770 118669432 118669690 3.370000e-113 418
4 TraesCS5B01G094200 chr4A 97.810 411 9 0 1773 2183 577759536 577759946 0.000000e+00 710
5 TraesCS5B01G094200 chr6B 97.129 418 10 2 1767 2183 186695021 186695437 0.000000e+00 704
6 TraesCS5B01G094200 chr4B 97.337 413 10 1 1773 2185 31878777 31879188 0.000000e+00 701
7 TraesCS5B01G094200 chr2B 97.101 414 12 0 1770 2183 635229543 635229956 0.000000e+00 699
8 TraesCS5B01G094200 chr2B 96.659 419 11 3 1773 2189 771821401 771820984 0.000000e+00 693
9 TraesCS5B01G094200 chr2B 96.852 413 11 2 1771 2183 649671574 649671164 0.000000e+00 689
10 TraesCS5B01G094200 chr7A 97.101 414 11 1 1771 2184 159723115 159722703 0.000000e+00 697
11 TraesCS5B01G094200 chr2A 97.087 412 11 1 1773 2183 198905660 198905249 0.000000e+00 693
12 TraesCS5B01G094200 chr7B 96.420 419 14 1 1772 2190 721929428 721929011 0.000000e+00 689
13 TraesCS5B01G094200 chr7B 84.151 265 33 7 1083 1345 293067335 293067078 4.670000e-62 248


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 TraesCS5B01G094200 chr5B 123757469 123759660 2191 False 4048 4048 100.0000 1 2192 1 chr5B.!!$F1 2191
1 TraesCS5B01G094200 chr5D 113388703 113390472 1769 False 2854 2854 95.7790 1 1771 1 chr5D.!!$F1 1770
2 TraesCS5B01G094200 chr5A 118667977 118669690 1713 False 1360 2302 95.3815 1 1770 2 chr5A.!!$F1 1769

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
687 692 1.004745 CTGGTTTGACATAGCTGGGGT 59.995 52.381 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2066 0.168788 AATTTGATGCGTGAGGTGCG 59.831 50.0 0.0 0.0 34.24 5.34 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
45 47 7.288852 TCTGTGGGTATTTTCTTTGATGGAAAA 59.711 33.333 0.00 0.00 43.65 2.29
191 195 1.915078 ATGCCGCCTTCTACAAGCCT 61.915 55.000 0.00 0.00 0.00 4.58
400 404 1.202867 TGTGCATGAGTGGCAGGTTAA 60.203 47.619 0.00 0.00 42.85 2.01
508 512 5.456921 TTTCCCTGCTCCATCTTAAGATT 57.543 39.130 15.49 0.00 31.21 2.40
612 616 7.491048 GCTATTGTTCTCTAGAGAGGTTTTGAG 59.509 40.741 21.34 14.48 42.30 3.02
625 630 2.887152 GGTTTTGAGGAGCAGTTGATGT 59.113 45.455 0.00 0.00 0.00 3.06
630 635 4.824479 TGAGGAGCAGTTGATGTATCAA 57.176 40.909 3.28 3.28 43.94 2.57
660 665 7.378966 TCTTCTTCATACTCTACTGTTTGTGG 58.621 38.462 0.00 0.00 0.00 4.17
674 679 3.243805 TGTTTGTGGATCATGCTGGTTTG 60.244 43.478 0.00 0.00 0.00 2.93
686 691 1.755179 CTGGTTTGACATAGCTGGGG 58.245 55.000 0.00 0.00 0.00 4.96
687 692 1.004745 CTGGTTTGACATAGCTGGGGT 59.995 52.381 0.00 0.00 0.00 4.95
699 704 6.357367 ACATAGCTGGGGTCACTAATTTTAG 58.643 40.000 0.00 0.00 36.82 1.85
769 774 5.916883 TCTAAACTCGGTTACGTCTTGAAAG 59.083 40.000 0.00 0.00 41.85 2.62
819 824 1.021202 CCAAGTGACCTTTGAACGCA 58.979 50.000 0.00 0.00 0.00 5.24
1207 1216 4.530161 AGGAGTAGTTCTGAAGTGCTGAAT 59.470 41.667 18.62 3.80 36.91 2.57
1340 1349 3.243839 GCACACCACCATTTGAGAACATT 60.244 43.478 0.00 0.00 0.00 2.71
1362 1371 8.130469 ACATTGAACCATTTTGAATTTGCTTTC 58.870 29.630 0.00 0.00 0.00 2.62
1483 1492 2.487986 CCTTTTGGAAGTGAGCTCACCT 60.488 50.000 37.09 28.46 44.60 4.00
1662 1671 0.658897 GGCTTTCACCGTCGTTTTCA 59.341 50.000 0.00 0.00 0.00 2.69
1740 1749 6.260050 CACTACCGTCATTAACCATTATTGCT 59.740 38.462 0.00 0.00 0.00 3.91
1774 1783 7.967890 ATCAAAGTTGATGATGTATATGCGA 57.032 32.000 5.74 0.00 45.63 5.10
1775 1784 7.784633 TCAAAGTTGATGATGTATATGCGAA 57.215 32.000 0.00 0.00 31.01 4.70
1776 1785 8.207521 TCAAAGTTGATGATGTATATGCGAAA 57.792 30.769 0.00 0.00 31.01 3.46
1777 1786 8.672815 TCAAAGTTGATGATGTATATGCGAAAA 58.327 29.630 0.00 0.00 31.01 2.29
1778 1787 9.454585 CAAAGTTGATGATGTATATGCGAAAAT 57.545 29.630 0.00 0.00 0.00 1.82
1779 1788 9.669353 AAAGTTGATGATGTATATGCGAAAATC 57.331 29.630 0.00 0.00 0.00 2.17
1780 1789 7.810658 AGTTGATGATGTATATGCGAAAATCC 58.189 34.615 0.00 0.00 0.00 3.01
1781 1790 7.445096 AGTTGATGATGTATATGCGAAAATCCA 59.555 33.333 0.00 0.00 0.00 3.41
1782 1791 7.742556 TGATGATGTATATGCGAAAATCCAA 57.257 32.000 0.00 0.00 0.00 3.53
1783 1792 8.164058 TGATGATGTATATGCGAAAATCCAAA 57.836 30.769 0.00 0.00 0.00 3.28
1784 1793 8.795513 TGATGATGTATATGCGAAAATCCAAAT 58.204 29.630 0.00 0.00 0.00 2.32
1785 1794 9.282247 GATGATGTATATGCGAAAATCCAAATC 57.718 33.333 0.00 0.00 0.00 2.17
1786 1795 8.394971 TGATGTATATGCGAAAATCCAAATCT 57.605 30.769 0.00 0.00 0.00 2.40
1787 1796 8.291740 TGATGTATATGCGAAAATCCAAATCTG 58.708 33.333 0.00 0.00 0.00 2.90
1788 1797 7.800155 TGTATATGCGAAAATCCAAATCTGA 57.200 32.000 0.00 0.00 0.00 3.27
1789 1798 7.864686 TGTATATGCGAAAATCCAAATCTGAG 58.135 34.615 0.00 0.00 0.00 3.35
1790 1799 3.492421 TGCGAAAATCCAAATCTGAGC 57.508 42.857 0.00 0.00 0.00 4.26
1791 1800 2.164219 TGCGAAAATCCAAATCTGAGCC 59.836 45.455 0.00 0.00 0.00 4.70
1792 1801 2.480244 GCGAAAATCCAAATCTGAGCCC 60.480 50.000 0.00 0.00 0.00 5.19
1793 1802 2.223340 CGAAAATCCAAATCTGAGCCCG 60.223 50.000 0.00 0.00 0.00 6.13
1794 1803 2.806945 AAATCCAAATCTGAGCCCGA 57.193 45.000 0.00 0.00 0.00 5.14
1795 1804 2.338577 AATCCAAATCTGAGCCCGAG 57.661 50.000 0.00 0.00 0.00 4.63
1796 1805 0.179034 ATCCAAATCTGAGCCCGAGC 60.179 55.000 0.00 0.00 40.32 5.03
1806 1815 2.894387 GCCCGAGCTCATCTGCAC 60.894 66.667 15.40 0.00 35.50 4.57
1807 1816 2.202987 CCCGAGCTCATCTGCACC 60.203 66.667 15.40 0.00 34.99 5.01
1808 1817 2.729479 CCCGAGCTCATCTGCACCT 61.729 63.158 15.40 0.00 34.99 4.00
1809 1818 1.521010 CCGAGCTCATCTGCACCTG 60.521 63.158 15.40 0.00 34.99 4.00
1810 1819 2.172372 CGAGCTCATCTGCACCTGC 61.172 63.158 15.40 0.00 42.50 4.85
1811 1820 2.125229 AGCTCATCTGCACCTGCG 60.125 61.111 0.00 0.00 45.83 5.18
1812 1821 3.873883 GCTCATCTGCACCTGCGC 61.874 66.667 0.00 0.00 45.83 6.09
1813 1822 2.125229 CTCATCTGCACCTGCGCT 60.125 61.111 9.73 0.00 45.83 5.92
1814 1823 2.125391 TCATCTGCACCTGCGCTC 60.125 61.111 9.73 0.00 45.83 5.03
1815 1824 2.435410 CATCTGCACCTGCGCTCA 60.435 61.111 9.73 0.00 45.83 4.26
1816 1825 2.435586 ATCTGCACCTGCGCTCAC 60.436 61.111 9.73 0.00 45.83 3.51
1817 1826 3.965539 ATCTGCACCTGCGCTCACC 62.966 63.158 9.73 0.00 45.83 4.02
1818 1827 4.994471 CTGCACCTGCGCTCACCA 62.994 66.667 9.73 0.00 45.83 4.17
1819 1828 4.560743 TGCACCTGCGCTCACCAA 62.561 61.111 9.73 0.00 45.83 3.67
1820 1829 3.286751 GCACCTGCGCTCACCAAA 61.287 61.111 9.73 0.00 0.00 3.28
1821 1830 2.844451 GCACCTGCGCTCACCAAAA 61.844 57.895 9.73 0.00 0.00 2.44
1822 1831 1.732917 CACCTGCGCTCACCAAAAA 59.267 52.632 9.73 0.00 0.00 1.94
1883 1892 4.787135 AAAAATTGGGGTGGTGAACAAT 57.213 36.364 0.00 0.00 35.24 2.71
1884 1893 4.787135 AAAATTGGGGTGGTGAACAATT 57.213 36.364 0.00 0.00 43.20 2.32
1885 1894 4.787135 AAATTGGGGTGGTGAACAATTT 57.213 36.364 8.03 8.03 44.26 1.82
1886 1895 3.767902 ATTGGGGTGGTGAACAATTTG 57.232 42.857 0.00 0.00 29.89 2.32
1887 1896 2.461300 TGGGGTGGTGAACAATTTGA 57.539 45.000 2.79 0.00 0.00 2.69
1888 1897 2.969628 TGGGGTGGTGAACAATTTGAT 58.030 42.857 2.79 0.00 0.00 2.57
1889 1898 2.632028 TGGGGTGGTGAACAATTTGATG 59.368 45.455 2.79 0.00 0.00 3.07
1890 1899 2.632512 GGGGTGGTGAACAATTTGATGT 59.367 45.455 2.79 0.00 34.24 3.06
1891 1900 3.554752 GGGGTGGTGAACAATTTGATGTG 60.555 47.826 2.79 0.00 32.81 3.21
1892 1901 3.069443 GGGTGGTGAACAATTTGATGTGT 59.931 43.478 2.79 0.00 32.81 3.72
1893 1902 4.050553 GGTGGTGAACAATTTGATGTGTG 58.949 43.478 2.79 0.00 32.81 3.82
1894 1903 4.202101 GGTGGTGAACAATTTGATGTGTGA 60.202 41.667 2.79 0.00 32.81 3.58
1895 1904 4.977963 GTGGTGAACAATTTGATGTGTGAG 59.022 41.667 2.79 0.00 32.81 3.51
1896 1905 4.037803 TGGTGAACAATTTGATGTGTGAGG 59.962 41.667 2.79 0.00 32.81 3.86
1897 1906 4.037923 GGTGAACAATTTGATGTGTGAGGT 59.962 41.667 2.79 0.00 32.81 3.85
1898 1907 4.977963 GTGAACAATTTGATGTGTGAGGTG 59.022 41.667 2.79 0.00 32.81 4.00
1899 1908 3.648339 ACAATTTGATGTGTGAGGTGC 57.352 42.857 2.79 0.00 30.82 5.01
1900 1909 2.030893 ACAATTTGATGTGTGAGGTGCG 60.031 45.455 2.79 0.00 30.82 5.34
1901 1910 0.523072 ATTTGATGTGTGAGGTGCGC 59.477 50.000 0.00 0.00 0.00 6.09
1902 1911 1.514678 TTTGATGTGTGAGGTGCGCC 61.515 55.000 8.71 8.71 0.00 6.53
1903 1912 3.127533 GATGTGTGAGGTGCGCCC 61.128 66.667 14.07 5.76 34.57 6.13
1904 1913 4.722700 ATGTGTGAGGTGCGCCCC 62.723 66.667 14.07 1.21 34.57 5.80
1906 1915 4.947147 GTGTGAGGTGCGCCCCAA 62.947 66.667 12.68 0.00 34.57 4.12
1907 1916 3.965258 TGTGAGGTGCGCCCCAAT 61.965 61.111 12.68 0.00 34.57 3.16
1908 1917 2.676471 GTGAGGTGCGCCCCAATT 60.676 61.111 12.68 0.00 34.57 2.32
1909 1918 2.117206 TGAGGTGCGCCCCAATTT 59.883 55.556 12.68 0.00 34.57 1.82
1910 1919 1.532794 TGAGGTGCGCCCCAATTTT 60.533 52.632 12.68 0.00 34.57 1.82
1911 1920 1.215382 GAGGTGCGCCCCAATTTTC 59.785 57.895 12.68 0.00 34.57 2.29
1912 1921 1.531739 GAGGTGCGCCCCAATTTTCA 61.532 55.000 12.68 0.00 34.57 2.69
1913 1922 1.118356 AGGTGCGCCCCAATTTTCAA 61.118 50.000 12.68 0.00 34.57 2.69
1914 1923 0.250081 GGTGCGCCCCAATTTTCAAA 60.250 50.000 3.18 0.00 0.00 2.69
1915 1924 1.587547 GTGCGCCCCAATTTTCAAAA 58.412 45.000 4.18 0.00 0.00 2.44
1916 1925 1.262950 GTGCGCCCCAATTTTCAAAAC 59.737 47.619 4.18 0.00 0.00 2.43
1917 1926 1.134401 TGCGCCCCAATTTTCAAAACA 60.134 42.857 4.18 0.00 0.00 2.83
1918 1927 2.150390 GCGCCCCAATTTTCAAAACAT 58.850 42.857 0.00 0.00 0.00 2.71
1919 1928 2.551887 GCGCCCCAATTTTCAAAACATT 59.448 40.909 0.00 0.00 0.00 2.71
1920 1929 3.004210 GCGCCCCAATTTTCAAAACATTT 59.996 39.130 0.00 0.00 0.00 2.32
1921 1930 4.535116 CGCCCCAATTTTCAAAACATTTG 58.465 39.130 0.00 0.00 0.00 2.32
1922 1931 4.556302 CGCCCCAATTTTCAAAACATTTGG 60.556 41.667 6.72 6.72 34.69 3.28
1923 1932 4.582240 GCCCCAATTTTCAAAACATTTGGA 59.418 37.500 13.28 0.00 36.55 3.53
1924 1933 5.507149 GCCCCAATTTTCAAAACATTTGGAC 60.507 40.000 13.28 4.07 36.55 4.02
1925 1934 5.827267 CCCCAATTTTCAAAACATTTGGACT 59.173 36.000 13.28 0.00 36.55 3.85
1926 1935 6.320926 CCCCAATTTTCAAAACATTTGGACTT 59.679 34.615 13.28 0.00 36.55 3.01
1927 1936 7.500559 CCCCAATTTTCAAAACATTTGGACTTA 59.499 33.333 13.28 0.00 36.55 2.24
1928 1937 9.065798 CCCAATTTTCAAAACATTTGGACTTAT 57.934 29.630 13.28 0.00 36.55 1.73
1929 1938 9.881529 CCAATTTTCAAAACATTTGGACTTATG 57.118 29.630 7.67 0.00 36.55 1.90
1932 1941 7.475771 TTTCAAAACATTTGGACTTATGTGC 57.524 32.000 3.25 0.00 35.29 4.57
1933 1942 6.154203 TCAAAACATTTGGACTTATGTGCA 57.846 33.333 0.00 0.00 42.73 4.57
1934 1943 6.215121 TCAAAACATTTGGACTTATGTGCAG 58.785 36.000 3.26 0.00 44.96 4.41
1935 1944 3.855689 ACATTTGGACTTATGTGCAGC 57.144 42.857 3.26 0.00 44.96 5.25
1936 1945 3.424703 ACATTTGGACTTATGTGCAGCT 58.575 40.909 3.26 0.00 44.96 4.24
1937 1946 3.441572 ACATTTGGACTTATGTGCAGCTC 59.558 43.478 3.26 0.00 44.96 4.09
1938 1947 3.423539 TTTGGACTTATGTGCAGCTCT 57.576 42.857 3.26 0.00 44.96 4.09
1939 1948 3.423539 TTGGACTTATGTGCAGCTCTT 57.576 42.857 3.26 0.00 44.96 2.85
1940 1949 4.551702 TTGGACTTATGTGCAGCTCTTA 57.448 40.909 3.26 0.00 44.96 2.10
1941 1950 4.128925 TGGACTTATGTGCAGCTCTTAG 57.871 45.455 0.00 0.00 39.59 2.18
1942 1951 2.869192 GGACTTATGTGCAGCTCTTAGC 59.131 50.000 0.00 0.00 42.84 3.09
1943 1952 3.525537 GACTTATGTGCAGCTCTTAGCA 58.474 45.455 1.22 0.00 45.56 3.49
1944 1953 3.935203 GACTTATGTGCAGCTCTTAGCAA 59.065 43.478 0.00 0.00 45.56 3.91
1945 1954 4.326826 ACTTATGTGCAGCTCTTAGCAAA 58.673 39.130 0.00 0.00 45.56 3.68
1946 1955 4.761739 ACTTATGTGCAGCTCTTAGCAAAA 59.238 37.500 0.00 0.00 45.56 2.44
1947 1956 5.241506 ACTTATGTGCAGCTCTTAGCAAAAA 59.758 36.000 0.00 0.00 45.56 1.94
1966 1975 3.771577 AAAGACAAATCGGAGGTCTGT 57.228 42.857 9.58 3.24 40.80 3.41
1967 1976 4.884668 AAAGACAAATCGGAGGTCTGTA 57.115 40.909 9.58 0.00 40.80 2.74
1968 1977 4.884668 AAGACAAATCGGAGGTCTGTAA 57.115 40.909 9.58 0.00 40.80 2.41
1969 1978 4.884668 AGACAAATCGGAGGTCTGTAAA 57.115 40.909 8.42 0.00 40.21 2.01
1970 1979 5.223449 AGACAAATCGGAGGTCTGTAAAA 57.777 39.130 8.42 0.00 40.21 1.52
1971 1980 5.617252 AGACAAATCGGAGGTCTGTAAAAA 58.383 37.500 8.42 0.00 40.21 1.94
1972 1981 6.238648 AGACAAATCGGAGGTCTGTAAAAAT 58.761 36.000 8.42 0.00 40.21 1.82
1973 1982 6.149474 AGACAAATCGGAGGTCTGTAAAAATG 59.851 38.462 8.42 0.00 40.21 2.32
1974 1983 5.768164 ACAAATCGGAGGTCTGTAAAAATGT 59.232 36.000 0.00 0.00 0.00 2.71
1975 1984 5.880054 AATCGGAGGTCTGTAAAAATGTG 57.120 39.130 0.00 0.00 0.00 3.21
1976 1985 4.345859 TCGGAGGTCTGTAAAAATGTGT 57.654 40.909 0.00 0.00 0.00 3.72
1977 1986 5.471556 TCGGAGGTCTGTAAAAATGTGTA 57.528 39.130 0.00 0.00 0.00 2.90
1978 1987 5.232463 TCGGAGGTCTGTAAAAATGTGTAC 58.768 41.667 0.00 0.00 0.00 2.90
1979 1988 5.011329 TCGGAGGTCTGTAAAAATGTGTACT 59.989 40.000 0.00 0.00 0.00 2.73
1980 1989 5.120208 CGGAGGTCTGTAAAAATGTGTACTG 59.880 44.000 0.00 0.00 0.00 2.74
1981 1990 5.995897 GGAGGTCTGTAAAAATGTGTACTGT 59.004 40.000 0.00 0.00 0.00 3.55
1982 1991 6.485648 GGAGGTCTGTAAAAATGTGTACTGTT 59.514 38.462 0.00 0.00 0.00 3.16
1983 1992 7.307811 GGAGGTCTGTAAAAATGTGTACTGTTC 60.308 40.741 0.00 0.00 0.00 3.18
1984 1993 7.051623 AGGTCTGTAAAAATGTGTACTGTTCA 58.948 34.615 0.00 0.00 0.00 3.18
1985 1994 7.719633 AGGTCTGTAAAAATGTGTACTGTTCAT 59.280 33.333 0.00 0.00 0.00 2.57
1986 1995 8.995220 GGTCTGTAAAAATGTGTACTGTTCATA 58.005 33.333 0.00 0.00 0.00 2.15
1997 2006 8.317891 TGTGTACTGTTCATATACTGTTTTGG 57.682 34.615 0.00 0.00 33.15 3.28
1998 2007 7.934665 TGTGTACTGTTCATATACTGTTTTGGT 59.065 33.333 0.00 0.00 33.15 3.67
1999 2008 8.440833 GTGTACTGTTCATATACTGTTTTGGTC 58.559 37.037 0.00 0.00 33.15 4.02
2000 2009 8.372459 TGTACTGTTCATATACTGTTTTGGTCT 58.628 33.333 0.00 0.00 33.15 3.85
2001 2010 7.672983 ACTGTTCATATACTGTTTTGGTCTG 57.327 36.000 0.00 0.00 0.00 3.51
2002 2011 7.450074 ACTGTTCATATACTGTTTTGGTCTGA 58.550 34.615 0.00 0.00 0.00 3.27
2003 2012 8.103305 ACTGTTCATATACTGTTTTGGTCTGAT 58.897 33.333 0.00 0.00 0.00 2.90
2004 2013 8.862325 TGTTCATATACTGTTTTGGTCTGATT 57.138 30.769 0.00 0.00 0.00 2.57
2005 2014 9.295825 TGTTCATATACTGTTTTGGTCTGATTT 57.704 29.630 0.00 0.00 0.00 2.17
2006 2015 9.559958 GTTCATATACTGTTTTGGTCTGATTTG 57.440 33.333 0.00 0.00 0.00 2.32
2007 2016 8.862325 TCATATACTGTTTTGGTCTGATTTGT 57.138 30.769 0.00 0.00 0.00 2.83
2008 2017 8.946085 TCATATACTGTTTTGGTCTGATTTGTC 58.054 33.333 0.00 0.00 0.00 3.18
2009 2018 8.950210 CATATACTGTTTTGGTCTGATTTGTCT 58.050 33.333 0.00 0.00 0.00 3.41
2010 2019 7.823745 ATACTGTTTTGGTCTGATTTGTCTT 57.176 32.000 0.00 0.00 0.00 3.01
2011 2020 6.530019 ACTGTTTTGGTCTGATTTGTCTTT 57.470 33.333 0.00 0.00 0.00 2.52
2012 2021 6.935167 ACTGTTTTGGTCTGATTTGTCTTTT 58.065 32.000 0.00 0.00 0.00 2.27
2013 2022 7.386059 ACTGTTTTGGTCTGATTTGTCTTTTT 58.614 30.769 0.00 0.00 0.00 1.94
2029 2038 1.391577 TTTTTGCTGAGAGCTGCACA 58.608 45.000 1.02 0.00 46.64 4.57
2030 2039 1.612676 TTTTGCTGAGAGCTGCACAT 58.387 45.000 1.02 0.00 46.64 3.21
2031 2040 2.477845 TTTGCTGAGAGCTGCACATA 57.522 45.000 1.02 0.00 46.64 2.29
2032 2041 2.477845 TTGCTGAGAGCTGCACATAA 57.522 45.000 1.02 0.00 46.64 1.90
2033 2042 2.019948 TGCTGAGAGCTGCACATAAG 57.980 50.000 1.02 0.00 42.93 1.73
2034 2043 1.277273 TGCTGAGAGCTGCACATAAGT 59.723 47.619 1.02 0.00 42.93 2.24
2035 2044 1.932511 GCTGAGAGCTGCACATAAGTC 59.067 52.381 1.02 0.00 38.45 3.01
2036 2045 2.548875 CTGAGAGCTGCACATAAGTCC 58.451 52.381 1.02 0.00 0.00 3.85
2037 2046 1.208052 TGAGAGCTGCACATAAGTCCC 59.792 52.381 1.02 0.00 0.00 4.46
2038 2047 1.208052 GAGAGCTGCACATAAGTCCCA 59.792 52.381 1.02 0.00 0.00 4.37
2039 2048 1.630369 AGAGCTGCACATAAGTCCCAA 59.370 47.619 1.02 0.00 0.00 4.12
2040 2049 2.240667 AGAGCTGCACATAAGTCCCAAT 59.759 45.455 1.02 0.00 0.00 3.16
2041 2050 2.357009 GAGCTGCACATAAGTCCCAATG 59.643 50.000 1.02 0.00 0.00 2.82
2042 2051 2.094675 GCTGCACATAAGTCCCAATGT 58.905 47.619 0.00 0.00 36.78 2.71
2043 2052 2.493278 GCTGCACATAAGTCCCAATGTT 59.507 45.455 0.00 0.00 34.12 2.71
2044 2053 3.056607 GCTGCACATAAGTCCCAATGTTT 60.057 43.478 0.00 0.00 34.12 2.83
2045 2054 4.561326 GCTGCACATAAGTCCCAATGTTTT 60.561 41.667 0.00 0.00 34.12 2.43
2046 2055 4.880759 TGCACATAAGTCCCAATGTTTTG 58.119 39.130 0.00 0.00 34.12 2.44
2047 2056 4.586421 TGCACATAAGTCCCAATGTTTTGA 59.414 37.500 0.00 0.00 34.12 2.69
2048 2057 5.069648 TGCACATAAGTCCCAATGTTTTGAA 59.930 36.000 0.00 0.00 34.12 2.69
2049 2058 5.988561 GCACATAAGTCCCAATGTTTTGAAA 59.011 36.000 0.00 0.00 34.12 2.69
2050 2059 6.481644 GCACATAAGTCCCAATGTTTTGAAAA 59.518 34.615 0.00 0.00 34.12 2.29
2051 2060 7.173047 GCACATAAGTCCCAATGTTTTGAAAAT 59.827 33.333 0.00 0.00 34.12 1.82
2052 2061 9.054922 CACATAAGTCCCAATGTTTTGAAAATT 57.945 29.630 0.00 0.00 34.12 1.82
2053 2062 9.054922 ACATAAGTCCCAATGTTTTGAAAATTG 57.945 29.630 0.00 0.00 32.43 2.32
2054 2063 6.940831 AAGTCCCAATGTTTTGAAAATTGG 57.059 33.333 13.49 13.49 46.59 3.16
2057 2066 4.502171 CCAATGTTTTGAAAATTGGGGC 57.498 40.909 12.88 0.00 44.37 5.80
2058 2067 3.058363 CCAATGTTTTGAAAATTGGGGCG 60.058 43.478 12.88 0.00 44.37 6.13
2059 2068 1.587547 TGTTTTGAAAATTGGGGCGC 58.412 45.000 0.00 0.00 0.00 6.53
2060 2069 1.134401 TGTTTTGAAAATTGGGGCGCA 60.134 42.857 10.83 0.00 0.00 6.09
2061 2070 1.262950 GTTTTGAAAATTGGGGCGCAC 59.737 47.619 10.83 4.83 0.00 5.34
2062 2071 0.250081 TTTGAAAATTGGGGCGCACC 60.250 50.000 25.59 25.59 39.11 5.01
2063 2072 1.118356 TTGAAAATTGGGGCGCACCT 61.118 50.000 32.18 9.19 40.03 4.00
2064 2073 1.215382 GAAAATTGGGGCGCACCTC 59.785 57.895 32.18 15.41 40.03 3.85
2074 2083 3.252964 CGCACCTCACGCATCAAA 58.747 55.556 0.00 0.00 0.00 2.69
2075 2084 1.796151 CGCACCTCACGCATCAAAT 59.204 52.632 0.00 0.00 0.00 2.32
2076 2085 0.168788 CGCACCTCACGCATCAAATT 59.831 50.000 0.00 0.00 0.00 1.82
2077 2086 1.621107 GCACCTCACGCATCAAATTG 58.379 50.000 0.00 0.00 0.00 2.32
2078 2087 1.068333 GCACCTCACGCATCAAATTGT 60.068 47.619 0.00 0.00 0.00 2.71
2079 2088 2.855180 CACCTCACGCATCAAATTGTC 58.145 47.619 0.00 0.00 0.00 3.18
2080 2089 1.812571 ACCTCACGCATCAAATTGTCC 59.187 47.619 0.00 0.00 0.00 4.02
2081 2090 1.811965 CCTCACGCATCAAATTGTCCA 59.188 47.619 0.00 0.00 0.00 4.02
2082 2091 2.414559 CCTCACGCATCAAATTGTCCAC 60.415 50.000 0.00 0.00 0.00 4.02
2083 2092 1.539388 TCACGCATCAAATTGTCCACC 59.461 47.619 0.00 0.00 0.00 4.61
2084 2093 1.269174 CACGCATCAAATTGTCCACCA 59.731 47.619 0.00 0.00 0.00 4.17
2085 2094 1.269448 ACGCATCAAATTGTCCACCAC 59.731 47.619 0.00 0.00 0.00 4.16
2086 2095 1.402720 CGCATCAAATTGTCCACCACC 60.403 52.381 0.00 0.00 0.00 4.61
2087 2096 1.895131 GCATCAAATTGTCCACCACCT 59.105 47.619 0.00 0.00 0.00 4.00
2088 2097 2.094545 GCATCAAATTGTCCACCACCTC 60.095 50.000 0.00 0.00 0.00 3.85
2089 2098 3.156293 CATCAAATTGTCCACCACCTCA 58.844 45.455 0.00 0.00 0.00 3.86
2090 2099 3.304911 TCAAATTGTCCACCACCTCAA 57.695 42.857 0.00 0.00 0.00 3.02
2091 2100 3.843422 TCAAATTGTCCACCACCTCAAT 58.157 40.909 0.00 0.00 32.86 2.57
2092 2101 4.222336 TCAAATTGTCCACCACCTCAATT 58.778 39.130 0.00 0.00 40.62 2.32
2093 2102 4.653341 TCAAATTGTCCACCACCTCAATTT 59.347 37.500 8.31 8.31 45.25 1.82
2094 2103 5.130145 TCAAATTGTCCACCACCTCAATTTT 59.870 36.000 10.59 0.00 43.34 1.82
2095 2104 5.628797 AATTGTCCACCACCTCAATTTTT 57.371 34.783 0.00 0.00 37.25 1.94
2156 2165 2.791383 TTTTTGAACGGGTGCAGATG 57.209 45.000 0.00 0.00 0.00 2.90
2157 2166 0.313672 TTTTGAACGGGTGCAGATGC 59.686 50.000 0.00 0.00 42.50 3.91
2182 2191 4.072088 CACCGAAACGCCGCACTC 62.072 66.667 0.00 0.00 0.00 3.51
2183 2192 4.595538 ACCGAAACGCCGCACTCA 62.596 61.111 0.00 0.00 0.00 3.41
2184 2193 3.118454 CCGAAACGCCGCACTCAT 61.118 61.111 0.00 0.00 0.00 2.90
2185 2194 2.096406 CGAAACGCCGCACTCATG 59.904 61.111 0.00 0.00 0.00 3.07
2186 2195 2.667318 CGAAACGCCGCACTCATGT 61.667 57.895 0.00 0.00 0.00 3.21
2187 2196 1.348538 CGAAACGCCGCACTCATGTA 61.349 55.000 0.00 0.00 0.00 2.29
2188 2197 1.006832 GAAACGCCGCACTCATGTAT 58.993 50.000 0.00 0.00 0.00 2.29
2189 2198 2.198406 GAAACGCCGCACTCATGTATA 58.802 47.619 0.00 0.00 0.00 1.47
2190 2199 2.526304 AACGCCGCACTCATGTATAT 57.474 45.000 0.00 0.00 0.00 0.86
2191 2200 1.783284 ACGCCGCACTCATGTATATG 58.217 50.000 0.00 0.00 35.57 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 195 8.250332 GCCAAAAGAAGATGGACAATAACATTA 58.750 33.333 0.00 0.00 39.12 1.90
400 404 2.903784 TGTATGCAGTGTACCCTTCACT 59.096 45.455 0.00 0.00 45.43 3.41
508 512 3.451540 ACCGCCCAAGTTTTTAAAAAGGA 59.548 39.130 13.58 0.00 0.00 3.36
586 590 7.324178 TCAAAACCTCTCTAGAGAACAATAGC 58.676 38.462 22.54 0.00 44.74 2.97
612 616 4.702131 AGGTTTTGATACATCAACTGCTCC 59.298 41.667 4.14 3.92 45.63 4.70
630 635 7.784470 ACAGTAGAGTATGAAGAAGAGGTTT 57.216 36.000 0.00 0.00 0.00 3.27
660 665 3.881688 AGCTATGTCAAACCAGCATGATC 59.118 43.478 0.00 0.00 39.69 2.92
674 679 4.423625 AATTAGTGACCCCAGCTATGTC 57.576 45.455 0.00 0.00 0.00 3.06
699 704 9.741647 AATCAAGAACTTCAAGATTTTGAGTTC 57.258 29.630 20.94 20.94 43.76 3.01
732 737 5.537674 ACCGAGTTTAGACTGGAAGAACTAA 59.462 40.000 8.30 0.00 35.88 2.24
748 753 4.436332 ACTTTCAAGACGTAACCGAGTTT 58.564 39.130 0.00 0.00 37.88 2.66
769 774 5.631512 TGCACAAAAACAAGTCAGTACAAAC 59.368 36.000 0.00 0.00 0.00 2.93
819 824 8.954834 TTAGGCCATGATATATGGTTTTTCAT 57.045 30.769 5.01 0.00 41.17 2.57
1041 1050 1.270907 AGATCTCCTTCACCACGCTT 58.729 50.000 0.00 0.00 0.00 4.68
1207 1216 5.941058 AGACTTCGAGATGTAGAACTTCTGA 59.059 40.000 1.17 0.00 33.42 3.27
1340 1349 6.822676 ACAGAAAGCAAATTCAAAATGGTTCA 59.177 30.769 0.00 0.00 34.01 3.18
1362 1371 7.702348 TGAGACAAGACATATTTGATACGACAG 59.298 37.037 0.00 0.00 0.00 3.51
1483 1492 4.070716 CCACCATTGCATTAAGCCAAAAA 58.929 39.130 0.00 0.00 44.83 1.94
1644 1653 2.681152 ATGAAAACGACGGTGAAAGC 57.319 45.000 0.00 0.00 0.00 3.51
1662 1671 6.823689 AGAAAACTAAACTCATGACCGCATAT 59.176 34.615 0.00 0.00 32.27 1.78
1757 1766 7.742556 TGGATTTTCGCATATACATCATCAA 57.257 32.000 0.00 0.00 0.00 2.57
1760 1769 9.017509 AGATTTGGATTTTCGCATATACATCAT 57.982 29.630 0.00 0.00 0.00 2.45
1771 1780 2.480244 GGGCTCAGATTTGGATTTTCGC 60.480 50.000 0.00 0.00 0.00 4.70
1772 1781 2.223340 CGGGCTCAGATTTGGATTTTCG 60.223 50.000 0.00 0.00 0.00 3.46
1773 1782 3.016736 TCGGGCTCAGATTTGGATTTTC 58.983 45.455 0.00 0.00 0.00 2.29
1774 1783 3.019564 CTCGGGCTCAGATTTGGATTTT 58.980 45.455 0.00 0.00 0.00 1.82
1775 1784 2.648059 CTCGGGCTCAGATTTGGATTT 58.352 47.619 0.00 0.00 0.00 2.17
1776 1785 1.748591 GCTCGGGCTCAGATTTGGATT 60.749 52.381 0.00 0.00 35.22 3.01
1777 1786 0.179034 GCTCGGGCTCAGATTTGGAT 60.179 55.000 0.00 0.00 35.22 3.41
1778 1787 1.221840 GCTCGGGCTCAGATTTGGA 59.778 57.895 0.00 0.00 35.22 3.53
1779 1788 3.819188 GCTCGGGCTCAGATTTGG 58.181 61.111 0.00 0.00 35.22 3.28
1789 1798 2.894387 GTGCAGATGAGCTCGGGC 60.894 66.667 9.64 0.00 39.06 6.13
1790 1799 2.202987 GGTGCAGATGAGCTCGGG 60.203 66.667 9.64 0.00 34.99 5.14
1791 1800 1.521010 CAGGTGCAGATGAGCTCGG 60.521 63.158 9.64 0.00 34.99 4.63
1792 1801 2.172372 GCAGGTGCAGATGAGCTCG 61.172 63.158 9.64 0.00 41.59 5.03
1793 1802 2.172372 CGCAGGTGCAGATGAGCTC 61.172 63.158 6.82 6.82 42.21 4.09
1794 1803 2.125229 CGCAGGTGCAGATGAGCT 60.125 61.111 2.33 0.00 42.21 4.09
1795 1804 3.873883 GCGCAGGTGCAGATGAGC 61.874 66.667 0.30 10.34 42.21 4.26
1796 1805 2.125229 AGCGCAGGTGCAGATGAG 60.125 61.111 11.47 0.18 42.21 2.90
1797 1806 2.125391 GAGCGCAGGTGCAGATGA 60.125 61.111 11.47 0.00 39.88 2.92
1798 1807 2.435410 TGAGCGCAGGTGCAGATG 60.435 61.111 11.47 0.00 39.88 2.90
1799 1808 2.435586 GTGAGCGCAGGTGCAGAT 60.436 61.111 11.47 0.00 39.88 2.90
1800 1809 4.687215 GGTGAGCGCAGGTGCAGA 62.687 66.667 11.47 0.00 39.88 4.26
1801 1810 4.994471 TGGTGAGCGCAGGTGCAG 62.994 66.667 11.47 0.00 39.88 4.41
1802 1811 4.560743 TTGGTGAGCGCAGGTGCA 62.561 61.111 11.47 0.00 39.88 4.57
1803 1812 2.348605 TTTTTGGTGAGCGCAGGTGC 62.349 55.000 11.47 0.00 39.88 5.01
1804 1813 1.732917 TTTTTGGTGAGCGCAGGTG 59.267 52.632 11.47 0.00 39.88 4.00
1805 1814 4.251246 TTTTTGGTGAGCGCAGGT 57.749 50.000 11.47 0.00 46.54 4.00
1862 1871 4.787135 ATTGTTCACCACCCCAATTTTT 57.213 36.364 0.00 0.00 0.00 1.94
1863 1872 4.787135 AATTGTTCACCACCCCAATTTT 57.213 36.364 0.00 0.00 34.73 1.82
1864 1873 4.164988 TCAAATTGTTCACCACCCCAATTT 59.835 37.500 0.00 0.00 44.18 1.82
1865 1874 3.713764 TCAAATTGTTCACCACCCCAATT 59.286 39.130 0.00 0.00 38.72 2.32
1866 1875 3.312890 TCAAATTGTTCACCACCCCAAT 58.687 40.909 0.00 0.00 0.00 3.16
1867 1876 2.752030 TCAAATTGTTCACCACCCCAA 58.248 42.857 0.00 0.00 0.00 4.12
1868 1877 2.461300 TCAAATTGTTCACCACCCCA 57.539 45.000 0.00 0.00 0.00 4.96
1869 1878 2.632512 ACATCAAATTGTTCACCACCCC 59.367 45.455 0.00 0.00 0.00 4.95
1870 1879 3.069443 ACACATCAAATTGTTCACCACCC 59.931 43.478 0.00 0.00 0.00 4.61
1871 1880 4.050553 CACACATCAAATTGTTCACCACC 58.949 43.478 0.00 0.00 0.00 4.61
1872 1881 4.930963 TCACACATCAAATTGTTCACCAC 58.069 39.130 0.00 0.00 0.00 4.16
1873 1882 4.037803 CCTCACACATCAAATTGTTCACCA 59.962 41.667 0.00 0.00 0.00 4.17
1874 1883 4.037923 ACCTCACACATCAAATTGTTCACC 59.962 41.667 0.00 0.00 0.00 4.02
1875 1884 4.977963 CACCTCACACATCAAATTGTTCAC 59.022 41.667 0.00 0.00 0.00 3.18
1876 1885 4.499526 GCACCTCACACATCAAATTGTTCA 60.500 41.667 0.00 0.00 0.00 3.18
1877 1886 3.983344 GCACCTCACACATCAAATTGTTC 59.017 43.478 0.00 0.00 0.00 3.18
1878 1887 3.550639 CGCACCTCACACATCAAATTGTT 60.551 43.478 0.00 0.00 0.00 2.83
1879 1888 2.030893 CGCACCTCACACATCAAATTGT 60.031 45.455 0.00 0.00 0.00 2.71
1880 1889 2.587956 CGCACCTCACACATCAAATTG 58.412 47.619 0.00 0.00 0.00 2.32
1881 1890 1.068333 GCGCACCTCACACATCAAATT 60.068 47.619 0.30 0.00 0.00 1.82
1882 1891 0.523072 GCGCACCTCACACATCAAAT 59.477 50.000 0.30 0.00 0.00 2.32
1883 1892 1.514678 GGCGCACCTCACACATCAAA 61.515 55.000 10.83 0.00 0.00 2.69
1884 1893 1.965930 GGCGCACCTCACACATCAA 60.966 57.895 10.83 0.00 0.00 2.57
1885 1894 2.358615 GGCGCACCTCACACATCA 60.359 61.111 10.83 0.00 0.00 3.07
1886 1895 3.127533 GGGCGCACCTCACACATC 61.128 66.667 10.83 0.00 35.85 3.06
1887 1896 4.722700 GGGGCGCACCTCACACAT 62.723 66.667 24.98 0.00 35.91 3.21
1893 1902 1.215382 GAAAATTGGGGCGCACCTC 59.785 57.895 32.18 15.41 40.03 3.85
1894 1903 1.118356 TTGAAAATTGGGGCGCACCT 61.118 50.000 32.18 9.19 40.03 4.00
1895 1904 0.250081 TTTGAAAATTGGGGCGCACC 60.250 50.000 25.59 25.59 39.11 5.01
1896 1905 1.262950 GTTTTGAAAATTGGGGCGCAC 59.737 47.619 10.83 4.83 0.00 5.34
1897 1906 1.134401 TGTTTTGAAAATTGGGGCGCA 60.134 42.857 10.83 0.00 0.00 6.09
1898 1907 1.587547 TGTTTTGAAAATTGGGGCGC 58.412 45.000 0.00 0.00 0.00 6.53
1899 1908 4.535116 CAAATGTTTTGAAAATTGGGGCG 58.465 39.130 0.00 0.00 0.00 6.13
1900 1909 4.582240 TCCAAATGTTTTGAAAATTGGGGC 59.418 37.500 16.94 0.00 38.25 5.80
1901 1910 5.827267 AGTCCAAATGTTTTGAAAATTGGGG 59.173 36.000 16.94 6.77 38.25 4.96
1902 1911 6.940831 AGTCCAAATGTTTTGAAAATTGGG 57.059 33.333 16.94 6.43 38.25 4.12
1903 1912 9.881529 CATAAGTCCAAATGTTTTGAAAATTGG 57.118 29.630 12.90 12.90 38.88 3.16
1906 1915 8.558700 GCACATAAGTCCAAATGTTTTGAAAAT 58.441 29.630 0.00 0.00 34.12 1.82
1907 1916 7.550551 TGCACATAAGTCCAAATGTTTTGAAAA 59.449 29.630 1.65 0.00 34.12 2.29
1908 1917 7.044181 TGCACATAAGTCCAAATGTTTTGAAA 58.956 30.769 1.65 0.00 34.12 2.69
1909 1918 6.577103 TGCACATAAGTCCAAATGTTTTGAA 58.423 32.000 1.65 0.00 34.12 2.69
1910 1919 6.154203 TGCACATAAGTCCAAATGTTTTGA 57.846 33.333 1.65 0.00 34.12 2.69
1911 1920 5.107375 GCTGCACATAAGTCCAAATGTTTTG 60.107 40.000 0.00 0.00 34.12 2.44
1912 1921 4.990426 GCTGCACATAAGTCCAAATGTTTT 59.010 37.500 0.00 0.00 34.12 2.43
1913 1922 4.281688 AGCTGCACATAAGTCCAAATGTTT 59.718 37.500 1.02 0.00 34.12 2.83
1914 1923 3.828451 AGCTGCACATAAGTCCAAATGTT 59.172 39.130 1.02 0.00 34.12 2.71
1915 1924 3.424703 AGCTGCACATAAGTCCAAATGT 58.575 40.909 1.02 0.00 36.78 2.71
1916 1925 3.693085 AGAGCTGCACATAAGTCCAAATG 59.307 43.478 1.02 0.00 0.00 2.32
1917 1926 3.960571 AGAGCTGCACATAAGTCCAAAT 58.039 40.909 1.02 0.00 0.00 2.32
1918 1927 3.423539 AGAGCTGCACATAAGTCCAAA 57.576 42.857 1.02 0.00 0.00 3.28
1919 1928 3.423539 AAGAGCTGCACATAAGTCCAA 57.576 42.857 1.02 0.00 0.00 3.53
1920 1929 3.679917 GCTAAGAGCTGCACATAAGTCCA 60.680 47.826 1.02 0.00 38.45 4.02
1921 1930 2.869192 GCTAAGAGCTGCACATAAGTCC 59.131 50.000 1.02 0.00 38.45 3.85
1922 1931 3.525537 TGCTAAGAGCTGCACATAAGTC 58.474 45.455 1.02 0.00 42.97 3.01
1923 1932 3.616956 TGCTAAGAGCTGCACATAAGT 57.383 42.857 1.02 0.00 42.97 2.24
1924 1933 4.952262 TTTGCTAAGAGCTGCACATAAG 57.048 40.909 1.02 0.00 42.97 1.73
1925 1934 5.703978 TTTTTGCTAAGAGCTGCACATAA 57.296 34.783 1.02 0.00 42.97 1.90
1944 1953 4.461198 ACAGACCTCCGATTTGTCTTTTT 58.539 39.130 0.00 0.00 37.25 1.94
1945 1954 4.086706 ACAGACCTCCGATTTGTCTTTT 57.913 40.909 0.00 0.00 37.25 2.27
1946 1955 3.771577 ACAGACCTCCGATTTGTCTTT 57.228 42.857 0.00 0.00 37.25 2.52
1947 1956 4.884668 TTACAGACCTCCGATTTGTCTT 57.115 40.909 0.00 0.00 37.25 3.01
1948 1957 4.884668 TTTACAGACCTCCGATTTGTCT 57.115 40.909 0.00 0.00 39.86 3.41
1949 1958 5.934935 TTTTTACAGACCTCCGATTTGTC 57.065 39.130 0.00 0.00 0.00 3.18
1950 1959 5.768164 ACATTTTTACAGACCTCCGATTTGT 59.232 36.000 0.00 0.00 0.00 2.83
1951 1960 6.086222 CACATTTTTACAGACCTCCGATTTG 58.914 40.000 0.00 0.00 0.00 2.32
1952 1961 5.768164 ACACATTTTTACAGACCTCCGATTT 59.232 36.000 0.00 0.00 0.00 2.17
1953 1962 5.313712 ACACATTTTTACAGACCTCCGATT 58.686 37.500 0.00 0.00 0.00 3.34
1954 1963 4.906618 ACACATTTTTACAGACCTCCGAT 58.093 39.130 0.00 0.00 0.00 4.18
1955 1964 4.345859 ACACATTTTTACAGACCTCCGA 57.654 40.909 0.00 0.00 0.00 4.55
1956 1965 5.120208 CAGTACACATTTTTACAGACCTCCG 59.880 44.000 0.00 0.00 0.00 4.63
1957 1966 5.995897 ACAGTACACATTTTTACAGACCTCC 59.004 40.000 0.00 0.00 0.00 4.30
1958 1967 7.225931 TGAACAGTACACATTTTTACAGACCTC 59.774 37.037 0.00 0.00 0.00 3.85
1959 1968 7.051623 TGAACAGTACACATTTTTACAGACCT 58.948 34.615 0.00 0.00 0.00 3.85
1960 1969 7.254227 TGAACAGTACACATTTTTACAGACC 57.746 36.000 0.00 0.00 0.00 3.85
1971 1980 8.946085 CCAAAACAGTATATGAACAGTACACAT 58.054 33.333 0.00 0.00 0.00 3.21
1972 1981 7.934665 ACCAAAACAGTATATGAACAGTACACA 59.065 33.333 0.00 0.00 0.00 3.72
1973 1982 8.319143 ACCAAAACAGTATATGAACAGTACAC 57.681 34.615 0.00 0.00 0.00 2.90
1974 1983 8.372459 AGACCAAAACAGTATATGAACAGTACA 58.628 33.333 0.00 0.00 0.00 2.90
1975 1984 8.656849 CAGACCAAAACAGTATATGAACAGTAC 58.343 37.037 0.00 0.00 0.00 2.73
1976 1985 8.590204 TCAGACCAAAACAGTATATGAACAGTA 58.410 33.333 0.00 0.00 0.00 2.74
1977 1986 7.450074 TCAGACCAAAACAGTATATGAACAGT 58.550 34.615 0.00 0.00 0.00 3.55
1978 1987 7.905604 TCAGACCAAAACAGTATATGAACAG 57.094 36.000 0.00 0.00 0.00 3.16
1979 1988 8.862325 AATCAGACCAAAACAGTATATGAACA 57.138 30.769 0.00 0.00 0.00 3.18
1980 1989 9.559958 CAAATCAGACCAAAACAGTATATGAAC 57.440 33.333 0.00 0.00 0.00 3.18
1981 1990 9.295825 ACAAATCAGACCAAAACAGTATATGAA 57.704 29.630 0.00 0.00 0.00 2.57
1982 1991 8.862325 ACAAATCAGACCAAAACAGTATATGA 57.138 30.769 0.00 0.00 0.00 2.15
1983 1992 8.950210 AGACAAATCAGACCAAAACAGTATATG 58.050 33.333 0.00 0.00 0.00 1.78
1984 1993 9.520515 AAGACAAATCAGACCAAAACAGTATAT 57.479 29.630 0.00 0.00 0.00 0.86
1985 1994 8.918202 AAGACAAATCAGACCAAAACAGTATA 57.082 30.769 0.00 0.00 0.00 1.47
1986 1995 7.823745 AAGACAAATCAGACCAAAACAGTAT 57.176 32.000 0.00 0.00 0.00 2.12
1987 1996 7.639113 AAAGACAAATCAGACCAAAACAGTA 57.361 32.000 0.00 0.00 0.00 2.74
1988 1997 6.530019 AAAGACAAATCAGACCAAAACAGT 57.470 33.333 0.00 0.00 0.00 3.55
1989 1998 7.832503 AAAAAGACAAATCAGACCAAAACAG 57.167 32.000 0.00 0.00 0.00 3.16
2010 2019 1.391577 TGTGCAGCTCTCAGCAAAAA 58.608 45.000 0.00 0.00 45.56 1.94
2011 2020 1.612676 ATGTGCAGCTCTCAGCAAAA 58.387 45.000 0.00 0.00 45.56 2.44
2012 2021 2.477845 TATGTGCAGCTCTCAGCAAA 57.522 45.000 0.00 0.00 45.56 3.68
2013 2022 2.289882 ACTTATGTGCAGCTCTCAGCAA 60.290 45.455 0.00 0.00 45.56 3.91
2014 2023 1.277273 ACTTATGTGCAGCTCTCAGCA 59.723 47.619 0.00 0.00 45.56 4.41
2015 2024 1.932511 GACTTATGTGCAGCTCTCAGC 59.067 52.381 0.00 0.00 42.84 4.26
2016 2025 2.548875 GGACTTATGTGCAGCTCTCAG 58.451 52.381 0.00 0.00 34.50 3.35
2017 2026 1.208052 GGGACTTATGTGCAGCTCTCA 59.792 52.381 2.74 0.00 36.16 3.27
2018 2027 1.208052 TGGGACTTATGTGCAGCTCTC 59.792 52.381 2.74 0.00 36.16 3.20
2019 2028 1.279496 TGGGACTTATGTGCAGCTCT 58.721 50.000 2.74 0.00 36.16 4.09
2020 2029 2.113860 TTGGGACTTATGTGCAGCTC 57.886 50.000 2.74 0.00 36.16 4.09
2021 2030 2.291153 ACATTGGGACTTATGTGCAGCT 60.291 45.455 2.74 0.00 36.16 4.24
2022 2031 2.094675 ACATTGGGACTTATGTGCAGC 58.905 47.619 2.74 0.00 36.16 5.25
2023 2032 4.789012 AAACATTGGGACTTATGTGCAG 57.211 40.909 2.74 0.00 35.29 4.41
2024 2033 4.586421 TCAAAACATTGGGACTTATGTGCA 59.414 37.500 2.74 0.00 35.29 4.57
2025 2034 5.132897 TCAAAACATTGGGACTTATGTGC 57.867 39.130 0.00 0.00 35.29 4.57
2026 2035 8.606040 ATTTTCAAAACATTGGGACTTATGTG 57.394 30.769 0.00 0.00 35.29 3.21
2027 2036 9.054922 CAATTTTCAAAACATTGGGACTTATGT 57.945 29.630 0.00 0.00 36.26 2.29
2028 2037 8.505625 CCAATTTTCAAAACATTGGGACTTATG 58.494 33.333 7.20 0.00 42.28 1.90
2029 2038 8.620116 CCAATTTTCAAAACATTGGGACTTAT 57.380 30.769 7.20 0.00 42.28 1.73
2031 2040 6.940831 CCAATTTTCAAAACATTGGGACTT 57.059 33.333 7.20 0.00 42.28 3.01
2036 2045 3.058363 CGCCCCAATTTTCAAAACATTGG 60.058 43.478 7.92 7.92 44.61 3.16
2037 2046 3.608941 GCGCCCCAATTTTCAAAACATTG 60.609 43.478 0.00 0.00 0.00 2.82
2038 2047 2.551887 GCGCCCCAATTTTCAAAACATT 59.448 40.909 0.00 0.00 0.00 2.71
2039 2048 2.150390 GCGCCCCAATTTTCAAAACAT 58.850 42.857 0.00 0.00 0.00 2.71
2040 2049 1.134401 TGCGCCCCAATTTTCAAAACA 60.134 42.857 4.18 0.00 0.00 2.83
2041 2050 1.262950 GTGCGCCCCAATTTTCAAAAC 59.737 47.619 4.18 0.00 0.00 2.43
2042 2051 1.587547 GTGCGCCCCAATTTTCAAAA 58.412 45.000 4.18 0.00 0.00 2.44
2043 2052 0.250081 GGTGCGCCCCAATTTTCAAA 60.250 50.000 3.18 0.00 0.00 2.69
2044 2053 1.118356 AGGTGCGCCCCAATTTTCAA 61.118 50.000 12.68 0.00 34.57 2.69
2045 2054 1.531739 GAGGTGCGCCCCAATTTTCA 61.532 55.000 12.68 0.00 34.57 2.69
2046 2055 1.215382 GAGGTGCGCCCCAATTTTC 59.785 57.895 12.68 0.00 34.57 2.29
2047 2056 1.532794 TGAGGTGCGCCCCAATTTT 60.533 52.632 12.68 0.00 34.57 1.82
2048 2057 2.117206 TGAGGTGCGCCCCAATTT 59.883 55.556 12.68 0.00 34.57 1.82
2049 2058 2.676471 GTGAGGTGCGCCCCAATT 60.676 61.111 12.68 0.00 34.57 2.32
2057 2066 0.168788 AATTTGATGCGTGAGGTGCG 59.831 50.000 0.00 0.00 34.24 5.34
2058 2067 1.068333 ACAATTTGATGCGTGAGGTGC 60.068 47.619 2.79 0.00 0.00 5.01
2059 2068 2.414559 GGACAATTTGATGCGTGAGGTG 60.415 50.000 2.79 0.00 0.00 4.00
2060 2069 1.812571 GGACAATTTGATGCGTGAGGT 59.187 47.619 2.79 0.00 0.00 3.85
2061 2070 1.811965 TGGACAATTTGATGCGTGAGG 59.188 47.619 2.79 0.00 0.00 3.86
2062 2071 2.414559 GGTGGACAATTTGATGCGTGAG 60.415 50.000 2.79 0.00 0.00 3.51
2063 2072 1.539388 GGTGGACAATTTGATGCGTGA 59.461 47.619 2.79 0.00 0.00 4.35
2064 2073 1.269174 TGGTGGACAATTTGATGCGTG 59.731 47.619 2.79 0.00 0.00 5.34
2065 2074 1.269448 GTGGTGGACAATTTGATGCGT 59.731 47.619 2.79 0.00 0.00 5.24
2066 2075 1.402720 GGTGGTGGACAATTTGATGCG 60.403 52.381 2.79 0.00 0.00 4.73
2067 2076 1.895131 AGGTGGTGGACAATTTGATGC 59.105 47.619 2.79 0.00 0.00 3.91
2068 2077 3.156293 TGAGGTGGTGGACAATTTGATG 58.844 45.455 2.79 0.00 0.00 3.07
2069 2078 3.524095 TGAGGTGGTGGACAATTTGAT 57.476 42.857 2.79 0.00 0.00 2.57
2070 2079 3.304911 TTGAGGTGGTGGACAATTTGA 57.695 42.857 2.79 0.00 0.00 2.69
2071 2080 4.605640 AATTGAGGTGGTGGACAATTTG 57.394 40.909 0.00 0.00 39.03 2.32
2073 2082 5.628797 AAAAATTGAGGTGGTGGACAATT 57.371 34.783 0.00 0.00 42.25 2.32
2137 2146 1.269517 GCATCTGCACCCGTTCAAAAA 60.270 47.619 0.00 0.00 41.59 1.94
2138 2147 0.313672 GCATCTGCACCCGTTCAAAA 59.686 50.000 0.00 0.00 41.59 2.44
2139 2148 1.956043 GCATCTGCACCCGTTCAAA 59.044 52.632 0.00 0.00 41.59 2.69
2140 2149 3.667087 GCATCTGCACCCGTTCAA 58.333 55.556 0.00 0.00 41.59 2.69
2165 2174 4.072088 GAGTGCGGCGTTTCGGTG 62.072 66.667 9.37 0.00 0.00 4.94
2166 2175 3.876589 ATGAGTGCGGCGTTTCGGT 62.877 57.895 9.37 0.00 0.00 4.69
2167 2176 3.118454 ATGAGTGCGGCGTTTCGG 61.118 61.111 9.37 0.00 0.00 4.30
2168 2177 1.348538 TACATGAGTGCGGCGTTTCG 61.349 55.000 9.37 0.00 0.00 3.46
2169 2178 1.006832 ATACATGAGTGCGGCGTTTC 58.993 50.000 9.37 4.59 0.00 2.78
2170 2179 2.303163 TATACATGAGTGCGGCGTTT 57.697 45.000 9.37 0.00 0.00 3.60
2171 2180 2.135139 CATATACATGAGTGCGGCGTT 58.865 47.619 9.37 0.00 33.67 4.84
2172 2181 1.783284 CATATACATGAGTGCGGCGT 58.217 50.000 9.37 0.00 33.67 5.68


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

AutoCloner maintained by Alex Coulton.