Multiple sequence alignment - TraesCS5B01G410700

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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 TraesCS5B01G410700 chr5B 100.000 2267 0 0 1 2267 586297995 586295729 0.000000e+00 4187.0
1 TraesCS5B01G410700 chr1D 92.299 1792 123 8 1 1779 92054252 92056041 0.000000e+00 2531.0
2 TraesCS5B01G410700 chr1D 75.723 173 27 12 2093 2263 392035362 392035521 3.120000e-09 73.1
3 TraesCS5B01G410700 chr1D 76.119 134 20 10 2140 2265 427305564 427305693 2.430000e-05 60.2
4 TraesCS5B01G410700 chr1D 83.607 61 8 2 2206 2265 92056236 92056295 3.150000e-04 56.5
5 TraesCS5B01G410700 chr2B 92.114 1788 132 4 1 1779 747523229 747525016 0.000000e+00 2512.0
6 TraesCS5B01G410700 chr2B 88.956 1820 165 22 3 1813 655221595 655219803 0.000000e+00 2215.0
7 TraesCS5B01G410700 chr2B 84.085 377 48 9 1897 2264 747535992 747536365 9.960000e-94 353.0
8 TraesCS5B01G410700 chr7D 91.918 1794 121 12 1 1779 411315788 411314004 0.000000e+00 2488.0
9 TraesCS5B01G410700 chr7D 78.358 134 21 6 2140 2267 226109481 226109612 1.870000e-11 80.5
10 TraesCS5B01G410700 chr7D 77.099 131 15 13 2140 2265 173029012 173028892 6.760000e-06 62.1
11 TraesCS5B01G410700 chr5D 91.750 1794 123 13 1 1779 522787157 522788940 0.000000e+00 2470.0
12 TraesCS5B01G410700 chr5D 90.635 1794 120 18 1 1779 517098994 517100754 0.000000e+00 2338.0
13 TraesCS5B01G410700 chr5D 91.118 1216 93 7 449 1650 46684446 46683232 0.000000e+00 1633.0
14 TraesCS5B01G410700 chr3B 90.447 1790 145 15 7 1779 213720117 213718337 0.000000e+00 2335.0
15 TraesCS5B01G410700 chr3B 89.532 1796 138 24 1 1779 738417839 738419601 0.000000e+00 2230.0
16 TraesCS5B01G410700 chr3B 91.111 45 3 1 1876 1920 715193800 715193757 2.430000e-05 60.2
17 TraesCS5B01G410700 chr3D 89.186 1794 144 25 3 1786 536284170 536285923 0.000000e+00 2193.0
18 TraesCS5B01G410700 chr3D 88.734 1793 148 26 3 1786 16222356 16220609 0.000000e+00 2143.0
19 TraesCS5B01G410700 chr3D 75.723 173 27 11 2093 2263 89551110 89551269 3.120000e-09 73.1
20 TraesCS5B01G410700 chr7B 88.883 1790 163 15 1 1778 122756888 122758653 0.000000e+00 2170.0
21 TraesCS5B01G410700 chr7B 79.851 134 22 5 1895 2026 654077536 654077666 2.400000e-15 93.5
22 TraesCS5B01G410700 chr1B 91.069 1254 101 4 1 1249 425364730 425365977 0.000000e+00 1685.0
23 TraesCS5B01G410700 chr4A 91.042 960 83 3 1 959 692682101 692681144 0.000000e+00 1293.0
24 TraesCS5B01G410700 chr6D 81.343 134 17 4 2140 2267 364527419 364527550 3.980000e-18 102.0
25 TraesCS5B01G410700 chr2D 84.146 82 6 5 2190 2265 44508915 44508995 3.120000e-09 73.1
26 TraesCS5B01G410700 chr2D 100.000 28 0 0 2238 2265 50976766 50976739 4.000000e-03 52.8
27 TraesCS5B01G410700 chr6A 100.000 28 0 0 2238 2265 611911206 611911233 4.000000e-03 52.8


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 TraesCS5B01G410700 chr5B 586295729 586297995 2266 True 4187.00 4187 100.000 1 2267 1 chr5B.!!$R1 2266
1 TraesCS5B01G410700 chr1D 92054252 92056295 2043 False 1293.75 2531 87.953 1 2265 2 chr1D.!!$F3 2264
2 TraesCS5B01G410700 chr2B 747523229 747525016 1787 False 2512.00 2512 92.114 1 1779 1 chr2B.!!$F1 1778
3 TraesCS5B01G410700 chr2B 655219803 655221595 1792 True 2215.00 2215 88.956 3 1813 1 chr2B.!!$R1 1810
4 TraesCS5B01G410700 chr7D 411314004 411315788 1784 True 2488.00 2488 91.918 1 1779 1 chr7D.!!$R2 1778
5 TraesCS5B01G410700 chr5D 522787157 522788940 1783 False 2470.00 2470 91.750 1 1779 1 chr5D.!!$F2 1778
6 TraesCS5B01G410700 chr5D 517098994 517100754 1760 False 2338.00 2338 90.635 1 1779 1 chr5D.!!$F1 1778
7 TraesCS5B01G410700 chr5D 46683232 46684446 1214 True 1633.00 1633 91.118 449 1650 1 chr5D.!!$R1 1201
8 TraesCS5B01G410700 chr3B 213718337 213720117 1780 True 2335.00 2335 90.447 7 1779 1 chr3B.!!$R1 1772
9 TraesCS5B01G410700 chr3B 738417839 738419601 1762 False 2230.00 2230 89.532 1 1779 1 chr3B.!!$F1 1778
10 TraesCS5B01G410700 chr3D 536284170 536285923 1753 False 2193.00 2193 89.186 3 1786 1 chr3D.!!$F2 1783
11 TraesCS5B01G410700 chr3D 16220609 16222356 1747 True 2143.00 2143 88.734 3 1786 1 chr3D.!!$R1 1783
12 TraesCS5B01G410700 chr7B 122756888 122758653 1765 False 2170.00 2170 88.883 1 1778 1 chr7B.!!$F1 1777
13 TraesCS5B01G410700 chr1B 425364730 425365977 1247 False 1685.00 1685 91.069 1 1249 1 chr1B.!!$F1 1248
14 TraesCS5B01G410700 chr4A 692681144 692682101 957 True 1293.00 1293 91.042 1 959 1 chr4A.!!$R1 958

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
701 708 0.335361 GAGGAGGTAGGAGTGGTGGA 59.665 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2146 0.034337 TGAGCAACCCTACCGTTGTC 59.966 55.0 3.65 1.7 44.1 3.18 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
107 108 9.462174 TCACATCAACAAATCATTAGTTTCAAC 57.538 29.630 0.00 0.00 0.00 3.18
266 267 1.810853 CTCGCATGTGATGACCGCA 60.811 57.895 9.87 0.00 39.93 5.69
296 297 6.020041 GGTTTAGAATCTTGAACGTATCCGAC 60.020 42.308 0.00 0.00 37.88 4.79
297 298 4.713824 AGAATCTTGAACGTATCCGACA 57.286 40.909 0.00 0.00 37.88 4.35
301 302 4.611310 TCTTGAACGTATCCGACAGTAG 57.389 45.455 0.00 0.00 37.88 2.57
533 540 4.622260 ACAATTTGGTAGCAGCCATTTT 57.378 36.364 0.78 0.00 38.48 1.82
576 583 4.356405 AGTTGTGGTCAATGTGATGAGA 57.644 40.909 0.00 0.00 35.92 3.27
628 635 1.745115 CACGGACCGATGCCAACAT 60.745 57.895 23.38 0.00 39.98 2.71
701 708 0.335361 GAGGAGGTAGGAGTGGTGGA 59.665 60.000 0.00 0.00 0.00 4.02
720 727 4.292178 GCGGAGGATGAGGAGGCG 62.292 72.222 0.00 0.00 0.00 5.52
729 736 1.416401 GATGAGGAGGCGGTATTGGAA 59.584 52.381 0.00 0.00 0.00 3.53
779 786 1.834263 AGTGGACAAGGAGGCACTATC 59.166 52.381 0.00 0.00 41.55 2.08
815 822 1.752683 GGTCGACTCTTAGAGGAGCA 58.247 55.000 16.46 0.00 36.87 4.26
819 826 2.504585 TCGACTCTTAGAGGAGCAGGTA 59.495 50.000 14.24 0.00 36.87 3.08
870 877 2.918712 AGGAAGGCCTATTGACATCG 57.081 50.000 5.16 0.00 44.74 3.84
905 913 6.616947 GGATGGTTGAAATAATGTGAACGAA 58.383 36.000 0.00 0.00 0.00 3.85
982 1007 9.469807 CATGTTATTTTACTTTGCTAACAACCA 57.530 29.630 0.00 0.00 36.29 3.67
1059 1086 2.573869 CGCGAGGATATGCCGGAT 59.426 61.111 5.05 0.00 43.43 4.18
1062 1089 1.403647 CGCGAGGATATGCCGGATAAA 60.404 52.381 5.05 0.00 43.43 1.40
1194 1221 8.992349 TCATGGACAGAAGGAAGAAGATATTTA 58.008 33.333 0.00 0.00 0.00 1.40
1219 1247 5.387113 TTGTCCCAACTATGCCTATGATT 57.613 39.130 0.00 0.00 0.00 2.57
1376 1408 5.763204 CCACTTTGTAAGTACTTCACATGGT 59.237 40.000 12.39 12.27 40.46 3.55
1438 1476 3.300388 TCGAGATTGTCTAAGGAGGCAT 58.700 45.455 0.00 0.00 37.09 4.40
1450 1488 1.372087 GGAGGCATCGGCTGTTTGAG 61.372 60.000 0.00 0.00 38.98 3.02
1523 1563 0.388649 GCGAAAGAAGCGTGAGGAGA 60.389 55.000 0.00 0.00 0.00 3.71
1612 1660 1.489649 CAAGAGGAGGATGAGGCATGT 59.510 52.381 0.00 0.00 0.00 3.21
1618 1666 2.422519 GGAGGATGAGGCATGTGACAAT 60.423 50.000 0.00 0.00 0.00 2.71
1787 1903 8.932945 TTGAGATGAACTATGTCATGAACTAC 57.067 34.615 0.00 0.00 38.68 2.73
1794 1910 9.936759 TGAACTATGTCATGAACTACATTTGTA 57.063 29.630 0.00 0.00 37.50 2.41
1800 1916 8.785329 TGTCATGAACTACATTTGTATTGCTA 57.215 30.769 0.00 0.00 37.07 3.49
1814 1930 6.875948 TGTATTGCTATTGTTGTGACTTGT 57.124 33.333 0.00 0.00 0.00 3.16
1815 1931 7.270757 TGTATTGCTATTGTTGTGACTTGTT 57.729 32.000 0.00 0.00 0.00 2.83
1817 1933 7.647318 TGTATTGCTATTGTTGTGACTTGTTTG 59.353 33.333 0.00 0.00 0.00 2.93
1818 1934 5.574891 TGCTATTGTTGTGACTTGTTTGT 57.425 34.783 0.00 0.00 0.00 2.83
1820 1936 6.393990 TGCTATTGTTGTGACTTGTTTGTTT 58.606 32.000 0.00 0.00 0.00 2.83
1821 1937 6.309980 TGCTATTGTTGTGACTTGTTTGTTTG 59.690 34.615 0.00 0.00 0.00 2.93
1822 1938 6.237808 GCTATTGTTGTGACTTGTTTGTTTGG 60.238 38.462 0.00 0.00 0.00 3.28
1823 1939 3.321497 TGTTGTGACTTGTTTGTTTGGC 58.679 40.909 0.00 0.00 0.00 4.52
1824 1940 3.006323 TGTTGTGACTTGTTTGTTTGGCT 59.994 39.130 0.00 0.00 0.00 4.75
1825 1941 3.951775 TGTGACTTGTTTGTTTGGCTT 57.048 38.095 0.00 0.00 0.00 4.35
1826 1942 3.583806 TGTGACTTGTTTGTTTGGCTTG 58.416 40.909 0.00 0.00 0.00 4.01
1828 1944 3.612423 GTGACTTGTTTGTTTGGCTTGTC 59.388 43.478 0.00 0.00 0.00 3.18
1829 1945 3.509575 TGACTTGTTTGTTTGGCTTGTCT 59.490 39.130 0.00 0.00 0.00 3.41
1830 1946 3.848726 ACTTGTTTGTTTGGCTTGTCTG 58.151 40.909 0.00 0.00 0.00 3.51
1831 1947 3.509575 ACTTGTTTGTTTGGCTTGTCTGA 59.490 39.130 0.00 0.00 0.00 3.27
1832 1948 4.021544 ACTTGTTTGTTTGGCTTGTCTGAA 60.022 37.500 0.00 0.00 0.00 3.02
1833 1949 4.527509 TGTTTGTTTGGCTTGTCTGAAA 57.472 36.364 0.00 0.00 0.00 2.69
1834 1950 4.241681 TGTTTGTTTGGCTTGTCTGAAAC 58.758 39.130 0.00 0.00 0.00 2.78
1835 1951 2.842208 TGTTTGGCTTGTCTGAAACG 57.158 45.000 0.00 0.00 32.12 3.60
1836 1952 1.403679 TGTTTGGCTTGTCTGAAACGG 59.596 47.619 0.00 0.00 32.12 4.44
1837 1953 1.404035 GTTTGGCTTGTCTGAAACGGT 59.596 47.619 0.00 0.00 0.00 4.83
1838 1954 1.021202 TTGGCTTGTCTGAAACGGTG 58.979 50.000 0.00 0.00 0.00 4.94
1839 1955 0.179234 TGGCTTGTCTGAAACGGTGA 59.821 50.000 0.00 0.00 0.00 4.02
1841 1957 1.264288 GGCTTGTCTGAAACGGTGAAG 59.736 52.381 0.00 0.00 0.00 3.02
1844 1960 2.526304 TGTCTGAAACGGTGAAGGAG 57.474 50.000 0.00 0.00 0.00 3.69
1856 1972 3.630312 CGGTGAAGGAGGAAGAAAAACAA 59.370 43.478 0.00 0.00 0.00 2.83
1859 1975 5.043903 GTGAAGGAGGAAGAAAAACAAAGC 58.956 41.667 0.00 0.00 0.00 3.51
1865 1981 5.874810 GGAGGAAGAAAAACAAAGCAAACTT 59.125 36.000 0.00 0.00 37.90 2.66
1867 1983 7.364522 AGGAAGAAAAACAAAGCAAACTTTC 57.635 32.000 0.00 0.00 44.41 2.62
1868 1984 7.161404 AGGAAGAAAAACAAAGCAAACTTTCT 58.839 30.769 0.00 0.00 44.41 2.52
1870 1986 8.289618 GGAAGAAAAACAAAGCAAACTTTCTTT 58.710 29.630 8.52 0.00 44.41 2.52
1871 1987 9.663904 GAAGAAAAACAAAGCAAACTTTCTTTT 57.336 25.926 8.52 7.23 44.41 2.27
1881 1997 3.982576 AACTTTCTTTTGCACCTACCG 57.017 42.857 0.00 0.00 0.00 4.02
1882 1998 1.607148 ACTTTCTTTTGCACCTACCGC 59.393 47.619 0.00 0.00 0.00 5.68
1883 1999 0.955905 TTTCTTTTGCACCTACCGCC 59.044 50.000 0.00 0.00 0.00 6.13
1884 2000 0.179015 TTCTTTTGCACCTACCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
1885 2001 0.179015 TCTTTTGCACCTACCGCCAA 60.179 50.000 0.00 0.00 0.00 4.52
1886 2002 0.240945 CTTTTGCACCTACCGCCAAG 59.759 55.000 0.00 0.00 0.00 3.61
1888 2004 2.058125 TTTGCACCTACCGCCAAGGA 62.058 55.000 3.26 0.00 45.00 3.36
1889 2005 2.125106 GCACCTACCGCCAAGGAG 60.125 66.667 3.26 0.00 45.00 3.69
1890 2006 2.584608 CACCTACCGCCAAGGAGG 59.415 66.667 7.38 7.38 45.00 4.30
1891 2007 1.987855 CACCTACCGCCAAGGAGGA 60.988 63.158 16.15 0.00 45.00 3.71
1892 2008 1.988406 ACCTACCGCCAAGGAGGAC 60.988 63.158 16.15 0.00 45.00 3.85
1893 2009 2.494918 CTACCGCCAAGGAGGACG 59.505 66.667 16.15 2.17 45.00 4.79
1896 2012 4.760047 CCGCCAAGGAGGACGGTG 62.760 72.222 2.29 0.00 45.82 4.94
1897 2013 4.760047 CGCCAAGGAGGACGGTGG 62.760 72.222 0.00 0.00 41.22 4.61
1898 2014 3.637273 GCCAAGGAGGACGGTGGT 61.637 66.667 0.00 0.00 41.22 4.16
1899 2015 2.288025 GCCAAGGAGGACGGTGGTA 61.288 63.158 0.00 0.00 41.22 3.25
1900 2016 1.898154 CCAAGGAGGACGGTGGTAG 59.102 63.158 0.00 0.00 41.22 3.18
1901 2017 1.614241 CCAAGGAGGACGGTGGTAGG 61.614 65.000 0.00 0.00 41.22 3.18
1902 2018 1.305887 AAGGAGGACGGTGGTAGGG 60.306 63.158 0.00 0.00 0.00 3.53
1903 2019 2.038490 GGAGGACGGTGGTAGGGT 59.962 66.667 0.00 0.00 0.00 4.34
1904 2020 1.611556 GGAGGACGGTGGTAGGGTT 60.612 63.158 0.00 0.00 0.00 4.11
1905 2021 1.595357 GAGGACGGTGGTAGGGTTG 59.405 63.158 0.00 0.00 0.00 3.77
1906 2022 1.152183 AGGACGGTGGTAGGGTTGT 60.152 57.895 0.00 0.00 0.00 3.32
1907 2023 1.190178 AGGACGGTGGTAGGGTTGTC 61.190 60.000 0.00 0.00 0.00 3.18
1908 2024 1.294459 GACGGTGGTAGGGTTGTCC 59.706 63.158 0.00 0.00 0.00 4.02
1909 2025 1.459921 ACGGTGGTAGGGTTGTCCA 60.460 57.895 0.00 0.00 38.24 4.02
1918 2034 2.046604 GGTTGTCCACCCTACCGC 60.047 66.667 0.00 0.00 40.19 5.68
1919 2035 2.046604 GTTGTCCACCCTACCGCC 60.047 66.667 0.00 0.00 0.00 6.13
1920 2036 2.527123 TTGTCCACCCTACCGCCA 60.527 61.111 0.00 0.00 0.00 5.69
1921 2037 2.148052 TTGTCCACCCTACCGCCAA 61.148 57.895 0.00 0.00 0.00 4.52
1922 2038 2.119484 TTGTCCACCCTACCGCCAAG 62.119 60.000 0.00 0.00 0.00 3.61
1924 2040 4.796495 CCACCCTACCGCCAAGGC 62.796 72.222 0.00 0.00 46.52 4.35
1941 2057 4.807039 CGGACGGCGGTAGGGTTG 62.807 72.222 13.24 0.00 0.00 3.77
1943 2059 4.078516 GACGGCGGTAGGGTTGCT 62.079 66.667 13.24 0.00 0.00 3.91
1944 2060 4.078516 ACGGCGGTAGGGTTGCTC 62.079 66.667 13.24 0.00 0.00 4.26
1945 2061 4.077184 CGGCGGTAGGGTTGCTCA 62.077 66.667 0.00 0.00 0.00 4.26
1946 2062 2.436115 GGCGGTAGGGTTGCTCAC 60.436 66.667 0.00 0.00 0.00 3.51
1947 2063 2.436115 GCGGTAGGGTTGCTCACC 60.436 66.667 0.00 0.00 46.46 4.02
1971 2087 4.767255 CCGTCCTGGCTGCCTGTC 62.767 72.222 21.03 12.92 0.00 3.51
1972 2088 4.767255 CGTCCTGGCTGCCTGTCC 62.767 72.222 21.03 10.45 0.00 4.02
1973 2089 3.325753 GTCCTGGCTGCCTGTCCT 61.326 66.667 21.03 0.00 0.00 3.85
1974 2090 3.324930 TCCTGGCTGCCTGTCCTG 61.325 66.667 21.03 6.72 0.00 3.86
1975 2091 3.644606 CCTGGCTGCCTGTCCTGT 61.645 66.667 21.03 0.00 0.00 4.00
1976 2092 2.359602 CTGGCTGCCTGTCCTGTG 60.360 66.667 21.03 0.00 0.00 3.66
1977 2093 2.848679 TGGCTGCCTGTCCTGTGA 60.849 61.111 21.03 0.00 0.00 3.58
1978 2094 2.359230 GGCTGCCTGTCCTGTGAC 60.359 66.667 12.43 0.00 42.12 3.67
1979 2095 2.359230 GCTGCCTGTCCTGTGACC 60.359 66.667 0.00 0.00 41.01 4.02
1980 2096 3.150949 CTGCCTGTCCTGTGACCA 58.849 61.111 0.00 0.00 41.01 4.02
1981 2097 1.451504 CTGCCTGTCCTGTGACCAA 59.548 57.895 0.00 0.00 41.01 3.67
1982 2098 0.037303 CTGCCTGTCCTGTGACCAAT 59.963 55.000 0.00 0.00 41.01 3.16
1983 2099 0.478072 TGCCTGTCCTGTGACCAATT 59.522 50.000 0.00 0.00 41.01 2.32
1984 2100 1.168714 GCCTGTCCTGTGACCAATTC 58.831 55.000 0.00 0.00 41.01 2.17
1985 2101 1.442769 CCTGTCCTGTGACCAATTCG 58.557 55.000 0.00 0.00 41.01 3.34
1986 2102 0.798776 CTGTCCTGTGACCAATTCGC 59.201 55.000 0.00 0.00 41.01 4.70
1987 2103 0.605319 TGTCCTGTGACCAATTCGCC 60.605 55.000 0.00 0.00 41.01 5.54
1988 2104 0.605319 GTCCTGTGACCAATTCGCCA 60.605 55.000 0.00 0.00 35.34 5.69
1989 2105 0.605319 TCCTGTGACCAATTCGCCAC 60.605 55.000 0.00 0.00 33.31 5.01
1990 2106 1.586154 CCTGTGACCAATTCGCCACC 61.586 60.000 0.00 0.00 33.31 4.61
1991 2107 1.586154 CTGTGACCAATTCGCCACCC 61.586 60.000 0.00 0.00 33.31 4.61
1992 2108 1.303317 GTGACCAATTCGCCACCCT 60.303 57.895 0.00 0.00 0.00 4.34
1993 2109 1.303236 TGACCAATTCGCCACCCTG 60.303 57.895 0.00 0.00 0.00 4.45
1994 2110 1.303317 GACCAATTCGCCACCCTGT 60.303 57.895 0.00 0.00 0.00 4.00
1995 2111 0.893727 GACCAATTCGCCACCCTGTT 60.894 55.000 0.00 0.00 0.00 3.16
1996 2112 0.893727 ACCAATTCGCCACCCTGTTC 60.894 55.000 0.00 0.00 0.00 3.18
1997 2113 0.893270 CCAATTCGCCACCCTGTTCA 60.893 55.000 0.00 0.00 0.00 3.18
1998 2114 0.523072 CAATTCGCCACCCTGTTCAG 59.477 55.000 0.00 0.00 0.00 3.02
1999 2115 1.244019 AATTCGCCACCCTGTTCAGC 61.244 55.000 0.00 0.00 0.00 4.26
2002 2118 4.643387 GCCACCCTGTTCAGCGGT 62.643 66.667 7.00 7.00 0.00 5.68
2003 2119 3.065306 CCACCCTGTTCAGCGGTA 58.935 61.111 10.82 0.00 0.00 4.02
2004 2120 1.079127 CCACCCTGTTCAGCGGTAG 60.079 63.158 10.82 3.40 0.00 3.18
2005 2121 1.079127 CACCCTGTTCAGCGGTAGG 60.079 63.158 10.82 0.00 0.00 3.18
2006 2122 2.584608 CCCTGTTCAGCGGTAGGG 59.415 66.667 5.82 5.82 43.56 3.53
2007 2123 2.291043 CCCTGTTCAGCGGTAGGGT 61.291 63.158 11.39 0.00 43.96 4.34
2008 2124 1.677552 CCTGTTCAGCGGTAGGGTT 59.322 57.895 0.00 0.00 0.00 4.11
2009 2125 0.673644 CCTGTTCAGCGGTAGGGTTG 60.674 60.000 0.00 0.00 0.00 3.77
2010 2126 0.673644 CTGTTCAGCGGTAGGGTTGG 60.674 60.000 0.00 0.00 0.00 3.77
2011 2127 1.373812 GTTCAGCGGTAGGGTTGGT 59.626 57.895 0.00 0.00 0.00 3.67
2012 2128 0.672711 GTTCAGCGGTAGGGTTGGTC 60.673 60.000 0.00 0.00 0.00 4.02
2013 2129 1.122632 TTCAGCGGTAGGGTTGGTCA 61.123 55.000 0.00 0.00 0.00 4.02
2014 2130 1.375523 CAGCGGTAGGGTTGGTCAC 60.376 63.158 0.00 0.00 0.00 3.67
2015 2131 2.046604 GCGGTAGGGTTGGTCACC 60.047 66.667 0.00 0.00 46.46 4.02
2022 2138 2.046604 GGTTGGTCACCCTACCGC 60.047 66.667 0.00 0.00 44.90 5.68
2023 2139 2.046604 GTTGGTCACCCTACCGCC 60.047 66.667 0.00 0.00 42.91 6.13
2024 2140 2.527123 TTGGTCACCCTACCGCCA 60.527 61.111 0.00 0.00 42.91 5.69
2025 2141 2.148052 TTGGTCACCCTACCGCCAA 61.148 57.895 0.00 0.00 42.91 4.52
2026 2142 2.119484 TTGGTCACCCTACCGCCAAG 62.119 60.000 0.00 0.00 42.91 3.61
2037 2153 3.353836 CGCCAAGGTGGACAACGG 61.354 66.667 0.00 0.00 40.96 4.44
2038 2154 2.203294 GCCAAGGTGGACAACGGT 60.203 61.111 0.00 0.00 40.96 4.83
2039 2155 1.071814 GCCAAGGTGGACAACGGTA 59.928 57.895 0.00 0.00 40.96 4.02
2040 2156 0.953960 GCCAAGGTGGACAACGGTAG 60.954 60.000 0.00 0.00 40.96 3.18
2041 2157 0.321298 CCAAGGTGGACAACGGTAGG 60.321 60.000 0.00 0.00 40.96 3.18
2042 2158 0.321298 CAAGGTGGACAACGGTAGGG 60.321 60.000 0.00 0.00 0.00 3.53
2043 2159 0.765519 AAGGTGGACAACGGTAGGGT 60.766 55.000 0.00 0.00 0.00 4.34
2044 2160 0.765519 AGGTGGACAACGGTAGGGTT 60.766 55.000 0.00 0.00 0.00 4.11
2050 2166 2.540145 CAACGGTAGGGTTGCTCAC 58.460 57.895 0.00 0.00 40.62 3.51
2051 2167 0.953960 CAACGGTAGGGTTGCTCACC 60.954 60.000 0.00 0.00 46.46 4.02
2058 2174 3.595819 GGTTGCTCACCCTGCATC 58.404 61.111 0.00 0.00 40.19 3.91
2059 2175 2.048603 GGTTGCTCACCCTGCATCC 61.049 63.158 0.00 0.00 40.19 3.51
2060 2176 1.303561 GTTGCTCACCCTGCATCCA 60.304 57.895 0.00 0.00 40.34 3.41
2061 2177 0.682209 GTTGCTCACCCTGCATCCAT 60.682 55.000 0.00 0.00 40.34 3.41
2062 2178 0.394762 TTGCTCACCCTGCATCCATC 60.395 55.000 0.00 0.00 40.34 3.51
2063 2179 1.527844 GCTCACCCTGCATCCATCC 60.528 63.158 0.00 0.00 0.00 3.51
2064 2180 1.992519 GCTCACCCTGCATCCATCCT 61.993 60.000 0.00 0.00 0.00 3.24
2065 2181 0.108207 CTCACCCTGCATCCATCCTC 59.892 60.000 0.00 0.00 0.00 3.71
2066 2182 1.227764 CACCCTGCATCCATCCTCG 60.228 63.158 0.00 0.00 0.00 4.63
2067 2183 2.281345 CCCTGCATCCATCCTCGC 60.281 66.667 0.00 0.00 0.00 5.03
2068 2184 2.815945 CCCTGCATCCATCCTCGCT 61.816 63.158 0.00 0.00 0.00 4.93
2069 2185 1.475169 CCCTGCATCCATCCTCGCTA 61.475 60.000 0.00 0.00 0.00 4.26
2070 2186 0.037512 CCTGCATCCATCCTCGCTAG 60.038 60.000 0.00 0.00 0.00 3.42
2071 2187 0.037512 CTGCATCCATCCTCGCTAGG 60.038 60.000 0.00 0.00 45.21 3.02
2072 2188 0.760567 TGCATCCATCCTCGCTAGGT 60.761 55.000 3.89 0.00 44.09 3.08
2073 2189 0.320247 GCATCCATCCTCGCTAGGTG 60.320 60.000 3.89 2.44 44.09 4.00
2074 2190 1.043816 CATCCATCCTCGCTAGGTGT 58.956 55.000 3.89 0.00 44.09 4.16
2075 2191 1.000283 CATCCATCCTCGCTAGGTGTC 60.000 57.143 3.89 0.00 44.09 3.67
2076 2192 0.755698 TCCATCCTCGCTAGGTGTCC 60.756 60.000 3.89 0.00 44.09 4.02
2077 2193 0.757188 CCATCCTCGCTAGGTGTCCT 60.757 60.000 3.89 0.00 44.09 3.85
2078 2194 0.387202 CATCCTCGCTAGGTGTCCTG 59.613 60.000 3.89 0.00 44.09 3.86
2079 2195 0.033011 ATCCTCGCTAGGTGTCCTGT 60.033 55.000 3.89 0.00 44.09 4.00
2080 2196 0.965866 TCCTCGCTAGGTGTCCTGTG 60.966 60.000 3.89 0.00 44.09 3.66
2081 2197 0.965866 CCTCGCTAGGTGTCCTGTGA 60.966 60.000 0.00 1.18 38.19 3.58
2082 2198 0.171455 CTCGCTAGGTGTCCTGTGAC 59.829 60.000 0.00 0.00 42.12 3.67
2083 2199 1.215647 CGCTAGGTGTCCTGTGACC 59.784 63.158 0.00 0.00 41.01 4.02
2084 2200 1.532604 CGCTAGGTGTCCTGTGACCA 61.533 60.000 0.00 0.00 41.01 4.02
2085 2201 0.685097 GCTAGGTGTCCTGTGACCAA 59.315 55.000 0.00 0.00 41.01 3.67
2086 2202 1.279271 GCTAGGTGTCCTGTGACCAAT 59.721 52.381 0.00 0.00 41.01 3.16
2087 2203 2.290323 GCTAGGTGTCCTGTGACCAATT 60.290 50.000 0.00 0.00 41.01 2.32
2088 2204 3.810743 GCTAGGTGTCCTGTGACCAATTT 60.811 47.826 0.00 0.00 41.01 1.82
2089 2205 3.312736 AGGTGTCCTGTGACCAATTTT 57.687 42.857 0.00 0.00 41.01 1.82
2090 2206 3.222603 AGGTGTCCTGTGACCAATTTTC 58.777 45.455 0.00 0.00 41.01 2.29
2091 2207 2.955660 GGTGTCCTGTGACCAATTTTCA 59.044 45.455 0.00 0.00 41.01 2.69
2092 2208 3.243401 GGTGTCCTGTGACCAATTTTCAC 60.243 47.826 9.24 9.24 43.22 3.18
2093 2209 2.955660 TGTCCTGTGACCAATTTTCACC 59.044 45.455 12.44 1.23 42.40 4.02
2094 2210 2.296190 GTCCTGTGACCAATTTTCACCC 59.704 50.000 12.44 0.00 42.40 4.61
2095 2211 1.618343 CCTGTGACCAATTTTCACCCC 59.382 52.381 12.44 0.00 42.40 4.95
2096 2212 2.597455 CTGTGACCAATTTTCACCCCT 58.403 47.619 12.44 0.00 42.40 4.79
2097 2213 3.499563 CCTGTGACCAATTTTCACCCCTA 60.500 47.826 12.44 0.00 42.40 3.53
2098 2214 4.344104 CTGTGACCAATTTTCACCCCTAT 58.656 43.478 12.44 0.00 42.40 2.57
2099 2215 4.746466 TGTGACCAATTTTCACCCCTATT 58.254 39.130 12.44 0.00 42.40 1.73
2100 2216 4.770010 TGTGACCAATTTTCACCCCTATTC 59.230 41.667 12.44 0.00 42.40 1.75
2101 2217 5.016831 GTGACCAATTTTCACCCCTATTCT 58.983 41.667 5.87 0.00 37.93 2.40
2102 2218 5.016173 TGACCAATTTTCACCCCTATTCTG 58.984 41.667 0.00 0.00 0.00 3.02
2103 2219 3.769300 ACCAATTTTCACCCCTATTCTGC 59.231 43.478 0.00 0.00 0.00 4.26
2104 2220 3.181487 CCAATTTTCACCCCTATTCTGCG 60.181 47.826 0.00 0.00 0.00 5.18
2105 2221 2.122783 TTTTCACCCCTATTCTGCGG 57.877 50.000 0.00 0.00 0.00 5.69
2106 2222 0.988832 TTTCACCCCTATTCTGCGGT 59.011 50.000 0.00 0.00 0.00 5.68
2107 2223 1.868713 TTCACCCCTATTCTGCGGTA 58.131 50.000 0.00 0.00 0.00 4.02
2108 2224 1.410004 TCACCCCTATTCTGCGGTAG 58.590 55.000 0.00 0.00 0.00 3.18
2109 2225 0.393077 CACCCCTATTCTGCGGTAGG 59.607 60.000 2.75 2.75 37.74 3.18
2113 2229 2.240493 CCTATTCTGCGGTAGGGTTG 57.760 55.000 1.89 0.00 34.99 3.77
2114 2230 1.202651 CCTATTCTGCGGTAGGGTTGG 60.203 57.143 1.89 0.00 34.99 3.77
2115 2231 0.179468 TATTCTGCGGTAGGGTTGGC 59.821 55.000 0.00 0.00 0.00 4.52
2129 2245 1.854979 TTGGCCACCCTACCACCAT 60.855 57.895 3.88 0.00 35.10 3.55
2130 2246 2.148723 TTGGCCACCCTACCACCATG 62.149 60.000 3.88 0.00 35.10 3.66
2132 2248 2.275418 CCACCCTACCACCATGCC 59.725 66.667 0.00 0.00 0.00 4.40
2133 2249 2.275418 CACCCTACCACCATGCCC 59.725 66.667 0.00 0.00 0.00 5.36
2135 2251 3.020647 CCCTACCACCATGCCCCA 61.021 66.667 0.00 0.00 0.00 4.96
2138 2254 1.644437 CCTACCACCATGCCCCATGA 61.644 60.000 6.77 0.00 43.81 3.07
2146 2262 3.120086 ATGCCCCATGACGGTAGGC 62.120 63.158 0.00 0.00 41.34 3.93
2148 2264 3.043999 GCCCCATGACGGTAGGCTT 62.044 63.158 0.00 0.00 38.68 4.35
2149 2265 1.153168 CCCCATGACGGTAGGCTTG 60.153 63.158 0.00 0.00 0.00 4.01
2151 2267 1.819632 CCATGACGGTAGGCTTGGC 60.820 63.158 0.00 0.00 42.77 4.52
2154 2270 1.836999 ATGACGGTAGGCTTGGCACA 61.837 55.000 0.00 0.00 0.00 4.57
2166 2282 3.752704 GGCACAACCTAACGCCAA 58.247 55.556 0.00 0.00 44.25 4.52
2167 2283 1.579429 GGCACAACCTAACGCCAAG 59.421 57.895 0.00 0.00 44.25 3.61
2189 2305 4.506255 ATGGCGGTAGGCTTGGGC 62.506 66.667 0.00 0.00 44.18 5.36
2208 2324 1.134670 GCACCCTACTGCCTTCTACTG 60.135 57.143 0.00 0.00 0.00 2.74
2219 2335 2.248248 CCTTCTACTGTCCTGTGACCA 58.752 52.381 0.00 0.00 41.01 4.02
2222 2338 4.263068 CCTTCTACTGTCCTGTGACCAAAT 60.263 45.833 0.00 0.00 41.01 2.32
2224 2340 3.901222 TCTACTGTCCTGTGACCAAATCA 59.099 43.478 0.00 0.00 41.01 2.57
2225 2341 3.795688 ACTGTCCTGTGACCAAATCAT 57.204 42.857 0.00 0.00 40.28 2.45
2226 2342 3.415212 ACTGTCCTGTGACCAAATCATG 58.585 45.455 0.00 0.00 40.28 3.07
2228 2344 2.161855 GTCCTGTGACCAAATCATGCA 58.838 47.619 0.00 0.00 40.28 3.96
2230 2346 1.887854 CCTGTGACCAAATCATGCACA 59.112 47.619 0.00 0.00 40.28 4.57
2232 2348 3.056393 CCTGTGACCAAATCATGCACATT 60.056 43.478 0.00 0.00 40.28 2.71
2234 2350 4.558178 TGTGACCAAATCATGCACATTTC 58.442 39.130 0.00 0.00 40.28 2.17
2235 2351 4.281435 TGTGACCAAATCATGCACATTTCT 59.719 37.500 0.00 0.00 40.28 2.52
2236 2352 5.476254 TGTGACCAAATCATGCACATTTCTA 59.524 36.000 0.00 0.00 40.28 2.10
2265 2381 4.354162 GGCCACCCTACCGCCAAA 62.354 66.667 0.00 0.00 42.52 3.28
2266 2382 2.750237 GCCACCCTACCGCCAAAG 60.750 66.667 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.675228 GCTTGATGCTTCAACCAATCCTG 60.675 47.826 10.76 1.12 36.94 3.86
107 108 8.221100 TCGACTTGATAGATTTGTTCTTTTTCG 58.779 33.333 0.00 0.00 35.79 3.46
266 267 5.866207 ACGTTCAAGATTCTAAACCTTCCT 58.134 37.500 6.37 0.00 0.00 3.36
268 269 7.907194 GGATACGTTCAAGATTCTAAACCTTC 58.093 38.462 0.00 2.78 0.00 3.46
533 540 1.048160 TGATGTCTGGCGCCTCCATA 61.048 55.000 29.70 9.90 45.50 2.74
542 549 3.347216 ACCACAACTATTGATGTCTGGC 58.653 45.455 0.00 0.00 0.00 4.85
576 583 3.495434 TTTCCTAACATTGTGTCCCGT 57.505 42.857 0.00 0.00 0.00 5.28
628 635 3.615592 CGTTTGACTAGTGGGATTCGGAA 60.616 47.826 0.00 0.00 0.00 4.30
701 708 2.835431 CCTCCTCATCCTCCGCGT 60.835 66.667 4.92 0.00 0.00 6.01
720 727 0.463833 CCTCCACGCCTTCCAATACC 60.464 60.000 0.00 0.00 0.00 2.73
779 786 4.227134 CGTCCTCCATGCCCTCCG 62.227 72.222 0.00 0.00 0.00 4.63
815 822 0.330604 TCCTACGACCACAGCTACCT 59.669 55.000 0.00 0.00 0.00 3.08
819 826 1.303074 TCGTCCTACGACCACAGCT 60.303 57.895 0.00 0.00 46.73 4.24
982 1007 8.542926 AGAAGCCATGCCTATAAAGAAAATTTT 58.457 29.630 2.28 2.28 0.00 1.82
1050 1077 3.389656 TGTCTGTCCATTTATCCGGCATA 59.610 43.478 0.00 0.00 0.00 3.14
1059 1086 4.346709 TCCAACTCAGTGTCTGTCCATTTA 59.653 41.667 0.00 0.00 32.61 1.40
1062 1089 2.329267 TCCAACTCAGTGTCTGTCCAT 58.671 47.619 0.00 0.00 32.61 3.41
1219 1247 1.658114 CGTGAGTTGGACGAGGACA 59.342 57.895 0.00 0.00 39.21 4.02
1376 1408 8.579850 ACATCTTTTGGCACATCTTTATCTAA 57.420 30.769 0.00 0.00 39.30 2.10
1438 1476 0.036732 ATGCTTCCTCAAACAGCCGA 59.963 50.000 0.00 0.00 32.11 5.54
1450 1488 2.416680 AGCCTCTCTGAAATGCTTCC 57.583 50.000 0.00 0.00 0.00 3.46
1523 1563 1.768684 TTCTCCTTGCGTGCCCTCTT 61.769 55.000 0.00 0.00 0.00 2.85
1612 1660 4.157656 CGAGGCCATTTTCCTTTATTGTCA 59.842 41.667 5.01 0.00 33.24 3.58
1618 1666 2.817258 CACACGAGGCCATTTTCCTTTA 59.183 45.455 5.01 0.00 33.24 1.85
1787 1903 8.641155 CAAGTCACAACAATAGCAATACAAATG 58.359 33.333 0.00 0.00 0.00 2.32
1794 1910 6.572519 ACAAACAAGTCACAACAATAGCAAT 58.427 32.000 0.00 0.00 0.00 3.56
1795 1911 5.960113 ACAAACAAGTCACAACAATAGCAA 58.040 33.333 0.00 0.00 0.00 3.91
1800 1916 4.391523 GCCAAACAAACAAGTCACAACAAT 59.608 37.500 0.00 0.00 0.00 2.71
1814 1930 3.506810 CGTTTCAGACAAGCCAAACAAA 58.493 40.909 0.00 0.00 0.00 2.83
1815 1931 2.159310 CCGTTTCAGACAAGCCAAACAA 60.159 45.455 0.00 0.00 0.00 2.83
1817 1933 1.404035 ACCGTTTCAGACAAGCCAAAC 59.596 47.619 0.00 0.00 0.00 2.93
1818 1934 1.403679 CACCGTTTCAGACAAGCCAAA 59.596 47.619 0.00 0.00 0.00 3.28
1820 1936 0.179234 TCACCGTTTCAGACAAGCCA 59.821 50.000 0.00 0.00 0.00 4.75
1821 1937 1.264288 CTTCACCGTTTCAGACAAGCC 59.736 52.381 0.00 0.00 0.00 4.35
1822 1938 1.264288 CCTTCACCGTTTCAGACAAGC 59.736 52.381 0.00 0.00 0.00 4.01
1823 1939 2.802816 CTCCTTCACCGTTTCAGACAAG 59.197 50.000 0.00 0.00 0.00 3.16
1824 1940 2.484770 CCTCCTTCACCGTTTCAGACAA 60.485 50.000 0.00 0.00 0.00 3.18
1825 1941 1.070134 CCTCCTTCACCGTTTCAGACA 59.930 52.381 0.00 0.00 0.00 3.41
1826 1942 1.343465 TCCTCCTTCACCGTTTCAGAC 59.657 52.381 0.00 0.00 0.00 3.51
1828 1944 2.037251 TCTTCCTCCTTCACCGTTTCAG 59.963 50.000 0.00 0.00 0.00 3.02
1829 1945 2.043992 TCTTCCTCCTTCACCGTTTCA 58.956 47.619 0.00 0.00 0.00 2.69
1830 1946 2.833631 TCTTCCTCCTTCACCGTTTC 57.166 50.000 0.00 0.00 0.00 2.78
1831 1947 3.570912 TTTCTTCCTCCTTCACCGTTT 57.429 42.857 0.00 0.00 0.00 3.60
1832 1948 3.570912 TTTTCTTCCTCCTTCACCGTT 57.429 42.857 0.00 0.00 0.00 4.44
1833 1949 3.211865 GTTTTTCTTCCTCCTTCACCGT 58.788 45.455 0.00 0.00 0.00 4.83
1834 1950 3.211045 TGTTTTTCTTCCTCCTTCACCG 58.789 45.455 0.00 0.00 0.00 4.94
1835 1951 5.592054 CTTTGTTTTTCTTCCTCCTTCACC 58.408 41.667 0.00 0.00 0.00 4.02
1836 1952 5.043903 GCTTTGTTTTTCTTCCTCCTTCAC 58.956 41.667 0.00 0.00 0.00 3.18
1837 1953 4.709397 TGCTTTGTTTTTCTTCCTCCTTCA 59.291 37.500 0.00 0.00 0.00 3.02
1838 1954 5.262588 TGCTTTGTTTTTCTTCCTCCTTC 57.737 39.130 0.00 0.00 0.00 3.46
1839 1955 5.675684 TTGCTTTGTTTTTCTTCCTCCTT 57.324 34.783 0.00 0.00 0.00 3.36
1841 1957 5.419542 AGTTTGCTTTGTTTTTCTTCCTCC 58.580 37.500 0.00 0.00 0.00 4.30
1844 1960 7.364522 AGAAAGTTTGCTTTGTTTTTCTTCC 57.635 32.000 0.00 0.00 44.25 3.46
1859 1975 4.041723 CGGTAGGTGCAAAAGAAAGTTTG 58.958 43.478 0.00 0.00 40.72 2.93
1865 1981 0.179015 TGGCGGTAGGTGCAAAAGAA 60.179 50.000 0.00 0.00 0.00 2.52
1867 1983 0.240945 CTTGGCGGTAGGTGCAAAAG 59.759 55.000 0.00 0.00 0.00 2.27
1868 1984 1.175983 CCTTGGCGGTAGGTGCAAAA 61.176 55.000 0.00 0.00 0.00 2.44
1870 1986 2.033448 CCTTGGCGGTAGGTGCAA 59.967 61.111 0.00 0.00 0.00 4.08
1871 1987 2.925706 TCCTTGGCGGTAGGTGCA 60.926 61.111 0.00 0.00 34.29 4.57
1874 1990 1.988406 GTCCTCCTTGGCGGTAGGT 60.988 63.158 0.00 0.00 33.96 3.08
1875 1991 2.901042 GTCCTCCTTGGCGGTAGG 59.099 66.667 0.00 0.00 35.26 3.18
1876 1992 2.494918 CGTCCTCCTTGGCGGTAG 59.505 66.667 0.00 0.00 33.74 3.18
1877 1993 3.072468 CCGTCCTCCTTGGCGGTA 61.072 66.667 0.00 0.00 44.62 4.02
1880 1996 4.760047 CCACCGTCCTCCTTGGCG 62.760 72.222 0.00 0.00 35.92 5.69
1881 1997 2.240162 CTACCACCGTCCTCCTTGGC 62.240 65.000 0.00 0.00 35.26 4.52
1882 1998 1.614241 CCTACCACCGTCCTCCTTGG 61.614 65.000 0.00 0.00 35.06 3.61
1883 1999 1.614241 CCCTACCACCGTCCTCCTTG 61.614 65.000 0.00 0.00 0.00 3.61
1884 2000 1.305887 CCCTACCACCGTCCTCCTT 60.306 63.158 0.00 0.00 0.00 3.36
1885 2001 2.103079 AACCCTACCACCGTCCTCCT 62.103 60.000 0.00 0.00 0.00 3.69
1886 2002 1.611556 AACCCTACCACCGTCCTCC 60.612 63.158 0.00 0.00 0.00 4.30
1887 2003 1.190178 ACAACCCTACCACCGTCCTC 61.190 60.000 0.00 0.00 0.00 3.71
1888 2004 1.152183 ACAACCCTACCACCGTCCT 60.152 57.895 0.00 0.00 0.00 3.85
1889 2005 1.294459 GACAACCCTACCACCGTCC 59.706 63.158 0.00 0.00 0.00 4.79
1890 2006 1.294459 GGACAACCCTACCACCGTC 59.706 63.158 0.00 0.00 0.00 4.79
1891 2007 1.459921 TGGACAACCCTACCACCGT 60.460 57.895 0.00 0.00 35.38 4.83
1892 2008 1.004200 GTGGACAACCCTACCACCG 60.004 63.158 0.00 0.00 45.53 4.94
1902 2018 2.046604 GGCGGTAGGGTGGACAAC 60.047 66.667 0.00 0.00 0.00 3.32
1903 2019 2.119484 CTTGGCGGTAGGGTGGACAA 62.119 60.000 0.00 0.00 0.00 3.18
1904 2020 2.527123 TTGGCGGTAGGGTGGACA 60.527 61.111 0.00 0.00 0.00 4.02
1905 2021 2.267961 CTTGGCGGTAGGGTGGAC 59.732 66.667 0.00 0.00 0.00 4.02
1906 2022 3.006728 CCTTGGCGGTAGGGTGGA 61.007 66.667 0.00 0.00 0.00 4.02
1907 2023 4.796495 GCCTTGGCGGTAGGGTGG 62.796 72.222 0.00 0.00 33.19 4.61
1924 2040 4.807039 CAACCCTACCGCCGTCCG 62.807 72.222 0.00 0.00 0.00 4.79
1926 2042 4.078516 AGCAACCCTACCGCCGTC 62.079 66.667 0.00 0.00 0.00 4.79
1927 2043 4.078516 GAGCAACCCTACCGCCGT 62.079 66.667 0.00 0.00 0.00 5.68
1928 2044 4.077184 TGAGCAACCCTACCGCCG 62.077 66.667 0.00 0.00 0.00 6.46
1929 2045 2.436115 GTGAGCAACCCTACCGCC 60.436 66.667 0.00 0.00 0.00 6.13
1930 2046 2.436115 GGTGAGCAACCCTACCGC 60.436 66.667 0.00 0.00 44.02 5.68
1954 2070 4.767255 GACAGGCAGCCAGGACGG 62.767 72.222 15.80 0.00 38.11 4.79
1955 2071 4.767255 GGACAGGCAGCCAGGACG 62.767 72.222 15.80 0.00 0.00 4.79
1956 2072 3.325753 AGGACAGGCAGCCAGGAC 61.326 66.667 15.80 5.61 0.00 3.85
1957 2073 3.324930 CAGGACAGGCAGCCAGGA 61.325 66.667 15.80 0.00 0.00 3.86
1958 2074 3.644606 ACAGGACAGGCAGCCAGG 61.645 66.667 15.80 8.00 0.00 4.45
1959 2075 2.359602 CACAGGACAGGCAGCCAG 60.360 66.667 15.80 8.60 0.00 4.85
1960 2076 2.848679 TCACAGGACAGGCAGCCA 60.849 61.111 15.80 0.00 0.00 4.75
1961 2077 2.359230 GTCACAGGACAGGCAGCC 60.359 66.667 1.84 1.84 43.73 4.85
1962 2078 2.359230 GGTCACAGGACAGGCAGC 60.359 66.667 0.00 0.00 46.17 5.25
1963 2079 0.037303 ATTGGTCACAGGACAGGCAG 59.963 55.000 0.00 0.00 46.17 4.85
1964 2080 0.478072 AATTGGTCACAGGACAGGCA 59.522 50.000 0.00 0.00 46.17 4.75
1965 2081 1.168714 GAATTGGTCACAGGACAGGC 58.831 55.000 0.00 0.00 46.17 4.85
1966 2082 1.442769 CGAATTGGTCACAGGACAGG 58.557 55.000 0.00 0.00 46.17 4.00
1967 2083 0.798776 GCGAATTGGTCACAGGACAG 59.201 55.000 0.00 0.00 46.17 3.51
1968 2084 0.605319 GGCGAATTGGTCACAGGACA 60.605 55.000 0.00 0.00 46.17 4.02
1969 2085 0.605319 TGGCGAATTGGTCACAGGAC 60.605 55.000 0.00 0.00 43.55 3.85
1970 2086 0.605319 GTGGCGAATTGGTCACAGGA 60.605 55.000 18.85 0.00 42.03 3.86
1971 2087 1.586154 GGTGGCGAATTGGTCACAGG 61.586 60.000 23.86 0.00 44.18 4.00
1972 2088 1.586154 GGGTGGCGAATTGGTCACAG 61.586 60.000 23.86 0.00 44.18 3.66
1973 2089 1.602323 GGGTGGCGAATTGGTCACA 60.602 57.895 23.86 3.02 44.18 3.58
1974 2090 1.303317 AGGGTGGCGAATTGGTCAC 60.303 57.895 15.97 15.97 41.72 3.67
1975 2091 1.303236 CAGGGTGGCGAATTGGTCA 60.303 57.895 0.00 0.00 0.00 4.02
1976 2092 0.893727 AACAGGGTGGCGAATTGGTC 60.894 55.000 0.00 0.00 0.00 4.02
1977 2093 0.893727 GAACAGGGTGGCGAATTGGT 60.894 55.000 0.00 0.00 0.00 3.67
1978 2094 0.893270 TGAACAGGGTGGCGAATTGG 60.893 55.000 0.00 0.00 0.00 3.16
1979 2095 0.523072 CTGAACAGGGTGGCGAATTG 59.477 55.000 0.00 0.00 0.00 2.32
1980 2096 1.244019 GCTGAACAGGGTGGCGAATT 61.244 55.000 3.99 0.00 0.00 2.17
1981 2097 1.675641 GCTGAACAGGGTGGCGAAT 60.676 57.895 3.99 0.00 0.00 3.34
1982 2098 2.281484 GCTGAACAGGGTGGCGAA 60.281 61.111 3.99 0.00 0.00 4.70
1985 2101 3.248446 TACCGCTGAACAGGGTGGC 62.248 63.158 18.28 0.73 39.45 5.01
1986 2102 1.079127 CTACCGCTGAACAGGGTGG 60.079 63.158 18.28 14.08 39.45 4.61
1987 2103 1.079127 CCTACCGCTGAACAGGGTG 60.079 63.158 18.28 12.37 39.45 4.61
1988 2104 2.291043 CCCTACCGCTGAACAGGGT 61.291 63.158 15.55 15.41 42.50 4.34
1989 2105 2.584608 CCCTACCGCTGAACAGGG 59.415 66.667 11.10 11.10 41.83 4.45
1990 2106 0.673644 CAACCCTACCGCTGAACAGG 60.674 60.000 3.99 0.00 0.00 4.00
1991 2107 0.673644 CCAACCCTACCGCTGAACAG 60.674 60.000 0.00 0.00 0.00 3.16
1992 2108 1.373435 CCAACCCTACCGCTGAACA 59.627 57.895 0.00 0.00 0.00 3.18
1993 2109 0.672711 GACCAACCCTACCGCTGAAC 60.673 60.000 0.00 0.00 0.00 3.18
1994 2110 1.122632 TGACCAACCCTACCGCTGAA 61.123 55.000 0.00 0.00 0.00 3.02
1995 2111 1.534476 TGACCAACCCTACCGCTGA 60.534 57.895 0.00 0.00 0.00 4.26
1996 2112 1.375523 GTGACCAACCCTACCGCTG 60.376 63.158 0.00 0.00 0.00 5.18
1997 2113 2.590114 GGTGACCAACCCTACCGCT 61.590 63.158 0.00 0.00 44.02 5.52
1998 2114 2.046604 GGTGACCAACCCTACCGC 60.047 66.667 0.00 0.00 44.02 5.68
2010 2126 2.267961 CCTTGGCGGTAGGGTGAC 59.732 66.667 0.00 0.00 0.00 3.67
2011 2127 2.203877 ACCTTGGCGGTAGGGTGA 60.204 61.111 5.31 0.00 46.73 4.02
2012 2128 2.046314 CACCTTGGCGGTAGGGTG 60.046 66.667 0.00 0.00 46.94 4.61
2013 2129 3.327404 CCACCTTGGCGGTAGGGT 61.327 66.667 5.31 0.00 46.94 4.34
2014 2130 3.006728 TCCACCTTGGCGGTAGGG 61.007 66.667 5.31 0.00 46.94 3.53
2015 2131 2.119484 TTGTCCACCTTGGCGGTAGG 62.119 60.000 0.00 0.00 46.94 3.18
2016 2132 0.953960 GTTGTCCACCTTGGCGGTAG 60.954 60.000 0.00 0.00 46.94 3.18
2017 2133 1.071814 GTTGTCCACCTTGGCGGTA 59.928 57.895 0.00 0.00 46.94 4.02
2019 2135 3.353836 CGTTGTCCACCTTGGCGG 61.354 66.667 0.00 0.00 37.47 6.13
2020 2136 2.718747 TACCGTTGTCCACCTTGGCG 62.719 60.000 0.00 0.00 37.47 5.69
2021 2137 0.953960 CTACCGTTGTCCACCTTGGC 60.954 60.000 0.00 0.00 37.47 4.52
2022 2138 0.321298 CCTACCGTTGTCCACCTTGG 60.321 60.000 0.00 0.00 39.43 3.61
2023 2139 0.321298 CCCTACCGTTGTCCACCTTG 60.321 60.000 0.00 0.00 0.00 3.61
2024 2140 0.765519 ACCCTACCGTTGTCCACCTT 60.766 55.000 0.00 0.00 0.00 3.50
2025 2141 0.765519 AACCCTACCGTTGTCCACCT 60.766 55.000 0.00 0.00 0.00 4.00
2026 2142 0.604511 CAACCCTACCGTTGTCCACC 60.605 60.000 0.00 0.00 38.64 4.61
2027 2143 1.232621 GCAACCCTACCGTTGTCCAC 61.233 60.000 3.65 0.00 44.10 4.02
2028 2144 1.071814 GCAACCCTACCGTTGTCCA 59.928 57.895 3.65 0.00 44.10 4.02
2029 2145 0.672711 GAGCAACCCTACCGTTGTCC 60.673 60.000 3.65 0.00 44.10 4.02
2030 2146 0.034337 TGAGCAACCCTACCGTTGTC 59.966 55.000 3.65 1.70 44.10 3.18
2031 2147 0.250166 GTGAGCAACCCTACCGTTGT 60.250 55.000 3.65 0.00 44.10 3.32
2032 2148 0.953960 GGTGAGCAACCCTACCGTTG 60.954 60.000 0.00 0.00 44.02 4.10
2033 2149 1.373812 GGTGAGCAACCCTACCGTT 59.626 57.895 0.00 0.00 44.02 4.44
2034 2150 3.066198 GGTGAGCAACCCTACCGT 58.934 61.111 0.00 0.00 44.02 4.83
2042 2158 0.682209 ATGGATGCAGGGTGAGCAAC 60.682 55.000 0.00 0.00 46.27 4.17
2043 2159 0.394762 GATGGATGCAGGGTGAGCAA 60.395 55.000 0.00 0.00 46.27 3.91
2045 2161 1.527844 GGATGGATGCAGGGTGAGC 60.528 63.158 0.00 0.00 0.00 4.26
2046 2162 0.108207 GAGGATGGATGCAGGGTGAG 59.892 60.000 0.00 0.00 0.00 3.51
2047 2163 1.689243 CGAGGATGGATGCAGGGTGA 61.689 60.000 0.00 0.00 0.00 4.02
2048 2164 1.227764 CGAGGATGGATGCAGGGTG 60.228 63.158 0.00 0.00 0.00 4.61
2049 2165 3.112205 GCGAGGATGGATGCAGGGT 62.112 63.158 0.00 0.00 0.00 4.34
2050 2166 1.475169 TAGCGAGGATGGATGCAGGG 61.475 60.000 0.00 0.00 0.00 4.45
2051 2167 0.037512 CTAGCGAGGATGGATGCAGG 60.038 60.000 0.00 0.00 0.00 4.85
2052 2168 3.511182 CTAGCGAGGATGGATGCAG 57.489 57.895 0.00 0.00 0.00 4.41
2062 2178 3.151414 GTCACAGGACACCTAGCGAGG 62.151 61.905 11.86 11.86 43.73 4.63
2063 2179 0.171455 GTCACAGGACACCTAGCGAG 59.829 60.000 0.00 0.00 43.73 5.03
2064 2180 1.248785 GGTCACAGGACACCTAGCGA 61.249 60.000 0.00 0.00 46.17 4.93
2065 2181 1.215647 GGTCACAGGACACCTAGCG 59.784 63.158 0.00 0.00 46.17 4.26
2066 2182 0.685097 TTGGTCACAGGACACCTAGC 59.315 55.000 0.00 0.00 46.17 3.42
2067 2183 3.703001 AATTGGTCACAGGACACCTAG 57.297 47.619 0.00 0.00 46.17 3.02
2068 2184 4.141367 TGAAAATTGGTCACAGGACACCTA 60.141 41.667 0.00 0.00 46.17 3.08
2069 2185 3.222603 GAAAATTGGTCACAGGACACCT 58.777 45.455 0.00 0.00 46.17 4.00
2070 2186 2.955660 TGAAAATTGGTCACAGGACACC 59.044 45.455 0.00 0.00 46.17 4.16
2071 2187 3.243401 GGTGAAAATTGGTCACAGGACAC 60.243 47.826 19.05 0.00 45.94 3.67
2072 2188 2.955660 GGTGAAAATTGGTCACAGGACA 59.044 45.455 19.05 0.00 45.94 4.02
2073 2189 2.296190 GGGTGAAAATTGGTCACAGGAC 59.704 50.000 19.05 6.47 45.94 3.85
2074 2190 2.593026 GGGTGAAAATTGGTCACAGGA 58.407 47.619 19.05 0.00 45.94 3.86
2075 2191 1.618343 GGGGTGAAAATTGGTCACAGG 59.382 52.381 19.05 0.00 45.94 4.00
2076 2192 2.597455 AGGGGTGAAAATTGGTCACAG 58.403 47.619 19.05 0.00 45.94 3.66
2077 2193 2.765689 AGGGGTGAAAATTGGTCACA 57.234 45.000 19.05 0.00 45.94 3.58
2078 2194 5.016831 AGAATAGGGGTGAAAATTGGTCAC 58.983 41.667 12.16 12.16 43.87 3.67
2079 2195 5.016173 CAGAATAGGGGTGAAAATTGGTCA 58.984 41.667 0.00 0.00 0.00 4.02
2080 2196 4.142160 GCAGAATAGGGGTGAAAATTGGTC 60.142 45.833 0.00 0.00 0.00 4.02
2081 2197 3.769300 GCAGAATAGGGGTGAAAATTGGT 59.231 43.478 0.00 0.00 0.00 3.67
2082 2198 3.181487 CGCAGAATAGGGGTGAAAATTGG 60.181 47.826 0.00 0.00 0.00 3.16
2083 2199 3.181487 CCGCAGAATAGGGGTGAAAATTG 60.181 47.826 0.00 0.00 36.89 2.32
2084 2200 3.023832 CCGCAGAATAGGGGTGAAAATT 58.976 45.455 0.00 0.00 36.89 1.82
2085 2201 2.654863 CCGCAGAATAGGGGTGAAAAT 58.345 47.619 0.00 0.00 36.89 1.82
2086 2202 2.122783 CCGCAGAATAGGGGTGAAAA 57.877 50.000 0.00 0.00 36.89 2.29
2087 2203 3.873781 CCGCAGAATAGGGGTGAAA 57.126 52.632 0.00 0.00 36.89 2.69
2092 2208 2.058675 CCCTACCGCAGAATAGGGG 58.941 63.158 8.28 0.00 46.33 4.79
2094 2210 1.202651 CCAACCCTACCGCAGAATAGG 60.203 57.143 0.00 0.00 36.37 2.57
2095 2211 1.810412 GCCAACCCTACCGCAGAATAG 60.810 57.143 0.00 0.00 0.00 1.73
2096 2212 0.179468 GCCAACCCTACCGCAGAATA 59.821 55.000 0.00 0.00 0.00 1.75
2097 2213 1.077716 GCCAACCCTACCGCAGAAT 60.078 57.895 0.00 0.00 0.00 2.40
2098 2214 2.349755 GCCAACCCTACCGCAGAA 59.650 61.111 0.00 0.00 0.00 3.02
2099 2215 3.712907 GGCCAACCCTACCGCAGA 61.713 66.667 0.00 0.00 0.00 4.26
2100 2216 4.028490 TGGCCAACCCTACCGCAG 62.028 66.667 0.61 0.00 33.59 5.18
2101 2217 4.338710 GTGGCCAACCCTACCGCA 62.339 66.667 7.24 0.00 34.06 5.69
2110 2226 2.035155 GGTGGTAGGGTGGCCAAC 59.965 66.667 14.15 14.15 36.41 3.77
2111 2227 1.854979 ATGGTGGTAGGGTGGCCAA 60.855 57.895 7.24 0.00 36.41 4.52
2112 2228 2.204228 ATGGTGGTAGGGTGGCCA 60.204 61.111 0.00 0.00 0.00 5.36
2113 2229 2.275418 CATGGTGGTAGGGTGGCC 59.725 66.667 0.00 0.00 0.00 5.36
2114 2230 2.440247 GCATGGTGGTAGGGTGGC 60.440 66.667 0.00 0.00 0.00 5.01
2115 2231 2.275418 GGCATGGTGGTAGGGTGG 59.725 66.667 0.00 0.00 0.00 4.61
2125 2241 1.983119 CTACCGTCATGGGGCATGGT 61.983 60.000 0.00 2.92 44.64 3.55
2129 2245 3.792736 GCCTACCGTCATGGGGCA 61.793 66.667 0.00 0.00 42.82 5.36
2130 2246 3.043999 AAGCCTACCGTCATGGGGC 62.044 63.158 3.90 0.00 43.43 5.80
2132 2248 1.153168 CCAAGCCTACCGTCATGGG 60.153 63.158 0.00 0.00 44.64 4.00
2133 2249 1.819632 GCCAAGCCTACCGTCATGG 60.820 63.158 0.00 0.00 46.41 3.66
2135 2251 1.078426 GTGCCAAGCCTACCGTCAT 60.078 57.895 0.00 0.00 0.00 3.06
2138 2254 1.599797 GTTGTGCCAAGCCTACCGT 60.600 57.895 0.00 0.00 0.00 4.83
2146 2262 1.579429 GGCGTTAGGTTGTGCCAAG 59.421 57.895 0.00 0.00 46.76 3.61
2151 2267 1.862602 GCCCTTGGCGTTAGGTTGTG 61.863 60.000 0.00 0.00 39.62 3.33
2172 2288 4.506255 GCCCAAGCCTACCGCCAT 62.506 66.667 0.00 0.00 38.78 4.40
2189 2305 2.166664 GACAGTAGAAGGCAGTAGGGTG 59.833 54.545 0.00 0.00 0.00 4.61
2190 2306 2.458620 GACAGTAGAAGGCAGTAGGGT 58.541 52.381 0.00 0.00 0.00 4.34
2191 2307 1.757699 GGACAGTAGAAGGCAGTAGGG 59.242 57.143 0.00 0.00 0.00 3.53
2192 2308 2.428890 CAGGACAGTAGAAGGCAGTAGG 59.571 54.545 0.00 0.00 0.00 3.18
2193 2309 3.093057 ACAGGACAGTAGAAGGCAGTAG 58.907 50.000 0.00 0.00 0.00 2.57
2194 2310 2.826128 CACAGGACAGTAGAAGGCAGTA 59.174 50.000 0.00 0.00 0.00 2.74
2195 2311 1.620819 CACAGGACAGTAGAAGGCAGT 59.379 52.381 0.00 0.00 0.00 4.40
2196 2312 1.895798 TCACAGGACAGTAGAAGGCAG 59.104 52.381 0.00 0.00 0.00 4.85
2197 2313 1.618837 GTCACAGGACAGTAGAAGGCA 59.381 52.381 0.00 0.00 43.73 4.75
2198 2314 1.066787 GGTCACAGGACAGTAGAAGGC 60.067 57.143 0.00 0.00 46.17 4.35
2199 2315 2.248248 TGGTCACAGGACAGTAGAAGG 58.752 52.381 0.00 0.00 46.17 3.46
2200 2316 4.336889 TTTGGTCACAGGACAGTAGAAG 57.663 45.455 0.00 0.00 46.17 2.85
2201 2317 4.346709 TGATTTGGTCACAGGACAGTAGAA 59.653 41.667 0.00 0.00 46.17 2.10
2202 2318 3.901222 TGATTTGGTCACAGGACAGTAGA 59.099 43.478 0.00 0.00 46.17 2.59
2203 2319 4.271696 TGATTTGGTCACAGGACAGTAG 57.728 45.455 0.00 0.00 46.17 2.57
2204 2320 4.578871 CATGATTTGGTCACAGGACAGTA 58.421 43.478 0.00 0.00 46.17 2.74
2208 2324 2.095059 GTGCATGATTTGGTCACAGGAC 60.095 50.000 0.00 0.00 40.28 3.85
2219 2335 3.696051 ACCGCTAGAAATGTGCATGATTT 59.304 39.130 0.00 6.40 0.00 2.17
2222 2338 2.401583 ACCGCTAGAAATGTGCATGA 57.598 45.000 0.00 0.00 0.00 3.07
2224 2340 2.485479 CCCTACCGCTAGAAATGTGCAT 60.485 50.000 0.00 0.00 0.00 3.96
2225 2341 1.134521 CCCTACCGCTAGAAATGTGCA 60.135 52.381 0.00 0.00 0.00 4.57
2226 2342 1.134491 ACCCTACCGCTAGAAATGTGC 60.134 52.381 0.00 0.00 0.00 4.57
2228 2344 2.093128 CCAACCCTACCGCTAGAAATGT 60.093 50.000 0.00 0.00 0.00 2.71
2230 2346 1.134189 GCCAACCCTACCGCTAGAAAT 60.134 52.381 0.00 0.00 0.00 2.17
2232 2348 1.619807 GGCCAACCCTACCGCTAGAA 61.620 60.000 0.00 0.00 0.00 2.10
2234 2350 2.363975 TGGCCAACCCTACCGCTAG 61.364 63.158 0.61 0.00 33.59 3.42
2235 2351 2.284773 TGGCCAACCCTACCGCTA 60.285 61.111 0.61 0.00 33.59 4.26
2236 2352 4.029809 GTGGCCAACCCTACCGCT 62.030 66.667 7.24 0.00 33.59 5.52


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

AutoCloner maintained by Alex Coulton.