Multiple sequence alignment - TraesCS6A01G238700

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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 TraesCS6A01G238700 chr6A 100.000 2594 0 0 1 2594 448233153 448230560 0.000000e+00 4791
1 TraesCS6A01G238700 chr6A 87.172 725 76 11 3 718 60238409 60239125 0.000000e+00 808
2 TraesCS6A01G238700 chr3D 93.017 1074 69 3 749 1817 6288120 6289192 0.000000e+00 1563
3 TraesCS6A01G238700 chr3D 88.771 757 68 14 3 748 149635445 149634695 0.000000e+00 911
4 TraesCS6A01G238700 chr7A 92.910 1072 69 6 749 1814 141057905 141056835 0.000000e+00 1552
5 TraesCS6A01G238700 chr7A 92.731 1073 70 7 749 1814 141903178 141902107 0.000000e+00 1543
6 TraesCS6A01G238700 chr7A 92.257 1072 76 6 749 1814 141312076 141311006 0.000000e+00 1513
7 TraesCS6A01G238700 chr7D 92.658 1076 64 6 749 1817 561524692 561523625 0.000000e+00 1535
8 TraesCS6A01G238700 chr7D 92.465 1075 73 5 749 1817 188555634 188554562 0.000000e+00 1530
9 TraesCS6A01G238700 chr7D 85.547 768 86 23 3 749 100346798 100346035 0.000000e+00 780
10 TraesCS6A01G238700 chr4A 92.544 1073 73 6 749 1815 588659605 588658534 0.000000e+00 1531
11 TraesCS6A01G238700 chr6D 92.458 1074 74 4 749 1817 275680942 275679871 0.000000e+00 1528
12 TraesCS6A01G238700 chr6D 89.848 591 42 10 2014 2594 311556619 311556037 0.000000e+00 743
13 TraesCS6A01G238700 chr4D 92.179 1074 78 3 749 1817 490088744 490087672 0.000000e+00 1513
14 TraesCS6A01G238700 chr4D 88.089 764 71 17 3 748 266937520 266938281 0.000000e+00 889
15 TraesCS6A01G238700 chr3A 89.564 757 65 12 3 748 732881931 732882684 0.000000e+00 948
16 TraesCS6A01G238700 chr5D 88.583 762 67 12 3 749 436264712 436265468 0.000000e+00 907
17 TraesCS6A01G238700 chr5D 86.939 758 80 10 3 746 81186368 81185616 0.000000e+00 833
18 TraesCS6A01G238700 chr2A 88.142 759 70 13 3 748 650770809 650771560 0.000000e+00 885
19 TraesCS6A01G238700 chr1D 86.649 749 76 13 3 731 130319949 130319205 0.000000e+00 808
20 TraesCS6A01G238700 chr6B 88.689 557 40 9 2042 2594 515058618 515059155 0.000000e+00 658
21 TraesCS6A01G238700 chr2B 88.235 102 12 0 1797 1898 636459223 636459122 3.510000e-24 122
22 TraesCS6A01G238700 chr2B 86.869 99 12 1 1801 1898 65430782 65430684 2.730000e-20 110
23 TraesCS6A01G238700 chr1A 86.869 99 12 1 1801 1898 327010309 327010211 2.730000e-20 110
24 TraesCS6A01G238700 chr1A 84.314 102 15 1 1797 1898 387996804 387996904 5.910000e-17 99
25 TraesCS6A01G238700 chr5B 85.149 101 15 0 1798 1898 34492004 34492104 1.270000e-18 104


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 TraesCS6A01G238700 chr6A 448230560 448233153 2593 True 4791 4791 100.000 1 2594 1 chr6A.!!$R1 2593
1 TraesCS6A01G238700 chr6A 60238409 60239125 716 False 808 808 87.172 3 718 1 chr6A.!!$F1 715
2 TraesCS6A01G238700 chr3D 6288120 6289192 1072 False 1563 1563 93.017 749 1817 1 chr3D.!!$F1 1068
3 TraesCS6A01G238700 chr3D 149634695 149635445 750 True 911 911 88.771 3 748 1 chr3D.!!$R1 745
4 TraesCS6A01G238700 chr7A 141056835 141057905 1070 True 1552 1552 92.910 749 1814 1 chr7A.!!$R1 1065
5 TraesCS6A01G238700 chr7A 141902107 141903178 1071 True 1543 1543 92.731 749 1814 1 chr7A.!!$R3 1065
6 TraesCS6A01G238700 chr7A 141311006 141312076 1070 True 1513 1513 92.257 749 1814 1 chr7A.!!$R2 1065
7 TraesCS6A01G238700 chr7D 561523625 561524692 1067 True 1535 1535 92.658 749 1817 1 chr7D.!!$R3 1068
8 TraesCS6A01G238700 chr7D 188554562 188555634 1072 True 1530 1530 92.465 749 1817 1 chr7D.!!$R2 1068
9 TraesCS6A01G238700 chr7D 100346035 100346798 763 True 780 780 85.547 3 749 1 chr7D.!!$R1 746
10 TraesCS6A01G238700 chr4A 588658534 588659605 1071 True 1531 1531 92.544 749 1815 1 chr4A.!!$R1 1066
11 TraesCS6A01G238700 chr6D 275679871 275680942 1071 True 1528 1528 92.458 749 1817 1 chr6D.!!$R1 1068
12 TraesCS6A01G238700 chr6D 311556037 311556619 582 True 743 743 89.848 2014 2594 1 chr6D.!!$R2 580
13 TraesCS6A01G238700 chr4D 490087672 490088744 1072 True 1513 1513 92.179 749 1817 1 chr4D.!!$R1 1068
14 TraesCS6A01G238700 chr4D 266937520 266938281 761 False 889 889 88.089 3 748 1 chr4D.!!$F1 745
15 TraesCS6A01G238700 chr3A 732881931 732882684 753 False 948 948 89.564 3 748 1 chr3A.!!$F1 745
16 TraesCS6A01G238700 chr5D 436264712 436265468 756 False 907 907 88.583 3 749 1 chr5D.!!$F1 746
17 TraesCS6A01G238700 chr5D 81185616 81186368 752 True 833 833 86.939 3 746 1 chr5D.!!$R1 743
18 TraesCS6A01G238700 chr2A 650770809 650771560 751 False 885 885 88.142 3 748 1 chr2A.!!$F1 745
19 TraesCS6A01G238700 chr1D 130319205 130319949 744 True 808 808 86.649 3 731 1 chr1D.!!$R1 728
20 TraesCS6A01G238700 chr6B 515058618 515059155 537 False 658 658 88.689 2042 2594 1 chr6B.!!$F1 552

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
234 262 0.550147 TCCCTTCCCCCTCTTCCTTG 60.55 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2038 0.031585 TGTTCGATAATCGGAGCGGG 59.968 55.0 0.0 0.0 40.88 6.13 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
148 149 2.736826 GGGAAGAGAGGAAGGGCCG 61.737 68.421 0.00 0.00 43.43 6.13
234 262 0.550147 TCCCTTCCCCCTCTTCCTTG 60.550 60.000 0.00 0.00 0.00 3.61
269 298 3.021177 AGACTTGGAGTCCTAGTAGGC 57.979 52.381 23.82 13.18 46.18 3.93
286 316 2.381941 GCTTCCCCTCTCCTGGCAT 61.382 63.158 0.00 0.00 0.00 4.40
322 366 1.743589 CCTCCCCTCCCCCTTTATAC 58.256 60.000 0.00 0.00 0.00 1.47
326 370 1.693404 CCCCTCCCCCTTTATACACGA 60.693 57.143 0.00 0.00 0.00 4.35
367 415 7.338800 AGAACACACAAGATCAATTGTCTTT 57.661 32.000 15.99 8.74 41.41 2.52
583 635 0.604073 TACGTTCGGTGCTTGGATCA 59.396 50.000 0.00 0.00 0.00 2.92
624 676 4.587584 TGACTACATCAACCACGTTACA 57.412 40.909 0.00 0.00 33.02 2.41
682 736 1.228894 ACTCTCCCCTCTCGTTGCA 60.229 57.895 0.00 0.00 0.00 4.08
685 739 1.757118 CTCTCCCCTCTCGTTGCAATA 59.243 52.381 0.59 0.00 0.00 1.90
722 777 5.699915 AGATCTTGCATGATCGTAGGAATTG 59.300 40.000 27.51 0.00 45.35 2.32
770 825 3.272017 CCCAAGGGAAGGGGTTGT 58.728 61.111 0.00 0.00 42.90 3.32
771 826 1.546738 CCCAAGGGAAGGGGTTGTT 59.453 57.895 0.00 0.00 42.90 2.83
777 832 1.118965 GGGAAGGGGTTGTTGTTGGG 61.119 60.000 0.00 0.00 0.00 4.12
785 840 0.755327 GTTGTTGTTGGGGCTGGAGT 60.755 55.000 0.00 0.00 0.00 3.85
836 891 3.823873 GGTTGACAGTGAGAGAAGAGAGA 59.176 47.826 0.00 0.00 0.00 3.10
859 914 1.219935 GGGTAAGTAGTGGTGGGCG 59.780 63.158 0.00 0.00 0.00 6.13
880 935 2.983898 GGGGTGAGTAAATATAGGGGCA 59.016 50.000 0.00 0.00 0.00 5.36
900 957 2.086610 ATGGAGAGGAGGAGAAGAGC 57.913 55.000 0.00 0.00 0.00 4.09
905 962 1.178276 GAGGAGGAGAAGAGCGACAA 58.822 55.000 0.00 0.00 0.00 3.18
919 976 4.032703 AGCGACAATCATGCCATTTTAC 57.967 40.909 0.00 0.00 0.00 2.01
949 1006 4.260538 GCTCTTCAATAAGCCATGAACTCG 60.261 45.833 0.00 0.00 32.46 4.18
950 1007 5.084818 TCTTCAATAAGCCATGAACTCGA 57.915 39.130 0.00 0.00 32.46 4.04
974 1031 5.863965 TGTTGTGTCTGACTCCATGAATTA 58.136 37.500 9.51 0.00 0.00 1.40
1010 1067 2.484062 GCAATGAGATGGGCACGGG 61.484 63.158 0.00 0.00 0.00 5.28
1059 1116 1.214305 AGCAGCCCCTTCACCCAATA 61.214 55.000 0.00 0.00 0.00 1.90
1243 1303 1.372087 GAAGCTTGAGTGCATCCCCG 61.372 60.000 2.10 0.00 34.99 5.73
1299 1359 1.673033 CCGACGGAATTCAAGCTCAGT 60.673 52.381 8.64 0.00 0.00 3.41
1461 1525 3.118992 CCTCAAGGTCATCATCTTCGACA 60.119 47.826 0.00 0.00 0.00 4.35
1464 1528 3.961480 AGGTCATCATCTTCGACAACA 57.039 42.857 0.00 0.00 0.00 3.33
1468 1532 4.631377 GGTCATCATCTTCGACAACAATGA 59.369 41.667 0.00 0.00 0.00 2.57
1493 1557 1.593209 GGTCGTCAACAAGTGCGGA 60.593 57.895 0.00 0.00 0.00 5.54
1572 1636 3.938963 TCGAGTCTGCTTTGAACTGTTTT 59.061 39.130 0.00 0.00 0.00 2.43
1631 1696 8.924303 AGTGTGGTACTGCTTATCTGAAATATA 58.076 33.333 0.00 0.00 38.49 0.86
1636 1701 9.632807 GGTACTGCTTATCTGAAATATACTCTG 57.367 37.037 0.00 0.00 0.00 3.35
1669 1734 8.948401 TGATCCTCTATTTATACTCTGCTCTT 57.052 34.615 0.00 0.00 0.00 2.85
1708 1774 0.882927 GGTTGTGCCGAAGTGTGCTA 60.883 55.000 0.00 0.00 0.00 3.49
1731 1797 3.306472 AACCTCACCAACTAGCCAAAA 57.694 42.857 0.00 0.00 0.00 2.44
1756 1822 0.250901 ACCACACTCCAGATGTTGCC 60.251 55.000 0.00 0.00 0.00 4.52
1773 1839 2.235016 TGCCTACAACCAAACACCATC 58.765 47.619 0.00 0.00 0.00 3.51
1774 1840 2.158534 TGCCTACAACCAAACACCATCT 60.159 45.455 0.00 0.00 0.00 2.90
1795 1862 8.335532 CATCTTTTGGATTTGTCCACTAACTA 57.664 34.615 0.00 0.00 39.90 2.24
1799 1866 6.428083 TTGGATTTGTCCACTAACTACAGA 57.572 37.500 0.00 0.00 39.90 3.41
1817 1884 2.361757 CAGACAACCAAACATCAGGCAA 59.638 45.455 0.00 0.00 0.00 4.52
1818 1885 3.030291 AGACAACCAAACATCAGGCAAA 58.970 40.909 0.00 0.00 0.00 3.68
1819 1886 3.642848 AGACAACCAAACATCAGGCAAAT 59.357 39.130 0.00 0.00 0.00 2.32
1820 1887 3.731089 ACAACCAAACATCAGGCAAATG 58.269 40.909 0.00 0.00 0.00 2.32
1821 1888 3.068560 CAACCAAACATCAGGCAAATGG 58.931 45.455 4.47 0.00 0.00 3.16
1822 1889 2.328319 ACCAAACATCAGGCAAATGGT 58.672 42.857 4.47 0.00 34.98 3.55
1823 1890 2.037511 ACCAAACATCAGGCAAATGGTG 59.962 45.455 0.00 0.00 38.22 4.17
1837 1904 4.558178 CAAATGGTGCATTTAAGACTGCA 58.442 39.130 0.00 5.60 41.40 4.41
1854 1921 2.486951 GCATTTGCATAGCCAGACTG 57.513 50.000 0.00 0.00 41.59 3.51
1855 1922 2.019249 GCATTTGCATAGCCAGACTGA 58.981 47.619 3.32 0.00 41.59 3.41
1856 1923 2.033049 GCATTTGCATAGCCAGACTGAG 59.967 50.000 3.32 0.00 41.59 3.35
1857 1924 3.276857 CATTTGCATAGCCAGACTGAGT 58.723 45.455 3.32 0.00 0.00 3.41
1858 1925 3.423539 TTTGCATAGCCAGACTGAGTT 57.576 42.857 3.32 0.00 0.00 3.01
1859 1926 2.391616 TGCATAGCCAGACTGAGTTG 57.608 50.000 3.32 0.00 0.00 3.16
1860 1927 1.901833 TGCATAGCCAGACTGAGTTGA 59.098 47.619 3.32 0.00 0.00 3.18
1861 1928 2.302733 TGCATAGCCAGACTGAGTTGAA 59.697 45.455 3.32 0.00 0.00 2.69
1862 1929 3.244526 TGCATAGCCAGACTGAGTTGAAA 60.245 43.478 3.32 0.00 0.00 2.69
1863 1930 3.753272 GCATAGCCAGACTGAGTTGAAAA 59.247 43.478 3.32 0.00 0.00 2.29
1864 1931 4.142730 GCATAGCCAGACTGAGTTGAAAAG 60.143 45.833 3.32 0.00 0.00 2.27
1865 1932 2.856222 AGCCAGACTGAGTTGAAAAGG 58.144 47.619 3.32 0.00 0.00 3.11
1866 1933 1.268079 GCCAGACTGAGTTGAAAAGGC 59.732 52.381 3.32 0.00 0.00 4.35
1867 1934 2.856222 CCAGACTGAGTTGAAAAGGCT 58.144 47.619 3.32 0.00 0.00 4.58
1868 1935 3.807209 GCCAGACTGAGTTGAAAAGGCTA 60.807 47.826 3.32 0.00 36.72 3.93
1869 1936 4.583871 CCAGACTGAGTTGAAAAGGCTAT 58.416 43.478 3.32 0.00 0.00 2.97
1870 1937 4.394300 CCAGACTGAGTTGAAAAGGCTATG 59.606 45.833 3.32 0.00 0.00 2.23
1871 1938 4.006319 AGACTGAGTTGAAAAGGCTATGC 58.994 43.478 0.00 0.00 0.00 3.14
1872 1939 3.753272 GACTGAGTTGAAAAGGCTATGCA 59.247 43.478 0.00 0.00 0.00 3.96
1873 1940 4.144297 ACTGAGTTGAAAAGGCTATGCAA 58.856 39.130 0.00 0.00 0.00 4.08
1874 1941 4.768968 ACTGAGTTGAAAAGGCTATGCAAT 59.231 37.500 0.00 0.00 0.00 3.56
1875 1942 5.945784 ACTGAGTTGAAAAGGCTATGCAATA 59.054 36.000 0.00 0.00 0.00 1.90
1876 1943 6.127897 ACTGAGTTGAAAAGGCTATGCAATAC 60.128 38.462 0.00 0.00 0.00 1.89
1877 1944 5.709631 TGAGTTGAAAAGGCTATGCAATACA 59.290 36.000 0.00 0.00 0.00 2.29
1878 1945 6.127925 TGAGTTGAAAAGGCTATGCAATACAG 60.128 38.462 0.00 0.00 0.00 2.74
1879 1946 4.637483 TGAAAAGGCTATGCAATACAGC 57.363 40.909 0.00 0.00 34.48 4.40
1880 1947 4.272489 TGAAAAGGCTATGCAATACAGCT 58.728 39.130 11.28 0.00 35.60 4.24
1881 1948 5.436175 TGAAAAGGCTATGCAATACAGCTA 58.564 37.500 11.28 0.00 35.60 3.32
1882 1949 5.296780 TGAAAAGGCTATGCAATACAGCTAC 59.703 40.000 11.28 0.00 35.60 3.58
1883 1950 4.696479 AAGGCTATGCAATACAGCTACT 57.304 40.909 11.28 1.28 35.60 2.57
1884 1951 4.000331 AGGCTATGCAATACAGCTACTG 58.000 45.455 11.28 0.00 35.60 2.74
1886 1953 4.130118 GGCTATGCAATACAGCTACTGTT 58.870 43.478 5.44 0.00 42.59 3.16
1887 1954 4.024556 GGCTATGCAATACAGCTACTGTTG 60.025 45.833 5.44 0.49 42.59 3.33
1888 1955 4.024556 GCTATGCAATACAGCTACTGTTGG 60.025 45.833 5.44 0.00 42.59 3.77
1889 1956 2.083774 TGCAATACAGCTACTGTTGGC 58.916 47.619 5.44 8.01 42.59 4.52
1890 1957 2.290260 TGCAATACAGCTACTGTTGGCT 60.290 45.455 5.44 2.83 42.59 4.75
1891 1958 3.055458 TGCAATACAGCTACTGTTGGCTA 60.055 43.478 5.44 0.00 42.59 3.93
1892 1959 3.309954 GCAATACAGCTACTGTTGGCTAC 59.690 47.826 5.44 0.00 42.59 3.58
1893 1960 2.933495 TACAGCTACTGTTGGCTACG 57.067 50.000 5.44 0.00 42.59 3.51
1894 1961 0.246635 ACAGCTACTGTTGGCTACGG 59.753 55.000 6.36 6.36 42.59 4.02
1895 1962 1.084370 CAGCTACTGTTGGCTACGGC 61.084 60.000 7.84 3.43 37.00 5.68
1896 1963 1.079405 GCTACTGTTGGCTACGGCA 60.079 57.895 7.84 0.00 40.87 5.69
1897 1964 0.672401 GCTACTGTTGGCTACGGCAA 60.672 55.000 7.84 0.00 45.54 4.52
1913 1980 3.458872 CAAGTATTGCTCCGCTCCA 57.541 52.632 0.00 0.00 40.39 3.86
1914 1981 1.009829 CAAGTATTGCTCCGCTCCAC 58.990 55.000 0.00 0.00 40.39 4.02
1915 1982 0.613260 AAGTATTGCTCCGCTCCACA 59.387 50.000 0.00 0.00 0.00 4.17
1916 1983 0.613260 AGTATTGCTCCGCTCCACAA 59.387 50.000 0.00 0.00 0.00 3.33
1917 1984 0.727398 GTATTGCTCCGCTCCACAAC 59.273 55.000 0.00 0.00 0.00 3.32
1918 1985 0.613260 TATTGCTCCGCTCCACAACT 59.387 50.000 0.00 0.00 0.00 3.16
1919 1986 0.674895 ATTGCTCCGCTCCACAACTC 60.675 55.000 0.00 0.00 0.00 3.01
1920 1987 2.435059 GCTCCGCTCCACAACTCC 60.435 66.667 0.00 0.00 0.00 3.85
1921 1988 2.948720 GCTCCGCTCCACAACTCCT 61.949 63.158 0.00 0.00 0.00 3.69
1922 1989 1.674057 CTCCGCTCCACAACTCCTT 59.326 57.895 0.00 0.00 0.00 3.36
1923 1990 0.895530 CTCCGCTCCACAACTCCTTA 59.104 55.000 0.00 0.00 0.00 2.69
1924 1991 0.895530 TCCGCTCCACAACTCCTTAG 59.104 55.000 0.00 0.00 0.00 2.18
1925 1992 0.741221 CCGCTCCACAACTCCTTAGC 60.741 60.000 0.00 0.00 0.00 3.09
1926 1993 0.037326 CGCTCCACAACTCCTTAGCA 60.037 55.000 0.00 0.00 0.00 3.49
1927 1994 1.731720 GCTCCACAACTCCTTAGCAG 58.268 55.000 0.00 0.00 0.00 4.24
1928 1995 1.276421 GCTCCACAACTCCTTAGCAGA 59.724 52.381 0.00 0.00 0.00 4.26
1929 1996 2.676463 GCTCCACAACTCCTTAGCAGAG 60.676 54.545 0.00 0.00 37.39 3.35
1930 1997 2.564947 CTCCACAACTCCTTAGCAGAGT 59.435 50.000 0.00 0.00 46.50 3.24
1936 2003 1.751924 ACTCCTTAGCAGAGTTAGCGG 59.248 52.381 0.00 0.00 41.87 5.52
1937 2004 2.025155 CTCCTTAGCAGAGTTAGCGGA 58.975 52.381 0.00 0.00 37.01 5.54
1938 2005 2.025155 TCCTTAGCAGAGTTAGCGGAG 58.975 52.381 0.00 0.00 37.01 4.63
1955 2022 4.701956 CGGAGCTACAATTCAAAATGGT 57.298 40.909 0.00 0.00 0.00 3.55
1956 2023 4.414852 CGGAGCTACAATTCAAAATGGTG 58.585 43.478 0.00 0.00 0.00 4.17
1957 2024 4.675146 CGGAGCTACAATTCAAAATGGTGG 60.675 45.833 0.00 0.00 0.00 4.61
1958 2025 4.462483 GGAGCTACAATTCAAAATGGTGGA 59.538 41.667 0.00 0.00 0.00 4.02
1959 2026 5.393461 GGAGCTACAATTCAAAATGGTGGAG 60.393 44.000 0.00 0.00 0.00 3.86
1960 2027 5.079643 AGCTACAATTCAAAATGGTGGAGT 58.920 37.500 0.00 0.00 0.00 3.85
1961 2028 5.539955 AGCTACAATTCAAAATGGTGGAGTT 59.460 36.000 0.00 0.00 0.00 3.01
1962 2029 5.634859 GCTACAATTCAAAATGGTGGAGTTG 59.365 40.000 0.00 0.00 35.27 3.16
1963 2030 4.379652 ACAATTCAAAATGGTGGAGTTGC 58.620 39.130 0.00 0.00 33.23 4.17
1964 2031 4.141756 ACAATTCAAAATGGTGGAGTTGCA 60.142 37.500 0.00 0.00 33.23 4.08
1965 2032 4.686191 ATTCAAAATGGTGGAGTTGCAA 57.314 36.364 0.00 0.00 0.00 4.08
1966 2033 4.686191 TTCAAAATGGTGGAGTTGCAAT 57.314 36.364 0.59 0.00 0.00 3.56
1967 2034 4.686191 TCAAAATGGTGGAGTTGCAATT 57.314 36.364 0.59 0.00 0.00 2.32
1968 2035 5.033589 TCAAAATGGTGGAGTTGCAATTT 57.966 34.783 0.59 0.00 0.00 1.82
1969 2036 5.435291 TCAAAATGGTGGAGTTGCAATTTT 58.565 33.333 0.59 0.00 0.00 1.82
1970 2037 5.526846 TCAAAATGGTGGAGTTGCAATTTTC 59.473 36.000 0.59 1.03 0.00 2.29
1971 2038 3.683365 ATGGTGGAGTTGCAATTTTCC 57.317 42.857 16.40 16.40 0.00 3.13
1972 2039 1.691434 TGGTGGAGTTGCAATTTTCCC 59.309 47.619 18.99 11.12 0.00 3.97
1973 2040 1.001974 GGTGGAGTTGCAATTTTCCCC 59.998 52.381 18.99 16.17 0.00 4.81
1974 2041 0.965439 TGGAGTTGCAATTTTCCCCG 59.035 50.000 18.99 0.00 0.00 5.73
1975 2042 0.389817 GGAGTTGCAATTTTCCCCGC 60.390 55.000 0.59 0.00 0.00 6.13
1976 2043 0.603065 GAGTTGCAATTTTCCCCGCT 59.397 50.000 0.59 0.00 0.00 5.52
1977 2044 0.603065 AGTTGCAATTTTCCCCGCTC 59.397 50.000 0.59 0.00 0.00 5.03
1978 2045 0.389817 GTTGCAATTTTCCCCGCTCC 60.390 55.000 0.59 0.00 0.00 4.70
1979 2046 1.872197 TTGCAATTTTCCCCGCTCCG 61.872 55.000 0.00 0.00 0.00 4.63
1980 2047 2.043980 GCAATTTTCCCCGCTCCGA 61.044 57.895 0.00 0.00 0.00 4.55
1981 2048 1.384222 GCAATTTTCCCCGCTCCGAT 61.384 55.000 0.00 0.00 0.00 4.18
1982 2049 1.102978 CAATTTTCCCCGCTCCGATT 58.897 50.000 0.00 0.00 0.00 3.34
1983 2050 2.294074 CAATTTTCCCCGCTCCGATTA 58.706 47.619 0.00 0.00 0.00 1.75
1984 2051 2.884639 CAATTTTCCCCGCTCCGATTAT 59.115 45.455 0.00 0.00 0.00 1.28
1985 2052 2.249844 TTTTCCCCGCTCCGATTATC 57.750 50.000 0.00 0.00 0.00 1.75
1986 2053 0.032952 TTTCCCCGCTCCGATTATCG 59.967 55.000 7.74 7.74 40.07 2.92
1987 2054 0.824595 TTCCCCGCTCCGATTATCGA 60.825 55.000 16.78 1.62 43.74 3.59
1988 2055 0.824595 TCCCCGCTCCGATTATCGAA 60.825 55.000 16.78 0.00 43.74 3.71
1989 2056 0.666577 CCCCGCTCCGATTATCGAAC 60.667 60.000 16.78 3.99 43.74 3.95
1990 2057 0.031585 CCCGCTCCGATTATCGAACA 59.968 55.000 16.78 0.00 43.74 3.18
1991 2058 1.409412 CCGCTCCGATTATCGAACAG 58.591 55.000 16.78 9.57 43.74 3.16
1992 2059 1.409412 CGCTCCGATTATCGAACAGG 58.591 55.000 16.78 0.00 43.74 4.00
1993 2060 1.784525 GCTCCGATTATCGAACAGGG 58.215 55.000 16.78 0.00 43.74 4.45
1994 2061 1.784525 CTCCGATTATCGAACAGGGC 58.215 55.000 16.78 0.00 43.74 5.19
1995 2062 0.391597 TCCGATTATCGAACAGGGCC 59.608 55.000 16.78 0.00 43.74 5.80
1996 2063 0.393077 CCGATTATCGAACAGGGCCT 59.607 55.000 16.78 0.00 43.74 5.19
1997 2064 1.202651 CCGATTATCGAACAGGGCCTT 60.203 52.381 16.78 0.00 43.74 4.35
1998 2065 2.036733 CCGATTATCGAACAGGGCCTTA 59.963 50.000 16.78 0.00 43.74 2.69
1999 2066 3.306780 CCGATTATCGAACAGGGCCTTAT 60.307 47.826 16.78 0.00 43.74 1.73
2000 2067 4.315803 CGATTATCGAACAGGGCCTTATT 58.684 43.478 9.20 0.06 43.74 1.40
2001 2068 4.755123 CGATTATCGAACAGGGCCTTATTT 59.245 41.667 9.20 0.00 43.74 1.40
2002 2069 5.334105 CGATTATCGAACAGGGCCTTATTTG 60.334 44.000 9.20 5.70 43.74 2.32
2003 2070 3.644966 ATCGAACAGGGCCTTATTTGA 57.355 42.857 16.24 16.24 0.00 2.69
2004 2071 3.644966 TCGAACAGGGCCTTATTTGAT 57.355 42.857 1.32 0.00 0.00 2.57
2005 2072 3.963129 TCGAACAGGGCCTTATTTGATT 58.037 40.909 1.32 0.00 0.00 2.57
2006 2073 3.694072 TCGAACAGGGCCTTATTTGATTG 59.306 43.478 1.32 0.00 0.00 2.67
2007 2074 3.443681 CGAACAGGGCCTTATTTGATTGT 59.556 43.478 1.32 0.00 0.00 2.71
2008 2075 4.082245 CGAACAGGGCCTTATTTGATTGTT 60.082 41.667 1.32 1.83 0.00 2.83
2009 2076 5.566627 CGAACAGGGCCTTATTTGATTGTTT 60.567 40.000 1.32 0.00 0.00 2.83
2010 2077 5.405935 ACAGGGCCTTATTTGATTGTTTC 57.594 39.130 1.32 0.00 0.00 2.78
2011 2078 4.837860 ACAGGGCCTTATTTGATTGTTTCA 59.162 37.500 1.32 0.00 0.00 2.69
2012 2079 5.306678 ACAGGGCCTTATTTGATTGTTTCAA 59.693 36.000 1.32 0.00 42.62 2.69
2046 2113 3.006752 CAGACTTCCTTCTTGAGCAGAGT 59.993 47.826 0.00 0.00 31.12 3.24
2051 2118 3.733337 TCCTTCTTGAGCAGAGTTCAAC 58.267 45.455 0.00 0.00 31.12 3.18
2085 2152 8.112016 TGTATAATAGAGAAGGAATCAGTCGG 57.888 38.462 0.00 0.00 0.00 4.79
2108 2175 0.609131 AATTAGTGCTTGGCGCCAGT 60.609 50.000 30.75 13.38 40.23 4.00
2122 2189 1.136057 CGCCAGTTACGAAGCCTTTTC 60.136 52.381 0.00 0.00 0.00 2.29
2123 2190 1.877443 GCCAGTTACGAAGCCTTTTCA 59.123 47.619 0.00 0.00 0.00 2.69
2124 2191 2.095718 GCCAGTTACGAAGCCTTTTCAG 60.096 50.000 0.00 0.00 0.00 3.02
2125 2192 2.484264 CCAGTTACGAAGCCTTTTCAGG 59.516 50.000 0.00 0.00 44.28 3.86
2133 2203 4.584743 ACGAAGCCTTTTCAGGAAAGAAAT 59.415 37.500 2.28 0.00 46.24 2.17
2142 2212 7.172019 CCTTTTCAGGAAAGAAATCCACATTTG 59.828 37.037 2.28 0.00 46.24 2.32
2144 2214 6.729690 TCAGGAAAGAAATCCACATTTGTT 57.270 33.333 0.00 0.00 42.27 2.83
2145 2215 7.123355 TCAGGAAAGAAATCCACATTTGTTT 57.877 32.000 3.06 3.06 44.25 2.83
2151 2221 6.983906 AGAAATCCACATTTGTTTCCTTCT 57.016 33.333 0.00 0.00 31.94 2.85
2152 2222 7.365497 AGAAATCCACATTTGTTTCCTTCTT 57.635 32.000 0.00 0.00 31.94 2.52
2172 2244 6.751514 TCTTAGCTCCGCATCAAAATAAAA 57.248 33.333 0.00 0.00 0.00 1.52
2193 2265 1.406065 ATCATCCAGACCAGAGGCGG 61.406 60.000 0.00 0.00 0.00 6.13
2281 2355 0.106708 GTCTGTCCACTGTGAAGGCA 59.893 55.000 9.86 0.00 0.00 4.75
2282 2356 0.836606 TCTGTCCACTGTGAAGGCAA 59.163 50.000 9.86 0.00 0.00 4.52
2308 2382 5.801380 ACGGCTACAACTAATAATATGGGG 58.199 41.667 0.00 0.00 0.00 4.96
2331 2407 5.418676 GCATTGCCCACATAAAACTGTAAT 58.581 37.500 0.00 0.00 0.00 1.89
2333 2409 7.038659 GCATTGCCCACATAAAACTGTAATAA 58.961 34.615 0.00 0.00 0.00 1.40
2334 2410 7.010091 GCATTGCCCACATAAAACTGTAATAAC 59.990 37.037 0.00 0.00 0.00 1.89
2335 2411 7.526142 TTGCCCACATAAAACTGTAATAACA 57.474 32.000 0.00 0.00 0.00 2.41
2336 2412 7.710676 TGCCCACATAAAACTGTAATAACAT 57.289 32.000 0.00 0.00 34.37 2.71
2337 2413 8.809468 TGCCCACATAAAACTGTAATAACATA 57.191 30.769 0.00 0.00 34.37 2.29
2338 2414 9.244292 TGCCCACATAAAACTGTAATAACATAA 57.756 29.630 0.00 0.00 34.37 1.90
2362 2438 3.323751 AGCCGTAAACAGGAATAACGT 57.676 42.857 0.00 0.00 31.87 3.99
2391 2467 2.611971 GGCTGTACTCACGAATCCAACA 60.612 50.000 0.00 0.00 0.00 3.33
2428 2505 5.051641 GGCATAGAATAGAAGTTCGTTCACG 60.052 44.000 19.46 11.64 37.67 4.35
2451 2528 1.270839 GGGCAGAGAAGCAGTGTACAA 60.271 52.381 0.00 0.00 35.83 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.908786 AACATCGTCCAATACATCAATCTTAT 57.091 30.769 0.00 0.00 0.00 1.73
1 2 9.996554 ATAACATCGTCCAATACATCAATCTTA 57.003 29.630 0.00 0.00 0.00 2.10
11 12 5.045215 TGTCCGAATAACATCGTCCAATAC 58.955 41.667 0.00 0.00 41.16 1.89
53 54 5.978814 GGCACTCCGATAATTATCTGGTAT 58.021 41.667 23.62 15.74 32.25 2.73
127 128 1.901085 CCCTTCCTCTCTTCCCACG 59.099 63.158 0.00 0.00 0.00 4.94
234 262 3.055312 CCAAGTCTAGTAGGTTTCCACCC 60.055 52.174 0.00 0.00 45.63 4.61
269 298 1.530771 CATGCCAGGAGAGGGGAAG 59.469 63.158 0.00 0.00 0.00 3.46
308 352 1.692519 CCTCGTGTATAAAGGGGGAGG 59.307 57.143 0.00 0.00 34.27 4.30
310 354 1.797320 CCCTCGTGTATAAAGGGGGA 58.203 55.000 2.83 0.00 45.18 4.81
438 487 1.206132 TGATGATGAAGTTACCGGCGT 59.794 47.619 6.01 0.00 0.00 5.68
521 570 0.817654 ATTCAGCTCGATGACGTCCA 59.182 50.000 14.12 1.26 40.69 4.02
583 635 4.024048 GTCAAACATGTTCACGATCCAACT 60.024 41.667 12.39 0.00 0.00 3.16
662 715 1.216710 CAACGAGAGGGGAGAGTGC 59.783 63.158 0.00 0.00 0.00 4.40
682 736 8.891985 TGCAAGATCTATCTAGGAGATGTATT 57.108 34.615 11.48 3.50 35.37 1.89
685 739 6.952938 TCATGCAAGATCTATCTAGGAGATGT 59.047 38.462 11.48 6.21 35.37 3.06
722 777 8.086851 TGTTAGGGAACGTAGTATTTCAAAAC 57.913 34.615 0.00 0.00 45.00 2.43
770 825 1.351017 CTCTAACTCCAGCCCCAACAA 59.649 52.381 0.00 0.00 0.00 2.83
771 826 0.984230 CTCTAACTCCAGCCCCAACA 59.016 55.000 0.00 0.00 0.00 3.33
777 832 1.202627 CCATGAGCTCTAACTCCAGCC 60.203 57.143 16.19 0.00 36.17 4.85
785 840 0.394192 CCCATCGCCATGAGCTCTAA 59.606 55.000 16.19 0.00 40.39 2.10
836 891 1.652947 CACCACTACTTACCCACCCT 58.347 55.000 0.00 0.00 0.00 4.34
859 914 2.983898 TGCCCCTATATTTACTCACCCC 59.016 50.000 0.00 0.00 0.00 4.95
880 935 2.397597 GCTCTTCTCCTCCTCTCCATT 58.602 52.381 0.00 0.00 0.00 3.16
900 957 4.637483 AGGTAAAATGGCATGATTGTCG 57.363 40.909 0.00 0.00 0.00 4.35
905 962 5.142639 AGCATGTAGGTAAAATGGCATGAT 58.857 37.500 0.00 0.00 36.71 2.45
919 976 4.454678 TGGCTTATTGAAGAGCATGTAGG 58.545 43.478 5.83 0.00 40.63 3.18
949 1006 3.930336 TCATGGAGTCAGACACAACATC 58.070 45.455 2.66 0.00 0.00 3.06
950 1007 4.356405 TTCATGGAGTCAGACACAACAT 57.644 40.909 2.66 0.00 0.00 2.71
974 1031 0.388659 GCTCTCCTCGATCTGCACAT 59.611 55.000 0.00 0.00 0.00 3.21
1059 1116 3.231736 AGCACAACCTCGTCGGGT 61.232 61.111 0.00 0.00 42.05 5.28
1095 1152 3.358076 CTCAGGCGTCTTCGGGTCC 62.358 68.421 0.00 0.00 37.56 4.46
1123 1180 3.036429 GCTCCTCCATGCCCTCGTT 62.036 63.158 0.00 0.00 0.00 3.85
1243 1303 2.034221 GGTGAAGTCCAGGGGCAC 59.966 66.667 0.00 0.00 0.00 5.01
1287 1347 3.498397 CGGTGTTGTTACTGAGCTTGAAT 59.502 43.478 0.00 0.00 0.00 2.57
1299 1359 1.302192 GGAGCAGCCGGTGTTGTTA 60.302 57.895 1.90 0.00 0.00 2.41
1390 1450 4.944619 TGTAGCCGATCTTGATCTGATT 57.055 40.909 8.70 0.00 0.00 2.57
1461 1525 3.738982 TGACGACCTCAATGTCATTGTT 58.261 40.909 22.01 10.20 41.02 2.83
1464 1528 3.738982 TGTTGACGACCTCAATGTCATT 58.261 40.909 0.00 0.00 41.10 2.57
1468 1532 2.872245 CACTTGTTGACGACCTCAATGT 59.128 45.455 0.00 0.00 41.10 2.71
1493 1557 2.235546 GAAGGCTTCGTCGTGCTTT 58.764 52.632 12.12 9.18 0.00 3.51
1515 1579 2.687566 CCGGCCCTACTCCTTGGT 60.688 66.667 0.00 0.00 0.00 3.67
1572 1636 9.776158 CAGTTTTACGCATAAACCATAAACATA 57.224 29.630 0.00 0.00 36.40 2.29
1593 1657 5.238650 GCAGTACCACACTTCATAACAGTTT 59.761 40.000 0.00 0.00 34.26 2.66
1669 1734 5.357742 ACCATGTAGCACACATCATAAGA 57.642 39.130 1.26 0.00 44.99 2.10
1708 1774 4.650972 TTGGCTAGTTGGTGAGGTTATT 57.349 40.909 0.00 0.00 0.00 1.40
1731 1797 4.706842 ACATCTGGAGTGTGGTAACTTT 57.293 40.909 0.00 0.00 37.61 2.66
1756 1822 5.288804 CCAAAAGATGGTGTTTGGTTGTAG 58.711 41.667 6.95 0.00 45.80 2.74
1795 1862 1.956477 GCCTGATGTTTGGTTGTCTGT 59.044 47.619 0.00 0.00 0.00 3.41
1799 1866 3.494749 CCATTTGCCTGATGTTTGGTTGT 60.495 43.478 0.00 0.00 0.00 3.32
1835 1902 2.019249 TCAGTCTGGCTATGCAAATGC 58.981 47.619 0.00 0.00 42.50 3.56
1836 1903 3.276857 ACTCAGTCTGGCTATGCAAATG 58.723 45.455 0.00 0.00 0.00 2.32
1837 1904 3.641434 ACTCAGTCTGGCTATGCAAAT 57.359 42.857 0.00 0.00 0.00 2.32
1838 1905 3.076621 CAACTCAGTCTGGCTATGCAAA 58.923 45.455 0.00 0.00 0.00 3.68
1839 1906 2.302733 TCAACTCAGTCTGGCTATGCAA 59.697 45.455 0.00 0.00 0.00 4.08
1840 1907 1.901833 TCAACTCAGTCTGGCTATGCA 59.098 47.619 0.00 0.00 0.00 3.96
1841 1908 2.680312 TCAACTCAGTCTGGCTATGC 57.320 50.000 0.00 0.00 0.00 3.14
1842 1909 4.394300 CCTTTTCAACTCAGTCTGGCTATG 59.606 45.833 0.00 0.00 0.00 2.23
1843 1910 4.583871 CCTTTTCAACTCAGTCTGGCTAT 58.416 43.478 0.00 0.00 0.00 2.97
1844 1911 3.807209 GCCTTTTCAACTCAGTCTGGCTA 60.807 47.826 0.00 0.00 35.44 3.93
1845 1912 2.856222 CCTTTTCAACTCAGTCTGGCT 58.144 47.619 0.00 0.00 0.00 4.75
1846 1913 1.268079 GCCTTTTCAACTCAGTCTGGC 59.732 52.381 0.00 0.00 0.00 4.85
1847 1914 2.856222 AGCCTTTTCAACTCAGTCTGG 58.144 47.619 0.00 0.00 0.00 3.86
1848 1915 4.142730 GCATAGCCTTTTCAACTCAGTCTG 60.143 45.833 0.00 0.00 0.00 3.51
1849 1916 4.006319 GCATAGCCTTTTCAACTCAGTCT 58.994 43.478 0.00 0.00 0.00 3.24
1850 1917 3.753272 TGCATAGCCTTTTCAACTCAGTC 59.247 43.478 0.00 0.00 0.00 3.51
1851 1918 3.754965 TGCATAGCCTTTTCAACTCAGT 58.245 40.909 0.00 0.00 0.00 3.41
1852 1919 4.771590 TTGCATAGCCTTTTCAACTCAG 57.228 40.909 0.00 0.00 0.00 3.35
1853 1920 5.709631 TGTATTGCATAGCCTTTTCAACTCA 59.290 36.000 0.00 0.00 0.00 3.41
1854 1921 6.194796 TGTATTGCATAGCCTTTTCAACTC 57.805 37.500 0.00 0.00 0.00 3.01
1855 1922 5.393461 GCTGTATTGCATAGCCTTTTCAACT 60.393 40.000 0.00 0.00 35.44 3.16
1856 1923 4.800471 GCTGTATTGCATAGCCTTTTCAAC 59.200 41.667 0.00 0.00 35.44 3.18
1857 1924 4.706476 AGCTGTATTGCATAGCCTTTTCAA 59.294 37.500 8.55 0.00 42.10 2.69
1858 1925 4.272489 AGCTGTATTGCATAGCCTTTTCA 58.728 39.130 8.55 0.00 42.10 2.69
1859 1926 4.907879 AGCTGTATTGCATAGCCTTTTC 57.092 40.909 8.55 0.00 42.10 2.29
1860 1927 5.297776 CAGTAGCTGTATTGCATAGCCTTTT 59.702 40.000 0.00 0.00 42.10 2.27
1861 1928 4.818546 CAGTAGCTGTATTGCATAGCCTTT 59.181 41.667 0.00 0.00 42.10 3.11
1862 1929 4.141620 ACAGTAGCTGTATTGCATAGCCTT 60.142 41.667 0.00 0.00 43.46 4.35
1863 1930 3.389329 ACAGTAGCTGTATTGCATAGCCT 59.611 43.478 0.00 0.00 43.46 4.58
1864 1931 3.733337 ACAGTAGCTGTATTGCATAGCC 58.267 45.455 0.00 0.00 43.46 3.93
1865 1932 4.024556 CCAACAGTAGCTGTATTGCATAGC 60.025 45.833 0.00 0.00 44.62 2.97
1866 1933 4.024556 GCCAACAGTAGCTGTATTGCATAG 60.025 45.833 0.00 0.00 44.62 2.23
1867 1934 3.876914 GCCAACAGTAGCTGTATTGCATA 59.123 43.478 0.00 0.00 44.62 3.14
1868 1935 2.684881 GCCAACAGTAGCTGTATTGCAT 59.315 45.455 0.00 0.00 44.62 3.96
1869 1936 2.083774 GCCAACAGTAGCTGTATTGCA 58.916 47.619 0.00 0.00 44.62 4.08
1870 1937 2.359900 AGCCAACAGTAGCTGTATTGC 58.640 47.619 0.00 5.99 44.62 3.56
1871 1938 3.551890 CGTAGCCAACAGTAGCTGTATTG 59.448 47.826 8.05 0.00 44.62 1.90
1872 1939 3.430374 CCGTAGCCAACAGTAGCTGTATT 60.430 47.826 8.05 0.00 44.62 1.89
1873 1940 2.100916 CCGTAGCCAACAGTAGCTGTAT 59.899 50.000 8.05 0.00 44.62 2.29
1874 1941 1.475280 CCGTAGCCAACAGTAGCTGTA 59.525 52.381 8.05 0.00 44.62 2.74
1876 1943 1.084370 GCCGTAGCCAACAGTAGCTG 61.084 60.000 8.05 0.00 40.28 4.24
1877 1944 1.218316 GCCGTAGCCAACAGTAGCT 59.782 57.895 3.61 3.61 43.20 3.32
1878 1945 0.672401 TTGCCGTAGCCAACAGTAGC 60.672 55.000 0.00 0.00 38.69 3.58
1879 1946 1.337823 ACTTGCCGTAGCCAACAGTAG 60.338 52.381 0.00 0.00 38.69 2.57
1880 1947 0.682852 ACTTGCCGTAGCCAACAGTA 59.317 50.000 0.00 0.00 38.69 2.74
1881 1948 0.682852 TACTTGCCGTAGCCAACAGT 59.317 50.000 0.00 0.00 38.69 3.55
1882 1949 2.024176 ATACTTGCCGTAGCCAACAG 57.976 50.000 0.00 0.00 38.69 3.16
1883 1950 2.080693 CAATACTTGCCGTAGCCAACA 58.919 47.619 0.00 0.00 38.69 3.33
1884 1951 2.825086 CAATACTTGCCGTAGCCAAC 57.175 50.000 0.00 0.00 38.69 3.77
1904 1971 0.895530 TAAGGAGTTGTGGAGCGGAG 59.104 55.000 0.00 0.00 0.00 4.63
1905 1972 0.895530 CTAAGGAGTTGTGGAGCGGA 59.104 55.000 0.00 0.00 0.00 5.54
1906 1973 0.741221 GCTAAGGAGTTGTGGAGCGG 60.741 60.000 0.00 0.00 0.00 5.52
1907 1974 0.037326 TGCTAAGGAGTTGTGGAGCG 60.037 55.000 0.00 0.00 32.53 5.03
1908 1975 1.276421 TCTGCTAAGGAGTTGTGGAGC 59.724 52.381 0.00 0.00 0.00 4.70
1909 1976 2.564947 ACTCTGCTAAGGAGTTGTGGAG 59.435 50.000 0.00 0.00 40.65 3.86
1910 1977 2.609747 ACTCTGCTAAGGAGTTGTGGA 58.390 47.619 0.00 0.00 40.65 4.02
1916 1983 1.751924 CCGCTAACTCTGCTAAGGAGT 59.248 52.381 0.00 0.00 44.73 3.85
1917 1984 2.025155 TCCGCTAACTCTGCTAAGGAG 58.975 52.381 0.00 0.00 36.92 3.69
1918 1985 2.025155 CTCCGCTAACTCTGCTAAGGA 58.975 52.381 0.00 0.00 0.00 3.36
1919 1986 1.537135 GCTCCGCTAACTCTGCTAAGG 60.537 57.143 0.00 0.00 0.00 2.69
1920 1987 1.407258 AGCTCCGCTAACTCTGCTAAG 59.593 52.381 0.00 0.00 36.99 2.18
1921 1988 1.475403 AGCTCCGCTAACTCTGCTAA 58.525 50.000 0.00 0.00 36.99 3.09
1922 1989 1.948145 GTAGCTCCGCTAACTCTGCTA 59.052 52.381 0.00 0.00 43.07 3.49
1923 1990 0.741915 GTAGCTCCGCTAACTCTGCT 59.258 55.000 0.00 0.00 43.07 4.24
1924 1991 0.456221 TGTAGCTCCGCTAACTCTGC 59.544 55.000 0.00 0.00 43.07 4.26
1925 1992 2.941453 TTGTAGCTCCGCTAACTCTG 57.059 50.000 0.00 0.00 43.07 3.35
1926 1993 3.447586 TGAATTGTAGCTCCGCTAACTCT 59.552 43.478 0.00 0.00 43.07 3.24
1927 1994 3.782046 TGAATTGTAGCTCCGCTAACTC 58.218 45.455 0.00 0.00 43.07 3.01
1928 1995 3.887621 TGAATTGTAGCTCCGCTAACT 57.112 42.857 0.00 0.00 43.07 2.24
1929 1996 4.939509 TTTGAATTGTAGCTCCGCTAAC 57.060 40.909 0.00 0.00 43.07 2.34
1930 1997 5.163663 CCATTTTGAATTGTAGCTCCGCTAA 60.164 40.000 0.00 0.00 43.07 3.09
1931 1998 4.335315 CCATTTTGAATTGTAGCTCCGCTA 59.665 41.667 0.00 0.00 40.44 4.26
1932 1999 3.129287 CCATTTTGAATTGTAGCTCCGCT 59.871 43.478 0.00 0.00 43.41 5.52
1933 2000 3.119495 ACCATTTTGAATTGTAGCTCCGC 60.119 43.478 0.00 0.00 0.00 5.54
1934 2001 4.414852 CACCATTTTGAATTGTAGCTCCG 58.585 43.478 0.00 0.00 0.00 4.63
1935 2002 4.462483 TCCACCATTTTGAATTGTAGCTCC 59.538 41.667 0.00 0.00 0.00 4.70
1936 2003 5.183904 ACTCCACCATTTTGAATTGTAGCTC 59.816 40.000 0.00 0.00 0.00 4.09
1937 2004 5.079643 ACTCCACCATTTTGAATTGTAGCT 58.920 37.500 0.00 0.00 0.00 3.32
1938 2005 5.391312 ACTCCACCATTTTGAATTGTAGC 57.609 39.130 0.00 0.00 0.00 3.58
1939 2006 5.634859 GCAACTCCACCATTTTGAATTGTAG 59.365 40.000 0.00 0.00 0.00 2.74
1940 2007 5.069648 TGCAACTCCACCATTTTGAATTGTA 59.930 36.000 0.00 0.00 0.00 2.41
1941 2008 4.141756 TGCAACTCCACCATTTTGAATTGT 60.142 37.500 0.00 0.00 0.00 2.71
1942 2009 4.378774 TGCAACTCCACCATTTTGAATTG 58.621 39.130 0.00 0.00 0.00 2.32
1943 2010 4.686191 TGCAACTCCACCATTTTGAATT 57.314 36.364 0.00 0.00 0.00 2.17
1944 2011 4.686191 TTGCAACTCCACCATTTTGAAT 57.314 36.364 0.00 0.00 0.00 2.57
1945 2012 4.686191 ATTGCAACTCCACCATTTTGAA 57.314 36.364 0.00 0.00 0.00 2.69
1946 2013 4.686191 AATTGCAACTCCACCATTTTGA 57.314 36.364 0.00 0.00 0.00 2.69
1947 2014 5.277925 GGAAAATTGCAACTCCACCATTTTG 60.278 40.000 15.79 0.00 0.00 2.44
1948 2015 4.821260 GGAAAATTGCAACTCCACCATTTT 59.179 37.500 15.79 10.02 0.00 1.82
1949 2016 4.388485 GGAAAATTGCAACTCCACCATTT 58.612 39.130 15.79 2.61 0.00 2.32
1950 2017 3.244526 GGGAAAATTGCAACTCCACCATT 60.245 43.478 20.14 0.00 0.00 3.16
1951 2018 2.302733 GGGAAAATTGCAACTCCACCAT 59.697 45.455 20.14 0.00 0.00 3.55
1952 2019 1.691434 GGGAAAATTGCAACTCCACCA 59.309 47.619 20.14 0.00 0.00 4.17
1953 2020 1.001974 GGGGAAAATTGCAACTCCACC 59.998 52.381 20.14 15.81 0.00 4.61
1954 2021 1.336795 CGGGGAAAATTGCAACTCCAC 60.337 52.381 20.14 17.15 0.00 4.02
1955 2022 0.965439 CGGGGAAAATTGCAACTCCA 59.035 50.000 20.14 0.00 0.00 3.86
1956 2023 0.389817 GCGGGGAAAATTGCAACTCC 60.390 55.000 0.00 8.42 0.00 3.85
1957 2024 0.603065 AGCGGGGAAAATTGCAACTC 59.397 50.000 0.00 0.00 0.00 3.01
1958 2025 0.603065 GAGCGGGGAAAATTGCAACT 59.397 50.000 0.00 0.00 0.00 3.16
1959 2026 0.389817 GGAGCGGGGAAAATTGCAAC 60.390 55.000 0.00 0.00 0.00 4.17
1960 2027 1.872197 CGGAGCGGGGAAAATTGCAA 61.872 55.000 0.00 0.00 0.00 4.08
1961 2028 2.339556 CGGAGCGGGGAAAATTGCA 61.340 57.895 0.00 0.00 0.00 4.08
1962 2029 1.384222 ATCGGAGCGGGGAAAATTGC 61.384 55.000 0.00 0.00 0.00 3.56
1963 2030 1.102978 AATCGGAGCGGGGAAAATTG 58.897 50.000 0.00 0.00 0.00 2.32
1964 2031 2.721425 TAATCGGAGCGGGGAAAATT 57.279 45.000 0.00 0.00 0.00 1.82
1965 2032 2.779506 GATAATCGGAGCGGGGAAAAT 58.220 47.619 0.00 0.00 0.00 1.82
1966 2033 1.539496 CGATAATCGGAGCGGGGAAAA 60.539 52.381 0.00 0.00 36.00 2.29
1967 2034 0.032952 CGATAATCGGAGCGGGGAAA 59.967 55.000 0.00 0.00 36.00 3.13
1968 2035 0.824595 TCGATAATCGGAGCGGGGAA 60.825 55.000 0.00 0.00 40.88 3.97
1969 2036 0.824595 TTCGATAATCGGAGCGGGGA 60.825 55.000 0.00 0.00 40.88 4.81
1970 2037 0.666577 GTTCGATAATCGGAGCGGGG 60.667 60.000 0.00 0.00 40.88 5.73
1971 2038 0.031585 TGTTCGATAATCGGAGCGGG 59.968 55.000 0.00 0.00 40.88 6.13
1972 2039 1.409412 CTGTTCGATAATCGGAGCGG 58.591 55.000 0.00 0.00 40.88 5.52
1973 2040 1.409412 CCTGTTCGATAATCGGAGCG 58.591 55.000 0.00 0.00 40.88 5.03
1974 2041 1.784525 CCCTGTTCGATAATCGGAGC 58.215 55.000 0.00 0.00 40.88 4.70
1975 2042 1.605712 GGCCCTGTTCGATAATCGGAG 60.606 57.143 0.00 0.00 40.88 4.63
1976 2043 0.391597 GGCCCTGTTCGATAATCGGA 59.608 55.000 0.00 0.00 40.88 4.55
1977 2044 0.393077 AGGCCCTGTTCGATAATCGG 59.607 55.000 0.00 0.00 40.88 4.18
1978 2045 2.240493 AAGGCCCTGTTCGATAATCG 57.760 50.000 0.00 0.00 42.10 3.34
1979 2046 5.763204 TCAAATAAGGCCCTGTTCGATAATC 59.237 40.000 0.00 0.00 0.00 1.75
1980 2047 5.690865 TCAAATAAGGCCCTGTTCGATAAT 58.309 37.500 0.00 0.00 0.00 1.28
1981 2048 5.105567 TCAAATAAGGCCCTGTTCGATAA 57.894 39.130 0.00 0.00 0.00 1.75
1982 2049 4.764050 TCAAATAAGGCCCTGTTCGATA 57.236 40.909 0.00 0.00 0.00 2.92
1983 2050 3.644966 TCAAATAAGGCCCTGTTCGAT 57.355 42.857 0.00 0.00 0.00 3.59
1984 2051 3.644966 ATCAAATAAGGCCCTGTTCGA 57.355 42.857 0.00 0.00 0.00 3.71
1985 2052 3.443681 ACAATCAAATAAGGCCCTGTTCG 59.556 43.478 0.00 0.00 0.00 3.95
1986 2053 5.405935 AACAATCAAATAAGGCCCTGTTC 57.594 39.130 0.00 0.00 0.00 3.18
1987 2054 5.306678 TGAAACAATCAAATAAGGCCCTGTT 59.693 36.000 0.00 0.00 34.30 3.16
1988 2055 4.837860 TGAAACAATCAAATAAGGCCCTGT 59.162 37.500 0.00 0.00 34.30 4.00
1989 2056 5.404466 TGAAACAATCAAATAAGGCCCTG 57.596 39.130 0.00 0.00 34.30 4.45
2016 2083 4.758674 TCAAGAAGGAAGTCTGAAGCATTG 59.241 41.667 0.00 0.00 0.00 2.82
2046 2113 8.909923 TCTCTATTATACAATCACGAGGTTGAA 58.090 33.333 12.99 0.00 0.00 2.69
2051 2118 8.112016 TCCTTCTCTATTATACAATCACGAGG 57.888 38.462 0.00 0.00 0.00 4.63
2108 2175 4.710324 TCTTTCCTGAAAAGGCTTCGTAA 58.290 39.130 0.00 0.00 43.88 3.18
2122 2189 6.424812 GGAAACAAATGTGGATTTCTTTCCTG 59.575 38.462 14.90 0.00 44.87 3.86
2123 2190 6.524734 GGAAACAAATGTGGATTTCTTTCCT 58.475 36.000 14.90 0.00 44.87 3.36
2124 2191 6.524734 AGGAAACAAATGTGGATTTCTTTCC 58.475 36.000 14.57 14.57 46.67 3.13
2125 2192 7.928167 AGAAGGAAACAAATGTGGATTTCTTTC 59.072 33.333 12.40 12.40 42.73 2.62
2133 2203 5.385198 AGCTAAGAAGGAAACAAATGTGGA 58.615 37.500 0.00 0.00 0.00 4.02
2172 2244 1.898472 CGCCTCTGGTCTGGATGATAT 59.102 52.381 0.00 0.00 0.00 1.63
2187 2259 2.480244 GGAGAAAATTCATTGCCGCCTC 60.480 50.000 0.00 0.00 0.00 4.70
2193 2265 5.063060 GCTGTCAATGGAGAAAATTCATTGC 59.937 40.000 10.46 7.58 44.17 3.56
2252 2324 3.704566 ACAGTGGACAGACAACAGTAGAA 59.295 43.478 0.00 0.00 0.00 2.10
2262 2334 0.106708 TGCCTTCACAGTGGACAGAC 59.893 55.000 0.00 0.00 0.00 3.51
2281 2355 8.626526 CCCATATTATTAGTTGTAGCCGTTTTT 58.373 33.333 0.00 0.00 0.00 1.94
2282 2356 7.229907 CCCCATATTATTAGTTGTAGCCGTTTT 59.770 37.037 0.00 0.00 0.00 2.43
2308 2382 3.317603 ACAGTTTTATGTGGGCAATGC 57.682 42.857 0.00 0.00 30.46 3.56
2335 2411 9.362539 CGTTATTCCTGTTTACGGCTATATTAT 57.637 33.333 0.00 0.00 0.00 1.28
2336 2412 8.359642 ACGTTATTCCTGTTTACGGCTATATTA 58.640 33.333 0.00 0.00 36.60 0.98
2337 2413 7.212274 ACGTTATTCCTGTTTACGGCTATATT 58.788 34.615 0.00 0.00 36.60 1.28
2338 2414 6.752168 ACGTTATTCCTGTTTACGGCTATAT 58.248 36.000 0.00 0.00 36.60 0.86
2339 2415 6.147864 ACGTTATTCCTGTTTACGGCTATA 57.852 37.500 0.00 0.00 36.60 1.31
2362 2438 0.250295 GTGAGTACAGCCTGCCACAA 60.250 55.000 0.00 0.00 0.00 3.33
2410 2487 3.060895 CCAGCGTGAACGAACTTCTATTC 59.939 47.826 7.10 0.00 43.02 1.75
2428 2505 2.039405 CACTGCTTCTCTGCCCAGC 61.039 63.158 0.00 0.00 0.00 4.85
2451 2528 0.884704 GTGCTCGGTTGTGTCACCAT 60.885 55.000 0.00 0.00 36.49 3.55
2498 2575 5.276773 CGAGATGATCAAGCAAAGCTAGAAC 60.277 44.000 0.00 0.00 38.25 3.01


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

AutoCloner maintained by Alex Coulton.