Multiple sequence alignment - TraesCS4A01G154300

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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 TraesCS4A01G154300 chr4A 100.000 2183 0 0 1 2183 310731441 310729259 0.000000e+00 4032
1 TraesCS4A01G154300 chr4A 94.269 1745 77 11 1 1738 309507981 309506253 0.000000e+00 2647
2 TraesCS4A01G154300 chr4A 90.210 429 41 1 1755 2182 298298517 298298089 1.890000e-155 558
3 TraesCS4A01G154300 chr4A 89.087 449 48 1 1736 2183 197697593 197697145 6.810000e-155 556
4 TraesCS4A01G154300 chr4A 89.091 440 47 1 1741 2179 268268203 268268642 1.470000e-151 545
5 TraesCS4A01G154300 chr4A 88.444 450 50 2 1736 2183 138782710 138782261 1.910000e-150 542
6 TraesCS4A01G154300 chr5D 96.279 1747 52 10 1 1735 503286453 503288198 0.000000e+00 2854
7 TraesCS4A01G154300 chr5D 96.053 1748 51 15 1 1735 6181791 6180049 0.000000e+00 2830
8 TraesCS4A01G154300 chr5D 95.993 1747 54 13 1 1735 120799023 120800765 0.000000e+00 2824
9 TraesCS4A01G154300 chr5D 94.616 1746 82 9 1 1735 167071086 167072830 0.000000e+00 2693
10 TraesCS4A01G154300 chr6D 95.876 1746 53 14 1 1735 45512411 45510674 0.000000e+00 2808
11 TraesCS4A01G154300 chr1D 95.647 1746 61 11 1 1735 51878919 51877178 0.000000e+00 2789
12 TraesCS4A01G154300 chr1D 95.592 1747 53 12 1 1735 254416217 254417951 0.000000e+00 2778
13 TraesCS4A01G154300 chr1D 93.693 1744 99 9 1 1735 260891260 260893001 0.000000e+00 2601
14 TraesCS4A01G154300 chr2A 95.793 1640 55 11 1 1631 335831475 335829841 0.000000e+00 2634
15 TraesCS4A01G154300 chr2A 91.537 449 37 1 1736 2183 677274680 677274232 3.080000e-173 617
16 TraesCS4A01G154300 chr2A 89.556 450 45 2 1736 2183 441221680 441221231 8.740000e-159 569
17 TraesCS4A01G154300 chr7A 91.091 449 36 3 1736 2183 265084038 265084483 2.400000e-169 604
18 TraesCS4A01G154300 chr7A 89.310 449 47 1 1736 2183 465616827 465617275 1.460000e-156 562
19 TraesCS4A01G154300 chr3A 88.641 449 50 1 1736 2183 481988487 481988039 1.470000e-151 545


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 TraesCS4A01G154300 chr4A 310729259 310731441 2182 True 4032 4032 100.000 1 2183 1 chr4A.!!$R5 2182
1 TraesCS4A01G154300 chr4A 309506253 309507981 1728 True 2647 2647 94.269 1 1738 1 chr4A.!!$R4 1737
2 TraesCS4A01G154300 chr5D 503286453 503288198 1745 False 2854 2854 96.279 1 1735 1 chr5D.!!$F3 1734
3 TraesCS4A01G154300 chr5D 6180049 6181791 1742 True 2830 2830 96.053 1 1735 1 chr5D.!!$R1 1734
4 TraesCS4A01G154300 chr5D 120799023 120800765 1742 False 2824 2824 95.993 1 1735 1 chr5D.!!$F1 1734
5 TraesCS4A01G154300 chr5D 167071086 167072830 1744 False 2693 2693 94.616 1 1735 1 chr5D.!!$F2 1734
6 TraesCS4A01G154300 chr6D 45510674 45512411 1737 True 2808 2808 95.876 1 1735 1 chr6D.!!$R1 1734
7 TraesCS4A01G154300 chr1D 51877178 51878919 1741 True 2789 2789 95.647 1 1735 1 chr1D.!!$R1 1734
8 TraesCS4A01G154300 chr1D 254416217 254417951 1734 False 2778 2778 95.592 1 1735 1 chr1D.!!$F1 1734
9 TraesCS4A01G154300 chr1D 260891260 260893001 1741 False 2601 2601 93.693 1 1735 1 chr1D.!!$F2 1734
10 TraesCS4A01G154300 chr2A 335829841 335831475 1634 True 2634 2634 95.793 1 1631 1 chr2A.!!$R1 1630

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
947 959 5.279506 GCCTTTTCCCTCTTTCCCTTAAAAG 60.28 44.0 0.0 0.0 37.55 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1931 0.028505 GGCATGCGAACATAGCTGTG 59.971 55.0 12.44 9.17 35.22 3.66 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
26 27 6.198216 CCGCCAAGATCCAATTTATTTAAACG 59.802 38.462 0.00 0.00 0.00 3.60
74 75 7.326063 GGATGAAACATAGTTTGAAAAAGACGG 59.674 37.037 0.00 0.00 0.00 4.79
82 83 6.144078 AGTTTGAAAAAGACGGCTAAACAT 57.856 33.333 14.40 0.00 0.00 2.71
168 169 7.684937 ATCTTGAAGTGAGAAAAGAAGGATG 57.315 36.000 0.00 0.00 32.72 3.51
573 582 8.788806 ACTATATGATTTCACCGTTTGTTTCAA 58.211 29.630 0.00 0.00 0.00 2.69
774 784 5.800941 GCTAGTATTCTACACATGCGGATAC 59.199 44.000 0.00 0.00 0.00 2.24
783 793 6.940867 TCTACACATGCGGATACTATAGAGTT 59.059 38.462 6.78 0.00 37.10 3.01
877 888 5.779241 TTTGAGAGTGGGAATACAAGGAT 57.221 39.130 0.00 0.00 0.00 3.24
932 943 5.411831 AGATTTTGAATCTGCCTTTTCCC 57.588 39.130 2.56 0.00 0.00 3.97
947 959 5.279506 GCCTTTTCCCTCTTTCCCTTAAAAG 60.280 44.000 0.00 0.00 37.55 2.27
1171 1185 1.340889 CCTTTGTTTGGCAAGCTGCTA 59.659 47.619 15.19 0.00 44.28 3.49
1332 1348 7.618019 TCTTCTACATTGAATGGGTAGCTAT 57.382 36.000 10.27 0.00 35.58 2.97
1440 1456 8.352942 CACCTAACCCTATTTTTGCTATTGATC 58.647 37.037 0.00 0.00 0.00 2.92
1602 1624 9.331282 AGATTATGTAATGCTTACTCTCAAACC 57.669 33.333 7.33 0.00 37.06 3.27
1607 1629 7.871853 TGTAATGCTTACTCTCAAACCTTTTC 58.128 34.615 7.33 0.00 37.06 2.29
1677 1699 6.896021 TTTATCTAATGACCTAGGACGGAG 57.104 41.667 17.98 8.06 0.00 4.63
1695 1717 3.062466 TCCTGGACGCGAGGAGTG 61.062 66.667 15.93 0.00 33.54 3.51
1735 1760 9.834628 TTTCTTATTGGATTTGTTTCGTACATC 57.165 29.630 0.00 0.00 36.44 3.06
1738 1763 9.490663 CTTATTGGATTTGTTTCGTACATCTTC 57.509 33.333 0.00 0.00 36.44 2.87
1739 1764 6.869315 TTGGATTTGTTTCGTACATCTTCA 57.131 33.333 0.00 0.00 36.44 3.02
1740 1765 6.869315 TGGATTTGTTTCGTACATCTTCAA 57.131 33.333 0.00 0.00 36.44 2.69
1741 1766 6.898041 TGGATTTGTTTCGTACATCTTCAAG 58.102 36.000 0.00 0.00 36.44 3.02
1742 1767 6.708502 TGGATTTGTTTCGTACATCTTCAAGA 59.291 34.615 0.00 0.00 36.44 3.02
1743 1768 7.095229 TGGATTTGTTTCGTACATCTTCAAGAG 60.095 37.037 0.00 0.00 36.44 2.85
1744 1769 6.539649 TTTGTTTCGTACATCTTCAAGAGG 57.460 37.500 0.00 0.00 36.44 3.69
1745 1770 5.209818 TGTTTCGTACATCTTCAAGAGGT 57.790 39.130 10.07 10.07 42.43 3.85
1746 1771 6.335471 TGTTTCGTACATCTTCAAGAGGTA 57.665 37.500 7.85 7.85 40.10 3.08
1747 1772 6.751157 TGTTTCGTACATCTTCAAGAGGTAA 58.249 36.000 13.38 0.00 42.23 2.85
1748 1773 6.866770 TGTTTCGTACATCTTCAAGAGGTAAG 59.133 38.462 13.38 14.97 42.23 2.34
1749 1774 5.578005 TCGTACATCTTCAAGAGGTAAGG 57.422 43.478 20.34 12.99 42.23 2.69
1750 1775 4.401519 TCGTACATCTTCAAGAGGTAAGGG 59.598 45.833 20.34 10.99 42.23 3.95
1751 1776 3.636153 ACATCTTCAAGAGGTAAGGGC 57.364 47.619 2.01 0.00 37.49 5.19
1752 1777 2.239907 ACATCTTCAAGAGGTAAGGGCC 59.760 50.000 2.01 0.00 37.49 5.80
1753 1778 2.038863 TCTTCAAGAGGTAAGGGCCA 57.961 50.000 6.18 0.00 0.00 5.36
1754 1779 2.562296 TCTTCAAGAGGTAAGGGCCAT 58.438 47.619 6.18 0.00 0.00 4.40
1755 1780 3.731431 TCTTCAAGAGGTAAGGGCCATA 58.269 45.455 6.18 0.00 0.00 2.74
1756 1781 3.454812 TCTTCAAGAGGTAAGGGCCATAC 59.545 47.826 10.42 10.42 0.00 2.39
1757 1782 1.760613 TCAAGAGGTAAGGGCCATACG 59.239 52.381 12.39 0.00 0.00 3.06
1758 1783 0.468648 AAGAGGTAAGGGCCATACGC 59.531 55.000 12.39 7.43 0.00 4.42
1759 1784 1.300697 GAGGTAAGGGCCATACGCG 60.301 63.158 12.39 3.53 38.94 6.01
1760 1785 2.280592 GGTAAGGGCCATACGCGG 60.281 66.667 12.47 0.00 38.94 6.46
1785 1810 3.632080 CACCCACCACCTGGCGTA 61.632 66.667 0.00 0.00 39.01 4.42
1786 1811 3.319198 ACCCACCACCTGGCGTAG 61.319 66.667 0.00 0.00 39.01 3.51
1830 1855 3.906649 CTGCGCGTCTGCATCGAC 61.907 66.667 8.43 5.90 45.26 4.20
1831 1856 4.715892 TGCGCGTCTGCATCGACA 62.716 61.111 8.43 8.83 40.62 4.35
1832 1857 3.257561 GCGCGTCTGCATCGACAT 61.258 61.111 8.43 0.00 42.97 3.06
1833 1858 2.802667 GCGCGTCTGCATCGACATT 61.803 57.895 8.43 0.00 42.97 2.71
1834 1859 1.270968 CGCGTCTGCATCGACATTC 59.729 57.895 14.10 0.00 42.97 2.67
1835 1860 1.638467 GCGTCTGCATCGACATTCC 59.362 57.895 14.10 0.00 42.15 3.01
1836 1861 1.083806 GCGTCTGCATCGACATTCCA 61.084 55.000 14.10 0.00 42.15 3.53
1837 1862 0.926155 CGTCTGCATCGACATTCCAG 59.074 55.000 6.87 0.00 33.54 3.86
1838 1863 1.293924 GTCTGCATCGACATTCCAGG 58.706 55.000 1.41 0.00 34.11 4.45
1839 1864 0.178767 TCTGCATCGACATTCCAGGG 59.821 55.000 0.00 0.00 0.00 4.45
1840 1865 1.442526 CTGCATCGACATTCCAGGGC 61.443 60.000 0.00 0.00 0.00 5.19
1841 1866 1.153086 GCATCGACATTCCAGGGCT 60.153 57.895 0.00 0.00 0.00 5.19
1842 1867 1.162800 GCATCGACATTCCAGGGCTC 61.163 60.000 0.00 0.00 0.00 4.70
1843 1868 0.178767 CATCGACATTCCAGGGCTCA 59.821 55.000 0.00 0.00 0.00 4.26
1844 1869 0.911769 ATCGACATTCCAGGGCTCAA 59.088 50.000 0.00 0.00 0.00 3.02
1845 1870 0.036388 TCGACATTCCAGGGCTCAAC 60.036 55.000 0.00 0.00 0.00 3.18
1846 1871 0.321564 CGACATTCCAGGGCTCAACA 60.322 55.000 0.00 0.00 0.00 3.33
1847 1872 1.457346 GACATTCCAGGGCTCAACAG 58.543 55.000 0.00 0.00 0.00 3.16
1848 1873 0.038744 ACATTCCAGGGCTCAACAGG 59.961 55.000 0.00 0.00 0.00 4.00
1849 1874 0.682209 CATTCCAGGGCTCAACAGGG 60.682 60.000 0.00 0.00 0.00 4.45
1850 1875 2.505364 ATTCCAGGGCTCAACAGGGC 62.505 60.000 0.00 0.00 0.00 5.19
1856 1881 3.512516 GCTCAACAGGGCCGCATC 61.513 66.667 0.00 0.00 0.00 3.91
1857 1882 2.270205 CTCAACAGGGCCGCATCT 59.730 61.111 0.00 0.00 0.00 2.90
1858 1883 1.817099 CTCAACAGGGCCGCATCTC 60.817 63.158 0.00 0.00 0.00 2.75
1859 1884 2.046023 CAACAGGGCCGCATCTCA 60.046 61.111 0.00 0.00 0.00 3.27
1860 1885 1.452651 CAACAGGGCCGCATCTCAT 60.453 57.895 0.00 0.00 0.00 2.90
1861 1886 1.452651 AACAGGGCCGCATCTCATG 60.453 57.895 0.00 0.00 0.00 3.07
1862 1887 1.913951 AACAGGGCCGCATCTCATGA 61.914 55.000 0.00 0.00 0.00 3.07
1863 1888 1.597302 CAGGGCCGCATCTCATGAG 60.597 63.158 17.07 17.07 0.00 2.90
1864 1889 2.976903 GGGCCGCATCTCATGAGC 60.977 66.667 18.36 6.60 0.00 4.26
1865 1890 2.976903 GGCCGCATCTCATGAGCC 60.977 66.667 18.36 11.64 41.78 4.70
1866 1891 2.976903 GCCGCATCTCATGAGCCC 60.977 66.667 18.36 7.35 0.00 5.19
1867 1892 2.827423 CCGCATCTCATGAGCCCT 59.173 61.111 18.36 2.21 0.00 5.19
1868 1893 1.147824 CCGCATCTCATGAGCCCTT 59.852 57.895 18.36 0.00 0.00 3.95
1869 1894 0.883814 CCGCATCTCATGAGCCCTTC 60.884 60.000 18.36 4.35 0.00 3.46
1870 1895 0.106335 CGCATCTCATGAGCCCTTCT 59.894 55.000 18.36 0.00 0.00 2.85
1871 1896 1.595466 GCATCTCATGAGCCCTTCTG 58.405 55.000 18.36 8.85 0.00 3.02
1872 1897 1.814634 GCATCTCATGAGCCCTTCTGG 60.815 57.143 18.36 2.27 37.09 3.86
1884 1909 4.980805 TTCTGGCCTTCGCGCGTT 62.981 61.111 30.98 0.00 35.02 4.84
1890 1915 4.383602 CCTTCGCGCGTTGGTTGG 62.384 66.667 30.98 18.30 0.00 3.77
1891 1916 3.645975 CTTCGCGCGTTGGTTGGT 61.646 61.111 30.98 0.00 0.00 3.67
1892 1917 3.855209 CTTCGCGCGTTGGTTGGTG 62.855 63.158 30.98 6.51 0.00 4.17
1894 1919 4.954680 CGCGCGTTGGTTGGTGTG 62.955 66.667 24.19 0.00 0.00 3.82
1895 1920 3.578272 GCGCGTTGGTTGGTGTGA 61.578 61.111 8.43 0.00 0.00 3.58
1896 1921 2.631428 CGCGTTGGTTGGTGTGAG 59.369 61.111 0.00 0.00 0.00 3.51
1897 1922 2.892334 CGCGTTGGTTGGTGTGAGG 61.892 63.158 0.00 0.00 0.00 3.86
1898 1923 2.551912 GCGTTGGTTGGTGTGAGGG 61.552 63.158 0.00 0.00 0.00 4.30
1899 1924 1.153046 CGTTGGTTGGTGTGAGGGT 60.153 57.895 0.00 0.00 0.00 4.34
1900 1925 1.164041 CGTTGGTTGGTGTGAGGGTC 61.164 60.000 0.00 0.00 0.00 4.46
1901 1926 0.822121 GTTGGTTGGTGTGAGGGTCC 60.822 60.000 0.00 0.00 0.00 4.46
1902 1927 1.282653 TTGGTTGGTGTGAGGGTCCA 61.283 55.000 0.00 0.00 0.00 4.02
1903 1928 1.228154 GGTTGGTGTGAGGGTCCAC 60.228 63.158 0.00 0.00 37.55 4.02
1913 1938 4.130255 GGGTCCACCTCACAGCTA 57.870 61.111 0.00 0.00 35.85 3.32
1914 1939 2.609046 GGGTCCACCTCACAGCTAT 58.391 57.895 0.00 0.00 35.85 2.97
1915 1940 0.179000 GGGTCCACCTCACAGCTATG 59.821 60.000 0.00 0.00 35.85 2.23
1916 1941 0.905357 GGTCCACCTCACAGCTATGT 59.095 55.000 0.00 0.00 41.57 2.29
1917 1942 1.279271 GGTCCACCTCACAGCTATGTT 59.721 52.381 0.00 0.00 37.65 2.71
1918 1943 2.622436 GTCCACCTCACAGCTATGTTC 58.378 52.381 0.00 0.00 37.65 3.18
1919 1944 1.204704 TCCACCTCACAGCTATGTTCG 59.795 52.381 0.00 0.00 37.65 3.95
1920 1945 1.002366 CACCTCACAGCTATGTTCGC 58.998 55.000 0.00 0.00 37.65 4.70
1921 1946 0.608130 ACCTCACAGCTATGTTCGCA 59.392 50.000 0.00 0.00 37.65 5.10
1922 1947 1.208052 ACCTCACAGCTATGTTCGCAT 59.792 47.619 0.00 0.00 37.65 4.73
1923 1948 1.596260 CCTCACAGCTATGTTCGCATG 59.404 52.381 0.00 0.00 37.65 4.06
1924 1949 1.004185 CTCACAGCTATGTTCGCATGC 60.004 52.381 7.91 7.91 37.65 4.06
1925 1950 0.028505 CACAGCTATGTTCGCATGCC 59.971 55.000 13.15 0.00 37.65 4.40
1926 1951 0.392863 ACAGCTATGTTCGCATGCCA 60.393 50.000 13.15 4.66 35.63 4.92
1927 1952 0.949397 CAGCTATGTTCGCATGCCAT 59.051 50.000 13.15 12.36 38.47 4.40
1928 1953 1.335810 CAGCTATGTTCGCATGCCATT 59.664 47.619 13.15 0.00 38.47 3.16
1929 1954 2.026641 AGCTATGTTCGCATGCCATTT 58.973 42.857 13.15 0.00 38.47 2.32
1930 1955 2.121786 GCTATGTTCGCATGCCATTTG 58.878 47.619 13.15 7.70 38.47 2.32
1931 1956 2.734670 CTATGTTCGCATGCCATTTGG 58.265 47.619 13.15 0.00 38.47 3.28
1942 1967 3.053662 CCATTTGGCTTGCCGAATG 57.946 52.632 32.47 32.47 39.82 2.67
1943 1968 1.085501 CCATTTGGCTTGCCGAATGC 61.086 55.000 33.38 3.94 39.17 3.56
1944 1969 1.153784 ATTTGGCTTGCCGAATGCG 60.154 52.632 22.34 0.00 45.60 4.73
1954 1979 3.197790 CGAATGCGGCCTCACCTG 61.198 66.667 0.00 0.00 35.61 4.00
1955 1980 3.512516 GAATGCGGCCTCACCTGC 61.513 66.667 0.00 0.00 38.12 4.85
1963 1988 3.957586 CCTCACCTGCCAGTGCCA 61.958 66.667 0.00 0.00 37.68 4.92
1964 1989 2.670934 CTCACCTGCCAGTGCCAC 60.671 66.667 0.00 0.00 37.68 5.01
1965 1990 4.269523 TCACCTGCCAGTGCCACC 62.270 66.667 0.00 0.00 37.68 4.61
1966 1991 4.275508 CACCTGCCAGTGCCACCT 62.276 66.667 0.00 0.00 36.33 4.00
1967 1992 4.275508 ACCTGCCAGTGCCACCTG 62.276 66.667 0.00 0.00 36.33 4.00
1972 1997 3.052082 CCAGTGCCACCTGCGAAG 61.052 66.667 0.00 0.00 45.60 3.79
1985 2010 4.308526 CGAAGCATTCTGGTGGCT 57.691 55.556 0.00 0.00 44.75 4.75
1987 2012 1.737838 CGAAGCATTCTGGTGGCTTA 58.262 50.000 0.00 0.00 47.00 3.09
1988 2013 1.667724 CGAAGCATTCTGGTGGCTTAG 59.332 52.381 0.00 0.00 47.00 2.18
1989 2014 2.019984 GAAGCATTCTGGTGGCTTAGG 58.980 52.381 0.00 0.00 47.00 2.69
1990 2015 1.289160 AGCATTCTGGTGGCTTAGGA 58.711 50.000 0.00 0.00 33.21 2.94
1991 2016 1.211457 AGCATTCTGGTGGCTTAGGAG 59.789 52.381 0.00 0.00 33.21 3.69
1992 2017 1.748591 GCATTCTGGTGGCTTAGGAGG 60.749 57.143 0.00 0.00 0.00 4.30
2000 2025 4.916358 GCTTAGGAGGCCATGCAT 57.084 55.556 5.01 0.00 0.00 3.96
2001 2026 2.638744 GCTTAGGAGGCCATGCATC 58.361 57.895 5.01 0.00 38.72 3.91
2002 2027 0.179009 GCTTAGGAGGCCATGCATCA 60.179 55.000 5.01 0.00 41.39 3.07
2003 2028 1.602311 CTTAGGAGGCCATGCATCAC 58.398 55.000 5.01 0.00 41.39 3.06
2004 2029 0.179048 TTAGGAGGCCATGCATCACG 60.179 55.000 5.01 0.00 41.39 4.35
2005 2030 2.665008 TAGGAGGCCATGCATCACGC 62.665 60.000 5.01 0.00 41.39 5.34
2006 2031 2.515523 GAGGCCATGCATCACGCT 60.516 61.111 5.01 0.00 39.28 5.07
2007 2032 2.827190 AGGCCATGCATCACGCTG 60.827 61.111 5.01 0.00 43.06 5.18
2008 2033 3.136123 GGCCATGCATCACGCTGT 61.136 61.111 0.00 0.00 43.06 4.40
2009 2034 2.406401 GCCATGCATCACGCTGTC 59.594 61.111 0.00 0.00 43.06 3.51
2010 2035 3.104766 CCATGCATCACGCTGTCC 58.895 61.111 0.00 0.00 43.06 4.02
2011 2036 1.450848 CCATGCATCACGCTGTCCT 60.451 57.895 0.00 0.00 43.06 3.85
2012 2037 1.712018 CCATGCATCACGCTGTCCTG 61.712 60.000 0.00 0.00 43.06 3.86
2013 2038 1.450848 ATGCATCACGCTGTCCTGG 60.451 57.895 0.00 0.00 43.06 4.45
2014 2039 3.503363 GCATCACGCTGTCCTGGC 61.503 66.667 0.00 0.00 37.77 4.85
2015 2040 2.046988 CATCACGCTGTCCTGGCA 60.047 61.111 0.00 0.00 0.00 4.92
2016 2041 2.104859 CATCACGCTGTCCTGGCAG 61.105 63.158 7.75 7.75 39.37 4.85
2017 2042 2.285773 ATCACGCTGTCCTGGCAGA 61.286 57.895 17.94 0.00 38.70 4.26
2018 2043 2.236223 ATCACGCTGTCCTGGCAGAG 62.236 60.000 17.94 17.10 41.13 3.35
2019 2044 2.601666 ACGCTGTCCTGGCAGAGA 60.602 61.111 17.94 8.89 38.32 3.10
2020 2045 2.210013 ACGCTGTCCTGGCAGAGAA 61.210 57.895 17.94 0.00 38.32 2.87
2021 2046 1.447489 CGCTGTCCTGGCAGAGAAG 60.447 63.158 17.94 10.74 38.32 2.85
2022 2047 1.078567 GCTGTCCTGGCAGAGAAGG 60.079 63.158 17.94 0.00 38.70 3.46
2023 2048 1.078567 CTGTCCTGGCAGAGAAGGC 60.079 63.158 17.94 0.37 38.70 4.35
2024 2049 2.125350 GTCCTGGCAGAGAAGGCG 60.125 66.667 17.94 0.00 36.77 5.52
2025 2050 2.283894 TCCTGGCAGAGAAGGCGA 60.284 61.111 17.94 0.00 36.77 5.54
2026 2051 1.687146 TCCTGGCAGAGAAGGCGAT 60.687 57.895 17.94 0.00 36.77 4.58
2027 2052 1.523258 CCTGGCAGAGAAGGCGATG 60.523 63.158 17.94 0.00 36.77 3.84
2028 2053 1.523258 CTGGCAGAGAAGGCGATGG 60.523 63.158 9.42 0.00 36.77 3.51
2029 2054 2.249413 CTGGCAGAGAAGGCGATGGT 62.249 60.000 9.42 0.00 36.77 3.55
2030 2055 1.522580 GGCAGAGAAGGCGATGGTC 60.523 63.158 0.00 0.00 0.00 4.02
2031 2056 1.519719 GCAGAGAAGGCGATGGTCT 59.480 57.895 0.00 0.00 0.00 3.85
2032 2057 0.107945 GCAGAGAAGGCGATGGTCTT 60.108 55.000 0.00 0.00 41.82 3.01
2037 2062 3.558674 AAGGCGATGGTCTTCAAGG 57.441 52.632 0.00 0.00 30.69 3.61
2038 2063 0.984230 AAGGCGATGGTCTTCAAGGA 59.016 50.000 0.00 0.00 30.69 3.36
2039 2064 0.984230 AGGCGATGGTCTTCAAGGAA 59.016 50.000 0.00 0.00 0.00 3.36
2040 2065 1.087501 GGCGATGGTCTTCAAGGAAC 58.912 55.000 0.00 0.00 0.00 3.62
2041 2066 1.087501 GCGATGGTCTTCAAGGAACC 58.912 55.000 0.00 0.00 0.00 3.62
2042 2067 1.610624 GCGATGGTCTTCAAGGAACCA 60.611 52.381 0.54 0.54 34.72 3.67
2043 2068 2.076863 CGATGGTCTTCAAGGAACCAC 58.923 52.381 0.03 0.00 32.85 4.16
2044 2069 2.437413 GATGGTCTTCAAGGAACCACC 58.563 52.381 0.03 0.00 39.35 4.61
2045 2070 0.476771 TGGTCTTCAAGGAACCACCC 59.523 55.000 0.00 0.00 40.05 4.61
2046 2071 0.605589 GGTCTTCAAGGAACCACCCG 60.606 60.000 0.00 0.00 40.05 5.28
2047 2072 0.395312 GTCTTCAAGGAACCACCCGA 59.605 55.000 0.00 0.00 40.05 5.14
2048 2073 0.685097 TCTTCAAGGAACCACCCGAG 59.315 55.000 0.00 0.00 40.05 4.63
2049 2074 0.955919 CTTCAAGGAACCACCCGAGC 60.956 60.000 0.00 0.00 40.05 5.03
2050 2075 2.359975 CAAGGAACCACCCGAGCC 60.360 66.667 0.00 0.00 40.05 4.70
2051 2076 3.647771 AAGGAACCACCCGAGCCC 61.648 66.667 0.00 0.00 40.05 5.19
2081 2106 0.463620 CTGAGGCTCAGGGTTCTAGC 59.536 60.000 32.31 0.00 40.71 3.42
2082 2107 1.323271 TGAGGCTCAGGGTTCTAGCG 61.323 60.000 14.43 0.00 37.11 4.26
2083 2108 2.022240 GAGGCTCAGGGTTCTAGCGG 62.022 65.000 10.25 0.00 37.11 5.52
2084 2109 2.202946 GCTCAGGGTTCTAGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
2085 2110 2.726351 GCTCAGGGTTCTAGCGGCT 61.726 63.158 7.98 7.98 0.00 5.52
2086 2111 1.439644 CTCAGGGTTCTAGCGGCTC 59.560 63.158 5.39 0.00 0.00 4.70
2087 2112 2.105128 CAGGGTTCTAGCGGCTCG 59.895 66.667 5.39 0.00 0.00 5.03
2088 2113 2.362632 AGGGTTCTAGCGGCTCGT 60.363 61.111 5.39 0.00 0.00 4.18
2089 2114 2.202756 GGGTTCTAGCGGCTCGTG 60.203 66.667 5.39 0.00 0.00 4.35
2090 2115 2.707849 GGGTTCTAGCGGCTCGTGA 61.708 63.158 5.39 0.51 0.00 4.35
2091 2116 1.226717 GGTTCTAGCGGCTCGTGAG 60.227 63.158 5.39 0.00 0.00 3.51
2092 2117 1.226717 GTTCTAGCGGCTCGTGAGG 60.227 63.158 5.39 0.00 0.00 3.86
2093 2118 1.378119 TTCTAGCGGCTCGTGAGGA 60.378 57.895 5.39 0.00 0.00 3.71
2094 2119 1.377366 TTCTAGCGGCTCGTGAGGAG 61.377 60.000 5.39 0.00 46.06 3.69
2101 2126 3.897936 CTCGTGAGGAGCGACTCT 58.102 61.111 11.17 0.00 38.32 3.24
2102 2127 2.176140 CTCGTGAGGAGCGACTCTT 58.824 57.895 11.17 0.00 38.32 2.85
2103 2128 0.098025 CTCGTGAGGAGCGACTCTTC 59.902 60.000 11.17 10.56 37.16 2.87
2105 2130 1.137825 GTGAGGAGCGACTCTTCGG 59.862 63.158 11.17 0.00 45.98 4.30
2106 2131 2.103340 GAGGAGCGACTCTTCGGC 59.897 66.667 6.78 0.00 45.98 5.54
2107 2132 2.676822 AGGAGCGACTCTTCGGCA 60.677 61.111 6.78 0.00 45.98 5.69
2108 2133 2.507324 GGAGCGACTCTTCGGCAC 60.507 66.667 6.78 0.00 45.98 5.01
2121 2146 2.280119 GGCACGCATCATCGGCTA 60.280 61.111 0.00 0.00 0.00 3.93
2122 2147 2.598632 GGCACGCATCATCGGCTAC 61.599 63.158 0.00 0.00 0.00 3.58
2123 2148 1.592669 GCACGCATCATCGGCTACT 60.593 57.895 0.00 0.00 0.00 2.57
2124 2149 1.552348 GCACGCATCATCGGCTACTC 61.552 60.000 0.00 0.00 0.00 2.59
2125 2150 0.941463 CACGCATCATCGGCTACTCC 60.941 60.000 0.00 0.00 0.00 3.85
2126 2151 1.363807 CGCATCATCGGCTACTCCA 59.636 57.895 0.00 0.00 34.01 3.86
2127 2152 0.249447 CGCATCATCGGCTACTCCAA 60.249 55.000 0.00 0.00 34.01 3.53
2128 2153 1.221414 GCATCATCGGCTACTCCAAC 58.779 55.000 0.00 0.00 34.01 3.77
2129 2154 1.473257 GCATCATCGGCTACTCCAACA 60.473 52.381 0.00 0.00 34.01 3.33
2130 2155 2.205074 CATCATCGGCTACTCCAACAC 58.795 52.381 0.00 0.00 34.01 3.32
2131 2156 0.535335 TCATCGGCTACTCCAACACC 59.465 55.000 0.00 0.00 34.01 4.16
2132 2157 0.249120 CATCGGCTACTCCAACACCA 59.751 55.000 0.00 0.00 34.01 4.17
2133 2158 0.249398 ATCGGCTACTCCAACACCAC 59.751 55.000 0.00 0.00 34.01 4.16
2134 2159 0.830444 TCGGCTACTCCAACACCACT 60.830 55.000 0.00 0.00 34.01 4.00
2135 2160 0.389948 CGGCTACTCCAACACCACTC 60.390 60.000 0.00 0.00 34.01 3.51
2136 2161 0.977395 GGCTACTCCAACACCACTCT 59.023 55.000 0.00 0.00 34.01 3.24
2137 2162 1.338200 GGCTACTCCAACACCACTCTG 60.338 57.143 0.00 0.00 34.01 3.35
2138 2163 1.338200 GCTACTCCAACACCACTCTGG 60.338 57.143 0.00 0.00 45.02 3.86
2139 2164 0.685097 TACTCCAACACCACTCTGGC 59.315 55.000 0.00 0.00 42.67 4.85
2140 2165 1.344953 ACTCCAACACCACTCTGGCA 61.345 55.000 0.00 0.00 42.67 4.92
2141 2166 0.179020 CTCCAACACCACTCTGGCAA 60.179 55.000 0.00 0.00 42.67 4.52
2142 2167 0.465460 TCCAACACCACTCTGGCAAC 60.465 55.000 0.00 0.00 42.67 4.17
2143 2168 1.648720 CAACACCACTCTGGCAACG 59.351 57.895 0.00 0.00 42.67 4.10
2144 2169 1.095228 CAACACCACTCTGGCAACGT 61.095 55.000 0.00 0.00 42.67 3.99
2145 2170 0.393808 AACACCACTCTGGCAACGTT 60.394 50.000 0.00 0.00 42.67 3.99
2146 2171 0.466543 ACACCACTCTGGCAACGTTA 59.533 50.000 0.00 0.00 42.67 3.18
2147 2172 1.071699 ACACCACTCTGGCAACGTTAT 59.928 47.619 0.00 0.00 42.67 1.89
2148 2173 1.732259 CACCACTCTGGCAACGTTATC 59.268 52.381 0.00 0.00 42.67 1.75
2149 2174 1.346395 ACCACTCTGGCAACGTTATCA 59.654 47.619 0.00 1.25 42.67 2.15
2150 2175 2.002586 CCACTCTGGCAACGTTATCAG 58.997 52.381 18.43 18.43 42.51 2.90
2151 2176 2.002586 CACTCTGGCAACGTTATCAGG 58.997 52.381 21.92 16.83 42.51 3.86
2152 2177 1.623811 ACTCTGGCAACGTTATCAGGT 59.376 47.619 21.92 17.27 42.51 4.00
2153 2178 2.002586 CTCTGGCAACGTTATCAGGTG 58.997 52.381 21.92 14.72 42.51 4.00
2154 2179 1.621317 TCTGGCAACGTTATCAGGTGA 59.379 47.619 21.92 7.78 42.51 4.02
2155 2180 1.732259 CTGGCAACGTTATCAGGTGAC 59.268 52.381 17.34 1.68 42.51 3.67
2156 2181 1.084289 GGCAACGTTATCAGGTGACC 58.916 55.000 0.00 0.00 0.00 4.02
2157 2182 1.084289 GCAACGTTATCAGGTGACCC 58.916 55.000 0.00 0.00 0.00 4.46
2158 2183 1.338769 GCAACGTTATCAGGTGACCCT 60.339 52.381 0.00 0.00 44.02 4.34
2159 2184 2.874457 GCAACGTTATCAGGTGACCCTT 60.874 50.000 0.00 0.00 39.89 3.95
2160 2185 3.408634 CAACGTTATCAGGTGACCCTTT 58.591 45.455 0.00 0.00 39.89 3.11
2161 2186 3.782656 ACGTTATCAGGTGACCCTTTT 57.217 42.857 0.00 0.00 39.89 2.27
2162 2187 3.671716 ACGTTATCAGGTGACCCTTTTC 58.328 45.455 0.00 0.00 39.89 2.29
2163 2188 3.326880 ACGTTATCAGGTGACCCTTTTCT 59.673 43.478 0.00 0.00 39.89 2.52
2164 2189 3.684788 CGTTATCAGGTGACCCTTTTCTG 59.315 47.826 0.00 0.00 39.89 3.02
2165 2190 4.652822 GTTATCAGGTGACCCTTTTCTGT 58.347 43.478 0.00 0.00 39.89 3.41
2166 2191 3.884037 ATCAGGTGACCCTTTTCTGTT 57.116 42.857 0.00 0.00 39.89 3.16
2167 2192 3.208747 TCAGGTGACCCTTTTCTGTTC 57.791 47.619 0.00 0.00 39.89 3.18
2168 2193 2.507886 TCAGGTGACCCTTTTCTGTTCA 59.492 45.455 0.00 0.00 39.89 3.18
2169 2194 3.138283 TCAGGTGACCCTTTTCTGTTCAT 59.862 43.478 0.00 0.00 39.89 2.57
2170 2195 3.891366 CAGGTGACCCTTTTCTGTTCATT 59.109 43.478 0.00 0.00 39.89 2.57
2171 2196 4.022849 CAGGTGACCCTTTTCTGTTCATTC 60.023 45.833 0.00 0.00 39.89 2.67
2172 2197 3.888930 GGTGACCCTTTTCTGTTCATTCA 59.111 43.478 0.00 0.00 0.00 2.57
2173 2198 4.022849 GGTGACCCTTTTCTGTTCATTCAG 60.023 45.833 0.00 0.00 36.85 3.02
2174 2199 4.580580 GTGACCCTTTTCTGTTCATTCAGT 59.419 41.667 0.00 0.00 36.85 3.41
2175 2200 5.067805 GTGACCCTTTTCTGTTCATTCAGTT 59.932 40.000 0.00 0.00 36.85 3.16
2176 2201 5.067674 TGACCCTTTTCTGTTCATTCAGTTG 59.932 40.000 0.00 0.00 36.85 3.16
2177 2202 4.342092 ACCCTTTTCTGTTCATTCAGTTGG 59.658 41.667 0.00 0.00 36.85 3.77
2178 2203 4.262164 CCCTTTTCTGTTCATTCAGTTGGG 60.262 45.833 0.00 0.00 36.85 4.12
2179 2204 4.342092 CCTTTTCTGTTCATTCAGTTGGGT 59.658 41.667 0.00 0.00 36.85 4.51
2180 2205 4.916983 TTTCTGTTCATTCAGTTGGGTG 57.083 40.909 0.00 0.00 36.85 4.61
2181 2206 2.229792 TCTGTTCATTCAGTTGGGTGC 58.770 47.619 0.00 0.00 36.85 5.01
2182 2207 0.950836 TGTTCATTCAGTTGGGTGCG 59.049 50.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 7.148967 GCCGTCTTTTTCAAACTATGTTTCATC 60.149 37.037 0.00 0.00 0.00 2.92
591 600 1.751924 CTCGGAGGTTCGAATCCTTCT 59.248 52.381 16.93 4.72 38.77 2.85
621 630 1.302993 TGGTAAGGCAGCGGGTTTC 60.303 57.895 0.00 0.00 0.00 2.78
735 745 8.734593 AGAATACTAGCAAGAGAATATCCCTT 57.265 34.615 0.00 0.00 0.00 3.95
877 888 5.450688 CGGACTTTCCCAAACACAAAATACA 60.451 40.000 0.00 0.00 31.13 2.29
1236 1250 8.350852 TCTCGGCTTTTACCCATTTTTAAATA 57.649 30.769 0.00 0.00 0.00 1.40
1332 1348 9.034800 AGAAAGGTTGATCCAAATTTATTGCTA 57.965 29.630 0.00 0.00 39.02 3.49
1351 1367 0.984995 GTGCAGGGGAGTAGAAAGGT 59.015 55.000 0.00 0.00 0.00 3.50
1654 1676 6.371278 ACTCCGTCCTAGGTCATTAGATAAA 58.629 40.000 9.08 0.00 0.00 1.40
1677 1699 3.063084 ACTCCTCGCGTCCAGGAC 61.063 66.667 9.92 9.92 34.91 3.85
1735 1760 3.741388 CGTATGGCCCTTACCTCTTGAAG 60.741 52.174 0.00 0.00 0.00 3.02
1738 1763 1.810412 GCGTATGGCCCTTACCTCTTG 60.810 57.143 0.00 0.00 34.80 3.02
1739 1764 0.468648 GCGTATGGCCCTTACCTCTT 59.531 55.000 0.00 0.00 34.80 2.85
1740 1765 1.745320 CGCGTATGGCCCTTACCTCT 61.745 60.000 0.00 0.00 38.94 3.69
1741 1766 1.300697 CGCGTATGGCCCTTACCTC 60.301 63.158 0.00 0.00 38.94 3.85
1742 1767 2.803817 CCGCGTATGGCCCTTACCT 61.804 63.158 4.92 0.00 38.94 3.08
1743 1768 2.280592 CCGCGTATGGCCCTTACC 60.281 66.667 4.92 0.00 38.94 2.85
1813 1838 3.906649 GTCGATGCAGACGCGCAG 61.907 66.667 5.73 2.42 46.99 5.18
1815 1840 2.671345 GAATGTCGATGCAGACGCGC 62.671 60.000 5.73 0.00 43.70 6.86
1816 1841 1.270968 GAATGTCGATGCAGACGCG 59.729 57.895 3.53 3.53 43.70 6.01
1817 1842 1.083806 TGGAATGTCGATGCAGACGC 61.084 55.000 10.53 7.19 43.70 5.19
1818 1843 0.926155 CTGGAATGTCGATGCAGACG 59.074 55.000 9.33 9.33 43.70 4.18
1819 1844 1.293924 CCTGGAATGTCGATGCAGAC 58.706 55.000 7.51 0.00 38.38 3.51
1820 1845 0.178767 CCCTGGAATGTCGATGCAGA 59.821 55.000 7.51 0.00 38.38 4.26
1821 1846 1.442526 GCCCTGGAATGTCGATGCAG 61.443 60.000 0.00 0.00 36.16 4.41
1822 1847 1.451927 GCCCTGGAATGTCGATGCA 60.452 57.895 0.00 0.00 0.00 3.96
1823 1848 1.153086 AGCCCTGGAATGTCGATGC 60.153 57.895 0.00 0.00 0.00 3.91
1824 1849 0.178767 TGAGCCCTGGAATGTCGATG 59.821 55.000 0.00 0.00 0.00 3.84
1825 1850 0.911769 TTGAGCCCTGGAATGTCGAT 59.088 50.000 0.00 0.00 0.00 3.59
1826 1851 0.036388 GTTGAGCCCTGGAATGTCGA 60.036 55.000 0.00 0.00 0.00 4.20
1827 1852 0.321564 TGTTGAGCCCTGGAATGTCG 60.322 55.000 0.00 0.00 0.00 4.35
1828 1853 1.457346 CTGTTGAGCCCTGGAATGTC 58.543 55.000 0.00 0.00 0.00 3.06
1829 1854 0.038744 CCTGTTGAGCCCTGGAATGT 59.961 55.000 0.00 0.00 0.00 2.71
1830 1855 0.682209 CCCTGTTGAGCCCTGGAATG 60.682 60.000 0.00 0.00 0.00 2.67
1831 1856 1.693640 CCCTGTTGAGCCCTGGAAT 59.306 57.895 0.00 0.00 0.00 3.01
1832 1857 3.170362 CCCTGTTGAGCCCTGGAA 58.830 61.111 0.00 0.00 0.00 3.53
1833 1858 3.650950 GCCCTGTTGAGCCCTGGA 61.651 66.667 0.00 0.00 0.00 3.86
1834 1859 4.748144 GGCCCTGTTGAGCCCTGG 62.748 72.222 0.00 0.00 43.76 4.45
1839 1864 3.512516 GATGCGGCCCTGTTGAGC 61.513 66.667 0.00 0.00 0.00 4.26
1840 1865 1.817099 GAGATGCGGCCCTGTTGAG 60.817 63.158 0.00 0.00 0.00 3.02
1841 1866 1.913951 ATGAGATGCGGCCCTGTTGA 61.914 55.000 0.00 0.00 0.00 3.18
1842 1867 1.452651 ATGAGATGCGGCCCTGTTG 60.453 57.895 0.00 0.00 0.00 3.33
1843 1868 1.452651 CATGAGATGCGGCCCTGTT 60.453 57.895 0.00 0.00 0.00 3.16
1844 1869 2.191375 CATGAGATGCGGCCCTGT 59.809 61.111 0.00 0.00 0.00 4.00
1845 1870 1.597302 CTCATGAGATGCGGCCCTG 60.597 63.158 18.34 0.00 0.00 4.45
1846 1871 2.827423 CTCATGAGATGCGGCCCT 59.173 61.111 18.34 0.00 0.00 5.19
1847 1872 2.976903 GCTCATGAGATGCGGCCC 60.977 66.667 27.04 1.80 0.00 5.80
1848 1873 2.976903 GGCTCATGAGATGCGGCC 60.977 66.667 27.04 15.90 39.91 6.13
1849 1874 2.955022 AAGGGCTCATGAGATGCGGC 62.955 60.000 27.04 11.77 39.52 6.53
1850 1875 0.883814 GAAGGGCTCATGAGATGCGG 60.884 60.000 27.04 0.00 0.00 5.69
1851 1876 0.106335 AGAAGGGCTCATGAGATGCG 59.894 55.000 27.04 0.09 0.00 4.73
1852 1877 1.595466 CAGAAGGGCTCATGAGATGC 58.405 55.000 27.04 11.92 0.00 3.91
1853 1878 2.257691 CCAGAAGGGCTCATGAGATG 57.742 55.000 27.04 12.79 0.00 2.90
1867 1892 4.980805 AACGCGCGAAGGCCAGAA 62.981 61.111 39.36 0.00 35.02 3.02
1873 1898 4.383602 CCAACCAACGCGCGAAGG 62.384 66.667 39.36 35.01 0.00 3.46
1874 1899 3.645975 ACCAACCAACGCGCGAAG 61.646 61.111 39.36 26.47 0.00 3.79
1875 1900 3.943034 CACCAACCAACGCGCGAA 61.943 61.111 39.36 0.00 0.00 4.70
1877 1902 4.954680 CACACCAACCAACGCGCG 62.955 66.667 30.96 30.96 0.00 6.86
1878 1903 3.521308 CTCACACCAACCAACGCGC 62.521 63.158 5.73 0.00 0.00 6.86
1879 1904 2.631428 CTCACACCAACCAACGCG 59.369 61.111 3.53 3.53 0.00 6.01
1880 1905 2.551912 CCCTCACACCAACCAACGC 61.552 63.158 0.00 0.00 0.00 4.84
1881 1906 1.153046 ACCCTCACACCAACCAACG 60.153 57.895 0.00 0.00 0.00 4.10
1882 1907 0.822121 GGACCCTCACACCAACCAAC 60.822 60.000 0.00 0.00 0.00 3.77
1883 1908 1.282653 TGGACCCTCACACCAACCAA 61.283 55.000 0.00 0.00 0.00 3.67
1884 1909 1.694525 TGGACCCTCACACCAACCA 60.695 57.895 0.00 0.00 0.00 3.67
1885 1910 1.228154 GTGGACCCTCACACCAACC 60.228 63.158 0.00 0.00 37.57 3.77
1886 1911 4.475527 GTGGACCCTCACACCAAC 57.524 61.111 0.00 0.00 37.57 3.77
1896 1921 0.179000 CATAGCTGTGAGGTGGACCC 59.821 60.000 4.09 0.00 36.42 4.46
1897 1922 0.905357 ACATAGCTGTGAGGTGGACC 59.095 55.000 18.24 0.00 33.22 4.46
1898 1923 2.622436 GAACATAGCTGTGAGGTGGAC 58.378 52.381 18.24 0.00 35.22 4.02
1899 1924 1.204704 CGAACATAGCTGTGAGGTGGA 59.795 52.381 18.24 0.00 35.22 4.02
1900 1925 1.645034 CGAACATAGCTGTGAGGTGG 58.355 55.000 18.24 0.00 35.22 4.61
1901 1926 1.002366 GCGAACATAGCTGTGAGGTG 58.998 55.000 18.24 5.09 35.22 4.00
1902 1927 0.608130 TGCGAACATAGCTGTGAGGT 59.392 50.000 18.24 1.60 35.22 3.85
1903 1928 1.596260 CATGCGAACATAGCTGTGAGG 59.404 52.381 18.24 6.63 35.22 3.86
1904 1929 1.004185 GCATGCGAACATAGCTGTGAG 60.004 52.381 18.24 8.94 35.22 3.51
1905 1930 1.009078 GCATGCGAACATAGCTGTGA 58.991 50.000 18.24 0.00 35.22 3.58
1906 1931 0.028505 GGCATGCGAACATAGCTGTG 59.971 55.000 12.44 9.17 35.22 3.66
1907 1932 0.392863 TGGCATGCGAACATAGCTGT 60.393 50.000 12.44 0.00 33.67 4.40
1908 1933 0.949397 ATGGCATGCGAACATAGCTG 59.051 50.000 12.44 0.00 33.67 4.24
1909 1934 1.683943 AATGGCATGCGAACATAGCT 58.316 45.000 12.44 0.00 33.67 3.32
1910 1935 2.121786 CAAATGGCATGCGAACATAGC 58.878 47.619 12.44 0.00 33.67 2.97
1911 1936 2.734670 CCAAATGGCATGCGAACATAG 58.265 47.619 12.44 6.27 33.67 2.23
1912 1937 2.867287 CCAAATGGCATGCGAACATA 57.133 45.000 12.44 0.00 33.67 2.29
1913 1938 3.744941 CCAAATGGCATGCGAACAT 57.255 47.368 12.44 6.86 36.79 2.71
1924 1949 1.085501 GCATTCGGCAAGCCAAATGG 61.086 55.000 22.28 7.95 43.97 3.16
1925 1950 1.415288 CGCATTCGGCAAGCCAAATG 61.415 55.000 18.10 18.10 45.17 2.32
1926 1951 1.153784 CGCATTCGGCAAGCCAAAT 60.154 52.632 12.19 1.03 45.17 2.32
1927 1952 2.257980 CGCATTCGGCAAGCCAAA 59.742 55.556 12.19 0.00 45.17 3.28
1937 1962 3.197790 CAGGTGAGGCCGCATTCG 61.198 66.667 13.89 0.00 43.70 3.34
1938 1963 3.512516 GCAGGTGAGGCCGCATTC 61.513 66.667 13.89 8.58 43.70 2.67
1946 1971 3.957586 TGGCACTGGCAGGTGAGG 61.958 66.667 20.34 3.85 43.71 3.86
1947 1972 2.670934 GTGGCACTGGCAGGTGAG 60.671 66.667 20.34 6.80 43.71 3.51
1948 1973 4.269523 GGTGGCACTGGCAGGTGA 62.270 66.667 20.34 0.00 43.71 4.02
1949 1974 4.275508 AGGTGGCACTGGCAGGTG 62.276 66.667 20.34 15.02 43.71 4.00
1950 1975 4.275508 CAGGTGGCACTGGCAGGT 62.276 66.667 20.34 1.28 43.71 4.00
1955 1980 3.052082 CTTCGCAGGTGGCACTGG 61.052 66.667 18.45 10.94 45.17 4.00
1956 1981 3.730761 GCTTCGCAGGTGGCACTG 61.731 66.667 18.45 14.22 45.17 3.66
1957 1982 3.557903 ATGCTTCGCAGGTGGCACT 62.558 57.895 18.45 0.26 43.65 4.40
1958 1983 2.533391 GAATGCTTCGCAGGTGGCAC 62.533 60.000 9.70 9.70 43.65 5.01
1959 1984 2.282391 AATGCTTCGCAGGTGGCA 60.282 55.556 0.00 0.00 43.65 4.92
1960 1985 2.042831 AGAATGCTTCGCAGGTGGC 61.043 57.895 0.00 0.00 43.65 5.01
1961 1986 1.651240 CCAGAATGCTTCGCAGGTGG 61.651 60.000 0.00 0.00 43.65 4.61
1962 1987 0.957395 ACCAGAATGCTTCGCAGGTG 60.957 55.000 0.00 0.00 43.65 4.00
1963 1988 0.957395 CACCAGAATGCTTCGCAGGT 60.957 55.000 0.00 0.00 43.65 4.00
1964 1989 1.651240 CCACCAGAATGCTTCGCAGG 61.651 60.000 0.00 0.00 43.65 4.85
1965 1990 1.798735 CCACCAGAATGCTTCGCAG 59.201 57.895 0.00 0.00 43.65 5.18
1966 1991 2.334946 GCCACCAGAATGCTTCGCA 61.335 57.895 0.00 0.00 44.86 5.10
1967 1992 1.589716 AAGCCACCAGAATGCTTCGC 61.590 55.000 0.00 0.00 41.23 4.70
1968 1993 1.667724 CTAAGCCACCAGAATGCTTCG 59.332 52.381 0.00 0.00 43.80 3.79
1969 1994 2.019984 CCTAAGCCACCAGAATGCTTC 58.980 52.381 0.00 0.00 43.80 3.86
1970 1995 1.635487 TCCTAAGCCACCAGAATGCTT 59.365 47.619 0.00 0.00 46.37 3.91
1971 1996 1.211457 CTCCTAAGCCACCAGAATGCT 59.789 52.381 0.00 0.00 36.79 3.79
1972 1997 1.673168 CTCCTAAGCCACCAGAATGC 58.327 55.000 0.00 0.00 31.97 3.56
1973 1998 1.748591 GCCTCCTAAGCCACCAGAATG 60.749 57.143 0.00 0.00 0.00 2.67
1974 1999 0.548510 GCCTCCTAAGCCACCAGAAT 59.451 55.000 0.00 0.00 0.00 2.40
1975 2000 1.991230 GCCTCCTAAGCCACCAGAA 59.009 57.895 0.00 0.00 0.00 3.02
1976 2001 3.727387 GCCTCCTAAGCCACCAGA 58.273 61.111 0.00 0.00 0.00 3.86
1983 2008 0.179009 TGATGCATGGCCTCCTAAGC 60.179 55.000 2.46 0.00 0.00 3.09
1984 2009 1.602311 GTGATGCATGGCCTCCTAAG 58.398 55.000 2.46 0.00 0.00 2.18
1985 2010 0.179048 CGTGATGCATGGCCTCCTAA 60.179 55.000 2.46 0.00 0.00 2.69
1986 2011 1.447217 CGTGATGCATGGCCTCCTA 59.553 57.895 2.46 0.00 0.00 2.94
1987 2012 2.191375 CGTGATGCATGGCCTCCT 59.809 61.111 2.46 0.00 0.00 3.69
1988 2013 3.589881 GCGTGATGCATGGCCTCC 61.590 66.667 2.46 0.00 45.45 4.30
1997 2022 3.503363 GCCAGGACAGCGTGATGC 61.503 66.667 0.00 0.00 46.98 3.91
1998 2023 2.046988 TGCCAGGACAGCGTGATG 60.047 61.111 0.00 0.00 31.73 3.07
1999 2024 2.236223 CTCTGCCAGGACAGCGTGAT 62.236 60.000 6.12 0.00 37.59 3.06
2000 2025 2.917227 TCTGCCAGGACAGCGTGA 60.917 61.111 6.12 0.00 37.59 4.35
2001 2026 2.433838 CTCTGCCAGGACAGCGTG 60.434 66.667 6.12 0.00 37.59 5.34
2002 2027 2.164865 CTTCTCTGCCAGGACAGCGT 62.165 60.000 6.12 0.00 37.59 5.07
2003 2028 1.447489 CTTCTCTGCCAGGACAGCG 60.447 63.158 6.12 1.34 37.59 5.18
2004 2029 1.078567 CCTTCTCTGCCAGGACAGC 60.079 63.158 6.12 0.00 37.59 4.40
2005 2030 1.078567 GCCTTCTCTGCCAGGACAG 60.079 63.158 0.00 0.00 39.12 3.51
2006 2031 2.947532 CGCCTTCTCTGCCAGGACA 61.948 63.158 0.00 0.00 30.81 4.02
2007 2032 1.965754 ATCGCCTTCTCTGCCAGGAC 61.966 60.000 0.00 0.00 30.81 3.85
2008 2033 1.687146 ATCGCCTTCTCTGCCAGGA 60.687 57.895 0.00 0.00 30.81 3.86
2009 2034 1.523258 CATCGCCTTCTCTGCCAGG 60.523 63.158 0.00 0.00 0.00 4.45
2010 2035 1.523258 CCATCGCCTTCTCTGCCAG 60.523 63.158 0.00 0.00 0.00 4.85
2011 2036 2.244117 GACCATCGCCTTCTCTGCCA 62.244 60.000 0.00 0.00 0.00 4.92
2012 2037 1.522580 GACCATCGCCTTCTCTGCC 60.523 63.158 0.00 0.00 0.00 4.85
2013 2038 0.107945 AAGACCATCGCCTTCTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
2014 2039 1.205655 TGAAGACCATCGCCTTCTCTG 59.794 52.381 0.00 0.00 39.47 3.35
2015 2040 1.561643 TGAAGACCATCGCCTTCTCT 58.438 50.000 0.00 0.00 39.47 3.10
2016 2041 2.275318 CTTGAAGACCATCGCCTTCTC 58.725 52.381 0.00 0.00 39.47 2.87
2017 2042 1.065854 CCTTGAAGACCATCGCCTTCT 60.066 52.381 0.00 0.00 39.47 2.85
2018 2043 1.066143 TCCTTGAAGACCATCGCCTTC 60.066 52.381 0.00 0.00 39.26 3.46
2019 2044 0.984230 TCCTTGAAGACCATCGCCTT 59.016 50.000 0.00 0.00 0.00 4.35
2020 2045 0.984230 TTCCTTGAAGACCATCGCCT 59.016 50.000 0.00 0.00 0.00 5.52
2021 2046 1.087501 GTTCCTTGAAGACCATCGCC 58.912 55.000 0.00 0.00 0.00 5.54
2022 2047 1.087501 GGTTCCTTGAAGACCATCGC 58.912 55.000 0.00 0.00 33.61 4.58
2023 2048 2.076863 GTGGTTCCTTGAAGACCATCG 58.923 52.381 8.73 0.00 44.56 3.84
2024 2049 2.437413 GGTGGTTCCTTGAAGACCATC 58.563 52.381 8.73 5.00 44.56 3.51
2025 2050 1.075536 GGGTGGTTCCTTGAAGACCAT 59.924 52.381 8.73 0.00 44.56 3.55
2026 2051 0.476771 GGGTGGTTCCTTGAAGACCA 59.523 55.000 1.95 1.95 40.95 4.02
2027 2052 0.605589 CGGGTGGTTCCTTGAAGACC 60.606 60.000 0.00 0.00 36.25 3.85
2028 2053 0.395312 TCGGGTGGTTCCTTGAAGAC 59.605 55.000 0.00 0.00 36.25 3.01
2029 2054 0.685097 CTCGGGTGGTTCCTTGAAGA 59.315 55.000 0.00 0.00 36.25 2.87
2030 2055 0.955919 GCTCGGGTGGTTCCTTGAAG 60.956 60.000 0.00 0.00 36.25 3.02
2031 2056 1.072505 GCTCGGGTGGTTCCTTGAA 59.927 57.895 0.00 0.00 36.25 2.69
2032 2057 2.747686 GCTCGGGTGGTTCCTTGA 59.252 61.111 0.00 0.00 36.25 3.02
2033 2058 2.359975 GGCTCGGGTGGTTCCTTG 60.360 66.667 0.00 0.00 36.25 3.61
2034 2059 3.647771 GGGCTCGGGTGGTTCCTT 61.648 66.667 0.00 0.00 36.25 3.36
2062 2087 0.463620 GCTAGAACCCTGAGCCTCAG 59.536 60.000 14.99 14.99 43.91 3.35
2063 2088 1.323271 CGCTAGAACCCTGAGCCTCA 61.323 60.000 0.00 0.00 32.35 3.86
2064 2089 1.439644 CGCTAGAACCCTGAGCCTC 59.560 63.158 0.00 0.00 32.35 4.70
2065 2090 2.060980 CCGCTAGAACCCTGAGCCT 61.061 63.158 0.00 0.00 32.35 4.58
2066 2091 2.501610 CCGCTAGAACCCTGAGCC 59.498 66.667 0.00 0.00 32.35 4.70
2067 2092 2.202946 GCCGCTAGAACCCTGAGC 60.203 66.667 0.00 0.00 0.00 4.26
2068 2093 1.439644 GAGCCGCTAGAACCCTGAG 59.560 63.158 0.00 0.00 0.00 3.35
2069 2094 2.415608 CGAGCCGCTAGAACCCTGA 61.416 63.158 0.00 0.00 0.00 3.86
2070 2095 2.105128 CGAGCCGCTAGAACCCTG 59.895 66.667 0.00 0.00 0.00 4.45
2071 2096 2.362632 ACGAGCCGCTAGAACCCT 60.363 61.111 7.57 0.00 0.00 4.34
2072 2097 2.202756 CACGAGCCGCTAGAACCC 60.203 66.667 7.57 0.00 0.00 4.11
2073 2098 1.226717 CTCACGAGCCGCTAGAACC 60.227 63.158 7.57 0.00 0.00 3.62
2074 2099 1.226717 CCTCACGAGCCGCTAGAAC 60.227 63.158 7.57 0.00 0.00 3.01
2075 2100 1.377366 CTCCTCACGAGCCGCTAGAA 61.377 60.000 7.57 0.00 0.00 2.10
2076 2101 1.820056 CTCCTCACGAGCCGCTAGA 60.820 63.158 7.57 0.00 0.00 2.43
2077 2102 2.718731 CTCCTCACGAGCCGCTAG 59.281 66.667 0.00 0.00 0.00 3.42
2084 2109 0.098025 GAAGAGTCGCTCCTCACGAG 59.902 60.000 0.00 0.00 40.80 4.18
2085 2110 1.636570 CGAAGAGTCGCTCCTCACGA 61.637 60.000 0.00 0.00 41.08 4.35
2086 2111 1.226156 CGAAGAGTCGCTCCTCACG 60.226 63.158 3.66 4.29 41.08 4.35
2087 2112 1.137825 CCGAAGAGTCGCTCCTCAC 59.862 63.158 3.66 0.00 46.28 3.51
2088 2113 2.701780 GCCGAAGAGTCGCTCCTCA 61.702 63.158 3.66 0.00 46.28 3.86
2089 2114 2.103340 GCCGAAGAGTCGCTCCTC 59.897 66.667 3.66 0.54 46.28 3.71
2090 2115 2.676822 TGCCGAAGAGTCGCTCCT 60.677 61.111 3.66 0.00 46.28 3.69
2091 2116 2.507324 GTGCCGAAGAGTCGCTCC 60.507 66.667 3.66 0.00 46.28 4.70
2092 2117 2.876645 CGTGCCGAAGAGTCGCTC 60.877 66.667 0.00 0.00 46.28 5.03
2096 2121 0.807667 ATGATGCGTGCCGAAGAGTC 60.808 55.000 0.00 0.00 0.00 3.36
2097 2122 0.807667 GATGATGCGTGCCGAAGAGT 60.808 55.000 0.00 0.00 0.00 3.24
2098 2123 1.815212 CGATGATGCGTGCCGAAGAG 61.815 60.000 0.00 0.00 0.00 2.85
2099 2124 1.878069 CGATGATGCGTGCCGAAGA 60.878 57.895 0.00 0.00 0.00 2.87
2100 2125 2.622629 CGATGATGCGTGCCGAAG 59.377 61.111 0.00 0.00 0.00 3.79
2101 2126 2.889988 CCGATGATGCGTGCCGAA 60.890 61.111 0.00 0.00 0.00 4.30
2104 2129 2.280119 TAGCCGATGATGCGTGCC 60.280 61.111 0.00 0.00 0.00 5.01
2105 2130 1.552348 GAGTAGCCGATGATGCGTGC 61.552 60.000 0.00 0.00 0.00 5.34
2106 2131 0.941463 GGAGTAGCCGATGATGCGTG 60.941 60.000 0.00 0.00 0.00 5.34
2107 2132 1.364171 GGAGTAGCCGATGATGCGT 59.636 57.895 0.00 0.00 0.00 5.24
2108 2133 0.249447 TTGGAGTAGCCGATGATGCG 60.249 55.000 0.00 0.00 40.66 4.73
2109 2134 1.221414 GTTGGAGTAGCCGATGATGC 58.779 55.000 0.00 0.00 40.66 3.91
2110 2135 2.205074 GTGTTGGAGTAGCCGATGATG 58.795 52.381 0.00 0.00 40.66 3.07
2111 2136 1.139058 GGTGTTGGAGTAGCCGATGAT 59.861 52.381 0.00 0.00 40.66 2.45
2112 2137 0.535335 GGTGTTGGAGTAGCCGATGA 59.465 55.000 0.00 0.00 40.66 2.92
2113 2138 0.249120 TGGTGTTGGAGTAGCCGATG 59.751 55.000 0.00 0.00 40.66 3.84
2114 2139 0.249398 GTGGTGTTGGAGTAGCCGAT 59.751 55.000 0.00 0.00 40.66 4.18
2115 2140 0.830444 AGTGGTGTTGGAGTAGCCGA 60.830 55.000 0.00 0.00 40.66 5.54
2116 2141 0.389948 GAGTGGTGTTGGAGTAGCCG 60.390 60.000 0.00 0.00 40.66 5.52
2117 2142 0.977395 AGAGTGGTGTTGGAGTAGCC 59.023 55.000 0.00 0.00 37.10 3.93
2118 2143 1.338200 CCAGAGTGGTGTTGGAGTAGC 60.338 57.143 0.00 0.00 33.76 3.58
2119 2144 1.338200 GCCAGAGTGGTGTTGGAGTAG 60.338 57.143 0.00 0.00 40.46 2.57
2120 2145 0.685097 GCCAGAGTGGTGTTGGAGTA 59.315 55.000 0.00 0.00 40.46 2.59
2121 2146 1.344953 TGCCAGAGTGGTGTTGGAGT 61.345 55.000 0.00 0.00 40.46 3.85
2122 2147 0.179020 TTGCCAGAGTGGTGTTGGAG 60.179 55.000 0.00 0.00 40.46 3.86
2123 2148 0.465460 GTTGCCAGAGTGGTGTTGGA 60.465 55.000 0.00 0.00 40.46 3.53
2124 2149 1.785041 CGTTGCCAGAGTGGTGTTGG 61.785 60.000 0.00 0.00 40.46 3.77
2125 2150 1.095228 ACGTTGCCAGAGTGGTGTTG 61.095 55.000 0.00 0.00 40.46 3.33
2126 2151 0.393808 AACGTTGCCAGAGTGGTGTT 60.394 50.000 0.00 0.00 40.46 3.32
2127 2152 0.466543 TAACGTTGCCAGAGTGGTGT 59.533 50.000 11.99 0.00 40.46 4.16
2128 2153 1.732259 GATAACGTTGCCAGAGTGGTG 59.268 52.381 11.99 0.00 40.46 4.17
2129 2154 1.346395 TGATAACGTTGCCAGAGTGGT 59.654 47.619 11.99 0.00 40.46 4.16
2130 2155 2.002586 CTGATAACGTTGCCAGAGTGG 58.997 52.381 20.31 0.00 41.55 4.00
2131 2156 2.002586 CCTGATAACGTTGCCAGAGTG 58.997 52.381 24.24 10.71 0.00 3.51
2132 2157 1.623811 ACCTGATAACGTTGCCAGAGT 59.376 47.619 24.24 18.74 0.00 3.24
2133 2158 2.002586 CACCTGATAACGTTGCCAGAG 58.997 52.381 24.24 18.30 0.00 3.35
2134 2159 1.621317 TCACCTGATAACGTTGCCAGA 59.379 47.619 24.24 9.46 0.00 3.86
2135 2160 1.732259 GTCACCTGATAACGTTGCCAG 59.268 52.381 11.99 16.40 0.00 4.85
2136 2161 1.609580 GGTCACCTGATAACGTTGCCA 60.610 52.381 11.99 7.63 0.00 4.92
2137 2162 1.084289 GGTCACCTGATAACGTTGCC 58.916 55.000 11.99 2.81 0.00 4.52
2138 2163 1.084289 GGGTCACCTGATAACGTTGC 58.916 55.000 11.99 3.40 0.00 4.17
2148 2173 8.173410 CTGAATGAACAGAAAAGGGTCACCTG 62.173 46.154 0.00 0.00 42.42 4.00
2149 2174 6.210980 CTGAATGAACAGAAAAGGGTCACCT 61.211 44.000 0.00 0.00 43.92 4.00
2150 2175 3.888930 TGAATGAACAGAAAAGGGTCACC 59.111 43.478 0.00 0.00 0.00 4.02
2151 2176 4.580580 ACTGAATGAACAGAAAAGGGTCAC 59.419 41.667 0.00 0.00 40.63 3.67
2152 2177 4.792068 ACTGAATGAACAGAAAAGGGTCA 58.208 39.130 0.00 0.00 40.63 4.02
2153 2178 5.507985 CCAACTGAATGAACAGAAAAGGGTC 60.508 44.000 0.00 0.00 40.63 4.46
2154 2179 4.342092 CCAACTGAATGAACAGAAAAGGGT 59.658 41.667 0.00 0.00 40.63 4.34
2155 2180 4.262164 CCCAACTGAATGAACAGAAAAGGG 60.262 45.833 0.00 0.00 40.63 3.95
2156 2181 4.342092 ACCCAACTGAATGAACAGAAAAGG 59.658 41.667 0.00 0.00 40.63 3.11
2157 2182 5.284079 CACCCAACTGAATGAACAGAAAAG 58.716 41.667 0.00 0.00 40.63 2.27
2158 2183 4.441356 GCACCCAACTGAATGAACAGAAAA 60.441 41.667 0.00 0.00 40.63 2.29
2159 2184 3.068024 GCACCCAACTGAATGAACAGAAA 59.932 43.478 0.00 0.00 40.63 2.52
2160 2185 2.622942 GCACCCAACTGAATGAACAGAA 59.377 45.455 0.00 0.00 40.63 3.02
2161 2186 2.229792 GCACCCAACTGAATGAACAGA 58.770 47.619 0.00 0.00 40.63 3.41
2162 2187 1.069022 CGCACCCAACTGAATGAACAG 60.069 52.381 0.00 0.00 42.78 3.16
2163 2188 0.950836 CGCACCCAACTGAATGAACA 59.049 50.000 0.00 0.00 0.00 3.18
2164 2189 3.773117 CGCACCCAACTGAATGAAC 57.227 52.632 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.