Multiple sequence alignment - TraesCS5D01G220900

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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 TraesCS5D01G220900 chr5D 100.000 2144 0 0 1 2144 329132058 329134201 0.000000e+00 3960
1 TraesCS5D01G220900 chr5D 97.462 197 5 0 1948 2144 503247658 503247462 9.480000e-89 337
2 TraesCS5D01G220900 chr5D 97.462 197 5 0 1948 2144 503262390 503262586 9.480000e-89 337
3 TraesCS5D01G220900 chr6D 97.154 1792 27 7 1 1787 431399676 431397904 0.000000e+00 3005
4 TraesCS5D01G220900 chr6D 97.449 196 5 0 1949 2144 389243437 389243632 3.410000e-88 335
5 TraesCS5D01G220900 chr2D 97.154 1792 23 6 1 1787 628285315 628283547 0.000000e+00 3001
6 TraesCS5D01G220900 chr2D 96.898 1612 35 9 1 1609 334225571 334223972 0.000000e+00 2686
7 TraesCS5D01G220900 chr1D 96.985 1791 34 6 1 1787 254489347 254487573 0.000000e+00 2990
8 TraesCS5D01G220900 chr1D 94.475 1792 65 12 1 1787 244401812 244400050 0.000000e+00 2730
9 TraesCS5D01G220900 chr1D 93.698 1793 79 11 1 1787 244423800 244422036 0.000000e+00 2654
10 TraesCS5D01G220900 chr1D 97.186 995 18 4 1 993 394178556 394177570 0.000000e+00 1674
11 TraesCS5D01G220900 chr3D 96.760 1790 38 6 1 1787 21897206 21895434 0.000000e+00 2966
12 TraesCS5D01G220900 chr2A 96.482 1791 51 5 1 1787 276441427 276443209 0.000000e+00 2948
13 TraesCS5D01G220900 chr2A 95.552 1776 52 8 1 1773 335825925 335824174 0.000000e+00 2817
14 TraesCS5D01G220900 chrUn 96.389 360 6 1 1 360 317473544 317473896 8.530000e-164 586
15 TraesCS5D01G220900 chrUn 97.449 196 5 0 1949 2144 365941481 365941286 3.410000e-88 335
16 TraesCS5D01G220900 chrUn 97.449 196 5 0 1949 2144 428084507 428084702 3.410000e-88 335
17 TraesCS5D01G220900 chrUn 97.449 196 5 0 1949 2144 433990574 433990379 3.410000e-88 335
18 TraesCS5D01G220900 chr7D 95.057 263 10 2 1 260 88605235 88604973 5.510000e-111 411
19 TraesCS5D01G220900 chr7D 97.449 196 5 0 1949 2144 231605532 231605727 3.410000e-88 335
20 TraesCS5D01G220900 chr7D 97.449 196 5 0 1949 2144 231606601 231606796 3.410000e-88 335
21 TraesCS5D01G220900 chr7B 97.449 196 5 0 1949 2144 662729298 662729103 3.410000e-88 335


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 TraesCS5D01G220900 chr5D 329132058 329134201 2143 False 3960 3960 100.000 1 2144 1 chr5D.!!$F1 2143
1 TraesCS5D01G220900 chr6D 431397904 431399676 1772 True 3005 3005 97.154 1 1787 1 chr6D.!!$R1 1786
2 TraesCS5D01G220900 chr2D 628283547 628285315 1768 True 3001 3001 97.154 1 1787 1 chr2D.!!$R2 1786
3 TraesCS5D01G220900 chr2D 334223972 334225571 1599 True 2686 2686 96.898 1 1609 1 chr2D.!!$R1 1608
4 TraesCS5D01G220900 chr1D 254487573 254489347 1774 True 2990 2990 96.985 1 1787 1 chr1D.!!$R3 1786
5 TraesCS5D01G220900 chr1D 244400050 244401812 1762 True 2730 2730 94.475 1 1787 1 chr1D.!!$R1 1786
6 TraesCS5D01G220900 chr1D 244422036 244423800 1764 True 2654 2654 93.698 1 1787 1 chr1D.!!$R2 1786
7 TraesCS5D01G220900 chr1D 394177570 394178556 986 True 1674 1674 97.186 1 993 1 chr1D.!!$R4 992
8 TraesCS5D01G220900 chr3D 21895434 21897206 1772 True 2966 2966 96.760 1 1787 1 chr3D.!!$R1 1786
9 TraesCS5D01G220900 chr2A 276441427 276443209 1782 False 2948 2948 96.482 1 1787 1 chr2A.!!$F1 1786
10 TraesCS5D01G220900 chr2A 335824174 335825925 1751 True 2817 2817 95.552 1 1773 1 chr2A.!!$R1 1772
11 TraesCS5D01G220900 chr7D 231605532 231606796 1264 False 335 335 97.449 1949 2144 2 chr7D.!!$F1 195

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
689 704 0.816825 AGTGCGATGGCTGGCTATTG 60.817 55.0 0.15 2.37 40.82 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1937 0.033504 TGGCGAACTGGAGTGAAGTC 59.966 55.0 0.0 0.0 0.0 3.01 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
120 122 5.199982 TGGGGTTTTCTATTGATGCCTTA 57.800 39.130 0.00 0.00 0.00 2.69
579 594 6.117488 ACAAGGAATTCCGTTAATAACCGAT 58.883 36.000 18.82 0.00 42.08 4.18
621 636 9.302345 GAACAACTCGATGAATTTAGTAGATCA 57.698 33.333 0.00 0.00 0.00 2.92
623 638 9.469807 ACAACTCGATGAATTTAGTAGATCATC 57.530 33.333 0.00 4.87 42.91 2.92
689 704 0.816825 AGTGCGATGGCTGGCTATTG 60.817 55.000 0.15 2.37 40.82 1.90
751 767 3.093814 TCAGCAATGCAGTTCATCCAAT 58.906 40.909 8.35 0.00 33.40 3.16
796 812 6.126863 AGAACTATGACAGAATCAAACCCA 57.873 37.500 0.00 0.00 41.93 4.51
990 1006 4.973168 TGTTTTTGTCTCTAGCATGACCT 58.027 39.130 0.00 0.00 32.67 3.85
1140 1157 7.513781 TCATATTCTGGATTGGGTTCATCTCTA 59.486 37.037 0.00 0.00 0.00 2.43
1141 1158 6.776887 ATTCTGGATTGGGTTCATCTCTAT 57.223 37.500 0.00 0.00 0.00 1.98
1142 1159 7.878621 ATTCTGGATTGGGTTCATCTCTATA 57.121 36.000 0.00 0.00 0.00 1.31
1143 1160 6.924913 TCTGGATTGGGTTCATCTCTATAG 57.075 41.667 0.00 0.00 0.00 1.31
1144 1161 6.385443 TCTGGATTGGGTTCATCTCTATAGT 58.615 40.000 0.00 0.00 0.00 2.12
1145 1162 7.535738 TCTGGATTGGGTTCATCTCTATAGTA 58.464 38.462 0.00 0.00 0.00 1.82
1322 1339 5.066968 AGAAAAAGAGATCACTCGAGGAC 57.933 43.478 18.41 4.93 46.64 3.85
1630 1653 3.933332 CCAAGAGACAGACCCGAATAAAC 59.067 47.826 0.00 0.00 0.00 2.01
1757 1780 0.620556 GAAGACCTGCAATCCCTCCA 59.379 55.000 0.00 0.00 0.00 3.86
1802 1825 9.581289 TTTTATTGTTCCATCTTCTTAACCTGA 57.419 29.630 0.00 0.00 0.00 3.86
1803 1826 9.581289 TTTATTGTTCCATCTTCTTAACCTGAA 57.419 29.630 0.00 0.00 0.00 3.02
1804 1827 9.581289 TTATTGTTCCATCTTCTTAACCTGAAA 57.419 29.630 0.00 0.00 0.00 2.69
1805 1828 7.510549 TTGTTCCATCTTCTTAACCTGAAAG 57.489 36.000 0.00 0.00 0.00 2.62
1827 1850 9.490663 GAAAGGAAAGTGAATCAATAATGTACG 57.509 33.333 0.00 0.00 0.00 3.67
1828 1851 7.553881 AGGAAAGTGAATCAATAATGTACGG 57.446 36.000 0.00 0.00 0.00 4.02
1829 1852 6.038271 AGGAAAGTGAATCAATAATGTACGGC 59.962 38.462 0.00 0.00 0.00 5.68
1830 1853 6.038271 GGAAAGTGAATCAATAATGTACGGCT 59.962 38.462 0.00 0.00 0.00 5.52
1831 1854 7.225931 GGAAAGTGAATCAATAATGTACGGCTA 59.774 37.037 0.00 0.00 0.00 3.93
1832 1855 7.715265 AAGTGAATCAATAATGTACGGCTAG 57.285 36.000 0.00 0.00 0.00 3.42
1833 1856 5.696724 AGTGAATCAATAATGTACGGCTAGC 59.303 40.000 6.04 6.04 0.00 3.42
1834 1857 5.465390 GTGAATCAATAATGTACGGCTAGCA 59.535 40.000 18.24 0.00 0.00 3.49
1835 1858 6.147821 GTGAATCAATAATGTACGGCTAGCAT 59.852 38.462 18.24 6.50 0.00 3.79
1836 1859 6.147656 TGAATCAATAATGTACGGCTAGCATG 59.852 38.462 18.24 10.92 0.00 4.06
1837 1860 5.208463 TCAATAATGTACGGCTAGCATGA 57.792 39.130 18.24 0.00 0.00 3.07
1838 1861 4.988540 TCAATAATGTACGGCTAGCATGAC 59.011 41.667 18.24 10.85 0.00 3.06
1839 1862 1.852942 AATGTACGGCTAGCATGACG 58.147 50.000 18.24 13.18 45.23 4.35
1848 1871 4.758561 CGGCTAGCATGACGTATTTAAAC 58.241 43.478 18.24 0.00 33.11 2.01
1849 1872 4.506654 CGGCTAGCATGACGTATTTAAACT 59.493 41.667 18.24 0.00 33.11 2.66
1850 1873 5.006358 CGGCTAGCATGACGTATTTAAACTT 59.994 40.000 18.24 0.00 33.11 2.66
1851 1874 6.192360 GGCTAGCATGACGTATTTAAACTTG 58.808 40.000 18.24 0.00 0.00 3.16
1852 1875 6.183360 GGCTAGCATGACGTATTTAAACTTGT 60.183 38.462 18.24 0.00 0.00 3.16
1853 1876 6.900299 GCTAGCATGACGTATTTAAACTTGTC 59.100 38.462 10.63 8.02 0.00 3.18
1854 1877 6.178239 AGCATGACGTATTTAAACTTGTCC 57.822 37.500 0.00 0.45 0.00 4.02
1855 1878 5.019498 GCATGACGTATTTAAACTTGTCCG 58.981 41.667 0.00 5.81 0.00 4.79
1856 1879 5.163933 GCATGACGTATTTAAACTTGTCCGA 60.164 40.000 0.00 0.00 0.00 4.55
1857 1880 5.827568 TGACGTATTTAAACTTGTCCGAC 57.172 39.130 11.04 0.00 0.00 4.79
1858 1881 5.531634 TGACGTATTTAAACTTGTCCGACT 58.468 37.500 11.04 0.00 0.00 4.18
1859 1882 5.403166 TGACGTATTTAAACTTGTCCGACTG 59.597 40.000 11.04 0.00 0.00 3.51
1860 1883 4.151157 ACGTATTTAAACTTGTCCGACTGC 59.849 41.667 0.00 0.00 0.00 4.40
1861 1884 4.150980 CGTATTTAAACTTGTCCGACTGCA 59.849 41.667 0.00 0.00 0.00 4.41
1862 1885 5.163893 CGTATTTAAACTTGTCCGACTGCAT 60.164 40.000 0.00 0.00 0.00 3.96
1863 1886 4.481930 TTTAAACTTGTCCGACTGCATG 57.518 40.909 0.00 0.00 0.00 4.06
1864 1887 1.967319 AAACTTGTCCGACTGCATGT 58.033 45.000 0.00 0.00 0.00 3.21
1865 1888 1.967319 AACTTGTCCGACTGCATGTT 58.033 45.000 0.00 0.00 0.00 2.71
1866 1889 1.512926 ACTTGTCCGACTGCATGTTC 58.487 50.000 0.00 0.00 0.00 3.18
1867 1890 1.070758 ACTTGTCCGACTGCATGTTCT 59.929 47.619 0.00 0.00 0.00 3.01
1868 1891 1.728971 CTTGTCCGACTGCATGTTCTC 59.271 52.381 0.00 0.00 0.00 2.87
1869 1892 0.969149 TGTCCGACTGCATGTTCTCT 59.031 50.000 0.00 0.00 0.00 3.10
1870 1893 1.067565 TGTCCGACTGCATGTTCTCTC 60.068 52.381 0.00 0.00 0.00 3.20
1871 1894 0.532573 TCCGACTGCATGTTCTCTCC 59.467 55.000 0.00 0.00 0.00 3.71
1872 1895 0.460987 CCGACTGCATGTTCTCTCCC 60.461 60.000 0.00 0.00 0.00 4.30
1873 1896 0.247460 CGACTGCATGTTCTCTCCCA 59.753 55.000 0.00 0.00 0.00 4.37
1874 1897 1.338105 CGACTGCATGTTCTCTCCCAA 60.338 52.381 0.00 0.00 0.00 4.12
1875 1898 2.679059 CGACTGCATGTTCTCTCCCAAT 60.679 50.000 0.00 0.00 0.00 3.16
1876 1899 3.350833 GACTGCATGTTCTCTCCCAATT 58.649 45.455 0.00 0.00 0.00 2.32
1877 1900 3.087031 ACTGCATGTTCTCTCCCAATTG 58.913 45.455 0.00 0.00 0.00 2.32
1878 1901 3.245016 ACTGCATGTTCTCTCCCAATTGA 60.245 43.478 7.12 0.00 0.00 2.57
1879 1902 3.952323 CTGCATGTTCTCTCCCAATTGAT 59.048 43.478 7.12 0.00 0.00 2.57
1880 1903 5.114764 TGCATGTTCTCTCCCAATTGATA 57.885 39.130 7.12 0.00 0.00 2.15
1881 1904 4.883585 TGCATGTTCTCTCCCAATTGATAC 59.116 41.667 7.12 0.00 0.00 2.24
1882 1905 4.276926 GCATGTTCTCTCCCAATTGATACC 59.723 45.833 7.12 0.00 0.00 2.73
1883 1906 4.503714 TGTTCTCTCCCAATTGATACCC 57.496 45.455 7.12 0.00 0.00 3.69
1884 1907 3.849574 TGTTCTCTCCCAATTGATACCCA 59.150 43.478 7.12 0.00 0.00 4.51
1885 1908 4.290985 TGTTCTCTCCCAATTGATACCCAA 59.709 41.667 7.12 0.00 39.41 4.12
1886 1909 5.044179 TGTTCTCTCCCAATTGATACCCAAT 60.044 40.000 7.12 0.00 46.86 3.16
1901 1924 8.610248 TGATACCCAATTTACATAATGTACGG 57.390 34.615 0.00 0.00 31.69 4.02
1902 1925 5.761165 ACCCAATTTACATAATGTACGGC 57.239 39.130 0.00 0.00 31.69 5.68
1903 1926 5.442391 ACCCAATTTACATAATGTACGGCT 58.558 37.500 0.00 0.00 31.69 5.52
1904 1927 6.593807 ACCCAATTTACATAATGTACGGCTA 58.406 36.000 0.00 0.00 31.69 3.93
1905 1928 6.484308 ACCCAATTTACATAATGTACGGCTAC 59.516 38.462 0.00 0.00 31.69 3.58
1906 1929 6.072893 CCCAATTTACATAATGTACGGCTACC 60.073 42.308 0.00 0.00 31.69 3.18
1907 1930 6.708949 CCAATTTACATAATGTACGGCTACCT 59.291 38.462 0.00 0.00 31.69 3.08
1908 1931 7.227910 CCAATTTACATAATGTACGGCTACCTT 59.772 37.037 0.00 0.00 31.69 3.50
1909 1932 7.958053 ATTTACATAATGTACGGCTACCTTC 57.042 36.000 0.00 0.00 31.69 3.46
1910 1933 6.720112 TTACATAATGTACGGCTACCTTCT 57.280 37.500 0.00 0.00 31.69 2.85
1911 1934 5.197682 ACATAATGTACGGCTACCTTCTC 57.802 43.478 0.00 0.00 0.00 2.87
1912 1935 4.647853 ACATAATGTACGGCTACCTTCTCA 59.352 41.667 0.00 0.00 0.00 3.27
1913 1936 3.521947 AATGTACGGCTACCTTCTCAC 57.478 47.619 0.00 0.00 0.00 3.51
1914 1937 0.806868 TGTACGGCTACCTTCTCACG 59.193 55.000 0.00 0.00 0.00 4.35
1915 1938 1.089920 GTACGGCTACCTTCTCACGA 58.910 55.000 0.00 0.00 0.00 4.35
1916 1939 1.089920 TACGGCTACCTTCTCACGAC 58.910 55.000 0.00 0.00 0.00 4.34
1917 1940 0.608582 ACGGCTACCTTCTCACGACT 60.609 55.000 0.00 0.00 0.00 4.18
1918 1941 0.526662 CGGCTACCTTCTCACGACTT 59.473 55.000 0.00 0.00 0.00 3.01
1919 1942 1.467713 CGGCTACCTTCTCACGACTTC 60.468 57.143 0.00 0.00 0.00 3.01
1920 1943 1.544691 GGCTACCTTCTCACGACTTCA 59.455 52.381 0.00 0.00 0.00 3.02
1921 1944 2.597520 GCTACCTTCTCACGACTTCAC 58.402 52.381 0.00 0.00 0.00 3.18
1922 1945 2.229302 GCTACCTTCTCACGACTTCACT 59.771 50.000 0.00 0.00 0.00 3.41
1923 1946 3.671164 GCTACCTTCTCACGACTTCACTC 60.671 52.174 0.00 0.00 0.00 3.51
1924 1947 1.614413 ACCTTCTCACGACTTCACTCC 59.386 52.381 0.00 0.00 0.00 3.85
1925 1948 1.613925 CCTTCTCACGACTTCACTCCA 59.386 52.381 0.00 0.00 0.00 3.86
1926 1949 2.352225 CCTTCTCACGACTTCACTCCAG 60.352 54.545 0.00 0.00 0.00 3.86
1927 1950 1.982660 TCTCACGACTTCACTCCAGT 58.017 50.000 0.00 0.00 0.00 4.00
1928 1951 2.307768 TCTCACGACTTCACTCCAGTT 58.692 47.619 0.00 0.00 0.00 3.16
1929 1952 2.293677 TCTCACGACTTCACTCCAGTTC 59.706 50.000 0.00 0.00 0.00 3.01
1930 1953 1.001706 TCACGACTTCACTCCAGTTCG 60.002 52.381 0.00 0.00 0.00 3.95
1931 1954 0.318784 ACGACTTCACTCCAGTTCGC 60.319 55.000 0.00 0.00 0.00 4.70
1932 1955 1.009389 CGACTTCACTCCAGTTCGCC 61.009 60.000 0.00 0.00 0.00 5.54
1933 1956 0.033504 GACTTCACTCCAGTTCGCCA 59.966 55.000 0.00 0.00 0.00 5.69
1934 1957 0.034059 ACTTCACTCCAGTTCGCCAG 59.966 55.000 0.00 0.00 0.00 4.85
1935 1958 0.671781 CTTCACTCCAGTTCGCCAGG 60.672 60.000 0.00 0.00 0.00 4.45
1936 1959 1.407656 TTCACTCCAGTTCGCCAGGT 61.408 55.000 0.00 0.00 0.00 4.00
1937 1960 1.071471 CACTCCAGTTCGCCAGGTT 59.929 57.895 0.00 0.00 0.00 3.50
1938 1961 1.071471 ACTCCAGTTCGCCAGGTTG 59.929 57.895 0.00 0.00 0.00 3.77
1939 1962 1.071471 CTCCAGTTCGCCAGGTTGT 59.929 57.895 0.00 0.00 0.00 3.32
1940 1963 0.951040 CTCCAGTTCGCCAGGTTGTC 60.951 60.000 0.00 0.00 0.00 3.18
1941 1964 1.071471 CCAGTTCGCCAGGTTGTCT 59.929 57.895 0.00 0.00 0.00 3.41
1942 1965 0.320374 CCAGTTCGCCAGGTTGTCTA 59.680 55.000 0.00 0.00 0.00 2.59
1943 1966 1.429463 CAGTTCGCCAGGTTGTCTAC 58.571 55.000 0.00 0.00 0.00 2.59
1944 1967 0.038526 AGTTCGCCAGGTTGTCTACG 60.039 55.000 0.00 0.00 0.00 3.51
1945 1968 1.373748 TTCGCCAGGTTGTCTACGC 60.374 57.895 0.00 0.00 0.00 4.42
1946 1969 3.179265 CGCCAGGTTGTCTACGCG 61.179 66.667 3.53 3.53 37.19 6.01
1947 1970 2.048503 GCCAGGTTGTCTACGCGT 60.049 61.111 19.17 19.17 0.00 6.01
2016 3108 7.230712 CCCCTGTTATTTTTGGGTCATATCTAC 59.769 40.741 0.00 0.00 38.03 2.59
2028 3120 8.410673 TGGGTCATATCTACTATTCAGAGTTC 57.589 38.462 0.00 0.00 0.00 3.01
2100 3192 2.419297 CCTAGATGTCCAGTCAACTGCC 60.419 54.545 4.58 0.00 42.47 4.85
2119 3211 4.440214 CGCCTCAACGCATTTCAC 57.560 55.556 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 178 7.062488 GCGTGGTTCCGAAACATAATTATTTTT 59.938 33.333 8.91 8.91 37.10 1.94
165 179 6.528774 GCGTGGTTCCGAAACATAATTATTTT 59.471 34.615 1.33 0.97 37.10 1.82
166 180 6.031471 GCGTGGTTCCGAAACATAATTATTT 58.969 36.000 1.33 0.00 37.10 1.40
167 181 5.124138 TGCGTGGTTCCGAAACATAATTATT 59.876 36.000 1.33 0.00 37.10 1.40
168 182 4.636648 TGCGTGGTTCCGAAACATAATTAT 59.363 37.500 1.33 0.00 37.10 1.28
318 333 6.693315 GGAATTGATTCCGTAAAAGATGGA 57.307 37.500 6.98 0.00 46.01 3.41
579 594 7.223193 TCGAGTTGTTCTAAAGAATCAAAACGA 59.777 33.333 18.64 18.64 35.73 3.85
621 636 2.708325 GTCATTGAGGGCCTCCTAAGAT 59.292 50.000 30.03 13.23 45.05 2.40
623 638 1.141858 GGTCATTGAGGGCCTCCTAAG 59.858 57.143 30.03 17.00 45.05 2.18
689 704 2.613133 CAGTAGGTACAGCTAGTCCGTC 59.387 54.545 0.00 0.00 0.00 4.79
785 801 7.929159 ACATTTTGTTCATTTGGGTTTGATTC 58.071 30.769 0.00 0.00 0.00 2.52
990 1006 9.627123 CCTACTTTCCTCCACATTTTATCAATA 57.373 33.333 0.00 0.00 0.00 1.90
1140 1157 6.797707 TGGTCCCTCCGATTACTATTACTAT 58.202 40.000 0.00 0.00 39.52 2.12
1141 1158 6.044754 TCTGGTCCCTCCGATTACTATTACTA 59.955 42.308 0.00 0.00 39.52 1.82
1142 1159 5.070823 TGGTCCCTCCGATTACTATTACT 57.929 43.478 0.00 0.00 39.52 2.24
1143 1160 5.075493 TCTGGTCCCTCCGATTACTATTAC 58.925 45.833 0.00 0.00 39.52 1.89
1144 1161 5.329191 TCTGGTCCCTCCGATTACTATTA 57.671 43.478 0.00 0.00 39.52 0.98
1145 1162 4.194678 TCTGGTCCCTCCGATTACTATT 57.805 45.455 0.00 0.00 39.52 1.73
1213 1230 5.465935 GTCCTTTCCGCTCTAATCAGATAG 58.534 45.833 0.00 0.00 0.00 2.08
1322 1339 5.865085 TCCTTCGTGGAATAAGATATTGGG 58.135 41.667 0.00 0.00 42.94 4.12
1432 1450 8.990163 AAGTAAACTCTTCCATTGAAGGTTTA 57.010 30.769 18.72 18.72 46.61 2.01
1787 1810 7.445402 TCACTTTCCTTTCAGGTTAAGAAGATG 59.555 37.037 11.75 3.67 36.53 2.90
1788 1811 7.518188 TCACTTTCCTTTCAGGTTAAGAAGAT 58.482 34.615 11.75 0.00 36.53 2.40
1789 1812 6.895782 TCACTTTCCTTTCAGGTTAAGAAGA 58.104 36.000 11.75 7.92 36.53 2.87
1790 1813 7.568199 TTCACTTTCCTTTCAGGTTAAGAAG 57.432 36.000 11.75 0.00 36.53 2.85
1791 1814 7.777910 TGATTCACTTTCCTTTCAGGTTAAGAA 59.222 33.333 11.75 0.00 36.53 2.52
1792 1815 7.287061 TGATTCACTTTCCTTTCAGGTTAAGA 58.713 34.615 11.75 0.00 36.53 2.10
1793 1816 7.510549 TGATTCACTTTCCTTTCAGGTTAAG 57.489 36.000 6.12 6.12 36.53 1.85
1794 1817 7.889873 TTGATTCACTTTCCTTTCAGGTTAA 57.110 32.000 0.00 0.00 36.53 2.01
1795 1818 9.581289 TTATTGATTCACTTTCCTTTCAGGTTA 57.419 29.630 0.00 0.00 36.53 2.85
1796 1819 6.983906 ATTGATTCACTTTCCTTTCAGGTT 57.016 33.333 0.00 0.00 36.53 3.50
1797 1820 8.526147 CATTATTGATTCACTTTCCTTTCAGGT 58.474 33.333 0.00 0.00 36.53 4.00
1798 1821 8.526147 ACATTATTGATTCACTTTCCTTTCAGG 58.474 33.333 0.00 0.00 36.46 3.86
1801 1824 9.490663 CGTACATTATTGATTCACTTTCCTTTC 57.509 33.333 0.00 0.00 0.00 2.62
1802 1825 8.458843 CCGTACATTATTGATTCACTTTCCTTT 58.541 33.333 0.00 0.00 0.00 3.11
1803 1826 7.415206 GCCGTACATTATTGATTCACTTTCCTT 60.415 37.037 0.00 0.00 0.00 3.36
1804 1827 6.038271 GCCGTACATTATTGATTCACTTTCCT 59.962 38.462 0.00 0.00 0.00 3.36
1805 1828 6.038271 AGCCGTACATTATTGATTCACTTTCC 59.962 38.462 0.00 0.00 0.00 3.13
1806 1829 7.016361 AGCCGTACATTATTGATTCACTTTC 57.984 36.000 0.00 0.00 0.00 2.62
1807 1830 7.254795 GCTAGCCGTACATTATTGATTCACTTT 60.255 37.037 2.29 0.00 0.00 2.66
1808 1831 6.202954 GCTAGCCGTACATTATTGATTCACTT 59.797 38.462 2.29 0.00 0.00 3.16
1809 1832 5.696724 GCTAGCCGTACATTATTGATTCACT 59.303 40.000 2.29 0.00 0.00 3.41
1810 1833 5.465390 TGCTAGCCGTACATTATTGATTCAC 59.535 40.000 13.29 0.00 0.00 3.18
1811 1834 5.606505 TGCTAGCCGTACATTATTGATTCA 58.393 37.500 13.29 0.00 0.00 2.57
1812 1835 6.368791 TCATGCTAGCCGTACATTATTGATTC 59.631 38.462 13.29 0.00 0.00 2.52
1813 1836 6.147821 GTCATGCTAGCCGTACATTATTGATT 59.852 38.462 13.29 0.00 0.00 2.57
1814 1837 5.639506 GTCATGCTAGCCGTACATTATTGAT 59.360 40.000 13.29 0.00 0.00 2.57
1815 1838 4.988540 GTCATGCTAGCCGTACATTATTGA 59.011 41.667 13.29 0.00 0.00 2.57
1816 1839 4.143326 CGTCATGCTAGCCGTACATTATTG 60.143 45.833 13.29 0.00 0.00 1.90
1817 1840 3.987868 CGTCATGCTAGCCGTACATTATT 59.012 43.478 13.29 0.00 0.00 1.40
1818 1841 3.005472 ACGTCATGCTAGCCGTACATTAT 59.995 43.478 13.29 0.00 0.00 1.28
1819 1842 2.359848 ACGTCATGCTAGCCGTACATTA 59.640 45.455 13.29 0.00 0.00 1.90
1820 1843 1.136305 ACGTCATGCTAGCCGTACATT 59.864 47.619 13.29 0.00 0.00 2.71
1821 1844 0.744874 ACGTCATGCTAGCCGTACAT 59.255 50.000 13.29 0.00 0.00 2.29
1822 1845 1.381522 TACGTCATGCTAGCCGTACA 58.618 50.000 16.66 2.17 34.95 2.90
1823 1846 2.701073 ATACGTCATGCTAGCCGTAC 57.299 50.000 21.05 11.78 38.45 3.67
1824 1847 3.720949 AAATACGTCATGCTAGCCGTA 57.279 42.857 20.94 20.94 39.74 4.02
1825 1848 2.596904 AAATACGTCATGCTAGCCGT 57.403 45.000 18.42 18.42 37.33 5.68
1826 1849 4.506654 AGTTTAAATACGTCATGCTAGCCG 59.493 41.667 13.29 10.94 0.00 5.52
1827 1850 5.986004 AGTTTAAATACGTCATGCTAGCC 57.014 39.130 13.29 0.00 0.00 3.93
1828 1851 6.772078 ACAAGTTTAAATACGTCATGCTAGC 58.228 36.000 8.10 8.10 0.00 3.42
1829 1852 7.399523 GGACAAGTTTAAATACGTCATGCTAG 58.600 38.462 0.00 0.00 0.00 3.42
1830 1853 6.035220 CGGACAAGTTTAAATACGTCATGCTA 59.965 38.462 0.00 0.00 0.00 3.49
1831 1854 5.163893 CGGACAAGTTTAAATACGTCATGCT 60.164 40.000 0.00 0.00 0.00 3.79
1832 1855 5.019498 CGGACAAGTTTAAATACGTCATGC 58.981 41.667 0.00 0.00 0.00 4.06
1833 1856 6.090358 AGTCGGACAAGTTTAAATACGTCATG 59.910 38.462 11.27 0.00 0.00 3.07
1834 1857 6.090358 CAGTCGGACAAGTTTAAATACGTCAT 59.910 38.462 11.27 0.00 0.00 3.06
1835 1858 5.403166 CAGTCGGACAAGTTTAAATACGTCA 59.597 40.000 11.27 0.00 0.00 4.35
1836 1859 5.667156 GCAGTCGGACAAGTTTAAATACGTC 60.667 44.000 11.27 0.00 0.00 4.34
1837 1860 4.151157 GCAGTCGGACAAGTTTAAATACGT 59.849 41.667 11.27 0.00 0.00 3.57
1838 1861 4.150980 TGCAGTCGGACAAGTTTAAATACG 59.849 41.667 11.27 0.00 0.00 3.06
1839 1862 5.600908 TGCAGTCGGACAAGTTTAAATAC 57.399 39.130 11.27 0.00 0.00 1.89
1840 1863 5.703592 ACATGCAGTCGGACAAGTTTAAATA 59.296 36.000 11.27 0.00 0.00 1.40
1841 1864 4.518970 ACATGCAGTCGGACAAGTTTAAAT 59.481 37.500 11.27 0.00 0.00 1.40
1842 1865 3.880490 ACATGCAGTCGGACAAGTTTAAA 59.120 39.130 11.27 0.00 0.00 1.52
1843 1866 3.472652 ACATGCAGTCGGACAAGTTTAA 58.527 40.909 11.27 0.00 0.00 1.52
1844 1867 3.120321 ACATGCAGTCGGACAAGTTTA 57.880 42.857 11.27 0.00 0.00 2.01
1845 1868 1.967319 ACATGCAGTCGGACAAGTTT 58.033 45.000 11.27 0.00 0.00 2.66
1846 1869 1.873591 GAACATGCAGTCGGACAAGTT 59.126 47.619 11.27 7.08 31.00 2.66
1847 1870 1.070758 AGAACATGCAGTCGGACAAGT 59.929 47.619 11.27 0.00 0.00 3.16
1848 1871 1.728971 GAGAACATGCAGTCGGACAAG 59.271 52.381 11.27 3.61 0.00 3.16
1849 1872 1.344438 AGAGAACATGCAGTCGGACAA 59.656 47.619 11.27 0.00 0.00 3.18
1850 1873 0.969149 AGAGAACATGCAGTCGGACA 59.031 50.000 11.27 0.00 0.00 4.02
1851 1874 1.634702 GAGAGAACATGCAGTCGGAC 58.365 55.000 0.00 0.00 0.00 4.79
1852 1875 0.532573 GGAGAGAACATGCAGTCGGA 59.467 55.000 0.00 0.00 0.00 4.55
1853 1876 0.460987 GGGAGAGAACATGCAGTCGG 60.461 60.000 0.00 0.00 0.00 4.79
1854 1877 0.247460 TGGGAGAGAACATGCAGTCG 59.753 55.000 0.00 0.00 0.00 4.18
1855 1878 2.479566 TTGGGAGAGAACATGCAGTC 57.520 50.000 0.00 0.00 0.00 3.51
1856 1879 3.087031 CAATTGGGAGAGAACATGCAGT 58.913 45.455 0.00 0.00 0.00 4.40
1857 1880 3.349927 TCAATTGGGAGAGAACATGCAG 58.650 45.455 5.42 0.00 0.00 4.41
1858 1881 3.438216 TCAATTGGGAGAGAACATGCA 57.562 42.857 5.42 0.00 0.00 3.96
1859 1882 4.276926 GGTATCAATTGGGAGAGAACATGC 59.723 45.833 5.42 0.00 0.00 4.06
1860 1883 4.823989 GGGTATCAATTGGGAGAGAACATG 59.176 45.833 5.42 0.00 0.00 3.21
1861 1884 4.478317 TGGGTATCAATTGGGAGAGAACAT 59.522 41.667 5.42 0.00 0.00 2.71
1862 1885 3.849574 TGGGTATCAATTGGGAGAGAACA 59.150 43.478 5.42 0.00 0.00 3.18
1863 1886 4.503714 TGGGTATCAATTGGGAGAGAAC 57.496 45.455 5.42 0.00 0.00 3.01
1864 1887 5.732331 ATTGGGTATCAATTGGGAGAGAA 57.268 39.130 5.42 0.00 43.04 2.87
1875 1898 9.058174 CCGTACATTATGTAAATTGGGTATCAA 57.942 33.333 6.64 0.00 34.21 2.57
1876 1899 7.173562 GCCGTACATTATGTAAATTGGGTATCA 59.826 37.037 6.64 0.00 34.21 2.15
1877 1900 7.389607 AGCCGTACATTATGTAAATTGGGTATC 59.610 37.037 6.64 0.00 34.21 2.24
1878 1901 7.228590 AGCCGTACATTATGTAAATTGGGTAT 58.771 34.615 6.64 0.00 34.21 2.73
1879 1902 6.593807 AGCCGTACATTATGTAAATTGGGTA 58.406 36.000 6.64 0.00 34.21 3.69
1880 1903 5.442391 AGCCGTACATTATGTAAATTGGGT 58.558 37.500 6.64 9.24 34.21 4.51
1881 1904 6.072893 GGTAGCCGTACATTATGTAAATTGGG 60.073 42.308 6.64 5.27 34.21 4.12
1882 1905 6.708949 AGGTAGCCGTACATTATGTAAATTGG 59.291 38.462 6.64 7.95 34.21 3.16
1883 1906 7.724305 AGGTAGCCGTACATTATGTAAATTG 57.276 36.000 6.64 0.00 34.21 2.32
1884 1907 8.208903 AGAAGGTAGCCGTACATTATGTAAATT 58.791 33.333 6.64 0.00 33.34 1.82
1885 1908 7.732996 AGAAGGTAGCCGTACATTATGTAAAT 58.267 34.615 6.64 0.00 33.34 1.40
1886 1909 7.116075 AGAAGGTAGCCGTACATTATGTAAA 57.884 36.000 6.64 0.00 33.34 2.01
1887 1910 6.321945 TGAGAAGGTAGCCGTACATTATGTAA 59.678 38.462 6.64 0.00 33.34 2.41
1888 1911 5.829391 TGAGAAGGTAGCCGTACATTATGTA 59.171 40.000 0.29 0.29 33.34 2.29
1889 1912 4.647853 TGAGAAGGTAGCCGTACATTATGT 59.352 41.667 2.58 2.58 33.34 2.29
1890 1913 4.982916 GTGAGAAGGTAGCCGTACATTATG 59.017 45.833 0.00 0.00 33.34 1.90
1891 1914 4.261489 CGTGAGAAGGTAGCCGTACATTAT 60.261 45.833 0.00 0.00 33.34 1.28
1892 1915 3.065786 CGTGAGAAGGTAGCCGTACATTA 59.934 47.826 0.00 0.00 33.34 1.90
1893 1916 2.159282 CGTGAGAAGGTAGCCGTACATT 60.159 50.000 0.00 0.00 35.87 2.71
1894 1917 1.404391 CGTGAGAAGGTAGCCGTACAT 59.596 52.381 0.00 0.00 0.00 2.29
1895 1918 0.806868 CGTGAGAAGGTAGCCGTACA 59.193 55.000 0.00 0.00 0.00 2.90
1896 1919 1.089920 TCGTGAGAAGGTAGCCGTAC 58.910 55.000 0.00 0.00 37.03 3.67
1897 1920 1.089920 GTCGTGAGAAGGTAGCCGTA 58.910 55.000 0.00 0.00 45.01 4.02
1898 1921 0.608582 AGTCGTGAGAAGGTAGCCGT 60.609 55.000 0.00 0.00 45.01 5.68
1899 1922 0.526662 AAGTCGTGAGAAGGTAGCCG 59.473 55.000 0.00 0.00 45.01 5.52
1900 1923 1.544691 TGAAGTCGTGAGAAGGTAGCC 59.455 52.381 0.00 0.00 45.01 3.93
1901 1924 2.229302 AGTGAAGTCGTGAGAAGGTAGC 59.771 50.000 0.00 0.00 45.01 3.58
1902 1925 3.119779 GGAGTGAAGTCGTGAGAAGGTAG 60.120 52.174 0.00 0.00 45.01 3.18
1903 1926 2.818432 GGAGTGAAGTCGTGAGAAGGTA 59.182 50.000 0.00 0.00 45.01 3.08
1904 1927 1.614413 GGAGTGAAGTCGTGAGAAGGT 59.386 52.381 0.00 0.00 45.01 3.50
1905 1928 1.613925 TGGAGTGAAGTCGTGAGAAGG 59.386 52.381 0.00 0.00 45.01 3.46
1906 1929 2.294791 ACTGGAGTGAAGTCGTGAGAAG 59.705 50.000 0.00 0.00 45.01 2.85
1907 1930 2.307768 ACTGGAGTGAAGTCGTGAGAA 58.692 47.619 0.00 0.00 45.01 2.87
1908 1931 1.982660 ACTGGAGTGAAGTCGTGAGA 58.017 50.000 0.00 0.00 38.16 3.27
1909 1932 2.667137 GAACTGGAGTGAAGTCGTGAG 58.333 52.381 0.00 0.00 0.00 3.51
1910 1933 1.001706 CGAACTGGAGTGAAGTCGTGA 60.002 52.381 0.00 0.00 0.00 4.35
1911 1934 1.409412 CGAACTGGAGTGAAGTCGTG 58.591 55.000 0.00 0.00 0.00 4.35
1912 1935 0.318784 GCGAACTGGAGTGAAGTCGT 60.319 55.000 0.00 0.00 0.00 4.34
1913 1936 1.009389 GGCGAACTGGAGTGAAGTCG 61.009 60.000 0.00 0.00 0.00 4.18
1914 1937 0.033504 TGGCGAACTGGAGTGAAGTC 59.966 55.000 0.00 0.00 0.00 3.01
1915 1938 0.034059 CTGGCGAACTGGAGTGAAGT 59.966 55.000 0.00 0.00 0.00 3.01
1916 1939 0.671781 CCTGGCGAACTGGAGTGAAG 60.672 60.000 0.00 0.00 40.42 3.02
1917 1940 1.371183 CCTGGCGAACTGGAGTGAA 59.629 57.895 0.00 0.00 40.42 3.18
1918 1941 1.407656 AACCTGGCGAACTGGAGTGA 61.408 55.000 9.79 0.00 40.42 3.41
1919 1942 1.071471 AACCTGGCGAACTGGAGTG 59.929 57.895 9.79 0.00 40.42 3.51
1920 1943 1.071471 CAACCTGGCGAACTGGAGT 59.929 57.895 9.79 0.00 40.42 3.85
1921 1944 0.951040 GACAACCTGGCGAACTGGAG 60.951 60.000 9.79 5.31 40.42 3.86
1922 1945 1.070786 GACAACCTGGCGAACTGGA 59.929 57.895 9.79 0.00 40.42 3.86
1923 1946 0.320374 TAGACAACCTGGCGAACTGG 59.680 55.000 0.00 0.00 43.37 4.00
1924 1947 1.429463 GTAGACAACCTGGCGAACTG 58.571 55.000 0.00 0.00 0.00 3.16
1925 1948 0.038526 CGTAGACAACCTGGCGAACT 60.039 55.000 0.00 0.00 0.00 3.01
1926 1949 1.623973 GCGTAGACAACCTGGCGAAC 61.624 60.000 0.00 0.00 0.00 3.95
1927 1950 1.373748 GCGTAGACAACCTGGCGAA 60.374 57.895 0.00 0.00 0.00 4.70
1928 1951 2.260434 GCGTAGACAACCTGGCGA 59.740 61.111 0.00 0.00 0.00 5.54
1929 1952 3.179265 CGCGTAGACAACCTGGCG 61.179 66.667 0.00 0.00 40.71 5.69
1930 1953 1.074872 GTACGCGTAGACAACCTGGC 61.075 60.000 21.25 0.00 0.00 4.85
1931 1954 0.795735 CGTACGCGTAGACAACCTGG 60.796 60.000 21.25 0.00 0.00 4.45
1932 1955 0.166597 TCGTACGCGTAGACAACCTG 59.833 55.000 21.25 3.85 39.49 4.00
1933 1956 1.089920 ATCGTACGCGTAGACAACCT 58.910 50.000 21.25 1.51 39.49 3.50
1934 1957 1.186030 CATCGTACGCGTAGACAACC 58.814 55.000 21.25 5.68 39.49 3.77
1935 1958 2.163826 TCATCGTACGCGTAGACAAC 57.836 50.000 21.25 9.32 39.49 3.32
1936 1959 2.777494 CTTCATCGTACGCGTAGACAA 58.223 47.619 21.25 13.34 39.49 3.18
1937 1960 1.530441 GCTTCATCGTACGCGTAGACA 60.530 52.381 21.25 6.71 39.49 3.41
1938 1961 1.110876 GCTTCATCGTACGCGTAGAC 58.889 55.000 21.25 11.00 39.49 2.59
1939 1962 1.012086 AGCTTCATCGTACGCGTAGA 58.988 50.000 21.25 18.53 39.49 2.59
1940 1963 1.823828 AAGCTTCATCGTACGCGTAG 58.176 50.000 21.25 13.77 39.49 3.51
1941 1964 3.548587 GATAAGCTTCATCGTACGCGTA 58.451 45.455 16.41 16.41 39.49 4.42
1942 1965 2.382519 GATAAGCTTCATCGTACGCGT 58.617 47.619 19.17 19.17 39.49 6.01
1943 1966 1.714460 GGATAAGCTTCATCGTACGCG 59.286 52.381 11.24 3.53 39.92 6.01
1944 1967 2.059541 GGGATAAGCTTCATCGTACGC 58.940 52.381 11.24 0.00 0.00 4.42
1945 1968 2.609737 GGGGGATAAGCTTCATCGTACG 60.610 54.545 9.53 9.53 0.00 3.67
1946 1969 2.367567 TGGGGGATAAGCTTCATCGTAC 59.632 50.000 0.00 0.00 0.00 3.67
1947 1970 2.684943 TGGGGGATAAGCTTCATCGTA 58.315 47.619 0.00 0.00 0.00 3.43
2016 3108 3.634568 ATCGAGGCGAACTCTGAATAG 57.365 47.619 6.09 0.00 44.33 1.73
2028 3120 2.522638 GCGGTACCAAATCGAGGCG 61.523 63.158 13.54 0.00 0.00 5.52
2118 3210 0.323908 AGAGCTAGCTGGTTCTCCGT 60.324 55.000 24.99 0.00 36.30 4.69
2119 3211 0.102120 CAGAGCTAGCTGGTTCTCCG 59.898 60.000 24.99 0.33 36.30 4.63


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

AutoCloner maintained by Alex Coulton.