Multiple sequence alignment - TraesCS3D01G157300

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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 TraesCS3D01G157300 chr3D 100.000 2753 0 0 1 2753 125481328 125484080 0.000000e+00 5084.0
1 TraesCS3D01G157300 chr3D 100.000 457 0 0 3190 3646 125484517 125484973 0.000000e+00 845.0
2 TraesCS3D01G157300 chr3A 92.287 1828 76 25 1 1771 134236684 134238503 0.000000e+00 2534.0
3 TraesCS3D01G157300 chr3A 90.295 577 43 7 2154 2730 134238956 134239519 0.000000e+00 743.0
4 TraesCS3D01G157300 chr3A 93.158 380 26 0 3242 3621 134240047 134240426 3.180000e-155 558.0
5 TraesCS3D01G157300 chr3A 90.164 122 11 1 1972 2092 134238827 134238948 1.360000e-34 158.0
6 TraesCS3D01G157300 chr3B 92.371 1809 75 20 1 1772 179368578 179370360 0.000000e+00 2518.0
7 TraesCS3D01G157300 chr3B 93.873 408 23 1 2300 2705 179370974 179371381 6.690000e-172 614.0
8 TraesCS3D01G157300 chr3B 91.632 239 20 0 3190 3428 179371871 179372109 7.550000e-87 331.0
9 TraesCS3D01G157300 chr7D 88.889 54 6 0 260 313 427631583 427631636 2.350000e-07 67.6
10 TraesCS3D01G157300 chr7B 90.000 50 5 0 264 313 445423165 445423214 8.450000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G157300 chr3D 125481328 125484973 3645 False 2964.500000 5084 100.000000 1 3646 2 chr3D.!!$F1 3645
1 TraesCS3D01G157300 chr3A 134236684 134240426 3742 False 998.250000 2534 91.476000 1 3621 4 chr3A.!!$F1 3620
2 TraesCS3D01G157300 chr3B 179368578 179372109 3531 False 1154.333333 2518 92.625333 1 3428 3 chr3B.!!$F1 3427

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
41 44 1.291132 GCTTCAATAGCCAGTCGGTC 58.709 55.0 0.0 0.0 44.48 4.79 F
1011 1049 0.034616 GGATCGGCATGGAGAAGGAG 59.965 60.0 0.0 0.0 0.00 3.69 F
1814 1880 0.035056 ATGCCCTTTTCCTCCACGAG 60.035 55.0 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1995 0.106894 GGGCACTTATCTAGGCGCTT 59.893 55.0 7.64 0.52 36.42 4.68 R
2245 2477 0.105964 TGCAACAGTACGGAGCAACT 59.894 50.0 13.16 0.00 31.42 3.16 R
3317 3567 0.038599 AGATGGCACCTGTTCATGCA 59.961 50.0 0.00 0.00 43.93 3.96 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
41 44 1.291132 GCTTCAATAGCCAGTCGGTC 58.709 55.000 0.00 0.00 44.48 4.79
92 95 3.584848 AGCCTCTCCACAGTTTACAGAAT 59.415 43.478 0.00 0.00 0.00 2.40
117 120 3.151554 CCTACCAACCAAACTAACCACC 58.848 50.000 0.00 0.00 0.00 4.61
195 199 1.944024 AGATCAAACCACGCGAACAAA 59.056 42.857 15.93 0.00 0.00 2.83
678 706 3.608073 GCCGTCTGCAACATTCATTAAAC 59.392 43.478 0.00 0.00 40.77 2.01
800 828 4.085009 AGAGCTTTCCAAATCCTTCCTTG 58.915 43.478 0.00 0.00 0.00 3.61
979 1013 4.498520 ACATCTCTCCCGCGTGCG 62.499 66.667 4.92 7.38 39.44 5.34
1011 1049 0.034616 GGATCGGCATGGAGAAGGAG 59.965 60.000 0.00 0.00 0.00 3.69
1175 1216 2.973316 GCGCCTTACGTTTGGTGGG 61.973 63.158 17.67 6.25 46.11 4.61
1201 1242 2.554142 TGCTCATTCTTGCCGATACAG 58.446 47.619 0.00 0.00 0.00 2.74
1210 1251 4.960938 TCTTGCCGATACAGCTATGATTT 58.039 39.130 0.00 0.00 0.00 2.17
1211 1252 4.991056 TCTTGCCGATACAGCTATGATTTC 59.009 41.667 0.00 0.00 0.00 2.17
1343 1403 1.345422 TGGGACTCCATAGCTCCCAAT 60.345 52.381 5.20 0.00 43.89 3.16
1566 1626 1.804748 CGGAGTTACAAGGCTGAAACC 59.195 52.381 0.00 0.00 0.00 3.27
1567 1627 2.550208 CGGAGTTACAAGGCTGAAACCT 60.550 50.000 0.00 0.00 43.91 3.50
1590 1652 7.012799 ACCTTATTCGTACCACTTAGCTAGTAC 59.987 40.741 9.78 9.78 34.56 2.73
1593 1655 9.613428 TTATTCGTACCACTTAGCTAGTACTAA 57.387 33.333 15.21 12.15 34.56 2.24
1595 1657 6.644347 TCGTACCACTTAGCTAGTACTAACT 58.356 40.000 10.54 10.54 39.91 2.24
1596 1658 7.106239 TCGTACCACTTAGCTAGTACTAACTT 58.894 38.462 10.95 0.00 37.15 2.66
1626 1692 5.222547 ACCTGAGGTAATTCCCCTTTGAAAT 60.223 40.000 0.07 0.00 32.11 2.17
1695 1761 5.362717 TGAGGATTGTGTGATATTCGGTACT 59.637 40.000 0.00 0.00 0.00 2.73
1705 1771 7.378995 GTGTGATATTCGGTACTGCTAGTTAAG 59.621 40.741 0.00 0.00 0.00 1.85
1709 1775 4.959596 TCGGTACTGCTAGTTAAGTGAG 57.040 45.455 0.00 0.00 0.00 3.51
1718 1784 3.802685 GCTAGTTAAGTGAGGCCGTATTG 59.197 47.826 0.00 0.00 0.00 1.90
1723 1789 2.981859 AGTGAGGCCGTATTGTTAGG 57.018 50.000 0.00 0.00 0.00 2.69
1727 1793 1.761198 GAGGCCGTATTGTTAGGGAGT 59.239 52.381 0.00 0.00 35.74 3.85
1738 1804 7.914346 CGTATTGTTAGGGAGTAACTTGTCTAG 59.086 40.741 0.00 0.00 41.60 2.43
1742 1808 8.064336 TGTTAGGGAGTAACTTGTCTAGAATC 57.936 38.462 0.00 0.00 41.60 2.52
1745 1811 5.659079 AGGGAGTAACTTGTCTAGAATCTGG 59.341 44.000 0.00 0.00 0.00 3.86
1746 1812 5.353111 GGAGTAACTTGTCTAGAATCTGGC 58.647 45.833 0.00 0.00 0.00 4.85
1748 1814 6.215495 AGTAACTTGTCTAGAATCTGGCTC 57.785 41.667 0.00 0.00 0.00 4.70
1750 1816 5.753721 AACTTGTCTAGAATCTGGCTCTT 57.246 39.130 0.00 0.00 0.00 2.85
1764 1830 2.104792 TGGCTCTTAGGTGGATATGTGC 59.895 50.000 0.00 0.00 0.00 4.57
1772 1838 8.354711 TCTTAGGTGGATATGTGCTATCTAAG 57.645 38.462 0.00 0.00 37.08 2.18
1773 1839 7.397476 TCTTAGGTGGATATGTGCTATCTAAGG 59.603 40.741 0.00 0.00 37.08 2.69
1774 1840 4.223923 AGGTGGATATGTGCTATCTAAGGC 59.776 45.833 0.00 0.00 37.08 4.35
1775 1841 4.508662 GTGGATATGTGCTATCTAAGGCC 58.491 47.826 0.00 0.00 37.08 5.19
1776 1842 4.020218 GTGGATATGTGCTATCTAAGGCCA 60.020 45.833 5.01 0.00 37.08 5.36
1777 1843 4.784838 TGGATATGTGCTATCTAAGGCCAT 59.215 41.667 5.01 0.00 37.08 4.40
1778 1844 5.104776 TGGATATGTGCTATCTAAGGCCATC 60.105 44.000 5.01 0.00 37.08 3.51
1779 1845 5.130145 GGATATGTGCTATCTAAGGCCATCT 59.870 44.000 5.01 0.00 37.08 2.90
1780 1846 4.550076 ATGTGCTATCTAAGGCCATCTC 57.450 45.455 5.01 0.00 0.00 2.75
1781 1847 2.634940 TGTGCTATCTAAGGCCATCTCC 59.365 50.000 5.01 0.00 0.00 3.71
1782 1848 2.634940 GTGCTATCTAAGGCCATCTCCA 59.365 50.000 5.01 0.00 0.00 3.86
1783 1849 3.071602 GTGCTATCTAAGGCCATCTCCAA 59.928 47.826 5.01 0.00 0.00 3.53
1784 1850 3.071602 TGCTATCTAAGGCCATCTCCAAC 59.928 47.826 5.01 0.00 0.00 3.77
1785 1851 2.918712 ATCTAAGGCCATCTCCAACG 57.081 50.000 5.01 0.00 0.00 4.10
1786 1852 0.178068 TCTAAGGCCATCTCCAACGC 59.822 55.000 5.01 0.00 0.00 4.84
1787 1853 0.815615 CTAAGGCCATCTCCAACGCC 60.816 60.000 5.01 0.00 41.96 5.68
1788 1854 1.558167 TAAGGCCATCTCCAACGCCA 61.558 55.000 5.01 0.00 44.18 5.69
1789 1855 2.825836 GGCCATCTCCAACGCCAG 60.826 66.667 0.00 0.00 41.25 4.85
1790 1856 2.825836 GCCATCTCCAACGCCAGG 60.826 66.667 0.00 0.00 0.00 4.45
1807 1873 4.242602 GCGCTATGCCCTTTTCCT 57.757 55.556 0.00 0.00 37.76 3.36
1809 1875 1.448119 GCGCTATGCCCTTTTCCTCC 61.448 60.000 0.00 0.00 37.76 4.30
1812 1878 1.668419 CTATGCCCTTTTCCTCCACG 58.332 55.000 0.00 0.00 0.00 4.94
1814 1880 0.035056 ATGCCCTTTTCCTCCACGAG 60.035 55.000 0.00 0.00 0.00 4.18
1815 1881 2.041115 GCCCTTTTCCTCCACGAGC 61.041 63.158 0.00 0.00 0.00 5.03
1816 1882 1.679898 CCCTTTTCCTCCACGAGCT 59.320 57.895 0.00 0.00 0.00 4.09
1817 1883 0.674895 CCCTTTTCCTCCACGAGCTG 60.675 60.000 0.00 0.00 0.00 4.24
1819 1885 1.674221 CCTTTTCCTCCACGAGCTGAG 60.674 57.143 0.00 0.00 0.00 3.35
1820 1886 1.273606 CTTTTCCTCCACGAGCTGAGA 59.726 52.381 0.00 0.00 0.00 3.27
1821 1887 0.603569 TTTCCTCCACGAGCTGAGAC 59.396 55.000 0.00 0.00 0.00 3.36
1822 1888 1.587043 TTCCTCCACGAGCTGAGACG 61.587 60.000 0.00 0.00 0.00 4.18
1824 1890 1.587043 CCTCCACGAGCTGAGACGAA 61.587 60.000 0.00 0.00 0.00 3.85
1825 1891 0.179176 CTCCACGAGCTGAGACGAAG 60.179 60.000 0.00 0.00 0.00 3.79
1827 1893 2.148982 CACGAGCTGAGACGAAGCG 61.149 63.158 0.00 0.00 45.59 4.68
1828 1894 3.243892 CGAGCTGAGACGAAGCGC 61.244 66.667 0.00 0.00 45.59 5.92
1830 1896 2.126149 AGCTGAGACGAAGCGCTG 60.126 61.111 12.58 0.57 45.59 5.18
1831 1897 2.431601 GCTGAGACGAAGCGCTGT 60.432 61.111 12.58 5.04 0.00 4.40
1832 1898 2.440569 GCTGAGACGAAGCGCTGTC 61.441 63.158 12.58 15.81 35.33 3.51
1838 1904 0.737715 GACGAAGCGCTGTCTCCAAT 60.738 55.000 12.58 0.00 32.37 3.16
1840 1906 1.424493 CGAAGCGCTGTCTCCAATCC 61.424 60.000 12.58 0.00 0.00 3.01
1842 1908 0.036732 AAGCGCTGTCTCCAATCCAA 59.963 50.000 12.58 0.00 0.00 3.53
1843 1909 0.392193 AGCGCTGTCTCCAATCCAAG 60.392 55.000 10.39 0.00 0.00 3.61
1845 1911 1.405526 GCGCTGTCTCCAATCCAAGTA 60.406 52.381 0.00 0.00 0.00 2.24
1846 1912 2.743183 GCGCTGTCTCCAATCCAAGTAT 60.743 50.000 0.00 0.00 0.00 2.12
1847 1913 3.535561 CGCTGTCTCCAATCCAAGTATT 58.464 45.455 0.00 0.00 0.00 1.89
1848 1914 3.941483 CGCTGTCTCCAATCCAAGTATTT 59.059 43.478 0.00 0.00 0.00 1.40
1849 1915 5.116180 CGCTGTCTCCAATCCAAGTATTTA 58.884 41.667 0.00 0.00 0.00 1.40
1850 1916 5.235186 CGCTGTCTCCAATCCAAGTATTTAG 59.765 44.000 0.00 0.00 0.00 1.85
1851 1917 5.008118 GCTGTCTCCAATCCAAGTATTTAGC 59.992 44.000 0.00 0.00 0.00 3.09
1853 1919 5.116882 GTCTCCAATCCAAGTATTTAGCGT 58.883 41.667 0.00 0.00 0.00 5.07
1854 1920 5.234543 GTCTCCAATCCAAGTATTTAGCGTC 59.765 44.000 0.00 0.00 0.00 5.19
1855 1921 4.116961 TCCAATCCAAGTATTTAGCGTCG 58.883 43.478 0.00 0.00 0.00 5.12
1857 1923 3.814005 ATCCAAGTATTTAGCGTCGGT 57.186 42.857 1.19 1.19 0.00 4.69
1859 1925 1.931172 CCAAGTATTTAGCGTCGGTGG 59.069 52.381 7.30 0.00 0.00 4.61
1861 1927 2.997986 CAAGTATTTAGCGTCGGTGGTT 59.002 45.455 7.30 0.00 0.00 3.67
1863 1929 4.037858 AGTATTTAGCGTCGGTGGTTAG 57.962 45.455 7.30 0.00 0.00 2.34
1864 1930 1.648504 ATTTAGCGTCGGTGGTTAGC 58.351 50.000 7.30 0.00 0.00 3.09
1866 1932 3.688475 TAGCGTCGGTGGTTAGCGC 62.688 63.158 7.30 0.00 46.67 5.92
1868 1934 4.430765 CGTCGGTGGTTAGCGCCT 62.431 66.667 12.30 0.00 46.67 5.52
1869 1935 2.887360 GTCGGTGGTTAGCGCCTA 59.113 61.111 12.30 0.00 46.67 3.93
1870 1936 1.226888 GTCGGTGGTTAGCGCCTAG 60.227 63.158 12.30 0.00 46.67 3.02
1871 1937 3.072486 TCGGTGGTTAGCGCCTAGC 62.072 63.158 12.30 2.08 46.67 3.42
1886 1952 1.009829 CTAGCGTTGGAACAGATGGC 58.990 55.000 0.00 0.00 42.39 4.40
1887 1953 0.323302 TAGCGTTGGAACAGATGGCA 59.677 50.000 0.00 0.00 42.39 4.92
1888 1954 1.210155 GCGTTGGAACAGATGGCAC 59.790 57.895 0.00 0.00 42.39 5.01
1890 1956 1.238439 CGTTGGAACAGATGGCACTT 58.762 50.000 0.00 0.00 42.39 3.16
1892 1958 2.416547 CGTTGGAACAGATGGCACTTAG 59.583 50.000 0.00 0.00 42.39 2.18
1893 1959 3.412386 GTTGGAACAGATGGCACTTAGT 58.588 45.455 0.00 0.00 42.39 2.24
1894 1960 4.575885 GTTGGAACAGATGGCACTTAGTA 58.424 43.478 0.00 0.00 42.39 1.82
1895 1961 5.186198 GTTGGAACAGATGGCACTTAGTAT 58.814 41.667 0.00 0.00 42.39 2.12
1896 1962 5.435686 TGGAACAGATGGCACTTAGTATT 57.564 39.130 0.00 0.00 0.00 1.89
1897 1963 5.815581 TGGAACAGATGGCACTTAGTATTT 58.184 37.500 0.00 0.00 0.00 1.40
1899 1965 6.719370 TGGAACAGATGGCACTTAGTATTTTT 59.281 34.615 0.00 0.00 0.00 1.94
1943 2009 6.903883 TTTCTGTTTAAGCGCCTAGATAAG 57.096 37.500 2.29 0.00 0.00 1.73
1944 2010 5.593679 TCTGTTTAAGCGCCTAGATAAGT 57.406 39.130 2.29 0.00 0.00 2.24
1945 2011 5.348986 TCTGTTTAAGCGCCTAGATAAGTG 58.651 41.667 2.29 0.00 0.00 3.16
1946 2012 3.869246 TGTTTAAGCGCCTAGATAAGTGC 59.131 43.478 2.29 0.00 0.00 4.40
1949 2015 1.301795 GCGCCTAGATAAGTGCCCC 60.302 63.158 0.00 0.00 0.00 5.80
1951 2017 1.407656 CGCCTAGATAAGTGCCCCCA 61.408 60.000 0.00 0.00 0.00 4.96
1954 2020 2.815589 GCCTAGATAAGTGCCCCCATTG 60.816 54.545 0.00 0.00 0.00 2.82
1955 2021 2.443255 CCTAGATAAGTGCCCCCATTGT 59.557 50.000 0.00 0.00 0.00 2.71
1956 2022 3.650942 CCTAGATAAGTGCCCCCATTGTA 59.349 47.826 0.00 0.00 0.00 2.41
1957 2023 4.289672 CCTAGATAAGTGCCCCCATTGTAT 59.710 45.833 0.00 0.00 0.00 2.29
1958 2024 4.814224 AGATAAGTGCCCCCATTGTATT 57.186 40.909 0.00 0.00 0.00 1.89
1959 2025 5.142806 AGATAAGTGCCCCCATTGTATTT 57.857 39.130 0.00 0.00 0.00 1.40
1983 2211 5.440234 TCAGAAGTCGATCAATAGTAGCC 57.560 43.478 0.00 0.00 0.00 3.93
1988 2216 3.884091 AGTCGATCAATAGTAGCCGAACT 59.116 43.478 0.00 0.00 0.00 3.01
1989 2217 4.023878 AGTCGATCAATAGTAGCCGAACTC 60.024 45.833 0.00 0.00 0.00 3.01
1990 2218 4.023878 GTCGATCAATAGTAGCCGAACTCT 60.024 45.833 0.00 0.00 0.00 3.24
1991 2219 5.178996 GTCGATCAATAGTAGCCGAACTCTA 59.821 44.000 0.00 0.00 0.00 2.43
2014 2242 0.400213 ACCGAATCCTCTGCAAACCA 59.600 50.000 0.00 0.00 0.00 3.67
2016 2244 2.238646 ACCGAATCCTCTGCAAACCATA 59.761 45.455 0.00 0.00 0.00 2.74
2018 2246 3.313526 CCGAATCCTCTGCAAACCATAAG 59.686 47.826 0.00 0.00 0.00 1.73
2034 2263 4.089361 CCATAAGCCCTCCTGTTTTTCTT 58.911 43.478 0.00 0.00 0.00 2.52
2085 2314 1.342174 GTCCCACAGTTAGTCGAACCA 59.658 52.381 0.00 0.00 39.02 3.67
2092 2321 4.082408 CACAGTTAGTCGAACCATAGGTCA 60.082 45.833 0.00 0.00 39.02 4.02
2104 2333 5.836024 ACCATAGGTCACCACTTTCTTTA 57.164 39.130 0.00 0.00 0.00 1.85
2105 2334 5.557866 ACCATAGGTCACCACTTTCTTTAC 58.442 41.667 0.00 0.00 0.00 2.01
2106 2335 5.072600 ACCATAGGTCACCACTTTCTTTACA 59.927 40.000 0.00 0.00 0.00 2.41
2111 2340 6.863275 AGGTCACCACTTTCTTTACAAAAAG 58.137 36.000 0.00 0.00 42.99 2.27
2133 2362 8.488651 AAAGAATTAGTTAGGTACCATTCACG 57.511 34.615 15.94 0.00 32.78 4.35
2134 2363 6.579865 AGAATTAGTTAGGTACCATTCACGG 58.420 40.000 15.94 0.00 32.78 4.94
2136 2365 1.134907 AGTTAGGTACCATTCACGGCG 60.135 52.381 15.94 4.80 0.00 6.46
2138 2367 1.184431 TAGGTACCATTCACGGCGAA 58.816 50.000 16.62 0.00 38.22 4.70
2139 2368 0.539986 AGGTACCATTCACGGCGAAT 59.460 50.000 16.62 0.00 45.60 3.34
2140 2369 1.065709 AGGTACCATTCACGGCGAATT 60.066 47.619 16.62 0.00 41.83 2.17
2141 2370 1.741145 GGTACCATTCACGGCGAATTT 59.259 47.619 16.62 0.00 41.83 1.82
2142 2371 2.162809 GGTACCATTCACGGCGAATTTT 59.837 45.455 16.62 0.00 41.83 1.82
2143 2372 2.346099 ACCATTCACGGCGAATTTTG 57.654 45.000 16.62 0.00 41.83 2.44
2147 2376 3.500982 CATTCACGGCGAATTTTGTCAT 58.499 40.909 16.62 0.00 41.83 3.06
2171 2400 4.574674 TCAGTTTCTCAATGTATGGGCT 57.425 40.909 0.00 0.00 0.00 5.19
2172 2401 4.922206 TCAGTTTCTCAATGTATGGGCTT 58.078 39.130 0.00 0.00 0.00 4.35
2179 2411 6.147864 TCTCAATGTATGGGCTTATTTTGC 57.852 37.500 0.00 0.00 0.00 3.68
2204 2436 7.275560 GCTATGAAAATTTGTCACATTACCCAC 59.724 37.037 0.00 0.00 0.00 4.61
2208 2440 2.577606 TTGTCACATTACCCACCTGG 57.422 50.000 0.00 0.00 41.37 4.45
2212 2444 2.026636 GTCACATTACCCACCTGGCTAA 60.027 50.000 0.00 0.00 37.83 3.09
2233 2465 7.417342 GGCTAAATTGTATGGAATGCACCTTTA 60.417 37.037 0.00 0.00 39.15 1.85
2254 2486 8.979574 CCTTTAGATTTTATACTAGTTGCTCCG 58.020 37.037 0.00 0.00 0.00 4.63
2257 2489 9.956720 TTAGATTTTATACTAGTTGCTCCGTAC 57.043 33.333 0.00 0.00 0.00 3.67
2270 2502 0.032952 TCCGTACTGTTGCAGTGTCC 59.967 55.000 11.57 0.08 45.01 4.02
2276 2508 2.722094 ACTGTTGCAGTGTCCTTTTCA 58.278 42.857 0.53 0.00 43.63 2.69
2278 2510 3.129287 ACTGTTGCAGTGTCCTTTTCAAG 59.871 43.478 0.53 0.00 43.63 3.02
2281 2513 4.702612 TGTTGCAGTGTCCTTTTCAAGTTA 59.297 37.500 0.00 0.00 0.00 2.24
2282 2514 5.184096 TGTTGCAGTGTCCTTTTCAAGTTAA 59.816 36.000 0.00 0.00 0.00 2.01
2283 2515 5.906113 TGCAGTGTCCTTTTCAAGTTAAA 57.094 34.783 0.00 0.00 0.00 1.52
2284 2516 6.463995 TGCAGTGTCCTTTTCAAGTTAAAT 57.536 33.333 0.00 0.00 0.00 1.40
2285 2517 6.872920 TGCAGTGTCCTTTTCAAGTTAAATT 58.127 32.000 0.00 0.00 0.00 1.82
2286 2518 7.327214 TGCAGTGTCCTTTTCAAGTTAAATTT 58.673 30.769 0.00 0.00 0.00 1.82
2287 2519 7.491048 TGCAGTGTCCTTTTCAAGTTAAATTTC 59.509 33.333 0.00 0.00 0.00 2.17
2288 2520 7.706607 GCAGTGTCCTTTTCAAGTTAAATTTCT 59.293 33.333 0.00 0.00 0.00 2.52
2289 2521 9.023967 CAGTGTCCTTTTCAAGTTAAATTTCTG 57.976 33.333 0.00 0.00 0.00 3.02
2290 2522 8.197439 AGTGTCCTTTTCAAGTTAAATTTCTGG 58.803 33.333 0.00 0.00 0.00 3.86
2291 2523 7.979537 GTGTCCTTTTCAAGTTAAATTTCTGGT 59.020 33.333 0.00 0.00 0.00 4.00
2292 2524 8.536175 TGTCCTTTTCAAGTTAAATTTCTGGTT 58.464 29.630 0.00 0.00 0.00 3.67
2323 2555 7.634671 TGTGATCATGAGAAGTTATTGCATT 57.365 32.000 0.00 0.00 0.00 3.56
2343 2577 4.471904 TTACAATGTAGCTGGACTCTGG 57.528 45.455 0.00 0.00 0.00 3.86
2345 2579 2.906389 ACAATGTAGCTGGACTCTGGAA 59.094 45.455 0.00 0.00 0.00 3.53
2366 2600 5.465390 GGAAAAATTGGGTGCTAACAGAAAC 59.535 40.000 0.00 0.00 0.00 2.78
2370 2604 4.846779 TTGGGTGCTAACAGAAACAATC 57.153 40.909 0.00 0.00 0.00 2.67
2410 2644 5.978919 TGTTTGTTTCATAAAGAAGCTGCAG 59.021 36.000 10.11 10.11 38.19 4.41
2435 2669 6.749118 GCTGATCTTTGTGTGGATGTATTTTC 59.251 38.462 0.00 0.00 0.00 2.29
2443 2677 5.106869 TGTGTGGATGTATTTTCGCTGTTAC 60.107 40.000 0.00 0.00 0.00 2.50
2519 2753 7.803659 TCATCGCGAAGTATATTTCTGTCTTAG 59.196 37.037 15.24 0.00 0.00 2.18
2720 2954 3.659786 TGGTTTAGTGTTGGATCTGTCG 58.340 45.455 0.00 0.00 0.00 4.35
2730 2964 4.748102 TGTTGGATCTGTCGTTTGTAGTTC 59.252 41.667 0.00 0.00 0.00 3.01
2731 2965 4.594123 TGGATCTGTCGTTTGTAGTTCA 57.406 40.909 0.00 0.00 0.00 3.18
2732 2966 5.147330 TGGATCTGTCGTTTGTAGTTCAT 57.853 39.130 0.00 0.00 0.00 2.57
2733 2967 5.547465 TGGATCTGTCGTTTGTAGTTCATT 58.453 37.500 0.00 0.00 0.00 2.57
2734 2968 5.995282 TGGATCTGTCGTTTGTAGTTCATTT 59.005 36.000 0.00 0.00 0.00 2.32
2735 2969 6.147164 TGGATCTGTCGTTTGTAGTTCATTTC 59.853 38.462 0.00 0.00 0.00 2.17
2736 2970 6.369065 GGATCTGTCGTTTGTAGTTCATTTCT 59.631 38.462 0.00 0.00 0.00 2.52
2737 2971 6.525121 TCTGTCGTTTGTAGTTCATTTCTG 57.475 37.500 0.00 0.00 0.00 3.02
2738 2972 6.277605 TCTGTCGTTTGTAGTTCATTTCTGA 58.722 36.000 0.00 0.00 0.00 3.27
2739 2973 6.929049 TCTGTCGTTTGTAGTTCATTTCTGAT 59.071 34.615 0.00 0.00 0.00 2.90
2740 2974 7.441157 TCTGTCGTTTGTAGTTCATTTCTGATT 59.559 33.333 0.00 0.00 0.00 2.57
2741 2975 7.925993 TGTCGTTTGTAGTTCATTTCTGATTT 58.074 30.769 0.00 0.00 0.00 2.17
2742 2976 9.047371 TGTCGTTTGTAGTTCATTTCTGATTTA 57.953 29.630 0.00 0.00 0.00 1.40
2743 2977 9.530129 GTCGTTTGTAGTTCATTTCTGATTTAG 57.470 33.333 0.00 0.00 0.00 1.85
2744 2978 9.483916 TCGTTTGTAGTTCATTTCTGATTTAGA 57.516 29.630 0.00 0.00 0.00 2.10
2748 2982 8.964476 TGTAGTTCATTTCTGATTTAGATCCC 57.036 34.615 0.00 0.00 34.80 3.85
2749 2983 7.993183 TGTAGTTCATTTCTGATTTAGATCCCC 59.007 37.037 0.00 0.00 34.80 4.81
2750 2984 6.368805 AGTTCATTTCTGATTTAGATCCCCC 58.631 40.000 0.00 0.00 34.80 5.40
3284 3534 1.234615 TTTGCTGCTGCCGTTCCTAC 61.235 55.000 13.47 0.00 38.71 3.18
3299 3549 5.424757 CGTTCCTACCCAGTTTCATGATTA 58.575 41.667 0.00 0.00 0.00 1.75
3316 3566 8.078060 TCATGATTACAGGTGTCTGAAATAGA 57.922 34.615 0.00 0.00 43.49 1.98
3317 3567 8.708378 TCATGATTACAGGTGTCTGAAATAGAT 58.292 33.333 0.00 0.00 43.49 1.98
3328 3578 5.587443 TGTCTGAAATAGATGCATGAACAGG 59.413 40.000 2.46 0.00 37.83 4.00
3350 3600 4.943705 GGTGCCATCTCTTCACAGATTTAA 59.056 41.667 0.00 0.00 30.07 1.52
3382 3632 1.358877 TCTGTGCCAAATCGTCGATG 58.641 50.000 8.83 0.00 0.00 3.84
3432 3682 7.615757 AGCTAATTTTTGGCCTGTTTAGTATCT 59.384 33.333 3.32 0.00 37.96 1.98
3470 3720 4.563337 ATTTGATGCGTTCATGGAGATG 57.437 40.909 0.00 0.00 33.34 2.90
3483 3733 1.281899 GGAGATGTCTTGTACTGCGC 58.718 55.000 0.00 0.00 0.00 6.09
3487 3737 0.175760 ATGTCTTGTACTGCGCCGAT 59.824 50.000 4.18 0.00 0.00 4.18
3502 3752 1.796617 GCCGATGCTGATGTTTCTTGC 60.797 52.381 0.00 0.00 33.53 4.01
3521 3771 3.740115 TGCCTTGTCTTACCTTTGTCTC 58.260 45.455 0.00 0.00 0.00 3.36
3593 3843 0.846015 CCCTGGGCTTATGTGATCCA 59.154 55.000 0.00 0.00 0.00 3.41
3610 3860 2.747177 TCCACACAGGTAGGAGTATGG 58.253 52.381 0.00 0.00 39.02 2.74
3617 3867 3.700038 ACAGGTAGGAGTATGGAAGAACG 59.300 47.826 0.00 0.00 0.00 3.95
3621 3871 4.159135 GGTAGGAGTATGGAAGAACGTTGA 59.841 45.833 5.00 0.00 0.00 3.18
3622 3872 5.163437 GGTAGGAGTATGGAAGAACGTTGAT 60.163 44.000 5.00 0.00 0.00 2.57
3623 3873 4.759782 AGGAGTATGGAAGAACGTTGATG 58.240 43.478 5.00 0.00 0.00 3.07
3624 3874 4.223032 AGGAGTATGGAAGAACGTTGATGT 59.777 41.667 5.00 0.00 0.00 3.06
3625 3875 4.935808 GGAGTATGGAAGAACGTTGATGTT 59.064 41.667 5.00 0.00 34.02 2.71
3626 3876 6.070995 AGGAGTATGGAAGAACGTTGATGTTA 60.071 38.462 5.00 0.00 30.75 2.41
3627 3877 6.035758 GGAGTATGGAAGAACGTTGATGTTAC 59.964 42.308 5.00 0.80 30.75 2.50
3628 3878 6.698380 AGTATGGAAGAACGTTGATGTTACT 58.302 36.000 5.00 3.21 30.75 2.24
3629 3879 7.833786 AGTATGGAAGAACGTTGATGTTACTA 58.166 34.615 5.00 0.00 30.75 1.82
3630 3880 6.963049 ATGGAAGAACGTTGATGTTACTAC 57.037 37.500 5.00 0.00 30.75 2.73
3631 3881 5.845103 TGGAAGAACGTTGATGTTACTACA 58.155 37.500 5.00 0.00 38.95 2.74
3632 3882 5.693104 TGGAAGAACGTTGATGTTACTACAC 59.307 40.000 5.00 0.00 37.03 2.90
3633 3883 5.119743 GGAAGAACGTTGATGTTACTACACC 59.880 44.000 5.00 0.00 37.03 4.16
3634 3884 5.204409 AGAACGTTGATGTTACTACACCA 57.796 39.130 5.00 0.00 37.03 4.17
3635 3885 5.603596 AGAACGTTGATGTTACTACACCAA 58.396 37.500 5.00 0.00 35.37 3.67
3636 3886 6.050432 AGAACGTTGATGTTACTACACCAAA 58.950 36.000 5.00 0.00 39.47 3.28
3637 3887 6.708949 AGAACGTTGATGTTACTACACCAAAT 59.291 34.615 5.00 0.00 39.47 2.32
3638 3888 6.236017 ACGTTGATGTTACTACACCAAATG 57.764 37.500 0.00 0.00 39.47 2.32
3639 3889 5.992829 ACGTTGATGTTACTACACCAAATGA 59.007 36.000 0.00 0.00 39.47 2.57
3640 3890 6.653320 ACGTTGATGTTACTACACCAAATGAT 59.347 34.615 0.00 0.00 39.47 2.45
3641 3891 6.960992 CGTTGATGTTACTACACCAAATGATG 59.039 38.462 0.00 0.00 39.47 3.07
3642 3892 7.360861 CGTTGATGTTACTACACCAAATGATGT 60.361 37.037 0.00 0.00 39.47 3.06
3643 3893 7.994425 TGATGTTACTACACCAAATGATGTT 57.006 32.000 0.00 0.00 37.03 2.71
3644 3894 8.402798 TGATGTTACTACACCAAATGATGTTT 57.597 30.769 0.00 0.00 37.03 2.83
3645 3895 8.296000 TGATGTTACTACACCAAATGATGTTTG 58.704 33.333 0.00 0.00 37.03 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 6.072397 TGTGGGTAGAAATGTTGGTAAATTCG 60.072 38.462 0.00 0.00 0.00 3.34
92 95 4.351407 TGGTTAGTTTGGTTGGTAGGATGA 59.649 41.667 0.00 0.00 0.00 2.92
117 120 1.137513 GGTTTGAACCGAGTGTCGAG 58.862 55.000 0.00 0.00 43.74 4.04
195 199 1.197430 CCCTGCTCAGACCCTCACTT 61.197 60.000 0.00 0.00 0.00 3.16
678 706 0.463833 AGAATTTAAGAGGGCCGCCG 60.464 55.000 2.73 0.00 0.00 6.46
830 858 1.197036 GGGCGAGAAGAAAGAAAACCG 59.803 52.381 0.00 0.00 0.00 4.44
935 966 1.443828 GGGAGCTGCTACTACCTGC 59.556 63.158 12.40 0.00 37.72 4.85
979 1013 1.102978 CCGATCCAATCCAACCAACC 58.897 55.000 0.00 0.00 0.00 3.77
1069 1107 1.680314 GGTCGTAGGGGTTCTCGGT 60.680 63.158 0.00 0.00 0.00 4.69
1104 1142 4.838486 CGGAGCACGTCGAGGAGC 62.838 72.222 17.99 17.99 37.93 4.70
1115 1153 4.147449 CGATGCACTCCCGGAGCA 62.147 66.667 14.86 9.09 44.79 4.26
1164 1205 2.440613 AAACGGCCCACCAAACGT 60.441 55.556 0.00 0.00 41.88 3.99
1175 1216 0.733909 GGCAAGAATGAGCAAACGGC 60.734 55.000 0.00 0.00 45.30 5.68
1201 1242 6.753180 TCAGTACAGGATCAGAAATCATAGC 58.247 40.000 0.00 0.00 0.00 2.97
1210 1251 4.323569 AGACCTTCAGTACAGGATCAGA 57.676 45.455 4.80 0.00 35.14 3.27
1211 1252 5.419155 TGTAAGACCTTCAGTACAGGATCAG 59.581 44.000 4.80 0.00 35.14 2.90
1255 1312 4.536090 TCAGTGGTGGGTGATATCTTTTCT 59.464 41.667 3.98 0.00 0.00 2.52
1257 1314 4.289672 ACTCAGTGGTGGGTGATATCTTTT 59.710 41.667 3.98 0.00 35.37 2.27
1258 1315 3.846588 ACTCAGTGGTGGGTGATATCTTT 59.153 43.478 3.98 0.00 35.37 2.52
1566 1626 8.152309 AGTACTAGCTAAGTGGTACGAATAAG 57.848 38.462 12.70 0.00 39.39 1.73
1567 1627 9.613428 TTAGTACTAGCTAAGTGGTACGAATAA 57.387 33.333 12.70 6.37 39.39 1.40
1568 1628 9.046296 GTTAGTACTAGCTAAGTGGTACGAATA 57.954 37.037 14.92 3.62 39.39 1.75
1569 1629 7.772757 AGTTAGTACTAGCTAAGTGGTACGAAT 59.227 37.037 16.77 6.99 39.39 3.34
1571 1631 6.644347 AGTTAGTACTAGCTAAGTGGTACGA 58.356 40.000 16.77 7.29 39.39 3.43
1572 1632 6.917217 AGTTAGTACTAGCTAAGTGGTACG 57.083 41.667 16.77 0.00 39.39 3.67
1605 1671 5.891551 GCTATTTCAAAGGGGAATTACCTCA 59.108 40.000 6.68 0.00 42.78 3.86
1695 1761 1.263356 ACGGCCTCACTTAACTAGCA 58.737 50.000 0.00 0.00 0.00 3.49
1705 1771 1.483415 TCCCTAACAATACGGCCTCAC 59.517 52.381 0.00 0.00 0.00 3.51
1709 1775 3.133542 AGTTACTCCCTAACAATACGGCC 59.866 47.826 0.00 0.00 37.76 6.13
1718 1784 8.192110 CAGATTCTAGACAAGTTACTCCCTAAC 58.808 40.741 0.00 0.00 35.77 2.34
1723 1789 5.128008 AGCCAGATTCTAGACAAGTTACTCC 59.872 44.000 0.00 0.00 0.00 3.85
1727 1793 6.859112 AAGAGCCAGATTCTAGACAAGTTA 57.141 37.500 0.00 0.00 0.00 2.24
1738 1804 5.012561 ACATATCCACCTAAGAGCCAGATTC 59.987 44.000 0.00 0.00 0.00 2.52
1742 1808 3.805108 GCACATATCCACCTAAGAGCCAG 60.805 52.174 0.00 0.00 0.00 4.85
1745 1811 3.760580 AGCACATATCCACCTAAGAGC 57.239 47.619 0.00 0.00 0.00 4.09
1746 1812 6.849085 AGATAGCACATATCCACCTAAGAG 57.151 41.667 0.00 0.00 41.20 2.85
1748 1814 7.551585 CCTTAGATAGCACATATCCACCTAAG 58.448 42.308 0.00 0.00 41.20 2.18
1750 1816 5.422331 GCCTTAGATAGCACATATCCACCTA 59.578 44.000 0.00 0.00 41.20 3.08
1764 1830 3.862642 GCGTTGGAGATGGCCTTAGATAG 60.863 52.174 3.32 0.00 0.00 2.08
1772 1838 2.825836 CTGGCGTTGGAGATGGCC 60.826 66.667 0.00 0.00 45.76 5.36
1773 1839 2.825836 CCTGGCGTTGGAGATGGC 60.826 66.667 0.00 0.00 40.12 4.40
1774 1840 2.825836 GCCTGGCGTTGGAGATGG 60.826 66.667 1.35 0.00 0.00 3.51
1790 1856 1.448119 GGAGGAAAAGGGCATAGCGC 61.448 60.000 0.00 0.00 41.91 5.92
1792 1858 1.393603 GTGGAGGAAAAGGGCATAGC 58.606 55.000 0.00 0.00 0.00 2.97
1793 1859 1.209504 TCGTGGAGGAAAAGGGCATAG 59.790 52.381 0.00 0.00 0.00 2.23
1794 1860 1.209504 CTCGTGGAGGAAAAGGGCATA 59.790 52.381 0.00 0.00 0.00 3.14
1796 1862 1.374947 CTCGTGGAGGAAAAGGGCA 59.625 57.895 0.00 0.00 0.00 5.36
1798 1864 0.674895 CAGCTCGTGGAGGAAAAGGG 60.675 60.000 0.00 0.00 0.00 3.95
1799 1865 0.321671 TCAGCTCGTGGAGGAAAAGG 59.678 55.000 0.00 0.00 0.00 3.11
1800 1866 1.273606 TCTCAGCTCGTGGAGGAAAAG 59.726 52.381 0.00 0.00 0.00 2.27
1802 1868 0.603569 GTCTCAGCTCGTGGAGGAAA 59.396 55.000 0.00 0.00 0.00 3.13
1803 1869 1.587043 CGTCTCAGCTCGTGGAGGAA 61.587 60.000 0.00 0.00 0.00 3.36
1804 1870 2.041115 CGTCTCAGCTCGTGGAGGA 61.041 63.158 0.00 0.00 0.00 3.71
1806 1872 0.179176 CTTCGTCTCAGCTCGTGGAG 60.179 60.000 0.00 0.00 0.00 3.86
1807 1873 1.876664 CTTCGTCTCAGCTCGTGGA 59.123 57.895 0.00 0.00 0.00 4.02
1809 1875 2.148982 CGCTTCGTCTCAGCTCGTG 61.149 63.158 0.00 0.00 34.88 4.35
1812 1878 2.157701 CAGCGCTTCGTCTCAGCTC 61.158 63.158 7.50 0.00 35.82 4.09
1814 1880 2.431601 ACAGCGCTTCGTCTCAGC 60.432 61.111 7.50 0.00 0.00 4.26
1815 1881 1.211449 AGACAGCGCTTCGTCTCAG 59.789 57.895 21.19 5.16 38.03 3.35
1816 1882 3.355756 AGACAGCGCTTCGTCTCA 58.644 55.556 21.19 0.00 38.03 3.27
1819 1885 0.737715 ATTGGAGACAGCGCTTCGTC 60.738 55.000 17.66 17.66 44.54 4.20
1820 1886 0.737715 GATTGGAGACAGCGCTTCGT 60.738 55.000 7.50 2.68 44.54 3.85
1821 1887 1.424493 GGATTGGAGACAGCGCTTCG 61.424 60.000 7.50 0.00 44.54 3.79
1822 1888 0.391661 TGGATTGGAGACAGCGCTTC 60.392 55.000 7.50 9.45 44.54 3.86
1824 1890 0.392193 CTTGGATTGGAGACAGCGCT 60.392 55.000 2.64 2.64 44.54 5.92
1825 1891 0.674895 ACTTGGATTGGAGACAGCGC 60.675 55.000 0.00 0.00 44.54 5.92
1827 1893 5.008118 GCTAAATACTTGGATTGGAGACAGC 59.992 44.000 0.00 0.00 44.54 4.40
1828 1894 5.235186 CGCTAAATACTTGGATTGGAGACAG 59.765 44.000 0.00 0.00 44.54 3.51
1830 1896 5.116882 ACGCTAAATACTTGGATTGGAGAC 58.883 41.667 0.00 0.00 0.00 3.36
1831 1897 5.353394 ACGCTAAATACTTGGATTGGAGA 57.647 39.130 0.00 0.00 0.00 3.71
1832 1898 4.209288 CGACGCTAAATACTTGGATTGGAG 59.791 45.833 0.00 0.00 0.00 3.86
1833 1899 4.116961 CGACGCTAAATACTTGGATTGGA 58.883 43.478 0.00 0.00 0.00 3.53
1838 1904 2.417651 CCACCGACGCTAAATACTTGGA 60.418 50.000 0.00 0.00 0.00 3.53
1840 1906 2.613691 ACCACCGACGCTAAATACTTG 58.386 47.619 0.00 0.00 0.00 3.16
1842 1908 3.736126 GCTAACCACCGACGCTAAATACT 60.736 47.826 0.00 0.00 0.00 2.12
1843 1909 2.537214 GCTAACCACCGACGCTAAATAC 59.463 50.000 0.00 0.00 0.00 1.89
1845 1911 1.648504 GCTAACCACCGACGCTAAAT 58.351 50.000 0.00 0.00 0.00 1.40
1846 1912 0.733566 CGCTAACCACCGACGCTAAA 60.734 55.000 0.00 0.00 0.00 1.85
1847 1913 1.153978 CGCTAACCACCGACGCTAA 60.154 57.895 0.00 0.00 0.00 3.09
1848 1914 2.486504 CGCTAACCACCGACGCTA 59.513 61.111 0.00 0.00 0.00 4.26
1851 1917 2.931713 CTAGGCGCTAACCACCGACG 62.932 65.000 7.64 0.00 37.60 5.12
1853 1919 3.072486 GCTAGGCGCTAACCACCGA 62.072 63.158 7.64 0.00 35.14 4.69
1854 1920 2.585247 GCTAGGCGCTAACCACCG 60.585 66.667 7.64 0.00 35.14 4.94
1865 1931 1.009829 CATCTGTTCCAACGCTAGGC 58.990 55.000 0.00 0.00 0.00 3.93
1866 1932 1.656652 CCATCTGTTCCAACGCTAGG 58.343 55.000 0.00 0.00 0.00 3.02
1868 1934 0.323302 TGCCATCTGTTCCAACGCTA 59.677 50.000 0.00 0.00 0.00 4.26
1869 1935 1.073025 TGCCATCTGTTCCAACGCT 59.927 52.632 0.00 0.00 0.00 5.07
1870 1936 1.210155 GTGCCATCTGTTCCAACGC 59.790 57.895 0.00 0.00 0.00 4.84
1871 1937 1.238439 AAGTGCCATCTGTTCCAACG 58.762 50.000 0.00 0.00 0.00 4.10
1873 1939 3.788227 ACTAAGTGCCATCTGTTCCAA 57.212 42.857 0.00 0.00 0.00 3.53
1875 1941 6.759497 AAAATACTAAGTGCCATCTGTTCC 57.241 37.500 0.00 0.00 0.00 3.62
1918 1984 7.389607 ACTTATCTAGGCGCTTAAACAGAAAAA 59.610 33.333 7.64 0.00 0.00 1.94
1919 1985 6.877322 ACTTATCTAGGCGCTTAAACAGAAAA 59.123 34.615 7.64 0.00 0.00 2.29
1922 1988 5.348986 CACTTATCTAGGCGCTTAAACAGA 58.651 41.667 7.64 0.00 0.00 3.41
1923 1989 4.025647 GCACTTATCTAGGCGCTTAAACAG 60.026 45.833 7.64 0.25 0.00 3.16
1924 1990 3.869246 GCACTTATCTAGGCGCTTAAACA 59.131 43.478 7.64 0.00 0.00 2.83
1925 1991 3.247886 GGCACTTATCTAGGCGCTTAAAC 59.752 47.826 7.64 0.00 0.00 2.01
1926 1992 3.463944 GGCACTTATCTAGGCGCTTAAA 58.536 45.455 7.64 0.00 0.00 1.52
1927 1993 2.224209 GGGCACTTATCTAGGCGCTTAA 60.224 50.000 7.64 0.00 36.42 1.85
1928 1994 1.343465 GGGCACTTATCTAGGCGCTTA 59.657 52.381 7.64 2.19 36.42 3.09
1929 1995 0.106894 GGGCACTTATCTAGGCGCTT 59.893 55.000 7.64 0.52 36.42 4.68
1931 1997 1.301795 GGGGCACTTATCTAGGCGC 60.302 63.158 0.00 0.00 38.34 6.53
1932 1998 1.371558 GGGGGCACTTATCTAGGCG 59.628 63.158 0.00 0.00 0.00 5.52
1933 1999 1.068121 ATGGGGGCACTTATCTAGGC 58.932 55.000 0.00 0.00 0.00 3.93
1935 2001 3.864789 ACAATGGGGGCACTTATCTAG 57.135 47.619 0.00 0.00 0.00 2.43
1936 2002 5.922960 AATACAATGGGGGCACTTATCTA 57.077 39.130 0.00 0.00 0.00 1.98
1937 2003 4.814224 AATACAATGGGGGCACTTATCT 57.186 40.909 0.00 0.00 0.00 1.98
1938 2004 6.719370 TGATAAATACAATGGGGGCACTTATC 59.281 38.462 0.00 0.00 0.00 1.75
1940 2006 6.019656 TGATAAATACAATGGGGGCACTTA 57.980 37.500 0.00 0.00 0.00 2.24
1943 2009 4.469657 TCTGATAAATACAATGGGGGCAC 58.530 43.478 0.00 0.00 0.00 5.01
1944 2010 4.805140 TCTGATAAATACAATGGGGGCA 57.195 40.909 0.00 0.00 0.00 5.36
1945 2011 5.140454 ACTTCTGATAAATACAATGGGGGC 58.860 41.667 0.00 0.00 0.00 5.80
1946 2012 5.470098 CGACTTCTGATAAATACAATGGGGG 59.530 44.000 0.00 0.00 0.00 5.40
1949 2015 8.593492 TGATCGACTTCTGATAAATACAATGG 57.407 34.615 0.00 0.00 0.00 3.16
1956 2022 9.632807 GCTACTATTGATCGACTTCTGATAAAT 57.367 33.333 0.00 0.00 32.74 1.40
1957 2023 8.082852 GGCTACTATTGATCGACTTCTGATAAA 58.917 37.037 0.00 0.00 0.00 1.40
1958 2024 7.573283 CGGCTACTATTGATCGACTTCTGATAA 60.573 40.741 0.00 0.00 0.00 1.75
1959 2025 6.128254 CGGCTACTATTGATCGACTTCTGATA 60.128 42.308 0.00 0.00 0.00 2.15
1983 2211 2.688958 AGGATTCGGTTCCTAGAGTTCG 59.311 50.000 5.39 0.00 44.50 3.95
1988 2216 2.032620 GCAGAGGATTCGGTTCCTAGA 58.967 52.381 7.01 0.00 46.35 2.43
1989 2217 1.757118 TGCAGAGGATTCGGTTCCTAG 59.243 52.381 7.01 5.06 46.35 3.02
1990 2218 1.860641 TGCAGAGGATTCGGTTCCTA 58.139 50.000 7.01 0.00 46.35 2.94
2014 2242 3.511540 GCAAGAAAAACAGGAGGGCTTAT 59.488 43.478 0.00 0.00 0.00 1.73
2016 2244 1.688735 GCAAGAAAAACAGGAGGGCTT 59.311 47.619 0.00 0.00 0.00 4.35
2018 2246 0.318441 GGCAAGAAAAACAGGAGGGC 59.682 55.000 0.00 0.00 0.00 5.19
2034 2263 0.543883 ACAAGAGGAGCTGAGAGGCA 60.544 55.000 0.00 0.00 34.17 4.75
2085 2314 8.528044 TTTTTGTAAAGAAAGTGGTGACCTAT 57.472 30.769 2.11 0.00 0.00 2.57
2111 2340 5.235831 GCCGTGAATGGTACCTAACTAATTC 59.764 44.000 14.36 12.69 34.43 2.17
2114 2343 3.429272 CGCCGTGAATGGTACCTAACTAA 60.429 47.826 14.36 0.00 0.00 2.24
2118 2347 1.184431 TCGCCGTGAATGGTACCTAA 58.816 50.000 14.36 0.00 0.00 2.69
2124 2353 1.611491 ACAAAATTCGCCGTGAATGGT 59.389 42.857 7.93 4.86 46.65 3.55
2125 2354 2.250188 GACAAAATTCGCCGTGAATGG 58.750 47.619 7.93 4.30 46.65 3.16
2133 2362 5.905480 AACTGAAAATGACAAAATTCGCC 57.095 34.783 0.00 0.00 0.00 5.54
2134 2363 7.043458 TGAGAAACTGAAAATGACAAAATTCGC 60.043 33.333 0.00 0.00 0.00 4.70
2138 2367 9.603921 ACATTGAGAAACTGAAAATGACAAAAT 57.396 25.926 0.00 0.00 33.47 1.82
2141 2370 9.681692 CATACATTGAGAAACTGAAAATGACAA 57.318 29.630 0.00 0.00 33.47 3.18
2142 2371 8.298854 CCATACATTGAGAAACTGAAAATGACA 58.701 33.333 0.00 0.00 33.47 3.58
2143 2372 7.756722 CCCATACATTGAGAAACTGAAAATGAC 59.243 37.037 0.00 0.00 33.47 3.06
2147 2376 5.774690 AGCCCATACATTGAGAAACTGAAAA 59.225 36.000 0.00 0.00 0.00 2.29
2179 2411 7.759433 GGTGGGTAATGTGACAAATTTTCATAG 59.241 37.037 0.00 0.00 0.00 2.23
2200 2432 2.958355 CCATACAATTTAGCCAGGTGGG 59.042 50.000 0.00 0.00 40.85 4.61
2204 2436 4.341806 TGCATTCCATACAATTTAGCCAGG 59.658 41.667 0.00 0.00 0.00 4.45
2208 2440 5.520376 AGGTGCATTCCATACAATTTAGC 57.480 39.130 0.00 0.00 0.00 3.09
2212 2444 7.902920 ATCTAAAGGTGCATTCCATACAATT 57.097 32.000 0.00 0.00 0.00 2.32
2233 2465 8.136165 CAGTACGGAGCAACTAGTATAAAATCT 58.864 37.037 0.00 0.00 0.00 2.40
2245 2477 0.105964 TGCAACAGTACGGAGCAACT 59.894 50.000 13.16 0.00 31.42 3.16
2254 2486 3.625764 TGAAAAGGACACTGCAACAGTAC 59.374 43.478 0.00 0.00 43.43 2.73
2257 2489 3.699067 CTTGAAAAGGACACTGCAACAG 58.301 45.455 0.00 0.00 41.27 3.16
2295 2527 8.358895 TGCAATAACTTCTCATGATCACAAAAA 58.641 29.630 0.00 0.00 0.00 1.94
2296 2528 7.884257 TGCAATAACTTCTCATGATCACAAAA 58.116 30.769 0.00 0.00 0.00 2.44
2297 2529 7.451501 TGCAATAACTTCTCATGATCACAAA 57.548 32.000 0.00 0.00 0.00 2.83
2298 2530 7.634671 ATGCAATAACTTCTCATGATCACAA 57.365 32.000 0.00 0.00 0.00 3.33
2303 2535 9.961265 CATTGTAATGCAATAACTTCTCATGAT 57.039 29.630 0.00 0.00 45.33 2.45
2304 2536 8.959548 ACATTGTAATGCAATAACTTCTCATGA 58.040 29.630 4.58 0.00 45.33 3.07
2317 2549 4.588899 AGTCCAGCTACATTGTAATGCAA 58.411 39.130 9.82 0.00 40.04 4.08
2319 2551 4.272018 CAGAGTCCAGCTACATTGTAATGC 59.728 45.833 4.58 0.00 40.04 3.56
2323 2555 3.708451 TCCAGAGTCCAGCTACATTGTA 58.292 45.455 0.00 0.00 0.00 2.41
2335 2567 2.029020 GCACCCAATTTTTCCAGAGTCC 60.029 50.000 0.00 0.00 0.00 3.85
2343 2577 6.045955 TGTTTCTGTTAGCACCCAATTTTTC 58.954 36.000 0.00 0.00 0.00 2.29
2345 2579 5.606348 TGTTTCTGTTAGCACCCAATTTT 57.394 34.783 0.00 0.00 0.00 1.82
2381 2615 9.897744 CAGCTTCTTTATGAAACAAACAGATAA 57.102 29.630 0.00 0.00 33.79 1.75
2382 2616 8.023128 GCAGCTTCTTTATGAAACAAACAGATA 58.977 33.333 0.00 0.00 33.79 1.98
2386 2620 5.900425 TGCAGCTTCTTTATGAAACAAACA 58.100 33.333 0.00 0.00 33.79 2.83
2405 2639 1.199327 CCACACAAAGATCAGCTGCAG 59.801 52.381 10.11 10.11 0.00 4.41
2410 2644 5.824904 AATACATCCACACAAAGATCAGC 57.175 39.130 0.00 0.00 0.00 4.26
2414 2648 5.415701 AGCGAAAATACATCCACACAAAGAT 59.584 36.000 0.00 0.00 0.00 2.40
2435 2669 7.748847 ACAAATTTAGTTGGATAGTAACAGCG 58.251 34.615 0.00 0.00 32.50 5.18
2638 2872 5.359576 TGAAATATTGCGGGCTTCTATTTGT 59.640 36.000 0.00 0.00 0.00 2.83
3284 3534 4.335416 ACACCTGTAATCATGAAACTGGG 58.665 43.478 26.94 21.17 36.76 4.45
3299 3549 4.558226 TGCATCTATTTCAGACACCTGT 57.442 40.909 0.00 0.00 41.16 4.00
3316 3566 1.108776 GATGGCACCTGTTCATGCAT 58.891 50.000 0.00 0.00 43.93 3.96
3317 3567 0.038599 AGATGGCACCTGTTCATGCA 59.961 50.000 0.00 0.00 43.93 3.96
3328 3578 5.448360 GCTTAAATCTGTGAAGAGATGGCAC 60.448 44.000 0.00 0.00 32.77 5.01
3350 3600 3.221771 TGGCACAGAACAATTACAAGCT 58.778 40.909 0.00 0.00 0.00 3.74
3382 3632 4.700213 TCGAAATCATCAAGTTCCCCTTTC 59.300 41.667 0.00 0.00 0.00 2.62
3432 3682 4.080687 TCAAATTGCACATGTCAGGATCA 58.919 39.130 0.00 0.00 0.00 2.92
3470 3720 1.999051 CATCGGCGCAGTACAAGAC 59.001 57.895 10.83 0.00 0.00 3.01
3483 3733 1.202222 GGCAAGAAACATCAGCATCGG 60.202 52.381 0.00 0.00 0.00 4.18
3487 3737 2.294233 GACAAGGCAAGAAACATCAGCA 59.706 45.455 0.00 0.00 0.00 4.41
3502 3752 5.233988 CAGAGAGACAAAGGTAAGACAAGG 58.766 45.833 0.00 0.00 0.00 3.61
3521 3771 7.877097 AGCTGAAAGAATATATACTTGCCAGAG 59.123 37.037 13.86 0.00 34.07 3.35
3593 3843 4.332683 TCTTCCATACTCCTACCTGTGT 57.667 45.455 0.00 0.00 0.00 3.72
3598 3848 4.159135 TCAACGTTCTTCCATACTCCTACC 59.841 45.833 0.00 0.00 0.00 3.18
3605 3855 6.963049 AGTAACATCAACGTTCTTCCATAC 57.037 37.500 0.00 0.00 0.00 2.39
3610 3860 5.693104 TGGTGTAGTAACATCAACGTTCTTC 59.307 40.000 0.00 0.00 43.78 2.87


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

AutoCloner maintained by Alex Coulton.