Multiple sequence alignment - TraesCS2B01G556200

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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 TraesCS2B01G556200 chr2B 100.000 2472 0 0 1 2472 751271836 751269365 0.000000e+00 4566.0
1 TraesCS2B01G556200 chr2A 88.155 1680 96 34 1 1647 746612261 746610652 0.000000e+00 1905.0
2 TraesCS2B01G556200 chr2A 84.127 252 26 8 1895 2139 746610141 746609897 5.320000e-57 231.0
3 TraesCS2B01G556200 chr2A 82.412 199 19 5 1724 1907 24137555 24137752 2.540000e-35 159.0
4 TraesCS2B01G556200 chr2A 98.276 58 1 0 1648 1705 746610618 746610561 4.350000e-18 102.0
5 TraesCS2B01G556200 chr2D 86.985 1675 86 38 1 1647 616516604 616515034 0.000000e+00 1764.0
6 TraesCS2B01G556200 chr2D 84.588 571 68 12 1907 2467 616514896 616514336 1.290000e-152 549.0
7 TraesCS2B01G556200 chr2D 88.235 119 8 5 1787 1899 642821790 642821908 1.190000e-28 137.0
8 TraesCS2B01G556200 chr2D 94.118 68 3 1 1648 1714 616514996 616514929 4.350000e-18 102.0
9 TraesCS2B01G556200 chr3A 88.757 169 12 2 1724 1885 394486513 394486345 1.500000e-47 200.0
10 TraesCS2B01G556200 chr3A 79.365 189 12 11 1724 1885 551651959 551651771 9.350000e-20 108.0
11 TraesCS2B01G556200 chr5A 93.137 102 4 1 1787 1885 535742090 535742191 1.980000e-31 147.0
12 TraesCS2B01G556200 chr5A 89.024 82 5 2 1724 1801 285572204 285572123 5.630000e-17 99.0
13 TraesCS2B01G556200 chr7A 92.157 102 5 1 1787 1885 247304140 247304241 9.220000e-30 141.0
14 TraesCS2B01G556200 chr6A 92.157 102 5 1 1787 1885 38766639 38766740 9.220000e-30 141.0
15 TraesCS2B01G556200 chr6A 92.157 102 5 1 1787 1885 142076032 142076133 9.220000e-30 141.0
16 TraesCS2B01G556200 chr6A 92.157 102 5 1 1787 1885 316927988 316927887 9.220000e-30 141.0
17 TraesCS2B01G556200 chr6A 79.894 189 11 8 1724 1885 441540121 441540309 2.010000e-21 113.0
18 TraesCS2B01G556200 chr4B 92.157 102 5 1 1787 1885 409252836 409252937 9.220000e-30 141.0
19 TraesCS2B01G556200 chr4B 79.894 189 11 9 1724 1885 111250448 111250260 2.010000e-21 113.0
20 TraesCS2B01G556200 chr4A 80.952 189 9 7 1724 1885 231610831 231610643 9.280000e-25 124.0
21 TraesCS2B01G556200 chr3B 80.108 186 10 7 1724 1882 570927219 570927034 2.010000e-21 113.0
22 TraesCS2B01G556200 chr5B 78.462 195 15 7 1718 1885 436548903 436549097 4.350000e-18 102.0
23 TraesCS2B01G556200 chrUn 78.307 189 14 7 1724 1885 168299660 168299472 2.020000e-16 97.1
24 TraesCS2B01G556200 chr5D 100.000 28 0 0 1256 1283 213470829 213470802 4.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G556200 chr2B 751269365 751271836 2471 True 4566 4566 100.000000 1 2472 1 chr2B.!!$R1 2471
1 TraesCS2B01G556200 chr2A 746609897 746612261 2364 True 746 1905 90.186000 1 2139 3 chr2A.!!$R1 2138
2 TraesCS2B01G556200 chr2D 616514336 616516604 2268 True 805 1764 88.563667 1 2467 3 chr2D.!!$R1 2466

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
230 243 0.108585 TCCTGTTCCACTCCAGTTGC 59.891 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1857 0.034337 TACTCACCAACCAACCGAGC 59.966 55.0 0.0 0.0 0.0 5.03 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
64 73 1.827969 CCATTTCCACTCTCGTCCTCT 59.172 52.381 0.00 0.00 0.00 3.69
106 115 7.174599 CCTGATTATTCCCTGCTTTTCTCATAG 59.825 40.741 0.00 0.00 0.00 2.23
186 197 3.481453 TCTCTCTACTCACGGATGGATG 58.519 50.000 0.00 0.00 0.00 3.51
187 198 2.556189 CTCTCTACTCACGGATGGATGG 59.444 54.545 0.00 0.00 0.00 3.51
204 217 5.078949 TGGATGGCCATTAACTAATCCATG 58.921 41.667 21.84 0.00 38.86 3.66
230 243 0.108585 TCCTGTTCCACTCCAGTTGC 59.891 55.000 0.00 0.00 0.00 4.17
243 256 2.356673 GTTGCAGCCAAAGCCTGC 60.357 61.111 6.44 6.44 41.25 4.85
263 280 1.154357 CAGACGTACGCGCACAGTA 60.154 57.895 16.72 0.00 42.83 2.74
379 396 3.624861 AGTAAATGAGCTCGGCTTCATTG 59.375 43.478 9.64 0.00 39.88 2.82
524 541 3.733960 GGTTTTCCCGCCGTGCTC 61.734 66.667 0.00 0.00 0.00 4.26
525 542 3.733960 GTTTTCCCGCCGTGCTCC 61.734 66.667 0.00 0.00 0.00 4.70
626 651 4.744795 TTAATGGCTTGTCTCTCTCTCC 57.255 45.455 0.00 0.00 0.00 3.71
951 983 1.498865 CTTGAGTGTCACCGTGCACC 61.499 60.000 12.15 11.80 36.35 5.01
953 985 3.785189 GAGTGTCACCGTGCACCGT 62.785 63.158 12.15 8.32 36.35 4.83
954 986 2.027897 GTGTCACCGTGCACCGTA 59.972 61.111 12.15 0.00 33.66 4.02
955 987 2.027897 TGTCACCGTGCACCGTAC 59.972 61.111 12.15 10.30 33.66 3.67
976 1012 3.248171 CGCGAGCTCTTGGTACGC 61.248 66.667 12.85 7.93 44.64 4.42
979 1015 3.248171 GAGCTCTTGGTACGCGCG 61.248 66.667 30.96 30.96 0.00 6.86
994 1030 4.520846 GCGCACGCGGGATTCTTG 62.521 66.667 15.48 0.00 40.19 3.02
1004 1042 2.565841 CGGGATTCTTGGGAAGATGAC 58.434 52.381 0.00 0.00 37.38 3.06
1019 1057 2.126031 GACGAAGAGGCACGGTCC 60.126 66.667 0.00 0.00 0.00 4.46
1044 1082 2.654912 CCGAGTTCACCGCGTTCAC 61.655 63.158 4.92 0.00 0.00 3.18
1173 1211 3.743521 CCATCTTCTTCGCATGGGAATA 58.256 45.455 23.68 15.09 34.47 1.75
1177 1215 5.034852 TCTTCTTCGCATGGGAATATGAA 57.965 39.130 23.68 20.62 0.00 2.57
1187 1225 6.427853 CGCATGGGAATATGAATCTAACTTGA 59.572 38.462 3.11 0.00 0.00 3.02
1193 1231 9.342308 GGGAATATGAATCTAACTTGAATCACA 57.658 33.333 0.00 0.00 29.90 3.58
1459 1513 1.377333 GGGCAAGTGCTACCCTGTC 60.377 63.158 2.85 0.00 40.75 3.51
1465 1519 1.612442 GTGCTACCCTGTCCCCTCA 60.612 63.158 0.00 0.00 0.00 3.86
1497 1551 2.421107 GCTCAGCTGAGATGATTTCCCA 60.421 50.000 41.20 5.31 44.74 4.37
1604 1668 5.928264 TGTTCGATCACCATGATGATATGAC 59.072 40.000 1.38 2.65 39.48 3.06
1606 1670 3.861689 CGATCACCATGATGATATGACGG 59.138 47.826 1.38 0.00 39.48 4.79
1705 1810 8.887717 CCAAATCTTTTGTTGATTGTTGGTTTA 58.112 29.630 0.00 0.00 34.74 2.01
1708 1813 9.883142 AATCTTTTGTTGATTGTTGGTTTAAGA 57.117 25.926 0.00 0.00 33.44 2.10
1712 1817 8.810652 TTTGTTGATTGTTGGTTTAAGATAGC 57.189 30.769 0.00 0.00 0.00 2.97
1713 1818 7.759489 TGTTGATTGTTGGTTTAAGATAGCT 57.241 32.000 0.00 0.00 0.00 3.32
1714 1819 7.592938 TGTTGATTGTTGGTTTAAGATAGCTG 58.407 34.615 0.00 0.00 0.00 4.24
1715 1820 6.194796 TGATTGTTGGTTTAAGATAGCTGC 57.805 37.500 0.00 0.00 0.00 5.25
1716 1821 5.945784 TGATTGTTGGTTTAAGATAGCTGCT 59.054 36.000 7.57 7.57 0.00 4.24
1718 1823 3.932710 TGTTGGTTTAAGATAGCTGCTCG 59.067 43.478 4.91 0.00 0.00 5.03
1719 1824 3.179443 TGGTTTAAGATAGCTGCTCGG 57.821 47.619 4.91 0.00 0.00 4.63
1720 1825 2.500098 TGGTTTAAGATAGCTGCTCGGT 59.500 45.455 4.91 0.00 0.00 4.69
1722 1827 3.939592 GGTTTAAGATAGCTGCTCGGTTT 59.060 43.478 4.91 0.00 0.00 3.27
1724 1829 5.758784 GGTTTAAGATAGCTGCTCGGTTTAT 59.241 40.000 4.91 0.00 0.00 1.40
1725 1830 6.260271 GGTTTAAGATAGCTGCTCGGTTTATT 59.740 38.462 4.91 0.00 0.00 1.40
1726 1831 6.844696 TTAAGATAGCTGCTCGGTTTATTG 57.155 37.500 4.91 0.00 0.00 1.90
1727 1832 4.408182 AGATAGCTGCTCGGTTTATTGT 57.592 40.909 4.91 0.00 0.00 2.71
1728 1833 4.770795 AGATAGCTGCTCGGTTTATTGTT 58.229 39.130 4.91 0.00 0.00 2.83
1730 1835 6.346096 AGATAGCTGCTCGGTTTATTGTTAA 58.654 36.000 4.91 0.00 0.00 2.01
1731 1836 4.946784 AGCTGCTCGGTTTATTGTTAAG 57.053 40.909 0.00 0.00 0.00 1.85
1732 1837 4.575885 AGCTGCTCGGTTTATTGTTAAGA 58.424 39.130 0.00 0.00 0.00 2.10
1733 1838 5.001232 AGCTGCTCGGTTTATTGTTAAGAA 58.999 37.500 0.00 0.00 0.00 2.52
1734 1839 5.472137 AGCTGCTCGGTTTATTGTTAAGAAA 59.528 36.000 0.00 0.00 0.00 2.52
1735 1840 6.016610 AGCTGCTCGGTTTATTGTTAAGAAAA 60.017 34.615 0.00 0.00 0.00 2.29
1737 1842 7.008357 GCTGCTCGGTTTATTGTTAAGAAAATC 59.992 37.037 0.00 0.00 0.00 2.17
1738 1843 7.018826 TGCTCGGTTTATTGTTAAGAAAATCG 58.981 34.615 0.00 0.00 0.00 3.34
1739 1844 7.019418 GCTCGGTTTATTGTTAAGAAAATCGT 58.981 34.615 3.32 0.00 0.00 3.73
1750 1855 7.799784 TGTTAAGAAAATCGTTAACAGGTAGC 58.200 34.615 6.39 0.00 41.82 3.58
1751 1856 7.658575 TGTTAAGAAAATCGTTAACAGGTAGCT 59.341 33.333 6.39 0.00 41.82 3.32
1752 1857 6.481954 AAGAAAATCGTTAACAGGTAGCTG 57.518 37.500 20.16 20.16 0.00 4.24
1753 1858 4.392138 AGAAAATCGTTAACAGGTAGCTGC 59.608 41.667 21.58 4.61 0.00 5.25
1754 1859 3.611766 AATCGTTAACAGGTAGCTGCT 57.388 42.857 21.58 12.46 0.00 4.24
1755 1860 2.649331 TCGTTAACAGGTAGCTGCTC 57.351 50.000 21.58 8.63 0.00 4.26
1756 1861 1.135489 TCGTTAACAGGTAGCTGCTCG 60.135 52.381 21.58 18.51 0.00 5.03
1757 1862 1.641577 GTTAACAGGTAGCTGCTCGG 58.358 55.000 21.58 0.00 0.00 4.63
1758 1863 1.067071 GTTAACAGGTAGCTGCTCGGT 60.067 52.381 21.58 0.00 0.00 4.69
1759 1864 1.263356 TAACAGGTAGCTGCTCGGTT 58.737 50.000 21.58 8.70 0.00 4.44
1760 1865 0.320771 AACAGGTAGCTGCTCGGTTG 60.321 55.000 21.58 3.65 0.00 3.77
1761 1866 1.448540 CAGGTAGCTGCTCGGTTGG 60.449 63.158 4.91 0.00 0.00 3.77
1762 1867 1.913762 AGGTAGCTGCTCGGTTGGT 60.914 57.895 4.91 0.00 0.00 3.67
1763 1868 1.003718 GGTAGCTGCTCGGTTGGTT 60.004 57.895 4.91 0.00 0.00 3.67
1764 1869 1.298859 GGTAGCTGCTCGGTTGGTTG 61.299 60.000 4.91 0.00 0.00 3.77
1765 1870 1.003839 TAGCTGCTCGGTTGGTTGG 60.004 57.895 4.91 0.00 0.00 3.77
1766 1871 1.764571 TAGCTGCTCGGTTGGTTGGT 61.765 55.000 4.91 0.00 0.00 3.67
1767 1872 2.908073 GCTGCTCGGTTGGTTGGTG 61.908 63.158 0.00 0.00 0.00 4.17
1768 1873 1.227823 CTGCTCGGTTGGTTGGTGA 60.228 57.895 0.00 0.00 0.00 4.02
1769 1874 1.227823 TGCTCGGTTGGTTGGTGAG 60.228 57.895 0.00 0.00 0.00 3.51
1770 1875 1.227853 GCTCGGTTGGTTGGTGAGT 60.228 57.895 0.00 0.00 0.00 3.41
1771 1876 0.034337 GCTCGGTTGGTTGGTGAGTA 59.966 55.000 0.00 0.00 0.00 2.59
1772 1877 1.939838 GCTCGGTTGGTTGGTGAGTAG 60.940 57.143 0.00 0.00 0.00 2.57
1773 1878 0.682852 TCGGTTGGTTGGTGAGTAGG 59.317 55.000 0.00 0.00 0.00 3.18
1774 1879 0.321298 CGGTTGGTTGGTGAGTAGGG 60.321 60.000 0.00 0.00 0.00 3.53
1775 1880 1.061546 GGTTGGTTGGTGAGTAGGGA 58.938 55.000 0.00 0.00 0.00 4.20
1776 1881 1.422402 GGTTGGTTGGTGAGTAGGGAA 59.578 52.381 0.00 0.00 0.00 3.97
1777 1882 2.041216 GGTTGGTTGGTGAGTAGGGAAT 59.959 50.000 0.00 0.00 0.00 3.01
1778 1883 3.499745 GGTTGGTTGGTGAGTAGGGAATT 60.500 47.826 0.00 0.00 0.00 2.17
1779 1884 4.263594 GGTTGGTTGGTGAGTAGGGAATTA 60.264 45.833 0.00 0.00 0.00 1.40
1780 1885 5.318630 GTTGGTTGGTGAGTAGGGAATTAA 58.681 41.667 0.00 0.00 0.00 1.40
1781 1886 5.789574 TGGTTGGTGAGTAGGGAATTAAT 57.210 39.130 0.00 0.00 0.00 1.40
1782 1887 6.894735 TGGTTGGTGAGTAGGGAATTAATA 57.105 37.500 0.00 0.00 0.00 0.98
1783 1888 6.895782 TGGTTGGTGAGTAGGGAATTAATAG 58.104 40.000 0.00 0.00 0.00 1.73
1784 1889 6.126594 TGGTTGGTGAGTAGGGAATTAATAGG 60.127 42.308 0.00 0.00 0.00 2.57
1785 1890 5.562298 TGGTGAGTAGGGAATTAATAGGC 57.438 43.478 0.00 0.00 0.00 3.93
1786 1891 5.224441 TGGTGAGTAGGGAATTAATAGGCT 58.776 41.667 0.00 0.00 0.00 4.58
1787 1892 6.387127 TGGTGAGTAGGGAATTAATAGGCTA 58.613 40.000 0.00 0.00 0.00 3.93
1788 1893 6.847567 TGGTGAGTAGGGAATTAATAGGCTAA 59.152 38.462 0.00 0.00 0.00 3.09
1789 1894 7.516209 TGGTGAGTAGGGAATTAATAGGCTAAT 59.484 37.037 0.00 0.00 0.00 1.73
1790 1895 8.041919 GGTGAGTAGGGAATTAATAGGCTAATC 58.958 40.741 0.00 0.00 0.00 1.75
1791 1896 8.594550 GTGAGTAGGGAATTAATAGGCTAATCA 58.405 37.037 0.00 0.00 0.00 2.57
1792 1897 8.816894 TGAGTAGGGAATTAATAGGCTAATCAG 58.183 37.037 0.00 0.00 0.00 2.90
1793 1898 8.743636 AGTAGGGAATTAATAGGCTAATCAGT 57.256 34.615 0.00 0.00 0.00 3.41
1794 1899 9.172060 AGTAGGGAATTAATAGGCTAATCAGTT 57.828 33.333 0.00 0.00 0.00 3.16
1803 1908 9.692749 TTAATAGGCTAATCAGTTAATCAGACG 57.307 33.333 0.00 0.00 0.00 4.18
1804 1909 4.950050 AGGCTAATCAGTTAATCAGACGG 58.050 43.478 0.00 0.00 0.00 4.79
1805 1910 4.406003 AGGCTAATCAGTTAATCAGACGGT 59.594 41.667 0.00 0.00 0.00 4.83
1806 1911 5.104900 AGGCTAATCAGTTAATCAGACGGTT 60.105 40.000 0.00 0.00 0.00 4.44
1807 1912 5.585047 GGCTAATCAGTTAATCAGACGGTTT 59.415 40.000 0.00 0.00 0.00 3.27
1808 1913 6.759827 GGCTAATCAGTTAATCAGACGGTTTA 59.240 38.462 0.00 0.00 0.00 2.01
1809 1914 7.441458 GGCTAATCAGTTAATCAGACGGTTTAT 59.559 37.037 0.00 0.00 0.00 1.40
1810 1915 8.488764 GCTAATCAGTTAATCAGACGGTTTATC 58.511 37.037 0.00 0.00 0.00 1.75
1811 1916 9.529325 CTAATCAGTTAATCAGACGGTTTATCA 57.471 33.333 0.00 0.00 0.00 2.15
1812 1917 8.425577 AATCAGTTAATCAGACGGTTTATCAG 57.574 34.615 0.00 0.00 0.00 2.90
1813 1918 6.931838 TCAGTTAATCAGACGGTTTATCAGT 58.068 36.000 0.00 0.00 0.00 3.41
1814 1919 7.383687 TCAGTTAATCAGACGGTTTATCAGTT 58.616 34.615 0.00 0.00 0.00 3.16
1815 1920 7.876068 TCAGTTAATCAGACGGTTTATCAGTTT 59.124 33.333 0.00 0.00 0.00 2.66
1816 1921 9.146984 CAGTTAATCAGACGGTTTATCAGTTTA 57.853 33.333 0.00 0.00 0.00 2.01
1817 1922 9.886132 AGTTAATCAGACGGTTTATCAGTTTAT 57.114 29.630 0.00 0.00 0.00 1.40
1819 1924 7.464830 AATCAGACGGTTTATCAGTTTATCG 57.535 36.000 0.00 0.00 0.00 2.92
1820 1925 5.345702 TCAGACGGTTTATCAGTTTATCGG 58.654 41.667 0.00 0.00 0.00 4.18
1821 1926 4.025979 CAGACGGTTTATCAGTTTATCGGC 60.026 45.833 0.00 0.00 0.00 5.54
1822 1927 4.117685 GACGGTTTATCAGTTTATCGGCT 58.882 43.478 0.00 0.00 0.00 5.52
1823 1928 5.068198 AGACGGTTTATCAGTTTATCGGCTA 59.932 40.000 0.00 0.00 32.63 3.93
1824 1929 5.045872 ACGGTTTATCAGTTTATCGGCTAC 58.954 41.667 0.00 0.00 0.00 3.58
1825 1930 5.163478 ACGGTTTATCAGTTTATCGGCTACT 60.163 40.000 0.00 0.00 0.00 2.57
1826 1931 5.401674 CGGTTTATCAGTTTATCGGCTACTC 59.598 44.000 0.00 0.00 0.00 2.59
1827 1932 5.401674 GGTTTATCAGTTTATCGGCTACTCG 59.598 44.000 0.00 0.00 0.00 4.18
1828 1933 3.644884 ATCAGTTTATCGGCTACTCGG 57.355 47.619 0.00 0.00 0.00 4.63
1829 1934 2.372264 TCAGTTTATCGGCTACTCGGT 58.628 47.619 0.00 0.00 0.00 4.69
1830 1935 2.098607 TCAGTTTATCGGCTACTCGGTG 59.901 50.000 0.00 0.00 0.00 4.94
1831 1936 2.098607 CAGTTTATCGGCTACTCGGTGA 59.901 50.000 0.00 0.00 0.00 4.02
1832 1937 2.098770 AGTTTATCGGCTACTCGGTGAC 59.901 50.000 0.00 0.00 0.00 3.67
1833 1938 1.027357 TTATCGGCTACTCGGTGACC 58.973 55.000 0.00 0.00 0.00 4.02
1834 1939 0.820891 TATCGGCTACTCGGTGACCC 60.821 60.000 0.00 0.00 0.00 4.46
1835 1940 2.569218 ATCGGCTACTCGGTGACCCT 62.569 60.000 0.00 0.00 0.00 4.34
1836 1941 1.452651 CGGCTACTCGGTGACCCTA 60.453 63.158 0.00 0.00 0.00 3.53
1837 1942 1.722636 CGGCTACTCGGTGACCCTAC 61.723 65.000 0.00 0.00 0.00 3.18
1838 1943 1.722636 GGCTACTCGGTGACCCTACG 61.723 65.000 0.00 0.00 0.00 3.51
1839 1944 0.745845 GCTACTCGGTGACCCTACGA 60.746 60.000 0.00 0.00 35.14 3.43
1841 1946 4.315588 CTCGGTGACCCTACGAGT 57.684 61.111 0.00 0.00 46.43 4.18
1842 1947 3.465990 CTCGGTGACCCTACGAGTA 57.534 57.895 0.00 0.00 46.43 2.59
1843 1948 1.297664 CTCGGTGACCCTACGAGTAG 58.702 60.000 0.00 3.39 46.43 2.57
1852 1957 0.597072 CCTACGAGTAGGGAATCGGC 59.403 60.000 18.99 0.00 46.96 5.54
1853 1958 1.315690 CTACGAGTAGGGAATCGGCA 58.684 55.000 2.46 0.00 43.12 5.69
1854 1959 1.679680 CTACGAGTAGGGAATCGGCAA 59.320 52.381 2.46 0.00 43.12 4.52
1855 1960 0.460311 ACGAGTAGGGAATCGGCAAG 59.540 55.000 0.00 0.00 43.12 4.01
1856 1961 0.460311 CGAGTAGGGAATCGGCAAGT 59.540 55.000 0.00 0.00 35.33 3.16
1857 1962 1.134788 CGAGTAGGGAATCGGCAAGTT 60.135 52.381 0.00 0.00 35.33 2.66
1858 1963 2.100252 CGAGTAGGGAATCGGCAAGTTA 59.900 50.000 0.00 0.00 35.33 2.24
1859 1964 3.429822 CGAGTAGGGAATCGGCAAGTTAA 60.430 47.826 0.00 0.00 35.33 2.01
1860 1965 3.869832 GAGTAGGGAATCGGCAAGTTAAC 59.130 47.826 0.00 0.00 0.00 2.01
1861 1966 3.518303 AGTAGGGAATCGGCAAGTTAACT 59.482 43.478 1.12 1.12 0.00 2.24
1862 1967 2.711542 AGGGAATCGGCAAGTTAACTG 58.288 47.619 9.34 4.88 0.00 3.16
1863 1968 1.743394 GGGAATCGGCAAGTTAACTGG 59.257 52.381 9.34 7.35 0.00 4.00
1864 1969 2.433436 GGAATCGGCAAGTTAACTGGT 58.567 47.619 9.34 0.00 0.00 4.00
1865 1970 2.817844 GGAATCGGCAAGTTAACTGGTT 59.182 45.455 9.34 0.00 0.00 3.67
1866 1971 4.004982 GGAATCGGCAAGTTAACTGGTTA 58.995 43.478 9.34 0.00 0.00 2.85
1867 1972 4.456566 GGAATCGGCAAGTTAACTGGTTAA 59.543 41.667 9.34 2.26 33.10 2.01
1868 1973 5.124936 GGAATCGGCAAGTTAACTGGTTAAT 59.875 40.000 9.34 0.00 37.37 1.40
1869 1974 6.349860 GGAATCGGCAAGTTAACTGGTTAATT 60.350 38.462 9.34 7.15 37.37 1.40
1870 1975 5.365403 TCGGCAAGTTAACTGGTTAATTG 57.635 39.130 9.34 2.83 37.37 2.32
1871 1976 4.216687 TCGGCAAGTTAACTGGTTAATTGG 59.783 41.667 9.34 11.39 37.37 3.16
1872 1977 4.216687 CGGCAAGTTAACTGGTTAATTGGA 59.783 41.667 9.34 0.00 37.37 3.53
1873 1978 5.466819 GGCAAGTTAACTGGTTAATTGGAC 58.533 41.667 9.34 9.87 37.37 4.02
1874 1979 5.151389 GCAAGTTAACTGGTTAATTGGACG 58.849 41.667 9.34 0.00 37.37 4.79
1875 1980 5.049267 GCAAGTTAACTGGTTAATTGGACGA 60.049 40.000 9.34 0.00 37.37 4.20
1876 1981 6.513720 GCAAGTTAACTGGTTAATTGGACGAA 60.514 38.462 9.34 0.00 37.37 3.85
1877 1982 7.590279 CAAGTTAACTGGTTAATTGGACGAAT 58.410 34.615 9.34 0.00 37.37 3.34
1878 1983 7.754851 AGTTAACTGGTTAATTGGACGAATT 57.245 32.000 7.48 0.92 37.37 2.17
1879 1984 7.813645 AGTTAACTGGTTAATTGGACGAATTC 58.186 34.615 7.48 0.00 37.37 2.17
1880 1985 7.664318 AGTTAACTGGTTAATTGGACGAATTCT 59.336 33.333 7.48 0.00 37.37 2.40
1881 1986 6.894339 AACTGGTTAATTGGACGAATTCTT 57.106 33.333 3.52 0.00 35.74 2.52
1882 1987 6.254281 ACTGGTTAATTGGACGAATTCTTG 57.746 37.500 3.52 0.00 35.74 3.02
1883 1988 6.001460 ACTGGTTAATTGGACGAATTCTTGA 58.999 36.000 3.52 0.00 35.74 3.02
1884 1989 6.488683 ACTGGTTAATTGGACGAATTCTTGAA 59.511 34.615 3.52 0.00 35.74 2.69
1885 1990 7.013846 ACTGGTTAATTGGACGAATTCTTGAAA 59.986 33.333 3.52 0.00 35.74 2.69
1886 1991 7.891561 TGGTTAATTGGACGAATTCTTGAAAT 58.108 30.769 3.52 0.00 35.74 2.17
1887 1992 9.015367 TGGTTAATTGGACGAATTCTTGAAATA 57.985 29.630 3.52 0.00 35.74 1.40
1892 1997 6.363577 TGGACGAATTCTTGAAATATCTGC 57.636 37.500 3.52 0.00 0.00 4.26
1893 1998 5.879777 TGGACGAATTCTTGAAATATCTGCA 59.120 36.000 3.52 0.00 0.00 4.41
1905 2240 6.699366 TGAAATATCTGCAAAATCTTTGGCA 58.301 32.000 4.73 4.73 44.42 4.92
1916 2251 2.823924 TCTTTGGCACACGCTAAGTA 57.176 45.000 0.00 0.00 40.01 2.24
1917 2252 3.328382 TCTTTGGCACACGCTAAGTAT 57.672 42.857 0.00 0.00 40.01 2.12
1932 2267 8.447833 CACGCTAAGTATCACTTTTTGGAAATA 58.552 33.333 0.00 0.00 39.51 1.40
1992 2330 7.499895 TGAACCCTAAAAATAGTTGTCGTCTTT 59.500 33.333 0.00 0.00 0.00 2.52
2006 2344 8.007716 AGTTGTCGTCTTTTATGATTTTACGTG 58.992 33.333 0.00 0.00 0.00 4.49
2049 2392 4.162698 ACTGTACTGCGGGATAATACCAAA 59.837 41.667 0.00 0.00 0.00 3.28
2050 2393 5.100344 TGTACTGCGGGATAATACCAAAA 57.900 39.130 0.00 0.00 0.00 2.44
2091 2434 0.321653 AGCCGAAAACCTGCACCTAG 60.322 55.000 0.00 0.00 0.00 3.02
2104 2447 3.515330 GCACCTAGCATTGCAAAAGAT 57.485 42.857 11.91 0.00 44.79 2.40
2117 2460 8.458843 GCATTGCAAAAGATAAACTACCTTAGA 58.541 33.333 1.71 0.00 0.00 2.10
2155 2499 2.951229 AACCTTGTAGGGTTGAGGTG 57.049 50.000 0.00 0.00 46.51 4.00
2156 2500 1.815757 ACCTTGTAGGGTTGAGGTGT 58.184 50.000 0.00 0.00 40.84 4.16
2170 2514 0.634465 AGGTGTGGACCCCAAACTTT 59.366 50.000 6.29 0.00 44.40 2.66
2171 2515 1.854280 AGGTGTGGACCCCAAACTTTA 59.146 47.619 6.29 0.00 44.40 1.85
2173 2517 2.235891 GTGTGGACCCCAAACTTTAGG 58.764 52.381 0.00 0.00 38.64 2.69
2182 2526 7.956881 TGGACCCCAAACTTTAGGTAAAAATAT 59.043 33.333 0.00 0.00 31.10 1.28
2206 2550 3.440522 TGTCGTTTCATGTGTTGTGGAAA 59.559 39.130 0.00 0.00 0.00 3.13
2207 2551 4.082733 TGTCGTTTCATGTGTTGTGGAAAA 60.083 37.500 0.00 0.00 31.73 2.29
2208 2552 4.859798 GTCGTTTCATGTGTTGTGGAAAAA 59.140 37.500 0.00 0.00 31.73 1.94
2209 2553 5.004345 GTCGTTTCATGTGTTGTGGAAAAAG 59.996 40.000 0.00 0.00 31.73 2.27
2218 2562 6.542821 TGTGTTGTGGAAAAAGAGAGGATAT 58.457 36.000 0.00 0.00 0.00 1.63
2257 2603 4.222145 GTCTTACACCATACTCTTCCCACA 59.778 45.833 0.00 0.00 0.00 4.17
2260 2606 4.021102 ACACCATACTCTTCCCACAAAG 57.979 45.455 0.00 0.00 0.00 2.77
2264 2610 5.643777 CACCATACTCTTCCCACAAAGTAAG 59.356 44.000 0.00 0.00 0.00 2.34
2297 2643 7.429636 TCCTTTCAAAACTTAGAATGTACGG 57.570 36.000 0.00 0.00 0.00 4.02
2299 2645 7.881232 TCCTTTCAAAACTTAGAATGTACGGAT 59.119 33.333 0.00 0.00 0.00 4.18
2310 2656 2.816204 TGTACGGATTTTGACGTGGA 57.184 45.000 0.00 0.00 43.93 4.02
2313 2659 2.465860 ACGGATTTTGACGTGGATCA 57.534 45.000 0.00 0.00 42.39 2.92
2324 2670 4.368315 TGACGTGGATCATACATAAGCAC 58.632 43.478 0.00 0.00 0.00 4.40
2325 2671 4.142049 TGACGTGGATCATACATAAGCACA 60.142 41.667 0.00 0.00 0.00 4.57
2398 2745 2.544721 TGGCCCTTCAAATATTGGCAA 58.455 42.857 13.90 0.68 43.96 4.52
2402 2749 4.565444 GGCCCTTCAAATATTGGCAAAGTT 60.565 41.667 3.01 0.00 43.96 2.66
2406 2753 7.336679 GCCCTTCAAATATTGGCAAAGTTTAAT 59.663 33.333 3.01 0.00 41.76 1.40
2414 2761 9.581099 AATATTGGCAAAGTTTAATTTAGGTCG 57.419 29.630 3.01 0.00 0.00 4.79
2415 2762 4.800784 TGGCAAAGTTTAATTTAGGTCGC 58.199 39.130 0.00 0.00 0.00 5.19
2422 2769 7.829378 AAGTTTAATTTAGGTCGCTCTACTG 57.171 36.000 0.00 0.00 0.00 2.74
2437 2784 6.916387 TCGCTCTACTGCAACACTATAAATAC 59.084 38.462 0.00 0.00 0.00 1.89
2441 2788 6.984474 TCTACTGCAACACTATAAATACTGGC 59.016 38.462 0.00 0.00 0.00 4.85
2443 2790 4.204012 TGCAACACTATAAATACTGGCCC 58.796 43.478 0.00 0.00 0.00 5.80
2453 2800 2.263895 ATACTGGCCCCTCAAGTGTA 57.736 50.000 0.00 0.00 0.00 2.90
2467 2814 6.239572 CCCTCAAGTGTAAAACCATTTGGATT 60.240 38.462 3.01 0.00 38.94 3.01
2468 2815 7.216494 CCTCAAGTGTAAAACCATTTGGATTT 58.784 34.615 3.01 6.83 41.97 2.17
2469 2816 7.714813 CCTCAAGTGTAAAACCATTTGGATTTT 59.285 33.333 9.72 10.93 40.15 1.82
2470 2817 9.757227 CTCAAGTGTAAAACCATTTGGATTTTA 57.243 29.630 9.72 10.15 40.15 1.52
2471 2818 9.535878 TCAAGTGTAAAACCATTTGGATTTTAC 57.464 29.630 23.26 23.26 43.95 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.872952 CACGCAGAAATCCAACTGACA 59.127 47.619 0.00 0.00 36.38 3.58
64 73 4.574674 ATCAGGTTCAGTTCTTGGCATA 57.425 40.909 0.00 0.00 0.00 3.14
149 160 2.743928 GAGTGAAGTGCTGGCCGG 60.744 66.667 7.41 7.41 0.00 6.13
156 167 3.425625 CGTGAGTAGAGAGAGTGAAGTGC 60.426 52.174 0.00 0.00 0.00 4.40
186 197 4.144297 TGCTCATGGATTAGTTAATGGCC 58.856 43.478 0.00 0.00 0.00 5.36
187 198 4.217118 CCTGCTCATGGATTAGTTAATGGC 59.783 45.833 0.00 0.00 0.00 4.40
204 217 0.036858 GAGTGGAACAGGACCTGCTC 60.037 60.000 21.95 18.47 41.80 4.26
243 256 4.710695 TGTGCGCGTACGTCTGGG 62.711 66.667 22.16 0.00 42.83 4.45
263 280 0.106769 TCCTCTGCGCTCTGAGAGAT 60.107 55.000 20.64 0.00 38.42 2.75
626 651 1.392589 GAGGCAGTCAGAGAGAGAGG 58.607 60.000 0.00 0.00 0.00 3.69
802 827 3.585990 CGGCCATTGATGCGGGAC 61.586 66.667 2.24 0.00 0.00 4.46
953 985 4.492160 CAAGAGCTCGCGCCGGTA 62.492 66.667 8.37 0.00 36.60 4.02
979 1015 3.508840 CCCAAGAATCCCGCGTGC 61.509 66.667 4.92 0.00 0.00 5.34
980 1016 1.369091 CTTCCCAAGAATCCCGCGTG 61.369 60.000 4.92 0.00 0.00 5.34
986 1022 3.543680 TCGTCATCTTCCCAAGAATCC 57.456 47.619 0.00 0.00 41.63 3.01
988 1024 4.383552 CCTCTTCGTCATCTTCCCAAGAAT 60.384 45.833 0.00 0.00 41.63 2.40
989 1025 3.055819 CCTCTTCGTCATCTTCCCAAGAA 60.056 47.826 0.00 0.00 41.63 2.52
991 1027 2.898705 CCTCTTCGTCATCTTCCCAAG 58.101 52.381 0.00 0.00 0.00 3.61
992 1028 1.066143 GCCTCTTCGTCATCTTCCCAA 60.066 52.381 0.00 0.00 0.00 4.12
993 1029 0.537188 GCCTCTTCGTCATCTTCCCA 59.463 55.000 0.00 0.00 0.00 4.37
994 1030 0.537188 TGCCTCTTCGTCATCTTCCC 59.463 55.000 0.00 0.00 0.00 3.97
1004 1042 2.125912 CAGGACCGTGCCTCTTCG 60.126 66.667 0.00 0.00 35.66 3.79
1040 1078 1.657804 GAGGAGAAGAAGGGGGTGAA 58.342 55.000 0.00 0.00 0.00 3.18
1044 1082 1.045911 CGAGGAGGAGAAGAAGGGGG 61.046 65.000 0.00 0.00 0.00 5.40
1129 1167 5.183331 GGCATTGCACATAGAGATCATTCAT 59.817 40.000 11.39 0.00 0.00 2.57
1130 1168 4.517832 GGCATTGCACATAGAGATCATTCA 59.482 41.667 11.39 0.00 0.00 2.57
1131 1169 4.517832 TGGCATTGCACATAGAGATCATTC 59.482 41.667 11.39 0.00 0.00 2.67
1132 1170 4.466827 TGGCATTGCACATAGAGATCATT 58.533 39.130 11.39 0.00 0.00 2.57
1173 1211 8.900781 CCAGAATGTGATTCAAGTTAGATTCAT 58.099 33.333 0.00 0.00 41.71 2.57
1177 1215 6.182627 TGCCAGAATGTGATTCAAGTTAGAT 58.817 36.000 0.00 0.00 41.71 1.98
1187 1225 3.318275 GCATCATCTGCCAGAATGTGATT 59.682 43.478 6.56 0.00 45.66 2.57
1216 1255 4.389576 CGCTGCACTGCCGGTTTC 62.390 66.667 1.90 0.00 0.00 2.78
1274 1316 3.839432 CCCCTTCTCCTCCGTCGC 61.839 72.222 0.00 0.00 0.00 5.19
1275 1317 1.946475 GAACCCCTTCTCCTCCGTCG 61.946 65.000 0.00 0.00 0.00 5.12
1276 1318 1.615165 GGAACCCCTTCTCCTCCGTC 61.615 65.000 0.00 0.00 0.00 4.79
1277 1319 1.612739 GGAACCCCTTCTCCTCCGT 60.613 63.158 0.00 0.00 0.00 4.69
1278 1320 1.306226 AGGAACCCCTTCTCCTCCG 60.306 63.158 0.00 0.00 40.78 4.63
1279 1321 1.916206 GCAGGAACCCCTTCTCCTCC 61.916 65.000 0.00 0.00 42.02 4.30
1378 1432 1.467734 GAGCACTTGAAGCTGACCATG 59.532 52.381 0.00 0.00 43.58 3.66
1456 1510 0.252239 TGAGCTAGCTTGAGGGGACA 60.252 55.000 20.42 6.54 0.00 4.02
1484 1538 1.089481 TGCGCGTGGGAAATCATCTC 61.089 55.000 8.43 0.00 0.00 2.75
1604 1668 5.681105 CCGAGTCATAATTTACAAAATGCCG 59.319 40.000 0.00 0.00 0.00 5.69
1606 1670 6.472163 CCACCGAGTCATAATTTACAAAATGC 59.528 38.462 0.00 0.00 0.00 3.56
1705 1810 4.770795 ACAATAAACCGAGCAGCTATCTT 58.229 39.130 0.00 0.00 0.00 2.40
1707 1812 6.479001 TCTTAACAATAAACCGAGCAGCTATC 59.521 38.462 0.00 0.00 0.00 2.08
1708 1813 6.346096 TCTTAACAATAAACCGAGCAGCTAT 58.654 36.000 0.00 0.00 0.00 2.97
1709 1814 5.726397 TCTTAACAATAAACCGAGCAGCTA 58.274 37.500 0.00 0.00 0.00 3.32
1710 1815 4.575885 TCTTAACAATAAACCGAGCAGCT 58.424 39.130 0.00 0.00 0.00 4.24
1711 1816 4.939509 TCTTAACAATAAACCGAGCAGC 57.060 40.909 0.00 0.00 0.00 5.25
1712 1817 7.216317 CGATTTTCTTAACAATAAACCGAGCAG 59.784 37.037 0.00 0.00 0.00 4.24
1713 1818 7.018826 CGATTTTCTTAACAATAAACCGAGCA 58.981 34.615 0.00 0.00 0.00 4.26
1714 1819 7.019418 ACGATTTTCTTAACAATAAACCGAGC 58.981 34.615 0.00 0.00 0.00 5.03
1715 1820 8.944212 AACGATTTTCTTAACAATAAACCGAG 57.056 30.769 0.00 0.00 0.00 4.63
1724 1829 8.284693 GCTACCTGTTAACGATTTTCTTAACAA 58.715 33.333 0.26 0.00 40.57 2.83
1725 1830 7.658575 AGCTACCTGTTAACGATTTTCTTAACA 59.341 33.333 0.26 6.61 39.45 2.41
1726 1831 7.955864 CAGCTACCTGTTAACGATTTTCTTAAC 59.044 37.037 0.26 0.00 34.65 2.01
1727 1832 7.360607 GCAGCTACCTGTTAACGATTTTCTTAA 60.361 37.037 0.26 0.00 41.26 1.85
1728 1833 6.091713 GCAGCTACCTGTTAACGATTTTCTTA 59.908 38.462 0.26 0.00 41.26 2.10
1730 1835 4.392138 GCAGCTACCTGTTAACGATTTTCT 59.608 41.667 0.26 0.00 41.26 2.52
1731 1836 4.392138 AGCAGCTACCTGTTAACGATTTTC 59.608 41.667 0.00 0.00 41.26 2.29
1732 1837 4.324267 AGCAGCTACCTGTTAACGATTTT 58.676 39.130 0.00 0.00 41.26 1.82
1733 1838 3.933332 GAGCAGCTACCTGTTAACGATTT 59.067 43.478 0.00 0.00 41.26 2.17
1734 1839 3.522553 GAGCAGCTACCTGTTAACGATT 58.477 45.455 0.00 0.00 41.26 3.34
1735 1840 2.479730 CGAGCAGCTACCTGTTAACGAT 60.480 50.000 0.00 0.00 41.26 3.73
1737 1842 1.269166 CGAGCAGCTACCTGTTAACG 58.731 55.000 0.00 0.00 41.26 3.18
1738 1843 1.067071 ACCGAGCAGCTACCTGTTAAC 60.067 52.381 0.00 0.00 41.26 2.01
1739 1844 1.263356 ACCGAGCAGCTACCTGTTAA 58.737 50.000 0.00 0.00 41.26 2.01
1741 1846 0.320771 CAACCGAGCAGCTACCTGTT 60.321 55.000 0.00 0.00 41.26 3.16
1742 1847 1.293498 CAACCGAGCAGCTACCTGT 59.707 57.895 0.00 0.00 41.26 4.00
1743 1848 1.448540 CCAACCGAGCAGCTACCTG 60.449 63.158 0.00 0.00 42.13 4.00
1744 1849 1.481056 AACCAACCGAGCAGCTACCT 61.481 55.000 0.00 0.00 0.00 3.08
1745 1850 1.003718 AACCAACCGAGCAGCTACC 60.004 57.895 0.00 0.00 0.00 3.18
1746 1851 1.298859 CCAACCAACCGAGCAGCTAC 61.299 60.000 0.00 0.00 0.00 3.58
1747 1852 1.003839 CCAACCAACCGAGCAGCTA 60.004 57.895 0.00 0.00 0.00 3.32
1748 1853 2.281761 CCAACCAACCGAGCAGCT 60.282 61.111 0.00 0.00 0.00 4.24
1749 1854 2.594592 ACCAACCAACCGAGCAGC 60.595 61.111 0.00 0.00 0.00 5.25
1750 1855 1.227823 TCACCAACCAACCGAGCAG 60.228 57.895 0.00 0.00 0.00 4.24
1751 1856 1.227823 CTCACCAACCAACCGAGCA 60.228 57.895 0.00 0.00 0.00 4.26
1752 1857 0.034337 TACTCACCAACCAACCGAGC 59.966 55.000 0.00 0.00 0.00 5.03
1753 1858 1.337823 CCTACTCACCAACCAACCGAG 60.338 57.143 0.00 0.00 0.00 4.63
1754 1859 0.682852 CCTACTCACCAACCAACCGA 59.317 55.000 0.00 0.00 0.00 4.69
1755 1860 0.321298 CCCTACTCACCAACCAACCG 60.321 60.000 0.00 0.00 0.00 4.44
1756 1861 1.061546 TCCCTACTCACCAACCAACC 58.938 55.000 0.00 0.00 0.00 3.77
1757 1862 2.943036 TTCCCTACTCACCAACCAAC 57.057 50.000 0.00 0.00 0.00 3.77
1758 1863 5.586155 TTAATTCCCTACTCACCAACCAA 57.414 39.130 0.00 0.00 0.00 3.67
1759 1864 5.789574 ATTAATTCCCTACTCACCAACCA 57.210 39.130 0.00 0.00 0.00 3.67
1760 1865 6.296803 CCTATTAATTCCCTACTCACCAACC 58.703 44.000 0.00 0.00 0.00 3.77
1761 1866 5.763698 GCCTATTAATTCCCTACTCACCAAC 59.236 44.000 0.00 0.00 0.00 3.77
1762 1867 5.670361 AGCCTATTAATTCCCTACTCACCAA 59.330 40.000 0.00 0.00 0.00 3.67
1763 1868 5.224441 AGCCTATTAATTCCCTACTCACCA 58.776 41.667 0.00 0.00 0.00 4.17
1764 1869 5.827326 AGCCTATTAATTCCCTACTCACC 57.173 43.478 0.00 0.00 0.00 4.02
1765 1870 8.594550 TGATTAGCCTATTAATTCCCTACTCAC 58.405 37.037 0.00 0.00 0.00 3.51
1766 1871 8.736097 TGATTAGCCTATTAATTCCCTACTCA 57.264 34.615 0.00 0.23 0.00 3.41
1767 1872 8.817876 ACTGATTAGCCTATTAATTCCCTACTC 58.182 37.037 0.00 0.00 0.00 2.59
1768 1873 8.743636 ACTGATTAGCCTATTAATTCCCTACT 57.256 34.615 0.00 0.00 0.00 2.57
1777 1882 9.692749 CGTCTGATTAACTGATTAGCCTATTAA 57.307 33.333 0.00 0.00 0.00 1.40
1778 1883 8.304596 CCGTCTGATTAACTGATTAGCCTATTA 58.695 37.037 0.00 0.00 0.00 0.98
1779 1884 7.155328 CCGTCTGATTAACTGATTAGCCTATT 58.845 38.462 0.00 0.00 0.00 1.73
1780 1885 6.267928 ACCGTCTGATTAACTGATTAGCCTAT 59.732 38.462 0.00 0.00 0.00 2.57
1781 1886 5.597182 ACCGTCTGATTAACTGATTAGCCTA 59.403 40.000 0.00 0.00 0.00 3.93
1782 1887 4.406003 ACCGTCTGATTAACTGATTAGCCT 59.594 41.667 0.00 0.00 0.00 4.58
1783 1888 4.694339 ACCGTCTGATTAACTGATTAGCC 58.306 43.478 0.00 0.00 0.00 3.93
1784 1889 6.663944 AAACCGTCTGATTAACTGATTAGC 57.336 37.500 0.00 0.00 0.00 3.09
1785 1890 9.529325 TGATAAACCGTCTGATTAACTGATTAG 57.471 33.333 0.00 0.00 0.00 1.73
1786 1891 9.529325 CTGATAAACCGTCTGATTAACTGATTA 57.471 33.333 0.00 0.00 0.00 1.75
1787 1892 8.041323 ACTGATAAACCGTCTGATTAACTGATT 58.959 33.333 0.00 0.00 0.00 2.57
1788 1893 7.556844 ACTGATAAACCGTCTGATTAACTGAT 58.443 34.615 0.00 0.00 0.00 2.90
1789 1894 6.931838 ACTGATAAACCGTCTGATTAACTGA 58.068 36.000 0.00 0.00 0.00 3.41
1790 1895 7.596749 AACTGATAAACCGTCTGATTAACTG 57.403 36.000 0.00 0.00 0.00 3.16
1791 1896 9.886132 ATAAACTGATAAACCGTCTGATTAACT 57.114 29.630 0.00 0.00 0.00 2.24
1793 1898 9.027129 CGATAAACTGATAAACCGTCTGATTAA 57.973 33.333 0.00 0.00 0.00 1.40
1794 1899 7.650504 CCGATAAACTGATAAACCGTCTGATTA 59.349 37.037 0.00 0.00 0.00 1.75
1795 1900 6.479001 CCGATAAACTGATAAACCGTCTGATT 59.521 38.462 0.00 0.00 0.00 2.57
1796 1901 5.983720 CCGATAAACTGATAAACCGTCTGAT 59.016 40.000 0.00 0.00 0.00 2.90
1797 1902 5.345702 CCGATAAACTGATAAACCGTCTGA 58.654 41.667 0.00 0.00 0.00 3.27
1798 1903 4.025979 GCCGATAAACTGATAAACCGTCTG 60.026 45.833 0.00 0.00 0.00 3.51
1799 1904 4.117685 GCCGATAAACTGATAAACCGTCT 58.882 43.478 0.00 0.00 0.00 4.18
1800 1905 4.117685 AGCCGATAAACTGATAAACCGTC 58.882 43.478 0.00 0.00 0.00 4.79
1801 1906 4.133013 AGCCGATAAACTGATAAACCGT 57.867 40.909 0.00 0.00 0.00 4.83
1802 1907 5.287226 AGTAGCCGATAAACTGATAAACCG 58.713 41.667 0.00 0.00 0.00 4.44
1803 1908 5.401674 CGAGTAGCCGATAAACTGATAAACC 59.598 44.000 0.00 0.00 0.00 3.27
1804 1909 5.401674 CCGAGTAGCCGATAAACTGATAAAC 59.598 44.000 0.00 0.00 0.00 2.01
1805 1910 5.068198 ACCGAGTAGCCGATAAACTGATAAA 59.932 40.000 0.00 0.00 0.00 1.40
1806 1911 4.581824 ACCGAGTAGCCGATAAACTGATAA 59.418 41.667 0.00 0.00 0.00 1.75
1807 1912 4.023450 CACCGAGTAGCCGATAAACTGATA 60.023 45.833 0.00 0.00 0.00 2.15
1808 1913 2.957006 ACCGAGTAGCCGATAAACTGAT 59.043 45.455 0.00 0.00 0.00 2.90
1809 1914 2.098607 CACCGAGTAGCCGATAAACTGA 59.901 50.000 0.00 0.00 0.00 3.41
1810 1915 2.098607 TCACCGAGTAGCCGATAAACTG 59.901 50.000 0.00 0.00 0.00 3.16
1811 1916 2.098770 GTCACCGAGTAGCCGATAAACT 59.901 50.000 0.00 0.00 0.00 2.66
1812 1917 2.457970 GTCACCGAGTAGCCGATAAAC 58.542 52.381 0.00 0.00 0.00 2.01
1813 1918 1.406539 GGTCACCGAGTAGCCGATAAA 59.593 52.381 0.00 0.00 0.00 1.40
1814 1919 1.027357 GGTCACCGAGTAGCCGATAA 58.973 55.000 0.00 0.00 0.00 1.75
1815 1920 0.820891 GGGTCACCGAGTAGCCGATA 60.821 60.000 0.00 0.00 0.00 2.92
1816 1921 2.125961 GGGTCACCGAGTAGCCGAT 61.126 63.158 0.00 0.00 0.00 4.18
1817 1922 1.913951 TAGGGTCACCGAGTAGCCGA 61.914 60.000 0.00 0.00 43.47 5.54
1818 1923 1.452651 TAGGGTCACCGAGTAGCCG 60.453 63.158 0.00 0.00 43.47 5.52
1819 1924 1.722636 CGTAGGGTCACCGAGTAGCC 61.723 65.000 0.00 0.00 43.47 3.93
1820 1925 0.745845 TCGTAGGGTCACCGAGTAGC 60.746 60.000 0.00 0.00 43.47 3.58
1821 1926 1.297664 CTCGTAGGGTCACCGAGTAG 58.702 60.000 0.00 0.00 42.26 2.57
1822 1927 3.465990 CTCGTAGGGTCACCGAGTA 57.534 57.895 0.00 0.00 42.26 2.59
1823 1928 4.315588 CTCGTAGGGTCACCGAGT 57.684 61.111 0.00 0.00 42.26 4.18
1825 1930 0.107508 CCTACTCGTAGGGTCACCGA 60.108 60.000 14.08 0.00 46.96 4.69
1826 1931 2.401967 CCTACTCGTAGGGTCACCG 58.598 63.158 14.08 0.00 46.96 4.94
1834 1939 1.315690 TGCCGATTCCCTACTCGTAG 58.684 55.000 0.00 0.00 33.11 3.51
1835 1940 1.679680 CTTGCCGATTCCCTACTCGTA 59.320 52.381 0.00 0.00 33.11 3.43
1836 1941 0.460311 CTTGCCGATTCCCTACTCGT 59.540 55.000 0.00 0.00 33.11 4.18
1837 1942 0.460311 ACTTGCCGATTCCCTACTCG 59.540 55.000 0.00 0.00 34.73 4.18
1838 1943 2.693267 AACTTGCCGATTCCCTACTC 57.307 50.000 0.00 0.00 0.00 2.59
1839 1944 3.518303 AGTTAACTTGCCGATTCCCTACT 59.482 43.478 1.12 0.00 0.00 2.57
1840 1945 3.621715 CAGTTAACTTGCCGATTCCCTAC 59.378 47.826 5.07 0.00 0.00 3.18
1841 1946 3.370103 CCAGTTAACTTGCCGATTCCCTA 60.370 47.826 5.07 0.00 0.00 3.53
1842 1947 2.618045 CCAGTTAACTTGCCGATTCCCT 60.618 50.000 5.07 0.00 0.00 4.20
1843 1948 1.743394 CCAGTTAACTTGCCGATTCCC 59.257 52.381 5.07 0.00 0.00 3.97
1844 1949 2.433436 ACCAGTTAACTTGCCGATTCC 58.567 47.619 5.07 0.00 0.00 3.01
1845 1950 5.616488 TTAACCAGTTAACTTGCCGATTC 57.384 39.130 5.07 0.00 30.78 2.52
1846 1951 6.386654 CAATTAACCAGTTAACTTGCCGATT 58.613 36.000 5.07 1.86 37.80 3.34
1847 1952 5.105917 CCAATTAACCAGTTAACTTGCCGAT 60.106 40.000 5.07 0.00 37.80 4.18
1848 1953 4.216687 CCAATTAACCAGTTAACTTGCCGA 59.783 41.667 5.07 0.00 37.80 5.54
1849 1954 4.216687 TCCAATTAACCAGTTAACTTGCCG 59.783 41.667 5.07 0.00 37.80 5.69
1850 1955 5.466819 GTCCAATTAACCAGTTAACTTGCC 58.533 41.667 5.07 3.12 37.80 4.52
1851 1956 5.049267 TCGTCCAATTAACCAGTTAACTTGC 60.049 40.000 5.07 1.47 37.80 4.01
1852 1957 6.548441 TCGTCCAATTAACCAGTTAACTTG 57.452 37.500 5.07 5.14 37.80 3.16
1853 1958 7.754851 ATTCGTCCAATTAACCAGTTAACTT 57.245 32.000 5.07 0.00 37.80 2.66
1854 1959 7.664318 AGAATTCGTCCAATTAACCAGTTAACT 59.336 33.333 1.12 1.12 37.80 2.24
1855 1960 7.813645 AGAATTCGTCCAATTAACCAGTTAAC 58.186 34.615 5.16 0.00 37.80 2.01
1856 1961 7.989416 AGAATTCGTCCAATTAACCAGTTAA 57.011 32.000 5.51 5.51 39.12 2.01
1857 1962 7.662258 TCAAGAATTCGTCCAATTAACCAGTTA 59.338 33.333 0.00 0.00 34.60 2.24
1858 1963 6.488683 TCAAGAATTCGTCCAATTAACCAGTT 59.511 34.615 0.00 0.00 34.60 3.16
1859 1964 6.001460 TCAAGAATTCGTCCAATTAACCAGT 58.999 36.000 0.00 0.00 34.60 4.00
1860 1965 6.494893 TCAAGAATTCGTCCAATTAACCAG 57.505 37.500 0.00 0.00 34.60 4.00
1861 1966 6.885952 TTCAAGAATTCGTCCAATTAACCA 57.114 33.333 0.00 0.00 34.60 3.67
1866 1971 7.917505 GCAGATATTTCAAGAATTCGTCCAATT 59.082 33.333 0.00 0.00 37.41 2.32
1867 1972 7.067372 TGCAGATATTTCAAGAATTCGTCCAAT 59.933 33.333 0.00 0.49 0.00 3.16
1868 1973 6.374053 TGCAGATATTTCAAGAATTCGTCCAA 59.626 34.615 0.00 0.00 0.00 3.53
1869 1974 5.879777 TGCAGATATTTCAAGAATTCGTCCA 59.120 36.000 0.00 0.00 0.00 4.02
1870 1975 6.363577 TGCAGATATTTCAAGAATTCGTCC 57.636 37.500 0.00 0.00 0.00 4.79
1871 1976 8.673626 TTTTGCAGATATTTCAAGAATTCGTC 57.326 30.769 0.00 0.00 0.00 4.20
1872 1977 9.294030 GATTTTGCAGATATTTCAAGAATTCGT 57.706 29.630 0.00 0.00 0.00 3.85
1873 1978 9.512435 AGATTTTGCAGATATTTCAAGAATTCG 57.488 29.630 0.00 0.00 0.00 3.34
1877 1982 9.426837 CCAAAGATTTTGCAGATATTTCAAGAA 57.573 29.630 2.83 0.00 0.00 2.52
1878 1983 7.546667 GCCAAAGATTTTGCAGATATTTCAAGA 59.453 33.333 2.83 0.00 0.00 3.02
1879 1984 7.332430 TGCCAAAGATTTTGCAGATATTTCAAG 59.668 33.333 0.32 0.00 34.40 3.02
1880 1985 7.118101 GTGCCAAAGATTTTGCAGATATTTCAA 59.882 33.333 4.47 0.00 39.15 2.69
1881 1986 6.591062 GTGCCAAAGATTTTGCAGATATTTCA 59.409 34.615 4.47 0.00 39.15 2.69
1882 1987 6.591062 TGTGCCAAAGATTTTGCAGATATTTC 59.409 34.615 4.47 0.00 39.15 2.17
1883 1988 6.369615 GTGTGCCAAAGATTTTGCAGATATTT 59.630 34.615 4.47 0.00 39.15 1.40
1884 1989 5.870978 GTGTGCCAAAGATTTTGCAGATATT 59.129 36.000 4.47 0.00 39.15 1.28
1885 1990 5.413499 GTGTGCCAAAGATTTTGCAGATAT 58.587 37.500 4.47 0.00 39.15 1.63
1886 1991 4.615682 CGTGTGCCAAAGATTTTGCAGATA 60.616 41.667 4.47 0.00 39.15 1.98
1887 1992 3.656559 GTGTGCCAAAGATTTTGCAGAT 58.343 40.909 4.47 0.00 39.15 2.90
1888 1993 2.543445 CGTGTGCCAAAGATTTTGCAGA 60.543 45.455 4.47 1.22 39.15 4.26
1889 1994 1.788308 CGTGTGCCAAAGATTTTGCAG 59.212 47.619 4.47 0.00 39.15 4.41
1890 1995 1.850377 CGTGTGCCAAAGATTTTGCA 58.150 45.000 0.32 0.32 36.60 4.08
1891 1996 0.508213 GCGTGTGCCAAAGATTTTGC 59.492 50.000 0.00 0.00 33.98 3.68
1892 1997 2.138596 AGCGTGTGCCAAAGATTTTG 57.861 45.000 0.00 0.00 44.31 2.44
1893 1998 3.317993 ACTTAGCGTGTGCCAAAGATTTT 59.682 39.130 6.88 0.00 44.31 1.82
1905 2240 5.302360 TCCAAAAAGTGATACTTAGCGTGT 58.698 37.500 0.00 0.00 37.47 4.49
2025 2363 4.472496 TGGTATTATCCCGCAGTACAGTA 58.528 43.478 0.00 0.00 0.00 2.74
2049 2392 4.755266 AGTCCACTACTGACAGTGTTTT 57.245 40.909 18.58 0.00 43.68 2.43
2050 2393 5.739358 GCTTAGTCCACTACTGACAGTGTTT 60.739 44.000 18.58 0.00 43.68 2.83
2068 2411 1.235724 GTGCAGGTTTTCGGCTTAGT 58.764 50.000 0.00 0.00 0.00 2.24
2069 2412 0.521735 GGTGCAGGTTTTCGGCTTAG 59.478 55.000 0.00 0.00 0.00 2.18
2091 2434 8.458843 TCTAAGGTAGTTTATCTTTTGCAATGC 58.541 33.333 0.00 0.00 30.42 3.56
2139 2483 1.697432 TCCACACCTCAACCCTACAAG 59.303 52.381 0.00 0.00 0.00 3.16
2141 2485 1.053424 GTCCACACCTCAACCCTACA 58.947 55.000 0.00 0.00 0.00 2.74
2155 2499 2.670019 ACCTAAAGTTTGGGGTCCAC 57.330 50.000 20.82 0.00 35.25 4.02
2156 2500 4.810584 TTTACCTAAAGTTTGGGGTCCA 57.189 40.909 20.82 6.62 35.25 4.02
2171 2515 9.405587 CACATGAAACGACAAATATTTTTACCT 57.594 29.630 0.00 0.00 0.00 3.08
2182 2526 3.440522 TCCACAACACATGAAACGACAAA 59.559 39.130 0.00 0.00 0.00 2.83
2187 2531 5.098893 TCTTTTTCCACAACACATGAAACG 58.901 37.500 0.00 0.00 0.00 3.60
2189 2533 6.405731 CCTCTCTTTTTCCACAACACATGAAA 60.406 38.462 0.00 0.00 0.00 2.69
2218 2562 8.653191 TGGTGTAAGACTTTATGTTAGAAAGGA 58.347 33.333 0.00 0.00 38.07 3.36
2240 2584 4.021102 ACTTTGTGGGAAGAGTATGGTG 57.979 45.455 0.00 0.00 0.00 4.17
2273 2619 7.218614 TCCGTACATTCTAAGTTTTGAAAGGA 58.781 34.615 0.00 0.00 0.00 3.36
2274 2620 7.429636 TCCGTACATTCTAAGTTTTGAAAGG 57.570 36.000 0.00 0.00 0.00 3.11
2277 2623 9.672086 CAAAATCCGTACATTCTAAGTTTTGAA 57.328 29.630 0.00 0.00 36.60 2.69
2297 2643 7.072030 GCTTATGTATGATCCACGTCAAAATC 58.928 38.462 0.00 0.00 0.00 2.17
2299 2645 5.877564 TGCTTATGTATGATCCACGTCAAAA 59.122 36.000 0.00 0.00 0.00 2.44
2310 2656 9.565090 ACAAATAGTCATGTGCTTATGTATGAT 57.435 29.630 0.00 0.00 32.76 2.45
2324 2670 5.647658 TCAAGCCAGGTTACAAATAGTCATG 59.352 40.000 0.00 0.00 0.00 3.07
2325 2671 5.815581 TCAAGCCAGGTTACAAATAGTCAT 58.184 37.500 0.00 0.00 0.00 3.06
2335 2681 9.944376 TTCATATATAGAATCAAGCCAGGTTAC 57.056 33.333 0.00 0.00 0.00 2.50
2369 2716 4.551702 ATTTGAAGGGCCAAATTGTACC 57.448 40.909 6.18 0.00 42.26 3.34
2375 2722 3.522750 TGCCAATATTTGAAGGGCCAAAT 59.477 39.130 6.18 5.89 45.52 2.32
2398 2745 6.313164 GCAGTAGAGCGACCTAAATTAAACTT 59.687 38.462 0.00 0.00 0.00 2.66
2402 2749 5.333299 TGCAGTAGAGCGACCTAAATTAA 57.667 39.130 0.00 0.00 37.31 1.40
2406 2753 2.297880 TGTTGCAGTAGAGCGACCTAAA 59.702 45.455 4.06 0.00 46.19 1.85
2409 2756 0.038159 GTGTTGCAGTAGAGCGACCT 60.038 55.000 4.06 0.00 46.19 3.85
2414 2761 7.169982 CCAGTATTTATAGTGTTGCAGTAGAGC 59.830 40.741 4.39 0.00 32.96 4.09
2415 2762 7.169982 GCCAGTATTTATAGTGTTGCAGTAGAG 59.830 40.741 4.39 0.00 32.96 2.43
2422 2769 3.568430 GGGGCCAGTATTTATAGTGTTGC 59.432 47.826 4.39 2.08 32.96 4.17
2437 2784 1.886542 GTTTTACACTTGAGGGGCCAG 59.113 52.381 4.39 0.00 0.00 4.85
2441 2788 4.262420 CCAAATGGTTTTACACTTGAGGGG 60.262 45.833 0.00 0.00 0.00 4.79
2443 2790 5.782893 TCCAAATGGTTTTACACTTGAGG 57.217 39.130 0.00 0.00 36.34 3.86


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

AutoCloner maintained by Alex Coulton.