Multiple sequence alignment - TraesCS3B01G574100

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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 TraesCS3B01G574100 chr3B 100.000 2288 0 0 1 2288 804610341 804612628 0.000000e+00 4226.0
1 TraesCS3B01G574100 chr3D 93.163 1726 86 7 1 1704 81833379 81835094 0.000000e+00 2505.0
2 TraesCS3B01G574100 chr3D 91.447 1742 98 16 1 1707 41618540 41616815 0.000000e+00 2344.0
3 TraesCS3B01G574100 chr3D 92.228 1261 60 6 475 1704 6288084 6289337 0.000000e+00 1751.0
4 TraesCS3B01G574100 chr3D 81.651 109 14 3 1704 1810 10830659 10830763 4.050000e-13 86.1
5 TraesCS3B01G574100 chr7B 92.932 1712 107 7 1 1707 43687284 43688986 0.000000e+00 2479.0
6 TraesCS3B01G574100 chr6B 92.515 1710 110 8 1 1702 457228458 457230157 0.000000e+00 2433.0
7 TraesCS3B01G574100 chr6B 91.312 1715 133 8 1 1707 89607954 89606248 0.000000e+00 2327.0
8 TraesCS3B01G574100 chr2D 92.388 1721 81 21 13 1710 88299485 88301178 0.000000e+00 2407.0
9 TraesCS3B01G574100 chr7A 91.715 1726 112 8 1 1704 221704937 221706653 0.000000e+00 2366.0
10 TraesCS3B01G574100 chr3A 91.873 1698 106 14 37 1709 71154457 71156147 0.000000e+00 2342.0
11 TraesCS3B01G574100 chr1B 94.009 1519 81 4 1 1518 155744912 155746421 0.000000e+00 2292.0
12 TraesCS3B01G574100 chr2B 91.326 1591 104 14 22 1582 777366059 777367645 0.000000e+00 2143.0
13 TraesCS3B01G574100 chr2B 87.651 1741 130 33 1 1704 23892243 23890551 0.000000e+00 1945.0
14 TraesCS3B01G574100 chr7D 90.524 496 28 3 1226 1704 535799892 535799399 2.480000e-179 638.0


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 TraesCS3B01G574100 chr3B 804610341 804612628 2287 False 4226 4226 100.000 1 2288 1 chr3B.!!$F1 2287
1 TraesCS3B01G574100 chr3D 81833379 81835094 1715 False 2505 2505 93.163 1 1704 1 chr3D.!!$F3 1703
2 TraesCS3B01G574100 chr3D 41616815 41618540 1725 True 2344 2344 91.447 1 1707 1 chr3D.!!$R1 1706
3 TraesCS3B01G574100 chr3D 6288084 6289337 1253 False 1751 1751 92.228 475 1704 1 chr3D.!!$F1 1229
4 TraesCS3B01G574100 chr7B 43687284 43688986 1702 False 2479 2479 92.932 1 1707 1 chr7B.!!$F1 1706
5 TraesCS3B01G574100 chr6B 457228458 457230157 1699 False 2433 2433 92.515 1 1702 1 chr6B.!!$F1 1701
6 TraesCS3B01G574100 chr6B 89606248 89607954 1706 True 2327 2327 91.312 1 1707 1 chr6B.!!$R1 1706
7 TraesCS3B01G574100 chr2D 88299485 88301178 1693 False 2407 2407 92.388 13 1710 1 chr2D.!!$F1 1697
8 TraesCS3B01G574100 chr7A 221704937 221706653 1716 False 2366 2366 91.715 1 1704 1 chr7A.!!$F1 1703
9 TraesCS3B01G574100 chr3A 71154457 71156147 1690 False 2342 2342 91.873 37 1709 1 chr3A.!!$F1 1672
10 TraesCS3B01G574100 chr1B 155744912 155746421 1509 False 2292 2292 94.009 1 1518 1 chr1B.!!$F1 1517
11 TraesCS3B01G574100 chr2B 777366059 777367645 1586 False 2143 2143 91.326 22 1582 1 chr2B.!!$F1 1560
12 TraesCS3B01G574100 chr2B 23890551 23892243 1692 True 1945 1945 87.651 1 1704 1 chr2B.!!$R1 1703

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
389 413 0.401356 TCTGCAGTGGCCTTCATGAA 59.599 50.0 14.67 8.12 40.13 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2331 0.031616 TTGGGTTCCAGGCCAGTTTT 60.032 50.0 5.01 0.0 33.81 2.43 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
73 86 2.879462 GCGGGTCATCGTCGTCAC 60.879 66.667 0.00 0.00 0.00 3.67
220 242 2.244117 CTCCCAGTACACTGCGGCAT 62.244 60.000 1.75 0.00 42.47 4.40
259 281 4.503296 CCCAGTAGTTCTTGTACTTGCACT 60.503 45.833 0.00 0.00 0.00 4.40
325 347 3.006940 GCCCAACGAATGATGTCAACTA 58.993 45.455 0.00 0.00 0.00 2.24
337 361 2.895372 CAACTACCATCGCGCCCC 60.895 66.667 0.00 0.00 0.00 5.80
389 413 0.401356 TCTGCAGTGGCCTTCATGAA 59.599 50.000 14.67 8.12 40.13 2.57
492 517 2.363795 CCAGCCGACCACCCTAGA 60.364 66.667 0.00 0.00 0.00 2.43
508 533 2.192263 CTAGAAAGAAGGCCCTCCAGT 58.808 52.381 0.00 0.00 33.74 4.00
774 847 2.988839 AATGAGGTGCTCCTGGCCC 61.989 63.158 13.11 0.00 45.24 5.80
810 883 1.077265 CAGCCCCTTCACCCAATGT 59.923 57.895 0.00 0.00 0.00 2.71
830 903 1.672030 CGATGAGGTTGTGCTGCCA 60.672 57.895 0.00 0.00 0.00 4.92
998 1071 1.699656 CCGAAGCTTGAGTGCATCCG 61.700 60.000 2.10 0.00 34.99 4.18
1139 1213 3.643554 GGGTTGGGCCACCTACGT 61.644 66.667 19.97 0.00 42.49 3.57
1229 1303 2.612212 TCATCATCTTCGACGACGATGA 59.388 45.455 34.85 34.85 46.16 2.92
1236 1310 2.622546 TCGACGACGATGACATTGAA 57.377 45.000 5.75 0.00 43.81 2.69
1273 1347 0.944311 GAAGCACGACGAAGCCTTCA 60.944 55.000 0.00 0.00 0.00 3.02
1359 1455 7.534723 AGAACTGTTATGAAGTGTGGTACTA 57.465 36.000 0.00 0.00 39.18 1.82
1439 1540 0.110295 TGTGCTACATGGTTGTGCCT 59.890 50.000 0.00 0.00 36.53 4.75
1443 1544 1.401905 GCTACATGGTTGTGCCTAAGC 59.598 52.381 0.00 0.00 36.53 3.09
1491 1592 3.876309 AAAGGTTATCACACACCAGGT 57.124 42.857 0.00 0.00 35.25 4.00
1537 1638 4.658063 CCTTGGGTTTGTCCACTAACATA 58.342 43.478 6.41 0.00 36.38 2.29
1710 1813 1.588674 CAACCAAACACGCACTAGGA 58.411 50.000 0.00 0.00 0.00 2.94
1711 1814 1.531149 CAACCAAACACGCACTAGGAG 59.469 52.381 0.00 0.00 0.00 3.69
1712 1815 0.602905 ACCAAACACGCACTAGGAGC 60.603 55.000 0.00 0.00 0.00 4.70
1713 1816 0.320771 CCAAACACGCACTAGGAGCT 60.321 55.000 7.68 0.00 0.00 4.09
1714 1817 0.792640 CAAACACGCACTAGGAGCTG 59.207 55.000 0.00 7.33 0.00 4.24
1715 1818 0.320771 AAACACGCACTAGGAGCTGG 60.321 55.000 0.00 2.82 0.00 4.85
1716 1819 1.185618 AACACGCACTAGGAGCTGGA 61.186 55.000 0.00 0.00 0.00 3.86
1717 1820 1.185618 ACACGCACTAGGAGCTGGAA 61.186 55.000 0.00 0.00 0.00 3.53
1718 1821 0.737715 CACGCACTAGGAGCTGGAAC 60.738 60.000 0.00 0.00 0.00 3.62
1719 1822 1.185618 ACGCACTAGGAGCTGGAACA 61.186 55.000 0.00 0.00 0.00 3.18
1720 1823 0.737715 CGCACTAGGAGCTGGAACAC 60.738 60.000 0.00 0.00 0.00 3.32
1721 1824 0.737715 GCACTAGGAGCTGGAACACG 60.738 60.000 0.00 0.00 0.00 4.49
1722 1825 0.108615 CACTAGGAGCTGGAACACGG 60.109 60.000 0.00 0.00 0.00 4.94
1728 1831 3.365535 GCTGGAACACGGCCAATT 58.634 55.556 2.24 0.00 46.06 2.32
1729 1832 2.562125 GCTGGAACACGGCCAATTA 58.438 52.632 2.24 0.00 46.06 1.40
1730 1833 0.451783 GCTGGAACACGGCCAATTAG 59.548 55.000 2.24 0.00 46.06 1.73
1731 1834 1.821216 CTGGAACACGGCCAATTAGT 58.179 50.000 2.24 0.00 34.44 2.24
1732 1835 2.159382 CTGGAACACGGCCAATTAGTT 58.841 47.619 2.24 0.00 34.44 2.24
1733 1836 3.340034 CTGGAACACGGCCAATTAGTTA 58.660 45.455 2.24 0.00 34.44 2.24
1734 1837 3.340034 TGGAACACGGCCAATTAGTTAG 58.660 45.455 2.24 0.00 31.13 2.34
1735 1838 3.244630 TGGAACACGGCCAATTAGTTAGT 60.245 43.478 2.24 0.00 31.13 2.24
1736 1839 3.754850 GGAACACGGCCAATTAGTTAGTT 59.245 43.478 2.24 0.00 0.00 2.24
1737 1840 4.216902 GGAACACGGCCAATTAGTTAGTTT 59.783 41.667 2.24 0.00 0.00 2.66
1738 1841 4.759516 ACACGGCCAATTAGTTAGTTTG 57.240 40.909 2.24 0.00 0.00 2.93
1739 1842 4.139038 ACACGGCCAATTAGTTAGTTTGT 58.861 39.130 2.24 0.00 0.00 2.83
1740 1843 4.023536 ACACGGCCAATTAGTTAGTTTGTG 60.024 41.667 2.24 0.00 0.00 3.33
1741 1844 4.023536 CACGGCCAATTAGTTAGTTTGTGT 60.024 41.667 2.24 0.00 0.00 3.72
1742 1845 4.581409 ACGGCCAATTAGTTAGTTTGTGTT 59.419 37.500 2.24 0.00 0.00 3.32
1743 1846 4.915085 CGGCCAATTAGTTAGTTTGTGTTG 59.085 41.667 2.24 0.00 0.00 3.33
1744 1847 5.278071 CGGCCAATTAGTTAGTTTGTGTTGA 60.278 40.000 2.24 0.00 0.00 3.18
1745 1848 6.569610 CGGCCAATTAGTTAGTTTGTGTTGAT 60.570 38.462 2.24 0.00 0.00 2.57
1746 1849 7.361371 CGGCCAATTAGTTAGTTTGTGTTGATA 60.361 37.037 2.24 0.00 0.00 2.15
1747 1850 8.466798 GGCCAATTAGTTAGTTTGTGTTGATAT 58.533 33.333 0.00 0.00 0.00 1.63
1748 1851 9.289303 GCCAATTAGTTAGTTTGTGTTGATATG 57.711 33.333 0.00 0.00 0.00 1.78
1749 1852 9.289303 CCAATTAGTTAGTTTGTGTTGATATGC 57.711 33.333 0.00 0.00 0.00 3.14
1750 1853 9.838975 CAATTAGTTAGTTTGTGTTGATATGCA 57.161 29.630 0.00 0.00 0.00 3.96
1753 1856 6.324819 AGTTAGTTTGTGTTGATATGCATGC 58.675 36.000 11.82 11.82 0.00 4.06
1754 1857 4.787260 AGTTTGTGTTGATATGCATGCA 57.213 36.364 25.04 25.04 0.00 3.96
1755 1858 5.333299 AGTTTGTGTTGATATGCATGCAT 57.667 34.783 33.92 33.92 40.19 3.96
1756 1859 5.106442 AGTTTGTGTTGATATGCATGCATG 58.894 37.500 37.43 22.70 37.82 4.06
1775 1878 5.258685 CATGCATGCACAAAGTTTGTTAG 57.741 39.130 25.37 9.82 43.23 2.34
1776 1879 3.122297 TGCATGCACAAAGTTTGTTAGC 58.878 40.909 18.46 18.91 43.23 3.09
1777 1880 3.122297 GCATGCACAAAGTTTGTTAGCA 58.878 40.909 26.55 26.55 43.67 3.49
1778 1881 3.555139 GCATGCACAAAGTTTGTTAGCAA 59.445 39.130 27.52 16.42 43.06 3.91
1779 1882 4.318263 GCATGCACAAAGTTTGTTAGCAAG 60.318 41.667 27.52 24.75 43.06 4.01
1780 1883 4.448537 TGCACAAAGTTTGTTAGCAAGT 57.551 36.364 23.87 0.00 43.23 3.16
1781 1884 4.815269 TGCACAAAGTTTGTTAGCAAGTT 58.185 34.783 23.87 0.00 43.23 2.66
1782 1885 5.233988 TGCACAAAGTTTGTTAGCAAGTTT 58.766 33.333 23.87 0.00 43.23 2.66
1783 1886 5.119898 TGCACAAAGTTTGTTAGCAAGTTTG 59.880 36.000 23.87 19.09 43.23 2.93
1784 1887 5.347364 GCACAAAGTTTGTTAGCAAGTTTGA 59.653 36.000 23.82 0.00 43.23 2.69
1785 1888 6.035975 GCACAAAGTTTGTTAGCAAGTTTGAT 59.964 34.615 23.82 12.73 43.23 2.57
1786 1889 7.393327 CACAAAGTTTGTTAGCAAGTTTGATG 58.607 34.615 23.82 17.34 43.23 3.07
1787 1890 6.534793 ACAAAGTTTGTTAGCAAGTTTGATGG 59.465 34.615 23.82 8.38 42.22 3.51
1788 1891 5.200368 AGTTTGTTAGCAAGTTTGATGGG 57.800 39.130 0.00 0.00 35.82 4.00
1789 1892 4.649218 AGTTTGTTAGCAAGTTTGATGGGT 59.351 37.500 0.00 0.00 35.82 4.51
1790 1893 4.582701 TTGTTAGCAAGTTTGATGGGTG 57.417 40.909 0.00 0.00 0.00 4.61
1791 1894 2.890311 TGTTAGCAAGTTTGATGGGTGG 59.110 45.455 0.00 0.00 0.00 4.61
1792 1895 1.544724 TAGCAAGTTTGATGGGTGGC 58.455 50.000 0.00 0.00 0.00 5.01
1793 1896 1.080569 GCAAGTTTGATGGGTGGCG 60.081 57.895 0.00 0.00 0.00 5.69
1794 1897 1.805428 GCAAGTTTGATGGGTGGCGT 61.805 55.000 0.00 0.00 0.00 5.68
1795 1898 0.039256 CAAGTTTGATGGGTGGCGTG 60.039 55.000 0.00 0.00 0.00 5.34
1796 1899 1.178534 AAGTTTGATGGGTGGCGTGG 61.179 55.000 0.00 0.00 0.00 4.94
1797 1900 2.988684 TTTGATGGGTGGCGTGGC 60.989 61.111 0.00 0.00 0.00 5.01
1798 1901 3.799286 TTTGATGGGTGGCGTGGCA 62.799 57.895 0.00 0.00 0.00 4.92
1799 1902 4.720902 TGATGGGTGGCGTGGCAG 62.721 66.667 0.00 0.00 0.00 4.85
1800 1903 4.722700 GATGGGTGGCGTGGCAGT 62.723 66.667 0.00 0.00 0.00 4.40
1801 1904 4.284550 ATGGGTGGCGTGGCAGTT 62.285 61.111 0.00 0.00 0.00 3.16
1803 1906 4.947147 GGGTGGCGTGGCAGTTGA 62.947 66.667 0.00 0.00 0.00 3.18
1804 1907 2.904866 GGTGGCGTGGCAGTTGAA 60.905 61.111 0.00 0.00 0.00 2.69
1805 1908 2.485795 GGTGGCGTGGCAGTTGAAA 61.486 57.895 0.00 0.00 0.00 2.69
1806 1909 1.659794 GTGGCGTGGCAGTTGAAAT 59.340 52.632 0.00 0.00 0.00 2.17
1807 1910 0.878416 GTGGCGTGGCAGTTGAAATA 59.122 50.000 0.00 0.00 0.00 1.40
1808 1911 1.268352 GTGGCGTGGCAGTTGAAATAA 59.732 47.619 0.00 0.00 0.00 1.40
1809 1912 2.094752 GTGGCGTGGCAGTTGAAATAAT 60.095 45.455 0.00 0.00 0.00 1.28
1810 1913 2.560542 TGGCGTGGCAGTTGAAATAATT 59.439 40.909 0.00 0.00 0.00 1.40
1811 1914 3.006323 TGGCGTGGCAGTTGAAATAATTT 59.994 39.130 0.00 0.00 0.00 1.82
1812 1915 3.993736 GGCGTGGCAGTTGAAATAATTTT 59.006 39.130 0.00 0.00 0.00 1.82
1813 1916 4.450757 GGCGTGGCAGTTGAAATAATTTTT 59.549 37.500 0.00 0.00 0.00 1.94
1814 1917 5.389411 GGCGTGGCAGTTGAAATAATTTTTC 60.389 40.000 0.00 6.30 0.00 2.29
1815 1918 5.176590 GCGTGGCAGTTGAAATAATTTTTCA 59.823 36.000 10.04 10.04 36.71 2.69
1816 1919 6.128580 GCGTGGCAGTTGAAATAATTTTTCAT 60.129 34.615 13.12 2.20 38.12 2.57
1817 1920 7.062839 GCGTGGCAGTTGAAATAATTTTTCATA 59.937 33.333 13.12 5.79 38.12 2.15
1818 1921 9.086336 CGTGGCAGTTGAAATAATTTTTCATAT 57.914 29.630 13.12 6.04 38.12 1.78
1899 2002 9.452287 AACATATGAGCAAATTTAAAATTGGCT 57.548 25.926 15.90 12.87 0.00 4.75
1903 2006 8.845413 ATGAGCAAATTTAAAATTGGCTACAA 57.155 26.923 15.90 5.47 41.59 2.41
1904 2007 8.082334 TGAGCAAATTTAAAATTGGCTACAAC 57.918 30.769 15.90 4.58 39.87 3.32
1905 2008 7.930865 TGAGCAAATTTAAAATTGGCTACAACT 59.069 29.630 15.90 4.48 39.87 3.16
1906 2009 8.675705 AGCAAATTTAAAATTGGCTACAACTT 57.324 26.923 15.90 0.00 39.87 2.66
1907 2010 9.119418 AGCAAATTTAAAATTGGCTACAACTTT 57.881 25.926 15.90 0.00 39.17 2.66
1908 2011 9.729023 GCAAATTTAAAATTGGCTACAACTTTT 57.271 25.926 15.90 0.00 37.27 2.27
1911 2014 9.620259 AATTTAAAATTGGCTACAACTTTTGGA 57.380 25.926 0.00 0.00 37.27 3.53
1912 2015 9.620259 ATTTAAAATTGGCTACAACTTTTGGAA 57.380 25.926 0.00 0.00 37.27 3.53
1913 2016 9.449719 TTTAAAATTGGCTACAACTTTTGGAAA 57.550 25.926 0.00 0.00 37.27 3.13
1914 2017 7.929941 AAAATTGGCTACAACTTTTGGAAAA 57.070 28.000 0.00 0.00 39.87 2.29
1915 2018 8.518430 AAAATTGGCTACAACTTTTGGAAAAT 57.482 26.923 0.00 0.00 39.87 1.82
1916 2019 7.495135 AATTGGCTACAACTTTTGGAAAATG 57.505 32.000 0.00 0.00 39.87 2.32
1917 2020 5.606348 TGGCTACAACTTTTGGAAAATGT 57.394 34.783 0.00 0.00 34.12 2.71
1918 2021 5.355596 TGGCTACAACTTTTGGAAAATGTG 58.644 37.500 0.00 0.00 34.12 3.21
1919 2022 4.211164 GGCTACAACTTTTGGAAAATGTGC 59.789 41.667 0.00 0.00 34.12 4.57
1920 2023 4.808364 GCTACAACTTTTGGAAAATGTGCA 59.192 37.500 0.00 0.00 34.12 4.57
1921 2024 5.466393 GCTACAACTTTTGGAAAATGTGCAT 59.534 36.000 0.00 0.00 34.12 3.96
1922 2025 6.644592 GCTACAACTTTTGGAAAATGTGCATA 59.355 34.615 0.00 0.00 34.12 3.14
1923 2026 7.331687 GCTACAACTTTTGGAAAATGTGCATAT 59.668 33.333 0.00 0.00 34.12 1.78
1924 2027 9.206870 CTACAACTTTTGGAAAATGTGCATATT 57.793 29.630 2.38 2.38 34.12 1.28
1925 2028 8.449251 ACAACTTTTGGAAAATGTGCATATTT 57.551 26.923 14.94 14.94 34.12 1.40
1926 2029 8.901793 ACAACTTTTGGAAAATGTGCATATTTT 58.098 25.926 27.79 27.79 41.55 1.82
1927 2030 9.733219 CAACTTTTGGAAAATGTGCATATTTTT 57.267 25.926 27.99 16.60 39.60 1.94
1957 2060 7.421530 TTTTTGAAAACCACAATCGTTTCAA 57.578 28.000 6.37 6.37 32.33 2.69
1958 2061 6.639671 TTTGAAAACCACAATCGTTTCAAG 57.360 33.333 9.55 0.00 32.33 3.02
1959 2062 5.568685 TGAAAACCACAATCGTTTCAAGA 57.431 34.783 0.00 0.00 32.33 3.02
1960 2063 5.955488 TGAAAACCACAATCGTTTCAAGAA 58.045 33.333 0.00 0.00 32.33 2.52
1961 2064 6.390721 TGAAAACCACAATCGTTTCAAGAAA 58.609 32.000 0.00 0.00 32.33 2.52
1962 2065 6.868864 TGAAAACCACAATCGTTTCAAGAAAA 59.131 30.769 0.00 0.00 32.33 2.29
1963 2066 7.385205 TGAAAACCACAATCGTTTCAAGAAAAA 59.615 29.630 0.00 0.00 32.33 1.94
1964 2067 6.641176 AACCACAATCGTTTCAAGAAAAAC 57.359 33.333 0.00 0.00 36.09 2.43
1965 2068 5.106442 ACCACAATCGTTTCAAGAAAAACC 58.894 37.500 0.00 0.00 36.06 3.27
1966 2069 5.105752 CCACAATCGTTTCAAGAAAAACCA 58.894 37.500 0.00 0.00 36.06 3.67
1967 2070 5.578727 CCACAATCGTTTCAAGAAAAACCAA 59.421 36.000 0.00 0.00 36.06 3.67
1968 2071 6.091441 CCACAATCGTTTCAAGAAAAACCAAA 59.909 34.615 0.00 0.00 36.06 3.28
1969 2072 6.953189 CACAATCGTTTCAAGAAAAACCAAAC 59.047 34.615 0.00 0.00 36.06 2.93
1970 2073 6.647067 ACAATCGTTTCAAGAAAAACCAAACA 59.353 30.769 0.00 0.00 36.06 2.83
1971 2074 7.171678 ACAATCGTTTCAAGAAAAACCAAACAA 59.828 29.630 0.00 0.00 36.06 2.83
1972 2075 7.841915 ATCGTTTCAAGAAAAACCAAACAAT 57.158 28.000 0.00 0.00 36.06 2.71
1973 2076 7.659652 TCGTTTCAAGAAAAACCAAACAATT 57.340 28.000 0.00 0.00 36.06 2.32
1974 2077 8.089115 TCGTTTCAAGAAAAACCAAACAATTT 57.911 26.923 0.00 0.00 36.06 1.82
1975 2078 8.560374 TCGTTTCAAGAAAAACCAAACAATTTT 58.440 25.926 0.00 0.00 36.06 1.82
1976 2079 9.175060 CGTTTCAAGAAAAACCAAACAATTTTT 57.825 25.926 0.00 0.00 39.97 1.94
2006 2109 8.961294 AATGAGAAAACATTTGAAATTGTGGA 57.039 26.923 0.00 0.00 37.20 4.02
2007 2110 7.769272 TGAGAAAACATTTGAAATTGTGGAC 57.231 32.000 0.00 0.00 0.00 4.02
2008 2111 7.326454 TGAGAAAACATTTGAAATTGTGGACA 58.674 30.769 0.00 0.00 0.00 4.02
2009 2112 7.986320 TGAGAAAACATTTGAAATTGTGGACAT 59.014 29.630 0.00 0.00 0.00 3.06
2010 2113 9.474920 GAGAAAACATTTGAAATTGTGGACATA 57.525 29.630 0.00 0.00 0.00 2.29
2060 2163 9.579610 CAAAAAGCAAACAATTTTACTAATCGG 57.420 29.630 0.00 0.00 0.00 4.18
2061 2164 7.883229 AAAGCAAACAATTTTACTAATCGGG 57.117 32.000 0.00 0.00 0.00 5.14
2062 2165 6.827586 AGCAAACAATTTTACTAATCGGGA 57.172 33.333 0.00 0.00 0.00 5.14
2063 2166 6.617879 AGCAAACAATTTTACTAATCGGGAC 58.382 36.000 0.00 0.00 0.00 4.46
2064 2167 6.207810 AGCAAACAATTTTACTAATCGGGACA 59.792 34.615 0.00 0.00 0.00 4.02
2065 2168 7.033185 GCAAACAATTTTACTAATCGGGACAT 58.967 34.615 0.00 0.00 0.00 3.06
2066 2169 7.544217 GCAAACAATTTTACTAATCGGGACATT 59.456 33.333 0.00 0.00 0.00 2.71
2067 2170 9.072294 CAAACAATTTTACTAATCGGGACATTC 57.928 33.333 0.00 0.00 0.00 2.67
2068 2171 8.575649 AACAATTTTACTAATCGGGACATTCT 57.424 30.769 0.00 0.00 0.00 2.40
2069 2172 8.575649 ACAATTTTACTAATCGGGACATTCTT 57.424 30.769 0.00 0.00 0.00 2.52
2070 2173 9.020731 ACAATTTTACTAATCGGGACATTCTTT 57.979 29.630 0.00 0.00 0.00 2.52
2071 2174 9.855021 CAATTTTACTAATCGGGACATTCTTTT 57.145 29.630 0.00 0.00 0.00 2.27
2077 2180 8.857694 ACTAATCGGGACATTCTTTTAAAAGA 57.142 30.769 23.65 23.65 42.91 2.52
2100 2203 9.830294 AAGAAAGCACTTTTTGAAGAAAAATTG 57.170 25.926 0.00 0.00 41.35 2.32
2101 2204 9.218440 AGAAAGCACTTTTTGAAGAAAAATTGA 57.782 25.926 12.08 0.00 41.11 2.57
2102 2205 9.481800 GAAAGCACTTTTTGAAGAAAAATTGAG 57.518 29.630 12.08 0.00 41.11 3.02
2103 2206 7.543947 AGCACTTTTTGAAGAAAAATTGAGG 57.456 32.000 12.08 0.00 41.11 3.86
2104 2207 7.330262 AGCACTTTTTGAAGAAAAATTGAGGA 58.670 30.769 12.08 0.00 41.11 3.71
2105 2208 7.989170 AGCACTTTTTGAAGAAAAATTGAGGAT 59.011 29.630 12.08 0.00 41.11 3.24
2106 2209 8.615211 GCACTTTTTGAAGAAAAATTGAGGATT 58.385 29.630 12.08 0.00 41.11 3.01
2177 2280 9.452287 ACACAAAGTAAACTAGTAGAAAAACCA 57.548 29.630 3.59 0.00 0.00 3.67
2180 2283 9.726232 CAAAGTAAACTAGTAGAAAAACCAACC 57.274 33.333 3.59 0.00 0.00 3.77
2181 2284 9.465199 AAAGTAAACTAGTAGAAAAACCAACCA 57.535 29.630 3.59 0.00 0.00 3.67
2182 2285 8.672823 AGTAAACTAGTAGAAAAACCAACCAG 57.327 34.615 3.59 0.00 0.00 4.00
2183 2286 8.488668 AGTAAACTAGTAGAAAAACCAACCAGA 58.511 33.333 3.59 0.00 0.00 3.86
2184 2287 9.112725 GTAAACTAGTAGAAAAACCAACCAGAA 57.887 33.333 3.59 0.00 0.00 3.02
2185 2288 8.584063 AAACTAGTAGAAAAACCAACCAGAAA 57.416 30.769 3.59 0.00 0.00 2.52
2186 2289 8.584063 AACTAGTAGAAAAACCAACCAGAAAA 57.416 30.769 3.59 0.00 0.00 2.29
2187 2290 7.993101 ACTAGTAGAAAAACCAACCAGAAAAC 58.007 34.615 3.59 0.00 0.00 2.43
2188 2291 6.844097 AGTAGAAAAACCAACCAGAAAACA 57.156 33.333 0.00 0.00 0.00 2.83
2189 2292 7.234661 AGTAGAAAAACCAACCAGAAAACAA 57.765 32.000 0.00 0.00 0.00 2.83
2190 2293 7.672240 AGTAGAAAAACCAACCAGAAAACAAA 58.328 30.769 0.00 0.00 0.00 2.83
2191 2294 8.151596 AGTAGAAAAACCAACCAGAAAACAAAA 58.848 29.630 0.00 0.00 0.00 2.44
2192 2295 7.809546 AGAAAAACCAACCAGAAAACAAAAA 57.190 28.000 0.00 0.00 0.00 1.94
2212 2315 5.613358 AAAACTGTAATCTTCTGCCGAAG 57.387 39.130 11.34 11.34 46.41 3.79
2240 2343 3.996614 CCGGTAAAACTGGCCTGG 58.003 61.111 14.82 4.64 37.90 4.45
2241 2344 1.377229 CCGGTAAAACTGGCCTGGA 59.623 57.895 14.82 0.00 37.90 3.86
2242 2345 0.250989 CCGGTAAAACTGGCCTGGAA 60.251 55.000 14.82 0.00 37.90 3.53
2243 2346 0.879090 CGGTAAAACTGGCCTGGAAC 59.121 55.000 14.82 6.05 0.00 3.62
2244 2347 1.254026 GGTAAAACTGGCCTGGAACC 58.746 55.000 14.82 11.08 0.00 3.62
2245 2348 1.254026 GTAAAACTGGCCTGGAACCC 58.746 55.000 14.82 0.00 0.00 4.11
2246 2349 0.854218 TAAAACTGGCCTGGAACCCA 59.146 50.000 14.82 0.00 0.00 4.51
2247 2350 0.031616 AAAACTGGCCTGGAACCCAA 60.032 50.000 14.82 0.00 30.80 4.12
2248 2351 0.031616 AAACTGGCCTGGAACCCAAA 60.032 50.000 14.82 0.00 30.80 3.28
2249 2352 0.031616 AACTGGCCTGGAACCCAAAA 60.032 50.000 14.82 0.00 30.80 2.44
2250 2353 0.759060 ACTGGCCTGGAACCCAAAAC 60.759 55.000 14.82 0.00 30.80 2.43
2251 2354 1.458588 TGGCCTGGAACCCAAAACC 60.459 57.895 3.32 0.00 30.80 3.27
2252 2355 2.570284 GGCCTGGAACCCAAAACCG 61.570 63.158 0.00 0.00 30.80 4.44
2253 2356 2.570284 GCCTGGAACCCAAAACCGG 61.570 63.158 0.00 0.00 30.80 5.28
2254 2357 1.151908 CCTGGAACCCAAAACCGGA 59.848 57.895 9.46 0.00 30.80 5.14
2255 2358 0.251608 CCTGGAACCCAAAACCGGAT 60.252 55.000 9.46 0.00 30.80 4.18
2256 2359 1.173913 CTGGAACCCAAAACCGGATC 58.826 55.000 9.46 0.00 30.80 3.36
2257 2360 0.478942 TGGAACCCAAAACCGGATCA 59.521 50.000 9.46 0.00 0.00 2.92
2258 2361 1.133450 TGGAACCCAAAACCGGATCAA 60.133 47.619 9.46 0.00 0.00 2.57
2259 2362 1.964933 GGAACCCAAAACCGGATCAAA 59.035 47.619 9.46 0.00 0.00 2.69
2260 2363 2.365941 GGAACCCAAAACCGGATCAAAA 59.634 45.455 9.46 0.00 0.00 2.44
2261 2364 3.386486 GAACCCAAAACCGGATCAAAAC 58.614 45.455 9.46 0.00 0.00 2.43
2262 2365 2.673258 ACCCAAAACCGGATCAAAACT 58.327 42.857 9.46 0.00 0.00 2.66
2263 2366 3.035363 ACCCAAAACCGGATCAAAACTT 58.965 40.909 9.46 0.00 0.00 2.66
2264 2367 3.069016 ACCCAAAACCGGATCAAAACTTC 59.931 43.478 9.46 0.00 0.00 3.01
2265 2368 3.554129 CCCAAAACCGGATCAAAACTTCC 60.554 47.826 9.46 0.00 0.00 3.46
2266 2369 3.554129 CCAAAACCGGATCAAAACTTCCC 60.554 47.826 9.46 0.00 0.00 3.97
2267 2370 2.971901 AACCGGATCAAAACTTCCCT 57.028 45.000 9.46 0.00 0.00 4.20
2268 2371 4.376225 AAACCGGATCAAAACTTCCCTA 57.624 40.909 9.46 0.00 0.00 3.53
2269 2372 4.586306 AACCGGATCAAAACTTCCCTAT 57.414 40.909 9.46 0.00 0.00 2.57
2270 2373 4.152284 ACCGGATCAAAACTTCCCTATC 57.848 45.455 9.46 0.00 0.00 2.08
2271 2374 3.780850 ACCGGATCAAAACTTCCCTATCT 59.219 43.478 9.46 0.00 0.00 1.98
2272 2375 4.966805 ACCGGATCAAAACTTCCCTATCTA 59.033 41.667 9.46 0.00 0.00 1.98
2273 2376 5.163332 ACCGGATCAAAACTTCCCTATCTAC 60.163 44.000 9.46 0.00 0.00 2.59
2274 2377 5.298347 CGGATCAAAACTTCCCTATCTACC 58.702 45.833 0.00 0.00 0.00 3.18
2275 2378 5.298347 GGATCAAAACTTCCCTATCTACCG 58.702 45.833 0.00 0.00 0.00 4.02
2276 2379 4.133013 TCAAAACTTCCCTATCTACCGC 57.867 45.455 0.00 0.00 0.00 5.68
2277 2380 3.773119 TCAAAACTTCCCTATCTACCGCT 59.227 43.478 0.00 0.00 0.00 5.52
2278 2381 4.957954 TCAAAACTTCCCTATCTACCGCTA 59.042 41.667 0.00 0.00 0.00 4.26
2279 2382 4.933505 AAACTTCCCTATCTACCGCTAC 57.066 45.455 0.00 0.00 0.00 3.58
2280 2383 3.880168 ACTTCCCTATCTACCGCTACT 57.120 47.619 0.00 0.00 0.00 2.57
2281 2384 4.181799 ACTTCCCTATCTACCGCTACTT 57.818 45.455 0.00 0.00 0.00 2.24
2282 2385 5.316158 ACTTCCCTATCTACCGCTACTTA 57.684 43.478 0.00 0.00 0.00 2.24
2283 2386 5.069318 ACTTCCCTATCTACCGCTACTTAC 58.931 45.833 0.00 0.00 0.00 2.34
2284 2387 4.989875 TCCCTATCTACCGCTACTTACT 57.010 45.455 0.00 0.00 0.00 2.24
2285 2388 4.904241 TCCCTATCTACCGCTACTTACTC 58.096 47.826 0.00 0.00 0.00 2.59
2286 2389 4.596643 TCCCTATCTACCGCTACTTACTCT 59.403 45.833 0.00 0.00 0.00 3.24
2287 2390 5.072872 TCCCTATCTACCGCTACTTACTCTT 59.927 44.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 147 1.483827 AGGAAGAAGCGATGCAGATGA 59.516 47.619 0.00 0.00 0.00 2.92
190 212 2.240279 GTACTGGGAGATGGCTATCGT 58.760 52.381 4.21 0.00 38.38 3.73
220 242 0.616395 TGGGCTCCTAATGACCGTCA 60.616 55.000 3.10 3.10 0.00 4.35
259 281 4.521639 TGACGCTAAACAGAGGAAGAAGTA 59.478 41.667 0.00 0.00 0.00 2.24
337 361 1.638133 CTGATTCCTGACACAGCGAG 58.362 55.000 0.00 0.00 0.00 5.03
344 368 1.618343 TGAAGACGCTGATTCCTGACA 59.382 47.619 0.00 0.00 0.00 3.58
389 413 6.299805 TGCAGAAGGAATCTAATACAGTGT 57.700 37.500 0.00 0.00 36.32 3.55
492 517 1.149101 TTGACTGGAGGGCCTTCTTT 58.851 50.000 14.33 0.00 34.31 2.52
508 533 1.304891 CCCTTCCCTTGGGGTATTGA 58.695 55.000 5.78 0.00 44.74 2.57
810 883 1.375908 GCAGCACAACCTCATCGGA 60.376 57.895 0.00 0.00 36.31 4.55
830 903 2.116772 TCTTCCTCGACGGTGGGT 59.883 61.111 0.00 0.00 0.00 4.51
945 1018 2.811317 CAGAAGTGAGTCGGGCGC 60.811 66.667 0.00 0.00 0.00 6.53
946 1019 2.811317 GCAGAAGTGAGTCGGGCG 60.811 66.667 0.00 0.00 0.00 6.13
998 1071 2.048603 GTGAAGTCCAGGGGCATGC 61.049 63.158 9.90 9.90 0.00 4.06
1139 1213 5.278022 CCGATCTTGATCTGATGAACGACTA 60.278 44.000 8.70 0.00 0.00 2.59
1229 1303 3.242739 GCACTTGTTGACGACTTCAATGT 60.243 43.478 0.00 0.00 46.14 2.71
1236 1310 1.594293 CCCGCACTTGTTGACGACT 60.594 57.895 0.00 0.00 0.00 4.18
1273 1347 2.444256 GGCCCTACTCCTTGGCGAT 61.444 63.158 0.00 0.00 46.31 4.58
1299 1373 3.816523 AGCAGACTCGATAGTACTTAGGC 59.183 47.826 0.00 0.00 35.56 3.93
1384 1482 6.155475 AGCAGAGTATAAACAGAGGATCAC 57.845 41.667 0.00 0.00 37.82 3.06
1439 1540 0.970640 TGAGGTTACCAGCACGCTTA 59.029 50.000 3.51 0.00 0.00 3.09
1443 1544 1.369692 TGGTGAGGTTACCAGCACG 59.630 57.895 16.96 0.00 45.46 5.34
1537 1638 2.102578 GCCTGATGTTTGGTTGCCTAT 58.897 47.619 0.00 0.00 0.00 2.57
1646 1749 2.679059 GCATAGCCTTCTCAACTCAGCA 60.679 50.000 0.00 0.00 0.00 4.41
1710 1813 0.037590 TAATTGGCCGTGTTCCAGCT 59.962 50.000 0.00 0.00 34.66 4.24
1711 1814 0.451783 CTAATTGGCCGTGTTCCAGC 59.548 55.000 0.00 0.00 34.66 4.85
1712 1815 1.821216 ACTAATTGGCCGTGTTCCAG 58.179 50.000 0.00 0.00 34.66 3.86
1713 1816 2.279935 AACTAATTGGCCGTGTTCCA 57.720 45.000 0.00 0.00 0.00 3.53
1714 1817 3.340928 ACTAACTAATTGGCCGTGTTCC 58.659 45.455 0.00 0.00 0.00 3.62
1715 1818 5.151389 CAAACTAACTAATTGGCCGTGTTC 58.849 41.667 0.00 0.00 0.00 3.18
1716 1819 4.581409 ACAAACTAACTAATTGGCCGTGTT 59.419 37.500 0.00 1.06 0.00 3.32
1717 1820 4.023536 CACAAACTAACTAATTGGCCGTGT 60.024 41.667 0.00 0.00 0.00 4.49
1718 1821 4.023536 ACACAAACTAACTAATTGGCCGTG 60.024 41.667 0.00 0.00 0.00 4.94
1719 1822 4.139038 ACACAAACTAACTAATTGGCCGT 58.861 39.130 0.00 0.00 0.00 5.68
1720 1823 4.759516 ACACAAACTAACTAATTGGCCG 57.240 40.909 0.00 0.00 0.00 6.13
1721 1824 6.079424 TCAACACAAACTAACTAATTGGCC 57.921 37.500 0.00 0.00 0.00 5.36
1722 1825 9.289303 CATATCAACACAAACTAACTAATTGGC 57.711 33.333 0.00 0.00 0.00 4.52
1723 1826 9.289303 GCATATCAACACAAACTAACTAATTGG 57.711 33.333 0.00 0.00 0.00 3.16
1724 1827 9.838975 TGCATATCAACACAAACTAACTAATTG 57.161 29.630 0.00 0.00 0.00 2.32
1727 1830 7.967854 GCATGCATATCAACACAAACTAACTAA 59.032 33.333 14.21 0.00 0.00 2.24
1728 1831 7.120432 TGCATGCATATCAACACAAACTAACTA 59.880 33.333 18.46 0.00 0.00 2.24
1729 1832 6.072008 TGCATGCATATCAACACAAACTAACT 60.072 34.615 18.46 0.00 0.00 2.24
1730 1833 6.092092 TGCATGCATATCAACACAAACTAAC 58.908 36.000 18.46 0.00 0.00 2.34
1731 1834 6.264841 TGCATGCATATCAACACAAACTAA 57.735 33.333 18.46 0.00 0.00 2.24
1732 1835 5.893897 TGCATGCATATCAACACAAACTA 57.106 34.783 18.46 0.00 0.00 2.24
1733 1836 4.787260 TGCATGCATATCAACACAAACT 57.213 36.364 18.46 0.00 0.00 2.66
1734 1837 5.383984 CATGCATGCATATCAACACAAAC 57.616 39.130 31.73 0.00 34.91 2.93
1753 1856 4.376615 GCTAACAAACTTTGTGCATGCATG 60.377 41.667 25.64 22.70 44.59 4.06
1754 1857 3.742369 GCTAACAAACTTTGTGCATGCAT 59.258 39.130 25.64 3.87 44.59 3.96
1755 1858 3.122297 GCTAACAAACTTTGTGCATGCA 58.878 40.909 18.46 18.46 44.59 3.96
1756 1859 3.122297 TGCTAACAAACTTTGTGCATGC 58.878 40.909 11.82 11.82 44.59 4.06
1757 1860 4.805192 ACTTGCTAACAAACTTTGTGCATG 59.195 37.500 20.24 20.24 44.59 4.06
1758 1861 5.009854 ACTTGCTAACAAACTTTGTGCAT 57.990 34.783 16.30 4.64 44.59 3.96
1759 1862 4.448537 ACTTGCTAACAAACTTTGTGCA 57.551 36.364 13.11 13.11 44.59 4.57
1760 1863 5.347364 TCAAACTTGCTAACAAACTTTGTGC 59.653 36.000 7.93 8.62 44.59 4.57
1761 1864 6.942886 TCAAACTTGCTAACAAACTTTGTG 57.057 33.333 7.93 0.00 44.59 3.33
1763 1866 6.018832 CCCATCAAACTTGCTAACAAACTTTG 60.019 38.462 0.00 0.00 36.10 2.77
1764 1867 6.048509 CCCATCAAACTTGCTAACAAACTTT 58.951 36.000 0.00 0.00 34.74 2.66
1765 1868 5.128663 ACCCATCAAACTTGCTAACAAACTT 59.871 36.000 0.00 0.00 34.74 2.66
1766 1869 4.649218 ACCCATCAAACTTGCTAACAAACT 59.351 37.500 0.00 0.00 34.74 2.66
1767 1870 4.744631 CACCCATCAAACTTGCTAACAAAC 59.255 41.667 0.00 0.00 34.74 2.93
1768 1871 4.202202 CCACCCATCAAACTTGCTAACAAA 60.202 41.667 0.00 0.00 34.74 2.83
1769 1872 3.320541 CCACCCATCAAACTTGCTAACAA 59.679 43.478 0.00 0.00 0.00 2.83
1770 1873 2.890311 CCACCCATCAAACTTGCTAACA 59.110 45.455 0.00 0.00 0.00 2.41
1771 1874 2.352715 GCCACCCATCAAACTTGCTAAC 60.353 50.000 0.00 0.00 0.00 2.34
1772 1875 1.892474 GCCACCCATCAAACTTGCTAA 59.108 47.619 0.00 0.00 0.00 3.09
1773 1876 1.544724 GCCACCCATCAAACTTGCTA 58.455 50.000 0.00 0.00 0.00 3.49
1774 1877 1.526575 CGCCACCCATCAAACTTGCT 61.527 55.000 0.00 0.00 0.00 3.91
1775 1878 1.080569 CGCCACCCATCAAACTTGC 60.081 57.895 0.00 0.00 0.00 4.01
1776 1879 0.039256 CACGCCACCCATCAAACTTG 60.039 55.000 0.00 0.00 0.00 3.16
1777 1880 1.178534 CCACGCCACCCATCAAACTT 61.179 55.000 0.00 0.00 0.00 2.66
1778 1881 1.603455 CCACGCCACCCATCAAACT 60.603 57.895 0.00 0.00 0.00 2.66
1779 1882 2.961768 CCACGCCACCCATCAAAC 59.038 61.111 0.00 0.00 0.00 2.93
1780 1883 2.988684 GCCACGCCACCCATCAAA 60.989 61.111 0.00 0.00 0.00 2.69
1781 1884 4.277009 TGCCACGCCACCCATCAA 62.277 61.111 0.00 0.00 0.00 2.57
1782 1885 4.720902 CTGCCACGCCACCCATCA 62.721 66.667 0.00 0.00 0.00 3.07
1783 1886 4.722700 ACTGCCACGCCACCCATC 62.723 66.667 0.00 0.00 0.00 3.51
1784 1887 4.284550 AACTGCCACGCCACCCAT 62.285 61.111 0.00 0.00 0.00 4.00
1786 1889 4.947147 TCAACTGCCACGCCACCC 62.947 66.667 0.00 0.00 0.00 4.61
1787 1890 1.805428 ATTTCAACTGCCACGCCACC 61.805 55.000 0.00 0.00 0.00 4.61
1788 1891 0.878416 TATTTCAACTGCCACGCCAC 59.122 50.000 0.00 0.00 0.00 5.01
1789 1892 1.610363 TTATTTCAACTGCCACGCCA 58.390 45.000 0.00 0.00 0.00 5.69
1790 1893 2.939460 ATTATTTCAACTGCCACGCC 57.061 45.000 0.00 0.00 0.00 5.68
1791 1894 5.176590 TGAAAAATTATTTCAACTGCCACGC 59.823 36.000 11.11 0.00 35.69 5.34
1792 1895 6.761731 TGAAAAATTATTTCAACTGCCACG 57.238 33.333 11.11 0.00 35.69 4.94
1873 1976 9.452287 AGCCAATTTTAAATTTGCTCATATGTT 57.548 25.926 19.08 0.57 0.00 2.71
1877 1980 9.935241 TTGTAGCCAATTTTAAATTTGCTCATA 57.065 25.926 25.32 14.10 0.00 2.15
1878 1981 8.720562 GTTGTAGCCAATTTTAAATTTGCTCAT 58.279 29.630 25.32 10.66 32.11 2.90
1879 1982 7.930865 AGTTGTAGCCAATTTTAAATTTGCTCA 59.069 29.630 25.32 20.23 32.11 4.26
1880 1983 8.310406 AGTTGTAGCCAATTTTAAATTTGCTC 57.690 30.769 25.32 18.58 32.11 4.26
1881 1984 8.675705 AAGTTGTAGCCAATTTTAAATTTGCT 57.324 26.923 25.06 25.06 32.11 3.91
1882 1985 9.729023 AAAAGTTGTAGCCAATTTTAAATTTGC 57.271 25.926 15.75 15.75 38.93 3.68
1885 1988 9.620259 TCCAAAAGTTGTAGCCAATTTTAAATT 57.380 25.926 0.00 0.00 38.93 1.82
1886 1989 9.620259 TTCCAAAAGTTGTAGCCAATTTTAAAT 57.380 25.926 0.00 0.00 38.93 1.40
1887 1990 9.449719 TTTCCAAAAGTTGTAGCCAATTTTAAA 57.550 25.926 0.00 0.00 38.93 1.52
1888 1991 9.449719 TTTTCCAAAAGTTGTAGCCAATTTTAA 57.550 25.926 0.00 0.00 38.93 1.52
1889 1992 9.620259 ATTTTCCAAAAGTTGTAGCCAATTTTA 57.380 25.926 0.00 0.00 38.93 1.52
1890 1993 7.929941 TTTTCCAAAAGTTGTAGCCAATTTT 57.070 28.000 0.00 0.00 40.83 1.82
1891 1994 7.555914 ACATTTTCCAAAAGTTGTAGCCAATTT 59.444 29.630 0.00 0.00 32.49 1.82
1892 1995 7.012232 CACATTTTCCAAAAGTTGTAGCCAATT 59.988 33.333 0.00 0.00 32.11 2.32
1893 1996 6.482973 CACATTTTCCAAAAGTTGTAGCCAAT 59.517 34.615 0.00 0.00 32.11 3.16
1894 1997 5.814705 CACATTTTCCAAAAGTTGTAGCCAA 59.185 36.000 0.00 0.00 0.00 4.52
1895 1998 5.355596 CACATTTTCCAAAAGTTGTAGCCA 58.644 37.500 0.00 0.00 0.00 4.75
1896 1999 4.211164 GCACATTTTCCAAAAGTTGTAGCC 59.789 41.667 0.00 0.00 0.00 3.93
1897 2000 4.808364 TGCACATTTTCCAAAAGTTGTAGC 59.192 37.500 0.00 0.00 0.00 3.58
1898 2001 8.761575 ATATGCACATTTTCCAAAAGTTGTAG 57.238 30.769 0.00 0.00 0.00 2.74
1899 2002 9.553064 AAATATGCACATTTTCCAAAAGTTGTA 57.447 25.926 0.00 0.00 0.00 2.41
1900 2003 8.449251 AAATATGCACATTTTCCAAAAGTTGT 57.551 26.923 0.00 0.00 0.00 3.32
1901 2004 9.733219 AAAAATATGCACATTTTCCAAAAGTTG 57.267 25.926 15.64 0.00 37.17 3.16
1933 2036 7.385205 TCTTGAAACGATTGTGGTTTTCAAAAA 59.615 29.630 10.47 2.36 37.70 1.94
1934 2037 6.868864 TCTTGAAACGATTGTGGTTTTCAAAA 59.131 30.769 10.47 0.00 37.70 2.44
1935 2038 6.390721 TCTTGAAACGATTGTGGTTTTCAAA 58.609 32.000 10.47 2.55 37.70 2.69
1936 2039 5.955488 TCTTGAAACGATTGTGGTTTTCAA 58.045 33.333 9.35 9.35 37.70 2.69
1937 2040 5.568685 TCTTGAAACGATTGTGGTTTTCA 57.431 34.783 0.00 0.00 37.70 2.69
1938 2041 6.879188 TTTCTTGAAACGATTGTGGTTTTC 57.121 33.333 0.00 0.00 37.70 2.29
1939 2042 7.360522 GGTTTTTCTTGAAACGATTGTGGTTTT 60.361 33.333 0.00 0.00 39.76 2.43
1940 2043 6.091577 GGTTTTTCTTGAAACGATTGTGGTTT 59.908 34.615 0.00 0.00 39.76 3.27
1941 2044 5.579119 GGTTTTTCTTGAAACGATTGTGGTT 59.421 36.000 0.00 0.00 39.76 3.67
1942 2045 5.106442 GGTTTTTCTTGAAACGATTGTGGT 58.894 37.500 0.00 0.00 39.76 4.16
1943 2046 5.105752 TGGTTTTTCTTGAAACGATTGTGG 58.894 37.500 0.00 0.00 39.76 4.17
1944 2047 6.639671 TTGGTTTTTCTTGAAACGATTGTG 57.360 33.333 0.00 0.00 39.76 3.33
1945 2048 6.647067 TGTTTGGTTTTTCTTGAAACGATTGT 59.353 30.769 0.00 0.00 39.76 2.71
1946 2049 7.054855 TGTTTGGTTTTTCTTGAAACGATTG 57.945 32.000 0.00 0.00 39.76 2.67
1947 2050 7.659652 TTGTTTGGTTTTTCTTGAAACGATT 57.340 28.000 0.00 0.00 39.76 3.34
1948 2051 7.841915 ATTGTTTGGTTTTTCTTGAAACGAT 57.158 28.000 0.00 0.00 39.76 3.73
1949 2052 7.659652 AATTGTTTGGTTTTTCTTGAAACGA 57.340 28.000 0.00 0.00 39.76 3.85
1950 2053 8.720909 AAAATTGTTTGGTTTTTCTTGAAACG 57.279 26.923 0.00 0.00 39.76 3.60
1980 2083 9.393512 TCCACAATTTCAAATGTTTTCTCATTT 57.606 25.926 0.00 0.00 45.23 2.32
1981 2084 8.829612 GTCCACAATTTCAAATGTTTTCTCATT 58.170 29.630 0.00 0.00 39.35 2.57
1982 2085 7.986320 TGTCCACAATTTCAAATGTTTTCTCAT 59.014 29.630 0.00 0.00 0.00 2.90
1983 2086 7.326454 TGTCCACAATTTCAAATGTTTTCTCA 58.674 30.769 0.00 0.00 0.00 3.27
1984 2087 7.769272 TGTCCACAATTTCAAATGTTTTCTC 57.231 32.000 0.00 0.00 0.00 2.87
2034 2137 9.579610 CCGATTAGTAAAATTGTTTGCTTTTTG 57.420 29.630 0.00 0.00 39.91 2.44
2035 2138 8.769891 CCCGATTAGTAAAATTGTTTGCTTTTT 58.230 29.630 0.00 0.00 39.91 1.94
2036 2139 8.145122 TCCCGATTAGTAAAATTGTTTGCTTTT 58.855 29.630 0.00 0.00 39.91 2.27
2037 2140 7.597369 GTCCCGATTAGTAAAATTGTTTGCTTT 59.403 33.333 0.00 0.00 39.91 3.51
2038 2141 7.088272 GTCCCGATTAGTAAAATTGTTTGCTT 58.912 34.615 0.00 0.00 39.91 3.91
2039 2142 6.207810 TGTCCCGATTAGTAAAATTGTTTGCT 59.792 34.615 0.00 0.00 41.80 3.91
2040 2143 6.383415 TGTCCCGATTAGTAAAATTGTTTGC 58.617 36.000 0.00 0.00 0.00 3.68
2041 2144 8.980143 AATGTCCCGATTAGTAAAATTGTTTG 57.020 30.769 0.00 0.00 0.00 2.93
2042 2145 9.020731 AGAATGTCCCGATTAGTAAAATTGTTT 57.979 29.630 0.00 0.00 0.00 2.83
2043 2146 8.575649 AGAATGTCCCGATTAGTAAAATTGTT 57.424 30.769 0.00 0.00 0.00 2.83
2044 2147 8.575649 AAGAATGTCCCGATTAGTAAAATTGT 57.424 30.769 0.00 0.00 0.00 2.71
2045 2148 9.855021 AAAAGAATGTCCCGATTAGTAAAATTG 57.145 29.630 0.00 0.00 0.00 2.32
2051 2154 9.947433 TCTTTTAAAAGAATGTCCCGATTAGTA 57.053 29.630 24.89 0.00 41.75 1.82
2052 2155 8.857694 TCTTTTAAAAGAATGTCCCGATTAGT 57.142 30.769 24.89 0.00 41.75 2.24
2074 2177 9.830294 CAATTTTTCTTCAAAAAGTGCTTTCTT 57.170 25.926 7.26 0.00 45.44 2.52
2151 2254 9.452287 TGGTTTTTCTACTAGTTTACTTTGTGT 57.548 29.630 0.00 0.00 0.00 3.72
2154 2257 9.726232 GGTTGGTTTTTCTACTAGTTTACTTTG 57.274 33.333 0.00 0.00 0.00 2.77
2155 2258 9.465199 TGGTTGGTTTTTCTACTAGTTTACTTT 57.535 29.630 0.00 0.00 0.00 2.66
2156 2259 9.117183 CTGGTTGGTTTTTCTACTAGTTTACTT 57.883 33.333 0.00 0.00 0.00 2.24
2157 2260 8.488668 TCTGGTTGGTTTTTCTACTAGTTTACT 58.511 33.333 0.00 0.00 0.00 2.24
2158 2261 8.667076 TCTGGTTGGTTTTTCTACTAGTTTAC 57.333 34.615 0.00 0.00 0.00 2.01
2159 2262 9.683870 TTTCTGGTTGGTTTTTCTACTAGTTTA 57.316 29.630 0.00 0.00 0.00 2.01
2160 2263 8.584063 TTTCTGGTTGGTTTTTCTACTAGTTT 57.416 30.769 0.00 0.00 0.00 2.66
2161 2264 8.464404 GTTTTCTGGTTGGTTTTTCTACTAGTT 58.536 33.333 0.00 0.00 0.00 2.24
2162 2265 7.612633 TGTTTTCTGGTTGGTTTTTCTACTAGT 59.387 33.333 0.00 0.00 0.00 2.57
2163 2266 7.992008 TGTTTTCTGGTTGGTTTTTCTACTAG 58.008 34.615 0.00 0.00 0.00 2.57
2164 2267 7.941431 TGTTTTCTGGTTGGTTTTTCTACTA 57.059 32.000 0.00 0.00 0.00 1.82
2165 2268 6.844097 TGTTTTCTGGTTGGTTTTTCTACT 57.156 33.333 0.00 0.00 0.00 2.57
2166 2269 7.892778 TTTGTTTTCTGGTTGGTTTTTCTAC 57.107 32.000 0.00 0.00 0.00 2.59
2167 2270 8.904099 TTTTTGTTTTCTGGTTGGTTTTTCTA 57.096 26.923 0.00 0.00 0.00 2.10
2168 2271 7.809546 TTTTTGTTTTCTGGTTGGTTTTTCT 57.190 28.000 0.00 0.00 0.00 2.52
2202 2305 0.107081 TTTCGGAACCTTCGGCAGAA 59.893 50.000 0.00 0.00 34.76 3.02
2203 2306 0.107081 TTTTCGGAACCTTCGGCAGA 59.893 50.000 0.00 0.00 0.00 4.26
2204 2307 0.237498 GTTTTCGGAACCTTCGGCAG 59.763 55.000 0.00 0.00 0.00 4.85
2205 2308 1.167781 GGTTTTCGGAACCTTCGGCA 61.168 55.000 12.56 0.00 37.34 5.69
2206 2309 1.577922 GGTTTTCGGAACCTTCGGC 59.422 57.895 12.56 0.00 37.34 5.54
2207 2310 1.864176 CGGTTTTCGGAACCTTCGG 59.136 57.895 16.17 1.64 38.15 4.30
2217 2320 1.335233 GGCCAGTTTTACCGGTTTTCG 60.335 52.381 15.04 0.00 38.88 3.46
2218 2321 1.958579 AGGCCAGTTTTACCGGTTTTC 59.041 47.619 15.04 1.07 0.00 2.29
2219 2322 1.684450 CAGGCCAGTTTTACCGGTTTT 59.316 47.619 15.04 0.00 0.00 2.43
2220 2323 1.324383 CAGGCCAGTTTTACCGGTTT 58.676 50.000 15.04 0.00 0.00 3.27
2221 2324 0.538746 CCAGGCCAGTTTTACCGGTT 60.539 55.000 15.04 0.00 0.00 4.44
2222 2325 1.074248 CCAGGCCAGTTTTACCGGT 59.926 57.895 13.98 13.98 0.00 5.28
2223 2326 0.250989 TTCCAGGCCAGTTTTACCGG 60.251 55.000 5.01 0.00 0.00 5.28
2224 2327 0.879090 GTTCCAGGCCAGTTTTACCG 59.121 55.000 5.01 0.00 0.00 4.02
2225 2328 1.254026 GGTTCCAGGCCAGTTTTACC 58.746 55.000 5.01 0.23 0.00 2.85
2226 2329 1.254026 GGGTTCCAGGCCAGTTTTAC 58.746 55.000 5.01 0.00 0.00 2.01
2227 2330 0.854218 TGGGTTCCAGGCCAGTTTTA 59.146 50.000 5.01 0.00 0.00 1.52
2228 2331 0.031616 TTGGGTTCCAGGCCAGTTTT 60.032 50.000 5.01 0.00 33.81 2.43
2229 2332 0.031616 TTTGGGTTCCAGGCCAGTTT 60.032 50.000 5.01 0.00 33.81 2.66
2230 2333 0.031616 TTTTGGGTTCCAGGCCAGTT 60.032 50.000 5.01 0.00 33.81 3.16
2231 2334 0.759060 GTTTTGGGTTCCAGGCCAGT 60.759 55.000 5.01 0.00 33.81 4.00
2232 2335 1.471829 GGTTTTGGGTTCCAGGCCAG 61.472 60.000 5.01 0.00 33.81 4.85
2233 2336 1.458588 GGTTTTGGGTTCCAGGCCA 60.459 57.895 5.01 0.00 33.81 5.36
2234 2337 2.570284 CGGTTTTGGGTTCCAGGCC 61.570 63.158 0.00 0.00 33.81 5.19
2235 2338 2.570284 CCGGTTTTGGGTTCCAGGC 61.570 63.158 0.00 0.00 33.81 4.85
2236 2339 0.251608 ATCCGGTTTTGGGTTCCAGG 60.252 55.000 0.00 0.00 33.81 4.45
2237 2340 1.173913 GATCCGGTTTTGGGTTCCAG 58.826 55.000 0.00 0.00 33.81 3.86
2238 2341 0.478942 TGATCCGGTTTTGGGTTCCA 59.521 50.000 0.00 0.00 0.00 3.53
2239 2342 1.623163 TTGATCCGGTTTTGGGTTCC 58.377 50.000 0.00 0.00 0.00 3.62
2240 2343 3.069016 AGTTTTGATCCGGTTTTGGGTTC 59.931 43.478 0.00 0.00 0.00 3.62
2241 2344 3.035363 AGTTTTGATCCGGTTTTGGGTT 58.965 40.909 0.00 0.00 0.00 4.11
2242 2345 2.673258 AGTTTTGATCCGGTTTTGGGT 58.327 42.857 0.00 0.00 0.00 4.51
2243 2346 3.554129 GGAAGTTTTGATCCGGTTTTGGG 60.554 47.826 0.00 0.00 0.00 4.12
2244 2347 3.554129 GGGAAGTTTTGATCCGGTTTTGG 60.554 47.826 0.00 0.00 0.00 3.28
2245 2348 3.320826 AGGGAAGTTTTGATCCGGTTTTG 59.679 43.478 0.00 0.00 0.00 2.44
2246 2349 3.572642 AGGGAAGTTTTGATCCGGTTTT 58.427 40.909 0.00 0.00 0.00 2.43
2247 2350 3.238788 AGGGAAGTTTTGATCCGGTTT 57.761 42.857 0.00 0.00 0.00 3.27
2248 2351 2.971901 AGGGAAGTTTTGATCCGGTT 57.028 45.000 0.00 0.00 0.00 4.44
2249 2352 3.780850 AGATAGGGAAGTTTTGATCCGGT 59.219 43.478 0.00 0.00 0.00 5.28
2250 2353 4.423625 AGATAGGGAAGTTTTGATCCGG 57.576 45.455 0.00 0.00 0.00 5.14
2251 2354 5.298347 GGTAGATAGGGAAGTTTTGATCCG 58.702 45.833 0.00 0.00 0.00 4.18
2252 2355 5.298347 CGGTAGATAGGGAAGTTTTGATCC 58.702 45.833 0.00 0.00 0.00 3.36
2253 2356 4.750598 GCGGTAGATAGGGAAGTTTTGATC 59.249 45.833 0.00 0.00 0.00 2.92
2254 2357 4.409247 AGCGGTAGATAGGGAAGTTTTGAT 59.591 41.667 0.00 0.00 0.00 2.57
2255 2358 3.773119 AGCGGTAGATAGGGAAGTTTTGA 59.227 43.478 0.00 0.00 0.00 2.69
2256 2359 4.138487 AGCGGTAGATAGGGAAGTTTTG 57.862 45.455 0.00 0.00 0.00 2.44
2257 2360 4.961099 AGTAGCGGTAGATAGGGAAGTTTT 59.039 41.667 0.00 0.00 0.00 2.43
2258 2361 4.544683 AGTAGCGGTAGATAGGGAAGTTT 58.455 43.478 0.00 0.00 0.00 2.66
2259 2362 4.181799 AGTAGCGGTAGATAGGGAAGTT 57.818 45.455 0.00 0.00 0.00 2.66
2260 2363 3.880168 AGTAGCGGTAGATAGGGAAGT 57.120 47.619 0.00 0.00 0.00 3.01
2261 2364 5.315348 AGTAAGTAGCGGTAGATAGGGAAG 58.685 45.833 0.00 0.00 0.00 3.46
2262 2365 5.072872 AGAGTAAGTAGCGGTAGATAGGGAA 59.927 44.000 0.00 0.00 0.00 3.97
2263 2366 4.596643 AGAGTAAGTAGCGGTAGATAGGGA 59.403 45.833 0.00 0.00 0.00 4.20
2264 2367 4.909001 AGAGTAAGTAGCGGTAGATAGGG 58.091 47.826 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.