Multiple sequence alignment - TraesCS4D01G252200

Loading Multiple Alignment...

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 TraesCS4D01G252200 chr4D 100.000 2287 0 0 1 2287 421048641 421046355 0 4224
1 TraesCS4D01G252200 chr4D 92.997 1742 108 8 1 1736 493971114 493969381 0 2529
2 TraesCS4D01G252200 chr4D 92.874 1726 115 4 1 1724 116524562 116522843 0 2499
3 TraesCS4D01G252200 chr4D 92.241 1727 119 9 1 1723 48683933 48682218 0 2433
4 TraesCS4D01G252200 chr3A 93.685 1726 107 2 1 1724 418765665 418763940 0 2582
5 TraesCS4D01G252200 chr5A 92.308 1729 129 4 1 1727 604232065 604230339 0 2453
6 TraesCS4D01G252200 chr4A 92.254 1730 131 3 1 1728 327748379 327746651 0 2449
7 TraesCS4D01G252200 chr7D 92.192 1729 131 4 1 1727 432740548 432738822 0 2442
8 TraesCS4D01G252200 chr1A 92.019 1729 127 7 1 1724 327011923 327010201 0 2418
9 TraesCS4D01G252200 chr5B 91.570 1732 132 7 1 1724 375712250 375710525 0 2377


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 TraesCS4D01G252200 chr4D 421046355 421048641 2286 True 4224 4224 100.000 1 2287 1 chr4D.!!$R3 2286
1 TraesCS4D01G252200 chr4D 493969381 493971114 1733 True 2529 2529 92.997 1 1736 1 chr4D.!!$R4 1735
2 TraesCS4D01G252200 chr4D 116522843 116524562 1719 True 2499 2499 92.874 1 1724 1 chr4D.!!$R2 1723
3 TraesCS4D01G252200 chr4D 48682218 48683933 1715 True 2433 2433 92.241 1 1723 1 chr4D.!!$R1 1722
4 TraesCS4D01G252200 chr3A 418763940 418765665 1725 True 2582 2582 93.685 1 1724 1 chr3A.!!$R1 1723
5 TraesCS4D01G252200 chr5A 604230339 604232065 1726 True 2453 2453 92.308 1 1727 1 chr5A.!!$R1 1726
6 TraesCS4D01G252200 chr4A 327746651 327748379 1728 True 2449 2449 92.254 1 1728 1 chr4A.!!$R1 1727
7 TraesCS4D01G252200 chr7D 432738822 432740548 1726 True 2442 2442 92.192 1 1727 1 chr7D.!!$R1 1726
8 TraesCS4D01G252200 chr1A 327010201 327011923 1722 True 2418 2418 92.019 1 1724 1 chr1A.!!$R1 1723
9 TraesCS4D01G252200 chr5B 375710525 375712250 1725 True 2377 2377 91.570 1 1724 1 chr5B.!!$R1 1723

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
172 173 0.104725 CTCCTCCTTAGGCTCCCCAT 60.105 60.0 0.0 0.0 43.31 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1517 0.036732 AACGCCTGATGTGTGGTCAT 59.963 50.0 0.0 0.0 37.86 3.06 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
106 107 1.414181 CGAGGTCAATCTGCCAGGTAT 59.586 52.381 0.00 0.00 0.00 2.73
113 114 1.050988 ATCTGCCAGGTATGACGGCT 61.051 55.000 0.00 0.00 46.39 5.52
133 134 4.221422 GCTCCGGCGCCATCACTA 62.221 66.667 28.98 3.10 0.00 2.74
172 173 0.104725 CTCCTCCTTAGGCTCCCCAT 60.105 60.000 0.00 0.00 43.31 4.00
338 340 2.821366 GACTGCCATCGCACCCTG 60.821 66.667 0.00 0.00 41.12 4.45
385 387 3.052082 CTTGTGCAGTGGCCCTCG 61.052 66.667 0.00 0.00 40.13 4.63
398 400 2.104859 CCCTCGTGAGCACTGCATG 61.105 63.158 3.30 0.00 0.00 4.06
412 414 1.948145 CTGCATGAGATTCCTTCTGCC 59.052 52.381 0.00 0.00 33.74 4.85
500 502 0.903454 GACCACCCGAGGAAGAAGGA 60.903 60.000 0.00 0.00 0.00 3.36
539 541 2.114411 GAAGGGGTTGGCGTTGGA 59.886 61.111 0.00 0.00 0.00 3.53
590 598 4.027437 AGGAGGAAGGTTGATAGTGAGAC 58.973 47.826 0.00 0.00 0.00 3.36
639 649 3.651423 GGGCAGGGTGAGTAAATATAGGT 59.349 47.826 0.00 0.00 0.00 3.08
703 716 6.830912 ACTACATGCTCTTCAATAAGCCATA 58.169 36.000 0.00 0.00 37.73 2.74
763 776 2.382882 TCGAGGAGAGCAATGAGATGT 58.617 47.619 0.00 0.00 0.00 3.06
804 817 1.069049 GTTGACAACAAGGGCAAGCAT 59.931 47.619 13.52 0.00 36.64 3.79
940 953 3.083122 ACTACGACCACTACCATGAGT 57.917 47.619 0.00 0.00 0.00 3.41
1101 1115 2.350522 GTGACGGTGAAGCTGATGAAT 58.649 47.619 0.00 0.00 0.00 2.57
1113 1127 0.697658 TGATGAATGGCAGGGTGACA 59.302 50.000 0.00 0.00 41.29 3.58
1162 1177 4.981054 CGATGTTCATCAGATCAAGATCGT 59.019 41.667 15.79 0.00 42.48 3.73
1187 1202 1.334160 TGGTGACGTTCAAGCTCCTA 58.666 50.000 0.00 0.00 0.00 2.94
1271 1286 1.228657 GGAAGCACGACGAAGCCTTT 61.229 55.000 0.00 0.00 0.00 3.11
1353 1368 4.675114 GGTTTATGCGTTGAACTGTTTGAG 59.325 41.667 0.00 0.00 0.00 3.02
1372 1387 5.514274 TGAGCTATCGTTATGATGTGTGA 57.486 39.130 0.00 0.00 37.99 3.58
1426 1447 6.857777 AGTTGATGCTCTGTTTATGCTATC 57.142 37.500 0.00 0.00 0.00 2.08
1457 1479 3.826524 TGATTGTGGTACATGGTTGTGT 58.173 40.909 0.00 0.00 44.52 3.72
1495 1517 2.303022 CCTCACCAACTAGCCAAAGAGA 59.697 50.000 0.00 0.00 0.00 3.10
1497 1519 3.937706 CTCACCAACTAGCCAAAGAGATG 59.062 47.826 0.00 0.00 0.00 2.90
1539 1562 1.412343 ACAACCAAACACCATGCCTTC 59.588 47.619 0.00 0.00 0.00 3.46
1550 1573 1.176527 CATGCCTTCGGTTTGTCCAT 58.823 50.000 0.00 0.00 35.57 3.41
1598 1623 1.152589 TGTGGTTCAGCCCATGCAA 60.153 52.632 0.00 0.00 41.13 4.08
1607 1632 1.679977 GCCCATGCAAGCAAGAGGA 60.680 57.895 11.19 0.00 37.47 3.71
1612 1637 1.816835 CATGCAAGCAAGAGGACATGT 59.183 47.619 0.00 0.00 32.28 3.21
1619 1644 2.240667 AGCAAGAGGACATGTAGGCAAT 59.759 45.455 0.00 0.00 0.00 3.56
1672 1697 1.752498 CATTTGCATAGCCAGGCTGAA 59.248 47.619 25.59 5.05 40.10 3.02
1681 1706 1.632409 AGCCAGGCTGAATTGAGAAGA 59.368 47.619 15.24 0.00 37.57 2.87
1724 1750 1.503818 CTACGGCAACCAAACACGCT 61.504 55.000 0.00 0.00 0.00 5.07
1729 1755 1.334689 GGCAACCAAACACGCTCTTAC 60.335 52.381 0.00 0.00 0.00 2.34
1732 1758 1.878953 ACCAAACACGCTCTTACTGG 58.121 50.000 0.00 0.00 0.00 4.00
1735 1761 2.616842 CCAAACACGCTCTTACTGGTTT 59.383 45.455 0.00 0.00 0.00 3.27
1736 1762 3.810941 CCAAACACGCTCTTACTGGTTTA 59.189 43.478 0.00 0.00 0.00 2.01
1737 1763 4.084013 CCAAACACGCTCTTACTGGTTTAG 60.084 45.833 0.00 0.00 0.00 1.85
1738 1764 4.332428 AACACGCTCTTACTGGTTTAGT 57.668 40.909 0.00 0.00 43.56 2.24
1739 1765 5.458041 AACACGCTCTTACTGGTTTAGTA 57.542 39.130 0.00 0.00 40.89 1.82
1740 1766 5.056894 ACACGCTCTTACTGGTTTAGTAG 57.943 43.478 0.00 0.00 42.57 2.57
1741 1767 4.522022 ACACGCTCTTACTGGTTTAGTAGT 59.478 41.667 0.00 0.00 42.57 2.73
1742 1768 5.707298 ACACGCTCTTACTGGTTTAGTAGTA 59.293 40.000 0.00 0.00 42.57 1.82
1743 1769 6.207417 ACACGCTCTTACTGGTTTAGTAGTAA 59.793 38.462 0.00 0.00 42.57 2.24
1749 1775 7.951347 CTTACTGGTTTAGTAGTAAGGAGGA 57.049 40.000 13.58 0.00 46.36 3.71
1750 1776 7.709149 TTACTGGTTTAGTAGTAAGGAGGAC 57.291 40.000 0.00 0.00 42.57 3.85
1751 1777 4.704057 ACTGGTTTAGTAGTAAGGAGGACG 59.296 45.833 0.00 0.00 38.04 4.79
1752 1778 4.922206 TGGTTTAGTAGTAAGGAGGACGA 58.078 43.478 0.00 0.00 0.00 4.20
1753 1779 5.513233 TGGTTTAGTAGTAAGGAGGACGAT 58.487 41.667 0.00 0.00 0.00 3.73
1754 1780 5.359009 TGGTTTAGTAGTAAGGAGGACGATG 59.641 44.000 0.00 0.00 0.00 3.84
1755 1781 5.280164 GTTTAGTAGTAAGGAGGACGATGC 58.720 45.833 0.00 0.00 0.00 3.91
1756 1782 1.948145 AGTAGTAAGGAGGACGATGCG 59.052 52.381 0.00 0.00 0.00 4.73
1757 1783 0.666913 TAGTAAGGAGGACGATGCGC 59.333 55.000 0.00 0.00 0.00 6.09
1768 1794 2.873367 CGATGCGCGTTCTATGAGT 58.127 52.632 8.43 0.00 34.64 3.41
1769 1795 1.200483 CGATGCGCGTTCTATGAGTT 58.800 50.000 8.43 0.00 34.64 3.01
1770 1796 1.588404 CGATGCGCGTTCTATGAGTTT 59.412 47.619 8.43 0.00 34.64 2.66
1771 1797 2.029244 CGATGCGCGTTCTATGAGTTTT 59.971 45.455 8.43 0.00 34.64 2.43
1772 1798 3.483574 CGATGCGCGTTCTATGAGTTTTT 60.484 43.478 8.43 0.00 34.64 1.94
1807 1833 3.715628 AAACTTGCACAACATGTCTCC 57.284 42.857 0.00 0.00 35.71 3.71
1808 1834 1.229428 ACTTGCACAACATGTCTCCG 58.771 50.000 0.00 0.00 31.29 4.63
1809 1835 0.518636 CTTGCACAACATGTCTCCGG 59.481 55.000 0.00 0.00 0.00 5.14
1810 1836 0.179032 TTGCACAACATGTCTCCGGT 60.179 50.000 0.00 0.00 0.00 5.28
1811 1837 0.884259 TGCACAACATGTCTCCGGTG 60.884 55.000 0.00 0.00 0.00 4.94
1812 1838 1.577328 GCACAACATGTCTCCGGTGG 61.577 60.000 0.00 0.00 0.00 4.61
1813 1839 1.302511 ACAACATGTCTCCGGTGGC 60.303 57.895 0.00 0.00 0.00 5.01
1814 1840 2.040544 CAACATGTCTCCGGTGGCC 61.041 63.158 5.53 0.00 0.00 5.36
1815 1841 2.224159 AACATGTCTCCGGTGGCCT 61.224 57.895 3.32 0.00 0.00 5.19
1816 1842 1.779061 AACATGTCTCCGGTGGCCTT 61.779 55.000 3.32 0.00 0.00 4.35
1817 1843 1.746615 CATGTCTCCGGTGGCCTTG 60.747 63.158 3.32 0.00 0.00 3.61
1818 1844 2.971598 ATGTCTCCGGTGGCCTTGG 61.972 63.158 3.32 2.78 0.00 3.61
1821 1847 4.785453 CTCCGGTGGCCTTGGCTC 62.785 72.222 11.71 5.38 0.00 4.70
1825 1851 4.748144 GGTGGCCTTGGCTCCAGG 62.748 72.222 11.71 0.00 40.66 4.45
1837 1863 4.729552 TGGCTCCAGGCAGAATATTATT 57.270 40.909 0.00 0.00 46.12 1.40
1838 1864 5.065613 TGGCTCCAGGCAGAATATTATTT 57.934 39.130 0.00 0.00 46.12 1.40
1839 1865 5.072741 TGGCTCCAGGCAGAATATTATTTC 58.927 41.667 0.00 0.00 46.12 2.17
1840 1866 5.163055 TGGCTCCAGGCAGAATATTATTTCT 60.163 40.000 0.00 0.00 46.12 2.52
1841 1867 5.414144 GGCTCCAGGCAGAATATTATTTCTC 59.586 44.000 0.00 0.00 44.01 2.87
1842 1868 5.121454 GCTCCAGGCAGAATATTATTTCTCG 59.879 44.000 0.00 0.00 41.35 4.04
1843 1869 4.997395 TCCAGGCAGAATATTATTTCTCGC 59.003 41.667 0.00 0.00 33.69 5.03
1844 1870 4.154918 CCAGGCAGAATATTATTTCTCGCC 59.845 45.833 14.42 14.42 43.13 5.54
1845 1871 5.234466 AGGCAGAATATTATTTCTCGCCT 57.766 39.130 17.07 17.07 45.28 5.52
1846 1872 6.166279 CAGGCAGAATATTATTTCTCGCCTA 58.834 40.000 19.92 0.00 46.60 3.93
1847 1873 6.091441 CAGGCAGAATATTATTTCTCGCCTAC 59.909 42.308 19.92 4.17 46.60 3.18
1848 1874 6.014156 AGGCAGAATATTATTTCTCGCCTACT 60.014 38.462 19.40 5.76 46.54 2.57
1849 1875 7.178628 AGGCAGAATATTATTTCTCGCCTACTA 59.821 37.037 19.40 0.00 46.54 1.82
1850 1876 7.275999 GGCAGAATATTATTTCTCGCCTACTAC 59.724 40.741 14.73 0.00 41.54 2.73
1851 1877 7.813148 GCAGAATATTATTTCTCGCCTACTACA 59.187 37.037 0.00 0.00 33.69 2.74
1852 1878 9.692749 CAGAATATTATTTCTCGCCTACTACAA 57.307 33.333 0.00 0.00 33.69 2.41
1857 1883 8.732746 ATTATTTCTCGCCTACTACAAAATGT 57.267 30.769 0.00 0.00 0.00 2.71
1858 1884 9.826574 ATTATTTCTCGCCTACTACAAAATGTA 57.173 29.630 0.00 0.00 0.00 2.29
1859 1885 9.656040 TTATTTCTCGCCTACTACAAAATGTAA 57.344 29.630 0.00 0.00 31.67 2.41
1860 1886 6.956299 TTCTCGCCTACTACAAAATGTAAC 57.044 37.500 0.00 0.00 31.67 2.50
1861 1887 6.028146 TCTCGCCTACTACAAAATGTAACA 57.972 37.500 0.00 0.00 31.67 2.41
1862 1888 5.865552 TCTCGCCTACTACAAAATGTAACAC 59.134 40.000 0.00 0.00 31.67 3.32
1863 1889 4.931002 TCGCCTACTACAAAATGTAACACC 59.069 41.667 0.00 0.00 31.67 4.16
1864 1890 4.691685 CGCCTACTACAAAATGTAACACCA 59.308 41.667 0.00 0.00 31.67 4.17
1865 1891 5.163893 CGCCTACTACAAAATGTAACACCAG 60.164 44.000 0.00 0.00 31.67 4.00
1866 1892 5.391629 GCCTACTACAAAATGTAACACCAGC 60.392 44.000 0.00 0.00 31.67 4.85
1867 1893 5.938125 CCTACTACAAAATGTAACACCAGCT 59.062 40.000 0.00 0.00 31.67 4.24
1868 1894 5.941948 ACTACAAAATGTAACACCAGCTC 57.058 39.130 0.00 0.00 31.67 4.09
1869 1895 3.896648 ACAAAATGTAACACCAGCTCG 57.103 42.857 0.00 0.00 0.00 5.03
1870 1896 2.031157 ACAAAATGTAACACCAGCTCGC 60.031 45.455 0.00 0.00 0.00 5.03
1871 1897 1.165270 AAATGTAACACCAGCTCGCC 58.835 50.000 0.00 0.00 0.00 5.54
1872 1898 0.324943 AATGTAACACCAGCTCGCCT 59.675 50.000 0.00 0.00 0.00 5.52
1873 1899 0.391661 ATGTAACACCAGCTCGCCTG 60.392 55.000 0.00 0.00 41.41 4.85
1874 1900 2.047274 TAACACCAGCTCGCCTGC 60.047 61.111 0.00 0.00 40.36 4.85
1875 1901 2.878089 TAACACCAGCTCGCCTGCA 61.878 57.895 0.00 0.00 40.36 4.41
1876 1902 2.390306 TAACACCAGCTCGCCTGCAA 62.390 55.000 0.00 0.00 40.36 4.08
1877 1903 3.429141 CACCAGCTCGCCTGCAAG 61.429 66.667 0.00 0.00 40.36 4.01
1878 1904 3.630013 ACCAGCTCGCCTGCAAGA 61.630 61.111 0.00 0.00 40.36 3.02
1879 1905 2.818714 CCAGCTCGCCTGCAAGAG 60.819 66.667 8.61 8.61 40.36 2.85
1893 1919 0.600057 CAAGAGCACTTTCCTTGCCC 59.400 55.000 0.00 0.00 41.18 5.36
1894 1920 0.185901 AAGAGCACTTTCCTTGCCCA 59.814 50.000 0.00 0.00 41.18 5.36
1895 1921 0.185901 AGAGCACTTTCCTTGCCCAA 59.814 50.000 0.00 0.00 41.18 4.12
1896 1922 0.315251 GAGCACTTTCCTTGCCCAAC 59.685 55.000 0.00 0.00 41.18 3.77
1897 1923 1.115326 AGCACTTTCCTTGCCCAACC 61.115 55.000 0.00 0.00 41.18 3.77
1898 1924 2.049435 CACTTTCCTTGCCCAACCC 58.951 57.895 0.00 0.00 0.00 4.11
1899 1925 0.758685 CACTTTCCTTGCCCAACCCA 60.759 55.000 0.00 0.00 0.00 4.51
1900 1926 0.469892 ACTTTCCTTGCCCAACCCAG 60.470 55.000 0.00 0.00 0.00 4.45
1901 1927 1.820010 CTTTCCTTGCCCAACCCAGC 61.820 60.000 0.00 0.00 0.00 4.85
1902 1928 3.826265 TTCCTTGCCCAACCCAGCC 62.826 63.158 0.00 0.00 0.00 4.85
1903 1929 4.619320 CCTTGCCCAACCCAGCCA 62.619 66.667 0.00 0.00 0.00 4.75
1904 1930 2.993264 CTTGCCCAACCCAGCCAG 60.993 66.667 0.00 0.00 0.00 4.85
1907 1933 4.047125 GCCCAACCCAGCCAGCTA 62.047 66.667 0.00 0.00 0.00 3.32
1908 1934 2.763215 CCCAACCCAGCCAGCTAA 59.237 61.111 0.00 0.00 0.00 3.09
1909 1935 1.307647 CCCAACCCAGCCAGCTAAT 59.692 57.895 0.00 0.00 0.00 1.73
1910 1936 0.324645 CCCAACCCAGCCAGCTAATT 60.325 55.000 0.00 0.00 0.00 1.40
1911 1937 1.560505 CCAACCCAGCCAGCTAATTT 58.439 50.000 0.00 0.00 0.00 1.82
1912 1938 1.901833 CCAACCCAGCCAGCTAATTTT 59.098 47.619 0.00 0.00 0.00 1.82
1913 1939 2.094026 CCAACCCAGCCAGCTAATTTTC 60.094 50.000 0.00 0.00 0.00 2.29
1914 1940 1.852633 ACCCAGCCAGCTAATTTTCC 58.147 50.000 0.00 0.00 0.00 3.13
1915 1941 1.359130 ACCCAGCCAGCTAATTTTCCT 59.641 47.619 0.00 0.00 0.00 3.36
1916 1942 2.580783 ACCCAGCCAGCTAATTTTCCTA 59.419 45.455 0.00 0.00 0.00 2.94
1917 1943 3.205282 ACCCAGCCAGCTAATTTTCCTAT 59.795 43.478 0.00 0.00 0.00 2.57
1918 1944 3.571401 CCCAGCCAGCTAATTTTCCTATG 59.429 47.826 0.00 0.00 0.00 2.23
1919 1945 4.210331 CCAGCCAGCTAATTTTCCTATGT 58.790 43.478 0.00 0.00 0.00 2.29
1920 1946 4.276926 CCAGCCAGCTAATTTTCCTATGTC 59.723 45.833 0.00 0.00 0.00 3.06
1921 1947 4.024556 CAGCCAGCTAATTTTCCTATGTCG 60.025 45.833 0.00 0.00 0.00 4.35
1922 1948 3.304057 GCCAGCTAATTTTCCTATGTCGC 60.304 47.826 0.00 0.00 0.00 5.19
1923 1949 4.130118 CCAGCTAATTTTCCTATGTCGCT 58.870 43.478 0.00 0.00 0.00 4.93
1924 1950 4.212214 CCAGCTAATTTTCCTATGTCGCTC 59.788 45.833 0.00 0.00 0.00 5.03
1925 1951 4.051922 AGCTAATTTTCCTATGTCGCTCG 58.948 43.478 0.00 0.00 0.00 5.03
1926 1952 4.049186 GCTAATTTTCCTATGTCGCTCGA 58.951 43.478 0.00 0.00 0.00 4.04
1927 1953 4.085004 GCTAATTTTCCTATGTCGCTCGAC 60.085 45.833 14.77 14.77 44.77 4.20
1935 1961 4.684265 GTCGCTCGACGCTCATAA 57.316 55.556 6.67 0.00 43.23 1.90
1936 1962 3.165559 GTCGCTCGACGCTCATAAT 57.834 52.632 6.67 0.00 43.23 1.28
1937 1963 1.478137 GTCGCTCGACGCTCATAATT 58.522 50.000 6.67 0.00 43.23 1.40
1938 1964 1.852895 GTCGCTCGACGCTCATAATTT 59.147 47.619 6.67 0.00 43.23 1.82
1939 1965 2.097829 GTCGCTCGACGCTCATAATTTC 60.098 50.000 6.67 0.00 43.23 2.17
1940 1966 2.120232 CGCTCGACGCTCATAATTTCT 58.880 47.619 5.53 0.00 36.13 2.52
1941 1967 2.535984 CGCTCGACGCTCATAATTTCTT 59.464 45.455 5.53 0.00 36.13 2.52
1942 1968 3.361147 CGCTCGACGCTCATAATTTCTTC 60.361 47.826 5.53 0.00 36.13 2.87
1943 1969 3.551890 GCTCGACGCTCATAATTTCTTCA 59.448 43.478 0.00 0.00 35.14 3.02
1944 1970 4.032900 GCTCGACGCTCATAATTTCTTCAA 59.967 41.667 0.00 0.00 35.14 2.69
1945 1971 5.445939 GCTCGACGCTCATAATTTCTTCAAA 60.446 40.000 0.00 0.00 35.14 2.69
1946 1972 6.094739 TCGACGCTCATAATTTCTTCAAAG 57.905 37.500 0.00 0.00 0.00 2.77
1947 1973 5.637810 TCGACGCTCATAATTTCTTCAAAGT 59.362 36.000 0.00 0.00 0.00 2.66
1948 1974 6.147164 TCGACGCTCATAATTTCTTCAAAGTT 59.853 34.615 0.00 0.00 0.00 2.66
1949 1975 6.797033 CGACGCTCATAATTTCTTCAAAGTTT 59.203 34.615 0.00 0.00 0.00 2.66
1950 1976 7.323656 CGACGCTCATAATTTCTTCAAAGTTTT 59.676 33.333 0.00 0.00 0.00 2.43
1951 1977 8.507470 ACGCTCATAATTTCTTCAAAGTTTTC 57.493 30.769 0.00 0.00 0.00 2.29
1952 1978 8.352942 ACGCTCATAATTTCTTCAAAGTTTTCT 58.647 29.630 0.00 0.00 0.00 2.52
1953 1979 8.633408 CGCTCATAATTTCTTCAAAGTTTTCTG 58.367 33.333 0.00 0.00 0.00 3.02
1954 1980 9.683069 GCTCATAATTTCTTCAAAGTTTTCTGA 57.317 29.630 0.00 0.00 0.00 3.27
1965 1991 9.334693 CTTCAAAGTTTTCTGATTTATTCTCGG 57.665 33.333 0.00 0.00 0.00 4.63
1966 1992 7.816640 TCAAAGTTTTCTGATTTATTCTCGGG 58.183 34.615 0.00 0.00 0.00 5.14
1967 1993 7.447238 TCAAAGTTTTCTGATTTATTCTCGGGT 59.553 33.333 0.00 0.00 0.00 5.28
1968 1994 7.761038 AAGTTTTCTGATTTATTCTCGGGTT 57.239 32.000 0.00 0.00 0.00 4.11
1969 1995 7.761038 AGTTTTCTGATTTATTCTCGGGTTT 57.239 32.000 0.00 0.00 0.00 3.27
1970 1996 7.817641 AGTTTTCTGATTTATTCTCGGGTTTC 58.182 34.615 0.00 0.00 0.00 2.78
1971 1997 6.753107 TTTCTGATTTATTCTCGGGTTTCC 57.247 37.500 0.00 0.00 0.00 3.13
1972 1998 5.693769 TCTGATTTATTCTCGGGTTTCCT 57.306 39.130 0.00 0.00 0.00 3.36
1973 1999 6.062258 TCTGATTTATTCTCGGGTTTCCTT 57.938 37.500 0.00 0.00 0.00 3.36
1974 2000 6.481643 TCTGATTTATTCTCGGGTTTCCTTT 58.518 36.000 0.00 0.00 0.00 3.11
1975 2001 6.946009 TCTGATTTATTCTCGGGTTTCCTTTT 59.054 34.615 0.00 0.00 0.00 2.27
1976 2002 7.450323 TCTGATTTATTCTCGGGTTTCCTTTTT 59.550 33.333 0.00 0.00 0.00 1.94
1977 2003 7.599171 TGATTTATTCTCGGGTTTCCTTTTTC 58.401 34.615 0.00 0.00 0.00 2.29
1978 2004 5.970317 TTATTCTCGGGTTTCCTTTTTCC 57.030 39.130 0.00 0.00 0.00 3.13
1979 2005 3.588210 TTCTCGGGTTTCCTTTTTCCT 57.412 42.857 0.00 0.00 0.00 3.36
1980 2006 3.588210 TCTCGGGTTTCCTTTTTCCTT 57.412 42.857 0.00 0.00 0.00 3.36
1981 2007 3.905968 TCTCGGGTTTCCTTTTTCCTTT 58.094 40.909 0.00 0.00 0.00 3.11
1982 2008 3.887110 TCTCGGGTTTCCTTTTTCCTTTC 59.113 43.478 0.00 0.00 0.00 2.62
1983 2009 3.633418 TCGGGTTTCCTTTTTCCTTTCA 58.367 40.909 0.00 0.00 0.00 2.69
1984 2010 3.634910 TCGGGTTTCCTTTTTCCTTTCAG 59.365 43.478 0.00 0.00 0.00 3.02
1985 2011 3.243737 CGGGTTTCCTTTTTCCTTTCAGG 60.244 47.826 0.00 0.00 36.46 3.86
1986 2012 3.709653 GGGTTTCCTTTTTCCTTTCAGGT 59.290 43.478 0.00 0.00 36.53 4.00
1987 2013 4.163458 GGGTTTCCTTTTTCCTTTCAGGTT 59.837 41.667 0.00 0.00 36.53 3.50
1988 2014 5.364446 GGGTTTCCTTTTTCCTTTCAGGTTA 59.636 40.000 0.00 0.00 36.53 2.85
1989 2015 6.042781 GGGTTTCCTTTTTCCTTTCAGGTTAT 59.957 38.462 0.00 0.00 36.53 1.89
1990 2016 7.419750 GGGTTTCCTTTTTCCTTTCAGGTTATT 60.420 37.037 0.00 0.00 36.53 1.40
1991 2017 7.990886 GGTTTCCTTTTTCCTTTCAGGTTATTT 59.009 33.333 0.00 0.00 36.53 1.40
1992 2018 9.391006 GTTTCCTTTTTCCTTTCAGGTTATTTT 57.609 29.630 0.00 0.00 36.53 1.82
1993 2019 9.607988 TTTCCTTTTTCCTTTCAGGTTATTTTC 57.392 29.630 0.00 0.00 36.53 2.29
1994 2020 8.547481 TCCTTTTTCCTTTCAGGTTATTTTCT 57.453 30.769 0.00 0.00 36.53 2.52
1995 2021 8.988060 TCCTTTTTCCTTTCAGGTTATTTTCTT 58.012 29.630 0.00 0.00 36.53 2.52
1996 2022 9.613428 CCTTTTTCCTTTCAGGTTATTTTCTTT 57.387 29.630 0.00 0.00 36.53 2.52
2014 2040 9.942850 ATTTTCTTTTCTTTTCAACTTTCCTCA 57.057 25.926 0.00 0.00 0.00 3.86
2015 2041 9.942850 TTTTCTTTTCTTTTCAACTTTCCTCAT 57.057 25.926 0.00 0.00 0.00 2.90
2016 2042 9.942850 TTTCTTTTCTTTTCAACTTTCCTCATT 57.057 25.926 0.00 0.00 0.00 2.57
2017 2043 9.586435 TTCTTTTCTTTTCAACTTTCCTCATTC 57.414 29.630 0.00 0.00 0.00 2.67
2018 2044 8.748412 TCTTTTCTTTTCAACTTTCCTCATTCA 58.252 29.630 0.00 0.00 0.00 2.57
2019 2045 9.538508 CTTTTCTTTTCAACTTTCCTCATTCAT 57.461 29.630 0.00 0.00 0.00 2.57
2059 2085 9.981114 TGTTTCCTTTCCTCATTTTCTATTTTC 57.019 29.630 0.00 0.00 0.00 2.29
2060 2086 9.424319 GTTTCCTTTCCTCATTTTCTATTTTCC 57.576 33.333 0.00 0.00 0.00 3.13
2061 2087 8.956446 TTCCTTTCCTCATTTTCTATTTTCCT 57.044 30.769 0.00 0.00 0.00 3.36
2062 2088 8.956446 TCCTTTCCTCATTTTCTATTTTCCTT 57.044 30.769 0.00 0.00 0.00 3.36
2063 2089 9.379770 TCCTTTCCTCATTTTCTATTTTCCTTT 57.620 29.630 0.00 0.00 0.00 3.11
2100 2126 7.809546 TTCTTCTTTCTCTTCTTTCCTTTCC 57.190 36.000 0.00 0.00 0.00 3.13
2101 2127 6.299922 TCTTCTTTCTCTTCTTTCCTTTCCC 58.700 40.000 0.00 0.00 0.00 3.97
2102 2128 5.913946 TCTTTCTCTTCTTTCCTTTCCCT 57.086 39.130 0.00 0.00 0.00 4.20
2103 2129 6.267492 TCTTTCTCTTCTTTCCTTTCCCTT 57.733 37.500 0.00 0.00 0.00 3.95
2104 2130 6.673583 TCTTTCTCTTCTTTCCTTTCCCTTT 58.326 36.000 0.00 0.00 0.00 3.11
2105 2131 7.126061 TCTTTCTCTTCTTTCCTTTCCCTTTT 58.874 34.615 0.00 0.00 0.00 2.27
2106 2132 7.619698 TCTTTCTCTTCTTTCCTTTCCCTTTTT 59.380 33.333 0.00 0.00 0.00 1.94
2129 2155 6.844696 TTCGAATTCTGATTTATTCTCGGG 57.155 37.500 3.52 0.00 0.00 5.14
2130 2156 5.914033 TCGAATTCTGATTTATTCTCGGGT 58.086 37.500 3.52 0.00 0.00 5.28
2131 2157 6.346096 TCGAATTCTGATTTATTCTCGGGTT 58.654 36.000 3.52 0.00 0.00 4.11
2132 2158 6.821665 TCGAATTCTGATTTATTCTCGGGTTT 59.178 34.615 3.52 0.00 0.00 3.27
2133 2159 7.011109 TCGAATTCTGATTTATTCTCGGGTTTC 59.989 37.037 3.52 0.00 0.00 2.78
2134 2160 6.944234 ATTCTGATTTATTCTCGGGTTTCC 57.056 37.500 0.00 0.00 0.00 3.13
2135 2161 5.693769 TCTGATTTATTCTCGGGTTTCCT 57.306 39.130 0.00 0.00 0.00 3.36
2136 2162 6.062258 TCTGATTTATTCTCGGGTTTCCTT 57.938 37.500 0.00 0.00 0.00 3.36
2137 2163 6.481643 TCTGATTTATTCTCGGGTTTCCTTT 58.518 36.000 0.00 0.00 0.00 3.11
2138 2164 6.946009 TCTGATTTATTCTCGGGTTTCCTTTT 59.054 34.615 0.00 0.00 0.00 2.27
2139 2165 7.450323 TCTGATTTATTCTCGGGTTTCCTTTTT 59.550 33.333 0.00 0.00 0.00 1.94
2140 2166 7.599171 TGATTTATTCTCGGGTTTCCTTTTTC 58.401 34.615 0.00 0.00 0.00 2.29
2141 2167 5.970317 TTATTCTCGGGTTTCCTTTTTCC 57.030 39.130 0.00 0.00 0.00 3.13
2142 2168 3.588210 TTCTCGGGTTTCCTTTTTCCT 57.412 42.857 0.00 0.00 0.00 3.36
2143 2169 3.588210 TCTCGGGTTTCCTTTTTCCTT 57.412 42.857 0.00 0.00 0.00 3.36
2144 2170 3.905968 TCTCGGGTTTCCTTTTTCCTTT 58.094 40.909 0.00 0.00 0.00 3.11
2145 2171 3.887110 TCTCGGGTTTCCTTTTTCCTTTC 59.113 43.478 0.00 0.00 0.00 2.62
2146 2172 3.633418 TCGGGTTTCCTTTTTCCTTTCA 58.367 40.909 0.00 0.00 0.00 2.69
2147 2173 3.634910 TCGGGTTTCCTTTTTCCTTTCAG 59.365 43.478 0.00 0.00 0.00 3.02
2148 2174 3.243737 CGGGTTTCCTTTTTCCTTTCAGG 60.244 47.826 0.00 0.00 36.46 3.86
2149 2175 3.709653 GGGTTTCCTTTTTCCTTTCAGGT 59.290 43.478 0.00 0.00 36.53 4.00
2150 2176 4.897076 GGGTTTCCTTTTTCCTTTCAGGTA 59.103 41.667 0.00 0.00 36.53 3.08
2151 2177 5.364446 GGGTTTCCTTTTTCCTTTCAGGTAA 59.636 40.000 0.00 0.00 36.53 2.85
2152 2178 6.042781 GGGTTTCCTTTTTCCTTTCAGGTAAT 59.957 38.462 0.00 0.00 36.53 1.89
2153 2179 7.419750 GGGTTTCCTTTTTCCTTTCAGGTAATT 60.420 37.037 0.00 0.00 36.53 1.40
2154 2180 7.990886 GGTTTCCTTTTTCCTTTCAGGTAATTT 59.009 33.333 0.00 0.00 36.53 1.82
2155 2181 9.391006 GTTTCCTTTTTCCTTTCAGGTAATTTT 57.609 29.630 0.00 0.00 36.53 1.82
2156 2182 9.967451 TTTCCTTTTTCCTTTCAGGTAATTTTT 57.033 25.926 0.00 0.00 36.53 1.94
2184 2210 9.579768 TCGAATTTCTGATTTGAAAGAAAAACA 57.420 25.926 2.31 0.00 43.57 2.83
2250 2276 9.965824 AAAAGATACGATGAACAATTTTTCAGT 57.034 25.926 12.27 8.35 38.87 3.41
2253 2279 9.214957 AGATACGATGAACAATTTTTCAGTACA 57.785 29.630 12.27 0.03 38.87 2.90
2254 2280 9.820229 GATACGATGAACAATTTTTCAGTACAA 57.180 29.630 12.27 0.00 38.87 2.41
2256 2282 8.335256 ACGATGAACAATTTTTCAGTACAAAC 57.665 30.769 12.27 0.00 38.87 2.93
2257 2283 7.971168 ACGATGAACAATTTTTCAGTACAAACA 59.029 29.630 12.27 0.00 38.87 2.83
2258 2284 8.259194 CGATGAACAATTTTTCAGTACAAACAC 58.741 33.333 12.27 0.00 38.87 3.32
2259 2285 8.994429 ATGAACAATTTTTCAGTACAAACACA 57.006 26.923 12.27 0.00 38.87 3.72
2260 2286 8.994429 TGAACAATTTTTCAGTACAAACACAT 57.006 26.923 2.88 0.00 31.68 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 0.105593 CCGGTGCAGATGCTAGTGAT 59.894 55.000 6.35 0.00 42.66 3.06
133 134 0.674895 GAAGAACCGGTGCAGATGCT 60.675 55.000 16.99 0.00 42.66 3.79
172 173 4.170062 GTCGCCGACGGTCATCGA 62.170 66.667 16.73 12.86 45.13 3.59
338 340 0.378610 GCTGATTTCTAACCCAGCGC 59.621 55.000 0.00 0.00 41.86 5.92
350 352 4.024556 CACAAGAGTTGAAGACGCTGATTT 60.025 41.667 0.00 0.00 38.49 2.17
385 387 1.669779 GGAATCTCATGCAGTGCTCAC 59.330 52.381 17.60 0.00 0.00 3.51
500 502 0.849094 TTGGGGTATTGGCTGGAGGT 60.849 55.000 0.00 0.00 0.00 3.85
529 531 2.032528 CTCCAGCTCCAACGCCAA 59.967 61.111 0.00 0.00 0.00 4.52
530 532 4.704833 GCTCCAGCTCCAACGCCA 62.705 66.667 0.00 0.00 38.21 5.69
590 598 0.912486 CTTACCCACCCCCTCTCTTG 59.088 60.000 0.00 0.00 0.00 3.02
639 649 0.033109 TCTTCCTCCTCTCCATCGCA 60.033 55.000 0.00 0.00 0.00 5.10
703 716 2.105477 AGTCAGGCACATCACAGAGTTT 59.895 45.455 0.00 0.00 0.00 2.66
804 817 2.880770 GGGCATTGGATGAACCGAA 58.119 52.632 0.00 0.00 42.61 4.30
940 953 0.770557 AAGTGAGTTGGGCCACCCTA 60.771 55.000 5.23 0.00 45.70 3.53
1040 1054 1.768275 TGTTCCTCAGCTTGAACTCCA 59.232 47.619 16.98 0.70 41.10 3.86
1101 1115 1.206811 TGATCCATGTCACCCTGCCA 61.207 55.000 0.00 0.00 0.00 4.92
1113 1127 1.935400 TGGCCCAACCCTGATCCAT 60.935 57.895 0.00 0.00 37.83 3.41
1141 1156 6.159299 AGACGATCTTGATCTGATGAACAT 57.841 37.500 8.70 0.00 0.00 2.71
1142 1157 5.588958 AGACGATCTTGATCTGATGAACA 57.411 39.130 8.70 0.00 0.00 3.18
1162 1177 2.299013 AGCTTGAACGTCACCATGTAGA 59.701 45.455 0.00 0.00 0.00 2.59
1187 1202 1.481056 CCTTGAGGGTGTCGGGAGTT 61.481 60.000 0.00 0.00 0.00 3.01
1229 1244 3.146066 GCACTTGTTGACCACCTCAATA 58.854 45.455 0.00 0.00 41.10 1.90
1353 1368 9.014533 CATAGTATCACACATCATAACGATAGC 57.985 37.037 0.00 0.00 42.67 2.97
1401 1422 7.605691 GGATAGCATAAACAGAGCATCAACTAT 59.394 37.037 0.00 0.00 37.82 2.12
1426 1447 4.769688 TGTACCACAATCATAAGCAGAGG 58.230 43.478 0.00 0.00 0.00 3.69
1457 1479 1.000506 GAGGTTACCAGCACACTTCGA 59.999 52.381 3.51 0.00 0.00 3.71
1495 1517 0.036732 AACGCCTGATGTGTGGTCAT 59.963 50.000 0.00 0.00 37.86 3.06
1497 1519 1.868997 CAACGCCTGATGTGTGGTC 59.131 57.895 0.00 0.00 37.86 4.02
1539 1562 3.500982 CTGCATGTTAATGGACAAACCG 58.499 45.455 0.00 0.00 42.61 4.44
1550 1573 2.432146 TGTTTGGTTGCCTGCATGTTAA 59.568 40.909 0.00 0.00 0.00 2.01
1598 1623 1.279496 TGCCTACATGTCCTCTTGCT 58.721 50.000 0.00 0.00 0.00 3.91
1607 1632 5.531634 CAAGTTGTTTGATTGCCTACATGT 58.468 37.500 2.69 2.69 39.21 3.21
1612 1637 3.382865 TGTGCAAGTTGTTTGATTGCCTA 59.617 39.130 4.48 0.00 46.82 3.93
1619 1644 3.162202 CACCATGTGCAAGTTGTTTGA 57.838 42.857 4.48 0.00 39.21 2.69
1672 1697 4.036498 GCTGCATTGCATAGTCTTCTCAAT 59.964 41.667 12.53 0.00 38.13 2.57
1681 1706 3.272574 ACAGTAGCTGCATTGCATAGT 57.727 42.857 12.53 2.82 38.13 2.12
1729 1755 4.946157 TCGTCCTCCTTACTACTAAACCAG 59.054 45.833 0.00 0.00 0.00 4.00
1732 1758 5.280164 GCATCGTCCTCCTTACTACTAAAC 58.720 45.833 0.00 0.00 0.00 2.01
1735 1761 3.136763 CGCATCGTCCTCCTTACTACTA 58.863 50.000 0.00 0.00 0.00 1.82
1736 1762 1.948145 CGCATCGTCCTCCTTACTACT 59.052 52.381 0.00 0.00 0.00 2.57
1737 1763 1.599916 GCGCATCGTCCTCCTTACTAC 60.600 57.143 0.30 0.00 0.00 2.73
1738 1764 0.666913 GCGCATCGTCCTCCTTACTA 59.333 55.000 0.30 0.00 0.00 1.82
1739 1765 1.437986 GCGCATCGTCCTCCTTACT 59.562 57.895 0.30 0.00 0.00 2.24
1740 1766 1.944676 CGCGCATCGTCCTCCTTAC 60.945 63.158 8.75 0.00 0.00 2.34
1741 1767 2.411701 CGCGCATCGTCCTCCTTA 59.588 61.111 8.75 0.00 0.00 2.69
1750 1776 1.200483 AACTCATAGAACGCGCATCG 58.800 50.000 5.73 0.00 45.38 3.84
1751 1777 3.658351 AAAACTCATAGAACGCGCATC 57.342 42.857 5.73 4.95 0.00 3.91
1785 1811 4.432712 GGAGACATGTTGTGCAAGTTTTT 58.567 39.130 0.00 0.00 0.00 1.94
1786 1812 3.489059 CGGAGACATGTTGTGCAAGTTTT 60.489 43.478 0.00 0.00 0.00 2.43
1787 1813 2.033299 CGGAGACATGTTGTGCAAGTTT 59.967 45.455 0.00 0.00 0.00 2.66
1788 1814 1.603802 CGGAGACATGTTGTGCAAGTT 59.396 47.619 0.00 0.00 0.00 2.66
1789 1815 1.229428 CGGAGACATGTTGTGCAAGT 58.771 50.000 0.00 0.00 0.00 3.16
1790 1816 0.518636 CCGGAGACATGTTGTGCAAG 59.481 55.000 0.00 0.00 0.00 4.01
1791 1817 0.179032 ACCGGAGACATGTTGTGCAA 60.179 50.000 9.46 0.00 0.00 4.08
1792 1818 0.884259 CACCGGAGACATGTTGTGCA 60.884 55.000 9.46 0.00 0.00 4.57
1793 1819 1.577328 CCACCGGAGACATGTTGTGC 61.577 60.000 9.46 0.00 0.00 4.57
1794 1820 1.577328 GCCACCGGAGACATGTTGTG 61.577 60.000 9.46 3.36 0.00 3.33
1795 1821 1.302511 GCCACCGGAGACATGTTGT 60.303 57.895 9.46 0.00 0.00 3.32
1796 1822 2.040544 GGCCACCGGAGACATGTTG 61.041 63.158 9.46 0.00 0.00 3.33
1797 1823 1.779061 AAGGCCACCGGAGACATGTT 61.779 55.000 9.46 0.00 0.00 2.71
1798 1824 2.224159 AAGGCCACCGGAGACATGT 61.224 57.895 9.46 0.00 0.00 3.21
1799 1825 1.746615 CAAGGCCACCGGAGACATG 60.747 63.158 9.46 0.00 0.00 3.21
1800 1826 2.671070 CAAGGCCACCGGAGACAT 59.329 61.111 9.46 0.00 0.00 3.06
1801 1827 3.636231 CCAAGGCCACCGGAGACA 61.636 66.667 9.46 0.00 0.00 3.41
1804 1830 4.785453 GAGCCAAGGCCACCGGAG 62.785 72.222 9.46 0.00 43.17 4.63
1808 1834 4.748144 CCTGGAGCCAAGGCCACC 62.748 72.222 5.01 12.18 43.17 4.61
1813 1839 0.548031 TATTCTGCCTGGAGCCAAGG 59.452 55.000 0.00 0.00 42.71 3.61
1814 1840 2.653234 ATATTCTGCCTGGAGCCAAG 57.347 50.000 0.00 0.00 42.71 3.61
1815 1841 4.729552 ATAATATTCTGCCTGGAGCCAA 57.270 40.909 0.00 0.00 42.71 4.52
1816 1842 4.729552 AATAATATTCTGCCTGGAGCCA 57.270 40.909 0.00 0.00 42.71 4.75
1817 1843 5.320277 AGAAATAATATTCTGCCTGGAGCC 58.680 41.667 0.00 0.00 42.71 4.70
1818 1844 5.121454 CGAGAAATAATATTCTGCCTGGAGC 59.879 44.000 0.00 0.00 39.70 4.70
1819 1845 5.121454 GCGAGAAATAATATTCTGCCTGGAG 59.879 44.000 0.00 0.00 39.70 3.86
1820 1846 4.997395 GCGAGAAATAATATTCTGCCTGGA 59.003 41.667 0.00 0.00 39.70 3.86
1821 1847 4.154918 GGCGAGAAATAATATTCTGCCTGG 59.845 45.833 16.35 0.00 43.11 4.45
1822 1848 5.288543 GGCGAGAAATAATATTCTGCCTG 57.711 43.478 16.35 0.13 43.11 4.85
1823 1849 5.234466 AGGCGAGAAATAATATTCTGCCT 57.766 39.130 18.67 18.67 46.83 4.75
1824 1850 6.166982 AGTAGGCGAGAAATAATATTCTGCC 58.833 40.000 16.08 16.08 44.74 4.85
1825 1851 7.813148 TGTAGTAGGCGAGAAATAATATTCTGC 59.187 37.037 0.00 0.00 39.70 4.26
1826 1852 9.692749 TTGTAGTAGGCGAGAAATAATATTCTG 57.307 33.333 0.00 0.00 39.70 3.02
1831 1857 9.826574 ACATTTTGTAGTAGGCGAGAAATAATA 57.173 29.630 0.00 0.00 0.00 0.98
1832 1858 8.732746 ACATTTTGTAGTAGGCGAGAAATAAT 57.267 30.769 0.00 0.00 0.00 1.28
1833 1859 9.656040 TTACATTTTGTAGTAGGCGAGAAATAA 57.344 29.630 0.00 0.00 33.92 1.40
1834 1860 9.090692 GTTACATTTTGTAGTAGGCGAGAAATA 57.909 33.333 0.00 0.00 33.92 1.40
1835 1861 7.604927 TGTTACATTTTGTAGTAGGCGAGAAAT 59.395 33.333 0.00 0.00 33.92 2.17
1836 1862 6.930164 TGTTACATTTTGTAGTAGGCGAGAAA 59.070 34.615 0.00 0.00 33.92 2.52
1837 1863 6.366877 GTGTTACATTTTGTAGTAGGCGAGAA 59.633 38.462 0.00 0.00 33.92 2.87
1838 1864 5.865552 GTGTTACATTTTGTAGTAGGCGAGA 59.134 40.000 0.00 0.00 33.92 4.04
1839 1865 5.063060 GGTGTTACATTTTGTAGTAGGCGAG 59.937 44.000 0.00 0.00 33.92 5.03
1840 1866 4.931002 GGTGTTACATTTTGTAGTAGGCGA 59.069 41.667 0.00 0.00 33.92 5.54
1841 1867 4.691685 TGGTGTTACATTTTGTAGTAGGCG 59.308 41.667 0.00 0.00 33.92 5.52
1842 1868 5.391629 GCTGGTGTTACATTTTGTAGTAGGC 60.392 44.000 0.00 0.00 33.92 3.93
1843 1869 5.938125 AGCTGGTGTTACATTTTGTAGTAGG 59.062 40.000 0.00 0.00 33.92 3.18
1844 1870 6.183360 CGAGCTGGTGTTACATTTTGTAGTAG 60.183 42.308 0.00 0.00 33.92 2.57
1845 1871 5.636121 CGAGCTGGTGTTACATTTTGTAGTA 59.364 40.000 0.00 0.00 33.92 1.82
1846 1872 4.451096 CGAGCTGGTGTTACATTTTGTAGT 59.549 41.667 0.00 0.00 33.92 2.73
1847 1873 4.669197 GCGAGCTGGTGTTACATTTTGTAG 60.669 45.833 0.00 0.00 33.92 2.74
1848 1874 3.187637 GCGAGCTGGTGTTACATTTTGTA 59.812 43.478 0.00 0.00 0.00 2.41
1849 1875 2.031157 GCGAGCTGGTGTTACATTTTGT 60.031 45.455 0.00 0.00 0.00 2.83
1850 1876 2.584791 GCGAGCTGGTGTTACATTTTG 58.415 47.619 0.00 0.00 0.00 2.44
1851 1877 1.539827 GGCGAGCTGGTGTTACATTTT 59.460 47.619 0.00 0.00 0.00 1.82
1852 1878 1.165270 GGCGAGCTGGTGTTACATTT 58.835 50.000 0.00 0.00 0.00 2.32
1853 1879 0.324943 AGGCGAGCTGGTGTTACATT 59.675 50.000 0.00 0.00 0.00 2.71
1854 1880 0.391661 CAGGCGAGCTGGTGTTACAT 60.392 55.000 0.00 0.00 0.00 2.29
1855 1881 1.005037 CAGGCGAGCTGGTGTTACA 60.005 57.895 0.00 0.00 0.00 2.41
1856 1882 2.391389 GCAGGCGAGCTGGTGTTAC 61.391 63.158 0.00 0.00 0.00 2.50
1857 1883 2.047274 GCAGGCGAGCTGGTGTTA 60.047 61.111 0.00 0.00 0.00 2.41
1858 1884 3.772853 TTGCAGGCGAGCTGGTGTT 62.773 57.895 0.00 0.00 34.99 3.32
1859 1885 4.254709 TTGCAGGCGAGCTGGTGT 62.255 61.111 0.00 0.00 34.99 4.16
1860 1886 3.429141 CTTGCAGGCGAGCTGGTG 61.429 66.667 0.00 0.00 34.99 4.17
1861 1887 3.602513 CTCTTGCAGGCGAGCTGGT 62.603 63.158 3.56 0.00 34.99 4.00
1862 1888 2.818714 CTCTTGCAGGCGAGCTGG 60.819 66.667 3.56 0.00 34.99 4.85
1863 1889 3.497932 GCTCTTGCAGGCGAGCTG 61.498 66.667 20.69 5.74 46.87 4.24
1874 1900 0.600057 GGGCAAGGAAAGTGCTCTTG 59.400 55.000 1.02 0.00 39.52 3.02
1875 1901 0.185901 TGGGCAAGGAAAGTGCTCTT 59.814 50.000 0.00 0.00 43.27 2.85
1876 1902 0.185901 TTGGGCAAGGAAAGTGCTCT 59.814 50.000 0.00 0.00 43.27 4.09
1877 1903 0.315251 GTTGGGCAAGGAAAGTGCTC 59.685 55.000 0.00 0.00 43.16 4.26
1878 1904 1.115326 GGTTGGGCAAGGAAAGTGCT 61.115 55.000 0.00 0.00 41.88 4.40
1879 1905 1.367471 GGTTGGGCAAGGAAAGTGC 59.633 57.895 0.00 0.00 41.45 4.40
1880 1906 0.758685 TGGGTTGGGCAAGGAAAGTG 60.759 55.000 0.00 0.00 0.00 3.16
1881 1907 0.469892 CTGGGTTGGGCAAGGAAAGT 60.470 55.000 0.00 0.00 0.00 2.66
1882 1908 1.820010 GCTGGGTTGGGCAAGGAAAG 61.820 60.000 0.00 0.00 0.00 2.62
1883 1909 1.836604 GCTGGGTTGGGCAAGGAAA 60.837 57.895 0.00 0.00 0.00 3.13
1884 1910 2.203625 GCTGGGTTGGGCAAGGAA 60.204 61.111 0.00 0.00 0.00 3.36
1885 1911 4.299796 GGCTGGGTTGGGCAAGGA 62.300 66.667 0.00 0.00 0.00 3.36
1886 1912 4.619320 TGGCTGGGTTGGGCAAGG 62.619 66.667 0.00 0.00 36.34 3.61
1887 1913 2.993264 CTGGCTGGGTTGGGCAAG 60.993 66.667 0.00 0.00 38.72 4.01
1890 1916 2.861271 ATTAGCTGGCTGGGTTGGGC 62.861 60.000 5.25 0.00 0.00 5.36
1891 1917 0.324645 AATTAGCTGGCTGGGTTGGG 60.325 55.000 5.25 0.00 0.00 4.12
1892 1918 1.560505 AAATTAGCTGGCTGGGTTGG 58.439 50.000 5.25 0.00 0.00 3.77
1893 1919 2.094026 GGAAAATTAGCTGGCTGGGTTG 60.094 50.000 5.25 0.00 0.00 3.77
1894 1920 2.179427 GGAAAATTAGCTGGCTGGGTT 58.821 47.619 5.25 0.00 0.00 4.11
1895 1921 1.359130 AGGAAAATTAGCTGGCTGGGT 59.641 47.619 5.25 0.00 0.00 4.51
1896 1922 2.149973 AGGAAAATTAGCTGGCTGGG 57.850 50.000 5.25 0.00 0.00 4.45
1897 1923 4.210331 ACATAGGAAAATTAGCTGGCTGG 58.790 43.478 5.25 0.00 0.00 4.85
1898 1924 4.024556 CGACATAGGAAAATTAGCTGGCTG 60.025 45.833 5.25 0.00 0.00 4.85
1899 1925 4.130118 CGACATAGGAAAATTAGCTGGCT 58.870 43.478 0.00 0.00 0.00 4.75
1900 1926 3.304057 GCGACATAGGAAAATTAGCTGGC 60.304 47.826 0.00 0.00 0.00 4.85
1901 1927 4.130118 AGCGACATAGGAAAATTAGCTGG 58.870 43.478 0.00 0.00 0.00 4.85
1902 1928 4.084849 CGAGCGACATAGGAAAATTAGCTG 60.085 45.833 0.00 0.00 32.14 4.24
1903 1929 4.051922 CGAGCGACATAGGAAAATTAGCT 58.948 43.478 0.00 0.00 34.92 3.32
1904 1930 4.049186 TCGAGCGACATAGGAAAATTAGC 58.951 43.478 0.00 0.00 0.00 3.09
1905 1931 4.146616 CGTCGAGCGACATAGGAAAATTAG 59.853 45.833 21.09 0.00 44.77 1.73
1906 1932 4.039703 CGTCGAGCGACATAGGAAAATTA 58.960 43.478 21.09 0.00 44.77 1.40
1907 1933 2.858344 CGTCGAGCGACATAGGAAAATT 59.142 45.455 21.09 0.00 44.77 1.82
1908 1934 2.460918 CGTCGAGCGACATAGGAAAAT 58.539 47.619 21.09 0.00 44.77 1.82
1909 1935 1.904144 CGTCGAGCGACATAGGAAAA 58.096 50.000 21.09 0.00 44.77 2.29
1910 1936 0.524816 GCGTCGAGCGACATAGGAAA 60.525 55.000 21.09 0.00 44.77 3.13
1911 1937 1.063649 GCGTCGAGCGACATAGGAA 59.936 57.895 21.09 0.00 44.77 3.36
1912 1938 2.713770 GCGTCGAGCGACATAGGA 59.286 61.111 21.09 0.00 44.77 2.94
1922 1948 5.702622 TTGAAGAAATTATGAGCGTCGAG 57.297 39.130 0.00 0.00 0.00 4.04
1923 1949 5.637810 ACTTTGAAGAAATTATGAGCGTCGA 59.362 36.000 0.00 0.00 0.00 4.20
1924 1950 5.858475 ACTTTGAAGAAATTATGAGCGTCG 58.142 37.500 0.00 0.00 0.00 5.12
1925 1951 8.507470 AAAACTTTGAAGAAATTATGAGCGTC 57.493 30.769 0.00 0.00 0.00 5.19
1926 1952 8.352942 AGAAAACTTTGAAGAAATTATGAGCGT 58.647 29.630 0.00 0.00 0.00 5.07
1927 1953 8.633408 CAGAAAACTTTGAAGAAATTATGAGCG 58.367 33.333 0.00 0.00 0.00 5.03
1928 1954 9.683069 TCAGAAAACTTTGAAGAAATTATGAGC 57.317 29.630 0.00 0.00 0.00 4.26
1939 1965 9.334693 CCGAGAATAAATCAGAAAACTTTGAAG 57.665 33.333 0.00 0.00 0.00 3.02
1940 1966 8.296713 CCCGAGAATAAATCAGAAAACTTTGAA 58.703 33.333 0.00 0.00 0.00 2.69
1941 1967 7.447238 ACCCGAGAATAAATCAGAAAACTTTGA 59.553 33.333 0.00 0.00 0.00 2.69
1942 1968 7.593825 ACCCGAGAATAAATCAGAAAACTTTG 58.406 34.615 0.00 0.00 0.00 2.77
1943 1969 7.761038 ACCCGAGAATAAATCAGAAAACTTT 57.239 32.000 0.00 0.00 0.00 2.66
1944 1970 7.761038 AACCCGAGAATAAATCAGAAAACTT 57.239 32.000 0.00 0.00 0.00 2.66
1945 1971 7.094334 GGAAACCCGAGAATAAATCAGAAAACT 60.094 37.037 0.00 0.00 0.00 2.66
1946 1972 7.027760 GGAAACCCGAGAATAAATCAGAAAAC 58.972 38.462 0.00 0.00 0.00 2.43
1947 1973 6.946009 AGGAAACCCGAGAATAAATCAGAAAA 59.054 34.615 0.00 0.00 0.00 2.29
1948 1974 6.481643 AGGAAACCCGAGAATAAATCAGAAA 58.518 36.000 0.00 0.00 0.00 2.52
1949 1975 6.062258 AGGAAACCCGAGAATAAATCAGAA 57.938 37.500 0.00 0.00 0.00 3.02
1950 1976 5.693769 AGGAAACCCGAGAATAAATCAGA 57.306 39.130 0.00 0.00 0.00 3.27
1951 1977 6.759497 AAAGGAAACCCGAGAATAAATCAG 57.241 37.500 0.00 0.00 0.00 2.90
1952 1978 7.309560 GGAAAAAGGAAACCCGAGAATAAATCA 60.310 37.037 0.00 0.00 0.00 2.57
1953 1979 7.033791 GGAAAAAGGAAACCCGAGAATAAATC 58.966 38.462 0.00 0.00 0.00 2.17
1954 1980 6.724441 AGGAAAAAGGAAACCCGAGAATAAAT 59.276 34.615 0.00 0.00 0.00 1.40
1955 1981 6.072649 AGGAAAAAGGAAACCCGAGAATAAA 58.927 36.000 0.00 0.00 0.00 1.40
1956 1982 5.637127 AGGAAAAAGGAAACCCGAGAATAA 58.363 37.500 0.00 0.00 0.00 1.40
1957 1983 5.251182 AGGAAAAAGGAAACCCGAGAATA 57.749 39.130 0.00 0.00 0.00 1.75
1958 1984 4.114015 AGGAAAAAGGAAACCCGAGAAT 57.886 40.909 0.00 0.00 0.00 2.40
1959 1985 3.588210 AGGAAAAAGGAAACCCGAGAA 57.412 42.857 0.00 0.00 0.00 2.87
1960 1986 3.588210 AAGGAAAAAGGAAACCCGAGA 57.412 42.857 0.00 0.00 0.00 4.04
1961 1987 3.634910 TGAAAGGAAAAAGGAAACCCGAG 59.365 43.478 0.00 0.00 0.00 4.63
1962 1988 3.633418 TGAAAGGAAAAAGGAAACCCGA 58.367 40.909 0.00 0.00 0.00 5.14
1963 1989 3.977427 CTGAAAGGAAAAAGGAAACCCG 58.023 45.455 0.00 0.00 0.00 5.28
1988 2014 9.942850 TGAGGAAAGTTGAAAAGAAAAGAAAAT 57.057 25.926 0.00 0.00 0.00 1.82
1989 2015 9.942850 ATGAGGAAAGTTGAAAAGAAAAGAAAA 57.057 25.926 0.00 0.00 0.00 2.29
1990 2016 9.942850 AATGAGGAAAGTTGAAAAGAAAAGAAA 57.057 25.926 0.00 0.00 0.00 2.52
1991 2017 9.586435 GAATGAGGAAAGTTGAAAAGAAAAGAA 57.414 29.630 0.00 0.00 0.00 2.52
1992 2018 8.748412 TGAATGAGGAAAGTTGAAAAGAAAAGA 58.252 29.630 0.00 0.00 0.00 2.52
1993 2019 8.931385 TGAATGAGGAAAGTTGAAAAGAAAAG 57.069 30.769 0.00 0.00 0.00 2.27
2033 2059 9.981114 GAAAATAGAAAATGAGGAAAGGAAACA 57.019 29.630 0.00 0.00 0.00 2.83
2034 2060 9.424319 GGAAAATAGAAAATGAGGAAAGGAAAC 57.576 33.333 0.00 0.00 0.00 2.78
2035 2061 9.379770 AGGAAAATAGAAAATGAGGAAAGGAAA 57.620 29.630 0.00 0.00 0.00 3.13
2036 2062 8.956446 AGGAAAATAGAAAATGAGGAAAGGAA 57.044 30.769 0.00 0.00 0.00 3.36
2037 2063 8.956446 AAGGAAAATAGAAAATGAGGAAAGGA 57.044 30.769 0.00 0.00 0.00 3.36
2074 2100 9.508642 GGAAAGGAAAGAAGAGAAAGAAGAATA 57.491 33.333 0.00 0.00 0.00 1.75
2075 2101 7.450014 GGGAAAGGAAAGAAGAGAAAGAAGAAT 59.550 37.037 0.00 0.00 0.00 2.40
2076 2102 6.773200 GGGAAAGGAAAGAAGAGAAAGAAGAA 59.227 38.462 0.00 0.00 0.00 2.52
2077 2103 6.101881 AGGGAAAGGAAAGAAGAGAAAGAAGA 59.898 38.462 0.00 0.00 0.00 2.87
2078 2104 6.303054 AGGGAAAGGAAAGAAGAGAAAGAAG 58.697 40.000 0.00 0.00 0.00 2.85
2079 2105 6.267492 AGGGAAAGGAAAGAAGAGAAAGAA 57.733 37.500 0.00 0.00 0.00 2.52
2080 2106 5.913946 AGGGAAAGGAAAGAAGAGAAAGA 57.086 39.130 0.00 0.00 0.00 2.52
2081 2107 6.968263 AAAGGGAAAGGAAAGAAGAGAAAG 57.032 37.500 0.00 0.00 0.00 2.62
2082 2108 7.733773 AAAAAGGGAAAGGAAAGAAGAGAAA 57.266 32.000 0.00 0.00 0.00 2.52
2103 2129 8.181573 CCCGAGAATAAATCAGAATTCGAAAAA 58.818 33.333 0.00 0.00 37.22 1.94
2104 2130 7.335924 ACCCGAGAATAAATCAGAATTCGAAAA 59.664 33.333 0.00 0.00 37.22 2.29
2105 2131 6.821665 ACCCGAGAATAAATCAGAATTCGAAA 59.178 34.615 0.00 0.00 37.22 3.46
2106 2132 6.346096 ACCCGAGAATAAATCAGAATTCGAA 58.654 36.000 0.00 0.00 37.22 3.71
2107 2133 5.914033 ACCCGAGAATAAATCAGAATTCGA 58.086 37.500 0.00 1.20 37.22 3.71
2108 2134 6.604735 AACCCGAGAATAAATCAGAATTCG 57.395 37.500 0.00 0.00 37.22 3.34
2109 2135 7.283354 AGGAAACCCGAGAATAAATCAGAATTC 59.717 37.037 0.00 0.00 33.21 2.17
2110 2136 7.119387 AGGAAACCCGAGAATAAATCAGAATT 58.881 34.615 0.00 0.00 0.00 2.17
2111 2137 6.663734 AGGAAACCCGAGAATAAATCAGAAT 58.336 36.000 0.00 0.00 0.00 2.40
2112 2138 6.062258 AGGAAACCCGAGAATAAATCAGAA 57.938 37.500 0.00 0.00 0.00 3.02
2113 2139 5.693769 AGGAAACCCGAGAATAAATCAGA 57.306 39.130 0.00 0.00 0.00 3.27
2114 2140 6.759497 AAAGGAAACCCGAGAATAAATCAG 57.241 37.500 0.00 0.00 0.00 2.90
2115 2141 7.309560 GGAAAAAGGAAACCCGAGAATAAATCA 60.310 37.037 0.00 0.00 0.00 2.57
2116 2142 7.033791 GGAAAAAGGAAACCCGAGAATAAATC 58.966 38.462 0.00 0.00 0.00 2.17
2117 2143 6.724441 AGGAAAAAGGAAACCCGAGAATAAAT 59.276 34.615 0.00 0.00 0.00 1.40
2118 2144 6.072649 AGGAAAAAGGAAACCCGAGAATAAA 58.927 36.000 0.00 0.00 0.00 1.40
2119 2145 5.637127 AGGAAAAAGGAAACCCGAGAATAA 58.363 37.500 0.00 0.00 0.00 1.40
2120 2146 5.251182 AGGAAAAAGGAAACCCGAGAATA 57.749 39.130 0.00 0.00 0.00 1.75
2121 2147 4.114015 AGGAAAAAGGAAACCCGAGAAT 57.886 40.909 0.00 0.00 0.00 2.40
2122 2148 3.588210 AGGAAAAAGGAAACCCGAGAA 57.412 42.857 0.00 0.00 0.00 2.87
2123 2149 3.588210 AAGGAAAAAGGAAACCCGAGA 57.412 42.857 0.00 0.00 0.00 4.04
2124 2150 3.634910 TGAAAGGAAAAAGGAAACCCGAG 59.365 43.478 0.00 0.00 0.00 4.63
2125 2151 3.633418 TGAAAGGAAAAAGGAAACCCGA 58.367 40.909 0.00 0.00 0.00 5.14
2126 2152 3.977427 CTGAAAGGAAAAAGGAAACCCG 58.023 45.455 0.00 0.00 0.00 5.28
2158 2184 9.579768 TGTTTTTCTTTCAAATCAGAAATTCGA 57.420 25.926 0.00 0.00 38.51 3.71
2224 2250 9.965824 ACTGAAAAATTGTTCATCGTATCTTTT 57.034 25.926 11.50 0.00 36.92 2.27
2227 2253 9.214957 TGTACTGAAAAATTGTTCATCGTATCT 57.785 29.630 11.50 0.00 36.92 1.98
2228 2254 9.820229 TTGTACTGAAAAATTGTTCATCGTATC 57.180 29.630 11.50 7.21 36.92 2.24
2230 2256 9.440784 GTTTGTACTGAAAAATTGTTCATCGTA 57.559 29.630 11.50 8.58 36.92 3.43
2231 2257 7.971168 TGTTTGTACTGAAAAATTGTTCATCGT 59.029 29.630 11.50 9.50 36.92 3.73
2232 2258 8.259194 GTGTTTGTACTGAAAAATTGTTCATCG 58.741 33.333 11.50 4.02 36.92 3.84
2233 2259 9.081997 TGTGTTTGTACTGAAAAATTGTTCATC 57.918 29.630 11.50 6.48 36.92 2.92
2234 2260 8.994429 TGTGTTTGTACTGAAAAATTGTTCAT 57.006 26.923 11.50 5.29 36.92 2.57
2235 2261 8.994429 ATGTGTTTGTACTGAAAAATTGTTCA 57.006 26.923 10.64 10.64 36.15 3.18


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

AutoCloner maintained by Alex Coulton.