Multiple sequence alignment - TraesCS3A01G396400

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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 TraesCS3A01G396400 chr3A 100.000 2507 0 0 1 2507 643544784 643547290 0.000000e+00 4630
1 TraesCS3A01G396400 chr3A 94.065 337 20 0 1723 2059 748868882 748869218 1.720000e-141 512
2 TraesCS3A01G396400 chr3A 93.491 338 22 0 1722 2059 416186721 416187058 1.040000e-138 503
3 TraesCS3A01G396400 chr3A 93.255 341 23 0 1720 2060 547895108 547894768 1.040000e-138 503
4 TraesCS3A01G396400 chr3D 95.887 1094 35 9 634 1722 505404296 505405384 0.000000e+00 1762
5 TraesCS3A01G396400 chr3D 89.588 461 22 7 2059 2507 505405375 505405821 1.680000e-156 562
6 TraesCS3A01G396400 chr3D 93.784 370 13 4 1 367 505403532 505403894 4.710000e-152 547
7 TraesCS3A01G396400 chr3D 96.104 154 5 1 484 636 505404114 505404267 1.490000e-62 250
8 TraesCS3A01G396400 chr3D 97.368 76 1 1 419 494 505404018 505404092 7.280000e-26 128
9 TraesCS3A01G396400 chr3D 98.529 68 1 0 364 431 505403939 505404006 1.220000e-23 121
10 TraesCS3A01G396400 chr3B 94.355 992 31 12 737 1722 667173442 667174414 0.000000e+00 1498
11 TraesCS3A01G396400 chr3B 95.687 371 12 3 1 367 667172662 667173032 5.970000e-166 593
12 TraesCS3A01G396400 chr3B 91.932 409 27 3 2060 2468 667174406 667174808 3.620000e-158 568
13 TraesCS3A01G396400 chr3B 99.057 106 1 0 415 520 667173157 667173262 9.150000e-45 191
14 TraesCS3A01G396400 chr3B 98.529 68 1 0 364 431 667173076 667173143 1.220000e-23 121
15 TraesCS3A01G396400 chr1A 94.362 337 19 0 1723 2059 28945300 28945636 3.700000e-143 518
16 TraesCS3A01G396400 chr1A 92.045 352 26 2 1717 2066 443122829 443123180 6.230000e-136 494
17 TraesCS3A01G396400 chr4A 94.065 337 20 0 1723 2059 583458522 583458858 1.720000e-141 512
18 TraesCS3A01G396400 chr2A 93.787 338 21 0 1722 2059 417289424 417289761 2.220000e-140 508
19 TraesCS3A01G396400 chr2A 93.491 338 22 0 1722 2059 585735494 585735157 1.040000e-138 503
20 TraesCS3A01G396400 chr5A 93.472 337 22 0 1723 2059 675297114 675297450 3.720000e-138 501


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 TraesCS3A01G396400 chr3A 643544784 643547290 2506 False 4630.000000 4630 100.000 1 2507 1 chr3A.!!$F2 2506
1 TraesCS3A01G396400 chr3D 505403532 505405821 2289 False 561.666667 1762 95.210 1 2507 6 chr3D.!!$F1 2506
2 TraesCS3A01G396400 chr3B 667172662 667174808 2146 False 594.200000 1498 95.912 1 2468 5 chr3B.!!$F1 2467

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
677 827 0.250553 ACGGCCAAGATCGTGGAAAA 60.251 50.0 29.13 0.0 41.65 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2102 0.036765 CCTAACACTTAGGCGCCACA 60.037 55.0 31.54 13.75 45.72 4.17 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
66 67 3.991924 ATCACTGGAGGCCCGAGCT 62.992 63.158 0.00 0.00 39.73 4.09
149 151 7.905493 GTCCTAAGTGCTTTCTTTATTTCATCG 59.095 37.037 0.00 0.00 0.00 3.84
152 154 5.858475 AGTGCTTTCTTTATTTCATCGTCG 58.142 37.500 0.00 0.00 0.00 5.12
195 197 6.824557 ACTCGTTTTTATCGGTGTTAATGTC 58.175 36.000 0.00 0.00 0.00 3.06
235 237 9.457110 CTGTGTGCATTTGTACTGTTAAATTTA 57.543 29.630 0.00 0.00 0.00 1.40
370 423 6.662755 TGCCTACTTGAATTCAATGGTATCT 58.337 36.000 20.76 3.07 35.02 1.98
456 539 1.634702 GTGCACAGCTAGTCTACTGC 58.365 55.000 13.17 1.21 37.42 4.40
615 734 7.094032 GGAAGAGTTAGGTTTACTGTAGCTACA 60.094 40.741 24.63 24.63 34.56 2.74
616 735 7.771927 AGAGTTAGGTTTACTGTAGCTACAA 57.228 36.000 25.95 10.96 35.50 2.41
640 790 5.957771 AACATCCCTTGATAAGTCTAGCA 57.042 39.130 0.00 0.00 0.00 3.49
677 827 0.250553 ACGGCCAAGATCGTGGAAAA 60.251 50.000 29.13 0.00 41.65 2.29
818 1002 2.362077 GACTGTTGGACAAAATGGCACT 59.638 45.455 0.00 0.00 0.00 4.40
869 1053 1.270678 GGCCCACCCGTCATATACTTC 60.271 57.143 0.00 0.00 0.00 3.01
915 1099 1.095600 TCCTCTGGTTCGATCGACTG 58.904 55.000 19.26 11.48 0.00 3.51
966 1151 4.368391 CACCCACTGAGAGTGCAC 57.632 61.111 9.40 9.40 44.63 4.57
969 1154 1.067283 CACCCACTGAGAGTGCACTAG 60.067 57.143 21.73 16.44 44.63 2.57
970 1155 1.203063 ACCCACTGAGAGTGCACTAGA 60.203 52.381 21.73 5.52 44.63 2.43
971 1156 1.476085 CCCACTGAGAGTGCACTAGAG 59.524 57.143 21.73 17.36 44.63 2.43
972 1157 1.476085 CCACTGAGAGTGCACTAGAGG 59.524 57.143 21.73 17.42 44.63 3.69
1540 1733 1.111277 AAGAATTGCATTACCCCGGC 58.889 50.000 0.00 0.00 0.00 6.13
1541 1734 0.755327 AGAATTGCATTACCCCGGCC 60.755 55.000 0.00 0.00 0.00 6.13
1603 1796 2.092882 CGCCGTCCGTCCTCTTTTC 61.093 63.158 0.00 0.00 0.00 2.29
1631 1824 9.520204 TTTCTTGATGATTGTTTGTCTCTTTTC 57.480 29.630 0.00 0.00 0.00 2.29
1632 1825 7.651808 TCTTGATGATTGTTTGTCTCTTTTCC 58.348 34.615 0.00 0.00 0.00 3.13
1705 1898 3.343941 TTACTGCCACACTGTTATCCC 57.656 47.619 0.00 0.00 0.00 3.85
1710 1903 1.544246 GCCACACTGTTATCCCAAACC 59.456 52.381 0.00 0.00 0.00 3.27
1712 1905 2.500229 CACACTGTTATCCCAAACCGT 58.500 47.619 0.00 0.00 0.00 4.83
1713 1906 2.225491 CACACTGTTATCCCAAACCGTG 59.775 50.000 8.97 8.97 44.98 4.94
1714 1907 2.105134 ACACTGTTATCCCAAACCGTGA 59.895 45.455 15.19 0.00 43.30 4.35
1715 1908 2.742053 CACTGTTATCCCAAACCGTGAG 59.258 50.000 5.65 0.00 43.30 3.51
1716 1909 2.370849 ACTGTTATCCCAAACCGTGAGT 59.629 45.455 0.00 0.00 0.00 3.41
1717 1910 2.742053 CTGTTATCCCAAACCGTGAGTG 59.258 50.000 0.00 0.00 0.00 3.51
1718 1911 1.467342 GTTATCCCAAACCGTGAGTGC 59.533 52.381 0.00 0.00 0.00 4.40
1719 1912 0.687920 TATCCCAAACCGTGAGTGCA 59.312 50.000 0.00 0.00 0.00 4.57
1720 1913 0.889186 ATCCCAAACCGTGAGTGCAC 60.889 55.000 9.40 9.40 41.67 4.57
1721 1914 1.821759 CCCAAACCGTGAGTGCACA 60.822 57.895 21.04 0.00 45.41 4.57
1722 1915 1.648720 CCAAACCGTGAGTGCACAG 59.351 57.895 21.04 7.13 45.41 3.66
1723 1916 1.648720 CAAACCGTGAGTGCACAGG 59.351 57.895 21.04 17.91 45.41 4.00
1724 1917 2.186826 AAACCGTGAGTGCACAGGC 61.187 57.895 21.04 8.52 45.41 4.85
1736 1929 2.292103 GCACAGGCAAAGTTGACAAA 57.708 45.000 0.00 0.00 39.18 2.83
1737 1930 2.825205 GCACAGGCAAAGTTGACAAAT 58.175 42.857 0.00 0.00 39.18 2.32
1738 1931 3.197265 GCACAGGCAAAGTTGACAAATT 58.803 40.909 0.00 0.00 39.18 1.82
1739 1932 3.622612 GCACAGGCAAAGTTGACAAATTT 59.377 39.130 7.76 7.76 39.18 1.82
1740 1933 4.494526 GCACAGGCAAAGTTGACAAATTTG 60.495 41.667 28.07 28.07 39.18 2.32
1741 1934 4.869297 CACAGGCAAAGTTGACAAATTTGA 59.131 37.500 33.53 0.00 39.18 2.69
1742 1935 4.869861 ACAGGCAAAGTTGACAAATTTGAC 59.130 37.500 33.53 31.99 41.35 3.18
1743 1936 4.270808 CAGGCAAAGTTGACAAATTTGACC 59.729 41.667 32.48 29.92 41.87 4.02
1744 1937 4.162131 AGGCAAAGTTGACAAATTTGACCT 59.838 37.500 32.48 31.08 41.87 3.85
1745 1938 4.507756 GGCAAAGTTGACAAATTTGACCTC 59.492 41.667 33.53 20.36 36.20 3.85
1746 1939 5.108517 GCAAAGTTGACAAATTTGACCTCA 58.891 37.500 33.53 14.55 36.28 3.86
1747 1940 5.580297 GCAAAGTTGACAAATTTGACCTCAA 59.420 36.000 33.53 19.14 36.28 3.02
1748 1941 8.746177 GGCAAAGTTGACAAATTTGACCTCAAA 61.746 37.037 33.53 6.16 41.91 2.69
1778 1971 9.435688 AAAGCATTTCACAAACTAAACTTCTTT 57.564 25.926 0.00 0.00 27.08 2.52
1779 1972 9.435688 AAGCATTTCACAAACTAAACTTCTTTT 57.564 25.926 0.00 0.00 0.00 2.27
1780 1973 8.872845 AGCATTTCACAAACTAAACTTCTTTTG 58.127 29.630 0.00 0.00 35.49 2.44
1781 1974 8.868916 GCATTTCACAAACTAAACTTCTTTTGA 58.131 29.630 0.00 0.00 33.90 2.69
1797 1990 9.034544 ACTTCTTTTGAAAATATTTCACACTGC 57.965 29.630 0.10 0.00 38.07 4.40
1798 1991 9.252962 CTTCTTTTGAAAATATTTCACACTGCT 57.747 29.630 0.10 0.00 38.07 4.24
1799 1992 8.578308 TCTTTTGAAAATATTTCACACTGCTG 57.422 30.769 0.10 0.00 0.00 4.41
1800 1993 8.412456 TCTTTTGAAAATATTTCACACTGCTGA 58.588 29.630 0.10 0.00 0.00 4.26
1801 1994 9.199982 CTTTTGAAAATATTTCACACTGCTGAT 57.800 29.630 0.10 0.00 0.00 2.90
1802 1995 8.746922 TTTGAAAATATTTCACACTGCTGATC 57.253 30.769 0.10 0.00 0.00 2.92
1803 1996 6.855836 TGAAAATATTTCACACTGCTGATCC 58.144 36.000 0.10 0.00 0.00 3.36
1804 1997 6.660521 TGAAAATATTTCACACTGCTGATCCT 59.339 34.615 0.10 0.00 0.00 3.24
1805 1998 7.177216 TGAAAATATTTCACACTGCTGATCCTT 59.823 33.333 0.10 0.00 0.00 3.36
1806 1999 7.472334 AAATATTTCACACTGCTGATCCTTT 57.528 32.000 0.00 0.00 0.00 3.11
1807 2000 7.472334 AATATTTCACACTGCTGATCCTTTT 57.528 32.000 0.00 0.00 0.00 2.27
1808 2001 4.572985 TTTCACACTGCTGATCCTTTTG 57.427 40.909 0.00 0.00 0.00 2.44
1809 2002 3.213206 TCACACTGCTGATCCTTTTGT 57.787 42.857 0.00 0.00 0.00 2.83
1810 2003 2.880268 TCACACTGCTGATCCTTTTGTG 59.120 45.455 0.00 0.00 35.31 3.33
1811 2004 2.620115 CACACTGCTGATCCTTTTGTGT 59.380 45.455 0.00 0.00 37.61 3.72
1812 2005 3.814842 CACACTGCTGATCCTTTTGTGTA 59.185 43.478 0.00 0.00 35.74 2.90
1813 2006 4.067896 ACACTGCTGATCCTTTTGTGTAG 58.932 43.478 0.00 0.00 35.74 2.74
1814 2007 3.077359 ACTGCTGATCCTTTTGTGTAGC 58.923 45.455 0.00 0.00 0.00 3.58
1815 2008 2.076100 TGCTGATCCTTTTGTGTAGCG 58.924 47.619 0.00 0.00 32.66 4.26
1816 2009 1.202076 GCTGATCCTTTTGTGTAGCGC 60.202 52.381 0.00 0.00 0.00 5.92
1817 2010 1.398390 CTGATCCTTTTGTGTAGCGCC 59.602 52.381 2.29 0.00 0.00 6.53
1818 2011 0.733150 GATCCTTTTGTGTAGCGCCC 59.267 55.000 2.29 0.00 0.00 6.13
1819 2012 1.024579 ATCCTTTTGTGTAGCGCCCG 61.025 55.000 2.29 0.00 0.00 6.13
1820 2013 1.669760 CCTTTTGTGTAGCGCCCGA 60.670 57.895 2.29 0.00 0.00 5.14
1821 2014 1.495951 CTTTTGTGTAGCGCCCGAC 59.504 57.895 2.29 0.00 0.00 4.79
1822 2015 1.225376 CTTTTGTGTAGCGCCCGACA 61.225 55.000 2.29 3.02 0.00 4.35
1823 2016 1.225376 TTTTGTGTAGCGCCCGACAG 61.225 55.000 2.29 0.00 0.00 3.51
1824 2017 4.735132 TGTGTAGCGCCCGACAGC 62.735 66.667 2.29 2.45 0.00 4.40
1825 2018 4.735132 GTGTAGCGCCCGACAGCA 62.735 66.667 2.29 0.00 35.48 4.41
1826 2019 3.997397 TGTAGCGCCCGACAGCAA 61.997 61.111 2.29 0.00 35.48 3.91
1827 2020 3.188786 GTAGCGCCCGACAGCAAG 61.189 66.667 2.29 0.00 35.48 4.01
1828 2021 4.451150 TAGCGCCCGACAGCAAGG 62.451 66.667 2.29 0.00 35.48 3.61
1840 2033 2.434884 GCAAGGCGCTGCACTCTA 60.435 61.111 15.97 0.00 42.17 2.43
1841 2034 2.744768 GCAAGGCGCTGCACTCTAC 61.745 63.158 15.97 0.00 42.17 2.59
1842 2035 1.079543 CAAGGCGCTGCACTCTACT 60.080 57.895 7.64 0.00 0.00 2.57
1843 2036 1.079543 AAGGCGCTGCACTCTACTG 60.080 57.895 7.64 0.00 0.00 2.74
1844 2037 1.821061 AAGGCGCTGCACTCTACTGT 61.821 55.000 7.64 0.00 0.00 3.55
1845 2038 2.097038 GGCGCTGCACTCTACTGTG 61.097 63.158 7.64 0.00 40.62 3.66
1854 2047 3.393089 CACTCTACTGTGCAACTCCTT 57.607 47.619 0.00 0.00 38.04 3.36
1855 2048 4.521130 CACTCTACTGTGCAACTCCTTA 57.479 45.455 0.00 0.00 38.04 2.69
1856 2049 4.238514 CACTCTACTGTGCAACTCCTTAC 58.761 47.826 0.00 0.00 38.04 2.34
1857 2050 3.895656 ACTCTACTGTGCAACTCCTTACA 59.104 43.478 0.00 0.00 38.04 2.41
1858 2051 4.021894 ACTCTACTGTGCAACTCCTTACAG 60.022 45.833 0.00 0.00 44.52 2.74
1859 2052 1.884235 ACTGTGCAACTCCTTACAGC 58.116 50.000 0.00 0.00 43.18 4.40
1860 2053 1.417890 ACTGTGCAACTCCTTACAGCT 59.582 47.619 0.00 0.00 43.18 4.24
1861 2054 2.632996 ACTGTGCAACTCCTTACAGCTA 59.367 45.455 0.00 0.00 43.18 3.32
1862 2055 3.257393 CTGTGCAACTCCTTACAGCTAG 58.743 50.000 0.00 0.00 38.04 3.42
1863 2056 2.028112 TGTGCAACTCCTTACAGCTAGG 60.028 50.000 0.00 0.00 38.04 3.02
1864 2057 1.066143 TGCAACTCCTTACAGCTAGGC 60.066 52.381 0.00 0.00 32.59 3.93
1865 2058 1.927895 CAACTCCTTACAGCTAGGCG 58.072 55.000 0.00 0.00 32.59 5.52
1866 2059 0.175989 AACTCCTTACAGCTAGGCGC 59.824 55.000 0.00 0.00 39.57 6.53
1875 2068 3.494336 GCTAGGCGCTGCACAGTG 61.494 66.667 7.64 6.84 41.63 3.66
1876 2069 2.047844 CTAGGCGCTGCACAGTGT 60.048 61.111 7.64 0.00 40.84 3.55
1877 2070 1.215382 CTAGGCGCTGCACAGTGTA 59.785 57.895 7.64 0.00 40.84 2.90
1878 2071 0.803768 CTAGGCGCTGCACAGTGTAG 60.804 60.000 14.02 14.02 40.84 2.74
1879 2072 1.532604 TAGGCGCTGCACAGTGTAGT 61.533 55.000 18.74 3.00 40.84 2.73
1880 2073 2.671177 GGCGCTGCACAGTGTAGTG 61.671 63.158 23.67 23.67 42.30 2.74
1903 2096 2.500509 CTCCTTAGAGTTAGGCGCTG 57.499 55.000 7.64 0.00 35.21 5.18
1904 2097 0.460311 TCCTTAGAGTTAGGCGCTGC 59.540 55.000 7.64 0.00 32.59 5.25
1905 2098 0.175760 CCTTAGAGTTAGGCGCTGCA 59.824 55.000 7.64 0.00 0.00 4.41
1906 2099 1.281899 CTTAGAGTTAGGCGCTGCAC 58.718 55.000 7.64 0.76 0.00 4.57
1907 2100 0.606096 TTAGAGTTAGGCGCTGCACA 59.394 50.000 7.64 0.00 0.00 4.57
1908 2101 0.173481 TAGAGTTAGGCGCTGCACAG 59.827 55.000 7.64 0.00 0.00 3.66
1909 2102 1.374758 GAGTTAGGCGCTGCACAGT 60.375 57.895 7.64 0.00 0.00 3.55
1910 2103 1.630244 GAGTTAGGCGCTGCACAGTG 61.630 60.000 7.64 6.84 41.63 3.66
1911 2104 1.961277 GTTAGGCGCTGCACAGTGT 60.961 57.895 7.64 0.00 40.84 3.55
1912 2105 1.960763 TTAGGCGCTGCACAGTGTG 60.961 57.895 19.27 19.27 40.84 3.82
1913 2106 3.881952 TAGGCGCTGCACAGTGTGG 62.882 63.158 24.24 10.07 40.84 4.17
1919 2112 3.881952 CTGCACAGTGTGGCGCCTA 62.882 63.158 29.70 14.39 33.64 3.93
1920 2113 2.668212 GCACAGTGTGGCGCCTAA 60.668 61.111 29.70 13.28 33.64 2.69
1921 2114 2.680913 GCACAGTGTGGCGCCTAAG 61.681 63.158 29.70 15.10 33.64 2.18
1922 2115 1.301716 CACAGTGTGGCGCCTAAGT 60.302 57.895 29.70 15.67 0.00 2.24
1923 2116 1.301716 ACAGTGTGGCGCCTAAGTG 60.302 57.895 29.70 27.32 0.00 3.16
1924 2117 1.301716 CAGTGTGGCGCCTAAGTGT 60.302 57.895 29.70 4.22 0.00 3.55
1925 2118 0.884704 CAGTGTGGCGCCTAAGTGTT 60.885 55.000 29.70 3.66 0.00 3.32
1926 2119 0.682852 AGTGTGGCGCCTAAGTGTTA 59.317 50.000 29.70 0.07 0.00 2.41
1927 2120 1.076332 GTGTGGCGCCTAAGTGTTAG 58.924 55.000 29.70 0.00 0.00 2.34
1935 2128 1.803334 CCTAAGTGTTAGGCGTTGCA 58.197 50.000 0.00 0.00 45.72 4.08
1936 2129 1.463444 CCTAAGTGTTAGGCGTTGCAC 59.537 52.381 0.00 5.31 45.72 4.57
1937 2130 2.139917 CTAAGTGTTAGGCGTTGCACA 58.860 47.619 13.03 0.24 34.59 4.57
1938 2131 0.944386 AAGTGTTAGGCGTTGCACAG 59.056 50.000 13.03 0.00 34.59 3.66
1939 2132 0.179056 AGTGTTAGGCGTTGCACAGT 60.179 50.000 13.03 2.89 34.59 3.55
1940 2133 1.069513 AGTGTTAGGCGTTGCACAGTA 59.930 47.619 13.03 0.00 34.59 2.74
1941 2134 1.459592 GTGTTAGGCGTTGCACAGTAG 59.540 52.381 0.00 0.00 32.62 2.57
1942 2135 1.341852 TGTTAGGCGTTGCACAGTAGA 59.658 47.619 0.00 0.00 0.00 2.59
1943 2136 1.993370 GTTAGGCGTTGCACAGTAGAG 59.007 52.381 0.00 0.00 0.00 2.43
1944 2137 1.254026 TAGGCGTTGCACAGTAGAGT 58.746 50.000 0.00 0.00 0.00 3.24
1945 2138 0.319900 AGGCGTTGCACAGTAGAGTG 60.320 55.000 0.00 0.00 42.37 3.51
1952 2145 2.832931 CACAGTAGAGTGCAGTGCC 58.167 57.895 13.72 3.92 32.04 5.01
1953 2146 0.319728 CACAGTAGAGTGCAGTGCCT 59.680 55.000 13.72 9.31 32.04 4.75
1954 2147 1.051812 ACAGTAGAGTGCAGTGCCTT 58.948 50.000 13.72 0.00 0.00 4.35
1955 2148 1.270518 ACAGTAGAGTGCAGTGCCTTG 60.271 52.381 13.72 7.00 0.00 3.61
1956 2149 0.321122 AGTAGAGTGCAGTGCCTTGC 60.321 55.000 13.72 2.80 44.33 4.01
1957 2150 0.321122 GTAGAGTGCAGTGCCTTGCT 60.321 55.000 13.72 7.34 44.38 3.91
1958 2151 0.321034 TAGAGTGCAGTGCCTTGCTG 60.321 55.000 13.72 1.50 44.38 4.41
1959 2152 1.895707 GAGTGCAGTGCCTTGCTGT 60.896 57.895 13.72 0.00 44.38 4.40
1960 2153 1.849976 GAGTGCAGTGCCTTGCTGTC 61.850 60.000 13.72 4.21 44.38 3.51
1961 2154 2.188829 GTGCAGTGCCTTGCTGTCA 61.189 57.895 13.72 0.00 44.38 3.58
1962 2155 1.895231 TGCAGTGCCTTGCTGTCAG 60.895 57.895 13.72 0.00 44.38 3.51
1963 2156 1.598962 GCAGTGCCTTGCTGTCAGA 60.599 57.895 2.85 0.00 40.89 3.27
1964 2157 1.849976 GCAGTGCCTTGCTGTCAGAC 61.850 60.000 2.85 0.00 40.89 3.51
1965 2158 0.533531 CAGTGCCTTGCTGTCAGACA 60.534 55.000 3.32 2.48 0.00 3.41
1966 2159 0.533755 AGTGCCTTGCTGTCAGACAC 60.534 55.000 3.32 3.48 0.00 3.67
1967 2160 0.533755 GTGCCTTGCTGTCAGACACT 60.534 55.000 3.32 0.00 0.00 3.55
1968 2161 0.533531 TGCCTTGCTGTCAGACACTG 60.534 55.000 3.32 0.00 0.00 3.66
1972 2165 4.443857 GCTGTCAGACACTGCACA 57.556 55.556 3.32 0.00 46.59 4.57
1973 2166 2.924185 GCTGTCAGACACTGCACAT 58.076 52.632 3.32 0.00 46.59 3.21
1974 2167 1.233019 GCTGTCAGACACTGCACATT 58.767 50.000 3.32 0.00 46.59 2.71
1975 2168 2.416747 GCTGTCAGACACTGCACATTA 58.583 47.619 3.32 0.00 46.59 1.90
1976 2169 2.807967 GCTGTCAGACACTGCACATTAA 59.192 45.455 3.32 0.00 46.59 1.40
1977 2170 3.250762 GCTGTCAGACACTGCACATTAAA 59.749 43.478 3.32 0.00 46.59 1.52
1978 2171 4.612259 GCTGTCAGACACTGCACATTAAAG 60.612 45.833 3.32 0.00 46.59 1.85
1979 2172 4.702831 TGTCAGACACTGCACATTAAAGA 58.297 39.130 0.00 0.00 0.00 2.52
1980 2173 5.308014 TGTCAGACACTGCACATTAAAGAT 58.692 37.500 0.00 0.00 0.00 2.40
1981 2174 5.409520 TGTCAGACACTGCACATTAAAGATC 59.590 40.000 0.00 0.00 0.00 2.75
1982 2175 5.409520 GTCAGACACTGCACATTAAAGATCA 59.590 40.000 0.00 0.00 0.00 2.92
1983 2176 5.997129 TCAGACACTGCACATTAAAGATCAA 59.003 36.000 0.00 0.00 0.00 2.57
1984 2177 6.656270 TCAGACACTGCACATTAAAGATCAAT 59.344 34.615 0.00 0.00 0.00 2.57
1985 2178 6.965500 CAGACACTGCACATTAAAGATCAATC 59.035 38.462 0.00 0.00 0.00 2.67
1986 2179 5.872635 ACACTGCACATTAAAGATCAATCG 58.127 37.500 0.00 0.00 0.00 3.34
1987 2180 5.163723 ACACTGCACATTAAAGATCAATCGG 60.164 40.000 0.00 0.00 0.00 4.18
1988 2181 4.336433 ACTGCACATTAAAGATCAATCGGG 59.664 41.667 0.00 0.00 0.00 5.14
1989 2182 4.269183 TGCACATTAAAGATCAATCGGGT 58.731 39.130 0.00 0.00 0.00 5.28
1990 2183 4.096231 TGCACATTAAAGATCAATCGGGTG 59.904 41.667 0.00 0.00 0.00 4.61
1991 2184 4.335315 GCACATTAAAGATCAATCGGGTGA 59.665 41.667 0.00 0.00 0.00 4.02
1992 2185 5.163663 GCACATTAAAGATCAATCGGGTGAA 60.164 40.000 0.00 0.00 0.00 3.18
1993 2186 6.624861 GCACATTAAAGATCAATCGGGTGAAA 60.625 38.462 0.00 0.00 0.00 2.69
1994 2187 7.483307 CACATTAAAGATCAATCGGGTGAAAT 58.517 34.615 0.00 0.00 0.00 2.17
1995 2188 8.620416 CACATTAAAGATCAATCGGGTGAAATA 58.380 33.333 0.00 0.00 0.00 1.40
1996 2189 8.621286 ACATTAAAGATCAATCGGGTGAAATAC 58.379 33.333 0.00 0.00 0.00 1.89
1997 2190 8.840321 CATTAAAGATCAATCGGGTGAAATACT 58.160 33.333 0.00 0.00 0.00 2.12
1998 2191 8.801882 TTAAAGATCAATCGGGTGAAATACTT 57.198 30.769 0.00 0.00 0.00 2.24
1999 2192 7.703058 AAAGATCAATCGGGTGAAATACTTT 57.297 32.000 0.00 0.00 0.00 2.66
2000 2193 7.703058 AAGATCAATCGGGTGAAATACTTTT 57.297 32.000 0.00 0.00 0.00 2.27
2001 2194 8.801882 AAGATCAATCGGGTGAAATACTTTTA 57.198 30.769 0.00 0.00 0.00 1.52
2002 2195 8.801882 AGATCAATCGGGTGAAATACTTTTAA 57.198 30.769 0.00 0.00 0.00 1.52
2003 2196 9.238368 AGATCAATCGGGTGAAATACTTTTAAA 57.762 29.630 0.00 0.00 0.00 1.52
2004 2197 9.849166 GATCAATCGGGTGAAATACTTTTAAAA 57.151 29.630 0.00 0.00 0.00 1.52
2038 2231 8.936864 AGTTTGTGAAATAGTTTCGATCTAAGG 58.063 33.333 0.00 0.00 42.55 2.69
2039 2232 8.718734 GTTTGTGAAATAGTTTCGATCTAAGGT 58.281 33.333 0.00 0.00 42.55 3.50
2040 2233 8.475331 TTGTGAAATAGTTTCGATCTAAGGTC 57.525 34.615 0.00 0.00 42.55 3.85
2041 2234 7.608153 TGTGAAATAGTTTCGATCTAAGGTCA 58.392 34.615 0.00 0.00 42.55 4.02
2042 2235 8.092068 TGTGAAATAGTTTCGATCTAAGGTCAA 58.908 33.333 0.00 0.00 42.55 3.18
2043 2236 8.932791 GTGAAATAGTTTCGATCTAAGGTCAAA 58.067 33.333 0.00 0.00 42.55 2.69
2044 2237 9.667107 TGAAATAGTTTCGATCTAAGGTCAAAT 57.333 29.630 0.00 0.00 42.55 2.32
2048 2241 7.745620 AGTTTCGATCTAAGGTCAAATTTGT 57.254 32.000 17.47 1.31 0.00 2.83
2049 2242 7.584987 AGTTTCGATCTAAGGTCAAATTTGTG 58.415 34.615 17.47 0.00 0.00 3.33
2050 2243 5.545658 TCGATCTAAGGTCAAATTTGTGC 57.454 39.130 17.47 11.50 0.00 4.57
2051 2244 4.394920 TCGATCTAAGGTCAAATTTGTGCC 59.605 41.667 17.47 18.72 0.00 5.01
2052 2245 4.396166 CGATCTAAGGTCAAATTTGTGCCT 59.604 41.667 22.31 22.31 36.67 4.75
2053 2246 5.106157 CGATCTAAGGTCAAATTTGTGCCTT 60.106 40.000 31.67 31.67 42.42 4.35
2054 2247 6.570378 CGATCTAAGGTCAAATTTGTGCCTTT 60.570 38.462 32.92 23.74 41.23 3.11
2055 2248 6.478512 TCTAAGGTCAAATTTGTGCCTTTT 57.521 33.333 32.92 22.35 41.23 2.27
2056 2249 6.279882 TCTAAGGTCAAATTTGTGCCTTTTG 58.720 36.000 32.92 27.59 41.23 2.44
2057 2250 3.205338 AGGTCAAATTTGTGCCTTTTGC 58.795 40.909 22.31 5.65 41.77 3.68
2079 2272 0.381801 AGTGCACAAGAACAAAGGCG 59.618 50.000 21.04 0.00 0.00 5.52
2087 2280 1.299089 GAACAAAGGCGGTGTGTGC 60.299 57.895 0.00 0.00 0.00 4.57
2164 2357 2.623416 AGCAATGCATGATGACTGATGG 59.377 45.455 8.35 0.00 0.00 3.51
2230 2423 2.072298 GGAGCACTGCACTTAGACAAG 58.928 52.381 3.30 0.00 37.81 3.16
2233 2426 1.879796 GCACTGCACTTAGACAAGGCT 60.880 52.381 0.00 0.00 35.97 4.58
2237 2430 3.056465 ACTGCACTTAGACAAGGCTAGAC 60.056 47.826 0.00 0.00 35.97 2.59
2245 2438 0.036010 ACAAGGCTAGACGCAGCAAT 60.036 50.000 0.00 0.00 43.67 3.56
2246 2439 0.376152 CAAGGCTAGACGCAGCAATG 59.624 55.000 0.00 1.66 43.67 2.82
2285 2478 2.322355 ACTGATGATGTACCTGCAGC 57.678 50.000 8.66 0.00 0.00 5.25
2287 2480 2.026915 ACTGATGATGTACCTGCAGCAA 60.027 45.455 8.66 0.00 38.31 3.91
2290 2483 1.097232 TGATGTACCTGCAGCAATGC 58.903 50.000 8.66 0.00 31.37 3.56
2350 2545 4.698583 ACTTGAACCAGCGTAGTAGTAG 57.301 45.455 0.00 0.00 0.00 2.57
2351 2546 4.330250 ACTTGAACCAGCGTAGTAGTAGA 58.670 43.478 0.00 0.00 0.00 2.59
2352 2547 4.763793 ACTTGAACCAGCGTAGTAGTAGAA 59.236 41.667 0.00 0.00 0.00 2.10
2353 2548 4.691860 TGAACCAGCGTAGTAGTAGAAC 57.308 45.455 0.00 0.00 0.00 3.01
2354 2549 3.441572 TGAACCAGCGTAGTAGTAGAACC 59.558 47.826 0.00 0.00 0.00 3.62
2360 2555 4.272991 CAGCGTAGTAGTAGAACCTACAGG 59.727 50.000 6.86 0.00 39.84 4.00
2489 2695 5.642919 TGCGTTATTAGTTTAACCGACCAAT 59.357 36.000 0.00 0.00 0.00 3.16
2495 2701 0.112606 TTTAACCGACCAATGGGCCA 59.887 50.000 9.61 9.61 37.90 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 6.821665 GGATTATGGTTTTATAGCTATCGCCA 59.178 38.462 10.16 13.92 36.60 5.69
149 151 7.138692 AGTATCCGGACTAATTATACACGAC 57.861 40.000 6.12 0.00 0.00 4.34
152 154 7.138692 ACGAGTATCCGGACTAATTATACAC 57.861 40.000 6.12 1.11 0.00 2.90
195 197 0.758123 ACACAGCATTGGGGGTTTTG 59.242 50.000 0.00 0.00 29.54 2.44
235 237 5.894298 TTATGGAGCCAGACACATAAGAT 57.106 39.130 0.00 0.00 32.58 2.40
370 423 8.851541 ACGATTTCCACTAACAGGTAAATTTA 57.148 30.769 0.00 0.00 0.00 1.40
456 539 2.930950 TCAGGGGAAAACAGAACACAG 58.069 47.619 0.00 0.00 0.00 3.66
615 734 7.934120 GTGCTAGACTTATCAAGGGATGTTATT 59.066 37.037 0.00 0.00 34.89 1.40
616 735 7.071196 TGTGCTAGACTTATCAAGGGATGTTAT 59.929 37.037 0.00 0.00 34.89 1.89
640 790 2.135581 TCCGACGGGGACAAACTGT 61.136 57.895 15.25 0.00 40.94 3.55
677 827 2.496899 ACGACCAAATCCTCTGCAAT 57.503 45.000 0.00 0.00 0.00 3.56
714 895 6.239008 CCAGGAAATACGTGCCATTTTATCAT 60.239 38.462 0.00 0.00 33.64 2.45
915 1099 1.448013 GGGCACTTCTGTACCGAGC 60.448 63.158 0.00 0.00 30.28 5.03
966 1151 2.639839 CTCCCTCTCTCTCTCCCTCTAG 59.360 59.091 0.00 0.00 0.00 2.43
969 1154 0.178990 GCTCCCTCTCTCTCTCCCTC 60.179 65.000 0.00 0.00 0.00 4.30
970 1155 0.923729 TGCTCCCTCTCTCTCTCCCT 60.924 60.000 0.00 0.00 0.00 4.20
971 1156 0.468029 CTGCTCCCTCTCTCTCTCCC 60.468 65.000 0.00 0.00 0.00 4.30
972 1157 1.109323 GCTGCTCCCTCTCTCTCTCC 61.109 65.000 0.00 0.00 0.00 3.71
1413 1602 4.598894 CGCATCAGGAGGCTCCGG 62.599 72.222 27.11 26.31 42.75 5.14
1603 1796 7.211966 AGAGACAAACAATCATCAAGAAAGG 57.788 36.000 0.00 0.00 0.00 3.11
1705 1898 1.648720 CCTGTGCACTCACGGTTTG 59.351 57.895 19.41 0.00 45.84 2.93
1717 1910 2.292103 TTTGTCAACTTTGCCTGTGC 57.708 45.000 0.00 0.00 38.26 4.57
1718 1911 4.869297 TCAAATTTGTCAACTTTGCCTGTG 59.131 37.500 18.69 1.44 31.50 3.66
1719 1912 4.869861 GTCAAATTTGTCAACTTTGCCTGT 59.130 37.500 18.69 0.00 31.50 4.00
1720 1913 4.270808 GGTCAAATTTGTCAACTTTGCCTG 59.729 41.667 18.69 2.32 31.50 4.85
1721 1914 4.162131 AGGTCAAATTTGTCAACTTTGCCT 59.838 37.500 23.37 23.37 34.51 4.75
1722 1915 4.441792 AGGTCAAATTTGTCAACTTTGCC 58.558 39.130 18.69 20.10 31.50 4.52
1723 1916 5.108517 TGAGGTCAAATTTGTCAACTTTGC 58.891 37.500 18.69 14.54 31.50 3.68
1724 1917 7.593875 TTTGAGGTCAAATTTGTCAACTTTG 57.406 32.000 17.47 17.82 40.55 2.77
1725 1918 6.313658 GCTTTGAGGTCAAATTTGTCAACTTT 59.686 34.615 17.47 2.74 43.92 2.66
1726 1919 5.812127 GCTTTGAGGTCAAATTTGTCAACTT 59.188 36.000 17.47 5.54 43.92 2.66
1727 1920 5.351458 GCTTTGAGGTCAAATTTGTCAACT 58.649 37.500 17.47 7.57 43.92 3.16
1728 1921 4.207019 CGCTTTGAGGTCAAATTTGTCAAC 59.793 41.667 17.47 8.77 43.92 3.18
1729 1922 4.097135 TCGCTTTGAGGTCAAATTTGTCAA 59.903 37.500 17.47 16.12 43.92 3.18
1730 1923 3.629855 TCGCTTTGAGGTCAAATTTGTCA 59.370 39.130 17.47 11.33 43.92 3.58
1731 1924 4.223320 TCGCTTTGAGGTCAAATTTGTC 57.777 40.909 17.47 12.07 43.92 3.18
1732 1925 4.647424 TTCGCTTTGAGGTCAAATTTGT 57.353 36.364 17.47 0.00 43.92 2.83
1733 1926 4.084900 GCTTTCGCTTTGAGGTCAAATTTG 60.085 41.667 12.15 12.15 43.92 2.32
1734 1927 4.051237 GCTTTCGCTTTGAGGTCAAATTT 58.949 39.130 5.63 0.00 43.92 1.82
1735 1928 3.068024 TGCTTTCGCTTTGAGGTCAAATT 59.932 39.130 5.63 0.00 43.92 1.82
1736 1929 2.622942 TGCTTTCGCTTTGAGGTCAAAT 59.377 40.909 5.63 0.00 43.92 2.32
1737 1930 2.020720 TGCTTTCGCTTTGAGGTCAAA 58.979 42.857 5.09 5.09 42.90 2.69
1738 1931 1.674359 TGCTTTCGCTTTGAGGTCAA 58.326 45.000 0.00 0.00 36.97 3.18
1739 1932 1.896220 ATGCTTTCGCTTTGAGGTCA 58.104 45.000 0.00 0.00 36.97 4.02
1740 1933 2.997485 AATGCTTTCGCTTTGAGGTC 57.003 45.000 0.00 0.00 36.97 3.85
1741 1934 2.622942 TGAAATGCTTTCGCTTTGAGGT 59.377 40.909 4.81 0.00 42.55 3.85
1742 1935 2.982470 GTGAAATGCTTTCGCTTTGAGG 59.018 45.455 12.19 0.00 44.55 3.86
1750 1943 7.432252 AGAAGTTTAGTTTGTGAAATGCTTTCG 59.568 33.333 4.81 0.00 42.55 3.46
1751 1944 8.634475 AGAAGTTTAGTTTGTGAAATGCTTTC 57.366 30.769 2.75 2.75 40.08 2.62
1752 1945 9.435688 AAAGAAGTTTAGTTTGTGAAATGCTTT 57.564 25.926 0.00 0.00 0.00 3.51
1753 1946 9.435688 AAAAGAAGTTTAGTTTGTGAAATGCTT 57.564 25.926 0.00 0.00 0.00 3.91
1754 1947 8.872845 CAAAAGAAGTTTAGTTTGTGAAATGCT 58.127 29.630 0.00 0.00 0.00 3.79
1755 1948 8.868916 TCAAAAGAAGTTTAGTTTGTGAAATGC 58.131 29.630 0.00 0.00 33.62 3.56
1771 1964 9.034544 GCAGTGTGAAATATTTTCAAAAGAAGT 57.965 29.630 1.43 0.00 0.00 3.01
1772 1965 9.252962 AGCAGTGTGAAATATTTTCAAAAGAAG 57.747 29.630 1.43 0.00 0.00 2.85
1773 1966 9.033481 CAGCAGTGTGAAATATTTTCAAAAGAA 57.967 29.630 1.43 0.00 0.00 2.52
1774 1967 8.412456 TCAGCAGTGTGAAATATTTTCAAAAGA 58.588 29.630 1.43 0.00 0.00 2.52
1775 1968 8.578308 TCAGCAGTGTGAAATATTTTCAAAAG 57.422 30.769 1.43 0.00 0.00 2.27
1776 1969 9.195411 GATCAGCAGTGTGAAATATTTTCAAAA 57.805 29.630 1.43 0.00 0.00 2.44
1777 1970 7.814107 GGATCAGCAGTGTGAAATATTTTCAAA 59.186 33.333 1.43 0.00 0.00 2.69
1778 1971 7.177216 AGGATCAGCAGTGTGAAATATTTTCAA 59.823 33.333 1.43 0.00 0.00 2.69
1779 1972 6.660521 AGGATCAGCAGTGTGAAATATTTTCA 59.339 34.615 1.43 2.91 0.00 2.69
1780 1973 7.093322 AGGATCAGCAGTGTGAAATATTTTC 57.907 36.000 1.43 0.32 0.00 2.29
1781 1974 7.472334 AAGGATCAGCAGTGTGAAATATTTT 57.528 32.000 1.43 0.00 0.00 1.82
1782 1975 7.472334 AAAGGATCAGCAGTGTGAAATATTT 57.528 32.000 0.00 0.00 0.00 1.40
1783 1976 7.039504 ACAAAAGGATCAGCAGTGTGAAATATT 60.040 33.333 0.00 0.00 0.00 1.28
1784 1977 6.435277 ACAAAAGGATCAGCAGTGTGAAATAT 59.565 34.615 0.00 0.00 0.00 1.28
1785 1978 5.769662 ACAAAAGGATCAGCAGTGTGAAATA 59.230 36.000 0.00 0.00 0.00 1.40
1786 1979 4.586001 ACAAAAGGATCAGCAGTGTGAAAT 59.414 37.500 0.00 0.00 0.00 2.17
1787 1980 3.953612 ACAAAAGGATCAGCAGTGTGAAA 59.046 39.130 0.00 0.00 0.00 2.69
1788 1981 3.316029 CACAAAAGGATCAGCAGTGTGAA 59.684 43.478 9.07 0.00 37.64 3.18
1789 1982 2.880268 CACAAAAGGATCAGCAGTGTGA 59.120 45.455 9.07 0.00 37.64 3.58
1790 1983 2.620115 ACACAAAAGGATCAGCAGTGTG 59.380 45.455 11.82 11.82 40.48 3.82
1791 1984 2.936202 ACACAAAAGGATCAGCAGTGT 58.064 42.857 0.00 0.00 34.26 3.55
1792 1985 3.120060 GCTACACAAAAGGATCAGCAGTG 60.120 47.826 0.00 0.00 0.00 3.66
1793 1986 3.077359 GCTACACAAAAGGATCAGCAGT 58.923 45.455 0.00 0.00 0.00 4.40
1794 1987 2.094894 CGCTACACAAAAGGATCAGCAG 59.905 50.000 0.00 0.00 0.00 4.24
1795 1988 2.076100 CGCTACACAAAAGGATCAGCA 58.924 47.619 0.00 0.00 0.00 4.41
1796 1989 1.202076 GCGCTACACAAAAGGATCAGC 60.202 52.381 0.00 0.00 0.00 4.26
1797 1990 1.398390 GGCGCTACACAAAAGGATCAG 59.602 52.381 7.64 0.00 0.00 2.90
1798 1991 1.448985 GGCGCTACACAAAAGGATCA 58.551 50.000 7.64 0.00 0.00 2.92
1799 1992 0.733150 GGGCGCTACACAAAAGGATC 59.267 55.000 7.64 0.00 0.00 3.36
1800 1993 1.024579 CGGGCGCTACACAAAAGGAT 61.025 55.000 7.64 0.00 0.00 3.24
1801 1994 1.669760 CGGGCGCTACACAAAAGGA 60.670 57.895 7.64 0.00 0.00 3.36
1802 1995 1.669760 TCGGGCGCTACACAAAAGG 60.670 57.895 7.64 0.00 0.00 3.11
1803 1996 1.225376 TGTCGGGCGCTACACAAAAG 61.225 55.000 7.64 0.00 0.00 2.27
1804 1997 1.225376 CTGTCGGGCGCTACACAAAA 61.225 55.000 7.64 0.00 0.00 2.44
1805 1998 1.666553 CTGTCGGGCGCTACACAAA 60.667 57.895 7.64 0.00 0.00 2.83
1806 1999 2.048597 CTGTCGGGCGCTACACAA 60.049 61.111 7.64 0.00 0.00 3.33
1807 2000 4.735132 GCTGTCGGGCGCTACACA 62.735 66.667 7.64 6.51 0.00 3.72
1808 2001 4.735132 TGCTGTCGGGCGCTACAC 62.735 66.667 7.64 1.37 34.52 2.90
1809 2002 3.932580 CTTGCTGTCGGGCGCTACA 62.933 63.158 7.64 7.89 34.52 2.74
1810 2003 3.188786 CTTGCTGTCGGGCGCTAC 61.189 66.667 7.64 4.10 34.52 3.58
1811 2004 4.451150 CCTTGCTGTCGGGCGCTA 62.451 66.667 7.64 0.00 34.52 4.26
1823 2016 2.434884 TAGAGTGCAGCGCCTTGC 60.435 61.111 14.21 14.21 46.98 4.01
1824 2017 1.079543 AGTAGAGTGCAGCGCCTTG 60.080 57.895 2.29 0.00 0.00 3.61
1825 2018 1.079543 CAGTAGAGTGCAGCGCCTT 60.080 57.895 2.29 0.00 0.00 4.35
1826 2019 2.279069 ACAGTAGAGTGCAGCGCCT 61.279 57.895 2.29 2.26 0.00 5.52
1827 2020 2.097038 CACAGTAGAGTGCAGCGCC 61.097 63.158 2.29 0.00 32.04 6.53
1828 2021 3.468007 CACAGTAGAGTGCAGCGC 58.532 61.111 0.00 0.00 32.04 5.92
1834 2027 3.393089 AAGGAGTTGCACAGTAGAGTG 57.607 47.619 0.00 0.00 42.37 3.51
1835 2028 3.895656 TGTAAGGAGTTGCACAGTAGAGT 59.104 43.478 0.00 0.00 0.00 3.24
1836 2029 4.489810 CTGTAAGGAGTTGCACAGTAGAG 58.510 47.826 0.00 0.00 34.91 2.43
1837 2030 3.306088 GCTGTAAGGAGTTGCACAGTAGA 60.306 47.826 0.00 0.00 40.40 2.59
1838 2031 2.996621 GCTGTAAGGAGTTGCACAGTAG 59.003 50.000 0.00 0.00 40.40 2.57
1839 2032 2.632996 AGCTGTAAGGAGTTGCACAGTA 59.367 45.455 0.00 0.00 40.40 2.74
1840 2033 1.417890 AGCTGTAAGGAGTTGCACAGT 59.582 47.619 0.00 0.00 40.40 3.55
1841 2034 2.175878 AGCTGTAAGGAGTTGCACAG 57.824 50.000 0.00 0.00 41.06 3.66
1842 2035 2.028112 CCTAGCTGTAAGGAGTTGCACA 60.028 50.000 0.00 0.00 36.08 4.57
1843 2036 2.622436 CCTAGCTGTAAGGAGTTGCAC 58.378 52.381 0.00 0.00 36.08 4.57
1844 2037 1.066143 GCCTAGCTGTAAGGAGTTGCA 60.066 52.381 5.13 0.00 36.08 4.08
1845 2038 1.657822 GCCTAGCTGTAAGGAGTTGC 58.342 55.000 5.13 0.00 36.08 4.17
1846 2039 1.927895 CGCCTAGCTGTAAGGAGTTG 58.072 55.000 5.13 0.00 36.08 3.16
1847 2040 0.175989 GCGCCTAGCTGTAAGGAGTT 59.824 55.000 5.13 0.00 44.04 3.01
1848 2041 1.817209 GCGCCTAGCTGTAAGGAGT 59.183 57.895 5.13 0.00 44.04 3.85
1849 2042 4.740235 GCGCCTAGCTGTAAGGAG 57.260 61.111 5.13 2.79 44.04 3.69
1859 2052 0.803768 CTACACTGTGCAGCGCCTAG 60.804 60.000 2.29 0.00 0.00 3.02
1860 2053 1.215382 CTACACTGTGCAGCGCCTA 59.785 57.895 2.29 0.00 0.00 3.93
1861 2054 2.047844 CTACACTGTGCAGCGCCT 60.048 61.111 2.29 0.00 0.00 5.52
1862 2055 2.357517 ACTACACTGTGCAGCGCC 60.358 61.111 2.29 0.00 0.00 6.53
1863 2056 2.856032 CACTACACTGTGCAGCGC 59.144 61.111 7.90 0.00 0.00 5.92
1869 2062 2.533266 AGGAGTTGCACTACACTGTG 57.467 50.000 6.19 6.19 40.62 3.66
1870 2063 3.895656 TCTAAGGAGTTGCACTACACTGT 59.104 43.478 0.00 0.00 29.09 3.55
1871 2064 4.489810 CTCTAAGGAGTTGCACTACACTG 58.510 47.826 0.00 0.00 29.09 3.66
1872 2065 4.792521 CTCTAAGGAGTTGCACTACACT 57.207 45.455 0.00 0.00 29.09 3.55
1884 2077 1.537135 GCAGCGCCTAACTCTAAGGAG 60.537 57.143 2.29 0.00 44.62 3.69
1885 2078 0.460311 GCAGCGCCTAACTCTAAGGA 59.540 55.000 2.29 0.00 36.08 3.36
1886 2079 0.175760 TGCAGCGCCTAACTCTAAGG 59.824 55.000 2.29 0.00 37.17 2.69
1887 2080 1.281899 GTGCAGCGCCTAACTCTAAG 58.718 55.000 2.29 0.00 0.00 2.18
1888 2081 0.606096 TGTGCAGCGCCTAACTCTAA 59.394 50.000 2.29 0.00 0.00 2.10
1889 2082 0.173481 CTGTGCAGCGCCTAACTCTA 59.827 55.000 2.29 0.00 0.00 2.43
1890 2083 1.079543 CTGTGCAGCGCCTAACTCT 60.080 57.895 2.29 0.00 0.00 3.24
1891 2084 1.374758 ACTGTGCAGCGCCTAACTC 60.375 57.895 2.29 0.00 0.00 3.01
1892 2085 1.669115 CACTGTGCAGCGCCTAACT 60.669 57.895 2.29 0.00 0.00 2.24
1893 2086 1.961277 ACACTGTGCAGCGCCTAAC 60.961 57.895 2.29 0.00 0.00 2.34
1894 2087 1.960763 CACACTGTGCAGCGCCTAA 60.961 57.895 2.29 0.00 0.00 2.69
1895 2088 2.357396 CACACTGTGCAGCGCCTA 60.357 61.111 2.29 0.00 0.00 3.93
1901 2094 3.881952 TAGGCGCCACACTGTGCAG 62.882 63.158 31.54 0.16 43.47 4.41
1902 2095 3.468326 TTAGGCGCCACACTGTGCA 62.468 57.895 31.54 0.00 43.47 4.57
1903 2096 2.668212 TTAGGCGCCACACTGTGC 60.668 61.111 31.54 0.00 40.99 4.57
1904 2097 1.301716 ACTTAGGCGCCACACTGTG 60.302 57.895 31.54 13.17 0.00 3.66
1905 2098 1.301716 CACTTAGGCGCCACACTGT 60.302 57.895 31.54 16.43 0.00 3.55
1906 2099 0.884704 AACACTTAGGCGCCACACTG 60.885 55.000 31.54 19.85 0.00 3.66
1907 2100 0.682852 TAACACTTAGGCGCCACACT 59.317 50.000 31.54 10.73 0.00 3.55
1908 2101 1.076332 CTAACACTTAGGCGCCACAC 58.924 55.000 31.54 0.00 0.00 3.82
1909 2102 0.036765 CCTAACACTTAGGCGCCACA 60.037 55.000 31.54 13.75 45.72 4.17
1910 2103 2.763651 CCTAACACTTAGGCGCCAC 58.236 57.895 31.54 1.27 45.72 5.01
1916 2109 3.125956 TGTGCAACGCCTAACACTTAGG 61.126 50.000 3.95 3.95 45.13 2.69
1917 2110 2.139917 TGTGCAACGCCTAACACTTAG 58.860 47.619 0.00 0.00 42.39 2.18
1918 2111 2.139917 CTGTGCAACGCCTAACACTTA 58.860 47.619 0.00 0.00 42.39 2.24
1919 2112 0.944386 CTGTGCAACGCCTAACACTT 59.056 50.000 0.00 0.00 42.39 3.16
1920 2113 0.179056 ACTGTGCAACGCCTAACACT 60.179 50.000 0.00 0.00 42.39 3.55
1921 2114 1.459592 CTACTGTGCAACGCCTAACAC 59.540 52.381 0.00 0.00 42.39 3.32
1922 2115 1.341852 TCTACTGTGCAACGCCTAACA 59.658 47.619 0.00 0.00 42.39 2.41
1923 2116 1.993370 CTCTACTGTGCAACGCCTAAC 59.007 52.381 0.00 0.00 42.39 2.34
1924 2117 1.616865 ACTCTACTGTGCAACGCCTAA 59.383 47.619 0.00 0.00 42.39 2.69
1925 2118 1.067846 CACTCTACTGTGCAACGCCTA 60.068 52.381 0.00 0.00 42.39 3.93
1926 2119 0.319900 CACTCTACTGTGCAACGCCT 60.320 55.000 0.00 0.00 42.39 5.52
1927 2120 2.153913 CACTCTACTGTGCAACGCC 58.846 57.895 0.00 0.00 42.39 5.68
1934 2127 0.319728 AGGCACTGCACTCTACTGTG 59.680 55.000 2.82 0.00 37.18 3.66
1935 2128 1.051812 AAGGCACTGCACTCTACTGT 58.948 50.000 2.82 0.00 40.86 3.55
1936 2129 1.436600 CAAGGCACTGCACTCTACTG 58.563 55.000 2.82 0.00 40.86 2.74
1937 2130 0.321122 GCAAGGCACTGCACTCTACT 60.321 55.000 2.82 0.00 40.86 2.57
1938 2131 0.321122 AGCAAGGCACTGCACTCTAC 60.321 55.000 13.21 0.00 40.86 2.59
1939 2132 0.321034 CAGCAAGGCACTGCACTCTA 60.321 55.000 13.21 0.00 40.86 2.43
1940 2133 1.600076 CAGCAAGGCACTGCACTCT 60.600 57.895 13.21 0.00 40.86 3.24
1941 2134 1.849976 GACAGCAAGGCACTGCACTC 61.850 60.000 13.21 4.19 40.86 3.51
1942 2135 1.895707 GACAGCAAGGCACTGCACT 60.896 57.895 13.21 0.00 40.86 4.40
1943 2136 2.126417 CTGACAGCAAGGCACTGCAC 62.126 60.000 13.21 5.72 40.86 4.57
1944 2137 1.895231 CTGACAGCAAGGCACTGCA 60.895 57.895 13.21 6.71 40.86 4.41
1945 2138 1.598962 TCTGACAGCAAGGCACTGC 60.599 57.895 0.00 3.59 40.86 4.40
1946 2139 0.533531 TGTCTGACAGCAAGGCACTG 60.534 55.000 6.36 1.25 40.86 3.66
1948 2141 0.533755 AGTGTCTGACAGCAAGGCAC 60.534 55.000 11.41 0.00 0.00 5.01
1949 2142 0.533531 CAGTGTCTGACAGCAAGGCA 60.534 55.000 11.41 0.00 32.44 4.75
1950 2143 1.849976 GCAGTGTCTGACAGCAAGGC 61.850 60.000 11.41 6.99 37.06 4.35
1951 2144 0.533531 TGCAGTGTCTGACAGCAAGG 60.534 55.000 18.75 6.13 43.53 3.61
1952 2145 2.996444 TGCAGTGTCTGACAGCAAG 58.004 52.632 18.75 7.93 43.53 4.01
1954 2147 0.107268 ATGTGCAGTGTCTGACAGCA 59.893 50.000 17.56 17.56 44.21 4.41
1955 2148 1.233019 AATGTGCAGTGTCTGACAGC 58.767 50.000 11.41 12.56 37.59 4.40
1956 2149 4.751600 TCTTTAATGTGCAGTGTCTGACAG 59.248 41.667 11.41 1.47 32.44 3.51
1957 2150 4.702831 TCTTTAATGTGCAGTGTCTGACA 58.297 39.130 6.36 6.36 32.44 3.58
1958 2151 5.409520 TGATCTTTAATGTGCAGTGTCTGAC 59.590 40.000 0.00 0.00 32.44 3.51
1959 2152 5.550290 TGATCTTTAATGTGCAGTGTCTGA 58.450 37.500 0.66 0.00 32.44 3.27
1960 2153 5.868043 TGATCTTTAATGTGCAGTGTCTG 57.132 39.130 0.00 0.00 34.12 3.51
1961 2154 6.183360 CGATTGATCTTTAATGTGCAGTGTCT 60.183 38.462 0.00 0.00 0.00 3.41
1962 2155 5.961843 CGATTGATCTTTAATGTGCAGTGTC 59.038 40.000 0.00 0.00 0.00 3.67
1963 2156 5.163723 CCGATTGATCTTTAATGTGCAGTGT 60.164 40.000 0.00 0.00 0.00 3.55
1964 2157 5.268544 CCGATTGATCTTTAATGTGCAGTG 58.731 41.667 0.00 0.00 0.00 3.66
1965 2158 4.336433 CCCGATTGATCTTTAATGTGCAGT 59.664 41.667 0.00 0.00 0.00 4.40
1966 2159 4.336433 ACCCGATTGATCTTTAATGTGCAG 59.664 41.667 0.00 0.00 0.00 4.41
1967 2160 4.096231 CACCCGATTGATCTTTAATGTGCA 59.904 41.667 0.00 0.00 0.00 4.57
1968 2161 4.335315 TCACCCGATTGATCTTTAATGTGC 59.665 41.667 0.00 0.00 0.00 4.57
1969 2162 6.435430 TTCACCCGATTGATCTTTAATGTG 57.565 37.500 0.00 0.00 0.00 3.21
1970 2163 7.645058 ATTTCACCCGATTGATCTTTAATGT 57.355 32.000 0.00 0.00 0.00 2.71
1971 2164 8.840321 AGTATTTCACCCGATTGATCTTTAATG 58.160 33.333 0.00 0.00 0.00 1.90
1972 2165 8.980481 AGTATTTCACCCGATTGATCTTTAAT 57.020 30.769 0.00 0.00 0.00 1.40
1973 2166 8.801882 AAGTATTTCACCCGATTGATCTTTAA 57.198 30.769 0.00 0.00 0.00 1.52
1974 2167 8.801882 AAAGTATTTCACCCGATTGATCTTTA 57.198 30.769 0.00 0.00 27.08 1.85
1975 2168 7.703058 AAAGTATTTCACCCGATTGATCTTT 57.297 32.000 0.00 0.00 27.08 2.52
1976 2169 7.703058 AAAAGTATTTCACCCGATTGATCTT 57.297 32.000 0.00 0.00 37.28 2.40
1977 2170 8.801882 TTAAAAGTATTTCACCCGATTGATCT 57.198 30.769 0.00 0.00 37.28 2.75
1978 2171 9.849166 TTTTAAAAGTATTTCACCCGATTGATC 57.151 29.630 0.00 0.00 37.28 2.92
2012 2205 8.936864 CCTTAGATCGAAACTATTTCACAAACT 58.063 33.333 0.00 0.00 39.63 2.66
2013 2206 8.718734 ACCTTAGATCGAAACTATTTCACAAAC 58.281 33.333 0.00 0.00 39.63 2.93
2014 2207 8.842358 ACCTTAGATCGAAACTATTTCACAAA 57.158 30.769 0.00 0.00 39.63 2.83
2015 2208 8.092068 TGACCTTAGATCGAAACTATTTCACAA 58.908 33.333 0.00 0.00 39.63 3.33
2016 2209 7.608153 TGACCTTAGATCGAAACTATTTCACA 58.392 34.615 0.00 0.00 39.63 3.58
2017 2210 8.475331 TTGACCTTAGATCGAAACTATTTCAC 57.525 34.615 0.00 0.00 39.63 3.18
2018 2211 9.667107 ATTTGACCTTAGATCGAAACTATTTCA 57.333 29.630 0.00 0.00 39.63 2.69
2022 2215 9.449719 ACAAATTTGACCTTAGATCGAAACTAT 57.550 29.630 24.64 0.00 0.00 2.12
2023 2216 8.717821 CACAAATTTGACCTTAGATCGAAACTA 58.282 33.333 24.64 0.00 0.00 2.24
2024 2217 7.584987 CACAAATTTGACCTTAGATCGAAACT 58.415 34.615 24.64 0.00 0.00 2.66
2025 2218 6.305638 GCACAAATTTGACCTTAGATCGAAAC 59.694 38.462 24.64 0.00 0.00 2.78
2026 2219 6.378582 GCACAAATTTGACCTTAGATCGAAA 58.621 36.000 24.64 0.00 0.00 3.46
2027 2220 5.106317 GGCACAAATTTGACCTTAGATCGAA 60.106 40.000 24.64 0.00 0.00 3.71
2028 2221 4.394920 GGCACAAATTTGACCTTAGATCGA 59.605 41.667 24.64 0.00 0.00 3.59
2029 2222 4.396166 AGGCACAAATTTGACCTTAGATCG 59.604 41.667 24.64 0.00 35.70 3.69
2030 2223 5.904362 AGGCACAAATTTGACCTTAGATC 57.096 39.130 24.64 2.48 35.70 2.75
2031 2224 6.670695 AAAGGCACAAATTTGACCTTAGAT 57.329 33.333 31.79 21.83 42.82 1.98
2032 2225 6.279882 CAAAAGGCACAAATTTGACCTTAGA 58.720 36.000 31.79 0.00 42.82 2.10
2033 2226 5.050159 GCAAAAGGCACAAATTTGACCTTAG 60.050 40.000 31.79 28.11 42.82 2.18
2034 2227 4.813697 GCAAAAGGCACAAATTTGACCTTA 59.186 37.500 31.79 0.00 42.82 2.69
2035 2228 3.627123 GCAAAAGGCACAAATTTGACCTT 59.373 39.130 28.90 28.90 44.27 3.50
2036 2229 3.205338 GCAAAAGGCACAAATTTGACCT 58.795 40.909 24.64 23.84 43.97 3.85
2037 2230 3.607422 GCAAAAGGCACAAATTTGACC 57.393 42.857 24.64 22.20 43.97 4.02
2056 2249 0.380378 TTTGTTCTTGTGCACTCGGC 59.620 50.000 19.41 5.32 45.13 5.54
2057 2250 1.002468 CCTTTGTTCTTGTGCACTCGG 60.002 52.381 19.41 8.08 0.00 4.63
2079 2272 2.746277 GATCACCGGGCACACACC 60.746 66.667 6.32 0.00 0.00 4.16
2087 2280 3.543680 ATTACTGACAAGATCACCGGG 57.456 47.619 6.32 0.00 32.37 5.73
2164 2357 5.070847 AGCTACTACTCTACTCTGGAGTACC 59.929 48.000 6.39 0.00 42.96 3.34
2245 2438 0.969149 CCACTCTACTGGAGCACACA 59.031 55.000 0.00 0.00 45.48 3.72
2246 2439 0.969894 ACCACTCTACTGGAGCACAC 59.030 55.000 0.00 0.00 45.48 3.82
2283 2476 1.993956 TAACCTGTGTTGGCATTGCT 58.006 45.000 8.82 0.00 35.87 3.91
2285 2478 2.159393 CGGATAACCTGTGTTGGCATTG 60.159 50.000 0.00 0.00 35.87 2.82
2287 2480 1.280710 TCGGATAACCTGTGTTGGCAT 59.719 47.619 0.00 0.00 35.87 4.40
2290 2483 3.328382 TTCTCGGATAACCTGTGTTGG 57.672 47.619 0.00 0.00 35.87 3.77
2350 2545 2.162264 AGCTCTACCCCTGTAGGTTC 57.838 55.000 0.00 0.00 43.90 3.62
2351 2546 2.644060 AAGCTCTACCCCTGTAGGTT 57.356 50.000 0.00 0.00 43.90 3.50
2352 2547 2.644060 AAAGCTCTACCCCTGTAGGT 57.356 50.000 0.00 0.00 43.90 3.08
2353 2548 5.632034 AAATAAAGCTCTACCCCTGTAGG 57.368 43.478 0.00 0.00 43.90 3.18
2354 2549 7.736893 ACATAAATAAAGCTCTACCCCTGTAG 58.263 38.462 0.00 0.00 44.90 2.74
2360 2555 5.470437 GGCAGACATAAATAAAGCTCTACCC 59.530 44.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.