Multiple sequence alignment - TraesCS6D01G243500

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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 TraesCS6D01G243500 chr6D 100.000 2629 0 0 1 2629 345396733 345394105 0.000000e+00 4855.0
1 TraesCS6D01G243500 chr6D 100.000 144 0 0 1720 1863 345394871 345394728 1.550000e-67 267.0
2 TraesCS6D01G243500 chr6D 100.000 144 0 0 1863 2006 345395014 345394871 1.550000e-67 267.0
3 TraesCS6D01G243500 chr6A 92.538 1836 92 24 5 1816 486012809 486010995 0.000000e+00 2590.0
4 TraesCS6D01G243500 chr6A 92.142 649 27 8 1989 2629 486011000 486010368 0.000000e+00 894.0
5 TraesCS6D01G243500 chr6A 96.939 98 2 1 1863 1959 486011092 486010995 2.090000e-36 163.0
6 TraesCS6D01G243500 chr6B 93.602 1563 63 20 291 1839 521521015 521519476 0.000000e+00 2298.0
7 TraesCS6D01G243500 chr6B 92.051 780 24 11 1863 2629 521519596 521518842 0.000000e+00 1062.0
8 TraesCS6D01G243500 chr6B 97.917 48 1 0 128 175 654610134 654610087 1.680000e-12 84.2
9 TraesCS6D01G243500 chr3B 85.256 156 23 0 18 173 611139244 611139399 7.530000e-36 161.0
10 TraesCS6D01G243500 chr7D 87.402 127 16 0 47 173 585434757 585434631 2.110000e-31 147.0
11 TraesCS6D01G243500 chr1B 84.314 153 13 5 32 173 282315946 282315794 3.530000e-29 139.0
12 TraesCS6D01G243500 chr2B 81.366 161 19 3 26 175 325915083 325915243 1.280000e-23 121.0
13 TraesCS6D01G243500 chr2B 92.593 54 3 1 119 171 281872837 281872784 2.810000e-10 76.8
14 TraesCS6D01G243500 chr7A 82.394 142 14 5 47 178 664753297 664753437 2.140000e-21 113.0
15 TraesCS6D01G243500 chr4B 80.851 141 14 9 44 171 95690592 95690732 5.990000e-17 99.0
16 TraesCS6D01G243500 chr4B 83.871 93 13 2 43 134 165282570 165282661 1.300000e-13 87.9
17 TraesCS6D01G243500 chr2D 84.043 94 12 3 96 187 580400287 580400195 1.300000e-13 87.9
18 TraesCS6D01G243500 chr2D 97.959 49 1 0 128 176 78009955 78010003 4.660000e-13 86.1
19 TraesCS6D01G243500 chr5B 85.333 75 11 0 32 106 681221210 681221284 7.800000e-11 78.7
20 TraesCS6D01G243500 chr1D 94.118 51 3 0 123 173 196079970 196079920 7.800000e-11 78.7
21 TraesCS6D01G243500 chr1D 91.228 57 5 0 32 88 395503352 395503296 7.800000e-11 78.7


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 TraesCS6D01G243500 chr6D 345394105 345396733 2628 True 1796.333333 4855 100.0000 1 2629 3 chr6D.!!$R1 2628
1 TraesCS6D01G243500 chr6A 486010368 486012809 2441 True 1215.666667 2590 93.8730 5 2629 3 chr6A.!!$R1 2624
2 TraesCS6D01G243500 chr6B 521518842 521521015 2173 True 1680.000000 2298 92.8265 291 2629 2 chr6B.!!$R2 2338

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
106 107 0.175073 GAAATCTAGGCGGACACGGT 59.825 55.0 0.0 0.0 41.36 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1851 0.038526 AAGCTCTGCATGCAAGCAAC 60.039 50.0 34.98 20.64 45.13 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
36 37 3.127589 TGGTTTATATGCACATCGGACG 58.872 45.455 0.00 0.00 0.00 4.79
56 57 1.297893 GATGCAGTCGAAATGCGGC 60.298 57.895 16.49 8.94 46.87 6.53
94 95 0.249868 CCGGCGCATCCAGAAATCTA 60.250 55.000 10.83 0.00 34.01 1.98
106 107 0.175073 GAAATCTAGGCGGACACGGT 59.825 55.000 0.00 0.00 41.36 4.83
108 109 0.683504 AATCTAGGCGGACACGGTCT 60.684 55.000 4.41 0.00 41.36 3.85
114 115 2.740714 GCGGACACGGTCTCATTGC 61.741 63.158 4.41 0.00 41.36 3.56
121 122 2.043953 GGTCTCATTGCCACCCCC 60.044 66.667 0.00 0.00 0.00 5.40
123 124 1.076549 GTCTCATTGCCACCCCCAA 59.923 57.895 0.00 0.00 0.00 4.12
124 125 0.967380 GTCTCATTGCCACCCCCAAG 60.967 60.000 0.00 0.00 0.00 3.61
125 126 2.283821 TCATTGCCACCCCCAAGC 60.284 61.111 0.00 0.00 0.00 4.01
126 127 2.604079 CATTGCCACCCCCAAGCA 60.604 61.111 0.00 0.00 33.97 3.91
127 128 2.284112 ATTGCCACCCCCAAGCAG 60.284 61.111 0.00 0.00 37.89 4.24
128 129 2.855770 ATTGCCACCCCCAAGCAGA 61.856 57.895 0.00 0.00 37.89 4.26
129 130 3.808218 TTGCCACCCCCAAGCAGAC 62.808 63.158 0.00 0.00 37.89 3.51
131 132 3.636231 CCACCCCCAAGCAGACGA 61.636 66.667 0.00 0.00 0.00 4.20
134 135 1.228154 ACCCCCAAGCAGACGAAAC 60.228 57.895 0.00 0.00 0.00 2.78
136 137 2.325082 CCCCAAGCAGACGAAACGG 61.325 63.158 0.00 0.00 0.00 4.44
138 139 1.566018 CCCAAGCAGACGAAACGGAC 61.566 60.000 0.00 0.00 0.00 4.79
154 155 4.974989 ACGTCCGTTTGGGGTCGC 62.975 66.667 0.00 0.00 37.16 5.19
175 176 1.094785 CGTTGGAGTTGGCCTAATGG 58.905 55.000 3.32 0.00 0.00 3.16
225 227 7.654923 GTGAATACATGATATCAGTGAAGAGCA 59.345 37.037 11.78 0.00 0.00 4.26
252 258 2.966309 GCCCGTCGTTGAGCAAAGG 61.966 63.158 0.00 0.00 0.00 3.11
255 261 1.291877 CCGTCGTTGAGCAAAGGAGG 61.292 60.000 7.27 7.27 37.96 4.30
475 481 1.405461 ATGCTATTGCTACGTACGCG 58.595 50.000 16.72 3.53 41.26 6.01
537 543 4.780815 TGGTGACAAGACAGAGAACAAAT 58.219 39.130 0.00 0.00 37.44 2.32
683 689 2.771762 AGGAGGAGATGGCTGGGC 60.772 66.667 0.00 0.00 0.00 5.36
730 736 4.141135 CCTCTTCCTCCTCATGTAGGTAGA 60.141 50.000 14.91 14.91 46.62 2.59
793 802 3.959293 TCCTCAGTGTTGCATTGATGAT 58.041 40.909 0.00 0.00 30.21 2.45
823 832 5.633182 CGGAGAAAGCATAAATAGAGAGCTC 59.367 44.000 5.27 5.27 33.83 4.09
831 840 5.393569 GCATAAATAGAGAGCTCGCTATCCA 60.394 44.000 31.94 24.14 37.87 3.41
834 843 2.940994 AGAGAGCTCGCTATCCAGTA 57.059 50.000 19.21 0.00 35.09 2.74
839 848 3.756434 AGAGCTCGCTATCCAGTATTCTC 59.244 47.826 8.37 0.00 0.00 2.87
860 869 7.979786 TCTCCTCCAAGTAGTTATTCATTCT 57.020 36.000 0.00 0.00 0.00 2.40
869 878 8.939929 CAAGTAGTTATTCATTCTTTCTCTGCA 58.060 33.333 0.00 0.00 0.00 4.41
883 893 5.537300 TTCTCTGCACACTTCTACTTCTT 57.463 39.130 0.00 0.00 0.00 2.52
888 898 3.181466 TGCACACTTCTACTTCTTCTGCA 60.181 43.478 0.00 0.00 0.00 4.41
909 919 4.530875 CATCTGTTCCCTTGGCTATCTTT 58.469 43.478 0.00 0.00 0.00 2.52
924 934 4.979815 GCTATCTTTAGCCTCTCTCGTTTC 59.020 45.833 0.00 0.00 44.29 2.78
927 937 2.233305 TTAGCCTCTCTCGTTTCCCT 57.767 50.000 0.00 0.00 0.00 4.20
928 938 1.765230 TAGCCTCTCTCGTTTCCCTC 58.235 55.000 0.00 0.00 0.00 4.30
953 963 6.392354 TCTTGTTTCTGCATTCCATTTCATC 58.608 36.000 0.00 0.00 0.00 2.92
1076 1094 0.679960 GGGTGGACAATGTACCTGGC 60.680 60.000 5.42 0.00 34.87 4.85
1161 1179 2.487934 AGCAATGTCGATGATGGCTAC 58.512 47.619 7.35 0.00 0.00 3.58
1204 1222 1.618074 GCAGGAAAGGAGGCAAGGAAT 60.618 52.381 0.00 0.00 0.00 3.01
1205 1223 2.357154 GCAGGAAAGGAGGCAAGGAATA 60.357 50.000 0.00 0.00 0.00 1.75
1206 1224 3.282885 CAGGAAAGGAGGCAAGGAATAC 58.717 50.000 0.00 0.00 0.00 1.89
1285 1309 3.513750 AAGGTCAAGGTGCAGCCCC 62.514 63.158 13.29 7.80 38.26 5.80
1374 1410 2.661718 GAGGAGGACGAGGAAGAAGAT 58.338 52.381 0.00 0.00 0.00 2.40
1379 1415 3.370104 AGGACGAGGAAGAAGATGACAT 58.630 45.455 0.00 0.00 0.00 3.06
1382 1418 1.857217 CGAGGAAGAAGATGACATGCG 59.143 52.381 0.00 0.00 0.00 4.73
1590 1626 3.819564 TCATCGGTCGATCTTTTCCAT 57.180 42.857 2.59 0.00 31.62 3.41
1600 1636 6.143919 GGTCGATCTTTTCCATTTTGTTGTTC 59.856 38.462 0.00 0.00 0.00 3.18
1604 1640 7.306749 CGATCTTTTCCATTTTGTTGTTCAAGG 60.307 37.037 0.00 0.00 37.35 3.61
1776 1821 7.350744 TCTACTGCAACCTTCGGTTATTATA 57.649 36.000 0.00 0.00 45.01 0.98
1777 1822 7.959175 TCTACTGCAACCTTCGGTTATTATAT 58.041 34.615 0.00 0.00 45.01 0.86
1778 1823 8.426489 TCTACTGCAACCTTCGGTTATTATATT 58.574 33.333 0.00 0.00 45.01 1.28
1779 1824 9.701098 CTACTGCAACCTTCGGTTATTATATTA 57.299 33.333 0.00 0.00 45.01 0.98
1781 1826 9.569122 ACTGCAACCTTCGGTTATTATATTATT 57.431 29.630 0.00 0.00 45.01 1.40
1805 1850 8.635765 TTATTCAATGTCTTCCTGCTTTTACT 57.364 30.769 0.00 0.00 0.00 2.24
1806 1851 5.947228 TCAATGTCTTCCTGCTTTTACTG 57.053 39.130 0.00 0.00 0.00 2.74
1807 1852 5.376625 TCAATGTCTTCCTGCTTTTACTGT 58.623 37.500 0.00 0.00 0.00 3.55
1808 1853 5.827797 TCAATGTCTTCCTGCTTTTACTGTT 59.172 36.000 0.00 0.00 0.00 3.16
1809 1854 5.695851 ATGTCTTCCTGCTTTTACTGTTG 57.304 39.130 0.00 0.00 0.00 3.33
1810 1855 3.315191 TGTCTTCCTGCTTTTACTGTTGC 59.685 43.478 0.00 0.00 0.00 4.17
1811 1856 3.565902 GTCTTCCTGCTTTTACTGTTGCT 59.434 43.478 0.00 0.00 0.00 3.91
1812 1857 4.036852 GTCTTCCTGCTTTTACTGTTGCTT 59.963 41.667 0.00 0.00 0.00 3.91
1813 1858 3.988379 TCCTGCTTTTACTGTTGCTTG 57.012 42.857 0.00 0.00 0.00 4.01
1814 1859 2.034558 TCCTGCTTTTACTGTTGCTTGC 59.965 45.455 0.00 0.00 0.00 4.01
1815 1860 2.223782 CCTGCTTTTACTGTTGCTTGCA 60.224 45.455 0.00 0.00 0.00 4.08
1816 1861 3.553508 CCTGCTTTTACTGTTGCTTGCAT 60.554 43.478 0.00 0.00 0.00 3.96
1817 1862 3.382855 TGCTTTTACTGTTGCTTGCATG 58.617 40.909 0.00 0.00 0.00 4.06
1818 1863 2.156310 GCTTTTACTGTTGCTTGCATGC 59.844 45.455 17.19 17.19 0.00 4.06
1819 1864 3.382855 CTTTTACTGTTGCTTGCATGCA 58.617 40.909 22.17 22.17 41.65 3.96
1820 1865 2.710220 TTACTGTTGCTTGCATGCAG 57.290 45.000 24.21 16.66 44.27 4.41
1821 1866 1.894881 TACTGTTGCTTGCATGCAGA 58.105 45.000 24.21 15.37 44.27 4.26
1822 1867 0.596577 ACTGTTGCTTGCATGCAGAG 59.403 50.000 24.21 23.68 44.27 3.35
1823 1868 0.732880 CTGTTGCTTGCATGCAGAGC 60.733 55.000 31.04 31.04 44.27 4.09
1824 1869 1.176619 TGTTGCTTGCATGCAGAGCT 61.177 50.000 34.01 0.00 44.27 4.09
1825 1870 0.038526 GTTGCTTGCATGCAGAGCTT 60.039 50.000 34.01 0.00 44.27 3.74
1826 1871 0.038618 TTGCTTGCATGCAGAGCTTG 60.039 50.000 34.01 19.64 44.27 4.01
1837 1882 2.546195 CAGAGCTTGCAATCTTCTGC 57.454 50.000 16.89 9.32 42.95 4.26
1838 1883 2.085320 CAGAGCTTGCAATCTTCTGCT 58.915 47.619 16.89 13.28 43.07 4.24
1839 1884 2.085320 AGAGCTTGCAATCTTCTGCTG 58.915 47.619 12.74 0.00 43.07 4.41
1840 1885 1.811359 GAGCTTGCAATCTTCTGCTGT 59.189 47.619 12.74 0.00 43.07 4.40
1841 1886 1.540267 AGCTTGCAATCTTCTGCTGTG 59.460 47.619 7.72 0.00 43.07 3.66
1842 1887 1.268899 GCTTGCAATCTTCTGCTGTGT 59.731 47.619 0.00 0.00 43.07 3.72
1843 1888 2.288030 GCTTGCAATCTTCTGCTGTGTT 60.288 45.455 0.00 0.00 43.07 3.32
1844 1889 3.797865 GCTTGCAATCTTCTGCTGTGTTT 60.798 43.478 0.00 0.00 43.07 2.83
1845 1890 3.631145 TGCAATCTTCTGCTGTGTTTC 57.369 42.857 0.00 0.00 43.07 2.78
1846 1891 3.216800 TGCAATCTTCTGCTGTGTTTCT 58.783 40.909 0.00 0.00 43.07 2.52
1847 1892 3.633525 TGCAATCTTCTGCTGTGTTTCTT 59.366 39.130 0.00 0.00 43.07 2.52
1848 1893 3.979495 GCAATCTTCTGCTGTGTTTCTTG 59.021 43.478 0.00 0.00 39.34 3.02
1849 1894 3.911661 ATCTTCTGCTGTGTTTCTTGC 57.088 42.857 0.00 0.00 0.00 4.01
1850 1895 2.642427 TCTTCTGCTGTGTTTCTTGCA 58.358 42.857 0.00 0.00 0.00 4.08
1851 1896 3.016031 TCTTCTGCTGTGTTTCTTGCAA 58.984 40.909 0.00 0.00 34.90 4.08
1852 1897 3.633525 TCTTCTGCTGTGTTTCTTGCAAT 59.366 39.130 0.00 0.00 34.90 3.56
1853 1898 3.631145 TCTGCTGTGTTTCTTGCAATC 57.369 42.857 0.00 0.00 34.90 2.67
1854 1899 3.216800 TCTGCTGTGTTTCTTGCAATCT 58.783 40.909 0.00 0.00 34.90 2.40
1855 1900 3.633525 TCTGCTGTGTTTCTTGCAATCTT 59.366 39.130 0.00 0.00 34.90 2.40
1856 1901 3.968649 TGCTGTGTTTCTTGCAATCTTC 58.031 40.909 0.00 0.00 32.12 2.87
1857 1902 3.633525 TGCTGTGTTTCTTGCAATCTTCT 59.366 39.130 0.00 0.00 32.12 2.85
1858 1903 3.979495 GCTGTGTTTCTTGCAATCTTCTG 59.021 43.478 0.00 0.00 0.00 3.02
1859 1904 3.968649 TGTGTTTCTTGCAATCTTCTGC 58.031 40.909 0.00 0.00 42.95 4.26
1860 1905 3.633525 TGTGTTTCTTGCAATCTTCTGCT 59.366 39.130 0.00 0.00 43.07 4.24
1861 1906 4.821260 TGTGTTTCTTGCAATCTTCTGCTA 59.179 37.500 0.00 0.00 43.07 3.49
1862 1907 5.474532 TGTGTTTCTTGCAATCTTCTGCTAT 59.525 36.000 0.00 0.00 43.07 2.97
1863 1908 6.654582 TGTGTTTCTTGCAATCTTCTGCTATA 59.345 34.615 0.00 0.00 43.07 1.31
1864 1909 6.963805 GTGTTTCTTGCAATCTTCTGCTATAC 59.036 38.462 0.00 0.00 43.07 1.47
1865 1910 6.881065 TGTTTCTTGCAATCTTCTGCTATACT 59.119 34.615 0.00 0.00 43.07 2.12
1866 1911 8.040727 TGTTTCTTGCAATCTTCTGCTATACTA 58.959 33.333 0.00 0.00 43.07 1.82
1867 1912 8.547069 GTTTCTTGCAATCTTCTGCTATACTAG 58.453 37.037 0.00 0.00 43.07 2.57
1868 1913 7.353414 TCTTGCAATCTTCTGCTATACTAGT 57.647 36.000 0.00 0.00 43.07 2.57
1869 1914 8.465273 TCTTGCAATCTTCTGCTATACTAGTA 57.535 34.615 4.77 4.77 43.07 1.82
1870 1915 8.572185 TCTTGCAATCTTCTGCTATACTAGTAG 58.428 37.037 8.85 0.00 43.07 2.57
1871 1916 7.220741 TGCAATCTTCTGCTATACTAGTAGG 57.779 40.000 8.85 5.18 43.07 3.18
1872 1917 6.209589 TGCAATCTTCTGCTATACTAGTAGGG 59.790 42.308 8.85 4.83 43.07 3.53
1873 1918 6.209788 GCAATCTTCTGCTATACTAGTAGGGT 59.790 42.308 8.85 0.00 38.79 4.34
1874 1919 7.256012 GCAATCTTCTGCTATACTAGTAGGGTT 60.256 40.741 8.85 0.00 38.79 4.11
1875 1920 9.298250 CAATCTTCTGCTATACTAGTAGGGTTA 57.702 37.037 8.85 0.00 38.79 2.85
1876 1921 9.878737 AATCTTCTGCTATACTAGTAGGGTTAA 57.121 33.333 8.85 0.00 38.79 2.01
1877 1922 8.688747 TCTTCTGCTATACTAGTAGGGTTAAC 57.311 38.462 8.85 0.00 38.79 2.01
1878 1923 8.501070 TCTTCTGCTATACTAGTAGGGTTAACT 58.499 37.037 8.85 0.00 38.79 2.24
1879 1924 8.461249 TTCTGCTATACTAGTAGGGTTAACTG 57.539 38.462 8.85 0.00 38.79 3.16
1880 1925 7.580910 TCTGCTATACTAGTAGGGTTAACTGT 58.419 38.462 8.85 0.00 38.79 3.55
1881 1926 8.057623 TCTGCTATACTAGTAGGGTTAACTGTT 58.942 37.037 8.85 0.00 38.79 3.16
1882 1927 8.004087 TGCTATACTAGTAGGGTTAACTGTTG 57.996 38.462 8.85 0.00 0.00 3.33
1883 1928 6.922407 GCTATACTAGTAGGGTTAACTGTTGC 59.078 42.308 8.85 0.00 0.00 4.17
1884 1929 7.201893 GCTATACTAGTAGGGTTAACTGTTGCT 60.202 40.741 8.85 3.46 0.00 3.91
1885 1930 5.148651 ACTAGTAGGGTTAACTGTTGCTG 57.851 43.478 5.42 0.00 0.00 4.41
1886 1931 2.779506 AGTAGGGTTAACTGTTGCTGC 58.220 47.619 5.42 0.00 0.00 5.25
1887 1932 1.810755 GTAGGGTTAACTGTTGCTGCC 59.189 52.381 5.42 0.21 0.00 4.85
1888 1933 0.184933 AGGGTTAACTGTTGCTGCCA 59.815 50.000 5.42 0.00 0.00 4.92
1889 1934 1.203050 AGGGTTAACTGTTGCTGCCAT 60.203 47.619 5.42 0.00 0.00 4.40
1890 1935 1.067635 GGGTTAACTGTTGCTGCCATG 60.068 52.381 5.42 0.00 0.00 3.66
1891 1936 1.613437 GGTTAACTGTTGCTGCCATGT 59.387 47.619 5.42 0.00 0.00 3.21
1892 1937 2.817258 GGTTAACTGTTGCTGCCATGTA 59.183 45.455 5.42 0.00 0.00 2.29
1893 1938 3.254657 GGTTAACTGTTGCTGCCATGTAA 59.745 43.478 5.42 0.00 0.00 2.41
1894 1939 4.261825 GGTTAACTGTTGCTGCCATGTAAA 60.262 41.667 5.42 0.00 0.00 2.01
1895 1940 5.469479 GTTAACTGTTGCTGCCATGTAAAT 58.531 37.500 2.69 0.00 0.00 1.40
1896 1941 3.855689 ACTGTTGCTGCCATGTAAATC 57.144 42.857 0.00 0.00 0.00 2.17
1897 1942 3.424703 ACTGTTGCTGCCATGTAAATCT 58.575 40.909 0.00 0.00 0.00 2.40
1898 1943 4.588899 ACTGTTGCTGCCATGTAAATCTA 58.411 39.130 0.00 0.00 0.00 1.98
1899 1944 4.396166 ACTGTTGCTGCCATGTAAATCTAC 59.604 41.667 0.00 0.00 0.00 2.59
1900 1945 4.588899 TGTTGCTGCCATGTAAATCTACT 58.411 39.130 0.00 0.00 0.00 2.57
1901 1946 4.395854 TGTTGCTGCCATGTAAATCTACTG 59.604 41.667 0.00 0.00 0.00 2.74
1902 1947 2.945008 TGCTGCCATGTAAATCTACTGC 59.055 45.455 0.00 0.00 0.00 4.40
1903 1948 2.945008 GCTGCCATGTAAATCTACTGCA 59.055 45.455 0.00 0.00 0.00 4.41
1904 1949 3.378112 GCTGCCATGTAAATCTACTGCAA 59.622 43.478 0.00 0.00 31.80 4.08
1905 1950 4.731773 GCTGCCATGTAAATCTACTGCAAC 60.732 45.833 0.00 0.00 31.80 4.17
1906 1951 3.694072 TGCCATGTAAATCTACTGCAACC 59.306 43.478 0.00 0.00 30.28 3.77
1907 1952 3.947834 GCCATGTAAATCTACTGCAACCT 59.052 43.478 0.00 0.00 0.00 3.50
1908 1953 4.399303 GCCATGTAAATCTACTGCAACCTT 59.601 41.667 0.00 0.00 0.00 3.50
1909 1954 5.449177 GCCATGTAAATCTACTGCAACCTTC 60.449 44.000 0.00 0.00 0.00 3.46
1910 1955 5.220662 CCATGTAAATCTACTGCAACCTTCG 60.221 44.000 0.00 0.00 0.00 3.79
1911 1956 4.250464 TGTAAATCTACTGCAACCTTCGG 58.750 43.478 0.00 0.00 0.00 4.30
1912 1957 3.418684 AAATCTACTGCAACCTTCGGT 57.581 42.857 0.00 0.00 37.65 4.69
1914 1959 4.546829 AATCTACTGCAACCTTCGGTTA 57.453 40.909 0.00 0.00 45.01 2.85
1915 1960 4.755266 ATCTACTGCAACCTTCGGTTAT 57.245 40.909 0.00 0.00 45.01 1.89
1916 1961 4.546829 TCTACTGCAACCTTCGGTTATT 57.453 40.909 0.00 0.00 45.01 1.40
1917 1962 5.664294 TCTACTGCAACCTTCGGTTATTA 57.336 39.130 0.00 0.00 45.01 0.98
1965 2010 0.596577 ACTGTTGCTTGCATGCAGAG 59.403 50.000 24.21 23.68 44.27 3.35
1982 2029 2.085320 AGAGCTTGCAATCTTCTGCTG 58.915 47.619 12.74 0.00 43.07 4.41
1987 2034 3.797865 GCTTGCAATCTTCTGCTGTGTTT 60.798 43.478 0.00 0.00 43.07 2.83
1988 2035 3.631145 TGCAATCTTCTGCTGTGTTTC 57.369 42.857 0.00 0.00 43.07 2.78
1989 2036 3.216800 TGCAATCTTCTGCTGTGTTTCT 58.783 40.909 0.00 0.00 43.07 2.52
1990 2037 3.633525 TGCAATCTTCTGCTGTGTTTCTT 59.366 39.130 0.00 0.00 43.07 2.52
1991 2038 3.979495 GCAATCTTCTGCTGTGTTTCTTG 59.021 43.478 0.00 0.00 39.34 3.02
1992 2039 3.911661 ATCTTCTGCTGTGTTTCTTGC 57.088 42.857 0.00 0.00 0.00 4.01
1993 2040 2.642427 TCTTCTGCTGTGTTTCTTGCA 58.358 42.857 0.00 0.00 0.00 4.08
1994 2041 3.016031 TCTTCTGCTGTGTTTCTTGCAA 58.984 40.909 0.00 0.00 34.90 4.08
1995 2042 3.633525 TCTTCTGCTGTGTTTCTTGCAAT 59.366 39.130 0.00 0.00 34.90 3.56
1996 2043 3.631145 TCTGCTGTGTTTCTTGCAATC 57.369 42.857 0.00 0.00 34.90 2.67
1997 2044 3.216800 TCTGCTGTGTTTCTTGCAATCT 58.783 40.909 0.00 0.00 34.90 2.40
1998 2045 3.633525 TCTGCTGTGTTTCTTGCAATCTT 59.366 39.130 0.00 0.00 34.90 2.40
1999 2046 3.968649 TGCTGTGTTTCTTGCAATCTTC 58.031 40.909 0.00 0.00 32.12 2.87
2000 2047 3.633525 TGCTGTGTTTCTTGCAATCTTCT 59.366 39.130 0.00 0.00 32.12 2.85
2001 2048 3.979495 GCTGTGTTTCTTGCAATCTTCTG 59.021 43.478 0.00 0.00 0.00 3.02
2002 2049 3.968649 TGTGTTTCTTGCAATCTTCTGC 58.031 40.909 0.00 0.00 42.95 4.26
2003 2050 3.633525 TGTGTTTCTTGCAATCTTCTGCT 59.366 39.130 0.00 0.00 43.07 4.24
2004 2051 4.821260 TGTGTTTCTTGCAATCTTCTGCTA 59.179 37.500 0.00 0.00 43.07 3.49
2005 2052 5.474532 TGTGTTTCTTGCAATCTTCTGCTAT 59.525 36.000 0.00 0.00 43.07 2.97
2006 2053 6.016024 TGTGTTTCTTGCAATCTTCTGCTATT 60.016 34.615 0.00 0.00 43.07 1.73
2007 2054 6.307318 GTGTTTCTTGCAATCTTCTGCTATTG 59.693 38.462 0.00 0.00 43.07 1.90
2008 2055 6.016024 TGTTTCTTGCAATCTTCTGCTATTGT 60.016 34.615 0.00 0.00 43.07 2.71
2009 2056 6.579666 TTCTTGCAATCTTCTGCTATTGTT 57.420 33.333 0.00 0.00 43.07 2.83
2010 2057 6.579666 TCTTGCAATCTTCTGCTATTGTTT 57.420 33.333 0.00 0.00 43.07 2.83
2059 2106 3.566322 ACTCATAAGCTACACTCTAGCCG 59.434 47.826 0.00 0.00 41.25 5.52
2066 2117 2.485038 GCTACACTCTAGCCGGATAGAC 59.515 54.545 25.19 10.93 34.65 2.59
2079 2130 2.609459 CGGATAGACTTGCGAGCAAAAT 59.391 45.455 11.83 3.15 35.33 1.82
2141 2192 9.520515 AGAAGAAGAAGCCAAGTCAAATTAATA 57.479 29.630 0.00 0.00 0.00 0.98
2278 2336 5.640357 TGCAATCTTTCTGCCAAAATCATTC 59.360 36.000 0.00 0.00 39.13 2.67
2297 2355 0.938637 CGCACGGCATTTCAGCAAAA 60.939 50.000 0.00 0.00 35.83 2.44
2310 2368 4.320608 TCAGCAAAACCAAATCACTTCC 57.679 40.909 0.00 0.00 0.00 3.46
2515 2578 5.461526 GTGACCTTGGCTTGAAGTAATTTC 58.538 41.667 0.00 0.00 36.29 2.17
2609 2672 6.410853 CCAGAGGGGAATATTTGTCTAACCAT 60.411 42.308 0.00 0.00 40.01 3.55
2620 2683 5.755409 TTGTCTAACCATACCACTCATGT 57.245 39.130 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.538381 CCGATGTGCATATAAACCAGCATATA 59.462 38.462 0.00 0.00 38.63 0.86
9 10 5.355071 CCGATGTGCATATAAACCAGCATAT 59.645 40.000 0.00 0.00 40.71 1.78
10 11 4.694982 CCGATGTGCATATAAACCAGCATA 59.305 41.667 0.00 0.00 39.43 3.14
11 12 3.503363 CCGATGTGCATATAAACCAGCAT 59.497 43.478 0.00 0.00 39.43 3.79
12 13 2.877786 CCGATGTGCATATAAACCAGCA 59.122 45.455 0.00 0.00 34.10 4.41
13 14 3.058914 GTCCGATGTGCATATAAACCAGC 60.059 47.826 0.00 0.00 0.00 4.85
14 15 3.184379 CGTCCGATGTGCATATAAACCAG 59.816 47.826 0.00 0.00 0.00 4.00
30 31 1.303091 TTCGACTGCATCTCGTCCGA 61.303 55.000 12.27 4.68 32.77 4.55
36 37 0.302890 CCGCATTTCGACTGCATCTC 59.697 55.000 16.81 0.00 41.67 2.75
87 88 0.175073 ACCGTGTCCGCCTAGATTTC 59.825 55.000 0.00 0.00 0.00 2.17
94 95 2.283529 AATGAGACCGTGTCCGCCT 61.284 57.895 0.00 0.00 32.18 5.52
106 107 1.383799 CTTGGGGGTGGCAATGAGA 59.616 57.895 0.00 0.00 0.00 3.27
108 109 2.283821 GCTTGGGGGTGGCAATGA 60.284 61.111 0.00 0.00 0.00 2.57
114 115 2.690653 TTTCGTCTGCTTGGGGGTGG 62.691 60.000 0.00 0.00 0.00 4.61
121 122 1.213094 ACGTCCGTTTCGTCTGCTTG 61.213 55.000 0.00 0.00 36.85 4.01
123 124 2.726274 ACGTCCGTTTCGTCTGCT 59.274 55.556 0.00 0.00 36.85 4.24
136 137 2.735857 CGACCCCAAACGGACGTC 60.736 66.667 7.13 7.13 0.00 4.34
149 150 4.072088 CAACTCCAACGCGCGACC 62.072 66.667 39.36 0.00 0.00 4.79
154 155 1.024579 ATTAGGCCAACTCCAACGCG 61.025 55.000 5.01 3.53 0.00 6.01
213 215 2.490509 CCATTTGCATGCTCTTCACTGA 59.509 45.455 20.33 0.00 0.00 3.41
225 227 1.976474 AACGACGGGCCATTTGCAT 60.976 52.632 4.39 0.00 43.89 3.96
475 481 1.239968 CCTGTTTCCTCCTGTGCAGC 61.240 60.000 0.00 0.00 0.00 5.25
537 543 4.825085 GTGTCTCATAACTTTCCCAACCAA 59.175 41.667 0.00 0.00 0.00 3.67
672 678 2.685017 TCTGACGCCCAGCCATCT 60.685 61.111 0.94 0.00 42.62 2.90
683 689 3.923461 GGACATTGAAGAAGTCTCTGACG 59.077 47.826 0.00 0.00 37.67 4.35
730 736 7.826252 TCTTCTTTGTGCTAGCTCTTTGAATAT 59.174 33.333 17.23 0.00 0.00 1.28
793 802 0.329931 TTATGCTTTCTCCGGGGCAA 59.670 50.000 0.00 0.00 38.21 4.52
823 832 3.157881 TGGAGGAGAATACTGGATAGCG 58.842 50.000 0.00 0.00 0.00 4.26
831 840 8.840200 TGAATAACTACTTGGAGGAGAATACT 57.160 34.615 0.00 0.00 0.00 2.12
834 843 8.997734 AGAATGAATAACTACTTGGAGGAGAAT 58.002 33.333 0.00 0.00 0.00 2.40
839 848 9.103861 GAGAAAGAATGAATAACTACTTGGAGG 57.896 37.037 0.00 0.00 0.00 4.30
860 869 5.537300 AGAAGTAGAAGTGTGCAGAGAAA 57.463 39.130 0.00 0.00 0.00 2.52
869 878 5.011533 ACAGATGCAGAAGAAGTAGAAGTGT 59.988 40.000 0.00 0.00 0.00 3.55
883 893 0.322816 GCCAAGGGAACAGATGCAGA 60.323 55.000 0.00 0.00 0.00 4.26
888 898 4.870021 AAAGATAGCCAAGGGAACAGAT 57.130 40.909 0.00 0.00 0.00 2.90
909 919 1.285373 AGAGGGAAACGAGAGAGGCTA 59.715 52.381 0.00 0.00 0.00 3.93
919 929 2.224314 GCAGAAACAAGAGAGGGAAACG 59.776 50.000 0.00 0.00 0.00 3.60
924 934 2.751806 GGAATGCAGAAACAAGAGAGGG 59.248 50.000 0.00 0.00 0.00 4.30
927 937 5.535783 TGAAATGGAATGCAGAAACAAGAGA 59.464 36.000 0.00 0.00 0.00 3.10
928 938 5.775686 TGAAATGGAATGCAGAAACAAGAG 58.224 37.500 0.00 0.00 0.00 2.85
953 963 6.424509 GCAATGAGAAGATCTAGTGAATGAGG 59.575 42.308 0.00 0.00 0.00 3.86
1076 1094 3.142838 CGCTTTGCATGGGGGAGG 61.143 66.667 0.00 0.00 0.00 4.30
1161 1179 0.100146 GGACGAGGTAAGTGTAGCCG 59.900 60.000 0.00 0.00 0.00 5.52
1204 1222 2.375014 TCGCCATCATCCTGGTAGTA 57.625 50.000 0.00 0.00 38.63 1.82
1205 1223 1.345741 CATCGCCATCATCCTGGTAGT 59.654 52.381 0.00 0.00 38.63 2.73
1206 1224 1.620323 TCATCGCCATCATCCTGGTAG 59.380 52.381 0.00 0.00 38.63 3.18
1298 1322 0.673644 ACCGTTCTTTCGATGGCCTG 60.674 55.000 3.32 0.00 0.00 4.85
1312 1348 2.963320 GCCGTCGTTGTCACCGTT 60.963 61.111 0.00 0.00 0.00 4.44
1340 1376 2.124942 CCTCCTTTGGCCTCTCGC 60.125 66.667 3.32 0.00 0.00 5.03
1341 1377 1.519719 CTCCTCCTTTGGCCTCTCG 59.480 63.158 3.32 0.00 0.00 4.04
1342 1378 0.618968 TCCTCCTCCTTTGGCCTCTC 60.619 60.000 3.32 0.00 0.00 3.20
1343 1379 0.912006 GTCCTCCTCCTTTGGCCTCT 60.912 60.000 3.32 0.00 0.00 3.69
1344 1380 1.604915 GTCCTCCTCCTTTGGCCTC 59.395 63.158 3.32 0.00 0.00 4.70
1345 1381 2.294078 CGTCCTCCTCCTTTGGCCT 61.294 63.158 3.32 0.00 0.00 5.19
1346 1382 2.245438 CTCGTCCTCCTCCTTTGGCC 62.245 65.000 0.00 0.00 0.00 5.36
1347 1383 1.219393 CTCGTCCTCCTCCTTTGGC 59.781 63.158 0.00 0.00 0.00 4.52
1348 1384 0.614979 TCCTCGTCCTCCTCCTTTGG 60.615 60.000 0.00 0.00 0.00 3.28
1349 1385 1.205893 CTTCCTCGTCCTCCTCCTTTG 59.794 57.143 0.00 0.00 0.00 2.77
1350 1386 1.077334 TCTTCCTCGTCCTCCTCCTTT 59.923 52.381 0.00 0.00 0.00 3.11
1351 1387 0.705253 TCTTCCTCGTCCTCCTCCTT 59.295 55.000 0.00 0.00 0.00 3.36
1352 1388 0.705253 TTCTTCCTCGTCCTCCTCCT 59.295 55.000 0.00 0.00 0.00 3.69
1374 1410 1.965930 GAACCTGGTGCGCATGTCA 60.966 57.895 15.91 12.08 0.00 3.58
1379 1415 3.611674 TCGAGAACCTGGTGCGCA 61.612 61.111 5.66 5.66 0.00 6.09
1382 1418 1.444553 CTCGTCGAGAACCTGGTGC 60.445 63.158 17.52 0.00 0.00 5.01
1546 1582 4.737054 GCATAAGGCACATACATATTGGC 58.263 43.478 0.00 0.00 43.97 4.52
1590 1626 4.223923 ACATTCCCACCTTGAACAACAAAA 59.776 37.500 0.00 0.00 38.08 2.44
1709 1754 2.021341 ACCCTACTAGTAATTGGGGGCT 60.021 50.000 23.13 10.33 42.00 5.19
1710 1755 2.415624 ACCCTACTAGTAATTGGGGGC 58.584 52.381 23.13 0.00 42.00 5.80
1779 1824 9.247861 AGTAAAAGCAGGAAGACATTGAATAAT 57.752 29.630 0.00 0.00 0.00 1.28
1780 1825 8.514594 CAGTAAAAGCAGGAAGACATTGAATAA 58.485 33.333 0.00 0.00 0.00 1.40
1781 1826 7.665559 ACAGTAAAAGCAGGAAGACATTGAATA 59.334 33.333 0.00 0.00 0.00 1.75
1782 1827 6.491403 ACAGTAAAAGCAGGAAGACATTGAAT 59.509 34.615 0.00 0.00 0.00 2.57
1783 1828 5.827797 ACAGTAAAAGCAGGAAGACATTGAA 59.172 36.000 0.00 0.00 0.00 2.69
1784 1829 5.376625 ACAGTAAAAGCAGGAAGACATTGA 58.623 37.500 0.00 0.00 0.00 2.57
1785 1830 5.695851 ACAGTAAAAGCAGGAAGACATTG 57.304 39.130 0.00 0.00 0.00 2.82
1786 1831 5.507985 GCAACAGTAAAAGCAGGAAGACATT 60.508 40.000 0.00 0.00 0.00 2.71
1787 1832 4.022849 GCAACAGTAAAAGCAGGAAGACAT 60.023 41.667 0.00 0.00 0.00 3.06
1788 1833 3.315191 GCAACAGTAAAAGCAGGAAGACA 59.685 43.478 0.00 0.00 0.00 3.41
1789 1834 3.565902 AGCAACAGTAAAAGCAGGAAGAC 59.434 43.478 0.00 0.00 0.00 3.01
1790 1835 3.820557 AGCAACAGTAAAAGCAGGAAGA 58.179 40.909 0.00 0.00 0.00 2.87
1791 1836 4.293415 CAAGCAACAGTAAAAGCAGGAAG 58.707 43.478 0.00 0.00 0.00 3.46
1792 1837 3.490761 GCAAGCAACAGTAAAAGCAGGAA 60.491 43.478 0.00 0.00 0.00 3.36
1793 1838 2.034558 GCAAGCAACAGTAAAAGCAGGA 59.965 45.455 0.00 0.00 0.00 3.86
1794 1839 2.223782 TGCAAGCAACAGTAAAAGCAGG 60.224 45.455 0.00 0.00 0.00 4.85
1795 1840 3.082698 TGCAAGCAACAGTAAAAGCAG 57.917 42.857 0.00 0.00 0.00 4.24
1796 1841 3.382855 CATGCAAGCAACAGTAAAAGCA 58.617 40.909 0.00 0.00 35.03 3.91
1797 1842 2.156310 GCATGCAAGCAACAGTAAAAGC 59.844 45.455 14.21 0.00 0.00 3.51
1798 1843 3.382855 TGCATGCAAGCAACAGTAAAAG 58.617 40.909 20.30 0.00 42.46 2.27
1799 1844 3.067883 TCTGCATGCAAGCAACAGTAAAA 59.932 39.130 22.88 6.11 45.13 1.52
1800 1845 2.622470 TCTGCATGCAAGCAACAGTAAA 59.378 40.909 22.88 6.38 45.13 2.01
1801 1846 2.227149 CTCTGCATGCAAGCAACAGTAA 59.773 45.455 22.88 8.23 45.13 2.24
1802 1847 1.808343 CTCTGCATGCAAGCAACAGTA 59.192 47.619 22.88 11.41 45.13 2.74
1803 1848 0.596577 CTCTGCATGCAAGCAACAGT 59.403 50.000 22.88 0.00 45.13 3.55
1804 1849 0.732880 GCTCTGCATGCAAGCAACAG 60.733 55.000 31.92 16.42 45.13 3.16
1805 1850 1.176619 AGCTCTGCATGCAAGCAACA 61.177 50.000 34.98 12.77 45.13 3.33
1806 1851 0.038526 AAGCTCTGCATGCAAGCAAC 60.039 50.000 34.98 20.64 45.13 4.17
1807 1852 0.038618 CAAGCTCTGCATGCAAGCAA 60.039 50.000 34.98 18.77 45.13 3.91
1808 1853 1.584495 CAAGCTCTGCATGCAAGCA 59.416 52.632 34.98 16.74 43.35 3.91
1809 1854 4.478195 CAAGCTCTGCATGCAAGC 57.522 55.556 30.81 30.81 36.27 4.01
1818 1863 2.085320 AGCAGAAGATTGCAAGCTCTG 58.915 47.619 26.18 26.18 46.47 3.35
1819 1864 2.085320 CAGCAGAAGATTGCAAGCTCT 58.915 47.619 19.00 13.52 46.47 4.09
1820 1865 1.811359 ACAGCAGAAGATTGCAAGCTC 59.189 47.619 19.00 11.44 46.47 4.09
1821 1866 1.540267 CACAGCAGAAGATTGCAAGCT 59.460 47.619 12.34 12.34 46.47 3.74
1822 1867 1.268899 ACACAGCAGAAGATTGCAAGC 59.731 47.619 6.58 6.58 46.47 4.01
1823 1868 3.637998 AACACAGCAGAAGATTGCAAG 57.362 42.857 4.94 0.00 46.47 4.01
1824 1869 3.633525 AGAAACACAGCAGAAGATTGCAA 59.366 39.130 0.00 0.00 46.47 4.08
1825 1870 3.216800 AGAAACACAGCAGAAGATTGCA 58.783 40.909 0.52 0.00 46.47 4.08
1826 1871 3.911661 AGAAACACAGCAGAAGATTGC 57.088 42.857 0.00 0.00 44.41 3.56
1827 1872 3.979495 GCAAGAAACACAGCAGAAGATTG 59.021 43.478 0.00 0.00 0.00 2.67
1828 1873 3.633525 TGCAAGAAACACAGCAGAAGATT 59.366 39.130 0.00 0.00 32.48 2.40
1829 1874 3.216800 TGCAAGAAACACAGCAGAAGAT 58.783 40.909 0.00 0.00 32.48 2.40
1830 1875 2.642427 TGCAAGAAACACAGCAGAAGA 58.358 42.857 0.00 0.00 32.48 2.87
1831 1876 3.425577 TTGCAAGAAACACAGCAGAAG 57.574 42.857 0.00 0.00 38.35 2.85
1832 1877 3.633525 AGATTGCAAGAAACACAGCAGAA 59.366 39.130 4.94 0.00 38.35 3.02
1833 1878 3.216800 AGATTGCAAGAAACACAGCAGA 58.783 40.909 4.94 0.00 38.35 4.26
1834 1879 3.637998 AGATTGCAAGAAACACAGCAG 57.362 42.857 4.94 0.00 38.35 4.24
1835 1880 3.633525 AGAAGATTGCAAGAAACACAGCA 59.366 39.130 4.94 0.00 34.79 4.41
1836 1881 3.979495 CAGAAGATTGCAAGAAACACAGC 59.021 43.478 4.94 0.00 0.00 4.40
1837 1882 3.979495 GCAGAAGATTGCAAGAAACACAG 59.021 43.478 4.94 0.00 43.53 3.66
1838 1883 3.633525 AGCAGAAGATTGCAAGAAACACA 59.366 39.130 4.94 0.00 46.47 3.72
1839 1884 4.234530 AGCAGAAGATTGCAAGAAACAC 57.765 40.909 4.94 0.00 46.47 3.32
1840 1885 6.881065 AGTATAGCAGAAGATTGCAAGAAACA 59.119 34.615 4.94 0.00 46.47 2.83
1841 1886 7.313951 AGTATAGCAGAAGATTGCAAGAAAC 57.686 36.000 4.94 0.00 46.47 2.78
1842 1887 8.260818 ACTAGTATAGCAGAAGATTGCAAGAAA 58.739 33.333 4.94 0.00 44.39 2.52
1843 1888 7.786030 ACTAGTATAGCAGAAGATTGCAAGAA 58.214 34.615 4.94 0.00 44.39 2.52
1844 1889 7.353414 ACTAGTATAGCAGAAGATTGCAAGA 57.647 36.000 4.94 0.00 44.39 3.02
1845 1890 7.812191 CCTACTAGTATAGCAGAAGATTGCAAG 59.188 40.741 4.94 0.00 44.39 4.01
1846 1891 7.255977 CCCTACTAGTATAGCAGAAGATTGCAA 60.256 40.741 0.00 0.00 44.39 4.08
1847 1892 6.209589 CCCTACTAGTATAGCAGAAGATTGCA 59.790 42.308 2.33 0.00 44.39 4.08
1848 1893 6.209788 ACCCTACTAGTATAGCAGAAGATTGC 59.790 42.308 2.33 0.00 44.39 3.56
1849 1894 7.768807 ACCCTACTAGTATAGCAGAAGATTG 57.231 40.000 2.33 0.00 44.39 2.67
1850 1895 9.878737 TTAACCCTACTAGTATAGCAGAAGATT 57.121 33.333 2.33 0.00 44.39 2.40
1851 1896 9.299465 GTTAACCCTACTAGTATAGCAGAAGAT 57.701 37.037 2.33 0.00 44.39 2.40
1852 1897 8.501070 AGTTAACCCTACTAGTATAGCAGAAGA 58.499 37.037 2.33 0.00 44.39 2.87
1853 1898 8.569641 CAGTTAACCCTACTAGTATAGCAGAAG 58.430 40.741 2.33 0.00 44.39 2.85
1854 1899 8.057623 ACAGTTAACCCTACTAGTATAGCAGAA 58.942 37.037 2.33 0.00 44.39 3.02
1855 1900 7.580910 ACAGTTAACCCTACTAGTATAGCAGA 58.419 38.462 2.33 0.00 44.39 4.26
1856 1901 7.820578 ACAGTTAACCCTACTAGTATAGCAG 57.179 40.000 2.33 0.00 44.39 4.24
1857 1902 7.417116 GCAACAGTTAACCCTACTAGTATAGCA 60.417 40.741 2.33 0.00 44.39 3.49
1858 1903 6.922407 GCAACAGTTAACCCTACTAGTATAGC 59.078 42.308 2.33 0.00 44.39 2.97
1859 1904 8.136165 CAGCAACAGTTAACCCTACTAGTATAG 58.864 40.741 2.33 0.47 46.50 1.31
1860 1905 7.417116 GCAGCAACAGTTAACCCTACTAGTATA 60.417 40.741 2.33 0.00 0.00 1.47
1861 1906 6.629739 GCAGCAACAGTTAACCCTACTAGTAT 60.630 42.308 2.33 0.00 0.00 2.12
1862 1907 5.337009 GCAGCAACAGTTAACCCTACTAGTA 60.337 44.000 0.88 1.89 0.00 1.82
1863 1908 4.562963 GCAGCAACAGTTAACCCTACTAGT 60.563 45.833 0.00 0.00 0.00 2.57
1864 1909 3.933332 GCAGCAACAGTTAACCCTACTAG 59.067 47.826 0.88 0.00 0.00 2.57
1865 1910 3.307199 GGCAGCAACAGTTAACCCTACTA 60.307 47.826 0.88 0.00 0.00 1.82
1866 1911 2.552373 GGCAGCAACAGTTAACCCTACT 60.552 50.000 0.88 0.00 0.00 2.57
1867 1912 1.810755 GGCAGCAACAGTTAACCCTAC 59.189 52.381 0.88 0.00 0.00 3.18
1868 1913 1.422024 TGGCAGCAACAGTTAACCCTA 59.578 47.619 0.88 0.00 0.00 3.53
1869 1914 0.184933 TGGCAGCAACAGTTAACCCT 59.815 50.000 0.88 0.00 0.00 4.34
1870 1915 1.067635 CATGGCAGCAACAGTTAACCC 60.068 52.381 0.88 0.00 0.00 4.11
1871 1916 1.613437 ACATGGCAGCAACAGTTAACC 59.387 47.619 0.88 0.00 0.00 2.85
1872 1917 4.497473 TTACATGGCAGCAACAGTTAAC 57.503 40.909 0.00 0.00 0.00 2.01
1873 1918 5.476599 AGATTTACATGGCAGCAACAGTTAA 59.523 36.000 0.00 0.00 0.00 2.01
1874 1919 5.009631 AGATTTACATGGCAGCAACAGTTA 58.990 37.500 0.00 0.00 0.00 2.24
1875 1920 3.828451 AGATTTACATGGCAGCAACAGTT 59.172 39.130 0.00 0.00 0.00 3.16
1876 1921 3.424703 AGATTTACATGGCAGCAACAGT 58.575 40.909 0.00 0.00 0.00 3.55
1877 1922 4.637534 AGTAGATTTACATGGCAGCAACAG 59.362 41.667 0.00 0.00 31.96 3.16
1878 1923 4.395854 CAGTAGATTTACATGGCAGCAACA 59.604 41.667 0.00 0.00 31.96 3.33
1879 1924 4.731773 GCAGTAGATTTACATGGCAGCAAC 60.732 45.833 0.00 0.00 31.96 4.17
1880 1925 3.378112 GCAGTAGATTTACATGGCAGCAA 59.622 43.478 0.00 0.00 31.96 3.91
1881 1926 2.945008 GCAGTAGATTTACATGGCAGCA 59.055 45.455 0.00 0.00 31.96 4.41
1882 1927 2.945008 TGCAGTAGATTTACATGGCAGC 59.055 45.455 0.00 0.00 33.06 5.25
1883 1928 4.201950 GGTTGCAGTAGATTTACATGGCAG 60.202 45.833 0.00 0.00 36.05 4.85
1884 1929 3.694072 GGTTGCAGTAGATTTACATGGCA 59.306 43.478 0.00 0.00 34.21 4.92
1885 1930 3.947834 AGGTTGCAGTAGATTTACATGGC 59.052 43.478 0.00 0.00 31.96 4.40
1886 1931 5.220662 CGAAGGTTGCAGTAGATTTACATGG 60.221 44.000 0.00 0.00 31.96 3.66
1887 1932 5.799960 CGAAGGTTGCAGTAGATTTACATG 58.200 41.667 0.00 0.00 31.96 3.21
1933 1978 3.820557 AGCAACAGTAAAAGCAGGAAGA 58.179 40.909 0.00 0.00 0.00 2.87
1965 2010 1.268899 ACACAGCAGAAGATTGCAAGC 59.731 47.619 6.58 6.58 46.47 4.01
1982 2029 4.234530 AGCAGAAGATTGCAAGAAACAC 57.765 40.909 4.94 0.00 46.47 3.32
1987 2034 6.432162 AGAAACAATAGCAGAAGATTGCAAGA 59.568 34.615 4.94 0.00 46.47 3.02
1988 2035 6.618811 AGAAACAATAGCAGAAGATTGCAAG 58.381 36.000 4.94 0.00 46.47 4.01
1989 2036 6.579666 AGAAACAATAGCAGAAGATTGCAA 57.420 33.333 0.00 0.00 46.47 4.08
1990 2037 6.183360 GCTAGAAACAATAGCAGAAGATTGCA 60.183 38.462 0.00 0.00 46.47 4.08
1991 2038 6.038050 AGCTAGAAACAATAGCAGAAGATTGC 59.962 38.462 7.62 0.00 46.57 3.56
1992 2039 7.551035 AGCTAGAAACAATAGCAGAAGATTG 57.449 36.000 7.62 0.00 46.57 2.67
1993 2040 9.844257 AATAGCTAGAAACAATAGCAGAAGATT 57.156 29.630 0.00 0.00 46.57 2.40
1998 2045 9.494271 CCATTAATAGCTAGAAACAATAGCAGA 57.506 33.333 0.00 0.00 46.57 4.26
1999 2046 9.494271 TCCATTAATAGCTAGAAACAATAGCAG 57.506 33.333 0.00 0.00 46.57 4.24
2000 2047 9.494271 CTCCATTAATAGCTAGAAACAATAGCA 57.506 33.333 0.00 0.00 46.57 3.49
2001 2048 8.447053 GCTCCATTAATAGCTAGAAACAATAGC 58.553 37.037 0.00 0.00 44.89 2.97
2002 2049 9.494271 TGCTCCATTAATAGCTAGAAACAATAG 57.506 33.333 10.74 0.00 39.53 1.73
2003 2050 9.273016 GTGCTCCATTAATAGCTAGAAACAATA 57.727 33.333 10.74 0.00 39.53 1.90
2004 2051 7.995488 AGTGCTCCATTAATAGCTAGAAACAAT 59.005 33.333 10.74 0.00 39.53 2.71
2005 2052 7.280876 CAGTGCTCCATTAATAGCTAGAAACAA 59.719 37.037 10.74 0.00 39.53 2.83
2006 2053 6.763135 CAGTGCTCCATTAATAGCTAGAAACA 59.237 38.462 10.74 0.00 39.53 2.83
2007 2054 6.293135 GCAGTGCTCCATTAATAGCTAGAAAC 60.293 42.308 8.18 1.98 39.53 2.78
2008 2055 5.760253 GCAGTGCTCCATTAATAGCTAGAAA 59.240 40.000 8.18 0.00 39.53 2.52
2009 2056 5.070981 AGCAGTGCTCCATTAATAGCTAGAA 59.929 40.000 13.14 0.00 39.53 2.10
2010 2057 4.590647 AGCAGTGCTCCATTAATAGCTAGA 59.409 41.667 13.14 0.00 39.53 2.43
2042 2089 2.723322 TCCGGCTAGAGTGTAGCTTA 57.277 50.000 17.92 2.56 40.25 3.09
2059 2106 5.683859 CATATTTTGCTCGCAAGTCTATCC 58.316 41.667 4.39 0.00 37.24 2.59
2153 2204 0.394899 GAGTCTGGGCAATGGGAAGG 60.395 60.000 0.00 0.00 0.00 3.46
2278 2336 0.938637 TTTTGCTGAAATGCCGTGCG 60.939 50.000 0.00 0.00 0.00 5.34
2297 2355 2.683211 AGGCAAGGAAGTGATTTGGT 57.317 45.000 0.00 0.00 0.00 3.67
2310 2368 2.422276 CCGTTGGAGAAAAAGGCAAG 57.578 50.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.