Multiple sequence alignment - TraesCS1A01G148700

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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 TraesCS1A01G148700 chr1A 100.000 2117 0 0 1 2117 256026287 256028403 0.000000e+00 3910
1 TraesCS1A01G148700 chr1A 87.204 211 25 2 1886 2094 499323952 499324162 2.710000e-59 239
2 TraesCS1A01G148700 chr1A 100.000 93 0 0 1959 2051 256028079 256028171 2.790000e-39 172
3 TraesCS1A01G148700 chr1A 100.000 93 0 0 1793 1885 256028245 256028337 2.790000e-39 172
4 TraesCS1A01G148700 chr1A 91.398 93 7 1 1794 1885 499324027 499324119 2.210000e-25 126
5 TraesCS1A01G148700 chr2D 99.026 1746 12 5 1 1742 628285549 628283805 0.000000e+00 3125
6 TraesCS1A01G148700 chr2D 97.273 1760 26 8 1 1742 334225805 334224050 0.000000e+00 2964
7 TraesCS1A01G148700 chr6D 98.460 1753 16 5 1 1742 431399910 431398158 0.000000e+00 3077
8 TraesCS1A01G148700 chr1D 98.401 1751 19 3 1 1742 254489581 254487831 0.000000e+00 3070
9 TraesCS1A01G148700 chr1D 95.985 1644 56 7 103 1742 244401944 244400307 0.000000e+00 2662
10 TraesCS1A01G148700 chr1D 95.925 1644 58 6 103 1742 244408395 244406757 0.000000e+00 2656
11 TraesCS1A01G148700 chr1D 94.894 1645 73 7 103 1742 244423932 244422294 0.000000e+00 2562
12 TraesCS1A01G148700 chr1D 98.440 1218 11 2 1 1210 394178790 394177573 0.000000e+00 2137
13 TraesCS1A01G148700 chr3D 98.057 1750 24 5 1 1742 21897439 21895692 0.000000e+00 3035
14 TraesCS1A01G148700 chr2A 97.364 1745 40 6 1 1742 335826159 335824418 0.000000e+00 2963
15 TraesCS1A01G148700 chr5A 97.249 1745 32 9 1 1742 684325468 684323737 0.000000e+00 2942
16 TraesCS1A01G148700 chrUn 98.126 587 4 1 1 580 317473310 317473896 0.000000e+00 1016
17 TraesCS1A01G148700 chr7D 87.603 242 26 4 1878 2117 334869810 334869571 5.750000e-71 278
18 TraesCS1A01G148700 chr7D 92.079 101 7 1 1794 1893 334869728 334869628 7.880000e-30 141
19 TraesCS1A01G148700 chr4A 86.266 233 27 4 1888 2117 533455668 533455898 4.510000e-62 248
20 TraesCS1A01G148700 chr4A 86.829 205 21 6 1893 2092 521613404 521613201 7.600000e-55 224
21 TraesCS1A01G148700 chr4A 86.528 193 20 6 1906 2093 536859969 536859778 7.660000e-50 207
22 TraesCS1A01G148700 chr2B 87.805 205 20 5 1893 2093 325838339 325838136 3.510000e-58 235
23 TraesCS1A01G148700 chr2B 88.696 115 12 1 1893 2006 371354959 371355073 2.830000e-29 139
24 TraesCS1A01G148700 chr3B 88.800 125 11 3 1887 2009 679520266 679520389 1.310000e-32 150


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 TraesCS1A01G148700 chr1A 256026287 256028403 2116 False 1418 3910 100.000 1 2117 3 chr1A.!!$F1 2116
1 TraesCS1A01G148700 chr2D 628283805 628285549 1744 True 3125 3125 99.026 1 1742 1 chr2D.!!$R2 1741
2 TraesCS1A01G148700 chr2D 334224050 334225805 1755 True 2964 2964 97.273 1 1742 1 chr2D.!!$R1 1741
3 TraesCS1A01G148700 chr6D 431398158 431399910 1752 True 3077 3077 98.460 1 1742 1 chr6D.!!$R1 1741
4 TraesCS1A01G148700 chr1D 254487831 254489581 1750 True 3070 3070 98.401 1 1742 1 chr1D.!!$R4 1741
5 TraesCS1A01G148700 chr1D 244400307 244401944 1637 True 2662 2662 95.985 103 1742 1 chr1D.!!$R1 1639
6 TraesCS1A01G148700 chr1D 244406757 244408395 1638 True 2656 2656 95.925 103 1742 1 chr1D.!!$R2 1639
7 TraesCS1A01G148700 chr1D 244422294 244423932 1638 True 2562 2562 94.894 103 1742 1 chr1D.!!$R3 1639
8 TraesCS1A01G148700 chr1D 394177573 394178790 1217 True 2137 2137 98.440 1 1210 1 chr1D.!!$R5 1209
9 TraesCS1A01G148700 chr3D 21895692 21897439 1747 True 3035 3035 98.057 1 1742 1 chr3D.!!$R1 1741
10 TraesCS1A01G148700 chr2A 335824418 335826159 1741 True 2963 2963 97.364 1 1742 1 chr2A.!!$R1 1741
11 TraesCS1A01G148700 chr5A 684323737 684325468 1731 True 2942 2942 97.249 1 1742 1 chr5A.!!$R1 1741
12 TraesCS1A01G148700 chrUn 317473310 317473896 586 False 1016 1016 98.126 1 580 1 chrUn.!!$F1 579

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
841 859 9.522804 GAACAACTCGATGAATTTAGTAGATCT 57.477 33.333 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1936 0.036164 CCAGATCCCAACACCAACGA 59.964 55.0 0.0 0.0 0.0 3.85 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
301 304 9.991906 ATTCCGAATTACTCTATTATTCCGAAA 57.008 29.630 0.00 0.00 32.98 3.46
841 859 9.522804 GAACAACTCGATGAATTTAGTAGATCT 57.477 33.333 0.00 0.00 0.00 2.75
1135 1154 9.482627 TCAATTGAGAGAAAGAAAGAGACTAAC 57.517 33.333 3.38 0.00 0.00 2.34
1358 1379 6.301486 TCATATTCTGGATTGGGTTCATCTG 58.699 40.000 0.00 0.00 0.00 2.90
1743 1770 5.199424 GCAATTTGCTCACAATCACAATC 57.801 39.130 14.11 0.00 40.96 2.67
1744 1771 4.687018 GCAATTTGCTCACAATCACAATCA 59.313 37.500 14.11 0.00 40.96 2.57
1745 1772 5.177881 GCAATTTGCTCACAATCACAATCAA 59.822 36.000 14.11 0.00 40.96 2.57
1746 1773 6.292973 GCAATTTGCTCACAATCACAATCAAA 60.293 34.615 14.11 0.00 40.96 2.69
1747 1774 7.631822 CAATTTGCTCACAATCACAATCAAAA 58.368 30.769 0.00 0.00 35.21 2.44
1748 1775 6.586868 TTTGCTCACAATCACAATCAAAAC 57.413 33.333 0.00 0.00 35.21 2.43
1749 1776 5.518848 TGCTCACAATCACAATCAAAACT 57.481 34.783 0.00 0.00 0.00 2.66
1750 1777 6.631971 TGCTCACAATCACAATCAAAACTA 57.368 33.333 0.00 0.00 0.00 2.24
1751 1778 7.218228 TGCTCACAATCACAATCAAAACTAT 57.782 32.000 0.00 0.00 0.00 2.12
1752 1779 7.660112 TGCTCACAATCACAATCAAAACTATT 58.340 30.769 0.00 0.00 0.00 1.73
1753 1780 7.809331 TGCTCACAATCACAATCAAAACTATTC 59.191 33.333 0.00 0.00 0.00 1.75
1754 1781 7.809331 GCTCACAATCACAATCAAAACTATTCA 59.191 33.333 0.00 0.00 0.00 2.57
1755 1782 9.681692 CTCACAATCACAATCAAAACTATTCAA 57.318 29.630 0.00 0.00 0.00 2.69
1756 1783 9.462174 TCACAATCACAATCAAAACTATTCAAC 57.538 29.630 0.00 0.00 0.00 3.18
1757 1784 9.467258 CACAATCACAATCAAAACTATTCAACT 57.533 29.630 0.00 0.00 0.00 3.16
1760 1787 9.846248 AATCACAATCAAAACTATTCAACTAGC 57.154 29.630 0.00 0.00 0.00 3.42
1761 1788 7.816640 TCACAATCAAAACTATTCAACTAGCC 58.183 34.615 0.00 0.00 0.00 3.93
1762 1789 7.665559 TCACAATCAAAACTATTCAACTAGCCT 59.334 33.333 0.00 0.00 0.00 4.58
1763 1790 8.946085 CACAATCAAAACTATTCAACTAGCCTA 58.054 33.333 0.00 0.00 0.00 3.93
1764 1791 9.515226 ACAATCAAAACTATTCAACTAGCCTAA 57.485 29.630 0.00 0.00 0.00 2.69
1796 1823 9.554395 AAAAATCCTTGATTTAACGGAATGTTT 57.446 25.926 2.73 0.00 40.77 2.83
1797 1824 9.554395 AAAATCCTTGATTTAACGGAATGTTTT 57.446 25.926 2.73 0.00 40.77 2.43
1801 1828 9.849166 TCCTTGATTTAACGGAATGTTTTATTC 57.151 29.630 0.00 0.00 42.09 1.75
1802 1829 9.632807 CCTTGATTTAACGGAATGTTTTATTCA 57.367 29.630 0.00 0.00 42.09 2.57
1821 1848 9.921637 TTTATTCATTTTATGTTCTTTTCCGCT 57.078 25.926 0.00 0.00 0.00 5.52
1822 1849 9.921637 TTATTCATTTTATGTTCTTTTCCGCTT 57.078 25.926 0.00 0.00 0.00 4.68
1827 1854 8.958043 CATTTTATGTTCTTTTCCGCTTATAGC 58.042 33.333 0.00 0.00 38.02 2.97
1839 1866 2.210961 GCTTATAGCGAAAGGTGGACC 58.789 52.381 0.00 0.00 44.53 4.46
1840 1867 2.419574 GCTTATAGCGAAAGGTGGACCA 60.420 50.000 0.00 0.00 44.53 4.02
1841 1868 2.973694 TATAGCGAAAGGTGGACCAC 57.026 50.000 16.86 16.86 44.53 4.16
1842 1869 0.108329 ATAGCGAAAGGTGGACCACG 60.108 55.000 18.40 7.78 44.53 4.94
1843 1870 2.775032 TAGCGAAAGGTGGACCACGC 62.775 60.000 18.40 17.27 46.62 5.34
1853 1880 4.465512 GACCACGCCGCATGCAAG 62.466 66.667 19.57 9.55 41.33 4.01
1861 1888 4.113815 CGCATGCAAGGGGAGGGA 62.114 66.667 19.57 0.00 29.20 4.20
1862 1889 2.440980 GCATGCAAGGGGAGGGAC 60.441 66.667 14.21 0.00 0.00 4.46
1863 1890 2.276740 CATGCAAGGGGAGGGACC 59.723 66.667 0.00 0.00 38.08 4.46
1864 1891 3.411517 ATGCAAGGGGAGGGACCG 61.412 66.667 0.00 0.00 40.11 4.79
1876 1903 4.162690 GGACCGGGCAGGCACTAG 62.163 72.222 11.00 0.00 46.52 2.57
1877 1904 4.162690 GACCGGGCAGGCACTAGG 62.163 72.222 0.00 0.00 46.52 3.02
1900 1927 3.599704 GCCGGGGCAGATGCAATC 61.600 66.667 2.18 0.00 46.04 2.67
1909 1936 3.403277 GATGCAATCACGAGCGCT 58.597 55.556 11.27 11.27 44.70 5.92
1910 1937 1.275066 GATGCAATCACGAGCGCTC 59.725 57.895 27.64 27.64 44.70 5.03
1919 1946 3.036084 CGAGCGCTCGTTGGTGTT 61.036 61.111 43.16 4.68 46.99 3.32
1920 1947 2.551270 GAGCGCTCGTTGGTGTTG 59.449 61.111 23.61 0.00 0.00 3.33
1921 1948 2.954753 GAGCGCTCGTTGGTGTTGG 61.955 63.158 23.61 0.00 0.00 3.77
1922 1949 4.025401 GCGCTCGTTGGTGTTGGG 62.025 66.667 0.00 0.00 0.00 4.12
1923 1950 2.280524 CGCTCGTTGGTGTTGGGA 60.281 61.111 0.00 0.00 0.00 4.37
1924 1951 1.671054 CGCTCGTTGGTGTTGGGAT 60.671 57.895 0.00 0.00 0.00 3.85
1925 1952 1.635663 CGCTCGTTGGTGTTGGGATC 61.636 60.000 0.00 0.00 0.00 3.36
1926 1953 0.321653 GCTCGTTGGTGTTGGGATCT 60.322 55.000 0.00 0.00 0.00 2.75
1927 1954 1.442769 CTCGTTGGTGTTGGGATCTG 58.557 55.000 0.00 0.00 0.00 2.90
1928 1955 0.036164 TCGTTGGTGTTGGGATCTGG 59.964 55.000 0.00 0.00 0.00 3.86
1929 1956 0.250727 CGTTGGTGTTGGGATCTGGT 60.251 55.000 0.00 0.00 0.00 4.00
1930 1957 1.534729 GTTGGTGTTGGGATCTGGTC 58.465 55.000 0.00 0.00 0.00 4.02
1939 1966 3.644953 GGATCTGGTCCCTCCTCTT 57.355 57.895 0.00 0.00 41.50 2.85
1940 1967 2.777459 GGATCTGGTCCCTCCTCTTA 57.223 55.000 0.00 0.00 41.50 2.10
1941 1968 2.321719 GGATCTGGTCCCTCCTCTTAC 58.678 57.143 0.00 0.00 41.50 2.34
1942 1969 2.321719 GATCTGGTCCCTCCTCTTACC 58.678 57.143 0.00 0.00 37.07 2.85
1943 1970 1.394532 TCTGGTCCCTCCTCTTACCT 58.605 55.000 0.00 0.00 37.07 3.08
1944 1971 1.288335 TCTGGTCCCTCCTCTTACCTC 59.712 57.143 0.00 0.00 37.07 3.85
1945 1972 1.007238 CTGGTCCCTCCTCTTACCTCA 59.993 57.143 0.00 0.00 37.07 3.86
1946 1973 1.651770 TGGTCCCTCCTCTTACCTCAT 59.348 52.381 0.00 0.00 37.07 2.90
1947 1974 2.045885 TGGTCCCTCCTCTTACCTCATT 59.954 50.000 0.00 0.00 37.07 2.57
1948 1975 3.116174 GGTCCCTCCTCTTACCTCATTT 58.884 50.000 0.00 0.00 0.00 2.32
1949 1976 3.118223 GGTCCCTCCTCTTACCTCATTTG 60.118 52.174 0.00 0.00 0.00 2.32
1950 1977 2.505819 TCCCTCCTCTTACCTCATTTGC 59.494 50.000 0.00 0.00 0.00 3.68
1951 1978 2.507471 CCCTCCTCTTACCTCATTTGCT 59.493 50.000 0.00 0.00 0.00 3.91
1952 1979 3.054065 CCCTCCTCTTACCTCATTTGCTT 60.054 47.826 0.00 0.00 0.00 3.91
1953 1980 4.568592 CCCTCCTCTTACCTCATTTGCTTT 60.569 45.833 0.00 0.00 0.00 3.51
1954 1981 5.012893 CCTCCTCTTACCTCATTTGCTTTT 58.987 41.667 0.00 0.00 0.00 2.27
1955 1982 5.478332 CCTCCTCTTACCTCATTTGCTTTTT 59.522 40.000 0.00 0.00 0.00 1.94
1987 2014 9.921637 TTTATTCATTTTATGTTCTTTTCCGCT 57.078 25.926 0.00 0.00 0.00 5.52
1988 2015 9.921637 TTATTCATTTTATGTTCTTTTCCGCTT 57.078 25.926 0.00 0.00 0.00 4.68
1993 2020 8.958043 CATTTTATGTTCTTTTCCGCTTATAGC 58.042 33.333 0.00 0.00 38.02 2.97
2005 2032 2.210961 GCTTATAGCGAAAGGTGGACC 58.789 52.381 0.00 0.00 44.53 4.46
2006 2033 2.419574 GCTTATAGCGAAAGGTGGACCA 60.420 50.000 0.00 0.00 44.53 4.02
2007 2034 2.973694 TATAGCGAAAGGTGGACCAC 57.026 50.000 16.86 16.86 44.53 4.16
2008 2035 0.108329 ATAGCGAAAGGTGGACCACG 60.108 55.000 18.40 7.78 44.53 4.94
2009 2036 2.775032 TAGCGAAAGGTGGACCACGC 62.775 60.000 18.40 17.27 46.62 5.34
2019 2046 4.465512 GACCACGCCGCATGCAAG 62.466 66.667 19.57 9.55 41.33 4.01
2027 2054 4.113815 CGCATGCAAGGGGAGGGA 62.114 66.667 19.57 0.00 29.20 4.20
2028 2055 2.440980 GCATGCAAGGGGAGGGAC 60.441 66.667 14.21 0.00 0.00 4.46
2029 2056 2.276740 CATGCAAGGGGAGGGACC 59.723 66.667 0.00 0.00 38.08 4.46
2030 2057 3.411517 ATGCAAGGGGAGGGACCG 61.412 66.667 0.00 0.00 40.11 4.79
2042 2069 4.162690 GGACCGGGCAGGCACTAG 62.163 72.222 11.00 0.00 46.52 2.57
2043 2070 4.162690 GACCGGGCAGGCACTAGG 62.163 72.222 0.00 0.00 46.52 3.02
2052 2079 2.202810 GGCACTAGGCTGTCGCTC 60.203 66.667 0.00 0.00 44.01 5.03
2053 2080 2.716017 GGCACTAGGCTGTCGCTCT 61.716 63.158 0.00 0.00 44.01 4.09
2054 2081 1.216710 GCACTAGGCTGTCGCTCTT 59.783 57.895 0.00 0.00 40.25 2.85
2055 2082 1.080995 GCACTAGGCTGTCGCTCTTG 61.081 60.000 0.00 0.00 40.25 3.02
2056 2083 1.080995 CACTAGGCTGTCGCTCTTGC 61.081 60.000 0.00 0.00 36.09 4.01
2057 2084 1.216444 CTAGGCTGTCGCTCTTGCA 59.784 57.895 0.00 0.00 39.64 4.08
2058 2085 0.390340 CTAGGCTGTCGCTCTTGCAA 60.390 55.000 0.00 0.00 39.64 4.08
2059 2086 0.670546 TAGGCTGTCGCTCTTGCAAC 60.671 55.000 0.00 0.00 39.64 4.17
2060 2087 2.558313 GCTGTCGCTCTTGCAACC 59.442 61.111 0.00 0.00 39.64 3.77
2061 2088 1.963338 GCTGTCGCTCTTGCAACCT 60.963 57.895 0.00 0.00 39.64 3.50
2062 2089 0.670546 GCTGTCGCTCTTGCAACCTA 60.671 55.000 0.00 0.00 39.64 3.08
2063 2090 1.354040 CTGTCGCTCTTGCAACCTAG 58.646 55.000 0.00 0.00 39.64 3.02
2064 2091 0.679505 TGTCGCTCTTGCAACCTAGT 59.320 50.000 0.00 0.00 39.64 2.57
2065 2092 1.890489 TGTCGCTCTTGCAACCTAGTA 59.110 47.619 0.00 0.00 39.64 1.82
2066 2093 2.094700 TGTCGCTCTTGCAACCTAGTAG 60.095 50.000 0.00 0.00 39.64 2.57
2067 2094 2.163815 GTCGCTCTTGCAACCTAGTAGA 59.836 50.000 0.00 0.00 39.64 2.59
2068 2095 2.163815 TCGCTCTTGCAACCTAGTAGAC 59.836 50.000 0.00 0.00 39.64 2.59
2069 2096 2.094700 CGCTCTTGCAACCTAGTAGACA 60.095 50.000 0.00 0.00 39.64 3.41
2070 2097 3.516615 GCTCTTGCAACCTAGTAGACAG 58.483 50.000 0.00 0.00 39.41 3.51
2071 2098 3.677424 GCTCTTGCAACCTAGTAGACAGG 60.677 52.174 0.00 0.00 39.41 4.00
2072 2099 3.764434 CTCTTGCAACCTAGTAGACAGGA 59.236 47.826 0.00 0.00 36.61 3.86
2073 2100 3.510360 TCTTGCAACCTAGTAGACAGGAC 59.490 47.826 0.00 0.00 36.61 3.85
2074 2101 2.176889 TGCAACCTAGTAGACAGGACC 58.823 52.381 0.00 0.00 36.61 4.46
2075 2102 2.176889 GCAACCTAGTAGACAGGACCA 58.823 52.381 0.00 0.00 36.61 4.02
2076 2103 2.094130 GCAACCTAGTAGACAGGACCAC 60.094 54.545 0.00 0.00 36.61 4.16
2077 2104 2.496470 CAACCTAGTAGACAGGACCACC 59.504 54.545 0.00 0.00 36.61 4.61
2078 2105 1.340795 ACCTAGTAGACAGGACCACCG 60.341 57.143 0.00 0.00 41.83 4.94
2079 2106 1.064906 CCTAGTAGACAGGACCACCGA 60.065 57.143 0.00 0.00 41.83 4.69
2080 2107 2.423088 CCTAGTAGACAGGACCACCGAT 60.423 54.545 0.00 0.00 41.83 4.18
2081 2108 1.475403 AGTAGACAGGACCACCGATG 58.525 55.000 0.00 0.00 41.83 3.84
2082 2109 0.179108 GTAGACAGGACCACCGATGC 60.179 60.000 0.00 0.00 41.83 3.91
2083 2110 1.327690 TAGACAGGACCACCGATGCC 61.328 60.000 0.00 0.00 41.83 4.40
2084 2111 2.927856 ACAGGACCACCGATGCCA 60.928 61.111 0.00 0.00 41.83 4.92
2085 2112 2.350895 CAGGACCACCGATGCCAA 59.649 61.111 0.00 0.00 41.83 4.52
2086 2113 1.303236 CAGGACCACCGATGCCAAA 60.303 57.895 0.00 0.00 41.83 3.28
2087 2114 0.893270 CAGGACCACCGATGCCAAAA 60.893 55.000 0.00 0.00 41.83 2.44
2088 2115 0.609131 AGGACCACCGATGCCAAAAG 60.609 55.000 0.00 0.00 41.83 2.27
2089 2116 1.595093 GGACCACCGATGCCAAAAGG 61.595 60.000 0.00 0.00 0.00 3.11
2090 2117 0.608035 GACCACCGATGCCAAAAGGA 60.608 55.000 0.00 0.00 0.00 3.36
2091 2118 0.178975 ACCACCGATGCCAAAAGGAA 60.179 50.000 0.00 0.00 0.00 3.36
2092 2119 0.965439 CCACCGATGCCAAAAGGAAA 59.035 50.000 0.00 0.00 0.00 3.13
2093 2120 1.342819 CCACCGATGCCAAAAGGAAAA 59.657 47.619 0.00 0.00 0.00 2.29
2094 2121 2.224161 CCACCGATGCCAAAAGGAAAAA 60.224 45.455 0.00 0.00 0.00 1.94
2095 2122 3.556843 CCACCGATGCCAAAAGGAAAAAT 60.557 43.478 0.00 0.00 0.00 1.82
2096 2123 3.432933 CACCGATGCCAAAAGGAAAAATG 59.567 43.478 0.00 0.00 0.00 2.32
2097 2124 3.070878 ACCGATGCCAAAAGGAAAAATGT 59.929 39.130 0.00 0.00 0.00 2.71
2098 2125 4.064388 CCGATGCCAAAAGGAAAAATGTT 58.936 39.130 0.00 0.00 0.00 2.71
2099 2126 4.152223 CCGATGCCAAAAGGAAAAATGTTC 59.848 41.667 0.00 0.00 0.00 3.18
2100 2127 4.152223 CGATGCCAAAAGGAAAAATGTTCC 59.848 41.667 0.00 0.00 38.86 3.62
2108 2135 4.402616 AGGAAAAATGTTCCTCCATGGA 57.597 40.909 15.27 15.27 45.32 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 262 4.415881 TCGGAATAGCAGCCAAAATCTA 57.584 40.909 0.00 0.00 0.00 1.98
301 304 8.434392 TGTAGGTTCTACTTACTTTTCATTGGT 58.566 33.333 6.63 0.00 32.59 3.67
646 664 5.147330 TGCTATGAATAACCCAGTATCGG 57.853 43.478 0.00 0.00 0.00 4.18
841 859 3.563479 GGTCATTGAGGGCCTCCTAAAAA 60.563 47.826 30.03 17.59 45.05 1.94
1135 1154 7.886629 TCCAAATGGGATAAGAGAATTCTTG 57.113 36.000 9.87 0.00 41.51 3.02
1358 1379 4.660168 TCTGGTCCCTCCGATTACTATAC 58.340 47.826 0.00 0.00 39.52 1.47
1432 1453 1.134491 CGGGTCCTTTCCGCTCTAATT 60.134 52.381 0.00 0.00 41.07 1.40
1770 1797 9.554395 AAACATTCCGTTAAATCAAGGATTTTT 57.446 25.926 9.24 0.00 41.64 1.94
1771 1798 9.554395 AAAACATTCCGTTAAATCAAGGATTTT 57.446 25.926 9.24 0.00 41.64 1.82
1775 1802 9.849166 GAATAAAACATTCCGTTAAATCAAGGA 57.151 29.630 0.00 0.00 36.59 3.36
1776 1803 9.632807 TGAATAAAACATTCCGTTAAATCAAGG 57.367 29.630 0.00 0.00 36.59 3.61
1795 1822 9.921637 AGCGGAAAAGAACATAAAATGAATAAA 57.078 25.926 0.00 0.00 0.00 1.40
1796 1823 9.921637 AAGCGGAAAAGAACATAAAATGAATAA 57.078 25.926 0.00 0.00 0.00 1.40
1801 1828 8.958043 GCTATAAGCGGAAAAGAACATAAAATG 58.042 33.333 0.00 0.00 0.00 2.32
1819 1846 2.210961 GGTCCACCTTTCGCTATAAGC 58.789 52.381 0.00 0.00 38.02 3.09
1820 1847 3.195661 GTGGTCCACCTTTCGCTATAAG 58.804 50.000 11.30 0.00 36.82 1.73
1821 1848 2.417651 CGTGGTCCACCTTTCGCTATAA 60.418 50.000 16.60 0.00 36.82 0.98
1822 1849 1.135527 CGTGGTCCACCTTTCGCTATA 59.864 52.381 16.60 0.00 36.82 1.31
1823 1850 0.108329 CGTGGTCCACCTTTCGCTAT 60.108 55.000 16.60 0.00 36.82 2.97
1824 1851 1.290955 CGTGGTCCACCTTTCGCTA 59.709 57.895 16.60 0.00 36.82 4.26
1825 1852 2.030562 CGTGGTCCACCTTTCGCT 59.969 61.111 16.60 0.00 36.82 4.93
1826 1853 3.723348 GCGTGGTCCACCTTTCGC 61.723 66.667 16.60 11.99 40.92 4.70
1827 1854 3.047877 GGCGTGGTCCACCTTTCG 61.048 66.667 16.60 5.44 36.82 3.46
1828 1855 3.047877 CGGCGTGGTCCACCTTTC 61.048 66.667 16.60 3.36 36.82 2.62
1844 1871 4.113815 TCCCTCCCCTTGCATGCG 62.114 66.667 14.09 0.00 0.00 4.73
1845 1872 2.440980 GTCCCTCCCCTTGCATGC 60.441 66.667 11.82 11.82 0.00 4.06
1846 1873 2.276740 GGTCCCTCCCCTTGCATG 59.723 66.667 0.00 0.00 0.00 4.06
1847 1874 3.411517 CGGTCCCTCCCCTTGCAT 61.412 66.667 0.00 0.00 0.00 3.96
1859 1886 4.162690 CTAGTGCCTGCCCGGTCC 62.163 72.222 0.00 0.00 34.25 4.46
1860 1887 4.162690 CCTAGTGCCTGCCCGGTC 62.163 72.222 0.00 0.00 34.25 4.79
1863 1890 4.845580 CAGCCTAGTGCCTGCCCG 62.846 72.222 0.21 0.00 42.71 6.13
1864 1891 3.689002 GACAGCCTAGTGCCTGCCC 62.689 68.421 0.21 0.00 42.71 5.36
1865 1892 2.124942 GACAGCCTAGTGCCTGCC 60.125 66.667 0.21 0.00 42.71 4.85
1866 1893 2.510238 CGACAGCCTAGTGCCTGC 60.510 66.667 0.21 0.00 42.71 4.85
1867 1894 2.510238 GCGACAGCCTAGTGCCTG 60.510 66.667 0.00 1.14 42.71 4.85
1883 1910 3.599704 GATTGCATCTGCCCCGGC 61.600 66.667 0.00 0.00 41.18 6.13
1884 1911 2.124193 TGATTGCATCTGCCCCGG 60.124 61.111 0.00 0.00 41.18 5.73
1885 1912 2.827051 CGTGATTGCATCTGCCCCG 61.827 63.158 0.00 0.00 41.18 5.73
1886 1913 1.442526 CTCGTGATTGCATCTGCCCC 61.443 60.000 0.00 0.00 41.18 5.80
1887 1914 2.020131 CTCGTGATTGCATCTGCCC 58.980 57.895 0.00 0.00 41.18 5.36
1888 1915 1.354506 GCTCGTGATTGCATCTGCC 59.645 57.895 0.00 0.00 41.18 4.85
1889 1916 1.011463 CGCTCGTGATTGCATCTGC 60.011 57.895 0.00 0.00 42.50 4.26
1890 1917 1.011463 GCGCTCGTGATTGCATCTG 60.011 57.895 0.00 0.00 0.00 2.90
1891 1918 1.150567 GAGCGCTCGTGATTGCATCT 61.151 55.000 23.61 0.00 0.00 2.90
1892 1919 1.275066 GAGCGCTCGTGATTGCATC 59.725 57.895 23.61 0.00 0.00 3.91
1893 1920 2.520039 CGAGCGCTCGTGATTGCAT 61.520 57.895 43.16 4.06 46.99 3.96
1894 1921 3.181290 CGAGCGCTCGTGATTGCA 61.181 61.111 43.16 0.00 46.99 4.08
1903 1930 2.551270 CAACACCAACGAGCGCTC 59.449 61.111 27.64 27.64 0.00 5.03
1904 1931 2.972505 CCAACACCAACGAGCGCT 60.973 61.111 11.27 11.27 0.00 5.92
1905 1932 4.025401 CCCAACACCAACGAGCGC 62.025 66.667 0.00 0.00 0.00 5.92
1906 1933 1.635663 GATCCCAACACCAACGAGCG 61.636 60.000 0.00 0.00 0.00 5.03
1907 1934 0.321653 AGATCCCAACACCAACGAGC 60.322 55.000 0.00 0.00 0.00 5.03
1908 1935 1.442769 CAGATCCCAACACCAACGAG 58.557 55.000 0.00 0.00 0.00 4.18
1909 1936 0.036164 CCAGATCCCAACACCAACGA 59.964 55.000 0.00 0.00 0.00 3.85
1910 1937 0.250727 ACCAGATCCCAACACCAACG 60.251 55.000 0.00 0.00 0.00 4.10
1911 1938 1.534729 GACCAGATCCCAACACCAAC 58.465 55.000 0.00 0.00 0.00 3.77
1912 1939 0.404040 GGACCAGATCCCAACACCAA 59.596 55.000 0.00 0.00 42.46 3.67
1913 1940 2.074967 GGACCAGATCCCAACACCA 58.925 57.895 0.00 0.00 42.46 4.17
1922 1949 2.090999 AGGTAAGAGGAGGGACCAGATC 60.091 54.545 0.00 0.00 42.04 2.75
1923 1950 1.940957 AGGTAAGAGGAGGGACCAGAT 59.059 52.381 0.00 0.00 42.04 2.90
1924 1951 1.288335 GAGGTAAGAGGAGGGACCAGA 59.712 57.143 0.00 0.00 42.04 3.86
1925 1952 1.007238 TGAGGTAAGAGGAGGGACCAG 59.993 57.143 0.00 0.00 42.04 4.00
1926 1953 1.089978 TGAGGTAAGAGGAGGGACCA 58.910 55.000 0.00 0.00 42.04 4.02
1927 1954 2.480642 ATGAGGTAAGAGGAGGGACC 57.519 55.000 0.00 0.00 39.35 4.46
1928 1955 3.682999 GCAAATGAGGTAAGAGGAGGGAC 60.683 52.174 0.00 0.00 0.00 4.46
1929 1956 2.505819 GCAAATGAGGTAAGAGGAGGGA 59.494 50.000 0.00 0.00 0.00 4.20
1930 1957 2.507471 AGCAAATGAGGTAAGAGGAGGG 59.493 50.000 0.00 0.00 0.00 4.30
1931 1958 3.922171 AGCAAATGAGGTAAGAGGAGG 57.078 47.619 0.00 0.00 0.00 4.30
1932 1959 6.581171 AAAAAGCAAATGAGGTAAGAGGAG 57.419 37.500 0.00 0.00 0.00 3.69
1961 1988 9.921637 AGCGGAAAAGAACATAAAATGAATAAA 57.078 25.926 0.00 0.00 0.00 1.40
1962 1989 9.921637 AAGCGGAAAAGAACATAAAATGAATAA 57.078 25.926 0.00 0.00 0.00 1.40
1967 1994 8.958043 GCTATAAGCGGAAAAGAACATAAAATG 58.042 33.333 0.00 0.00 0.00 2.32
1985 2012 2.210961 GGTCCACCTTTCGCTATAAGC 58.789 52.381 0.00 0.00 38.02 3.09
1986 2013 3.195661 GTGGTCCACCTTTCGCTATAAG 58.804 50.000 11.30 0.00 36.82 1.73
1987 2014 2.417651 CGTGGTCCACCTTTCGCTATAA 60.418 50.000 16.60 0.00 36.82 0.98
1988 2015 1.135527 CGTGGTCCACCTTTCGCTATA 59.864 52.381 16.60 0.00 36.82 1.31
1989 2016 0.108329 CGTGGTCCACCTTTCGCTAT 60.108 55.000 16.60 0.00 36.82 2.97
1990 2017 1.290955 CGTGGTCCACCTTTCGCTA 59.709 57.895 16.60 0.00 36.82 4.26
1991 2018 2.030562 CGTGGTCCACCTTTCGCT 59.969 61.111 16.60 0.00 36.82 4.93
1992 2019 3.723348 GCGTGGTCCACCTTTCGC 61.723 66.667 16.60 11.99 40.92 4.70
1993 2020 3.047877 GGCGTGGTCCACCTTTCG 61.048 66.667 16.60 5.44 36.82 3.46
1994 2021 3.047877 CGGCGTGGTCCACCTTTC 61.048 66.667 16.60 3.36 36.82 2.62
2010 2037 4.113815 TCCCTCCCCTTGCATGCG 62.114 66.667 14.09 0.00 0.00 4.73
2011 2038 2.440980 GTCCCTCCCCTTGCATGC 60.441 66.667 11.82 11.82 0.00 4.06
2012 2039 2.276740 GGTCCCTCCCCTTGCATG 59.723 66.667 0.00 0.00 0.00 4.06
2013 2040 3.411517 CGGTCCCTCCCCTTGCAT 61.412 66.667 0.00 0.00 0.00 3.96
2025 2052 4.162690 CTAGTGCCTGCCCGGTCC 62.163 72.222 0.00 0.00 34.25 4.46
2026 2053 4.162690 CCTAGTGCCTGCCCGGTC 62.163 72.222 0.00 0.00 34.25 4.79
2029 2056 4.845580 CAGCCTAGTGCCTGCCCG 62.846 72.222 0.21 0.00 42.71 6.13
2030 2057 3.689002 GACAGCCTAGTGCCTGCCC 62.689 68.421 0.21 0.00 42.71 5.36
2031 2058 2.124942 GACAGCCTAGTGCCTGCC 60.125 66.667 0.21 0.00 42.71 4.85
2032 2059 2.510238 CGACAGCCTAGTGCCTGC 60.510 66.667 0.21 0.00 42.71 4.85
2033 2060 2.510238 GCGACAGCCTAGTGCCTG 60.510 66.667 0.00 1.14 42.71 4.85
2034 2061 2.681778 AGCGACAGCCTAGTGCCT 60.682 61.111 0.00 0.00 46.67 4.75
2035 2062 2.202810 GAGCGACAGCCTAGTGCC 60.203 66.667 0.00 0.00 46.67 5.01
2036 2063 1.080995 CAAGAGCGACAGCCTAGTGC 61.081 60.000 0.00 0.00 46.67 4.40
2037 2064 1.080995 GCAAGAGCGACAGCCTAGTG 61.081 60.000 0.00 0.00 46.67 2.74
2038 2065 1.216710 GCAAGAGCGACAGCCTAGT 59.783 57.895 0.00 0.00 46.67 2.57
2039 2066 0.390340 TTGCAAGAGCGACAGCCTAG 60.390 55.000 0.00 0.00 46.67 3.02
2040 2067 1.671166 TTGCAAGAGCGACAGCCTA 59.329 52.632 0.00 0.00 46.67 3.93
2041 2068 2.427320 TTGCAAGAGCGACAGCCT 59.573 55.556 0.00 0.00 46.67 4.58
2047 2074 2.163815 GTCTACTAGGTTGCAAGAGCGA 59.836 50.000 0.00 0.00 46.23 4.93
2048 2075 2.094700 TGTCTACTAGGTTGCAAGAGCG 60.095 50.000 0.00 0.00 46.23 5.03
2049 2076 3.516615 CTGTCTACTAGGTTGCAAGAGC 58.483 50.000 0.00 0.00 42.57 4.09
2050 2077 3.764434 TCCTGTCTACTAGGTTGCAAGAG 59.236 47.826 0.00 0.00 36.67 2.85
2051 2078 3.510360 GTCCTGTCTACTAGGTTGCAAGA 59.490 47.826 0.00 0.00 36.67 3.02
2052 2079 3.368531 GGTCCTGTCTACTAGGTTGCAAG 60.369 52.174 0.00 0.00 36.67 4.01
2053 2080 2.565834 GGTCCTGTCTACTAGGTTGCAA 59.434 50.000 0.00 0.00 36.67 4.08
2054 2081 2.176889 GGTCCTGTCTACTAGGTTGCA 58.823 52.381 0.00 0.00 36.67 4.08
2055 2082 2.094130 GTGGTCCTGTCTACTAGGTTGC 60.094 54.545 0.00 0.00 36.67 4.17
2056 2083 2.496470 GGTGGTCCTGTCTACTAGGTTG 59.504 54.545 0.00 0.00 36.67 3.77
2057 2084 2.817665 GGTGGTCCTGTCTACTAGGTT 58.182 52.381 0.00 0.00 36.67 3.50
2058 2085 1.340795 CGGTGGTCCTGTCTACTAGGT 60.341 57.143 0.00 0.00 36.67 3.08
2059 2086 1.064906 TCGGTGGTCCTGTCTACTAGG 60.065 57.143 0.00 0.00 36.63 3.02
2060 2087 2.414994 TCGGTGGTCCTGTCTACTAG 57.585 55.000 0.00 0.00 0.00 2.57
2061 2088 2.651455 CATCGGTGGTCCTGTCTACTA 58.349 52.381 0.00 0.00 0.00 1.82
2062 2089 1.475403 CATCGGTGGTCCTGTCTACT 58.525 55.000 0.00 0.00 0.00 2.57
2063 2090 0.179108 GCATCGGTGGTCCTGTCTAC 60.179 60.000 0.00 0.00 0.00 2.59
2064 2091 1.327690 GGCATCGGTGGTCCTGTCTA 61.328 60.000 0.00 0.00 0.00 2.59
2065 2092 2.660064 GGCATCGGTGGTCCTGTCT 61.660 63.158 0.00 0.00 0.00 3.41
2066 2093 2.125106 GGCATCGGTGGTCCTGTC 60.125 66.667 0.00 0.00 0.00 3.51
2067 2094 2.063015 TTTGGCATCGGTGGTCCTGT 62.063 55.000 0.00 0.00 0.00 4.00
2068 2095 0.893270 TTTTGGCATCGGTGGTCCTG 60.893 55.000 0.00 0.00 0.00 3.86
2069 2096 0.609131 CTTTTGGCATCGGTGGTCCT 60.609 55.000 0.00 0.00 0.00 3.85
2070 2097 1.595093 CCTTTTGGCATCGGTGGTCC 61.595 60.000 0.00 0.00 0.00 4.46
2071 2098 0.608035 TCCTTTTGGCATCGGTGGTC 60.608 55.000 0.00 0.00 40.12 4.02
2072 2099 0.178975 TTCCTTTTGGCATCGGTGGT 60.179 50.000 0.00 0.00 40.12 4.16
2073 2100 0.965439 TTTCCTTTTGGCATCGGTGG 59.035 50.000 0.00 0.00 40.12 4.61
2074 2101 2.810439 TTTTCCTTTTGGCATCGGTG 57.190 45.000 0.00 0.00 40.12 4.94
2075 2102 3.070878 ACATTTTTCCTTTTGGCATCGGT 59.929 39.130 0.00 0.00 40.12 4.69
2076 2103 3.663025 ACATTTTTCCTTTTGGCATCGG 58.337 40.909 0.00 0.00 40.12 4.18
2077 2104 4.152223 GGAACATTTTTCCTTTTGGCATCG 59.848 41.667 0.00 0.00 40.12 3.84
2078 2105 5.308014 AGGAACATTTTTCCTTTTGGCATC 58.692 37.500 0.00 0.00 46.21 3.91
2079 2106 5.308976 AGGAACATTTTTCCTTTTGGCAT 57.691 34.783 0.00 0.00 46.21 4.40
2080 2107 4.769345 AGGAACATTTTTCCTTTTGGCA 57.231 36.364 0.00 0.00 46.21 4.92


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

AutoCloner maintained by Alex Coulton.