Multiple sequence alignment - TraesCS4D01G294800

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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 TraesCS4D01G294800 chr4D 100.000 1645 0 0 740 2384 465046807 465045163 0.000000e+00 3038
1 TraesCS4D01G294800 chr4D 100.000 323 0 0 1 323 465047546 465047224 4.390000e-167 597
2 TraesCS4D01G294800 chr4D 93.814 97 6 0 1850 1946 437299904 437300000 1.910000e-31 147
3 TraesCS4D01G294800 chr4B 95.174 1119 42 4 740 1851 581332596 581331483 0.000000e+00 1757
4 TraesCS4D01G294800 chr4B 87.957 465 38 6 1933 2384 581331484 581331025 1.250000e-147 532
5 TraesCS4D01G294800 chr4B 85.976 328 33 7 7 323 581333015 581332690 2.940000e-89 339
6 TraesCS4D01G294800 chr2A 91.935 124 8 2 1698 1820 740021643 740021521 3.150000e-39 172
7 TraesCS4D01G294800 chr3D 97.753 89 2 0 1850 1938 219572265 219572177 1.140000e-33 154
8 TraesCS4D01G294800 chr3D 95.349 86 3 1 1849 1934 488998556 488998472 4.130000e-28 135
9 TraesCS4D01G294800 chr3A 97.701 87 2 0 1848 1934 436662150 436662064 1.480000e-32 150
10 TraesCS4D01G294800 chr1D 96.629 89 3 0 1849 1937 473933016 473932928 5.310000e-32 148
11 TraesCS4D01G294800 chr1B 94.737 95 5 0 1843 1937 142723548 142723454 5.310000e-32 148
12 TraesCS4D01G294800 chr6D 94.681 94 5 0 1843 1936 149721658 149721751 1.910000e-31 147
13 TraesCS4D01G294800 chr6B 93.000 100 4 3 1850 1949 715204259 715204355 2.470000e-30 143
14 TraesCS4D01G294800 chr6A 92.929 99 5 2 1843 1940 297654357 297654454 2.470000e-30 143


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 TraesCS4D01G294800 chr4D 465045163 465047546 2383 True 1817.5 3038 100.000000 1 2384 2 chr4D.!!$R1 2383
1 TraesCS4D01G294800 chr4B 581331025 581333015 1990 True 876.0 1757 89.702333 7 2384 3 chr4B.!!$R1 2377

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
291 302 0.179089 CTGCCAGCTAGACGAAGCAT 60.179 55.0 10.78 0.0 45.3 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 1996 0.250513 GCGTGATCTGGAAAGGGTCT 59.749 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
29 30 9.093458 AGTTTTAATTGTGAGGGAAGATCAAAT 57.907 29.630 0.00 0.00 0.00 2.32
31 32 8.648698 TTTAATTGTGAGGGAAGATCAAATGA 57.351 30.769 0.00 0.00 0.00 2.57
38 39 3.261897 AGGGAAGATCAAATGACGACAGT 59.738 43.478 0.00 0.00 0.00 3.55
47 48 7.586300 AGATCAAATGACGACAGTTTTAAAACG 59.414 33.333 22.04 18.79 43.51 3.60
52 54 8.450385 AATGACGACAGTTTTAAAACGAAAAA 57.550 26.923 22.04 9.13 43.51 1.94
53 55 8.623310 ATGACGACAGTTTTAAAACGAAAAAT 57.377 26.923 22.04 10.04 43.51 1.82
81 90 9.645059 TCTTCACTGAAGAAACTATCATGTAAG 57.355 33.333 17.58 0.00 44.37 2.34
90 99 8.928270 AGAAACTATCATGTAAGAAACTACCG 57.072 34.615 0.00 0.00 0.00 4.02
92 101 8.699283 AAACTATCATGTAAGAAACTACCGTC 57.301 34.615 0.00 0.00 0.00 4.79
112 122 4.010349 GTCCCCTCACAACTAAAATCCAG 58.990 47.826 0.00 0.00 0.00 3.86
120 130 6.664515 TCACAACTAAAATCCAGCTAAAACG 58.335 36.000 0.00 0.00 0.00 3.60
122 132 6.577427 CACAACTAAAATCCAGCTAAAACGTC 59.423 38.462 0.00 0.00 0.00 4.34
133 143 2.492001 CTAAAACGTCCGCAAATGTCG 58.508 47.619 0.00 0.00 0.00 4.35
136 146 4.160635 CGTCCGCAAATGTCGCCC 62.161 66.667 0.00 0.00 0.00 6.13
145 155 1.488705 AAATGTCGCCCTCCCTGACA 61.489 55.000 0.00 0.00 45.71 3.58
149 159 2.742372 CGCCCTCCCTGACAAACG 60.742 66.667 0.00 0.00 0.00 3.60
152 162 1.235281 GCCCTCCCTGACAAACGTTC 61.235 60.000 0.00 0.00 0.00 3.95
156 166 2.549282 CCTGACAAACGTTCGCCG 59.451 61.111 0.00 0.00 44.03 6.46
165 175 1.223417 AACGTTCGCCGGTTAACAGG 61.223 55.000 19.28 19.28 42.24 4.00
168 178 1.004679 TTCGCCGGTTAACAGGGTC 60.005 57.895 23.75 9.18 0.00 4.46
171 181 1.377612 GCCGGTTAACAGGGTCCTT 59.622 57.895 23.75 0.00 0.00 3.36
172 182 0.958876 GCCGGTTAACAGGGTCCTTG 60.959 60.000 23.75 0.00 0.00 3.61
177 187 3.633065 CGGTTAACAGGGTCCTTGAAAAA 59.367 43.478 8.21 0.00 0.00 1.94
178 188 4.279922 CGGTTAACAGGGTCCTTGAAAAAT 59.720 41.667 8.21 0.00 0.00 1.82
179 189 5.221362 CGGTTAACAGGGTCCTTGAAAAATT 60.221 40.000 8.21 0.00 0.00 1.82
181 191 7.470286 CGGTTAACAGGGTCCTTGAAAAATTAA 60.470 37.037 8.21 0.00 0.00 1.40
187 197 9.996554 ACAGGGTCCTTGAAAAATTAAATTTAG 57.003 29.630 8.21 0.00 0.00 1.85
210 220 6.478129 AGAACCTTACCAAAATATCCAACGA 58.522 36.000 0.00 0.00 0.00 3.85
211 221 7.116736 AGAACCTTACCAAAATATCCAACGAT 58.883 34.615 0.00 0.00 0.00 3.73
212 222 6.693315 ACCTTACCAAAATATCCAACGATG 57.307 37.500 0.00 0.00 0.00 3.84
223 234 3.306917 TCCAACGATGCTCGAACTTTA 57.693 42.857 11.64 0.00 43.74 1.85
291 302 0.179089 CTGCCAGCTAGACGAAGCAT 60.179 55.000 10.78 0.00 45.30 3.79
897 908 2.667724 CGTCTTCCTCTAACGACACCAC 60.668 54.545 0.00 0.00 38.65 4.16
902 913 1.607251 CCTCTAACGACACCACCCAAC 60.607 57.143 0.00 0.00 0.00 3.77
907 918 2.191109 GACACCACCCAACCACGT 59.809 61.111 0.00 0.00 0.00 4.49
915 926 2.738521 CCAACCACGTGAGGCGAG 60.739 66.667 19.30 0.71 44.77 5.03
929 940 0.857935 GGCGAGAAGAATCAGCATCG 59.142 55.000 0.00 0.00 34.46 3.84
941 952 2.074948 AGCATCGGGGCCTTGATCT 61.075 57.895 0.84 4.77 0.00 2.75
942 953 0.764369 AGCATCGGGGCCTTGATCTA 60.764 55.000 0.84 0.00 0.00 1.98
943 954 0.321122 GCATCGGGGCCTTGATCTAG 60.321 60.000 0.84 0.00 0.00 2.43
944 955 1.342074 CATCGGGGCCTTGATCTAGA 58.658 55.000 0.84 0.00 0.00 2.43
945 956 1.001406 CATCGGGGCCTTGATCTAGAC 59.999 57.143 0.84 0.00 0.00 2.59
964 975 1.440938 CTAGAGCCGTCCTCGACCAG 61.441 65.000 0.00 0.00 45.54 4.00
986 997 3.371059 GGATCCAAGAAGAGGGAGGTTTC 60.371 52.174 6.95 0.00 36.45 2.78
987 998 1.985895 TCCAAGAAGAGGGAGGTTTCC 59.014 52.381 0.00 0.00 43.23 3.13
1016 1027 4.101790 CATGTCGGCGGTGGTTGC 62.102 66.667 7.21 0.00 0.00 4.17
1026 1037 4.012895 GTGGTTGCGCAGGACGTG 62.013 66.667 11.31 0.00 46.11 4.49
1248 1259 2.646143 GAGGTAGAGGCGGCGATC 59.354 66.667 12.98 7.90 0.00 3.69
1345 1356 4.847444 GCCAGAGCGGGAGGAAGC 62.847 72.222 0.00 0.00 34.06 3.86
1528 1542 4.589908 AGACGCTTAATTTGGAGACCAAT 58.410 39.130 4.03 0.00 43.55 3.16
1615 1629 9.863845 TGTAGATGACACGAGAAAAATGTATAA 57.136 29.630 0.00 0.00 31.20 0.98
1627 1641 7.103641 AGAAAAATGTATAAACGGAGCTGAGA 58.896 34.615 0.00 0.00 0.00 3.27
1641 1655 5.300752 GGAGCTGAGATCGAATAATTCCAA 58.699 41.667 0.00 0.00 0.00 3.53
1689 1703 6.291648 TCAAATAATGGCAAAGGTATTGCA 57.708 33.333 14.34 2.42 46.58 4.08
1693 1707 3.825143 ATGGCAAAGGTATTGCATTCC 57.175 42.857 14.34 0.00 46.58 3.01
1700 1714 2.815158 AGGTATTGCATTCCGGGTTTT 58.185 42.857 0.00 0.00 0.00 2.43
1720 1736 0.675633 CTTTGACCTGGCACTTTGGG 59.324 55.000 0.00 0.00 0.00 4.12
1728 1744 0.178992 TGGCACTTTGGGACTTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
1778 1796 1.817357 TTCAGACAAGCATGCCAGAG 58.183 50.000 15.66 4.32 0.00 3.35
1809 1827 2.158696 AGCAGCTGTCTTTTTCTCACCT 60.159 45.455 16.64 0.00 0.00 4.00
1811 1829 2.031333 CAGCTGTCTTTTTCTCACCTGC 60.031 50.000 5.25 0.00 0.00 4.85
1851 1869 9.520204 ACAAGCAACAATAATGCAAGATTATAC 57.480 29.630 0.00 0.00 46.22 1.47
1852 1870 9.740239 CAAGCAACAATAATGCAAGATTATACT 57.260 29.630 0.00 0.00 46.22 2.12
1853 1871 9.956720 AAGCAACAATAATGCAAGATTATACTC 57.043 29.630 0.00 0.00 46.22 2.59
1854 1872 8.571336 AGCAACAATAATGCAAGATTATACTCC 58.429 33.333 0.00 0.00 46.22 3.85
1855 1873 7.809806 GCAACAATAATGCAAGATTATACTCCC 59.190 37.037 0.00 0.00 43.29 4.30
1856 1874 9.071276 CAACAATAATGCAAGATTATACTCCCT 57.929 33.333 0.00 0.00 0.00 4.20
1857 1875 8.854614 ACAATAATGCAAGATTATACTCCCTC 57.145 34.615 0.00 0.00 0.00 4.30
1858 1876 8.664079 ACAATAATGCAAGATTATACTCCCTCT 58.336 33.333 0.00 0.00 0.00 3.69
1859 1877 8.944029 CAATAATGCAAGATTATACTCCCTCTG 58.056 37.037 0.00 0.00 0.00 3.35
1860 1878 6.506538 AATGCAAGATTATACTCCCTCTGT 57.493 37.500 0.00 0.00 0.00 3.41
1861 1879 5.537300 TGCAAGATTATACTCCCTCTGTC 57.463 43.478 0.00 0.00 0.00 3.51
1862 1880 4.345257 TGCAAGATTATACTCCCTCTGTCC 59.655 45.833 0.00 0.00 0.00 4.02
1863 1881 4.262678 GCAAGATTATACTCCCTCTGTCCC 60.263 50.000 0.00 0.00 0.00 4.46
1864 1882 4.834406 AGATTATACTCCCTCTGTCCCA 57.166 45.455 0.00 0.00 0.00 4.37
1865 1883 5.361630 AGATTATACTCCCTCTGTCCCAT 57.638 43.478 0.00 0.00 0.00 4.00
1866 1884 6.485388 AGATTATACTCCCTCTGTCCCATA 57.515 41.667 0.00 0.00 0.00 2.74
1867 1885 6.875469 AGATTATACTCCCTCTGTCCCATAA 58.125 40.000 0.00 0.00 0.00 1.90
1868 1886 7.491681 AGATTATACTCCCTCTGTCCCATAAT 58.508 38.462 0.00 0.00 0.00 1.28
1869 1887 8.633724 AGATTATACTCCCTCTGTCCCATAATA 58.366 37.037 0.00 0.00 0.00 0.98
1870 1888 9.440761 GATTATACTCCCTCTGTCCCATAATAT 57.559 37.037 0.00 0.00 0.00 1.28
1873 1891 8.846423 ATACTCCCTCTGTCCCATAATATAAG 57.154 38.462 0.00 0.00 0.00 1.73
1874 1892 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
1875 1893 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
1876 1894 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
1877 1895 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
1878 1896 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
1879 1897 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
1880 1898 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
1881 1899 8.882415 TCTGTCCCATAATATAAGAACGTTTC 57.118 34.615 0.46 0.00 0.00 2.78
1882 1900 8.701895 TCTGTCCCATAATATAAGAACGTTTCT 58.298 33.333 0.46 0.00 43.15 2.52
1883 1901 8.657074 TGTCCCATAATATAAGAACGTTTCTG 57.343 34.615 0.46 0.00 40.59 3.02
1884 1902 8.479689 TGTCCCATAATATAAGAACGTTTCTGA 58.520 33.333 0.46 0.00 40.59 3.27
1885 1903 8.762426 GTCCCATAATATAAGAACGTTTCTGAC 58.238 37.037 0.46 0.00 40.59 3.51
1886 1904 8.479689 TCCCATAATATAAGAACGTTTCTGACA 58.520 33.333 0.46 0.00 40.59 3.58
1887 1905 8.548721 CCCATAATATAAGAACGTTTCTGACAC 58.451 37.037 0.46 0.00 40.59 3.67
1888 1906 9.314321 CCATAATATAAGAACGTTTCTGACACT 57.686 33.333 0.46 0.00 40.59 3.55
1892 1910 8.912787 ATATAAGAACGTTTCTGACACTAGTG 57.087 34.615 21.44 21.44 40.59 2.74
1893 1911 4.650754 AGAACGTTTCTGACACTAGTGT 57.349 40.909 28.27 28.27 38.91 3.55
1894 1912 5.762825 AGAACGTTTCTGACACTAGTGTA 57.237 39.130 27.98 10.72 39.38 2.90
1895 1913 5.759963 AGAACGTTTCTGACACTAGTGTAG 58.240 41.667 27.98 22.31 39.38 2.74
1896 1914 5.298777 AGAACGTTTCTGACACTAGTGTAGT 59.701 40.000 27.98 15.35 39.38 2.73
1921 1939 9.120422 GTGTTAAACACGTTCTTATATTTTGGG 57.880 33.333 0.00 0.00 39.53 4.12
1922 1940 9.064706 TGTTAAACACGTTCTTATATTTTGGGA 57.935 29.630 0.00 0.00 0.00 4.37
1923 1941 9.333497 GTTAAACACGTTCTTATATTTTGGGAC 57.667 33.333 0.00 0.00 0.00 4.46
1924 1942 7.513371 AAACACGTTCTTATATTTTGGGACA 57.487 32.000 0.00 0.00 0.00 4.02
1925 1943 6.737254 ACACGTTCTTATATTTTGGGACAG 57.263 37.500 0.00 0.00 42.39 3.51
1926 1944 6.469410 ACACGTTCTTATATTTTGGGACAGA 58.531 36.000 0.00 0.00 42.39 3.41
1927 1945 6.594159 ACACGTTCTTATATTTTGGGACAGAG 59.406 38.462 0.00 0.00 42.39 3.35
1928 1946 6.037172 CACGTTCTTATATTTTGGGACAGAGG 59.963 42.308 0.00 0.00 42.39 3.69
1929 1947 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
1930 1948 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
1931 1949 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
1932 1950 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
1933 1951 7.136885 TCTTATATTTTGGGACAGAGGGAGTA 58.863 38.462 0.00 0.00 42.39 2.59
1942 1960 4.965532 GGGACAGAGGGAGTATATGCATAT 59.034 45.833 22.31 22.31 0.00 1.78
1947 1965 9.581289 GACAGAGGGAGTATATGCATATATAGT 57.419 37.037 25.35 15.17 37.85 2.12
1978 1996 5.946298 AGTATCATTCACGACAAACGAGTA 58.054 37.500 0.00 0.00 45.77 2.59
1992 2010 3.103080 ACGAGTAGACCCTTTCCAGAT 57.897 47.619 0.00 0.00 0.00 2.90
2017 2035 1.600663 CGGACAGGTCGATGCATCTAC 60.601 57.143 23.73 21.87 0.00 2.59
2046 2070 4.040952 AGAGTCACTGTTGTGCTTCCTTAT 59.959 41.667 0.00 0.00 43.49 1.73
2104 2132 4.217118 AGCCACTTCAAGTAGAAAGCAATG 59.783 41.667 0.00 0.00 35.40 2.82
2105 2133 4.022849 GCCACTTCAAGTAGAAAGCAATGT 60.023 41.667 0.00 0.00 35.40 2.71
2120 2148 8.466798 AGAAAGCAATGTTAGTAACAAGTTGTT 58.533 29.630 23.85 23.85 45.86 2.83
2129 2157 5.186996 AGTAACAAGTTGTTCATTGCAGG 57.813 39.130 24.06 0.00 40.22 4.85
2132 2160 3.030291 ACAAGTTGTTCATTGCAGGGAA 58.970 40.909 1.64 0.00 0.00 3.97
2139 2167 4.469657 TGTTCATTGCAGGGAAGTTACTT 58.530 39.130 0.00 0.00 0.00 2.24
2145 2173 6.206634 TCATTGCAGGGAAGTTACTTAAAGTG 59.793 38.462 0.00 0.00 0.00 3.16
2176 2204 2.504367 CCACCTGAAGTTGTGGTAAGG 58.496 52.381 3.25 0.00 45.61 2.69
2177 2205 1.880027 CACCTGAAGTTGTGGTAAGGC 59.120 52.381 0.00 0.00 32.13 4.35
2181 2209 1.771854 TGAAGTTGTGGTAAGGCCTCA 59.228 47.619 5.23 0.00 38.82 3.86
2186 2214 3.517296 TTGTGGTAAGGCCTCAATTGA 57.483 42.857 5.23 8.12 43.43 2.57
2191 2219 2.164422 GGTAAGGCCTCAATTGAAGTGC 59.836 50.000 5.23 11.89 0.00 4.40
2195 2223 2.298163 AGGCCTCAATTGAAGTGCAAAG 59.702 45.455 19.78 4.03 40.48 2.77
2199 2227 4.261572 GCCTCAATTGAAGTGCAAAGTGTA 60.262 41.667 9.88 0.00 40.48 2.90
2204 2232 5.633830 ATTGAAGTGCAAAGTGTATCCAG 57.366 39.130 0.00 0.00 40.48 3.86
2226 2254 6.262273 CCAGCTAAGTTACTTGAAGTGGAAAA 59.738 38.462 8.33 0.00 0.00 2.29
2227 2255 7.132863 CAGCTAAGTTACTTGAAGTGGAAAAC 58.867 38.462 8.33 4.39 0.00 2.43
2229 2257 7.338449 AGCTAAGTTACTTGAAGTGGAAAACAA 59.662 33.333 8.33 0.00 0.00 2.83
2230 2258 7.644157 GCTAAGTTACTTGAAGTGGAAAACAAG 59.356 37.037 8.33 7.25 43.30 3.16
2231 2259 7.696992 AAGTTACTTGAAGTGGAAAACAAGA 57.303 32.000 8.33 0.00 41.16 3.02
2232 2260 7.696992 AGTTACTTGAAGTGGAAAACAAGAA 57.303 32.000 8.33 0.00 41.16 2.52
2233 2261 7.762382 AGTTACTTGAAGTGGAAAACAAGAAG 58.238 34.615 8.33 0.00 41.16 2.85
2234 2262 7.393515 AGTTACTTGAAGTGGAAAACAAGAAGT 59.606 33.333 8.33 0.00 41.16 3.01
2255 2283 5.133221 AGTAACTTGCACACAGAAAAGGAT 58.867 37.500 0.00 0.00 0.00 3.24
2286 2314 8.585881 ACTAGAAGTGTAAAGCAAGAACAGATA 58.414 33.333 0.00 0.00 0.00 1.98
2311 2342 5.125100 CAAGCCAATTGCAGAAAGTAAGA 57.875 39.130 0.00 0.00 44.83 2.10
2314 2345 6.350629 AGCCAATTGCAGAAAGTAAGAAAT 57.649 33.333 0.00 0.00 44.83 2.17
2320 2351 9.962759 CAATTGCAGAAAGTAAGAAATATTTGC 57.037 29.630 5.17 0.00 0.00 3.68
2343 2374 0.762082 TATCTGCTAGCTGGCCTGCT 60.762 55.000 35.49 35.49 46.11 4.24
2374 2405 2.412605 GCATGTTCTGATGCTCCCC 58.587 57.895 0.00 0.00 44.57 4.81
2378 2409 1.144936 GTTCTGATGCTCCCCCTCG 59.855 63.158 0.00 0.00 0.00 4.63
2379 2410 1.306141 TTCTGATGCTCCCCCTCGT 60.306 57.895 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.522789 TCTTCCCTCACAATTAAAACTGCC 59.477 41.667 0.00 0.00 0.00 4.85
1 2 5.705609 TCTTCCCTCACAATTAAAACTGC 57.294 39.130 0.00 0.00 0.00 4.40
2 3 7.452880 TGATCTTCCCTCACAATTAAAACTG 57.547 36.000 0.00 0.00 0.00 3.16
3 4 8.477419 TTTGATCTTCCCTCACAATTAAAACT 57.523 30.769 0.00 0.00 0.00 2.66
4 5 9.143631 CATTTGATCTTCCCTCACAATTAAAAC 57.856 33.333 0.00 0.00 0.00 2.43
5 6 9.087871 TCATTTGATCTTCCCTCACAATTAAAA 57.912 29.630 0.00 0.00 0.00 1.52
11 12 4.002982 CGTCATTTGATCTTCCCTCACAA 58.997 43.478 0.00 0.00 0.00 3.33
18 19 5.613358 AAACTGTCGTCATTTGATCTTCC 57.387 39.130 0.00 0.00 0.00 3.46
19 20 9.445786 TTTTAAAACTGTCGTCATTTGATCTTC 57.554 29.630 0.00 0.00 0.00 2.87
29 30 7.537991 ACATTTTTCGTTTTAAAACTGTCGTCA 59.462 29.630 24.57 6.99 37.56 4.35
31 32 7.800015 ACATTTTTCGTTTTAAAACTGTCGT 57.200 28.000 24.57 11.96 37.56 4.34
38 39 9.627395 TCAGTGAAGACATTTTTCGTTTTAAAA 57.373 25.926 0.00 0.00 0.00 1.52
52 54 8.099537 ACATGATAGTTTCTTCAGTGAAGACAT 58.900 33.333 30.75 24.86 46.54 3.06
53 55 7.445121 ACATGATAGTTTCTTCAGTGAAGACA 58.555 34.615 30.75 23.47 46.54 3.41
58 60 9.996554 TTTCTTACATGATAGTTTCTTCAGTGA 57.003 29.630 0.00 0.00 0.00 3.41
70 72 6.214399 GGGACGGTAGTTTCTTACATGATAG 58.786 44.000 0.00 0.00 0.00 2.08
72 74 4.141779 GGGGACGGTAGTTTCTTACATGAT 60.142 45.833 0.00 0.00 0.00 2.45
81 90 0.971386 TGTGAGGGGACGGTAGTTTC 59.029 55.000 0.00 0.00 0.00 2.78
90 99 4.010349 CTGGATTTTAGTTGTGAGGGGAC 58.990 47.826 0.00 0.00 0.00 4.46
92 101 2.755103 GCTGGATTTTAGTTGTGAGGGG 59.245 50.000 0.00 0.00 0.00 4.79
112 122 2.239201 GACATTTGCGGACGTTTTAGC 58.761 47.619 0.00 0.00 0.00 3.09
120 130 2.746277 AGGGCGACATTTGCGGAC 60.746 61.111 0.00 0.00 0.00 4.79
122 132 3.508840 GGAGGGCGACATTTGCGG 61.509 66.667 0.00 0.00 0.00 5.69
133 143 1.228154 AACGTTTGTCAGGGAGGGC 60.228 57.895 0.00 0.00 0.00 5.19
136 146 1.566018 GGCGAACGTTTGTCAGGGAG 61.566 60.000 15.30 0.00 0.00 4.30
145 155 0.582960 CTGTTAACCGGCGAACGTTT 59.417 50.000 9.30 0.00 42.24 3.60
149 159 1.293963 GACCCTGTTAACCGGCGAAC 61.294 60.000 9.30 6.76 0.00 3.95
152 162 2.435410 GGACCCTGTTAACCGGCG 60.435 66.667 10.40 0.00 0.00 6.46
156 166 5.801531 ATTTTTCAAGGACCCTGTTAACC 57.198 39.130 2.48 0.00 0.00 2.85
187 197 6.746745 TCGTTGGATATTTTGGTAAGGTTC 57.253 37.500 0.00 0.00 0.00 3.62
210 220 4.307432 CCCACGATATAAAGTTCGAGCAT 58.693 43.478 1.01 0.00 38.67 3.79
211 221 3.713288 CCCACGATATAAAGTTCGAGCA 58.287 45.455 1.01 0.00 38.67 4.26
212 222 2.475487 GCCCACGATATAAAGTTCGAGC 59.525 50.000 0.68 0.00 38.67 5.03
291 302 1.573829 GCTTTGGGTGTTCGATGCGA 61.574 55.000 0.00 0.00 0.00 5.10
897 908 4.308458 TCGCCTCACGTGGTTGGG 62.308 66.667 17.00 13.55 44.19 4.12
902 913 0.108615 ATTCTTCTCGCCTCACGTGG 60.109 55.000 17.00 6.38 44.19 4.94
907 918 0.897621 TGCTGATTCTTCTCGCCTCA 59.102 50.000 0.00 0.00 0.00 3.86
915 926 1.169034 GGCCCCGATGCTGATTCTTC 61.169 60.000 0.00 0.00 0.00 2.87
929 940 3.161866 CTCTAGTCTAGATCAAGGCCCC 58.838 54.545 10.06 0.00 33.66 5.80
941 952 1.117994 TCGAGGACGGCTCTAGTCTA 58.882 55.000 0.00 0.00 38.58 2.59
942 953 0.462403 GTCGAGGACGGCTCTAGTCT 60.462 60.000 0.00 0.00 41.20 3.24
943 954 1.438562 GGTCGAGGACGGCTCTAGTC 61.439 65.000 0.00 0.00 44.06 2.59
944 955 1.451747 GGTCGAGGACGGCTCTAGT 60.452 63.158 0.00 0.00 44.06 2.57
945 956 1.440938 CTGGTCGAGGACGGCTCTAG 61.441 65.000 0.00 0.00 44.06 2.43
964 975 1.886422 ACCTCCCTCTTCTTGGATCC 58.114 55.000 4.20 4.20 0.00 3.36
987 998 3.434319 GACATGCCAGCACGGTGG 61.434 66.667 10.95 10.95 41.01 4.61
1092 1103 2.046507 GCAGTGCACTCCTCCCTG 60.047 66.667 18.64 5.96 0.00 4.45
1209 1220 3.917760 GTGGCCGATCCTCCTCCG 61.918 72.222 0.00 0.00 35.26 4.63
1528 1542 8.186163 CACAAATAAGCTGAAGATATTGCAGAA 58.814 33.333 0.00 0.00 0.00 3.02
1615 1629 4.592485 ATTATTCGATCTCAGCTCCGTT 57.408 40.909 0.00 0.00 0.00 4.44
1617 1631 3.923461 GGAATTATTCGATCTCAGCTCCG 59.077 47.826 0.00 0.00 0.00 4.63
1627 1641 8.621286 ACGCTTCTTAAATTGGAATTATTCGAT 58.379 29.630 0.00 0.00 0.00 3.59
1641 1655 9.774742 GATTCAATAGTTTGACGCTTCTTAAAT 57.225 29.630 0.00 0.00 41.50 1.40
1650 1664 8.745837 CCATTATTTGATTCAATAGTTTGACGC 58.254 33.333 0.00 0.00 41.50 5.19
1651 1665 8.745837 GCCATTATTTGATTCAATAGTTTGACG 58.254 33.333 0.00 0.00 41.50 4.35
1689 1703 2.890945 CAGGTCAAAGAAAACCCGGAAT 59.109 45.455 0.73 0.00 36.11 3.01
1693 1707 0.313987 GCCAGGTCAAAGAAAACCCG 59.686 55.000 0.00 0.00 36.11 5.28
1700 1714 1.691196 CCAAAGTGCCAGGTCAAAGA 58.309 50.000 0.00 0.00 0.00 2.52
1720 1736 1.168714 ATTCCGCAAAGCCTGAAGTC 58.831 50.000 0.00 0.00 0.00 3.01
1728 1744 2.292103 TATGCCAAATTCCGCAAAGC 57.708 45.000 3.75 0.00 38.75 3.51
1753 1771 1.202268 GCATGCTTGTCTGAATGCCTC 60.202 52.381 11.37 0.00 41.85 4.70
1778 1796 7.543520 AGAAAAAGACAGCTGCTATTAAAATGC 59.456 33.333 15.27 0.00 0.00 3.56
1809 1827 7.261325 TGTTGCTTGTAAATTTTAGAACTGCA 58.739 30.769 0.00 8.14 0.00 4.41
1856 1874 8.701895 AGAAACGTTCTTATATTATGGGACAGA 58.298 33.333 0.00 0.00 38.47 3.41
1857 1875 8.765219 CAGAAACGTTCTTATATTATGGGACAG 58.235 37.037 0.00 0.00 39.41 3.51
1858 1876 8.479689 TCAGAAACGTTCTTATATTATGGGACA 58.520 33.333 0.00 0.00 40.23 4.02
1859 1877 8.762426 GTCAGAAACGTTCTTATATTATGGGAC 58.238 37.037 0.00 0.00 38.11 4.46
1860 1878 8.479689 TGTCAGAAACGTTCTTATATTATGGGA 58.520 33.333 0.00 0.00 38.11 4.37
1861 1879 8.548721 GTGTCAGAAACGTTCTTATATTATGGG 58.451 37.037 0.00 0.00 38.11 4.00
1862 1880 9.314321 AGTGTCAGAAACGTTCTTATATTATGG 57.686 33.333 0.00 0.00 38.11 2.74
1866 1884 9.355215 CACTAGTGTCAGAAACGTTCTTATATT 57.645 33.333 15.06 0.00 38.11 1.28
1867 1885 8.521176 ACACTAGTGTCAGAAACGTTCTTATAT 58.479 33.333 22.95 0.00 40.24 0.86
1868 1886 7.879070 ACACTAGTGTCAGAAACGTTCTTATA 58.121 34.615 22.95 0.00 40.24 0.98
1869 1887 6.746120 ACACTAGTGTCAGAAACGTTCTTAT 58.254 36.000 22.95 0.00 40.24 1.73
1870 1888 6.140303 ACACTAGTGTCAGAAACGTTCTTA 57.860 37.500 22.95 0.00 40.24 2.10
1871 1889 5.007385 ACACTAGTGTCAGAAACGTTCTT 57.993 39.130 22.95 0.00 40.24 2.52
1872 1890 4.650754 ACACTAGTGTCAGAAACGTTCT 57.349 40.909 22.95 0.00 40.24 3.01
1873 1891 5.517904 ACTACACTAGTGTCAGAAACGTTC 58.482 41.667 31.11 0.00 43.74 3.95
1874 1892 5.511234 ACTACACTAGTGTCAGAAACGTT 57.489 39.130 31.11 6.17 43.74 3.99
1886 1904 6.799512 AGAACGTGTTTAACACTACACTAGT 58.200 36.000 23.27 10.86 46.46 2.57
1887 1905 7.689953 AAGAACGTGTTTAACACTACACTAG 57.310 36.000 23.27 10.28 46.46 2.57
1889 1907 9.918630 ATATAAGAACGTGTTTAACACTACACT 57.081 29.630 23.27 14.58 46.46 3.55
1894 1912 9.887406 CCAAAATATAAGAACGTGTTTAACACT 57.113 29.630 23.27 8.06 46.46 3.55
1895 1913 9.120422 CCCAAAATATAAGAACGTGTTTAACAC 57.880 33.333 17.34 17.34 45.26 3.32
1896 1914 9.064706 TCCCAAAATATAAGAACGTGTTTAACA 57.935 29.630 0.00 0.00 0.00 2.41
1897 1915 9.333497 GTCCCAAAATATAAGAACGTGTTTAAC 57.667 33.333 0.00 0.00 0.00 2.01
1898 1916 9.064706 TGTCCCAAAATATAAGAACGTGTTTAA 57.935 29.630 0.00 0.00 0.00 1.52
1899 1917 8.618702 TGTCCCAAAATATAAGAACGTGTTTA 57.381 30.769 0.00 0.00 0.00 2.01
1900 1918 7.446013 TCTGTCCCAAAATATAAGAACGTGTTT 59.554 33.333 0.00 0.00 0.00 2.83
1901 1919 6.938030 TCTGTCCCAAAATATAAGAACGTGTT 59.062 34.615 0.00 0.00 0.00 3.32
1902 1920 6.469410 TCTGTCCCAAAATATAAGAACGTGT 58.531 36.000 0.00 0.00 0.00 4.49
1903 1921 6.037172 CCTCTGTCCCAAAATATAAGAACGTG 59.963 42.308 0.00 0.00 0.00 4.49
1904 1922 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
1905 1923 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
1906 1924 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
1907 1925 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
1908 1926 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
1909 1927 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
1910 1928 7.947782 ATACTCCCTCTGTCCCAAAATATAA 57.052 36.000 0.00 0.00 0.00 0.98
1911 1929 9.046846 CATATACTCCCTCTGTCCCAAAATATA 57.953 37.037 0.00 0.00 0.00 0.86
1912 1930 7.529560 GCATATACTCCCTCTGTCCCAAAATAT 60.530 40.741 0.00 0.00 0.00 1.28
1913 1931 6.239887 GCATATACTCCCTCTGTCCCAAAATA 60.240 42.308 0.00 0.00 0.00 1.40
1914 1932 5.456763 GCATATACTCCCTCTGTCCCAAAAT 60.457 44.000 0.00 0.00 0.00 1.82
1915 1933 4.141482 GCATATACTCCCTCTGTCCCAAAA 60.141 45.833 0.00 0.00 0.00 2.44
1916 1934 3.391296 GCATATACTCCCTCTGTCCCAAA 59.609 47.826 0.00 0.00 0.00 3.28
1917 1935 2.972713 GCATATACTCCCTCTGTCCCAA 59.027 50.000 0.00 0.00 0.00 4.12
1918 1936 2.090775 TGCATATACTCCCTCTGTCCCA 60.091 50.000 0.00 0.00 0.00 4.37
1919 1937 2.609747 TGCATATACTCCCTCTGTCCC 58.390 52.381 0.00 0.00 0.00 4.46
1920 1938 7.847711 ATATATGCATATACTCCCTCTGTCC 57.152 40.000 25.15 0.00 0.00 4.02
1921 1939 9.581289 ACTATATATGCATATACTCCCTCTGTC 57.419 37.037 25.15 0.00 0.00 3.51
1922 1940 9.581289 GACTATATATGCATATACTCCCTCTGT 57.419 37.037 25.15 15.14 0.00 3.41
1923 1941 9.806448 AGACTATATATGCATATACTCCCTCTG 57.194 37.037 25.15 12.78 0.00 3.35
1947 1965 7.625828 TTGTCGTGAATGATACTCTTCTAGA 57.374 36.000 0.00 0.00 0.00 2.43
1950 1968 5.573282 CGTTTGTCGTGAATGATACTCTTCT 59.427 40.000 0.00 0.00 34.52 2.85
1978 1996 0.250513 GCGTGATCTGGAAAGGGTCT 59.749 55.000 0.00 0.00 0.00 3.85
1992 2010 3.060000 ATCGACCTGTCCGCGTGA 61.060 61.111 4.92 0.00 0.00 4.35
2046 2070 1.470051 TGCACTCTGATGCTACCGTA 58.530 50.000 11.45 0.00 46.28 4.02
2074 2102 1.160329 ACTTGAAGTGGCTCGCACAC 61.160 55.000 0.00 0.00 39.10 3.82
2104 2132 6.636850 CCTGCAATGAACAACTTGTTACTAAC 59.363 38.462 7.15 0.00 41.28 2.34
2105 2133 6.238897 CCCTGCAATGAACAACTTGTTACTAA 60.239 38.462 7.15 0.00 41.28 2.24
2120 2148 6.206634 CACTTTAAGTAACTTCCCTGCAATGA 59.793 38.462 0.00 0.00 0.00 2.57
2132 2160 9.802039 TGGATACATTTTCCACTTTAAGTAACT 57.198 29.630 0.00 0.00 46.17 2.24
2176 2204 3.054878 CACTTTGCACTTCAATTGAGGC 58.945 45.455 16.83 16.98 34.12 4.70
2177 2205 4.311816 ACACTTTGCACTTCAATTGAGG 57.688 40.909 15.47 15.47 34.12 3.86
2181 2209 5.565439 GCTGGATACACTTTGCACTTCAATT 60.565 40.000 0.00 0.00 46.17 2.32
2183 2211 3.253188 GCTGGATACACTTTGCACTTCAA 59.747 43.478 0.00 0.00 46.17 2.69
2186 2214 3.146104 AGCTGGATACACTTTGCACTT 57.854 42.857 0.00 0.00 46.17 3.16
2191 2219 7.602644 TCAAGTAACTTAGCTGGATACACTTTG 59.397 37.037 0.00 0.91 46.17 2.77
2195 2223 7.063544 CACTTCAAGTAACTTAGCTGGATACAC 59.936 40.741 0.00 0.00 46.17 2.90
2199 2227 5.248477 TCCACTTCAAGTAACTTAGCTGGAT 59.752 40.000 0.00 0.00 0.00 3.41
2204 2232 7.023197 TGTTTTCCACTTCAAGTAACTTAGC 57.977 36.000 0.00 0.00 0.00 3.09
2226 2254 4.513442 TCTGTGTGCAAGTTACTTCTTGT 58.487 39.130 0.00 0.00 44.41 3.16
2227 2255 5.484173 TTCTGTGTGCAAGTTACTTCTTG 57.516 39.130 0.00 2.58 45.09 3.02
2229 2257 5.066505 CCTTTTCTGTGTGCAAGTTACTTCT 59.933 40.000 0.00 0.00 0.00 2.85
2230 2258 5.065988 TCCTTTTCTGTGTGCAAGTTACTTC 59.934 40.000 0.00 0.00 0.00 3.01
2231 2259 4.947388 TCCTTTTCTGTGTGCAAGTTACTT 59.053 37.500 0.00 0.00 0.00 2.24
2232 2260 4.523083 TCCTTTTCTGTGTGCAAGTTACT 58.477 39.130 0.00 0.00 0.00 2.24
2233 2261 4.893424 TCCTTTTCTGTGTGCAAGTTAC 57.107 40.909 0.00 0.00 0.00 2.50
2234 2262 5.129634 TCATCCTTTTCTGTGTGCAAGTTA 58.870 37.500 0.00 0.00 0.00 2.24
2255 2283 7.050970 TCTTGCTTTACACTTCTAGTCTTCA 57.949 36.000 0.00 0.00 0.00 3.02
2311 2342 7.174599 CCAGCTAGCAGATAAGAGCAAATATTT 59.825 37.037 18.83 0.00 37.40 1.40
2314 2345 5.545588 CCAGCTAGCAGATAAGAGCAAATA 58.454 41.667 18.83 0.00 37.40 1.40
2320 2351 1.969923 AGGCCAGCTAGCAGATAAGAG 59.030 52.381 18.83 0.00 0.00 2.85
2343 2374 3.700539 CAGAACATGCATGGTTCCCATTA 59.299 43.478 29.41 0.00 42.23 1.90


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

AutoCloner maintained by Alex Coulton.