Multiple sequence alignment - TraesCS2A01G427100

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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 TraesCS2A01G427100 chr2A 100.000 2690 0 0 1 2690 680088686 680085997 0.000000e+00 4968
1 TraesCS2A01G427100 chr2D 94.212 933 37 8 1 929 537525511 537524592 0.000000e+00 1408
2 TraesCS2A01G427100 chr2D 93.992 799 28 3 950 1728 537524528 537523730 0.000000e+00 1192
3 TraesCS2A01G427100 chr2B 86.895 702 78 10 2001 2690 640377117 640376418 0.000000e+00 774
4 TraesCS2A01G427100 chr2B 84.921 756 71 26 1258 2005 640377772 640377052 0.000000e+00 725
5 TraesCS2A01G427100 chr2B 93.939 330 19 1 601 929 640378577 640378248 5.170000e-137 497
6 TraesCS2A01G427100 chr2B 88.344 326 14 8 950 1251 640378184 640377859 1.180000e-98 370
7 TraesCS2A01G427100 chr4A 85.816 141 18 2 376 515 608559164 608559303 6.000000e-32 148


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 TraesCS2A01G427100 chr2A 680085997 680088686 2689 True 4968.0 4968 100.00000 1 2690 1 chr2A.!!$R1 2689
1 TraesCS2A01G427100 chr2D 537523730 537525511 1781 True 1300.0 1408 94.10200 1 1728 2 chr2D.!!$R1 1727
2 TraesCS2A01G427100 chr2B 640376418 640378577 2159 True 591.5 774 88.52475 601 2690 4 chr2B.!!$R1 2089

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
390 393 0.777446 TAAGGCAAGGCTGAAAGGGT 59.223 50.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2133 0.031178 GCGGCACCATGAATTCATCC 59.969 55.0 18.16 14.6 33.61 3.51 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
82 83 9.657419 AAAACATTTGAAAGCCCTAAATATCTG 57.343 29.630 0.00 0.00 0.00 2.90
174 177 5.537188 TCCAGTAAACATTGAATTTGCACC 58.463 37.500 0.00 0.00 0.00 5.01
263 266 9.794719 AGCTAAAACTTTTCCAGAATACTAACT 57.205 29.630 0.00 0.00 0.00 2.24
340 343 9.447157 TTTTCATCTCAAATTTGACCAAAACTT 57.553 25.926 16.91 0.00 33.56 2.66
341 344 8.422973 TTCATCTCAAATTTGACCAAAACTTG 57.577 30.769 16.91 4.55 33.56 3.16
342 345 7.780064 TCATCTCAAATTTGACCAAAACTTGA 58.220 30.769 16.91 9.67 36.09 3.02
343 346 8.256605 TCATCTCAAATTTGACCAAAACTTGAA 58.743 29.630 16.91 11.76 36.57 2.69
344 347 8.881743 CATCTCAAATTTGACCAAAACTTGAAA 58.118 29.630 16.91 9.87 36.57 2.69
390 393 0.777446 TAAGGCAAGGCTGAAAGGGT 59.223 50.000 0.00 0.00 0.00 4.34
483 486 7.228706 CCAATAATTATTTTCTACTGTCGGCCT 59.771 37.037 8.01 0.00 0.00 5.19
495 498 3.121030 CGGCCTGTCCAGCTTTCG 61.121 66.667 0.00 0.00 34.01 3.46
496 499 2.347490 GGCCTGTCCAGCTTTCGA 59.653 61.111 0.00 0.00 34.01 3.71
579 582 5.773575 TGGTTTTGCTAATTCGTATTTGCA 58.226 33.333 17.06 17.06 46.03 4.08
596 599 8.272176 CGTATTTGCAGTTTTATGCTTTCAAAA 58.728 29.630 0.00 0.00 46.63 2.44
671 675 5.426833 ACACCTCTGGCAAGTTAATATCTCT 59.573 40.000 0.00 0.00 0.00 3.10
672 676 6.069963 ACACCTCTGGCAAGTTAATATCTCTT 60.070 38.462 0.00 0.00 0.00 2.85
769 773 1.874345 AAGGTACGTGAGGTCGGCAG 61.874 60.000 0.00 0.00 34.94 4.85
795 799 4.843728 TGGGCAGATTAAGATTCGTTTCT 58.156 39.130 0.00 0.00 0.00 2.52
796 800 4.876107 TGGGCAGATTAAGATTCGTTTCTC 59.124 41.667 0.00 0.00 0.00 2.87
807 811 7.883229 AAGATTCGTTTCTCTTTCTTCTCTC 57.117 36.000 0.00 0.00 0.00 3.20
814 818 3.654414 TCTCTTTCTTCTCTCGGCAAAC 58.346 45.455 0.00 0.00 0.00 2.93
817 821 1.056660 TTCTTCTCTCGGCAAACCCT 58.943 50.000 0.00 0.00 0.00 4.34
832 836 1.264749 ACCCTTCACGAGCATGGCTA 61.265 55.000 0.00 0.00 39.88 3.93
966 1014 2.361992 CCCCCGGCCTACAAAACC 60.362 66.667 0.00 0.00 0.00 3.27
1060 1126 1.990060 CCGACCACCAGACCCAGAT 60.990 63.158 0.00 0.00 0.00 2.90
1071 1137 0.250081 GACCCAGATCGATGGCTTCC 60.250 60.000 0.54 0.00 39.17 3.46
1074 1140 0.755079 CCAGATCGATGGCTTCCTCA 59.245 55.000 0.54 0.00 32.48 3.86
1278 1431 3.044986 CTGGTGTTTGTTCTTTGCGATG 58.955 45.455 0.00 0.00 0.00 3.84
1298 1451 4.245845 TGTTACGTATGCTGACTGTTCA 57.754 40.909 0.00 0.00 0.00 3.18
1302 1455 3.002791 ACGTATGCTGACTGTTCATTGG 58.997 45.455 0.00 0.00 0.00 3.16
1600 1753 2.096496 AGCTCAACATTTGCGTATCAGC 59.904 45.455 0.00 0.00 37.71 4.26
1602 1755 3.426695 GCTCAACATTTGCGTATCAGCTT 60.427 43.478 0.00 0.00 38.13 3.74
1610 1763 4.404507 TTGCGTATCAGCTTTTCAGTTC 57.595 40.909 0.00 0.00 38.13 3.01
1619 1772 1.729149 GCTTTTCAGTTCGCCGATTGG 60.729 52.381 0.00 0.00 38.77 3.16
1625 1778 3.130633 TCAGTTCGCCGATTGGATATTG 58.869 45.455 1.98 0.00 37.49 1.90
1663 1816 1.295792 GCGAGTGTCTGTTTTGTGGA 58.704 50.000 0.00 0.00 0.00 4.02
1670 1823 6.114187 AGTGTCTGTTTTGTGGATCTCATA 57.886 37.500 0.00 0.00 0.00 2.15
1717 1870 3.275999 AGCTACAACGTTGGTCAAAAGT 58.724 40.909 30.34 10.77 31.20 2.66
1748 1903 5.964887 GAGCATCTACAACTGAACATCTC 57.035 43.478 0.00 0.00 0.00 2.75
1749 1904 5.411831 AGCATCTACAACTGAACATCTCA 57.588 39.130 0.00 0.00 0.00 3.27
1750 1905 5.987098 AGCATCTACAACTGAACATCTCAT 58.013 37.500 0.00 0.00 32.14 2.90
1751 1906 5.816258 AGCATCTACAACTGAACATCTCATG 59.184 40.000 0.00 0.00 32.14 3.07
1758 1913 0.460109 TGAACATCTCATGCCCGTCG 60.460 55.000 0.00 0.00 0.00 5.12
1770 1925 1.375396 CCCGTCGCAAATGTCCAGA 60.375 57.895 0.00 0.00 0.00 3.86
1777 1932 1.926511 GCAAATGTCCAGACGGGCTG 61.927 60.000 3.13 3.13 44.49 4.85
1778 1933 1.675641 AAATGTCCAGACGGGCTGC 60.676 57.895 4.98 0.00 43.50 5.25
1781 1936 4.767255 GTCCAGACGGGCTGCCAG 62.767 72.222 22.05 19.70 43.50 4.85
1784 1939 2.032528 CAGACGGGCTGCCAGAAA 59.967 61.111 25.53 0.00 37.90 2.52
1811 1971 1.484653 CACTCAACACCCCATATCCGA 59.515 52.381 0.00 0.00 0.00 4.55
1814 1974 0.179029 CAACACCCCATATCCGACCC 60.179 60.000 0.00 0.00 0.00 4.46
1819 1979 0.548989 CCCCATATCCGACCCAAACA 59.451 55.000 0.00 0.00 0.00 2.83
1822 1982 2.356741 CCCATATCCGACCCAAACAACT 60.357 50.000 0.00 0.00 0.00 3.16
1832 1992 4.094887 CGACCCAAACAACTGGATTGATAG 59.905 45.833 0.00 0.00 41.23 2.08
1840 2000 2.769209 ACTGGATTGATAGGCACTCCT 58.231 47.619 0.00 0.00 44.42 3.69
1841 2001 2.703007 ACTGGATTGATAGGCACTCCTC 59.297 50.000 0.00 0.00 44.42 3.71
1842 2002 2.971330 CTGGATTGATAGGCACTCCTCT 59.029 50.000 0.00 0.00 44.42 3.69
1848 2008 4.808767 TGATAGGCACTCCTCTTACCTA 57.191 45.455 0.00 0.00 43.06 3.08
1850 2010 4.168283 TGATAGGCACTCCTCTTACCTAGT 59.832 45.833 0.00 0.00 43.06 2.57
1851 2011 3.476485 AGGCACTCCTCTTACCTAGTT 57.524 47.619 0.00 0.00 38.72 2.24
1859 2019 7.666388 GCACTCCTCTTACCTAGTTCATATCTA 59.334 40.741 0.00 0.00 0.00 1.98
1868 2028 5.446860 CCTAGTTCATATCTAGGGCGGATA 58.553 45.833 10.19 0.00 46.27 2.59
1875 2035 3.697190 ATCTAGGGCGGATATGAGGAT 57.303 47.619 0.00 0.00 0.00 3.24
1878 2038 1.078143 GGGCGGATATGAGGATGCC 60.078 63.158 0.00 0.00 41.72 4.40
1882 2042 1.002430 GCGGATATGAGGATGCCTGAA 59.998 52.381 0.00 0.00 31.76 3.02
1884 2044 2.693069 GGATATGAGGATGCCTGAACG 58.307 52.381 0.00 0.00 31.76 3.95
1885 2045 2.072298 GATATGAGGATGCCTGAACGC 58.928 52.381 0.00 0.00 31.76 4.84
1906 2066 4.018609 CGTCATGCCGGACTGATC 57.981 61.111 5.05 1.29 35.63 2.92
1907 2067 1.141665 CGTCATGCCGGACTGATCA 59.858 57.895 5.05 0.00 35.63 2.92
1908 2068 1.148157 CGTCATGCCGGACTGATCAC 61.148 60.000 5.05 0.00 35.63 3.06
1909 2069 0.108186 GTCATGCCGGACTGATCACA 60.108 55.000 5.05 0.00 34.92 3.58
1910 2070 0.612744 TCATGCCGGACTGATCACAA 59.387 50.000 5.05 0.00 0.00 3.33
1911 2071 1.012086 CATGCCGGACTGATCACAAG 58.988 55.000 5.05 0.00 0.00 3.16
1912 2072 0.904649 ATGCCGGACTGATCACAAGA 59.095 50.000 5.05 0.00 0.00 3.02
1913 2073 0.247460 TGCCGGACTGATCACAAGAG 59.753 55.000 5.05 0.00 0.00 2.85
1914 2074 1.086634 GCCGGACTGATCACAAGAGC 61.087 60.000 5.05 0.00 0.00 4.09
1915 2075 0.460987 CCGGACTGATCACAAGAGCC 60.461 60.000 0.00 0.00 0.00 4.70
1916 2076 0.460987 CGGACTGATCACAAGAGCCC 60.461 60.000 0.00 0.00 0.00 5.19
1917 2077 0.615331 GGACTGATCACAAGAGCCCA 59.385 55.000 0.00 0.00 0.00 5.36
1918 2078 1.677217 GGACTGATCACAAGAGCCCAC 60.677 57.143 0.00 0.00 0.00 4.61
1919 2079 0.036952 ACTGATCACAAGAGCCCACG 60.037 55.000 0.00 0.00 0.00 4.94
1920 2080 1.364626 CTGATCACAAGAGCCCACGC 61.365 60.000 0.00 0.00 0.00 5.34
1956 2116 3.449042 CGGTCTGACGAACGCTTC 58.551 61.111 1.07 0.00 44.19 3.86
1957 2117 2.087009 CGGTCTGACGAACGCTTCC 61.087 63.158 1.07 0.00 44.19 3.46
1958 2118 1.289380 GGTCTGACGAACGCTTCCT 59.711 57.895 1.07 0.00 0.00 3.36
1959 2119 0.733223 GGTCTGACGAACGCTTCCTC 60.733 60.000 1.07 0.00 0.00 3.71
1960 2120 0.733223 GTCTGACGAACGCTTCCTCC 60.733 60.000 0.00 0.00 0.00 4.30
1961 2121 1.176619 TCTGACGAACGCTTCCTCCA 61.177 55.000 0.00 0.00 0.00 3.86
1962 2122 0.734253 CTGACGAACGCTTCCTCCAG 60.734 60.000 0.00 0.00 0.00 3.86
1963 2123 1.289380 GACGAACGCTTCCTCCAGT 59.711 57.895 0.00 0.00 0.00 4.00
1964 2124 0.319641 GACGAACGCTTCCTCCAGTT 60.320 55.000 0.00 0.00 0.00 3.16
1965 2125 0.319641 ACGAACGCTTCCTCCAGTTC 60.320 55.000 0.00 0.00 39.46 3.01
1966 2126 0.038159 CGAACGCTTCCTCCAGTTCT 60.038 55.000 5.78 0.00 40.36 3.01
1967 2127 1.715993 GAACGCTTCCTCCAGTTCTC 58.284 55.000 0.55 0.00 39.66 2.87
1968 2128 0.038159 AACGCTTCCTCCAGTTCTCG 60.038 55.000 0.00 0.00 0.00 4.04
1969 2129 1.153745 CGCTTCCTCCAGTTCTCGG 60.154 63.158 0.00 0.00 0.00 4.63
1970 2130 1.878656 CGCTTCCTCCAGTTCTCGGT 61.879 60.000 0.00 0.00 0.00 4.69
1971 2131 0.390472 GCTTCCTCCAGTTCTCGGTG 60.390 60.000 0.00 0.00 0.00 4.94
1972 2132 0.969894 CTTCCTCCAGTTCTCGGTGT 59.030 55.000 0.00 0.00 0.00 4.16
1973 2133 0.679505 TTCCTCCAGTTCTCGGTGTG 59.320 55.000 0.00 0.00 0.00 3.82
1974 2134 1.185618 TCCTCCAGTTCTCGGTGTGG 61.186 60.000 0.00 0.00 0.00 4.17
1975 2135 1.185618 CCTCCAGTTCTCGGTGTGGA 61.186 60.000 0.00 0.00 37.52 4.02
1976 2136 0.898320 CTCCAGTTCTCGGTGTGGAT 59.102 55.000 0.00 0.00 38.42 3.41
1977 2137 0.608130 TCCAGTTCTCGGTGTGGATG 59.392 55.000 0.00 0.00 34.03 3.51
1978 2138 0.608130 CCAGTTCTCGGTGTGGATGA 59.392 55.000 0.00 0.00 31.04 2.92
1979 2139 1.001974 CCAGTTCTCGGTGTGGATGAA 59.998 52.381 0.00 0.00 31.04 2.57
1980 2140 2.355108 CCAGTTCTCGGTGTGGATGAAT 60.355 50.000 0.00 0.00 31.04 2.57
1981 2141 3.338249 CAGTTCTCGGTGTGGATGAATT 58.662 45.455 0.00 0.00 0.00 2.17
1982 2142 3.372206 CAGTTCTCGGTGTGGATGAATTC 59.628 47.826 0.00 0.00 0.00 2.17
1983 2143 3.007940 AGTTCTCGGTGTGGATGAATTCA 59.992 43.478 11.26 11.26 0.00 2.57
1984 2144 3.912496 TCTCGGTGTGGATGAATTCAT 57.088 42.857 20.85 20.85 39.70 2.57
1985 2145 3.534554 TCTCGGTGTGGATGAATTCATG 58.465 45.455 25.37 9.26 36.57 3.07
1986 2146 2.615447 CTCGGTGTGGATGAATTCATGG 59.385 50.000 25.37 5.99 36.57 3.66
1987 2147 2.026356 TCGGTGTGGATGAATTCATGGT 60.026 45.455 25.37 2.27 36.57 3.55
1988 2148 2.097954 CGGTGTGGATGAATTCATGGTG 59.902 50.000 25.37 4.65 36.57 4.17
1989 2149 2.159198 GGTGTGGATGAATTCATGGTGC 60.159 50.000 25.37 10.64 36.57 5.01
1990 2150 2.101783 TGTGGATGAATTCATGGTGCC 58.898 47.619 25.37 19.00 36.57 5.01
1991 2151 1.066002 GTGGATGAATTCATGGTGCCG 59.934 52.381 25.37 0.00 36.57 5.69
1992 2152 0.031178 GGATGAATTCATGGTGCCGC 59.969 55.000 25.37 8.87 36.57 6.53
1993 2153 0.317269 GATGAATTCATGGTGCCGCG 60.317 55.000 25.37 0.00 36.57 6.46
1994 2154 1.031571 ATGAATTCATGGTGCCGCGT 61.032 50.000 20.11 0.00 34.83 6.01
1995 2155 1.226379 GAATTCATGGTGCCGCGTG 60.226 57.895 4.92 0.00 0.00 5.34
1996 2156 2.597117 GAATTCATGGTGCCGCGTGG 62.597 60.000 11.67 11.67 38.77 4.94
2033 2193 0.900647 CCTCCTCCAGTTCTCGGTGT 60.901 60.000 0.00 0.00 0.00 4.16
2035 2195 0.178973 TCCTCCAGTTCTCGGTGTGA 60.179 55.000 0.00 0.00 0.00 3.58
2053 2213 0.872881 GAATGCATTCATGGTGCCGC 60.873 55.000 30.15 3.29 41.83 6.53
2104 2264 6.764379 AGGGAGCAAGTCTATCTATTTAAGC 58.236 40.000 0.00 0.00 0.00 3.09
2105 2265 5.935206 GGGAGCAAGTCTATCTATTTAAGCC 59.065 44.000 0.00 0.00 0.00 4.35
2110 2270 6.479001 GCAAGTCTATCTATTTAAGCCGAACA 59.521 38.462 0.00 0.00 0.00 3.18
2112 2272 7.349412 AGTCTATCTATTTAAGCCGAACAGT 57.651 36.000 0.00 0.00 0.00 3.55
2130 2290 0.960861 GTGGCAGTGAAACCCTAGCC 60.961 60.000 0.00 0.00 40.16 3.93
2136 2298 1.162329 TGAAACCCTAGCCTCCCCA 59.838 57.895 0.00 0.00 0.00 4.96
2140 2302 0.994050 AACCCTAGCCTCCCCATTCC 60.994 60.000 0.00 0.00 0.00 3.01
2145 2307 0.697854 TAGCCTCCCCATTCCTTCCC 60.698 60.000 0.00 0.00 0.00 3.97
2169 2331 4.179579 GCCGCAACTTCCATCCGC 62.180 66.667 0.00 0.00 0.00 5.54
2172 2334 2.044946 GCAACTTCCATCCGCCCT 60.045 61.111 0.00 0.00 0.00 5.19
2173 2335 2.409870 GCAACTTCCATCCGCCCTG 61.410 63.158 0.00 0.00 0.00 4.45
2221 2383 2.979814 TCACCACCTATCCAATGTCG 57.020 50.000 0.00 0.00 0.00 4.35
2223 2385 3.038280 TCACCACCTATCCAATGTCGAT 58.962 45.455 0.00 0.00 0.00 3.59
2224 2386 3.133691 CACCACCTATCCAATGTCGATG 58.866 50.000 0.00 0.00 0.00 3.84
2229 2391 0.602638 TATCCAATGTCGATGCCGGC 60.603 55.000 22.73 22.73 41.51 6.13
2254 2416 1.883275 CGATTGTAGCTCGAGGAGGAT 59.117 52.381 15.58 0.00 38.38 3.24
2285 2447 4.771356 GCGCCGCTCGTGTCACTA 62.771 66.667 0.00 0.00 41.07 2.74
2286 2448 2.102357 CGCCGCTCGTGTCACTAT 59.898 61.111 0.65 0.00 0.00 2.12
2305 2467 4.110493 GGTCTGCCTCCGAATTCG 57.890 61.111 20.92 20.92 39.44 3.34
2306 2468 2.174319 GGTCTGCCTCCGAATTCGC 61.174 63.158 22.36 9.12 38.18 4.70
2307 2469 2.174319 GTCTGCCTCCGAATTCGCC 61.174 63.158 22.36 10.14 38.18 5.54
2332 2494 2.269940 CCAGAGGAAAAGGAGGAGGAA 58.730 52.381 0.00 0.00 0.00 3.36
2334 2496 1.912731 AGAGGAAAAGGAGGAGGAAGC 59.087 52.381 0.00 0.00 0.00 3.86
2336 2498 0.325272 GGAAAAGGAGGAGGAAGCGT 59.675 55.000 0.00 0.00 0.00 5.07
2337 2499 1.443802 GAAAAGGAGGAGGAAGCGTG 58.556 55.000 0.00 0.00 0.00 5.34
2345 2507 2.203337 AGGAAGCGTGGCAGCAAA 60.203 55.556 10.71 0.00 40.15 3.68
2346 2508 1.795170 GAGGAAGCGTGGCAGCAAAA 61.795 55.000 10.71 0.00 40.15 2.44
2362 2524 2.097629 GCAAAAGGAAGCGGATTAGGAC 59.902 50.000 0.00 0.00 0.00 3.85
2374 2537 0.998945 ATTAGGACCCCCACCCATGG 60.999 60.000 4.14 4.14 46.81 3.66
2390 2553 1.149711 CATGGAGGAGGAGGAGGATCT 59.850 57.143 0.00 0.00 33.73 2.75
2398 2561 1.745264 GAGGAGGATCTGGAAGCGG 59.255 63.158 0.00 0.00 33.73 5.52
2401 2564 1.066587 GAGGATCTGGAAGCGGACG 59.933 63.158 0.00 0.00 0.00 4.79
2426 2595 2.477176 CGGAGTCGGAGGAGCAGAG 61.477 68.421 0.00 0.00 0.00 3.35
2427 2596 1.077357 GGAGTCGGAGGAGCAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
2428 2597 1.381165 GGAGTCGGAGGAGCAGAGAC 61.381 65.000 0.00 0.00 0.00 3.36
2431 2600 4.200283 CGGAGGAGCAGAGACCGC 62.200 72.222 0.00 0.00 37.32 5.68
2432 2601 3.071206 GGAGGAGCAGAGACCGCA 61.071 66.667 0.00 0.00 0.00 5.69
2452 2621 1.153958 GCTTTGCCATGGAGAACGC 60.154 57.895 18.40 12.47 0.00 4.84
2511 2680 1.134699 CGAAGCAGACTGCCATCCTTA 60.135 52.381 23.74 0.00 46.52 2.69
2535 2704 6.708885 AATTCATCCAAGATGAGGCCTATA 57.291 37.500 4.42 0.00 0.00 1.31
2545 2714 3.344535 TGAGGCCTATATGGAGTCCAA 57.655 47.619 17.71 6.23 36.95 3.53
2546 2715 2.972713 TGAGGCCTATATGGAGTCCAAC 59.027 50.000 17.71 1.69 36.95 3.77
2553 2722 1.202099 TATGGAGTCCAACCGCCCAA 61.202 55.000 17.71 0.00 36.95 4.12
2569 2739 1.898574 CAAGCTTGCACCGACCCTT 60.899 57.895 14.65 0.00 0.00 3.95
2577 2747 2.463752 TGCACCGACCCTTCTAATACT 58.536 47.619 0.00 0.00 0.00 2.12
2596 2766 9.662947 CTAATACTCTTCCAATATGCATCATCA 57.337 33.333 0.19 0.00 0.00 3.07
2617 2787 4.646040 TCATCATCATCCAAACATCAACCC 59.354 41.667 0.00 0.00 0.00 4.11
2626 2796 3.007182 CCAAACATCAACCCTTTGCTCAT 59.993 43.478 0.00 0.00 32.17 2.90
2627 2797 4.240096 CAAACATCAACCCTTTGCTCATC 58.760 43.478 0.00 0.00 32.17 2.92
2628 2798 3.446442 ACATCAACCCTTTGCTCATCT 57.554 42.857 0.00 0.00 32.17 2.90
2630 2800 3.508793 ACATCAACCCTTTGCTCATCTTG 59.491 43.478 0.00 0.00 32.17 3.02
2631 2801 2.517959 TCAACCCTTTGCTCATCTTGG 58.482 47.619 0.00 0.00 32.17 3.61
2632 2802 2.108075 TCAACCCTTTGCTCATCTTGGA 59.892 45.455 0.00 0.00 32.17 3.53
2680 2851 4.161565 CCACAAATCAGTACTAGGCCACTA 59.838 45.833 5.01 0.00 0.00 2.74
2682 2853 6.349300 CACAAATCAGTACTAGGCCACTATT 58.651 40.000 5.01 0.00 0.00 1.73
2686 2857 6.667558 ATCAGTACTAGGCCACTATTTACC 57.332 41.667 5.01 0.00 0.00 2.85
2687 2858 5.774179 TCAGTACTAGGCCACTATTTACCT 58.226 41.667 5.01 0.00 36.27 3.08
2688 2859 6.914665 TCAGTACTAGGCCACTATTTACCTA 58.085 40.000 5.01 0.00 33.60 3.08
2689 2860 7.533083 TCAGTACTAGGCCACTATTTACCTAT 58.467 38.462 5.01 0.00 34.36 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 8.584157 TCTTGAAGAATCTAAGCTCATCTATCC 58.416 37.037 0.00 0.00 0.00 2.59
200 203 3.629398 GCCATTGAGGAGTTTGGACTATG 59.371 47.826 0.00 0.00 41.22 2.23
420 423 4.437659 GGCCGAAAACGAAATATGCACTTA 60.438 41.667 0.00 0.00 0.00 2.24
421 424 3.498082 GCCGAAAACGAAATATGCACTT 58.502 40.909 0.00 0.00 0.00 3.16
426 429 4.285807 TCATGGCCGAAAACGAAATATG 57.714 40.909 0.00 0.00 0.00 1.78
475 478 2.731691 GAAAGCTGGACAGGCCGACA 62.732 60.000 0.00 0.00 40.66 4.35
483 486 2.050836 TTGGCCTCGAAAGCTGGACA 62.051 55.000 3.32 0.00 39.91 4.02
586 589 5.181056 TCGCAGATTGTAGATTTTGAAAGCA 59.819 36.000 0.00 0.00 0.00 3.91
596 599 4.036852 TCAACTCGATCGCAGATTGTAGAT 59.963 41.667 11.09 0.00 45.12 1.98
598 601 3.695816 TCAACTCGATCGCAGATTGTAG 58.304 45.455 11.09 2.20 45.12 2.74
635 638 2.480932 CCAGAGGTGTCATCACTCATCG 60.481 54.545 0.00 0.00 43.41 3.84
671 675 1.831106 AGGTCACATACATCCGAGCAA 59.169 47.619 0.00 0.00 0.00 3.91
672 676 1.485124 AGGTCACATACATCCGAGCA 58.515 50.000 0.00 0.00 0.00 4.26
734 738 1.203013 ACCTTTAGGCCTGTTTGGGAC 60.203 52.381 17.99 0.00 39.32 4.46
769 773 2.227388 CGAATCTTAATCTGCCCATGCC 59.773 50.000 0.00 0.00 36.33 4.40
795 799 2.550208 GGGTTTGCCGAGAGAAGAAAGA 60.550 50.000 0.00 0.00 34.97 2.52
796 800 1.807142 GGGTTTGCCGAGAGAAGAAAG 59.193 52.381 0.00 0.00 34.97 2.62
807 811 2.966309 GCTCGTGAAGGGTTTGCCG 61.966 63.158 0.00 0.00 34.97 5.69
814 818 0.811616 GTAGCCATGCTCGTGAAGGG 60.812 60.000 0.00 0.00 40.44 3.95
817 821 1.153647 CGGTAGCCATGCTCGTGAA 60.154 57.895 0.00 0.00 40.44 3.18
841 845 2.101209 CTGTCGACCGTTTGTGTGGC 62.101 60.000 14.12 0.00 0.00 5.01
966 1014 4.363990 ACGAGAGGTGCAGTGCCG 62.364 66.667 13.72 10.15 0.00 5.69
1060 1126 1.043116 ACGGATGAGGAAGCCATCGA 61.043 55.000 0.00 0.00 40.86 3.59
1278 1431 5.445939 CCAATGAACAGTCAGCATACGTAAC 60.446 44.000 0.00 0.00 37.14 2.50
1298 1451 1.464608 CTGACGCACGAATGAACCAAT 59.535 47.619 0.00 0.00 0.00 3.16
1302 1455 1.132640 GCCTGACGCACGAATGAAC 59.867 57.895 0.00 0.00 37.47 3.18
1483 1636 3.997064 CTCCTCCGTCGCCTGCTTG 62.997 68.421 0.00 0.00 0.00 4.01
1600 1753 1.804151 TCCAATCGGCGAACTGAAAAG 59.196 47.619 15.93 2.04 33.99 2.27
1602 1755 2.107950 ATCCAATCGGCGAACTGAAA 57.892 45.000 15.93 6.76 33.99 2.69
1610 1763 3.813800 CATGTTCAATATCCAATCGGCG 58.186 45.455 0.00 0.00 0.00 6.46
1739 1894 0.460109 CGACGGGCATGAGATGTTCA 60.460 55.000 0.00 0.00 40.85 3.18
1741 1896 1.815421 GCGACGGGCATGAGATGTT 60.815 57.895 0.00 0.00 42.87 2.71
1751 1906 3.039202 CTGGACATTTGCGACGGGC 62.039 63.158 0.00 0.00 43.96 6.13
1758 1913 1.675641 AGCCCGTCTGGACATTTGC 60.676 57.895 1.63 0.00 37.49 3.68
1784 1939 1.340211 TGGGGTGTTGAGTGACGTTTT 60.340 47.619 0.00 0.00 0.00 2.43
1788 1943 2.550978 GATATGGGGTGTTGAGTGACG 58.449 52.381 0.00 0.00 0.00 4.35
1792 1947 1.485066 GTCGGATATGGGGTGTTGAGT 59.515 52.381 0.00 0.00 0.00 3.41
1793 1948 1.202651 GGTCGGATATGGGGTGTTGAG 60.203 57.143 0.00 0.00 0.00 3.02
1794 1949 0.834612 GGTCGGATATGGGGTGTTGA 59.165 55.000 0.00 0.00 0.00 3.18
1798 1953 0.548989 TTTGGGTCGGATATGGGGTG 59.451 55.000 0.00 0.00 0.00 4.61
1799 1954 0.549469 GTTTGGGTCGGATATGGGGT 59.451 55.000 0.00 0.00 0.00 4.95
1800 1955 0.548989 TGTTTGGGTCGGATATGGGG 59.451 55.000 0.00 0.00 0.00 4.96
1801 1956 2.021457 GTTGTTTGGGTCGGATATGGG 58.979 52.381 0.00 0.00 0.00 4.00
1802 1957 2.682856 CAGTTGTTTGGGTCGGATATGG 59.317 50.000 0.00 0.00 0.00 2.74
1811 1971 4.344104 CCTATCAATCCAGTTGTTTGGGT 58.656 43.478 0.00 0.00 38.81 4.51
1814 1974 4.460382 AGTGCCTATCAATCCAGTTGTTTG 59.540 41.667 0.00 0.00 38.95 2.93
1832 1992 3.097614 TGAACTAGGTAAGAGGAGTGCC 58.902 50.000 0.00 0.00 0.00 5.01
1859 2019 1.557269 GGCATCCTCATATCCGCCCT 61.557 60.000 0.00 0.00 33.31 5.19
1868 2028 1.522355 CGCGTTCAGGCATCCTCAT 60.522 57.895 0.00 0.00 0.00 2.90
1878 2038 3.853330 CATGACGGGCGCGTTCAG 61.853 66.667 30.06 17.72 0.00 3.02
1891 2051 0.612744 TTGTGATCAGTCCGGCATGA 59.387 50.000 10.38 10.38 0.00 3.07
1894 2054 0.247460 CTCTTGTGATCAGTCCGGCA 59.753 55.000 0.00 0.00 0.00 5.69
1896 2056 0.460987 GGCTCTTGTGATCAGTCCGG 60.461 60.000 0.00 0.00 0.00 5.14
1898 2058 0.615331 TGGGCTCTTGTGATCAGTCC 59.385 55.000 0.00 0.00 0.00 3.85
1904 2064 0.745845 GATGCGTGGGCTCTTGTGAT 60.746 55.000 0.00 0.00 40.82 3.06
1905 2065 1.375908 GATGCGTGGGCTCTTGTGA 60.376 57.895 0.00 0.00 40.82 3.58
1906 2066 1.672030 TGATGCGTGGGCTCTTGTG 60.672 57.895 0.00 0.00 40.82 3.33
1907 2067 1.672356 GTGATGCGTGGGCTCTTGT 60.672 57.895 0.00 0.00 40.82 3.16
1908 2068 1.672030 TGTGATGCGTGGGCTCTTG 60.672 57.895 0.00 0.00 40.82 3.02
1909 2069 1.672356 GTGTGATGCGTGGGCTCTT 60.672 57.895 0.00 0.00 40.82 2.85
1910 2070 2.046892 GTGTGATGCGTGGGCTCT 60.047 61.111 0.00 0.00 40.82 4.09
1911 2071 3.490759 CGTGTGATGCGTGGGCTC 61.491 66.667 0.00 0.00 40.82 4.70
1914 2074 3.792047 CTGCGTGTGATGCGTGGG 61.792 66.667 0.00 0.00 31.36 4.61
1915 2075 2.733671 CTCTGCGTGTGATGCGTGG 61.734 63.158 0.00 0.00 31.36 4.94
1916 2076 1.734117 TCTCTGCGTGTGATGCGTG 60.734 57.895 0.00 0.00 31.36 5.34
1917 2077 1.734477 GTCTCTGCGTGTGATGCGT 60.734 57.895 0.00 0.00 31.36 5.24
1918 2078 2.447887 GGTCTCTGCGTGTGATGCG 61.448 63.158 0.00 0.00 31.36 4.73
1919 2079 2.447887 CGGTCTCTGCGTGTGATGC 61.448 63.158 0.00 0.00 0.00 3.91
1920 2080 1.807165 CCGGTCTCTGCGTGTGATG 60.807 63.158 0.00 0.00 0.00 3.07
1944 2104 1.289066 CTGGAGGAAGCGTTCGTCA 59.711 57.895 16.53 0.40 44.18 4.35
1945 2105 0.319641 AACTGGAGGAAGCGTTCGTC 60.320 55.000 10.16 10.16 42.28 4.20
1948 2108 1.715993 GAGAACTGGAGGAAGCGTTC 58.284 55.000 0.00 0.00 36.81 3.95
1949 2109 0.038159 CGAGAACTGGAGGAAGCGTT 60.038 55.000 0.00 0.00 0.00 4.84
1950 2110 1.587054 CGAGAACTGGAGGAAGCGT 59.413 57.895 0.00 0.00 0.00 5.07
1951 2111 1.153745 CCGAGAACTGGAGGAAGCG 60.154 63.158 0.00 0.00 0.00 4.68
1952 2112 0.390472 CACCGAGAACTGGAGGAAGC 60.390 60.000 0.00 0.00 0.00 3.86
1953 2113 0.969894 ACACCGAGAACTGGAGGAAG 59.030 55.000 0.00 0.00 0.00 3.46
1954 2114 0.679505 CACACCGAGAACTGGAGGAA 59.320 55.000 0.00 0.00 0.00 3.36
1955 2115 1.185618 CCACACCGAGAACTGGAGGA 61.186 60.000 0.00 0.00 0.00 3.71
1956 2116 1.185618 TCCACACCGAGAACTGGAGG 61.186 60.000 0.00 0.00 0.00 4.30
1957 2117 0.898320 ATCCACACCGAGAACTGGAG 59.102 55.000 0.00 0.00 36.24 3.86
1958 2118 0.608130 CATCCACACCGAGAACTGGA 59.392 55.000 0.00 0.00 37.22 3.86
1959 2119 0.608130 TCATCCACACCGAGAACTGG 59.392 55.000 0.00 0.00 0.00 4.00
1960 2120 2.455674 TTCATCCACACCGAGAACTG 57.544 50.000 0.00 0.00 0.00 3.16
1961 2121 3.007940 TGAATTCATCCACACCGAGAACT 59.992 43.478 3.38 0.00 0.00 3.01
1962 2122 3.334691 TGAATTCATCCACACCGAGAAC 58.665 45.455 3.38 0.00 0.00 3.01
1963 2123 3.694043 TGAATTCATCCACACCGAGAA 57.306 42.857 3.38 0.00 0.00 2.87
1964 2124 3.534554 CATGAATTCATCCACACCGAGA 58.465 45.455 18.16 0.00 33.61 4.04
1965 2125 2.615447 CCATGAATTCATCCACACCGAG 59.385 50.000 18.16 4.04 33.61 4.63
1966 2126 2.026356 ACCATGAATTCATCCACACCGA 60.026 45.455 18.16 0.00 33.61 4.69
1967 2127 2.097954 CACCATGAATTCATCCACACCG 59.902 50.000 18.16 5.43 33.61 4.94
1968 2128 2.159198 GCACCATGAATTCATCCACACC 60.159 50.000 18.16 1.91 33.61 4.16
1969 2129 2.159198 GGCACCATGAATTCATCCACAC 60.159 50.000 18.16 7.12 33.61 3.82
1970 2130 2.101783 GGCACCATGAATTCATCCACA 58.898 47.619 18.16 0.00 33.61 4.17
1971 2131 1.066002 CGGCACCATGAATTCATCCAC 59.934 52.381 18.16 8.11 33.61 4.02
1972 2132 1.391577 CGGCACCATGAATTCATCCA 58.608 50.000 18.16 0.00 33.61 3.41
1973 2133 0.031178 GCGGCACCATGAATTCATCC 59.969 55.000 18.16 14.60 33.61 3.51
1974 2134 0.317269 CGCGGCACCATGAATTCATC 60.317 55.000 18.16 7.10 33.61 2.92
1975 2135 1.031571 ACGCGGCACCATGAATTCAT 61.032 50.000 15.36 15.36 36.96 2.57
1976 2136 1.673993 ACGCGGCACCATGAATTCA 60.674 52.632 11.26 11.26 0.00 2.57
1977 2137 1.226379 CACGCGGCACCATGAATTC 60.226 57.895 12.47 0.00 0.00 2.17
1978 2138 2.699768 CCACGCGGCACCATGAATT 61.700 57.895 12.47 0.00 0.00 2.17
1979 2139 3.133464 CCACGCGGCACCATGAAT 61.133 61.111 12.47 0.00 0.00 2.57
2009 2169 1.950973 GAGAACTGGAGGAGGCGTCC 61.951 65.000 17.88 17.88 44.33 4.79
2021 2181 1.511850 TGCATTCACACCGAGAACTG 58.488 50.000 0.00 0.00 0.00 3.16
2035 2195 1.142314 GCGGCACCATGAATGCATT 59.858 52.632 12.83 12.83 45.27 3.56
2081 2241 5.935206 GGCTTAAATAGATAGACTTGCTCCC 59.065 44.000 0.00 0.00 0.00 4.30
2104 2264 0.307760 GTTTCACTGCCACTGTTCGG 59.692 55.000 0.00 0.00 0.00 4.30
2105 2265 0.307760 GGTTTCACTGCCACTGTTCG 59.692 55.000 0.00 0.00 0.00 3.95
2110 2270 0.036875 GCTAGGGTTTCACTGCCACT 59.963 55.000 0.00 0.00 0.00 4.00
2112 2272 1.133809 AGGCTAGGGTTTCACTGCCA 61.134 55.000 0.00 0.00 42.46 4.92
2120 2280 0.927029 GAATGGGGAGGCTAGGGTTT 59.073 55.000 0.00 0.00 0.00 3.27
2130 2290 0.548510 GAGTGGGAAGGAATGGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
2136 2298 2.125106 GCGCGAGTGGGAAGGAAT 60.125 61.111 12.10 0.00 0.00 3.01
2145 2307 4.430423 GAAGTTGCGGCGCGAGTG 62.430 66.667 28.69 0.00 0.00 3.51
2157 2319 0.541863 CTACAGGGCGGATGGAAGTT 59.458 55.000 0.00 0.00 0.00 2.66
2158 2320 1.972660 GCTACAGGGCGGATGGAAGT 61.973 60.000 0.00 0.00 0.00 3.01
2169 2331 2.511452 ATGGCTAGCGGCTACAGGG 61.511 63.158 9.00 0.00 41.46 4.45
2172 2334 2.821685 CCATGGCTAGCGGCTACA 59.178 61.111 9.00 4.14 41.46 2.74
2173 2335 2.666526 GCCATGGCTAGCGGCTAC 60.667 66.667 29.98 3.18 42.78 3.58
2193 2355 2.252714 GATAGGTGGTGATCCTCTCCC 58.747 57.143 0.00 0.00 36.60 4.30
2213 2375 2.823593 TGCCGGCATCGACATTGG 60.824 61.111 29.03 0.00 39.00 3.16
2214 2376 2.404789 GTGCCGGCATCGACATTG 59.595 61.111 35.23 0.00 39.00 2.82
2221 2383 2.890474 AATCGACGTGCCGGCATC 60.890 61.111 35.23 25.77 32.52 3.91
2223 2385 3.284133 TACAATCGACGTGCCGGCA 62.284 57.895 29.03 29.03 32.52 5.69
2224 2386 2.507547 TACAATCGACGTGCCGGC 60.508 61.111 22.73 22.73 0.00 6.13
2229 2391 1.457738 CTCGAGCTACAATCGACGTG 58.542 55.000 0.00 0.00 43.79 4.49
2232 2394 1.002251 CCTCCTCGAGCTACAATCGAC 60.002 57.143 6.99 0.00 43.79 4.20
2233 2395 1.134189 TCCTCCTCGAGCTACAATCGA 60.134 52.381 6.99 0.00 46.26 3.59
2236 2398 4.020543 GGATATCCTCCTCGAGCTACAAT 58.979 47.826 14.97 0.00 41.29 2.71
2272 2434 0.589229 GACCGATAGTGACACGAGCG 60.589 60.000 17.76 17.76 32.62 5.03
2305 2467 0.679321 CCTTTTCCTCTGGCTCTGGC 60.679 60.000 0.00 0.00 37.82 4.85
2306 2468 0.987294 TCCTTTTCCTCTGGCTCTGG 59.013 55.000 0.00 0.00 0.00 3.86
2307 2469 1.065564 CCTCCTTTTCCTCTGGCTCTG 60.066 57.143 0.00 0.00 0.00 3.35
2332 2494 1.799258 CTTCCTTTTGCTGCCACGCT 61.799 55.000 0.00 0.00 0.00 5.07
2334 2496 1.372128 GCTTCCTTTTGCTGCCACG 60.372 57.895 0.00 0.00 0.00 4.94
2336 2498 2.563798 CCGCTTCCTTTTGCTGCCA 61.564 57.895 0.00 0.00 0.00 4.92
2337 2499 1.598701 ATCCGCTTCCTTTTGCTGCC 61.599 55.000 0.00 0.00 0.00 4.85
2345 2507 0.837940 GGGTCCTAATCCGCTTCCTT 59.162 55.000 0.00 0.00 0.00 3.36
2346 2508 1.054978 GGGGTCCTAATCCGCTTCCT 61.055 60.000 0.00 0.00 35.46 3.36
2374 2537 0.856982 TCCAGATCCTCCTCCTCCTC 59.143 60.000 0.00 0.00 0.00 3.71
2413 2582 2.438614 CGGTCTCTGCTCCTCCGA 60.439 66.667 0.00 0.00 43.22 4.55
2414 2583 4.200283 GCGGTCTCTGCTCCTCCG 62.200 72.222 0.00 0.00 43.37 4.63
2435 2604 1.243342 TGGCGTTCTCCATGGCAAAG 61.243 55.000 6.96 5.87 43.84 2.77
2451 2620 2.546494 CCTCGAATTCCGCCATGGC 61.546 63.158 27.67 27.67 37.80 4.40
2452 2621 1.153168 ACCTCGAATTCCGCCATGG 60.153 57.895 7.63 7.63 38.37 3.66
2500 2669 5.595542 TCTTGGATGAATTTAAGGATGGCAG 59.404 40.000 0.00 0.00 0.00 4.85
2511 2680 4.261411 AGGCCTCATCTTGGATGAATTT 57.739 40.909 0.00 0.00 0.00 1.82
2535 2704 2.484287 CTTGGGCGGTTGGACTCCAT 62.484 60.000 0.00 0.00 31.53 3.41
2553 2722 1.192146 TAGAAGGGTCGGTGCAAGCT 61.192 55.000 0.00 0.00 0.00 3.74
2569 2739 9.881649 GATGATGCATATTGGAAGAGTATTAGA 57.118 33.333 0.00 0.00 0.00 2.10
2577 2747 7.172342 TGATGATGATGATGCATATTGGAAGA 58.828 34.615 0.00 0.00 0.00 2.87
2596 2766 4.875389 AGGGTTGATGTTTGGATGATGAT 58.125 39.130 0.00 0.00 0.00 2.45
2617 2787 5.393461 GGGTGTATTTCCAAGATGAGCAAAG 60.393 44.000 0.00 0.00 0.00 2.77
2626 2796 6.395780 TTTCCATAGGGTGTATTTCCAAGA 57.604 37.500 0.00 0.00 34.93 3.02
2627 2797 6.127451 GGTTTTCCATAGGGTGTATTTCCAAG 60.127 42.308 0.00 0.00 40.31 3.61
2628 2798 5.717654 GGTTTTCCATAGGGTGTATTTCCAA 59.282 40.000 0.00 0.00 40.31 3.53
2630 2800 5.516044 AGGTTTTCCATAGGGTGTATTTCC 58.484 41.667 0.00 0.00 43.73 3.13
2631 2801 6.095021 GTGAGGTTTTCCATAGGGTGTATTTC 59.905 42.308 0.00 0.00 43.73 2.17
2632 2802 5.949952 GTGAGGTTTTCCATAGGGTGTATTT 59.050 40.000 0.00 0.00 43.73 1.40


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

AutoCloner maintained by Alex Coulton.