Multiple sequence alignment - TraesCS5D01G133500

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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 TraesCS5D01G133500 chr5D 100.000 2618 0 0 1 2618 213272368 213274985 0.000000e+00 4835
1 TraesCS5D01G133500 chr5A 91.321 1809 55 37 7 1772 276334047 276332298 0.000000e+00 2377
2 TraesCS5D01G133500 chr5A 94.643 112 5 1 1768 1879 276332143 276332033 3.460000e-39 172
3 TraesCS5D01G133500 chr5B 92.020 401 25 6 5 400 227496796 227497194 8.190000e-155 556
4 TraesCS5D01G133500 chr5B 91.000 200 18 0 2419 2618 227497447 227497646 1.190000e-68 270
5 TraesCS5D01G133500 chr5B 87.245 196 10 7 399 579 227497252 227497447 2.640000e-50 209
6 TraesCS5D01G133500 chr6D 77.913 575 97 19 1063 1619 80112737 80113299 5.400000e-87 331
7 TraesCS5D01G133500 chr4B 76.592 534 83 23 2122 2618 402963500 402962972 3.340000e-64 255


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 TraesCS5D01G133500 chr5D 213272368 213274985 2617 False 4835.0 4835 100.000000 1 2618 1 chr5D.!!$F1 2617
1 TraesCS5D01G133500 chr5A 276332033 276334047 2014 True 1274.5 2377 92.982000 7 1879 2 chr5A.!!$R1 1872
2 TraesCS5D01G133500 chr5B 227496796 227497646 850 False 345.0 556 90.088333 5 2618 3 chr5B.!!$F1 2613
3 TraesCS5D01G133500 chr6D 80112737 80113299 562 False 331.0 331 77.913000 1063 1619 1 chr6D.!!$F1 556
4 TraesCS5D01G133500 chr4B 402962972 402963500 528 True 255.0 255 76.592000 2122 2618 1 chr4B.!!$R1 496

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
892 993 1.035139 ACTCCAAGCTGGCAAGTTTG 58.965 50.0 10.59 10.59 42.51 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2246 0.032403 TGGGTCGGTCAGTTTACACG 59.968 55.0 0.0 0.0 0.0 4.49 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
295 300 7.856145 TTTGAACACCTGTGCATTTTAAAAT 57.144 28.000 7.64 7.64 32.71 1.82
544 641 2.303890 TGTAGGTAGACGAGGTCAGTCA 59.696 50.000 0.00 0.00 40.84 3.41
644 741 3.782244 CGCCTGACAGCAACGCTC 61.782 66.667 0.00 0.00 36.40 5.03
674 771 2.233271 ACAAAGACTTGTGGCATCCAG 58.767 47.619 0.00 0.00 44.28 3.86
709 806 2.841795 CCTAGGGTAAAGGGGACAAGA 58.158 52.381 0.00 0.00 0.00 3.02
724 821 1.143183 AAGAGTTGACACACGCGGT 59.857 52.632 12.47 2.05 0.00 5.68
785 882 4.536765 GACATGTCCTTCCACCCATAAAT 58.463 43.478 15.31 0.00 0.00 1.40
892 993 1.035139 ACTCCAAGCTGGCAAGTTTG 58.965 50.000 10.59 10.59 42.51 2.93
893 994 1.035139 CTCCAAGCTGGCAAGTTTGT 58.965 50.000 15.66 0.00 41.61 2.83
894 995 1.410153 CTCCAAGCTGGCAAGTTTGTT 59.590 47.619 15.66 0.00 41.61 2.83
895 996 2.622942 CTCCAAGCTGGCAAGTTTGTTA 59.377 45.455 15.66 3.83 41.61 2.41
896 997 2.360801 TCCAAGCTGGCAAGTTTGTTAC 59.639 45.455 15.66 0.00 41.61 2.50
908 1009 8.781196 TGGCAAGTTTGTTACGTATATAAAACA 58.219 29.630 17.64 9.43 31.53 2.83
909 1010 9.054191 GGCAAGTTTGTTACGTATATAAAACAC 57.946 33.333 17.64 4.88 31.92 3.32
910 1011 9.596677 GCAAGTTTGTTACGTATATAAAACACA 57.403 29.630 17.64 6.92 31.92 3.72
914 1015 9.412390 GTTTGTTACGTATATAAAACACATCGG 57.588 33.333 0.00 0.00 31.92 4.18
915 1016 7.164226 TGTTACGTATATAAAACACATCGGC 57.836 36.000 0.00 0.00 0.00 5.54
916 1017 6.200665 TGTTACGTATATAAAACACATCGGCC 59.799 38.462 0.00 0.00 0.00 6.13
917 1018 4.695396 ACGTATATAAAACACATCGGCCA 58.305 39.130 2.24 0.00 0.00 5.36
918 1019 4.508861 ACGTATATAAAACACATCGGCCAC 59.491 41.667 2.24 0.00 0.00 5.01
919 1020 4.748102 CGTATATAAAACACATCGGCCACT 59.252 41.667 2.24 0.00 0.00 4.00
920 1021 5.107607 CGTATATAAAACACATCGGCCACTC 60.108 44.000 2.24 0.00 0.00 3.51
962 1063 3.039526 CTCTCCCTCCCCTCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
963 1064 3.036959 TCTCCCTCCCCTCCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
964 1065 4.179599 CTCCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
968 1069 3.795924 CTCCCCTCCCCTCCCCAT 61.796 72.222 0.00 0.00 0.00 4.00
969 1070 3.791076 TCCCCTCCCCTCCCCATC 61.791 72.222 0.00 0.00 0.00 3.51
971 1072 4.172232 CCCTCCCCTCCCCATCGA 62.172 72.222 0.00 0.00 0.00 3.59
972 1073 2.525381 CCTCCCCTCCCCATCGAG 60.525 72.222 0.00 0.00 0.00 4.04
973 1074 3.237741 CTCCCCTCCCCATCGAGC 61.238 72.222 0.00 0.00 0.00 5.03
1028 1129 2.265739 CTGCGGCAGCCTCAAGTA 59.734 61.111 18.16 0.00 44.33 2.24
1037 1138 0.397941 AGCCTCAAGTACTGCTGCAA 59.602 50.000 3.02 0.00 31.70 4.08
1107 1208 2.441001 CCTCATCTACTGGGCCATCTTT 59.559 50.000 6.72 0.00 0.00 2.52
1696 1806 5.333263 CGGTTTGCATCTTTTTCATGTTTCC 60.333 40.000 0.00 0.00 0.00 3.13
1719 1829 3.887621 TGGAGATTAGCGTGCTAGTTT 57.112 42.857 1.39 0.00 0.00 2.66
1747 1857 7.091443 TCGGTTTGTGTTTTGTGTAAAGATTT 58.909 30.769 0.00 0.00 0.00 2.17
1777 2045 1.338136 GGATGGTGATCGTCCCCTGT 61.338 60.000 0.00 0.00 44.08 4.00
1858 2126 4.465660 TGTGGCAATGGTATAAACATGCTT 59.534 37.500 0.00 0.00 33.93 3.91
1864 2132 6.578545 GCAATGGTATAAACATGCTTCATACG 59.421 38.462 0.00 0.00 31.99 3.06
1867 2135 5.007234 TGGTATAAACATGCTTCATACGCAC 59.993 40.000 0.00 0.00 40.65 5.34
1869 2137 1.438651 AACATGCTTCATACGCACGT 58.561 45.000 0.00 0.00 40.65 4.49
1879 2147 2.030096 TCATACGCACGTTGTAAGGTCA 60.030 45.455 0.00 0.00 0.00 4.02
1880 2148 2.505628 TACGCACGTTGTAAGGTCAA 57.494 45.000 0.00 0.00 0.00 3.18
1881 2149 0.932399 ACGCACGTTGTAAGGTCAAC 59.068 50.000 0.00 0.00 42.67 3.18
1882 2150 0.233848 CGCACGTTGTAAGGTCAACC 59.766 55.000 0.00 0.00 43.02 3.77
1883 2151 0.589708 GCACGTTGTAAGGTCAACCC 59.410 55.000 0.00 0.00 43.02 4.11
1884 2152 1.956297 CACGTTGTAAGGTCAACCCA 58.044 50.000 0.00 0.00 43.02 4.51
1885 2153 2.290464 CACGTTGTAAGGTCAACCCAA 58.710 47.619 0.00 0.00 43.02 4.12
1886 2154 2.289547 CACGTTGTAAGGTCAACCCAAG 59.710 50.000 0.00 0.00 43.02 3.61
1887 2155 1.877443 CGTTGTAAGGTCAACCCAAGG 59.123 52.381 0.00 0.00 43.02 3.61
1888 2156 1.611977 GTTGTAAGGTCAACCCAAGGC 59.388 52.381 0.00 0.00 40.97 4.35
1889 2157 0.250553 TGTAAGGTCAACCCAAGGCG 60.251 55.000 0.00 0.00 36.42 5.52
1890 2158 1.302993 TAAGGTCAACCCAAGGCGC 60.303 57.895 0.00 0.00 36.42 6.53
1891 2159 2.757980 TAAGGTCAACCCAAGGCGCC 62.758 60.000 21.89 21.89 36.42 6.53
1915 2183 3.487985 GCAAACAGTGCGAAATTTGTC 57.512 42.857 0.00 0.00 45.10 3.18
1916 2184 3.115554 GCAAACAGTGCGAAATTTGTCT 58.884 40.909 0.00 0.00 45.10 3.41
1917 2185 3.180387 GCAAACAGTGCGAAATTTGTCTC 59.820 43.478 0.00 0.00 45.10 3.36
1918 2186 3.626028 AACAGTGCGAAATTTGTCTCC 57.374 42.857 0.00 0.00 0.00 3.71
1919 2187 2.851195 ACAGTGCGAAATTTGTCTCCT 58.149 42.857 0.00 0.00 0.00 3.69
1920 2188 3.214328 ACAGTGCGAAATTTGTCTCCTT 58.786 40.909 0.00 0.00 0.00 3.36
1921 2189 3.632145 ACAGTGCGAAATTTGTCTCCTTT 59.368 39.130 0.00 0.00 0.00 3.11
1922 2190 4.097892 ACAGTGCGAAATTTGTCTCCTTTT 59.902 37.500 0.00 0.00 0.00 2.27
1923 2191 5.043248 CAGTGCGAAATTTGTCTCCTTTTT 58.957 37.500 0.00 0.00 0.00 1.94
1924 2192 5.043248 AGTGCGAAATTTGTCTCCTTTTTG 58.957 37.500 0.00 0.00 0.00 2.44
1925 2193 4.803613 GTGCGAAATTTGTCTCCTTTTTGT 59.196 37.500 0.00 0.00 0.00 2.83
1926 2194 5.040635 TGCGAAATTTGTCTCCTTTTTGTC 58.959 37.500 0.00 0.00 0.00 3.18
1927 2195 4.444388 GCGAAATTTGTCTCCTTTTTGTCC 59.556 41.667 0.00 0.00 0.00 4.02
1928 2196 5.736207 GCGAAATTTGTCTCCTTTTTGTCCT 60.736 40.000 0.00 0.00 0.00 3.85
1929 2197 6.273071 CGAAATTTGTCTCCTTTTTGTCCTT 58.727 36.000 0.00 0.00 0.00 3.36
1930 2198 6.756542 CGAAATTTGTCTCCTTTTTGTCCTTT 59.243 34.615 0.00 0.00 0.00 3.11
1931 2199 7.254084 CGAAATTTGTCTCCTTTTTGTCCTTTG 60.254 37.037 0.00 0.00 0.00 2.77
1932 2200 5.337578 TTTGTCTCCTTTTTGTCCTTTGG 57.662 39.130 0.00 0.00 0.00 3.28
1933 2201 4.243793 TGTCTCCTTTTTGTCCTTTGGA 57.756 40.909 0.00 0.00 0.00 3.53
1934 2202 4.803452 TGTCTCCTTTTTGTCCTTTGGAT 58.197 39.130 0.00 0.00 32.73 3.41
1935 2203 5.208121 TGTCTCCTTTTTGTCCTTTGGATT 58.792 37.500 0.00 0.00 32.73 3.01
1936 2204 5.068987 TGTCTCCTTTTTGTCCTTTGGATTG 59.931 40.000 0.00 0.00 32.73 2.67
1937 2205 4.588528 TCTCCTTTTTGTCCTTTGGATTGG 59.411 41.667 0.00 0.00 32.73 3.16
1938 2206 3.070878 TCCTTTTTGTCCTTTGGATTGGC 59.929 43.478 0.00 0.00 32.73 4.52
1939 2207 3.181456 CCTTTTTGTCCTTTGGATTGGCA 60.181 43.478 0.00 0.00 32.73 4.92
1940 2208 3.749665 TTTTGTCCTTTGGATTGGCAG 57.250 42.857 0.00 0.00 32.73 4.85
1941 2209 2.380064 TTGTCCTTTGGATTGGCAGT 57.620 45.000 0.00 0.00 32.73 4.40
1942 2210 3.517296 TTGTCCTTTGGATTGGCAGTA 57.483 42.857 0.00 0.00 32.73 2.74
1943 2211 3.071874 TGTCCTTTGGATTGGCAGTAG 57.928 47.619 0.00 0.00 32.73 2.57
1944 2212 2.290896 TGTCCTTTGGATTGGCAGTAGG 60.291 50.000 0.00 0.00 32.73 3.18
1945 2213 1.284785 TCCTTTGGATTGGCAGTAGGG 59.715 52.381 0.00 0.00 0.00 3.53
1946 2214 1.005924 CCTTTGGATTGGCAGTAGGGT 59.994 52.381 0.00 0.00 0.00 4.34
1947 2215 2.094675 CTTTGGATTGGCAGTAGGGTG 58.905 52.381 0.00 0.00 0.00 4.61
1948 2216 0.331278 TTGGATTGGCAGTAGGGTGG 59.669 55.000 0.00 0.00 0.00 4.61
1949 2217 1.453928 GGATTGGCAGTAGGGTGGC 60.454 63.158 0.00 0.00 43.25 5.01
1950 2218 1.819632 GATTGGCAGTAGGGTGGCG 60.820 63.158 0.00 0.00 45.86 5.69
1951 2219 2.536997 GATTGGCAGTAGGGTGGCGT 62.537 60.000 0.00 0.00 45.86 5.68
1952 2220 2.536997 ATTGGCAGTAGGGTGGCGTC 62.537 60.000 0.00 0.00 45.86 5.19
1953 2221 4.468689 GGCAGTAGGGTGGCGTCC 62.469 72.222 0.00 0.00 32.71 4.79
1954 2222 4.814294 GCAGTAGGGTGGCGTCCG 62.814 72.222 0.00 0.00 0.00 4.79
1955 2223 3.379445 CAGTAGGGTGGCGTCCGT 61.379 66.667 0.00 0.09 0.00 4.69
1956 2224 2.602568 AGTAGGGTGGCGTCCGTT 60.603 61.111 0.00 0.00 0.00 4.44
1957 2225 2.433664 GTAGGGTGGCGTCCGTTG 60.434 66.667 0.00 0.00 0.00 4.10
1958 2226 2.918802 TAGGGTGGCGTCCGTTGT 60.919 61.111 0.00 0.00 0.00 3.32
1959 2227 2.509651 TAGGGTGGCGTCCGTTGTT 61.510 57.895 0.00 0.00 0.00 2.83
1960 2228 2.718747 TAGGGTGGCGTCCGTTGTTG 62.719 60.000 0.00 0.00 0.00 3.33
1961 2229 3.656045 GGTGGCGTCCGTTGTTGG 61.656 66.667 0.00 0.00 0.00 3.77
1962 2230 4.322385 GTGGCGTCCGTTGTTGGC 62.322 66.667 0.00 0.00 0.00 4.52
1966 2234 4.007940 CGTCCGTTGTTGGCCGTG 62.008 66.667 0.00 0.00 0.00 4.94
1967 2235 4.322385 GTCCGTTGTTGGCCGTGC 62.322 66.667 0.00 0.00 0.00 5.34
1968 2236 4.858680 TCCGTTGTTGGCCGTGCA 62.859 61.111 0.00 0.00 0.00 4.57
1969 2237 3.669344 CCGTTGTTGGCCGTGCAT 61.669 61.111 0.00 0.00 0.00 3.96
1970 2238 2.428902 CGTTGTTGGCCGTGCATG 60.429 61.111 0.00 0.00 0.00 4.06
1971 2239 2.727544 GTTGTTGGCCGTGCATGT 59.272 55.556 4.96 0.00 0.00 3.21
1972 2240 1.371635 GTTGTTGGCCGTGCATGTC 60.372 57.895 4.96 0.00 0.00 3.06
1973 2241 1.528076 TTGTTGGCCGTGCATGTCT 60.528 52.632 4.96 0.00 0.00 3.41
1974 2242 1.794151 TTGTTGGCCGTGCATGTCTG 61.794 55.000 4.96 0.00 0.00 3.51
1975 2243 2.112928 TTGGCCGTGCATGTCTGT 59.887 55.556 4.96 0.00 0.00 3.41
1976 2244 0.953471 GTTGGCCGTGCATGTCTGTA 60.953 55.000 4.96 0.00 0.00 2.74
1977 2245 0.673333 TTGGCCGTGCATGTCTGTAG 60.673 55.000 4.96 0.00 0.00 2.74
1978 2246 2.464459 GGCCGTGCATGTCTGTAGC 61.464 63.158 4.96 0.00 0.00 3.58
1979 2247 2.802667 GCCGTGCATGTCTGTAGCG 61.803 63.158 4.96 0.00 0.00 4.26
1980 2248 1.446099 CCGTGCATGTCTGTAGCGT 60.446 57.895 4.96 0.00 0.00 5.07
1981 2249 1.686566 CCGTGCATGTCTGTAGCGTG 61.687 60.000 4.96 0.00 0.00 5.34
1982 2250 1.008875 CGTGCATGTCTGTAGCGTGT 61.009 55.000 0.00 0.00 0.00 4.49
1983 2251 1.731098 CGTGCATGTCTGTAGCGTGTA 60.731 52.381 0.00 0.00 0.00 2.90
1984 2252 2.333926 GTGCATGTCTGTAGCGTGTAA 58.666 47.619 0.00 0.00 0.00 2.41
1985 2253 2.734606 GTGCATGTCTGTAGCGTGTAAA 59.265 45.455 0.00 0.00 0.00 2.01
1986 2254 2.734606 TGCATGTCTGTAGCGTGTAAAC 59.265 45.455 0.00 0.00 0.00 2.01
1987 2255 2.993899 GCATGTCTGTAGCGTGTAAACT 59.006 45.455 0.00 0.00 0.00 2.66
1988 2256 3.181530 GCATGTCTGTAGCGTGTAAACTG 60.182 47.826 0.00 0.00 0.00 3.16
1989 2257 3.994204 TGTCTGTAGCGTGTAAACTGA 57.006 42.857 0.00 0.00 0.00 3.41
1990 2258 3.635331 TGTCTGTAGCGTGTAAACTGAC 58.365 45.455 0.00 0.00 40.47 3.51
1991 2259 2.985139 GTCTGTAGCGTGTAAACTGACC 59.015 50.000 0.00 0.00 36.59 4.02
1992 2260 1.983605 CTGTAGCGTGTAAACTGACCG 59.016 52.381 0.00 0.00 0.00 4.79
1993 2261 1.608109 TGTAGCGTGTAAACTGACCGA 59.392 47.619 0.00 0.00 0.00 4.69
1994 2262 1.981533 GTAGCGTGTAAACTGACCGAC 59.018 52.381 0.00 0.00 0.00 4.79
1995 2263 0.319297 AGCGTGTAAACTGACCGACC 60.319 55.000 0.00 0.00 0.00 4.79
1996 2264 1.287041 GCGTGTAAACTGACCGACCC 61.287 60.000 0.00 0.00 0.00 4.46
1997 2265 0.032403 CGTGTAAACTGACCGACCCA 59.968 55.000 0.00 0.00 0.00 4.51
1998 2266 1.337447 CGTGTAAACTGACCGACCCAT 60.337 52.381 0.00 0.00 0.00 4.00
1999 2267 2.774687 GTGTAAACTGACCGACCCATT 58.225 47.619 0.00 0.00 0.00 3.16
2000 2268 3.143728 GTGTAAACTGACCGACCCATTT 58.856 45.455 0.00 0.00 0.00 2.32
2001 2269 3.058501 GTGTAAACTGACCGACCCATTTG 60.059 47.826 0.00 0.00 0.00 2.32
2002 2270 2.649531 AAACTGACCGACCCATTTGA 57.350 45.000 0.00 0.00 0.00 2.69
2003 2271 2.879103 AACTGACCGACCCATTTGAT 57.121 45.000 0.00 0.00 0.00 2.57
2004 2272 2.403252 ACTGACCGACCCATTTGATC 57.597 50.000 0.00 0.00 0.00 2.92
2005 2273 1.065418 ACTGACCGACCCATTTGATCC 60.065 52.381 0.00 0.00 0.00 3.36
2006 2274 0.107897 TGACCGACCCATTTGATCCG 60.108 55.000 0.00 0.00 0.00 4.18
2007 2275 0.107848 GACCGACCCATTTGATCCGT 60.108 55.000 0.00 0.00 0.00 4.69
2008 2276 0.107848 ACCGACCCATTTGATCCGTC 60.108 55.000 0.00 0.00 0.00 4.79
2009 2277 0.178068 CCGACCCATTTGATCCGTCT 59.822 55.000 0.00 0.00 0.00 4.18
2010 2278 1.411246 CCGACCCATTTGATCCGTCTA 59.589 52.381 0.00 0.00 0.00 2.59
2011 2279 2.545952 CCGACCCATTTGATCCGTCTAG 60.546 54.545 0.00 0.00 0.00 2.43
2012 2280 2.100916 CGACCCATTTGATCCGTCTAGT 59.899 50.000 0.00 0.00 0.00 2.57
2013 2281 3.718815 GACCCATTTGATCCGTCTAGTC 58.281 50.000 0.00 0.00 0.00 2.59
2014 2282 3.104512 ACCCATTTGATCCGTCTAGTCA 58.895 45.455 0.00 0.00 0.00 3.41
2015 2283 3.517901 ACCCATTTGATCCGTCTAGTCAA 59.482 43.478 0.00 0.00 0.00 3.18
2016 2284 4.019681 ACCCATTTGATCCGTCTAGTCAAA 60.020 41.667 7.64 7.64 43.51 2.69
2017 2285 4.941263 CCCATTTGATCCGTCTAGTCAAAA 59.059 41.667 8.90 0.00 42.88 2.44
2018 2286 5.414454 CCCATTTGATCCGTCTAGTCAAAAA 59.586 40.000 8.90 0.00 42.88 1.94
2048 2316 9.558396 TGTCAATTTTTCTTTATTTGGCATTCT 57.442 25.926 0.00 0.00 27.82 2.40
2113 2381 8.587952 AACAAACAAGTCATATAGTTTTTGGC 57.412 30.769 0.00 0.00 32.34 4.52
2114 2382 7.951591 ACAAACAAGTCATATAGTTTTTGGCT 58.048 30.769 0.00 0.00 32.34 4.75
2115 2383 8.082242 ACAAACAAGTCATATAGTTTTTGGCTC 58.918 33.333 0.00 0.00 32.34 4.70
2116 2384 8.299570 CAAACAAGTCATATAGTTTTTGGCTCT 58.700 33.333 0.00 0.00 32.34 4.09
2117 2385 9.515226 AAACAAGTCATATAGTTTTTGGCTCTA 57.485 29.630 0.00 0.00 30.64 2.43
2118 2386 8.494016 ACAAGTCATATAGTTTTTGGCTCTAC 57.506 34.615 0.00 0.00 0.00 2.59
2119 2387 8.100791 ACAAGTCATATAGTTTTTGGCTCTACA 58.899 33.333 0.00 0.00 0.00 2.74
2120 2388 8.607459 CAAGTCATATAGTTTTTGGCTCTACAG 58.393 37.037 0.00 0.00 0.00 2.74
2138 2406 2.975489 ACAGACAAGACAAGGAGGTCAT 59.025 45.455 0.00 0.00 40.29 3.06
2143 2411 1.187087 AGACAAGGAGGTCATCGGAC 58.813 55.000 0.00 0.00 43.55 4.79
2145 2413 0.611062 ACAAGGAGGTCATCGGACGA 60.611 55.000 0.00 0.00 45.28 4.20
2148 2416 0.818296 AGGAGGTCATCGGACGAAAG 59.182 55.000 0.00 0.00 45.28 2.62
2169 2437 1.282382 GTAAGGTGGGCTGGAAGGTA 58.718 55.000 0.00 0.00 0.00 3.08
2172 2440 0.910088 AGGTGGGCTGGAAGGTAGTC 60.910 60.000 0.00 0.00 0.00 2.59
2207 2476 4.489771 CGGGGACTGGGCATCCAC 62.490 72.222 4.35 0.00 38.32 4.02
2212 2481 2.607750 ACTGGGCATCCACGACCT 60.608 61.111 0.00 0.00 38.32 3.85
2213 2482 2.124983 CTGGGCATCCACGACCTG 60.125 66.667 0.00 0.00 38.32 4.00
2214 2483 3.687321 CTGGGCATCCACGACCTGG 62.687 68.421 0.00 0.00 42.29 4.45
2219 2488 1.077501 CATCCACGACCTGGCCAAT 60.078 57.895 7.01 0.00 40.39 3.16
2221 2490 0.394352 ATCCACGACCTGGCCAATTC 60.394 55.000 7.01 4.88 40.39 2.17
2222 2491 2.398554 CCACGACCTGGCCAATTCG 61.399 63.158 26.50 26.50 37.50 3.34
2223 2492 2.746277 ACGACCTGGCCAATTCGC 60.746 61.111 27.54 7.86 34.81 4.70
2224 2493 2.436646 CGACCTGGCCAATTCGCT 60.437 61.111 19.62 0.00 0.00 4.93
2225 2494 2.464459 CGACCTGGCCAATTCGCTC 61.464 63.158 19.62 0.00 0.00 5.03
2226 2495 2.436646 ACCTGGCCAATTCGCTCG 60.437 61.111 7.01 0.00 0.00 5.03
2227 2496 2.436646 CCTGGCCAATTCGCTCGT 60.437 61.111 7.01 0.00 0.00 4.18
2228 2497 2.753966 CCTGGCCAATTCGCTCGTG 61.754 63.158 7.01 0.00 0.00 4.35
2229 2498 3.386867 CTGGCCAATTCGCTCGTGC 62.387 63.158 7.01 0.00 0.00 5.34
2231 2500 4.179579 GCCAATTCGCTCGTGCCC 62.180 66.667 3.52 0.00 35.36 5.36
2295 2565 2.584608 GTGGGTAGGCACGAGCAT 59.415 61.111 7.26 1.27 44.61 3.79
2296 2566 1.521681 GTGGGTAGGCACGAGCATC 60.522 63.158 7.26 0.00 44.61 3.91
2301 2571 0.811616 GTAGGCACGAGCATCCCTTG 60.812 60.000 7.26 0.00 44.61 3.61
2309 2579 2.202878 GCATCCCTTGCGACGCTA 60.203 61.111 22.08 13.01 42.54 4.26
2310 2580 1.595382 GCATCCCTTGCGACGCTAT 60.595 57.895 22.08 4.07 42.54 2.97
2311 2581 1.560860 GCATCCCTTGCGACGCTATC 61.561 60.000 22.08 0.00 42.54 2.08
2328 2605 3.554692 CGATCGCGCCCTGTTCAC 61.555 66.667 0.26 0.00 0.00 3.18
2329 2606 2.125512 GATCGCGCCCTGTTCACT 60.126 61.111 0.00 0.00 0.00 3.41
2334 2611 3.052082 CGCCCTGTTCACTGCCTG 61.052 66.667 0.00 0.00 0.00 4.85
2335 2612 3.368571 GCCCTGTTCACTGCCTGC 61.369 66.667 0.00 0.00 0.00 4.85
2340 2617 2.591715 GTTCACTGCCTGCACGGT 60.592 61.111 4.45 0.00 34.25 4.83
2341 2618 2.591429 TTCACTGCCTGCACGGTG 60.591 61.111 9.47 9.47 46.37 4.94
2356 2633 3.747976 GTGGTCACCATTGGCGGC 61.748 66.667 0.00 0.00 35.28 6.53
2382 2659 2.726351 CGGCCTCCTTCTGGTCCTC 61.726 68.421 0.00 0.00 34.23 3.71
2385 2662 1.334384 GCCTCCTTCTGGTCCTCCTC 61.334 65.000 0.00 0.00 34.23 3.71
2391 2668 2.997315 CTGGTCCTCCTCGTGGCA 60.997 66.667 0.00 0.00 34.23 4.92
2392 2669 3.302347 CTGGTCCTCCTCGTGGCAC 62.302 68.421 7.79 7.79 34.23 5.01
2393 2670 3.311110 GGTCCTCCTCGTGGCACA 61.311 66.667 19.09 4.04 0.00 4.57
2406 2683 1.975660 TGGCACACCTAGTGGTTTTC 58.024 50.000 0.00 0.00 46.05 2.29
2408 2685 0.237498 GCACACCTAGTGGTTTTCGC 59.763 55.000 0.00 0.00 46.05 4.70
2413 2714 1.074889 ACCTAGTGGTTTTCGCCCAAT 59.925 47.619 0.00 0.00 46.05 3.16
2434 2735 6.376299 CCAATCCATCAGAAAGAACAGATCAA 59.624 38.462 0.00 0.00 0.00 2.57
2436 2737 7.804843 ATCCATCAGAAAGAACAGATCAATC 57.195 36.000 0.00 0.00 0.00 2.67
2438 2739 5.007430 CCATCAGAAAGAACAGATCAATCCG 59.993 44.000 0.00 0.00 0.00 4.18
2454 2755 3.113745 CGGGAGGCATTGCATCAC 58.886 61.111 23.12 19.45 41.39 3.06
2540 2841 1.236628 GCTAGGGAGATACGAAGCGA 58.763 55.000 0.00 0.00 0.00 4.93
2567 2868 1.094269 ACACTAGAAGAGGGGAGGGT 58.906 55.000 0.00 0.00 29.93 4.34
2568 2869 1.273324 ACACTAGAAGAGGGGAGGGTG 60.273 57.143 0.00 0.00 29.93 4.61
2598 2899 1.907936 AGATGGACTCTTTGCAGCTCT 59.092 47.619 0.00 0.00 37.90 4.09
2601 2902 0.322975 GGACTCTTTGCAGCTCTGGA 59.677 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 202 9.804758 AACGTTCCTATTTTTATGTTTTGTTCA 57.195 25.926 0.00 0.00 0.00 3.18
519 614 1.401199 GACCTCGTCTACCTACAGCAC 59.599 57.143 0.00 0.00 0.00 4.40
544 641 5.065731 GTGCTAGCAGTAATTTTGAGCAGAT 59.934 40.000 20.03 0.00 39.00 2.90
644 741 3.067106 ACAAGTCTTTGTGTATGCCTCG 58.933 45.455 0.00 0.00 45.54 4.63
709 806 1.328374 GTTAAACCGCGTGTGTCAACT 59.672 47.619 4.92 0.00 0.00 3.16
724 821 0.250989 CCGGGGAACAGGCTGTTAAA 60.251 55.000 31.24 0.00 41.28 1.52
785 882 7.445402 AGTGTAGTAGTAGTTGAAGTCCGTTTA 59.555 37.037 0.00 0.00 0.00 2.01
805 902 7.672983 ATTGACATTGACTAACCAAGTGTAG 57.327 36.000 0.00 0.00 39.07 2.74
840 941 2.542205 CGCGTACGTGATTGATTCCCTA 60.542 50.000 23.95 0.00 33.53 3.53
892 993 6.200665 TGGCCGATGTGTTTTATATACGTAAC 59.799 38.462 0.00 0.00 0.00 2.50
893 994 6.200665 GTGGCCGATGTGTTTTATATACGTAA 59.799 38.462 0.00 0.00 0.00 3.18
894 995 5.691305 GTGGCCGATGTGTTTTATATACGTA 59.309 40.000 0.00 0.00 0.00 3.57
895 996 4.508861 GTGGCCGATGTGTTTTATATACGT 59.491 41.667 0.00 0.00 0.00 3.57
896 997 4.748102 AGTGGCCGATGTGTTTTATATACG 59.252 41.667 0.00 0.00 0.00 3.06
908 1009 2.512286 CATGCGAGTGGCCGATGT 60.512 61.111 0.00 0.00 42.61 3.06
909 1010 1.815003 TTCATGCGAGTGGCCGATG 60.815 57.895 0.00 0.00 42.61 3.84
910 1011 1.815421 GTTCATGCGAGTGGCCGAT 60.815 57.895 0.00 0.00 42.61 4.18
911 1012 2.434185 GTTCATGCGAGTGGCCGA 60.434 61.111 0.00 0.00 42.61 5.54
912 1013 3.853330 CGTTCATGCGAGTGGCCG 61.853 66.667 0.00 0.00 42.61 6.13
913 1014 1.766143 GATCGTTCATGCGAGTGGCC 61.766 60.000 0.00 0.00 44.43 5.36
914 1015 1.083806 TGATCGTTCATGCGAGTGGC 61.084 55.000 2.02 0.00 44.43 5.01
915 1016 0.926155 CTGATCGTTCATGCGAGTGG 59.074 55.000 0.00 0.00 44.43 4.00
916 1017 0.926155 CCTGATCGTTCATGCGAGTG 59.074 55.000 0.00 0.00 44.43 3.51
917 1018 0.817654 TCCTGATCGTTCATGCGAGT 59.182 50.000 0.00 0.00 44.43 4.18
918 1019 1.203928 GTCCTGATCGTTCATGCGAG 58.796 55.000 0.00 0.00 44.43 5.03
919 1020 0.530288 TGTCCTGATCGTTCATGCGA 59.470 50.000 0.00 0.00 45.32 5.10
920 1021 0.647410 GTGTCCTGATCGTTCATGCG 59.353 55.000 0.00 0.00 0.00 4.73
966 1067 4.899239 GTGGGGCTCGGCTCGATG 62.899 72.222 0.00 0.00 34.61 3.84
1028 1129 1.510480 GCCGAAGAACTTGCAGCAGT 61.510 55.000 0.00 0.00 0.00 4.40
1032 1133 2.863153 CCGCCGAAGAACTTGCAG 59.137 61.111 0.00 0.00 0.00 4.41
1037 1138 3.050275 GCAAGCCGCCGAAGAACT 61.050 61.111 0.00 0.00 32.94 3.01
1107 1208 2.354729 CGGATTTGGTGGGGCTGA 59.645 61.111 0.00 0.00 0.00 4.26
1113 1214 4.114997 GTGGCGCGGATTTGGTGG 62.115 66.667 8.83 0.00 0.00 4.61
1623 1733 2.415168 CACCGACAGCGATTGTAATTGT 59.585 45.455 0.00 0.00 41.05 2.71
1627 1737 2.333926 CTTCACCGACAGCGATTGTAA 58.666 47.619 0.00 0.00 41.05 2.41
1696 1806 3.786635 ACTAGCACGCTAATCTCCAAAG 58.213 45.455 0.00 0.00 0.00 2.77
1719 1829 5.562506 TTACACAAAACACAAACCGATGA 57.437 34.783 0.00 0.00 0.00 2.92
1747 1857 3.569277 CGATCACCATCCCAAATAATGCA 59.431 43.478 0.00 0.00 0.00 3.96
1858 2126 2.030096 TGACCTTACAACGTGCGTATGA 60.030 45.455 0.00 0.00 0.00 2.15
1869 2137 1.816183 CGCCTTGGGTTGACCTTACAA 60.816 52.381 0.00 0.00 41.11 2.41
1896 2164 3.730715 GGAGACAAATTTCGCACTGTTTG 59.269 43.478 0.00 0.00 37.52 2.93
1897 2165 3.632145 AGGAGACAAATTTCGCACTGTTT 59.368 39.130 0.00 0.00 0.00 2.83
1898 2166 3.214328 AGGAGACAAATTTCGCACTGTT 58.786 40.909 0.00 0.00 0.00 3.16
1899 2167 2.851195 AGGAGACAAATTTCGCACTGT 58.149 42.857 0.00 0.00 0.00 3.55
1900 2168 3.904136 AAGGAGACAAATTTCGCACTG 57.096 42.857 0.00 0.00 0.00 3.66
1901 2169 4.918810 AAAAGGAGACAAATTTCGCACT 57.081 36.364 0.00 0.00 0.00 4.40
1902 2170 4.803613 ACAAAAAGGAGACAAATTTCGCAC 59.196 37.500 0.00 0.00 0.00 5.34
1903 2171 5.004922 ACAAAAAGGAGACAAATTTCGCA 57.995 34.783 0.00 0.00 0.00 5.10
1904 2172 4.444388 GGACAAAAAGGAGACAAATTTCGC 59.556 41.667 0.00 0.00 0.00 4.70
1905 2173 5.831997 AGGACAAAAAGGAGACAAATTTCG 58.168 37.500 0.00 0.00 0.00 3.46
1906 2174 7.011389 CCAAAGGACAAAAAGGAGACAAATTTC 59.989 37.037 0.00 0.00 0.00 2.17
1907 2175 6.823182 CCAAAGGACAAAAAGGAGACAAATTT 59.177 34.615 0.00 0.00 0.00 1.82
1908 2176 6.156083 TCCAAAGGACAAAAAGGAGACAAATT 59.844 34.615 0.00 0.00 0.00 1.82
1909 2177 5.660864 TCCAAAGGACAAAAAGGAGACAAAT 59.339 36.000 0.00 0.00 0.00 2.32
1910 2178 5.020132 TCCAAAGGACAAAAAGGAGACAAA 58.980 37.500 0.00 0.00 0.00 2.83
1911 2179 4.605183 TCCAAAGGACAAAAAGGAGACAA 58.395 39.130 0.00 0.00 0.00 3.18
1912 2180 4.243793 TCCAAAGGACAAAAAGGAGACA 57.756 40.909 0.00 0.00 0.00 3.41
1913 2181 5.509670 CCAATCCAAAGGACAAAAAGGAGAC 60.510 44.000 0.00 0.00 32.98 3.36
1914 2182 4.588528 CCAATCCAAAGGACAAAAAGGAGA 59.411 41.667 0.00 0.00 32.98 3.71
1915 2183 4.800582 GCCAATCCAAAGGACAAAAAGGAG 60.801 45.833 0.00 0.00 32.98 3.69
1916 2184 3.070878 GCCAATCCAAAGGACAAAAAGGA 59.929 43.478 0.00 0.00 32.98 3.36
1917 2185 3.181456 TGCCAATCCAAAGGACAAAAAGG 60.181 43.478 0.00 0.00 32.98 3.11
1918 2186 4.060205 CTGCCAATCCAAAGGACAAAAAG 58.940 43.478 0.00 0.00 32.98 2.27
1919 2187 3.454082 ACTGCCAATCCAAAGGACAAAAA 59.546 39.130 0.00 0.00 32.98 1.94
1920 2188 3.037549 ACTGCCAATCCAAAGGACAAAA 58.962 40.909 0.00 0.00 32.98 2.44
1921 2189 2.676748 ACTGCCAATCCAAAGGACAAA 58.323 42.857 0.00 0.00 32.98 2.83
1922 2190 2.380064 ACTGCCAATCCAAAGGACAA 57.620 45.000 0.00 0.00 32.98 3.18
1923 2191 2.290896 CCTACTGCCAATCCAAAGGACA 60.291 50.000 0.00 0.00 32.98 4.02
1924 2192 2.369394 CCTACTGCCAATCCAAAGGAC 58.631 52.381 0.00 0.00 32.98 3.85
1925 2193 1.284785 CCCTACTGCCAATCCAAAGGA 59.715 52.381 0.00 0.00 35.55 3.36
1926 2194 1.005924 ACCCTACTGCCAATCCAAAGG 59.994 52.381 0.00 0.00 0.00 3.11
1927 2195 2.094675 CACCCTACTGCCAATCCAAAG 58.905 52.381 0.00 0.00 0.00 2.77
1928 2196 1.272425 CCACCCTACTGCCAATCCAAA 60.272 52.381 0.00 0.00 0.00 3.28
1929 2197 0.331278 CCACCCTACTGCCAATCCAA 59.669 55.000 0.00 0.00 0.00 3.53
1930 2198 1.998530 CCACCCTACTGCCAATCCA 59.001 57.895 0.00 0.00 0.00 3.41
1931 2199 1.453928 GCCACCCTACTGCCAATCC 60.454 63.158 0.00 0.00 0.00 3.01
1932 2200 1.819632 CGCCACCCTACTGCCAATC 60.820 63.158 0.00 0.00 0.00 2.67
1933 2201 2.272146 CGCCACCCTACTGCCAAT 59.728 61.111 0.00 0.00 0.00 3.16
1934 2202 3.246112 ACGCCACCCTACTGCCAA 61.246 61.111 0.00 0.00 0.00 4.52
1935 2203 3.702048 GACGCCACCCTACTGCCA 61.702 66.667 0.00 0.00 0.00 4.92
1936 2204 4.468689 GGACGCCACCCTACTGCC 62.469 72.222 0.00 0.00 0.00 4.85
1937 2205 4.814294 CGGACGCCACCCTACTGC 62.814 72.222 0.00 0.00 0.00 4.40
1938 2206 2.939261 AACGGACGCCACCCTACTG 61.939 63.158 0.00 0.00 0.00 2.74
1939 2207 2.602568 AACGGACGCCACCCTACT 60.603 61.111 0.00 0.00 0.00 2.57
1940 2208 2.433664 CAACGGACGCCACCCTAC 60.434 66.667 0.00 0.00 0.00 3.18
1941 2209 2.509651 AACAACGGACGCCACCCTA 61.510 57.895 0.00 0.00 0.00 3.53
1942 2210 3.868985 AACAACGGACGCCACCCT 61.869 61.111 0.00 0.00 0.00 4.34
1943 2211 3.656045 CAACAACGGACGCCACCC 61.656 66.667 0.00 0.00 0.00 4.61
1944 2212 3.656045 CCAACAACGGACGCCACC 61.656 66.667 0.00 0.00 0.00 4.61
1945 2213 4.322385 GCCAACAACGGACGCCAC 62.322 66.667 0.00 0.00 0.00 5.01
1950 2218 4.322385 GCACGGCCAACAACGGAC 62.322 66.667 2.24 0.00 0.00 4.79
1951 2219 4.858680 TGCACGGCCAACAACGGA 62.859 61.111 2.24 0.00 0.00 4.69
1952 2220 3.669344 ATGCACGGCCAACAACGG 61.669 61.111 2.24 0.00 0.00 4.44
1953 2221 2.428902 CATGCACGGCCAACAACG 60.429 61.111 2.24 0.00 0.00 4.10
1954 2222 1.371635 GACATGCACGGCCAACAAC 60.372 57.895 2.24 0.00 0.00 3.32
1955 2223 1.528076 AGACATGCACGGCCAACAA 60.528 52.632 2.24 0.00 0.00 2.83
1956 2224 2.112928 AGACATGCACGGCCAACA 59.887 55.556 2.24 0.00 0.00 3.33
1957 2225 0.953471 TACAGACATGCACGGCCAAC 60.953 55.000 2.24 0.00 0.00 3.77
1958 2226 0.673333 CTACAGACATGCACGGCCAA 60.673 55.000 2.24 0.00 0.00 4.52
1959 2227 1.079197 CTACAGACATGCACGGCCA 60.079 57.895 2.24 0.00 0.00 5.36
1960 2228 2.464459 GCTACAGACATGCACGGCC 61.464 63.158 0.00 0.00 0.00 6.13
1961 2229 2.802667 CGCTACAGACATGCACGGC 61.803 63.158 0.00 0.00 0.00 5.68
1962 2230 1.446099 ACGCTACAGACATGCACGG 60.446 57.895 0.00 0.00 0.00 4.94
1963 2231 1.008875 ACACGCTACAGACATGCACG 61.009 55.000 0.00 0.00 0.00 5.34
1964 2232 1.990799 TACACGCTACAGACATGCAC 58.009 50.000 0.00 0.00 0.00 4.57
1965 2233 2.734276 TTACACGCTACAGACATGCA 57.266 45.000 0.00 0.00 0.00 3.96
1966 2234 2.993899 AGTTTACACGCTACAGACATGC 59.006 45.455 0.00 0.00 0.00 4.06
1967 2235 4.090066 GTCAGTTTACACGCTACAGACATG 59.910 45.833 0.00 0.00 31.18 3.21
1968 2236 4.235360 GTCAGTTTACACGCTACAGACAT 58.765 43.478 0.00 0.00 31.18 3.06
1969 2237 3.551454 GGTCAGTTTACACGCTACAGACA 60.551 47.826 0.00 0.00 32.08 3.41
1970 2238 2.985139 GGTCAGTTTACACGCTACAGAC 59.015 50.000 0.00 0.00 0.00 3.51
1971 2239 2.351060 CGGTCAGTTTACACGCTACAGA 60.351 50.000 0.00 0.00 0.00 3.41
1972 2240 1.983605 CGGTCAGTTTACACGCTACAG 59.016 52.381 0.00 0.00 0.00 2.74
1973 2241 1.608109 TCGGTCAGTTTACACGCTACA 59.392 47.619 0.00 0.00 0.00 2.74
1974 2242 1.981533 GTCGGTCAGTTTACACGCTAC 59.018 52.381 0.00 0.00 0.00 3.58
1975 2243 1.068333 GGTCGGTCAGTTTACACGCTA 60.068 52.381 0.00 0.00 0.00 4.26
1976 2244 0.319297 GGTCGGTCAGTTTACACGCT 60.319 55.000 0.00 0.00 0.00 5.07
1977 2245 1.287041 GGGTCGGTCAGTTTACACGC 61.287 60.000 0.00 0.00 0.00 5.34
1978 2246 0.032403 TGGGTCGGTCAGTTTACACG 59.968 55.000 0.00 0.00 0.00 4.49
1979 2247 2.467566 ATGGGTCGGTCAGTTTACAC 57.532 50.000 0.00 0.00 0.00 2.90
1980 2248 3.142951 CAAATGGGTCGGTCAGTTTACA 58.857 45.455 0.00 0.00 0.00 2.41
1981 2249 3.404899 TCAAATGGGTCGGTCAGTTTAC 58.595 45.455 0.00 0.00 0.00 2.01
1982 2250 3.773418 TCAAATGGGTCGGTCAGTTTA 57.227 42.857 0.00 0.00 0.00 2.01
1983 2251 2.649531 TCAAATGGGTCGGTCAGTTT 57.350 45.000 0.00 0.00 0.00 2.66
1984 2252 2.618045 GGATCAAATGGGTCGGTCAGTT 60.618 50.000 0.00 0.00 0.00 3.16
1985 2253 1.065418 GGATCAAATGGGTCGGTCAGT 60.065 52.381 0.00 0.00 0.00 3.41
1986 2254 1.668419 GGATCAAATGGGTCGGTCAG 58.332 55.000 0.00 0.00 0.00 3.51
1987 2255 0.107897 CGGATCAAATGGGTCGGTCA 60.108 55.000 0.00 0.00 0.00 4.02
1988 2256 0.107848 ACGGATCAAATGGGTCGGTC 60.108 55.000 0.00 0.00 0.00 4.79
1989 2257 0.107848 GACGGATCAAATGGGTCGGT 60.108 55.000 0.00 0.00 0.00 4.69
1990 2258 0.178068 AGACGGATCAAATGGGTCGG 59.822 55.000 0.00 0.00 33.04 4.79
1991 2259 2.100916 ACTAGACGGATCAAATGGGTCG 59.899 50.000 0.00 0.00 33.04 4.79
1992 2260 3.132289 TGACTAGACGGATCAAATGGGTC 59.868 47.826 0.00 0.00 0.00 4.46
1993 2261 3.104512 TGACTAGACGGATCAAATGGGT 58.895 45.455 0.00 0.00 0.00 4.51
1994 2262 3.819564 TGACTAGACGGATCAAATGGG 57.180 47.619 0.00 0.00 0.00 4.00
1995 2263 6.494893 TTTTTGACTAGACGGATCAAATGG 57.505 37.500 0.00 0.00 40.88 3.16
2022 2290 9.558396 AGAATGCCAAATAAAGAAAAATTGACA 57.442 25.926 0.00 0.00 0.00 3.58
2087 2355 9.685828 GCCAAAAACTATATGACTTGTTTGTTA 57.314 29.630 0.00 0.00 33.61 2.41
2088 2356 8.421002 AGCCAAAAACTATATGACTTGTTTGTT 58.579 29.630 0.00 0.00 33.61 2.83
2089 2357 7.951591 AGCCAAAAACTATATGACTTGTTTGT 58.048 30.769 0.00 0.00 33.61 2.83
2090 2358 8.299570 AGAGCCAAAAACTATATGACTTGTTTG 58.700 33.333 0.00 0.00 33.61 2.93
2091 2359 8.409358 AGAGCCAAAAACTATATGACTTGTTT 57.591 30.769 0.00 0.00 34.59 2.83
2092 2360 8.947115 GTAGAGCCAAAAACTATATGACTTGTT 58.053 33.333 0.00 0.00 0.00 2.83
2093 2361 8.100791 TGTAGAGCCAAAAACTATATGACTTGT 58.899 33.333 0.00 0.00 0.00 3.16
2094 2362 8.492673 TGTAGAGCCAAAAACTATATGACTTG 57.507 34.615 0.00 0.00 0.00 3.16
2095 2363 8.540388 TCTGTAGAGCCAAAAACTATATGACTT 58.460 33.333 0.00 0.00 0.00 3.01
2096 2364 7.982354 GTCTGTAGAGCCAAAAACTATATGACT 59.018 37.037 0.00 0.00 0.00 3.41
2097 2365 7.764443 TGTCTGTAGAGCCAAAAACTATATGAC 59.236 37.037 0.00 0.00 0.00 3.06
2098 2366 7.847096 TGTCTGTAGAGCCAAAAACTATATGA 58.153 34.615 0.00 0.00 0.00 2.15
2099 2367 8.492673 TTGTCTGTAGAGCCAAAAACTATATG 57.507 34.615 0.00 0.00 0.00 1.78
2100 2368 8.540388 TCTTGTCTGTAGAGCCAAAAACTATAT 58.460 33.333 0.00 0.00 0.00 0.86
2101 2369 7.817962 GTCTTGTCTGTAGAGCCAAAAACTATA 59.182 37.037 0.00 0.00 0.00 1.31
2102 2370 6.651225 GTCTTGTCTGTAGAGCCAAAAACTAT 59.349 38.462 0.00 0.00 0.00 2.12
2103 2371 5.989777 GTCTTGTCTGTAGAGCCAAAAACTA 59.010 40.000 0.00 0.00 0.00 2.24
2104 2372 4.816925 GTCTTGTCTGTAGAGCCAAAAACT 59.183 41.667 0.00 0.00 0.00 2.66
2105 2373 4.574828 TGTCTTGTCTGTAGAGCCAAAAAC 59.425 41.667 0.00 0.00 0.00 2.43
2106 2374 4.776349 TGTCTTGTCTGTAGAGCCAAAAA 58.224 39.130 0.00 0.00 0.00 1.94
2107 2375 4.415881 TGTCTTGTCTGTAGAGCCAAAA 57.584 40.909 0.00 0.00 0.00 2.44
2108 2376 4.380531 CTTGTCTTGTCTGTAGAGCCAAA 58.619 43.478 0.00 0.00 0.00 3.28
2109 2377 3.244215 CCTTGTCTTGTCTGTAGAGCCAA 60.244 47.826 0.00 0.00 0.00 4.52
2110 2378 2.300152 CCTTGTCTTGTCTGTAGAGCCA 59.700 50.000 0.00 0.00 0.00 4.75
2111 2379 2.563179 TCCTTGTCTTGTCTGTAGAGCC 59.437 50.000 0.00 0.00 0.00 4.70
2112 2380 3.367910 CCTCCTTGTCTTGTCTGTAGAGC 60.368 52.174 0.00 0.00 0.00 4.09
2113 2381 3.829601 ACCTCCTTGTCTTGTCTGTAGAG 59.170 47.826 0.00 0.00 0.00 2.43
2114 2382 3.827302 GACCTCCTTGTCTTGTCTGTAGA 59.173 47.826 0.00 0.00 32.39 2.59
2115 2383 3.574396 TGACCTCCTTGTCTTGTCTGTAG 59.426 47.826 0.00 0.00 36.21 2.74
2116 2384 3.572642 TGACCTCCTTGTCTTGTCTGTA 58.427 45.455 0.00 0.00 36.21 2.74
2117 2385 2.398588 TGACCTCCTTGTCTTGTCTGT 58.601 47.619 0.00 0.00 36.21 3.41
2118 2386 3.594134 GATGACCTCCTTGTCTTGTCTG 58.406 50.000 0.00 0.00 36.21 3.51
2119 2387 2.232452 CGATGACCTCCTTGTCTTGTCT 59.768 50.000 0.00 0.00 36.21 3.41
2120 2388 2.611518 CGATGACCTCCTTGTCTTGTC 58.388 52.381 0.00 0.00 36.21 3.18
2127 2395 0.530744 TTCGTCCGATGACCTCCTTG 59.469 55.000 0.00 0.00 38.32 3.61
2128 2396 1.204941 CTTTCGTCCGATGACCTCCTT 59.795 52.381 0.00 0.00 38.32 3.36
2138 2406 1.000060 CCACCTTACACTTTCGTCCGA 60.000 52.381 0.00 0.00 0.00 4.55
2143 2411 1.156736 CAGCCCACCTTACACTTTCG 58.843 55.000 0.00 0.00 0.00 3.46
2145 2413 1.145571 TCCAGCCCACCTTACACTTT 58.854 50.000 0.00 0.00 0.00 2.66
2148 2416 0.322546 CCTTCCAGCCCACCTTACAC 60.323 60.000 0.00 0.00 0.00 2.90
2169 2437 3.991051 CGCTCCGGTGTGGTGACT 61.991 66.667 9.22 0.00 39.52 3.41
2187 2455 4.489771 GATGCCCAGTCCCCGGTG 62.490 72.222 0.00 0.00 0.00 4.94
2207 2476 2.436646 AGCGAATTGGCCAGGTCG 60.437 61.111 27.16 27.16 36.59 4.79
2212 2481 3.430862 GCACGAGCGAATTGGCCA 61.431 61.111 0.00 0.00 0.00 5.36
2213 2482 4.179579 GGCACGAGCGAATTGGCC 62.180 66.667 9.00 0.00 43.41 5.36
2214 2483 4.179579 GGGCACGAGCGAATTGGC 62.180 66.667 3.97 3.97 43.41 4.52
2240 2510 2.156098 AGGAGAGCCAAAGCCACCA 61.156 57.895 0.00 0.00 41.25 4.17
2283 2553 1.522092 CAAGGGATGCTCGTGCCTA 59.478 57.895 7.05 0.00 39.23 3.93
2284 2554 2.270205 CAAGGGATGCTCGTGCCT 59.730 61.111 7.05 0.00 42.31 4.75
2295 2565 2.411701 CGATAGCGTCGCAAGGGA 59.588 61.111 21.09 0.00 44.33 4.20
2306 2576 2.807045 CAGGGCGCGATCGATAGC 60.807 66.667 21.57 19.26 38.10 2.97
2307 2577 1.004277 GAACAGGGCGCGATCGATAG 61.004 60.000 21.57 10.29 38.10 2.08
2308 2578 1.007734 GAACAGGGCGCGATCGATA 60.008 57.895 21.57 0.00 38.10 2.92
2309 2579 2.279517 GAACAGGGCGCGATCGAT 60.280 61.111 21.57 0.00 38.10 3.59
2310 2580 3.754530 TGAACAGGGCGCGATCGA 61.755 61.111 21.57 0.00 38.10 3.59
2311 2581 3.554692 GTGAACAGGGCGCGATCG 61.555 66.667 12.10 11.69 39.07 3.69
2312 2582 2.125512 AGTGAACAGGGCGCGATC 60.126 61.111 12.10 0.00 0.00 3.69
2313 2583 2.434884 CAGTGAACAGGGCGCGAT 60.435 61.111 12.10 0.00 0.00 4.58
2317 2594 3.052082 CAGGCAGTGAACAGGGCG 61.052 66.667 0.00 0.00 0.00 6.13
2328 2605 4.624364 TGACCACCGTGCAGGCAG 62.624 66.667 0.00 0.00 46.52 4.85
2329 2606 4.927782 GTGACCACCGTGCAGGCA 62.928 66.667 0.00 0.00 46.52 4.75
2358 2635 1.672356 CAGAAGGAGGCCGTTGTGG 60.672 63.158 0.00 0.00 42.50 4.17
2359 2636 1.672356 CCAGAAGGAGGCCGTTGTG 60.672 63.158 0.00 1.16 36.89 3.33
2360 2637 2.113243 GACCAGAAGGAGGCCGTTGT 62.113 60.000 0.00 0.00 38.69 3.32
2365 2642 2.371259 GGAGGACCAGAAGGAGGCC 61.371 68.421 0.00 0.00 38.69 5.19
2367 2644 1.040339 CGAGGAGGACCAGAAGGAGG 61.040 65.000 0.00 0.00 38.69 4.30
2382 2659 1.079819 CACTAGGTGTGCCACGAGG 60.080 63.158 0.00 0.00 40.06 4.63
2394 2671 1.743394 GATTGGGCGAAAACCACTAGG 59.257 52.381 0.00 0.00 37.82 3.02
2395 2672 1.743394 GGATTGGGCGAAAACCACTAG 59.257 52.381 0.00 0.00 37.82 2.57
2396 2673 1.074084 TGGATTGGGCGAAAACCACTA 59.926 47.619 7.25 0.00 37.82 2.74
2397 2674 0.178975 TGGATTGGGCGAAAACCACT 60.179 50.000 7.25 0.00 37.82 4.00
2398 2675 0.894835 ATGGATTGGGCGAAAACCAC 59.105 50.000 11.98 0.00 37.82 4.16
2399 2676 1.181786 GATGGATTGGGCGAAAACCA 58.818 50.000 12.08 12.08 35.88 3.67
2402 2679 2.505650 TCTGATGGATTGGGCGAAAA 57.494 45.000 0.00 0.00 0.00 2.29
2403 2680 2.505650 TTCTGATGGATTGGGCGAAA 57.494 45.000 0.00 0.00 0.00 3.46
2404 2681 2.026356 TCTTTCTGATGGATTGGGCGAA 60.026 45.455 0.00 0.00 0.00 4.70
2405 2682 1.559219 TCTTTCTGATGGATTGGGCGA 59.441 47.619 0.00 0.00 0.00 5.54
2406 2683 2.042686 TCTTTCTGATGGATTGGGCG 57.957 50.000 0.00 0.00 0.00 6.13
2408 2685 4.592942 TCTGTTCTTTCTGATGGATTGGG 58.407 43.478 0.00 0.00 0.00 4.12
2413 2714 6.118170 GGATTGATCTGTTCTTTCTGATGGA 58.882 40.000 0.00 0.00 0.00 3.41
2434 2735 1.228367 GATGCAATGCCTCCCGGAT 60.228 57.895 0.73 0.00 0.00 4.18
2436 2737 2.124193 TGATGCAATGCCTCCCGG 60.124 61.111 1.53 0.00 0.00 5.73
2438 2739 1.451927 TCGTGATGCAATGCCTCCC 60.452 57.895 1.53 0.00 0.00 4.30
2532 2833 1.007336 GTGTGATTCCGTCGCTTCGT 61.007 55.000 0.00 0.00 38.20 3.85
2540 2841 2.761208 CCCTCTTCTAGTGTGATTCCGT 59.239 50.000 0.00 0.00 0.00 4.69
2567 2868 1.751351 GAGTCCATCTGATCGTGTCCA 59.249 52.381 0.00 0.00 0.00 4.02
2568 2869 2.028130 AGAGTCCATCTGATCGTGTCC 58.972 52.381 0.00 0.00 36.69 4.02
2598 2899 4.710695 CGCGCGGTGTACTGTCCA 62.711 66.667 24.84 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.