Multiple sequence alignment - TraesCS6A01G028900

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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 TraesCS6A01G028900 chr6A 100.000 2216 0 0 1 2216 15384381 15382166 0.000000e+00 4093
1 TraesCS6A01G028900 chr6A 96.774 124 1 2 1714 1834 15382548 15382425 1.040000e-48 204
2 TraesCS6A01G028900 chr6A 96.774 124 1 2 1834 1957 15382668 15382548 1.040000e-48 204
3 TraesCS6A01G028900 chr7A 96.778 1862 23 10 1 1834 610461067 610459215 0.000000e+00 3072
4 TraesCS6A01G028900 chr7A 96.911 259 7 1 1834 2091 610459338 610459080 1.220000e-117 433
5 TraesCS6A01G028900 chr7A 96.341 82 3 0 2135 2216 610459086 610459005 3.840000e-28 135
6 TraesCS6A01G028900 chr4A 96.618 1863 34 10 1 1834 180269128 180267266 0.000000e+00 3064
7 TraesCS6A01G028900 chr4A 93.348 1864 87 16 1 1834 729542984 729541128 0.000000e+00 2721
8 TraesCS6A01G028900 chr4A 92.228 386 23 4 1835 2216 729541249 729540867 6.960000e-150 540
9 TraesCS6A01G028900 chr4A 96.525 259 8 1 1834 2091 180267389 180267131 5.650000e-116 427
10 TraesCS6A01G028900 chr4A 96.341 82 3 0 2135 2216 180267137 180267056 3.840000e-28 135
11 TraesCS6A01G028900 chr7D 95.918 1862 46 14 1 1834 194639835 194641694 0.000000e+00 2990
12 TraesCS6A01G028900 chr7D 96.615 384 12 1 1834 2216 194641571 194641954 8.630000e-179 636
13 TraesCS6A01G028900 chr3B 94.984 1854 69 14 1 1834 607807956 607806107 0.000000e+00 2887
14 TraesCS6A01G028900 chr3B 94.819 386 15 3 1835 2216 607806229 607805845 4.070000e-167 597
15 TraesCS6A01G028900 chr5A 98.445 1222 16 2 616 1834 567267782 567269003 0.000000e+00 2148
16 TraesCS6A01G028900 chr5A 96.525 259 8 1 1834 2091 567268880 567269138 5.650000e-116 427
17 TraesCS6A01G028900 chr5A 96.341 82 3 0 2135 2216 567269132 567269213 3.840000e-28 135
18 TraesCS6A01G028900 chr1D 80.442 588 79 20 967 1522 271791987 271792570 1.220000e-112 416
19 TraesCS6A01G028900 chr1D 80.899 178 31 2 2039 2216 271793001 271793175 1.070000e-28 137
20 TraesCS6A01G028900 chr1A 80.603 531 67 20 1021 1522 344134603 344135126 5.780000e-101 377


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 TraesCS6A01G028900 chr6A 15382166 15384381 2215 True 1500.333333 4093 97.849333 1 2216 3 chr6A.!!$R1 2215
1 TraesCS6A01G028900 chr7A 610459005 610461067 2062 True 1213.333333 3072 96.676667 1 2216 3 chr7A.!!$R1 2215
2 TraesCS6A01G028900 chr4A 729540867 729542984 2117 True 1630.500000 2721 92.788000 1 2216 2 chr4A.!!$R2 2215
3 TraesCS6A01G028900 chr4A 180267056 180269128 2072 True 1208.666667 3064 96.494667 1 2216 3 chr4A.!!$R1 2215
4 TraesCS6A01G028900 chr7D 194639835 194641954 2119 False 1813.000000 2990 96.266500 1 2216 2 chr7D.!!$F1 2215
5 TraesCS6A01G028900 chr3B 607805845 607807956 2111 True 1742.000000 2887 94.901500 1 2216 2 chr3B.!!$R1 2215
6 TraesCS6A01G028900 chr5A 567267782 567269213 1431 False 903.333333 2148 97.103667 616 2216 3 chr5A.!!$F1 1600
7 TraesCS6A01G028900 chr1D 271791987 271793175 1188 False 276.500000 416 80.670500 967 2216 2 chr1D.!!$F1 1249
8 TraesCS6A01G028900 chr1A 344134603 344135126 523 False 377.000000 377 80.603000 1021 1522 1 chr1A.!!$F1 501

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
468 473 5.376625 AGAAAGTGCTATTTCTGGTTCACA 58.623 37.5 13.68 0.0 45.52 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1957 1.070134 TCACCACAAGTACCAGCAGTC 59.93 52.381 0.0 0.0 0.0 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
372 377 8.470805 CCAGTTGACATCTCTTGTATTACTACT 58.529 37.037 0.00 0.00 39.18 2.57
373 378 9.862371 CAGTTGACATCTCTTGTATTACTACTT 57.138 33.333 0.00 0.00 39.18 2.24
468 473 5.376625 AGAAAGTGCTATTTCTGGTTCACA 58.623 37.500 13.68 0.00 45.52 3.58
469 474 6.006449 AGAAAGTGCTATTTCTGGTTCACAT 58.994 36.000 13.68 0.00 45.52 3.21
470 475 6.491403 AGAAAGTGCTATTTCTGGTTCACATT 59.509 34.615 13.68 0.00 45.52 2.71
473 478 7.944729 AGTGCTATTTCTGGTTCACATTATT 57.055 32.000 0.00 0.00 0.00 1.40
474 479 8.353423 AGTGCTATTTCTGGTTCACATTATTT 57.647 30.769 0.00 0.00 0.00 1.40
478 508 8.462016 GCTATTTCTGGTTCACATTATTTCACT 58.538 33.333 0.00 0.00 0.00 3.41
1008 1045 3.626729 CCCAAGAGAAAGCAATGGAGGAT 60.627 47.826 0.00 0.00 32.82 3.24
1042 1080 8.245701 ACAGAAGTTTAAAGAGAAAGCTATCG 57.754 34.615 0.00 0.00 0.00 2.92
1623 1744 5.945466 AATTTTTGTTGGTCCAATGATGC 57.055 34.783 7.77 0.00 0.00 3.91
1806 1930 9.734620 TTGTTACTCTTCAACAATGAGAAAATG 57.265 29.630 0.00 0.00 40.12 2.32
1807 1931 9.119418 TGTTACTCTTCAACAATGAGAAAATGA 57.881 29.630 0.00 0.00 36.78 2.57
1810 1934 8.632906 ACTCTTCAACAATGAGAAAATGATCT 57.367 30.769 0.00 0.00 36.78 2.75
1811 1935 8.512956 ACTCTTCAACAATGAGAAAATGATCTG 58.487 33.333 0.00 0.00 36.78 2.90
1812 1936 8.400184 TCTTCAACAATGAGAAAATGATCTGT 57.600 30.769 0.00 0.00 36.78 3.41
1813 1937 8.853126 TCTTCAACAATGAGAAAATGATCTGTT 58.147 29.630 0.00 0.00 36.78 3.16
1814 1938 9.472361 CTTCAACAATGAGAAAATGATCTGTTT 57.528 29.630 0.00 0.00 36.78 2.83
1815 1939 9.820725 TTCAACAATGAGAAAATGATCTGTTTT 57.179 25.926 8.50 8.50 36.78 2.43
1816 1940 9.251792 TCAACAATGAGAAAATGATCTGTTTTG 57.748 29.630 12.17 2.93 0.00 2.44
1817 1941 9.037737 CAACAATGAGAAAATGATCTGTTTTGT 57.962 29.630 12.17 9.23 30.13 2.83
1818 1942 9.603921 AACAATGAGAAAATGATCTGTTTTGTT 57.396 25.926 12.17 7.87 32.83 2.83
1819 1943 9.037737 ACAATGAGAAAATGATCTGTTTTGTTG 57.962 29.630 12.17 12.41 0.00 3.33
1820 1944 8.492748 CAATGAGAAAATGATCTGTTTTGTTGG 58.507 33.333 12.17 0.66 0.00 3.77
1821 1945 5.984926 TGAGAAAATGATCTGTTTTGTTGGC 59.015 36.000 12.17 1.44 0.00 4.52
1822 1946 6.165700 AGAAAATGATCTGTTTTGTTGGCT 57.834 33.333 12.17 3.18 0.00 4.75
1823 1947 7.014134 TGAGAAAATGATCTGTTTTGTTGGCTA 59.986 33.333 12.17 0.00 0.00 3.93
1824 1948 7.725251 AGAAAATGATCTGTTTTGTTGGCTAA 58.275 30.769 12.17 0.00 0.00 3.09
1825 1949 8.370182 AGAAAATGATCTGTTTTGTTGGCTAAT 58.630 29.630 12.17 0.00 0.00 1.73
1826 1950 8.907222 AAAATGATCTGTTTTGTTGGCTAATT 57.093 26.923 8.10 0.00 0.00 1.40
1827 1951 9.995003 AAAATGATCTGTTTTGTTGGCTAATTA 57.005 25.926 8.10 0.00 0.00 1.40
1829 1953 9.590451 AATGATCTGTTTTGTTGGCTAATTATG 57.410 29.630 0.00 0.00 0.00 1.90
1830 1954 7.035004 TGATCTGTTTTGTTGGCTAATTATGC 58.965 34.615 0.00 0.00 0.00 3.14
1831 1955 6.338214 TCTGTTTTGTTGGCTAATTATGCA 57.662 33.333 0.00 0.00 0.00 3.96
1832 1956 6.934056 TCTGTTTTGTTGGCTAATTATGCAT 58.066 32.000 3.79 3.79 0.00 3.96
1833 1957 6.812656 TCTGTTTTGTTGGCTAATTATGCATG 59.187 34.615 10.16 0.00 0.00 4.06
1834 1958 6.695429 TGTTTTGTTGGCTAATTATGCATGA 58.305 32.000 10.16 0.00 0.00 3.07
1835 1959 6.589523 TGTTTTGTTGGCTAATTATGCATGAC 59.410 34.615 10.16 0.00 0.00 3.06
1836 1960 6.528537 TTTGTTGGCTAATTATGCATGACT 57.471 33.333 10.16 0.00 0.00 3.41
1837 1961 5.503662 TGTTGGCTAATTATGCATGACTG 57.496 39.130 10.16 0.00 0.00 3.51
1848 1972 1.813513 GCATGACTGCTGGTACTTGT 58.186 50.000 0.00 0.00 45.32 3.16
1849 1973 1.466167 GCATGACTGCTGGTACTTGTG 59.534 52.381 0.00 0.00 45.32 3.33
1850 1974 2.079158 CATGACTGCTGGTACTTGTGG 58.921 52.381 0.00 0.00 0.00 4.17
1851 1975 1.128200 TGACTGCTGGTACTTGTGGT 58.872 50.000 0.00 0.00 0.00 4.16
1852 1976 1.202639 TGACTGCTGGTACTTGTGGTG 60.203 52.381 0.00 0.00 0.00 4.17
1853 1977 1.070134 GACTGCTGGTACTTGTGGTGA 59.930 52.381 0.00 0.00 0.00 4.02
1854 1978 1.699634 ACTGCTGGTACTTGTGGTGAT 59.300 47.619 0.00 0.00 0.00 3.06
1855 1979 2.079158 CTGCTGGTACTTGTGGTGATG 58.921 52.381 0.00 0.00 0.00 3.07
1856 1980 1.696884 TGCTGGTACTTGTGGTGATGA 59.303 47.619 0.00 0.00 0.00 2.92
1857 1981 2.305635 TGCTGGTACTTGTGGTGATGAT 59.694 45.455 0.00 0.00 0.00 2.45
1858 1982 2.679837 GCTGGTACTTGTGGTGATGATG 59.320 50.000 0.00 0.00 0.00 3.07
1859 1983 3.619733 GCTGGTACTTGTGGTGATGATGA 60.620 47.826 0.00 0.00 0.00 2.92
1860 1984 4.186926 CTGGTACTTGTGGTGATGATGAG 58.813 47.826 0.00 0.00 0.00 2.90
1861 1985 2.939103 GGTACTTGTGGTGATGATGAGC 59.061 50.000 0.00 0.00 0.00 4.26
1862 1986 3.369892 GGTACTTGTGGTGATGATGAGCT 60.370 47.826 0.00 0.00 0.00 4.09
1863 1987 2.708051 ACTTGTGGTGATGATGAGCTG 58.292 47.619 0.00 0.00 0.00 4.24
1864 1988 2.303890 ACTTGTGGTGATGATGAGCTGA 59.696 45.455 0.00 0.00 0.00 4.26
1865 1989 3.054582 ACTTGTGGTGATGATGAGCTGAT 60.055 43.478 0.00 0.00 0.00 2.90
1866 1990 2.914059 TGTGGTGATGATGAGCTGATG 58.086 47.619 0.00 0.00 0.00 3.07
1867 1991 2.237893 TGTGGTGATGATGAGCTGATGT 59.762 45.455 0.00 0.00 0.00 3.06
1868 1992 2.612672 GTGGTGATGATGAGCTGATGTG 59.387 50.000 0.00 0.00 0.00 3.21
1869 1993 2.237893 TGGTGATGATGAGCTGATGTGT 59.762 45.455 0.00 0.00 0.00 3.72
1870 1994 3.276857 GGTGATGATGAGCTGATGTGTT 58.723 45.455 0.00 0.00 0.00 3.32
1871 1995 4.080975 TGGTGATGATGAGCTGATGTGTTA 60.081 41.667 0.00 0.00 0.00 2.41
1872 1996 4.272018 GGTGATGATGAGCTGATGTGTTAC 59.728 45.833 0.00 0.00 0.00 2.50
1873 1997 4.026228 GTGATGATGAGCTGATGTGTTACG 60.026 45.833 0.00 0.00 0.00 3.18
1874 1998 3.866883 TGATGAGCTGATGTGTTACGA 57.133 42.857 0.00 0.00 0.00 3.43
1875 1999 3.774066 TGATGAGCTGATGTGTTACGAG 58.226 45.455 0.00 0.00 0.00 4.18
1876 2000 3.443681 TGATGAGCTGATGTGTTACGAGA 59.556 43.478 0.00 0.00 0.00 4.04
1877 2001 4.098501 TGATGAGCTGATGTGTTACGAGAT 59.901 41.667 0.00 0.00 0.00 2.75
1878 2002 3.774066 TGAGCTGATGTGTTACGAGATG 58.226 45.455 0.00 0.00 0.00 2.90
1879 2003 3.119291 GAGCTGATGTGTTACGAGATGG 58.881 50.000 0.00 0.00 0.00 3.51
1880 2004 2.760650 AGCTGATGTGTTACGAGATGGA 59.239 45.455 0.00 0.00 0.00 3.41
1881 2005 3.386078 AGCTGATGTGTTACGAGATGGAT 59.614 43.478 0.00 0.00 0.00 3.41
1882 2006 4.584743 AGCTGATGTGTTACGAGATGGATA 59.415 41.667 0.00 0.00 0.00 2.59
1883 2007 5.244851 AGCTGATGTGTTACGAGATGGATAT 59.755 40.000 0.00 0.00 0.00 1.63
1884 2008 5.574830 GCTGATGTGTTACGAGATGGATATC 59.425 44.000 0.00 0.00 0.00 1.63
1885 2009 6.648879 TGATGTGTTACGAGATGGATATCA 57.351 37.500 4.83 0.00 35.70 2.15
1886 2010 6.447162 TGATGTGTTACGAGATGGATATCAC 58.553 40.000 4.83 0.00 35.70 3.06
1887 2011 5.845391 TGTGTTACGAGATGGATATCACA 57.155 39.130 4.83 0.72 35.70 3.58
1888 2012 6.405278 TGTGTTACGAGATGGATATCACAT 57.595 37.500 4.83 5.78 35.70 3.21
1889 2013 6.215845 TGTGTTACGAGATGGATATCACATG 58.784 40.000 4.83 0.00 35.70 3.21
1890 2014 6.040391 TGTGTTACGAGATGGATATCACATGA 59.960 38.462 4.83 0.00 35.70 3.07
1891 2015 6.923508 GTGTTACGAGATGGATATCACATGAA 59.076 38.462 4.83 0.00 35.70 2.57
1892 2016 7.438160 GTGTTACGAGATGGATATCACATGAAA 59.562 37.037 4.83 0.00 35.70 2.69
1893 2017 7.984617 TGTTACGAGATGGATATCACATGAAAA 59.015 33.333 4.83 0.00 35.70 2.29
1894 2018 8.826710 GTTACGAGATGGATATCACATGAAAAA 58.173 33.333 4.83 0.00 35.70 1.94
1895 2019 9.559732 TTACGAGATGGATATCACATGAAAAAT 57.440 29.630 4.83 0.00 35.70 1.82
1896 2020 7.868775 ACGAGATGGATATCACATGAAAAATG 58.131 34.615 4.83 0.00 35.70 2.32
1897 2021 7.500227 ACGAGATGGATATCACATGAAAAATGT 59.500 33.333 4.83 0.00 35.70 2.71
1898 2022 8.347771 CGAGATGGATATCACATGAAAAATGTT 58.652 33.333 4.83 0.00 35.70 2.71
2092 2263 4.968812 CATGTCAGCCATGTACAAATCA 57.031 40.909 0.00 0.00 44.96 2.57
2093 2264 4.916870 CATGTCAGCCATGTACAAATCAG 58.083 43.478 0.00 0.00 44.96 2.90
2094 2265 2.749076 TGTCAGCCATGTACAAATCAGC 59.251 45.455 0.00 0.00 0.00 4.26
2095 2266 2.749076 GTCAGCCATGTACAAATCAGCA 59.251 45.455 0.00 0.00 0.00 4.41
2096 2267 3.379372 GTCAGCCATGTACAAATCAGCAT 59.621 43.478 0.00 0.00 0.00 3.79
2097 2268 4.018490 TCAGCCATGTACAAATCAGCATT 58.982 39.130 0.00 0.00 0.00 3.56
2098 2269 5.066375 GTCAGCCATGTACAAATCAGCATTA 59.934 40.000 0.00 0.00 0.00 1.90
2099 2270 5.651576 TCAGCCATGTACAAATCAGCATTAA 59.348 36.000 0.00 0.00 0.00 1.40
2100 2271 6.321945 TCAGCCATGTACAAATCAGCATTAAT 59.678 34.615 0.00 0.00 0.00 1.40
2101 2272 6.982141 CAGCCATGTACAAATCAGCATTAATT 59.018 34.615 0.00 0.00 0.00 1.40
2102 2273 7.493320 CAGCCATGTACAAATCAGCATTAATTT 59.507 33.333 0.00 0.00 0.00 1.82
2103 2274 8.042515 AGCCATGTACAAATCAGCATTAATTTT 58.957 29.630 0.00 0.00 0.00 1.82
2104 2275 8.117988 GCCATGTACAAATCAGCATTAATTTTG 58.882 33.333 0.00 7.64 34.34 2.44
2105 2276 8.117988 CCATGTACAAATCAGCATTAATTTTGC 58.882 33.333 0.00 5.22 40.45 3.68
2106 2277 8.657729 CATGTACAAATCAGCATTAATTTTGCA 58.342 29.630 0.00 0.00 42.62 4.08
2107 2278 8.774890 TGTACAAATCAGCATTAATTTTGCAT 57.225 26.923 13.56 0.00 42.62 3.96
2108 2279 9.217278 TGTACAAATCAGCATTAATTTTGCATT 57.783 25.926 13.56 4.96 42.62 3.56
2109 2280 9.693157 GTACAAATCAGCATTAATTTTGCATTC 57.307 29.630 13.56 0.00 42.62 2.67
2110 2281 8.325421 ACAAATCAGCATTAATTTTGCATTCA 57.675 26.923 13.56 0.00 42.62 2.57
2111 2282 8.952278 ACAAATCAGCATTAATTTTGCATTCAT 58.048 25.926 13.56 0.47 42.62 2.57
2112 2283 9.781834 CAAATCAGCATTAATTTTGCATTCATT 57.218 25.926 13.56 5.13 42.62 2.57
2113 2284 9.781834 AAATCAGCATTAATTTTGCATTCATTG 57.218 25.926 13.56 4.44 42.62 2.82
2114 2285 7.908827 TCAGCATTAATTTTGCATTCATTGT 57.091 28.000 13.56 0.00 42.62 2.71
2115 2286 7.966111 TCAGCATTAATTTTGCATTCATTGTC 58.034 30.769 13.56 0.00 42.62 3.18
2116 2287 6.897663 CAGCATTAATTTTGCATTCATTGTCG 59.102 34.615 13.56 0.00 42.62 4.35
2117 2288 6.591062 AGCATTAATTTTGCATTCATTGTCGT 59.409 30.769 13.56 0.00 42.62 4.34
2118 2289 7.118101 AGCATTAATTTTGCATTCATTGTCGTT 59.882 29.630 13.56 0.00 42.62 3.85
2119 2290 7.423314 GCATTAATTTTGCATTCATTGTCGTTC 59.577 33.333 7.88 0.00 39.90 3.95
2120 2291 7.936950 TTAATTTTGCATTCATTGTCGTTCA 57.063 28.000 0.00 0.00 0.00 3.18
2121 2292 8.531622 TTAATTTTGCATTCATTGTCGTTCAT 57.468 26.923 0.00 0.00 0.00 2.57
2122 2293 7.424227 AATTTTGCATTCATTGTCGTTCATT 57.576 28.000 0.00 0.00 0.00 2.57
2123 2294 6.841443 TTTTGCATTCATTGTCGTTCATTT 57.159 29.167 0.00 0.00 0.00 2.32
2124 2295 5.825905 TTGCATTCATTGTCGTTCATTTG 57.174 34.783 0.00 0.00 0.00 2.32
2125 2296 5.118642 TGCATTCATTGTCGTTCATTTGA 57.881 34.783 0.00 0.00 0.00 2.69
2126 2297 5.712004 TGCATTCATTGTCGTTCATTTGAT 58.288 33.333 0.00 0.00 0.00 2.57
2127 2298 5.573669 TGCATTCATTGTCGTTCATTTGATG 59.426 36.000 0.00 0.00 0.00 3.07
2128 2299 5.801444 GCATTCATTGTCGTTCATTTGATGA 59.199 36.000 0.00 0.00 37.55 2.92
2129 2300 6.020916 GCATTCATTGTCGTTCATTTGATGAG 60.021 38.462 0.00 0.00 40.94 2.90
2130 2301 6.799926 TTCATTGTCGTTCATTTGATGAGA 57.200 33.333 0.00 0.00 40.94 3.27
2131 2302 6.990341 TCATTGTCGTTCATTTGATGAGAT 57.010 33.333 0.00 0.00 40.94 2.75
2132 2303 8.491331 TTCATTGTCGTTCATTTGATGAGATA 57.509 30.769 0.00 0.00 40.94 1.98
2133 2304 8.491331 TCATTGTCGTTCATTTGATGAGATAA 57.509 30.769 0.00 0.00 40.94 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
372 377 6.834451 CCAATAGGACCTCACTTCTAGTAGAA 59.166 42.308 12.05 12.05 36.89 2.10
373 378 6.159928 TCCAATAGGACCTCACTTCTAGTAGA 59.840 42.308 0.00 0.00 39.61 2.59
374 379 6.366340 TCCAATAGGACCTCACTTCTAGTAG 58.634 44.000 0.00 0.00 39.61 2.57
455 460 7.092716 GCAGTGAAATAATGTGAACCAGAAAT 58.907 34.615 0.00 0.00 0.00 2.17
468 473 8.462016 GTTTTCTAGGTCATGCAGTGAAATAAT 58.538 33.333 0.00 0.00 38.90 1.28
469 474 7.665559 AGTTTTCTAGGTCATGCAGTGAAATAA 59.334 33.333 0.00 0.00 38.90 1.40
470 475 7.119699 CAGTTTTCTAGGTCATGCAGTGAAATA 59.880 37.037 0.00 0.00 38.90 1.40
473 478 4.756642 CAGTTTTCTAGGTCATGCAGTGAA 59.243 41.667 0.00 0.00 38.90 3.18
474 479 4.040339 TCAGTTTTCTAGGTCATGCAGTGA 59.960 41.667 0.00 0.00 0.00 3.41
478 508 4.890158 TCTCAGTTTTCTAGGTCATGCA 57.110 40.909 0.00 0.00 0.00 3.96
1008 1045 8.651589 TCTCTTTAAACTTCTGTCTAGGATCA 57.348 34.615 0.00 0.00 0.00 2.92
1042 1080 7.014038 AGTGAATCCAAGCCTTGATAATTCATC 59.986 37.037 21.67 17.29 36.84 2.92
1623 1744 6.964741 ATCTTCTAATTGCATCATCTAGCG 57.035 37.500 0.00 0.00 0.00 4.26
1788 1912 9.472361 AAACAGATCATTTTCTCATTGTTGAAG 57.528 29.630 0.00 0.00 0.00 3.02
1789 1913 9.820725 AAAACAGATCATTTTCTCATTGTTGAA 57.179 25.926 0.00 0.00 0.00 2.69
1790 1914 9.251792 CAAAACAGATCATTTTCTCATTGTTGA 57.748 29.630 5.07 0.00 0.00 3.18
1791 1915 9.037737 ACAAAACAGATCATTTTCTCATTGTTG 57.962 29.630 5.07 0.00 0.00 3.33
1792 1916 9.603921 AACAAAACAGATCATTTTCTCATTGTT 57.396 25.926 5.07 0.00 32.99 2.83
1793 1917 9.037737 CAACAAAACAGATCATTTTCTCATTGT 57.962 29.630 5.07 0.00 30.30 2.71
1794 1918 8.492748 CCAACAAAACAGATCATTTTCTCATTG 58.507 33.333 5.07 7.42 0.00 2.82
1795 1919 7.172019 GCCAACAAAACAGATCATTTTCTCATT 59.828 33.333 5.07 0.00 0.00 2.57
1796 1920 6.647895 GCCAACAAAACAGATCATTTTCTCAT 59.352 34.615 5.07 0.00 0.00 2.90
1797 1921 5.984926 GCCAACAAAACAGATCATTTTCTCA 59.015 36.000 5.07 0.00 0.00 3.27
1798 1922 6.218746 AGCCAACAAAACAGATCATTTTCTC 58.781 36.000 5.07 0.00 0.00 2.87
1799 1923 6.165700 AGCCAACAAAACAGATCATTTTCT 57.834 33.333 5.07 0.00 0.00 2.52
1800 1924 7.945033 TTAGCCAACAAAACAGATCATTTTC 57.055 32.000 5.07 0.00 0.00 2.29
1801 1925 8.907222 AATTAGCCAACAAAACAGATCATTTT 57.093 26.923 0.00 0.00 0.00 1.82
1803 1927 9.590451 CATAATTAGCCAACAAAACAGATCATT 57.410 29.630 0.00 0.00 0.00 2.57
1804 1928 7.707893 GCATAATTAGCCAACAAAACAGATCAT 59.292 33.333 0.00 0.00 0.00 2.45
1805 1929 7.035004 GCATAATTAGCCAACAAAACAGATCA 58.965 34.615 0.00 0.00 0.00 2.92
1806 1930 7.035004 TGCATAATTAGCCAACAAAACAGATC 58.965 34.615 0.00 0.00 0.00 2.75
1807 1931 6.934056 TGCATAATTAGCCAACAAAACAGAT 58.066 32.000 0.00 0.00 0.00 2.90
1808 1932 6.338214 TGCATAATTAGCCAACAAAACAGA 57.662 33.333 0.00 0.00 0.00 3.41
1809 1933 6.812656 TCATGCATAATTAGCCAACAAAACAG 59.187 34.615 0.00 0.00 0.00 3.16
1810 1934 6.589523 GTCATGCATAATTAGCCAACAAAACA 59.410 34.615 0.00 0.00 0.00 2.83
1811 1935 6.813152 AGTCATGCATAATTAGCCAACAAAAC 59.187 34.615 0.00 0.00 0.00 2.43
1812 1936 6.812656 CAGTCATGCATAATTAGCCAACAAAA 59.187 34.615 0.00 0.00 0.00 2.44
1813 1937 6.331845 CAGTCATGCATAATTAGCCAACAAA 58.668 36.000 0.00 0.00 0.00 2.83
1814 1938 5.893687 CAGTCATGCATAATTAGCCAACAA 58.106 37.500 0.00 0.00 0.00 2.83
1815 1939 5.503662 CAGTCATGCATAATTAGCCAACA 57.496 39.130 0.00 0.00 0.00 3.33
1830 1954 2.079158 CCACAAGTACCAGCAGTCATG 58.921 52.381 0.00 0.00 0.00 3.07
1831 1955 1.699634 ACCACAAGTACCAGCAGTCAT 59.300 47.619 0.00 0.00 0.00 3.06
1832 1956 1.128200 ACCACAAGTACCAGCAGTCA 58.872 50.000 0.00 0.00 0.00 3.41
1833 1957 1.070134 TCACCACAAGTACCAGCAGTC 59.930 52.381 0.00 0.00 0.00 3.51
1834 1958 1.128200 TCACCACAAGTACCAGCAGT 58.872 50.000 0.00 0.00 0.00 4.40
1835 1959 2.079158 CATCACCACAAGTACCAGCAG 58.921 52.381 0.00 0.00 0.00 4.24
1836 1960 1.696884 TCATCACCACAAGTACCAGCA 59.303 47.619 0.00 0.00 0.00 4.41
1837 1961 2.472695 TCATCACCACAAGTACCAGC 57.527 50.000 0.00 0.00 0.00 4.85
1838 1962 4.186926 CTCATCATCACCACAAGTACCAG 58.813 47.826 0.00 0.00 0.00 4.00
1839 1963 3.619733 GCTCATCATCACCACAAGTACCA 60.620 47.826 0.00 0.00 0.00 3.25
1840 1964 2.939103 GCTCATCATCACCACAAGTACC 59.061 50.000 0.00 0.00 0.00 3.34
1841 1965 3.620374 CAGCTCATCATCACCACAAGTAC 59.380 47.826 0.00 0.00 0.00 2.73
1842 1966 3.515104 TCAGCTCATCATCACCACAAGTA 59.485 43.478 0.00 0.00 0.00 2.24
1843 1967 2.303890 TCAGCTCATCATCACCACAAGT 59.696 45.455 0.00 0.00 0.00 3.16
1844 1968 2.981898 TCAGCTCATCATCACCACAAG 58.018 47.619 0.00 0.00 0.00 3.16
1845 1969 3.275999 CATCAGCTCATCATCACCACAA 58.724 45.455 0.00 0.00 0.00 3.33
1846 1970 2.237893 ACATCAGCTCATCATCACCACA 59.762 45.455 0.00 0.00 0.00 4.17
1847 1971 2.612672 CACATCAGCTCATCATCACCAC 59.387 50.000 0.00 0.00 0.00 4.16
1848 1972 2.237893 ACACATCAGCTCATCATCACCA 59.762 45.455 0.00 0.00 0.00 4.17
1849 1973 2.915349 ACACATCAGCTCATCATCACC 58.085 47.619 0.00 0.00 0.00 4.02
1850 1974 4.026228 CGTAACACATCAGCTCATCATCAC 60.026 45.833 0.00 0.00 0.00 3.06
1851 1975 4.114794 CGTAACACATCAGCTCATCATCA 58.885 43.478 0.00 0.00 0.00 3.07
1852 1976 4.363138 TCGTAACACATCAGCTCATCATC 58.637 43.478 0.00 0.00 0.00 2.92
1853 1977 4.098501 TCTCGTAACACATCAGCTCATCAT 59.901 41.667 0.00 0.00 0.00 2.45
1854 1978 3.443681 TCTCGTAACACATCAGCTCATCA 59.556 43.478 0.00 0.00 0.00 3.07
1855 1979 4.033990 TCTCGTAACACATCAGCTCATC 57.966 45.455 0.00 0.00 0.00 2.92
1856 1980 4.366586 CATCTCGTAACACATCAGCTCAT 58.633 43.478 0.00 0.00 0.00 2.90
1857 1981 3.429410 CCATCTCGTAACACATCAGCTCA 60.429 47.826 0.00 0.00 0.00 4.26
1858 1982 3.119291 CCATCTCGTAACACATCAGCTC 58.881 50.000 0.00 0.00 0.00 4.09
1859 1983 2.760650 TCCATCTCGTAACACATCAGCT 59.239 45.455 0.00 0.00 0.00 4.24
1860 1984 3.165058 TCCATCTCGTAACACATCAGC 57.835 47.619 0.00 0.00 0.00 4.26
1861 1985 6.584184 GTGATATCCATCTCGTAACACATCAG 59.416 42.308 0.00 0.00 31.93 2.90
1862 1986 6.040391 TGTGATATCCATCTCGTAACACATCA 59.960 38.462 0.00 0.00 29.76 3.07
1863 1987 6.447162 TGTGATATCCATCTCGTAACACATC 58.553 40.000 0.00 0.00 29.76 3.06
1864 1988 6.405278 TGTGATATCCATCTCGTAACACAT 57.595 37.500 0.00 0.00 29.76 3.21
1865 1989 5.845391 TGTGATATCCATCTCGTAACACA 57.155 39.130 0.00 0.00 31.48 3.72
1866 1990 6.447162 TCATGTGATATCCATCTCGTAACAC 58.553 40.000 0.00 0.00 31.93 3.32
1867 1991 6.648879 TCATGTGATATCCATCTCGTAACA 57.351 37.500 0.00 0.00 31.93 2.41
1868 1992 7.946655 TTTCATGTGATATCCATCTCGTAAC 57.053 36.000 0.00 0.00 31.93 2.50
1869 1993 8.956533 TTTTTCATGTGATATCCATCTCGTAA 57.043 30.769 0.00 0.00 31.93 3.18
1870 1994 8.992073 CATTTTTCATGTGATATCCATCTCGTA 58.008 33.333 0.00 0.00 31.93 3.43
1871 1995 7.500227 ACATTTTTCATGTGATATCCATCTCGT 59.500 33.333 0.00 0.00 31.93 4.18
1872 1996 7.868775 ACATTTTTCATGTGATATCCATCTCG 58.131 34.615 0.00 0.00 31.93 4.04
1901 2025 9.119418 TCATTTTCTCATTGTTGAAGAGTAACA 57.881 29.630 0.00 0.00 36.34 2.41
1904 2028 9.730705 AGATCATTTTCTCATTGTTGAAGAGTA 57.269 29.630 0.00 0.00 0.00 2.59
1905 2029 8.512956 CAGATCATTTTCTCATTGTTGAAGAGT 58.487 33.333 0.00 0.00 0.00 3.24
1906 2030 8.512956 ACAGATCATTTTCTCATTGTTGAAGAG 58.487 33.333 0.00 0.00 0.00 2.85
1907 2031 8.400184 ACAGATCATTTTCTCATTGTTGAAGA 57.600 30.769 0.00 0.00 0.00 2.87
2084 2255 9.433153 TGAATGCAAAATTAATGCTGATTTGTA 57.567 25.926 14.91 6.97 44.14 2.41
2086 2257 9.781834 AATGAATGCAAAATTAATGCTGATTTG 57.218 25.926 14.91 5.54 44.14 2.32
2088 2259 8.952278 ACAATGAATGCAAAATTAATGCTGATT 58.048 25.926 14.91 8.73 44.14 2.57
2089 2260 8.500753 ACAATGAATGCAAAATTAATGCTGAT 57.499 26.923 14.91 1.80 44.14 2.90
2090 2261 7.201453 CGACAATGAATGCAAAATTAATGCTGA 60.201 33.333 14.91 0.00 44.14 4.26
2091 2262 6.897663 CGACAATGAATGCAAAATTAATGCTG 59.102 34.615 14.91 7.94 44.14 4.41
2092 2263 6.591062 ACGACAATGAATGCAAAATTAATGCT 59.409 30.769 14.91 0.00 44.14 3.79
2093 2264 6.764094 ACGACAATGAATGCAAAATTAATGC 58.236 32.000 8.75 8.75 44.08 3.56
2094 2265 8.433893 TGAACGACAATGAATGCAAAATTAATG 58.566 29.630 0.00 0.00 0.00 1.90
2095 2266 8.531622 TGAACGACAATGAATGCAAAATTAAT 57.468 26.923 0.00 0.00 0.00 1.40
2096 2267 7.936950 TGAACGACAATGAATGCAAAATTAA 57.063 28.000 0.00 0.00 0.00 1.40
2097 2268 8.531622 AATGAACGACAATGAATGCAAAATTA 57.468 26.923 0.00 0.00 0.00 1.40
2098 2269 7.424227 AATGAACGACAATGAATGCAAAATT 57.576 28.000 0.00 0.00 0.00 1.82
2099 2270 7.171167 TCAAATGAACGACAATGAATGCAAAAT 59.829 29.630 0.00 0.00 0.00 1.82
2100 2271 6.478016 TCAAATGAACGACAATGAATGCAAAA 59.522 30.769 0.00 0.00 0.00 2.44
2101 2272 5.981915 TCAAATGAACGACAATGAATGCAAA 59.018 32.000 0.00 0.00 0.00 3.68
2102 2273 5.527033 TCAAATGAACGACAATGAATGCAA 58.473 33.333 0.00 0.00 0.00 4.08
2103 2274 5.118642 TCAAATGAACGACAATGAATGCA 57.881 34.783 0.00 0.00 0.00 3.96
2104 2275 5.801444 TCATCAAATGAACGACAATGAATGC 59.199 36.000 0.00 0.00 36.11 3.56
2105 2276 7.245604 TCTCATCAAATGAACGACAATGAATG 58.754 34.615 0.00 1.26 39.11 2.67
2106 2277 7.381766 TCTCATCAAATGAACGACAATGAAT 57.618 32.000 0.00 0.00 39.11 2.57
2107 2278 6.799926 TCTCATCAAATGAACGACAATGAA 57.200 33.333 0.00 0.00 39.11 2.57
2108 2279 6.990341 ATCTCATCAAATGAACGACAATGA 57.010 33.333 0.00 0.00 39.11 2.57
2111 2282 9.599866 AGTATTATCTCATCAAATGAACGACAA 57.400 29.630 0.00 0.00 39.11 3.18
2125 2296 9.920133 CACAATGTAGCAGTAGTATTATCTCAT 57.080 33.333 0.00 0.00 0.00 2.90
2126 2297 8.914011 ACACAATGTAGCAGTAGTATTATCTCA 58.086 33.333 0.00 0.00 0.00 3.27
2131 2302 9.976511 GGATTACACAATGTAGCAGTAGTATTA 57.023 33.333 0.00 0.00 33.92 0.98
2132 2303 7.931948 GGGATTACACAATGTAGCAGTAGTATT 59.068 37.037 0.00 0.00 33.92 1.89
2133 2304 7.070696 TGGGATTACACAATGTAGCAGTAGTAT 59.929 37.037 0.00 0.00 33.92 2.12


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

AutoCloner maintained by Alex Coulton.