Multiple sequence alignment - TraesCS5D01G185200

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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 TraesCS5D01G185200 chr5D 100.000 2525 0 0 1 2525 287439152 287441676 0.000000e+00 4663.0
1 TraesCS5D01G185200 chr5D 93.220 118 7 1 1761 1877 118840568 118840451 3.340000e-39 172.0
2 TraesCS5D01G185200 chr5B 92.857 1806 67 24 1 1754 326570370 326572165 0.000000e+00 2564.0
3 TraesCS5D01G185200 chr5B 88.746 622 53 12 1911 2525 326572186 326572797 0.000000e+00 745.0
4 TraesCS5D01G185200 chr5B 90.400 125 11 1 1754 1877 234303465 234303341 2.010000e-36 163.0
5 TraesCS5D01G185200 chr5A 87.847 1728 97 43 83 1754 379351663 379353333 0.000000e+00 1923.0
6 TraesCS5D01G185200 chr5A 92.824 655 33 8 1874 2525 379353335 379353978 0.000000e+00 937.0
7 TraesCS5D01G185200 chr7B 91.736 121 9 1 1759 1878 81424987 81425107 1.550000e-37 167.0
8 TraesCS5D01G185200 chr6A 92.373 118 8 1 1761 1877 147303660 147303777 1.550000e-37 167.0
9 TraesCS5D01G185200 chr2A 91.736 121 9 1 1758 1877 78845692 78845572 1.550000e-37 167.0
10 TraesCS5D01G185200 chr4B 90.476 126 10 2 1761 1885 392368023 392367899 5.590000e-37 165.0
11 TraesCS5D01G185200 chr2D 91.057 123 9 2 1757 1877 12692235 12692357 5.590000e-37 165.0
12 TraesCS5D01G185200 chr1D 88.636 132 13 2 1747 1877 240590492 240590622 2.600000e-35 159.0
13 TraesCS5D01G185200 chr3B 88.550 131 13 2 1748 1877 829966113 829966242 9.350000e-35 158.0
14 TraesCS5D01G185200 chrUn 94.737 76 3 1 898 973 103504829 103504903 1.590000e-22 117.0
15 TraesCS5D01G185200 chr4D 100.000 28 0 0 17 44 496030974 496030947 5.000000e-03 52.8


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 TraesCS5D01G185200 chr5D 287439152 287441676 2524 False 4663.0 4663 100.0000 1 2525 1 chr5D.!!$F1 2524
1 TraesCS5D01G185200 chr5B 326570370 326572797 2427 False 1654.5 2564 90.8015 1 2525 2 chr5B.!!$F1 2524
2 TraesCS5D01G185200 chr5A 379351663 379353978 2315 False 1430.0 1923 90.3355 83 2525 2 chr5A.!!$F1 2442

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
967 999 0.673956 CAGCAGCAGCATCAGTCAGT 60.674 55.0 3.17 0.0 45.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1924 0.601841 TCGTCCGAAAAGCTTGTCCC 60.602 55.0 11.14 0.0 0.0 4.46 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
27 28 1.636988 GATTAGTTACGTGCGGCTGT 58.363 50.000 0.00 2.43 0.00 4.40
58 59 6.985117 TCTTAGAGCAGTGCAATTTGAAATT 58.015 32.000 19.20 0.00 0.00 1.82
266 267 5.880332 AGAATTAGCCTGCGATTGTTCTTAA 59.120 36.000 0.00 0.00 0.00 1.85
277 280 4.858692 CGATTGTTCTTAAAGTTGGCCATG 59.141 41.667 6.09 0.00 0.00 3.66
330 338 4.082408 GCCTAGAAATACCGGCAAAAACTT 60.082 41.667 0.00 0.00 42.06 2.66
349 357 5.104259 ACTTTGGTCTGAAGTTGTCTCTT 57.896 39.130 0.00 0.00 33.76 2.85
453 467 6.554419 TCGCTCACAAAATTTCAGGAATATG 58.446 36.000 0.00 0.00 0.00 1.78
544 559 6.547141 TGTTCTCCAAAACAATCTTCAGATGT 59.453 34.615 0.00 0.00 36.25 3.06
649 675 3.995199 TGGCCGATAAATCAGTCTCATC 58.005 45.455 0.00 0.00 0.00 2.92
665 691 6.318144 CAGTCTCATCTCCTGCAAAAATATGT 59.682 38.462 0.00 0.00 0.00 2.29
674 700 2.496871 TGCAAAAATATGTCCCTGCAGG 59.503 45.455 26.87 26.87 35.02 4.85
704 730 4.595762 AGCTTGTTTCAATCACTGCAAT 57.404 36.364 0.00 0.00 0.00 3.56
800 827 6.261826 AGCTCAAGCATGATCAACCTATAAAC 59.738 38.462 0.00 0.00 45.16 2.01
886 915 4.873129 CCCCGGATCAGCGTCACG 62.873 72.222 0.73 0.00 0.00 4.35
957 989 2.050351 CAACACAGCAGCAGCAGC 60.050 61.111 3.17 0.46 45.49 5.25
958 990 2.517638 AACACAGCAGCAGCAGCA 60.518 55.556 12.92 0.00 45.49 4.41
959 991 1.901948 AACACAGCAGCAGCAGCAT 60.902 52.632 12.92 0.00 45.49 3.79
960 992 1.863662 AACACAGCAGCAGCAGCATC 61.864 55.000 12.92 0.00 45.49 3.91
961 993 2.033602 ACAGCAGCAGCAGCATCA 59.966 55.556 12.92 0.00 45.49 3.07
962 994 2.041115 ACAGCAGCAGCAGCATCAG 61.041 57.895 12.92 1.59 45.49 2.90
963 995 2.041115 CAGCAGCAGCAGCATCAGT 61.041 57.895 12.92 0.00 45.49 3.41
965 997 2.038837 GCAGCAGCAGCATCAGTCA 61.039 57.895 4.63 0.00 45.49 3.41
966 998 1.983196 GCAGCAGCAGCATCAGTCAG 61.983 60.000 4.63 0.00 45.49 3.51
967 999 0.673956 CAGCAGCAGCATCAGTCAGT 60.674 55.000 3.17 0.00 45.49 3.41
968 1000 0.900421 AGCAGCAGCATCAGTCAGTA 59.100 50.000 3.17 0.00 45.49 2.74
969 1001 1.277273 AGCAGCAGCATCAGTCAGTAA 59.723 47.619 3.17 0.00 45.49 2.24
975 1012 1.905215 AGCATCAGTCAGTAACCAGCT 59.095 47.619 0.00 0.00 0.00 4.24
1021 1058 2.964389 GGAGCAAGAGATCGCCGC 60.964 66.667 0.85 0.85 0.00 6.53
1045 1082 4.752879 CGGCCGTGGTGGTGGTAG 62.753 72.222 19.50 0.00 41.21 3.18
1047 1084 2.358247 GCCGTGGTGGTGGTAGTG 60.358 66.667 0.00 0.00 41.21 2.74
1048 1085 2.345991 CCGTGGTGGTGGTAGTGG 59.654 66.667 0.00 0.00 0.00 4.00
1050 1087 1.301401 CGTGGTGGTGGTAGTGGTG 60.301 63.158 0.00 0.00 0.00 4.17
1203 1240 2.244651 ACTGTTGCTCAACGCGTCC 61.245 57.895 14.44 1.82 43.94 4.79
1532 1599 2.181021 CGTCTACTGACCACGCCC 59.819 66.667 0.00 0.00 39.94 6.13
1555 1622 2.359975 CGCCCCTTCCCACAGTTC 60.360 66.667 0.00 0.00 0.00 3.01
1565 1632 4.218417 CCTTCCCACAGTTCCATTTTACTG 59.782 45.833 0.00 0.00 45.61 2.74
1613 1681 6.494835 AGCAATTTTCCATTTTCTGGTCTAGT 59.505 34.615 0.00 0.00 46.08 2.57
1614 1682 7.015584 AGCAATTTTCCATTTTCTGGTCTAGTT 59.984 33.333 0.00 0.00 46.08 2.24
1661 1729 8.839310 ACATTATATAGTTCTGTTCTGGATGC 57.161 34.615 0.00 0.00 0.00 3.91
1739 1812 1.197721 GAACTTGGCATTCTCCACACG 59.802 52.381 0.00 0.00 35.50 4.49
1760 1835 7.303634 CACGCTGGTGTAATTTCTAAATAGT 57.696 36.000 0.00 0.00 39.38 2.12
1761 1836 8.415192 CACGCTGGTGTAATTTCTAAATAGTA 57.585 34.615 0.00 0.00 39.38 1.82
1762 1837 8.325997 CACGCTGGTGTAATTTCTAAATAGTAC 58.674 37.037 0.00 0.00 39.38 2.73
1763 1838 8.255905 ACGCTGGTGTAATTTCTAAATAGTACT 58.744 33.333 0.00 0.00 0.00 2.73
1764 1839 9.095065 CGCTGGTGTAATTTCTAAATAGTACTT 57.905 33.333 0.00 0.00 0.00 2.24
1773 1848 6.705863 TTCTAAATAGTACTTCCTCCGTCC 57.294 41.667 0.00 0.00 0.00 4.79
1774 1849 4.818546 TCTAAATAGTACTTCCTCCGTCCG 59.181 45.833 0.00 0.00 0.00 4.79
1775 1850 3.287867 AATAGTACTTCCTCCGTCCGA 57.712 47.619 0.00 0.00 0.00 4.55
1776 1851 2.787473 TAGTACTTCCTCCGTCCGAA 57.213 50.000 0.00 0.00 0.00 4.30
1777 1852 1.915141 AGTACTTCCTCCGTCCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
1778 1853 2.242043 AGTACTTCCTCCGTCCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
1779 1854 2.629617 AGTACTTCCTCCGTCCGAAAAA 59.370 45.455 0.00 0.00 0.00 1.94
1797 1872 3.801114 AAAACTTGTCCCAAGCTTGTC 57.199 42.857 24.35 14.49 0.00 3.18
1798 1873 1.692411 AACTTGTCCCAAGCTTGTCC 58.308 50.000 24.35 12.15 0.00 4.02
1799 1874 0.550914 ACTTGTCCCAAGCTTGTCCA 59.449 50.000 24.35 14.48 0.00 4.02
1800 1875 1.145738 ACTTGTCCCAAGCTTGTCCAT 59.854 47.619 24.35 2.27 0.00 3.41
1801 1876 1.815003 CTTGTCCCAAGCTTGTCCATC 59.185 52.381 24.35 10.65 0.00 3.51
1802 1877 0.770499 TGTCCCAAGCTTGTCCATCA 59.230 50.000 24.35 12.85 0.00 3.07
1803 1878 1.144708 TGTCCCAAGCTTGTCCATCAA 59.855 47.619 24.35 1.41 34.61 2.57
1804 1879 2.238521 GTCCCAAGCTTGTCCATCAAA 58.761 47.619 24.35 0.00 35.48 2.69
1805 1880 2.827921 GTCCCAAGCTTGTCCATCAAAT 59.172 45.455 24.35 0.00 35.48 2.32
1806 1881 2.827322 TCCCAAGCTTGTCCATCAAATG 59.173 45.455 24.35 5.47 35.48 2.32
1821 1896 5.898174 CATCAAATGGATGTATGTTGCACT 58.102 37.500 0.00 0.00 46.81 4.40
1822 1897 7.030075 CATCAAATGGATGTATGTTGCACTA 57.970 36.000 0.00 0.00 46.81 2.74
1823 1898 7.482474 CATCAAATGGATGTATGTTGCACTAA 58.518 34.615 0.00 0.00 46.81 2.24
1824 1899 6.851609 TCAAATGGATGTATGTTGCACTAAC 58.148 36.000 0.00 0.00 39.80 2.34
1825 1900 6.658816 TCAAATGGATGTATGTTGCACTAACT 59.341 34.615 0.00 0.00 40.05 2.24
1826 1901 7.176515 TCAAATGGATGTATGTTGCACTAACTT 59.823 33.333 0.00 0.00 40.05 2.66
1827 1902 5.878332 TGGATGTATGTTGCACTAACTTG 57.122 39.130 0.00 0.00 40.05 3.16
1828 1903 4.699735 TGGATGTATGTTGCACTAACTTGG 59.300 41.667 0.00 0.00 40.05 3.61
1829 1904 4.941263 GGATGTATGTTGCACTAACTTGGA 59.059 41.667 0.00 0.00 40.05 3.53
1830 1905 5.065218 GGATGTATGTTGCACTAACTTGGAG 59.935 44.000 0.00 0.00 40.05 3.86
1831 1906 3.751175 TGTATGTTGCACTAACTTGGAGC 59.249 43.478 0.00 0.00 40.05 4.70
1832 1907 2.638480 TGTTGCACTAACTTGGAGCT 57.362 45.000 0.00 0.00 40.05 4.09
1833 1908 3.762407 TGTTGCACTAACTTGGAGCTA 57.238 42.857 0.00 0.00 40.05 3.32
1834 1909 3.664107 TGTTGCACTAACTTGGAGCTAG 58.336 45.455 0.00 0.00 40.05 3.42
1835 1910 3.323691 TGTTGCACTAACTTGGAGCTAGA 59.676 43.478 0.00 0.00 40.05 2.43
1836 1911 4.020218 TGTTGCACTAACTTGGAGCTAGAT 60.020 41.667 0.00 0.00 40.05 1.98
1837 1912 5.186992 TGTTGCACTAACTTGGAGCTAGATA 59.813 40.000 0.00 0.00 40.05 1.98
1838 1913 5.263968 TGCACTAACTTGGAGCTAGATAC 57.736 43.478 0.00 0.00 0.00 2.24
1839 1914 4.709886 TGCACTAACTTGGAGCTAGATACA 59.290 41.667 0.00 0.00 0.00 2.29
1840 1915 5.363868 TGCACTAACTTGGAGCTAGATACAT 59.636 40.000 0.00 0.00 0.00 2.29
1841 1916 5.923684 GCACTAACTTGGAGCTAGATACATC 59.076 44.000 0.00 0.00 0.00 3.06
1842 1917 6.239176 GCACTAACTTGGAGCTAGATACATCT 60.239 42.308 0.00 0.00 40.86 2.90
1843 1918 7.040340 GCACTAACTTGGAGCTAGATACATCTA 60.040 40.741 0.00 0.00 38.32 1.98
1844 1919 9.019656 CACTAACTTGGAGCTAGATACATCTAT 57.980 37.037 0.00 0.00 38.60 1.98
1845 1920 9.594936 ACTAACTTGGAGCTAGATACATCTATT 57.405 33.333 0.00 0.00 38.60 1.73
1848 1923 8.484214 ACTTGGAGCTAGATACATCTATTTGA 57.516 34.615 0.00 0.00 38.60 2.69
1849 1924 8.584157 ACTTGGAGCTAGATACATCTATTTGAG 58.416 37.037 0.00 0.00 38.60 3.02
1850 1925 7.473735 TGGAGCTAGATACATCTATTTGAGG 57.526 40.000 0.00 0.00 38.60 3.86
1851 1926 6.438741 TGGAGCTAGATACATCTATTTGAGGG 59.561 42.308 0.00 0.00 38.60 4.30
1852 1927 6.665680 GGAGCTAGATACATCTATTTGAGGGA 59.334 42.308 0.00 0.00 38.60 4.20
1853 1928 7.363443 GGAGCTAGATACATCTATTTGAGGGAC 60.363 44.444 0.00 0.00 38.60 4.46
1854 1929 7.013220 AGCTAGATACATCTATTTGAGGGACA 58.987 38.462 0.00 0.00 38.60 4.02
1855 1930 7.510685 AGCTAGATACATCTATTTGAGGGACAA 59.489 37.037 0.00 0.00 38.60 3.18
1856 1931 7.816995 GCTAGATACATCTATTTGAGGGACAAG 59.183 40.741 0.00 0.00 38.60 3.16
1857 1932 6.529220 AGATACATCTATTTGAGGGACAAGC 58.471 40.000 0.00 0.00 36.19 4.01
1858 1933 4.851639 ACATCTATTTGAGGGACAAGCT 57.148 40.909 0.00 0.00 39.77 3.74
1859 1934 5.184892 ACATCTATTTGAGGGACAAGCTT 57.815 39.130 0.00 0.00 39.77 3.74
1860 1935 5.574188 ACATCTATTTGAGGGACAAGCTTT 58.426 37.500 0.00 0.00 39.77 3.51
1861 1936 6.012745 ACATCTATTTGAGGGACAAGCTTTT 58.987 36.000 0.00 0.00 39.77 2.27
1862 1937 6.151817 ACATCTATTTGAGGGACAAGCTTTTC 59.848 38.462 3.91 3.91 39.77 2.29
1863 1938 3.923017 ATTTGAGGGACAAGCTTTTCG 57.077 42.857 6.53 0.00 39.77 3.46
1864 1939 1.604604 TTGAGGGACAAGCTTTTCGG 58.395 50.000 6.53 0.00 34.20 4.30
1865 1940 0.762418 TGAGGGACAAGCTTTTCGGA 59.238 50.000 6.53 0.00 0.00 4.55
1866 1941 1.157585 GAGGGACAAGCTTTTCGGAC 58.842 55.000 6.53 0.34 0.00 4.79
1867 1942 0.602905 AGGGACAAGCTTTTCGGACG 60.603 55.000 6.53 0.00 0.00 4.79
1868 1943 0.601841 GGGACAAGCTTTTCGGACGA 60.602 55.000 6.53 0.00 0.00 4.20
1869 1944 1.223187 GGACAAGCTTTTCGGACGAA 58.777 50.000 6.53 2.62 0.00 3.85
1870 1945 1.194772 GGACAAGCTTTTCGGACGAAG 59.805 52.381 6.53 0.00 35.38 3.79
1871 1946 2.132762 GACAAGCTTTTCGGACGAAGA 58.867 47.619 7.25 2.48 35.38 2.87
1872 1947 2.135933 ACAAGCTTTTCGGACGAAGAG 58.864 47.619 17.44 17.44 38.77 2.85
1877 1952 3.255149 AGCTTTTCGGACGAAGAGAGTAA 59.745 43.478 23.61 7.72 38.23 2.24
1891 1966 9.984190 ACGAAGAGAGTAAAAACTTATCTTTCT 57.016 29.630 0.00 0.00 30.99 2.52
1895 1970 9.713713 AGAGAGTAAAAACTTATCTTTCTGTCC 57.286 33.333 0.00 0.00 0.00 4.02
1915 1990 2.456010 CGTTTGGTTTGGCAGTACAAC 58.544 47.619 0.00 0.00 0.00 3.32
1929 2004 5.276489 GGCAGTACAACTTTTTAAAAACCGC 60.276 40.000 9.31 3.96 0.00 5.68
1937 2012 7.223193 ACAACTTTTTAAAAACCGCAGTAATCC 59.777 33.333 9.31 0.00 0.00 3.01
2042 2117 6.321848 AGTTTATAAAACCGTGGTTTCTGG 57.678 37.500 16.83 0.00 46.22 3.86
2085 2162 1.408422 CAAACGCAGCCTTAACTTGC 58.592 50.000 0.00 0.00 34.58 4.01
2086 2163 0.313987 AAACGCAGCCTTAACTTGCC 59.686 50.000 0.00 0.00 34.42 4.52
2118 2195 8.756927 TGGTATTGAAAATTTATGGCAATCTCA 58.243 29.630 0.00 8.25 32.13 3.27
2223 2301 3.238108 TCGCACAAACCAACACAAAAT 57.762 38.095 0.00 0.00 0.00 1.82
2378 2460 6.687081 AGACTGTACAATTTCCGACAAAAA 57.313 33.333 0.00 0.00 0.00 1.94
2434 2516 3.513515 ACCCTGACATCTCTCAGAAAGAC 59.486 47.826 0.00 0.00 40.28 3.01
2518 2600 5.240844 AGTCGAAACCTTCCCAATTAAGTTG 59.759 40.000 0.00 0.00 37.57 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 7.727331 AAAGCTGCAGAATCTATATGTTCTC 57.273 36.000 20.43 0.00 32.60 2.87
266 267 2.885135 TCAGATGACATGGCCAACTT 57.115 45.000 10.96 2.57 0.00 2.66
277 280 2.346847 GCATGACACGACTTCAGATGAC 59.653 50.000 0.00 0.00 0.00 3.06
330 338 4.487714 ACAAGAGACAACTTCAGACCAA 57.512 40.909 0.00 0.00 0.00 3.67
349 357 4.020839 TGTTCATCTGCATCTCTGAGAACA 60.021 41.667 12.00 11.84 37.80 3.18
399 407 1.462670 CTTCTTCAGAAAGCAGCGGTC 59.537 52.381 0.00 0.00 33.07 4.79
453 467 1.410517 TGAGTCATAGCAGCAGCCTAC 59.589 52.381 0.00 0.00 43.56 3.18
544 559 1.913778 TACACTGACGGGCTCTGTTA 58.086 50.000 0.00 0.00 0.00 2.41
649 675 3.181483 GCAGGGACATATTTTTGCAGGAG 60.181 47.826 0.00 0.00 0.00 3.69
674 700 5.406477 GTGATTGAAACAAGCTTTGAATCCC 59.594 40.000 0.00 0.00 33.19 3.85
704 730 3.869912 GCAGTGGAGGAGTTGCAGAAATA 60.870 47.826 0.00 0.00 36.59 1.40
800 827 0.609131 AGGCCGATTTGTTGGAGTGG 60.609 55.000 0.00 0.00 0.00 4.00
957 989 2.534298 CGAGCTGGTTACTGACTGATG 58.466 52.381 0.00 0.00 0.00 3.07
958 990 1.478510 CCGAGCTGGTTACTGACTGAT 59.521 52.381 0.00 0.00 0.00 2.90
959 991 0.888619 CCGAGCTGGTTACTGACTGA 59.111 55.000 0.00 0.00 0.00 3.41
960 992 0.108615 CCCGAGCTGGTTACTGACTG 60.109 60.000 0.00 0.00 35.15 3.51
961 993 0.251653 TCCCGAGCTGGTTACTGACT 60.252 55.000 0.00 0.00 35.15 3.41
962 994 0.606604 TTCCCGAGCTGGTTACTGAC 59.393 55.000 0.00 0.00 35.15 3.51
963 995 0.895530 CTTCCCGAGCTGGTTACTGA 59.104 55.000 0.00 0.00 35.15 3.41
975 1012 2.973899 GCTCTGTCTGCTTCCCGA 59.026 61.111 0.00 0.00 0.00 5.14
1004 1041 2.964389 GCGGCGATCTCTTGCTCC 60.964 66.667 12.98 0.00 31.87 4.70
1037 1074 2.146724 AGCAGCACCACTACCACCA 61.147 57.895 0.00 0.00 0.00 4.17
1042 1079 0.886490 AACAGCAGCAGCACCACTAC 60.886 55.000 3.17 0.00 45.49 2.73
1044 1081 1.895707 GAACAGCAGCAGCACCACT 60.896 57.895 3.17 0.00 45.49 4.00
1045 1082 2.641559 GAACAGCAGCAGCACCAC 59.358 61.111 3.17 0.00 45.49 4.16
1047 1084 2.959357 GACGAACAGCAGCAGCACC 61.959 63.158 3.17 0.00 45.49 5.01
1048 1085 2.553268 GACGAACAGCAGCAGCAC 59.447 61.111 3.17 0.00 45.49 4.40
1050 1087 2.358003 AGGACGAACAGCAGCAGC 60.358 61.111 0.00 0.00 42.56 5.25
1485 1552 1.880340 GAAGGAGATGTCGCAGCCG 60.880 63.158 0.00 0.00 0.00 5.52
1542 1609 4.218417 CAGTAAAATGGAACTGTGGGAAGG 59.782 45.833 0.00 0.00 0.00 3.46
1552 1619 6.432107 TGCTACGTTTTCAGTAAAATGGAAC 58.568 36.000 0.00 0.00 43.15 3.62
1555 1622 4.851558 GCTGCTACGTTTTCAGTAAAATGG 59.148 41.667 0.00 0.00 43.15 3.16
1701 1769 9.066892 GCCAAGTTCACTATTAATCATTATGGA 57.933 33.333 0.00 0.00 0.00 3.41
1754 1829 3.624777 TCGGACGGAGGAAGTACTATTT 58.375 45.455 0.00 0.00 0.00 1.40
1755 1830 3.287867 TCGGACGGAGGAAGTACTATT 57.712 47.619 0.00 0.00 0.00 1.73
1756 1831 3.287867 TTCGGACGGAGGAAGTACTAT 57.712 47.619 0.00 0.00 0.00 2.12
1757 1832 2.787473 TTCGGACGGAGGAAGTACTA 57.213 50.000 0.00 0.00 0.00 1.82
1758 1833 1.915141 TTTCGGACGGAGGAAGTACT 58.085 50.000 0.00 0.00 0.00 2.73
1759 1834 2.730550 TTTTCGGACGGAGGAAGTAC 57.269 50.000 0.00 0.00 0.00 2.73
1780 1855 6.762480 TTGATGGACAAGCTTGGGACAAGT 62.762 45.833 29.18 11.32 37.48 3.16
1781 1856 4.312039 TTGATGGACAAGCTTGGGACAAG 61.312 47.826 29.18 3.71 37.48 3.16
1782 1857 2.424091 TTGATGGACAAGCTTGGGACAA 60.424 45.455 29.18 21.59 37.48 3.18
1783 1858 0.770499 TGATGGACAAGCTTGGGACA 59.230 50.000 29.18 23.01 0.00 4.02
1784 1859 1.909700 TTGATGGACAAGCTTGGGAC 58.090 50.000 29.18 18.54 34.20 4.46
1785 1860 2.673775 TTTGATGGACAAGCTTGGGA 57.326 45.000 29.18 13.39 39.77 4.37
1786 1861 3.241067 CATTTGATGGACAAGCTTGGG 57.759 47.619 29.18 6.83 39.77 4.12
1797 1872 5.045215 GTGCAACATACATCCATTTGATGG 58.955 41.667 7.06 0.41 45.98 3.51
1799 1874 7.340232 AGTTAGTGCAACATACATCCATTTGAT 59.660 33.333 0.00 0.00 41.43 2.57
1800 1875 6.658816 AGTTAGTGCAACATACATCCATTTGA 59.341 34.615 0.00 0.00 41.43 2.69
1801 1876 6.855836 AGTTAGTGCAACATACATCCATTTG 58.144 36.000 0.00 0.00 41.43 2.32
1802 1877 7.315142 CAAGTTAGTGCAACATACATCCATTT 58.685 34.615 0.00 0.00 41.43 2.32
1803 1878 6.127647 CCAAGTTAGTGCAACATACATCCATT 60.128 38.462 0.00 0.00 41.43 3.16
1804 1879 5.357878 CCAAGTTAGTGCAACATACATCCAT 59.642 40.000 0.00 0.00 41.43 3.41
1805 1880 4.699735 CCAAGTTAGTGCAACATACATCCA 59.300 41.667 0.00 0.00 41.43 3.41
1806 1881 4.941263 TCCAAGTTAGTGCAACATACATCC 59.059 41.667 0.00 0.00 41.43 3.51
1807 1882 5.447818 GCTCCAAGTTAGTGCAACATACATC 60.448 44.000 0.00 0.00 41.43 3.06
1808 1883 4.396166 GCTCCAAGTTAGTGCAACATACAT 59.604 41.667 0.00 0.00 41.43 2.29
1809 1884 3.751175 GCTCCAAGTTAGTGCAACATACA 59.249 43.478 0.00 0.00 41.43 2.29
1810 1885 4.003648 AGCTCCAAGTTAGTGCAACATAC 58.996 43.478 0.00 0.00 41.43 2.39
1811 1886 4.286297 AGCTCCAAGTTAGTGCAACATA 57.714 40.909 0.00 0.00 41.43 2.29
1812 1887 3.146104 AGCTCCAAGTTAGTGCAACAT 57.854 42.857 0.00 0.00 41.43 2.71
1813 1888 2.638480 AGCTCCAAGTTAGTGCAACA 57.362 45.000 0.00 0.00 41.43 3.33
1814 1889 3.926616 TCTAGCTCCAAGTTAGTGCAAC 58.073 45.455 0.00 0.00 37.41 4.17
1815 1890 4.826274 ATCTAGCTCCAAGTTAGTGCAA 57.174 40.909 0.00 0.00 31.87 4.08
1816 1891 4.709886 TGTATCTAGCTCCAAGTTAGTGCA 59.290 41.667 0.00 0.00 31.87 4.57
1817 1892 5.263968 TGTATCTAGCTCCAAGTTAGTGC 57.736 43.478 0.00 0.00 31.87 4.40
1818 1893 7.283625 AGATGTATCTAGCTCCAAGTTAGTG 57.716 40.000 0.00 0.00 34.85 2.74
1819 1894 9.594936 AATAGATGTATCTAGCTCCAAGTTAGT 57.405 33.333 7.57 0.00 42.20 2.24
1822 1897 8.928448 TCAAATAGATGTATCTAGCTCCAAGTT 58.072 33.333 7.57 0.00 42.20 2.66
1823 1898 8.484214 TCAAATAGATGTATCTAGCTCCAAGT 57.516 34.615 7.57 0.00 42.20 3.16
1824 1899 8.034215 CCTCAAATAGATGTATCTAGCTCCAAG 58.966 40.741 7.57 0.00 42.20 3.61
1825 1900 7.038729 CCCTCAAATAGATGTATCTAGCTCCAA 60.039 40.741 7.57 0.00 42.20 3.53
1826 1901 6.438741 CCCTCAAATAGATGTATCTAGCTCCA 59.561 42.308 7.57 0.00 42.20 3.86
1827 1902 6.665680 TCCCTCAAATAGATGTATCTAGCTCC 59.334 42.308 7.57 0.00 42.20 4.70
1828 1903 7.177568 TGTCCCTCAAATAGATGTATCTAGCTC 59.822 40.741 7.57 0.00 42.20 4.09
1829 1904 7.013220 TGTCCCTCAAATAGATGTATCTAGCT 58.987 38.462 7.57 0.00 42.20 3.32
1830 1905 7.233389 TGTCCCTCAAATAGATGTATCTAGC 57.767 40.000 7.57 0.00 42.20 3.42
1831 1906 7.816995 GCTTGTCCCTCAAATAGATGTATCTAG 59.183 40.741 7.57 0.00 36.19 2.43
1832 1907 7.510685 AGCTTGTCCCTCAAATAGATGTATCTA 59.489 37.037 4.22 4.22 36.64 1.98
1833 1908 6.328672 AGCTTGTCCCTCAAATAGATGTATCT 59.671 38.462 0.00 0.00 36.97 1.98
1834 1909 6.529220 AGCTTGTCCCTCAAATAGATGTATC 58.471 40.000 0.00 0.00 35.48 2.24
1835 1910 6.506538 AGCTTGTCCCTCAAATAGATGTAT 57.493 37.500 0.00 0.00 35.48 2.29
1836 1911 5.957771 AGCTTGTCCCTCAAATAGATGTA 57.042 39.130 0.00 0.00 35.48 2.29
1837 1912 4.851639 AGCTTGTCCCTCAAATAGATGT 57.148 40.909 0.00 0.00 35.48 3.06
1838 1913 6.521151 AAAAGCTTGTCCCTCAAATAGATG 57.479 37.500 0.00 0.00 35.48 2.90
1839 1914 5.355350 CGAAAAGCTTGTCCCTCAAATAGAT 59.645 40.000 11.14 0.00 35.48 1.98
1840 1915 4.695455 CGAAAAGCTTGTCCCTCAAATAGA 59.305 41.667 11.14 0.00 35.48 1.98
1841 1916 4.142600 CCGAAAAGCTTGTCCCTCAAATAG 60.143 45.833 11.14 0.00 35.48 1.73
1842 1917 3.756434 CCGAAAAGCTTGTCCCTCAAATA 59.244 43.478 11.14 0.00 35.48 1.40
1843 1918 2.558359 CCGAAAAGCTTGTCCCTCAAAT 59.442 45.455 11.14 0.00 35.48 2.32
1844 1919 1.953686 CCGAAAAGCTTGTCCCTCAAA 59.046 47.619 11.14 0.00 35.48 2.69
1845 1920 1.142060 TCCGAAAAGCTTGTCCCTCAA 59.858 47.619 11.14 0.00 34.61 3.02
1846 1921 0.762418 TCCGAAAAGCTTGTCCCTCA 59.238 50.000 11.14 0.00 0.00 3.86
1847 1922 1.157585 GTCCGAAAAGCTTGTCCCTC 58.842 55.000 11.14 0.00 0.00 4.30
1848 1923 0.602905 CGTCCGAAAAGCTTGTCCCT 60.603 55.000 11.14 0.00 0.00 4.20
1849 1924 0.601841 TCGTCCGAAAAGCTTGTCCC 60.602 55.000 11.14 0.00 0.00 4.46
1850 1925 1.194772 CTTCGTCCGAAAAGCTTGTCC 59.805 52.381 11.14 0.00 33.34 4.02
1851 1926 2.132762 TCTTCGTCCGAAAAGCTTGTC 58.867 47.619 6.56 6.56 33.34 3.18
1852 1927 2.135933 CTCTTCGTCCGAAAAGCTTGT 58.864 47.619 0.00 0.00 33.34 3.16
1853 1928 2.404215 TCTCTTCGTCCGAAAAGCTTG 58.596 47.619 0.00 0.00 33.34 4.01
1854 1929 2.036089 ACTCTCTTCGTCCGAAAAGCTT 59.964 45.455 3.52 0.00 33.34 3.74
1855 1930 1.614413 ACTCTCTTCGTCCGAAAAGCT 59.386 47.619 3.52 0.00 33.34 3.74
1856 1931 2.067414 ACTCTCTTCGTCCGAAAAGC 57.933 50.000 3.52 0.00 33.34 3.51
1857 1932 6.200475 AGTTTTTACTCTCTTCGTCCGAAAAG 59.800 38.462 3.52 0.00 33.34 2.27
1858 1933 6.044682 AGTTTTTACTCTCTTCGTCCGAAAA 58.955 36.000 3.52 0.00 33.34 2.29
1859 1934 5.594926 AGTTTTTACTCTCTTCGTCCGAAA 58.405 37.500 3.52 0.00 33.34 3.46
1860 1935 5.192327 AGTTTTTACTCTCTTCGTCCGAA 57.808 39.130 1.81 1.81 0.00 4.30
1861 1936 4.843220 AGTTTTTACTCTCTTCGTCCGA 57.157 40.909 0.00 0.00 0.00 4.55
1862 1937 7.028361 AGATAAGTTTTTACTCTCTTCGTCCG 58.972 38.462 0.00 0.00 0.00 4.79
1863 1938 8.760103 AAGATAAGTTTTTACTCTCTTCGTCC 57.240 34.615 0.00 0.00 0.00 4.79
1865 1940 9.984190 AGAAAGATAAGTTTTTACTCTCTTCGT 57.016 29.630 0.00 0.00 0.00 3.85
1869 1944 9.713713 GGACAGAAAGATAAGTTTTTACTCTCT 57.286 33.333 0.00 0.00 0.00 3.10
1870 1945 8.648968 CGGACAGAAAGATAAGTTTTTACTCTC 58.351 37.037 0.00 0.00 0.00 3.20
1871 1946 8.148999 ACGGACAGAAAGATAAGTTTTTACTCT 58.851 33.333 0.00 0.00 0.00 3.24
1872 1947 8.307921 ACGGACAGAAAGATAAGTTTTTACTC 57.692 34.615 0.00 0.00 0.00 2.59
1877 1952 6.320418 ACCAAACGGACAGAAAGATAAGTTTT 59.680 34.615 0.00 0.00 0.00 2.43
1891 1966 0.681564 ACTGCCAAACCAAACGGACA 60.682 50.000 0.00 0.00 0.00 4.02
1895 1970 2.098443 AGTTGTACTGCCAAACCAAACG 59.902 45.455 0.00 0.00 0.00 3.60
1915 1990 9.465985 TTTAGGATTACTGCGGTTTTTAAAAAG 57.534 29.630 13.58 4.50 0.00 2.27
1929 2004 7.792032 TGGAATACTGAGGTTTAGGATTACTG 58.208 38.462 0.00 0.00 31.64 2.74
1937 2012 4.080863 AGGCACTGGAATACTGAGGTTTAG 60.081 45.833 0.00 0.00 37.18 1.85
1986 2061 6.573664 TTAGCATCAACAAATAGCACTGTT 57.426 33.333 0.00 0.00 36.19 3.16
1988 2063 6.306356 GTGTTTAGCATCAACAAATAGCACTG 59.694 38.462 0.00 0.00 35.91 3.66
2086 2163 6.591001 CCATAAATTTTCAATACCAAGGGGG 58.409 40.000 0.00 0.00 44.81 5.40
2093 2170 9.252962 CTGAGATTGCCATAAATTTTCAATACC 57.747 33.333 0.00 0.00 0.00 2.73
2166 2243 5.227569 TGTCATATTTCAGTGACCTGTGT 57.772 39.130 0.00 0.00 43.09 3.72
2242 2320 6.484288 TGGAAGCTCCATCTTCTATTTTTCA 58.516 36.000 1.25 0.00 42.67 2.69


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

AutoCloner maintained by Alex Coulton.