Multiple sequence alignment - TraesCS3D01G236400

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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 TraesCS3D01G236400 chr3D 100.000 2411 0 0 1 2411 326869878 326872288 0.000000e+00 4453.0
1 TraesCS3D01G236400 chr3B 95.894 1656 47 9 6 1650 422514086 422512441 0.000000e+00 2662.0
2 TraesCS3D01G236400 chr3B 82.288 542 56 23 1906 2411 769454953 769455490 1.320000e-117 433.0
3 TraesCS3D01G236400 chr3B 86.850 327 37 6 1906 2230 666727322 666727000 6.340000e-96 361.0
4 TraesCS3D01G236400 chr3A 94.591 1479 46 4 173 1650 440607098 440608543 0.000000e+00 2257.0
5 TraesCS3D01G236400 chr3A 96.262 107 4 0 70 176 440606833 440606939 2.460000e-40 176.0
6 TraesCS3D01G236400 chr2D 87.086 573 51 13 1857 2411 324007055 324006488 5.660000e-176 627.0
7 TraesCS3D01G236400 chr2D 86.446 332 40 5 1902 2230 591936400 591936071 2.280000e-95 359.0
8 TraesCS3D01G236400 chr1D 82.255 541 65 15 1899 2411 402720137 402720674 2.850000e-119 438.0
9 TraesCS3D01G236400 chr1D 86.405 331 41 4 1902 2230 217291497 217291169 2.280000e-95 359.0
10 TraesCS3D01G236400 chr1D 95.000 80 4 0 550 629 2194681 2194602 2.520000e-25 126.0
11 TraesCS3D01G236400 chr6D 82.651 513 48 24 1902 2381 7348611 7348107 1.330000e-112 416.0
12 TraesCS3D01G236400 chr7A 80.220 546 63 24 1902 2411 535397766 535398302 3.790000e-98 368.0
13 TraesCS3D01G236400 chr5D 86.103 331 43 3 1902 2231 265118956 265118628 1.060000e-93 353.0
14 TraesCS3D01G236400 chr1A 77.717 552 72 23 1899 2411 386382688 386383227 8.430000e-75 291.0
15 TraesCS3D01G236400 chr1A 90.000 50 4 1 1844 1893 64719147 64719195 2.000000e-06 63.9
16 TraesCS3D01G236400 chr5B 76.566 495 76 20 1910 2369 683906313 683906802 4.010000e-58 235.0


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 TraesCS3D01G236400 chr3D 326869878 326872288 2410 False 4453.0 4453 100.0000 1 2411 1 chr3D.!!$F1 2410
1 TraesCS3D01G236400 chr3B 422512441 422514086 1645 True 2662.0 2662 95.8940 6 1650 1 chr3B.!!$R1 1644
2 TraesCS3D01G236400 chr3B 769454953 769455490 537 False 433.0 433 82.2880 1906 2411 1 chr3B.!!$F1 505
3 TraesCS3D01G236400 chr3A 440606833 440608543 1710 False 1216.5 2257 95.4265 70 1650 2 chr3A.!!$F1 1580
4 TraesCS3D01G236400 chr2D 324006488 324007055 567 True 627.0 627 87.0860 1857 2411 1 chr2D.!!$R1 554
5 TraesCS3D01G236400 chr1D 402720137 402720674 537 False 438.0 438 82.2550 1899 2411 1 chr1D.!!$F1 512
6 TraesCS3D01G236400 chr6D 7348107 7348611 504 True 416.0 416 82.6510 1902 2381 1 chr6D.!!$R1 479
7 TraesCS3D01G236400 chr7A 535397766 535398302 536 False 368.0 368 80.2200 1902 2411 1 chr7A.!!$F1 509
8 TraesCS3D01G236400 chr1A 386382688 386383227 539 False 291.0 291 77.7170 1899 2411 1 chr1A.!!$F2 512

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
733 898 0.181587 TCCGGACTCCACAAAGCAAA 59.818 50.0 0.0 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1863 0.034198 TTGGAAACTGTGCCGATCGA 59.966 50.0 18.66 0.0 0.0 3.59 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
98 100 4.206375 TGAAGGAGCAACAAGTTGAATGA 58.794 39.130 16.54 0.00 42.93 2.57
106 108 4.293415 CAACAAGTTGAATGAAGGACTGC 58.707 43.478 10.54 0.00 42.93 4.40
285 450 2.808244 CTCACTCGGCTTCTGAAGATC 58.192 52.381 21.06 10.65 0.00 2.75
313 478 4.696877 TGAGCATGTTATTTCTGTGGTCAG 59.303 41.667 0.00 0.00 40.91 3.51
343 508 3.451141 TGTTGGTGTTGATTTGCTTCC 57.549 42.857 0.00 0.00 0.00 3.46
360 525 1.186200 TCCGAATCCTGTCTGTCCAG 58.814 55.000 0.00 0.00 0.00 3.86
400 565 5.624344 TTTGACAAATATTTCCGCGGTAA 57.376 34.783 27.15 23.35 0.00 2.85
426 591 7.773864 TTTCGAGTTATAACACTGTTTGACA 57.226 32.000 17.65 0.00 0.00 3.58
476 641 1.203523 GGTCTCGAAGATGCTGTCAGT 59.796 52.381 0.93 0.00 33.89 3.41
477 642 2.525055 GTCTCGAAGATGCTGTCAGTC 58.475 52.381 0.93 0.00 33.89 3.51
489 654 2.545946 GCTGTCAGTCTTCAGTGAAACC 59.454 50.000 7.06 0.31 37.80 3.27
539 704 4.401519 CCTCATTCTGAAAGCATGGATTGT 59.598 41.667 0.00 0.00 38.18 2.71
611 776 2.413765 CCAGCAAACGCAGAATTCTCAG 60.414 50.000 4.57 5.09 0.00 3.35
733 898 0.181587 TCCGGACTCCACAAAGCAAA 59.818 50.000 0.00 0.00 0.00 3.68
896 1061 1.203441 TGGTCATGCCTCCTGCTTCT 61.203 55.000 7.54 0.00 42.00 2.85
1471 1636 3.120511 GCTTTGGCTTCGTTGAAGACTAG 60.121 47.826 13.18 11.00 46.92 2.57
1556 1721 3.678056 TGTTGTTCTCAAGGCTACGAT 57.322 42.857 0.00 0.00 33.97 3.73
1592 1759 3.481839 TCGTATCGTTACAAGTGTGTCG 58.518 45.455 4.63 0.00 39.30 4.35
1598 1765 1.862827 GTTACAAGTGTGTCGGTGTCC 59.137 52.381 0.00 0.00 39.30 4.02
1650 1817 4.262617 GGGTTTGGTGGATTCTACTTCTC 58.737 47.826 0.00 0.00 0.00 2.87
1651 1818 4.263331 GGGTTTGGTGGATTCTACTTCTCA 60.263 45.833 0.00 0.00 0.00 3.27
1652 1819 5.501156 GGTTTGGTGGATTCTACTTCTCAT 58.499 41.667 0.00 0.00 0.00 2.90
1653 1820 5.946377 GGTTTGGTGGATTCTACTTCTCATT 59.054 40.000 0.00 0.00 0.00 2.57
1654 1821 6.127897 GGTTTGGTGGATTCTACTTCTCATTG 60.128 42.308 0.00 0.00 0.00 2.82
1655 1822 5.762179 TGGTGGATTCTACTTCTCATTGT 57.238 39.130 0.00 0.00 0.00 2.71
1656 1823 5.491070 TGGTGGATTCTACTTCTCATTGTG 58.509 41.667 0.00 0.00 0.00 3.33
1657 1824 5.013079 TGGTGGATTCTACTTCTCATTGTGT 59.987 40.000 0.00 0.00 0.00 3.72
1658 1825 5.940470 GGTGGATTCTACTTCTCATTGTGTT 59.060 40.000 0.00 0.00 0.00 3.32
1659 1826 6.431234 GGTGGATTCTACTTCTCATTGTGTTT 59.569 38.462 0.00 0.00 0.00 2.83
1660 1827 7.301054 GTGGATTCTACTTCTCATTGTGTTTG 58.699 38.462 0.00 0.00 0.00 2.93
1661 1828 6.072508 TGGATTCTACTTCTCATTGTGTTTGC 60.073 38.462 0.00 0.00 0.00 3.68
1662 1829 4.990543 TCTACTTCTCATTGTGTTTGCG 57.009 40.909 0.00 0.00 0.00 4.85
1663 1830 2.405892 ACTTCTCATTGTGTTTGCGC 57.594 45.000 0.00 0.00 0.00 6.09
1664 1831 1.949525 ACTTCTCATTGTGTTTGCGCT 59.050 42.857 9.73 0.00 0.00 5.92
1665 1832 2.287188 ACTTCTCATTGTGTTTGCGCTG 60.287 45.455 9.73 0.00 0.00 5.18
1666 1833 0.592637 TCTCATTGTGTTTGCGCTGG 59.407 50.000 9.73 0.00 0.00 4.85
1667 1834 1.005294 CTCATTGTGTTTGCGCTGGC 61.005 55.000 9.73 0.00 40.52 4.85
1668 1835 2.023223 CATTGTGTTTGCGCTGGCC 61.023 57.895 9.73 0.00 38.85 5.36
1669 1836 3.556543 ATTGTGTTTGCGCTGGCCG 62.557 57.895 9.73 0.00 38.85 6.13
1696 1863 4.313020 AGGATTTCCTTCTGCAAGATGT 57.687 40.909 0.00 0.00 46.36 3.06
1697 1864 4.268359 AGGATTTCCTTCTGCAAGATGTC 58.732 43.478 0.00 0.00 46.36 3.06
1698 1865 3.064545 GGATTTCCTTCTGCAAGATGTCG 59.935 47.826 0.00 0.00 46.36 4.35
1699 1866 3.401033 TTTCCTTCTGCAAGATGTCGA 57.599 42.857 0.00 0.00 46.36 4.20
1700 1867 3.616956 TTCCTTCTGCAAGATGTCGAT 57.383 42.857 0.00 0.00 46.36 3.59
1701 1868 3.170791 TCCTTCTGCAAGATGTCGATC 57.829 47.619 0.00 0.00 46.36 3.69
1702 1869 1.857217 CCTTCTGCAAGATGTCGATCG 59.143 52.381 9.36 9.36 46.36 3.69
1703 1870 1.857217 CTTCTGCAAGATGTCGATCGG 59.143 52.381 16.41 0.00 46.36 4.18
1704 1871 0.528466 TCTGCAAGATGTCGATCGGC 60.528 55.000 13.98 13.98 38.67 5.54
1705 1872 0.807275 CTGCAAGATGTCGATCGGCA 60.807 55.000 26.41 26.41 39.76 5.69
1706 1873 1.083806 TGCAAGATGTCGATCGGCAC 61.084 55.000 26.77 18.23 38.24 5.01
1707 1874 1.083806 GCAAGATGTCGATCGGCACA 61.084 55.000 26.77 18.26 35.23 4.57
1708 1875 0.926155 CAAGATGTCGATCGGCACAG 59.074 55.000 26.77 11.18 33.34 3.66
1709 1876 0.532573 AAGATGTCGATCGGCACAGT 59.467 50.000 26.77 9.69 33.34 3.55
1710 1877 0.532573 AGATGTCGATCGGCACAGTT 59.467 50.000 26.77 9.25 33.34 3.16
1711 1878 1.066858 AGATGTCGATCGGCACAGTTT 60.067 47.619 26.77 8.80 33.34 2.66
1712 1879 1.324736 GATGTCGATCGGCACAGTTTC 59.675 52.381 26.77 14.61 30.16 2.78
1713 1880 0.669318 TGTCGATCGGCACAGTTTCC 60.669 55.000 20.25 0.00 0.00 3.13
1714 1881 0.669318 GTCGATCGGCACAGTTTCCA 60.669 55.000 16.20 0.00 0.00 3.53
1715 1882 0.034198 TCGATCGGCACAGTTTCCAA 59.966 50.000 16.41 0.00 0.00 3.53
1716 1883 0.165944 CGATCGGCACAGTTTCCAAC 59.834 55.000 7.38 0.00 0.00 3.77
1717 1884 1.234821 GATCGGCACAGTTTCCAACA 58.765 50.000 0.00 0.00 0.00 3.33
1718 1885 1.606668 GATCGGCACAGTTTCCAACAA 59.393 47.619 0.00 0.00 0.00 2.83
1719 1886 1.464734 TCGGCACAGTTTCCAACAAA 58.535 45.000 0.00 0.00 0.00 2.83
1720 1887 1.819288 TCGGCACAGTTTCCAACAAAA 59.181 42.857 0.00 0.00 0.00 2.44
1721 1888 2.231478 TCGGCACAGTTTCCAACAAAAA 59.769 40.909 0.00 0.00 0.00 1.94
1745 1912 4.111016 CGACAGCACGCCGGTAGA 62.111 66.667 1.90 0.00 0.00 2.59
1746 1913 2.202623 GACAGCACGCCGGTAGAG 60.203 66.667 1.90 0.00 0.00 2.43
1747 1914 4.436998 ACAGCACGCCGGTAGAGC 62.437 66.667 1.90 8.38 0.00 4.09
1748 1915 4.135153 CAGCACGCCGGTAGAGCT 62.135 66.667 15.51 15.51 35.63 4.09
1749 1916 3.382832 AGCACGCCGGTAGAGCTT 61.383 61.111 15.51 3.87 29.98 3.74
1750 1917 3.188786 GCACGCCGGTAGAGCTTG 61.189 66.667 1.90 0.00 32.98 4.01
1751 1918 3.188786 CACGCCGGTAGAGCTTGC 61.189 66.667 1.90 0.00 0.00 4.01
1752 1919 3.382832 ACGCCGGTAGAGCTTGCT 61.383 61.111 1.90 0.00 0.00 3.91
1753 1920 2.125512 CGCCGGTAGAGCTTGCTT 60.126 61.111 1.90 0.00 0.00 3.91
1754 1921 2.167861 CGCCGGTAGAGCTTGCTTC 61.168 63.158 1.90 0.00 0.00 3.86
1755 1922 2.167861 GCCGGTAGAGCTTGCTTCG 61.168 63.158 1.90 0.00 0.00 3.79
1756 1923 1.511305 CCGGTAGAGCTTGCTTCGA 59.489 57.895 0.00 0.00 0.00 3.71
1757 1924 0.802607 CCGGTAGAGCTTGCTTCGAC 60.803 60.000 0.00 0.00 0.00 4.20
1758 1925 1.134530 CGGTAGAGCTTGCTTCGACG 61.135 60.000 0.00 0.00 0.00 5.12
1759 1926 0.109226 GGTAGAGCTTGCTTCGACGT 60.109 55.000 0.00 0.00 0.00 4.34
1760 1927 1.261097 GTAGAGCTTGCTTCGACGTC 58.739 55.000 5.18 5.18 0.00 4.34
1761 1928 0.179197 TAGAGCTTGCTTCGACGTCG 60.179 55.000 31.30 31.30 41.45 5.12
1762 1929 3.060663 GAGCTTGCTTCGACGTCGC 62.061 63.158 32.19 19.15 39.60 5.19
1763 1930 3.106407 GCTTGCTTCGACGTCGCT 61.106 61.111 32.19 0.00 39.60 4.93
1764 1931 2.658707 GCTTGCTTCGACGTCGCTT 61.659 57.895 32.19 0.00 39.60 4.68
1765 1932 1.412606 CTTGCTTCGACGTCGCTTC 59.587 57.895 32.19 21.47 39.60 3.86
1766 1933 1.004277 CTTGCTTCGACGTCGCTTCT 61.004 55.000 32.19 0.00 39.60 2.85
1767 1934 0.596600 TTGCTTCGACGTCGCTTCTT 60.597 50.000 32.19 0.00 39.60 2.52
1768 1935 0.239082 TGCTTCGACGTCGCTTCTTA 59.761 50.000 32.19 12.04 39.60 2.10
1769 1936 0.908505 GCTTCGACGTCGCTTCTTAG 59.091 55.000 32.19 20.17 39.60 2.18
1770 1937 1.536149 CTTCGACGTCGCTTCTTAGG 58.464 55.000 32.19 11.29 39.60 2.69
1771 1938 0.169672 TTCGACGTCGCTTCTTAGGG 59.830 55.000 32.19 3.14 39.60 3.53
1772 1939 1.872679 CGACGTCGCTTCTTAGGGC 60.873 63.158 26.59 0.00 34.50 5.19
1773 1940 1.214589 GACGTCGCTTCTTAGGGCA 59.785 57.895 0.00 0.00 34.50 5.36
1774 1941 0.179108 GACGTCGCTTCTTAGGGCAT 60.179 55.000 0.00 0.00 34.50 4.40
1775 1942 0.460284 ACGTCGCTTCTTAGGGCATG 60.460 55.000 0.00 0.00 34.50 4.06
1776 1943 0.460284 CGTCGCTTCTTAGGGCATGT 60.460 55.000 0.00 0.00 34.50 3.21
1777 1944 1.291132 GTCGCTTCTTAGGGCATGTC 58.709 55.000 0.00 0.00 34.50 3.06
1778 1945 0.901827 TCGCTTCTTAGGGCATGTCA 59.098 50.000 0.00 0.00 34.50 3.58
1779 1946 1.134699 TCGCTTCTTAGGGCATGTCAG 60.135 52.381 0.00 0.00 34.50 3.51
1780 1947 1.406069 CGCTTCTTAGGGCATGTCAGT 60.406 52.381 0.00 0.00 0.00 3.41
1781 1948 2.012673 GCTTCTTAGGGCATGTCAGTG 58.987 52.381 0.00 0.00 0.00 3.66
1782 1949 2.636830 CTTCTTAGGGCATGTCAGTGG 58.363 52.381 0.00 0.00 0.00 4.00
1783 1950 1.656587 TCTTAGGGCATGTCAGTGGT 58.343 50.000 0.00 0.00 0.00 4.16
1784 1951 1.985159 TCTTAGGGCATGTCAGTGGTT 59.015 47.619 0.00 0.00 0.00 3.67
1785 1952 2.086869 CTTAGGGCATGTCAGTGGTTG 58.913 52.381 0.00 0.00 0.00 3.77
1786 1953 1.357137 TAGGGCATGTCAGTGGTTGA 58.643 50.000 0.00 0.00 0.00 3.18
1787 1954 0.700564 AGGGCATGTCAGTGGTTGAT 59.299 50.000 0.00 0.00 38.29 2.57
1788 1955 1.915489 AGGGCATGTCAGTGGTTGATA 59.085 47.619 0.00 0.00 38.29 2.15
1789 1956 2.308570 AGGGCATGTCAGTGGTTGATAA 59.691 45.455 0.00 0.00 38.29 1.75
1790 1957 3.053395 AGGGCATGTCAGTGGTTGATAAT 60.053 43.478 0.00 0.00 38.29 1.28
1791 1958 4.165950 AGGGCATGTCAGTGGTTGATAATA 59.834 41.667 0.00 0.00 38.29 0.98
1792 1959 5.072741 GGGCATGTCAGTGGTTGATAATAT 58.927 41.667 0.00 0.00 38.29 1.28
1793 1960 6.044287 AGGGCATGTCAGTGGTTGATAATATA 59.956 38.462 0.00 0.00 38.29 0.86
1794 1961 6.372659 GGGCATGTCAGTGGTTGATAATATAG 59.627 42.308 0.00 0.00 38.29 1.31
1795 1962 6.936900 GGCATGTCAGTGGTTGATAATATAGT 59.063 38.462 0.00 0.00 38.29 2.12
1796 1963 7.095060 GGCATGTCAGTGGTTGATAATATAGTG 60.095 40.741 0.00 0.00 38.29 2.74
1797 1964 7.442364 GCATGTCAGTGGTTGATAATATAGTGT 59.558 37.037 0.00 0.00 38.29 3.55
1798 1965 9.330063 CATGTCAGTGGTTGATAATATAGTGTT 57.670 33.333 0.00 0.00 38.29 3.32
1800 1967 9.811995 TGTCAGTGGTTGATAATATAGTGTTAC 57.188 33.333 0.00 0.00 38.29 2.50
1801 1968 9.257651 GTCAGTGGTTGATAATATAGTGTTACC 57.742 37.037 0.00 0.00 38.29 2.85
1802 1969 8.983789 TCAGTGGTTGATAATATAGTGTTACCA 58.016 33.333 0.00 0.00 0.00 3.25
1803 1970 9.778741 CAGTGGTTGATAATATAGTGTTACCAT 57.221 33.333 7.67 0.00 35.78 3.55
1810 1977 9.634163 TGATAATATAGTGTTACCATAAGCACG 57.366 33.333 0.00 0.00 36.99 5.34
1811 1978 9.635520 GATAATATAGTGTTACCATAAGCACGT 57.364 33.333 0.00 0.00 36.99 4.49
1812 1979 7.941795 AATATAGTGTTACCATAAGCACGTC 57.058 36.000 0.00 0.00 36.99 4.34
1813 1980 2.602878 AGTGTTACCATAAGCACGTCG 58.397 47.619 0.00 0.00 36.99 5.12
1814 1981 2.029649 AGTGTTACCATAAGCACGTCGT 60.030 45.455 0.00 0.00 36.99 4.34
1815 1982 2.091588 GTGTTACCATAAGCACGTCGTG 59.908 50.000 21.02 21.02 36.51 4.35
1816 1983 2.288334 TGTTACCATAAGCACGTCGTGT 60.288 45.455 25.18 10.25 35.75 4.49
1817 1984 3.057666 TGTTACCATAAGCACGTCGTGTA 60.058 43.478 25.18 12.12 35.75 2.90
1818 1985 2.273370 ACCATAAGCACGTCGTGTAG 57.727 50.000 25.18 11.33 35.75 2.74
1819 1986 1.814394 ACCATAAGCACGTCGTGTAGA 59.186 47.619 25.18 11.70 35.75 2.59
1820 1987 2.182825 CCATAAGCACGTCGTGTAGAC 58.817 52.381 25.18 9.67 46.16 2.59
1872 2039 1.335810 TCTTACTAGCACATACGCCCG 59.664 52.381 0.00 0.00 0.00 6.13
1875 2042 1.141019 CTAGCACATACGCCCGTGT 59.859 57.895 3.22 0.00 35.51 4.49
1932 2100 5.817816 TCTTTCATCCGAGGAGATTTAAAGC 59.182 40.000 0.00 0.00 32.07 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.601662 ACGCATACACTGATATAGCAGTTT 58.398 37.500 20.69 16.99 46.42 2.66
23 24 4.322009 CGAACGCATACACTGATATAGCAG 59.678 45.833 16.33 16.33 41.63 4.24
24 25 4.023536 TCGAACGCATACACTGATATAGCA 60.024 41.667 0.00 0.00 0.00 3.49
98 100 2.203294 AAAACCGCGGCAGTCCTT 60.203 55.556 28.58 8.04 0.00 3.36
106 108 2.051703 CCGACAACAAAACCGCGG 60.052 61.111 26.86 26.86 0.00 6.46
285 450 3.620374 ACAGAAATAACATGCTCAGAGCG 59.380 43.478 17.81 6.84 46.26 5.03
328 493 3.191371 AGGATTCGGAAGCAAATCAACAC 59.809 43.478 8.39 0.00 34.28 3.32
330 495 3.191371 ACAGGATTCGGAAGCAAATCAAC 59.809 43.478 8.39 0.00 34.28 3.18
400 565 8.832521 TGTCAAACAGTGTTATAACTCGAAAAT 58.167 29.630 16.33 0.00 0.00 1.82
426 591 6.712547 AGACAAAAGAGAACGGAAATCATCTT 59.287 34.615 0.00 0.00 0.00 2.40
476 641 1.679680 ACTCGTCGGTTTCACTGAAGA 59.320 47.619 0.00 2.06 39.16 2.87
477 642 2.135664 ACTCGTCGGTTTCACTGAAG 57.864 50.000 0.00 0.00 34.87 3.02
489 654 1.262683 GTAGGATTCCCGTACTCGTCG 59.737 57.143 0.00 0.00 37.58 5.12
539 704 0.822532 GGGATCCGAGCTCTCCGTAA 60.823 60.000 12.85 0.00 0.00 3.18
611 776 1.401018 CGGGAATTTGGAAAGTGCGAC 60.401 52.381 0.00 0.00 0.00 5.19
733 898 1.080298 TGTGTTGCGACTTGAAACGT 58.920 45.000 5.50 0.00 39.18 3.99
857 1022 0.386858 AACGAGTCATGTCACGGACG 60.387 55.000 13.31 7.27 39.01 4.79
896 1061 2.092807 GGGGTTTATAAGGCGTGGAGAA 60.093 50.000 0.00 0.00 0.00 2.87
1107 1272 4.175489 ACCTCGATCACGTCCGCG 62.175 66.667 0.00 0.00 44.93 6.46
1471 1636 1.358046 CGGCGCCAGGTAGTAGTAC 59.642 63.158 28.98 0.00 0.00 2.73
1592 1759 0.509929 GAAAGTACAACGCGGACACC 59.490 55.000 12.47 0.00 0.00 4.16
1650 1817 2.023223 GGCCAGCGCAAACACAATG 61.023 57.895 11.47 0.00 36.38 2.82
1651 1818 2.339712 GGCCAGCGCAAACACAAT 59.660 55.556 11.47 0.00 36.38 2.71
1652 1819 4.263209 CGGCCAGCGCAAACACAA 62.263 61.111 11.47 0.00 36.38 3.33
1663 1830 2.925162 GAAATCCTCGTCCCGGCCAG 62.925 65.000 2.24 0.00 0.00 4.85
1664 1831 3.006728 AAATCCTCGTCCCGGCCA 61.007 61.111 2.24 0.00 0.00 5.36
1665 1832 2.203029 GAAATCCTCGTCCCGGCC 60.203 66.667 0.00 0.00 0.00 6.13
1666 1833 2.203029 GGAAATCCTCGTCCCGGC 60.203 66.667 0.00 0.00 0.00 6.13
1667 1834 3.630289 AGGAAATCCTCGTCCCGG 58.370 61.111 0.00 0.00 44.77 5.73
1676 1843 3.064545 CGACATCTTGCAGAAGGAAATCC 59.935 47.826 0.00 0.00 0.00 3.01
1677 1844 3.935203 TCGACATCTTGCAGAAGGAAATC 59.065 43.478 0.00 0.00 0.00 2.17
1678 1845 3.942829 TCGACATCTTGCAGAAGGAAAT 58.057 40.909 0.00 0.00 0.00 2.17
1679 1846 3.401033 TCGACATCTTGCAGAAGGAAA 57.599 42.857 0.00 0.00 0.00 3.13
1680 1847 3.525537 GATCGACATCTTGCAGAAGGAA 58.474 45.455 0.00 0.00 0.00 3.36
1681 1848 2.480244 CGATCGACATCTTGCAGAAGGA 60.480 50.000 10.26 0.00 0.00 3.36
1682 1849 1.857217 CGATCGACATCTTGCAGAAGG 59.143 52.381 10.26 0.00 0.00 3.46
1683 1850 1.857217 CCGATCGACATCTTGCAGAAG 59.143 52.381 18.66 0.00 0.00 2.85
1684 1851 1.926561 CCGATCGACATCTTGCAGAA 58.073 50.000 18.66 0.00 0.00 3.02
1685 1852 0.528466 GCCGATCGACATCTTGCAGA 60.528 55.000 18.66 0.00 0.00 4.26
1686 1853 0.807275 TGCCGATCGACATCTTGCAG 60.807 55.000 18.66 0.00 32.48 4.41
1687 1854 1.083806 GTGCCGATCGACATCTTGCA 61.084 55.000 18.66 12.80 34.07 4.08
1688 1855 1.083806 TGTGCCGATCGACATCTTGC 61.084 55.000 18.66 10.05 0.00 4.01
1689 1856 0.926155 CTGTGCCGATCGACATCTTG 59.074 55.000 18.66 0.00 0.00 3.02
1690 1857 0.532573 ACTGTGCCGATCGACATCTT 59.467 50.000 18.66 0.00 0.00 2.40
1691 1858 0.532573 AACTGTGCCGATCGACATCT 59.467 50.000 18.66 1.13 0.00 2.90
1692 1859 1.324736 GAAACTGTGCCGATCGACATC 59.675 52.381 18.66 6.86 0.00 3.06
1693 1860 1.359848 GAAACTGTGCCGATCGACAT 58.640 50.000 18.66 0.00 0.00 3.06
1694 1861 0.669318 GGAAACTGTGCCGATCGACA 60.669 55.000 18.66 8.80 0.00 4.35
1695 1862 0.669318 TGGAAACTGTGCCGATCGAC 60.669 55.000 18.66 5.29 0.00 4.20
1696 1863 0.034198 TTGGAAACTGTGCCGATCGA 59.966 50.000 18.66 0.00 0.00 3.59
1697 1864 0.165944 GTTGGAAACTGTGCCGATCG 59.834 55.000 8.51 8.51 45.32 3.69
1729 1896 2.202623 CTCTACCGGCGTGCTGTC 60.203 66.667 6.01 0.00 0.00 3.51
1730 1897 4.436998 GCTCTACCGGCGTGCTGT 62.437 66.667 6.01 0.00 0.00 4.40
1731 1898 3.649277 AAGCTCTACCGGCGTGCTG 62.649 63.158 18.04 0.00 33.96 4.41
1732 1899 3.382832 AAGCTCTACCGGCGTGCT 61.383 61.111 13.29 13.29 35.30 4.40
1733 1900 3.188786 CAAGCTCTACCGGCGTGC 61.189 66.667 6.01 5.76 33.23 5.34
1734 1901 3.188786 GCAAGCTCTACCGGCGTG 61.189 66.667 6.01 0.00 40.91 5.34
1735 1902 2.837371 GAAGCAAGCTCTACCGGCGT 62.837 60.000 6.01 0.00 34.52 5.68
1736 1903 2.125512 AAGCAAGCTCTACCGGCG 60.126 61.111 0.00 0.00 34.52 6.46
1737 1904 2.167861 CGAAGCAAGCTCTACCGGC 61.168 63.158 0.00 0.00 0.00 6.13
1738 1905 0.802607 GTCGAAGCAAGCTCTACCGG 60.803 60.000 0.00 0.00 0.00 5.28
1739 1906 1.134530 CGTCGAAGCAAGCTCTACCG 61.135 60.000 0.00 0.00 0.00 4.02
1740 1907 0.109226 ACGTCGAAGCAAGCTCTACC 60.109 55.000 0.00 0.00 0.00 3.18
1741 1908 1.261097 GACGTCGAAGCAAGCTCTAC 58.739 55.000 0.00 0.00 0.00 2.59
1742 1909 0.179197 CGACGTCGAAGCAAGCTCTA 60.179 55.000 33.35 0.00 43.02 2.43
1743 1910 1.442857 CGACGTCGAAGCAAGCTCT 60.443 57.895 33.35 0.00 43.02 4.09
1744 1911 3.060663 GCGACGTCGAAGCAAGCTC 62.061 63.158 39.74 15.89 43.02 4.09
1745 1912 3.106407 GCGACGTCGAAGCAAGCT 61.106 61.111 39.74 0.00 43.02 3.74
1746 1913 2.535688 GAAGCGACGTCGAAGCAAGC 62.536 60.000 39.74 20.57 43.02 4.01
1747 1914 1.004277 AGAAGCGACGTCGAAGCAAG 61.004 55.000 39.74 11.11 43.02 4.01
1748 1915 0.596600 AAGAAGCGACGTCGAAGCAA 60.597 50.000 39.74 0.00 43.02 3.91
1749 1916 0.239082 TAAGAAGCGACGTCGAAGCA 59.761 50.000 39.74 16.56 43.02 3.91
1750 1917 0.908505 CTAAGAAGCGACGTCGAAGC 59.091 55.000 39.74 25.50 43.02 3.86
1751 1918 1.536149 CCTAAGAAGCGACGTCGAAG 58.464 55.000 39.74 23.06 43.02 3.79
1752 1919 0.169672 CCCTAAGAAGCGACGTCGAA 59.830 55.000 39.74 16.04 43.02 3.71
1753 1920 1.798735 CCCTAAGAAGCGACGTCGA 59.201 57.895 39.74 17.88 43.02 4.20
1754 1921 1.872679 GCCCTAAGAAGCGACGTCG 60.873 63.158 32.57 32.57 43.27 5.12
1755 1922 0.179108 ATGCCCTAAGAAGCGACGTC 60.179 55.000 5.18 5.18 0.00 4.34
1756 1923 0.460284 CATGCCCTAAGAAGCGACGT 60.460 55.000 0.00 0.00 0.00 4.34
1757 1924 0.460284 ACATGCCCTAAGAAGCGACG 60.460 55.000 0.00 0.00 0.00 5.12
1758 1925 1.291132 GACATGCCCTAAGAAGCGAC 58.709 55.000 0.00 0.00 0.00 5.19
1759 1926 0.901827 TGACATGCCCTAAGAAGCGA 59.098 50.000 0.00 0.00 0.00 4.93
1760 1927 1.293924 CTGACATGCCCTAAGAAGCG 58.706 55.000 0.00 0.00 0.00 4.68
1761 1928 2.012673 CACTGACATGCCCTAAGAAGC 58.987 52.381 0.00 0.00 0.00 3.86
1762 1929 2.026822 ACCACTGACATGCCCTAAGAAG 60.027 50.000 0.00 0.00 0.00 2.85
1763 1930 1.985159 ACCACTGACATGCCCTAAGAA 59.015 47.619 0.00 0.00 0.00 2.52
1764 1931 1.656587 ACCACTGACATGCCCTAAGA 58.343 50.000 0.00 0.00 0.00 2.10
1765 1932 2.086869 CAACCACTGACATGCCCTAAG 58.913 52.381 0.00 0.00 0.00 2.18
1766 1933 1.702401 TCAACCACTGACATGCCCTAA 59.298 47.619 0.00 0.00 0.00 2.69
1767 1934 1.357137 TCAACCACTGACATGCCCTA 58.643 50.000 0.00 0.00 0.00 3.53
1768 1935 0.700564 ATCAACCACTGACATGCCCT 59.299 50.000 0.00 0.00 36.69 5.19
1769 1936 2.418368 TATCAACCACTGACATGCCC 57.582 50.000 0.00 0.00 36.69 5.36
1770 1937 6.936900 ACTATATTATCAACCACTGACATGCC 59.063 38.462 0.00 0.00 36.69 4.40
1771 1938 7.442364 ACACTATATTATCAACCACTGACATGC 59.558 37.037 0.00 0.00 36.69 4.06
1772 1939 8.893219 ACACTATATTATCAACCACTGACATG 57.107 34.615 0.00 0.00 36.69 3.21
1774 1941 9.811995 GTAACACTATATTATCAACCACTGACA 57.188 33.333 0.00 0.00 36.69 3.58
1775 1942 9.257651 GGTAACACTATATTATCAACCACTGAC 57.742 37.037 0.00 0.00 36.69 3.51
1776 1943 8.983789 TGGTAACACTATATTATCAACCACTGA 58.016 33.333 0.00 0.00 46.17 3.41
1790 1957 9.224535 ACACGACGTGCTTATGGTAACACTATA 62.225 40.741 27.11 0.00 44.13 1.31
1791 1958 8.500474 ACACGACGTGCTTATGGTAACACTAT 62.500 42.308 27.11 0.00 44.13 2.12
1792 1959 7.278737 ACACGACGTGCTTATGGTAACACTA 62.279 44.000 27.11 0.00 44.13 2.74
1793 1960 6.577957 ACACGACGTGCTTATGGTAACACT 62.578 45.833 27.11 0.00 44.13 3.55
1794 1961 4.401617 ACACGACGTGCTTATGGTAACAC 61.402 47.826 27.11 0.00 44.13 3.32
1795 1962 2.288334 ACACGACGTGCTTATGGTAACA 60.288 45.455 27.11 0.00 45.07 2.41
1796 1963 2.331194 ACACGACGTGCTTATGGTAAC 58.669 47.619 27.11 0.00 36.98 2.50
1797 1964 2.728690 ACACGACGTGCTTATGGTAA 57.271 45.000 27.11 0.00 36.98 2.85
1798 1965 3.009026 TCTACACGACGTGCTTATGGTA 58.991 45.455 27.11 9.65 36.98 3.25
1799 1966 1.814394 TCTACACGACGTGCTTATGGT 59.186 47.619 27.11 8.97 36.98 3.55
1800 1967 2.182825 GTCTACACGACGTGCTTATGG 58.817 52.381 27.11 10.35 36.98 2.74
1801 1968 2.858839 TGTCTACACGACGTGCTTATG 58.141 47.619 27.11 12.75 45.87 1.90
1802 1969 3.240069 GTTGTCTACACGACGTGCTTAT 58.760 45.455 27.11 10.82 45.87 1.73
1803 1970 2.033174 TGTTGTCTACACGACGTGCTTA 59.967 45.455 27.11 12.45 45.87 3.09
1804 1971 1.202325 TGTTGTCTACACGACGTGCTT 60.202 47.619 27.11 11.94 45.87 3.91
1805 1972 0.382873 TGTTGTCTACACGACGTGCT 59.617 50.000 27.11 16.40 45.87 4.40
1806 1973 1.202203 TTGTTGTCTACACGACGTGC 58.798 50.000 27.11 11.78 45.87 5.34
1807 1974 3.061028 TGTTTTGTTGTCTACACGACGTG 59.939 43.478 25.72 25.72 45.87 4.49
1808 1975 3.252400 TGTTTTGTTGTCTACACGACGT 58.748 40.909 0.00 0.00 45.87 4.34
1809 1976 3.910862 TGTTTTGTTGTCTACACGACG 57.089 42.857 0.00 0.00 45.87 5.12
1810 1977 5.151632 ACATGTTTTGTTGTCTACACGAC 57.848 39.130 0.00 0.00 43.14 4.34
1811 1978 5.804692 AACATGTTTTGTTGTCTACACGA 57.195 34.783 4.92 0.00 46.80 4.35
1845 2012 6.532657 GGCGTATGTGCTAGTAAGACTAAAAA 59.467 38.462 0.00 0.00 29.00 1.94
1846 2013 6.038356 GGCGTATGTGCTAGTAAGACTAAAA 58.962 40.000 0.00 0.00 29.00 1.52
1847 2014 5.450965 GGGCGTATGTGCTAGTAAGACTAAA 60.451 44.000 0.00 0.00 29.00 1.85
1848 2015 4.037208 GGGCGTATGTGCTAGTAAGACTAA 59.963 45.833 0.00 0.00 29.00 2.24
1849 2016 3.567164 GGGCGTATGTGCTAGTAAGACTA 59.433 47.826 0.00 0.00 34.52 2.59
1850 2017 2.361438 GGGCGTATGTGCTAGTAAGACT 59.639 50.000 0.00 0.00 34.52 3.24
1851 2018 2.740452 GGGCGTATGTGCTAGTAAGAC 58.260 52.381 0.00 0.00 34.52 3.01
1852 2019 1.335810 CGGGCGTATGTGCTAGTAAGA 59.664 52.381 0.00 0.00 34.52 2.10
1853 2020 1.066605 ACGGGCGTATGTGCTAGTAAG 59.933 52.381 0.00 0.00 34.52 2.34
1854 2021 1.105457 ACGGGCGTATGTGCTAGTAA 58.895 50.000 0.00 0.00 34.52 2.24
1855 2022 0.382873 CACGGGCGTATGTGCTAGTA 59.617 55.000 0.00 0.00 34.52 1.82
1867 2034 4.954680 CGTTGCAACACACGGGCG 62.955 66.667 28.01 8.82 0.00 6.13
1872 2039 0.736053 TTTCTCCCGTTGCAACACAC 59.264 50.000 28.01 3.05 0.00 3.82
1904 2072 8.807948 TTAAATCTCCTCGGATGAAAGAAAAT 57.192 30.769 0.00 0.00 0.00 1.82
1915 2083 6.098409 ACTTCATAGCTTTAAATCTCCTCGGA 59.902 38.462 0.00 0.00 0.00 4.55
2006 2176 7.629027 ATTTTCTTCGTGATTTTCTCAAAGC 57.371 32.000 0.00 0.00 35.07 3.51
2075 2245 9.824534 CCATGTTTTTATTAAAAAGATTGGTGC 57.175 29.630 17.13 5.19 40.91 5.01
2131 2304 7.277539 TGAATTTTCAACACATGTTCCTGTTTC 59.722 33.333 0.00 0.00 35.83 2.78
2309 2517 7.122055 TGTTGCTATTTTGAAGAATATTCGGGT 59.878 33.333 9.78 0.00 0.00 5.28
2310 2518 7.479980 TGTTGCTATTTTGAAGAATATTCGGG 58.520 34.615 9.78 0.00 0.00 5.14
2341 2550 7.938563 TTTTGTAAAATGTTCGGAATTCCAG 57.061 32.000 24.09 16.06 35.14 3.86


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

AutoCloner maintained by Alex Coulton.