Multiple sequence alignment - TraesCS2D01G411700

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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 TraesCS2D01G411700 chr2D 100.000 2680 0 0 1 2680 526379169 526376490 0.000000e+00 4950.0
1 TraesCS2D01G411700 chr2D 83.971 836 108 14 54 884 391803804 391802990 0.000000e+00 778.0
2 TraesCS2D01G411700 chr2D 84.387 807 100 14 82 883 11505788 11506573 0.000000e+00 769.0
3 TraesCS2D01G411700 chr2B 92.282 1192 70 10 1 1191 622716546 622715376 0.000000e+00 1672.0
4 TraesCS2D01G411700 chr2B 88.845 762 50 22 1930 2680 622704123 622703386 0.000000e+00 904.0
5 TraesCS2D01G411700 chr2B 90.676 547 39 1 1184 1718 622704834 622704288 0.000000e+00 717.0
6 TraesCS2D01G411700 chr3D 91.150 791 61 6 54 844 389254369 389255150 0.000000e+00 1064.0
7 TraesCS2D01G411700 chr5B 87.365 831 90 12 54 883 467160400 467161216 0.000000e+00 939.0
8 TraesCS2D01G411700 chr2A 90.415 699 38 13 1999 2680 671341698 671341012 0.000000e+00 893.0
9 TraesCS2D01G411700 chr2A 86.948 521 49 3 1198 1699 671384926 671384406 3.870000e-158 568.0
10 TraesCS2D01G411700 chr2A 93.852 244 7 5 919 1154 671385167 671384924 7.050000e-96 361.0
11 TraesCS2D01G411700 chr2A 100.000 37 0 0 1 37 671385258 671385222 4.790000e-08 69.4
12 TraesCS2D01G411700 chr1B 89.778 675 68 1 57 731 329712949 329712276 0.000000e+00 863.0
13 TraesCS2D01G411700 chr1B 79.249 453 53 23 1967 2389 575704906 575705347 7.310000e-71 278.0
14 TraesCS2D01G411700 chr1B 81.333 300 37 13 2107 2389 575706180 575706477 2.680000e-55 226.0
15 TraesCS2D01G411700 chr6D 84.925 796 101 13 54 844 15361696 15360915 0.000000e+00 787.0
16 TraesCS2D01G411700 chr1D 84.925 796 101 13 54 844 418301924 418302705 0.000000e+00 787.0
17 TraesCS2D01G411700 chr5D 83.313 833 119 11 54 884 557939634 557938820 0.000000e+00 750.0
18 TraesCS2D01G411700 chr5A 80.444 450 50 23 1967 2389 647813807 647814245 2.590000e-80 309.0
19 TraesCS2D01G411700 chr5A 79.787 376 44 21 1967 2320 559017852 559017487 7.410000e-61 244.0
20 TraesCS2D01G411700 chr1A 80.266 451 48 26 1967 2389 138261078 138260641 4.340000e-78 302.0


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 TraesCS2D01G411700 chr2D 526376490 526379169 2679 True 4950.0 4950 100.0000 1 2680 1 chr2D.!!$R2 2679
1 TraesCS2D01G411700 chr2D 391802990 391803804 814 True 778.0 778 83.9710 54 884 1 chr2D.!!$R1 830
2 TraesCS2D01G411700 chr2D 11505788 11506573 785 False 769.0 769 84.3870 82 883 1 chr2D.!!$F1 801
3 TraesCS2D01G411700 chr2B 622715376 622716546 1170 True 1672.0 1672 92.2820 1 1191 1 chr2B.!!$R1 1190
4 TraesCS2D01G411700 chr2B 622703386 622704834 1448 True 810.5 904 89.7605 1184 2680 2 chr2B.!!$R2 1496
5 TraesCS2D01G411700 chr3D 389254369 389255150 781 False 1064.0 1064 91.1500 54 844 1 chr3D.!!$F1 790
6 TraesCS2D01G411700 chr5B 467160400 467161216 816 False 939.0 939 87.3650 54 883 1 chr5B.!!$F1 829
7 TraesCS2D01G411700 chr2A 671341012 671341698 686 True 893.0 893 90.4150 1999 2680 1 chr2A.!!$R1 681
8 TraesCS2D01G411700 chr2A 671384406 671385258 852 True 332.8 568 93.6000 1 1699 3 chr2A.!!$R2 1698
9 TraesCS2D01G411700 chr1B 329712276 329712949 673 True 863.0 863 89.7780 57 731 1 chr1B.!!$R1 674
10 TraesCS2D01G411700 chr1B 575704906 575706477 1571 False 252.0 278 80.2910 1967 2389 2 chr1B.!!$F1 422
11 TraesCS2D01G411700 chr6D 15360915 15361696 781 True 787.0 787 84.9250 54 844 1 chr6D.!!$R1 790
12 TraesCS2D01G411700 chr1D 418301924 418302705 781 False 787.0 787 84.9250 54 844 1 chr1D.!!$F1 790
13 TraesCS2D01G411700 chr5D 557938820 557939634 814 True 750.0 750 83.3130 54 884 1 chr5D.!!$R1 830

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
777 779 0.105224 TTCGGACACCATGTTCACGT 59.895 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1886 0.03601 AGCTCACGATGGACCAAAGG 60.036 55.0 0.0 0.0 0.0 3.11 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
166 167 1.155390 CTCCCTAGGCCCATCGGTA 59.845 63.158 2.05 0.00 0.00 4.02
502 503 2.046285 GTGCCGTTCCATTCCTGGG 61.046 63.158 0.00 0.00 43.34 4.45
596 597 4.695231 CGACGGCGTCTCGGTGTT 62.695 66.667 33.90 0.00 0.00 3.32
695 696 3.761218 TGTTGTTTGGTTTGCTTCTCTGA 59.239 39.130 0.00 0.00 0.00 3.27
777 779 0.105224 TTCGGACACCATGTTCACGT 59.895 50.000 0.00 0.00 0.00 4.49
799 808 1.218875 TTGCGTCCGTGTCATGTGTC 61.219 55.000 0.00 0.00 0.00 3.67
800 809 1.663388 GCGTCCGTGTCATGTGTCA 60.663 57.895 0.00 0.00 0.00 3.58
807 816 3.055458 TCCGTGTCATGTGTCATACCATT 60.055 43.478 0.00 0.00 0.00 3.16
812 821 6.112734 GTGTCATGTGTCATACCATTCCTTA 58.887 40.000 0.00 0.00 0.00 2.69
847 856 9.823098 CTAACTTCTTCTATCAATGCAATATGC 57.177 33.333 0.00 0.00 45.29 3.14
1170 1216 1.390664 CGTTCCTACGTACGTGCGTG 61.391 60.000 36.35 25.63 45.33 5.34
1178 1224 0.586748 CGTACGTGCGTGCAACAAAA 60.587 50.000 18.32 0.00 35.74 2.44
1182 1228 1.202245 ACGTGCGTGCAACAAAAGAAT 60.202 42.857 0.00 0.00 35.74 2.40
1209 1255 4.817063 GCGCGCGTGACATGCATT 62.817 61.111 32.35 0.00 0.00 3.56
1221 1267 0.932399 CATGCATTGTCTGATCGCGA 59.068 50.000 13.09 13.09 0.00 5.87
1232 1278 1.995484 CTGATCGCGATGACACTTTGT 59.005 47.619 29.09 0.00 0.00 2.83
1233 1279 1.726248 TGATCGCGATGACACTTTGTG 59.274 47.619 29.09 0.00 39.75 3.33
1235 1281 1.154413 CGCGATGACACTTTGTGCC 60.154 57.895 0.00 0.00 36.98 5.01
1245 1291 4.023279 TGACACTTTGTGCCAATGTACATC 60.023 41.667 9.23 0.00 36.94 3.06
1337 1395 2.975799 GGAAACTTCGGCGTGGCA 60.976 61.111 6.85 0.00 0.00 4.92
1472 1530 1.730902 CTCATACGCGCTGGGATCG 60.731 63.158 5.73 0.00 0.00 3.69
1496 1554 2.946762 GCCGTCTTCACAAGGTGC 59.053 61.111 0.00 0.00 32.98 5.01
1646 1710 2.515854 GGCATCCCTCTCATCTACGTA 58.484 52.381 0.00 0.00 0.00 3.57
1685 1750 4.217510 TCATTGGCATCCCCTAAATGAAG 58.782 43.478 0.00 0.00 34.70 3.02
1709 1774 5.180680 GGTAGCCGTATTCTGTTGTTTTCTT 59.819 40.000 0.00 0.00 0.00 2.52
1718 1783 3.115554 CTGTTGTTTTCTTTCGGCCAAG 58.884 45.455 2.24 0.00 0.00 3.61
1719 1784 2.494073 TGTTGTTTTCTTTCGGCCAAGT 59.506 40.909 2.24 0.00 0.00 3.16
1720 1785 3.056465 TGTTGTTTTCTTTCGGCCAAGTT 60.056 39.130 2.24 0.00 0.00 2.66
1721 1786 3.878160 TGTTTTCTTTCGGCCAAGTTT 57.122 38.095 2.24 0.00 0.00 2.66
1722 1787 3.516615 TGTTTTCTTTCGGCCAAGTTTG 58.483 40.909 2.24 0.00 0.00 2.93
1723 1788 2.217429 TTTCTTTCGGCCAAGTTTGC 57.783 45.000 2.24 0.00 0.00 3.68
1724 1789 1.107114 TTCTTTCGGCCAAGTTTGCA 58.893 45.000 2.24 0.00 0.00 4.08
1725 1790 0.667993 TCTTTCGGCCAAGTTTGCAG 59.332 50.000 2.24 0.00 0.00 4.41
1726 1791 0.385390 CTTTCGGCCAAGTTTGCAGT 59.615 50.000 2.24 0.00 0.00 4.40
1727 1792 1.606668 CTTTCGGCCAAGTTTGCAGTA 59.393 47.619 2.24 0.00 0.00 2.74
1728 1793 1.681538 TTCGGCCAAGTTTGCAGTAA 58.318 45.000 2.24 0.00 0.00 2.24
1729 1794 1.904287 TCGGCCAAGTTTGCAGTAAT 58.096 45.000 2.24 0.00 0.00 1.89
1730 1795 1.810151 TCGGCCAAGTTTGCAGTAATC 59.190 47.619 2.24 0.00 0.00 1.75
1731 1796 1.812571 CGGCCAAGTTTGCAGTAATCT 59.187 47.619 2.24 0.00 0.00 2.40
1732 1797 2.414559 CGGCCAAGTTTGCAGTAATCTG 60.415 50.000 2.24 0.00 43.87 2.90
1733 1798 2.558359 GGCCAAGTTTGCAGTAATCTGT 59.442 45.455 0.00 0.00 43.05 3.41
1734 1799 3.756434 GGCCAAGTTTGCAGTAATCTGTA 59.244 43.478 0.00 0.00 43.05 2.74
1735 1800 4.142600 GGCCAAGTTTGCAGTAATCTGTAG 60.143 45.833 0.00 0.00 43.05 2.74
1736 1801 4.672801 GCCAAGTTTGCAGTAATCTGTAGC 60.673 45.833 0.00 0.00 43.05 3.58
1737 1802 4.142600 CCAAGTTTGCAGTAATCTGTAGCC 60.143 45.833 0.00 0.00 43.05 3.93
1738 1803 4.286297 AGTTTGCAGTAATCTGTAGCCA 57.714 40.909 0.00 0.00 43.05 4.75
1739 1804 4.848357 AGTTTGCAGTAATCTGTAGCCAT 58.152 39.130 0.00 0.00 43.05 4.40
1740 1805 4.878397 AGTTTGCAGTAATCTGTAGCCATC 59.122 41.667 0.00 0.00 43.05 3.51
1741 1806 3.475566 TGCAGTAATCTGTAGCCATCC 57.524 47.619 0.00 0.00 43.05 3.51
1742 1807 2.771372 TGCAGTAATCTGTAGCCATCCA 59.229 45.455 0.00 0.00 43.05 3.41
1743 1808 3.392285 TGCAGTAATCTGTAGCCATCCAT 59.608 43.478 0.00 0.00 43.05 3.41
1744 1809 3.750130 GCAGTAATCTGTAGCCATCCATG 59.250 47.826 0.00 0.00 43.05 3.66
1756 1821 1.472201 CCATCCATGTCAGTGAGGTCG 60.472 57.143 0.00 0.00 0.00 4.79
1778 1843 3.609175 GCGTTATGCATGTGTGAACAACT 60.609 43.478 10.16 0.00 45.45 3.16
1782 1847 2.226330 TGCATGTGTGAACAACTACCC 58.774 47.619 0.00 0.00 0.00 3.69
1793 1858 5.938125 GTGAACAACTACCCATAATGTGAGT 59.062 40.000 0.00 0.00 0.00 3.41
1802 1867 8.764558 ACTACCCATAATGTGAGTGTATTTGTA 58.235 33.333 0.00 0.00 0.00 2.41
1804 1869 6.537301 ACCCATAATGTGAGTGTATTTGTACG 59.463 38.462 0.00 0.00 0.00 3.67
1805 1870 6.537301 CCCATAATGTGAGTGTATTTGTACGT 59.463 38.462 0.00 0.00 0.00 3.57
1806 1871 7.398746 CCATAATGTGAGTGTATTTGTACGTG 58.601 38.462 0.00 0.00 0.00 4.49
1807 1872 7.064134 CCATAATGTGAGTGTATTTGTACGTGT 59.936 37.037 0.00 0.00 0.00 4.49
1808 1873 6.854496 AATGTGAGTGTATTTGTACGTGTT 57.146 33.333 0.00 0.00 0.00 3.32
1809 1874 5.644902 TGTGAGTGTATTTGTACGTGTTG 57.355 39.130 0.00 0.00 0.00 3.33
1811 1876 5.811100 TGTGAGTGTATTTGTACGTGTTGAA 59.189 36.000 0.00 0.00 0.00 2.69
1813 1878 5.050634 TGAGTGTATTTGTACGTGTTGAAGC 60.051 40.000 0.00 0.00 0.00 3.86
1814 1879 4.212636 AGTGTATTTGTACGTGTTGAAGCC 59.787 41.667 0.00 0.00 0.00 4.35
1816 1881 2.335316 TTTGTACGTGTTGAAGCCCT 57.665 45.000 0.00 0.00 0.00 5.19
1817 1882 1.873698 TTGTACGTGTTGAAGCCCTC 58.126 50.000 0.00 0.00 0.00 4.30
1820 1885 0.320421 TACGTGTTGAAGCCCTCTGC 60.320 55.000 0.00 0.00 41.71 4.26
1821 1886 2.328099 CGTGTTGAAGCCCTCTGCC 61.328 63.158 0.00 0.00 42.71 4.85
1823 1888 2.156098 TGTTGAAGCCCTCTGCCCT 61.156 57.895 0.00 0.00 42.71 5.19
1826 1891 0.540365 TTGAAGCCCTCTGCCCTTTG 60.540 55.000 0.00 0.00 42.71 2.77
1827 1892 1.680314 GAAGCCCTCTGCCCTTTGG 60.680 63.158 0.00 0.00 42.71 3.28
1828 1893 2.432174 GAAGCCCTCTGCCCTTTGGT 62.432 60.000 0.00 0.00 42.71 3.67
1833 1898 0.394899 CCTCTGCCCTTTGGTCCATC 60.395 60.000 0.00 0.00 0.00 3.51
1834 1899 0.745845 CTCTGCCCTTTGGTCCATCG 60.746 60.000 0.00 0.00 0.00 3.84
1836 1901 1.303236 TGCCCTTTGGTCCATCGTG 60.303 57.895 0.00 0.00 0.00 4.35
1837 1902 1.002624 GCCCTTTGGTCCATCGTGA 60.003 57.895 0.00 0.00 0.00 4.35
1838 1903 1.026718 GCCCTTTGGTCCATCGTGAG 61.027 60.000 0.00 0.00 0.00 3.51
1840 1905 0.036010 CCTTTGGTCCATCGTGAGCT 60.036 55.000 0.00 0.00 33.93 4.09
1842 1907 0.396435 TTTGGTCCATCGTGAGCTGT 59.604 50.000 0.00 0.00 33.93 4.40
1845 1910 0.320771 GGTCCATCGTGAGCTGTTGT 60.321 55.000 0.00 0.00 0.00 3.32
1846 1911 1.067142 GGTCCATCGTGAGCTGTTGTA 60.067 52.381 0.00 0.00 0.00 2.41
1847 1912 1.993370 GTCCATCGTGAGCTGTTGTAC 59.007 52.381 0.00 0.00 0.00 2.90
1848 1913 1.616374 TCCATCGTGAGCTGTTGTACA 59.384 47.619 0.00 0.00 0.00 2.90
1849 1914 2.233676 TCCATCGTGAGCTGTTGTACAT 59.766 45.455 0.00 0.00 0.00 2.29
1852 1917 3.926821 TCGTGAGCTGTTGTACATGTA 57.073 42.857 0.08 0.08 0.00 2.29
1853 1918 4.450082 TCGTGAGCTGTTGTACATGTAT 57.550 40.909 9.18 0.00 0.00 2.29
1854 1919 5.570234 TCGTGAGCTGTTGTACATGTATA 57.430 39.130 9.18 3.08 0.00 1.47
1855 1920 6.144078 TCGTGAGCTGTTGTACATGTATAT 57.856 37.500 9.18 0.00 0.00 0.86
1856 1921 7.266922 TCGTGAGCTGTTGTACATGTATATA 57.733 36.000 9.18 0.00 0.00 0.86
1857 1922 7.882179 TCGTGAGCTGTTGTACATGTATATAT 58.118 34.615 9.18 0.00 0.00 0.86
1858 1923 9.005777 TCGTGAGCTGTTGTACATGTATATATA 57.994 33.333 9.18 0.00 0.00 0.86
1859 1924 9.788960 CGTGAGCTGTTGTACATGTATATATAT 57.211 33.333 9.18 0.00 0.00 0.86
1915 1980 3.305094 TGTAATTCTTTACACTAGCGCGC 59.695 43.478 26.66 26.66 42.10 6.86
1916 1981 0.921347 ATTCTTTACACTAGCGCGCG 59.079 50.000 28.44 28.44 0.00 6.86
1917 1982 0.109643 TTCTTTACACTAGCGCGCGA 60.110 50.000 37.18 21.03 0.00 5.87
1918 1983 0.099968 TCTTTACACTAGCGCGCGAT 59.900 50.000 37.18 32.71 0.00 4.58
1919 1984 0.921347 CTTTACACTAGCGCGCGATT 59.079 50.000 37.18 23.07 0.00 3.34
1920 1985 2.114056 CTTTACACTAGCGCGCGATTA 58.886 47.619 37.18 22.94 0.00 1.75
1921 1986 1.469917 TTACACTAGCGCGCGATTAC 58.530 50.000 37.18 16.41 0.00 1.89
1923 1988 0.179145 ACACTAGCGCGCGATTACTT 60.179 50.000 37.18 10.34 0.00 2.24
1926 1991 0.498927 CTAGCGCGCGATTACTTCAC 59.501 55.000 37.18 12.54 0.00 3.18
1927 1992 0.099968 TAGCGCGCGATTACTTCACT 59.900 50.000 37.18 19.67 0.00 3.41
1928 1993 1.013323 GCGCGCGATTACTTCACTG 60.013 57.895 37.18 0.00 0.00 3.66
1934 1999 2.595188 CGCGATTACTTCACTGAATGCG 60.595 50.000 0.00 0.00 35.74 4.73
1935 2000 2.603110 GCGATTACTTCACTGAATGCGA 59.397 45.455 0.00 0.00 0.00 5.10
1936 2001 3.542291 GCGATTACTTCACTGAATGCGAC 60.542 47.826 0.00 0.00 0.00 5.19
1954 2019 2.683968 GACCGAGCAATACAACAGACA 58.316 47.619 0.00 0.00 0.00 3.41
1959 2024 3.265791 GAGCAATACAACAGACAGGGAG 58.734 50.000 0.00 0.00 0.00 4.30
1961 2026 2.359900 CAATACAACAGACAGGGAGCC 58.640 52.381 0.00 0.00 0.00 4.70
1985 2050 1.203441 TGCTCAGGGCTTCACTCCAT 61.203 55.000 0.00 0.00 42.39 3.41
1991 2056 1.211457 AGGGCTTCACTCCATCACATC 59.789 52.381 0.00 0.00 0.00 3.06
1994 2059 2.355513 GGCTTCACTCCATCACATCAGT 60.356 50.000 0.00 0.00 0.00 3.41
2061 2145 8.579850 ACTTCAAAATGGCATATTTCAGTAGA 57.420 30.769 0.00 0.00 0.00 2.59
2062 2146 8.680903 ACTTCAAAATGGCATATTTCAGTAGAG 58.319 33.333 0.00 0.00 0.00 2.43
2112 2196 9.533831 AGTTTCAAGTACCAATTCCAGATTATT 57.466 29.630 0.00 0.00 0.00 1.40
2129 2224 7.919091 CCAGATTATTTGAAACATCACATGAGG 59.081 37.037 0.00 0.00 0.00 3.86
2131 2226 8.680903 AGATTATTTGAAACATCACATGAGGTC 58.319 33.333 0.00 0.00 38.19 3.85
2138 2240 1.753649 CATCACATGAGGTCTCGAGGT 59.246 52.381 13.56 0.00 0.00 3.85
2145 2247 4.341520 ACATGAGGTCTCGAGGTAATTACC 59.658 45.833 24.71 24.71 46.82 2.85
2422 3674 4.321718 CAAGAGTCATGGTGTGAACTCAT 58.678 43.478 11.32 0.00 38.90 2.90
2443 3695 4.806571 GCATCAGCATTGTGCCAG 57.193 55.556 0.00 0.00 46.52 4.85
2525 3777 4.210331 ACACTTCCACTGCAAGAGAAAAT 58.790 39.130 0.00 0.00 37.43 1.82
2526 3778 5.376625 ACACTTCCACTGCAAGAGAAAATA 58.623 37.500 0.00 0.00 37.43 1.40
2527 3779 5.239525 ACACTTCCACTGCAAGAGAAAATAC 59.760 40.000 0.00 0.00 37.43 1.89
2528 3780 5.239306 CACTTCCACTGCAAGAGAAAATACA 59.761 40.000 0.00 0.00 37.43 2.29
2529 3781 6.006449 ACTTCCACTGCAAGAGAAAATACAT 58.994 36.000 0.00 0.00 37.43 2.29
2530 3782 5.885230 TCCACTGCAAGAGAAAATACATG 57.115 39.130 0.00 0.00 37.43 3.21
2531 3783 4.701651 TCCACTGCAAGAGAAAATACATGG 59.298 41.667 0.00 0.00 37.43 3.66
2564 3817 5.178096 TCAGGGTGAACATACATGAACAT 57.822 39.130 0.00 0.00 0.00 2.71
2664 3917 4.746089 GCAGCATCATGGTTATCCTTCTCT 60.746 45.833 0.00 0.00 34.23 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
553 554 2.037367 TCCGGAGACCTGGACCTG 59.963 66.667 0.00 0.00 42.79 4.00
695 696 0.524862 ACACGACTAAACTCGCCGAT 59.475 50.000 0.00 0.00 37.15 4.18
777 779 1.374125 CATGACACGGACGCAAGGA 60.374 57.895 0.00 0.00 46.39 3.36
964 1001 1.219522 GGTGCCGTGTCAGTGTACAC 61.220 60.000 18.56 18.56 45.10 2.90
1154 1199 2.127634 TTGCACGCACGTACGTAGGA 62.128 55.000 22.34 9.83 46.34 2.94
1156 1201 1.270110 TGTTGCACGCACGTACGTAG 61.270 55.000 22.34 19.66 46.34 3.51
1163 1209 1.476074 ATTCTTTTGTTGCACGCACG 58.524 45.000 0.00 0.00 0.00 5.34
1170 1216 4.074272 CGCGCATTTTATTCTTTTGTTGC 58.926 39.130 8.75 0.00 0.00 4.17
1178 1224 4.285291 GCGCGCGCATTTTATTCT 57.715 50.000 46.11 0.00 41.49 2.40
1209 1255 0.811281 AGTGTCATCGCGATCAGACA 59.189 50.000 28.42 28.42 38.56 3.41
1232 1278 2.843730 ACCTGGTAGATGTACATTGGCA 59.156 45.455 10.30 0.00 0.00 4.92
1233 1279 3.206150 CACCTGGTAGATGTACATTGGC 58.794 50.000 10.30 3.13 0.00 4.52
1235 1281 4.191544 CCACACCTGGTAGATGTACATTG 58.808 47.826 10.30 4.14 32.03 2.82
1322 1380 2.203153 ACTGCCACGCCGAAGTTT 60.203 55.556 0.00 0.00 0.00 2.66
1343 1401 4.803426 GAGGCCAGCACCGACTCG 62.803 72.222 5.01 0.00 33.69 4.18
1538 1596 2.675423 CTCGGGGGTGACGTCTGA 60.675 66.667 17.92 0.00 0.00 3.27
1616 1680 3.570212 GGGATGCCCAGGCCGTAT 61.570 66.667 6.14 0.00 44.65 3.06
1646 1710 5.881923 CAATGATTGGGATGAAAGGGAAT 57.118 39.130 0.00 0.00 0.00 3.01
1685 1750 4.694037 AGAAAACAACAGAATACGGCTACC 59.306 41.667 0.00 0.00 0.00 3.18
1709 1774 1.681538 TTACTGCAAACTTGGCCGAA 58.318 45.000 0.00 0.00 0.00 4.30
1718 1783 4.035675 GGATGGCTACAGATTACTGCAAAC 59.964 45.833 0.00 0.00 46.95 2.93
1719 1784 4.199310 GGATGGCTACAGATTACTGCAAA 58.801 43.478 0.00 0.00 46.95 3.68
1720 1785 3.199727 TGGATGGCTACAGATTACTGCAA 59.800 43.478 0.00 0.00 46.95 4.08
1721 1786 2.771372 TGGATGGCTACAGATTACTGCA 59.229 45.455 0.00 0.00 46.95 4.41
1722 1787 3.475566 TGGATGGCTACAGATTACTGC 57.524 47.619 0.00 0.00 46.95 4.40
1723 1788 4.993584 GACATGGATGGCTACAGATTACTG 59.006 45.833 0.00 0.00 40.26 2.74
1724 1789 4.655649 TGACATGGATGGCTACAGATTACT 59.344 41.667 0.00 0.00 36.54 2.24
1725 1790 4.960938 TGACATGGATGGCTACAGATTAC 58.039 43.478 0.00 0.00 36.54 1.89
1726 1791 4.655649 ACTGACATGGATGGCTACAGATTA 59.344 41.667 0.00 0.00 36.54 1.75
1727 1792 3.457380 ACTGACATGGATGGCTACAGATT 59.543 43.478 0.00 0.00 36.54 2.40
1728 1793 3.044156 ACTGACATGGATGGCTACAGAT 58.956 45.455 0.00 0.00 36.54 2.90
1729 1794 2.169144 CACTGACATGGATGGCTACAGA 59.831 50.000 0.00 0.00 36.54 3.41
1730 1795 2.169144 TCACTGACATGGATGGCTACAG 59.831 50.000 0.00 0.00 36.54 2.74
1731 1796 2.169144 CTCACTGACATGGATGGCTACA 59.831 50.000 0.00 0.00 36.54 2.74
1732 1797 2.484417 CCTCACTGACATGGATGGCTAC 60.484 54.545 0.00 0.00 36.54 3.58
1733 1798 1.764723 CCTCACTGACATGGATGGCTA 59.235 52.381 0.00 0.00 36.54 3.93
1734 1799 0.545171 CCTCACTGACATGGATGGCT 59.455 55.000 0.00 0.00 36.54 4.75
1735 1800 0.254178 ACCTCACTGACATGGATGGC 59.746 55.000 0.00 0.00 35.98 4.40
1736 1801 1.472201 CGACCTCACTGACATGGATGG 60.472 57.143 0.00 0.00 0.00 3.51
1737 1802 1.931906 CGACCTCACTGACATGGATG 58.068 55.000 0.00 0.00 0.00 3.51
1738 1803 0.176680 GCGACCTCACTGACATGGAT 59.823 55.000 0.00 0.00 0.00 3.41
1739 1804 1.591703 GCGACCTCACTGACATGGA 59.408 57.895 0.00 0.00 0.00 3.41
1740 1805 1.807165 CGCGACCTCACTGACATGG 60.807 63.158 0.00 0.00 0.00 3.66
1741 1806 0.667487 AACGCGACCTCACTGACATG 60.667 55.000 15.93 0.00 0.00 3.21
1742 1807 0.885879 TAACGCGACCTCACTGACAT 59.114 50.000 15.93 0.00 0.00 3.06
1743 1808 0.885879 ATAACGCGACCTCACTGACA 59.114 50.000 15.93 0.00 0.00 3.58
1744 1809 1.269166 CATAACGCGACCTCACTGAC 58.731 55.000 15.93 0.00 0.00 3.51
1756 1821 2.610219 TGTTCACACATGCATAACGC 57.390 45.000 0.00 0.00 42.89 4.84
1778 1843 7.707464 CGTACAAATACACTCACATTATGGGTA 59.293 37.037 0.00 0.00 41.54 3.69
1782 1847 7.959733 ACACGTACAAATACACTCACATTATG 58.040 34.615 0.00 0.00 0.00 1.90
1793 1858 3.499157 GGGCTTCAACACGTACAAATACA 59.501 43.478 0.00 0.00 0.00 2.29
1802 1867 1.598130 GCAGAGGGCTTCAACACGT 60.598 57.895 0.00 0.00 40.25 4.49
1804 1869 1.973812 GGGCAGAGGGCTTCAACAC 60.974 63.158 0.00 0.00 44.01 3.32
1805 1870 1.719063 AAGGGCAGAGGGCTTCAACA 61.719 55.000 0.00 0.00 44.01 3.33
1806 1871 0.540597 AAAGGGCAGAGGGCTTCAAC 60.541 55.000 0.00 0.00 44.01 3.18
1807 1872 0.540365 CAAAGGGCAGAGGGCTTCAA 60.540 55.000 0.00 0.00 44.01 2.69
1808 1873 1.075482 CAAAGGGCAGAGGGCTTCA 59.925 57.895 0.00 0.00 44.01 3.02
1809 1874 1.680314 CCAAAGGGCAGAGGGCTTC 60.680 63.158 0.00 0.00 44.01 3.86
1811 1876 2.860971 ACCAAAGGGCAGAGGGCT 60.861 61.111 0.00 0.00 44.01 5.19
1813 1878 1.867595 ATGGACCAAAGGGCAGAGGG 61.868 60.000 0.00 0.00 37.90 4.30
1814 1879 0.394899 GATGGACCAAAGGGCAGAGG 60.395 60.000 0.00 0.00 37.90 3.69
1816 1881 1.299648 CGATGGACCAAAGGGCAGA 59.700 57.895 0.00 0.00 37.90 4.26
1817 1882 1.002134 ACGATGGACCAAAGGGCAG 60.002 57.895 0.00 0.00 37.90 4.85
1820 1885 1.026718 GCTCACGATGGACCAAAGGG 61.027 60.000 0.00 0.00 41.29 3.95
1821 1886 0.036010 AGCTCACGATGGACCAAAGG 60.036 55.000 0.00 0.00 0.00 3.11
1823 1888 0.396435 ACAGCTCACGATGGACCAAA 59.604 50.000 0.00 0.00 0.00 3.28
1826 1891 0.320771 ACAACAGCTCACGATGGACC 60.321 55.000 0.00 0.00 0.00 4.46
1827 1892 1.993370 GTACAACAGCTCACGATGGAC 59.007 52.381 0.00 0.00 0.00 4.02
1828 1893 1.616374 TGTACAACAGCTCACGATGGA 59.384 47.619 0.00 0.00 0.00 3.41
1833 1898 9.788960 ATATATATACATGTACAACAGCTCACG 57.211 33.333 7.96 0.00 0.00 4.35
1893 1958 3.305094 GCGCGCTAGTGTAAAGAATTACA 59.695 43.478 26.67 0.00 46.96 2.41
1894 1959 3.598670 CGCGCGCTAGTGTAAAGAATTAC 60.599 47.826 30.48 0.00 41.50 1.89
1895 1960 2.532723 CGCGCGCTAGTGTAAAGAATTA 59.467 45.455 30.48 0.00 0.00 1.40
1896 1961 1.323534 CGCGCGCTAGTGTAAAGAATT 59.676 47.619 30.48 0.00 0.00 2.17
1897 1962 0.921347 CGCGCGCTAGTGTAAAGAAT 59.079 50.000 30.48 0.00 0.00 2.40
1903 1968 0.659427 AGTAATCGCGCGCTAGTGTA 59.341 50.000 30.48 6.17 0.00 2.90
1904 1969 0.179145 AAGTAATCGCGCGCTAGTGT 60.179 50.000 30.48 11.97 0.00 3.55
1906 1971 0.099968 TGAAGTAATCGCGCGCTAGT 59.900 50.000 30.48 20.89 0.00 2.57
1907 1972 0.498927 GTGAAGTAATCGCGCGCTAG 59.501 55.000 30.48 15.15 0.00 3.42
1909 1974 1.153823 AGTGAAGTAATCGCGCGCT 60.154 52.632 30.48 14.34 43.53 5.92
1910 1975 1.013323 CAGTGAAGTAATCGCGCGC 60.013 57.895 27.95 23.91 43.53 6.86
1911 1976 0.989164 TTCAGTGAAGTAATCGCGCG 59.011 50.000 26.76 26.76 43.53 6.86
1912 1977 2.847254 GCATTCAGTGAAGTAATCGCGC 60.847 50.000 11.91 0.00 43.53 6.86
1913 1978 2.595188 CGCATTCAGTGAAGTAATCGCG 60.595 50.000 11.91 13.20 43.53 5.87
1914 1979 2.603110 TCGCATTCAGTGAAGTAATCGC 59.397 45.455 11.91 6.02 38.91 4.58
1915 1980 3.000322 GGTCGCATTCAGTGAAGTAATCG 60.000 47.826 11.91 9.53 38.73 3.34
1916 1981 3.000322 CGGTCGCATTCAGTGAAGTAATC 60.000 47.826 11.91 2.25 38.73 1.75
1917 1982 2.930040 CGGTCGCATTCAGTGAAGTAAT 59.070 45.455 11.91 0.00 38.73 1.89
1918 1983 2.029739 TCGGTCGCATTCAGTGAAGTAA 60.030 45.455 11.91 0.00 38.73 2.24
1919 1984 1.542472 TCGGTCGCATTCAGTGAAGTA 59.458 47.619 11.91 0.00 38.73 2.24
1920 1985 0.317160 TCGGTCGCATTCAGTGAAGT 59.683 50.000 11.91 0.00 38.73 3.01
1921 1986 0.994995 CTCGGTCGCATTCAGTGAAG 59.005 55.000 11.91 5.01 38.73 3.02
1923 1988 1.446099 GCTCGGTCGCATTCAGTGA 60.446 57.895 0.00 0.00 0.00 3.41
1926 1991 1.258982 GTATTGCTCGGTCGCATTCAG 59.741 52.381 0.00 0.00 40.04 3.02
1927 1992 1.286501 GTATTGCTCGGTCGCATTCA 58.713 50.000 0.00 0.00 40.04 2.57
1928 1993 1.286501 TGTATTGCTCGGTCGCATTC 58.713 50.000 0.00 0.00 40.04 2.67
1934 1999 2.668457 CTGTCTGTTGTATTGCTCGGTC 59.332 50.000 0.00 0.00 0.00 4.79
1935 2000 2.612972 CCTGTCTGTTGTATTGCTCGGT 60.613 50.000 0.00 0.00 0.00 4.69
1936 2001 2.002586 CCTGTCTGTTGTATTGCTCGG 58.997 52.381 0.00 0.00 0.00 4.63
1973 2038 2.286872 CTGATGTGATGGAGTGAAGCC 58.713 52.381 0.00 0.00 0.00 4.35
2059 2143 6.041637 TGTGTGGACACTCAATTTAGTACTCT 59.958 38.462 11.09 0.00 46.55 3.24
2060 2144 6.220930 TGTGTGGACACTCAATTTAGTACTC 58.779 40.000 11.09 0.00 46.55 2.59
2061 2145 6.169557 TGTGTGGACACTCAATTTAGTACT 57.830 37.500 11.09 0.00 46.55 2.73
2062 2146 7.817962 ACTATGTGTGGACACTCAATTTAGTAC 59.182 37.037 11.09 0.00 46.55 2.73
2075 2159 5.163290 TGGTACTTGAAACTATGTGTGGACA 60.163 40.000 0.00 0.00 36.22 4.02
2086 2170 9.533831 AATAATCTGGAATTGGTACTTGAAACT 57.466 29.630 0.00 0.00 0.00 2.66
2112 2196 3.996363 CGAGACCTCATGTGATGTTTCAA 59.004 43.478 8.76 0.00 32.48 2.69
2129 2224 4.523558 AGCTATGGGTAATTACCTCGAGAC 59.476 45.833 29.26 15.02 45.72 3.36
2131 2226 4.523173 TGAGCTATGGGTAATTACCTCGAG 59.477 45.833 29.26 23.02 45.72 4.04
2138 2240 5.130311 TGCTTGAGTGAGCTATGGGTAATTA 59.870 40.000 0.00 0.00 43.11 1.40
2145 2247 1.297664 GCTGCTTGAGTGAGCTATGG 58.702 55.000 0.00 0.00 43.11 2.74
2148 2250 0.390866 GCTGCTGCTTGAGTGAGCTA 60.391 55.000 8.53 0.00 43.11 3.32
2422 3674 2.097444 GCACAATGCTGATGCCGTA 58.903 52.632 0.00 0.00 40.96 4.02
2443 3695 0.323360 TACCTCCATGCACAAAGGGC 60.323 55.000 13.11 0.00 32.97 5.19
2525 3777 3.973973 CCCTGATTCTTACCTCCCATGTA 59.026 47.826 0.00 0.00 0.00 2.29
2526 3778 2.780010 CCCTGATTCTTACCTCCCATGT 59.220 50.000 0.00 0.00 0.00 3.21
2527 3779 2.780010 ACCCTGATTCTTACCTCCCATG 59.220 50.000 0.00 0.00 0.00 3.66
2528 3780 2.780010 CACCCTGATTCTTACCTCCCAT 59.220 50.000 0.00 0.00 0.00 4.00
2529 3781 2.196595 CACCCTGATTCTTACCTCCCA 58.803 52.381 0.00 0.00 0.00 4.37
2530 3782 2.478292 TCACCCTGATTCTTACCTCCC 58.522 52.381 0.00 0.00 0.00 4.30
2531 3783 3.263425 TGTTCACCCTGATTCTTACCTCC 59.737 47.826 0.00 0.00 0.00 4.30
2579 3832 5.306419 AGGAATAGAGGGGTACGTATTTTCC 59.694 44.000 0.00 2.38 35.46 3.13


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

AutoCloner maintained by Alex Coulton.