Multiple sequence alignment - TraesCS3D01G322100

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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 TraesCS3D01G322100 chr3D 100.000 2600 0 0 1 2600 435292745 435290146 0.000000e+00 4802.0
1 TraesCS3D01G322100 chr3D 93.016 673 43 4 1929 2600 501079270 501078601 0.000000e+00 979.0
2 TraesCS3D01G322100 chr3D 85.906 149 18 3 1730 1876 608073770 608073623 3.460000e-34 156.0
3 TraesCS3D01G322100 chr3B 93.352 1053 48 13 678 1724 571297172 571296136 0.000000e+00 1537.0
4 TraesCS3D01G322100 chr3B 91.392 697 34 10 1 679 571297896 571297208 0.000000e+00 931.0
5 TraesCS3D01G322100 chr3A 92.201 1013 37 19 678 1687 574010361 574009388 0.000000e+00 1395.0
6 TraesCS3D01G322100 chr3A 84.943 704 31 18 1 679 574011053 574010400 0.000000e+00 643.0
7 TraesCS3D01G322100 chr3A 86.207 145 19 1 1742 1885 729706431 729706575 3.460000e-34 156.0
8 TraesCS3D01G322100 chr3A 85.714 147 15 4 1731 1876 380925924 380926065 1.610000e-32 150.0
9 TraesCS3D01G322100 chr3A 83.673 147 19 3 1731 1876 380925062 380925204 1.620000e-27 134.0
10 TraesCS3D01G322100 chr2D 93.769 674 35 6 1930 2600 634276613 634275944 0.000000e+00 1005.0
11 TraesCS3D01G322100 chr5D 93.452 672 42 2 1930 2600 168013455 168014125 0.000000e+00 996.0
12 TraesCS3D01G322100 chr5D 93.145 671 44 2 1928 2598 311379249 311378581 0.000000e+00 983.0
13 TraesCS3D01G322100 chr7D 92.598 689 49 2 1913 2600 75957876 75958563 0.000000e+00 989.0
14 TraesCS3D01G322100 chr7D 93.304 672 41 4 1929 2600 454093251 454092584 0.000000e+00 989.0
15 TraesCS3D01G322100 chr7D 93.155 672 44 2 1929 2600 438546400 438545731 0.000000e+00 985.0
16 TraesCS3D01G322100 chr7D 77.778 234 39 9 438 661 20038102 20037872 5.840000e-27 132.0
17 TraesCS3D01G322100 chr6D 93.016 673 41 6 1930 2600 58833644 58834312 0.000000e+00 977.0
18 TraesCS3D01G322100 chr4D 92.647 680 44 5 1920 2598 322076178 322076852 0.000000e+00 974.0
19 TraesCS3D01G322100 chr2B 84.568 162 25 0 1724 1885 363794994 363794833 7.450000e-36 161.0
20 TraesCS3D01G322100 chr2B 95.349 43 1 1 54 96 794623420 794623461 1.670000e-07 67.6
21 TraesCS3D01G322100 chr2B 91.667 48 3 1 47 93 796837388 796837341 6.010000e-07 65.8
22 TraesCS3D01G322100 chr1D 84.516 155 24 0 1731 1885 110976190 110976036 1.250000e-33 154.0
23 TraesCS3D01G322100 chr6B 81.977 172 29 1 1752 1921 127118154 127117983 7.500000e-31 145.0
24 TraesCS3D01G322100 chr6B 100.000 30 0 0 1892 1921 667201079 667201050 3.610000e-04 56.5
25 TraesCS3D01G322100 chr4B 86.364 132 18 0 1754 1885 584122868 584122737 7.500000e-31 145.0
26 TraesCS3D01G322100 chr1B 83.439 157 21 5 1730 1885 495753112 495753264 9.700000e-30 141.0
27 TraesCS3D01G322100 chrUn 77.348 181 26 9 490 659 39537096 39537272 2.750000e-15 93.5
28 TraesCS3D01G322100 chr2A 91.667 48 3 1 47 93 764149055 764149008 6.010000e-07 65.8
29 TraesCS3D01G322100 chr6A 100.000 31 0 0 1891 1921 610290518 610290488 1.000000e-04 58.4


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 TraesCS3D01G322100 chr3D 435290146 435292745 2599 True 4802 4802 100.000 1 2600 1 chr3D.!!$R1 2599
1 TraesCS3D01G322100 chr3D 501078601 501079270 669 True 979 979 93.016 1929 2600 1 chr3D.!!$R2 671
2 TraesCS3D01G322100 chr3B 571296136 571297896 1760 True 1234 1537 92.372 1 1724 2 chr3B.!!$R1 1723
3 TraesCS3D01G322100 chr3A 574009388 574011053 1665 True 1019 1395 88.572 1 1687 2 chr3A.!!$R1 1686
4 TraesCS3D01G322100 chr2D 634275944 634276613 669 True 1005 1005 93.769 1930 2600 1 chr2D.!!$R1 670
5 TraesCS3D01G322100 chr5D 168013455 168014125 670 False 996 996 93.452 1930 2600 1 chr5D.!!$F1 670
6 TraesCS3D01G322100 chr5D 311378581 311379249 668 True 983 983 93.145 1928 2598 1 chr5D.!!$R1 670
7 TraesCS3D01G322100 chr7D 75957876 75958563 687 False 989 989 92.598 1913 2600 1 chr7D.!!$F1 687
8 TraesCS3D01G322100 chr7D 454092584 454093251 667 True 989 989 93.304 1929 2600 1 chr7D.!!$R3 671
9 TraesCS3D01G322100 chr7D 438545731 438546400 669 True 985 985 93.155 1929 2600 1 chr7D.!!$R2 671
10 TraesCS3D01G322100 chr6D 58833644 58834312 668 False 977 977 93.016 1930 2600 1 chr6D.!!$F1 670
11 TraesCS3D01G322100 chr4D 322076178 322076852 674 False 974 974 92.647 1920 2598 1 chr4D.!!$F1 678

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
147 148 0.851469 AGTACCGGATAGAGGCTGGA 59.149 55.0 9.46 0.0 35.69 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1922 0.095417 GCGCCTTCGTCTTGCTTTAG 59.905 55.0 0.0 0.0 38.14 1.85 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
147 148 0.851469 AGTACCGGATAGAGGCTGGA 59.149 55.000 9.46 0.00 35.69 3.86
171 172 6.615088 ACATGCAAGAGCTAAACTAATTGTG 58.385 36.000 0.00 0.00 42.74 3.33
186 193 7.251321 ACTAATTGTGGAGAAGAACTGAGAT 57.749 36.000 0.00 0.00 0.00 2.75
187 194 7.684529 ACTAATTGTGGAGAAGAACTGAGATT 58.315 34.615 0.00 0.00 0.00 2.40
188 195 6.814506 AATTGTGGAGAAGAACTGAGATTG 57.185 37.500 0.00 0.00 0.00 2.67
189 196 5.551305 TTGTGGAGAAGAACTGAGATTGA 57.449 39.130 0.00 0.00 0.00 2.57
190 197 5.144692 TGTGGAGAAGAACTGAGATTGAG 57.855 43.478 0.00 0.00 0.00 3.02
191 198 4.835056 TGTGGAGAAGAACTGAGATTGAGA 59.165 41.667 0.00 0.00 0.00 3.27
266 281 3.627577 AGGTAATATGTGCGCTTTCAAGG 59.372 43.478 9.73 0.00 0.00 3.61
304 320 3.989817 GTCAGTTTGGTGAATTGGAATGC 59.010 43.478 0.00 0.00 0.00 3.56
305 321 2.988493 CAGTTTGGTGAATTGGAATGCG 59.012 45.455 0.00 0.00 0.00 4.73
306 322 2.890311 AGTTTGGTGAATTGGAATGCGA 59.110 40.909 0.00 0.00 0.00 5.10
346 362 1.226746 CTCGGTTCCACTGAAACCAC 58.773 55.000 0.00 0.00 34.53 4.16
383 413 3.674997 ACCACACTTCACATGATACCAC 58.325 45.455 0.00 0.00 0.00 4.16
400 430 1.278127 CCACGGTACCACTCCTCAAAT 59.722 52.381 13.54 0.00 0.00 2.32
425 455 5.916318 TCAAATTTGCAAGTCTCCACAAAT 58.084 33.333 13.54 0.00 42.81 2.32
494 524 7.239763 TCCCTTAAATTTTCAGACCCAAATC 57.760 36.000 0.00 0.00 0.00 2.17
601 631 4.882671 TGTCTTCTTTGTTTCTCTGTGC 57.117 40.909 0.00 0.00 0.00 4.57
630 660 9.896263 ATTTCGAATTTGGGATTGAAAATTTTG 57.104 25.926 8.47 0.00 36.40 2.44
674 706 9.868277 TTGTGAACATTCAGAGTTTTATGTTTT 57.132 25.926 0.00 0.00 40.29 2.43
675 707 9.515020 TGTGAACATTCAGAGTTTTATGTTTTC 57.485 29.630 0.00 0.00 40.29 2.29
676 708 9.515020 GTGAACATTCAGAGTTTTATGTTTTCA 57.485 29.630 0.00 0.00 40.29 2.69
723 794 4.476361 CATGCATGCACAGCACAG 57.524 55.556 25.37 9.67 45.95 3.66
724 795 1.153842 CATGCATGCACAGCACAGG 60.154 57.895 25.37 7.15 45.95 4.00
725 796 1.303806 ATGCATGCACAGCACAGGA 60.304 52.632 25.37 0.00 45.95 3.86
941 1013 0.938713 CTGCGCTAGCTAGACGTACT 59.061 55.000 25.15 0.00 45.42 2.73
942 1014 2.133553 CTGCGCTAGCTAGACGTACTA 58.866 52.381 25.15 12.87 45.42 1.82
943 1015 1.863454 TGCGCTAGCTAGACGTACTAC 59.137 52.381 25.15 13.13 45.42 2.73
957 1029 1.336125 GTACTACGTCCTCCCCATTCG 59.664 57.143 0.00 0.00 0.00 3.34
1084 1156 1.617536 TGCTTCTGCCTCCCAGGAT 60.618 57.895 0.00 0.00 42.05 3.24
1131 1206 2.909577 GAGAGCCAGCAGGAGCAT 59.090 61.111 0.00 0.00 45.49 3.79
1270 1345 0.247736 CTTCGACTTCCTGGTGGAGG 59.752 60.000 0.00 0.00 44.24 4.30
1365 1440 4.647615 CTGATACGGGCCGGCGAG 62.648 72.222 31.78 19.26 0.00 5.03
1655 1730 1.661112 GAAAACGATGCGAGAGGGAAG 59.339 52.381 0.00 0.00 0.00 3.46
1696 1772 3.182967 GTGTCGCATTTGGTTTTCACAA 58.817 40.909 0.00 0.00 0.00 3.33
1701 1777 5.676310 GTCGCATTTGGTTTTCACAATTTTG 59.324 36.000 0.00 0.00 0.00 2.44
1705 1781 7.194962 GCATTTGGTTTTCACAATTTTGACAT 58.805 30.769 0.00 0.00 0.00 3.06
1706 1782 8.341173 GCATTTGGTTTTCACAATTTTGACATA 58.659 29.630 0.00 0.00 0.00 2.29
1724 1800 9.709495 TTTGACATAAGAAATCCAATTCCTTTG 57.291 29.630 0.00 0.00 34.93 2.77
1770 1846 9.948964 ACATTCCATTCTATTCATATTCGATCA 57.051 29.630 0.00 0.00 0.00 2.92
1774 1850 9.591792 TCCATTCTATTCATATTCGATCATGAC 57.408 33.333 0.00 0.00 31.04 3.06
1775 1851 9.374838 CCATTCTATTCATATTCGATCATGACA 57.625 33.333 0.00 2.98 31.04 3.58
1783 1859 8.061125 TCATATTCGATCATGACAGTAAAACG 57.939 34.615 0.00 0.00 0.00 3.60
1784 1860 7.918562 TCATATTCGATCATGACAGTAAAACGA 59.081 33.333 0.00 0.00 0.00 3.85
1785 1861 6.961359 ATTCGATCATGACAGTAAAACGAA 57.039 33.333 0.00 0.00 40.40 3.85
1786 1862 6.961359 TTCGATCATGACAGTAAAACGAAT 57.039 33.333 0.00 0.00 33.55 3.34
1787 1863 8.642908 ATTCGATCATGACAGTAAAACGAATA 57.357 30.769 0.00 0.00 42.89 1.75
1788 1864 7.445900 TCGATCATGACAGTAAAACGAATAC 57.554 36.000 0.00 0.00 0.00 1.89
1789 1865 6.474427 TCGATCATGACAGTAAAACGAATACC 59.526 38.462 0.00 0.00 0.00 2.73
1790 1866 6.254804 CGATCATGACAGTAAAACGAATACCA 59.745 38.462 0.00 0.00 0.00 3.25
1791 1867 6.961359 TCATGACAGTAAAACGAATACCAG 57.039 37.500 0.00 0.00 0.00 4.00
1792 1868 6.693466 TCATGACAGTAAAACGAATACCAGA 58.307 36.000 0.00 0.00 0.00 3.86
1793 1869 7.156000 TCATGACAGTAAAACGAATACCAGAA 58.844 34.615 0.00 0.00 0.00 3.02
1794 1870 7.658167 TCATGACAGTAAAACGAATACCAGAAA 59.342 33.333 0.00 0.00 0.00 2.52
1795 1871 7.972832 TGACAGTAAAACGAATACCAGAAAT 57.027 32.000 0.00 0.00 0.00 2.17
1796 1872 9.661563 ATGACAGTAAAACGAATACCAGAAATA 57.338 29.630 0.00 0.00 0.00 1.40
1797 1873 9.491675 TGACAGTAAAACGAATACCAGAAATAA 57.508 29.630 0.00 0.00 0.00 1.40
1824 1900 8.738645 AAAAATTGTATCCAGATCTGTAGACC 57.261 34.615 21.11 7.53 0.00 3.85
1825 1901 7.437713 AAATTGTATCCAGATCTGTAGACCA 57.562 36.000 21.11 5.66 0.00 4.02
1826 1902 5.854010 TTGTATCCAGATCTGTAGACCAC 57.146 43.478 21.11 13.10 0.00 4.16
1827 1903 3.883489 TGTATCCAGATCTGTAGACCACG 59.117 47.826 21.11 3.65 0.00 4.94
1828 1904 2.509166 TCCAGATCTGTAGACCACGT 57.491 50.000 21.11 0.00 0.00 4.49
1829 1905 3.639672 TCCAGATCTGTAGACCACGTA 57.360 47.619 21.11 0.00 0.00 3.57
1830 1906 3.542648 TCCAGATCTGTAGACCACGTAG 58.457 50.000 21.11 1.71 0.00 3.51
1831 1907 2.033550 CCAGATCTGTAGACCACGTAGC 59.966 54.545 21.11 0.00 0.00 3.58
1832 1908 1.941294 AGATCTGTAGACCACGTAGCG 59.059 52.381 0.00 0.00 0.00 4.26
1833 1909 1.938577 GATCTGTAGACCACGTAGCGA 59.061 52.381 0.00 0.00 0.00 4.93
1834 1910 1.081892 TCTGTAGACCACGTAGCGAC 58.918 55.000 0.00 0.00 0.00 5.19
1845 1921 3.689224 GTAGCGACGACTACAAGCA 57.311 52.632 18.38 0.00 41.81 3.91
1846 1922 1.257539 GTAGCGACGACTACAAGCAC 58.742 55.000 18.38 0.42 41.81 4.40
1847 1923 1.135746 GTAGCGACGACTACAAGCACT 60.136 52.381 18.38 0.00 41.81 4.40
1848 1924 1.162698 AGCGACGACTACAAGCACTA 58.837 50.000 0.00 0.00 0.00 2.74
1849 1925 1.538512 AGCGACGACTACAAGCACTAA 59.461 47.619 0.00 0.00 0.00 2.24
1850 1926 2.030540 AGCGACGACTACAAGCACTAAA 60.031 45.455 0.00 0.00 0.00 1.85
1851 1927 2.341760 GCGACGACTACAAGCACTAAAG 59.658 50.000 0.00 0.00 0.00 1.85
1852 1928 2.341760 CGACGACTACAAGCACTAAAGC 59.658 50.000 0.00 0.00 0.00 3.51
1853 1929 3.314553 GACGACTACAAGCACTAAAGCA 58.685 45.455 0.00 0.00 36.85 3.91
1854 1930 3.724374 ACGACTACAAGCACTAAAGCAA 58.276 40.909 0.00 0.00 36.85 3.91
1855 1931 3.741344 ACGACTACAAGCACTAAAGCAAG 59.259 43.478 0.00 0.00 36.85 4.01
1856 1932 3.987868 CGACTACAAGCACTAAAGCAAGA 59.012 43.478 0.00 0.00 36.85 3.02
1857 1933 4.143305 CGACTACAAGCACTAAAGCAAGAC 60.143 45.833 0.00 0.00 36.85 3.01
1858 1934 3.741344 ACTACAAGCACTAAAGCAAGACG 59.259 43.478 0.00 0.00 36.85 4.18
1859 1935 2.833794 ACAAGCACTAAAGCAAGACGA 58.166 42.857 0.00 0.00 36.85 4.20
1860 1936 3.202906 ACAAGCACTAAAGCAAGACGAA 58.797 40.909 0.00 0.00 36.85 3.85
1861 1937 3.248602 ACAAGCACTAAAGCAAGACGAAG 59.751 43.478 0.00 0.00 36.85 3.79
1862 1938 2.417719 AGCACTAAAGCAAGACGAAGG 58.582 47.619 0.00 0.00 36.85 3.46
1863 1939 1.135944 GCACTAAAGCAAGACGAAGGC 60.136 52.381 0.00 0.00 0.00 4.35
1864 1940 1.126846 CACTAAAGCAAGACGAAGGCG 59.873 52.381 0.00 0.00 44.79 5.52
1865 1941 0.095417 CTAAAGCAAGACGAAGGCGC 59.905 55.000 0.00 0.00 42.48 6.53
1866 1942 1.623081 TAAAGCAAGACGAAGGCGCG 61.623 55.000 0.00 0.00 42.48 6.86
1869 1945 4.139420 CAAGACGAAGGCGCGCTG 62.139 66.667 32.29 19.99 42.48 5.18
1883 1959 4.101448 GCTGCCATCACCGTCCCT 62.101 66.667 0.00 0.00 0.00 4.20
1884 1960 2.187946 CTGCCATCACCGTCCCTC 59.812 66.667 0.00 0.00 0.00 4.30
1885 1961 2.284625 TGCCATCACCGTCCCTCT 60.285 61.111 0.00 0.00 0.00 3.69
1886 1962 2.187946 GCCATCACCGTCCCTCTG 59.812 66.667 0.00 0.00 0.00 3.35
1887 1963 2.660064 GCCATCACCGTCCCTCTGT 61.660 63.158 0.00 0.00 0.00 3.41
1888 1964 1.219124 CCATCACCGTCCCTCTGTG 59.781 63.158 0.00 0.00 33.55 3.66
1889 1965 1.257750 CCATCACCGTCCCTCTGTGA 61.258 60.000 0.00 0.00 42.58 3.58
1890 1966 0.108615 CATCACCGTCCCTCTGTGAC 60.109 60.000 0.00 0.00 41.57 3.67
1898 1974 2.143925 GTCCCTCTGTGACGAAAAAGG 58.856 52.381 0.00 0.00 0.00 3.11
1899 1975 1.071699 TCCCTCTGTGACGAAAAAGGG 59.928 52.381 0.00 0.00 44.06 3.95
1900 1976 1.202770 CCCTCTGTGACGAAAAAGGGT 60.203 52.381 0.00 0.00 38.92 4.34
1901 1977 2.572290 CCTCTGTGACGAAAAAGGGTT 58.428 47.619 0.00 0.00 0.00 4.11
1902 1978 2.949644 CCTCTGTGACGAAAAAGGGTTT 59.050 45.455 0.00 0.00 0.00 3.27
1903 1979 3.380320 CCTCTGTGACGAAAAAGGGTTTT 59.620 43.478 0.00 0.00 39.70 2.43
1904 1980 4.497507 CCTCTGTGACGAAAAAGGGTTTTC 60.498 45.833 0.00 2.51 46.17 2.29
1905 1981 3.379057 TCTGTGACGAAAAAGGGTTTTCC 59.621 43.478 6.40 0.00 46.69 3.13
1949 2025 1.296056 GACAACGCTAACGCCCACAT 61.296 55.000 0.00 0.00 45.53 3.21
1980 2056 2.972505 CAAACCCGCTCACACGCT 60.973 61.111 0.00 0.00 0.00 5.07
2102 2178 6.781138 TCCGATTGAAGATTCATTTTTACCG 58.219 36.000 0.00 0.00 37.00 4.02
2207 2285 5.733226 TGTCTATTGCACATGAATTACCG 57.267 39.130 0.00 0.00 0.00 4.02
2251 2329 9.941325 TTGCCATGATATGTTTCAACTATTTTT 57.059 25.926 0.00 0.00 0.00 1.94
2350 2429 6.509656 ACTAAAATTGCCATGATACATGCAG 58.490 36.000 0.00 0.00 34.81 4.41
2455 2535 8.121305 TGCCATGATCTACAAACTAAAATTGT 57.879 30.769 0.00 0.00 43.14 2.71
2475 2555 4.930963 TGTCACATGGCAACTTTAGTTTG 58.069 39.130 0.00 0.00 35.83 2.93
2486 2566 5.048713 GCAACTTTAGTTTGAGCACTATGGT 60.049 40.000 0.00 0.00 35.83 3.55
2554 2638 3.621268 CGTCGAAACATATCAACATGGGT 59.379 43.478 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 6.349611 CCACAATTAGTTTAGCTCTTGCATGT 60.350 38.462 0.00 0.00 42.74 3.21
171 172 6.279513 TCTTCTCAATCTCAGTTCTTCTCC 57.720 41.667 0.00 0.00 0.00 3.71
304 320 2.987149 GAGTACATCCGTATTGCCATCG 59.013 50.000 0.00 0.00 0.00 3.84
305 321 3.326747 GGAGTACATCCGTATTGCCATC 58.673 50.000 0.00 0.00 38.67 3.51
306 322 3.402628 GGAGTACATCCGTATTGCCAT 57.597 47.619 0.00 0.00 38.67 4.40
346 362 3.314635 GTGTGGTATCCCTCGTACTGTAG 59.685 52.174 0.00 0.00 0.00 2.74
378 408 0.405198 TGAGGAGTGGTACCGTGGTA 59.595 55.000 7.57 0.00 0.00 3.25
380 410 0.682852 TTTGAGGAGTGGTACCGTGG 59.317 55.000 7.57 0.00 0.00 4.94
383 413 3.670625 TGAAATTTGAGGAGTGGTACCG 58.329 45.455 7.57 0.00 0.00 4.02
400 430 5.336150 TGTGGAGACTTGCAAATTTGAAA 57.664 34.783 22.31 16.63 0.00 2.69
425 455 6.773080 TGAACGTTCACAACTTTTATCGAAA 58.227 32.000 26.53 0.00 31.01 3.46
463 493 8.002459 GGGTCTGAAAATTTAAGGGATGGTATA 58.998 37.037 0.00 0.00 0.00 1.47
468 498 6.603940 TTGGGTCTGAAAATTTAAGGGATG 57.396 37.500 0.00 0.00 0.00 3.51
494 524 9.289303 CCTTTTGTTTCTCATTGTATATTTCGG 57.711 33.333 0.00 0.00 0.00 4.30
522 552 5.180117 GTGACACTGTTCATGCTAGATTTGT 59.820 40.000 0.00 0.00 0.00 2.83
601 631 3.768406 TCAATCCCAAATTCGAAATGCG 58.232 40.909 0.00 0.00 42.69 4.73
630 660 5.724328 TCACAACATGAGTCTACAATCTCC 58.276 41.667 0.00 0.00 31.91 3.71
668 700 8.344831 CGTCATACCATGATACAATGAAAACAT 58.655 33.333 0.00 0.00 42.04 2.71
670 702 7.915508 TCGTCATACCATGATACAATGAAAAC 58.084 34.615 0.00 0.00 42.04 2.43
674 706 6.991938 TGATCGTCATACCATGATACAATGA 58.008 36.000 0.00 0.00 42.04 2.57
675 707 7.675637 GCATGATCGTCATACCATGATACAATG 60.676 40.741 0.00 0.00 42.04 2.82
676 708 6.314648 GCATGATCGTCATACCATGATACAAT 59.685 38.462 0.00 0.00 42.04 2.71
713 784 0.040958 CTTCGTTTCCTGTGCTGTGC 60.041 55.000 0.00 0.00 0.00 4.57
714 785 1.261619 GACTTCGTTTCCTGTGCTGTG 59.738 52.381 0.00 0.00 0.00 3.66
715 786 1.583054 GACTTCGTTTCCTGTGCTGT 58.417 50.000 0.00 0.00 0.00 4.40
716 787 0.508641 CGACTTCGTTTCCTGTGCTG 59.491 55.000 0.00 0.00 34.11 4.41
717 788 0.387929 TCGACTTCGTTTCCTGTGCT 59.612 50.000 0.00 0.00 40.80 4.40
718 789 0.784778 CTCGACTTCGTTTCCTGTGC 59.215 55.000 0.00 0.00 40.80 4.57
719 790 2.052157 GACTCGACTTCGTTTCCTGTG 58.948 52.381 0.00 0.00 40.80 3.66
720 791 1.679680 TGACTCGACTTCGTTTCCTGT 59.320 47.619 0.00 0.00 40.80 4.00
721 792 2.417339 TGACTCGACTTCGTTTCCTG 57.583 50.000 0.00 0.00 40.80 3.86
722 793 2.740452 GTTGACTCGACTTCGTTTCCT 58.260 47.619 0.00 0.00 40.80 3.36
723 794 1.450905 CGTTGACTCGACTTCGTTTCC 59.549 52.381 0.00 0.00 40.80 3.13
724 795 2.378806 TCGTTGACTCGACTTCGTTTC 58.621 47.619 0.00 0.00 40.80 2.78
725 796 2.480224 TCGTTGACTCGACTTCGTTT 57.520 45.000 0.00 0.00 40.80 3.60
941 1013 1.380785 AGCGAATGGGGAGGACGTA 60.381 57.895 0.00 0.00 0.00 3.57
942 1014 2.683933 AGCGAATGGGGAGGACGT 60.684 61.111 0.00 0.00 0.00 4.34
943 1015 2.107141 GAGCGAATGGGGAGGACG 59.893 66.667 0.00 0.00 0.00 4.79
957 1029 0.521735 AAATTCGAACGCCTTGGAGC 59.478 50.000 0.00 0.00 0.00 4.70
1060 1132 1.739562 GGAGGCAGAAGCACGTGAG 60.740 63.158 22.23 3.87 44.61 3.51
1069 1141 1.207791 GAGAATCCTGGGAGGCAGAA 58.792 55.000 0.00 0.00 34.61 3.02
1084 1156 1.348064 TCCGGCTTCTTCTTGGAGAA 58.652 50.000 0.00 0.00 34.63 2.87
1297 1372 2.030562 GTATCCATGGACCGCCCG 59.969 66.667 18.99 0.00 37.93 6.13
1298 1373 1.071471 CAGTATCCATGGACCGCCC 59.929 63.158 18.99 3.18 0.00 6.13
1299 1374 1.598130 GCAGTATCCATGGACCGCC 60.598 63.158 18.99 5.10 0.00 6.13
1300 1375 1.598130 GGCAGTATCCATGGACCGC 60.598 63.158 18.99 16.45 0.00 5.68
1301 1376 1.071471 GGGCAGTATCCATGGACCG 59.929 63.158 18.99 6.88 0.00 4.79
1302 1377 1.071471 CGGGCAGTATCCATGGACC 59.929 63.158 18.99 13.38 0.00 4.46
1438 1513 0.820871 GACGCCATCCTCTTCAGAGT 59.179 55.000 3.15 0.00 40.48 3.24
1655 1730 0.725784 CAACTTCATGCAACGACGGC 60.726 55.000 0.00 0.00 0.00 5.68
1744 1820 9.948964 TGATCGAATATGAATAGAATGGAATGT 57.051 29.630 0.00 0.00 0.00 2.71
1748 1824 9.591792 GTCATGATCGAATATGAATAGAATGGA 57.408 33.333 14.26 0.00 35.29 3.41
1749 1825 9.374838 TGTCATGATCGAATATGAATAGAATGG 57.625 33.333 14.26 0.00 35.29 3.16
1757 1833 8.539674 CGTTTTACTGTCATGATCGAATATGAA 58.460 33.333 14.26 6.70 35.29 2.57
1758 1834 7.918562 TCGTTTTACTGTCATGATCGAATATGA 59.081 33.333 0.00 9.99 0.00 2.15
1759 1835 8.061125 TCGTTTTACTGTCATGATCGAATATG 57.939 34.615 0.00 6.05 0.00 1.78
1760 1836 8.642908 TTCGTTTTACTGTCATGATCGAATAT 57.357 30.769 0.00 0.00 31.63 1.28
1761 1837 8.642908 ATTCGTTTTACTGTCATGATCGAATA 57.357 30.769 0.00 0.00 41.39 1.75
1762 1838 6.961359 TTCGTTTTACTGTCATGATCGAAT 57.039 33.333 0.00 0.00 31.63 3.34
1763 1839 6.961359 ATTCGTTTTACTGTCATGATCGAA 57.039 33.333 0.00 6.56 38.67 3.71
1764 1840 6.474427 GGTATTCGTTTTACTGTCATGATCGA 59.526 38.462 0.00 0.00 0.00 3.59
1765 1841 6.254804 TGGTATTCGTTTTACTGTCATGATCG 59.745 38.462 0.00 0.00 0.00 3.69
1766 1842 7.491372 TCTGGTATTCGTTTTACTGTCATGATC 59.509 37.037 0.00 0.00 0.00 2.92
1767 1843 7.327975 TCTGGTATTCGTTTTACTGTCATGAT 58.672 34.615 0.00 0.00 0.00 2.45
1768 1844 6.693466 TCTGGTATTCGTTTTACTGTCATGA 58.307 36.000 0.00 0.00 0.00 3.07
1769 1845 6.961359 TCTGGTATTCGTTTTACTGTCATG 57.039 37.500 0.00 0.00 0.00 3.07
1770 1846 7.972832 TTTCTGGTATTCGTTTTACTGTCAT 57.027 32.000 0.00 0.00 0.00 3.06
1771 1847 7.972832 ATTTCTGGTATTCGTTTTACTGTCA 57.027 32.000 0.00 0.00 0.00 3.58
1806 1882 3.884091 ACGTGGTCTACAGATCTGGATAC 59.116 47.826 26.08 19.74 34.19 2.24
1807 1883 4.166246 ACGTGGTCTACAGATCTGGATA 57.834 45.455 26.08 8.40 34.19 2.59
1808 1884 3.019799 ACGTGGTCTACAGATCTGGAT 57.980 47.619 26.08 9.29 34.19 3.41
1809 1885 2.509166 ACGTGGTCTACAGATCTGGA 57.491 50.000 26.08 17.86 34.19 3.86
1810 1886 2.033550 GCTACGTGGTCTACAGATCTGG 59.966 54.545 26.08 9.99 34.19 3.86
1811 1887 2.286477 CGCTACGTGGTCTACAGATCTG 60.286 54.545 21.37 21.37 0.00 2.90
1812 1888 1.941294 CGCTACGTGGTCTACAGATCT 59.059 52.381 0.00 0.00 0.00 2.75
1813 1889 1.938577 TCGCTACGTGGTCTACAGATC 59.061 52.381 0.00 0.00 0.00 2.75
1814 1890 1.669779 GTCGCTACGTGGTCTACAGAT 59.330 52.381 0.00 0.00 0.00 2.90
1815 1891 1.081892 GTCGCTACGTGGTCTACAGA 58.918 55.000 0.00 0.00 0.00 3.41
1816 1892 0.247576 CGTCGCTACGTGGTCTACAG 60.248 60.000 2.05 0.00 44.21 2.74
1817 1893 1.789751 CGTCGCTACGTGGTCTACA 59.210 57.895 2.05 0.00 44.21 2.74
1818 1894 4.659002 CGTCGCTACGTGGTCTAC 57.341 61.111 2.05 0.00 44.21 2.59
1827 1903 1.135746 AGTGCTTGTAGTCGTCGCTAC 60.136 52.381 15.52 15.52 41.13 3.58
1828 1904 1.162698 AGTGCTTGTAGTCGTCGCTA 58.837 50.000 0.00 0.00 0.00 4.26
1829 1905 1.162698 TAGTGCTTGTAGTCGTCGCT 58.837 50.000 0.00 0.00 0.00 4.93
1830 1906 1.973138 TTAGTGCTTGTAGTCGTCGC 58.027 50.000 0.00 0.00 0.00 5.19
1831 1907 2.341760 GCTTTAGTGCTTGTAGTCGTCG 59.658 50.000 0.00 0.00 0.00 5.12
1832 1908 3.314553 TGCTTTAGTGCTTGTAGTCGTC 58.685 45.455 0.00 0.00 0.00 4.20
1833 1909 3.380479 TGCTTTAGTGCTTGTAGTCGT 57.620 42.857 0.00 0.00 0.00 4.34
1834 1910 3.987868 TCTTGCTTTAGTGCTTGTAGTCG 59.012 43.478 0.00 0.00 0.00 4.18
1835 1911 4.143305 CGTCTTGCTTTAGTGCTTGTAGTC 60.143 45.833 0.00 0.00 0.00 2.59
1836 1912 3.741344 CGTCTTGCTTTAGTGCTTGTAGT 59.259 43.478 0.00 0.00 0.00 2.73
1837 1913 3.987868 TCGTCTTGCTTTAGTGCTTGTAG 59.012 43.478 0.00 0.00 0.00 2.74
1838 1914 3.985008 TCGTCTTGCTTTAGTGCTTGTA 58.015 40.909 0.00 0.00 0.00 2.41
1839 1915 2.833794 TCGTCTTGCTTTAGTGCTTGT 58.166 42.857 0.00 0.00 0.00 3.16
1840 1916 3.364366 CCTTCGTCTTGCTTTAGTGCTTG 60.364 47.826 0.00 0.00 0.00 4.01
1841 1917 2.808543 CCTTCGTCTTGCTTTAGTGCTT 59.191 45.455 0.00 0.00 0.00 3.91
1842 1918 2.417719 CCTTCGTCTTGCTTTAGTGCT 58.582 47.619 0.00 0.00 0.00 4.40
1843 1919 1.135944 GCCTTCGTCTTGCTTTAGTGC 60.136 52.381 0.00 0.00 0.00 4.40
1844 1920 1.126846 CGCCTTCGTCTTGCTTTAGTG 59.873 52.381 0.00 0.00 0.00 2.74
1845 1921 1.429463 CGCCTTCGTCTTGCTTTAGT 58.571 50.000 0.00 0.00 0.00 2.24
1846 1922 0.095417 GCGCCTTCGTCTTGCTTTAG 59.905 55.000 0.00 0.00 38.14 1.85
1847 1923 1.623081 CGCGCCTTCGTCTTGCTTTA 61.623 55.000 0.00 0.00 38.14 1.85
1848 1924 2.946762 GCGCCTTCGTCTTGCTTT 59.053 55.556 0.00 0.00 38.14 3.51
1849 1925 3.414700 CGCGCCTTCGTCTTGCTT 61.415 61.111 0.00 0.00 38.14 3.91
1852 1928 4.139420 CAGCGCGCCTTCGTCTTG 62.139 66.667 30.33 13.35 38.14 3.02
1866 1942 4.101448 AGGGACGGTGATGGCAGC 62.101 66.667 0.00 0.00 39.10 5.25
1867 1943 2.187946 GAGGGACGGTGATGGCAG 59.812 66.667 0.00 0.00 0.00 4.85
1868 1944 2.284625 AGAGGGACGGTGATGGCA 60.285 61.111 0.00 0.00 0.00 4.92
1869 1945 2.187946 CAGAGGGACGGTGATGGC 59.812 66.667 0.00 0.00 0.00 4.40
1870 1946 1.219124 CACAGAGGGACGGTGATGG 59.781 63.158 0.00 0.00 45.00 3.51
1871 1947 2.276869 TCACAGAGGGACGGTGATG 58.723 57.895 0.00 0.00 45.55 3.07
1872 1948 4.865629 TCACAGAGGGACGGTGAT 57.134 55.556 0.00 0.00 45.55 3.06
1878 1954 2.143925 CCTTTTTCGTCACAGAGGGAC 58.856 52.381 0.00 0.00 0.00 4.46
1879 1955 1.071699 CCCTTTTTCGTCACAGAGGGA 59.928 52.381 0.00 0.00 45.37 4.20
1880 1956 1.523758 CCCTTTTTCGTCACAGAGGG 58.476 55.000 0.00 0.00 38.03 4.30
1881 1957 2.256117 ACCCTTTTTCGTCACAGAGG 57.744 50.000 0.00 0.00 0.00 3.69
1882 1958 4.598062 GAAAACCCTTTTTCGTCACAGAG 58.402 43.478 0.00 0.00 40.90 3.35
1883 1959 4.625972 GAAAACCCTTTTTCGTCACAGA 57.374 40.909 0.00 0.00 40.90 3.41
1891 1967 2.902705 AAGCGGGAAAACCCTTTTTC 57.097 45.000 0.00 1.91 46.88 2.29
1892 1968 4.967084 ATAAAGCGGGAAAACCCTTTTT 57.033 36.364 0.00 0.00 39.19 1.94
1893 1969 6.614694 AATATAAAGCGGGAAAACCCTTTT 57.385 33.333 0.00 0.00 39.19 2.27
1894 1970 7.907841 ATAATATAAAGCGGGAAAACCCTTT 57.092 32.000 0.00 0.00 40.53 3.11
1895 1971 8.999905 TTATAATATAAAGCGGGAAAACCCTT 57.000 30.769 0.00 0.00 34.99 3.95
1916 1992 7.254185 CGTTAGCGTTGTCCTTGCTTTATTATA 60.254 37.037 0.00 0.00 40.06 0.98
1925 2001 1.154469 GCGTTAGCGTTGTCCTTGC 60.154 57.895 0.00 0.00 40.81 4.01
1926 2002 1.495951 GGCGTTAGCGTTGTCCTTG 59.504 57.895 0.00 0.00 46.35 3.61
1949 2025 1.040339 GGTTTGGCTTCCACCACACA 61.040 55.000 2.62 0.00 41.32 3.72
1980 2056 4.011698 TGGCGTAGTCTGTGTGTTATAGA 58.988 43.478 0.00 0.00 0.00 1.98
2098 2174 1.102154 TCGCGAGGGATTTAACGGTA 58.898 50.000 3.71 0.00 0.00 4.02
2102 2178 3.334078 TCGTCGCGAGGGATTTAAC 57.666 52.632 26.64 3.83 0.00 2.01
2207 2285 6.494893 TGGCAACTTCAGTGTAAATATCAC 57.505 37.500 0.00 0.00 35.07 3.06
2293 2371 6.749118 GCATGGCAAGTCTAGTTTCTTAATTG 59.251 38.462 0.00 0.00 0.00 2.32
2377 2456 9.357652 CCAGTACTTTGACCATGAAAATATTTG 57.642 33.333 0.39 0.00 0.00 2.32
2455 2535 4.261572 GCTCAAACTAAAGTTGCCATGTGA 60.262 41.667 0.00 0.00 38.44 3.58
2475 2555 5.326200 ACACTGTAGTTACCATAGTGCTC 57.674 43.478 7.47 0.00 41.74 4.26
2486 2566 6.468543 TGCCATGATGTTTACACTGTAGTTA 58.531 36.000 0.00 0.00 0.00 2.24
2554 2638 6.148976 TCTCGACGAGATCTTCAAAACTAGAA 59.851 38.462 23.27 0.00 33.35 2.10


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

AutoCloner maintained by Alex Coulton.