Multiple sequence alignment - TraesCS4D01G167800

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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 TraesCS4D01G167800 chr4D 100.000 2396 0 0 1 2396 291764412 291766807 0.000000e+00 4425.0
1 TraesCS4D01G167800 chr4B 90.539 835 45 14 1 804 273645977 273645146 0.000000e+00 1074.0
2 TraesCS4D01G167800 chr4A 92.995 571 37 3 1 569 210957020 210956451 0.000000e+00 830.0
3 TraesCS4D01G167800 chr4A 88.911 496 25 10 743 1233 210931522 210931052 3.430000e-163 584.0
4 TraesCS4D01G167800 chr4A 90.517 348 20 6 1239 1582 211052293 211052631 4.700000e-122 448.0
5 TraesCS4D01G167800 chr4A 92.369 249 17 2 1578 1825 211052745 211052992 1.050000e-93 353.0
6 TraesCS4D01G167800 chr4A 88.060 134 11 3 621 750 210955364 210955232 1.150000e-33 154.0
7 TraesCS4D01G167800 chr4A 97.778 45 1 0 565 609 210955604 210955560 7.100000e-11 78.7
8 TraesCS4D01G167800 chr4A 100.000 34 0 0 608 641 210955400 210955367 1.990000e-06 63.9
9 TraesCS4D01G167800 chr1B 95.127 472 20 3 1924 2394 674959974 674960443 0.000000e+00 741.0
10 TraesCS4D01G167800 chr1B 95.370 108 5 0 1825 1932 674957257 674957364 3.170000e-39 172.0
11 TraesCS4D01G167800 chr3D 73.962 265 61 8 281 543 340285037 340284779 1.520000e-17 100.0


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 TraesCS4D01G167800 chr4D 291764412 291766807 2395 False 4425.00 4425 100.00000 1 2396 1 chr4D.!!$F1 2395
1 TraesCS4D01G167800 chr4B 273645146 273645977 831 True 1074.00 1074 90.53900 1 804 1 chr4B.!!$R1 803
2 TraesCS4D01G167800 chr4A 211052293 211052992 699 False 400.50 448 91.44300 1239 1825 2 chr4A.!!$F1 586
3 TraesCS4D01G167800 chr4A 210955232 210957020 1788 True 281.65 830 94.70825 1 750 4 chr4A.!!$R2 749
4 TraesCS4D01G167800 chr1B 674957257 674960443 3186 False 456.50 741 95.24850 1825 2394 2 chr1B.!!$F1 569

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
120 121 0.038159 CCCTTCTCGAAAGTCGCTGT 60.038 55.0 0.00 0.00 40.21 4.40 F
1006 2055 0.037326 TCTCTCGTCAACCATGGCAC 60.037 55.0 13.04 5.27 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1010 2059 0.032952 TACGAACAGGAGCAGCGTTT 59.967 50.000 0.00 0.0 36.51 3.60 R
2106 5896 1.588139 GGTGACGGCGTTCCTATCG 60.588 63.158 16.19 0.0 0.00 2.92 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
28 29 2.153645 GATCACACATTCACACAGCCA 58.846 47.619 0.00 0.00 0.00 4.75
119 120 0.243907 TCCCTTCTCGAAAGTCGCTG 59.756 55.000 0.00 0.00 40.21 5.18
120 121 0.038159 CCCTTCTCGAAAGTCGCTGT 60.038 55.000 0.00 0.00 40.21 4.40
178 180 4.215109 AGGCGTAGATTTGGGCATTTTAT 58.785 39.130 0.00 0.00 0.00 1.40
241 243 4.866508 TTCATGTATAGGTTCTAGGCGG 57.133 45.455 0.00 0.00 0.00 6.13
321 323 4.344390 ACGTAGGAACAGAAAGTCTTCCTT 59.656 41.667 3.59 0.00 41.84 3.36
364 366 3.930035 TGGTTGAAAGGTTTGGGGTAAT 58.070 40.909 0.00 0.00 0.00 1.89
536 539 8.908903 ACATTTTACTGTGGTTTGACTTTGATA 58.091 29.630 0.00 0.00 0.00 2.15
595 1450 1.013596 TCTGTGTGTGTTTTCCTGCG 58.986 50.000 0.00 0.00 0.00 5.18
641 1657 3.906846 AGGCCCTTAGATGATACTTCCTG 59.093 47.826 0.00 0.00 0.00 3.86
646 1685 6.653989 CCCTTAGATGATACTTCCTGTGTTT 58.346 40.000 0.00 0.00 0.00 2.83
726 1769 4.755123 AGAAACTTTCATGTGGAACCGTAG 59.245 41.667 4.34 0.00 34.56 3.51
731 1774 1.070914 TCATGTGGAACCGTAGCAACA 59.929 47.619 0.00 0.00 34.36 3.33
755 1798 7.601130 ACAAAACATCTCATTCAATCAATGGTG 59.399 33.333 0.00 0.00 42.18 4.17
756 1799 6.845758 AACATCTCATTCAATCAATGGTGT 57.154 33.333 0.00 0.00 42.18 4.16
763 1806 6.741109 TCATTCAATCAATGGTGTATGCATC 58.259 36.000 0.19 0.00 42.18 3.91
769 1813 5.313520 TCAATGGTGTATGCATCTTGTTG 57.686 39.130 0.19 2.94 0.00 3.33
801 1850 3.057969 CTCAGGTTAACATGAGTGGCA 57.942 47.619 32.14 9.04 46.27 4.92
804 1853 0.168128 GGTTAACATGAGTGGCACGC 59.832 55.000 14.83 14.83 40.45 5.34
813 1862 2.049433 GTGGCACGCTCGTGTAGT 60.049 61.111 21.30 0.00 46.90 2.73
814 1863 1.663702 GTGGCACGCTCGTGTAGTT 60.664 57.895 21.30 0.00 46.90 2.24
815 1864 1.068417 TGGCACGCTCGTGTAGTTT 59.932 52.632 21.30 0.00 46.90 2.66
816 1865 1.218875 TGGCACGCTCGTGTAGTTTG 61.219 55.000 21.30 0.00 46.90 2.93
817 1866 0.942410 GGCACGCTCGTGTAGTTTGA 60.942 55.000 21.30 0.00 46.90 2.69
818 1867 0.856641 GCACGCTCGTGTAGTTTGAA 59.143 50.000 21.30 0.00 46.90 2.69
819 1868 1.396815 GCACGCTCGTGTAGTTTGAAC 60.397 52.381 21.30 0.59 46.90 3.18
820 1869 1.855978 CACGCTCGTGTAGTTTGAACA 59.144 47.619 13.66 0.00 40.91 3.18
821 1870 1.856597 ACGCTCGTGTAGTTTGAACAC 59.143 47.619 0.00 0.00 43.04 3.32
822 1871 1.855978 CGCTCGTGTAGTTTGAACACA 59.144 47.619 7.10 0.00 46.05 3.72
823 1872 2.283086 CGCTCGTGTAGTTTGAACACAA 59.717 45.455 7.10 0.00 46.05 3.33
824 1873 3.242155 CGCTCGTGTAGTTTGAACACAAA 60.242 43.478 7.10 0.00 46.05 2.83
825 1874 4.551990 CGCTCGTGTAGTTTGAACACAAAT 60.552 41.667 7.10 0.00 46.05 2.32
826 1875 4.904154 GCTCGTGTAGTTTGAACACAAATC 59.096 41.667 7.10 0.00 46.05 2.17
827 1876 5.412526 TCGTGTAGTTTGAACACAAATCC 57.587 39.130 7.10 0.00 46.05 3.01
828 1877 4.025563 TCGTGTAGTTTGAACACAAATCCG 60.026 41.667 7.10 0.00 46.05 4.18
829 1878 4.533222 GTGTAGTTTGAACACAAATCCGG 58.467 43.478 0.00 0.00 45.26 5.14
830 1879 3.566322 TGTAGTTTGAACACAAATCCGGG 59.434 43.478 0.00 0.00 36.22 5.73
831 1880 1.339929 AGTTTGAACACAAATCCGGGC 59.660 47.619 0.00 0.00 36.22 6.13
832 1881 0.676736 TTTGAACACAAATCCGGGCC 59.323 50.000 0.00 0.00 0.00 5.80
833 1882 1.519751 TTGAACACAAATCCGGGCCG 61.520 55.000 21.46 21.46 0.00 6.13
834 1883 1.673009 GAACACAAATCCGGGCCGA 60.673 57.895 30.79 14.42 0.00 5.54
835 1884 1.918868 GAACACAAATCCGGGCCGAC 61.919 60.000 30.79 1.49 0.00 4.79
836 1885 2.046314 CACAAATCCGGGCCGACT 60.046 61.111 30.79 11.42 0.00 4.18
837 1886 2.106683 CACAAATCCGGGCCGACTC 61.107 63.158 30.79 0.00 0.00 3.36
838 1887 2.291043 ACAAATCCGGGCCGACTCT 61.291 57.895 30.79 6.07 0.00 3.24
839 1888 0.974010 ACAAATCCGGGCCGACTCTA 60.974 55.000 30.79 7.46 0.00 2.43
840 1889 0.529992 CAAATCCGGGCCGACTCTAC 60.530 60.000 30.79 0.00 0.00 2.59
841 1890 0.974010 AAATCCGGGCCGACTCTACA 60.974 55.000 30.79 1.68 0.00 2.74
842 1891 1.392710 AATCCGGGCCGACTCTACAG 61.393 60.000 30.79 8.01 0.00 2.74
843 1892 2.280404 ATCCGGGCCGACTCTACAGA 62.280 60.000 30.79 13.98 0.00 3.41
844 1893 2.772691 CCGGGCCGACTCTACAGAC 61.773 68.421 30.79 0.00 0.00 3.51
845 1894 2.799371 GGGCCGACTCTACAGACG 59.201 66.667 0.00 0.00 37.52 4.18
846 1895 2.102553 GGCCGACTCTACAGACGC 59.897 66.667 0.00 0.00 36.60 5.19
847 1896 2.102553 GCCGACTCTACAGACGCC 59.897 66.667 0.00 0.00 36.60 5.68
848 1897 2.799371 CCGACTCTACAGACGCCC 59.201 66.667 0.00 0.00 36.60 6.13
849 1898 2.403987 CGACTCTACAGACGCCCG 59.596 66.667 0.00 0.00 31.18 6.13
850 1899 2.104859 CGACTCTACAGACGCCCGA 61.105 63.158 0.00 0.00 31.18 5.14
851 1900 1.428620 GACTCTACAGACGCCCGAC 59.571 63.158 0.00 0.00 0.00 4.79
852 1901 1.002379 ACTCTACAGACGCCCGACT 60.002 57.895 0.00 0.00 0.00 4.18
853 1902 1.025647 ACTCTACAGACGCCCGACTC 61.026 60.000 0.00 0.00 0.00 3.36
854 1903 1.716826 CTCTACAGACGCCCGACTCC 61.717 65.000 0.00 0.00 0.00 3.85
855 1904 2.753043 TACAGACGCCCGACTCCC 60.753 66.667 0.00 0.00 0.00 4.30
856 1905 3.572447 TACAGACGCCCGACTCCCA 62.572 63.158 0.00 0.00 0.00 4.37
857 1906 4.436998 CAGACGCCCGACTCCCAC 62.437 72.222 0.00 0.00 0.00 4.61
858 1907 4.680537 AGACGCCCGACTCCCACT 62.681 66.667 0.00 0.00 0.00 4.00
859 1908 4.131088 GACGCCCGACTCCCACTC 62.131 72.222 0.00 0.00 0.00 3.51
862 1911 3.462678 GCCCGACTCCCACTCCTC 61.463 72.222 0.00 0.00 0.00 3.71
863 1912 3.141488 CCCGACTCCCACTCCTCG 61.141 72.222 0.00 0.00 0.00 4.63
864 1913 3.827898 CCGACTCCCACTCCTCGC 61.828 72.222 0.00 0.00 0.00 5.03
865 1914 4.180946 CGACTCCCACTCCTCGCG 62.181 72.222 0.00 0.00 0.00 5.87
866 1915 3.063084 GACTCCCACTCCTCGCGT 61.063 66.667 5.77 0.00 0.00 6.01
867 1916 2.600769 ACTCCCACTCCTCGCGTT 60.601 61.111 5.77 0.00 0.00 4.84
868 1917 2.156051 GACTCCCACTCCTCGCGTTT 62.156 60.000 5.77 0.00 0.00 3.60
869 1918 0.896940 ACTCCCACTCCTCGCGTTTA 60.897 55.000 5.77 0.00 0.00 2.01
870 1919 0.245539 CTCCCACTCCTCGCGTTTAA 59.754 55.000 5.77 0.00 0.00 1.52
871 1920 0.680618 TCCCACTCCTCGCGTTTAAA 59.319 50.000 5.77 0.00 0.00 1.52
872 1921 1.070445 TCCCACTCCTCGCGTTTAAAA 59.930 47.619 5.77 0.00 0.00 1.52
873 1922 1.874872 CCCACTCCTCGCGTTTAAAAA 59.125 47.619 5.77 0.00 0.00 1.94
897 1946 3.500635 CCCCCTTCCTCTGTTGCT 58.499 61.111 0.00 0.00 0.00 3.91
898 1947 1.001641 CCCCCTTCCTCTGTTGCTG 60.002 63.158 0.00 0.00 0.00 4.41
899 1948 1.676967 CCCCTTCCTCTGTTGCTGC 60.677 63.158 0.00 0.00 0.00 5.25
900 1949 1.073722 CCCTTCCTCTGTTGCTGCA 59.926 57.895 0.00 0.00 0.00 4.41
901 1950 1.239968 CCCTTCCTCTGTTGCTGCAC 61.240 60.000 0.00 0.00 0.00 4.57
902 1951 1.239968 CCTTCCTCTGTTGCTGCACC 61.240 60.000 0.00 0.00 0.00 5.01
903 1952 1.572085 CTTCCTCTGTTGCTGCACCG 61.572 60.000 0.00 0.00 0.00 4.94
904 1953 3.730761 CCTCTGTTGCTGCACCGC 61.731 66.667 0.00 0.00 0.00 5.68
905 1954 3.730761 CTCTGTTGCTGCACCGCC 61.731 66.667 0.00 0.00 0.00 6.13
909 1958 4.347453 GTTGCTGCACCGCCCAAG 62.347 66.667 0.00 0.00 0.00 3.61
916 1965 4.003788 CACCGCCCAAGGTCGACT 62.004 66.667 16.46 0.00 43.89 4.18
917 1966 4.003788 ACCGCCCAAGGTCGACTG 62.004 66.667 16.46 6.67 41.46 3.51
922 1971 4.680237 CCAAGGTCGACTGCGGCA 62.680 66.667 16.46 1.29 45.70 5.69
923 1972 3.414700 CAAGGTCGACTGCGGCAC 61.415 66.667 16.46 0.00 45.70 5.01
938 1987 3.753434 CACGCTCGCTCCTGTCCT 61.753 66.667 0.00 0.00 0.00 3.85
939 1988 3.753434 ACGCTCGCTCCTGTCCTG 61.753 66.667 0.00 0.00 0.00 3.86
940 1989 4.504916 CGCTCGCTCCTGTCCTGG 62.505 72.222 0.00 0.00 0.00 4.45
941 1990 4.828925 GCTCGCTCCTGTCCTGGC 62.829 72.222 0.00 0.00 0.00 4.85
942 1991 3.073735 CTCGCTCCTGTCCTGGCT 61.074 66.667 0.00 0.00 0.00 4.75
943 1992 3.071206 TCGCTCCTGTCCTGGCTC 61.071 66.667 0.00 0.00 0.00 4.70
944 1993 4.154347 CGCTCCTGTCCTGGCTCC 62.154 72.222 0.00 0.00 0.00 4.70
945 1994 3.005539 GCTCCTGTCCTGGCTCCA 61.006 66.667 0.00 0.00 0.00 3.86
946 1995 2.985456 CTCCTGTCCTGGCTCCAC 59.015 66.667 0.00 0.00 0.00 4.02
947 1996 2.607750 TCCTGTCCTGGCTCCACC 60.608 66.667 0.00 0.00 39.84 4.61
949 1998 2.348998 CTGTCCTGGCTCCACCAC 59.651 66.667 0.00 0.00 46.36 4.16
950 1999 3.249189 TGTCCTGGCTCCACCACC 61.249 66.667 0.00 0.00 46.36 4.61
951 2000 4.035102 GTCCTGGCTCCACCACCC 62.035 72.222 0.00 0.00 46.36 4.61
954 2003 4.351054 CTGGCTCCACCACCCCAC 62.351 72.222 0.00 0.00 46.36 4.61
958 2007 4.033776 CTCCACCACCCCACGCAT 62.034 66.667 0.00 0.00 0.00 4.73
959 2008 3.976701 CTCCACCACCCCACGCATC 62.977 68.421 0.00 0.00 0.00 3.91
963 2012 4.802051 CCACCCCACGCATCCCAG 62.802 72.222 0.00 0.00 0.00 4.45
964 2013 3.716195 CACCCCACGCATCCCAGA 61.716 66.667 0.00 0.00 0.00 3.86
965 2014 3.402681 ACCCCACGCATCCCAGAG 61.403 66.667 0.00 0.00 0.00 3.35
966 2015 4.864334 CCCCACGCATCCCAGAGC 62.864 72.222 0.00 0.00 0.00 4.09
973 2022 2.895865 CATCCCAGAGCGCTGCAG 60.896 66.667 18.48 10.11 40.91 4.41
974 2023 4.853050 ATCCCAGAGCGCTGCAGC 62.853 66.667 29.12 29.12 40.91 5.25
980 2029 4.853050 GAGCGCTGCAGCCTCCAT 62.853 66.667 31.17 17.12 37.91 3.41
981 2030 4.421515 AGCGCTGCAGCCTCCATT 62.422 61.111 32.07 9.09 37.91 3.16
982 2031 4.189188 GCGCTGCAGCCTCCATTG 62.189 66.667 32.07 17.36 37.91 2.82
983 2032 4.189188 CGCTGCAGCCTCCATTGC 62.189 66.667 32.07 5.88 40.67 3.56
984 2033 3.834799 GCTGCAGCCTCCATTGCC 61.835 66.667 28.76 0.00 39.54 4.52
985 2034 3.515286 CTGCAGCCTCCATTGCCG 61.515 66.667 0.00 0.00 39.54 5.69
988 2037 3.207669 CAGCCTCCATTGCCGCTC 61.208 66.667 0.00 0.00 0.00 5.03
989 2038 3.406200 AGCCTCCATTGCCGCTCT 61.406 61.111 0.00 0.00 0.00 4.09
990 2039 2.899339 GCCTCCATTGCCGCTCTC 60.899 66.667 0.00 0.00 0.00 3.20
991 2040 2.906458 CCTCCATTGCCGCTCTCT 59.094 61.111 0.00 0.00 0.00 3.10
992 2041 1.227497 CCTCCATTGCCGCTCTCTC 60.227 63.158 0.00 0.00 0.00 3.20
993 2042 1.591059 CTCCATTGCCGCTCTCTCG 60.591 63.158 0.00 0.00 0.00 4.04
994 2043 2.185350 CCATTGCCGCTCTCTCGT 59.815 61.111 0.00 0.00 0.00 4.18
995 2044 1.880340 CCATTGCCGCTCTCTCGTC 60.880 63.158 0.00 0.00 0.00 4.20
996 2045 1.153765 CATTGCCGCTCTCTCGTCA 60.154 57.895 0.00 0.00 0.00 4.35
997 2046 0.737367 CATTGCCGCTCTCTCGTCAA 60.737 55.000 0.00 0.00 31.88 3.18
998 2047 0.737715 ATTGCCGCTCTCTCGTCAAC 60.738 55.000 0.00 0.00 30.06 3.18
999 2048 2.507324 GCCGCTCTCTCGTCAACC 60.507 66.667 0.00 0.00 0.00 3.77
1000 2049 2.962569 CCGCTCTCTCGTCAACCA 59.037 61.111 0.00 0.00 0.00 3.67
1001 2050 1.513158 CCGCTCTCTCGTCAACCAT 59.487 57.895 0.00 0.00 0.00 3.55
1002 2051 0.803768 CCGCTCTCTCGTCAACCATG 60.804 60.000 0.00 0.00 0.00 3.66
1003 2052 0.803768 CGCTCTCTCGTCAACCATGG 60.804 60.000 11.19 11.19 0.00 3.66
1004 2053 1.086634 GCTCTCTCGTCAACCATGGC 61.087 60.000 13.04 0.00 0.00 4.40
1005 2054 0.247460 CTCTCTCGTCAACCATGGCA 59.753 55.000 13.04 0.00 0.00 4.92
1006 2055 0.037326 TCTCTCGTCAACCATGGCAC 60.037 55.000 13.04 5.27 0.00 5.01
1007 2056 1.354337 CTCTCGTCAACCATGGCACG 61.354 60.000 20.29 20.29 0.00 5.34
1008 2057 2.358125 TCGTCAACCATGGCACGG 60.358 61.111 23.88 0.00 33.02 4.94
1009 2058 4.101790 CGTCAACCATGGCACGGC 62.102 66.667 13.04 0.21 0.00 5.68
1010 2059 2.983030 GTCAACCATGGCACGGCA 60.983 61.111 13.04 0.00 0.00 5.69
1011 2060 2.203408 TCAACCATGGCACGGCAA 60.203 55.556 13.04 0.00 0.00 4.52
1012 2061 1.829970 TCAACCATGGCACGGCAAA 60.830 52.632 13.04 0.00 0.00 3.68
1013 2062 1.664333 CAACCATGGCACGGCAAAC 60.664 57.895 13.04 0.00 0.00 2.93
1027 2076 1.205064 CAAACGCTGCTCCTGTTCG 59.795 57.895 0.00 0.00 0.00 3.95
1028 2077 1.227556 AAACGCTGCTCCTGTTCGT 60.228 52.632 0.00 0.00 34.63 3.85
1029 2078 0.032952 AAACGCTGCTCCTGTTCGTA 59.967 50.000 0.00 0.00 32.71 3.43
1030 2079 0.388649 AACGCTGCTCCTGTTCGTAG 60.389 55.000 0.00 0.00 32.71 3.51
1031 2080 2.161486 CGCTGCTCCTGTTCGTAGC 61.161 63.158 0.00 0.00 35.84 3.58
1032 2081 1.811679 GCTGCTCCTGTTCGTAGCC 60.812 63.158 0.00 0.00 35.33 3.93
1033 2082 1.591703 CTGCTCCTGTTCGTAGCCA 59.408 57.895 0.00 0.00 35.33 4.75
1034 2083 0.737715 CTGCTCCTGTTCGTAGCCAC 60.738 60.000 0.00 0.00 35.33 5.01
1053 2102 4.056125 CTCGTCGCCTCTGCCACA 62.056 66.667 0.00 0.00 0.00 4.17
1054 2103 3.978723 CTCGTCGCCTCTGCCACAG 62.979 68.421 0.00 0.00 0.00 3.66
1084 2133 4.477975 CGGTGGAGCTCGTCGTCC 62.478 72.222 7.83 4.61 0.00 4.79
1085 2134 3.371063 GGTGGAGCTCGTCGTCCA 61.371 66.667 7.83 0.00 40.72 4.02
1086 2135 2.179517 GTGGAGCTCGTCGTCCAG 59.820 66.667 7.83 0.00 43.69 3.86
1087 2136 3.062466 TGGAGCTCGTCGTCCAGG 61.062 66.667 7.83 0.00 37.96 4.45
1088 2137 3.827898 GGAGCTCGTCGTCCAGGG 61.828 72.222 7.83 0.00 32.55 4.45
1089 2138 3.827898 GAGCTCGTCGTCCAGGGG 61.828 72.222 0.00 0.00 0.00 4.79
1115 2164 3.809013 GGATGTGGCGGGGTGGAT 61.809 66.667 0.00 0.00 0.00 3.41
1116 2165 2.516930 GATGTGGCGGGGTGGATG 60.517 66.667 0.00 0.00 0.00 3.51
1117 2166 4.820744 ATGTGGCGGGGTGGATGC 62.821 66.667 0.00 0.00 0.00 3.91
1130 2179 3.861797 GATGCGTCCGGGACCCAT 61.862 66.667 23.68 23.68 34.32 4.00
1131 2180 3.809374 GATGCGTCCGGGACCCATC 62.809 68.421 29.23 29.23 39.53 3.51
1133 2182 4.222847 GCGTCCGGGACCCATCTC 62.223 72.222 21.06 0.73 0.00 2.75
1134 2183 3.537874 CGTCCGGGACCCATCTCC 61.538 72.222 21.06 0.00 0.00 3.71
1135 2184 2.041819 GTCCGGGACCCATCTCCT 60.042 66.667 16.55 0.00 0.00 3.69
1136 2185 2.041922 TCCGGGACCCATCTCCTG 60.042 66.667 12.15 0.00 36.54 3.86
1137 2186 3.866582 CCGGGACCCATCTCCTGC 61.867 72.222 12.15 0.00 35.55 4.85
1138 2187 3.866582 CGGGACCCATCTCCTGCC 61.867 72.222 12.15 0.00 29.62 4.85
1139 2188 2.692368 GGGACCCATCTCCTGCCA 60.692 66.667 5.33 0.00 0.00 4.92
1140 2189 2.308722 GGGACCCATCTCCTGCCAA 61.309 63.158 5.33 0.00 0.00 4.52
1141 2190 1.225704 GGACCCATCTCCTGCCAAG 59.774 63.158 0.00 0.00 0.00 3.61
1142 2191 1.225704 GACCCATCTCCTGCCAAGG 59.774 63.158 0.00 0.00 46.06 3.61
1143 2192 2.123982 CCCATCTCCTGCCAAGGC 60.124 66.667 3.61 3.61 44.11 4.35
1154 2203 3.636231 CCAAGGCACGGTGGAGGA 61.636 66.667 10.60 0.00 40.19 3.71
1155 2204 2.046892 CAAGGCACGGTGGAGGAG 60.047 66.667 10.60 0.00 0.00 3.69
1156 2205 2.526873 AAGGCACGGTGGAGGAGT 60.527 61.111 10.60 0.00 0.00 3.85
1157 2206 2.883828 AAGGCACGGTGGAGGAGTG 61.884 63.158 10.60 0.00 38.77 3.51
1199 2248 2.660552 CGACGACGTGTTTGGGCT 60.661 61.111 4.58 0.00 34.56 5.19
1200 2249 2.654912 CGACGACGTGTTTGGGCTC 61.655 63.158 4.58 0.00 34.56 4.70
1201 2250 1.593209 GACGACGTGTTTGGGCTCA 60.593 57.895 4.58 0.00 0.00 4.26
1202 2251 1.557443 GACGACGTGTTTGGGCTCAG 61.557 60.000 4.58 0.00 0.00 3.35
1203 2252 2.317609 CGACGTGTTTGGGCTCAGG 61.318 63.158 0.00 0.00 0.00 3.86
1204 2253 2.594592 ACGTGTTTGGGCTCAGGC 60.595 61.111 0.00 0.00 37.82 4.85
1205 2254 3.726517 CGTGTTTGGGCTCAGGCG 61.727 66.667 0.00 0.00 39.81 5.52
1206 2255 3.365265 GTGTTTGGGCTCAGGCGG 61.365 66.667 0.00 0.00 39.81 6.13
1223 2272 4.789075 GCGCCTTGTCTACGCGGA 62.789 66.667 12.47 0.00 45.81 5.54
1224 2273 2.579787 CGCCTTGTCTACGCGGAG 60.580 66.667 13.63 13.63 42.14 4.63
1225 2274 2.202756 GCCTTGTCTACGCGGAGG 60.203 66.667 20.39 11.96 0.00 4.30
1226 2275 2.707849 GCCTTGTCTACGCGGAGGA 61.708 63.158 20.39 6.14 0.00 3.71
1227 2276 1.888018 CCTTGTCTACGCGGAGGAA 59.112 57.895 20.39 10.93 0.00 3.36
1228 2277 0.179134 CCTTGTCTACGCGGAGGAAG 60.179 60.000 20.39 19.46 0.00 3.46
1229 2278 0.809385 CTTGTCTACGCGGAGGAAGA 59.191 55.000 20.39 5.90 0.00 2.87
1230 2279 0.809385 TTGTCTACGCGGAGGAAGAG 59.191 55.000 20.39 0.00 0.00 2.85
1231 2280 1.030488 TGTCTACGCGGAGGAAGAGG 61.030 60.000 20.39 0.00 0.00 3.69
1232 2281 0.747283 GTCTACGCGGAGGAAGAGGA 60.747 60.000 20.39 0.00 0.00 3.71
1233 2282 0.464013 TCTACGCGGAGGAAGAGGAG 60.464 60.000 20.39 0.00 0.00 3.69
1234 2283 1.448922 CTACGCGGAGGAAGAGGAGG 61.449 65.000 11.59 0.00 0.00 4.30
1235 2284 1.918467 TACGCGGAGGAAGAGGAGGA 61.918 60.000 12.47 0.00 0.00 3.71
1236 2285 2.776913 CGCGGAGGAAGAGGAGGAC 61.777 68.421 0.00 0.00 0.00 3.85
1237 2286 2.776913 GCGGAGGAAGAGGAGGACG 61.777 68.421 0.00 0.00 0.00 4.79
1261 2310 1.378882 CGGCTACCCTACGCAGTACA 61.379 60.000 0.00 0.00 45.11 2.90
1287 2339 3.781770 CTCCGCGCTGATGAGGGAC 62.782 68.421 5.56 0.00 33.95 4.46
1383 2435 1.144716 CTGCTCCGCTATCAGCCAA 59.855 57.895 0.00 0.00 38.18 4.52
1396 2448 3.941836 GCCAATGCCGCGACTAGC 61.942 66.667 8.23 1.98 43.95 3.42
1405 2457 4.509737 GCGACTAGCCGGACCACC 62.510 72.222 5.05 0.00 40.81 4.61
1415 2467 2.678470 GGACCACCGCCCCATTTA 59.322 61.111 0.00 0.00 0.00 1.40
1416 2468 1.000646 GGACCACCGCCCCATTTAA 60.001 57.895 0.00 0.00 0.00 1.52
1422 2474 2.561037 CCGCCCCATTTAATCCCGC 61.561 63.158 0.00 0.00 0.00 6.13
1461 2513 0.903454 CCGTCCTCTAGTTGTGGGGT 60.903 60.000 0.00 0.00 0.00 4.95
1462 2514 0.974383 CGTCCTCTAGTTGTGGGGTT 59.026 55.000 0.00 0.00 0.00 4.11
1463 2515 1.337823 CGTCCTCTAGTTGTGGGGTTG 60.338 57.143 0.00 0.00 0.00 3.77
1464 2516 1.697982 GTCCTCTAGTTGTGGGGTTGT 59.302 52.381 0.00 0.00 0.00 3.32
1465 2517 2.105993 GTCCTCTAGTTGTGGGGTTGTT 59.894 50.000 0.00 0.00 0.00 2.83
1466 2518 2.370849 TCCTCTAGTTGTGGGGTTGTTC 59.629 50.000 0.00 0.00 0.00 3.18
1467 2519 2.372172 CCTCTAGTTGTGGGGTTGTTCT 59.628 50.000 0.00 0.00 0.00 3.01
1513 2566 2.813908 GGGTGACGGTCGATGCAC 60.814 66.667 3.34 2.81 0.00 4.57
1549 2602 3.264193 AGCACTCTTATGTGGATGGAACA 59.736 43.478 0.00 0.00 39.83 3.18
1567 2620 5.652014 TGGAACAAAATTGAAGTGACAGAGT 59.348 36.000 0.00 0.00 31.92 3.24
1576 2629 8.764524 AATTGAAGTGACAGAGTCTTGTATAC 57.235 34.615 0.00 0.00 33.15 1.47
1591 2761 9.451002 AGTCTTGTATACTACTATATGCACGAT 57.549 33.333 4.17 0.00 31.44 3.73
1600 2770 8.534333 ACTACTATATGCACGATTAATTGGTG 57.466 34.615 13.38 13.38 34.85 4.17
1605 2775 7.985634 ATATGCACGATTAATTGGTGTTTTC 57.014 32.000 16.96 6.03 34.25 2.29
1609 2780 5.116983 GCACGATTAATTGGTGTTTTCAGTG 59.883 40.000 16.96 0.00 34.25 3.66
1614 2785 7.042791 CGATTAATTGGTGTTTTCAGTGCTTTT 60.043 33.333 0.00 0.00 0.00 2.27
1634 2805 5.438761 TTTTCTTCTTTTGGACAGCTAGC 57.561 39.130 6.62 6.62 0.00 3.42
1652 2823 2.947448 GCTTTTGCATCTTACCCCAG 57.053 50.000 0.00 0.00 46.58 4.45
1656 2827 0.255890 TTGCATCTTACCCCAGGAGC 59.744 55.000 0.00 0.00 0.00 4.70
1695 2866 6.154445 CCTTCATATTGTAAATGCATGCTCC 58.846 40.000 20.33 2.63 0.00 4.70
1778 2949 2.230025 TCCTCAGAGACGAAGCAAGAAG 59.770 50.000 0.00 0.00 0.00 2.85
1785 2956 6.366332 TCAGAGACGAAGCAAGAAGTAAAATC 59.634 38.462 0.00 0.00 0.00 2.17
1788 2959 5.409826 AGACGAAGCAAGAAGTAAAATCCTG 59.590 40.000 0.00 0.00 0.00 3.86
1790 2961 5.049405 ACGAAGCAAGAAGTAAAATCCTGTG 60.049 40.000 0.00 0.00 0.00 3.66
1794 2965 4.407365 CAAGAAGTAAAATCCTGTGGGGT 58.593 43.478 0.00 0.00 36.25 4.95
1826 2997 2.287547 GCAATGGTGTCGTGTTCACATT 60.288 45.455 3.87 0.00 37.52 2.71
1840 3011 6.290540 CGTGTTCACATTTCTTTCACGAAAAG 60.291 38.462 8.72 8.21 46.10 2.27
1903 3074 7.743749 ACATCATGTAGAGCAATCTTTCCTAT 58.256 34.615 0.00 0.00 0.00 2.57
1918 3089 9.533253 AATCTTTCCTATTGTTTTGTTGAACAG 57.467 29.630 0.00 0.00 40.33 3.16
1927 3098 5.398169 TGTTTTGTTGAACAGCTTGTACAG 58.602 37.500 0.00 0.00 34.77 2.74
2037 5827 9.995957 GAAGCTCCAGAATTATCTTTTAAAGTC 57.004 33.333 4.53 0.00 32.03 3.01
2125 5915 1.588139 GATAGGAACGCCGTCACCG 60.588 63.158 0.00 0.00 39.96 4.94
2160 5950 1.669999 AAATGCTCCCAATCGCCTGC 61.670 55.000 0.00 0.00 0.00 4.85
2165 5955 3.136123 CCCAATCGCCTGCCACAG 61.136 66.667 0.00 0.00 0.00 3.66
2183 5973 3.017323 CCACATCCGCTCATTCGC 58.983 61.111 0.00 0.00 0.00 4.70
2203 5993 8.635983 CATTCGCATATCATTGTTCATTTCATC 58.364 33.333 0.00 0.00 0.00 2.92
2270 6060 4.424761 TTCTACTACCTACCCCCAAAGT 57.575 45.455 0.00 0.00 0.00 2.66
2290 6080 3.821033 AGTTTGGGTATCTGTCAAGTTGC 59.179 43.478 0.00 0.00 0.00 4.17
2343 6133 8.902540 ATTAGATCATCCGTTTAGCATAACAA 57.097 30.769 0.00 0.00 0.00 2.83
2371 6161 3.387050 GGTCTAGGAATGACCGTGGTAAT 59.613 47.826 0.00 0.00 43.55 1.89
2394 6184 5.838531 TTTTTAGTGAAAATGACCGTGGT 57.161 34.783 0.00 0.00 34.54 4.16
2395 6185 6.939132 TTTTTAGTGAAAATGACCGTGGTA 57.061 33.333 0.00 0.00 34.54 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.876068 TGACAAATTATTCCTACGTGAGTTCTT 59.124 33.333 0.00 0.00 46.40 2.52
241 243 6.706716 GCCCTTACTACTGAATTCTATTGGAC 59.293 42.308 7.05 0.00 0.00 4.02
321 323 6.210385 ACCAAATGCATGAACAATAGTACCAA 59.790 34.615 0.00 0.00 0.00 3.67
474 477 7.925622 TCTTATGATGCCATCAAGGATCTTAT 58.074 34.615 12.08 0.00 43.50 1.73
517 520 6.942005 TGATCATATCAAAGTCAAACCACAGT 59.058 34.615 0.00 0.00 36.11 3.55
536 539 3.181493 GCGCAAACCAGAGAATTGATCAT 60.181 43.478 0.30 0.00 0.00 2.45
595 1450 8.731605 CCTCTTTGGTTTCTAGGATCTAAAAAC 58.268 37.037 0.00 0.00 0.00 2.43
726 1769 7.410800 TTGATTGAATGAGATGTTTTGTTGC 57.589 32.000 0.00 0.00 0.00 4.17
731 1774 7.673180 ACACCATTGATTGAATGAGATGTTTT 58.327 30.769 0.00 0.00 43.87 2.43
769 1813 0.740737 AACCTGAGTTTGCTGTGTGC 59.259 50.000 0.00 0.00 43.25 4.57
781 1825 2.744202 GTGCCACTCATGTTAACCTGAG 59.256 50.000 28.79 28.79 42.10 3.35
784 1828 1.808411 CGTGCCACTCATGTTAACCT 58.192 50.000 2.48 0.00 0.00 3.50
801 1850 1.856597 GTGTTCAAACTACACGAGCGT 59.143 47.619 0.00 0.00 36.84 5.07
804 1853 5.440685 GGATTTGTGTTCAAACTACACGAG 58.559 41.667 0.00 0.00 46.85 4.18
805 1854 4.025563 CGGATTTGTGTTCAAACTACACGA 60.026 41.667 0.00 0.00 46.85 4.35
806 1855 4.208355 CGGATTTGTGTTCAAACTACACG 58.792 43.478 0.00 0.00 46.85 4.49
807 1856 4.533222 CCGGATTTGTGTTCAAACTACAC 58.467 43.478 0.00 0.00 44.69 2.90
808 1857 3.566322 CCCGGATTTGTGTTCAAACTACA 59.434 43.478 0.73 0.00 44.69 2.74
809 1858 3.610821 GCCCGGATTTGTGTTCAAACTAC 60.611 47.826 0.73 0.00 44.69 2.73
810 1859 2.554893 GCCCGGATTTGTGTTCAAACTA 59.445 45.455 0.73 0.00 44.69 2.24
811 1860 1.339929 GCCCGGATTTGTGTTCAAACT 59.660 47.619 0.73 0.00 44.69 2.66
812 1861 1.604438 GGCCCGGATTTGTGTTCAAAC 60.604 52.381 0.73 0.00 44.69 2.93
813 1862 0.676736 GGCCCGGATTTGTGTTCAAA 59.323 50.000 0.73 0.00 45.71 2.69
814 1863 1.519751 CGGCCCGGATTTGTGTTCAA 61.520 55.000 0.73 0.00 0.00 2.69
815 1864 1.969064 CGGCCCGGATTTGTGTTCA 60.969 57.895 0.73 0.00 0.00 3.18
816 1865 1.673009 TCGGCCCGGATTTGTGTTC 60.673 57.895 0.73 0.00 0.00 3.18
817 1866 1.969589 GTCGGCCCGGATTTGTGTT 60.970 57.895 0.73 0.00 0.00 3.32
818 1867 2.359478 GTCGGCCCGGATTTGTGT 60.359 61.111 0.73 0.00 0.00 3.72
819 1868 2.046314 AGTCGGCCCGGATTTGTG 60.046 61.111 0.73 0.00 0.00 3.33
820 1869 0.974010 TAGAGTCGGCCCGGATTTGT 60.974 55.000 0.73 0.00 0.00 2.83
821 1870 0.529992 GTAGAGTCGGCCCGGATTTG 60.530 60.000 0.73 0.00 0.00 2.32
822 1871 0.974010 TGTAGAGTCGGCCCGGATTT 60.974 55.000 0.73 0.00 0.00 2.17
823 1872 1.380785 TGTAGAGTCGGCCCGGATT 60.381 57.895 0.73 0.00 0.00 3.01
824 1873 1.828660 CTGTAGAGTCGGCCCGGAT 60.829 63.158 0.73 0.00 0.00 4.18
825 1874 2.439701 CTGTAGAGTCGGCCCGGA 60.440 66.667 0.73 0.00 0.00 5.14
826 1875 2.439701 TCTGTAGAGTCGGCCCGG 60.440 66.667 1.90 0.00 0.00 5.73
827 1876 2.799371 GTCTGTAGAGTCGGCCCG 59.201 66.667 0.00 0.00 0.00 6.13
828 1877 2.799371 CGTCTGTAGAGTCGGCCC 59.201 66.667 0.00 0.00 0.00 5.80
829 1878 2.102553 GCGTCTGTAGAGTCGGCC 59.897 66.667 8.46 0.00 32.19 6.13
830 1879 2.102553 GGCGTCTGTAGAGTCGGC 59.897 66.667 15.80 15.80 45.74 5.54
831 1880 2.799371 GGGCGTCTGTAGAGTCGG 59.201 66.667 8.46 0.00 32.19 4.79
832 1881 2.104859 TCGGGCGTCTGTAGAGTCG 61.105 63.158 2.22 2.22 34.34 4.18
833 1882 1.025647 AGTCGGGCGTCTGTAGAGTC 61.026 60.000 0.00 0.00 0.00 3.36
834 1883 1.002379 AGTCGGGCGTCTGTAGAGT 60.002 57.895 0.00 0.00 0.00 3.24
835 1884 1.716826 GGAGTCGGGCGTCTGTAGAG 61.717 65.000 0.00 0.00 0.00 2.43
836 1885 1.748122 GGAGTCGGGCGTCTGTAGA 60.748 63.158 0.00 0.00 0.00 2.59
837 1886 2.772691 GGGAGTCGGGCGTCTGTAG 61.773 68.421 0.00 0.00 0.00 2.74
838 1887 2.753043 GGGAGTCGGGCGTCTGTA 60.753 66.667 0.00 0.00 0.00 2.74
839 1888 4.988716 TGGGAGTCGGGCGTCTGT 62.989 66.667 0.00 0.00 0.00 3.41
840 1889 4.436998 GTGGGAGTCGGGCGTCTG 62.437 72.222 0.00 0.00 0.00 3.51
841 1890 4.680537 AGTGGGAGTCGGGCGTCT 62.681 66.667 0.00 0.00 0.00 4.18
842 1891 4.131088 GAGTGGGAGTCGGGCGTC 62.131 72.222 0.00 0.00 0.00 5.19
845 1894 3.462678 GAGGAGTGGGAGTCGGGC 61.463 72.222 0.00 0.00 0.00 6.13
846 1895 3.141488 CGAGGAGTGGGAGTCGGG 61.141 72.222 0.00 0.00 0.00 5.14
847 1896 3.827898 GCGAGGAGTGGGAGTCGG 61.828 72.222 0.00 0.00 32.99 4.79
848 1897 4.180946 CGCGAGGAGTGGGAGTCG 62.181 72.222 0.00 0.00 35.51 4.18
849 1898 2.156051 AAACGCGAGGAGTGGGAGTC 62.156 60.000 15.93 0.00 33.90 3.36
850 1899 0.896940 TAAACGCGAGGAGTGGGAGT 60.897 55.000 15.93 0.00 33.90 3.85
851 1900 0.245539 TTAAACGCGAGGAGTGGGAG 59.754 55.000 15.93 0.00 33.90 4.30
852 1901 0.680618 TTTAAACGCGAGGAGTGGGA 59.319 50.000 15.93 0.00 33.90 4.37
853 1902 1.515081 TTTTAAACGCGAGGAGTGGG 58.485 50.000 15.93 0.00 33.90 4.61
880 1929 1.001641 CAGCAACAGAGGAAGGGGG 60.002 63.158 0.00 0.00 0.00 5.40
881 1930 1.676967 GCAGCAACAGAGGAAGGGG 60.677 63.158 0.00 0.00 0.00 4.79
882 1931 1.073722 TGCAGCAACAGAGGAAGGG 59.926 57.895 0.00 0.00 0.00 3.95
883 1932 1.239968 GGTGCAGCAACAGAGGAAGG 61.240 60.000 11.86 0.00 0.00 3.46
884 1933 1.572085 CGGTGCAGCAACAGAGGAAG 61.572 60.000 17.33 0.00 0.00 3.46
885 1934 1.597854 CGGTGCAGCAACAGAGGAA 60.598 57.895 17.33 0.00 0.00 3.36
886 1935 2.031012 CGGTGCAGCAACAGAGGA 59.969 61.111 17.33 0.00 0.00 3.71
887 1936 3.730761 GCGGTGCAGCAACAGAGG 61.731 66.667 17.33 0.00 37.05 3.69
888 1937 3.730761 GGCGGTGCAGCAACAGAG 61.731 66.667 17.33 0.00 39.27 3.35
892 1941 4.347453 CTTGGGCGGTGCAGCAAC 62.347 66.667 17.33 0.00 39.27 4.17
899 1948 4.003788 AGTCGACCTTGGGCGGTG 62.004 66.667 15.45 0.00 37.42 4.94
900 1949 4.003788 CAGTCGACCTTGGGCGGT 62.004 66.667 15.45 0.00 40.80 5.68
905 1954 4.680237 TGCCGCAGTCGACCTTGG 62.680 66.667 13.01 12.39 38.10 3.61
906 1955 3.414700 GTGCCGCAGTCGACCTTG 61.415 66.667 13.01 6.16 38.10 3.61
921 1970 3.753434 AGGACAGGAGCGAGCGTG 61.753 66.667 0.00 0.00 0.00 5.34
922 1971 3.753434 CAGGACAGGAGCGAGCGT 61.753 66.667 0.00 0.00 0.00 5.07
923 1972 4.504916 CCAGGACAGGAGCGAGCG 62.505 72.222 0.00 0.00 0.00 5.03
924 1973 4.828925 GCCAGGACAGGAGCGAGC 62.829 72.222 0.00 0.00 0.00 5.03
925 1974 3.073735 AGCCAGGACAGGAGCGAG 61.074 66.667 0.00 0.00 0.00 5.03
926 1975 3.071206 GAGCCAGGACAGGAGCGA 61.071 66.667 0.00 0.00 0.00 4.93
927 1976 4.154347 GGAGCCAGGACAGGAGCG 62.154 72.222 0.00 0.00 0.00 5.03
928 1977 3.005539 TGGAGCCAGGACAGGAGC 61.006 66.667 0.00 0.00 0.00 4.70
929 1978 2.664081 GGTGGAGCCAGGACAGGAG 61.664 68.421 0.00 0.00 37.17 3.69
930 1979 2.607750 GGTGGAGCCAGGACAGGA 60.608 66.667 0.00 0.00 37.17 3.86
931 1980 2.930019 TGGTGGAGCCAGGACAGG 60.930 66.667 0.00 0.00 43.61 4.00
941 1990 3.976701 GATGCGTGGGGTGGTGGAG 62.977 68.421 0.00 0.00 0.00 3.86
942 1991 4.028490 GATGCGTGGGGTGGTGGA 62.028 66.667 0.00 0.00 0.00 4.02
946 1995 4.802051 CTGGGATGCGTGGGGTGG 62.802 72.222 0.00 0.00 0.00 4.61
947 1996 3.687321 CTCTGGGATGCGTGGGGTG 62.687 68.421 0.00 0.00 0.00 4.61
948 1997 3.402681 CTCTGGGATGCGTGGGGT 61.403 66.667 0.00 0.00 0.00 4.95
949 1998 4.864334 GCTCTGGGATGCGTGGGG 62.864 72.222 0.00 0.00 0.00 4.96
956 2005 2.895865 CTGCAGCGCTCTGGGATG 60.896 66.667 7.13 0.00 40.65 3.51
957 2006 4.853050 GCTGCAGCGCTCTGGGAT 62.853 66.667 25.23 0.00 40.65 3.85
963 2012 4.853050 ATGGAGGCTGCAGCGCTC 62.853 66.667 32.39 32.39 43.26 5.03
964 2013 4.421515 AATGGAGGCTGCAGCGCT 62.422 61.111 31.19 27.31 43.26 5.92
965 2014 4.189188 CAATGGAGGCTGCAGCGC 62.189 66.667 31.19 24.42 43.26 5.92
966 2015 4.189188 GCAATGGAGGCTGCAGCG 62.189 66.667 31.19 17.04 43.26 5.18
967 2016 3.834799 GGCAATGGAGGCTGCAGC 61.835 66.667 30.88 30.88 40.46 5.25
968 2017 3.515286 CGGCAATGGAGGCTGCAG 61.515 66.667 15.56 10.11 40.46 4.41
971 2020 3.207669 GAGCGGCAATGGAGGCTG 61.208 66.667 1.45 0.00 40.63 4.85
972 2021 3.397613 GAGAGCGGCAATGGAGGCT 62.398 63.158 1.45 0.00 38.70 4.58
973 2022 2.899339 GAGAGCGGCAATGGAGGC 60.899 66.667 1.45 0.00 0.00 4.70
974 2023 1.227497 GAGAGAGCGGCAATGGAGG 60.227 63.158 1.45 0.00 0.00 4.30
975 2024 1.591059 CGAGAGAGCGGCAATGGAG 60.591 63.158 1.45 0.00 0.00 3.86
976 2025 2.284798 GACGAGAGAGCGGCAATGGA 62.285 60.000 1.45 0.00 39.62 3.41
977 2026 1.880340 GACGAGAGAGCGGCAATGG 60.880 63.158 1.45 0.00 39.62 3.16
978 2027 3.698382 GACGAGAGAGCGGCAATG 58.302 61.111 1.45 0.00 39.62 2.82
982 2031 2.507324 GGTTGACGAGAGAGCGGC 60.507 66.667 0.00 0.00 40.45 6.53
983 2032 0.803768 CATGGTTGACGAGAGAGCGG 60.804 60.000 0.00 0.00 35.12 5.52
984 2033 0.803768 CCATGGTTGACGAGAGAGCG 60.804 60.000 2.57 0.00 37.29 5.03
985 2034 1.086634 GCCATGGTTGACGAGAGAGC 61.087 60.000 14.67 0.00 0.00 4.09
986 2035 0.247460 TGCCATGGTTGACGAGAGAG 59.753 55.000 14.67 0.00 0.00 3.20
987 2036 0.037326 GTGCCATGGTTGACGAGAGA 60.037 55.000 14.67 0.00 0.00 3.10
988 2037 1.354337 CGTGCCATGGTTGACGAGAG 61.354 60.000 21.53 0.03 33.64 3.20
989 2038 1.374125 CGTGCCATGGTTGACGAGA 60.374 57.895 21.53 0.00 33.64 4.04
990 2039 2.390599 CCGTGCCATGGTTGACGAG 61.391 63.158 25.44 15.77 33.64 4.18
991 2040 2.358125 CCGTGCCATGGTTGACGA 60.358 61.111 25.44 0.00 33.64 4.20
992 2041 4.101790 GCCGTGCCATGGTTGACG 62.102 66.667 14.67 18.01 0.00 4.35
993 2042 2.081425 TTTGCCGTGCCATGGTTGAC 62.081 55.000 14.67 7.10 0.00 3.18
994 2043 1.829970 TTTGCCGTGCCATGGTTGA 60.830 52.632 14.67 0.00 0.00 3.18
995 2044 1.664333 GTTTGCCGTGCCATGGTTG 60.664 57.895 14.67 3.24 0.00 3.77
996 2045 2.733945 GTTTGCCGTGCCATGGTT 59.266 55.556 14.67 0.00 0.00 3.67
997 2046 3.669344 CGTTTGCCGTGCCATGGT 61.669 61.111 14.67 0.00 0.00 3.55
999 2048 4.041917 AGCGTTTGCCGTGCCATG 62.042 61.111 0.00 0.00 44.31 3.66
1000 2049 4.041917 CAGCGTTTGCCGTGCCAT 62.042 61.111 0.00 0.00 44.31 4.40
1009 2058 1.205064 CGAACAGGAGCAGCGTTTG 59.795 57.895 0.00 0.00 0.00 2.93
1010 2059 0.032952 TACGAACAGGAGCAGCGTTT 59.967 50.000 0.00 0.00 36.51 3.60
1011 2060 0.388649 CTACGAACAGGAGCAGCGTT 60.389 55.000 0.00 0.00 36.51 4.84
1012 2061 1.213013 CTACGAACAGGAGCAGCGT 59.787 57.895 0.00 0.00 38.81 5.07
1013 2062 4.079090 CTACGAACAGGAGCAGCG 57.921 61.111 0.00 0.00 0.00 5.18
1067 2116 4.477975 GGACGACGAGCTCCACCG 62.478 72.222 8.47 11.46 0.00 4.94
1068 2117 3.343788 CTGGACGACGAGCTCCACC 62.344 68.421 8.47 5.35 32.84 4.61
1069 2118 2.179517 CTGGACGACGAGCTCCAC 59.820 66.667 8.47 1.23 32.84 4.02
1070 2119 3.062466 CCTGGACGACGAGCTCCA 61.062 66.667 8.47 3.40 35.20 3.86
1071 2120 3.827898 CCCTGGACGACGAGCTCC 61.828 72.222 8.47 0.00 0.00 4.70
1072 2121 3.827898 CCCCTGGACGACGAGCTC 61.828 72.222 2.73 2.73 0.00 4.09
1098 2147 3.809013 ATCCACCCCGCCACATCC 61.809 66.667 0.00 0.00 0.00 3.51
1099 2148 2.516930 CATCCACCCCGCCACATC 60.517 66.667 0.00 0.00 0.00 3.06
1100 2149 4.820744 GCATCCACCCCGCCACAT 62.821 66.667 0.00 0.00 0.00 3.21
1109 2158 4.832608 GTCCCGGACGCATCCACC 62.833 72.222 0.73 0.00 46.67 4.61
1110 2159 4.832608 GGTCCCGGACGCATCCAC 62.833 72.222 11.55 0.00 46.67 4.02
1116 2165 4.222847 GAGATGGGTCCCGGACGC 62.223 72.222 24.30 24.30 44.15 5.19
1117 2166 3.537874 GGAGATGGGTCCCGGACG 61.538 72.222 11.55 0.00 32.65 4.79
1118 2167 2.041819 AGGAGATGGGTCCCGGAC 60.042 66.667 9.30 9.30 37.31 4.79
1119 2168 2.041922 CAGGAGATGGGTCCCGGA 60.042 66.667 0.73 0.00 37.31 5.14
1120 2169 3.866582 GCAGGAGATGGGTCCCGG 61.867 72.222 2.65 0.00 37.31 5.73
1121 2170 3.866582 GGCAGGAGATGGGTCCCG 61.867 72.222 2.65 0.00 37.31 5.14
1122 2171 2.276309 CTTGGCAGGAGATGGGTCCC 62.276 65.000 0.00 0.00 37.31 4.46
1123 2172 1.225704 CTTGGCAGGAGATGGGTCC 59.774 63.158 0.00 0.00 36.79 4.46
1124 2173 1.225704 CCTTGGCAGGAGATGGGTC 59.774 63.158 0.00 0.00 44.19 4.46
1125 2174 2.988839 GCCTTGGCAGGAGATGGGT 61.989 63.158 6.79 0.00 44.19 4.51
1126 2175 2.123982 GCCTTGGCAGGAGATGGG 60.124 66.667 6.79 0.00 44.19 4.00
1127 2176 1.751927 GTGCCTTGGCAGGAGATGG 60.752 63.158 15.31 0.00 44.19 3.51
1128 2177 2.110967 CGTGCCTTGGCAGGAGATG 61.111 63.158 24.76 1.57 44.19 2.90
1129 2178 2.270205 CGTGCCTTGGCAGGAGAT 59.730 61.111 24.76 0.00 44.19 2.75
1130 2179 4.020617 CCGTGCCTTGGCAGGAGA 62.021 66.667 28.93 0.37 44.19 3.71
1131 2180 4.335647 ACCGTGCCTTGGCAGGAG 62.336 66.667 28.93 21.70 44.19 3.69
1132 2181 4.641645 CACCGTGCCTTGGCAGGA 62.642 66.667 28.93 1.11 44.19 3.86
1134 2183 4.641645 TCCACCGTGCCTTGGCAG 62.642 66.667 15.31 6.96 32.37 4.85
1135 2184 4.641645 CTCCACCGTGCCTTGGCA 62.642 66.667 10.65 10.65 32.37 4.92
1137 2186 3.612247 CTCCTCCACCGTGCCTTGG 62.612 68.421 0.00 0.00 0.00 3.61
1138 2187 2.046892 CTCCTCCACCGTGCCTTG 60.047 66.667 0.00 0.00 0.00 3.61
1139 2188 2.526873 ACTCCTCCACCGTGCCTT 60.527 61.111 0.00 0.00 0.00 4.35
1140 2189 3.314331 CACTCCTCCACCGTGCCT 61.314 66.667 0.00 0.00 0.00 4.75
1143 2192 3.314331 AGGCACTCCTCCACCGTG 61.314 66.667 0.00 0.00 38.72 4.94
1144 2193 3.314331 CAGGCACTCCTCCACCGT 61.314 66.667 0.00 0.00 41.93 4.83
1145 2194 4.767255 GCAGGCACTCCTCCACCG 62.767 72.222 0.00 0.00 41.93 4.94
1146 2195 3.640407 TGCAGGCACTCCTCCACC 61.640 66.667 0.00 0.00 41.93 4.61
1147 2196 2.359230 GTGCAGGCACTCCTCCAC 60.359 66.667 16.71 0.00 43.38 4.02
1148 2197 4.007644 CGTGCAGGCACTCCTCCA 62.008 66.667 20.79 0.00 41.93 3.86
1149 2198 3.240134 TTCGTGCAGGCACTCCTCC 62.240 63.158 20.79 0.00 41.93 4.30
1150 2199 2.029844 GTTCGTGCAGGCACTCCTC 61.030 63.158 20.79 6.45 41.93 3.71
1151 2200 2.031163 GTTCGTGCAGGCACTCCT 59.969 61.111 20.79 0.00 45.66 3.69
1152 2201 3.414700 CGTTCGTGCAGGCACTCC 61.415 66.667 20.79 8.40 44.16 3.85
1153 2202 4.077188 GCGTTCGTGCAGGCACTC 62.077 66.667 20.79 10.79 44.16 3.51
1182 2231 2.654912 GAGCCCAAACACGTCGTCG 61.655 63.158 0.00 0.00 43.34 5.12
1183 2232 1.557443 CTGAGCCCAAACACGTCGTC 61.557 60.000 0.00 0.00 0.00 4.20
1184 2233 1.594293 CTGAGCCCAAACACGTCGT 60.594 57.895 0.00 0.00 0.00 4.34
1185 2234 2.317609 CCTGAGCCCAAACACGTCG 61.318 63.158 0.00 0.00 0.00 5.12
1186 2235 2.617274 GCCTGAGCCCAAACACGTC 61.617 63.158 0.00 0.00 0.00 4.34
1187 2236 2.594592 GCCTGAGCCCAAACACGT 60.595 61.111 0.00 0.00 0.00 4.49
1188 2237 3.726517 CGCCTGAGCCCAAACACG 61.727 66.667 0.00 0.00 34.57 4.49
1189 2238 3.365265 CCGCCTGAGCCCAAACAC 61.365 66.667 0.00 0.00 34.57 3.32
1208 2257 2.202756 CCTCCGCGTAGACAAGGC 60.203 66.667 4.92 0.00 35.60 4.35
1209 2258 0.179134 CTTCCTCCGCGTAGACAAGG 60.179 60.000 4.92 1.97 0.00 3.61
1210 2259 0.809385 TCTTCCTCCGCGTAGACAAG 59.191 55.000 4.92 4.72 0.00 3.16
1211 2260 0.809385 CTCTTCCTCCGCGTAGACAA 59.191 55.000 4.92 0.00 0.00 3.18
1212 2261 1.030488 CCTCTTCCTCCGCGTAGACA 61.030 60.000 4.92 0.00 0.00 3.41
1213 2262 0.747283 TCCTCTTCCTCCGCGTAGAC 60.747 60.000 4.92 0.00 0.00 2.59
1214 2263 0.464013 CTCCTCTTCCTCCGCGTAGA 60.464 60.000 4.92 0.00 0.00 2.59
1215 2264 1.448922 CCTCCTCTTCCTCCGCGTAG 61.449 65.000 4.92 0.00 0.00 3.51
1216 2265 1.453379 CCTCCTCTTCCTCCGCGTA 60.453 63.158 4.92 0.00 0.00 4.42
1217 2266 2.756283 CCTCCTCTTCCTCCGCGT 60.756 66.667 4.92 0.00 0.00 6.01
1218 2267 2.440430 TCCTCCTCTTCCTCCGCG 60.440 66.667 0.00 0.00 0.00 6.46
1219 2268 2.776913 CGTCCTCCTCTTCCTCCGC 61.777 68.421 0.00 0.00 0.00 5.54
1220 2269 2.122167 CCGTCCTCCTCTTCCTCCG 61.122 68.421 0.00 0.00 0.00 4.63
1221 2270 2.428085 GCCGTCCTCCTCTTCCTCC 61.428 68.421 0.00 0.00 0.00 4.30
1222 2271 2.776913 CGCCGTCCTCCTCTTCCTC 61.777 68.421 0.00 0.00 0.00 3.71
1223 2272 2.756283 CGCCGTCCTCCTCTTCCT 60.756 66.667 0.00 0.00 0.00 3.36
1224 2273 3.839432 CCGCCGTCCTCCTCTTCC 61.839 72.222 0.00 0.00 0.00 3.46
1225 2274 4.516195 GCCGCCGTCCTCCTCTTC 62.516 72.222 0.00 0.00 0.00 2.87
1309 2361 0.801067 CAGTTGTAGTAGGACGCGCC 60.801 60.000 5.73 9.03 0.00 6.53
1314 2366 2.481449 CGGATGGCAGTTGTAGTAGGAC 60.481 54.545 0.00 0.00 0.00 3.85
1405 2457 1.795170 CTGCGGGATTAAATGGGGCG 61.795 60.000 0.00 0.00 0.00 6.13
1406 2458 1.463553 CCTGCGGGATTAAATGGGGC 61.464 60.000 5.28 0.00 33.58 5.80
1445 2497 2.112279 ACAACCCCACAACTAGAGGA 57.888 50.000 0.00 0.00 0.00 3.71
1461 2513 3.513515 AGTGGGCAAAGAACAAAGAACAA 59.486 39.130 0.00 0.00 0.00 2.83
1462 2514 3.096092 AGTGGGCAAAGAACAAAGAACA 58.904 40.909 0.00 0.00 0.00 3.18
1463 2515 3.801114 AGTGGGCAAAGAACAAAGAAC 57.199 42.857 0.00 0.00 0.00 3.01
1464 2516 4.020662 ACAAAGTGGGCAAAGAACAAAGAA 60.021 37.500 0.00 0.00 0.00 2.52
1465 2517 3.513515 ACAAAGTGGGCAAAGAACAAAGA 59.486 39.130 0.00 0.00 0.00 2.52
1466 2518 3.618150 CACAAAGTGGGCAAAGAACAAAG 59.382 43.478 0.00 0.00 0.00 2.77
1467 2519 3.259374 TCACAAAGTGGGCAAAGAACAAA 59.741 39.130 0.00 0.00 33.87 2.83
1516 2569 0.250640 AAGAGTGCTGAACCTGCAGG 60.251 55.000 31.60 31.60 38.86 4.85
1519 2572 2.417933 CACATAAGAGTGCTGAACCTGC 59.582 50.000 0.00 0.00 32.04 4.85
1520 2573 3.005554 CCACATAAGAGTGCTGAACCTG 58.994 50.000 0.00 0.00 38.18 4.00
1528 2581 3.609853 TGTTCCATCCACATAAGAGTGC 58.390 45.455 0.00 0.00 38.18 4.40
1549 2602 8.682936 ATACAAGACTCTGTCACTTCAATTTT 57.317 30.769 0.46 0.00 34.60 1.82
1561 2614 9.794719 TGCATATAGTAGTATACAAGACTCTGT 57.205 33.333 5.50 0.00 46.26 3.41
1576 2629 8.534333 ACACCAATTAATCGTGCATATAGTAG 57.466 34.615 13.05 0.00 0.00 2.57
1591 2761 7.821846 AGAAAAAGCACTGAAAACACCAATTAA 59.178 29.630 0.00 0.00 0.00 1.40
1600 2770 7.117667 TCCAAAAGAAGAAAAAGCACTGAAAAC 59.882 33.333 0.00 0.00 0.00 2.43
1605 2775 5.410067 TGTCCAAAAGAAGAAAAAGCACTG 58.590 37.500 0.00 0.00 0.00 3.66
1609 2780 4.686972 AGCTGTCCAAAAGAAGAAAAAGC 58.313 39.130 0.00 0.00 0.00 3.51
1614 2785 4.357918 AGCTAGCTGTCCAAAAGAAGAA 57.642 40.909 18.57 0.00 0.00 2.52
1634 2805 3.019564 CTCCTGGGGTAAGATGCAAAAG 58.980 50.000 0.00 0.00 0.00 2.27
1647 2818 1.352352 CTAATATGGTGGCTCCTGGGG 59.648 57.143 7.19 0.00 37.07 4.96
1652 2823 1.545651 GGGTGCTAATATGGTGGCTCC 60.546 57.143 0.00 0.00 37.54 4.70
1656 2827 3.576078 TGAAGGGTGCTAATATGGTGG 57.424 47.619 0.00 0.00 0.00 4.61
1695 2866 2.552743 CTGCAGCCTTGACATCCATATG 59.447 50.000 0.00 0.00 39.17 1.78
1732 2903 2.172505 TGGAGGCACCAAATATGACGAT 59.827 45.455 0.00 0.00 46.75 3.73
1778 2949 2.092323 GCTGACCCCACAGGATTTTAC 58.908 52.381 0.00 0.00 39.89 2.01
1785 2956 0.911769 TATGAAGCTGACCCCACAGG 59.088 55.000 0.00 0.00 43.78 4.00
1788 2959 3.086733 GCTATGAAGCTGACCCCAC 57.913 57.895 0.00 0.00 45.85 4.61
1807 2978 3.882888 AGAAATGTGAACACGACACCATT 59.117 39.130 0.00 0.00 37.45 3.16
1826 2997 4.034742 GGTACTGCACTTTTCGTGAAAGAA 59.965 41.667 16.86 5.46 46.24 2.52
1903 3074 5.773575 TGTACAAGCTGTTCAACAAAACAA 58.226 33.333 0.00 0.00 38.60 2.83
1918 3089 8.950208 AGGAAGAGAAATATAACTGTACAAGC 57.050 34.615 0.00 0.00 0.00 4.01
2045 5835 8.466798 ACCATTGTTAATTCTGTTGGCTATAAC 58.533 33.333 0.00 0.00 0.00 1.89
2106 5896 1.588139 GGTGACGGCGTTCCTATCG 60.588 63.158 16.19 0.00 0.00 2.92
2128 5918 2.432972 CATTTGCAACCAGCCGGC 60.433 61.111 21.89 21.89 44.83 6.13
2141 5931 1.669999 GCAGGCGATTGGGAGCATTT 61.670 55.000 0.00 0.00 34.54 2.32
2142 5932 2.123428 GCAGGCGATTGGGAGCATT 61.123 57.895 0.00 0.00 34.54 3.56
2160 5950 2.821366 GAGCGGATGTGGCTGTGG 60.821 66.667 0.00 0.00 41.72 4.17
2165 5955 3.017323 CGAATGAGCGGATGTGGC 58.983 61.111 0.00 0.00 0.00 5.01
2270 6060 3.820467 CAGCAACTTGACAGATACCCAAA 59.180 43.478 0.00 0.00 0.00 3.28
2290 6080 8.356533 ACAAAAATATTGTCTGCTTTGAACAG 57.643 30.769 12.67 0.00 36.44 3.16


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

AutoCloner maintained by Alex Coulton.