Multiple sequence alignment - TraesCS3A01G079500

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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 TraesCS3A01G079500 chr3A 100.000 2921 0 0 1 2921 51409942 51407022 0.000000e+00 5395
1 TraesCS3A01G079500 chr3A 90.311 867 47 11 1 833 646276161 646275298 0.000000e+00 1101
2 TraesCS3A01G079500 chr3A 87.654 162 18 2 2256 2417 740927422 740927263 1.380000e-43 187
3 TraesCS3A01G079500 chr3D 92.176 1112 62 11 838 1924 39621477 39620366 0.000000e+00 1548
4 TraesCS3A01G079500 chr3D 85.841 226 30 2 2188 2413 608387038 608387261 3.760000e-59 239
5 TraesCS3A01G079500 chr3B 91.689 1119 60 12 835 1924 63399672 63398558 0.000000e+00 1520
6 TraesCS3A01G079500 chr3B 91.495 823 40 13 1 795 94872488 94873308 0.000000e+00 1105
7 TraesCS3A01G079500 chr2B 91.599 857 47 10 1 833 215942203 215943058 0.000000e+00 1160
8 TraesCS3A01G079500 chr2B 91.008 645 33 9 214 834 254291718 254291075 0.000000e+00 846
9 TraesCS3A01G079500 chr7B 90.687 859 52 9 1 833 477425817 477426673 0.000000e+00 1118
10 TraesCS3A01G079500 chr7B 80.649 925 134 29 1017 1922 434831476 434830578 0.000000e+00 675
11 TraesCS3A01G079500 chr4A 90.542 867 45 16 1 833 487883636 487884499 0.000000e+00 1112
12 TraesCS3A01G079500 chr2A 90.069 866 49 11 1 832 33689575 33690437 0.000000e+00 1088
13 TraesCS3A01G079500 chr2A 89.093 871 58 11 1 837 60281523 60282390 0.000000e+00 1048
14 TraesCS3A01G079500 chr1D 88.575 744 69 9 2188 2921 462861872 462861135 0.000000e+00 889
15 TraesCS3A01G079500 chr4D 87.752 743 77 5 2188 2921 51904093 51904830 0.000000e+00 856
16 TraesCS3A01G079500 chr5D 87.618 743 78 5 2188 2921 249788521 249787784 0.000000e+00 850
17 TraesCS3A01G079500 chr5B 85.593 708 85 7 2189 2889 282387627 282386930 0.000000e+00 726
18 TraesCS3A01G079500 chr5B 90.514 253 23 1 2188 2440 548927420 548927671 1.680000e-87 333
19 TraesCS3A01G079500 chr7A 81.020 922 123 36 1027 1922 514702196 514703091 0.000000e+00 686
20 TraesCS3A01G079500 chr7D 80.043 922 145 28 1017 1922 418948909 418948011 0.000000e+00 647
21 TraesCS3A01G079500 chr6D 87.712 236 17 5 354 580 463854355 463854587 6.210000e-67 265


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 TraesCS3A01G079500 chr3A 51407022 51409942 2920 True 5395 5395 100.000 1 2921 1 chr3A.!!$R1 2920
1 TraesCS3A01G079500 chr3A 646275298 646276161 863 True 1101 1101 90.311 1 833 1 chr3A.!!$R2 832
2 TraesCS3A01G079500 chr3D 39620366 39621477 1111 True 1548 1548 92.176 838 1924 1 chr3D.!!$R1 1086
3 TraesCS3A01G079500 chr3B 63398558 63399672 1114 True 1520 1520 91.689 835 1924 1 chr3B.!!$R1 1089
4 TraesCS3A01G079500 chr3B 94872488 94873308 820 False 1105 1105 91.495 1 795 1 chr3B.!!$F1 794
5 TraesCS3A01G079500 chr2B 215942203 215943058 855 False 1160 1160 91.599 1 833 1 chr2B.!!$F1 832
6 TraesCS3A01G079500 chr2B 254291075 254291718 643 True 846 846 91.008 214 834 1 chr2B.!!$R1 620
7 TraesCS3A01G079500 chr7B 477425817 477426673 856 False 1118 1118 90.687 1 833 1 chr7B.!!$F1 832
8 TraesCS3A01G079500 chr7B 434830578 434831476 898 True 675 675 80.649 1017 1922 1 chr7B.!!$R1 905
9 TraesCS3A01G079500 chr4A 487883636 487884499 863 False 1112 1112 90.542 1 833 1 chr4A.!!$F1 832
10 TraesCS3A01G079500 chr2A 33689575 33690437 862 False 1088 1088 90.069 1 832 1 chr2A.!!$F1 831
11 TraesCS3A01G079500 chr2A 60281523 60282390 867 False 1048 1048 89.093 1 837 1 chr2A.!!$F2 836
12 TraesCS3A01G079500 chr1D 462861135 462861872 737 True 889 889 88.575 2188 2921 1 chr1D.!!$R1 733
13 TraesCS3A01G079500 chr4D 51904093 51904830 737 False 856 856 87.752 2188 2921 1 chr4D.!!$F1 733
14 TraesCS3A01G079500 chr5D 249787784 249788521 737 True 850 850 87.618 2188 2921 1 chr5D.!!$R1 733
15 TraesCS3A01G079500 chr5B 282386930 282387627 697 True 726 726 85.593 2189 2889 1 chr5B.!!$R1 700
16 TraesCS3A01G079500 chr7A 514702196 514703091 895 False 686 686 81.020 1027 1922 1 chr7A.!!$F1 895
17 TraesCS3A01G079500 chr7D 418948011 418948909 898 True 647 647 80.043 1017 1922 1 chr7D.!!$R1 905

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
599 646 0.316607 TCGTTTCATTGTGTGTGCGC 60.317 50.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 2489 0.105778 TCCATGACACGACAACAGCA 59.894 50.0 0.0 0.0 0.0 4.41 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
94 99 6.334202 CCAAGATCCTAACTACTGAACTGAC 58.666 44.000 0.00 0.00 0.00 3.51
155 160 1.807142 GCAAGTGTAGAGAAAGCACCC 59.193 52.381 0.00 0.00 33.96 4.61
210 215 4.676986 CGTGCAGCAAACTACTATCCACTA 60.677 45.833 0.00 0.00 0.00 2.74
350 357 2.853914 GCGTTTCTCGTGCTCCAC 59.146 61.111 0.00 0.00 42.13 4.02
385 392 0.959553 GCATGTCGGGCTAGCTACTA 59.040 55.000 15.72 0.00 0.00 1.82
599 646 0.316607 TCGTTTCATTGTGTGTGCGC 60.317 50.000 0.00 0.00 0.00 6.09
688 737 0.678950 CTGGTGGGGATTGCGTTTTT 59.321 50.000 0.00 0.00 0.00 1.94
752 801 6.525578 TTGACTGAGATTAATGAGTACGGT 57.474 37.500 0.00 0.00 0.00 4.83
784 833 9.263446 GATTTTAGGGATTAAAAGGTAAGGGTT 57.737 33.333 0.00 0.00 42.73 4.11
842 891 3.084786 CAGACTTTTCCCATTCAGTCCC 58.915 50.000 0.00 0.00 37.02 4.46
846 895 2.603075 TTTCCCATTCAGTCCCCAAG 57.397 50.000 0.00 0.00 0.00 3.61
882 931 1.706443 AATTCGTCGACGTTTCCTCC 58.294 50.000 34.40 0.00 40.80 4.30
896 945 0.404040 TCCTCCCCATGTTTGACCAC 59.596 55.000 0.00 0.00 0.00 4.16
920 969 2.095853 CACCCCGTCATTCATTTTCTCG 59.904 50.000 0.00 0.00 0.00 4.04
969 1018 4.433413 CGAATCTCGTGACAAATGTCTGTG 60.433 45.833 14.15 8.12 44.99 3.66
970 1019 3.452755 TCTCGTGACAAATGTCTGTGT 57.547 42.857 14.15 0.00 44.99 3.72
986 1035 3.817084 TCTGTGTATCCGACTAATACCCG 59.183 47.826 0.00 0.00 0.00 5.28
1022 1104 0.109226 GCGTCTTCTGGTAAGCTCGT 60.109 55.000 0.00 0.00 0.00 4.18
1036 1118 1.064611 AGCTCGTGGGTCTAGCTCTAA 60.065 52.381 0.00 0.00 40.45 2.10
1049 1134 5.009610 GTCTAGCTCTAATACTGCTGCTCTT 59.990 44.000 0.00 0.00 37.62 2.85
1076 1167 4.891727 GACGATCATGGCGGCGGT 62.892 66.667 9.78 0.00 0.00 5.68
1193 1284 3.225235 GCTCTTCCAGCCCGAGAT 58.775 61.111 0.00 0.00 43.17 2.75
1245 1336 4.168291 GGCTTCCTGCTCCTCCCG 62.168 72.222 0.00 0.00 42.39 5.14
1399 1490 2.954753 CTGTTCAACAGCCGGACGC 61.955 63.158 5.05 0.00 39.62 5.19
1529 1620 2.505557 GTACGTCGGCCTCAACGG 60.506 66.667 21.29 8.03 42.99 4.44
1924 2030 4.497300 CATGGAACCCAAGCAATAGTTTG 58.503 43.478 0.00 0.00 36.95 2.93
1925 2031 3.571590 TGGAACCCAAGCAATAGTTTGT 58.428 40.909 0.00 0.00 34.54 2.83
1926 2032 4.730966 TGGAACCCAAGCAATAGTTTGTA 58.269 39.130 0.00 0.00 34.54 2.41
1927 2033 4.764823 TGGAACCCAAGCAATAGTTTGTAG 59.235 41.667 0.00 0.00 34.54 2.74
1928 2034 4.765339 GGAACCCAAGCAATAGTTTGTAGT 59.235 41.667 0.00 0.00 34.54 2.73
1929 2035 5.941647 GGAACCCAAGCAATAGTTTGTAGTA 59.058 40.000 0.00 0.00 34.54 1.82
1930 2036 6.128090 GGAACCCAAGCAATAGTTTGTAGTAC 60.128 42.308 0.00 0.00 34.54 2.73
1931 2037 6.123045 ACCCAAGCAATAGTTTGTAGTACT 57.877 37.500 0.00 0.00 34.54 2.73
1932 2038 5.938125 ACCCAAGCAATAGTTTGTAGTACTG 59.062 40.000 5.39 0.00 34.54 2.74
1933 2039 5.163754 CCCAAGCAATAGTTTGTAGTACTGC 60.164 44.000 5.39 4.49 33.65 4.40
1934 2040 5.163754 CCAAGCAATAGTTTGTAGTACTGCC 60.164 44.000 5.39 0.00 33.89 4.85
1935 2041 5.160607 AGCAATAGTTTGTAGTACTGCCA 57.839 39.130 5.39 0.00 33.89 4.92
1936 2042 5.745227 AGCAATAGTTTGTAGTACTGCCAT 58.255 37.500 5.39 0.00 33.89 4.40
1937 2043 5.586243 AGCAATAGTTTGTAGTACTGCCATG 59.414 40.000 5.39 0.00 33.89 3.66
1938 2044 5.354234 GCAATAGTTTGTAGTACTGCCATGT 59.646 40.000 5.39 0.00 35.17 3.21
1939 2045 6.675486 GCAATAGTTTGTAGTACTGCCATGTG 60.675 42.308 5.39 0.00 35.17 3.21
1940 2046 4.351874 AGTTTGTAGTACTGCCATGTGT 57.648 40.909 5.39 0.00 0.00 3.72
1941 2047 4.714632 AGTTTGTAGTACTGCCATGTGTT 58.285 39.130 5.39 0.00 0.00 3.32
1942 2048 4.755123 AGTTTGTAGTACTGCCATGTGTTC 59.245 41.667 5.39 0.00 0.00 3.18
1943 2049 4.344359 TTGTAGTACTGCCATGTGTTCA 57.656 40.909 5.39 0.00 0.00 3.18
1944 2050 4.344359 TGTAGTACTGCCATGTGTTCAA 57.656 40.909 5.39 0.00 0.00 2.69
1945 2051 4.062293 TGTAGTACTGCCATGTGTTCAAC 58.938 43.478 5.39 0.00 0.00 3.18
1946 2052 2.504367 AGTACTGCCATGTGTTCAACC 58.496 47.619 0.00 0.00 0.00 3.77
1947 2053 1.539827 GTACTGCCATGTGTTCAACCC 59.460 52.381 0.00 0.00 0.00 4.11
1948 2054 0.106268 ACTGCCATGTGTTCAACCCA 60.106 50.000 0.00 0.00 0.00 4.51
1949 2055 1.259609 CTGCCATGTGTTCAACCCAT 58.740 50.000 0.00 0.00 0.00 4.00
1950 2056 0.967662 TGCCATGTGTTCAACCCATG 59.032 50.000 6.03 6.03 36.56 3.66
1951 2057 0.390209 GCCATGTGTTCAACCCATGC 60.390 55.000 7.43 0.48 35.70 4.06
1952 2058 0.967662 CCATGTGTTCAACCCATGCA 59.032 50.000 7.43 0.00 35.70 3.96
1953 2059 1.551430 CCATGTGTTCAACCCATGCAT 59.449 47.619 7.43 0.00 35.70 3.96
1954 2060 2.759535 CCATGTGTTCAACCCATGCATA 59.240 45.455 7.43 0.00 35.70 3.14
1955 2061 3.429272 CCATGTGTTCAACCCATGCATAC 60.429 47.826 7.43 0.00 35.70 2.39
1956 2062 2.166829 TGTGTTCAACCCATGCATACC 58.833 47.619 0.00 0.00 0.00 2.73
1957 2063 2.166829 GTGTTCAACCCATGCATACCA 58.833 47.619 0.00 0.00 0.00 3.25
1958 2064 2.760092 GTGTTCAACCCATGCATACCAT 59.240 45.455 0.00 0.00 33.39 3.55
1971 2077 7.953158 CATGCATACCATGTATAGTATAGCC 57.047 40.000 0.00 0.00 45.05 3.93
1972 2078 6.479972 TGCATACCATGTATAGTATAGCCC 57.520 41.667 0.00 0.00 0.00 5.19
1973 2079 6.202331 TGCATACCATGTATAGTATAGCCCT 58.798 40.000 0.00 0.00 0.00 5.19
1974 2080 6.098266 TGCATACCATGTATAGTATAGCCCTG 59.902 42.308 0.00 0.00 0.00 4.45
1975 2081 6.098409 GCATACCATGTATAGTATAGCCCTGT 59.902 42.308 0.00 0.00 0.00 4.00
1976 2082 7.287005 GCATACCATGTATAGTATAGCCCTGTA 59.713 40.741 0.00 0.00 0.00 2.74
1977 2083 8.851145 CATACCATGTATAGTATAGCCCTGTAG 58.149 40.741 0.00 0.00 0.00 2.74
1978 2084 7.040913 ACCATGTATAGTATAGCCCTGTAGA 57.959 40.000 0.00 0.00 0.00 2.59
1979 2085 6.890814 ACCATGTATAGTATAGCCCTGTAGAC 59.109 42.308 0.00 0.00 0.00 2.59
1980 2086 6.038382 CCATGTATAGTATAGCCCTGTAGACG 59.962 46.154 0.00 0.00 0.00 4.18
1981 2087 6.119240 TGTATAGTATAGCCCTGTAGACGT 57.881 41.667 0.00 0.00 0.00 4.34
1982 2088 6.169094 TGTATAGTATAGCCCTGTAGACGTC 58.831 44.000 7.70 7.70 0.00 4.34
1983 2089 3.860968 AGTATAGCCCTGTAGACGTCT 57.139 47.619 23.66 23.66 0.00 4.18
1984 2090 4.970860 AGTATAGCCCTGTAGACGTCTA 57.029 45.455 21.25 21.25 0.00 2.59
1985 2091 4.640364 AGTATAGCCCTGTAGACGTCTAC 58.360 47.826 37.47 37.47 46.78 2.59
1986 2092 3.860968 ATAGCCCTGTAGACGTCTACT 57.139 47.619 40.53 28.65 46.74 2.57
1987 2093 4.970860 ATAGCCCTGTAGACGTCTACTA 57.029 45.455 40.53 29.54 46.74 1.82
1988 2094 3.860968 AGCCCTGTAGACGTCTACTAT 57.139 47.619 40.53 25.39 46.74 2.12
1989 2095 3.742385 AGCCCTGTAGACGTCTACTATC 58.258 50.000 40.53 29.49 46.74 2.08
1990 2096 3.391955 AGCCCTGTAGACGTCTACTATCT 59.608 47.826 40.53 30.68 46.74 1.98
1991 2097 4.136051 GCCCTGTAGACGTCTACTATCTT 58.864 47.826 40.53 14.71 46.74 2.40
1992 2098 4.579753 GCCCTGTAGACGTCTACTATCTTT 59.420 45.833 40.53 14.05 46.74 2.52
1993 2099 5.762218 GCCCTGTAGACGTCTACTATCTTTA 59.238 44.000 40.53 25.45 46.74 1.85
1994 2100 6.261826 GCCCTGTAGACGTCTACTATCTTTAA 59.738 42.308 40.53 24.87 46.74 1.52
1995 2101 7.201767 GCCCTGTAGACGTCTACTATCTTTAAA 60.202 40.741 40.53 24.30 46.74 1.52
1996 2102 8.127954 CCCTGTAGACGTCTACTATCTTTAAAC 58.872 40.741 40.53 22.93 46.74 2.01
1997 2103 8.127954 CCTGTAGACGTCTACTATCTTTAAACC 58.872 40.741 40.53 20.54 46.74 3.27
1998 2104 8.565896 TGTAGACGTCTACTATCTTTAAACCA 57.434 34.615 40.53 22.44 46.74 3.67
1999 2105 8.454106 TGTAGACGTCTACTATCTTTAAACCAC 58.546 37.037 40.53 21.86 46.74 4.16
2000 2106 7.700022 AGACGTCTACTATCTTTAAACCACT 57.300 36.000 18.46 0.00 0.00 4.00
2001 2107 7.536855 AGACGTCTACTATCTTTAAACCACTG 58.463 38.462 18.46 0.00 0.00 3.66
2002 2108 7.176340 AGACGTCTACTATCTTTAAACCACTGT 59.824 37.037 18.46 0.00 0.00 3.55
2003 2109 7.088905 ACGTCTACTATCTTTAAACCACTGTG 58.911 38.462 0.00 0.00 0.00 3.66
2004 2110 7.088905 CGTCTACTATCTTTAAACCACTGTGT 58.911 38.462 7.08 0.00 0.00 3.72
2005 2111 7.597743 CGTCTACTATCTTTAAACCACTGTGTT 59.402 37.037 7.08 0.00 0.00 3.32
2006 2112 9.269453 GTCTACTATCTTTAAACCACTGTGTTT 57.731 33.333 7.08 9.65 41.18 2.83
2007 2113 9.841295 TCTACTATCTTTAAACCACTGTGTTTT 57.159 29.630 8.38 8.38 39.15 2.43
2010 2116 9.623000 ACTATCTTTAAACCACTGTGTTTTACT 57.377 29.630 9.65 0.28 39.15 2.24
2014 2120 9.398538 TCTTTAAACCACTGTGTTTTACTATGT 57.601 29.630 9.65 0.00 39.15 2.29
2018 2124 8.741603 AAACCACTGTGTTTTACTATGTTACT 57.258 30.769 7.08 0.00 34.92 2.24
2019 2125 8.741603 AACCACTGTGTTTTACTATGTTACTT 57.258 30.769 7.08 0.00 0.00 2.24
2020 2126 8.374327 ACCACTGTGTTTTACTATGTTACTTC 57.626 34.615 7.08 0.00 0.00 3.01
2021 2127 7.443272 ACCACTGTGTTTTACTATGTTACTTCC 59.557 37.037 7.08 0.00 0.00 3.46
2022 2128 7.442969 CCACTGTGTTTTACTATGTTACTTCCA 59.557 37.037 7.08 0.00 0.00 3.53
2023 2129 8.999431 CACTGTGTTTTACTATGTTACTTCCAT 58.001 33.333 0.00 0.00 0.00 3.41
2024 2130 8.999431 ACTGTGTTTTACTATGTTACTTCCATG 58.001 33.333 0.00 0.00 0.00 3.66
2025 2131 8.911918 TGTGTTTTACTATGTTACTTCCATGT 57.088 30.769 0.00 0.00 0.00 3.21
2026 2132 9.344772 TGTGTTTTACTATGTTACTTCCATGTT 57.655 29.630 0.00 0.00 0.00 2.71
2034 2140 9.295825 ACTATGTTACTTCCATGTTTGAATTCA 57.704 29.630 3.38 3.38 0.00 2.57
2066 2172 8.553459 ACGATTGAATTAAGATCAGTGTTTCT 57.447 30.769 0.00 0.00 0.00 2.52
2067 2173 9.003658 ACGATTGAATTAAGATCAGTGTTTCTT 57.996 29.630 13.19 13.19 36.26 2.52
2072 2178 9.658799 TGAATTAAGATCAGTGTTTCTTAGGAG 57.341 33.333 13.94 0.00 36.20 3.69
2073 2179 9.877178 GAATTAAGATCAGTGTTTCTTAGGAGA 57.123 33.333 13.94 5.13 36.20 3.71
2074 2180 9.883142 AATTAAGATCAGTGTTTCTTAGGAGAG 57.117 33.333 13.94 0.00 36.20 3.20
2075 2181 8.651589 TTAAGATCAGTGTTTCTTAGGAGAGA 57.348 34.615 13.94 2.24 36.20 3.10
2076 2182 7.546250 AAGATCAGTGTTTCTTAGGAGAGAA 57.454 36.000 8.66 0.00 34.00 2.87
2077 2183 7.546250 AGATCAGTGTTTCTTAGGAGAGAAA 57.454 36.000 0.00 0.00 41.88 2.52
2078 2184 7.610865 AGATCAGTGTTTCTTAGGAGAGAAAG 58.389 38.462 0.00 0.00 43.99 2.62
2079 2185 5.542779 TCAGTGTTTCTTAGGAGAGAAAGC 58.457 41.667 0.65 0.00 43.99 3.51
2080 2186 5.305644 TCAGTGTTTCTTAGGAGAGAAAGCT 59.694 40.000 0.65 0.00 43.99 3.74
2081 2187 6.493802 TCAGTGTTTCTTAGGAGAGAAAGCTA 59.506 38.462 0.65 0.00 43.99 3.32
2082 2188 6.588373 CAGTGTTTCTTAGGAGAGAAAGCTAC 59.412 42.308 0.65 2.23 43.99 3.58
2083 2189 6.495526 AGTGTTTCTTAGGAGAGAAAGCTACT 59.504 38.462 0.65 0.00 43.99 2.57
2084 2190 7.015779 AGTGTTTCTTAGGAGAGAAAGCTACTT 59.984 37.037 0.65 0.00 43.99 2.24
2085 2191 7.117092 GTGTTTCTTAGGAGAGAAAGCTACTTG 59.883 40.741 0.65 0.00 43.99 3.16
2086 2192 5.923733 TCTTAGGAGAGAAAGCTACTTGG 57.076 43.478 0.00 0.00 30.01 3.61
2087 2193 5.334421 TCTTAGGAGAGAAAGCTACTTGGT 58.666 41.667 0.00 0.00 30.01 3.67
2088 2194 3.971245 AGGAGAGAAAGCTACTTGGTG 57.029 47.619 0.00 0.00 0.00 4.17
2089 2195 2.027653 AGGAGAGAAAGCTACTTGGTGC 60.028 50.000 0.00 0.00 0.00 5.01
2090 2196 2.289694 GGAGAGAAAGCTACTTGGTGCA 60.290 50.000 0.00 0.00 0.00 4.57
2091 2197 2.739379 GAGAGAAAGCTACTTGGTGCAC 59.261 50.000 8.80 8.80 0.00 4.57
2092 2198 2.370189 AGAGAAAGCTACTTGGTGCACT 59.630 45.455 17.98 0.00 0.00 4.40
2093 2199 3.142174 GAGAAAGCTACTTGGTGCACTT 58.858 45.455 17.98 0.00 0.00 3.16
2094 2200 3.555966 AGAAAGCTACTTGGTGCACTTT 58.444 40.909 17.98 6.47 0.00 2.66
2095 2201 4.714632 AGAAAGCTACTTGGTGCACTTTA 58.285 39.130 17.98 0.49 0.00 1.85
2096 2202 5.316987 AGAAAGCTACTTGGTGCACTTTAT 58.683 37.500 17.98 0.95 0.00 1.40
2097 2203 5.770162 AGAAAGCTACTTGGTGCACTTTATT 59.230 36.000 17.98 0.29 0.00 1.40
2098 2204 6.940298 AGAAAGCTACTTGGTGCACTTTATTA 59.060 34.615 17.98 1.52 0.00 0.98
2099 2205 7.447238 AGAAAGCTACTTGGTGCACTTTATTAA 59.553 33.333 17.98 2.41 0.00 1.40
2100 2206 6.496338 AGCTACTTGGTGCACTTTATTAAC 57.504 37.500 17.98 0.00 0.00 2.01
2101 2207 6.238648 AGCTACTTGGTGCACTTTATTAACT 58.761 36.000 17.98 3.28 0.00 2.24
2102 2208 6.149474 AGCTACTTGGTGCACTTTATTAACTG 59.851 38.462 17.98 0.00 0.00 3.16
2103 2209 6.148811 GCTACTTGGTGCACTTTATTAACTGA 59.851 38.462 17.98 0.00 0.00 3.41
2104 2210 6.952773 ACTTGGTGCACTTTATTAACTGAA 57.047 33.333 17.98 0.00 0.00 3.02
2105 2211 7.341445 ACTTGGTGCACTTTATTAACTGAAA 57.659 32.000 17.98 0.00 0.00 2.69
2106 2212 7.951591 ACTTGGTGCACTTTATTAACTGAAAT 58.048 30.769 17.98 0.00 0.00 2.17
2107 2213 8.082242 ACTTGGTGCACTTTATTAACTGAAATC 58.918 33.333 17.98 0.00 0.00 2.17
2108 2214 7.517614 TGGTGCACTTTATTAACTGAAATCA 57.482 32.000 17.98 0.00 0.00 2.57
2109 2215 7.946207 TGGTGCACTTTATTAACTGAAATCAA 58.054 30.769 17.98 0.00 0.00 2.57
2110 2216 8.417106 TGGTGCACTTTATTAACTGAAATCAAA 58.583 29.630 17.98 0.00 0.00 2.69
2111 2217 8.915654 GGTGCACTTTATTAACTGAAATCAAAG 58.084 33.333 17.98 0.00 0.00 2.77
2112 2218 9.463443 GTGCACTTTATTAACTGAAATCAAAGT 57.537 29.630 10.32 0.00 35.68 2.66
2123 2229 8.408043 AACTGAAATCAAAGTTACATCATCCA 57.592 30.769 0.00 0.00 34.90 3.41
2124 2230 8.585471 ACTGAAATCAAAGTTACATCATCCAT 57.415 30.769 0.00 0.00 0.00 3.41
2125 2231 9.685276 ACTGAAATCAAAGTTACATCATCCATA 57.315 29.630 0.00 0.00 0.00 2.74
2131 2237 8.450578 TCAAAGTTACATCATCCATAATGACC 57.549 34.615 0.00 0.00 47.00 4.02
2132 2238 7.226523 TCAAAGTTACATCATCCATAATGACCG 59.773 37.037 0.00 0.00 47.00 4.79
2133 2239 5.551233 AGTTACATCATCCATAATGACCGG 58.449 41.667 0.00 0.00 47.00 5.28
2134 2240 5.306937 AGTTACATCATCCATAATGACCGGA 59.693 40.000 9.46 0.00 47.00 5.14
2135 2241 4.705110 ACATCATCCATAATGACCGGAA 57.295 40.909 9.46 0.00 47.00 4.30
2136 2242 5.047566 ACATCATCCATAATGACCGGAAA 57.952 39.130 9.46 0.00 47.00 3.13
2137 2243 5.634118 ACATCATCCATAATGACCGGAAAT 58.366 37.500 9.46 0.00 47.00 2.17
2138 2244 6.070656 ACATCATCCATAATGACCGGAAATT 58.929 36.000 9.46 10.13 47.00 1.82
2139 2245 7.230747 ACATCATCCATAATGACCGGAAATTA 58.769 34.615 9.46 12.18 47.00 1.40
2140 2246 7.723616 ACATCATCCATAATGACCGGAAATTAA 59.276 33.333 9.46 0.00 47.00 1.40
2141 2247 8.575589 CATCATCCATAATGACCGGAAATTAAA 58.424 33.333 9.46 2.95 47.00 1.52
2142 2248 8.526667 TCATCCATAATGACCGGAAATTAAAA 57.473 30.769 9.46 2.61 39.52 1.52
2143 2249 8.972127 TCATCCATAATGACCGGAAATTAAAAA 58.028 29.630 9.46 2.28 39.52 1.94
2162 2268 2.123597 CGGGGGATCACCGTCCTA 60.124 66.667 17.17 0.00 46.03 2.94
2163 2269 1.759299 CGGGGGATCACCGTCCTAA 60.759 63.158 17.17 0.00 46.03 2.69
2164 2270 1.332144 CGGGGGATCACCGTCCTAAA 61.332 60.000 17.17 0.00 46.03 1.85
2165 2271 0.179702 GGGGGATCACCGTCCTAAAC 59.820 60.000 8.21 0.00 41.60 2.01
2166 2272 0.906775 GGGGATCACCGTCCTAAACA 59.093 55.000 0.00 0.00 41.60 2.83
2167 2273 1.279846 GGGGATCACCGTCCTAAACAA 59.720 52.381 0.00 0.00 41.60 2.83
2168 2274 2.290450 GGGGATCACCGTCCTAAACAAA 60.290 50.000 0.00 0.00 41.60 2.83
2169 2275 3.414269 GGGATCACCGTCCTAAACAAAA 58.586 45.455 0.00 0.00 38.38 2.44
2170 2276 3.439129 GGGATCACCGTCCTAAACAAAAG 59.561 47.826 0.00 0.00 38.38 2.27
2171 2277 4.070009 GGATCACCGTCCTAAACAAAAGT 58.930 43.478 0.00 0.00 35.32 2.66
2172 2278 5.240121 GGATCACCGTCCTAAACAAAAGTA 58.760 41.667 0.00 0.00 35.32 2.24
2173 2279 5.350640 GGATCACCGTCCTAAACAAAAGTAG 59.649 44.000 0.00 0.00 35.32 2.57
2174 2280 5.534207 TCACCGTCCTAAACAAAAGTAGA 57.466 39.130 0.00 0.00 0.00 2.59
2175 2281 5.535333 TCACCGTCCTAAACAAAAGTAGAG 58.465 41.667 0.00 0.00 0.00 2.43
2176 2282 5.069516 TCACCGTCCTAAACAAAAGTAGAGT 59.930 40.000 0.00 0.00 0.00 3.24
2177 2283 5.756833 CACCGTCCTAAACAAAAGTAGAGTT 59.243 40.000 0.00 0.00 0.00 3.01
2178 2284 5.987953 ACCGTCCTAAACAAAAGTAGAGTTC 59.012 40.000 0.00 0.00 0.00 3.01
2179 2285 5.118203 CCGTCCTAAACAAAAGTAGAGTTCG 59.882 44.000 0.00 0.00 0.00 3.95
2180 2286 5.916883 CGTCCTAAACAAAAGTAGAGTTCGA 59.083 40.000 0.00 0.00 0.00 3.71
2181 2287 6.418819 CGTCCTAAACAAAAGTAGAGTTCGAA 59.581 38.462 0.00 0.00 0.00 3.71
2182 2288 7.115947 CGTCCTAAACAAAAGTAGAGTTCGAAT 59.884 37.037 0.00 0.00 0.00 3.34
2183 2289 8.433893 GTCCTAAACAAAAGTAGAGTTCGAATC 58.566 37.037 0.00 0.15 0.00 2.52
2184 2290 8.145767 TCCTAAACAAAAGTAGAGTTCGAATCA 58.854 33.333 0.00 0.00 0.00 2.57
2185 2291 8.770828 CCTAAACAAAAGTAGAGTTCGAATCAA 58.229 33.333 0.00 0.00 0.00 2.57
2205 2311 4.564769 TCAAAACAATGCGTGAAAGAAACC 59.435 37.500 0.00 0.00 0.00 3.27
2206 2312 2.399396 ACAATGCGTGAAAGAAACCG 57.601 45.000 0.00 0.00 0.00 4.44
2207 2313 1.944024 ACAATGCGTGAAAGAAACCGA 59.056 42.857 0.00 0.00 0.00 4.69
2212 2318 0.231279 CGTGAAAGAAACCGACACCG 59.769 55.000 0.00 0.00 0.00 4.94
2218 2324 1.167851 AGAAACCGACACCGATACGA 58.832 50.000 0.00 0.00 38.22 3.43
2240 2346 3.233507 AGAGCCTTTTGAAAGCAATCCA 58.766 40.909 0.00 0.00 34.69 3.41
2249 2355 9.001542 CCTTTTGAAAGCAATCCATCAAAATAA 57.998 29.630 11.53 0.00 45.43 1.40
2264 2370 6.374417 TCAAAATAACAGAGTAAGGGCTCT 57.626 37.500 0.00 0.00 45.87 4.09
2266 2372 7.556844 TCAAAATAACAGAGTAAGGGCTCTAG 58.443 38.462 0.00 0.00 43.37 2.43
2275 2381 7.565398 ACAGAGTAAGGGCTCTAGATTTCAATA 59.435 37.037 0.00 0.00 43.37 1.90
2351 2457 2.711009 TGACATCCAAGGTCTTCCAACT 59.289 45.455 0.00 0.00 36.26 3.16
2383 2489 0.108424 GCTGAAGTGTGATCGCCTCT 60.108 55.000 3.31 0.00 0.00 3.69
2392 2498 0.390340 TGATCGCCTCTGCTGTTGTC 60.390 55.000 0.00 0.00 34.43 3.18
2394 2500 2.159819 ATCGCCTCTGCTGTTGTCGT 62.160 55.000 0.00 0.00 34.43 4.34
2395 2501 2.661566 CGCCTCTGCTGTTGTCGTG 61.662 63.158 0.00 0.00 34.43 4.35
2408 2514 3.055891 TGTTGTCGTGTCATGGAGATGAT 60.056 43.478 0.00 0.00 40.78 2.45
2467 2573 1.264288 CTGTTTCGGAGAACAACAGCC 59.736 52.381 7.21 0.00 44.74 4.85
2469 2575 0.179067 TTTCGGAGAACAACAGCCGT 60.179 50.000 0.00 0.00 45.90 5.68
2485 2597 0.882927 CCGTCGCACCCTTCTCAAAA 60.883 55.000 0.00 0.00 0.00 2.44
2486 2598 0.941542 CGTCGCACCCTTCTCAAAAA 59.058 50.000 0.00 0.00 0.00 1.94
2509 2621 2.611292 AGCTGCATCGATGTTTAGCTTC 59.389 45.455 30.58 14.87 37.96 3.86
2511 2623 3.545624 GCTGCATCGATGTTTAGCTTCTG 60.546 47.826 28.28 15.91 32.60 3.02
2515 2627 3.165058 TCGATGTTTAGCTTCTGCGAT 57.835 42.857 0.00 0.00 45.42 4.58
2578 2690 3.119459 TCAGATTAGTGGCTCGACTGAAC 60.119 47.826 0.00 0.00 31.51 3.18
2594 2706 5.106555 CGACTGAACTTAATTGTGATTGCCT 60.107 40.000 0.00 0.00 0.00 4.75
2595 2707 6.092122 CGACTGAACTTAATTGTGATTGCCTA 59.908 38.462 0.00 0.00 0.00 3.93
2600 2712 9.679661 TGAACTTAATTGTGATTGCCTAGATAA 57.320 29.630 0.00 0.00 0.00 1.75
2615 2727 6.040054 TGCCTAGATAACGAATGCAGTACTTA 59.960 38.462 0.00 0.00 0.00 2.24
2624 2736 8.813643 AACGAATGCAGTACTTATAGGATTAC 57.186 34.615 0.00 0.00 0.00 1.89
2642 2754 2.165319 ACGGACTTTTTCTCCCTTCG 57.835 50.000 0.00 0.00 0.00 3.79
2653 2765 1.546476 TCTCCCTTCGCAAACTCTCTC 59.454 52.381 0.00 0.00 0.00 3.20
2654 2766 1.273606 CTCCCTTCGCAAACTCTCTCA 59.726 52.381 0.00 0.00 0.00 3.27
2656 2768 1.001406 CCCTTCGCAAACTCTCTCAGT 59.999 52.381 0.00 0.00 36.64 3.41
2666 2778 1.071385 ACTCTCTCAGTTGCCACCAAG 59.929 52.381 0.00 0.00 26.56 3.61
2682 2794 2.229792 CCAAGTATACCATGCGCCAAT 58.770 47.619 4.18 0.00 0.00 3.16
2685 2797 2.494059 AGTATACCATGCGCCAATGAC 58.506 47.619 4.18 0.00 0.00 3.06
2702 2814 0.035915 GACCAAAGACTCCCTGAGGC 60.036 60.000 0.00 0.00 38.12 4.70
2719 2831 3.814268 CCCAATCGGCCAAGCACG 61.814 66.667 2.24 0.00 0.00 5.34
2738 2850 3.859414 GAGGATGGCTCGCTGGCT 61.859 66.667 3.84 0.00 42.34 4.75
2764 2876 5.012046 TGTGAGAAGCTCCTCAAGAATAACA 59.988 40.000 3.37 0.00 43.94 2.41
2789 2902 7.770433 CACTCCTGACCTGTCAATATTAATCAA 59.230 37.037 1.14 0.00 39.39 2.57
2790 2903 8.497745 ACTCCTGACCTGTCAATATTAATCAAT 58.502 33.333 1.14 0.00 39.39 2.57
2791 2904 8.908786 TCCTGACCTGTCAATATTAATCAATC 57.091 34.615 1.14 0.00 39.39 2.67
2792 2905 8.493607 TCCTGACCTGTCAATATTAATCAATCA 58.506 33.333 1.14 0.00 39.39 2.57
2819 2932 2.159382 CTGTTAACGGTTGCATTCCCT 58.841 47.619 6.25 0.00 0.00 4.20
2832 2945 2.881403 GCATTCCCTGTTCTGTCCACAT 60.881 50.000 0.00 0.00 0.00 3.21
2869 2982 2.557924 ACATGTGAACATCAAATGGCGT 59.442 40.909 13.55 0.00 44.47 5.68
2882 2995 6.096673 TCAAATGGCGTATATCTTCTGCTA 57.903 37.500 0.00 0.00 0.00 3.49
2904 3019 0.179023 TGCTCACACAGGACATTGCA 60.179 50.000 0.00 0.00 0.00 4.08
2906 3021 1.162698 CTCACACAGGACATTGCAGG 58.837 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 99 3.592381 GACCAATCGATCAACCATTCG 57.408 47.619 0.00 0.00 36.72 3.34
124 129 2.162008 TCTACACTTGCGTACGTGCATA 59.838 45.455 17.90 1.98 45.78 3.14
155 160 1.337635 GCTAGCCTCAAGGATCCATCG 60.338 57.143 15.82 1.23 37.39 3.84
183 188 0.105964 AGTAGTTTGCTGCACGTGGA 59.894 50.000 18.88 14.63 0.00 4.02
210 215 0.467384 CCCAGATCGACCAAGCATCT 59.533 55.000 0.00 0.00 0.00 2.90
350 357 0.179084 ATGCTAACGACGATGGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
385 392 3.208884 GAGTGGCTGGTGTCGTCGT 62.209 63.158 0.00 0.00 0.00 4.34
505 516 3.058160 CGTGCAGCCCTGGGAAAG 61.058 66.667 19.27 6.00 0.00 2.62
670 719 0.676736 GAAAAACGCAATCCCCACCA 59.323 50.000 0.00 0.00 0.00 4.17
688 737 5.567430 TCTAGACTAGTTTGGTGCACTAGA 58.433 41.667 17.98 8.77 44.60 2.43
784 833 2.228582 TCGTACTTCCCGTCGAAATTGA 59.771 45.455 0.00 0.00 0.00 2.57
882 931 0.673437 GTGTGGTGGTCAAACATGGG 59.327 55.000 0.00 0.00 33.78 4.00
896 945 1.544724 AAATGAATGACGGGGTGTGG 58.455 50.000 0.00 0.00 0.00 4.17
935 984 2.093869 CACGAGATTCGGAGGGGTTTTA 60.094 50.000 3.37 0.00 45.59 1.52
969 1018 5.048504 TGTTGATCGGGTATTAGTCGGATAC 60.049 44.000 0.00 0.00 0.00 2.24
970 1019 5.072055 TGTTGATCGGGTATTAGTCGGATA 58.928 41.667 0.00 0.00 0.00 2.59
986 1035 4.310769 AGACGCCATTAGCTATGTTGATC 58.689 43.478 0.00 0.00 40.39 2.92
1012 1094 0.102663 GCTAGACCCACGAGCTTACC 59.897 60.000 0.00 0.00 42.48 2.85
1022 1104 3.891977 CAGCAGTATTAGAGCTAGACCCA 59.108 47.826 0.00 0.00 36.73 4.51
1036 1118 1.809271 CGCCATGAAGAGCAGCAGTAT 60.809 52.381 0.00 0.00 0.00 2.12
1049 1134 3.150647 ATGATCGTCGCCGCCATGA 62.151 57.895 0.00 0.00 0.00 3.07
1076 1167 3.931190 TAGGACTCGACGCCTGCCA 62.931 63.158 10.78 0.00 35.73 4.92
1636 1736 3.917760 GTCGATGAGGGCTCCGGG 61.918 72.222 0.00 0.00 0.00 5.73
1924 2030 3.435671 GGTTGAACACATGGCAGTACTAC 59.564 47.826 0.00 0.00 0.00 2.73
1925 2031 3.558321 GGGTTGAACACATGGCAGTACTA 60.558 47.826 0.00 0.00 0.00 1.82
1926 2032 2.504367 GGTTGAACACATGGCAGTACT 58.496 47.619 0.00 0.00 0.00 2.73
1927 2033 1.539827 GGGTTGAACACATGGCAGTAC 59.460 52.381 0.00 0.00 0.00 2.73
1928 2034 1.143889 TGGGTTGAACACATGGCAGTA 59.856 47.619 0.00 0.00 0.00 2.74
1929 2035 0.106268 TGGGTTGAACACATGGCAGT 60.106 50.000 0.00 0.00 0.00 4.40
1930 2036 1.259609 ATGGGTTGAACACATGGCAG 58.740 50.000 13.00 0.00 41.44 4.85
1931 2037 3.453916 ATGGGTTGAACACATGGCA 57.546 47.368 13.00 0.00 41.44 4.92
1935 2041 2.760092 GGTATGCATGGGTTGAACACAT 59.240 45.455 7.35 7.35 44.40 3.21
1936 2042 2.166829 GGTATGCATGGGTTGAACACA 58.833 47.619 10.16 1.37 35.08 3.72
1937 2043 2.166829 TGGTATGCATGGGTTGAACAC 58.833 47.619 10.16 0.00 0.00 3.32
1938 2044 2.593925 TGGTATGCATGGGTTGAACA 57.406 45.000 10.16 0.00 0.00 3.18
1939 2045 2.760092 ACATGGTATGCATGGGTTGAAC 59.240 45.455 10.16 0.00 34.56 3.18
1940 2046 3.098774 ACATGGTATGCATGGGTTGAA 57.901 42.857 10.16 0.00 34.56 2.69
1941 2047 2.824689 ACATGGTATGCATGGGTTGA 57.175 45.000 10.16 0.00 34.56 3.18
1942 2048 5.316167 ACTATACATGGTATGCATGGGTTG 58.684 41.667 10.16 4.80 34.56 3.77
1943 2049 5.582950 ACTATACATGGTATGCATGGGTT 57.417 39.130 10.16 0.00 34.56 4.11
1944 2050 6.891306 ATACTATACATGGTATGCATGGGT 57.109 37.500 10.16 2.79 33.86 4.51
1945 2051 6.931281 GCTATACTATACATGGTATGCATGGG 59.069 42.308 10.16 0.00 35.59 4.00
1946 2052 6.931281 GGCTATACTATACATGGTATGCATGG 59.069 42.308 10.16 0.00 35.59 3.66
1947 2053 6.931281 GGGCTATACTATACATGGTATGCATG 59.069 42.308 10.16 0.00 35.59 4.06
1948 2054 6.846505 AGGGCTATACTATACATGGTATGCAT 59.153 38.462 3.79 3.79 35.59 3.96
1949 2055 6.098266 CAGGGCTATACTATACATGGTATGCA 59.902 42.308 8.11 0.00 35.59 3.96
1950 2056 6.098409 ACAGGGCTATACTATACATGGTATGC 59.902 42.308 8.11 8.93 35.59 3.14
1951 2057 7.661536 ACAGGGCTATACTATACATGGTATG 57.338 40.000 8.11 0.00 35.59 2.39
1952 2058 8.788799 TCTACAGGGCTATACTATACATGGTAT 58.211 37.037 0.00 4.02 37.99 2.73
1953 2059 8.051535 GTCTACAGGGCTATACTATACATGGTA 58.948 40.741 0.00 0.00 0.00 3.25
1954 2060 6.890814 GTCTACAGGGCTATACTATACATGGT 59.109 42.308 0.00 0.00 0.00 3.55
1955 2061 6.038382 CGTCTACAGGGCTATACTATACATGG 59.962 46.154 0.00 0.00 0.00 3.66
1956 2062 6.598457 ACGTCTACAGGGCTATACTATACATG 59.402 42.308 0.00 0.00 0.00 3.21
1957 2063 6.719301 ACGTCTACAGGGCTATACTATACAT 58.281 40.000 0.00 0.00 0.00 2.29
1958 2064 6.013898 AGACGTCTACAGGGCTATACTATACA 60.014 42.308 18.46 0.00 0.00 2.29
1959 2065 6.405538 AGACGTCTACAGGGCTATACTATAC 58.594 44.000 18.46 0.00 0.00 1.47
1960 2066 6.617782 AGACGTCTACAGGGCTATACTATA 57.382 41.667 18.46 0.00 0.00 1.31
1961 2067 5.502089 AGACGTCTACAGGGCTATACTAT 57.498 43.478 18.46 0.00 0.00 2.12
1962 2068 4.970860 AGACGTCTACAGGGCTATACTA 57.029 45.455 18.46 0.00 0.00 1.82
1963 2069 3.860968 AGACGTCTACAGGGCTATACT 57.139 47.619 18.46 0.00 0.00 2.12
1974 2080 8.672815 AGTGGTTTAAAGATAGTAGACGTCTAC 58.327 37.037 37.34 37.34 46.93 2.59
1975 2081 8.671921 CAGTGGTTTAAAGATAGTAGACGTCTA 58.328 37.037 21.25 21.25 0.00 2.59
1976 2082 7.176340 ACAGTGGTTTAAAGATAGTAGACGTCT 59.824 37.037 23.66 23.66 0.00 4.18
1977 2083 7.272948 CACAGTGGTTTAAAGATAGTAGACGTC 59.727 40.741 7.70 7.70 0.00 4.34
1978 2084 7.088905 CACAGTGGTTTAAAGATAGTAGACGT 58.911 38.462 0.00 0.00 0.00 4.34
1979 2085 7.088905 ACACAGTGGTTTAAAGATAGTAGACG 58.911 38.462 5.31 0.00 0.00 4.18
1980 2086 8.828688 AACACAGTGGTTTAAAGATAGTAGAC 57.171 34.615 5.31 0.00 0.00 2.59
1981 2087 9.841295 AAAACACAGTGGTTTAAAGATAGTAGA 57.159 29.630 15.28 0.00 35.15 2.59
1984 2090 9.623000 AGTAAAACACAGTGGTTTAAAGATAGT 57.377 29.630 22.78 4.79 40.74 2.12
1988 2094 9.398538 ACATAGTAAAACACAGTGGTTTAAAGA 57.601 29.630 22.78 12.67 40.74 2.52
1992 2098 9.835389 AGTAACATAGTAAAACACAGTGGTTTA 57.165 29.630 18.26 18.26 38.40 2.01
1993 2099 8.741603 AGTAACATAGTAAAACACAGTGGTTT 57.258 30.769 20.35 20.35 40.82 3.27
1994 2100 8.741603 AAGTAACATAGTAAAACACAGTGGTT 57.258 30.769 5.31 0.51 0.00 3.67
1995 2101 7.443272 GGAAGTAACATAGTAAAACACAGTGGT 59.557 37.037 5.31 0.00 0.00 4.16
1996 2102 7.442969 TGGAAGTAACATAGTAAAACACAGTGG 59.557 37.037 5.31 0.00 0.00 4.00
1997 2103 8.373048 TGGAAGTAACATAGTAAAACACAGTG 57.627 34.615 0.00 0.00 0.00 3.66
1998 2104 8.999431 CATGGAAGTAACATAGTAAAACACAGT 58.001 33.333 0.00 0.00 0.00 3.55
1999 2105 8.999431 ACATGGAAGTAACATAGTAAAACACAG 58.001 33.333 0.00 0.00 0.00 3.66
2000 2106 8.911918 ACATGGAAGTAACATAGTAAAACACA 57.088 30.769 0.00 0.00 0.00 3.72
2008 2114 9.295825 TGAATTCAAACATGGAAGTAACATAGT 57.704 29.630 5.45 0.00 0.00 2.12
2040 2146 9.003658 AGAAACACTGATCTTAATTCAATCGTT 57.996 29.630 0.00 0.00 0.00 3.85
2041 2147 8.553459 AGAAACACTGATCTTAATTCAATCGT 57.447 30.769 0.00 0.00 0.00 3.73
2046 2152 9.658799 CTCCTAAGAAACACTGATCTTAATTCA 57.341 33.333 0.00 0.00 37.61 2.57
2047 2153 9.877178 TCTCCTAAGAAACACTGATCTTAATTC 57.123 33.333 0.00 0.00 37.61 2.17
2048 2154 9.883142 CTCTCCTAAGAAACACTGATCTTAATT 57.117 33.333 0.00 0.00 37.61 1.40
2049 2155 9.261035 TCTCTCCTAAGAAACACTGATCTTAAT 57.739 33.333 0.00 0.00 37.61 1.40
2050 2156 8.651589 TCTCTCCTAAGAAACACTGATCTTAA 57.348 34.615 0.00 0.00 37.61 1.85
2051 2157 8.651589 TTCTCTCCTAAGAAACACTGATCTTA 57.348 34.615 0.00 8.05 37.16 2.10
2052 2158 7.546250 TTCTCTCCTAAGAAACACTGATCTT 57.454 36.000 0.00 6.93 39.19 2.40
2053 2159 7.546250 TTTCTCTCCTAAGAAACACTGATCT 57.454 36.000 0.00 0.00 39.67 2.75
2054 2160 6.312672 GCTTTCTCTCCTAAGAAACACTGATC 59.687 42.308 0.00 0.00 39.67 2.92
2055 2161 6.013812 AGCTTTCTCTCCTAAGAAACACTGAT 60.014 38.462 0.00 0.00 39.67 2.90
2056 2162 5.305644 AGCTTTCTCTCCTAAGAAACACTGA 59.694 40.000 0.00 0.00 39.67 3.41
2057 2163 5.546526 AGCTTTCTCTCCTAAGAAACACTG 58.453 41.667 0.00 0.00 39.67 3.66
2058 2164 5.816955 AGCTTTCTCTCCTAAGAAACACT 57.183 39.130 0.00 0.00 39.67 3.55
2059 2165 6.693466 AGTAGCTTTCTCTCCTAAGAAACAC 58.307 40.000 0.00 0.00 39.67 3.32
2060 2166 6.919775 AGTAGCTTTCTCTCCTAAGAAACA 57.080 37.500 0.00 0.00 39.67 2.83
2061 2167 6.592220 CCAAGTAGCTTTCTCTCCTAAGAAAC 59.408 42.308 0.00 0.00 39.67 2.78
2062 2168 6.270231 ACCAAGTAGCTTTCTCTCCTAAGAAA 59.730 38.462 0.00 0.00 41.70 2.52
2063 2169 5.780793 ACCAAGTAGCTTTCTCTCCTAAGAA 59.219 40.000 0.00 0.00 33.50 2.52
2064 2170 5.186021 CACCAAGTAGCTTTCTCTCCTAAGA 59.814 44.000 0.00 0.00 0.00 2.10
2065 2171 5.415221 CACCAAGTAGCTTTCTCTCCTAAG 58.585 45.833 0.00 0.00 0.00 2.18
2066 2172 4.322801 GCACCAAGTAGCTTTCTCTCCTAA 60.323 45.833 0.00 0.00 0.00 2.69
2067 2173 3.195825 GCACCAAGTAGCTTTCTCTCCTA 59.804 47.826 0.00 0.00 0.00 2.94
2068 2174 2.027653 GCACCAAGTAGCTTTCTCTCCT 60.028 50.000 0.00 0.00 0.00 3.69
2069 2175 2.289694 TGCACCAAGTAGCTTTCTCTCC 60.290 50.000 0.00 0.00 0.00 3.71
2070 2176 2.739379 GTGCACCAAGTAGCTTTCTCTC 59.261 50.000 5.22 0.00 0.00 3.20
2071 2177 2.370189 AGTGCACCAAGTAGCTTTCTCT 59.630 45.455 14.63 0.00 0.00 3.10
2072 2178 2.772287 AGTGCACCAAGTAGCTTTCTC 58.228 47.619 14.63 0.00 0.00 2.87
2073 2179 2.938956 AGTGCACCAAGTAGCTTTCT 57.061 45.000 14.63 0.00 0.00 2.52
2074 2180 3.990318 AAAGTGCACCAAGTAGCTTTC 57.010 42.857 14.63 0.00 0.00 2.62
2075 2181 7.230712 AGTTAATAAAGTGCACCAAGTAGCTTT 59.769 33.333 14.63 7.43 0.00 3.51
2076 2182 6.715264 AGTTAATAAAGTGCACCAAGTAGCTT 59.285 34.615 14.63 0.00 0.00 3.74
2077 2183 6.149474 CAGTTAATAAAGTGCACCAAGTAGCT 59.851 38.462 14.63 7.39 0.00 3.32
2078 2184 6.148811 TCAGTTAATAAAGTGCACCAAGTAGC 59.851 38.462 14.63 5.16 36.20 3.58
2079 2185 7.667043 TCAGTTAATAAAGTGCACCAAGTAG 57.333 36.000 14.63 0.00 36.20 2.57
2080 2186 8.453238 TTTCAGTTAATAAAGTGCACCAAGTA 57.547 30.769 14.63 0.00 36.20 2.24
2081 2187 6.952773 TTCAGTTAATAAAGTGCACCAAGT 57.047 33.333 14.63 0.71 36.20 3.16
2082 2188 8.081633 TGATTTCAGTTAATAAAGTGCACCAAG 58.918 33.333 14.63 0.00 36.20 3.61
2083 2189 7.946207 TGATTTCAGTTAATAAAGTGCACCAA 58.054 30.769 14.63 0.00 36.20 3.67
2084 2190 7.517614 TGATTTCAGTTAATAAAGTGCACCA 57.482 32.000 14.63 0.00 36.20 4.17
2085 2191 8.810652 TTTGATTTCAGTTAATAAAGTGCACC 57.189 30.769 14.63 0.00 36.20 5.01
2086 2192 9.463443 ACTTTGATTTCAGTTAATAAAGTGCAC 57.537 29.630 9.40 9.40 36.06 4.57
2097 2203 9.513906 TGGATGATGTAACTTTGATTTCAGTTA 57.486 29.630 0.00 0.00 34.92 2.24
2098 2204 8.408043 TGGATGATGTAACTTTGATTTCAGTT 57.592 30.769 0.00 0.00 37.08 3.16
2099 2205 8.585471 ATGGATGATGTAACTTTGATTTCAGT 57.415 30.769 0.00 0.00 0.00 3.41
2105 2211 9.071276 GGTCATTATGGATGATGTAACTTTGAT 57.929 33.333 0.00 0.00 46.01 2.57
2106 2212 7.226523 CGGTCATTATGGATGATGTAACTTTGA 59.773 37.037 0.00 0.00 46.01 2.69
2107 2213 7.355017 CGGTCATTATGGATGATGTAACTTTG 58.645 38.462 0.00 0.00 46.01 2.77
2108 2214 6.486657 CCGGTCATTATGGATGATGTAACTTT 59.513 38.462 0.00 0.00 46.01 2.66
2109 2215 5.997746 CCGGTCATTATGGATGATGTAACTT 59.002 40.000 0.00 0.00 46.01 2.66
2110 2216 5.306937 TCCGGTCATTATGGATGATGTAACT 59.693 40.000 0.00 0.00 46.01 2.24
2111 2217 5.547465 TCCGGTCATTATGGATGATGTAAC 58.453 41.667 0.00 0.00 46.01 2.50
2112 2218 5.816955 TCCGGTCATTATGGATGATGTAA 57.183 39.130 0.00 0.00 46.01 2.41
2113 2219 5.816955 TTCCGGTCATTATGGATGATGTA 57.183 39.130 0.00 0.00 46.01 2.29
2114 2220 4.705110 TTCCGGTCATTATGGATGATGT 57.295 40.909 0.00 0.00 46.01 3.06
2115 2221 6.579666 AATTTCCGGTCATTATGGATGATG 57.420 37.500 0.00 0.00 46.01 3.07
2116 2222 8.704849 TTTAATTTCCGGTCATTATGGATGAT 57.295 30.769 0.00 0.00 46.01 2.45
2117 2223 8.526667 TTTTAATTTCCGGTCATTATGGATGA 57.473 30.769 0.00 0.00 42.42 2.92
2140 2246 4.408378 CGGTGATCCCCCGTTTTT 57.592 55.556 11.66 0.00 40.59 1.94
2146 2252 0.179702 GTTTAGGACGGTGATCCCCC 59.820 60.000 0.00 0.00 39.91 5.40
2147 2253 0.906775 TGTTTAGGACGGTGATCCCC 59.093 55.000 0.00 0.00 39.91 4.81
2148 2254 2.773993 TTGTTTAGGACGGTGATCCC 57.226 50.000 0.00 0.00 39.91 3.85
2149 2255 4.070009 ACTTTTGTTTAGGACGGTGATCC 58.930 43.478 0.00 0.00 39.28 3.36
2150 2256 6.161381 TCTACTTTTGTTTAGGACGGTGATC 58.839 40.000 0.00 0.00 0.00 2.92
2151 2257 6.105397 TCTACTTTTGTTTAGGACGGTGAT 57.895 37.500 0.00 0.00 0.00 3.06
2152 2258 5.069516 ACTCTACTTTTGTTTAGGACGGTGA 59.930 40.000 0.00 0.00 0.00 4.02
2153 2259 5.295152 ACTCTACTTTTGTTTAGGACGGTG 58.705 41.667 0.00 0.00 0.00 4.94
2154 2260 5.541953 ACTCTACTTTTGTTTAGGACGGT 57.458 39.130 0.00 0.00 0.00 4.83
2155 2261 5.118203 CGAACTCTACTTTTGTTTAGGACGG 59.882 44.000 0.00 0.00 0.00 4.79
2156 2262 5.916883 TCGAACTCTACTTTTGTTTAGGACG 59.083 40.000 0.00 0.00 0.00 4.79
2157 2263 7.704789 TTCGAACTCTACTTTTGTTTAGGAC 57.295 36.000 0.00 0.00 0.00 3.85
2158 2264 8.145767 TGATTCGAACTCTACTTTTGTTTAGGA 58.854 33.333 0.00 0.00 0.00 2.94
2159 2265 8.306680 TGATTCGAACTCTACTTTTGTTTAGG 57.693 34.615 0.00 0.00 0.00 2.69
2162 2268 9.285770 GTTTTGATTCGAACTCTACTTTTGTTT 57.714 29.630 0.00 0.00 0.00 2.83
2163 2269 8.455682 TGTTTTGATTCGAACTCTACTTTTGTT 58.544 29.630 0.00 0.00 0.00 2.83
2164 2270 7.981142 TGTTTTGATTCGAACTCTACTTTTGT 58.019 30.769 0.00 0.00 0.00 2.83
2165 2271 8.835467 TTGTTTTGATTCGAACTCTACTTTTG 57.165 30.769 0.00 0.00 0.00 2.44
2166 2272 9.450807 CATTGTTTTGATTCGAACTCTACTTTT 57.549 29.630 0.00 0.00 0.00 2.27
2167 2273 7.591426 GCATTGTTTTGATTCGAACTCTACTTT 59.409 33.333 0.00 0.00 0.00 2.66
2168 2274 7.078228 GCATTGTTTTGATTCGAACTCTACTT 58.922 34.615 0.00 0.00 0.00 2.24
2169 2275 6.603095 GCATTGTTTTGATTCGAACTCTACT 58.397 36.000 0.00 0.00 0.00 2.57
2170 2276 5.504755 CGCATTGTTTTGATTCGAACTCTAC 59.495 40.000 0.00 0.00 0.00 2.59
2171 2277 5.178623 ACGCATTGTTTTGATTCGAACTCTA 59.821 36.000 0.00 0.00 0.00 2.43
2172 2278 4.024048 ACGCATTGTTTTGATTCGAACTCT 60.024 37.500 0.00 0.00 0.00 3.24
2173 2279 4.087085 CACGCATTGTTTTGATTCGAACTC 59.913 41.667 0.00 0.12 0.00 3.01
2174 2280 3.974401 CACGCATTGTTTTGATTCGAACT 59.026 39.130 0.00 0.00 0.00 3.01
2175 2281 3.971871 TCACGCATTGTTTTGATTCGAAC 59.028 39.130 0.00 0.00 0.00 3.95
2176 2282 4.216366 TCACGCATTGTTTTGATTCGAA 57.784 36.364 0.00 0.00 0.00 3.71
2177 2283 3.887339 TCACGCATTGTTTTGATTCGA 57.113 38.095 0.00 0.00 0.00 3.71
2178 2284 4.674662 TCTTTCACGCATTGTTTTGATTCG 59.325 37.500 0.00 0.00 0.00 3.34
2179 2285 6.509317 TTCTTTCACGCATTGTTTTGATTC 57.491 33.333 0.00 0.00 0.00 2.52
2180 2286 6.238076 GGTTTCTTTCACGCATTGTTTTGATT 60.238 34.615 0.00 0.00 0.00 2.57
2181 2287 5.234116 GGTTTCTTTCACGCATTGTTTTGAT 59.766 36.000 0.00 0.00 0.00 2.57
2182 2288 4.564769 GGTTTCTTTCACGCATTGTTTTGA 59.435 37.500 0.00 0.00 0.00 2.69
2183 2289 4.547966 CGGTTTCTTTCACGCATTGTTTTG 60.548 41.667 0.00 0.00 0.00 2.44
2184 2290 3.549873 CGGTTTCTTTCACGCATTGTTTT 59.450 39.130 0.00 0.00 0.00 2.43
2185 2291 3.112580 CGGTTTCTTTCACGCATTGTTT 58.887 40.909 0.00 0.00 0.00 2.83
2186 2292 2.356382 TCGGTTTCTTTCACGCATTGTT 59.644 40.909 0.00 0.00 0.00 2.83
2205 2311 0.591741 GGCTCTTCGTATCGGTGTCG 60.592 60.000 0.00 0.00 37.82 4.35
2206 2312 0.739561 AGGCTCTTCGTATCGGTGTC 59.260 55.000 0.00 0.00 0.00 3.67
2207 2313 1.183549 AAGGCTCTTCGTATCGGTGT 58.816 50.000 0.00 0.00 0.00 4.16
2212 2318 4.154195 TGCTTTCAAAAGGCTCTTCGTATC 59.846 41.667 4.76 0.00 36.53 2.24
2218 2324 3.642848 TGGATTGCTTTCAAAAGGCTCTT 59.357 39.130 4.76 0.00 36.53 2.85
2240 2346 6.963322 AGAGCCCTTACTCTGTTATTTTGAT 58.037 36.000 0.00 0.00 45.36 2.57
2249 2355 5.273208 TGAAATCTAGAGCCCTTACTCTGT 58.727 41.667 0.00 0.00 46.50 3.41
2264 2370 7.035004 GCTTGCAATGGTGTTATTGAAATCTA 58.965 34.615 0.00 0.00 39.79 1.98
2266 2372 5.870978 AGCTTGCAATGGTGTTATTGAAATC 59.129 36.000 0.00 0.00 39.79 2.17
2275 2381 3.756933 ATTCAAGCTTGCAATGGTGTT 57.243 38.095 21.99 0.00 0.00 3.32
2335 2441 2.158667 GGAACAGTTGGAAGACCTTGGA 60.159 50.000 0.00 0.00 37.04 3.53
2383 2489 0.105778 TCCATGACACGACAACAGCA 59.894 50.000 0.00 0.00 0.00 4.41
2392 2498 4.122046 TGCTAAATCATCTCCATGACACG 58.878 43.478 0.00 0.00 42.05 4.49
2394 2500 4.132336 GCTGCTAAATCATCTCCATGACA 58.868 43.478 0.00 0.00 42.05 3.58
2395 2501 3.501445 GGCTGCTAAATCATCTCCATGAC 59.499 47.826 0.00 0.00 42.05 3.06
2408 2514 2.740826 GGCGTCGTGGCTGCTAAA 60.741 61.111 0.00 0.00 40.72 1.85
2467 2573 0.941542 TTTTTGAGAAGGGTGCGACG 59.058 50.000 0.00 0.00 0.00 5.12
2485 2597 3.441572 AGCTAAACATCGATGCAGCTTTT 59.558 39.130 29.69 22.14 37.42 2.27
2486 2598 3.012518 AGCTAAACATCGATGCAGCTTT 58.987 40.909 29.69 22.42 37.42 3.51
2490 2602 3.545624 GCAGAAGCTAAACATCGATGCAG 60.546 47.826 25.11 19.06 37.91 4.41
2499 2611 4.391830 CAGGTAAATCGCAGAAGCTAAACA 59.608 41.667 0.00 0.00 43.58 2.83
2578 2690 8.365399 TCGTTATCTAGGCAATCACAATTAAG 57.635 34.615 0.00 0.00 0.00 1.85
2594 2706 9.511272 TCCTATAAGTACTGCATTCGTTATCTA 57.489 33.333 0.00 0.00 0.00 1.98
2595 2707 8.405418 TCCTATAAGTACTGCATTCGTTATCT 57.595 34.615 0.00 0.00 0.00 1.98
2600 2712 7.082602 CGTAATCCTATAAGTACTGCATTCGT 58.917 38.462 0.00 0.00 0.00 3.85
2615 2727 5.666265 AGGGAGAAAAAGTCCGTAATCCTAT 59.334 40.000 0.00 0.00 34.56 2.57
2624 2736 0.796927 GCGAAGGGAGAAAAAGTCCG 59.203 55.000 0.00 0.00 34.56 4.79
2642 2754 1.265365 GTGGCAACTGAGAGAGTTTGC 59.735 52.381 0.00 0.00 42.70 3.68
2653 2765 3.066291 TGGTATACTTGGTGGCAACTG 57.934 47.619 3.27 0.00 37.61 3.16
2654 2766 3.620488 CATGGTATACTTGGTGGCAACT 58.380 45.455 3.27 0.00 37.61 3.16
2656 2768 2.374184 GCATGGTATACTTGGTGGCAA 58.626 47.619 2.25 0.00 0.00 4.52
2666 2778 1.535462 GGTCATTGGCGCATGGTATAC 59.465 52.381 10.83 0.00 0.00 1.47
2682 2794 1.352083 CCTCAGGGAGTCTTTGGTCA 58.648 55.000 0.00 0.00 33.58 4.02
2685 2797 1.301293 GGCCTCAGGGAGTCTTTGG 59.699 63.158 0.00 0.00 33.58 3.28
2702 2814 3.814268 CGTGCTTGGCCGATTGGG 61.814 66.667 0.00 0.00 39.58 4.12
2719 2831 4.247380 CCAGCGAGCCATCCTCCC 62.247 72.222 0.00 0.00 37.27 4.30
2724 2836 3.200593 CACAGCCAGCGAGCCATC 61.201 66.667 0.00 0.00 0.00 3.51
2738 2850 2.319844 TCTTGAGGAGCTTCTCACACA 58.680 47.619 24.93 9.48 42.74 3.72
2764 2876 7.437713 TGATTAATATTGACAGGTCAGGAGT 57.562 36.000 2.01 0.00 41.13 3.85
2789 2902 4.213482 GCAACCGTTAACAGAAGAAGTGAT 59.787 41.667 6.39 0.00 0.00 3.06
2790 2903 3.558418 GCAACCGTTAACAGAAGAAGTGA 59.442 43.478 6.39 0.00 0.00 3.41
2791 2904 3.311322 TGCAACCGTTAACAGAAGAAGTG 59.689 43.478 6.39 0.00 0.00 3.16
2792 2905 3.537580 TGCAACCGTTAACAGAAGAAGT 58.462 40.909 6.39 0.00 0.00 3.01
2801 2914 1.883926 ACAGGGAATGCAACCGTTAAC 59.116 47.619 0.00 0.00 0.00 2.01
2819 2932 4.180057 GCAAAACAAATGTGGACAGAACA 58.820 39.130 0.00 0.00 0.00 3.18
2832 2945 4.646945 TCACATGTAGAAGGGCAAAACAAA 59.353 37.500 0.00 0.00 0.00 2.83
2882 2995 2.224606 CAATGTCCTGTGTGAGCAAGT 58.775 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.