Multiple sequence alignment - TraesCS5A01G507300

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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 TraesCS5A01G507300 chr5A 100.000 2264 0 0 1 2264 671875944 671873681 0.000000e+00 4181
1 TraesCS5A01G507300 chr5A 98.221 1911 18 5 1 1900 547532925 547534830 0.000000e+00 3326
2 TraesCS5A01G507300 chr5A 89.858 917 80 7 489 1402 181455576 181456482 0.000000e+00 1166
3 TraesCS5A01G507300 chr5A 83.422 187 27 4 1718 1902 316506806 316506622 1.080000e-38 171
4 TraesCS5A01G507300 chr6A 98.286 1867 20 4 1 1855 83359974 83361840 0.000000e+00 3260
5 TraesCS5A01G507300 chr1A 97.344 1920 20 4 1 1908 75741291 75739391 0.000000e+00 3234
6 TraesCS5A01G507300 chr1A 94.554 202 8 3 1708 1907 20881144 20880944 2.180000e-80 309
7 TraesCS5A01G507300 chr1A 83.246 191 28 4 1718 1906 446143997 446144185 2.990000e-39 172
8 TraesCS5A01G507300 chr4B 88.947 1927 174 30 1 1907 295124559 295122652 0.000000e+00 2342
9 TraesCS5A01G507300 chr4B 88.296 675 71 7 723 1394 510389129 510389798 0.000000e+00 802
10 TraesCS5A01G507300 chr2B 90.754 1406 118 7 1 1402 551156856 551158253 0.000000e+00 1866
11 TraesCS5A01G507300 chr2B 84.796 638 66 23 1287 1902 47064050 47063422 1.490000e-171 612
12 TraesCS5A01G507300 chr5D 89.749 917 78 9 489 1402 177305676 177306579 0.000000e+00 1158
13 TraesCS5A01G507300 chr2D 92.760 732 53 0 1 732 52067258 52067989 0.000000e+00 1059
14 TraesCS5A01G507300 chr2A 92.486 732 55 0 1 732 615517849 615517118 0.000000e+00 1048
15 TraesCS5A01G507300 chr2A 90.634 363 31 2 1902 2263 613185647 613185287 1.570000e-131 479
16 TraesCS5A01G507300 chr4A 92.350 732 56 0 1 732 91227481 91226750 0.000000e+00 1042
17 TraesCS5A01G507300 chr4A 87.812 681 79 3 723 1401 91226808 91226130 0.000000e+00 795
18 TraesCS5A01G507300 chr6B 92.350 732 54 1 1 732 129396303 129397032 0.000000e+00 1040
19 TraesCS5A01G507300 chr7B 88.444 675 69 8 723 1394 72302822 72302154 0.000000e+00 806
20 TraesCS5A01G507300 chr7B 95.616 365 14 2 1902 2264 629429506 629429142 3.240000e-163 584
21 TraesCS5A01G507300 chr3A 87.187 718 64 21 1112 1810 671626027 671626735 0.000000e+00 791
22 TraesCS5A01G507300 chr3A 90.358 363 30 3 1902 2263 106300257 106300615 2.630000e-129 472
23 TraesCS5A01G507300 chr3A 86.076 316 40 2 1945 2259 361620681 361620369 1.000000e-88 337
24 TraesCS5A01G507300 chr5B 95.068 365 16 2 1902 2264 343138668 343139032 7.010000e-160 573
25 TraesCS5A01G507300 chr1D 95.055 364 16 2 1902 2264 265801768 265802130 2.520000e-159 571
26 TraesCS5A01G507300 chr3B 92.308 364 13 3 1902 2264 598041018 598041367 9.330000e-139 503
27 TraesCS5A01G507300 chrUn 87.043 301 35 4 1962 2261 314012064 314012361 1.000000e-88 337
28 TraesCS5A01G507300 chrUn 87.043 301 35 4 1962 2261 337229369 337229666 1.000000e-88 337


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 TraesCS5A01G507300 chr5A 671873681 671875944 2263 True 4181.0 4181 100.000 1 2264 1 chr5A.!!$R2 2263
1 TraesCS5A01G507300 chr5A 547532925 547534830 1905 False 3326.0 3326 98.221 1 1900 1 chr5A.!!$F2 1899
2 TraesCS5A01G507300 chr5A 181455576 181456482 906 False 1166.0 1166 89.858 489 1402 1 chr5A.!!$F1 913
3 TraesCS5A01G507300 chr6A 83359974 83361840 1866 False 3260.0 3260 98.286 1 1855 1 chr6A.!!$F1 1854
4 TraesCS5A01G507300 chr1A 75739391 75741291 1900 True 3234.0 3234 97.344 1 1908 1 chr1A.!!$R2 1907
5 TraesCS5A01G507300 chr4B 295122652 295124559 1907 True 2342.0 2342 88.947 1 1907 1 chr4B.!!$R1 1906
6 TraesCS5A01G507300 chr4B 510389129 510389798 669 False 802.0 802 88.296 723 1394 1 chr4B.!!$F1 671
7 TraesCS5A01G507300 chr2B 551156856 551158253 1397 False 1866.0 1866 90.754 1 1402 1 chr2B.!!$F1 1401
8 TraesCS5A01G507300 chr2B 47063422 47064050 628 True 612.0 612 84.796 1287 1902 1 chr2B.!!$R1 615
9 TraesCS5A01G507300 chr5D 177305676 177306579 903 False 1158.0 1158 89.749 489 1402 1 chr5D.!!$F1 913
10 TraesCS5A01G507300 chr2D 52067258 52067989 731 False 1059.0 1059 92.760 1 732 1 chr2D.!!$F1 731
11 TraesCS5A01G507300 chr2A 615517118 615517849 731 True 1048.0 1048 92.486 1 732 1 chr2A.!!$R2 731
12 TraesCS5A01G507300 chr4A 91226130 91227481 1351 True 918.5 1042 90.081 1 1401 2 chr4A.!!$R1 1400
13 TraesCS5A01G507300 chr6B 129396303 129397032 729 False 1040.0 1040 92.350 1 732 1 chr6B.!!$F1 731
14 TraesCS5A01G507300 chr7B 72302154 72302822 668 True 806.0 806 88.444 723 1394 1 chr7B.!!$R1 671
15 TraesCS5A01G507300 chr3A 671626027 671626735 708 False 791.0 791 87.187 1112 1810 1 chr3A.!!$F2 698

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
47 48 1.450312 GTCATGAAGGCCGACCCTG 60.45 63.158 0.0 0.0 45.62 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1680 0.183492 TCTGGGCTGAAAACTGCTGT 59.817 50.0 0.0 0.0 0.0 4.4 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
47 48 1.450312 GTCATGAAGGCCGACCCTG 60.450 63.158 0.00 0.00 45.62 4.45
578 581 2.076100 TGCATTTCACCTACGCTTCAG 58.924 47.619 0.00 0.00 0.00 3.02
642 645 4.380761 CCATGCAATCGAAAATGACAAGGA 60.381 41.667 0.00 0.00 0.00 3.36
858 863 4.737855 TCTAGCACCATACAAAGGAGAC 57.262 45.455 0.00 0.00 0.00 3.36
1442 1478 8.331740 ACATTGCCTATTGCTATAATCCAGTAT 58.668 33.333 0.00 0.00 42.00 2.12
1594 1636 7.689313 GCATGGTTCTTTGTACATCCCTCTATA 60.689 40.741 0.00 0.00 0.00 1.31
1595 1637 7.931015 TGGTTCTTTGTACATCCCTCTATAT 57.069 36.000 0.00 0.00 0.00 0.86
1908 1954 4.103311 GGATCAGAACAGGCCCTAAGTAAT 59.897 45.833 0.00 0.00 0.00 1.89
1909 1955 4.487714 TCAGAACAGGCCCTAAGTAATG 57.512 45.455 0.00 0.00 0.00 1.90
1910 1956 3.199946 TCAGAACAGGCCCTAAGTAATGG 59.800 47.826 0.00 0.00 0.00 3.16
1911 1957 2.092375 AGAACAGGCCCTAAGTAATGGC 60.092 50.000 0.00 0.00 44.59 4.40
1912 1958 0.180406 ACAGGCCCTAAGTAATGGCG 59.820 55.000 0.00 0.00 46.31 5.69
1913 1959 0.535102 CAGGCCCTAAGTAATGGCGG 60.535 60.000 0.00 0.00 46.31 6.13
1914 1960 0.986550 AGGCCCTAAGTAATGGCGGT 60.987 55.000 0.00 0.00 46.31 5.68
1915 1961 0.534427 GGCCCTAAGTAATGGCGGTC 60.534 60.000 0.00 0.00 46.31 4.79
1916 1962 0.179468 GCCCTAAGTAATGGCGGTCA 59.821 55.000 0.00 0.00 35.08 4.02
1917 1963 1.810412 GCCCTAAGTAATGGCGGTCAG 60.810 57.143 0.00 0.00 35.08 3.51
1918 1964 1.760613 CCCTAAGTAATGGCGGTCAGA 59.239 52.381 0.00 0.00 0.00 3.27
1919 1965 2.368875 CCCTAAGTAATGGCGGTCAGAT 59.631 50.000 0.00 0.00 0.00 2.90
1920 1966 3.576982 CCCTAAGTAATGGCGGTCAGATA 59.423 47.826 0.00 0.00 0.00 1.98
1921 1967 4.557205 CCTAAGTAATGGCGGTCAGATAC 58.443 47.826 0.00 0.00 0.00 2.24
1922 1968 4.038763 CCTAAGTAATGGCGGTCAGATACA 59.961 45.833 9.93 0.00 0.00 2.29
1923 1969 3.735237 AGTAATGGCGGTCAGATACAG 57.265 47.619 9.93 0.00 0.00 2.74
1924 1970 3.031736 AGTAATGGCGGTCAGATACAGT 58.968 45.455 9.93 0.00 0.00 3.55
1925 1971 2.315925 AATGGCGGTCAGATACAGTG 57.684 50.000 0.00 0.00 0.00 3.66
1926 1972 1.195115 ATGGCGGTCAGATACAGTGT 58.805 50.000 0.00 0.00 0.00 3.55
1927 1973 1.842052 TGGCGGTCAGATACAGTGTA 58.158 50.000 5.24 5.24 0.00 2.90
1928 1974 2.384828 TGGCGGTCAGATACAGTGTAT 58.615 47.619 15.73 15.73 0.00 2.29
1929 1975 2.100749 TGGCGGTCAGATACAGTGTATG 59.899 50.000 20.46 8.92 0.00 2.39
1930 1976 2.361119 GGCGGTCAGATACAGTGTATGA 59.639 50.000 20.46 11.17 0.00 2.15
1931 1977 3.181479 GGCGGTCAGATACAGTGTATGAA 60.181 47.826 20.46 2.94 0.00 2.57
1932 1978 4.430007 GCGGTCAGATACAGTGTATGAAA 58.570 43.478 20.46 2.59 0.00 2.69
1933 1979 4.868171 GCGGTCAGATACAGTGTATGAAAA 59.132 41.667 20.46 0.86 0.00 2.29
1934 1980 5.350365 GCGGTCAGATACAGTGTATGAAAAA 59.650 40.000 20.46 0.00 0.00 1.94
1962 2008 9.786105 TGCTCATGTTGTTGTATAATTATTGTG 57.214 29.630 2.68 0.00 0.00 3.33
1963 2009 9.236691 GCTCATGTTGTTGTATAATTATTGTGG 57.763 33.333 2.68 0.00 0.00 4.17
1979 2025 8.685838 ATTATTGTGGTACTTGTTGTGTTAGT 57.314 30.769 0.00 0.00 0.00 2.24
1980 2026 8.508883 TTATTGTGGTACTTGTTGTGTTAGTT 57.491 30.769 0.00 0.00 0.00 2.24
1981 2027 6.821031 TTGTGGTACTTGTTGTGTTAGTTT 57.179 33.333 0.00 0.00 0.00 2.66
1982 2028 6.184580 TGTGGTACTTGTTGTGTTAGTTTG 57.815 37.500 0.00 0.00 0.00 2.93
1983 2029 5.706369 TGTGGTACTTGTTGTGTTAGTTTGT 59.294 36.000 0.00 0.00 0.00 2.83
1984 2030 6.025280 GTGGTACTTGTTGTGTTAGTTTGTG 58.975 40.000 0.00 0.00 0.00 3.33
1985 2031 5.706369 TGGTACTTGTTGTGTTAGTTTGTGT 59.294 36.000 0.00 0.00 0.00 3.72
1986 2032 6.877855 TGGTACTTGTTGTGTTAGTTTGTGTA 59.122 34.615 0.00 0.00 0.00 2.90
1987 2033 7.553402 TGGTACTTGTTGTGTTAGTTTGTGTAT 59.447 33.333 0.00 0.00 0.00 2.29
1988 2034 8.066000 GGTACTTGTTGTGTTAGTTTGTGTATC 58.934 37.037 0.00 0.00 0.00 2.24
1989 2035 7.859325 ACTTGTTGTGTTAGTTTGTGTATCT 57.141 32.000 0.00 0.00 0.00 1.98
1990 2036 7.916552 ACTTGTTGTGTTAGTTTGTGTATCTC 58.083 34.615 0.00 0.00 0.00 2.75
1991 2037 7.769044 ACTTGTTGTGTTAGTTTGTGTATCTCT 59.231 33.333 0.00 0.00 0.00 3.10
1992 2038 7.477144 TGTTGTGTTAGTTTGTGTATCTCTG 57.523 36.000 0.00 0.00 0.00 3.35
1993 2039 7.045416 TGTTGTGTTAGTTTGTGTATCTCTGT 58.955 34.615 0.00 0.00 0.00 3.41
1994 2040 7.551262 TGTTGTGTTAGTTTGTGTATCTCTGTT 59.449 33.333 0.00 0.00 0.00 3.16
1995 2041 9.037737 GTTGTGTTAGTTTGTGTATCTCTGTTA 57.962 33.333 0.00 0.00 0.00 2.41
1996 2042 8.812147 TGTGTTAGTTTGTGTATCTCTGTTAG 57.188 34.615 0.00 0.00 0.00 2.34
1997 2043 8.418662 TGTGTTAGTTTGTGTATCTCTGTTAGT 58.581 33.333 0.00 0.00 0.00 2.24
1998 2044 9.903682 GTGTTAGTTTGTGTATCTCTGTTAGTA 57.096 33.333 0.00 0.00 0.00 1.82
2006 2052 8.683550 TGTGTATCTCTGTTAGTATTTTGTCG 57.316 34.615 0.00 0.00 0.00 4.35
2007 2053 7.758076 TGTGTATCTCTGTTAGTATTTTGTCGG 59.242 37.037 0.00 0.00 0.00 4.79
2008 2054 7.758528 GTGTATCTCTGTTAGTATTTTGTCGGT 59.241 37.037 0.00 0.00 0.00 4.69
2009 2055 7.972277 TGTATCTCTGTTAGTATTTTGTCGGTC 59.028 37.037 0.00 0.00 0.00 4.79
2010 2056 5.396484 TCTCTGTTAGTATTTTGTCGGTCG 58.604 41.667 0.00 0.00 0.00 4.79
2011 2057 4.487948 TCTGTTAGTATTTTGTCGGTCGG 58.512 43.478 0.00 0.00 0.00 4.79
2012 2058 2.995258 TGTTAGTATTTTGTCGGTCGGC 59.005 45.455 0.00 0.00 0.00 5.54
2013 2059 2.298411 TAGTATTTTGTCGGTCGGCC 57.702 50.000 0.00 0.00 0.00 6.13
2014 2060 0.322322 AGTATTTTGTCGGTCGGCCA 59.678 50.000 6.96 0.00 34.09 5.36
2015 2061 1.065709 AGTATTTTGTCGGTCGGCCAT 60.066 47.619 6.96 0.00 34.09 4.40
2016 2062 2.168936 AGTATTTTGTCGGTCGGCCATA 59.831 45.455 6.96 0.00 34.09 2.74
2017 2063 2.341846 ATTTTGTCGGTCGGCCATAT 57.658 45.000 6.96 0.00 34.09 1.78
2018 2064 2.116827 TTTTGTCGGTCGGCCATATT 57.883 45.000 6.96 0.00 34.09 1.28
2019 2065 2.116827 TTTGTCGGTCGGCCATATTT 57.883 45.000 6.96 0.00 34.09 1.40
2020 2066 2.983907 TTGTCGGTCGGCCATATTTA 57.016 45.000 6.96 0.00 34.09 1.40
2021 2067 3.478857 TTGTCGGTCGGCCATATTTAT 57.521 42.857 6.96 0.00 34.09 1.40
2022 2068 3.478857 TGTCGGTCGGCCATATTTATT 57.521 42.857 6.96 0.00 34.09 1.40
2023 2069 3.811083 TGTCGGTCGGCCATATTTATTT 58.189 40.909 6.96 0.00 34.09 1.40
2024 2070 3.562141 TGTCGGTCGGCCATATTTATTTG 59.438 43.478 6.96 0.00 34.09 2.32
2025 2071 2.550606 TCGGTCGGCCATATTTATTTGC 59.449 45.455 6.96 0.00 34.09 3.68
2026 2072 2.292016 CGGTCGGCCATATTTATTTGCA 59.708 45.455 6.96 0.00 34.09 4.08
2027 2073 3.243234 CGGTCGGCCATATTTATTTGCAA 60.243 43.478 6.96 0.00 34.09 4.08
2028 2074 4.558496 CGGTCGGCCATATTTATTTGCAAT 60.558 41.667 6.96 0.00 34.09 3.56
2029 2075 5.335269 CGGTCGGCCATATTTATTTGCAATA 60.335 40.000 6.96 0.00 34.09 1.90
2030 2076 6.092748 GGTCGGCCATATTTATTTGCAATAG 58.907 40.000 0.00 0.00 34.09 1.73
2031 2077 6.294508 GGTCGGCCATATTTATTTGCAATAGT 60.295 38.462 0.00 0.00 34.09 2.12
2032 2078 7.145323 GTCGGCCATATTTATTTGCAATAGTT 58.855 34.615 2.24 0.00 0.00 2.24
2033 2079 7.326063 GTCGGCCATATTTATTTGCAATAGTTC 59.674 37.037 2.24 0.00 0.00 3.01
2034 2080 7.230510 TCGGCCATATTTATTTGCAATAGTTCT 59.769 33.333 2.24 0.00 0.00 3.01
2035 2081 7.867403 CGGCCATATTTATTTGCAATAGTTCTT 59.133 33.333 2.24 0.00 0.00 2.52
2036 2082 9.196552 GGCCATATTTATTTGCAATAGTTCTTC 57.803 33.333 0.00 0.00 0.00 2.87
2037 2083 9.971922 GCCATATTTATTTGCAATAGTTCTTCT 57.028 29.630 0.00 0.00 0.00 2.85
2050 2096 3.254827 GTTCTTCTGAACGCAACCTTC 57.745 47.619 0.00 0.00 42.39 3.46
2051 2097 1.878953 TCTTCTGAACGCAACCTTCC 58.121 50.000 0.00 0.00 0.00 3.46
2052 2098 1.140052 TCTTCTGAACGCAACCTTCCA 59.860 47.619 0.00 0.00 0.00 3.53
2053 2099 1.532868 CTTCTGAACGCAACCTTCCAG 59.467 52.381 0.00 0.00 0.00 3.86
2054 2100 0.468226 TCTGAACGCAACCTTCCAGT 59.532 50.000 0.00 0.00 0.00 4.00
2055 2101 1.134220 TCTGAACGCAACCTTCCAGTT 60.134 47.619 0.00 0.00 0.00 3.16
2056 2102 2.103432 TCTGAACGCAACCTTCCAGTTA 59.897 45.455 0.00 0.00 0.00 2.24
2057 2103 2.480419 CTGAACGCAACCTTCCAGTTAG 59.520 50.000 0.00 0.00 0.00 2.34
2058 2104 1.804748 GAACGCAACCTTCCAGTTAGG 59.195 52.381 0.00 0.00 38.79 2.69
2060 2106 1.156736 CGCAACCTTCCAGTTAGGTG 58.843 55.000 0.00 0.00 45.17 4.00
2061 2107 1.270625 CGCAACCTTCCAGTTAGGTGA 60.271 52.381 0.00 0.00 45.17 4.02
2062 2108 2.615493 CGCAACCTTCCAGTTAGGTGAT 60.615 50.000 0.00 0.00 45.17 3.06
2063 2109 2.749621 GCAACCTTCCAGTTAGGTGATG 59.250 50.000 0.00 0.00 45.17 3.07
2064 2110 2.749621 CAACCTTCCAGTTAGGTGATGC 59.250 50.000 0.00 0.00 45.17 3.91
2065 2111 2.269940 ACCTTCCAGTTAGGTGATGCT 58.730 47.619 0.00 0.00 44.25 3.79
2066 2112 2.644798 ACCTTCCAGTTAGGTGATGCTT 59.355 45.455 0.00 0.00 44.25 3.91
2067 2113 3.012518 CCTTCCAGTTAGGTGATGCTTG 58.987 50.000 0.00 0.00 39.02 4.01
2068 2114 2.113860 TCCAGTTAGGTGATGCTTGC 57.886 50.000 0.00 0.00 39.02 4.01
2069 2115 1.630369 TCCAGTTAGGTGATGCTTGCT 59.370 47.619 0.00 0.00 39.02 3.91
2070 2116 2.837591 TCCAGTTAGGTGATGCTTGCTA 59.162 45.455 0.00 0.00 39.02 3.49
2071 2117 3.455910 TCCAGTTAGGTGATGCTTGCTAT 59.544 43.478 0.00 0.00 39.02 2.97
2072 2118 4.080356 TCCAGTTAGGTGATGCTTGCTATT 60.080 41.667 0.00 0.00 39.02 1.73
2073 2119 4.641989 CCAGTTAGGTGATGCTTGCTATTT 59.358 41.667 0.00 0.00 0.00 1.40
2074 2120 5.822519 CCAGTTAGGTGATGCTTGCTATTTA 59.177 40.000 0.00 0.00 0.00 1.40
2075 2121 6.017605 CCAGTTAGGTGATGCTTGCTATTTAG 60.018 42.308 0.00 0.00 0.00 1.85
2076 2122 6.540189 CAGTTAGGTGATGCTTGCTATTTAGT 59.460 38.462 0.00 0.00 0.00 2.24
2077 2123 7.066284 CAGTTAGGTGATGCTTGCTATTTAGTT 59.934 37.037 0.00 0.00 0.00 2.24
2078 2124 5.824904 AGGTGATGCTTGCTATTTAGTTG 57.175 39.130 0.00 0.00 0.00 3.16
2079 2125 4.096984 AGGTGATGCTTGCTATTTAGTTGC 59.903 41.667 0.00 0.00 0.00 4.17
2080 2126 4.096984 GGTGATGCTTGCTATTTAGTTGCT 59.903 41.667 0.00 0.00 0.00 3.91
2081 2127 5.393461 GGTGATGCTTGCTATTTAGTTGCTT 60.393 40.000 0.00 0.00 0.00 3.91
2082 2128 5.741040 GTGATGCTTGCTATTTAGTTGCTTC 59.259 40.000 0.00 0.00 0.00 3.86
2083 2129 5.415389 TGATGCTTGCTATTTAGTTGCTTCA 59.585 36.000 0.00 0.00 32.78 3.02
2084 2130 5.300969 TGCTTGCTATTTAGTTGCTTCAG 57.699 39.130 0.00 0.00 0.00 3.02
2085 2131 4.761739 TGCTTGCTATTTAGTTGCTTCAGT 59.238 37.500 0.00 0.00 0.00 3.41
2086 2132 5.241506 TGCTTGCTATTTAGTTGCTTCAGTT 59.758 36.000 0.00 0.00 0.00 3.16
2087 2133 5.797434 GCTTGCTATTTAGTTGCTTCAGTTC 59.203 40.000 0.00 0.00 0.00 3.01
2088 2134 6.568462 GCTTGCTATTTAGTTGCTTCAGTTCA 60.568 38.462 0.00 0.00 0.00 3.18
2089 2135 6.241207 TGCTATTTAGTTGCTTCAGTTCAC 57.759 37.500 0.00 0.00 0.00 3.18
2090 2136 5.997746 TGCTATTTAGTTGCTTCAGTTCACT 59.002 36.000 0.00 0.00 0.00 3.41
2091 2137 6.486657 TGCTATTTAGTTGCTTCAGTTCACTT 59.513 34.615 0.00 0.00 0.00 3.16
2092 2138 6.798959 GCTATTTAGTTGCTTCAGTTCACTTG 59.201 38.462 0.00 0.00 0.00 3.16
2093 2139 6.699575 ATTTAGTTGCTTCAGTTCACTTGT 57.300 33.333 0.00 0.00 0.00 3.16
2094 2140 5.484173 TTAGTTGCTTCAGTTCACTTGTG 57.516 39.130 0.00 0.00 0.00 3.33
2095 2141 3.609853 AGTTGCTTCAGTTCACTTGTGA 58.390 40.909 0.00 0.00 0.00 3.58
2096 2142 4.009675 AGTTGCTTCAGTTCACTTGTGAA 58.990 39.130 11.62 11.62 0.00 3.18
2097 2143 4.458989 AGTTGCTTCAGTTCACTTGTGAAA 59.541 37.500 16.46 0.62 30.00 2.69
2098 2144 5.048083 AGTTGCTTCAGTTCACTTGTGAAAA 60.048 36.000 16.46 8.00 30.00 2.29
2099 2145 5.581126 TGCTTCAGTTCACTTGTGAAAAT 57.419 34.783 16.46 7.11 30.00 1.82
2100 2146 5.342433 TGCTTCAGTTCACTTGTGAAAATG 58.658 37.500 16.46 16.80 30.00 2.32
2101 2147 5.125257 TGCTTCAGTTCACTTGTGAAAATGA 59.875 36.000 16.46 18.40 30.00 2.57
2102 2148 5.456822 GCTTCAGTTCACTTGTGAAAATGAC 59.543 40.000 21.73 11.20 30.48 3.06
2103 2149 6.678900 GCTTCAGTTCACTTGTGAAAATGACT 60.679 38.462 21.73 12.77 30.48 3.41
2104 2150 6.122850 TCAGTTCACTTGTGAAAATGACTG 57.877 37.500 16.46 17.83 0.00 3.51
2105 2151 5.647658 TCAGTTCACTTGTGAAAATGACTGT 59.352 36.000 21.63 0.00 0.00 3.55
2106 2152 5.740569 CAGTTCACTTGTGAAAATGACTGTG 59.259 40.000 16.46 0.00 0.00 3.66
2107 2153 5.647658 AGTTCACTTGTGAAAATGACTGTGA 59.352 36.000 16.46 0.00 0.00 3.58
2108 2154 6.319658 AGTTCACTTGTGAAAATGACTGTGAT 59.680 34.615 16.46 0.00 33.98 3.06
2109 2155 6.698008 TCACTTGTGAAAATGACTGTGATT 57.302 33.333 0.44 0.00 0.00 2.57
2110 2156 6.728200 TCACTTGTGAAAATGACTGTGATTC 58.272 36.000 0.44 0.00 0.00 2.52
2111 2157 6.543465 TCACTTGTGAAAATGACTGTGATTCT 59.457 34.615 0.44 0.00 0.00 2.40
2112 2158 7.714813 TCACTTGTGAAAATGACTGTGATTCTA 59.285 33.333 0.44 0.00 0.00 2.10
2113 2159 8.509690 CACTTGTGAAAATGACTGTGATTCTAT 58.490 33.333 0.00 0.00 0.00 1.98
2114 2160 9.071276 ACTTGTGAAAATGACTGTGATTCTATT 57.929 29.630 0.00 0.00 0.00 1.73
2115 2161 9.552114 CTTGTGAAAATGACTGTGATTCTATTC 57.448 33.333 0.00 0.00 0.00 1.75
2116 2162 8.620116 TGTGAAAATGACTGTGATTCTATTCA 57.380 30.769 2.75 2.75 0.00 2.57
2117 2163 9.234827 TGTGAAAATGACTGTGATTCTATTCAT 57.765 29.630 8.21 0.00 0.00 2.57
2125 2171 9.730705 TGACTGTGATTCTATTCATTTCTTTCT 57.269 29.630 0.00 0.00 0.00 2.52
2138 2184 8.450578 TTCATTTCTTTCTTTTGTAGAGAGCA 57.549 30.769 0.00 0.00 35.57 4.26
2139 2185 8.627208 TCATTTCTTTCTTTTGTAGAGAGCAT 57.373 30.769 0.00 0.00 35.57 3.79
2140 2186 9.071276 TCATTTCTTTCTTTTGTAGAGAGCATT 57.929 29.630 0.00 0.00 35.57 3.56
2141 2187 9.688592 CATTTCTTTCTTTTGTAGAGAGCATTT 57.311 29.630 0.00 0.00 35.57 2.32
2142 2188 9.688592 ATTTCTTTCTTTTGTAGAGAGCATTTG 57.311 29.630 0.00 0.00 35.57 2.32
2143 2189 7.807977 TCTTTCTTTTGTAGAGAGCATTTGT 57.192 32.000 0.00 0.00 35.57 2.83
2144 2190 8.902540 TCTTTCTTTTGTAGAGAGCATTTGTA 57.097 30.769 0.00 0.00 35.57 2.41
2145 2191 8.774586 TCTTTCTTTTGTAGAGAGCATTTGTAC 58.225 33.333 0.00 0.00 35.57 2.90
2146 2192 8.677148 TTTCTTTTGTAGAGAGCATTTGTACT 57.323 30.769 0.00 0.00 33.51 2.73
2147 2193 7.658179 TCTTTTGTAGAGAGCATTTGTACTG 57.342 36.000 0.00 0.00 0.00 2.74
2148 2194 6.650807 TCTTTTGTAGAGAGCATTTGTACTGG 59.349 38.462 0.00 0.00 0.00 4.00
2149 2195 5.483685 TTGTAGAGAGCATTTGTACTGGT 57.516 39.130 0.00 0.00 0.00 4.00
2150 2196 4.820897 TGTAGAGAGCATTTGTACTGGTG 58.179 43.478 0.00 0.00 0.00 4.17
2151 2197 3.340814 AGAGAGCATTTGTACTGGTGG 57.659 47.619 0.00 0.00 0.00 4.61
2152 2198 2.026822 AGAGAGCATTTGTACTGGTGGG 60.027 50.000 0.00 0.00 0.00 4.61
2153 2199 1.705186 AGAGCATTTGTACTGGTGGGT 59.295 47.619 0.00 0.00 0.00 4.51
2154 2200 2.108250 AGAGCATTTGTACTGGTGGGTT 59.892 45.455 0.00 0.00 0.00 4.11
2155 2201 2.890945 GAGCATTTGTACTGGTGGGTTT 59.109 45.455 0.00 0.00 0.00 3.27
2156 2202 4.076394 GAGCATTTGTACTGGTGGGTTTA 58.924 43.478 0.00 0.00 0.00 2.01
2157 2203 4.475345 AGCATTTGTACTGGTGGGTTTAA 58.525 39.130 0.00 0.00 0.00 1.52
2158 2204 5.083821 AGCATTTGTACTGGTGGGTTTAAT 58.916 37.500 0.00 0.00 0.00 1.40
2159 2205 5.542251 AGCATTTGTACTGGTGGGTTTAATT 59.458 36.000 0.00 0.00 0.00 1.40
2160 2206 6.042666 AGCATTTGTACTGGTGGGTTTAATTT 59.957 34.615 0.00 0.00 0.00 1.82
2161 2207 6.147000 GCATTTGTACTGGTGGGTTTAATTTG 59.853 38.462 0.00 0.00 0.00 2.32
2162 2208 6.793505 TTTGTACTGGTGGGTTTAATTTGT 57.206 33.333 0.00 0.00 0.00 2.83
2163 2209 6.793505 TTGTACTGGTGGGTTTAATTTGTT 57.206 33.333 0.00 0.00 0.00 2.83
2164 2210 7.893124 TTGTACTGGTGGGTTTAATTTGTTA 57.107 32.000 0.00 0.00 0.00 2.41
2165 2211 7.893124 TGTACTGGTGGGTTTAATTTGTTAA 57.107 32.000 0.00 0.00 0.00 2.01
2166 2212 8.480133 TGTACTGGTGGGTTTAATTTGTTAAT 57.520 30.769 0.00 0.00 0.00 1.40
2167 2213 8.578151 TGTACTGGTGGGTTTAATTTGTTAATC 58.422 33.333 0.00 0.00 0.00 1.75
2168 2214 6.999950 ACTGGTGGGTTTAATTTGTTAATCC 58.000 36.000 0.00 0.00 0.00 3.01
2169 2215 6.555360 ACTGGTGGGTTTAATTTGTTAATCCA 59.445 34.615 9.15 0.00 31.17 3.41
2170 2216 6.998802 TGGTGGGTTTAATTTGTTAATCCAG 58.001 36.000 9.15 0.00 31.17 3.86
2171 2217 6.555360 TGGTGGGTTTAATTTGTTAATCCAGT 59.445 34.615 9.15 0.00 31.17 4.00
2172 2218 6.871492 GGTGGGTTTAATTTGTTAATCCAGTG 59.129 38.462 9.15 0.00 31.17 3.66
2173 2219 6.871492 GTGGGTTTAATTTGTTAATCCAGTGG 59.129 38.462 1.40 1.40 31.17 4.00
2174 2220 6.014156 TGGGTTTAATTTGTTAATCCAGTGGG 60.014 38.462 9.92 0.00 31.17 4.61
2175 2221 6.403049 GGTTTAATTTGTTAATCCAGTGGGG 58.597 40.000 9.92 0.00 38.37 4.96
2176 2222 6.014070 GGTTTAATTTGTTAATCCAGTGGGGT 60.014 38.462 9.92 0.00 38.11 4.95
2177 2223 7.178805 GGTTTAATTTGTTAATCCAGTGGGGTA 59.821 37.037 9.92 0.00 38.11 3.69
2178 2224 7.706100 TTAATTTGTTAATCCAGTGGGGTAC 57.294 36.000 9.92 3.67 38.11 3.34
2179 2225 4.726035 TTTGTTAATCCAGTGGGGTACA 57.274 40.909 9.92 6.30 38.11 2.90
2180 2226 3.992943 TGTTAATCCAGTGGGGTACAG 57.007 47.619 9.92 0.00 38.11 2.74
2181 2227 2.026636 TGTTAATCCAGTGGGGTACAGC 60.027 50.000 9.92 0.00 38.11 4.40
2182 2228 1.209621 TAATCCAGTGGGGTACAGCC 58.790 55.000 9.92 0.00 38.11 4.85
2183 2229 0.550147 AATCCAGTGGGGTACAGCCT 60.550 55.000 9.92 0.00 38.11 4.58
2184 2230 1.274703 ATCCAGTGGGGTACAGCCTG 61.275 60.000 9.92 0.00 38.11 4.85
2185 2231 2.671070 CAGTGGGGTACAGCCTGG 59.329 66.667 0.00 0.00 37.43 4.45
2186 2232 2.207189 AGTGGGGTACAGCCTGGT 59.793 61.111 0.00 0.00 37.43 4.00
2187 2233 2.224159 AGTGGGGTACAGCCTGGTG 61.224 63.158 0.00 0.00 37.43 4.17
2188 2234 2.933287 TGGGGTACAGCCTGGTGG 60.933 66.667 0.00 0.00 37.43 4.61
2189 2235 2.609610 GGGGTACAGCCTGGTGGA 60.610 66.667 0.00 0.00 37.43 4.02
2190 2236 2.228480 GGGGTACAGCCTGGTGGAA 61.228 63.158 0.00 0.00 37.43 3.53
2191 2237 1.002502 GGGTACAGCCTGGTGGAAC 60.003 63.158 0.00 0.00 37.43 3.62
2203 2249 3.838795 GTGGAACCATGCAAATGGG 57.161 52.632 11.02 3.63 45.84 4.00
2204 2250 1.265236 GTGGAACCATGCAAATGGGA 58.735 50.000 11.02 0.00 45.84 4.37
2205 2251 1.832998 GTGGAACCATGCAAATGGGAT 59.167 47.619 11.02 0.00 45.84 3.85
2206 2252 2.109774 TGGAACCATGCAAATGGGATC 58.890 47.619 11.02 8.22 45.84 3.36
2207 2253 2.292389 TGGAACCATGCAAATGGGATCT 60.292 45.455 11.02 0.00 45.84 2.75
2208 2254 2.767960 GGAACCATGCAAATGGGATCTT 59.232 45.455 11.02 0.00 45.84 2.40
2209 2255 3.181472 GGAACCATGCAAATGGGATCTTC 60.181 47.826 11.02 5.33 45.84 2.87
2210 2256 2.026641 ACCATGCAAATGGGATCTTCG 58.973 47.619 11.02 0.00 45.84 3.79
2211 2257 2.026641 CCATGCAAATGGGATCTTCGT 58.973 47.619 0.00 0.00 38.04 3.85
2212 2258 2.428171 CCATGCAAATGGGATCTTCGTT 59.572 45.455 0.00 0.00 38.04 3.85
2213 2259 3.119029 CCATGCAAATGGGATCTTCGTTT 60.119 43.478 0.00 0.00 38.04 3.60
2214 2260 3.848272 TGCAAATGGGATCTTCGTTTC 57.152 42.857 0.00 0.00 0.00 2.78
2215 2261 3.420893 TGCAAATGGGATCTTCGTTTCT 58.579 40.909 0.00 0.00 0.00 2.52
2216 2262 3.440173 TGCAAATGGGATCTTCGTTTCTC 59.560 43.478 0.00 0.00 0.00 2.87
2217 2263 3.440173 GCAAATGGGATCTTCGTTTCTCA 59.560 43.478 0.00 0.00 0.00 3.27
2218 2264 4.437930 GCAAATGGGATCTTCGTTTCTCAG 60.438 45.833 0.00 0.00 0.00 3.35
2219 2265 3.550437 ATGGGATCTTCGTTTCTCAGG 57.450 47.619 0.00 0.00 0.00 3.86
2220 2266 2.257207 TGGGATCTTCGTTTCTCAGGT 58.743 47.619 0.00 0.00 0.00 4.00
2221 2267 3.437213 TGGGATCTTCGTTTCTCAGGTA 58.563 45.455 0.00 0.00 0.00 3.08
2222 2268 3.194968 TGGGATCTTCGTTTCTCAGGTAC 59.805 47.826 0.00 0.00 0.00 3.34
2223 2269 3.194968 GGGATCTTCGTTTCTCAGGTACA 59.805 47.826 0.00 0.00 0.00 2.90
2224 2270 4.425520 GGATCTTCGTTTCTCAGGTACAG 58.574 47.826 0.00 0.00 0.00 2.74
2225 2271 4.082136 GGATCTTCGTTTCTCAGGTACAGT 60.082 45.833 0.00 0.00 0.00 3.55
2226 2272 4.931661 TCTTCGTTTCTCAGGTACAGTT 57.068 40.909 0.00 0.00 0.00 3.16
2227 2273 6.349944 GGATCTTCGTTTCTCAGGTACAGTTA 60.350 42.308 0.00 0.00 0.00 2.24
2228 2274 5.766222 TCTTCGTTTCTCAGGTACAGTTAC 58.234 41.667 0.00 0.00 0.00 2.50
2229 2275 5.533903 TCTTCGTTTCTCAGGTACAGTTACT 59.466 40.000 0.00 0.00 0.00 2.24
2230 2276 6.712095 TCTTCGTTTCTCAGGTACAGTTACTA 59.288 38.462 0.00 0.00 0.00 1.82
2231 2277 6.246420 TCGTTTCTCAGGTACAGTTACTAC 57.754 41.667 0.00 0.00 0.00 2.73
2232 2278 5.764686 TCGTTTCTCAGGTACAGTTACTACA 59.235 40.000 0.00 0.00 0.00 2.74
2233 2279 6.432162 TCGTTTCTCAGGTACAGTTACTACAT 59.568 38.462 0.00 0.00 0.00 2.29
2234 2280 6.746364 CGTTTCTCAGGTACAGTTACTACATC 59.254 42.308 0.00 0.00 0.00 3.06
2235 2281 7.574404 CGTTTCTCAGGTACAGTTACTACATCA 60.574 40.741 0.00 0.00 0.00 3.07
2236 2282 7.956328 TTCTCAGGTACAGTTACTACATCAT 57.044 36.000 0.00 0.00 0.00 2.45
2237 2283 7.569639 TCTCAGGTACAGTTACTACATCATC 57.430 40.000 0.00 0.00 0.00 2.92
2238 2284 7.347252 TCTCAGGTACAGTTACTACATCATCT 58.653 38.462 0.00 0.00 0.00 2.90
2239 2285 7.834681 TCTCAGGTACAGTTACTACATCATCTT 59.165 37.037 0.00 0.00 0.00 2.40
2240 2286 9.121658 CTCAGGTACAGTTACTACATCATCTTA 57.878 37.037 0.00 0.00 0.00 2.10
2241 2287 9.470399 TCAGGTACAGTTACTACATCATCTTAA 57.530 33.333 0.00 0.00 0.00 1.85
2247 2293 9.672673 ACAGTTACTACATCATCTTAATTTGCT 57.327 29.630 0.00 0.00 0.00 3.91
2256 2302 9.807649 ACATCATCTTAATTTGCTAATTGTTCC 57.192 29.630 15.16 0.00 35.61 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.486726 CCCACTCAACCTAGATGTCCC 59.513 57.143 0.00 0.00 0.00 4.46
578 581 2.081462 CATAGAACCCGGTTGTCCAAC 58.919 52.381 7.78 1.49 40.45 3.77
642 645 1.224592 GGAGGATGCGGGAATGTGT 59.775 57.895 0.00 0.00 0.00 3.72
858 863 1.006102 GTCGGGGACATGATAGCGG 60.006 63.158 0.00 0.00 32.09 5.52
1442 1478 9.000486 CGAGTATCTATTATCCTACACAAGACA 58.000 37.037 0.00 0.00 0.00 3.41
1594 1636 9.649167 ACTAGTTTCTGCGTATTTTTAGTGTAT 57.351 29.630 0.00 0.00 0.00 2.29
1595 1637 9.132521 GACTAGTTTCTGCGTATTTTTAGTGTA 57.867 33.333 0.00 0.00 0.00 2.90
1636 1679 0.313043 CTGGGCTGAAAACTGCTGTG 59.687 55.000 0.00 0.00 0.00 3.66
1637 1680 0.183492 TCTGGGCTGAAAACTGCTGT 59.817 50.000 0.00 0.00 0.00 4.40
1908 1954 1.842052 TACACTGTATCTGACCGCCA 58.158 50.000 0.00 0.00 0.00 5.69
1909 1955 2.361119 TCATACACTGTATCTGACCGCC 59.639 50.000 0.00 0.00 0.00 6.13
1910 1956 3.710326 TCATACACTGTATCTGACCGC 57.290 47.619 0.00 0.00 0.00 5.68
1911 1957 6.961359 TTTTTCATACACTGTATCTGACCG 57.039 37.500 0.00 0.00 0.00 4.79
1936 1982 9.786105 CACAATAATTATACAACAACATGAGCA 57.214 29.630 0.00 0.00 0.00 4.26
1937 1983 9.236691 CCACAATAATTATACAACAACATGAGC 57.763 33.333 0.00 0.00 0.00 4.26
1953 1999 9.127277 ACTAACACAACAAGTACCACAATAATT 57.873 29.630 0.00 0.00 0.00 1.40
1954 2000 8.685838 ACTAACACAACAAGTACCACAATAAT 57.314 30.769 0.00 0.00 0.00 1.28
1955 2001 8.508883 AACTAACACAACAAGTACCACAATAA 57.491 30.769 0.00 0.00 0.00 1.40
1956 2002 8.399425 CAAACTAACACAACAAGTACCACAATA 58.601 33.333 0.00 0.00 0.00 1.90
1957 2003 7.094118 ACAAACTAACACAACAAGTACCACAAT 60.094 33.333 0.00 0.00 0.00 2.71
1958 2004 6.207025 ACAAACTAACACAACAAGTACCACAA 59.793 34.615 0.00 0.00 0.00 3.33
1959 2005 5.706369 ACAAACTAACACAACAAGTACCACA 59.294 36.000 0.00 0.00 0.00 4.17
1960 2006 6.025280 CACAAACTAACACAACAAGTACCAC 58.975 40.000 0.00 0.00 0.00 4.16
1961 2007 5.706369 ACACAAACTAACACAACAAGTACCA 59.294 36.000 0.00 0.00 0.00 3.25
1962 2008 6.185852 ACACAAACTAACACAACAAGTACC 57.814 37.500 0.00 0.00 0.00 3.34
1963 2009 8.823818 AGATACACAAACTAACACAACAAGTAC 58.176 33.333 0.00 0.00 0.00 2.73
1964 2010 8.951787 AGATACACAAACTAACACAACAAGTA 57.048 30.769 0.00 0.00 0.00 2.24
1965 2011 7.769044 AGAGATACACAAACTAACACAACAAGT 59.231 33.333 0.00 0.00 0.00 3.16
1966 2012 8.064222 CAGAGATACACAAACTAACACAACAAG 58.936 37.037 0.00 0.00 0.00 3.16
1967 2013 7.551262 ACAGAGATACACAAACTAACACAACAA 59.449 33.333 0.00 0.00 0.00 2.83
1968 2014 7.045416 ACAGAGATACACAAACTAACACAACA 58.955 34.615 0.00 0.00 0.00 3.33
1969 2015 7.478520 ACAGAGATACACAAACTAACACAAC 57.521 36.000 0.00 0.00 0.00 3.32
1970 2016 9.256477 CTAACAGAGATACACAAACTAACACAA 57.744 33.333 0.00 0.00 0.00 3.33
1971 2017 8.418662 ACTAACAGAGATACACAAACTAACACA 58.581 33.333 0.00 0.00 0.00 3.72
1972 2018 8.813643 ACTAACAGAGATACACAAACTAACAC 57.186 34.615 0.00 0.00 0.00 3.32
1980 2026 9.135843 CGACAAAATACTAACAGAGATACACAA 57.864 33.333 0.00 0.00 0.00 3.33
1981 2027 7.758076 CCGACAAAATACTAACAGAGATACACA 59.242 37.037 0.00 0.00 0.00 3.72
1982 2028 7.758528 ACCGACAAAATACTAACAGAGATACAC 59.241 37.037 0.00 0.00 0.00 2.90
1983 2029 7.833786 ACCGACAAAATACTAACAGAGATACA 58.166 34.615 0.00 0.00 0.00 2.29
1984 2030 7.165483 CGACCGACAAAATACTAACAGAGATAC 59.835 40.741 0.00 0.00 0.00 2.24
1985 2031 7.191551 CGACCGACAAAATACTAACAGAGATA 58.808 38.462 0.00 0.00 0.00 1.98
1986 2032 6.034591 CGACCGACAAAATACTAACAGAGAT 58.965 40.000 0.00 0.00 0.00 2.75
1987 2033 5.396484 CGACCGACAAAATACTAACAGAGA 58.604 41.667 0.00 0.00 0.00 3.10
1988 2034 4.561606 CCGACCGACAAAATACTAACAGAG 59.438 45.833 0.00 0.00 0.00 3.35
1989 2035 4.487948 CCGACCGACAAAATACTAACAGA 58.512 43.478 0.00 0.00 0.00 3.41
1990 2036 3.061697 GCCGACCGACAAAATACTAACAG 59.938 47.826 0.00 0.00 0.00 3.16
1991 2037 2.995258 GCCGACCGACAAAATACTAACA 59.005 45.455 0.00 0.00 0.00 2.41
1992 2038 2.349580 GGCCGACCGACAAAATACTAAC 59.650 50.000 0.00 0.00 0.00 2.34
1993 2039 2.028294 TGGCCGACCGACAAAATACTAA 60.028 45.455 0.00 0.00 39.70 2.24
1994 2040 1.549620 TGGCCGACCGACAAAATACTA 59.450 47.619 0.00 0.00 39.70 1.82
1995 2041 0.322322 TGGCCGACCGACAAAATACT 59.678 50.000 0.00 0.00 39.70 2.12
1996 2042 1.375551 ATGGCCGACCGACAAAATAC 58.624 50.000 0.00 0.00 39.70 1.89
1997 2043 2.983907 TATGGCCGACCGACAAAATA 57.016 45.000 0.00 0.00 39.70 1.40
1998 2044 2.341846 ATATGGCCGACCGACAAAAT 57.658 45.000 0.00 0.00 39.70 1.82
1999 2045 2.116827 AATATGGCCGACCGACAAAA 57.883 45.000 0.00 0.00 39.70 2.44
2000 2046 2.116827 AAATATGGCCGACCGACAAA 57.883 45.000 0.00 0.00 39.70 2.83
2001 2047 2.983907 TAAATATGGCCGACCGACAA 57.016 45.000 0.00 0.00 39.70 3.18
2002 2048 3.478857 AATAAATATGGCCGACCGACA 57.521 42.857 0.00 0.00 39.70 4.35
2003 2049 3.608474 GCAAATAAATATGGCCGACCGAC 60.608 47.826 0.00 0.00 39.70 4.79
2004 2050 2.550606 GCAAATAAATATGGCCGACCGA 59.449 45.455 0.00 0.00 39.70 4.69
2005 2051 2.292016 TGCAAATAAATATGGCCGACCG 59.708 45.455 0.00 0.00 39.70 4.79
2006 2052 4.314740 TTGCAAATAAATATGGCCGACC 57.685 40.909 0.00 0.00 0.00 4.79
2007 2053 6.677913 ACTATTGCAAATAAATATGGCCGAC 58.322 36.000 1.71 0.00 0.00 4.79
2008 2054 6.892658 ACTATTGCAAATAAATATGGCCGA 57.107 33.333 1.71 0.00 0.00 5.54
2009 2055 7.370383 AGAACTATTGCAAATAAATATGGCCG 58.630 34.615 1.71 0.00 0.00 6.13
2010 2056 9.196552 GAAGAACTATTGCAAATAAATATGGCC 57.803 33.333 1.71 0.00 0.00 5.36
2011 2057 9.971922 AGAAGAACTATTGCAAATAAATATGGC 57.028 29.630 1.71 0.00 0.00 4.40
2031 2077 2.218603 GGAAGGTTGCGTTCAGAAGAA 58.781 47.619 4.37 0.00 30.94 2.52
2032 2078 1.140052 TGGAAGGTTGCGTTCAGAAGA 59.860 47.619 4.37 0.00 30.94 2.87
2033 2079 1.532868 CTGGAAGGTTGCGTTCAGAAG 59.467 52.381 4.37 0.00 30.94 2.85
2034 2080 1.134220 ACTGGAAGGTTGCGTTCAGAA 60.134 47.619 0.00 0.00 39.30 3.02
2035 2081 0.468226 ACTGGAAGGTTGCGTTCAGA 59.532 50.000 0.00 0.00 39.30 3.27
2036 2082 1.308998 AACTGGAAGGTTGCGTTCAG 58.691 50.000 4.37 0.00 39.30 3.02
2037 2083 2.489971 CTAACTGGAAGGTTGCGTTCA 58.510 47.619 4.37 0.00 39.30 3.18
2038 2084 1.804748 CCTAACTGGAAGGTTGCGTTC 59.195 52.381 0.00 0.00 39.30 3.95
2039 2085 1.142262 ACCTAACTGGAAGGTTGCGTT 59.858 47.619 0.00 0.00 45.26 4.84
2040 2086 0.763035 ACCTAACTGGAAGGTTGCGT 59.237 50.000 0.00 0.00 45.26 5.24
2041 2087 1.156736 CACCTAACTGGAAGGTTGCG 58.843 55.000 0.88 0.00 45.26 4.85
2042 2088 2.561478 TCACCTAACTGGAAGGTTGC 57.439 50.000 0.88 0.00 45.26 4.17
2043 2089 2.749621 GCATCACCTAACTGGAAGGTTG 59.250 50.000 0.88 0.66 45.26 3.77
2044 2090 2.644798 AGCATCACCTAACTGGAAGGTT 59.355 45.455 0.88 0.00 45.26 3.50
2046 2092 3.012518 CAAGCATCACCTAACTGGAAGG 58.987 50.000 0.00 0.00 39.30 3.46
2047 2093 2.421424 GCAAGCATCACCTAACTGGAAG 59.579 50.000 0.00 0.00 39.71 3.46
2048 2094 2.040278 AGCAAGCATCACCTAACTGGAA 59.960 45.455 0.00 0.00 39.71 3.53
2049 2095 1.630369 AGCAAGCATCACCTAACTGGA 59.370 47.619 0.00 0.00 39.71 3.86
2050 2096 2.119801 AGCAAGCATCACCTAACTGG 57.880 50.000 0.00 0.00 42.93 4.00
2051 2097 5.824904 AAATAGCAAGCATCACCTAACTG 57.175 39.130 0.00 0.00 0.00 3.16
2052 2098 6.653989 ACTAAATAGCAAGCATCACCTAACT 58.346 36.000 0.00 0.00 0.00 2.24
2053 2099 6.927294 ACTAAATAGCAAGCATCACCTAAC 57.073 37.500 0.00 0.00 0.00 2.34
2054 2100 6.183360 GCAACTAAATAGCAAGCATCACCTAA 60.183 38.462 0.00 0.00 0.00 2.69
2055 2101 5.296780 GCAACTAAATAGCAAGCATCACCTA 59.703 40.000 0.00 0.00 0.00 3.08
2056 2102 4.096984 GCAACTAAATAGCAAGCATCACCT 59.903 41.667 0.00 0.00 0.00 4.00
2057 2103 4.096984 AGCAACTAAATAGCAAGCATCACC 59.903 41.667 0.00 0.00 0.00 4.02
2058 2104 5.240713 AGCAACTAAATAGCAAGCATCAC 57.759 39.130 0.00 0.00 0.00 3.06
2059 2105 5.415389 TGAAGCAACTAAATAGCAAGCATCA 59.585 36.000 0.00 0.00 0.00 3.07
2060 2106 5.883661 TGAAGCAACTAAATAGCAAGCATC 58.116 37.500 0.00 0.00 0.00 3.91
2061 2107 5.416952 ACTGAAGCAACTAAATAGCAAGCAT 59.583 36.000 0.00 0.00 0.00 3.79
2062 2108 4.761739 ACTGAAGCAACTAAATAGCAAGCA 59.238 37.500 0.00 0.00 0.00 3.91
2063 2109 5.302357 ACTGAAGCAACTAAATAGCAAGC 57.698 39.130 0.00 0.00 0.00 4.01
2064 2110 6.798959 GTGAACTGAAGCAACTAAATAGCAAG 59.201 38.462 0.00 0.00 0.00 4.01
2065 2111 6.486657 AGTGAACTGAAGCAACTAAATAGCAA 59.513 34.615 0.00 0.00 0.00 3.91
2066 2112 5.997746 AGTGAACTGAAGCAACTAAATAGCA 59.002 36.000 0.00 0.00 0.00 3.49
2067 2113 6.487689 AGTGAACTGAAGCAACTAAATAGC 57.512 37.500 0.00 0.00 0.00 2.97
2068 2114 7.800380 CACAAGTGAACTGAAGCAACTAAATAG 59.200 37.037 0.00 0.00 0.00 1.73
2069 2115 7.497579 TCACAAGTGAACTGAAGCAACTAAATA 59.502 33.333 0.00 0.00 36.53 1.40
2070 2116 6.318648 TCACAAGTGAACTGAAGCAACTAAAT 59.681 34.615 0.00 0.00 36.53 1.40
2071 2117 5.645929 TCACAAGTGAACTGAAGCAACTAAA 59.354 36.000 0.00 0.00 36.53 1.85
2072 2118 5.182487 TCACAAGTGAACTGAAGCAACTAA 58.818 37.500 0.00 0.00 36.53 2.24
2073 2119 4.765273 TCACAAGTGAACTGAAGCAACTA 58.235 39.130 0.00 0.00 36.53 2.24
2074 2120 3.609853 TCACAAGTGAACTGAAGCAACT 58.390 40.909 0.00 0.00 36.53 3.16
2075 2121 4.355543 TTCACAAGTGAACTGAAGCAAC 57.644 40.909 11.34 0.00 43.90 4.17
2085 2131 6.698008 ATCACAGTCATTTTCACAAGTGAA 57.302 33.333 11.34 11.34 46.72 3.18
2086 2132 6.543465 AGAATCACAGTCATTTTCACAAGTGA 59.457 34.615 0.00 0.00 36.28 3.41
2087 2133 6.732154 AGAATCACAGTCATTTTCACAAGTG 58.268 36.000 0.00 0.00 0.00 3.16
2088 2134 6.949352 AGAATCACAGTCATTTTCACAAGT 57.051 33.333 0.00 0.00 0.00 3.16
2089 2135 9.552114 GAATAGAATCACAGTCATTTTCACAAG 57.448 33.333 0.00 0.00 0.00 3.16
2090 2136 9.065798 TGAATAGAATCACAGTCATTTTCACAA 57.934 29.630 0.00 0.00 0.00 3.33
2091 2137 8.620116 TGAATAGAATCACAGTCATTTTCACA 57.380 30.769 0.00 0.00 0.00 3.58
2099 2145 9.730705 AGAAAGAAATGAATAGAATCACAGTCA 57.269 29.630 0.00 0.00 30.82 3.41
2112 2158 9.071276 TGCTCTCTACAAAAGAAAGAAATGAAT 57.929 29.630 0.00 0.00 32.46 2.57
2113 2159 8.450578 TGCTCTCTACAAAAGAAAGAAATGAA 57.549 30.769 0.00 0.00 32.46 2.57
2114 2160 8.627208 ATGCTCTCTACAAAAGAAAGAAATGA 57.373 30.769 0.00 0.00 32.46 2.57
2115 2161 9.688592 AAATGCTCTCTACAAAAGAAAGAAATG 57.311 29.630 0.00 0.00 32.46 2.32
2116 2162 9.688592 CAAATGCTCTCTACAAAAGAAAGAAAT 57.311 29.630 0.00 0.00 32.46 2.17
2117 2163 8.686334 ACAAATGCTCTCTACAAAAGAAAGAAA 58.314 29.630 0.00 0.00 32.46 2.52
2118 2164 8.225603 ACAAATGCTCTCTACAAAAGAAAGAA 57.774 30.769 0.00 0.00 32.46 2.52
2119 2165 7.807977 ACAAATGCTCTCTACAAAAGAAAGA 57.192 32.000 0.00 0.00 32.46 2.52
2120 2166 8.778358 AGTACAAATGCTCTCTACAAAAGAAAG 58.222 33.333 0.00 0.00 32.46 2.62
2121 2167 8.559536 CAGTACAAATGCTCTCTACAAAAGAAA 58.440 33.333 0.00 0.00 32.46 2.52
2122 2168 7.173218 CCAGTACAAATGCTCTCTACAAAAGAA 59.827 37.037 0.00 0.00 32.46 2.52
2123 2169 6.650807 CCAGTACAAATGCTCTCTACAAAAGA 59.349 38.462 0.00 0.00 0.00 2.52
2124 2170 6.428159 ACCAGTACAAATGCTCTCTACAAAAG 59.572 38.462 0.00 0.00 0.00 2.27
2125 2171 6.204688 CACCAGTACAAATGCTCTCTACAAAA 59.795 38.462 0.00 0.00 0.00 2.44
2126 2172 5.700832 CACCAGTACAAATGCTCTCTACAAA 59.299 40.000 0.00 0.00 0.00 2.83
2127 2173 5.237815 CACCAGTACAAATGCTCTCTACAA 58.762 41.667 0.00 0.00 0.00 2.41
2128 2174 4.322725 CCACCAGTACAAATGCTCTCTACA 60.323 45.833 0.00 0.00 0.00 2.74
2129 2175 4.184629 CCACCAGTACAAATGCTCTCTAC 58.815 47.826 0.00 0.00 0.00 2.59
2130 2176 3.197766 CCCACCAGTACAAATGCTCTCTA 59.802 47.826 0.00 0.00 0.00 2.43
2131 2177 2.026822 CCCACCAGTACAAATGCTCTCT 60.027 50.000 0.00 0.00 0.00 3.10
2132 2178 2.290323 ACCCACCAGTACAAATGCTCTC 60.290 50.000 0.00 0.00 0.00 3.20
2133 2179 1.705186 ACCCACCAGTACAAATGCTCT 59.295 47.619 0.00 0.00 0.00 4.09
2134 2180 2.200373 ACCCACCAGTACAAATGCTC 57.800 50.000 0.00 0.00 0.00 4.26
2135 2181 2.675658 AACCCACCAGTACAAATGCT 57.324 45.000 0.00 0.00 0.00 3.79
2136 2182 4.857509 TTAAACCCACCAGTACAAATGC 57.142 40.909 0.00 0.00 0.00 3.56
2137 2183 7.213678 ACAAATTAAACCCACCAGTACAAATG 58.786 34.615 0.00 0.00 0.00 2.32
2138 2184 7.368198 ACAAATTAAACCCACCAGTACAAAT 57.632 32.000 0.00 0.00 0.00 2.32
2139 2185 6.793505 ACAAATTAAACCCACCAGTACAAA 57.206 33.333 0.00 0.00 0.00 2.83
2140 2186 6.793505 AACAAATTAAACCCACCAGTACAA 57.206 33.333 0.00 0.00 0.00 2.41
2141 2187 7.893124 TTAACAAATTAAACCCACCAGTACA 57.107 32.000 0.00 0.00 0.00 2.90
2142 2188 8.030692 GGATTAACAAATTAAACCCACCAGTAC 58.969 37.037 0.00 0.00 37.29 2.73
2143 2189 7.728981 TGGATTAACAAATTAAACCCACCAGTA 59.271 33.333 4.28 0.00 40.73 2.74
2144 2190 6.555360 TGGATTAACAAATTAAACCCACCAGT 59.445 34.615 4.28 0.00 40.73 4.00
2145 2191 6.998802 TGGATTAACAAATTAAACCCACCAG 58.001 36.000 4.28 0.00 40.73 4.00
2146 2192 6.555360 ACTGGATTAACAAATTAAACCCACCA 59.445 34.615 4.28 0.00 40.73 4.17
2147 2193 6.871492 CACTGGATTAACAAATTAAACCCACC 59.129 38.462 4.28 0.00 40.73 4.61
2148 2194 6.871492 CCACTGGATTAACAAATTAAACCCAC 59.129 38.462 0.00 0.00 40.73 4.61
2149 2195 6.014156 CCCACTGGATTAACAAATTAAACCCA 60.014 38.462 0.00 4.68 40.73 4.51
2150 2196 6.403049 CCCACTGGATTAACAAATTAAACCC 58.597 40.000 0.00 1.09 40.73 4.11
2151 2197 6.014070 ACCCCACTGGATTAACAAATTAAACC 60.014 38.462 0.00 0.48 41.44 3.27
2152 2198 6.999950 ACCCCACTGGATTAACAAATTAAAC 58.000 36.000 0.00 0.00 34.00 2.01
2153 2199 7.728981 TGTACCCCACTGGATTAACAAATTAAA 59.271 33.333 0.00 0.00 34.00 1.52
2154 2200 7.239438 TGTACCCCACTGGATTAACAAATTAA 58.761 34.615 0.00 0.00 38.00 1.40
2155 2201 6.791371 TGTACCCCACTGGATTAACAAATTA 58.209 36.000 0.00 0.00 38.00 1.40
2156 2202 5.646215 TGTACCCCACTGGATTAACAAATT 58.354 37.500 0.00 0.00 38.00 1.82
2157 2203 5.261216 CTGTACCCCACTGGATTAACAAAT 58.739 41.667 0.00 0.00 38.00 2.32
2158 2204 4.658063 CTGTACCCCACTGGATTAACAAA 58.342 43.478 0.00 0.00 38.00 2.83
2159 2205 3.560453 GCTGTACCCCACTGGATTAACAA 60.560 47.826 0.00 0.00 38.00 2.83
2160 2206 2.026636 GCTGTACCCCACTGGATTAACA 60.027 50.000 0.00 0.00 38.00 2.41
2161 2207 2.640184 GCTGTACCCCACTGGATTAAC 58.360 52.381 0.00 0.00 38.00 2.01
2162 2208 1.562475 GGCTGTACCCCACTGGATTAA 59.438 52.381 0.00 0.00 38.00 1.40
2163 2209 1.209621 GGCTGTACCCCACTGGATTA 58.790 55.000 0.00 0.00 38.00 1.75
2164 2210 0.550147 AGGCTGTACCCCACTGGATT 60.550 55.000 0.00 0.00 40.58 3.01
2165 2211 1.082954 AGGCTGTACCCCACTGGAT 59.917 57.895 0.00 0.00 40.58 3.41
2166 2212 1.918293 CAGGCTGTACCCCACTGGA 60.918 63.158 6.28 0.00 40.58 3.86
2167 2213 2.671070 CAGGCTGTACCCCACTGG 59.329 66.667 6.28 0.00 40.58 4.00
2168 2214 2.224159 ACCAGGCTGTACCCCACTG 61.224 63.158 14.43 0.00 40.58 3.66
2169 2215 2.207189 ACCAGGCTGTACCCCACT 59.793 61.111 14.43 0.00 40.58 4.00
2170 2216 2.351276 CACCAGGCTGTACCCCAC 59.649 66.667 14.43 0.00 40.58 4.61
2171 2217 2.933287 CCACCAGGCTGTACCCCA 60.933 66.667 14.43 0.00 40.58 4.96
2172 2218 2.228480 TTCCACCAGGCTGTACCCC 61.228 63.158 14.43 0.00 40.58 4.95
2173 2219 1.002502 GTTCCACCAGGCTGTACCC 60.003 63.158 14.43 0.00 40.58 3.69
2174 2220 1.002502 GGTTCCACCAGGCTGTACC 60.003 63.158 14.43 8.70 38.42 3.34
2175 2221 1.758592 TGGTTCCACCAGGCTGTAC 59.241 57.895 14.43 3.39 44.79 2.90
2176 2222 4.322681 TGGTTCCACCAGGCTGTA 57.677 55.556 14.43 0.00 44.79 2.74
2184 2230 3.838795 CCATTTGCATGGTTCCACC 57.161 52.632 0.00 0.00 44.81 4.61
2192 2238 3.788333 AACGAAGATCCCATTTGCATG 57.212 42.857 0.00 0.00 0.00 4.06
2193 2239 4.019174 AGAAACGAAGATCCCATTTGCAT 58.981 39.130 0.00 0.00 0.00 3.96
2194 2240 3.420893 AGAAACGAAGATCCCATTTGCA 58.579 40.909 0.00 0.00 0.00 4.08
2195 2241 3.440173 TGAGAAACGAAGATCCCATTTGC 59.560 43.478 0.00 0.00 0.00 3.68
2196 2242 4.095483 CCTGAGAAACGAAGATCCCATTTG 59.905 45.833 0.00 0.00 0.00 2.32
2197 2243 4.263506 ACCTGAGAAACGAAGATCCCATTT 60.264 41.667 0.00 0.00 0.00 2.32
2198 2244 3.264450 ACCTGAGAAACGAAGATCCCATT 59.736 43.478 0.00 0.00 0.00 3.16
2199 2245 2.840651 ACCTGAGAAACGAAGATCCCAT 59.159 45.455 0.00 0.00 0.00 4.00
2200 2246 2.257207 ACCTGAGAAACGAAGATCCCA 58.743 47.619 0.00 0.00 0.00 4.37
2201 2247 3.194968 TGTACCTGAGAAACGAAGATCCC 59.805 47.826 0.00 0.00 0.00 3.85
2202 2248 4.082136 ACTGTACCTGAGAAACGAAGATCC 60.082 45.833 0.00 0.00 0.00 3.36
2203 2249 5.061920 ACTGTACCTGAGAAACGAAGATC 57.938 43.478 0.00 0.00 0.00 2.75
2204 2250 5.470047 AACTGTACCTGAGAAACGAAGAT 57.530 39.130 0.00 0.00 0.00 2.40
2205 2251 4.931661 AACTGTACCTGAGAAACGAAGA 57.068 40.909 0.00 0.00 0.00 2.87
2206 2252 5.770417 AGTAACTGTACCTGAGAAACGAAG 58.230 41.667 0.00 0.00 0.00 3.79
2207 2253 5.779529 AGTAACTGTACCTGAGAAACGAA 57.220 39.130 0.00 0.00 0.00 3.85
2208 2254 5.764686 TGTAGTAACTGTACCTGAGAAACGA 59.235 40.000 0.00 0.00 0.00 3.85
2209 2255 6.005583 TGTAGTAACTGTACCTGAGAAACG 57.994 41.667 0.00 0.00 0.00 3.60
2210 2256 7.600065 TGATGTAGTAACTGTACCTGAGAAAC 58.400 38.462 0.00 0.00 0.00 2.78
2211 2257 7.770366 TGATGTAGTAACTGTACCTGAGAAA 57.230 36.000 0.00 0.00 0.00 2.52
2212 2258 7.834681 AGATGATGTAGTAACTGTACCTGAGAA 59.165 37.037 0.00 0.00 0.00 2.87
2213 2259 7.347252 AGATGATGTAGTAACTGTACCTGAGA 58.653 38.462 0.00 0.00 0.00 3.27
2214 2260 7.575414 AGATGATGTAGTAACTGTACCTGAG 57.425 40.000 0.00 0.00 0.00 3.35
2215 2261 7.956328 AAGATGATGTAGTAACTGTACCTGA 57.044 36.000 0.00 0.00 0.00 3.86
2221 2267 9.672673 AGCAAATTAAGATGATGTAGTAACTGT 57.327 29.630 0.00 0.00 0.00 3.55
2230 2276 9.807649 GGAACAATTAGCAAATTAAGATGATGT 57.192 29.630 0.00 0.00 33.45 3.06


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

AutoCloner maintained by Alex Coulton.