Multiple sequence alignment - TraesCS4A01G102800

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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 TraesCS4A01G102800 chr4A 100.000 3744 0 0 1 3744 115573042 115576785 0.000000e+00 6914
1 TraesCS4A01G102800 chr4B 94.381 1655 84 9 2095 3743 432257404 432255753 0.000000e+00 2532
2 TraesCS4A01G102800 chr4B 89.615 1897 80 36 1 1808 432259323 432257455 0.000000e+00 2303
3 TraesCS4A01G102800 chr4D 94.004 1651 71 9 2095 3740 349410671 349409044 0.000000e+00 2475
4 TraesCS4A01G102800 chr4D 90.623 1269 70 18 574 1823 349411966 349410728 0.000000e+00 1639
5 TraesCS4A01G102800 chr4D 92.000 600 20 7 1 577 349421125 349420531 0.000000e+00 817
6 TraesCS4A01G102800 chr4D 95.984 249 9 1 1845 2092 30506674 30506426 1.620000e-108 403
7 TraesCS4A01G102800 chr4D 96.296 243 9 0 1850 2092 76612185 76611943 2.090000e-107 399
8 TraesCS4A01G102800 chr4D 94.902 255 11 2 1840 2092 11504369 11504115 7.530000e-107 398
9 TraesCS4A01G102800 chr4D 93.233 266 13 4 1834 2095 58632832 58633096 1.630000e-103 387
10 TraesCS4A01G102800 chr7D 96.281 242 9 0 1851 2092 397205687 397205446 7.530000e-107 398
11 TraesCS4A01G102800 chr2D 96.296 243 8 1 1850 2092 642827315 642827074 7.530000e-107 398
12 TraesCS4A01G102800 chr6D 95.510 245 11 0 1851 2095 80054319 80054075 3.510000e-105 392
13 TraesCS4A01G102800 chr5D 93.487 261 15 2 1845 2104 112358180 112357921 1.630000e-103 387
14 TraesCS4A01G102800 chr3D 92.565 269 19 1 1838 2105 129016839 129016571 5.870000e-103 385


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 TraesCS4A01G102800 chr4A 115573042 115576785 3743 False 6914.0 6914 100.0000 1 3744 1 chr4A.!!$F1 3743
1 TraesCS4A01G102800 chr4B 432255753 432259323 3570 True 2417.5 2532 91.9980 1 3743 2 chr4B.!!$R1 3742
2 TraesCS4A01G102800 chr4D 349409044 349411966 2922 True 2057.0 2475 92.3135 574 3740 2 chr4D.!!$R5 3166
3 TraesCS4A01G102800 chr4D 349420531 349421125 594 True 817.0 817 92.0000 1 577 1 chr4D.!!$R4 576

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
482 506 0.250793 TGACGTGTTGGTGGTGTTCT 59.749 50.0 0.0 0.0 0.0 3.01 F
1169 1265 0.107312 CTCGACTTCCTCCCCGACTA 60.107 60.0 0.0 0.0 0.0 2.59 F
1892 2023 0.032017 AGTGCTTCCTCTATCCCCGT 60.032 55.0 0.0 0.0 0.0 5.28 F
1898 2029 0.032515 TCCTCTATCCCCGTGCTTCA 60.033 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2004 0.032017 ACGGGGATAGAGGAAGCACT 60.032 55.000 0.00 0.0 0.00 4.40 R
2008 2139 0.110056 TAACGAACGAGACCGACTGC 60.110 55.000 0.14 0.0 39.50 4.40 R
2707 2839 2.097825 GAAAGCTCCTCAACCATGCAT 58.902 47.619 0.00 0.0 0.00 3.96 R
3031 3164 2.107141 GATCGAAGAGCGTGGGGG 59.893 66.667 0.00 0.0 43.63 5.40 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
56 64 2.430248 AACGGTTGACTTTTCCACCT 57.570 45.000 0.00 0.00 35.71 4.00
89 97 2.099263 TCGTCATCTCCGTTCATTCTCC 59.901 50.000 0.00 0.00 0.00 3.71
157 174 2.157668 GTGAATATCGTTAGGGCATGCG 59.842 50.000 12.44 0.00 0.00 4.73
257 274 3.600388 GCAGGTGTAAGTTGCTCAGTAT 58.400 45.455 0.00 0.00 35.05 2.12
263 280 5.334879 GGTGTAAGTTGCTCAGTATGGTTTG 60.335 44.000 0.00 0.00 36.16 2.93
302 319 9.864034 CTTGTGTTGTACTGTAAAAGAATGTAG 57.136 33.333 0.00 0.00 0.00 2.74
370 387 1.200760 TGTAGGTGGCTGCAGTGGAT 61.201 55.000 16.64 0.71 0.00 3.41
371 388 0.462759 GTAGGTGGCTGCAGTGGATC 60.463 60.000 16.64 0.00 0.00 3.36
397 414 7.103641 TCCTCTGCCTTTGTTGTACTATAAAG 58.896 38.462 15.96 15.96 0.00 1.85
398 415 7.038587 TCCTCTGCCTTTGTTGTACTATAAAGA 60.039 37.037 21.76 7.57 33.18 2.52
482 506 0.250793 TGACGTGTTGGTGGTGTTCT 59.749 50.000 0.00 0.00 0.00 3.01
483 507 1.481363 TGACGTGTTGGTGGTGTTCTA 59.519 47.619 0.00 0.00 0.00 2.10
484 508 2.103432 TGACGTGTTGGTGGTGTTCTAT 59.897 45.455 0.00 0.00 0.00 1.98
485 509 3.321396 TGACGTGTTGGTGGTGTTCTATA 59.679 43.478 0.00 0.00 0.00 1.31
493 517 9.042008 GTGTTGGTGGTGTTCTATATATACTTG 57.958 37.037 0.00 0.00 0.00 3.16
516 540 8.862325 TTGTATGTATTTTCCTGTGAGTGAAT 57.138 30.769 0.00 0.00 0.00 2.57
568 592 6.183360 ACAAGTGATGTAAAACTGGTTTCCTG 60.183 38.462 0.00 0.00 41.63 3.86
569 593 4.827284 AGTGATGTAAAACTGGTTTCCTGG 59.173 41.667 0.00 0.00 31.45 4.45
665 692 7.064371 ACTCATGTCAAGAATCGAGATCTTTTG 59.936 37.037 12.23 5.31 34.99 2.44
685 712 6.367374 TTTGTTCTTTCTTCCTTTTTGGGT 57.633 33.333 0.00 0.00 36.20 4.51
850 939 1.302033 CAGCAGCCGGGCTATAAGG 60.302 63.158 23.37 10.25 43.68 2.69
851 940 1.459539 AGCAGCCGGGCTATAAGGA 60.460 57.895 23.37 0.00 43.70 3.36
933 1022 4.292178 CCTCCGCTGATCCGCTCC 62.292 72.222 7.56 0.00 0.00 4.70
964 1057 0.548031 CCAAGATCCAAGCTAGGCCA 59.452 55.000 5.01 0.00 0.00 5.36
966 1059 1.211457 CAAGATCCAAGCTAGGCCACT 59.789 52.381 5.01 0.00 0.00 4.00
1086 1179 2.163815 CGTCTTCCTCAACTACATCGGT 59.836 50.000 0.00 0.00 0.00 4.69
1168 1264 1.378778 CTCGACTTCCTCCCCGACT 60.379 63.158 0.00 0.00 0.00 4.18
1169 1265 0.107312 CTCGACTTCCTCCCCGACTA 60.107 60.000 0.00 0.00 0.00 2.59
1249 1345 3.121030 CTGGCTGTACTGCGTGGC 61.121 66.667 17.25 5.39 0.00 5.01
1250 1346 4.697756 TGGCTGTACTGCGTGGCC 62.698 66.667 17.25 0.00 42.73 5.36
1334 1430 2.757099 GTCTTCGACCCCGCCCTA 60.757 66.667 0.00 0.00 35.37 3.53
1477 1573 2.409870 GCCAAGATGAACCGGCTGG 61.410 63.158 11.02 11.02 41.50 4.85
1490 1598 0.745845 CGGCTGGAGAACCTTCCATG 60.746 60.000 0.00 0.00 45.80 3.66
1522 1630 1.511318 CGTTTGACGGAATGGCCACA 61.511 55.000 8.16 0.00 38.08 4.17
1556 1664 2.109126 GCCTGTGTTCTCATCGGCC 61.109 63.158 0.00 0.00 36.47 6.13
1706 1814 1.580132 CGCGCTTTACGTCCATTGC 60.580 57.895 5.56 0.00 46.11 3.56
1769 1877 6.296026 AGTGCATAACTACAAAACTCCTTCA 58.704 36.000 0.00 0.00 37.36 3.02
1867 1998 9.686136 ATATCATCTATACTCCATCCATTCCAT 57.314 33.333 0.00 0.00 0.00 3.41
1869 2000 8.915813 TCATCTATACTCCATCCATTCCATAA 57.084 34.615 0.00 0.00 0.00 1.90
1870 2001 9.511404 TCATCTATACTCCATCCATTCCATAAT 57.489 33.333 0.00 0.00 0.00 1.28
1871 2002 9.557061 CATCTATACTCCATCCATTCCATAATG 57.443 37.037 0.00 0.00 41.90 1.90
1872 2003 8.685257 TCTATACTCCATCCATTCCATAATGT 57.315 34.615 0.00 0.00 40.84 2.71
1873 2004 9.782900 TCTATACTCCATCCATTCCATAATGTA 57.217 33.333 0.00 0.00 40.84 2.29
1875 2006 6.770286 ACTCCATCCATTCCATAATGTAGT 57.230 37.500 0.00 0.00 40.84 2.73
1876 2007 6.537355 ACTCCATCCATTCCATAATGTAGTG 58.463 40.000 0.00 0.00 40.84 2.74
1877 2008 5.316167 TCCATCCATTCCATAATGTAGTGC 58.684 41.667 0.00 0.00 40.84 4.40
1878 2009 5.073554 TCCATCCATTCCATAATGTAGTGCT 59.926 40.000 0.00 0.00 40.84 4.40
1879 2010 5.771666 CCATCCATTCCATAATGTAGTGCTT 59.228 40.000 0.00 0.00 40.84 3.91
1880 2011 6.072286 CCATCCATTCCATAATGTAGTGCTTC 60.072 42.308 0.00 0.00 40.84 3.86
1881 2012 5.376625 TCCATTCCATAATGTAGTGCTTCC 58.623 41.667 0.00 0.00 40.84 3.46
1882 2013 5.132648 TCCATTCCATAATGTAGTGCTTCCT 59.867 40.000 0.00 0.00 40.84 3.36
1883 2014 5.471456 CCATTCCATAATGTAGTGCTTCCTC 59.529 44.000 0.00 0.00 40.84 3.71
1884 2015 5.957771 TTCCATAATGTAGTGCTTCCTCT 57.042 39.130 0.00 0.00 0.00 3.69
1885 2016 7.445121 CATTCCATAATGTAGTGCTTCCTCTA 58.555 38.462 0.00 0.00 38.15 2.43
1886 2017 7.618019 TTCCATAATGTAGTGCTTCCTCTAT 57.382 36.000 0.00 0.00 0.00 1.98
1887 2018 7.233389 TCCATAATGTAGTGCTTCCTCTATC 57.767 40.000 0.00 0.00 0.00 2.08
1888 2019 6.211584 TCCATAATGTAGTGCTTCCTCTATCC 59.788 42.308 0.00 0.00 0.00 2.59
1889 2020 4.965200 AATGTAGTGCTTCCTCTATCCC 57.035 45.455 0.00 0.00 0.00 3.85
1890 2021 2.679082 TGTAGTGCTTCCTCTATCCCC 58.321 52.381 0.00 0.00 0.00 4.81
1891 2022 1.614413 GTAGTGCTTCCTCTATCCCCG 59.386 57.143 0.00 0.00 0.00 5.73
1892 2023 0.032017 AGTGCTTCCTCTATCCCCGT 60.032 55.000 0.00 0.00 0.00 5.28
1893 2024 0.105039 GTGCTTCCTCTATCCCCGTG 59.895 60.000 0.00 0.00 0.00 4.94
1894 2025 1.069935 GCTTCCTCTATCCCCGTGC 59.930 63.158 0.00 0.00 0.00 5.34
1895 2026 1.403687 GCTTCCTCTATCCCCGTGCT 61.404 60.000 0.00 0.00 0.00 4.40
1896 2027 1.123928 CTTCCTCTATCCCCGTGCTT 58.876 55.000 0.00 0.00 0.00 3.91
1897 2028 1.069358 CTTCCTCTATCCCCGTGCTTC 59.931 57.143 0.00 0.00 0.00 3.86
1898 2029 0.032515 TCCTCTATCCCCGTGCTTCA 60.033 55.000 0.00 0.00 0.00 3.02
1899 2030 0.830648 CCTCTATCCCCGTGCTTCAA 59.169 55.000 0.00 0.00 0.00 2.69
1900 2031 1.473434 CCTCTATCCCCGTGCTTCAAC 60.473 57.143 0.00 0.00 0.00 3.18
1901 2032 1.482593 CTCTATCCCCGTGCTTCAACT 59.517 52.381 0.00 0.00 0.00 3.16
1902 2033 1.906574 TCTATCCCCGTGCTTCAACTT 59.093 47.619 0.00 0.00 0.00 2.66
1903 2034 2.304761 TCTATCCCCGTGCTTCAACTTT 59.695 45.455 0.00 0.00 0.00 2.66
1904 2035 1.247567 ATCCCCGTGCTTCAACTTTG 58.752 50.000 0.00 0.00 0.00 2.77
1905 2036 0.181587 TCCCCGTGCTTCAACTTTGA 59.818 50.000 0.00 0.00 34.92 2.69
1906 2037 0.310854 CCCCGTGCTTCAACTTTGAC 59.689 55.000 0.00 0.00 36.83 3.18
1907 2038 0.310854 CCCGTGCTTCAACTTTGACC 59.689 55.000 0.00 0.00 36.83 4.02
1908 2039 0.041312 CCGTGCTTCAACTTTGACCG 60.041 55.000 0.00 0.00 36.83 4.79
1909 2040 0.655733 CGTGCTTCAACTTTGACCGT 59.344 50.000 0.00 0.00 36.83 4.83
1910 2041 1.862201 CGTGCTTCAACTTTGACCGTA 59.138 47.619 0.00 0.00 36.83 4.02
1911 2042 2.285756 CGTGCTTCAACTTTGACCGTAA 59.714 45.455 0.00 0.00 36.83 3.18
1912 2043 3.242478 CGTGCTTCAACTTTGACCGTAAA 60.242 43.478 0.00 0.00 36.83 2.01
1913 2044 4.553938 CGTGCTTCAACTTTGACCGTAAAT 60.554 41.667 0.00 0.00 36.83 1.40
1914 2045 5.278604 GTGCTTCAACTTTGACCGTAAATT 58.721 37.500 0.00 0.00 36.83 1.82
1915 2046 5.746721 GTGCTTCAACTTTGACCGTAAATTT 59.253 36.000 0.00 0.00 36.83 1.82
1916 2047 6.913673 GTGCTTCAACTTTGACCGTAAATTTA 59.086 34.615 0.00 0.00 36.83 1.40
1917 2048 7.432838 GTGCTTCAACTTTGACCGTAAATTTAA 59.567 33.333 0.00 0.00 36.83 1.52
1918 2049 7.432838 TGCTTCAACTTTGACCGTAAATTTAAC 59.567 33.333 0.00 0.00 36.83 2.01
1919 2050 7.646526 GCTTCAACTTTGACCGTAAATTTAACT 59.353 33.333 0.00 0.00 36.83 2.24
1929 2060 9.027129 TGACCGTAAATTTAACTATCAAGATCG 57.973 33.333 0.00 0.00 0.00 3.69
1930 2061 9.241317 GACCGTAAATTTAACTATCAAGATCGA 57.759 33.333 0.00 0.00 0.00 3.59
1931 2062 9.760077 ACCGTAAATTTAACTATCAAGATCGAT 57.240 29.630 0.00 0.00 0.00 3.59
1935 2066 8.993852 AAATTTAACTATCAAGATCGATTGCG 57.006 30.769 0.00 0.00 39.35 4.85
1936 2067 6.525121 TTTAACTATCAAGATCGATTGCGG 57.475 37.500 0.00 0.00 38.28 5.69
1937 2068 2.408050 ACTATCAAGATCGATTGCGGC 58.592 47.619 0.00 0.00 38.28 6.53
1938 2069 1.388093 CTATCAAGATCGATTGCGGCG 59.612 52.381 0.51 0.51 38.28 6.46
1939 2070 1.224069 ATCAAGATCGATTGCGGCGG 61.224 55.000 9.78 0.00 38.28 6.13
1940 2071 2.588877 AAGATCGATTGCGGCGGG 60.589 61.111 9.78 0.00 38.28 6.13
1941 2072 3.088941 AAGATCGATTGCGGCGGGA 62.089 57.895 9.78 0.00 38.28 5.14
1942 2073 2.978452 AAGATCGATTGCGGCGGGAG 62.978 60.000 9.78 0.00 38.28 4.30
1959 2090 5.409643 CGGGAGCAAAAGTTATATCAGTG 57.590 43.478 0.00 0.00 0.00 3.66
1960 2091 5.116180 CGGGAGCAAAAGTTATATCAGTGA 58.884 41.667 0.00 0.00 0.00 3.41
1961 2092 5.584649 CGGGAGCAAAAGTTATATCAGTGAA 59.415 40.000 0.00 0.00 0.00 3.18
1962 2093 6.260936 CGGGAGCAAAAGTTATATCAGTGAAT 59.739 38.462 0.00 0.00 0.00 2.57
1963 2094 7.201732 CGGGAGCAAAAGTTATATCAGTGAATT 60.202 37.037 0.00 0.00 0.00 2.17
1964 2095 8.131731 GGGAGCAAAAGTTATATCAGTGAATTC 58.868 37.037 0.00 0.00 0.00 2.17
1965 2096 7.852945 GGAGCAAAAGTTATATCAGTGAATTCG 59.147 37.037 0.00 0.00 0.00 3.34
1966 2097 8.268850 AGCAAAAGTTATATCAGTGAATTCGT 57.731 30.769 0.00 0.00 0.00 3.85
1967 2098 9.378551 AGCAAAAGTTATATCAGTGAATTCGTA 57.621 29.630 0.00 0.00 0.00 3.43
1972 2103 9.961265 AAGTTATATCAGTGAATTCGTATTCGA 57.039 29.630 9.79 2.59 42.55 3.71
2008 2139 6.796705 ATTATATAACTTTTTCTCCCGCCG 57.203 37.500 0.00 0.00 0.00 6.46
2009 2140 1.092348 ATAACTTTTTCTCCCGCCGC 58.908 50.000 0.00 0.00 0.00 6.53
2010 2141 0.250381 TAACTTTTTCTCCCGCCGCA 60.250 50.000 0.00 0.00 0.00 5.69
2011 2142 1.515521 AACTTTTTCTCCCGCCGCAG 61.516 55.000 0.00 0.00 0.00 5.18
2012 2143 1.966451 CTTTTTCTCCCGCCGCAGT 60.966 57.895 0.00 0.00 0.00 4.40
2013 2144 1.912371 CTTTTTCTCCCGCCGCAGTC 61.912 60.000 0.00 0.00 0.00 3.51
2014 2145 4.735132 TTTCTCCCGCCGCAGTCG 62.735 66.667 0.00 0.00 0.00 4.18
2024 2155 2.870161 CGCAGTCGGTCTCGTTCG 60.870 66.667 0.00 0.00 37.69 3.95
2025 2156 2.254651 GCAGTCGGTCTCGTTCGT 59.745 61.111 0.00 0.00 37.69 3.85
2026 2157 1.371389 GCAGTCGGTCTCGTTCGTT 60.371 57.895 0.00 0.00 37.69 3.85
2027 2158 0.110056 GCAGTCGGTCTCGTTCGTTA 60.110 55.000 0.00 0.00 37.69 3.18
2028 2159 1.664016 GCAGTCGGTCTCGTTCGTTAA 60.664 52.381 0.00 0.00 37.69 2.01
2029 2160 2.653890 CAGTCGGTCTCGTTCGTTAAA 58.346 47.619 0.00 0.00 37.69 1.52
2030 2161 3.240069 CAGTCGGTCTCGTTCGTTAAAT 58.760 45.455 0.00 0.00 37.69 1.40
2031 2162 3.671928 CAGTCGGTCTCGTTCGTTAAATT 59.328 43.478 0.00 0.00 37.69 1.82
2032 2163 4.149396 CAGTCGGTCTCGTTCGTTAAATTT 59.851 41.667 0.00 0.00 37.69 1.82
2033 2164 5.343058 CAGTCGGTCTCGTTCGTTAAATTTA 59.657 40.000 0.00 0.00 37.69 1.40
2034 2165 6.034256 CAGTCGGTCTCGTTCGTTAAATTTAT 59.966 38.462 0.00 0.00 37.69 1.40
2035 2166 6.034256 AGTCGGTCTCGTTCGTTAAATTTATG 59.966 38.462 0.00 0.00 37.69 1.90
2036 2167 5.289193 TCGGTCTCGTTCGTTAAATTTATGG 59.711 40.000 0.00 0.00 37.69 2.74
2037 2168 5.062558 CGGTCTCGTTCGTTAAATTTATGGT 59.937 40.000 0.00 0.00 0.00 3.55
2038 2169 6.472680 GGTCTCGTTCGTTAAATTTATGGTC 58.527 40.000 0.00 0.00 0.00 4.02
2039 2170 6.091169 GGTCTCGTTCGTTAAATTTATGGTCA 59.909 38.462 0.00 0.00 0.00 4.02
2040 2171 7.360269 GGTCTCGTTCGTTAAATTTATGGTCAA 60.360 37.037 0.00 0.00 0.00 3.18
2041 2172 8.011106 GTCTCGTTCGTTAAATTTATGGTCAAA 58.989 33.333 0.00 0.00 0.00 2.69
2042 2173 8.557864 TCTCGTTCGTTAAATTTATGGTCAAAA 58.442 29.630 0.00 0.00 0.00 2.44
2043 2174 9.337091 CTCGTTCGTTAAATTTATGGTCAAAAT 57.663 29.630 0.00 0.00 0.00 1.82
2044 2175 9.680315 TCGTTCGTTAAATTTATGGTCAAAATT 57.320 25.926 0.00 0.00 37.98 1.82
2045 2176 9.931710 CGTTCGTTAAATTTATGGTCAAAATTC 57.068 29.630 0.00 0.00 35.91 2.17
2046 2177 9.931710 GTTCGTTAAATTTATGGTCAAAATTCG 57.068 29.630 0.00 0.00 35.91 3.34
2047 2178 9.894783 TTCGTTAAATTTATGGTCAAAATTCGA 57.105 25.926 0.00 0.00 35.91 3.71
2048 2179 9.332301 TCGTTAAATTTATGGTCAAAATTCGAC 57.668 29.630 0.00 0.37 35.91 4.20
2055 2186 2.088950 GTCAAAATTCGACCTCGGGA 57.911 50.000 0.00 0.00 40.29 5.14
2056 2187 2.419667 GTCAAAATTCGACCTCGGGAA 58.580 47.619 0.00 0.00 40.29 3.97
2057 2188 2.415512 GTCAAAATTCGACCTCGGGAAG 59.584 50.000 0.00 0.00 40.29 3.46
2058 2189 1.130561 CAAAATTCGACCTCGGGAAGC 59.869 52.381 0.00 0.00 40.29 3.86
2059 2190 0.323629 AAATTCGACCTCGGGAAGCA 59.676 50.000 0.00 0.00 40.29 3.91
2060 2191 0.391263 AATTCGACCTCGGGAAGCAC 60.391 55.000 0.00 0.00 40.29 4.40
2061 2192 2.558554 ATTCGACCTCGGGAAGCACG 62.559 60.000 0.00 0.00 40.29 5.34
2062 2193 4.796231 CGACCTCGGGAAGCACGG 62.796 72.222 0.00 0.00 35.37 4.94
2063 2194 4.452733 GACCTCGGGAAGCACGGG 62.453 72.222 0.00 0.00 0.00 5.28
2074 2205 4.043168 GCACGGGCGCACTATATT 57.957 55.556 8.62 0.00 0.00 1.28
2075 2206 2.317230 GCACGGGCGCACTATATTT 58.683 52.632 8.62 0.00 0.00 1.40
2076 2207 0.661020 GCACGGGCGCACTATATTTT 59.339 50.000 8.62 0.00 0.00 1.82
2077 2208 1.596954 GCACGGGCGCACTATATTTTG 60.597 52.381 8.62 0.00 0.00 2.44
2078 2209 1.937223 CACGGGCGCACTATATTTTGA 59.063 47.619 8.62 0.00 0.00 2.69
2079 2210 2.353269 CACGGGCGCACTATATTTTGAA 59.647 45.455 8.62 0.00 0.00 2.69
2080 2211 3.011119 ACGGGCGCACTATATTTTGAAA 58.989 40.909 8.62 0.00 0.00 2.69
2081 2212 3.630312 ACGGGCGCACTATATTTTGAAAT 59.370 39.130 8.62 0.00 0.00 2.17
2082 2213 3.974401 CGGGCGCACTATATTTTGAAATG 59.026 43.478 8.62 0.00 0.00 2.32
2083 2214 4.298332 GGGCGCACTATATTTTGAAATGG 58.702 43.478 10.83 0.00 0.00 3.16
2084 2215 4.037446 GGGCGCACTATATTTTGAAATGGA 59.963 41.667 10.83 0.00 0.00 3.41
2085 2216 5.215160 GGCGCACTATATTTTGAAATGGAG 58.785 41.667 10.83 0.06 0.00 3.86
2086 2217 5.215160 GCGCACTATATTTTGAAATGGAGG 58.785 41.667 0.30 0.00 0.00 4.30
2087 2218 5.762045 CGCACTATATTTTGAAATGGAGGG 58.238 41.667 0.00 0.00 0.00 4.30
2088 2219 5.530915 CGCACTATATTTTGAAATGGAGGGA 59.469 40.000 0.00 0.00 0.00 4.20
2089 2220 6.293626 CGCACTATATTTTGAAATGGAGGGAG 60.294 42.308 0.00 0.00 0.00 4.30
2090 2221 6.547510 GCACTATATTTTGAAATGGAGGGAGT 59.452 38.462 0.00 0.00 0.00 3.85
2091 2222 7.719633 GCACTATATTTTGAAATGGAGGGAGTA 59.280 37.037 0.00 0.00 0.00 2.59
2092 2223 9.627123 CACTATATTTTGAAATGGAGGGAGTAA 57.373 33.333 0.00 0.00 0.00 2.24
2142 2273 6.261381 AGCGAATAAACTTGTGTTTTGTAGGA 59.739 34.615 0.00 0.00 43.13 2.94
2251 2382 2.953648 CGGAAAAAGGGGTGTACTTTGT 59.046 45.455 0.00 0.00 38.13 2.83
2282 2413 6.518493 TCACAAGTACAATAACCTTCTTCGT 58.482 36.000 0.00 0.00 0.00 3.85
2369 2500 0.037590 AATCTACTTTGTGGGCCGCA 59.962 50.000 17.45 17.45 0.00 5.69
2370 2501 0.037590 ATCTACTTTGTGGGCCGCAA 59.962 50.000 27.77 27.77 31.73 4.85
2463 2594 2.359900 AGATGGTGCCGCTAAAAGAAG 58.640 47.619 0.00 0.00 0.00 2.85
2509 2641 7.715249 TGAGATAATGTAATGAGTAACCAAGGC 59.285 37.037 0.00 0.00 0.00 4.35
2523 2655 0.310854 CAAGGCGGTTGTGAAGAACC 59.689 55.000 0.00 0.00 41.89 3.62
2524 2656 0.106918 AAGGCGGTTGTGAAGAACCA 60.107 50.000 9.74 0.00 45.08 3.67
2620 2752 5.468072 AGTGGCTTATCATTTGAATAGCTCG 59.532 40.000 13.52 0.00 35.89 5.03
2729 2861 1.888512 GCATGGTTGAGGAGCTTTCAA 59.111 47.619 9.72 9.72 32.44 2.69
2808 2940 6.094742 TCAACAGTGCAAGAAAAAGTGTATCA 59.905 34.615 0.00 0.00 0.00 2.15
2987 3120 8.368668 GGGAGCATAATTCTACATGTAAGTACT 58.631 37.037 7.06 0.00 0.00 2.73
3002 3135 8.721478 CATGTAAGTACTGCAAAGTGTAGAAAT 58.279 33.333 0.00 0.00 34.09 2.17
3073 3206 1.474077 CTGGGCATGCAAAAGTAGTCC 59.526 52.381 21.36 8.46 0.00 3.85
3074 3207 0.817654 GGGCATGCAAAAGTAGTCCC 59.182 55.000 21.36 3.08 0.00 4.46
3082 3216 2.034179 GCAAAAGTAGTCCCGTGCTTTT 59.966 45.455 0.00 0.00 40.46 2.27
3113 3247 7.518052 CGTGTCAAATTTTGCACCATGTTAATT 60.518 33.333 20.73 0.00 35.63 1.40
3174 3308 8.660295 AGGCATTCATCAATGGTAATATCAAT 57.340 30.769 0.00 0.00 40.03 2.57
3240 3374 3.982516 TCCTGACAGAGTGTATAGGCTT 58.017 45.455 3.32 0.00 35.78 4.35
3275 3409 1.271597 TGGGCTCAAGAAAGCTCCTTC 60.272 52.381 0.00 0.00 42.41 3.46
3335 3470 1.271926 GGGCTTCAAACTAGGAGCCAA 60.272 52.381 14.74 0.00 43.60 4.52
3364 3499 6.409704 TCCACTCTCTTCACCAAATCTTATG 58.590 40.000 0.00 0.00 0.00 1.90
3564 3702 2.492088 GGAAAAATACCTCAAAGCCGCT 59.508 45.455 0.00 0.00 0.00 5.52
3692 3830 0.109132 GCTCCATTGGCTTTCCGTTG 60.109 55.000 0.00 0.00 34.14 4.10
3720 3858 2.102578 GTGCATCTAGGCCCAACATTT 58.897 47.619 0.00 0.00 0.00 2.32
3729 3867 3.773560 AGGCCCAACATTTTGCTTAGTA 58.226 40.909 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.895798 TGCCAGTCTGACTAAGGAGTG 59.104 52.381 16.10 1.87 35.45 3.51
49 57 2.038033 CGAGACTTAAACCCAGGTGGAA 59.962 50.000 0.00 0.00 37.39 3.53
56 64 3.194968 GGAGATGACGAGACTTAAACCCA 59.805 47.826 0.00 0.00 0.00 4.51
231 248 1.697432 AGCAACTTACACCTGCCTACA 59.303 47.619 0.00 0.00 36.73 2.74
257 274 2.408565 AGGTTCTCTCAGGACAAACCA 58.591 47.619 5.47 0.00 41.46 3.67
263 280 3.134458 CAACACAAGGTTCTCTCAGGAC 58.866 50.000 0.00 0.00 37.72 3.85
370 387 2.972713 AGTACAACAAAGGCAGAGGAGA 59.027 45.455 0.00 0.00 0.00 3.71
371 388 3.409026 AGTACAACAAAGGCAGAGGAG 57.591 47.619 0.00 0.00 0.00 3.69
493 517 8.268850 ACATTCACTCACAGGAAAATACATAC 57.731 34.615 0.00 0.00 0.00 2.39
516 540 3.671008 TGCTCTTAGGCGTTTCTTACA 57.329 42.857 0.00 0.00 34.52 2.41
547 571 4.825085 TCCAGGAAACCAGTTTTACATCAC 59.175 41.667 0.00 0.00 28.97 3.06
665 692 4.119862 GCACCCAAAAAGGAAGAAAGAAC 58.880 43.478 0.00 0.00 41.22 3.01
685 712 1.944709 CATTGGCTTGATCAGATCGCA 59.055 47.619 11.19 0.00 0.00 5.10
737 790 0.991146 TGGAGGCTGATTAGTTGGCA 59.009 50.000 0.00 0.00 0.00 4.92
850 939 9.583765 AACTCAGGTTATAACGAAACTAGAATC 57.416 33.333 9.46 0.00 33.39 2.52
851 940 9.367444 CAACTCAGGTTATAACGAAACTAGAAT 57.633 33.333 9.46 0.00 33.88 2.40
933 1022 1.672881 GGATCTTGGGTTCTTGATGCG 59.327 52.381 0.00 0.00 0.00 4.73
964 1057 1.452651 CATCCATGGCTTCCGCAGT 60.453 57.895 6.96 0.00 38.10 4.40
966 1059 0.535780 GATCATCCATGGCTTCCGCA 60.536 55.000 6.96 0.00 38.10 5.69
1039 1132 2.124983 CGAGTGTGGCAGGGGATG 60.125 66.667 0.00 0.00 0.00 3.51
1040 1133 3.402681 CCGAGTGTGGCAGGGGAT 61.403 66.667 0.00 0.00 0.00 3.85
1041 1134 4.954118 ACCGAGTGTGGCAGGGGA 62.954 66.667 0.00 0.00 0.00 4.81
1086 1179 3.887335 GAACCGTGGCCGCCAGTAA 62.887 63.158 13.92 0.00 32.34 2.24
1168 1264 3.434309 GAGTTGTACCCCCGGCTATATA 58.566 50.000 0.00 0.00 0.00 0.86
1169 1265 2.254508 GAGTTGTACCCCCGGCTATAT 58.745 52.381 0.00 0.00 0.00 0.86
1339 1435 1.004918 AGCAACACCTCGTAGCCAC 60.005 57.895 0.00 0.00 0.00 5.01
1447 1543 3.657610 TCATCTTGGCCCTCATTCTCTA 58.342 45.455 0.00 0.00 0.00 2.43
1477 1573 3.922171 AGTCATCCATGGAAGGTTCTC 57.078 47.619 20.67 5.53 0.00 2.87
1490 1598 2.474526 CGTCAAACGATGCAAGTCATCC 60.475 50.000 0.00 0.00 46.93 3.51
1522 1630 1.672356 GGCAGCGTCCATTGTGACT 60.672 57.895 0.00 0.00 32.97 3.41
1667 1775 2.540515 CCTCGCCAATACACACTGTAG 58.459 52.381 0.00 0.00 36.14 2.74
1841 1972 9.686136 ATGGAATGGATGGAGTATAGATGATAT 57.314 33.333 0.00 0.00 0.00 1.63
1845 1976 9.557061 CATTATGGAATGGATGGAGTATAGATG 57.443 37.037 0.00 0.00 39.10 2.90
1846 1977 9.289049 ACATTATGGAATGGATGGAGTATAGAT 57.711 33.333 0.00 0.00 45.83 1.98
1847 1978 8.685257 ACATTATGGAATGGATGGAGTATAGA 57.315 34.615 0.00 0.00 45.83 1.98
1849 1980 9.560860 ACTACATTATGGAATGGATGGAGTATA 57.439 33.333 0.00 0.00 45.83 1.47
1850 1981 8.324306 CACTACATTATGGAATGGATGGAGTAT 58.676 37.037 0.15 0.00 45.83 2.12
1855 1986 5.319453 AGCACTACATTATGGAATGGATGG 58.681 41.667 0.00 0.00 45.83 3.51
1857 1988 6.006449 GGAAGCACTACATTATGGAATGGAT 58.994 40.000 0.00 0.00 45.83 3.41
1858 1989 5.132648 AGGAAGCACTACATTATGGAATGGA 59.867 40.000 0.00 0.00 45.83 3.41
1859 1990 5.380043 AGGAAGCACTACATTATGGAATGG 58.620 41.667 0.00 0.00 45.83 3.16
1860 1991 6.294473 AGAGGAAGCACTACATTATGGAATG 58.706 40.000 0.00 0.00 46.77 2.67
1861 1992 6.506538 AGAGGAAGCACTACATTATGGAAT 57.493 37.500 0.00 0.00 0.00 3.01
1862 1993 5.957771 AGAGGAAGCACTACATTATGGAA 57.042 39.130 0.00 0.00 0.00 3.53
1863 1994 6.211584 GGATAGAGGAAGCACTACATTATGGA 59.788 42.308 0.00 0.00 0.00 3.41
1864 1995 6.402222 GGATAGAGGAAGCACTACATTATGG 58.598 44.000 0.00 0.00 0.00 2.74
1865 1996 6.402222 GGGATAGAGGAAGCACTACATTATG 58.598 44.000 0.00 0.00 0.00 1.90
1866 1997 5.485708 GGGGATAGAGGAAGCACTACATTAT 59.514 44.000 0.00 0.00 0.00 1.28
1867 1998 4.838986 GGGGATAGAGGAAGCACTACATTA 59.161 45.833 0.00 0.00 0.00 1.90
1868 1999 3.648545 GGGGATAGAGGAAGCACTACATT 59.351 47.826 0.00 0.00 0.00 2.71
1869 2000 3.243724 GGGGATAGAGGAAGCACTACAT 58.756 50.000 0.00 0.00 0.00 2.29
1870 2001 2.679082 GGGGATAGAGGAAGCACTACA 58.321 52.381 0.00 0.00 0.00 2.74
1871 2002 1.614413 CGGGGATAGAGGAAGCACTAC 59.386 57.143 0.00 0.00 0.00 2.73
1872 2003 1.217183 ACGGGGATAGAGGAAGCACTA 59.783 52.381 0.00 0.00 0.00 2.74
1873 2004 0.032017 ACGGGGATAGAGGAAGCACT 60.032 55.000 0.00 0.00 0.00 4.40
1874 2005 0.105039 CACGGGGATAGAGGAAGCAC 59.895 60.000 0.00 0.00 0.00 4.40
1875 2006 1.686325 GCACGGGGATAGAGGAAGCA 61.686 60.000 0.00 0.00 0.00 3.91
1876 2007 1.069935 GCACGGGGATAGAGGAAGC 59.930 63.158 0.00 0.00 0.00 3.86
1877 2008 1.069358 GAAGCACGGGGATAGAGGAAG 59.931 57.143 0.00 0.00 0.00 3.46
1878 2009 1.120530 GAAGCACGGGGATAGAGGAA 58.879 55.000 0.00 0.00 0.00 3.36
1879 2010 0.032515 TGAAGCACGGGGATAGAGGA 60.033 55.000 0.00 0.00 0.00 3.71
1880 2011 0.830648 TTGAAGCACGGGGATAGAGG 59.169 55.000 0.00 0.00 0.00 3.69
1881 2012 1.482593 AGTTGAAGCACGGGGATAGAG 59.517 52.381 0.00 0.00 0.00 2.43
1882 2013 1.568504 AGTTGAAGCACGGGGATAGA 58.431 50.000 0.00 0.00 0.00 1.98
1883 2014 2.403252 AAGTTGAAGCACGGGGATAG 57.597 50.000 0.00 0.00 0.00 2.08
1884 2015 2.039216 TCAAAGTTGAAGCACGGGGATA 59.961 45.455 0.00 0.00 33.55 2.59
1885 2016 1.202879 TCAAAGTTGAAGCACGGGGAT 60.203 47.619 0.00 0.00 33.55 3.85
1886 2017 0.181587 TCAAAGTTGAAGCACGGGGA 59.818 50.000 0.00 0.00 33.55 4.81
1887 2018 0.310854 GTCAAAGTTGAAGCACGGGG 59.689 55.000 0.00 0.00 39.21 5.73
1888 2019 0.310854 GGTCAAAGTTGAAGCACGGG 59.689 55.000 0.00 0.00 39.21 5.28
1889 2020 0.041312 CGGTCAAAGTTGAAGCACGG 60.041 55.000 0.00 0.00 39.21 4.94
1890 2021 0.655733 ACGGTCAAAGTTGAAGCACG 59.344 50.000 0.00 2.00 39.21 5.34
1891 2022 3.955771 TTACGGTCAAAGTTGAAGCAC 57.044 42.857 0.00 0.00 39.21 4.40
1892 2023 5.508200 AATTTACGGTCAAAGTTGAAGCA 57.492 34.783 0.00 0.00 39.21 3.91
1893 2024 7.646526 AGTTAAATTTACGGTCAAAGTTGAAGC 59.353 33.333 0.00 0.00 39.21 3.86
1903 2034 9.027129 CGATCTTGATAGTTAAATTTACGGTCA 57.973 33.333 0.00 0.00 0.00 4.02
1904 2035 9.241317 TCGATCTTGATAGTTAAATTTACGGTC 57.759 33.333 0.00 0.00 0.00 4.79
1905 2036 9.760077 ATCGATCTTGATAGTTAAATTTACGGT 57.240 29.630 0.00 0.00 0.00 4.83
1910 2041 8.070171 CCGCAATCGATCTTGATAGTTAAATTT 58.930 33.333 0.00 0.00 38.10 1.82
1911 2042 7.576236 CCGCAATCGATCTTGATAGTTAAATT 58.424 34.615 0.00 0.00 38.10 1.82
1912 2043 6.347725 GCCGCAATCGATCTTGATAGTTAAAT 60.348 38.462 0.00 0.00 38.10 1.40
1913 2044 5.050363 GCCGCAATCGATCTTGATAGTTAAA 60.050 40.000 0.00 0.00 38.10 1.52
1914 2045 4.447724 GCCGCAATCGATCTTGATAGTTAA 59.552 41.667 0.00 0.00 38.10 2.01
1915 2046 3.987868 GCCGCAATCGATCTTGATAGTTA 59.012 43.478 0.00 0.00 38.10 2.24
1916 2047 2.802816 GCCGCAATCGATCTTGATAGTT 59.197 45.455 0.00 0.00 38.10 2.24
1917 2048 2.408050 GCCGCAATCGATCTTGATAGT 58.592 47.619 0.00 0.00 38.10 2.12
1918 2049 1.388093 CGCCGCAATCGATCTTGATAG 59.612 52.381 0.00 0.00 38.10 2.08
1919 2050 1.418373 CGCCGCAATCGATCTTGATA 58.582 50.000 0.00 0.00 38.10 2.15
1920 2051 1.224069 CCGCCGCAATCGATCTTGAT 61.224 55.000 0.00 0.00 38.10 2.57
1921 2052 1.882625 CCGCCGCAATCGATCTTGA 60.883 57.895 0.00 0.00 38.10 3.02
1922 2053 2.628106 CCGCCGCAATCGATCTTG 59.372 61.111 0.00 0.00 38.10 3.02
1923 2054 2.588877 CCCGCCGCAATCGATCTT 60.589 61.111 0.00 0.00 38.10 2.40
1924 2055 3.506059 CTCCCGCCGCAATCGATCT 62.506 63.158 0.00 0.00 38.10 2.75
1925 2056 3.038417 CTCCCGCCGCAATCGATC 61.038 66.667 0.00 0.00 38.10 3.69
1929 2060 2.872337 CTTTTGCTCCCGCCGCAATC 62.872 60.000 5.33 0.00 45.67 2.67
1930 2061 2.988684 TTTTGCTCCCGCCGCAAT 60.989 55.556 5.33 0.00 45.67 3.56
1931 2062 3.669344 CTTTTGCTCCCGCCGCAA 61.669 61.111 0.00 0.00 44.83 4.85
1932 2063 4.887932 TATAACTTTTGCTCCCGCCGCA 62.888 50.000 0.00 0.00 35.22 5.69
1933 2064 1.654023 ATAACTTTTGCTCCCGCCGC 61.654 55.000 0.00 0.00 34.43 6.53
1934 2065 1.658994 TATAACTTTTGCTCCCGCCG 58.341 50.000 0.00 0.00 34.43 6.46
1935 2066 3.211045 TGATATAACTTTTGCTCCCGCC 58.789 45.455 0.00 0.00 34.43 6.13
1936 2067 3.877508 ACTGATATAACTTTTGCTCCCGC 59.122 43.478 0.00 0.00 0.00 6.13
1937 2068 5.116180 TCACTGATATAACTTTTGCTCCCG 58.884 41.667 0.00 0.00 0.00 5.14
1938 2069 7.573968 ATTCACTGATATAACTTTTGCTCCC 57.426 36.000 0.00 0.00 0.00 4.30
1939 2070 7.852945 CGAATTCACTGATATAACTTTTGCTCC 59.147 37.037 6.22 0.00 0.00 4.70
1940 2071 8.391106 ACGAATTCACTGATATAACTTTTGCTC 58.609 33.333 6.22 0.00 0.00 4.26
1941 2072 8.268850 ACGAATTCACTGATATAACTTTTGCT 57.731 30.769 6.22 0.00 0.00 3.91
1946 2077 9.961265 TCGAATACGAATTCACTGATATAACTT 57.039 29.630 6.22 0.00 45.74 2.66
1982 2113 8.776470 CGGCGGGAGAAAAAGTTATATAATTAA 58.224 33.333 0.00 0.00 0.00 1.40
1983 2114 7.095102 GCGGCGGGAGAAAAAGTTATATAATTA 60.095 37.037 9.78 0.00 0.00 1.40
1984 2115 6.293790 GCGGCGGGAGAAAAAGTTATATAATT 60.294 38.462 9.78 0.00 0.00 1.40
1985 2116 5.180680 GCGGCGGGAGAAAAAGTTATATAAT 59.819 40.000 9.78 0.00 0.00 1.28
1986 2117 4.512571 GCGGCGGGAGAAAAAGTTATATAA 59.487 41.667 9.78 0.00 0.00 0.98
1987 2118 4.060205 GCGGCGGGAGAAAAAGTTATATA 58.940 43.478 9.78 0.00 0.00 0.86
1988 2119 2.876550 GCGGCGGGAGAAAAAGTTATAT 59.123 45.455 9.78 0.00 0.00 0.86
1989 2120 2.282407 GCGGCGGGAGAAAAAGTTATA 58.718 47.619 9.78 0.00 0.00 0.98
1990 2121 1.092348 GCGGCGGGAGAAAAAGTTAT 58.908 50.000 9.78 0.00 0.00 1.89
1991 2122 0.250381 TGCGGCGGGAGAAAAAGTTA 60.250 50.000 9.78 0.00 0.00 2.24
1992 2123 1.515521 CTGCGGCGGGAGAAAAAGTT 61.516 55.000 9.78 0.00 32.53 2.66
1993 2124 1.966451 CTGCGGCGGGAGAAAAAGT 60.966 57.895 9.78 0.00 32.53 2.66
1994 2125 1.912371 GACTGCGGCGGGAGAAAAAG 61.912 60.000 19.55 0.00 35.29 2.27
1995 2126 1.964373 GACTGCGGCGGGAGAAAAA 60.964 57.895 19.55 0.00 35.29 1.94
1996 2127 2.358247 GACTGCGGCGGGAGAAAA 60.358 61.111 19.55 0.00 35.29 2.29
1997 2128 4.735132 CGACTGCGGCGGGAGAAA 62.735 66.667 19.55 0.00 35.29 2.52
2007 2138 2.870161 CGAACGAGACCGACTGCG 60.870 66.667 0.00 0.00 39.50 5.18
2008 2139 0.110056 TAACGAACGAGACCGACTGC 60.110 55.000 0.14 0.00 39.50 4.40
2009 2140 2.320805 TTAACGAACGAGACCGACTG 57.679 50.000 0.14 0.00 39.50 3.51
2010 2141 3.565905 ATTTAACGAACGAGACCGACT 57.434 42.857 0.14 0.00 39.50 4.18
2011 2142 4.635961 AAATTTAACGAACGAGACCGAC 57.364 40.909 0.14 0.00 39.50 4.79
2012 2143 5.289193 CCATAAATTTAACGAACGAGACCGA 59.711 40.000 1.21 0.00 39.50 4.69
2013 2144 5.062558 ACCATAAATTTAACGAACGAGACCG 59.937 40.000 1.21 0.00 42.50 4.79
2014 2145 6.091169 TGACCATAAATTTAACGAACGAGACC 59.909 38.462 1.21 0.00 0.00 3.85
2015 2146 7.052565 TGACCATAAATTTAACGAACGAGAC 57.947 36.000 1.21 0.00 0.00 3.36
2016 2147 7.655236 TTGACCATAAATTTAACGAACGAGA 57.345 32.000 1.21 0.00 0.00 4.04
2017 2148 8.716619 TTTTGACCATAAATTTAACGAACGAG 57.283 30.769 1.21 0.00 0.00 4.18
2018 2149 9.680315 AATTTTGACCATAAATTTAACGAACGA 57.320 25.926 1.21 0.00 32.75 3.85
2019 2150 9.931710 GAATTTTGACCATAAATTTAACGAACG 57.068 29.630 1.21 0.00 35.83 3.95
2020 2151 9.931710 CGAATTTTGACCATAAATTTAACGAAC 57.068 29.630 1.21 0.00 35.83 3.95
2021 2152 9.894783 TCGAATTTTGACCATAAATTTAACGAA 57.105 25.926 1.21 0.00 35.83 3.85
2022 2153 9.332301 GTCGAATTTTGACCATAAATTTAACGA 57.668 29.630 1.21 0.00 35.83 3.85
2036 2167 2.088950 TCCCGAGGTCGAATTTTGAC 57.911 50.000 8.09 8.09 43.02 3.18
2037 2168 2.695359 CTTCCCGAGGTCGAATTTTGA 58.305 47.619 0.00 0.00 43.02 2.69
2038 2169 1.130561 GCTTCCCGAGGTCGAATTTTG 59.869 52.381 0.00 0.00 43.02 2.44
2039 2170 1.271163 TGCTTCCCGAGGTCGAATTTT 60.271 47.619 0.00 0.00 43.02 1.82
2040 2171 0.323629 TGCTTCCCGAGGTCGAATTT 59.676 50.000 0.00 0.00 43.02 1.82
2041 2172 0.391263 GTGCTTCCCGAGGTCGAATT 60.391 55.000 0.00 0.00 43.02 2.17
2042 2173 1.218316 GTGCTTCCCGAGGTCGAAT 59.782 57.895 0.00 0.00 43.02 3.34
2043 2174 2.654877 GTGCTTCCCGAGGTCGAA 59.345 61.111 0.00 0.00 43.02 3.71
2044 2175 3.744719 CGTGCTTCCCGAGGTCGA 61.745 66.667 0.00 0.00 43.02 4.20
2045 2176 4.796231 CCGTGCTTCCCGAGGTCG 62.796 72.222 0.00 0.00 39.44 4.79
2046 2177 4.452733 CCCGTGCTTCCCGAGGTC 62.453 72.222 0.00 0.00 0.00 3.85
2053 2184 2.638330 TATAGTGCGCCCGTGCTTCC 62.638 60.000 4.18 0.00 35.36 3.46
2054 2185 0.600255 ATATAGTGCGCCCGTGCTTC 60.600 55.000 4.18 0.00 35.36 3.86
2055 2186 0.179056 AATATAGTGCGCCCGTGCTT 60.179 50.000 4.18 0.00 35.36 3.91
2056 2187 0.179056 AAATATAGTGCGCCCGTGCT 60.179 50.000 4.18 0.00 35.36 4.40
2057 2188 0.661020 AAAATATAGTGCGCCCGTGC 59.339 50.000 4.18 0.00 0.00 5.34
2058 2189 1.937223 TCAAAATATAGTGCGCCCGTG 59.063 47.619 4.18 0.00 0.00 4.94
2059 2190 2.319136 TCAAAATATAGTGCGCCCGT 57.681 45.000 4.18 0.00 0.00 5.28
2060 2191 3.684103 TTTCAAAATATAGTGCGCCCG 57.316 42.857 4.18 0.00 0.00 6.13
2061 2192 4.037446 TCCATTTCAAAATATAGTGCGCCC 59.963 41.667 4.18 0.00 0.00 6.13
2062 2193 5.181690 TCCATTTCAAAATATAGTGCGCC 57.818 39.130 4.18 0.00 0.00 6.53
2063 2194 5.215160 CCTCCATTTCAAAATATAGTGCGC 58.785 41.667 0.00 0.00 0.00 6.09
2064 2195 5.530915 TCCCTCCATTTCAAAATATAGTGCG 59.469 40.000 0.00 0.00 0.00 5.34
2065 2196 6.547510 ACTCCCTCCATTTCAAAATATAGTGC 59.452 38.462 0.00 0.00 0.00 4.40
2066 2197 9.627123 TTACTCCCTCCATTTCAAAATATAGTG 57.373 33.333 0.00 0.00 0.00 2.74
2076 2207 9.847224 GTCTAAAATATTACTCCCTCCATTTCA 57.153 33.333 0.00 0.00 0.00 2.69
2112 2243 9.308318 ACAAAACACAAGTTTATTCGCTAAAAT 57.692 25.926 0.00 0.00 46.79 1.82
2251 2382 8.458573 AAGGTTATTGTACTTGTGAATTGTCA 57.541 30.769 0.00 0.00 0.00 3.58
2270 2401 3.878699 GGTTCCAAACACGAAGAAGGTTA 59.121 43.478 0.00 0.00 0.00 2.85
2282 2413 4.163441 TGATTCACTGAGGTTCCAAACA 57.837 40.909 0.00 0.00 0.00 2.83
2463 2594 6.459066 TCTCATCGGAGTTCCATTCAATATC 58.541 40.000 0.00 0.00 42.05 1.63
2523 2655 6.094881 ACCCAAGAAATAAATGTGACCGTATG 59.905 38.462 0.00 0.00 0.00 2.39
2524 2656 6.184789 ACCCAAGAAATAAATGTGACCGTAT 58.815 36.000 0.00 0.00 0.00 3.06
2620 2752 5.001874 AGTTTTCCGAGGTATTGGACTTTC 58.998 41.667 0.00 0.00 38.85 2.62
2707 2839 2.097825 GAAAGCTCCTCAACCATGCAT 58.902 47.619 0.00 0.00 0.00 3.96
2729 2861 5.538813 TGCGTACATATTATGGAGGAGTCTT 59.461 40.000 11.86 0.00 30.63 3.01
2808 2940 7.606456 TGGCTGAAAATAAGACTCGAACTTTAT 59.394 33.333 9.27 0.77 0.00 1.40
2987 3120 9.325198 CCAGTACATATATTTCTACACTTTGCA 57.675 33.333 0.00 0.00 0.00 4.08
3031 3164 2.107141 GATCGAAGAGCGTGGGGG 59.893 66.667 0.00 0.00 43.63 5.40
3073 3206 3.529634 TGACACGATTTAAAAGCACGG 57.470 42.857 0.00 0.00 0.00 4.94
3074 3207 6.432802 AATTTGACACGATTTAAAAGCACG 57.567 33.333 0.00 0.00 0.00 5.34
3082 3216 5.592054 TGGTGCAAAATTTGACACGATTTA 58.408 33.333 10.26 1.07 38.04 1.40
3136 3270 3.391965 TGAATGCCTTTTCACATGCAAC 58.608 40.909 0.00 0.00 37.27 4.17
3174 3308 5.298276 GGGTTGTTTGACACATAGTTCTTCA 59.702 40.000 0.00 0.00 34.43 3.02
3240 3374 3.073798 TGAGCCCATAAAGGACTTTGTGA 59.926 43.478 19.06 0.86 42.04 3.58
3275 3409 5.664457 TCTTGAGTGTATCATACCAAGCTG 58.336 41.667 7.19 0.00 37.89 4.24
3335 3470 4.916041 TTGGTGAAGAGAGTGGAATCAT 57.084 40.909 0.00 0.00 0.00 2.45
3434 3570 9.809096 TTCGGCTATTAATTTGCAAATTATTCA 57.191 25.926 33.89 24.09 39.73 2.57
3470 3608 3.882102 TTAGTTCCCCCATCATGGATG 57.118 47.619 4.75 0.00 40.96 3.51
3471 3609 4.898014 TTTTAGTTCCCCCATCATGGAT 57.102 40.909 4.75 0.00 40.96 3.41
3512 3650 8.960591 AGATAAAGATGTCATTCCGTTTTTGAT 58.039 29.630 0.00 0.00 0.00 2.57
3517 3655 7.331026 TGAGAGATAAAGATGTCATTCCGTTT 58.669 34.615 0.00 0.00 0.00 3.60
3564 3702 8.838365 CCAATTTTCCATGAAACATTTCTTCAA 58.162 29.630 5.97 0.00 36.43 2.69
3692 3830 2.548920 GGGCCTAGATGCACACAGATAC 60.549 54.545 0.84 0.00 33.82 2.24


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

AutoCloner maintained by Alex Coulton.