Multiple sequence alignment - TraesCS2B01G397000

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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 TraesCS2B01G397000 chr2B 100.000 2537 0 0 1 2537 563678053 563680589 0.000000e+00 4686.0
1 TraesCS2B01G397000 chr2A 90.200 2051 132 26 11 2009 623151417 623153450 0.000000e+00 2610.0
2 TraesCS2B01G397000 chr2A 88.496 113 5 3 2417 2525 623153816 623153924 2.050000e-26 130.0
3 TraesCS2B01G397000 chr2D 89.725 1382 65 34 669 2009 480573581 480574926 0.000000e+00 1694.0
4 TraesCS2B01G397000 chr2D 85.910 511 49 12 11 502 480568088 480568594 8.040000e-145 523.0
5 TraesCS2B01G397000 chr2D 87.097 93 8 1 2417 2509 480575505 480575593 4.470000e-18 102.0
6 TraesCS2B01G397000 chr6B 84.375 96 9 4 1389 1478 466967550 466967645 3.480000e-14 89.8


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 TraesCS2B01G397000 chr2B 563678053 563680589 2536 False 4686 4686 100.000 1 2537 1 chr2B.!!$F1 2536
1 TraesCS2B01G397000 chr2A 623151417 623153924 2507 False 1370 2610 89.348 11 2525 2 chr2A.!!$F1 2514
2 TraesCS2B01G397000 chr2D 480573581 480575593 2012 False 898 1694 88.411 669 2509 2 chr2D.!!$F2 1840
3 TraesCS2B01G397000 chr2D 480568088 480568594 506 False 523 523 85.910 11 502 1 chr2D.!!$F1 491

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
133 142 0.366871 CGAGATGTTTTGGAGCGACG 59.633 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2152 0.107897 TTGATAACGCGATGCAGGGT 60.108 50.0 15.93 0.0 39.03 4.34 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
38 39 7.383572 TGGTGTGTACATATTTTGTTCATTTGC 59.616 33.333 0.00 0.00 37.84 3.68
42 43 8.977505 GTGTACATATTTTGTTCATTTGCTTGT 58.022 29.630 0.00 0.00 37.84 3.16
56 57 2.556257 TGCTTGTGTGTTTTAGCTCGA 58.444 42.857 0.00 0.00 34.77 4.04
70 71 2.018544 CTCGAAAAACACCGCCACA 58.981 52.632 0.00 0.00 0.00 4.17
73 74 0.591170 CGAAAAACACCGCCACAGAT 59.409 50.000 0.00 0.00 0.00 2.90
133 142 0.366871 CGAGATGTTTTGGAGCGACG 59.633 55.000 0.00 0.00 0.00 5.12
134 143 1.710013 GAGATGTTTTGGAGCGACGA 58.290 50.000 0.00 0.00 0.00 4.20
168 177 4.034626 CACACAATTCCGTAATATTGGCGA 59.965 41.667 13.46 0.00 36.34 5.54
195 204 2.939103 GCTATGTCAAGGTTAGTGGCAG 59.061 50.000 0.00 0.00 33.33 4.85
223 232 9.465166 ATGATCATTCATTGGCATTGTGCAAGA 62.465 37.037 1.18 3.28 41.70 3.02
271 282 2.281484 GGCGGTGTTTGAGGCAGA 60.281 61.111 0.00 0.00 0.00 4.26
295 306 1.338107 TATGTCGGCCCTTCGATCAT 58.662 50.000 0.00 0.91 41.40 2.45
313 324 1.839994 CATCCATGTCCACCTACACCT 59.160 52.381 0.00 0.00 30.75 4.00
318 338 3.008594 CCATGTCCACCTACACCTTGTAA 59.991 47.826 0.00 0.00 31.67 2.41
369 389 1.078497 TGGCATGTGTCATCGACCC 60.078 57.895 0.00 0.00 0.00 4.46
371 391 1.447838 GCATGTGTCATCGACCCGT 60.448 57.895 0.00 0.00 0.00 5.28
457 477 5.906113 ACCACACAATGTTCACAAGTTTA 57.094 34.783 0.00 0.00 0.00 2.01
475 495 6.952773 AGTTTACTAAAATTGCCACACTCA 57.047 33.333 0.00 0.00 0.00 3.41
514 534 6.968263 TTGTTTTAGTCCATTCCATGACAA 57.032 33.333 0.00 0.00 0.00 3.18
523 543 6.153340 AGTCCATTCCATGACAAGTAATTTGG 59.847 38.462 0.00 0.00 41.25 3.28
524 544 6.015918 TCCATTCCATGACAAGTAATTTGGT 58.984 36.000 0.00 0.00 41.25 3.67
526 546 7.122055 TCCATTCCATGACAAGTAATTTGGTAC 59.878 37.037 0.00 0.00 41.25 3.34
531 551 5.471556 TGACAAGTAATTTGGTACGGAGA 57.528 39.130 0.00 0.00 41.25 3.71
532 552 6.045072 TGACAAGTAATTTGGTACGGAGAT 57.955 37.500 0.00 0.00 41.25 2.75
533 553 5.872617 TGACAAGTAATTTGGTACGGAGATG 59.127 40.000 0.00 0.00 41.25 2.90
539 559 8.431910 AGTAATTTGGTACGGAGATGGTATAT 57.568 34.615 0.00 0.00 0.00 0.86
563 583 8.931385 ATGTTTCCTACAAATCAAATGCATAC 57.069 30.769 0.00 0.00 40.89 2.39
564 584 8.121305 TGTTTCCTACAAATCAAATGCATACT 57.879 30.769 0.00 0.00 32.64 2.12
565 585 8.028354 TGTTTCCTACAAATCAAATGCATACTG 58.972 33.333 0.00 0.35 32.64 2.74
596 616 9.492730 AACTTTCCTTTGGGTCATATTCATTAT 57.507 29.630 0.00 0.00 0.00 1.28
624 644 4.009675 TCTCATGAAAATCCTCCAAACCG 58.990 43.478 0.00 0.00 0.00 4.44
632 652 1.675641 CCTCCAAACCGAGGCCTTG 60.676 63.158 13.75 13.75 43.01 3.61
654 674 6.916360 TGGAGAAATGCAATTAAAAGGTCT 57.084 33.333 0.00 0.00 33.67 3.85
794 814 1.405821 CGAGGCTAGAACCGTCATTCT 59.594 52.381 0.00 0.00 41.81 2.40
857 883 4.468689 GGACCCGCACACTAGGCC 62.469 72.222 0.00 0.00 0.00 5.19
1128 1168 3.450115 GAGTCGGACGTCTGGGGG 61.450 72.222 23.78 4.85 0.00 5.40
1137 1177 3.308705 GTCTGGGGGTCGTTCGGT 61.309 66.667 0.00 0.00 0.00 4.69
1627 1681 0.392336 AGGCCTGAAGCGAGATCATC 59.608 55.000 3.11 0.00 45.17 2.92
1632 1686 3.856638 GCCTGAAGCGAGATCATCACTAG 60.857 52.174 0.00 0.00 0.00 2.57
1633 1687 3.307674 CTGAAGCGAGATCATCACTAGC 58.692 50.000 0.00 0.00 36.53 3.42
1642 1696 6.190264 CGAGATCATCACTAGCAATTGTTTG 58.810 40.000 7.40 4.70 35.85 2.93
1643 1697 6.183360 CGAGATCATCACTAGCAATTGTTTGT 60.183 38.462 7.40 5.40 35.17 2.83
1701 1755 0.997196 GCAAACCGTAGTAGCGAAGG 59.003 55.000 0.00 0.00 0.00 3.46
1751 1813 1.206578 GTGTTCGTTCATGGCGTGG 59.793 57.895 6.90 0.00 0.00 4.94
1765 1827 1.531739 GCGTGGCAAATTTCAGGGGA 61.532 55.000 0.00 0.00 0.00 4.81
1767 1829 1.342819 CGTGGCAAATTTCAGGGGAAA 59.657 47.619 0.00 0.00 46.36 3.13
1768 1830 2.224161 CGTGGCAAATTTCAGGGGAAAA 60.224 45.455 0.00 0.00 45.52 2.29
1769 1831 3.402110 GTGGCAAATTTCAGGGGAAAAG 58.598 45.455 0.00 0.00 45.52 2.27
1789 1865 0.400594 GCTAGGTTGGTTGGTCAGGT 59.599 55.000 0.00 0.00 0.00 4.00
1814 1890 3.717404 CGGCGTGCGTATTTTATTTCTTC 59.283 43.478 0.00 0.00 0.00 2.87
1821 1897 7.238571 GTGCGTATTTTATTTCTTCCTTTCGA 58.761 34.615 0.00 0.00 0.00 3.71
1828 1904 7.859325 TTTATTTCTTCCTTTCGAGTATGGG 57.141 36.000 0.00 0.00 0.00 4.00
1829 1905 4.903045 TTTCTTCCTTTCGAGTATGGGT 57.097 40.909 0.00 0.00 0.00 4.51
1830 1906 6.555463 ATTTCTTCCTTTCGAGTATGGGTA 57.445 37.500 0.00 0.00 0.00 3.69
1833 1909 4.643784 TCTTCCTTTCGAGTATGGGTAGTC 59.356 45.833 0.00 0.00 0.00 2.59
1866 1942 0.593128 GTGGGCTGTACTGCTGTTTG 59.407 55.000 22.05 0.00 0.00 2.93
1869 1945 0.040067 GGCTGTACTGCTGTTTGTGC 60.040 55.000 22.05 2.26 0.00 4.57
1880 1956 1.585002 GTTTGTGCGCGAAGTTGCA 60.585 52.632 12.10 0.00 38.55 4.08
1905 1981 3.505293 ACAGAGAAGAAATGCTTGCCTTC 59.495 43.478 0.00 0.00 36.83 3.46
1906 1982 2.746362 AGAGAAGAAATGCTTGCCTTCG 59.254 45.455 0.00 0.00 39.78 3.79
1907 1983 1.200948 AGAAGAAATGCTTGCCTTCGC 59.799 47.619 0.00 0.00 39.78 4.70
1908 1984 0.244721 AAGAAATGCTTGCCTTCGCC 59.755 50.000 0.00 0.00 34.93 5.54
1909 1985 1.514873 GAAATGCTTGCCTTCGCCG 60.515 57.895 0.00 0.00 0.00 6.46
1926 2002 4.464262 GGCCATCCCGTTCTCATC 57.536 61.111 0.00 0.00 0.00 2.92
1932 2008 3.557898 GCCATCCCGTTCTCATCATACAT 60.558 47.826 0.00 0.00 0.00 2.29
1960 2037 9.506018 AGCATAAATGGTAAAGAAATTGCTTTT 57.494 25.926 16.68 0.51 38.85 2.27
1980 2057 5.814764 TTTTGTTGAGCGTTACACCTTTA 57.185 34.783 0.00 0.00 0.00 1.85
1992 2069 6.566942 GCGTTACACCTTTATGATGTGACAAA 60.567 38.462 0.00 0.00 33.67 2.83
2029 2106 3.936902 TGTTAGAAACAACACAGACGC 57.063 42.857 0.00 0.00 38.72 5.19
2030 2107 3.527533 TGTTAGAAACAACACAGACGCT 58.472 40.909 0.00 0.00 38.72 5.07
2031 2108 3.554324 TGTTAGAAACAACACAGACGCTC 59.446 43.478 0.00 0.00 38.72 5.03
2032 2109 2.309528 AGAAACAACACAGACGCTCA 57.690 45.000 0.00 0.00 0.00 4.26
2033 2110 2.838736 AGAAACAACACAGACGCTCAT 58.161 42.857 0.00 0.00 0.00 2.90
2034 2111 3.990092 AGAAACAACACAGACGCTCATA 58.010 40.909 0.00 0.00 0.00 2.15
2035 2112 4.569943 AGAAACAACACAGACGCTCATAT 58.430 39.130 0.00 0.00 0.00 1.78
2036 2113 5.720202 AGAAACAACACAGACGCTCATATA 58.280 37.500 0.00 0.00 0.00 0.86
2037 2114 5.807520 AGAAACAACACAGACGCTCATATAG 59.192 40.000 0.00 0.00 0.00 1.31
2038 2115 4.983671 ACAACACAGACGCTCATATAGA 57.016 40.909 0.00 0.00 0.00 1.98
2039 2116 4.673441 ACAACACAGACGCTCATATAGAC 58.327 43.478 0.00 0.00 0.00 2.59
2040 2117 3.610786 ACACAGACGCTCATATAGACG 57.389 47.619 0.00 0.00 0.00 4.18
2041 2118 2.287069 ACACAGACGCTCATATAGACGC 60.287 50.000 0.00 0.00 0.00 5.19
2042 2119 1.947456 ACAGACGCTCATATAGACGCA 59.053 47.619 0.00 0.00 0.00 5.24
2043 2120 2.287069 ACAGACGCTCATATAGACGCAC 60.287 50.000 0.00 0.00 0.00 5.34
2044 2121 1.947456 AGACGCTCATATAGACGCACA 59.053 47.619 0.00 0.00 0.00 4.57
2045 2122 2.554462 AGACGCTCATATAGACGCACAT 59.446 45.455 0.00 0.00 0.00 3.21
2046 2123 3.751698 AGACGCTCATATAGACGCACATA 59.248 43.478 0.00 0.00 0.00 2.29
2047 2124 4.396478 AGACGCTCATATAGACGCACATAT 59.604 41.667 0.00 0.00 0.00 1.78
2048 2125 4.663166 ACGCTCATATAGACGCACATATC 58.337 43.478 0.00 0.00 0.00 1.63
2049 2126 4.038361 CGCTCATATAGACGCACATATCC 58.962 47.826 0.00 0.00 0.00 2.59
2050 2127 4.201960 CGCTCATATAGACGCACATATCCT 60.202 45.833 0.00 0.00 0.00 3.24
2051 2128 5.655488 GCTCATATAGACGCACATATCCTT 58.345 41.667 0.00 0.00 0.00 3.36
2052 2129 6.458342 CGCTCATATAGACGCACATATCCTTA 60.458 42.308 0.00 0.00 0.00 2.69
2053 2130 6.693545 GCTCATATAGACGCACATATCCTTAC 59.306 42.308 0.00 0.00 0.00 2.34
2054 2131 7.096884 TCATATAGACGCACATATCCTTACC 57.903 40.000 0.00 0.00 0.00 2.85
2055 2132 6.661805 TCATATAGACGCACATATCCTTACCA 59.338 38.462 0.00 0.00 0.00 3.25
2056 2133 7.342026 TCATATAGACGCACATATCCTTACCAT 59.658 37.037 0.00 0.00 0.00 3.55
2057 2134 8.630037 CATATAGACGCACATATCCTTACCATA 58.370 37.037 0.00 0.00 0.00 2.74
2058 2135 7.661536 ATAGACGCACATATCCTTACCATAT 57.338 36.000 0.00 0.00 0.00 1.78
2059 2136 6.360370 AGACGCACATATCCTTACCATATT 57.640 37.500 0.00 0.00 0.00 1.28
2060 2137 7.476540 AGACGCACATATCCTTACCATATTA 57.523 36.000 0.00 0.00 0.00 0.98
2061 2138 7.321153 AGACGCACATATCCTTACCATATTAC 58.679 38.462 0.00 0.00 0.00 1.89
2062 2139 6.403878 ACGCACATATCCTTACCATATTACC 58.596 40.000 0.00 0.00 0.00 2.85
2063 2140 5.815740 CGCACATATCCTTACCATATTACCC 59.184 44.000 0.00 0.00 0.00 3.69
2064 2141 6.351881 CGCACATATCCTTACCATATTACCCT 60.352 42.308 0.00 0.00 0.00 4.34
2065 2142 7.147794 CGCACATATCCTTACCATATTACCCTA 60.148 40.741 0.00 0.00 0.00 3.53
2066 2143 8.714906 GCACATATCCTTACCATATTACCCTAT 58.285 37.037 0.00 0.00 0.00 2.57
2072 2149 8.751215 TCCTTACCATATTACCCTATGAATGT 57.249 34.615 0.00 0.00 31.92 2.71
2073 2150 9.846725 TCCTTACCATATTACCCTATGAATGTA 57.153 33.333 0.00 0.00 31.92 2.29
2074 2151 9.886132 CCTTACCATATTACCCTATGAATGTAC 57.114 37.037 0.00 0.00 31.92 2.90
2077 2154 7.686434 ACCATATTACCCTATGAATGTACACC 58.314 38.462 0.00 0.00 31.92 4.16
2078 2155 7.110155 CCATATTACCCTATGAATGTACACCC 58.890 42.308 0.00 0.00 31.92 4.61
2079 2156 7.037586 CCATATTACCCTATGAATGTACACCCT 60.038 40.741 0.00 0.00 31.92 4.34
2080 2157 5.623956 TTACCCTATGAATGTACACCCTG 57.376 43.478 0.00 0.00 0.00 4.45
2081 2158 2.172717 ACCCTATGAATGTACACCCTGC 59.827 50.000 0.00 0.00 0.00 4.85
2082 2159 2.172505 CCCTATGAATGTACACCCTGCA 59.827 50.000 0.00 0.00 0.00 4.41
2083 2160 3.181440 CCCTATGAATGTACACCCTGCAT 60.181 47.826 0.00 0.00 0.00 3.96
2084 2161 4.067896 CCTATGAATGTACACCCTGCATC 58.932 47.826 0.00 0.00 0.00 3.91
2085 2162 2.022764 TGAATGTACACCCTGCATCG 57.977 50.000 0.00 0.00 0.00 3.84
2086 2163 0.657840 GAATGTACACCCTGCATCGC 59.342 55.000 0.00 0.00 0.00 4.58
2087 2164 1.089481 AATGTACACCCTGCATCGCG 61.089 55.000 0.00 0.00 0.00 5.87
2088 2165 2.125673 GTACACCCTGCATCGCGT 60.126 61.111 5.77 0.00 0.00 6.01
2089 2166 1.740296 GTACACCCTGCATCGCGTT 60.740 57.895 5.77 0.00 0.00 4.84
2090 2167 0.458889 GTACACCCTGCATCGCGTTA 60.459 55.000 5.77 0.00 0.00 3.18
2091 2168 0.462375 TACACCCTGCATCGCGTTAT 59.538 50.000 5.77 0.00 0.00 1.89
2092 2169 0.810031 ACACCCTGCATCGCGTTATC 60.810 55.000 5.77 0.00 0.00 1.75
2093 2170 0.809636 CACCCTGCATCGCGTTATCA 60.810 55.000 5.77 0.00 0.00 2.15
2094 2171 0.107897 ACCCTGCATCGCGTTATCAA 60.108 50.000 5.77 0.00 0.00 2.57
2095 2172 0.304705 CCCTGCATCGCGTTATCAAC 59.695 55.000 5.77 0.00 0.00 3.18
2110 2187 6.435562 GTTATCAACGGATACATCGTCTTC 57.564 41.667 0.00 0.00 40.18 2.87
2111 2188 3.431922 TCAACGGATACATCGTCTTCC 57.568 47.619 0.00 0.00 40.18 3.46
2112 2189 2.756207 TCAACGGATACATCGTCTTCCA 59.244 45.455 0.00 0.00 40.18 3.53
2113 2190 3.383505 TCAACGGATACATCGTCTTCCAT 59.616 43.478 0.00 0.00 40.18 3.41
2114 2191 4.119862 CAACGGATACATCGTCTTCCATT 58.880 43.478 0.00 0.00 40.18 3.16
2115 2192 3.717707 ACGGATACATCGTCTTCCATTG 58.282 45.455 0.00 0.00 35.87 2.82
2116 2193 3.132289 ACGGATACATCGTCTTCCATTGT 59.868 43.478 0.00 0.00 35.87 2.71
2117 2194 4.340097 ACGGATACATCGTCTTCCATTGTA 59.660 41.667 0.00 0.00 35.87 2.41
2118 2195 4.680110 CGGATACATCGTCTTCCATTGTAC 59.320 45.833 0.00 0.00 0.00 2.90
2119 2196 4.989168 GGATACATCGTCTTCCATTGTACC 59.011 45.833 0.00 0.00 0.00 3.34
2120 2197 3.973206 ACATCGTCTTCCATTGTACCA 57.027 42.857 0.00 0.00 0.00 3.25
2121 2198 4.280436 ACATCGTCTTCCATTGTACCAA 57.720 40.909 0.00 0.00 0.00 3.67
2122 2199 4.647611 ACATCGTCTTCCATTGTACCAAA 58.352 39.130 0.00 0.00 0.00 3.28
2123 2200 4.454504 ACATCGTCTTCCATTGTACCAAAC 59.545 41.667 0.00 0.00 0.00 2.93
2124 2201 3.404899 TCGTCTTCCATTGTACCAAACC 58.595 45.455 0.00 0.00 0.00 3.27
2125 2202 3.142951 CGTCTTCCATTGTACCAAACCA 58.857 45.455 0.00 0.00 0.00 3.67
2126 2203 3.566322 CGTCTTCCATTGTACCAAACCAA 59.434 43.478 0.00 0.00 0.00 3.67
2127 2204 4.555906 CGTCTTCCATTGTACCAAACCAAC 60.556 45.833 0.00 0.00 0.00 3.77
2128 2205 4.583073 GTCTTCCATTGTACCAAACCAACT 59.417 41.667 0.00 0.00 0.00 3.16
2129 2206 4.825085 TCTTCCATTGTACCAAACCAACTC 59.175 41.667 0.00 0.00 0.00 3.01
2130 2207 4.171878 TCCATTGTACCAAACCAACTCA 57.828 40.909 0.00 0.00 0.00 3.41
2131 2208 4.141287 TCCATTGTACCAAACCAACTCAG 58.859 43.478 0.00 0.00 0.00 3.35
2132 2209 3.888930 CCATTGTACCAAACCAACTCAGT 59.111 43.478 0.00 0.00 0.00 3.41
2133 2210 4.340950 CCATTGTACCAAACCAACTCAGTT 59.659 41.667 0.00 0.00 0.00 3.16
2134 2211 5.533154 CCATTGTACCAAACCAACTCAGTTA 59.467 40.000 0.00 0.00 0.00 2.24
2135 2212 6.435428 CATTGTACCAAACCAACTCAGTTAC 58.565 40.000 0.00 0.00 0.00 2.50
2136 2213 5.100344 TGTACCAAACCAACTCAGTTACA 57.900 39.130 0.00 0.00 0.00 2.41
2137 2214 5.498393 TGTACCAAACCAACTCAGTTACAA 58.502 37.500 0.00 0.00 0.00 2.41
2138 2215 6.123651 TGTACCAAACCAACTCAGTTACAAT 58.876 36.000 0.00 0.00 0.00 2.71
2139 2216 5.767816 ACCAAACCAACTCAGTTACAATC 57.232 39.130 0.00 0.00 0.00 2.67
2140 2217 5.197451 ACCAAACCAACTCAGTTACAATCA 58.803 37.500 0.00 0.00 0.00 2.57
2141 2218 5.833131 ACCAAACCAACTCAGTTACAATCAT 59.167 36.000 0.00 0.00 0.00 2.45
2142 2219 6.016276 ACCAAACCAACTCAGTTACAATCATC 60.016 38.462 0.00 0.00 0.00 2.92
2143 2220 6.381801 CAAACCAACTCAGTTACAATCATCC 58.618 40.000 0.00 0.00 0.00 3.51
2144 2221 4.589908 ACCAACTCAGTTACAATCATCCC 58.410 43.478 0.00 0.00 0.00 3.85
2145 2222 4.042809 ACCAACTCAGTTACAATCATCCCA 59.957 41.667 0.00 0.00 0.00 4.37
2146 2223 5.009631 CCAACTCAGTTACAATCATCCCAA 58.990 41.667 0.00 0.00 0.00 4.12
2147 2224 5.653769 CCAACTCAGTTACAATCATCCCAAT 59.346 40.000 0.00 0.00 0.00 3.16
2148 2225 6.183360 CCAACTCAGTTACAATCATCCCAATC 60.183 42.308 0.00 0.00 0.00 2.67
2149 2226 5.440610 ACTCAGTTACAATCATCCCAATCC 58.559 41.667 0.00 0.00 0.00 3.01
2150 2227 5.192522 ACTCAGTTACAATCATCCCAATCCT 59.807 40.000 0.00 0.00 0.00 3.24
2151 2228 5.684704 TCAGTTACAATCATCCCAATCCTC 58.315 41.667 0.00 0.00 0.00 3.71
2152 2229 4.823989 CAGTTACAATCATCCCAATCCTCC 59.176 45.833 0.00 0.00 0.00 4.30
2153 2230 4.478317 AGTTACAATCATCCCAATCCTCCA 59.522 41.667 0.00 0.00 0.00 3.86
2154 2231 5.135020 AGTTACAATCATCCCAATCCTCCAT 59.865 40.000 0.00 0.00 0.00 3.41
2155 2232 4.547886 ACAATCATCCCAATCCTCCATT 57.452 40.909 0.00 0.00 0.00 3.16
2156 2233 5.668135 ACAATCATCCCAATCCTCCATTA 57.332 39.130 0.00 0.00 0.00 1.90
2157 2234 6.223574 ACAATCATCCCAATCCTCCATTAT 57.776 37.500 0.00 0.00 0.00 1.28
2158 2235 7.347319 ACAATCATCCCAATCCTCCATTATA 57.653 36.000 0.00 0.00 0.00 0.98
2159 2236 7.947484 ACAATCATCCCAATCCTCCATTATAT 58.053 34.615 0.00 0.00 0.00 0.86
2160 2237 8.057623 ACAATCATCCCAATCCTCCATTATATC 58.942 37.037 0.00 0.00 0.00 1.63
2161 2238 7.776291 ATCATCCCAATCCTCCATTATATCA 57.224 36.000 0.00 0.00 0.00 2.15
2162 2239 7.587375 TCATCCCAATCCTCCATTATATCAA 57.413 36.000 0.00 0.00 0.00 2.57
2163 2240 7.999042 TCATCCCAATCCTCCATTATATCAAA 58.001 34.615 0.00 0.00 0.00 2.69
2164 2241 7.890127 TCATCCCAATCCTCCATTATATCAAAC 59.110 37.037 0.00 0.00 0.00 2.93
2165 2242 7.406620 TCCCAATCCTCCATTATATCAAACT 57.593 36.000 0.00 0.00 0.00 2.66
2166 2243 7.461749 TCCCAATCCTCCATTATATCAAACTC 58.538 38.462 0.00 0.00 0.00 3.01
2167 2244 7.073598 TCCCAATCCTCCATTATATCAAACTCA 59.926 37.037 0.00 0.00 0.00 3.41
2168 2245 7.175641 CCCAATCCTCCATTATATCAAACTCAC 59.824 40.741 0.00 0.00 0.00 3.51
2169 2246 7.175641 CCAATCCTCCATTATATCAAACTCACC 59.824 40.741 0.00 0.00 0.00 4.02
2170 2247 6.187727 TCCTCCATTATATCAAACTCACCC 57.812 41.667 0.00 0.00 0.00 4.61
2171 2248 5.911178 TCCTCCATTATATCAAACTCACCCT 59.089 40.000 0.00 0.00 0.00 4.34
2172 2249 6.000219 CCTCCATTATATCAAACTCACCCTG 59.000 44.000 0.00 0.00 0.00 4.45
2173 2250 6.183361 CCTCCATTATATCAAACTCACCCTGA 60.183 42.308 0.00 0.00 0.00 3.86
2174 2251 7.392766 TCCATTATATCAAACTCACCCTGAT 57.607 36.000 0.00 0.00 34.29 2.90
2175 2252 7.226441 TCCATTATATCAAACTCACCCTGATG 58.774 38.462 0.00 0.00 32.22 3.07
2176 2253 6.432162 CCATTATATCAAACTCACCCTGATGG 59.568 42.308 0.00 0.00 41.37 3.51
2188 2265 1.427809 CCTGATGGGCTGAGGATACA 58.572 55.000 0.00 0.00 41.41 2.29
2189 2266 1.770658 CCTGATGGGCTGAGGATACAA 59.229 52.381 0.00 0.00 41.41 2.41
2190 2267 2.486191 CCTGATGGGCTGAGGATACAAC 60.486 54.545 0.00 0.00 41.41 3.32
2191 2268 2.437281 CTGATGGGCTGAGGATACAACT 59.563 50.000 0.00 0.00 41.41 3.16
2192 2269 3.643320 CTGATGGGCTGAGGATACAACTA 59.357 47.826 0.00 0.00 41.41 2.24
2193 2270 4.234550 TGATGGGCTGAGGATACAACTAT 58.765 43.478 0.00 0.00 41.41 2.12
2194 2271 4.284490 TGATGGGCTGAGGATACAACTATC 59.716 45.833 0.00 0.00 41.41 2.08
2195 2272 2.972713 TGGGCTGAGGATACAACTATCC 59.027 50.000 0.00 0.00 46.62 2.59
2210 2287 9.922477 ATACAACTATCCTCCTATAATCATCGA 57.078 33.333 0.00 0.00 0.00 3.59
2211 2288 8.651589 ACAACTATCCTCCTATAATCATCGAA 57.348 34.615 0.00 0.00 0.00 3.71
2212 2289 9.261035 ACAACTATCCTCCTATAATCATCGAAT 57.739 33.333 0.00 0.00 0.00 3.34
2218 2295 8.067751 TCCTCCTATAATCATCGAATAACAGG 57.932 38.462 0.00 0.00 0.00 4.00
2219 2296 7.674348 TCCTCCTATAATCATCGAATAACAGGT 59.326 37.037 0.00 0.00 0.00 4.00
2220 2297 8.314751 CCTCCTATAATCATCGAATAACAGGTT 58.685 37.037 0.00 0.00 0.00 3.50
2221 2298 9.144747 CTCCTATAATCATCGAATAACAGGTTG 57.855 37.037 0.00 0.00 0.00 3.77
2222 2299 8.647796 TCCTATAATCATCGAATAACAGGTTGT 58.352 33.333 0.00 0.00 0.00 3.32
2223 2300 9.273016 CCTATAATCATCGAATAACAGGTTGTT 57.727 33.333 0.00 0.00 43.88 2.83
2226 2303 7.687941 AATCATCGAATAACAGGTTGTTTCT 57.312 32.000 0.00 0.00 41.45 2.52
2227 2304 7.687941 ATCATCGAATAACAGGTTGTTTCTT 57.312 32.000 0.00 0.00 41.45 2.52
2228 2305 8.786826 ATCATCGAATAACAGGTTGTTTCTTA 57.213 30.769 0.00 0.00 41.45 2.10
2229 2306 8.251750 TCATCGAATAACAGGTTGTTTCTTAG 57.748 34.615 0.00 0.00 41.45 2.18
2230 2307 8.092068 TCATCGAATAACAGGTTGTTTCTTAGA 58.908 33.333 0.00 2.22 41.45 2.10
2231 2308 8.883731 CATCGAATAACAGGTTGTTTCTTAGAT 58.116 33.333 0.00 4.09 41.45 1.98
2232 2309 8.842358 TCGAATAACAGGTTGTTTCTTAGATT 57.158 30.769 0.00 0.00 41.45 2.40
2233 2310 9.280174 TCGAATAACAGGTTGTTTCTTAGATTT 57.720 29.630 0.00 0.00 41.45 2.17
2234 2311 9.543018 CGAATAACAGGTTGTTTCTTAGATTTC 57.457 33.333 0.00 0.00 41.45 2.17
2239 2316 8.753497 ACAGGTTGTTTCTTAGATTTCTTTCT 57.247 30.769 0.00 0.00 0.00 2.52
2240 2317 8.841300 ACAGGTTGTTTCTTAGATTTCTTTCTC 58.159 33.333 0.00 0.00 0.00 2.87
2241 2318 8.293157 CAGGTTGTTTCTTAGATTTCTTTCTCC 58.707 37.037 0.00 0.00 0.00 3.71
2242 2319 7.998964 AGGTTGTTTCTTAGATTTCTTTCTCCA 59.001 33.333 0.00 0.00 0.00 3.86
2243 2320 8.630037 GGTTGTTTCTTAGATTTCTTTCTCCAA 58.370 33.333 0.00 0.00 0.00 3.53
2306 2396 4.665212 CATGCACTGACATAATTGACCAC 58.335 43.478 0.00 0.00 0.00 4.16
2346 2840 9.667107 CAAAAGTAGACTCAATTATGGGAAGTA 57.333 33.333 0.00 0.00 0.00 2.24
2368 2862 9.635404 AAGTATAGCTTCTGTAGTCTACAATCT 57.365 33.333 13.63 10.03 38.38 2.40
2369 2863 9.280174 AGTATAGCTTCTGTAGTCTACAATCTC 57.720 37.037 13.63 4.50 38.38 2.75
2371 2865 8.760980 ATAGCTTCTGTAGTCTACAATCTCTT 57.239 34.615 13.63 2.04 38.38 2.85
2372 2866 7.475137 AGCTTCTGTAGTCTACAATCTCTTT 57.525 36.000 13.63 0.00 38.38 2.52
2373 2867 7.902087 AGCTTCTGTAGTCTACAATCTCTTTT 58.098 34.615 13.63 0.00 38.38 2.27
2374 2868 8.371699 AGCTTCTGTAGTCTACAATCTCTTTTT 58.628 33.333 13.63 0.00 38.38 1.94
2404 2949 3.067320 TCTCGTACGTGCTAGCTAGTAGA 59.933 47.826 21.62 11.96 0.00 2.59
2406 2951 2.475864 CGTACGTGCTAGCTAGTAGAGG 59.524 54.545 21.62 13.34 0.00 3.69
2407 2952 2.713863 ACGTGCTAGCTAGTAGAGGT 57.286 50.000 21.62 13.90 39.82 3.85
2410 2955 2.232399 GTGCTAGCTAGTAGAGGTCCC 58.768 57.143 21.62 2.71 37.09 4.46
2412 2957 1.072015 GCTAGCTAGTAGAGGTCCCGA 59.928 57.143 21.62 0.00 37.09 5.14
2413 2958 2.486907 GCTAGCTAGTAGAGGTCCCGAA 60.487 54.545 21.62 0.00 37.09 4.30
2434 2984 1.135575 CCAAAAGTTGATGGAGAGCGC 60.136 52.381 0.00 0.00 39.12 5.92
2455 3005 5.729454 GCGCCAGCTCGATTTTAAATTTCTA 60.729 40.000 0.00 0.00 41.01 2.10
2456 3006 6.430451 CGCCAGCTCGATTTTAAATTTCTAT 58.570 36.000 0.00 0.00 0.00 1.98
2457 3007 6.575201 CGCCAGCTCGATTTTAAATTTCTATC 59.425 38.462 0.00 0.00 0.00 2.08
2458 3008 7.519008 CGCCAGCTCGATTTTAAATTTCTATCT 60.519 37.037 0.00 0.00 0.00 1.98
2501 3055 0.318275 CTCCGCGCAAGAGTAGGATC 60.318 60.000 8.75 0.00 43.02 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.199766 ACAAAATATGTACACACCAACTGTTG 58.800 34.615 13.50 13.50 41.63 3.33
6 7 7.341445 ACAAAATATGTACACACCAACTGTT 57.659 32.000 0.00 0.00 41.63 3.16
7 8 6.952773 ACAAAATATGTACACACCAACTGT 57.047 33.333 0.00 0.00 41.63 3.55
8 9 7.421599 TGAACAAAATATGTACACACCAACTG 58.578 34.615 0.00 0.00 42.99 3.16
9 10 7.575414 TGAACAAAATATGTACACACCAACT 57.425 32.000 0.00 0.00 42.99 3.16
38 39 5.797934 TGTTTTTCGAGCTAAAACACACAAG 59.202 36.000 17.89 0.00 45.46 3.16
56 57 2.820330 CAAATCTGTGGCGGTGTTTTT 58.180 42.857 0.00 0.00 0.00 1.94
133 142 3.492313 GAATTGTGTGCCAACTCGATTC 58.508 45.455 0.00 5.57 40.68 2.52
134 143 2.228822 GGAATTGTGTGCCAACTCGATT 59.771 45.455 0.00 0.00 36.86 3.34
138 147 0.951558 ACGGAATTGTGTGCCAACTC 59.048 50.000 0.00 0.00 35.44 3.01
141 150 5.393569 CCAATATTACGGAATTGTGTGCCAA 60.394 40.000 0.00 0.00 37.49 4.52
168 177 3.510360 ACTAACCTTGACATAGCTCGTGT 59.490 43.478 4.48 4.48 0.00 4.49
195 204 4.211164 CACAATGCCAATGAATGATCATGC 59.789 41.667 9.46 8.04 45.60 4.06
223 232 3.814842 TCAATCTTTGACGCACTTGACAT 59.185 39.130 0.00 0.00 34.08 3.06
250 259 4.636435 CCTCAAACACCGCCCCGT 62.636 66.667 0.00 0.00 0.00 5.28
271 282 0.107848 CGAAGGGCCGACATAAACCT 60.108 55.000 0.00 0.00 0.00 3.50
295 306 1.628340 CAAGGTGTAGGTGGACATGGA 59.372 52.381 0.00 0.00 0.00 3.41
313 324 2.565834 AGAAGCTAAGGCGGACTTACAA 59.434 45.455 0.00 0.00 44.37 2.41
318 338 1.219393 GCAGAAGCTAAGGCGGACT 59.781 57.895 0.00 0.00 44.37 3.85
457 477 7.701539 TTATCATGAGTGTGGCAATTTTAGT 57.298 32.000 0.09 0.00 0.00 2.24
495 515 8.877864 AATTACTTGTCATGGAATGGACTAAA 57.122 30.769 0.00 0.00 46.73 1.85
502 522 6.966632 CGTACCAAATTACTTGTCATGGAATG 59.033 38.462 0.00 0.00 37.70 2.67
503 523 6.094881 CCGTACCAAATTACTTGTCATGGAAT 59.905 38.462 0.00 0.00 32.65 3.01
506 526 4.938832 TCCGTACCAAATTACTTGTCATGG 59.061 41.667 0.00 0.00 32.65 3.66
508 528 6.045072 TCTCCGTACCAAATTACTTGTCAT 57.955 37.500 0.00 0.00 32.65 3.06
509 529 5.471556 TCTCCGTACCAAATTACTTGTCA 57.528 39.130 0.00 0.00 32.65 3.58
514 534 6.742559 ATACCATCTCCGTACCAAATTACT 57.257 37.500 0.00 0.00 0.00 2.24
523 543 6.342338 AGGAAACATATACCATCTCCGTAC 57.658 41.667 0.00 0.00 0.00 3.67
524 544 7.005902 TGTAGGAAACATATACCATCTCCGTA 58.994 38.462 0.00 0.00 31.43 4.02
526 546 6.340962 TGTAGGAAACATATACCATCTCCG 57.659 41.667 0.00 0.00 31.43 4.63
533 553 9.463443 GCATTTGATTTGTAGGAAACATATACC 57.537 33.333 0.00 0.00 38.10 2.73
539 559 8.028354 CAGTATGCATTTGATTTGTAGGAAACA 58.972 33.333 3.54 0.00 35.88 2.83
580 600 9.473007 TGAGAAAAACATAATGAATATGACCCA 57.527 29.630 2.67 0.00 43.52 4.51
624 644 1.549203 TTGCATTTCTCCAAGGCCTC 58.451 50.000 5.23 0.00 41.76 4.70
632 652 9.875691 AATAAGACCTTTTAATTGCATTTCTCC 57.124 29.630 0.00 0.00 0.00 3.71
848 874 2.109229 ATAGGAGCATGGCCTAGTGT 57.891 50.000 3.32 0.00 41.07 3.55
857 883 5.242393 CCAGGTTGGATTTTATAGGAGCATG 59.758 44.000 0.00 0.00 40.96 4.06
1350 1396 1.208358 CTTGCCGTAGTCGTCGTCA 59.792 57.895 0.00 0.00 35.01 4.35
1500 1546 2.182030 CTCTTCCAGACGGCGTCC 59.818 66.667 34.04 17.68 32.18 4.79
1589 1643 2.094258 CCTATACTGCGGCGCATATTTG 59.906 50.000 36.35 24.88 38.13 2.32
1590 1644 2.346803 CCTATACTGCGGCGCATATTT 58.653 47.619 36.35 22.22 38.13 1.40
1591 1645 2.007049 GCCTATACTGCGGCGCATATT 61.007 52.381 36.35 23.69 38.13 1.28
1592 1646 0.460284 GCCTATACTGCGGCGCATAT 60.460 55.000 36.35 30.45 38.13 1.78
1612 1666 3.243334 TGCTAGTGATGATCTCGCTTCAG 60.243 47.826 11.71 7.11 42.09 3.02
1613 1667 2.689983 TGCTAGTGATGATCTCGCTTCA 59.310 45.455 11.71 8.72 42.09 3.02
1627 1681 4.732285 ACGAGACAAACAATTGCTAGTG 57.268 40.909 5.05 1.16 40.34 2.74
1632 1686 2.719046 CCGAAACGAGACAAACAATTGC 59.281 45.455 5.05 0.00 40.34 3.56
1633 1687 3.296628 CCCGAAACGAGACAAACAATTG 58.703 45.455 3.24 3.24 42.46 2.32
1642 1696 2.125633 GAGGGCCCGAAACGAGAC 60.126 66.667 18.44 0.00 0.00 3.36
1643 1697 3.387947 GGAGGGCCCGAAACGAGA 61.388 66.667 18.44 0.00 0.00 4.04
1682 1736 0.997196 CCTTCGCTACTACGGTTTGC 59.003 55.000 0.00 0.00 0.00 3.68
1701 1755 2.106938 TCCGTCAGGATCGCATGC 59.893 61.111 7.91 7.91 42.75 4.06
1751 1813 2.038952 AGCCTTTTCCCCTGAAATTTGC 59.961 45.455 0.00 0.00 40.08 3.68
1765 1827 2.091555 TGACCAACCAACCTAGCCTTTT 60.092 45.455 0.00 0.00 0.00 2.27
1767 1829 1.073923 CTGACCAACCAACCTAGCCTT 59.926 52.381 0.00 0.00 0.00 4.35
1768 1830 0.693049 CTGACCAACCAACCTAGCCT 59.307 55.000 0.00 0.00 0.00 4.58
1769 1831 0.322546 CCTGACCAACCAACCTAGCC 60.323 60.000 0.00 0.00 0.00 3.93
1789 1865 1.642728 ATAAAATACGCACGCCGACA 58.357 45.000 2.93 0.00 41.02 4.35
1814 1890 5.507650 GCTTAGACTACCCATACTCGAAAGG 60.508 48.000 0.00 0.00 0.00 3.11
1821 1897 5.880887 GCAAAAAGCTTAGACTACCCATACT 59.119 40.000 0.00 0.00 41.15 2.12
1825 1901 4.072131 CTGCAAAAAGCTTAGACTACCCA 58.928 43.478 0.00 0.00 45.94 4.51
1826 1902 4.072839 ACTGCAAAAAGCTTAGACTACCC 58.927 43.478 0.00 0.00 45.94 3.69
1827 1903 4.083271 CCACTGCAAAAAGCTTAGACTACC 60.083 45.833 0.00 0.00 45.94 3.18
1828 1904 4.083271 CCCACTGCAAAAAGCTTAGACTAC 60.083 45.833 0.00 0.00 45.94 2.73
1829 1905 4.072131 CCCACTGCAAAAAGCTTAGACTA 58.928 43.478 0.00 0.00 45.94 2.59
1830 1906 2.887152 CCCACTGCAAAAAGCTTAGACT 59.113 45.455 0.00 0.00 45.94 3.24
1833 1909 1.615392 AGCCCACTGCAAAAAGCTTAG 59.385 47.619 0.00 0.00 45.94 2.18
1866 1942 1.722507 GTTCTGCAACTTCGCGCAC 60.723 57.895 8.75 0.00 33.75 5.34
1869 1945 0.162507 CTCTGTTCTGCAACTTCGCG 59.837 55.000 0.00 0.00 33.17 5.87
1880 1956 3.505293 GGCAAGCATTTCTTCTCTGTTCT 59.495 43.478 0.00 0.00 31.27 3.01
1907 1983 2.996168 GATGAGAACGGGATGGCCGG 62.996 65.000 0.00 0.00 40.16 6.13
1908 1984 1.595382 GATGAGAACGGGATGGCCG 60.595 63.158 0.00 0.00 33.83 6.13
1909 1985 0.109342 ATGATGAGAACGGGATGGCC 59.891 55.000 0.00 0.00 0.00 5.36
1919 1995 7.940688 ACCATTTATGCTCATGTATGATGAGAA 59.059 33.333 16.81 9.41 46.25 2.87
1932 2008 7.839907 AGCAATTTCTTTACCATTTATGCTCA 58.160 30.769 0.00 0.00 35.69 4.26
1960 2037 5.057819 TCATAAAGGTGTAACGCTCAACAA 58.942 37.500 0.00 0.00 38.12 2.83
1961 2038 4.633175 TCATAAAGGTGTAACGCTCAACA 58.367 39.130 0.00 0.00 38.12 3.33
2010 2087 3.554324 TGAGCGTCTGTGTTGTTTCTAAC 59.446 43.478 0.00 0.00 0.00 2.34
2011 2088 3.787785 TGAGCGTCTGTGTTGTTTCTAA 58.212 40.909 0.00 0.00 0.00 2.10
2012 2089 3.446310 TGAGCGTCTGTGTTGTTTCTA 57.554 42.857 0.00 0.00 0.00 2.10
2014 2091 4.928661 ATATGAGCGTCTGTGTTGTTTC 57.071 40.909 0.00 0.00 0.00 2.78
2015 2092 5.577164 GTCTATATGAGCGTCTGTGTTGTTT 59.423 40.000 0.00 0.00 0.00 2.83
2017 2094 4.673441 GTCTATATGAGCGTCTGTGTTGT 58.327 43.478 0.00 0.00 0.00 3.32
2018 2095 3.726235 CGTCTATATGAGCGTCTGTGTTG 59.274 47.826 0.00 0.00 0.00 3.33
2019 2096 3.792459 GCGTCTATATGAGCGTCTGTGTT 60.792 47.826 0.00 0.00 0.00 3.32
2020 2097 2.287069 GCGTCTATATGAGCGTCTGTGT 60.287 50.000 0.00 0.00 0.00 3.72
2021 2098 2.287009 TGCGTCTATATGAGCGTCTGTG 60.287 50.000 0.00 0.00 0.00 3.66
2022 2099 1.947456 TGCGTCTATATGAGCGTCTGT 59.053 47.619 0.00 0.00 0.00 3.41
2023 2100 2.287009 TGTGCGTCTATATGAGCGTCTG 60.287 50.000 0.00 0.00 0.00 3.51
2024 2101 1.947456 TGTGCGTCTATATGAGCGTCT 59.053 47.619 0.00 0.00 0.00 4.18
2025 2102 2.401017 TGTGCGTCTATATGAGCGTC 57.599 50.000 0.00 0.00 0.00 5.19
2026 2103 4.438880 GGATATGTGCGTCTATATGAGCGT 60.439 45.833 0.00 0.00 0.00 5.07
2027 2104 4.038361 GGATATGTGCGTCTATATGAGCG 58.962 47.826 0.00 0.00 0.00 5.03
2028 2105 5.255710 AGGATATGTGCGTCTATATGAGC 57.744 43.478 0.00 0.00 0.00 4.26
2029 2106 7.148069 TGGTAAGGATATGTGCGTCTATATGAG 60.148 40.741 0.00 0.00 0.00 2.90
2030 2107 6.661805 TGGTAAGGATATGTGCGTCTATATGA 59.338 38.462 0.00 0.00 0.00 2.15
2031 2108 6.863275 TGGTAAGGATATGTGCGTCTATATG 58.137 40.000 0.00 0.00 0.00 1.78
2032 2109 7.661536 ATGGTAAGGATATGTGCGTCTATAT 57.338 36.000 0.00 0.00 0.00 0.86
2033 2110 8.762481 ATATGGTAAGGATATGTGCGTCTATA 57.238 34.615 0.00 0.00 0.00 1.31
2034 2111 7.661536 ATATGGTAAGGATATGTGCGTCTAT 57.338 36.000 0.00 0.00 0.00 1.98
2035 2112 7.476540 AATATGGTAAGGATATGTGCGTCTA 57.523 36.000 0.00 0.00 0.00 2.59
2036 2113 6.360370 AATATGGTAAGGATATGTGCGTCT 57.640 37.500 0.00 0.00 0.00 4.18
2037 2114 6.534079 GGTAATATGGTAAGGATATGTGCGTC 59.466 42.308 0.00 0.00 0.00 5.19
2038 2115 6.403878 GGTAATATGGTAAGGATATGTGCGT 58.596 40.000 0.00 0.00 0.00 5.24
2039 2116 5.815740 GGGTAATATGGTAAGGATATGTGCG 59.184 44.000 0.00 0.00 0.00 5.34
2040 2117 6.958767 AGGGTAATATGGTAAGGATATGTGC 58.041 40.000 0.00 0.00 0.00 4.57
2046 2123 9.351572 ACATTCATAGGGTAATATGGTAAGGAT 57.648 33.333 0.00 0.00 34.51 3.24
2047 2124 8.751215 ACATTCATAGGGTAATATGGTAAGGA 57.249 34.615 0.00 0.00 34.51 3.36
2048 2125 9.886132 GTACATTCATAGGGTAATATGGTAAGG 57.114 37.037 0.00 0.00 34.51 2.69
2051 2128 8.818860 GGTGTACATTCATAGGGTAATATGGTA 58.181 37.037 0.00 0.00 34.51 3.25
2052 2129 7.256908 GGGTGTACATTCATAGGGTAATATGGT 60.257 40.741 0.00 0.00 34.51 3.55
2053 2130 7.037586 AGGGTGTACATTCATAGGGTAATATGG 60.038 40.741 0.00 0.00 34.51 2.74
2054 2131 7.824289 CAGGGTGTACATTCATAGGGTAATATG 59.176 40.741 0.00 0.00 34.96 1.78
2055 2132 7.528881 GCAGGGTGTACATTCATAGGGTAATAT 60.529 40.741 0.00 0.00 0.00 1.28
2056 2133 6.239772 GCAGGGTGTACATTCATAGGGTAATA 60.240 42.308 0.00 0.00 0.00 0.98
2057 2134 5.456186 GCAGGGTGTACATTCATAGGGTAAT 60.456 44.000 0.00 0.00 0.00 1.89
2058 2135 4.141574 GCAGGGTGTACATTCATAGGGTAA 60.142 45.833 0.00 0.00 0.00 2.85
2059 2136 3.389983 GCAGGGTGTACATTCATAGGGTA 59.610 47.826 0.00 0.00 0.00 3.69
2060 2137 2.172717 GCAGGGTGTACATTCATAGGGT 59.827 50.000 0.00 0.00 0.00 4.34
2061 2138 2.172505 TGCAGGGTGTACATTCATAGGG 59.827 50.000 0.00 0.00 0.00 3.53
2062 2139 3.558931 TGCAGGGTGTACATTCATAGG 57.441 47.619 0.00 0.00 0.00 2.57
2063 2140 3.742882 CGATGCAGGGTGTACATTCATAG 59.257 47.826 0.00 0.00 0.00 2.23
2064 2141 3.727726 CGATGCAGGGTGTACATTCATA 58.272 45.455 0.00 0.00 0.00 2.15
2065 2142 2.564771 CGATGCAGGGTGTACATTCAT 58.435 47.619 0.00 0.00 0.00 2.57
2066 2143 2.011548 GCGATGCAGGGTGTACATTCA 61.012 52.381 0.00 0.00 0.00 2.57
2067 2144 0.657840 GCGATGCAGGGTGTACATTC 59.342 55.000 0.00 0.00 0.00 2.67
2068 2145 1.089481 CGCGATGCAGGGTGTACATT 61.089 55.000 0.00 0.00 0.00 2.71
2069 2146 1.521457 CGCGATGCAGGGTGTACAT 60.521 57.895 0.00 0.00 0.00 2.29
2070 2147 2.125713 CGCGATGCAGGGTGTACA 60.126 61.111 0.00 0.00 0.00 2.90
2071 2148 0.458889 TAACGCGATGCAGGGTGTAC 60.459 55.000 15.93 0.00 37.37 2.90
2072 2149 0.462375 ATAACGCGATGCAGGGTGTA 59.538 50.000 15.93 0.00 37.37 2.90
2073 2150 0.810031 GATAACGCGATGCAGGGTGT 60.810 55.000 15.93 0.00 37.37 4.16
2074 2151 0.809636 TGATAACGCGATGCAGGGTG 60.810 55.000 15.93 0.00 37.37 4.61
2075 2152 0.107897 TTGATAACGCGATGCAGGGT 60.108 50.000 15.93 0.00 39.03 4.34
2076 2153 0.304705 GTTGATAACGCGATGCAGGG 59.695 55.000 15.93 0.00 0.00 4.45
2077 2154 3.806257 GTTGATAACGCGATGCAGG 57.194 52.632 15.93 0.00 0.00 4.85
2087 2164 5.401674 GGAAGACGATGTATCCGTTGATAAC 59.598 44.000 0.00 0.00 40.67 1.89
2088 2165 5.068067 TGGAAGACGATGTATCCGTTGATAA 59.932 40.000 0.00 0.00 40.67 1.75
2089 2166 4.581409 TGGAAGACGATGTATCCGTTGATA 59.419 41.667 0.00 0.00 40.67 2.15
2090 2167 3.383505 TGGAAGACGATGTATCCGTTGAT 59.616 43.478 0.00 0.00 40.67 2.57
2091 2168 2.756207 TGGAAGACGATGTATCCGTTGA 59.244 45.455 0.00 0.00 40.67 3.18
2092 2169 3.159353 TGGAAGACGATGTATCCGTTG 57.841 47.619 0.00 0.00 40.67 4.10
2093 2170 4.119862 CAATGGAAGACGATGTATCCGTT 58.880 43.478 0.00 0.00 40.85 4.44
2094 2171 3.132289 ACAATGGAAGACGATGTATCCGT 59.868 43.478 0.00 0.00 43.56 4.69
2095 2172 3.717707 ACAATGGAAGACGATGTATCCG 58.282 45.455 0.00 0.00 34.60 4.18
2096 2173 4.989168 GGTACAATGGAAGACGATGTATCC 59.011 45.833 0.00 0.00 0.00 2.59
2097 2174 5.597806 TGGTACAATGGAAGACGATGTATC 58.402 41.667 0.00 0.00 31.92 2.24
2098 2175 5.607939 TGGTACAATGGAAGACGATGTAT 57.392 39.130 0.00 0.00 31.92 2.29
2100 2177 3.973206 TGGTACAATGGAAGACGATGT 57.027 42.857 0.00 0.00 31.92 3.06
2114 2191 5.100344 TGTAACTGAGTTGGTTTGGTACA 57.900 39.130 8.33 0.00 0.00 2.90
2115 2192 6.261381 TGATTGTAACTGAGTTGGTTTGGTAC 59.739 38.462 8.33 0.00 0.00 3.34
2116 2193 6.358178 TGATTGTAACTGAGTTGGTTTGGTA 58.642 36.000 8.33 0.00 0.00 3.25
2117 2194 5.197451 TGATTGTAACTGAGTTGGTTTGGT 58.803 37.500 8.33 0.00 0.00 3.67
2118 2195 5.766150 TGATTGTAACTGAGTTGGTTTGG 57.234 39.130 8.33 0.00 0.00 3.28
2119 2196 6.381801 GGATGATTGTAACTGAGTTGGTTTG 58.618 40.000 8.33 0.00 0.00 2.93
2120 2197 5.476945 GGGATGATTGTAACTGAGTTGGTTT 59.523 40.000 8.33 0.00 0.00 3.27
2121 2198 5.010282 GGGATGATTGTAACTGAGTTGGTT 58.990 41.667 8.33 0.00 0.00 3.67
2122 2199 4.042809 TGGGATGATTGTAACTGAGTTGGT 59.957 41.667 8.33 0.00 0.00 3.67
2123 2200 4.588899 TGGGATGATTGTAACTGAGTTGG 58.411 43.478 8.33 0.00 0.00 3.77
2124 2201 6.183360 GGATTGGGATGATTGTAACTGAGTTG 60.183 42.308 8.33 0.00 0.00 3.16
2125 2202 5.888161 GGATTGGGATGATTGTAACTGAGTT 59.112 40.000 2.37 2.37 0.00 3.01
2126 2203 5.192522 AGGATTGGGATGATTGTAACTGAGT 59.807 40.000 0.00 0.00 0.00 3.41
2127 2204 5.688807 AGGATTGGGATGATTGTAACTGAG 58.311 41.667 0.00 0.00 0.00 3.35
2128 2205 5.397899 GGAGGATTGGGATGATTGTAACTGA 60.398 44.000 0.00 0.00 0.00 3.41
2129 2206 4.823989 GGAGGATTGGGATGATTGTAACTG 59.176 45.833 0.00 0.00 0.00 3.16
2130 2207 4.478317 TGGAGGATTGGGATGATTGTAACT 59.522 41.667 0.00 0.00 0.00 2.24
2131 2208 4.792068 TGGAGGATTGGGATGATTGTAAC 58.208 43.478 0.00 0.00 0.00 2.50
2132 2209 5.668135 ATGGAGGATTGGGATGATTGTAA 57.332 39.130 0.00 0.00 0.00 2.41
2133 2210 5.668135 AATGGAGGATTGGGATGATTGTA 57.332 39.130 0.00 0.00 0.00 2.41
2134 2211 4.547886 AATGGAGGATTGGGATGATTGT 57.452 40.909 0.00 0.00 0.00 2.71
2135 2212 8.057011 TGATATAATGGAGGATTGGGATGATTG 58.943 37.037 0.00 0.00 0.00 2.67
2136 2213 8.178662 TGATATAATGGAGGATTGGGATGATT 57.821 34.615 0.00 0.00 0.00 2.57
2137 2214 7.776291 TGATATAATGGAGGATTGGGATGAT 57.224 36.000 0.00 0.00 0.00 2.45
2138 2215 7.587375 TTGATATAATGGAGGATTGGGATGA 57.413 36.000 0.00 0.00 0.00 2.92
2139 2216 7.892241 AGTTTGATATAATGGAGGATTGGGATG 59.108 37.037 0.00 0.00 0.00 3.51
2140 2217 8.004697 AGTTTGATATAATGGAGGATTGGGAT 57.995 34.615 0.00 0.00 0.00 3.85
2141 2218 7.073598 TGAGTTTGATATAATGGAGGATTGGGA 59.926 37.037 0.00 0.00 0.00 4.37
2142 2219 7.175641 GTGAGTTTGATATAATGGAGGATTGGG 59.824 40.741 0.00 0.00 0.00 4.12
2143 2220 7.175641 GGTGAGTTTGATATAATGGAGGATTGG 59.824 40.741 0.00 0.00 0.00 3.16
2144 2221 7.175641 GGGTGAGTTTGATATAATGGAGGATTG 59.824 40.741 0.00 0.00 0.00 2.67
2145 2222 7.074237 AGGGTGAGTTTGATATAATGGAGGATT 59.926 37.037 0.00 0.00 0.00 3.01
2146 2223 6.564152 AGGGTGAGTTTGATATAATGGAGGAT 59.436 38.462 0.00 0.00 0.00 3.24
2147 2224 5.911178 AGGGTGAGTTTGATATAATGGAGGA 59.089 40.000 0.00 0.00 0.00 3.71
2148 2225 6.000219 CAGGGTGAGTTTGATATAATGGAGG 59.000 44.000 0.00 0.00 0.00 4.30
2149 2226 6.830912 TCAGGGTGAGTTTGATATAATGGAG 58.169 40.000 0.00 0.00 0.00 3.86
2150 2227 6.823286 TCAGGGTGAGTTTGATATAATGGA 57.177 37.500 0.00 0.00 0.00 3.41
2151 2228 6.432162 CCATCAGGGTGAGTTTGATATAATGG 59.568 42.308 0.00 0.00 30.77 3.16
2152 2229 7.444629 CCATCAGGGTGAGTTTGATATAATG 57.555 40.000 0.00 0.00 30.77 1.90
2169 2246 1.427809 TGTATCCTCAGCCCATCAGG 58.572 55.000 0.00 0.00 39.47 3.86
2170 2247 2.437281 AGTTGTATCCTCAGCCCATCAG 59.563 50.000 0.00 0.00 0.00 2.90
2171 2248 2.481441 AGTTGTATCCTCAGCCCATCA 58.519 47.619 0.00 0.00 0.00 3.07
2172 2249 4.826556 GATAGTTGTATCCTCAGCCCATC 58.173 47.826 0.00 0.00 30.28 3.51
2173 2250 4.899352 GATAGTTGTATCCTCAGCCCAT 57.101 45.455 0.00 0.00 30.28 4.00
2184 2261 9.922477 TCGATGATTATAGGAGGATAGTTGTAT 57.078 33.333 0.00 0.00 0.00 2.29
2185 2262 9.749340 TTCGATGATTATAGGAGGATAGTTGTA 57.251 33.333 0.00 0.00 0.00 2.41
2186 2263 8.651589 TTCGATGATTATAGGAGGATAGTTGT 57.348 34.615 0.00 0.00 0.00 3.32
2192 2269 8.700051 CCTGTTATTCGATGATTATAGGAGGAT 58.300 37.037 0.00 0.00 0.00 3.24
2193 2270 7.674348 ACCTGTTATTCGATGATTATAGGAGGA 59.326 37.037 6.06 0.00 0.00 3.71
2194 2271 7.841956 ACCTGTTATTCGATGATTATAGGAGG 58.158 38.462 6.06 3.63 0.00 4.30
2195 2272 9.144747 CAACCTGTTATTCGATGATTATAGGAG 57.855 37.037 6.06 0.00 0.00 3.69
2196 2273 8.647796 ACAACCTGTTATTCGATGATTATAGGA 58.352 33.333 6.06 0.00 0.00 2.94
2197 2274 8.833231 ACAACCTGTTATTCGATGATTATAGG 57.167 34.615 0.00 0.00 0.00 2.57
2200 2277 9.396022 AGAAACAACCTGTTATTCGATGATTAT 57.604 29.630 0.00 0.00 40.14 1.28
2201 2278 8.786826 AGAAACAACCTGTTATTCGATGATTA 57.213 30.769 0.00 0.00 40.14 1.75
2202 2279 7.687941 AGAAACAACCTGTTATTCGATGATT 57.312 32.000 0.00 0.00 40.14 2.57
2203 2280 7.687941 AAGAAACAACCTGTTATTCGATGAT 57.312 32.000 0.00 0.00 40.14 2.45
2204 2281 8.092068 TCTAAGAAACAACCTGTTATTCGATGA 58.908 33.333 0.00 0.00 40.14 2.92
2205 2282 8.251750 TCTAAGAAACAACCTGTTATTCGATG 57.748 34.615 0.00 0.00 40.14 3.84
2206 2283 9.449719 AATCTAAGAAACAACCTGTTATTCGAT 57.550 29.630 0.00 0.00 40.14 3.59
2207 2284 8.842358 AATCTAAGAAACAACCTGTTATTCGA 57.158 30.769 0.00 0.00 40.14 3.71
2208 2285 9.543018 GAAATCTAAGAAACAACCTGTTATTCG 57.457 33.333 0.00 0.00 40.14 3.34
2213 2290 9.190317 AGAAAGAAATCTAAGAAACAACCTGTT 57.810 29.630 0.00 0.00 43.41 3.16
2214 2291 8.753497 AGAAAGAAATCTAAGAAACAACCTGT 57.247 30.769 0.00 0.00 0.00 4.00
2215 2292 8.293157 GGAGAAAGAAATCTAAGAAACAACCTG 58.707 37.037 0.00 0.00 0.00 4.00
2216 2293 7.998964 TGGAGAAAGAAATCTAAGAAACAACCT 59.001 33.333 0.00 0.00 0.00 3.50
2217 2294 8.166422 TGGAGAAAGAAATCTAAGAAACAACC 57.834 34.615 0.00 0.00 0.00 3.77
2238 2315 9.550811 GGTGTCGTTTATAACTTTATTTTGGAG 57.449 33.333 0.00 0.00 0.00 3.86
2239 2316 8.229137 CGGTGTCGTTTATAACTTTATTTTGGA 58.771 33.333 0.00 0.00 0.00 3.53
2240 2317 8.371961 CGGTGTCGTTTATAACTTTATTTTGG 57.628 34.615 0.00 0.00 0.00 3.28
2286 2376 4.019792 AGTGGTCAATTATGTCAGTGCA 57.980 40.909 0.00 0.00 0.00 4.57
2316 2406 8.383175 TCCCATAATTGAGTCTACTTTTGTTCT 58.617 33.333 0.00 0.00 0.00 3.01
2317 2407 8.561738 TCCCATAATTGAGTCTACTTTTGTTC 57.438 34.615 0.00 0.00 0.00 3.18
2319 2409 8.164070 ACTTCCCATAATTGAGTCTACTTTTGT 58.836 33.333 0.00 0.00 0.00 2.83
2324 2414 8.808092 GCTATACTTCCCATAATTGAGTCTACT 58.192 37.037 0.00 0.00 0.00 2.57
2327 2417 7.863901 AGCTATACTTCCCATAATTGAGTCT 57.136 36.000 0.00 0.00 0.00 3.24
2346 2840 8.760980 AAGAGATTGTAGACTACAGAAGCTAT 57.239 34.615 14.74 4.87 40.24 2.97
2375 2869 5.404946 AGCTAGCACGTACGAGATTAAAAA 58.595 37.500 24.41 0.00 0.00 1.94
2376 2870 4.990257 AGCTAGCACGTACGAGATTAAAA 58.010 39.130 24.41 0.00 0.00 1.52
2377 2871 4.627611 AGCTAGCACGTACGAGATTAAA 57.372 40.909 24.41 0.00 0.00 1.52
2378 2872 4.813161 ACTAGCTAGCACGTACGAGATTAA 59.187 41.667 24.41 0.00 0.00 1.40
2379 2873 4.375272 ACTAGCTAGCACGTACGAGATTA 58.625 43.478 24.41 9.43 0.00 1.75
2380 2874 3.204526 ACTAGCTAGCACGTACGAGATT 58.795 45.455 24.41 8.74 0.00 2.40
2381 2875 2.836262 ACTAGCTAGCACGTACGAGAT 58.164 47.619 24.41 16.20 0.00 2.75
2382 2876 2.306341 ACTAGCTAGCACGTACGAGA 57.694 50.000 24.41 2.64 0.00 4.04
2383 2877 3.379240 TCTACTAGCTAGCACGTACGAG 58.621 50.000 24.41 16.14 0.00 4.18
2384 2878 3.379240 CTCTACTAGCTAGCACGTACGA 58.621 50.000 24.41 13.74 0.00 3.43
2385 2879 2.475864 CCTCTACTAGCTAGCACGTACG 59.524 54.545 20.91 15.01 0.00 3.67
2386 2880 3.465871 ACCTCTACTAGCTAGCACGTAC 58.534 50.000 20.91 0.00 0.00 3.67
2387 2881 3.494048 GGACCTCTACTAGCTAGCACGTA 60.494 52.174 20.91 15.50 0.00 3.57
2388 2882 2.563702 GACCTCTACTAGCTAGCACGT 58.436 52.381 20.91 15.19 0.00 4.49
2389 2883 1.874872 GGACCTCTACTAGCTAGCACG 59.125 57.143 20.91 9.63 0.00 5.34
2390 2884 2.232399 GGGACCTCTACTAGCTAGCAC 58.768 57.143 20.91 0.00 0.00 4.40
2391 2885 1.202782 CGGGACCTCTACTAGCTAGCA 60.203 57.143 20.91 7.12 0.00 3.49
2392 2886 1.072015 TCGGGACCTCTACTAGCTAGC 59.928 57.143 20.91 6.62 0.00 3.42
2406 2951 2.030274 CCATCAACTTTTGGTTCGGGAC 60.030 50.000 0.00 0.00 35.74 4.46
2407 2952 2.158593 TCCATCAACTTTTGGTTCGGGA 60.159 45.455 0.00 0.00 35.74 5.14
2410 2955 3.365364 GCTCTCCATCAACTTTTGGTTCG 60.365 47.826 0.00 0.00 35.74 3.95
2412 2957 2.554032 CGCTCTCCATCAACTTTTGGTT 59.446 45.455 0.00 0.00 38.93 3.67
2413 2958 2.154462 CGCTCTCCATCAACTTTTGGT 58.846 47.619 0.00 0.00 34.48 3.67
2421 2971 2.124983 GCTGGCGCTCTCCATCAA 60.125 61.111 7.64 0.00 35.22 2.57
2455 3005 0.104934 ACCTCCTGCCCCGATTAGAT 60.105 55.000 0.00 0.00 0.00 1.98
2456 3006 0.326238 AACCTCCTGCCCCGATTAGA 60.326 55.000 0.00 0.00 0.00 2.10
2457 3007 0.179045 CAACCTCCTGCCCCGATTAG 60.179 60.000 0.00 0.00 0.00 1.73
2458 3008 1.632018 CCAACCTCCTGCCCCGATTA 61.632 60.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.