Multiple sequence alignment - TraesCS5D01G258700

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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 TraesCS5D01G258700 chr5D 100.000 2476 0 0 1 2476 365120441 365117966 0.000000e+00 4573
1 TraesCS5D01G258700 chr5D 96.704 1972 57 4 1 1967 304884325 304882357 0.000000e+00 3275
2 TraesCS5D01G258700 chr5D 96.650 1970 56 7 1 1966 12933485 12931522 0.000000e+00 3264
3 TraesCS5D01G258700 chr5D 95.918 392 10 5 2088 2476 443048644 443049032 4.490000e-177 630
4 TraesCS5D01G258700 chr6D 97.316 1975 42 5 1 1965 31859057 31861030 0.000000e+00 3343
5 TraesCS5D01G258700 chr6D 96.604 1973 59 4 1 1966 441815051 441813080 0.000000e+00 3265
6 TraesCS5D01G258700 chr6D 95.949 395 8 4 2088 2476 349393143 349392751 3.470000e-178 634
7 TraesCS5D01G258700 chr2D 97.007 1971 49 7 1 1965 588796860 588794894 0.000000e+00 3304
8 TraesCS5D01G258700 chr2D 96.904 1970 52 6 1 1965 476878767 476880732 0.000000e+00 3291
9 TraesCS5D01G258700 chr2D 96.800 1969 56 5 1 1964 16904391 16906357 0.000000e+00 3280
10 TraesCS5D01G258700 chr2D 96.954 394 6 3 2088 2476 486183832 486183440 0.000000e+00 656
11 TraesCS5D01G258700 chr2D 96.931 391 7 3 2089 2476 486193609 486193221 0.000000e+00 651
12 TraesCS5D01G258700 chr2D 95.949 395 8 5 2088 2476 260014879 260014487 3.470000e-178 634
13 TraesCS5D01G258700 chr2D 95.707 396 8 6 2088 2476 260005148 260004755 1.620000e-176 628
14 TraesCS5D01G258700 chr1D 96.907 1972 50 8 1 1965 471280898 471282865 0.000000e+00 3293
15 TraesCS5D01G258700 chr7D 96.695 1967 63 2 1 1965 464035252 464037218 0.000000e+00 3271
16 TraesCS5D01G258700 chr4D 96.193 394 9 3 2088 2476 4879577 4879969 7.470000e-180 640
17 TraesCS5D01G258700 chr4D 96.173 392 10 2 2089 2476 4869715 4870105 9.660000e-179 636
18 TraesCS5D01G258700 chr3D 95.707 396 8 5 2089 2476 98591670 98592064 1.620000e-176 628
19 TraesCS5D01G258700 chr5B 94.167 120 6 1 1964 2082 431069287 431069168 5.440000e-42 182
20 TraesCS5D01G258700 chr5A 93.277 119 7 1 1964 2082 466580066 466579949 9.100000e-40 174


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 TraesCS5D01G258700 chr5D 365117966 365120441 2475 True 4573 4573 100.000 1 2476 1 chr5D.!!$R3 2475
1 TraesCS5D01G258700 chr5D 304882357 304884325 1968 True 3275 3275 96.704 1 1967 1 chr5D.!!$R2 1966
2 TraesCS5D01G258700 chr5D 12931522 12933485 1963 True 3264 3264 96.650 1 1966 1 chr5D.!!$R1 1965
3 TraesCS5D01G258700 chr6D 31859057 31861030 1973 False 3343 3343 97.316 1 1965 1 chr6D.!!$F1 1964
4 TraesCS5D01G258700 chr6D 441813080 441815051 1971 True 3265 3265 96.604 1 1966 1 chr6D.!!$R2 1965
5 TraesCS5D01G258700 chr2D 588794894 588796860 1966 True 3304 3304 97.007 1 1965 1 chr2D.!!$R5 1964
6 TraesCS5D01G258700 chr2D 476878767 476880732 1965 False 3291 3291 96.904 1 1965 1 chr2D.!!$F2 1964
7 TraesCS5D01G258700 chr2D 16904391 16906357 1966 False 3280 3280 96.800 1 1964 1 chr2D.!!$F1 1963
8 TraesCS5D01G258700 chr1D 471280898 471282865 1967 False 3293 3293 96.907 1 1965 1 chr1D.!!$F1 1964
9 TraesCS5D01G258700 chr7D 464035252 464037218 1966 False 3271 3271 96.695 1 1965 1 chr7D.!!$F1 1964

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
299 304 1.874345 TTGTCGAGGAGCTCCGAACC 61.874 60.0 26.95 16.41 42.08 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2272 0.036483 GGCATGGCCCGAACATTTTT 60.036 50.0 8.35 0.0 44.06 1.94 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
251 256 2.037687 ACCGACCCCGTCCACATA 59.962 61.111 0.00 0.00 0.00 2.29
299 304 1.874345 TTGTCGAGGAGCTCCGAACC 61.874 60.000 26.95 16.41 42.08 3.62
514 520 4.624024 CGTTTGCTCTCGTTAGGTATTTCA 59.376 41.667 0.00 0.00 0.00 2.69
523 529 4.726334 GGTATTTCACCGTGGCCA 57.274 55.556 0.00 0.00 37.63 5.36
570 576 3.075005 GGGTAGCCACCGAGCTCA 61.075 66.667 15.40 0.00 46.86 4.26
1741 1759 9.693739 TTGCATAATTTAAGGAAGTTAGATCCA 57.306 29.630 0.00 0.00 39.55 3.41
1967 1989 7.372451 CTCGTCCATTAGGAGTAGAGATTAG 57.628 44.000 0.00 0.00 46.92 1.73
1968 1990 7.075851 TCGTCCATTAGGAGTAGAGATTAGA 57.924 40.000 0.00 0.00 46.92 2.10
1969 1991 7.162761 TCGTCCATTAGGAGTAGAGATTAGAG 58.837 42.308 0.00 0.00 46.92 2.43
1970 1992 7.016366 TCGTCCATTAGGAGTAGAGATTAGAGA 59.984 40.741 0.00 0.00 46.92 3.10
1971 1993 7.827236 CGTCCATTAGGAGTAGAGATTAGAGAT 59.173 40.741 0.00 0.00 46.92 2.75
1974 1996 9.104965 CCATTAGGAGTAGAGATTAGAGATACG 57.895 40.741 0.00 0.00 36.89 3.06
1975 1997 9.104965 CATTAGGAGTAGAGATTAGAGATACGG 57.895 40.741 0.00 0.00 0.00 4.02
1976 1998 6.938698 AGGAGTAGAGATTAGAGATACGGA 57.061 41.667 0.00 0.00 0.00 4.69
1977 1999 7.319052 AGGAGTAGAGATTAGAGATACGGAA 57.681 40.000 0.00 0.00 0.00 4.30
1978 2000 7.747690 AGGAGTAGAGATTAGAGATACGGAAA 58.252 38.462 0.00 0.00 0.00 3.13
1979 2001 8.219178 AGGAGTAGAGATTAGAGATACGGAAAA 58.781 37.037 0.00 0.00 0.00 2.29
1980 2002 8.848182 GGAGTAGAGATTAGAGATACGGAAAAA 58.152 37.037 0.00 0.00 0.00 1.94
1995 2017 2.317230 AAAAAGTGTCACTCGGCCG 58.683 52.632 22.12 22.12 0.00 6.13
1996 2018 0.179067 AAAAAGTGTCACTCGGCCGA 60.179 50.000 29.03 29.03 0.00 5.54
1997 2019 0.600255 AAAAGTGTCACTCGGCCGAG 60.600 55.000 45.26 45.26 46.91 4.63
2006 2028 3.137484 CTCGGCCGAGATTTTCACA 57.863 52.632 45.28 12.76 44.53 3.58
2007 2029 1.438651 CTCGGCCGAGATTTTCACAA 58.561 50.000 45.28 12.18 44.53 3.33
2008 2030 1.394917 CTCGGCCGAGATTTTCACAAG 59.605 52.381 45.28 18.41 44.53 3.16
2009 2031 1.001520 TCGGCCGAGATTTTCACAAGA 59.998 47.619 27.28 0.00 0.00 3.02
2010 2032 1.128692 CGGCCGAGATTTTCACAAGAC 59.871 52.381 24.07 0.00 0.00 3.01
2011 2033 2.151202 GGCCGAGATTTTCACAAGACA 58.849 47.619 0.00 0.00 0.00 3.41
2012 2034 2.749621 GGCCGAGATTTTCACAAGACAT 59.250 45.455 0.00 0.00 0.00 3.06
2013 2035 3.426695 GGCCGAGATTTTCACAAGACATG 60.427 47.826 0.00 0.00 0.00 3.21
2014 2036 3.189287 GCCGAGATTTTCACAAGACATGT 59.811 43.478 0.00 0.00 45.34 3.21
2015 2037 4.320494 GCCGAGATTTTCACAAGACATGTT 60.320 41.667 0.00 0.00 41.46 2.71
2016 2038 5.762045 CCGAGATTTTCACAAGACATGTTT 58.238 37.500 0.00 0.00 41.46 2.83
2017 2039 5.626543 CCGAGATTTTCACAAGACATGTTTG 59.373 40.000 0.00 9.26 41.46 2.93
2018 2040 6.201517 CGAGATTTTCACAAGACATGTTTGT 58.798 36.000 15.98 15.98 41.46 2.83
2019 2041 6.692681 CGAGATTTTCACAAGACATGTTTGTT 59.307 34.615 17.97 8.35 41.46 2.83
2020 2042 7.220683 CGAGATTTTCACAAGACATGTTTGTTT 59.779 33.333 17.97 2.93 41.46 2.83
2021 2043 8.776376 AGATTTTCACAAGACATGTTTGTTTT 57.224 26.923 17.97 6.91 41.46 2.43
2022 2044 9.218440 AGATTTTCACAAGACATGTTTGTTTTT 57.782 25.926 17.97 7.15 41.46 1.94
2042 2064 6.844097 TTTTTCACCTTTTACTGTTCACCT 57.156 33.333 0.00 0.00 0.00 4.00
2043 2065 5.828299 TTTCACCTTTTACTGTTCACCTG 57.172 39.130 0.00 0.00 0.00 4.00
2044 2066 3.815809 TCACCTTTTACTGTTCACCTGG 58.184 45.455 0.00 0.00 0.00 4.45
2045 2067 2.884639 CACCTTTTACTGTTCACCTGGG 59.115 50.000 0.00 0.00 0.00 4.45
2046 2068 2.158519 ACCTTTTACTGTTCACCTGGGG 60.159 50.000 0.00 0.00 0.00 4.96
2047 2069 2.158519 CCTTTTACTGTTCACCTGGGGT 60.159 50.000 0.00 0.00 35.62 4.95
2048 2070 2.943036 TTTACTGTTCACCTGGGGTC 57.057 50.000 0.00 0.00 31.02 4.46
2049 2071 1.809133 TTACTGTTCACCTGGGGTCA 58.191 50.000 0.00 0.00 31.02 4.02
2050 2072 2.038863 TACTGTTCACCTGGGGTCAT 57.961 50.000 0.00 0.00 31.02 3.06
2051 2073 0.693049 ACTGTTCACCTGGGGTCATC 59.307 55.000 0.00 0.00 31.02 2.92
2052 2074 0.987294 CTGTTCACCTGGGGTCATCT 59.013 55.000 0.00 0.00 31.02 2.90
2053 2075 0.692476 TGTTCACCTGGGGTCATCTG 59.308 55.000 0.00 0.00 31.02 2.90
2054 2076 0.693049 GTTCACCTGGGGTCATCTGT 59.307 55.000 0.00 0.00 31.02 3.41
2055 2077 0.692476 TTCACCTGGGGTCATCTGTG 59.308 55.000 0.00 0.00 31.02 3.66
2056 2078 1.377725 CACCTGGGGTCATCTGTGC 60.378 63.158 0.00 0.00 31.02 4.57
2057 2079 1.539869 ACCTGGGGTCATCTGTGCT 60.540 57.895 0.00 0.00 0.00 4.40
2058 2080 1.136329 ACCTGGGGTCATCTGTGCTT 61.136 55.000 0.00 0.00 0.00 3.91
2059 2081 0.679002 CCTGGGGTCATCTGTGCTTG 60.679 60.000 0.00 0.00 0.00 4.01
2060 2082 0.037303 CTGGGGTCATCTGTGCTTGT 59.963 55.000 0.00 0.00 0.00 3.16
2061 2083 0.250858 TGGGGTCATCTGTGCTTGTG 60.251 55.000 0.00 0.00 0.00 3.33
2062 2084 0.036732 GGGGTCATCTGTGCTTGTGA 59.963 55.000 0.00 0.00 0.00 3.58
2063 2085 1.340405 GGGGTCATCTGTGCTTGTGAT 60.340 52.381 0.00 0.00 0.00 3.06
2064 2086 2.012673 GGGTCATCTGTGCTTGTGATC 58.987 52.381 0.00 0.00 0.00 2.92
2065 2087 2.616256 GGGTCATCTGTGCTTGTGATCA 60.616 50.000 0.00 0.00 0.00 2.92
2066 2088 2.676839 GGTCATCTGTGCTTGTGATCAG 59.323 50.000 0.00 0.00 0.00 2.90
2067 2089 2.095532 GTCATCTGTGCTTGTGATCAGC 59.904 50.000 0.00 0.00 0.00 4.26
2068 2090 2.027469 TCATCTGTGCTTGTGATCAGCT 60.027 45.455 0.00 0.00 0.00 4.24
2069 2091 3.196254 TCATCTGTGCTTGTGATCAGCTA 59.804 43.478 0.00 0.00 0.00 3.32
2070 2092 3.900966 TCTGTGCTTGTGATCAGCTAT 57.099 42.857 0.00 0.00 0.00 2.97
2071 2093 3.528532 TCTGTGCTTGTGATCAGCTATG 58.471 45.455 0.00 0.00 0.00 2.23
2072 2094 2.612672 CTGTGCTTGTGATCAGCTATGG 59.387 50.000 0.00 0.00 0.00 2.74
2073 2095 2.236893 TGTGCTTGTGATCAGCTATGGA 59.763 45.455 0.00 0.00 0.00 3.41
2074 2096 3.118149 TGTGCTTGTGATCAGCTATGGAT 60.118 43.478 0.00 0.00 0.00 3.41
2075 2097 3.881688 GTGCTTGTGATCAGCTATGGATT 59.118 43.478 0.00 0.00 0.00 3.01
2076 2098 5.059161 GTGCTTGTGATCAGCTATGGATTA 58.941 41.667 0.00 0.00 0.00 1.75
2077 2099 5.049818 GTGCTTGTGATCAGCTATGGATTAC 60.050 44.000 0.00 0.00 33.33 1.89
2078 2100 4.453819 GCTTGTGATCAGCTATGGATTACC 59.546 45.833 0.00 0.00 32.14 2.85
2100 2122 2.014010 AGGTACTTGTAACACCCCGA 57.986 50.000 0.00 0.00 27.25 5.14
2101 2123 1.897802 AGGTACTTGTAACACCCCGAG 59.102 52.381 0.00 0.00 27.25 4.63
2102 2124 1.895131 GGTACTTGTAACACCCCGAGA 59.105 52.381 0.00 0.00 0.00 4.04
2103 2125 2.299867 GGTACTTGTAACACCCCGAGAA 59.700 50.000 0.00 0.00 0.00 2.87
2104 2126 3.055602 GGTACTTGTAACACCCCGAGAAT 60.056 47.826 0.00 0.00 0.00 2.40
2105 2127 3.329929 ACTTGTAACACCCCGAGAATC 57.670 47.619 0.00 0.00 0.00 2.52
2106 2128 2.635915 ACTTGTAACACCCCGAGAATCA 59.364 45.455 0.00 0.00 33.17 2.57
2107 2129 3.263425 ACTTGTAACACCCCGAGAATCAT 59.737 43.478 0.00 0.00 33.17 2.45
2108 2130 3.260475 TGTAACACCCCGAGAATCATG 57.740 47.619 0.00 0.00 33.17 3.07
2109 2131 1.940613 GTAACACCCCGAGAATCATGC 59.059 52.381 0.00 0.00 33.17 4.06
2110 2132 0.620556 AACACCCCGAGAATCATGCT 59.379 50.000 0.00 0.00 33.17 3.79
2111 2133 1.496060 ACACCCCGAGAATCATGCTA 58.504 50.000 0.00 0.00 33.17 3.49
2112 2134 1.139058 ACACCCCGAGAATCATGCTAC 59.861 52.381 0.00 0.00 33.17 3.58
2113 2135 1.138859 CACCCCGAGAATCATGCTACA 59.861 52.381 0.00 0.00 33.17 2.74
2114 2136 1.414181 ACCCCGAGAATCATGCTACAG 59.586 52.381 0.00 0.00 33.17 2.74
2115 2137 1.414181 CCCCGAGAATCATGCTACAGT 59.586 52.381 0.00 0.00 33.17 3.55
2116 2138 2.628178 CCCCGAGAATCATGCTACAGTA 59.372 50.000 0.00 0.00 33.17 2.74
2117 2139 3.069586 CCCCGAGAATCATGCTACAGTAA 59.930 47.826 0.00 0.00 33.17 2.24
2118 2140 4.051922 CCCGAGAATCATGCTACAGTAAC 58.948 47.826 0.00 0.00 33.17 2.50
2119 2141 4.202161 CCCGAGAATCATGCTACAGTAACT 60.202 45.833 0.00 0.00 33.17 2.24
2120 2142 4.979197 CCGAGAATCATGCTACAGTAACTC 59.021 45.833 0.00 0.00 33.17 3.01
2121 2143 5.221145 CCGAGAATCATGCTACAGTAACTCT 60.221 44.000 0.00 0.00 33.17 3.24
2122 2144 5.912396 CGAGAATCATGCTACAGTAACTCTC 59.088 44.000 0.00 0.00 33.17 3.20
2123 2145 6.238621 CGAGAATCATGCTACAGTAACTCTCT 60.239 42.308 0.00 0.00 33.17 3.10
2124 2146 6.804677 AGAATCATGCTACAGTAACTCTCTG 58.195 40.000 0.00 0.00 38.68 3.35
2125 2147 6.379703 AGAATCATGCTACAGTAACTCTCTGT 59.620 38.462 4.11 4.11 46.10 3.41
2126 2148 5.316327 TCATGCTACAGTAACTCTCTGTG 57.684 43.478 8.54 1.49 44.41 3.66
2127 2149 5.010282 TCATGCTACAGTAACTCTCTGTGA 58.990 41.667 8.54 0.00 44.41 3.58
2128 2150 5.654209 TCATGCTACAGTAACTCTCTGTGAT 59.346 40.000 8.54 0.00 44.41 3.06
2129 2151 5.984695 TGCTACAGTAACTCTCTGTGATT 57.015 39.130 8.54 0.00 44.41 2.57
2130 2152 7.339466 TCATGCTACAGTAACTCTCTGTGATTA 59.661 37.037 8.54 0.00 44.41 1.75
2131 2153 7.462571 TGCTACAGTAACTCTCTGTGATTAA 57.537 36.000 8.54 0.00 44.41 1.40
2132 2154 7.539436 TGCTACAGTAACTCTCTGTGATTAAG 58.461 38.462 8.54 0.08 44.41 1.85
2133 2155 6.474102 GCTACAGTAACTCTCTGTGATTAAGC 59.526 42.308 8.54 5.68 44.41 3.09
2134 2156 6.597832 ACAGTAACTCTCTGTGATTAAGCT 57.402 37.500 0.00 0.00 43.32 3.74
2135 2157 7.704578 ACAGTAACTCTCTGTGATTAAGCTA 57.295 36.000 0.00 0.00 43.32 3.32
2136 2158 8.123639 ACAGTAACTCTCTGTGATTAAGCTAA 57.876 34.615 0.00 0.00 43.32 3.09
2137 2159 8.754080 ACAGTAACTCTCTGTGATTAAGCTAAT 58.246 33.333 0.00 0.00 43.32 1.73
2138 2160 9.243637 CAGTAACTCTCTGTGATTAAGCTAATC 57.756 37.037 0.00 0.00 43.73 1.75
2151 2173 8.955388 TGATTAAGCTAATCATGTTGCTAAACA 58.045 29.630 11.99 0.00 46.92 2.83
2152 2174 9.443283 GATTAAGCTAATCATGTTGCTAAACAG 57.557 33.333 9.63 0.00 40.90 3.16
2159 2181 2.356665 TGTTGCTAAACAGGGCTTGA 57.643 45.000 2.65 0.00 41.41 3.02
2160 2182 2.875296 TGTTGCTAAACAGGGCTTGAT 58.125 42.857 2.65 0.00 41.41 2.57
2161 2183 2.819608 TGTTGCTAAACAGGGCTTGATC 59.180 45.455 2.65 0.00 41.41 2.92
2162 2184 2.819608 GTTGCTAAACAGGGCTTGATCA 59.180 45.455 2.65 0.00 36.24 2.92
2163 2185 2.436417 TGCTAAACAGGGCTTGATCAC 58.564 47.619 2.65 0.00 0.00 3.06
2164 2186 2.224744 TGCTAAACAGGGCTTGATCACA 60.225 45.455 2.65 0.00 0.00 3.58
2165 2187 3.019564 GCTAAACAGGGCTTGATCACAT 58.980 45.455 2.65 0.00 0.00 3.21
2166 2188 3.445096 GCTAAACAGGGCTTGATCACATT 59.555 43.478 2.65 0.00 0.00 2.71
2167 2189 4.082026 GCTAAACAGGGCTTGATCACATTT 60.082 41.667 2.65 0.00 0.00 2.32
2168 2190 3.947910 AACAGGGCTTGATCACATTTG 57.052 42.857 2.65 0.00 0.00 2.32
2169 2191 3.159213 ACAGGGCTTGATCACATTTGA 57.841 42.857 2.65 0.00 35.73 2.69
2170 2192 3.499338 ACAGGGCTTGATCACATTTGAA 58.501 40.909 2.65 0.00 34.61 2.69
2171 2193 4.091549 ACAGGGCTTGATCACATTTGAAT 58.908 39.130 2.65 0.00 34.61 2.57
2172 2194 4.159135 ACAGGGCTTGATCACATTTGAATC 59.841 41.667 2.65 0.00 34.61 2.52
2173 2195 4.158949 CAGGGCTTGATCACATTTGAATCA 59.841 41.667 0.00 0.00 34.61 2.57
2174 2196 4.159135 AGGGCTTGATCACATTTGAATCAC 59.841 41.667 0.00 0.00 34.61 3.06
2175 2197 4.082081 GGGCTTGATCACATTTGAATCACA 60.082 41.667 0.00 0.00 34.61 3.58
2176 2198 5.394883 GGGCTTGATCACATTTGAATCACAT 60.395 40.000 0.00 0.00 34.61 3.21
2177 2199 6.103997 GGCTTGATCACATTTGAATCACATT 58.896 36.000 0.00 0.00 34.61 2.71
2178 2200 6.592607 GGCTTGATCACATTTGAATCACATTT 59.407 34.615 0.00 0.00 34.61 2.32
2179 2201 7.201496 GGCTTGATCACATTTGAATCACATTTC 60.201 37.037 0.00 0.00 34.61 2.17
2180 2202 7.544566 GCTTGATCACATTTGAATCACATTTCT 59.455 33.333 0.00 0.00 34.61 2.52
2181 2203 9.419297 CTTGATCACATTTGAATCACATTTCTT 57.581 29.630 0.00 0.00 34.61 2.52
2182 2204 9.767228 TTGATCACATTTGAATCACATTTCTTT 57.233 25.926 0.00 0.00 34.61 2.52
2183 2205 9.767228 TGATCACATTTGAATCACATTTCTTTT 57.233 25.926 0.00 0.00 34.61 2.27
2186 2208 8.754096 TCACATTTGAATCACATTTCTTTTTCG 58.246 29.630 0.00 0.00 0.00 3.46
2187 2209 8.754096 CACATTTGAATCACATTTCTTTTTCGA 58.246 29.630 0.00 0.00 0.00 3.71
2188 2210 9.311916 ACATTTGAATCACATTTCTTTTTCGAA 57.688 25.926 0.00 0.00 0.00 3.71
2189 2211 9.571804 CATTTGAATCACATTTCTTTTTCGAAC 57.428 29.630 0.00 0.00 0.00 3.95
2190 2212 8.925161 TTTGAATCACATTTCTTTTTCGAACT 57.075 26.923 0.00 0.00 0.00 3.01
2191 2213 8.560576 TTGAATCACATTTCTTTTTCGAACTC 57.439 30.769 0.00 0.00 0.00 3.01
2192 2214 7.138736 TGAATCACATTTCTTTTTCGAACTCC 58.861 34.615 0.00 0.00 0.00 3.85
2193 2215 6.884280 ATCACATTTCTTTTTCGAACTCCT 57.116 33.333 0.00 0.00 0.00 3.69
2194 2216 7.979444 ATCACATTTCTTTTTCGAACTCCTA 57.021 32.000 0.00 0.00 0.00 2.94
2195 2217 7.795482 TCACATTTCTTTTTCGAACTCCTAA 57.205 32.000 0.00 0.00 0.00 2.69
2196 2218 8.391075 TCACATTTCTTTTTCGAACTCCTAAT 57.609 30.769 0.00 0.00 0.00 1.73
2197 2219 8.846211 TCACATTTCTTTTTCGAACTCCTAATT 58.154 29.630 0.00 0.00 0.00 1.40
2198 2220 9.118236 CACATTTCTTTTTCGAACTCCTAATTC 57.882 33.333 0.00 0.00 0.00 2.17
2199 2221 8.846211 ACATTTCTTTTTCGAACTCCTAATTCA 58.154 29.630 0.00 0.00 0.00 2.57
2200 2222 9.677567 CATTTCTTTTTCGAACTCCTAATTCAA 57.322 29.630 0.00 0.00 0.00 2.69
2202 2224 9.511144 TTTCTTTTTCGAACTCCTAATTCAAAC 57.489 29.630 0.00 0.00 0.00 2.93
2203 2225 8.446599 TCTTTTTCGAACTCCTAATTCAAACT 57.553 30.769 0.00 0.00 0.00 2.66
2204 2226 8.899771 TCTTTTTCGAACTCCTAATTCAAACTT 58.100 29.630 0.00 0.00 0.00 2.66
2205 2227 9.170584 CTTTTTCGAACTCCTAATTCAAACTTC 57.829 33.333 0.00 0.00 0.00 3.01
2206 2228 7.795482 TTTCGAACTCCTAATTCAAACTTCA 57.205 32.000 0.00 0.00 0.00 3.02
2207 2229 7.795482 TTCGAACTCCTAATTCAAACTTCAA 57.205 32.000 0.00 0.00 0.00 2.69
2208 2230 7.979444 TCGAACTCCTAATTCAAACTTCAAT 57.021 32.000 0.00 0.00 0.00 2.57
2209 2231 8.391075 TCGAACTCCTAATTCAAACTTCAATT 57.609 30.769 0.00 0.00 0.00 2.32
2210 2232 9.496873 TCGAACTCCTAATTCAAACTTCAATTA 57.503 29.630 0.00 0.00 0.00 1.40
2262 2284 9.774742 TCAAAAATTTAAACAAAAATGTTCGGG 57.225 25.926 0.00 0.00 28.23 5.14
2263 2285 8.527488 CAAAAATTTAAACAAAAATGTTCGGGC 58.473 29.630 0.00 0.00 28.23 6.13
2264 2286 5.933187 ATTTAAACAAAAATGTTCGGGCC 57.067 34.783 0.00 0.00 0.00 5.80
2265 2287 2.990066 AAACAAAAATGTTCGGGCCA 57.010 40.000 4.39 0.00 0.00 5.36
2266 2288 3.483808 AAACAAAAATGTTCGGGCCAT 57.516 38.095 4.39 0.00 0.00 4.40
2267 2289 2.453983 ACAAAAATGTTCGGGCCATG 57.546 45.000 4.39 0.00 0.00 3.66
2268 2290 1.077915 CAAAAATGTTCGGGCCATGC 58.922 50.000 4.39 0.00 0.00 4.06
2280 2302 3.879912 GCCATGCCAGATATTGCAC 57.120 52.632 0.00 0.00 40.88 4.57
2281 2303 1.325355 GCCATGCCAGATATTGCACT 58.675 50.000 0.00 0.00 40.88 4.40
2282 2304 1.000607 GCCATGCCAGATATTGCACTG 60.001 52.381 0.00 0.00 40.88 3.66
2283 2305 2.578786 CCATGCCAGATATTGCACTGA 58.421 47.619 3.73 0.00 40.88 3.41
2284 2306 3.154710 CCATGCCAGATATTGCACTGAT 58.845 45.455 3.73 0.00 40.88 2.90
2285 2307 4.329392 CCATGCCAGATATTGCACTGATA 58.671 43.478 3.73 0.00 40.88 2.15
2286 2308 4.763279 CCATGCCAGATATTGCACTGATAA 59.237 41.667 3.73 0.00 40.88 1.75
2287 2309 5.417894 CCATGCCAGATATTGCACTGATAAT 59.582 40.000 3.73 0.00 40.88 1.28
2288 2310 6.071560 CCATGCCAGATATTGCACTGATAATT 60.072 38.462 3.73 0.00 40.88 1.40
2289 2311 7.121611 CCATGCCAGATATTGCACTGATAATTA 59.878 37.037 3.73 0.00 40.88 1.40
2290 2312 8.683615 CATGCCAGATATTGCACTGATAATTAT 58.316 33.333 0.00 0.00 40.88 1.28
2291 2313 8.640063 TGCCAGATATTGCACTGATAATTATT 57.360 30.769 3.73 0.00 36.38 1.40
2292 2314 8.517056 TGCCAGATATTGCACTGATAATTATTG 58.483 33.333 3.73 0.00 36.38 1.90
2293 2315 8.517878 GCCAGATATTGCACTGATAATTATTGT 58.482 33.333 3.73 0.00 36.38 2.71
2294 2316 9.836076 CCAGATATTGCACTGATAATTATTGTG 57.164 33.333 19.57 19.57 36.38 3.33
2295 2317 9.836076 CAGATATTGCACTGATAATTATTGTGG 57.164 33.333 22.56 12.01 36.38 4.17
2296 2318 9.797642 AGATATTGCACTGATAATTATTGTGGA 57.202 29.630 22.56 19.75 0.00 4.02
2298 2320 9.797642 ATATTGCACTGATAATTATTGTGGAGA 57.202 29.630 22.56 16.14 31.29 3.71
2299 2321 7.936496 TTGCACTGATAATTATTGTGGAGAA 57.064 32.000 22.56 11.36 31.29 2.87
2300 2322 7.936496 TGCACTGATAATTATTGTGGAGAAA 57.064 32.000 22.56 0.00 0.00 2.52
2301 2323 8.347004 TGCACTGATAATTATTGTGGAGAAAA 57.653 30.769 22.56 0.00 0.00 2.29
2302 2324 8.243426 TGCACTGATAATTATTGTGGAGAAAAC 58.757 33.333 22.56 11.87 0.00 2.43
2303 2325 8.243426 GCACTGATAATTATTGTGGAGAAAACA 58.757 33.333 22.56 5.35 0.00 2.83
2304 2326 9.559958 CACTGATAATTATTGTGGAGAAAACAC 57.440 33.333 17.60 0.00 39.26 3.32
2305 2327 9.295825 ACTGATAATTATTGTGGAGAAAACACA 57.704 29.630 0.00 0.00 46.22 3.72
2417 2439 2.889170 AAAAGGAGAAGGAGAAGCCC 57.111 50.000 0.00 0.00 37.37 5.19
2418 2440 0.995803 AAAGGAGAAGGAGAAGCCCC 59.004 55.000 0.00 0.00 37.37 5.80
2419 2441 0.916845 AAGGAGAAGGAGAAGCCCCC 60.917 60.000 0.00 0.00 37.37 5.40
2435 2457 2.360191 CCCCCATTGGACCACTGG 59.640 66.667 21.37 21.37 34.54 4.00
2436 2458 2.362889 CCCCATTGGACCACTGGC 60.363 66.667 22.60 0.00 33.60 4.85
2437 2459 2.362889 CCCATTGGACCACTGGCC 60.363 66.667 22.60 0.00 33.60 5.36
2438 2460 2.362889 CCATTGGACCACTGGCCC 60.363 66.667 17.24 0.00 27.99 5.80
2439 2461 2.440147 CATTGGACCACTGGCCCA 59.560 61.111 0.00 0.00 0.00 5.36
2440 2462 1.228831 CATTGGACCACTGGCCCAA 60.229 57.895 17.45 17.45 43.25 4.12
2441 2463 1.228862 ATTGGACCACTGGCCCAAC 60.229 57.895 17.48 0.00 42.08 3.77
2442 2464 1.729267 ATTGGACCACTGGCCCAACT 61.729 55.000 17.48 5.35 42.08 3.16
2443 2465 2.282462 GGACCACTGGCCCAACTG 60.282 66.667 0.00 0.00 0.00 3.16
2444 2466 2.282462 GACCACTGGCCCAACTGG 60.282 66.667 0.00 5.69 37.09 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.456253 GAGAAGACGACCGCGCGA 62.456 66.667 34.63 0.00 42.48 5.87
275 280 4.432601 AGCTCCTCGACAAGCTCT 57.567 55.556 10.32 0.00 45.57 4.09
354 359 1.888436 TTGAGGAAGACGGCAGCGAT 61.888 55.000 0.00 0.00 0.00 4.58
1231 1244 2.654385 TGAAGGAAATCACCCCTCCATT 59.346 45.455 0.00 0.00 31.17 3.16
1327 1340 6.371595 AAACCCCATTTGCATAGAAATCAA 57.628 33.333 0.00 0.00 0.00 2.57
1849 1868 4.643463 TGGTCTGCGGTTTATTTTCACTA 58.357 39.130 0.00 0.00 0.00 2.74
1866 1885 4.354943 CCCCTCCCACCCTGGTCT 62.355 72.222 0.00 0.00 35.17 3.85
1977 1999 0.179067 TCGGCCGAGTGACACTTTTT 60.179 50.000 27.28 0.00 0.00 1.94
1978 2000 0.600255 CTCGGCCGAGTGACACTTTT 60.600 55.000 40.77 0.00 37.47 2.27
1979 2001 1.006102 CTCGGCCGAGTGACACTTT 60.006 57.895 40.77 0.00 37.47 2.66
1980 2002 1.251527 ATCTCGGCCGAGTGACACTT 61.252 55.000 44.61 23.48 42.49 3.16
1981 2003 1.251527 AATCTCGGCCGAGTGACACT 61.252 55.000 44.61 25.11 42.49 3.55
1982 2004 0.389948 AAATCTCGGCCGAGTGACAC 60.390 55.000 44.61 0.00 42.49 3.67
1983 2005 0.320374 AAAATCTCGGCCGAGTGACA 59.680 50.000 44.61 31.15 42.49 3.58
1984 2006 1.000145 GAAAATCTCGGCCGAGTGAC 59.000 55.000 44.61 29.84 42.49 3.67
1985 2007 0.606096 TGAAAATCTCGGCCGAGTGA 59.394 50.000 44.61 32.31 42.49 3.41
1986 2008 0.721718 GTGAAAATCTCGGCCGAGTG 59.278 55.000 44.61 28.48 42.49 3.51
1987 2009 0.320374 TGTGAAAATCTCGGCCGAGT 59.680 50.000 44.61 32.17 42.49 4.18
1988 2010 1.394917 CTTGTGAAAATCTCGGCCGAG 59.605 52.381 42.89 42.89 43.21 4.63
1989 2011 1.001520 TCTTGTGAAAATCTCGGCCGA 59.998 47.619 29.03 29.03 0.00 5.54
1990 2012 1.128692 GTCTTGTGAAAATCTCGGCCG 59.871 52.381 22.12 22.12 0.00 6.13
1991 2013 2.151202 TGTCTTGTGAAAATCTCGGCC 58.849 47.619 0.00 0.00 0.00 6.13
1992 2014 3.189287 ACATGTCTTGTGAAAATCTCGGC 59.811 43.478 0.00 0.00 37.11 5.54
1993 2015 5.362556 AACATGTCTTGTGAAAATCTCGG 57.637 39.130 0.00 0.00 38.99 4.63
1994 2016 6.201517 ACAAACATGTCTTGTGAAAATCTCG 58.798 36.000 19.09 0.00 38.99 4.04
1995 2017 7.992180 AACAAACATGTCTTGTGAAAATCTC 57.008 32.000 19.95 0.00 38.99 2.75
1996 2018 8.776376 AAAACAAACATGTCTTGTGAAAATCT 57.224 26.923 19.95 6.65 38.99 2.40
2019 2041 6.350612 CCAGGTGAACAGTAAAAGGTGAAAAA 60.351 38.462 0.00 0.00 0.00 1.94
2020 2042 5.126384 CCAGGTGAACAGTAAAAGGTGAAAA 59.874 40.000 0.00 0.00 0.00 2.29
2021 2043 4.642885 CCAGGTGAACAGTAAAAGGTGAAA 59.357 41.667 0.00 0.00 0.00 2.69
2022 2044 4.204012 CCAGGTGAACAGTAAAAGGTGAA 58.796 43.478 0.00 0.00 0.00 3.18
2023 2045 3.434453 CCCAGGTGAACAGTAAAAGGTGA 60.434 47.826 0.00 0.00 0.00 4.02
2024 2046 2.884639 CCCAGGTGAACAGTAAAAGGTG 59.115 50.000 0.00 0.00 0.00 4.00
2025 2047 2.158519 CCCCAGGTGAACAGTAAAAGGT 60.159 50.000 0.00 0.00 0.00 3.50
2026 2048 2.158519 ACCCCAGGTGAACAGTAAAAGG 60.159 50.000 0.00 0.00 32.98 3.11
2027 2049 3.146847 GACCCCAGGTGAACAGTAAAAG 58.853 50.000 0.00 0.00 35.25 2.27
2028 2050 2.510382 TGACCCCAGGTGAACAGTAAAA 59.490 45.455 0.00 0.00 35.25 1.52
2029 2051 2.128535 TGACCCCAGGTGAACAGTAAA 58.871 47.619 0.00 0.00 35.25 2.01
2030 2052 1.809133 TGACCCCAGGTGAACAGTAA 58.191 50.000 0.00 0.00 35.25 2.24
2031 2053 1.906574 GATGACCCCAGGTGAACAGTA 59.093 52.381 0.00 0.00 35.25 2.74
2032 2054 0.693049 GATGACCCCAGGTGAACAGT 59.307 55.000 0.00 0.00 35.25 3.55
2033 2055 0.987294 AGATGACCCCAGGTGAACAG 59.013 55.000 0.00 0.00 35.25 3.16
2034 2056 0.692476 CAGATGACCCCAGGTGAACA 59.308 55.000 0.00 0.00 35.25 3.18
2035 2057 0.693049 ACAGATGACCCCAGGTGAAC 59.307 55.000 0.00 0.00 35.25 3.18
2036 2058 0.692476 CACAGATGACCCCAGGTGAA 59.308 55.000 0.00 0.00 35.25 3.18
2037 2059 1.841302 GCACAGATGACCCCAGGTGA 61.841 60.000 0.00 0.00 35.25 4.02
2038 2060 1.377725 GCACAGATGACCCCAGGTG 60.378 63.158 0.00 0.00 35.25 4.00
2039 2061 1.136329 AAGCACAGATGACCCCAGGT 61.136 55.000 0.00 0.00 39.44 4.00
2040 2062 0.679002 CAAGCACAGATGACCCCAGG 60.679 60.000 0.00 0.00 0.00 4.45
2041 2063 0.037303 ACAAGCACAGATGACCCCAG 59.963 55.000 0.00 0.00 0.00 4.45
2042 2064 0.250858 CACAAGCACAGATGACCCCA 60.251 55.000 0.00 0.00 0.00 4.96
2043 2065 0.036732 TCACAAGCACAGATGACCCC 59.963 55.000 0.00 0.00 0.00 4.95
2044 2066 2.012673 GATCACAAGCACAGATGACCC 58.987 52.381 0.00 0.00 0.00 4.46
2045 2067 2.676839 CTGATCACAAGCACAGATGACC 59.323 50.000 0.00 0.00 32.90 4.02
2046 2068 2.095532 GCTGATCACAAGCACAGATGAC 59.904 50.000 0.00 0.00 32.90 3.06
2047 2069 2.027469 AGCTGATCACAAGCACAGATGA 60.027 45.455 8.02 0.00 32.90 2.92
2048 2070 2.357075 AGCTGATCACAAGCACAGATG 58.643 47.619 8.02 0.00 32.90 2.90
2049 2071 2.783609 AGCTGATCACAAGCACAGAT 57.216 45.000 8.02 0.00 32.90 2.90
2050 2072 3.528532 CATAGCTGATCACAAGCACAGA 58.471 45.455 8.02 0.00 32.90 3.41
2051 2073 2.612672 CCATAGCTGATCACAAGCACAG 59.387 50.000 8.02 0.00 0.00 3.66
2052 2074 2.236893 TCCATAGCTGATCACAAGCACA 59.763 45.455 8.02 0.00 0.00 4.57
2053 2075 2.910199 TCCATAGCTGATCACAAGCAC 58.090 47.619 8.02 0.00 0.00 4.40
2054 2076 3.851458 ATCCATAGCTGATCACAAGCA 57.149 42.857 8.02 0.00 0.00 3.91
2055 2077 4.453819 GGTAATCCATAGCTGATCACAAGC 59.546 45.833 0.00 0.00 0.00 4.01
2056 2078 5.614308 TGGTAATCCATAGCTGATCACAAG 58.386 41.667 0.00 0.00 39.03 3.16
2057 2079 5.628797 TGGTAATCCATAGCTGATCACAA 57.371 39.130 0.00 0.00 39.03 3.33
2058 2080 5.628797 TTGGTAATCCATAGCTGATCACA 57.371 39.130 0.00 0.00 43.91 3.58
2059 2081 5.471456 CCTTTGGTAATCCATAGCTGATCAC 59.529 44.000 0.00 0.00 43.91 3.06
2060 2082 5.132648 ACCTTTGGTAATCCATAGCTGATCA 59.867 40.000 0.00 0.00 43.91 2.92
2061 2083 5.625150 ACCTTTGGTAATCCATAGCTGATC 58.375 41.667 0.00 0.00 43.91 2.92
2062 2084 5.653255 ACCTTTGGTAATCCATAGCTGAT 57.347 39.130 0.00 0.00 43.91 2.90
2063 2085 5.665812 AGTACCTTTGGTAATCCATAGCTGA 59.334 40.000 0.00 0.00 43.91 4.26
2064 2086 5.930135 AGTACCTTTGGTAATCCATAGCTG 58.070 41.667 0.00 0.00 43.91 4.24
2065 2087 6.069615 ACAAGTACCTTTGGTAATCCATAGCT 60.070 38.462 0.00 0.00 43.91 3.32
2066 2088 6.120220 ACAAGTACCTTTGGTAATCCATAGC 58.880 40.000 0.00 0.00 43.91 2.97
2067 2089 9.106070 GTTACAAGTACCTTTGGTAATCCATAG 57.894 37.037 0.00 0.00 43.91 2.23
2068 2090 8.604184 TGTTACAAGTACCTTTGGTAATCCATA 58.396 33.333 0.00 0.00 43.91 2.74
2069 2091 7.392393 GTGTTACAAGTACCTTTGGTAATCCAT 59.608 37.037 0.00 0.00 43.91 3.41
2070 2092 6.711645 GTGTTACAAGTACCTTTGGTAATCCA 59.288 38.462 0.00 0.00 40.12 3.41
2071 2093 6.149973 GGTGTTACAAGTACCTTTGGTAATCC 59.850 42.308 0.00 0.00 40.12 3.01
2072 2094 6.149973 GGGTGTTACAAGTACCTTTGGTAATC 59.850 42.308 0.00 0.00 40.12 1.75
2073 2095 6.005823 GGGTGTTACAAGTACCTTTGGTAAT 58.994 40.000 0.00 0.00 40.12 1.89
2074 2096 5.375773 GGGTGTTACAAGTACCTTTGGTAA 58.624 41.667 0.00 0.00 40.12 2.85
2075 2097 4.202451 GGGGTGTTACAAGTACCTTTGGTA 60.202 45.833 0.00 0.00 37.09 3.25
2076 2098 3.435457 GGGGTGTTACAAGTACCTTTGGT 60.435 47.826 0.00 0.00 40.16 3.67
2077 2099 3.151554 GGGGTGTTACAAGTACCTTTGG 58.848 50.000 0.00 0.00 34.87 3.28
2078 2100 2.809696 CGGGGTGTTACAAGTACCTTTG 59.190 50.000 0.00 0.00 34.87 2.77
2079 2101 2.705127 TCGGGGTGTTACAAGTACCTTT 59.295 45.455 0.00 0.00 34.87 3.11
2080 2102 2.301009 CTCGGGGTGTTACAAGTACCTT 59.699 50.000 0.00 0.00 34.87 3.50
2081 2103 1.897802 CTCGGGGTGTTACAAGTACCT 59.102 52.381 0.00 0.00 34.87 3.08
2082 2104 1.895131 TCTCGGGGTGTTACAAGTACC 59.105 52.381 0.00 0.00 0.00 3.34
2083 2105 3.665745 TTCTCGGGGTGTTACAAGTAC 57.334 47.619 0.00 0.00 0.00 2.73
2084 2106 3.833650 TGATTCTCGGGGTGTTACAAGTA 59.166 43.478 0.00 0.00 0.00 2.24
2085 2107 2.635915 TGATTCTCGGGGTGTTACAAGT 59.364 45.455 0.00 0.00 0.00 3.16
2086 2108 3.328382 TGATTCTCGGGGTGTTACAAG 57.672 47.619 0.00 0.00 0.00 3.16
2087 2109 3.605634 CATGATTCTCGGGGTGTTACAA 58.394 45.455 0.00 0.00 0.00 2.41
2088 2110 2.679639 GCATGATTCTCGGGGTGTTACA 60.680 50.000 0.00 0.00 0.00 2.41
2089 2111 1.940613 GCATGATTCTCGGGGTGTTAC 59.059 52.381 0.00 0.00 0.00 2.50
2090 2112 1.837439 AGCATGATTCTCGGGGTGTTA 59.163 47.619 0.00 0.00 0.00 2.41
2091 2113 0.620556 AGCATGATTCTCGGGGTGTT 59.379 50.000 0.00 0.00 0.00 3.32
2092 2114 1.139058 GTAGCATGATTCTCGGGGTGT 59.861 52.381 0.00 0.00 0.00 4.16
2093 2115 1.138859 TGTAGCATGATTCTCGGGGTG 59.861 52.381 0.00 0.00 0.00 4.61
2094 2116 1.414181 CTGTAGCATGATTCTCGGGGT 59.586 52.381 0.00 0.00 0.00 4.95
2095 2117 1.414181 ACTGTAGCATGATTCTCGGGG 59.586 52.381 0.00 0.00 0.00 5.73
2096 2118 2.898729 ACTGTAGCATGATTCTCGGG 57.101 50.000 0.00 0.00 0.00 5.14
2097 2119 4.938080 AGTTACTGTAGCATGATTCTCGG 58.062 43.478 0.00 0.00 0.00 4.63
2098 2120 5.826586 AGAGTTACTGTAGCATGATTCTCG 58.173 41.667 0.00 0.00 0.00 4.04
2099 2121 6.917477 CAGAGAGTTACTGTAGCATGATTCTC 59.083 42.308 0.00 7.00 0.00 2.87
2100 2122 6.379703 ACAGAGAGTTACTGTAGCATGATTCT 59.620 38.462 0.00 0.00 45.10 2.40
2101 2123 6.475076 CACAGAGAGTTACTGTAGCATGATTC 59.525 42.308 0.00 0.00 45.15 2.52
2102 2124 6.153510 TCACAGAGAGTTACTGTAGCATGATT 59.846 38.462 0.00 0.00 45.15 2.57
2103 2125 5.654209 TCACAGAGAGTTACTGTAGCATGAT 59.346 40.000 0.00 0.00 45.15 2.45
2104 2126 5.010282 TCACAGAGAGTTACTGTAGCATGA 58.990 41.667 0.00 0.00 45.15 3.07
2105 2127 5.316327 TCACAGAGAGTTACTGTAGCATG 57.684 43.478 4.49 0.00 45.15 4.06
2106 2128 6.537453 AATCACAGAGAGTTACTGTAGCAT 57.463 37.500 4.49 0.00 45.15 3.79
2107 2129 5.984695 AATCACAGAGAGTTACTGTAGCA 57.015 39.130 4.49 0.00 45.15 3.49
2108 2130 6.474102 GCTTAATCACAGAGAGTTACTGTAGC 59.526 42.308 0.00 0.00 45.15 3.58
2109 2131 7.767261 AGCTTAATCACAGAGAGTTACTGTAG 58.233 38.462 0.00 0.00 45.15 2.74
2110 2132 7.704578 AGCTTAATCACAGAGAGTTACTGTA 57.295 36.000 0.00 0.00 45.15 2.74
2112 2134 9.243637 GATTAGCTTAATCACAGAGAGTTACTG 57.756 37.037 0.00 0.00 43.12 2.74
2113 2135 8.972127 TGATTAGCTTAATCACAGAGAGTTACT 58.028 33.333 11.99 0.00 46.92 2.24
2126 2148 9.443283 CTGTTTAGCAACATGATTAGCTTAATC 57.557 33.333 0.00 0.04 42.21 1.75
2127 2149 8.408601 CCTGTTTAGCAACATGATTAGCTTAAT 58.591 33.333 0.00 0.00 42.21 1.40
2128 2150 7.148086 CCCTGTTTAGCAACATGATTAGCTTAA 60.148 37.037 0.00 0.53 42.21 1.85
2129 2151 6.318648 CCCTGTTTAGCAACATGATTAGCTTA 59.681 38.462 0.00 0.00 42.21 3.09
2130 2152 5.126061 CCCTGTTTAGCAACATGATTAGCTT 59.874 40.000 0.00 0.00 42.21 3.74
2131 2153 4.641989 CCCTGTTTAGCAACATGATTAGCT 59.358 41.667 0.00 5.47 42.21 3.32
2132 2154 4.734695 GCCCTGTTTAGCAACATGATTAGC 60.735 45.833 0.00 0.00 42.21 3.09
2133 2155 4.641989 AGCCCTGTTTAGCAACATGATTAG 59.358 41.667 0.00 0.00 42.21 1.73
2134 2156 4.599041 AGCCCTGTTTAGCAACATGATTA 58.401 39.130 0.00 0.00 42.21 1.75
2135 2157 3.434309 AGCCCTGTTTAGCAACATGATT 58.566 40.909 0.00 0.00 42.21 2.57
2136 2158 3.091633 AGCCCTGTTTAGCAACATGAT 57.908 42.857 0.00 0.00 42.21 2.45
2137 2159 2.557924 CAAGCCCTGTTTAGCAACATGA 59.442 45.455 0.00 0.00 42.21 3.07
2138 2160 2.557924 TCAAGCCCTGTTTAGCAACATG 59.442 45.455 0.00 0.00 42.21 3.21
2139 2161 2.875296 TCAAGCCCTGTTTAGCAACAT 58.125 42.857 0.00 0.00 42.21 2.71
2140 2162 2.356665 TCAAGCCCTGTTTAGCAACA 57.643 45.000 0.00 0.00 40.82 3.33
2141 2163 2.819608 TGATCAAGCCCTGTTTAGCAAC 59.180 45.455 0.00 0.00 0.00 4.17
2142 2164 2.819608 GTGATCAAGCCCTGTTTAGCAA 59.180 45.455 0.00 0.00 0.00 3.91
2143 2165 2.224744 TGTGATCAAGCCCTGTTTAGCA 60.225 45.455 0.00 0.00 0.00 3.49
2144 2166 2.436417 TGTGATCAAGCCCTGTTTAGC 58.564 47.619 0.00 0.00 0.00 3.09
2145 2167 5.183713 TCAAATGTGATCAAGCCCTGTTTAG 59.816 40.000 0.00 0.00 0.00 1.85
2146 2168 5.076182 TCAAATGTGATCAAGCCCTGTTTA 58.924 37.500 0.00 0.00 0.00 2.01
2147 2169 3.896888 TCAAATGTGATCAAGCCCTGTTT 59.103 39.130 0.00 0.00 0.00 2.83
2148 2170 3.499338 TCAAATGTGATCAAGCCCTGTT 58.501 40.909 0.00 0.00 0.00 3.16
2149 2171 3.159213 TCAAATGTGATCAAGCCCTGT 57.841 42.857 0.00 0.00 0.00 4.00
2150 2172 4.158949 TGATTCAAATGTGATCAAGCCCTG 59.841 41.667 0.00 0.00 32.48 4.45
2151 2173 4.159135 GTGATTCAAATGTGATCAAGCCCT 59.841 41.667 0.00 0.00 32.48 5.19
2152 2174 4.082081 TGTGATTCAAATGTGATCAAGCCC 60.082 41.667 0.00 0.00 32.48 5.19
2153 2175 5.063180 TGTGATTCAAATGTGATCAAGCC 57.937 39.130 0.00 0.00 32.48 4.35
2154 2176 7.544566 AGAAATGTGATTCAAATGTGATCAAGC 59.455 33.333 0.00 0.00 32.48 4.01
2155 2177 8.981724 AGAAATGTGATTCAAATGTGATCAAG 57.018 30.769 0.00 0.00 32.48 3.02
2156 2178 9.767228 AAAGAAATGTGATTCAAATGTGATCAA 57.233 25.926 0.00 0.00 32.48 2.57
2157 2179 9.767228 AAAAGAAATGTGATTCAAATGTGATCA 57.233 25.926 0.00 0.00 32.48 2.92
2160 2182 8.754096 CGAAAAAGAAATGTGATTCAAATGTGA 58.246 29.630 0.00 0.00 0.00 3.58
2161 2183 8.754096 TCGAAAAAGAAATGTGATTCAAATGTG 58.246 29.630 0.00 0.00 0.00 3.21
2162 2184 8.870160 TCGAAAAAGAAATGTGATTCAAATGT 57.130 26.923 0.00 0.00 0.00 2.71
2163 2185 9.571804 GTTCGAAAAAGAAATGTGATTCAAATG 57.428 29.630 0.00 0.00 0.00 2.32
2164 2186 9.533253 AGTTCGAAAAAGAAATGTGATTCAAAT 57.467 25.926 0.00 0.00 0.00 2.32
2165 2187 8.925161 AGTTCGAAAAAGAAATGTGATTCAAA 57.075 26.923 0.00 0.00 0.00 2.69
2166 2188 7.647715 GGAGTTCGAAAAAGAAATGTGATTCAA 59.352 33.333 0.00 0.00 0.00 2.69
2167 2189 7.013274 AGGAGTTCGAAAAAGAAATGTGATTCA 59.987 33.333 0.00 0.00 0.00 2.57
2168 2190 7.363431 AGGAGTTCGAAAAAGAAATGTGATTC 58.637 34.615 0.00 0.00 0.00 2.52
2169 2191 7.277174 AGGAGTTCGAAAAAGAAATGTGATT 57.723 32.000 0.00 0.00 0.00 2.57
2170 2192 6.884280 AGGAGTTCGAAAAAGAAATGTGAT 57.116 33.333 0.00 0.00 0.00 3.06
2171 2193 7.795482 TTAGGAGTTCGAAAAAGAAATGTGA 57.205 32.000 0.00 0.00 0.00 3.58
2172 2194 9.118236 GAATTAGGAGTTCGAAAAAGAAATGTG 57.882 33.333 0.00 0.00 0.00 3.21
2173 2195 8.846211 TGAATTAGGAGTTCGAAAAAGAAATGT 58.154 29.630 0.00 0.00 0.00 2.71
2174 2196 9.677567 TTGAATTAGGAGTTCGAAAAAGAAATG 57.322 29.630 0.00 0.00 0.00 2.32
2176 2198 9.511144 GTTTGAATTAGGAGTTCGAAAAAGAAA 57.489 29.630 0.00 0.00 32.37 2.52
2177 2199 8.899771 AGTTTGAATTAGGAGTTCGAAAAAGAA 58.100 29.630 0.00 0.00 32.37 2.52
2178 2200 8.446599 AGTTTGAATTAGGAGTTCGAAAAAGA 57.553 30.769 0.00 0.00 32.37 2.52
2179 2201 9.170584 GAAGTTTGAATTAGGAGTTCGAAAAAG 57.829 33.333 0.00 0.00 32.37 2.27
2180 2202 8.679100 TGAAGTTTGAATTAGGAGTTCGAAAAA 58.321 29.630 0.00 0.00 32.37 1.94
2181 2203 8.215926 TGAAGTTTGAATTAGGAGTTCGAAAA 57.784 30.769 0.00 0.00 32.37 2.29
2182 2204 7.795482 TGAAGTTTGAATTAGGAGTTCGAAA 57.205 32.000 0.00 0.00 32.37 3.46
2183 2205 7.795482 TTGAAGTTTGAATTAGGAGTTCGAA 57.205 32.000 0.00 0.00 0.00 3.71
2184 2206 7.979444 ATTGAAGTTTGAATTAGGAGTTCGA 57.021 32.000 0.00 0.00 0.00 3.71
2236 2258 9.774742 CCCGAACATTTTTGTTTAAATTTTTGA 57.225 25.926 0.00 0.00 31.35 2.69
2237 2259 8.527488 GCCCGAACATTTTTGTTTAAATTTTTG 58.473 29.630 0.00 0.00 31.35 2.44
2238 2260 7.702772 GGCCCGAACATTTTTGTTTAAATTTTT 59.297 29.630 0.00 0.00 31.35 1.94
2239 2261 7.148069 TGGCCCGAACATTTTTGTTTAAATTTT 60.148 29.630 0.00 0.00 31.35 1.82
2240 2262 6.318900 TGGCCCGAACATTTTTGTTTAAATTT 59.681 30.769 0.00 0.00 31.35 1.82
2241 2263 5.823045 TGGCCCGAACATTTTTGTTTAAATT 59.177 32.000 0.00 0.00 31.35 1.82
2242 2264 5.368989 TGGCCCGAACATTTTTGTTTAAAT 58.631 33.333 0.00 0.00 31.35 1.40
2243 2265 4.766375 TGGCCCGAACATTTTTGTTTAAA 58.234 34.783 0.00 0.00 31.35 1.52
2244 2266 4.402056 TGGCCCGAACATTTTTGTTTAA 57.598 36.364 0.00 0.00 31.35 1.52
2245 2267 4.310769 CATGGCCCGAACATTTTTGTTTA 58.689 39.130 0.00 0.00 31.35 2.01
2246 2268 2.990066 TGGCCCGAACATTTTTGTTT 57.010 40.000 0.00 0.00 31.35 2.83
2247 2269 2.765122 CATGGCCCGAACATTTTTGTT 58.235 42.857 0.00 0.00 34.29 2.83
2248 2270 1.607767 GCATGGCCCGAACATTTTTGT 60.608 47.619 0.00 0.00 0.00 2.83
2249 2271 1.077915 GCATGGCCCGAACATTTTTG 58.922 50.000 0.00 0.00 0.00 2.44
2250 2272 0.036483 GGCATGGCCCGAACATTTTT 60.036 50.000 8.35 0.00 44.06 1.94
2251 2273 1.596408 GGCATGGCCCGAACATTTT 59.404 52.632 8.35 0.00 44.06 1.82
2252 2274 3.297904 GGCATGGCCCGAACATTT 58.702 55.556 8.35 0.00 44.06 2.32
2262 2284 1.000607 CAGTGCAATATCTGGCATGGC 60.001 52.381 13.29 13.29 42.75 4.40
2263 2285 2.578786 TCAGTGCAATATCTGGCATGG 58.421 47.619 2.55 0.00 42.75 3.66
2264 2286 5.952526 TTATCAGTGCAATATCTGGCATG 57.047 39.130 2.55 0.00 42.75 4.06
2265 2287 8.818622 ATAATTATCAGTGCAATATCTGGCAT 57.181 30.769 2.55 0.00 42.75 4.40
2266 2288 8.517056 CAATAATTATCAGTGCAATATCTGGCA 58.483 33.333 0.00 0.00 37.77 4.92
2267 2289 8.517878 ACAATAATTATCAGTGCAATATCTGGC 58.482 33.333 0.00 0.00 33.13 4.85
2268 2290 9.836076 CACAATAATTATCAGTGCAATATCTGG 57.164 33.333 14.40 0.00 33.13 3.86
2269 2291 9.836076 CCACAATAATTATCAGTGCAATATCTG 57.164 33.333 18.57 0.00 0.00 2.90
2270 2292 9.797642 TCCACAATAATTATCAGTGCAATATCT 57.202 29.630 18.57 0.00 0.00 1.98
2272 2294 9.797642 TCTCCACAATAATTATCAGTGCAATAT 57.202 29.630 18.57 0.00 0.00 1.28
2273 2295 9.625747 TTCTCCACAATAATTATCAGTGCAATA 57.374 29.630 18.57 8.28 0.00 1.90
2274 2296 8.523915 TTCTCCACAATAATTATCAGTGCAAT 57.476 30.769 18.57 0.00 0.00 3.56
2275 2297 7.936496 TTCTCCACAATAATTATCAGTGCAA 57.064 32.000 18.57 11.44 0.00 4.08
2276 2298 7.936496 TTTCTCCACAATAATTATCAGTGCA 57.064 32.000 18.57 8.93 0.00 4.57
2277 2299 8.243426 TGTTTTCTCCACAATAATTATCAGTGC 58.757 33.333 18.57 9.01 0.00 4.40
2278 2300 9.559958 GTGTTTTCTCCACAATAATTATCAGTG 57.440 33.333 17.66 17.66 33.00 3.66
2279 2301 9.295825 TGTGTTTTCTCCACAATAATTATCAGT 57.704 29.630 0.00 0.00 39.73 3.41
2397 2419 2.225142 GGGGCTTCTCCTTCTCCTTTTT 60.225 50.000 0.00 0.00 34.39 1.94
2398 2420 1.356059 GGGGCTTCTCCTTCTCCTTTT 59.644 52.381 0.00 0.00 34.39 2.27
2399 2421 0.995803 GGGGCTTCTCCTTCTCCTTT 59.004 55.000 0.00 0.00 34.39 3.11
2400 2422 0.916845 GGGGGCTTCTCCTTCTCCTT 60.917 60.000 0.00 0.00 34.39 3.36
2401 2423 1.307430 GGGGGCTTCTCCTTCTCCT 60.307 63.158 0.00 0.00 34.39 3.69
2402 2424 3.325806 GGGGGCTTCTCCTTCTCC 58.674 66.667 0.00 0.00 34.39 3.71
2418 2440 2.360191 CCAGTGGTCCAATGGGGG 59.640 66.667 27.61 5.13 44.60 5.40
2427 2449 2.282462 CCAGTTGGGCCAGTGGTC 60.282 66.667 22.93 8.49 0.00 4.02


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

AutoCloner maintained by Alex Coulton.