Multiple sequence alignment - TraesCS4D01G135600

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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 TraesCS4D01G135600 chr4D 100.000 2264 0 0 1 2264 122177800 122180063 0.000000e+00 4181
1 TraesCS4D01G135600 chr4D 96.336 1965 53 4 1 1946 470196654 470194690 0.000000e+00 3212
2 TraesCS4D01G135600 chr2D 96.283 1964 54 6 1 1946 619853615 619855577 0.000000e+00 3205
3 TraesCS4D01G135600 chr2D 98.769 325 2 2 1941 2264 580494552 580494229 5.420000e-161 577
4 TraesCS4D01G135600 chr6D 96.130 1964 58 1 1 1946 377212189 377214152 0.000000e+00 3190
5 TraesCS4D01G135600 chr6D 95.672 1964 55 3 1 1946 62141224 62143175 0.000000e+00 3129
6 TraesCS4D01G135600 chr6D 97.633 338 4 4 1928 2264 384695131 384695465 5.420000e-161 577
7 TraesCS4D01G135600 chr3D 95.925 1963 54 4 1 1945 446922408 446924362 0.000000e+00 3158
8 TraesCS4D01G135600 chr3D 98.187 331 5 1 1935 2264 132595149 132594819 5.420000e-161 577
9 TraesCS4D01G135600 chr3D 96.784 342 4 6 1925 2264 391442918 391442582 4.220000e-157 564
10 TraesCS4D01G135600 chr3D 96.784 342 4 6 1925 2264 391710643 391710979 4.220000e-157 564
11 TraesCS4D01G135600 chr7D 95.573 1965 67 4 1 1946 528561171 528563134 0.000000e+00 3129
12 TraesCS4D01G135600 chr7D 95.211 1963 75 2 1 1945 131689378 131691339 0.000000e+00 3086
13 TraesCS4D01G135600 chr7D 99.074 324 2 1 1941 2264 414999592 414999270 4.190000e-162 580
14 TraesCS4D01G135600 chrUn 95.110 1963 76 3 1 1945 10399157 10401117 0.000000e+00 3075
15 TraesCS4D01G135600 chr5D 96.966 1813 37 7 1 1795 348341227 348343039 0.000000e+00 3027
16 TraesCS4D01G135600 chr5D 98.476 328 3 2 1937 2264 243630842 243630517 5.420000e-161 577
17 TraesCS4D01G135600 chr5D 98.769 325 2 2 1941 2264 530469157 530468834 5.420000e-161 577
18 TraesCS4D01G135600 chr5D 97.345 339 6 3 1926 2264 365431583 365431918 7.010000e-160 573
19 TraesCS4D01G135600 chr1D 93.887 1963 86 13 1 1944 446419292 446421239 0.000000e+00 2929
20 TraesCS4D01G135600 chr4B 93.743 1918 112 8 1 1915 588824074 588825986 0.000000e+00 2870
21 TraesCS4D01G135600 chr4B 93.445 1434 83 6 399 1830 467349633 467348209 0.000000e+00 2117
22 TraesCS4D01G135600 chr1A 95.087 1608 60 4 357 1946 311772302 311770696 0.000000e+00 2514
23 TraesCS4D01G135600 chr5B 93.620 815 45 4 3 816 234885633 234884825 0.000000e+00 1210


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 TraesCS4D01G135600 chr4D 122177800 122180063 2263 False 4181 4181 100.000 1 2264 1 chr4D.!!$F1 2263
1 TraesCS4D01G135600 chr4D 470194690 470196654 1964 True 3212 3212 96.336 1 1946 1 chr4D.!!$R1 1945
2 TraesCS4D01G135600 chr2D 619853615 619855577 1962 False 3205 3205 96.283 1 1946 1 chr2D.!!$F1 1945
3 TraesCS4D01G135600 chr6D 377212189 377214152 1963 False 3190 3190 96.130 1 1946 1 chr6D.!!$F2 1945
4 TraesCS4D01G135600 chr6D 62141224 62143175 1951 False 3129 3129 95.672 1 1946 1 chr6D.!!$F1 1945
5 TraesCS4D01G135600 chr3D 446922408 446924362 1954 False 3158 3158 95.925 1 1945 1 chr3D.!!$F2 1944
6 TraesCS4D01G135600 chr7D 528561171 528563134 1963 False 3129 3129 95.573 1 1946 1 chr7D.!!$F2 1945
7 TraesCS4D01G135600 chr7D 131689378 131691339 1961 False 3086 3086 95.211 1 1945 1 chr7D.!!$F1 1944
8 TraesCS4D01G135600 chrUn 10399157 10401117 1960 False 3075 3075 95.110 1 1945 1 chrUn.!!$F1 1944
9 TraesCS4D01G135600 chr5D 348341227 348343039 1812 False 3027 3027 96.966 1 1795 1 chr5D.!!$F1 1794
10 TraesCS4D01G135600 chr1D 446419292 446421239 1947 False 2929 2929 93.887 1 1944 1 chr1D.!!$F1 1943
11 TraesCS4D01G135600 chr4B 588824074 588825986 1912 False 2870 2870 93.743 1 1915 1 chr4B.!!$F1 1914
12 TraesCS4D01G135600 chr4B 467348209 467349633 1424 True 2117 2117 93.445 399 1830 1 chr4B.!!$R1 1431
13 TraesCS4D01G135600 chr1A 311770696 311772302 1606 True 2514 2514 95.087 357 1946 1 chr1A.!!$R1 1589
14 TraesCS4D01G135600 chr5B 234884825 234885633 808 True 1210 1210 93.620 3 816 1 chr5B.!!$R1 813

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
300 301 1.210478 AGTATCATTGGCCTTGCTCGT 59.79 47.619 3.32 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1623 0.034059 CCTTCTTGTCACGTGCCTCT 59.966 55.0 11.67 0.0 0.0 3.69 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
233 234 4.475016 AGGTCTTATGGTGGAGTTGCTTAT 59.525 41.667 0.00 0.00 0.00 1.73
250 251 3.424962 GCTTATGAGGTGCGTCTGAAAAC 60.425 47.826 0.00 0.00 0.00 2.43
300 301 1.210478 AGTATCATTGGCCTTGCTCGT 59.790 47.619 3.32 0.00 0.00 4.18
305 306 3.088532 TCATTGGCCTTGCTCGTATTTT 58.911 40.909 3.32 0.00 0.00 1.82
1098 1136 4.104738 TCTTTGGACAAGGTGAAGGAGAAT 59.895 41.667 0.00 0.00 0.00 2.40
1203 1241 4.711846 GGAAGGAGATATTTTGTTTGCCCT 59.288 41.667 0.00 0.00 0.00 5.19
1237 1275 0.032952 TCGTGCGCTTCCAACTAACT 59.967 50.000 9.73 0.00 0.00 2.24
1318 1357 8.120465 GTCAACACTAACATCCGTTTTATATGG 58.880 37.037 0.00 0.00 36.52 2.74
1388 1427 4.467438 AGTGCCAAAAGATATCCAAAAGGG 59.533 41.667 0.00 0.00 38.37 3.95
1417 1456 0.905357 AGATTGTCTTAGGCGCCAGT 59.095 50.000 31.54 12.06 0.00 4.00
1434 1473 2.483876 CAGTGGCTGTTCGAAGAAAGA 58.516 47.619 0.00 0.00 45.90 2.52
1500 1539 2.509336 CGGAAGCAACGCGAGGAT 60.509 61.111 15.93 0.00 0.00 3.24
1576 1615 0.459489 AAAAGCTCGCAAGGCACAAA 59.541 45.000 0.00 0.00 36.22 2.83
1584 1623 1.039856 GCAAGGCACAAAAGGAGGAA 58.960 50.000 0.00 0.00 0.00 3.36
1695 1735 8.306038 GCCATGCCAAATTTATCATGAACTATA 58.694 33.333 22.98 0.00 38.77 1.31
1749 1800 2.610219 TGTCGTGAATGAATTTGCCG 57.390 45.000 0.00 0.00 0.00 5.69
1918 1971 7.344913 TGTTTTTAGAGTTTACAACCCTACCA 58.655 34.615 0.00 0.00 0.00 3.25
1946 1999 4.082523 TGGCGGTAGGCTGCTGTC 62.083 66.667 9.25 9.25 45.94 3.51
1948 2001 4.436998 GCGGTAGGCTGCTGTCGT 62.437 66.667 13.13 0.00 43.44 4.34
1949 2002 2.261671 CGGTAGGCTGCTGTCGTT 59.738 61.111 2.91 0.00 0.00 3.85
1950 2003 2.094659 CGGTAGGCTGCTGTCGTTG 61.095 63.158 2.91 0.00 0.00 4.10
1951 2004 1.741770 GGTAGGCTGCTGTCGTTGG 60.742 63.158 1.79 0.00 0.00 3.77
1952 2005 1.292223 GTAGGCTGCTGTCGTTGGA 59.708 57.895 0.00 0.00 0.00 3.53
1953 2006 0.320421 GTAGGCTGCTGTCGTTGGAA 60.320 55.000 0.00 0.00 0.00 3.53
1954 2007 0.394938 TAGGCTGCTGTCGTTGGAAA 59.605 50.000 0.00 0.00 0.00 3.13
1955 2008 0.250901 AGGCTGCTGTCGTTGGAAAT 60.251 50.000 0.00 0.00 0.00 2.17
1956 2009 1.003118 AGGCTGCTGTCGTTGGAAATA 59.997 47.619 0.00 0.00 0.00 1.40
1957 2010 2.017049 GGCTGCTGTCGTTGGAAATAT 58.983 47.619 0.00 0.00 0.00 1.28
1958 2011 2.223340 GGCTGCTGTCGTTGGAAATATG 60.223 50.000 0.00 0.00 0.00 1.78
1959 2012 2.792542 GCTGCTGTCGTTGGAAATATGC 60.793 50.000 0.00 0.00 0.00 3.14
1960 2013 1.742831 TGCTGTCGTTGGAAATATGCC 59.257 47.619 0.00 0.00 0.00 4.40
1961 2014 1.065551 GCTGTCGTTGGAAATATGCCC 59.934 52.381 0.00 0.00 0.00 5.36
1962 2015 2.643551 CTGTCGTTGGAAATATGCCCT 58.356 47.619 0.00 0.00 0.00 5.19
1963 2016 3.804036 CTGTCGTTGGAAATATGCCCTA 58.196 45.455 0.00 0.00 0.00 3.53
1964 2017 3.804036 TGTCGTTGGAAATATGCCCTAG 58.196 45.455 0.00 0.00 0.00 3.02
1965 2018 3.452990 TGTCGTTGGAAATATGCCCTAGA 59.547 43.478 0.00 0.00 0.00 2.43
1966 2019 4.058817 GTCGTTGGAAATATGCCCTAGAG 58.941 47.826 0.00 0.00 0.00 2.43
1967 2020 3.071023 TCGTTGGAAATATGCCCTAGAGG 59.929 47.826 0.00 0.00 39.47 3.69
2036 2089 8.902540 TCGTTTATTATCCATGCTAGAATTGT 57.097 30.769 0.00 0.00 0.00 2.71
2037 2090 9.990360 TCGTTTATTATCCATGCTAGAATTGTA 57.010 29.630 0.00 0.00 0.00 2.41
2046 2099 8.206126 TCCATGCTAGAATTGTATTGATAGGA 57.794 34.615 0.00 0.00 0.00 2.94
2047 2100 8.659527 TCCATGCTAGAATTGTATTGATAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
2048 2101 9.288576 CCATGCTAGAATTGTATTGATAGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
2051 2104 9.547753 TGCTAGAATTGTATTGATAGGAAACTC 57.452 33.333 0.00 0.00 43.67 3.01
2052 2105 9.547753 GCTAGAATTGTATTGATAGGAAACTCA 57.452 33.333 0.00 0.00 43.67 3.41
2060 2113 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
2061 2114 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
2062 2115 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
2063 2116 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
2064 2117 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
2065 2118 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
2066 2119 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
2067 2120 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
2068 2121 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
2069 2122 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
2085 2138 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
2086 2139 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
2087 2140 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
2088 2141 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
2094 2147 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
2095 2148 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
2096 2149 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
2097 2150 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
2098 2151 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
2099 2152 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
2100 2153 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
2101 2154 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
2102 2155 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
2103 2156 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
2104 2157 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
2105 2158 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
2106 2159 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
2107 2160 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
2108 2161 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
2109 2162 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
2110 2163 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
2111 2164 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
2112 2165 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
2113 2166 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
2114 2167 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
2115 2168 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
2116 2169 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
2117 2170 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
2118 2171 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
2119 2172 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
2120 2173 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
2121 2174 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
2122 2175 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
2123 2176 5.078411 AGTTGACTAGCTCGTTGATCAAT 57.922 39.130 12.12 0.00 0.00 2.57
2124 2177 6.208988 AGTTGACTAGCTCGTTGATCAATA 57.791 37.500 12.12 2.38 0.00 1.90
2125 2178 6.269315 AGTTGACTAGCTCGTTGATCAATAG 58.731 40.000 12.12 13.07 0.00 1.73
2126 2179 6.095580 AGTTGACTAGCTCGTTGATCAATAGA 59.904 38.462 19.51 16.55 0.00 1.98
2127 2180 6.641169 TGACTAGCTCGTTGATCAATAGAT 57.359 37.500 19.51 16.66 37.13 1.98
2128 2181 6.442112 TGACTAGCTCGTTGATCAATAGATG 58.558 40.000 19.51 12.48 33.72 2.90
2129 2182 5.777802 ACTAGCTCGTTGATCAATAGATGG 58.222 41.667 19.51 17.62 33.72 3.51
2130 2183 4.679373 AGCTCGTTGATCAATAGATGGT 57.321 40.909 19.51 14.02 33.72 3.55
2131 2184 5.028549 AGCTCGTTGATCAATAGATGGTT 57.971 39.130 19.51 6.05 33.72 3.67
2132 2185 6.161855 AGCTCGTTGATCAATAGATGGTTA 57.838 37.500 19.51 0.00 33.72 2.85
2133 2186 5.986135 AGCTCGTTGATCAATAGATGGTTAC 59.014 40.000 19.51 1.79 33.72 2.50
2134 2187 5.107837 GCTCGTTGATCAATAGATGGTTACG 60.108 44.000 19.51 12.22 33.72 3.18
2135 2188 5.286438 TCGTTGATCAATAGATGGTTACGG 58.714 41.667 12.12 0.00 33.72 4.02
2136 2189 5.047847 CGTTGATCAATAGATGGTTACGGT 58.952 41.667 12.12 0.00 33.72 4.83
2137 2190 5.522460 CGTTGATCAATAGATGGTTACGGTT 59.478 40.000 12.12 0.00 33.72 4.44
2138 2191 6.036735 CGTTGATCAATAGATGGTTACGGTTT 59.963 38.462 12.12 0.00 33.72 3.27
2139 2192 7.407337 GTTGATCAATAGATGGTTACGGTTTC 58.593 38.462 12.12 0.00 33.72 2.78
2140 2193 6.053005 TGATCAATAGATGGTTACGGTTTCC 58.947 40.000 0.00 0.00 33.72 3.13
2141 2194 5.687166 TCAATAGATGGTTACGGTTTCCT 57.313 39.130 0.00 0.00 0.00 3.36
2142 2195 5.424757 TCAATAGATGGTTACGGTTTCCTG 58.575 41.667 0.00 0.00 0.00 3.86
2143 2196 5.188163 TCAATAGATGGTTACGGTTTCCTGA 59.812 40.000 0.00 0.00 0.00 3.86
2144 2197 3.329929 AGATGGTTACGGTTTCCTGAC 57.670 47.619 0.00 0.00 0.00 3.51
2145 2198 2.027469 AGATGGTTACGGTTTCCTGACC 60.027 50.000 0.00 0.00 36.31 4.02
2146 2199 1.129917 TGGTTACGGTTTCCTGACCA 58.870 50.000 0.00 0.00 39.78 4.02
2147 2200 1.700739 TGGTTACGGTTTCCTGACCAT 59.299 47.619 0.00 0.00 39.78 3.55
2148 2201 2.081462 GGTTACGGTTTCCTGACCATG 58.919 52.381 0.00 0.00 39.78 3.66
2149 2202 2.081462 GTTACGGTTTCCTGACCATGG 58.919 52.381 11.19 11.19 39.78 3.66
2150 2203 1.646912 TACGGTTTCCTGACCATGGA 58.353 50.000 21.47 0.00 39.78 3.41
2151 2204 0.036306 ACGGTTTCCTGACCATGGAC 59.964 55.000 21.47 13.94 39.78 4.02
2152 2205 0.036164 CGGTTTCCTGACCATGGACA 59.964 55.000 21.47 18.47 39.78 4.02
2153 2206 1.340017 CGGTTTCCTGACCATGGACAT 60.340 52.381 21.47 0.00 39.78 3.06
2154 2207 2.807676 GGTTTCCTGACCATGGACATT 58.192 47.619 21.47 0.00 39.57 2.71
2155 2208 2.493278 GGTTTCCTGACCATGGACATTG 59.507 50.000 21.47 12.72 39.57 2.82
2156 2209 2.493278 GTTTCCTGACCATGGACATTGG 59.507 50.000 21.47 16.85 32.65 3.16
2157 2210 1.667595 TCCTGACCATGGACATTGGA 58.332 50.000 21.47 18.93 0.00 3.53
2158 2211 2.207988 TCCTGACCATGGACATTGGAT 58.792 47.619 21.47 0.00 0.00 3.41
2159 2212 2.092267 TCCTGACCATGGACATTGGATG 60.092 50.000 21.47 5.31 0.00 3.51
2186 2239 7.121974 GTTGATAACGGGATCACATCATTAG 57.878 40.000 0.00 0.00 35.56 1.73
2187 2240 5.793817 TGATAACGGGATCACATCATTAGG 58.206 41.667 0.00 0.00 30.75 2.69
2188 2241 5.542251 TGATAACGGGATCACATCATTAGGA 59.458 40.000 0.00 0.00 30.75 2.94
2189 2242 4.342862 AACGGGATCACATCATTAGGAG 57.657 45.455 0.00 0.00 0.00 3.69
2190 2243 3.576861 ACGGGATCACATCATTAGGAGA 58.423 45.455 0.00 0.00 0.00 3.71
2191 2244 3.967326 ACGGGATCACATCATTAGGAGAA 59.033 43.478 0.00 0.00 0.00 2.87
2192 2245 4.594920 ACGGGATCACATCATTAGGAGAAT 59.405 41.667 0.00 0.00 0.00 2.40
2193 2246 4.934001 CGGGATCACATCATTAGGAGAATG 59.066 45.833 0.00 0.00 0.00 2.67
2194 2247 5.279657 CGGGATCACATCATTAGGAGAATGA 60.280 44.000 0.00 2.66 40.50 2.57
2195 2248 6.575847 CGGGATCACATCATTAGGAGAATGAT 60.576 42.308 6.90 6.90 45.40 2.45
2203 2256 6.752285 TCATTAGGAGAATGATGTGATGGA 57.248 37.500 0.00 0.00 32.21 3.41
2204 2257 6.528321 TCATTAGGAGAATGATGTGATGGAC 58.472 40.000 0.00 0.00 32.21 4.02
2205 2258 5.955961 TTAGGAGAATGATGTGATGGACA 57.044 39.130 0.00 0.00 39.53 4.02
2206 2259 4.849813 AGGAGAATGATGTGATGGACAA 57.150 40.909 0.00 0.00 38.36 3.18
2207 2260 4.778579 AGGAGAATGATGTGATGGACAAG 58.221 43.478 0.00 0.00 38.36 3.16
2208 2261 4.472470 AGGAGAATGATGTGATGGACAAGA 59.528 41.667 0.00 0.00 38.36 3.02
2209 2262 4.574013 GGAGAATGATGTGATGGACAAGAC 59.426 45.833 0.00 0.00 38.36 3.01
2210 2263 4.521146 AGAATGATGTGATGGACAAGACC 58.479 43.478 0.00 0.00 38.36 3.85
2211 2264 2.787473 TGATGTGATGGACAAGACCC 57.213 50.000 0.00 0.00 38.36 4.46
2212 2265 1.984424 TGATGTGATGGACAAGACCCA 59.016 47.619 0.00 0.00 38.36 4.51
2213 2266 2.374839 TGATGTGATGGACAAGACCCAA 59.625 45.455 0.00 0.00 38.36 4.12
2214 2267 3.010472 TGATGTGATGGACAAGACCCAAT 59.990 43.478 0.00 0.00 38.36 3.16
2215 2268 3.071874 TGTGATGGACAAGACCCAATC 57.928 47.619 0.00 0.00 37.22 2.67
2216 2269 2.290896 TGTGATGGACAAGACCCAATCC 60.291 50.000 0.00 0.00 37.22 3.01
2217 2270 2.025887 GTGATGGACAAGACCCAATCCT 60.026 50.000 0.00 0.00 37.22 3.24
2218 2271 3.199946 GTGATGGACAAGACCCAATCCTA 59.800 47.826 0.00 0.00 37.22 2.94
2219 2272 3.849574 TGATGGACAAGACCCAATCCTAA 59.150 43.478 0.00 0.00 37.22 2.69
2220 2273 4.080356 TGATGGACAAGACCCAATCCTAAG 60.080 45.833 0.00 0.00 37.22 2.18
2221 2274 2.026262 TGGACAAGACCCAATCCTAAGC 60.026 50.000 0.00 0.00 32.06 3.09
2222 2275 2.644676 GACAAGACCCAATCCTAAGCC 58.355 52.381 0.00 0.00 0.00 4.35
2223 2276 2.239907 GACAAGACCCAATCCTAAGCCT 59.760 50.000 0.00 0.00 0.00 4.58
2224 2277 3.454812 GACAAGACCCAATCCTAAGCCTA 59.545 47.826 0.00 0.00 0.00 3.93
2225 2278 3.456277 ACAAGACCCAATCCTAAGCCTAG 59.544 47.826 0.00 0.00 0.00 3.02
2226 2279 2.050918 AGACCCAATCCTAAGCCTAGC 58.949 52.381 0.00 0.00 0.00 3.42
2227 2280 1.768870 GACCCAATCCTAAGCCTAGCA 59.231 52.381 0.00 0.00 0.00 3.49
2228 2281 1.490910 ACCCAATCCTAAGCCTAGCAC 59.509 52.381 0.00 0.00 0.00 4.40
2229 2282 1.490490 CCCAATCCTAAGCCTAGCACA 59.510 52.381 0.00 0.00 0.00 4.57
2230 2283 2.092429 CCCAATCCTAAGCCTAGCACAA 60.092 50.000 0.00 0.00 0.00 3.33
2231 2284 3.209410 CCAATCCTAAGCCTAGCACAAG 58.791 50.000 0.00 0.00 0.00 3.16
2232 2285 3.118261 CCAATCCTAAGCCTAGCACAAGA 60.118 47.826 0.00 0.00 0.00 3.02
2233 2286 4.445448 CCAATCCTAAGCCTAGCACAAGAT 60.445 45.833 0.00 0.00 0.00 2.40
2234 2287 4.615588 ATCCTAAGCCTAGCACAAGATC 57.384 45.455 0.00 0.00 0.00 2.75
2235 2288 2.362397 TCCTAAGCCTAGCACAAGATCG 59.638 50.000 0.00 0.00 0.00 3.69
2236 2289 2.101582 CCTAAGCCTAGCACAAGATCGT 59.898 50.000 0.00 0.00 0.00 3.73
2237 2290 2.015736 AAGCCTAGCACAAGATCGTG 57.984 50.000 7.13 7.13 40.00 4.35
2238 2291 0.898320 AGCCTAGCACAAGATCGTGT 59.102 50.000 8.60 8.60 39.19 4.49
2239 2292 2.100197 AGCCTAGCACAAGATCGTGTA 58.900 47.619 14.10 0.00 39.19 2.90
2240 2293 2.099921 AGCCTAGCACAAGATCGTGTAG 59.900 50.000 14.10 8.32 39.19 2.74
2241 2294 2.159226 GCCTAGCACAAGATCGTGTAGT 60.159 50.000 14.10 7.07 39.19 2.73
2242 2295 3.676324 GCCTAGCACAAGATCGTGTAGTT 60.676 47.826 14.10 9.24 39.19 2.24
2243 2296 4.106197 CCTAGCACAAGATCGTGTAGTTC 58.894 47.826 14.10 4.56 39.19 3.01
2244 2297 2.596452 AGCACAAGATCGTGTAGTTCG 58.404 47.619 14.10 3.06 39.19 3.95
2245 2298 2.030185 AGCACAAGATCGTGTAGTTCGT 60.030 45.455 14.10 0.00 39.19 3.85
2246 2299 2.729882 GCACAAGATCGTGTAGTTCGTT 59.270 45.455 14.10 0.00 39.19 3.85
2247 2300 3.183775 GCACAAGATCGTGTAGTTCGTTT 59.816 43.478 14.10 0.00 39.19 3.60
2248 2301 4.688063 CACAAGATCGTGTAGTTCGTTTG 58.312 43.478 14.10 0.00 32.00 2.93
2249 2302 3.183775 ACAAGATCGTGTAGTTCGTTTGC 59.816 43.478 12.88 0.00 0.00 3.68
2250 2303 3.299340 AGATCGTGTAGTTCGTTTGCT 57.701 42.857 0.00 0.00 0.00 3.91
2251 2304 4.430137 AGATCGTGTAGTTCGTTTGCTA 57.570 40.909 0.00 0.00 0.00 3.49
2252 2305 4.801891 AGATCGTGTAGTTCGTTTGCTAA 58.198 39.130 0.00 0.00 0.00 3.09
2253 2306 4.857588 AGATCGTGTAGTTCGTTTGCTAAG 59.142 41.667 0.00 0.00 0.00 2.18
2254 2307 4.227512 TCGTGTAGTTCGTTTGCTAAGA 57.772 40.909 0.00 0.00 0.00 2.10
2255 2308 4.224433 TCGTGTAGTTCGTTTGCTAAGAG 58.776 43.478 0.00 0.00 0.00 2.85
2256 2309 3.181543 CGTGTAGTTCGTTTGCTAAGAGC 60.182 47.826 0.00 0.00 42.82 4.09
2257 2310 3.988517 GTGTAGTTCGTTTGCTAAGAGCT 59.011 43.478 0.00 0.00 42.97 4.09
2258 2311 4.448060 GTGTAGTTCGTTTGCTAAGAGCTT 59.552 41.667 0.00 0.00 42.97 3.74
2259 2312 5.050295 GTGTAGTTCGTTTGCTAAGAGCTTT 60.050 40.000 0.00 0.00 42.97 3.51
2260 2313 5.526111 TGTAGTTCGTTTGCTAAGAGCTTTT 59.474 36.000 0.00 0.00 42.97 2.27
2261 2314 5.096954 AGTTCGTTTGCTAAGAGCTTTTC 57.903 39.130 0.00 0.00 42.97 2.29
2262 2315 4.816925 AGTTCGTTTGCTAAGAGCTTTTCT 59.183 37.500 0.00 0.00 42.97 2.52
2263 2316 5.989777 AGTTCGTTTGCTAAGAGCTTTTCTA 59.010 36.000 0.00 0.00 42.97 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 0.534203 GGGTTTTCAGACGCACCTCA 60.534 55.000 0.00 0.00 33.16 3.86
250 251 3.286751 CACACTGGCACCAACGGG 61.287 66.667 0.00 0.00 41.29 5.28
355 356 2.664851 TGAACTCCTGCAACCGCG 60.665 61.111 0.00 0.00 42.97 6.46
365 366 2.875933 TGTTCGTTCCAATGTGAACTCC 59.124 45.455 11.02 2.68 41.95 3.85
1098 1136 2.291365 CATGGCGGAATCTTCACATCA 58.709 47.619 0.00 0.00 0.00 3.07
1203 1241 3.120616 GCGCACGATCGTAAGCATAATTA 59.879 43.478 29.91 0.00 32.57 1.40
1237 1275 0.042131 ACCGGTGGAAGGTCATAGGA 59.958 55.000 6.12 0.00 37.44 2.94
1318 1357 0.671251 CATAGAGGAGGCGGTGACTC 59.329 60.000 0.00 0.00 36.87 3.36
1388 1427 5.277538 CGCCTAAGACAATCTTCTAATTGGC 60.278 44.000 0.00 0.00 43.74 4.52
1417 1456 4.133820 TGAAATCTTTCTTCGAACAGCCA 58.866 39.130 0.00 0.00 38.02 4.75
1434 1473 3.814504 TCCTCCAAGCCTCTTTGAAAT 57.185 42.857 0.00 0.00 0.00 2.17
1500 1539 4.704833 GCTTGGCGTGCCCTCTCA 62.705 66.667 8.69 0.00 34.56 3.27
1576 1615 0.832135 TCACGTGCCTCTTCCTCCTT 60.832 55.000 11.67 0.00 0.00 3.36
1584 1623 0.034059 CCTTCTTGTCACGTGCCTCT 59.966 55.000 11.67 0.00 0.00 3.69
1749 1800 9.649024 CATTTTCACACCAAATTCAATACAAAC 57.351 29.630 0.00 0.00 0.00 2.93
1853 1905 0.618968 TCCCTCTTCTCTTCCCAGCC 60.619 60.000 0.00 0.00 0.00 4.85
1946 1999 3.403038 CCTCTAGGGCATATTTCCAACG 58.597 50.000 0.00 0.00 0.00 4.10
2010 2063 9.507329 ACAATTCTAGCATGGATAATAAACGAT 57.493 29.630 0.00 0.00 0.00 3.73
2011 2064 8.902540 ACAATTCTAGCATGGATAATAAACGA 57.097 30.769 0.00 0.00 0.00 3.85
2020 2073 8.829746 TCCTATCAATACAATTCTAGCATGGAT 58.170 33.333 0.00 0.00 0.00 3.41
2021 2074 8.206126 TCCTATCAATACAATTCTAGCATGGA 57.794 34.615 0.00 0.00 0.00 3.41
2022 2075 8.853077 TTCCTATCAATACAATTCTAGCATGG 57.147 34.615 0.00 0.00 0.00 3.66
2025 2078 9.547753 GAGTTTCCTATCAATACAATTCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
2026 2079 9.547753 TGAGTTTCCTATCAATACAATTCTAGC 57.452 33.333 0.00 0.00 0.00 3.42
2034 2087 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
2035 2088 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
2036 2089 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
2037 2090 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
2038 2091 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
2039 2092 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
2040 2093 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
2041 2094 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
2042 2095 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
2043 2096 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
2044 2097 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
2045 2098 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
2046 2099 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
2047 2100 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
2048 2101 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
2049 2102 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
2050 2103 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
2051 2104 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
2052 2105 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
2053 2106 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
2054 2107 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
2055 2108 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
2056 2109 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
2057 2110 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
2058 2111 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
2059 2112 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
2060 2113 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
2061 2114 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
2062 2115 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
2063 2116 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
2064 2117 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
2065 2118 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
2066 2119 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
2067 2120 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
2068 2121 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
2069 2122 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
2070 2123 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
2071 2124 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
2072 2125 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
2073 2126 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
2074 2127 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
2075 2128 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
2076 2129 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
2077 2130 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
2078 2131 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
2079 2132 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
2080 2133 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
2081 2134 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
2082 2135 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
2083 2136 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
2084 2137 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
2085 2138 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
2086 2139 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
2087 2140 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
2088 2141 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
2089 2142 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
2090 2143 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
2091 2144 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
2092 2145 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
2093 2146 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
2094 2147 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
2095 2148 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
2096 2149 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
2097 2150 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
2098 2151 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
2099 2152 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
2100 2153 5.638596 TTGATCAACGAGCTAGTCAACTA 57.361 39.130 3.38 0.00 0.00 2.24
2101 2154 4.521130 TTGATCAACGAGCTAGTCAACT 57.479 40.909 3.38 0.00 0.00 3.16
2102 2155 6.266323 TCTATTGATCAACGAGCTAGTCAAC 58.734 40.000 11.07 0.00 0.00 3.18
2103 2156 6.451064 TCTATTGATCAACGAGCTAGTCAA 57.549 37.500 11.07 0.55 0.00 3.18
2104 2157 6.442112 CATCTATTGATCAACGAGCTAGTCA 58.558 40.000 11.07 0.00 0.00 3.41
2105 2158 5.861251 CCATCTATTGATCAACGAGCTAGTC 59.139 44.000 11.07 0.00 0.00 2.59
2106 2159 5.303078 ACCATCTATTGATCAACGAGCTAGT 59.697 40.000 11.07 6.23 0.00 2.57
2107 2160 5.777802 ACCATCTATTGATCAACGAGCTAG 58.222 41.667 11.07 8.38 0.00 3.42
2108 2161 5.791336 ACCATCTATTGATCAACGAGCTA 57.209 39.130 11.07 0.00 0.00 3.32
2109 2162 4.679373 ACCATCTATTGATCAACGAGCT 57.321 40.909 11.07 0.00 0.00 4.09
2110 2163 5.107837 CGTAACCATCTATTGATCAACGAGC 60.108 44.000 11.07 0.00 0.00 5.03
2111 2164 5.402568 CCGTAACCATCTATTGATCAACGAG 59.597 44.000 11.07 11.28 0.00 4.18
2112 2165 5.163488 ACCGTAACCATCTATTGATCAACGA 60.163 40.000 11.07 10.80 0.00 3.85
2113 2166 5.047847 ACCGTAACCATCTATTGATCAACG 58.952 41.667 11.07 6.28 0.00 4.10
2114 2167 6.920569 AACCGTAACCATCTATTGATCAAC 57.079 37.500 11.07 0.00 0.00 3.18
2115 2168 6.540914 GGAAACCGTAACCATCTATTGATCAA 59.459 38.462 11.26 11.26 0.00 2.57
2116 2169 6.053005 GGAAACCGTAACCATCTATTGATCA 58.947 40.000 0.00 0.00 0.00 2.92
2117 2170 6.202954 CAGGAAACCGTAACCATCTATTGATC 59.797 42.308 0.00 0.00 0.00 2.92
2118 2171 6.055588 CAGGAAACCGTAACCATCTATTGAT 58.944 40.000 0.00 0.00 0.00 2.57
2119 2172 5.188163 TCAGGAAACCGTAACCATCTATTGA 59.812 40.000 0.00 0.00 0.00 2.57
2120 2173 5.293569 GTCAGGAAACCGTAACCATCTATTG 59.706 44.000 0.00 0.00 0.00 1.90
2121 2174 5.425630 GTCAGGAAACCGTAACCATCTATT 58.574 41.667 0.00 0.00 0.00 1.73
2122 2175 4.141779 GGTCAGGAAACCGTAACCATCTAT 60.142 45.833 0.00 0.00 0.00 1.98
2123 2176 3.196254 GGTCAGGAAACCGTAACCATCTA 59.804 47.826 0.00 0.00 0.00 1.98
2124 2177 2.027469 GGTCAGGAAACCGTAACCATCT 60.027 50.000 0.00 0.00 0.00 2.90
2125 2178 2.289819 TGGTCAGGAAACCGTAACCATC 60.290 50.000 0.00 0.00 42.62 3.51
2126 2179 1.700739 TGGTCAGGAAACCGTAACCAT 59.299 47.619 0.00 0.00 42.62 3.55
2127 2180 1.129917 TGGTCAGGAAACCGTAACCA 58.870 50.000 0.00 0.00 42.62 3.67
2128 2181 2.081462 CATGGTCAGGAAACCGTAACC 58.919 52.381 0.00 0.00 42.62 2.85
2129 2182 2.081462 CCATGGTCAGGAAACCGTAAC 58.919 52.381 2.57 0.00 42.62 2.50
2130 2183 1.979308 TCCATGGTCAGGAAACCGTAA 59.021 47.619 12.58 0.00 42.62 3.18
2131 2184 1.276989 GTCCATGGTCAGGAAACCGTA 59.723 52.381 12.58 0.00 42.62 4.02
2132 2185 0.036306 GTCCATGGTCAGGAAACCGT 59.964 55.000 12.58 0.00 42.62 4.83
2133 2186 0.036164 TGTCCATGGTCAGGAAACCG 59.964 55.000 12.58 0.00 42.62 4.44
2134 2187 2.493278 CAATGTCCATGGTCAGGAAACC 59.507 50.000 16.79 0.00 36.80 3.27
2135 2188 2.493278 CCAATGTCCATGGTCAGGAAAC 59.507 50.000 16.79 4.30 36.80 2.78
2136 2189 2.378208 TCCAATGTCCATGGTCAGGAAA 59.622 45.455 16.79 1.08 39.09 3.13
2137 2190 1.991813 TCCAATGTCCATGGTCAGGAA 59.008 47.619 16.79 0.75 39.09 3.36
2138 2191 1.667595 TCCAATGTCCATGGTCAGGA 58.332 50.000 16.79 15.06 39.09 3.86
2139 2192 2.304092 CATCCAATGTCCATGGTCAGG 58.696 52.381 16.79 13.14 39.09 3.86
2140 2193 3.008835 ACATCCAATGTCCATGGTCAG 57.991 47.619 16.79 4.75 39.92 3.51
2162 2215 6.147821 CCTAATGATGTGATCCCGTTATCAAC 59.852 42.308 0.00 0.00 37.61 3.18
2163 2216 6.042666 TCCTAATGATGTGATCCCGTTATCAA 59.957 38.462 0.00 0.00 37.61 2.57
2164 2217 5.542251 TCCTAATGATGTGATCCCGTTATCA 59.458 40.000 0.00 0.00 33.48 2.15
2165 2218 6.037786 TCCTAATGATGTGATCCCGTTATC 57.962 41.667 0.00 0.00 0.00 1.75
2166 2219 5.780282 TCTCCTAATGATGTGATCCCGTTAT 59.220 40.000 0.00 0.00 0.00 1.89
2167 2220 5.144832 TCTCCTAATGATGTGATCCCGTTA 58.855 41.667 0.00 0.00 0.00 3.18
2168 2221 3.967326 TCTCCTAATGATGTGATCCCGTT 59.033 43.478 0.00 0.00 0.00 4.44
2169 2222 3.576861 TCTCCTAATGATGTGATCCCGT 58.423 45.455 0.00 0.00 0.00 5.28
2170 2223 4.607293 TTCTCCTAATGATGTGATCCCG 57.393 45.455 0.00 0.00 0.00 5.14
2171 2224 6.119240 TCATTCTCCTAATGATGTGATCCC 57.881 41.667 0.00 0.00 32.21 3.85
2179 2232 7.166851 GTCCATCACATCATTCTCCTAATGAT 58.833 38.462 7.28 7.28 45.40 2.45
2180 2233 6.100134 TGTCCATCACATCATTCTCCTAATGA 59.900 38.462 3.13 3.13 40.50 2.57
2181 2234 6.293698 TGTCCATCACATCATTCTCCTAATG 58.706 40.000 0.00 0.00 0.00 1.90
2182 2235 6.505048 TGTCCATCACATCATTCTCCTAAT 57.495 37.500 0.00 0.00 0.00 1.73
2183 2236 5.955961 TGTCCATCACATCATTCTCCTAA 57.044 39.130 0.00 0.00 0.00 2.69
2184 2237 5.662657 TCTTGTCCATCACATCATTCTCCTA 59.337 40.000 0.00 0.00 33.90 2.94
2185 2238 4.472470 TCTTGTCCATCACATCATTCTCCT 59.528 41.667 0.00 0.00 33.90 3.69
2186 2239 4.574013 GTCTTGTCCATCACATCATTCTCC 59.426 45.833 0.00 0.00 33.90 3.71
2187 2240 4.574013 GGTCTTGTCCATCACATCATTCTC 59.426 45.833 0.00 0.00 33.90 2.87
2188 2241 4.521146 GGTCTTGTCCATCACATCATTCT 58.479 43.478 0.00 0.00 33.90 2.40
2189 2242 3.629398 GGGTCTTGTCCATCACATCATTC 59.371 47.826 0.00 0.00 33.90 2.67
2190 2243 3.010472 TGGGTCTTGTCCATCACATCATT 59.990 43.478 0.00 0.00 33.90 2.57
2191 2244 2.577563 TGGGTCTTGTCCATCACATCAT 59.422 45.455 0.00 0.00 33.90 2.45
2192 2245 1.984424 TGGGTCTTGTCCATCACATCA 59.016 47.619 0.00 0.00 33.90 3.07
2193 2246 2.787473 TGGGTCTTGTCCATCACATC 57.213 50.000 0.00 0.00 33.90 3.06
2194 2247 3.624777 GATTGGGTCTTGTCCATCACAT 58.375 45.455 0.00 0.00 33.90 3.21
2195 2248 2.290896 GGATTGGGTCTTGTCCATCACA 60.291 50.000 0.00 0.00 33.82 3.58
2196 2249 2.025887 AGGATTGGGTCTTGTCCATCAC 60.026 50.000 0.00 0.00 33.82 3.06
2197 2250 2.278245 AGGATTGGGTCTTGTCCATCA 58.722 47.619 0.00 0.00 33.82 3.07
2198 2251 4.455606 CTTAGGATTGGGTCTTGTCCATC 58.544 47.826 0.00 0.00 33.82 3.51
2199 2252 3.372025 GCTTAGGATTGGGTCTTGTCCAT 60.372 47.826 0.00 0.00 33.82 3.41
2200 2253 2.026262 GCTTAGGATTGGGTCTTGTCCA 60.026 50.000 0.00 0.00 33.12 4.02
2201 2254 2.644676 GCTTAGGATTGGGTCTTGTCC 58.355 52.381 0.00 0.00 0.00 4.02
2202 2255 2.239907 AGGCTTAGGATTGGGTCTTGTC 59.760 50.000 0.00 0.00 0.00 3.18
2203 2256 2.279173 AGGCTTAGGATTGGGTCTTGT 58.721 47.619 0.00 0.00 0.00 3.16
2204 2257 3.745797 GCTAGGCTTAGGATTGGGTCTTG 60.746 52.174 4.88 0.00 0.00 3.02
2205 2258 2.439880 GCTAGGCTTAGGATTGGGTCTT 59.560 50.000 4.88 0.00 0.00 3.01
2206 2259 2.050918 GCTAGGCTTAGGATTGGGTCT 58.949 52.381 4.88 0.00 0.00 3.85
2207 2260 1.768870 TGCTAGGCTTAGGATTGGGTC 59.231 52.381 4.88 0.00 0.00 4.46
2208 2261 1.490910 GTGCTAGGCTTAGGATTGGGT 59.509 52.381 4.88 0.00 29.47 4.51
2209 2262 1.490490 TGTGCTAGGCTTAGGATTGGG 59.510 52.381 4.88 0.00 29.47 4.12
2210 2263 3.118261 TCTTGTGCTAGGCTTAGGATTGG 60.118 47.826 4.88 0.00 29.47 3.16
2211 2264 4.142609 TCTTGTGCTAGGCTTAGGATTG 57.857 45.455 4.88 0.00 29.47 2.67
2212 2265 4.502259 CGATCTTGTGCTAGGCTTAGGATT 60.502 45.833 4.88 0.00 29.47 3.01
2213 2266 3.006323 CGATCTTGTGCTAGGCTTAGGAT 59.994 47.826 4.88 0.00 29.47 3.24
2214 2267 2.362397 CGATCTTGTGCTAGGCTTAGGA 59.638 50.000 4.88 0.00 0.00 2.94
2215 2268 2.101582 ACGATCTTGTGCTAGGCTTAGG 59.898 50.000 4.88 0.00 0.00 2.69
2216 2269 3.119291 CACGATCTTGTGCTAGGCTTAG 58.881 50.000 0.00 0.00 32.31 2.18
2217 2270 2.496070 ACACGATCTTGTGCTAGGCTTA 59.504 45.455 3.70 0.00 43.74 3.09
2218 2271 1.276421 ACACGATCTTGTGCTAGGCTT 59.724 47.619 3.70 0.00 43.74 4.35
2219 2272 0.898320 ACACGATCTTGTGCTAGGCT 59.102 50.000 3.70 0.00 43.74 4.58
2220 2273 2.159226 ACTACACGATCTTGTGCTAGGC 60.159 50.000 14.69 0.00 43.74 3.93
2221 2274 3.784701 ACTACACGATCTTGTGCTAGG 57.215 47.619 14.69 3.20 43.74 3.02
2222 2275 3.786576 CGAACTACACGATCTTGTGCTAG 59.213 47.826 14.69 7.03 43.74 3.42
2223 2276 3.189910 ACGAACTACACGATCTTGTGCTA 59.810 43.478 14.69 0.00 43.74 3.49
2224 2277 2.030185 ACGAACTACACGATCTTGTGCT 60.030 45.455 14.69 0.00 43.74 4.40
2225 2278 2.325761 ACGAACTACACGATCTTGTGC 58.674 47.619 14.69 1.64 43.74 4.57
2226 2279 4.688063 CAAACGAACTACACGATCTTGTG 58.312 43.478 14.69 7.12 45.41 3.33
2227 2280 3.183775 GCAAACGAACTACACGATCTTGT 59.816 43.478 10.01 10.01 34.70 3.16
2228 2281 3.428870 AGCAAACGAACTACACGATCTTG 59.571 43.478 0.00 0.00 34.70 3.02
2229 2282 3.650139 AGCAAACGAACTACACGATCTT 58.350 40.909 0.00 0.00 34.70 2.40
2230 2283 3.299340 AGCAAACGAACTACACGATCT 57.701 42.857 0.00 0.00 34.70 2.75
2231 2284 4.855388 TCTTAGCAAACGAACTACACGATC 59.145 41.667 0.00 0.00 34.70 3.69
2232 2285 4.801891 TCTTAGCAAACGAACTACACGAT 58.198 39.130 0.00 0.00 34.70 3.73
2233 2286 4.224433 CTCTTAGCAAACGAACTACACGA 58.776 43.478 0.00 0.00 34.70 4.35
2234 2287 3.181543 GCTCTTAGCAAACGAACTACACG 60.182 47.826 0.00 0.00 41.89 4.49
2235 2288 3.988517 AGCTCTTAGCAAACGAACTACAC 59.011 43.478 1.22 0.00 45.56 2.90
2236 2289 4.252971 AGCTCTTAGCAAACGAACTACA 57.747 40.909 1.22 0.00 45.56 2.74
2237 2290 5.593183 AAAGCTCTTAGCAAACGAACTAC 57.407 39.130 1.22 0.00 45.56 2.73
2238 2291 5.989777 AGAAAAGCTCTTAGCAAACGAACTA 59.010 36.000 1.22 0.00 45.56 2.24
2239 2292 4.816925 AGAAAAGCTCTTAGCAAACGAACT 59.183 37.500 1.22 0.00 45.56 3.01
2240 2293 5.096954 AGAAAAGCTCTTAGCAAACGAAC 57.903 39.130 1.22 0.00 45.56 3.95


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

AutoCloner maintained by Alex Coulton.