Multiple sequence alignment - TraesCS6D01G045300

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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 TraesCS6D01G045300 chr6D 100.000 2369 0 0 1 2369 20360812 20358444 0.000000e+00 4375
1 TraesCS6D01G045300 chr6D 88.739 1998 179 27 3 1979 146941220 146943192 0.000000e+00 2401
2 TraesCS6D01G045300 chr6D 93.402 485 24 5 1891 2368 177796568 177797051 0.000000e+00 712
3 TraesCS6D01G045300 chr6D 87.671 146 12 3 3 148 200487920 200488059 5.240000e-37 165
4 TraesCS6D01G045300 chr3D 89.960 2002 165 17 3 1985 121209333 121211317 0.000000e+00 2551
5 TraesCS6D01G045300 chr3D 88.917 1994 172 30 3 1971 562217395 562219364 0.000000e+00 2412
6 TraesCS6D01G045300 chr3D 88.124 2004 188 29 3 1985 586295524 586293550 0.000000e+00 2337
7 TraesCS6D01G045300 chr3D 94.021 485 21 5 1891 2368 126394252 126394735 0.000000e+00 728
8 TraesCS6D01G045300 chr7D 89.709 1992 168 25 3 1985 465568294 465566331 0.000000e+00 2508
9 TraesCS6D01G045300 chr7D 92.739 482 29 5 1891 2368 262739535 262739056 0.000000e+00 691
10 TraesCS6D01G045300 chr7D 84.494 445 45 11 3 429 392216060 392216498 3.640000e-113 418
11 TraesCS6D01G045300 chr1D 88.905 2010 177 26 3 1985 415632886 415630896 0.000000e+00 2435
12 TraesCS6D01G045300 chr1A 89.357 1945 174 22 52 1985 105913272 105915194 0.000000e+00 2414
13 TraesCS6D01G045300 chr6B 87.681 2005 202 22 3 1985 12592503 12590522 0.000000e+00 2292
14 TraesCS6D01G045300 chr6B 92.577 485 29 6 1890 2368 485127727 485128210 0.000000e+00 689
15 TraesCS6D01G045300 chr4A 87.638 1990 212 18 3 1985 441932098 441934060 0.000000e+00 2281
16 TraesCS6D01G045300 chr5D 85.469 1920 208 31 3 1890 430529860 430531740 0.000000e+00 1934
17 TraesCS6D01G045300 chr5D 93.361 482 25 6 1891 2368 531883331 531883809 0.000000e+00 706
18 TraesCS6D01G045300 chr5D 87.755 147 8 6 3 147 497931635 497931497 1.880000e-36 163
19 TraesCS6D01G045300 chr2A 88.351 1528 139 18 1 1516 148159252 148160752 0.000000e+00 1799
20 TraesCS6D01G045300 chr2A 80.043 466 50 25 3 437 513820469 513820016 2.960000e-79 305
21 TraesCS6D01G045300 chr7B 92.754 483 29 5 1890 2367 544723785 544724266 0.000000e+00 693
22 TraesCS6D01G045300 chr5B 92.769 484 27 7 1891 2368 88343896 88343415 0.000000e+00 693
23 TraesCS6D01G045300 chr2D 92.754 483 29 5 1891 2368 504198366 504197885 0.000000e+00 693
24 TraesCS6D01G045300 chr2D 92.181 486 30 7 1891 2369 337392574 337393058 0.000000e+00 680
25 TraesCS6D01G045300 chr5A 85.517 145 15 4 3 147 445422543 445422405 1.900000e-31 147


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 TraesCS6D01G045300 chr6D 20358444 20360812 2368 True 4375 4375 100.000 1 2369 1 chr6D.!!$R1 2368
1 TraesCS6D01G045300 chr6D 146941220 146943192 1972 False 2401 2401 88.739 3 1979 1 chr6D.!!$F1 1976
2 TraesCS6D01G045300 chr3D 121209333 121211317 1984 False 2551 2551 89.960 3 1985 1 chr3D.!!$F1 1982
3 TraesCS6D01G045300 chr3D 562217395 562219364 1969 False 2412 2412 88.917 3 1971 1 chr3D.!!$F3 1968
4 TraesCS6D01G045300 chr3D 586293550 586295524 1974 True 2337 2337 88.124 3 1985 1 chr3D.!!$R1 1982
5 TraesCS6D01G045300 chr7D 465566331 465568294 1963 True 2508 2508 89.709 3 1985 1 chr7D.!!$R2 1982
6 TraesCS6D01G045300 chr1D 415630896 415632886 1990 True 2435 2435 88.905 3 1985 1 chr1D.!!$R1 1982
7 TraesCS6D01G045300 chr1A 105913272 105915194 1922 False 2414 2414 89.357 52 1985 1 chr1A.!!$F1 1933
8 TraesCS6D01G045300 chr6B 12590522 12592503 1981 True 2292 2292 87.681 3 1985 1 chr6B.!!$R1 1982
9 TraesCS6D01G045300 chr4A 441932098 441934060 1962 False 2281 2281 87.638 3 1985 1 chr4A.!!$F1 1982
10 TraesCS6D01G045300 chr5D 430529860 430531740 1880 False 1934 1934 85.469 3 1890 1 chr5D.!!$F1 1887
11 TraesCS6D01G045300 chr2A 148159252 148160752 1500 False 1799 1799 88.351 1 1516 1 chr2A.!!$F1 1515

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
981 1053 0.462225 TCACGCCGTCCAACTTTGAA 60.462 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2119 0.11001 GCAAGAGCCACTTCTTTCGC 60.11 55.0 0.0 0.0 35.28 4.7 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
46 48 2.045926 GCCTGCCGACACATTCCT 60.046 61.111 0.00 0.00 0.00 3.36
178 196 2.947610 CCCCCAAAAACCCTCCCA 59.052 61.111 0.00 0.00 0.00 4.37
345 386 1.827315 CGAAAAAGACGCTGACGCCA 61.827 55.000 0.00 0.00 45.53 5.69
385 427 2.593956 GCCAAGAGGAAGGGTCGGT 61.594 63.158 0.00 0.00 36.89 4.69
534 597 2.176546 CACGGCCTTGTCAATGCG 59.823 61.111 0.00 5.31 0.00 4.73
542 605 1.227704 TTGTCAATGCGGTCGTGGT 60.228 52.632 0.00 0.00 0.00 4.16
730 793 2.264480 CGCCCATCGACCTCAACA 59.736 61.111 0.00 0.00 41.67 3.33
837 901 2.106683 CCTGTTCGACGGAATGCCC 61.107 63.158 0.00 0.00 34.05 5.36
941 1010 1.469251 CGATCCCGACGAGACACAAAT 60.469 52.381 0.00 0.00 38.22 2.32
949 1018 1.691976 ACGAGACACAAATCCAGGACA 59.308 47.619 0.00 0.00 0.00 4.02
974 1043 3.053291 GGCATTCACGCCGTCCAA 61.053 61.111 0.00 0.00 43.52 3.53
981 1053 0.462225 TCACGCCGTCCAACTTTGAA 60.462 50.000 0.00 0.00 0.00 2.69
1098 1170 1.064296 GGACGAGTGCGACATCGAT 59.936 57.895 5.26 0.00 41.40 3.59
1199 1271 4.457496 CACGGCGGCTGAGGACAT 62.457 66.667 17.15 0.00 0.00 3.06
1246 1318 2.747686 GGCAAGACCCCAAGACGA 59.252 61.111 0.00 0.00 0.00 4.20
1367 1439 3.013921 GGGTGTCCATTTCAAAGCGATA 58.986 45.455 0.00 0.00 0.00 2.92
1386 1458 4.698575 GATAGAGGGTGATCCAACAAGAC 58.301 47.826 0.00 0.00 38.24 3.01
1494 1569 2.238521 GCCCTCTTTTGTGTCATTCCA 58.761 47.619 0.00 0.00 0.00 3.53
1523 1602 3.632855 TGCGTGTTCATTTGCATACAA 57.367 38.095 0.00 0.00 31.31 2.41
1681 1760 1.686325 ATATGCCGCCCTCAAGTCGT 61.686 55.000 0.00 0.00 0.00 4.34
1686 1765 2.741092 GCCCTCAAGTCGTGTGGA 59.259 61.111 8.26 0.00 42.57 4.02
1695 1774 1.194781 AGTCGTGTGGAGGGAAGCAT 61.195 55.000 0.00 0.00 0.00 3.79
1698 1777 1.001641 GTGTGGAGGGAAGCATGCT 60.002 57.895 16.30 16.30 0.00 3.79
1711 1790 0.253044 GCATGCTGTGGAGGAGGTTA 59.747 55.000 11.37 0.00 0.00 2.85
1775 1857 1.201429 AAGGAGGACAAGCGGGATGT 61.201 55.000 0.00 0.00 0.00 3.06
1845 1927 2.364317 TCAAGGGAGGAGGAGCGG 60.364 66.667 0.00 0.00 0.00 5.52
1903 1985 6.373005 TGGAGATCCATACAAAGAAGAACA 57.627 37.500 0.00 0.00 42.01 3.18
1904 1986 6.778821 TGGAGATCCATACAAAGAAGAACAA 58.221 36.000 0.00 0.00 42.01 2.83
1905 1987 7.230747 TGGAGATCCATACAAAGAAGAACAAA 58.769 34.615 0.00 0.00 42.01 2.83
1906 1988 7.890127 TGGAGATCCATACAAAGAAGAACAAAT 59.110 33.333 0.00 0.00 42.01 2.32
1907 1989 8.186821 GGAGATCCATACAAAGAAGAACAAATG 58.813 37.037 0.00 0.00 35.64 2.32
1908 1990 8.868522 AGATCCATACAAAGAAGAACAAATGA 57.131 30.769 0.00 0.00 0.00 2.57
1909 1991 9.300681 AGATCCATACAAAGAAGAACAAATGAA 57.699 29.630 0.00 0.00 0.00 2.57
1911 1993 9.865321 ATCCATACAAAGAAGAACAAATGAATG 57.135 29.630 0.00 0.00 0.00 2.67
1912 1994 7.814107 TCCATACAAAGAAGAACAAATGAATGC 59.186 33.333 0.00 0.00 0.00 3.56
1913 1995 7.063780 CCATACAAAGAAGAACAAATGAATGCC 59.936 37.037 0.00 0.00 0.00 4.40
1914 1996 6.165700 ACAAAGAAGAACAAATGAATGCCT 57.834 33.333 0.00 0.00 0.00 4.75
1915 1997 6.585416 ACAAAGAAGAACAAATGAATGCCTT 58.415 32.000 0.00 0.00 0.00 4.35
1916 1998 6.703165 ACAAAGAAGAACAAATGAATGCCTTC 59.297 34.615 0.00 0.00 35.38 3.46
1917 1999 6.409524 AAGAAGAACAAATGAATGCCTTCA 57.590 33.333 6.89 6.89 45.15 3.02
1926 2008 3.219176 TGAATGCCTTCATGGAGATCC 57.781 47.619 1.24 0.00 36.46 3.36
2018 2100 1.544724 AGATGCTAGAGATCGAGGCC 58.455 55.000 0.00 0.00 0.00 5.19
2019 2101 0.170116 GATGCTAGAGATCGAGGCCG 59.830 60.000 0.00 0.00 37.07 6.13
2020 2102 1.872197 ATGCTAGAGATCGAGGCCGC 61.872 60.000 0.00 0.00 35.37 6.53
2021 2103 2.958576 CTAGAGATCGAGGCCGCC 59.041 66.667 0.00 0.00 35.37 6.13
2022 2104 1.899054 CTAGAGATCGAGGCCGCCA 60.899 63.158 13.15 0.00 35.37 5.69
2023 2105 1.455032 TAGAGATCGAGGCCGCCAA 60.455 57.895 13.15 0.00 35.37 4.52
2024 2106 0.827925 TAGAGATCGAGGCCGCCAAT 60.828 55.000 13.15 1.63 35.37 3.16
2025 2107 1.958205 GAGATCGAGGCCGCCAATG 60.958 63.158 13.15 0.26 35.37 2.82
2026 2108 3.654020 GATCGAGGCCGCCAATGC 61.654 66.667 13.15 0.00 35.37 3.56
2033 2115 4.133796 GCCGCCAATGCCAAGACC 62.134 66.667 0.00 0.00 0.00 3.85
2034 2116 2.676121 CCGCCAATGCCAAGACCA 60.676 61.111 0.00 0.00 0.00 4.02
2035 2117 2.274645 CCGCCAATGCCAAGACCAA 61.275 57.895 0.00 0.00 0.00 3.67
2036 2118 1.213537 CGCCAATGCCAAGACCAAG 59.786 57.895 0.00 0.00 0.00 3.61
2037 2119 1.593265 GCCAATGCCAAGACCAAGG 59.407 57.895 0.00 0.00 0.00 3.61
2042 2124 3.758172 GCCAAGACCAAGGCGAAA 58.242 55.556 0.00 0.00 41.70 3.46
2043 2125 1.581447 GCCAAGACCAAGGCGAAAG 59.419 57.895 0.00 0.00 41.70 2.62
2044 2126 0.889186 GCCAAGACCAAGGCGAAAGA 60.889 55.000 0.00 0.00 41.70 2.52
2045 2127 1.604604 CCAAGACCAAGGCGAAAGAA 58.395 50.000 0.00 0.00 0.00 2.52
2046 2128 1.537202 CCAAGACCAAGGCGAAAGAAG 59.463 52.381 0.00 0.00 0.00 2.85
2047 2129 2.222027 CAAGACCAAGGCGAAAGAAGT 58.778 47.619 0.00 0.00 0.00 3.01
2048 2130 1.884235 AGACCAAGGCGAAAGAAGTG 58.116 50.000 0.00 0.00 0.00 3.16
2049 2131 0.875059 GACCAAGGCGAAAGAAGTGG 59.125 55.000 0.00 0.00 34.11 4.00
2050 2132 1.172812 ACCAAGGCGAAAGAAGTGGC 61.173 55.000 0.00 0.00 31.96 5.01
2051 2133 0.890996 CCAAGGCGAAAGAAGTGGCT 60.891 55.000 0.00 0.00 40.62 4.75
2052 2134 0.519077 CAAGGCGAAAGAAGTGGCTC 59.481 55.000 0.00 0.00 37.56 4.70
2053 2135 0.398318 AAGGCGAAAGAAGTGGCTCT 59.602 50.000 0.00 0.00 37.56 4.09
2054 2136 0.398318 AGGCGAAAGAAGTGGCTCTT 59.602 50.000 0.67 0.67 37.24 2.85
2055 2137 0.519077 GGCGAAAGAAGTGGCTCTTG 59.481 55.000 6.53 0.00 35.79 3.02
2056 2138 0.110010 GCGAAAGAAGTGGCTCTTGC 60.110 55.000 6.53 0.00 35.79 4.01
2057 2139 0.164647 CGAAAGAAGTGGCTCTTGCG 59.835 55.000 6.53 3.74 45.52 4.85
2058 2140 1.512926 GAAAGAAGTGGCTCTTGCGA 58.487 50.000 6.53 0.00 40.82 5.10
2059 2141 1.462670 GAAAGAAGTGGCTCTTGCGAG 59.537 52.381 6.53 0.00 40.82 5.03
2069 2151 1.937278 CTCTTGCGAGCATGATGACT 58.063 50.000 12.92 0.00 31.27 3.41
2070 2152 1.593469 CTCTTGCGAGCATGATGACTG 59.407 52.381 12.92 0.00 31.27 3.51
2071 2153 0.656259 CTTGCGAGCATGATGACTGG 59.344 55.000 0.00 0.00 0.00 4.00
2072 2154 0.745486 TTGCGAGCATGATGACTGGG 60.745 55.000 0.00 0.00 0.00 4.45
2073 2155 1.890979 GCGAGCATGATGACTGGGG 60.891 63.158 0.00 0.00 0.00 4.96
2074 2156 1.524002 CGAGCATGATGACTGGGGT 59.476 57.895 0.00 0.00 0.00 4.95
2075 2157 0.812811 CGAGCATGATGACTGGGGTG 60.813 60.000 0.00 0.00 0.00 4.61
2076 2158 0.465097 GAGCATGATGACTGGGGTGG 60.465 60.000 0.00 0.00 0.00 4.61
2077 2159 0.915872 AGCATGATGACTGGGGTGGA 60.916 55.000 0.00 0.00 0.00 4.02
2078 2160 0.465097 GCATGATGACTGGGGTGGAG 60.465 60.000 0.00 0.00 0.00 3.86
2079 2161 1.206878 CATGATGACTGGGGTGGAGA 58.793 55.000 0.00 0.00 0.00 3.71
2080 2162 1.773052 CATGATGACTGGGGTGGAGAT 59.227 52.381 0.00 0.00 0.00 2.75
2081 2163 1.500474 TGATGACTGGGGTGGAGATC 58.500 55.000 0.00 0.00 0.00 2.75
2082 2164 1.273781 TGATGACTGGGGTGGAGATCA 60.274 52.381 0.00 0.00 0.00 2.92
2083 2165 2.053244 GATGACTGGGGTGGAGATCAT 58.947 52.381 0.00 0.00 0.00 2.45
2084 2166 1.206878 TGACTGGGGTGGAGATCATG 58.793 55.000 0.00 0.00 0.00 3.07
2085 2167 1.273781 TGACTGGGGTGGAGATCATGA 60.274 52.381 0.00 0.00 0.00 3.07
2086 2168 1.839994 GACTGGGGTGGAGATCATGAA 59.160 52.381 0.00 0.00 0.00 2.57
2087 2169 1.842562 ACTGGGGTGGAGATCATGAAG 59.157 52.381 0.00 0.00 0.00 3.02
2088 2170 1.142465 CTGGGGTGGAGATCATGAAGG 59.858 57.143 0.00 0.00 0.00 3.46
2089 2171 1.216990 GGGGTGGAGATCATGAAGGT 58.783 55.000 0.00 0.00 0.00 3.50
2090 2172 1.133976 GGGGTGGAGATCATGAAGGTG 60.134 57.143 0.00 0.00 0.00 4.00
2091 2173 1.133976 GGGTGGAGATCATGAAGGTGG 60.134 57.143 0.00 0.00 0.00 4.61
2092 2174 1.839994 GGTGGAGATCATGAAGGTGGA 59.160 52.381 0.00 0.00 0.00 4.02
2093 2175 2.441001 GGTGGAGATCATGAAGGTGGAT 59.559 50.000 0.00 0.00 0.00 3.41
2094 2176 3.495806 GGTGGAGATCATGAAGGTGGATC 60.496 52.174 0.00 0.00 38.13 3.36
2099 2181 5.705397 AGATCATGAAGGTGGATCTCAAA 57.295 39.130 0.00 0.00 43.06 2.69
2100 2182 5.435291 AGATCATGAAGGTGGATCTCAAAC 58.565 41.667 0.00 0.00 43.06 2.93
2101 2183 4.639078 TCATGAAGGTGGATCTCAAACA 57.361 40.909 0.00 0.00 0.00 2.83
2102 2184 4.326826 TCATGAAGGTGGATCTCAAACAC 58.673 43.478 0.00 0.00 0.00 3.32
2105 2187 3.625745 GGTGGATCTCAAACACCGT 57.374 52.632 2.80 0.00 44.41 4.83
2106 2188 1.156736 GGTGGATCTCAAACACCGTG 58.843 55.000 2.80 0.00 44.41 4.94
2107 2189 1.542547 GGTGGATCTCAAACACCGTGT 60.543 52.381 0.00 0.00 44.41 4.49
2108 2190 1.798813 GTGGATCTCAAACACCGTGTC 59.201 52.381 4.23 0.00 0.00 3.67
2109 2191 1.414550 TGGATCTCAAACACCGTGTCA 59.585 47.619 4.23 0.00 0.00 3.58
2110 2192 1.798813 GGATCTCAAACACCGTGTCAC 59.201 52.381 4.23 0.00 0.00 3.67
2111 2193 1.798813 GATCTCAAACACCGTGTCACC 59.201 52.381 4.23 0.00 0.00 4.02
2112 2194 0.537653 TCTCAAACACCGTGTCACCA 59.462 50.000 4.23 0.00 0.00 4.17
2113 2195 1.066071 TCTCAAACACCGTGTCACCAA 60.066 47.619 4.23 0.00 0.00 3.67
2114 2196 1.330521 CTCAAACACCGTGTCACCAAG 59.669 52.381 4.23 0.00 0.00 3.61
2115 2197 0.380378 CAAACACCGTGTCACCAAGG 59.620 55.000 4.23 0.00 44.80 3.61
2116 2198 0.253610 AAACACCGTGTCACCAAGGA 59.746 50.000 4.23 0.00 42.22 3.36
2117 2199 0.253610 AACACCGTGTCACCAAGGAA 59.746 50.000 4.23 0.00 42.22 3.36
2118 2200 0.179056 ACACCGTGTCACCAAGGAAG 60.179 55.000 0.00 0.00 42.22 3.46
2119 2201 0.105964 CACCGTGTCACCAAGGAAGA 59.894 55.000 1.67 0.00 42.22 2.87
2120 2202 0.393077 ACCGTGTCACCAAGGAAGAG 59.607 55.000 1.67 0.00 42.22 2.85
2121 2203 0.320771 CCGTGTCACCAAGGAAGAGG 60.321 60.000 0.00 0.00 42.22 3.69
2122 2204 0.951040 CGTGTCACCAAGGAAGAGGC 60.951 60.000 0.00 0.00 0.00 4.70
2123 2205 0.606673 GTGTCACCAAGGAAGAGGCC 60.607 60.000 0.00 0.00 0.00 5.19
2124 2206 1.376037 GTCACCAAGGAAGAGGCCG 60.376 63.158 0.00 0.00 0.00 6.13
2125 2207 1.841556 TCACCAAGGAAGAGGCCGT 60.842 57.895 0.00 0.00 0.00 5.68
2126 2208 1.672356 CACCAAGGAAGAGGCCGTG 60.672 63.158 0.00 0.00 37.20 4.94
2128 2210 2.750350 CAAGGAAGAGGCCGTGGT 59.250 61.111 0.00 0.00 34.34 4.16
2129 2211 1.073199 CAAGGAAGAGGCCGTGGTT 59.927 57.895 0.00 0.00 34.34 3.67
2130 2212 0.955919 CAAGGAAGAGGCCGTGGTTC 60.956 60.000 0.00 0.00 34.34 3.62
2131 2213 2.434359 GGAAGAGGCCGTGGTTCG 60.434 66.667 0.00 0.00 39.52 3.95
2132 2214 2.654877 GAAGAGGCCGTGGTTCGA 59.345 61.111 0.00 0.00 42.86 3.71
2133 2215 1.446272 GAAGAGGCCGTGGTTCGAG 60.446 63.158 0.00 0.00 42.86 4.04
2134 2216 1.874345 GAAGAGGCCGTGGTTCGAGA 61.874 60.000 0.00 0.00 42.86 4.04
2135 2217 1.469335 AAGAGGCCGTGGTTCGAGAA 61.469 55.000 0.00 0.00 42.86 2.87
2136 2218 1.446272 GAGGCCGTGGTTCGAGAAG 60.446 63.158 0.00 0.00 42.86 2.85
2137 2219 1.874345 GAGGCCGTGGTTCGAGAAGA 61.874 60.000 0.00 0.00 42.86 2.87
2138 2220 1.218316 GGCCGTGGTTCGAGAAGAT 59.782 57.895 0.00 0.00 42.86 2.40
2139 2221 1.084370 GGCCGTGGTTCGAGAAGATG 61.084 60.000 0.00 0.00 42.86 2.90
2140 2222 1.696832 GCCGTGGTTCGAGAAGATGC 61.697 60.000 0.00 0.00 42.86 3.91
2141 2223 0.389817 CCGTGGTTCGAGAAGATGCA 60.390 55.000 0.00 0.00 42.86 3.96
2142 2224 0.994995 CGTGGTTCGAGAAGATGCAG 59.005 55.000 0.00 0.00 42.86 4.41
2143 2225 1.363744 GTGGTTCGAGAAGATGCAGG 58.636 55.000 0.00 0.00 0.00 4.85
2144 2226 0.391661 TGGTTCGAGAAGATGCAGGC 60.392 55.000 0.00 0.00 0.00 4.85
2145 2227 1.092345 GGTTCGAGAAGATGCAGGCC 61.092 60.000 0.00 0.00 0.00 5.19
2146 2228 0.391661 GTTCGAGAAGATGCAGGCCA 60.392 55.000 5.01 0.00 0.00 5.36
2147 2229 0.324614 TTCGAGAAGATGCAGGCCAA 59.675 50.000 5.01 0.00 0.00 4.52
2148 2230 0.391661 TCGAGAAGATGCAGGCCAAC 60.392 55.000 5.01 0.00 0.00 3.77
2149 2231 0.674581 CGAGAAGATGCAGGCCAACA 60.675 55.000 5.01 1.90 0.00 3.33
2150 2232 1.760192 GAGAAGATGCAGGCCAACAT 58.240 50.000 5.01 8.07 0.00 2.71
2151 2233 1.674962 GAGAAGATGCAGGCCAACATC 59.325 52.381 23.64 23.64 42.45 3.06
2154 2236 3.179925 GATGCAGGCCAACATCTCA 57.820 52.632 23.74 4.80 39.66 3.27
2155 2237 1.466856 GATGCAGGCCAACATCTCAA 58.533 50.000 23.74 0.00 39.66 3.02
2156 2238 1.404391 GATGCAGGCCAACATCTCAAG 59.596 52.381 23.74 0.00 39.66 3.02
2157 2239 0.111061 TGCAGGCCAACATCTCAAGT 59.889 50.000 5.01 0.00 0.00 3.16
2158 2240 1.251251 GCAGGCCAACATCTCAAGTT 58.749 50.000 5.01 0.00 0.00 2.66
2159 2241 1.200948 GCAGGCCAACATCTCAAGTTC 59.799 52.381 5.01 0.00 0.00 3.01
2160 2242 1.466167 CAGGCCAACATCTCAAGTTCG 59.534 52.381 5.01 0.00 0.00 3.95
2161 2243 1.347707 AGGCCAACATCTCAAGTTCGA 59.652 47.619 5.01 0.00 0.00 3.71
2162 2244 1.464997 GGCCAACATCTCAAGTTCGAC 59.535 52.381 0.00 0.00 0.00 4.20
2163 2245 1.126846 GCCAACATCTCAAGTTCGACG 59.873 52.381 0.00 0.00 0.00 5.12
2164 2246 2.672714 CCAACATCTCAAGTTCGACGA 58.327 47.619 0.00 0.00 0.00 4.20
2165 2247 2.408704 CCAACATCTCAAGTTCGACGAC 59.591 50.000 0.00 0.00 0.00 4.34
2166 2248 1.965083 ACATCTCAAGTTCGACGACG 58.035 50.000 0.00 0.00 41.26 5.12
2178 2260 1.865340 TCGACGACGAGTGATCTATGG 59.135 52.381 5.75 0.00 43.81 2.74
2179 2261 1.865340 CGACGACGAGTGATCTATGGA 59.135 52.381 0.00 0.00 42.66 3.41
2180 2262 2.096664 CGACGACGAGTGATCTATGGAG 60.097 54.545 0.00 0.00 42.66 3.86
2181 2263 2.222886 ACGACGAGTGATCTATGGAGG 58.777 52.381 0.00 0.00 0.00 4.30
2182 2264 1.068885 CGACGAGTGATCTATGGAGGC 60.069 57.143 0.00 0.00 0.00 4.70
2183 2265 0.955178 ACGAGTGATCTATGGAGGCG 59.045 55.000 0.00 0.00 0.00 5.52
2184 2266 1.239347 CGAGTGATCTATGGAGGCGA 58.761 55.000 0.00 0.00 0.00 5.54
2185 2267 1.198867 CGAGTGATCTATGGAGGCGAG 59.801 57.143 0.00 0.00 0.00 5.03
2186 2268 0.965439 AGTGATCTATGGAGGCGAGC 59.035 55.000 0.00 0.00 0.00 5.03
2187 2269 0.387878 GTGATCTATGGAGGCGAGCG 60.388 60.000 0.00 0.00 0.00 5.03
2188 2270 1.445238 GATCTATGGAGGCGAGCGC 60.445 63.158 6.27 6.27 41.06 5.92
2198 2280 2.877691 GCGAGCGCCATCCTTTTT 59.122 55.556 2.29 0.00 34.56 1.94
2213 2295 3.043998 TTTTTGTATGCCGGCAGGT 57.956 47.368 35.36 21.86 40.50 4.00
2214 2296 0.600557 TTTTTGTATGCCGGCAGGTG 59.399 50.000 35.36 0.00 40.50 4.00
2215 2297 0.538516 TTTTGTATGCCGGCAGGTGT 60.539 50.000 35.36 20.64 40.50 4.16
2216 2298 1.240641 TTTGTATGCCGGCAGGTGTG 61.241 55.000 35.36 0.00 40.50 3.82
2226 2308 3.271014 CAGGTGTGCTGGCATGAC 58.729 61.111 0.00 0.00 0.00 3.06
2227 2309 2.034687 AGGTGTGCTGGCATGACC 59.965 61.111 14.86 14.86 39.84 4.02
2229 2311 2.629656 GGTGTGCTGGCATGACCAC 61.630 63.158 16.70 11.60 46.36 4.16
2230 2312 2.669229 TGTGCTGGCATGACCACG 60.669 61.111 0.00 0.00 46.36 4.94
2231 2313 3.434319 GTGCTGGCATGACCACGG 61.434 66.667 0.00 0.00 46.36 4.94
2232 2314 4.720902 TGCTGGCATGACCACGGG 62.721 66.667 0.00 0.00 46.36 5.28
2253 2335 3.849953 GCGATGGCGTGGTCGAAC 61.850 66.667 0.00 0.00 40.11 3.95
2254 2336 2.126071 CGATGGCGTGGTCGAACT 60.126 61.111 0.33 0.00 40.11 3.01
2255 2337 2.158959 CGATGGCGTGGTCGAACTC 61.159 63.158 0.33 0.00 40.11 3.01
2256 2338 1.080093 GATGGCGTGGTCGAACTCA 60.080 57.895 0.33 0.00 39.71 3.41
2257 2339 0.669318 GATGGCGTGGTCGAACTCAA 60.669 55.000 0.33 0.00 39.71 3.02
2258 2340 0.670546 ATGGCGTGGTCGAACTCAAG 60.671 55.000 0.33 0.00 39.71 3.02
2259 2341 1.300697 GGCGTGGTCGAACTCAAGT 60.301 57.895 0.33 0.00 39.71 3.16
2260 2342 1.282930 GGCGTGGTCGAACTCAAGTC 61.283 60.000 0.33 0.00 39.71 3.01
2261 2343 1.282930 GCGTGGTCGAACTCAAGTCC 61.283 60.000 0.33 0.00 39.71 3.85
2262 2344 0.666577 CGTGGTCGAACTCAAGTCCC 60.667 60.000 0.33 0.00 39.71 4.46
2263 2345 0.391597 GTGGTCGAACTCAAGTCCCA 59.608 55.000 0.33 0.00 0.00 4.37
2264 2346 0.391597 TGGTCGAACTCAAGTCCCAC 59.608 55.000 0.33 0.00 0.00 4.61
2265 2347 0.320508 GGTCGAACTCAAGTCCCACC 60.321 60.000 0.00 0.00 0.00 4.61
2266 2348 0.320508 GTCGAACTCAAGTCCCACCC 60.321 60.000 0.00 0.00 0.00 4.61
2267 2349 0.471211 TCGAACTCAAGTCCCACCCT 60.471 55.000 0.00 0.00 0.00 4.34
2268 2350 0.396811 CGAACTCAAGTCCCACCCTT 59.603 55.000 0.00 0.00 0.00 3.95
2269 2351 1.202770 CGAACTCAAGTCCCACCCTTT 60.203 52.381 0.00 0.00 0.00 3.11
2270 2352 2.748465 CGAACTCAAGTCCCACCCTTTT 60.748 50.000 0.00 0.00 0.00 2.27
2271 2353 3.296854 GAACTCAAGTCCCACCCTTTTT 58.703 45.455 0.00 0.00 0.00 1.94
2287 2369 2.007360 TTTTTGTGTGCTGGCAAGTG 57.993 45.000 0.00 0.00 0.00 3.16
2288 2370 0.894141 TTTTGTGTGCTGGCAAGTGT 59.106 45.000 0.00 0.00 0.00 3.55
2289 2371 0.173029 TTTGTGTGCTGGCAAGTGTG 59.827 50.000 0.00 0.00 0.00 3.82
2299 2381 3.716006 CAAGTGTGCCGTCCGCTG 61.716 66.667 0.00 0.00 38.78 5.18
2300 2382 4.988598 AAGTGTGCCGTCCGCTGG 62.989 66.667 0.00 0.00 38.78 4.85
2323 2405 2.177531 GCGCCAGCATGAACTGTG 59.822 61.111 0.00 0.00 44.35 3.66
2324 2406 2.620112 GCGCCAGCATGAACTGTGT 61.620 57.895 0.00 0.00 44.35 3.72
2325 2407 1.208358 CGCCAGCATGAACTGTGTG 59.792 57.895 0.00 0.00 39.69 3.82
2326 2408 1.582968 GCCAGCATGAACTGTGTGG 59.417 57.895 0.00 0.00 39.69 4.17
2327 2409 1.174712 GCCAGCATGAACTGTGTGGT 61.175 55.000 0.00 0.00 39.69 4.16
2328 2410 0.594602 CCAGCATGAACTGTGTGGTG 59.405 55.000 0.00 11.13 39.69 4.17
2329 2411 1.311859 CAGCATGAACTGTGTGGTGT 58.688 50.000 0.00 0.00 39.69 4.16
2330 2412 1.677576 CAGCATGAACTGTGTGGTGTT 59.322 47.619 0.00 0.00 39.69 3.32
2331 2413 2.099592 CAGCATGAACTGTGTGGTGTTT 59.900 45.455 0.00 0.00 39.69 2.83
2332 2414 2.760092 AGCATGAACTGTGTGGTGTTTT 59.240 40.909 0.00 0.00 0.00 2.43
2333 2415 3.195396 AGCATGAACTGTGTGGTGTTTTT 59.805 39.130 0.00 0.00 0.00 1.94
2334 2416 3.306703 GCATGAACTGTGTGGTGTTTTTG 59.693 43.478 0.00 0.00 0.00 2.44
2335 2417 4.742417 CATGAACTGTGTGGTGTTTTTGA 58.258 39.130 0.00 0.00 0.00 2.69
2336 2418 4.855715 TGAACTGTGTGGTGTTTTTGAA 57.144 36.364 0.00 0.00 0.00 2.69
2337 2419 4.804108 TGAACTGTGTGGTGTTTTTGAAG 58.196 39.130 0.00 0.00 0.00 3.02
2338 2420 3.230743 ACTGTGTGGTGTTTTTGAAGC 57.769 42.857 0.00 0.00 0.00 3.86
2339 2421 2.825532 ACTGTGTGGTGTTTTTGAAGCT 59.174 40.909 0.00 0.00 0.00 3.74
2340 2422 3.181397 CTGTGTGGTGTTTTTGAAGCTG 58.819 45.455 0.00 0.00 0.00 4.24
2341 2423 1.926510 GTGTGGTGTTTTTGAAGCTGC 59.073 47.619 0.00 0.00 0.00 5.25
2342 2424 1.134848 TGTGGTGTTTTTGAAGCTGCC 60.135 47.619 0.00 0.00 0.00 4.85
2343 2425 1.134848 GTGGTGTTTTTGAAGCTGCCA 60.135 47.619 0.00 0.00 0.00 4.92
2344 2426 1.761784 TGGTGTTTTTGAAGCTGCCAT 59.238 42.857 0.00 0.00 0.00 4.40
2345 2427 2.170187 TGGTGTTTTTGAAGCTGCCATT 59.830 40.909 0.00 0.00 0.00 3.16
2346 2428 2.545106 GGTGTTTTTGAAGCTGCCATTG 59.455 45.455 0.00 0.00 0.00 2.82
2347 2429 3.197265 GTGTTTTTGAAGCTGCCATTGT 58.803 40.909 0.00 0.00 0.00 2.71
2348 2430 4.367450 GTGTTTTTGAAGCTGCCATTGTA 58.633 39.130 0.00 0.00 0.00 2.41
2349 2431 4.990426 GTGTTTTTGAAGCTGCCATTGTAT 59.010 37.500 0.00 0.00 0.00 2.29
2350 2432 4.989797 TGTTTTTGAAGCTGCCATTGTATG 59.010 37.500 0.00 0.00 0.00 2.39
2351 2433 2.945447 TTGAAGCTGCCATTGTATGC 57.055 45.000 0.00 0.00 0.00 3.14
2352 2434 1.105457 TGAAGCTGCCATTGTATGCC 58.895 50.000 0.00 0.00 0.00 4.40
2353 2435 0.029834 GAAGCTGCCATTGTATGCCG 59.970 55.000 0.00 0.00 0.00 5.69
2354 2436 1.386525 AAGCTGCCATTGTATGCCGG 61.387 55.000 0.00 0.00 0.00 6.13
2355 2437 2.723746 CTGCCATTGTATGCCGGC 59.276 61.111 22.73 22.73 45.11 6.13
2357 2439 4.629115 GCCATTGTATGCCGGCGC 62.629 66.667 23.90 15.15 34.26 6.53
2358 2440 2.901840 CCATTGTATGCCGGCGCT 60.902 61.111 23.90 14.61 35.36 5.92
2359 2441 2.328989 CATTGTATGCCGGCGCTG 59.671 61.111 23.90 9.96 35.36 5.18
2360 2442 2.901840 ATTGTATGCCGGCGCTGG 60.902 61.111 31.57 31.57 35.36 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 2.282039 CCGGCTCAAAAATGGGCCA 61.282 57.895 19.01 9.61 44.27 5.36
102 104 4.798682 GAGGGGGAGGGAAGGCGA 62.799 72.222 0.00 0.00 0.00 5.54
106 108 4.845307 GGGGGAGGGGGAGGGAAG 62.845 77.778 0.00 0.00 0.00 3.46
330 371 1.069090 TTCTGGCGTCAGCGTCTTT 59.931 52.632 13.43 0.00 46.35 2.52
345 386 3.249189 TCCCTTGCCCGCTGTTCT 61.249 61.111 0.00 0.00 0.00 3.01
468 531 4.329545 GCCTCCCTCGTTGCCACA 62.330 66.667 0.00 0.00 0.00 4.17
910 979 2.797278 CGGGATCGTAGCAAGCCCT 61.797 63.158 0.00 0.00 36.62 5.19
974 1043 2.154462 CCGCCTGATCTTGTTCAAAGT 58.846 47.619 0.00 0.00 0.00 2.66
981 1053 1.078143 GAAGGCCGCCTGATCTTGT 60.078 57.895 14.19 0.00 32.13 3.16
1098 1170 1.374947 CTCGAACAAAGGCTCCCCA 59.625 57.895 0.00 0.00 0.00 4.96
1199 1271 2.945008 CTCCAACACTCACAAAGAAGCA 59.055 45.455 0.00 0.00 0.00 3.91
1367 1439 2.304180 CAGTCTTGTTGGATCACCCTCT 59.696 50.000 0.00 0.00 35.38 3.69
1386 1458 1.660104 GTGGCACAAAACTTGTTGCAG 59.340 47.619 13.86 0.00 44.16 4.41
1494 1569 4.091800 GCAAATGAACACGCAAGCATAAAT 59.908 37.500 0.00 0.00 45.62 1.40
1523 1602 4.409718 TCATGCAAGCATATTGGCAAAT 57.590 36.364 3.01 0.00 40.02 2.32
1681 1760 1.001764 CAGCATGCTTCCCTCCACA 60.002 57.895 19.98 0.00 0.00 4.17
1686 1765 1.302285 CTCCACAGCATGCTTCCCT 59.698 57.895 19.98 0.00 42.53 4.20
1695 1774 0.909610 CCCTAACCTCCTCCACAGCA 60.910 60.000 0.00 0.00 0.00 4.41
1698 1777 0.613853 CGTCCCTAACCTCCTCCACA 60.614 60.000 0.00 0.00 0.00 4.17
1801 1883 0.554305 TTGCTCATCATGCCCTCCAT 59.446 50.000 0.00 0.00 33.39 3.41
1845 1927 4.640805 TTGTTCTTCTTTGTATCGACGC 57.359 40.909 0.00 0.00 0.00 5.19
1848 1930 7.287950 CGTTCATTTGTTCTTCTTTGTATCGA 58.712 34.615 0.00 0.00 0.00 3.59
1890 1972 7.288810 AGGCATTCATTTGTTCTTCTTTGTA 57.711 32.000 0.00 0.00 0.00 2.41
1891 1973 6.165700 AGGCATTCATTTGTTCTTCTTTGT 57.834 33.333 0.00 0.00 0.00 2.83
1892 1974 6.702723 TGAAGGCATTCATTTGTTCTTCTTTG 59.297 34.615 10.22 0.00 40.54 2.77
1893 1975 6.819284 TGAAGGCATTCATTTGTTCTTCTTT 58.181 32.000 10.22 0.00 40.54 2.52
1894 1976 6.409524 TGAAGGCATTCATTTGTTCTTCTT 57.590 33.333 10.22 0.00 40.54 2.52
1907 1989 3.219176 TGGATCTCCATGAAGGCATTC 57.781 47.619 3.66 3.66 42.01 2.67
1908 1990 3.675348 TTGGATCTCCATGAAGGCATT 57.325 42.857 0.00 0.00 46.97 3.56
1909 1991 3.563223 CTTTGGATCTCCATGAAGGCAT 58.437 45.455 0.00 0.00 46.97 4.40
1910 1992 2.357465 CCTTTGGATCTCCATGAAGGCA 60.357 50.000 14.03 0.00 43.30 4.75
1911 1993 2.092212 TCCTTTGGATCTCCATGAAGGC 60.092 50.000 18.89 0.00 46.44 4.35
1913 1995 3.457380 TCCTCCTTTGGATCTCCATGAAG 59.543 47.826 0.00 2.05 46.97 3.02
1914 1996 3.457380 CTCCTCCTTTGGATCTCCATGAA 59.543 47.826 0.00 0.00 46.97 2.57
1915 1997 3.044156 CTCCTCCTTTGGATCTCCATGA 58.956 50.000 0.00 0.00 46.97 3.07
1916 1998 2.106166 CCTCCTCCTTTGGATCTCCATG 59.894 54.545 0.00 0.00 46.97 3.66
1917 1999 2.416638 CCTCCTCCTTTGGATCTCCAT 58.583 52.381 0.00 0.00 46.97 3.41
1918 2000 1.885049 CCTCCTCCTTTGGATCTCCA 58.115 55.000 0.00 0.00 45.94 3.86
1919 2001 0.472044 GCCTCCTCCTTTGGATCTCC 59.528 60.000 0.00 0.00 35.30 3.71
1920 2002 1.506025 AGCCTCCTCCTTTGGATCTC 58.494 55.000 0.00 0.00 35.30 2.75
1921 2003 1.563410 CAAGCCTCCTCCTTTGGATCT 59.437 52.381 0.00 0.00 35.30 2.75
1922 2004 1.561542 TCAAGCCTCCTCCTTTGGATC 59.438 52.381 0.00 0.00 35.30 3.36
1923 2005 1.563410 CTCAAGCCTCCTCCTTTGGAT 59.437 52.381 0.00 0.00 35.30 3.41
1924 2006 0.987294 CTCAAGCCTCCTCCTTTGGA 59.013 55.000 0.00 0.00 34.52 3.53
1925 2007 0.987294 TCTCAAGCCTCCTCCTTTGG 59.013 55.000 0.00 0.00 0.00 3.28
1926 2008 2.641305 CATCTCAAGCCTCCTCCTTTG 58.359 52.381 0.00 0.00 0.00 2.77
1927 2009 1.563410 CCATCTCAAGCCTCCTCCTTT 59.437 52.381 0.00 0.00 0.00 3.11
2018 2100 1.213537 CTTGGTCTTGGCATTGGCG 59.786 57.895 5.68 0.00 42.47 5.69
2019 2101 1.593265 CCTTGGTCTTGGCATTGGC 59.407 57.895 2.73 2.73 40.13 4.52
2025 2107 0.889186 TCTTTCGCCTTGGTCTTGGC 60.889 55.000 0.00 0.00 45.25 4.52
2026 2108 1.537202 CTTCTTTCGCCTTGGTCTTGG 59.463 52.381 0.00 0.00 0.00 3.61
2027 2109 2.031682 CACTTCTTTCGCCTTGGTCTTG 60.032 50.000 0.00 0.00 0.00 3.02
2028 2110 2.222027 CACTTCTTTCGCCTTGGTCTT 58.778 47.619 0.00 0.00 0.00 3.01
2029 2111 1.543429 CCACTTCTTTCGCCTTGGTCT 60.543 52.381 0.00 0.00 0.00 3.85
2030 2112 0.875059 CCACTTCTTTCGCCTTGGTC 59.125 55.000 0.00 0.00 0.00 4.02
2031 2113 1.172812 GCCACTTCTTTCGCCTTGGT 61.173 55.000 0.00 0.00 0.00 3.67
2032 2114 0.890996 AGCCACTTCTTTCGCCTTGG 60.891 55.000 0.00 0.00 0.00 3.61
2033 2115 0.519077 GAGCCACTTCTTTCGCCTTG 59.481 55.000 0.00 0.00 0.00 3.61
2034 2116 0.398318 AGAGCCACTTCTTTCGCCTT 59.602 50.000 0.00 0.00 0.00 4.35
2035 2117 0.398318 AAGAGCCACTTCTTTCGCCT 59.602 50.000 0.00 0.00 33.74 5.52
2036 2118 0.519077 CAAGAGCCACTTCTTTCGCC 59.481 55.000 0.00 0.00 35.28 5.54
2037 2119 0.110010 GCAAGAGCCACTTCTTTCGC 60.110 55.000 0.00 0.00 35.28 4.70
2038 2120 0.164647 CGCAAGAGCCACTTCTTTCG 59.835 55.000 0.00 0.00 37.45 3.46
2039 2121 1.512926 TCGCAAGAGCCACTTCTTTC 58.487 50.000 0.00 0.00 45.01 2.62
2040 2122 3.706055 TCGCAAGAGCCACTTCTTT 57.294 47.368 0.00 0.00 45.01 2.52
2052 2134 0.656259 CCAGTCATCATGCTCGCAAG 59.344 55.000 0.00 0.00 0.00 4.01
2053 2135 0.745486 CCCAGTCATCATGCTCGCAA 60.745 55.000 0.00 0.00 0.00 4.85
2054 2136 1.153309 CCCAGTCATCATGCTCGCA 60.153 57.895 0.00 0.00 0.00 5.10
2055 2137 1.890979 CCCCAGTCATCATGCTCGC 60.891 63.158 0.00 0.00 0.00 5.03
2056 2138 0.812811 CACCCCAGTCATCATGCTCG 60.813 60.000 0.00 0.00 0.00 5.03
2057 2139 0.465097 CCACCCCAGTCATCATGCTC 60.465 60.000 0.00 0.00 0.00 4.26
2058 2140 0.915872 TCCACCCCAGTCATCATGCT 60.916 55.000 0.00 0.00 0.00 3.79
2059 2141 0.465097 CTCCACCCCAGTCATCATGC 60.465 60.000 0.00 0.00 0.00 4.06
2060 2142 1.206878 TCTCCACCCCAGTCATCATG 58.793 55.000 0.00 0.00 0.00 3.07
2061 2143 2.053244 GATCTCCACCCCAGTCATCAT 58.947 52.381 0.00 0.00 0.00 2.45
2062 2144 1.273781 TGATCTCCACCCCAGTCATCA 60.274 52.381 0.00 0.00 0.00 3.07
2063 2145 1.500474 TGATCTCCACCCCAGTCATC 58.500 55.000 0.00 0.00 0.00 2.92
2064 2146 1.773052 CATGATCTCCACCCCAGTCAT 59.227 52.381 0.00 0.00 0.00 3.06
2065 2147 1.206878 CATGATCTCCACCCCAGTCA 58.793 55.000 0.00 0.00 0.00 3.41
2066 2148 1.500474 TCATGATCTCCACCCCAGTC 58.500 55.000 0.00 0.00 0.00 3.51
2067 2149 1.842562 CTTCATGATCTCCACCCCAGT 59.157 52.381 0.00 0.00 0.00 4.00
2068 2150 1.142465 CCTTCATGATCTCCACCCCAG 59.858 57.143 0.00 0.00 0.00 4.45
2069 2151 1.216064 CCTTCATGATCTCCACCCCA 58.784 55.000 0.00 0.00 0.00 4.96
2070 2152 1.133976 CACCTTCATGATCTCCACCCC 60.134 57.143 0.00 0.00 0.00 4.95
2071 2153 1.133976 CCACCTTCATGATCTCCACCC 60.134 57.143 0.00 0.00 0.00 4.61
2072 2154 1.839994 TCCACCTTCATGATCTCCACC 59.160 52.381 0.00 0.00 0.00 4.61
2073 2155 3.390639 AGATCCACCTTCATGATCTCCAC 59.609 47.826 0.00 0.00 40.88 4.02
2074 2156 3.662078 AGATCCACCTTCATGATCTCCA 58.338 45.455 0.00 0.00 40.88 3.86
2077 2159 5.045359 TGTTTGAGATCCACCTTCATGATCT 60.045 40.000 0.00 1.12 45.91 2.75
2078 2160 5.065731 GTGTTTGAGATCCACCTTCATGATC 59.934 44.000 0.00 0.00 36.08 2.92
2079 2161 4.946157 GTGTTTGAGATCCACCTTCATGAT 59.054 41.667 0.00 0.00 0.00 2.45
2080 2162 4.326826 GTGTTTGAGATCCACCTTCATGA 58.673 43.478 0.00 0.00 0.00 3.07
2081 2163 3.441572 GGTGTTTGAGATCCACCTTCATG 59.558 47.826 9.99 0.00 44.21 3.07
2082 2164 3.690460 GGTGTTTGAGATCCACCTTCAT 58.310 45.455 9.99 0.00 44.21 2.57
2083 2165 2.549992 CGGTGTTTGAGATCCACCTTCA 60.550 50.000 13.94 0.00 45.18 3.02
2084 2166 2.076863 CGGTGTTTGAGATCCACCTTC 58.923 52.381 13.94 0.00 45.18 3.46
2085 2167 1.420138 ACGGTGTTTGAGATCCACCTT 59.580 47.619 13.94 4.41 45.18 3.50
2086 2168 1.056660 ACGGTGTTTGAGATCCACCT 58.943 50.000 13.94 2.00 45.18 4.00
2087 2169 1.156736 CACGGTGTTTGAGATCCACC 58.843 55.000 7.76 7.76 44.16 4.61
2088 2170 1.798813 GACACGGTGTTTGAGATCCAC 59.201 52.381 15.94 0.00 0.00 4.02
2089 2171 1.414550 TGACACGGTGTTTGAGATCCA 59.585 47.619 15.94 3.11 0.00 3.41
2090 2172 1.798813 GTGACACGGTGTTTGAGATCC 59.201 52.381 15.94 0.28 0.00 3.36
2091 2173 1.798813 GGTGACACGGTGTTTGAGATC 59.201 52.381 15.94 1.04 0.00 2.75
2092 2174 1.140052 TGGTGACACGGTGTTTGAGAT 59.860 47.619 15.94 0.00 33.40 2.75
2093 2175 0.537653 TGGTGACACGGTGTTTGAGA 59.462 50.000 15.94 0.00 33.40 3.27
2094 2176 1.330521 CTTGGTGACACGGTGTTTGAG 59.669 52.381 15.94 6.05 42.67 3.02
2095 2177 1.374560 CTTGGTGACACGGTGTTTGA 58.625 50.000 15.94 0.00 42.67 2.69
2096 2178 0.380378 CCTTGGTGACACGGTGTTTG 59.620 55.000 15.94 2.80 44.43 2.93
2097 2179 2.788515 CCTTGGTGACACGGTGTTT 58.211 52.632 15.94 0.00 44.43 2.83
2098 2180 4.551729 CCTTGGTGACACGGTGTT 57.448 55.556 15.94 0.00 44.43 3.32
2103 2185 0.951040 GCCTCTTCCTTGGTGACACG 60.951 60.000 0.00 0.00 42.67 4.49
2104 2186 0.606673 GGCCTCTTCCTTGGTGACAC 60.607 60.000 0.00 0.00 42.67 3.67
2105 2187 1.761174 GGCCTCTTCCTTGGTGACA 59.239 57.895 0.00 0.00 39.83 3.58
2106 2188 1.376037 CGGCCTCTTCCTTGGTGAC 60.376 63.158 0.00 0.00 0.00 3.67
2107 2189 1.841556 ACGGCCTCTTCCTTGGTGA 60.842 57.895 0.00 0.00 0.00 4.02
2108 2190 1.672356 CACGGCCTCTTCCTTGGTG 60.672 63.158 0.00 0.00 0.00 4.17
2109 2191 2.750350 CACGGCCTCTTCCTTGGT 59.250 61.111 0.00 0.00 0.00 3.67
2110 2192 2.045926 CCACGGCCTCTTCCTTGG 60.046 66.667 0.00 0.00 38.88 3.61
2111 2193 0.955919 GAACCACGGCCTCTTCCTTG 60.956 60.000 0.00 0.00 0.00 3.61
2112 2194 1.375326 GAACCACGGCCTCTTCCTT 59.625 57.895 0.00 0.00 0.00 3.36
2113 2195 2.943978 CGAACCACGGCCTCTTCCT 61.944 63.158 0.00 0.00 38.46 3.36
2114 2196 2.434359 CGAACCACGGCCTCTTCC 60.434 66.667 0.00 0.00 38.46 3.46
2115 2197 1.446272 CTCGAACCACGGCCTCTTC 60.446 63.158 0.00 0.00 42.82 2.87
2116 2198 1.469335 TTCTCGAACCACGGCCTCTT 61.469 55.000 0.00 0.00 42.82 2.85
2117 2199 1.878656 CTTCTCGAACCACGGCCTCT 61.879 60.000 0.00 0.00 42.82 3.69
2118 2200 1.446272 CTTCTCGAACCACGGCCTC 60.446 63.158 0.00 0.00 42.82 4.70
2119 2201 1.258445 ATCTTCTCGAACCACGGCCT 61.258 55.000 0.00 0.00 42.82 5.19
2120 2202 1.084370 CATCTTCTCGAACCACGGCC 61.084 60.000 0.00 0.00 42.82 6.13
2121 2203 1.696832 GCATCTTCTCGAACCACGGC 61.697 60.000 0.00 0.00 42.82 5.68
2122 2204 0.389817 TGCATCTTCTCGAACCACGG 60.390 55.000 0.00 0.00 42.82 4.94
2123 2205 0.994995 CTGCATCTTCTCGAACCACG 59.005 55.000 0.00 0.00 44.09 4.94
2124 2206 1.363744 CCTGCATCTTCTCGAACCAC 58.636 55.000 0.00 0.00 0.00 4.16
2125 2207 0.391661 GCCTGCATCTTCTCGAACCA 60.392 55.000 0.00 0.00 0.00 3.67
2126 2208 1.092345 GGCCTGCATCTTCTCGAACC 61.092 60.000 0.00 0.00 0.00 3.62
2127 2209 0.391661 TGGCCTGCATCTTCTCGAAC 60.392 55.000 3.32 0.00 0.00 3.95
2128 2210 0.324614 TTGGCCTGCATCTTCTCGAA 59.675 50.000 3.32 0.00 0.00 3.71
2129 2211 0.391661 GTTGGCCTGCATCTTCTCGA 60.392 55.000 3.32 0.00 0.00 4.04
2130 2212 0.674581 TGTTGGCCTGCATCTTCTCG 60.675 55.000 3.32 0.00 0.00 4.04
2131 2213 1.674962 GATGTTGGCCTGCATCTTCTC 59.325 52.381 23.67 7.17 38.63 2.87
2132 2214 1.284198 AGATGTTGGCCTGCATCTTCT 59.716 47.619 26.26 13.40 46.66 2.85
2133 2215 1.760192 AGATGTTGGCCTGCATCTTC 58.240 50.000 26.26 11.80 46.66 2.87
2134 2216 3.994165 AGATGTTGGCCTGCATCTT 57.006 47.368 26.26 15.98 46.66 2.40
2136 2218 1.404391 CTTGAGATGTTGGCCTGCATC 59.596 52.381 23.58 23.58 41.13 3.91
2137 2219 1.272313 ACTTGAGATGTTGGCCTGCAT 60.272 47.619 3.32 8.42 0.00 3.96
2138 2220 0.111061 ACTTGAGATGTTGGCCTGCA 59.889 50.000 3.32 2.81 0.00 4.41
2139 2221 1.200948 GAACTTGAGATGTTGGCCTGC 59.799 52.381 3.32 0.00 0.00 4.85
2140 2222 1.466167 CGAACTTGAGATGTTGGCCTG 59.534 52.381 3.32 0.00 0.00 4.85
2141 2223 1.347707 TCGAACTTGAGATGTTGGCCT 59.652 47.619 3.32 0.00 0.00 5.19
2142 2224 1.464997 GTCGAACTTGAGATGTTGGCC 59.535 52.381 0.00 0.00 0.00 5.36
2143 2225 1.126846 CGTCGAACTTGAGATGTTGGC 59.873 52.381 0.00 0.00 0.00 4.52
2144 2226 2.408704 GTCGTCGAACTTGAGATGTTGG 59.591 50.000 0.00 0.00 0.00 3.77
2145 2227 2.089121 CGTCGTCGAACTTGAGATGTTG 59.911 50.000 0.00 0.00 39.71 3.33
2146 2228 2.031420 TCGTCGTCGAACTTGAGATGTT 60.031 45.455 1.37 0.00 43.34 2.71
2147 2229 1.534163 TCGTCGTCGAACTTGAGATGT 59.466 47.619 1.37 0.00 43.34 3.06
2148 2230 2.169974 CTCGTCGTCGAACTTGAGATG 58.830 52.381 6.19 0.00 45.61 2.90
2149 2231 1.805345 ACTCGTCGTCGAACTTGAGAT 59.195 47.619 16.98 4.36 45.61 2.75
2150 2232 1.070108 CACTCGTCGTCGAACTTGAGA 60.070 52.381 16.98 3.14 45.61 3.27
2151 2233 1.070108 TCACTCGTCGTCGAACTTGAG 60.070 52.381 6.19 5.10 45.61 3.02
2152 2234 0.939419 TCACTCGTCGTCGAACTTGA 59.061 50.000 6.19 6.43 45.61 3.02
2153 2235 1.905687 GATCACTCGTCGTCGAACTTG 59.094 52.381 6.19 4.25 45.61 3.16
2154 2236 1.805345 AGATCACTCGTCGTCGAACTT 59.195 47.619 6.19 0.00 45.61 2.66
2155 2237 1.440708 AGATCACTCGTCGTCGAACT 58.559 50.000 6.19 0.00 45.61 3.01
2156 2238 3.281601 CATAGATCACTCGTCGTCGAAC 58.718 50.000 6.19 0.00 45.61 3.95
2157 2239 2.287103 CCATAGATCACTCGTCGTCGAA 59.713 50.000 6.19 0.00 45.61 3.71
2158 2240 1.865340 CCATAGATCACTCGTCGTCGA 59.135 52.381 4.42 4.42 44.12 4.20
2159 2241 1.865340 TCCATAGATCACTCGTCGTCG 59.135 52.381 0.00 0.00 38.55 5.12
2160 2242 2.224549 CCTCCATAGATCACTCGTCGTC 59.775 54.545 0.00 0.00 0.00 4.20
2161 2243 2.222886 CCTCCATAGATCACTCGTCGT 58.777 52.381 0.00 0.00 0.00 4.34
2162 2244 1.068885 GCCTCCATAGATCACTCGTCG 60.069 57.143 0.00 0.00 0.00 5.12
2163 2245 1.068885 CGCCTCCATAGATCACTCGTC 60.069 57.143 0.00 0.00 0.00 4.20
2164 2246 0.955178 CGCCTCCATAGATCACTCGT 59.045 55.000 0.00 0.00 0.00 4.18
2165 2247 1.198867 CTCGCCTCCATAGATCACTCG 59.801 57.143 0.00 0.00 0.00 4.18
2166 2248 1.067915 GCTCGCCTCCATAGATCACTC 60.068 57.143 0.00 0.00 0.00 3.51
2167 2249 0.965439 GCTCGCCTCCATAGATCACT 59.035 55.000 0.00 0.00 0.00 3.41
2168 2250 0.387878 CGCTCGCCTCCATAGATCAC 60.388 60.000 0.00 0.00 0.00 3.06
2169 2251 1.959848 CGCTCGCCTCCATAGATCA 59.040 57.895 0.00 0.00 0.00 2.92
2170 2252 1.445238 GCGCTCGCCTCCATAGATC 60.445 63.158 0.00 0.00 34.56 2.75
2171 2253 2.653702 GCGCTCGCCTCCATAGAT 59.346 61.111 0.00 0.00 34.56 1.98
2181 2263 2.877691 AAAAAGGATGGCGCTCGC 59.122 55.556 7.64 5.60 41.06 5.03
2195 2277 0.600557 CACCTGCCGGCATACAAAAA 59.399 50.000 32.87 3.62 0.00 1.94
2196 2278 0.538516 ACACCTGCCGGCATACAAAA 60.539 50.000 32.87 4.54 0.00 2.44
2197 2279 1.074072 ACACCTGCCGGCATACAAA 59.926 52.632 32.87 5.45 0.00 2.83
2198 2280 1.673993 CACACCTGCCGGCATACAA 60.674 57.895 32.87 6.37 0.00 2.41
2199 2281 2.046411 CACACCTGCCGGCATACA 60.046 61.111 32.87 6.85 0.00 2.29
2200 2282 3.508840 GCACACCTGCCGGCATAC 61.509 66.667 32.87 12.06 37.45 2.39
2201 2283 3.716195 AGCACACCTGCCGGCATA 61.716 61.111 32.87 8.24 45.53 3.14
2207 2289 3.755628 CATGCCAGCACACCTGCC 61.756 66.667 0.00 0.00 45.53 4.85
2208 2290 2.674033 TCATGCCAGCACACCTGC 60.674 61.111 0.00 0.00 44.63 4.85
2209 2291 2.338015 GGTCATGCCAGCACACCTG 61.338 63.158 13.17 0.82 41.41 4.00
2210 2292 2.034687 GGTCATGCCAGCACACCT 59.965 61.111 13.17 0.00 37.17 4.00
2211 2293 2.282391 TGGTCATGCCAGCACACC 60.282 61.111 13.44 13.44 43.61 4.16
2236 2318 3.849953 GTTCGACCACGCCATCGC 61.850 66.667 0.00 0.00 38.24 4.58
2237 2319 2.126071 AGTTCGACCACGCCATCG 60.126 61.111 0.00 0.00 42.43 3.84
2238 2320 0.669318 TTGAGTTCGACCACGCCATC 60.669 55.000 0.00 0.00 39.58 3.51
2239 2321 0.670546 CTTGAGTTCGACCACGCCAT 60.671 55.000 0.00 0.00 39.58 4.40
2240 2322 1.300620 CTTGAGTTCGACCACGCCA 60.301 57.895 0.00 0.00 39.58 5.69
2241 2323 1.282930 GACTTGAGTTCGACCACGCC 61.283 60.000 0.00 0.00 39.58 5.68
2242 2324 1.282930 GGACTTGAGTTCGACCACGC 61.283 60.000 0.00 0.00 39.58 5.34
2243 2325 0.666577 GGGACTTGAGTTCGACCACG 60.667 60.000 0.00 0.00 41.26 4.94
2244 2326 0.391597 TGGGACTTGAGTTCGACCAC 59.608 55.000 0.00 0.00 0.00 4.16
2245 2327 0.391597 GTGGGACTTGAGTTCGACCA 59.608 55.000 0.00 0.00 0.00 4.02
2246 2328 0.320508 GGTGGGACTTGAGTTCGACC 60.321 60.000 7.72 7.72 43.60 4.79
2247 2329 0.320508 GGGTGGGACTTGAGTTCGAC 60.321 60.000 0.00 0.00 32.27 4.20
2248 2330 0.471211 AGGGTGGGACTTGAGTTCGA 60.471 55.000 0.00 0.00 0.00 3.71
2249 2331 0.396811 AAGGGTGGGACTTGAGTTCG 59.603 55.000 0.00 0.00 0.00 3.95
2250 2332 2.658807 AAAGGGTGGGACTTGAGTTC 57.341 50.000 0.00 0.00 0.00 3.01
2251 2333 3.398318 AAAAAGGGTGGGACTTGAGTT 57.602 42.857 0.00 0.00 0.00 3.01
2268 2350 1.274728 ACACTTGCCAGCACACAAAAA 59.725 42.857 0.00 0.00 0.00 1.94
2269 2351 0.894141 ACACTTGCCAGCACACAAAA 59.106 45.000 0.00 0.00 0.00 2.44
2270 2352 0.173029 CACACTTGCCAGCACACAAA 59.827 50.000 0.00 0.00 0.00 2.83
2271 2353 1.808546 CACACTTGCCAGCACACAA 59.191 52.632 0.00 0.00 0.00 3.33
2272 2354 2.773745 GCACACTTGCCAGCACACA 61.774 57.895 0.00 0.00 43.66 3.72
2273 2355 2.026590 GCACACTTGCCAGCACAC 59.973 61.111 0.00 0.00 43.66 3.82
2306 2388 2.177531 CACAGTTCATGCTGGCGC 59.822 61.111 0.00 0.00 40.59 6.53
2307 2389 1.208358 CACACAGTTCATGCTGGCG 59.792 57.895 5.48 0.00 40.59 5.69
2308 2390 1.174712 ACCACACAGTTCATGCTGGC 61.175 55.000 5.48 0.00 40.59 4.85
2309 2391 0.594602 CACCACACAGTTCATGCTGG 59.405 55.000 5.48 0.00 40.59 4.85
2310 2392 1.311859 ACACCACACAGTTCATGCTG 58.688 50.000 0.00 0.00 41.92 4.41
2311 2393 2.057137 AACACCACACAGTTCATGCT 57.943 45.000 0.00 0.00 0.00 3.79
2312 2394 2.869233 AAACACCACACAGTTCATGC 57.131 45.000 0.00 0.00 0.00 4.06
2313 2395 4.742417 TCAAAAACACCACACAGTTCATG 58.258 39.130 0.00 0.00 0.00 3.07
2314 2396 5.398603 TTCAAAAACACCACACAGTTCAT 57.601 34.783 0.00 0.00 0.00 2.57
2315 2397 4.804108 CTTCAAAAACACCACACAGTTCA 58.196 39.130 0.00 0.00 0.00 3.18
2316 2398 3.612423 GCTTCAAAAACACCACACAGTTC 59.388 43.478 0.00 0.00 0.00 3.01
2317 2399 3.258123 AGCTTCAAAAACACCACACAGTT 59.742 39.130 0.00 0.00 0.00 3.16
2318 2400 2.825532 AGCTTCAAAAACACCACACAGT 59.174 40.909 0.00 0.00 0.00 3.55
2319 2401 3.181397 CAGCTTCAAAAACACCACACAG 58.819 45.455 0.00 0.00 0.00 3.66
2320 2402 2.673610 GCAGCTTCAAAAACACCACACA 60.674 45.455 0.00 0.00 0.00 3.72
2321 2403 1.926510 GCAGCTTCAAAAACACCACAC 59.073 47.619 0.00 0.00 0.00 3.82
2322 2404 1.134848 GGCAGCTTCAAAAACACCACA 60.135 47.619 0.00 0.00 0.00 4.17
2323 2405 1.134848 TGGCAGCTTCAAAAACACCAC 60.135 47.619 0.00 0.00 0.00 4.16
2324 2406 1.189752 TGGCAGCTTCAAAAACACCA 58.810 45.000 0.00 0.00 0.00 4.17
2325 2407 2.531522 ATGGCAGCTTCAAAAACACC 57.468 45.000 0.00 0.00 0.00 4.16
2326 2408 3.197265 ACAATGGCAGCTTCAAAAACAC 58.803 40.909 0.00 0.00 0.00 3.32
2327 2409 3.540314 ACAATGGCAGCTTCAAAAACA 57.460 38.095 0.00 0.00 0.00 2.83
2328 2410 4.143052 GCATACAATGGCAGCTTCAAAAAC 60.143 41.667 0.00 0.00 0.00 2.43
2329 2411 3.995705 GCATACAATGGCAGCTTCAAAAA 59.004 39.130 0.00 0.00 0.00 1.94
2330 2412 3.587923 GCATACAATGGCAGCTTCAAAA 58.412 40.909 0.00 0.00 0.00 2.44
2331 2413 3.235157 GCATACAATGGCAGCTTCAAA 57.765 42.857 0.00 0.00 0.00 2.69
2332 2414 2.945447 GCATACAATGGCAGCTTCAA 57.055 45.000 0.00 0.00 0.00 2.69
2341 2423 2.901840 AGCGCCGGCATACAATGG 60.902 61.111 28.98 8.44 43.41 3.16
2342 2424 2.328989 CAGCGCCGGCATACAATG 59.671 61.111 28.98 9.29 43.41 2.82
2343 2425 2.901840 CCAGCGCCGGCATACAAT 60.902 61.111 28.98 1.24 43.41 2.71


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

AutoCloner maintained by Alex Coulton.