Multiple sequence alignment - TraesCS4B01G128300

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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 TraesCS4B01G128300 chr4B 100.000 2679 0 0 1 2679 167943173 167940495 0.000000e+00 4948
1 TraesCS4B01G128300 chr4A 88.772 1906 94 36 3 1830 467540987 467539124 0.000000e+00 2224
2 TraesCS4B01G128300 chr4A 96.795 624 14 2 2056 2679 467539053 467538436 0.000000e+00 1037
3 TraesCS4B01G128300 chr4D 93.456 978 44 7 1 969 108850740 108851706 0.000000e+00 1434
4 TraesCS4B01G128300 chr4D 98.237 624 11 0 2056 2679 108852665 108853288 0.000000e+00 1092
5 TraesCS4B01G128300 chr4D 89.394 726 32 14 967 1656 108851734 108852450 0.000000e+00 872
6 TraesCS4B01G128300 chr4D 94.009 217 8 2 1712 1928 108852451 108852662 9.250000e-85 324
7 TraesCS4B01G128300 chrUn 100.000 129 0 0 1929 2057 396963000 396963128 3.450000e-59 239
8 TraesCS4B01G128300 chr3A 97.794 136 2 1 1930 2065 159530328 159530462 1.600000e-57 233
9 TraesCS4B01G128300 chr3A 89.474 171 9 8 1897 2061 686615272 686615439 9.720000e-50 207
10 TraesCS4B01G128300 chr6D 97.727 132 3 0 1930 2061 160470645 160470776 7.460000e-56 228
11 TraesCS4B01G128300 chr6B 97.037 135 4 0 1924 2058 542584875 542584741 7.460000e-56 228
12 TraesCS4B01G128300 chr6B 92.105 152 10 2 1931 2081 220575562 220575412 2.090000e-51 213
13 TraesCS4B01G128300 chr3B 97.744 133 2 1 1926 2057 236361941 236362073 7.460000e-56 228
14 TraesCS4B01G128300 chr2D 92.903 155 9 2 1915 2067 62390566 62390412 9.650000e-55 224
15 TraesCS4B01G128300 chr2B 95.588 136 6 0 1932 2067 97944880 97944745 4.490000e-53 219


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 TraesCS4B01G128300 chr4B 167940495 167943173 2678 True 4948.0 4948 100.0000 1 2679 1 chr4B.!!$R1 2678
1 TraesCS4B01G128300 chr4A 467538436 467540987 2551 True 1630.5 2224 92.7835 3 2679 2 chr4A.!!$R1 2676
2 TraesCS4B01G128300 chr4D 108850740 108853288 2548 False 930.5 1434 93.7740 1 2679 4 chr4D.!!$F1 2678


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
932 964 0.459585 CCATGTTCCCACGTACTCCG 60.46 60.0 0.0 0.0 44.03 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2152 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.0 0.0 0.0 2.17 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
63 64 6.252599 TCAGATCACTGCCATTTTATAGGT 57.747 37.500 0.00 0.00 43.17 3.08
67 68 7.386299 CAGATCACTGCCATTTTATAGGTACTC 59.614 40.741 0.00 0.00 37.30 2.59
73 74 6.068010 TGCCATTTTATAGGTACTCCATTGG 58.932 40.000 0.00 0.00 41.75 3.16
75 76 5.476945 CCATTTTATAGGTACTCCATTGGGC 59.523 44.000 2.09 0.00 41.75 5.36
76 77 4.345859 TTTATAGGTACTCCATTGGGCG 57.654 45.455 2.09 0.00 41.75 6.13
117 127 9.398170 CACATTTTCAATTAACTGGTAGTTCAG 57.602 33.333 0.00 0.00 39.51 3.02
188 198 6.437928 TGAATCAACTTTCCAAACTTGATCG 58.562 36.000 7.13 0.00 33.35 3.69
345 363 6.966632 TCCGTGTATGATACGTTTGTAACTAC 59.033 38.462 0.00 0.00 39.76 2.73
378 396 1.734137 CCCTCCACGATCTACCACG 59.266 63.158 0.00 0.00 0.00 4.94
391 409 7.012138 CACGATCTACCACGCCTATACTTATAT 59.988 40.741 0.00 0.00 0.00 0.86
392 410 8.206867 ACGATCTACCACGCCTATACTTATATA 58.793 37.037 0.00 0.00 0.00 0.86
393 411 9.049523 CGATCTACCACGCCTATACTTATATAA 57.950 37.037 0.00 0.00 0.00 0.98
538 557 3.416156 ACCAGTCAAAAAGATCAGCTCC 58.584 45.455 0.00 0.00 0.00 4.70
728 754 1.361668 CGGGGCGCTGCACATATATC 61.362 60.000 7.64 0.00 30.93 1.63
736 762 4.742167 GCGCTGCACATATATCCTATGTAG 59.258 45.833 0.00 0.00 36.49 2.74
744 770 7.041303 GCACATATATCCTATGTAGCGCTAGTA 60.041 40.741 19.48 12.87 36.49 1.82
858 890 1.043816 CCCATATGCTCCGTGACTCT 58.956 55.000 0.00 0.00 0.00 3.24
871 903 3.070018 CGTGACTCTCTTTTGCTCCATT 58.930 45.455 0.00 0.00 0.00 3.16
886 918 4.280174 TGCTCCATTCCCGACTAGTATAAC 59.720 45.833 0.00 0.00 0.00 1.89
887 919 4.523558 GCTCCATTCCCGACTAGTATAACT 59.476 45.833 0.00 0.00 0.00 2.24
888 920 5.010820 GCTCCATTCCCGACTAGTATAACTT 59.989 44.000 0.00 0.00 0.00 2.66
889 921 6.208204 GCTCCATTCCCGACTAGTATAACTTA 59.792 42.308 0.00 0.00 0.00 2.24
890 922 7.255730 GCTCCATTCCCGACTAGTATAACTTAA 60.256 40.741 0.00 0.00 0.00 1.85
894 926 8.627403 CATTCCCGACTAGTATAACTTAAGACA 58.373 37.037 10.09 0.00 0.00 3.41
932 964 0.459585 CCATGTTCCCACGTACTCCG 60.460 60.000 0.00 0.00 44.03 4.63
933 965 1.082117 CATGTTCCCACGTACTCCGC 61.082 60.000 0.00 0.00 41.42 5.54
1068 1141 2.083774 GGTTCGATCAAGTGCCATGAA 58.916 47.619 0.00 0.00 0.00 2.57
1138 1228 1.834378 CTGCCTCCTCGCCTCCATA 60.834 63.158 0.00 0.00 0.00 2.74
1319 1412 0.391597 GGAGACCAACGAGTTCCACA 59.608 55.000 0.00 0.00 0.00 4.17
1329 1422 0.036388 GAGTTCCACATCAAGGGCGA 60.036 55.000 0.00 0.00 0.00 5.54
1411 1504 0.681243 AATTTCCCAAGAGCGGCTCC 60.681 55.000 25.49 8.71 0.00 4.70
1423 1516 1.000274 AGCGGCTCCAACAAAAATCAC 60.000 47.619 0.00 0.00 0.00 3.06
1431 1524 6.705825 GGCTCCAACAAAAATCACAATTAGTT 59.294 34.615 0.00 0.00 0.00 2.24
1469 1580 4.734398 TCCTTCTCTCTTTGATCAGCTC 57.266 45.455 0.00 0.00 0.00 4.09
1662 1773 7.598189 GATAGATCATCTGTCCATGTCAATG 57.402 40.000 0.00 0.00 29.60 2.82
1663 1774 5.625568 AGATCATCTGTCCATGTCAATGA 57.374 39.130 0.00 4.35 35.67 2.57
1665 1776 6.602278 AGATCATCTGTCCATGTCAATGAAT 58.398 36.000 0.00 0.00 35.67 2.57
1666 1777 7.742767 AGATCATCTGTCCATGTCAATGAATA 58.257 34.615 0.00 0.00 35.67 1.75
1667 1778 8.383947 AGATCATCTGTCCATGTCAATGAATAT 58.616 33.333 0.00 0.00 35.67 1.28
1697 1808 2.499289 AGTTTTGCCACAACCATCACAA 59.501 40.909 0.00 0.00 0.00 3.33
1702 1813 2.762887 TGCCACAACCATCACAAGAAAA 59.237 40.909 0.00 0.00 0.00 2.29
1703 1814 3.387374 TGCCACAACCATCACAAGAAAAT 59.613 39.130 0.00 0.00 0.00 1.82
1704 1815 4.141756 TGCCACAACCATCACAAGAAAATT 60.142 37.500 0.00 0.00 0.00 1.82
1705 1816 4.448732 GCCACAACCATCACAAGAAAATTC 59.551 41.667 0.00 0.00 0.00 2.17
1706 1817 4.681025 CCACAACCATCACAAGAAAATTCG 59.319 41.667 0.00 0.00 0.00 3.34
1707 1818 5.507149 CCACAACCATCACAAGAAAATTCGA 60.507 40.000 0.00 0.00 0.00 3.71
1743 1854 3.700038 ACCTGTACTACCTCAAATCCGAG 59.300 47.826 0.00 0.00 0.00 4.63
1757 1872 2.953466 TCCGAGTTTCTTGTATCCCG 57.047 50.000 0.00 0.00 0.00 5.14
1786 1902 1.029947 CGGCGAGCCCCACTAAATTT 61.030 55.000 0.00 0.00 0.00 1.82
1842 1958 7.415095 CGGTTAAATCAAACATCCTTCATGCTA 60.415 37.037 0.00 0.00 35.65 3.49
1843 1959 7.702348 GGTTAAATCAAACATCCTTCATGCTAC 59.298 37.037 0.00 0.00 35.65 3.58
1844 1960 8.462016 GTTAAATCAAACATCCTTCATGCTACT 58.538 33.333 0.00 0.00 35.65 2.57
1845 1961 6.446781 AATCAAACATCCTTCATGCTACTG 57.553 37.500 0.00 0.00 35.65 2.74
1846 1962 4.910195 TCAAACATCCTTCATGCTACTGT 58.090 39.130 0.00 0.00 35.65 3.55
1847 1963 6.048732 TCAAACATCCTTCATGCTACTGTA 57.951 37.500 0.00 0.00 35.65 2.74
1928 2045 5.009610 ACAGCAGGACGAACATTACAAAATT 59.990 36.000 0.00 0.00 0.00 1.82
1932 2049 8.395633 AGCAGGACGAACATTACAAAATTATAC 58.604 33.333 0.00 0.00 0.00 1.47
1934 2051 9.916397 CAGGACGAACATTACAAAATTATACTC 57.084 33.333 0.00 0.00 0.00 2.59
1935 2052 9.106070 AGGACGAACATTACAAAATTATACTCC 57.894 33.333 0.00 0.00 0.00 3.85
1936 2053 8.340443 GGACGAACATTACAAAATTATACTCCC 58.660 37.037 0.00 0.00 0.00 4.30
1937 2054 9.106070 GACGAACATTACAAAATTATACTCCCT 57.894 33.333 0.00 0.00 0.00 4.20
1938 2055 9.106070 ACGAACATTACAAAATTATACTCCCTC 57.894 33.333 0.00 0.00 0.00 4.30
1939 2056 8.557029 CGAACATTACAAAATTATACTCCCTCC 58.443 37.037 0.00 0.00 0.00 4.30
1940 2057 8.446599 AACATTACAAAATTATACTCCCTCCG 57.553 34.615 0.00 0.00 0.00 4.63
1941 2058 7.571025 ACATTACAAAATTATACTCCCTCCGT 58.429 34.615 0.00 0.00 0.00 4.69
1942 2059 7.713942 ACATTACAAAATTATACTCCCTCCGTC 59.286 37.037 0.00 0.00 0.00 4.79
1943 2060 5.032327 ACAAAATTATACTCCCTCCGTCC 57.968 43.478 0.00 0.00 0.00 4.79
1944 2061 4.141551 ACAAAATTATACTCCCTCCGTCCC 60.142 45.833 0.00 0.00 0.00 4.46
1945 2062 3.339713 AATTATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
1946 2063 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
1947 2064 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
1948 2065 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1949 2066 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1950 2067 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1951 2068 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1952 2069 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1953 2070 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1954 2071 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1955 2072 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1956 2073 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1957 2074 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1958 2075 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1959 2076 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1960 2077 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
1961 2078 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
1962 2079 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
1963 2080 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
1964 2081 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
1965 2082 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
1966 2083 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
1967 2084 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
1968 2085 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
1976 2093 9.582431 TCTTGTCTTAAATTTGTCTAGATACGG 57.418 33.333 0.00 0.00 0.00 4.02
1977 2094 9.582431 CTTGTCTTAAATTTGTCTAGATACGGA 57.418 33.333 0.00 0.00 0.00 4.69
1979 2096 9.529325 TGTCTTAAATTTGTCTAGATACGGATG 57.471 33.333 0.00 0.00 0.00 3.51
1980 2097 9.530633 GTCTTAAATTTGTCTAGATACGGATGT 57.469 33.333 0.00 0.00 0.00 3.06
1983 2100 9.754382 TTAAATTTGTCTAGATACGGATGTACC 57.246 33.333 0.00 0.00 32.26 3.34
1984 2101 7.598759 AATTTGTCTAGATACGGATGTACCT 57.401 36.000 0.00 0.00 36.31 3.08
1985 2102 8.701908 AATTTGTCTAGATACGGATGTACCTA 57.298 34.615 0.00 0.00 36.31 3.08
1986 2103 8.701908 ATTTGTCTAGATACGGATGTACCTAA 57.298 34.615 0.00 0.00 36.31 2.69
1987 2104 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
1988 2105 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
1989 2106 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
1990 2107 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
1998 2115 8.882415 ACGGATGTACCTAATACTAAAATGTG 57.118 34.615 0.00 0.00 34.56 3.21
1999 2116 8.698210 ACGGATGTACCTAATACTAAAATGTGA 58.302 33.333 0.00 0.00 34.56 3.58
2000 2117 8.975439 CGGATGTACCTAATACTAAAATGTGAC 58.025 37.037 0.00 0.00 34.56 3.67
2003 2120 9.745880 ATGTACCTAATACTAAAATGTGACTCG 57.254 33.333 0.00 0.00 34.56 4.18
2004 2121 8.959548 TGTACCTAATACTAAAATGTGACTCGA 58.040 33.333 0.00 0.00 34.56 4.04
2005 2122 9.962783 GTACCTAATACTAAAATGTGACTCGAT 57.037 33.333 0.00 0.00 0.00 3.59
2007 2124 9.962783 ACCTAATACTAAAATGTGACTCGATAC 57.037 33.333 0.00 0.00 0.00 2.24
2008 2125 9.961265 CCTAATACTAAAATGTGACTCGATACA 57.039 33.333 0.00 0.00 0.00 2.29
2011 2128 9.477484 AATACTAAAATGTGACTCGATACATCC 57.523 33.333 9.59 0.00 36.56 3.51
2012 2129 5.977725 ACTAAAATGTGACTCGATACATCCG 59.022 40.000 9.59 0.00 36.56 4.18
2013 2130 4.386867 AAATGTGACTCGATACATCCGT 57.613 40.909 9.59 0.00 36.56 4.69
2014 2131 5.509716 AAATGTGACTCGATACATCCGTA 57.490 39.130 9.59 0.00 36.56 4.02
2015 2132 5.707242 AATGTGACTCGATACATCCGTAT 57.293 39.130 9.59 0.00 41.16 3.06
2016 2133 5.707242 ATGTGACTCGATACATCCGTATT 57.293 39.130 4.76 0.00 38.48 1.89
2017 2134 5.509716 TGTGACTCGATACATCCGTATTT 57.490 39.130 0.00 0.00 38.48 1.40
2018 2135 6.622833 TGTGACTCGATACATCCGTATTTA 57.377 37.500 0.00 0.00 38.48 1.40
2019 2136 6.665465 TGTGACTCGATACATCCGTATTTAG 58.335 40.000 0.00 0.00 38.48 1.85
2020 2137 6.484308 TGTGACTCGATACATCCGTATTTAGA 59.516 38.462 0.00 0.00 38.48 2.10
2021 2138 6.796072 GTGACTCGATACATCCGTATTTAGAC 59.204 42.308 0.00 0.00 38.48 2.59
2022 2139 6.484308 TGACTCGATACATCCGTATTTAGACA 59.516 38.462 0.00 0.00 38.48 3.41
2023 2140 7.012610 TGACTCGATACATCCGTATTTAGACAA 59.987 37.037 0.00 0.00 38.48 3.18
2024 2141 7.709947 ACTCGATACATCCGTATTTAGACAAA 58.290 34.615 0.00 0.00 38.48 2.83
2025 2142 8.358148 ACTCGATACATCCGTATTTAGACAAAT 58.642 33.333 0.00 0.00 38.48 2.32
2026 2143 8.738199 TCGATACATCCGTATTTAGACAAATC 57.262 34.615 0.00 0.00 38.48 2.17
2027 2144 8.573885 TCGATACATCCGTATTTAGACAAATCT 58.426 33.333 0.00 0.00 38.48 2.40
2028 2145 9.836076 CGATACATCCGTATTTAGACAAATCTA 57.164 33.333 0.00 0.00 38.48 1.98
2032 2149 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
2033 2150 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
2035 2152 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
2036 2153 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
2044 2161 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2045 2162 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2046 2163 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2047 2164 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2048 2165 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2049 2166 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2050 2167 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2051 2168 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2052 2169 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2053 2170 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2054 2171 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2139 2256 5.334724 CCATCTATCGGTAAGTTCTACGACC 60.335 48.000 0.00 0.00 38.24 4.79
2334 2451 2.004017 CAAGCCGTACGCCTATTTTCA 58.996 47.619 10.49 0.00 38.78 2.69
2507 2624 0.110486 GCACCTGAACTGGAGGGAAA 59.890 55.000 4.82 0.00 34.56 3.13
2526 2643 4.503910 GAAAAACCCAGTGCTTGAAGTTT 58.496 39.130 0.00 0.00 35.74 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 0.546122 AATGAGCGCCCAATGGAGTA 59.454 50.000 2.29 0.00 33.30 2.59
67 68 0.179020 TCCTAATGAGCGCCCAATGG 60.179 55.000 2.29 2.52 0.00 3.16
73 74 2.072298 GTGATGATCCTAATGAGCGCC 58.928 52.381 2.29 0.00 29.76 6.53
75 76 5.936686 AAATGTGATGATCCTAATGAGCG 57.063 39.130 0.00 0.00 29.76 5.03
76 77 7.268199 TGAAAATGTGATGATCCTAATGAGC 57.732 36.000 0.00 0.00 0.00 4.26
143 153 2.416747 TCTCAACACATGCTGCTACAC 58.583 47.619 0.00 0.00 0.00 2.90
254 272 8.961634 GTCTGGACTCATCATACTAGCATTATA 58.038 37.037 0.00 0.00 0.00 0.98
260 278 3.891977 TGGTCTGGACTCATCATACTAGC 59.108 47.826 0.67 0.00 0.00 3.42
266 284 3.070734 GCTGTATGGTCTGGACTCATCAT 59.929 47.826 0.67 0.00 0.00 2.45
538 557 3.628487 ACCTACGATCTTCCTCTTCTTCG 59.372 47.826 0.00 0.00 0.00 3.79
584 603 9.276590 CCATGTGATGCTTATCTTTGACTAATA 57.723 33.333 0.00 0.00 0.00 0.98
728 754 7.818642 AGAAACTAATACTAGCGCTACATAGG 58.181 38.462 14.45 6.02 0.00 2.57
736 762 8.576936 AATTCTGTAGAAACTAATACTAGCGC 57.423 34.615 0.00 0.00 37.61 5.92
858 890 1.351017 AGTCGGGAATGGAGCAAAAGA 59.649 47.619 0.00 0.00 0.00 2.52
871 903 7.230108 CCATGTCTTAAGTTATACTAGTCGGGA 59.770 40.741 0.00 0.00 0.00 5.14
894 926 1.442769 GAGTGAACATGTGACGCCAT 58.557 50.000 0.00 0.00 0.00 4.40
1107 1197 4.477975 GGCAGGAGACGACGACGG 62.478 72.222 12.58 0.00 44.46 4.79
1110 1200 2.750637 GGAGGCAGGAGACGACGA 60.751 66.667 0.00 0.00 0.00 4.20
1138 1228 0.636101 AGAGGAGATGGAGCAGGAGT 59.364 55.000 0.00 0.00 0.00 3.85
1360 1453 3.307906 TCGAACCCCACCTCCACG 61.308 66.667 0.00 0.00 0.00 4.94
1411 1504 8.334632 GTTCCCAACTAATTGTGATTTTTGTTG 58.665 33.333 0.00 0.00 33.60 3.33
1423 1516 6.183347 AGGAGATTCAGTTCCCAACTAATTG 58.817 40.000 0.00 0.00 40.46 2.32
1431 1524 2.921221 AGGAAGGAGATTCAGTTCCCA 58.079 47.619 7.66 0.00 39.54 4.37
1503 1614 5.247337 TCTCTACAAGTGAGAGAGAGAGTGA 59.753 44.000 11.29 0.00 43.57 3.41
1674 1785 3.055530 TGTGATGGTTGTGGCAAAACTTT 60.056 39.130 19.43 7.85 0.00 2.66
1682 1793 3.451141 TTTTCTTGTGATGGTTGTGGC 57.549 42.857 0.00 0.00 0.00 5.01
1697 1808 8.186821 GGTCAGATGAATTGAATCGAATTTTCT 58.813 33.333 0.00 0.00 0.00 2.52
1702 1813 6.118170 ACAGGTCAGATGAATTGAATCGAAT 58.882 36.000 0.00 0.00 0.00 3.34
1703 1814 5.491070 ACAGGTCAGATGAATTGAATCGAA 58.509 37.500 0.00 0.00 0.00 3.71
1704 1815 5.089970 ACAGGTCAGATGAATTGAATCGA 57.910 39.130 0.00 0.00 0.00 3.59
1705 1816 6.045318 AGTACAGGTCAGATGAATTGAATCG 58.955 40.000 0.00 0.00 0.00 3.34
1706 1817 7.439655 GGTAGTACAGGTCAGATGAATTGAATC 59.560 40.741 2.06 0.00 0.00 2.52
1707 1818 7.126421 AGGTAGTACAGGTCAGATGAATTGAAT 59.874 37.037 2.06 0.00 0.00 2.57
1743 1854 6.238022 CGGAAATCTAACGGGATACAAGAAAC 60.238 42.308 0.00 0.00 39.74 2.78
1757 1872 1.158484 GGGCTCGCCGGAAATCTAAC 61.158 60.000 5.05 0.00 36.85 2.34
1817 1933 6.633856 AGCATGAAGGATGTTTGATTTAACC 58.366 36.000 0.00 0.00 34.14 2.85
1842 1958 4.935808 GGTGTTGCTGCTAGTTTATACAGT 59.064 41.667 0.00 0.00 32.65 3.55
1843 1959 4.935205 TGGTGTTGCTGCTAGTTTATACAG 59.065 41.667 0.00 0.00 0.00 2.74
1844 1960 4.900684 TGGTGTTGCTGCTAGTTTATACA 58.099 39.130 0.00 0.00 0.00 2.29
1845 1961 5.873179 TTGGTGTTGCTGCTAGTTTATAC 57.127 39.130 0.00 0.00 0.00 1.47
1846 1962 6.176896 TCATTGGTGTTGCTGCTAGTTTATA 58.823 36.000 0.00 0.00 0.00 0.98
1847 1963 5.009631 TCATTGGTGTTGCTGCTAGTTTAT 58.990 37.500 0.00 0.00 0.00 1.40
1928 2045 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
1932 2049 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1934 2051 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1935 2052 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1936 2053 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1937 2054 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1938 2055 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
1939 2056 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
1940 2057 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
1941 2058 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
1942 2059 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
1950 2067 9.582431 CCGTATCTAGACAAATTTAAGACAAGA 57.418 33.333 0.00 0.00 0.00 3.02
1951 2068 9.582431 TCCGTATCTAGACAAATTTAAGACAAG 57.418 33.333 0.00 0.00 0.00 3.16
1953 2070 9.529325 CATCCGTATCTAGACAAATTTAAGACA 57.471 33.333 0.00 0.00 0.00 3.41
1954 2071 9.530633 ACATCCGTATCTAGACAAATTTAAGAC 57.469 33.333 0.00 0.00 0.00 3.01
1957 2074 9.754382 GGTACATCCGTATCTAGACAAATTTAA 57.246 33.333 0.00 0.00 0.00 1.52
1958 2075 9.139734 AGGTACATCCGTATCTAGACAAATTTA 57.860 33.333 0.00 0.00 37.29 1.40
1959 2076 8.019656 AGGTACATCCGTATCTAGACAAATTT 57.980 34.615 0.00 0.00 37.29 1.82
1960 2077 7.598759 AGGTACATCCGTATCTAGACAAATT 57.401 36.000 0.00 0.00 37.29 1.82
1961 2078 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
1962 2079 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
1963 2080 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
1964 2081 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
1972 2089 9.970395 CACATTTTAGTATTAGGTACATCCGTA 57.030 33.333 0.00 0.00 41.99 4.02
1973 2090 8.698210 TCACATTTTAGTATTAGGTACATCCGT 58.302 33.333 0.00 0.00 41.99 4.69
1974 2091 8.975439 GTCACATTTTAGTATTAGGTACATCCG 58.025 37.037 0.00 0.00 41.99 4.18
1977 2094 9.745880 CGAGTCACATTTTAGTATTAGGTACAT 57.254 33.333 0.00 0.00 35.67 2.29
1978 2095 8.959548 TCGAGTCACATTTTAGTATTAGGTACA 58.040 33.333 0.00 0.00 35.67 2.90
1979 2096 9.962783 ATCGAGTCACATTTTAGTATTAGGTAC 57.037 33.333 0.00 0.00 0.00 3.34
1981 2098 9.962783 GTATCGAGTCACATTTTAGTATTAGGT 57.037 33.333 0.00 0.00 0.00 3.08
1982 2099 9.961265 TGTATCGAGTCACATTTTAGTATTAGG 57.039 33.333 0.00 0.00 0.00 2.69
1985 2102 9.477484 GGATGTATCGAGTCACATTTTAGTATT 57.523 33.333 10.38 0.00 35.55 1.89
1986 2103 7.808381 CGGATGTATCGAGTCACATTTTAGTAT 59.192 37.037 10.38 0.00 35.55 2.12
1987 2104 7.136772 CGGATGTATCGAGTCACATTTTAGTA 58.863 38.462 10.38 0.00 35.55 1.82
1988 2105 5.977725 CGGATGTATCGAGTCACATTTTAGT 59.022 40.000 10.38 0.00 35.55 2.24
1989 2106 5.977725 ACGGATGTATCGAGTCACATTTTAG 59.022 40.000 10.38 6.39 35.55 1.85
1990 2107 5.898174 ACGGATGTATCGAGTCACATTTTA 58.102 37.500 10.38 0.00 35.55 1.52
1991 2108 4.755411 ACGGATGTATCGAGTCACATTTT 58.245 39.130 10.38 0.00 35.55 1.82
1992 2109 4.386867 ACGGATGTATCGAGTCACATTT 57.613 40.909 10.38 0.00 35.55 2.32
1993 2110 5.707242 ATACGGATGTATCGAGTCACATT 57.293 39.130 10.38 0.55 36.56 2.71
1994 2111 5.707242 AATACGGATGTATCGAGTCACAT 57.293 39.130 9.18 9.18 40.42 3.21
1995 2112 5.509716 AAATACGGATGTATCGAGTCACA 57.490 39.130 0.00 0.00 40.42 3.58
1996 2113 6.796072 GTCTAAATACGGATGTATCGAGTCAC 59.204 42.308 0.00 0.00 40.42 3.67
1997 2114 6.484308 TGTCTAAATACGGATGTATCGAGTCA 59.516 38.462 0.00 0.00 40.42 3.41
1998 2115 6.895898 TGTCTAAATACGGATGTATCGAGTC 58.104 40.000 0.00 0.00 40.42 3.36
1999 2116 6.872628 TGTCTAAATACGGATGTATCGAGT 57.127 37.500 0.00 0.00 40.42 4.18
2000 2117 8.744008 ATTTGTCTAAATACGGATGTATCGAG 57.256 34.615 0.00 0.00 40.42 4.04
2001 2118 8.573885 AGATTTGTCTAAATACGGATGTATCGA 58.426 33.333 0.00 0.00 40.42 3.59
2002 2119 8.744008 AGATTTGTCTAAATACGGATGTATCG 57.256 34.615 0.00 0.00 40.42 2.92
2006 2123 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
2007 2124 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
2009 2126 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
2010 2127 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
2018 2135 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2019 2136 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2020 2137 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2021 2138 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2022 2139 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2023 2140 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2024 2141 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2025 2142 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2026 2143 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2027 2144 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2028 2145 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2029 2146 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2030 2147 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2031 2148 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2032 2149 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2033 2150 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2034 2151 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2035 2152 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2036 2153 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2037 2154 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2038 2155 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
2039 2156 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2040 2157 2.767960 GTTATTACTCCCTCCGTCCCAA 59.232 50.000 0.00 0.00 0.00 4.12
2041 2158 2.292389 TGTTATTACTCCCTCCGTCCCA 60.292 50.000 0.00 0.00 0.00 4.37
2042 2159 2.391678 TGTTATTACTCCCTCCGTCCC 58.608 52.381 0.00 0.00 0.00 4.46
2043 2160 4.476628 TTTGTTATTACTCCCTCCGTCC 57.523 45.455 0.00 0.00 0.00 4.79
2044 2161 7.254218 CGTTTATTTGTTATTACTCCCTCCGTC 60.254 40.741 0.00 0.00 0.00 4.79
2045 2162 6.536224 CGTTTATTTGTTATTACTCCCTCCGT 59.464 38.462 0.00 0.00 0.00 4.69
2046 2163 6.536224 ACGTTTATTTGTTATTACTCCCTCCG 59.464 38.462 0.00 0.00 0.00 4.63
2047 2164 7.550196 TCACGTTTATTTGTTATTACTCCCTCC 59.450 37.037 0.00 0.00 0.00 4.30
2048 2165 8.483307 TCACGTTTATTTGTTATTACTCCCTC 57.517 34.615 0.00 0.00 0.00 4.30
2049 2166 8.724229 GTTCACGTTTATTTGTTATTACTCCCT 58.276 33.333 0.00 0.00 0.00 4.20
2050 2167 8.505625 TGTTCACGTTTATTTGTTATTACTCCC 58.494 33.333 0.00 0.00 0.00 4.30
2051 2168 9.881529 TTGTTCACGTTTATTTGTTATTACTCC 57.118 29.630 0.00 0.00 0.00 3.85
2139 2256 6.934645 TGATATTAACATTTTAGGGCTCCTCG 59.065 38.462 0.00 0.00 34.61 4.63
2507 2624 2.168313 CCAAACTTCAAGCACTGGGTTT 59.832 45.455 0.00 0.00 34.26 3.27



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

AutoCloner maintained by Alex Coulton.