Multiple sequence alignment - TraesCS1D01G212500

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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 TraesCS1D01G212500 chr1D 100.000 2105 0 0 1 2105 298347808 298345704 0.000000e+00 3888.0
1 TraesCS1D01G212500 chr1D 97.921 1058 16 2 882 1934 254440850 254441906 0.000000e+00 1827.0
2 TraesCS1D01G212500 chr3D 98.765 1053 12 1 882 1934 323520860 323521911 0.000000e+00 1871.0
3 TraesCS1D01G212500 chr2D 98.206 1059 13 2 882 1934 638430239 638431297 0.000000e+00 1845.0
4 TraesCS1D01G212500 chr2D 80.435 138 17 2 1975 2102 272992507 272992644 1.720000e-16 97.1
5 TraesCS1D01G212500 chr5D 98.019 1060 14 3 882 1934 503297714 503298773 0.000000e+00 1834.0
6 TraesCS1D01G212500 chr5D 97.545 1059 19 3 882 1934 6270167 6269110 0.000000e+00 1805.0
7 TraesCS1D01G212500 chr5D 97.876 1036 19 3 901 1934 329162135 329161101 0.000000e+00 1788.0
8 TraesCS1D01G212500 chr4A 97.441 1055 25 1 882 1934 309484216 309483162 0.000000e+00 1797.0
9 TraesCS1D01G212500 chr4A 87.500 88 6 3 2019 2102 642104145 642104231 1.720000e-16 97.1
10 TraesCS1D01G212500 chr4D 96.961 1053 24 3 882 1934 19874318 19875362 0.000000e+00 1760.0
11 TraesCS1D01G212500 chr4B 96.128 1059 23 6 882 1934 308673960 308672914 0.000000e+00 1712.0
12 TraesCS1D01G212500 chrUn 98.737 871 11 0 1 871 264057220 264056350 0.000000e+00 1548.0
13 TraesCS1D01G212500 chrUn 98.622 871 12 0 1 871 266527150 266526280 0.000000e+00 1543.0
14 TraesCS1D01G212500 chrUn 98.622 871 12 0 1 871 282368247 282367377 0.000000e+00 1543.0
15 TraesCS1D01G212500 chrUn 98.507 871 13 0 1 871 86513563 86512693 0.000000e+00 1537.0
16 TraesCS1D01G212500 chr7B 98.737 871 11 0 1 871 644453730 644454600 0.000000e+00 1548.0
17 TraesCS1D01G212500 chr7B 87.209 86 8 1 2020 2102 706793868 706793953 6.180000e-16 95.3
18 TraesCS1D01G212500 chr7D 98.622 871 12 0 1 871 203549127 203548257 0.000000e+00 1543.0
19 TraesCS1D01G212500 chr7D 98.622 871 12 0 1 871 381931276 381932146 0.000000e+00 1543.0
20 TraesCS1D01G212500 chr7D 98.622 871 12 0 1 871 381966482 381965612 0.000000e+00 1543.0
21 TraesCS1D01G212500 chr7D 98.507 871 13 0 1 871 382057353 382058223 0.000000e+00 1537.0
22 TraesCS1D01G212500 chr7D 86.047 86 9 1 2019 2101 163089494 163089409 2.880000e-14 89.8
23 TraesCS1D01G212500 chr2A 82.090 134 13 5 1981 2103 319054212 319054079 1.030000e-18 104.0
24 TraesCS1D01G212500 chr2B 81.818 132 13 2 1982 2102 317187348 317187479 1.330000e-17 100.0
25 TraesCS1D01G212500 chr6B 95.000 60 2 1 2012 2071 590011816 590011758 2.220000e-15 93.5
26 TraesCS1D01G212500 chr6A 79.545 132 15 5 1985 2105 540310585 540310455 1.340000e-12 84.2
27 TraesCS1D01G212500 chr7A 83.721 86 11 1 2019 2101 163993174 163993089 6.230000e-11 78.7


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 TraesCS1D01G212500 chr1D 298345704 298347808 2104 True 3888 3888 100.000 1 2105 1 chr1D.!!$R1 2104
1 TraesCS1D01G212500 chr1D 254440850 254441906 1056 False 1827 1827 97.921 882 1934 1 chr1D.!!$F1 1052
2 TraesCS1D01G212500 chr3D 323520860 323521911 1051 False 1871 1871 98.765 882 1934 1 chr3D.!!$F1 1052
3 TraesCS1D01G212500 chr2D 638430239 638431297 1058 False 1845 1845 98.206 882 1934 1 chr2D.!!$F2 1052
4 TraesCS1D01G212500 chr5D 503297714 503298773 1059 False 1834 1834 98.019 882 1934 1 chr5D.!!$F1 1052
5 TraesCS1D01G212500 chr5D 6269110 6270167 1057 True 1805 1805 97.545 882 1934 1 chr5D.!!$R1 1052
6 TraesCS1D01G212500 chr5D 329161101 329162135 1034 True 1788 1788 97.876 901 1934 1 chr5D.!!$R2 1033
7 TraesCS1D01G212500 chr4A 309483162 309484216 1054 True 1797 1797 97.441 882 1934 1 chr4A.!!$R1 1052
8 TraesCS1D01G212500 chr4D 19874318 19875362 1044 False 1760 1760 96.961 882 1934 1 chr4D.!!$F1 1052
9 TraesCS1D01G212500 chr4B 308672914 308673960 1046 True 1712 1712 96.128 882 1934 1 chr4B.!!$R1 1052
10 TraesCS1D01G212500 chrUn 264056350 264057220 870 True 1548 1548 98.737 1 871 1 chrUn.!!$R2 870
11 TraesCS1D01G212500 chrUn 266526280 266527150 870 True 1543 1543 98.622 1 871 1 chrUn.!!$R3 870
12 TraesCS1D01G212500 chrUn 282367377 282368247 870 True 1543 1543 98.622 1 871 1 chrUn.!!$R4 870
13 TraesCS1D01G212500 chrUn 86512693 86513563 870 True 1537 1537 98.507 1 871 1 chrUn.!!$R1 870
14 TraesCS1D01G212500 chr7B 644453730 644454600 870 False 1548 1548 98.737 1 871 1 chr7B.!!$F1 870
15 TraesCS1D01G212500 chr7D 203548257 203549127 870 True 1543 1543 98.622 1 871 1 chr7D.!!$R2 870
16 TraesCS1D01G212500 chr7D 381931276 381932146 870 False 1543 1543 98.622 1 871 1 chr7D.!!$F1 870
17 TraesCS1D01G212500 chr7D 381965612 381966482 870 True 1543 1543 98.622 1 871 1 chr7D.!!$R3 870
18 TraesCS1D01G212500 chr7D 382057353 382058223 870 False 1537 1537 98.507 1 871 1 chr7D.!!$F2 870

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
775 776 0.103572 GTACACACCGCCCGTCATAT 59.896 55.0 0.0 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2046 0.033796 ACACCATCCAAGAGGCCATG 60.034 55.0 5.01 0.0 33.74 3.66 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
469 470 5.736813 TGGTGTGGAATGTAGTGGTAATAC 58.263 41.667 0.00 0.00 0.00 1.89
619 620 3.510753 TGCTACAATGGCAATGACAATGT 59.489 39.130 14.78 14.78 38.36 2.71
663 664 1.221414 GATCCGGAAAGATTGCCTCG 58.779 55.000 9.01 0.00 0.00 4.63
773 774 2.263540 GTACACACCGCCCGTCAT 59.736 61.111 0.00 0.00 0.00 3.06
775 776 0.103572 GTACACACCGCCCGTCATAT 59.896 55.000 0.00 0.00 0.00 1.78
829 830 4.474651 ACCAATGATCACCCATGACTTCTA 59.525 41.667 0.00 0.00 37.79 2.10
850 851 3.562343 TGTACCACTAGTGCCACAAAA 57.438 42.857 17.86 0.00 0.00 2.44
871 872 2.378547 AGCCTTTGGTGGTCTTATTGGA 59.621 45.455 0.00 0.00 0.00 3.53
872 873 3.161866 GCCTTTGGTGGTCTTATTGGAA 58.838 45.455 0.00 0.00 0.00 3.53
873 874 3.769300 GCCTTTGGTGGTCTTATTGGAAT 59.231 43.478 0.00 0.00 0.00 3.01
874 875 4.953579 GCCTTTGGTGGTCTTATTGGAATA 59.046 41.667 0.00 0.00 0.00 1.75
875 876 5.420739 GCCTTTGGTGGTCTTATTGGAATAA 59.579 40.000 0.00 0.00 0.00 1.40
876 877 6.098266 GCCTTTGGTGGTCTTATTGGAATAAT 59.902 38.462 0.00 0.00 31.03 1.28
877 878 7.286775 GCCTTTGGTGGTCTTATTGGAATAATA 59.713 37.037 0.00 0.00 31.03 0.98
878 879 9.367160 CCTTTGGTGGTCTTATTGGAATAATAT 57.633 33.333 0.00 0.00 31.03 1.28
880 881 9.928618 TTTGGTGGTCTTATTGGAATAATATGA 57.071 29.630 0.00 0.00 31.03 2.15
1938 1955 2.058593 CCCTAAGGCCATGGAAAGTC 57.941 55.000 18.40 0.00 0.00 3.01
1939 1956 1.566231 CCCTAAGGCCATGGAAAGTCT 59.434 52.381 18.40 0.88 0.00 3.24
1940 1957 2.422093 CCCTAAGGCCATGGAAAGTCTC 60.422 54.545 18.40 0.00 0.00 3.36
1941 1958 2.555199 CTAAGGCCATGGAAAGTCTCG 58.445 52.381 18.40 0.00 0.00 4.04
1942 1959 0.678048 AAGGCCATGGAAAGTCTCGC 60.678 55.000 18.40 0.00 0.00 5.03
1943 1960 2.115291 GGCCATGGAAAGTCTCGCC 61.115 63.158 18.40 1.37 0.00 5.54
1944 1961 2.115291 GCCATGGAAAGTCTCGCCC 61.115 63.158 18.40 0.00 0.00 6.13
1945 1962 1.604378 CCATGGAAAGTCTCGCCCT 59.396 57.895 5.56 0.00 0.00 5.19
1946 1963 0.830648 CCATGGAAAGTCTCGCCCTA 59.169 55.000 5.56 0.00 0.00 3.53
1947 1964 1.202580 CCATGGAAAGTCTCGCCCTAG 60.203 57.143 5.56 0.00 0.00 3.02
1948 1965 0.466124 ATGGAAAGTCTCGCCCTAGC 59.534 55.000 0.00 0.00 0.00 3.42
1949 1966 1.144276 GGAAAGTCTCGCCCTAGCC 59.856 63.158 0.00 0.00 34.57 3.93
1950 1967 1.614241 GGAAAGTCTCGCCCTAGCCA 61.614 60.000 0.00 0.00 34.57 4.75
1951 1968 0.249398 GAAAGTCTCGCCCTAGCCAA 59.751 55.000 0.00 0.00 34.57 4.52
1952 1969 0.690762 AAAGTCTCGCCCTAGCCAAA 59.309 50.000 0.00 0.00 34.57 3.28
1953 1970 0.912486 AAGTCTCGCCCTAGCCAAAT 59.088 50.000 0.00 0.00 34.57 2.32
1954 1971 0.179000 AGTCTCGCCCTAGCCAAATG 59.821 55.000 0.00 0.00 34.57 2.32
1955 1972 0.178068 GTCTCGCCCTAGCCAAATGA 59.822 55.000 0.00 0.00 34.57 2.57
1956 1973 0.908910 TCTCGCCCTAGCCAAATGAA 59.091 50.000 0.00 0.00 34.57 2.57
1957 1974 1.017387 CTCGCCCTAGCCAAATGAAC 58.983 55.000 0.00 0.00 34.57 3.18
1958 1975 0.326595 TCGCCCTAGCCAAATGAACA 59.673 50.000 0.00 0.00 34.57 3.18
1959 1976 1.173043 CGCCCTAGCCAAATGAACAA 58.827 50.000 0.00 0.00 34.57 2.83
1960 1977 1.135402 CGCCCTAGCCAAATGAACAAC 60.135 52.381 0.00 0.00 34.57 3.32
1961 1978 1.892474 GCCCTAGCCAAATGAACAACA 59.108 47.619 0.00 0.00 0.00 3.33
1962 1979 2.352715 GCCCTAGCCAAATGAACAACAC 60.353 50.000 0.00 0.00 0.00 3.32
1963 1980 2.890311 CCCTAGCCAAATGAACAACACA 59.110 45.455 0.00 0.00 0.00 3.72
1964 1981 3.511146 CCCTAGCCAAATGAACAACACAT 59.489 43.478 0.00 0.00 0.00 3.21
1965 1982 4.704540 CCCTAGCCAAATGAACAACACATA 59.295 41.667 0.00 0.00 0.00 2.29
1966 1983 5.360714 CCCTAGCCAAATGAACAACACATAT 59.639 40.000 0.00 0.00 0.00 1.78
1967 1984 6.460123 CCCTAGCCAAATGAACAACACATATC 60.460 42.308 0.00 0.00 0.00 1.63
1968 1985 6.319658 CCTAGCCAAATGAACAACACATATCT 59.680 38.462 0.00 0.00 0.00 1.98
1969 1986 6.594788 AGCCAAATGAACAACACATATCTT 57.405 33.333 0.00 0.00 0.00 2.40
1970 1987 6.392354 AGCCAAATGAACAACACATATCTTG 58.608 36.000 0.00 0.00 0.00 3.02
1971 1988 5.062558 GCCAAATGAACAACACATATCTTGC 59.937 40.000 0.00 0.00 0.00 4.01
1972 1989 5.577945 CCAAATGAACAACACATATCTTGCC 59.422 40.000 0.00 0.00 0.00 4.52
1973 1990 4.989279 ATGAACAACACATATCTTGCCC 57.011 40.909 0.00 0.00 0.00 5.36
1974 1991 2.746904 TGAACAACACATATCTTGCCCG 59.253 45.455 0.00 0.00 0.00 6.13
1975 1992 1.750193 ACAACACATATCTTGCCCGG 58.250 50.000 0.00 0.00 0.00 5.73
1976 1993 1.004277 ACAACACATATCTTGCCCGGT 59.996 47.619 0.00 0.00 0.00 5.28
1977 1994 1.401552 CAACACATATCTTGCCCGGTG 59.598 52.381 0.00 0.00 0.00 4.94
1978 1995 0.908910 ACACATATCTTGCCCGGTGA 59.091 50.000 0.00 0.00 0.00 4.02
1979 1996 1.299541 CACATATCTTGCCCGGTGAC 58.700 55.000 0.00 0.00 0.00 3.67
1980 1997 1.134401 CACATATCTTGCCCGGTGACT 60.134 52.381 0.00 0.00 0.00 3.41
1981 1998 2.102420 CACATATCTTGCCCGGTGACTA 59.898 50.000 0.00 0.00 0.00 2.59
1982 1999 2.365617 ACATATCTTGCCCGGTGACTAG 59.634 50.000 0.00 0.00 0.00 2.57
1983 2000 0.750850 TATCTTGCCCGGTGACTAGC 59.249 55.000 0.00 0.00 0.00 3.42
1984 2001 2.298158 ATCTTGCCCGGTGACTAGCG 62.298 60.000 0.00 0.00 46.68 4.26
1985 2002 4.752879 TTGCCCGGTGACTAGCGC 62.753 66.667 0.00 0.00 45.83 5.92
2002 2019 3.357079 CAGCACTTGCCCACCGAC 61.357 66.667 0.00 0.00 43.38 4.79
2003 2020 4.643387 AGCACTTGCCCACCGACC 62.643 66.667 0.00 0.00 43.38 4.79
2005 2022 4.308458 CACTTGCCCACCGACCGA 62.308 66.667 0.00 0.00 0.00 4.69
2006 2023 3.319198 ACTTGCCCACCGACCGAT 61.319 61.111 0.00 0.00 0.00 4.18
2007 2024 2.046314 CTTGCCCACCGACCGATT 60.046 61.111 0.00 0.00 0.00 3.34
2008 2025 1.219664 CTTGCCCACCGACCGATTA 59.780 57.895 0.00 0.00 0.00 1.75
2009 2026 0.810031 CTTGCCCACCGACCGATTAG 60.810 60.000 0.00 0.00 0.00 1.73
2010 2027 1.546589 TTGCCCACCGACCGATTAGT 61.547 55.000 0.00 0.00 0.00 2.24
2011 2028 0.683828 TGCCCACCGACCGATTAGTA 60.684 55.000 0.00 0.00 0.00 1.82
2012 2029 0.677842 GCCCACCGACCGATTAGTAT 59.322 55.000 0.00 0.00 0.00 2.12
2013 2030 1.604693 GCCCACCGACCGATTAGTATG 60.605 57.143 0.00 0.00 0.00 2.39
2014 2031 1.000506 CCCACCGACCGATTAGTATGG 59.999 57.143 0.00 0.00 0.00 2.74
2015 2032 1.684983 CCACCGACCGATTAGTATGGT 59.315 52.381 0.00 0.00 39.12 3.55
2016 2033 2.288030 CCACCGACCGATTAGTATGGTC 60.288 54.545 0.55 0.55 46.91 4.02
2019 2036 2.787601 GACCGATTAGTATGGTCGCA 57.212 50.000 0.00 0.00 42.42 5.10
2020 2037 3.088194 GACCGATTAGTATGGTCGCAA 57.912 47.619 0.00 0.00 42.42 4.85
2021 2038 3.650139 GACCGATTAGTATGGTCGCAAT 58.350 45.455 0.00 0.00 42.42 3.56
2022 2039 4.801891 GACCGATTAGTATGGTCGCAATA 58.198 43.478 0.00 0.00 42.42 1.90
2023 2040 4.553323 ACCGATTAGTATGGTCGCAATAC 58.447 43.478 0.00 0.00 34.25 1.89
2024 2041 4.280174 ACCGATTAGTATGGTCGCAATACT 59.720 41.667 10.46 10.46 42.23 2.12
2025 2042 5.221382 ACCGATTAGTATGGTCGCAATACTT 60.221 40.000 10.77 0.00 40.49 2.24
2026 2043 5.118664 CCGATTAGTATGGTCGCAATACTTG 59.881 44.000 10.77 2.58 40.49 3.16
2038 2055 2.928334 CAATACTTGCTCATGGCCTCT 58.072 47.619 3.32 0.00 40.92 3.69
2039 2056 3.285484 CAATACTTGCTCATGGCCTCTT 58.715 45.455 3.32 0.00 40.92 2.85
2040 2057 2.408271 TACTTGCTCATGGCCTCTTG 57.592 50.000 3.32 0.00 40.92 3.02
2041 2058 0.323178 ACTTGCTCATGGCCTCTTGG 60.323 55.000 3.32 0.00 40.92 3.61
2042 2059 0.034767 CTTGCTCATGGCCTCTTGGA 60.035 55.000 3.32 0.00 40.92 3.53
2043 2060 0.627451 TTGCTCATGGCCTCTTGGAT 59.373 50.000 3.32 0.00 40.92 3.41
2044 2061 0.106868 TGCTCATGGCCTCTTGGATG 60.107 55.000 3.32 0.00 40.92 3.51
2045 2062 0.822532 GCTCATGGCCTCTTGGATGG 60.823 60.000 3.32 0.00 34.57 3.51
2046 2063 0.549950 CTCATGGCCTCTTGGATGGT 59.450 55.000 3.32 0.00 34.57 3.55
2047 2064 0.256752 TCATGGCCTCTTGGATGGTG 59.743 55.000 3.32 0.00 34.57 4.17
2048 2065 0.033796 CATGGCCTCTTGGATGGTGT 60.034 55.000 3.32 0.00 34.57 4.16
2049 2066 1.212688 CATGGCCTCTTGGATGGTGTA 59.787 52.381 3.32 0.00 34.57 2.90
2050 2067 0.618458 TGGCCTCTTGGATGGTGTAC 59.382 55.000 3.32 0.00 34.57 2.90
2051 2068 0.107165 GGCCTCTTGGATGGTGTACC 60.107 60.000 0.00 0.00 34.57 3.34
2072 2089 1.651987 TCGATGGTTGAGCGAATTCC 58.348 50.000 0.00 0.00 40.17 3.01
2073 2090 0.657840 CGATGGTTGAGCGAATTCCC 59.342 55.000 0.00 0.00 34.57 3.97
2074 2091 1.750193 GATGGTTGAGCGAATTCCCA 58.250 50.000 0.00 0.44 0.00 4.37
2075 2092 1.401905 GATGGTTGAGCGAATTCCCAC 59.598 52.381 0.00 0.00 0.00 4.61
2076 2093 0.953471 TGGTTGAGCGAATTCCCACG 60.953 55.000 0.00 0.00 0.00 4.94
2077 2094 0.672401 GGTTGAGCGAATTCCCACGA 60.672 55.000 0.00 0.00 0.00 4.35
2078 2095 1.369625 GTTGAGCGAATTCCCACGAT 58.630 50.000 0.00 0.00 0.00 3.73
2079 2096 1.737793 GTTGAGCGAATTCCCACGATT 59.262 47.619 0.00 0.00 0.00 3.34
2080 2097 2.933906 GTTGAGCGAATTCCCACGATTA 59.066 45.455 0.00 0.00 0.00 1.75
2081 2098 3.469008 TGAGCGAATTCCCACGATTAT 57.531 42.857 0.00 0.00 0.00 1.28
2082 2099 4.594123 TGAGCGAATTCCCACGATTATA 57.406 40.909 0.00 0.00 0.00 0.98
2083 2100 4.556233 TGAGCGAATTCCCACGATTATAG 58.444 43.478 0.00 0.00 0.00 1.31
2084 2101 4.279922 TGAGCGAATTCCCACGATTATAGA 59.720 41.667 0.00 0.00 0.00 1.98
2085 2102 5.047306 TGAGCGAATTCCCACGATTATAGAT 60.047 40.000 0.00 0.00 0.00 1.98
2086 2103 5.171476 AGCGAATTCCCACGATTATAGATG 58.829 41.667 0.00 0.00 0.00 2.90
2087 2104 5.047306 AGCGAATTCCCACGATTATAGATGA 60.047 40.000 0.00 0.00 0.00 2.92
2088 2105 5.289675 GCGAATTCCCACGATTATAGATGAG 59.710 44.000 0.00 0.00 0.00 2.90
2089 2106 6.390721 CGAATTCCCACGATTATAGATGAGT 58.609 40.000 0.00 0.00 0.00 3.41
2090 2107 6.868864 CGAATTCCCACGATTATAGATGAGTT 59.131 38.462 0.00 0.00 0.00 3.01
2091 2108 7.062371 CGAATTCCCACGATTATAGATGAGTTC 59.938 40.741 0.00 0.00 0.00 3.01
2092 2109 5.372547 TCCCACGATTATAGATGAGTTCG 57.627 43.478 0.00 0.00 0.00 3.95
2093 2110 4.825634 TCCCACGATTATAGATGAGTTCGT 59.174 41.667 0.00 0.00 40.11 3.85
2094 2111 5.301045 TCCCACGATTATAGATGAGTTCGTT 59.699 40.000 0.00 0.00 37.69 3.85
2095 2112 5.402568 CCCACGATTATAGATGAGTTCGTTG 59.597 44.000 0.00 0.00 37.69 4.10
2096 2113 5.107837 CCACGATTATAGATGAGTTCGTTGC 60.108 44.000 0.00 0.00 37.69 4.17
2097 2114 4.675565 ACGATTATAGATGAGTTCGTTGCG 59.324 41.667 0.00 0.00 36.52 4.85
2098 2115 4.088638 CGATTATAGATGAGTTCGTTGCGG 59.911 45.833 0.00 0.00 0.00 5.69
2099 2116 2.961526 ATAGATGAGTTCGTTGCGGT 57.038 45.000 0.00 0.00 0.00 5.68
2100 2117 5.503662 TTATAGATGAGTTCGTTGCGGTA 57.496 39.130 0.00 0.00 0.00 4.02
2101 2118 2.279582 AGATGAGTTCGTTGCGGTAG 57.720 50.000 0.00 0.00 0.00 3.18
2102 2119 1.816835 AGATGAGTTCGTTGCGGTAGA 59.183 47.619 0.00 0.00 0.00 2.59
2103 2120 2.159366 AGATGAGTTCGTTGCGGTAGAG 60.159 50.000 0.00 0.00 0.00 2.43
2104 2121 0.388134 TGAGTTCGTTGCGGTAGAGC 60.388 55.000 0.00 0.00 37.71 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
619 620 0.955428 CGCCTTACAGCCTTGCTTCA 60.955 55.000 0.00 0.00 36.40 3.02
644 645 1.221414 CGAGGCAATCTTTCCGGATC 58.779 55.000 4.15 0.00 0.00 3.36
663 664 1.808411 TGCAGAGAACAATCCGAACC 58.192 50.000 0.00 0.00 0.00 3.62
773 774 2.650322 GCGAAACCAATTCCCAGGATA 58.350 47.619 0.00 0.00 34.34 2.59
775 776 0.610785 GGCGAAACCAATTCCCAGGA 60.611 55.000 0.00 0.00 38.86 3.86
829 830 3.780804 TTTGTGGCACTAGTGGTACAT 57.219 42.857 23.95 0.00 44.52 2.29
850 851 2.378547 TCCAATAAGACCACCAAAGGCT 59.621 45.455 0.00 0.00 0.00 4.58
1088 1089 8.839343 GGAATTCCAATTAATTATTTTGGCTGG 58.161 33.333 20.04 6.00 39.79 4.85
1386 1397 6.840780 TTTCTTTCCTTCCATGGATTCTTC 57.159 37.500 17.06 0.00 35.83 2.87
1888 1905 4.515567 CCTTTTTGACTCTGTACCCTTGAC 59.484 45.833 0.00 0.00 0.00 3.18
1934 1951 0.912486 ATTTGGCTAGGGCGAGACTT 59.088 50.000 0.00 0.00 39.81 3.01
1935 1952 0.179000 CATTTGGCTAGGGCGAGACT 59.821 55.000 0.00 0.00 39.81 3.24
1936 1953 0.178068 TCATTTGGCTAGGGCGAGAC 59.822 55.000 0.00 0.00 39.81 3.36
1937 1954 0.908910 TTCATTTGGCTAGGGCGAGA 59.091 50.000 0.00 0.00 39.81 4.04
1938 1955 1.017387 GTTCATTTGGCTAGGGCGAG 58.983 55.000 0.00 0.00 39.81 5.03
1939 1956 0.326595 TGTTCATTTGGCTAGGGCGA 59.673 50.000 0.00 0.00 39.81 5.54
1940 1957 1.135402 GTTGTTCATTTGGCTAGGGCG 60.135 52.381 0.00 0.00 39.81 6.13
1941 1958 1.892474 TGTTGTTCATTTGGCTAGGGC 59.108 47.619 0.00 0.00 37.82 5.19
1942 1959 2.890311 TGTGTTGTTCATTTGGCTAGGG 59.110 45.455 0.00 0.00 0.00 3.53
1943 1960 4.789012 ATGTGTTGTTCATTTGGCTAGG 57.211 40.909 0.00 0.00 0.00 3.02
1944 1961 7.325660 AGATATGTGTTGTTCATTTGGCTAG 57.674 36.000 0.00 0.00 0.00 3.42
1945 1962 7.537715 CAAGATATGTGTTGTTCATTTGGCTA 58.462 34.615 0.00 0.00 0.00 3.93
1946 1963 6.392354 CAAGATATGTGTTGTTCATTTGGCT 58.608 36.000 0.00 0.00 0.00 4.75
1947 1964 5.062558 GCAAGATATGTGTTGTTCATTTGGC 59.937 40.000 1.38 0.00 31.62 4.52
1948 1965 5.577945 GGCAAGATATGTGTTGTTCATTTGG 59.422 40.000 1.38 0.00 31.62 3.28
1949 1966 5.577945 GGGCAAGATATGTGTTGTTCATTTG 59.422 40.000 1.38 0.00 31.62 2.32
1950 1967 5.622007 CGGGCAAGATATGTGTTGTTCATTT 60.622 40.000 1.38 0.00 31.62 2.32
1951 1968 4.142403 CGGGCAAGATATGTGTTGTTCATT 60.142 41.667 1.38 0.00 31.62 2.57
1952 1969 3.378112 CGGGCAAGATATGTGTTGTTCAT 59.622 43.478 1.38 0.00 31.62 2.57
1953 1970 2.746904 CGGGCAAGATATGTGTTGTTCA 59.253 45.455 1.38 0.00 31.62 3.18
1954 1971 2.097466 CCGGGCAAGATATGTGTTGTTC 59.903 50.000 0.00 0.00 31.62 3.18
1955 1972 2.091541 CCGGGCAAGATATGTGTTGTT 58.908 47.619 0.00 0.00 31.62 2.83
1956 1973 1.004277 ACCGGGCAAGATATGTGTTGT 59.996 47.619 6.32 0.00 31.62 3.32
1957 1974 1.401552 CACCGGGCAAGATATGTGTTG 59.598 52.381 6.32 0.00 0.00 3.33
1958 1975 1.280710 TCACCGGGCAAGATATGTGTT 59.719 47.619 6.32 0.00 0.00 3.32
1959 1976 0.908910 TCACCGGGCAAGATATGTGT 59.091 50.000 6.32 0.00 0.00 3.72
1960 1977 1.134401 AGTCACCGGGCAAGATATGTG 60.134 52.381 6.32 0.00 0.00 3.21
1961 1978 1.204146 AGTCACCGGGCAAGATATGT 58.796 50.000 6.32 0.00 0.00 2.29
1962 1979 2.868044 GCTAGTCACCGGGCAAGATATG 60.868 54.545 6.32 0.00 0.00 1.78
1963 1980 1.344763 GCTAGTCACCGGGCAAGATAT 59.655 52.381 6.32 0.00 0.00 1.63
1964 1981 0.750850 GCTAGTCACCGGGCAAGATA 59.249 55.000 6.32 0.00 0.00 1.98
1965 1982 1.522569 GCTAGTCACCGGGCAAGAT 59.477 57.895 6.32 0.00 0.00 2.40
1966 1983 2.978824 GCTAGTCACCGGGCAAGA 59.021 61.111 6.32 0.00 0.00 3.02
1967 1984 2.509336 CGCTAGTCACCGGGCAAG 60.509 66.667 6.32 0.00 0.00 4.01
1968 1985 4.752879 GCGCTAGTCACCGGGCAA 62.753 66.667 6.32 0.00 38.74 4.52
1972 1989 4.435436 TGCTGCGCTAGTCACCGG 62.435 66.667 9.73 0.00 0.00 5.28
1973 1990 3.181967 GTGCTGCGCTAGTCACCG 61.182 66.667 9.73 0.00 31.47 4.94
1974 1991 1.374758 AAGTGCTGCGCTAGTCACC 60.375 57.895 17.04 3.41 35.43 4.02
1975 1992 1.784062 CAAGTGCTGCGCTAGTCAC 59.216 57.895 17.04 15.25 35.21 3.67
1976 1993 2.029288 GCAAGTGCTGCGCTAGTCA 61.029 57.895 17.04 4.63 42.37 3.41
1977 1994 2.781300 GCAAGTGCTGCGCTAGTC 59.219 61.111 17.04 4.93 42.37 2.59
1985 2002 3.357079 GTCGGTGGGCAAGTGCTG 61.357 66.667 2.85 0.00 41.70 4.41
1986 2003 4.643387 GGTCGGTGGGCAAGTGCT 62.643 66.667 2.85 0.00 41.70 4.40
1988 2005 3.605749 ATCGGTCGGTGGGCAAGTG 62.606 63.158 0.00 0.00 0.00 3.16
1989 2006 1.546589 TAATCGGTCGGTGGGCAAGT 61.547 55.000 0.00 0.00 0.00 3.16
1990 2007 0.810031 CTAATCGGTCGGTGGGCAAG 60.810 60.000 0.00 0.00 0.00 4.01
1991 2008 1.219664 CTAATCGGTCGGTGGGCAA 59.780 57.895 0.00 0.00 0.00 4.52
1992 2009 0.683828 TACTAATCGGTCGGTGGGCA 60.684 55.000 0.00 0.00 0.00 5.36
1993 2010 0.677842 ATACTAATCGGTCGGTGGGC 59.322 55.000 0.00 0.00 0.00 5.36
1994 2011 1.000506 CCATACTAATCGGTCGGTGGG 59.999 57.143 0.00 0.00 0.00 4.61
1995 2012 1.684983 ACCATACTAATCGGTCGGTGG 59.315 52.381 0.00 0.00 0.00 4.61
1996 2013 3.009301 GACCATACTAATCGGTCGGTG 57.991 52.381 0.00 0.00 39.86 4.94
2000 2017 2.787601 TGCGACCATACTAATCGGTC 57.212 50.000 0.00 0.00 44.79 4.79
2001 2018 3.746045 ATTGCGACCATACTAATCGGT 57.254 42.857 0.00 0.00 36.37 4.69
2002 2019 4.806330 AGTATTGCGACCATACTAATCGG 58.194 43.478 0.00 0.00 36.37 4.18
2003 2020 6.140896 CAAGTATTGCGACCATACTAATCG 57.859 41.667 0.00 0.00 40.39 3.34
2019 2036 3.285484 CAAGAGGCCATGAGCAAGTATT 58.715 45.455 5.01 0.00 46.50 1.89
2020 2037 2.422519 CCAAGAGGCCATGAGCAAGTAT 60.423 50.000 5.01 0.00 46.50 2.12
2021 2038 1.065199 CCAAGAGGCCATGAGCAAGTA 60.065 52.381 5.01 0.00 46.50 2.24
2022 2039 0.323178 CCAAGAGGCCATGAGCAAGT 60.323 55.000 5.01 0.00 46.50 3.16
2023 2040 0.034767 TCCAAGAGGCCATGAGCAAG 60.035 55.000 5.01 0.00 46.50 4.01
2024 2041 0.627451 ATCCAAGAGGCCATGAGCAA 59.373 50.000 5.01 0.00 46.50 3.91
2025 2042 0.106868 CATCCAAGAGGCCATGAGCA 60.107 55.000 5.01 0.00 46.50 4.26
2026 2043 0.822532 CCATCCAAGAGGCCATGAGC 60.823 60.000 5.01 0.00 42.60 4.26
2027 2044 0.549950 ACCATCCAAGAGGCCATGAG 59.450 55.000 5.01 0.00 33.74 2.90
2028 2045 0.256752 CACCATCCAAGAGGCCATGA 59.743 55.000 5.01 0.00 33.74 3.07
2029 2046 0.033796 ACACCATCCAAGAGGCCATG 60.034 55.000 5.01 0.00 33.74 3.66
2030 2047 1.212935 GTACACCATCCAAGAGGCCAT 59.787 52.381 5.01 0.00 33.74 4.40
2031 2048 0.618458 GTACACCATCCAAGAGGCCA 59.382 55.000 5.01 0.00 33.74 5.36
2032 2049 0.107165 GGTACACCATCCAAGAGGCC 60.107 60.000 0.00 0.00 35.64 5.19
2033 2050 0.618458 TGGTACACCATCCAAGAGGC 59.382 55.000 0.00 0.00 42.01 4.70
2051 2068 2.032549 GGAATTCGCTCAACCATCGATG 60.033 50.000 18.76 18.76 31.96 3.84
2052 2069 2.213499 GGAATTCGCTCAACCATCGAT 58.787 47.619 0.00 0.00 31.96 3.59
2053 2070 1.651987 GGAATTCGCTCAACCATCGA 58.348 50.000 0.00 0.00 0.00 3.59
2054 2071 0.657840 GGGAATTCGCTCAACCATCG 59.342 55.000 14.84 0.00 0.00 3.84
2055 2072 1.401905 GTGGGAATTCGCTCAACCATC 59.598 52.381 21.56 4.24 0.00 3.51
2056 2073 1.463674 GTGGGAATTCGCTCAACCAT 58.536 50.000 21.56 0.00 0.00 3.55
2057 2074 0.953471 CGTGGGAATTCGCTCAACCA 60.953 55.000 21.56 9.12 0.00 3.67
2058 2075 0.672401 TCGTGGGAATTCGCTCAACC 60.672 55.000 21.56 6.64 0.00 3.77
2059 2076 1.369625 ATCGTGGGAATTCGCTCAAC 58.630 50.000 21.56 11.67 0.00 3.18
2060 2077 2.107950 AATCGTGGGAATTCGCTCAA 57.892 45.000 21.56 5.91 0.00 3.02
2061 2078 2.971660 TAATCGTGGGAATTCGCTCA 57.028 45.000 21.56 10.44 0.00 4.26
2062 2079 4.806330 TCTATAATCGTGGGAATTCGCTC 58.194 43.478 21.56 17.16 0.00 5.03
2063 2080 4.866508 TCTATAATCGTGGGAATTCGCT 57.133 40.909 21.56 5.40 0.00 4.93
2064 2081 5.168569 TCATCTATAATCGTGGGAATTCGC 58.831 41.667 15.22 15.22 0.00 4.70
2065 2082 6.390721 ACTCATCTATAATCGTGGGAATTCG 58.609 40.000 0.00 0.00 0.00 3.34
2066 2083 7.062371 CGAACTCATCTATAATCGTGGGAATTC 59.938 40.741 0.00 0.00 0.00 2.17
2067 2084 6.868864 CGAACTCATCTATAATCGTGGGAATT 59.131 38.462 0.00 0.00 0.00 2.17
2068 2085 6.015350 ACGAACTCATCTATAATCGTGGGAAT 60.015 38.462 0.00 0.00 41.41 3.01
2069 2086 5.301045 ACGAACTCATCTATAATCGTGGGAA 59.699 40.000 0.00 0.00 41.41 3.97
2070 2087 4.825634 ACGAACTCATCTATAATCGTGGGA 59.174 41.667 0.00 0.00 41.41 4.37
2071 2088 5.122512 ACGAACTCATCTATAATCGTGGG 57.877 43.478 0.00 0.00 41.41 4.61
2072 2089 5.107837 GCAACGAACTCATCTATAATCGTGG 60.108 44.000 0.00 0.00 42.04 4.94
2073 2090 5.386424 CGCAACGAACTCATCTATAATCGTG 60.386 44.000 0.00 0.00 42.04 4.35
2074 2091 4.675565 CGCAACGAACTCATCTATAATCGT 59.324 41.667 0.00 0.00 44.43 3.73
2075 2092 4.088638 CCGCAACGAACTCATCTATAATCG 59.911 45.833 0.00 0.00 36.45 3.34
2076 2093 4.982916 ACCGCAACGAACTCATCTATAATC 59.017 41.667 0.00 0.00 0.00 1.75
2077 2094 4.945246 ACCGCAACGAACTCATCTATAAT 58.055 39.130 0.00 0.00 0.00 1.28
2078 2095 4.380841 ACCGCAACGAACTCATCTATAA 57.619 40.909 0.00 0.00 0.00 0.98
2079 2096 4.818005 TCTACCGCAACGAACTCATCTATA 59.182 41.667 0.00 0.00 0.00 1.31
2080 2097 2.961526 ACCGCAACGAACTCATCTAT 57.038 45.000 0.00 0.00 0.00 1.98
2081 2098 3.011818 TCTACCGCAACGAACTCATCTA 58.988 45.455 0.00 0.00 0.00 1.98
2082 2099 1.816835 TCTACCGCAACGAACTCATCT 59.183 47.619 0.00 0.00 0.00 2.90
2083 2100 2.186076 CTCTACCGCAACGAACTCATC 58.814 52.381 0.00 0.00 0.00 2.92
2084 2101 1.736032 GCTCTACCGCAACGAACTCAT 60.736 52.381 0.00 0.00 0.00 2.90
2085 2102 0.388134 GCTCTACCGCAACGAACTCA 60.388 55.000 0.00 0.00 0.00 3.41
2086 2103 2.360794 GCTCTACCGCAACGAACTC 58.639 57.895 0.00 0.00 0.00 3.01
2087 2104 4.573162 GCTCTACCGCAACGAACT 57.427 55.556 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.