Multiple sequence alignment - TraesCS2D01G161600

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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 TraesCS2D01G161600 chr2D 100.000 2357 0 0 1 2357 106345048 106347404 0.000000e+00 4353
1 TraesCS2D01G161600 chr2D 96.720 1067 24 1 890 1945 73126609 73125543 0.000000e+00 1766
2 TraesCS2D01G161600 chr2D 97.865 890 17 2 1 889 13815814 13816702 0.000000e+00 1537
3 TraesCS2D01G161600 chr2D 97.863 889 18 1 1 889 106337611 106338498 0.000000e+00 1535
4 TraesCS2D01G161600 chr2D 97.753 890 18 2 1 889 621467994 621468882 0.000000e+00 1531
5 TraesCS2D01G161600 chr1D 96.626 1067 25 1 890 1945 60171553 60170487 0.000000e+00 1760
6 TraesCS2D01G161600 chr1D 95.689 1067 30 2 890 1945 205134434 205133373 0.000000e+00 1701
7 TraesCS2D01G161600 chr1D 98.200 889 16 0 1 889 874447 873559 0.000000e+00 1554
8 TraesCS2D01G161600 chr1D 98.088 889 17 0 1 889 867029 866141 0.000000e+00 1548
9 TraesCS2D01G161600 chr3D 96.439 1067 27 1 890 1945 584701129 584700063 0.000000e+00 1749
10 TraesCS2D01G161600 chr3D 93.396 212 9 5 1736 1945 613712347 613712555 2.280000e-80 309
11 TraesCS2D01G161600 chr7D 96.345 1067 28 1 890 1945 497561168 497562234 0.000000e+00 1744
12 TraesCS2D01G161600 chr7D 97.865 890 17 2 1 889 30197621 30196733 0.000000e+00 1537
13 TraesCS2D01G161600 chr5D 95.783 1067 34 1 890 1945 275171486 275170420 0.000000e+00 1711
14 TraesCS2D01G161600 chr6D 95.689 1067 32 2 890 1945 142136429 142135366 0.000000e+00 1703
15 TraesCS2D01G161600 chr6D 95.408 1067 36 6 890 1945 28034779 28033715 0.000000e+00 1687
16 TraesCS2D01G161600 chr6D 98.088 889 17 0 1 889 315677977 315677089 0.000000e+00 1548
17 TraesCS2D01G161600 chr4A 95.545 1055 47 0 890 1944 561102860 561103914 0.000000e+00 1688
18 TraesCS2D01G161600 chr4D 95.131 1068 39 3 890 1945 23003783 23002717 0.000000e+00 1672
19 TraesCS2D01G161600 chrUn 94.939 1067 42 2 890 1945 63293438 63294503 0.000000e+00 1661
20 TraesCS2D01G161600 chrUn 94.658 1067 45 5 890 1945 63398761 63397696 0.000000e+00 1644
21 TraesCS2D01G161600 chrUn 97.980 891 15 3 1 889 69328599 69327710 0.000000e+00 1543
22 TraesCS2D01G161600 chrUn 97.868 891 18 1 1 890 30565693 30566583 0.000000e+00 1539
23 TraesCS2D01G161600 chrUn 97.126 174 4 1 1772 1945 319148537 319148709 2.290000e-75 292
24 TraesCS2D01G161600 chr3B 94.528 1060 45 3 897 1945 222272490 222273547 0.000000e+00 1624
25 TraesCS2D01G161600 chr1A 94.107 1069 46 5 888 1945 3977722 3978784 0.000000e+00 1609
26 TraesCS2D01G161600 chr3A 93.914 1068 52 3 890 1945 738099378 738100444 0.000000e+00 1600


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 TraesCS2D01G161600 chr2D 106345048 106347404 2356 False 4353 4353 100.000 1 2357 1 chr2D.!!$F3 2356
1 TraesCS2D01G161600 chr2D 73125543 73126609 1066 True 1766 1766 96.720 890 1945 1 chr2D.!!$R1 1055
2 TraesCS2D01G161600 chr2D 13815814 13816702 888 False 1537 1537 97.865 1 889 1 chr2D.!!$F1 888
3 TraesCS2D01G161600 chr2D 106337611 106338498 887 False 1535 1535 97.863 1 889 1 chr2D.!!$F2 888
4 TraesCS2D01G161600 chr2D 621467994 621468882 888 False 1531 1531 97.753 1 889 1 chr2D.!!$F4 888
5 TraesCS2D01G161600 chr1D 60170487 60171553 1066 True 1760 1760 96.626 890 1945 1 chr1D.!!$R3 1055
6 TraesCS2D01G161600 chr1D 205133373 205134434 1061 True 1701 1701 95.689 890 1945 1 chr1D.!!$R4 1055
7 TraesCS2D01G161600 chr1D 873559 874447 888 True 1554 1554 98.200 1 889 1 chr1D.!!$R2 888
8 TraesCS2D01G161600 chr1D 866141 867029 888 True 1548 1548 98.088 1 889 1 chr1D.!!$R1 888
9 TraesCS2D01G161600 chr3D 584700063 584701129 1066 True 1749 1749 96.439 890 1945 1 chr3D.!!$R1 1055
10 TraesCS2D01G161600 chr7D 497561168 497562234 1066 False 1744 1744 96.345 890 1945 1 chr7D.!!$F1 1055
11 TraesCS2D01G161600 chr7D 30196733 30197621 888 True 1537 1537 97.865 1 889 1 chr7D.!!$R1 888
12 TraesCS2D01G161600 chr5D 275170420 275171486 1066 True 1711 1711 95.783 890 1945 1 chr5D.!!$R1 1055
13 TraesCS2D01G161600 chr6D 142135366 142136429 1063 True 1703 1703 95.689 890 1945 1 chr6D.!!$R2 1055
14 TraesCS2D01G161600 chr6D 28033715 28034779 1064 True 1687 1687 95.408 890 1945 1 chr6D.!!$R1 1055
15 TraesCS2D01G161600 chr6D 315677089 315677977 888 True 1548 1548 98.088 1 889 1 chr6D.!!$R3 888
16 TraesCS2D01G161600 chr4A 561102860 561103914 1054 False 1688 1688 95.545 890 1944 1 chr4A.!!$F1 1054
17 TraesCS2D01G161600 chr4D 23002717 23003783 1066 True 1672 1672 95.131 890 1945 1 chr4D.!!$R1 1055
18 TraesCS2D01G161600 chrUn 63293438 63294503 1065 False 1661 1661 94.939 890 1945 1 chrUn.!!$F2 1055
19 TraesCS2D01G161600 chrUn 63397696 63398761 1065 True 1644 1644 94.658 890 1945 1 chrUn.!!$R1 1055
20 TraesCS2D01G161600 chrUn 69327710 69328599 889 True 1543 1543 97.980 1 889 1 chrUn.!!$R2 888
21 TraesCS2D01G161600 chrUn 30565693 30566583 890 False 1539 1539 97.868 1 890 1 chrUn.!!$F1 889
22 TraesCS2D01G161600 chr3B 222272490 222273547 1057 False 1624 1624 94.528 897 1945 1 chr3B.!!$F1 1048
23 TraesCS2D01G161600 chr1A 3977722 3978784 1062 False 1609 1609 94.107 888 1945 1 chr1A.!!$F1 1057
24 TraesCS2D01G161600 chr3A 738099378 738100444 1066 False 1600 1600 93.914 890 1945 1 chr3A.!!$F1 1055

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
162 163 0.417035 ATTTTTGGGCCCCTCATGGA 59.583 50.0 22.27 0.0 35.39 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1400 0.563173 TAGGATGGGGACTGGAGGAG 59.437 60.0 0.0 0.0 0.0 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 0.846015 TGGGGATGACATGGATGGAC 59.154 55.000 0.00 0.00 0.00 4.02
162 163 0.417035 ATTTTTGGGCCCCTCATGGA 59.583 50.000 22.27 0.00 35.39 3.41
493 496 2.954316 CACCGTATGTGTGCAACTCTA 58.046 47.619 0.00 0.00 40.26 2.43
562 565 2.906388 TCCGTGTGACCGTCCGAA 60.906 61.111 0.00 0.00 0.00 4.30
598 601 1.534235 AAGGGCTGTCCGAGTGACT 60.534 57.895 0.00 0.00 44.75 3.41
893 897 1.674817 GCTGCGTTACCCTACACACAT 60.675 52.381 0.00 0.00 0.00 3.21
949 953 2.461300 TCTTCCACCGATCCATCTCT 57.539 50.000 0.00 0.00 0.00 3.10
1017 1021 3.709633 ATGGCGCCAGACAGCTCA 61.710 61.111 35.36 7.66 39.80 4.26
1344 1351 0.326238 TCGCCTCCAGGAAGGGTAAT 60.326 55.000 2.14 0.00 36.88 1.89
1368 1375 1.733041 CAAGTGACGTCGCCGATGT 60.733 57.895 24.75 12.49 37.88 3.06
1393 1400 0.232303 CGAACACGCTGACCAAAGTC 59.768 55.000 0.00 0.00 43.83 3.01
1400 1407 0.687354 GCTGACCAAAGTCTCCTCCA 59.313 55.000 0.00 0.00 43.91 3.86
1467 1474 1.079127 CCACGATCTGAAACCCGCT 60.079 57.895 0.00 0.00 0.00 5.52
1783 1806 1.760086 CTCTGGATCCCGCTGTCCT 60.760 63.158 9.90 0.00 35.49 3.85
1950 1973 4.745751 CGCGGGGGCGACACTAAA 62.746 66.667 1.68 0.00 34.88 1.85
1951 1974 2.124860 GCGGGGGCGACACTAAAT 60.125 61.111 0.00 0.00 0.00 1.40
1952 1975 1.747745 GCGGGGGCGACACTAAATT 60.748 57.895 0.00 0.00 0.00 1.82
1953 1976 1.712018 GCGGGGGCGACACTAAATTC 61.712 60.000 0.00 0.00 0.00 2.17
1954 1977 0.391927 CGGGGGCGACACTAAATTCA 60.392 55.000 0.00 0.00 0.00 2.57
1955 1978 1.828979 GGGGGCGACACTAAATTCAA 58.171 50.000 0.00 0.00 0.00 2.69
1956 1979 2.375146 GGGGGCGACACTAAATTCAAT 58.625 47.619 0.00 0.00 0.00 2.57
1957 1980 3.547746 GGGGGCGACACTAAATTCAATA 58.452 45.455 0.00 0.00 0.00 1.90
1958 1981 3.949113 GGGGGCGACACTAAATTCAATAA 59.051 43.478 0.00 0.00 0.00 1.40
1959 1982 4.201980 GGGGGCGACACTAAATTCAATAAC 60.202 45.833 0.00 0.00 0.00 1.89
1960 1983 4.396790 GGGGCGACACTAAATTCAATAACA 59.603 41.667 0.00 0.00 0.00 2.41
1961 1984 5.106078 GGGGCGACACTAAATTCAATAACAA 60.106 40.000 0.00 0.00 0.00 2.83
1962 1985 6.383415 GGGCGACACTAAATTCAATAACAAA 58.617 36.000 0.00 0.00 0.00 2.83
1963 1986 6.864165 GGGCGACACTAAATTCAATAACAAAA 59.136 34.615 0.00 0.00 0.00 2.44
1964 1987 7.061789 GGGCGACACTAAATTCAATAACAAAAG 59.938 37.037 0.00 0.00 0.00 2.27
1965 1988 7.806014 GGCGACACTAAATTCAATAACAAAAGA 59.194 33.333 0.00 0.00 0.00 2.52
1966 1989 9.341899 GCGACACTAAATTCAATAACAAAAGAT 57.658 29.630 0.00 0.00 0.00 2.40
1974 1997 9.675464 AAATTCAATAACAAAAGATCCATGCAT 57.325 25.926 0.00 0.00 0.00 3.96
1975 1998 8.657074 ATTCAATAACAAAAGATCCATGCATG 57.343 30.769 20.19 20.19 0.00 4.06
1976 1999 7.407393 TCAATAACAAAAGATCCATGCATGA 57.593 32.000 28.31 14.16 0.00 3.07
1977 2000 8.014070 TCAATAACAAAAGATCCATGCATGAT 57.986 30.769 28.31 18.12 0.00 2.45
1978 2001 8.479689 TCAATAACAAAAGATCCATGCATGATT 58.520 29.630 28.31 14.32 0.00 2.57
1979 2002 9.752961 CAATAACAAAAGATCCATGCATGATTA 57.247 29.630 28.31 13.05 0.00 1.75
1980 2003 9.976511 AATAACAAAAGATCCATGCATGATTAG 57.023 29.630 28.31 11.20 0.00 1.73
1981 2004 7.649533 AACAAAAGATCCATGCATGATTAGA 57.350 32.000 28.31 16.32 0.00 2.10
1982 2005 7.273320 ACAAAAGATCCATGCATGATTAGAG 57.727 36.000 28.31 10.06 0.00 2.43
1983 2006 6.264744 ACAAAAGATCCATGCATGATTAGAGG 59.735 38.462 28.31 9.49 0.00 3.69
1984 2007 4.571369 AGATCCATGCATGATTAGAGGG 57.429 45.455 28.31 8.70 0.00 4.30
1985 2008 4.173594 AGATCCATGCATGATTAGAGGGA 58.826 43.478 28.31 14.10 0.00 4.20
1986 2009 4.600547 AGATCCATGCATGATTAGAGGGAA 59.399 41.667 28.31 0.00 0.00 3.97
1987 2010 4.362470 TCCATGCATGATTAGAGGGAAG 57.638 45.455 28.31 6.55 0.00 3.46
1988 2011 3.073503 TCCATGCATGATTAGAGGGAAGG 59.926 47.826 28.31 6.39 0.00 3.46
1989 2012 3.181436 CCATGCATGATTAGAGGGAAGGT 60.181 47.826 28.31 0.00 0.00 3.50
1990 2013 4.042062 CCATGCATGATTAGAGGGAAGGTA 59.958 45.833 28.31 0.00 0.00 3.08
1991 2014 5.456619 CCATGCATGATTAGAGGGAAGGTAA 60.457 44.000 28.31 0.00 0.00 2.85
1992 2015 5.296151 TGCATGATTAGAGGGAAGGTAAG 57.704 43.478 0.00 0.00 0.00 2.34
1993 2016 4.721776 TGCATGATTAGAGGGAAGGTAAGT 59.278 41.667 0.00 0.00 0.00 2.24
1994 2017 5.191722 TGCATGATTAGAGGGAAGGTAAGTT 59.808 40.000 0.00 0.00 0.00 2.66
1995 2018 6.385759 TGCATGATTAGAGGGAAGGTAAGTTA 59.614 38.462 0.00 0.00 0.00 2.24
1996 2019 6.706716 GCATGATTAGAGGGAAGGTAAGTTAC 59.293 42.308 4.32 4.32 0.00 2.50
1997 2020 7.419172 GCATGATTAGAGGGAAGGTAAGTTACT 60.419 40.741 12.65 0.00 0.00 2.24
1998 2021 9.144298 CATGATTAGAGGGAAGGTAAGTTACTA 57.856 37.037 12.65 0.00 0.00 1.82
1999 2022 9.725206 ATGATTAGAGGGAAGGTAAGTTACTAA 57.275 33.333 12.65 2.03 0.00 2.24
2000 2023 9.725206 TGATTAGAGGGAAGGTAAGTTACTAAT 57.275 33.333 12.65 6.36 32.97 1.73
2003 2026 9.995594 TTAGAGGGAAGGTAAGTTACTAATACA 57.004 33.333 12.65 0.00 0.00 2.29
2004 2027 8.303780 AGAGGGAAGGTAAGTTACTAATACAC 57.696 38.462 12.65 2.63 0.00 2.90
2005 2028 8.121185 AGAGGGAAGGTAAGTTACTAATACACT 58.879 37.037 12.65 6.80 0.00 3.55
2006 2029 8.676397 AGGGAAGGTAAGTTACTAATACACTT 57.324 34.615 12.65 5.72 35.00 3.16
2007 2030 9.109246 AGGGAAGGTAAGTTACTAATACACTTT 57.891 33.333 12.65 0.00 32.88 2.66
2008 2031 9.376075 GGGAAGGTAAGTTACTAATACACTTTC 57.624 37.037 12.65 4.74 32.88 2.62
2009 2032 9.933723 GGAAGGTAAGTTACTAATACACTTTCA 57.066 33.333 12.65 0.00 32.88 2.69
2024 2047 6.422776 ACACTTTCATAATGGTAAGCTTCG 57.577 37.500 0.00 0.00 0.00 3.79
2025 2048 5.354234 ACACTTTCATAATGGTAAGCTTCGG 59.646 40.000 0.00 0.00 0.00 4.30
2026 2049 5.354234 CACTTTCATAATGGTAAGCTTCGGT 59.646 40.000 0.00 0.00 0.00 4.69
2027 2050 5.354234 ACTTTCATAATGGTAAGCTTCGGTG 59.646 40.000 0.00 0.00 0.00 4.94
2028 2051 4.481368 TCATAATGGTAAGCTTCGGTGT 57.519 40.909 0.00 0.00 0.00 4.16
2029 2052 4.439057 TCATAATGGTAAGCTTCGGTGTC 58.561 43.478 0.00 0.00 0.00 3.67
2030 2053 4.161565 TCATAATGGTAAGCTTCGGTGTCT 59.838 41.667 0.00 0.00 0.00 3.41
2031 2054 5.361571 TCATAATGGTAAGCTTCGGTGTCTA 59.638 40.000 0.00 0.00 0.00 2.59
2032 2055 4.755266 AATGGTAAGCTTCGGTGTCTAT 57.245 40.909 0.00 0.00 0.00 1.98
2033 2056 3.520290 TGGTAAGCTTCGGTGTCTATG 57.480 47.619 0.00 0.00 0.00 2.23
2034 2057 3.093814 TGGTAAGCTTCGGTGTCTATGA 58.906 45.455 0.00 0.00 0.00 2.15
2035 2058 3.119245 TGGTAAGCTTCGGTGTCTATGAC 60.119 47.826 0.00 0.00 0.00 3.06
2036 2059 3.130693 GGTAAGCTTCGGTGTCTATGACT 59.869 47.826 0.00 0.00 33.15 3.41
2037 2060 3.963428 AAGCTTCGGTGTCTATGACTT 57.037 42.857 0.00 0.00 33.15 3.01
2038 2061 5.163581 GGTAAGCTTCGGTGTCTATGACTTA 60.164 44.000 0.00 0.00 33.15 2.24
2039 2062 5.401531 AAGCTTCGGTGTCTATGACTTAA 57.598 39.130 0.00 0.00 33.15 1.85
2040 2063 4.745649 AGCTTCGGTGTCTATGACTTAAC 58.254 43.478 0.00 0.00 33.15 2.01
2041 2064 4.219944 AGCTTCGGTGTCTATGACTTAACA 59.780 41.667 0.00 0.00 33.15 2.41
2042 2065 4.563184 GCTTCGGTGTCTATGACTTAACAG 59.437 45.833 0.00 0.00 33.15 3.16
2043 2066 5.621555 GCTTCGGTGTCTATGACTTAACAGA 60.622 44.000 0.00 0.00 33.15 3.41
2044 2067 5.970317 TCGGTGTCTATGACTTAACAGAA 57.030 39.130 0.00 0.00 33.15 3.02
2045 2068 5.950883 TCGGTGTCTATGACTTAACAGAAG 58.049 41.667 0.00 0.00 33.15 2.85
2046 2069 5.708697 TCGGTGTCTATGACTTAACAGAAGA 59.291 40.000 0.00 0.00 33.15 2.87
2047 2070 6.377429 TCGGTGTCTATGACTTAACAGAAGAT 59.623 38.462 0.00 0.00 33.15 2.40
2048 2071 7.036220 CGGTGTCTATGACTTAACAGAAGATT 58.964 38.462 0.00 0.00 33.15 2.40
2049 2072 7.545965 CGGTGTCTATGACTTAACAGAAGATTT 59.454 37.037 0.00 0.00 33.15 2.17
2050 2073 9.220767 GGTGTCTATGACTTAACAGAAGATTTT 57.779 33.333 0.00 0.00 33.15 1.82
2057 2080 9.846248 ATGACTTAACAGAAGATTTTTACATGC 57.154 29.630 0.00 0.00 0.00 4.06
2058 2081 8.845227 TGACTTAACAGAAGATTTTTACATGCA 58.155 29.630 0.00 0.00 0.00 3.96
2059 2082 9.118236 GACTTAACAGAAGATTTTTACATGCAC 57.882 33.333 0.00 0.00 0.00 4.57
2060 2083 7.803189 ACTTAACAGAAGATTTTTACATGCACG 59.197 33.333 0.00 0.00 0.00 5.34
2061 2084 5.689383 ACAGAAGATTTTTACATGCACGT 57.311 34.783 0.00 0.00 0.00 4.49
2062 2085 6.795098 ACAGAAGATTTTTACATGCACGTA 57.205 33.333 0.00 0.00 0.00 3.57
2063 2086 7.197071 ACAGAAGATTTTTACATGCACGTAA 57.803 32.000 0.32 0.32 0.00 3.18
2064 2087 7.816640 ACAGAAGATTTTTACATGCACGTAAT 58.183 30.769 6.16 0.00 31.65 1.89
2065 2088 8.296713 ACAGAAGATTTTTACATGCACGTAATT 58.703 29.630 6.16 0.00 31.65 1.40
2066 2089 9.767684 CAGAAGATTTTTACATGCACGTAATTA 57.232 29.630 6.16 0.00 31.65 1.40
2067 2090 9.769093 AGAAGATTTTTACATGCACGTAATTAC 57.231 29.630 6.16 5.47 31.65 1.89
2068 2091 9.769093 GAAGATTTTTACATGCACGTAATTACT 57.231 29.630 6.16 2.02 31.65 2.24
2069 2092 9.554724 AAGATTTTTACATGCACGTAATTACTG 57.445 29.630 6.16 11.18 31.65 2.74
2070 2093 8.181573 AGATTTTTACATGCACGTAATTACTGG 58.818 33.333 6.16 6.54 31.65 4.00
2071 2094 7.436430 TTTTTACATGCACGTAATTACTGGA 57.564 32.000 6.16 11.59 31.65 3.86
2072 2095 7.436430 TTTTACATGCACGTAATTACTGGAA 57.564 32.000 6.16 4.92 31.65 3.53
2073 2096 7.618502 TTTACATGCACGTAATTACTGGAAT 57.381 32.000 6.16 3.00 31.65 3.01
2074 2097 5.734855 ACATGCACGTAATTACTGGAATC 57.265 39.130 13.56 0.59 0.00 2.52
2075 2098 5.182487 ACATGCACGTAATTACTGGAATCA 58.818 37.500 13.56 5.27 0.00 2.57
2076 2099 5.822519 ACATGCACGTAATTACTGGAATCAT 59.177 36.000 13.56 6.93 0.00 2.45
2077 2100 6.318648 ACATGCACGTAATTACTGGAATCATT 59.681 34.615 13.56 0.00 0.00 2.57
2078 2101 6.751514 TGCACGTAATTACTGGAATCATTT 57.248 33.333 13.56 0.00 0.00 2.32
2079 2102 6.781138 TGCACGTAATTACTGGAATCATTTC 58.219 36.000 13.56 0.00 0.00 2.17
2080 2103 6.372937 TGCACGTAATTACTGGAATCATTTCA 59.627 34.615 13.56 0.20 33.23 2.69
2081 2104 7.094592 TGCACGTAATTACTGGAATCATTTCAA 60.095 33.333 13.56 0.00 33.23 2.69
2082 2105 7.915397 GCACGTAATTACTGGAATCATTTCAAT 59.085 33.333 13.56 0.00 33.23 2.57
2083 2106 9.438291 CACGTAATTACTGGAATCATTTCAATC 57.562 33.333 13.56 0.00 33.23 2.67
2084 2107 9.173021 ACGTAATTACTGGAATCATTTCAATCA 57.827 29.630 13.56 0.00 33.23 2.57
2085 2108 9.438291 CGTAATTACTGGAATCATTTCAATCAC 57.562 33.333 13.56 0.00 33.23 3.06
2088 2111 9.865321 AATTACTGGAATCATTTCAATCACAAG 57.135 29.630 0.00 0.00 33.23 3.16
2089 2112 8.634335 TTACTGGAATCATTTCAATCACAAGA 57.366 30.769 0.00 0.00 33.23 3.02
2090 2113 7.528996 ACTGGAATCATTTCAATCACAAGAA 57.471 32.000 0.00 0.00 33.23 2.52
2091 2114 8.130671 ACTGGAATCATTTCAATCACAAGAAT 57.869 30.769 0.00 0.00 33.23 2.40
2092 2115 8.591072 ACTGGAATCATTTCAATCACAAGAATT 58.409 29.630 0.00 0.00 33.23 2.17
2093 2116 8.766000 TGGAATCATTTCAATCACAAGAATTG 57.234 30.769 0.00 0.00 42.14 2.32
2094 2117 7.332430 TGGAATCATTTCAATCACAAGAATTGC 59.668 33.333 0.00 0.00 40.95 3.56
2095 2118 7.332430 GGAATCATTTCAATCACAAGAATTGCA 59.668 33.333 0.00 0.00 40.95 4.08
2106 2129 4.508461 CAAGAATTGCACACCAGAATCA 57.492 40.909 0.00 0.00 40.39 2.57
2107 2130 5.068234 CAAGAATTGCACACCAGAATCAT 57.932 39.130 0.00 0.00 40.39 2.45
2108 2131 5.475719 CAAGAATTGCACACCAGAATCATT 58.524 37.500 0.00 0.00 40.39 2.57
2109 2132 5.068234 AGAATTGCACACCAGAATCATTG 57.932 39.130 0.00 0.00 0.00 2.82
2110 2133 4.525487 AGAATTGCACACCAGAATCATTGT 59.475 37.500 0.00 0.00 0.00 2.71
2111 2134 5.711506 AGAATTGCACACCAGAATCATTGTA 59.288 36.000 0.00 0.00 0.00 2.41
2112 2135 5.981088 ATTGCACACCAGAATCATTGTAA 57.019 34.783 0.00 0.00 0.00 2.41
2113 2136 5.981088 TTGCACACCAGAATCATTGTAAT 57.019 34.783 0.00 0.00 0.00 1.89
2114 2137 5.981088 TGCACACCAGAATCATTGTAATT 57.019 34.783 0.00 0.00 0.00 1.40
2115 2138 6.343716 TGCACACCAGAATCATTGTAATTT 57.656 33.333 0.00 0.00 0.00 1.82
2116 2139 6.757237 TGCACACCAGAATCATTGTAATTTT 58.243 32.000 0.00 0.00 0.00 1.82
2117 2140 7.890515 TGCACACCAGAATCATTGTAATTTTA 58.109 30.769 0.00 0.00 0.00 1.52
2118 2141 8.530311 TGCACACCAGAATCATTGTAATTTTAT 58.470 29.630 0.00 0.00 0.00 1.40
2119 2142 9.369904 GCACACCAGAATCATTGTAATTTTATT 57.630 29.630 0.00 0.00 0.00 1.40
2237 2260 7.009179 CATACATAAGGGTATGTCCATCACT 57.991 40.000 2.74 0.00 46.01 3.41
2238 2261 5.975988 ACATAAGGGTATGTCCATCACTT 57.024 39.130 0.00 0.00 46.01 3.16
2239 2262 6.327386 ACATAAGGGTATGTCCATCACTTT 57.673 37.500 0.00 0.00 46.01 2.66
2240 2263 6.731467 ACATAAGGGTATGTCCATCACTTTT 58.269 36.000 0.00 0.00 46.01 2.27
2241 2264 7.867921 ACATAAGGGTATGTCCATCACTTTTA 58.132 34.615 0.00 0.00 46.01 1.52
2242 2265 8.502738 ACATAAGGGTATGTCCATCACTTTTAT 58.497 33.333 0.00 0.00 46.01 1.40
2243 2266 9.003658 CATAAGGGTATGTCCATCACTTTTATC 57.996 37.037 0.00 0.00 38.11 1.75
2244 2267 6.831664 AGGGTATGTCCATCACTTTTATCT 57.168 37.500 0.00 0.00 38.11 1.98
2245 2268 6.595682 AGGGTATGTCCATCACTTTTATCTG 58.404 40.000 0.00 0.00 38.11 2.90
2246 2269 5.239525 GGGTATGTCCATCACTTTTATCTGC 59.760 44.000 0.00 0.00 38.11 4.26
2247 2270 5.050091 GGTATGTCCATCACTTTTATCTGCG 60.050 44.000 0.00 0.00 35.97 5.18
2248 2271 3.937814 TGTCCATCACTTTTATCTGCGT 58.062 40.909 0.00 0.00 0.00 5.24
2249 2272 4.323417 TGTCCATCACTTTTATCTGCGTT 58.677 39.130 0.00 0.00 0.00 4.84
2250 2273 4.154015 TGTCCATCACTTTTATCTGCGTTG 59.846 41.667 0.00 0.00 0.00 4.10
2251 2274 4.154195 GTCCATCACTTTTATCTGCGTTGT 59.846 41.667 0.00 0.00 0.00 3.32
2252 2275 5.350365 GTCCATCACTTTTATCTGCGTTGTA 59.650 40.000 0.00 0.00 0.00 2.41
2253 2276 6.037172 GTCCATCACTTTTATCTGCGTTGTAT 59.963 38.462 0.00 0.00 0.00 2.29
2254 2277 6.037062 TCCATCACTTTTATCTGCGTTGTATG 59.963 38.462 0.00 0.00 0.00 2.39
2255 2278 6.037062 CCATCACTTTTATCTGCGTTGTATGA 59.963 38.462 0.00 0.00 0.00 2.15
2256 2279 7.254898 CCATCACTTTTATCTGCGTTGTATGAT 60.255 37.037 0.00 0.00 0.00 2.45
2257 2280 7.609760 TCACTTTTATCTGCGTTGTATGATT 57.390 32.000 0.00 0.00 0.00 2.57
2258 2281 7.684670 TCACTTTTATCTGCGTTGTATGATTC 58.315 34.615 0.00 0.00 0.00 2.52
2259 2282 6.907212 CACTTTTATCTGCGTTGTATGATTCC 59.093 38.462 0.00 0.00 0.00 3.01
2260 2283 6.597672 ACTTTTATCTGCGTTGTATGATTCCA 59.402 34.615 0.00 0.00 0.00 3.53
2261 2284 6.993786 TTTATCTGCGTTGTATGATTCCAA 57.006 33.333 0.00 0.00 0.00 3.53
2262 2285 6.993786 TTATCTGCGTTGTATGATTCCAAA 57.006 33.333 0.00 0.00 0.00 3.28
2263 2286 7.566760 TTATCTGCGTTGTATGATTCCAAAT 57.433 32.000 0.00 0.00 0.00 2.32
2264 2287 5.484173 TCTGCGTTGTATGATTCCAAATC 57.516 39.130 0.00 0.00 0.00 2.17
2265 2288 4.940654 TCTGCGTTGTATGATTCCAAATCA 59.059 37.500 4.94 4.94 0.00 2.57
2266 2289 5.589855 TCTGCGTTGTATGATTCCAAATCAT 59.410 36.000 16.80 16.80 41.25 2.45
2267 2290 6.765512 TCTGCGTTGTATGATTCCAAATCATA 59.234 34.615 15.13 15.13 39.30 2.15
2268 2291 7.281999 TCTGCGTTGTATGATTCCAAATCATAA 59.718 33.333 18.93 8.24 41.15 1.90
2269 2292 7.939782 TGCGTTGTATGATTCCAAATCATAAT 58.060 30.769 18.93 2.79 41.15 1.28
2270 2293 9.061435 TGCGTTGTATGATTCCAAATCATAATA 57.939 29.630 18.93 11.45 41.15 0.98
2296 2319 6.007936 TCATACCACACAAACTTAACATGC 57.992 37.500 0.00 0.00 0.00 4.06
2297 2320 3.726291 ACCACACAAACTTAACATGCC 57.274 42.857 0.00 0.00 0.00 4.40
2298 2321 3.295973 ACCACACAAACTTAACATGCCT 58.704 40.909 0.00 0.00 0.00 4.75
2299 2322 4.465886 ACCACACAAACTTAACATGCCTA 58.534 39.130 0.00 0.00 0.00 3.93
2300 2323 4.890581 ACCACACAAACTTAACATGCCTAA 59.109 37.500 0.00 0.00 0.00 2.69
2301 2324 5.538433 ACCACACAAACTTAACATGCCTAAT 59.462 36.000 0.00 0.00 0.00 1.73
2302 2325 6.717540 ACCACACAAACTTAACATGCCTAATA 59.282 34.615 0.00 0.00 0.00 0.98
2303 2326 7.094377 ACCACACAAACTTAACATGCCTAATAG 60.094 37.037 0.00 0.00 0.00 1.73
2304 2327 7.120579 CCACACAAACTTAACATGCCTAATAGA 59.879 37.037 0.00 0.00 0.00 1.98
2305 2328 8.677300 CACACAAACTTAACATGCCTAATAGAT 58.323 33.333 0.00 0.00 0.00 1.98
2306 2329 8.893727 ACACAAACTTAACATGCCTAATAGATC 58.106 33.333 0.00 0.00 0.00 2.75
2307 2330 8.892723 CACAAACTTAACATGCCTAATAGATCA 58.107 33.333 0.00 0.00 0.00 2.92
2308 2331 9.113838 ACAAACTTAACATGCCTAATAGATCAG 57.886 33.333 0.00 0.00 0.00 2.90
2309 2332 9.113838 CAAACTTAACATGCCTAATAGATCAGT 57.886 33.333 0.00 0.00 0.00 3.41
2310 2333 9.686683 AAACTTAACATGCCTAATAGATCAGTT 57.313 29.630 0.00 0.00 0.00 3.16
2315 2338 8.854614 AACATGCCTAATAGATCAGTTATTCC 57.145 34.615 0.00 0.00 0.00 3.01
2316 2339 7.977818 ACATGCCTAATAGATCAGTTATTCCA 58.022 34.615 0.00 0.00 0.00 3.53
2317 2340 8.439971 ACATGCCTAATAGATCAGTTATTCCAA 58.560 33.333 0.00 0.00 0.00 3.53
2318 2341 8.944029 CATGCCTAATAGATCAGTTATTCCAAG 58.056 37.037 0.00 0.00 0.00 3.61
2319 2342 8.034313 TGCCTAATAGATCAGTTATTCCAAGT 57.966 34.615 0.00 0.00 0.00 3.16
2320 2343 9.154632 TGCCTAATAGATCAGTTATTCCAAGTA 57.845 33.333 0.00 0.00 0.00 2.24
2321 2344 9.998106 GCCTAATAGATCAGTTATTCCAAGTAA 57.002 33.333 0.00 0.00 0.00 2.24
2327 2350 8.910351 AGATCAGTTATTCCAAGTAAATAGGC 57.090 34.615 0.00 0.00 0.00 3.93
2328 2351 8.494433 AGATCAGTTATTCCAAGTAAATAGGCA 58.506 33.333 0.00 0.00 0.00 4.75
2329 2352 9.120538 GATCAGTTATTCCAAGTAAATAGGCAA 57.879 33.333 0.00 0.00 0.00 4.52
2330 2353 8.506168 TCAGTTATTCCAAGTAAATAGGCAAG 57.494 34.615 0.00 0.00 0.00 4.01
2331 2354 7.067008 TCAGTTATTCCAAGTAAATAGGCAAGC 59.933 37.037 0.00 0.00 0.00 4.01
2332 2355 7.067494 CAGTTATTCCAAGTAAATAGGCAAGCT 59.933 37.037 0.00 0.00 0.00 3.74
2333 2356 8.272173 AGTTATTCCAAGTAAATAGGCAAGCTA 58.728 33.333 0.00 0.00 0.00 3.32
2334 2357 8.560374 GTTATTCCAAGTAAATAGGCAAGCTAG 58.440 37.037 0.00 0.00 0.00 3.42
2335 2358 5.950544 TCCAAGTAAATAGGCAAGCTAGA 57.049 39.130 0.00 0.00 0.00 2.43
2336 2359 6.308015 TCCAAGTAAATAGGCAAGCTAGAA 57.692 37.500 0.00 0.00 0.00 2.10
2337 2360 6.900194 TCCAAGTAAATAGGCAAGCTAGAAT 58.100 36.000 0.00 0.00 0.00 2.40
2338 2361 6.992715 TCCAAGTAAATAGGCAAGCTAGAATC 59.007 38.462 0.00 0.00 0.00 2.52
2339 2362 6.767902 CCAAGTAAATAGGCAAGCTAGAATCA 59.232 38.462 0.00 0.00 0.00 2.57
2340 2363 7.254932 CCAAGTAAATAGGCAAGCTAGAATCAC 60.255 40.741 0.00 0.00 0.00 3.06
2341 2364 6.889198 AGTAAATAGGCAAGCTAGAATCACA 58.111 36.000 0.00 0.00 0.00 3.58
2342 2365 6.763610 AGTAAATAGGCAAGCTAGAATCACAC 59.236 38.462 0.00 0.00 0.00 3.82
2343 2366 4.760530 ATAGGCAAGCTAGAATCACACA 57.239 40.909 0.00 0.00 0.00 3.72
2344 2367 3.641434 AGGCAAGCTAGAATCACACAT 57.359 42.857 0.00 0.00 0.00 3.21
2345 2368 4.760530 AGGCAAGCTAGAATCACACATA 57.239 40.909 0.00 0.00 0.00 2.29
2346 2369 5.301835 AGGCAAGCTAGAATCACACATAT 57.698 39.130 0.00 0.00 0.00 1.78
2347 2370 5.061853 AGGCAAGCTAGAATCACACATATG 58.938 41.667 0.00 0.00 0.00 1.78
2348 2371 4.818546 GGCAAGCTAGAATCACACATATGT 59.181 41.667 1.41 1.41 40.80 2.29
2349 2372 5.991606 GGCAAGCTAGAATCACACATATGTA 59.008 40.000 8.32 0.00 36.72 2.29
2350 2373 6.146837 GGCAAGCTAGAATCACACATATGTAG 59.853 42.308 8.32 4.60 36.72 2.74
2351 2374 6.347240 GCAAGCTAGAATCACACATATGTAGC 60.347 42.308 8.32 11.11 36.72 3.58
2352 2375 6.410942 AGCTAGAATCACACATATGTAGCA 57.589 37.500 19.74 4.52 36.02 3.49
2353 2376 6.820335 AGCTAGAATCACACATATGTAGCAA 58.180 36.000 19.74 4.41 36.02 3.91
2354 2377 6.703607 AGCTAGAATCACACATATGTAGCAAC 59.296 38.462 19.74 7.52 36.02 4.17
2355 2378 6.479990 GCTAGAATCACACATATGTAGCAACA 59.520 38.462 8.32 0.00 36.72 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
493 496 5.613329 AGACCGAAACTACGATCTCTCTAT 58.387 41.667 0.00 0.00 29.34 1.98
562 565 1.207329 CTTCGGGAGGACCTTCGAAAT 59.793 52.381 24.14 0.00 38.57 2.17
926 930 1.486726 GATGGATCGGTGGAAGAAGGT 59.513 52.381 0.00 0.00 0.00 3.50
949 953 0.809385 GTGCGTCAGTACCTGCTCTA 59.191 55.000 0.00 0.00 0.00 2.43
1017 1021 4.681978 GACGAGCGCAGGGTGGTT 62.682 66.667 11.47 0.00 32.53 3.67
1383 1390 1.971357 GACTGGAGGAGACTTTGGTCA 59.029 52.381 0.00 0.00 44.43 4.02
1393 1400 0.563173 TAGGATGGGGACTGGAGGAG 59.437 60.000 0.00 0.00 0.00 3.69
1400 1407 1.062488 GGTGGCATAGGATGGGGACT 61.062 60.000 0.00 0.00 0.00 3.85
1467 1474 3.582998 CCCCATGGCTCTTTCATCTTA 57.417 47.619 6.09 0.00 0.00 2.10
1948 1971 9.675464 ATGCATGGATCTTTTGTTATTGAATTT 57.325 25.926 0.00 0.00 0.00 1.82
1949 1972 9.104965 CATGCATGGATCTTTTGTTATTGAATT 57.895 29.630 19.40 0.00 0.00 2.17
1950 1973 8.479689 TCATGCATGGATCTTTTGTTATTGAAT 58.520 29.630 25.97 0.00 0.00 2.57
1951 1974 7.838884 TCATGCATGGATCTTTTGTTATTGAA 58.161 30.769 25.97 0.00 0.00 2.69
1952 1975 7.407393 TCATGCATGGATCTTTTGTTATTGA 57.593 32.000 25.97 0.00 0.00 2.57
1953 1976 8.657074 AATCATGCATGGATCTTTTGTTATTG 57.343 30.769 25.97 0.00 0.00 1.90
1954 1977 9.976511 CTAATCATGCATGGATCTTTTGTTATT 57.023 29.630 25.97 15.04 0.00 1.40
1955 1978 9.358406 TCTAATCATGCATGGATCTTTTGTTAT 57.642 29.630 25.97 5.13 0.00 1.89
1956 1979 8.750515 TCTAATCATGCATGGATCTTTTGTTA 57.249 30.769 25.97 2.76 0.00 2.41
1957 1980 7.201884 CCTCTAATCATGCATGGATCTTTTGTT 60.202 37.037 25.97 9.68 0.00 2.83
1958 1981 6.264744 CCTCTAATCATGCATGGATCTTTTGT 59.735 38.462 25.97 5.64 0.00 2.83
1959 1982 6.294564 CCCTCTAATCATGCATGGATCTTTTG 60.295 42.308 25.97 12.55 0.00 2.44
1960 1983 5.773680 CCCTCTAATCATGCATGGATCTTTT 59.226 40.000 25.97 12.36 0.00 2.27
1961 1984 5.074102 TCCCTCTAATCATGCATGGATCTTT 59.926 40.000 25.97 13.89 0.00 2.52
1962 1985 4.600547 TCCCTCTAATCATGCATGGATCTT 59.399 41.667 25.97 15.91 0.00 2.40
1963 1986 4.173594 TCCCTCTAATCATGCATGGATCT 58.826 43.478 25.97 10.74 0.00 2.75
1964 1987 4.564782 TCCCTCTAATCATGCATGGATC 57.435 45.455 25.97 0.00 0.00 3.36
1965 1988 4.263816 CCTTCCCTCTAATCATGCATGGAT 60.264 45.833 25.97 16.96 0.00 3.41
1966 1989 3.073503 CCTTCCCTCTAATCATGCATGGA 59.926 47.826 25.97 14.12 0.00 3.41
1967 1990 3.181436 ACCTTCCCTCTAATCATGCATGG 60.181 47.826 25.97 10.42 0.00 3.66
1968 1991 4.096190 ACCTTCCCTCTAATCATGCATG 57.904 45.455 21.07 21.07 0.00 4.06
1969 1992 5.370880 ACTTACCTTCCCTCTAATCATGCAT 59.629 40.000 0.00 0.00 0.00 3.96
1970 1993 4.721776 ACTTACCTTCCCTCTAATCATGCA 59.278 41.667 0.00 0.00 0.00 3.96
1971 1994 5.297569 ACTTACCTTCCCTCTAATCATGC 57.702 43.478 0.00 0.00 0.00 4.06
1972 1995 8.024145 AGTAACTTACCTTCCCTCTAATCATG 57.976 38.462 0.00 0.00 0.00 3.07
1973 1996 9.725206 TTAGTAACTTACCTTCCCTCTAATCAT 57.275 33.333 0.00 0.00 0.00 2.45
1974 1997 9.725206 ATTAGTAACTTACCTTCCCTCTAATCA 57.275 33.333 0.00 0.00 0.00 2.57
1977 2000 9.995594 TGTATTAGTAACTTACCTTCCCTCTAA 57.004 33.333 0.00 0.00 0.00 2.10
1978 2001 9.413734 GTGTATTAGTAACTTACCTTCCCTCTA 57.586 37.037 0.00 0.00 0.00 2.43
1979 2002 8.121185 AGTGTATTAGTAACTTACCTTCCCTCT 58.879 37.037 0.00 0.00 0.00 3.69
1980 2003 8.303780 AGTGTATTAGTAACTTACCTTCCCTC 57.696 38.462 0.00 0.00 0.00 4.30
1981 2004 8.676397 AAGTGTATTAGTAACTTACCTTCCCT 57.324 34.615 0.00 0.00 32.48 4.20
1982 2005 9.376075 GAAAGTGTATTAGTAACTTACCTTCCC 57.624 37.037 0.00 0.00 33.09 3.97
1983 2006 9.933723 TGAAAGTGTATTAGTAACTTACCTTCC 57.066 33.333 0.00 0.00 33.09 3.46
1998 2021 8.612619 CGAAGCTTACCATTATGAAAGTGTATT 58.387 33.333 0.00 0.00 0.00 1.89
1999 2022 7.226720 CCGAAGCTTACCATTATGAAAGTGTAT 59.773 37.037 0.00 0.00 0.00 2.29
2000 2023 6.537301 CCGAAGCTTACCATTATGAAAGTGTA 59.463 38.462 0.00 0.00 0.00 2.90
2001 2024 5.354234 CCGAAGCTTACCATTATGAAAGTGT 59.646 40.000 0.00 0.00 0.00 3.55
2002 2025 5.354234 ACCGAAGCTTACCATTATGAAAGTG 59.646 40.000 0.00 0.00 0.00 3.16
2003 2026 5.354234 CACCGAAGCTTACCATTATGAAAGT 59.646 40.000 0.00 0.00 0.00 2.66
2004 2027 5.354234 ACACCGAAGCTTACCATTATGAAAG 59.646 40.000 0.00 0.00 0.00 2.62
2005 2028 5.250200 ACACCGAAGCTTACCATTATGAAA 58.750 37.500 0.00 0.00 0.00 2.69
2006 2029 4.839121 ACACCGAAGCTTACCATTATGAA 58.161 39.130 0.00 0.00 0.00 2.57
2007 2030 4.161565 AGACACCGAAGCTTACCATTATGA 59.838 41.667 0.00 0.00 0.00 2.15
2008 2031 4.442706 AGACACCGAAGCTTACCATTATG 58.557 43.478 0.00 0.00 0.00 1.90
2009 2032 4.755266 AGACACCGAAGCTTACCATTAT 57.245 40.909 0.00 0.00 0.00 1.28
2010 2033 5.361571 TCATAGACACCGAAGCTTACCATTA 59.638 40.000 0.00 0.00 0.00 1.90
2011 2034 4.161565 TCATAGACACCGAAGCTTACCATT 59.838 41.667 0.00 0.00 0.00 3.16
2012 2035 3.704566 TCATAGACACCGAAGCTTACCAT 59.295 43.478 0.00 0.00 0.00 3.55
2013 2036 3.093814 TCATAGACACCGAAGCTTACCA 58.906 45.455 0.00 0.00 0.00 3.25
2014 2037 3.130693 AGTCATAGACACCGAAGCTTACC 59.869 47.826 0.00 0.00 34.60 2.85
2015 2038 4.373348 AGTCATAGACACCGAAGCTTAC 57.627 45.455 0.00 0.00 34.60 2.34
2016 2039 6.071784 TGTTAAGTCATAGACACCGAAGCTTA 60.072 38.462 0.00 0.00 34.60 3.09
2017 2040 3.963428 AAGTCATAGACACCGAAGCTT 57.037 42.857 0.00 0.00 34.60 3.74
2018 2041 4.219944 TGTTAAGTCATAGACACCGAAGCT 59.780 41.667 0.00 0.00 34.60 3.74
2019 2042 4.491676 TGTTAAGTCATAGACACCGAAGC 58.508 43.478 0.00 0.00 34.60 3.86
2020 2043 5.950883 TCTGTTAAGTCATAGACACCGAAG 58.049 41.667 0.00 0.00 34.60 3.79
2021 2044 5.970317 TCTGTTAAGTCATAGACACCGAA 57.030 39.130 0.00 0.00 34.60 4.30
2022 2045 5.708697 TCTTCTGTTAAGTCATAGACACCGA 59.291 40.000 0.00 0.00 34.60 4.69
2023 2046 5.950883 TCTTCTGTTAAGTCATAGACACCG 58.049 41.667 0.00 0.00 34.60 4.94
2024 2047 8.779354 AAATCTTCTGTTAAGTCATAGACACC 57.221 34.615 0.00 0.00 34.60 4.16
2031 2054 9.846248 GCATGTAAAAATCTTCTGTTAAGTCAT 57.154 29.630 0.00 0.00 0.00 3.06
2032 2055 8.845227 TGCATGTAAAAATCTTCTGTTAAGTCA 58.155 29.630 0.00 0.00 0.00 3.41
2033 2056 9.118236 GTGCATGTAAAAATCTTCTGTTAAGTC 57.882 33.333 0.00 0.00 0.00 3.01
2034 2057 7.803189 CGTGCATGTAAAAATCTTCTGTTAAGT 59.197 33.333 0.00 0.00 0.00 2.24
2035 2058 7.803189 ACGTGCATGTAAAAATCTTCTGTTAAG 59.197 33.333 10.57 0.00 0.00 1.85
2036 2059 7.644490 ACGTGCATGTAAAAATCTTCTGTTAA 58.356 30.769 10.57 0.00 0.00 2.01
2037 2060 7.197071 ACGTGCATGTAAAAATCTTCTGTTA 57.803 32.000 10.57 0.00 0.00 2.41
2038 2061 6.072112 ACGTGCATGTAAAAATCTTCTGTT 57.928 33.333 10.57 0.00 0.00 3.16
2039 2062 5.689383 ACGTGCATGTAAAAATCTTCTGT 57.311 34.783 10.57 0.00 0.00 3.41
2040 2063 8.673626 AATTACGTGCATGTAAAAATCTTCTG 57.326 30.769 29.86 0.00 37.81 3.02
2041 2064 9.769093 GTAATTACGTGCATGTAAAAATCTTCT 57.231 29.630 29.86 12.34 37.81 2.85
2042 2065 9.769093 AGTAATTACGTGCATGTAAAAATCTTC 57.231 29.630 29.86 17.27 37.81 2.87
2043 2066 9.554724 CAGTAATTACGTGCATGTAAAAATCTT 57.445 29.630 29.86 21.89 37.81 2.40
2044 2067 8.181573 CCAGTAATTACGTGCATGTAAAAATCT 58.818 33.333 29.86 21.91 37.81 2.40
2045 2068 8.178964 TCCAGTAATTACGTGCATGTAAAAATC 58.821 33.333 29.86 20.49 37.81 2.17
2046 2069 8.046294 TCCAGTAATTACGTGCATGTAAAAAT 57.954 30.769 29.86 21.65 37.81 1.82
2047 2070 7.436430 TCCAGTAATTACGTGCATGTAAAAA 57.564 32.000 29.86 19.75 37.81 1.94
2048 2071 7.436430 TTCCAGTAATTACGTGCATGTAAAA 57.564 32.000 29.86 20.05 37.81 1.52
2049 2072 7.334671 TGATTCCAGTAATTACGTGCATGTAAA 59.665 33.333 29.86 15.60 37.81 2.01
2050 2073 6.819146 TGATTCCAGTAATTACGTGCATGTAA 59.181 34.615 28.71 28.71 38.58 2.41
2051 2074 6.342111 TGATTCCAGTAATTACGTGCATGTA 58.658 36.000 14.85 14.85 0.00 2.29
2052 2075 5.182487 TGATTCCAGTAATTACGTGCATGT 58.818 37.500 17.19 17.19 0.00 3.21
2053 2076 5.733226 TGATTCCAGTAATTACGTGCATG 57.267 39.130 9.91 3.82 0.00 4.06
2054 2077 6.942532 AATGATTCCAGTAATTACGTGCAT 57.057 33.333 9.91 6.75 0.00 3.96
2055 2078 6.372937 TGAAATGATTCCAGTAATTACGTGCA 59.627 34.615 9.91 4.91 34.49 4.57
2056 2079 6.781138 TGAAATGATTCCAGTAATTACGTGC 58.219 36.000 9.91 0.00 34.49 5.34
2057 2080 9.438291 GATTGAAATGATTCCAGTAATTACGTG 57.562 33.333 9.91 8.58 34.49 4.49
2058 2081 9.173021 TGATTGAAATGATTCCAGTAATTACGT 57.827 29.630 9.91 0.00 34.49 3.57
2059 2082 9.438291 GTGATTGAAATGATTCCAGTAATTACG 57.562 33.333 9.91 5.41 34.49 3.18
2062 2085 9.865321 CTTGTGATTGAAATGATTCCAGTAATT 57.135 29.630 0.00 0.00 34.49 1.40
2063 2086 9.246670 TCTTGTGATTGAAATGATTCCAGTAAT 57.753 29.630 0.00 0.00 34.49 1.89
2064 2087 8.634335 TCTTGTGATTGAAATGATTCCAGTAA 57.366 30.769 0.00 0.00 34.49 2.24
2065 2088 8.634335 TTCTTGTGATTGAAATGATTCCAGTA 57.366 30.769 0.00 0.00 34.49 2.74
2066 2089 7.528996 TTCTTGTGATTGAAATGATTCCAGT 57.471 32.000 0.00 0.00 34.49 4.00
2067 2090 8.869897 CAATTCTTGTGATTGAAATGATTCCAG 58.130 33.333 0.00 0.00 34.49 3.86
2068 2091 7.332430 GCAATTCTTGTGATTGAAATGATTCCA 59.668 33.333 1.32 0.00 34.49 3.53
2069 2092 7.332430 TGCAATTCTTGTGATTGAAATGATTCC 59.668 33.333 1.32 0.00 34.49 3.01
2070 2093 8.166706 GTGCAATTCTTGTGATTGAAATGATTC 58.833 33.333 0.00 0.00 36.04 2.52
2071 2094 7.658167 TGTGCAATTCTTGTGATTGAAATGATT 59.342 29.630 0.00 0.00 0.00 2.57
2072 2095 7.117236 GTGTGCAATTCTTGTGATTGAAATGAT 59.883 33.333 0.00 0.00 0.00 2.45
2073 2096 6.421501 GTGTGCAATTCTTGTGATTGAAATGA 59.578 34.615 0.00 0.00 0.00 2.57
2074 2097 6.347079 GGTGTGCAATTCTTGTGATTGAAATG 60.347 38.462 0.00 0.00 0.00 2.32
2075 2098 5.697633 GGTGTGCAATTCTTGTGATTGAAAT 59.302 36.000 0.00 0.00 0.00 2.17
2076 2099 5.049167 GGTGTGCAATTCTTGTGATTGAAA 58.951 37.500 0.00 0.00 0.00 2.69
2077 2100 4.099113 TGGTGTGCAATTCTTGTGATTGAA 59.901 37.500 0.00 0.00 0.00 2.69
2078 2101 3.635836 TGGTGTGCAATTCTTGTGATTGA 59.364 39.130 0.00 0.00 0.00 2.57
2079 2102 3.979948 TGGTGTGCAATTCTTGTGATTG 58.020 40.909 0.00 0.00 0.00 2.67
2080 2103 3.890756 TCTGGTGTGCAATTCTTGTGATT 59.109 39.130 0.00 0.00 0.00 2.57
2081 2104 3.489355 TCTGGTGTGCAATTCTTGTGAT 58.511 40.909 0.00 0.00 0.00 3.06
2082 2105 2.929641 TCTGGTGTGCAATTCTTGTGA 58.070 42.857 0.00 0.00 0.00 3.58
2083 2106 3.713858 TTCTGGTGTGCAATTCTTGTG 57.286 42.857 0.00 0.00 0.00 3.33
2084 2107 3.890756 TGATTCTGGTGTGCAATTCTTGT 59.109 39.130 0.00 0.00 0.00 3.16
2085 2108 4.508461 TGATTCTGGTGTGCAATTCTTG 57.492 40.909 0.00 0.00 0.00 3.02
2086 2109 5.011329 ACAATGATTCTGGTGTGCAATTCTT 59.989 36.000 0.00 0.00 0.00 2.52
2087 2110 4.525487 ACAATGATTCTGGTGTGCAATTCT 59.475 37.500 0.00 0.00 0.00 2.40
2088 2111 4.813027 ACAATGATTCTGGTGTGCAATTC 58.187 39.130 0.00 0.00 0.00 2.17
2089 2112 4.877378 ACAATGATTCTGGTGTGCAATT 57.123 36.364 0.00 0.00 0.00 2.32
2090 2113 5.981088 TTACAATGATTCTGGTGTGCAAT 57.019 34.783 0.00 0.00 0.00 3.56
2091 2114 5.981088 ATTACAATGATTCTGGTGTGCAA 57.019 34.783 0.00 0.00 0.00 4.08
2092 2115 5.981088 AATTACAATGATTCTGGTGTGCA 57.019 34.783 0.00 0.00 0.00 4.57
2093 2116 8.931385 ATAAAATTACAATGATTCTGGTGTGC 57.069 30.769 0.00 0.00 0.00 4.57
2213 2236 7.009179 AGTGATGGACATACCCTTATGTATG 57.991 40.000 9.08 9.08 47.00 2.39
2214 2237 7.633018 AAGTGATGGACATACCCTTATGTAT 57.367 36.000 0.00 0.00 47.00 2.29
2215 2238 7.446106 AAAGTGATGGACATACCCTTATGTA 57.554 36.000 0.00 0.00 47.00 2.29
2217 2240 8.924511 ATAAAAGTGATGGACATACCCTTATG 57.075 34.615 0.00 0.00 41.01 1.90
2218 2241 8.949421 AGATAAAAGTGATGGACATACCCTTAT 58.051 33.333 0.00 0.00 38.00 1.73
2219 2242 8.210946 CAGATAAAAGTGATGGACATACCCTTA 58.789 37.037 0.00 0.00 38.00 2.69
2220 2243 7.056635 CAGATAAAAGTGATGGACATACCCTT 58.943 38.462 0.00 0.00 38.00 3.95
2221 2244 6.595682 CAGATAAAAGTGATGGACATACCCT 58.404 40.000 0.00 0.00 38.00 4.34
2222 2245 5.239525 GCAGATAAAAGTGATGGACATACCC 59.760 44.000 0.00 0.00 38.00 3.69
2223 2246 5.050091 CGCAGATAAAAGTGATGGACATACC 60.050 44.000 0.00 0.00 39.54 2.73
2224 2247 5.523916 ACGCAGATAAAAGTGATGGACATAC 59.476 40.000 0.00 0.00 0.00 2.39
2225 2248 5.670485 ACGCAGATAAAAGTGATGGACATA 58.330 37.500 0.00 0.00 0.00 2.29
2226 2249 4.517285 ACGCAGATAAAAGTGATGGACAT 58.483 39.130 0.00 0.00 0.00 3.06
2227 2250 3.937814 ACGCAGATAAAAGTGATGGACA 58.062 40.909 0.00 0.00 0.00 4.02
2228 2251 4.154195 ACAACGCAGATAAAAGTGATGGAC 59.846 41.667 0.00 0.00 0.00 4.02
2229 2252 4.323417 ACAACGCAGATAAAAGTGATGGA 58.677 39.130 0.00 0.00 0.00 3.41
2230 2253 4.685169 ACAACGCAGATAAAAGTGATGG 57.315 40.909 0.00 0.00 0.00 3.51
2231 2254 7.003939 TCATACAACGCAGATAAAAGTGATG 57.996 36.000 0.00 0.00 0.00 3.07
2232 2255 7.792374 ATCATACAACGCAGATAAAAGTGAT 57.208 32.000 0.00 0.00 0.00 3.06
2233 2256 7.201609 GGAATCATACAACGCAGATAAAAGTGA 60.202 37.037 0.00 0.00 0.00 3.41
2234 2257 6.907212 GGAATCATACAACGCAGATAAAAGTG 59.093 38.462 0.00 0.00 0.00 3.16
2235 2258 6.597672 TGGAATCATACAACGCAGATAAAAGT 59.402 34.615 0.00 0.00 0.00 2.66
2236 2259 7.015226 TGGAATCATACAACGCAGATAAAAG 57.985 36.000 0.00 0.00 0.00 2.27
2237 2260 6.993786 TGGAATCATACAACGCAGATAAAA 57.006 33.333 0.00 0.00 0.00 1.52
2238 2261 6.993786 TTGGAATCATACAACGCAGATAAA 57.006 33.333 0.00 0.00 0.00 1.40
2239 2262 6.993786 TTTGGAATCATACAACGCAGATAA 57.006 33.333 0.00 0.00 0.00 1.75
2240 2263 6.765512 TGATTTGGAATCATACAACGCAGATA 59.234 34.615 0.00 0.00 0.00 1.98
2241 2264 5.589855 TGATTTGGAATCATACAACGCAGAT 59.410 36.000 0.00 0.00 0.00 2.90
2242 2265 4.940654 TGATTTGGAATCATACAACGCAGA 59.059 37.500 0.00 0.00 0.00 4.26
2243 2266 5.233957 TGATTTGGAATCATACAACGCAG 57.766 39.130 0.00 0.00 0.00 5.18
2244 2267 5.833406 ATGATTTGGAATCATACAACGCA 57.167 34.783 13.00 0.00 37.03 5.24
2270 2293 7.598493 GCATGTTAAGTTTGTGTGGTATGAAAT 59.402 33.333 0.00 0.00 0.00 2.17
2271 2294 6.920758 GCATGTTAAGTTTGTGTGGTATGAAA 59.079 34.615 0.00 0.00 0.00 2.69
2272 2295 6.442952 GCATGTTAAGTTTGTGTGGTATGAA 58.557 36.000 0.00 0.00 0.00 2.57
2273 2296 5.048364 GGCATGTTAAGTTTGTGTGGTATGA 60.048 40.000 0.00 0.00 0.00 2.15
2274 2297 5.048083 AGGCATGTTAAGTTTGTGTGGTATG 60.048 40.000 0.00 0.00 0.00 2.39
2275 2298 5.076873 AGGCATGTTAAGTTTGTGTGGTAT 58.923 37.500 0.00 0.00 0.00 2.73
2276 2299 4.465886 AGGCATGTTAAGTTTGTGTGGTA 58.534 39.130 0.00 0.00 0.00 3.25
2277 2300 3.295973 AGGCATGTTAAGTTTGTGTGGT 58.704 40.909 0.00 0.00 0.00 4.16
2278 2301 5.446143 TTAGGCATGTTAAGTTTGTGTGG 57.554 39.130 0.00 0.00 0.00 4.17
2279 2302 8.039603 TCTATTAGGCATGTTAAGTTTGTGTG 57.960 34.615 0.00 0.00 0.00 3.82
2280 2303 8.807948 ATCTATTAGGCATGTTAAGTTTGTGT 57.192 30.769 0.00 0.00 0.00 3.72
2281 2304 8.892723 TGATCTATTAGGCATGTTAAGTTTGTG 58.107 33.333 0.00 0.00 0.00 3.33
2282 2305 9.113838 CTGATCTATTAGGCATGTTAAGTTTGT 57.886 33.333 0.00 0.00 0.00 2.83
2283 2306 9.113838 ACTGATCTATTAGGCATGTTAAGTTTG 57.886 33.333 0.00 0.00 0.00 2.93
2284 2307 9.686683 AACTGATCTATTAGGCATGTTAAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
2289 2312 9.944376 GGAATAACTGATCTATTAGGCATGTTA 57.056 33.333 0.00 0.00 0.00 2.41
2290 2313 8.439971 TGGAATAACTGATCTATTAGGCATGTT 58.560 33.333 0.00 0.00 0.00 2.71
2291 2314 7.977818 TGGAATAACTGATCTATTAGGCATGT 58.022 34.615 0.00 0.00 0.00 3.21
2292 2315 8.853077 TTGGAATAACTGATCTATTAGGCATG 57.147 34.615 0.00 0.00 0.00 4.06
2293 2316 8.664079 ACTTGGAATAACTGATCTATTAGGCAT 58.336 33.333 0.00 0.00 0.00 4.40
2294 2317 8.034313 ACTTGGAATAACTGATCTATTAGGCA 57.966 34.615 0.00 0.00 0.00 4.75
2295 2318 9.998106 TTACTTGGAATAACTGATCTATTAGGC 57.002 33.333 0.00 0.00 0.00 3.93
2301 2324 9.998106 GCCTATTTACTTGGAATAACTGATCTA 57.002 33.333 0.00 0.00 0.00 1.98
2302 2325 8.494433 TGCCTATTTACTTGGAATAACTGATCT 58.506 33.333 0.00 0.00 0.00 2.75
2303 2326 8.677148 TGCCTATTTACTTGGAATAACTGATC 57.323 34.615 0.00 0.00 0.00 2.92
2304 2327 9.125026 CTTGCCTATTTACTTGGAATAACTGAT 57.875 33.333 0.00 0.00 0.00 2.90
2305 2328 7.067008 GCTTGCCTATTTACTTGGAATAACTGA 59.933 37.037 0.00 0.00 0.00 3.41
2306 2329 7.067494 AGCTTGCCTATTTACTTGGAATAACTG 59.933 37.037 0.00 0.00 0.00 3.16
2307 2330 7.119387 AGCTTGCCTATTTACTTGGAATAACT 58.881 34.615 0.00 0.00 0.00 2.24
2308 2331 7.334844 AGCTTGCCTATTTACTTGGAATAAC 57.665 36.000 0.00 0.00 0.00 1.89
2309 2332 8.491134 TCTAGCTTGCCTATTTACTTGGAATAA 58.509 33.333 0.00 0.00 0.00 1.40
2310 2333 8.029782 TCTAGCTTGCCTATTTACTTGGAATA 57.970 34.615 0.00 0.00 0.00 1.75
2311 2334 6.900194 TCTAGCTTGCCTATTTACTTGGAAT 58.100 36.000 0.00 0.00 0.00 3.01
2312 2335 6.308015 TCTAGCTTGCCTATTTACTTGGAA 57.692 37.500 0.00 0.00 0.00 3.53
2313 2336 5.950544 TCTAGCTTGCCTATTTACTTGGA 57.049 39.130 0.00 0.00 0.00 3.53
2314 2337 6.767902 TGATTCTAGCTTGCCTATTTACTTGG 59.232 38.462 0.00 0.00 0.00 3.61
2315 2338 7.280876 TGTGATTCTAGCTTGCCTATTTACTTG 59.719 37.037 0.00 0.00 0.00 3.16
2316 2339 7.281100 GTGTGATTCTAGCTTGCCTATTTACTT 59.719 37.037 0.00 0.00 0.00 2.24
2317 2340 6.763610 GTGTGATTCTAGCTTGCCTATTTACT 59.236 38.462 0.00 0.00 0.00 2.24
2318 2341 6.538742 TGTGTGATTCTAGCTTGCCTATTTAC 59.461 38.462 0.00 0.00 0.00 2.01
2319 2342 6.649155 TGTGTGATTCTAGCTTGCCTATTTA 58.351 36.000 0.00 0.00 0.00 1.40
2320 2343 5.500234 TGTGTGATTCTAGCTTGCCTATTT 58.500 37.500 0.00 0.00 0.00 1.40
2321 2344 5.102953 TGTGTGATTCTAGCTTGCCTATT 57.897 39.130 0.00 0.00 0.00 1.73
2322 2345 4.760530 TGTGTGATTCTAGCTTGCCTAT 57.239 40.909 0.00 0.00 0.00 2.57
2323 2346 4.760530 ATGTGTGATTCTAGCTTGCCTA 57.239 40.909 0.00 0.00 0.00 3.93
2324 2347 3.641434 ATGTGTGATTCTAGCTTGCCT 57.359 42.857 0.00 0.00 0.00 4.75
2325 2348 4.818546 ACATATGTGTGATTCTAGCTTGCC 59.181 41.667 7.78 0.00 37.14 4.52
2326 2349 5.998454 ACATATGTGTGATTCTAGCTTGC 57.002 39.130 7.78 0.00 37.14 4.01
2327 2350 6.703165 TGCTACATATGTGTGATTCTAGCTTG 59.297 38.462 18.81 0.00 39.39 4.01
2328 2351 6.820335 TGCTACATATGTGTGATTCTAGCTT 58.180 36.000 18.81 0.00 39.39 3.74
2329 2352 6.410942 TGCTACATATGTGTGATTCTAGCT 57.589 37.500 18.81 0.00 39.39 3.32
2330 2353 6.479990 TGTTGCTACATATGTGTGATTCTAGC 59.520 38.462 18.81 15.79 39.39 3.42
2331 2354 8.599055 ATGTTGCTACATATGTGTGATTCTAG 57.401 34.615 18.81 6.15 43.12 2.43


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

AutoCloner maintained by Alex Coulton.