Multiple sequence alignment - TraesCS6D01G239300

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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 TraesCS6D01G239300 chr6D 100.000 2342 0 0 1 2342 340195913 340198254 0.000000e+00 4325
1 TraesCS6D01G239300 chr6B 95.917 1200 27 6 745 1923 480787366 480786168 0.000000e+00 1925
2 TraesCS6D01G239300 chr6B 92.095 759 42 9 4 747 626809931 626809176 0.000000e+00 1053
3 TraesCS6D01G239300 chr3D 93.617 752 39 4 1 743 97120518 97119767 0.000000e+00 1114
4 TraesCS6D01G239300 chr4A 93.103 754 40 5 1 744 704518678 704519429 0.000000e+00 1094
5 TraesCS6D01G239300 chr4A 97.115 416 10 2 1928 2342 642948712 642948298 0.000000e+00 701
6 TraesCS6D01G239300 chr2D 92.895 760 42 6 4 751 534727798 534727039 0.000000e+00 1094
7 TraesCS6D01G239300 chr2D 92.157 765 41 10 1 747 285349324 285350087 0.000000e+00 1062
8 TraesCS6D01G239300 chr2D 92.740 730 42 6 1 723 531683099 531682374 0.000000e+00 1044
9 TraesCS6D01G239300 chr1D 92.026 765 47 10 1 754 444890504 444891265 0.000000e+00 1062
10 TraesCS6D01G239300 chr1D 96.394 416 13 2 1928 2342 109569741 109569327 0.000000e+00 684
11 TraesCS6D01G239300 chr1D 96.154 416 15 1 1928 2342 449151257 449151672 0.000000e+00 678
12 TraesCS6D01G239300 chr7D 92.896 732 40 6 21 743 163364819 163364091 0.000000e+00 1053
13 TraesCS6D01G239300 chr3B 92.204 744 40 8 21 746 521658653 521657910 0.000000e+00 1037
14 TraesCS6D01G239300 chr3B 96.394 416 14 1 1928 2342 463125507 463125922 0.000000e+00 684
15 TraesCS6D01G239300 chr6A 88.854 646 16 3 756 1368 480197404 480198026 0.000000e+00 743
16 TraesCS6D01G239300 chr6A 89.688 417 21 10 1440 1846 480198029 480198433 1.610000e-141 512
17 TraesCS6D01G239300 chr5D 96.394 416 13 2 1928 2342 50996985 50996571 0.000000e+00 684
18 TraesCS6D01G239300 chr5B 96.394 416 14 1 1928 2342 113685279 113684864 0.000000e+00 684
19 TraesCS6D01G239300 chr2B 96.394 416 14 1 1928 2342 464183116 464183531 0.000000e+00 684
20 TraesCS6D01G239300 chr2B 96.394 416 13 2 1928 2342 763497135 763496721 0.000000e+00 684
21 TraesCS6D01G239300 chr1A 96.154 416 15 1 1928 2342 17266863 17267278 0.000000e+00 678


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 TraesCS6D01G239300 chr6D 340195913 340198254 2341 False 4325.0 4325 100.000 1 2342 1 chr6D.!!$F1 2341
1 TraesCS6D01G239300 chr6B 480786168 480787366 1198 True 1925.0 1925 95.917 745 1923 1 chr6B.!!$R1 1178
2 TraesCS6D01G239300 chr6B 626809176 626809931 755 True 1053.0 1053 92.095 4 747 1 chr6B.!!$R2 743
3 TraesCS6D01G239300 chr3D 97119767 97120518 751 True 1114.0 1114 93.617 1 743 1 chr3D.!!$R1 742
4 TraesCS6D01G239300 chr4A 704518678 704519429 751 False 1094.0 1094 93.103 1 744 1 chr4A.!!$F1 743
5 TraesCS6D01G239300 chr2D 534727039 534727798 759 True 1094.0 1094 92.895 4 751 1 chr2D.!!$R2 747
6 TraesCS6D01G239300 chr2D 285349324 285350087 763 False 1062.0 1062 92.157 1 747 1 chr2D.!!$F1 746
7 TraesCS6D01G239300 chr2D 531682374 531683099 725 True 1044.0 1044 92.740 1 723 1 chr2D.!!$R1 722
8 TraesCS6D01G239300 chr1D 444890504 444891265 761 False 1062.0 1062 92.026 1 754 1 chr1D.!!$F1 753
9 TraesCS6D01G239300 chr7D 163364091 163364819 728 True 1053.0 1053 92.896 21 743 1 chr7D.!!$R1 722
10 TraesCS6D01G239300 chr3B 521657910 521658653 743 True 1037.0 1037 92.204 21 746 1 chr3B.!!$R1 725
11 TraesCS6D01G239300 chr6A 480197404 480198433 1029 False 627.5 743 89.271 756 1846 2 chr6A.!!$F1 1090

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
487 521 1.152525 GGGAGAGGAGACGGGCATA 60.153 63.158 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2310 0.034863 TACTCCAAAACGATGCCCCC 60.035 55.0 0.0 0.0 0.0 5.4 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
173 174 3.858247 GGTTGCCACCTACTAACACTAG 58.142 50.000 0.00 0.00 40.44 2.57
229 231 6.041979 AGTTGCCATGATTTGAAAACCTTAGT 59.958 34.615 0.00 0.00 0.00 2.24
296 299 6.183360 ACAAAGAGACATGGCAAAACAACATA 60.183 34.615 0.00 0.00 0.00 2.29
487 521 1.152525 GGGAGAGGAGACGGGCATA 60.153 63.158 0.00 0.00 0.00 3.14
499 533 1.679311 GGGCATATGGGCGAGATGA 59.321 57.895 8.36 0.00 44.56 2.92
631 665 2.062971 GGTGAATGCCCAGACATCAT 57.937 50.000 0.00 0.00 0.00 2.45
632 666 2.381911 GGTGAATGCCCAGACATCATT 58.618 47.619 0.00 0.00 33.57 2.57
633 667 2.762327 GGTGAATGCCCAGACATCATTT 59.238 45.455 0.00 0.00 31.30 2.32
668 704 4.252073 GCACCACAATATGCCAAAATTCA 58.748 39.130 0.00 0.00 35.73 2.57
754 792 5.623673 CGTTAGTGTTTCCGAAAGAAAATGG 59.376 40.000 0.00 0.00 45.93 3.16
862 900 2.393557 CCACGCACGGCAAGATAAT 58.606 52.632 0.00 0.00 0.00 1.28
1284 1355 2.125350 GCCTGGCTCTCCGTCTTG 60.125 66.667 12.43 0.00 34.14 3.02
1568 1657 4.268359 CTTCTGGAATTCTCCTTTCCTGG 58.732 47.826 5.23 0.00 42.63 4.45
1693 1787 1.743252 GTGCAGAAGCTTCTCCCCG 60.743 63.158 26.18 15.75 42.74 5.73
1720 1814 6.315642 CACAGATCACTATCAAGACTGCAAAT 59.684 38.462 0.00 0.00 34.28 2.32
1789 1883 2.126189 CCGTCCGGTCGTTTCTCC 60.126 66.667 19.43 0.00 0.00 3.71
1880 1975 5.088739 GTGTCGACTAATCATTTTTGCTGG 58.911 41.667 17.92 0.00 0.00 4.85
1882 1977 3.128589 TCGACTAATCATTTTTGCTGGGC 59.871 43.478 0.00 0.00 0.00 5.36
1887 1982 1.702182 TCATTTTTGCTGGGCTGACA 58.298 45.000 0.00 0.00 0.00 3.58
1897 1992 2.513753 CTGGGCTGACACACCATTAAA 58.486 47.619 0.00 0.00 33.07 1.52
1902 1997 3.758554 GGCTGACACACCATTAAATGAGT 59.241 43.478 0.00 0.00 0.00 3.41
1927 2022 9.453325 GTAAAGAGAAGATTAAGTATCAGACGG 57.547 37.037 0.00 0.00 35.59 4.79
1928 2023 7.883391 AAGAGAAGATTAAGTATCAGACGGA 57.117 36.000 0.00 0.00 35.59 4.69
1929 2024 7.504924 AGAGAAGATTAAGTATCAGACGGAG 57.495 40.000 0.00 0.00 35.59 4.63
1930 2025 6.016610 AGAGAAGATTAAGTATCAGACGGAGC 60.017 42.308 0.00 0.00 35.59 4.70
1931 2026 4.491234 AGATTAAGTATCAGACGGAGCG 57.509 45.455 0.00 0.00 35.59 5.03
1932 2027 4.135306 AGATTAAGTATCAGACGGAGCGA 58.865 43.478 0.00 0.00 35.59 4.93
1933 2028 4.762765 AGATTAAGTATCAGACGGAGCGAT 59.237 41.667 0.00 0.00 35.59 4.58
1934 2029 2.783828 AAGTATCAGACGGAGCGATG 57.216 50.000 0.00 0.00 0.00 3.84
1935 2030 0.955178 AGTATCAGACGGAGCGATGG 59.045 55.000 0.00 0.00 0.00 3.51
1936 2031 0.664767 GTATCAGACGGAGCGATGGC 60.665 60.000 0.00 0.00 40.37 4.40
1937 2032 2.130073 TATCAGACGGAGCGATGGCG 62.130 60.000 0.00 0.00 46.35 5.69
1958 2053 1.785951 GCTTTTGCGTCGTAGTCCC 59.214 57.895 0.00 0.00 34.86 4.46
1959 2054 0.669625 GCTTTTGCGTCGTAGTCCCT 60.670 55.000 0.00 0.00 34.86 4.20
1960 2055 1.347320 CTTTTGCGTCGTAGTCCCTC 58.653 55.000 0.00 0.00 0.00 4.30
1961 2056 0.963962 TTTTGCGTCGTAGTCCCTCT 59.036 50.000 0.00 0.00 0.00 3.69
1962 2057 0.963962 TTTGCGTCGTAGTCCCTCTT 59.036 50.000 0.00 0.00 0.00 2.85
1963 2058 0.963962 TTGCGTCGTAGTCCCTCTTT 59.036 50.000 0.00 0.00 0.00 2.52
1964 2059 1.825090 TGCGTCGTAGTCCCTCTTTA 58.175 50.000 0.00 0.00 0.00 1.85
1965 2060 1.741706 TGCGTCGTAGTCCCTCTTTAG 59.258 52.381 0.00 0.00 0.00 1.85
1966 2061 1.065251 GCGTCGTAGTCCCTCTTTAGG 59.935 57.143 0.00 0.00 43.25 2.69
1978 2073 4.192429 CCTCTTTAGGGCATTGTTTTGG 57.808 45.455 0.00 0.00 39.48 3.28
1979 2074 3.831911 CCTCTTTAGGGCATTGTTTTGGA 59.168 43.478 0.00 0.00 39.48 3.53
1980 2075 4.082026 CCTCTTTAGGGCATTGTTTTGGAG 60.082 45.833 0.00 0.00 39.48 3.86
1981 2076 4.479158 TCTTTAGGGCATTGTTTTGGAGT 58.521 39.130 0.00 0.00 0.00 3.85
1982 2077 4.898861 TCTTTAGGGCATTGTTTTGGAGTT 59.101 37.500 0.00 0.00 0.00 3.01
1983 2078 5.365314 TCTTTAGGGCATTGTTTTGGAGTTT 59.635 36.000 0.00 0.00 0.00 2.66
1984 2079 3.473923 AGGGCATTGTTTTGGAGTTTG 57.526 42.857 0.00 0.00 0.00 2.93
1985 2080 1.872952 GGGCATTGTTTTGGAGTTTGC 59.127 47.619 0.00 0.00 0.00 3.68
1986 2081 2.485302 GGGCATTGTTTTGGAGTTTGCT 60.485 45.455 0.00 0.00 0.00 3.91
1987 2082 2.802247 GGCATTGTTTTGGAGTTTGCTC 59.198 45.455 0.00 0.00 40.93 4.26
1997 2092 0.875059 GAGTTTGCTCCGGTTGAAGG 59.125 55.000 0.00 0.00 35.76 3.46
1998 2093 0.537371 AGTTTGCTCCGGTTGAAGGG 60.537 55.000 0.00 0.00 0.00 3.95
1999 2094 0.536460 GTTTGCTCCGGTTGAAGGGA 60.536 55.000 0.00 0.00 0.00 4.20
2000 2095 0.536460 TTTGCTCCGGTTGAAGGGAC 60.536 55.000 0.00 0.00 0.00 4.46
2001 2096 2.046217 GCTCCGGTTGAAGGGACC 60.046 66.667 0.00 0.00 0.00 4.46
2002 2097 2.890766 GCTCCGGTTGAAGGGACCA 61.891 63.158 0.00 0.00 36.99 4.02
2003 2098 1.296715 CTCCGGTTGAAGGGACCAG 59.703 63.158 0.00 0.00 36.99 4.00
2004 2099 2.359975 CCGGTTGAAGGGACCAGC 60.360 66.667 0.00 0.00 36.99 4.85
2005 2100 2.742372 CGGTTGAAGGGACCAGCG 60.742 66.667 0.00 0.00 36.99 5.18
2006 2101 2.747686 GGTTGAAGGGACCAGCGA 59.252 61.111 0.00 0.00 37.14 4.93
2007 2102 1.671379 GGTTGAAGGGACCAGCGAC 60.671 63.158 0.00 0.00 37.14 5.19
2008 2103 2.027625 GTTGAAGGGACCAGCGACG 61.028 63.158 0.00 0.00 0.00 5.12
2009 2104 2.504274 TTGAAGGGACCAGCGACGT 61.504 57.895 0.00 0.00 0.00 4.34
2010 2105 2.126031 GAAGGGACCAGCGACGTC 60.126 66.667 5.18 5.18 0.00 4.34
2011 2106 2.915659 AAGGGACCAGCGACGTCA 60.916 61.111 17.16 0.00 31.55 4.35
2012 2107 2.820767 GAAGGGACCAGCGACGTCAG 62.821 65.000 17.16 9.59 31.55 3.51
2037 2132 2.247790 ACGTCTGGTGAGCAATTGC 58.752 52.632 23.05 23.05 42.49 3.56
2038 2133 1.237285 ACGTCTGGTGAGCAATTGCC 61.237 55.000 26.45 17.77 43.38 4.52
2039 2134 1.503542 GTCTGGTGAGCAATTGCCG 59.496 57.895 26.45 8.66 43.38 5.69
2040 2135 0.955428 GTCTGGTGAGCAATTGCCGA 60.955 55.000 26.45 10.83 43.38 5.54
2041 2136 0.035152 TCTGGTGAGCAATTGCCGAT 60.035 50.000 26.45 8.72 43.38 4.18
2042 2137 0.099968 CTGGTGAGCAATTGCCGATG 59.900 55.000 26.45 8.82 43.38 3.84
2043 2138 0.322366 TGGTGAGCAATTGCCGATGA 60.322 50.000 26.45 5.90 43.38 2.92
2044 2139 0.810648 GGTGAGCAATTGCCGATGAA 59.189 50.000 26.45 3.66 43.38 2.57
2045 2140 1.202114 GGTGAGCAATTGCCGATGAAA 59.798 47.619 26.45 2.23 43.38 2.69
2046 2141 2.352617 GGTGAGCAATTGCCGATGAAAA 60.353 45.455 26.45 1.16 43.38 2.29
2047 2142 3.514645 GTGAGCAATTGCCGATGAAAAT 58.485 40.909 26.45 4.68 43.38 1.82
2048 2143 3.549070 GTGAGCAATTGCCGATGAAAATC 59.451 43.478 26.45 14.21 43.38 2.17
2049 2144 2.785477 GAGCAATTGCCGATGAAAATCG 59.215 45.455 26.45 1.19 43.38 3.34
2050 2145 1.256117 GCAATTGCCGATGAAAATCGC 59.744 47.619 20.06 0.22 42.26 4.58
2051 2146 1.513994 CAATTGCCGATGAAAATCGCG 59.486 47.619 0.00 0.00 42.26 5.87
2052 2147 0.592247 ATTGCCGATGAAAATCGCGC 60.592 50.000 0.00 0.00 42.26 6.86
2053 2148 2.352343 GCCGATGAAAATCGCGCC 60.352 61.111 0.00 0.00 42.26 6.53
2054 2149 2.053116 CCGATGAAAATCGCGCCG 60.053 61.111 0.00 0.00 42.26 6.46
2055 2150 2.521771 CCGATGAAAATCGCGCCGA 61.522 57.895 0.00 2.55 42.26 5.54
2056 2151 1.366494 CGATGAAAATCGCGCCGAC 60.366 57.895 0.00 0.00 39.18 4.79
2057 2152 1.752501 CGATGAAAATCGCGCCGACT 61.753 55.000 0.00 0.00 39.18 4.18
2058 2153 1.205657 GATGAAAATCGCGCCGACTA 58.794 50.000 0.00 0.00 39.18 2.59
2059 2154 0.928229 ATGAAAATCGCGCCGACTAC 59.072 50.000 0.00 0.00 39.18 2.73
2060 2155 1.268946 GAAAATCGCGCCGACTACG 59.731 57.895 0.00 0.00 39.18 3.51
2070 2165 2.278596 CGACTACGGTCATGGCGG 60.279 66.667 2.94 2.94 42.21 6.13
2071 2166 2.767445 CGACTACGGTCATGGCGGA 61.767 63.158 12.28 0.00 42.21 5.54
2072 2167 1.226888 GACTACGGTCATGGCGGAC 60.227 63.158 12.28 0.88 41.75 4.79
2073 2168 2.278596 CTACGGTCATGGCGGACG 60.279 66.667 12.28 2.14 38.70 4.79
2074 2169 2.751036 TACGGTCATGGCGGACGA 60.751 61.111 12.28 0.00 38.70 4.20
2075 2170 2.071844 CTACGGTCATGGCGGACGAT 62.072 60.000 12.28 0.00 38.70 3.73
2076 2171 2.344521 TACGGTCATGGCGGACGATG 62.345 60.000 12.28 0.00 38.70 3.84
2077 2172 2.588877 GGTCATGGCGGACGATGG 60.589 66.667 0.00 0.00 38.70 3.51
2078 2173 3.272334 GTCATGGCGGACGATGGC 61.272 66.667 0.00 0.00 0.00 4.40
2079 2174 4.889856 TCATGGCGGACGATGGCG 62.890 66.667 0.00 0.00 44.79 5.69
2088 2183 2.104331 ACGATGGCGGCGTCTTAG 59.896 61.111 26.35 14.92 43.17 2.18
2089 2184 2.411701 CGATGGCGGCGTCTTAGA 59.588 61.111 26.35 0.00 0.00 2.10
2090 2185 1.007271 CGATGGCGGCGTCTTAGAT 60.007 57.895 26.35 0.00 0.00 1.98
2091 2186 1.278172 CGATGGCGGCGTCTTAGATG 61.278 60.000 26.35 8.21 0.00 2.90
2092 2187 0.249489 GATGGCGGCGTCTTAGATGT 60.249 55.000 22.88 0.00 0.00 3.06
2093 2188 0.249489 ATGGCGGCGTCTTAGATGTC 60.249 55.000 14.51 0.00 0.00 3.06
2095 2190 1.226603 GCGGCGTCTTAGATGTCGT 60.227 57.895 25.84 0.00 46.56 4.34
2096 2191 0.801067 GCGGCGTCTTAGATGTCGTT 60.801 55.000 25.84 0.00 46.56 3.85
2097 2192 1.189403 CGGCGTCTTAGATGTCGTTC 58.811 55.000 18.88 0.00 41.06 3.95
2098 2193 1.557651 GGCGTCTTAGATGTCGTTCC 58.442 55.000 3.23 0.00 0.00 3.62
2099 2194 1.557651 GCGTCTTAGATGTCGTTCCC 58.442 55.000 3.23 0.00 0.00 3.97
2100 2195 1.134560 GCGTCTTAGATGTCGTTCCCT 59.865 52.381 3.23 0.00 0.00 4.20
2101 2196 2.416972 GCGTCTTAGATGTCGTTCCCTT 60.417 50.000 3.23 0.00 0.00 3.95
2102 2197 3.179830 CGTCTTAGATGTCGTTCCCTTG 58.820 50.000 0.00 0.00 0.00 3.61
2103 2198 3.367087 CGTCTTAGATGTCGTTCCCTTGT 60.367 47.826 0.00 0.00 0.00 3.16
2104 2199 4.174762 GTCTTAGATGTCGTTCCCTTGTC 58.825 47.826 0.00 0.00 0.00 3.18
2105 2200 2.933495 TAGATGTCGTTCCCTTGTCG 57.067 50.000 0.00 0.00 0.00 4.35
2106 2201 1.254026 AGATGTCGTTCCCTTGTCGA 58.746 50.000 0.00 0.00 0.00 4.20
2107 2202 1.202582 AGATGTCGTTCCCTTGTCGAG 59.797 52.381 0.00 0.00 34.33 4.04
2108 2203 0.246635 ATGTCGTTCCCTTGTCGAGG 59.753 55.000 0.00 0.00 45.86 4.63
2109 2204 1.737008 GTCGTTCCCTTGTCGAGGC 60.737 63.158 0.00 0.00 44.85 4.70
2110 2205 2.204461 TCGTTCCCTTGTCGAGGCA 61.204 57.895 0.00 0.00 44.85 4.75
2111 2206 1.079127 CGTTCCCTTGTCGAGGCAT 60.079 57.895 0.00 0.00 44.85 4.40
2112 2207 1.084370 CGTTCCCTTGTCGAGGCATC 61.084 60.000 0.00 0.00 44.85 3.91
2121 2216 2.809174 CGAGGCATCGTCGTTGCA 60.809 61.111 25.10 0.00 44.09 4.08
2122 2217 2.792290 CGAGGCATCGTCGTTGCAG 61.792 63.158 25.10 14.27 44.09 4.41
2123 2218 1.738099 GAGGCATCGTCGTTGCAGT 60.738 57.895 25.10 14.35 41.95 4.40
2124 2219 1.687494 GAGGCATCGTCGTTGCAGTC 61.687 60.000 25.10 18.04 41.95 3.51
2125 2220 1.738099 GGCATCGTCGTTGCAGTCT 60.738 57.895 25.10 0.00 41.95 3.24
2126 2221 1.417592 GCATCGTCGTTGCAGTCTG 59.582 57.895 20.54 0.00 39.90 3.51
2127 2222 1.417592 CATCGTCGTTGCAGTCTGC 59.582 57.895 18.32 18.32 45.29 4.26
2136 2231 3.791539 GCAGTCTGCGTCATCAGG 58.208 61.111 9.53 0.00 34.91 3.86
2137 2232 2.459442 GCAGTCTGCGTCATCAGGC 61.459 63.158 9.53 0.00 38.90 4.85
2138 2233 3.705502 AGTCTGCGTCATCAGGCT 58.294 55.556 0.00 0.00 43.58 4.58
2139 2234 0.805322 CAGTCTGCGTCATCAGGCTC 60.805 60.000 0.00 0.00 45.05 4.70
2140 2235 1.875813 GTCTGCGTCATCAGGCTCG 60.876 63.158 0.00 0.00 35.88 5.03
2141 2236 2.584418 CTGCGTCATCAGGCTCGG 60.584 66.667 0.00 0.00 34.31 4.63
2142 2237 4.147449 TGCGTCATCAGGCTCGGG 62.147 66.667 0.00 0.00 34.31 5.14
2143 2238 3.838271 GCGTCATCAGGCTCGGGA 61.838 66.667 0.00 0.00 0.00 5.14
2144 2239 3.133014 CGTCATCAGGCTCGGGAT 58.867 61.111 0.00 0.00 0.00 3.85
2145 2240 1.300465 CGTCATCAGGCTCGGGATG 60.300 63.158 6.91 6.91 41.73 3.51
2146 2241 1.596477 GTCATCAGGCTCGGGATGC 60.596 63.158 8.11 1.75 40.50 3.91
2147 2242 1.763655 TCATCAGGCTCGGGATGCT 60.764 57.895 8.11 0.00 40.50 3.79
2148 2243 1.301558 CATCAGGCTCGGGATGCTC 60.302 63.158 0.94 0.00 35.03 4.26
2149 2244 2.515071 ATCAGGCTCGGGATGCTCC 61.515 63.158 0.00 0.00 35.23 4.70
2157 2252 3.416880 GGGATGCTCCGGGGGAAA 61.417 66.667 0.00 0.00 37.43 3.13
2158 2253 2.124278 GGATGCTCCGGGGGAAAC 60.124 66.667 0.00 0.00 0.00 2.78
2176 2271 5.186942 GGAAACCTTAGATCTTGGTCTTCC 58.813 45.833 24.43 24.43 35.77 3.46
2177 2272 4.473477 AACCTTAGATCTTGGTCTTCCG 57.527 45.455 17.06 0.00 36.30 4.30
2178 2273 2.766828 ACCTTAGATCTTGGTCTTCCGG 59.233 50.000 12.62 0.00 36.30 5.14
2179 2274 3.031736 CCTTAGATCTTGGTCTTCCGGA 58.968 50.000 0.00 0.00 36.30 5.14
2180 2275 3.643792 CCTTAGATCTTGGTCTTCCGGAT 59.356 47.826 4.15 0.00 36.30 4.18
2181 2276 4.262249 CCTTAGATCTTGGTCTTCCGGATC 60.262 50.000 4.15 0.00 41.39 3.36
2182 2277 1.683917 AGATCTTGGTCTTCCGGATCG 59.316 52.381 4.15 0.00 43.45 3.69
2193 2288 4.559835 CGGATCGGACGATGATGG 57.440 61.111 12.40 0.00 34.60 3.51
2194 2289 1.734477 CGGATCGGACGATGATGGC 60.734 63.158 12.40 0.00 34.60 4.40
2195 2290 1.734477 GGATCGGACGATGATGGCG 60.734 63.158 12.40 0.00 34.60 5.69
2196 2291 1.007271 GATCGGACGATGATGGCGT 60.007 57.895 12.40 0.00 45.79 5.68
2197 2292 0.597637 GATCGGACGATGATGGCGTT 60.598 55.000 12.40 0.00 42.77 4.84
2198 2293 0.179084 ATCGGACGATGATGGCGTTT 60.179 50.000 6.39 0.00 42.77 3.60
2199 2294 0.390603 TCGGACGATGATGGCGTTTT 60.391 50.000 0.00 0.00 42.77 2.43
2200 2295 1.135053 TCGGACGATGATGGCGTTTTA 60.135 47.619 0.00 0.00 42.77 1.52
2201 2296 1.864711 CGGACGATGATGGCGTTTTAT 59.135 47.619 0.00 0.00 42.77 1.40
2202 2297 2.096909 CGGACGATGATGGCGTTTTATC 60.097 50.000 0.00 0.00 42.77 1.75
2203 2298 2.096909 GGACGATGATGGCGTTTTATCG 60.097 50.000 15.60 15.60 42.77 2.92
2214 2309 2.629051 CGTTTTATCGCTTTCCCTCCT 58.371 47.619 0.00 0.00 0.00 3.69
2215 2310 2.351726 CGTTTTATCGCTTTCCCTCCTG 59.648 50.000 0.00 0.00 0.00 3.86
2216 2311 2.683362 GTTTTATCGCTTTCCCTCCTGG 59.317 50.000 0.00 0.00 0.00 4.45
2226 2321 3.411517 CCTCCTGGGGGCATCGTT 61.412 66.667 0.00 0.00 0.00 3.85
2227 2322 2.677228 CTCCTGGGGGCATCGTTT 59.323 61.111 0.00 0.00 0.00 3.60
2228 2323 1.000896 CTCCTGGGGGCATCGTTTT 60.001 57.895 0.00 0.00 0.00 2.43
2229 2324 1.304052 TCCTGGGGGCATCGTTTTG 60.304 57.895 0.00 0.00 0.00 2.44
2230 2325 2.350458 CCTGGGGGCATCGTTTTGG 61.350 63.158 0.00 0.00 0.00 3.28
2231 2326 1.304052 CTGGGGGCATCGTTTTGGA 60.304 57.895 0.00 0.00 0.00 3.53
2232 2327 1.304052 TGGGGGCATCGTTTTGGAG 60.304 57.895 0.00 0.00 0.00 3.86
2233 2328 1.304134 GGGGGCATCGTTTTGGAGT 60.304 57.895 0.00 0.00 0.00 3.85
2234 2329 0.034863 GGGGGCATCGTTTTGGAGTA 60.035 55.000 0.00 0.00 0.00 2.59
2235 2330 1.614850 GGGGGCATCGTTTTGGAGTAA 60.615 52.381 0.00 0.00 0.00 2.24
2236 2331 1.743394 GGGGCATCGTTTTGGAGTAAG 59.257 52.381 0.00 0.00 0.00 2.34
2237 2332 2.433436 GGGCATCGTTTTGGAGTAAGT 58.567 47.619 0.00 0.00 0.00 2.24
2238 2333 2.161609 GGGCATCGTTTTGGAGTAAGTG 59.838 50.000 0.00 0.00 0.00 3.16
2239 2334 2.414161 GGCATCGTTTTGGAGTAAGTGC 60.414 50.000 0.00 0.00 0.00 4.40
2240 2335 2.484264 GCATCGTTTTGGAGTAAGTGCT 59.516 45.455 0.00 0.00 0.00 4.40
2241 2336 3.667960 GCATCGTTTTGGAGTAAGTGCTG 60.668 47.826 0.00 0.00 0.00 4.41
2242 2337 2.489971 TCGTTTTGGAGTAAGTGCTGG 58.510 47.619 0.00 0.00 0.00 4.85
2243 2338 1.069227 CGTTTTGGAGTAAGTGCTGGC 60.069 52.381 0.00 0.00 0.00 4.85
2244 2339 2.230660 GTTTTGGAGTAAGTGCTGGCT 58.769 47.619 0.00 0.00 0.00 4.75
2245 2340 1.896220 TTTGGAGTAAGTGCTGGCTG 58.104 50.000 0.00 0.00 0.00 4.85
2246 2341 0.036732 TTGGAGTAAGTGCTGGCTGG 59.963 55.000 0.00 0.00 0.00 4.85
2247 2342 1.127567 TGGAGTAAGTGCTGGCTGGT 61.128 55.000 0.00 0.00 0.00 4.00
2248 2343 0.674895 GGAGTAAGTGCTGGCTGGTG 60.675 60.000 0.00 0.00 0.00 4.17
2249 2344 0.674895 GAGTAAGTGCTGGCTGGTGG 60.675 60.000 0.00 0.00 0.00 4.61
2250 2345 1.675641 GTAAGTGCTGGCTGGTGGG 60.676 63.158 0.00 0.00 0.00 4.61
2251 2346 1.845664 TAAGTGCTGGCTGGTGGGA 60.846 57.895 0.00 0.00 0.00 4.37
2252 2347 1.207488 TAAGTGCTGGCTGGTGGGAT 61.207 55.000 0.00 0.00 0.00 3.85
2253 2348 2.753043 GTGCTGGCTGGTGGGATG 60.753 66.667 0.00 0.00 0.00 3.51
2254 2349 4.051167 TGCTGGCTGGTGGGATGG 62.051 66.667 0.00 0.00 0.00 3.51
2255 2350 4.052518 GCTGGCTGGTGGGATGGT 62.053 66.667 0.00 0.00 0.00 3.55
2256 2351 2.044650 CTGGCTGGTGGGATGGTG 60.045 66.667 0.00 0.00 0.00 4.17
2257 2352 3.650298 CTGGCTGGTGGGATGGTGG 62.650 68.421 0.00 0.00 0.00 4.61
2258 2353 3.338250 GGCTGGTGGGATGGTGGA 61.338 66.667 0.00 0.00 0.00 4.02
2259 2354 2.273449 GCTGGTGGGATGGTGGAG 59.727 66.667 0.00 0.00 0.00 3.86
2260 2355 2.273449 CTGGTGGGATGGTGGAGC 59.727 66.667 0.00 0.00 0.00 4.70
2261 2356 3.687321 CTGGTGGGATGGTGGAGCG 62.687 68.421 0.00 0.00 0.00 5.03
2262 2357 4.489771 GGTGGGATGGTGGAGCGG 62.490 72.222 0.00 0.00 0.00 5.52
2263 2358 3.717294 GTGGGATGGTGGAGCGGT 61.717 66.667 0.00 0.00 0.00 5.68
2264 2359 3.716195 TGGGATGGTGGAGCGGTG 61.716 66.667 0.00 0.00 0.00 4.94
2266 2361 4.101448 GGATGGTGGAGCGGTGCT 62.101 66.667 7.84 0.00 43.88 4.40
2267 2362 2.045926 GATGGTGGAGCGGTGCTT 60.046 61.111 7.84 0.00 39.88 3.91
2268 2363 2.045926 ATGGTGGAGCGGTGCTTC 60.046 61.111 7.84 0.54 39.88 3.86
2269 2364 2.803155 GATGGTGGAGCGGTGCTTCA 62.803 60.000 7.84 6.08 42.52 3.02
2270 2365 2.045926 GGTGGAGCGGTGCTTCAT 60.046 61.111 7.84 0.00 46.58 2.57
2271 2366 2.109126 GGTGGAGCGGTGCTTCATC 61.109 63.158 7.84 0.00 46.58 2.92
2272 2367 1.078848 GTGGAGCGGTGCTTCATCT 60.079 57.895 7.84 0.00 46.58 2.90
2273 2368 1.086634 GTGGAGCGGTGCTTCATCTC 61.087 60.000 7.84 0.00 46.58 2.75
2274 2369 1.219124 GGAGCGGTGCTTCATCTCA 59.781 57.895 0.00 0.00 39.88 3.27
2275 2370 1.086634 GGAGCGGTGCTTCATCTCAC 61.087 60.000 0.00 0.00 39.88 3.51
2276 2371 0.390340 GAGCGGTGCTTCATCTCACA 60.390 55.000 0.00 0.00 39.88 3.58
2277 2372 0.671781 AGCGGTGCTTCATCTCACAC 60.672 55.000 0.00 0.00 33.89 3.82
2278 2373 0.950555 GCGGTGCTTCATCTCACACA 60.951 55.000 0.00 0.00 34.69 3.72
2279 2374 1.730501 CGGTGCTTCATCTCACACAT 58.269 50.000 0.00 0.00 34.69 3.21
2280 2375 1.662629 CGGTGCTTCATCTCACACATC 59.337 52.381 0.00 0.00 34.69 3.06
2281 2376 1.662629 GGTGCTTCATCTCACACATCG 59.337 52.381 0.00 0.00 34.69 3.84
2282 2377 2.610433 GTGCTTCATCTCACACATCGA 58.390 47.619 0.00 0.00 33.63 3.59
2283 2378 3.193263 GTGCTTCATCTCACACATCGAT 58.807 45.455 0.00 0.00 33.63 3.59
2284 2379 3.001026 GTGCTTCATCTCACACATCGATG 59.999 47.826 23.68 23.68 36.70 3.84
2285 2380 3.119029 TGCTTCATCTCACACATCGATGA 60.119 43.478 31.33 9.41 41.09 2.92
2286 2381 3.244814 GCTTCATCTCACACATCGATGAC 59.755 47.826 31.33 1.40 42.13 3.06
2287 2382 3.070429 TCATCTCACACATCGATGACG 57.930 47.619 31.33 22.15 38.77 4.35
2288 2383 2.122564 CATCTCACACATCGATGACGG 58.877 52.381 31.33 20.56 37.35 4.79
2289 2384 0.179137 TCTCACACATCGATGACGGC 60.179 55.000 31.33 0.00 40.21 5.68
2290 2385 1.474648 CTCACACATCGATGACGGCG 61.475 60.000 31.33 15.92 40.21 6.46
2291 2386 2.202743 ACACATCGATGACGGCGG 60.203 61.111 31.33 14.45 40.21 6.13
2292 2387 2.104132 CACATCGATGACGGCGGA 59.896 61.111 31.33 0.00 40.21 5.54
2293 2388 1.300156 CACATCGATGACGGCGGAT 60.300 57.895 31.33 3.59 40.21 4.18
2294 2389 0.039527 CACATCGATGACGGCGGATA 60.040 55.000 31.33 0.00 40.21 2.59
2295 2390 0.888619 ACATCGATGACGGCGGATAT 59.111 50.000 31.33 2.01 40.21 1.63
2296 2391 1.272490 ACATCGATGACGGCGGATATT 59.728 47.619 31.33 1.45 40.21 1.28
2297 2392 1.655597 CATCGATGACGGCGGATATTG 59.344 52.381 21.02 6.52 40.21 1.90
2298 2393 0.038618 TCGATGACGGCGGATATTGG 60.039 55.000 13.24 0.00 40.21 3.16
2299 2394 1.626654 CGATGACGGCGGATATTGGC 61.627 60.000 13.24 0.00 35.72 4.52
2304 2399 2.672996 GGCGGATATTGGCGGCAT 60.673 61.111 14.32 5.79 33.79 4.40
2305 2400 2.562912 GCGGATATTGGCGGCATG 59.437 61.111 14.32 0.00 0.00 4.06
2306 2401 2.981560 GCGGATATTGGCGGCATGG 61.982 63.158 14.32 0.00 0.00 3.66
2307 2402 2.964978 GGATATTGGCGGCATGGC 59.035 61.111 14.32 9.69 45.12 4.40
2316 2411 2.963854 CGGCATGGCGCTGTAGAG 60.964 66.667 29.30 0.00 42.55 2.43
2317 2412 2.590007 GGCATGGCGCTGTAGAGG 60.590 66.667 7.64 0.00 41.91 3.69
2318 2413 3.275338 GCATGGCGCTGTAGAGGC 61.275 66.667 7.64 2.31 40.61 4.70
2319 2414 2.503061 CATGGCGCTGTAGAGGCT 59.497 61.111 7.64 0.00 40.82 4.58
2320 2415 1.593750 CATGGCGCTGTAGAGGCTC 60.594 63.158 7.64 6.34 40.82 4.70
2321 2416 3.144120 ATGGCGCTGTAGAGGCTCG 62.144 63.158 7.64 0.00 40.82 5.03
2322 2417 4.577246 GGCGCTGTAGAGGCTCGG 62.577 72.222 7.64 2.38 37.43 4.63
2325 2420 3.827898 GCTGTAGAGGCTCGGCGT 61.828 66.667 9.22 0.00 0.00 5.68
2326 2421 2.409651 CTGTAGAGGCTCGGCGTC 59.590 66.667 9.22 9.61 42.77 5.19
2327 2422 3.127352 CTGTAGAGGCTCGGCGTCC 62.127 68.421 9.22 9.88 43.36 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.310933 GCATCTGGCACTTGACCTGG 61.311 60.000 0.00 0.00 43.97 4.45
141 142 3.917329 GGTGGCAACCTCTAAAGTTTC 57.083 47.619 1.77 0.00 43.84 2.78
229 231 4.708421 CCTAGTGTTAGTAGGTGGCAACTA 59.292 45.833 8.51 8.51 36.69 2.24
296 299 5.011738 TGACAACTCTCTCTTTTACCCGAAT 59.988 40.000 0.00 0.00 0.00 3.34
487 521 1.027357 GCATTTGTCATCTCGCCCAT 58.973 50.000 0.00 0.00 0.00 4.00
499 533 1.747325 GCTGGTGTGTGGGCATTTGT 61.747 55.000 0.00 0.00 0.00 2.83
584 618 1.879430 ACACGTCCGTTTCACCACG 60.879 57.895 0.00 0.00 40.02 4.94
624 658 3.865745 CCACGTAGGACTGAAATGATGTC 59.134 47.826 0.00 0.00 41.22 3.06
628 662 1.621317 TGCCACGTAGGACTGAAATGA 59.379 47.619 8.04 0.00 41.22 2.57
631 665 0.034337 GGTGCCACGTAGGACTGAAA 59.966 55.000 5.55 0.00 41.22 2.69
632 666 1.116536 TGGTGCCACGTAGGACTGAA 61.117 55.000 5.55 0.00 41.22 3.02
633 667 1.532078 TGGTGCCACGTAGGACTGA 60.532 57.895 5.55 0.00 41.22 3.41
663 699 1.000731 CCGTTTGTGGGTGCATGAATT 59.999 47.619 0.00 0.00 0.00 2.17
668 704 2.258013 CGTCCGTTTGTGGGTGCAT 61.258 57.895 0.00 0.00 0.00 3.96
754 792 1.546476 ACACTGATCCTCGAGTTCCAC 59.454 52.381 12.31 0.00 0.00 4.02
862 900 1.079405 GTCCAAGTTGATCGGCGGA 60.079 57.895 7.21 0.00 0.00 5.54
1568 1657 2.413837 AGTCTGTTGCGTTACCATCAC 58.586 47.619 0.00 0.00 0.00 3.06
1693 1787 4.118410 CAGTCTTGATAGTGATCTGTGCC 58.882 47.826 0.00 0.00 32.79 5.01
1720 1814 0.881118 GCTGGATCAAGCGTGGAAAA 59.119 50.000 6.28 0.00 32.56 2.29
1779 1873 1.421485 CTGCGCATGGAGAAACGAC 59.579 57.895 12.24 0.00 35.14 4.34
1857 1952 5.088739 CCAGCAAAAATGATTAGTCGACAC 58.911 41.667 19.50 6.72 0.00 3.67
1880 1975 3.758554 ACTCATTTAATGGTGTGTCAGCC 59.241 43.478 5.02 0.00 0.00 4.85
1882 1977 8.322906 TCTTTACTCATTTAATGGTGTGTCAG 57.677 34.615 5.02 0.00 0.00 3.51
1887 1982 9.965902 ATCTTCTCTTTACTCATTTAATGGTGT 57.034 29.630 5.02 7.29 0.00 4.16
1902 1997 9.404848 TCCGTCTGATACTTAATCTTCTCTTTA 57.595 33.333 0.00 0.00 35.45 1.85
1936 2031 3.680072 CTACGACGCAAAAGCGCCG 62.680 63.158 16.23 16.23 43.90 6.46
1937 2032 2.095843 CTACGACGCAAAAGCGCC 59.904 61.111 2.29 0.00 36.58 6.53
1938 2033 1.225395 GACTACGACGCAAAAGCGC 60.225 57.895 10.01 0.00 36.58 5.92
1939 2034 1.414897 GGACTACGACGCAAAAGCG 59.585 57.895 8.45 8.45 39.31 4.68
1940 2035 0.669625 AGGGACTACGACGCAAAAGC 60.670 55.000 0.00 0.00 36.02 3.51
1941 2036 1.067776 AGAGGGACTACGACGCAAAAG 60.068 52.381 0.00 0.00 41.55 2.27
1942 2037 0.963962 AGAGGGACTACGACGCAAAA 59.036 50.000 0.00 0.00 41.55 2.44
1943 2038 0.963962 AAGAGGGACTACGACGCAAA 59.036 50.000 0.00 0.00 41.55 3.68
1944 2039 0.963962 AAAGAGGGACTACGACGCAA 59.036 50.000 0.00 0.00 41.55 4.85
1945 2040 1.741706 CTAAAGAGGGACTACGACGCA 59.258 52.381 0.00 0.00 41.55 5.24
1946 2041 1.065251 CCTAAAGAGGGACTACGACGC 59.935 57.143 0.00 0.00 41.55 5.19
1957 2052 3.831911 TCCAAAACAATGCCCTAAAGAGG 59.168 43.478 0.00 0.00 43.33 3.69
1958 2053 4.524328 ACTCCAAAACAATGCCCTAAAGAG 59.476 41.667 0.00 0.00 0.00 2.85
1959 2054 4.479158 ACTCCAAAACAATGCCCTAAAGA 58.521 39.130 0.00 0.00 0.00 2.52
1960 2055 4.871933 ACTCCAAAACAATGCCCTAAAG 57.128 40.909 0.00 0.00 0.00 1.85
1961 2056 5.363939 CAAACTCCAAAACAATGCCCTAAA 58.636 37.500 0.00 0.00 0.00 1.85
1962 2057 4.742138 GCAAACTCCAAAACAATGCCCTAA 60.742 41.667 0.00 0.00 0.00 2.69
1963 2058 3.244044 GCAAACTCCAAAACAATGCCCTA 60.244 43.478 0.00 0.00 0.00 3.53
1964 2059 2.485302 GCAAACTCCAAAACAATGCCCT 60.485 45.455 0.00 0.00 0.00 5.19
1965 2060 1.872952 GCAAACTCCAAAACAATGCCC 59.127 47.619 0.00 0.00 0.00 5.36
1966 2061 2.802247 GAGCAAACTCCAAAACAATGCC 59.198 45.455 0.00 0.00 36.90 4.40
1978 2073 0.875059 CCTTCAACCGGAGCAAACTC 59.125 55.000 9.46 0.00 42.66 3.01
1979 2074 0.537371 CCCTTCAACCGGAGCAAACT 60.537 55.000 9.46 0.00 0.00 2.66
1980 2075 0.536460 TCCCTTCAACCGGAGCAAAC 60.536 55.000 9.46 0.00 0.00 2.93
1981 2076 0.536460 GTCCCTTCAACCGGAGCAAA 60.536 55.000 9.46 0.00 0.00 3.68
1982 2077 1.072505 GTCCCTTCAACCGGAGCAA 59.927 57.895 9.46 0.00 0.00 3.91
1983 2078 2.747686 GTCCCTTCAACCGGAGCA 59.252 61.111 9.46 0.00 0.00 4.26
1984 2079 2.046217 GGTCCCTTCAACCGGAGC 60.046 66.667 9.46 0.00 39.31 4.70
1985 2080 1.296715 CTGGTCCCTTCAACCGGAG 59.703 63.158 9.46 0.00 44.59 4.63
1986 2081 2.890766 GCTGGTCCCTTCAACCGGA 61.891 63.158 9.46 0.00 44.59 5.14
1987 2082 2.359975 GCTGGTCCCTTCAACCGG 60.360 66.667 0.00 0.00 44.61 5.28
1988 2083 2.742372 CGCTGGTCCCTTCAACCG 60.742 66.667 0.00 0.00 39.81 4.44
1989 2084 1.671379 GTCGCTGGTCCCTTCAACC 60.671 63.158 0.00 0.00 37.31 3.77
1990 2085 2.027625 CGTCGCTGGTCCCTTCAAC 61.028 63.158 0.00 0.00 0.00 3.18
1991 2086 2.342279 CGTCGCTGGTCCCTTCAA 59.658 61.111 0.00 0.00 0.00 2.69
1992 2087 2.915659 ACGTCGCTGGTCCCTTCA 60.916 61.111 0.00 0.00 0.00 3.02
1993 2088 2.126031 GACGTCGCTGGTCCCTTC 60.126 66.667 0.00 0.00 0.00 3.46
1994 2089 2.915659 TGACGTCGCTGGTCCCTT 60.916 61.111 11.62 0.00 33.46 3.95
1995 2090 3.374402 CTGACGTCGCTGGTCCCT 61.374 66.667 11.62 0.00 33.46 4.20
2016 2111 1.568612 AATTGCTCACCAGACGTGCG 61.569 55.000 0.00 0.00 42.69 5.34
2017 2112 0.110056 CAATTGCTCACCAGACGTGC 60.110 55.000 0.00 0.00 42.69 5.34
2018 2113 0.110056 GCAATTGCTCACCAGACGTG 60.110 55.000 23.21 0.00 44.50 4.49
2019 2114 1.237285 GGCAATTGCTCACCAGACGT 61.237 55.000 28.42 0.00 41.70 4.34
2020 2115 1.503542 GGCAATTGCTCACCAGACG 59.496 57.895 28.42 0.00 41.70 4.18
2021 2116 0.955428 TCGGCAATTGCTCACCAGAC 60.955 55.000 28.42 9.44 41.70 3.51
2022 2117 0.035152 ATCGGCAATTGCTCACCAGA 60.035 50.000 28.42 17.62 41.70 3.86
2023 2118 0.099968 CATCGGCAATTGCTCACCAG 59.900 55.000 28.42 13.52 41.70 4.00
2024 2119 0.322366 TCATCGGCAATTGCTCACCA 60.322 50.000 28.42 8.87 41.70 4.17
2025 2120 0.810648 TTCATCGGCAATTGCTCACC 59.189 50.000 28.42 11.95 41.70 4.02
2026 2121 2.634982 TTTCATCGGCAATTGCTCAC 57.365 45.000 28.42 12.31 41.70 3.51
2027 2122 3.772932 GATTTTCATCGGCAATTGCTCA 58.227 40.909 28.42 16.20 41.70 4.26
2039 2134 1.071436 GTAGTCGGCGCGATTTTCATC 60.071 52.381 12.10 0.00 38.42 2.92
2040 2135 0.928229 GTAGTCGGCGCGATTTTCAT 59.072 50.000 12.10 0.00 38.42 2.57
2041 2136 1.407721 CGTAGTCGGCGCGATTTTCA 61.408 55.000 12.10 0.00 38.42 2.69
2042 2137 1.268946 CGTAGTCGGCGCGATTTTC 59.731 57.895 12.10 0.00 38.42 2.29
2043 2138 3.380671 CGTAGTCGGCGCGATTTT 58.619 55.556 12.10 0.00 38.42 1.82
2053 2148 2.278596 CCGCCATGACCGTAGTCG 60.279 66.667 0.00 0.00 46.74 4.18
2054 2149 1.226888 GTCCGCCATGACCGTAGTC 60.227 63.158 0.00 0.00 43.83 2.59
2055 2150 2.890371 GTCCGCCATGACCGTAGT 59.110 61.111 0.00 0.00 0.00 2.73
2056 2151 2.071844 ATCGTCCGCCATGACCGTAG 62.072 60.000 0.00 0.00 31.35 3.51
2057 2152 2.122797 ATCGTCCGCCATGACCGTA 61.123 57.895 0.00 0.00 31.35 4.02
2058 2153 3.458163 ATCGTCCGCCATGACCGT 61.458 61.111 0.00 0.00 31.35 4.83
2059 2154 2.961721 CATCGTCCGCCATGACCG 60.962 66.667 0.00 0.00 31.35 4.79
2060 2155 2.588877 CCATCGTCCGCCATGACC 60.589 66.667 0.00 0.00 31.35 4.02
2061 2156 3.272334 GCCATCGTCCGCCATGAC 61.272 66.667 0.00 0.00 0.00 3.06
2062 2157 4.889856 CGCCATCGTCCGCCATGA 62.890 66.667 0.00 0.00 0.00 3.07
2071 2166 1.735376 ATCTAAGACGCCGCCATCGT 61.735 55.000 0.00 0.00 43.49 3.73
2072 2167 1.007271 ATCTAAGACGCCGCCATCG 60.007 57.895 0.00 0.00 0.00 3.84
2073 2168 0.249489 ACATCTAAGACGCCGCCATC 60.249 55.000 0.00 0.00 0.00 3.51
2074 2169 0.249489 GACATCTAAGACGCCGCCAT 60.249 55.000 0.00 0.00 0.00 4.40
2075 2170 1.141019 GACATCTAAGACGCCGCCA 59.859 57.895 0.00 0.00 0.00 5.69
2076 2171 1.944676 CGACATCTAAGACGCCGCC 60.945 63.158 0.00 0.00 0.00 6.13
2077 2172 0.801067 AACGACATCTAAGACGCCGC 60.801 55.000 0.00 0.00 0.00 6.53
2078 2173 1.189403 GAACGACATCTAAGACGCCG 58.811 55.000 0.00 0.00 0.00 6.46
2079 2174 1.557651 GGAACGACATCTAAGACGCC 58.442 55.000 0.00 0.00 0.00 5.68
2080 2175 1.134560 AGGGAACGACATCTAAGACGC 59.865 52.381 0.00 0.00 0.00 5.19
2081 2176 3.179830 CAAGGGAACGACATCTAAGACG 58.820 50.000 0.00 0.00 0.00 4.18
2082 2177 4.174762 GACAAGGGAACGACATCTAAGAC 58.825 47.826 0.00 0.00 0.00 3.01
2083 2178 3.119602 CGACAAGGGAACGACATCTAAGA 60.120 47.826 0.00 0.00 0.00 2.10
2084 2179 3.119602 TCGACAAGGGAACGACATCTAAG 60.120 47.826 0.00 0.00 0.00 2.18
2085 2180 2.821378 TCGACAAGGGAACGACATCTAA 59.179 45.455 0.00 0.00 0.00 2.10
2086 2181 2.422479 CTCGACAAGGGAACGACATCTA 59.578 50.000 0.00 0.00 32.72 1.98
2087 2182 1.202582 CTCGACAAGGGAACGACATCT 59.797 52.381 0.00 0.00 32.72 2.90
2088 2183 1.630148 CTCGACAAGGGAACGACATC 58.370 55.000 0.00 0.00 32.72 3.06
2089 2184 0.246635 CCTCGACAAGGGAACGACAT 59.753 55.000 0.00 0.00 42.03 3.06
2090 2185 1.663739 CCTCGACAAGGGAACGACA 59.336 57.895 0.00 0.00 42.03 4.35
2091 2186 1.737008 GCCTCGACAAGGGAACGAC 60.737 63.158 0.00 0.00 46.32 4.34
2092 2187 2.204461 TGCCTCGACAAGGGAACGA 61.204 57.895 0.00 0.00 43.57 3.85
2093 2188 2.342279 TGCCTCGACAAGGGAACG 59.658 61.111 0.00 0.00 43.57 3.95
2105 2200 1.687494 GACTGCAACGACGATGCCTC 61.687 60.000 24.68 15.97 43.16 4.70
2106 2201 1.738099 GACTGCAACGACGATGCCT 60.738 57.895 24.68 11.66 43.16 4.75
2107 2202 1.738099 AGACTGCAACGACGATGCC 60.738 57.895 24.68 11.41 43.16 4.40
2108 2203 1.417592 CAGACTGCAACGACGATGC 59.582 57.895 21.63 21.63 44.08 3.91
2109 2204 1.417592 GCAGACTGCAACGACGATG 59.582 57.895 22.62 0.00 44.26 3.84
2110 2205 2.088763 CGCAGACTGCAACGACGAT 61.089 57.895 26.32 0.00 45.36 3.73
2111 2206 2.729491 CGCAGACTGCAACGACGA 60.729 61.111 26.32 0.00 45.36 4.20
2112 2207 2.988549 GACGCAGACTGCAACGACG 61.989 63.158 26.32 11.72 45.36 5.12
2113 2208 1.284982 ATGACGCAGACTGCAACGAC 61.285 55.000 26.32 11.48 45.36 4.34
2114 2209 1.006220 ATGACGCAGACTGCAACGA 60.006 52.632 26.32 7.96 45.36 3.85
2115 2210 1.284297 TGATGACGCAGACTGCAACG 61.284 55.000 26.32 13.14 45.36 4.10
2116 2211 0.441533 CTGATGACGCAGACTGCAAC 59.558 55.000 26.32 18.59 45.36 4.17
2117 2212 0.671472 CCTGATGACGCAGACTGCAA 60.671 55.000 26.32 12.10 45.36 4.08
2118 2213 1.079612 CCTGATGACGCAGACTGCA 60.080 57.895 26.32 8.34 45.36 4.41
2119 2214 2.459442 GCCTGATGACGCAGACTGC 61.459 63.158 17.84 17.84 40.69 4.40
2120 2215 0.805322 GAGCCTGATGACGCAGACTG 60.805 60.000 0.00 0.00 38.14 3.51
2121 2216 1.515020 GAGCCTGATGACGCAGACT 59.485 57.895 0.00 0.00 38.14 3.24
2122 2217 1.875813 CGAGCCTGATGACGCAGAC 60.876 63.158 0.00 0.00 38.14 3.51
2123 2218 2.491621 CGAGCCTGATGACGCAGA 59.508 61.111 0.00 0.00 38.14 4.26
2124 2219 2.584418 CCGAGCCTGATGACGCAG 60.584 66.667 0.00 0.00 35.66 5.18
2125 2220 4.147449 CCCGAGCCTGATGACGCA 62.147 66.667 0.00 0.00 0.00 5.24
2126 2221 3.157217 ATCCCGAGCCTGATGACGC 62.157 63.158 0.00 0.00 0.00 5.19
2127 2222 1.300465 CATCCCGAGCCTGATGACG 60.300 63.158 0.00 0.00 40.64 4.35
2128 2223 1.596477 GCATCCCGAGCCTGATGAC 60.596 63.158 3.80 0.00 40.64 3.06
2129 2224 1.752358 GAGCATCCCGAGCCTGATGA 61.752 60.000 3.80 0.00 40.64 2.92
2130 2225 1.301558 GAGCATCCCGAGCCTGATG 60.302 63.158 0.00 0.00 41.02 3.07
2131 2226 3.146182 GAGCATCCCGAGCCTGAT 58.854 61.111 0.00 0.00 0.00 2.90
2142 2237 2.124278 GGTTTCCCCCGGAGCATC 60.124 66.667 0.73 0.00 31.21 3.91
2143 2238 0.917333 TAAGGTTTCCCCCGGAGCAT 60.917 55.000 0.73 0.00 31.21 3.79
2144 2239 1.539372 TAAGGTTTCCCCCGGAGCA 60.539 57.895 0.73 0.00 31.21 4.26
2145 2240 1.223763 CTAAGGTTTCCCCCGGAGC 59.776 63.158 0.73 0.00 31.21 4.70
2146 2241 1.416772 GATCTAAGGTTTCCCCCGGAG 59.583 57.143 0.73 0.00 31.21 4.63
2147 2242 1.009183 AGATCTAAGGTTTCCCCCGGA 59.991 52.381 0.73 0.00 0.00 5.14
2148 2243 1.508256 AGATCTAAGGTTTCCCCCGG 58.492 55.000 0.00 0.00 0.00 5.73
2149 2244 2.421529 CCAAGATCTAAGGTTTCCCCCG 60.422 54.545 0.00 0.00 0.00 5.73
2150 2245 2.581246 ACCAAGATCTAAGGTTTCCCCC 59.419 50.000 12.73 0.00 29.58 5.40
2151 2246 3.523972 AGACCAAGATCTAAGGTTTCCCC 59.476 47.826 18.00 7.66 35.36 4.81
2152 2247 4.846168 AGACCAAGATCTAAGGTTTCCC 57.154 45.455 18.00 7.96 35.36 3.97
2153 2248 5.186942 GGAAGACCAAGATCTAAGGTTTCC 58.813 45.833 24.91 24.91 36.45 3.13
2154 2249 4.870991 CGGAAGACCAAGATCTAAGGTTTC 59.129 45.833 18.00 19.13 35.36 2.78
2155 2250 4.323562 CCGGAAGACCAAGATCTAAGGTTT 60.324 45.833 18.00 11.55 35.36 3.27
2156 2251 3.197983 CCGGAAGACCAAGATCTAAGGTT 59.802 47.826 18.00 6.28 35.36 3.50
2157 2252 2.766828 CCGGAAGACCAAGATCTAAGGT 59.233 50.000 17.21 17.21 38.63 3.50
2158 2253 3.031736 TCCGGAAGACCAAGATCTAAGG 58.968 50.000 0.00 11.55 35.59 2.69
2159 2254 4.557695 CGATCCGGAAGACCAAGATCTAAG 60.558 50.000 9.01 0.00 40.50 2.18
2160 2255 3.318275 CGATCCGGAAGACCAAGATCTAA 59.682 47.826 9.01 0.00 40.50 2.10
2161 2256 2.885266 CGATCCGGAAGACCAAGATCTA 59.115 50.000 9.01 0.00 40.50 1.98
2162 2257 1.683917 CGATCCGGAAGACCAAGATCT 59.316 52.381 9.01 0.00 40.50 2.75
2163 2258 2.141535 CGATCCGGAAGACCAAGATC 57.858 55.000 9.01 0.00 39.87 2.75
2176 2271 1.734477 GCCATCATCGTCCGATCCG 60.734 63.158 0.00 0.00 31.62 4.18
2177 2272 1.734477 CGCCATCATCGTCCGATCC 60.734 63.158 0.00 0.00 31.62 3.36
2178 2273 0.597637 AACGCCATCATCGTCCGATC 60.598 55.000 0.00 0.00 39.48 3.69
2179 2274 0.179084 AAACGCCATCATCGTCCGAT 60.179 50.000 0.00 0.00 39.48 4.18
2180 2275 0.390603 AAAACGCCATCATCGTCCGA 60.391 50.000 0.00 0.00 39.48 4.55
2181 2276 1.282817 TAAAACGCCATCATCGTCCG 58.717 50.000 0.00 0.00 39.48 4.79
2182 2277 2.096909 CGATAAAACGCCATCATCGTCC 60.097 50.000 0.00 0.00 39.48 4.79
2183 2278 3.155344 CGATAAAACGCCATCATCGTC 57.845 47.619 0.00 0.00 39.48 4.20
2194 2289 2.351726 CAGGAGGGAAAGCGATAAAACG 59.648 50.000 0.00 0.00 0.00 3.60
2195 2290 2.683362 CCAGGAGGGAAAGCGATAAAAC 59.317 50.000 0.00 0.00 40.01 2.43
2196 2291 2.999331 CCAGGAGGGAAAGCGATAAAA 58.001 47.619 0.00 0.00 40.01 1.52
2197 2292 2.710096 CCAGGAGGGAAAGCGATAAA 57.290 50.000 0.00 0.00 40.01 1.40
2209 2304 2.499303 AAAACGATGCCCCCAGGAGG 62.499 60.000 0.00 0.00 33.47 4.30
2210 2305 1.000896 AAAACGATGCCCCCAGGAG 60.001 57.895 0.00 0.00 33.47 3.69
2211 2306 1.304052 CAAAACGATGCCCCCAGGA 60.304 57.895 0.00 0.00 33.47 3.86
2212 2307 2.350458 CCAAAACGATGCCCCCAGG 61.350 63.158 0.00 0.00 0.00 4.45
2213 2308 1.304052 TCCAAAACGATGCCCCCAG 60.304 57.895 0.00 0.00 0.00 4.45
2214 2309 1.304052 CTCCAAAACGATGCCCCCA 60.304 57.895 0.00 0.00 0.00 4.96
2215 2310 0.034863 TACTCCAAAACGATGCCCCC 60.035 55.000 0.00 0.00 0.00 5.40
2216 2311 1.743394 CTTACTCCAAAACGATGCCCC 59.257 52.381 0.00 0.00 0.00 5.80
2217 2312 2.161609 CACTTACTCCAAAACGATGCCC 59.838 50.000 0.00 0.00 0.00 5.36
2218 2313 2.414161 GCACTTACTCCAAAACGATGCC 60.414 50.000 0.00 0.00 0.00 4.40
2219 2314 2.484264 AGCACTTACTCCAAAACGATGC 59.516 45.455 0.00 0.00 0.00 3.91
2220 2315 3.120199 CCAGCACTTACTCCAAAACGATG 60.120 47.826 0.00 0.00 0.00 3.84
2221 2316 3.074412 CCAGCACTTACTCCAAAACGAT 58.926 45.455 0.00 0.00 0.00 3.73
2222 2317 2.489971 CCAGCACTTACTCCAAAACGA 58.510 47.619 0.00 0.00 0.00 3.85
2223 2318 1.069227 GCCAGCACTTACTCCAAAACG 60.069 52.381 0.00 0.00 0.00 3.60
2224 2319 2.030805 CAGCCAGCACTTACTCCAAAAC 60.031 50.000 0.00 0.00 0.00 2.43
2225 2320 2.229792 CAGCCAGCACTTACTCCAAAA 58.770 47.619 0.00 0.00 0.00 2.44
2226 2321 1.545428 CCAGCCAGCACTTACTCCAAA 60.545 52.381 0.00 0.00 0.00 3.28
2227 2322 0.036732 CCAGCCAGCACTTACTCCAA 59.963 55.000 0.00 0.00 0.00 3.53
2228 2323 1.127567 ACCAGCCAGCACTTACTCCA 61.128 55.000 0.00 0.00 0.00 3.86
2229 2324 0.674895 CACCAGCCAGCACTTACTCC 60.675 60.000 0.00 0.00 0.00 3.85
2230 2325 0.674895 CCACCAGCCAGCACTTACTC 60.675 60.000 0.00 0.00 0.00 2.59
2231 2326 1.376466 CCACCAGCCAGCACTTACT 59.624 57.895 0.00 0.00 0.00 2.24
2232 2327 1.675641 CCCACCAGCCAGCACTTAC 60.676 63.158 0.00 0.00 0.00 2.34
2233 2328 1.207488 ATCCCACCAGCCAGCACTTA 61.207 55.000 0.00 0.00 0.00 2.24
2234 2329 2.541907 ATCCCACCAGCCAGCACTT 61.542 57.895 0.00 0.00 0.00 3.16
2235 2330 2.937689 ATCCCACCAGCCAGCACT 60.938 61.111 0.00 0.00 0.00 4.40
2236 2331 2.753043 CATCCCACCAGCCAGCAC 60.753 66.667 0.00 0.00 0.00 4.40
2237 2332 4.051167 CCATCCCACCAGCCAGCA 62.051 66.667 0.00 0.00 0.00 4.41
2238 2333 4.052518 ACCATCCCACCAGCCAGC 62.053 66.667 0.00 0.00 0.00 4.85
2239 2334 2.044650 CACCATCCCACCAGCCAG 60.045 66.667 0.00 0.00 0.00 4.85
2240 2335 3.660571 CCACCATCCCACCAGCCA 61.661 66.667 0.00 0.00 0.00 4.75
2241 2336 3.338250 TCCACCATCCCACCAGCC 61.338 66.667 0.00 0.00 0.00 4.85
2242 2337 2.273449 CTCCACCATCCCACCAGC 59.727 66.667 0.00 0.00 0.00 4.85
2243 2338 2.273449 GCTCCACCATCCCACCAG 59.727 66.667 0.00 0.00 0.00 4.00
2244 2339 3.716195 CGCTCCACCATCCCACCA 61.716 66.667 0.00 0.00 0.00 4.17
2245 2340 4.489771 CCGCTCCACCATCCCACC 62.490 72.222 0.00 0.00 0.00 4.61
2246 2341 3.717294 ACCGCTCCACCATCCCAC 61.717 66.667 0.00 0.00 0.00 4.61
2247 2342 3.716195 CACCGCTCCACCATCCCA 61.716 66.667 0.00 0.00 0.00 4.37
2249 2344 3.628646 AAGCACCGCTCCACCATCC 62.629 63.158 0.00 0.00 38.25 3.51
2250 2345 2.045926 AAGCACCGCTCCACCATC 60.046 61.111 0.00 0.00 38.25 3.51
2251 2346 2.045926 GAAGCACCGCTCCACCAT 60.046 61.111 0.00 0.00 38.25 3.55
2252 2347 2.803155 GATGAAGCACCGCTCCACCA 62.803 60.000 0.00 0.00 38.25 4.17
2253 2348 2.045926 ATGAAGCACCGCTCCACC 60.046 61.111 0.00 0.00 38.25 4.61
2254 2349 1.078848 AGATGAAGCACCGCTCCAC 60.079 57.895 0.00 0.00 38.25 4.02
2255 2350 1.219124 GAGATGAAGCACCGCTCCA 59.781 57.895 0.00 0.00 38.25 3.86
2256 2351 1.086634 GTGAGATGAAGCACCGCTCC 61.087 60.000 0.00 0.00 38.25 4.70
2257 2352 0.390340 TGTGAGATGAAGCACCGCTC 60.390 55.000 0.00 0.00 38.25 5.03
2258 2353 0.671781 GTGTGAGATGAAGCACCGCT 60.672 55.000 0.00 0.00 42.56 5.52
2259 2354 0.950555 TGTGTGAGATGAAGCACCGC 60.951 55.000 0.00 0.00 34.19 5.68
2260 2355 1.662629 GATGTGTGAGATGAAGCACCG 59.337 52.381 0.00 0.00 34.19 4.94
2261 2356 1.662629 CGATGTGTGAGATGAAGCACC 59.337 52.381 0.00 0.00 34.19 5.01
2262 2357 2.610433 TCGATGTGTGAGATGAAGCAC 58.390 47.619 0.00 0.00 35.63 4.40
2263 2358 3.119029 TCATCGATGTGTGAGATGAAGCA 60.119 43.478 24.09 0.00 45.14 3.91
2264 2359 3.451526 TCATCGATGTGTGAGATGAAGC 58.548 45.455 24.09 0.00 45.14 3.86
2267 2362 2.223572 CCGTCATCGATGTGTGAGATGA 60.224 50.000 24.09 0.03 45.69 2.92
2268 2363 2.122564 CCGTCATCGATGTGTGAGATG 58.877 52.381 24.09 9.64 42.11 2.90
2269 2364 1.536922 GCCGTCATCGATGTGTGAGAT 60.537 52.381 24.09 0.00 39.71 2.75
2270 2365 0.179137 GCCGTCATCGATGTGTGAGA 60.179 55.000 24.09 1.50 39.71 3.27
2271 2366 1.474648 CGCCGTCATCGATGTGTGAG 61.475 60.000 24.09 11.64 39.71 3.51
2272 2367 1.516169 CGCCGTCATCGATGTGTGA 60.516 57.895 24.09 3.62 39.71 3.58
2273 2368 2.516589 CCGCCGTCATCGATGTGTG 61.517 63.158 24.09 18.45 39.71 3.82
2274 2369 2.016393 ATCCGCCGTCATCGATGTGT 62.016 55.000 24.09 0.76 39.71 3.72
2275 2370 0.039527 TATCCGCCGTCATCGATGTG 60.040 55.000 24.09 17.24 39.71 3.21
2276 2371 0.888619 ATATCCGCCGTCATCGATGT 59.111 50.000 24.09 5.75 39.71 3.06
2277 2372 1.655597 CAATATCCGCCGTCATCGATG 59.344 52.381 19.61 19.61 39.71 3.84
2278 2373 1.404181 CCAATATCCGCCGTCATCGAT 60.404 52.381 0.00 0.00 39.71 3.59
2279 2374 0.038618 CCAATATCCGCCGTCATCGA 60.039 55.000 0.00 0.00 39.71 3.59
2280 2375 1.626654 GCCAATATCCGCCGTCATCG 61.627 60.000 0.00 0.00 0.00 3.84
2281 2376 1.626654 CGCCAATATCCGCCGTCATC 61.627 60.000 0.00 0.00 0.00 2.92
2282 2377 1.667830 CGCCAATATCCGCCGTCAT 60.668 57.895 0.00 0.00 0.00 3.06
2283 2378 2.279851 CGCCAATATCCGCCGTCA 60.280 61.111 0.00 0.00 0.00 4.35
2284 2379 3.041940 CCGCCAATATCCGCCGTC 61.042 66.667 0.00 0.00 0.00 4.79
2287 2382 2.672996 ATGCCGCCAATATCCGCC 60.673 61.111 0.00 0.00 0.00 6.13
2288 2383 2.562912 CATGCCGCCAATATCCGC 59.437 61.111 0.00 0.00 0.00 5.54
2289 2384 2.981560 GCCATGCCGCCAATATCCG 61.982 63.158 0.00 0.00 0.00 4.18
2290 2385 2.964978 GCCATGCCGCCAATATCC 59.035 61.111 0.00 0.00 0.00 2.59
2291 2386 2.562912 CGCCATGCCGCCAATATC 59.437 61.111 0.00 0.00 0.00 1.63
2301 2396 3.275338 GCCTCTACAGCGCCATGC 61.275 66.667 2.29 0.00 46.98 4.06
2302 2397 1.593750 GAGCCTCTACAGCGCCATG 60.594 63.158 2.29 0.00 34.64 3.66
2303 2398 2.818132 GAGCCTCTACAGCGCCAT 59.182 61.111 2.29 0.00 34.64 4.40
2304 2399 3.826754 CGAGCCTCTACAGCGCCA 61.827 66.667 2.29 0.00 34.64 5.69
2305 2400 4.577246 CCGAGCCTCTACAGCGCC 62.577 72.222 2.29 0.00 34.64 6.53
2307 2402 4.914420 CGCCGAGCCTCTACAGCG 62.914 72.222 1.90 1.90 37.39 5.18
2308 2403 3.759766 GACGCCGAGCCTCTACAGC 62.760 68.421 0.00 0.00 0.00 4.40
2309 2404 2.409651 GACGCCGAGCCTCTACAG 59.590 66.667 0.00 0.00 0.00 2.74
2310 2405 3.138798 GGACGCCGAGCCTCTACA 61.139 66.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.