Multiple sequence alignment - TraesCS3B01G093600

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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 TraesCS3B01G093600 chr3B 100.000 2527 0 0 1 2527 62531658 62529132 0.000000e+00 4667.0
1 TraesCS3B01G093600 chr3B 91.596 1059 83 5 806 1863 612314088 612315141 0.000000e+00 1458.0
2 TraesCS3B01G093600 chr3B 87.696 382 33 7 1867 2247 62522456 62522088 1.390000e-117 433.0
3 TraesCS3B01G093600 chr3B 83.562 73 8 4 1868 1936 81225426 81225354 5.840000e-07 65.8
4 TraesCS3B01G093600 chr7A 93.941 1865 107 5 1 1865 641404512 641402654 0.000000e+00 2813.0
5 TraesCS3B01G093600 chr4B 93.686 1869 111 6 1 1865 575618929 575617064 0.000000e+00 2791.0
6 TraesCS3B01G093600 chr4B 88.660 97 9 2 2067 2162 196476901 196476806 1.590000e-22 117.0
7 TraesCS3B01G093600 chr4D 93.450 1878 115 3 1 1877 379508835 379506965 0.000000e+00 2780.0
8 TraesCS3B01G093600 chr1A 92.652 1878 128 9 1 1876 520787031 520788900 0.000000e+00 2695.0
9 TraesCS3B01G093600 chr3A 92.759 1823 122 8 1 1820 170229597 170227782 0.000000e+00 2627.0
10 TraesCS3B01G093600 chr3A 87.952 83 10 0 2043 2125 341446141 341446223 5.750000e-17 99.0
11 TraesCS3B01G093600 chr5B 91.698 1867 134 8 1 1865 395331226 395333073 0.000000e+00 2569.0
12 TraesCS3B01G093600 chr2A 93.854 1025 59 4 1 1023 123740559 123739537 0.000000e+00 1541.0
13 TraesCS3B01G093600 chr1D 92.624 1071 76 3 806 1875 467476026 467474958 0.000000e+00 1537.0
14 TraesCS3B01G093600 chr1B 91.628 1075 82 6 806 1877 199668178 199667109 0.000000e+00 1480.0
15 TraesCS3B01G093600 chr1B 85.714 91 11 2 2040 2128 372549774 372549684 7.440000e-16 95.3
16 TraesCS3B01G093600 chr1B 96.429 56 2 0 2067 2122 184519387 184519332 2.680000e-15 93.5
17 TraesCS3B01G093600 chr1B 90.000 40 4 0 1867 1906 393254194 393254233 5.000000e-03 52.8
18 TraesCS3B01G093600 chr6A 92.653 245 18 0 260 504 161103946 161103702 1.110000e-93 353.0
19 TraesCS3B01G093600 chr6A 95.513 156 7 0 1 156 161104156 161104001 1.500000e-62 250.0
20 TraesCS3B01G093600 chr6B 88.889 99 8 2 1957 2055 356744077 356744172 4.420000e-23 119.0
21 TraesCS3B01G093600 chr2B 86.957 92 9 3 2040 2129 459883586 459883496 1.600000e-17 100.0
22 TraesCS3B01G093600 chr2B 91.667 60 3 2 1957 2016 293705360 293705303 5.790000e-12 82.4
23 TraesCS3B01G093600 chr7D 93.443 61 4 0 2067 2127 415075684 415075624 9.630000e-15 91.6
24 TraesCS3B01G093600 chr2D 93.443 61 4 0 2067 2127 121510403 121510343 9.630000e-15 91.6
25 TraesCS3B01G093600 chr2D 93.443 61 4 0 2067 2127 371171014 371170954 9.630000e-15 91.6
26 TraesCS3B01G093600 chr2D 100.000 28 0 0 2455 2482 514911952 514911925 5.000000e-03 52.8


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 TraesCS3B01G093600 chr3B 62529132 62531658 2526 True 4667 4667 100.000 1 2527 1 chr3B.!!$R2 2526
1 TraesCS3B01G093600 chr3B 612314088 612315141 1053 False 1458 1458 91.596 806 1863 1 chr3B.!!$F1 1057
2 TraesCS3B01G093600 chr7A 641402654 641404512 1858 True 2813 2813 93.941 1 1865 1 chr7A.!!$R1 1864
3 TraesCS3B01G093600 chr4B 575617064 575618929 1865 True 2791 2791 93.686 1 1865 1 chr4B.!!$R2 1864
4 TraesCS3B01G093600 chr4D 379506965 379508835 1870 True 2780 2780 93.450 1 1877 1 chr4D.!!$R1 1876
5 TraesCS3B01G093600 chr1A 520787031 520788900 1869 False 2695 2695 92.652 1 1876 1 chr1A.!!$F1 1875
6 TraesCS3B01G093600 chr3A 170227782 170229597 1815 True 2627 2627 92.759 1 1820 1 chr3A.!!$R1 1819
7 TraesCS3B01G093600 chr5B 395331226 395333073 1847 False 2569 2569 91.698 1 1865 1 chr5B.!!$F1 1864
8 TraesCS3B01G093600 chr2A 123739537 123740559 1022 True 1541 1541 93.854 1 1023 1 chr2A.!!$R1 1022
9 TraesCS3B01G093600 chr1D 467474958 467476026 1068 True 1537 1537 92.624 806 1875 1 chr1D.!!$R1 1069
10 TraesCS3B01G093600 chr1B 199667109 199668178 1069 True 1480 1480 91.628 806 1877 1 chr1B.!!$R2 1071

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
338 339 0.383949 TCTGCTTTGTTGGCCGAAAC 59.616 50.0 0.0 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 1993 0.032117 ATCTGATCGGGTGGACCAGA 60.032 55.0 0.62 0.88 44.05 3.86 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
88 89 3.443681 GCTGCTATAATGTGGGTGTGTTT 59.556 43.478 0.00 0.00 0.00 2.83
132 133 3.330701 TGAATCCTTGCTTCTAGGTTGGT 59.669 43.478 0.00 0.00 34.29 3.67
147 148 7.861629 TCTAGGTTGGTCTATGAAATGATGTT 58.138 34.615 0.00 0.00 0.00 2.71
157 158 8.668353 GTCTATGAAATGATGTTGTTTCTGCTA 58.332 33.333 0.00 0.00 35.80 3.49
228 229 7.513856 TCATAACTGCATTTAATGGGTAGCTA 58.486 34.615 7.08 0.00 0.00 3.32
235 236 6.152661 TGCATTTAATGGGTAGCTATTATGCC 59.847 38.462 24.20 13.72 31.77 4.40
263 264 2.489722 GCTCAAAGAAAGGTTGCCTAGG 59.510 50.000 3.67 3.67 31.13 3.02
304 305 7.775053 TTAAGAAATAGGCTGACACCAAATT 57.225 32.000 0.00 0.00 0.00 1.82
338 339 0.383949 TCTGCTTTGTTGGCCGAAAC 59.616 50.000 0.00 0.00 0.00 2.78
380 381 7.601856 TCTTGTTATGTTTAGCCATTCCAAAG 58.398 34.615 0.00 0.00 0.00 2.77
443 444 3.198200 AGCTGGCCATATTTTTGAATGCA 59.802 39.130 5.51 0.00 0.00 3.96
488 489 2.851263 ATGTAGTTTGCCGGAAGTCA 57.149 45.000 5.05 0.00 0.00 3.41
515 516 3.646162 ACCAATGGATAGGCATCGTCTTA 59.354 43.478 6.16 0.00 31.33 2.10
517 518 5.483937 ACCAATGGATAGGCATCGTCTTATA 59.516 40.000 6.16 0.00 31.33 0.98
518 519 6.156949 ACCAATGGATAGGCATCGTCTTATAT 59.843 38.462 6.16 0.00 31.33 0.86
594 596 4.003648 AGATCTTGGTTGGTGATTCGTTC 58.996 43.478 0.00 0.00 0.00 3.95
603 605 1.173043 GTGATTCGTTCCAATGGCCA 58.827 50.000 8.56 8.56 0.00 5.36
757 760 9.750125 GTTTTTGATTCCAGTCTTCATACTTTT 57.250 29.630 0.00 0.00 0.00 2.27
843 846 5.335583 GCCTGTGTGCTGTAACATTAATCAA 60.336 40.000 0.00 0.00 31.49 2.57
1059 1062 8.531146 TCTTCATTTGGATAATTTGTTTCCCTC 58.469 33.333 0.00 0.00 0.00 4.30
1068 1072 5.728637 AATTTGTTTCCCTCTGACCAATC 57.271 39.130 0.00 0.00 0.00 2.67
1071 1075 4.453480 TGTTTCCCTCTGACCAATCTTT 57.547 40.909 0.00 0.00 0.00 2.52
1072 1076 5.576563 TGTTTCCCTCTGACCAATCTTTA 57.423 39.130 0.00 0.00 0.00 1.85
1136 1146 1.080772 CGCTTCGTGTGCTACCTCA 60.081 57.895 0.00 0.00 0.00 3.86
1159 1169 2.508439 CGCGGCCACTATGTTCGT 60.508 61.111 2.24 0.00 0.00 3.85
1201 1211 3.374402 CTCGACGCCCTCCACTGT 61.374 66.667 0.00 0.00 0.00 3.55
1203 1213 3.991051 CGACGCCCTCCACTGTGT 61.991 66.667 7.08 0.00 0.00 3.72
1211 1221 1.662608 CTCCACTGTGTGCTCTCGT 59.337 57.895 7.08 0.00 31.34 4.18
1215 1225 0.031314 CACTGTGTGCTCTCGTCAGT 59.969 55.000 0.00 0.00 39.48 3.41
1397 1407 1.202405 CCACGGAGCATATTTTTGCCC 60.202 52.381 0.00 0.00 43.83 5.36
1413 1423 1.631388 TGCCCTGATTTCCTTCGGTTA 59.369 47.619 0.00 0.00 0.00 2.85
1432 1442 5.583457 CGGTTAGATTTCGTGGATTTAGGTT 59.417 40.000 0.00 0.00 0.00 3.50
1517 1527 0.319297 GGCTGCTTCTTTGTGGCTTG 60.319 55.000 0.00 0.00 0.00 4.01
1545 1555 7.977789 ACTTGAAATGTTTGTTTGGAAGTTT 57.022 28.000 0.00 0.00 0.00 2.66
1655 1667 4.340097 TGGTGGTATGGTCTCAATAGTACG 59.660 45.833 0.00 0.00 0.00 3.67
1789 1801 1.757118 TGGCCACATTTGGTTTTCGAA 59.243 42.857 0.00 0.00 45.98 3.71
1882 1894 7.978982 CATCTAGTGATGTTAAAAACTCAGGG 58.021 38.462 0.00 0.00 43.68 4.45
1883 1895 7.311092 TCTAGTGATGTTAAAAACTCAGGGA 57.689 36.000 0.00 0.00 0.00 4.20
1884 1896 7.159372 TCTAGTGATGTTAAAAACTCAGGGAC 58.841 38.462 0.00 0.00 0.00 4.46
1885 1897 5.941788 AGTGATGTTAAAAACTCAGGGACT 58.058 37.500 0.00 0.00 43.88 3.85
1886 1898 6.365520 AGTGATGTTAAAAACTCAGGGACTT 58.634 36.000 0.00 0.00 34.60 3.01
1887 1899 7.514721 AGTGATGTTAAAAACTCAGGGACTTA 58.485 34.615 0.00 0.00 34.60 2.24
1888 1900 7.661847 AGTGATGTTAAAAACTCAGGGACTTAG 59.338 37.037 0.00 0.00 34.60 2.18
1889 1901 7.444487 GTGATGTTAAAAACTCAGGGACTTAGT 59.556 37.037 0.00 0.00 45.89 2.24
1890 1902 7.444183 TGATGTTAAAAACTCAGGGACTTAGTG 59.556 37.037 0.00 0.00 42.75 2.74
1891 1903 6.059484 TGTTAAAAACTCAGGGACTTAGTGG 58.941 40.000 0.00 0.00 42.75 4.00
1892 1904 6.126710 TGTTAAAAACTCAGGGACTTAGTGGA 60.127 38.462 0.00 0.00 42.75 4.02
1893 1905 5.382664 AAAAACTCAGGGACTTAGTGGAA 57.617 39.130 0.00 0.00 42.75 3.53
1894 1906 5.584551 AAAACTCAGGGACTTAGTGGAAT 57.415 39.130 0.00 0.00 42.75 3.01
1895 1907 5.584551 AAACTCAGGGACTTAGTGGAATT 57.415 39.130 0.00 0.00 42.75 2.17
1896 1908 5.584551 AACTCAGGGACTTAGTGGAATTT 57.415 39.130 0.00 0.00 42.75 1.82
1897 1909 6.697641 AACTCAGGGACTTAGTGGAATTTA 57.302 37.500 0.00 0.00 42.75 1.40
1898 1910 6.301169 ACTCAGGGACTTAGTGGAATTTAG 57.699 41.667 0.00 0.00 41.88 1.85
1899 1911 6.023603 ACTCAGGGACTTAGTGGAATTTAGA 58.976 40.000 0.00 0.00 41.88 2.10
1900 1912 6.070710 ACTCAGGGACTTAGTGGAATTTAGAC 60.071 42.308 0.00 0.00 41.88 2.59
1901 1913 5.189145 TCAGGGACTTAGTGGAATTTAGACC 59.811 44.000 0.00 0.00 34.60 3.85
1902 1914 5.189934 CAGGGACTTAGTGGAATTTAGACCT 59.810 44.000 0.00 0.00 34.60 3.85
1903 1915 5.425862 AGGGACTTAGTGGAATTTAGACCTC 59.574 44.000 0.00 0.00 27.25 3.85
1904 1916 5.349809 GGACTTAGTGGAATTTAGACCTCG 58.650 45.833 0.00 0.00 0.00 4.63
1905 1917 4.756502 ACTTAGTGGAATTTAGACCTCGC 58.243 43.478 0.00 0.00 0.00 5.03
1906 1918 4.222145 ACTTAGTGGAATTTAGACCTCGCA 59.778 41.667 0.00 0.00 0.00 5.10
1907 1919 3.252974 AGTGGAATTTAGACCTCGCAG 57.747 47.619 0.00 0.00 0.00 5.18
1908 1920 2.832129 AGTGGAATTTAGACCTCGCAGA 59.168 45.455 0.00 0.00 0.00 4.26
1909 1921 3.260884 AGTGGAATTTAGACCTCGCAGAA 59.739 43.478 0.00 0.00 34.09 3.02
1910 1922 4.000988 GTGGAATTTAGACCTCGCAGAAA 58.999 43.478 0.00 0.00 34.09 2.52
1911 1923 4.000988 TGGAATTTAGACCTCGCAGAAAC 58.999 43.478 0.00 0.00 34.09 2.78
1912 1924 4.254492 GGAATTTAGACCTCGCAGAAACT 58.746 43.478 0.00 0.00 34.09 2.66
1913 1925 4.093556 GGAATTTAGACCTCGCAGAAACTG 59.906 45.833 0.00 0.00 34.09 3.16
1914 1926 2.743636 TTAGACCTCGCAGAAACTGG 57.256 50.000 0.00 0.00 34.09 4.00
1915 1927 1.919240 TAGACCTCGCAGAAACTGGA 58.081 50.000 0.00 0.00 34.09 3.86
1916 1928 1.270907 AGACCTCGCAGAAACTGGAT 58.729 50.000 0.00 0.00 34.09 3.41
1917 1929 1.066573 AGACCTCGCAGAAACTGGATG 60.067 52.381 0.00 0.00 34.09 3.51
1918 1930 0.036010 ACCTCGCAGAAACTGGATGG 60.036 55.000 0.00 0.00 34.09 3.51
1919 1931 0.745845 CCTCGCAGAAACTGGATGGG 60.746 60.000 0.00 0.00 34.09 4.00
1920 1932 0.745845 CTCGCAGAAACTGGATGGGG 60.746 60.000 0.00 0.00 34.09 4.96
1921 1933 2.409870 CGCAGAAACTGGATGGGGC 61.410 63.158 0.00 0.00 31.21 5.80
1922 1934 2.409870 GCAGAAACTGGATGGGGCG 61.410 63.158 0.00 0.00 31.21 6.13
1923 1935 1.299648 CAGAAACTGGATGGGGCGA 59.700 57.895 0.00 0.00 0.00 5.54
1924 1936 0.107017 CAGAAACTGGATGGGGCGAT 60.107 55.000 0.00 0.00 0.00 4.58
1925 1937 0.107017 AGAAACTGGATGGGGCGATG 60.107 55.000 0.00 0.00 0.00 3.84
1926 1938 1.728490 GAAACTGGATGGGGCGATGC 61.728 60.000 0.00 0.00 0.00 3.91
1927 1939 4.552365 ACTGGATGGGGCGATGCG 62.552 66.667 0.00 0.00 0.00 4.73
1931 1943 4.335647 GATGGGGCGATGCGGGAT 62.336 66.667 0.00 0.00 0.00 3.85
1932 1944 4.648626 ATGGGGCGATGCGGGATG 62.649 66.667 0.00 0.00 0.00 3.51
1935 1947 4.996434 GGGCGATGCGGGATGGAG 62.996 72.222 0.00 0.00 0.00 3.86
1936 1948 4.996434 GGCGATGCGGGATGGAGG 62.996 72.222 0.00 0.00 0.00 4.30
1937 1949 4.996434 GCGATGCGGGATGGAGGG 62.996 72.222 0.00 0.00 0.00 4.30
1938 1950 3.233980 CGATGCGGGATGGAGGGA 61.234 66.667 0.00 0.00 0.00 4.20
1939 1951 2.587247 CGATGCGGGATGGAGGGAT 61.587 63.158 0.00 0.00 0.00 3.85
1940 1952 1.298014 GATGCGGGATGGAGGGATC 59.702 63.158 0.00 0.00 0.00 3.36
1941 1953 2.190488 GATGCGGGATGGAGGGATCC 62.190 65.000 1.92 1.92 41.28 3.36
1942 1954 2.849162 GCGGGATGGAGGGATCCA 60.849 66.667 15.23 0.00 43.51 3.41
1956 1968 4.088164 TCCATGATGGAGGGGTGG 57.912 61.111 10.75 0.00 42.67 4.61
1957 1969 2.196776 CCATGATGGAGGGGTGGC 59.803 66.667 5.27 0.00 40.96 5.01
1958 1970 2.203252 CATGATGGAGGGGTGGCG 60.203 66.667 0.00 0.00 0.00 5.69
1959 1971 2.692368 ATGATGGAGGGGTGGCGT 60.692 61.111 0.00 0.00 0.00 5.68
1960 1972 2.308722 ATGATGGAGGGGTGGCGTT 61.309 57.895 0.00 0.00 0.00 4.84
1961 1973 1.863155 ATGATGGAGGGGTGGCGTTT 61.863 55.000 0.00 0.00 0.00 3.60
1962 1974 2.035626 ATGGAGGGGTGGCGTTTG 59.964 61.111 0.00 0.00 0.00 2.93
1963 1975 3.583882 ATGGAGGGGTGGCGTTTGG 62.584 63.158 0.00 0.00 0.00 3.28
1964 1976 4.280019 GGAGGGGTGGCGTTTGGT 62.280 66.667 0.00 0.00 0.00 3.67
1965 1977 2.203437 GAGGGGTGGCGTTTGGTT 60.203 61.111 0.00 0.00 0.00 3.67
1966 1978 2.203437 AGGGGTGGCGTTTGGTTC 60.203 61.111 0.00 0.00 0.00 3.62
1967 1979 3.666253 GGGGTGGCGTTTGGTTCG 61.666 66.667 0.00 0.00 0.00 3.95
1973 1985 4.379143 GCGTTTGGTTCGCGGGAC 62.379 66.667 6.13 5.54 43.94 4.46
1974 1986 2.663852 CGTTTGGTTCGCGGGACT 60.664 61.111 6.13 0.00 0.00 3.85
1975 1987 2.943653 GTTTGGTTCGCGGGACTG 59.056 61.111 6.13 0.00 0.00 3.51
1976 1988 2.281208 TTTGGTTCGCGGGACTGG 60.281 61.111 6.13 0.00 0.00 4.00
1977 1989 3.109592 TTTGGTTCGCGGGACTGGT 62.110 57.895 6.13 0.00 0.00 4.00
1978 1990 3.818121 TTGGTTCGCGGGACTGGTG 62.818 63.158 6.13 0.00 0.00 4.17
1980 1992 3.998672 GTTCGCGGGACTGGTGGA 61.999 66.667 6.13 0.00 0.00 4.02
1981 1993 3.000819 TTCGCGGGACTGGTGGAT 61.001 61.111 6.13 0.00 0.00 3.41
1982 1994 3.014085 TTCGCGGGACTGGTGGATC 62.014 63.158 6.13 0.00 0.00 3.36
1983 1995 3.461773 CGCGGGACTGGTGGATCT 61.462 66.667 0.00 0.00 0.00 2.75
1984 1996 2.187946 GCGGGACTGGTGGATCTG 59.812 66.667 0.00 0.00 0.00 2.90
1985 1997 2.903357 CGGGACTGGTGGATCTGG 59.097 66.667 0.00 0.00 0.00 3.86
1986 1998 1.990060 CGGGACTGGTGGATCTGGT 60.990 63.158 0.00 0.00 0.00 4.00
1987 1999 1.908483 GGGACTGGTGGATCTGGTC 59.092 63.158 0.00 0.00 0.00 4.02
1995 2007 3.971894 GGATCTGGTCCACCCGAT 58.028 61.111 1.02 2.50 46.96 4.18
1997 2009 4.807321 ATCTGGTCCACCCGATCA 57.193 55.556 0.00 0.00 35.42 2.92
2000 2012 4.807321 TGGTCCACCCGATCAGAT 57.193 55.556 0.00 0.00 35.15 2.90
2001 2013 2.516448 TGGTCCACCCGATCAGATC 58.484 57.895 0.00 0.00 35.15 2.75
2002 2014 1.048724 TGGTCCACCCGATCAGATCC 61.049 60.000 4.73 0.00 35.15 3.36
2003 2015 1.364171 GTCCACCCGATCAGATCCG 59.636 63.158 4.73 0.00 0.00 4.18
2004 2016 1.832608 TCCACCCGATCAGATCCGG 60.833 63.158 14.45 14.45 44.94 5.14
2047 2059 3.148279 GGTGAGGTCGCCGGAGAT 61.148 66.667 12.23 0.00 36.72 2.75
2048 2060 2.105128 GTGAGGTCGCCGGAGATG 59.895 66.667 12.23 0.00 0.00 2.90
2049 2061 3.147595 TGAGGTCGCCGGAGATGG 61.148 66.667 12.23 0.00 0.00 3.51
2057 2069 4.227134 CCGGAGATGGCAGGGACG 62.227 72.222 0.00 0.00 0.00 4.79
2058 2070 3.147595 CGGAGATGGCAGGGACGA 61.148 66.667 0.00 0.00 0.00 4.20
2059 2071 2.502492 CGGAGATGGCAGGGACGAT 61.502 63.158 0.00 0.00 0.00 3.73
2060 2072 1.070445 GGAGATGGCAGGGACGATG 59.930 63.158 0.00 0.00 0.00 3.84
2061 2073 1.070445 GAGATGGCAGGGACGATGG 59.930 63.158 0.00 0.00 0.00 3.51
2062 2074 2.111878 GATGGCAGGGACGATGGG 59.888 66.667 0.00 0.00 0.00 4.00
2063 2075 2.692368 ATGGCAGGGACGATGGGT 60.692 61.111 0.00 0.00 0.00 4.51
2064 2076 2.666596 GATGGCAGGGACGATGGGTC 62.667 65.000 0.00 0.00 45.31 4.46
2065 2077 3.083997 GGCAGGGACGATGGGTCT 61.084 66.667 0.00 0.00 45.35 3.85
2066 2078 2.187946 GCAGGGACGATGGGTCTG 59.812 66.667 0.00 0.00 45.35 3.51
2067 2079 2.903357 CAGGGACGATGGGTCTGG 59.097 66.667 0.00 0.00 45.35 3.86
2068 2080 3.083997 AGGGACGATGGGTCTGGC 61.084 66.667 0.00 0.00 45.35 4.85
2069 2081 4.176752 GGGACGATGGGTCTGGCC 62.177 72.222 0.00 0.00 45.35 5.36
2070 2082 4.530857 GGACGATGGGTCTGGCCG 62.531 72.222 0.00 0.00 45.35 6.13
2071 2083 4.530857 GACGATGGGTCTGGCCGG 62.531 72.222 4.71 4.71 42.62 6.13
2073 2085 3.550431 CGATGGGTCTGGCCGGAT 61.550 66.667 19.55 0.01 38.44 4.18
2074 2086 2.427753 GATGGGTCTGGCCGGATC 59.572 66.667 19.55 18.39 38.44 3.36
2075 2087 2.040464 ATGGGTCTGGCCGGATCT 60.040 61.111 24.24 2.38 38.44 2.75
2076 2088 2.105806 GATGGGTCTGGCCGGATCTC 62.106 65.000 24.24 14.86 38.44 2.75
2077 2089 3.917760 GGGTCTGGCCGGATCTCG 61.918 72.222 24.24 0.00 38.44 4.04
2078 2090 4.593864 GGTCTGGCCGGATCTCGC 62.594 72.222 19.55 3.78 37.59 5.03
2079 2091 4.593864 GTCTGGCCGGATCTCGCC 62.594 72.222 19.55 14.52 37.59 5.54
2136 2148 4.821589 CGAGGCTGGGCGAAGGAC 62.822 72.222 0.00 0.00 0.00 3.85
2137 2149 4.821589 GAGGCTGGGCGAAGGACG 62.822 72.222 0.00 0.00 45.66 4.79
2145 2157 2.956964 GCGAAGGACGGCGAGATG 60.957 66.667 16.62 0.00 42.83 2.90
2146 2158 2.798689 CGAAGGACGGCGAGATGA 59.201 61.111 16.62 0.00 38.46 2.92
2147 2159 1.586564 CGAAGGACGGCGAGATGAC 60.587 63.158 16.62 0.00 38.46 3.06
2155 2167 4.933064 GCGAGATGACGGCGGAGG 62.933 72.222 13.24 0.00 0.00 4.30
2156 2168 4.271816 CGAGATGACGGCGGAGGG 62.272 72.222 13.24 0.00 0.00 4.30
2157 2169 4.593864 GAGATGACGGCGGAGGGC 62.594 72.222 13.24 0.00 42.51 5.19
2159 2171 4.899239 GATGACGGCGGAGGGCAG 62.899 72.222 13.24 0.00 46.16 4.85
2209 2221 3.571119 CGAAGCTGGTTGCAGAGG 58.429 61.111 0.00 0.00 45.94 3.69
2210 2222 2.684843 CGAAGCTGGTTGCAGAGGC 61.685 63.158 0.00 0.00 45.94 4.70
2257 2269 2.903855 GCGATGGGCAGTCATGGG 60.904 66.667 0.00 0.00 42.87 4.00
2258 2270 2.903855 CGATGGGCAGTCATGGGC 60.904 66.667 0.00 0.00 0.00 5.36
2259 2271 2.903855 GATGGGCAGTCATGGGCG 60.904 66.667 0.00 0.00 0.00 6.13
2260 2272 4.511246 ATGGGCAGTCATGGGCGG 62.511 66.667 0.00 0.00 0.00 6.13
2265 2277 3.434319 CAGTCATGGGCGGCACAC 61.434 66.667 7.28 0.00 0.00 3.82
2278 2290 3.792047 CACACGCGGTCCATGCTG 61.792 66.667 12.47 0.00 0.00 4.41
2283 2295 4.864334 GCGGTCCATGCTGGGGAG 62.864 72.222 2.86 0.00 38.32 4.30
2284 2296 4.181010 CGGTCCATGCTGGGGAGG 62.181 72.222 2.86 0.00 38.32 4.30
2285 2297 4.512914 GGTCCATGCTGGGGAGGC 62.513 72.222 2.86 0.00 38.32 4.70
2286 2298 4.864334 GTCCATGCTGGGGAGGCG 62.864 72.222 2.86 0.00 38.32 5.52
2343 2355 2.356673 GGTGACCGGACCGACAAC 60.357 66.667 17.49 14.05 0.00 3.32
2344 2356 2.732094 GTGACCGGACCGACAACG 60.732 66.667 17.49 0.00 39.43 4.10
2369 2381 3.869272 GCAACTGGAGCGGCGATG 61.869 66.667 12.98 0.00 0.00 3.84
2370 2382 3.869272 CAACTGGAGCGGCGATGC 61.869 66.667 12.98 11.62 0.00 3.91
2400 2412 4.351938 CGACAGTGCCGACGGGAA 62.352 66.667 17.22 0.00 34.06 3.97
2401 2413 2.737376 GACAGTGCCGACGGGAAC 60.737 66.667 17.22 7.91 42.97 3.62
2501 2513 4.530857 GGGGAGTCGGCGGTGATG 62.531 72.222 7.21 0.00 0.00 3.07
2502 2514 3.458163 GGGAGTCGGCGGTGATGA 61.458 66.667 7.21 0.00 0.00 2.92
2503 2515 2.202756 GGAGTCGGCGGTGATGAC 60.203 66.667 7.21 0.00 0.00 3.06
2504 2516 2.579787 GAGTCGGCGGTGATGACG 60.580 66.667 7.21 0.00 43.33 4.35
2505 2517 3.338126 GAGTCGGCGGTGATGACGT 62.338 63.158 7.21 0.00 42.32 4.34
2506 2518 3.179265 GTCGGCGGTGATGACGTG 61.179 66.667 7.21 0.00 42.32 4.49
2507 2519 4.429212 TCGGCGGTGATGACGTGG 62.429 66.667 7.21 0.00 42.32 4.94
2510 2522 2.819595 GCGGTGATGACGTGGCAT 60.820 61.111 0.00 0.00 0.00 4.40
2511 2523 2.813179 GCGGTGATGACGTGGCATC 61.813 63.158 8.79 8.79 43.84 3.91
2512 2524 2.516589 CGGTGATGACGTGGCATCG 61.517 63.158 10.92 6.48 45.93 3.84
2513 2525 2.173669 GGTGATGACGTGGCATCGG 61.174 63.158 10.92 0.00 45.93 4.18
2514 2526 1.153647 GTGATGACGTGGCATCGGA 60.154 57.895 10.92 0.00 45.93 4.55
2515 2527 1.141665 TGATGACGTGGCATCGGAG 59.858 57.895 10.92 0.00 45.93 4.63
2516 2528 1.592669 GATGACGTGGCATCGGAGG 60.593 63.158 0.00 0.00 35.77 4.30
2517 2529 2.016393 GATGACGTGGCATCGGAGGA 62.016 60.000 0.00 0.00 35.77 3.71
2518 2530 1.402896 ATGACGTGGCATCGGAGGAT 61.403 55.000 12.66 0.00 34.94 3.24
2519 2531 1.144057 GACGTGGCATCGGAGGATT 59.856 57.895 12.66 0.00 34.94 3.01
2520 2532 1.153369 ACGTGGCATCGGAGGATTG 60.153 57.895 12.66 0.00 34.94 2.67
2521 2533 1.889105 CGTGGCATCGGAGGATTGG 60.889 63.158 0.00 0.00 0.00 3.16
2522 2534 2.189499 GTGGCATCGGAGGATTGGC 61.189 63.158 0.00 0.00 0.00 4.52
2523 2535 2.595754 GGCATCGGAGGATTGGCC 60.596 66.667 0.00 0.00 35.38 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.157840 ACAAAAACTCACAGAAACTCCACC 59.842 41.667 0.00 0.00 0.00 4.61
88 89 4.766891 CACCTTAAATGAAGAAGGAAGCCA 59.233 41.667 7.64 0.00 44.36 4.75
124 125 7.402054 ACAACATCATTTCATAGACCAACCTA 58.598 34.615 0.00 0.00 0.00 3.08
132 133 7.692460 AGCAGAAACAACATCATTTCATAGA 57.308 32.000 0.00 0.00 37.30 1.98
228 229 4.088634 TCTTTGAGCAAAGTGGGCATAAT 58.911 39.130 19.15 0.00 45.88 1.28
235 236 4.114794 CAACCTTTCTTTGAGCAAAGTGG 58.885 43.478 19.15 19.47 45.88 4.00
258 259 1.672881 GCACAAAGTAGCATGCCTAGG 59.327 52.381 15.66 3.67 31.71 3.02
263 264 5.046910 TCTTAAAGCACAAAGTAGCATGC 57.953 39.130 10.51 10.51 38.39 4.06
304 305 5.248477 ACAAAGCAGAAGTCCAGGATTACTA 59.752 40.000 0.00 0.00 0.00 1.82
364 365 7.223387 CAGATAAATGCTTTGGAATGGCTAAAC 59.777 37.037 0.00 0.00 0.00 2.01
443 444 7.255199 AGCATGATATCTATGTGAGGTTCAT 57.745 36.000 3.98 0.00 0.00 2.57
479 480 4.013728 TCCATTGGTTTTATGACTTCCGG 58.986 43.478 1.86 0.00 0.00 5.14
488 489 5.385198 ACGATGCCTATCCATTGGTTTTAT 58.615 37.500 1.86 0.00 32.05 1.40
515 516 7.285340 AGAAGGGTGAAAGGAACCTTAATAT 57.715 36.000 6.53 0.00 43.03 1.28
517 518 5.600669 AGAAGGGTGAAAGGAACCTTAAT 57.399 39.130 6.53 0.00 43.03 1.40
518 519 5.397553 AAGAAGGGTGAAAGGAACCTTAA 57.602 39.130 6.53 0.00 43.03 1.85
594 596 3.073062 AGCCTTACTATACTGGCCATTGG 59.927 47.826 5.51 0.00 45.94 3.16
637 639 3.328637 AGGGCAGGCAAAAAGAATTGAAT 59.671 39.130 0.00 0.00 31.84 2.57
642 644 2.049372 ACAAGGGCAGGCAAAAAGAAT 58.951 42.857 0.00 0.00 0.00 2.40
731 734 9.750125 AAAAGTATGAAGACTGGAATCAAAAAC 57.250 29.630 0.00 0.00 0.00 2.43
792 795 0.171455 ACATCTTCGTCTGGAGCGAC 59.829 55.000 0.00 0.00 38.14 5.19
843 846 1.851304 AAATGTTGGGTCCGATGCAT 58.149 45.000 0.00 0.00 0.00 3.96
911 914 7.107639 TCATGTACTGACGAAAATCATAGGA 57.892 36.000 0.00 0.00 0.00 2.94
915 918 7.615582 ACAATCATGTACTGACGAAAATCAT 57.384 32.000 0.00 0.00 38.24 2.45
1038 1041 7.093333 GGTCAGAGGGAAACAAATTATCCAAAT 60.093 37.037 0.00 0.00 34.82 2.32
1059 1062 7.552687 TGTAGGCAAGTAATAAAGATTGGTCAG 59.447 37.037 0.00 0.00 0.00 3.51
1068 1072 7.688372 CACAGATGTGTAGGCAAGTAATAAAG 58.312 38.462 4.77 0.00 40.96 1.85
1115 1119 1.666872 GGTAGCACACGAAGCGGTT 60.667 57.895 0.00 0.00 37.01 4.44
1136 1146 4.143333 ATAGTGGCCGCGCGACTT 62.143 61.111 34.63 17.34 44.67 3.01
1201 1211 2.340078 GCCACTGACGAGAGCACA 59.660 61.111 0.00 0.00 0.00 4.57
1203 1213 2.749110 GAACGCCACTGACGAGAGCA 62.749 60.000 0.00 0.00 0.00 4.26
1211 1221 2.892334 GCTTTGCGAACGCCACTGA 61.892 57.895 16.27 0.00 41.09 3.41
1215 1225 2.904866 AAGGCTTTGCGAACGCCA 60.905 55.556 21.84 2.60 46.14 5.69
1383 1393 4.718276 AGGAAATCAGGGCAAAAATATGCT 59.282 37.500 0.00 0.00 45.68 3.79
1388 1398 4.192429 CGAAGGAAATCAGGGCAAAAAT 57.808 40.909 0.00 0.00 0.00 1.82
1413 1423 7.519032 TTCAAAACCTAAATCCACGAAATCT 57.481 32.000 0.00 0.00 0.00 2.40
1432 1442 6.429385 GCATCCACAACCCATAATTTTTCAAA 59.571 34.615 0.00 0.00 0.00 2.69
1727 1739 0.889186 GAAGCCGCCTTTTCTCACCA 60.889 55.000 0.00 0.00 0.00 4.17
1877 1889 5.189145 GGTCTAAATTCCACTAAGTCCCTGA 59.811 44.000 0.00 0.00 0.00 3.86
1878 1890 5.189934 AGGTCTAAATTCCACTAAGTCCCTG 59.810 44.000 0.00 0.00 0.00 4.45
1879 1891 5.351405 AGGTCTAAATTCCACTAAGTCCCT 58.649 41.667 0.00 0.00 0.00 4.20
1880 1892 5.672503 GAGGTCTAAATTCCACTAAGTCCC 58.327 45.833 0.00 0.00 0.00 4.46
1881 1893 5.349809 CGAGGTCTAAATTCCACTAAGTCC 58.650 45.833 0.00 0.00 0.00 3.85
1882 1894 4.804665 GCGAGGTCTAAATTCCACTAAGTC 59.195 45.833 0.00 0.00 0.00 3.01
1883 1895 4.222145 TGCGAGGTCTAAATTCCACTAAGT 59.778 41.667 0.00 0.00 0.00 2.24
1884 1896 4.755411 TGCGAGGTCTAAATTCCACTAAG 58.245 43.478 0.00 0.00 0.00 2.18
1885 1897 4.464951 TCTGCGAGGTCTAAATTCCACTAA 59.535 41.667 0.00 0.00 0.00 2.24
1886 1898 4.021229 TCTGCGAGGTCTAAATTCCACTA 58.979 43.478 0.00 0.00 0.00 2.74
1887 1899 2.832129 TCTGCGAGGTCTAAATTCCACT 59.168 45.455 0.00 0.00 0.00 4.00
1888 1900 3.247006 TCTGCGAGGTCTAAATTCCAC 57.753 47.619 0.00 0.00 0.00 4.02
1889 1901 3.973206 TTCTGCGAGGTCTAAATTCCA 57.027 42.857 0.00 0.00 0.00 3.53
1890 1902 4.093556 CAGTTTCTGCGAGGTCTAAATTCC 59.906 45.833 0.00 0.00 0.00 3.01
1891 1903 4.093556 CCAGTTTCTGCGAGGTCTAAATTC 59.906 45.833 0.00 0.00 0.00 2.17
1892 1904 4.003648 CCAGTTTCTGCGAGGTCTAAATT 58.996 43.478 0.00 0.00 0.00 1.82
1893 1905 3.260884 TCCAGTTTCTGCGAGGTCTAAAT 59.739 43.478 0.00 0.00 0.00 1.40
1894 1906 2.631062 TCCAGTTTCTGCGAGGTCTAAA 59.369 45.455 0.00 0.00 0.00 1.85
1895 1907 2.244695 TCCAGTTTCTGCGAGGTCTAA 58.755 47.619 0.00 0.00 0.00 2.10
1896 1908 1.919240 TCCAGTTTCTGCGAGGTCTA 58.081 50.000 0.00 0.00 0.00 2.59
1897 1909 1.066573 CATCCAGTTTCTGCGAGGTCT 60.067 52.381 0.00 0.00 0.00 3.85
1898 1910 1.363744 CATCCAGTTTCTGCGAGGTC 58.636 55.000 0.00 0.00 0.00 3.85
1899 1911 0.036010 CCATCCAGTTTCTGCGAGGT 60.036 55.000 0.00 0.00 0.00 3.85
1900 1912 0.745845 CCCATCCAGTTTCTGCGAGG 60.746 60.000 0.00 0.00 0.00 4.63
1901 1913 0.745845 CCCCATCCAGTTTCTGCGAG 60.746 60.000 0.00 0.00 0.00 5.03
1902 1914 1.299648 CCCCATCCAGTTTCTGCGA 59.700 57.895 0.00 0.00 0.00 5.10
1903 1915 2.409870 GCCCCATCCAGTTTCTGCG 61.410 63.158 0.00 0.00 0.00 5.18
1904 1916 2.409870 CGCCCCATCCAGTTTCTGC 61.410 63.158 0.00 0.00 0.00 4.26
1905 1917 0.107017 ATCGCCCCATCCAGTTTCTG 60.107 55.000 0.00 0.00 0.00 3.02
1906 1918 0.107017 CATCGCCCCATCCAGTTTCT 60.107 55.000 0.00 0.00 0.00 2.52
1907 1919 1.728490 GCATCGCCCCATCCAGTTTC 61.728 60.000 0.00 0.00 0.00 2.78
1908 1920 1.754234 GCATCGCCCCATCCAGTTT 60.754 57.895 0.00 0.00 0.00 2.66
1909 1921 2.124151 GCATCGCCCCATCCAGTT 60.124 61.111 0.00 0.00 0.00 3.16
1910 1922 4.552365 CGCATCGCCCCATCCAGT 62.552 66.667 0.00 0.00 0.00 4.00
1914 1926 4.335647 ATCCCGCATCGCCCCATC 62.336 66.667 0.00 0.00 0.00 3.51
1915 1927 4.648626 CATCCCGCATCGCCCCAT 62.649 66.667 0.00 0.00 0.00 4.00
1918 1930 4.996434 CTCCATCCCGCATCGCCC 62.996 72.222 0.00 0.00 0.00 6.13
1919 1931 4.996434 CCTCCATCCCGCATCGCC 62.996 72.222 0.00 0.00 0.00 5.54
1920 1932 4.996434 CCCTCCATCCCGCATCGC 62.996 72.222 0.00 0.00 0.00 4.58
1921 1933 2.513026 GATCCCTCCATCCCGCATCG 62.513 65.000 0.00 0.00 0.00 3.84
1922 1934 1.298014 GATCCCTCCATCCCGCATC 59.702 63.158 0.00 0.00 0.00 3.91
1923 1935 2.227036 GGATCCCTCCATCCCGCAT 61.227 63.158 0.00 0.00 41.64 4.73
1924 1936 2.849162 GGATCCCTCCATCCCGCA 60.849 66.667 0.00 0.00 41.64 5.69
1925 1937 2.849162 TGGATCCCTCCATCCCGC 60.849 66.667 9.90 0.00 46.95 6.13
1939 1951 2.386100 GCCACCCCTCCATCATGGA 61.386 63.158 6.13 6.13 45.98 3.41
1940 1952 2.196776 GCCACCCCTCCATCATGG 59.803 66.667 0.00 0.00 39.43 3.66
1941 1953 2.203252 CGCCACCCCTCCATCATG 60.203 66.667 0.00 0.00 0.00 3.07
1942 1954 1.863155 AAACGCCACCCCTCCATCAT 61.863 55.000 0.00 0.00 0.00 2.45
1943 1955 2.534396 AAACGCCACCCCTCCATCA 61.534 57.895 0.00 0.00 0.00 3.07
1944 1956 2.046285 CAAACGCCACCCCTCCATC 61.046 63.158 0.00 0.00 0.00 3.51
1945 1957 2.035626 CAAACGCCACCCCTCCAT 59.964 61.111 0.00 0.00 0.00 3.41
1946 1958 4.278513 CCAAACGCCACCCCTCCA 62.279 66.667 0.00 0.00 0.00 3.86
1947 1959 3.802852 AACCAAACGCCACCCCTCC 62.803 63.158 0.00 0.00 0.00 4.30
1948 1960 2.203437 AACCAAACGCCACCCCTC 60.203 61.111 0.00 0.00 0.00 4.30
1949 1961 2.203437 GAACCAAACGCCACCCCT 60.203 61.111 0.00 0.00 0.00 4.79
1950 1962 3.666253 CGAACCAAACGCCACCCC 61.666 66.667 0.00 0.00 0.00 4.95
1957 1969 2.663852 AGTCCCGCGAACCAAACG 60.664 61.111 8.23 0.00 0.00 3.60
1958 1970 2.613506 CCAGTCCCGCGAACCAAAC 61.614 63.158 8.23 0.00 0.00 2.93
1959 1971 2.281208 CCAGTCCCGCGAACCAAA 60.281 61.111 8.23 0.00 0.00 3.28
1960 1972 3.552384 ACCAGTCCCGCGAACCAA 61.552 61.111 8.23 0.00 0.00 3.67
1961 1973 4.308458 CACCAGTCCCGCGAACCA 62.308 66.667 8.23 0.00 0.00 3.67
1963 1975 3.310860 ATCCACCAGTCCCGCGAAC 62.311 63.158 8.23 5.43 0.00 3.95
1964 1976 3.000819 ATCCACCAGTCCCGCGAA 61.001 61.111 8.23 0.00 0.00 4.70
1965 1977 3.458163 GATCCACCAGTCCCGCGA 61.458 66.667 8.23 0.00 0.00 5.87
1966 1978 3.461773 AGATCCACCAGTCCCGCG 61.462 66.667 0.00 0.00 0.00 6.46
1967 1979 2.187946 CAGATCCACCAGTCCCGC 59.812 66.667 0.00 0.00 0.00 6.13
1968 1980 1.961180 GACCAGATCCACCAGTCCCG 61.961 65.000 0.00 0.00 0.00 5.14
1969 1981 1.908483 GACCAGATCCACCAGTCCC 59.092 63.158 0.00 0.00 0.00 4.46
1978 1990 3.971894 ATCGGGTGGACCAGATCC 58.028 61.111 5.70 0.00 45.72 3.36
1981 1993 0.032117 ATCTGATCGGGTGGACCAGA 60.032 55.000 0.62 0.88 44.05 3.86
1982 1994 0.390860 GATCTGATCGGGTGGACCAG 59.609 60.000 1.26 0.00 40.22 4.00
1983 1995 1.048724 GGATCTGATCGGGTGGACCA 61.049 60.000 11.28 0.00 40.22 4.02
1984 1996 1.749033 GGATCTGATCGGGTGGACC 59.251 63.158 11.28 0.00 0.00 4.46
1985 1997 1.364171 CGGATCTGATCGGGTGGAC 59.636 63.158 15.25 0.00 0.00 4.02
1986 1998 1.832608 CCGGATCTGATCGGGTGGA 60.833 63.158 27.22 0.00 42.82 4.02
1987 1999 1.399744 TTCCGGATCTGATCGGGTGG 61.400 60.000 31.26 20.58 46.49 4.61
1988 2000 0.249489 GTTCCGGATCTGATCGGGTG 60.249 60.000 31.26 15.77 46.49 4.61
1989 2001 1.735376 CGTTCCGGATCTGATCGGGT 61.735 60.000 31.26 0.00 46.49 5.28
1991 2003 4.635925 CGTTCCGGATCTGATCGG 57.364 61.111 4.15 15.90 46.89 4.18
2019 2031 4.778415 CCTCACCGTCGTCGCTGG 62.778 72.222 0.00 1.55 35.54 4.85
2020 2032 3.948086 GACCTCACCGTCGTCGCTG 62.948 68.421 0.00 0.00 35.54 5.18
2021 2033 3.735029 GACCTCACCGTCGTCGCT 61.735 66.667 0.00 0.00 35.54 4.93
2030 2042 3.148279 ATCTCCGGCGACCTCACC 61.148 66.667 9.30 0.00 0.00 4.02
2031 2043 2.105128 CATCTCCGGCGACCTCAC 59.895 66.667 9.30 0.00 0.00 3.51
2032 2044 3.147595 CCATCTCCGGCGACCTCA 61.148 66.667 9.30 0.00 0.00 3.86
2033 2045 4.593864 GCCATCTCCGGCGACCTC 62.594 72.222 9.30 0.00 43.52 3.85
2040 2052 4.227134 CGTCCCTGCCATCTCCGG 62.227 72.222 0.00 0.00 0.00 5.14
2041 2053 2.502492 ATCGTCCCTGCCATCTCCG 61.502 63.158 0.00 0.00 0.00 4.63
2042 2054 1.070445 CATCGTCCCTGCCATCTCC 59.930 63.158 0.00 0.00 0.00 3.71
2043 2055 1.070445 CCATCGTCCCTGCCATCTC 59.930 63.158 0.00 0.00 0.00 2.75
2044 2056 2.446848 CCCATCGTCCCTGCCATCT 61.447 63.158 0.00 0.00 0.00 2.90
2045 2057 2.111878 CCCATCGTCCCTGCCATC 59.888 66.667 0.00 0.00 0.00 3.51
2046 2058 2.692368 ACCCATCGTCCCTGCCAT 60.692 61.111 0.00 0.00 0.00 4.40
2047 2059 3.399181 GACCCATCGTCCCTGCCA 61.399 66.667 0.00 0.00 35.23 4.92
2048 2060 3.083997 AGACCCATCGTCCCTGCC 61.084 66.667 0.00 0.00 43.08 4.85
2049 2061 2.187946 CAGACCCATCGTCCCTGC 59.812 66.667 0.00 0.00 43.08 4.85
2050 2062 2.903357 CCAGACCCATCGTCCCTG 59.097 66.667 0.00 0.00 43.08 4.45
2051 2063 3.083997 GCCAGACCCATCGTCCCT 61.084 66.667 0.00 0.00 43.08 4.20
2052 2064 4.176752 GGCCAGACCCATCGTCCC 62.177 72.222 0.00 0.00 43.08 4.46
2053 2065 4.530857 CGGCCAGACCCATCGTCC 62.531 72.222 2.24 0.00 43.08 4.79
2054 2066 4.530857 CCGGCCAGACCCATCGTC 62.531 72.222 2.24 0.00 42.32 4.20
2056 2068 3.521529 GATCCGGCCAGACCCATCG 62.522 68.421 2.24 0.00 33.26 3.84
2057 2069 2.105806 GAGATCCGGCCAGACCCATC 62.106 65.000 2.24 0.00 33.26 3.51
2058 2070 2.040464 AGATCCGGCCAGACCCAT 60.040 61.111 2.24 0.00 33.26 4.00
2059 2071 2.764128 GAGATCCGGCCAGACCCA 60.764 66.667 2.24 0.00 33.26 4.51
2060 2072 3.917760 CGAGATCCGGCCAGACCC 61.918 72.222 2.24 0.00 33.26 4.46
2061 2073 4.593864 GCGAGATCCGGCCAGACC 62.594 72.222 2.24 0.00 39.04 3.85
2119 2131 4.821589 GTCCTTCGCCCAGCCTCG 62.822 72.222 0.00 0.00 0.00 4.63
2120 2132 4.821589 CGTCCTTCGCCCAGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
2127 2139 4.208686 ATCTCGCCGTCCTTCGCC 62.209 66.667 0.00 0.00 38.35 5.54
2128 2140 2.956964 CATCTCGCCGTCCTTCGC 60.957 66.667 0.00 0.00 38.35 4.70
2129 2141 1.586564 GTCATCTCGCCGTCCTTCG 60.587 63.158 0.00 0.00 39.52 3.79
2130 2142 1.586564 CGTCATCTCGCCGTCCTTC 60.587 63.158 0.00 0.00 0.00 3.46
2131 2143 2.490217 CGTCATCTCGCCGTCCTT 59.510 61.111 0.00 0.00 0.00 3.36
2132 2144 3.518998 CCGTCATCTCGCCGTCCT 61.519 66.667 0.00 0.00 0.00 3.85
2137 2149 4.933064 CTCCGCCGTCATCTCGCC 62.933 72.222 0.00 0.00 0.00 5.54
2138 2150 4.933064 CCTCCGCCGTCATCTCGC 62.933 72.222 0.00 0.00 0.00 5.03
2139 2151 4.271816 CCCTCCGCCGTCATCTCG 62.272 72.222 0.00 0.00 0.00 4.04
2140 2152 4.593864 GCCCTCCGCCGTCATCTC 62.594 72.222 0.00 0.00 0.00 2.75
2142 2154 4.899239 CTGCCCTCCGCCGTCATC 62.899 72.222 0.00 0.00 36.24 2.92
2183 2195 4.530857 CCAGCTTCGCCCTACCGG 62.531 72.222 0.00 0.00 0.00 5.28
2184 2196 3.310860 AACCAGCTTCGCCCTACCG 62.311 63.158 0.00 0.00 0.00 4.02
2185 2197 1.745489 CAACCAGCTTCGCCCTACC 60.745 63.158 0.00 0.00 0.00 3.18
2186 2198 2.399356 GCAACCAGCTTCGCCCTAC 61.399 63.158 0.00 0.00 41.15 3.18
2187 2199 2.046314 GCAACCAGCTTCGCCCTA 60.046 61.111 0.00 0.00 41.15 3.53
2188 2200 4.269523 TGCAACCAGCTTCGCCCT 62.270 61.111 0.00 0.00 45.94 5.19
2189 2201 3.741476 CTGCAACCAGCTTCGCCC 61.741 66.667 0.00 0.00 45.94 6.13
2190 2202 2.669569 TCTGCAACCAGCTTCGCC 60.670 61.111 0.00 0.00 45.94 5.54
2191 2203 2.684843 CCTCTGCAACCAGCTTCGC 61.685 63.158 0.00 0.00 45.94 4.70
2192 2204 2.684843 GCCTCTGCAACCAGCTTCG 61.685 63.158 0.00 0.00 45.94 3.79
2193 2205 1.601759 TGCCTCTGCAACCAGCTTC 60.602 57.895 0.00 0.00 46.66 3.86
2194 2206 2.517414 TGCCTCTGCAACCAGCTT 59.483 55.556 0.00 0.00 46.66 3.74
2232 2244 4.802051 TGCCCATCGCTGCCCTTC 62.802 66.667 0.00 0.00 38.78 3.46
2233 2245 4.809496 CTGCCCATCGCTGCCCTT 62.809 66.667 0.00 0.00 38.78 3.95
2236 2248 4.783621 TGACTGCCCATCGCTGCC 62.784 66.667 0.00 0.00 39.93 4.85
2237 2249 2.515523 ATGACTGCCCATCGCTGC 60.516 61.111 0.00 0.00 39.93 5.25
2238 2250 2.184830 CCATGACTGCCCATCGCTG 61.185 63.158 0.00 0.00 41.91 5.18
2239 2251 2.191375 CCATGACTGCCCATCGCT 59.809 61.111 0.00 0.00 38.78 4.93
2240 2252 2.903855 CCCATGACTGCCCATCGC 60.904 66.667 0.00 0.00 38.31 4.58
2241 2253 2.903855 GCCCATGACTGCCCATCG 60.904 66.667 0.00 0.00 0.00 3.84
2242 2254 2.903855 CGCCCATGACTGCCCATC 60.904 66.667 0.00 0.00 0.00 3.51
2243 2255 4.511246 CCGCCCATGACTGCCCAT 62.511 66.667 0.00 0.00 0.00 4.00
2248 2260 3.434319 GTGTGCCGCCCATGACTG 61.434 66.667 0.00 0.00 0.00 3.51
2261 2273 3.792047 CAGCATGGACCGCGTGTG 61.792 66.667 4.92 0.00 0.00 3.82
2326 2338 2.356673 GTTGTCGGTCCGGTCACC 60.357 66.667 12.29 0.74 0.00 4.02
2327 2339 2.732094 CGTTGTCGGTCCGGTCAC 60.732 66.667 12.29 2.76 0.00 3.67
2352 2364 3.869272 CATCGCCGCTCCAGTTGC 61.869 66.667 0.00 0.00 0.00 4.17
2353 2365 3.869272 GCATCGCCGCTCCAGTTG 61.869 66.667 0.00 0.00 0.00 3.16
2383 2395 4.351938 TTCCCGTCGGCACTGTCG 62.352 66.667 5.50 0.00 0.00 4.35
2384 2396 2.737376 GTTCCCGTCGGCACTGTC 60.737 66.667 5.50 0.00 0.00 3.51
2385 2397 4.657824 CGTTCCCGTCGGCACTGT 62.658 66.667 5.50 0.00 0.00 3.55
2390 2402 4.814294 ATCTGCGTTCCCGTCGGC 62.814 66.667 5.50 0.00 36.15 5.54
2391 2403 2.885644 CATCTGCGTTCCCGTCGG 60.886 66.667 3.60 3.60 36.15 4.79
2392 2404 2.885644 CCATCTGCGTTCCCGTCG 60.886 66.667 0.00 0.00 36.15 5.12
2393 2405 3.195698 GCCATCTGCGTTCCCGTC 61.196 66.667 0.00 0.00 36.15 4.79
2484 2496 4.530857 CATCACCGCCGACTCCCC 62.531 72.222 0.00 0.00 0.00 4.81
2485 2497 3.458163 TCATCACCGCCGACTCCC 61.458 66.667 0.00 0.00 0.00 4.30
2486 2498 2.202756 GTCATCACCGCCGACTCC 60.203 66.667 0.00 0.00 0.00 3.85
2487 2499 2.579787 CGTCATCACCGCCGACTC 60.580 66.667 0.00 0.00 0.00 3.36
2488 2500 3.371063 ACGTCATCACCGCCGACT 61.371 61.111 0.00 0.00 0.00 4.18
2489 2501 3.179265 CACGTCATCACCGCCGAC 61.179 66.667 0.00 0.00 0.00 4.79
2490 2502 4.429212 CCACGTCATCACCGCCGA 62.429 66.667 0.00 0.00 0.00 5.54
2493 2505 2.813179 GATGCCACGTCATCACCGC 61.813 63.158 11.30 0.00 41.77 5.68
2494 2506 2.516589 CGATGCCACGTCATCACCG 61.517 63.158 15.22 0.16 42.15 4.94
2495 2507 2.173669 CCGATGCCACGTCATCACC 61.174 63.158 15.22 0.00 42.15 4.02
2496 2508 1.148157 CTCCGATGCCACGTCATCAC 61.148 60.000 15.22 0.00 42.15 3.06
2497 2509 1.141665 CTCCGATGCCACGTCATCA 59.858 57.895 15.22 1.42 42.15 3.07
2498 2510 1.592669 CCTCCGATGCCACGTCATC 60.593 63.158 7.08 7.08 39.47 2.92
2499 2511 1.402896 ATCCTCCGATGCCACGTCAT 61.403 55.000 0.00 0.00 0.00 3.06
2500 2512 1.613317 AATCCTCCGATGCCACGTCA 61.613 55.000 0.00 0.00 0.00 4.35
2501 2513 1.144057 AATCCTCCGATGCCACGTC 59.856 57.895 0.00 0.00 0.00 4.34
2502 2514 1.153369 CAATCCTCCGATGCCACGT 60.153 57.895 0.00 0.00 0.00 4.49
2503 2515 1.889105 CCAATCCTCCGATGCCACG 60.889 63.158 0.00 0.00 0.00 4.94
2504 2516 2.189499 GCCAATCCTCCGATGCCAC 61.189 63.158 0.00 0.00 0.00 5.01
2505 2517 2.192979 GCCAATCCTCCGATGCCA 59.807 61.111 0.00 0.00 0.00 4.92
2506 2518 2.595754 GGCCAATCCTCCGATGCC 60.596 66.667 0.00 0.00 32.22 4.40


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

AutoCloner maintained by Alex Coulton.