Multiple sequence alignment - TraesCS2D01G156500

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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 TraesCS2D01G156500 chr2D 100.000 3196 0 0 1 3196 99735059 99731864 0.000000e+00 5903.0
1 TraesCS2D01G156500 chr2D 93.182 88 6 0 1830 1917 420169400 420169487 2.950000e-26 130.0
2 TraesCS2D01G156500 chr2D 100.000 67 0 0 3578 3644 99731482 99731416 1.370000e-24 124.0
3 TraesCS2D01G156500 chr2B 93.874 1812 90 9 1 1808 150938630 150940424 0.000000e+00 2712.0
4 TraesCS2D01G156500 chr2B 91.460 808 44 15 147 939 5327416 5326619 0.000000e+00 1086.0
5 TraesCS2D01G156500 chr2B 91.688 794 47 10 157 938 633253600 633252814 0.000000e+00 1083.0
6 TraesCS2D01G156500 chr2B 86.203 790 68 30 2284 3054 150940958 150941725 0.000000e+00 817.0
7 TraesCS2D01G156500 chr2B 81.227 277 36 9 2008 2270 150940440 150940714 3.690000e-50 209.0
8 TraesCS2D01G156500 chr2A 93.902 1066 50 5 750 1815 99150592 99149542 0.000000e+00 1594.0
9 TraesCS2D01G156500 chr2A 95.926 761 26 2 1 761 99151476 99150721 0.000000e+00 1229.0
10 TraesCS2D01G156500 chr2A 93.852 732 36 4 1078 1809 99151615 99152337 0.000000e+00 1094.0
11 TraesCS2D01G156500 chr2A 89.870 849 51 13 2279 3120 99149184 99148364 0.000000e+00 1059.0
12 TraesCS2D01G156500 chr2A 80.986 284 35 10 2008 2275 99149533 99149253 1.330000e-49 207.0
13 TraesCS2D01G156500 chr2A 81.226 261 32 8 2008 2254 99152352 99152609 1.030000e-45 195.0
14 TraesCS2D01G156500 chr2A 93.333 60 2 2 3132 3190 99147999 99147941 1.800000e-13 87.9
15 TraesCS2D01G156500 chr7B 91.563 806 47 11 147 939 120370706 120369909 0.000000e+00 1092.0
16 TraesCS2D01G156500 chr7B 91.837 98 8 0 1822 1919 211795508 211795411 1.760000e-28 137.0
17 TraesCS2D01G156500 chr4B 91.364 799 46 9 153 939 515893046 515892259 0.000000e+00 1072.0
18 TraesCS2D01G156500 chr4B 90.370 810 53 17 147 939 48007662 48006861 0.000000e+00 1040.0
19 TraesCS2D01G156500 chr1B 89.357 451 30 5 501 939 634032122 634032566 5.320000e-153 551.0
20 TraesCS2D01G156500 chr1B 93.593 359 19 2 147 504 634026855 634027210 1.930000e-147 532.0
21 TraesCS2D01G156500 chrUn 91.990 387 28 1 153 539 37014457 37014840 1.150000e-149 540.0
22 TraesCS2D01G156500 chrUn 91.067 403 20 4 551 939 37014906 37015306 6.930000e-147 531.0
23 TraesCS2D01G156500 chrUn 91.594 345 25 1 1471 1815 477541466 477541126 1.180000e-129 473.0
24 TraesCS2D01G156500 chr7A 91.176 102 8 1 1819 1919 82204216 82204115 1.760000e-28 137.0
25 TraesCS2D01G156500 chr7A 89.691 97 10 0 1823 1919 250689107 250689011 1.370000e-24 124.0
26 TraesCS2D01G156500 chr5D 91.176 102 8 1 1823 1924 330393518 330393618 1.760000e-28 137.0
27 TraesCS2D01G156500 chr5B 91.176 102 8 1 1823 1924 383512935 383513035 1.760000e-28 137.0
28 TraesCS2D01G156500 chr5B 90.196 102 9 1 1823 1924 386391916 386392016 8.210000e-27 132.0
29 TraesCS2D01G156500 chr6D 91.579 95 8 0 1822 1916 437332695 437332601 8.210000e-27 132.0
30 TraesCS2D01G156500 chr7D 90.722 97 9 0 1823 1919 235577013 235576917 2.950000e-26 130.0
31 TraesCS2D01G156500 chr1D 88.350 103 8 2 1823 1921 324624128 324624230 1.780000e-23 121.0
32 TraesCS2D01G156500 chr1A 85.484 62 5 4 3135 3196 338513486 338513429 1.090000e-05 62.1


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 TraesCS2D01G156500 chr2D 99731416 99735059 3643 True 3013.50 5903 100.000000 1 3644 2 chr2D.!!$R1 3643
1 TraesCS2D01G156500 chr2B 150938630 150941725 3095 False 1246.00 2712 87.101333 1 3054 3 chr2B.!!$F1 3053
2 TraesCS2D01G156500 chr2B 5326619 5327416 797 True 1086.00 1086 91.460000 147 939 1 chr2B.!!$R1 792
3 TraesCS2D01G156500 chr2B 633252814 633253600 786 True 1083.00 1083 91.688000 157 938 1 chr2B.!!$R2 781
4 TraesCS2D01G156500 chr2A 99147941 99151476 3535 True 835.38 1594 90.803400 1 3190 5 chr2A.!!$R1 3189
5 TraesCS2D01G156500 chr2A 99151615 99152609 994 False 644.50 1094 87.539000 1078 2254 2 chr2A.!!$F1 1176
6 TraesCS2D01G156500 chr7B 120369909 120370706 797 True 1092.00 1092 91.563000 147 939 1 chr7B.!!$R1 792
7 TraesCS2D01G156500 chr4B 515892259 515893046 787 True 1072.00 1072 91.364000 153 939 1 chr4B.!!$R2 786
8 TraesCS2D01G156500 chr4B 48006861 48007662 801 True 1040.00 1040 90.370000 147 939 1 chr4B.!!$R1 792
9 TraesCS2D01G156500 chrUn 37014457 37015306 849 False 535.50 540 91.528500 153 939 2 chrUn.!!$F1 786

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
41 42 0.472471 AAACCCCGAGAAAGCACTGA 59.528 50.0 0.0 0.0 0.0 3.41 F
1546 1764 0.249322 ACGACGTGACAAGGGTTCTG 60.249 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1974 0.172578 TACATGCTGCGCTTAGTCGT 59.827 50.0 9.73 1.33 0.00 4.34 R
2915 3404 0.038599 TGCTGTTCCAGGCACATCAT 59.961 50.0 0.00 0.00 33.23 2.45 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
41 42 0.472471 AAACCCCGAGAAAGCACTGA 59.528 50.000 0.00 0.00 0.00 3.41
105 106 3.735029 GACTCCGACGCCGTCACT 61.735 66.667 18.40 0.00 32.09 3.41
106 107 3.264866 GACTCCGACGCCGTCACTT 62.265 63.158 18.40 0.00 32.09 3.16
403 404 1.806542 CAGTACAGCAACCAATTCGCT 59.193 47.619 0.00 0.00 36.10 4.93
808 1017 9.243637 GCACTGAACTTCAATTTTACAATGTAA 57.756 29.630 1.08 1.08 0.00 2.41
971 1182 9.601217 TTACTGCTTCATTTAATAGGTCTTCTC 57.399 33.333 0.00 0.00 0.00 2.87
997 1208 2.949644 GTTGGTAGCACTCTTTTGGTGT 59.050 45.455 0.00 0.00 37.07 4.16
1166 1378 4.386867 TCACTCATCACTCGGTATTTCC 57.613 45.455 0.00 0.00 0.00 3.13
1254 1466 7.347485 ACTTATCAGGTTAGTAGGCAAATACCT 59.653 37.037 0.00 0.00 44.31 3.08
1255 1467 6.576778 ATCAGGTTAGTAGGCAAATACCTT 57.423 37.500 0.00 0.00 41.50 3.50
1360 1578 0.610232 CAAGGGGAGGTTTGCCAGAG 60.610 60.000 0.00 0.00 36.32 3.35
1391 1609 3.737559 TGAAGGTATTGCCATCCTTGT 57.262 42.857 6.34 0.00 41.00 3.16
1546 1764 0.249322 ACGACGTGACAAGGGTTCTG 60.249 55.000 0.00 0.00 0.00 3.02
1552 1770 1.376037 GACAAGGGTTCTGGAGCGG 60.376 63.158 0.00 0.00 0.00 5.52
1581 1799 1.451067 GCTGCTGCTTCTCATTCTGT 58.549 50.000 8.53 0.00 36.03 3.41
1647 1865 2.738587 TTGGTGCCACTTCAGGTTAA 57.261 45.000 0.00 0.00 0.00 2.01
1649 1867 3.237268 TGGTGCCACTTCAGGTTAATT 57.763 42.857 0.00 0.00 0.00 1.40
1674 1892 8.848474 TTTGTTTCTTAACTTGCTATAGCTCT 57.152 30.769 24.61 9.45 37.26 4.09
1704 1922 7.457024 AAGAGTTTAGAGAGTAGAGACAACC 57.543 40.000 0.00 0.00 0.00 3.77
1705 1923 6.544650 AGAGTTTAGAGAGTAGAGACAACCA 58.455 40.000 0.00 0.00 0.00 3.67
1747 1965 5.130975 TGGAGCTCCATTATGTACATCTGTT 59.869 40.000 32.00 0.00 42.01 3.16
1756 1974 9.173021 CCATTATGTACATCTGTTAGGTCAAAA 57.827 33.333 12.68 0.00 0.00 2.44
1758 1976 6.721571 ATGTACATCTGTTAGGTCAAAACG 57.278 37.500 1.41 0.00 0.00 3.60
1765 1983 4.986659 TCTGTTAGGTCAAAACGACTAAGC 59.013 41.667 0.00 0.00 44.70 3.09
1787 2005 5.460571 CGCAGCATGTATCTGGTATAATG 57.539 43.478 0.00 0.00 39.31 1.90
1809 2027 6.426980 TGATGTCTGTCTACATTTCAATGC 57.573 37.500 0.00 0.00 40.17 3.56
1812 2030 3.125146 GTCTGTCTACATTTCAATGCGCA 59.875 43.478 14.96 14.96 40.04 6.09
1815 2033 2.420022 GTCTACATTTCAATGCGCACCT 59.580 45.455 14.90 0.00 40.04 4.00
1816 2034 3.621268 GTCTACATTTCAATGCGCACCTA 59.379 43.478 14.90 0.00 40.04 3.08
1817 2035 4.094294 GTCTACATTTCAATGCGCACCTAA 59.906 41.667 14.90 3.76 40.04 2.69
1818 2036 4.881273 TCTACATTTCAATGCGCACCTAAT 59.119 37.500 14.90 7.67 40.04 1.73
1819 2037 4.454728 ACATTTCAATGCGCACCTAATT 57.545 36.364 14.90 0.00 40.04 1.40
1820 2038 5.574891 ACATTTCAATGCGCACCTAATTA 57.425 34.783 14.90 0.00 40.04 1.40
1821 2039 5.339990 ACATTTCAATGCGCACCTAATTAC 58.660 37.500 14.90 0.00 40.04 1.89
1823 2041 6.317642 ACATTTCAATGCGCACCTAATTACTA 59.682 34.615 14.90 0.00 40.04 1.82
1824 2042 5.728351 TTCAATGCGCACCTAATTACTAC 57.272 39.130 14.90 0.00 0.00 2.73
1825 2043 5.018539 TCAATGCGCACCTAATTACTACT 57.981 39.130 14.90 0.00 0.00 2.57
1826 2044 5.047847 TCAATGCGCACCTAATTACTACTC 58.952 41.667 14.90 0.00 0.00 2.59
1827 2045 4.939052 ATGCGCACCTAATTACTACTCT 57.061 40.909 14.90 0.00 0.00 3.24
1828 2046 4.303086 TGCGCACCTAATTACTACTCTC 57.697 45.455 5.66 0.00 0.00 3.20
1829 2047 3.952323 TGCGCACCTAATTACTACTCTCT 59.048 43.478 5.66 0.00 0.00 3.10
1830 2048 4.036498 TGCGCACCTAATTACTACTCTCTC 59.964 45.833 5.66 0.00 0.00 3.20
1831 2049 4.557097 GCGCACCTAATTACTACTCTCTCC 60.557 50.000 0.30 0.00 0.00 3.71
1832 2050 4.579340 CGCACCTAATTACTACTCTCTCCA 59.421 45.833 0.00 0.00 0.00 3.86
1833 2051 5.241949 CGCACCTAATTACTACTCTCTCCAT 59.758 44.000 0.00 0.00 0.00 3.41
1834 2052 6.568844 CGCACCTAATTACTACTCTCTCCATC 60.569 46.154 0.00 0.00 0.00 3.51
1835 2053 6.294843 GCACCTAATTACTACTCTCTCCATCC 60.295 46.154 0.00 0.00 0.00 3.51
1836 2054 6.209788 CACCTAATTACTACTCTCTCCATCCC 59.790 46.154 0.00 0.00 0.00 3.85
1837 2055 6.125860 ACCTAATTACTACTCTCTCCATCCCA 60.126 42.308 0.00 0.00 0.00 4.37
1838 2056 6.957020 CCTAATTACTACTCTCTCCATCCCAT 59.043 42.308 0.00 0.00 0.00 4.00
1839 2057 8.116669 CCTAATTACTACTCTCTCCATCCCATA 58.883 40.741 0.00 0.00 0.00 2.74
1840 2058 9.535170 CTAATTACTACTCTCTCCATCCCATAA 57.465 37.037 0.00 0.00 0.00 1.90
1841 2059 8.980832 AATTACTACTCTCTCCATCCCATAAT 57.019 34.615 0.00 0.00 0.00 1.28
1846 2064 9.707957 ACTACTCTCTCCATCCCATAATATAAG 57.292 37.037 0.00 0.00 0.00 1.73
1847 2065 9.928618 CTACTCTCTCCATCCCATAATATAAGA 57.071 37.037 0.00 0.00 0.00 2.10
1849 2067 9.432982 ACTCTCTCCATCCCATAATATAAGATC 57.567 37.037 0.00 0.00 0.00 2.75
1850 2068 9.659135 CTCTCTCCATCCCATAATATAAGATCT 57.341 37.037 0.00 0.00 0.00 2.75
1873 2091 9.832445 ATCTTATTACATCCAAAATACTCACGT 57.168 29.630 0.00 0.00 0.00 4.49
1878 2096 6.677781 ACATCCAAAATACTCACGTATTGG 57.322 37.500 0.00 0.00 43.65 3.16
1879 2097 6.411376 ACATCCAAAATACTCACGTATTGGA 58.589 36.000 7.43 7.43 43.65 3.53
1880 2098 7.054124 ACATCCAAAATACTCACGTATTGGAT 58.946 34.615 11.08 11.08 46.50 3.41
1881 2099 6.918892 TCCAAAATACTCACGTATTGGATG 57.081 37.500 1.12 3.02 43.65 3.51
1882 2100 6.411376 TCCAAAATACTCACGTATTGGATGT 58.589 36.000 1.12 0.00 43.65 3.06
1883 2101 7.557724 TCCAAAATACTCACGTATTGGATGTA 58.442 34.615 1.12 0.00 43.65 2.29
1884 2102 8.041919 TCCAAAATACTCACGTATTGGATGTAA 58.958 33.333 1.12 0.00 43.65 2.41
1885 2103 8.836413 CCAAAATACTCACGTATTGGATGTAAT 58.164 33.333 0.00 0.00 43.65 1.89
1892 2110 8.861086 ACTCACGTATTGGATGTAATAAGATCT 58.139 33.333 0.00 0.00 0.00 2.75
1893 2111 9.698309 CTCACGTATTGGATGTAATAAGATCTT 57.302 33.333 13.56 13.56 0.00 2.40
1912 2130 9.524903 AAGATCTTATATTATGGGATGGATGGA 57.475 33.333 6.06 0.00 0.00 3.41
1913 2131 9.168553 AGATCTTATATTATGGGATGGATGGAG 57.831 37.037 0.00 0.00 0.00 3.86
1914 2132 8.882704 ATCTTATATTATGGGATGGATGGAGT 57.117 34.615 0.00 0.00 0.00 3.85
1915 2133 9.973880 ATCTTATATTATGGGATGGATGGAGTA 57.026 33.333 0.00 0.00 0.00 2.59
1916 2134 9.213777 TCTTATATTATGGGATGGATGGAGTAC 57.786 37.037 0.00 0.00 0.00 2.73
1917 2135 8.925447 TTATATTATGGGATGGATGGAGTACA 57.075 34.615 0.00 0.00 0.00 2.90
1918 2136 9.519488 TTATATTATGGGATGGATGGAGTACAT 57.481 33.333 0.00 0.00 44.18 2.29
1930 2148 3.291584 TGGAGTACATCTCTAGCTGTGG 58.708 50.000 0.00 0.00 42.40 4.17
1931 2149 3.053619 TGGAGTACATCTCTAGCTGTGGA 60.054 47.826 0.00 0.00 42.40 4.02
1932 2150 4.148838 GGAGTACATCTCTAGCTGTGGAT 58.851 47.826 0.00 0.00 42.40 3.41
1933 2151 4.022416 GGAGTACATCTCTAGCTGTGGATG 60.022 50.000 17.20 17.20 42.40 3.51
1934 2152 4.541705 AGTACATCTCTAGCTGTGGATGT 58.458 43.478 23.44 23.44 46.67 3.06
1935 2153 5.696030 AGTACATCTCTAGCTGTGGATGTA 58.304 41.667 22.06 22.06 44.36 2.29
1936 2154 6.129874 AGTACATCTCTAGCTGTGGATGTAA 58.870 40.000 24.93 14.54 46.33 2.41
1937 2155 5.939764 ACATCTCTAGCTGTGGATGTAAA 57.060 39.130 20.68 0.00 44.36 2.01
1938 2156 5.911752 ACATCTCTAGCTGTGGATGTAAAG 58.088 41.667 20.68 0.00 44.36 1.85
1939 2157 5.423610 ACATCTCTAGCTGTGGATGTAAAGT 59.576 40.000 20.68 4.62 44.36 2.66
1940 2158 5.584253 TCTCTAGCTGTGGATGTAAAGTC 57.416 43.478 0.00 0.00 0.00 3.01
1941 2159 5.265191 TCTCTAGCTGTGGATGTAAAGTCT 58.735 41.667 0.00 0.00 0.00 3.24
1942 2160 5.358442 TCTCTAGCTGTGGATGTAAAGTCTC 59.642 44.000 0.00 0.00 0.00 3.36
1943 2161 3.618690 AGCTGTGGATGTAAAGTCTCC 57.381 47.619 0.00 0.00 0.00 3.71
1944 2162 2.906389 AGCTGTGGATGTAAAGTCTCCA 59.094 45.455 0.00 0.00 36.73 3.86
1945 2163 3.521126 AGCTGTGGATGTAAAGTCTCCAT 59.479 43.478 0.00 0.00 40.96 3.41
1946 2164 4.018960 AGCTGTGGATGTAAAGTCTCCATT 60.019 41.667 0.00 0.00 40.96 3.16
1947 2165 5.189736 AGCTGTGGATGTAAAGTCTCCATTA 59.810 40.000 0.00 0.00 40.96 1.90
1948 2166 6.058183 GCTGTGGATGTAAAGTCTCCATTAT 58.942 40.000 0.00 0.00 40.96 1.28
1949 2167 6.543831 GCTGTGGATGTAAAGTCTCCATTATT 59.456 38.462 0.00 0.00 40.96 1.40
1950 2168 7.467811 GCTGTGGATGTAAAGTCTCCATTATTG 60.468 40.741 0.00 0.00 40.96 1.90
1951 2169 7.629157 TGTGGATGTAAAGTCTCCATTATTGA 58.371 34.615 0.00 0.00 40.96 2.57
1952 2170 8.106462 TGTGGATGTAAAGTCTCCATTATTGAA 58.894 33.333 0.00 0.00 40.96 2.69
1953 2171 8.956426 GTGGATGTAAAGTCTCCATTATTGAAA 58.044 33.333 0.00 0.00 40.96 2.69
1954 2172 9.527157 TGGATGTAAAGTCTCCATTATTGAAAA 57.473 29.630 0.00 0.00 34.17 2.29
1987 2205 7.906199 AGGTCTAATTACAACATCTCTAGCT 57.094 36.000 0.00 0.00 0.00 3.32
1988 2206 7.721402 AGGTCTAATTACAACATCTCTAGCTG 58.279 38.462 0.00 0.00 0.00 4.24
1989 2207 7.343316 AGGTCTAATTACAACATCTCTAGCTGT 59.657 37.037 0.00 0.00 0.00 4.40
1990 2208 7.982354 GGTCTAATTACAACATCTCTAGCTGTT 59.018 37.037 0.00 0.00 35.06 3.16
1995 2213 9.726438 AATTACAACATCTCTAGCTGTTACTTT 57.274 29.630 0.00 0.00 33.23 2.66
1996 2214 8.758633 TTACAACATCTCTAGCTGTTACTTTC 57.241 34.615 0.00 0.00 33.23 2.62
1997 2215 6.759272 ACAACATCTCTAGCTGTTACTTTCA 58.241 36.000 0.00 0.00 33.23 2.69
1998 2216 7.217200 ACAACATCTCTAGCTGTTACTTTCAA 58.783 34.615 0.00 0.00 33.23 2.69
1999 2217 7.880195 ACAACATCTCTAGCTGTTACTTTCAAT 59.120 33.333 0.00 0.00 33.23 2.57
2000 2218 9.371136 CAACATCTCTAGCTGTTACTTTCAATA 57.629 33.333 0.00 0.00 33.23 1.90
2039 2257 4.507710 TGCTTTACTGCTTATCTGGTCAG 58.492 43.478 0.00 0.00 0.00 3.51
2048 2266 8.427902 ACTGCTTATCTGGTCAGATATTCATA 57.572 34.615 18.07 5.64 46.38 2.15
2085 2303 7.778185 ACTATAGTCAGGATTACATACCACC 57.222 40.000 0.00 0.00 0.00 4.61
2086 2304 5.723672 ATAGTCAGGATTACATACCACCG 57.276 43.478 0.00 0.00 0.00 4.94
2087 2305 3.638860 AGTCAGGATTACATACCACCGA 58.361 45.455 0.00 0.00 0.00 4.69
2088 2306 4.223953 AGTCAGGATTACATACCACCGAT 58.776 43.478 0.00 0.00 0.00 4.18
2089 2307 5.391256 AGTCAGGATTACATACCACCGATA 58.609 41.667 0.00 0.00 0.00 2.92
2090 2308 5.243283 AGTCAGGATTACATACCACCGATAC 59.757 44.000 0.00 0.00 0.00 2.24
2091 2309 4.216902 TCAGGATTACATACCACCGATACG 59.783 45.833 0.00 0.00 0.00 3.06
2188 2427 2.857748 GCTGTGCAACCAACAGTTAAAC 59.142 45.455 5.55 0.00 36.18 2.01
2189 2428 3.428862 GCTGTGCAACCAACAGTTAAACT 60.429 43.478 5.55 0.00 36.18 2.66
2209 2448 5.480642 ACTGACTCAGTTCTGAATGTCAT 57.519 39.130 18.38 10.54 42.59 3.06
2217 2456 5.821995 TCAGTTCTGAATGTCATGTCAACAA 59.178 36.000 0.00 0.00 0.00 2.83
2219 2458 7.013559 TCAGTTCTGAATGTCATGTCAACAATT 59.986 33.333 0.00 0.00 0.00 2.32
2224 2463 9.628746 TCTGAATGTCATGTCAACAATTAATTG 57.371 29.630 23.60 23.60 43.26 2.32
2225 2464 8.760103 TGAATGTCATGTCAACAATTAATTGG 57.240 30.769 27.43 13.86 41.96 3.16
2226 2465 8.366401 TGAATGTCATGTCAACAATTAATTGGT 58.634 29.630 27.43 21.21 41.96 3.67
2232 2471 9.775854 TCATGTCAACAATTAATTGGTTCAATT 57.224 25.926 27.43 12.06 44.74 2.32
2254 2493 8.531146 CAATTTGGGATATTTTACTGTCAGGTT 58.469 33.333 4.53 0.00 0.00 3.50
2270 2509 7.106439 TGTCAGGTTTATTCAAGAGCAAAAA 57.894 32.000 0.00 0.00 0.00 1.94
2299 2768 5.987098 AGTATCTCACATCTTGCTTCATGT 58.013 37.500 0.00 0.00 33.29 3.21
2301 2770 5.562506 ATCTCACATCTTGCTTCATGTTG 57.437 39.130 0.00 0.00 30.48 3.33
2303 2772 3.151554 TCACATCTTGCTTCATGTTGCT 58.848 40.909 12.28 0.00 30.48 3.91
2304 2773 3.057806 TCACATCTTGCTTCATGTTGCTG 60.058 43.478 12.28 6.31 30.48 4.41
2324 2793 4.502259 GCTGTGTAGGCTGTCATTATAGCT 60.502 45.833 0.00 0.00 39.63 3.32
2351 2820 1.476085 TGCAATCCCAAATGGCTAACG 59.524 47.619 0.00 0.00 0.00 3.18
2379 2848 2.730094 CAACCCTGGCAAGCACAC 59.270 61.111 0.00 0.00 0.00 3.82
2414 2883 1.679139 TGTGCCTCAAGGACAACAAG 58.321 50.000 0.00 0.00 37.39 3.16
2423 2892 1.140312 AGGACAACAAGGGAAGCTCA 58.860 50.000 0.00 0.00 0.00 4.26
2456 2925 0.034896 AAGTGGCGAATGTCCGAACT 59.965 50.000 0.00 0.00 32.10 3.01
2480 2949 0.472471 TGGCCATCGGGATAAAGGTC 59.528 55.000 0.00 0.00 35.59 3.85
2497 2970 5.638530 AAGGTCACCTTTCTTTCTTCTCT 57.361 39.130 2.03 0.00 41.69 3.10
2498 2971 5.222079 AGGTCACCTTTCTTTCTTCTCTC 57.778 43.478 0.00 0.00 0.00 3.20
2499 2972 4.656112 AGGTCACCTTTCTTTCTTCTCTCA 59.344 41.667 0.00 0.00 0.00 3.27
2527 3000 2.432510 GCAGTGCCCTATACTGTCTCTT 59.567 50.000 2.85 0.00 45.60 2.85
2598 3071 8.743085 ACAGCATAATCAATAAGACTGTTGAT 57.257 30.769 9.44 9.44 43.11 2.57
2648 3121 5.296780 CAGTGGCCGATGAACAGTAAATTAT 59.703 40.000 0.00 0.00 0.00 1.28
2669 3143 0.546598 CCCCATTCCCAGTCCAGTAC 59.453 60.000 0.00 0.00 0.00 2.73
2676 3150 3.699025 TCCCAGTCCAGTACCATGATA 57.301 47.619 0.00 0.00 0.00 2.15
2725 3200 7.151976 TCAACATTACAAGAACATCTCGAAGA 58.848 34.615 0.00 0.00 0.00 2.87
2762 3238 1.902432 CGGGGATACGGGAGAGGTC 60.902 68.421 0.00 0.00 37.60 3.85
2800 3278 2.482336 TGTTGTCGAATTGTAGCGCATT 59.518 40.909 11.47 0.00 0.00 3.56
2801 3279 2.804421 TGTCGAATTGTAGCGCATTG 57.196 45.000 11.47 0.00 0.00 2.82
2853 3337 3.005050 TTGCTGGCAAAACTCATGAAGAG 59.995 43.478 5.47 0.00 40.52 2.85
2864 3348 3.529533 CTCATGAAGAGTAGGCTTGTGG 58.470 50.000 0.00 0.00 39.62 4.17
2865 3349 2.012673 CATGAAGAGTAGGCTTGTGGC 58.987 52.381 0.00 0.00 40.90 5.01
2913 3402 1.305201 GGTGCAGTTCGGTTGAAGAA 58.695 50.000 0.00 0.00 33.98 2.52
2914 3403 1.264288 GGTGCAGTTCGGTTGAAGAAG 59.736 52.381 0.00 0.00 33.98 2.85
2915 3404 2.210116 GTGCAGTTCGGTTGAAGAAGA 58.790 47.619 0.00 0.00 33.98 2.87
2954 3443 6.878923 ACAGCATTTTCTATAACACTGCACTA 59.121 34.615 0.00 0.00 0.00 2.74
3045 3536 4.497473 TCGCGGAAATCATTTTTGTTCT 57.503 36.364 6.13 0.00 0.00 3.01
3056 3547 7.775397 ATCATTTTTGTTCTTTGTGGAGTTG 57.225 32.000 0.00 0.00 0.00 3.16
3058 3549 3.518634 TTTGTTCTTTGTGGAGTTGCC 57.481 42.857 0.00 0.00 37.10 4.52
3120 3614 6.438108 TGGGATGATTTTCTGACAATGTGAAT 59.562 34.615 0.00 0.00 0.00 2.57
3121 3615 7.038870 TGGGATGATTTTCTGACAATGTGAATT 60.039 33.333 0.00 0.00 0.00 2.17
3122 3616 7.820872 GGGATGATTTTCTGACAATGTGAATTT 59.179 33.333 0.00 0.00 0.00 1.82
3129 3623 9.487790 TTTTCTGACAATGTGAATTTATTTCCC 57.512 29.630 0.00 0.00 33.04 3.97
3130 3624 7.169158 TCTGACAATGTGAATTTATTTCCCC 57.831 36.000 0.00 0.00 33.04 4.81
3131 3625 5.960113 TGACAATGTGAATTTATTTCCCCG 58.040 37.500 0.00 0.00 33.04 5.73
3190 4037 7.002250 TGTTGATTGATTTGCAAGGGATTTA 57.998 32.000 0.00 0.00 40.42 1.40
3191 4038 7.622713 TGTTGATTGATTTGCAAGGGATTTAT 58.377 30.769 0.00 0.00 40.42 1.40
3192 4039 8.102047 TGTTGATTGATTTGCAAGGGATTTATT 58.898 29.630 0.00 0.00 40.42 1.40
3193 4040 8.949177 GTTGATTGATTTGCAAGGGATTTATTT 58.051 29.630 0.00 0.00 40.42 1.40
3194 4041 8.721019 TGATTGATTTGCAAGGGATTTATTTC 57.279 30.769 0.00 0.00 40.42 2.17
3195 4042 7.769970 TGATTGATTTGCAAGGGATTTATTTCC 59.230 33.333 0.00 0.00 40.42 3.13
3613 4460 7.670009 TGCATGATTTAAAAGAAAATGGTGG 57.330 32.000 0.00 0.00 0.00 4.61
3614 4461 6.654161 TGCATGATTTAAAAGAAAATGGTGGG 59.346 34.615 0.00 0.00 0.00 4.61
3615 4462 6.093909 GCATGATTTAAAAGAAAATGGTGGGG 59.906 38.462 0.00 0.00 0.00 4.96
3616 4463 6.120507 TGATTTAAAAGAAAATGGTGGGGG 57.879 37.500 0.00 0.00 0.00 5.40
3617 4464 5.846714 TGATTTAAAAGAAAATGGTGGGGGA 59.153 36.000 0.00 0.00 0.00 4.81
3618 4465 5.816955 TTTAAAAGAAAATGGTGGGGGAG 57.183 39.130 0.00 0.00 0.00 4.30
3619 4466 2.325661 AAAGAAAATGGTGGGGGAGG 57.674 50.000 0.00 0.00 0.00 4.30
3620 4467 1.466858 AAGAAAATGGTGGGGGAGGA 58.533 50.000 0.00 0.00 0.00 3.71
3621 4468 1.002857 AGAAAATGGTGGGGGAGGAG 58.997 55.000 0.00 0.00 0.00 3.69
3622 4469 0.684479 GAAAATGGTGGGGGAGGAGC 60.684 60.000 0.00 0.00 0.00 4.70
3623 4470 1.442886 AAAATGGTGGGGGAGGAGCA 61.443 55.000 0.00 0.00 0.00 4.26
3624 4471 1.224003 AAATGGTGGGGGAGGAGCAT 61.224 55.000 0.00 0.00 31.68 3.79
3625 4472 1.941403 AATGGTGGGGGAGGAGCATG 61.941 60.000 0.00 0.00 30.84 4.06
3626 4473 3.017581 GGTGGGGGAGGAGCATGT 61.018 66.667 0.00 0.00 0.00 3.21
3627 4474 1.692749 GGTGGGGGAGGAGCATGTA 60.693 63.158 0.00 0.00 0.00 2.29
3628 4475 1.062488 GGTGGGGGAGGAGCATGTAT 61.062 60.000 0.00 0.00 0.00 2.29
3629 4476 0.398318 GTGGGGGAGGAGCATGTATC 59.602 60.000 0.00 0.00 0.00 2.24
3630 4477 1.121407 TGGGGGAGGAGCATGTATCG 61.121 60.000 0.00 0.00 0.00 2.92
3631 4478 1.674057 GGGGAGGAGCATGTATCGG 59.326 63.158 0.00 0.00 0.00 4.18
3632 4479 1.122019 GGGGAGGAGCATGTATCGGT 61.122 60.000 0.00 0.00 0.00 4.69
3633 4480 0.034059 GGGAGGAGCATGTATCGGTG 59.966 60.000 0.00 0.00 0.00 4.94
3634 4481 0.034059 GGAGGAGCATGTATCGGTGG 59.966 60.000 0.00 0.00 0.00 4.61
3635 4482 0.601311 GAGGAGCATGTATCGGTGGC 60.601 60.000 0.00 0.00 0.00 5.01
3636 4483 1.146041 GGAGCATGTATCGGTGGCA 59.854 57.895 0.00 0.00 0.00 4.92
3637 4484 0.882042 GGAGCATGTATCGGTGGCAG 60.882 60.000 0.00 0.00 0.00 4.85
3638 4485 0.179073 GAGCATGTATCGGTGGCAGT 60.179 55.000 0.00 0.00 0.00 4.40
3639 4486 1.068588 GAGCATGTATCGGTGGCAGTA 59.931 52.381 0.00 0.00 0.00 2.74
3640 4487 1.202533 AGCATGTATCGGTGGCAGTAC 60.203 52.381 0.00 0.00 0.00 2.73
3641 4488 1.202533 GCATGTATCGGTGGCAGTACT 60.203 52.381 0.00 0.00 0.00 2.73
3642 4489 2.473816 CATGTATCGGTGGCAGTACTG 58.526 52.381 18.93 18.93 0.00 2.74
3643 4490 1.842052 TGTATCGGTGGCAGTACTGA 58.158 50.000 27.08 3.31 40.04 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.106149 GGGATATGCGTTCGGGAAGT 59.894 55.000 0.00 0.00 0.00 3.01
247 248 1.000771 GGGAAACTGAGGAAGGGCC 60.001 63.158 0.00 0.00 0.00 5.80
403 404 2.380064 AAATTCACCTTCCACCTGCA 57.620 45.000 0.00 0.00 0.00 4.41
776 985 8.128582 TGTAAAATTGAAGTTCAGTGCTAACAG 58.871 33.333 5.56 0.00 0.00 3.16
808 1017 2.346803 GTGACATACATCAGCACCGTT 58.653 47.619 0.00 0.00 0.00 4.44
948 1159 7.278875 AGGAGAAGACCTATTAAATGAAGCAG 58.721 38.462 0.00 0.00 38.65 4.24
971 1182 3.409026 AAAGAGTGCTACCAACTGAGG 57.591 47.619 0.00 0.00 0.00 3.86
997 1208 4.257267 TGTTCTTCTTCTTGCTCATCGA 57.743 40.909 0.00 0.00 0.00 3.59
1138 1350 2.989840 CCGAGTGATGAGTGAACTGAAC 59.010 50.000 0.00 0.00 0.00 3.18
1166 1378 3.578716 TCTGAAGTTACTCTGTTCAGGGG 59.421 47.826 10.68 0.00 44.87 4.79
1254 1466 7.123547 ACACAAAGAAATGTTGGGAGAGTAAAA 59.876 33.333 0.00 0.00 33.43 1.52
1255 1467 6.605594 ACACAAAGAAATGTTGGGAGAGTAAA 59.394 34.615 0.00 0.00 33.43 2.01
1360 1578 6.240894 TGGCAATACCTTCATCCATATCTTC 58.759 40.000 0.00 0.00 40.22 2.87
1483 1701 4.082081 TGCTACAAGGGCAAAAATCATGAG 60.082 41.667 0.09 0.00 36.71 2.90
1575 1793 3.181451 TGCTTCAGTGGAACAGACAGAAT 60.181 43.478 0.00 0.00 41.80 2.40
1581 1799 0.249868 CGGTGCTTCAGTGGAACAGA 60.250 55.000 0.00 0.00 41.80 3.41
1649 1867 8.721478 CAGAGCTATAGCAAGTTAAGAAACAAA 58.279 33.333 26.07 0.00 45.16 2.83
1670 1888 5.105513 ACTCTCTAAACTCTTAAGCCAGAGC 60.106 44.000 0.00 0.00 43.83 4.09
1671 1889 6.524101 ACTCTCTAAACTCTTAAGCCAGAG 57.476 41.667 0.00 5.22 45.29 3.35
1672 1890 7.403671 TCTACTCTCTAAACTCTTAAGCCAGA 58.596 38.462 0.00 0.00 0.00 3.86
1673 1891 7.554835 TCTCTACTCTCTAAACTCTTAAGCCAG 59.445 40.741 0.00 0.00 0.00 4.85
1674 1892 7.337436 GTCTCTACTCTCTAAACTCTTAAGCCA 59.663 40.741 0.00 0.00 0.00 4.75
1678 1896 9.012161 GGTTGTCTCTACTCTCTAAACTCTTAA 57.988 37.037 0.00 0.00 0.00 1.85
1680 1898 7.005296 TGGTTGTCTCTACTCTCTAAACTCTT 58.995 38.462 0.00 0.00 0.00 2.85
1704 1922 5.065731 GCTCCAAGTCCATAAGAAGACAATG 59.934 44.000 0.00 0.00 35.38 2.82
1705 1923 5.045286 AGCTCCAAGTCCATAAGAAGACAAT 60.045 40.000 0.00 0.00 35.38 2.71
1709 1927 3.452627 GGAGCTCCAAGTCCATAAGAAGA 59.547 47.826 28.43 0.00 35.64 2.87
1756 1974 0.172578 TACATGCTGCGCTTAGTCGT 59.827 50.000 9.73 1.33 0.00 4.34
1758 1976 2.474359 CAGATACATGCTGCGCTTAGTC 59.526 50.000 9.73 0.00 0.00 2.59
1765 1983 5.170748 TCATTATACCAGATACATGCTGCG 58.829 41.667 0.00 0.00 32.06 5.18
1786 2004 5.063817 CGCATTGAAATGTAGACAGACATCA 59.936 40.000 5.02 0.00 39.16 3.07
1787 2005 5.496387 CGCATTGAAATGTAGACAGACATC 58.504 41.667 5.02 0.00 39.16 3.06
1809 2027 4.579340 TGGAGAGAGTAGTAATTAGGTGCG 59.421 45.833 0.00 0.00 0.00 5.34
1812 2030 6.125860 TGGGATGGAGAGAGTAGTAATTAGGT 60.126 42.308 0.00 0.00 0.00 3.08
1816 2034 8.980832 ATTATGGGATGGAGAGAGTAGTAATT 57.019 34.615 0.00 0.00 0.00 1.40
1820 2038 9.707957 CTTATATTATGGGATGGAGAGAGTAGT 57.292 37.037 0.00 0.00 0.00 2.73
1821 2039 9.928618 TCTTATATTATGGGATGGAGAGAGTAG 57.071 37.037 0.00 0.00 0.00 2.57
1823 2041 9.432982 GATCTTATATTATGGGATGGAGAGAGT 57.567 37.037 0.00 0.00 0.00 3.24
1824 2042 9.659135 AGATCTTATATTATGGGATGGAGAGAG 57.341 37.037 0.00 0.00 0.00 3.20
1847 2065 9.832445 ACGTGAGTATTTTGGATGTAATAAGAT 57.168 29.630 0.00 0.00 46.88 2.40
1867 2085 9.698309 AAGATCTTATTACATCCAATACGTGAG 57.302 33.333 6.06 0.00 0.00 3.51
1886 2104 9.524903 TCCATCCATCCCATAATATAAGATCTT 57.475 33.333 13.56 13.56 0.00 2.40
1887 2105 9.168553 CTCCATCCATCCCATAATATAAGATCT 57.831 37.037 0.00 0.00 0.00 2.75
1888 2106 8.943085 ACTCCATCCATCCCATAATATAAGATC 58.057 37.037 0.00 0.00 0.00 2.75
1889 2107 8.882704 ACTCCATCCATCCCATAATATAAGAT 57.117 34.615 0.00 0.00 0.00 2.40
1890 2108 9.213777 GTACTCCATCCATCCCATAATATAAGA 57.786 37.037 0.00 0.00 0.00 2.10
1891 2109 8.992349 TGTACTCCATCCATCCCATAATATAAG 58.008 37.037 0.00 0.00 0.00 1.73
1892 2110 8.925447 TGTACTCCATCCATCCCATAATATAA 57.075 34.615 0.00 0.00 0.00 0.98
1893 2111 9.159254 GATGTACTCCATCCATCCCATAATATA 57.841 37.037 0.00 0.00 43.59 0.86
1894 2112 8.038862 GATGTACTCCATCCATCCCATAATAT 57.961 38.462 0.00 0.00 43.59 1.28
1895 2113 7.437713 GATGTACTCCATCCATCCCATAATA 57.562 40.000 0.00 0.00 43.59 0.98
1896 2114 6.319048 GATGTACTCCATCCATCCCATAAT 57.681 41.667 0.00 0.00 43.59 1.28
1897 2115 5.762179 GATGTACTCCATCCATCCCATAA 57.238 43.478 0.00 0.00 43.59 1.90
1908 2126 3.894427 CCACAGCTAGAGATGTACTCCAT 59.106 47.826 0.00 0.00 43.53 3.41
1909 2127 3.053619 TCCACAGCTAGAGATGTACTCCA 60.054 47.826 0.00 0.00 43.53 3.86
1910 2128 3.556999 TCCACAGCTAGAGATGTACTCC 58.443 50.000 0.00 0.00 43.53 3.85
1911 2129 4.582656 ACATCCACAGCTAGAGATGTACTC 59.417 45.833 18.17 0.00 45.62 2.59
1912 2130 4.541705 ACATCCACAGCTAGAGATGTACT 58.458 43.478 18.17 0.74 45.62 2.73
1913 2131 4.927978 ACATCCACAGCTAGAGATGTAC 57.072 45.455 18.17 0.00 45.62 2.90
1914 2132 6.607600 ACTTTACATCCACAGCTAGAGATGTA 59.392 38.462 19.96 19.96 45.62 2.29
1916 2134 5.911752 ACTTTACATCCACAGCTAGAGATG 58.088 41.667 14.33 14.33 41.50 2.90
1917 2135 5.896678 AGACTTTACATCCACAGCTAGAGAT 59.103 40.000 0.00 0.00 0.00 2.75
1918 2136 5.265191 AGACTTTACATCCACAGCTAGAGA 58.735 41.667 0.00 0.00 0.00 3.10
1919 2137 5.451242 GGAGACTTTACATCCACAGCTAGAG 60.451 48.000 0.00 0.00 33.08 2.43
1920 2138 4.402793 GGAGACTTTACATCCACAGCTAGA 59.597 45.833 0.00 0.00 33.08 2.43
1921 2139 4.160439 TGGAGACTTTACATCCACAGCTAG 59.840 45.833 0.00 0.00 38.19 3.42
1922 2140 4.093743 TGGAGACTTTACATCCACAGCTA 58.906 43.478 0.00 0.00 38.19 3.32
1923 2141 2.906389 TGGAGACTTTACATCCACAGCT 59.094 45.455 0.00 0.00 38.19 4.24
1924 2142 3.334583 TGGAGACTTTACATCCACAGC 57.665 47.619 0.00 0.00 38.19 4.40
1925 2143 7.770433 TCAATAATGGAGACTTTACATCCACAG 59.230 37.037 0.00 0.00 45.53 3.66
1926 2144 7.629157 TCAATAATGGAGACTTTACATCCACA 58.371 34.615 0.00 0.00 45.53 4.17
1927 2145 8.506168 TTCAATAATGGAGACTTTACATCCAC 57.494 34.615 0.00 0.00 45.53 4.02
1928 2146 9.527157 TTTTCAATAATGGAGACTTTACATCCA 57.473 29.630 0.00 0.00 46.69 3.41
1961 2179 9.422681 AGCTAGAGATGTTGTAATTAGACCTAA 57.577 33.333 0.00 0.00 0.00 2.69
1962 2180 8.851145 CAGCTAGAGATGTTGTAATTAGACCTA 58.149 37.037 0.00 0.00 0.00 3.08
1963 2181 7.343316 ACAGCTAGAGATGTTGTAATTAGACCT 59.657 37.037 0.00 0.00 42.67 3.85
1964 2182 7.493367 ACAGCTAGAGATGTTGTAATTAGACC 58.507 38.462 0.00 0.00 42.67 3.85
1985 2203 9.290483 GCCTTTCTTTATATTGAAAGTAACAGC 57.710 33.333 18.48 13.46 44.34 4.40
2015 2233 5.500234 TGACCAGATAAGCAGTAAAGCATT 58.500 37.500 0.00 0.00 36.85 3.56
2016 2234 5.102953 TGACCAGATAAGCAGTAAAGCAT 57.897 39.130 0.00 0.00 36.85 3.79
2064 2282 5.391256 TCGGTGGTATGTAATCCTGACTAT 58.609 41.667 0.00 0.00 0.00 2.12
2070 2288 3.508793 CCGTATCGGTGGTATGTAATCCT 59.491 47.826 0.00 0.00 42.73 3.24
2073 2291 2.564062 CCCCGTATCGGTGGTATGTAAT 59.436 50.000 7.40 0.00 46.80 1.89
2085 2303 0.037605 GGCCTTACATCCCCGTATCG 60.038 60.000 0.00 0.00 0.00 2.92
2086 2304 1.349067 AGGCCTTACATCCCCGTATC 58.651 55.000 0.00 0.00 0.00 2.24
2087 2305 1.815757 AAGGCCTTACATCCCCGTAT 58.184 50.000 18.87 0.00 0.00 3.06
2088 2306 2.322658 CTAAGGCCTTACATCCCCGTA 58.677 52.381 21.68 0.00 0.00 4.02
2089 2307 1.129058 CTAAGGCCTTACATCCCCGT 58.871 55.000 21.68 0.00 0.00 5.28
2090 2308 1.129058 ACTAAGGCCTTACATCCCCG 58.871 55.000 21.68 12.13 0.00 5.73
2091 2309 3.559384 GCATACTAAGGCCTTACATCCCC 60.559 52.174 21.68 5.02 0.00 4.81
2092 2310 3.328050 AGCATACTAAGGCCTTACATCCC 59.672 47.826 21.68 9.87 31.05 3.85
2093 2311 4.202367 ACAGCATACTAAGGCCTTACATCC 60.202 45.833 21.68 8.01 31.05 3.51
2162 2401 1.134753 CTGTTGGTTGCACAGCTGAAA 59.865 47.619 23.35 8.93 35.52 2.69
2171 2410 4.013728 AGTCAGTTTAACTGTTGGTTGCA 58.986 39.130 22.36 0.28 46.03 4.08
2188 2427 5.236282 ACATGACATTCAGAACTGAGTCAG 58.764 41.667 18.83 18.83 43.35 3.51
2189 2428 5.219343 ACATGACATTCAGAACTGAGTCA 57.781 39.130 20.70 20.70 43.85 3.41
2195 2434 6.889301 ATTGTTGACATGACATTCAGAACT 57.111 33.333 0.00 0.00 0.00 3.01
2209 2448 8.834465 CCAAATTGAACCAATTAATTGTTGACA 58.166 29.630 23.24 15.37 42.32 3.58
2223 2462 8.429237 ACAGTAAAATATCCCAAATTGAACCA 57.571 30.769 0.00 0.00 0.00 3.67
2224 2463 8.527810 TGACAGTAAAATATCCCAAATTGAACC 58.472 33.333 0.00 0.00 0.00 3.62
2225 2464 9.573133 CTGACAGTAAAATATCCCAAATTGAAC 57.427 33.333 0.00 0.00 0.00 3.18
2226 2465 8.748412 CCTGACAGTAAAATATCCCAAATTGAA 58.252 33.333 0.93 0.00 0.00 2.69
2232 2471 9.762381 AATAAACCTGACAGTAAAATATCCCAA 57.238 29.630 0.93 0.00 0.00 4.12
2243 2482 6.109156 TGCTCTTGAATAAACCTGACAGTA 57.891 37.500 0.93 0.00 0.00 2.74
2270 2509 7.663081 TGAAGCAAGATGTGAGATACTTCTTTT 59.337 33.333 5.71 0.97 46.01 2.27
2273 2512 6.291648 TGAAGCAAGATGTGAGATACTTCT 57.708 37.500 0.00 0.00 43.42 2.85
2274 2513 6.538021 ACATGAAGCAAGATGTGAGATACTTC 59.462 38.462 0.00 0.00 31.47 3.01
2277 2746 6.484540 CAACATGAAGCAAGATGTGAGATAC 58.515 40.000 0.00 0.00 33.03 2.24
2281 2750 3.190744 AGCAACATGAAGCAAGATGTGAG 59.809 43.478 14.61 0.00 33.03 3.51
2291 2760 1.135575 GCCTACACAGCAACATGAAGC 60.136 52.381 0.00 2.43 0.00 3.86
2292 2761 2.161012 CAGCCTACACAGCAACATGAAG 59.839 50.000 0.00 0.00 0.00 3.02
2299 2768 2.566833 AATGACAGCCTACACAGCAA 57.433 45.000 0.00 0.00 0.00 3.91
2301 2770 3.743396 GCTATAATGACAGCCTACACAGC 59.257 47.826 0.00 0.00 0.00 4.40
2303 2772 4.740634 GCAGCTATAATGACAGCCTACACA 60.741 45.833 0.00 0.00 38.61 3.72
2304 2773 3.743396 GCAGCTATAATGACAGCCTACAC 59.257 47.826 0.00 0.00 38.61 2.90
2324 2793 2.093394 CCATTTGGGATTGCAATCAGCA 60.093 45.455 34.08 18.64 46.99 4.41
2379 2848 1.086696 CACAATACAGGGACTTGCCG 58.913 55.000 0.00 0.00 34.60 5.69
2390 2859 3.146066 GTTGTCCTTGAGGCACAATACA 58.854 45.455 14.02 3.65 37.46 2.29
2414 2883 1.208293 CCTAACCTCAGTGAGCTTCCC 59.792 57.143 15.10 0.00 0.00 3.97
2423 2892 1.348036 GCCACTTGACCTAACCTCAGT 59.652 52.381 0.00 0.00 0.00 3.41
2480 2949 5.465056 GTCAGTGAGAGAAGAAAGAAAGGTG 59.535 44.000 0.00 0.00 0.00 4.00
2527 3000 9.950680 GAAACAAAGATTTCATGAGTGACTTTA 57.049 29.630 14.20 0.00 38.28 1.85
2558 3031 4.550076 ATGCTGTCTCTGGCCTAATATC 57.450 45.455 3.32 0.00 0.00 1.63
2563 3036 3.308401 TGATTATGCTGTCTCTGGCCTA 58.692 45.455 3.32 0.00 0.00 3.93
2598 3071 9.998106 GGCTTATAATAATCCTTCAGTACTTCA 57.002 33.333 0.00 0.00 0.00 3.02
2604 3077 7.227156 CCACTGGCTTATAATAATCCTTCAGT 58.773 38.462 0.00 0.00 32.80 3.41
2648 3121 1.619363 CTGGACTGGGAATGGGGGA 60.619 63.158 0.00 0.00 0.00 4.81
2669 3143 8.584157 ACAGAGTTAAGATCTAGCTTATCATGG 58.416 37.037 0.00 0.00 31.00 3.66
2676 3150 5.186797 AGCACACAGAGTTAAGATCTAGCTT 59.813 40.000 0.00 0.00 0.00 3.74
2738 3214 0.179029 CTCCCGTATCCCCGCAAAAT 60.179 55.000 0.00 0.00 0.00 1.82
2771 3247 5.120830 GCTACAATTCGACAACACTTGATCT 59.879 40.000 0.00 0.00 0.00 2.75
2800 3278 3.581332 ACCCAAAAGTCGAGATTAGACCA 59.419 43.478 0.00 0.00 39.31 4.02
2801 3279 3.933332 CACCCAAAAGTCGAGATTAGACC 59.067 47.826 0.00 0.00 39.31 3.85
2913 3402 1.681166 GCTGTTCCAGGCACATCATCT 60.681 52.381 0.00 0.00 31.21 2.90
2914 3403 0.737219 GCTGTTCCAGGCACATCATC 59.263 55.000 0.00 0.00 31.21 2.92
2915 3404 0.038599 TGCTGTTCCAGGCACATCAT 59.961 50.000 0.00 0.00 33.23 2.45
2954 3443 6.603940 ACCAATAAAACAGCATTGTGGTAT 57.396 33.333 0.00 0.00 37.67 2.73
3021 3512 6.616947 AGAACAAAAATGATTTCCGCGAATA 58.383 32.000 8.23 0.00 0.00 1.75
3025 3516 5.051106 ACAAAGAACAAAAATGATTTCCGCG 60.051 36.000 0.00 0.00 0.00 6.46
3045 3536 3.442273 GGATTAATCGGCAACTCCACAAA 59.558 43.478 9.32 0.00 34.01 2.83
3056 3547 4.900635 ACATGAAACTGGATTAATCGGC 57.099 40.909 9.32 0.00 0.00 5.54
3058 3549 9.277565 CAACTTAACATGAAACTGGATTAATCG 57.722 33.333 9.32 0.00 0.00 3.34
3094 3588 5.953548 TCACATTGTCAGAAAATCATCCCAT 59.046 36.000 0.00 0.00 0.00 4.00
3095 3589 5.323581 TCACATTGTCAGAAAATCATCCCA 58.676 37.500 0.00 0.00 0.00 4.37
3096 3590 5.902613 TCACATTGTCAGAAAATCATCCC 57.097 39.130 0.00 0.00 0.00 3.85
3124 3618 6.459923 CAATTGTAAGAAATTTCCGGGGAAA 58.540 36.000 14.76 14.76 46.37 3.13
3125 3619 5.046950 CCAATTGTAAGAAATTTCCGGGGAA 60.047 40.000 14.61 0.00 0.00 3.97
3126 3620 4.464597 CCAATTGTAAGAAATTTCCGGGGA 59.535 41.667 14.61 0.00 0.00 4.81
3127 3621 4.754322 CCAATTGTAAGAAATTTCCGGGG 58.246 43.478 14.61 2.40 0.00 5.73
3129 3623 3.857093 CGCCAATTGTAAGAAATTTCCGG 59.143 43.478 14.61 0.00 0.00 5.14
3130 3624 4.728534 TCGCCAATTGTAAGAAATTTCCG 58.271 39.130 14.61 7.12 0.00 4.30
3131 3625 7.117667 ACAAATCGCCAATTGTAAGAAATTTCC 59.882 33.333 14.61 0.43 37.96 3.13
3136 3982 6.980978 TCAAACAAATCGCCAATTGTAAGAAA 59.019 30.769 4.43 0.00 38.75 2.52
3142 3988 5.990996 AGAAATCAAACAAATCGCCAATTGT 59.009 32.000 4.43 0.00 41.31 2.71
3144 3990 5.990996 ACAGAAATCAAACAAATCGCCAATT 59.009 32.000 0.00 0.00 0.00 2.32
3587 4434 8.732531 CCACCATTTTCTTTTAAATCATGCAAT 58.267 29.630 0.00 0.00 0.00 3.56
3588 4435 7.174599 CCCACCATTTTCTTTTAAATCATGCAA 59.825 33.333 0.00 0.00 0.00 4.08
3589 4436 6.654161 CCCACCATTTTCTTTTAAATCATGCA 59.346 34.615 0.00 0.00 0.00 3.96
3590 4437 6.093909 CCCCACCATTTTCTTTTAAATCATGC 59.906 38.462 0.00 0.00 0.00 4.06
3591 4438 6.598850 CCCCCACCATTTTCTTTTAAATCATG 59.401 38.462 0.00 0.00 0.00 3.07
3592 4439 6.503570 TCCCCCACCATTTTCTTTTAAATCAT 59.496 34.615 0.00 0.00 0.00 2.45
3593 4440 5.846714 TCCCCCACCATTTTCTTTTAAATCA 59.153 36.000 0.00 0.00 0.00 2.57
3594 4441 6.367374 TCCCCCACCATTTTCTTTTAAATC 57.633 37.500 0.00 0.00 0.00 2.17
3595 4442 5.250543 CCTCCCCCACCATTTTCTTTTAAAT 59.749 40.000 0.00 0.00 0.00 1.40
3596 4443 4.595350 CCTCCCCCACCATTTTCTTTTAAA 59.405 41.667 0.00 0.00 0.00 1.52
3597 4444 4.140663 TCCTCCCCCACCATTTTCTTTTAA 60.141 41.667 0.00 0.00 0.00 1.52
3598 4445 3.403051 TCCTCCCCCACCATTTTCTTTTA 59.597 43.478 0.00 0.00 0.00 1.52
3599 4446 2.181196 TCCTCCCCCACCATTTTCTTTT 59.819 45.455 0.00 0.00 0.00 2.27
3600 4447 1.792651 TCCTCCCCCACCATTTTCTTT 59.207 47.619 0.00 0.00 0.00 2.52
3601 4448 1.359130 CTCCTCCCCCACCATTTTCTT 59.641 52.381 0.00 0.00 0.00 2.52
3602 4449 1.002857 CTCCTCCCCCACCATTTTCT 58.997 55.000 0.00 0.00 0.00 2.52
3603 4450 0.684479 GCTCCTCCCCCACCATTTTC 60.684 60.000 0.00 0.00 0.00 2.29
3604 4451 1.388133 GCTCCTCCCCCACCATTTT 59.612 57.895 0.00 0.00 0.00 1.82
3605 4452 1.224003 ATGCTCCTCCCCCACCATTT 61.224 55.000 0.00 0.00 0.00 2.32
3606 4453 1.623686 ATGCTCCTCCCCCACCATT 60.624 57.895 0.00 0.00 0.00 3.16
3607 4454 2.045132 ATGCTCCTCCCCCACCAT 59.955 61.111 0.00 0.00 0.00 3.55
3608 4455 2.484868 TACATGCTCCTCCCCCACCA 62.485 60.000 0.00 0.00 0.00 4.17
3609 4456 1.062488 ATACATGCTCCTCCCCCACC 61.062 60.000 0.00 0.00 0.00 4.61
3610 4457 0.398318 GATACATGCTCCTCCCCCAC 59.602 60.000 0.00 0.00 0.00 4.61
3611 4458 1.121407 CGATACATGCTCCTCCCCCA 61.121 60.000 0.00 0.00 0.00 4.96
3612 4459 1.674057 CGATACATGCTCCTCCCCC 59.326 63.158 0.00 0.00 0.00 5.40
3613 4460 1.122019 ACCGATACATGCTCCTCCCC 61.122 60.000 0.00 0.00 0.00 4.81
3614 4461 0.034059 CACCGATACATGCTCCTCCC 59.966 60.000 0.00 0.00 0.00 4.30
3615 4462 0.034059 CCACCGATACATGCTCCTCC 59.966 60.000 0.00 0.00 0.00 4.30
3616 4463 0.601311 GCCACCGATACATGCTCCTC 60.601 60.000 0.00 0.00 0.00 3.71
3617 4464 1.337384 TGCCACCGATACATGCTCCT 61.337 55.000 0.00 0.00 0.00 3.69
3618 4465 0.882042 CTGCCACCGATACATGCTCC 60.882 60.000 0.00 0.00 0.00 4.70
3619 4466 0.179073 ACTGCCACCGATACATGCTC 60.179 55.000 0.00 0.00 0.00 4.26
3620 4467 1.119684 TACTGCCACCGATACATGCT 58.880 50.000 0.00 0.00 0.00 3.79
3621 4468 1.202533 AGTACTGCCACCGATACATGC 60.203 52.381 0.00 0.00 0.00 4.06
3622 4469 2.100749 TCAGTACTGCCACCGATACATG 59.899 50.000 18.45 0.00 0.00 3.21
3623 4470 2.384828 TCAGTACTGCCACCGATACAT 58.615 47.619 18.45 0.00 0.00 2.29
3624 4471 1.842052 TCAGTACTGCCACCGATACA 58.158 50.000 18.45 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.