Multiple sequence alignment - TraesCS2A01G263600

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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 TraesCS2A01G263600 chr2A 100.000 2425 0 0 1 2425 418796183 418793759 0.000000e+00 4479.0
1 TraesCS2A01G263600 chr2A 77.888 303 29 14 1845 2113 730645357 730645655 1.160000e-33 154.0
2 TraesCS2A01G263600 chr2A 86.441 59 8 0 1162 1220 700976012 700975954 5.600000e-07 65.8
3 TraesCS2A01G263600 chr2B 95.777 1113 36 5 736 1848 384400063 384401164 0.000000e+00 1784.0
4 TraesCS2A01G263600 chr2B 92.586 607 39 6 140 743 131288589 131287986 0.000000e+00 867.0
5 TraesCS2A01G263600 chr2B 96.774 124 3 1 1 124 384399929 384400051 3.160000e-49 206.0
6 TraesCS2A01G263600 chr2B 79.259 270 33 10 1875 2123 364133949 364133682 1.490000e-37 167.0
7 TraesCS2A01G263600 chr2B 86.916 107 11 3 2020 2124 110322342 110322237 1.520000e-22 117.0
8 TraesCS2A01G263600 chr2B 92.593 54 2 2 1843 1896 232937666 232937615 2.590000e-10 76.8
9 TraesCS2A01G263600 chr2B 93.333 45 3 0 1844 1888 510901073 510901117 1.560000e-07 67.6
10 TraesCS2A01G263600 chr2B 84.746 59 9 0 1162 1220 669649031 669648973 2.600000e-05 60.2
11 TraesCS2A01G263600 chr2D 95.094 1121 39 8 736 1848 316327992 316329104 0.000000e+00 1751.0
12 TraesCS2A01G263600 chr2D 93.656 599 34 3 140 737 447851664 447851069 0.000000e+00 893.0
13 TraesCS2A01G263600 chr2D 86.667 240 24 6 1875 2110 501303911 501303676 2.390000e-65 259.0
14 TraesCS2A01G263600 chr2D 91.667 144 4 5 1 139 316327861 316328001 2.460000e-45 193.0
15 TraesCS2A01G263600 chr2D 90.000 60 2 1 2363 2422 316329132 316329187 9.300000e-10 75.0
16 TraesCS2A01G263600 chr2D 97.500 40 1 0 2111 2150 316329101 316329140 4.330000e-08 69.4
17 TraesCS2A01G263600 chr2D 84.746 59 9 0 1162 1220 560991630 560991572 2.600000e-05 60.2
18 TraesCS2A01G263600 chr5B 93.035 603 39 3 140 740 282847114 282846513 0.000000e+00 878.0
19 TraesCS2A01G263600 chr5B 74.882 211 44 6 1012 1220 580844064 580843861 1.190000e-13 87.9
20 TraesCS2A01G263600 chr3D 92.346 601 43 3 139 737 131348462 131349061 0.000000e+00 852.0
21 TraesCS2A01G263600 chr3D 91.694 602 46 4 140 738 521590662 521591262 0.000000e+00 832.0
22 TraesCS2A01G263600 chr7B 91.100 618 50 5 140 754 138036096 138036711 0.000000e+00 832.0
23 TraesCS2A01G263600 chr7D 91.486 599 47 4 139 734 165112921 165113518 0.000000e+00 821.0
24 TraesCS2A01G263600 chr7D 87.866 239 24 5 1875 2110 511190558 511190322 2.370000e-70 276.0
25 TraesCS2A01G263600 chr7D 86.325 234 28 4 1875 2105 578388101 578387869 4.000000e-63 252.0
26 TraesCS2A01G263600 chr4D 91.362 602 48 4 139 737 221285317 221284717 0.000000e+00 821.0
27 TraesCS2A01G263600 chr4D 91.348 601 48 4 140 737 386936735 386936136 0.000000e+00 819.0
28 TraesCS2A01G263600 chrUn 92.735 234 13 4 2144 2375 74669470 74669701 3.860000e-88 335.0
29 TraesCS2A01G263600 chrUn 93.333 45 3 0 1844 1888 480716376 480716420 1.560000e-07 67.6
30 TraesCS2A01G263600 chr4A 95.238 210 8 2 2151 2360 604639730 604639937 5.000000e-87 331.0
31 TraesCS2A01G263600 chr4A 94.811 212 9 2 2151 2362 604639513 604639722 1.800000e-86 329.0
32 TraesCS2A01G263600 chr4A 94.340 212 11 1 2151 2362 604638801 604639011 8.360000e-85 324.0
33 TraesCS2A01G263600 chr4A 93.458 214 13 1 2151 2364 602738682 602738470 1.400000e-82 316.0
34 TraesCS2A01G263600 chr4A 93.427 213 12 2 2150 2362 609798086 609797876 5.030000e-82 315.0
35 TraesCS2A01G263600 chr4A 77.903 267 37 7 1875 2120 697996730 697996995 1.940000e-31 147.0
36 TraesCS2A01G263600 chr4A 95.349 43 2 0 1846 1888 420299873 420299915 4.330000e-08 69.4
37 TraesCS2A01G263600 chr7A 93.151 219 13 1 2150 2366 15633523 15633305 1.080000e-83 320.0
38 TraesCS2A01G263600 chr7A 86.000 250 27 8 1875 2118 523716784 523717031 6.650000e-66 261.0
39 TraesCS2A01G263600 chr5A 93.056 216 12 3 2151 2365 33131967 33132180 1.810000e-81 313.0
40 TraesCS2A01G263600 chr5A 93.023 215 13 1 2150 2364 644353053 644353265 1.810000e-81 313.0
41 TraesCS2A01G263600 chr5A 86.364 242 28 5 1875 2113 552964518 552964757 2.390000e-65 259.0
42 TraesCS2A01G263600 chr5A 86.383 235 28 4 1875 2107 36072103 36072335 1.110000e-63 254.0
43 TraesCS2A01G263600 chr5A 74.299 214 47 5 1015 1227 593340523 593340317 1.550000e-12 84.2
44 TraesCS2A01G263600 chr5A 95.745 47 2 0 1845 1891 441171619 441171665 2.590000e-10 76.8
45 TraesCS2A01G263600 chr5A 80.189 106 16 3 1121 1222 139083444 139083548 9.300000e-10 75.0
46 TraesCS2A01G263600 chr6A 86.122 245 30 4 1870 2111 392126763 392126520 6.650000e-66 261.0
47 TraesCS2A01G263600 chr6A 93.333 45 3 0 1844 1888 115506986 115507030 1.560000e-07 67.6
48 TraesCS2A01G263600 chr6A 93.333 45 3 0 1844 1888 115539169 115539213 1.560000e-07 67.6
49 TraesCS2A01G263600 chr1A 86.611 239 29 3 1875 2111 54069792 54070029 6.650000e-66 261.0
50 TraesCS2A01G263600 chr1A 79.197 274 30 14 1875 2124 570277597 570277327 5.360000e-37 165.0
51 TraesCS2A01G263600 chr5D 85.833 240 30 4 1875 2111 419976275 419976037 4.000000e-63 252.0
52 TraesCS2A01G263600 chr5D 81.579 266 26 10 1875 2119 340533328 340533591 5.290000e-47 198.0
53 TraesCS2A01G263600 chr5D 90.385 52 5 0 1299 1350 473848570 473848519 4.330000e-08 69.4
54 TraesCS2A01G263600 chr3B 93.478 92 4 2 2036 2127 48883687 48883598 4.210000e-28 135.0
55 TraesCS2A01G263600 chr1B 75.824 273 42 11 1875 2127 48104011 48104279 1.520000e-22 117.0


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 TraesCS2A01G263600 chr2A 418793759 418796183 2424 True 4479.0 4479 100.000000 1 2425 1 chr2A.!!$R1 2424
1 TraesCS2A01G263600 chr2B 384399929 384401164 1235 False 995.0 1784 96.275500 1 1848 2 chr2B.!!$F2 1847
2 TraesCS2A01G263600 chr2B 131287986 131288589 603 True 867.0 867 92.586000 140 743 1 chr2B.!!$R2 603
3 TraesCS2A01G263600 chr2D 447851069 447851664 595 True 893.0 893 93.656000 140 737 1 chr2D.!!$R1 597
4 TraesCS2A01G263600 chr2D 316327861 316329187 1326 False 522.1 1751 93.565250 1 2422 4 chr2D.!!$F1 2421
5 TraesCS2A01G263600 chr5B 282846513 282847114 601 True 878.0 878 93.035000 140 740 1 chr5B.!!$R1 600
6 TraesCS2A01G263600 chr3D 131348462 131349061 599 False 852.0 852 92.346000 139 737 1 chr3D.!!$F1 598
7 TraesCS2A01G263600 chr3D 521590662 521591262 600 False 832.0 832 91.694000 140 738 1 chr3D.!!$F2 598
8 TraesCS2A01G263600 chr7B 138036096 138036711 615 False 832.0 832 91.100000 140 754 1 chr7B.!!$F1 614
9 TraesCS2A01G263600 chr7D 165112921 165113518 597 False 821.0 821 91.486000 139 734 1 chr7D.!!$F1 595
10 TraesCS2A01G263600 chr4D 221284717 221285317 600 True 821.0 821 91.362000 139 737 1 chr4D.!!$R1 598
11 TraesCS2A01G263600 chr4D 386936136 386936735 599 True 819.0 819 91.348000 140 737 1 chr4D.!!$R2 597
12 TraesCS2A01G263600 chr4A 604638801 604639937 1136 False 328.0 331 94.796333 2151 2362 3 chr4A.!!$F3 211

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
702 710 1.155042 GAGTTGAGCTGAGCCAACTG 58.845 55.0 31.48 0.0 43.97 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1549 0.516001 CGCGCTATCTACCGAGCTAA 59.484 55.0 5.56 0.0 36.5 3.09 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
98 101 6.250527 GCGTAATTTGCCGCCTTATAATATTG 59.749 38.462 0.00 0.00 43.96 1.90
157 160 2.220653 ATAGGGCTGCAAGAAAAGCA 57.779 45.000 0.50 0.00 41.36 3.91
460 465 3.988976 AGTGCAGAGAAGATTTAGGCA 57.011 42.857 0.00 0.00 0.00 4.75
614 622 4.959596 AGCTCGAGATCGTTACAAACTA 57.040 40.909 18.75 0.00 40.80 2.24
627 635 7.317390 TCGTTACAAACTAAGCATGAGTCATA 58.683 34.615 5.03 0.00 0.00 2.15
702 710 1.155042 GAGTTGAGCTGAGCCAACTG 58.845 55.000 31.48 0.00 43.97 3.16
718 726 1.735920 CTGCAACTCGCTCGAGCTT 60.736 57.895 32.88 19.17 45.54 3.74
757 766 5.471456 CCTAATTACATACGTACCGGAGAGT 59.529 44.000 9.46 7.10 0.00 3.24
811 820 4.749310 AAGAGCGCCGTGAGCTGG 62.749 66.667 2.29 0.00 46.13 4.85
826 835 2.915659 TGGTCGAGGCTGGACGTT 60.916 61.111 21.08 0.00 35.24 3.99
937 946 4.729798 GCCAAACCGCGTACGTGC 62.730 66.667 23.00 4.74 37.70 5.34
951 960 1.868469 ACGTGCCTTGCGTTAACTAA 58.132 45.000 3.71 0.00 39.79 2.24
952 961 2.419667 ACGTGCCTTGCGTTAACTAAT 58.580 42.857 3.71 0.00 39.79 1.73
953 962 2.809696 ACGTGCCTTGCGTTAACTAATT 59.190 40.909 3.71 0.00 39.79 1.40
999 1011 2.627699 GAGAATCAGCCGGAAGAGATCT 59.372 50.000 5.05 9.81 33.17 2.75
1228 1240 2.824041 CGCACCCCTACATGCACC 60.824 66.667 0.00 0.00 42.17 5.01
1261 1279 1.300620 TAGCGTATGACGGCATGGC 60.301 57.895 15.86 17.36 42.82 4.40
1523 1543 4.201679 CTCATGTCGCCCGCCGTA 62.202 66.667 0.00 0.00 38.35 4.02
1525 1545 4.508128 CATGTCGCCCGCCGTACT 62.508 66.667 0.00 0.00 38.35 2.73
1526 1546 4.203076 ATGTCGCCCGCCGTACTC 62.203 66.667 0.00 0.00 38.35 2.59
1528 1548 4.549516 GTCGCCCGCCGTACTCTC 62.550 72.222 0.00 0.00 38.35 3.20
1529 1549 4.790962 TCGCCCGCCGTACTCTCT 62.791 66.667 0.00 0.00 38.35 3.10
1569 1589 4.761845 TCGCCGCCGCCACAAATA 62.762 61.111 0.00 0.00 0.00 1.40
1663 1683 2.241880 CGACGACGGCAAGTTTGGT 61.242 57.895 0.00 0.00 35.72 3.67
1694 1714 0.463833 GGCACCCAAGGATAAGGTCG 60.464 60.000 0.00 0.00 0.00 4.79
1785 1805 2.661866 GCAGCGAGTGTCCGTTGT 60.662 61.111 0.00 0.00 41.69 3.32
1805 1825 3.238441 GTCTTCGTGACAGTGATCTGAC 58.762 50.000 0.00 0.00 44.73 3.51
1838 1858 4.202503 ACTCTTGAATATTCCGATGCCCAT 60.203 41.667 12.90 0.00 0.00 4.00
1848 1868 5.782893 TTCCGATGCCCATAAAATTAAGG 57.217 39.130 0.00 0.00 0.00 2.69
1849 1869 4.148838 TCCGATGCCCATAAAATTAAGGG 58.851 43.478 8.75 8.75 43.01 3.95
1850 1870 3.895041 CCGATGCCCATAAAATTAAGGGT 59.105 43.478 13.43 0.00 42.32 4.34
1851 1871 4.343814 CCGATGCCCATAAAATTAAGGGTT 59.656 41.667 13.43 3.85 42.32 4.11
1852 1872 5.163353 CCGATGCCCATAAAATTAAGGGTTT 60.163 40.000 13.43 3.56 42.32 3.27
1853 1873 5.752955 CGATGCCCATAAAATTAAGGGTTTG 59.247 40.000 13.43 4.28 42.32 2.93
1854 1874 6.629291 CGATGCCCATAAAATTAAGGGTTTGT 60.629 38.462 13.43 0.51 42.32 2.83
1855 1875 6.441088 TGCCCATAAAATTAAGGGTTTGTT 57.559 33.333 13.43 0.00 42.32 2.83
1856 1876 6.842676 TGCCCATAAAATTAAGGGTTTGTTT 58.157 32.000 13.43 0.00 42.32 2.83
1857 1877 6.712547 TGCCCATAAAATTAAGGGTTTGTTTG 59.287 34.615 13.43 0.00 42.32 2.93
1858 1878 6.150307 GCCCATAAAATTAAGGGTTTGTTTGG 59.850 38.462 13.43 0.00 42.32 3.28
1859 1879 7.227873 CCCATAAAATTAAGGGTTTGTTTGGT 58.772 34.615 5.49 0.00 37.00 3.67
1860 1880 7.721842 CCCATAAAATTAAGGGTTTGTTTGGTT 59.278 33.333 5.49 0.00 37.00 3.67
1861 1881 9.126151 CCATAAAATTAAGGGTTTGTTTGGTTT 57.874 29.630 0.00 0.00 0.00 3.27
1863 1883 9.907229 ATAAAATTAAGGGTTTGTTTGGTTTCA 57.093 25.926 0.00 0.00 0.00 2.69
1864 1884 8.637196 AAAATTAAGGGTTTGTTTGGTTTCAA 57.363 26.923 0.00 0.00 0.00 2.69
1865 1885 8.815565 AAATTAAGGGTTTGTTTGGTTTCAAT 57.184 26.923 0.00 0.00 32.28 2.57
1866 1886 9.907229 AAATTAAGGGTTTGTTTGGTTTCAATA 57.093 25.926 0.00 0.00 32.28 1.90
1867 1887 9.907229 AATTAAGGGTTTGTTTGGTTTCAATAA 57.093 25.926 0.00 0.00 32.28 1.40
1868 1888 8.950208 TTAAGGGTTTGTTTGGTTTCAATAAG 57.050 30.769 0.00 0.00 32.28 1.73
1869 1889 6.553953 AGGGTTTGTTTGGTTTCAATAAGT 57.446 33.333 0.00 0.00 32.28 2.24
1870 1890 6.578944 AGGGTTTGTTTGGTTTCAATAAGTC 58.421 36.000 0.00 0.00 32.28 3.01
1871 1891 6.155393 AGGGTTTGTTTGGTTTCAATAAGTCA 59.845 34.615 0.00 0.00 32.28 3.41
1872 1892 6.256975 GGGTTTGTTTGGTTTCAATAAGTCAC 59.743 38.462 0.00 0.00 32.28 3.67
1873 1893 7.039270 GGTTTGTTTGGTTTCAATAAGTCACT 58.961 34.615 0.00 0.00 32.28 3.41
1874 1894 7.547722 GGTTTGTTTGGTTTCAATAAGTCACTT 59.452 33.333 0.00 0.00 32.28 3.16
1875 1895 8.379902 GTTTGTTTGGTTTCAATAAGTCACTTG 58.620 33.333 0.00 0.00 32.28 3.16
1876 1896 7.397892 TGTTTGGTTTCAATAAGTCACTTGA 57.602 32.000 0.00 0.00 32.28 3.02
1877 1897 7.254852 TGTTTGGTTTCAATAAGTCACTTGAC 58.745 34.615 0.00 0.77 37.75 3.18
1878 1898 7.122055 TGTTTGGTTTCAATAAGTCACTTGACT 59.878 33.333 6.04 6.04 43.62 3.41
1902 1922 9.131791 ACTTATAAGTCAAGTCATTTTGGTTGT 57.868 29.630 12.50 0.00 32.86 3.32
1903 1923 9.612620 CTTATAAGTCAAGTCATTTTGGTTGTC 57.387 33.333 4.18 0.00 0.00 3.18
1904 1924 5.913137 AAGTCAAGTCATTTTGGTTGTCA 57.087 34.783 0.00 0.00 0.00 3.58
1905 1925 6.469782 AAGTCAAGTCATTTTGGTTGTCAT 57.530 33.333 0.00 0.00 0.00 3.06
1906 1926 6.076981 AGTCAAGTCATTTTGGTTGTCATC 57.923 37.500 0.00 0.00 0.00 2.92
1907 1927 5.829924 AGTCAAGTCATTTTGGTTGTCATCT 59.170 36.000 0.00 0.00 0.00 2.90
1908 1928 5.916883 GTCAAGTCATTTTGGTTGTCATCTG 59.083 40.000 0.00 0.00 0.00 2.90
1909 1929 5.827267 TCAAGTCATTTTGGTTGTCATCTGA 59.173 36.000 0.00 0.00 0.00 3.27
1910 1930 6.491062 TCAAGTCATTTTGGTTGTCATCTGAT 59.509 34.615 0.00 0.00 0.00 2.90
1911 1931 6.906157 AGTCATTTTGGTTGTCATCTGATT 57.094 33.333 0.00 0.00 0.00 2.57
1912 1932 7.294017 AGTCATTTTGGTTGTCATCTGATTT 57.706 32.000 0.00 0.00 0.00 2.17
1913 1933 8.408043 AGTCATTTTGGTTGTCATCTGATTTA 57.592 30.769 0.00 0.00 0.00 1.40
1914 1934 9.028284 AGTCATTTTGGTTGTCATCTGATTTAT 57.972 29.630 0.00 0.00 0.00 1.40
1920 1940 9.513906 TTTGGTTGTCATCTGATTTATAAGTCA 57.486 29.630 9.97 9.97 0.00 3.41
1921 1941 9.685276 TTGGTTGTCATCTGATTTATAAGTCAT 57.315 29.630 10.71 0.00 0.00 3.06
1922 1942 9.330063 TGGTTGTCATCTGATTTATAAGTCATC 57.670 33.333 10.71 0.54 0.00 2.92
1923 1943 9.553064 GGTTGTCATCTGATTTATAAGTCATCT 57.447 33.333 10.71 0.05 0.00 2.90
1926 1946 9.755804 TGTCATCTGATTTATAAGTCATCTGAC 57.244 33.333 26.15 26.15 45.08 3.51
1927 1947 9.202273 GTCATCTGATTTATAAGTCATCTGACC 57.798 37.037 24.50 15.48 45.85 4.02
1928 1948 8.927411 TCATCTGATTTATAAGTCATCTGACCA 58.073 33.333 10.71 0.00 45.85 4.02
1929 1949 8.986847 CATCTGATTTATAAGTCATCTGACCAC 58.013 37.037 10.71 0.00 45.85 4.16
1930 1950 8.078060 TCTGATTTATAAGTCATCTGACCACA 57.922 34.615 10.71 0.00 45.85 4.17
1931 1951 8.708378 TCTGATTTATAAGTCATCTGACCACAT 58.292 33.333 10.71 1.46 45.85 3.21
1932 1952 8.893219 TGATTTATAAGTCATCTGACCACATC 57.107 34.615 6.58 2.41 45.85 3.06
1933 1953 8.708378 TGATTTATAAGTCATCTGACCACATCT 58.292 33.333 6.58 0.00 45.85 2.90
1934 1954 9.553064 GATTTATAAGTCATCTGACCACATCTT 57.447 33.333 6.71 0.00 45.85 2.40
1935 1955 9.911788 ATTTATAAGTCATCTGACCACATCTTT 57.088 29.630 6.71 0.00 45.85 2.52
1936 1956 9.739276 TTTATAAGTCATCTGACCACATCTTTT 57.261 29.630 6.71 0.00 45.85 2.27
1937 1957 9.739276 TTATAAGTCATCTGACCACATCTTTTT 57.261 29.630 6.71 0.00 45.85 1.94
1939 1959 7.440523 AAGTCATCTGACCACATCTTTTTAC 57.559 36.000 6.71 0.00 45.85 2.01
1940 1960 5.940470 AGTCATCTGACCACATCTTTTTACC 59.060 40.000 6.71 0.00 45.85 2.85
1941 1961 5.940470 GTCATCTGACCACATCTTTTTACCT 59.060 40.000 0.00 0.00 39.07 3.08
1942 1962 6.431234 GTCATCTGACCACATCTTTTTACCTT 59.569 38.462 0.00 0.00 39.07 3.50
1943 1963 7.606456 GTCATCTGACCACATCTTTTTACCTTA 59.394 37.037 0.00 0.00 39.07 2.69
1944 1964 8.328758 TCATCTGACCACATCTTTTTACCTTAT 58.671 33.333 0.00 0.00 0.00 1.73
1945 1965 8.960591 CATCTGACCACATCTTTTTACCTTATT 58.039 33.333 0.00 0.00 0.00 1.40
1946 1966 8.934023 TCTGACCACATCTTTTTACCTTATTT 57.066 30.769 0.00 0.00 0.00 1.40
1947 1967 9.362151 TCTGACCACATCTTTTTACCTTATTTT 57.638 29.630 0.00 0.00 0.00 1.82
1948 1968 9.981114 CTGACCACATCTTTTTACCTTATTTTT 57.019 29.630 0.00 0.00 0.00 1.94
1971 1991 9.747898 TTTTTATATAAAGGTGGTGTGACTCAT 57.252 29.630 7.91 0.00 0.00 2.90
1972 1992 9.747898 TTTTATATAAAGGTGGTGTGACTCATT 57.252 29.630 7.91 0.00 0.00 2.57
1976 1996 9.747898 ATATAAAGGTGGTGTGACTCATTAAAA 57.252 29.630 0.00 0.00 0.00 1.52
1977 1997 6.783708 AAAGGTGGTGTGACTCATTAAAAA 57.216 33.333 0.00 0.00 0.00 1.94
2013 2033 6.819397 AGTTTTAAGTTAGGATGGAGCAAC 57.181 37.500 0.00 0.00 0.00 4.17
2014 2034 6.543735 AGTTTTAAGTTAGGATGGAGCAACT 58.456 36.000 0.00 0.00 32.73 3.16
2015 2035 7.004691 AGTTTTAAGTTAGGATGGAGCAACTT 58.995 34.615 4.24 4.24 42.32 2.66
2016 2036 8.161425 AGTTTTAAGTTAGGATGGAGCAACTTA 58.839 33.333 0.00 0.00 40.63 2.24
2017 2037 8.957466 GTTTTAAGTTAGGATGGAGCAACTTAT 58.043 33.333 6.60 0.00 40.95 1.73
2020 2040 9.609346 TTAAGTTAGGATGGAGCAACTTATAAC 57.391 33.333 6.60 0.00 40.95 1.89
2021 2041 7.439108 AGTTAGGATGGAGCAACTTATAACT 57.561 36.000 0.00 0.00 0.00 2.24
2022 2042 7.862675 AGTTAGGATGGAGCAACTTATAACTT 58.137 34.615 0.00 0.00 29.17 2.66
2023 2043 8.989131 AGTTAGGATGGAGCAACTTATAACTTA 58.011 33.333 0.00 0.00 29.17 2.24
2024 2044 9.780186 GTTAGGATGGAGCAACTTATAACTTAT 57.220 33.333 0.00 0.00 0.00 1.73
2044 2064 9.606631 AACTTATAAGTTGAATTTGTTTGGCAA 57.393 25.926 26.30 0.00 46.80 4.52
2045 2065 9.606631 ACTTATAAGTTGAATTTGTTTGGCAAA 57.393 25.926 12.50 8.93 42.82 3.68
2082 2102 9.724839 TTTTTCCACTTTTCGACTTATAAGTTG 57.275 29.630 22.32 22.32 39.88 3.16
2083 2103 7.429636 TTCCACTTTTCGACTTATAAGTTGG 57.570 36.000 25.99 21.99 39.88 3.77
2084 2104 6.527423 TCCACTTTTCGACTTATAAGTTGGT 58.473 36.000 25.99 16.17 39.88 3.67
2085 2105 6.425721 TCCACTTTTCGACTTATAAGTTGGTG 59.574 38.462 25.99 23.47 39.88 4.17
2086 2106 6.425721 CCACTTTTCGACTTATAAGTTGGTGA 59.574 38.462 26.00 17.35 39.88 4.02
2087 2107 7.288672 CACTTTTCGACTTATAAGTTGGTGAC 58.711 38.462 25.99 10.35 39.88 3.67
2088 2108 7.170998 CACTTTTCGACTTATAAGTTGGTGACT 59.829 37.037 25.99 9.24 39.88 3.41
2100 2120 6.783708 AAGTTGGTGACTTATTTGAAACCA 57.216 33.333 0.00 0.00 46.61 3.67
2101 2121 6.783708 AGTTGGTGACTTATTTGAAACCAA 57.216 33.333 1.07 1.07 43.50 3.67
2102 2122 7.176589 AGTTGGTGACTTATTTGAAACCAAA 57.823 32.000 6.65 0.00 46.21 3.28
2103 2123 7.039270 AGTTGGTGACTTATTTGAAACCAAAC 58.961 34.615 6.65 2.75 46.21 2.93
2104 2124 6.531503 TGGTGACTTATTTGAAACCAAACA 57.468 33.333 0.00 0.00 36.48 2.83
2105 2125 7.118496 TGGTGACTTATTTGAAACCAAACAT 57.882 32.000 0.00 0.00 36.48 2.71
2106 2126 6.983307 TGGTGACTTATTTGAAACCAAACATG 59.017 34.615 0.00 0.00 36.48 3.21
2107 2127 6.423604 GGTGACTTATTTGAAACCAAACATGG 59.576 38.462 0.00 0.00 36.48 3.66
2108 2128 5.988561 TGACTTATTTGAAACCAAACATGGC 59.011 36.000 0.00 0.00 36.48 4.40
2109 2129 5.304778 ACTTATTTGAAACCAAACATGGCC 58.695 37.500 0.00 0.00 36.48 5.36
2110 2130 5.071653 ACTTATTTGAAACCAAACATGGCCT 59.928 36.000 3.32 0.00 36.48 5.19
2111 2131 6.268847 ACTTATTTGAAACCAAACATGGCCTA 59.731 34.615 3.32 0.00 36.48 3.93
2141 2161 1.453155 AAAATCTGCGCTACACAGGG 58.547 50.000 9.73 0.00 35.78 4.45
2142 2162 0.324943 AAATCTGCGCTACACAGGGT 59.675 50.000 9.73 0.00 37.07 4.34
2143 2163 1.191535 AATCTGCGCTACACAGGGTA 58.808 50.000 9.73 0.00 37.07 3.69
2144 2164 0.460311 ATCTGCGCTACACAGGGTAC 59.540 55.000 9.73 0.00 37.07 3.34
2145 2165 0.611062 TCTGCGCTACACAGGGTACT 60.611 55.000 9.73 0.00 37.07 2.73
2146 2166 0.179134 CTGCGCTACACAGGGTACTC 60.179 60.000 9.73 0.00 37.07 2.59
2147 2167 1.226603 GCGCTACACAGGGTACTCG 60.227 63.158 0.00 0.00 37.07 4.18
2148 2168 1.651240 GCGCTACACAGGGTACTCGA 61.651 60.000 0.00 0.00 37.07 4.04
2149 2169 0.377554 CGCTACACAGGGTACTCGAG 59.622 60.000 11.84 11.84 0.00 4.04
2172 2192 2.674380 CGGCTTGCCTGCTCCTTT 60.674 61.111 10.12 0.00 0.00 3.11
2215 2947 2.431057 CCACTTAATCCTACGGCTGTCT 59.569 50.000 0.00 0.00 0.00 3.41
2309 3257 3.101437 TGCTCCAATCAAATCAAGCCAT 58.899 40.909 0.00 0.00 0.00 4.40
2360 3308 1.446966 GGAGCAGGCAAGTCTCGTC 60.447 63.158 0.00 0.00 0.00 4.20
2361 3309 1.446966 GAGCAGGCAAGTCTCGTCC 60.447 63.158 0.00 0.00 0.00 4.79
2392 3340 4.342092 AGTGCTTTAGAAAGGTTGCAACAT 59.658 37.500 29.55 21.72 36.53 2.71
2393 3341 5.534654 AGTGCTTTAGAAAGGTTGCAACATA 59.465 36.000 29.55 6.11 36.53 2.29
2394 3342 5.629435 GTGCTTTAGAAAGGTTGCAACATAC 59.371 40.000 29.55 19.65 36.53 2.39
2395 3343 5.300539 TGCTTTAGAAAGGTTGCAACATACA 59.699 36.000 29.55 7.33 36.53 2.29
2408 3356 6.007936 TGCAACATACACTTGTATTTCCAC 57.992 37.500 0.00 0.00 39.06 4.02
2409 3357 5.048364 TGCAACATACACTTGTATTTCCACC 60.048 40.000 0.00 0.00 39.06 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 127 5.303589 TGCAGCCCTATACGTAATTAAGTCT 59.696 40.000 7.35 1.28 0.00 3.24
126 129 5.540400 TGCAGCCCTATACGTAATTAAGT 57.460 39.130 9.06 9.06 0.00 2.24
127 130 6.220930 TCTTGCAGCCCTATACGTAATTAAG 58.779 40.000 0.00 0.00 0.00 1.85
128 131 6.164417 TCTTGCAGCCCTATACGTAATTAA 57.836 37.500 0.00 0.00 0.00 1.40
130 133 4.682778 TCTTGCAGCCCTATACGTAATT 57.317 40.909 0.00 0.00 0.00 1.40
131 134 4.682778 TTCTTGCAGCCCTATACGTAAT 57.317 40.909 0.00 0.00 0.00 1.89
132 135 4.475051 TTTCTTGCAGCCCTATACGTAA 57.525 40.909 0.00 0.00 0.00 3.18
133 136 4.439057 CTTTTCTTGCAGCCCTATACGTA 58.561 43.478 0.00 0.00 0.00 3.57
134 137 3.270877 CTTTTCTTGCAGCCCTATACGT 58.729 45.455 0.00 0.00 0.00 3.57
135 138 2.032178 GCTTTTCTTGCAGCCCTATACG 59.968 50.000 0.00 0.00 0.00 3.06
136 139 3.016736 TGCTTTTCTTGCAGCCCTATAC 58.983 45.455 0.00 0.00 35.31 1.47
137 140 3.016736 GTGCTTTTCTTGCAGCCCTATA 58.983 45.455 0.00 0.00 41.41 1.31
245 249 2.034939 TCGTTTCTCGGTCAAGCTACAA 59.965 45.455 0.00 0.00 40.32 2.41
460 465 5.258456 AGTCGACCACGTGACATAATTAT 57.742 39.130 19.30 0.00 40.69 1.28
614 622 6.172136 AGCTGTAGAATATGACTCATGCTT 57.828 37.500 1.42 0.00 0.00 3.91
653 661 5.689383 AATTCAAGCGAGCTCAAACTAAA 57.311 34.783 15.40 6.57 0.00 1.85
718 726 2.102109 TTAGGGCCGCAAACGAGTCA 62.102 55.000 0.00 0.00 43.93 3.41
811 820 2.432628 CCAACGTCCAGCCTCGAC 60.433 66.667 0.00 0.00 0.00 4.20
929 938 0.179268 GTTAACGCAAGGCACGTACG 60.179 55.000 15.01 15.01 44.30 3.67
930 939 1.142474 AGTTAACGCAAGGCACGTAC 58.858 50.000 0.00 0.00 44.30 3.67
1146 1158 1.127567 AGGACAGCACTGCCAACCTA 61.128 55.000 11.84 0.00 31.93 3.08
1228 1240 0.450482 CGCTACGCTTCAACGTTTGG 60.450 55.000 0.00 0.00 45.75 3.28
1252 1270 4.230603 CATGAAGAGCCATGCCGT 57.769 55.556 0.00 0.00 37.68 5.68
1261 1279 1.113253 CTACGTACGCGCATGAAGAG 58.887 55.000 16.72 0.00 42.83 2.85
1271 1289 0.738412 AACATGCACCCTACGTACGC 60.738 55.000 16.72 0.00 0.00 4.42
1500 1520 3.771160 GGGCGACATGAGTCCGGT 61.771 66.667 0.00 0.00 41.87 5.28
1523 1543 4.320870 GCTATCTACCGAGCTAAGAGAGT 58.679 47.826 9.76 0.00 35.73 3.24
1525 1545 3.327626 CGCTATCTACCGAGCTAAGAGA 58.672 50.000 0.00 0.00 36.50 3.10
1526 1546 2.159626 GCGCTATCTACCGAGCTAAGAG 60.160 54.545 0.00 0.00 36.50 2.85
1527 1547 1.805345 GCGCTATCTACCGAGCTAAGA 59.195 52.381 0.00 0.00 36.50 2.10
1528 1548 1.464355 CGCGCTATCTACCGAGCTAAG 60.464 57.143 5.56 0.00 36.50 2.18
1529 1549 0.516001 CGCGCTATCTACCGAGCTAA 59.484 55.000 5.56 0.00 36.50 3.09
1609 1629 1.064952 CACCAAGACAAACCGAACACC 59.935 52.381 0.00 0.00 0.00 4.16
1615 1635 1.841663 CGCTCCACCAAGACAAACCG 61.842 60.000 0.00 0.00 0.00 4.44
1663 1683 1.154221 GGGTGCCCCTACCACAAAA 59.846 57.895 3.16 0.00 42.69 2.44
1681 1701 2.166459 TCTCTGTGCGACCTTATCCTTG 59.834 50.000 0.00 0.00 0.00 3.61
1694 1714 0.543749 ATTAGTGGCCCTCTCTGTGC 59.456 55.000 0.00 0.00 0.00 4.57
1785 1805 2.884639 TGTCAGATCACTGTCACGAAGA 59.115 45.455 0.00 0.00 43.81 2.87
1805 1825 6.346120 CGGAATATTCAAGAGTAGCATCGTTG 60.346 42.308 17.07 0.00 0.00 4.10
1838 1858 9.734984 TTGAAACCAAACAAACCCTTAATTTTA 57.265 25.926 0.00 0.00 0.00 1.52
1848 1868 7.039270 AGTGACTTATTGAAACCAAACAAACC 58.961 34.615 0.00 0.00 0.00 3.27
1849 1869 8.379902 CAAGTGACTTATTGAAACCAAACAAAC 58.620 33.333 0.00 0.00 0.00 2.93
1850 1870 8.307483 TCAAGTGACTTATTGAAACCAAACAAA 58.693 29.630 0.00 0.00 32.66 2.83
1851 1871 7.757624 GTCAAGTGACTTATTGAAACCAAACAA 59.242 33.333 0.00 0.00 41.65 2.83
1852 1872 7.254852 GTCAAGTGACTTATTGAAACCAAACA 58.745 34.615 0.00 0.00 41.65 2.83
1853 1873 7.679659 GTCAAGTGACTTATTGAAACCAAAC 57.320 36.000 0.00 0.00 41.65 2.93
1876 1896 9.131791 ACAACCAAAATGACTTGACTTATAAGT 57.868 29.630 18.05 18.05 43.16 2.24
1877 1897 9.612620 GACAACCAAAATGACTTGACTTATAAG 57.387 33.333 11.05 11.05 0.00 1.73
1878 1898 9.126151 TGACAACCAAAATGACTTGACTTATAA 57.874 29.630 0.00 0.00 0.00 0.98
1879 1899 8.684386 TGACAACCAAAATGACTTGACTTATA 57.316 30.769 0.00 0.00 0.00 0.98
1880 1900 7.581213 TGACAACCAAAATGACTTGACTTAT 57.419 32.000 0.00 0.00 0.00 1.73
1881 1901 7.502226 AGATGACAACCAAAATGACTTGACTTA 59.498 33.333 0.00 0.00 0.00 2.24
1882 1902 5.913137 TGACAACCAAAATGACTTGACTT 57.087 34.783 0.00 0.00 0.00 3.01
1883 1903 5.829924 AGATGACAACCAAAATGACTTGACT 59.170 36.000 0.00 0.00 0.00 3.41
1884 1904 5.916883 CAGATGACAACCAAAATGACTTGAC 59.083 40.000 0.00 0.00 0.00 3.18
1885 1905 5.827267 TCAGATGACAACCAAAATGACTTGA 59.173 36.000 0.00 0.00 0.00 3.02
1886 1906 6.075762 TCAGATGACAACCAAAATGACTTG 57.924 37.500 0.00 0.00 0.00 3.16
1887 1907 6.906157 ATCAGATGACAACCAAAATGACTT 57.094 33.333 0.00 0.00 0.00 3.01
1888 1908 6.906157 AATCAGATGACAACCAAAATGACT 57.094 33.333 0.00 0.00 0.00 3.41
1894 1914 9.513906 TGACTTATAAATCAGATGACAACCAAA 57.486 29.630 0.00 0.00 0.00 3.28
1895 1915 9.685276 ATGACTTATAAATCAGATGACAACCAA 57.315 29.630 2.76 0.00 0.00 3.67
1896 1916 9.330063 GATGACTTATAAATCAGATGACAACCA 57.670 33.333 2.76 0.00 0.00 3.67
1897 1917 9.553064 AGATGACTTATAAATCAGATGACAACC 57.447 33.333 2.76 0.00 0.00 3.77
1900 1920 9.755804 GTCAGATGACTTATAAATCAGATGACA 57.244 33.333 24.72 6.42 40.51 3.58
1901 1921 9.202273 GGTCAGATGACTTATAAATCAGATGAC 57.798 37.037 23.12 23.12 44.20 3.06
1902 1922 8.927411 TGGTCAGATGACTTATAAATCAGATGA 58.073 33.333 12.43 6.32 44.20 2.92
1903 1923 8.986847 GTGGTCAGATGACTTATAAATCAGATG 58.013 37.037 12.43 4.24 44.20 2.90
1904 1924 8.708378 TGTGGTCAGATGACTTATAAATCAGAT 58.292 33.333 12.43 0.00 44.20 2.90
1905 1925 8.078060 TGTGGTCAGATGACTTATAAATCAGA 57.922 34.615 12.43 0.00 44.20 3.27
1906 1926 8.899427 ATGTGGTCAGATGACTTATAAATCAG 57.101 34.615 12.43 0.00 44.20 2.90
1907 1927 8.708378 AGATGTGGTCAGATGACTTATAAATCA 58.292 33.333 12.43 0.00 44.20 2.57
1908 1928 9.553064 AAGATGTGGTCAGATGACTTATAAATC 57.447 33.333 12.43 7.28 44.20 2.17
1909 1929 9.911788 AAAGATGTGGTCAGATGACTTATAAAT 57.088 29.630 12.43 0.00 44.20 1.40
1910 1930 9.739276 AAAAGATGTGGTCAGATGACTTATAAA 57.261 29.630 12.43 0.00 44.20 1.40
1911 1931 9.739276 AAAAAGATGTGGTCAGATGACTTATAA 57.261 29.630 12.43 0.00 44.20 0.98
1913 1933 9.167311 GTAAAAAGATGTGGTCAGATGACTTAT 57.833 33.333 12.43 5.21 44.20 1.73
1914 1934 7.606456 GGTAAAAAGATGTGGTCAGATGACTTA 59.394 37.037 12.43 0.40 44.20 2.24
1915 1935 6.431234 GGTAAAAAGATGTGGTCAGATGACTT 59.569 38.462 12.43 0.00 44.20 3.01
1916 1936 5.940470 GGTAAAAAGATGTGGTCAGATGACT 59.060 40.000 12.43 0.00 44.20 3.41
1917 1937 5.940470 AGGTAAAAAGATGTGGTCAGATGAC 59.060 40.000 4.33 4.33 44.04 3.06
1918 1938 6.126863 AGGTAAAAAGATGTGGTCAGATGA 57.873 37.500 0.00 0.00 0.00 2.92
1919 1939 6.824305 AAGGTAAAAAGATGTGGTCAGATG 57.176 37.500 0.00 0.00 0.00 2.90
1920 1940 9.533831 AAATAAGGTAAAAAGATGTGGTCAGAT 57.466 29.630 0.00 0.00 0.00 2.90
1921 1941 8.934023 AAATAAGGTAAAAAGATGTGGTCAGA 57.066 30.769 0.00 0.00 0.00 3.27
1922 1942 9.981114 AAAAATAAGGTAAAAAGATGTGGTCAG 57.019 29.630 0.00 0.00 0.00 3.51
1945 1965 9.747898 ATGAGTCACACCACCTTTATATAAAAA 57.252 29.630 9.15 0.00 0.00 1.94
1946 1966 9.747898 AATGAGTCACACCACCTTTATATAAAA 57.252 29.630 9.15 0.00 0.00 1.52
1950 1970 9.747898 TTTTAATGAGTCACACCACCTTTATAT 57.252 29.630 0.00 0.00 0.00 0.86
1951 1971 9.575868 TTTTTAATGAGTCACACCACCTTTATA 57.424 29.630 0.00 0.00 0.00 0.98
1952 1972 8.472007 TTTTTAATGAGTCACACCACCTTTAT 57.528 30.769 0.00 0.00 0.00 1.40
1953 1973 7.883391 TTTTTAATGAGTCACACCACCTTTA 57.117 32.000 0.00 0.00 0.00 1.85
1954 1974 6.783708 TTTTTAATGAGTCACACCACCTTT 57.216 33.333 0.00 0.00 0.00 3.11
1987 2007 8.957466 GTTGCTCCATCCTAACTTAAAACTTAT 58.043 33.333 0.00 0.00 0.00 1.73
1988 2008 8.161425 AGTTGCTCCATCCTAACTTAAAACTTA 58.839 33.333 0.00 0.00 29.65 2.24
1989 2009 7.004691 AGTTGCTCCATCCTAACTTAAAACTT 58.995 34.615 0.00 0.00 29.65 2.66
1990 2010 6.543735 AGTTGCTCCATCCTAACTTAAAACT 58.456 36.000 0.00 0.00 29.65 2.66
1991 2011 6.819397 AGTTGCTCCATCCTAACTTAAAAC 57.181 37.500 0.00 0.00 29.65 2.43
1994 2014 9.609346 GTTATAAGTTGCTCCATCCTAACTTAA 57.391 33.333 11.09 0.00 44.18 1.85
1995 2015 8.989131 AGTTATAAGTTGCTCCATCCTAACTTA 58.011 33.333 9.88 9.88 44.72 2.24
1996 2016 7.862675 AGTTATAAGTTGCTCCATCCTAACTT 58.137 34.615 0.00 0.00 43.48 2.66
1997 2017 7.439108 AGTTATAAGTTGCTCCATCCTAACT 57.561 36.000 0.00 0.00 35.06 2.24
1998 2018 9.780186 ATAAGTTATAAGTTGCTCCATCCTAAC 57.220 33.333 14.62 0.00 0.00 2.34
2018 2038 9.606631 TTGCCAAACAAATTCAACTTATAAGTT 57.393 25.926 22.49 22.49 41.78 2.66
2019 2039 9.606631 TTTGCCAAACAAATTCAACTTATAAGT 57.393 25.926 12.50 12.50 43.35 2.24
2056 2076 9.724839 CAACTTATAAGTCGAAAAGTGGAAAAA 57.275 29.630 18.28 0.00 38.57 1.94
2057 2077 8.347035 CCAACTTATAAGTCGAAAAGTGGAAAA 58.653 33.333 18.28 0.00 38.57 2.29
2058 2078 7.499895 ACCAACTTATAAGTCGAAAAGTGGAAA 59.500 33.333 26.18 0.00 38.57 3.13
2059 2079 6.993902 ACCAACTTATAAGTCGAAAAGTGGAA 59.006 34.615 26.18 0.00 38.57 3.53
2060 2080 6.425721 CACCAACTTATAAGTCGAAAAGTGGA 59.574 38.462 26.18 0.00 38.57 4.02
2061 2081 6.425721 TCACCAACTTATAAGTCGAAAAGTGG 59.574 38.462 18.28 19.93 38.57 4.00
2062 2082 7.170998 AGTCACCAACTTATAAGTCGAAAAGTG 59.829 37.037 18.28 16.78 38.57 3.16
2063 2083 7.215085 AGTCACCAACTTATAAGTCGAAAAGT 58.785 34.615 18.28 7.29 38.57 2.66
2064 2084 7.653767 AGTCACCAACTTATAAGTCGAAAAG 57.346 36.000 18.28 7.33 38.57 2.27
2077 2097 7.547722 GTTTGGTTTCAAATAAGTCACCAACTT 59.452 33.333 1.03 0.00 42.59 2.66
2078 2098 6.783708 TTGGTTTCAAATAAGTCACCAACT 57.216 33.333 0.00 0.00 38.97 3.16
2079 2099 6.814146 TGTTTGGTTTCAAATAAGTCACCAAC 59.186 34.615 1.03 0.00 42.59 3.77
2080 2100 6.936279 TGTTTGGTTTCAAATAAGTCACCAA 58.064 32.000 0.00 0.00 43.73 3.67
2081 2101 6.531503 TGTTTGGTTTCAAATAAGTCACCA 57.468 33.333 0.00 0.00 43.73 4.17
2082 2102 6.423604 CCATGTTTGGTTTCAAATAAGTCACC 59.576 38.462 0.00 0.00 43.73 4.02
2083 2103 6.073819 GCCATGTTTGGTTTCAAATAAGTCAC 60.074 38.462 0.00 0.00 45.57 3.67
2084 2104 5.988561 GCCATGTTTGGTTTCAAATAAGTCA 59.011 36.000 0.00 0.00 45.57 3.41
2085 2105 5.408299 GGCCATGTTTGGTTTCAAATAAGTC 59.592 40.000 0.00 0.00 45.57 3.01
2086 2106 5.071653 AGGCCATGTTTGGTTTCAAATAAGT 59.928 36.000 5.01 0.00 45.57 2.24
2087 2107 5.550290 AGGCCATGTTTGGTTTCAAATAAG 58.450 37.500 5.01 0.00 45.57 1.73
2088 2108 5.559148 AGGCCATGTTTGGTTTCAAATAA 57.441 34.783 5.01 0.00 45.57 1.40
2089 2109 6.672266 TTAGGCCATGTTTGGTTTCAAATA 57.328 33.333 5.01 0.00 45.57 1.40
2090 2110 5.550290 CTTAGGCCATGTTTGGTTTCAAAT 58.450 37.500 5.01 0.00 45.57 2.32
2091 2111 4.742138 GCTTAGGCCATGTTTGGTTTCAAA 60.742 41.667 5.01 0.00 45.57 2.69
2092 2112 3.244044 GCTTAGGCCATGTTTGGTTTCAA 60.244 43.478 5.01 0.00 45.57 2.69
2093 2113 2.298729 GCTTAGGCCATGTTTGGTTTCA 59.701 45.455 5.01 0.00 45.57 2.69
2094 2114 2.562738 AGCTTAGGCCATGTTTGGTTTC 59.437 45.455 5.01 0.00 45.57 2.78
2095 2115 2.608623 AGCTTAGGCCATGTTTGGTTT 58.391 42.857 5.01 0.00 45.57 3.27
2096 2116 2.309136 AGCTTAGGCCATGTTTGGTT 57.691 45.000 5.01 0.00 45.57 3.67
2097 2117 2.945890 GCTAGCTTAGGCCATGTTTGGT 60.946 50.000 7.70 0.00 45.57 3.67
2098 2118 1.678101 GCTAGCTTAGGCCATGTTTGG 59.322 52.381 7.70 0.00 46.66 3.28
2099 2119 1.678101 GGCTAGCTTAGGCCATGTTTG 59.322 52.381 15.72 0.00 46.84 2.93
2100 2120 2.058593 GGCTAGCTTAGGCCATGTTT 57.941 50.000 15.72 0.00 46.84 2.83
2101 2121 3.808984 GGCTAGCTTAGGCCATGTT 57.191 52.632 15.72 0.00 46.84 2.71
2108 2128 4.212214 CGCAGATTTTAAGGCTAGCTTAGG 59.788 45.833 15.72 0.00 0.00 2.69
2109 2129 4.319118 GCGCAGATTTTAAGGCTAGCTTAG 60.319 45.833 15.72 0.62 0.00 2.18
2110 2130 3.560068 GCGCAGATTTTAAGGCTAGCTTA 59.440 43.478 15.72 8.45 0.00 3.09
2111 2131 2.356069 GCGCAGATTTTAAGGCTAGCTT 59.644 45.455 15.72 3.40 0.00 3.74
2121 2141 2.027561 ACCCTGTGTAGCGCAGATTTTA 60.028 45.455 11.47 0.00 43.78 1.52
2141 2161 1.108132 AAGCCGGATCCCTCGAGTAC 61.108 60.000 5.05 0.00 0.00 2.73
2142 2162 1.107538 CAAGCCGGATCCCTCGAGTA 61.108 60.000 5.05 0.00 0.00 2.59
2143 2163 2.042843 AAGCCGGATCCCTCGAGT 60.043 61.111 5.05 0.00 0.00 4.18
2144 2164 2.419198 CAAGCCGGATCCCTCGAG 59.581 66.667 5.05 5.13 0.00 4.04
2145 2165 3.849951 GCAAGCCGGATCCCTCGA 61.850 66.667 5.05 0.00 0.00 4.04
2146 2166 4.918201 GGCAAGCCGGATCCCTCG 62.918 72.222 5.05 0.00 0.00 4.63
2147 2167 3.483869 AGGCAAGCCGGATCCCTC 61.484 66.667 5.05 0.00 41.95 4.30
2148 2168 3.801997 CAGGCAAGCCGGATCCCT 61.802 66.667 5.05 5.70 41.95 4.20
2170 2190 2.674754 GGATGGGAGCACGGGAAA 59.325 61.111 0.00 0.00 0.00 3.13
2234 2966 7.690454 TCAGGAGGGAACATGATTAGATTAA 57.310 36.000 0.00 0.00 0.00 1.40
2253 3201 1.643811 CCCACCCCCTTAAAATCAGGA 59.356 52.381 0.00 0.00 32.41 3.86
2280 3228 7.546667 GCTTGATTTGATTGGAGCAAAATAAGA 59.453 33.333 15.76 0.00 38.57 2.10
2309 3257 1.379443 ATCCGTGCTCCCGTCTACA 60.379 57.895 0.00 0.00 0.00 2.74
2360 3308 3.482722 TTCTAAAGCACTCGAGTACGG 57.517 47.619 19.57 7.44 40.21 4.02
2361 3309 3.852536 CCTTTCTAAAGCACTCGAGTACG 59.147 47.826 19.57 8.25 36.45 3.67
2392 3340 8.871629 ATTAACATGGTGGAAATACAAGTGTA 57.128 30.769 0.00 0.00 34.67 2.90
2393 3341 7.775053 ATTAACATGGTGGAAATACAAGTGT 57.225 32.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.