Multiple sequence alignment - TraesCS1D01G134500

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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 TraesCS1D01G134500 chr1D 100.000 4143 0 0 1 4143 171165337 171161195 0.000000e+00 7651.0
1 TraesCS1D01G134500 chr1D 93.571 280 8 4 1781 2050 344235918 344235639 3.860000e-110 409.0
2 TraesCS1D01G134500 chr1D 81.057 227 37 6 3922 4143 153016852 153016627 4.260000e-40 176.0
3 TraesCS1D01G134500 chr1A 95.490 1796 60 11 4 1783 229172152 229170362 0.000000e+00 2848.0
4 TraesCS1D01G134500 chr1A 92.422 1953 104 9 2093 4004 229170300 229168351 0.000000e+00 2747.0
5 TraesCS1D01G134500 chr1A 81.416 226 34 7 3922 4142 283475238 283475460 1.180000e-40 178.0
6 TraesCS1D01G134500 chr1A 79.918 244 43 6 3905 4143 218048182 218047940 1.530000e-39 174.0
7 TraesCS1D01G134500 chr1B 91.633 1984 145 9 2180 4143 226358206 226356224 0.000000e+00 2724.0
8 TraesCS1D01G134500 chr1B 93.410 1730 90 11 1 1720 226360027 226358312 0.000000e+00 2542.0
9 TraesCS1D01G134500 chr1B 100.000 31 0 0 2136 2166 226358302 226358272 1.610000e-04 58.4
10 TraesCS1D01G134500 chr1B 100.000 29 0 0 2152 2180 226358258 226358230 2.000000e-03 54.7
11 TraesCS1D01G134500 chr4D 81.905 525 77 14 2598 3115 443520825 443521338 1.060000e-115 427.0
12 TraesCS1D01G134500 chr4D 93.929 280 7 4 1781 2050 293775792 293776071 8.290000e-112 414.0
13 TraesCS1D01G134500 chr4D 93.571 280 8 4 1781 2050 201924657 201924378 3.860000e-110 409.0
14 TraesCS1D01G134500 chr4D 93.571 280 8 4 1781 2050 212032175 212031896 3.860000e-110 409.0
15 TraesCS1D01G134500 chr4D 93.214 280 9 5 1781 2050 222210881 222210602 1.790000e-108 403.0
16 TraesCS1D01G134500 chr4D 80.606 165 29 1 2470 2631 116270798 116270962 1.560000e-24 124.0
17 TraesCS1D01G134500 chr4B 81.524 525 79 14 2598 3115 552845971 552846484 2.300000e-112 416.0
18 TraesCS1D01G134500 chr4B 81.437 167 26 5 129 293 77343717 77343554 9.350000e-27 132.0
19 TraesCS1D01G134500 chr4B 80.723 166 27 3 2470 2631 178071729 178071893 1.560000e-24 124.0
20 TraesCS1D01G134500 chr4A 81.524 525 79 16 2598 3115 24217020 24216507 2.300000e-112 416.0
21 TraesCS1D01G134500 chr4A 79.394 165 31 1 2470 2631 460239586 460239422 3.390000e-21 113.0
22 TraesCS1D01G134500 chr6B 93.929 280 7 4 1781 2050 6917726 6918005 8.290000e-112 414.0
23 TraesCS1D01G134500 chr6B 81.073 317 37 16 1781 2084 19070997 19071303 8.960000e-57 231.0
24 TraesCS1D01G134500 chr6B 80.162 247 42 7 3903 4143 325028614 325028369 1.180000e-40 178.0
25 TraesCS1D01G134500 chr7D 93.571 280 8 4 1781 2050 119293464 119293743 3.860000e-110 409.0
26 TraesCS1D01G134500 chr7D 94.595 37 1 1 1616 1651 617019060 617019024 5.790000e-04 56.5
27 TraesCS1D01G134500 chr2D 93.525 278 10 3 1781 2050 530699180 530699457 1.390000e-109 407.0
28 TraesCS1D01G134500 chr2D 93.525 278 11 4 1779 2049 535557686 535557963 1.390000e-109 407.0
29 TraesCS1D01G134500 chr2D 80.328 244 42 6 3905 4143 274738564 274738806 3.290000e-41 180.0
30 TraesCS1D01G134500 chr2D 79.874 159 32 0 2548 2706 39320896 39320738 2.620000e-22 117.0
31 TraesCS1D01G134500 chr2D 79.245 159 33 0 2548 2706 50238187 50238345 1.220000e-20 111.0
32 TraesCS1D01G134500 chr3B 81.529 314 41 14 1781 2081 122382960 122382651 4.140000e-60 243.0
33 TraesCS1D01G134500 chr5A 81.858 226 33 7 3922 4142 218933092 218933314 2.540000e-42 183.0
34 TraesCS1D01G134500 chr2B 81.498 227 36 6 3922 4143 318518846 318518621 9.150000e-42 182.0
35 TraesCS1D01G134500 chr2B 80.660 212 39 2 83 293 315497481 315497691 3.310000e-36 163.0
36 TraesCS1D01G134500 chr2B 79.874 159 32 0 2548 2706 78072107 78072265 2.620000e-22 117.0
37 TraesCS1D01G134500 chr2B 100.000 29 0 0 1515 1543 551634260 551634232 2.000000e-03 54.7
38 TraesCS1D01G134500 chr3D 77.778 297 60 5 2 295 246307126 246306833 1.180000e-40 178.0
39 TraesCS1D01G134500 chr3D 89.362 47 4 1 2047 2092 416948719 416948673 1.610000e-04 58.4
40 TraesCS1D01G134500 chr6D 81.057 227 37 6 3922 4143 209576547 209576322 4.260000e-40 176.0
41 TraesCS1D01G134500 chr6D 80.905 199 37 1 94 292 167050291 167050094 5.550000e-34 156.0
42 TraesCS1D01G134500 chr6D 78.922 204 35 8 94 293 203373063 203373262 9.350000e-27 132.0
43 TraesCS1D01G134500 chr6D 90.323 62 5 1 1722 1783 470516676 470516616 3.430000e-11 80.5
44 TraesCS1D01G134500 chr3A 82.587 201 33 2 94 293 301379575 301379376 4.260000e-40 176.0
45 TraesCS1D01G134500 chr5B 81.643 207 29 8 94 295 164775408 164775206 3.310000e-36 163.0
46 TraesCS1D01G134500 chr2A 79.245 159 33 0 2548 2706 51945270 51945428 1.220000e-20 111.0
47 TraesCS1D01G134500 chr2A 97.143 35 1 0 2065 2099 654021990 654021956 4.470000e-05 60.2
48 TraesCS1D01G134500 chr2A 100.000 29 0 0 1515 1543 613988747 613988719 2.000000e-03 54.7
49 TraesCS1D01G134500 chr7A 88.462 52 6 0 1732 1783 672279155 672279104 3.460000e-06 63.9
50 TraesCS1D01G134500 chr7A 96.970 33 0 1 1616 1647 709734258 709734226 2.000000e-03 54.7
51 TraesCS1D01G134500 chr6A 97.297 37 0 1 2065 2101 337208838 337208803 1.240000e-05 62.1
52 TraesCS1D01G134500 chr7B 94.595 37 1 1 1616 1651 711062949 711062913 5.790000e-04 56.5


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 TraesCS1D01G134500 chr1D 171161195 171165337 4142 True 7651.000 7651 100.00000 1 4143 1 chr1D.!!$R2 4142
1 TraesCS1D01G134500 chr1A 229168351 229172152 3801 True 2797.500 2848 93.95600 4 4004 2 chr1A.!!$R2 4000
2 TraesCS1D01G134500 chr1B 226356224 226360027 3803 True 1344.775 2724 96.26075 1 4143 4 chr1B.!!$R1 4142
3 TraesCS1D01G134500 chr4D 443520825 443521338 513 False 427.000 427 81.90500 2598 3115 1 chr4D.!!$F3 517
4 TraesCS1D01G134500 chr4B 552845971 552846484 513 False 416.000 416 81.52400 2598 3115 1 chr4B.!!$F2 517
5 TraesCS1D01G134500 chr4A 24216507 24217020 513 True 416.000 416 81.52400 2598 3115 1 chr4A.!!$R1 517

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
802 814 1.064296 CTGGTTCGATCGTCCGGAG 59.936 63.158 25.14 15.35 0.0 4.63 F
1323 1340 1.055338 GACAGTTGTGGTACGTACGC 58.945 55.000 16.72 14.40 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1829 0.109153 GTCCCAAGTGGTTACCGGTT 59.891 55.0 15.04 0.0 34.77 4.44 R
3263 3412 0.036105 CACTACACATGCCTGCCTGA 60.036 55.0 1.32 0.0 0.00 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
152 153 4.093743 TGAGGTAGTAGCCATGTCTCAAA 58.906 43.478 0.00 0.00 0.00 2.69
163 164 5.080969 CCATGTCTCAAATGGCTCAAATT 57.919 39.130 0.00 0.00 38.32 1.82
212 213 3.259123 TCAGTCTCAATAGCTCTTGCACA 59.741 43.478 6.95 0.00 42.74 4.57
281 283 2.825457 CCATGGGGATGACCGTAGGATA 60.825 54.545 2.85 0.00 46.09 2.59
485 487 2.303600 TGTAACCGGCTACCAGAAACAT 59.696 45.455 12.38 0.00 0.00 2.71
625 629 6.720012 ACTACTGCCTTTTGTTTGTTTTTG 57.280 33.333 0.00 0.00 0.00 2.44
668 673 5.413833 TCCTCTTGTTGAAGTAGTACTACCG 59.586 44.000 25.97 7.77 36.75 4.02
686 691 1.229315 CGAGTACCGATCCTCCTCCG 61.229 65.000 0.00 0.00 41.76 4.63
753 765 1.354101 TTTCTCTCCGTGGGCCTTTA 58.646 50.000 4.53 0.00 0.00 1.85
802 814 1.064296 CTGGTTCGATCGTCCGGAG 59.936 63.158 25.14 15.35 0.00 4.63
909 921 8.532819 TCTCTATTTTTCCAGTCTTTACCTCTC 58.467 37.037 0.00 0.00 0.00 3.20
916 928 5.202004 TCCAGTCTTTACCTCTCTACCATC 58.798 45.833 0.00 0.00 0.00 3.51
917 929 5.044030 TCCAGTCTTTACCTCTCTACCATCT 60.044 44.000 0.00 0.00 0.00 2.90
918 930 5.659079 CCAGTCTTTACCTCTCTACCATCTT 59.341 44.000 0.00 0.00 0.00 2.40
919 931 6.183360 CCAGTCTTTACCTCTCTACCATCTTC 60.183 46.154 0.00 0.00 0.00 2.87
920 932 6.605594 CAGTCTTTACCTCTCTACCATCTTCT 59.394 42.308 0.00 0.00 0.00 2.85
921 933 7.123547 CAGTCTTTACCTCTCTACCATCTTCTT 59.876 40.741 0.00 0.00 0.00 2.52
1268 1285 3.368843 GCTCCAGCAAAATCCATTTTTCG 59.631 43.478 0.00 0.00 37.86 3.46
1323 1340 1.055338 GACAGTTGTGGTACGTACGC 58.945 55.000 16.72 14.40 0.00 4.42
1604 1621 2.028484 GTCAAGGTGCACGACGGA 59.972 61.111 11.45 2.84 0.00 4.69
1778 1801 2.290008 TGTGGCACCGAGTGATACAATT 60.290 45.455 16.26 0.00 35.23 2.32
1780 1803 4.127171 GTGGCACCGAGTGATACAATTAT 58.873 43.478 6.29 0.00 35.23 1.28
1781 1804 5.163395 TGTGGCACCGAGTGATACAATTATA 60.163 40.000 16.26 0.00 35.23 0.98
1782 1805 5.756347 GTGGCACCGAGTGATACAATTATAA 59.244 40.000 6.29 0.00 35.23 0.98
1783 1806 6.259167 GTGGCACCGAGTGATACAATTATAAA 59.741 38.462 6.29 0.00 35.23 1.40
1784 1807 6.481976 TGGCACCGAGTGATACAATTATAAAG 59.518 38.462 8.04 0.00 35.23 1.85
1785 1808 6.363473 GCACCGAGTGATACAATTATAAAGC 58.637 40.000 8.04 0.00 35.23 3.51
1786 1809 6.202954 GCACCGAGTGATACAATTATAAAGCT 59.797 38.462 8.04 0.00 35.23 3.74
1787 1810 7.384115 GCACCGAGTGATACAATTATAAAGCTA 59.616 37.037 8.04 0.00 35.23 3.32
1788 1811 8.916654 CACCGAGTGATACAATTATAAAGCTAG 58.083 37.037 0.00 0.00 35.23 3.42
1789 1812 7.599245 ACCGAGTGATACAATTATAAAGCTAGC 59.401 37.037 6.62 6.62 0.00 3.42
1790 1813 7.063544 CCGAGTGATACAATTATAAAGCTAGCC 59.936 40.741 12.13 0.00 0.00 3.93
1791 1814 7.598869 CGAGTGATACAATTATAAAGCTAGCCA 59.401 37.037 12.13 0.00 0.00 4.75
1792 1815 9.442047 GAGTGATACAATTATAAAGCTAGCCAT 57.558 33.333 12.13 5.20 0.00 4.40
1797 1820 7.986085 ACAATTATAAAGCTAGCCATAGTGG 57.014 36.000 12.13 4.30 41.55 4.00
1798 1821 6.942576 ACAATTATAAAGCTAGCCATAGTGGG 59.057 38.462 12.13 3.57 38.19 4.61
1799 1822 5.499004 TTATAAAGCTAGCCATAGTGGGG 57.501 43.478 12.13 0.00 38.19 4.96
1800 1823 1.596496 AAAGCTAGCCATAGTGGGGT 58.404 50.000 12.13 0.00 38.19 4.95
1801 1824 2.489528 AAGCTAGCCATAGTGGGGTA 57.510 50.000 12.13 0.00 38.19 3.69
1802 1825 2.489528 AGCTAGCCATAGTGGGGTAA 57.510 50.000 12.13 0.00 40.18 2.85
1803 1826 2.047830 AGCTAGCCATAGTGGGGTAAC 58.952 52.381 12.13 0.00 40.18 2.50
1804 1827 1.766496 GCTAGCCATAGTGGGGTAACA 59.234 52.381 2.29 0.00 40.18 2.41
1805 1828 2.372172 GCTAGCCATAGTGGGGTAACAT 59.628 50.000 2.29 0.00 40.18 2.71
1806 1829 3.581332 GCTAGCCATAGTGGGGTAACATA 59.419 47.826 2.29 0.00 40.18 2.29
1807 1830 4.041198 GCTAGCCATAGTGGGGTAACATAA 59.959 45.833 2.29 0.00 40.18 1.90
1808 1831 4.432980 AGCCATAGTGGGGTAACATAAC 57.567 45.455 0.00 0.00 38.19 1.89
1809 1832 3.137728 AGCCATAGTGGGGTAACATAACC 59.862 47.826 0.00 0.00 38.19 2.85
1810 1833 3.735591 CCATAGTGGGGTAACATAACCG 58.264 50.000 0.00 0.00 40.73 4.44
1811 1834 3.495453 CCATAGTGGGGTAACATAACCGG 60.495 52.174 0.00 0.00 40.73 5.28
1812 1835 1.660242 AGTGGGGTAACATAACCGGT 58.340 50.000 0.00 0.00 40.73 5.28
1813 1836 2.831565 AGTGGGGTAACATAACCGGTA 58.168 47.619 8.00 0.00 40.73 4.02
1814 1837 3.180507 AGTGGGGTAACATAACCGGTAA 58.819 45.455 8.00 0.00 40.73 2.85
1815 1838 3.055167 AGTGGGGTAACATAACCGGTAAC 60.055 47.826 8.00 0.00 40.73 2.50
1816 1839 2.238395 TGGGGTAACATAACCGGTAACC 59.762 50.000 8.00 1.93 40.73 2.85
1817 1840 2.238395 GGGGTAACATAACCGGTAACCA 59.762 50.000 8.00 0.00 40.73 3.67
1818 1841 3.270027 GGGTAACATAACCGGTAACCAC 58.730 50.000 8.00 1.12 40.73 4.16
1819 1842 3.055167 GGGTAACATAACCGGTAACCACT 60.055 47.826 8.00 0.00 40.73 4.00
1820 1843 4.565444 GGGTAACATAACCGGTAACCACTT 60.565 45.833 8.00 0.00 40.73 3.16
1821 1844 4.392754 GGTAACATAACCGGTAACCACTTG 59.607 45.833 8.00 0.50 0.00 3.16
1822 1845 3.062122 ACATAACCGGTAACCACTTGG 57.938 47.619 8.00 0.00 42.17 3.61
1823 1846 2.290450 ACATAACCGGTAACCACTTGGG 60.290 50.000 8.00 0.00 44.81 4.12
1824 1847 1.727062 TAACCGGTAACCACTTGGGA 58.273 50.000 8.00 0.00 41.15 4.37
1825 1848 0.109153 AACCGGTAACCACTTGGGAC 59.891 55.000 8.00 0.00 41.15 4.46
1826 1849 0.765519 ACCGGTAACCACTTGGGACT 60.766 55.000 4.49 0.00 41.15 3.85
1827 1850 1.269012 CCGGTAACCACTTGGGACTA 58.731 55.000 0.00 0.00 41.15 2.59
1828 1851 1.206371 CCGGTAACCACTTGGGACTAG 59.794 57.143 0.00 0.00 41.15 2.57
1829 1852 1.405121 CGGTAACCACTTGGGACTAGC 60.405 57.143 0.00 0.00 41.15 3.42
1830 1853 1.626825 GGTAACCACTTGGGACTAGCA 59.373 52.381 0.00 0.00 41.15 3.49
1831 1854 2.039348 GGTAACCACTTGGGACTAGCAA 59.961 50.000 0.00 0.00 41.15 3.91
1832 1855 3.497227 GGTAACCACTTGGGACTAGCAAA 60.497 47.826 0.00 0.00 41.15 3.68
1833 1856 2.271944 ACCACTTGGGACTAGCAAAC 57.728 50.000 0.00 0.00 41.15 2.93
1834 1857 1.493022 ACCACTTGGGACTAGCAAACA 59.507 47.619 0.00 0.00 41.15 2.83
1835 1858 2.108250 ACCACTTGGGACTAGCAAACAT 59.892 45.455 0.00 0.00 41.15 2.71
1836 1859 2.489329 CCACTTGGGACTAGCAAACATG 59.511 50.000 0.00 0.00 40.01 3.21
1837 1860 2.095059 CACTTGGGACTAGCAAACATGC 60.095 50.000 0.00 0.00 0.00 4.06
1839 1862 2.584835 TGGGACTAGCAAACATGCTT 57.415 45.000 8.79 0.00 43.52 3.91
1840 1863 3.712016 TGGGACTAGCAAACATGCTTA 57.288 42.857 8.79 0.00 43.52 3.09
1841 1864 4.235079 TGGGACTAGCAAACATGCTTAT 57.765 40.909 8.79 0.00 43.52 1.73
1842 1865 3.947196 TGGGACTAGCAAACATGCTTATG 59.053 43.478 8.79 3.17 43.52 1.90
1843 1866 3.947834 GGGACTAGCAAACATGCTTATGT 59.052 43.478 8.79 6.15 43.52 2.29
1844 1867 4.201950 GGGACTAGCAAACATGCTTATGTG 60.202 45.833 8.79 0.00 43.52 3.21
1845 1868 4.201950 GGACTAGCAAACATGCTTATGTGG 60.202 45.833 8.79 0.00 43.52 4.17
1846 1869 2.660189 AGCAAACATGCTTATGTGGC 57.340 45.000 0.00 8.42 43.52 5.01
1847 1870 1.894466 AGCAAACATGCTTATGTGGCA 59.106 42.857 15.17 0.00 43.52 4.92
1848 1871 1.994779 GCAAACATGCTTATGTGGCAC 59.005 47.619 11.55 11.55 42.69 5.01
1849 1872 2.609984 GCAAACATGCTTATGTGGCACA 60.610 45.455 24.36 24.36 42.69 4.57
1867 1890 7.615582 TGGCACACAATTAAATAAGAGAGAG 57.384 36.000 0.00 0.00 0.00 3.20
1868 1891 6.599244 TGGCACACAATTAAATAAGAGAGAGG 59.401 38.462 0.00 0.00 0.00 3.69
1869 1892 6.038714 GGCACACAATTAAATAAGAGAGAGGG 59.961 42.308 0.00 0.00 0.00 4.30
1870 1893 6.599638 GCACACAATTAAATAAGAGAGAGGGT 59.400 38.462 0.00 0.00 0.00 4.34
1871 1894 7.121315 GCACACAATTAAATAAGAGAGAGGGTT 59.879 37.037 0.00 0.00 0.00 4.11
1872 1895 9.667107 CACACAATTAAATAAGAGAGAGGGTTA 57.333 33.333 0.00 0.00 0.00 2.85
1884 1907 8.943594 AAGAGAGAGGGTTATAGTAACATAGG 57.056 38.462 2.68 0.00 0.00 2.57
1885 1908 8.059565 AGAGAGAGGGTTATAGTAACATAGGT 57.940 38.462 2.68 0.00 0.00 3.08
1886 1909 9.180282 AGAGAGAGGGTTATAGTAACATAGGTA 57.820 37.037 2.68 0.00 0.00 3.08
1887 1910 9.452287 GAGAGAGGGTTATAGTAACATAGGTAG 57.548 40.741 2.68 0.00 0.00 3.18
1888 1911 9.180282 AGAGAGGGTTATAGTAACATAGGTAGA 57.820 37.037 2.68 0.00 0.00 2.59
1889 1912 9.978336 GAGAGGGTTATAGTAACATAGGTAGAT 57.022 37.037 2.68 0.00 0.00 1.98
1917 1940 9.758651 TCGTATCATGTTAAATGTTATGCTACT 57.241 29.630 0.00 0.00 0.00 2.57
1929 1952 7.806409 ATGTTATGCTACTTTATGTCATGCA 57.194 32.000 0.00 0.00 35.34 3.96
1930 1953 7.806409 TGTTATGCTACTTTATGTCATGCAT 57.194 32.000 10.02 10.02 40.50 3.96
1931 1954 7.641760 TGTTATGCTACTTTATGTCATGCATG 58.358 34.615 21.07 21.07 39.07 4.06
1932 1955 5.700722 ATGCTACTTTATGTCATGCATGG 57.299 39.130 25.97 10.76 38.13 3.66
1933 1956 3.316029 TGCTACTTTATGTCATGCATGGC 59.684 43.478 24.40 24.40 38.47 4.40
1935 1958 4.202040 GCTACTTTATGTCATGCATGGCAA 60.202 41.667 35.40 21.90 46.52 4.52
1936 1959 5.508489 GCTACTTTATGTCATGCATGGCAAT 60.508 40.000 35.40 24.63 46.52 3.56
1937 1960 6.294120 GCTACTTTATGTCATGCATGGCAATA 60.294 38.462 35.40 23.35 46.52 1.90
1938 1961 6.468333 ACTTTATGTCATGCATGGCAATAA 57.532 33.333 35.40 27.69 46.52 1.40
1939 1962 6.876155 ACTTTATGTCATGCATGGCAATAAA 58.124 32.000 35.40 30.47 46.52 1.40
1940 1963 7.502696 ACTTTATGTCATGCATGGCAATAAAT 58.497 30.769 35.40 21.84 46.52 1.40
1941 1964 8.640651 ACTTTATGTCATGCATGGCAATAAATA 58.359 29.630 35.40 20.80 46.52 1.40
1942 1965 9.647797 CTTTATGTCATGCATGGCAATAAATAT 57.352 29.630 35.40 20.43 46.52 1.28
1943 1966 8.989653 TTATGTCATGCATGGCAATAAATATG 57.010 30.769 35.40 3.21 46.52 1.78
1944 1967 5.785243 TGTCATGCATGGCAATAAATATGG 58.215 37.500 30.82 0.00 43.62 2.74
1945 1968 5.304871 TGTCATGCATGGCAATAAATATGGT 59.695 36.000 30.82 0.00 43.62 3.55
1946 1969 6.492772 TGTCATGCATGGCAATAAATATGGTA 59.507 34.615 30.82 3.13 43.62 3.25
1947 1970 7.015001 TGTCATGCATGGCAATAAATATGGTAA 59.985 33.333 30.82 2.65 43.62 2.85
1948 1971 8.036575 GTCATGCATGGCAATAAATATGGTAAT 58.963 33.333 26.04 0.00 43.62 1.89
1949 1972 8.252417 TCATGCATGGCAATAAATATGGTAATC 58.748 33.333 25.97 0.00 43.62 1.75
1950 1973 7.779754 TGCATGGCAATAAATATGGTAATCT 57.220 32.000 0.00 0.00 34.76 2.40
1951 1974 8.876303 TGCATGGCAATAAATATGGTAATCTA 57.124 30.769 0.00 0.00 34.76 1.98
1952 1975 9.478238 TGCATGGCAATAAATATGGTAATCTAT 57.522 29.630 0.00 0.00 34.76 1.98
1953 1976 9.740239 GCATGGCAATAAATATGGTAATCTATG 57.260 33.333 0.00 0.00 0.00 2.23
1982 2005 8.777865 TTTATGATACTATGCACTATGAAGGC 57.222 34.615 0.00 0.00 0.00 4.35
1983 2006 5.806654 TGATACTATGCACTATGAAGGCA 57.193 39.130 0.00 0.00 42.43 4.75
1984 2007 5.787380 TGATACTATGCACTATGAAGGCAG 58.213 41.667 0.00 0.00 41.40 4.85
1985 2008 5.305386 TGATACTATGCACTATGAAGGCAGT 59.695 40.000 0.00 0.00 41.40 4.40
1986 2009 6.493458 TGATACTATGCACTATGAAGGCAGTA 59.507 38.462 0.00 0.00 41.40 2.74
1987 2010 5.815233 ACTATGCACTATGAAGGCAGTAT 57.185 39.130 0.00 0.00 41.40 2.12
1988 2011 5.788450 ACTATGCACTATGAAGGCAGTATC 58.212 41.667 0.00 0.00 41.40 2.24
1989 2012 4.694760 ATGCACTATGAAGGCAGTATCA 57.305 40.909 0.00 0.00 41.40 2.15
1990 2013 4.694760 TGCACTATGAAGGCAGTATCAT 57.305 40.909 0.00 0.00 39.50 2.45
1991 2014 5.806654 TGCACTATGAAGGCAGTATCATA 57.193 39.130 0.00 0.00 37.46 2.15
1992 2015 5.541845 TGCACTATGAAGGCAGTATCATAC 58.458 41.667 0.00 0.00 37.46 2.39
1993 2016 5.070313 TGCACTATGAAGGCAGTATCATACA 59.930 40.000 0.00 0.00 37.46 2.29
1994 2017 5.406780 GCACTATGAAGGCAGTATCATACAC 59.593 44.000 0.00 0.00 37.46 2.90
1995 2018 6.739843 GCACTATGAAGGCAGTATCATACACT 60.740 42.308 0.00 0.00 37.46 3.55
1996 2019 7.523873 GCACTATGAAGGCAGTATCATACACTA 60.524 40.741 0.00 0.00 37.46 2.74
1997 2020 8.026026 CACTATGAAGGCAGTATCATACACTAG 58.974 40.741 0.00 0.00 37.46 2.57
1998 2021 6.985653 ATGAAGGCAGTATCATACACTAGT 57.014 37.500 0.00 0.00 34.61 2.57
1999 2022 9.232473 CTATGAAGGCAGTATCATACACTAGTA 57.768 37.037 0.00 0.00 37.46 1.82
2000 2023 8.657387 ATGAAGGCAGTATCATACACTAGTAT 57.343 34.615 0.00 0.00 41.57 2.12
2001 2024 8.112016 TGAAGGCAGTATCATACACTAGTATC 57.888 38.462 0.00 0.00 38.88 2.24
2002 2025 7.724061 TGAAGGCAGTATCATACACTAGTATCA 59.276 37.037 0.00 0.00 38.88 2.15
2003 2026 8.657387 AAGGCAGTATCATACACTAGTATCAT 57.343 34.615 0.00 0.00 38.88 2.45
2004 2027 9.755122 AAGGCAGTATCATACACTAGTATCATA 57.245 33.333 0.00 0.00 38.88 2.15
2005 2028 9.928618 AGGCAGTATCATACACTAGTATCATAT 57.071 33.333 0.00 0.00 38.88 1.78
2006 2029 9.958234 GGCAGTATCATACACTAGTATCATATG 57.042 37.037 0.00 0.00 38.88 1.78
2007 2030 9.457110 GCAGTATCATACACTAGTATCATATGC 57.543 37.037 0.00 0.00 38.88 3.14
2032 2055 9.765795 GCATGATATTAGTATATGTTACTCCCC 57.234 37.037 0.00 0.00 0.00 4.81
2040 2063 9.529823 TTAGTATATGTTACTCCCCACTATGAG 57.470 37.037 0.00 0.00 34.73 2.90
2041 2064 7.536625 AGTATATGTTACTCCCCACTATGAGT 58.463 38.462 0.00 0.00 43.85 3.41
2042 2065 8.676020 AGTATATGTTACTCCCCACTATGAGTA 58.324 37.037 0.00 0.00 41.80 2.59
2043 2066 8.958506 GTATATGTTACTCCCCACTATGAGTAG 58.041 40.741 0.00 0.00 43.04 2.57
2044 2067 3.958798 TGTTACTCCCCACTATGAGTAGC 59.041 47.826 6.58 6.58 43.04 3.58
2045 2068 2.089600 ACTCCCCACTATGAGTAGCC 57.910 55.000 0.00 0.00 39.96 3.93
2056 2079 8.056400 CCCACTATGAGTAGCCTAAGAGTATAT 58.944 40.741 0.00 0.00 0.00 0.86
2070 2093 8.484575 CCTAAGAGTATATACCCGATCTCTACA 58.515 40.741 9.32 0.00 32.92 2.74
2086 2109 7.324856 CGATCTCTACATAGTTAAGATGCACAC 59.675 40.741 0.00 0.00 0.00 3.82
2088 2111 7.836842 TCTCTACATAGTTAAGATGCACACAA 58.163 34.615 0.00 0.00 0.00 3.33
2093 2116 4.568152 AGTTAAGATGCACACAACCAAC 57.432 40.909 0.00 0.00 0.00 3.77
2096 2119 2.057137 AGATGCACACAACCAACACT 57.943 45.000 0.00 0.00 0.00 3.55
2097 2120 3.207265 AGATGCACACAACCAACACTA 57.793 42.857 0.00 0.00 0.00 2.74
2098 2121 3.550820 AGATGCACACAACCAACACTAA 58.449 40.909 0.00 0.00 0.00 2.24
2099 2122 3.951037 AGATGCACACAACCAACACTAAA 59.049 39.130 0.00 0.00 0.00 1.85
2100 2123 4.584325 AGATGCACACAACCAACACTAAAT 59.416 37.500 0.00 0.00 0.00 1.40
2101 2124 4.727507 TGCACACAACCAACACTAAATT 57.272 36.364 0.00 0.00 0.00 1.82
2104 2127 5.125578 TGCACACAACCAACACTAAATTACA 59.874 36.000 0.00 0.00 0.00 2.41
2105 2128 6.183360 TGCACACAACCAACACTAAATTACAT 60.183 34.615 0.00 0.00 0.00 2.29
2109 2151 8.637986 ACACAACCAACACTAAATTACATCAAT 58.362 29.630 0.00 0.00 0.00 2.57
2396 2490 2.292828 ACCACCTCCATTTTCCACAG 57.707 50.000 0.00 0.00 0.00 3.66
2499 2593 0.029567 GACGAGGATGAAGATCGCGT 59.970 55.000 5.77 0.00 40.69 6.01
2733 2827 0.835941 AGGTGCCATGCCAAAAACAA 59.164 45.000 0.00 0.00 0.00 2.83
2739 2833 3.071312 TGCCATGCCAAAAACAAAGAGAT 59.929 39.130 0.00 0.00 0.00 2.75
2741 2835 4.083696 GCCATGCCAAAAACAAAGAGATTG 60.084 41.667 0.00 0.00 44.95 2.67
2759 2853 8.340618 AGAGATTGCAAACTCAAATTAAGCTA 57.659 30.769 30.94 0.00 35.83 3.32
2800 2894 4.176271 GGTGGCTAAATTGATTTGACTGC 58.824 43.478 0.00 0.00 0.00 4.40
2872 3021 1.298014 GCTGCTGGAGCTGGTAACT 59.702 57.895 14.33 0.00 45.21 2.24
2978 3127 0.464452 GGTGTTGGGGATCCTAGACG 59.536 60.000 12.58 0.00 33.98 4.18
3127 3276 0.251033 TGCAGCAACTGGAGCTCATT 60.251 50.000 17.19 3.56 41.14 2.57
3151 3300 1.398390 GCCAACGTGTGATCCTCATTC 59.602 52.381 0.00 0.00 0.00 2.67
3175 3324 0.689080 TTTTGGTCCAGGCCTTGCAA 60.689 50.000 0.00 0.00 0.00 4.08
3196 3345 1.953138 GCTGTCAGATCCATCGCCG 60.953 63.158 3.32 0.00 0.00 6.46
3263 3412 4.502105 TGTGTGTGATTGCCTGGTATAT 57.498 40.909 0.00 0.00 0.00 0.86
3274 3423 1.632409 CCTGGTATATCAGGCAGGCAT 59.368 52.381 19.14 0.00 46.47 4.40
3289 3438 2.485426 CAGGCATGTGTAGTGTTCTTGG 59.515 50.000 0.00 0.00 0.00 3.61
3293 3442 1.577468 TGTGTAGTGTTCTTGGTGCG 58.423 50.000 0.00 0.00 0.00 5.34
3427 3577 7.086685 AGACCTGTAAAACCCTCTTGAATTA 57.913 36.000 0.00 0.00 0.00 1.40
3456 3606 5.727630 ACTGGTAGGTGGGTATATCAGATT 58.272 41.667 0.00 0.00 0.00 2.40
3457 3607 5.780793 ACTGGTAGGTGGGTATATCAGATTC 59.219 44.000 0.00 0.00 0.00 2.52
3494 3644 0.107410 TGGAACACCAACACGAAGCT 60.107 50.000 0.00 0.00 0.00 3.74
3528 3678 0.671781 CACGAGGCAAGTCAGGAAGG 60.672 60.000 0.00 0.00 0.00 3.46
3653 3808 9.176181 GAAATTCGTATGTTAAAAGCTGAAACA 57.824 29.630 10.21 10.21 37.51 2.83
3669 3824 8.953368 AGCTGAAACAGATCTTTTGAAAATTT 57.047 26.923 0.00 0.00 32.44 1.82
3731 3899 4.523168 AACTAGAGTTAGAGGATCCGGT 57.477 45.455 5.98 0.00 36.32 5.28
3743 3911 0.037046 GATCCGGTACCCACAAACGT 60.037 55.000 6.25 0.00 0.00 3.99
3803 3971 3.234353 ACATGCCTGATATCCTCTCGAA 58.766 45.455 0.00 0.00 0.00 3.71
3824 3992 1.003866 GTGAGCCAAACGTTGTCAGAC 60.004 52.381 0.00 0.00 0.00 3.51
3945 4113 4.523083 CCGATCTTTCAATGAGGGGTAAA 58.477 43.478 0.00 0.00 0.00 2.01
3964 4133 8.847196 GGGGTAAATATCTTTTTGTGGAGTATC 58.153 37.037 0.00 0.00 0.00 2.24
3997 4166 2.349249 CGACTACGAACGTGTGAAGACT 60.349 50.000 10.14 0.00 42.66 3.24
4004 4173 0.102481 ACGTGTGAAGACTTCGTGCT 59.898 50.000 10.56 0.00 34.15 4.40
4005 4174 1.335810 ACGTGTGAAGACTTCGTGCTA 59.664 47.619 10.56 0.00 34.15 3.49
4029 4198 5.343307 AGCAATCACCAAACAAACTTTCT 57.657 34.783 0.00 0.00 0.00 2.52
4033 4202 4.981806 TCACCAAACAAACTTTCTGAGG 57.018 40.909 0.00 0.00 0.00 3.86
4044 4213 8.747538 ACAAACTTTCTGAGGTTACTAACAAT 57.252 30.769 1.40 0.00 32.12 2.71
4062 4231 5.627182 ACAATAGAGGAGCATGATCAACT 57.373 39.130 13.85 12.93 0.00 3.16
4070 4239 3.076621 GAGCATGATCAACTTGACCACA 58.923 45.455 5.98 0.00 0.00 4.17
4073 4242 3.983344 GCATGATCAACTTGACCACAAAC 59.017 43.478 0.00 0.00 35.49 2.93
4075 4244 3.275143 TGATCAACTTGACCACAAACGT 58.725 40.909 0.00 0.00 35.49 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.038130 CCTCGGAGACACTCGGGATT 61.038 60.000 6.58 0.00 32.74 3.01
72 73 1.454111 CCTCGGAGACACTCGGGAT 60.454 63.158 6.58 0.00 32.74 3.85
152 153 9.034800 TCCTTAATGAACTTTAATTTGAGCCAT 57.965 29.630 0.00 0.00 0.00 4.40
163 164 8.041323 GGTGACATCTCTCCTTAATGAACTTTA 58.959 37.037 0.00 0.00 0.00 1.85
212 213 1.202580 GCGGACCTATGACAAGAGCAT 60.203 52.381 0.00 0.00 0.00 3.79
281 283 1.134128 TGCACCAATATGATGCGGAGT 60.134 47.619 0.00 0.00 40.65 3.85
302 304 4.517832 ACATCATCAATTCACCATGGATCG 59.482 41.667 21.47 6.49 0.00 3.69
340 342 7.572814 TGATTATCAATGATACAAGGTGGTGA 58.427 34.615 1.88 0.00 0.00 4.02
509 511 6.438763 ACGCTAGGCAAAAGCATATAAAATC 58.561 36.000 7.19 0.00 40.08 2.17
560 562 8.624776 CATCACTTTCTTCCCTTTATCATTACC 58.375 37.037 0.00 0.00 0.00 2.85
625 629 5.527951 AGAGGAGAAAGGAAAGAACGAAAAC 59.472 40.000 0.00 0.00 0.00 2.43
668 673 2.631427 CGGAGGAGGATCGGTACTC 58.369 63.158 0.00 0.00 34.28 2.59
686 691 3.350219 ACACAGAGAGAGAGAGAGACC 57.650 52.381 0.00 0.00 0.00 3.85
687 692 4.323417 TGAACACAGAGAGAGAGAGAGAC 58.677 47.826 0.00 0.00 0.00 3.36
753 765 2.174685 AACAAAACAGGGAAAGGGCT 57.825 45.000 0.00 0.00 0.00 5.19
802 814 1.670380 GGGCTCAAGAGTTGACGAGAC 60.670 57.143 0.00 0.00 35.46 3.36
909 921 7.181569 AGGAAGAAGAAGAAGAAGATGGTAG 57.818 40.000 0.00 0.00 0.00 3.18
916 928 3.855858 CCCGAGGAAGAAGAAGAAGAAG 58.144 50.000 0.00 0.00 0.00 2.85
917 929 2.028020 GCCCGAGGAAGAAGAAGAAGAA 60.028 50.000 0.00 0.00 0.00 2.52
918 930 1.550976 GCCCGAGGAAGAAGAAGAAGA 59.449 52.381 0.00 0.00 0.00 2.87
919 931 1.552792 AGCCCGAGGAAGAAGAAGAAG 59.447 52.381 0.00 0.00 0.00 2.85
920 932 1.276421 CAGCCCGAGGAAGAAGAAGAA 59.724 52.381 0.00 0.00 0.00 2.52
921 933 0.898320 CAGCCCGAGGAAGAAGAAGA 59.102 55.000 0.00 0.00 0.00 2.87
1231 1248 1.642238 TGGAGCTAGTGGTAGTGGGTA 59.358 52.381 0.00 0.00 0.00 3.69
1268 1285 6.314896 CCACACCAACTGAATTATCTCTCTTC 59.685 42.308 0.00 0.00 0.00 2.87
1323 1340 0.534412 ATCTTGGGAGTCTCTGCACG 59.466 55.000 0.00 0.00 0.00 5.34
1579 1596 4.980805 GCACCTTGACGGCGACCA 62.981 66.667 16.62 8.43 35.61 4.02
1604 1621 0.548510 GGCCCTGGAAGCTGTTATCT 59.451 55.000 0.00 0.00 0.00 1.98
1717 1739 8.561932 AAAACACTCTTTATCGAAGAAAAAGC 57.438 30.769 0.00 0.00 43.56 3.51
1758 1781 2.024176 ATTGTATCACTCGGTGCCAC 57.976 50.000 0.00 0.00 32.98 5.01
1778 1801 4.499472 ACCCCACTATGGCTAGCTTTATA 58.501 43.478 15.72 10.11 35.79 0.98
1780 1803 2.771688 ACCCCACTATGGCTAGCTTTA 58.228 47.619 15.72 5.88 35.79 1.85
1781 1804 1.596496 ACCCCACTATGGCTAGCTTT 58.404 50.000 15.72 4.92 35.79 3.51
1782 1805 2.438392 GTTACCCCACTATGGCTAGCTT 59.562 50.000 15.72 5.30 35.79 3.74
1783 1806 2.047830 GTTACCCCACTATGGCTAGCT 58.952 52.381 15.72 0.00 35.79 3.32
1784 1807 1.766496 TGTTACCCCACTATGGCTAGC 59.234 52.381 6.04 6.04 35.79 3.42
1785 1808 5.512576 GGTTATGTTACCCCACTATGGCTAG 60.513 48.000 0.00 0.00 35.79 3.42
1786 1809 4.348754 GGTTATGTTACCCCACTATGGCTA 59.651 45.833 0.00 0.00 35.79 3.93
1787 1810 3.137728 GGTTATGTTACCCCACTATGGCT 59.862 47.826 0.00 0.00 35.79 4.75
1788 1811 3.483421 GGTTATGTTACCCCACTATGGC 58.517 50.000 0.00 0.00 35.79 4.40
1789 1812 3.495453 CCGGTTATGTTACCCCACTATGG 60.495 52.174 0.00 0.00 37.25 2.74
1790 1813 3.135167 ACCGGTTATGTTACCCCACTATG 59.865 47.826 0.00 0.00 34.56 2.23
1791 1814 3.387012 ACCGGTTATGTTACCCCACTAT 58.613 45.455 0.00 0.00 34.56 2.12
1792 1815 2.831565 ACCGGTTATGTTACCCCACTA 58.168 47.619 0.00 0.00 34.56 2.74
1793 1816 1.660242 ACCGGTTATGTTACCCCACT 58.340 50.000 0.00 0.00 34.56 4.00
1794 1817 3.270027 GTTACCGGTTATGTTACCCCAC 58.730 50.000 15.04 0.00 34.56 4.61
1795 1818 2.238395 GGTTACCGGTTATGTTACCCCA 59.762 50.000 15.04 0.00 34.56 4.96
1796 1819 2.238395 TGGTTACCGGTTATGTTACCCC 59.762 50.000 15.04 0.00 35.15 4.95
1797 1820 3.055167 AGTGGTTACCGGTTATGTTACCC 60.055 47.826 15.04 0.00 35.15 3.69
1798 1821 4.206477 AGTGGTTACCGGTTATGTTACC 57.794 45.455 15.04 11.66 36.26 2.85
1799 1822 4.392754 CCAAGTGGTTACCGGTTATGTTAC 59.607 45.833 15.04 5.32 0.00 2.50
1800 1823 4.565236 CCCAAGTGGTTACCGGTTATGTTA 60.565 45.833 15.04 0.00 0.00 2.41
1801 1824 3.414269 CCAAGTGGTTACCGGTTATGTT 58.586 45.455 15.04 0.00 0.00 2.71
1802 1825 2.290450 CCCAAGTGGTTACCGGTTATGT 60.290 50.000 15.04 0.00 0.00 2.29
1803 1826 2.027007 TCCCAAGTGGTTACCGGTTATG 60.027 50.000 15.04 0.00 34.77 1.90
1804 1827 2.026915 GTCCCAAGTGGTTACCGGTTAT 60.027 50.000 15.04 0.00 34.77 1.89
1805 1828 1.347378 GTCCCAAGTGGTTACCGGTTA 59.653 52.381 15.04 0.00 34.77 2.85
1806 1829 0.109153 GTCCCAAGTGGTTACCGGTT 59.891 55.000 15.04 0.00 34.77 4.44
1807 1830 0.765519 AGTCCCAAGTGGTTACCGGT 60.766 55.000 13.98 13.98 34.77 5.28
1808 1831 1.206371 CTAGTCCCAAGTGGTTACCGG 59.794 57.143 0.00 0.00 34.77 5.28
1809 1832 1.405121 GCTAGTCCCAAGTGGTTACCG 60.405 57.143 0.00 0.00 34.77 4.02
1810 1833 1.626825 TGCTAGTCCCAAGTGGTTACC 59.373 52.381 0.00 0.00 34.77 2.85
1811 1834 3.412237 TTGCTAGTCCCAAGTGGTTAC 57.588 47.619 0.00 0.00 34.77 2.50
1812 1835 3.136809 TGTTTGCTAGTCCCAAGTGGTTA 59.863 43.478 0.00 0.00 34.77 2.85
1813 1836 2.092103 TGTTTGCTAGTCCCAAGTGGTT 60.092 45.455 0.00 0.00 34.77 3.67
1814 1837 1.493022 TGTTTGCTAGTCCCAAGTGGT 59.507 47.619 0.00 0.00 34.77 4.16
1815 1838 2.270352 TGTTTGCTAGTCCCAAGTGG 57.730 50.000 0.00 0.00 0.00 4.00
1816 1839 2.095059 GCATGTTTGCTAGTCCCAAGTG 60.095 50.000 0.00 0.00 45.77 3.16
1817 1840 2.162681 GCATGTTTGCTAGTCCCAAGT 58.837 47.619 0.00 0.00 45.77 3.16
1818 1841 2.927553 GCATGTTTGCTAGTCCCAAG 57.072 50.000 0.00 0.00 45.77 3.61
1826 1849 7.559253 GTGTGCCACATAAGCATGTTTGCTA 62.559 44.000 0.00 0.00 45.30 3.49
1827 1850 6.868736 GTGTGCCACATAAGCATGTTTGCT 62.869 45.833 0.00 0.00 46.69 3.91
1828 1851 4.703027 GTGTGCCACATAAGCATGTTTGC 61.703 47.826 0.00 0.00 42.98 3.68
1829 1852 2.988493 GTGTGCCACATAAGCATGTTTG 59.012 45.455 0.00 0.00 42.98 2.93
1830 1853 2.627221 TGTGTGCCACATAAGCATGTTT 59.373 40.909 0.00 0.00 42.98 2.83
1831 1854 2.237643 TGTGTGCCACATAAGCATGTT 58.762 42.857 0.00 0.00 42.98 2.71
1832 1855 1.908344 TGTGTGCCACATAAGCATGT 58.092 45.000 0.00 0.00 46.58 3.21
1833 1856 3.513680 ATTGTGTGCCACATAAGCATG 57.486 42.857 12.58 0.00 44.16 4.06
1834 1857 5.657826 TTAATTGTGTGCCACATAAGCAT 57.342 34.783 12.58 4.64 44.16 3.79
1835 1858 5.459536 TTTAATTGTGTGCCACATAAGCA 57.540 34.783 12.58 0.00 44.16 3.91
1836 1859 7.973388 TCTTATTTAATTGTGTGCCACATAAGC 59.027 33.333 12.58 0.00 44.16 3.09
1837 1860 9.507280 CTCTTATTTAATTGTGTGCCACATAAG 57.493 33.333 12.58 8.32 44.16 1.73
1838 1861 9.237187 TCTCTTATTTAATTGTGTGCCACATAA 57.763 29.630 9.52 9.52 44.16 1.90
1839 1862 8.800370 TCTCTTATTTAATTGTGTGCCACATA 57.200 30.769 0.00 0.00 44.16 2.29
1840 1863 7.611467 TCTCTCTTATTTAATTGTGTGCCACAT 59.389 33.333 0.00 0.00 44.16 3.21
1841 1864 6.939730 TCTCTCTTATTTAATTGTGTGCCACA 59.060 34.615 0.00 0.00 43.02 4.17
1842 1865 7.377766 TCTCTCTTATTTAATTGTGTGCCAC 57.622 36.000 0.00 0.00 34.56 5.01
1843 1866 6.599244 CCTCTCTCTTATTTAATTGTGTGCCA 59.401 38.462 0.00 0.00 0.00 4.92
1844 1867 6.038714 CCCTCTCTCTTATTTAATTGTGTGCC 59.961 42.308 0.00 0.00 0.00 5.01
1845 1868 6.599638 ACCCTCTCTCTTATTTAATTGTGTGC 59.400 38.462 0.00 0.00 0.00 4.57
1846 1869 8.567285 AACCCTCTCTCTTATTTAATTGTGTG 57.433 34.615 0.00 0.00 0.00 3.82
1859 1882 8.512813 ACCTATGTTACTATAACCCTCTCTCTT 58.487 37.037 0.00 0.00 0.00 2.85
1860 1883 8.059565 ACCTATGTTACTATAACCCTCTCTCT 57.940 38.462 0.00 0.00 0.00 3.10
1861 1884 9.452287 CTACCTATGTTACTATAACCCTCTCTC 57.548 40.741 0.00 0.00 0.00 3.20
1862 1885 9.180282 TCTACCTATGTTACTATAACCCTCTCT 57.820 37.037 0.00 0.00 0.00 3.10
1863 1886 9.978336 ATCTACCTATGTTACTATAACCCTCTC 57.022 37.037 0.00 0.00 0.00 3.20
1891 1914 9.758651 AGTAGCATAACATTTAACATGATACGA 57.241 29.630 0.00 0.00 42.29 3.43
1903 1926 8.685427 TGCATGACATAAAGTAGCATAACATTT 58.315 29.630 0.00 0.00 30.65 2.32
1904 1927 8.224389 TGCATGACATAAAGTAGCATAACATT 57.776 30.769 0.00 0.00 30.65 2.71
1905 1928 7.806409 TGCATGACATAAAGTAGCATAACAT 57.194 32.000 0.00 0.00 30.65 2.71
1906 1929 7.255208 CCATGCATGACATAAAGTAGCATAACA 60.255 37.037 28.31 0.00 39.67 2.41
1907 1930 7.080099 CCATGCATGACATAAAGTAGCATAAC 58.920 38.462 28.31 0.00 39.67 1.89
1908 1931 6.294120 GCCATGCATGACATAAAGTAGCATAA 60.294 38.462 28.31 0.00 39.67 1.90
1909 1932 5.181811 GCCATGCATGACATAAAGTAGCATA 59.818 40.000 28.31 0.00 39.67 3.14
1910 1933 4.022589 GCCATGCATGACATAAAGTAGCAT 60.023 41.667 28.31 3.51 41.24 3.79
1911 1934 3.316029 GCCATGCATGACATAAAGTAGCA 59.684 43.478 28.31 0.00 36.64 3.49
1912 1935 3.316029 TGCCATGCATGACATAAAGTAGC 59.684 43.478 28.31 17.58 36.64 3.58
1913 1936 5.503662 TTGCCATGCATGACATAAAGTAG 57.496 39.130 28.31 8.01 38.76 2.57
1914 1937 7.579761 TTATTGCCATGCATGACATAAAGTA 57.420 32.000 28.31 6.77 38.76 2.24
1915 1938 6.468333 TTATTGCCATGCATGACATAAAGT 57.532 33.333 28.31 8.98 38.76 2.66
1916 1939 7.956420 ATTTATTGCCATGCATGACATAAAG 57.044 32.000 28.31 10.23 38.76 1.85
1917 1940 9.425577 CATATTTATTGCCATGCATGACATAAA 57.574 29.630 28.31 25.96 38.76 1.40
1918 1941 8.035984 CCATATTTATTGCCATGCATGACATAA 58.964 33.333 28.31 20.47 38.76 1.90
1919 1942 7.178805 ACCATATTTATTGCCATGCATGACATA 59.821 33.333 28.31 16.30 38.76 2.29
1920 1943 6.014070 ACCATATTTATTGCCATGCATGACAT 60.014 34.615 28.31 17.25 38.76 3.06
1921 1944 5.304871 ACCATATTTATTGCCATGCATGACA 59.695 36.000 28.31 20.53 38.76 3.58
1922 1945 5.786311 ACCATATTTATTGCCATGCATGAC 58.214 37.500 28.31 17.77 38.76 3.06
1923 1946 7.536159 TTACCATATTTATTGCCATGCATGA 57.464 32.000 28.31 8.76 38.76 3.07
1924 1947 8.255206 AGATTACCATATTTATTGCCATGCATG 58.745 33.333 20.19 20.19 38.76 4.06
1925 1948 8.370266 AGATTACCATATTTATTGCCATGCAT 57.630 30.769 0.00 0.00 38.76 3.96
1926 1949 7.779754 AGATTACCATATTTATTGCCATGCA 57.220 32.000 0.00 0.00 36.47 3.96
1927 1950 9.740239 CATAGATTACCATATTTATTGCCATGC 57.260 33.333 0.00 0.00 0.00 4.06
1956 1979 9.388506 GCCTTCATAGTGCATAGTATCATAAAT 57.611 33.333 0.00 0.00 0.00 1.40
1957 1980 8.374743 TGCCTTCATAGTGCATAGTATCATAAA 58.625 33.333 0.00 0.00 0.00 1.40
1958 1981 7.906327 TGCCTTCATAGTGCATAGTATCATAA 58.094 34.615 0.00 0.00 0.00 1.90
1959 1982 7.179160 ACTGCCTTCATAGTGCATAGTATCATA 59.821 37.037 0.00 0.00 33.97 2.15
1960 1983 6.013898 ACTGCCTTCATAGTGCATAGTATCAT 60.014 38.462 0.00 0.00 33.97 2.45
1961 1984 5.305386 ACTGCCTTCATAGTGCATAGTATCA 59.695 40.000 0.00 0.00 33.97 2.15
1962 1985 5.788450 ACTGCCTTCATAGTGCATAGTATC 58.212 41.667 0.00 0.00 33.97 2.24
1963 1986 5.815233 ACTGCCTTCATAGTGCATAGTAT 57.185 39.130 0.00 0.00 33.97 2.12
1964 1987 6.493458 TGATACTGCCTTCATAGTGCATAGTA 59.507 38.462 0.00 0.00 33.97 1.82
1965 1988 5.305386 TGATACTGCCTTCATAGTGCATAGT 59.695 40.000 0.00 0.00 33.97 2.12
1966 1989 5.787380 TGATACTGCCTTCATAGTGCATAG 58.213 41.667 0.00 0.00 33.97 2.23
1967 1990 5.806654 TGATACTGCCTTCATAGTGCATA 57.193 39.130 0.00 0.00 33.97 3.14
1968 1991 4.694760 TGATACTGCCTTCATAGTGCAT 57.305 40.909 0.00 0.00 33.97 3.96
1969 1992 4.694760 ATGATACTGCCTTCATAGTGCA 57.305 40.909 0.00 0.00 30.93 4.57
1970 1993 5.406780 GTGTATGATACTGCCTTCATAGTGC 59.593 44.000 4.03 0.00 35.94 4.40
1971 1994 6.753180 AGTGTATGATACTGCCTTCATAGTG 58.247 40.000 4.03 0.00 35.94 2.74
1972 1995 6.985653 AGTGTATGATACTGCCTTCATAGT 57.014 37.500 4.03 0.00 35.94 2.12
1973 1996 8.116651 ACTAGTGTATGATACTGCCTTCATAG 57.883 38.462 4.03 0.00 35.94 2.23
1974 1997 9.755122 ATACTAGTGTATGATACTGCCTTCATA 57.245 33.333 5.39 0.00 37.92 2.15
1975 1998 6.985653 ACTAGTGTATGATACTGCCTTCAT 57.014 37.500 4.03 0.00 36.57 2.57
1976 1999 7.724061 TGATACTAGTGTATGATACTGCCTTCA 59.276 37.037 5.39 0.00 39.29 3.02
1977 2000 8.112016 TGATACTAGTGTATGATACTGCCTTC 57.888 38.462 5.39 0.00 39.29 3.46
1978 2001 8.657387 ATGATACTAGTGTATGATACTGCCTT 57.343 34.615 5.39 0.00 39.29 4.35
1979 2002 9.928618 ATATGATACTAGTGTATGATACTGCCT 57.071 33.333 5.39 0.57 37.80 4.75
1980 2003 9.958234 CATATGATACTAGTGTATGATACTGCC 57.042 37.037 5.39 0.00 37.80 4.85
1981 2004 9.457110 GCATATGATACTAGTGTATGATACTGC 57.543 37.037 6.97 5.14 37.80 4.40
2006 2029 9.765795 GGGGAGTAACATATACTAATATCATGC 57.234 37.037 0.00 0.00 0.00 4.06
2014 2037 9.529823 CTCATAGTGGGGAGTAACATATACTAA 57.470 37.037 0.00 0.00 0.00 2.24
2015 2038 8.676020 ACTCATAGTGGGGAGTAACATATACTA 58.324 37.037 0.00 0.00 42.30 1.82
2016 2039 7.536625 ACTCATAGTGGGGAGTAACATATACT 58.463 38.462 0.00 0.00 42.30 2.12
2017 2040 7.778185 ACTCATAGTGGGGAGTAACATATAC 57.222 40.000 0.00 0.00 42.30 1.47
2018 2041 7.614583 GCTACTCATAGTGGGGAGTAACATATA 59.385 40.741 0.00 0.00 43.77 0.86
2019 2042 6.437793 GCTACTCATAGTGGGGAGTAACATAT 59.562 42.308 0.00 0.00 43.77 1.78
2020 2043 5.773680 GCTACTCATAGTGGGGAGTAACATA 59.226 44.000 0.00 0.00 43.77 2.29
2021 2044 4.589374 GCTACTCATAGTGGGGAGTAACAT 59.411 45.833 0.00 0.00 43.77 2.71
2022 2045 3.958798 GCTACTCATAGTGGGGAGTAACA 59.041 47.826 0.00 0.00 43.77 2.41
2023 2046 3.321396 GGCTACTCATAGTGGGGAGTAAC 59.679 52.174 0.00 0.00 43.77 2.50
2024 2047 3.206866 AGGCTACTCATAGTGGGGAGTAA 59.793 47.826 0.00 0.00 43.77 2.24
2025 2048 2.789992 AGGCTACTCATAGTGGGGAGTA 59.210 50.000 0.00 0.00 42.30 2.59
2026 2049 1.576272 AGGCTACTCATAGTGGGGAGT 59.424 52.381 0.00 0.00 45.72 3.85
2027 2050 2.390225 AGGCTACTCATAGTGGGGAG 57.610 55.000 0.00 0.00 37.18 4.30
2028 2051 3.465966 TCTTAGGCTACTCATAGTGGGGA 59.534 47.826 0.00 0.00 0.00 4.81
2029 2052 3.829601 CTCTTAGGCTACTCATAGTGGGG 59.170 52.174 0.00 0.00 0.00 4.96
2030 2053 4.475345 ACTCTTAGGCTACTCATAGTGGG 58.525 47.826 0.00 0.00 0.00 4.61
2034 2057 9.563748 GGGTATATACTCTTAGGCTACTCATAG 57.436 40.741 12.54 0.00 0.00 2.23
2035 2058 8.209584 CGGGTATATACTCTTAGGCTACTCATA 58.790 40.741 11.00 0.00 0.00 2.15
2036 2059 7.055378 CGGGTATATACTCTTAGGCTACTCAT 58.945 42.308 11.00 0.00 0.00 2.90
2037 2060 6.214208 TCGGGTATATACTCTTAGGCTACTCA 59.786 42.308 11.00 0.00 0.00 3.41
2038 2061 6.648192 TCGGGTATATACTCTTAGGCTACTC 58.352 44.000 11.00 0.00 0.00 2.59
2039 2062 6.633325 TCGGGTATATACTCTTAGGCTACT 57.367 41.667 11.00 0.00 0.00 2.57
2040 2063 7.281841 AGATCGGGTATATACTCTTAGGCTAC 58.718 42.308 11.00 0.00 0.00 3.58
2041 2064 7.347748 AGAGATCGGGTATATACTCTTAGGCTA 59.652 40.741 11.00 0.00 31.93 3.93
2042 2065 6.159046 AGAGATCGGGTATATACTCTTAGGCT 59.841 42.308 11.00 0.00 31.93 4.58
2043 2066 6.358991 AGAGATCGGGTATATACTCTTAGGC 58.641 44.000 11.00 0.00 31.93 3.93
2044 2067 8.484575 TGTAGAGATCGGGTATATACTCTTAGG 58.515 40.741 11.00 0.00 36.39 2.69
2056 2079 7.120873 GCATCTTAACTATGTAGAGATCGGGTA 59.879 40.741 0.00 0.00 0.00 3.69
2058 2081 6.071896 TGCATCTTAACTATGTAGAGATCGGG 60.072 42.308 0.00 0.00 0.00 5.14
2070 2093 5.767665 TGTTGGTTGTGTGCATCTTAACTAT 59.232 36.000 0.00 0.00 0.00 2.12
2077 2100 2.057137 AGTGTTGGTTGTGTGCATCT 57.943 45.000 0.00 0.00 0.00 2.90
2116 2158 8.441312 AAACACTTCGGTCTTATTTGACTTTA 57.559 30.769 0.00 0.00 37.16 1.85
2310 2404 2.223829 GCATGTACTCGTAGACCAGCAT 60.224 50.000 0.00 0.00 0.00 3.79
2396 2490 1.273688 GACACGCACCAAACCAAAAC 58.726 50.000 0.00 0.00 0.00 2.43
2546 2640 2.951457 TGAAATCGCGGTAGATGACA 57.049 45.000 6.13 0.00 0.00 3.58
2640 2734 2.186903 GTGGGACATGTCGCCGAT 59.813 61.111 32.59 0.00 44.52 4.18
2733 2827 7.664758 AGCTTAATTTGAGTTTGCAATCTCTT 58.335 30.769 28.77 20.37 0.00 2.85
2739 2833 8.109705 TGATCTAGCTTAATTTGAGTTTGCAA 57.890 30.769 0.00 0.00 0.00 4.08
2741 2835 9.657121 GTATGATCTAGCTTAATTTGAGTTTGC 57.343 33.333 0.00 0.00 0.00 3.68
2759 2853 4.533707 CCACCAGACCCATATGTATGATCT 59.466 45.833 1.24 2.25 35.75 2.75
2771 2865 1.707989 TCAATTTAGCCACCAGACCCA 59.292 47.619 0.00 0.00 0.00 4.51
2800 2894 3.842923 AGGTGCCCTGATCGCTCG 61.843 66.667 0.00 0.00 29.57 5.03
2836 2985 1.968050 GCACCACCCCGTAGCTGTAT 61.968 60.000 0.00 0.00 0.00 2.29
2978 3127 2.817396 GTCAGAGCCGAGCCTTGC 60.817 66.667 0.00 0.00 0.00 4.01
3127 3276 2.047655 GATCACACGTTGGCGGGA 60.048 61.111 0.00 0.00 45.97 5.14
3175 3324 0.179089 GCGATGGATCTGACAGCACT 60.179 55.000 0.00 0.00 0.00 4.40
3257 3406 2.224621 ACACATGCCTGCCTGATATACC 60.225 50.000 1.32 0.00 0.00 2.73
3263 3412 0.036105 CACTACACATGCCTGCCTGA 60.036 55.000 1.32 0.00 0.00 3.86
3274 3423 1.577468 CGCACCAAGAACACTACACA 58.423 50.000 0.00 0.00 0.00 3.72
3427 3577 9.268282 CTGATATACCCACCTACCAGTAATAAT 57.732 37.037 0.00 0.00 0.00 1.28
3436 3586 6.936968 AAGAATCTGATATACCCACCTACC 57.063 41.667 0.00 0.00 0.00 3.18
3494 3644 3.270027 CCTCGTGCAAATTACAGGATCA 58.730 45.455 0.00 0.00 32.07 2.92
3551 3701 2.306219 GACTCTAACTTGCTTTCCCCCT 59.694 50.000 0.00 0.00 0.00 4.79
3731 3899 1.102222 GTGGCCAACGTTTGTGGGTA 61.102 55.000 7.24 0.00 41.76 3.69
3803 3971 1.134521 TCTGACAACGTTTGGCTCACT 60.135 47.619 0.00 0.00 40.19 3.41
3824 3992 5.413213 TCAGATTGTAAATGTTAACCCACGG 59.587 40.000 2.48 0.00 0.00 4.94
3964 4133 1.399440 TCGTAGTCGGATCGTGAAAGG 59.601 52.381 0.00 0.00 37.69 3.11
4004 4173 8.081633 CAGAAAGTTTGTTTGGTGATTGCTATA 58.918 33.333 0.00 0.00 0.00 1.31
4005 4174 6.925165 CAGAAAGTTTGTTTGGTGATTGCTAT 59.075 34.615 0.00 0.00 0.00 2.97
4013 4182 4.718940 ACCTCAGAAAGTTTGTTTGGTG 57.281 40.909 0.00 0.00 0.00 4.17
4014 4183 5.949952 AGTAACCTCAGAAAGTTTGTTTGGT 59.050 36.000 0.00 0.00 0.00 3.67
4015 4184 6.451064 AGTAACCTCAGAAAGTTTGTTTGG 57.549 37.500 0.00 0.00 0.00 3.28
4016 4185 8.455682 TGTTAGTAACCTCAGAAAGTTTGTTTG 58.544 33.333 10.51 0.00 0.00 2.93
4029 4198 5.955959 TGCTCCTCTATTGTTAGTAACCTCA 59.044 40.000 10.51 0.00 0.00 3.86
4033 4202 8.144478 TGATCATGCTCCTCTATTGTTAGTAAC 58.856 37.037 6.06 6.06 0.00 2.50
4044 4213 4.141846 GGTCAAGTTGATCATGCTCCTCTA 60.142 45.833 11.38 0.00 0.00 2.43
4046 4215 2.941720 GGTCAAGTTGATCATGCTCCTC 59.058 50.000 11.38 0.00 0.00 3.71
4062 4231 4.513692 CAGGAATTAGACGTTTGTGGTCAA 59.486 41.667 0.00 0.00 36.87 3.18
4070 4239 3.081061 TGCATGCAGGAATTAGACGTTT 58.919 40.909 18.46 0.00 0.00 3.60
4073 4242 3.763097 TTTGCATGCAGGAATTAGACG 57.237 42.857 21.50 0.00 0.00 4.18
4075 4244 5.653330 TCTTCATTTGCATGCAGGAATTAGA 59.347 36.000 21.50 17.86 0.00 2.10


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

AutoCloner maintained by Alex Coulton.