Multiple sequence alignment - TraesCS1B01G289300

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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 TraesCS1B01G289300 chr1B 100.000 5463 0 0 1 5463 504097856 504092394 0.000000e+00 10089
1 TraesCS1B01G289300 chr1D 92.049 2830 133 41 1897 4711 377194606 377191854 0.000000e+00 3895
2 TraesCS1B01G289300 chr1D 91.989 1835 101 23 10 1814 377196423 377194605 0.000000e+00 2532
3 TraesCS1B01G289300 chr1D 89.607 356 19 9 5108 5463 377191390 377191053 2.340000e-118 436
4 TraesCS1B01G289300 chr1D 84.211 418 34 12 4696 5098 377191832 377191432 1.440000e-100 377
5 TraesCS1B01G289300 chr1A 93.519 1944 92 14 1897 3830 477738344 477736425 0.000000e+00 2861
6 TraesCS1B01G289300 chr1A 90.702 1581 96 22 269 1814 477739907 477738343 0.000000e+00 2058
7 TraesCS1B01G289300 chr1A 83.959 985 93 30 3858 4817 477736331 477735387 0.000000e+00 883
8 TraesCS1B01G289300 chr1A 79.679 187 25 9 5218 5402 477735122 477734947 7.430000e-24 122
9 TraesCS1B01G289300 chr4B 96.809 94 2 1 1813 1905 237031170 237031077 7.330000e-34 156
10 TraesCS1B01G289300 chr4B 90.265 113 5 6 1813 1922 6009933 6010042 5.700000e-30 143
11 TraesCS1B01G289300 chr4A 94.175 103 4 2 1807 1907 607427298 607427400 7.330000e-34 156
12 TraesCS1B01G289300 chr4A 94.059 101 2 4 1809 1907 4152059 4151961 3.410000e-32 150
13 TraesCS1B01G289300 chr4D 94.118 102 2 4 1809 1908 421421008 421420909 9.480000e-33 152
14 TraesCS1B01G289300 chr2B 92.661 109 3 4 1813 1919 303097351 303097246 9.480000e-33 152
15 TraesCS1B01G289300 chr7A 92.523 107 2 5 1813 1917 272502843 272502741 1.230000e-31 148
16 TraesCS1B01G289300 chr5B 91.743 109 6 3 1807 1914 330847748 330847854 1.230000e-31 148
17 TraesCS1B01G289300 chr2A 90.909 110 8 2 1807 1916 659614585 659614692 4.410000e-31 147


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 TraesCS1B01G289300 chr1B 504092394 504097856 5462 True 10089 10089 100.00000 1 5463 1 chr1B.!!$R1 5462
1 TraesCS1B01G289300 chr1D 377191053 377196423 5370 True 1810 3895 89.46400 10 5463 4 chr1D.!!$R1 5453
2 TraesCS1B01G289300 chr1A 477734947 477739907 4960 True 1481 2861 86.96475 269 5402 4 chr1A.!!$R1 5133


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
248 257 0.107800 TCCTCAGTAGACGAGACGGG 60.108 60.000 0.00 0.0 31.84 5.28 F
301 314 0.766131 TAAACACCCGAAAGCCTCCA 59.234 50.000 0.00 0.0 0.00 3.86 F
1039 1073 1.219393 GAGGCTTCCAAGGTCTCCG 59.781 63.158 0.00 0.0 0.00 4.63 F
1935 1985 1.933181 CTGTTTGTCGACTTGCTGTCA 59.067 47.619 17.92 5.7 45.60 3.58 F
3400 3460 1.531423 ATGTGCTTGAAGTGCTCCTG 58.469 50.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1678 0.028902 GCGACAAATTCCCGCCATAC 59.971 55.0 7.55 0.00 42.77 2.39 R
1644 1684 0.591170 ACACAAGCGACAAATTCCCG 59.409 50.0 0.00 0.00 0.00 5.14 R
2168 2218 1.023513 GTCCGAGCATGCTCAAAGCT 61.024 55.0 38.97 10.84 42.97 3.74 R
3661 3722 0.105964 CCTACGATTCGGGCATGGAA 59.894 55.0 11.29 0.00 0.00 3.53 R
5379 5663 0.250640 CCAGGCATAGGATCTGGTGC 60.251 60.0 8.47 7.81 42.17 5.01 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
45 46 1.077930 CACCTCCATGCACCCTCTG 60.078 63.158 0.00 0.00 0.00 3.35
48 49 1.153489 CTCCATGCACCCTCTGACG 60.153 63.158 0.00 0.00 0.00 4.35
56 57 1.378646 ACCCTCTGACGATGCGAGA 60.379 57.895 0.00 0.00 0.00 4.04
57 58 1.064946 CCCTCTGACGATGCGAGAC 59.935 63.158 0.00 0.00 0.00 3.36
101 102 7.148000 GCTAGGCAAAGAGAACCTTATTTCATT 60.148 37.037 0.00 0.00 34.92 2.57
113 114 9.449719 GAACCTTATTTCATTCTTAGGAAGTCA 57.550 33.333 0.00 0.00 34.70 3.41
123 124 1.192146 TAGGAAGTCACCGCTGCCTT 61.192 55.000 0.00 0.00 41.80 4.35
124 125 2.328099 GGAAGTCACCGCTGCCTTG 61.328 63.158 0.00 0.00 31.25 3.61
129 130 3.297620 CACCGCTGCCTTGCCTTT 61.298 61.111 0.00 0.00 0.00 3.11
130 131 2.985847 ACCGCTGCCTTGCCTTTC 60.986 61.111 0.00 0.00 0.00 2.62
131 132 2.674380 CCGCTGCCTTGCCTTTCT 60.674 61.111 0.00 0.00 0.00 2.52
134 135 1.518056 CGCTGCCTTGCCTTTCTGAA 61.518 55.000 0.00 0.00 0.00 3.02
135 136 0.675633 GCTGCCTTGCCTTTCTGAAA 59.324 50.000 2.44 2.44 0.00 2.69
155 156 5.534654 TGAAAAGGACACAAACCCTAATCAG 59.465 40.000 0.00 0.00 31.36 2.90
194 197 0.337428 AAAAGCATGAGCCCTCCCAT 59.663 50.000 0.00 0.00 43.56 4.00
196 199 1.284111 AAGCATGAGCCCTCCCATCA 61.284 55.000 0.00 0.00 43.56 3.07
228 231 3.499737 CCACCGCGCTTCCATGAC 61.500 66.667 5.56 0.00 0.00 3.06
232 241 2.185350 CGCGCTTCCATGACTCCT 59.815 61.111 5.56 0.00 0.00 3.69
236 245 0.534412 CGCTTCCATGACTCCTCAGT 59.466 55.000 0.00 0.00 34.57 3.41
240 249 3.181480 GCTTCCATGACTCCTCAGTAGAC 60.181 52.174 0.00 0.00 30.63 2.59
244 253 3.536570 CATGACTCCTCAGTAGACGAGA 58.463 50.000 0.00 0.00 33.03 4.04
248 257 0.107800 TCCTCAGTAGACGAGACGGG 60.108 60.000 0.00 0.00 31.84 5.28
290 300 1.254026 GCAGGAAACCCTAAACACCC 58.746 55.000 0.00 0.00 31.47 4.61
292 302 1.072648 CAGGAAACCCTAAACACCCGA 59.927 52.381 0.00 0.00 31.47 5.14
301 314 0.766131 TAAACACCCGAAAGCCTCCA 59.234 50.000 0.00 0.00 0.00 3.86
314 327 1.295292 AGCCTCCATCTTTCTAGGGGA 59.705 52.381 0.00 0.00 0.00 4.81
331 344 4.470602 AGGGGAGAAAGAAAACGACAATT 58.529 39.130 0.00 0.00 0.00 2.32
332 345 4.278419 AGGGGAGAAAGAAAACGACAATTG 59.722 41.667 3.24 3.24 0.00 2.32
345 358 7.972832 AAACGACAATTGATAACTGAACCTA 57.027 32.000 13.59 0.00 0.00 3.08
398 411 1.815003 AGCTATGCAAACAAGCTCCAC 59.185 47.619 9.62 0.00 42.89 4.02
573 589 4.354943 CACCCTCCCCCACCTCCT 62.355 72.222 0.00 0.00 0.00 3.69
591 607 3.147595 GCCCGCCTTTTCCCCATC 61.148 66.667 0.00 0.00 0.00 3.51
622 638 1.879380 CTCTCCCGCATTTCACAAACA 59.121 47.619 0.00 0.00 0.00 2.83
649 665 7.597288 TCATTATCTCGTTTCCCTTGATCTA 57.403 36.000 0.00 0.00 0.00 1.98
773 799 3.181967 CAGAGCGACGGCCTTTCG 61.182 66.667 17.05 17.05 41.24 3.46
983 1017 2.030562 CGTTGTCGGAGCAGGGTT 59.969 61.111 0.00 0.00 0.00 4.11
1039 1073 1.219393 GAGGCTTCCAAGGTCTCCG 59.781 63.158 0.00 0.00 0.00 4.63
1252 1289 2.058675 CCCCGATCCAGTATCCCAC 58.941 63.158 0.00 0.00 0.00 4.61
1293 1330 7.060633 GTGAACTTATTAATTTCGTTGTGGCTG 59.939 37.037 0.00 0.00 0.00 4.85
1459 1496 5.048713 AGGTTGTTAAGCATTTGTAGCAGTC 60.049 40.000 0.00 0.00 0.00 3.51
1492 1529 7.112452 TGCAGATTAGACTACATTCTAGCAA 57.888 36.000 0.00 0.00 29.67 3.91
1532 1572 9.859152 CAGAAATATAGAGGGGAAATTTCTCTT 57.141 33.333 17.45 10.38 42.21 2.85
1589 1629 7.887996 TTTGAAGGACATATGCATTTGAAAC 57.112 32.000 21.91 11.70 0.00 2.78
1627 1667 6.205853 ACTGTTTAATTTGAACCGCTGATACA 59.794 34.615 2.04 0.00 0.00 2.29
1630 1670 7.753132 TGTTTAATTTGAACCGCTGATACAATC 59.247 33.333 2.04 0.00 0.00 2.67
1631 1671 5.895636 AATTTGAACCGCTGATACAATCA 57.104 34.783 0.00 0.00 37.76 2.57
1637 1677 6.054941 TGAACCGCTGATACAATCATTATGT 58.945 36.000 0.00 0.00 38.85 2.29
1638 1678 5.929697 ACCGCTGATACAATCATTATGTG 57.070 39.130 0.00 0.00 38.85 3.21
1639 1679 5.368145 ACCGCTGATACAATCATTATGTGT 58.632 37.500 0.00 0.00 38.85 3.72
1640 1680 6.521162 ACCGCTGATACAATCATTATGTGTA 58.479 36.000 0.00 0.00 38.85 2.90
1641 1681 7.161404 ACCGCTGATACAATCATTATGTGTAT 58.839 34.615 7.80 7.80 40.34 2.29
1643 1683 7.413328 CCGCTGATACAATCATTATGTGTATGG 60.413 40.741 11.53 5.11 38.31 2.74
1644 1684 7.246311 GCTGATACAATCATTATGTGTATGGC 58.754 38.462 11.53 11.23 38.31 4.40
1645 1685 7.363205 TGATACAATCATTATGTGTATGGCG 57.637 36.000 11.53 0.00 38.31 5.69
1647 1687 3.820467 ACAATCATTATGTGTATGGCGGG 59.180 43.478 0.00 0.00 0.00 6.13
1669 1719 4.320202 GGAATTTGTCGCTTGTGTGTATGT 60.320 41.667 0.00 0.00 0.00 2.29
1812 1862 5.109903 GTGTTCTGCATCGGTCTATAACTT 58.890 41.667 0.00 0.00 0.00 2.66
1813 1863 6.270815 GTGTTCTGCATCGGTCTATAACTTA 58.729 40.000 0.00 0.00 0.00 2.24
1814 1864 6.198591 GTGTTCTGCATCGGTCTATAACTTAC 59.801 42.308 0.00 0.00 0.00 2.34
1815 1865 6.096423 TGTTCTGCATCGGTCTATAACTTACT 59.904 38.462 0.00 0.00 0.00 2.24
1816 1866 6.315091 TCTGCATCGGTCTATAACTTACTC 57.685 41.667 0.00 0.00 0.00 2.59
1817 1867 5.241064 TCTGCATCGGTCTATAACTTACTCC 59.759 44.000 0.00 0.00 0.00 3.85
1818 1868 4.280174 TGCATCGGTCTATAACTTACTCCC 59.720 45.833 0.00 0.00 0.00 4.30
1819 1869 4.523558 GCATCGGTCTATAACTTACTCCCT 59.476 45.833 0.00 0.00 0.00 4.20
1820 1870 5.335819 GCATCGGTCTATAACTTACTCCCTC 60.336 48.000 0.00 0.00 0.00 4.30
1821 1871 4.723309 TCGGTCTATAACTTACTCCCTCC 58.277 47.826 0.00 0.00 0.00 4.30
1822 1872 3.501445 CGGTCTATAACTTACTCCCTCCG 59.499 52.174 0.00 0.00 0.00 4.63
1823 1873 4.468713 GGTCTATAACTTACTCCCTCCGT 58.531 47.826 0.00 0.00 0.00 4.69
1824 1874 4.892345 GGTCTATAACTTACTCCCTCCGTT 59.108 45.833 0.00 0.00 0.00 4.44
1825 1875 5.009510 GGTCTATAACTTACTCCCTCCGTTC 59.990 48.000 0.00 0.00 0.00 3.95
1826 1876 5.009510 GTCTATAACTTACTCCCTCCGTTCC 59.990 48.000 0.00 0.00 0.00 3.62
1827 1877 2.019807 AACTTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
1828 1878 2.019807 ACTTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
1829 1879 2.332117 ACTTACTCCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
1830 1880 2.707257 ACTTACTCCCTCCGTTCCAAAA 59.293 45.455 0.00 0.00 0.00 2.44
1831 1881 3.329814 ACTTACTCCCTCCGTTCCAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
1832 1882 4.533311 ACTTACTCCCTCCGTTCCAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
1833 1883 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1834 1884 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1835 1885 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1836 1886 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1837 1887 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1838 1888 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1839 1889 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1840 1890 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1841 1891 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1842 1892 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1843 1893 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1844 1894 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1845 1895 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1846 1896 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1847 1897 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1848 1898 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1849 1899 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1850 1900 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
1851 1901 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
1852 1902 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
1853 1903 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
1854 1904 9.449719 AAATAGATGACCCAACTTTGTACTAAG 57.550 33.333 14.42 14.42 0.00 2.18
1855 1905 5.805728 AGATGACCCAACTTTGTACTAAGG 58.194 41.667 19.08 6.74 0.00 2.69
1856 1906 5.309806 AGATGACCCAACTTTGTACTAAGGT 59.690 40.000 19.08 11.48 0.00 3.50
1857 1907 5.376756 TGACCCAACTTTGTACTAAGGTT 57.623 39.130 19.08 9.89 0.00 3.50
1858 1908 6.497624 TGACCCAACTTTGTACTAAGGTTA 57.502 37.500 19.08 4.72 0.00 2.85
1859 1909 6.527423 TGACCCAACTTTGTACTAAGGTTAG 58.473 40.000 19.08 9.91 36.82 2.34
1860 1910 6.100134 TGACCCAACTTTGTACTAAGGTTAGT 59.900 38.462 19.08 12.61 45.39 2.24
1861 1911 7.289782 TGACCCAACTTTGTACTAAGGTTAGTA 59.710 37.037 19.08 5.64 43.36 1.82
1887 1937 9.696917 ACAAAGTTTGATCATCTATTTTGGAAC 57.303 29.630 22.23 8.03 0.00 3.62
1888 1938 8.853345 CAAAGTTTGATCATCTATTTTGGAACG 58.147 33.333 10.19 0.00 0.00 3.95
1889 1939 7.088589 AGTTTGATCATCTATTTTGGAACGG 57.911 36.000 0.00 0.00 0.00 4.44
1890 1940 6.884295 AGTTTGATCATCTATTTTGGAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
1891 1941 6.925610 TTGATCATCTATTTTGGAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
1892 1942 5.368145 TGATCATCTATTTTGGAACGGAGG 58.632 41.667 0.00 0.00 0.00 4.30
1893 1943 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
1894 1944 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1895 1945 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1916 1966 9.457776 AGGGAGTATATGCATGGATAATATTCT 57.542 33.333 11.23 5.58 0.00 2.40
1935 1985 1.933181 CTGTTTGTCGACTTGCTGTCA 59.067 47.619 17.92 5.70 45.60 3.58
2033 2083 7.269477 AGAAAATTAATCCTGCTCTGTATGC 57.731 36.000 0.00 0.00 0.00 3.14
2083 2133 3.317603 TCTCTGTGATTGCATTCGTCA 57.682 42.857 4.27 5.43 0.00 4.35
2102 2152 4.652822 GTCAAACCCTCCTTTAGTGTCAT 58.347 43.478 0.00 0.00 0.00 3.06
2106 2156 4.993705 ACCCTCCTTTAGTGTCATCAAA 57.006 40.909 0.00 0.00 0.00 2.69
2136 2186 3.689161 GGTGTGTTCACAAGCTGCATATA 59.311 43.478 7.22 0.00 45.45 0.86
2168 2218 7.770433 CAGAACCAGAATCATATCAAGTAACCA 59.230 37.037 0.00 0.00 0.00 3.67
2342 2393 7.862372 CACTTATTGTGTTATGCTTGACAGTTT 59.138 33.333 0.00 0.00 41.53 2.66
2507 2558 7.483059 CGTGGATTTCTTTTATCTTTTGAGAGC 59.517 37.037 0.00 0.00 0.00 4.09
2724 2781 5.930837 TTCCCATGTGTTTGTTTCTTTCT 57.069 34.783 0.00 0.00 0.00 2.52
2875 2932 6.265876 TCCAAAAAGGACTTGGTGGTTAATAC 59.734 38.462 11.75 0.00 43.07 1.89
2879 2936 3.265995 AGGACTTGGTGGTTAATACCCTG 59.734 47.826 8.78 5.15 44.35 4.45
3019 3079 2.489722 GCAGTGGACCTTTCATCCTTTC 59.510 50.000 0.00 0.00 37.13 2.62
3115 3175 7.147479 GCATCCTCCCTAACCATGTATGTATAT 60.147 40.741 0.00 0.00 0.00 0.86
3144 3204 2.027561 TGCACGCCCAGATAAGTTACTT 60.028 45.455 2.32 2.32 0.00 2.24
3229 3289 2.897969 AGGTCCAAACTATCACTGTCGT 59.102 45.455 0.00 0.00 0.00 4.34
3262 3322 6.054941 CCTTGTTTCACCTTAGCCAATTTTT 58.945 36.000 0.00 0.00 0.00 1.94
3288 3348 3.056536 TGAGCTCTTTCTCAGCATTACGT 60.057 43.478 16.19 0.00 39.56 3.57
3300 3360 2.567615 AGCATTACGTCCTGGAAGAACT 59.432 45.455 16.67 3.30 34.07 3.01
3304 3364 5.585047 GCATTACGTCCTGGAAGAACTTATT 59.415 40.000 16.67 0.00 34.07 1.40
3400 3460 1.531423 ATGTGCTTGAAGTGCTCCTG 58.469 50.000 0.00 0.00 0.00 3.86
3403 3463 1.736681 GTGCTTGAAGTGCTCCTGATC 59.263 52.381 0.00 0.00 0.00 2.92
3417 3477 4.943705 GCTCCTGATCAATTGTAAGTTCCA 59.056 41.667 5.13 0.00 0.00 3.53
3421 3481 8.421249 TCCTGATCAATTGTAAGTTCCATTTT 57.579 30.769 5.13 0.00 0.00 1.82
3450 3511 3.622612 GGCTTGACATTTTGTGCAAGTTT 59.377 39.130 15.01 0.00 40.71 2.66
3451 3512 4.094739 GGCTTGACATTTTGTGCAAGTTTT 59.905 37.500 15.01 0.00 40.71 2.43
3454 3515 5.793026 TGACATTTTGTGCAAGTTTTTCC 57.207 34.783 0.00 0.00 0.00 3.13
3480 3541 9.226606 CAACTTACCATCCAGAACTTTGTATTA 57.773 33.333 0.00 0.00 0.00 0.98
3482 3543 9.614792 ACTTACCATCCAGAACTTTGTATTATC 57.385 33.333 0.00 0.00 0.00 1.75
3498 3559 3.627395 TTATCCATTGCAGTTCCTCGT 57.373 42.857 0.00 0.00 0.00 4.18
3564 3625 9.055248 CATATGATTTTCACTCTTGTTTTCGTC 57.945 33.333 0.00 0.00 0.00 4.20
3626 3687 2.289819 ACCCATGCTTGGCTTGAAATTG 60.290 45.455 13.15 0.00 42.15 2.32
3680 3741 0.105964 TTCCATGCCCGAATCGTAGG 59.894 55.000 0.82 0.00 0.00 3.18
3784 3847 0.944311 CTCGCAAGCACTACACCGTT 60.944 55.000 0.00 0.00 37.18 4.44
3830 3893 4.571176 GCTGGTAGCTTACATTTCACCTAC 59.429 45.833 0.00 0.00 38.45 3.18
3831 3894 5.627040 GCTGGTAGCTTACATTTCACCTACT 60.627 44.000 0.00 0.00 38.45 2.57
3833 3896 7.670605 TGGTAGCTTACATTTCACCTACTAT 57.329 36.000 0.00 0.00 0.00 2.12
3835 3898 7.343574 TGGTAGCTTACATTTCACCTACTATCA 59.656 37.037 0.00 0.00 0.00 2.15
3839 3902 7.287927 AGCTTACATTTCACCTACTATCAGCTA 59.712 37.037 0.00 0.00 29.71 3.32
3841 3904 8.534954 TTACATTTCACCTACTATCAGCTACT 57.465 34.615 0.00 0.00 0.00 2.57
3856 3919 4.305769 CAGCTACTATTTGGCTGCTCTAG 58.694 47.826 0.00 0.00 45.04 2.43
3910 4039 5.234329 CAGGTATGCCGTTAATCTAGTTGTG 59.766 44.000 0.00 0.00 40.50 3.33
3931 4060 0.468226 TCTTCGTGGACACCAAGCTT 59.532 50.000 5.14 0.00 34.18 3.74
3971 4104 9.230122 TCATGACACACAGTATATGATTTGTTT 57.770 29.630 0.00 0.00 32.28 2.83
4016 4149 5.828299 TTGTAACAAGAGTTCTTTGTGGG 57.172 39.130 0.00 0.00 39.15 4.61
4017 4150 4.850680 TGTAACAAGAGTTCTTTGTGGGT 58.149 39.130 0.00 0.00 39.15 4.51
4043 4176 2.332654 GCAGAAATGCCGGACCGTT 61.333 57.895 13.94 0.00 0.00 4.44
4116 4249 4.256920 CCAAAGGATGAGAAAGACGTGAT 58.743 43.478 0.00 0.00 0.00 3.06
4239 4373 3.499918 GCCCGTTGATCATCCATCTTAAG 59.500 47.826 0.00 0.00 31.92 1.85
4245 4379 6.291849 CGTTGATCATCCATCTTAAGTTCGAC 60.292 42.308 1.63 0.00 31.92 4.20
4247 4381 4.402056 TCATCCATCTTAAGTTCGACCC 57.598 45.455 1.63 0.00 0.00 4.46
4248 4382 3.134081 TCATCCATCTTAAGTTCGACCCC 59.866 47.826 1.63 0.00 0.00 4.95
4270 4427 3.993736 CCCTTAAAAATTGAAACCCGCAG 59.006 43.478 0.00 0.00 0.00 5.18
4272 4429 4.684242 CCTTAAAAATTGAAACCCGCAGTC 59.316 41.667 0.00 0.00 0.00 3.51
4273 4430 2.415697 AAAATTGAAACCCGCAGTCG 57.584 45.000 0.00 0.00 0.00 4.18
4274 4431 1.314730 AAATTGAAACCCGCAGTCGT 58.685 45.000 0.00 0.00 0.00 4.34
4275 4432 1.314730 AATTGAAACCCGCAGTCGTT 58.685 45.000 0.00 0.00 0.00 3.85
4276 4433 1.314730 ATTGAAACCCGCAGTCGTTT 58.685 45.000 0.00 0.00 34.95 3.60
4277 4434 1.950828 TTGAAACCCGCAGTCGTTTA 58.049 45.000 0.00 0.00 32.46 2.01
4278 4435 2.172851 TGAAACCCGCAGTCGTTTAT 57.827 45.000 0.00 0.00 32.46 1.40
4279 4436 2.070783 TGAAACCCGCAGTCGTTTATC 58.929 47.619 0.00 0.00 32.46 1.75
4299 4459 1.605457 CCGTTGAGCTGAGCTTGTACA 60.605 52.381 9.00 0.00 39.88 2.90
4328 4488 3.467226 GCCGGGCTGCCTGTACTA 61.467 66.667 25.08 0.00 0.00 1.82
4329 4489 2.499685 CCGGGCTGCCTGTACTAC 59.500 66.667 25.08 2.77 0.00 2.73
4330 4490 2.355986 CCGGGCTGCCTGTACTACA 61.356 63.158 25.08 0.00 0.00 2.74
4331 4491 1.141881 CGGGCTGCCTGTACTACAG 59.858 63.158 19.55 9.02 45.53 2.74
4424 4586 1.685765 CACCCCGAGGAGGACATGA 60.686 63.158 0.00 0.00 45.00 3.07
4425 4587 1.381872 ACCCCGAGGAGGACATGAG 60.382 63.158 0.00 0.00 45.00 2.90
4426 4588 2.801631 CCCCGAGGAGGACATGAGC 61.802 68.421 0.00 0.00 45.00 4.26
4476 4641 1.134995 CACATGAGCGCTTCTCCAGTA 60.135 52.381 13.26 0.00 41.18 2.74
4477 4642 1.135915 ACATGAGCGCTTCTCCAGTAG 59.864 52.381 13.26 1.88 41.18 2.57
4478 4643 1.135915 CATGAGCGCTTCTCCAGTAGT 59.864 52.381 13.26 0.00 41.18 2.73
4479 4644 0.811915 TGAGCGCTTCTCCAGTAGTC 59.188 55.000 13.26 0.00 41.18 2.59
4480 4645 0.101579 GAGCGCTTCTCCAGTAGTCC 59.898 60.000 13.26 0.00 35.77 3.85
4481 4646 0.612174 AGCGCTTCTCCAGTAGTCCA 60.612 55.000 2.64 0.00 0.00 4.02
4561 4726 4.424711 TGCCCGGCCCATTCTGTC 62.425 66.667 7.03 0.00 0.00 3.51
4569 4734 1.035932 GCCCATTCTGTCTGCATGCT 61.036 55.000 20.33 0.00 0.00 3.79
4582 4764 3.267233 ATGCTGAAGCCCCACCCA 61.267 61.111 0.00 0.00 41.18 4.51
4591 4773 3.077907 CCCCACCCATCGTTCAGT 58.922 61.111 0.00 0.00 0.00 3.41
4605 4787 1.779061 TTCAGTTGAGCCACCCTCCC 61.779 60.000 0.00 0.00 39.98 4.30
4607 4789 1.920835 AGTTGAGCCACCCTCCCTC 60.921 63.158 0.00 0.00 39.98 4.30
4636 4819 1.342474 TGGCCTTCCCTTCAACAACAA 60.342 47.619 3.32 0.00 0.00 2.83
4647 4830 4.391523 CCTTCAACAACAACACCAAAAAGG 59.608 41.667 0.00 0.00 45.67 3.11
4648 4831 4.873746 TCAACAACAACACCAAAAAGGA 57.126 36.364 0.00 0.00 41.22 3.36
4649 4832 5.413309 TCAACAACAACACCAAAAAGGAT 57.587 34.783 0.00 0.00 41.22 3.24
4650 4833 5.799213 TCAACAACAACACCAAAAAGGATT 58.201 33.333 0.00 0.00 41.22 3.01
4651 4834 5.641209 TCAACAACAACACCAAAAAGGATTG 59.359 36.000 0.00 0.00 41.22 2.67
4652 4835 5.413309 ACAACAACACCAAAAAGGATTGA 57.587 34.783 8.95 0.00 41.22 2.57
4658 4844 5.410355 ACACCAAAAAGGATTGATGATGG 57.590 39.130 0.00 0.00 41.22 3.51
4676 4862 3.620427 TGGATGTGGGTGTACATGTAC 57.380 47.619 25.99 25.99 41.15 2.90
4693 4879 1.599071 GTACATATCGTCCGACCGACA 59.401 52.381 0.00 0.00 42.07 4.35
4711 4930 4.985409 CCGACAGACCAGCTTAATTCTATC 59.015 45.833 0.00 0.00 0.00 2.08
4716 4935 7.743749 ACAGACCAGCTTAATTCTATCATCAT 58.256 34.615 0.00 0.00 0.00 2.45
4749 4968 0.243907 CATATCGATTCTCCGCCGGT 59.756 55.000 1.71 0.00 0.00 5.28
4811 5030 6.227522 TGGACGAGTTTCATTCATTCTGTTA 58.772 36.000 0.00 0.00 0.00 2.41
4819 5038 1.011968 TTCATTCTGTTAGCGCGCGT 61.012 50.000 32.35 20.00 0.00 6.01
5012 5257 1.602668 CCATTGGGTTTTGCGTGTGAG 60.603 52.381 0.00 0.00 0.00 3.51
5021 5269 1.691195 TTGCGTGTGAGTTCCCTCCA 61.691 55.000 0.00 0.00 36.86 3.86
5024 5272 0.393077 CGTGTGAGTTCCCTCCACTT 59.607 55.000 0.00 0.00 37.04 3.16
5068 5316 1.125093 TTTCGTGCTGGGGAGAAGGA 61.125 55.000 0.00 0.00 0.00 3.36
5098 5346 3.188786 CTACACGCCGCAGCTTCC 61.189 66.667 0.00 0.00 36.60 3.46
5104 5352 3.752339 GCCGCAGCTTCCCCTTTG 61.752 66.667 0.00 0.00 35.50 2.77
5105 5353 3.752339 CCGCAGCTTCCCCTTTGC 61.752 66.667 0.00 0.00 0.00 3.68
5175 5459 3.787001 CCGGCCCTGGAGAGGAAC 61.787 72.222 0.00 0.00 42.93 3.62
5176 5460 3.003173 CGGCCCTGGAGAGGAACA 61.003 66.667 0.00 0.00 42.93 3.18
5178 5462 1.767692 GGCCCTGGAGAGGAACAAA 59.232 57.895 0.00 0.00 42.93 2.83
5179 5463 0.609406 GGCCCTGGAGAGGAACAAAC 60.609 60.000 0.00 0.00 42.93 2.93
5180 5464 0.955919 GCCCTGGAGAGGAACAAACG 60.956 60.000 0.00 0.00 42.93 3.60
5181 5465 0.955919 CCCTGGAGAGGAACAAACGC 60.956 60.000 0.00 0.00 42.93 4.84
5182 5466 0.250295 CCTGGAGAGGAACAAACGCA 60.250 55.000 0.00 0.00 42.93 5.24
5183 5467 1.611673 CCTGGAGAGGAACAAACGCAT 60.612 52.381 0.00 0.00 42.93 4.73
5184 5468 1.734465 CTGGAGAGGAACAAACGCATC 59.266 52.381 0.00 0.00 0.00 3.91
5257 5541 2.951457 TCACCGATTCTCGTATGCAA 57.049 45.000 0.00 0.00 38.40 4.08
5332 5616 0.904649 TGCTACTACCACTGCTGCAT 59.095 50.000 1.31 0.00 0.00 3.96
5333 5617 1.134699 TGCTACTACCACTGCTGCATC 60.135 52.381 1.31 0.00 0.00 3.91
5370 5654 1.815421 CGGTCCTGGGAATTCTGCG 60.815 63.158 5.23 0.00 0.00 5.18
5379 5663 1.502163 GGAATTCTGCGGCCTCATCG 61.502 60.000 5.23 0.00 0.00 3.84
5397 5681 0.602106 CGCACCAGATCCTATGCCTG 60.602 60.000 7.00 0.00 34.49 4.85
5444 5728 4.172512 AGAGCCATCTGCCCTGCG 62.173 66.667 0.00 0.00 42.71 5.18
5448 5732 4.478371 CCATCTGCCCTGCGCTCA 62.478 66.667 9.73 0.20 38.78 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.099921 CCGACGAGTCTCATGGAATTCT 59.900 50.000 5.23 0.00 0.00 2.40
3 4 1.678627 CTCCGACGAGTCTCATGGAAT 59.321 52.381 0.00 0.00 0.00 3.01
4 5 1.095600 CTCCGACGAGTCTCATGGAA 58.904 55.000 0.00 0.00 0.00 3.53
6 7 0.378962 GTCTCCGACGAGTCTCATGG 59.621 60.000 0.00 0.00 37.40 3.66
7 8 1.087501 TGTCTCCGACGAGTCTCATG 58.912 55.000 0.00 0.00 37.40 3.07
8 9 1.088306 GTGTCTCCGACGAGTCTCAT 58.912 55.000 0.00 0.00 37.40 2.90
9 10 0.250166 TGTGTCTCCGACGAGTCTCA 60.250 55.000 0.00 0.00 37.40 3.27
10 11 0.166379 GTGTGTCTCCGACGAGTCTC 59.834 60.000 0.00 0.00 37.40 3.36
11 12 1.235948 GGTGTGTCTCCGACGAGTCT 61.236 60.000 0.00 0.00 37.40 3.24
12 13 1.209640 GGTGTGTCTCCGACGAGTC 59.790 63.158 0.00 0.00 37.40 3.36
13 14 1.228184 AGGTGTGTCTCCGACGAGT 60.228 57.895 0.00 0.00 37.40 4.18
14 15 1.502640 GAGGTGTGTCTCCGACGAG 59.497 63.158 0.00 0.00 34.95 4.18
35 36 2.265739 GCATCGTCAGAGGGTGCA 59.734 61.111 21.11 0.00 35.93 4.57
36 37 2.887568 CGCATCGTCAGAGGGTGC 60.888 66.667 17.00 17.00 0.00 5.01
37 38 1.226802 CTCGCATCGTCAGAGGGTG 60.227 63.158 0.00 0.00 0.00 4.61
38 39 1.378646 TCTCGCATCGTCAGAGGGT 60.379 57.895 0.00 0.00 33.16 4.34
73 74 1.362224 AGGTTCTCTTTGCCTAGCCA 58.638 50.000 0.00 0.00 0.00 4.75
77 78 8.109634 AGAATGAAATAAGGTTCTCTTTGCCTA 58.890 33.333 0.00 0.00 36.93 3.93
101 102 0.246635 GCAGCGGTGACTTCCTAAGA 59.753 55.000 20.69 0.00 0.00 2.10
113 114 2.985847 GAAAGGCAAGGCAGCGGT 60.986 61.111 0.00 0.00 34.64 5.68
129 130 3.662759 AGGGTTTGTGTCCTTTTCAGA 57.337 42.857 0.00 0.00 0.00 3.27
130 131 5.534654 TGATTAGGGTTTGTGTCCTTTTCAG 59.465 40.000 0.00 0.00 34.75 3.02
131 132 5.450453 TGATTAGGGTTTGTGTCCTTTTCA 58.550 37.500 0.00 0.00 34.75 2.69
134 135 5.070685 GTCTGATTAGGGTTTGTGTCCTTT 58.929 41.667 0.00 0.00 34.75 3.11
135 136 4.351111 AGTCTGATTAGGGTTTGTGTCCTT 59.649 41.667 0.00 0.00 34.75 3.36
138 139 7.739498 TTTTAGTCTGATTAGGGTTTGTGTC 57.261 36.000 0.00 0.00 0.00 3.67
175 178 0.337428 ATGGGAGGGCTCATGCTTTT 59.663 50.000 0.00 0.00 32.79 2.27
180 183 1.228184 GCTGATGGGAGGGCTCATG 60.228 63.158 0.00 0.00 34.66 3.07
181 184 1.066585 ATGCTGATGGGAGGGCTCAT 61.067 55.000 0.00 0.00 38.13 2.90
194 197 2.443394 GGATCCCGACCCATGCTGA 61.443 63.158 0.00 0.00 0.00 4.26
196 199 2.366837 TGGATCCCGACCCATGCT 60.367 61.111 9.90 0.00 0.00 3.79
220 223 3.017442 CGTCTACTGAGGAGTCATGGAA 58.983 50.000 0.00 0.00 33.21 3.53
232 241 0.738762 CGACCCGTCTCGTCTACTGA 60.739 60.000 0.00 0.00 0.00 3.41
236 245 2.821366 GCCGACCCGTCTCGTCTA 60.821 66.667 0.00 0.00 31.35 2.59
258 267 4.803426 CCTGCCTCTCGTCGGTGC 62.803 72.222 0.00 0.00 0.00 5.01
263 272 1.079057 GGGTTTCCTGCCTCTCGTC 60.079 63.158 0.00 0.00 0.00 4.20
292 302 2.511637 CCCCTAGAAAGATGGAGGCTTT 59.488 50.000 0.00 0.00 38.22 3.51
314 327 8.836413 TCAGTTATCAATTGTCGTTTTCTTTCT 58.164 29.630 5.13 0.00 0.00 2.52
360 373 9.008965 TGCATAGCTTTACAACTCTTTCAAATA 57.991 29.630 0.00 0.00 0.00 1.40
365 378 7.138736 TGTTTGCATAGCTTTACAACTCTTTC 58.861 34.615 0.00 0.00 0.00 2.62
383 396 1.761449 TTCAGTGGAGCTTGTTTGCA 58.239 45.000 0.00 0.00 34.99 4.08
384 397 2.099756 AGTTTCAGTGGAGCTTGTTTGC 59.900 45.455 0.00 0.00 0.00 3.68
573 589 3.955543 GATGGGGAAAAGGCGGGCA 62.956 63.158 3.78 0.00 0.00 5.36
591 607 3.787001 GGGAGAGCGAGGGGGTTG 61.787 72.222 0.00 0.00 0.00 3.77
622 638 5.989477 TCAAGGGAAACGAGATAATGATGT 58.011 37.500 0.00 0.00 0.00 3.06
649 665 0.980423 GGCAGGGAGTTCAAGAGAGT 59.020 55.000 0.00 0.00 0.00 3.24
983 1017 0.735978 CATGGCAGTAGACGACGCAA 60.736 55.000 0.00 0.00 31.70 4.85
1101 1135 4.982241 AAGAAAGGATTGTGAGTCCTCA 57.018 40.909 0.00 0.00 45.23 3.86
1107 1141 4.039609 AGCCCAAAAAGAAAGGATTGTGAG 59.960 41.667 0.00 0.00 0.00 3.51
1117 1151 1.138661 CCTGCACAGCCCAAAAAGAAA 59.861 47.619 0.00 0.00 0.00 2.52
1211 1246 2.162681 CTCACCTGAAACACAATCCCC 58.837 52.381 0.00 0.00 0.00 4.81
1252 1289 2.041966 GTTCACACACACGACGTAGAG 58.958 52.381 0.00 0.00 0.00 2.43
1293 1330 1.296056 ATACTGAAACGCGCACCACC 61.296 55.000 5.73 0.00 0.00 4.61
1395 1432 3.259123 CCAATTCCAGGGAAGAAACAAGG 59.741 47.826 6.91 0.00 37.56 3.61
1459 1496 6.166279 TGTAGTCTAATCTGCAACAGGAAAG 58.834 40.000 0.00 0.00 31.51 2.62
1492 1529 5.779529 ATATTTCTGCCGATCAGCAAAAT 57.220 34.783 19.01 19.01 43.52 1.82
1512 1552 9.460413 TTCCATAAGAGAAATTTCCCCTCTATA 57.540 33.333 14.61 7.21 36.36 1.31
1532 1572 3.068873 GTGGGTGCAAAACAGTTTCCATA 59.931 43.478 0.00 0.00 0.00 2.74
1610 1650 6.455360 AATGATTGTATCAGCGGTTCAAAT 57.545 33.333 0.00 0.00 43.53 2.32
1627 1667 4.365514 TCCCGCCATACACATAATGATT 57.634 40.909 0.00 0.00 0.00 2.57
1630 1670 5.221224 ACAAATTCCCGCCATACACATAATG 60.221 40.000 0.00 0.00 0.00 1.90
1631 1671 4.892934 ACAAATTCCCGCCATACACATAAT 59.107 37.500 0.00 0.00 0.00 1.28
1637 1677 1.374560 CGACAAATTCCCGCCATACA 58.625 50.000 0.00 0.00 0.00 2.29
1638 1678 0.028902 GCGACAAATTCCCGCCATAC 59.971 55.000 7.55 0.00 42.77 2.39
1639 1679 2.399856 GCGACAAATTCCCGCCATA 58.600 52.632 7.55 0.00 42.77 2.74
1640 1680 3.196648 GCGACAAATTCCCGCCAT 58.803 55.556 7.55 0.00 42.77 4.40
1644 1684 0.591170 ACACAAGCGACAAATTCCCG 59.409 50.000 0.00 0.00 0.00 5.14
1645 1685 1.336755 ACACACAAGCGACAAATTCCC 59.663 47.619 0.00 0.00 0.00 3.97
1647 1687 4.783242 ACATACACACAAGCGACAAATTC 58.217 39.130 0.00 0.00 0.00 2.17
1669 1719 3.994204 TCGACGATCAATTATTCCCGA 57.006 42.857 0.00 0.00 0.00 5.14
1812 1862 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1813 1863 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1814 1864 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1815 1865 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1816 1866 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1817 1867 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1818 1868 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1819 1869 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1820 1870 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1821 1871 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1822 1872 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1823 1873 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1824 1874 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1825 1875 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1826 1876 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
1827 1877 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
1828 1878 9.449719 CTTAGTACAAAGTTGGGTCATCTATTT 57.550 33.333 0.00 0.00 0.00 1.40
1829 1879 8.047310 CCTTAGTACAAAGTTGGGTCATCTATT 58.953 37.037 0.00 0.00 0.00 1.73
1830 1880 7.182206 ACCTTAGTACAAAGTTGGGTCATCTAT 59.818 37.037 0.00 0.00 0.00 1.98
1831 1881 6.499350 ACCTTAGTACAAAGTTGGGTCATCTA 59.501 38.462 0.00 0.00 0.00 1.98
1832 1882 5.309806 ACCTTAGTACAAAGTTGGGTCATCT 59.690 40.000 0.00 0.00 0.00 2.90
1833 1883 5.557866 ACCTTAGTACAAAGTTGGGTCATC 58.442 41.667 0.00 0.00 0.00 2.92
1834 1884 5.578157 ACCTTAGTACAAAGTTGGGTCAT 57.422 39.130 0.00 0.00 0.00 3.06
1835 1885 5.376756 AACCTTAGTACAAAGTTGGGTCA 57.623 39.130 0.00 0.00 0.00 4.02
1836 1886 6.528321 ACTAACCTTAGTACAAAGTTGGGTC 58.472 40.000 0.00 0.00 41.92 4.46
1837 1887 6.505048 ACTAACCTTAGTACAAAGTTGGGT 57.495 37.500 0.00 0.00 41.92 4.51
1861 1911 9.696917 GTTCCAAAATAGATGATCAAACTTTGT 57.303 29.630 0.00 0.00 0.00 2.83
1862 1912 8.853345 CGTTCCAAAATAGATGATCAAACTTTG 58.147 33.333 0.00 5.91 0.00 2.77
1863 1913 8.028938 CCGTTCCAAAATAGATGATCAAACTTT 58.971 33.333 0.00 0.00 0.00 2.66
1864 1914 7.393234 TCCGTTCCAAAATAGATGATCAAACTT 59.607 33.333 0.00 0.00 0.00 2.66
1865 1915 6.884295 TCCGTTCCAAAATAGATGATCAAACT 59.116 34.615 0.00 5.25 0.00 2.66
1866 1916 7.083875 TCCGTTCCAAAATAGATGATCAAAC 57.916 36.000 0.00 0.00 0.00 2.93
1867 1917 6.318648 CCTCCGTTCCAAAATAGATGATCAAA 59.681 38.462 0.00 0.00 0.00 2.69
1868 1918 5.822519 CCTCCGTTCCAAAATAGATGATCAA 59.177 40.000 0.00 0.00 0.00 2.57
1869 1919 5.368145 CCTCCGTTCCAAAATAGATGATCA 58.632 41.667 0.00 0.00 0.00 2.92
1870 1920 4.757149 CCCTCCGTTCCAAAATAGATGATC 59.243 45.833 0.00 0.00 0.00 2.92
1871 1921 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
1872 1922 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1873 1923 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1874 1924 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1875 1925 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1876 1926 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1877 1927 6.743208 GCATATACTCCCTCCGTTCCAAAATA 60.743 42.308 0.00 0.00 0.00 1.40
1878 1928 5.621193 CATATACTCCCTCCGTTCCAAAAT 58.379 41.667 0.00 0.00 0.00 1.82
1879 1929 4.685030 GCATATACTCCCTCCGTTCCAAAA 60.685 45.833 0.00 0.00 0.00 2.44
1880 1930 3.181458 GCATATACTCCCTCCGTTCCAAA 60.181 47.826 0.00 0.00 0.00 3.28
1881 1931 2.367567 GCATATACTCCCTCCGTTCCAA 59.632 50.000 0.00 0.00 0.00 3.53
1882 1932 1.968493 GCATATACTCCCTCCGTTCCA 59.032 52.381 0.00 0.00 0.00 3.53
1883 1933 1.968493 TGCATATACTCCCTCCGTTCC 59.032 52.381 0.00 0.00 0.00 3.62
1884 1934 3.589988 CATGCATATACTCCCTCCGTTC 58.410 50.000 0.00 0.00 0.00 3.95
1885 1935 2.303022 CCATGCATATACTCCCTCCGTT 59.697 50.000 0.00 0.00 0.00 4.44
1886 1936 1.902508 CCATGCATATACTCCCTCCGT 59.097 52.381 0.00 0.00 0.00 4.69
1887 1937 2.179427 TCCATGCATATACTCCCTCCG 58.821 52.381 0.00 0.00 0.00 4.63
1888 1938 5.957771 TTATCCATGCATATACTCCCTCC 57.042 43.478 0.00 0.00 0.00 4.30
1889 1939 9.717942 GAATATTATCCATGCATATACTCCCTC 57.282 37.037 0.00 0.00 0.00 4.30
1890 1940 9.457776 AGAATATTATCCATGCATATACTCCCT 57.542 33.333 0.00 0.00 0.00 4.20
1891 1941 9.499479 CAGAATATTATCCATGCATATACTCCC 57.501 37.037 0.00 0.00 0.00 4.30
1992 2042 6.892658 ATTTTCTATGCACAACTTGGTACA 57.107 33.333 0.00 0.00 0.00 2.90
1996 2046 8.253113 AGGATTAATTTTCTATGCACAACTTGG 58.747 33.333 0.00 0.00 0.00 3.61
1997 2047 9.079833 CAGGATTAATTTTCTATGCACAACTTG 57.920 33.333 0.00 0.00 0.00 3.16
1998 2048 7.761249 GCAGGATTAATTTTCTATGCACAACTT 59.239 33.333 0.00 0.00 32.79 2.66
1999 2049 7.123247 AGCAGGATTAATTTTCTATGCACAACT 59.877 33.333 14.80 0.00 34.93 3.16
2000 2050 7.260603 AGCAGGATTAATTTTCTATGCACAAC 58.739 34.615 14.80 0.00 34.93 3.32
2033 2083 2.086869 AGCCCGATGAAACATTCACAG 58.913 47.619 0.00 0.00 43.48 3.66
2083 2133 4.993705 TGATGACACTAAAGGAGGGTTT 57.006 40.909 0.00 0.00 44.07 3.27
2102 2152 3.066621 GTGAACACACCAGCAGAATTTGA 59.933 43.478 0.00 0.00 0.00 2.69
2106 2156 2.346766 TGTGAACACACCAGCAGAAT 57.653 45.000 3.39 0.00 36.21 2.40
2136 2186 3.947612 ATGATTCTGGTTCTGGCAGAT 57.052 42.857 19.50 0.24 0.00 2.90
2168 2218 1.023513 GTCCGAGCATGCTCAAAGCT 61.024 55.000 38.97 10.84 42.97 3.74
2661 2714 6.534634 AGGCAGAAGTAGTCAAAACAAGTAT 58.465 36.000 0.00 0.00 0.00 2.12
2875 2932 1.682854 ACAAATGACACACAAGCAGGG 59.317 47.619 0.00 0.00 0.00 4.45
2879 2936 5.424121 AGAACTACAAATGACACACAAGC 57.576 39.130 0.00 0.00 0.00 4.01
3115 3175 5.825679 ACTTATCTGGGCGTGCAAAATATTA 59.174 36.000 0.00 0.00 0.00 0.98
3127 3187 7.387948 AGCAATATTAAGTAACTTATCTGGGCG 59.612 37.037 0.00 0.00 0.00 6.13
3144 3204 5.126067 GTGAAGCCTGGAGAAGCAATATTA 58.874 41.667 0.00 0.00 0.00 0.98
3262 3322 1.002773 TGCTGAGAAAGAGCTCATGCA 59.997 47.619 17.77 6.65 43.43 3.96
3288 3348 7.741785 TGACTAAACAATAAGTTCTTCCAGGA 58.258 34.615 0.00 0.00 40.26 3.86
3304 3364 7.423844 AGATGACTCCATGTATGACTAAACA 57.576 36.000 0.00 0.00 32.09 2.83
3417 3477 8.723311 CACAAAATGTCAAGCCAATGATAAAAT 58.277 29.630 0.00 0.00 0.00 1.82
3421 3481 5.170021 GCACAAAATGTCAAGCCAATGATA 58.830 37.500 0.00 0.00 0.00 2.15
3450 3511 5.319043 AGTTCTGGATGGTAAGTTGGAAA 57.681 39.130 0.00 0.00 0.00 3.13
3451 3512 4.993705 AGTTCTGGATGGTAAGTTGGAA 57.006 40.909 0.00 0.00 0.00 3.53
3454 3515 7.687941 ATACAAAGTTCTGGATGGTAAGTTG 57.312 36.000 0.00 0.00 0.00 3.16
3480 3541 1.679944 CCACGAGGAACTGCAATGGAT 60.680 52.381 0.00 0.00 41.55 3.41
3482 3543 0.321564 TCCACGAGGAACTGCAATGG 60.322 55.000 0.00 0.00 42.23 3.16
3498 3559 2.714250 ACCACACCCAAGATTTACTCCA 59.286 45.455 0.00 0.00 0.00 3.86
3564 3625 5.469760 TGAGCCATATTTGTGATATGTTCGG 59.530 40.000 5.57 0.00 31.77 4.30
3626 3687 5.008980 GGATTTCCCAGATGGAGATTCATC 58.991 45.833 0.00 0.00 46.24 2.92
3657 3718 1.156736 CGATTCGGGCATGGAATACC 58.843 55.000 0.00 0.00 34.41 2.73
3658 3719 1.878953 ACGATTCGGGCATGGAATAC 58.121 50.000 11.29 0.00 34.41 1.89
3659 3720 2.028476 CCTACGATTCGGGCATGGAATA 60.028 50.000 11.29 0.00 34.41 1.75
3660 3721 1.270839 CCTACGATTCGGGCATGGAAT 60.271 52.381 11.29 0.00 36.85 3.01
3661 3722 0.105964 CCTACGATTCGGGCATGGAA 59.894 55.000 11.29 0.00 0.00 3.53
3662 3723 1.046472 ACCTACGATTCGGGCATGGA 61.046 55.000 11.29 0.00 0.00 3.41
3680 3741 2.922740 TACAAGGTCCACCAGTTCAC 57.077 50.000 0.00 0.00 38.89 3.18
3784 3847 1.774110 ACCAGGCAACAACAACATCA 58.226 45.000 0.00 0.00 41.41 3.07
3808 3871 5.978814 AGTAGGTGAAATGTAAGCTACCAG 58.021 41.667 6.05 0.00 44.63 4.00
3835 3898 3.964031 ACTAGAGCAGCCAAATAGTAGCT 59.036 43.478 0.00 0.00 37.32 3.32
3839 3902 4.100189 CAGGTACTAGAGCAGCCAAATAGT 59.900 45.833 0.00 0.00 36.02 2.12
3841 3904 4.030913 ACAGGTACTAGAGCAGCCAAATA 58.969 43.478 0.00 0.00 36.02 1.40
3850 3913 6.126568 CTGTTAGAAGACAGGTACTAGAGC 57.873 45.833 0.00 0.00 42.58 4.09
3853 3916 6.071840 AGCAACTGTTAGAAGACAGGTACTAG 60.072 42.308 9.53 0.00 45.45 2.57
3856 3919 4.884247 AGCAACTGTTAGAAGACAGGTAC 58.116 43.478 9.53 0.00 45.45 3.34
3910 4039 0.586802 GCTTGGTGTCCACGAAGAAC 59.413 55.000 21.55 5.52 45.97 3.01
3931 4060 4.141597 TGTGTCATGAAAACAGTACCTGGA 60.142 41.667 0.00 0.00 35.51 3.86
3971 4104 8.203485 ACAAAGTGCCTTCAAATAGAAAATCAA 58.797 29.630 0.00 0.00 35.40 2.57
3986 4119 5.193679 AGAACTCTTGTTACAAAGTGCCTT 58.806 37.500 11.48 0.47 36.39 4.35
4007 4140 3.072330 TCTGCACAAGATACCCACAAAGA 59.928 43.478 0.00 0.00 0.00 2.52
4165 4298 1.405872 AATGCCGTACCCGATCAGTA 58.594 50.000 0.00 0.00 35.63 2.74
4195 4328 2.737252 CGAAAACCCTAGAGTGTTCAGC 59.263 50.000 7.94 0.00 34.19 4.26
4247 4381 3.244249 TGCGGGTTTCAATTTTTAAGGGG 60.244 43.478 0.00 0.00 0.00 4.79
4248 4382 3.993736 CTGCGGGTTTCAATTTTTAAGGG 59.006 43.478 0.00 0.00 0.00 3.95
4257 4414 1.314730 AAACGACTGCGGGTTTCAAT 58.685 45.000 0.00 0.00 43.17 2.57
4260 4417 1.395954 GGATAAACGACTGCGGGTTTC 59.604 52.381 3.52 0.00 43.17 2.78
4265 4422 0.368907 CAACGGATAAACGACTGCGG 59.631 55.000 0.00 0.00 43.17 5.69
4270 4427 2.599082 CTCAGCTCAACGGATAAACGAC 59.401 50.000 0.00 0.00 37.61 4.34
4272 4429 1.324736 GCTCAGCTCAACGGATAAACG 59.675 52.381 0.00 0.00 40.31 3.60
4273 4430 2.622436 AGCTCAGCTCAACGGATAAAC 58.378 47.619 0.00 0.00 30.62 2.01
4274 4431 3.002791 CAAGCTCAGCTCAACGGATAAA 58.997 45.455 0.00 0.00 38.25 1.40
4275 4432 2.028112 ACAAGCTCAGCTCAACGGATAA 60.028 45.455 0.00 0.00 38.25 1.75
4276 4433 1.550524 ACAAGCTCAGCTCAACGGATA 59.449 47.619 0.00 0.00 38.25 2.59
4277 4434 0.322975 ACAAGCTCAGCTCAACGGAT 59.677 50.000 0.00 0.00 38.25 4.18
4278 4435 0.966179 TACAAGCTCAGCTCAACGGA 59.034 50.000 0.00 0.00 38.25 4.69
4279 4436 1.071605 GTACAAGCTCAGCTCAACGG 58.928 55.000 0.00 0.00 38.25 4.44
4330 4490 1.134431 CCAAAAGGTGGCAGCAAAACT 60.134 47.619 20.04 0.00 41.72 2.66
4331 4491 1.298602 CCAAAAGGTGGCAGCAAAAC 58.701 50.000 20.04 0.00 41.72 2.43
4476 4641 1.350310 AAAACTCCCGGTGGTGGACT 61.350 55.000 0.00 0.00 0.00 3.85
4477 4642 1.149854 AAAACTCCCGGTGGTGGAC 59.850 57.895 0.00 0.00 0.00 4.02
4478 4643 1.149627 CAAAACTCCCGGTGGTGGA 59.850 57.895 0.00 0.00 0.00 4.02
4479 4644 1.152839 ACAAAACTCCCGGTGGTGG 60.153 57.895 0.00 0.00 0.00 4.61
4480 4645 1.170290 GGACAAAACTCCCGGTGGTG 61.170 60.000 0.00 0.00 0.00 4.17
4481 4646 1.149854 GGACAAAACTCCCGGTGGT 59.850 57.895 0.00 0.00 0.00 4.16
4539 4704 2.679996 AATGGGCCGGGCAGTTTC 60.680 61.111 30.95 12.51 0.00 2.78
4554 4719 1.743958 GCTTCAGCATGCAGACAGAAT 59.256 47.619 21.98 0.00 41.59 2.40
4561 4726 2.361992 TGGGGCTTCAGCATGCAG 60.362 61.111 21.98 12.90 44.36 4.41
4569 4734 2.478335 GAACGATGGGTGGGGCTTCA 62.478 60.000 0.00 0.00 0.00 3.02
4582 4764 0.321653 GGGTGGCTCAACTGAACGAT 60.322 55.000 0.00 0.00 0.00 3.73
4591 4773 2.610859 GGAGGGAGGGTGGCTCAA 60.611 66.667 0.00 0.00 0.00 3.02
4636 4819 5.085920 TCCATCATCAATCCTTTTTGGTGT 58.914 37.500 0.00 0.00 38.57 4.16
4647 4830 3.559069 ACACCCACATCCATCATCAATC 58.441 45.455 0.00 0.00 0.00 2.67
4648 4831 3.675348 ACACCCACATCCATCATCAAT 57.325 42.857 0.00 0.00 0.00 2.57
4649 4832 3.265479 TGTACACCCACATCCATCATCAA 59.735 43.478 0.00 0.00 0.00 2.57
4650 4833 2.843113 TGTACACCCACATCCATCATCA 59.157 45.455 0.00 0.00 0.00 3.07
4651 4834 3.558931 TGTACACCCACATCCATCATC 57.441 47.619 0.00 0.00 0.00 2.92
4652 4835 3.202818 ACATGTACACCCACATCCATCAT 59.797 43.478 0.00 0.00 37.02 2.45
4693 4879 8.204903 AGATGATGATAGAATTAAGCTGGTCT 57.795 34.615 0.00 0.00 0.00 3.85
4716 4935 9.310716 GAGAATCGATATGAATGCATCAATAGA 57.689 33.333 0.00 0.00 42.54 1.98
4791 5010 5.251081 CGCTAACAGAATGAATGAAACTCG 58.749 41.667 0.00 0.00 39.69 4.18
4991 5236 1.068921 ACACGCAAAACCCAATGGC 59.931 52.632 0.00 0.00 33.59 4.40
4999 5244 1.021968 AGGGAACTCACACGCAAAAC 58.978 50.000 0.00 0.00 32.90 2.43
5000 5245 3.487576 AGGGAACTCACACGCAAAA 57.512 47.368 0.00 0.00 32.90 2.44
5012 5257 0.961753 CAAGGCAAAGTGGAGGGAAC 59.038 55.000 0.00 0.00 0.00 3.62
5087 5335 3.752339 CAAAGGGGAAGCTGCGGC 61.752 66.667 10.33 10.33 39.06 6.53
5089 5337 3.752339 GGCAAAGGGGAAGCTGCG 61.752 66.667 0.00 0.00 35.60 5.18
5092 5340 1.228988 CCAAGGCAAAGGGGAAGCT 60.229 57.895 0.00 0.00 0.00 3.74
5098 5346 4.764143 CCCTACCAAGGCAAAGGG 57.236 61.111 7.23 7.23 42.14 3.95
5100 5348 2.030274 CGAAAACCCTACCAAGGCAAAG 60.030 50.000 0.00 0.00 42.14 2.77
5101 5349 1.957877 CGAAAACCCTACCAAGGCAAA 59.042 47.619 0.00 0.00 42.14 3.68
5102 5350 1.611519 CGAAAACCCTACCAAGGCAA 58.388 50.000 0.00 0.00 42.14 4.52
5104 5352 0.608308 AGCGAAAACCCTACCAAGGC 60.608 55.000 0.00 0.00 42.14 4.35
5105 5353 1.810755 GAAGCGAAAACCCTACCAAGG 59.189 52.381 0.00 0.00 43.25 3.61
5164 5448 1.734465 GATGCGTTTGTTCCTCTCCAG 59.266 52.381 0.00 0.00 0.00 3.86
5180 5464 2.087385 GAGGTACCCTTGCATGGATGC 61.087 57.143 19.85 6.35 43.87 3.91
5181 5465 1.492176 AGAGGTACCCTTGCATGGATG 59.508 52.381 19.85 6.76 31.76 3.51
5182 5466 1.771255 GAGAGGTACCCTTGCATGGAT 59.229 52.381 19.85 5.33 31.76 3.41
5183 5467 1.204146 GAGAGGTACCCTTGCATGGA 58.796 55.000 19.85 0.00 31.76 3.41
5184 5468 0.911769 TGAGAGGTACCCTTGCATGG 59.088 55.000 8.74 11.68 31.76 3.66
5252 5536 2.522185 CTGGGCCAGCTATAATTGCAT 58.478 47.619 22.68 0.00 0.00 3.96
5332 5616 2.288013 GCAATGAATCGCGACGAGA 58.712 52.632 12.93 3.14 39.91 4.04
5333 5617 4.860150 GCAATGAATCGCGACGAG 57.140 55.556 12.93 0.00 39.91 4.18
5370 5654 1.596477 GATCTGGTGCGATGAGGCC 60.596 63.158 0.00 0.00 0.00 5.19
5379 5663 0.250640 CCAGGCATAGGATCTGGTGC 60.251 60.000 8.47 7.81 42.17 5.01



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

AutoCloner maintained by Alex Coulton.