Multiple sequence alignment - TraesCS4B01G155300

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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 TraesCS4B01G155300 chr4B 100.000 5632 0 0 1 5632 277316186 277321817 0.000000e+00 10401.0
1 TraesCS4B01G155300 chr4B 95.000 40 2 0 5321 5360 277321466 277321505 4.710000e-06 63.9
2 TraesCS4B01G155300 chr4B 95.000 40 2 0 5281 5320 277321506 277321545 4.710000e-06 63.9
3 TraesCS4B01G155300 chr4B 100.000 28 0 0 5099 5126 277321240 277321267 1.000000e-02 52.8
4 TraesCS4B01G155300 chr4B 100.000 28 0 0 5055 5082 277321284 277321311 1.000000e-02 52.8
5 TraesCS4B01G155300 chr4A 94.767 3115 88 36 1914 4988 321902651 321899572 0.000000e+00 4780.0
6 TraesCS4B01G155300 chr4A 95.845 1853 50 9 1 1832 321904496 321902650 0.000000e+00 2970.0
7 TraesCS4B01G155300 chr4A 89.268 205 15 2 5123 5320 321898459 321898255 3.370000e-62 250.0
8 TraesCS4B01G155300 chr4A 90.566 159 15 0 5321 5479 321898294 321898136 1.590000e-50 211.0
9 TraesCS4B01G155300 chr4D 96.322 1849 44 6 1 1832 292909072 292910913 0.000000e+00 3016.0
10 TraesCS4B01G155300 chr4D 97.789 1628 22 7 1914 3539 292910912 292912527 0.000000e+00 2795.0
11 TraesCS4B01G155300 chr4D 92.050 1610 44 37 3528 5083 292912688 292914267 0.000000e+00 2187.0
12 TraesCS4B01G155300 chr4D 92.727 165 7 3 5472 5632 497017067 497016904 3.390000e-57 233.0
13 TraesCS4B01G155300 chr4D 92.547 161 10 1 5321 5479 292914750 292914910 4.390000e-56 230.0
14 TraesCS4B01G155300 chr4D 87.192 203 12 5 5123 5318 292914592 292914787 9.500000e-53 219.0
15 TraesCS4B01G155300 chr4D 93.056 72 5 0 5123 5194 292914395 292914466 7.720000e-19 106.0
16 TraesCS4B01G155300 chr4D 94.231 52 3 0 5123 5174 292914496 292914547 4.680000e-11 80.5
17 TraesCS4B01G155300 chr5D 94.304 158 5 2 5479 5632 98271933 98272090 7.290000e-59 239.0
18 TraesCS4B01G155300 chr5D 92.727 165 11 1 332 495 399614685 399614521 2.620000e-58 237.0
19 TraesCS4B01G155300 chr5D 93.671 158 6 2 5479 5632 132888460 132888303 3.390000e-57 233.0
20 TraesCS4B01G155300 chr5D 93.711 159 5 3 5478 5632 484573809 484573652 3.390000e-57 233.0
21 TraesCS4B01G155300 chr5D 92.593 162 8 2 5475 5632 393806754 393806915 4.390000e-56 230.0
22 TraesCS4B01G155300 chr2A 93.671 158 6 2 5479 5632 763806975 763807132 3.390000e-57 233.0
23 TraesCS4B01G155300 chr2A 95.604 91 4 0 1831 1921 71560834 71560744 4.550000e-31 147.0
24 TraesCS4B01G155300 chr2A 92.857 98 7 0 1823 1920 81757219 81757316 5.880000e-30 143.0
25 TraesCS4B01G155300 chr7B 93.671 158 5 3 5479 5632 531663793 531663949 1.220000e-56 231.0
26 TraesCS4B01G155300 chr7B 92.121 165 7 4 5472 5632 504668611 504668773 1.580000e-55 228.0
27 TraesCS4B01G155300 chr5B 92.121 165 12 1 332 495 479726998 479726834 1.220000e-56 231.0
28 TraesCS4B01G155300 chr5B 97.701 87 2 0 1830 1916 372649056 372648970 3.510000e-32 150.0
29 TraesCS4B01G155300 chr1D 93.125 160 6 4 5478 5632 243305121 243304962 4.390000e-56 230.0
30 TraesCS4B01G155300 chr3A 91.071 168 11 3 329 495 675873017 675873181 2.040000e-54 224.0
31 TraesCS4B01G155300 chr3A 90.854 164 12 3 333 495 621329019 621328858 3.420000e-52 217.0
32 TraesCS4B01G155300 chr3A 96.629 89 3 0 1830 1918 16809188 16809100 1.260000e-31 148.0
33 TraesCS4B01G155300 chr1A 91.463 164 13 1 332 494 520812189 520812352 2.040000e-54 224.0
34 TraesCS4B01G155300 chr1A 94.792 96 3 2 1831 1926 486046077 486046170 1.260000e-31 148.0
35 TraesCS4B01G155300 chr6A 91.875 160 9 3 331 489 47466951 47466795 2.640000e-53 220.0
36 TraesCS4B01G155300 chr6A 90.476 105 8 1 1811 1915 418954102 418954000 2.740000e-28 137.0
37 TraesCS4B01G155300 chr1B 90.854 164 14 1 332 494 574286834 574286997 9.500000e-53 219.0
38 TraesCS4B01G155300 chr7D 96.739 92 3 0 1830 1921 463109129 463109038 2.720000e-33 154.0
39 TraesCS4B01G155300 chr5A 93.000 100 5 1 1828 1927 499657513 499657416 1.640000e-30 145.0
40 TraesCS4B01G155300 chr3B 89.815 108 10 1 1831 1938 76468602 76468496 2.740000e-28 137.0


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 TraesCS4B01G155300 chr4B 277316186 277321817 5631 False 2126.880000 10401 98.000000 1 5632 5 chr4B.!!$F1 5631
1 TraesCS4B01G155300 chr4A 321898136 321904496 6360 True 2052.750000 4780 92.611500 1 5479 4 chr4A.!!$R1 5478
2 TraesCS4B01G155300 chr4D 292909072 292914910 5838 False 1233.357143 3016 93.312429 1 5479 7 chr4D.!!$F1 5478

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
243 245 0.322816 GCAAGAGGGATGGCTTGTGA 60.323 55.000 0.0 0.0 42.57 3.58 F
453 455 3.920197 TGTCTAGAAATTCCCTTCCCCAA 59.080 43.478 0.0 0.0 0.00 4.12 F
857 876 4.186856 AGACTAAAGAGAGCTTGAGCAC 57.813 45.455 5.7 0.0 45.16 4.40 F
1618 1640 4.269183 TCACCATATCATGTTTGTGACCC 58.731 43.478 0.0 0.0 28.53 4.46 F
3114 3141 0.332293 TCTGCATTGGGGAATGAGCA 59.668 50.000 0.0 0.0 31.98 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1922 1.572415 AGTAATACTCCCTCCGTCCCA 59.428 52.381 0.00 0.0 0.00 4.37 R
1900 1923 2.158490 AGAGTAATACTCCCTCCGTCCC 60.158 54.545 16.12 0.0 46.18 4.46 R
1901 1924 3.226682 AGAGTAATACTCCCTCCGTCC 57.773 52.381 16.12 0.0 46.18 4.79 R
3142 3170 2.089980 CCTGCAAAGGGATTGACTGAG 58.910 52.381 0.00 0.0 41.85 3.35 R
4898 5155 1.089123 TTAATCCAAAGCCTGGGGGT 58.911 50.000 2.71 0.0 46.44 4.95 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
75 76 8.073768 TGCTACTTTTCTTTGAGGAAAATTACG 58.926 33.333 2.14 0.00 42.07 3.18
106 107 8.980143 ATTTTGTTTTACTACGATGGAAATGG 57.020 30.769 0.00 0.00 0.00 3.16
147 149 3.559384 GGCTTCTTACCACCTTGTAGCTT 60.559 47.826 0.00 0.00 0.00 3.74
164 166 5.705441 TGTAGCTTAAACAGATTGGTTCCAG 59.295 40.000 0.00 0.00 0.00 3.86
182 184 6.250819 GTTCCAGTAATGATGATTGTTGTCG 58.749 40.000 0.00 0.00 0.00 4.35
242 244 0.323178 AGCAAGAGGGATGGCTTGTG 60.323 55.000 0.00 0.00 42.57 3.33
243 245 0.322816 GCAAGAGGGATGGCTTGTGA 60.323 55.000 0.00 0.00 42.57 3.58
266 268 5.917541 TTCACAGAGTAATTGAACGGTTC 57.082 39.130 13.86 13.86 0.00 3.62
285 287 4.870991 GGTTCTATCTGTGTAAGGTTGAGC 59.129 45.833 0.00 0.00 0.00 4.26
286 288 4.371855 TCTATCTGTGTAAGGTTGAGCG 57.628 45.455 0.00 0.00 0.00 5.03
453 455 3.920197 TGTCTAGAAATTCCCTTCCCCAA 59.080 43.478 0.00 0.00 0.00 4.12
682 701 4.881273 TGGTGCTATAAGTACAATTGCTGG 59.119 41.667 5.05 0.00 32.12 4.85
857 876 4.186856 AGACTAAAGAGAGCTTGAGCAC 57.813 45.455 5.70 0.00 45.16 4.40
884 903 7.352739 TCGAAGAAGCACAAAAGAAGATTTAC 58.647 34.615 0.00 0.00 0.00 2.01
949 968 8.423906 AGAAGAAAGCCGGAATTATAGATAGA 57.576 34.615 5.05 0.00 0.00 1.98
950 969 8.871125 AGAAGAAAGCCGGAATTATAGATAGAA 58.129 33.333 5.05 0.00 0.00 2.10
951 970 9.145865 GAAGAAAGCCGGAATTATAGATAGAAG 57.854 37.037 5.05 0.00 0.00 2.85
1156 1175 5.045578 AGTGCAGGGATATCTGTAACTGTTT 60.046 40.000 2.05 0.00 37.12 2.83
1338 1357 7.311092 TCAACTATCTACCCTGTTCTTTTCA 57.689 36.000 0.00 0.00 0.00 2.69
1343 1362 5.367945 TCTACCCTGTTCTTTTCAACTGT 57.632 39.130 0.00 0.00 0.00 3.55
1618 1640 4.269183 TCACCATATCATGTTTGTGACCC 58.731 43.478 0.00 0.00 28.53 4.46
1834 1857 9.982651 TGTGCTTATTGAGGATAAGTTATACTC 57.017 33.333 23.38 23.38 44.78 2.59
1835 1858 9.425577 GTGCTTATTGAGGATAAGTTATACTCC 57.574 37.037 25.92 13.66 44.07 3.85
1836 1859 8.594550 TGCTTATTGAGGATAAGTTATACTCCC 58.405 37.037 25.92 10.54 44.07 4.30
1837 1860 8.817876 GCTTATTGAGGATAAGTTATACTCCCT 58.182 37.037 25.92 17.54 44.07 4.20
1840 1863 7.841282 TTGAGGATAAGTTATACTCCCTCTG 57.159 40.000 25.92 0.00 44.07 3.35
1841 1864 6.923670 TGAGGATAAGTTATACTCCCTCTGT 58.076 40.000 25.92 0.00 44.07 3.41
1842 1865 7.005296 TGAGGATAAGTTATACTCCCTCTGTC 58.995 42.308 25.92 6.30 44.07 3.51
1843 1866 6.316513 AGGATAAGTTATACTCCCTCTGTCC 58.683 44.000 1.36 0.00 0.00 4.02
1844 1867 5.481122 GGATAAGTTATACTCCCTCTGTCCC 59.519 48.000 0.00 0.00 0.00 4.46
1845 1868 4.348020 AAGTTATACTCCCTCTGTCCCA 57.652 45.455 0.00 0.00 0.00 4.37
1846 1869 4.348020 AGTTATACTCCCTCTGTCCCAA 57.652 45.455 0.00 0.00 0.00 4.12
1847 1870 4.695606 AGTTATACTCCCTCTGTCCCAAA 58.304 43.478 0.00 0.00 0.00 3.28
1848 1871 5.098663 AGTTATACTCCCTCTGTCCCAAAA 58.901 41.667 0.00 0.00 0.00 2.44
1849 1872 5.731678 AGTTATACTCCCTCTGTCCCAAAAT 59.268 40.000 0.00 0.00 0.00 1.82
1850 1873 6.906901 AGTTATACTCCCTCTGTCCCAAAATA 59.093 38.462 0.00 0.00 0.00 1.40
1851 1874 7.572861 AGTTATACTCCCTCTGTCCCAAAATAT 59.427 37.037 0.00 0.00 0.00 1.28
1852 1875 8.877195 GTTATACTCCCTCTGTCCCAAAATATA 58.123 37.037 0.00 0.00 0.00 0.86
1853 1876 7.947782 ATACTCCCTCTGTCCCAAAATATAA 57.052 36.000 0.00 0.00 0.00 0.98
1854 1877 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
1855 1878 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
1856 1879 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
1857 1880 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
1858 1881 6.216662 TCCCTCTGTCCCAAAATATAAGAACA 59.783 38.462 0.00 0.00 0.00 3.18
1859 1882 7.062957 CCCTCTGTCCCAAAATATAAGAACAT 58.937 38.462 0.00 0.00 0.00 2.71
1860 1883 7.561356 CCCTCTGTCCCAAAATATAAGAACATT 59.439 37.037 0.00 0.00 0.00 2.71
1861 1884 8.971073 CCTCTGTCCCAAAATATAAGAACATTT 58.029 33.333 0.00 0.00 0.00 2.32
1889 1912 5.511234 ACTACAGTAGTGTCAAGAACGTT 57.489 39.130 12.75 0.00 37.69 3.99
1890 1913 5.517904 ACTACAGTAGTGTCAAGAACGTTC 58.482 41.667 20.71 20.71 37.69 3.95
1891 1914 4.650754 ACAGTAGTGTCAAGAACGTTCT 57.349 40.909 24.93 24.93 32.59 3.01
1892 1915 6.140303 TACAGTAGTGTCAAGAACGTTCTT 57.860 37.500 32.60 32.60 41.92 2.52
1893 1916 6.140303 ACAGTAGTGTCAAGAACGTTCTTA 57.860 37.500 35.97 22.29 45.23 2.10
1894 1917 6.746120 ACAGTAGTGTCAAGAACGTTCTTAT 58.254 36.000 35.97 23.02 45.23 1.73
1895 1918 7.879070 ACAGTAGTGTCAAGAACGTTCTTATA 58.121 34.615 35.97 25.93 45.23 0.98
1896 1919 8.521176 ACAGTAGTGTCAAGAACGTTCTTATAT 58.479 33.333 35.97 23.58 45.23 0.86
1897 1920 9.355215 CAGTAGTGTCAAGAACGTTCTTATATT 57.645 33.333 35.97 24.14 45.23 1.28
1901 1924 9.314321 AGTGTCAAGAACGTTCTTATATTATGG 57.686 33.333 35.97 23.38 45.23 2.74
1902 1925 8.548721 GTGTCAAGAACGTTCTTATATTATGGG 58.451 37.037 35.97 22.77 45.23 4.00
1903 1926 8.479689 TGTCAAGAACGTTCTTATATTATGGGA 58.520 33.333 35.97 24.34 45.23 4.37
1904 1927 8.762426 GTCAAGAACGTTCTTATATTATGGGAC 58.238 37.037 35.97 29.18 45.23 4.46
1905 1928 7.650504 TCAAGAACGTTCTTATATTATGGGACG 59.349 37.037 35.97 21.56 45.23 4.79
1906 1929 6.453092 AGAACGTTCTTATATTATGGGACGG 58.547 40.000 24.93 1.76 32.55 4.79
1907 1930 6.266103 AGAACGTTCTTATATTATGGGACGGA 59.734 38.462 24.93 0.00 32.55 4.69
1908 1931 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
1909 1932 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
1910 1933 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
1911 1934 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
1912 1935 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1913 1936 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1914 1937 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2034 2061 7.765307 TCAATGCCAACAGATCTTTCTTATTC 58.235 34.615 0.00 0.00 0.00 1.75
2253 2280 7.028361 CGGTTGTGACTTTTAACCTGTTTTTA 58.972 34.615 0.00 0.00 41.26 1.52
2254 2281 7.541437 CGGTTGTGACTTTTAACCTGTTTTTAA 59.459 33.333 0.00 0.00 41.26 1.52
2407 2434 5.391312 ACAATTTGAGTTGGTATTGCCTC 57.609 39.130 2.79 0.00 38.35 4.70
2429 2456 6.712547 CCTCTCTGACTTTGGAGTTACATTTT 59.287 38.462 0.00 0.00 35.88 1.82
2430 2457 7.095017 CCTCTCTGACTTTGGAGTTACATTTTC 60.095 40.741 0.00 0.00 35.88 2.29
2431 2458 7.279615 TCTCTGACTTTGGAGTTACATTTTCA 58.720 34.615 0.00 0.00 35.88 2.69
3054 3081 5.745514 CAATCTCTTGAATATTGGTCGCAG 58.254 41.667 0.00 0.00 34.04 5.18
3114 3141 0.332293 TCTGCATTGGGGAATGAGCA 59.668 50.000 0.00 0.00 31.98 4.26
3142 3170 2.210116 TCAAGTTTGGCGTTCTCAGTC 58.790 47.619 0.00 0.00 0.00 3.51
3183 3211 3.767131 GGTACCCATATTTGGCTGTTGTT 59.233 43.478 0.00 0.00 42.15 2.83
3513 3543 2.935201 CAGCAAGTCACCTCTATGCTTC 59.065 50.000 0.00 0.00 44.43 3.86
3823 4063 5.426504 TGGTTCATGTGTTGCTTTGAATTT 58.573 33.333 0.00 0.00 0.00 1.82
3865 4105 7.441157 AGTGTATATACAATGCGCTTGTTGTAT 59.559 33.333 30.14 30.14 45.98 2.29
3893 4133 8.623030 AGTGATTTTATTTGCTTGCACATTTTT 58.377 25.926 0.00 0.00 0.00 1.94
3925 4165 3.118905 TGTGTTCACAACCGATGATGA 57.881 42.857 2.99 0.00 0.00 2.92
3951 4191 2.492088 ACTGCAGACAACGATGCTACTA 59.508 45.455 23.35 0.00 42.98 1.82
4258 4501 3.064207 TCGTGATGTTGTGTTAGGAAGC 58.936 45.455 0.00 0.00 0.00 3.86
4279 4522 6.237313 AGCGGTGAAATTGTAAGTTTCTAC 57.763 37.500 0.00 0.00 36.71 2.59
4296 4539 7.793036 AGTTTCTACTAGTGGTCAGTTTTCTT 58.207 34.615 5.39 0.00 31.21 2.52
4298 4541 8.890718 GTTTCTACTAGTGGTCAGTTTTCTTTT 58.109 33.333 5.39 0.00 0.00 2.27
4326 4569 7.331026 TCCTTTATCATTCTCTCACATTCGTT 58.669 34.615 0.00 0.00 0.00 3.85
4438 4681 6.154706 ACGAAGATAAATAAGACACTCCACCT 59.845 38.462 0.00 0.00 0.00 4.00
4454 4697 7.785028 ACACTCCACCTAATATCTGAGAATGTA 59.215 37.037 0.00 0.00 0.00 2.29
4725 4968 2.689983 CACACTGAGGCAAAAGAAAGGT 59.310 45.455 0.00 0.00 0.00 3.50
4746 4990 5.189145 AGGTGATTCCGGTGACTAATAGTTT 59.811 40.000 0.00 0.00 41.99 2.66
4816 5061 0.398318 GGCTCAGTTTCAGGAGGTGT 59.602 55.000 0.00 0.00 0.00 4.16
4823 5068 3.247648 CAGTTTCAGGAGGTGTTGTTACG 59.752 47.826 0.00 0.00 0.00 3.18
4842 5087 3.939066 ACGTGGGTTTTTCTATGAGAGG 58.061 45.455 0.00 0.00 0.00 3.69
4898 5155 6.704493 GCTCCGATAATTACTGATGTAACCAA 59.296 38.462 0.00 0.00 40.91 3.67
4903 5160 3.724732 TTACTGATGTAACCAACCCCC 57.275 47.619 0.00 0.00 34.10 5.40
4906 5163 0.701731 TGATGTAACCAACCCCCAGG 59.298 55.000 0.00 0.00 40.04 4.45
4930 5189 6.374333 GGCTTTGGATTAACATACACTGAAGA 59.626 38.462 0.00 0.00 0.00 2.87
5007 6169 4.739046 AGTTTTGAAGTGATTCAGAGCG 57.261 40.909 0.00 0.00 31.87 5.03
5032 6194 2.662700 CTAATCGTAGCAAGGCGTAGG 58.337 52.381 0.00 0.00 0.00 3.18
5052 6214 2.354805 GGCGTAAACTGTCCTGATCCTT 60.355 50.000 0.00 0.00 0.00 3.36
5101 6518 7.761981 AATGCCTAGGATATCCAACATATCT 57.238 36.000 23.81 2.86 38.89 1.98
5104 6521 8.679344 TGCCTAGGATATCCAACATATCTTAA 57.321 34.615 23.81 0.00 38.89 1.85
5105 6522 9.111519 TGCCTAGGATATCCAACATATCTTAAA 57.888 33.333 23.81 0.00 38.89 1.52
5106 6523 9.959721 GCCTAGGATATCCAACATATCTTAAAA 57.040 33.333 23.81 0.00 38.89 1.52
5174 6627 7.303182 TCCAACATATCCTAGGTAGAACATG 57.697 40.000 9.08 6.99 0.00 3.21
5181 6634 4.037222 TCCTAGGTAGAACATGCCATCAA 58.963 43.478 9.08 0.00 35.79 2.57
5234 6694 3.033909 TCATGACCTGATCGTTCCATCT 58.966 45.455 0.00 0.00 0.00 2.90
5264 6724 4.240888 ACATGTGTGAACTTGAGATCGAG 58.759 43.478 0.00 0.00 0.00 4.04
5305 6765 3.762407 TGGCTTGTGTAGTGCTTTCTA 57.238 42.857 0.00 0.00 0.00 2.10
5306 6766 3.399330 TGGCTTGTGTAGTGCTTTCTAC 58.601 45.455 7.13 7.13 40.22 2.59
5307 6767 2.742589 GGCTTGTGTAGTGCTTTCTACC 59.257 50.000 10.16 4.85 39.39 3.18
5308 6768 3.557264 GGCTTGTGTAGTGCTTTCTACCT 60.557 47.826 10.16 0.00 39.39 3.08
5309 6769 4.322499 GGCTTGTGTAGTGCTTTCTACCTA 60.322 45.833 10.16 0.00 39.39 3.08
5310 6770 4.626172 GCTTGTGTAGTGCTTTCTACCTAC 59.374 45.833 10.16 0.00 39.39 3.18
5311 6771 5.779922 CTTGTGTAGTGCTTTCTACCTACA 58.220 41.667 10.16 0.00 39.39 2.74
5312 6772 5.995565 TGTGTAGTGCTTTCTACCTACAT 57.004 39.130 0.00 0.00 39.39 2.29
5313 6773 7.470935 TTGTGTAGTGCTTTCTACCTACATA 57.529 36.000 0.00 0.00 39.39 2.29
5314 6774 7.655521 TGTGTAGTGCTTTCTACCTACATAT 57.344 36.000 0.00 0.00 39.39 1.78
5315 6775 7.489160 TGTGTAGTGCTTTCTACCTACATATG 58.511 38.462 0.00 0.00 39.39 1.78
5316 6776 7.123697 TGTGTAGTGCTTTCTACCTACATATGT 59.876 37.037 13.93 13.93 39.39 2.29
5317 6777 7.980099 GTGTAGTGCTTTCTACCTACATATGTT 59.020 37.037 14.77 0.00 39.39 2.71
5318 6778 9.192642 TGTAGTGCTTTCTACCTACATATGTTA 57.807 33.333 14.77 0.00 39.39 2.41
5319 6779 9.460906 GTAGTGCTTTCTACCTACATATGTTAC 57.539 37.037 14.77 1.51 35.57 2.50
5320 6780 7.498443 AGTGCTTTCTACCTACATATGTTACC 58.502 38.462 14.77 0.00 0.00 2.85
5321 6781 7.125204 AGTGCTTTCTACCTACATATGTTACCA 59.875 37.037 14.77 0.00 0.00 3.25
5322 6782 7.931948 GTGCTTTCTACCTACATATGTTACCAT 59.068 37.037 14.77 0.00 34.97 3.55
5323 6783 9.150028 TGCTTTCTACCTACATATGTTACCATA 57.850 33.333 14.77 0.00 37.92 2.74
5328 6788 8.537016 TCTACCTACATATGTTACCATATTGGC 58.463 37.037 14.77 0.00 42.67 4.52
5329 6789 7.329746 ACCTACATATGTTACCATATTGGCT 57.670 36.000 14.77 0.00 42.67 4.75
5330 6790 7.755618 ACCTACATATGTTACCATATTGGCTT 58.244 34.615 14.77 0.00 42.67 4.35
5331 6791 7.665559 ACCTACATATGTTACCATATTGGCTTG 59.334 37.037 14.77 0.00 42.67 4.01
5332 6792 7.665559 CCTACATATGTTACCATATTGGCTTGT 59.334 37.037 14.77 0.00 42.67 3.16
5333 6793 7.275888 ACATATGTTACCATATTGGCTTGTG 57.724 36.000 1.41 0.00 42.67 3.33
5334 6794 6.833416 ACATATGTTACCATATTGGCTTGTGT 59.167 34.615 1.41 0.00 42.67 3.72
5335 6795 7.996066 ACATATGTTACCATATTGGCTTGTGTA 59.004 33.333 1.41 0.00 42.67 2.90
5336 6796 6.942532 ATGTTACCATATTGGCTTGTGTAG 57.057 37.500 0.00 0.00 42.67 2.74
5337 6797 5.811190 TGTTACCATATTGGCTTGTGTAGT 58.189 37.500 0.00 0.00 42.67 2.73
5338 6798 5.645929 TGTTACCATATTGGCTTGTGTAGTG 59.354 40.000 0.00 0.00 42.67 2.74
5339 6799 3.016736 ACCATATTGGCTTGTGTAGTGC 58.983 45.455 0.00 0.00 42.67 4.40
5340 6800 3.282021 CCATATTGGCTTGTGTAGTGCT 58.718 45.455 0.00 0.00 0.00 4.40
5341 6801 3.696051 CCATATTGGCTTGTGTAGTGCTT 59.304 43.478 0.00 0.00 0.00 3.91
5342 6802 4.158394 CCATATTGGCTTGTGTAGTGCTTT 59.842 41.667 0.00 0.00 0.00 3.51
5343 6803 3.923017 ATTGGCTTGTGTAGTGCTTTC 57.077 42.857 0.00 0.00 0.00 2.62
5344 6804 2.638480 TGGCTTGTGTAGTGCTTTCT 57.362 45.000 0.00 0.00 0.00 2.52
5390 6850 0.321671 TTGGCACTCTAGCAGTCACC 59.678 55.000 0.00 0.00 35.83 4.02
5391 6851 1.153745 GGCACTCTAGCAGTCACCG 60.154 63.158 0.00 0.00 35.83 4.94
5467 6929 2.658285 CTCACAAGAACACAAGCATGC 58.342 47.619 10.51 10.51 0.00 4.06
5488 6950 2.149973 ATGGAATGAAGGGCCAGTTC 57.850 50.000 6.18 7.69 34.74 3.01
5489 6951 1.075601 TGGAATGAAGGGCCAGTTCT 58.924 50.000 15.94 0.00 0.00 3.01
5490 6952 1.428912 TGGAATGAAGGGCCAGTTCTT 59.571 47.619 15.94 5.28 0.00 2.52
5491 6953 2.158325 TGGAATGAAGGGCCAGTTCTTT 60.158 45.455 15.94 15.20 0.00 2.52
5492 6954 2.899900 GGAATGAAGGGCCAGTTCTTTT 59.100 45.455 15.94 10.55 0.00 2.27
5493 6955 3.306294 GGAATGAAGGGCCAGTTCTTTTG 60.306 47.826 15.94 0.00 0.00 2.44
5494 6956 1.703411 TGAAGGGCCAGTTCTTTTGG 58.297 50.000 15.94 0.00 38.78 3.28
5495 6957 1.063266 TGAAGGGCCAGTTCTTTTGGT 60.063 47.619 15.94 0.00 38.02 3.67
5496 6958 1.341209 GAAGGGCCAGTTCTTTTGGTG 59.659 52.381 6.18 0.00 38.02 4.17
5497 6959 0.469892 AGGGCCAGTTCTTTTGGTGG 60.470 55.000 6.18 0.00 38.02 4.61
5501 6963 2.800881 CCAGTTCTTTTGGTGGCTTC 57.199 50.000 0.00 0.00 0.00 3.86
5502 6964 2.310538 CCAGTTCTTTTGGTGGCTTCT 58.689 47.619 0.00 0.00 0.00 2.85
5503 6965 3.486383 CCAGTTCTTTTGGTGGCTTCTA 58.514 45.455 0.00 0.00 0.00 2.10
5504 6966 3.503748 CCAGTTCTTTTGGTGGCTTCTAG 59.496 47.826 0.00 0.00 0.00 2.43
5505 6967 4.389374 CAGTTCTTTTGGTGGCTTCTAGA 58.611 43.478 0.00 0.00 0.00 2.43
5506 6968 4.821805 CAGTTCTTTTGGTGGCTTCTAGAA 59.178 41.667 4.81 4.81 0.00 2.10
5507 6969 5.474876 CAGTTCTTTTGGTGGCTTCTAGAAT 59.525 40.000 5.44 0.00 0.00 2.40
5508 6970 6.655003 CAGTTCTTTTGGTGGCTTCTAGAATA 59.345 38.462 5.44 0.00 0.00 1.75
5509 6971 7.174946 CAGTTCTTTTGGTGGCTTCTAGAATAA 59.825 37.037 5.44 0.00 0.00 1.40
5510 6972 7.391833 AGTTCTTTTGGTGGCTTCTAGAATAAG 59.608 37.037 5.44 0.00 0.00 1.73
5511 6973 5.648092 TCTTTTGGTGGCTTCTAGAATAAGC 59.352 40.000 5.44 5.98 46.90 3.09
5512 6974 4.844349 TTGGTGGCTTCTAGAATAAGCT 57.156 40.909 13.28 0.00 46.81 3.74
5513 6975 4.142609 TGGTGGCTTCTAGAATAAGCTG 57.857 45.455 13.28 0.00 46.81 4.24
5514 6976 3.774766 TGGTGGCTTCTAGAATAAGCTGA 59.225 43.478 13.28 0.44 46.81 4.26
5515 6977 4.225042 TGGTGGCTTCTAGAATAAGCTGAA 59.775 41.667 13.28 0.00 46.81 3.02
5516 6978 5.104360 TGGTGGCTTCTAGAATAAGCTGAAT 60.104 40.000 13.28 0.00 46.81 2.57
5517 6979 6.099701 TGGTGGCTTCTAGAATAAGCTGAATA 59.900 38.462 13.28 0.00 46.81 1.75
5518 6980 6.992715 GGTGGCTTCTAGAATAAGCTGAATAA 59.007 38.462 13.28 0.00 46.81 1.40
5519 6981 7.172361 GGTGGCTTCTAGAATAAGCTGAATAAG 59.828 40.741 13.28 0.00 46.81 1.73
5530 6992 2.262423 CTGAATAAGCTGCCCCCTAC 57.738 55.000 0.00 0.00 0.00 3.18
5531 6993 0.843984 TGAATAAGCTGCCCCCTACC 59.156 55.000 0.00 0.00 0.00 3.18
5532 6994 0.110678 GAATAAGCTGCCCCCTACCC 59.889 60.000 0.00 0.00 0.00 3.69
5533 6995 0.328548 AATAAGCTGCCCCCTACCCT 60.329 55.000 0.00 0.00 0.00 4.34
5534 6996 0.328548 ATAAGCTGCCCCCTACCCTT 60.329 55.000 0.00 0.00 0.00 3.95
5535 6997 0.344080 TAAGCTGCCCCCTACCCTTA 59.656 55.000 0.00 0.00 0.00 2.69
5536 6998 0.328548 AAGCTGCCCCCTACCCTTAT 60.329 55.000 0.00 0.00 0.00 1.73
5537 6999 0.328548 AGCTGCCCCCTACCCTTATT 60.329 55.000 0.00 0.00 0.00 1.40
5538 7000 0.110678 GCTGCCCCCTACCCTTATTC 59.889 60.000 0.00 0.00 0.00 1.75
5539 7001 1.821088 CTGCCCCCTACCCTTATTCT 58.179 55.000 0.00 0.00 0.00 2.40
5540 7002 2.986050 CTGCCCCCTACCCTTATTCTA 58.014 52.381 0.00 0.00 0.00 2.10
5541 7003 2.907042 CTGCCCCCTACCCTTATTCTAG 59.093 54.545 0.00 0.00 0.00 2.43
5542 7004 2.525310 TGCCCCCTACCCTTATTCTAGA 59.475 50.000 0.00 0.00 0.00 2.43
5543 7005 3.050876 TGCCCCCTACCCTTATTCTAGAA 60.051 47.826 7.82 7.82 0.00 2.10
5544 7006 3.583526 GCCCCCTACCCTTATTCTAGAAG 59.416 52.174 11.53 0.00 0.00 2.85
5545 7007 3.583526 CCCCCTACCCTTATTCTAGAAGC 59.416 52.174 11.53 0.00 0.00 3.86
5546 7008 3.583526 CCCCTACCCTTATTCTAGAAGCC 59.416 52.174 11.53 0.00 0.00 4.35
5547 7009 3.583526 CCCTACCCTTATTCTAGAAGCCC 59.416 52.174 11.53 0.00 0.00 5.19
5548 7010 4.232091 CCTACCCTTATTCTAGAAGCCCA 58.768 47.826 11.53 0.00 0.00 5.36
5549 7011 4.658901 CCTACCCTTATTCTAGAAGCCCAA 59.341 45.833 11.53 2.03 0.00 4.12
5550 7012 4.505324 ACCCTTATTCTAGAAGCCCAAC 57.495 45.455 11.53 0.00 0.00 3.77
5551 7013 3.202373 ACCCTTATTCTAGAAGCCCAACC 59.798 47.826 11.53 0.00 0.00 3.77
5552 7014 3.202151 CCCTTATTCTAGAAGCCCAACCA 59.798 47.826 11.53 0.00 0.00 3.67
5553 7015 4.325030 CCCTTATTCTAGAAGCCCAACCAA 60.325 45.833 11.53 0.00 0.00 3.67
5554 7016 5.261216 CCTTATTCTAGAAGCCCAACCAAA 58.739 41.667 11.53 0.00 0.00 3.28
5555 7017 5.714806 CCTTATTCTAGAAGCCCAACCAAAA 59.285 40.000 11.53 0.00 0.00 2.44
5556 7018 6.381133 CCTTATTCTAGAAGCCCAACCAAAAT 59.619 38.462 11.53 0.00 0.00 1.82
5557 7019 7.093333 CCTTATTCTAGAAGCCCAACCAAAATT 60.093 37.037 11.53 0.00 0.00 1.82
5558 7020 8.887264 TTATTCTAGAAGCCCAACCAAAATTA 57.113 30.769 11.53 0.00 0.00 1.40
5559 7021 7.978099 ATTCTAGAAGCCCAACCAAAATTAT 57.022 32.000 11.53 0.00 0.00 1.28
5560 7022 7.790782 TTCTAGAAGCCCAACCAAAATTATT 57.209 32.000 0.00 0.00 0.00 1.40
5561 7023 7.790782 TCTAGAAGCCCAACCAAAATTATTT 57.209 32.000 0.00 0.00 0.00 1.40
5562 7024 8.201242 TCTAGAAGCCCAACCAAAATTATTTT 57.799 30.769 0.00 0.00 0.00 1.82
5563 7025 8.655901 TCTAGAAGCCCAACCAAAATTATTTTT 58.344 29.630 0.00 0.00 35.41 1.94
5588 7050 9.924650 TTTTAGAAGCCTAGTAGTTAAGACTTG 57.075 33.333 0.00 0.00 37.33 3.16
5589 7051 8.874744 TTAGAAGCCTAGTAGTTAAGACTTGA 57.125 34.615 0.00 0.00 37.33 3.02
5590 7052 7.964666 AGAAGCCTAGTAGTTAAGACTTGAT 57.035 36.000 0.00 0.00 37.33 2.57
5591 7053 8.368962 AGAAGCCTAGTAGTTAAGACTTGATT 57.631 34.615 0.00 0.00 37.33 2.57
5592 7054 9.476928 AGAAGCCTAGTAGTTAAGACTTGATTA 57.523 33.333 0.00 0.00 37.33 1.75
5593 7055 9.738832 GAAGCCTAGTAGTTAAGACTTGATTAG 57.261 37.037 0.00 0.00 37.33 1.73
5594 7056 8.826293 AGCCTAGTAGTTAAGACTTGATTAGT 57.174 34.615 0.00 0.00 40.71 2.24
5595 7057 9.917887 AGCCTAGTAGTTAAGACTTGATTAGTA 57.082 33.333 0.00 0.00 37.17 1.82
5623 7085 9.173021 ACTTCTAAAAAGAAAATTTTGGTTGGG 57.827 29.630 8.47 0.00 33.84 4.12
5624 7086 7.561021 TCTAAAAAGAAAATTTTGGTTGGGC 57.439 32.000 8.47 0.00 33.84 5.36
5625 7087 7.342581 TCTAAAAAGAAAATTTTGGTTGGGCT 58.657 30.769 8.47 0.00 33.84 5.19
5626 7088 6.849085 AAAAAGAAAATTTTGGTTGGGCTT 57.151 29.167 8.47 0.70 31.55 4.35
5627 7089 6.449635 AAAAGAAAATTTTGGTTGGGCTTC 57.550 33.333 8.47 0.00 0.00 3.86
5628 7090 5.372343 AAGAAAATTTTGGTTGGGCTTCT 57.628 34.783 8.47 0.00 0.00 2.85
5629 7091 6.493189 AAGAAAATTTTGGTTGGGCTTCTA 57.507 33.333 8.47 0.00 0.00 2.10
5630 7092 6.101650 AGAAAATTTTGGTTGGGCTTCTAG 57.898 37.500 8.47 0.00 0.00 2.43
5631 7093 5.838521 AGAAAATTTTGGTTGGGCTTCTAGA 59.161 36.000 8.47 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 8.911247 AGAAGCCAAAATCGTCAATAATAAAC 57.089 30.769 0.00 0.00 0.00 2.01
123 125 3.809324 GCTACAAGGTGGTAAGAAGCCAA 60.809 47.826 0.00 0.00 37.81 4.52
147 149 8.106462 TCATCATTACTGGAACCAATCTGTTTA 58.894 33.333 0.00 0.00 0.00 2.01
214 216 4.785301 CCATCCCTCTTGCTAAATCTTCA 58.215 43.478 0.00 0.00 0.00 3.02
242 244 6.369065 AGAACCGTTCAATTACTCTGTGAATC 59.631 38.462 13.69 0.00 34.04 2.52
243 245 6.231211 AGAACCGTTCAATTACTCTGTGAAT 58.769 36.000 13.69 0.00 34.04 2.57
266 268 3.119101 ACCGCTCAACCTTACACAGATAG 60.119 47.826 0.00 0.00 0.00 2.08
285 287 6.809689 GGTAACAAATAATCCAAGGAAAACCG 59.190 38.462 0.00 0.00 0.00 4.44
286 288 7.903145 AGGTAACAAATAATCCAAGGAAAACC 58.097 34.615 0.00 0.00 41.41 3.27
559 561 0.928505 ATGCCCATCTCCATTGTGGA 59.071 50.000 0.00 0.00 45.98 4.02
857 876 5.348418 TCTTCTTTTGTGCTTCTTCGATG 57.652 39.130 0.00 0.00 0.00 3.84
884 903 2.827921 CAGGATTCAAAAACTGAGGGGG 59.172 50.000 0.00 0.00 34.81 5.40
949 968 1.131638 TGCTTGTGGTCTGTCCTCTT 58.868 50.000 0.00 0.00 37.07 2.85
950 969 1.071385 CTTGCTTGTGGTCTGTCCTCT 59.929 52.381 0.00 0.00 37.07 3.69
951 970 1.202698 ACTTGCTTGTGGTCTGTCCTC 60.203 52.381 0.00 0.00 37.07 3.71
1156 1175 4.843728 AGAAACAAGGACAGAACAAGTGA 58.156 39.130 0.00 0.00 0.00 3.41
1338 1357 5.723295 ACTGAAATTGAAAGTGCAACAGTT 58.277 33.333 0.00 0.00 41.43 3.16
1343 1362 5.964758 AGACAACTGAAATTGAAAGTGCAA 58.035 33.333 0.00 0.00 33.57 4.08
1729 1752 7.501559 ACTTACTAGAGTACAAACACTCACAGA 59.498 37.037 0.00 0.00 46.15 3.41
1832 1855 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
1833 1856 6.216662 TGTTCTTATATTTTGGGACAGAGGGA 59.783 38.462 0.00 0.00 42.39 4.20
1834 1857 6.423182 TGTTCTTATATTTTGGGACAGAGGG 58.577 40.000 0.00 0.00 42.39 4.30
1835 1858 8.525290 AATGTTCTTATATTTTGGGACAGAGG 57.475 34.615 0.00 0.00 42.39 3.69
1867 1890 5.298777 AGAACGTTCTTGACACTACTGTAGT 59.701 40.000 24.93 14.53 34.80 2.73
1868 1891 5.759963 AGAACGTTCTTGACACTACTGTAG 58.240 41.667 24.93 13.13 32.55 2.74
1869 1892 5.762825 AGAACGTTCTTGACACTACTGTA 57.237 39.130 24.93 0.00 32.55 2.74
1870 1893 4.650754 AGAACGTTCTTGACACTACTGT 57.349 40.909 24.93 0.00 32.55 3.55
1871 1894 8.912787 ATATAAGAACGTTCTTGACACTACTG 57.087 34.615 40.39 0.00 46.34 2.74
1875 1898 9.314321 CCATAATATAAGAACGTTCTTGACACT 57.686 33.333 40.39 26.48 46.34 3.55
1876 1899 8.548721 CCCATAATATAAGAACGTTCTTGACAC 58.451 37.037 40.39 12.65 46.34 3.67
1877 1900 8.479689 TCCCATAATATAAGAACGTTCTTGACA 58.520 33.333 40.39 28.56 46.34 3.58
1878 1901 8.762426 GTCCCATAATATAAGAACGTTCTTGAC 58.238 37.037 40.39 31.50 46.34 3.18
1879 1902 7.650504 CGTCCCATAATATAAGAACGTTCTTGA 59.349 37.037 40.39 31.02 46.34 3.02
1880 1903 7.095774 CCGTCCCATAATATAAGAACGTTCTTG 60.096 40.741 40.39 27.49 46.34 3.02
1882 1905 6.266103 TCCGTCCCATAATATAAGAACGTTCT 59.734 38.462 24.93 24.93 39.74 3.01
1883 1906 6.449698 TCCGTCCCATAATATAAGAACGTTC 58.550 40.000 20.71 20.71 0.00 3.95
1884 1907 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
1885 1908 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
1886 1909 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
1887 1910 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
1888 1911 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
1889 1912 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1890 1913 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1891 1914 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1892 1915 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1893 1916 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1894 1917 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
1895 1918 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1896 1919 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
1897 1920 3.400322 AGTAATACTCCCTCCGTCCCATA 59.600 47.826 0.00 0.00 0.00 2.74
1898 1921 2.179424 AGTAATACTCCCTCCGTCCCAT 59.821 50.000 0.00 0.00 0.00 4.00
1899 1922 1.572415 AGTAATACTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
1900 1923 2.158490 AGAGTAATACTCCCTCCGTCCC 60.158 54.545 16.12 0.00 46.18 4.46
1901 1924 3.226682 AGAGTAATACTCCCTCCGTCC 57.773 52.381 16.12 0.00 46.18 4.79
1902 1925 5.827267 ACTAAAGAGTAATACTCCCTCCGTC 59.173 44.000 16.12 0.00 46.18 4.79
1903 1926 5.593502 CACTAAAGAGTAATACTCCCTCCGT 59.406 44.000 16.12 5.68 46.18 4.69
1904 1927 5.507650 GCACTAAAGAGTAATACTCCCTCCG 60.508 48.000 16.12 5.12 46.18 4.63
1905 1928 5.599242 AGCACTAAAGAGTAATACTCCCTCC 59.401 44.000 16.12 0.53 46.18 4.30
1906 1929 6.718522 AGCACTAAAGAGTAATACTCCCTC 57.281 41.667 16.12 0.00 46.18 4.30
1907 1930 7.497773 AAAGCACTAAAGAGTAATACTCCCT 57.502 36.000 16.12 6.90 46.18 4.20
1908 1931 7.606839 ACAAAAGCACTAAAGAGTAATACTCCC 59.393 37.037 16.12 0.00 46.18 4.30
1909 1932 8.549338 ACAAAAGCACTAAAGAGTAATACTCC 57.451 34.615 16.12 0.24 46.18 3.85
1911 1934 9.000486 GGAACAAAAGCACTAAAGAGTAATACT 58.000 33.333 0.00 0.00 33.32 2.12
1912 1935 9.000486 AGGAACAAAAGCACTAAAGAGTAATAC 58.000 33.333 0.00 0.00 33.32 1.89
1913 1936 9.569122 AAGGAACAAAAGCACTAAAGAGTAATA 57.431 29.630 0.00 0.00 33.32 0.98
1914 1937 8.465273 AAGGAACAAAAGCACTAAAGAGTAAT 57.535 30.769 0.00 0.00 33.32 1.89
1972 1999 9.770097 ATCATAGTCACCATATACACAGAAAAG 57.230 33.333 0.00 0.00 0.00 2.27
2136 2163 4.235079 ACCAACCTAAGCATGCTATCAA 57.765 40.909 23.00 6.22 0.00 2.57
2301 2328 5.789574 AGAAGAAACCCATGTATTACCCA 57.210 39.130 0.00 0.00 0.00 4.51
2332 2359 8.437360 TTGACGATTGATATTTCTGCATTACT 57.563 30.769 0.00 0.00 0.00 2.24
2399 2426 3.840666 ACTCCAAAGTCAGAGAGGCAATA 59.159 43.478 0.00 0.00 34.13 1.90
2407 2434 7.496529 TGAAAATGTAACTCCAAAGTCAGAG 57.503 36.000 0.00 0.00 33.48 3.35
2472 2499 7.599998 CCAAACTAAAGCAGCAAACAGAATAAT 59.400 33.333 0.00 0.00 0.00 1.28
2565 2592 9.975218 AAAATAAATAAGGAAACCTGAGAGCTA 57.025 29.630 0.00 0.00 32.13 3.32
3114 3141 7.206687 TGAGAACGCCAAACTTGAAATATTTT 58.793 30.769 1.43 0.00 0.00 1.82
3142 3170 2.089980 CCTGCAAAGGGATTGACTGAG 58.910 52.381 0.00 0.00 41.85 3.35
3183 3211 4.272489 CCCATGTCTGGCTGAAATTTAGA 58.728 43.478 0.00 0.00 41.64 2.10
3463 3493 8.947055 AAACAAGTAAAAGCAAGTGAATCAAT 57.053 26.923 0.00 0.00 0.00 2.57
3513 3543 5.105554 GCATGTACTCCTATGAGGGTAGATG 60.106 48.000 17.57 17.57 43.29 2.90
3865 4105 5.840715 TGTGCAAGCAAATAAAATCACTGA 58.159 33.333 0.00 0.00 0.00 3.41
3925 4165 3.753272 AGCATCGTTGTCTGCAGTAAATT 59.247 39.130 14.67 0.00 40.88 1.82
3951 4191 9.377312 GACTCTTCTTAAACAATTAGAGAGCAT 57.623 33.333 0.00 0.00 32.90 3.79
4258 4501 8.433126 CACTAGTAGAAACTTACAATTTCACCG 58.567 37.037 3.59 0.00 38.32 4.94
4279 4522 5.470437 GGAGGAAAAGAAAACTGACCACTAG 59.530 44.000 0.00 0.00 0.00 2.57
4296 4539 7.257790 TGTGAGAGAATGATAAAGGAGGAAA 57.742 36.000 0.00 0.00 0.00 3.13
4298 4541 7.443302 AATGTGAGAGAATGATAAAGGAGGA 57.557 36.000 0.00 0.00 0.00 3.71
4326 4569 6.182507 AGAAGGTACCATAACACAAGTGAA 57.817 37.500 15.94 0.00 0.00 3.18
4454 4697 4.649692 TCTTCTGCTTCTCAATCTGCTTT 58.350 39.130 0.00 0.00 0.00 3.51
4725 4968 4.873827 GCAAACTATTAGTCACCGGAATCA 59.126 41.667 9.46 0.00 0.00 2.57
4746 4990 2.586245 CTCCGAAGCCATCCTGCA 59.414 61.111 0.00 0.00 0.00 4.41
4816 5061 6.289834 TCTCATAGAAAAACCCACGTAACAA 58.710 36.000 0.00 0.00 0.00 2.83
4823 5068 3.621558 CCCCTCTCATAGAAAAACCCAC 58.378 50.000 0.00 0.00 0.00 4.61
4842 5087 1.532604 GCCTGTACCAAACAAGGCCC 61.533 60.000 0.00 0.00 42.17 5.80
4898 5155 1.089123 TTAATCCAAAGCCTGGGGGT 58.911 50.000 2.71 0.00 46.44 4.95
4903 5160 5.647658 TCAGTGTATGTTAATCCAAAGCCTG 59.352 40.000 0.00 0.00 0.00 4.85
4906 5163 7.334421 TCTCTTCAGTGTATGTTAATCCAAAGC 59.666 37.037 0.00 0.00 0.00 3.51
4930 5189 6.961360 TCATCCAGTCGTACAAATATCTCT 57.039 37.500 0.00 0.00 0.00 3.10
5017 6179 2.327002 TACGCCTACGCCTTGCTACG 62.327 60.000 0.00 0.00 45.53 3.51
5031 6193 1.207329 AGGATCAGGACAGTTTACGCC 59.793 52.381 0.00 0.00 0.00 5.68
5032 6194 2.673368 CAAGGATCAGGACAGTTTACGC 59.327 50.000 0.00 0.00 0.00 4.42
5034 6196 5.983540 AGATCAAGGATCAGGACAGTTTAC 58.016 41.667 8.75 0.00 41.12 2.01
5035 6197 6.627087 AAGATCAAGGATCAGGACAGTTTA 57.373 37.500 8.75 0.00 41.12 2.01
5036 6198 5.511386 AAGATCAAGGATCAGGACAGTTT 57.489 39.130 8.75 0.00 41.12 2.66
5037 6199 6.627087 TTAAGATCAAGGATCAGGACAGTT 57.373 37.500 8.75 0.00 41.12 3.16
5038 6200 6.627087 TTTAAGATCAAGGATCAGGACAGT 57.373 37.500 8.75 0.00 41.12 3.55
5039 6201 8.517062 AATTTTAAGATCAAGGATCAGGACAG 57.483 34.615 8.75 0.00 41.12 3.51
5068 6231 7.004086 TGGATATCCTAGGCATTTGGTTAAAG 58.996 38.462 22.35 0.00 36.82 1.85
5106 6523 9.995003 TGTTCTTGCATTTGGTTAAAGAATAAT 57.005 25.926 0.00 0.00 38.66 1.28
5107 6524 9.255304 GTGTTCTTGCATTTGGTTAAAGAATAA 57.745 29.630 0.00 0.00 38.66 1.40
5108 6525 8.637986 AGTGTTCTTGCATTTGGTTAAAGAATA 58.362 29.630 0.00 0.00 38.66 1.75
5110 6527 6.872920 AGTGTTCTTGCATTTGGTTAAAGAA 58.127 32.000 0.00 0.00 35.17 2.52
5111 6528 6.463995 AGTGTTCTTGCATTTGGTTAAAGA 57.536 33.333 0.00 0.00 0.00 2.52
5112 6529 7.591426 GTCTAGTGTTCTTGCATTTGGTTAAAG 59.409 37.037 0.00 0.00 0.00 1.85
5114 6531 6.016610 GGTCTAGTGTTCTTGCATTTGGTTAA 60.017 38.462 0.00 0.00 0.00 2.01
5115 6532 5.472137 GGTCTAGTGTTCTTGCATTTGGTTA 59.528 40.000 0.00 0.00 0.00 2.85
5116 6533 4.278419 GGTCTAGTGTTCTTGCATTTGGTT 59.722 41.667 0.00 0.00 0.00 3.67
5117 6534 3.821033 GGTCTAGTGTTCTTGCATTTGGT 59.179 43.478 0.00 0.00 0.00 3.67
5118 6535 3.120199 CGGTCTAGTGTTCTTGCATTTGG 60.120 47.826 0.00 0.00 0.00 3.28
5119 6536 3.745975 TCGGTCTAGTGTTCTTGCATTTG 59.254 43.478 0.00 0.00 0.00 2.32
5120 6537 3.746492 GTCGGTCTAGTGTTCTTGCATTT 59.254 43.478 0.00 0.00 0.00 2.32
5174 6627 5.944599 ACATGAGATCAATATCCTTGATGGC 59.055 40.000 0.00 0.00 39.08 4.40
5234 6694 3.207265 AGTTCACACATGTGTTGGCTA 57.793 42.857 28.64 9.39 45.76 3.93
5264 6724 5.399858 CCAATATGCTTGCTGCTATTGATC 58.600 41.667 15.88 0.00 40.73 2.92
5315 6775 5.448632 GCACTACACAAGCCAATATGGTAAC 60.449 44.000 0.00 0.00 40.46 2.50
5316 6776 4.638421 GCACTACACAAGCCAATATGGTAA 59.362 41.667 0.00 0.00 40.46 2.85
5317 6777 4.080582 AGCACTACACAAGCCAATATGGTA 60.081 41.667 0.00 0.00 40.46 3.25
5318 6778 3.016736 GCACTACACAAGCCAATATGGT 58.983 45.455 0.00 0.00 40.46 3.55
5319 6779 3.282021 AGCACTACACAAGCCAATATGG 58.718 45.455 0.00 0.00 41.55 2.74
5320 6780 4.970662 AAGCACTACACAAGCCAATATG 57.029 40.909 0.00 0.00 0.00 1.78
5321 6781 5.256474 AGAAAGCACTACACAAGCCAATAT 58.744 37.500 0.00 0.00 0.00 1.28
5322 6782 4.651778 AGAAAGCACTACACAAGCCAATA 58.348 39.130 0.00 0.00 0.00 1.90
5323 6783 3.490348 AGAAAGCACTACACAAGCCAAT 58.510 40.909 0.00 0.00 0.00 3.16
5324 6784 2.930950 AGAAAGCACTACACAAGCCAA 58.069 42.857 0.00 0.00 0.00 4.52
5325 6785 2.638480 AGAAAGCACTACACAAGCCA 57.362 45.000 0.00 0.00 0.00 4.75
5326 6786 2.742589 GGTAGAAAGCACTACACAAGCC 59.257 50.000 14.34 0.00 42.91 4.35
5327 6787 3.665190 AGGTAGAAAGCACTACACAAGC 58.335 45.455 14.34 0.00 42.91 4.01
5328 6788 6.398918 ACATAGGTAGAAAGCACTACACAAG 58.601 40.000 14.34 6.86 42.91 3.16
5329 6789 6.354794 ACATAGGTAGAAAGCACTACACAA 57.645 37.500 14.34 3.68 42.91 3.33
5330 6790 5.995565 ACATAGGTAGAAAGCACTACACA 57.004 39.130 14.34 5.21 42.91 3.72
5331 6791 7.490000 ACATACATAGGTAGAAAGCACTACAC 58.510 38.462 14.34 6.92 42.91 2.90
5332 6792 7.655521 ACATACATAGGTAGAAAGCACTACA 57.344 36.000 14.34 0.49 42.91 2.74
5333 6793 9.460906 GTAACATACATAGGTAGAAAGCACTAC 57.539 37.037 0.00 0.00 41.13 2.73
5334 6794 9.192642 TGTAACATACATAGGTAGAAAGCACTA 57.807 33.333 0.00 0.00 32.89 2.74
5335 6795 8.074613 TGTAACATACATAGGTAGAAAGCACT 57.925 34.615 0.00 0.00 32.89 4.40
5336 6796 7.980099 ACTGTAACATACATAGGTAGAAAGCAC 59.020 37.037 0.00 0.00 38.15 4.40
5337 6797 8.074613 ACTGTAACATACATAGGTAGAAAGCA 57.925 34.615 0.00 0.00 38.15 3.91
5338 6798 8.943909 AACTGTAACATACATAGGTAGAAAGC 57.056 34.615 0.00 0.00 38.15 3.51
5341 6801 9.647797 CACAAACTGTAACATACATAGGTAGAA 57.352 33.333 0.00 0.00 38.15 2.10
5342 6802 9.027202 TCACAAACTGTAACATACATAGGTAGA 57.973 33.333 0.00 0.00 38.15 2.59
5343 6803 9.084164 GTCACAAACTGTAACATACATAGGTAG 57.916 37.037 0.00 0.00 38.15 3.18
5344 6804 8.586744 TGTCACAAACTGTAACATACATAGGTA 58.413 33.333 0.00 0.00 38.15 3.08
5372 6832 1.877576 CGGTGACTGCTAGAGTGCCA 61.878 60.000 0.00 0.00 33.83 4.92
5390 6850 1.802960 GGCACAATAGATGATGCTCCG 59.197 52.381 0.00 0.00 36.73 4.63
5391 6851 2.854963 TGGCACAATAGATGATGCTCC 58.145 47.619 0.00 0.00 36.73 4.70
5441 6903 4.931601 TGCTTGTGTTCTTGTGAGCTATAG 59.068 41.667 0.00 0.00 0.00 1.31
5467 6929 0.032813 ACTGGCCCTTCATTCCATGG 60.033 55.000 4.97 4.97 0.00 3.66
5479 6941 2.049435 CCACCAAAAGAACTGGCCC 58.951 57.895 0.00 0.00 37.48 5.80
5480 6942 1.367471 GCCACCAAAAGAACTGGCC 59.633 57.895 0.00 0.00 43.01 5.36
5482 6944 2.310538 AGAAGCCACCAAAAGAACTGG 58.689 47.619 0.00 0.00 40.05 4.00
5483 6945 4.389374 TCTAGAAGCCACCAAAAGAACTG 58.611 43.478 0.00 0.00 0.00 3.16
5484 6946 4.706842 TCTAGAAGCCACCAAAAGAACT 57.293 40.909 0.00 0.00 0.00 3.01
5485 6947 5.966742 ATTCTAGAAGCCACCAAAAGAAC 57.033 39.130 11.53 0.00 0.00 3.01
5486 6948 6.151144 GCTTATTCTAGAAGCCACCAAAAGAA 59.849 38.462 11.53 0.00 42.90 2.52
5487 6949 5.648092 GCTTATTCTAGAAGCCACCAAAAGA 59.352 40.000 11.53 0.00 42.90 2.52
5488 6950 5.884771 GCTTATTCTAGAAGCCACCAAAAG 58.115 41.667 11.53 5.59 42.90 2.27
5489 6951 5.897377 GCTTATTCTAGAAGCCACCAAAA 57.103 39.130 11.53 0.00 42.90 2.44
5511 6973 1.202818 GGTAGGGGGCAGCTTATTCAG 60.203 57.143 0.00 0.00 0.00 3.02
5512 6974 0.843984 GGTAGGGGGCAGCTTATTCA 59.156 55.000 0.00 0.00 0.00 2.57
5513 6975 0.110678 GGGTAGGGGGCAGCTTATTC 59.889 60.000 0.00 0.00 0.00 1.75
5514 6976 0.328548 AGGGTAGGGGGCAGCTTATT 60.329 55.000 0.00 0.00 0.00 1.40
5515 6977 0.328548 AAGGGTAGGGGGCAGCTTAT 60.329 55.000 0.00 0.00 0.00 1.73
5516 6978 0.344080 TAAGGGTAGGGGGCAGCTTA 59.656 55.000 0.00 0.00 0.00 3.09
5517 6979 0.328548 ATAAGGGTAGGGGGCAGCTT 60.329 55.000 0.00 0.00 0.00 3.74
5518 6980 0.328548 AATAAGGGTAGGGGGCAGCT 60.329 55.000 0.00 0.00 0.00 4.24
5519 6981 0.110678 GAATAAGGGTAGGGGGCAGC 59.889 60.000 0.00 0.00 0.00 5.25
5520 6982 1.821088 AGAATAAGGGTAGGGGGCAG 58.179 55.000 0.00 0.00 0.00 4.85
5521 6983 2.525310 TCTAGAATAAGGGTAGGGGGCA 59.475 50.000 0.00 0.00 0.00 5.36
5522 6984 3.271153 TCTAGAATAAGGGTAGGGGGC 57.729 52.381 0.00 0.00 0.00 5.80
5523 6985 3.583526 GCTTCTAGAATAAGGGTAGGGGG 59.416 52.174 5.44 0.00 0.00 5.40
5524 6986 3.583526 GGCTTCTAGAATAAGGGTAGGGG 59.416 52.174 5.44 0.00 0.00 4.79
5525 6987 3.583526 GGGCTTCTAGAATAAGGGTAGGG 59.416 52.174 5.44 0.00 0.00 3.53
5526 6988 4.232091 TGGGCTTCTAGAATAAGGGTAGG 58.768 47.826 5.44 0.00 0.00 3.18
5527 6989 5.454897 GGTTGGGCTTCTAGAATAAGGGTAG 60.455 48.000 5.44 0.00 0.00 3.18
5528 6990 4.411212 GGTTGGGCTTCTAGAATAAGGGTA 59.589 45.833 5.44 0.00 0.00 3.69
5529 6991 3.202373 GGTTGGGCTTCTAGAATAAGGGT 59.798 47.826 5.44 0.00 0.00 4.34
5530 6992 3.202151 TGGTTGGGCTTCTAGAATAAGGG 59.798 47.826 5.44 0.00 0.00 3.95
5531 6993 4.503714 TGGTTGGGCTTCTAGAATAAGG 57.496 45.455 5.44 0.00 0.00 2.69
5532 6994 6.834168 TTTTGGTTGGGCTTCTAGAATAAG 57.166 37.500 5.44 0.00 0.00 1.73
5533 6995 7.790782 AATTTTGGTTGGGCTTCTAGAATAA 57.209 32.000 5.44 0.00 0.00 1.40
5534 6996 9.487442 AATAATTTTGGTTGGGCTTCTAGAATA 57.513 29.630 5.44 0.00 0.00 1.75
5535 6997 7.978099 ATAATTTTGGTTGGGCTTCTAGAAT 57.022 32.000 5.44 0.00 0.00 2.40
5536 6998 7.790782 AATAATTTTGGTTGGGCTTCTAGAA 57.209 32.000 4.81 4.81 0.00 2.10
5537 6999 7.790782 AAATAATTTTGGTTGGGCTTCTAGA 57.209 32.000 0.00 0.00 0.00 2.43
5538 7000 8.846943 AAAAATAATTTTGGTTGGGCTTCTAG 57.153 30.769 0.00 0.00 37.36 2.43
5562 7024 9.924650 CAAGTCTTAACTACTAGGCTTCTAAAA 57.075 33.333 0.00 0.00 34.27 1.52
5563 7025 9.305555 TCAAGTCTTAACTACTAGGCTTCTAAA 57.694 33.333 0.00 0.00 34.27 1.85
5564 7026 8.874744 TCAAGTCTTAACTACTAGGCTTCTAA 57.125 34.615 0.00 0.00 34.27 2.10
5565 7027 9.476928 AATCAAGTCTTAACTACTAGGCTTCTA 57.523 33.333 0.00 0.00 34.27 2.10
5566 7028 7.964666 ATCAAGTCTTAACTACTAGGCTTCT 57.035 36.000 0.00 0.00 34.27 2.85
5567 7029 9.738832 CTAATCAAGTCTTAACTACTAGGCTTC 57.261 37.037 0.00 0.00 34.27 3.86
5568 7030 9.257428 ACTAATCAAGTCTTAACTACTAGGCTT 57.743 33.333 0.00 0.00 36.80 4.35
5569 7031 8.826293 ACTAATCAAGTCTTAACTACTAGGCT 57.174 34.615 0.00 0.00 33.48 4.58
5597 7059 9.173021 CCCAACCAAAATTTTCTTTTTAGAAGT 57.827 29.630 0.00 0.00 0.00 3.01
5598 7060 8.128582 GCCCAACCAAAATTTTCTTTTTAGAAG 58.871 33.333 0.00 0.00 0.00 2.85
5599 7061 7.831690 AGCCCAACCAAAATTTTCTTTTTAGAA 59.168 29.630 0.00 0.00 0.00 2.10
5600 7062 7.342581 AGCCCAACCAAAATTTTCTTTTTAGA 58.657 30.769 0.00 0.00 0.00 2.10
5601 7063 7.566760 AGCCCAACCAAAATTTTCTTTTTAG 57.433 32.000 0.00 0.00 0.00 1.85
5602 7064 7.831690 AGAAGCCCAACCAAAATTTTCTTTTTA 59.168 29.630 0.00 0.00 0.00 1.52
5603 7065 6.663093 AGAAGCCCAACCAAAATTTTCTTTTT 59.337 30.769 0.00 0.00 0.00 1.94
5604 7066 6.186957 AGAAGCCCAACCAAAATTTTCTTTT 58.813 32.000 0.00 0.00 0.00 2.27
5605 7067 5.754782 AGAAGCCCAACCAAAATTTTCTTT 58.245 33.333 0.00 0.00 0.00 2.52
5606 7068 5.372343 AGAAGCCCAACCAAAATTTTCTT 57.628 34.783 0.00 0.00 0.00 2.52
5607 7069 5.838521 TCTAGAAGCCCAACCAAAATTTTCT 59.161 36.000 0.00 0.00 0.00 2.52
5608 7070 6.096673 TCTAGAAGCCCAACCAAAATTTTC 57.903 37.500 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.