Multiple sequence alignment - TraesCS3D01G532500

Loading Multiple Alignment...

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 TraesCS3D01G532500 chr3D 100.000 2481 0 0 1 2481 608433970 608431490 0.000000e+00 4582.0
1 TraesCS3D01G532500 chr3D 85.060 415 41 10 5 415 608207317 608207714 1.070000e-108 403.0
2 TraesCS3D01G532500 chr3D 82.250 400 44 13 222 602 608309556 608309165 1.110000e-83 320.0
3 TraesCS3D01G532500 chr3D 100.000 124 0 0 604 727 608427623 608427746 1.920000e-56 230.0
4 TraesCS3D01G532500 chr3D 87.500 200 22 1 406 602 608207745 608207944 6.900000e-56 228.0
5 TraesCS3D01G532500 chr5D 99.205 1132 8 1 606 1736 412102482 412103613 0.000000e+00 2039.0
6 TraesCS3D01G532500 chr5D 99.491 589 3 0 1893 2481 412103621 412104209 0.000000e+00 1072.0
7 TraesCS3D01G532500 chr5D 99.194 124 1 0 604 727 412107945 412107822 8.930000e-55 224.0
8 TraesCS3D01G532500 chr7B 83.749 1163 126 28 601 1725 36969780 36970917 0.000000e+00 1042.0
9 TraesCS3D01G532500 chr3A 87.740 416 37 9 5 418 740811516 740811113 8.030000e-130 473.0
10 TraesCS3D01G532500 chr3A 84.881 377 41 6 42 415 740394296 740394659 1.400000e-97 366.0
11 TraesCS3D01G532500 chr3A 89.796 196 17 1 410 602 741094157 741094352 5.300000e-62 248.0
12 TraesCS3D01G532500 chr3A 89.340 197 18 1 410 603 740811081 740810885 6.850000e-61 244.0
13 TraesCS3D01G532500 chr3A 88.776 196 19 1 410 602 741110119 741110314 1.150000e-58 237.0
14 TraesCS3D01G532500 chr3A 88.265 196 20 1 410 602 740394694 740394889 5.340000e-57 231.0
15 TraesCS3D01G532500 chr3B 88.010 392 38 5 5 396 818140111 818139729 2.910000e-124 455.0
16 TraesCS3D01G532500 chr3B 94.915 236 12 0 5 240 817902202 817902437 1.080000e-98 370.0
17 TraesCS3D01G532500 chr3B 83.955 268 32 6 151 415 818153630 818153889 1.910000e-61 246.0
18 TraesCS3D01G532500 chr3B 87.179 195 22 1 411 602 818153925 818154119 4.150000e-53 219.0
19 TraesCS3D01G532500 chr3B 97.500 120 3 0 271 390 817902439 817902558 3.230000e-49 206.0
20 TraesCS3D01G532500 chr3B 89.431 123 9 2 151 270 818141368 818141489 4.270000e-33 152.0
21 TraesCS3D01G532500 chrUn 82.303 356 47 5 60 415 327256330 327256669 6.710000e-76 294.0
22 TraesCS3D01G532500 chr2D 100.000 29 0 0 602 630 39165384 39165356 1.000000e-03 54.7


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 TraesCS3D01G532500 chr3D 608431490 608433970 2480 True 4582.0 4582 100.000 1 2481 1 chr3D.!!$R2 2480
1 TraesCS3D01G532500 chr3D 608207317 608207944 627 False 315.5 403 86.280 5 602 2 chr3D.!!$F2 597
2 TraesCS3D01G532500 chr5D 412102482 412104209 1727 False 1555.5 2039 99.348 606 2481 2 chr5D.!!$F1 1875
3 TraesCS3D01G532500 chr7B 36969780 36970917 1137 False 1042.0 1042 83.749 601 1725 1 chr7B.!!$F1 1124
4 TraesCS3D01G532500 chr3A 740810885 740811516 631 True 358.5 473 88.540 5 603 2 chr3A.!!$R1 598
5 TraesCS3D01G532500 chr3A 740394296 740394889 593 False 298.5 366 86.573 42 602 2 chr3A.!!$F3 560

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
234 238 0.036732 GTCATGGAGGCTGACCAACA 59.963 55.0 0.0 0.0 40.93 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1917 0.257328 TCCCTGTGAACTTGTGGCAA 59.743 50.0 0.0 0.0 0.0 4.52 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
22 23 4.207955 ACGACCTTCTCTACAGCATATCA 58.792 43.478 0.00 0.00 0.00 2.15
24 25 5.303078 ACGACCTTCTCTACAGCATATCAAT 59.697 40.000 0.00 0.00 0.00 2.57
26 27 5.777802 ACCTTCTCTACAGCATATCAATCG 58.222 41.667 0.00 0.00 0.00 3.34
35 36 0.792640 CATATCAATCGCCGGTGCTC 59.207 55.000 11.05 0.00 34.43 4.26
48 49 4.947147 TGCTCACGTGGTTGGGCC 62.947 66.667 17.00 0.00 42.93 5.80
131 132 1.739049 GAGAGGACCCTCGAGCATG 59.261 63.158 6.99 0.00 46.90 4.06
143 144 3.244156 CTCGAGCATGAGTATGAGCATC 58.756 50.000 0.00 0.00 36.36 3.91
150 151 1.067060 TGAGTATGAGCATCGGTTCCG 59.933 52.381 4.74 4.74 38.61 4.30
153 154 0.387929 TATGAGCATCGGTTCCGGAC 59.612 55.000 1.83 0.00 38.61 4.79
184 185 1.331680 CGTCAACCTGTTTTGTCGTCG 60.332 52.381 0.00 0.00 34.60 5.12
234 238 0.036732 GTCATGGAGGCTGACCAACA 59.963 55.000 0.00 0.00 40.93 3.33
235 239 0.994247 TCATGGAGGCTGACCAACAT 59.006 50.000 0.00 0.00 40.93 2.71
284 288 2.892425 CCCGCGATGAGCTTGTCC 60.892 66.667 8.23 0.00 45.59 4.02
291 295 0.251354 GATGAGCTTGTCCAGAGCCA 59.749 55.000 0.00 0.00 41.03 4.75
323 327 2.441717 TGCAGCTGTGGTTTGGCA 60.442 55.556 16.64 0.59 0.00 4.92
335 339 0.681175 GTTTGGCAAATCCACCTGCT 59.319 50.000 16.74 0.00 46.55 4.24
342 346 3.066760 GGCAAATCCACCTGCTATTACAC 59.933 47.826 0.00 0.00 38.65 2.90
343 347 3.947834 GCAAATCCACCTGCTATTACACT 59.052 43.478 0.00 0.00 35.62 3.55
345 349 5.588648 GCAAATCCACCTGCTATTACACTTA 59.411 40.000 0.00 0.00 35.62 2.24
346 350 6.458342 GCAAATCCACCTGCTATTACACTTAC 60.458 42.308 0.00 0.00 35.62 2.34
347 351 5.950544 ATCCACCTGCTATTACACTTACA 57.049 39.130 0.00 0.00 0.00 2.41
348 352 5.748670 TCCACCTGCTATTACACTTACAA 57.251 39.130 0.00 0.00 0.00 2.41
349 353 5.484715 TCCACCTGCTATTACACTTACAAC 58.515 41.667 0.00 0.00 0.00 3.32
350 354 4.634443 CCACCTGCTATTACACTTACAACC 59.366 45.833 0.00 0.00 0.00 3.77
396 400 7.810282 CGAGATTCTATGGGTGTCTATTAACAG 59.190 40.741 0.00 0.00 0.00 3.16
403 407 3.798202 GGTGTCTATTAACAGCCCTGAG 58.202 50.000 1.69 0.00 40.83 3.35
452 495 3.490078 CGAGGAGCCTCTATTGTCAGAAC 60.490 52.174 14.19 0.00 40.69 3.01
453 496 3.704061 GAGGAGCCTCTATTGTCAGAACT 59.296 47.826 9.28 0.00 39.80 3.01
463 506 0.464036 TGTCAGAACTGTCGCCACTT 59.536 50.000 1.73 0.00 0.00 3.16
486 529 4.779489 TGAGAAGATGAGATGGGTGAGAAA 59.221 41.667 0.00 0.00 0.00 2.52
493 536 1.849039 AGATGGGTGAGAAAGGATGGG 59.151 52.381 0.00 0.00 0.00 4.00
598 644 2.029649 GTGTGCCTACTTCGTCTACCAA 60.030 50.000 0.00 0.00 0.00 3.67
807 853 1.472878 GTCGACTCAGCCACACATCTA 59.527 52.381 8.70 0.00 0.00 1.98
938 984 1.226802 GCTCATCTGCTTCTCGCGA 60.227 57.895 9.26 9.26 43.27 5.87
1329 1401 5.221880 TGTTGATGCACTGTTAAATGAAGC 58.778 37.500 0.00 0.00 0.00 3.86
1509 1582 4.081420 CAGTTAGTAGTGAGTTGGAGGCAT 60.081 45.833 0.00 0.00 0.00 4.40
1742 1821 7.919690 TGTCAAAATGTTGAGAGTTTGTAGAG 58.080 34.615 0.00 0.00 44.44 2.43
1743 1822 7.552687 TGTCAAAATGTTGAGAGTTTGTAGAGT 59.447 33.333 0.00 0.00 44.44 3.24
1744 1823 9.042008 GTCAAAATGTTGAGAGTTTGTAGAGTA 57.958 33.333 0.00 0.00 44.44 2.59
1745 1824 9.607988 TCAAAATGTTGAGAGTTTGTAGAGTAA 57.392 29.630 0.00 0.00 38.88 2.24
1748 1827 9.614792 AAATGTTGAGAGTTTGTAGAGTAAAGT 57.385 29.630 0.00 0.00 0.00 2.66
1749 1828 9.614792 AATGTTGAGAGTTTGTAGAGTAAAGTT 57.385 29.630 0.00 0.00 0.00 2.66
1750 1829 9.614792 ATGTTGAGAGTTTGTAGAGTAAAGTTT 57.385 29.630 0.00 0.00 0.00 2.66
1751 1830 8.879759 TGTTGAGAGTTTGTAGAGTAAAGTTTG 58.120 33.333 0.00 0.00 0.00 2.93
1752 1831 7.478520 TGAGAGTTTGTAGAGTAAAGTTTGC 57.521 36.000 0.00 0.00 0.00 3.68
1753 1832 7.272978 TGAGAGTTTGTAGAGTAAAGTTTGCT 58.727 34.615 5.85 5.85 0.00 3.91
1754 1833 7.224753 TGAGAGTTTGTAGAGTAAAGTTTGCTG 59.775 37.037 11.21 0.00 0.00 4.41
1755 1834 7.048512 AGAGTTTGTAGAGTAAAGTTTGCTGT 58.951 34.615 11.21 9.67 0.00 4.40
1756 1835 7.224949 AGAGTTTGTAGAGTAAAGTTTGCTGTC 59.775 37.037 11.21 0.00 0.00 3.51
1757 1836 6.821665 AGTTTGTAGAGTAAAGTTTGCTGTCA 59.178 34.615 11.21 5.20 0.00 3.58
1758 1837 7.335924 AGTTTGTAGAGTAAAGTTTGCTGTCAA 59.664 33.333 11.21 10.22 0.00 3.18
1759 1838 7.618502 TTGTAGAGTAAAGTTTGCTGTCAAA 57.381 32.000 11.21 3.02 39.67 2.69
1760 1839 7.618502 TGTAGAGTAAAGTTTGCTGTCAAAA 57.381 32.000 11.21 0.00 43.12 2.44
1761 1840 8.220755 TGTAGAGTAAAGTTTGCTGTCAAAAT 57.779 30.769 11.21 0.00 43.12 1.82
1762 1841 8.128582 TGTAGAGTAAAGTTTGCTGTCAAAATG 58.871 33.333 11.21 0.00 43.12 2.32
1763 1842 7.100458 AGAGTAAAGTTTGCTGTCAAAATGT 57.900 32.000 11.21 0.00 43.12 2.71
1764 1843 7.547227 AGAGTAAAGTTTGCTGTCAAAATGTT 58.453 30.769 11.21 0.00 43.12 2.71
1765 1844 7.489113 AGAGTAAAGTTTGCTGTCAAAATGTTG 59.511 33.333 11.21 0.00 43.12 3.33
1766 1845 7.319646 AGTAAAGTTTGCTGTCAAAATGTTGA 58.680 30.769 5.32 0.00 43.12 3.18
1767 1846 6.651755 AAAGTTTGCTGTCAAAATGTTGAG 57.348 33.333 0.00 0.00 44.44 3.02
1768 1847 5.581126 AGTTTGCTGTCAAAATGTTGAGA 57.419 34.783 0.00 0.00 44.44 3.27
1769 1848 5.964758 AGTTTGCTGTCAAAATGTTGAGAA 58.035 33.333 0.00 0.00 44.44 2.87
1770 1849 6.576185 AGTTTGCTGTCAAAATGTTGAGAAT 58.424 32.000 0.00 0.00 44.44 2.40
1771 1850 7.043565 AGTTTGCTGTCAAAATGTTGAGAATT 58.956 30.769 0.00 0.00 44.44 2.17
1772 1851 7.550196 AGTTTGCTGTCAAAATGTTGAGAATTT 59.450 29.630 0.00 0.00 44.44 1.82
1773 1852 7.846644 TTGCTGTCAAAATGTTGAGAATTTT 57.153 28.000 0.00 0.00 44.44 1.82
1774 1853 7.467557 TGCTGTCAAAATGTTGAGAATTTTC 57.532 32.000 0.00 0.00 44.44 2.29
1775 1854 7.040494 TGCTGTCAAAATGTTGAGAATTTTCA 58.960 30.769 0.00 0.00 44.44 2.69
1776 1855 7.010367 TGCTGTCAAAATGTTGAGAATTTTCAC 59.990 33.333 0.00 0.00 44.44 3.18
1777 1856 7.010367 GCTGTCAAAATGTTGAGAATTTTCACA 59.990 33.333 0.00 1.59 44.44 3.58
1778 1857 8.945481 TGTCAAAATGTTGAGAATTTTCACAT 57.055 26.923 0.00 3.73 44.44 3.21
1779 1858 8.819015 TGTCAAAATGTTGAGAATTTTCACATG 58.181 29.630 0.00 0.00 44.44 3.21
1780 1859 8.277713 GTCAAAATGTTGAGAATTTTCACATGG 58.722 33.333 0.00 7.58 44.44 3.66
1781 1860 6.790285 AAATGTTGAGAATTTTCACATGGC 57.210 33.333 11.85 0.00 0.00 4.40
1782 1861 4.933505 TGTTGAGAATTTTCACATGGCA 57.066 36.364 0.00 0.00 0.00 4.92
1783 1862 5.471556 TGTTGAGAATTTTCACATGGCAT 57.528 34.783 0.00 0.00 0.00 4.40
1784 1863 6.587206 TGTTGAGAATTTTCACATGGCATA 57.413 33.333 0.00 0.00 0.00 3.14
1785 1864 7.172868 TGTTGAGAATTTTCACATGGCATAT 57.827 32.000 0.00 0.00 0.00 1.78
1786 1865 8.291191 TGTTGAGAATTTTCACATGGCATATA 57.709 30.769 0.00 0.00 0.00 0.86
1787 1866 8.916062 TGTTGAGAATTTTCACATGGCATATAT 58.084 29.630 0.00 0.00 0.00 0.86
1788 1867 9.403110 GTTGAGAATTTTCACATGGCATATATC 57.597 33.333 0.00 0.00 0.00 1.63
1789 1868 8.694581 TGAGAATTTTCACATGGCATATATCA 57.305 30.769 0.00 0.00 0.00 2.15
1790 1869 8.570488 TGAGAATTTTCACATGGCATATATCAC 58.430 33.333 0.00 0.00 0.00 3.06
1791 1870 7.587629 AGAATTTTCACATGGCATATATCACG 58.412 34.615 0.00 0.00 0.00 4.35
1792 1871 7.445096 AGAATTTTCACATGGCATATATCACGA 59.555 33.333 0.00 0.00 0.00 4.35
1793 1872 7.692460 ATTTTCACATGGCATATATCACGAT 57.308 32.000 0.00 0.00 0.00 3.73
1794 1873 6.726258 TTTCACATGGCATATATCACGATC 57.274 37.500 0.00 0.00 0.00 3.69
1795 1874 5.404466 TCACATGGCATATATCACGATCA 57.596 39.130 0.00 0.00 0.00 2.92
1796 1875 5.792741 TCACATGGCATATATCACGATCAA 58.207 37.500 0.00 0.00 0.00 2.57
1797 1876 6.229733 TCACATGGCATATATCACGATCAAA 58.770 36.000 0.00 0.00 0.00 2.69
1798 1877 6.147656 TCACATGGCATATATCACGATCAAAC 59.852 38.462 0.00 0.00 0.00 2.93
1799 1878 5.997129 ACATGGCATATATCACGATCAAACA 59.003 36.000 0.00 0.00 0.00 2.83
1800 1879 6.656270 ACATGGCATATATCACGATCAAACAT 59.344 34.615 0.00 0.00 0.00 2.71
1801 1880 7.823799 ACATGGCATATATCACGATCAAACATA 59.176 33.333 0.00 0.00 0.00 2.29
1802 1881 7.832503 TGGCATATATCACGATCAAACATAG 57.167 36.000 0.00 0.00 0.00 2.23
1803 1882 7.610865 TGGCATATATCACGATCAAACATAGA 58.389 34.615 0.00 0.00 0.00 1.98
1804 1883 7.545615 TGGCATATATCACGATCAAACATAGAC 59.454 37.037 0.00 0.00 0.00 2.59
1805 1884 7.545615 GGCATATATCACGATCAAACATAGACA 59.454 37.037 0.00 0.00 0.00 3.41
1806 1885 8.590470 GCATATATCACGATCAAACATAGACAG 58.410 37.037 0.00 0.00 0.00 3.51
1807 1886 8.590470 CATATATCACGATCAAACATAGACAGC 58.410 37.037 0.00 0.00 0.00 4.40
1808 1887 4.186856 TCACGATCAAACATAGACAGCA 57.813 40.909 0.00 0.00 0.00 4.41
1809 1888 4.176271 TCACGATCAAACATAGACAGCAG 58.824 43.478 0.00 0.00 0.00 4.24
1810 1889 4.082245 TCACGATCAAACATAGACAGCAGA 60.082 41.667 0.00 0.00 0.00 4.26
1811 1890 4.627035 CACGATCAAACATAGACAGCAGAA 59.373 41.667 0.00 0.00 0.00 3.02
1812 1891 5.120674 CACGATCAAACATAGACAGCAGAAA 59.879 40.000 0.00 0.00 0.00 2.52
1813 1892 5.700832 ACGATCAAACATAGACAGCAGAAAA 59.299 36.000 0.00 0.00 0.00 2.29
1814 1893 6.372659 ACGATCAAACATAGACAGCAGAAAAT 59.627 34.615 0.00 0.00 0.00 1.82
1815 1894 7.549134 ACGATCAAACATAGACAGCAGAAAATA 59.451 33.333 0.00 0.00 0.00 1.40
1816 1895 8.390354 CGATCAAACATAGACAGCAGAAAATAA 58.610 33.333 0.00 0.00 0.00 1.40
1817 1896 9.713740 GATCAAACATAGACAGCAGAAAATAAG 57.286 33.333 0.00 0.00 0.00 1.73
1818 1897 8.846943 TCAAACATAGACAGCAGAAAATAAGA 57.153 30.769 0.00 0.00 0.00 2.10
1819 1898 8.721478 TCAAACATAGACAGCAGAAAATAAGAC 58.279 33.333 0.00 0.00 0.00 3.01
1820 1899 7.617041 AACATAGACAGCAGAAAATAAGACC 57.383 36.000 0.00 0.00 0.00 3.85
1821 1900 6.711277 ACATAGACAGCAGAAAATAAGACCA 58.289 36.000 0.00 0.00 0.00 4.02
1822 1901 7.168219 ACATAGACAGCAGAAAATAAGACCAA 58.832 34.615 0.00 0.00 0.00 3.67
1823 1902 5.948992 AGACAGCAGAAAATAAGACCAAC 57.051 39.130 0.00 0.00 0.00 3.77
1824 1903 5.376625 AGACAGCAGAAAATAAGACCAACA 58.623 37.500 0.00 0.00 0.00 3.33
1825 1904 5.827797 AGACAGCAGAAAATAAGACCAACAA 59.172 36.000 0.00 0.00 0.00 2.83
1826 1905 6.016777 AGACAGCAGAAAATAAGACCAACAAG 60.017 38.462 0.00 0.00 0.00 3.16
1827 1906 5.594317 ACAGCAGAAAATAAGACCAACAAGT 59.406 36.000 0.00 0.00 0.00 3.16
1828 1907 6.096846 ACAGCAGAAAATAAGACCAACAAGTT 59.903 34.615 0.00 0.00 0.00 2.66
1829 1908 6.638468 CAGCAGAAAATAAGACCAACAAGTTC 59.362 38.462 0.00 0.00 0.00 3.01
1830 1909 6.321181 AGCAGAAAATAAGACCAACAAGTTCA 59.679 34.615 0.00 0.00 0.00 3.18
1831 1910 6.417930 GCAGAAAATAAGACCAACAAGTTCAC 59.582 38.462 0.00 0.00 0.00 3.18
1832 1911 7.479980 CAGAAAATAAGACCAACAAGTTCACA 58.520 34.615 0.00 0.00 0.00 3.58
1833 1912 8.137437 CAGAAAATAAGACCAACAAGTTCACAT 58.863 33.333 0.00 0.00 0.00 3.21
1834 1913 8.695456 AGAAAATAAGACCAACAAGTTCACATT 58.305 29.630 0.00 0.00 0.00 2.71
1835 1914 8.647143 AAAATAAGACCAACAAGTTCACATTG 57.353 30.769 0.00 0.00 0.00 2.82
1836 1915 3.715628 AGACCAACAAGTTCACATTGC 57.284 42.857 0.00 0.00 0.00 3.56
1837 1916 3.023119 AGACCAACAAGTTCACATTGCA 58.977 40.909 0.00 0.00 0.00 4.08
1838 1917 3.638160 AGACCAACAAGTTCACATTGCAT 59.362 39.130 0.00 0.00 0.00 3.96
1839 1918 4.099881 AGACCAACAAGTTCACATTGCATT 59.900 37.500 0.00 0.00 0.00 3.56
1840 1919 4.121317 ACCAACAAGTTCACATTGCATTG 58.879 39.130 7.04 7.04 0.00 2.82
1841 1920 3.059461 CCAACAAGTTCACATTGCATTGC 60.059 43.478 8.48 0.46 0.00 3.56
1842 1921 2.758009 ACAAGTTCACATTGCATTGCC 58.242 42.857 6.12 0.00 0.00 4.52
1843 1922 2.102757 ACAAGTTCACATTGCATTGCCA 59.897 40.909 6.12 0.00 0.00 4.92
1844 1923 2.443887 AGTTCACATTGCATTGCCAC 57.556 45.000 6.12 3.46 0.00 5.01
1845 1924 1.687660 AGTTCACATTGCATTGCCACA 59.312 42.857 6.12 0.00 0.00 4.17
1846 1925 2.102757 AGTTCACATTGCATTGCCACAA 59.897 40.909 6.12 0.00 0.00 3.33
1847 1926 2.442212 TCACATTGCATTGCCACAAG 57.558 45.000 6.12 0.00 0.00 3.16
1848 1927 1.687660 TCACATTGCATTGCCACAAGT 59.312 42.857 6.12 0.00 0.00 3.16
1849 1928 2.102757 TCACATTGCATTGCCACAAGTT 59.897 40.909 6.12 0.00 0.00 2.66
1850 1929 2.477375 CACATTGCATTGCCACAAGTTC 59.523 45.455 6.12 0.00 0.00 3.01
1851 1930 2.102757 ACATTGCATTGCCACAAGTTCA 59.897 40.909 6.12 0.00 0.00 3.18
1852 1931 2.222007 TTGCATTGCCACAAGTTCAC 57.778 45.000 6.12 0.00 0.00 3.18
1853 1932 1.109609 TGCATTGCCACAAGTTCACA 58.890 45.000 6.12 0.00 0.00 3.58
1854 1933 1.067364 TGCATTGCCACAAGTTCACAG 59.933 47.619 6.12 0.00 0.00 3.66
1855 1934 1.603678 GCATTGCCACAAGTTCACAGG 60.604 52.381 0.00 0.00 0.00 4.00
1856 1935 1.000060 CATTGCCACAAGTTCACAGGG 60.000 52.381 0.00 0.00 0.00 4.45
1857 1936 0.257328 TTGCCACAAGTTCACAGGGA 59.743 50.000 0.00 0.00 0.00 4.20
1858 1937 0.465460 TGCCACAAGTTCACAGGGAC 60.465 55.000 0.00 0.00 0.00 4.46
1859 1938 0.465460 GCCACAAGTTCACAGGGACA 60.465 55.000 0.00 0.00 0.00 4.02
1860 1939 1.308998 CCACAAGTTCACAGGGACAC 58.691 55.000 0.00 0.00 0.00 3.67
1861 1940 1.408127 CCACAAGTTCACAGGGACACA 60.408 52.381 0.00 0.00 0.00 3.72
1862 1941 1.670811 CACAAGTTCACAGGGACACAC 59.329 52.381 0.00 0.00 0.00 3.82
1863 1942 1.280710 ACAAGTTCACAGGGACACACA 59.719 47.619 0.00 0.00 0.00 3.72
1864 1943 2.092429 ACAAGTTCACAGGGACACACAT 60.092 45.455 0.00 0.00 0.00 3.21
1865 1944 3.135712 ACAAGTTCACAGGGACACACATA 59.864 43.478 0.00 0.00 0.00 2.29
1866 1945 3.685139 AGTTCACAGGGACACACATAG 57.315 47.619 0.00 0.00 0.00 2.23
1867 1946 3.239449 AGTTCACAGGGACACACATAGA 58.761 45.455 0.00 0.00 0.00 1.98
1868 1947 3.006967 AGTTCACAGGGACACACATAGAC 59.993 47.826 0.00 0.00 0.00 2.59
1869 1948 2.604139 TCACAGGGACACACATAGACA 58.396 47.619 0.00 0.00 0.00 3.41
1870 1949 2.562738 TCACAGGGACACACATAGACAG 59.437 50.000 0.00 0.00 0.00 3.51
1871 1950 1.276421 ACAGGGACACACATAGACAGC 59.724 52.381 0.00 0.00 0.00 4.40
1872 1951 1.276138 CAGGGACACACATAGACAGCA 59.724 52.381 0.00 0.00 0.00 4.41
1873 1952 1.977854 AGGGACACACATAGACAGCAA 59.022 47.619 0.00 0.00 0.00 3.91
1874 1953 2.371841 AGGGACACACATAGACAGCAAA 59.628 45.455 0.00 0.00 0.00 3.68
1875 1954 3.146066 GGGACACACATAGACAGCAAAA 58.854 45.455 0.00 0.00 0.00 2.44
1876 1955 3.758554 GGGACACACATAGACAGCAAAAT 59.241 43.478 0.00 0.00 0.00 1.82
1877 1956 4.941263 GGGACACACATAGACAGCAAAATA 59.059 41.667 0.00 0.00 0.00 1.40
1878 1957 5.414454 GGGACACACATAGACAGCAAAATAA 59.586 40.000 0.00 0.00 0.00 1.40
1879 1958 6.072175 GGGACACACATAGACAGCAAAATAAA 60.072 38.462 0.00 0.00 0.00 1.40
1880 1959 7.362920 GGGACACACATAGACAGCAAAATAAAT 60.363 37.037 0.00 0.00 0.00 1.40
1881 1960 8.028938 GGACACACATAGACAGCAAAATAAATT 58.971 33.333 0.00 0.00 0.00 1.82
1882 1961 8.970691 ACACACATAGACAGCAAAATAAATTC 57.029 30.769 0.00 0.00 0.00 2.17
1883 1962 8.028938 ACACACATAGACAGCAAAATAAATTCC 58.971 33.333 0.00 0.00 0.00 3.01
1884 1963 8.028354 CACACATAGACAGCAAAATAAATTCCA 58.972 33.333 0.00 0.00 0.00 3.53
1885 1964 8.246180 ACACATAGACAGCAAAATAAATTCCAG 58.754 33.333 0.00 0.00 0.00 3.86
1886 1965 8.246180 CACATAGACAGCAAAATAAATTCCAGT 58.754 33.333 0.00 0.00 0.00 4.00
1887 1966 8.246180 ACATAGACAGCAAAATAAATTCCAGTG 58.754 33.333 0.00 0.00 0.00 3.66
1888 1967 6.655078 AGACAGCAAAATAAATTCCAGTGT 57.345 33.333 0.00 0.00 0.00 3.55
1889 1968 7.054491 AGACAGCAAAATAAATTCCAGTGTT 57.946 32.000 0.00 0.00 0.00 3.32
1890 1969 7.500141 AGACAGCAAAATAAATTCCAGTGTTT 58.500 30.769 0.00 0.00 0.00 2.83
1891 1970 7.653311 AGACAGCAAAATAAATTCCAGTGTTTC 59.347 33.333 0.00 0.00 0.00 2.78
1928 2007 3.817709 ACATGGTTTTTCACCCAACAG 57.182 42.857 0.00 0.00 46.68 3.16
2032 2111 2.736347 GTTCCTCTCCCTGTAGCACTA 58.264 52.381 0.00 0.00 0.00 2.74
2273 2352 2.260844 TTGAGGAGCTTGTGTCCTTG 57.739 50.000 0.00 0.00 45.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.207955 TGATATGCTGTAGAGAAGGTCGT 58.792 43.478 0.00 0.00 0.00 4.34
1 2 4.837896 TGATATGCTGTAGAGAAGGTCG 57.162 45.455 0.00 0.00 0.00 4.79
2 3 5.861251 CGATTGATATGCTGTAGAGAAGGTC 59.139 44.000 0.00 0.00 0.00 3.85
3 4 5.777802 CGATTGATATGCTGTAGAGAAGGT 58.222 41.667 0.00 0.00 0.00 3.50
131 132 1.603172 CCGGAACCGATGCTCATACTC 60.603 57.143 15.07 0.00 42.83 2.59
150 151 1.469335 TTGACGAGGTGACCAGGTCC 61.469 60.000 17.59 8.24 30.46 4.46
153 154 1.004918 GGTTGACGAGGTGACCAGG 60.005 63.158 3.63 0.00 32.41 4.45
234 238 2.742372 GTGTGACGAGGCGCCAAT 60.742 61.111 31.54 13.76 0.00 3.16
235 239 4.980805 GGTGTGACGAGGCGCCAA 62.981 66.667 31.54 5.34 35.49 4.52
323 327 6.717289 TGTAAGTGTAATAGCAGGTGGATTT 58.283 36.000 0.00 0.00 0.00 2.17
335 339 7.681679 TCAAGGATGTGGTTGTAAGTGTAATA 58.318 34.615 0.00 0.00 0.00 0.98
342 346 4.003648 GGACTCAAGGATGTGGTTGTAAG 58.996 47.826 0.00 0.00 0.00 2.34
343 347 3.244770 GGGACTCAAGGATGTGGTTGTAA 60.245 47.826 0.00 0.00 0.00 2.41
345 349 1.073923 GGGACTCAAGGATGTGGTTGT 59.926 52.381 0.00 0.00 0.00 3.32
346 350 1.826385 GGGACTCAAGGATGTGGTTG 58.174 55.000 0.00 0.00 0.00 3.77
347 351 0.324943 CGGGACTCAAGGATGTGGTT 59.675 55.000 0.00 0.00 0.00 3.67
348 352 0.836400 ACGGGACTCAAGGATGTGGT 60.836 55.000 0.00 0.00 0.00 4.16
349 353 0.391661 CACGGGACTCAAGGATGTGG 60.392 60.000 0.00 0.00 0.00 4.17
350 354 0.391661 CCACGGGACTCAAGGATGTG 60.392 60.000 0.00 0.00 0.00 3.21
396 400 1.279271 ACACCTTGTCATACTCAGGGC 59.721 52.381 0.00 0.00 35.82 5.19
452 495 1.998315 CATCTTCTCAAGTGGCGACAG 59.002 52.381 0.00 0.00 44.46 3.51
453 496 1.618343 TCATCTTCTCAAGTGGCGACA 59.382 47.619 0.45 0.00 38.70 4.35
463 506 3.986435 TCTCACCCATCTCATCTTCTCA 58.014 45.455 0.00 0.00 0.00 3.27
486 529 2.435693 GCCAGACTACGCCCATCCT 61.436 63.158 0.00 0.00 0.00 3.24
532 578 1.602668 CCCGCATCCACAACAAAACTG 60.603 52.381 0.00 0.00 0.00 3.16
535 581 2.045280 CCCCGCATCCACAACAAAA 58.955 52.632 0.00 0.00 0.00 2.44
574 620 3.879844 ACGAAGTAGGCACACCCA 58.120 55.556 0.00 0.00 41.94 4.51
598 644 6.405842 GGTTCAAAACAGACTTCACTCCATTT 60.406 38.462 0.00 0.00 0.00 2.32
807 853 1.373497 CCGCTTCGAGTGCTTCTGT 60.373 57.895 10.06 0.00 0.00 3.41
997 1043 2.423898 CCGGCTCGTACTCCATGGT 61.424 63.158 12.58 0.00 0.00 3.55
1329 1401 1.714414 GCAGCAGCTCGTGAATCTG 59.286 57.895 0.00 0.00 37.91 2.90
1736 1815 7.618502 TTTTGACAGCAAACTTTACTCTACA 57.381 32.000 0.00 0.00 43.27 2.74
1737 1816 8.129211 ACATTTTGACAGCAAACTTTACTCTAC 58.871 33.333 0.00 0.00 43.27 2.59
1738 1817 8.220755 ACATTTTGACAGCAAACTTTACTCTA 57.779 30.769 0.00 0.00 43.27 2.43
1739 1818 7.100458 ACATTTTGACAGCAAACTTTACTCT 57.900 32.000 0.00 0.00 43.27 3.24
1740 1819 7.487829 TCAACATTTTGACAGCAAACTTTACTC 59.512 33.333 0.00 0.00 43.27 2.59
1742 1821 7.487829 TCTCAACATTTTGACAGCAAACTTTAC 59.512 33.333 0.00 0.00 43.27 2.01
1743 1822 7.542890 TCTCAACATTTTGACAGCAAACTTTA 58.457 30.769 0.00 0.00 43.27 1.85
1744 1823 6.397272 TCTCAACATTTTGACAGCAAACTTT 58.603 32.000 0.00 0.00 43.27 2.66
1745 1824 5.964758 TCTCAACATTTTGACAGCAAACTT 58.035 33.333 0.00 0.00 43.27 2.66
1746 1825 5.581126 TCTCAACATTTTGACAGCAAACT 57.419 34.783 0.00 0.00 43.27 2.66
1747 1826 6.833342 ATTCTCAACATTTTGACAGCAAAC 57.167 33.333 0.00 0.00 43.27 2.93
1748 1827 7.846644 AAATTCTCAACATTTTGACAGCAAA 57.153 28.000 0.00 0.00 41.97 3.68
1749 1828 7.548427 TGAAAATTCTCAACATTTTGACAGCAA 59.452 29.630 0.00 0.00 36.79 3.91
1750 1829 7.010367 GTGAAAATTCTCAACATTTTGACAGCA 59.990 33.333 3.72 0.00 37.54 4.41
1751 1830 7.010367 TGTGAAAATTCTCAACATTTTGACAGC 59.990 33.333 6.38 0.00 40.53 4.40
1752 1831 8.410030 TGTGAAAATTCTCAACATTTTGACAG 57.590 30.769 6.38 0.00 40.53 3.51
1753 1832 8.819015 CATGTGAAAATTCTCAACATTTTGACA 58.181 29.630 11.19 11.19 45.56 3.58
1754 1833 8.277713 CCATGTGAAAATTCTCAACATTTTGAC 58.722 33.333 2.44 2.05 37.89 3.18
1755 1834 7.041916 GCCATGTGAAAATTCTCAACATTTTGA 60.042 33.333 2.44 0.00 39.55 2.69
1756 1835 7.073265 GCCATGTGAAAATTCTCAACATTTTG 58.927 34.615 2.44 0.00 34.61 2.44
1757 1836 6.766944 TGCCATGTGAAAATTCTCAACATTTT 59.233 30.769 2.44 0.00 36.69 1.82
1758 1837 6.289834 TGCCATGTGAAAATTCTCAACATTT 58.710 32.000 2.44 0.00 34.77 2.32
1759 1838 5.856156 TGCCATGTGAAAATTCTCAACATT 58.144 33.333 2.44 0.00 34.77 2.71
1760 1839 5.471556 TGCCATGTGAAAATTCTCAACAT 57.528 34.783 2.44 0.00 34.77 2.71
1761 1840 4.933505 TGCCATGTGAAAATTCTCAACA 57.066 36.364 2.44 0.00 34.77 3.33
1762 1841 9.403110 GATATATGCCATGTGAAAATTCTCAAC 57.597 33.333 2.44 0.00 34.77 3.18
1763 1842 9.134055 TGATATATGCCATGTGAAAATTCTCAA 57.866 29.630 2.44 0.00 34.77 3.02
1764 1843 8.570488 GTGATATATGCCATGTGAAAATTCTCA 58.430 33.333 0.00 0.93 35.47 3.27
1765 1844 7.747799 CGTGATATATGCCATGTGAAAATTCTC 59.252 37.037 0.00 0.00 0.00 2.87
1766 1845 7.445096 TCGTGATATATGCCATGTGAAAATTCT 59.555 33.333 0.00 0.00 0.00 2.40
1767 1846 7.584108 TCGTGATATATGCCATGTGAAAATTC 58.416 34.615 0.00 0.00 0.00 2.17
1768 1847 7.509141 TCGTGATATATGCCATGTGAAAATT 57.491 32.000 0.00 0.00 0.00 1.82
1769 1848 7.391275 TGATCGTGATATATGCCATGTGAAAAT 59.609 33.333 0.00 0.00 0.00 1.82
1770 1849 6.709846 TGATCGTGATATATGCCATGTGAAAA 59.290 34.615 0.00 0.00 0.00 2.29
1771 1850 6.229733 TGATCGTGATATATGCCATGTGAAA 58.770 36.000 0.00 0.00 0.00 2.69
1772 1851 5.792741 TGATCGTGATATATGCCATGTGAA 58.207 37.500 0.00 0.00 0.00 3.18
1773 1852 5.404466 TGATCGTGATATATGCCATGTGA 57.596 39.130 0.00 0.00 0.00 3.58
1774 1853 6.073112 TGTTTGATCGTGATATATGCCATGTG 60.073 38.462 0.00 0.00 0.00 3.21
1775 1854 5.997129 TGTTTGATCGTGATATATGCCATGT 59.003 36.000 0.00 0.00 0.00 3.21
1776 1855 6.484818 TGTTTGATCGTGATATATGCCATG 57.515 37.500 0.00 0.00 0.00 3.66
1777 1856 8.260114 TCTATGTTTGATCGTGATATATGCCAT 58.740 33.333 0.00 0.00 0.00 4.40
1778 1857 7.545615 GTCTATGTTTGATCGTGATATATGCCA 59.454 37.037 0.00 0.00 0.00 4.92
1779 1858 7.545615 TGTCTATGTTTGATCGTGATATATGCC 59.454 37.037 0.00 0.00 0.00 4.40
1780 1859 8.466086 TGTCTATGTTTGATCGTGATATATGC 57.534 34.615 0.00 0.00 0.00 3.14
1781 1860 8.590470 GCTGTCTATGTTTGATCGTGATATATG 58.410 37.037 0.00 0.00 0.00 1.78
1782 1861 8.306761 TGCTGTCTATGTTTGATCGTGATATAT 58.693 33.333 0.00 0.00 0.00 0.86
1783 1862 7.657336 TGCTGTCTATGTTTGATCGTGATATA 58.343 34.615 0.00 0.00 0.00 0.86
1784 1863 6.515832 TGCTGTCTATGTTTGATCGTGATAT 58.484 36.000 0.00 0.00 0.00 1.63
1785 1864 5.901552 TGCTGTCTATGTTTGATCGTGATA 58.098 37.500 0.00 0.00 0.00 2.15
1786 1865 4.758688 TGCTGTCTATGTTTGATCGTGAT 58.241 39.130 0.00 0.00 0.00 3.06
1787 1866 4.082245 TCTGCTGTCTATGTTTGATCGTGA 60.082 41.667 0.00 0.00 0.00 4.35
1788 1867 4.176271 TCTGCTGTCTATGTTTGATCGTG 58.824 43.478 0.00 0.00 0.00 4.35
1789 1868 4.456280 TCTGCTGTCTATGTTTGATCGT 57.544 40.909 0.00 0.00 0.00 3.73
1790 1869 5.784750 TTTCTGCTGTCTATGTTTGATCG 57.215 39.130 0.00 0.00 0.00 3.69
1791 1870 9.713740 CTTATTTTCTGCTGTCTATGTTTGATC 57.286 33.333 0.00 0.00 0.00 2.92
1792 1871 9.453572 TCTTATTTTCTGCTGTCTATGTTTGAT 57.546 29.630 0.00 0.00 0.00 2.57
1793 1872 8.721478 GTCTTATTTTCTGCTGTCTATGTTTGA 58.279 33.333 0.00 0.00 0.00 2.69
1794 1873 7.965107 GGTCTTATTTTCTGCTGTCTATGTTTG 59.035 37.037 0.00 0.00 0.00 2.93
1795 1874 7.665559 TGGTCTTATTTTCTGCTGTCTATGTTT 59.334 33.333 0.00 0.00 0.00 2.83
1796 1875 7.168219 TGGTCTTATTTTCTGCTGTCTATGTT 58.832 34.615 0.00 0.00 0.00 2.71
1797 1876 6.711277 TGGTCTTATTTTCTGCTGTCTATGT 58.289 36.000 0.00 0.00 0.00 2.29
1798 1877 7.119699 TGTTGGTCTTATTTTCTGCTGTCTATG 59.880 37.037 0.00 0.00 0.00 2.23
1799 1878 7.168219 TGTTGGTCTTATTTTCTGCTGTCTAT 58.832 34.615 0.00 0.00 0.00 1.98
1800 1879 6.530120 TGTTGGTCTTATTTTCTGCTGTCTA 58.470 36.000 0.00 0.00 0.00 2.59
1801 1880 5.376625 TGTTGGTCTTATTTTCTGCTGTCT 58.623 37.500 0.00 0.00 0.00 3.41
1802 1881 5.689383 TGTTGGTCTTATTTTCTGCTGTC 57.311 39.130 0.00 0.00 0.00 3.51
1803 1882 5.594317 ACTTGTTGGTCTTATTTTCTGCTGT 59.406 36.000 0.00 0.00 0.00 4.40
1804 1883 6.076981 ACTTGTTGGTCTTATTTTCTGCTG 57.923 37.500 0.00 0.00 0.00 4.41
1805 1884 6.321181 TGAACTTGTTGGTCTTATTTTCTGCT 59.679 34.615 0.00 0.00 32.49 4.24
1806 1885 6.417930 GTGAACTTGTTGGTCTTATTTTCTGC 59.582 38.462 0.00 0.00 32.49 4.26
1807 1886 7.479980 TGTGAACTTGTTGGTCTTATTTTCTG 58.520 34.615 0.00 0.00 32.49 3.02
1808 1887 7.639113 TGTGAACTTGTTGGTCTTATTTTCT 57.361 32.000 0.00 0.00 32.49 2.52
1809 1888 8.755018 CAATGTGAACTTGTTGGTCTTATTTTC 58.245 33.333 0.00 0.00 32.49 2.29
1810 1889 7.224557 GCAATGTGAACTTGTTGGTCTTATTTT 59.775 33.333 0.00 0.00 32.49 1.82
1811 1890 6.701400 GCAATGTGAACTTGTTGGTCTTATTT 59.299 34.615 0.00 0.00 32.49 1.40
1812 1891 6.183360 TGCAATGTGAACTTGTTGGTCTTATT 60.183 34.615 0.00 0.00 32.49 1.40
1813 1892 5.301551 TGCAATGTGAACTTGTTGGTCTTAT 59.698 36.000 0.00 0.00 32.49 1.73
1814 1893 4.642437 TGCAATGTGAACTTGTTGGTCTTA 59.358 37.500 0.00 0.00 32.49 2.10
1815 1894 3.446873 TGCAATGTGAACTTGTTGGTCTT 59.553 39.130 0.00 0.00 32.49 3.01
1816 1895 3.023119 TGCAATGTGAACTTGTTGGTCT 58.977 40.909 0.00 0.00 32.49 3.85
1817 1896 3.435105 TGCAATGTGAACTTGTTGGTC 57.565 42.857 0.00 0.00 0.00 4.02
1818 1897 4.121317 CAATGCAATGTGAACTTGTTGGT 58.879 39.130 0.00 0.00 0.00 3.67
1819 1898 3.059461 GCAATGCAATGTGAACTTGTTGG 60.059 43.478 0.00 0.00 0.00 3.77
1820 1899 3.059461 GGCAATGCAATGTGAACTTGTTG 60.059 43.478 7.79 0.00 0.00 3.33
1821 1900 3.132925 GGCAATGCAATGTGAACTTGTT 58.867 40.909 7.79 0.00 0.00 2.83
1822 1901 2.102757 TGGCAATGCAATGTGAACTTGT 59.897 40.909 7.79 0.00 0.00 3.16
1823 1902 2.477375 GTGGCAATGCAATGTGAACTTG 59.523 45.455 7.79 0.00 0.00 3.16
1824 1903 2.102757 TGTGGCAATGCAATGTGAACTT 59.897 40.909 7.79 0.00 0.00 2.66
1825 1904 1.687660 TGTGGCAATGCAATGTGAACT 59.312 42.857 7.79 0.00 0.00 3.01
1826 1905 2.151881 TGTGGCAATGCAATGTGAAC 57.848 45.000 7.79 0.63 0.00 3.18
1827 1906 2.102757 ACTTGTGGCAATGCAATGTGAA 59.897 40.909 7.79 0.00 0.00 3.18
1828 1907 1.687660 ACTTGTGGCAATGCAATGTGA 59.312 42.857 7.79 0.00 0.00 3.58
1829 1908 2.157834 ACTTGTGGCAATGCAATGTG 57.842 45.000 7.79 0.00 0.00 3.21
1830 1909 2.102757 TGAACTTGTGGCAATGCAATGT 59.897 40.909 7.79 0.00 0.00 2.71
1831 1910 2.477375 GTGAACTTGTGGCAATGCAATG 59.523 45.455 7.79 0.00 0.00 2.82
1832 1911 2.102757 TGTGAACTTGTGGCAATGCAAT 59.897 40.909 7.79 0.00 0.00 3.56
1833 1912 1.479730 TGTGAACTTGTGGCAATGCAA 59.520 42.857 7.79 0.00 0.00 4.08
1834 1913 1.067364 CTGTGAACTTGTGGCAATGCA 59.933 47.619 7.79 0.00 0.00 3.96
1835 1914 1.603678 CCTGTGAACTTGTGGCAATGC 60.604 52.381 0.00 0.00 0.00 3.56
1836 1915 1.000060 CCCTGTGAACTTGTGGCAATG 60.000 52.381 0.00 0.00 0.00 2.82
1837 1916 1.133513 TCCCTGTGAACTTGTGGCAAT 60.134 47.619 0.00 0.00 0.00 3.56
1838 1917 0.257328 TCCCTGTGAACTTGTGGCAA 59.743 50.000 0.00 0.00 0.00 4.52
1839 1918 0.465460 GTCCCTGTGAACTTGTGGCA 60.465 55.000 0.00 0.00 0.00 4.92
1840 1919 0.465460 TGTCCCTGTGAACTTGTGGC 60.465 55.000 0.00 0.00 0.00 5.01
1841 1920 1.308998 GTGTCCCTGTGAACTTGTGG 58.691 55.000 0.00 0.00 0.00 4.17
1842 1921 1.670811 GTGTGTCCCTGTGAACTTGTG 59.329 52.381 0.00 0.00 0.00 3.33
1843 1922 1.280710 TGTGTGTCCCTGTGAACTTGT 59.719 47.619 0.00 0.00 0.00 3.16
1844 1923 2.036958 TGTGTGTCCCTGTGAACTTG 57.963 50.000 0.00 0.00 0.00 3.16
1845 1924 3.646162 TCTATGTGTGTCCCTGTGAACTT 59.354 43.478 0.00 0.00 0.00 2.66
1846 1925 3.006967 GTCTATGTGTGTCCCTGTGAACT 59.993 47.826 0.00 0.00 0.00 3.01
1847 1926 3.244078 TGTCTATGTGTGTCCCTGTGAAC 60.244 47.826 0.00 0.00 0.00 3.18
1848 1927 2.969262 TGTCTATGTGTGTCCCTGTGAA 59.031 45.455 0.00 0.00 0.00 3.18
1849 1928 2.562738 CTGTCTATGTGTGTCCCTGTGA 59.437 50.000 0.00 0.00 0.00 3.58
1850 1929 2.932622 GCTGTCTATGTGTGTCCCTGTG 60.933 54.545 0.00 0.00 0.00 3.66
1851 1930 1.276421 GCTGTCTATGTGTGTCCCTGT 59.724 52.381 0.00 0.00 0.00 4.00
1852 1931 1.276138 TGCTGTCTATGTGTGTCCCTG 59.724 52.381 0.00 0.00 0.00 4.45
1853 1932 1.644509 TGCTGTCTATGTGTGTCCCT 58.355 50.000 0.00 0.00 0.00 4.20
1854 1933 2.472695 TTGCTGTCTATGTGTGTCCC 57.527 50.000 0.00 0.00 0.00 4.46
1855 1934 6.494893 TTATTTTGCTGTCTATGTGTGTCC 57.505 37.500 0.00 0.00 0.00 4.02
1856 1935 8.970691 AATTTATTTTGCTGTCTATGTGTGTC 57.029 30.769 0.00 0.00 0.00 3.67
1857 1936 8.028938 GGAATTTATTTTGCTGTCTATGTGTGT 58.971 33.333 0.00 0.00 0.00 3.72
1858 1937 8.028354 TGGAATTTATTTTGCTGTCTATGTGTG 58.972 33.333 0.00 0.00 0.00 3.82
1859 1938 8.121305 TGGAATTTATTTTGCTGTCTATGTGT 57.879 30.769 0.00 0.00 0.00 3.72
1860 1939 8.246180 ACTGGAATTTATTTTGCTGTCTATGTG 58.754 33.333 0.00 0.00 0.00 3.21
1861 1940 8.246180 CACTGGAATTTATTTTGCTGTCTATGT 58.754 33.333 0.00 0.00 29.09 2.29
1862 1941 8.246180 ACACTGGAATTTATTTTGCTGTCTATG 58.754 33.333 0.00 0.00 29.09 2.23
1863 1942 8.353423 ACACTGGAATTTATTTTGCTGTCTAT 57.647 30.769 0.00 0.00 29.09 1.98
1864 1943 7.759489 ACACTGGAATTTATTTTGCTGTCTA 57.241 32.000 0.00 0.00 29.09 2.59
1865 1944 6.655078 ACACTGGAATTTATTTTGCTGTCT 57.345 33.333 0.00 0.00 29.09 3.41
1866 1945 7.437862 TGAAACACTGGAATTTATTTTGCTGTC 59.562 33.333 0.00 0.00 29.09 3.51
1867 1946 7.271511 TGAAACACTGGAATTTATTTTGCTGT 58.728 30.769 0.00 0.00 31.11 4.40
1868 1947 7.712264 TGAAACACTGGAATTTATTTTGCTG 57.288 32.000 0.00 0.00 0.00 4.41
1876 1955 9.521841 TGTGGTTATATGAAACACTGGAATTTA 57.478 29.630 10.61 0.00 0.00 1.40
1877 1956 8.415950 TGTGGTTATATGAAACACTGGAATTT 57.584 30.769 10.61 0.00 0.00 1.82
1878 1957 8.593945 ATGTGGTTATATGAAACACTGGAATT 57.406 30.769 10.61 0.00 0.00 2.17
1879 1958 8.593945 AATGTGGTTATATGAAACACTGGAAT 57.406 30.769 10.61 0.00 0.00 3.01
1880 1959 7.888021 AGAATGTGGTTATATGAAACACTGGAA 59.112 33.333 10.61 0.00 0.00 3.53
1881 1960 7.402054 AGAATGTGGTTATATGAAACACTGGA 58.598 34.615 10.61 0.00 0.00 3.86
1882 1961 7.630242 AGAATGTGGTTATATGAAACACTGG 57.370 36.000 10.61 0.00 0.00 4.00
1883 1962 9.988350 GTTAGAATGTGGTTATATGAAACACTG 57.012 33.333 10.61 0.00 0.00 3.66
1884 1963 9.733556 TGTTAGAATGTGGTTATATGAAACACT 57.266 29.630 10.61 0.00 0.00 3.55
1887 1966 9.950680 CCATGTTAGAATGTGGTTATATGAAAC 57.049 33.333 0.00 0.00 0.00 2.78
1888 1967 9.693739 ACCATGTTAGAATGTGGTTATATGAAA 57.306 29.630 0.00 0.00 42.03 2.69
1928 2007 9.615295 AATTGTTCTTTTTGCATGATATTTTGC 57.385 25.926 0.00 4.36 39.33 3.68
2032 2111 1.202818 GGGAGAGGAACAGCAACAACT 60.203 52.381 0.00 0.00 0.00 3.16
2273 2352 3.052036 CAGCAAATACACAACCTGCAAC 58.948 45.455 0.00 0.00 35.44 4.17


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

AutoCloner maintained by Alex Coulton.