Multiple sequence alignment - TraesCS3B01G532900

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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 TraesCS3B01G532900 chr3B 100.000 2627 0 0 1 2627 773547012 773549638 0.000000e+00 4852.0
1 TraesCS3B01G532900 chr1B 99.463 1677 9 0 1 1677 669918193 669919869 0.000000e+00 3048.0
2 TraesCS3B01G532900 chr1B 99.164 1675 12 1 1 1675 418167226 418165554 0.000000e+00 3014.0
3 TraesCS3B01G532900 chr5A 99.225 1677 13 0 1 1677 536712256 536710580 0.000000e+00 3025.0
4 TraesCS3B01G532900 chr7A 99.046 1677 14 1 1 1675 30716182 30714506 0.000000e+00 3007.0
5 TraesCS3B01G532900 chr7A 94.389 1301 69 3 377 1674 667967885 667966586 0.000000e+00 1995.0
6 TraesCS3B01G532900 chr7B 97.795 1678 33 2 1 1675 63493086 63494762 0.000000e+00 2891.0
7 TraesCS3B01G532900 chr2A 96.655 1674 54 2 3 1676 40957567 40955896 0.000000e+00 2780.0
8 TraesCS3B01G532900 chr2A 96.236 1355 49 2 325 1677 722079736 722078382 0.000000e+00 2218.0
9 TraesCS3B01G532900 chr2A 83.500 600 99 0 1 600 407750224 407750823 6.350000e-156 560.0
10 TraesCS3B01G532900 chr2A 95.527 313 13 1 1 313 722093048 722092737 1.400000e-137 499.0
11 TraesCS3B01G532900 chr1A 94.093 1676 91 6 1 1676 592501710 592500043 0.000000e+00 2540.0
12 TraesCS3B01G532900 chr5B 94.345 672 29 4 1959 2627 197092173 197092838 0.000000e+00 1022.0
13 TraesCS3B01G532900 chr4B 94.345 672 29 4 1959 2627 567185830 567185165 0.000000e+00 1022.0
14 TraesCS3B01G532900 chr4B 93.899 672 32 4 1959 2627 187622979 187622314 0.000000e+00 1005.0
15 TraesCS3B01G532900 chr6D 93.750 672 33 4 1959 2627 46047036 46047701 0.000000e+00 1000.0
16 TraesCS3B01G532900 chr3A 93.741 671 32 6 1959 2625 234974018 234973354 0.000000e+00 998.0
17 TraesCS3B01G532900 chr3A 93.731 670 33 4 1959 2625 715423190 715423853 0.000000e+00 996.0
18 TraesCS3B01G532900 chr3A 93.304 672 34 4 1959 2627 429487899 429487236 0.000000e+00 981.0
19 TraesCS3B01G532900 chr3A 91.139 158 8 3 1804 1955 714537552 714537709 2.650000e-50 209.0
20 TraesCS3B01G532900 chr7D 92.148 675 41 5 1959 2627 556847490 556848158 0.000000e+00 942.0
21 TraesCS3B01G532900 chr1D 91.815 672 46 4 1959 2627 340529133 340529798 0.000000e+00 928.0
22 TraesCS3B01G532900 chr3D 94.393 214 12 0 1672 1885 579293749 579293962 1.950000e-86 329.0
23 TraesCS3B01G532900 chr3D 97.872 47 1 0 1890 1936 579294086 579294132 6.030000e-12 82.4


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 TraesCS3B01G532900 chr3B 773547012 773549638 2626 False 4852 4852 100.000 1 2627 1 chr3B.!!$F1 2626
1 TraesCS3B01G532900 chr1B 669918193 669919869 1676 False 3048 3048 99.463 1 1677 1 chr1B.!!$F1 1676
2 TraesCS3B01G532900 chr1B 418165554 418167226 1672 True 3014 3014 99.164 1 1675 1 chr1B.!!$R1 1674
3 TraesCS3B01G532900 chr5A 536710580 536712256 1676 True 3025 3025 99.225 1 1677 1 chr5A.!!$R1 1676
4 TraesCS3B01G532900 chr7A 30714506 30716182 1676 True 3007 3007 99.046 1 1675 1 chr7A.!!$R1 1674
5 TraesCS3B01G532900 chr7A 667966586 667967885 1299 True 1995 1995 94.389 377 1674 1 chr7A.!!$R2 1297
6 TraesCS3B01G532900 chr7B 63493086 63494762 1676 False 2891 2891 97.795 1 1675 1 chr7B.!!$F1 1674
7 TraesCS3B01G532900 chr2A 40955896 40957567 1671 True 2780 2780 96.655 3 1676 1 chr2A.!!$R1 1673
8 TraesCS3B01G532900 chr2A 722078382 722079736 1354 True 2218 2218 96.236 325 1677 1 chr2A.!!$R2 1352
9 TraesCS3B01G532900 chr2A 407750224 407750823 599 False 560 560 83.500 1 600 1 chr2A.!!$F1 599
10 TraesCS3B01G532900 chr1A 592500043 592501710 1667 True 2540 2540 94.093 1 1676 1 chr1A.!!$R1 1675
11 TraesCS3B01G532900 chr5B 197092173 197092838 665 False 1022 1022 94.345 1959 2627 1 chr5B.!!$F1 668
12 TraesCS3B01G532900 chr4B 567185165 567185830 665 True 1022 1022 94.345 1959 2627 1 chr4B.!!$R2 668
13 TraesCS3B01G532900 chr4B 187622314 187622979 665 True 1005 1005 93.899 1959 2627 1 chr4B.!!$R1 668
14 TraesCS3B01G532900 chr6D 46047036 46047701 665 False 1000 1000 93.750 1959 2627 1 chr6D.!!$F1 668
15 TraesCS3B01G532900 chr3A 234973354 234974018 664 True 998 998 93.741 1959 2625 1 chr3A.!!$R1 666
16 TraesCS3B01G532900 chr3A 715423190 715423853 663 False 996 996 93.731 1959 2625 1 chr3A.!!$F2 666
17 TraesCS3B01G532900 chr3A 429487236 429487899 663 True 981 981 93.304 1959 2627 1 chr3A.!!$R2 668
18 TraesCS3B01G532900 chr7D 556847490 556848158 668 False 942 942 92.148 1959 2627 1 chr7D.!!$F1 668
19 TraesCS3B01G532900 chr1D 340529133 340529798 665 False 928 928 91.815 1959 2627 1 chr1D.!!$F1 668

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
137 138 2.03262 TGCTTTTTGGGCTTCGGTTTA 58.967 42.857 0.0 0.0 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 1950 0.033601 TGGAGCAATTACCCGCCAAT 60.034 50.0 0.0 0.0 0.0 3.16 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
137 138 2.032620 TGCTTTTTGGGCTTCGGTTTA 58.967 42.857 0.00 0.00 0.00 2.01
1283 1294 1.979855 TTTGCAGCTCAAGTGGCTAA 58.020 45.000 0.00 0.00 38.03 3.09
1526 1537 4.093743 AGGGTTGAACCTCAAGTTTGTTT 58.906 39.130 14.87 0.00 39.40 2.83
1703 1714 3.230743 ACAAGTGTGTGCCTTGAAAAC 57.769 42.857 7.11 0.00 41.44 2.43
1704 1715 2.560542 ACAAGTGTGTGCCTTGAAAACA 59.439 40.909 7.11 0.00 41.44 2.83
1705 1716 3.006323 ACAAGTGTGTGCCTTGAAAACAA 59.994 39.130 7.11 0.00 41.44 2.83
1706 1717 4.183101 CAAGTGTGTGCCTTGAAAACAAT 58.817 39.130 0.00 0.00 41.44 2.71
1707 1718 4.470334 AGTGTGTGCCTTGAAAACAATT 57.530 36.364 0.00 0.00 0.00 2.32
1708 1719 4.831107 AGTGTGTGCCTTGAAAACAATTT 58.169 34.783 0.00 0.00 0.00 1.82
1709 1720 5.971763 AGTGTGTGCCTTGAAAACAATTTA 58.028 33.333 0.00 0.00 0.00 1.40
1710 1721 5.810074 AGTGTGTGCCTTGAAAACAATTTAC 59.190 36.000 0.00 0.00 0.00 2.01
1711 1722 5.578727 GTGTGTGCCTTGAAAACAATTTACA 59.421 36.000 0.00 0.00 0.00 2.41
1712 1723 5.809562 TGTGTGCCTTGAAAACAATTTACAG 59.190 36.000 0.00 0.00 0.00 2.74
1713 1724 5.810074 GTGTGCCTTGAAAACAATTTACAGT 59.190 36.000 0.00 0.00 0.00 3.55
1714 1725 5.809562 TGTGCCTTGAAAACAATTTACAGTG 59.190 36.000 0.00 0.00 0.00 3.66
1715 1726 6.039616 GTGCCTTGAAAACAATTTACAGTGA 58.960 36.000 0.00 0.00 0.00 3.41
1716 1727 6.533367 GTGCCTTGAAAACAATTTACAGTGAA 59.467 34.615 0.00 0.00 0.00 3.18
1717 1728 6.533367 TGCCTTGAAAACAATTTACAGTGAAC 59.467 34.615 0.00 0.00 0.00 3.18
1718 1729 6.756542 GCCTTGAAAACAATTTACAGTGAACT 59.243 34.615 0.00 0.00 0.00 3.01
1719 1730 7.918562 GCCTTGAAAACAATTTACAGTGAACTA 59.081 33.333 0.00 0.00 0.00 2.24
1720 1731 9.965824 CCTTGAAAACAATTTACAGTGAACTAT 57.034 29.630 0.00 0.00 0.00 2.12
1746 1757 6.704512 TTTTCAAATAAATTGGCGAGCTTC 57.295 33.333 0.00 0.00 39.62 3.86
1747 1758 5.643379 TTCAAATAAATTGGCGAGCTTCT 57.357 34.783 0.00 0.00 39.62 2.85
1748 1759 4.985413 TCAAATAAATTGGCGAGCTTCTG 58.015 39.130 0.00 0.00 39.62 3.02
1749 1760 4.107622 CAAATAAATTGGCGAGCTTCTGG 58.892 43.478 0.00 0.00 35.27 3.86
1750 1761 2.489938 TAAATTGGCGAGCTTCTGGT 57.510 45.000 0.00 0.00 0.00 4.00
1751 1762 2.489938 AAATTGGCGAGCTTCTGGTA 57.510 45.000 0.00 0.00 0.00 3.25
1752 1763 2.717639 AATTGGCGAGCTTCTGGTAT 57.282 45.000 0.00 0.00 0.00 2.73
1753 1764 2.717639 ATTGGCGAGCTTCTGGTATT 57.282 45.000 0.00 0.00 0.00 1.89
1754 1765 3.838244 ATTGGCGAGCTTCTGGTATTA 57.162 42.857 0.00 0.00 0.00 0.98
1755 1766 3.838244 TTGGCGAGCTTCTGGTATTAT 57.162 42.857 0.00 0.00 0.00 1.28
1756 1767 3.838244 TGGCGAGCTTCTGGTATTATT 57.162 42.857 0.00 0.00 0.00 1.40
1757 1768 4.948341 TGGCGAGCTTCTGGTATTATTA 57.052 40.909 0.00 0.00 0.00 0.98
1758 1769 5.284861 TGGCGAGCTTCTGGTATTATTAA 57.715 39.130 0.00 0.00 0.00 1.40
1759 1770 5.676552 TGGCGAGCTTCTGGTATTATTAAA 58.323 37.500 0.00 0.00 0.00 1.52
1760 1771 6.296026 TGGCGAGCTTCTGGTATTATTAAAT 58.704 36.000 0.00 0.00 0.00 1.40
1761 1772 7.446769 TGGCGAGCTTCTGGTATTATTAAATA 58.553 34.615 0.00 0.00 0.00 1.40
1762 1773 8.100791 TGGCGAGCTTCTGGTATTATTAAATAT 58.899 33.333 0.00 0.00 30.42 1.28
1763 1774 9.595823 GGCGAGCTTCTGGTATTATTAAATATA 57.404 33.333 0.00 0.00 30.42 0.86
1773 1784 9.439500 TGGTATTATTAAATATACCGTTCTGGC 57.561 33.333 17.69 0.00 41.33 4.85
1774 1785 8.886719 GGTATTATTAAATATACCGTTCTGGCC 58.113 37.037 11.46 0.00 33.68 5.36
1775 1786 9.662947 GTATTATTAAATATACCGTTCTGGCCT 57.337 33.333 3.32 0.00 33.68 5.19
1779 1790 8.983702 ATTAAATATACCGTTCTGGCCTAAAA 57.016 30.769 3.32 0.00 43.94 1.52
1780 1791 8.804912 TTAAATATACCGTTCTGGCCTAAAAA 57.195 30.769 3.32 0.00 43.94 1.94
1781 1792 6.937436 AATATACCGTTCTGGCCTAAAAAG 57.063 37.500 3.32 0.00 43.94 2.27
1782 1793 2.943036 ACCGTTCTGGCCTAAAAAGA 57.057 45.000 3.32 0.00 43.94 2.52
1783 1794 3.217681 ACCGTTCTGGCCTAAAAAGAA 57.782 42.857 3.32 0.44 43.94 2.52
1784 1795 3.146847 ACCGTTCTGGCCTAAAAAGAAG 58.853 45.455 3.32 0.00 43.94 2.85
1785 1796 3.181448 ACCGTTCTGGCCTAAAAAGAAGA 60.181 43.478 3.32 0.00 43.94 2.87
1786 1797 3.818773 CCGTTCTGGCCTAAAAAGAAGAA 59.181 43.478 3.32 0.00 30.84 2.52
1787 1798 4.277423 CCGTTCTGGCCTAAAAAGAAGAAA 59.723 41.667 3.32 0.00 30.84 2.52
1788 1799 5.221165 CCGTTCTGGCCTAAAAAGAAGAAAA 60.221 40.000 3.32 0.00 30.84 2.29
1789 1800 6.270064 CGTTCTGGCCTAAAAAGAAGAAAAA 58.730 36.000 3.32 0.00 30.84 1.94
1790 1801 6.923508 CGTTCTGGCCTAAAAAGAAGAAAAAT 59.076 34.615 3.32 0.00 30.84 1.82
1791 1802 8.079809 CGTTCTGGCCTAAAAAGAAGAAAAATA 58.920 33.333 3.32 0.00 30.84 1.40
1792 1803 9.929180 GTTCTGGCCTAAAAAGAAGAAAAATAT 57.071 29.630 3.32 0.00 30.84 1.28
1794 1805 8.749354 TCTGGCCTAAAAAGAAGAAAAATATCC 58.251 33.333 3.32 0.00 0.00 2.59
1795 1806 8.664669 TGGCCTAAAAAGAAGAAAAATATCCT 57.335 30.769 3.32 0.00 0.00 3.24
1796 1807 9.100197 TGGCCTAAAAAGAAGAAAAATATCCTT 57.900 29.630 3.32 0.00 0.00 3.36
1797 1808 9.944376 GGCCTAAAAAGAAGAAAAATATCCTTT 57.056 29.630 0.00 0.00 0.00 3.11
1816 1827 8.640033 ATCCTTTTTAGGAACTTAGGATAGGT 57.360 34.615 0.00 0.00 41.90 3.08
1817 1828 8.458951 TCCTTTTTAGGAACTTAGGATAGGTT 57.541 34.615 0.00 0.00 44.09 3.50
1818 1829 8.897692 TCCTTTTTAGGAACTTAGGATAGGTTT 58.102 33.333 0.00 0.00 41.26 3.27
1819 1830 8.957466 CCTTTTTAGGAACTTAGGATAGGTTTG 58.043 37.037 0.00 0.00 41.26 2.93
1820 1831 9.734984 CTTTTTAGGAACTTAGGATAGGTTTGA 57.265 33.333 0.00 0.00 41.26 2.69
1822 1833 9.681062 TTTTAGGAACTTAGGATAGGTTTGATG 57.319 33.333 0.00 0.00 41.26 3.07
1823 1834 8.618240 TTAGGAACTTAGGATAGGTTTGATGA 57.382 34.615 0.00 0.00 41.26 2.92
1824 1835 7.510675 AGGAACTTAGGATAGGTTTGATGAA 57.489 36.000 0.00 0.00 41.26 2.57
1825 1836 7.928873 AGGAACTTAGGATAGGTTTGATGAAA 58.071 34.615 0.00 0.00 41.26 2.69
1826 1837 8.390921 AGGAACTTAGGATAGGTTTGATGAAAA 58.609 33.333 0.00 0.00 41.26 2.29
1827 1838 8.459635 GGAACTTAGGATAGGTTTGATGAAAAC 58.540 37.037 0.00 0.00 41.26 2.43
1838 1849 1.369625 GATGAAAACCATCTCGCCGT 58.630 50.000 0.00 0.00 46.33 5.68
1839 1850 1.737793 GATGAAAACCATCTCGCCGTT 59.262 47.619 0.00 0.00 46.33 4.44
1840 1851 0.871722 TGAAAACCATCTCGCCGTTG 59.128 50.000 0.00 0.00 0.00 4.10
1841 1852 0.168128 GAAAACCATCTCGCCGTTGG 59.832 55.000 2.76 2.76 38.27 3.77
1842 1853 0.250553 AAAACCATCTCGCCGTTGGA 60.251 50.000 9.73 0.00 36.24 3.53
1843 1854 0.035439 AAACCATCTCGCCGTTGGAT 60.035 50.000 9.73 0.00 36.24 3.41
1844 1855 0.462047 AACCATCTCGCCGTTGGATC 60.462 55.000 9.73 0.00 36.24 3.36
1845 1856 1.143838 CCATCTCGCCGTTGGATCA 59.856 57.895 0.00 0.00 34.93 2.92
1846 1857 0.461870 CCATCTCGCCGTTGGATCAA 60.462 55.000 0.00 0.00 34.93 2.57
1847 1858 1.368641 CATCTCGCCGTTGGATCAAA 58.631 50.000 0.00 0.00 0.00 2.69
1848 1859 1.942657 CATCTCGCCGTTGGATCAAAT 59.057 47.619 0.00 0.00 0.00 2.32
1849 1860 2.107950 TCTCGCCGTTGGATCAAATT 57.892 45.000 0.00 0.00 0.00 1.82
1850 1861 2.432444 TCTCGCCGTTGGATCAAATTT 58.568 42.857 0.00 0.00 0.00 1.82
1851 1862 3.601435 TCTCGCCGTTGGATCAAATTTA 58.399 40.909 0.00 0.00 0.00 1.40
1852 1863 4.004314 TCTCGCCGTTGGATCAAATTTAA 58.996 39.130 0.00 0.00 0.00 1.52
1853 1864 4.086199 TCGCCGTTGGATCAAATTTAAC 57.914 40.909 0.00 0.00 0.00 2.01
1854 1865 3.754323 TCGCCGTTGGATCAAATTTAACT 59.246 39.130 0.00 0.00 0.00 2.24
1855 1866 4.216687 TCGCCGTTGGATCAAATTTAACTT 59.783 37.500 0.00 0.00 0.00 2.66
1856 1867 4.557301 CGCCGTTGGATCAAATTTAACTTC 59.443 41.667 0.00 0.00 0.00 3.01
1857 1868 4.862574 GCCGTTGGATCAAATTTAACTTCC 59.137 41.667 0.00 0.00 0.00 3.46
1858 1869 5.407502 CCGTTGGATCAAATTTAACTTCCC 58.592 41.667 0.00 0.00 0.00 3.97
1859 1870 5.185056 CCGTTGGATCAAATTTAACTTCCCT 59.815 40.000 0.00 0.00 0.00 4.20
1860 1871 6.376018 CCGTTGGATCAAATTTAACTTCCCTA 59.624 38.462 0.00 0.00 0.00 3.53
1861 1872 7.415206 CCGTTGGATCAAATTTAACTTCCCTAG 60.415 40.741 0.00 0.00 0.00 3.02
1862 1873 7.335924 CGTTGGATCAAATTTAACTTCCCTAGA 59.664 37.037 0.00 0.00 0.00 2.43
1863 1874 9.020731 GTTGGATCAAATTTAACTTCCCTAGAA 57.979 33.333 0.00 0.00 0.00 2.10
1864 1875 8.575649 TGGATCAAATTTAACTTCCCTAGAAC 57.424 34.615 0.00 0.00 0.00 3.01
1865 1876 8.390921 TGGATCAAATTTAACTTCCCTAGAACT 58.609 33.333 0.00 0.00 0.00 3.01
1866 1877 9.901172 GGATCAAATTTAACTTCCCTAGAACTA 57.099 33.333 0.00 0.00 0.00 2.24
1872 1883 9.516546 AATTTAACTTCCCTAGAACTAACTTGG 57.483 33.333 0.00 0.00 33.77 3.61
1873 1884 7.860649 TTAACTTCCCTAGAACTAACTTGGA 57.139 36.000 0.00 0.00 35.43 3.53
1874 1885 6.954352 AACTTCCCTAGAACTAACTTGGAT 57.046 37.500 0.00 0.00 35.43 3.41
1875 1886 9.551339 TTAACTTCCCTAGAACTAACTTGGATA 57.449 33.333 0.00 0.00 35.43 2.59
1876 1887 8.625467 AACTTCCCTAGAACTAACTTGGATAT 57.375 34.615 0.00 0.00 35.43 1.63
1877 1888 8.252624 ACTTCCCTAGAACTAACTTGGATATC 57.747 38.462 0.00 0.00 35.43 1.63
1878 1889 8.068733 ACTTCCCTAGAACTAACTTGGATATCT 58.931 37.037 2.05 0.00 35.43 1.98
1879 1890 8.855804 TTCCCTAGAACTAACTTGGATATCTT 57.144 34.615 2.05 0.00 35.43 2.40
1880 1891 8.480133 TCCCTAGAACTAACTTGGATATCTTC 57.520 38.462 2.05 0.00 35.43 2.87
1881 1892 7.509659 TCCCTAGAACTAACTTGGATATCTTCC 59.490 40.741 2.05 0.00 45.69 3.46
1882 1893 7.511028 CCCTAGAACTAACTTGGATATCTTCCT 59.489 40.741 2.05 0.00 45.68 3.36
1883 1894 9.589461 CCTAGAACTAACTTGGATATCTTCCTA 57.411 37.037 2.05 0.00 45.68 2.94
1902 1913 9.131791 TCTTCCTAATATTTATTTGTCTTGCCC 57.868 33.333 0.00 0.00 0.00 5.36
1903 1914 8.830915 TTCCTAATATTTATTTGTCTTGCCCA 57.169 30.769 0.00 0.00 0.00 5.36
1904 1915 9.432982 TTCCTAATATTTATTTGTCTTGCCCAT 57.567 29.630 0.00 0.00 0.00 4.00
1913 1924 9.868277 TTTATTTGTCTTGCCCATACATTTAAG 57.132 29.630 0.00 0.00 0.00 1.85
1914 1925 7.716799 ATTTGTCTTGCCCATACATTTAAGA 57.283 32.000 0.00 0.00 0.00 2.10
1915 1926 6.509418 TTGTCTTGCCCATACATTTAAGAC 57.491 37.500 0.00 0.00 42.48 3.01
1916 1927 5.565509 TGTCTTGCCCATACATTTAAGACA 58.434 37.500 12.10 12.10 46.68 3.41
1917 1928 5.647658 TGTCTTGCCCATACATTTAAGACAG 59.352 40.000 12.10 0.00 45.09 3.51
1918 1929 4.640201 TCTTGCCCATACATTTAAGACAGC 59.360 41.667 0.00 0.00 0.00 4.40
1919 1930 3.961849 TGCCCATACATTTAAGACAGCA 58.038 40.909 0.00 0.00 0.00 4.41
1920 1931 4.535781 TGCCCATACATTTAAGACAGCAT 58.464 39.130 0.00 0.00 0.00 3.79
1921 1932 5.689835 TGCCCATACATTTAAGACAGCATA 58.310 37.500 0.00 0.00 0.00 3.14
1922 1933 6.125719 TGCCCATACATTTAAGACAGCATAA 58.874 36.000 0.00 0.00 0.00 1.90
1923 1934 6.777091 TGCCCATACATTTAAGACAGCATAAT 59.223 34.615 0.00 0.00 0.00 1.28
1924 1935 7.086376 GCCCATACATTTAAGACAGCATAATG 58.914 38.462 0.00 0.00 33.55 1.90
1925 1936 7.040478 GCCCATACATTTAAGACAGCATAATGA 60.040 37.037 0.00 0.00 32.15 2.57
1926 1937 8.509690 CCCATACATTTAAGACAGCATAATGAG 58.490 37.037 0.00 0.00 32.15 2.90
1927 1938 8.019669 CCATACATTTAAGACAGCATAATGAGC 58.980 37.037 0.00 0.00 32.15 4.26
1928 1939 8.781196 CATACATTTAAGACAGCATAATGAGCT 58.219 33.333 0.00 0.00 44.62 4.09
1929 1940 7.256756 ACATTTAAGACAGCATAATGAGCTC 57.743 36.000 6.82 6.82 41.14 4.09
1930 1941 6.825213 ACATTTAAGACAGCATAATGAGCTCA 59.175 34.615 20.79 20.79 41.14 4.26
1931 1942 6.915544 TTTAAGACAGCATAATGAGCTCAG 57.084 37.500 22.96 9.46 41.14 3.35
1932 1943 2.836262 AGACAGCATAATGAGCTCAGC 58.164 47.619 22.96 19.03 41.14 4.26
1933 1944 2.435069 AGACAGCATAATGAGCTCAGCT 59.565 45.455 22.96 20.98 41.14 4.24
1934 1945 3.640498 AGACAGCATAATGAGCTCAGCTA 59.360 43.478 23.21 16.71 41.14 3.32
1935 1946 3.989167 GACAGCATAATGAGCTCAGCTAG 59.011 47.826 23.21 19.26 41.14 3.42
1945 1956 4.842292 TCAGCTAGCTGATTGGCG 57.158 55.556 37.64 15.70 46.80 5.69
1946 1957 1.144716 TCAGCTAGCTGATTGGCGG 59.855 57.895 37.64 14.97 46.80 6.13
1947 1958 1.890979 CAGCTAGCTGATTGGCGGG 60.891 63.158 36.47 8.72 46.30 6.13
1948 1959 2.190578 GCTAGCTGATTGGCGGGT 59.809 61.111 7.70 0.00 37.29 5.28
1949 1960 1.048724 AGCTAGCTGATTGGCGGGTA 61.049 55.000 18.57 0.00 37.29 3.69
1950 1961 0.179056 GCTAGCTGATTGGCGGGTAA 60.179 55.000 7.70 0.00 35.56 2.85
1951 1962 1.543429 GCTAGCTGATTGGCGGGTAAT 60.543 52.381 7.70 0.00 35.56 1.89
1952 1963 2.851195 CTAGCTGATTGGCGGGTAATT 58.149 47.619 0.00 0.00 35.56 1.40
1953 1964 1.392589 AGCTGATTGGCGGGTAATTG 58.607 50.000 0.00 0.00 37.29 2.32
1954 1965 0.249031 GCTGATTGGCGGGTAATTGC 60.249 55.000 0.00 0.00 0.00 3.56
1955 1966 1.392589 CTGATTGGCGGGTAATTGCT 58.607 50.000 0.00 0.00 0.00 3.91
1956 1967 1.334869 CTGATTGGCGGGTAATTGCTC 59.665 52.381 0.00 0.00 0.00 4.26
1957 1968 0.668535 GATTGGCGGGTAATTGCTCC 59.331 55.000 0.00 0.00 0.00 4.70
2027 2038 0.472471 TTTGGAGAAGCCGTTGAGGT 59.528 50.000 0.00 0.00 43.70 3.85
2030 2041 1.371558 GAGAAGCCGTTGAGGTGGT 59.628 57.895 0.00 0.00 43.70 4.16
2047 2058 0.179045 GGTGGCCGATTATGCTGACT 60.179 55.000 0.00 0.00 0.00 3.41
2090 2104 5.710099 GCCAATTCCCGATTAAATATCTGGA 59.290 40.000 0.00 0.00 31.04 3.86
2124 2138 0.179076 ATCGGCGTCTCATCATTGCA 60.179 50.000 6.85 0.00 0.00 4.08
2172 2186 5.180117 GCTAGAGAAATGTTTGAGCAGTTGA 59.820 40.000 0.00 0.00 0.00 3.18
2224 2238 5.008217 CGGTTGGTTTTGATTAACTCTGTCA 59.992 40.000 0.00 0.00 0.00 3.58
2273 2287 4.867086 TCTTTCTTCCAACTCCCAAAAGT 58.133 39.130 0.00 0.00 0.00 2.66
2284 2298 0.675633 CCCAAAAGTGGTCCTGCAAG 59.324 55.000 0.00 0.00 44.30 4.01
2335 2349 4.705110 TGACAAGGAGATGGTGAAAAGA 57.295 40.909 0.00 0.00 0.00 2.52
2369 2383 4.076394 GTTGGCCAAATAGAGTGTGGTTA 58.924 43.478 22.47 0.00 34.71 2.85
2370 2384 4.374689 TGGCCAAATAGAGTGTGGTTAA 57.625 40.909 0.61 0.00 34.71 2.01
2371 2385 4.929479 TGGCCAAATAGAGTGTGGTTAAT 58.071 39.130 0.61 0.00 34.71 1.40
2372 2386 5.329399 TGGCCAAATAGAGTGTGGTTAATT 58.671 37.500 0.61 0.00 34.71 1.40
2387 2401 6.098409 TGTGGTTAATTTGTAGGCCAAAAGAA 59.902 34.615 5.01 0.00 45.72 2.52
2415 2430 2.621407 GGCCTTGGAATTCATGACCTGA 60.621 50.000 7.93 0.00 0.00 3.86
2418 2433 4.021192 GCCTTGGAATTCATGACCTGAAAA 60.021 41.667 7.93 0.00 46.62 2.29
2470 2488 7.660208 GTGGTTTAAACTTCTTACTGAGGATGA 59.340 37.037 17.50 0.00 0.00 2.92
2524 2542 1.566018 GGTCAAAAGGCGGTGTCTCG 61.566 60.000 0.00 0.00 0.00 4.04
2534 2552 1.498865 CGGTGTCTCGGGCATATTGC 61.499 60.000 0.00 0.00 44.08 3.56
2615 2633 4.142687 CGCTTTGGGTCTTTCACGATAAAT 60.143 41.667 0.00 0.00 0.00 1.40
2622 2640 4.332819 GGTCTTTCACGATAAATGACAGGG 59.667 45.833 0.00 0.00 0.00 4.45
2623 2641 4.935808 GTCTTTCACGATAAATGACAGGGT 59.064 41.667 0.00 0.00 0.00 4.34
2624 2642 5.063564 GTCTTTCACGATAAATGACAGGGTC 59.936 44.000 0.00 0.00 0.00 4.46
2626 2644 2.159156 TCACGATAAATGACAGGGTCGG 60.159 50.000 0.00 0.00 34.95 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1283 1294 4.217510 TGGCTGCCAAATATTGAGCTTAT 58.782 39.130 21.08 0.00 32.75 1.73
1526 1537 4.541973 TGTCTATGAGCTGAAGCAAAGA 57.458 40.909 4.90 0.00 45.16 2.52
1682 1693 5.090375 TTGTTTTCAAGGCACACACTTGTG 61.090 41.667 7.84 7.84 44.19 3.33
1683 1694 2.560542 TGTTTTCAAGGCACACACTTGT 59.439 40.909 5.24 0.00 44.29 3.16
1684 1695 3.229276 TGTTTTCAAGGCACACACTTG 57.771 42.857 0.00 0.00 45.08 3.16
1685 1696 3.951775 TTGTTTTCAAGGCACACACTT 57.048 38.095 0.00 0.00 34.60 3.16
1686 1697 4.470334 AATTGTTTTCAAGGCACACACT 57.530 36.364 0.00 0.00 43.41 3.55
1687 1698 5.578727 TGTAAATTGTTTTCAAGGCACACAC 59.421 36.000 0.00 0.00 43.41 3.82
1688 1699 5.724328 TGTAAATTGTTTTCAAGGCACACA 58.276 33.333 0.00 0.00 43.41 3.72
1689 1700 5.810074 ACTGTAAATTGTTTTCAAGGCACAC 59.190 36.000 0.00 0.00 43.41 3.82
1690 1701 5.809562 CACTGTAAATTGTTTTCAAGGCACA 59.190 36.000 0.00 0.00 43.41 4.57
1691 1702 6.039616 TCACTGTAAATTGTTTTCAAGGCAC 58.960 36.000 0.00 0.00 43.41 5.01
1692 1703 6.214191 TCACTGTAAATTGTTTTCAAGGCA 57.786 33.333 0.00 0.00 43.41 4.75
1693 1704 6.756542 AGTTCACTGTAAATTGTTTTCAAGGC 59.243 34.615 0.00 0.00 43.41 4.35
1694 1705 9.965824 ATAGTTCACTGTAAATTGTTTTCAAGG 57.034 29.630 0.00 0.00 43.41 3.61
1722 1733 6.928492 AGAAGCTCGCCAATTTATTTGAAAAA 59.072 30.769 0.00 0.00 37.53 1.94
1723 1734 6.365789 CAGAAGCTCGCCAATTTATTTGAAAA 59.634 34.615 0.00 0.00 37.53 2.29
1724 1735 5.863397 CAGAAGCTCGCCAATTTATTTGAAA 59.137 36.000 0.00 0.00 37.53 2.69
1725 1736 5.401550 CAGAAGCTCGCCAATTTATTTGAA 58.598 37.500 0.00 0.00 37.53 2.69
1726 1737 4.142403 CCAGAAGCTCGCCAATTTATTTGA 60.142 41.667 0.00 0.00 37.53 2.69
1727 1738 4.107622 CCAGAAGCTCGCCAATTTATTTG 58.892 43.478 0.00 0.00 34.93 2.32
1728 1739 3.763897 ACCAGAAGCTCGCCAATTTATTT 59.236 39.130 0.00 0.00 0.00 1.40
1729 1740 3.356290 ACCAGAAGCTCGCCAATTTATT 58.644 40.909 0.00 0.00 0.00 1.40
1730 1741 3.004752 ACCAGAAGCTCGCCAATTTAT 57.995 42.857 0.00 0.00 0.00 1.40
1731 1742 2.489938 ACCAGAAGCTCGCCAATTTA 57.510 45.000 0.00 0.00 0.00 1.40
1732 1743 2.489938 TACCAGAAGCTCGCCAATTT 57.510 45.000 0.00 0.00 0.00 1.82
1733 1744 2.717639 ATACCAGAAGCTCGCCAATT 57.282 45.000 0.00 0.00 0.00 2.32
1734 1745 2.717639 AATACCAGAAGCTCGCCAAT 57.282 45.000 0.00 0.00 0.00 3.16
1735 1746 3.838244 ATAATACCAGAAGCTCGCCAA 57.162 42.857 0.00 0.00 0.00 4.52
1736 1747 3.838244 AATAATACCAGAAGCTCGCCA 57.162 42.857 0.00 0.00 0.00 5.69
1737 1748 6.803154 ATTTAATAATACCAGAAGCTCGCC 57.197 37.500 0.00 0.00 0.00 5.54
1747 1758 9.439500 GCCAGAACGGTATATTTAATAATACCA 57.561 33.333 19.30 0.00 39.08 3.25
1748 1759 8.886719 GGCCAGAACGGTATATTTAATAATACC 58.113 37.037 0.00 13.27 36.97 2.73
1749 1760 9.662947 AGGCCAGAACGGTATATTTAATAATAC 57.337 33.333 5.01 1.01 36.97 1.89
1754 1765 8.983702 TTTTAGGCCAGAACGGTATATTTAAT 57.016 30.769 5.01 0.00 36.97 1.40
1755 1766 8.804912 TTTTTAGGCCAGAACGGTATATTTAA 57.195 30.769 5.01 0.00 36.97 1.52
1756 1767 8.266473 TCTTTTTAGGCCAGAACGGTATATTTA 58.734 33.333 5.01 0.00 36.97 1.40
1757 1768 7.114095 TCTTTTTAGGCCAGAACGGTATATTT 58.886 34.615 5.01 0.00 36.97 1.40
1758 1769 6.655930 TCTTTTTAGGCCAGAACGGTATATT 58.344 36.000 5.01 0.00 36.97 1.28
1759 1770 6.243216 TCTTTTTAGGCCAGAACGGTATAT 57.757 37.500 5.01 0.00 36.97 0.86
1760 1771 5.680594 TCTTTTTAGGCCAGAACGGTATA 57.319 39.130 5.01 0.00 36.97 1.47
1761 1772 4.563140 TCTTTTTAGGCCAGAACGGTAT 57.437 40.909 5.01 0.00 36.97 2.73
1762 1773 4.040706 TCTTCTTTTTAGGCCAGAACGGTA 59.959 41.667 5.01 0.00 36.97 4.02
1763 1774 2.943036 TCTTTTTAGGCCAGAACGGT 57.057 45.000 5.01 0.00 36.97 4.83
1764 1775 3.408634 TCTTCTTTTTAGGCCAGAACGG 58.591 45.455 5.01 0.00 38.11 4.44
1765 1776 5.432885 TTTCTTCTTTTTAGGCCAGAACG 57.567 39.130 5.01 0.00 0.00 3.95
1766 1777 9.929180 ATATTTTTCTTCTTTTTAGGCCAGAAC 57.071 29.630 5.01 0.00 0.00 3.01
1768 1779 8.749354 GGATATTTTTCTTCTTTTTAGGCCAGA 58.251 33.333 5.01 0.00 0.00 3.86
1769 1780 8.753133 AGGATATTTTTCTTCTTTTTAGGCCAG 58.247 33.333 5.01 0.00 0.00 4.85
1770 1781 8.664669 AGGATATTTTTCTTCTTTTTAGGCCA 57.335 30.769 5.01 0.00 0.00 5.36
1771 1782 9.944376 AAAGGATATTTTTCTTCTTTTTAGGCC 57.056 29.630 0.00 0.00 0.00 5.19
1790 1801 9.739737 ACCTATCCTAAGTTCCTAAAAAGGATA 57.260 33.333 8.25 8.25 42.43 2.59
1791 1802 8.640033 ACCTATCCTAAGTTCCTAAAAAGGAT 57.360 34.615 6.87 6.87 44.16 3.24
1792 1803 8.458951 AACCTATCCTAAGTTCCTAAAAAGGA 57.541 34.615 0.00 0.00 37.52 3.36
1793 1804 8.957466 CAAACCTATCCTAAGTTCCTAAAAAGG 58.043 37.037 0.00 0.00 0.00 3.11
1794 1805 9.734984 TCAAACCTATCCTAAGTTCCTAAAAAG 57.265 33.333 0.00 0.00 0.00 2.27
1796 1807 9.681062 CATCAAACCTATCCTAAGTTCCTAAAA 57.319 33.333 0.00 0.00 0.00 1.52
1797 1808 9.053472 TCATCAAACCTATCCTAAGTTCCTAAA 57.947 33.333 0.00 0.00 0.00 1.85
1798 1809 8.618240 TCATCAAACCTATCCTAAGTTCCTAA 57.382 34.615 0.00 0.00 0.00 2.69
1799 1810 8.618240 TTCATCAAACCTATCCTAAGTTCCTA 57.382 34.615 0.00 0.00 0.00 2.94
1800 1811 7.510675 TTCATCAAACCTATCCTAAGTTCCT 57.489 36.000 0.00 0.00 0.00 3.36
1801 1812 8.459635 GTTTTCATCAAACCTATCCTAAGTTCC 58.540 37.037 0.00 0.00 39.22 3.62
1820 1831 1.468520 CAACGGCGAGATGGTTTTCAT 59.531 47.619 16.62 0.00 39.13 2.57
1821 1832 0.871722 CAACGGCGAGATGGTTTTCA 59.128 50.000 16.62 0.00 0.00 2.69
1822 1833 0.168128 CCAACGGCGAGATGGTTTTC 59.832 55.000 16.62 0.00 37.93 2.29
1823 1834 0.250553 TCCAACGGCGAGATGGTTTT 60.251 50.000 16.62 0.00 42.73 2.43
1824 1835 0.035439 ATCCAACGGCGAGATGGTTT 60.035 50.000 16.62 8.43 42.73 3.27
1825 1836 0.462047 GATCCAACGGCGAGATGGTT 60.462 55.000 16.62 13.63 42.73 3.67
1826 1837 1.144057 GATCCAACGGCGAGATGGT 59.856 57.895 16.62 9.50 42.73 3.55
1827 1838 0.461870 TTGATCCAACGGCGAGATGG 60.462 55.000 16.62 18.63 43.45 3.51
1828 1839 1.368641 TTTGATCCAACGGCGAGATG 58.631 50.000 16.62 9.57 0.00 2.90
1829 1840 2.332063 ATTTGATCCAACGGCGAGAT 57.668 45.000 16.62 12.82 0.00 2.75
1830 1841 2.107950 AATTTGATCCAACGGCGAGA 57.892 45.000 16.62 7.79 0.00 4.04
1831 1842 2.919666 AAATTTGATCCAACGGCGAG 57.080 45.000 16.62 5.37 0.00 5.03
1832 1843 3.754323 AGTTAAATTTGATCCAACGGCGA 59.246 39.130 16.62 0.00 0.00 5.54
1833 1844 4.091453 AGTTAAATTTGATCCAACGGCG 57.909 40.909 4.80 4.80 0.00 6.46
1834 1845 4.862574 GGAAGTTAAATTTGATCCAACGGC 59.137 41.667 0.00 0.00 0.00 5.68
1835 1846 5.185056 AGGGAAGTTAAATTTGATCCAACGG 59.815 40.000 0.00 0.00 0.00 4.44
1836 1847 6.267496 AGGGAAGTTAAATTTGATCCAACG 57.733 37.500 0.00 0.00 0.00 4.10
1837 1848 8.575649 TCTAGGGAAGTTAAATTTGATCCAAC 57.424 34.615 0.00 0.00 0.00 3.77
1838 1849 9.020731 GTTCTAGGGAAGTTAAATTTGATCCAA 57.979 33.333 0.00 0.00 31.46 3.53
1839 1850 8.390921 AGTTCTAGGGAAGTTAAATTTGATCCA 58.609 33.333 0.00 0.00 31.68 3.41
1840 1851 8.809468 AGTTCTAGGGAAGTTAAATTTGATCC 57.191 34.615 0.00 3.24 31.68 3.36
1846 1857 9.516546 CCAAGTTAGTTCTAGGGAAGTTAAATT 57.483 33.333 0.00 0.00 36.59 1.82
1847 1858 8.887393 TCCAAGTTAGTTCTAGGGAAGTTAAAT 58.113 33.333 0.00 0.00 36.59 1.40
1848 1859 8.266363 TCCAAGTTAGTTCTAGGGAAGTTAAA 57.734 34.615 0.00 0.00 36.59 1.52
1849 1860 7.860649 TCCAAGTTAGTTCTAGGGAAGTTAA 57.139 36.000 0.00 0.00 36.59 2.01
1850 1861 9.725206 ATATCCAAGTTAGTTCTAGGGAAGTTA 57.275 33.333 0.00 0.00 36.59 2.24
1851 1862 6.954352 ATCCAAGTTAGTTCTAGGGAAGTT 57.046 37.500 0.00 0.00 36.59 2.66
1852 1863 8.068733 AGATATCCAAGTTAGTTCTAGGGAAGT 58.931 37.037 0.00 0.00 38.51 3.01
1853 1864 8.485578 AGATATCCAAGTTAGTTCTAGGGAAG 57.514 38.462 0.00 0.00 31.46 3.46
1854 1865 8.855804 AAGATATCCAAGTTAGTTCTAGGGAA 57.144 34.615 0.00 0.00 0.00 3.97
1855 1866 8.480133 GAAGATATCCAAGTTAGTTCTAGGGA 57.520 38.462 0.00 0.00 0.00 4.20
1876 1887 9.131791 GGGCAAGACAAATAAATATTAGGAAGA 57.868 33.333 0.00 0.00 0.00 2.87
1877 1888 8.912988 TGGGCAAGACAAATAAATATTAGGAAG 58.087 33.333 0.00 0.00 0.00 3.46
1878 1889 8.830915 TGGGCAAGACAAATAAATATTAGGAA 57.169 30.769 0.00 0.00 0.00 3.36
1887 1898 9.868277 CTTAAATGTATGGGCAAGACAAATAAA 57.132 29.630 0.00 0.00 0.00 1.40
1888 1899 9.249053 TCTTAAATGTATGGGCAAGACAAATAA 57.751 29.630 0.00 0.00 0.00 1.40
1889 1900 8.682710 GTCTTAAATGTATGGGCAAGACAAATA 58.317 33.333 0.00 0.00 40.85 1.40
1890 1901 7.178274 TGTCTTAAATGTATGGGCAAGACAAAT 59.822 33.333 11.40 0.00 45.19 2.32
1891 1902 6.491745 TGTCTTAAATGTATGGGCAAGACAAA 59.508 34.615 11.40 0.00 45.19 2.83
1892 1903 6.007076 TGTCTTAAATGTATGGGCAAGACAA 58.993 36.000 11.40 0.00 45.19 3.18
1893 1904 5.565509 TGTCTTAAATGTATGGGCAAGACA 58.434 37.500 10.10 10.10 45.68 3.41
1894 1905 5.449177 GCTGTCTTAAATGTATGGGCAAGAC 60.449 44.000 5.54 5.54 41.30 3.01
1895 1906 4.640201 GCTGTCTTAAATGTATGGGCAAGA 59.360 41.667 0.00 0.00 0.00 3.02
1896 1907 4.398988 TGCTGTCTTAAATGTATGGGCAAG 59.601 41.667 0.00 0.00 0.00 4.01
1897 1908 4.339748 TGCTGTCTTAAATGTATGGGCAA 58.660 39.130 0.00 0.00 0.00 4.52
1898 1909 3.961849 TGCTGTCTTAAATGTATGGGCA 58.038 40.909 0.00 0.00 0.00 5.36
1899 1910 6.633500 TTATGCTGTCTTAAATGTATGGGC 57.367 37.500 0.00 0.00 0.00 5.36
1900 1911 8.394971 TCATTATGCTGTCTTAAATGTATGGG 57.605 34.615 0.00 0.00 0.00 4.00
1901 1912 8.019669 GCTCATTATGCTGTCTTAAATGTATGG 58.980 37.037 0.00 0.00 0.00 2.74
1902 1913 8.781196 AGCTCATTATGCTGTCTTAAATGTATG 58.219 33.333 0.00 0.00 39.56 2.39
1903 1914 8.915057 AGCTCATTATGCTGTCTTAAATGTAT 57.085 30.769 0.00 0.00 39.56 2.29
1904 1915 7.986889 TGAGCTCATTATGCTGTCTTAAATGTA 59.013 33.333 13.74 0.00 41.30 2.29
1905 1916 6.825213 TGAGCTCATTATGCTGTCTTAAATGT 59.175 34.615 13.74 0.00 41.30 2.71
1906 1917 7.255491 TGAGCTCATTATGCTGTCTTAAATG 57.745 36.000 13.74 0.00 41.30 2.32
1907 1918 6.017275 GCTGAGCTCATTATGCTGTCTTAAAT 60.017 38.462 18.63 0.00 41.30 1.40
1908 1919 5.295292 GCTGAGCTCATTATGCTGTCTTAAA 59.705 40.000 18.63 0.00 41.30 1.52
1909 1920 4.813161 GCTGAGCTCATTATGCTGTCTTAA 59.187 41.667 18.63 0.00 41.30 1.85
1910 1921 4.100653 AGCTGAGCTCATTATGCTGTCTTA 59.899 41.667 23.09 0.00 41.30 2.10
1911 1922 3.118334 AGCTGAGCTCATTATGCTGTCTT 60.118 43.478 23.09 3.51 41.30 3.01
1912 1923 2.435069 AGCTGAGCTCATTATGCTGTCT 59.565 45.455 23.09 7.44 41.30 3.41
1913 1924 2.836262 AGCTGAGCTCATTATGCTGTC 58.164 47.619 23.09 5.59 41.30 3.51
1914 1925 3.992643 CTAGCTGAGCTCATTATGCTGT 58.007 45.455 28.86 13.30 41.30 4.40
1929 1940 1.890979 CCCGCCAATCAGCTAGCTG 60.891 63.158 34.48 34.48 44.86 4.24
1930 1941 1.048724 TACCCGCCAATCAGCTAGCT 61.049 55.000 12.68 12.68 0.00 3.32
1931 1942 0.179056 TTACCCGCCAATCAGCTAGC 60.179 55.000 6.62 6.62 0.00 3.42
1932 1943 2.549754 CAATTACCCGCCAATCAGCTAG 59.450 50.000 0.00 0.00 0.00 3.42
1933 1944 2.571212 CAATTACCCGCCAATCAGCTA 58.429 47.619 0.00 0.00 0.00 3.32
1934 1945 1.392589 CAATTACCCGCCAATCAGCT 58.607 50.000 0.00 0.00 0.00 4.24
1935 1946 0.249031 GCAATTACCCGCCAATCAGC 60.249 55.000 0.00 0.00 0.00 4.26
1936 1947 1.334869 GAGCAATTACCCGCCAATCAG 59.665 52.381 0.00 0.00 0.00 2.90
1937 1948 1.388547 GAGCAATTACCCGCCAATCA 58.611 50.000 0.00 0.00 0.00 2.57
1938 1949 0.668535 GGAGCAATTACCCGCCAATC 59.331 55.000 0.00 0.00 0.00 2.67
1939 1950 0.033601 TGGAGCAATTACCCGCCAAT 60.034 50.000 0.00 0.00 0.00 3.16
1940 1951 0.679640 CTGGAGCAATTACCCGCCAA 60.680 55.000 0.00 0.00 30.50 4.52
1941 1952 1.077787 CTGGAGCAATTACCCGCCA 60.078 57.895 0.00 0.00 0.00 5.69
1942 1953 2.481471 GCTGGAGCAATTACCCGCC 61.481 63.158 0.00 0.00 41.59 6.13
1943 1954 3.111038 GCTGGAGCAATTACCCGC 58.889 61.111 0.00 0.00 41.59 6.13
1953 1964 1.648467 GACCCGACATTTGCTGGAGC 61.648 60.000 0.00 0.00 42.50 4.70
1954 1965 0.036010 AGACCCGACATTTGCTGGAG 60.036 55.000 0.00 0.00 0.00 3.86
1955 1966 0.400213 AAGACCCGACATTTGCTGGA 59.600 50.000 0.00 0.00 0.00 3.86
1956 1967 2.107950 TAAGACCCGACATTTGCTGG 57.892 50.000 0.00 0.00 0.00 4.85
1957 1968 4.497473 TTTTAAGACCCGACATTTGCTG 57.503 40.909 0.00 0.00 0.00 4.41
2007 2018 0.875059 CCTCAACGGCTTCTCCAAAC 59.125 55.000 0.00 0.00 34.01 2.93
2027 2038 0.463654 GTCAGCATAATCGGCCACCA 60.464 55.000 2.24 0.00 0.00 4.17
2030 2041 1.065491 ACAAGTCAGCATAATCGGCCA 60.065 47.619 2.24 0.00 0.00 5.36
2047 2058 0.383590 CCATGTGTGCAACCGAACAA 59.616 50.000 0.00 0.00 34.36 2.83
2117 2131 2.089201 CATGCTTCCACTCTGCAATGA 58.911 47.619 0.00 0.00 40.24 2.57
2124 2138 3.030291 CTCCTCTACATGCTTCCACTCT 58.970 50.000 0.00 0.00 0.00 3.24
2172 2186 4.374399 CAACTGAGAGCAATTTGCCTTTT 58.626 39.130 17.51 0.00 46.52 2.27
2248 2262 4.788925 TTGGGAGTTGGAAGAAAGAGAA 57.211 40.909 0.00 0.00 0.00 2.87
2284 2298 6.732896 TCTGGATCTAAAATAGTCCAGTCC 57.267 41.667 21.76 9.82 44.87 3.85
2316 2330 6.790232 TTTTTCTTTTCACCATCTCCTTGT 57.210 33.333 0.00 0.00 0.00 3.16
2371 2385 4.027437 ACCTTGTTCTTTTGGCCTACAAA 58.973 39.130 3.32 0.00 46.82 2.83
2372 2386 3.383185 CACCTTGTTCTTTTGGCCTACAA 59.617 43.478 3.32 4.34 37.28 2.41
2415 2430 5.198602 AGTAGGGCCTCATTCTTGATTTT 57.801 39.130 10.74 0.00 0.00 1.82
2418 2433 4.971924 ACTAAGTAGGGCCTCATTCTTGAT 59.028 41.667 10.74 1.62 0.00 2.57
2524 2542 1.134729 CACCAGGTTTGCAATATGCCC 60.135 52.381 0.00 0.00 44.23 5.36
2534 2552 0.532862 AGTGCGAGTCACCAGGTTTG 60.533 55.000 0.00 0.00 46.81 2.93
2564 2582 5.012239 AGATGTTTCTTTGCTGCCATTAGA 58.988 37.500 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.