Multiple sequence alignment - TraesCS1B01G453800

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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 TraesCS1B01G453800 chr1B 100.000 2627 0 0 1 2627 669918193 669920819 0.000000e+00 4852.0
1 TraesCS1B01G453800 chr1B 99.285 1678 10 1 1 1678 418167226 418165551 0.000000e+00 3031.0
2 TraesCS1B01G453800 chr3B 99.463 1677 9 0 1 1677 773547012 773548688 0.000000e+00 3048.0
3 TraesCS1B01G453800 chr5A 99.404 1678 10 0 1 1678 536712256 536710579 0.000000e+00 3044.0
4 TraesCS1B01G453800 chr7A 99.225 1677 11 1 1 1675 30716182 30714506 0.000000e+00 3024.0
5 TraesCS1B01G453800 chr7A 94.620 1301 66 3 377 1674 667967885 667966586 0.000000e+00 2012.0
6 TraesCS1B01G453800 chr7B 97.735 1678 34 2 1 1675 63493086 63494762 0.000000e+00 2885.0
7 TraesCS1B01G453800 chr2A 96.673 1683 54 2 3 1685 40957567 40955887 0.000000e+00 2796.0
8 TraesCS1B01G453800 chr2A 96.465 1358 47 1 325 1681 722079736 722078379 0.000000e+00 2241.0
9 TraesCS1B01G453800 chr2A 83.833 600 97 0 1 600 407750224 407750823 2.930000e-159 571.0
10 TraesCS1B01G453800 chr2A 95.527 313 13 1 1 313 722093048 722092737 1.400000e-137 499.0
11 TraesCS1B01G453800 chr1A 94.212 1676 89 6 1 1676 592501710 592500043 0.000000e+00 2551.0
12 TraesCS1B01G453800 chr1D 91.125 800 42 9 1847 2627 481546859 481547648 0.000000e+00 1057.0
13 TraesCS1B01G453800 chr1D 79.121 273 23 8 2111 2375 481461897 481462143 9.730000e-35 158.0
14 TraesCS1B01G453800 chr1D 82.353 187 19 5 1766 1941 391290582 391290399 1.630000e-32 150.0
15 TraesCS1B01G453800 chr1D 77.358 265 38 13 2113 2375 481454657 481454413 1.270000e-28 137.0
16 TraesCS1B01G453800 chr1D 96.970 33 1 0 2369 2401 481462187 481462219 3.650000e-04 56.5
17 TraesCS1B01G453800 chr6B 77.511 1623 345 20 3 1615 702206114 702204502 0.000000e+00 957.0
18 TraesCS1B01G453800 chr3A 85.714 56 8 0 1889 1944 430338953 430338898 2.820000e-05 60.2


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 TraesCS1B01G453800 chr1B 669918193 669920819 2626 False 4852 4852 100.000 1 2627 1 chr1B.!!$F1 2626
1 TraesCS1B01G453800 chr1B 418165551 418167226 1675 True 3031 3031 99.285 1 1678 1 chr1B.!!$R1 1677
2 TraesCS1B01G453800 chr3B 773547012 773548688 1676 False 3048 3048 99.463 1 1677 1 chr3B.!!$F1 1676
3 TraesCS1B01G453800 chr5A 536710579 536712256 1677 True 3044 3044 99.404 1 1678 1 chr5A.!!$R1 1677
4 TraesCS1B01G453800 chr7A 30714506 30716182 1676 True 3024 3024 99.225 1 1675 1 chr7A.!!$R1 1674
5 TraesCS1B01G453800 chr7A 667966586 667967885 1299 True 2012 2012 94.620 377 1674 1 chr7A.!!$R2 1297
6 TraesCS1B01G453800 chr7B 63493086 63494762 1676 False 2885 2885 97.735 1 1675 1 chr7B.!!$F1 1674
7 TraesCS1B01G453800 chr2A 40955887 40957567 1680 True 2796 2796 96.673 3 1685 1 chr2A.!!$R1 1682
8 TraesCS1B01G453800 chr2A 722078379 722079736 1357 True 2241 2241 96.465 325 1681 1 chr2A.!!$R2 1356
9 TraesCS1B01G453800 chr2A 407750224 407750823 599 False 571 571 83.833 1 600 1 chr2A.!!$F1 599
10 TraesCS1B01G453800 chr1A 592500043 592501710 1667 True 2551 2551 94.212 1 1676 1 chr1A.!!$R1 1675
11 TraesCS1B01G453800 chr1D 481546859 481547648 789 False 1057 1057 91.125 1847 2627 1 chr1D.!!$F1 780
12 TraesCS1B01G453800 chr6B 702204502 702206114 1612 True 957 957 77.511 3 1615 1 chr6B.!!$R1 1612

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
133 134 1.9097 ATCTGCTTTTTGGGCTTCGA 58.09 45.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1710 0.105194 TGGGAGGGACTGACAGAACA 60.105 55.0 10.08 0.0 41.55 3.18 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
133 134 1.909700 ATCTGCTTTTTGGGCTTCGA 58.090 45.000 0.00 0.00 0.00 3.71
1250 1259 4.348486 ACTTCTCCTCTACATGCAGAAGA 58.652 43.478 12.73 7.73 41.77 2.87
1580 1591 3.577667 CTGTGCTGTCTCTTCTCTCAAG 58.422 50.000 0.00 0.00 0.00 3.02
1692 1703 3.036431 AAAAAGAGGCCGGGAACAG 57.964 52.632 2.18 0.00 0.00 3.16
1693 1704 0.539669 AAAAAGAGGCCGGGAACAGG 60.540 55.000 2.18 0.00 0.00 4.00
1694 1705 1.716028 AAAAGAGGCCGGGAACAGGT 61.716 55.000 2.18 0.00 0.00 4.00
1695 1706 2.125766 AAAGAGGCCGGGAACAGGTC 62.126 60.000 2.18 0.00 0.00 3.85
1697 1708 3.003763 AGGCCGGGAACAGGTCTC 61.004 66.667 2.18 0.00 40.09 3.36
1698 1709 4.097361 GGCCGGGAACAGGTCTCC 62.097 72.222 2.18 0.00 0.00 3.71
1699 1710 3.003763 GCCGGGAACAGGTCTCCT 61.004 66.667 2.18 0.00 33.11 3.69
1709 1720 2.739885 CAGGTCTCCTGTTCTGTCAG 57.260 55.000 7.55 0.00 45.82 3.51
1710 1721 1.967066 CAGGTCTCCTGTTCTGTCAGT 59.033 52.381 7.55 0.00 45.82 3.41
1711 1722 2.029470 CAGGTCTCCTGTTCTGTCAGTC 60.029 54.545 7.55 0.00 45.82 3.51
1712 1723 1.273886 GGTCTCCTGTTCTGTCAGTCC 59.726 57.143 0.00 0.00 34.02 3.85
1713 1724 1.273886 GTCTCCTGTTCTGTCAGTCCC 59.726 57.143 0.00 0.00 34.02 4.46
1714 1725 1.148027 TCTCCTGTTCTGTCAGTCCCT 59.852 52.381 0.00 0.00 34.02 4.20
1715 1726 1.548269 CTCCTGTTCTGTCAGTCCCTC 59.452 57.143 0.00 0.00 34.02 4.30
1716 1727 0.610687 CCTGTTCTGTCAGTCCCTCC 59.389 60.000 0.00 0.00 34.02 4.30
1717 1728 0.610687 CTGTTCTGTCAGTCCCTCCC 59.389 60.000 0.00 0.00 0.00 4.30
1718 1729 0.105194 TGTTCTGTCAGTCCCTCCCA 60.105 55.000 0.00 0.00 0.00 4.37
1719 1730 1.280457 GTTCTGTCAGTCCCTCCCAT 58.720 55.000 0.00 0.00 0.00 4.00
1720 1731 1.065854 GTTCTGTCAGTCCCTCCCATG 60.066 57.143 0.00 0.00 0.00 3.66
1721 1732 0.413434 TCTGTCAGTCCCTCCCATGA 59.587 55.000 0.00 0.00 0.00 3.07
1722 1733 1.008815 TCTGTCAGTCCCTCCCATGAT 59.991 52.381 0.00 0.00 0.00 2.45
1723 1734 1.842562 CTGTCAGTCCCTCCCATGATT 59.157 52.381 0.00 0.00 0.00 2.57
1724 1735 1.839994 TGTCAGTCCCTCCCATGATTC 59.160 52.381 0.00 0.00 0.00 2.52
1725 1736 1.141858 GTCAGTCCCTCCCATGATTCC 59.858 57.143 0.00 0.00 0.00 3.01
1726 1737 1.216064 CAGTCCCTCCCATGATTCCA 58.784 55.000 0.00 0.00 0.00 3.53
1727 1738 1.565759 CAGTCCCTCCCATGATTCCAA 59.434 52.381 0.00 0.00 0.00 3.53
1728 1739 2.025037 CAGTCCCTCCCATGATTCCAAA 60.025 50.000 0.00 0.00 0.00 3.28
1729 1740 2.654385 AGTCCCTCCCATGATTCCAAAA 59.346 45.455 0.00 0.00 0.00 2.44
1730 1741 3.026694 GTCCCTCCCATGATTCCAAAAG 58.973 50.000 0.00 0.00 0.00 2.27
1731 1742 2.654385 TCCCTCCCATGATTCCAAAAGT 59.346 45.455 0.00 0.00 0.00 2.66
1732 1743 3.026694 CCCTCCCATGATTCCAAAAGTC 58.973 50.000 0.00 0.00 0.00 3.01
1733 1744 3.026694 CCTCCCATGATTCCAAAAGTCC 58.973 50.000 0.00 0.00 0.00 3.85
1734 1745 3.309410 CCTCCCATGATTCCAAAAGTCCT 60.309 47.826 0.00 0.00 0.00 3.85
1735 1746 3.950395 CTCCCATGATTCCAAAAGTCCTC 59.050 47.826 0.00 0.00 0.00 3.71
1736 1747 3.026694 CCCATGATTCCAAAAGTCCTCC 58.973 50.000 0.00 0.00 0.00 4.30
1737 1748 3.309410 CCCATGATTCCAAAAGTCCTCCT 60.309 47.826 0.00 0.00 0.00 3.69
1738 1749 3.698040 CCATGATTCCAAAAGTCCTCCTG 59.302 47.826 0.00 0.00 0.00 3.86
1739 1750 2.795329 TGATTCCAAAAGTCCTCCTGC 58.205 47.619 0.00 0.00 0.00 4.85
1740 1751 2.095461 GATTCCAAAAGTCCTCCTGCC 58.905 52.381 0.00 0.00 0.00 4.85
1741 1752 0.112412 TTCCAAAAGTCCTCCTGCCC 59.888 55.000 0.00 0.00 0.00 5.36
1742 1753 1.675641 CCAAAAGTCCTCCTGCCCG 60.676 63.158 0.00 0.00 0.00 6.13
1743 1754 1.073199 CAAAAGTCCTCCTGCCCGT 59.927 57.895 0.00 0.00 0.00 5.28
1744 1755 0.323629 CAAAAGTCCTCCTGCCCGTA 59.676 55.000 0.00 0.00 0.00 4.02
1745 1756 0.323957 AAAAGTCCTCCTGCCCGTAC 59.676 55.000 0.00 0.00 0.00 3.67
1746 1757 0.544595 AAAGTCCTCCTGCCCGTACT 60.545 55.000 0.00 0.00 0.00 2.73
1747 1758 0.971447 AAGTCCTCCTGCCCGTACTC 60.971 60.000 0.00 0.00 0.00 2.59
1748 1759 2.043248 TCCTCCTGCCCGTACTCC 60.043 66.667 0.00 0.00 0.00 3.85
1749 1760 3.155167 CCTCCTGCCCGTACTCCC 61.155 72.222 0.00 0.00 0.00 4.30
1750 1761 3.528370 CTCCTGCCCGTACTCCCG 61.528 72.222 0.00 0.00 0.00 5.14
1753 1764 4.814294 CTGCCCGTACTCCCGCAC 62.814 72.222 0.00 0.00 0.00 5.34
1755 1766 4.509737 GCCCGTACTCCCGCACTC 62.510 72.222 0.00 0.00 0.00 3.51
1756 1767 4.189188 CCCGTACTCCCGCACTCG 62.189 72.222 0.00 0.00 0.00 4.18
1757 1768 3.437795 CCGTACTCCCGCACTCGT 61.438 66.667 0.00 0.00 0.00 4.18
1758 1769 2.099831 CGTACTCCCGCACTCGTC 59.900 66.667 0.00 0.00 0.00 4.20
1759 1770 2.099831 GTACTCCCGCACTCGTCG 59.900 66.667 0.00 0.00 0.00 5.12
1760 1771 3.807538 TACTCCCGCACTCGTCGC 61.808 66.667 0.00 0.00 0.00 5.19
1762 1773 2.857575 TACTCCCGCACTCGTCGCTA 62.858 60.000 0.00 0.00 0.00 4.26
1763 1774 3.456431 CTCCCGCACTCGTCGCTAG 62.456 68.421 0.00 0.00 0.00 3.42
1764 1775 4.554363 CCCGCACTCGTCGCTAGG 62.554 72.222 0.00 0.00 0.00 3.02
1765 1776 4.554363 CCGCACTCGTCGCTAGGG 62.554 72.222 0.00 0.00 0.00 3.53
1766 1777 3.812019 CGCACTCGTCGCTAGGGT 61.812 66.667 6.70 0.00 0.00 4.34
1767 1778 2.102553 GCACTCGTCGCTAGGGTC 59.897 66.667 6.70 0.00 0.00 4.46
1768 1779 2.408241 GCACTCGTCGCTAGGGTCT 61.408 63.158 6.70 0.00 0.00 3.85
1769 1780 1.935327 GCACTCGTCGCTAGGGTCTT 61.935 60.000 6.70 0.00 0.00 3.01
1770 1781 0.526662 CACTCGTCGCTAGGGTCTTT 59.473 55.000 6.70 0.00 0.00 2.52
1771 1782 1.067776 CACTCGTCGCTAGGGTCTTTT 60.068 52.381 6.70 0.00 0.00 2.27
1772 1783 1.201880 ACTCGTCGCTAGGGTCTTTTC 59.798 52.381 6.70 0.00 0.00 2.29
1773 1784 1.473278 CTCGTCGCTAGGGTCTTTTCT 59.527 52.381 6.70 0.00 0.00 2.52
1774 1785 2.681848 CTCGTCGCTAGGGTCTTTTCTA 59.318 50.000 6.70 0.00 0.00 2.10
1775 1786 2.681848 TCGTCGCTAGGGTCTTTTCTAG 59.318 50.000 6.70 0.00 36.84 2.43
1776 1787 2.681848 CGTCGCTAGGGTCTTTTCTAGA 59.318 50.000 6.70 0.00 36.08 2.43
1777 1788 3.315749 CGTCGCTAGGGTCTTTTCTAGAT 59.684 47.826 6.70 0.00 36.08 1.98
1778 1789 4.202030 CGTCGCTAGGGTCTTTTCTAGATT 60.202 45.833 6.70 0.00 36.08 2.40
1779 1790 5.044558 GTCGCTAGGGTCTTTTCTAGATTG 58.955 45.833 6.70 0.00 36.08 2.67
1780 1791 4.710375 TCGCTAGGGTCTTTTCTAGATTGT 59.290 41.667 6.70 0.00 36.08 2.71
1781 1792 5.889853 TCGCTAGGGTCTTTTCTAGATTGTA 59.110 40.000 6.70 0.00 36.08 2.41
1782 1793 5.978322 CGCTAGGGTCTTTTCTAGATTGTAC 59.022 44.000 0.00 0.00 36.08 2.90
1783 1794 6.282167 GCTAGGGTCTTTTCTAGATTGTACC 58.718 44.000 0.00 0.00 36.08 3.34
1784 1795 6.098552 GCTAGGGTCTTTTCTAGATTGTACCT 59.901 42.308 12.14 9.78 36.08 3.08
1785 1796 6.954352 AGGGTCTTTTCTAGATTGTACCTT 57.046 37.500 12.14 4.88 34.79 3.50
1786 1797 7.331089 AGGGTCTTTTCTAGATTGTACCTTT 57.669 36.000 12.14 2.69 34.79 3.11
1787 1798 7.756614 AGGGTCTTTTCTAGATTGTACCTTTT 58.243 34.615 12.14 0.95 34.79 2.27
1788 1799 7.883833 AGGGTCTTTTCTAGATTGTACCTTTTC 59.116 37.037 12.14 0.55 34.79 2.29
1789 1800 7.883833 GGGTCTTTTCTAGATTGTACCTTTTCT 59.116 37.037 12.14 0.00 34.79 2.52
1790 1801 9.286170 GGTCTTTTCTAGATTGTACCTTTTCTT 57.714 33.333 0.00 0.00 34.79 2.52
1793 1804 9.813080 CTTTTCTAGATTGTACCTTTTCTTTCG 57.187 33.333 0.00 0.00 0.00 3.46
1794 1805 9.550406 TTTTCTAGATTGTACCTTTTCTTTCGA 57.450 29.630 0.00 0.00 0.00 3.71
1795 1806 8.758633 TTCTAGATTGTACCTTTTCTTTCGAG 57.241 34.615 0.00 0.00 0.00 4.04
1796 1807 7.321153 TCTAGATTGTACCTTTTCTTTCGAGG 58.679 38.462 0.00 0.00 36.62 4.63
1797 1808 5.246307 AGATTGTACCTTTTCTTTCGAGGG 58.754 41.667 0.00 0.00 34.81 4.30
1798 1809 4.426736 TTGTACCTTTTCTTTCGAGGGT 57.573 40.909 0.00 0.00 34.81 4.34
1799 1810 3.999046 TGTACCTTTTCTTTCGAGGGTC 58.001 45.455 0.00 0.00 34.81 4.46
1800 1811 2.165319 ACCTTTTCTTTCGAGGGTCG 57.835 50.000 0.00 0.00 42.10 4.79
1801 1812 1.415289 ACCTTTTCTTTCGAGGGTCGT 59.585 47.619 0.00 0.00 41.35 4.34
1802 1813 1.798813 CCTTTTCTTTCGAGGGTCGTG 59.201 52.381 0.00 0.00 41.35 4.35
1803 1814 2.480845 CTTTTCTTTCGAGGGTCGTGT 58.519 47.619 0.00 0.00 41.35 4.49
1804 1815 2.607631 TTTCTTTCGAGGGTCGTGTT 57.392 45.000 0.00 0.00 41.35 3.32
1805 1816 1.860676 TTCTTTCGAGGGTCGTGTTG 58.139 50.000 0.00 0.00 41.35 3.33
1806 1817 1.034356 TCTTTCGAGGGTCGTGTTGA 58.966 50.000 0.00 0.00 41.35 3.18
1807 1818 1.409790 TCTTTCGAGGGTCGTGTTGAA 59.590 47.619 0.00 0.00 41.35 2.69
1808 1819 1.792949 CTTTCGAGGGTCGTGTTGAAG 59.207 52.381 0.00 0.00 41.35 3.02
1809 1820 0.599204 TTCGAGGGTCGTGTTGAAGC 60.599 55.000 0.00 0.00 41.35 3.86
1810 1821 1.300620 CGAGGGTCGTGTTGAAGCA 60.301 57.895 0.00 0.00 34.72 3.91
1811 1822 1.557443 CGAGGGTCGTGTTGAAGCAC 61.557 60.000 0.00 0.00 34.72 4.40
1812 1823 0.531974 GAGGGTCGTGTTGAAGCACA 60.532 55.000 0.00 0.00 39.19 4.57
1813 1824 0.108585 AGGGTCGTGTTGAAGCACAT 59.891 50.000 0.00 0.00 39.19 3.21
1814 1825 1.346395 AGGGTCGTGTTGAAGCACATA 59.654 47.619 0.00 0.00 39.19 2.29
1815 1826 1.732259 GGGTCGTGTTGAAGCACATAG 59.268 52.381 0.00 0.00 39.19 2.23
1816 1827 1.128692 GGTCGTGTTGAAGCACATAGC 59.871 52.381 0.00 0.00 46.19 2.97
1824 1835 1.139654 TGAAGCACATAGCCCAGCTAG 59.860 52.381 2.41 0.00 44.66 3.42
1825 1836 1.414181 GAAGCACATAGCCCAGCTAGA 59.586 52.381 2.41 0.00 44.66 2.43
1826 1837 1.727062 AGCACATAGCCCAGCTAGAT 58.273 50.000 2.41 0.00 44.66 1.98
1827 1838 2.053244 AGCACATAGCCCAGCTAGATT 58.947 47.619 2.41 0.00 44.66 2.40
1828 1839 2.441001 AGCACATAGCCCAGCTAGATTT 59.559 45.455 2.41 0.00 44.66 2.17
1829 1840 3.117738 AGCACATAGCCCAGCTAGATTTT 60.118 43.478 2.41 0.00 44.66 1.82
1830 1841 3.633986 GCACATAGCCCAGCTAGATTTTT 59.366 43.478 2.41 0.00 44.66 1.94
1831 1842 4.498682 GCACATAGCCCAGCTAGATTTTTG 60.499 45.833 2.41 0.00 44.66 2.44
1832 1843 3.633986 ACATAGCCCAGCTAGATTTTTGC 59.366 43.478 2.41 0.00 44.66 3.68
1833 1844 2.521547 AGCCCAGCTAGATTTTTGCT 57.478 45.000 0.00 0.00 36.99 3.91
1834 1845 2.812658 AGCCCAGCTAGATTTTTGCTT 58.187 42.857 0.00 0.00 36.99 3.91
1835 1846 3.168292 AGCCCAGCTAGATTTTTGCTTT 58.832 40.909 0.00 0.00 36.99 3.51
1836 1847 3.194329 AGCCCAGCTAGATTTTTGCTTTC 59.806 43.478 0.00 0.00 36.99 2.62
1837 1848 3.194329 GCCCAGCTAGATTTTTGCTTTCT 59.806 43.478 0.00 0.00 34.51 2.52
1838 1849 4.322273 GCCCAGCTAGATTTTTGCTTTCTT 60.322 41.667 0.00 0.00 34.51 2.52
1839 1850 5.787380 CCCAGCTAGATTTTTGCTTTCTTT 58.213 37.500 0.00 0.00 34.51 2.52
1840 1851 6.572314 GCCCAGCTAGATTTTTGCTTTCTTTA 60.572 38.462 0.00 0.00 34.51 1.85
1841 1852 7.031975 CCCAGCTAGATTTTTGCTTTCTTTAG 58.968 38.462 0.00 0.00 34.51 1.85
1842 1853 7.094205 CCCAGCTAGATTTTTGCTTTCTTTAGA 60.094 37.037 0.00 0.00 34.51 2.10
1843 1854 8.465201 CCAGCTAGATTTTTGCTTTCTTTAGAT 58.535 33.333 0.00 0.00 34.51 1.98
1844 1855 9.500864 CAGCTAGATTTTTGCTTTCTTTAGATC 57.499 33.333 0.00 0.00 34.51 2.75
1845 1856 9.460019 AGCTAGATTTTTGCTTTCTTTAGATCT 57.540 29.630 0.00 0.00 32.61 2.75
1848 1859 8.641498 AGATTTTTGCTTTCTTTAGATCTGGA 57.359 30.769 5.18 0.00 0.00 3.86
1860 1871 6.368791 TCTTTAGATCTGGAACGTCACATTTG 59.631 38.462 5.18 0.00 0.00 2.32
1880 1891 1.674962 GGCTTGACCAATCTCATGAGC 59.325 52.381 18.36 3.36 38.86 4.26
1881 1892 1.329906 GCTTGACCAATCTCATGAGCG 59.670 52.381 18.36 8.56 0.00 5.03
1891 1902 3.717400 TCTCATGAGCGGAACACTATC 57.283 47.619 18.36 0.00 0.00 2.08
1893 1904 2.363680 CTCATGAGCGGAACACTATCCT 59.636 50.000 10.38 0.00 37.34 3.24
1899 1910 4.891168 TGAGCGGAACACTATCCTACATTA 59.109 41.667 0.00 0.00 37.34 1.90
1901 1912 6.041637 TGAGCGGAACACTATCCTACATTATT 59.958 38.462 0.00 0.00 37.34 1.40
1903 1914 6.706270 AGCGGAACACTATCCTACATTATTTG 59.294 38.462 0.00 0.00 37.34 2.32
1934 1945 5.221441 GCTGAATAAAGTTTGTTTCACCCCT 60.221 40.000 10.20 0.00 0.00 4.79
1935 1946 6.015772 GCTGAATAAAGTTTGTTTCACCCCTA 60.016 38.462 10.20 0.00 0.00 3.53
1976 1987 1.973812 GTTGGGTGCCTCCAGCTTC 60.974 63.158 2.76 0.00 44.23 3.86
1977 1988 2.459969 TTGGGTGCCTCCAGCTTCA 61.460 57.895 0.00 0.00 44.23 3.02
1979 1990 2.360475 GGTGCCTCCAGCTTCACC 60.360 66.667 0.00 0.00 44.23 4.02
1983 1994 2.581354 CCTCCAGCTTCACCCGAG 59.419 66.667 0.00 0.00 0.00 4.63
1997 2008 2.034066 CGAGTGTTGCCCACCCAT 59.966 61.111 0.37 0.00 45.74 4.00
2044 2055 2.615912 GCTTTCAGGCCATGTCTACATC 59.384 50.000 5.01 0.00 33.61 3.06
2052 2063 1.609061 CCATGTCTACATCGGGGATGC 60.609 57.143 5.56 0.00 43.15 3.91
2062 2073 2.036256 GGGGATGCTGCACCAAGT 59.964 61.111 18.44 0.00 0.00 3.16
2071 2082 3.423154 GCACCAAGTTCGAGCCGG 61.423 66.667 0.00 0.00 0.00 6.13
2112 2123 2.125552 CTCGGCTCGCATTCACCA 60.126 61.111 0.00 0.00 0.00 4.17
2123 2134 3.190327 TCGCATTCACCATTACACAAAGG 59.810 43.478 0.00 0.00 0.00 3.11
2134 2145 4.584638 TTACACAAAGGGCATAGACCAT 57.415 40.909 0.00 0.00 29.21 3.55
2157 2168 3.642901 GCATGCAGCAGGAAATGAG 57.357 52.632 14.21 0.00 44.79 2.90
2158 2169 1.100510 GCATGCAGCAGGAAATGAGA 58.899 50.000 14.21 0.00 44.79 3.27
2160 2171 1.063616 CATGCAGCAGGAAATGAGACG 59.936 52.381 0.00 0.00 0.00 4.18
2167 2178 5.532557 CAGCAGGAAATGAGACGATATACA 58.467 41.667 0.00 0.00 0.00 2.29
2174 2185 3.074504 TGAGACGATATACAACACGGC 57.925 47.619 0.00 0.00 0.00 5.68
2180 2191 4.107622 ACGATATACAACACGGCTACAAC 58.892 43.478 0.00 0.00 0.00 3.32
2199 2210 0.540365 CTGGGCAACTTGGGTCACAT 60.540 55.000 0.00 0.00 0.00 3.21
2211 2222 4.852134 TGGGTCACATGACAGAAAATTG 57.148 40.909 13.77 0.00 46.47 2.32
2226 2237 5.399301 CAGAAAATTGCAAACGACGATTTCT 59.601 36.000 1.71 8.32 31.33 2.52
2227 2238 6.577055 CAGAAAATTGCAAACGACGATTTCTA 59.423 34.615 1.71 0.00 31.33 2.10
2228 2239 7.271223 CAGAAAATTGCAAACGACGATTTCTAT 59.729 33.333 1.71 0.00 31.33 1.98
2229 2240 8.447833 AGAAAATTGCAAACGACGATTTCTATA 58.552 29.630 1.71 0.00 31.33 1.31
2270 2281 2.207590 TGCATGAATGAGACGAGATGC 58.792 47.619 0.00 0.00 37.34 3.91
2292 2303 2.639286 CAACTGGGCGCACAAGAC 59.361 61.111 16.01 0.00 0.00 3.01
2307 2318 1.003545 CAAGACAGACGGTTGCAACAG 60.004 52.381 29.55 27.39 0.00 3.16
2328 2339 4.383052 CAGCGGCGTTTTCTATCTATACAG 59.617 45.833 9.37 0.00 0.00 2.74
2475 2501 1.628846 GGTGTAATCCAGACAGGTGGT 59.371 52.381 0.00 0.00 38.88 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1250 1259 2.230750 GCTGCAAAAGAAAGAGCCAGAT 59.769 45.455 0.00 0.00 0.00 2.90
1580 1591 4.983671 ACAAACTCCTGAACCTGAAAAC 57.016 40.909 0.00 0.00 0.00 2.43
1691 1702 2.243810 GACTGACAGAACAGGAGACCT 58.756 52.381 10.08 0.00 41.59 3.85
1692 1703 1.273886 GGACTGACAGAACAGGAGACC 59.726 57.143 10.08 0.00 41.59 3.85
1693 1704 1.273886 GGGACTGACAGAACAGGAGAC 59.726 57.143 10.08 0.00 41.59 3.36
1694 1705 1.148027 AGGGACTGACAGAACAGGAGA 59.852 52.381 10.08 0.00 41.59 3.71
1695 1706 1.548269 GAGGGACTGACAGAACAGGAG 59.452 57.143 10.08 0.00 41.55 3.69
1696 1707 1.633774 GAGGGACTGACAGAACAGGA 58.366 55.000 10.08 0.00 41.55 3.86
1697 1708 0.610687 GGAGGGACTGACAGAACAGG 59.389 60.000 10.08 0.00 41.55 4.00
1698 1709 0.610687 GGGAGGGACTGACAGAACAG 59.389 60.000 10.08 0.00 41.55 3.16
1699 1710 0.105194 TGGGAGGGACTGACAGAACA 60.105 55.000 10.08 0.00 41.55 3.18
1700 1711 1.065854 CATGGGAGGGACTGACAGAAC 60.066 57.143 10.08 2.75 41.55 3.01
1701 1712 1.203300 TCATGGGAGGGACTGACAGAA 60.203 52.381 10.08 0.00 41.55 3.02
1702 1713 0.413434 TCATGGGAGGGACTGACAGA 59.587 55.000 10.08 0.00 41.55 3.41
1703 1714 1.504912 ATCATGGGAGGGACTGACAG 58.495 55.000 0.00 0.00 41.55 3.51
1704 1715 1.839994 GAATCATGGGAGGGACTGACA 59.160 52.381 0.00 0.00 41.55 3.58
1705 1716 1.141858 GGAATCATGGGAGGGACTGAC 59.858 57.143 0.00 0.00 41.55 3.51
1706 1717 1.274358 TGGAATCATGGGAGGGACTGA 60.274 52.381 0.00 0.00 41.55 3.41
1707 1718 1.216064 TGGAATCATGGGAGGGACTG 58.784 55.000 0.00 0.00 41.55 3.51
1709 1720 2.826674 TTTGGAATCATGGGAGGGAC 57.173 50.000 0.00 0.00 0.00 4.46
1710 1721 2.654385 ACTTTTGGAATCATGGGAGGGA 59.346 45.455 0.00 0.00 0.00 4.20
1711 1722 3.026694 GACTTTTGGAATCATGGGAGGG 58.973 50.000 0.00 0.00 0.00 4.30
1712 1723 3.026694 GGACTTTTGGAATCATGGGAGG 58.973 50.000 0.00 0.00 0.00 4.30
1713 1724 3.950395 GAGGACTTTTGGAATCATGGGAG 59.050 47.826 0.00 0.00 0.00 4.30
1714 1725 3.309121 GGAGGACTTTTGGAATCATGGGA 60.309 47.826 0.00 0.00 0.00 4.37
1715 1726 3.026694 GGAGGACTTTTGGAATCATGGG 58.973 50.000 0.00 0.00 0.00 4.00
1716 1727 3.698040 CAGGAGGACTTTTGGAATCATGG 59.302 47.826 0.00 0.00 0.00 3.66
1717 1728 3.129988 GCAGGAGGACTTTTGGAATCATG 59.870 47.826 0.00 0.00 0.00 3.07
1718 1729 3.359950 GCAGGAGGACTTTTGGAATCAT 58.640 45.455 0.00 0.00 0.00 2.45
1719 1730 2.555227 GGCAGGAGGACTTTTGGAATCA 60.555 50.000 0.00 0.00 0.00 2.57
1720 1731 2.095461 GGCAGGAGGACTTTTGGAATC 58.905 52.381 0.00 0.00 0.00 2.52
1721 1732 1.272704 GGGCAGGAGGACTTTTGGAAT 60.273 52.381 0.00 0.00 0.00 3.01
1722 1733 0.112412 GGGCAGGAGGACTTTTGGAA 59.888 55.000 0.00 0.00 0.00 3.53
1723 1734 1.767692 GGGCAGGAGGACTTTTGGA 59.232 57.895 0.00 0.00 0.00 3.53
1724 1735 1.675641 CGGGCAGGAGGACTTTTGG 60.676 63.158 0.00 0.00 0.00 3.28
1725 1736 0.323629 TACGGGCAGGAGGACTTTTG 59.676 55.000 0.00 0.00 0.00 2.44
1726 1737 0.323957 GTACGGGCAGGAGGACTTTT 59.676 55.000 0.00 0.00 0.00 2.27
1727 1738 0.544595 AGTACGGGCAGGAGGACTTT 60.545 55.000 0.00 0.00 0.00 2.66
1728 1739 0.971447 GAGTACGGGCAGGAGGACTT 60.971 60.000 0.00 0.00 0.00 3.01
1729 1740 1.380112 GAGTACGGGCAGGAGGACT 60.380 63.158 0.00 0.00 0.00 3.85
1730 1741 2.424733 GGAGTACGGGCAGGAGGAC 61.425 68.421 0.00 0.00 0.00 3.85
1731 1742 2.043248 GGAGTACGGGCAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
1732 1743 3.155167 GGGAGTACGGGCAGGAGG 61.155 72.222 0.00 0.00 0.00 4.30
1733 1744 3.528370 CGGGAGTACGGGCAGGAG 61.528 72.222 0.00 0.00 0.00 3.69
1736 1747 4.814294 GTGCGGGAGTACGGGCAG 62.814 72.222 3.93 0.00 35.85 4.85
1742 1753 2.099831 CGACGAGTGCGGGAGTAC 59.900 66.667 0.00 0.00 46.44 2.73
1743 1754 2.857575 TAGCGACGAGTGCGGGAGTA 62.858 60.000 0.00 0.00 43.17 2.59
1745 1756 3.456431 CTAGCGACGAGTGCGGGAG 62.456 68.421 0.00 0.00 43.17 4.30
1746 1757 3.506096 CTAGCGACGAGTGCGGGA 61.506 66.667 0.00 0.00 43.17 5.14
1747 1758 4.554363 CCTAGCGACGAGTGCGGG 62.554 72.222 0.00 0.00 43.17 6.13
1748 1759 4.554363 CCCTAGCGACGAGTGCGG 62.554 72.222 0.00 0.00 43.17 5.69
1749 1760 3.736482 GACCCTAGCGACGAGTGCG 62.736 68.421 0.00 0.00 44.79 5.34
1750 1761 1.935327 AAGACCCTAGCGACGAGTGC 61.935 60.000 0.00 0.00 0.00 4.40
1751 1762 0.526662 AAAGACCCTAGCGACGAGTG 59.473 55.000 0.00 0.00 0.00 3.51
1752 1763 1.201880 GAAAAGACCCTAGCGACGAGT 59.798 52.381 0.00 0.00 0.00 4.18
1753 1764 1.473278 AGAAAAGACCCTAGCGACGAG 59.527 52.381 0.00 0.00 0.00 4.18
1754 1765 1.542492 AGAAAAGACCCTAGCGACGA 58.458 50.000 0.00 0.00 0.00 4.20
1755 1766 2.681848 TCTAGAAAAGACCCTAGCGACG 59.318 50.000 0.00 0.00 34.02 5.12
1756 1767 4.922471 ATCTAGAAAAGACCCTAGCGAC 57.078 45.455 0.00 0.00 36.93 5.19
1757 1768 4.710375 ACAATCTAGAAAAGACCCTAGCGA 59.290 41.667 0.00 0.00 36.93 4.93
1758 1769 5.012328 ACAATCTAGAAAAGACCCTAGCG 57.988 43.478 0.00 0.00 36.93 4.26
1759 1770 6.098552 AGGTACAATCTAGAAAAGACCCTAGC 59.901 42.308 0.00 0.00 36.93 3.42
1760 1771 7.663043 AGGTACAATCTAGAAAAGACCCTAG 57.337 40.000 0.00 0.00 36.93 3.02
1761 1772 8.445361 AAAGGTACAATCTAGAAAAGACCCTA 57.555 34.615 0.00 0.00 36.93 3.53
1762 1773 6.954352 AAGGTACAATCTAGAAAAGACCCT 57.046 37.500 0.00 0.00 36.93 4.34
1763 1774 7.883833 AGAAAAGGTACAATCTAGAAAAGACCC 59.116 37.037 0.00 0.00 36.93 4.46
1764 1775 8.850007 AGAAAAGGTACAATCTAGAAAAGACC 57.150 34.615 0.00 2.85 36.93 3.85
1767 1778 9.813080 CGAAAGAAAAGGTACAATCTAGAAAAG 57.187 33.333 0.00 0.00 0.00 2.27
1768 1779 9.550406 TCGAAAGAAAAGGTACAATCTAGAAAA 57.450 29.630 0.00 0.00 37.03 2.29
1769 1780 9.204570 CTCGAAAGAAAAGGTACAATCTAGAAA 57.795 33.333 0.00 0.00 41.32 2.52
1770 1781 7.817962 CCTCGAAAGAAAAGGTACAATCTAGAA 59.182 37.037 0.00 0.00 41.32 2.10
1771 1782 7.321153 CCTCGAAAGAAAAGGTACAATCTAGA 58.679 38.462 0.00 0.00 41.32 2.43
1772 1783 6.535508 CCCTCGAAAGAAAAGGTACAATCTAG 59.464 42.308 0.00 0.00 41.32 2.43
1773 1784 6.013984 ACCCTCGAAAGAAAAGGTACAATCTA 60.014 38.462 0.00 0.00 41.32 1.98
1774 1785 5.221864 ACCCTCGAAAGAAAAGGTACAATCT 60.222 40.000 0.00 0.00 41.32 2.40
1775 1786 5.001874 ACCCTCGAAAGAAAAGGTACAATC 58.998 41.667 0.00 0.00 41.32 2.67
1776 1787 4.981812 ACCCTCGAAAGAAAAGGTACAAT 58.018 39.130 0.00 0.00 41.32 2.71
1777 1788 4.383173 GACCCTCGAAAGAAAAGGTACAA 58.617 43.478 0.00 0.00 41.32 2.41
1778 1789 3.553508 CGACCCTCGAAAGAAAAGGTACA 60.554 47.826 0.00 0.00 43.74 2.90
1779 1790 2.991866 CGACCCTCGAAAGAAAAGGTAC 59.008 50.000 0.00 0.00 43.74 3.34
1780 1791 2.629617 ACGACCCTCGAAAGAAAAGGTA 59.370 45.455 0.00 0.00 43.74 3.08
1781 1792 1.415289 ACGACCCTCGAAAGAAAAGGT 59.585 47.619 0.00 0.00 43.74 3.50
1782 1793 1.798813 CACGACCCTCGAAAGAAAAGG 59.201 52.381 0.00 0.00 43.74 3.11
1783 1794 2.480845 ACACGACCCTCGAAAGAAAAG 58.519 47.619 0.00 0.00 43.74 2.27
1784 1795 2.607631 ACACGACCCTCGAAAGAAAA 57.392 45.000 0.00 0.00 43.74 2.29
1785 1796 2.159071 TCAACACGACCCTCGAAAGAAA 60.159 45.455 0.00 0.00 43.74 2.52
1786 1797 1.409790 TCAACACGACCCTCGAAAGAA 59.590 47.619 0.00 0.00 43.74 2.52
1787 1798 1.034356 TCAACACGACCCTCGAAAGA 58.966 50.000 0.00 0.00 43.74 2.52
1788 1799 1.792949 CTTCAACACGACCCTCGAAAG 59.207 52.381 0.00 0.00 43.74 2.62
1789 1800 1.860676 CTTCAACACGACCCTCGAAA 58.139 50.000 0.00 0.00 43.74 3.46
1790 1801 0.599204 GCTTCAACACGACCCTCGAA 60.599 55.000 0.00 0.00 43.74 3.71
1791 1802 1.006571 GCTTCAACACGACCCTCGA 60.007 57.895 0.00 0.00 43.74 4.04
1792 1803 1.300620 TGCTTCAACACGACCCTCG 60.301 57.895 0.00 0.00 46.93 4.63
1793 1804 0.531974 TGTGCTTCAACACGACCCTC 60.532 55.000 0.00 0.00 43.74 4.30
1794 1805 0.108585 ATGTGCTTCAACACGACCCT 59.891 50.000 0.00 0.00 43.74 4.34
1795 1806 1.732259 CTATGTGCTTCAACACGACCC 59.268 52.381 0.00 0.00 43.74 4.46
1796 1807 1.128692 GCTATGTGCTTCAACACGACC 59.871 52.381 0.00 0.00 43.74 4.79
1797 1808 1.128692 GGCTATGTGCTTCAACACGAC 59.871 52.381 0.00 0.00 43.74 4.34
1798 1809 1.438651 GGCTATGTGCTTCAACACGA 58.561 50.000 0.00 0.00 43.74 4.35
1799 1810 0.447801 GGGCTATGTGCTTCAACACG 59.552 55.000 0.00 0.00 43.74 4.49
1800 1811 1.470098 CTGGGCTATGTGCTTCAACAC 59.530 52.381 0.00 0.00 42.39 3.32
1801 1812 1.825090 CTGGGCTATGTGCTTCAACA 58.175 50.000 0.00 0.00 42.39 3.33
1802 1813 0.453390 GCTGGGCTATGTGCTTCAAC 59.547 55.000 0.00 0.00 42.39 3.18
1803 1814 0.329261 AGCTGGGCTATGTGCTTCAA 59.671 50.000 0.00 0.00 42.39 2.69
1804 1815 1.139654 CTAGCTGGGCTATGTGCTTCA 59.860 52.381 0.00 0.00 40.54 3.02
1805 1816 1.414181 TCTAGCTGGGCTATGTGCTTC 59.586 52.381 0.00 0.00 40.54 3.86
1806 1817 1.500474 TCTAGCTGGGCTATGTGCTT 58.500 50.000 0.00 0.00 40.54 3.91
1807 1818 1.727062 ATCTAGCTGGGCTATGTGCT 58.273 50.000 0.00 0.00 40.54 4.40
1808 1819 2.557920 AATCTAGCTGGGCTATGTGC 57.442 50.000 0.00 0.00 40.54 4.57
1809 1820 4.498682 GCAAAAATCTAGCTGGGCTATGTG 60.499 45.833 0.00 0.00 40.54 3.21
1810 1821 3.633986 GCAAAAATCTAGCTGGGCTATGT 59.366 43.478 0.00 0.00 40.54 2.29
1811 1822 3.887716 AGCAAAAATCTAGCTGGGCTATG 59.112 43.478 0.00 0.00 40.54 2.23
1812 1823 4.176120 AGCAAAAATCTAGCTGGGCTAT 57.824 40.909 0.00 0.00 40.54 2.97
1813 1824 3.652057 AGCAAAAATCTAGCTGGGCTA 57.348 42.857 0.00 0.00 40.44 3.93
1814 1825 2.521547 AGCAAAAATCTAGCTGGGCT 57.478 45.000 0.00 0.00 43.41 5.19
1815 1826 3.194329 AGAAAGCAAAAATCTAGCTGGGC 59.806 43.478 0.00 0.00 38.86 5.36
1816 1827 5.397142 AAGAAAGCAAAAATCTAGCTGGG 57.603 39.130 0.00 0.00 38.86 4.45
1817 1828 7.820648 TCTAAAGAAAGCAAAAATCTAGCTGG 58.179 34.615 0.00 0.00 38.86 4.85
1818 1829 9.500864 GATCTAAAGAAAGCAAAAATCTAGCTG 57.499 33.333 0.00 0.00 38.86 4.24
1819 1830 9.460019 AGATCTAAAGAAAGCAAAAATCTAGCT 57.540 29.630 0.00 0.00 41.03 3.32
1820 1831 9.500864 CAGATCTAAAGAAAGCAAAAATCTAGC 57.499 33.333 0.00 0.00 0.00 3.42
1822 1833 9.739276 TCCAGATCTAAAGAAAGCAAAAATCTA 57.261 29.630 0.00 0.00 0.00 1.98
1823 1834 8.641498 TCCAGATCTAAAGAAAGCAAAAATCT 57.359 30.769 0.00 0.00 0.00 2.40
1824 1835 9.133627 GTTCCAGATCTAAAGAAAGCAAAAATC 57.866 33.333 0.00 0.00 0.00 2.17
1825 1836 7.809806 CGTTCCAGATCTAAAGAAAGCAAAAAT 59.190 33.333 0.00 0.00 0.00 1.82
1826 1837 7.138736 CGTTCCAGATCTAAAGAAAGCAAAAA 58.861 34.615 0.00 0.00 0.00 1.94
1827 1838 6.262273 ACGTTCCAGATCTAAAGAAAGCAAAA 59.738 34.615 0.00 0.00 0.00 2.44
1828 1839 5.763204 ACGTTCCAGATCTAAAGAAAGCAAA 59.237 36.000 0.00 0.00 0.00 3.68
1829 1840 5.305585 ACGTTCCAGATCTAAAGAAAGCAA 58.694 37.500 0.00 0.00 0.00 3.91
1830 1841 4.894784 ACGTTCCAGATCTAAAGAAAGCA 58.105 39.130 0.00 0.00 0.00 3.91
1831 1842 4.929808 TGACGTTCCAGATCTAAAGAAAGC 59.070 41.667 0.00 0.29 0.00 3.51
1832 1843 5.926542 TGTGACGTTCCAGATCTAAAGAAAG 59.073 40.000 0.00 4.49 0.00 2.62
1833 1844 5.849510 TGTGACGTTCCAGATCTAAAGAAA 58.150 37.500 0.00 0.00 0.00 2.52
1834 1845 5.462530 TGTGACGTTCCAGATCTAAAGAA 57.537 39.130 0.00 0.00 0.00 2.52
1835 1846 5.661056 ATGTGACGTTCCAGATCTAAAGA 57.339 39.130 0.00 0.00 0.00 2.52
1836 1847 6.402550 CCAAATGTGACGTTCCAGATCTAAAG 60.403 42.308 0.00 0.00 0.00 1.85
1837 1848 5.411361 CCAAATGTGACGTTCCAGATCTAAA 59.589 40.000 0.00 0.00 0.00 1.85
1838 1849 4.935205 CCAAATGTGACGTTCCAGATCTAA 59.065 41.667 0.00 0.00 0.00 2.10
1839 1850 4.503910 CCAAATGTGACGTTCCAGATCTA 58.496 43.478 0.00 0.00 0.00 1.98
1840 1851 3.338249 CCAAATGTGACGTTCCAGATCT 58.662 45.455 0.00 0.00 0.00 2.75
1841 1852 2.159517 GCCAAATGTGACGTTCCAGATC 60.160 50.000 0.00 0.00 0.00 2.75
1842 1853 1.812571 GCCAAATGTGACGTTCCAGAT 59.187 47.619 0.00 0.00 0.00 2.90
1843 1854 1.202758 AGCCAAATGTGACGTTCCAGA 60.203 47.619 0.00 0.00 0.00 3.86
1844 1855 1.238439 AGCCAAATGTGACGTTCCAG 58.762 50.000 0.00 0.00 0.00 3.86
1845 1856 1.336440 CAAGCCAAATGTGACGTTCCA 59.664 47.619 0.00 0.00 0.00 3.53
1848 1859 1.336755 GGTCAAGCCAAATGTGACGTT 59.663 47.619 0.00 0.00 42.11 3.99
1860 1871 1.674962 GCTCATGAGATTGGTCAAGCC 59.325 52.381 27.04 0.00 37.90 4.35
1878 1889 6.420913 AATAATGTAGGATAGTGTTCCGCT 57.579 37.500 0.00 0.00 40.94 5.52
1879 1890 6.073222 CCAAATAATGTAGGATAGTGTTCCGC 60.073 42.308 0.00 0.00 40.94 5.54
1880 1891 6.990349 ACCAAATAATGTAGGATAGTGTTCCG 59.010 38.462 0.00 0.00 40.94 4.30
1881 1892 8.747538 AACCAAATAATGTAGGATAGTGTTCC 57.252 34.615 0.00 0.00 35.90 3.62
1891 1902 8.776376 ATTCAGCAAAAACCAAATAATGTAGG 57.224 30.769 0.00 0.00 0.00 3.18
1899 1910 8.955388 ACAAACTTTATTCAGCAAAAACCAAAT 58.045 25.926 0.00 0.00 0.00 2.32
1901 1912 7.913674 ACAAACTTTATTCAGCAAAAACCAA 57.086 28.000 0.00 0.00 0.00 3.67
1903 1914 8.447053 TGAAACAAACTTTATTCAGCAAAAACC 58.553 29.630 0.00 0.00 0.00 3.27
1949 1960 4.740822 GCACCCAACCCTGGCGAT 62.741 66.667 0.00 0.00 41.99 4.58
1976 1987 2.978010 GTGGGCAACACTCGGGTG 60.978 66.667 15.49 15.49 46.72 4.61
1997 2008 2.048222 GCAGGTAGCACGTCAGCA 60.048 61.111 0.36 0.00 44.79 4.41
2021 2032 1.740025 GTAGACATGGCCTGAAAGCAC 59.260 52.381 3.32 0.00 0.00 4.40
2023 2034 2.113860 TGTAGACATGGCCTGAAAGC 57.886 50.000 3.32 0.00 0.00 3.51
2044 2055 3.136123 CTTGGTGCAGCATCCCCG 61.136 66.667 20.91 2.55 0.00 5.73
2052 2063 2.671177 CGGCTCGAACTTGGTGCAG 61.671 63.158 0.00 0.00 0.00 4.41
2112 2123 4.584638 TGGTCTATGCCCTTTGTGTAAT 57.415 40.909 0.00 0.00 0.00 1.89
2123 2134 2.227388 GCATGCAGTTATGGTCTATGCC 59.773 50.000 14.21 0.00 36.04 4.40
2147 2158 6.074835 CGTGTTGTATATCGTCTCATTTCCTG 60.075 42.308 0.00 0.00 0.00 3.86
2157 2168 3.956233 TGTAGCCGTGTTGTATATCGTC 58.044 45.455 0.00 0.00 0.00 4.20
2158 2169 4.107622 GTTGTAGCCGTGTTGTATATCGT 58.892 43.478 0.00 0.00 0.00 3.73
2160 2171 4.506654 CCAGTTGTAGCCGTGTTGTATATC 59.493 45.833 0.00 0.00 0.00 1.63
2167 2178 1.599797 GCCCAGTTGTAGCCGTGTT 60.600 57.895 0.00 0.00 0.00 3.32
2174 2185 1.247567 CCCAAGTTGCCCAGTTGTAG 58.752 55.000 0.00 0.00 34.32 2.74
2180 2191 0.540365 ATGTGACCCAAGTTGCCCAG 60.540 55.000 0.00 0.00 0.00 4.45
2199 2210 3.064134 TCGTCGTTTGCAATTTTCTGTCA 59.936 39.130 0.00 0.00 0.00 3.58
2211 2222 8.584600 CCTGTATATATAGAAATCGTCGTTTGC 58.415 37.037 8.00 0.00 0.00 3.68
2292 2303 2.249309 CGCTGTTGCAACCGTCTG 59.751 61.111 26.14 12.08 39.64 3.51
2307 2318 3.673809 CCTGTATAGATAGAAAACGCCGC 59.326 47.826 0.00 0.00 0.00 6.53
2342 2353 4.148696 GGTGCTTCATTTTTGTGATTGACG 59.851 41.667 0.00 0.00 0.00 4.35
2436 2450 5.286438 ACACCGTTTTTCAGGATTTTAAGC 58.714 37.500 0.00 0.00 0.00 3.09
2475 2501 2.263540 GTAAGGAAGCGGCCGTCA 59.736 61.111 28.70 0.00 0.00 4.35
2509 2535 2.595463 TATACGGCGTCCTCGGGG 60.595 66.667 19.21 0.00 37.56 5.73
2554 2584 1.442769 ACTTGTATCAACGCTGGCAG 58.557 50.000 10.94 10.94 0.00 4.85
2557 2587 1.588404 CGCTACTTGTATCAACGCTGG 59.412 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.