Multiple sequence alignment - TraesCS5D01G026200

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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 TraesCS5D01G026200 chr5D 100.000 2354 0 0 1 2354 23844144 23841791 0 4348
1 TraesCS5D01G026200 chr2D 94.867 1695 72 6 1 1689 593126535 593128220 0 2634
2 TraesCS5D01G026200 chr2D 94.820 1699 68 9 1 1690 305961107 305959420 0 2632
3 TraesCS5D01G026200 chr2D 94.513 1695 78 6 1 1689 577792532 577790847 0 2601
4 TraesCS5D01G026200 chr2D 91.871 529 27 4 1829 2354 642124650 642124135 0 725
5 TraesCS5D01G026200 chrUn 94.802 1693 76 6 1 1689 241760755 241759071 0 2628
6 TraesCS5D01G026200 chr7D 94.746 1694 75 7 1 1689 589251037 589249353 0 2623
7 TraesCS5D01G026200 chr7D 94.582 1698 70 8 1 1689 31418816 31420500 0 2606
8 TraesCS5D01G026200 chr4D 94.690 1695 74 7 1 1689 441127897 441129581 0 2617
9 TraesCS5D01G026200 chr3D 94.631 1695 70 8 1 1689 234618658 234620337 0 2606
10 TraesCS5D01G026200 chr1D 94.569 1694 70 9 1 1689 303228493 303230169 0 2599


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 TraesCS5D01G026200 chr5D 23841791 23844144 2353 True 4348 4348 100.000 1 2354 1 chr5D.!!$R1 2353
1 TraesCS5D01G026200 chr2D 593126535 593128220 1685 False 2634 2634 94.867 1 1689 1 chr2D.!!$F1 1688
2 TraesCS5D01G026200 chr2D 305959420 305961107 1687 True 2632 2632 94.820 1 1690 1 chr2D.!!$R1 1689
3 TraesCS5D01G026200 chr2D 577790847 577792532 1685 True 2601 2601 94.513 1 1689 1 chr2D.!!$R2 1688
4 TraesCS5D01G026200 chr2D 642124135 642124650 515 True 725 725 91.871 1829 2354 1 chr2D.!!$R3 525
5 TraesCS5D01G026200 chrUn 241759071 241760755 1684 True 2628 2628 94.802 1 1689 1 chrUn.!!$R1 1688
6 TraesCS5D01G026200 chr7D 589249353 589251037 1684 True 2623 2623 94.746 1 1689 1 chr7D.!!$R1 1688
7 TraesCS5D01G026200 chr7D 31418816 31420500 1684 False 2606 2606 94.582 1 1689 1 chr7D.!!$F1 1688
8 TraesCS5D01G026200 chr4D 441127897 441129581 1684 False 2617 2617 94.690 1 1689 1 chr4D.!!$F1 1688
9 TraesCS5D01G026200 chr3D 234618658 234620337 1679 False 2606 2606 94.631 1 1689 1 chr3D.!!$F1 1688
10 TraesCS5D01G026200 chr1D 303228493 303230169 1676 False 2599 2599 94.569 1 1689 1 chr1D.!!$F1 1688

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
851 852 0.107017 GTCCTGCTGCACCCACATAT 60.107 55.0 0.0 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1813 0.039618 ATTCCAATGCCGGGTCAGTT 59.96 50.0 2.18 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
34 35 1.447663 CGTCATGTGATCCGTGGCA 60.448 57.895 8.21 0.00 34.17 4.92
87 88 3.046374 GGTAGGATGGTGTGTATCCCTT 58.954 50.000 0.00 0.00 44.19 3.95
114 115 3.966543 CGGGTCCTTGCCCTTGGT 61.967 66.667 0.00 0.00 46.47 3.67
323 324 0.178861 CCTAGTGATAGGGCCCCCAT 60.179 60.000 21.43 12.98 38.92 4.00
341 342 2.896677 ATCCAGGGTCGATGCAGGGA 62.897 60.000 0.00 0.00 0.00 4.20
364 365 2.362120 GCTGCCTTGCCAGGTGAT 60.362 61.111 5.61 0.00 43.18 3.06
441 442 3.532155 GGCGGAGGAGCGATGAGT 61.532 66.667 0.00 0.00 38.18 3.41
448 449 0.393132 AGGAGCGATGAGTCTCGACA 60.393 55.000 13.81 0.00 41.12 4.35
565 566 1.207089 TCGAGGCCTTTGATGACGAAT 59.793 47.619 6.77 0.00 0.00 3.34
583 584 0.611062 ATCCGGTGAACTCCTCGTCA 60.611 55.000 0.00 0.00 0.00 4.35
616 617 1.478510 CCAATAGAGGTGAGCGTGTCT 59.521 52.381 0.00 0.00 0.00 3.41
713 714 2.792947 GCCATCGAGCGGGAGGTAA 61.793 63.158 5.85 0.00 43.00 2.85
730 731 0.480690 TAAAGACCTGGGCAAAGGCA 59.519 50.000 0.47 0.00 41.46 4.75
765 766 3.717294 GGCGTCCATGGAGGTGGT 61.717 66.667 29.85 0.00 40.27 4.16
823 824 0.252881 AACCCTGGATGGCAGAGAGA 60.253 55.000 0.00 0.00 0.00 3.10
851 852 0.107017 GTCCTGCTGCACCCACATAT 60.107 55.000 0.00 0.00 0.00 1.78
858 863 1.268283 TGCACCCACATATGGTCGGA 61.268 55.000 7.80 0.00 45.66 4.55
926 931 1.981256 AGCGAACCATCAACAAACCT 58.019 45.000 0.00 0.00 0.00 3.50
938 943 2.103153 ACAAACCTGAGGAGAGACCA 57.897 50.000 4.99 0.00 42.04 4.02
1008 1013 1.226974 CGTGAGTCGGATGGCGATT 60.227 57.895 0.00 0.00 35.71 3.34
1098 1103 2.994995 ACAGGATCCACGACCGCA 60.995 61.111 15.82 0.00 0.00 5.69
1105 1110 2.901051 ATCCACGACCGCAACCGATC 62.901 60.000 0.00 0.00 36.29 3.69
1108 1113 4.444838 CGACCGCAACCGATCCCA 62.445 66.667 0.00 0.00 36.29 4.37
1485 1496 0.986550 GGCAGCCCTAGGGTTTAGGA 60.987 60.000 28.96 0.00 36.85 2.94
1489 1500 3.555966 CAGCCCTAGGGTTTAGGATTTG 58.444 50.000 28.96 4.81 36.85 2.32
1491 1502 2.243994 GCCCTAGGGTTTAGGATTTGGT 59.756 50.000 28.96 0.00 36.85 3.67
1492 1503 3.898482 CCCTAGGGTTTAGGATTTGGTG 58.102 50.000 20.88 0.00 36.85 4.17
1493 1504 3.288092 CCTAGGGTTTAGGATTTGGTGC 58.712 50.000 0.00 0.00 36.85 5.01
1494 1505 1.834188 AGGGTTTAGGATTTGGTGCG 58.166 50.000 0.00 0.00 0.00 5.34
1495 1506 0.815095 GGGTTTAGGATTTGGTGCGG 59.185 55.000 0.00 0.00 0.00 5.69
1496 1507 0.172578 GGTTTAGGATTTGGTGCGGC 59.827 55.000 0.00 0.00 0.00 6.53
1497 1508 0.179174 GTTTAGGATTTGGTGCGGCG 60.179 55.000 0.51 0.51 0.00 6.46
1596 1607 1.140312 ACTGGCTCAACCCTCAAAGA 58.860 50.000 0.00 0.00 37.83 2.52
1690 1709 6.047231 GGGCTACAATACGAAGTCTAACATT 58.953 40.000 0.00 0.00 43.93 2.71
1691 1710 6.200475 GGGCTACAATACGAAGTCTAACATTC 59.800 42.308 0.00 0.00 43.93 2.67
1692 1711 6.755141 GGCTACAATACGAAGTCTAACATTCA 59.245 38.462 0.00 0.00 43.93 2.57
1693 1712 7.254017 GGCTACAATACGAAGTCTAACATTCAC 60.254 40.741 0.00 0.00 43.93 3.18
1694 1713 6.963049 ACAATACGAAGTCTAACATTCACC 57.037 37.500 0.00 0.00 43.93 4.02
1695 1714 5.873164 ACAATACGAAGTCTAACATTCACCC 59.127 40.000 0.00 0.00 43.93 4.61
1696 1715 5.934402 ATACGAAGTCTAACATTCACCCT 57.066 39.130 0.00 0.00 43.93 4.34
1697 1716 7.093640 ACAATACGAAGTCTAACATTCACCCTA 60.094 37.037 0.00 0.00 43.93 3.53
1698 1717 5.934402 ACGAAGTCTAACATTCACCCTAT 57.066 39.130 0.00 0.00 29.74 2.57
1699 1718 5.903810 ACGAAGTCTAACATTCACCCTATC 58.096 41.667 0.00 0.00 29.74 2.08
1700 1719 5.421056 ACGAAGTCTAACATTCACCCTATCA 59.579 40.000 0.00 0.00 29.74 2.15
1701 1720 5.980116 CGAAGTCTAACATTCACCCTATCAG 59.020 44.000 0.00 0.00 0.00 2.90
1702 1721 6.405953 CGAAGTCTAACATTCACCCTATCAGT 60.406 42.308 0.00 0.00 0.00 3.41
1703 1722 6.227298 AGTCTAACATTCACCCTATCAGTG 57.773 41.667 0.00 0.00 36.54 3.66
1704 1723 5.129485 AGTCTAACATTCACCCTATCAGTGG 59.871 44.000 0.00 0.00 35.87 4.00
1705 1724 5.128827 GTCTAACATTCACCCTATCAGTGGA 59.871 44.000 0.00 0.00 35.87 4.02
1706 1725 5.905331 TCTAACATTCACCCTATCAGTGGAT 59.095 40.000 0.00 0.00 33.53 3.41
1707 1726 5.456921 AACATTCACCCTATCAGTGGATT 57.543 39.130 0.00 0.00 30.71 3.01
1708 1727 4.785301 ACATTCACCCTATCAGTGGATTG 58.215 43.478 0.00 0.00 30.71 2.67
1709 1728 3.281727 TTCACCCTATCAGTGGATTGC 57.718 47.619 0.00 0.00 35.87 3.56
1710 1729 1.138859 TCACCCTATCAGTGGATTGCG 59.861 52.381 0.00 0.00 35.87 4.85
1711 1730 0.179045 ACCCTATCAGTGGATTGCGC 60.179 55.000 0.00 0.00 34.89 6.09
1712 1731 0.179048 CCCTATCAGTGGATTGCGCA 60.179 55.000 5.66 5.66 34.89 6.09
1713 1732 1.224075 CCTATCAGTGGATTGCGCAG 58.776 55.000 11.31 0.00 34.89 5.18
1714 1733 1.202568 CCTATCAGTGGATTGCGCAGA 60.203 52.381 11.31 2.35 34.89 4.26
1715 1734 2.554142 CTATCAGTGGATTGCGCAGAA 58.446 47.619 11.31 0.00 34.89 3.02
1716 1735 1.089920 ATCAGTGGATTGCGCAGAAC 58.910 50.000 11.31 7.95 0.00 3.01
1717 1736 3.307554 TATCAGTGGATTGCGCAGAACG 61.308 50.000 11.31 5.05 38.81 3.95
1718 1737 5.533253 TATCAGTGGATTGCGCAGAACGA 62.533 47.826 11.31 9.77 38.37 3.85
1742 1761 2.003301 GGAGACACATTCTTTCTCCGC 58.997 52.381 1.22 0.00 44.62 5.54
1743 1762 2.354203 GGAGACACATTCTTTCTCCGCT 60.354 50.000 1.22 0.00 44.62 5.52
1744 1763 3.330267 GAGACACATTCTTTCTCCGCTT 58.670 45.455 0.00 0.00 33.22 4.68
1745 1764 3.070018 AGACACATTCTTTCTCCGCTTG 58.930 45.455 0.00 0.00 0.00 4.01
1746 1765 3.067106 GACACATTCTTTCTCCGCTTGA 58.933 45.455 0.00 0.00 0.00 3.02
1747 1766 3.070018 ACACATTCTTTCTCCGCTTGAG 58.930 45.455 0.00 0.00 42.90 3.02
1748 1767 3.070018 CACATTCTTTCTCCGCTTGAGT 58.930 45.455 0.73 0.00 42.12 3.41
1749 1768 3.499918 CACATTCTTTCTCCGCTTGAGTT 59.500 43.478 0.73 0.00 42.12 3.01
1750 1769 4.690748 CACATTCTTTCTCCGCTTGAGTTA 59.309 41.667 0.73 0.00 42.12 2.24
1751 1770 4.932200 ACATTCTTTCTCCGCTTGAGTTAG 59.068 41.667 0.73 0.89 42.12 2.34
1752 1771 2.960819 TCTTTCTCCGCTTGAGTTAGC 58.039 47.619 0.73 0.00 42.12 3.09
1753 1772 2.003301 CTTTCTCCGCTTGAGTTAGCC 58.997 52.381 0.00 0.00 42.12 3.93
1754 1773 1.267121 TTCTCCGCTTGAGTTAGCCT 58.733 50.000 0.00 0.00 42.12 4.58
1755 1774 2.139323 TCTCCGCTTGAGTTAGCCTA 57.861 50.000 0.00 0.00 42.12 3.93
1756 1775 1.749634 TCTCCGCTTGAGTTAGCCTAC 59.250 52.381 0.00 0.00 42.12 3.18
1757 1776 0.454600 TCCGCTTGAGTTAGCCTACG 59.545 55.000 0.00 0.00 37.90 3.51
1758 1777 0.454600 CCGCTTGAGTTAGCCTACGA 59.545 55.000 0.00 0.00 37.90 3.43
1759 1778 1.546834 CGCTTGAGTTAGCCTACGAC 58.453 55.000 0.00 0.00 37.90 4.34
1760 1779 1.798079 CGCTTGAGTTAGCCTACGACC 60.798 57.143 0.00 0.00 37.90 4.79
1761 1780 1.477295 GCTTGAGTTAGCCTACGACCT 59.523 52.381 0.00 0.00 35.06 3.85
1762 1781 2.094130 GCTTGAGTTAGCCTACGACCTT 60.094 50.000 0.00 0.00 35.06 3.50
1763 1782 3.129988 GCTTGAGTTAGCCTACGACCTTA 59.870 47.826 0.00 0.00 35.06 2.69
1764 1783 4.670347 CTTGAGTTAGCCTACGACCTTAC 58.330 47.826 0.00 0.00 0.00 2.34
1765 1784 2.679837 TGAGTTAGCCTACGACCTTACG 59.320 50.000 0.00 0.00 39.31 3.18
1766 1785 2.019984 AGTTAGCCTACGACCTTACGG 58.980 52.381 0.00 0.00 37.61 4.02
1767 1786 1.066152 GTTAGCCTACGACCTTACGGG 59.934 57.143 0.00 0.00 41.89 5.28
1768 1787 0.466189 TAGCCTACGACCTTACGGGG 60.466 60.000 0.00 0.00 40.03 5.73
1769 1788 2.810403 CCTACGACCTTACGGGGC 59.190 66.667 0.00 0.00 40.58 5.80
1770 1789 1.755783 CCTACGACCTTACGGGGCT 60.756 63.158 0.00 0.00 42.26 5.19
1771 1790 1.436336 CTACGACCTTACGGGGCTG 59.564 63.158 0.00 0.00 42.26 4.85
1772 1791 2.624437 CTACGACCTTACGGGGCTGC 62.624 65.000 0.00 0.00 42.26 5.25
1774 1793 4.832608 GACCTTACGGGGCTGCGG 62.833 72.222 0.00 0.00 40.87 5.69
1794 1813 3.803082 GCCTTCATGCTGCGCGAA 61.803 61.111 12.10 0.00 0.00 4.70
1795 1814 2.869646 CCTTCATGCTGCGCGAAA 59.130 55.556 12.10 0.00 0.00 3.46
1796 1815 1.512734 CCTTCATGCTGCGCGAAAC 60.513 57.895 12.10 0.00 0.00 2.78
1797 1816 1.499056 CTTCATGCTGCGCGAAACT 59.501 52.632 12.10 0.00 0.00 2.66
1798 1817 0.791983 CTTCATGCTGCGCGAAACTG 60.792 55.000 12.10 0.00 0.00 3.16
1799 1818 1.227342 TTCATGCTGCGCGAAACTGA 61.227 50.000 12.10 2.10 0.00 3.41
1800 1819 1.510623 CATGCTGCGCGAAACTGAC 60.511 57.895 12.10 0.00 0.00 3.51
1801 1820 2.680913 ATGCTGCGCGAAACTGACC 61.681 57.895 12.10 0.00 0.00 4.02
1802 1821 4.090057 GCTGCGCGAAACTGACCC 62.090 66.667 12.10 0.00 0.00 4.46
1803 1822 3.777925 CTGCGCGAAACTGACCCG 61.778 66.667 12.10 0.00 0.00 5.28
1807 1826 2.746277 GCGAAACTGACCCGGCAT 60.746 61.111 0.00 0.00 0.00 4.40
1808 1827 2.332654 GCGAAACTGACCCGGCATT 61.333 57.895 0.00 0.00 0.00 3.56
1809 1828 1.501741 CGAAACTGACCCGGCATTG 59.498 57.895 0.00 0.00 0.00 2.82
1810 1829 1.883021 GAAACTGACCCGGCATTGG 59.117 57.895 0.00 0.00 0.00 3.16
1811 1830 0.608035 GAAACTGACCCGGCATTGGA 60.608 55.000 0.00 0.00 0.00 3.53
1812 1831 0.178975 AAACTGACCCGGCATTGGAA 60.179 50.000 0.00 0.00 0.00 3.53
1813 1832 0.039618 AACTGACCCGGCATTGGAAT 59.960 50.000 0.00 0.00 0.00 3.01
1814 1833 0.394352 ACTGACCCGGCATTGGAATC 60.394 55.000 0.00 0.00 0.00 2.52
1815 1834 1.077068 TGACCCGGCATTGGAATCC 60.077 57.895 0.00 0.00 0.00 3.01
1816 1835 2.124320 ACCCGGCATTGGAATCCG 60.124 61.111 0.00 0.00 42.58 4.18
1817 1836 2.124320 CCCGGCATTGGAATCCGT 60.124 61.111 0.00 0.00 41.46 4.69
1818 1837 1.752694 CCCGGCATTGGAATCCGTT 60.753 57.895 0.00 0.00 41.46 4.44
1819 1838 1.433064 CCGGCATTGGAATCCGTTG 59.567 57.895 0.00 0.00 41.46 4.10
1820 1839 1.433064 CGGCATTGGAATCCGTTGG 59.567 57.895 0.00 0.00 38.47 3.77
1821 1840 1.141665 GGCATTGGAATCCGTTGGC 59.858 57.895 11.02 11.02 0.00 4.52
1822 1841 1.603236 GGCATTGGAATCCGTTGGCA 61.603 55.000 18.45 0.00 35.03 4.92
1823 1842 0.461135 GCATTGGAATCCGTTGGCAT 59.539 50.000 0.00 0.00 0.00 4.40
1824 1843 1.680735 GCATTGGAATCCGTTGGCATA 59.319 47.619 0.00 0.00 0.00 3.14
1825 1844 2.287788 GCATTGGAATCCGTTGGCATAG 60.288 50.000 0.00 0.00 0.00 2.23
1826 1845 2.799126 TTGGAATCCGTTGGCATAGT 57.201 45.000 0.00 0.00 0.00 2.12
1827 1846 3.916359 TTGGAATCCGTTGGCATAGTA 57.084 42.857 0.00 0.00 0.00 1.82
1865 1884 3.260100 CAGCAGGGTCAAGGGGGT 61.260 66.667 0.00 0.00 0.00 4.95
1872 1892 2.743179 GGTCAAGGGGGTCGGATCC 61.743 68.421 0.00 0.00 0.00 3.36
1900 1920 2.172505 TCAAGAGGAAACCTGCAAGTCA 59.827 45.455 0.00 0.00 31.76 3.41
1909 1929 0.107456 CCTGCAAGTCACACCAGTCT 59.893 55.000 0.00 0.00 0.00 3.24
1950 1971 0.388520 GGGAGCACCAAAATCGTTGC 60.389 55.000 1.58 0.00 39.85 4.17
1966 1987 2.576847 GCCCGAAATTTCAGCGCG 60.577 61.111 17.99 0.00 0.00 6.86
1977 1998 0.387112 TTCAGCGCGGCAAATCAAAG 60.387 50.000 8.83 0.00 0.00 2.77
2024 2045 1.290134 AGGGGAAACTCATCAGTCCC 58.710 55.000 0.00 0.00 36.35 4.46
2050 2072 1.203050 CCATCAGGAACACCAACCCTT 60.203 52.381 0.00 0.00 36.89 3.95
2066 2088 4.591321 ACCCTTATCTTCAATCCTTGCA 57.409 40.909 0.00 0.00 0.00 4.08
2087 2109 0.310854 CACCGAAAGAAGCACAACCC 59.689 55.000 0.00 0.00 0.00 4.11
2126 2148 1.742768 GGATCTCGCGAACCTCCAT 59.257 57.895 20.43 3.89 0.00 3.41
2145 2167 3.635373 CCATTGGGTCTCAATCCTCATTG 59.365 47.826 0.00 0.00 43.70 2.82
2148 2170 2.912295 TGGGTCTCAATCCTCATTGACA 59.088 45.455 0.00 0.00 42.99 3.58
2151 2173 4.141528 GGGTCTCAATCCTCATTGACAGAT 60.142 45.833 0.00 0.00 42.99 2.90
2203 2225 1.372087 GGCTCATGTTTCTCCTGCCG 61.372 60.000 0.00 0.00 0.00 5.69
2204 2226 0.674895 GCTCATGTTTCTCCTGCCGT 60.675 55.000 0.00 0.00 0.00 5.68
2205 2227 1.363744 CTCATGTTTCTCCTGCCGTC 58.636 55.000 0.00 0.00 0.00 4.79
2206 2228 0.976641 TCATGTTTCTCCTGCCGTCT 59.023 50.000 0.00 0.00 0.00 4.18
2207 2229 1.347707 TCATGTTTCTCCTGCCGTCTT 59.652 47.619 0.00 0.00 0.00 3.01
2208 2230 1.466167 CATGTTTCTCCTGCCGTCTTG 59.534 52.381 0.00 0.00 0.00 3.02
2209 2231 0.250295 TGTTTCTCCTGCCGTCTTGG 60.250 55.000 0.00 0.00 42.50 3.61
2210 2232 0.034896 GTTTCTCCTGCCGTCTTGGA 59.965 55.000 0.00 0.00 42.00 3.53
2211 2233 0.034896 TTTCTCCTGCCGTCTTGGAC 59.965 55.000 0.00 0.00 42.00 4.02
2212 2234 0.832135 TTCTCCTGCCGTCTTGGACT 60.832 55.000 0.00 0.00 42.00 3.85
2213 2235 0.039180 TCTCCTGCCGTCTTGGACTA 59.961 55.000 0.00 0.00 42.00 2.59
2214 2236 0.895530 CTCCTGCCGTCTTGGACTAA 59.104 55.000 0.00 0.00 42.00 2.24
2215 2237 0.606604 TCCTGCCGTCTTGGACTAAC 59.393 55.000 0.00 0.00 42.00 2.34
2228 2250 1.906574 GGACTAACATCCTGGTCCACA 59.093 52.381 6.16 0.00 45.23 4.17
2230 2252 2.567615 GACTAACATCCTGGTCCACAGT 59.432 50.000 0.00 0.00 46.06 3.55
2234 2256 0.250858 CATCCTGGTCCACAGTGCAA 60.251 55.000 0.00 0.00 46.06 4.08
2246 2268 0.752054 CAGTGCAAACCAACCCACAT 59.248 50.000 0.00 0.00 0.00 3.21
2253 2275 2.220653 AACCAACCCACATGATCTGG 57.779 50.000 0.00 0.00 0.00 3.86
2266 2288 2.579684 GATCTGGTCCACGGCTCACC 62.580 65.000 0.00 0.00 0.00 4.02
2340 2362 3.551890 GCACTGTTCCATGTCGTATACAG 59.448 47.826 3.32 0.00 42.70 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.550130 CCTGGTACATGGACACCGGT 61.550 60.000 10.99 0.00 39.22 5.28
114 115 2.347114 CGTCTGCCCACATCACCA 59.653 61.111 0.00 0.00 0.00 4.17
311 312 2.121321 CCTGGATGGGGGCCCTAT 60.121 66.667 23.04 23.04 36.94 2.57
323 324 3.083349 CCCTGCATCGACCCTGGA 61.083 66.667 10.47 0.00 0.00 3.86
437 438 0.040336 GAGCAACGTGTCGAGACTCA 60.040 55.000 11.29 0.00 0.00 3.41
441 442 2.254350 CCGAGCAACGTGTCGAGA 59.746 61.111 14.77 0.00 38.50 4.04
448 449 1.006102 CCTCTTCACCGAGCAACGT 60.006 57.895 3.00 0.00 40.78 3.99
565 566 1.228337 TGACGAGGAGTTCACCGGA 60.228 57.895 9.46 0.00 34.73 5.14
583 584 0.104304 CTATTGGTCGGCCGCTTAGT 59.896 55.000 23.51 8.90 37.67 2.24
616 617 0.111061 ACAAGATGAAGGTGCTGGCA 59.889 50.000 0.00 0.00 0.00 4.92
713 714 0.901580 CATGCCTTTGCCCAGGTCTT 60.902 55.000 0.47 0.00 36.15 3.01
730 731 2.284625 TGGACGACCCTGGAGCAT 60.285 61.111 0.34 0.00 35.38 3.79
765 766 1.302511 GGCCTTTGTCTCTTCGCCA 60.303 57.895 0.00 0.00 36.38 5.69
823 824 2.270205 CAGCAGGACCAGGCGATT 59.730 61.111 0.00 0.00 34.54 3.34
926 931 2.346541 CGCAGCTGGTCTCTCCTCA 61.347 63.158 17.12 0.00 37.07 3.86
1008 1013 2.746269 CCGTTCCACTTCGACAACTTA 58.254 47.619 0.00 0.00 0.00 2.24
1338 1346 1.004440 GCCTCAGTTCTTCGGCACT 60.004 57.895 0.00 0.00 42.06 4.40
1566 1577 0.263172 TGAGCCAGTTCCCCCAAAAA 59.737 50.000 0.00 0.00 0.00 1.94
1596 1607 9.674705 TCATTATATATATGTGATAGGCCACCT 57.325 33.333 5.01 0.00 36.26 4.00
1641 1660 6.753107 ACTGTGTAAACCATACCTTATTGC 57.247 37.500 0.00 0.00 0.00 3.56
1690 1709 1.138859 CGCAATCCACTGATAGGGTGA 59.861 52.381 0.00 0.00 36.89 4.02
1691 1710 1.586422 CGCAATCCACTGATAGGGTG 58.414 55.000 0.00 0.00 34.78 4.61
1692 1711 0.179045 GCGCAATCCACTGATAGGGT 60.179 55.000 0.30 0.00 0.00 4.34
1693 1712 0.179048 TGCGCAATCCACTGATAGGG 60.179 55.000 8.16 0.00 0.00 3.53
1694 1713 1.202568 TCTGCGCAATCCACTGATAGG 60.203 52.381 13.05 0.00 0.00 2.57
1695 1714 2.229675 TCTGCGCAATCCACTGATAG 57.770 50.000 13.05 0.00 0.00 2.08
1696 1715 2.279741 GTTCTGCGCAATCCACTGATA 58.720 47.619 13.05 0.00 0.00 2.15
1697 1716 1.089920 GTTCTGCGCAATCCACTGAT 58.910 50.000 13.05 0.00 0.00 2.90
1698 1717 1.291184 CGTTCTGCGCAATCCACTGA 61.291 55.000 13.05 0.00 0.00 3.41
1699 1718 1.133253 CGTTCTGCGCAATCCACTG 59.867 57.895 13.05 0.00 0.00 3.66
1700 1719 1.005037 TCGTTCTGCGCAATCCACT 60.005 52.632 13.05 0.00 41.07 4.00
1701 1720 1.291877 ACTCGTTCTGCGCAATCCAC 61.292 55.000 13.05 4.66 41.07 4.02
1702 1721 1.005037 ACTCGTTCTGCGCAATCCA 60.005 52.632 13.05 0.00 41.07 3.41
1703 1722 1.710339 GACTCGTTCTGCGCAATCC 59.290 57.895 13.05 0.00 41.07 3.01
1704 1723 1.341802 CGACTCGTTCTGCGCAATC 59.658 57.895 13.05 3.67 41.07 2.67
1705 1724 2.094659 CCGACTCGTTCTGCGCAAT 61.095 57.895 13.05 0.00 41.07 3.56
1706 1725 2.733218 CCGACTCGTTCTGCGCAA 60.733 61.111 13.05 0.00 41.07 4.85
1707 1726 3.610791 CTCCGACTCGTTCTGCGCA 62.611 63.158 10.98 10.98 41.07 6.09
1708 1727 2.876645 CTCCGACTCGTTCTGCGC 60.877 66.667 0.00 0.00 41.07 6.09
1709 1728 1.512310 GTCTCCGACTCGTTCTGCG 60.512 63.158 0.00 0.00 43.01 5.18
1710 1729 0.729816 GTGTCTCCGACTCGTTCTGC 60.730 60.000 0.00 0.00 33.15 4.26
1711 1730 0.591659 TGTGTCTCCGACTCGTTCTG 59.408 55.000 0.00 0.00 33.15 3.02
1712 1731 1.535833 ATGTGTCTCCGACTCGTTCT 58.464 50.000 0.00 0.00 33.15 3.01
1713 1732 2.095161 AGAATGTGTCTCCGACTCGTTC 60.095 50.000 16.94 16.94 44.96 3.95
1714 1733 1.887198 AGAATGTGTCTCCGACTCGTT 59.113 47.619 0.00 3.91 37.78 3.85
1715 1734 1.535833 AGAATGTGTCTCCGACTCGT 58.464 50.000 0.00 0.00 33.15 4.18
1716 1735 2.638556 AAGAATGTGTCTCCGACTCG 57.361 50.000 0.00 0.00 34.56 4.18
1717 1736 4.170256 GAGAAAGAATGTGTCTCCGACTC 58.830 47.826 0.00 0.00 34.56 3.36
1718 1737 3.056465 GGAGAAAGAATGTGTCTCCGACT 60.056 47.826 0.43 0.00 45.95 4.18
1719 1738 3.254892 GGAGAAAGAATGTGTCTCCGAC 58.745 50.000 0.43 0.00 45.95 4.79
1720 1739 3.594603 GGAGAAAGAATGTGTCTCCGA 57.405 47.619 0.43 0.00 45.95 4.55
1723 1742 2.966050 AGCGGAGAAAGAATGTGTCTC 58.034 47.619 0.00 0.00 34.56 3.36
1724 1743 3.070018 CAAGCGGAGAAAGAATGTGTCT 58.930 45.455 0.00 0.00 38.69 3.41
1725 1744 3.067106 TCAAGCGGAGAAAGAATGTGTC 58.933 45.455 0.00 0.00 0.00 3.67
1726 1745 3.126001 TCAAGCGGAGAAAGAATGTGT 57.874 42.857 0.00 0.00 0.00 3.72
1738 1757 0.454600 CGTAGGCTAACTCAAGCGGA 59.545 55.000 0.00 0.00 43.74 5.54
1739 1758 0.454600 TCGTAGGCTAACTCAAGCGG 59.545 55.000 0.00 0.00 43.74 5.52
1740 1759 1.546834 GTCGTAGGCTAACTCAAGCG 58.453 55.000 0.00 0.00 43.74 4.68
1741 1760 1.477295 AGGTCGTAGGCTAACTCAAGC 59.523 52.381 0.00 0.00 41.99 4.01
1742 1761 3.870633 AAGGTCGTAGGCTAACTCAAG 57.129 47.619 0.00 0.00 0.00 3.02
1743 1762 3.127548 CGTAAGGTCGTAGGCTAACTCAA 59.872 47.826 0.00 0.00 0.00 3.02
1744 1763 2.679837 CGTAAGGTCGTAGGCTAACTCA 59.320 50.000 0.00 0.00 0.00 3.41
1745 1764 3.331251 CGTAAGGTCGTAGGCTAACTC 57.669 52.381 0.00 0.00 0.00 3.01
1786 1805 3.777925 CGGGTCAGTTTCGCGCAG 61.778 66.667 8.75 0.00 34.88 5.18
1790 1809 2.332654 AATGCCGGGTCAGTTTCGC 61.333 57.895 2.18 0.00 0.00 4.70
1791 1810 1.501741 CAATGCCGGGTCAGTTTCG 59.498 57.895 2.18 0.00 0.00 3.46
1792 1811 0.608035 TCCAATGCCGGGTCAGTTTC 60.608 55.000 2.18 0.00 0.00 2.78
1793 1812 0.178975 TTCCAATGCCGGGTCAGTTT 60.179 50.000 2.18 0.00 0.00 2.66
1794 1813 0.039618 ATTCCAATGCCGGGTCAGTT 59.960 50.000 2.18 0.00 0.00 3.16
1795 1814 0.394352 GATTCCAATGCCGGGTCAGT 60.394 55.000 2.18 0.00 0.00 3.41
1796 1815 1.103398 GGATTCCAATGCCGGGTCAG 61.103 60.000 2.18 0.00 0.00 3.51
1797 1816 1.077068 GGATTCCAATGCCGGGTCA 60.077 57.895 2.18 0.00 0.00 4.02
1798 1817 2.186826 CGGATTCCAATGCCGGGTC 61.187 63.158 2.18 0.00 41.29 4.46
1799 1818 2.124320 CGGATTCCAATGCCGGGT 60.124 61.111 2.18 0.00 41.29 5.28
1803 1822 1.141665 GCCAACGGATTCCAATGCC 59.858 57.895 3.09 0.00 0.00 4.40
1804 1823 0.461135 ATGCCAACGGATTCCAATGC 59.539 50.000 3.09 0.36 0.00 3.56
1805 1824 2.951642 ACTATGCCAACGGATTCCAATG 59.048 45.455 3.09 0.76 0.00 2.82
1806 1825 3.297134 ACTATGCCAACGGATTCCAAT 57.703 42.857 3.09 0.00 0.00 3.16
1807 1826 2.799126 ACTATGCCAACGGATTCCAA 57.201 45.000 3.09 0.00 0.00 3.53
1808 1827 2.104111 CCTACTATGCCAACGGATTCCA 59.896 50.000 3.09 0.00 0.00 3.53
1809 1828 2.104281 ACCTACTATGCCAACGGATTCC 59.896 50.000 0.00 0.00 0.00 3.01
1810 1829 3.470645 ACCTACTATGCCAACGGATTC 57.529 47.619 0.00 0.00 0.00 2.52
1811 1830 3.541632 CAACCTACTATGCCAACGGATT 58.458 45.455 0.00 0.00 0.00 3.01
1812 1831 2.158813 CCAACCTACTATGCCAACGGAT 60.159 50.000 0.00 0.00 0.00 4.18
1813 1832 1.208535 CCAACCTACTATGCCAACGGA 59.791 52.381 0.00 0.00 0.00 4.69
1814 1833 1.663695 CCAACCTACTATGCCAACGG 58.336 55.000 0.00 0.00 0.00 4.44
1815 1834 1.663695 CCCAACCTACTATGCCAACG 58.336 55.000 0.00 0.00 0.00 4.10
1816 1835 1.340600 TGCCCAACCTACTATGCCAAC 60.341 52.381 0.00 0.00 0.00 3.77
1817 1836 0.995803 TGCCCAACCTACTATGCCAA 59.004 50.000 0.00 0.00 0.00 4.52
1818 1837 0.995803 TTGCCCAACCTACTATGCCA 59.004 50.000 0.00 0.00 0.00 4.92
1819 1838 1.211949 TCTTGCCCAACCTACTATGCC 59.788 52.381 0.00 0.00 0.00 4.40
1820 1839 2.092914 AGTCTTGCCCAACCTACTATGC 60.093 50.000 0.00 0.00 0.00 3.14
1821 1840 3.055094 ACAGTCTTGCCCAACCTACTATG 60.055 47.826 0.00 0.00 0.00 2.23
1822 1841 3.055094 CACAGTCTTGCCCAACCTACTAT 60.055 47.826 0.00 0.00 0.00 2.12
1823 1842 2.301870 CACAGTCTTGCCCAACCTACTA 59.698 50.000 0.00 0.00 0.00 1.82
1824 1843 1.072331 CACAGTCTTGCCCAACCTACT 59.928 52.381 0.00 0.00 0.00 2.57
1825 1844 1.523758 CACAGTCTTGCCCAACCTAC 58.476 55.000 0.00 0.00 0.00 3.18
1826 1845 0.250727 GCACAGTCTTGCCCAACCTA 60.251 55.000 0.00 0.00 36.42 3.08
1827 1846 1.529244 GCACAGTCTTGCCCAACCT 60.529 57.895 0.00 0.00 36.42 3.50
1856 1875 2.762459 CGGATCCGACCCCCTTGA 60.762 66.667 30.62 0.00 42.83 3.02
1865 1884 1.409064 CTCTTGAACATCCGGATCCGA 59.591 52.381 35.42 20.88 42.83 4.55
1872 1892 2.744202 CAGGTTTCCTCTTGAACATCCG 59.256 50.000 0.00 0.00 31.05 4.18
1950 1971 2.100216 CCGCGCTGAAATTTCGGG 59.900 61.111 24.87 20.34 36.73 5.14
1966 1987 2.925563 CGATTCCTTGCTTTGATTTGCC 59.074 45.455 0.00 0.00 0.00 4.52
1997 2018 1.217244 GAGTTTCCCCTTCGCGCTA 59.783 57.895 5.56 0.00 0.00 4.26
2024 2045 0.179045 GGTGTTCCTGATGGATCCGG 60.179 60.000 7.39 0.00 42.81 5.14
2066 2088 1.021968 GTTGTGCTTCTTTCGGTGGT 58.978 50.000 0.00 0.00 0.00 4.16
2126 2148 3.330405 TGTCAATGAGGATTGAGACCCAA 59.670 43.478 0.00 0.00 46.95 4.12
2145 2167 0.109272 TTCACGCGTCTCCATCTGTC 60.109 55.000 9.86 0.00 0.00 3.51
2148 2170 0.317160 TTGTTCACGCGTCTCCATCT 59.683 50.000 9.86 0.00 0.00 2.90
2151 2173 1.262950 CAATTTGTTCACGCGTCTCCA 59.737 47.619 9.86 2.39 0.00 3.86
2190 2212 0.250295 CCAAGACGGCAGGAGAAACA 60.250 55.000 0.00 0.00 0.00 2.83
2203 2225 3.369576 GGACCAGGATGTTAGTCCAAGAC 60.370 52.174 0.00 0.00 42.34 3.01
2204 2226 2.838202 GGACCAGGATGTTAGTCCAAGA 59.162 50.000 0.00 0.00 42.34 3.02
2205 2227 2.571653 TGGACCAGGATGTTAGTCCAAG 59.428 50.000 8.22 0.00 46.94 3.61
2206 2228 2.626785 TGGACCAGGATGTTAGTCCAA 58.373 47.619 8.22 0.00 46.94 3.53
2208 2230 1.906574 TGTGGACCAGGATGTTAGTCC 59.093 52.381 0.00 1.04 42.86 3.85
2209 2231 2.567615 ACTGTGGACCAGGATGTTAGTC 59.432 50.000 0.00 0.00 46.06 2.59
2210 2232 2.303022 CACTGTGGACCAGGATGTTAGT 59.697 50.000 0.00 0.00 46.06 2.24
2211 2233 2.936993 GCACTGTGGACCAGGATGTTAG 60.937 54.545 10.21 0.00 46.06 2.34
2212 2234 1.003118 GCACTGTGGACCAGGATGTTA 59.997 52.381 10.21 0.00 46.06 2.41
2213 2235 0.250901 GCACTGTGGACCAGGATGTT 60.251 55.000 10.21 0.00 46.06 2.71
2214 2236 1.376466 GCACTGTGGACCAGGATGT 59.624 57.895 10.21 0.00 46.06 3.06
2215 2237 0.250858 TTGCACTGTGGACCAGGATG 60.251 55.000 10.21 0.00 46.06 3.51
2228 2250 0.752054 CATGTGGGTTGGTTTGCACT 59.248 50.000 0.00 0.00 0.00 4.40
2230 2252 1.617850 GATCATGTGGGTTGGTTTGCA 59.382 47.619 0.00 0.00 0.00 4.08
2234 2256 1.428912 ACCAGATCATGTGGGTTGGTT 59.571 47.619 5.67 0.00 39.65 3.67
2246 2268 1.609210 TGAGCCGTGGACCAGATCA 60.609 57.895 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.