Multiple sequence alignment - TraesCS4B01G246200

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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 TraesCS4B01G246200 chr4B 100.000 2726 0 0 1 2726 510353638 510350913 0.000000e+00 5035
1 TraesCS4B01G246200 chr4B 92.308 78 2 3 1818 1894 47495743 47495817 1.030000e-19 108
2 TraesCS4B01G246200 chr4B 89.286 84 7 2 1811 1894 47495824 47495743 1.340000e-18 104
3 TraesCS4B01G246200 chr4D 93.309 1106 30 10 747 1819 414224849 414223755 0.000000e+00 1592
4 TraesCS4B01G246200 chr4D 91.892 851 41 12 1891 2726 414223758 414222921 0.000000e+00 1164
5 TraesCS4B01G246200 chr4A 93.061 980 54 5 851 1819 49221057 49222033 0.000000e+00 1421
6 TraesCS4B01G246200 chr4A 90.675 311 25 2 1513 1819 49236291 49236601 7.030000e-111 411
7 TraesCS4B01G246200 chr7D 90.823 741 67 1 1 741 192016734 192015995 0.000000e+00 990
8 TraesCS4B01G246200 chr7B 90.148 741 73 0 1 741 400954096 400954836 0.000000e+00 965
9 TraesCS4B01G246200 chr7B 89.716 739 75 1 1 739 60344858 60344121 0.000000e+00 942
10 TraesCS4B01G246200 chr7B 92.308 78 3 2 1817 1894 156633922 156633848 1.030000e-19 108
11 TraesCS4B01G246200 chr5D 90.013 741 69 3 1 741 420194135 420193400 0.000000e+00 953
12 TraesCS4B01G246200 chr6B 89.799 745 71 3 1 745 169484845 169485584 0.000000e+00 950
13 TraesCS4B01G246200 chr2B 89.744 741 74 2 1 741 6042412 6041674 0.000000e+00 946
14 TraesCS4B01G246200 chr2B 89.339 741 79 0 1 741 215842623 215843363 0.000000e+00 931
15 TraesCS4B01G246200 chr3B 89.623 742 76 1 1 741 534518045 534518786 0.000000e+00 942
16 TraesCS4B01G246200 chr3B 89.595 740 75 1 2 741 786039636 786040373 0.000000e+00 939
17 TraesCS4B01G246200 chr1A 94.937 79 2 2 1817 1894 489569184 489569107 3.690000e-24 122
18 TraesCS4B01G246200 chr1A 93.590 78 3 2 1818 1894 489569107 489569183 6.170000e-22 115
19 TraesCS4B01G246200 chr1A 91.250 80 5 2 1818 1897 530602365 530602288 1.030000e-19 108
20 TraesCS4B01G246200 chr1A 92.308 78 2 3 1818 1894 530602291 530602365 1.030000e-19 108
21 TraesCS4B01G246200 chr7A 92.405 79 4 2 1818 1895 104727486 104727409 7.980000e-21 111
22 TraesCS4B01G246200 chr1D 92.308 78 4 2 1817 1894 470796198 470796123 2.870000e-20 110


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 TraesCS4B01G246200 chr4B 510350913 510353638 2725 True 5035 5035 100.0000 1 2726 1 chr4B.!!$R2 2725
1 TraesCS4B01G246200 chr4D 414222921 414224849 1928 True 1378 1592 92.6005 747 2726 2 chr4D.!!$R1 1979
2 TraesCS4B01G246200 chr4A 49221057 49222033 976 False 1421 1421 93.0610 851 1819 1 chr4A.!!$F1 968
3 TraesCS4B01G246200 chr7D 192015995 192016734 739 True 990 990 90.8230 1 741 1 chr7D.!!$R1 740
4 TraesCS4B01G246200 chr7B 400954096 400954836 740 False 965 965 90.1480 1 741 1 chr7B.!!$F1 740
5 TraesCS4B01G246200 chr7B 60344121 60344858 737 True 942 942 89.7160 1 739 1 chr7B.!!$R1 738
6 TraesCS4B01G246200 chr5D 420193400 420194135 735 True 953 953 90.0130 1 741 1 chr5D.!!$R1 740
7 TraesCS4B01G246200 chr6B 169484845 169485584 739 False 950 950 89.7990 1 745 1 chr6B.!!$F1 744
8 TraesCS4B01G246200 chr2B 6041674 6042412 738 True 946 946 89.7440 1 741 1 chr2B.!!$R1 740
9 TraesCS4B01G246200 chr2B 215842623 215843363 740 False 931 931 89.3390 1 741 1 chr2B.!!$F1 740
10 TraesCS4B01G246200 chr3B 534518045 534518786 741 False 942 942 89.6230 1 741 1 chr3B.!!$F1 740
11 TraesCS4B01G246200 chr3B 786039636 786040373 737 False 939 939 89.5950 2 741 1 chr3B.!!$F2 739

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
718 725 0.323302 ACATGGTGTGTGGACGCATA 59.677 50.0 0.0 0.0 40.28 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2361 0.541863 TTCCGAATCAGGCCTCTTCC 59.458 55.0 0.0 0.0 0.0 3.46 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
21 22 0.391661 CAGCCACCTAGTTCATGCGT 60.392 55.000 0.00 0.00 0.00 5.24
56 60 0.745128 TTTTCGCCCACACGACACTT 60.745 50.000 0.00 0.00 42.78 3.16
64 68 3.615592 GCCCACACGACACTTCTACATTA 60.616 47.826 0.00 0.00 0.00 1.90
72 76 6.925718 CACGACACTTCTACATTATGGATGAT 59.074 38.462 0.00 0.00 39.15 2.45
93 97 9.224058 GATGATAACTACAGTTAGACGAACTTC 57.776 37.037 7.79 0.00 46.79 3.01
123 127 5.676552 AGGTAAACACACATGACAACTGTA 58.323 37.500 0.00 0.00 0.00 2.74
176 180 1.153353 ACGTGGCAACCAGATAAACG 58.847 50.000 0.00 0.00 32.34 3.60
195 199 2.013400 CGCACATGGCAACTATGGTTA 58.987 47.619 0.00 0.00 45.17 2.85
228 232 5.676552 TGACAACTAGGTAAACACACATGT 58.323 37.500 0.00 0.00 42.46 3.21
274 278 3.744426 GCAAGTAGTTAATCACACACGGT 59.256 43.478 0.00 0.00 0.00 4.83
277 281 6.091713 GCAAGTAGTTAATCACACACGGTAAT 59.908 38.462 0.00 0.00 0.00 1.89
290 294 3.264964 ACACGGTAATTATGGTTGGACCT 59.735 43.478 0.00 0.00 39.58 3.85
319 323 3.818773 GCAACTAGGTAAACACACATGGT 59.181 43.478 0.00 0.00 0.00 3.55
346 352 8.608255 AACTACTGTTTGACCATATGTGGCAAA 61.608 37.037 19.52 19.52 43.12 3.68
376 382 1.202510 ACACACGGCAACTACGGTTTA 60.203 47.619 0.00 0.00 32.73 2.01
435 442 7.968405 GGCAACTATAGTTAACCAAAACAGATG 59.032 37.037 22.97 8.76 36.32 2.90
442 449 6.126409 AGTTAACCAAAACAGATGGAGTTGA 58.874 36.000 0.88 0.00 40.56 3.18
456 463 5.843673 TGGAGTTGACATGCTTTTACAAA 57.156 34.783 0.00 0.00 0.00 2.83
459 466 8.121305 TGGAGTTGACATGCTTTTACAAATAT 57.879 30.769 0.00 0.00 0.00 1.28
485 492 2.354805 GCCATCCCGGATAACTACATCC 60.355 54.545 0.73 0.00 41.06 3.51
562 569 4.320861 CGTCAGAATGTGTGGGCATTTTTA 60.321 41.667 0.00 0.00 38.98 1.52
567 574 5.304101 AGAATGTGTGGGCATTTTTACTTCA 59.696 36.000 0.00 0.00 38.98 3.02
596 603 2.750948 GCGCGGGATAAAGATGAGTAA 58.249 47.619 8.83 0.00 0.00 2.24
636 643 3.910914 AAATAGCCGCGCCCACACA 62.911 57.895 0.00 0.00 0.00 3.72
638 645 2.318519 AATAGCCGCGCCCACACATA 62.319 55.000 0.00 0.00 0.00 2.29
641 648 2.203001 CCGCGCCCACACATATGA 60.203 61.111 10.38 0.00 0.00 2.15
664 671 6.097554 TGAACAATTTTAATATCCGCCCACAT 59.902 34.615 0.00 0.00 0.00 3.21
668 675 7.068839 ACAATTTTAATATCCGCCCACATACAA 59.931 33.333 0.00 0.00 0.00 2.41
688 695 2.377810 CCATGTGGGCTGCCTCCTA 61.378 63.158 19.68 3.30 0.00 2.94
693 700 1.003442 TGGGCTGCCTCCTACTCAT 59.997 57.895 19.68 0.00 0.00 2.90
718 725 0.323302 ACATGGTGTGTGGACGCATA 59.677 50.000 0.00 0.00 40.28 3.14
757 764 1.143277 TGGCGTCCTTACTTTTTCCCA 59.857 47.619 0.00 0.00 0.00 4.37
766 773 1.710816 ACTTTTTCCCATTGGCCGAA 58.289 45.000 0.00 0.00 0.00 4.30
772 779 1.376683 CCCATTGGCCGAAGAACGA 60.377 57.895 0.00 0.00 45.77 3.85
773 780 0.958382 CCCATTGGCCGAAGAACGAA 60.958 55.000 0.00 0.00 45.77 3.85
774 781 0.447801 CCATTGGCCGAAGAACGAAG 59.552 55.000 0.00 0.00 45.77 3.79
776 783 2.343101 CATTGGCCGAAGAACGAAGTA 58.657 47.619 0.00 0.00 45.00 2.24
777 784 2.754946 TTGGCCGAAGAACGAAGTAT 57.245 45.000 0.00 0.00 45.00 2.12
778 785 2.754946 TGGCCGAAGAACGAAGTATT 57.245 45.000 0.00 0.00 45.00 1.89
779 786 2.343101 TGGCCGAAGAACGAAGTATTG 58.657 47.619 0.00 0.00 45.00 1.90
780 787 2.289195 TGGCCGAAGAACGAAGTATTGT 60.289 45.455 0.00 0.00 45.00 2.71
801 809 0.543277 TCTGGTCTCATCCCACATGC 59.457 55.000 0.00 0.00 0.00 4.06
841 849 4.093556 GTGTCTTTGATCAGACCGAATTCC 59.906 45.833 11.42 0.00 42.39 3.01
958 999 7.006187 TCGTATTCAGCGATAGATCAGATAC 57.994 40.000 0.00 0.00 39.76 2.24
959 1000 6.819146 TCGTATTCAGCGATAGATCAGATACT 59.181 38.462 0.00 0.00 39.76 2.12
960 1001 7.980099 TCGTATTCAGCGATAGATCAGATACTA 59.020 37.037 0.00 0.00 39.76 1.82
961 1002 8.604890 CGTATTCAGCGATAGATCAGATACTAA 58.395 37.037 0.00 0.00 39.76 2.24
1473 1517 1.609320 GGAGCTCTGAACAGGTGGAAC 60.609 57.143 14.64 0.00 0.00 3.62
1699 1746 1.608717 GATCACGGAGGTGCTCAGGT 61.609 60.000 0.00 0.00 44.03 4.00
1730 1777 3.067833 AGGAAAACGAACTCTAAGCTGC 58.932 45.455 0.00 0.00 0.00 5.25
1789 1836 3.133003 AGAACGGATGGTGGTAGATCTTG 59.867 47.826 0.00 0.00 0.00 3.02
1794 1841 2.940514 TGGTGGTAGATCTTGGGAGA 57.059 50.000 0.00 0.00 36.09 3.71
1815 1863 0.834687 AGGGGACACGCAGGTTTCTA 60.835 55.000 0.00 0.00 0.00 2.10
1816 1864 0.391263 GGGGACACGCAGGTTTCTAG 60.391 60.000 0.00 0.00 0.00 2.43
1817 1865 0.320697 GGGACACGCAGGTTTCTAGT 59.679 55.000 0.00 0.00 0.00 2.57
1818 1866 1.547372 GGGACACGCAGGTTTCTAGTA 59.453 52.381 0.00 0.00 0.00 1.82
1819 1867 2.603953 GGACACGCAGGTTTCTAGTAC 58.396 52.381 0.00 0.00 0.00 2.73
1820 1868 2.230750 GGACACGCAGGTTTCTAGTACT 59.769 50.000 0.00 0.00 0.00 2.73
1821 1869 3.500014 GACACGCAGGTTTCTAGTACTC 58.500 50.000 0.00 0.00 0.00 2.59
1822 1870 2.230750 ACACGCAGGTTTCTAGTACTCC 59.769 50.000 0.00 0.00 0.00 3.85
1823 1871 1.823610 ACGCAGGTTTCTAGTACTCCC 59.176 52.381 0.00 0.00 0.00 4.30
1824 1872 2.100989 CGCAGGTTTCTAGTACTCCCT 58.899 52.381 0.00 0.00 0.00 4.20
1825 1873 2.099427 CGCAGGTTTCTAGTACTCCCTC 59.901 54.545 0.00 0.00 0.00 4.30
1826 1874 2.431419 GCAGGTTTCTAGTACTCCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
1827 1875 2.688958 CAGGTTTCTAGTACTCCCTCCG 59.311 54.545 0.00 0.00 0.00 4.63
1828 1876 2.311243 AGGTTTCTAGTACTCCCTCCGT 59.689 50.000 0.00 0.00 0.00 4.69
1829 1877 3.095332 GGTTTCTAGTACTCCCTCCGTT 58.905 50.000 0.00 0.00 0.00 4.44
1830 1878 3.513119 GGTTTCTAGTACTCCCTCCGTTT 59.487 47.826 0.00 0.00 0.00 3.60
1831 1879 4.381398 GGTTTCTAGTACTCCCTCCGTTTC 60.381 50.000 0.00 0.00 0.00 2.78
1832 1880 3.726557 TCTAGTACTCCCTCCGTTTCA 57.273 47.619 0.00 0.00 0.00 2.69
1833 1881 4.038271 TCTAGTACTCCCTCCGTTTCAA 57.962 45.455 0.00 0.00 0.00 2.69
1834 1882 4.410099 TCTAGTACTCCCTCCGTTTCAAA 58.590 43.478 0.00 0.00 0.00 2.69
1835 1883 4.834496 TCTAGTACTCCCTCCGTTTCAAAA 59.166 41.667 0.00 0.00 0.00 2.44
1836 1884 4.635699 AGTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
1837 1885 5.750352 AGTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
1838 1886 5.731591 AGTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
1839 1887 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1840 1888 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1841 1889 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1842 1890 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1843 1891 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
1844 1892 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
1845 1893 5.648092 CCCTCCGTTTCAAAATAGATGACTT 59.352 40.000 0.00 0.00 0.00 3.01
1846 1894 6.821665 CCCTCCGTTTCAAAATAGATGACTTA 59.178 38.462 0.00 0.00 0.00 2.24
1847 1895 7.335924 CCCTCCGTTTCAAAATAGATGACTTAA 59.664 37.037 0.00 0.00 0.00 1.85
1848 1896 8.175716 CCTCCGTTTCAAAATAGATGACTTAAC 58.824 37.037 0.00 0.00 0.00 2.01
1849 1897 8.842358 TCCGTTTCAAAATAGATGACTTAACT 57.158 30.769 0.00 0.00 0.00 2.24
1850 1898 9.280174 TCCGTTTCAAAATAGATGACTTAACTT 57.720 29.630 0.00 0.00 0.00 2.66
1851 1899 9.329913 CCGTTTCAAAATAGATGACTTAACTTG 57.670 33.333 0.00 0.00 0.00 3.16
1852 1900 9.878599 CGTTTCAAAATAGATGACTTAACTTGT 57.121 29.630 0.00 0.00 0.00 3.16
1862 1910 8.608844 AGATGACTTAACTTGTAGGTTCAAAG 57.391 34.615 0.00 0.00 0.00 2.77
1863 1911 8.211629 AGATGACTTAACTTGTAGGTTCAAAGT 58.788 33.333 0.00 0.00 33.42 2.66
1864 1912 8.747538 ATGACTTAACTTGTAGGTTCAAAGTT 57.252 30.769 5.47 5.47 31.92 2.66
1865 1913 7.981142 TGACTTAACTTGTAGGTTCAAAGTTG 58.019 34.615 9.63 0.00 31.92 3.16
1866 1914 7.825270 TGACTTAACTTGTAGGTTCAAAGTTGA 59.175 33.333 9.63 1.99 31.92 3.18
1867 1915 8.209917 ACTTAACTTGTAGGTTCAAAGTTGAG 57.790 34.615 14.20 14.20 38.61 3.02
1868 1916 7.827729 ACTTAACTTGTAGGTTCAAAGTTGAGT 59.172 33.333 15.18 15.18 38.61 3.41
1869 1917 6.679327 AACTTGTAGGTTCAAAGTTGAGTC 57.321 37.500 0.00 0.00 38.61 3.36
1870 1918 5.741011 ACTTGTAGGTTCAAAGTTGAGTCA 58.259 37.500 0.00 0.00 38.61 3.41
1871 1919 6.357367 ACTTGTAGGTTCAAAGTTGAGTCAT 58.643 36.000 0.00 0.00 38.61 3.06
1872 1920 6.483640 ACTTGTAGGTTCAAAGTTGAGTCATC 59.516 38.462 0.00 0.00 38.61 2.92
1873 1921 6.174720 TGTAGGTTCAAAGTTGAGTCATCT 57.825 37.500 0.00 0.00 38.61 2.90
1874 1922 7.297936 TGTAGGTTCAAAGTTGAGTCATCTA 57.702 36.000 4.14 0.00 38.61 1.98
1875 1923 7.907389 TGTAGGTTCAAAGTTGAGTCATCTAT 58.093 34.615 4.14 0.00 38.61 1.98
1876 1924 8.375506 TGTAGGTTCAAAGTTGAGTCATCTATT 58.624 33.333 4.14 0.00 38.61 1.73
1877 1925 9.220767 GTAGGTTCAAAGTTGAGTCATCTATTT 57.779 33.333 4.14 0.00 38.61 1.40
1878 1926 8.697507 AGGTTCAAAGTTGAGTCATCTATTTT 57.302 30.769 4.14 0.00 38.61 1.82
1879 1927 8.571336 AGGTTCAAAGTTGAGTCATCTATTTTG 58.429 33.333 4.14 6.08 38.39 2.44
1880 1928 8.567948 GGTTCAAAGTTGAGTCATCTATTTTGA 58.432 33.333 10.67 10.67 41.47 2.69
1881 1929 9.950680 GTTCAAAGTTGAGTCATCTATTTTGAA 57.049 29.630 17.70 17.70 45.30 2.69
1883 1931 9.950680 TCAAAGTTGAGTCATCTATTTTGAAAC 57.049 29.630 11.72 0.00 40.83 2.78
1884 1932 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
1885 1933 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
1886 1934 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
1887 1935 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
1888 1936 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
1889 1937 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
1923 1971 3.202151 ACCACTCCATCCGTTCCATAATT 59.798 43.478 0.00 0.00 0.00 1.40
1924 1972 3.565482 CCACTCCATCCGTTCCATAATTG 59.435 47.826 0.00 0.00 0.00 2.32
1925 1973 4.199310 CACTCCATCCGTTCCATAATTGT 58.801 43.478 0.00 0.00 0.00 2.71
1928 1976 6.017934 CACTCCATCCGTTCCATAATTGTAAG 60.018 42.308 0.00 0.00 0.00 2.34
1930 1978 6.053005 TCCATCCGTTCCATAATTGTAAGAC 58.947 40.000 0.00 0.00 0.00 3.01
1980 2029 9.598517 AATTGCCATGTAAACATATTTTACTGG 57.401 29.630 18.78 18.78 36.88 4.00
2028 2077 5.455056 TGTATTCTTAGAATCCTCCTCGC 57.545 43.478 11.06 0.00 0.00 5.03
2069 2118 9.500785 CCAACATTTTTACCCTTAAATCACATT 57.499 29.630 0.00 0.00 0.00 2.71
2086 2135 6.159299 TCACATTTTTGATGGCTTTTCTCA 57.841 33.333 0.00 0.00 0.00 3.27
2091 2140 8.203485 ACATTTTTGATGGCTTTTCTCAAGTTA 58.797 29.630 0.00 0.00 31.11 2.24
2096 2145 7.288810 TGATGGCTTTTCTCAAGTTATGTTT 57.711 32.000 0.00 0.00 0.00 2.83
2119 2168 9.072294 GTTTATCAAAATTTTGGATGTAGTCGG 57.928 33.333 26.45 1.25 38.66 4.79
2129 2178 0.632835 ATGTAGTCGGGACCCCACTA 59.367 55.000 13.59 13.59 35.37 2.74
2168 2219 3.368427 CCACTGCTATTCTCAACGAAGGA 60.368 47.826 0.00 0.00 34.56 3.36
2184 2235 5.776744 ACGAAGGAATAACAACGTAGTCTT 58.223 37.500 0.00 0.00 45.00 3.01
2186 2237 5.632347 CGAAGGAATAACAACGTAGTCTTGT 59.368 40.000 0.00 0.00 45.00 3.16
2191 2242 2.047679 ACAACGTAGTCTTGTCTCGC 57.952 50.000 0.00 0.00 45.00 5.03
2195 2246 0.858135 CGTAGTCTTGTCTCGCGAGC 60.858 60.000 30.97 24.35 0.00 5.03
2226 2277 3.747976 GCATGGGCGTTGTGGACC 61.748 66.667 0.00 0.00 34.79 4.46
2239 2290 1.810532 TGGACCAACCGCAACAAAC 59.189 52.632 0.00 0.00 42.61 2.93
2243 2294 2.295070 GGACCAACCGCAACAAACTAAT 59.705 45.455 0.00 0.00 0.00 1.73
2247 2298 5.903810 ACCAACCGCAACAAACTAATAAAA 58.096 33.333 0.00 0.00 0.00 1.52
2248 2299 6.338937 ACCAACCGCAACAAACTAATAAAAA 58.661 32.000 0.00 0.00 0.00 1.94
2291 2342 6.507023 TCTTTCAAATTGTTCCTCTTCTTGC 58.493 36.000 0.00 0.00 0.00 4.01
2358 2419 4.899502 TCCAGAAGATCAAAGAAGTCCAC 58.100 43.478 0.00 0.00 0.00 4.02
2370 2431 2.230508 AGAAGTCCACGCGATGAACTAA 59.769 45.455 15.93 0.00 0.00 2.24
2431 2492 7.887996 TCTTTTGTCATCATTTTGTAATGGC 57.112 32.000 0.00 0.00 41.23 4.40
2518 2579 2.564721 GCACCTCTTGCGCCCTTTT 61.565 57.895 4.18 0.00 42.79 2.27
2519 2580 2.041153 CACCTCTTGCGCCCTTTTT 58.959 52.632 4.18 0.00 0.00 1.94
2599 2660 7.537596 TTCCACATAAATTCATTCAACAGGT 57.462 32.000 0.00 0.00 0.00 4.00
2638 2699 3.559655 CCACACATTCGAACACTCTGAAA 59.440 43.478 0.00 0.00 0.00 2.69
2668 2729 7.209475 CCATGTCCAAAAACTTTTACACAGAT 58.791 34.615 0.00 0.00 29.64 2.90
2679 2740 7.639113 ACTTTTACACAGATCACCTTGAAAA 57.361 32.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.215196 GAAAAGTAGTTCGCCCACACA 58.785 47.619 0.00 0.00 0.00 3.72
64 68 7.818997 TCGTCTAACTGTAGTTATCATCCAT 57.181 36.000 5.05 0.00 39.49 3.41
91 95 3.794717 TGTGTGTTTACCTAGTTGCGAA 58.205 40.909 0.00 0.00 0.00 4.70
93 97 3.743911 TCATGTGTGTTTACCTAGTTGCG 59.256 43.478 0.00 0.00 0.00 4.85
176 180 3.065371 GTCTAACCATAGTTGCCATGTGC 59.935 47.826 0.00 0.00 36.68 4.57
195 199 2.972713 ACCTAGTTGTCATGTGTGGTCT 59.027 45.455 0.00 0.00 0.00 3.85
207 211 5.676552 TGACATGTGTGTTTACCTAGTTGT 58.323 37.500 1.15 0.00 39.09 3.32
228 232 5.937540 CCACATATGGTCAAACAGTAGTTGA 59.062 40.000 7.80 0.00 41.64 3.18
274 278 4.509616 CACGTGAGGTCCAACCATAATTA 58.490 43.478 10.90 0.00 41.95 1.40
277 281 1.002659 CCACGTGAGGTCCAACCATAA 59.997 52.381 19.30 0.00 41.95 1.90
290 294 2.102757 TGTTTACCTAGTTGCCACGTGA 59.897 45.455 19.30 0.00 0.00 4.35
346 352 4.575885 AGTTGCCGTGTGTGATTAACTAT 58.424 39.130 0.00 0.00 0.00 2.12
376 382 1.081094 GGTAGTTGCCGCGTGTAATT 58.919 50.000 4.92 2.10 0.00 1.40
435 442 9.503427 GTATATTTGTAAAAGCATGTCAACTCC 57.497 33.333 0.00 0.00 0.00 3.85
442 449 7.835822 TGGCAAGTATATTTGTAAAAGCATGT 58.164 30.769 9.44 0.00 0.00 3.21
456 463 4.783227 AGTTATCCGGGATGGCAAGTATAT 59.217 41.667 19.82 0.00 37.80 0.86
459 466 2.404559 AGTTATCCGGGATGGCAAGTA 58.595 47.619 19.82 0.00 37.80 2.24
491 498 3.055458 TGACGATTTAGTTGCCATCCTGA 60.055 43.478 0.00 0.00 0.00 3.86
562 569 3.726517 GCGCGTGTGGCATGAAGT 61.727 61.111 8.43 0.00 43.84 3.01
596 603 0.536233 TGCCACACGCCAACAAGTAT 60.536 50.000 0.00 0.00 36.24 2.12
620 627 2.111999 ATATGTGTGGGCGCGGCTAT 62.112 55.000 32.30 17.49 0.00 2.97
636 643 8.303876 GTGGGCGGATATTAAAATTGTTCATAT 58.696 33.333 0.00 0.00 0.00 1.78
638 645 6.097554 TGTGGGCGGATATTAAAATTGTTCAT 59.902 34.615 0.00 0.00 0.00 2.57
641 648 5.923733 TGTGGGCGGATATTAAAATTGTT 57.076 34.783 0.00 0.00 0.00 2.83
718 725 0.468226 ACACGGGTGGCATATTCGAT 59.532 50.000 0.00 0.00 34.19 3.59
741 748 3.056107 GGCCAATGGGAAAAAGTAAGGAC 60.056 47.826 0.00 0.00 35.59 3.85
742 749 3.169908 GGCCAATGGGAAAAAGTAAGGA 58.830 45.455 0.00 0.00 35.59 3.36
744 751 2.823154 TCGGCCAATGGGAAAAAGTAAG 59.177 45.455 2.24 0.00 35.59 2.34
745 752 2.877866 TCGGCCAATGGGAAAAAGTAA 58.122 42.857 2.24 0.00 35.59 2.24
757 764 2.754946 TACTTCGTTCTTCGGCCAAT 57.245 45.000 2.24 0.00 40.32 3.16
766 773 6.377429 TGAGACCAGATACAATACTTCGTTCT 59.623 38.462 0.00 0.00 0.00 3.01
772 779 5.905331 TGGGATGAGACCAGATACAATACTT 59.095 40.000 0.00 0.00 33.23 2.24
773 780 5.305644 GTGGGATGAGACCAGATACAATACT 59.694 44.000 0.00 0.00 39.00 2.12
774 781 5.070446 TGTGGGATGAGACCAGATACAATAC 59.930 44.000 0.00 0.00 39.00 1.89
775 782 5.215845 TGTGGGATGAGACCAGATACAATA 58.784 41.667 0.00 0.00 39.00 1.90
776 783 4.040047 TGTGGGATGAGACCAGATACAAT 58.960 43.478 0.00 0.00 39.00 2.71
777 784 3.449918 TGTGGGATGAGACCAGATACAA 58.550 45.455 0.00 0.00 39.00 2.41
778 785 3.114643 TGTGGGATGAGACCAGATACA 57.885 47.619 0.00 0.00 39.00 2.29
779 786 3.805108 GCATGTGGGATGAGACCAGATAC 60.805 52.174 0.00 0.00 39.70 2.24
780 787 2.369860 GCATGTGGGATGAGACCAGATA 59.630 50.000 0.00 0.00 39.70 1.98
841 849 1.879380 TGTTGGGCGAAGAACAGATTG 59.121 47.619 0.00 0.00 0.00 2.67
1041 1082 1.808133 GCCTTGACGATCATCCTGGAC 60.808 57.143 0.00 0.00 0.00 4.02
1102 1143 1.540267 CTGACGACCTTCAGAGTCCT 58.460 55.000 0.00 0.00 45.19 3.85
1206 1247 2.069165 GCTGTGAGGGGTCCTTGGTT 62.069 60.000 0.00 0.00 31.76 3.67
1407 1451 2.989253 TCGGCGAGCTTCCTGTCA 60.989 61.111 4.99 0.00 0.00 3.58
1463 1507 4.003788 CGCCTCGGTTCCACCTGT 62.004 66.667 0.00 0.00 35.66 4.00
1466 1510 3.047877 CAACGCCTCGGTTCCACC 61.048 66.667 0.00 0.00 34.05 4.61
1480 1524 1.146358 CCTACGCTTAGCTCGCCAAC 61.146 60.000 1.76 0.00 0.00 3.77
1699 1746 3.006537 AGTTCGTTTTCCTTCCTGATCGA 59.993 43.478 0.00 0.00 0.00 3.59
1730 1777 2.031120 CTGCTCCTCTACCTGGAAGAG 58.969 57.143 0.00 0.00 40.21 2.85
1789 1836 3.462678 GCGTGTCCCCTCTCTCCC 61.463 72.222 0.00 0.00 0.00 4.30
1794 1841 2.113243 GAAACCTGCGTGTCCCCTCT 62.113 60.000 0.00 0.00 0.00 3.69
1815 1863 4.635699 ATTTTGAAACGGAGGGAGTACT 57.364 40.909 0.00 0.00 0.00 2.73
1816 1864 5.727434 TCTATTTTGAAACGGAGGGAGTAC 58.273 41.667 0.00 0.00 0.00 2.73
1817 1865 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1818 1866 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1819 1867 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
1820 1868 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
1821 1869 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
1822 1870 6.743575 AAGTCATCTATTTTGAAACGGAGG 57.256 37.500 0.00 0.00 0.00 4.30
1823 1871 8.936864 AGTTAAGTCATCTATTTTGAAACGGAG 58.063 33.333 0.00 0.00 0.00 4.63
1824 1872 8.842358 AGTTAAGTCATCTATTTTGAAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
1825 1873 9.329913 CAAGTTAAGTCATCTATTTTGAAACGG 57.670 33.333 0.00 0.00 0.00 4.44
1826 1874 9.878599 ACAAGTTAAGTCATCTATTTTGAAACG 57.121 29.630 0.00 0.00 0.00 3.60
1836 1884 9.706691 CTTTGAACCTACAAGTTAAGTCATCTA 57.293 33.333 0.00 0.00 0.00 1.98
1837 1885 8.211629 ACTTTGAACCTACAAGTTAAGTCATCT 58.788 33.333 0.00 0.00 27.32 2.90
1838 1886 8.379457 ACTTTGAACCTACAAGTTAAGTCATC 57.621 34.615 0.00 0.00 27.32 2.92
1839 1887 8.621286 CAACTTTGAACCTACAAGTTAAGTCAT 58.379 33.333 0.00 0.00 30.78 3.06
1840 1888 7.825270 TCAACTTTGAACCTACAAGTTAAGTCA 59.175 33.333 0.00 0.00 30.78 3.41
1841 1889 8.205131 TCAACTTTGAACCTACAAGTTAAGTC 57.795 34.615 0.00 0.00 30.78 3.01
1842 1890 7.827729 ACTCAACTTTGAACCTACAAGTTAAGT 59.172 33.333 0.00 0.00 36.64 2.24
1843 1891 8.209917 ACTCAACTTTGAACCTACAAGTTAAG 57.790 34.615 0.00 0.00 36.64 1.85
1844 1892 7.825270 TGACTCAACTTTGAACCTACAAGTTAA 59.175 33.333 0.00 0.00 36.64 2.01
1845 1893 7.332557 TGACTCAACTTTGAACCTACAAGTTA 58.667 34.615 0.00 0.00 36.64 2.24
1846 1894 6.177610 TGACTCAACTTTGAACCTACAAGTT 58.822 36.000 0.00 0.00 36.64 2.66
1847 1895 5.741011 TGACTCAACTTTGAACCTACAAGT 58.259 37.500 0.00 0.00 36.64 3.16
1848 1896 6.708054 AGATGACTCAACTTTGAACCTACAAG 59.292 38.462 0.00 0.00 36.64 3.16
1849 1897 6.591935 AGATGACTCAACTTTGAACCTACAA 58.408 36.000 0.00 0.00 36.64 2.41
1850 1898 6.174720 AGATGACTCAACTTTGAACCTACA 57.825 37.500 0.00 0.00 36.64 2.74
1851 1899 8.779354 AATAGATGACTCAACTTTGAACCTAC 57.221 34.615 0.00 0.00 36.64 3.18
1852 1900 9.793259 AAAATAGATGACTCAACTTTGAACCTA 57.207 29.630 0.00 0.00 36.64 3.08
1853 1901 8.571336 CAAAATAGATGACTCAACTTTGAACCT 58.429 33.333 0.00 0.00 36.64 3.50
1854 1902 8.567948 TCAAAATAGATGACTCAACTTTGAACC 58.432 33.333 0.00 0.00 36.64 3.62
1855 1903 9.950680 TTCAAAATAGATGACTCAACTTTGAAC 57.049 29.630 9.14 0.00 36.64 3.18
1857 1905 9.950680 GTTTCAAAATAGATGACTCAACTTTGA 57.049 29.630 0.00 0.00 35.57 2.69
1858 1906 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
1859 1907 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
1860 1908 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
1861 1909 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
1862 1910 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
1863 1911 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
1864 1912 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
1865 1913 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
1866 1914 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
1867 1915 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
1868 1916 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1869 1917 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1870 1918 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1871 1919 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1872 1920 7.625828 AAATACTCCCTCCGTTTCAAAATAG 57.374 36.000 0.00 0.00 0.00 1.73
1873 1921 8.411991 AAAAATACTCCCTCCGTTTCAAAATA 57.588 30.769 0.00 0.00 0.00 1.40
1874 1922 6.911250 AAAATACTCCCTCCGTTTCAAAAT 57.089 33.333 0.00 0.00 0.00 1.82
1875 1923 6.718522 AAAAATACTCCCTCCGTTTCAAAA 57.281 33.333 0.00 0.00 0.00 2.44
1909 1957 8.575649 AAAAGTCTTACAATTATGGAACGGAT 57.424 30.769 0.00 0.00 0.00 4.18
1936 1984 4.685030 GCAATTAATAACCACTCCCTCCGA 60.685 45.833 0.00 0.00 0.00 4.55
2007 2056 5.224135 GTGCGAGGAGGATTCTAAGAATAC 58.776 45.833 0.00 0.00 0.00 1.89
2010 2059 2.431057 GGTGCGAGGAGGATTCTAAGAA 59.569 50.000 0.00 0.00 0.00 2.52
2069 2118 7.725251 ACATAACTTGAGAAAAGCCATCAAAA 58.275 30.769 0.00 0.00 32.87 2.44
2074 2123 9.023962 TGATAAACATAACTTGAGAAAAGCCAT 57.976 29.630 0.00 0.00 0.00 4.40
2096 2145 7.066525 GTCCCGACTACATCCAAAATTTTGATA 59.933 37.037 28.44 17.63 40.55 2.15
2117 2166 0.688487 TTGAAACTAGTGGGGTCCCG 59.312 55.000 0.48 0.00 39.42 5.14
2119 2168 3.782656 TTCTTGAAACTAGTGGGGTCC 57.217 47.619 0.00 0.00 0.00 4.46
2151 2202 6.903883 TGTTATTCCTTCGTTGAGAATAGC 57.096 37.500 0.00 0.00 38.34 2.97
2168 2219 4.620184 GCGAGACAAGACTACGTTGTTATT 59.380 41.667 3.70 0.14 38.26 1.40
2184 2235 3.244105 GCAAAAGCTCGCGAGACA 58.756 55.556 38.74 1.86 35.39 3.41
2191 2242 2.202518 CATGGCCGCAAAAGCTCG 60.203 61.111 0.00 0.00 0.00 5.03
2195 2246 1.812093 CATGCCATGGCCGCAAAAG 60.812 57.895 33.44 8.09 40.22 2.27
2252 2303 9.757227 CAATTTGAAAGAGGTGTTTTGGTATTA 57.243 29.630 0.00 0.00 0.00 0.98
2253 2304 8.264347 ACAATTTGAAAGAGGTGTTTTGGTATT 58.736 29.630 2.79 0.00 0.00 1.89
2254 2305 7.791029 ACAATTTGAAAGAGGTGTTTTGGTAT 58.209 30.769 2.79 0.00 0.00 2.73
2255 2306 7.176589 ACAATTTGAAAGAGGTGTTTTGGTA 57.823 32.000 2.79 0.00 0.00 3.25
2256 2307 6.048732 ACAATTTGAAAGAGGTGTTTTGGT 57.951 33.333 2.79 0.00 0.00 3.67
2273 2324 2.029918 GCCGCAAGAAGAGGAACAATTT 60.030 45.455 0.00 0.00 40.01 1.82
2309 2361 0.541863 TTCCGAATCAGGCCTCTTCC 59.458 55.000 0.00 0.00 0.00 3.46
2358 2419 4.084328 GGAATTGATCCTTAGTTCATCGCG 60.084 45.833 0.00 0.00 45.56 5.87
2431 2492 6.872920 ACAAGAGAGCAGATCCTTAGTTTAG 58.127 40.000 0.00 0.00 0.00 1.85
2502 2563 4.599036 AAAAAGGGCGCAAGAGGT 57.401 50.000 10.83 0.00 43.02 3.85
2577 2638 9.703892 TTTTACCTGTTGAATGAATTTATGTGG 57.296 29.630 0.00 0.00 0.00 4.17
2595 2656 5.974751 GTGGTGTGTGTTGTATTTTTACCTG 59.025 40.000 0.00 0.00 0.00 4.00
2599 2660 6.510879 TGTGTGGTGTGTGTTGTATTTTTA 57.489 33.333 0.00 0.00 0.00 1.52
2638 2699 4.835284 AAAGTTTTTGGACATGGGTGTT 57.165 36.364 0.00 0.00 39.09 3.32


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

AutoCloner maintained by Alex Coulton.