Multiple sequence alignment - TraesCS5D01G196900

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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 TraesCS5D01G196900 chr5D 100.000 2483 0 0 1 2483 300128872 300126390 0.000000e+00 4586
1 TraesCS5D01G196900 chr5D 97.959 882 18 0 1 882 539121728 539122609 0.000000e+00 1530
2 TraesCS5D01G196900 chr5D 97.619 882 20 1 1 882 300136294 300135414 0.000000e+00 1511
3 TraesCS5D01G196900 chr5D 91.652 563 44 3 1922 2483 204149378 204148818 0.000000e+00 776
4 TraesCS5D01G196900 chr7D 97.725 879 19 1 1 878 15690282 15689404 0.000000e+00 1511
5 TraesCS5D01G196900 chr7D 97.185 888 24 1 1 887 110807231 110806344 0.000000e+00 1500
6 TraesCS5D01G196900 chr7D 91.459 562 47 1 1922 2483 498068484 498069044 0.000000e+00 771
7 TraesCS5D01G196900 chr3D 97.722 878 20 0 1 878 321708607 321709484 0.000000e+00 1511
8 TraesCS5D01G196900 chr3D 97.608 878 21 0 1 878 321716052 321716929 0.000000e+00 1506
9 TraesCS5D01G196900 chr3D 91.815 562 44 2 1922 2483 337836079 337835520 0.000000e+00 782
10 TraesCS5D01G196900 chr3D 91.741 557 45 1 1922 2478 402459015 402458460 0.000000e+00 773
11 TraesCS5D01G196900 chr2D 97.725 879 19 1 1 878 6418489 6417611 0.000000e+00 1511
12 TraesCS5D01G196900 chr2D 97.725 879 19 1 1 878 75478945 75478067 0.000000e+00 1511
13 TraesCS5D01G196900 chr2D 85.034 882 125 5 883 1763 4661623 4662498 0.000000e+00 891
14 TraesCS5D01G196900 chr2D 86.675 773 96 6 1007 1777 552289453 552288686 0.000000e+00 850
15 TraesCS5D01G196900 chr2D 91.681 565 43 4 1922 2483 118353876 118353313 0.000000e+00 780
16 TraesCS5D01G196900 chr2D 91.652 563 43 3 1922 2483 488206486 488205927 0.000000e+00 776
17 TraesCS5D01G196900 chrUn 97.294 887 23 1 1 886 43352175 43351289 0.000000e+00 1504
18 TraesCS5D01G196900 chr2B 88.045 895 101 6 883 1775 513269952 513269062 0.000000e+00 1055
19 TraesCS5D01G196900 chr2B 86.384 896 114 6 883 1777 657863791 657862903 0.000000e+00 972
20 TraesCS5D01G196900 chr1D 86.704 895 90 16 885 1775 363506165 363507034 0.000000e+00 966
21 TraesCS5D01G196900 chr1D 91.459 562 46 2 1922 2483 2086730 2086171 0.000000e+00 771
22 TraesCS5D01G196900 chr6A 87.190 765 95 3 1000 1763 290265091 290265853 0.000000e+00 867
23 TraesCS5D01G196900 chr6A 82.905 895 142 8 886 1777 477113248 477112362 0.000000e+00 795
24 TraesCS5D01G196900 chr6D 84.222 900 129 10 882 1777 336823352 336822462 0.000000e+00 863
25 TraesCS5D01G196900 chr6D 91.667 564 44 3 1922 2483 104309520 104310082 0.000000e+00 778
26 TraesCS5D01G196900 chr3B 87.434 756 88 5 884 1635 41261180 41260428 0.000000e+00 863
27 TraesCS5D01G196900 chr4D 91.637 562 43 4 1922 2483 65064821 65064264 0.000000e+00 774
28 TraesCS5D01G196900 chr4A 87.356 87 11 0 1786 1872 547017521 547017435 1.570000e-17 100


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 TraesCS5D01G196900 chr5D 300126390 300128872 2482 True 4586 4586 100.000 1 2483 1 chr5D.!!$R2 2482
1 TraesCS5D01G196900 chr5D 539121728 539122609 881 False 1530 1530 97.959 1 882 1 chr5D.!!$F1 881
2 TraesCS5D01G196900 chr5D 300135414 300136294 880 True 1511 1511 97.619 1 882 1 chr5D.!!$R3 881
3 TraesCS5D01G196900 chr5D 204148818 204149378 560 True 776 776 91.652 1922 2483 1 chr5D.!!$R1 561
4 TraesCS5D01G196900 chr7D 15689404 15690282 878 True 1511 1511 97.725 1 878 1 chr7D.!!$R1 877
5 TraesCS5D01G196900 chr7D 110806344 110807231 887 True 1500 1500 97.185 1 887 1 chr7D.!!$R2 886
6 TraesCS5D01G196900 chr7D 498068484 498069044 560 False 771 771 91.459 1922 2483 1 chr7D.!!$F1 561
7 TraesCS5D01G196900 chr3D 321708607 321709484 877 False 1511 1511 97.722 1 878 1 chr3D.!!$F1 877
8 TraesCS5D01G196900 chr3D 321716052 321716929 877 False 1506 1506 97.608 1 878 1 chr3D.!!$F2 877
9 TraesCS5D01G196900 chr3D 337835520 337836079 559 True 782 782 91.815 1922 2483 1 chr3D.!!$R1 561
10 TraesCS5D01G196900 chr3D 402458460 402459015 555 True 773 773 91.741 1922 2478 1 chr3D.!!$R2 556
11 TraesCS5D01G196900 chr2D 6417611 6418489 878 True 1511 1511 97.725 1 878 1 chr2D.!!$R1 877
12 TraesCS5D01G196900 chr2D 75478067 75478945 878 True 1511 1511 97.725 1 878 1 chr2D.!!$R2 877
13 TraesCS5D01G196900 chr2D 4661623 4662498 875 False 891 891 85.034 883 1763 1 chr2D.!!$F1 880
14 TraesCS5D01G196900 chr2D 552288686 552289453 767 True 850 850 86.675 1007 1777 1 chr2D.!!$R5 770
15 TraesCS5D01G196900 chr2D 118353313 118353876 563 True 780 780 91.681 1922 2483 1 chr2D.!!$R3 561
16 TraesCS5D01G196900 chr2D 488205927 488206486 559 True 776 776 91.652 1922 2483 1 chr2D.!!$R4 561
17 TraesCS5D01G196900 chrUn 43351289 43352175 886 True 1504 1504 97.294 1 886 1 chrUn.!!$R1 885
18 TraesCS5D01G196900 chr2B 513269062 513269952 890 True 1055 1055 88.045 883 1775 1 chr2B.!!$R1 892
19 TraesCS5D01G196900 chr2B 657862903 657863791 888 True 972 972 86.384 883 1777 1 chr2B.!!$R2 894
20 TraesCS5D01G196900 chr1D 363506165 363507034 869 False 966 966 86.704 885 1775 1 chr1D.!!$F1 890
21 TraesCS5D01G196900 chr1D 2086171 2086730 559 True 771 771 91.459 1922 2483 1 chr1D.!!$R1 561
22 TraesCS5D01G196900 chr6A 290265091 290265853 762 False 867 867 87.190 1000 1763 1 chr6A.!!$F1 763
23 TraesCS5D01G196900 chr6A 477112362 477113248 886 True 795 795 82.905 886 1777 1 chr6A.!!$R1 891
24 TraesCS5D01G196900 chr6D 336822462 336823352 890 True 863 863 84.222 882 1777 1 chr6D.!!$R1 895
25 TraesCS5D01G196900 chr6D 104309520 104310082 562 False 778 778 91.667 1922 2483 1 chr6D.!!$F1 561
26 TraesCS5D01G196900 chr3B 41260428 41261180 752 True 863 863 87.434 884 1635 1 chr3B.!!$R1 751
27 TraesCS5D01G196900 chr4D 65064264 65064821 557 True 774 774 91.637 1922 2483 1 chr4D.!!$R1 561

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
469 471 0.31904 CCTGCCGGATAGATGACACG 60.319 60.0 5.05 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1941 0.032316 TGGTGGTAGCCGGGTATGTA 60.032 55.0 17.8 3.52 0.0 2.29 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
63 65 2.788786 CGCATTCTTGTTTGCTTTTCGT 59.211 40.909 0.00 0.00 36.71 3.85
124 126 7.698970 CGCGTTGAAAATTATTTTAGTGGGTAT 59.301 33.333 2.65 0.00 31.94 2.73
137 139 7.696992 TTTAGTGGGTATTGGAAATGTTCTC 57.303 36.000 0.00 0.00 0.00 2.87
381 383 2.131067 GGCTTCTCTCTCCCTCCCG 61.131 68.421 0.00 0.00 0.00 5.14
469 471 0.319040 CCTGCCGGATAGATGACACG 60.319 60.000 5.05 0.00 0.00 4.49
673 675 2.284921 CCTCCCAGAGGGCTGTCA 60.285 66.667 2.49 0.00 45.43 3.58
674 676 1.692042 CCTCCCAGAGGGCTGTCAT 60.692 63.158 2.49 0.00 45.43 3.06
909 913 4.499040 GGACGATCGGTTTTAATTGCAATG 59.501 41.667 20.98 0.00 0.00 2.82
926 930 3.609409 GCAATGAACCTCGGAACTTTGTC 60.609 47.826 0.00 0.00 0.00 3.18
966 970 4.749099 GCTCTCTTCGTAATGCAGATTGAT 59.251 41.667 0.00 0.00 0.00 2.57
975 979 5.332581 CGTAATGCAGATTGATACGGACAAG 60.333 44.000 0.00 0.00 36.59 3.16
980 984 4.680708 GCAGATTGATACGGACAAGAAGGA 60.681 45.833 0.00 0.00 0.00 3.36
988 992 1.618837 CGGACAAGAAGGACAAGGAGA 59.381 52.381 0.00 0.00 0.00 3.71
1021 1025 1.604915 GAGAAGGGCAAGGAGGTCC 59.395 63.158 0.00 0.00 0.00 4.46
1180 1225 0.908198 GGTGATCCTTGCTCCTCAGT 59.092 55.000 0.00 0.00 0.00 3.41
1242 1287 3.432186 GCGGTGCCACAAGAGTTT 58.568 55.556 0.00 0.00 0.00 2.66
1247 1292 1.269723 GGTGCCACAAGAGTTTAAGCC 59.730 52.381 0.00 0.00 0.00 4.35
1259 1304 2.039879 AGTTTAAGCCGAGGACCAACAT 59.960 45.455 0.00 0.00 0.00 2.71
1273 1318 1.452651 AACATCGGCTGCTCATGGG 60.453 57.895 13.46 0.00 0.00 4.00
1398 1443 2.126307 CTCACTCCGGACACGCTG 60.126 66.667 0.00 0.00 39.22 5.18
1440 1487 1.197721 GAAGGCATTGAAGTGGTGACG 59.802 52.381 0.00 0.00 0.00 4.35
1503 1550 1.070445 CTGCCCTTCCTATGCTCCG 59.930 63.158 0.00 0.00 0.00 4.63
1520 1567 3.146847 CTCCGGCTGGTTTAGTTTCTTT 58.853 45.455 12.43 0.00 36.30 2.52
1529 1576 7.118825 GGCTGGTTTAGTTTCTTTTCGTACTAT 59.881 37.037 0.00 0.00 0.00 2.12
1689 1741 5.346181 AAGAGGTTACCAGACAATAGCTC 57.654 43.478 3.51 0.00 34.48 4.09
1690 1742 3.707102 AGAGGTTACCAGACAATAGCTCC 59.293 47.826 3.51 0.00 34.73 4.70
1705 1757 1.188863 GCTCCTGCATGGAACCAAAT 58.811 50.000 6.39 0.00 45.63 2.32
1711 1763 2.491693 CTGCATGGAACCAAATACCGTT 59.508 45.455 0.00 0.00 0.00 4.44
1764 1816 3.428534 CCAAACGCTAAGCCAAAATTGAC 59.571 43.478 0.00 0.00 0.00 3.18
1784 1836 2.112380 CCCCCAATGCAAATTTCACC 57.888 50.000 0.00 0.00 0.00 4.02
1785 1837 1.629861 CCCCCAATGCAAATTTCACCT 59.370 47.619 0.00 0.00 0.00 4.00
1786 1838 2.040145 CCCCCAATGCAAATTTCACCTT 59.960 45.455 0.00 0.00 0.00 3.50
1787 1839 3.498301 CCCCCAATGCAAATTTCACCTTT 60.498 43.478 0.00 0.00 0.00 3.11
1788 1840 4.143543 CCCCAATGCAAATTTCACCTTTT 58.856 39.130 0.00 0.00 0.00 2.27
1789 1841 5.312079 CCCCAATGCAAATTTCACCTTTTA 58.688 37.500 0.00 0.00 0.00 1.52
1790 1842 5.412286 CCCCAATGCAAATTTCACCTTTTAG 59.588 40.000 0.00 0.00 0.00 1.85
1791 1843 5.412286 CCCAATGCAAATTTCACCTTTTAGG 59.588 40.000 0.00 0.00 42.49 2.69
1792 1844 5.106594 CCAATGCAAATTTCACCTTTTAGGC 60.107 40.000 0.00 0.00 39.63 3.93
1793 1845 4.953940 TGCAAATTTCACCTTTTAGGCT 57.046 36.364 0.00 0.00 39.63 4.58
1794 1846 4.630111 TGCAAATTTCACCTTTTAGGCTG 58.370 39.130 0.00 0.00 39.63 4.85
1795 1847 4.100808 TGCAAATTTCACCTTTTAGGCTGT 59.899 37.500 0.00 0.00 39.63 4.40
1796 1848 5.056480 GCAAATTTCACCTTTTAGGCTGTT 58.944 37.500 0.00 0.00 39.63 3.16
1797 1849 5.527214 GCAAATTTCACCTTTTAGGCTGTTT 59.473 36.000 0.00 0.00 39.63 2.83
1798 1850 6.038161 GCAAATTTCACCTTTTAGGCTGTTTT 59.962 34.615 0.00 0.00 39.63 2.43
1799 1851 7.630026 CAAATTTCACCTTTTAGGCTGTTTTC 58.370 34.615 0.00 0.00 39.63 2.29
1800 1852 4.929819 TTCACCTTTTAGGCTGTTTTCC 57.070 40.909 0.00 0.00 39.63 3.13
1801 1853 4.178956 TCACCTTTTAGGCTGTTTTCCT 57.821 40.909 0.00 0.00 39.63 3.36
1802 1854 4.542697 TCACCTTTTAGGCTGTTTTCCTT 58.457 39.130 0.00 0.00 39.63 3.36
1803 1855 4.583073 TCACCTTTTAGGCTGTTTTCCTTC 59.417 41.667 0.00 0.00 39.63 3.46
1804 1856 4.340950 CACCTTTTAGGCTGTTTTCCTTCA 59.659 41.667 0.00 0.00 39.63 3.02
1805 1857 4.959839 ACCTTTTAGGCTGTTTTCCTTCAA 59.040 37.500 0.00 0.00 39.63 2.69
1806 1858 5.163447 ACCTTTTAGGCTGTTTTCCTTCAAC 60.163 40.000 0.00 0.00 39.63 3.18
1807 1859 5.163457 CCTTTTAGGCTGTTTTCCTTCAACA 60.163 40.000 0.00 0.00 35.21 3.33
1808 1860 5.923733 TTTAGGCTGTTTTCCTTCAACAA 57.076 34.783 0.00 0.00 33.74 2.83
1809 1861 5.514274 TTAGGCTGTTTTCCTTCAACAAG 57.486 39.130 0.00 0.00 33.74 3.16
1810 1862 3.631250 AGGCTGTTTTCCTTCAACAAGA 58.369 40.909 0.00 0.00 33.74 3.02
1811 1863 3.381590 AGGCTGTTTTCCTTCAACAAGAC 59.618 43.478 0.00 0.00 33.74 3.01
1812 1864 3.381590 GGCTGTTTTCCTTCAACAAGACT 59.618 43.478 0.00 0.00 33.74 3.24
1813 1865 4.498177 GGCTGTTTTCCTTCAACAAGACTC 60.498 45.833 0.00 0.00 33.74 3.36
1814 1866 4.096382 GCTGTTTTCCTTCAACAAGACTCA 59.904 41.667 0.00 0.00 33.74 3.41
1815 1867 5.731686 GCTGTTTTCCTTCAACAAGACTCAG 60.732 44.000 0.00 0.00 33.74 3.35
1816 1868 5.253330 TGTTTTCCTTCAACAAGACTCAGT 58.747 37.500 0.00 0.00 31.05 3.41
1817 1869 5.710099 TGTTTTCCTTCAACAAGACTCAGTT 59.290 36.000 0.00 0.00 31.05 3.16
1818 1870 5.818136 TTTCCTTCAACAAGACTCAGTTG 57.182 39.130 12.27 12.27 44.84 3.16
1822 1874 2.838736 TCAACAAGACTCAGTTGAGCC 58.161 47.619 15.57 0.00 46.46 4.70
1823 1875 2.170397 TCAACAAGACTCAGTTGAGCCA 59.830 45.455 15.57 0.00 46.46 4.75
1824 1876 2.540265 ACAAGACTCAGTTGAGCCAG 57.460 50.000 8.99 0.00 45.79 4.85
1825 1877 1.071385 ACAAGACTCAGTTGAGCCAGG 59.929 52.381 8.99 0.48 45.79 4.45
1826 1878 0.036022 AAGACTCAGTTGAGCCAGGC 59.964 55.000 1.84 1.84 45.79 4.85
1827 1879 0.835543 AGACTCAGTTGAGCCAGGCT 60.836 55.000 16.12 16.12 45.79 4.58
1828 1880 0.898320 GACTCAGTTGAGCCAGGCTA 59.102 55.000 16.16 0.00 45.79 3.93
1829 1881 1.276421 GACTCAGTTGAGCCAGGCTAA 59.724 52.381 16.16 3.20 45.79 3.09
1830 1882 1.277557 ACTCAGTTGAGCCAGGCTAAG 59.722 52.381 16.16 7.82 45.79 2.18
1831 1883 0.036010 TCAGTTGAGCCAGGCTAAGC 60.036 55.000 16.16 9.75 39.88 3.09
1832 1884 0.035630 CAGTTGAGCCAGGCTAAGCT 60.036 55.000 16.16 12.47 39.88 3.74
1833 1885 1.208052 CAGTTGAGCCAGGCTAAGCTA 59.792 52.381 16.16 0.00 39.88 3.32
1834 1886 1.484240 AGTTGAGCCAGGCTAAGCTAG 59.516 52.381 16.16 0.00 39.88 3.42
1842 1894 2.112087 GCTAAGCTAGCCAGGCCC 59.888 66.667 12.13 0.00 45.95 5.80
1843 1895 2.423446 CTAAGCTAGCCAGGCCCG 59.577 66.667 12.13 0.00 0.00 6.13
1844 1896 3.161450 TAAGCTAGCCAGGCCCGG 61.161 66.667 12.13 0.00 0.00 5.73
1852 1904 4.860881 CCAGGCCCGGCTCCTAGA 62.861 72.222 9.86 0.00 31.52 2.43
1853 1905 3.230245 CAGGCCCGGCTCCTAGAG 61.230 72.222 9.86 0.00 31.52 2.43
1865 1917 2.069273 CTCCTAGAGCAACCAAACACG 58.931 52.381 0.00 0.00 0.00 4.49
1866 1918 0.517316 CCTAGAGCAACCAAACACGC 59.483 55.000 0.00 0.00 0.00 5.34
1867 1919 0.517316 CTAGAGCAACCAAACACGCC 59.483 55.000 0.00 0.00 0.00 5.68
1868 1920 0.887387 TAGAGCAACCAAACACGCCC 60.887 55.000 0.00 0.00 0.00 6.13
1869 1921 2.441164 AGCAACCAAACACGCCCA 60.441 55.556 0.00 0.00 0.00 5.36
1870 1922 1.805428 GAGCAACCAAACACGCCCAT 61.805 55.000 0.00 0.00 0.00 4.00
1871 1923 0.538516 AGCAACCAAACACGCCCATA 60.539 50.000 0.00 0.00 0.00 2.74
1872 1924 0.109319 GCAACCAAACACGCCCATAG 60.109 55.000 0.00 0.00 0.00 2.23
1873 1925 1.529226 CAACCAAACACGCCCATAGA 58.471 50.000 0.00 0.00 0.00 1.98
1874 1926 1.468520 CAACCAAACACGCCCATAGAG 59.531 52.381 0.00 0.00 0.00 2.43
1875 1927 0.981183 ACCAAACACGCCCATAGAGA 59.019 50.000 0.00 0.00 0.00 3.10
1876 1928 1.338769 ACCAAACACGCCCATAGAGAC 60.339 52.381 0.00 0.00 0.00 3.36
1877 1929 1.066143 CCAAACACGCCCATAGAGACT 60.066 52.381 0.00 0.00 0.00 3.24
1878 1930 2.615493 CCAAACACGCCCATAGAGACTT 60.615 50.000 0.00 0.00 0.00 3.01
1879 1931 2.673368 CAAACACGCCCATAGAGACTTC 59.327 50.000 0.00 0.00 0.00 3.01
1880 1932 1.557099 ACACGCCCATAGAGACTTCA 58.443 50.000 0.00 0.00 0.00 3.02
1881 1933 1.478510 ACACGCCCATAGAGACTTCAG 59.521 52.381 0.00 0.00 0.00 3.02
1882 1934 1.478510 CACGCCCATAGAGACTTCAGT 59.521 52.381 0.00 0.00 0.00 3.41
1883 1935 2.093973 CACGCCCATAGAGACTTCAGTT 60.094 50.000 0.00 0.00 0.00 3.16
1884 1936 2.093973 ACGCCCATAGAGACTTCAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
1885 1937 2.739932 CGCCCATAGAGACTTCAGTTGG 60.740 54.545 0.00 0.00 0.00 3.77
1886 1938 2.501723 GCCCATAGAGACTTCAGTTGGA 59.498 50.000 0.00 0.00 0.00 3.53
1887 1939 3.431486 GCCCATAGAGACTTCAGTTGGAG 60.431 52.174 0.00 0.00 0.00 3.86
1888 1940 3.772025 CCCATAGAGACTTCAGTTGGAGT 59.228 47.826 0.00 0.00 0.00 3.85
1889 1941 4.223923 CCCATAGAGACTTCAGTTGGAGTT 59.776 45.833 0.00 0.00 0.00 3.01
1890 1942 5.422331 CCCATAGAGACTTCAGTTGGAGTTA 59.578 44.000 0.00 0.00 0.00 2.24
1891 1943 6.334202 CCATAGAGACTTCAGTTGGAGTTAC 58.666 44.000 0.00 0.00 0.00 2.50
1892 1944 6.071334 CCATAGAGACTTCAGTTGGAGTTACA 60.071 42.308 0.00 0.00 0.00 2.41
1893 1945 7.364232 CCATAGAGACTTCAGTTGGAGTTACAT 60.364 40.741 0.00 0.00 0.00 2.29
1894 1946 8.687242 CATAGAGACTTCAGTTGGAGTTACATA 58.313 37.037 0.00 0.00 0.00 2.29
1895 1947 6.926313 AGAGACTTCAGTTGGAGTTACATAC 58.074 40.000 0.00 0.00 0.00 2.39
1896 1948 6.038997 AGACTTCAGTTGGAGTTACATACC 57.961 41.667 0.00 0.00 0.00 2.73
1897 1949 5.046520 AGACTTCAGTTGGAGTTACATACCC 60.047 44.000 0.00 0.00 0.00 3.69
1898 1950 3.880047 TCAGTTGGAGTTACATACCCG 57.120 47.619 0.00 0.00 0.00 5.28
1899 1951 2.498481 TCAGTTGGAGTTACATACCCGG 59.502 50.000 0.00 0.00 0.00 5.73
1900 1952 1.208776 AGTTGGAGTTACATACCCGGC 59.791 52.381 0.00 0.00 0.00 6.13
1901 1953 1.208776 GTTGGAGTTACATACCCGGCT 59.791 52.381 0.00 0.00 0.00 5.52
1902 1954 2.431782 GTTGGAGTTACATACCCGGCTA 59.568 50.000 0.00 0.00 0.00 3.93
1903 1955 2.034124 TGGAGTTACATACCCGGCTAC 58.966 52.381 0.00 0.00 0.00 3.58
1904 1956 1.342496 GGAGTTACATACCCGGCTACC 59.658 57.143 0.00 0.00 0.00 3.18
1905 1957 2.034124 GAGTTACATACCCGGCTACCA 58.966 52.381 0.00 0.00 0.00 3.25
1906 1958 1.758862 AGTTACATACCCGGCTACCAC 59.241 52.381 0.00 0.00 0.00 4.16
1907 1959 1.122227 TTACATACCCGGCTACCACC 58.878 55.000 0.00 0.00 0.00 4.61
1908 1960 0.032316 TACATACCCGGCTACCACCA 60.032 55.000 0.00 0.00 0.00 4.17
1909 1961 1.145377 CATACCCGGCTACCACCAC 59.855 63.158 0.00 0.00 0.00 4.16
1910 1962 1.002533 ATACCCGGCTACCACCACT 59.997 57.895 0.00 0.00 0.00 4.00
1911 1963 0.262580 ATACCCGGCTACCACCACTA 59.737 55.000 0.00 0.00 0.00 2.74
1912 1964 0.684153 TACCCGGCTACCACCACTAC 60.684 60.000 0.00 0.00 0.00 2.73
1913 1965 1.985662 CCCGGCTACCACCACTACA 60.986 63.158 0.00 0.00 0.00 2.74
1914 1966 1.546589 CCCGGCTACCACCACTACAA 61.547 60.000 0.00 0.00 0.00 2.41
1915 1967 0.322322 CCGGCTACCACCACTACAAA 59.678 55.000 0.00 0.00 0.00 2.83
1916 1968 1.270947 CCGGCTACCACCACTACAAAA 60.271 52.381 0.00 0.00 0.00 2.44
1917 1969 2.496111 CGGCTACCACCACTACAAAAA 58.504 47.619 0.00 0.00 0.00 1.94
2127 2181 4.563782 AGGAAAATATCGGGGAGTTCCTA 58.436 43.478 8.32 0.00 42.33 2.94
2135 2189 1.683011 CGGGGAGTTCCTAGTTACGGA 60.683 57.143 0.00 0.00 35.95 4.69
2147 2203 3.222599 TTACGGAGGGTGGTCGGGA 62.223 63.158 0.00 0.00 0.00 5.14
2148 2204 2.519119 TTACGGAGGGTGGTCGGGAT 62.519 60.000 0.00 0.00 0.00 3.85
2164 2220 0.026803 GGATCGAGCAATGCACGTTC 59.973 55.000 22.70 22.14 42.61 3.95
2241 2297 0.544595 AGGGGTTCGCCTACTGAACT 60.545 55.000 6.63 0.00 44.02 3.01
2309 2365 3.510388 TCGATCTGGCTGTTAACTGAG 57.490 47.619 15.89 5.88 0.00 3.35
2327 2383 1.068083 GCCTGATCGAGCGATTCCA 59.932 57.895 6.84 0.93 34.60 3.53
2388 2444 3.993081 CCTCTTGATGAACAGTGAGTGTC 59.007 47.826 0.00 0.00 39.03 3.67
2439 2497 0.698818 GGGTTGGATGAACAGGACCT 59.301 55.000 0.00 0.00 36.12 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 126 2.238521 GTGGGCTGAGAACATTTCCAA 58.761 47.619 0.00 0.00 0.00 3.53
137 139 6.692681 CGAACTGAAAATATTTATGTGGGCTG 59.307 38.462 0.01 0.00 0.00 4.85
469 471 4.082190 TCTCTACAGAGTTGCACACATACC 60.082 45.833 6.16 0.00 42.60 2.73
635 637 3.307906 TCGAACAGTCCCCCGGTG 61.308 66.667 0.00 0.00 0.00 4.94
636 638 3.308705 GTCGAACAGTCCCCCGGT 61.309 66.667 0.00 0.00 0.00 5.28
673 675 5.276694 TGTATACCCTCATCTGCTCCTAT 57.723 43.478 0.00 0.00 0.00 2.57
674 676 4.741928 TGTATACCCTCATCTGCTCCTA 57.258 45.455 0.00 0.00 0.00 2.94
893 897 4.323336 CGAGGTTCATTGCAATTAAAACCG 59.677 41.667 26.77 19.44 40.79 4.44
909 913 1.525619 CACGACAAAGTTCCGAGGTTC 59.474 52.381 0.00 0.00 0.00 3.62
926 930 0.933097 AGCGCATTATGAAGAGCACG 59.067 50.000 11.47 0.00 0.00 5.34
966 970 2.561419 CTCCTTGTCCTTCTTGTCCGTA 59.439 50.000 0.00 0.00 0.00 4.02
975 979 1.680249 GGCACCATCTCCTTGTCCTTC 60.680 57.143 0.00 0.00 0.00 3.46
980 984 2.045926 GCGGCACCATCTCCTTGT 60.046 61.111 0.00 0.00 0.00 3.16
1021 1025 4.431131 AACCTCCATGGGCGGCAG 62.431 66.667 13.02 0.53 41.11 4.85
1040 1085 1.994507 CTCCTCAGGCGTAGTCGGTG 61.995 65.000 0.00 0.00 36.95 4.94
1118 1163 0.107945 CTCCTCTTGGTAGTGGCTGC 60.108 60.000 0.00 0.00 35.45 5.25
1120 1165 0.618968 CCCTCCTCTTGGTAGTGGCT 60.619 60.000 0.00 0.00 35.45 4.75
1203 1248 2.650322 GGGAAGTGTTTGGTGAAGTCA 58.350 47.619 0.00 0.00 0.00 3.41
1233 1278 2.289506 GGTCCTCGGCTTAAACTCTTGT 60.290 50.000 0.00 0.00 0.00 3.16
1242 1287 0.174845 CGATGTTGGTCCTCGGCTTA 59.825 55.000 0.00 0.00 32.17 3.09
1247 1292 1.811266 CAGCCGATGTTGGTCCTCG 60.811 63.158 0.00 0.00 34.77 4.63
1273 1318 4.394712 CAGCCGGACAGTCACCCC 62.395 72.222 5.05 0.00 0.00 4.95
1333 1378 2.021068 CTGATCTGATGGACGGCGGT 62.021 60.000 13.24 0.00 0.00 5.68
1503 1550 4.563337 ACGAAAAGAAACTAAACCAGCC 57.437 40.909 0.00 0.00 0.00 4.85
1520 1567 6.629649 CAGTTCAAACGCAAAAATAGTACGAA 59.370 34.615 0.00 0.00 0.00 3.85
1529 1576 7.763172 AAACATATCAGTTCAAACGCAAAAA 57.237 28.000 0.00 0.00 0.00 1.94
1572 1619 2.024176 AACCATAGCTAACCGCAGTG 57.976 50.000 0.00 0.00 42.61 3.66
1689 1741 1.405105 CGGTATTTGGTTCCATGCAGG 59.595 52.381 0.00 0.00 39.47 4.85
1690 1742 2.091541 ACGGTATTTGGTTCCATGCAG 58.908 47.619 0.00 0.00 0.00 4.41
1705 1757 1.421382 GCTCACGCAACTAAACGGTA 58.579 50.000 0.00 0.00 35.78 4.02
1711 1763 1.736645 GCTCGGCTCACGCAACTAA 60.737 57.895 0.00 0.00 43.86 2.24
1769 1821 5.702209 AGCCTAAAAGGTGAAATTTGCATTG 59.298 36.000 0.00 0.00 37.80 2.82
1777 1829 5.602561 AGGAAAACAGCCTAAAAGGTGAAAT 59.397 36.000 0.00 0.00 37.80 2.17
1778 1830 4.959839 AGGAAAACAGCCTAAAAGGTGAAA 59.040 37.500 0.00 0.00 37.80 2.69
1779 1831 4.542697 AGGAAAACAGCCTAAAAGGTGAA 58.457 39.130 0.00 0.00 37.80 3.18
1780 1832 4.178956 AGGAAAACAGCCTAAAAGGTGA 57.821 40.909 0.00 0.00 37.80 4.02
1781 1833 4.340950 TGAAGGAAAACAGCCTAAAAGGTG 59.659 41.667 0.00 0.00 37.80 4.00
1782 1834 4.542697 TGAAGGAAAACAGCCTAAAAGGT 58.457 39.130 0.00 0.00 37.80 3.50
1783 1835 5.163457 TGTTGAAGGAAAACAGCCTAAAAGG 60.163 40.000 0.00 0.00 33.84 3.11
1784 1836 5.901552 TGTTGAAGGAAAACAGCCTAAAAG 58.098 37.500 0.00 0.00 33.76 2.27
1785 1837 5.923733 TGTTGAAGGAAAACAGCCTAAAA 57.076 34.783 0.00 0.00 33.76 1.52
1786 1838 5.654650 TCTTGTTGAAGGAAAACAGCCTAAA 59.345 36.000 0.00 0.00 38.67 1.85
1787 1839 5.067283 GTCTTGTTGAAGGAAAACAGCCTAA 59.933 40.000 0.00 0.00 38.67 2.69
1788 1840 4.578928 GTCTTGTTGAAGGAAAACAGCCTA 59.421 41.667 0.00 0.00 38.67 3.93
1789 1841 3.381590 GTCTTGTTGAAGGAAAACAGCCT 59.618 43.478 0.00 0.00 38.67 4.58
1790 1842 3.381590 AGTCTTGTTGAAGGAAAACAGCC 59.618 43.478 0.00 0.00 38.67 4.85
1791 1843 4.096382 TGAGTCTTGTTGAAGGAAAACAGC 59.904 41.667 0.00 0.00 38.67 4.40
1792 1844 5.355350 ACTGAGTCTTGTTGAAGGAAAACAG 59.645 40.000 0.00 0.00 38.67 3.16
1793 1845 5.253330 ACTGAGTCTTGTTGAAGGAAAACA 58.747 37.500 0.00 0.00 35.78 2.83
1794 1846 5.819825 ACTGAGTCTTGTTGAAGGAAAAC 57.180 39.130 0.00 0.00 0.00 2.43
1795 1847 5.943416 TCAACTGAGTCTTGTTGAAGGAAAA 59.057 36.000 21.36 5.74 46.17 2.29
1796 1848 5.496556 TCAACTGAGTCTTGTTGAAGGAAA 58.503 37.500 21.36 6.24 46.17 3.13
1797 1849 5.097742 TCAACTGAGTCTTGTTGAAGGAA 57.902 39.130 21.36 6.75 46.17 3.36
1798 1850 4.753516 TCAACTGAGTCTTGTTGAAGGA 57.246 40.909 21.36 7.01 46.17 3.36
1802 1854 2.170397 TGGCTCAACTGAGTCTTGTTGA 59.830 45.455 21.84 21.84 46.41 3.18
1803 1855 2.547211 CTGGCTCAACTGAGTCTTGTTG 59.453 50.000 12.29 17.55 46.41 3.33
1804 1856 2.486191 CCTGGCTCAACTGAGTCTTGTT 60.486 50.000 12.29 0.00 46.41 2.83
1805 1857 1.071385 CCTGGCTCAACTGAGTCTTGT 59.929 52.381 12.29 0.00 46.41 3.16
1806 1858 1.805869 CCTGGCTCAACTGAGTCTTG 58.194 55.000 12.29 5.63 46.41 3.02
1807 1859 0.036022 GCCTGGCTCAACTGAGTCTT 59.964 55.000 12.43 0.00 46.41 3.01
1808 1860 0.835543 AGCCTGGCTCAACTGAGTCT 60.836 55.000 17.22 0.00 46.41 3.24
1809 1861 0.898320 TAGCCTGGCTCAACTGAGTC 59.102 55.000 27.16 4.32 46.44 3.36
1810 1862 1.277557 CTTAGCCTGGCTCAACTGAGT 59.722 52.381 27.16 0.00 43.85 3.41
1811 1863 2.011046 GCTTAGCCTGGCTCAACTGAG 61.011 57.143 27.16 14.64 44.75 3.35
1812 1864 0.036010 GCTTAGCCTGGCTCAACTGA 60.036 55.000 27.16 2.88 40.44 3.41
1813 1865 0.035630 AGCTTAGCCTGGCTCAACTG 60.036 55.000 27.16 12.54 40.44 3.16
1814 1866 1.484240 CTAGCTTAGCCTGGCTCAACT 59.516 52.381 27.16 21.37 40.44 3.16
1815 1867 1.946745 CTAGCTTAGCCTGGCTCAAC 58.053 55.000 27.16 15.22 40.44 3.18
1816 1868 0.179000 GCTAGCTTAGCCTGGCTCAA 59.821 55.000 27.16 16.05 45.95 3.02
1817 1869 1.826024 GCTAGCTTAGCCTGGCTCA 59.174 57.895 27.16 14.20 45.95 4.26
1818 1870 4.769047 GCTAGCTTAGCCTGGCTC 57.231 61.111 27.16 11.43 45.95 4.70
1826 1878 2.423446 CGGGCCTGGCTAGCTTAG 59.577 66.667 19.68 13.01 0.00 2.18
1827 1879 3.161450 CCGGGCCTGGCTAGCTTA 61.161 66.667 20.35 3.29 0.00 3.09
1835 1887 4.860881 TCTAGGAGCCGGGCCTGG 62.861 72.222 27.88 27.88 36.96 4.45
1836 1888 3.230245 CTCTAGGAGCCGGGCCTG 61.230 72.222 17.02 3.88 36.96 4.85
1845 1897 2.069273 CGTGTTTGGTTGCTCTAGGAG 58.931 52.381 0.00 0.00 0.00 3.69
1846 1898 1.876416 GCGTGTTTGGTTGCTCTAGGA 60.876 52.381 0.00 0.00 0.00 2.94
1847 1899 0.517316 GCGTGTTTGGTTGCTCTAGG 59.483 55.000 0.00 0.00 0.00 3.02
1848 1900 0.517316 GGCGTGTTTGGTTGCTCTAG 59.483 55.000 0.00 0.00 0.00 2.43
1849 1901 0.887387 GGGCGTGTTTGGTTGCTCTA 60.887 55.000 0.00 0.00 0.00 2.43
1850 1902 2.193536 GGGCGTGTTTGGTTGCTCT 61.194 57.895 0.00 0.00 0.00 4.09
1851 1903 1.805428 ATGGGCGTGTTTGGTTGCTC 61.805 55.000 0.00 0.00 0.00 4.26
1852 1904 0.538516 TATGGGCGTGTTTGGTTGCT 60.539 50.000 0.00 0.00 0.00 3.91
1853 1905 0.109319 CTATGGGCGTGTTTGGTTGC 60.109 55.000 0.00 0.00 0.00 4.17
1854 1906 1.468520 CTCTATGGGCGTGTTTGGTTG 59.531 52.381 0.00 0.00 0.00 3.77
1855 1907 1.349688 TCTCTATGGGCGTGTTTGGTT 59.650 47.619 0.00 0.00 0.00 3.67
1856 1908 0.981183 TCTCTATGGGCGTGTTTGGT 59.019 50.000 0.00 0.00 0.00 3.67
1857 1909 1.066143 AGTCTCTATGGGCGTGTTTGG 60.066 52.381 0.00 0.00 0.00 3.28
1858 1910 2.386661 AGTCTCTATGGGCGTGTTTG 57.613 50.000 0.00 0.00 0.00 2.93
1859 1911 2.301870 TGAAGTCTCTATGGGCGTGTTT 59.698 45.455 0.00 0.00 0.00 2.83
1860 1912 1.899814 TGAAGTCTCTATGGGCGTGTT 59.100 47.619 0.00 0.00 0.00 3.32
1861 1913 1.478510 CTGAAGTCTCTATGGGCGTGT 59.521 52.381 0.00 0.00 0.00 4.49
1862 1914 1.478510 ACTGAAGTCTCTATGGGCGTG 59.521 52.381 0.00 0.00 0.00 5.34
1863 1915 1.853963 ACTGAAGTCTCTATGGGCGT 58.146 50.000 0.00 0.00 0.00 5.68
1864 1916 2.544685 CAACTGAAGTCTCTATGGGCG 58.455 52.381 0.00 0.00 0.00 6.13
1865 1917 2.501723 TCCAACTGAAGTCTCTATGGGC 59.498 50.000 0.00 0.00 0.00 5.36
1866 1918 3.772025 ACTCCAACTGAAGTCTCTATGGG 59.228 47.826 0.00 0.00 0.00 4.00
1867 1919 5.413309 AACTCCAACTGAAGTCTCTATGG 57.587 43.478 0.00 0.00 0.00 2.74
1868 1920 6.925211 TGTAACTCCAACTGAAGTCTCTATG 58.075 40.000 0.00 0.00 0.00 2.23
1869 1921 7.726033 ATGTAACTCCAACTGAAGTCTCTAT 57.274 36.000 0.00 0.00 0.00 1.98
1870 1922 7.122353 GGTATGTAACTCCAACTGAAGTCTCTA 59.878 40.741 0.00 0.00 0.00 2.43
1871 1923 6.071278 GGTATGTAACTCCAACTGAAGTCTCT 60.071 42.308 0.00 0.00 0.00 3.10
1872 1924 6.100668 GGTATGTAACTCCAACTGAAGTCTC 58.899 44.000 0.00 0.00 0.00 3.36
1873 1925 5.046520 GGGTATGTAACTCCAACTGAAGTCT 60.047 44.000 0.00 0.00 0.00 3.24
1874 1926 5.176592 GGGTATGTAACTCCAACTGAAGTC 58.823 45.833 0.00 0.00 0.00 3.01
1875 1927 4.322499 CGGGTATGTAACTCCAACTGAAGT 60.322 45.833 0.00 0.00 0.00 3.01
1876 1928 4.181578 CGGGTATGTAACTCCAACTGAAG 58.818 47.826 0.00 0.00 0.00 3.02
1877 1929 3.055675 CCGGGTATGTAACTCCAACTGAA 60.056 47.826 0.00 0.00 0.00 3.02
1878 1930 2.498481 CCGGGTATGTAACTCCAACTGA 59.502 50.000 0.00 0.00 0.00 3.41
1879 1931 2.901249 CCGGGTATGTAACTCCAACTG 58.099 52.381 0.00 0.00 0.00 3.16
1880 1932 1.208776 GCCGGGTATGTAACTCCAACT 59.791 52.381 2.18 0.00 0.00 3.16
1881 1933 1.208776 AGCCGGGTATGTAACTCCAAC 59.791 52.381 3.10 0.00 0.00 3.77
1882 1934 1.575419 AGCCGGGTATGTAACTCCAA 58.425 50.000 3.10 0.00 0.00 3.53
1883 1935 2.034124 GTAGCCGGGTATGTAACTCCA 58.966 52.381 17.80 0.00 0.00 3.86
1884 1936 1.342496 GGTAGCCGGGTATGTAACTCC 59.658 57.143 17.80 7.56 0.00 3.85
1885 1937 2.034124 TGGTAGCCGGGTATGTAACTC 58.966 52.381 17.80 1.42 0.00 3.01
1886 1938 1.758862 GTGGTAGCCGGGTATGTAACT 59.241 52.381 17.80 0.00 0.00 2.24
1887 1939 1.202568 GGTGGTAGCCGGGTATGTAAC 60.203 57.143 17.80 12.13 0.00 2.50
1888 1940 1.122227 GGTGGTAGCCGGGTATGTAA 58.878 55.000 17.80 0.00 0.00 2.41
1889 1941 0.032316 TGGTGGTAGCCGGGTATGTA 60.032 55.000 17.80 3.52 0.00 2.29
1890 1942 1.306312 TGGTGGTAGCCGGGTATGT 60.306 57.895 17.80 0.00 0.00 2.29
1891 1943 1.145377 GTGGTGGTAGCCGGGTATG 59.855 63.158 17.80 0.00 0.00 2.39
1892 1944 0.262580 TAGTGGTGGTAGCCGGGTAT 59.737 55.000 17.80 0.92 0.00 2.73
1893 1945 0.684153 GTAGTGGTGGTAGCCGGGTA 60.684 60.000 9.87 9.87 0.00 3.69
1894 1946 1.986210 GTAGTGGTGGTAGCCGGGT 60.986 63.158 12.58 12.58 0.00 5.28
1895 1947 1.546589 TTGTAGTGGTGGTAGCCGGG 61.547 60.000 2.18 0.00 0.00 5.73
1896 1948 0.322322 TTTGTAGTGGTGGTAGCCGG 59.678 55.000 0.00 0.00 0.00 6.13
1897 1949 2.172851 TTTTGTAGTGGTGGTAGCCG 57.827 50.000 0.00 0.00 0.00 5.52
1916 1968 2.828877 TCGTCACGGATGTGTCTTTTT 58.171 42.857 0.00 0.00 46.49 1.94
1917 1969 2.519377 TCGTCACGGATGTGTCTTTT 57.481 45.000 0.00 0.00 46.49 2.27
1918 1970 2.743636 ATCGTCACGGATGTGTCTTT 57.256 45.000 0.00 0.00 46.49 2.52
1919 1971 3.861276 TTATCGTCACGGATGTGTCTT 57.139 42.857 0.00 0.00 46.49 3.01
1920 1972 4.112634 CAATTATCGTCACGGATGTGTCT 58.887 43.478 0.00 0.00 46.49 3.41
1926 1978 4.118093 TGTCACAATTATCGTCACGGAT 57.882 40.909 0.00 0.00 0.00 4.18
1929 1981 4.843984 GGTTTTGTCACAATTATCGTCACG 59.156 41.667 0.00 0.00 0.00 4.35
1930 1982 5.851177 CAGGTTTTGTCACAATTATCGTCAC 59.149 40.000 0.00 0.00 0.00 3.67
1999 2052 0.552848 AGCCCATTTCCCGTCATGAT 59.447 50.000 0.00 0.00 0.00 2.45
2007 2060 2.169144 CAGGATGAAAAGCCCATTTCCC 59.831 50.000 5.18 1.47 39.69 3.97
2009 2062 2.169144 CCCAGGATGAAAAGCCCATTTC 59.831 50.000 0.00 1.42 39.69 2.17
2043 2097 2.230508 CCAAAGAATGTCATGCAGCTGT 59.769 45.455 16.64 0.00 0.00 4.40
2127 2181 1.980772 CCGACCACCCTCCGTAACT 60.981 63.158 0.00 0.00 0.00 2.24
2135 2189 2.442272 CTCGATCCCGACCACCCT 60.442 66.667 0.00 0.00 40.30 4.34
2147 2203 0.391661 AGGAACGTGCATTGCTCGAT 60.392 50.000 32.24 23.84 46.28 3.59
2148 2204 1.005037 AGGAACGTGCATTGCTCGA 60.005 52.632 32.24 1.49 46.28 4.04
2164 2220 0.928908 GCGCGTACGTGTATGAGAGG 60.929 60.000 27.72 2.07 42.83 3.69
2225 2281 0.524862 TCGAGTTCAGTAGGCGAACC 59.475 55.000 0.00 0.00 43.07 3.62
2241 2297 2.048316 TGCAGTGCAATCGCTCGA 60.048 55.556 17.26 0.00 39.64 4.04
2309 2365 0.320247 ATGGAATCGCTCGATCAGGC 60.320 55.000 5.17 0.00 33.08 4.85
2439 2497 0.322816 AACGGCCTCTACTACCACGA 60.323 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.