Multiple sequence alignment - TraesCS5A01G361700

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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 TraesCS5A01G361700 chr5A 100.000 3230 0 0 1 3230 562894495 562891266 0.000000e+00 5965
1 TraesCS5A01G361700 chr5A 86.688 939 88 15 884 1793 562992245 562991315 0.000000e+00 1007
2 TraesCS5A01G361700 chr5A 89.547 574 57 1 2160 2733 562977349 562976779 0.000000e+00 725
3 TraesCS5A01G361700 chr5A 78.116 690 147 4 2046 2733 563441172 563440485 4.950000e-118 435
4 TraesCS5A01G361700 chr5B 95.730 1850 58 10 1 1836 542954574 542952732 0.000000e+00 2959
5 TraesCS5A01G361700 chr5B 97.265 914 21 2 2037 2948 542952734 542951823 0.000000e+00 1546
6 TraesCS5A01G361700 chr5B 84.951 1422 125 44 397 1799 542983400 542982049 0.000000e+00 1358
7 TraesCS5A01G361700 chr5B 82.291 1135 153 23 2037 3165 542982005 542980913 0.000000e+00 939
8 TraesCS5A01G361700 chr5B 90.426 282 24 2 2946 3224 542951666 542951385 5.090000e-98 368
9 TraesCS5A01G361700 chr5B 98.990 198 1 1 1839 2036 251568512 251568708 1.430000e-93 353
10 TraesCS5A01G361700 chr5D 96.693 1391 35 4 456 1836 445320376 445318987 0.000000e+00 2303
11 TraesCS5A01G361700 chr5D 94.216 1193 61 3 2037 3224 445318989 445317800 0.000000e+00 1814
12 TraesCS5A01G361700 chr5D 88.241 978 87 11 884 1836 445378708 445377734 0.000000e+00 1144
13 TraesCS5A01G361700 chr5D 89.383 697 71 1 2037 2733 445377736 445377043 0.000000e+00 874
14 TraesCS5A01G361700 chr5D 84.813 777 68 16 92 841 445379456 445378703 0.000000e+00 736
15 TraesCS5A01G361700 chr5D 91.774 389 20 6 1 383 445320780 445320398 6.140000e-147 531
16 TraesCS5A01G361700 chr5D 79.059 425 61 23 2814 3224 445376997 445376587 1.910000e-67 267
17 TraesCS5A01G361700 chr4D 78.287 677 137 6 2046 2715 4030894 4030221 8.280000e-116 427
18 TraesCS5A01G361700 chr2D 77.810 685 146 6 2051 2732 7587600 7586919 4.980000e-113 418
19 TraesCS5A01G361700 chr4A 98.122 213 2 2 1839 2051 76927909 76927699 1.420000e-98 370
20 TraesCS5A01G361700 chr6A 99.500 200 0 1 1839 2038 49403817 49403619 2.370000e-96 363
21 TraesCS5A01G361700 chr7B 98.522 203 2 1 1839 2041 388817319 388817520 1.100000e-94 357
22 TraesCS5A01G361700 chr7B 98.030 203 3 1 1839 2041 388798059 388798260 5.130000e-93 351
23 TraesCS5A01G361700 chr2A 99.000 200 0 2 1839 2037 196117774 196117972 1.100000e-94 357
24 TraesCS5A01G361700 chr1B 99.000 200 1 1 1839 2038 229951330 229951132 1.100000e-94 357
25 TraesCS5A01G361700 chr7A 98.995 199 0 2 1839 2036 142528061 142528258 3.960000e-94 355
26 TraesCS5A01G361700 chr2B 98.030 203 3 1 1839 2041 290527007 290527208 5.130000e-93 351
27 TraesCS5A01G361700 chr2B 74.625 800 167 27 1007 1794 9106431 9105656 1.450000e-83 320
28 TraesCS5A01G361700 chr6D 91.667 144 11 1 130 273 12035372 12035514 7.070000e-47 198


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 TraesCS5A01G361700 chr5A 562891266 562894495 3229 True 5965.000000 5965 100.000000 1 3230 1 chr5A.!!$R1 3229
1 TraesCS5A01G361700 chr5A 562991315 562992245 930 True 1007.000000 1007 86.688000 884 1793 1 chr5A.!!$R3 909
2 TraesCS5A01G361700 chr5A 562976779 562977349 570 True 725.000000 725 89.547000 2160 2733 1 chr5A.!!$R2 573
3 TraesCS5A01G361700 chr5A 563440485 563441172 687 True 435.000000 435 78.116000 2046 2733 1 chr5A.!!$R4 687
4 TraesCS5A01G361700 chr5B 542951385 542954574 3189 True 1624.333333 2959 94.473667 1 3224 3 chr5B.!!$R1 3223
5 TraesCS5A01G361700 chr5B 542980913 542983400 2487 True 1148.500000 1358 83.621000 397 3165 2 chr5B.!!$R2 2768
6 TraesCS5A01G361700 chr5D 445317800 445320780 2980 True 1549.333333 2303 94.227667 1 3224 3 chr5D.!!$R1 3223
7 TraesCS5A01G361700 chr5D 445376587 445379456 2869 True 755.250000 1144 85.374000 92 3224 4 chr5D.!!$R2 3132
8 TraesCS5A01G361700 chr4D 4030221 4030894 673 True 427.000000 427 78.287000 2046 2715 1 chr4D.!!$R1 669
9 TraesCS5A01G361700 chr2D 7586919 7587600 681 True 418.000000 418 77.810000 2051 2732 1 chr2D.!!$R1 681
10 TraesCS5A01G361700 chr2B 9105656 9106431 775 True 320.000000 320 74.625000 1007 1794 1 chr2B.!!$R1 787

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
287 294 1.143684 ACTTTGCTTCCTCTGCTGGAA 59.856 47.619 6.32 6.32 43.16 3.53 F
1251 1320 0.748005 CCGGGATGCGGTTCTTCATT 60.748 55.000 0.00 0.00 0.00 2.57 F
1876 1963 0.121197 TCTCCCAGAATTGACCCCCT 59.879 55.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1630 0.108585 ACGCCAAAGACTGTCATGGT 59.891 50.000 24.46 10.53 35.34 3.55 R
2217 2304 1.137404 CATGGGCTACTTTGTGCGC 59.863 57.895 0.00 0.00 41.57 6.09 R
3145 3458 5.973565 GCTGAAAAATATATGTCTGTGTGCC 59.026 40.000 0.00 0.00 0.00 5.01 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
115 116 5.187186 CGTATATCCTGGCCTATGGTAAGTT 59.813 44.000 3.32 0.00 0.00 2.66
123 124 3.432326 GGCCTATGGTAAGTTCTCAGGTG 60.432 52.174 0.00 0.00 0.00 4.00
239 246 2.042297 TCCTCGATCTAGCAGGATGGAT 59.958 50.000 4.68 0.00 35.86 3.41
287 294 1.143684 ACTTTGCTTCCTCTGCTGGAA 59.856 47.619 6.32 6.32 43.16 3.53
328 335 4.471904 TTCTGCATCTGGTTAGTCGATT 57.528 40.909 0.00 0.00 0.00 3.34
411 428 2.811431 TGTCTGCATTTTAGTGGAACCG 59.189 45.455 0.00 0.00 37.80 4.44
432 453 4.035091 CCGTCGGCTTTATTCATTCATTCA 59.965 41.667 0.00 0.00 0.00 2.57
435 456 5.743872 GTCGGCTTTATTCATTCATTCAACC 59.256 40.000 0.00 0.00 0.00 3.77
438 459 7.012327 TCGGCTTTATTCATTCATTCAACCTAG 59.988 37.037 0.00 0.00 0.00 3.02
449 470 9.784531 CATTCATTCAACCTAGTATTATCTGGT 57.215 33.333 0.00 0.00 0.00 4.00
450 471 9.784531 ATTCATTCAACCTAGTATTATCTGGTG 57.215 33.333 0.00 0.00 0.00 4.17
451 472 8.547481 TCATTCAACCTAGTATTATCTGGTGA 57.453 34.615 0.00 0.00 0.00 4.02
452 473 8.988060 TCATTCAACCTAGTATTATCTGGTGAA 58.012 33.333 0.00 0.00 0.00 3.18
453 474 9.613428 CATTCAACCTAGTATTATCTGGTGAAA 57.387 33.333 0.00 0.00 0.00 2.69
566 596 2.046023 TTGAGCTGGATGCCCGTG 60.046 61.111 0.00 0.00 44.23 4.94
701 743 1.411246 GGAGGTACCATACGCATGACA 59.589 52.381 15.94 0.00 38.79 3.58
840 884 3.547601 GTGCACCAAAACGTATGTGTAC 58.452 45.455 5.22 10.38 37.21 2.90
981 1039 2.196595 CATCCAAGTAGTCCTCCCCAA 58.803 52.381 0.00 0.00 0.00 4.12
1251 1320 0.748005 CCGGGATGCGGTTCTTCATT 60.748 55.000 0.00 0.00 0.00 2.57
1561 1630 4.454161 CGAGGTTAATGTTTGACATCACCA 59.546 41.667 17.78 0.00 41.16 4.17
1804 1891 0.322546 GAAGACCAACGGAGGCCAAT 60.323 55.000 5.01 0.00 0.00 3.16
1836 1923 4.251103 AGAGGTTGTGGGGGATATTTTC 57.749 45.455 0.00 0.00 0.00 2.29
1837 1924 3.596046 AGAGGTTGTGGGGGATATTTTCA 59.404 43.478 0.00 0.00 0.00 2.69
1838 1925 3.954258 GAGGTTGTGGGGGATATTTTCAG 59.046 47.826 0.00 0.00 0.00 3.02
1839 1926 2.430694 GGTTGTGGGGGATATTTTCAGC 59.569 50.000 0.00 0.00 0.00 4.26
1840 1927 2.430694 GTTGTGGGGGATATTTTCAGCC 59.569 50.000 0.00 0.00 0.00 4.85
1841 1928 1.643286 TGTGGGGGATATTTTCAGCCA 59.357 47.619 0.00 0.00 0.00 4.75
1842 1929 2.310538 GTGGGGGATATTTTCAGCCAG 58.689 52.381 0.00 0.00 0.00 4.85
1843 1930 1.929494 TGGGGGATATTTTCAGCCAGT 59.071 47.619 0.00 0.00 0.00 4.00
1844 1931 2.314549 TGGGGGATATTTTCAGCCAGTT 59.685 45.455 0.00 0.00 0.00 3.16
1845 1932 2.959030 GGGGGATATTTTCAGCCAGTTC 59.041 50.000 0.00 0.00 0.00 3.01
1846 1933 3.373110 GGGGGATATTTTCAGCCAGTTCT 60.373 47.826 0.00 0.00 0.00 3.01
1847 1934 4.281657 GGGGATATTTTCAGCCAGTTCTT 58.718 43.478 0.00 0.00 0.00 2.52
1848 1935 4.711846 GGGGATATTTTCAGCCAGTTCTTT 59.288 41.667 0.00 0.00 0.00 2.52
1849 1936 5.187772 GGGGATATTTTCAGCCAGTTCTTTT 59.812 40.000 0.00 0.00 0.00 2.27
1850 1937 6.101997 GGGATATTTTCAGCCAGTTCTTTTG 58.898 40.000 0.00 0.00 0.00 2.44
1851 1938 6.101997 GGATATTTTCAGCCAGTTCTTTTGG 58.898 40.000 0.00 0.00 38.78 3.28
1852 1939 3.817709 TTTTCAGCCAGTTCTTTTGGG 57.182 42.857 0.00 0.00 36.19 4.12
1853 1940 1.039856 TTCAGCCAGTTCTTTTGGGC 58.960 50.000 0.00 0.00 46.77 5.36
1857 1944 2.549064 GCCAGTTCTTTTGGGCAATT 57.451 45.000 0.00 0.00 45.70 2.32
1858 1945 2.416747 GCCAGTTCTTTTGGGCAATTC 58.583 47.619 0.00 0.00 45.70 2.17
1859 1946 2.037641 GCCAGTTCTTTTGGGCAATTCT 59.962 45.455 0.00 0.00 45.70 2.40
1860 1947 3.862264 GCCAGTTCTTTTGGGCAATTCTC 60.862 47.826 0.00 0.00 45.70 2.87
1861 1948 3.306294 CCAGTTCTTTTGGGCAATTCTCC 60.306 47.826 0.00 0.00 31.87 3.71
1862 1949 2.899900 AGTTCTTTTGGGCAATTCTCCC 59.100 45.455 5.52 5.52 44.17 4.30
1875 1962 0.999712 TTCTCCCAGAATTGACCCCC 59.000 55.000 0.00 0.00 0.00 5.40
1876 1963 0.121197 TCTCCCAGAATTGACCCCCT 59.879 55.000 0.00 0.00 0.00 4.79
1877 1964 0.548510 CTCCCAGAATTGACCCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
1878 1965 0.919289 TCCCAGAATTGACCCCCTCC 60.919 60.000 0.00 0.00 0.00 4.30
1879 1966 1.615262 CCAGAATTGACCCCCTCCC 59.385 63.158 0.00 0.00 0.00 4.30
1880 1967 1.615262 CAGAATTGACCCCCTCCCC 59.385 63.158 0.00 0.00 0.00 4.81
1881 1968 1.165782 AGAATTGACCCCCTCCCCA 59.834 57.895 0.00 0.00 0.00 4.96
1882 1969 0.921256 AGAATTGACCCCCTCCCCAG 60.921 60.000 0.00 0.00 0.00 4.45
1883 1970 2.573893 GAATTGACCCCCTCCCCAGC 62.574 65.000 0.00 0.00 0.00 4.85
1884 1971 3.603330 ATTGACCCCCTCCCCAGCT 62.603 63.158 0.00 0.00 0.00 4.24
1885 1972 3.829311 TTGACCCCCTCCCCAGCTT 62.829 63.158 0.00 0.00 0.00 3.74
1886 1973 3.412408 GACCCCCTCCCCAGCTTC 61.412 72.222 0.00 0.00 0.00 3.86
1887 1974 3.952799 GACCCCCTCCCCAGCTTCT 62.953 68.421 0.00 0.00 0.00 2.85
1888 1975 3.093172 CCCCCTCCCCAGCTTCTC 61.093 72.222 0.00 0.00 0.00 2.87
1889 1976 3.093172 CCCCTCCCCAGCTTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
1890 1977 3.093172 CCCTCCCCAGCTTCTCCC 61.093 72.222 0.00 0.00 0.00 4.30
1891 1978 2.285668 CCTCCCCAGCTTCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
1892 1979 2.373707 CCTCCCCAGCTTCTCCCAG 61.374 68.421 0.00 0.00 0.00 4.45
1893 1980 1.306482 CTCCCCAGCTTCTCCCAGA 60.306 63.158 0.00 0.00 0.00 3.86
1894 1981 0.911525 CTCCCCAGCTTCTCCCAGAA 60.912 60.000 0.00 0.00 32.50 3.02
1895 1982 0.253347 TCCCCAGCTTCTCCCAGAAT 60.253 55.000 0.00 0.00 33.13 2.40
1896 1983 0.627986 CCCCAGCTTCTCCCAGAATT 59.372 55.000 0.00 0.00 33.13 2.17
1897 1984 1.684248 CCCCAGCTTCTCCCAGAATTG 60.684 57.143 0.00 0.00 33.13 2.32
1898 1985 1.101331 CCAGCTTCTCCCAGAATTGC 58.899 55.000 0.00 0.00 33.13 3.56
1899 1986 1.101331 CAGCTTCTCCCAGAATTGCC 58.899 55.000 0.00 0.00 33.13 4.52
1900 1987 0.700564 AGCTTCTCCCAGAATTGCCA 59.299 50.000 0.00 0.00 33.13 4.92
1901 1988 0.813821 GCTTCTCCCAGAATTGCCAC 59.186 55.000 0.00 0.00 33.13 5.01
1902 1989 1.615384 GCTTCTCCCAGAATTGCCACT 60.615 52.381 0.00 0.00 33.13 4.00
1903 1990 2.800250 CTTCTCCCAGAATTGCCACTT 58.200 47.619 0.00 0.00 33.13 3.16
1904 1991 3.873801 GCTTCTCCCAGAATTGCCACTTA 60.874 47.826 0.00 0.00 33.13 2.24
1905 1992 4.335416 CTTCTCCCAGAATTGCCACTTAA 58.665 43.478 0.00 0.00 33.13 1.85
1906 1993 4.591321 TCTCCCAGAATTGCCACTTAAT 57.409 40.909 0.00 0.00 0.00 1.40
1907 1994 5.708736 TCTCCCAGAATTGCCACTTAATA 57.291 39.130 0.00 0.00 0.00 0.98
1908 1995 6.266131 TCTCCCAGAATTGCCACTTAATAT 57.734 37.500 0.00 0.00 0.00 1.28
1909 1996 6.672593 TCTCCCAGAATTGCCACTTAATATT 58.327 36.000 0.00 0.00 0.00 1.28
1910 1997 7.125391 TCTCCCAGAATTGCCACTTAATATTT 58.875 34.615 0.00 0.00 0.00 1.40
1911 1998 7.619302 TCTCCCAGAATTGCCACTTAATATTTT 59.381 33.333 0.00 0.00 0.00 1.82
1912 1999 8.144862 TCCCAGAATTGCCACTTAATATTTTT 57.855 30.769 0.00 0.00 0.00 1.94
1937 2024 9.662947 TTTTACAATTCCTAGCTAGTTAAGGTC 57.337 33.333 19.31 0.00 37.13 3.85
1938 2025 8.605325 TTACAATTCCTAGCTAGTTAAGGTCT 57.395 34.615 19.31 0.00 37.13 3.85
1939 2026 9.705103 TTACAATTCCTAGCTAGTTAAGGTCTA 57.295 33.333 19.31 5.95 37.13 2.59
1940 2027 8.605325 ACAATTCCTAGCTAGTTAAGGTCTAA 57.395 34.615 19.31 0.00 37.13 2.10
1941 2028 9.214962 ACAATTCCTAGCTAGTTAAGGTCTAAT 57.785 33.333 19.31 0.19 37.13 1.73
1945 2032 8.406730 TCCTAGCTAGTTAAGGTCTAATTAGC 57.593 38.462 19.31 9.70 40.67 3.09
1947 2034 9.517868 CCTAGCTAGTTAAGGTCTAATTAGCTA 57.482 37.037 19.31 19.29 45.18 3.32
1949 2036 8.411991 AGCTAGTTAAGGTCTAATTAGCTAGG 57.588 38.462 15.72 0.00 45.18 3.02
1950 2037 8.226112 AGCTAGTTAAGGTCTAATTAGCTAGGA 58.774 37.037 15.72 0.00 45.18 2.94
1951 2038 8.858094 GCTAGTTAAGGTCTAATTAGCTAGGAA 58.142 37.037 7.67 0.00 41.05 3.36
1955 2042 9.833917 GTTAAGGTCTAATTAGCTAGGAATTGT 57.166 33.333 7.67 0.00 0.00 2.71
1983 2070 7.732222 AAAATATTAAGTGGCAATTCTGGGA 57.268 32.000 2.32 0.00 0.00 4.37
1984 2071 6.966534 AATATTAAGTGGCAATTCTGGGAG 57.033 37.500 2.32 0.00 0.00 4.30
1985 2072 4.591321 ATTAAGTGGCAATTCTGGGAGA 57.409 40.909 2.32 0.00 0.00 3.71
1986 2073 2.978156 AAGTGGCAATTCTGGGAGAA 57.022 45.000 0.00 0.00 38.78 2.87
1987 2074 2.503895 AGTGGCAATTCTGGGAGAAG 57.496 50.000 0.00 0.00 37.69 2.85
1988 2075 0.813821 GTGGCAATTCTGGGAGAAGC 59.186 55.000 0.00 0.00 37.69 3.86
1989 2076 0.700564 TGGCAATTCTGGGAGAAGCT 59.299 50.000 0.00 0.00 37.69 3.74
1990 2077 1.101331 GGCAATTCTGGGAGAAGCTG 58.899 55.000 0.00 0.00 37.69 4.24
1991 2078 1.101331 GCAATTCTGGGAGAAGCTGG 58.899 55.000 0.00 0.00 37.69 4.85
1992 2079 1.760192 CAATTCTGGGAGAAGCTGGG 58.240 55.000 0.00 0.00 37.69 4.45
1993 2080 0.627986 AATTCTGGGAGAAGCTGGGG 59.372 55.000 0.00 0.00 37.69 4.96
1994 2081 0.253347 ATTCTGGGAGAAGCTGGGGA 60.253 55.000 0.00 0.00 37.69 4.81
1995 2082 0.911525 TTCTGGGAGAAGCTGGGGAG 60.912 60.000 0.00 0.00 29.50 4.30
1996 2083 2.285668 TGGGAGAAGCTGGGGAGG 60.286 66.667 0.00 0.00 0.00 4.30
1997 2084 3.093172 GGGAGAAGCTGGGGAGGG 61.093 72.222 0.00 0.00 0.00 4.30
1998 2085 3.093172 GGAGAAGCTGGGGAGGGG 61.093 72.222 0.00 0.00 0.00 4.79
1999 2086 3.093172 GAGAAGCTGGGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
2014 2101 2.709992 GGGGGTCAATTCTGGGAGA 58.290 57.895 0.00 0.00 0.00 3.71
2015 2102 0.999712 GGGGGTCAATTCTGGGAGAA 59.000 55.000 0.00 0.00 38.78 2.87
2016 2103 1.570979 GGGGGTCAATTCTGGGAGAAT 59.429 52.381 0.00 0.00 46.22 2.40
2029 2116 3.319137 GGGAGAATTGCCCAAAAGAAC 57.681 47.619 7.89 0.00 45.31 3.01
2030 2117 2.899900 GGGAGAATTGCCCAAAAGAACT 59.100 45.455 7.89 0.00 45.31 3.01
2031 2118 3.306294 GGGAGAATTGCCCAAAAGAACTG 60.306 47.826 7.89 0.00 45.31 3.16
2032 2119 3.306294 GGAGAATTGCCCAAAAGAACTGG 60.306 47.826 0.00 0.00 0.00 4.00
2033 2120 2.037641 AGAATTGCCCAAAAGAACTGGC 59.962 45.455 0.00 0.00 44.27 4.85
2034 2121 0.686789 ATTGCCCAAAAGAACTGGCC 59.313 50.000 0.00 0.00 43.35 5.36
2035 2122 1.406860 TTGCCCAAAAGAACTGGCCC 61.407 55.000 0.00 0.00 43.35 5.80
2036 2123 1.533994 GCCCAAAAGAACTGGCCCT 60.534 57.895 0.00 0.00 37.94 5.19
2037 2124 1.121407 GCCCAAAAGAACTGGCCCTT 61.121 55.000 0.00 0.00 37.94 3.95
2038 2125 1.423584 CCCAAAAGAACTGGCCCTTT 58.576 50.000 0.00 0.00 34.39 3.11
2217 2304 5.233050 CGTAATGAACTCTCACCTATTGCAG 59.767 44.000 0.00 0.00 33.30 4.41
2262 2352 0.684535 TGCCACGGTCATCTTTGAGA 59.315 50.000 0.00 0.00 30.85 3.27
2629 2724 0.317020 GCAGTCGTGTGGAACTTTGC 60.317 55.000 0.00 0.00 38.04 3.68
2645 2740 4.106925 GCCCTGGAGCTGGTGGAG 62.107 72.222 0.00 0.00 0.00 3.86
2663 2758 1.817099 GAGCCAGAGCATCCAACCG 60.817 63.158 0.00 0.00 43.56 4.44
2811 2947 1.508632 AGAATGCGTGTGTGGTGTAC 58.491 50.000 0.00 0.00 0.00 2.90
2836 2974 7.766738 ACGTGTGTGTCCATATACATATTTTCA 59.233 33.333 0.00 0.00 0.00 2.69
2936 3077 1.811965 TGGATGGTGCAAATGTTCTCG 59.188 47.619 0.00 0.00 0.00 4.04
3010 3312 9.408648 AGATTATCCAAGTAAATGACCGAAAAT 57.591 29.630 0.00 0.00 0.00 1.82
3097 3406 3.648009 GAGACGATGCCTCCTTATTGAG 58.352 50.000 0.00 0.00 0.00 3.02
3144 3457 4.887748 TGAACTGTTTGTTTTTCTTGCCA 58.112 34.783 0.00 0.00 39.30 4.92
3145 3458 4.928615 TGAACTGTTTGTTTTTCTTGCCAG 59.071 37.500 0.00 0.00 39.30 4.85
3170 3488 5.678483 GCACACAGACATATATTTTTCAGCG 59.322 40.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 3.701205 AATGCATGTACACACCTGAGA 57.299 42.857 0.00 0.00 0.00 3.27
239 246 7.847096 TGATTTGAATCAAGTAGGTAGCTACA 58.153 34.615 28.68 12.81 42.11 2.74
287 294 0.996762 TCCCAACTTCAACCCCAGGT 60.997 55.000 0.00 0.00 37.65 4.00
328 335 9.137459 TCAAAACTAAAAATAGATGTTGGTCCA 57.863 29.630 0.00 0.00 0.00 4.02
411 428 5.743872 GGTTGAATGAATGAATAAAGCCGAC 59.256 40.000 0.00 0.00 0.00 4.79
446 467 9.941325 AGCATTATTTGTATTTCATTTTCACCA 57.059 25.926 0.00 0.00 0.00 4.17
566 596 1.735920 CAGGAGACTCGTGCACTGC 60.736 63.158 16.19 0.26 40.21 4.40
857 901 0.870393 CAGCAGCCACTACACACAAG 59.130 55.000 0.00 0.00 0.00 3.16
860 904 0.037326 TAGCAGCAGCCACTACACAC 60.037 55.000 0.00 0.00 43.56 3.82
872 916 3.181455 CCATTGGTACCATACTAGCAGCA 60.181 47.826 17.17 0.00 0.00 4.41
1251 1320 2.925706 TTGGCAGGGTCGCAGGTA 60.926 61.111 0.00 0.00 0.00 3.08
1561 1630 0.108585 ACGCCAAAGACTGTCATGGT 59.891 50.000 24.46 10.53 35.34 3.55
1783 1852 2.046217 GCCTCCGTTGGTCTTCCC 60.046 66.667 0.00 0.00 0.00 3.97
1804 1891 3.455910 CCCACAACCTCTTCATCCTCATA 59.544 47.826 0.00 0.00 0.00 2.15
1836 1923 0.752054 TTGCCCAAAAGAACTGGCTG 59.248 50.000 0.00 0.00 44.32 4.85
1837 1924 1.720781 ATTGCCCAAAAGAACTGGCT 58.279 45.000 0.00 0.00 44.32 4.75
1838 1925 2.037641 AGAATTGCCCAAAAGAACTGGC 59.962 45.455 0.00 0.00 44.27 4.85
1839 1926 3.306294 GGAGAATTGCCCAAAAGAACTGG 60.306 47.826 0.00 0.00 0.00 4.00
1840 1927 3.306294 GGGAGAATTGCCCAAAAGAACTG 60.306 47.826 7.89 0.00 45.31 3.16
1841 1928 2.899900 GGGAGAATTGCCCAAAAGAACT 59.100 45.455 7.89 0.00 45.31 3.01
1842 1929 3.319137 GGGAGAATTGCCCAAAAGAAC 57.681 47.619 7.89 0.00 45.31 3.01
1855 1942 1.570979 GGGGGTCAATTCTGGGAGAAT 59.429 52.381 0.00 0.00 46.22 2.40
1856 1943 0.999712 GGGGGTCAATTCTGGGAGAA 59.000 55.000 0.00 0.00 38.78 2.87
1857 1944 0.121197 AGGGGGTCAATTCTGGGAGA 59.879 55.000 0.00 0.00 0.00 3.71
1858 1945 0.548510 GAGGGGGTCAATTCTGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
1859 1946 0.919289 GGAGGGGGTCAATTCTGGGA 60.919 60.000 0.00 0.00 0.00 4.37
1860 1947 1.615262 GGAGGGGGTCAATTCTGGG 59.385 63.158 0.00 0.00 0.00 4.45
1861 1948 1.615262 GGGAGGGGGTCAATTCTGG 59.385 63.158 0.00 0.00 0.00 3.86
1862 1949 1.214305 TGGGGAGGGGGTCAATTCTG 61.214 60.000 0.00 0.00 0.00 3.02
1863 1950 0.921256 CTGGGGAGGGGGTCAATTCT 60.921 60.000 0.00 0.00 0.00 2.40
1864 1951 1.615262 CTGGGGAGGGGGTCAATTC 59.385 63.158 0.00 0.00 0.00 2.17
1865 1952 2.626467 GCTGGGGAGGGGGTCAATT 61.626 63.158 0.00 0.00 0.00 2.32
1866 1953 3.023735 GCTGGGGAGGGGGTCAAT 61.024 66.667 0.00 0.00 0.00 2.57
1867 1954 3.829311 AAGCTGGGGAGGGGGTCAA 62.829 63.158 0.00 0.00 0.00 3.18
1868 1955 4.285790 AAGCTGGGGAGGGGGTCA 62.286 66.667 0.00 0.00 0.00 4.02
1869 1956 3.412408 GAAGCTGGGGAGGGGGTC 61.412 72.222 0.00 0.00 0.00 4.46
1870 1957 3.952799 GAGAAGCTGGGGAGGGGGT 62.953 68.421 0.00 0.00 0.00 4.95
1871 1958 3.093172 GAGAAGCTGGGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
1872 1959 3.093172 GGAGAAGCTGGGGAGGGG 61.093 72.222 0.00 0.00 0.00 4.79
1873 1960 3.093172 GGGAGAAGCTGGGGAGGG 61.093 72.222 0.00 0.00 0.00 4.30
1874 1961 2.285668 TGGGAGAAGCTGGGGAGG 60.286 66.667 0.00 0.00 0.00 4.30
1875 1962 0.911525 TTCTGGGAGAAGCTGGGGAG 60.912 60.000 0.00 0.00 29.50 4.30
1876 1963 0.253347 ATTCTGGGAGAAGCTGGGGA 60.253 55.000 0.00 0.00 37.69 4.81
1877 1964 0.627986 AATTCTGGGAGAAGCTGGGG 59.372 55.000 0.00 0.00 37.69 4.96
1878 1965 1.760192 CAATTCTGGGAGAAGCTGGG 58.240 55.000 0.00 0.00 37.69 4.45
1879 1966 1.101331 GCAATTCTGGGAGAAGCTGG 58.899 55.000 0.00 0.00 37.69 4.85
1880 1967 1.101331 GGCAATTCTGGGAGAAGCTG 58.899 55.000 0.00 0.00 37.69 4.24
1881 1968 0.700564 TGGCAATTCTGGGAGAAGCT 59.299 50.000 0.00 0.00 37.69 3.74
1882 1969 0.813821 GTGGCAATTCTGGGAGAAGC 59.186 55.000 0.00 0.00 37.69 3.86
1883 1970 2.503895 AGTGGCAATTCTGGGAGAAG 57.496 50.000 0.00 0.00 37.69 2.85
1884 1971 2.978156 AAGTGGCAATTCTGGGAGAA 57.022 45.000 0.00 0.00 38.78 2.87
1885 1972 4.591321 ATTAAGTGGCAATTCTGGGAGA 57.409 40.909 2.32 0.00 0.00 3.71
1886 1973 6.966534 AATATTAAGTGGCAATTCTGGGAG 57.033 37.500 2.32 0.00 0.00 4.30
1887 1974 7.732222 AAAATATTAAGTGGCAATTCTGGGA 57.268 32.000 2.32 0.00 0.00 4.37
1911 1998 9.662947 GACCTTAACTAGCTAGGAATTGTAAAA 57.337 33.333 24.35 1.45 33.21 1.52
1912 1999 9.043548 AGACCTTAACTAGCTAGGAATTGTAAA 57.956 33.333 24.35 6.07 33.21 2.01
1913 2000 8.605325 AGACCTTAACTAGCTAGGAATTGTAA 57.395 34.615 24.35 10.98 33.21 2.41
1914 2001 9.705103 TTAGACCTTAACTAGCTAGGAATTGTA 57.295 33.333 24.35 8.34 33.21 2.41
1915 2002 8.605325 TTAGACCTTAACTAGCTAGGAATTGT 57.395 34.615 24.35 14.92 33.21 2.71
1919 2006 8.858094 GCTAATTAGACCTTAACTAGCTAGGAA 58.142 37.037 24.35 16.07 33.21 3.36
1920 2007 8.226112 AGCTAATTAGACCTTAACTAGCTAGGA 58.774 37.037 24.35 9.48 33.21 2.94
1921 2008 8.411991 AGCTAATTAGACCTTAACTAGCTAGG 57.588 38.462 24.35 11.75 35.14 3.02
1923 2010 9.517868 CCTAGCTAATTAGACCTTAACTAGCTA 57.482 37.037 16.85 13.29 29.48 3.32
1924 2011 8.226112 TCCTAGCTAATTAGACCTTAACTAGCT 58.774 37.037 16.85 12.62 29.48 3.32
1925 2012 8.406730 TCCTAGCTAATTAGACCTTAACTAGC 57.593 38.462 16.85 0.00 29.48 3.42
1929 2016 9.833917 ACAATTCCTAGCTAATTAGACCTTAAC 57.166 33.333 16.85 0.00 0.00 2.01
1958 2045 8.144862 TCCCAGAATTGCCACTTAATATTTTT 57.855 30.769 0.00 0.00 0.00 1.94
1959 2046 7.619302 TCTCCCAGAATTGCCACTTAATATTTT 59.381 33.333 0.00 0.00 0.00 1.82
1960 2047 7.125391 TCTCCCAGAATTGCCACTTAATATTT 58.875 34.615 0.00 0.00 0.00 1.40
1961 2048 6.672593 TCTCCCAGAATTGCCACTTAATATT 58.327 36.000 0.00 0.00 0.00 1.28
1962 2049 6.266131 TCTCCCAGAATTGCCACTTAATAT 57.734 37.500 0.00 0.00 0.00 1.28
1963 2050 5.708736 TCTCCCAGAATTGCCACTTAATA 57.291 39.130 0.00 0.00 0.00 0.98
1964 2051 4.591321 TCTCCCAGAATTGCCACTTAAT 57.409 40.909 0.00 0.00 0.00 1.40
1965 2052 4.335416 CTTCTCCCAGAATTGCCACTTAA 58.665 43.478 0.00 0.00 33.13 1.85
1966 2053 3.873801 GCTTCTCCCAGAATTGCCACTTA 60.874 47.826 0.00 0.00 33.13 2.24
1967 2054 2.800250 CTTCTCCCAGAATTGCCACTT 58.200 47.619 0.00 0.00 33.13 3.16
1968 2055 1.615384 GCTTCTCCCAGAATTGCCACT 60.615 52.381 0.00 0.00 33.13 4.00
1969 2056 0.813821 GCTTCTCCCAGAATTGCCAC 59.186 55.000 0.00 0.00 33.13 5.01
1970 2057 0.700564 AGCTTCTCCCAGAATTGCCA 59.299 50.000 0.00 0.00 33.13 4.92
1971 2058 1.101331 CAGCTTCTCCCAGAATTGCC 58.899 55.000 0.00 0.00 33.13 4.52
1972 2059 1.101331 CCAGCTTCTCCCAGAATTGC 58.899 55.000 0.00 0.00 33.13 3.56
1973 2060 1.684248 CCCCAGCTTCTCCCAGAATTG 60.684 57.143 0.00 0.00 33.13 2.32
1974 2061 0.627986 CCCCAGCTTCTCCCAGAATT 59.372 55.000 0.00 0.00 33.13 2.17
1975 2062 0.253347 TCCCCAGCTTCTCCCAGAAT 60.253 55.000 0.00 0.00 33.13 2.40
1976 2063 0.911525 CTCCCCAGCTTCTCCCAGAA 60.912 60.000 0.00 0.00 32.50 3.02
1977 2064 1.306482 CTCCCCAGCTTCTCCCAGA 60.306 63.158 0.00 0.00 0.00 3.86
1978 2065 2.373707 CCTCCCCAGCTTCTCCCAG 61.374 68.421 0.00 0.00 0.00 4.45
1979 2066 2.285668 CCTCCCCAGCTTCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
1980 2067 3.093172 CCCTCCCCAGCTTCTCCC 61.093 72.222 0.00 0.00 0.00 4.30
1981 2068 3.093172 CCCCTCCCCAGCTTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
1982 2069 3.093172 CCCCCTCCCCAGCTTCTC 61.093 72.222 0.00 0.00 0.00 2.87
1996 2083 0.999712 TTCTCCCAGAATTGACCCCC 59.000 55.000 0.00 0.00 0.00 5.40
2009 2096 2.899900 AGTTCTTTTGGGCAATTCTCCC 59.100 45.455 5.52 5.52 44.17 4.30
2010 2097 3.306294 CCAGTTCTTTTGGGCAATTCTCC 60.306 47.826 0.00 0.00 31.87 3.71
2011 2098 3.862264 GCCAGTTCTTTTGGGCAATTCTC 60.862 47.826 0.00 0.00 45.70 2.87
2012 2099 2.037641 GCCAGTTCTTTTGGGCAATTCT 59.962 45.455 0.00 0.00 45.70 2.40
2013 2100 2.416747 GCCAGTTCTTTTGGGCAATTC 58.583 47.619 0.00 0.00 45.70 2.17
2014 2101 2.549064 GCCAGTTCTTTTGGGCAATT 57.451 45.000 0.00 0.00 45.70 2.32
2019 2106 1.423584 AAAGGGCCAGTTCTTTTGGG 58.576 50.000 6.18 0.00 36.19 4.12
2020 2107 4.089361 AGATAAAGGGCCAGTTCTTTTGG 58.911 43.478 6.18 0.00 38.78 3.28
2021 2108 5.012893 AGAGATAAAGGGCCAGTTCTTTTG 58.987 41.667 6.18 0.00 35.22 2.44
2022 2109 5.014649 AGAGAGATAAAGGGCCAGTTCTTTT 59.985 40.000 6.18 0.00 35.22 2.27
2023 2110 4.538089 AGAGAGATAAAGGGCCAGTTCTTT 59.462 41.667 6.18 7.55 37.09 2.52
2024 2111 4.107820 AGAGAGATAAAGGGCCAGTTCTT 58.892 43.478 6.18 0.00 0.00 2.52
2025 2112 3.730269 AGAGAGATAAAGGGCCAGTTCT 58.270 45.455 6.18 1.71 0.00 3.01
2026 2113 4.406003 TGTAGAGAGATAAAGGGCCAGTTC 59.594 45.833 6.18 0.00 0.00 3.01
2027 2114 4.362677 TGTAGAGAGATAAAGGGCCAGTT 58.637 43.478 6.18 1.31 0.00 3.16
2028 2115 3.995636 TGTAGAGAGATAAAGGGCCAGT 58.004 45.455 6.18 0.00 0.00 4.00
2029 2116 4.590647 TGATGTAGAGAGATAAAGGGCCAG 59.409 45.833 6.18 0.00 0.00 4.85
2030 2117 4.556697 TGATGTAGAGAGATAAAGGGCCA 58.443 43.478 6.18 0.00 0.00 5.36
2031 2118 5.552870 TTGATGTAGAGAGATAAAGGGCC 57.447 43.478 0.00 0.00 0.00 5.80
2032 2119 6.648725 GTCATTGATGTAGAGAGATAAAGGGC 59.351 42.308 0.00 0.00 0.00 5.19
2033 2120 7.158021 GGTCATTGATGTAGAGAGATAAAGGG 58.842 42.308 0.00 0.00 0.00 3.95
2034 2121 7.158021 GGGTCATTGATGTAGAGAGATAAAGG 58.842 42.308 0.00 0.00 0.00 3.11
2035 2122 7.730084 TGGGTCATTGATGTAGAGAGATAAAG 58.270 38.462 0.00 0.00 0.00 1.85
2036 2123 7.565029 TCTGGGTCATTGATGTAGAGAGATAAA 59.435 37.037 0.00 0.00 0.00 1.40
2037 2124 7.014711 GTCTGGGTCATTGATGTAGAGAGATAA 59.985 40.741 0.00 0.00 0.00 1.75
2038 2125 6.491745 GTCTGGGTCATTGATGTAGAGAGATA 59.508 42.308 0.00 0.00 0.00 1.98
2217 2304 1.137404 CATGGGCTACTTTGTGCGC 59.863 57.895 0.00 0.00 41.57 6.09
2469 2564 1.915141 AGCCATCTGTTTGGGTTGAG 58.085 50.000 0.00 0.00 44.96 3.02
2629 2724 2.284921 TCTCCACCAGCTCCAGGG 60.285 66.667 0.00 0.00 0.00 4.45
2645 2740 1.817099 CGGTTGGATGCTCTGGCTC 60.817 63.158 0.00 0.00 39.59 4.70
2663 2758 6.536582 TCATCTGCAGTAAACAAGATAGCTTC 59.463 38.462 14.67 0.00 30.14 3.86
2811 2947 8.061857 GTGAAAATATGTATATGGACACACACG 58.938 37.037 0.00 0.00 30.52 4.49
2836 2974 6.485313 TGAATAAAGTTGTCCGACATGAAAGT 59.515 34.615 1.09 0.00 0.00 2.66
2997 3299 9.423061 CTGAATTCCTTAAATTTTCGGTCATTT 57.577 29.630 2.27 0.00 37.70 2.32
3144 3457 6.183360 GCTGAAAAATATATGTCTGTGTGCCT 60.183 38.462 0.00 0.00 0.00 4.75
3145 3458 5.973565 GCTGAAAAATATATGTCTGTGTGCC 59.026 40.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.