Multiple sequence alignment - TraesCS1A01G422000

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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 TraesCS1A01G422000 chr1A 100.000 2216 0 0 1 2216 577835497 577833282 0.000000e+00 4093.0
1 TraesCS1A01G422000 chr1A 92.849 881 42 6 724 1584 504740016 504740895 0.000000e+00 1258.0
2 TraesCS1A01G422000 chr1A 92.525 883 43 6 724 1584 504999344 505000225 0.000000e+00 1243.0
3 TraesCS1A01G422000 chr1A 93.182 44 3 0 2173 2216 514668012 514668055 5.110000e-07 65.8
4 TraesCS1A01G422000 chr3A 94.514 875 33 5 724 1584 170479253 170478380 0.000000e+00 1336.0
5 TraesCS1A01G422000 chr3A 87.571 877 83 10 725 1578 709154427 709155300 0.000000e+00 992.0
6 TraesCS1A01G422000 chr3A 91.957 373 18 2 724 1084 57174621 57174993 1.520000e-141 512.0
7 TraesCS1A01G422000 chr3A 95.259 232 10 1 1080 1310 57191214 57191445 1.250000e-97 366.0
8 TraesCS1A01G422000 chr1B 94.337 724 36 2 1 723 669748999 669748280 0.000000e+00 1105.0
9 TraesCS1A01G422000 chr1B 95.200 250 10 1 1576 1823 669748290 669748041 5.740000e-106 394.0
10 TraesCS1A01G422000 chr7A 87.371 871 94 6 724 1580 78562290 78563158 0.000000e+00 985.0
11 TraesCS1A01G422000 chr7A 83.391 873 122 17 725 1580 42711495 42710629 0.000000e+00 787.0
12 TraesCS1A01G422000 chr5B 87.330 884 83 13 724 1582 415647156 415648035 0.000000e+00 985.0
13 TraesCS1A01G422000 chr5B 92.857 42 3 0 2173 2214 42263937 42263896 6.610000e-06 62.1
14 TraesCS1A01G422000 chr1D 92.972 683 23 5 1 680 481378192 481377532 0.000000e+00 972.0
15 TraesCS1A01G422000 chr1D 90.698 43 4 0 2174 2216 466363066 466363024 8.550000e-05 58.4
16 TraesCS1A01G422000 chr7D 84.994 813 102 8 781 1579 12421473 12422279 0.000000e+00 808.0
17 TraesCS1A01G422000 chrUn 83.077 715 113 5 4 714 71291165 71290455 0.000000e+00 643.0
18 TraesCS1A01G422000 chr6A 92.340 235 15 3 1350 1582 555108594 555108361 4.560000e-87 331.0
19 TraesCS1A01G422000 chr6A 93.023 43 3 0 2174 2216 552712301 552712259 1.840000e-06 63.9
20 TraesCS1A01G422000 chr6A 92.857 42 3 0 2170 2211 119613973 119614014 6.610000e-06 62.1
21 TraesCS1A01G422000 chr3B 95.238 42 2 0 2170 2211 594965564 594965605 1.420000e-07 67.6
22 TraesCS1A01G422000 chr5D 97.368 38 1 0 2174 2211 335104242 335104279 5.110000e-07 65.8
23 TraesCS1A01G422000 chr5A 94.872 39 0 2 2174 2211 1802683 1802720 2.380000e-05 60.2
24 TraesCS1A01G422000 chr5A 94.737 38 2 0 2174 2211 677946199 677946236 2.380000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G422000 chr1A 577833282 577835497 2215 True 4093.0 4093 100.0000 1 2216 1 chr1A.!!$R1 2215
1 TraesCS1A01G422000 chr1A 504740016 504740895 879 False 1258.0 1258 92.8490 724 1584 1 chr1A.!!$F1 860
2 TraesCS1A01G422000 chr1A 504999344 505000225 881 False 1243.0 1243 92.5250 724 1584 1 chr1A.!!$F2 860
3 TraesCS1A01G422000 chr3A 170478380 170479253 873 True 1336.0 1336 94.5140 724 1584 1 chr3A.!!$R1 860
4 TraesCS1A01G422000 chr3A 709154427 709155300 873 False 992.0 992 87.5710 725 1578 1 chr3A.!!$F3 853
5 TraesCS1A01G422000 chr1B 669748041 669748999 958 True 749.5 1105 94.7685 1 1823 2 chr1B.!!$R1 1822
6 TraesCS1A01G422000 chr7A 78562290 78563158 868 False 985.0 985 87.3710 724 1580 1 chr7A.!!$F1 856
7 TraesCS1A01G422000 chr7A 42710629 42711495 866 True 787.0 787 83.3910 725 1580 1 chr7A.!!$R1 855
8 TraesCS1A01G422000 chr5B 415647156 415648035 879 False 985.0 985 87.3300 724 1582 1 chr5B.!!$F1 858
9 TraesCS1A01G422000 chr1D 481377532 481378192 660 True 972.0 972 92.9720 1 680 1 chr1D.!!$R2 679
10 TraesCS1A01G422000 chr7D 12421473 12422279 806 False 808.0 808 84.9940 781 1579 1 chr7D.!!$F1 798
11 TraesCS1A01G422000 chrUn 71290455 71291165 710 True 643.0 643 83.0770 4 714 1 chrUn.!!$R1 710

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
886 891 0.107557 AACGGTGGTTTGGAGAACGT 60.108 50.0 0.0 0.0 30.42 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1931 0.031314 CTCCATCGTCCTGTCCATCG 59.969 60.0 0.0 0.0 0.0 3.84 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
101 102 1.153309 CATCCTCGCTGCATGTCCA 60.153 57.895 0.00 0.00 0.00 4.02
204 208 3.250521 GCTTATCAAGAGCTTGCATCCTC 59.749 47.826 5.37 6.12 40.24 3.71
373 378 0.892755 CTGGCTTGGTGTACGACCTA 59.107 55.000 13.41 7.07 46.32 3.08
428 433 3.117657 CTCGGTGATAGAGGCCTGA 57.882 57.895 12.00 0.00 32.38 3.86
456 461 1.525197 CGTGCGTAACAAGAGCTTGAA 59.475 47.619 16.47 2.17 42.93 2.69
508 513 5.499004 TTGAGCTCAACTACCCAACTATT 57.501 39.130 25.16 0.00 0.00 1.73
526 531 2.584835 TTACTGTGCCATTGAAGCCT 57.415 45.000 0.00 0.00 0.00 4.58
530 535 2.571653 ACTGTGCCATTGAAGCCTACTA 59.428 45.455 0.00 0.00 0.00 1.82
584 589 1.269569 GGCCGTCATCATCGACATACA 60.270 52.381 0.00 0.00 35.54 2.29
603 608 1.068402 CATTGCGAAGTTGGACATGCA 60.068 47.619 0.00 0.00 0.00 3.96
604 609 1.246649 TTGCGAAGTTGGACATGCAT 58.753 45.000 0.00 0.00 31.70 3.96
605 610 0.522626 TGCGAAGTTGGACATGCATG 59.477 50.000 25.09 25.09 0.00 4.06
606 611 0.799534 GCGAAGTTGGACATGCATGC 60.800 55.000 26.53 18.01 0.00 4.06
613 618 0.330941 TGGACATGCATGCCCAAGTA 59.669 50.000 29.96 8.95 37.38 2.24
617 622 2.094675 ACATGCATGCCCAAGTAACTC 58.905 47.619 26.53 0.00 0.00 3.01
712 717 1.971167 GCAAGGGCGTTCATGGACA 60.971 57.895 4.68 0.00 0.00 4.02
713 718 1.523154 GCAAGGGCGTTCATGGACAA 61.523 55.000 4.68 0.00 0.00 3.18
714 719 0.958091 CAAGGGCGTTCATGGACAAA 59.042 50.000 4.68 0.00 0.00 2.83
715 720 1.339610 CAAGGGCGTTCATGGACAAAA 59.660 47.619 4.68 0.00 0.00 2.44
716 721 1.698506 AGGGCGTTCATGGACAAAAA 58.301 45.000 4.68 0.00 0.00 1.94
717 722 1.339929 AGGGCGTTCATGGACAAAAAC 59.660 47.619 4.68 0.00 0.00 2.43
718 723 1.067821 GGGCGTTCATGGACAAAAACA 59.932 47.619 4.68 0.00 0.00 2.83
719 724 2.288763 GGGCGTTCATGGACAAAAACAT 60.289 45.455 4.68 0.00 0.00 2.71
720 725 3.389221 GGCGTTCATGGACAAAAACATT 58.611 40.909 4.68 0.00 0.00 2.71
721 726 3.807071 GGCGTTCATGGACAAAAACATTT 59.193 39.130 4.68 0.00 0.00 2.32
722 727 4.318689 GGCGTTCATGGACAAAAACATTTG 60.319 41.667 4.68 0.03 37.89 2.32
860 865 3.584406 ACATCTCTTCTTCACCTGTCG 57.416 47.619 0.00 0.00 0.00 4.35
869 874 1.261619 CTTCACCTGTCGAGTTGCAAC 59.738 52.381 22.17 22.17 0.00 4.17
886 891 0.107557 AACGGTGGTTTGGAGAACGT 60.108 50.000 0.00 0.00 30.42 3.99
951 956 5.260424 TGGCAATATTTCTCTTGGTGCTAA 58.740 37.500 0.00 0.00 0.00 3.09
990 1007 1.209504 ACTTTTGGCCTAGCTGCGATA 59.790 47.619 3.32 0.00 0.00 2.92
1052 1070 3.532641 AGGCAAAAAGTTGAGATCCCT 57.467 42.857 0.00 0.00 36.83 4.20
1100 1118 2.168521 GCTACATGAACTACTGGGCAGA 59.831 50.000 0.00 0.00 0.00 4.26
1179 1197 1.523032 CGCTGCTGCCATGATGAGA 60.523 57.895 10.24 0.00 35.36 3.27
1263 1292 2.356535 CCTGCCTTATCTTCAGTGGCTT 60.357 50.000 0.00 0.00 43.57 4.35
1396 1436 8.090788 TCTTATTTTGCTCTGGTTAGGATAGT 57.909 34.615 0.00 0.00 0.00 2.12
1421 1462 4.202315 GGTTTTAGATGGCACTGGGTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
1422 1463 4.599047 TTTAGATGGCACTGGGTTTTTG 57.401 40.909 0.00 0.00 0.00 2.44
1493 1534 1.594331 GTGTCTTGAACCCGCTTTCT 58.406 50.000 0.00 0.00 0.00 2.52
1564 1653 3.531814 AGTAATGGAAAGGGGTAATGCCT 59.468 43.478 0.00 0.00 37.43 4.75
1600 1689 1.004044 CATGTGGAGGGAAGCTTGAGT 59.996 52.381 2.10 0.00 0.00 3.41
1633 1722 0.036732 GACATGTTGTGAGGAGCCCA 59.963 55.000 0.00 0.00 0.00 5.36
1713 1804 3.763360 TGTTATGGAAATGGCTGGAAGTG 59.237 43.478 0.00 0.00 35.30 3.16
1728 1819 6.317857 GCTGGAAGTGAATGATTTAAGTGTC 58.682 40.000 0.00 0.00 35.30 3.67
1729 1820 6.072508 GCTGGAAGTGAATGATTTAAGTGTCA 60.073 38.462 0.00 0.00 35.30 3.58
1811 1902 5.767665 TCCTGCGCATTTACATTAATACCAT 59.232 36.000 12.24 0.00 0.00 3.55
1838 1929 5.441718 AGTATATATGATGTTGCCCTGGG 57.558 43.478 8.86 8.86 0.00 4.45
1839 1930 4.852118 AGTATATATGATGTTGCCCTGGGT 59.148 41.667 15.56 0.00 0.00 4.51
1840 1931 2.664402 ATATGATGTTGCCCTGGGTC 57.336 50.000 15.56 7.41 0.00 4.46
1841 1932 0.180171 TATGATGTTGCCCTGGGTCG 59.820 55.000 15.56 0.00 0.00 4.79
1842 1933 1.561769 ATGATGTTGCCCTGGGTCGA 61.562 55.000 15.56 3.75 0.00 4.20
1843 1934 1.224592 GATGTTGCCCTGGGTCGAT 59.775 57.895 15.56 1.45 0.00 3.59
1844 1935 1.077501 ATGTTGCCCTGGGTCGATG 60.078 57.895 15.56 0.00 0.00 3.84
1845 1936 2.438434 GTTGCCCTGGGTCGATGG 60.438 66.667 15.56 0.00 0.00 3.51
1846 1937 2.609299 TTGCCCTGGGTCGATGGA 60.609 61.111 15.56 0.00 0.00 3.41
1847 1938 2.966732 TTGCCCTGGGTCGATGGAC 61.967 63.158 15.56 0.00 42.66 4.02
1848 1939 3.399181 GCCCTGGGTCGATGGACA 61.399 66.667 15.56 0.00 45.28 4.02
1849 1940 2.903357 CCCTGGGTCGATGGACAG 59.097 66.667 10.22 0.00 45.28 3.51
1850 1941 2.735772 CCCTGGGTCGATGGACAGG 61.736 68.421 10.22 16.18 45.28 4.00
1851 1942 1.685765 CCTGGGTCGATGGACAGGA 60.686 63.158 17.49 0.00 45.28 3.86
1852 1943 1.517832 CTGGGTCGATGGACAGGAC 59.482 63.158 10.22 0.00 45.28 3.85
1853 1944 2.284798 CTGGGTCGATGGACAGGACG 62.285 65.000 10.22 0.00 45.28 4.79
1854 1945 2.050350 GGGTCGATGGACAGGACGA 61.050 63.158 10.22 0.00 45.28 4.20
1855 1946 1.392710 GGGTCGATGGACAGGACGAT 61.393 60.000 10.22 0.00 45.28 3.73
1856 1947 0.249073 GGTCGATGGACAGGACGATG 60.249 60.000 10.22 0.00 45.28 3.84
1857 1948 0.249073 GTCGATGGACAGGACGATGG 60.249 60.000 2.59 0.00 42.91 3.51
1858 1949 0.395173 TCGATGGACAGGACGATGGA 60.395 55.000 0.00 0.00 0.00 3.41
1859 1950 0.031314 CGATGGACAGGACGATGGAG 59.969 60.000 0.00 0.00 0.00 3.86
1860 1951 0.249657 GATGGACAGGACGATGGAGC 60.250 60.000 0.00 0.00 0.00 4.70
1861 1952 2.021068 ATGGACAGGACGATGGAGCG 62.021 60.000 0.00 0.00 37.29 5.03
1862 1953 2.583593 GACAGGACGATGGAGCGC 60.584 66.667 0.00 0.00 33.86 5.92
1863 1954 4.148825 ACAGGACGATGGAGCGCC 62.149 66.667 2.29 0.00 33.86 6.53
1873 1964 3.550431 GGAGCGCCAGGGCAGATA 61.550 66.667 11.42 0.00 42.06 1.98
1874 1965 2.030262 GAGCGCCAGGGCAGATAG 59.970 66.667 11.42 0.00 42.06 2.08
1875 1966 2.444706 AGCGCCAGGGCAGATAGA 60.445 61.111 11.42 0.00 42.06 1.98
1876 1967 2.032860 GAGCGCCAGGGCAGATAGAA 62.033 60.000 11.42 0.00 42.06 2.10
1877 1968 1.072159 GCGCCAGGGCAGATAGAAT 59.928 57.895 11.42 0.00 42.06 2.40
1878 1969 0.952984 GCGCCAGGGCAGATAGAATC 60.953 60.000 11.42 0.00 42.06 2.52
1879 1970 0.668706 CGCCAGGGCAGATAGAATCG 60.669 60.000 11.42 0.00 42.06 3.34
1880 1971 0.321122 GCCAGGGCAGATAGAATCGG 60.321 60.000 5.20 0.00 41.49 4.18
1881 1972 1.051812 CCAGGGCAGATAGAATCGGT 58.948 55.000 0.00 0.00 0.00 4.69
1882 1973 1.270518 CCAGGGCAGATAGAATCGGTG 60.271 57.143 0.00 0.00 0.00 4.94
1883 1974 1.688735 CAGGGCAGATAGAATCGGTGA 59.311 52.381 0.00 0.00 0.00 4.02
1884 1975 1.689273 AGGGCAGATAGAATCGGTGAC 59.311 52.381 0.00 0.00 0.00 3.67
1885 1976 1.270358 GGGCAGATAGAATCGGTGACC 60.270 57.143 0.00 0.00 0.00 4.02
1895 1986 3.725819 CGGTGACCGTGAAGCAAA 58.274 55.556 17.28 0.00 42.73 3.68
1896 1987 2.018544 CGGTGACCGTGAAGCAAAA 58.981 52.632 17.28 0.00 42.73 2.44
1897 1988 0.591170 CGGTGACCGTGAAGCAAAAT 59.409 50.000 17.28 0.00 42.73 1.82
1898 1989 1.001815 CGGTGACCGTGAAGCAAAATT 60.002 47.619 17.28 0.00 42.73 1.82
1899 1990 2.393764 GGTGACCGTGAAGCAAAATTG 58.606 47.619 0.00 0.00 0.00 2.32
1900 1991 2.393764 GTGACCGTGAAGCAAAATTGG 58.606 47.619 0.00 0.00 0.00 3.16
1901 1992 2.028130 TGACCGTGAAGCAAAATTGGT 58.972 42.857 0.00 0.00 41.27 3.67
1902 1993 2.223688 TGACCGTGAAGCAAAATTGGTG 60.224 45.455 0.00 0.00 39.13 4.17
1903 1994 2.028130 ACCGTGAAGCAAAATTGGTGA 58.972 42.857 0.00 0.00 39.13 4.02
1904 1995 2.627699 ACCGTGAAGCAAAATTGGTGAT 59.372 40.909 0.00 0.00 39.13 3.06
1905 1996 2.988493 CCGTGAAGCAAAATTGGTGATG 59.012 45.455 0.00 0.00 39.13 3.07
1906 1997 2.988493 CGTGAAGCAAAATTGGTGATGG 59.012 45.455 0.00 0.00 39.13 3.51
1907 1998 3.552684 CGTGAAGCAAAATTGGTGATGGT 60.553 43.478 0.00 0.00 39.13 3.55
1908 1999 3.742369 GTGAAGCAAAATTGGTGATGGTG 59.258 43.478 0.00 0.00 39.13 4.17
1909 2000 3.640498 TGAAGCAAAATTGGTGATGGTGA 59.360 39.130 0.00 0.00 39.13 4.02
1910 2001 3.947910 AGCAAAATTGGTGATGGTGAG 57.052 42.857 0.00 0.00 37.53 3.51
1911 2002 3.499338 AGCAAAATTGGTGATGGTGAGA 58.501 40.909 0.00 0.00 37.53 3.27
1912 2003 4.091549 AGCAAAATTGGTGATGGTGAGAT 58.908 39.130 0.00 0.00 37.53 2.75
1913 2004 4.529377 AGCAAAATTGGTGATGGTGAGATT 59.471 37.500 0.00 0.00 37.53 2.40
1914 2005 4.628333 GCAAAATTGGTGATGGTGAGATTG 59.372 41.667 0.00 0.00 0.00 2.67
1915 2006 5.567224 GCAAAATTGGTGATGGTGAGATTGA 60.567 40.000 0.00 0.00 0.00 2.57
1916 2007 6.457355 CAAAATTGGTGATGGTGAGATTGAA 58.543 36.000 0.00 0.00 0.00 2.69
1917 2008 6.669125 AAATTGGTGATGGTGAGATTGAAA 57.331 33.333 0.00 0.00 0.00 2.69
1918 2009 6.669125 AATTGGTGATGGTGAGATTGAAAA 57.331 33.333 0.00 0.00 0.00 2.29
1919 2010 5.710513 TTGGTGATGGTGAGATTGAAAAG 57.289 39.130 0.00 0.00 0.00 2.27
1920 2011 4.984295 TGGTGATGGTGAGATTGAAAAGA 58.016 39.130 0.00 0.00 0.00 2.52
1921 2012 5.384336 TGGTGATGGTGAGATTGAAAAGAA 58.616 37.500 0.00 0.00 0.00 2.52
1922 2013 6.012113 TGGTGATGGTGAGATTGAAAAGAAT 58.988 36.000 0.00 0.00 0.00 2.40
1923 2014 6.151648 TGGTGATGGTGAGATTGAAAAGAATC 59.848 38.462 0.00 0.00 33.21 2.52
1924 2015 6.253746 GTGATGGTGAGATTGAAAAGAATCG 58.746 40.000 0.00 0.00 37.41 3.34
1925 2016 6.092670 GTGATGGTGAGATTGAAAAGAATCGA 59.907 38.462 0.00 0.00 37.41 3.59
1926 2017 5.862924 TGGTGAGATTGAAAAGAATCGAC 57.137 39.130 0.00 0.00 37.41 4.20
1927 2018 4.388773 TGGTGAGATTGAAAAGAATCGACG 59.611 41.667 0.00 0.00 37.41 5.12
1928 2019 4.201724 GGTGAGATTGAAAAGAATCGACGG 60.202 45.833 0.00 0.00 37.41 4.79
1929 2020 3.370978 TGAGATTGAAAAGAATCGACGGC 59.629 43.478 0.00 0.00 37.41 5.68
1930 2021 3.334691 AGATTGAAAAGAATCGACGGCA 58.665 40.909 0.00 0.00 37.41 5.69
1931 2022 3.751175 AGATTGAAAAGAATCGACGGCAA 59.249 39.130 0.00 0.00 37.41 4.52
1932 2023 4.396166 AGATTGAAAAGAATCGACGGCAAT 59.604 37.500 0.00 0.00 37.41 3.56
1933 2024 3.469899 TGAAAAGAATCGACGGCAATG 57.530 42.857 0.00 0.00 0.00 2.82
1934 2025 2.177173 GAAAAGAATCGACGGCAATGC 58.823 47.619 0.00 0.00 0.00 3.56
1935 2026 0.451783 AAAGAATCGACGGCAATGCC 59.548 50.000 15.52 15.52 46.75 4.40
1951 2042 4.047125 CCCAGGTCCGGCAATGGT 62.047 66.667 14.97 0.00 0.00 3.55
1952 2043 2.438434 CCAGGTCCGGCAATGGTC 60.438 66.667 0.00 0.00 0.00 4.02
1953 2044 2.671070 CAGGTCCGGCAATGGTCT 59.329 61.111 0.00 0.00 0.00 3.85
1954 2045 1.450312 CAGGTCCGGCAATGGTCTC 60.450 63.158 0.00 0.00 0.00 3.36
1955 2046 2.124695 GGTCCGGCAATGGTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
1956 2047 2.670148 GGTCCGGCAATGGTCTCCT 61.670 63.158 0.00 0.00 0.00 3.69
1957 2048 1.335132 GGTCCGGCAATGGTCTCCTA 61.335 60.000 0.00 0.00 0.00 2.94
1958 2049 0.179081 GTCCGGCAATGGTCTCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
1997 2088 8.806429 AAAAATGTTTCCCTTCTTGAAAATGT 57.194 26.923 0.00 0.00 33.80 2.71
1998 2089 8.437360 AAAATGTTTCCCTTCTTGAAAATGTC 57.563 30.769 0.00 0.00 33.80 3.06
1999 2090 5.529581 TGTTTCCCTTCTTGAAAATGTCC 57.470 39.130 0.00 0.00 33.80 4.02
2000 2091 4.959210 TGTTTCCCTTCTTGAAAATGTCCA 59.041 37.500 0.00 0.00 33.80 4.02
2001 2092 5.602145 TGTTTCCCTTCTTGAAAATGTCCAT 59.398 36.000 0.00 0.00 33.80 3.41
2002 2093 6.780031 TGTTTCCCTTCTTGAAAATGTCCATA 59.220 34.615 0.00 0.00 33.80 2.74
2003 2094 7.454380 TGTTTCCCTTCTTGAAAATGTCCATAT 59.546 33.333 0.00 0.00 33.80 1.78
2004 2095 8.314021 GTTTCCCTTCTTGAAAATGTCCATATT 58.686 33.333 0.00 0.00 33.80 1.28
2005 2096 7.645058 TCCCTTCTTGAAAATGTCCATATTC 57.355 36.000 0.00 0.00 0.00 1.75
2006 2097 7.181361 TCCCTTCTTGAAAATGTCCATATTCA 58.819 34.615 0.00 0.00 0.00 2.57
2007 2098 7.340232 TCCCTTCTTGAAAATGTCCATATTCAG 59.660 37.037 0.00 0.00 33.71 3.02
2008 2099 7.340232 CCCTTCTTGAAAATGTCCATATTCAGA 59.660 37.037 0.00 0.00 33.71 3.27
2009 2100 8.742777 CCTTCTTGAAAATGTCCATATTCAGAA 58.257 33.333 0.00 0.00 33.71 3.02
2014 2105 9.699410 TTGAAAATGTCCATATTCAGAATAGGT 57.301 29.630 12.68 0.00 33.71 3.08
2015 2106 9.699410 TGAAAATGTCCATATTCAGAATAGGTT 57.301 29.630 12.68 1.13 0.00 3.50
2018 2109 8.469309 AATGTCCATATTCAGAATAGGTTTGG 57.531 34.615 12.68 12.31 0.00 3.28
2019 2110 6.969043 TGTCCATATTCAGAATAGGTTTGGT 58.031 36.000 15.70 0.00 0.00 3.67
2020 2111 7.410174 TGTCCATATTCAGAATAGGTTTGGTT 58.590 34.615 15.70 0.00 0.00 3.67
2021 2112 8.553153 TGTCCATATTCAGAATAGGTTTGGTTA 58.447 33.333 15.70 7.43 0.00 2.85
2022 2113 9.057089 GTCCATATTCAGAATAGGTTTGGTTAG 57.943 37.037 15.70 0.88 0.00 2.34
2023 2114 8.217799 TCCATATTCAGAATAGGTTTGGTTAGG 58.782 37.037 15.70 0.33 0.00 2.69
2024 2115 7.998964 CCATATTCAGAATAGGTTTGGTTAGGT 59.001 37.037 12.68 0.00 0.00 3.08
2025 2116 9.057089 CATATTCAGAATAGGTTTGGTTAGGTC 57.943 37.037 8.82 0.00 0.00 3.85
2026 2117 6.697641 TTCAGAATAGGTTTGGTTAGGTCT 57.302 37.500 0.00 0.00 0.00 3.85
2027 2118 6.295719 TCAGAATAGGTTTGGTTAGGTCTC 57.704 41.667 0.00 0.00 0.00 3.36
2028 2119 5.783360 TCAGAATAGGTTTGGTTAGGTCTCA 59.217 40.000 0.00 0.00 0.00 3.27
2029 2120 6.070767 TCAGAATAGGTTTGGTTAGGTCTCAG 60.071 42.308 0.00 0.00 0.00 3.35
2030 2121 5.785940 AGAATAGGTTTGGTTAGGTCTCAGT 59.214 40.000 0.00 0.00 0.00 3.41
2031 2122 5.678955 ATAGGTTTGGTTAGGTCTCAGTC 57.321 43.478 0.00 0.00 0.00 3.51
2032 2123 3.314693 AGGTTTGGTTAGGTCTCAGTCA 58.685 45.455 0.00 0.00 0.00 3.41
2033 2124 3.714798 AGGTTTGGTTAGGTCTCAGTCAA 59.285 43.478 0.00 0.00 0.00 3.18
2034 2125 4.065789 GGTTTGGTTAGGTCTCAGTCAAG 58.934 47.826 0.00 0.00 0.00 3.02
2035 2126 4.444449 GGTTTGGTTAGGTCTCAGTCAAGT 60.444 45.833 0.00 0.00 0.00 3.16
2036 2127 4.336889 TTGGTTAGGTCTCAGTCAAGTG 57.663 45.455 0.00 0.00 0.00 3.16
2037 2128 2.037251 TGGTTAGGTCTCAGTCAAGTGC 59.963 50.000 0.00 0.00 0.00 4.40
2038 2129 2.037251 GGTTAGGTCTCAGTCAAGTGCA 59.963 50.000 0.00 0.00 0.00 4.57
2039 2130 3.307059 GGTTAGGTCTCAGTCAAGTGCAT 60.307 47.826 0.00 0.00 0.00 3.96
2040 2131 4.081642 GGTTAGGTCTCAGTCAAGTGCATA 60.082 45.833 0.00 0.00 0.00 3.14
2041 2132 5.479306 GTTAGGTCTCAGTCAAGTGCATAA 58.521 41.667 0.00 0.00 0.00 1.90
2042 2133 3.931578 AGGTCTCAGTCAAGTGCATAAC 58.068 45.455 0.00 0.00 0.00 1.89
2043 2134 3.324846 AGGTCTCAGTCAAGTGCATAACA 59.675 43.478 0.00 0.00 0.00 2.41
2044 2135 4.019860 AGGTCTCAGTCAAGTGCATAACAT 60.020 41.667 0.00 0.00 0.00 2.71
2045 2136 4.093998 GGTCTCAGTCAAGTGCATAACATG 59.906 45.833 0.00 0.00 0.00 3.21
2100 2191 7.854534 TGCATGATGTTAAATAAGATCTCACG 58.145 34.615 0.00 0.00 37.02 4.35
2101 2192 7.041848 TGCATGATGTTAAATAAGATCTCACGG 60.042 37.037 0.00 0.35 37.02 4.94
2102 2193 7.171508 GCATGATGTTAAATAAGATCTCACGGA 59.828 37.037 0.00 0.00 37.02 4.69
2103 2194 9.212641 CATGATGTTAAATAAGATCTCACGGAT 57.787 33.333 10.51 0.00 37.02 4.18
2115 2206 8.740123 AAGATCTCACGGATATAATATCGACT 57.260 34.615 0.00 0.00 34.33 4.18
2116 2207 8.148807 AGATCTCACGGATATAATATCGACTG 57.851 38.462 0.00 0.00 34.33 3.51
2117 2208 7.988028 AGATCTCACGGATATAATATCGACTGA 59.012 37.037 0.00 0.00 34.33 3.41
2118 2209 7.541122 TCTCACGGATATAATATCGACTGAG 57.459 40.000 0.00 0.00 0.00 3.35
2119 2210 7.328737 TCTCACGGATATAATATCGACTGAGA 58.671 38.462 10.16 10.16 0.00 3.27
2120 2211 7.278203 TCTCACGGATATAATATCGACTGAGAC 59.722 40.741 10.16 0.00 0.00 3.36
2121 2212 7.104290 TCACGGATATAATATCGACTGAGACT 58.896 38.462 0.00 0.00 0.00 3.24
2122 2213 7.606839 TCACGGATATAATATCGACTGAGACTT 59.393 37.037 0.00 0.00 0.00 3.01
2123 2214 8.880750 CACGGATATAATATCGACTGAGACTTA 58.119 37.037 0.00 0.00 0.00 2.24
2124 2215 9.616156 ACGGATATAATATCGACTGAGACTTAT 57.384 33.333 0.00 0.00 0.00 1.73
2142 2233 5.230942 ACTTATTGAAGTCTCAGTTGACCG 58.769 41.667 0.00 0.00 42.50 4.79
2143 2234 2.526304 TTGAAGTCTCAGTTGACCGG 57.474 50.000 0.00 0.00 37.66 5.28
2144 2235 0.679505 TGAAGTCTCAGTTGACCGGG 59.320 55.000 6.32 0.00 37.66 5.73
2145 2236 0.966920 GAAGTCTCAGTTGACCGGGA 59.033 55.000 6.32 0.00 37.66 5.14
2146 2237 0.680061 AAGTCTCAGTTGACCGGGAC 59.320 55.000 6.32 0.90 37.66 4.46
2147 2238 0.178958 AGTCTCAGTTGACCGGGACT 60.179 55.000 6.32 3.70 37.66 3.85
2148 2239 0.680061 GTCTCAGTTGACCGGGACTT 59.320 55.000 6.32 0.00 0.00 3.01
2149 2240 1.891150 GTCTCAGTTGACCGGGACTTA 59.109 52.381 6.32 0.00 0.00 2.24
2150 2241 2.094649 GTCTCAGTTGACCGGGACTTAG 60.095 54.545 6.32 7.99 0.00 2.18
2151 2242 0.606604 TCAGTTGACCGGGACTTAGC 59.393 55.000 6.32 0.00 0.00 3.09
2152 2243 0.320374 CAGTTGACCGGGACTTAGCA 59.680 55.000 6.32 0.00 0.00 3.49
2153 2244 1.053424 AGTTGACCGGGACTTAGCAA 58.947 50.000 6.32 0.00 0.00 3.91
2154 2245 1.002087 AGTTGACCGGGACTTAGCAAG 59.998 52.381 6.32 0.00 0.00 4.01
2155 2246 0.323629 TTGACCGGGACTTAGCAAGG 59.676 55.000 6.32 0.00 0.00 3.61
2156 2247 1.449778 GACCGGGACTTAGCAAGGC 60.450 63.158 6.32 0.00 35.07 4.35
2157 2248 1.900545 GACCGGGACTTAGCAAGGCT 61.901 60.000 6.32 0.00 43.41 4.58
2158 2249 1.450312 CCGGGACTTAGCAAGGCTG 60.450 63.158 0.07 0.00 40.10 4.85
2159 2250 1.596934 CGGGACTTAGCAAGGCTGA 59.403 57.895 0.07 0.00 40.10 4.26
2160 2251 0.179000 CGGGACTTAGCAAGGCTGAT 59.821 55.000 0.07 0.00 40.10 2.90
2161 2252 1.407437 CGGGACTTAGCAAGGCTGATT 60.407 52.381 0.07 0.00 40.10 2.57
2162 2253 2.728007 GGGACTTAGCAAGGCTGATTT 58.272 47.619 0.07 0.00 40.10 2.17
2163 2254 3.681594 CGGGACTTAGCAAGGCTGATTTA 60.682 47.826 0.07 0.00 40.10 1.40
2164 2255 4.464947 GGGACTTAGCAAGGCTGATTTAT 58.535 43.478 0.07 0.00 40.10 1.40
2165 2256 4.889995 GGGACTTAGCAAGGCTGATTTATT 59.110 41.667 0.07 0.00 40.10 1.40
2166 2257 6.062095 GGGACTTAGCAAGGCTGATTTATTA 58.938 40.000 0.07 0.00 40.10 0.98
2167 2258 6.205658 GGGACTTAGCAAGGCTGATTTATTAG 59.794 42.308 0.07 0.00 40.10 1.73
2168 2259 6.992715 GGACTTAGCAAGGCTGATTTATTAGA 59.007 38.462 0.07 0.00 40.10 2.10
2169 2260 7.499232 GGACTTAGCAAGGCTGATTTATTAGAA 59.501 37.037 0.07 0.00 40.10 2.10
2170 2261 8.986929 ACTTAGCAAGGCTGATTTATTAGAAT 57.013 30.769 0.07 0.00 40.10 2.40
2175 2266 9.495572 AGCAAGGCTGATTTATTAGAATAGTAC 57.504 33.333 0.00 0.00 37.57 2.73
2176 2267 9.495572 GCAAGGCTGATTTATTAGAATAGTACT 57.504 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 327 2.173519 CTTGTTGGATTCACATGGCCT 58.826 47.619 3.32 0.00 0.00 5.19
373 378 0.532573 CAGCATAGTCGGTGACACCT 59.467 55.000 22.14 6.58 35.66 4.00
404 409 1.953017 CTCTATCACCGAGGAGCCG 59.047 63.158 0.00 0.00 0.00 5.52
428 433 1.529438 CTTGTTACGCACGATGGTTGT 59.471 47.619 0.00 0.00 0.00 3.32
456 461 0.593128 CTTTGGTAGCTTTGCGCAGT 59.407 50.000 11.31 0.00 42.61 4.40
569 574 3.976169 TCGCAATGTATGTCGATGATGA 58.024 40.909 0.00 0.00 34.31 2.92
584 589 1.246649 TGCATGTCCAACTTCGCAAT 58.753 45.000 0.00 0.00 0.00 3.56
603 608 3.616560 CGTACTGTGAGTTACTTGGGCAT 60.617 47.826 0.00 0.00 0.00 4.40
604 609 2.288579 CGTACTGTGAGTTACTTGGGCA 60.289 50.000 0.00 0.00 0.00 5.36
605 610 2.334838 CGTACTGTGAGTTACTTGGGC 58.665 52.381 0.00 0.00 0.00 5.36
606 611 2.334838 GCGTACTGTGAGTTACTTGGG 58.665 52.381 0.00 0.00 0.00 4.12
613 618 0.318445 GGTGACGCGTACTGTGAGTT 60.318 55.000 13.97 0.00 0.00 3.01
617 622 2.431942 GGGGTGACGCGTACTGTG 60.432 66.667 13.97 0.00 0.00 3.66
712 717 8.476657 CAAAGGAAAATTTGGCAAATGTTTTT 57.523 26.923 25.05 21.26 36.68 1.94
742 747 1.541147 CAACACCGCATCTTGGAACAT 59.459 47.619 0.00 0.00 39.30 2.71
860 865 0.248866 CCAAACCACCGTTGCAACTC 60.249 55.000 26.09 2.29 30.72 3.01
869 874 1.018910 AAACGTTCTCCAAACCACCG 58.981 50.000 0.00 0.00 0.00 4.94
886 891 2.280835 TGCCAAACACACAGCCAAA 58.719 47.368 0.00 0.00 0.00 3.28
951 956 7.989741 CCAAAAGTATAGAATCTGACACCATCT 59.010 37.037 0.00 0.00 0.00 2.90
990 1007 0.325860 AAATCCACATGGCCCAGCAT 60.326 50.000 0.00 0.00 34.44 3.79
1052 1070 5.336150 TGCAGAAAAGACCACATCAAAAA 57.664 34.783 0.00 0.00 0.00 1.94
1100 1118 1.126329 ATCAGCTCCCGCCATCAGAT 61.126 55.000 0.00 0.00 36.60 2.90
1179 1197 3.062639 GCTGGGGCTGCACAAATT 58.937 55.556 3.46 0.00 35.22 1.82
1263 1292 6.469410 ACGGAACAAGTATCAGGACAATAAA 58.531 36.000 0.00 0.00 0.00 1.40
1396 1436 2.158385 ACCCAGTGCCATCTAAAACCAA 60.158 45.455 0.00 0.00 0.00 3.67
1421 1462 4.051167 CAGCTCACCATGGGGCCA 62.051 66.667 18.09 0.00 37.90 5.36
1493 1534 4.663592 AGGTCTTAAGGAAACTGGAAAGGA 59.336 41.667 1.85 0.00 42.68 3.36
1633 1722 5.059833 GGAAGATTAGGAACAGCGATGATT 58.940 41.667 8.12 0.00 0.00 2.57
1777 1868 0.813184 ATGCGCAGGAAGTTGATTGG 59.187 50.000 18.32 0.00 0.00 3.16
1779 1870 3.505680 TGTAAATGCGCAGGAAGTTGATT 59.494 39.130 18.32 0.00 0.00 2.57
1783 1874 5.637006 TTAATGTAAATGCGCAGGAAGTT 57.363 34.783 18.32 8.96 0.00 2.66
1823 1914 1.077501 CGACCCAGGGCAACATCAT 60.078 57.895 4.91 0.00 39.74 2.45
1824 1915 1.561769 ATCGACCCAGGGCAACATCA 61.562 55.000 4.91 0.00 39.74 3.07
1825 1916 1.097547 CATCGACCCAGGGCAACATC 61.098 60.000 4.91 0.00 39.74 3.06
1826 1917 1.077501 CATCGACCCAGGGCAACAT 60.078 57.895 4.91 0.00 39.74 2.71
1827 1918 2.350895 CATCGACCCAGGGCAACA 59.649 61.111 4.91 0.00 39.74 3.33
1828 1919 2.438434 CCATCGACCCAGGGCAAC 60.438 66.667 4.91 0.00 0.00 4.17
1829 1920 2.609299 TCCATCGACCCAGGGCAA 60.609 61.111 4.91 0.00 0.00 4.52
1830 1921 3.399181 GTCCATCGACCCAGGGCA 61.399 66.667 4.91 0.00 32.40 5.36
1831 1922 3.391665 CTGTCCATCGACCCAGGGC 62.392 68.421 4.91 0.00 38.32 5.19
1832 1923 2.735772 CCTGTCCATCGACCCAGGG 61.736 68.421 2.85 2.85 38.32 4.45
1833 1924 1.685765 TCCTGTCCATCGACCCAGG 60.686 63.158 12.82 12.82 38.32 4.45
1834 1925 1.517832 GTCCTGTCCATCGACCCAG 59.482 63.158 0.00 0.00 38.32 4.45
1835 1926 2.348104 CGTCCTGTCCATCGACCCA 61.348 63.158 0.00 0.00 38.32 4.51
1836 1927 1.392710 ATCGTCCTGTCCATCGACCC 61.393 60.000 0.00 0.00 38.32 4.46
1837 1928 0.249073 CATCGTCCTGTCCATCGACC 60.249 60.000 0.00 0.00 38.32 4.79
1838 1929 0.249073 CCATCGTCCTGTCCATCGAC 60.249 60.000 0.00 0.00 39.66 4.20
1839 1930 0.395173 TCCATCGTCCTGTCCATCGA 60.395 55.000 0.00 0.00 36.77 3.59
1840 1931 0.031314 CTCCATCGTCCTGTCCATCG 59.969 60.000 0.00 0.00 0.00 3.84
1841 1932 0.249657 GCTCCATCGTCCTGTCCATC 60.250 60.000 0.00 0.00 0.00 3.51
1842 1933 1.826024 GCTCCATCGTCCTGTCCAT 59.174 57.895 0.00 0.00 0.00 3.41
1843 1934 2.710902 CGCTCCATCGTCCTGTCCA 61.711 63.158 0.00 0.00 0.00 4.02
1844 1935 2.105128 CGCTCCATCGTCCTGTCC 59.895 66.667 0.00 0.00 0.00 4.02
1845 1936 2.583593 GCGCTCCATCGTCCTGTC 60.584 66.667 0.00 0.00 0.00 3.51
1846 1937 4.148825 GGCGCTCCATCGTCCTGT 62.149 66.667 7.64 0.00 0.00 4.00
1847 1938 4.147449 TGGCGCTCCATCGTCCTG 62.147 66.667 7.64 0.00 37.47 3.86
1848 1939 3.842923 CTGGCGCTCCATCGTCCT 61.843 66.667 7.64 0.00 42.51 3.85
1849 1940 4.899239 CCTGGCGCTCCATCGTCC 62.899 72.222 7.64 0.00 42.51 4.79
1850 1941 4.899239 CCCTGGCGCTCCATCGTC 62.899 72.222 7.64 0.00 42.51 4.20
1856 1947 3.527775 CTATCTGCCCTGGCGCTCC 62.528 68.421 7.64 0.00 45.51 4.70
1857 1948 2.030262 CTATCTGCCCTGGCGCTC 59.970 66.667 7.64 0.00 45.51 5.03
1858 1949 1.414061 ATTCTATCTGCCCTGGCGCT 61.414 55.000 7.64 0.00 45.51 5.92
1859 1950 0.952984 GATTCTATCTGCCCTGGCGC 60.953 60.000 0.00 0.00 45.51 6.53
1860 1951 0.668706 CGATTCTATCTGCCCTGGCG 60.669 60.000 3.32 0.00 45.51 5.69
1861 1952 0.321122 CCGATTCTATCTGCCCTGGC 60.321 60.000 0.00 0.00 42.35 4.85
1862 1953 1.051812 ACCGATTCTATCTGCCCTGG 58.948 55.000 0.00 0.00 0.00 4.45
1863 1954 1.688735 TCACCGATTCTATCTGCCCTG 59.311 52.381 0.00 0.00 0.00 4.45
1864 1955 1.689273 GTCACCGATTCTATCTGCCCT 59.311 52.381 0.00 0.00 0.00 5.19
1865 1956 1.270358 GGTCACCGATTCTATCTGCCC 60.270 57.143 0.00 0.00 0.00 5.36
1866 1957 2.156343 GGTCACCGATTCTATCTGCC 57.844 55.000 0.00 0.00 0.00 4.85
1879 1970 2.393764 CAATTTTGCTTCACGGTCACC 58.606 47.619 0.00 0.00 0.00 4.02
1880 1971 2.223711 ACCAATTTTGCTTCACGGTCAC 60.224 45.455 0.00 0.00 0.00 3.67
1881 1972 2.028130 ACCAATTTTGCTTCACGGTCA 58.972 42.857 0.00 0.00 0.00 4.02
1882 1973 2.034053 TCACCAATTTTGCTTCACGGTC 59.966 45.455 0.00 0.00 0.00 4.79
1883 1974 2.028130 TCACCAATTTTGCTTCACGGT 58.972 42.857 0.00 0.00 0.00 4.83
1884 1975 2.791383 TCACCAATTTTGCTTCACGG 57.209 45.000 0.00 0.00 0.00 4.94
1885 1976 2.988493 CCATCACCAATTTTGCTTCACG 59.012 45.455 0.00 0.00 0.00 4.35
1886 1977 3.742369 CACCATCACCAATTTTGCTTCAC 59.258 43.478 0.00 0.00 0.00 3.18
1887 1978 3.640498 TCACCATCACCAATTTTGCTTCA 59.360 39.130 0.00 0.00 0.00 3.02
1888 1979 4.022068 TCTCACCATCACCAATTTTGCTTC 60.022 41.667 0.00 0.00 0.00 3.86
1889 1980 3.896888 TCTCACCATCACCAATTTTGCTT 59.103 39.130 0.00 0.00 0.00 3.91
1890 1981 3.499338 TCTCACCATCACCAATTTTGCT 58.501 40.909 0.00 0.00 0.00 3.91
1891 1982 3.940209 TCTCACCATCACCAATTTTGC 57.060 42.857 0.00 0.00 0.00 3.68
1892 1983 6.028146 TCAATCTCACCATCACCAATTTTG 57.972 37.500 0.00 0.00 0.00 2.44
1893 1984 6.669125 TTCAATCTCACCATCACCAATTTT 57.331 33.333 0.00 0.00 0.00 1.82
1894 1985 6.669125 TTTCAATCTCACCATCACCAATTT 57.331 33.333 0.00 0.00 0.00 1.82
1895 1986 6.494491 TCTTTTCAATCTCACCATCACCAATT 59.506 34.615 0.00 0.00 0.00 2.32
1896 1987 6.012113 TCTTTTCAATCTCACCATCACCAAT 58.988 36.000 0.00 0.00 0.00 3.16
1897 1988 5.384336 TCTTTTCAATCTCACCATCACCAA 58.616 37.500 0.00 0.00 0.00 3.67
1898 1989 4.984295 TCTTTTCAATCTCACCATCACCA 58.016 39.130 0.00 0.00 0.00 4.17
1899 1990 5.964958 TTCTTTTCAATCTCACCATCACC 57.035 39.130 0.00 0.00 0.00 4.02
1900 1991 6.092670 TCGATTCTTTTCAATCTCACCATCAC 59.907 38.462 0.00 0.00 31.48 3.06
1901 1992 6.092670 GTCGATTCTTTTCAATCTCACCATCA 59.907 38.462 0.00 0.00 31.48 3.07
1902 1993 6.481984 GTCGATTCTTTTCAATCTCACCATC 58.518 40.000 0.00 0.00 31.48 3.51
1903 1994 5.063944 CGTCGATTCTTTTCAATCTCACCAT 59.936 40.000 0.00 0.00 31.48 3.55
1904 1995 4.388773 CGTCGATTCTTTTCAATCTCACCA 59.611 41.667 0.00 0.00 31.48 4.17
1905 1996 4.201724 CCGTCGATTCTTTTCAATCTCACC 60.202 45.833 0.00 0.00 31.48 4.02
1906 1997 4.725169 GCCGTCGATTCTTTTCAATCTCAC 60.725 45.833 0.00 0.00 31.48 3.51
1907 1998 3.370978 GCCGTCGATTCTTTTCAATCTCA 59.629 43.478 0.00 0.00 31.48 3.27
1908 1999 3.370978 TGCCGTCGATTCTTTTCAATCTC 59.629 43.478 0.00 0.00 31.48 2.75
1909 2000 3.334691 TGCCGTCGATTCTTTTCAATCT 58.665 40.909 0.00 0.00 31.48 2.40
1910 2001 3.740044 TGCCGTCGATTCTTTTCAATC 57.260 42.857 0.00 0.00 0.00 2.67
1911 2002 4.414852 CATTGCCGTCGATTCTTTTCAAT 58.585 39.130 0.00 0.00 0.00 2.57
1912 2003 3.820689 CATTGCCGTCGATTCTTTTCAA 58.179 40.909 0.00 0.00 0.00 2.69
1913 2004 2.414029 GCATTGCCGTCGATTCTTTTCA 60.414 45.455 0.00 0.00 0.00 2.69
1914 2005 2.177173 GCATTGCCGTCGATTCTTTTC 58.823 47.619 0.00 0.00 0.00 2.29
1915 2006 1.135402 GGCATTGCCGTCGATTCTTTT 60.135 47.619 12.82 0.00 39.62 2.27
1916 2007 0.451783 GGCATTGCCGTCGATTCTTT 59.548 50.000 12.82 0.00 39.62 2.52
1917 2008 2.098293 GGCATTGCCGTCGATTCTT 58.902 52.632 12.82 0.00 39.62 2.52
1918 2009 3.813596 GGCATTGCCGTCGATTCT 58.186 55.556 12.82 0.00 39.62 2.40
1934 2025 3.995506 GACCATTGCCGGACCTGGG 62.996 68.421 5.05 1.11 32.89 4.45
1935 2026 2.438434 GACCATTGCCGGACCTGG 60.438 66.667 5.05 10.59 34.84 4.45
1936 2027 1.450312 GAGACCATTGCCGGACCTG 60.450 63.158 5.05 0.00 0.00 4.00
1937 2028 2.670148 GGAGACCATTGCCGGACCT 61.670 63.158 5.05 0.00 0.00 3.85
1938 2029 1.335132 TAGGAGACCATTGCCGGACC 61.335 60.000 5.05 0.00 0.00 4.46
1939 2030 0.179081 GTAGGAGACCATTGCCGGAC 60.179 60.000 5.05 0.00 0.00 4.79
1940 2031 2.208527 GTAGGAGACCATTGCCGGA 58.791 57.895 5.05 0.00 0.00 5.14
1941 2032 4.857251 GTAGGAGACCATTGCCGG 57.143 61.111 0.00 0.00 0.00 6.13
1972 2063 8.806429 ACATTTTCAAGAAGGGAAACATTTTT 57.194 26.923 0.00 0.00 34.23 1.94
1973 2064 7.498900 GGACATTTTCAAGAAGGGAAACATTTT 59.501 33.333 0.00 0.00 34.23 1.82
1974 2065 6.992123 GGACATTTTCAAGAAGGGAAACATTT 59.008 34.615 0.00 0.00 34.23 2.32
1975 2066 6.099557 TGGACATTTTCAAGAAGGGAAACATT 59.900 34.615 0.00 0.00 34.23 2.71
1976 2067 5.602145 TGGACATTTTCAAGAAGGGAAACAT 59.398 36.000 0.00 0.00 34.23 2.71
1977 2068 4.959210 TGGACATTTTCAAGAAGGGAAACA 59.041 37.500 0.00 0.00 34.23 2.83
1978 2069 5.529581 TGGACATTTTCAAGAAGGGAAAC 57.470 39.130 0.00 0.00 34.23 2.78
1979 2070 8.434589 AATATGGACATTTTCAAGAAGGGAAA 57.565 30.769 0.00 0.00 32.74 3.13
1980 2071 7.673504 TGAATATGGACATTTTCAAGAAGGGAA 59.326 33.333 13.36 0.00 36.37 3.97
1981 2072 7.181361 TGAATATGGACATTTTCAAGAAGGGA 58.819 34.615 13.36 0.00 36.37 4.20
1982 2073 7.340232 TCTGAATATGGACATTTTCAAGAAGGG 59.660 37.037 15.54 6.69 37.96 3.95
1983 2074 8.284945 TCTGAATATGGACATTTTCAAGAAGG 57.715 34.615 15.54 7.20 37.96 3.46
1988 2079 9.699410 ACCTATTCTGAATATGGACATTTTCAA 57.301 29.630 21.98 6.17 37.96 2.69
1989 2080 9.699410 AACCTATTCTGAATATGGACATTTTCA 57.301 29.630 21.98 14.47 36.75 2.69
1992 2083 8.917088 CCAAACCTATTCTGAATATGGACATTT 58.083 33.333 21.98 14.05 0.00 2.32
1993 2084 8.061304 ACCAAACCTATTCTGAATATGGACATT 58.939 33.333 24.30 15.43 0.00 2.71
1994 2085 7.586349 ACCAAACCTATTCTGAATATGGACAT 58.414 34.615 24.30 8.32 0.00 3.06
1995 2086 6.969043 ACCAAACCTATTCTGAATATGGACA 58.031 36.000 24.30 2.49 0.00 4.02
1996 2087 7.881775 AACCAAACCTATTCTGAATATGGAC 57.118 36.000 24.30 0.00 0.00 4.02
1997 2088 8.217799 CCTAACCAAACCTATTCTGAATATGGA 58.782 37.037 24.30 10.03 0.00 3.41
1998 2089 7.998964 ACCTAACCAAACCTATTCTGAATATGG 59.001 37.037 19.19 19.19 0.00 2.74
1999 2090 8.980481 ACCTAACCAAACCTATTCTGAATATG 57.020 34.615 10.34 10.19 0.00 1.78
2000 2091 9.004231 AGACCTAACCAAACCTATTCTGAATAT 57.996 33.333 10.34 0.00 0.00 1.28
2001 2092 8.388656 AGACCTAACCAAACCTATTCTGAATA 57.611 34.615 9.58 9.58 0.00 1.75
2002 2093 7.037586 TGAGACCTAACCAAACCTATTCTGAAT 60.038 37.037 8.14 8.14 0.00 2.57
2003 2094 6.271391 TGAGACCTAACCAAACCTATTCTGAA 59.729 38.462 0.00 0.00 0.00 3.02
2004 2095 5.783360 TGAGACCTAACCAAACCTATTCTGA 59.217 40.000 0.00 0.00 0.00 3.27
2005 2096 6.049955 TGAGACCTAACCAAACCTATTCTG 57.950 41.667 0.00 0.00 0.00 3.02
2006 2097 5.785940 ACTGAGACCTAACCAAACCTATTCT 59.214 40.000 0.00 0.00 0.00 2.40
2007 2098 6.051179 ACTGAGACCTAACCAAACCTATTC 57.949 41.667 0.00 0.00 0.00 1.75
2008 2099 5.546499 TGACTGAGACCTAACCAAACCTATT 59.454 40.000 0.00 0.00 0.00 1.73
2009 2100 5.091552 TGACTGAGACCTAACCAAACCTAT 58.908 41.667 0.00 0.00 0.00 2.57
2010 2101 4.485875 TGACTGAGACCTAACCAAACCTA 58.514 43.478 0.00 0.00 0.00 3.08
2011 2102 3.314693 TGACTGAGACCTAACCAAACCT 58.685 45.455 0.00 0.00 0.00 3.50
2012 2103 3.764237 TGACTGAGACCTAACCAAACC 57.236 47.619 0.00 0.00 0.00 3.27
2013 2104 4.511826 CACTTGACTGAGACCTAACCAAAC 59.488 45.833 0.00 0.00 0.00 2.93
2014 2105 4.703897 CACTTGACTGAGACCTAACCAAA 58.296 43.478 0.00 0.00 0.00 3.28
2015 2106 3.494398 GCACTTGACTGAGACCTAACCAA 60.494 47.826 0.00 0.00 0.00 3.67
2016 2107 2.037251 GCACTTGACTGAGACCTAACCA 59.963 50.000 0.00 0.00 0.00 3.67
2017 2108 2.037251 TGCACTTGACTGAGACCTAACC 59.963 50.000 0.00 0.00 0.00 2.85
2018 2109 3.386768 TGCACTTGACTGAGACCTAAC 57.613 47.619 0.00 0.00 0.00 2.34
2019 2110 5.011635 TGTTATGCACTTGACTGAGACCTAA 59.988 40.000 0.00 0.00 0.00 2.69
2020 2111 4.526650 TGTTATGCACTTGACTGAGACCTA 59.473 41.667 0.00 0.00 0.00 3.08
2021 2112 3.324846 TGTTATGCACTTGACTGAGACCT 59.675 43.478 0.00 0.00 0.00 3.85
2022 2113 3.664107 TGTTATGCACTTGACTGAGACC 58.336 45.455 0.00 0.00 0.00 3.85
2023 2114 5.213913 CATGTTATGCACTTGACTGAGAC 57.786 43.478 0.00 0.00 33.21 3.36
2074 2165 8.337532 CGTGAGATCTTATTTAACATCATGCAA 58.662 33.333 0.00 0.00 0.00 4.08
2075 2166 7.041848 CCGTGAGATCTTATTTAACATCATGCA 60.042 37.037 0.00 0.00 0.00 3.96
2076 2167 7.171508 TCCGTGAGATCTTATTTAACATCATGC 59.828 37.037 0.00 0.00 0.00 4.06
2077 2168 8.593492 TCCGTGAGATCTTATTTAACATCATG 57.407 34.615 0.00 0.00 0.00 3.07
2089 2180 9.833917 AGTCGATATTATATCCGTGAGATCTTA 57.166 33.333 6.64 0.00 36.33 2.10
2090 2181 8.616942 CAGTCGATATTATATCCGTGAGATCTT 58.383 37.037 6.64 0.00 36.33 2.40
2091 2182 7.988028 TCAGTCGATATTATATCCGTGAGATCT 59.012 37.037 6.64 0.00 36.33 2.75
2092 2183 8.144155 TCAGTCGATATTATATCCGTGAGATC 57.856 38.462 6.64 0.00 36.33 2.75
2093 2184 7.988028 TCTCAGTCGATATTATATCCGTGAGAT 59.012 37.037 20.38 2.14 39.15 2.75
2094 2185 7.278203 GTCTCAGTCGATATTATATCCGTGAGA 59.722 40.741 20.38 20.38 35.51 3.27
2095 2186 7.279090 AGTCTCAGTCGATATTATATCCGTGAG 59.721 40.741 17.94 17.94 0.00 3.51
2096 2187 7.104290 AGTCTCAGTCGATATTATATCCGTGA 58.896 38.462 6.64 6.26 0.00 4.35
2097 2188 7.310072 AGTCTCAGTCGATATTATATCCGTG 57.690 40.000 6.64 2.68 0.00 4.94
2098 2189 7.925043 AAGTCTCAGTCGATATTATATCCGT 57.075 36.000 6.64 0.00 0.00 4.69
2120 2211 4.627467 CCGGTCAACTGAGACTTCAATAAG 59.373 45.833 0.00 0.00 38.57 1.73
2121 2212 4.562757 CCCGGTCAACTGAGACTTCAATAA 60.563 45.833 0.00 0.00 38.57 1.40
2122 2213 3.056107 CCCGGTCAACTGAGACTTCAATA 60.056 47.826 0.00 0.00 38.57 1.90
2123 2214 2.289694 CCCGGTCAACTGAGACTTCAAT 60.290 50.000 0.00 0.00 38.57 2.57
2124 2215 1.070134 CCCGGTCAACTGAGACTTCAA 59.930 52.381 0.00 0.00 38.57 2.69
2125 2216 0.679505 CCCGGTCAACTGAGACTTCA 59.320 55.000 0.00 0.00 38.57 3.02
2126 2217 0.966920 TCCCGGTCAACTGAGACTTC 59.033 55.000 0.00 0.00 38.57 3.01
2127 2218 0.680061 GTCCCGGTCAACTGAGACTT 59.320 55.000 0.00 0.00 38.57 3.01
2128 2219 0.178958 AGTCCCGGTCAACTGAGACT 60.179 55.000 0.00 0.69 38.57 3.24
2129 2220 0.680061 AAGTCCCGGTCAACTGAGAC 59.320 55.000 0.00 0.00 37.80 3.36
2130 2221 2.168496 CTAAGTCCCGGTCAACTGAGA 58.832 52.381 0.00 0.00 0.00 3.27
2131 2222 1.404315 GCTAAGTCCCGGTCAACTGAG 60.404 57.143 0.00 4.81 0.00 3.35
2132 2223 0.606604 GCTAAGTCCCGGTCAACTGA 59.393 55.000 0.00 0.00 0.00 3.41
2133 2224 0.320374 TGCTAAGTCCCGGTCAACTG 59.680 55.000 0.00 0.00 0.00 3.16
2134 2225 1.002087 CTTGCTAAGTCCCGGTCAACT 59.998 52.381 0.00 0.00 0.00 3.16
2135 2226 1.439679 CTTGCTAAGTCCCGGTCAAC 58.560 55.000 0.00 0.00 0.00 3.18
2136 2227 0.323629 CCTTGCTAAGTCCCGGTCAA 59.676 55.000 0.00 0.00 0.00 3.18
2137 2228 1.980052 CCTTGCTAAGTCCCGGTCA 59.020 57.895 0.00 0.00 0.00 4.02
2138 2229 1.449778 GCCTTGCTAAGTCCCGGTC 60.450 63.158 0.00 0.00 0.00 4.79
2139 2230 1.918800 AGCCTTGCTAAGTCCCGGT 60.919 57.895 0.00 0.00 36.99 5.28
2140 2231 1.450312 CAGCCTTGCTAAGTCCCGG 60.450 63.158 0.00 0.00 36.40 5.73
2141 2232 0.179000 ATCAGCCTTGCTAAGTCCCG 59.821 55.000 0.00 0.00 36.40 5.14
2142 2233 2.426842 AATCAGCCTTGCTAAGTCCC 57.573 50.000 0.00 0.00 36.40 4.46
2143 2234 6.992715 TCTAATAAATCAGCCTTGCTAAGTCC 59.007 38.462 0.00 0.00 36.40 3.85
2144 2235 8.438676 TTCTAATAAATCAGCCTTGCTAAGTC 57.561 34.615 0.00 0.00 36.40 3.01
2145 2236 8.986929 ATTCTAATAAATCAGCCTTGCTAAGT 57.013 30.769 0.00 0.00 36.40 2.24
2149 2240 9.495572 GTACTATTCTAATAAATCAGCCTTGCT 57.504 33.333 0.00 0.00 40.77 3.91
2150 2241 9.495572 AGTACTATTCTAATAAATCAGCCTTGC 57.504 33.333 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.