Multiple sequence alignment - TraesCS6A01G123300

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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 TraesCS6A01G123300 chr6A 100.000 2615 0 0 1 2615 96812363 96814977 0.000000e+00 4830.0
1 TraesCS6A01G123300 chr6D 90.825 1188 60 24 653 1798 80112313 80113493 0.000000e+00 1544.0
2 TraesCS6A01G123300 chr6D 96.552 58 2 0 2426 2483 80113538 80113595 2.140000e-16 97.1
3 TraesCS6A01G123300 chr6B 90.293 1195 59 26 653 1797 153311653 153312840 0.000000e+00 1511.0
4 TraesCS6A01G123300 chr6B 86.971 614 50 8 2025 2615 153323565 153324171 0.000000e+00 664.0
5 TraesCS6A01G123300 chr5A 94.444 666 36 1 1 666 610228143 610227479 0.000000e+00 1024.0
6 TraesCS6A01G123300 chr5A 92.274 686 33 2 1 666 705602167 705602852 0.000000e+00 955.0
7 TraesCS6A01G123300 chr5A 91.520 684 38 3 1 665 656711742 656712424 0.000000e+00 924.0
8 TraesCS6A01G123300 chr5A 88.724 674 66 5 2 666 593391055 593391727 0.000000e+00 815.0
9 TraesCS6A01G123300 chr5A 82.222 675 102 10 2 666 687662318 687662984 1.360000e-157 566.0
10 TraesCS6A01G123300 chr5A 82.074 675 103 10 2 666 687668718 687669384 6.320000e-156 560.0
11 TraesCS6A01G123300 chr5A 78.182 550 100 12 1074 1616 276332986 276332450 1.500000e-87 333.0
12 TraesCS6A01G123300 chr5A 92.683 41 1 2 2225 2264 641559460 641559499 1.010000e-04 58.4
13 TraesCS6A01G123300 chr5A 85.714 56 4 4 2217 2271 516800312 516800364 3.640000e-04 56.5
14 TraesCS6A01G123300 chr7A 92.847 685 28 3 1 666 98490934 98491616 0.000000e+00 974.0
15 TraesCS6A01G123300 chr7A 89.024 82 9 0 2221 2302 694777847 694777766 4.600000e-18 102.0
16 TraesCS6A01G123300 chr7A 94.872 39 2 0 2217 2255 570143662 570143700 7.810000e-06 62.1
17 TraesCS6A01G123300 chr4B 91.849 687 35 2 1 666 665618935 665619621 0.000000e+00 939.0
18 TraesCS6A01G123300 chr4B 96.429 56 2 0 2226 2281 134951605 134951550 2.770000e-15 93.5
19 TraesCS6A01G123300 chr2B 89.778 675 55 8 2 666 71375344 71374674 0.000000e+00 852.0
20 TraesCS6A01G123300 chr3D 89.577 662 62 6 4 660 23236489 23235830 0.000000e+00 833.0
21 TraesCS6A01G123300 chr4A 87.117 652 72 7 5 646 619317901 619317252 0.000000e+00 728.0
22 TraesCS6A01G123300 chr7D 83.993 581 76 11 93 666 125782932 125783502 2.290000e-150 542.0
23 TraesCS6A01G123300 chr5B 87.342 79 9 1 2226 2304 549611345 549611268 3.580000e-14 89.8
24 TraesCS6A01G123300 chr5B 94.595 37 2 0 2217 2253 610010382 610010346 1.010000e-04 58.4
25 TraesCS6A01G123300 chr7B 96.078 51 2 0 2231 2281 485043982 485043932 1.670000e-12 84.2
26 TraesCS6A01G123300 chr5D 86.842 76 9 1 2225 2300 245632663 245632737 1.670000e-12 84.2
27 TraesCS6A01G123300 chr3A 84.706 85 12 1 2216 2300 446539214 446539297 1.670000e-12 84.2


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 TraesCS6A01G123300 chr6A 96812363 96814977 2614 False 4830.00 4830 100.0000 1 2615 1 chr6A.!!$F1 2614
1 TraesCS6A01G123300 chr6D 80112313 80113595 1282 False 820.55 1544 93.6885 653 2483 2 chr6D.!!$F1 1830
2 TraesCS6A01G123300 chr6B 153311653 153312840 1187 False 1511.00 1511 90.2930 653 1797 1 chr6B.!!$F1 1144
3 TraesCS6A01G123300 chr6B 153323565 153324171 606 False 664.00 664 86.9710 2025 2615 1 chr6B.!!$F2 590
4 TraesCS6A01G123300 chr5A 610227479 610228143 664 True 1024.00 1024 94.4440 1 666 1 chr5A.!!$R2 665
5 TraesCS6A01G123300 chr5A 705602167 705602852 685 False 955.00 955 92.2740 1 666 1 chr5A.!!$F7 665
6 TraesCS6A01G123300 chr5A 656711742 656712424 682 False 924.00 924 91.5200 1 665 1 chr5A.!!$F4 664
7 TraesCS6A01G123300 chr5A 593391055 593391727 672 False 815.00 815 88.7240 2 666 1 chr5A.!!$F2 664
8 TraesCS6A01G123300 chr5A 687662318 687662984 666 False 566.00 566 82.2220 2 666 1 chr5A.!!$F5 664
9 TraesCS6A01G123300 chr5A 687668718 687669384 666 False 560.00 560 82.0740 2 666 1 chr5A.!!$F6 664
10 TraesCS6A01G123300 chr5A 276332450 276332986 536 True 333.00 333 78.1820 1074 1616 1 chr5A.!!$R1 542
11 TraesCS6A01G123300 chr7A 98490934 98491616 682 False 974.00 974 92.8470 1 666 1 chr7A.!!$F1 665
12 TraesCS6A01G123300 chr4B 665618935 665619621 686 False 939.00 939 91.8490 1 666 1 chr4B.!!$F1 665
13 TraesCS6A01G123300 chr2B 71374674 71375344 670 True 852.00 852 89.7780 2 666 1 chr2B.!!$R1 664
14 TraesCS6A01G123300 chr3D 23235830 23236489 659 True 833.00 833 89.5770 4 660 1 chr3D.!!$R1 656
15 TraesCS6A01G123300 chr4A 619317252 619317901 649 True 728.00 728 87.1170 5 646 1 chr4A.!!$R1 641
16 TraesCS6A01G123300 chr7D 125782932 125783502 570 False 542.00 542 83.9930 93 666 1 chr7D.!!$F1 573

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
790 867 0.031721 AGACGACGACTTGAACACCC 59.968 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2155 0.041312 CGTGGAGAAAGTTGCCAACG 60.041 55.0 1.2 0.0 36.23 4.1 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
179 180 2.350522 GATCATGAGCGTGGACTTGTT 58.649 47.619 0.09 0.00 0.00 2.83
300 303 4.764771 TTGGAGGCTGGCATGGGC 62.765 66.667 3.38 0.00 40.13 5.36
400 424 5.892348 AGGACAACTATTCATTTTGGAGGT 58.108 37.500 0.00 0.00 0.00 3.85
527 601 1.399714 ATAGACGCGGACAGGATGAA 58.600 50.000 12.47 0.00 39.69 2.57
574 648 2.094659 CACGACCACCGCATCTCAC 61.095 63.158 0.00 0.00 43.32 3.51
613 687 3.600617 ACCCCAAATCCCTATCCAAAGAA 59.399 43.478 0.00 0.00 0.00 2.52
697 772 1.577328 CGGTCCTTGCATCGCACTTT 61.577 55.000 0.00 0.00 38.71 2.66
720 795 0.252197 GGAACATTCCTGGCGGTACT 59.748 55.000 3.24 0.00 44.11 2.73
721 796 1.369625 GAACATTCCTGGCGGTACTG 58.630 55.000 0.00 0.00 0.00 2.74
722 797 0.981183 AACATTCCTGGCGGTACTGA 59.019 50.000 5.68 0.00 0.00 3.41
732 807 1.209128 GCGGTACTGAATCGTCATGG 58.791 55.000 5.68 0.00 31.85 3.66
790 867 0.031721 AGACGACGACTTGAACACCC 59.968 55.000 0.00 0.00 0.00 4.61
866 961 1.272781 GTTCTCTGATGCTTCCGACG 58.727 55.000 0.00 0.00 0.00 5.12
869 964 0.863538 CTCTGATGCTTCCGACGACG 60.864 60.000 0.00 0.00 39.43 5.12
1381 1507 3.685214 CTGGAGTTCGACGGGAGCG 62.685 68.421 0.00 0.00 0.00 5.03
1620 1746 5.100259 TGTAGCGTTAAGTACTGATGAAGC 58.900 41.667 0.00 0.00 0.00 3.86
1630 1756 1.074405 ACTGATGAAGCTTCTTGGGCA 59.926 47.619 26.09 13.44 0.00 5.36
1674 1806 2.621407 GCCATCTTGTTTGGAGATCCCA 60.621 50.000 0.00 0.00 44.93 4.37
1681 1813 0.036164 TTTGGAGATCCCACGGTGTG 59.964 55.000 7.45 0.00 46.62 3.82
1694 1826 1.579429 GGTGTGCCGGTTTGATGTC 59.421 57.895 1.90 0.00 0.00 3.06
1696 1828 1.069935 TGTGCCGGTTTGATGTCGA 59.930 52.632 1.90 0.00 0.00 4.20
1717 1849 9.201127 TGTCGATTTCATTTTTGCAAATATTCA 57.799 25.926 13.65 0.10 30.90 2.57
1756 1894 6.908825 TGTGTATTTCTGTAGGATTGTTTGC 58.091 36.000 0.00 0.00 0.00 3.68
1773 1911 9.199982 GATTGTTTGCCTATCATTGAATATTGG 57.800 33.333 0.00 0.00 0.00 3.16
1798 1936 6.811634 TGCATTCTTGGGGATTAATTCATT 57.188 33.333 0.00 0.00 0.00 2.57
1799 1937 6.584488 TGCATTCTTGGGGATTAATTCATTG 58.416 36.000 0.00 0.00 0.00 2.82
1800 1938 6.383436 TGCATTCTTGGGGATTAATTCATTGA 59.617 34.615 0.00 0.00 0.00 2.57
1801 1939 7.071447 TGCATTCTTGGGGATTAATTCATTGAT 59.929 33.333 0.00 0.00 0.00 2.57
1802 1940 7.935210 GCATTCTTGGGGATTAATTCATTGATT 59.065 33.333 0.00 0.00 0.00 2.57
1803 1941 9.268268 CATTCTTGGGGATTAATTCATTGATTG 57.732 33.333 0.00 0.00 0.00 2.67
1805 1943 5.549742 TGGGGATTAATTCATTGATTGGC 57.450 39.130 0.00 0.00 0.00 4.52
1806 1944 5.218179 TGGGGATTAATTCATTGATTGGCT 58.782 37.500 0.00 0.00 0.00 4.75
1807 1945 5.070714 TGGGGATTAATTCATTGATTGGCTG 59.929 40.000 0.00 0.00 0.00 4.85
1808 1946 5.305128 GGGGATTAATTCATTGATTGGCTGA 59.695 40.000 0.00 0.00 0.00 4.26
1809 1947 6.183360 GGGGATTAATTCATTGATTGGCTGAA 60.183 38.462 0.00 0.00 33.75 3.02
1810 1948 6.703165 GGGATTAATTCATTGATTGGCTGAAC 59.297 38.462 0.00 0.00 32.16 3.18
1811 1949 6.418819 GGATTAATTCATTGATTGGCTGAACG 59.581 38.462 0.00 0.00 32.16 3.95
1812 1950 3.788333 ATTCATTGATTGGCTGAACGG 57.212 42.857 0.00 0.00 32.16 4.44
1813 1951 2.198827 TCATTGATTGGCTGAACGGT 57.801 45.000 0.00 0.00 0.00 4.83
1814 1952 2.513753 TCATTGATTGGCTGAACGGTT 58.486 42.857 0.00 0.00 0.00 4.44
1815 1953 2.228582 TCATTGATTGGCTGAACGGTTG 59.771 45.455 0.00 0.00 0.00 3.77
1816 1954 1.974265 TTGATTGGCTGAACGGTTGA 58.026 45.000 0.00 0.00 0.00 3.18
1817 1955 2.198827 TGATTGGCTGAACGGTTGAT 57.801 45.000 0.00 0.00 0.00 2.57
1818 1956 1.811965 TGATTGGCTGAACGGTTGATG 59.188 47.619 0.00 0.00 0.00 3.07
1819 1957 1.812571 GATTGGCTGAACGGTTGATGT 59.187 47.619 0.00 0.00 0.00 3.06
1820 1958 1.234821 TTGGCTGAACGGTTGATGTC 58.765 50.000 0.00 0.00 0.00 3.06
1821 1959 0.107643 TGGCTGAACGGTTGATGTCA 59.892 50.000 0.00 0.00 0.00 3.58
1822 1960 1.271325 TGGCTGAACGGTTGATGTCAT 60.271 47.619 0.00 0.00 0.00 3.06
1823 1961 1.812571 GGCTGAACGGTTGATGTCATT 59.187 47.619 0.00 0.00 0.00 2.57
1824 1962 2.228822 GGCTGAACGGTTGATGTCATTT 59.771 45.455 0.00 0.00 0.00 2.32
1825 1963 3.492313 GCTGAACGGTTGATGTCATTTC 58.508 45.455 0.00 0.00 0.00 2.17
1826 1964 3.058293 GCTGAACGGTTGATGTCATTTCA 60.058 43.478 0.00 0.00 0.00 2.69
1827 1965 4.379813 GCTGAACGGTTGATGTCATTTCAT 60.380 41.667 0.00 0.00 0.00 2.57
1828 1966 5.295431 TGAACGGTTGATGTCATTTCATC 57.705 39.130 0.00 0.00 42.95 2.92
1829 1967 4.155826 TGAACGGTTGATGTCATTTCATCC 59.844 41.667 0.00 0.00 42.24 3.51
1830 1968 3.955471 ACGGTTGATGTCATTTCATCCT 58.045 40.909 4.59 0.00 42.24 3.24
1831 1969 5.097742 ACGGTTGATGTCATTTCATCCTA 57.902 39.130 4.59 0.00 42.24 2.94
1832 1970 5.496556 ACGGTTGATGTCATTTCATCCTAA 58.503 37.500 4.59 0.00 42.24 2.69
1833 1971 5.354234 ACGGTTGATGTCATTTCATCCTAAC 59.646 40.000 4.59 3.76 42.24 2.34
1834 1972 5.586243 CGGTTGATGTCATTTCATCCTAACT 59.414 40.000 4.59 0.00 42.24 2.24
1835 1973 6.238211 CGGTTGATGTCATTTCATCCTAACTC 60.238 42.308 4.59 0.00 42.24 3.01
1836 1974 6.825721 GGTTGATGTCATTTCATCCTAACTCT 59.174 38.462 4.59 0.00 42.24 3.24
1837 1975 7.337942 GGTTGATGTCATTTCATCCTAACTCTT 59.662 37.037 4.59 0.00 42.24 2.85
1838 1976 7.854557 TGATGTCATTTCATCCTAACTCTTG 57.145 36.000 4.59 0.00 42.24 3.02
1839 1977 7.623630 TGATGTCATTTCATCCTAACTCTTGA 58.376 34.615 4.59 0.00 42.24 3.02
1840 1978 8.270030 TGATGTCATTTCATCCTAACTCTTGAT 58.730 33.333 4.59 0.00 42.24 2.57
1841 1979 9.770097 GATGTCATTTCATCCTAACTCTTGATA 57.230 33.333 0.00 0.00 38.47 2.15
1843 1981 9.958180 TGTCATTTCATCCTAACTCTTGATAAA 57.042 29.630 0.00 0.00 0.00 1.40
1848 1986 9.958180 TTTCATCCTAACTCTTGATAAATGTCA 57.042 29.630 0.00 0.00 0.00 3.58
1849 1987 9.958180 TTCATCCTAACTCTTGATAAATGTCAA 57.042 29.630 0.00 0.00 36.70 3.18
1850 1988 9.958180 TCATCCTAACTCTTGATAAATGTCAAA 57.042 29.630 0.00 0.00 37.63 2.69
1853 1991 9.739276 TCCTAACTCTTGATAAATGTCAAATGT 57.261 29.630 0.00 0.00 37.63 2.71
1870 2008 9.012161 TGTCAAATGTTGATCAGATTATGTTCA 57.988 29.630 0.00 0.00 42.47 3.18
1871 2009 9.499585 GTCAAATGTTGATCAGATTATGTTCAG 57.500 33.333 0.00 0.00 42.47 3.02
1872 2010 8.680001 TCAAATGTTGATCAGATTATGTTCAGG 58.320 33.333 0.00 0.00 38.53 3.86
1873 2011 8.680001 CAAATGTTGATCAGATTATGTTCAGGA 58.320 33.333 0.00 0.00 38.53 3.86
1874 2012 8.447924 AATGTTGATCAGATTATGTTCAGGAG 57.552 34.615 0.00 0.00 38.53 3.69
1875 2013 7.186570 TGTTGATCAGATTATGTTCAGGAGA 57.813 36.000 0.00 0.00 38.53 3.71
1876 2014 7.044181 TGTTGATCAGATTATGTTCAGGAGAC 58.956 38.462 0.00 0.00 38.53 3.36
1877 2015 6.796785 TGATCAGATTATGTTCAGGAGACA 57.203 37.500 0.00 0.00 33.60 3.41
1878 2016 7.186570 TGATCAGATTATGTTCAGGAGACAA 57.813 36.000 0.00 0.00 33.60 3.18
1879 2017 7.270779 TGATCAGATTATGTTCAGGAGACAAG 58.729 38.462 0.00 0.00 33.60 3.16
1880 2018 6.857437 TCAGATTATGTTCAGGAGACAAGA 57.143 37.500 0.00 0.00 0.00 3.02
1881 2019 6.634805 TCAGATTATGTTCAGGAGACAAGAC 58.365 40.000 0.00 0.00 0.00 3.01
1882 2020 6.438741 TCAGATTATGTTCAGGAGACAAGACT 59.561 38.462 0.00 0.00 0.00 3.24
1883 2021 7.038729 TCAGATTATGTTCAGGAGACAAGACTT 60.039 37.037 0.00 0.00 0.00 3.01
1884 2022 8.253810 CAGATTATGTTCAGGAGACAAGACTTA 58.746 37.037 0.00 0.00 0.00 2.24
1885 2023 8.986991 AGATTATGTTCAGGAGACAAGACTTAT 58.013 33.333 0.00 0.00 0.00 1.73
1889 2027 6.878317 TGTTCAGGAGACAAGACTTATATGG 58.122 40.000 0.00 0.00 0.00 2.74
1890 2028 6.440647 TGTTCAGGAGACAAGACTTATATGGT 59.559 38.462 0.00 0.00 0.00 3.55
1891 2029 6.716934 TCAGGAGACAAGACTTATATGGTC 57.283 41.667 0.00 3.42 0.00 4.02
1892 2030 5.299531 TCAGGAGACAAGACTTATATGGTCG 59.700 44.000 0.00 0.00 38.58 4.79
1893 2031 5.299531 CAGGAGACAAGACTTATATGGTCGA 59.700 44.000 0.00 0.00 38.58 4.20
1894 2032 5.533154 AGGAGACAAGACTTATATGGTCGAG 59.467 44.000 0.00 5.16 38.58 4.04
1895 2033 5.531659 GGAGACAAGACTTATATGGTCGAGA 59.468 44.000 0.00 0.00 38.58 4.04
1896 2034 6.039493 GGAGACAAGACTTATATGGTCGAGAA 59.961 42.308 0.00 0.00 38.58 2.87
1897 2035 7.406031 AGACAAGACTTATATGGTCGAGAAA 57.594 36.000 0.00 0.00 38.58 2.52
1898 2036 7.259161 AGACAAGACTTATATGGTCGAGAAAC 58.741 38.462 0.00 0.00 38.58 2.78
1899 2037 6.931838 ACAAGACTTATATGGTCGAGAAACA 58.068 36.000 0.00 0.00 38.58 2.83
1900 2038 7.556844 ACAAGACTTATATGGTCGAGAAACAT 58.443 34.615 0.00 0.00 38.58 2.71
1901 2039 8.041323 ACAAGACTTATATGGTCGAGAAACATT 58.959 33.333 0.00 0.00 38.58 2.71
1902 2040 8.331022 CAAGACTTATATGGTCGAGAAACATTG 58.669 37.037 0.00 0.00 38.58 2.82
1903 2041 7.556844 AGACTTATATGGTCGAGAAACATTGT 58.443 34.615 0.00 0.00 38.58 2.71
1904 2042 8.041323 AGACTTATATGGTCGAGAAACATTGTT 58.959 33.333 0.00 0.00 38.58 2.83
1905 2043 9.309516 GACTTATATGGTCGAGAAACATTGTTA 57.690 33.333 1.76 0.00 0.00 2.41
1906 2044 9.095065 ACTTATATGGTCGAGAAACATTGTTAC 57.905 33.333 1.76 0.00 0.00 2.50
1907 2045 6.920569 ATATGGTCGAGAAACATTGTTACC 57.079 37.500 1.76 6.94 0.00 2.85
1908 2046 3.404899 TGGTCGAGAAACATTGTTACCC 58.595 45.455 13.35 3.23 0.00 3.69
1909 2047 3.181453 TGGTCGAGAAACATTGTTACCCA 60.181 43.478 13.35 6.75 0.00 4.51
1910 2048 4.007659 GGTCGAGAAACATTGTTACCCAT 58.992 43.478 1.76 0.00 0.00 4.00
1911 2049 4.457949 GGTCGAGAAACATTGTTACCCATT 59.542 41.667 1.76 0.00 0.00 3.16
1912 2050 5.644636 GGTCGAGAAACATTGTTACCCATTA 59.355 40.000 1.76 0.00 0.00 1.90
1913 2051 6.402875 GGTCGAGAAACATTGTTACCCATTAC 60.403 42.308 1.76 0.00 0.00 1.89
1914 2052 6.370718 GTCGAGAAACATTGTTACCCATTACT 59.629 38.462 1.76 0.00 0.00 2.24
1915 2053 7.546667 GTCGAGAAACATTGTTACCCATTACTA 59.453 37.037 1.76 0.00 0.00 1.82
1916 2054 7.546667 TCGAGAAACATTGTTACCCATTACTAC 59.453 37.037 1.76 0.00 0.00 2.73
1917 2055 7.332430 CGAGAAACATTGTTACCCATTACTACA 59.668 37.037 1.76 0.00 0.00 2.74
1918 2056 9.174166 GAGAAACATTGTTACCCATTACTACAT 57.826 33.333 1.76 0.00 0.00 2.29
1919 2057 9.174166 AGAAACATTGTTACCCATTACTACATC 57.826 33.333 1.76 0.00 0.00 3.06
1920 2058 7.875327 AACATTGTTACCCATTACTACATCC 57.125 36.000 0.00 0.00 0.00 3.51
1921 2059 6.964464 ACATTGTTACCCATTACTACATCCA 58.036 36.000 0.00 0.00 0.00 3.41
1922 2060 7.582719 ACATTGTTACCCATTACTACATCCAT 58.417 34.615 0.00 0.00 0.00 3.41
1923 2061 8.058847 ACATTGTTACCCATTACTACATCCATT 58.941 33.333 0.00 0.00 0.00 3.16
1924 2062 8.912988 CATTGTTACCCATTACTACATCCATTT 58.087 33.333 0.00 0.00 0.00 2.32
1925 2063 8.514330 TTGTTACCCATTACTACATCCATTTC 57.486 34.615 0.00 0.00 0.00 2.17
1926 2064 7.634718 TGTTACCCATTACTACATCCATTTCA 58.365 34.615 0.00 0.00 0.00 2.69
1927 2065 8.110271 TGTTACCCATTACTACATCCATTTCAA 58.890 33.333 0.00 0.00 0.00 2.69
1928 2066 8.621286 GTTACCCATTACTACATCCATTTCAAG 58.379 37.037 0.00 0.00 0.00 3.02
1929 2067 6.731467 ACCCATTACTACATCCATTTCAAGT 58.269 36.000 0.00 0.00 0.00 3.16
1930 2068 7.182060 ACCCATTACTACATCCATTTCAAGTT 58.818 34.615 0.00 0.00 0.00 2.66
1931 2069 7.339466 ACCCATTACTACATCCATTTCAAGTTC 59.661 37.037 0.00 0.00 0.00 3.01
1932 2070 7.557719 CCCATTACTACATCCATTTCAAGTTCT 59.442 37.037 0.00 0.00 0.00 3.01
1933 2071 8.400947 CCATTACTACATCCATTTCAAGTTCTG 58.599 37.037 0.00 0.00 0.00 3.02
1934 2072 9.166173 CATTACTACATCCATTTCAAGTTCTGA 57.834 33.333 0.00 0.00 0.00 3.27
1935 2073 8.547967 TTACTACATCCATTTCAAGTTCTGAC 57.452 34.615 0.00 0.00 32.21 3.51
1936 2074 6.533730 ACTACATCCATTTCAAGTTCTGACA 58.466 36.000 0.00 0.00 32.21 3.58
1937 2075 6.998074 ACTACATCCATTTCAAGTTCTGACAA 59.002 34.615 0.00 0.00 32.21 3.18
1938 2076 6.323203 ACATCCATTTCAAGTTCTGACAAG 57.677 37.500 0.00 0.00 32.21 3.16
1939 2077 5.242393 ACATCCATTTCAAGTTCTGACAAGG 59.758 40.000 0.00 0.00 32.21 3.61
1940 2078 4.792068 TCCATTTCAAGTTCTGACAAGGT 58.208 39.130 0.00 0.00 32.21 3.50
1941 2079 5.200483 TCCATTTCAAGTTCTGACAAGGTT 58.800 37.500 0.00 0.00 32.21 3.50
1942 2080 5.067674 TCCATTTCAAGTTCTGACAAGGTTG 59.932 40.000 0.00 0.00 32.21 3.77
1943 2081 5.067674 CCATTTCAAGTTCTGACAAGGTTGA 59.932 40.000 0.00 0.00 32.21 3.18
1944 2082 6.239120 CCATTTCAAGTTCTGACAAGGTTGAT 60.239 38.462 0.00 0.00 32.21 2.57
1945 2083 6.773976 TTTCAAGTTCTGACAAGGTTGATT 57.226 33.333 0.00 0.00 32.21 2.57
1946 2084 5.756195 TCAAGTTCTGACAAGGTTGATTG 57.244 39.130 0.00 0.00 36.22 2.67
1947 2085 5.192927 TCAAGTTCTGACAAGGTTGATTGT 58.807 37.500 0.00 0.00 45.89 2.71
1954 2092 3.011566 ACAAGGTTGATTGTCACACCA 57.988 42.857 0.00 0.00 39.13 4.17
1955 2093 3.565307 ACAAGGTTGATTGTCACACCAT 58.435 40.909 0.00 1.23 39.13 3.55
1956 2094 3.318839 ACAAGGTTGATTGTCACACCATG 59.681 43.478 0.00 11.32 39.13 3.66
1957 2095 2.517959 AGGTTGATTGTCACACCATGG 58.482 47.619 11.19 11.19 33.18 3.66
1958 2096 1.067635 GGTTGATTGTCACACCATGGC 60.068 52.381 13.04 0.00 31.97 4.40
1959 2097 1.888512 GTTGATTGTCACACCATGGCT 59.111 47.619 13.04 0.00 32.41 4.75
1960 2098 1.825090 TGATTGTCACACCATGGCTC 58.175 50.000 13.04 0.00 32.41 4.70
1961 2099 1.098050 GATTGTCACACCATGGCTCC 58.902 55.000 13.04 0.00 32.41 4.70
1962 2100 0.700564 ATTGTCACACCATGGCTCCT 59.299 50.000 13.04 0.00 32.41 3.69
1963 2101 0.478072 TTGTCACACCATGGCTCCTT 59.522 50.000 13.04 0.00 32.41 3.36
1964 2102 0.250858 TGTCACACCATGGCTCCTTG 60.251 55.000 13.04 4.49 32.41 3.61
1965 2103 0.962356 GTCACACCATGGCTCCTTGG 60.962 60.000 13.04 16.62 44.08 3.61
1966 2104 2.036256 ACACCATGGCTCCTTGGC 59.964 61.111 13.04 0.00 42.80 4.52
1967 2105 2.357836 CACCATGGCTCCTTGGCT 59.642 61.111 13.04 5.71 42.80 4.75
1968 2106 1.304713 CACCATGGCTCCTTGGCTT 60.305 57.895 13.04 0.52 42.80 4.35
1969 2107 1.000396 ACCATGGCTCCTTGGCTTC 60.000 57.895 13.04 0.00 42.80 3.86
1970 2108 1.305623 CCATGGCTCCTTGGCTTCT 59.694 57.895 0.00 0.00 42.34 2.85
1971 2109 0.750911 CCATGGCTCCTTGGCTTCTC 60.751 60.000 0.00 0.00 42.34 2.87
1972 2110 1.094073 CATGGCTCCTTGGCTTCTCG 61.094 60.000 0.00 0.00 42.34 4.04
1973 2111 1.557269 ATGGCTCCTTGGCTTCTCGT 61.557 55.000 0.00 0.00 42.34 4.18
1974 2112 1.448717 GGCTCCTTGGCTTCTCGTC 60.449 63.158 0.00 0.00 38.32 4.20
1975 2113 1.594310 GCTCCTTGGCTTCTCGTCT 59.406 57.895 0.00 0.00 0.00 4.18
1976 2114 0.459411 GCTCCTTGGCTTCTCGTCTC 60.459 60.000 0.00 0.00 0.00 3.36
1977 2115 0.174617 CTCCTTGGCTTCTCGTCTCC 59.825 60.000 0.00 0.00 0.00 3.71
1978 2116 0.251832 TCCTTGGCTTCTCGTCTCCT 60.252 55.000 0.00 0.00 0.00 3.69
1979 2117 0.174617 CCTTGGCTTCTCGTCTCCTC 59.825 60.000 0.00 0.00 0.00 3.71
1980 2118 1.181786 CTTGGCTTCTCGTCTCCTCT 58.818 55.000 0.00 0.00 0.00 3.69
1981 2119 1.548269 CTTGGCTTCTCGTCTCCTCTT 59.452 52.381 0.00 0.00 0.00 2.85
1982 2120 0.891373 TGGCTTCTCGTCTCCTCTTG 59.109 55.000 0.00 0.00 0.00 3.02
1983 2121 1.178276 GGCTTCTCGTCTCCTCTTGA 58.822 55.000 0.00 0.00 0.00 3.02
1984 2122 1.135228 GGCTTCTCGTCTCCTCTTGAC 60.135 57.143 0.00 0.00 0.00 3.18
1985 2123 1.542030 GCTTCTCGTCTCCTCTTGACA 59.458 52.381 0.00 0.00 34.37 3.58
1986 2124 2.029828 GCTTCTCGTCTCCTCTTGACAA 60.030 50.000 0.00 0.00 34.37 3.18
1987 2125 3.832276 CTTCTCGTCTCCTCTTGACAAG 58.168 50.000 9.03 9.03 34.37 3.16
1988 2126 1.542030 TCTCGTCTCCTCTTGACAAGC 59.458 52.381 10.50 0.00 34.37 4.01
1989 2127 1.543802 CTCGTCTCCTCTTGACAAGCT 59.456 52.381 10.50 0.00 34.37 3.74
1990 2128 1.270826 TCGTCTCCTCTTGACAAGCTG 59.729 52.381 10.50 5.79 34.37 4.24
1991 2129 1.437625 GTCTCCTCTTGACAAGCTGC 58.562 55.000 10.50 0.00 34.80 5.25
1992 2130 1.001860 GTCTCCTCTTGACAAGCTGCT 59.998 52.381 10.50 0.00 34.80 4.24
1993 2131 1.001746 TCTCCTCTTGACAAGCTGCTG 59.998 52.381 10.50 0.00 0.00 4.41
1994 2132 0.604780 TCCTCTTGACAAGCTGCTGC 60.605 55.000 10.50 7.62 40.05 5.25
1995 2133 0.887836 CCTCTTGACAAGCTGCTGCA 60.888 55.000 18.42 0.88 42.74 4.41
1996 2134 0.517755 CTCTTGACAAGCTGCTGCAG 59.482 55.000 24.80 24.80 42.74 4.41
2005 2143 3.108343 CTGCTGCAGCTGCCATAC 58.892 61.111 36.61 21.01 42.66 2.39
2006 2144 1.747745 CTGCTGCAGCTGCCATACA 60.748 57.895 36.61 24.09 42.66 2.29
2007 2145 1.077285 TGCTGCAGCTGCCATACAT 60.077 52.632 36.61 0.00 42.66 2.29
2008 2146 0.180878 TGCTGCAGCTGCCATACATA 59.819 50.000 36.61 14.22 42.66 2.29
2009 2147 0.590195 GCTGCAGCTGCCATACATAC 59.410 55.000 34.64 11.78 41.18 2.39
2010 2148 1.233019 CTGCAGCTGCCATACATACC 58.767 55.000 34.64 4.94 41.18 2.73
2011 2149 0.839277 TGCAGCTGCCATACATACCT 59.161 50.000 34.64 0.00 41.18 3.08
2012 2150 1.233019 GCAGCTGCCATACATACCTG 58.767 55.000 28.76 0.00 34.31 4.00
2013 2151 1.202687 GCAGCTGCCATACATACCTGA 60.203 52.381 28.76 0.00 34.31 3.86
2014 2152 2.746142 GCAGCTGCCATACATACCTGAA 60.746 50.000 28.76 0.00 34.31 3.02
2015 2153 3.136763 CAGCTGCCATACATACCTGAAG 58.863 50.000 0.00 0.00 0.00 3.02
2016 2154 3.041211 AGCTGCCATACATACCTGAAGA 58.959 45.455 0.00 0.00 0.00 2.87
2017 2155 3.134458 GCTGCCATACATACCTGAAGAC 58.866 50.000 0.00 0.00 0.00 3.01
2018 2156 3.384668 CTGCCATACATACCTGAAGACG 58.615 50.000 0.00 0.00 0.00 4.18
2019 2157 2.764010 TGCCATACATACCTGAAGACGT 59.236 45.455 0.00 0.00 0.00 4.34
2020 2158 3.196901 TGCCATACATACCTGAAGACGTT 59.803 43.478 0.00 0.00 0.00 3.99
2021 2159 3.555956 GCCATACATACCTGAAGACGTTG 59.444 47.826 0.00 0.00 0.00 4.10
2022 2160 4.119862 CCATACATACCTGAAGACGTTGG 58.880 47.826 0.00 0.00 0.00 3.77
2023 2161 2.094762 ACATACCTGAAGACGTTGGC 57.905 50.000 0.00 0.00 0.00 4.52
2035 2173 1.002792 GACGTTGGCAACTTTCTCCAC 60.003 52.381 26.26 2.29 37.61 4.02
2060 2198 8.936864 ACGGTCTTTATATGTTTTCTTCTCTTG 58.063 33.333 0.00 0.00 0.00 3.02
2062 2200 8.184848 GGTCTTTATATGTTTTCTTCTCTTGGC 58.815 37.037 0.00 0.00 0.00 4.52
2073 2211 1.204146 TCTCTTGGCCTGGGTATGAC 58.796 55.000 3.32 0.00 0.00 3.06
2074 2212 0.179073 CTCTTGGCCTGGGTATGACG 60.179 60.000 3.32 0.00 0.00 4.35
2099 2237 2.079925 GGTCTGAAGACAAGTGGCATC 58.920 52.381 12.32 0.00 46.47 3.91
2105 2243 1.656587 AGACAAGTGGCATCACCCTA 58.343 50.000 0.00 0.00 44.64 3.53
2109 2247 2.308570 ACAAGTGGCATCACCCTATGAA 59.691 45.455 0.00 0.00 44.64 2.57
2142 2280 6.418819 CACTGCTTTCACTTCAGTTAAAATGG 59.581 38.462 0.00 0.00 38.85 3.16
2152 2290 5.450818 TCAGTTAAAATGGCATAGGACCT 57.549 39.130 0.00 0.00 0.00 3.85
2165 2303 4.379918 GCATAGGACCTTGAGCAAAGAAAC 60.380 45.833 0.00 0.00 38.24 2.78
2194 2332 9.368674 CAACAAATCAATATTCATTTAGTGGCA 57.631 29.630 0.00 0.00 0.00 4.92
2198 2336 6.964807 TCAATATTCATTTAGTGGCAGCAT 57.035 33.333 0.00 0.00 0.00 3.79
2211 2349 2.892215 TGGCAGCATCATGAGAACAAAA 59.108 40.909 0.09 0.00 0.00 2.44
2212 2350 3.057104 TGGCAGCATCATGAGAACAAAAG 60.057 43.478 0.09 0.00 0.00 2.27
2219 2357 8.456471 CAGCATCATGAGAACAAAAGAGATTTA 58.544 33.333 0.09 0.00 0.00 1.40
2228 2366 9.548208 GAGAACAAAAGAGATTTAGTTATGTGC 57.452 33.333 0.00 0.00 0.00 4.57
2251 2389 2.703536 TCTTAATTATGCAGAGGCCGGA 59.296 45.455 5.05 0.00 40.13 5.14
2254 2392 0.767375 ATTATGCAGAGGCCGGATGT 59.233 50.000 5.05 0.00 40.13 3.06
2262 2400 3.006537 GCAGAGGCCGGATGTAATACTTA 59.993 47.826 5.05 0.00 0.00 2.24
2263 2401 4.502604 GCAGAGGCCGGATGTAATACTTAA 60.503 45.833 5.05 0.00 0.00 1.85
2264 2402 5.607477 CAGAGGCCGGATGTAATACTTAAA 58.393 41.667 5.05 0.00 0.00 1.52
2265 2403 6.231211 CAGAGGCCGGATGTAATACTTAAAT 58.769 40.000 5.05 0.00 0.00 1.40
2266 2404 7.383687 CAGAGGCCGGATGTAATACTTAAATA 58.616 38.462 5.05 0.00 0.00 1.40
2294 2432 8.973835 TTAAGTAATAAAATGCCTGTTTTCGG 57.026 30.769 0.00 0.00 33.62 4.30
2365 2524 5.647658 CAGATAACCATCTTGTAGCCAACAA 59.352 40.000 2.57 2.57 45.90 2.83
2396 2555 9.123902 CTGGGTGAGATCAATGAAACATAAATA 57.876 33.333 0.00 0.00 0.00 1.40
2397 2556 9.123902 TGGGTGAGATCAATGAAACATAAATAG 57.876 33.333 0.00 0.00 0.00 1.73
2423 2582 6.830912 TGTCAGTCCTTGGAGATAATATTGG 58.169 40.000 0.00 0.00 0.00 3.16
2468 2627 0.872388 AAACAGCCGATCGACCAAAC 59.128 50.000 18.66 0.00 0.00 2.93
2551 2710 8.185003 TGTAGAGAATAATGTTGTCAATCACG 57.815 34.615 0.00 0.00 0.00 4.35
2592 2751 3.621715 GTCAACTTTGAACGGACTGAACT 59.378 43.478 0.00 0.00 39.21 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 1.539827 TCGTCTTGTCGCTCATCTTCA 59.460 47.619 0.00 0.00 0.00 3.02
252 253 2.827051 CGCCGATCGGACGACCTAA 61.827 63.158 37.64 0.00 37.11 2.69
527 601 2.690778 GCGGACGCATCCTTTTGCT 61.691 57.895 12.31 0.00 43.73 3.91
613 687 4.383351 CGTCCGTTTTGTTCTGTTTTTGTT 59.617 37.500 0.00 0.00 0.00 2.83
651 725 3.555324 TGAGCCAACTCCACCGCA 61.555 61.111 0.00 0.00 42.74 5.69
714 789 1.407618 TCCCATGACGATTCAGTACCG 59.592 52.381 0.00 0.00 34.35 4.02
720 795 2.419990 GGTGATGTCCCATGACGATTCA 60.420 50.000 0.00 0.00 44.86 2.57
721 796 2.213499 GGTGATGTCCCATGACGATTC 58.787 52.381 0.00 0.00 44.86 2.52
722 797 1.134098 GGGTGATGTCCCATGACGATT 60.134 52.381 0.00 0.00 46.30 3.34
790 867 1.294659 GAAGACTTGCGACTGGCCTG 61.295 60.000 8.29 8.29 42.61 4.85
825 903 1.900237 ACATAAACCGCGTCGAGTAC 58.100 50.000 4.92 0.00 0.00 2.73
827 905 1.458064 CAAACATAAACCGCGTCGAGT 59.542 47.619 4.92 0.00 0.00 4.18
828 906 1.458064 ACAAACATAAACCGCGTCGAG 59.542 47.619 4.92 0.00 0.00 4.04
831 926 3.185797 AGAGAACAAACATAAACCGCGTC 59.814 43.478 4.92 0.00 0.00 5.19
869 964 3.842925 TTTGTCCTCTGGGCCGTGC 62.843 63.158 0.00 0.00 0.00 5.34
944 1046 3.400054 GGTCAACGGGGAGGGGAG 61.400 72.222 0.00 0.00 0.00 4.30
947 1049 4.029809 GTGGGTCAACGGGGAGGG 62.030 72.222 0.00 0.00 0.00 4.30
1593 1719 3.236816 TCAGTACTTAACGCTACAACGC 58.763 45.455 0.00 0.00 36.19 4.84
1596 1722 5.575606 GCTTCATCAGTACTTAACGCTACAA 59.424 40.000 0.00 0.00 0.00 2.41
1654 1786 3.370840 TGGGATCTCCAAACAAGATGG 57.629 47.619 0.00 0.00 43.84 3.51
1681 1813 1.466950 TGAAATCGACATCAAACCGGC 59.533 47.619 0.00 0.00 0.00 6.13
1717 1849 9.844790 CAGAAATACACATCACACAAACAATAT 57.155 29.630 0.00 0.00 0.00 1.28
1725 1857 6.353404 TCCTACAGAAATACACATCACACA 57.647 37.500 0.00 0.00 0.00 3.72
1756 1894 8.582437 AGAATGCAACCAATATTCAATGATAGG 58.418 33.333 0.00 0.00 34.18 2.57
1773 1911 5.976458 TGAATTAATCCCCAAGAATGCAAC 58.024 37.500 0.00 0.00 0.00 4.17
1798 1936 1.811965 CATCAACCGTTCAGCCAATCA 59.188 47.619 0.00 0.00 0.00 2.57
1799 1937 1.812571 ACATCAACCGTTCAGCCAATC 59.187 47.619 0.00 0.00 0.00 2.67
1800 1938 1.812571 GACATCAACCGTTCAGCCAAT 59.187 47.619 0.00 0.00 0.00 3.16
1801 1939 1.234821 GACATCAACCGTTCAGCCAA 58.765 50.000 0.00 0.00 0.00 4.52
1802 1940 0.107643 TGACATCAACCGTTCAGCCA 59.892 50.000 0.00 0.00 0.00 4.75
1803 1941 1.453155 ATGACATCAACCGTTCAGCC 58.547 50.000 0.00 0.00 0.00 4.85
1805 1943 4.747540 TGAAATGACATCAACCGTTCAG 57.252 40.909 0.00 0.00 0.00 3.02
1806 1944 4.155826 GGATGAAATGACATCAACCGTTCA 59.844 41.667 0.00 1.53 45.68 3.18
1807 1945 4.396166 AGGATGAAATGACATCAACCGTTC 59.604 41.667 0.00 0.00 45.68 3.95
1808 1946 4.335416 AGGATGAAATGACATCAACCGTT 58.665 39.130 0.00 0.00 45.68 4.44
1809 1947 3.955471 AGGATGAAATGACATCAACCGT 58.045 40.909 0.00 0.00 45.68 4.83
1810 1948 5.586243 AGTTAGGATGAAATGACATCAACCG 59.414 40.000 0.00 0.00 45.68 4.44
1811 1949 6.825721 AGAGTTAGGATGAAATGACATCAACC 59.174 38.462 0.00 0.00 45.68 3.77
1812 1950 7.856145 AGAGTTAGGATGAAATGACATCAAC 57.144 36.000 0.00 0.00 45.68 3.18
1813 1951 8.102676 TCAAGAGTTAGGATGAAATGACATCAA 58.897 33.333 0.00 0.00 45.68 2.57
1814 1952 7.623630 TCAAGAGTTAGGATGAAATGACATCA 58.376 34.615 0.00 0.00 45.68 3.07
1815 1953 8.674263 ATCAAGAGTTAGGATGAAATGACATC 57.326 34.615 0.00 0.00 43.88 3.06
1817 1955 9.958180 TTTATCAAGAGTTAGGATGAAATGACA 57.042 29.630 0.00 0.00 0.00 3.58
1822 1960 9.958180 TGACATTTATCAAGAGTTAGGATGAAA 57.042 29.630 0.00 0.00 0.00 2.69
1823 1961 9.958180 TTGACATTTATCAAGAGTTAGGATGAA 57.042 29.630 0.00 0.00 33.62 2.57
1824 1962 9.958180 TTTGACATTTATCAAGAGTTAGGATGA 57.042 29.630 0.00 0.00 39.68 2.92
1827 1965 9.739276 ACATTTGACATTTATCAAGAGTTAGGA 57.261 29.630 0.00 0.00 39.68 2.94
1844 1982 9.012161 TGAACATAATCTGATCAACATTTGACA 57.988 29.630 0.00 4.43 43.48 3.58
1845 1983 9.499585 CTGAACATAATCTGATCAACATTTGAC 57.500 33.333 0.00 2.56 43.48 3.18
1846 1984 8.680001 CCTGAACATAATCTGATCAACATTTGA 58.320 33.333 0.00 0.00 45.01 2.69
1847 1985 8.680001 TCCTGAACATAATCTGATCAACATTTG 58.320 33.333 0.00 3.20 36.36 2.32
1848 1986 8.812513 TCCTGAACATAATCTGATCAACATTT 57.187 30.769 0.00 0.00 36.36 2.32
1849 1987 8.270030 TCTCCTGAACATAATCTGATCAACATT 58.730 33.333 0.00 0.85 36.36 2.71
1850 1988 7.714377 GTCTCCTGAACATAATCTGATCAACAT 59.286 37.037 0.00 0.00 36.36 2.71
1851 1989 7.044181 GTCTCCTGAACATAATCTGATCAACA 58.956 38.462 0.00 0.00 36.36 3.33
1852 1990 7.044181 TGTCTCCTGAACATAATCTGATCAAC 58.956 38.462 0.00 0.00 36.36 3.18
1853 1991 7.186570 TGTCTCCTGAACATAATCTGATCAA 57.813 36.000 0.00 0.00 36.36 2.57
1854 1992 6.796785 TGTCTCCTGAACATAATCTGATCA 57.203 37.500 0.00 0.00 35.57 2.92
1855 1993 7.437862 GTCTTGTCTCCTGAACATAATCTGATC 59.562 40.741 0.00 0.00 0.00 2.92
1856 1994 7.125507 AGTCTTGTCTCCTGAACATAATCTGAT 59.874 37.037 0.00 0.00 0.00 2.90
1857 1995 6.438741 AGTCTTGTCTCCTGAACATAATCTGA 59.561 38.462 0.00 0.00 0.00 3.27
1858 1996 6.638610 AGTCTTGTCTCCTGAACATAATCTG 58.361 40.000 0.00 0.00 0.00 2.90
1859 1997 6.865834 AGTCTTGTCTCCTGAACATAATCT 57.134 37.500 0.00 0.00 0.00 2.40
1863 2001 8.642432 CCATATAAGTCTTGTCTCCTGAACATA 58.358 37.037 0.00 0.00 0.00 2.29
1864 2002 7.126421 ACCATATAAGTCTTGTCTCCTGAACAT 59.874 37.037 0.00 0.00 0.00 2.71
1865 2003 6.440647 ACCATATAAGTCTTGTCTCCTGAACA 59.559 38.462 0.00 0.00 0.00 3.18
1866 2004 6.879400 ACCATATAAGTCTTGTCTCCTGAAC 58.121 40.000 0.00 0.00 0.00 3.18
1867 2005 6.183360 CGACCATATAAGTCTTGTCTCCTGAA 60.183 42.308 0.00 0.00 31.83 3.02
1868 2006 5.299531 CGACCATATAAGTCTTGTCTCCTGA 59.700 44.000 0.00 0.00 31.83 3.86
1869 2007 5.299531 TCGACCATATAAGTCTTGTCTCCTG 59.700 44.000 0.00 0.00 31.83 3.86
1870 2008 5.446860 TCGACCATATAAGTCTTGTCTCCT 58.553 41.667 0.00 0.00 31.83 3.69
1871 2009 5.531659 TCTCGACCATATAAGTCTTGTCTCC 59.468 44.000 0.00 0.00 31.83 3.71
1872 2010 6.621316 TCTCGACCATATAAGTCTTGTCTC 57.379 41.667 0.00 0.00 31.83 3.36
1873 2011 7.093902 TGTTTCTCGACCATATAAGTCTTGTCT 60.094 37.037 0.00 0.00 31.83 3.41
1874 2012 7.033791 TGTTTCTCGACCATATAAGTCTTGTC 58.966 38.462 0.00 0.00 31.83 3.18
1875 2013 6.931838 TGTTTCTCGACCATATAAGTCTTGT 58.068 36.000 0.00 0.00 31.83 3.16
1876 2014 8.331022 CAATGTTTCTCGACCATATAAGTCTTG 58.669 37.037 0.00 0.00 31.83 3.02
1877 2015 8.041323 ACAATGTTTCTCGACCATATAAGTCTT 58.959 33.333 5.13 0.00 31.83 3.01
1878 2016 7.556844 ACAATGTTTCTCGACCATATAAGTCT 58.443 34.615 5.13 0.00 31.83 3.24
1879 2017 7.772332 ACAATGTTTCTCGACCATATAAGTC 57.228 36.000 0.00 0.00 0.00 3.01
1880 2018 9.095065 GTAACAATGTTTCTCGACCATATAAGT 57.905 33.333 3.17 0.00 0.00 2.24
1881 2019 8.548721 GGTAACAATGTTTCTCGACCATATAAG 58.451 37.037 3.17 0.00 0.00 1.73
1882 2020 7.496591 GGGTAACAATGTTTCTCGACCATATAA 59.503 37.037 14.66 0.00 39.74 0.98
1883 2021 6.987992 GGGTAACAATGTTTCTCGACCATATA 59.012 38.462 14.66 0.00 39.74 0.86
1884 2022 5.820947 GGGTAACAATGTTTCTCGACCATAT 59.179 40.000 14.66 0.00 39.74 1.78
1885 2023 5.180271 GGGTAACAATGTTTCTCGACCATA 58.820 41.667 14.66 0.00 39.74 2.74
1886 2024 4.007659 GGGTAACAATGTTTCTCGACCAT 58.992 43.478 14.66 0.00 39.74 3.55
1887 2025 3.181453 TGGGTAACAATGTTTCTCGACCA 60.181 43.478 14.66 6.02 39.74 4.02
1888 2026 3.404899 TGGGTAACAATGTTTCTCGACC 58.595 45.455 3.17 5.18 39.74 4.79
1889 2027 5.622770 AATGGGTAACAATGTTTCTCGAC 57.377 39.130 3.17 0.00 39.74 4.20
1890 2028 6.469410 AGTAATGGGTAACAATGTTTCTCGA 58.531 36.000 3.17 0.00 39.74 4.04
1891 2029 6.737254 AGTAATGGGTAACAATGTTTCTCG 57.263 37.500 3.17 0.00 39.74 4.04
1892 2030 8.556213 TGTAGTAATGGGTAACAATGTTTCTC 57.444 34.615 3.17 0.00 39.74 2.87
1893 2031 9.174166 GATGTAGTAATGGGTAACAATGTTTCT 57.826 33.333 3.17 0.00 39.74 2.52
1894 2032 8.403236 GGATGTAGTAATGGGTAACAATGTTTC 58.597 37.037 3.17 0.00 39.74 2.78
1895 2033 7.891183 TGGATGTAGTAATGGGTAACAATGTTT 59.109 33.333 3.17 0.00 39.74 2.83
1896 2034 7.406916 TGGATGTAGTAATGGGTAACAATGTT 58.593 34.615 3.43 3.43 39.74 2.71
1897 2035 6.964464 TGGATGTAGTAATGGGTAACAATGT 58.036 36.000 0.00 0.00 39.74 2.71
1898 2036 8.463930 AATGGATGTAGTAATGGGTAACAATG 57.536 34.615 0.00 0.00 39.74 2.82
1899 2037 9.131791 GAAATGGATGTAGTAATGGGTAACAAT 57.868 33.333 0.00 0.00 39.74 2.71
1900 2038 8.110271 TGAAATGGATGTAGTAATGGGTAACAA 58.890 33.333 0.00 0.00 39.74 2.83
1901 2039 7.634718 TGAAATGGATGTAGTAATGGGTAACA 58.365 34.615 0.00 0.00 39.74 2.41
1902 2040 8.514330 TTGAAATGGATGTAGTAATGGGTAAC 57.486 34.615 0.00 0.00 0.00 2.50
1903 2041 8.333235 ACTTGAAATGGATGTAGTAATGGGTAA 58.667 33.333 0.00 0.00 0.00 2.85
1904 2042 7.867921 ACTTGAAATGGATGTAGTAATGGGTA 58.132 34.615 0.00 0.00 0.00 3.69
1905 2043 6.731467 ACTTGAAATGGATGTAGTAATGGGT 58.269 36.000 0.00 0.00 0.00 4.51
1906 2044 7.557719 AGAACTTGAAATGGATGTAGTAATGGG 59.442 37.037 0.00 0.00 0.00 4.00
1907 2045 8.400947 CAGAACTTGAAATGGATGTAGTAATGG 58.599 37.037 0.00 0.00 0.00 3.16
1908 2046 9.166173 TCAGAACTTGAAATGGATGTAGTAATG 57.834 33.333 0.00 0.00 31.34 1.90
1909 2047 9.167311 GTCAGAACTTGAAATGGATGTAGTAAT 57.833 33.333 0.00 0.00 37.61 1.89
1910 2048 8.154203 TGTCAGAACTTGAAATGGATGTAGTAA 58.846 33.333 0.00 0.00 37.61 2.24
1911 2049 7.676004 TGTCAGAACTTGAAATGGATGTAGTA 58.324 34.615 0.00 0.00 37.61 1.82
1912 2050 6.533730 TGTCAGAACTTGAAATGGATGTAGT 58.466 36.000 0.00 0.00 37.61 2.73
1913 2051 7.361542 CCTTGTCAGAACTTGAAATGGATGTAG 60.362 40.741 0.00 0.00 39.60 2.74
1914 2052 6.430925 CCTTGTCAGAACTTGAAATGGATGTA 59.569 38.462 0.00 0.00 39.60 2.29
1915 2053 5.242393 CCTTGTCAGAACTTGAAATGGATGT 59.758 40.000 0.00 0.00 39.60 3.06
1916 2054 5.242393 ACCTTGTCAGAACTTGAAATGGATG 59.758 40.000 6.34 0.00 39.60 3.51
1917 2055 5.388654 ACCTTGTCAGAACTTGAAATGGAT 58.611 37.500 6.34 0.00 39.60 3.41
1918 2056 4.792068 ACCTTGTCAGAACTTGAAATGGA 58.208 39.130 6.34 0.00 39.60 3.41
1919 2057 5.067674 TCAACCTTGTCAGAACTTGAAATGG 59.932 40.000 0.00 0.00 41.84 3.16
1920 2058 6.135290 TCAACCTTGTCAGAACTTGAAATG 57.865 37.500 0.00 0.00 37.61 2.32
1921 2059 6.966534 ATCAACCTTGTCAGAACTTGAAAT 57.033 33.333 0.00 0.00 37.61 2.17
1922 2060 6.152661 ACAATCAACCTTGTCAGAACTTGAAA 59.847 34.615 0.00 0.00 37.61 2.69
1923 2061 5.652014 ACAATCAACCTTGTCAGAACTTGAA 59.348 36.000 0.00 0.00 37.61 2.69
1924 2062 5.192927 ACAATCAACCTTGTCAGAACTTGA 58.807 37.500 0.00 0.00 34.26 3.02
1925 2063 5.505173 ACAATCAACCTTGTCAGAACTTG 57.495 39.130 0.00 0.00 34.26 3.16
1934 2072 3.011566 TGGTGTGACAATCAACCTTGT 57.988 42.857 0.00 0.00 41.92 3.16
1935 2073 3.305539 CCATGGTGTGACAATCAACCTTG 60.306 47.826 2.57 13.27 35.32 3.61
1936 2074 2.892852 CCATGGTGTGACAATCAACCTT 59.107 45.455 2.57 3.78 32.50 3.50
1937 2075 2.517959 CCATGGTGTGACAATCAACCT 58.482 47.619 2.57 0.00 32.50 3.50
1938 2076 1.067635 GCCATGGTGTGACAATCAACC 60.068 52.381 14.67 0.00 32.16 3.77
1939 2077 1.888512 AGCCATGGTGTGACAATCAAC 59.111 47.619 14.67 0.00 0.00 3.18
1940 2078 2.161855 GAGCCATGGTGTGACAATCAA 58.838 47.619 14.67 0.00 0.00 2.57
1941 2079 1.614051 GGAGCCATGGTGTGACAATCA 60.614 52.381 14.67 0.00 0.00 2.57
1942 2080 1.098050 GGAGCCATGGTGTGACAATC 58.902 55.000 14.67 0.00 0.00 2.67
1943 2081 0.700564 AGGAGCCATGGTGTGACAAT 59.299 50.000 14.67 0.00 0.00 2.71
1944 2082 0.478072 AAGGAGCCATGGTGTGACAA 59.522 50.000 14.67 0.00 0.00 3.18
1945 2083 0.250858 CAAGGAGCCATGGTGTGACA 60.251 55.000 14.67 0.00 0.00 3.58
1946 2084 0.962356 CCAAGGAGCCATGGTGTGAC 60.962 60.000 14.67 0.00 30.89 3.67
1947 2085 1.379916 CCAAGGAGCCATGGTGTGA 59.620 57.895 14.67 0.00 30.89 3.58
1948 2086 2.345760 GCCAAGGAGCCATGGTGTG 61.346 63.158 14.67 4.59 37.16 3.82
1949 2087 2.036256 GCCAAGGAGCCATGGTGT 59.964 61.111 14.67 0.12 37.16 4.16
1950 2088 1.304713 AAGCCAAGGAGCCATGGTG 60.305 57.895 14.67 2.67 37.16 4.17
1951 2089 1.000396 GAAGCCAAGGAGCCATGGT 60.000 57.895 14.67 0.00 37.16 3.55
1952 2090 0.750911 GAGAAGCCAAGGAGCCATGG 60.751 60.000 7.63 7.63 37.80 3.66
1953 2091 1.094073 CGAGAAGCCAAGGAGCCATG 61.094 60.000 0.00 0.00 0.00 3.66
1954 2092 1.222936 CGAGAAGCCAAGGAGCCAT 59.777 57.895 0.00 0.00 0.00 4.40
1955 2093 2.172483 GACGAGAAGCCAAGGAGCCA 62.172 60.000 0.00 0.00 0.00 4.75
1956 2094 1.448717 GACGAGAAGCCAAGGAGCC 60.449 63.158 0.00 0.00 0.00 4.70
1957 2095 0.459411 GAGACGAGAAGCCAAGGAGC 60.459 60.000 0.00 0.00 0.00 4.70
1958 2096 0.174617 GGAGACGAGAAGCCAAGGAG 59.825 60.000 0.00 0.00 0.00 3.69
1959 2097 0.251832 AGGAGACGAGAAGCCAAGGA 60.252 55.000 0.00 0.00 0.00 3.36
1960 2098 0.174617 GAGGAGACGAGAAGCCAAGG 59.825 60.000 0.00 0.00 0.00 3.61
1961 2099 1.181786 AGAGGAGACGAGAAGCCAAG 58.818 55.000 0.00 0.00 0.00 3.61
1962 2100 1.273606 CAAGAGGAGACGAGAAGCCAA 59.726 52.381 0.00 0.00 0.00 4.52
1963 2101 0.891373 CAAGAGGAGACGAGAAGCCA 59.109 55.000 0.00 0.00 0.00 4.75
1964 2102 1.135228 GTCAAGAGGAGACGAGAAGCC 60.135 57.143 0.00 0.00 0.00 4.35
1965 2103 1.542030 TGTCAAGAGGAGACGAGAAGC 59.458 52.381 0.00 0.00 38.83 3.86
1966 2104 3.832276 CTTGTCAAGAGGAGACGAGAAG 58.168 50.000 6.76 0.00 46.07 2.85
1967 2105 2.029828 GCTTGTCAAGAGGAGACGAGAA 60.030 50.000 16.99 0.00 46.07 2.87
1968 2106 1.542030 GCTTGTCAAGAGGAGACGAGA 59.458 52.381 16.99 0.00 46.07 4.04
1969 2107 1.543802 AGCTTGTCAAGAGGAGACGAG 59.456 52.381 16.99 6.27 45.97 4.18
1970 2108 1.270826 CAGCTTGTCAAGAGGAGACGA 59.729 52.381 16.99 0.00 38.83 4.20
1971 2109 1.707632 CAGCTTGTCAAGAGGAGACG 58.292 55.000 16.99 0.00 38.83 4.18
1972 2110 1.001860 AGCAGCTTGTCAAGAGGAGAC 59.998 52.381 16.99 0.00 36.55 3.36
1973 2111 1.001746 CAGCAGCTTGTCAAGAGGAGA 59.998 52.381 16.99 0.00 0.00 3.71
1974 2112 1.440708 CAGCAGCTTGTCAAGAGGAG 58.559 55.000 16.99 3.58 0.00 3.69
1975 2113 0.604780 GCAGCAGCTTGTCAAGAGGA 60.605 55.000 16.99 0.00 37.91 3.71
1976 2114 0.887836 TGCAGCAGCTTGTCAAGAGG 60.888 55.000 16.99 8.02 42.74 3.69
1977 2115 0.517755 CTGCAGCAGCTTGTCAAGAG 59.482 55.000 16.99 8.71 42.74 2.85
1978 2116 2.625375 CTGCAGCAGCTTGTCAAGA 58.375 52.632 16.99 0.00 42.74 3.02
1988 2126 1.101635 ATGTATGGCAGCTGCAGCAG 61.102 55.000 38.24 31.89 45.16 4.24
1989 2127 0.180878 TATGTATGGCAGCTGCAGCA 59.819 50.000 38.24 27.67 45.16 4.41
1990 2128 0.590195 GTATGTATGGCAGCTGCAGC 59.410 55.000 37.63 31.53 44.36 5.25
1991 2129 1.202734 AGGTATGTATGGCAGCTGCAG 60.203 52.381 37.63 10.11 44.36 4.41
1992 2130 0.839277 AGGTATGTATGGCAGCTGCA 59.161 50.000 37.63 24.48 44.36 4.41
1993 2131 1.202687 TCAGGTATGTATGGCAGCTGC 60.203 52.381 30.88 30.88 37.63 5.25
1994 2132 2.916702 TCAGGTATGTATGGCAGCTG 57.083 50.000 10.11 10.11 38.76 4.24
1995 2133 3.041211 TCTTCAGGTATGTATGGCAGCT 58.959 45.455 0.00 0.00 0.00 4.24
1996 2134 3.134458 GTCTTCAGGTATGTATGGCAGC 58.866 50.000 0.00 0.00 0.00 5.25
1997 2135 3.181475 ACGTCTTCAGGTATGTATGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
1998 2136 2.764010 ACGTCTTCAGGTATGTATGGCA 59.236 45.455 0.00 0.00 0.00 4.92
1999 2137 3.454371 ACGTCTTCAGGTATGTATGGC 57.546 47.619 0.00 0.00 0.00 4.40
2000 2138 4.119862 CCAACGTCTTCAGGTATGTATGG 58.880 47.826 0.00 0.00 0.00 2.74
2001 2139 3.555956 GCCAACGTCTTCAGGTATGTATG 59.444 47.826 0.00 0.00 0.00 2.39
2002 2140 3.196901 TGCCAACGTCTTCAGGTATGTAT 59.803 43.478 0.00 0.00 0.00 2.29
2003 2141 2.563620 TGCCAACGTCTTCAGGTATGTA 59.436 45.455 0.00 0.00 0.00 2.29
2004 2142 1.346395 TGCCAACGTCTTCAGGTATGT 59.654 47.619 0.00 0.00 0.00 2.29
2005 2143 2.093306 TGCCAACGTCTTCAGGTATG 57.907 50.000 0.00 0.00 0.00 2.39
2006 2144 2.038557 AGTTGCCAACGTCTTCAGGTAT 59.961 45.455 1.20 0.00 36.23 2.73
2007 2145 1.414919 AGTTGCCAACGTCTTCAGGTA 59.585 47.619 1.20 0.00 36.23 3.08
2008 2146 0.180406 AGTTGCCAACGTCTTCAGGT 59.820 50.000 1.20 0.00 36.23 4.00
2009 2147 1.308998 AAGTTGCCAACGTCTTCAGG 58.691 50.000 1.20 0.00 36.23 3.86
2010 2148 2.614057 AGAAAGTTGCCAACGTCTTCAG 59.386 45.455 16.84 0.00 36.23 3.02
2011 2149 2.612212 GAGAAAGTTGCCAACGTCTTCA 59.388 45.455 15.16 0.00 32.90 3.02
2012 2150 2.031944 GGAGAAAGTTGCCAACGTCTTC 60.032 50.000 15.16 11.08 32.90 2.87
2013 2151 1.947456 GGAGAAAGTTGCCAACGTCTT 59.053 47.619 15.16 5.55 32.90 3.01
2014 2152 1.134220 TGGAGAAAGTTGCCAACGTCT 60.134 47.619 14.28 14.28 34.64 4.18
2015 2153 1.002792 GTGGAGAAAGTTGCCAACGTC 60.003 52.381 1.20 4.19 36.23 4.34
2016 2154 1.021968 GTGGAGAAAGTTGCCAACGT 58.978 50.000 1.20 0.00 36.23 3.99
2017 2155 0.041312 CGTGGAGAAAGTTGCCAACG 60.041 55.000 1.20 0.00 36.23 4.10
2018 2156 0.310854 CCGTGGAGAAAGTTGCCAAC 59.689 55.000 0.00 0.00 32.68 3.77
2019 2157 0.106918 ACCGTGGAGAAAGTTGCCAA 60.107 50.000 0.00 0.00 32.68 4.52
2020 2158 0.534203 GACCGTGGAGAAAGTTGCCA 60.534 55.000 0.00 0.00 0.00 4.92
2021 2159 0.250338 AGACCGTGGAGAAAGTTGCC 60.250 55.000 0.00 0.00 0.00 4.52
2022 2160 1.594331 AAGACCGTGGAGAAAGTTGC 58.406 50.000 0.00 0.00 0.00 4.17
2023 2161 6.594159 ACATATAAAGACCGTGGAGAAAGTTG 59.406 38.462 0.00 0.00 0.00 3.16
2035 2173 8.391106 CCAAGAGAAGAAAACATATAAAGACCG 58.609 37.037 0.00 0.00 0.00 4.79
2060 2198 0.808755 CAAAACGTCATACCCAGGCC 59.191 55.000 0.00 0.00 0.00 5.19
2062 2200 2.081462 GACCAAAACGTCATACCCAGG 58.919 52.381 0.00 0.00 32.74 4.45
2073 2211 3.242739 CCACTTGTCTTCAGACCAAAACG 60.243 47.826 4.48 0.00 44.15 3.60
2074 2212 3.489229 GCCACTTGTCTTCAGACCAAAAC 60.489 47.826 4.48 0.00 44.15 2.43
2099 2237 2.026822 AGTGCCTGTTCTTCATAGGGTG 60.027 50.000 0.00 0.00 32.15 4.61
2105 2243 2.283145 AAGCAGTGCCTGTTCTTCAT 57.717 45.000 12.58 0.00 33.43 2.57
2109 2247 1.133976 AGTGAAAGCAGTGCCTGTTCT 60.134 47.619 12.58 2.67 33.43 3.01
2125 2263 6.374333 GTCCTATGCCATTTTAACTGAAGTGA 59.626 38.462 0.00 0.00 0.00 3.41
2142 2280 2.991250 TCTTTGCTCAAGGTCCTATGC 58.009 47.619 0.00 0.00 32.64 3.14
2152 2290 7.040494 TGATTTGTTGATGTTTCTTTGCTCAA 58.960 30.769 0.00 0.00 0.00 3.02
2183 2321 3.881089 TCTCATGATGCTGCCACTAAATG 59.119 43.478 0.00 0.00 0.00 2.32
2194 2332 7.463961 AAATCTCTTTTGTTCTCATGATGCT 57.536 32.000 0.00 0.00 0.00 3.79
2228 2366 3.438087 CCGGCCTCTGCATAATTAAGATG 59.562 47.826 0.00 0.00 40.13 2.90
2300 2438 8.910944 CCATTAATTCATCTCCTTTGTTCTCAT 58.089 33.333 0.00 0.00 0.00 2.90
2301 2439 8.108999 TCCATTAATTCATCTCCTTTGTTCTCA 58.891 33.333 0.00 0.00 0.00 3.27
2312 2450 8.777413 TGTTTCATCGATCCATTAATTCATCTC 58.223 33.333 0.00 0.00 0.00 2.75
2317 2455 9.817365 CTGTATGTTTCATCGATCCATTAATTC 57.183 33.333 0.00 0.00 0.00 2.17
2341 2479 5.185454 TGTTGGCTACAAGATGGTTATCTG 58.815 41.667 0.00 0.00 42.80 2.90
2365 2524 3.117745 TCATTGATCTCACCCAGGACAT 58.882 45.455 0.00 0.00 0.00 3.06
2396 2555 8.373981 CAATATTATCTCCAAGGACTGACATCT 58.626 37.037 0.00 0.00 0.00 2.90
2397 2556 7.605691 CCAATATTATCTCCAAGGACTGACATC 59.394 40.741 0.00 0.00 0.00 3.06
2403 2562 5.912149 TGCCAATATTATCTCCAAGGACT 57.088 39.130 0.00 0.00 0.00 3.85
2423 2582 4.963276 TCTGTGCTAAACATGGTTATGC 57.037 40.909 3.09 10.28 38.39 3.14
2438 2597 1.266718 TCGGCTGTTTTTCATCTGTGC 59.733 47.619 0.00 0.00 0.00 4.57
2468 2627 6.993079 TGCATATACATGTAGTAGTTCCTGG 58.007 40.000 11.91 0.00 35.85 4.45
2570 2729 3.621715 AGTTCAGTCCGTTCAAAGTTGAC 59.378 43.478 0.00 0.00 36.83 3.18
2583 2742 9.654663 AGAAAACATGTATACTTAGTTCAGTCC 57.345 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.