Multiple sequence alignment - TraesCS3A01G509100

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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 TraesCS3A01G509100 chr3A 100.000 3480 0 0 1 3480 729958115 729954636 0.000000e+00 6427.0
1 TraesCS3A01G509100 chr3A 86.373 499 44 13 2068 2559 730398401 730398882 1.110000e-144 523.0
2 TraesCS3A01G509100 chr3A 79.592 490 80 11 2067 2548 730345729 730345252 2.000000e-87 333.0
3 TraesCS3A01G509100 chrUn 99.111 1799 15 1 1 1798 269605248 269607046 0.000000e+00 3232.0
4 TraesCS3A01G509100 chrUn 98.999 1799 15 3 1 1798 195665982 195664186 0.000000e+00 3219.0
5 TraesCS3A01G509100 chrUn 99.169 1564 12 1 1 1564 195650751 195649189 0.000000e+00 2815.0
6 TraesCS3A01G509100 chrUn 98.868 1237 14 0 562 1798 347577343 347578579 0.000000e+00 2207.0
7 TraesCS3A01G509100 chrUn 99.477 1148 4 2 1 1147 405100675 405101821 0.000000e+00 2085.0
8 TraesCS3A01G509100 chrUn 98.874 1155 12 1 644 1798 226786271 226785118 0.000000e+00 2060.0
9 TraesCS3A01G509100 chrUn 99.557 1129 4 1 1 1128 355715887 355717015 0.000000e+00 2056.0
10 TraesCS3A01G509100 chrUn 98.615 1155 15 1 644 1798 225678617 225679770 0.000000e+00 2043.0
11 TraesCS3A01G509100 chrUn 99.637 827 2 1 1 826 410620884 410620058 0.000000e+00 1509.0
12 TraesCS3A01G509100 chrUn 97.952 586 12 0 1213 1798 287107903 287108488 0.000000e+00 1016.0
13 TraesCS3A01G509100 chrUn 99.608 255 1 0 1 255 204044402 204044148 1.890000e-127 466.0
14 TraesCS3A01G509100 chrUn 99.608 255 1 0 1 255 413722287 413722033 1.890000e-127 466.0
15 TraesCS3A01G509100 chrUn 95.668 277 10 2 1795 2069 86513856 86513580 8.860000e-121 444.0
16 TraesCS3A01G509100 chrUn 95.668 277 10 2 1795 2069 189399466 189399742 8.860000e-121 444.0
17 TraesCS3A01G509100 chrUn 95.668 277 10 2 1795 2069 266527443 266527167 8.860000e-121 444.0
18 TraesCS3A01G509100 chrUn 95.668 277 10 2 1795 2069 282368540 282368264 8.860000e-121 444.0
19 TraesCS3A01G509100 chrUn 95.668 277 10 2 1795 2069 365915276 365915552 8.860000e-121 444.0
20 TraesCS3A01G509100 chrUn 97.788 226 5 0 1573 1798 301338308 301338533 1.170000e-104 390.0
21 TraesCS3A01G509100 chrUn 91.975 162 12 1 2081 2241 225679786 225679947 3.490000e-55 226.0
22 TraesCS3A01G509100 chrUn 91.975 162 12 1 2081 2241 269607062 269607223 3.490000e-55 226.0
23 TraesCS3A01G509100 chrUn 100.000 50 0 0 1 50 358348070 358348021 3.700000e-15 93.5
24 TraesCS3A01G509100 chr5A 94.438 863 47 1 2615 3477 7964123 7964984 0.000000e+00 1327.0
25 TraesCS3A01G509100 chr4D 94.335 865 48 1 2616 3480 57060213 57059350 0.000000e+00 1325.0
26 TraesCS3A01G509100 chr4D 95.668 277 10 2 1795 2069 398039940 398039664 8.860000e-121 444.0
27 TraesCS3A01G509100 chr1A 92.254 865 65 2 2616 3480 58376068 58375206 0.000000e+00 1225.0
28 TraesCS3A01G509100 chr7A 91.667 864 72 0 2617 3480 80367704 80366841 0.000000e+00 1197.0
29 TraesCS3A01G509100 chr1B 91.590 868 72 1 2614 3480 16657857 16656990 0.000000e+00 1197.0
30 TraesCS3A01G509100 chr2B 90.825 861 79 0 2617 3477 128368394 128369254 0.000000e+00 1153.0
31 TraesCS3A01G509100 chr2B 87.595 395 38 8 341 732 161476260 161476646 6.850000e-122 448.0
32 TraesCS3A01G509100 chr3B 90.582 807 61 11 996 1798 807440951 807440156 0.000000e+00 1055.0
33 TraesCS3A01G509100 chr3B 90.566 477 26 4 2068 2531 807440135 807439665 6.380000e-172 614.0
34 TraesCS3A01G509100 chr3B 86.681 458 48 6 2068 2522 807482577 807482130 2.410000e-136 496.0
35 TraesCS3A01G509100 chr3B 84.375 192 24 3 1096 1287 807500982 807500797 2.130000e-42 183.0
36 TraesCS3A01G509100 chr3B 95.238 84 4 0 248 331 672624586 672624669 2.180000e-27 134.0
37 TraesCS3A01G509100 chr3B 86.992 123 8 6 789 906 807441258 807441139 7.840000e-27 132.0
38 TraesCS3A01G509100 chr4B 88.747 862 94 3 2620 3480 28283254 28282395 0.000000e+00 1051.0
39 TraesCS3A01G509100 chr4B 100.000 28 0 0 87 114 649676635 649676608 6.000000e-03 52.8
40 TraesCS3A01G509100 chr4A 88.644 863 98 0 2618 3480 187560121 187560983 0.000000e+00 1051.0
41 TraesCS3A01G509100 chr3D 89.316 833 57 21 996 1798 600424650 600423820 0.000000e+00 1016.0
42 TraesCS3A01G509100 chr3D 88.235 578 35 16 2068 2619 600423799 600423229 0.000000e+00 660.0
43 TraesCS3A01G509100 chr3D 90.642 374 28 6 328 696 600147893 600148264 1.120000e-134 490.0
44 TraesCS3A01G509100 chr3D 90.160 376 30 6 327 696 600160931 600161305 1.880000e-132 483.0
45 TraesCS3A01G509100 chr3D 87.198 414 43 3 2067 2479 600528932 600528528 2.450000e-126 462.0
46 TraesCS3A01G509100 chr3D 86.813 91 5 6 906 989 600424802 600424712 1.030000e-15 95.3
47 TraesCS3A01G509100 chr5B 86.854 852 110 1 2629 3480 693173376 693174225 0.000000e+00 952.0
48 TraesCS3A01G509100 chr6D 95.668 277 10 2 1795 2069 124524508 124524784 8.860000e-121 444.0
49 TraesCS3A01G509100 chr6B 95.668 277 10 2 1795 2069 596616479 596616755 8.860000e-121 444.0
50 TraesCS3A01G509100 chr6B 90.722 97 7 2 234 330 529869583 529869677 1.010000e-25 128.0
51 TraesCS3A01G509100 chr1D 95.668 277 10 2 1795 2069 298348101 298347825 8.860000e-121 444.0
52 TraesCS3A01G509100 chr7D 83.333 468 53 16 2068 2518 37234423 37233964 3.230000e-110 409.0
53 TraesCS3A01G509100 chr6A 96.296 81 3 0 251 331 494040488 494040568 2.180000e-27 134.0


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 TraesCS3A01G509100 chr3A 729954636 729958115 3479 True 6427.000000 6427 100.000000 1 3480 1 chr3A.!!$R1 3479
1 TraesCS3A01G509100 chrUn 195664186 195665982 1796 True 3219.000000 3219 98.999000 1 1798 1 chrUn.!!$R3 1797
2 TraesCS3A01G509100 chrUn 195649189 195650751 1562 True 2815.000000 2815 99.169000 1 1564 1 chrUn.!!$R2 1563
3 TraesCS3A01G509100 chrUn 347577343 347578579 1236 False 2207.000000 2207 98.868000 562 1798 1 chrUn.!!$F4 1236
4 TraesCS3A01G509100 chrUn 405100675 405101821 1146 False 2085.000000 2085 99.477000 1 1147 1 chrUn.!!$F7 1146
5 TraesCS3A01G509100 chrUn 226785118 226786271 1153 True 2060.000000 2060 98.874000 644 1798 1 chrUn.!!$R5 1154
6 TraesCS3A01G509100 chrUn 355715887 355717015 1128 False 2056.000000 2056 99.557000 1 1128 1 chrUn.!!$F5 1127
7 TraesCS3A01G509100 chrUn 269605248 269607223 1975 False 1729.000000 3232 95.543000 1 2241 2 chrUn.!!$F9 2240
8 TraesCS3A01G509100 chrUn 410620058 410620884 826 True 1509.000000 1509 99.637000 1 826 1 chrUn.!!$R9 825
9 TraesCS3A01G509100 chrUn 225678617 225679947 1330 False 1134.500000 2043 95.295000 644 2241 2 chrUn.!!$F8 1597
10 TraesCS3A01G509100 chrUn 287107903 287108488 585 False 1016.000000 1016 97.952000 1213 1798 1 chrUn.!!$F2 585
11 TraesCS3A01G509100 chr5A 7964123 7964984 861 False 1327.000000 1327 94.438000 2615 3477 1 chr5A.!!$F1 862
12 TraesCS3A01G509100 chr4D 57059350 57060213 863 True 1325.000000 1325 94.335000 2616 3480 1 chr4D.!!$R1 864
13 TraesCS3A01G509100 chr1A 58375206 58376068 862 True 1225.000000 1225 92.254000 2616 3480 1 chr1A.!!$R1 864
14 TraesCS3A01G509100 chr7A 80366841 80367704 863 True 1197.000000 1197 91.667000 2617 3480 1 chr7A.!!$R1 863
15 TraesCS3A01G509100 chr1B 16656990 16657857 867 True 1197.000000 1197 91.590000 2614 3480 1 chr1B.!!$R1 866
16 TraesCS3A01G509100 chr2B 128368394 128369254 860 False 1153.000000 1153 90.825000 2617 3477 1 chr2B.!!$F1 860
17 TraesCS3A01G509100 chr3B 807439665 807441258 1593 True 600.333333 1055 89.380000 789 2531 3 chr3B.!!$R3 1742
18 TraesCS3A01G509100 chr4B 28282395 28283254 859 True 1051.000000 1051 88.747000 2620 3480 1 chr4B.!!$R1 860
19 TraesCS3A01G509100 chr4A 187560121 187560983 862 False 1051.000000 1051 88.644000 2618 3480 1 chr4A.!!$F1 862
20 TraesCS3A01G509100 chr3D 600423229 600424802 1573 True 590.433333 1016 88.121333 906 2619 3 chr3D.!!$R2 1713
21 TraesCS3A01G509100 chr5B 693173376 693174225 849 False 952.000000 952 86.854000 2629 3480 1 chr5B.!!$F1 851

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
690 694 6.713450 GGCCTTTAATTAAACTCCCGATATGA 59.287 38.462 6.54 0.0 0.00 2.15 F
1803 2003 0.246635 CGTGTCCTTCGAGGTGGAAT 59.753 55.000 5.63 0.0 36.53 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2044 0.038801 GAGCTGCCTTCACTTTTGGC 60.039 55.0 0.0 0.0 46.26 4.52 R
3316 3542 1.428448 TGGAGCGTCACGATTCAAAG 58.572 50.0 0.0 0.0 23.78 2.77 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
690 694 6.713450 GGCCTTTAATTAAACTCCCGATATGA 59.287 38.462 6.54 0.00 0.00 2.15
1291 1457 2.525629 TCCGCCTCCACTTCCACA 60.526 61.111 0.00 0.00 0.00 4.17
1798 1998 2.201022 ACTGCGTGTCCTTCGAGGT 61.201 57.895 0.00 0.00 36.53 3.85
1799 1999 1.734477 CTGCGTGTCCTTCGAGGTG 60.734 63.158 0.00 0.00 36.53 4.00
1800 2000 2.432628 GCGTGTCCTTCGAGGTGG 60.433 66.667 0.00 0.00 36.53 4.61
1801 2001 2.927580 GCGTGTCCTTCGAGGTGGA 61.928 63.158 0.00 0.00 36.53 4.02
1802 2002 1.663739 CGTGTCCTTCGAGGTGGAA 59.336 57.895 5.63 0.00 36.53 3.53
1803 2003 0.246635 CGTGTCCTTCGAGGTGGAAT 59.753 55.000 5.63 0.00 36.53 3.01
1805 2005 2.779506 GTGTCCTTCGAGGTGGAATTT 58.220 47.619 5.63 0.00 36.53 1.82
1806 2006 2.742589 GTGTCCTTCGAGGTGGAATTTC 59.257 50.000 5.63 0.00 36.53 2.17
1807 2007 2.000447 GTCCTTCGAGGTGGAATTTCG 59.000 52.381 5.63 0.00 36.53 3.46
1808 2008 1.621814 TCCTTCGAGGTGGAATTTCGT 59.378 47.619 0.00 0.00 36.53 3.85
1809 2009 1.732259 CCTTCGAGGTGGAATTTCGTG 59.268 52.381 0.00 0.00 35.90 4.35
1810 2010 2.413837 CTTCGAGGTGGAATTTCGTGT 58.586 47.619 0.00 0.00 35.90 4.49
1812 2012 1.069513 TCGAGGTGGAATTTCGTGTGT 59.930 47.619 0.00 0.00 35.90 3.72
1813 2013 2.296752 TCGAGGTGGAATTTCGTGTGTA 59.703 45.455 0.00 0.00 35.90 2.90
1815 2015 3.000727 GAGGTGGAATTTCGTGTGTAGG 58.999 50.000 0.00 0.00 0.00 3.18
1816 2016 2.081462 GGTGGAATTTCGTGTGTAGGG 58.919 52.381 0.00 0.00 0.00 3.53
1817 2017 2.081462 GTGGAATTTCGTGTGTAGGGG 58.919 52.381 0.00 0.00 0.00 4.79
1818 2018 1.700739 TGGAATTTCGTGTGTAGGGGT 59.299 47.619 0.00 0.00 0.00 4.95
1819 2019 2.081462 GGAATTTCGTGTGTAGGGGTG 58.919 52.381 0.00 0.00 0.00 4.61
1820 2020 2.289819 GGAATTTCGTGTGTAGGGGTGA 60.290 50.000 0.00 0.00 0.00 4.02
1821 2021 3.404899 GAATTTCGTGTGTAGGGGTGAA 58.595 45.455 0.00 0.00 0.00 3.18
1822 2022 3.495434 ATTTCGTGTGTAGGGGTGAAA 57.505 42.857 0.00 0.00 0.00 2.69
1823 2023 3.495434 TTTCGTGTGTAGGGGTGAAAT 57.505 42.857 0.00 0.00 0.00 2.17
1824 2024 2.754946 TCGTGTGTAGGGGTGAAATC 57.245 50.000 0.00 0.00 0.00 2.17
1825 2025 1.276989 TCGTGTGTAGGGGTGAAATCC 59.723 52.381 0.00 0.00 0.00 3.01
1826 2026 1.734163 GTGTGTAGGGGTGAAATCCG 58.266 55.000 0.00 0.00 0.00 4.18
1827 2027 1.002773 GTGTGTAGGGGTGAAATCCGT 59.997 52.381 0.00 0.00 0.00 4.69
1828 2028 2.234414 GTGTGTAGGGGTGAAATCCGTA 59.766 50.000 0.00 0.00 0.00 4.02
1829 2029 2.498481 TGTGTAGGGGTGAAATCCGTAG 59.502 50.000 0.00 0.00 0.00 3.51
1830 2030 2.762327 GTGTAGGGGTGAAATCCGTAGA 59.238 50.000 0.00 0.00 0.00 2.59
1831 2031 3.387050 GTGTAGGGGTGAAATCCGTAGAT 59.613 47.826 0.00 0.00 0.00 1.98
1832 2032 3.640029 TGTAGGGGTGAAATCCGTAGATC 59.360 47.826 0.00 0.00 0.00 2.75
1833 2033 3.047695 AGGGGTGAAATCCGTAGATCT 57.952 47.619 0.00 0.00 0.00 2.75
1834 2034 4.194678 AGGGGTGAAATCCGTAGATCTA 57.805 45.455 0.00 0.00 0.00 1.98
1835 2035 3.896272 AGGGGTGAAATCCGTAGATCTAC 59.104 47.826 21.00 21.00 0.00 2.59
1846 2046 2.997463 GTAGATCTACGAAGGAACGCC 58.003 52.381 16.87 0.00 36.70 5.68
1847 2047 1.471119 AGATCTACGAAGGAACGCCA 58.529 50.000 0.00 0.00 36.29 5.69
1848 2048 1.822990 AGATCTACGAAGGAACGCCAA 59.177 47.619 0.00 0.00 36.29 4.52
1849 2049 2.232941 AGATCTACGAAGGAACGCCAAA 59.767 45.455 0.00 0.00 36.29 3.28
1850 2050 2.529780 TCTACGAAGGAACGCCAAAA 57.470 45.000 0.00 0.00 36.29 2.44
1851 2051 2.409975 TCTACGAAGGAACGCCAAAAG 58.590 47.619 0.00 0.00 36.29 2.27
1852 2052 2.140717 CTACGAAGGAACGCCAAAAGT 58.859 47.619 0.00 0.00 36.29 2.66
1853 2053 0.661020 ACGAAGGAACGCCAAAAGTG 59.339 50.000 0.00 0.00 36.29 3.16
1854 2054 0.941542 CGAAGGAACGCCAAAAGTGA 59.058 50.000 0.00 0.00 36.29 3.41
1855 2055 1.332375 CGAAGGAACGCCAAAAGTGAA 59.668 47.619 0.00 0.00 36.29 3.18
1856 2056 2.602217 CGAAGGAACGCCAAAAGTGAAG 60.602 50.000 0.00 0.00 36.29 3.02
1857 2057 1.318576 AGGAACGCCAAAAGTGAAGG 58.681 50.000 0.00 0.00 36.29 3.46
1858 2058 0.318699 GGAACGCCAAAAGTGAAGGC 60.319 55.000 0.00 0.00 44.89 4.35
1864 2064 0.600057 CCAAAAGTGAAGGCAGCTCC 59.400 55.000 0.00 0.00 0.00 4.70
1865 2065 0.600057 CAAAAGTGAAGGCAGCTCCC 59.400 55.000 0.00 0.00 34.51 4.30
1866 2066 0.480252 AAAAGTGAAGGCAGCTCCCT 59.520 50.000 0.00 0.00 36.58 4.20
1867 2067 0.251077 AAAGTGAAGGCAGCTCCCTG 60.251 55.000 0.00 0.00 42.13 4.45
1868 2068 2.045536 GTGAAGGCAGCTCCCTGG 60.046 66.667 0.00 0.00 39.54 4.45
1869 2069 3.333219 TGAAGGCAGCTCCCTGGG 61.333 66.667 6.33 6.33 39.54 4.45
1870 2070 3.334054 GAAGGCAGCTCCCTGGGT 61.334 66.667 13.56 0.00 39.54 4.51
1871 2071 3.334054 AAGGCAGCTCCCTGGGTC 61.334 66.667 13.56 6.14 39.54 4.46
1875 2075 2.368594 CAGCTCCCTGGGTCCCTA 59.631 66.667 13.56 0.00 35.38 3.53
1876 2076 2.066999 CAGCTCCCTGGGTCCCTAC 61.067 68.421 13.56 0.00 35.38 3.18
1877 2077 2.768769 GCTCCCTGGGTCCCTACC 60.769 72.222 13.56 0.00 45.97 3.18
1885 2085 2.361771 GGTCCCTACCGACCCTGA 59.638 66.667 0.00 0.00 45.72 3.86
1886 2086 1.757340 GGTCCCTACCGACCCTGAG 60.757 68.421 0.00 0.00 45.72 3.35
1887 2087 1.000107 GTCCCTACCGACCCTGAGT 60.000 63.158 0.00 0.00 0.00 3.41
1888 2088 0.614134 GTCCCTACCGACCCTGAGTT 60.614 60.000 0.00 0.00 0.00 3.01
1889 2089 0.613853 TCCCTACCGACCCTGAGTTG 60.614 60.000 0.00 0.00 0.00 3.16
1890 2090 1.218316 CCTACCGACCCTGAGTTGC 59.782 63.158 0.00 0.00 0.00 4.17
1891 2091 1.153823 CTACCGACCCTGAGTTGCG 60.154 63.158 0.00 0.00 0.00 4.85
1892 2092 1.592400 CTACCGACCCTGAGTTGCGA 61.592 60.000 0.00 0.00 0.00 5.10
1893 2093 1.180456 TACCGACCCTGAGTTGCGAA 61.180 55.000 0.00 0.00 0.00 4.70
1894 2094 1.301401 CCGACCCTGAGTTGCGAAA 60.301 57.895 0.00 0.00 0.00 3.46
1895 2095 1.291877 CCGACCCTGAGTTGCGAAAG 61.292 60.000 0.00 0.00 0.00 2.62
1907 2107 2.125147 CGAAAGCATGGGGAGCGA 60.125 61.111 0.00 0.00 37.01 4.93
1908 2108 1.745115 CGAAAGCATGGGGAGCGAA 60.745 57.895 0.00 0.00 37.01 4.70
1909 2109 1.803289 GAAAGCATGGGGAGCGAAC 59.197 57.895 0.00 0.00 37.01 3.95
1910 2110 0.960364 GAAAGCATGGGGAGCGAACA 60.960 55.000 0.00 0.00 37.01 3.18
1911 2111 0.962356 AAAGCATGGGGAGCGAACAG 60.962 55.000 0.00 0.00 37.01 3.16
1912 2112 2.825836 GCATGGGGAGCGAACAGG 60.826 66.667 0.00 0.00 0.00 4.00
1913 2113 2.989639 CATGGGGAGCGAACAGGA 59.010 61.111 0.00 0.00 0.00 3.86
1914 2114 1.528824 CATGGGGAGCGAACAGGAT 59.471 57.895 0.00 0.00 0.00 3.24
1915 2115 0.107017 CATGGGGAGCGAACAGGATT 60.107 55.000 0.00 0.00 0.00 3.01
1916 2116 1.140852 CATGGGGAGCGAACAGGATTA 59.859 52.381 0.00 0.00 0.00 1.75
1917 2117 0.830648 TGGGGAGCGAACAGGATTAG 59.169 55.000 0.00 0.00 0.00 1.73
1918 2118 1.120530 GGGGAGCGAACAGGATTAGA 58.879 55.000 0.00 0.00 0.00 2.10
1919 2119 1.694696 GGGGAGCGAACAGGATTAGAT 59.305 52.381 0.00 0.00 0.00 1.98
1920 2120 2.897969 GGGGAGCGAACAGGATTAGATA 59.102 50.000 0.00 0.00 0.00 1.98
1921 2121 3.306156 GGGGAGCGAACAGGATTAGATAC 60.306 52.174 0.00 0.00 0.00 2.24
1922 2122 3.306156 GGGAGCGAACAGGATTAGATACC 60.306 52.174 0.00 0.00 0.00 2.73
1923 2123 3.306156 GGAGCGAACAGGATTAGATACCC 60.306 52.174 0.00 0.00 0.00 3.69
1924 2124 3.574826 GAGCGAACAGGATTAGATACCCT 59.425 47.826 0.00 0.00 0.00 4.34
1933 2133 6.485388 AGGATTAGATACCCTGATAGTCCA 57.515 41.667 0.00 0.00 0.00 4.02
1934 2134 7.062584 AGGATTAGATACCCTGATAGTCCAT 57.937 40.000 0.00 0.00 0.00 3.41
1935 2135 6.900186 AGGATTAGATACCCTGATAGTCCATG 59.100 42.308 0.00 0.00 0.00 3.66
1936 2136 6.407525 GGATTAGATACCCTGATAGTCCATGC 60.408 46.154 0.00 0.00 0.00 4.06
1937 2137 3.177228 AGATACCCTGATAGTCCATGCC 58.823 50.000 0.00 0.00 0.00 4.40
1938 2138 1.338107 TACCCTGATAGTCCATGCCG 58.662 55.000 0.00 0.00 0.00 5.69
1939 2139 0.691078 ACCCTGATAGTCCATGCCGT 60.691 55.000 0.00 0.00 0.00 5.68
1940 2140 1.338107 CCCTGATAGTCCATGCCGTA 58.662 55.000 0.00 0.00 0.00 4.02
1941 2141 1.691976 CCCTGATAGTCCATGCCGTAA 59.308 52.381 0.00 0.00 0.00 3.18
1942 2142 2.104111 CCCTGATAGTCCATGCCGTAAA 59.896 50.000 0.00 0.00 0.00 2.01
1943 2143 3.131396 CCTGATAGTCCATGCCGTAAAC 58.869 50.000 0.00 0.00 0.00 2.01
1944 2144 2.794910 CTGATAGTCCATGCCGTAAACG 59.205 50.000 0.00 0.00 39.44 3.60
1945 2145 2.427812 TGATAGTCCATGCCGTAAACGA 59.572 45.455 3.65 0.00 43.02 3.85
1946 2146 3.069016 TGATAGTCCATGCCGTAAACGAT 59.931 43.478 3.65 0.00 43.02 3.73
1947 2147 1.651987 AGTCCATGCCGTAAACGATG 58.348 50.000 3.65 0.87 43.02 3.84
1948 2148 1.206132 AGTCCATGCCGTAAACGATGA 59.794 47.619 3.65 0.00 43.02 2.92
1949 2149 1.593006 GTCCATGCCGTAAACGATGAG 59.407 52.381 3.65 0.00 43.02 2.90
1950 2150 1.206132 TCCATGCCGTAAACGATGAGT 59.794 47.619 3.65 0.00 43.02 3.41
1951 2151 1.327460 CCATGCCGTAAACGATGAGTG 59.673 52.381 3.65 0.00 43.02 3.51
1952 2152 1.999735 CATGCCGTAAACGATGAGTGT 59.000 47.619 3.65 0.00 43.02 3.55
1953 2153 2.157834 TGCCGTAAACGATGAGTGTT 57.842 45.000 3.65 0.00 43.02 3.32
1954 2154 2.485903 TGCCGTAAACGATGAGTGTTT 58.514 42.857 3.65 0.00 43.02 2.83
1955 2155 2.222213 TGCCGTAAACGATGAGTGTTTG 59.778 45.455 3.65 0.00 43.02 2.93
1956 2156 2.834689 CCGTAAACGATGAGTGTTTGC 58.165 47.619 3.65 0.00 43.02 3.68
1957 2157 2.412325 CCGTAAACGATGAGTGTTTGCC 60.412 50.000 3.65 0.00 43.02 4.52
1958 2158 2.412325 CGTAAACGATGAGTGTTTGCCC 60.412 50.000 0.00 0.00 43.02 5.36
1959 2159 1.981256 AAACGATGAGTGTTTGCCCT 58.019 45.000 0.00 0.00 38.08 5.19
1960 2160 1.981256 AACGATGAGTGTTTGCCCTT 58.019 45.000 0.00 0.00 0.00 3.95
1961 2161 1.238439 ACGATGAGTGTTTGCCCTTG 58.762 50.000 0.00 0.00 0.00 3.61
1962 2162 0.523072 CGATGAGTGTTTGCCCTTGG 59.477 55.000 0.00 0.00 0.00 3.61
1963 2163 1.620822 GATGAGTGTTTGCCCTTGGT 58.379 50.000 0.00 0.00 0.00 3.67
1964 2164 1.541588 GATGAGTGTTTGCCCTTGGTC 59.458 52.381 0.00 0.00 0.00 4.02
1965 2165 0.550914 TGAGTGTTTGCCCTTGGTCT 59.449 50.000 0.00 0.00 0.00 3.85
1966 2166 1.771854 TGAGTGTTTGCCCTTGGTCTA 59.228 47.619 0.00 0.00 0.00 2.59
1967 2167 2.152016 GAGTGTTTGCCCTTGGTCTAC 58.848 52.381 0.00 0.00 0.00 2.59
1968 2168 0.872388 GTGTTTGCCCTTGGTCTACG 59.128 55.000 0.00 0.00 0.00 3.51
1969 2169 0.887387 TGTTTGCCCTTGGTCTACGC 60.887 55.000 0.00 0.00 0.00 4.42
1970 2170 0.887387 GTTTGCCCTTGGTCTACGCA 60.887 55.000 0.00 0.00 0.00 5.24
1971 2171 0.605319 TTTGCCCTTGGTCTACGCAG 60.605 55.000 0.00 0.00 0.00 5.18
1972 2172 1.476845 TTGCCCTTGGTCTACGCAGA 61.477 55.000 0.00 0.00 0.00 4.26
1973 2173 1.264749 TGCCCTTGGTCTACGCAGAT 61.265 55.000 0.00 0.00 32.09 2.90
1974 2174 0.530870 GCCCTTGGTCTACGCAGATC 60.531 60.000 0.00 0.00 32.09 2.75
1975 2175 0.824109 CCCTTGGTCTACGCAGATCA 59.176 55.000 0.00 0.00 40.26 2.92
1976 2176 1.202463 CCCTTGGTCTACGCAGATCAG 60.202 57.143 0.00 0.00 42.85 2.90
1977 2177 1.202463 CCTTGGTCTACGCAGATCAGG 60.202 57.143 1.06 1.06 42.85 3.86
1978 2178 0.824109 TTGGTCTACGCAGATCAGGG 59.176 55.000 0.00 0.32 42.85 4.45
1979 2179 1.043116 TGGTCTACGCAGATCAGGGG 61.043 60.000 7.10 3.79 36.98 4.79
1980 2180 1.068250 GTCTACGCAGATCAGGGGC 59.932 63.158 7.10 0.00 32.09 5.80
1981 2181 2.134287 TCTACGCAGATCAGGGGCC 61.134 63.158 7.10 0.00 0.00 5.80
1982 2182 2.364973 TACGCAGATCAGGGGCCA 60.365 61.111 4.39 0.00 0.00 5.36
1983 2183 2.374830 CTACGCAGATCAGGGGCCAG 62.375 65.000 4.39 0.00 0.00 4.85
1985 2185 3.806667 GCAGATCAGGGGCCAGCT 61.807 66.667 4.39 0.00 0.00 4.24
1986 2186 2.446848 GCAGATCAGGGGCCAGCTA 61.447 63.158 4.39 0.00 0.00 3.32
1987 2187 1.987807 GCAGATCAGGGGCCAGCTAA 61.988 60.000 4.39 0.00 0.00 3.09
1988 2188 0.179034 CAGATCAGGGGCCAGCTAAC 60.179 60.000 4.39 0.00 0.00 2.34
1989 2189 1.227674 GATCAGGGGCCAGCTAACG 60.228 63.158 4.39 0.00 0.00 3.18
1990 2190 3.406595 ATCAGGGGCCAGCTAACGC 62.407 63.158 4.39 0.00 0.00 4.84
1994 2194 4.752879 GGGCCAGCTAACGCGTGA 62.753 66.667 14.98 3.37 42.32 4.35
1995 2195 2.740826 GGCCAGCTAACGCGTGAA 60.741 61.111 14.98 2.84 42.32 3.18
1996 2196 2.322081 GGCCAGCTAACGCGTGAAA 61.322 57.895 14.98 0.00 42.32 2.69
1997 2197 1.154469 GCCAGCTAACGCGTGAAAC 60.154 57.895 14.98 2.62 42.32 2.78
1998 2198 1.837538 GCCAGCTAACGCGTGAAACA 61.838 55.000 14.98 0.00 42.32 2.83
1999 2199 0.110823 CCAGCTAACGCGTGAAACAC 60.111 55.000 14.98 0.00 42.32 3.32
2000 2200 0.859232 CAGCTAACGCGTGAAACACT 59.141 50.000 14.98 1.63 42.32 3.55
2001 2201 1.136611 CAGCTAACGCGTGAAACACTC 60.137 52.381 14.98 0.00 42.32 3.51
2002 2202 0.163146 GCTAACGCGTGAAACACTCC 59.837 55.000 14.98 0.00 35.74 3.85
2003 2203 0.433492 CTAACGCGTGAAACACTCCG 59.567 55.000 14.98 0.00 35.74 4.63
2004 2204 1.550659 TAACGCGTGAAACACTCCGC 61.551 55.000 14.98 0.00 39.15 5.54
2005 2205 4.072088 CGCGTGAAACACTCCGCC 62.072 66.667 0.00 0.00 39.27 6.13
2006 2206 2.665185 GCGTGAAACACTCCGCCT 60.665 61.111 0.00 0.00 37.61 5.52
2007 2207 2.954753 GCGTGAAACACTCCGCCTG 61.955 63.158 0.00 0.00 37.61 4.85
2008 2208 2.317609 CGTGAAACACTCCGCCTGG 61.318 63.158 0.00 0.00 35.74 4.45
2009 2209 1.966451 GTGAAACACTCCGCCTGGG 60.966 63.158 0.00 0.00 36.32 4.45
2010 2210 2.359975 GAAACACTCCGCCTGGGG 60.360 66.667 3.33 3.33 43.71 4.96
2011 2211 2.852075 AAACACTCCGCCTGGGGA 60.852 61.111 12.98 7.97 38.40 4.81
2016 2216 3.528370 CTCCGCCTGGGGAGTACG 61.528 72.222 19.21 0.00 46.97 3.67
2019 2219 3.834799 CGCCTGGGGAGTACGGTC 61.835 72.222 4.46 0.00 0.00 4.79
2020 2220 3.834799 GCCTGGGGAGTACGGTCG 61.835 72.222 0.00 0.00 0.00 4.79
2021 2221 3.834799 CCTGGGGAGTACGGTCGC 61.835 72.222 0.00 0.00 0.00 5.19
2022 2222 3.066190 CTGGGGAGTACGGTCGCA 61.066 66.667 2.32 3.10 0.00 5.10
2023 2223 2.601067 TGGGGAGTACGGTCGCAA 60.601 61.111 2.32 0.00 0.00 4.85
2024 2224 2.183555 GGGGAGTACGGTCGCAAG 59.816 66.667 2.32 0.00 0.00 4.01
2036 2236 3.671262 TCGCAAGACCGAAACTCAA 57.329 47.368 0.00 0.00 45.01 3.02
2037 2237 1.942677 TCGCAAGACCGAAACTCAAA 58.057 45.000 0.00 0.00 45.01 2.69
2038 2238 2.281517 TCGCAAGACCGAAACTCAAAA 58.718 42.857 0.00 0.00 45.01 2.44
2039 2239 2.678836 TCGCAAGACCGAAACTCAAAAA 59.321 40.909 0.00 0.00 45.01 1.94
2054 2254 4.966247 AAAAATTGACGGGGGCCT 57.034 50.000 0.84 0.00 0.00 5.19
2055 2255 2.361189 AAAAATTGACGGGGGCCTG 58.639 52.632 0.84 0.00 0.00 4.85
2056 2256 1.826340 AAAAATTGACGGGGGCCTGC 61.826 55.000 0.84 0.00 0.00 4.85
2057 2257 3.521765 AAATTGACGGGGGCCTGCA 62.522 57.895 0.84 0.00 0.00 4.41
2058 2258 4.740822 ATTGACGGGGGCCTGCAC 62.741 66.667 0.84 0.00 0.00 4.57
2084 2284 4.176752 GACCCGACCATGAGCCCC 62.177 72.222 0.00 0.00 0.00 5.80
2104 2304 2.172483 GACTTCCTCGGCAGGCTGAA 62.172 60.000 20.86 0.80 40.12 3.02
2185 2386 6.385537 GACGTGTTCGACAACAAATACTAT 57.614 37.500 0.00 0.00 44.32 2.12
2245 2446 0.969894 AGGACCTCTTCACCAACGAG 59.030 55.000 0.00 0.00 0.00 4.18
2248 2449 1.122019 ACCTCTTCACCAACGAGGCT 61.122 55.000 4.56 0.00 46.49 4.58
2263 2464 4.603946 GCTACCCGGCCCATCGTC 62.604 72.222 0.00 0.00 0.00 4.20
2347 2548 1.985614 CCAGATCAGGGTGCTCACA 59.014 57.895 0.00 0.00 0.00 3.58
2418 2619 3.583383 CGACGGTAACCTCGGACT 58.417 61.111 0.00 0.00 0.00 3.85
2419 2620 1.427020 CGACGGTAACCTCGGACTC 59.573 63.158 0.00 0.00 0.00 3.36
2420 2621 1.805910 GACGGTAACCTCGGACTCC 59.194 63.158 0.00 0.00 0.00 3.85
2550 2770 0.102481 GCAAGGCAAGGCATGATGAG 59.898 55.000 0.00 0.00 0.00 2.90
2551 2771 0.102481 CAAGGCAAGGCATGATGAGC 59.898 55.000 0.00 0.00 0.00 4.26
2560 2783 1.303309 GCATGATGAGCCTGTGTACC 58.697 55.000 0.00 0.00 0.00 3.34
2566 2789 1.003718 GAGCCTGTGTACCACCCAC 60.004 63.158 0.00 0.00 32.73 4.61
2567 2790 2.358247 GCCTGTGTACCACCCACG 60.358 66.667 0.00 0.00 35.56 4.94
2568 2791 3.144285 CCTGTGTACCACCCACGT 58.856 61.111 0.00 0.00 35.56 4.49
2569 2792 1.818959 GCCTGTGTACCACCCACGTA 61.819 60.000 0.00 0.00 35.56 3.57
2573 2796 1.693062 TGTGTACCACCCACGTATGTT 59.307 47.619 0.00 0.00 35.56 2.71
2574 2797 2.896044 TGTGTACCACCCACGTATGTTA 59.104 45.455 0.00 0.00 35.56 2.41
2589 2814 6.035650 CACGTATGTTATGTTCACCAGTTAGG 59.964 42.308 0.00 0.00 45.67 2.69
2605 2830 4.088638 CAGTTAGGTTAATCGATCGATGCG 59.911 45.833 29.99 6.78 34.70 4.73
2686 2912 9.440784 TCGTTTACAACATGTTGAGAAATAAAC 57.559 29.630 38.30 32.97 42.93 2.01
2852 3078 0.533085 GATAGCCGCTTCTTGTCCCC 60.533 60.000 0.00 0.00 0.00 4.81
2853 3079 0.983378 ATAGCCGCTTCTTGTCCCCT 60.983 55.000 0.00 0.00 0.00 4.79
2951 3177 8.249592 CTTGCCAGCCAAATAGAAACCATTCT 62.250 42.308 0.00 0.00 39.98 2.40
2952 3178 4.440663 GCCAGCCAAATAGAAACCATTCTC 60.441 45.833 0.00 0.00 44.75 2.87
3174 3400 0.753867 TGGTTCGGTGTTAGTGAGCA 59.246 50.000 0.00 0.00 0.00 4.26
3316 3542 0.872021 CGGCCACAGATAGAGCGTTC 60.872 60.000 2.24 0.00 0.00 3.95
3334 3560 1.710013 TCTTTGAATCGTGACGCTCC 58.290 50.000 0.00 0.00 0.00 4.70
3342 3568 0.605589 TCGTGACGCTCCAAGAGAGA 60.606 55.000 0.00 0.00 46.50 3.10
3406 3632 0.892063 GAACTTCAGCCTCGAGTCCT 59.108 55.000 12.31 4.29 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 257 6.038161 GCACTGGGCTTTTTGTTTAAATTTCT 59.962 34.615 0.00 0.00 40.25 2.52
690 694 3.004419 TCGCTGCGCAGACTAATTAGTAT 59.996 43.478 40.21 12.54 36.50 2.12
1291 1457 0.403271 AGCACCTGGATGAAGCAGTT 59.597 50.000 0.00 0.00 0.00 3.16
1787 1987 2.000447 CGAAATTCCACCTCGAAGGAC 59.000 52.381 7.76 0.00 37.67 3.85
1798 1998 1.700739 ACCCCTACACACGAAATTCCA 59.299 47.619 0.00 0.00 0.00 3.53
1799 1999 2.081462 CACCCCTACACACGAAATTCC 58.919 52.381 0.00 0.00 0.00 3.01
1800 2000 3.048337 TCACCCCTACACACGAAATTC 57.952 47.619 0.00 0.00 0.00 2.17
1801 2001 3.495434 TTCACCCCTACACACGAAATT 57.505 42.857 0.00 0.00 0.00 1.82
1802 2002 3.495434 TTTCACCCCTACACACGAAAT 57.505 42.857 0.00 0.00 0.00 2.17
1803 2003 3.404899 GATTTCACCCCTACACACGAAA 58.595 45.455 0.00 0.00 0.00 3.46
1805 2005 1.276989 GGATTTCACCCCTACACACGA 59.723 52.381 0.00 0.00 0.00 4.35
1806 2006 1.734163 GGATTTCACCCCTACACACG 58.266 55.000 0.00 0.00 0.00 4.49
1807 2007 1.002773 ACGGATTTCACCCCTACACAC 59.997 52.381 0.00 0.00 0.00 3.82
1808 2008 1.354101 ACGGATTTCACCCCTACACA 58.646 50.000 0.00 0.00 0.00 3.72
1809 2009 2.762327 TCTACGGATTTCACCCCTACAC 59.238 50.000 0.00 0.00 0.00 2.90
1810 2010 3.104519 TCTACGGATTTCACCCCTACA 57.895 47.619 0.00 0.00 0.00 2.74
1812 2012 4.194678 AGATCTACGGATTTCACCCCTA 57.805 45.455 0.00 0.00 31.46 3.53
1813 2013 3.047695 AGATCTACGGATTTCACCCCT 57.952 47.619 0.00 0.00 31.46 4.79
1826 2026 2.357009 TGGCGTTCCTTCGTAGATCTAC 59.643 50.000 21.00 21.00 35.04 2.59
1827 2027 2.646930 TGGCGTTCCTTCGTAGATCTA 58.353 47.619 0.00 0.00 35.04 1.98
1828 2028 1.471119 TGGCGTTCCTTCGTAGATCT 58.529 50.000 0.00 0.00 35.04 2.75
1829 2029 2.288961 TTGGCGTTCCTTCGTAGATC 57.711 50.000 0.00 0.00 35.04 2.75
1830 2030 2.754946 TTTGGCGTTCCTTCGTAGAT 57.245 45.000 0.00 0.00 35.04 1.98
1831 2031 2.224113 ACTTTTGGCGTTCCTTCGTAGA 60.224 45.455 0.00 0.00 0.00 2.59
1832 2032 2.096417 CACTTTTGGCGTTCCTTCGTAG 60.096 50.000 0.00 0.00 0.00 3.51
1833 2033 1.868498 CACTTTTGGCGTTCCTTCGTA 59.132 47.619 0.00 0.00 0.00 3.43
1834 2034 0.661020 CACTTTTGGCGTTCCTTCGT 59.339 50.000 0.00 0.00 0.00 3.85
1835 2035 0.941542 TCACTTTTGGCGTTCCTTCG 59.058 50.000 0.00 0.00 0.00 3.79
1836 2036 2.287608 CCTTCACTTTTGGCGTTCCTTC 60.288 50.000 0.00 0.00 0.00 3.46
1837 2037 1.681264 CCTTCACTTTTGGCGTTCCTT 59.319 47.619 0.00 0.00 0.00 3.36
1838 2038 1.318576 CCTTCACTTTTGGCGTTCCT 58.681 50.000 0.00 0.00 0.00 3.36
1839 2039 0.318699 GCCTTCACTTTTGGCGTTCC 60.319 55.000 0.00 0.00 37.11 3.62
1840 2040 3.179433 GCCTTCACTTTTGGCGTTC 57.821 52.632 0.00 0.00 37.11 3.95
1844 2044 0.038801 GAGCTGCCTTCACTTTTGGC 60.039 55.000 0.00 0.00 46.26 4.52
1845 2045 0.600057 GGAGCTGCCTTCACTTTTGG 59.400 55.000 0.00 0.00 0.00 3.28
1846 2046 0.600057 GGGAGCTGCCTTCACTTTTG 59.400 55.000 18.47 0.00 36.66 2.44
1847 2047 0.480252 AGGGAGCTGCCTTCACTTTT 59.520 50.000 23.00 0.00 36.66 2.27
1848 2048 0.251077 CAGGGAGCTGCCTTCACTTT 60.251 55.000 26.30 0.00 36.66 2.66
1849 2049 1.377994 CAGGGAGCTGCCTTCACTT 59.622 57.895 26.30 0.00 36.66 3.16
1850 2050 2.600729 CCAGGGAGCTGCCTTCACT 61.601 63.158 26.30 0.00 36.66 3.41
1851 2051 2.045536 CCAGGGAGCTGCCTTCAC 60.046 66.667 26.30 0.00 36.66 3.18
1852 2052 3.333219 CCCAGGGAGCTGCCTTCA 61.333 66.667 26.30 0.00 36.66 3.02
1853 2053 3.334054 ACCCAGGGAGCTGCCTTC 61.334 66.667 26.30 0.00 36.66 3.46
1854 2054 3.334054 GACCCAGGGAGCTGCCTT 61.334 66.667 26.30 10.89 36.66 4.35
1858 2058 2.066999 GTAGGGACCCAGGGAGCTG 61.067 68.421 14.54 0.00 0.00 4.24
1859 2059 2.369001 GTAGGGACCCAGGGAGCT 59.631 66.667 14.54 0.00 0.00 4.09
1860 2060 2.768769 GGTAGGGACCCAGGGAGC 60.769 72.222 14.54 3.16 40.23 4.70
1861 2061 2.444140 CGGTAGGGACCCAGGGAG 60.444 72.222 14.54 0.00 43.64 4.30
1862 2062 2.948354 TCGGTAGGGACCCAGGGA 60.948 66.667 14.54 1.10 43.64 4.20
1863 2063 2.762875 GTCGGTAGGGACCCAGGG 60.763 72.222 14.60 2.85 43.64 4.45
1869 2069 0.614134 AACTCAGGGTCGGTAGGGAC 60.614 60.000 0.00 0.00 36.18 4.46
1870 2070 0.613853 CAACTCAGGGTCGGTAGGGA 60.614 60.000 0.00 0.00 0.00 4.20
1871 2071 1.898154 CAACTCAGGGTCGGTAGGG 59.102 63.158 0.00 0.00 0.00 3.53
1872 2072 1.218316 GCAACTCAGGGTCGGTAGG 59.782 63.158 0.00 0.00 0.00 3.18
1873 2073 1.153823 CGCAACTCAGGGTCGGTAG 60.154 63.158 0.00 0.00 0.00 3.18
1874 2074 1.180456 TTCGCAACTCAGGGTCGGTA 61.180 55.000 0.00 0.00 0.00 4.02
1875 2075 2.035237 TTTCGCAACTCAGGGTCGGT 62.035 55.000 0.00 0.00 0.00 4.69
1876 2076 1.291877 CTTTCGCAACTCAGGGTCGG 61.292 60.000 0.00 0.00 0.00 4.79
1877 2077 1.901650 GCTTTCGCAACTCAGGGTCG 61.902 60.000 0.00 0.00 35.78 4.79
1878 2078 0.884704 TGCTTTCGCAACTCAGGGTC 60.885 55.000 0.00 0.00 44.62 4.46
1879 2079 1.148273 TGCTTTCGCAACTCAGGGT 59.852 52.632 0.00 0.00 44.62 4.34
1880 2080 4.063529 TGCTTTCGCAACTCAGGG 57.936 55.556 0.00 0.00 44.62 4.45
1889 2089 3.880846 CGCTCCCCATGCTTTCGC 61.881 66.667 0.00 0.00 0.00 4.70
1890 2090 1.745115 TTCGCTCCCCATGCTTTCG 60.745 57.895 0.00 0.00 0.00 3.46
1891 2091 0.960364 TGTTCGCTCCCCATGCTTTC 60.960 55.000 0.00 0.00 0.00 2.62
1892 2092 0.962356 CTGTTCGCTCCCCATGCTTT 60.962 55.000 0.00 0.00 0.00 3.51
1893 2093 1.377725 CTGTTCGCTCCCCATGCTT 60.378 57.895 0.00 0.00 0.00 3.91
1894 2094 2.270205 CTGTTCGCTCCCCATGCT 59.730 61.111 0.00 0.00 0.00 3.79
1895 2095 2.615227 ATCCTGTTCGCTCCCCATGC 62.615 60.000 0.00 0.00 0.00 4.06
1896 2096 0.107017 AATCCTGTTCGCTCCCCATG 60.107 55.000 0.00 0.00 0.00 3.66
1897 2097 1.417890 CTAATCCTGTTCGCTCCCCAT 59.582 52.381 0.00 0.00 0.00 4.00
1898 2098 0.830648 CTAATCCTGTTCGCTCCCCA 59.169 55.000 0.00 0.00 0.00 4.96
1899 2099 1.120530 TCTAATCCTGTTCGCTCCCC 58.879 55.000 0.00 0.00 0.00 4.81
1900 2100 3.306156 GGTATCTAATCCTGTTCGCTCCC 60.306 52.174 0.00 0.00 0.00 4.30
1901 2101 3.306156 GGGTATCTAATCCTGTTCGCTCC 60.306 52.174 0.00 0.00 0.00 4.70
1902 2102 3.574826 AGGGTATCTAATCCTGTTCGCTC 59.425 47.826 0.00 0.00 0.00 5.03
1903 2103 3.322254 CAGGGTATCTAATCCTGTTCGCT 59.678 47.826 0.00 0.00 42.17 4.93
1904 2104 3.321111 TCAGGGTATCTAATCCTGTTCGC 59.679 47.826 4.31 0.00 45.97 4.70
1905 2105 5.730296 ATCAGGGTATCTAATCCTGTTCG 57.270 43.478 4.31 0.00 45.97 3.95
1906 2106 7.093684 GGACTATCAGGGTATCTAATCCTGTTC 60.094 44.444 4.31 0.00 45.97 3.18
1907 2107 6.726764 GGACTATCAGGGTATCTAATCCTGTT 59.273 42.308 4.31 0.00 45.97 3.16
1908 2108 6.183361 TGGACTATCAGGGTATCTAATCCTGT 60.183 42.308 4.31 0.00 45.97 4.00
1909 2109 6.256819 TGGACTATCAGGGTATCTAATCCTG 58.743 44.000 0.00 0.00 46.91 3.86
1910 2110 6.485388 TGGACTATCAGGGTATCTAATCCT 57.515 41.667 0.00 0.00 0.00 3.24
1911 2111 6.407525 GCATGGACTATCAGGGTATCTAATCC 60.408 46.154 0.00 0.00 0.00 3.01
1912 2112 6.407525 GGCATGGACTATCAGGGTATCTAATC 60.408 46.154 0.00 0.00 0.00 1.75
1913 2113 5.426833 GGCATGGACTATCAGGGTATCTAAT 59.573 44.000 0.00 0.00 0.00 1.73
1914 2114 4.777896 GGCATGGACTATCAGGGTATCTAA 59.222 45.833 0.00 0.00 0.00 2.10
1915 2115 4.353777 GGCATGGACTATCAGGGTATCTA 58.646 47.826 0.00 0.00 0.00 1.98
1916 2116 3.177228 GGCATGGACTATCAGGGTATCT 58.823 50.000 0.00 0.00 0.00 1.98
1917 2117 2.093973 CGGCATGGACTATCAGGGTATC 60.094 54.545 0.00 0.00 0.00 2.24
1918 2118 1.902508 CGGCATGGACTATCAGGGTAT 59.097 52.381 0.00 0.00 0.00 2.73
1919 2119 1.338107 CGGCATGGACTATCAGGGTA 58.662 55.000 0.00 0.00 0.00 3.69
1920 2120 0.691078 ACGGCATGGACTATCAGGGT 60.691 55.000 0.00 0.00 0.00 4.34
1921 2121 1.338107 TACGGCATGGACTATCAGGG 58.662 55.000 0.00 0.00 0.00 4.45
1922 2122 3.131396 GTTTACGGCATGGACTATCAGG 58.869 50.000 0.00 0.00 0.00 3.86
1923 2123 2.794910 CGTTTACGGCATGGACTATCAG 59.205 50.000 0.00 0.00 35.37 2.90
1924 2124 2.427812 TCGTTTACGGCATGGACTATCA 59.572 45.455 2.09 0.00 40.29 2.15
1925 2125 3.088194 TCGTTTACGGCATGGACTATC 57.912 47.619 2.09 0.00 40.29 2.08
1926 2126 3.069016 TCATCGTTTACGGCATGGACTAT 59.931 43.478 2.09 0.00 40.29 2.12
1927 2127 2.427812 TCATCGTTTACGGCATGGACTA 59.572 45.455 2.09 0.00 40.29 2.59
1928 2128 1.206132 TCATCGTTTACGGCATGGACT 59.794 47.619 2.09 0.00 40.29 3.85
1929 2129 1.593006 CTCATCGTTTACGGCATGGAC 59.407 52.381 2.09 0.00 40.29 4.02
1930 2130 1.206132 ACTCATCGTTTACGGCATGGA 59.794 47.619 2.09 0.00 40.29 3.41
1931 2131 1.327460 CACTCATCGTTTACGGCATGG 59.673 52.381 2.09 0.00 40.29 3.66
1932 2132 1.999735 ACACTCATCGTTTACGGCATG 59.000 47.619 2.09 0.50 40.29 4.06
1933 2133 2.380084 ACACTCATCGTTTACGGCAT 57.620 45.000 2.09 0.00 40.29 4.40
1934 2134 2.157834 AACACTCATCGTTTACGGCA 57.842 45.000 2.09 0.00 40.29 5.69
1935 2135 2.834689 CAAACACTCATCGTTTACGGC 58.165 47.619 2.09 0.00 40.29 5.68
1936 2136 2.412325 GGCAAACACTCATCGTTTACGG 60.412 50.000 2.09 0.00 40.29 4.02
1937 2137 2.412325 GGGCAAACACTCATCGTTTACG 60.412 50.000 0.00 0.00 34.87 3.18
1938 2138 2.812011 AGGGCAAACACTCATCGTTTAC 59.188 45.455 0.00 0.00 34.87 2.01
1939 2139 3.134574 AGGGCAAACACTCATCGTTTA 57.865 42.857 0.00 0.00 34.87 2.01
1940 2140 1.981256 AGGGCAAACACTCATCGTTT 58.019 45.000 0.00 0.00 37.04 3.60
1941 2141 1.608590 CAAGGGCAAACACTCATCGTT 59.391 47.619 0.00 0.00 0.00 3.85
1942 2142 1.238439 CAAGGGCAAACACTCATCGT 58.762 50.000 0.00 0.00 0.00 3.73
1943 2143 0.523072 CCAAGGGCAAACACTCATCG 59.477 55.000 0.00 0.00 0.00 3.84
1944 2144 1.541588 GACCAAGGGCAAACACTCATC 59.458 52.381 0.00 0.00 0.00 2.92
1945 2145 1.145738 AGACCAAGGGCAAACACTCAT 59.854 47.619 0.00 0.00 0.00 2.90
1946 2146 0.550914 AGACCAAGGGCAAACACTCA 59.449 50.000 0.00 0.00 0.00 3.41
1947 2147 2.152016 GTAGACCAAGGGCAAACACTC 58.848 52.381 0.00 0.00 0.00 3.51
1948 2148 1.542547 CGTAGACCAAGGGCAAACACT 60.543 52.381 0.00 0.00 0.00 3.55
1949 2149 0.872388 CGTAGACCAAGGGCAAACAC 59.128 55.000 0.00 0.00 0.00 3.32
1950 2150 0.887387 GCGTAGACCAAGGGCAAACA 60.887 55.000 0.00 0.00 0.00 2.83
1951 2151 0.887387 TGCGTAGACCAAGGGCAAAC 60.887 55.000 0.00 0.00 0.00 2.93
1952 2152 0.605319 CTGCGTAGACCAAGGGCAAA 60.605 55.000 0.00 0.00 32.59 3.68
1953 2153 1.003839 CTGCGTAGACCAAGGGCAA 60.004 57.895 0.00 0.00 32.59 4.52
1954 2154 1.264749 ATCTGCGTAGACCAAGGGCA 61.265 55.000 4.99 0.00 35.34 5.36
1955 2155 0.530870 GATCTGCGTAGACCAAGGGC 60.531 60.000 4.99 0.00 35.34 5.19
1956 2156 0.824109 TGATCTGCGTAGACCAAGGG 59.176 55.000 4.99 0.00 35.34 3.95
1957 2157 1.202463 CCTGATCTGCGTAGACCAAGG 60.202 57.143 4.99 9.30 35.34 3.61
1958 2158 1.202463 CCCTGATCTGCGTAGACCAAG 60.202 57.143 4.99 0.00 35.34 3.61
1959 2159 0.824109 CCCTGATCTGCGTAGACCAA 59.176 55.000 4.99 0.00 35.34 3.67
1960 2160 1.043116 CCCCTGATCTGCGTAGACCA 61.043 60.000 4.99 0.00 35.34 4.02
1961 2161 1.742768 CCCCTGATCTGCGTAGACC 59.257 63.158 4.99 0.00 35.34 3.85
1962 2162 1.068250 GCCCCTGATCTGCGTAGAC 59.932 63.158 4.99 0.73 35.34 2.59
1963 2163 2.134287 GGCCCCTGATCTGCGTAGA 61.134 63.158 5.45 5.45 37.35 2.59
1964 2164 2.374830 CTGGCCCCTGATCTGCGTAG 62.375 65.000 0.00 0.00 0.00 3.51
1965 2165 2.364973 TGGCCCCTGATCTGCGTA 60.365 61.111 0.00 0.00 0.00 4.42
1966 2166 3.790437 CTGGCCCCTGATCTGCGT 61.790 66.667 0.00 0.00 0.00 5.24
1968 2168 1.987807 TTAGCTGGCCCCTGATCTGC 61.988 60.000 0.00 0.00 0.00 4.26
1969 2169 0.179034 GTTAGCTGGCCCCTGATCTG 60.179 60.000 0.00 0.00 0.00 2.90
1970 2170 1.690219 CGTTAGCTGGCCCCTGATCT 61.690 60.000 0.00 0.00 0.00 2.75
1971 2171 1.227674 CGTTAGCTGGCCCCTGATC 60.228 63.158 0.00 0.00 0.00 2.92
1972 2172 2.911143 CGTTAGCTGGCCCCTGAT 59.089 61.111 0.00 0.00 0.00 2.90
1973 2173 4.096003 GCGTTAGCTGGCCCCTGA 62.096 66.667 0.00 0.00 41.01 3.86
1977 2177 4.752879 TCACGCGTTAGCTGGCCC 62.753 66.667 10.22 0.00 42.32 5.80
1978 2178 2.322081 TTTCACGCGTTAGCTGGCC 61.322 57.895 10.22 0.00 42.32 5.36
1979 2179 1.154469 GTTTCACGCGTTAGCTGGC 60.154 57.895 10.22 0.00 42.32 4.85
1980 2180 0.110823 GTGTTTCACGCGTTAGCTGG 60.111 55.000 10.22 0.00 42.32 4.85
1981 2181 0.859232 AGTGTTTCACGCGTTAGCTG 59.141 50.000 10.22 0.00 42.32 4.24
1982 2182 1.137513 GAGTGTTTCACGCGTTAGCT 58.862 50.000 10.22 1.71 42.32 3.32
1983 2183 0.163146 GGAGTGTTTCACGCGTTAGC 59.837 55.000 10.22 3.15 39.64 3.09
1984 2184 0.433492 CGGAGTGTTTCACGCGTTAG 59.567 55.000 10.22 0.00 39.64 2.34
1985 2185 1.550659 GCGGAGTGTTTCACGCGTTA 61.551 55.000 10.22 0.00 42.66 3.18
1986 2186 2.877974 GCGGAGTGTTTCACGCGTT 61.878 57.895 10.22 0.00 42.66 4.84
1987 2187 3.335534 GCGGAGTGTTTCACGCGT 61.336 61.111 5.58 5.58 42.66 6.01
1990 2190 2.317609 CCAGGCGGAGTGTTTCACG 61.318 63.158 0.00 0.00 39.64 4.35
1991 2191 1.966451 CCCAGGCGGAGTGTTTCAC 60.966 63.158 0.00 0.00 34.10 3.18
1992 2192 2.429930 CCCAGGCGGAGTGTTTCA 59.570 61.111 0.00 0.00 0.00 2.69
1993 2193 2.359975 CCCCAGGCGGAGTGTTTC 60.360 66.667 0.00 0.00 0.00 2.78
1994 2194 2.852075 TCCCCAGGCGGAGTGTTT 60.852 61.111 0.00 0.00 0.00 2.83
1995 2195 3.322466 CTCCCCAGGCGGAGTGTT 61.322 66.667 13.50 0.00 43.94 3.32
2002 2202 3.834799 GACCGTACTCCCCAGGCG 61.835 72.222 0.00 0.00 0.00 5.52
2003 2203 3.834799 CGACCGTACTCCCCAGGC 61.835 72.222 0.00 0.00 0.00 4.85
2004 2204 3.834799 GCGACCGTACTCCCCAGG 61.835 72.222 0.00 0.00 0.00 4.45
2005 2205 2.558554 CTTGCGACCGTACTCCCCAG 62.559 65.000 0.00 0.00 0.00 4.45
2006 2206 2.601067 TTGCGACCGTACTCCCCA 60.601 61.111 0.00 0.00 0.00 4.96
2007 2207 2.183555 CTTGCGACCGTACTCCCC 59.816 66.667 0.00 0.00 0.00 4.81
2008 2208 1.153881 GTCTTGCGACCGTACTCCC 60.154 63.158 0.00 0.00 33.98 4.30
2009 2209 4.472702 GTCTTGCGACCGTACTCC 57.527 61.111 0.00 0.00 33.98 3.85
2017 2217 1.214367 TTGAGTTTCGGTCTTGCGAC 58.786 50.000 0.00 0.00 39.49 5.19
2018 2218 1.942677 TTTGAGTTTCGGTCTTGCGA 58.057 45.000 0.00 0.00 0.00 5.10
2019 2219 2.748461 TTTTGAGTTTCGGTCTTGCG 57.252 45.000 0.00 0.00 0.00 4.85
2037 2237 1.826340 GCAGGCCCCCGTCAATTTTT 61.826 55.000 0.00 0.00 0.00 1.94
2038 2238 2.282783 GCAGGCCCCCGTCAATTTT 61.283 57.895 0.00 0.00 0.00 1.82
2039 2239 2.679996 GCAGGCCCCCGTCAATTT 60.680 61.111 0.00 0.00 0.00 1.82
2040 2240 3.978193 TGCAGGCCCCCGTCAATT 61.978 61.111 0.00 0.00 0.00 2.32
2041 2241 4.740822 GTGCAGGCCCCCGTCAAT 62.741 66.667 0.00 0.00 0.00 2.57
2052 2252 3.357079 GTCCACCGCTTGTGCAGG 61.357 66.667 0.00 0.00 44.01 4.85
2053 2253 3.357079 GGTCCACCGCTTGTGCAG 61.357 66.667 0.00 0.00 44.01 4.41
2054 2254 4.947147 GGGTCCACCGCTTGTGCA 62.947 66.667 0.00 0.00 44.01 4.57
2063 2263 2.584608 CTCATGGTCGGGTCCACC 59.415 66.667 0.00 0.00 40.51 4.61
2064 2264 2.125106 GCTCATGGTCGGGTCCAC 60.125 66.667 0.00 0.00 40.51 4.02
2065 2265 3.399181 GGCTCATGGTCGGGTCCA 61.399 66.667 0.00 0.00 42.01 4.02
2066 2266 4.176752 GGGCTCATGGTCGGGTCC 62.177 72.222 0.00 0.00 0.00 4.46
2185 2386 1.147376 CCGGTTCACCAGGTTGACA 59.853 57.895 0.00 0.00 35.14 3.58
2248 2449 4.818863 TCGACGATGGGCCGGGTA 62.819 66.667 2.18 0.00 0.00 3.69
2406 2607 0.531200 CCACTGGAGTCCGAGGTTAC 59.469 60.000 4.30 0.00 0.00 2.50
2407 2608 0.113776 ACCACTGGAGTCCGAGGTTA 59.886 55.000 12.76 0.00 0.00 2.85
2408 2609 1.152312 ACCACTGGAGTCCGAGGTT 60.152 57.895 12.76 0.61 0.00 3.50
2409 2610 1.606889 GACCACTGGAGTCCGAGGT 60.607 63.158 17.14 17.14 0.00 3.85
2415 2616 1.606889 AGGGACGACCACTGGAGTC 60.607 63.158 15.51 15.51 43.89 3.36
2416 2617 1.908793 CAGGGACGACCACTGGAGT 60.909 63.158 6.20 1.18 43.89 3.85
2417 2618 2.973899 CAGGGACGACCACTGGAG 59.026 66.667 6.20 0.00 43.89 3.86
2420 2621 2.343758 CACCAGGGACGACCACTG 59.656 66.667 6.20 10.31 43.89 3.66
2558 2781 3.008157 TGAACATAACATACGTGGGTGGT 59.992 43.478 0.00 0.00 0.00 4.16
2560 2783 3.372822 GGTGAACATAACATACGTGGGTG 59.627 47.826 0.00 0.00 0.00 4.61
2566 2789 6.583912 CCTAACTGGTGAACATAACATACG 57.416 41.667 0.00 0.00 0.00 3.06
2589 2814 5.298083 CAACATACGCATCGATCGATTAAC 58.702 41.667 27.45 18.00 31.62 2.01
2633 2859 9.679661 TCTTGCCATTATGTGAGAAATAAAGTA 57.320 29.630 0.00 0.00 0.00 2.24
2853 3079 3.638627 TGCTCTCAACTCTGAAACTCTCA 59.361 43.478 0.00 0.00 0.00 3.27
2887 3113 5.067936 CCTACACATTGAGTCGGATAGTTCT 59.932 44.000 0.00 0.00 0.00 3.01
2951 3177 2.352127 CGGCAGAGATGATTGCTATCGA 60.352 50.000 3.70 0.00 40.15 3.59
2952 3178 1.991264 CGGCAGAGATGATTGCTATCG 59.009 52.381 3.70 0.00 40.15 2.92
3174 3400 7.927048 ACGAGTTCTAGCAACAAACTTTATTT 58.073 30.769 0.00 0.00 33.54 1.40
3291 3517 3.615110 CGCTCTATCTGTGGCCGAATTAT 60.615 47.826 0.00 0.00 0.00 1.28
3316 3542 1.428448 TGGAGCGTCACGATTCAAAG 58.572 50.000 0.00 0.00 23.78 2.77
3334 3560 1.898472 TCCACTCTGGCTTCTCTCTTG 59.102 52.381 0.00 0.00 37.47 3.02
3342 3568 2.437359 GCGCATCCACTCTGGCTT 60.437 61.111 0.30 0.00 37.47 4.35
3406 3632 4.402793 GCGAAGGATATATGGAAGGAGCTA 59.597 45.833 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.