Multiple sequence alignment - TraesCS2B01G476700

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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 TraesCS2B01G476700 chr2B 100.000 2472 0 0 1 2472 673706872 673709343 0.000000e+00 4566
1 TraesCS2B01G476700 chr2B 91.038 212 15 4 1807 2018 547230473 547230680 1.450000e-72 283
2 TraesCS2B01G476700 chr2D 92.631 1167 71 10 645 1803 563142524 563143683 0.000000e+00 1664
3 TraesCS2B01G476700 chr2D 87.111 450 35 13 2019 2458 563143677 563144113 2.860000e-134 488
4 TraesCS2B01G476700 chr2A 92.545 1167 71 9 645 1803 703545421 703546579 0.000000e+00 1659
5 TraesCS2B01G476700 chr2A 85.934 455 34 10 2019 2458 703546573 703547012 2.240000e-125 459
6 TraesCS2B01G476700 chr5B 95.672 647 26 2 1 645 276898071 276897425 0.000000e+00 1038
7 TraesCS2B01G476700 chr5B 94.729 664 31 4 1 660 558705869 558705206 0.000000e+00 1029
8 TraesCS2B01G476700 chr5B 95.209 647 29 2 1 645 445178970 445179616 0.000000e+00 1022
9 TraesCS2B01G476700 chr5B 92.453 212 12 4 1808 2018 316603113 316603321 1.440000e-77 300
10 TraesCS2B01G476700 chr5B 91.509 212 14 4 1808 2018 667824302 667824510 3.110000e-74 289
11 TraesCS2B01G476700 chr5B 91.121 214 13 5 1807 2018 622202830 622203039 4.020000e-73 285
12 TraesCS2B01G476700 chr7B 95.399 652 28 2 1 650 608187057 608187708 0.000000e+00 1037
13 TraesCS2B01G476700 chr7B 95.216 648 28 3 1 646 217303937 217303291 0.000000e+00 1022
14 TraesCS2B01G476700 chr7B 94.761 649 32 2 1 647 453114310 453114958 0.000000e+00 1009
15 TraesCS2B01G476700 chr4B 94.745 647 32 2 1 645 424285869 424285223 0.000000e+00 1005
16 TraesCS2B01G476700 chr4B 94.607 649 32 3 1 646 119336729 119336081 0.000000e+00 1002
17 TraesCS2B01G476700 chr4B 91.509 212 17 1 1807 2018 328323926 328323716 8.650000e-75 291
18 TraesCS2B01G476700 chr1B 94.737 646 32 2 2 645 330838449 330837804 0.000000e+00 1003
19 TraesCS2B01G476700 chr1B 92.093 215 13 4 1808 2020 161317574 161317362 1.440000e-77 300
20 TraesCS2B01G476700 chr6B 91.038 212 16 3 1808 2018 720142062 720142271 1.450000e-72 283
21 TraesCS2B01G476700 chr6B 90.278 216 16 4 1805 2018 636742729 636742941 6.730000e-71 278
22 TraesCS2B01G476700 chr3B 90.698 215 15 5 1807 2019 735228032 735227821 5.200000e-72 281


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 TraesCS2B01G476700 chr2B 673706872 673709343 2471 False 4566 4566 100.0000 1 2472 1 chr2B.!!$F2 2471
1 TraesCS2B01G476700 chr2D 563142524 563144113 1589 False 1076 1664 89.8710 645 2458 2 chr2D.!!$F1 1813
2 TraesCS2B01G476700 chr2A 703545421 703547012 1591 False 1059 1659 89.2395 645 2458 2 chr2A.!!$F1 1813
3 TraesCS2B01G476700 chr5B 276897425 276898071 646 True 1038 1038 95.6720 1 645 1 chr5B.!!$R1 644
4 TraesCS2B01G476700 chr5B 558705206 558705869 663 True 1029 1029 94.7290 1 660 1 chr5B.!!$R2 659
5 TraesCS2B01G476700 chr5B 445178970 445179616 646 False 1022 1022 95.2090 1 645 1 chr5B.!!$F2 644
6 TraesCS2B01G476700 chr7B 608187057 608187708 651 False 1037 1037 95.3990 1 650 1 chr7B.!!$F2 649
7 TraesCS2B01G476700 chr7B 217303291 217303937 646 True 1022 1022 95.2160 1 646 1 chr7B.!!$R1 645
8 TraesCS2B01G476700 chr7B 453114310 453114958 648 False 1009 1009 94.7610 1 647 1 chr7B.!!$F1 646
9 TraesCS2B01G476700 chr4B 424285223 424285869 646 True 1005 1005 94.7450 1 645 1 chr4B.!!$R3 644
10 TraesCS2B01G476700 chr4B 119336081 119336729 648 True 1002 1002 94.6070 1 646 1 chr4B.!!$R1 645
11 TraesCS2B01G476700 chr1B 330837804 330838449 645 True 1003 1003 94.7370 2 645 1 chr1B.!!$R2 643

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
884 891 0.252375 AAAGTACGCCACCCTCCCTA 60.252 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1857 0.107508 ATGAAGTGGGAGCACGGATG 60.108 55.0 0.0 0.0 0.0 3.51 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
108 110 3.083997 GGGGCGTGGTGGATCTCT 61.084 66.667 0.00 0.00 0.00 3.10
149 151 4.902448 GGCTTCGTTTTTAGTCGTTTCTTC 59.098 41.667 0.00 0.00 0.00 2.87
150 152 5.277202 GGCTTCGTTTTTAGTCGTTTCTTCT 60.277 40.000 0.00 0.00 0.00 2.85
171 173 5.442391 TCTAGTTTTGCTAGGGTTTGTGTT 58.558 37.500 0.00 0.00 45.55 3.32
174 176 4.709886 AGTTTTGCTAGGGTTTGTGTTCTT 59.290 37.500 0.00 0.00 0.00 2.52
195 197 4.117661 AGGAAGACGAGACGGCGC 62.118 66.667 6.90 0.00 41.28 6.53
226 228 4.101741 CGGAAGATGGAATAAAGGTCTCCT 59.898 45.833 0.00 0.00 33.87 3.69
306 308 1.613925 CTCCGGCGGATCTATCTTTGA 59.386 52.381 31.23 1.63 0.00 2.69
393 395 7.013750 TCTGATCTACGTTATTCTTCATCTGCT 59.986 37.037 0.00 0.00 0.00 4.24
718 724 2.302587 TTTTCGAAGGGCTGGGAAAT 57.697 45.000 0.00 0.00 0.00 2.17
737 743 7.605691 TGGGAAATGCCAACTTTATTGTTTATG 59.394 33.333 0.00 0.00 38.95 1.90
884 891 0.252375 AAAGTACGCCACCCTCCCTA 60.252 55.000 0.00 0.00 0.00 3.53
891 898 3.320129 ACGCCACCCTCCCTAATATAAA 58.680 45.455 0.00 0.00 0.00 1.40
928 935 1.591280 TACTCTCCTCCCCCACTCCC 61.591 65.000 0.00 0.00 0.00 4.30
943 950 3.118592 CCACTCCCTTCAGTCATTCCTAC 60.119 52.174 0.00 0.00 0.00 3.18
966 973 7.446001 ACCTGAAAAGAAAGAGAAGCATTAG 57.554 36.000 0.00 0.00 0.00 1.73
1059 1067 1.550524 CACTCCGTCTCTCCCATCAAA 59.449 52.381 0.00 0.00 0.00 2.69
1063 1071 0.530744 CGTCTCTCCCATCAAACCGA 59.469 55.000 0.00 0.00 0.00 4.69
1166 1174 2.906389 ACTACCTGGACATCTGCTTCAA 59.094 45.455 0.00 0.00 0.00 2.69
1179 1187 2.633860 CTTCAACTGCCGGAAGCTT 58.366 52.632 10.27 0.00 44.23 3.74
1185 1193 3.939837 CTGCCGGAAGCTTCTCGCA 62.940 63.158 27.70 27.70 44.23 5.10
1188 1196 2.573869 CGGAAGCTTCTCGCAGGA 59.426 61.111 25.05 0.00 42.61 3.86
1241 1251 0.177141 GCTACTTGTCATACCGGCCA 59.823 55.000 0.00 0.00 0.00 5.36
1268 1278 2.439507 TCTCCTTTTTGTCACCTCTGCT 59.560 45.455 0.00 0.00 0.00 4.24
1269 1279 2.551459 CTCCTTTTTGTCACCTCTGCTG 59.449 50.000 0.00 0.00 0.00 4.41
1375 1385 2.238437 CGAGATCGACGAGGCGAGA 61.238 63.158 7.26 0.00 44.26 4.04
1487 1497 1.072332 TAGCAGCTTTCCGGCAACA 59.928 52.632 0.00 0.00 37.08 3.33
1524 1534 4.142227 GGATTTTCAGCAGCAGTTCATGAT 60.142 41.667 0.00 0.00 0.00 2.45
1554 1564 0.178767 TCGATGATGAGTTGGGCAGG 59.821 55.000 0.00 0.00 0.00 4.85
1611 1623 3.703127 GGGACGACCACCACCCTC 61.703 72.222 6.20 0.00 39.28 4.30
1617 1629 4.599500 ACCACCACCCTCCAGGCT 62.599 66.667 0.00 0.00 40.58 4.58
1655 1669 0.251354 ATGCTGTCTCTGAACCGCAT 59.749 50.000 12.40 12.40 42.81 4.73
1755 1769 1.862827 GTTCTTGTGTCGCGTAAGGTT 59.137 47.619 5.77 0.00 38.28 3.50
1756 1770 1.493772 TCTTGTGTCGCGTAAGGTTG 58.506 50.000 5.77 0.00 38.28 3.77
1757 1771 1.202440 TCTTGTGTCGCGTAAGGTTGT 60.202 47.619 5.77 0.00 38.28 3.32
1758 1772 2.034432 TCTTGTGTCGCGTAAGGTTGTA 59.966 45.455 5.77 0.00 38.28 2.41
1760 1774 1.337703 TGTGTCGCGTAAGGTTGTACT 59.662 47.619 5.77 0.00 38.28 2.73
1761 1775 2.551887 TGTGTCGCGTAAGGTTGTACTA 59.448 45.455 5.77 0.00 38.28 1.82
1762 1776 3.191162 TGTGTCGCGTAAGGTTGTACTAT 59.809 43.478 5.77 0.00 38.28 2.12
1763 1777 4.394610 TGTGTCGCGTAAGGTTGTACTATA 59.605 41.667 5.77 0.00 38.28 1.31
1784 1801 8.421784 ACTATAGCCTGTCGATATGAAAGAAAA 58.578 33.333 0.00 0.00 33.28 2.29
1786 1803 5.734720 AGCCTGTCGATATGAAAGAAAAGA 58.265 37.500 0.00 0.00 33.28 2.52
1803 1820 7.823745 AGAAAAGAGAGAGGCATAACAAAAA 57.176 32.000 0.00 0.00 0.00 1.94
1818 1835 2.976099 AAAAAGGGGATCCGGCTTG 58.024 52.632 5.45 0.00 38.33 4.01
1819 1836 0.614697 AAAAAGGGGATCCGGCTTGG 60.615 55.000 5.45 0.00 38.33 3.61
1820 1837 3.662117 AAAGGGGATCCGGCTTGGC 62.662 63.158 5.45 0.00 37.80 4.52
1822 1839 4.883354 GGGGATCCGGCTTGGCTG 62.883 72.222 5.45 0.00 37.80 4.85
1824 1841 4.496336 GGATCCGGCTTGGCTGCT 62.496 66.667 0.00 0.00 37.80 4.24
1825 1842 2.899339 GATCCGGCTTGGCTGCTC 60.899 66.667 0.00 0.00 37.80 4.26
1826 1843 4.496336 ATCCGGCTTGGCTGCTCC 62.496 66.667 0.00 0.00 37.80 4.70
1829 1846 4.729918 CGGCTTGGCTGCTCCCTT 62.730 66.667 0.00 0.00 0.00 3.95
1830 1847 2.753446 GGCTTGGCTGCTCCCTTC 60.753 66.667 0.00 0.00 0.00 3.46
1831 1848 2.753446 GCTTGGCTGCTCCCTTCC 60.753 66.667 0.00 0.00 0.00 3.46
1832 1849 3.085223 CTTGGCTGCTCCCTTCCT 58.915 61.111 0.00 0.00 0.00 3.36
1833 1850 1.915078 GCTTGGCTGCTCCCTTCCTA 61.915 60.000 0.00 0.00 0.00 2.94
1834 1851 0.842635 CTTGGCTGCTCCCTTCCTAT 59.157 55.000 0.00 0.00 0.00 2.57
1835 1852 0.548031 TTGGCTGCTCCCTTCCTATG 59.452 55.000 0.00 0.00 0.00 2.23
1836 1853 1.228094 GGCTGCTCCCTTCCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
1837 1854 1.704007 GGCTGCTCCCTTCCTATGCT 61.704 60.000 0.00 0.00 0.00 3.79
1838 1855 0.250252 GCTGCTCCCTTCCTATGCTC 60.250 60.000 0.00 0.00 0.00 4.26
1839 1856 0.396060 CTGCTCCCTTCCTATGCTCC 59.604 60.000 0.00 0.00 0.00 4.70
1840 1857 1.056700 TGCTCCCTTCCTATGCTCCC 61.057 60.000 0.00 0.00 0.00 4.30
1841 1858 1.056700 GCTCCCTTCCTATGCTCCCA 61.057 60.000 0.00 0.00 0.00 4.37
1842 1859 1.739750 CTCCCTTCCTATGCTCCCAT 58.260 55.000 0.00 0.00 35.44 4.00
1843 1860 1.627834 CTCCCTTCCTATGCTCCCATC 59.372 57.143 0.00 0.00 32.85 3.51
1844 1861 0.695347 CCCTTCCTATGCTCCCATCC 59.305 60.000 0.00 0.00 32.85 3.51
1845 1862 0.322975 CCTTCCTATGCTCCCATCCG 59.677 60.000 0.00 0.00 32.85 4.18
1846 1863 1.051812 CTTCCTATGCTCCCATCCGT 58.948 55.000 0.00 0.00 32.85 4.69
1847 1864 0.758734 TTCCTATGCTCCCATCCGTG 59.241 55.000 0.00 0.00 32.85 4.94
1848 1865 1.302033 CCTATGCTCCCATCCGTGC 60.302 63.158 0.00 0.00 32.85 5.34
1849 1866 1.750930 CTATGCTCCCATCCGTGCT 59.249 57.895 0.00 0.00 32.85 4.40
1850 1867 0.320247 CTATGCTCCCATCCGTGCTC 60.320 60.000 0.00 0.00 32.85 4.26
1851 1868 1.758440 TATGCTCCCATCCGTGCTCC 61.758 60.000 0.00 0.00 32.85 4.70
1852 1869 4.554036 GCTCCCATCCGTGCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
1853 1870 3.083349 CTCCCATCCGTGCTCCCA 61.083 66.667 0.00 0.00 0.00 4.37
1854 1871 3.391665 CTCCCATCCGTGCTCCCAC 62.392 68.421 0.00 0.00 38.62 4.61
1855 1872 3.402681 CCCATCCGTGCTCCCACT 61.403 66.667 0.00 0.00 39.86 4.00
1856 1873 2.671070 CCATCCGTGCTCCCACTT 59.329 61.111 0.00 0.00 39.86 3.16
1857 1874 1.450312 CCATCCGTGCTCCCACTTC 60.450 63.158 0.00 0.00 39.86 3.01
1858 1875 1.296392 CATCCGTGCTCCCACTTCA 59.704 57.895 0.00 0.00 39.86 3.02
1859 1876 0.107508 CATCCGTGCTCCCACTTCAT 60.108 55.000 0.00 0.00 39.86 2.57
1860 1877 0.179000 ATCCGTGCTCCCACTTCATC 59.821 55.000 0.00 0.00 39.86 2.92
1861 1878 1.450312 CCGTGCTCCCACTTCATCC 60.450 63.158 0.00 0.00 39.86 3.51
1862 1879 1.599047 CGTGCTCCCACTTCATCCT 59.401 57.895 0.00 0.00 39.86 3.24
1863 1880 0.824109 CGTGCTCCCACTTCATCCTA 59.176 55.000 0.00 0.00 39.86 2.94
1864 1881 1.471676 CGTGCTCCCACTTCATCCTAC 60.472 57.143 0.00 0.00 39.86 3.18
1865 1882 1.555075 GTGCTCCCACTTCATCCTACA 59.445 52.381 0.00 0.00 38.93 2.74
1866 1883 1.833630 TGCTCCCACTTCATCCTACAG 59.166 52.381 0.00 0.00 0.00 2.74
1867 1884 1.474143 GCTCCCACTTCATCCTACAGC 60.474 57.143 0.00 0.00 0.00 4.40
1868 1885 2.114616 CTCCCACTTCATCCTACAGCT 58.885 52.381 0.00 0.00 0.00 4.24
1869 1886 1.833630 TCCCACTTCATCCTACAGCTG 59.166 52.381 13.48 13.48 0.00 4.24
1870 1887 1.556911 CCCACTTCATCCTACAGCTGT 59.443 52.381 25.12 25.12 0.00 4.40
1871 1888 2.419297 CCCACTTCATCCTACAGCTGTC 60.419 54.545 25.56 0.00 0.00 3.51
1872 1889 2.499289 CCACTTCATCCTACAGCTGTCT 59.501 50.000 25.56 1.44 0.00 3.41
1873 1890 3.055530 CCACTTCATCCTACAGCTGTCTT 60.056 47.826 25.56 0.54 0.00 3.01
1874 1891 4.564406 CCACTTCATCCTACAGCTGTCTTT 60.564 45.833 25.56 4.03 0.00 2.52
1875 1892 4.999950 CACTTCATCCTACAGCTGTCTTTT 59.000 41.667 25.56 4.43 0.00 2.27
1876 1893 5.471456 CACTTCATCCTACAGCTGTCTTTTT 59.529 40.000 25.56 2.84 0.00 1.94
1877 1894 5.703130 ACTTCATCCTACAGCTGTCTTTTTC 59.297 40.000 25.56 0.00 0.00 2.29
1878 1895 4.579869 TCATCCTACAGCTGTCTTTTTCC 58.420 43.478 25.56 0.00 0.00 3.13
1879 1896 4.287067 TCATCCTACAGCTGTCTTTTTCCT 59.713 41.667 25.56 0.00 0.00 3.36
1880 1897 4.706842 TCCTACAGCTGTCTTTTTCCTT 57.293 40.909 25.56 0.00 0.00 3.36
1881 1898 5.048846 TCCTACAGCTGTCTTTTTCCTTT 57.951 39.130 25.56 0.00 0.00 3.11
1882 1899 5.445964 TCCTACAGCTGTCTTTTTCCTTTT 58.554 37.500 25.56 0.00 0.00 2.27
1883 1900 5.531287 TCCTACAGCTGTCTTTTTCCTTTTC 59.469 40.000 25.56 0.00 0.00 2.29
1884 1901 5.532779 CCTACAGCTGTCTTTTTCCTTTTCT 59.467 40.000 25.56 0.00 0.00 2.52
1885 1902 5.921962 ACAGCTGTCTTTTTCCTTTTCTT 57.078 34.783 15.25 0.00 0.00 2.52
1886 1903 6.286240 ACAGCTGTCTTTTTCCTTTTCTTT 57.714 33.333 15.25 0.00 0.00 2.52
1887 1904 6.701340 ACAGCTGTCTTTTTCCTTTTCTTTT 58.299 32.000 15.25 0.00 0.00 2.27
1888 1905 7.161404 ACAGCTGTCTTTTTCCTTTTCTTTTT 58.839 30.769 15.25 0.00 0.00 1.94
1889 1906 7.331934 ACAGCTGTCTTTTTCCTTTTCTTTTTC 59.668 33.333 15.25 0.00 0.00 2.29
1890 1907 7.547019 CAGCTGTCTTTTTCCTTTTCTTTTTCT 59.453 33.333 5.25 0.00 0.00 2.52
1891 1908 8.749354 AGCTGTCTTTTTCCTTTTCTTTTTCTA 58.251 29.630 0.00 0.00 0.00 2.10
1892 1909 9.366216 GCTGTCTTTTTCCTTTTCTTTTTCTAA 57.634 29.630 0.00 0.00 0.00 2.10
1922 1939 9.859152 AATTATCTCCCTCTCTTGATTTTAAGG 57.141 33.333 0.00 0.00 0.00 2.69
1923 1940 5.700402 TCTCCCTCTCTTGATTTTAAGGG 57.300 43.478 0.00 0.00 44.06 3.95
1924 1941 4.475016 TCTCCCTCTCTTGATTTTAAGGGG 59.525 45.833 5.46 0.00 43.10 4.79
1925 1942 3.527665 TCCCTCTCTTGATTTTAAGGGGG 59.472 47.826 5.46 0.00 43.10 5.40
1926 1943 3.269643 CCCTCTCTTGATTTTAAGGGGGT 59.730 47.826 0.00 0.00 39.87 4.95
1927 1944 4.273318 CCTCTCTTGATTTTAAGGGGGTG 58.727 47.826 0.00 0.00 25.80 4.61
1928 1945 4.273318 CTCTCTTGATTTTAAGGGGGTGG 58.727 47.826 0.00 0.00 0.00 4.61
1929 1946 3.011257 TCTCTTGATTTTAAGGGGGTGGG 59.989 47.826 0.00 0.00 0.00 4.61
1930 1947 2.043801 TCTTGATTTTAAGGGGGTGGGG 59.956 50.000 0.00 0.00 0.00 4.96
1931 1948 1.473550 TGATTTTAAGGGGGTGGGGT 58.526 50.000 0.00 0.00 0.00 4.95
1932 1949 1.359818 TGATTTTAAGGGGGTGGGGTC 59.640 52.381 0.00 0.00 0.00 4.46
1933 1950 0.333652 ATTTTAAGGGGGTGGGGTCG 59.666 55.000 0.00 0.00 0.00 4.79
1934 1951 1.791695 TTTTAAGGGGGTGGGGTCGG 61.792 60.000 0.00 0.00 0.00 4.79
1935 1952 4.745013 TAAGGGGGTGGGGTCGGG 62.745 72.222 0.00 0.00 0.00 5.14
1940 1957 3.332385 GGGTGGGGTCGGGCTTTA 61.332 66.667 0.00 0.00 0.00 1.85
1941 1958 2.686572 GGGTGGGGTCGGGCTTTAT 61.687 63.158 0.00 0.00 0.00 1.40
1942 1959 1.305287 GGTGGGGTCGGGCTTTATT 59.695 57.895 0.00 0.00 0.00 1.40
1943 1960 0.323999 GGTGGGGTCGGGCTTTATTT 60.324 55.000 0.00 0.00 0.00 1.40
1944 1961 1.552578 GTGGGGTCGGGCTTTATTTT 58.447 50.000 0.00 0.00 0.00 1.82
1945 1962 1.203758 GTGGGGTCGGGCTTTATTTTG 59.796 52.381 0.00 0.00 0.00 2.44
1946 1963 1.203075 TGGGGTCGGGCTTTATTTTGT 60.203 47.619 0.00 0.00 0.00 2.83
1947 1964 1.897133 GGGGTCGGGCTTTATTTTGTT 59.103 47.619 0.00 0.00 0.00 2.83
1948 1965 2.094390 GGGGTCGGGCTTTATTTTGTTC 60.094 50.000 0.00 0.00 0.00 3.18
1949 1966 2.094390 GGGTCGGGCTTTATTTTGTTCC 60.094 50.000 0.00 0.00 0.00 3.62
1950 1967 2.559231 GGTCGGGCTTTATTTTGTTCCA 59.441 45.455 0.00 0.00 0.00 3.53
1951 1968 3.006003 GGTCGGGCTTTATTTTGTTCCAA 59.994 43.478 0.00 0.00 0.00 3.53
1952 1969 4.322424 GGTCGGGCTTTATTTTGTTCCAAT 60.322 41.667 0.00 0.00 0.00 3.16
1953 1970 4.862574 GTCGGGCTTTATTTTGTTCCAATC 59.137 41.667 0.00 0.00 0.00 2.67
1954 1971 4.524714 TCGGGCTTTATTTTGTTCCAATCA 59.475 37.500 0.00 0.00 0.00 2.57
1955 1972 5.011125 TCGGGCTTTATTTTGTTCCAATCAA 59.989 36.000 0.00 0.00 0.00 2.57
1956 1973 5.698545 CGGGCTTTATTTTGTTCCAATCAAA 59.301 36.000 0.00 0.00 33.76 2.69
1957 1974 6.203723 CGGGCTTTATTTTGTTCCAATCAAAA 59.796 34.615 6.34 6.34 44.83 2.44
1958 1975 7.359595 GGGCTTTATTTTGTTCCAATCAAAAC 58.640 34.615 6.07 0.00 44.00 2.43
1959 1976 7.012799 GGGCTTTATTTTGTTCCAATCAAAACA 59.987 33.333 6.07 0.00 44.00 2.83
1960 1977 8.401709 GGCTTTATTTTGTTCCAATCAAAACAA 58.598 29.630 6.07 0.00 44.00 2.83
1961 1978 9.437045 GCTTTATTTTGTTCCAATCAAAACAAG 57.563 29.630 6.07 10.98 43.86 3.16
1962 1979 9.437045 CTTTATTTTGTTCCAATCAAAACAAGC 57.563 29.630 6.07 0.00 43.86 4.01
1963 1980 5.809719 TTTTGTTCCAATCAAAACAAGCC 57.190 34.783 0.00 0.00 43.86 4.35
1964 1981 4.478206 TTGTTCCAATCAAAACAAGCCA 57.522 36.364 0.00 0.00 39.70 4.75
1965 1982 3.791245 TGTTCCAATCAAAACAAGCCAC 58.209 40.909 0.00 0.00 32.69 5.01
1966 1983 2.791383 TCCAATCAAAACAAGCCACG 57.209 45.000 0.00 0.00 0.00 4.94
1967 1984 2.028130 TCCAATCAAAACAAGCCACGT 58.972 42.857 0.00 0.00 0.00 4.49
1968 1985 3.215151 TCCAATCAAAACAAGCCACGTA 58.785 40.909 0.00 0.00 0.00 3.57
1969 1986 3.003897 TCCAATCAAAACAAGCCACGTAC 59.996 43.478 0.00 0.00 0.00 3.67
1970 1987 2.961522 ATCAAAACAAGCCACGTACG 57.038 45.000 15.01 15.01 0.00 3.67
1971 1988 0.305313 TCAAAACAAGCCACGTACGC 59.695 50.000 16.72 0.00 0.00 4.42
1972 1989 0.989805 CAAAACAAGCCACGTACGCG 60.990 55.000 16.72 3.53 44.93 6.01
1973 1990 2.108344 AAAACAAGCCACGTACGCGG 62.108 55.000 17.94 17.94 43.45 6.46
1975 1992 4.728102 CAAGCCACGTACGCGGGA 62.728 66.667 25.61 0.00 45.97 5.14
1976 1993 4.430765 AAGCCACGTACGCGGGAG 62.431 66.667 25.61 2.82 45.97 4.30
1988 2005 4.147449 CGGGAGCACGGATGAGCA 62.147 66.667 0.00 0.00 33.73 4.26
1989 2006 2.512515 GGGAGCACGGATGAGCAC 60.513 66.667 0.00 0.00 33.73 4.40
1990 2007 2.265739 GGAGCACGGATGAGCACA 59.734 61.111 0.00 0.00 33.73 4.57
1991 2008 2.103042 GGAGCACGGATGAGCACAC 61.103 63.158 0.00 0.00 33.73 3.82
1992 2009 2.433145 AGCACGGATGAGCACACG 60.433 61.111 0.00 0.00 33.73 4.49
1993 2010 3.490759 GCACGGATGAGCACACGG 61.491 66.667 0.00 0.00 0.00 4.94
1994 2011 3.490759 CACGGATGAGCACACGGC 61.491 66.667 0.00 0.00 45.30 5.68
2009 2026 4.785453 GGCGGGGGAGCTGTCAAG 62.785 72.222 0.00 0.00 37.29 3.02
2010 2027 4.021925 GCGGGGGAGCTGTCAAGT 62.022 66.667 0.00 0.00 0.00 3.16
2011 2028 2.266055 CGGGGGAGCTGTCAAGTC 59.734 66.667 0.00 0.00 0.00 3.01
2012 2029 2.286523 CGGGGGAGCTGTCAAGTCT 61.287 63.158 0.00 0.00 0.00 3.24
2013 2030 1.599576 GGGGGAGCTGTCAAGTCTC 59.400 63.158 0.00 0.00 0.00 3.36
2014 2031 1.216710 GGGGAGCTGTCAAGTCTCG 59.783 63.158 0.00 0.00 31.29 4.04
2015 2032 1.536943 GGGGAGCTGTCAAGTCTCGT 61.537 60.000 0.00 0.00 31.29 4.18
2016 2033 0.109039 GGGAGCTGTCAAGTCTCGTC 60.109 60.000 0.00 0.00 31.29 4.20
2017 2034 0.109039 GGAGCTGTCAAGTCTCGTCC 60.109 60.000 0.00 0.00 31.29 4.79
2018 2035 0.598562 GAGCTGTCAAGTCTCGTCCA 59.401 55.000 0.00 0.00 0.00 4.02
2019 2036 1.000163 GAGCTGTCAAGTCTCGTCCAA 60.000 52.381 0.00 0.00 0.00 3.53
2020 2037 1.140816 GCTGTCAAGTCTCGTCCAAC 58.859 55.000 0.00 0.00 0.00 3.77
2021 2038 1.538204 GCTGTCAAGTCTCGTCCAACA 60.538 52.381 0.00 0.00 0.00 3.33
2022 2039 2.821546 CTGTCAAGTCTCGTCCAACAA 58.178 47.619 0.00 0.00 0.00 2.83
2023 2040 3.194861 CTGTCAAGTCTCGTCCAACAAA 58.805 45.455 0.00 0.00 0.00 2.83
2024 2041 3.601435 TGTCAAGTCTCGTCCAACAAAA 58.399 40.909 0.00 0.00 0.00 2.44
2025 2042 3.621268 TGTCAAGTCTCGTCCAACAAAAG 59.379 43.478 0.00 0.00 0.00 2.27
2026 2043 3.002348 GTCAAGTCTCGTCCAACAAAAGG 59.998 47.826 0.00 0.00 0.00 3.11
2035 2052 1.160137 CCAACAAAAGGGCTCTCTCG 58.840 55.000 0.00 0.00 0.00 4.04
2044 2061 0.458716 GGGCTCTCTCGGTTTTCTCG 60.459 60.000 0.00 0.00 0.00 4.04
2046 2063 1.336980 GGCTCTCTCGGTTTTCTCGTT 60.337 52.381 0.00 0.00 0.00 3.85
2052 2069 4.276678 TCTCTCGGTTTTCTCGTTAGTTCA 59.723 41.667 0.00 0.00 0.00 3.18
2069 2086 4.381411 AGTTCAGCTGTGTTCTTTCCTAC 58.619 43.478 14.67 0.00 0.00 3.18
2072 2089 3.388024 TCAGCTGTGTTCTTTCCTACTGT 59.612 43.478 14.67 0.00 0.00 3.55
2073 2090 4.130118 CAGCTGTGTTCTTTCCTACTGTT 58.870 43.478 5.25 0.00 0.00 3.16
2074 2091 4.212214 CAGCTGTGTTCTTTCCTACTGTTC 59.788 45.833 5.25 0.00 0.00 3.18
2075 2092 3.498777 GCTGTGTTCTTTCCTACTGTTCC 59.501 47.826 0.00 0.00 0.00 3.62
2076 2093 4.703897 CTGTGTTCTTTCCTACTGTTCCA 58.296 43.478 0.00 0.00 0.00 3.53
2077 2094 5.304686 TGTGTTCTTTCCTACTGTTCCAT 57.695 39.130 0.00 0.00 0.00 3.41
2078 2095 5.063204 TGTGTTCTTTCCTACTGTTCCATG 58.937 41.667 0.00 0.00 0.00 3.66
2079 2096 4.072131 TGTTCTTTCCTACTGTTCCATGC 58.928 43.478 0.00 0.00 0.00 4.06
2082 2099 4.985538 TCTTTCCTACTGTTCCATGCTTT 58.014 39.130 0.00 0.00 0.00 3.51
2094 2111 1.546923 CCATGCTTTCATGCTTCCACA 59.453 47.619 0.03 0.00 46.69 4.17
2099 2116 7.898676 CATGCTTTCATGCTTCCACAGATGG 62.899 48.000 0.00 0.00 44.22 3.51
2181 2199 0.511221 CGAACACAATCGCCGTTCTT 59.489 50.000 0.00 0.00 37.48 2.52
2265 2290 2.422597 TGCCTGTTACTGTGTGCATAC 58.577 47.619 6.65 6.65 0.00 2.39
2285 2310 1.130054 AGCAAAGGCAGAGGACCAGA 61.130 55.000 0.00 0.00 44.61 3.86
2328 2353 1.086634 GGAGCAGAGCGCAGGTAAAG 61.087 60.000 11.47 0.00 46.13 1.85
2331 2356 0.670546 GCAGAGCGCAGGTAAAGTCA 60.671 55.000 11.47 0.00 39.88 3.41
2348 2373 4.059773 AGTCAGGAAAGTCCAGAGAGAT 57.940 45.455 0.00 0.00 39.61 2.75
2409 2438 7.439955 TGATAGCCGTGAACGAATTGTTATTAT 59.560 33.333 4.03 0.00 42.09 1.28
2458 2493 4.776743 CAAAGTAGTGTGCTCAACATGAC 58.223 43.478 0.00 0.00 41.97 3.06
2459 2494 4.342862 AAGTAGTGTGCTCAACATGACT 57.657 40.909 0.00 0.00 41.97 3.41
2460 2495 5.468540 AAGTAGTGTGCTCAACATGACTA 57.531 39.130 0.00 0.00 41.97 2.59
2461 2496 4.810790 AGTAGTGTGCTCAACATGACTAC 58.189 43.478 0.00 4.35 42.23 2.73
2462 2497 4.524714 AGTAGTGTGCTCAACATGACTACT 59.475 41.667 11.71 11.71 44.58 2.57
2463 2498 3.919216 AGTGTGCTCAACATGACTACTC 58.081 45.455 0.00 0.00 41.97 2.59
2464 2499 2.996621 GTGTGCTCAACATGACTACTCC 59.003 50.000 0.00 0.00 41.97 3.85
2465 2500 2.899900 TGTGCTCAACATGACTACTCCT 59.100 45.455 0.00 0.00 32.36 3.69
2466 2501 4.082190 GTGTGCTCAACATGACTACTCCTA 60.082 45.833 0.00 0.00 41.97 2.94
2467 2502 4.526650 TGTGCTCAACATGACTACTCCTAA 59.473 41.667 0.00 0.00 32.36 2.69
2468 2503 5.187772 TGTGCTCAACATGACTACTCCTAAT 59.812 40.000 0.00 0.00 32.36 1.73
2469 2504 6.379988 TGTGCTCAACATGACTACTCCTAATA 59.620 38.462 0.00 0.00 32.36 0.98
2470 2505 7.093509 TGTGCTCAACATGACTACTCCTAATAA 60.094 37.037 0.00 0.00 32.36 1.40
2471 2506 7.436673 GTGCTCAACATGACTACTCCTAATAAG 59.563 40.741 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 132 7.992180 AACTAGAAGAAACGACTAAAAACGA 57.008 32.000 0.00 0.00 0.00 3.85
149 151 5.531287 AGAACACAAACCCTAGCAAAACTAG 59.469 40.000 0.00 0.00 46.95 2.57
150 152 5.442391 AGAACACAAACCCTAGCAAAACTA 58.558 37.500 0.00 0.00 0.00 2.24
174 176 1.306642 GCCGTCTCGTCTTCCTGAGA 61.307 60.000 0.00 0.00 38.85 3.27
204 206 5.616270 GAGGAGACCTTTATTCCATCTTCC 58.384 45.833 0.00 0.00 31.76 3.46
226 228 2.757099 GGAACGGGGACTAGGCGA 60.757 66.667 0.00 0.00 0.00 5.54
253 255 1.819632 GCCCACCAACGATGCTAGG 60.820 63.158 0.00 0.00 0.00 3.02
306 308 1.414181 ACGAGATCCGAGCAAATCCAT 59.586 47.619 10.05 0.00 41.76 3.41
393 395 2.186160 CACCAGAACAGCAACCGCA 61.186 57.895 0.00 0.00 42.27 5.69
703 709 2.418083 GGCATTTCCCAGCCCTTCG 61.418 63.158 0.00 0.00 45.18 3.79
718 724 5.157781 GCGACATAAACAATAAAGTTGGCA 58.842 37.500 0.00 0.00 0.00 4.92
737 743 1.798813 CAGACTTTGTACTTGGGCGAC 59.201 52.381 0.00 0.00 0.00 5.19
794 800 2.359975 GCAAGGTTCTCCCGGTGG 60.360 66.667 0.00 0.00 38.74 4.61
898 905 0.472471 AGGAGAGTAGAGAGGCGAGG 59.528 60.000 0.00 0.00 0.00 4.63
904 911 1.133606 GTGGGGGAGGAGAGTAGAGAG 60.134 61.905 0.00 0.00 0.00 3.20
928 935 6.467677 TCTTTTCAGGTAGGAATGACTGAAG 58.532 40.000 0.00 0.00 46.74 3.02
943 950 6.072286 TGCTAATGCTTCTCTTTCTTTTCAGG 60.072 38.462 0.00 0.00 40.48 3.86
966 973 4.319839 GGAGTAGTTTCTTCTGCAAACTGC 60.320 45.833 10.33 9.08 42.73 4.40
1166 1174 2.262915 CGAGAAGCTTCCGGCAGT 59.737 61.111 22.81 2.82 44.79 4.40
1179 1187 2.613026 TGTCTTTGTTTCCTGCGAGA 57.387 45.000 0.00 0.00 0.00 4.04
1185 1193 6.998074 TGTACATGAAGATGTCTTTGTTTCCT 59.002 34.615 0.00 0.00 42.14 3.36
1188 1196 6.772716 ACCTGTACATGAAGATGTCTTTGTTT 59.227 34.615 0.00 0.00 42.14 2.83
1241 1251 5.250313 AGAGGTGACAAAAAGGAGAGATCAT 59.750 40.000 0.00 0.00 0.00 2.45
1268 1278 4.582869 CCACCATCAGAGACAATTCTTCA 58.417 43.478 0.00 0.00 29.47 3.02
1269 1279 3.376546 GCCACCATCAGAGACAATTCTTC 59.623 47.826 0.00 0.00 29.47 2.87
1375 1385 1.098869 TCTGATTCGAGCGCTTCTCT 58.901 50.000 13.26 0.00 39.70 3.10
1384 1394 1.736586 CCTCCCGGTCTGATTCGAG 59.263 63.158 0.00 0.00 0.00 4.04
1487 1497 3.816523 TGAAAATCCTACGTTTCGGCTTT 59.183 39.130 0.00 0.00 36.69 3.51
1494 1504 3.146066 TGCTGCTGAAAATCCTACGTTT 58.854 40.909 0.00 0.00 0.00 3.60
1524 1534 4.318332 ACTCATCATCGAGCTTTTGTTCA 58.682 39.130 0.00 0.00 36.42 3.18
1525 1535 4.935885 ACTCATCATCGAGCTTTTGTTC 57.064 40.909 0.00 0.00 36.42 3.18
1526 1536 4.083110 CCAACTCATCATCGAGCTTTTGTT 60.083 41.667 0.00 0.00 36.42 2.83
1554 1564 2.484594 GCTTCCCTCAACTGGATCTAGC 60.485 54.545 5.91 0.00 0.00 3.42
1755 1769 7.664318 TCTTTCATATCGACAGGCTATAGTACA 59.336 37.037 0.84 0.00 0.00 2.90
1756 1770 8.041829 TCTTTCATATCGACAGGCTATAGTAC 57.958 38.462 0.84 0.00 0.00 2.73
1757 1771 8.631480 TTCTTTCATATCGACAGGCTATAGTA 57.369 34.615 0.84 0.00 0.00 1.82
1758 1772 7.526142 TTCTTTCATATCGACAGGCTATAGT 57.474 36.000 0.84 0.00 0.00 2.12
1760 1774 8.638873 TCTTTTCTTTCATATCGACAGGCTATA 58.361 33.333 0.00 0.00 0.00 1.31
1761 1775 7.500992 TCTTTTCTTTCATATCGACAGGCTAT 58.499 34.615 0.00 0.00 0.00 2.97
1762 1776 6.873997 TCTTTTCTTTCATATCGACAGGCTA 58.126 36.000 0.00 0.00 0.00 3.93
1763 1777 5.734720 TCTTTTCTTTCATATCGACAGGCT 58.265 37.500 0.00 0.00 0.00 4.58
1803 1820 4.129148 GCCAAGCCGGATCCCCTT 62.129 66.667 5.05 6.33 36.56 3.95
1805 1822 4.883354 CAGCCAAGCCGGATCCCC 62.883 72.222 5.05 0.00 36.56 4.81
1807 1824 4.496336 AGCAGCCAAGCCGGATCC 62.496 66.667 5.05 0.00 36.56 3.36
1808 1825 2.899339 GAGCAGCCAAGCCGGATC 60.899 66.667 5.05 0.00 36.56 3.36
1809 1826 4.496336 GGAGCAGCCAAGCCGGAT 62.496 66.667 5.05 0.00 36.56 4.18
1812 1829 4.729918 AAGGGAGCAGCCAAGCCG 62.730 66.667 0.00 0.00 38.95 5.52
1813 1830 2.753446 GAAGGGAGCAGCCAAGCC 60.753 66.667 0.00 0.00 38.95 4.35
1814 1831 1.915078 TAGGAAGGGAGCAGCCAAGC 61.915 60.000 0.00 0.00 38.95 4.01
1815 1832 0.842635 ATAGGAAGGGAGCAGCCAAG 59.157 55.000 0.00 0.00 38.95 3.61
1816 1833 0.548031 CATAGGAAGGGAGCAGCCAA 59.452 55.000 0.00 0.00 38.95 4.52
1817 1834 1.987807 GCATAGGAAGGGAGCAGCCA 61.988 60.000 0.00 0.00 38.95 4.75
1818 1835 1.228094 GCATAGGAAGGGAGCAGCC 60.228 63.158 0.00 0.00 0.00 4.85
1819 1836 0.250252 GAGCATAGGAAGGGAGCAGC 60.250 60.000 0.00 0.00 0.00 5.25
1820 1837 0.396060 GGAGCATAGGAAGGGAGCAG 59.604 60.000 0.00 0.00 0.00 4.24
1821 1838 1.056700 GGGAGCATAGGAAGGGAGCA 61.057 60.000 0.00 0.00 0.00 4.26
1822 1839 1.056700 TGGGAGCATAGGAAGGGAGC 61.057 60.000 0.00 0.00 0.00 4.70
1823 1840 1.627834 GATGGGAGCATAGGAAGGGAG 59.372 57.143 0.00 0.00 0.00 4.30
1824 1841 1.734655 GATGGGAGCATAGGAAGGGA 58.265 55.000 0.00 0.00 0.00 4.20
1825 1842 0.695347 GGATGGGAGCATAGGAAGGG 59.305 60.000 0.00 0.00 0.00 3.95
1826 1843 0.322975 CGGATGGGAGCATAGGAAGG 59.677 60.000 0.00 0.00 0.00 3.46
1827 1844 1.051812 ACGGATGGGAGCATAGGAAG 58.948 55.000 0.00 0.00 0.00 3.46
1828 1845 0.758734 CACGGATGGGAGCATAGGAA 59.241 55.000 0.00 0.00 0.00 3.36
1829 1846 1.758440 GCACGGATGGGAGCATAGGA 61.758 60.000 0.00 0.00 0.00 2.94
1830 1847 1.302033 GCACGGATGGGAGCATAGG 60.302 63.158 0.00 0.00 0.00 2.57
1831 1848 0.320247 GAGCACGGATGGGAGCATAG 60.320 60.000 0.00 0.00 0.00 2.23
1832 1849 1.748403 GAGCACGGATGGGAGCATA 59.252 57.895 0.00 0.00 0.00 3.14
1833 1850 2.507944 GAGCACGGATGGGAGCAT 59.492 61.111 0.00 0.00 0.00 3.79
1834 1851 3.785859 GGAGCACGGATGGGAGCA 61.786 66.667 0.00 0.00 0.00 4.26
1835 1852 4.554036 GGGAGCACGGATGGGAGC 62.554 72.222 0.00 0.00 0.00 4.70
1836 1853 3.083349 TGGGAGCACGGATGGGAG 61.083 66.667 0.00 0.00 0.00 4.30
1837 1854 3.399181 GTGGGAGCACGGATGGGA 61.399 66.667 0.00 0.00 0.00 4.37
1838 1855 2.876368 GAAGTGGGAGCACGGATGGG 62.876 65.000 0.00 0.00 0.00 4.00
1839 1856 1.450312 GAAGTGGGAGCACGGATGG 60.450 63.158 0.00 0.00 0.00 3.51
1840 1857 0.107508 ATGAAGTGGGAGCACGGATG 60.108 55.000 0.00 0.00 0.00 3.51
1841 1858 0.179000 GATGAAGTGGGAGCACGGAT 59.821 55.000 0.00 0.00 0.00 4.18
1842 1859 1.596934 GATGAAGTGGGAGCACGGA 59.403 57.895 0.00 0.00 0.00 4.69
1843 1860 1.450312 GGATGAAGTGGGAGCACGG 60.450 63.158 0.00 0.00 0.00 4.94
1844 1861 0.824109 TAGGATGAAGTGGGAGCACG 59.176 55.000 0.00 0.00 0.00 5.34
1845 1862 1.555075 TGTAGGATGAAGTGGGAGCAC 59.445 52.381 0.00 0.00 0.00 4.40
1846 1863 1.833630 CTGTAGGATGAAGTGGGAGCA 59.166 52.381 0.00 0.00 0.00 4.26
1847 1864 1.474143 GCTGTAGGATGAAGTGGGAGC 60.474 57.143 0.00 0.00 0.00 4.70
1848 1865 2.114616 AGCTGTAGGATGAAGTGGGAG 58.885 52.381 0.00 0.00 0.00 4.30
1849 1866 1.833630 CAGCTGTAGGATGAAGTGGGA 59.166 52.381 5.25 0.00 32.28 4.37
1850 1867 1.556911 ACAGCTGTAGGATGAAGTGGG 59.443 52.381 20.16 0.00 35.04 4.61
1851 1868 2.499289 AGACAGCTGTAGGATGAAGTGG 59.501 50.000 21.73 0.00 35.04 4.00
1852 1869 3.883830 AGACAGCTGTAGGATGAAGTG 57.116 47.619 21.73 0.00 35.04 3.16
1853 1870 4.899352 AAAGACAGCTGTAGGATGAAGT 57.101 40.909 21.73 0.00 35.04 3.01
1854 1871 5.123027 GGAAAAAGACAGCTGTAGGATGAAG 59.877 44.000 21.73 0.00 35.04 3.02
1855 1872 5.003804 GGAAAAAGACAGCTGTAGGATGAA 58.996 41.667 21.73 0.00 35.04 2.57
1856 1873 4.287067 AGGAAAAAGACAGCTGTAGGATGA 59.713 41.667 21.73 0.00 35.04 2.92
1857 1874 4.583871 AGGAAAAAGACAGCTGTAGGATG 58.416 43.478 21.73 0.00 37.36 3.51
1858 1875 4.917906 AGGAAAAAGACAGCTGTAGGAT 57.082 40.909 21.73 5.29 0.00 3.24
1859 1876 4.706842 AAGGAAAAAGACAGCTGTAGGA 57.293 40.909 21.73 0.00 0.00 2.94
1860 1877 5.532779 AGAAAAGGAAAAAGACAGCTGTAGG 59.467 40.000 21.73 0.00 0.00 3.18
1861 1878 6.625873 AGAAAAGGAAAAAGACAGCTGTAG 57.374 37.500 21.73 0.00 0.00 2.74
1862 1879 7.404671 AAAGAAAAGGAAAAAGACAGCTGTA 57.595 32.000 21.73 0.00 0.00 2.74
1863 1880 5.921962 AAGAAAAGGAAAAAGACAGCTGT 57.078 34.783 21.88 21.88 0.00 4.40
1864 1881 7.547019 AGAAAAAGAAAAGGAAAAAGACAGCTG 59.453 33.333 13.48 13.48 0.00 4.24
1865 1882 7.615403 AGAAAAAGAAAAGGAAAAAGACAGCT 58.385 30.769 0.00 0.00 0.00 4.24
1866 1883 7.834068 AGAAAAAGAAAAGGAAAAAGACAGC 57.166 32.000 0.00 0.00 0.00 4.40
1896 1913 9.859152 CCTTAAAATCAAGAGAGGGAGATAATT 57.141 33.333 0.00 0.00 0.00 1.40
1897 1914 8.443979 CCCTTAAAATCAAGAGAGGGAGATAAT 58.556 37.037 0.00 0.00 45.37 1.28
1898 1915 7.147302 CCCCTTAAAATCAAGAGAGGGAGATAA 60.147 40.741 7.79 0.00 45.37 1.75
1899 1916 6.330250 CCCCTTAAAATCAAGAGAGGGAGATA 59.670 42.308 7.79 0.00 45.37 1.98
1900 1917 5.133491 CCCCTTAAAATCAAGAGAGGGAGAT 59.867 44.000 7.79 0.00 45.37 2.75
1901 1918 4.475016 CCCCTTAAAATCAAGAGAGGGAGA 59.525 45.833 7.79 0.00 45.37 3.71
1902 1919 4.385754 CCCCCTTAAAATCAAGAGAGGGAG 60.386 50.000 7.79 0.00 45.37 4.30
1903 1920 3.527665 CCCCCTTAAAATCAAGAGAGGGA 59.472 47.826 7.79 0.00 45.37 4.20
1904 1921 3.269643 ACCCCCTTAAAATCAAGAGAGGG 59.730 47.826 0.00 0.00 42.79 4.30
1905 1922 4.273318 CACCCCCTTAAAATCAAGAGAGG 58.727 47.826 0.00 0.00 0.00 3.69
1906 1923 4.273318 CCACCCCCTTAAAATCAAGAGAG 58.727 47.826 0.00 0.00 0.00 3.20
1907 1924 3.011257 CCCACCCCCTTAAAATCAAGAGA 59.989 47.826 0.00 0.00 0.00 3.10
1908 1925 3.365472 CCCACCCCCTTAAAATCAAGAG 58.635 50.000 0.00 0.00 0.00 2.85
1909 1926 2.043801 CCCCACCCCCTTAAAATCAAGA 59.956 50.000 0.00 0.00 0.00 3.02
1910 1927 2.225522 ACCCCACCCCCTTAAAATCAAG 60.226 50.000 0.00 0.00 0.00 3.02
1911 1928 1.796415 ACCCCACCCCCTTAAAATCAA 59.204 47.619 0.00 0.00 0.00 2.57
1912 1929 1.359818 GACCCCACCCCCTTAAAATCA 59.640 52.381 0.00 0.00 0.00 2.57
1913 1930 1.683938 CGACCCCACCCCCTTAAAATC 60.684 57.143 0.00 0.00 0.00 2.17
1914 1931 0.333652 CGACCCCACCCCCTTAAAAT 59.666 55.000 0.00 0.00 0.00 1.82
1915 1932 1.769006 CGACCCCACCCCCTTAAAA 59.231 57.895 0.00 0.00 0.00 1.52
1916 1933 2.232836 CCGACCCCACCCCCTTAAA 61.233 63.158 0.00 0.00 0.00 1.52
1917 1934 2.611486 CCGACCCCACCCCCTTAA 60.611 66.667 0.00 0.00 0.00 1.85
1918 1935 4.745013 CCCGACCCCACCCCCTTA 62.745 72.222 0.00 0.00 0.00 2.69
1923 1940 2.219449 AATAAAGCCCGACCCCACCC 62.219 60.000 0.00 0.00 0.00 4.61
1924 1941 0.323999 AAATAAAGCCCGACCCCACC 60.324 55.000 0.00 0.00 0.00 4.61
1925 1942 1.203758 CAAAATAAAGCCCGACCCCAC 59.796 52.381 0.00 0.00 0.00 4.61
1926 1943 1.203075 ACAAAATAAAGCCCGACCCCA 60.203 47.619 0.00 0.00 0.00 4.96
1927 1944 1.552578 ACAAAATAAAGCCCGACCCC 58.447 50.000 0.00 0.00 0.00 4.95
1928 1945 2.094390 GGAACAAAATAAAGCCCGACCC 60.094 50.000 0.00 0.00 0.00 4.46
1929 1946 2.559231 TGGAACAAAATAAAGCCCGACC 59.441 45.455 0.00 0.00 31.92 4.79
1930 1947 3.926821 TGGAACAAAATAAAGCCCGAC 57.073 42.857 0.00 0.00 31.92 4.79
1944 1961 3.736433 CGTGGCTTGTTTTGATTGGAACA 60.736 43.478 0.00 0.00 34.22 3.18
1945 1962 2.794350 CGTGGCTTGTTTTGATTGGAAC 59.206 45.455 0.00 0.00 0.00 3.62
1946 1963 2.428890 ACGTGGCTTGTTTTGATTGGAA 59.571 40.909 0.00 0.00 0.00 3.53
1947 1964 2.028130 ACGTGGCTTGTTTTGATTGGA 58.972 42.857 0.00 0.00 0.00 3.53
1948 1965 2.507339 ACGTGGCTTGTTTTGATTGG 57.493 45.000 0.00 0.00 0.00 3.16
1949 1966 2.970609 CGTACGTGGCTTGTTTTGATTG 59.029 45.455 7.22 0.00 0.00 2.67
1950 1967 2.603652 GCGTACGTGGCTTGTTTTGATT 60.604 45.455 17.90 0.00 0.00 2.57
1951 1968 1.069500 GCGTACGTGGCTTGTTTTGAT 60.069 47.619 17.90 0.00 0.00 2.57
1952 1969 0.305313 GCGTACGTGGCTTGTTTTGA 59.695 50.000 17.90 0.00 0.00 2.69
1953 1970 0.989805 CGCGTACGTGGCTTGTTTTG 60.990 55.000 20.84 0.00 33.53 2.44
1954 1971 1.277440 CGCGTACGTGGCTTGTTTT 59.723 52.632 20.84 0.00 33.53 2.43
1955 1972 2.600475 CCGCGTACGTGGCTTGTTT 61.600 57.895 32.68 0.00 39.06 2.83
1956 1973 3.039588 CCGCGTACGTGGCTTGTT 61.040 61.111 32.68 0.00 39.06 2.83
1958 1975 4.728102 TCCCGCGTACGTGGCTTG 62.728 66.667 36.56 25.05 43.94 4.01
1959 1976 4.430765 CTCCCGCGTACGTGGCTT 62.431 66.667 36.56 0.00 43.94 4.35
1966 1983 4.203076 ATCCGTGCTCCCGCGTAC 62.203 66.667 4.92 0.00 43.11 3.67
1967 1984 4.201679 CATCCGTGCTCCCGCGTA 62.202 66.667 4.92 0.00 43.11 4.42
1971 1988 4.147449 TGCTCATCCGTGCTCCCG 62.147 66.667 0.00 0.00 32.76 5.14
1972 1989 2.512515 GTGCTCATCCGTGCTCCC 60.513 66.667 0.00 0.00 32.76 4.30
1973 1990 2.103042 GTGTGCTCATCCGTGCTCC 61.103 63.158 0.00 0.00 32.76 4.70
1974 1991 2.447887 CGTGTGCTCATCCGTGCTC 61.448 63.158 0.00 0.00 32.76 4.26
1975 1992 2.433145 CGTGTGCTCATCCGTGCT 60.433 61.111 0.00 0.00 32.76 4.40
1976 1993 3.490759 CCGTGTGCTCATCCGTGC 61.491 66.667 0.00 0.00 0.00 5.34
1977 1994 3.490759 GCCGTGTGCTCATCCGTG 61.491 66.667 0.00 0.00 36.87 4.94
1992 2009 4.785453 CTTGACAGCTCCCCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
1993 2010 3.959991 GACTTGACAGCTCCCCCGC 62.960 68.421 0.00 0.00 0.00 6.13
1994 2011 2.232298 GAGACTTGACAGCTCCCCCG 62.232 65.000 0.00 0.00 0.00 5.73
1995 2012 1.599576 GAGACTTGACAGCTCCCCC 59.400 63.158 0.00 0.00 0.00 5.40
1996 2013 1.216710 CGAGACTTGACAGCTCCCC 59.783 63.158 0.00 0.00 0.00 4.81
1997 2014 0.109039 GACGAGACTTGACAGCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
1998 2015 0.109039 GGACGAGACTTGACAGCTCC 60.109 60.000 0.00 0.00 0.00 4.70
1999 2016 0.598562 TGGACGAGACTTGACAGCTC 59.401 55.000 0.00 0.00 0.00 4.09
2000 2017 1.040646 TTGGACGAGACTTGACAGCT 58.959 50.000 0.00 0.00 0.00 4.24
2001 2018 1.140816 GTTGGACGAGACTTGACAGC 58.859 55.000 0.00 0.00 0.00 4.40
2002 2019 2.509052 TGTTGGACGAGACTTGACAG 57.491 50.000 0.00 0.00 0.00 3.51
2003 2020 2.971660 TTGTTGGACGAGACTTGACA 57.028 45.000 0.00 0.00 0.00 3.58
2004 2021 3.002348 CCTTTTGTTGGACGAGACTTGAC 59.998 47.826 0.00 0.00 0.00 3.18
2005 2022 3.202906 CCTTTTGTTGGACGAGACTTGA 58.797 45.455 0.00 0.00 0.00 3.02
2006 2023 2.290641 CCCTTTTGTTGGACGAGACTTG 59.709 50.000 0.00 0.00 0.00 3.16
2007 2024 2.572290 CCCTTTTGTTGGACGAGACTT 58.428 47.619 0.00 0.00 0.00 3.01
2008 2025 1.814248 GCCCTTTTGTTGGACGAGACT 60.814 52.381 0.00 0.00 0.00 3.24
2009 2026 0.591659 GCCCTTTTGTTGGACGAGAC 59.408 55.000 0.00 0.00 0.00 3.36
2010 2027 0.472471 AGCCCTTTTGTTGGACGAGA 59.528 50.000 0.00 0.00 0.00 4.04
2011 2028 0.875059 GAGCCCTTTTGTTGGACGAG 59.125 55.000 0.00 0.00 0.00 4.18
2012 2029 0.472471 AGAGCCCTTTTGTTGGACGA 59.528 50.000 0.00 0.00 0.00 4.20
2013 2030 0.875059 GAGAGCCCTTTTGTTGGACG 59.125 55.000 0.00 0.00 0.00 4.79
2014 2031 2.155279 GAGAGAGCCCTTTTGTTGGAC 58.845 52.381 0.00 0.00 0.00 4.02
2015 2032 1.270839 CGAGAGAGCCCTTTTGTTGGA 60.271 52.381 0.00 0.00 0.00 3.53
2016 2033 1.160137 CGAGAGAGCCCTTTTGTTGG 58.840 55.000 0.00 0.00 0.00 3.77
2017 2034 1.160137 CCGAGAGAGCCCTTTTGTTG 58.840 55.000 0.00 0.00 0.00 3.33
2018 2035 0.765510 ACCGAGAGAGCCCTTTTGTT 59.234 50.000 0.00 0.00 0.00 2.83
2019 2036 0.765510 AACCGAGAGAGCCCTTTTGT 59.234 50.000 0.00 0.00 0.00 2.83
2020 2037 1.897560 AAACCGAGAGAGCCCTTTTG 58.102 50.000 0.00 0.00 0.00 2.44
2021 2038 2.106684 AGAAAACCGAGAGAGCCCTTTT 59.893 45.455 0.00 0.00 0.00 2.27
2022 2039 1.700186 AGAAAACCGAGAGAGCCCTTT 59.300 47.619 0.00 0.00 0.00 3.11
2023 2040 1.276705 GAGAAAACCGAGAGAGCCCTT 59.723 52.381 0.00 0.00 0.00 3.95
2024 2041 0.899019 GAGAAAACCGAGAGAGCCCT 59.101 55.000 0.00 0.00 0.00 5.19
2025 2042 0.458716 CGAGAAAACCGAGAGAGCCC 60.459 60.000 0.00 0.00 0.00 5.19
2026 2043 0.244178 ACGAGAAAACCGAGAGAGCC 59.756 55.000 0.00 0.00 0.00 4.70
2035 2052 3.808174 ACAGCTGAACTAACGAGAAAACC 59.192 43.478 23.35 0.00 0.00 3.27
2044 2061 4.816925 AGGAAAGAACACAGCTGAACTAAC 59.183 41.667 23.35 6.51 0.00 2.34
2046 2063 4.689612 AGGAAAGAACACAGCTGAACTA 57.310 40.909 23.35 0.00 0.00 2.24
2052 2069 4.381411 GAACAGTAGGAAAGAACACAGCT 58.619 43.478 0.00 0.00 0.00 4.24
2076 2093 2.799017 TCTGTGGAAGCATGAAAGCAT 58.201 42.857 0.00 0.00 36.85 3.79
2077 2094 2.275134 TCTGTGGAAGCATGAAAGCA 57.725 45.000 0.00 0.00 36.85 3.91
2078 2095 3.146618 CATCTGTGGAAGCATGAAAGC 57.853 47.619 0.00 0.00 0.00 3.51
2104 2121 0.398696 TTGCGTCCACTGTTATGGGT 59.601 50.000 0.00 0.00 40.49 4.51
2106 2123 6.481976 TCTTAATATTGCGTCCACTGTTATGG 59.518 38.462 0.00 0.00 41.57 2.74
2265 2290 0.959372 CTGGTCCTCTGCCTTTGCTG 60.959 60.000 0.00 0.00 38.71 4.41
2270 2295 0.398318 GTTGTCTGGTCCTCTGCCTT 59.602 55.000 0.00 0.00 0.00 4.35
2285 2310 1.826487 GAACCAACAGGGCCGTTGT 60.826 57.895 27.29 14.60 43.89 3.32
2328 2353 5.186021 TGTTATCTCTCTGGACTTTCCTGAC 59.814 44.000 0.00 0.00 39.21 3.51
2331 2356 6.688073 TTTGTTATCTCTCTGGACTTTCCT 57.312 37.500 0.00 0.00 37.46 3.36
2348 2373 6.855763 AGAAATGGAAGGCATCATTTGTTA 57.144 33.333 14.28 0.00 41.80 2.41
2409 2438 5.804692 TCTTGTTGAAGCAAACGTCTAAA 57.195 34.783 0.00 0.00 32.47 1.85
2441 2473 4.082190 GGAGTAGTCATGTTGAGCACACTA 60.082 45.833 0.00 0.00 38.61 2.74


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

AutoCloner maintained by Alex Coulton.