Multiple sequence alignment - TraesCS1A01G085400

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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 TraesCS1A01G085400 chr1A 100.000 2417 0 0 1 2417 71549862 71547446 0.000000e+00 4464.0
1 TraesCS1A01G085400 chr1A 93.289 149 10 0 1087 1235 71548629 71548481 1.120000e-53 220.0
2 TraesCS1A01G085400 chr1A 93.289 149 10 0 1234 1382 71548776 71548628 1.120000e-53 220.0
3 TraesCS1A01G085400 chr1A 92.784 97 7 0 1894 1990 278527105 278527009 9.010000e-30 141.0
4 TraesCS1A01G085400 chr1A 93.443 61 4 0 1837 1897 554451162 554451102 9.200000e-15 91.6
5 TraesCS1A01G085400 chr1A 88.889 54 4 2 115 168 374273442 374273493 5.580000e-07 65.8
6 TraesCS1A01G085400 chr1B 94.229 1265 47 12 365 1614 112504968 112503715 0.000000e+00 1908.0
7 TraesCS1A01G085400 chr1B 91.463 246 14 3 126 368 112523973 112523732 4.980000e-87 331.0
8 TraesCS1A01G085400 chr1B 91.275 149 13 0 1087 1235 112504105 112503957 1.130000e-48 204.0
9 TraesCS1A01G085400 chr1B 95.082 61 3 0 1837 1897 218001066 218001126 1.980000e-16 97.1
10 TraesCS1A01G085400 chr1B 90.385 52 3 2 113 162 686882518 686882569 1.550000e-07 67.6
11 TraesCS1A01G085400 chr1D 94.413 698 28 4 695 1382 71037579 71036883 0.000000e+00 1062.0
12 TraesCS1A01G085400 chr1D 92.286 713 24 14 1 709 71038295 71037610 0.000000e+00 983.0
13 TraesCS1A01G085400 chr1D 93.939 528 24 4 1087 1607 71037031 71036505 0.000000e+00 791.0
14 TraesCS1A01G085400 chr1D 94.631 149 8 0 1234 1382 71037178 71037030 5.200000e-57 231.0
15 TraesCS1A01G085400 chr1D 91.946 149 12 0 1087 1235 71036884 71036736 2.430000e-50 209.0
16 TraesCS1A01G085400 chr1D 93.443 61 4 0 1837 1897 254473467 254473527 9.200000e-15 91.6
17 TraesCS1A01G085400 chr2D 89.336 422 35 7 2001 2417 567969946 567969530 2.750000e-144 521.0
18 TraesCS1A01G085400 chr3A 86.998 423 41 7 2001 2417 503755756 503756170 4.710000e-127 464.0
19 TraesCS1A01G085400 chr3A 92.857 98 7 0 1893 1990 638574714 638574811 2.500000e-30 143.0
20 TraesCS1A01G085400 chr3A 82.569 109 6 6 1608 1716 503755555 503755650 1.540000e-12 84.2
21 TraesCS1A01G085400 chr3D 95.652 92 4 0 1899 1990 520163977 520164068 5.380000e-32 148.0
22 TraesCS1A01G085400 chr5D 93.814 97 6 0 1894 1990 503230137 503230233 1.940000e-31 147.0
23 TraesCS1A01G085400 chr5D 93.443 61 4 0 1837 1897 6239233 6239173 9.200000e-15 91.6
24 TraesCS1A01G085400 chr5D 93.443 61 4 0 1837 1897 432308323 432308263 9.200000e-15 91.6
25 TraesCS1A01G085400 chr5D 93.443 61 4 0 1837 1897 503327560 503327620 9.200000e-15 91.6
26 TraesCS1A01G085400 chrUn 94.565 92 5 0 1899 1990 180666748 180666657 2.500000e-30 143.0
27 TraesCS1A01G085400 chrUn 94.565 92 5 0 1899 1990 354078071 354078162 2.500000e-30 143.0
28 TraesCS1A01G085400 chrUn 93.443 61 4 0 1837 1897 30304365 30304305 9.200000e-15 91.6
29 TraesCS1A01G085400 chrUn 97.561 41 1 0 119 159 360043065 360043105 1.200000e-08 71.3
30 TraesCS1A01G085400 chr6D 94.565 92 5 0 1899 1990 458922454 458922545 2.500000e-30 143.0
31 TraesCS1A01G085400 chr6D 93.443 61 4 0 1837 1897 429812097 429812037 9.200000e-15 91.6
32 TraesCS1A01G085400 chr4D 94.565 92 5 0 1899 1990 177442303 177442212 2.500000e-30 143.0
33 TraesCS1A01G085400 chr4D 90.426 94 9 0 1641 1734 12023034 12022941 9.070000e-25 124.0
34 TraesCS1A01G085400 chr4D 92.453 53 3 1 109 160 73208484 73208536 9.270000e-10 75.0
35 TraesCS1A01G085400 chr2A 92.784 97 7 0 1894 1990 121165876 121165780 9.010000e-30 141.0
36 TraesCS1A01G085400 chr2A 93.548 62 4 0 1836 1897 729770724 729770663 2.560000e-15 93.5
37 TraesCS1A01G085400 chr7D 97.561 41 1 0 118 158 628994590 628994630 1.200000e-08 71.3
38 TraesCS1A01G085400 chr7A 97.561 41 1 0 119 159 679071590 679071630 1.200000e-08 71.3
39 TraesCS1A01G085400 chr7A 90.566 53 5 0 107 159 679086871 679086923 1.200000e-08 71.3
40 TraesCS1A01G085400 chr6A 90.385 52 5 0 107 158 224613092 224613143 4.310000e-08 69.4


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 TraesCS1A01G085400 chr1A 71547446 71549862 2416 True 1634.666667 4464 95.5260 1 2417 3 chr1A.!!$R3 2416
1 TraesCS1A01G085400 chr1B 112503715 112504968 1253 True 1056.000000 1908 92.7520 365 1614 2 chr1B.!!$R2 1249
2 TraesCS1A01G085400 chr1D 71036505 71038295 1790 True 655.200000 1062 93.4430 1 1607 5 chr1D.!!$R1 1606
3 TraesCS1A01G085400 chr3A 503755555 503756170 615 False 274.100000 464 84.7835 1608 2417 2 chr3A.!!$F2 809

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
910 973 0.535102 ACCACCAAAACCGAGCTCAG 60.535 55.0 15.4 4.66 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 2583 0.027063 CGTTGTTGCGGAAACTCGTT 59.973 50.0 0.0 0.0 39.7 3.85 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
28 29 2.483014 TTTACCCACTTCCCATGTCG 57.517 50.000 0.00 0.00 0.00 4.35
63 65 4.296621 TGGGGCTACCTAAAGTTCTTTC 57.703 45.455 0.87 0.00 41.11 2.62
76 78 5.382618 AAGTTCTTTCCTGCATCAATCAC 57.617 39.130 0.00 0.00 0.00 3.06
178 181 8.197988 ACTGATCAATAATTACCGAAGTCAAC 57.802 34.615 0.00 0.00 0.00 3.18
184 187 9.451002 TCAATAATTACCGAAGTCAACCAAATA 57.549 29.630 0.00 0.00 0.00 1.40
193 196 9.538508 ACCGAAGTCAACCAAATATATTACTAC 57.461 33.333 0.00 0.00 0.00 2.73
194 197 9.537192 CCGAAGTCAACCAAATATATTACTACA 57.463 33.333 0.00 0.00 0.00 2.74
229 232 3.321648 TCATGCGCCCACCTGACT 61.322 61.111 4.18 0.00 0.00 3.41
291 294 2.691011 GGCCTAACAAGTGAAACCACAA 59.309 45.455 0.00 0.00 37.80 3.33
292 295 3.490249 GGCCTAACAAGTGAAACCACAAC 60.490 47.826 0.00 0.00 37.80 3.32
293 296 3.129638 GCCTAACAAGTGAAACCACAACA 59.870 43.478 0.00 0.00 37.80 3.33
294 297 4.668289 CCTAACAAGTGAAACCACAACAC 58.332 43.478 0.00 0.00 37.80 3.32
295 298 3.586100 AACAAGTGAAACCACAACACC 57.414 42.857 0.00 0.00 37.80 4.16
296 299 2.520069 ACAAGTGAAACCACAACACCA 58.480 42.857 0.00 0.00 37.80 4.17
297 300 2.491693 ACAAGTGAAACCACAACACCAG 59.508 45.455 0.00 0.00 37.80 4.00
298 301 2.491693 CAAGTGAAACCACAACACCAGT 59.508 45.455 0.00 0.00 37.80 4.00
342 346 6.318648 TCATCGAGCAATAATTATTATGCCCC 59.681 38.462 15.42 9.12 0.00 5.80
343 347 5.565509 TCGAGCAATAATTATTATGCCCCA 58.434 37.500 15.42 1.28 0.00 4.96
344 348 5.414454 TCGAGCAATAATTATTATGCCCCAC 59.586 40.000 15.42 7.08 0.00 4.61
345 349 5.393027 CGAGCAATAATTATTATGCCCCACC 60.393 44.000 15.42 3.69 0.00 4.61
346 350 5.401750 AGCAATAATTATTATGCCCCACCA 58.598 37.500 15.42 0.00 0.00 4.17
347 351 5.843421 AGCAATAATTATTATGCCCCACCAA 59.157 36.000 15.42 0.00 0.00 3.67
370 374 3.322541 TGTAACTCGACCCATCACTTGAA 59.677 43.478 0.00 0.00 0.00 2.69
418 422 3.181475 TGAGAGCCTGCCTAAGTTATTCG 60.181 47.826 0.00 0.00 0.00 3.34
832 893 4.019411 TCAGTGTGGAATTAAGCATCTCCA 60.019 41.667 0.00 0.00 35.58 3.86
837 898 3.137176 TGGAATTAAGCATCTCCAGAGGG 59.863 47.826 0.00 0.00 32.97 4.30
861 922 0.878523 CCGCGAAAACACACCTCTCA 60.879 55.000 8.23 0.00 0.00 3.27
872 935 4.537751 ACACACCTCTCATAGCTAAGCTA 58.462 43.478 0.00 0.00 45.55 3.32
910 973 0.535102 ACCACCAAAACCGAGCTCAG 60.535 55.000 15.40 4.66 0.00 3.35
971 1035 6.342111 GCTCCAGCTAGTTAGATAACTTTGT 58.658 40.000 10.34 0.00 45.19 2.83
1628 1851 8.593945 TTTTAGGAAAATGCTTGGTATCATCT 57.406 30.769 0.00 0.00 0.00 2.90
1630 1853 4.340381 AGGAAAATGCTTGGTATCATCTGC 59.660 41.667 0.00 0.00 0.00 4.26
1632 1855 3.589951 AATGCTTGGTATCATCTGCCT 57.410 42.857 0.00 0.00 0.00 4.75
1634 1857 1.839354 TGCTTGGTATCATCTGCCTGA 59.161 47.619 0.00 0.00 0.00 3.86
1635 1858 2.440627 TGCTTGGTATCATCTGCCTGAT 59.559 45.455 0.00 0.00 39.22 2.90
1637 1860 3.252701 GCTTGGTATCATCTGCCTGATTG 59.747 47.826 0.00 0.00 37.13 2.67
1638 1861 2.854963 TGGTATCATCTGCCTGATTGC 58.145 47.619 0.00 0.00 37.13 3.56
1639 1862 1.802960 GGTATCATCTGCCTGATTGCG 59.197 52.381 0.00 0.00 37.13 4.85
1640 1863 2.487934 GTATCATCTGCCTGATTGCGT 58.512 47.619 0.00 0.00 37.13 5.24
1641 1864 1.590932 ATCATCTGCCTGATTGCGTC 58.409 50.000 0.00 0.00 31.82 5.19
1642 1865 0.807275 TCATCTGCCTGATTGCGTCG 60.807 55.000 0.00 0.00 32.05 5.12
1643 1866 0.807275 CATCTGCCTGATTGCGTCGA 60.807 55.000 0.00 0.00 32.05 4.20
1644 1867 0.807667 ATCTGCCTGATTGCGTCGAC 60.808 55.000 5.18 5.18 29.59 4.20
1645 1868 2.434185 TGCCTGATTGCGTCGACC 60.434 61.111 10.58 3.43 0.00 4.79
1646 1869 3.554692 GCCTGATTGCGTCGACCG 61.555 66.667 10.58 6.51 40.40 4.79
1661 1884 4.172512 CCGCCTCTGCAGCCATCT 62.173 66.667 9.47 0.00 37.32 2.90
1686 1909 1.231221 ACTTTTAATCGTGCGGCACA 58.769 45.000 30.23 18.53 33.40 4.57
1687 1910 1.069500 ACTTTTAATCGTGCGGCACAC 60.069 47.619 30.23 7.22 46.45 3.82
1716 1939 8.978539 CAACTCTTATTATACGCATGAGCTTTA 58.021 33.333 0.00 0.00 39.10 1.85
1717 1940 8.522178 ACTCTTATTATACGCATGAGCTTTAC 57.478 34.615 0.00 0.00 39.10 2.01
1738 1994 1.398692 ACAGGACCGTGTTGCAAAAT 58.601 45.000 0.00 0.00 0.00 1.82
1744 2000 3.389221 GACCGTGTTGCAAAATCCAATT 58.611 40.909 0.00 0.00 0.00 2.32
1746 2002 3.181471 ACCGTGTTGCAAAATCCAATTCA 60.181 39.130 0.00 0.00 0.00 2.57
1748 2004 4.318689 CCGTGTTGCAAAATCCAATTCAAC 60.319 41.667 0.00 0.00 35.64 3.18
1752 2008 5.293814 TGTTGCAAAATCCAATTCAACTGTG 59.706 36.000 0.00 0.00 35.96 3.66
1755 2011 4.297510 CAAAATCCAATTCAACTGTGCGA 58.702 39.130 0.00 0.00 0.00 5.10
1769 2025 0.457166 GTGCGACACGTGCCTACATA 60.457 55.000 17.22 0.00 0.00 2.29
1770 2026 0.179148 TGCGACACGTGCCTACATAG 60.179 55.000 17.22 0.00 0.00 2.23
1771 2027 0.179145 GCGACACGTGCCTACATAGT 60.179 55.000 17.22 0.00 0.00 2.12
1772 2028 1.823828 CGACACGTGCCTACATAGTC 58.176 55.000 17.22 0.85 0.00 2.59
1773 2029 1.131693 CGACACGTGCCTACATAGTCA 59.868 52.381 17.22 0.00 0.00 3.41
1774 2030 2.223502 CGACACGTGCCTACATAGTCAT 60.224 50.000 17.22 0.00 0.00 3.06
1775 2031 3.002965 CGACACGTGCCTACATAGTCATA 59.997 47.826 17.22 0.00 0.00 2.15
1776 2032 4.537965 GACACGTGCCTACATAGTCATAG 58.462 47.826 17.22 0.00 0.00 2.23
1777 2033 4.204799 ACACGTGCCTACATAGTCATAGA 58.795 43.478 17.22 0.00 0.00 1.98
1778 2034 4.643334 ACACGTGCCTACATAGTCATAGAA 59.357 41.667 17.22 0.00 0.00 2.10
1779 2035 5.126545 ACACGTGCCTACATAGTCATAGAAA 59.873 40.000 17.22 0.00 0.00 2.52
1780 2036 6.040247 CACGTGCCTACATAGTCATAGAAAA 58.960 40.000 0.82 0.00 0.00 2.29
1781 2037 6.533723 CACGTGCCTACATAGTCATAGAAAAA 59.466 38.462 0.82 0.00 0.00 1.94
1808 2064 9.589461 ACTATATATAGTTCTTGCTACCACACT 57.411 33.333 18.01 0.00 40.54 3.55
1813 2069 7.907214 ATAGTTCTTGCTACCACACTTTAAG 57.093 36.000 0.00 0.00 0.00 1.85
1814 2070 5.925509 AGTTCTTGCTACCACACTTTAAGA 58.074 37.500 0.00 0.00 0.00 2.10
1815 2071 6.534634 AGTTCTTGCTACCACACTTTAAGAT 58.465 36.000 0.00 0.00 0.00 2.40
1816 2072 6.998673 AGTTCTTGCTACCACACTTTAAGATT 59.001 34.615 0.00 0.00 0.00 2.40
1817 2073 7.502561 AGTTCTTGCTACCACACTTTAAGATTT 59.497 33.333 0.00 0.00 0.00 2.17
1818 2074 7.435068 TCTTGCTACCACACTTTAAGATTTC 57.565 36.000 0.00 0.00 0.00 2.17
1819 2075 6.995686 TCTTGCTACCACACTTTAAGATTTCA 59.004 34.615 0.00 0.00 0.00 2.69
1820 2076 7.500892 TCTTGCTACCACACTTTAAGATTTCAA 59.499 33.333 0.00 0.00 0.00 2.69
1821 2077 6.966021 TGCTACCACACTTTAAGATTTCAAC 58.034 36.000 0.00 0.00 0.00 3.18
1822 2078 6.770785 TGCTACCACACTTTAAGATTTCAACT 59.229 34.615 0.00 0.00 0.00 3.16
1823 2079 7.934665 TGCTACCACACTTTAAGATTTCAACTA 59.065 33.333 0.00 0.00 0.00 2.24
1824 2080 8.443937 GCTACCACACTTTAAGATTTCAACTAG 58.556 37.037 0.00 0.00 0.00 2.57
1825 2081 9.706691 CTACCACACTTTAAGATTTCAACTAGA 57.293 33.333 0.00 0.00 0.00 2.43
1827 2083 9.220767 ACCACACTTTAAGATTTCAACTAGATC 57.779 33.333 0.00 0.00 0.00 2.75
1828 2084 8.669243 CCACACTTTAAGATTTCAACTAGATCC 58.331 37.037 0.00 0.00 0.00 3.36
1829 2085 9.442047 CACACTTTAAGATTTCAACTAGATCCT 57.558 33.333 0.00 0.00 0.00 3.24
1849 2105 9.745018 AGATCCTTTCATTTAAGACTTGAATGA 57.255 29.630 24.11 24.11 41.90 2.57
1869 2125 9.135189 TGAATGAAATTACATAAGGAATCCTGG 57.865 33.333 0.90 0.00 36.07 4.45
1870 2126 9.136323 GAATGAAATTACATAAGGAATCCTGGT 57.864 33.333 0.90 4.64 36.07 4.00
1871 2127 8.697507 ATGAAATTACATAAGGAATCCTGGTC 57.302 34.615 0.90 0.00 32.13 4.02
1872 2128 7.872138 TGAAATTACATAAGGAATCCTGGTCT 58.128 34.615 0.90 0.00 32.13 3.85
1873 2129 7.993183 TGAAATTACATAAGGAATCCTGGTCTC 59.007 37.037 0.90 0.00 32.13 3.36
1874 2130 7.451731 AATTACATAAGGAATCCTGGTCTCA 57.548 36.000 0.90 0.00 32.13 3.27
1875 2131 6.884472 TTACATAAGGAATCCTGGTCTCAA 57.116 37.500 0.90 0.00 32.13 3.02
1876 2132 5.779241 ACATAAGGAATCCTGGTCTCAAA 57.221 39.130 0.90 0.00 32.13 2.69
1877 2133 5.749462 ACATAAGGAATCCTGGTCTCAAAG 58.251 41.667 0.90 0.00 32.13 2.77
1878 2134 5.488919 ACATAAGGAATCCTGGTCTCAAAGA 59.511 40.000 0.90 0.00 32.13 2.52
1879 2135 6.012508 ACATAAGGAATCCTGGTCTCAAAGAA 60.013 38.462 0.90 0.00 32.13 2.52
1880 2136 4.566426 AGGAATCCTGGTCTCAAAGAAG 57.434 45.455 0.00 0.00 29.57 2.85
1881 2137 4.171234 AGGAATCCTGGTCTCAAAGAAGA 58.829 43.478 0.00 0.00 29.57 2.87
1882 2138 4.224818 AGGAATCCTGGTCTCAAAGAAGAG 59.775 45.833 0.00 0.00 32.50 2.85
1883 2139 4.512484 GAATCCTGGTCTCAAAGAAGAGG 58.488 47.826 0.00 0.00 36.30 3.69
1884 2140 2.260822 TCCTGGTCTCAAAGAAGAGGG 58.739 52.381 0.00 0.00 36.30 4.30
1885 2141 2.158158 TCCTGGTCTCAAAGAAGAGGGA 60.158 50.000 0.00 0.00 36.30 4.20
1886 2142 2.639839 CCTGGTCTCAAAGAAGAGGGAA 59.360 50.000 0.00 0.00 36.30 3.97
1887 2143 3.073062 CCTGGTCTCAAAGAAGAGGGAAA 59.927 47.826 0.00 0.00 36.30 3.13
1888 2144 4.263683 CCTGGTCTCAAAGAAGAGGGAAAT 60.264 45.833 0.00 0.00 36.30 2.17
1889 2145 4.655963 TGGTCTCAAAGAAGAGGGAAATG 58.344 43.478 0.00 0.00 36.30 2.32
1890 2146 4.013050 GGTCTCAAAGAAGAGGGAAATGG 58.987 47.826 0.00 0.00 36.30 3.16
1891 2147 4.013050 GTCTCAAAGAAGAGGGAAATGGG 58.987 47.826 0.00 0.00 36.30 4.00
1892 2148 3.010584 TCTCAAAGAAGAGGGAAATGGGG 59.989 47.826 0.00 0.00 36.30 4.96
1893 2149 2.993146 TCAAAGAAGAGGGAAATGGGGA 59.007 45.455 0.00 0.00 0.00 4.81
1894 2150 3.597868 TCAAAGAAGAGGGAAATGGGGAT 59.402 43.478 0.00 0.00 0.00 3.85
1895 2151 4.793520 TCAAAGAAGAGGGAAATGGGGATA 59.206 41.667 0.00 0.00 0.00 2.59
1896 2152 5.436374 TCAAAGAAGAGGGAAATGGGGATAT 59.564 40.000 0.00 0.00 0.00 1.63
1897 2153 6.623602 TCAAAGAAGAGGGAAATGGGGATATA 59.376 38.462 0.00 0.00 0.00 0.86
1898 2154 6.710499 AAGAAGAGGGAAATGGGGATATAG 57.290 41.667 0.00 0.00 0.00 1.31
1899 2155 5.742743 AGAAGAGGGAAATGGGGATATAGT 58.257 41.667 0.00 0.00 0.00 2.12
1900 2156 6.161167 AGAAGAGGGAAATGGGGATATAGTT 58.839 40.000 0.00 0.00 0.00 2.24
1901 2157 7.321530 AGAAGAGGGAAATGGGGATATAGTTA 58.678 38.462 0.00 0.00 0.00 2.24
1902 2158 7.799583 AGAAGAGGGAAATGGGGATATAGTTAA 59.200 37.037 0.00 0.00 0.00 2.01
1903 2159 7.331089 AGAGGGAAATGGGGATATAGTTAAC 57.669 40.000 0.00 0.00 0.00 2.01
1904 2160 6.274908 AGAGGGAAATGGGGATATAGTTAACC 59.725 42.308 0.88 0.00 0.00 2.85
1905 2161 5.013808 AGGGAAATGGGGATATAGTTAACCG 59.986 44.000 0.88 0.00 0.00 4.44
1906 2162 4.698780 GGAAATGGGGATATAGTTAACCGC 59.301 45.833 0.88 0.00 34.81 5.68
1907 2163 3.994931 ATGGGGATATAGTTAACCGCC 57.005 47.619 0.88 5.06 33.72 6.13
1908 2164 2.692024 TGGGGATATAGTTAACCGCCA 58.308 47.619 11.75 11.75 33.72 5.69
1909 2165 3.253220 TGGGGATATAGTTAACCGCCAT 58.747 45.455 11.75 0.72 33.72 4.40
1910 2166 3.008594 TGGGGATATAGTTAACCGCCATG 59.991 47.826 11.75 0.00 33.72 3.66
1911 2167 3.008704 GGGGATATAGTTAACCGCCATGT 59.991 47.826 0.88 0.00 29.87 3.21
1912 2168 4.506095 GGGGATATAGTTAACCGCCATGTT 60.506 45.833 0.88 0.00 29.87 2.71
1913 2169 5.280113 GGGGATATAGTTAACCGCCATGTTA 60.280 44.000 0.88 0.00 29.87 2.41
1914 2170 6.232692 GGGATATAGTTAACCGCCATGTTAA 58.767 40.000 0.88 0.00 38.13 2.01
1921 2177 5.721876 TTAACCGCCATGTTAACTAATCG 57.278 39.130 7.22 5.68 36.15 3.34
1922 2178 3.530265 ACCGCCATGTTAACTAATCGA 57.470 42.857 7.22 0.00 0.00 3.59
1923 2179 4.067972 ACCGCCATGTTAACTAATCGAT 57.932 40.909 7.22 0.00 0.00 3.59
1924 2180 4.448210 ACCGCCATGTTAACTAATCGATT 58.552 39.130 16.15 16.15 0.00 3.34
1925 2181 5.603596 ACCGCCATGTTAACTAATCGATTA 58.396 37.500 16.69 16.69 0.00 1.75
1926 2182 6.228258 ACCGCCATGTTAACTAATCGATTAT 58.772 36.000 17.84 7.35 0.00 1.28
1927 2183 6.147164 ACCGCCATGTTAACTAATCGATTATG 59.853 38.462 17.84 12.05 0.00 1.90
1928 2184 6.367695 CCGCCATGTTAACTAATCGATTATGA 59.632 38.462 17.84 4.30 0.00 2.15
1929 2185 7.095397 CCGCCATGTTAACTAATCGATTATGAA 60.095 37.037 17.84 9.70 0.00 2.57
1930 2186 8.279800 CGCCATGTTAACTAATCGATTATGAAA 58.720 33.333 17.84 9.55 0.00 2.69
1931 2187 9.944663 GCCATGTTAACTAATCGATTATGAAAA 57.055 29.630 17.84 8.34 0.00 2.29
1951 2207 8.600449 TGAAAAATTAAATCGGATTTTGCAGT 57.400 26.923 20.04 3.29 36.39 4.40
1952 2208 9.050601 TGAAAAATTAAATCGGATTTTGCAGTT 57.949 25.926 20.04 10.18 36.39 3.16
1953 2209 9.528847 GAAAAATTAAATCGGATTTTGCAGTTC 57.471 29.630 20.04 14.17 36.06 3.01
1954 2210 8.831715 AAAATTAAATCGGATTTTGCAGTTCT 57.168 26.923 20.04 0.00 34.97 3.01
1955 2211 8.831715 AAATTAAATCGGATTTTGCAGTTCTT 57.168 26.923 20.04 2.54 33.82 2.52
1956 2212 8.831715 AATTAAATCGGATTTTGCAGTTCTTT 57.168 26.923 20.04 0.00 33.82 2.52
1957 2213 8.831715 ATTAAATCGGATTTTGCAGTTCTTTT 57.168 26.923 20.04 0.00 33.82 2.27
1958 2214 8.655651 TTAAATCGGATTTTGCAGTTCTTTTT 57.344 26.923 20.04 0.00 33.82 1.94
1975 2231 2.060326 TTTTCTGCAGTACCTCGACG 57.940 50.000 14.67 0.00 0.00 5.12
1976 2232 0.956633 TTTCTGCAGTACCTCGACGT 59.043 50.000 14.67 0.00 0.00 4.34
1977 2233 1.812235 TTCTGCAGTACCTCGACGTA 58.188 50.000 14.67 0.00 0.00 3.57
1978 2234 1.812235 TCTGCAGTACCTCGACGTAA 58.188 50.000 14.67 0.00 0.00 3.18
1979 2235 1.466167 TCTGCAGTACCTCGACGTAAC 59.534 52.381 14.67 0.00 0.00 2.50
1980 2236 1.198408 CTGCAGTACCTCGACGTAACA 59.802 52.381 5.25 0.00 0.00 2.41
1981 2237 1.814394 TGCAGTACCTCGACGTAACAT 59.186 47.619 0.00 0.00 0.00 2.71
1982 2238 2.182825 GCAGTACCTCGACGTAACATG 58.817 52.381 0.00 0.00 0.00 3.21
1983 2239 2.159476 GCAGTACCTCGACGTAACATGA 60.159 50.000 0.00 0.00 0.00 3.07
1984 2240 3.681855 CAGTACCTCGACGTAACATGAG 58.318 50.000 0.00 0.00 0.00 2.90
1985 2241 2.097142 AGTACCTCGACGTAACATGAGC 59.903 50.000 0.00 0.00 0.00 4.26
1986 2242 0.179171 ACCTCGACGTAACATGAGCG 60.179 55.000 0.00 3.14 0.00 5.03
1987 2243 0.179171 CCTCGACGTAACATGAGCGT 60.179 55.000 0.00 6.69 41.81 5.07
1988 2244 0.907837 CTCGACGTAACATGAGCGTG 59.092 55.000 15.68 9.87 39.06 5.34
1996 2252 1.480212 AACATGAGCGTGAGGACCCA 61.480 55.000 0.00 0.00 0.00 4.51
2002 2258 3.625897 CGTGAGGACCCACAGCCA 61.626 66.667 12.00 0.00 36.89 4.75
2007 2263 0.614979 GAGGACCCACAGCCACTCTA 60.615 60.000 0.00 0.00 0.00 2.43
2008 2264 0.043334 AGGACCCACAGCCACTCTAT 59.957 55.000 0.00 0.00 0.00 1.98
2019 2275 5.931146 CACAGCCACTCTATCATTCTTATCC 59.069 44.000 0.00 0.00 0.00 2.59
2020 2276 5.012561 ACAGCCACTCTATCATTCTTATCCC 59.987 44.000 0.00 0.00 0.00 3.85
2021 2277 5.012458 CAGCCACTCTATCATTCTTATCCCA 59.988 44.000 0.00 0.00 0.00 4.37
2022 2278 5.608437 AGCCACTCTATCATTCTTATCCCAA 59.392 40.000 0.00 0.00 0.00 4.12
2023 2279 6.101734 AGCCACTCTATCATTCTTATCCCAAA 59.898 38.462 0.00 0.00 0.00 3.28
2024 2280 6.944862 GCCACTCTATCATTCTTATCCCAAAT 59.055 38.462 0.00 0.00 0.00 2.32
2035 2299 6.515272 TCTTATCCCAAATGAAAAGAGCAC 57.485 37.500 0.00 0.00 0.00 4.40
2049 2313 6.700960 TGAAAAGAGCACAACCACATATTTTG 59.299 34.615 0.00 0.00 0.00 2.44
2052 2316 2.028203 AGCACAACCACATATTTTGCCC 60.028 45.455 0.00 0.00 0.00 5.36
2061 2325 3.763360 CACATATTTTGCCCTGAACCTCA 59.237 43.478 0.00 0.00 0.00 3.86
2095 2359 4.202441 CAGGTCCCTTTCATGGATGTAAG 58.798 47.826 0.00 0.00 35.67 2.34
2096 2360 2.952310 GGTCCCTTTCATGGATGTAAGC 59.048 50.000 0.00 0.00 34.90 3.09
2119 2383 0.179129 CCAAGCACGCATCCAAATCC 60.179 55.000 0.00 0.00 0.00 3.01
2121 2385 1.098050 AAGCACGCATCCAAATCCTC 58.902 50.000 0.00 0.00 0.00 3.71
2151 2415 3.428725 CGTGAGAAGAGAGAGAACCCATG 60.429 52.174 0.00 0.00 0.00 3.66
2189 2454 1.768684 AAACTCCTGCGAGCTTGGGA 61.769 55.000 2.37 0.80 40.03 4.37
2196 2461 2.660064 GCGAGCTTGGGAAGAGGGA 61.660 63.158 2.37 0.00 0.00 4.20
2197 2462 1.219393 CGAGCTTGGGAAGAGGGAC 59.781 63.158 0.00 0.00 0.00 4.46
2201 2466 0.036306 GCTTGGGAAGAGGGACGAAA 59.964 55.000 0.00 0.00 0.00 3.46
2205 2470 1.346722 TGGGAAGAGGGACGAAACTTC 59.653 52.381 0.00 0.00 38.26 3.01
2208 2473 0.320508 AAGAGGGACGAAACTTCCGC 60.321 55.000 0.00 0.00 33.43 5.54
2210 2475 0.529378 GAGGGACGAAACTTCCGCTA 59.471 55.000 0.00 0.00 33.43 4.26
2215 2480 3.308053 GGGACGAAACTTCCGCTATTTAC 59.692 47.826 0.00 0.00 33.43 2.01
2216 2481 4.179298 GGACGAAACTTCCGCTATTTACT 58.821 43.478 0.00 0.00 0.00 2.24
2270 2539 2.417936 GACCTACCCAGCTAGCGC 59.582 66.667 9.55 0.00 0.00 5.92
2281 2550 2.949678 CTAGCGCGCGTCGTTCAT 60.950 61.111 32.35 8.09 41.07 2.57
2322 2591 0.730265 TTGTGCTGCGAAACGAGTTT 59.270 45.000 0.28 0.28 35.14 2.66
2337 2606 0.655733 AGTTTCCGCAACAACGACTG 59.344 50.000 0.00 0.00 37.93 3.51
2361 2630 1.081509 CAAATGGTGGTGGCGAACG 60.082 57.895 0.00 0.00 0.00 3.95
2363 2632 1.512156 AAATGGTGGTGGCGAACGAC 61.512 55.000 0.00 0.00 36.81 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.615331 AAGCTCACATGGGACGACAT 59.385 50.000 0.00 0.00 0.00 3.06
63 65 7.951530 AAAACTAAAAAGTGATTGATGCAGG 57.048 32.000 0.00 0.00 0.00 4.85
168 171 9.537192 TGTAGTAATATATTTGGTTGACTTCGG 57.463 33.333 2.68 0.00 0.00 4.30
229 232 2.486203 GGTTTATTGCACGACCACATGA 59.514 45.455 0.00 0.00 32.41 3.07
291 294 0.696485 AAGGGGTGGTGTACTGGTGT 60.696 55.000 0.00 0.00 0.00 4.16
292 295 0.476771 AAAGGGGTGGTGTACTGGTG 59.523 55.000 0.00 0.00 0.00 4.17
293 296 0.476771 CAAAGGGGTGGTGTACTGGT 59.523 55.000 0.00 0.00 0.00 4.00
294 297 0.893727 GCAAAGGGGTGGTGTACTGG 60.894 60.000 0.00 0.00 0.00 4.00
295 298 0.179004 TGCAAAGGGGTGGTGTACTG 60.179 55.000 0.00 0.00 0.00 2.74
296 299 0.777446 ATGCAAAGGGGTGGTGTACT 59.223 50.000 0.00 0.00 0.00 2.73
297 300 1.627864 AATGCAAAGGGGTGGTGTAC 58.372 50.000 0.00 0.00 0.00 2.90
298 301 2.243810 GAAATGCAAAGGGGTGGTGTA 58.756 47.619 0.00 0.00 0.00 2.90
342 346 2.465860 TGGGTCGAGTTACATTGGTG 57.534 50.000 0.00 0.00 0.00 4.17
343 347 2.569853 TGATGGGTCGAGTTACATTGGT 59.430 45.455 0.00 0.00 0.00 3.67
344 348 2.936498 GTGATGGGTCGAGTTACATTGG 59.064 50.000 0.00 0.00 0.00 3.16
345 349 3.861840 AGTGATGGGTCGAGTTACATTG 58.138 45.455 0.00 0.00 0.00 2.82
346 350 4.020573 TCAAGTGATGGGTCGAGTTACATT 60.021 41.667 0.00 0.00 0.00 2.71
347 351 3.513912 TCAAGTGATGGGTCGAGTTACAT 59.486 43.478 0.00 0.00 0.00 2.29
418 422 3.658757 AGAGCGAGGAATAAGCATCTC 57.341 47.619 0.00 0.00 0.00 2.75
685 690 7.675962 TTGGAAATAATAATATCGTTCCCCG 57.324 36.000 0.00 0.00 31.47 5.73
832 893 1.911766 TTTTCGCGGGACTCCCTCT 60.912 57.895 12.62 0.00 42.67 3.69
837 898 1.568025 GTGTGTTTTCGCGGGACTC 59.432 57.895 6.13 4.50 0.00 3.36
844 905 2.094417 GCTATGAGAGGTGTGTTTTCGC 59.906 50.000 0.00 0.00 0.00 4.70
848 909 4.223923 AGCTTAGCTATGAGAGGTGTGTTT 59.776 41.667 4.30 0.00 36.99 2.83
861 922 2.494073 GGCTCCATCGTAGCTTAGCTAT 59.506 50.000 17.44 0.00 43.30 2.97
872 935 3.646162 TGGTCATTTATAGGCTCCATCGT 59.354 43.478 0.00 0.00 0.00 3.73
910 973 0.249911 AGAGGAGTGCGTGGTTTCAC 60.250 55.000 0.00 0.00 40.36 3.18
1628 1851 2.434185 GGTCGACGCAATCAGGCA 60.434 61.111 9.92 0.00 0.00 4.75
1646 1869 0.465824 AATCAGATGGCTGCAGAGGC 60.466 55.000 20.43 5.00 45.19 4.70
1655 1878 6.414987 GCACGATTAAAAGTTAATCAGATGGC 59.585 38.462 16.81 10.26 34.51 4.40
1656 1879 6.628856 CGCACGATTAAAAGTTAATCAGATGG 59.371 38.462 16.81 6.39 34.51 3.51
1658 1881 6.715464 CCGCACGATTAAAAGTTAATCAGAT 58.285 36.000 16.81 3.66 34.51 2.90
1661 1884 4.154375 TGCCGCACGATTAAAAGTTAATCA 59.846 37.500 16.81 0.00 34.51 2.57
1686 1909 7.254455 GCTCATGCGTATAATAAGAGTTGTTGT 60.254 37.037 0.00 0.00 0.00 3.32
1687 1910 7.042456 AGCTCATGCGTATAATAAGAGTTGTTG 60.042 37.037 0.00 0.00 45.42 3.33
1688 1911 6.986817 AGCTCATGCGTATAATAAGAGTTGTT 59.013 34.615 0.00 0.00 45.42 2.83
1693 1916 8.520835 TGTAAAGCTCATGCGTATAATAAGAG 57.479 34.615 0.00 0.00 45.42 2.85
1738 1994 1.601903 GTGTCGCACAGTTGAATTGGA 59.398 47.619 5.30 0.00 34.08 3.53
1744 2000 2.521771 GCACGTGTCGCACAGTTGA 61.522 57.895 18.38 0.00 33.40 3.18
1746 2002 2.358193 TAGGCACGTGTCGCACAGTT 62.358 55.000 18.38 0.00 33.40 3.16
1748 2004 2.049526 TAGGCACGTGTCGCACAG 60.050 61.111 18.38 5.83 33.40 3.66
1752 2008 0.179145 ACTATGTAGGCACGTGTCGC 60.179 55.000 18.38 13.71 0.00 5.19
1755 2011 4.204799 TCTATGACTATGTAGGCACGTGT 58.795 43.478 18.38 0.00 45.63 4.49
1782 2038 9.589461 AGTGTGGTAGCAAGAACTATATATAGT 57.411 33.333 18.01 18.01 45.04 2.12
1787 2043 9.601217 CTTAAAGTGTGGTAGCAAGAACTATAT 57.399 33.333 0.00 0.00 0.00 0.86
1788 2044 8.809066 TCTTAAAGTGTGGTAGCAAGAACTATA 58.191 33.333 0.00 0.00 0.00 1.31
1789 2045 7.676947 TCTTAAAGTGTGGTAGCAAGAACTAT 58.323 34.615 0.00 0.00 0.00 2.12
1790 2046 7.058023 TCTTAAAGTGTGGTAGCAAGAACTA 57.942 36.000 0.00 0.00 0.00 2.24
1791 2047 5.925509 TCTTAAAGTGTGGTAGCAAGAACT 58.074 37.500 0.00 0.00 0.00 3.01
1792 2048 6.803154 ATCTTAAAGTGTGGTAGCAAGAAC 57.197 37.500 0.00 0.00 0.00 3.01
1793 2049 7.500892 TGAAATCTTAAAGTGTGGTAGCAAGAA 59.499 33.333 0.00 0.00 0.00 2.52
1794 2050 6.995686 TGAAATCTTAAAGTGTGGTAGCAAGA 59.004 34.615 0.00 0.00 0.00 3.02
1795 2051 7.202016 TGAAATCTTAAAGTGTGGTAGCAAG 57.798 36.000 0.00 0.00 0.00 4.01
1796 2052 7.284489 AGTTGAAATCTTAAAGTGTGGTAGCAA 59.716 33.333 0.00 0.00 0.00 3.91
1797 2053 6.770785 AGTTGAAATCTTAAAGTGTGGTAGCA 59.229 34.615 0.00 0.00 0.00 3.49
1798 2054 7.203255 AGTTGAAATCTTAAAGTGTGGTAGC 57.797 36.000 0.00 0.00 0.00 3.58
1799 2055 9.706691 TCTAGTTGAAATCTTAAAGTGTGGTAG 57.293 33.333 0.00 0.00 0.00 3.18
1801 2057 9.220767 GATCTAGTTGAAATCTTAAAGTGTGGT 57.779 33.333 0.00 0.00 0.00 4.16
1802 2058 8.669243 GGATCTAGTTGAAATCTTAAAGTGTGG 58.331 37.037 0.00 0.00 0.00 4.17
1803 2059 9.442047 AGGATCTAGTTGAAATCTTAAAGTGTG 57.558 33.333 0.00 0.00 0.00 3.82
1823 2079 9.745018 TCATTCAAGTCTTAAATGAAAGGATCT 57.255 29.630 8.48 0.00 36.69 2.75
1843 2099 9.135189 CCAGGATTCCTTATGTAATTTCATTCA 57.865 33.333 1.28 0.00 0.00 2.57
1844 2100 9.136323 ACCAGGATTCCTTATGTAATTTCATTC 57.864 33.333 1.28 0.00 0.00 2.67
1845 2101 9.136323 GACCAGGATTCCTTATGTAATTTCATT 57.864 33.333 1.28 0.00 0.00 2.57
1846 2102 8.506083 AGACCAGGATTCCTTATGTAATTTCAT 58.494 33.333 1.28 2.93 0.00 2.57
1847 2103 7.872138 AGACCAGGATTCCTTATGTAATTTCA 58.128 34.615 1.28 0.00 0.00 2.69
1848 2104 7.993183 TGAGACCAGGATTCCTTATGTAATTTC 59.007 37.037 1.28 0.00 0.00 2.17
1849 2105 7.872138 TGAGACCAGGATTCCTTATGTAATTT 58.128 34.615 1.28 0.00 0.00 1.82
1850 2106 7.451731 TGAGACCAGGATTCCTTATGTAATT 57.548 36.000 1.28 0.00 0.00 1.40
1851 2107 7.451731 TTGAGACCAGGATTCCTTATGTAAT 57.548 36.000 1.28 0.00 0.00 1.89
1852 2108 6.884472 TTGAGACCAGGATTCCTTATGTAA 57.116 37.500 1.28 0.00 0.00 2.41
1853 2109 6.672218 TCTTTGAGACCAGGATTCCTTATGTA 59.328 38.462 1.28 0.00 0.00 2.29
1854 2110 5.488919 TCTTTGAGACCAGGATTCCTTATGT 59.511 40.000 1.28 0.58 0.00 2.29
1855 2111 5.994250 TCTTTGAGACCAGGATTCCTTATG 58.006 41.667 1.28 0.00 0.00 1.90
1856 2112 6.445139 TCTTCTTTGAGACCAGGATTCCTTAT 59.555 38.462 1.28 0.00 0.00 1.73
1857 2113 5.785423 TCTTCTTTGAGACCAGGATTCCTTA 59.215 40.000 1.28 0.00 0.00 2.69
1858 2114 4.599241 TCTTCTTTGAGACCAGGATTCCTT 59.401 41.667 1.28 0.00 0.00 3.36
1859 2115 4.171234 TCTTCTTTGAGACCAGGATTCCT 58.829 43.478 0.00 0.00 0.00 3.36
1860 2116 4.512484 CTCTTCTTTGAGACCAGGATTCC 58.488 47.826 0.00 0.00 36.23 3.01
1861 2117 4.512484 CCTCTTCTTTGAGACCAGGATTC 58.488 47.826 0.00 0.00 36.23 2.52
1862 2118 3.265479 CCCTCTTCTTTGAGACCAGGATT 59.735 47.826 0.00 0.00 36.23 3.01
1863 2119 2.843113 CCCTCTTCTTTGAGACCAGGAT 59.157 50.000 0.00 0.00 36.23 3.24
1864 2120 2.158158 TCCCTCTTCTTTGAGACCAGGA 60.158 50.000 0.00 0.00 36.23 3.86
1865 2121 2.260822 TCCCTCTTCTTTGAGACCAGG 58.739 52.381 0.00 0.00 36.23 4.45
1866 2122 4.357918 TTTCCCTCTTCTTTGAGACCAG 57.642 45.455 0.00 0.00 36.23 4.00
1867 2123 4.507335 CCATTTCCCTCTTCTTTGAGACCA 60.507 45.833 0.00 0.00 36.23 4.02
1868 2124 4.013050 CCATTTCCCTCTTCTTTGAGACC 58.987 47.826 0.00 0.00 36.23 3.85
1869 2125 4.013050 CCCATTTCCCTCTTCTTTGAGAC 58.987 47.826 0.00 0.00 36.23 3.36
1870 2126 3.010584 CCCCATTTCCCTCTTCTTTGAGA 59.989 47.826 0.00 0.00 36.23 3.27
1871 2127 3.010584 TCCCCATTTCCCTCTTCTTTGAG 59.989 47.826 0.00 0.00 0.00 3.02
1872 2128 2.993146 TCCCCATTTCCCTCTTCTTTGA 59.007 45.455 0.00 0.00 0.00 2.69
1873 2129 3.456380 TCCCCATTTCCCTCTTCTTTG 57.544 47.619 0.00 0.00 0.00 2.77
1874 2130 6.625700 ACTATATCCCCATTTCCCTCTTCTTT 59.374 38.462 0.00 0.00 0.00 2.52
1875 2131 6.161167 ACTATATCCCCATTTCCCTCTTCTT 58.839 40.000 0.00 0.00 0.00 2.52
1876 2132 5.742743 ACTATATCCCCATTTCCCTCTTCT 58.257 41.667 0.00 0.00 0.00 2.85
1877 2133 6.455690 AACTATATCCCCATTTCCCTCTTC 57.544 41.667 0.00 0.00 0.00 2.87
1878 2134 7.202289 GGTTAACTATATCCCCATTTCCCTCTT 60.202 40.741 5.42 0.00 0.00 2.85
1879 2135 6.274908 GGTTAACTATATCCCCATTTCCCTCT 59.725 42.308 5.42 0.00 0.00 3.69
1880 2136 6.482524 GGTTAACTATATCCCCATTTCCCTC 58.517 44.000 5.42 0.00 0.00 4.30
1881 2137 5.013808 CGGTTAACTATATCCCCATTTCCCT 59.986 44.000 5.42 0.00 0.00 4.20
1882 2138 5.250982 CGGTTAACTATATCCCCATTTCCC 58.749 45.833 5.42 0.00 0.00 3.97
1883 2139 4.698780 GCGGTTAACTATATCCCCATTTCC 59.301 45.833 5.42 0.00 0.00 3.13
1884 2140 4.698780 GGCGGTTAACTATATCCCCATTTC 59.301 45.833 5.42 0.00 0.00 2.17
1885 2141 4.105057 TGGCGGTTAACTATATCCCCATTT 59.895 41.667 5.42 0.00 0.00 2.32
1886 2142 3.653836 TGGCGGTTAACTATATCCCCATT 59.346 43.478 5.42 0.00 0.00 3.16
1887 2143 3.253220 TGGCGGTTAACTATATCCCCAT 58.747 45.455 5.42 0.00 0.00 4.00
1888 2144 2.692024 TGGCGGTTAACTATATCCCCA 58.308 47.619 5.42 0.00 0.00 4.96
1889 2145 3.008704 ACATGGCGGTTAACTATATCCCC 59.991 47.826 5.42 0.00 0.00 4.81
1890 2146 4.281898 ACATGGCGGTTAACTATATCCC 57.718 45.455 5.42 0.00 0.00 3.85
1899 2155 5.417811 TCGATTAGTTAACATGGCGGTTAA 58.582 37.500 8.61 9.42 40.04 2.01
1900 2156 5.008619 TCGATTAGTTAACATGGCGGTTA 57.991 39.130 8.61 0.00 32.29 2.85
1901 2157 3.864243 TCGATTAGTTAACATGGCGGTT 58.136 40.909 8.61 0.07 34.81 4.44
1902 2158 3.530265 TCGATTAGTTAACATGGCGGT 57.470 42.857 8.61 0.00 0.00 5.68
1903 2159 6.367695 TCATAATCGATTAGTTAACATGGCGG 59.632 38.462 21.55 0.00 0.00 6.13
1904 2160 7.346208 TCATAATCGATTAGTTAACATGGCG 57.654 36.000 21.55 6.50 0.00 5.69
1905 2161 9.944663 TTTTCATAATCGATTAGTTAACATGGC 57.055 29.630 21.55 0.00 0.00 4.40
1925 2181 9.218440 ACTGCAAAATCCGATTTAATTTTTCAT 57.782 25.926 6.79 0.00 33.86 2.57
1926 2182 8.600449 ACTGCAAAATCCGATTTAATTTTTCA 57.400 26.923 6.79 0.00 33.86 2.69
1927 2183 9.528847 GAACTGCAAAATCCGATTTAATTTTTC 57.471 29.630 6.79 4.77 33.86 2.29
1928 2184 9.271828 AGAACTGCAAAATCCGATTTAATTTTT 57.728 25.926 6.79 0.00 33.86 1.94
1929 2185 8.831715 AGAACTGCAAAATCCGATTTAATTTT 57.168 26.923 6.79 0.00 35.91 1.82
1930 2186 8.831715 AAGAACTGCAAAATCCGATTTAATTT 57.168 26.923 6.79 0.00 0.00 1.82
1931 2187 8.831715 AAAGAACTGCAAAATCCGATTTAATT 57.168 26.923 6.79 0.00 0.00 1.40
1932 2188 8.831715 AAAAGAACTGCAAAATCCGATTTAAT 57.168 26.923 6.79 0.00 0.00 1.40
1933 2189 8.655651 AAAAAGAACTGCAAAATCCGATTTAA 57.344 26.923 6.79 0.00 0.00 1.52
1955 2211 2.223876 ACGTCGAGGTACTGCAGAAAAA 60.224 45.455 23.35 0.00 41.55 1.94
1956 2212 1.338973 ACGTCGAGGTACTGCAGAAAA 59.661 47.619 23.35 1.97 41.55 2.29
1957 2213 0.956633 ACGTCGAGGTACTGCAGAAA 59.043 50.000 23.35 4.90 41.55 2.52
1958 2214 1.812235 TACGTCGAGGTACTGCAGAA 58.188 50.000 23.35 0.00 41.55 3.02
1959 2215 1.466167 GTTACGTCGAGGTACTGCAGA 59.534 52.381 23.35 0.48 41.55 4.26
1960 2216 1.198408 TGTTACGTCGAGGTACTGCAG 59.802 52.381 17.03 13.48 41.55 4.41
1961 2217 1.237533 TGTTACGTCGAGGTACTGCA 58.762 50.000 17.03 13.12 41.55 4.41
1962 2218 2.159476 TCATGTTACGTCGAGGTACTGC 60.159 50.000 17.03 10.97 41.55 4.40
1963 2219 3.681855 CTCATGTTACGTCGAGGTACTG 58.318 50.000 17.03 14.13 41.55 2.74
1965 2221 2.448219 GCTCATGTTACGTCGAGGTAC 58.552 52.381 17.03 12.56 0.00 3.34
1966 2222 1.063027 CGCTCATGTTACGTCGAGGTA 59.937 52.381 13.68 13.68 0.00 3.08
1967 2223 0.179171 CGCTCATGTTACGTCGAGGT 60.179 55.000 15.89 15.89 0.00 3.85
1968 2224 0.179171 ACGCTCATGTTACGTCGAGG 60.179 55.000 3.03 3.03 34.35 4.63
1969 2225 0.907837 CACGCTCATGTTACGTCGAG 59.092 55.000 0.00 0.00 38.09 4.04
1970 2226 0.518195 TCACGCTCATGTTACGTCGA 59.482 50.000 0.00 6.67 38.09 4.20
1971 2227 0.907837 CTCACGCTCATGTTACGTCG 59.092 55.000 0.00 0.00 38.09 5.12
1972 2228 1.135489 TCCTCACGCTCATGTTACGTC 60.135 52.381 0.00 0.00 38.09 4.34
1973 2229 0.885879 TCCTCACGCTCATGTTACGT 59.114 50.000 0.00 0.00 41.45 3.57
1974 2230 1.269166 GTCCTCACGCTCATGTTACG 58.731 55.000 0.00 0.00 0.00 3.18
1975 2231 1.641577 GGTCCTCACGCTCATGTTAC 58.358 55.000 0.00 0.00 0.00 2.50
1976 2232 0.535335 GGGTCCTCACGCTCATGTTA 59.465 55.000 0.00 0.00 32.63 2.41
1977 2233 1.296715 GGGTCCTCACGCTCATGTT 59.703 57.895 0.00 0.00 32.63 2.71
1978 2234 1.913262 TGGGTCCTCACGCTCATGT 60.913 57.895 0.00 0.00 36.42 3.21
1979 2235 1.448540 GTGGGTCCTCACGCTCATG 60.449 63.158 0.00 0.00 36.42 3.07
1980 2236 1.892819 CTGTGGGTCCTCACGCTCAT 61.893 60.000 6.15 0.00 38.04 2.90
1981 2237 2.523168 TGTGGGTCCTCACGCTCA 60.523 61.111 6.15 0.00 40.31 4.26
1982 2238 2.262915 CTGTGGGTCCTCACGCTC 59.737 66.667 6.15 0.00 40.31 5.03
1983 2239 4.008933 GCTGTGGGTCCTCACGCT 62.009 66.667 14.14 0.00 40.31 5.07
1985 2241 3.625897 TGGCTGTGGGTCCTCACG 61.626 66.667 6.15 0.00 40.31 4.35
1986 2242 2.032681 GTGGCTGTGGGTCCTCAC 59.967 66.667 4.09 4.09 38.09 3.51
1987 2243 2.122413 AGTGGCTGTGGGTCCTCA 60.122 61.111 0.00 0.00 0.00 3.86
1988 2244 0.614979 TAGAGTGGCTGTGGGTCCTC 60.615 60.000 0.00 0.00 0.00 3.71
1996 2252 5.012561 GGGATAAGAATGATAGAGTGGCTGT 59.987 44.000 0.00 0.00 0.00 4.40
2007 2263 8.419442 GCTCTTTTCATTTGGGATAAGAATGAT 58.581 33.333 0.00 0.00 38.96 2.45
2008 2264 7.396907 TGCTCTTTTCATTTGGGATAAGAATGA 59.603 33.333 0.00 0.00 35.44 2.57
2019 2275 3.803778 GTGGTTGTGCTCTTTTCATTTGG 59.196 43.478 0.00 0.00 0.00 3.28
2020 2276 4.431809 TGTGGTTGTGCTCTTTTCATTTG 58.568 39.130 0.00 0.00 0.00 2.32
2021 2277 4.734398 TGTGGTTGTGCTCTTTTCATTT 57.266 36.364 0.00 0.00 0.00 2.32
2022 2278 4.942761 ATGTGGTTGTGCTCTTTTCATT 57.057 36.364 0.00 0.00 0.00 2.57
2023 2279 6.594788 AATATGTGGTTGTGCTCTTTTCAT 57.405 33.333 0.00 0.00 0.00 2.57
2024 2280 6.403866 AAATATGTGGTTGTGCTCTTTTCA 57.596 33.333 0.00 0.00 0.00 2.69
2035 2299 4.244862 GTTCAGGGCAAAATATGTGGTTG 58.755 43.478 0.00 0.00 0.00 3.77
2049 2313 1.414550 GTAGGAGATGAGGTTCAGGGC 59.585 57.143 0.00 0.00 0.00 5.19
2052 2316 2.962421 GGAGGTAGGAGATGAGGTTCAG 59.038 54.545 0.00 0.00 0.00 3.02
2119 2383 2.165234 TCTCTTCTCACGAATGGCAGAG 59.835 50.000 0.00 0.00 0.00 3.35
2121 2385 2.165234 TCTCTCTTCTCACGAATGGCAG 59.835 50.000 0.00 0.00 0.00 4.85
2144 2408 0.409484 AGCTAGGTTTGCCATGGGTT 59.591 50.000 15.13 0.00 37.19 4.11
2151 2415 4.037565 AGTTTTACAACAGCTAGGTTTGCC 59.962 41.667 13.31 0.00 35.05 4.52
2189 2454 0.320508 GCGGAAGTTTCGTCCCTCTT 60.321 55.000 5.27 0.00 0.00 2.85
2196 2461 3.370061 GCAGTAAATAGCGGAAGTTTCGT 59.630 43.478 5.27 0.00 0.00 3.85
2197 2462 3.924610 GCAGTAAATAGCGGAAGTTTCG 58.075 45.455 0.00 0.00 0.00 3.46
2242 2510 3.152400 GTAGGTCCCCGGTGCGAT 61.152 66.667 0.00 0.00 0.00 4.58
2273 2542 4.814294 AGGGCCGCGATGAACGAC 62.814 66.667 8.23 0.00 45.77 4.34
2274 2543 4.508128 GAGGGCCGCGATGAACGA 62.508 66.667 8.23 0.00 45.77 3.85
2302 2571 0.304705 AACTCGTTTCGCAGCACAAG 59.695 50.000 0.00 0.00 0.00 3.16
2303 2572 0.730265 AAACTCGTTTCGCAGCACAA 59.270 45.000 0.00 0.00 0.00 3.33
2304 2573 0.303493 GAAACTCGTTTCGCAGCACA 59.697 50.000 6.76 0.00 39.42 4.57
2314 2583 0.027063 CGTTGTTGCGGAAACTCGTT 59.973 50.000 0.00 0.00 39.70 3.85
2322 2591 0.741574 AACACAGTCGTTGTTGCGGA 60.742 50.000 0.00 0.00 38.16 5.54
2337 2606 0.879839 GCCACCACCATTTGCAACAC 60.880 55.000 0.00 0.00 0.00 3.32
2361 2630 2.507407 TCCCCTTGCAATTAGTGGTC 57.493 50.000 0.00 0.00 0.00 4.02
2363 2632 4.824479 AAAATCCCCTTGCAATTAGTGG 57.176 40.909 0.00 0.00 0.00 4.00
2391 2660 3.774066 ACAAGAAGCTTGTTGCAGAAAC 58.226 40.909 30.24 1.47 45.94 2.78


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

AutoCloner maintained by Alex Coulton.