Multiple sequence alignment - TraesCS1B01G439700

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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 TraesCS1B01G439700 chr1B 100.000 2892 0 0 800 3691 661508321 661511212 0.000000e+00 5341.0
1 TraesCS1B01G439700 chr1B 100.000 433 0 0 1 433 661507522 661507954 0.000000e+00 800.0
2 TraesCS1B01G439700 chr1B 80.387 362 32 15 79 427 661567350 661567015 4.760000e-59 239.0
3 TraesCS1B01G439700 chr1D 93.039 747 29 14 800 1540 475502366 475503095 0.000000e+00 1070.0
4 TraesCS1B01G439700 chr1D 93.065 620 21 7 2811 3408 475504029 475504648 0.000000e+00 887.0
5 TraesCS1B01G439700 chr1D 91.406 640 35 13 2111 2744 475503403 475504028 0.000000e+00 859.0
6 TraesCS1B01G439700 chr1D 95.735 422 16 2 3 424 475501496 475501915 0.000000e+00 678.0
7 TraesCS1B01G439700 chr1D 94.309 123 6 1 1790 1912 418042983 418043104 1.750000e-43 187.0
8 TraesCS1B01G439700 chr1D 93.600 125 7 1 1792 1916 184463018 184463141 6.290000e-43 185.0
9 TraesCS1B01G439700 chr1D 96.078 102 4 0 1654 1755 475503292 475503393 2.280000e-37 167.0
10 TraesCS1B01G439700 chr1D 89.091 55 5 1 1322 1376 46107121 46107068 2.380000e-07 67.6
11 TraesCS1B01G439700 chr1A 93.141 729 33 11 800 1527 571281106 571281818 0.000000e+00 1053.0
12 TraesCS1B01G439700 chr1A 85.923 888 69 30 1897 2744 571282213 571283084 0.000000e+00 896.0
13 TraesCS1B01G439700 chr1A 96.774 403 9 4 3013 3413 571283544 571283944 0.000000e+00 669.0
14 TraesCS1B01G439700 chr1A 92.706 425 22 6 3 424 571280586 571281004 4.080000e-169 604.0
15 TraesCS1B01G439700 chr1A 88.046 435 35 9 3 424 571349042 571348612 1.980000e-137 499.0
16 TraesCS1B01G439700 chr1A 82.857 280 31 9 3424 3691 571284291 571284565 6.160000e-58 235.0
17 TraesCS1B01G439700 chr1A 86.463 229 9 4 2811 3017 571283085 571283313 7.970000e-57 231.0
18 TraesCS1B01G439700 chr1A 90.625 128 7 4 1536 1658 571281912 571282039 8.200000e-37 165.0
19 TraesCS1B01G439700 chr1A 91.597 119 8 2 1654 1771 571282083 571282200 2.950000e-36 163.0
20 TraesCS1B01G439700 chr5B 97.479 119 3 0 1785 1903 511839674 511839792 1.740000e-48 204.0
21 TraesCS1B01G439700 chr5B 95.000 120 6 0 1791 1910 685441690 685441571 4.870000e-44 189.0
22 TraesCS1B01G439700 chrUn 99.099 111 1 0 1792 1902 27987519 27987409 2.250000e-47 200.0
23 TraesCS1B01G439700 chr2B 97.414 116 3 0 1789 1904 146781184 146781069 8.090000e-47 198.0
24 TraesCS1B01G439700 chr4B 96.581 117 4 0 1785 1901 78817614 78817730 1.050000e-45 195.0
25 TraesCS1B01G439700 chr2D 95.798 119 3 2 1781 1898 272263053 272263170 1.350000e-44 191.0
26 TraesCS1B01G439700 chr3A 95.763 118 4 1 1785 1902 265543331 265543447 4.870000e-44 189.0
27 TraesCS1B01G439700 chr5D 89.431 123 12 1 302 424 289584852 289584973 1.780000e-33 154.0
28 TraesCS1B01G439700 chr3D 88.618 123 14 0 302 424 34544669 34544547 2.300000e-32 150.0
29 TraesCS1B01G439700 chr6D 92.958 71 5 0 1313 1383 445057445 445057375 1.810000e-18 104.0
30 TraesCS1B01G439700 chr6D 88.333 60 6 1 1319 1378 112956263 112956321 1.840000e-08 71.3
31 TraesCS1B01G439700 chr4D 92.453 53 4 0 1326 1378 321815851 321815903 3.950000e-10 76.8
32 TraesCS1B01G439700 chr4D 87.302 63 7 1 1319 1381 442750855 442750794 1.840000e-08 71.3
33 TraesCS1B01G439700 chr7D 90.196 51 5 0 1326 1376 134503747 134503797 2.380000e-07 67.6


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 TraesCS1B01G439700 chr1B 661507522 661511212 3690 False 3070.5 5341 100.00000 1 3691 2 chr1B.!!$F1 3690
1 TraesCS1B01G439700 chr1D 475501496 475504648 3152 False 732.2 1070 93.86460 3 3408 5 chr1D.!!$F3 3405
2 TraesCS1B01G439700 chr1A 571280586 571284565 3979 False 502.0 1053 90.01075 3 3691 8 chr1A.!!$F1 3688

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
980 1059 0.173708 GCCCGACCTGTTGTAGAGAG 59.826 60.0 0.00 0.0 0.0 3.20 F
2367 2592 0.249398 CGATCGAAACCAGGACCCTT 59.751 55.0 10.26 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 2923 0.036875 ACTCTGCAAAGCTACACCCC 59.963 55.000 0.00 0.0 0.00 4.95 R
3413 3940 1.066303 GTAGCGAGCTGACATAGTGCT 59.934 52.381 7.99 0.0 40.02 4.40 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
20 21 0.976641 TCAGATCTTGTGCGGGTTCT 59.023 50.000 0.00 0.00 0.00 3.01
34 35 2.022129 GTTCTGTCCGTGCAGACCG 61.022 63.158 5.78 0.00 44.23 4.79
43 44 1.821241 CGTGCAGACCGTGACAACAG 61.821 60.000 0.00 0.00 0.00 3.16
44 45 0.810031 GTGCAGACCGTGACAACAGT 60.810 55.000 0.00 0.00 0.00 3.55
241 243 0.249868 TCCTTCAGGTTGTCTGCACG 60.250 55.000 0.00 0.00 43.06 5.34
376 378 2.436292 CCGTCGTCGTCCTCCTCT 60.436 66.667 0.71 0.00 35.01 3.69
424 426 1.663074 GAGCATCGCCGAGTCCATC 60.663 63.158 0.00 0.00 0.00 3.51
901 977 4.292178 CGGGCCATCGCTCTCTCC 62.292 72.222 4.39 0.00 30.96 3.71
903 979 4.292178 GGCCATCGCTCTCTCCCG 62.292 72.222 0.00 0.00 34.44 5.14
904 980 4.292178 GCCATCGCTCTCTCCCGG 62.292 72.222 0.00 0.00 0.00 5.73
968 1047 3.122971 GCAACTTACGGCCCGACC 61.123 66.667 11.71 0.00 0.00 4.79
969 1048 2.660802 CAACTTACGGCCCGACCT 59.339 61.111 11.71 0.00 35.61 3.85
970 1049 1.740296 CAACTTACGGCCCGACCTG 60.740 63.158 11.71 0.00 35.61 4.00
973 1052 1.740296 CTTACGGCCCGACCTGTTG 60.740 63.158 11.71 0.00 35.61 3.33
974 1053 2.444700 CTTACGGCCCGACCTGTTGT 62.445 60.000 11.71 0.00 35.61 3.32
980 1059 0.173708 GCCCGACCTGTTGTAGAGAG 59.826 60.000 0.00 0.00 0.00 3.20
982 1061 1.746220 CCCGACCTGTTGTAGAGAGAG 59.254 57.143 0.00 0.00 0.00 3.20
984 1063 2.680841 CCGACCTGTTGTAGAGAGAGAG 59.319 54.545 0.00 0.00 0.00 3.20
986 1065 4.004314 CGACCTGTTGTAGAGAGAGAGAA 58.996 47.826 0.00 0.00 0.00 2.87
987 1066 4.456222 CGACCTGTTGTAGAGAGAGAGAAA 59.544 45.833 0.00 0.00 0.00 2.52
988 1067 5.048643 CGACCTGTTGTAGAGAGAGAGAAAA 60.049 44.000 0.00 0.00 0.00 2.29
1047 1126 2.496817 CCGGAAGAGAGGAAGGCG 59.503 66.667 0.00 0.00 0.00 5.52
1189 1268 3.911698 CGCGGGGGATGATGACGA 61.912 66.667 0.00 0.00 0.00 4.20
1190 1269 2.280186 GCGGGGGATGATGACGAC 60.280 66.667 0.00 0.00 0.00 4.34
1437 1516 2.584064 CACATCAGGTAGCCCGCA 59.416 61.111 0.00 0.00 35.12 5.69
1527 1608 1.876714 GACGAATTGGAGCGCGCTA 60.877 57.895 36.69 20.50 0.00 4.26
1528 1609 2.078958 GACGAATTGGAGCGCGCTAC 62.079 60.000 36.22 36.22 0.00 3.58
1554 1720 2.860136 CGAATCTAGCAAGCAATCGACA 59.140 45.455 0.00 0.00 0.00 4.35
1564 1730 4.034394 GCAAGCAATCGACATGTCAGATTA 59.966 41.667 28.81 12.41 34.04 1.75
1568 1734 4.805719 GCAATCGACATGTCAGATTACTCA 59.194 41.667 28.81 9.21 34.04 3.41
1607 1778 2.128771 ATCCCAAGGATTGTGGTTCG 57.871 50.000 0.00 0.00 46.99 3.95
1615 1786 2.238646 AGGATTGTGGTTCGGCTAATGA 59.761 45.455 0.00 0.00 0.00 2.57
1661 1881 3.801114 AGCTGACAGTGCGATTATACA 57.199 42.857 3.99 0.00 35.28 2.29
1686 1907 4.532834 TGACTTCATAATTTAGCACCCCC 58.467 43.478 0.00 0.00 0.00 5.40
1728 1949 2.168313 TCGAGCTGCATCCTCATAACAA 59.832 45.455 13.10 0.00 0.00 2.83
1756 1977 3.854784 GCAATGCTTCCAGTGTGTTCTTC 60.855 47.826 0.00 0.00 39.15 2.87
1765 1986 1.692519 AGTGTGTTCTTCCGGCTTAGT 59.307 47.619 0.00 0.00 0.00 2.24
1766 1987 2.104281 AGTGTGTTCTTCCGGCTTAGTT 59.896 45.455 0.00 0.00 0.00 2.24
1767 1988 3.322828 AGTGTGTTCTTCCGGCTTAGTTA 59.677 43.478 0.00 0.00 0.00 2.24
1768 1989 3.678548 GTGTGTTCTTCCGGCTTAGTTAG 59.321 47.826 0.00 0.00 0.00 2.34
1793 2014 3.056035 ACTTAGCCCAGTGTAGCAACTAC 60.056 47.826 5.31 0.00 37.46 2.73
1794 2015 1.645710 AGCCCAGTGTAGCAACTACT 58.354 50.000 6.34 0.00 37.78 2.57
1795 2016 1.550976 AGCCCAGTGTAGCAACTACTC 59.449 52.381 6.34 3.00 37.78 2.59
1796 2017 1.405661 GCCCAGTGTAGCAACTACTCC 60.406 57.143 6.34 0.00 37.78 3.85
1797 2018 1.207329 CCCAGTGTAGCAACTACTCCC 59.793 57.143 6.34 0.00 37.78 4.30
1798 2019 2.180276 CCAGTGTAGCAACTACTCCCT 58.820 52.381 6.34 0.00 37.78 4.20
1799 2020 2.166664 CCAGTGTAGCAACTACTCCCTC 59.833 54.545 6.34 0.00 37.78 4.30
1800 2021 2.166664 CAGTGTAGCAACTACTCCCTCC 59.833 54.545 6.34 0.00 37.78 4.30
1801 2022 1.134560 GTGTAGCAACTACTCCCTCCG 59.865 57.143 6.34 0.00 37.78 4.63
1802 2023 1.272313 TGTAGCAACTACTCCCTCCGT 60.272 52.381 6.34 0.00 37.78 4.69
1803 2024 1.823610 GTAGCAACTACTCCCTCCGTT 59.176 52.381 0.00 0.00 34.45 4.44
1804 2025 0.896226 AGCAACTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
1805 2026 0.896226 GCAACTACTCCCTCCGTTCT 59.104 55.000 0.00 0.00 0.00 3.01
1806 2027 1.404315 GCAACTACTCCCTCCGTTCTG 60.404 57.143 0.00 0.00 0.00 3.02
1807 2028 2.168496 CAACTACTCCCTCCGTTCTGA 58.832 52.381 0.00 0.00 0.00 3.27
1808 2029 2.561419 CAACTACTCCCTCCGTTCTGAA 59.439 50.000 0.00 0.00 0.00 3.02
1809 2030 3.103080 ACTACTCCCTCCGTTCTGAAT 57.897 47.619 0.00 0.00 0.00 2.57
1810 2031 3.442076 ACTACTCCCTCCGTTCTGAATT 58.558 45.455 0.00 0.00 0.00 2.17
1811 2032 4.607239 ACTACTCCCTCCGTTCTGAATTA 58.393 43.478 0.00 0.00 0.00 1.40
1812 2033 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
1813 2034 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
1814 2035 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
1815 2036 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
1816 2037 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
1817 2038 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
1818 2039 3.612860 CCTCCGTTCTGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
1819 2040 2.991190 TCCGTTCTGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
1820 2041 2.734606 CCGTTCTGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
1821 2042 3.423123 CCGTTCTGAATTACTTGTCGCAC 60.423 47.826 0.00 0.00 0.00 5.34
1822 2043 3.718036 CGTTCTGAATTACTTGTCGCACG 60.718 47.826 0.00 0.00 0.00 5.34
1823 2044 3.021269 TCTGAATTACTTGTCGCACGT 57.979 42.857 0.00 0.00 0.00 4.49
1824 2045 4.163458 TCTGAATTACTTGTCGCACGTA 57.837 40.909 0.00 0.00 0.00 3.57
1825 2046 4.740268 TCTGAATTACTTGTCGCACGTAT 58.260 39.130 0.00 0.00 0.00 3.06
1826 2047 4.561213 TCTGAATTACTTGTCGCACGTATG 59.439 41.667 0.00 0.00 0.00 2.39
1827 2048 3.615056 TGAATTACTTGTCGCACGTATGG 59.385 43.478 0.00 0.00 0.00 2.74
1828 2049 3.513680 ATTACTTGTCGCACGTATGGA 57.486 42.857 0.00 0.00 0.00 3.41
1829 2050 3.513680 TTACTTGTCGCACGTATGGAT 57.486 42.857 0.00 0.00 0.00 3.41
1830 2051 1.640428 ACTTGTCGCACGTATGGATG 58.360 50.000 0.00 0.00 0.00 3.51
1831 2052 1.067142 ACTTGTCGCACGTATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
1832 2053 2.164827 ACTTGTCGCACGTATGGATGTA 59.835 45.455 0.00 0.00 0.00 2.29
1833 2054 3.181479 ACTTGTCGCACGTATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
1834 2055 3.007979 TGTCGCACGTATGGATGTATC 57.992 47.619 0.00 0.00 0.00 2.24
1835 2056 2.621526 TGTCGCACGTATGGATGTATCT 59.378 45.455 0.00 0.00 0.00 1.98
1836 2057 3.816523 TGTCGCACGTATGGATGTATCTA 59.183 43.478 0.00 0.00 0.00 1.98
1837 2058 4.083484 TGTCGCACGTATGGATGTATCTAG 60.083 45.833 0.00 0.00 0.00 2.43
1838 2059 4.153655 GTCGCACGTATGGATGTATCTAGA 59.846 45.833 0.00 0.00 0.00 2.43
1839 2060 4.941873 TCGCACGTATGGATGTATCTAGAT 59.058 41.667 10.73 10.73 0.00 1.98
1840 2061 5.030936 CGCACGTATGGATGTATCTAGATG 58.969 45.833 15.79 0.00 0.00 2.90
1841 2062 5.392057 CGCACGTATGGATGTATCTAGATGT 60.392 44.000 15.79 1.25 30.36 3.06
1842 2063 6.183360 CGCACGTATGGATGTATCTAGATGTA 60.183 42.308 15.79 4.44 29.44 2.29
1843 2064 7.467403 CGCACGTATGGATGTATCTAGATGTAT 60.467 40.741 15.79 9.11 29.44 2.29
1844 2065 8.191446 GCACGTATGGATGTATCTAGATGTATT 58.809 37.037 15.79 0.00 29.44 1.89
1870 2091 9.547753 TTTAGTTCTAGATACATCCATTTCAGC 57.452 33.333 0.00 0.00 0.00 4.26
1871 2092 6.219473 AGTTCTAGATACATCCATTTCAGCG 58.781 40.000 0.00 0.00 0.00 5.18
1872 2093 6.040955 AGTTCTAGATACATCCATTTCAGCGA 59.959 38.462 0.00 0.00 0.00 4.93
1873 2094 5.773575 TCTAGATACATCCATTTCAGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
1874 2095 3.384668 AGATACATCCATTTCAGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
1875 2096 2.951457 TACATCCATTTCAGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
1876 2097 1.645034 ACATCCATTTCAGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
1877 2098 1.066858 ACATCCATTTCAGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
1878 2099 2.165641 ACATCCATTTCAGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
1879 2100 3.186909 CATCCATTTCAGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
1880 2101 3.520290 TCCATTTCAGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
1881 2102 3.857052 TCCATTTCAGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
1882 2103 4.250464 TCCATTTCAGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
1883 2104 4.092821 TCCATTTCAGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
1884 2105 4.092821 CCATTTCAGCGACGAGTAATTTGA 59.907 41.667 0.00 0.00 0.00 2.69
1885 2106 5.390461 CCATTTCAGCGACGAGTAATTTGAA 60.390 40.000 0.00 0.00 0.00 2.69
1886 2107 5.660629 TTTCAGCGACGAGTAATTTGAAA 57.339 34.783 0.00 0.31 32.52 2.69
1887 2108 4.640805 TCAGCGACGAGTAATTTGAAAC 57.359 40.909 0.00 0.00 0.00 2.78
1888 2109 3.120616 TCAGCGACGAGTAATTTGAAACG 59.879 43.478 0.00 0.00 0.00 3.60
1889 2110 2.410730 AGCGACGAGTAATTTGAAACGG 59.589 45.455 0.00 0.00 0.00 4.44
1890 2111 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
1891 2112 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
1892 2113 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
1893 2114 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1894 2115 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1895 2116 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
1896 2117 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
1897 2118 5.622914 CGAGTAATTTGAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
1910 2131 4.381411 GGAGGGAGTAGTAATTGACATGC 58.619 47.826 0.00 0.00 0.00 4.06
1916 2137 5.698545 GGAGTAGTAATTGACATGCCAGATC 59.301 44.000 0.00 0.00 0.00 2.75
1920 2141 1.590932 ATTGACATGCCAGATCGCTC 58.409 50.000 0.00 0.00 0.00 5.03
1970 2192 1.538047 TTGTGGCTCTGCAAATCCTC 58.462 50.000 0.00 0.00 0.00 3.71
1972 2194 0.322816 GTGGCTCTGCAAATCCTCCA 60.323 55.000 0.00 0.00 0.00 3.86
1973 2195 0.322816 TGGCTCTGCAAATCCTCCAC 60.323 55.000 0.00 0.00 0.00 4.02
2012 2234 6.470160 CGAATGCACATACTACTGTTCTTTC 58.530 40.000 0.00 0.00 0.00 2.62
2016 2238 5.926542 TGCACATACTACTGTTCTTTCAGAC 59.073 40.000 0.65 0.00 38.63 3.51
2074 2296 8.492673 TGACTTTATAATTTAGCACCTGACTG 57.507 34.615 0.00 0.00 0.00 3.51
2075 2297 8.100791 TGACTTTATAATTTAGCACCTGACTGT 58.899 33.333 0.00 0.00 0.00 3.55
2081 2303 3.386768 TTAGCACCTGACTGTCTGAAC 57.613 47.619 15.25 5.19 0.00 3.18
2089 2313 5.010112 CACCTGACTGTCTGAACTCTAAGAA 59.990 44.000 15.25 0.00 0.00 2.52
2091 2315 5.010112 CCTGACTGTCTGAACTCTAAGAACA 59.990 44.000 15.25 0.00 0.00 3.18
2102 2326 9.261180 CTGAACTCTAAGAACAAAACTACATCA 57.739 33.333 0.00 0.00 0.00 3.07
2123 2347 7.228108 ACATCATCATAACACTAGAAAGCATGG 59.772 37.037 0.00 0.00 0.00 3.66
2135 2359 6.886459 ACTAGAAAGCATGGAATTCTTTGCTA 59.114 34.615 25.51 14.87 44.26 3.49
2140 2364 4.883585 AGCATGGAATTCTTTGCTAATCGA 59.116 37.500 24.63 0.00 43.28 3.59
2162 2386 6.374053 TCGACTGAATCATTATTTGCCAAGAA 59.626 34.615 0.00 0.00 0.00 2.52
2164 2388 7.541783 CGACTGAATCATTATTTGCCAAGAAAA 59.458 33.333 0.00 0.00 0.00 2.29
2165 2389 8.538409 ACTGAATCATTATTTGCCAAGAAAAC 57.462 30.769 0.00 0.00 0.00 2.43
2173 2397 9.904647 CATTATTTGCCAAGAAAACGATTATTG 57.095 29.630 0.00 0.00 0.00 1.90
2186 2410 4.253685 ACGATTATTGTCACTGAACCCTG 58.746 43.478 0.00 0.00 0.00 4.45
2187 2411 4.253685 CGATTATTGTCACTGAACCCTGT 58.746 43.478 0.00 0.00 0.00 4.00
2188 2412 4.330074 CGATTATTGTCACTGAACCCTGTC 59.670 45.833 0.00 0.00 0.00 3.51
2228 2452 2.701163 GATACCTGAAGAGCGGCCCG 62.701 65.000 0.00 0.00 0.00 6.13
2258 2482 2.038659 GAGAAGGACATGGAGAGGAGG 58.961 57.143 0.00 0.00 0.00 4.30
2333 2558 4.016851 CCCTGATAATCAATCCCCATCCAT 60.017 45.833 0.00 0.00 33.22 3.41
2335 2560 5.197224 TGATAATCAATCCCCATCCATCC 57.803 43.478 0.00 0.00 33.22 3.51
2336 2561 4.607141 TGATAATCAATCCCCATCCATCCA 59.393 41.667 0.00 0.00 33.22 3.41
2340 2565 0.557729 AATCCCCATCCATCCACCAC 59.442 55.000 0.00 0.00 0.00 4.16
2341 2566 0.328842 ATCCCCATCCATCCACCACT 60.329 55.000 0.00 0.00 0.00 4.00
2342 2567 0.345146 TCCCCATCCATCCACCACTA 59.655 55.000 0.00 0.00 0.00 2.74
2343 2568 1.060640 TCCCCATCCATCCACCACTAT 60.061 52.381 0.00 0.00 0.00 2.12
2344 2569 1.074405 CCCCATCCATCCACCACTATG 59.926 57.143 0.00 0.00 0.00 2.23
2367 2592 0.249398 CGATCGAAACCAGGACCCTT 59.751 55.000 10.26 0.00 0.00 3.95
2368 2593 1.338769 CGATCGAAACCAGGACCCTTT 60.339 52.381 10.26 0.00 0.00 3.11
2370 2595 0.841289 TCGAAACCAGGACCCTTTGT 59.159 50.000 0.00 0.00 0.00 2.83
2371 2596 1.202722 TCGAAACCAGGACCCTTTGTC 60.203 52.381 0.00 0.00 43.67 3.18
2372 2597 1.202770 CGAAACCAGGACCCTTTGTCT 60.203 52.381 0.00 0.00 43.89 3.41
2373 2598 2.505405 GAAACCAGGACCCTTTGTCTC 58.495 52.381 0.00 0.00 43.89 3.36
2376 2601 1.132689 ACCAGGACCCTTTGTCTCTCT 60.133 52.381 0.00 0.00 43.89 3.10
2388 2613 1.813178 TGTCTCTCTAAGCACGACCAG 59.187 52.381 0.00 0.00 0.00 4.00
2420 2645 4.990526 AGATCCCTTGTTCAAGTGTGATT 58.009 39.130 10.93 1.51 32.48 2.57
2443 2668 4.633126 TGTAATGTCAGAATTCAGCTCTGC 59.367 41.667 8.44 0.00 40.18 4.26
2459 2684 6.654582 TCAGCTCTGCAATACTAATTTCAACA 59.345 34.615 0.00 0.00 0.00 3.33
2554 2781 7.553402 AGACATTTTCTCTGGATTGATCTTCTG 59.447 37.037 0.00 0.00 0.00 3.02
2559 2786 7.678947 TTCTCTGGATTGATCTTCTGAAAAC 57.321 36.000 0.00 0.00 0.00 2.43
2609 2865 5.181009 ACACGATGATCAGATGTTTGATGT 58.819 37.500 0.09 0.00 37.90 3.06
2613 2869 5.558463 CGATGATCAGATGTTTGATGTCAGC 60.558 44.000 0.09 0.00 37.90 4.26
2628 2884 1.135859 GTCAGCTTGTTTCTGCATCCG 60.136 52.381 0.00 0.00 0.00 4.18
2632 2888 1.129437 GCTTGTTTCTGCATCCGAGAC 59.871 52.381 0.00 0.00 0.00 3.36
2640 2897 0.534873 TGCATCCGAGACGAAATGGA 59.465 50.000 0.00 0.00 34.45 3.41
2646 2903 1.267532 CCGAGACGAAATGGATTTGCG 60.268 52.381 0.00 0.00 0.00 4.85
2660 2917 1.159285 TTTGCGAGATTCACCTGCAG 58.841 50.000 6.78 6.78 36.83 4.41
2664 2921 2.012673 GCGAGATTCACCTGCAGAAAT 58.987 47.619 17.39 11.73 0.00 2.17
2665 2922 2.223203 GCGAGATTCACCTGCAGAAATG 60.223 50.000 17.39 10.71 0.00 2.32
2666 2923 2.353889 CGAGATTCACCTGCAGAAATGG 59.646 50.000 17.39 0.19 0.00 3.16
2682 2939 0.323725 ATGGGGGTGTAGCTTTGCAG 60.324 55.000 0.00 0.00 0.00 4.41
2744 3004 1.278127 CCGATTGGGTCACAGTAGGTT 59.722 52.381 0.00 0.00 28.94 3.50
2745 3005 2.618053 CGATTGGGTCACAGTAGGTTC 58.382 52.381 0.00 0.00 0.00 3.62
2746 3006 2.233922 CGATTGGGTCACAGTAGGTTCT 59.766 50.000 0.00 0.00 0.00 3.01
2747 3007 3.446161 CGATTGGGTCACAGTAGGTTCTA 59.554 47.826 0.00 0.00 0.00 2.10
2748 3008 4.677250 CGATTGGGTCACAGTAGGTTCTAC 60.677 50.000 0.00 0.00 0.00 2.59
2749 3009 3.537795 TGGGTCACAGTAGGTTCTACT 57.462 47.619 2.07 2.07 0.00 2.57
2750 3010 3.853207 TGGGTCACAGTAGGTTCTACTT 58.147 45.455 4.99 0.00 0.00 2.24
2751 3011 3.830755 TGGGTCACAGTAGGTTCTACTTC 59.169 47.826 4.99 0.00 0.00 3.01
2752 3012 4.087907 GGGTCACAGTAGGTTCTACTTCT 58.912 47.826 4.99 0.00 0.00 2.85
2753 3013 5.222192 TGGGTCACAGTAGGTTCTACTTCTA 60.222 44.000 4.99 0.00 0.00 2.10
2754 3014 5.125257 GGGTCACAGTAGGTTCTACTTCTAC 59.875 48.000 4.99 4.20 35.03 2.59
2755 3015 5.945191 GGTCACAGTAGGTTCTACTTCTACT 59.055 44.000 4.99 0.00 42.89 2.57
2759 3019 5.900865 AGTAGGTTCTACTTCTACTGTGC 57.099 43.478 2.07 0.00 41.24 4.57
2760 3020 5.322754 AGTAGGTTCTACTTCTACTGTGCA 58.677 41.667 2.07 0.00 41.24 4.57
2761 3021 5.773680 AGTAGGTTCTACTTCTACTGTGCAA 59.226 40.000 2.07 0.00 41.24 4.08
2762 3022 5.546621 AGGTTCTACTTCTACTGTGCAAA 57.453 39.130 0.00 0.00 0.00 3.68
2763 3023 5.542779 AGGTTCTACTTCTACTGTGCAAAG 58.457 41.667 1.09 1.09 0.00 2.77
2764 3024 5.304614 AGGTTCTACTTCTACTGTGCAAAGA 59.695 40.000 11.93 0.00 0.00 2.52
2765 3025 5.405873 GGTTCTACTTCTACTGTGCAAAGAC 59.594 44.000 11.93 0.00 0.00 3.01
2766 3026 5.784578 TCTACTTCTACTGTGCAAAGACA 57.215 39.130 11.93 0.00 0.00 3.41
2767 3027 6.156748 TCTACTTCTACTGTGCAAAGACAA 57.843 37.500 11.93 0.00 0.00 3.18
2768 3028 6.216569 TCTACTTCTACTGTGCAAAGACAAG 58.783 40.000 11.93 11.16 0.00 3.16
2769 3029 3.561725 ACTTCTACTGTGCAAAGACAAGC 59.438 43.478 11.93 0.00 0.00 4.01
2770 3030 3.475566 TCTACTGTGCAAAGACAAGCT 57.524 42.857 11.93 0.00 0.00 3.74
2771 3031 3.808728 TCTACTGTGCAAAGACAAGCTT 58.191 40.909 11.93 0.00 38.88 3.74
2772 3032 3.809832 TCTACTGTGCAAAGACAAGCTTC 59.190 43.478 11.93 0.00 35.24 3.86
2773 3033 2.648059 ACTGTGCAAAGACAAGCTTCT 58.352 42.857 11.93 0.00 35.24 2.85
2774 3034 3.019564 ACTGTGCAAAGACAAGCTTCTT 58.980 40.909 11.93 0.00 37.44 2.52
2775 3035 3.445096 ACTGTGCAAAGACAAGCTTCTTT 59.555 39.130 11.93 7.46 44.98 2.52
2776 3036 4.082026 ACTGTGCAAAGACAAGCTTCTTTT 60.082 37.500 11.93 2.77 42.09 2.27
2777 3037 4.819769 TGTGCAAAGACAAGCTTCTTTTT 58.180 34.783 10.13 0.00 42.09 1.94
2839 3099 6.417339 CAGCTCAGCTTCTTTTTCTTTTCTTC 59.583 38.462 0.00 0.00 36.40 2.87
2840 3100 6.096001 AGCTCAGCTTCTTTTTCTTTTCTTCA 59.904 34.615 0.00 0.00 33.89 3.02
2909 3182 5.604231 TGATGATGAGGAATAGTAGTGGCTT 59.396 40.000 0.00 0.00 0.00 4.35
2924 3197 1.811679 GCTTAGCTGGTCCAGTCGC 60.812 63.158 20.24 13.05 33.43 5.19
2934 3207 2.513204 CCAGTCGCATCAGGCCAG 60.513 66.667 5.01 0.00 40.31 4.85
3277 3803 4.368543 GGTCGACACGTGGGGGAC 62.369 72.222 21.57 21.05 0.00 4.46
3413 3940 1.290955 CAAGAACCTACACGGCCGA 59.709 57.895 35.90 8.90 35.61 5.54
3415 3942 2.502692 AAGAACCTACACGGCCGAGC 62.503 60.000 35.90 10.05 35.61 5.03
3418 4281 3.760035 CCTACACGGCCGAGCACT 61.760 66.667 35.90 11.16 0.00 4.40
3421 4284 0.595053 CTACACGGCCGAGCACTATG 60.595 60.000 35.90 20.43 0.00 2.23
3422 4285 1.317431 TACACGGCCGAGCACTATGT 61.317 55.000 35.90 25.24 0.00 2.29
3425 4288 1.589993 CGGCCGAGCACTATGTCAG 60.590 63.158 24.07 0.00 0.00 3.51
3430 4293 2.587574 GAGCACTATGTCAGCTCGC 58.412 57.895 0.00 0.00 44.37 5.03
3460 4323 3.667497 TTTTTATTGGCACGCAATCCA 57.333 38.095 0.00 0.00 0.00 3.41
3461 4324 2.937469 TTTATTGGCACGCAATCCAG 57.063 45.000 0.00 0.00 33.32 3.86
3464 4327 0.968405 ATTGGCACGCAATCCAGTTT 59.032 45.000 0.00 0.00 33.32 2.66
3497 4360 9.679661 TCTACAATACCACAATTATGTTCATGT 57.320 29.630 0.00 0.00 37.82 3.21
3536 4399 5.471556 AAAATGCAAATGTCCATGTCTCA 57.528 34.783 0.00 0.00 0.00 3.27
3544 4407 6.363357 GCAAATGTCCATGTCTCAAAAAGTAC 59.637 38.462 0.00 0.00 0.00 2.73
3545 4408 6.575162 AATGTCCATGTCTCAAAAAGTACC 57.425 37.500 0.00 0.00 0.00 3.34
3557 4420 8.476925 GTCTCAAAAAGTACCGCTTTATTTTTG 58.523 33.333 15.49 15.49 45.91 2.44
3602 4467 4.238385 CGTGTTGGACGTCGTCAT 57.762 55.556 25.64 0.00 43.50 3.06
3613 4486 1.202604 ACGTCGTCATCCACAAAGGTT 60.203 47.619 0.00 0.00 39.02 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.556911 AGAACCCGCACAAGATCTGAT 59.443 47.619 0.00 0.00 0.00 2.90
1 2 0.976641 AGAACCCGCACAAGATCTGA 59.023 50.000 0.00 0.00 0.00 3.27
20 21 3.220658 TCACGGTCTGCACGGACA 61.221 61.111 11.53 0.00 37.91 4.02
34 35 5.447818 CCTGAAACTCTGAAACTGTTGTCAC 60.448 44.000 0.00 0.00 0.00 3.67
43 44 3.149981 CCCCTTCCTGAAACTCTGAAAC 58.850 50.000 0.00 0.00 0.00 2.78
44 45 2.108250 CCCCCTTCCTGAAACTCTGAAA 59.892 50.000 0.00 0.00 0.00 2.69
67 69 1.070289 CGGCAGGTAGGTTTCCTATCC 59.930 57.143 2.84 4.92 37.93 2.59
68 70 1.761198 ACGGCAGGTAGGTTTCCTATC 59.239 52.381 0.00 0.00 38.48 2.08
73 75 1.066430 TCATCACGGCAGGTAGGTTTC 60.066 52.381 0.00 0.00 0.00 2.78
77 79 1.226974 CGTCATCACGGCAGGTAGG 60.227 63.158 0.00 0.00 42.73 3.18
78 80 0.248661 CTCGTCATCACGGCAGGTAG 60.249 60.000 0.00 0.00 46.70 3.18
847 923 2.733218 GCCAAAAGCGCGGGAAAC 60.733 61.111 8.83 0.00 0.00 2.78
885 961 3.934962 GGGAGAGAGCGATGGCCC 61.935 72.222 0.00 0.00 41.24 5.80
968 1047 6.987386 TCCTTTTTCTCTCTCTCTACAACAG 58.013 40.000 0.00 0.00 0.00 3.16
969 1048 6.015010 CCTCCTTTTTCTCTCTCTCTACAACA 60.015 42.308 0.00 0.00 0.00 3.33
970 1049 6.209788 TCCTCCTTTTTCTCTCTCTCTACAAC 59.790 42.308 0.00 0.00 0.00 3.32
973 1052 6.184789 TCTCCTCCTTTTTCTCTCTCTCTAC 58.815 44.000 0.00 0.00 0.00 2.59
974 1053 6.395780 TCTCCTCCTTTTTCTCTCTCTCTA 57.604 41.667 0.00 0.00 0.00 2.43
1040 1119 4.856607 CTCGGTCGCTCGCCTTCC 62.857 72.222 0.00 0.00 0.00 3.46
1047 1126 4.239203 ATCGTCGCTCGGTCGCTC 62.239 66.667 0.00 0.00 40.32 5.03
1409 1488 1.219124 CTGATGTGGAGGTCGGTGG 59.781 63.158 0.00 0.00 0.00 4.61
1504 1585 0.796312 GCGCTCCAATTCGTCTTCAA 59.204 50.000 0.00 0.00 0.00 2.69
1511 1592 2.621000 GTAGCGCGCTCCAATTCG 59.379 61.111 40.23 0.00 0.00 3.34
1527 1608 1.424493 GCTTGCTAGATTCGCTGCGT 61.424 55.000 22.48 2.86 0.00 5.24
1528 1609 1.275066 GCTTGCTAGATTCGCTGCG 59.725 57.895 17.25 17.25 0.00 5.18
1531 1612 1.863454 CGATTGCTTGCTAGATTCGCT 59.137 47.619 0.00 0.00 0.00 4.93
1538 1704 2.931969 TGACATGTCGATTGCTTGCTAG 59.068 45.455 20.54 0.00 0.00 3.42
1600 1771 1.599542 GCAGATCATTAGCCGAACCAC 59.400 52.381 0.00 0.00 0.00 4.16
1607 1778 4.396522 AGAGGATTTGCAGATCATTAGCC 58.603 43.478 18.08 1.28 0.00 3.93
1615 1786 4.487714 TTTCGGTAGAGGATTTGCAGAT 57.512 40.909 0.00 0.00 0.00 2.90
1661 1881 5.652452 GGGGTGCTAAATTATGAAGTCAGTT 59.348 40.000 0.00 0.00 0.00 3.16
1686 1907 1.694150 TCTTGGAACTCAGGTGGTCAG 59.306 52.381 0.00 0.00 0.00 3.51
1771 1992 1.978580 AGTTGCTACACTGGGCTAAGT 59.021 47.619 0.13 0.00 0.00 2.24
1772 1993 2.770164 AGTTGCTACACTGGGCTAAG 57.230 50.000 0.13 0.00 0.00 2.18
1793 2014 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
1794 2015 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
1795 2016 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
1796 2017 3.612860 CGACAAGTAATTCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
1797 2018 3.060895 GCGACAAGTAATTCAGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
1798 2019 2.991190 GCGACAAGTAATTCAGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
1799 2020 2.734606 TGCGACAAGTAATTCAGAACGG 59.265 45.455 0.00 0.00 0.00 4.44
1800 2021 3.718036 CGTGCGACAAGTAATTCAGAACG 60.718 47.826 0.00 0.00 0.00 3.95
1801 2022 3.183775 ACGTGCGACAAGTAATTCAGAAC 59.816 43.478 0.00 0.00 0.00 3.01
1802 2023 3.386486 ACGTGCGACAAGTAATTCAGAA 58.614 40.909 0.00 0.00 0.00 3.02
1803 2024 3.021269 ACGTGCGACAAGTAATTCAGA 57.979 42.857 0.00 0.00 0.00 3.27
1804 2025 4.259810 CCATACGTGCGACAAGTAATTCAG 60.260 45.833 0.00 0.88 32.82 3.02
1805 2026 3.615056 CCATACGTGCGACAAGTAATTCA 59.385 43.478 0.00 0.00 32.82 2.57
1806 2027 3.861113 TCCATACGTGCGACAAGTAATTC 59.139 43.478 0.00 0.00 32.82 2.17
1807 2028 3.852286 TCCATACGTGCGACAAGTAATT 58.148 40.909 0.00 0.00 32.82 1.40
1808 2029 3.513680 TCCATACGTGCGACAAGTAAT 57.486 42.857 0.00 0.00 32.82 1.89
1809 2030 3.183754 CATCCATACGTGCGACAAGTAA 58.816 45.455 0.00 0.00 32.82 2.24
1810 2031 2.164827 ACATCCATACGTGCGACAAGTA 59.835 45.455 0.00 7.72 33.49 2.24
1811 2032 1.067142 ACATCCATACGTGCGACAAGT 60.067 47.619 0.00 0.00 0.00 3.16
1812 2033 1.640428 ACATCCATACGTGCGACAAG 58.360 50.000 0.00 0.00 0.00 3.16
1813 2034 2.943449 TACATCCATACGTGCGACAA 57.057 45.000 0.00 0.00 0.00 3.18
1814 2035 2.621526 AGATACATCCATACGTGCGACA 59.378 45.455 0.00 0.00 0.00 4.35
1815 2036 3.284323 AGATACATCCATACGTGCGAC 57.716 47.619 0.00 0.00 0.00 5.19
1816 2037 4.320870 TCTAGATACATCCATACGTGCGA 58.679 43.478 0.00 0.00 0.00 5.10
1817 2038 4.680171 TCTAGATACATCCATACGTGCG 57.320 45.455 0.00 0.00 0.00 5.34
1818 2039 5.955488 ACATCTAGATACATCCATACGTGC 58.045 41.667 4.54 0.00 0.00 5.34
1844 2065 9.547753 GCTGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
1845 2066 7.867909 CGCTGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
1846 2067 7.230712 TCGCTGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
1847 2068 6.040955 TCGCTGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
1848 2069 6.144724 GTCGCTGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 0.00 3.01
1849 2070 6.216569 GTCGCTGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 0.00 2.10
1850 2071 5.562890 CGTCGCTGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 0.00 2.43
1851 2072 4.618912 CGTCGCTGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 0.00 2.43
1852 2073 4.277423 TCGTCGCTGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 0.00 1.98
1853 2074 3.068165 TCGTCGCTGAAATGGATGTATCT 59.932 43.478 0.00 0.00 0.00 1.98
1854 2075 3.381045 TCGTCGCTGAAATGGATGTATC 58.619 45.455 0.00 0.00 0.00 2.24
1855 2076 3.181475 ACTCGTCGCTGAAATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
1856 2077 2.165641 ACTCGTCGCTGAAATGGATGTA 59.834 45.455 0.00 0.00 0.00 2.29
1857 2078 1.066858 ACTCGTCGCTGAAATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
1858 2079 1.645034 ACTCGTCGCTGAAATGGATG 58.355 50.000 0.00 0.00 0.00 3.51
1859 2080 3.520290 TTACTCGTCGCTGAAATGGAT 57.480 42.857 0.00 0.00 0.00 3.41
1860 2081 3.520290 ATTACTCGTCGCTGAAATGGA 57.480 42.857 0.00 0.00 0.00 3.41
1861 2082 4.092821 TCAAATTACTCGTCGCTGAAATGG 59.907 41.667 0.00 0.00 0.00 3.16
1862 2083 5.203358 TCAAATTACTCGTCGCTGAAATG 57.797 39.130 0.00 0.00 0.00 2.32
1863 2084 5.856126 TTCAAATTACTCGTCGCTGAAAT 57.144 34.783 0.00 0.00 0.00 2.17
1864 2085 5.437263 GTTTCAAATTACTCGTCGCTGAAA 58.563 37.500 0.00 0.00 0.00 2.69
1865 2086 4.375606 CGTTTCAAATTACTCGTCGCTGAA 60.376 41.667 0.00 0.00 0.00 3.02
1866 2087 3.120616 CGTTTCAAATTACTCGTCGCTGA 59.879 43.478 0.00 0.00 0.00 4.26
1867 2088 3.395671 CGTTTCAAATTACTCGTCGCTG 58.604 45.455 0.00 0.00 0.00 5.18
1868 2089 2.410730 CCGTTTCAAATTACTCGTCGCT 59.589 45.455 0.00 0.00 0.00 4.93
1869 2090 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
1870 2091 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
1871 2092 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
1872 2093 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
1873 2094 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
1874 2095 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
1875 2096 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1876 2097 5.485620 ACTACTCCCTCCGTTTCAAATTAC 58.514 41.667 0.00 0.00 0.00 1.89
1877 2098 5.750352 ACTACTCCCTCCGTTTCAAATTA 57.250 39.130 0.00 0.00 0.00 1.40
1878 2099 4.635699 ACTACTCCCTCCGTTTCAAATT 57.364 40.909 0.00 0.00 0.00 1.82
1879 2100 5.750352 TTACTACTCCCTCCGTTTCAAAT 57.250 39.130 0.00 0.00 0.00 2.32
1880 2101 5.750352 ATTACTACTCCCTCCGTTTCAAA 57.250 39.130 0.00 0.00 0.00 2.69
1881 2102 5.246656 TCAATTACTACTCCCTCCGTTTCAA 59.753 40.000 0.00 0.00 0.00 2.69
1882 2103 4.773674 TCAATTACTACTCCCTCCGTTTCA 59.226 41.667 0.00 0.00 0.00 2.69
1883 2104 5.107824 GTCAATTACTACTCCCTCCGTTTC 58.892 45.833 0.00 0.00 0.00 2.78
1884 2105 4.529377 TGTCAATTACTACTCCCTCCGTTT 59.471 41.667 0.00 0.00 0.00 3.60
1885 2106 4.091549 TGTCAATTACTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
1886 2107 3.705051 TGTCAATTACTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
1887 2108 4.621991 CATGTCAATTACTACTCCCTCCG 58.378 47.826 0.00 0.00 0.00 4.63
1888 2109 4.381411 GCATGTCAATTACTACTCCCTCC 58.619 47.826 0.00 0.00 0.00 4.30
1889 2110 4.141711 TGGCATGTCAATTACTACTCCCTC 60.142 45.833 0.00 0.00 0.00 4.30
1890 2111 3.780294 TGGCATGTCAATTACTACTCCCT 59.220 43.478 0.00 0.00 0.00 4.20
1891 2112 4.130118 CTGGCATGTCAATTACTACTCCC 58.870 47.826 0.00 0.00 0.00 4.30
1892 2113 5.023533 TCTGGCATGTCAATTACTACTCC 57.976 43.478 0.00 0.00 0.00 3.85
1893 2114 5.403766 CGATCTGGCATGTCAATTACTACTC 59.596 44.000 0.00 0.00 0.00 2.59
1894 2115 5.292765 CGATCTGGCATGTCAATTACTACT 58.707 41.667 0.00 0.00 0.00 2.57
1895 2116 4.084328 GCGATCTGGCATGTCAATTACTAC 60.084 45.833 0.00 0.00 0.00 2.73
1896 2117 4.058124 GCGATCTGGCATGTCAATTACTA 58.942 43.478 0.00 0.00 0.00 1.82
1897 2118 2.874701 GCGATCTGGCATGTCAATTACT 59.125 45.455 0.00 0.00 0.00 2.24
1910 2131 1.081892 CCAACTGTTGAGCGATCTGG 58.918 55.000 21.49 0.00 0.00 3.86
1934 2155 3.256631 CCACAATCCTTGGGAAAGTGAAG 59.743 47.826 17.32 4.57 40.53 3.02
1939 2160 1.821136 GAGCCACAATCCTTGGGAAAG 59.179 52.381 0.00 0.00 35.62 2.62
2016 2238 5.104776 TGGAAAGGGTAGAATGACATCTCTG 60.105 44.000 9.20 0.00 0.00 3.35
2064 2286 1.342819 AGAGTTCAGACAGTCAGGTGC 59.657 52.381 2.66 0.00 0.00 5.01
2067 2289 5.010112 TGTTCTTAGAGTTCAGACAGTCAGG 59.990 44.000 2.66 0.00 0.00 3.86
2074 2296 8.644318 TGTAGTTTTGTTCTTAGAGTTCAGAC 57.356 34.615 0.00 0.00 0.00 3.51
2075 2297 9.477484 GATGTAGTTTTGTTCTTAGAGTTCAGA 57.523 33.333 0.00 0.00 0.00 3.27
2102 2326 8.757982 AATTCCATGCTTTCTAGTGTTATGAT 57.242 30.769 0.00 0.00 0.00 2.45
2107 2331 7.373493 CAAAGAATTCCATGCTTTCTAGTGTT 58.627 34.615 0.65 0.00 30.00 3.32
2108 2332 6.571150 GCAAAGAATTCCATGCTTTCTAGTGT 60.571 38.462 20.21 0.00 35.93 3.55
2123 2347 7.688372 TGATTCAGTCGATTAGCAAAGAATTC 58.312 34.615 0.00 0.00 0.00 2.17
2135 2359 6.698008 TGGCAAATAATGATTCAGTCGATT 57.302 33.333 0.00 0.00 0.00 3.34
2140 2364 7.329226 CGTTTTCTTGGCAAATAATGATTCAGT 59.671 33.333 0.00 0.00 0.00 3.41
2162 2386 5.181245 CAGGGTTCAGTGACAATAATCGTTT 59.819 40.000 0.00 0.00 0.00 3.60
2164 2388 4.253685 CAGGGTTCAGTGACAATAATCGT 58.746 43.478 0.00 0.00 0.00 3.73
2165 2389 4.253685 ACAGGGTTCAGTGACAATAATCG 58.746 43.478 0.00 0.00 0.00 3.34
2173 2397 2.550830 ACATGACAGGGTTCAGTGAC 57.449 50.000 0.00 0.00 0.00 3.67
2186 2410 7.445900 TCTGATTACGTCGATTAAACATGAC 57.554 36.000 0.00 0.00 0.00 3.06
2187 2411 9.177304 GTATCTGATTACGTCGATTAAACATGA 57.823 33.333 0.00 0.00 0.00 3.07
2188 2412 8.425491 GGTATCTGATTACGTCGATTAAACATG 58.575 37.037 0.00 0.00 0.00 3.21
2228 2452 0.840722 TGTCCTTCTCCAGGTTCCCC 60.841 60.000 0.00 0.00 44.37 4.81
2333 2558 1.040646 GATCGAGCCATAGTGGTGGA 58.959 55.000 0.00 0.00 42.02 4.02
2335 2560 0.668535 TCGATCGAGCCATAGTGGTG 59.331 55.000 15.15 0.00 40.46 4.17
2336 2561 1.399714 TTCGATCGAGCCATAGTGGT 58.600 50.000 18.54 0.00 40.46 4.16
2340 2565 2.398498 CTGGTTTCGATCGAGCCATAG 58.602 52.381 30.41 21.25 33.17 2.23
2341 2566 1.068588 CCTGGTTTCGATCGAGCCATA 59.931 52.381 30.41 16.99 33.17 2.74
2342 2567 0.179073 CCTGGTTTCGATCGAGCCAT 60.179 55.000 30.41 0.00 33.17 4.40
2343 2568 1.218047 CCTGGTTTCGATCGAGCCA 59.782 57.895 29.19 29.19 32.82 4.75
2344 2569 0.806492 GTCCTGGTTTCGATCGAGCC 60.806 60.000 24.86 24.86 0.00 4.70
2367 2592 2.229062 CTGGTCGTGCTTAGAGAGACAA 59.771 50.000 4.48 0.00 33.84 3.18
2368 2593 1.813178 CTGGTCGTGCTTAGAGAGACA 59.187 52.381 4.48 0.00 33.84 3.41
2370 2595 0.811915 GCTGGTCGTGCTTAGAGAGA 59.188 55.000 0.00 0.00 0.00 3.10
2371 2596 0.179124 GGCTGGTCGTGCTTAGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
2372 2597 1.605058 GGGCTGGTCGTGCTTAGAGA 61.605 60.000 0.00 0.00 0.00 3.10
2373 2598 1.153549 GGGCTGGTCGTGCTTAGAG 60.154 63.158 0.00 0.00 0.00 2.43
2376 2601 2.297895 ATGGGGCTGGTCGTGCTTA 61.298 57.895 0.00 0.00 0.00 3.09
2388 2613 1.075748 AAGGGATCTTGCATGGGGC 60.076 57.895 0.00 0.00 45.13 5.80
2420 2645 4.633126 GCAGAGCTGAATTCTGACATTACA 59.367 41.667 15.79 0.00 43.75 2.41
2459 2684 5.339008 TCTCGCTTGTGTAGATTAACCAT 57.661 39.130 0.00 0.00 0.00 3.55
2469 2694 4.645136 ACTGAATCCTATCTCGCTTGTGTA 59.355 41.667 0.00 0.00 0.00 2.90
2515 2740 2.770164 AATGTCTGTACAGGTCTGCC 57.230 50.000 22.48 5.11 39.49 4.85
2559 2786 6.973843 TCAACAGAAATCCAGAGAAAATGTG 58.026 36.000 0.00 0.00 0.00 3.21
2609 2865 1.159285 CGGATGCAGAAACAAGCTGA 58.841 50.000 0.00 0.00 35.39 4.26
2613 2869 1.391485 CGTCTCGGATGCAGAAACAAG 59.609 52.381 0.00 0.00 0.00 3.16
2628 2884 2.930040 TCTCGCAAATCCATTTCGTCTC 59.070 45.455 0.00 0.00 0.00 3.36
2632 2888 4.031028 GTGAATCTCGCAAATCCATTTCG 58.969 43.478 0.00 0.00 0.00 3.46
2640 2897 1.741706 CTGCAGGTGAATCTCGCAAAT 59.258 47.619 5.57 0.00 31.10 2.32
2646 2903 2.686915 CCCATTTCTGCAGGTGAATCTC 59.313 50.000 15.13 0.00 0.00 2.75
2660 2917 1.204704 GCAAAGCTACACCCCCATTTC 59.795 52.381 0.00 0.00 0.00 2.17
2664 2921 1.074775 CTGCAAAGCTACACCCCCA 59.925 57.895 0.00 0.00 0.00 4.96
2665 2922 0.678048 CTCTGCAAAGCTACACCCCC 60.678 60.000 0.00 0.00 0.00 5.40
2666 2923 0.036875 ACTCTGCAAAGCTACACCCC 59.963 55.000 0.00 0.00 0.00 4.95
2682 2939 4.392445 TGACACTCGCTTCTACTTCTACTC 59.608 45.833 0.00 0.00 0.00 2.59
2744 3004 5.784578 TGTCTTTGCACAGTAGAAGTAGA 57.215 39.130 0.00 0.00 0.00 2.59
2745 3005 5.107298 GCTTGTCTTTGCACAGTAGAAGTAG 60.107 44.000 0.00 0.00 0.00 2.57
2746 3006 4.750098 GCTTGTCTTTGCACAGTAGAAGTA 59.250 41.667 0.00 0.00 0.00 2.24
2747 3007 3.561725 GCTTGTCTTTGCACAGTAGAAGT 59.438 43.478 0.00 0.00 0.00 3.01
2748 3008 3.812053 AGCTTGTCTTTGCACAGTAGAAG 59.188 43.478 0.00 2.99 0.00 2.85
2749 3009 3.808728 AGCTTGTCTTTGCACAGTAGAA 58.191 40.909 0.00 0.00 0.00 2.10
2750 3010 3.475566 AGCTTGTCTTTGCACAGTAGA 57.524 42.857 0.00 0.00 0.00 2.59
2751 3011 3.812053 AGAAGCTTGTCTTTGCACAGTAG 59.188 43.478 2.10 0.00 34.56 2.57
2752 3012 3.808728 AGAAGCTTGTCTTTGCACAGTA 58.191 40.909 2.10 0.00 34.56 2.74
2753 3013 2.648059 AGAAGCTTGTCTTTGCACAGT 58.352 42.857 2.10 0.00 34.56 3.55
2754 3014 3.705043 AAGAAGCTTGTCTTTGCACAG 57.295 42.857 2.10 0.00 34.03 3.66
2755 3015 4.454728 AAAAGAAGCTTGTCTTTGCACA 57.545 36.364 12.96 0.00 45.09 4.57
2801 3061 2.165167 CTGAGCTGAGCCCATCAAAAA 58.835 47.619 0.00 0.00 37.52 1.94
2802 3062 1.830279 CTGAGCTGAGCCCATCAAAA 58.170 50.000 0.00 0.00 37.52 2.44
2803 3063 0.679002 GCTGAGCTGAGCCCATCAAA 60.679 55.000 14.99 0.00 37.52 2.69
2804 3064 1.077930 GCTGAGCTGAGCCCATCAA 60.078 57.895 14.99 0.00 37.52 2.57
2805 3065 1.559965 AAGCTGAGCTGAGCCCATCA 61.560 55.000 22.26 0.00 39.62 3.07
2806 3066 0.814812 GAAGCTGAGCTGAGCCCATC 60.815 60.000 22.26 13.81 39.62 3.51
2807 3067 1.224039 GAAGCTGAGCTGAGCCCAT 59.776 57.895 22.26 8.54 39.62 4.00
2808 3068 1.486997 AAGAAGCTGAGCTGAGCCCA 61.487 55.000 22.26 0.00 39.62 5.36
2809 3069 0.322366 AAAGAAGCTGAGCTGAGCCC 60.322 55.000 22.26 13.88 39.62 5.19
2909 3182 0.970427 TGATGCGACTGGACCAGCTA 60.970 55.000 21.95 5.76 34.37 3.32
2961 3239 1.065701 CTTATCCTCTGACACGACGGG 59.934 57.143 0.00 0.00 0.00 5.28
3376 3902 2.124942 GTGCAGCTAGCCTGGGAC 60.125 66.667 12.13 9.27 44.83 4.46
3413 3940 1.066303 GTAGCGAGCTGACATAGTGCT 59.934 52.381 7.99 0.00 40.02 4.40
3415 3942 1.747956 CGTAGCGAGCTGACATAGTG 58.252 55.000 7.99 0.00 0.00 2.74
3444 4307 1.832883 AACTGGATTGCGTGCCAATA 58.167 45.000 0.00 0.00 44.02 1.90
3471 4334 9.679661 ACATGAACATAATTGTGGTATTGTAGA 57.320 29.630 7.15 0.00 35.83 2.59
3474 4337 8.584157 ACAACATGAACATAATTGTGGTATTGT 58.416 29.630 7.15 4.69 35.83 2.71
3476 4339 9.023962 AGACAACATGAACATAATTGTGGTATT 57.976 29.630 16.10 0.00 35.83 1.89
3477 4340 8.579850 AGACAACATGAACATAATTGTGGTAT 57.420 30.769 16.10 0.30 35.83 2.73
3488 4351 4.126437 TGTGAACGAGACAACATGAACAT 58.874 39.130 0.00 0.00 0.00 2.71
3515 4378 5.471556 TTGAGACATGGACATTTGCATTT 57.528 34.783 0.00 0.00 29.79 2.32
3516 4379 5.471556 TTTGAGACATGGACATTTGCATT 57.528 34.783 0.00 0.00 29.79 3.56
3517 4380 5.471556 TTTTGAGACATGGACATTTGCAT 57.528 34.783 0.00 0.00 33.19 3.96
3518 4381 4.933505 TTTTGAGACATGGACATTTGCA 57.066 36.364 0.00 0.00 0.00 4.08
3527 4390 3.074412 AGCGGTACTTTTTGAGACATGG 58.926 45.455 0.00 0.00 0.00 3.66
3536 4399 9.589111 TTTCTCAAAAATAAAGCGGTACTTTTT 57.411 25.926 7.98 7.98 46.73 1.94


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

AutoCloner maintained by Alex Coulton.