Multiple sequence alignment - TraesCS1B01G326500

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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 TraesCS1B01G326500 chr1B 100.000 2555 0 0 1 2555 551871279 551868725 0.000000e+00 4719.0
1 TraesCS1B01G326500 chr1B 81.781 247 23 15 421 650 552277602 552277361 1.210000e-43 187.0
2 TraesCS1B01G326500 chr1B 84.091 176 26 2 1096 1270 552474263 552474089 4.370000e-38 169.0
3 TraesCS1B01G326500 chr1B 91.549 71 2 2 177 243 552277818 552277748 7.530000e-16 95.3
4 TraesCS1B01G326500 chr1D 89.974 1905 71 56 1 1807 409800377 409798495 0.000000e+00 2350.0
5 TraesCS1B01G326500 chr1D 93.204 412 17 3 2029 2429 409798495 409798084 1.690000e-166 595.0
6 TraesCS1B01G326500 chr1D 82.796 186 29 3 1096 1280 410072051 410071868 2.030000e-36 163.0
7 TraesCS1B01G326500 chr1D 95.000 80 2 1 2421 2500 409797929 409797852 9.600000e-25 124.0
8 TraesCS1B01G326500 chr1D 100.000 30 0 0 214 243 409986779 409986750 3.550000e-04 56.5
9 TraesCS1B01G326500 chr1A 92.369 1009 42 20 830 1807 505681541 505680537 0.000000e+00 1404.0
10 TraesCS1B01G326500 chr1A 83.118 853 42 39 1 812 505682316 505681525 0.000000e+00 684.0
11 TraesCS1B01G326500 chr1A 87.161 553 37 15 1992 2523 505680548 505680009 4.710000e-167 597.0
12 TraesCS1B01G326500 chr1A 77.996 459 35 32 471 901 505733344 505732924 7.110000e-56 228.0
13 TraesCS1B01G326500 chr1A 87.597 129 10 2 1345 1473 505732782 505732660 7.370000e-31 145.0
14 TraesCS1B01G326500 chr1A 95.122 41 2 0 203 243 505738841 505738801 5.900000e-07 65.8
15 TraesCS1B01G326500 chr1A 94.595 37 2 0 7 43 505738969 505738933 9.870000e-05 58.4
16 TraesCS1B01G326500 chr6A 91.444 187 16 0 1805 1991 554780637 554780823 9.070000e-65 257.0
17 TraesCS1B01G326500 chr6A 87.500 168 17 3 1102 1267 183188190 183188355 9.330000e-45 191.0
18 TraesCS1B01G326500 chr7B 89.655 203 17 4 1797 1996 25880284 25880485 3.260000e-64 255.0
19 TraesCS1B01G326500 chr7B 89.231 195 18 2 1800 1991 4094913 4095107 9.130000e-60 241.0
20 TraesCS1B01G326500 chr7B 89.529 191 18 2 1805 1995 589915953 589915765 9.130000e-60 241.0
21 TraesCS1B01G326500 chr3B 89.340 197 15 2 1805 1995 240267690 240267886 2.540000e-60 243.0
22 TraesCS1B01G326500 chr3B 89.362 188 19 1 1805 1991 728816663 728816850 4.250000e-58 235.0
23 TraesCS1B01G326500 chr3B 75.547 503 77 36 1065 1556 568282986 568283453 3.330000e-49 206.0
24 TraesCS1B01G326500 chr2A 89.947 189 16 2 1805 1991 68865394 68865581 9.130000e-60 241.0
25 TraesCS1B01G326500 chr5D 89.474 190 17 2 1805 1991 288133467 288133278 1.180000e-58 237.0
26 TraesCS1B01G326500 chr2B 89.119 193 17 2 1804 1992 170418125 170418317 1.180000e-58 237.0
27 TraesCS1B01G326500 chr3D 75.794 504 79 31 1061 1556 434895915 434896383 5.540000e-52 215.0
28 TraesCS1B01G326500 chr3A 84.651 215 25 7 1067 1280 573832520 573832727 9.260000e-50 207.0
29 TraesCS1B01G326500 chr6D 87.500 168 17 3 1102 1267 139916327 139916492 9.330000e-45 191.0
30 TraesCS1B01G326500 chr6B 87.500 168 17 3 1102 1267 239729264 239729429 9.330000e-45 191.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G326500 chr1B 551868725 551871279 2554 True 4719 4719 100.000000 1 2555 1 chr1B.!!$R1 2554
1 TraesCS1B01G326500 chr1D 409797852 409800377 2525 True 1023 2350 92.726000 1 2500 3 chr1D.!!$R3 2499
2 TraesCS1B01G326500 chr1A 505680009 505682316 2307 True 895 1404 87.549333 1 2523 3 chr1A.!!$R1 2522

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
140 152 0.467844 AAAACCTTTTACGGCCCGGT 60.468 50.0 8.57 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2156 0.036306 ATTTCGCAAAGTCTCGGGGT 59.964 50.0 0.0 0.0 0.0 4.95 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
140 152 0.467844 AAAACCTTTTACGGCCCGGT 60.468 50.000 8.57 0.00 0.00 5.28
354 410 3.884900 GGCACGTACCATCACCAC 58.115 61.111 0.00 0.00 0.00 4.16
355 411 1.743995 GGCACGTACCATCACCACC 60.744 63.158 0.00 0.00 0.00 4.61
356 412 1.004320 GCACGTACCATCACCACCA 60.004 57.895 0.00 0.00 0.00 4.17
535 621 2.122167 GGACGAGACGGAGCTGGAT 61.122 63.158 0.00 0.00 0.00 3.41
536 622 1.668101 GGACGAGACGGAGCTGGATT 61.668 60.000 0.00 0.00 0.00 3.01
544 630 1.202734 ACGGAGCTGGATTCATGATGG 60.203 52.381 0.00 0.00 0.00 3.51
545 631 1.071228 CGGAGCTGGATTCATGATGGA 59.929 52.381 0.00 0.00 0.00 3.41
546 632 2.502295 GGAGCTGGATTCATGATGGAC 58.498 52.381 0.00 0.00 0.00 4.02
843 964 1.392589 GAGAGGAGAGCCAGTGAGAG 58.607 60.000 0.00 0.00 36.29 3.20
844 965 0.704076 AGAGGAGAGCCAGTGAGAGT 59.296 55.000 0.00 0.00 36.29 3.24
860 981 1.301244 AGTGACCACGCTCAAGCTG 60.301 57.895 0.00 0.00 39.32 4.24
861 982 2.666190 TGACCACGCTCAAGCTGC 60.666 61.111 0.00 0.00 39.32 5.25
980 1111 3.402110 CAACCATACTGTGAAGTGAGCA 58.598 45.455 0.00 0.00 0.00 4.26
983 1114 3.324846 ACCATACTGTGAAGTGAGCAAGA 59.675 43.478 0.00 0.00 0.00 3.02
998 1140 1.756561 AAGAGAGAGGGAGAGGCGC 60.757 63.158 0.00 0.00 0.00 6.53
1267 1415 0.111253 CAAGGCCAGGACCAACTTCT 59.889 55.000 5.01 0.00 0.00 2.85
1270 1418 1.761174 GCCAGGACCAACTTCTCCA 59.239 57.895 0.00 0.00 0.00 3.86
1721 1880 7.532682 TTTTAGCAAAATTTCACCTTGTGTC 57.467 32.000 0.00 0.00 34.79 3.67
1729 1888 1.525995 CACCTTGTGTCCGCCTTGT 60.526 57.895 0.00 0.00 0.00 3.16
1801 1961 6.942532 TGTCTCTTTGCAAGACACTTTAAT 57.057 33.333 14.33 0.00 46.15 1.40
1802 1962 7.333528 TGTCTCTTTGCAAGACACTTTAATT 57.666 32.000 14.33 0.00 46.15 1.40
1806 1966 6.658831 TCTTTGCAAGACACTTTAATTCGAG 58.341 36.000 0.00 0.00 31.20 4.04
1807 1967 6.260050 TCTTTGCAAGACACTTTAATTCGAGT 59.740 34.615 0.00 0.00 31.20 4.18
1808 1968 7.439955 TCTTTGCAAGACACTTTAATTCGAGTA 59.560 33.333 0.00 0.00 31.20 2.59
1809 1969 7.485418 TTGCAAGACACTTTAATTCGAGTAA 57.515 32.000 0.00 0.00 0.00 2.24
1810 1970 7.667043 TGCAAGACACTTTAATTCGAGTAAT 57.333 32.000 0.00 0.00 0.00 1.89
1811 1971 7.518161 TGCAAGACACTTTAATTCGAGTAATG 58.482 34.615 0.00 0.00 0.00 1.90
1812 1972 6.466097 GCAAGACACTTTAATTCGAGTAATGC 59.534 38.462 0.00 0.00 0.00 3.56
1813 1973 7.624344 GCAAGACACTTTAATTCGAGTAATGCT 60.624 37.037 0.00 0.00 0.00 3.79
1814 1974 8.869897 CAAGACACTTTAATTCGAGTAATGCTA 58.130 33.333 0.00 0.00 0.00 3.49
1815 1975 8.408743 AGACACTTTAATTCGAGTAATGCTAC 57.591 34.615 0.00 0.00 0.00 3.58
1816 1976 8.033038 AGACACTTTAATTCGAGTAATGCTACA 58.967 33.333 0.00 0.00 0.00 2.74
1817 1977 7.960793 ACACTTTAATTCGAGTAATGCTACAC 58.039 34.615 0.00 0.00 0.00 2.90
1818 1978 7.111139 CACTTTAATTCGAGTAATGCTACACG 58.889 38.462 0.00 0.00 41.68 4.49
1819 1979 6.810182 ACTTTAATTCGAGTAATGCTACACGT 59.190 34.615 3.61 0.00 41.26 4.49
1820 1980 7.970061 ACTTTAATTCGAGTAATGCTACACGTA 59.030 33.333 0.00 0.00 41.26 3.57
1821 1981 7.669438 TTAATTCGAGTAATGCTACACGTAC 57.331 36.000 0.00 0.00 41.26 3.67
1822 1982 4.683501 TTCGAGTAATGCTACACGTACA 57.316 40.909 0.00 0.00 41.26 2.90
1823 1983 4.683501 TCGAGTAATGCTACACGTACAA 57.316 40.909 0.00 0.00 41.26 2.41
1824 1984 5.045668 TCGAGTAATGCTACACGTACAAA 57.954 39.130 0.00 0.00 41.26 2.83
1825 1985 4.853196 TCGAGTAATGCTACACGTACAAAC 59.147 41.667 0.00 0.00 41.26 2.93
1846 2006 9.940166 ACAAACGAGTTACAAGGTTTTATAAAG 57.060 29.630 0.00 0.00 30.73 1.85
1849 2009 9.768662 AACGAGTTACAAGGTTTTATAAAGAGA 57.231 29.630 0.00 0.00 0.00 3.10
1850 2010 9.939802 ACGAGTTACAAGGTTTTATAAAGAGAT 57.060 29.630 0.00 0.00 0.00 2.75
1879 2039 7.838079 TTTGATTGGTCAATATATGGGAAGG 57.162 36.000 0.00 0.00 43.49 3.46
1880 2040 5.324409 TGATTGGTCAATATATGGGAAGGC 58.676 41.667 0.00 0.00 0.00 4.35
1881 2041 3.417069 TGGTCAATATATGGGAAGGCG 57.583 47.619 0.00 0.00 0.00 5.52
1882 2042 2.039746 TGGTCAATATATGGGAAGGCGG 59.960 50.000 0.00 0.00 0.00 6.13
1883 2043 2.084546 GTCAATATATGGGAAGGCGGC 58.915 52.381 0.00 0.00 0.00 6.53
1884 2044 1.004277 TCAATATATGGGAAGGCGGCC 59.996 52.381 12.11 12.11 0.00 6.13
1885 2045 0.331616 AATATATGGGAAGGCGGCCC 59.668 55.000 17.02 10.36 46.22 5.80
1891 2051 4.570874 GGAAGGCGGCCCATCCTC 62.571 72.222 26.18 12.34 44.03 3.71
1892 2052 3.483869 GAAGGCGGCCCATCCTCT 61.484 66.667 17.02 0.00 0.00 3.69
1893 2053 3.764160 GAAGGCGGCCCATCCTCTG 62.764 68.421 17.02 0.00 0.00 3.35
1894 2054 4.804420 AGGCGGCCCATCCTCTGA 62.804 66.667 17.02 0.00 0.00 3.27
1895 2055 3.797353 GGCGGCCCATCCTCTGAA 61.797 66.667 8.12 0.00 0.00 3.02
1896 2056 2.272146 GCGGCCCATCCTCTGAAA 59.728 61.111 0.00 0.00 0.00 2.69
1897 2057 1.378514 GCGGCCCATCCTCTGAAAA 60.379 57.895 0.00 0.00 0.00 2.29
1898 2058 0.753111 GCGGCCCATCCTCTGAAAAT 60.753 55.000 0.00 0.00 0.00 1.82
1899 2059 1.312815 CGGCCCATCCTCTGAAAATC 58.687 55.000 0.00 0.00 0.00 2.17
1900 2060 1.408683 CGGCCCATCCTCTGAAAATCA 60.409 52.381 0.00 0.00 0.00 2.57
1901 2061 2.750807 CGGCCCATCCTCTGAAAATCAT 60.751 50.000 0.00 0.00 0.00 2.45
1902 2062 2.626743 GGCCCATCCTCTGAAAATCATG 59.373 50.000 0.00 0.00 0.00 3.07
1903 2063 2.626743 GCCCATCCTCTGAAAATCATGG 59.373 50.000 0.00 0.00 0.00 3.66
1904 2064 3.228453 CCCATCCTCTGAAAATCATGGG 58.772 50.000 0.40 0.40 35.92 4.00
1905 2065 3.228453 CCATCCTCTGAAAATCATGGGG 58.772 50.000 0.00 0.00 0.00 4.96
1906 2066 3.228453 CATCCTCTGAAAATCATGGGGG 58.772 50.000 0.00 0.00 0.00 5.40
1923 2083 2.466846 GGGGGCAAGTTTATGATTGGT 58.533 47.619 0.00 0.00 0.00 3.67
1924 2084 2.837591 GGGGGCAAGTTTATGATTGGTT 59.162 45.455 0.00 0.00 0.00 3.67
1925 2085 4.027437 GGGGGCAAGTTTATGATTGGTTA 58.973 43.478 0.00 0.00 0.00 2.85
1926 2086 4.468153 GGGGGCAAGTTTATGATTGGTTAA 59.532 41.667 0.00 0.00 0.00 2.01
1927 2087 5.130311 GGGGGCAAGTTTATGATTGGTTAAT 59.870 40.000 0.00 0.00 0.00 1.40
1928 2088 6.325286 GGGGGCAAGTTTATGATTGGTTAATA 59.675 38.462 0.00 0.00 0.00 0.98
1929 2089 7.433680 GGGGCAAGTTTATGATTGGTTAATAG 58.566 38.462 0.00 0.00 0.00 1.73
1930 2090 7.286775 GGGGCAAGTTTATGATTGGTTAATAGA 59.713 37.037 0.00 0.00 0.00 1.98
1931 2091 8.860088 GGGCAAGTTTATGATTGGTTAATAGAT 58.140 33.333 0.00 0.00 0.00 1.98
1932 2092 9.683069 GGCAAGTTTATGATTGGTTAATAGATG 57.317 33.333 0.00 0.00 0.00 2.90
1953 2113 8.417780 AGATGAAAGAAATTCTAGTCATCGTG 57.582 34.615 26.62 0.00 44.54 4.35
1954 2114 8.037758 AGATGAAAGAAATTCTAGTCATCGTGT 58.962 33.333 26.62 16.45 44.54 4.49
1955 2115 9.302345 GATGAAAGAAATTCTAGTCATCGTGTA 57.698 33.333 22.70 0.90 37.89 2.90
1956 2116 9.653287 ATGAAAGAAATTCTAGTCATCGTGTAA 57.347 29.630 13.32 0.00 38.92 2.41
1957 2117 9.653287 TGAAAGAAATTCTAGTCATCGTGTAAT 57.347 29.630 0.00 0.00 38.92 1.89
1960 2120 9.436957 AAGAAATTCTAGTCATCGTGTAATTGT 57.563 29.630 0.00 0.00 0.00 2.71
1961 2121 8.873830 AGAAATTCTAGTCATCGTGTAATTGTG 58.126 33.333 0.00 0.00 0.00 3.33
1962 2122 8.547967 AAATTCTAGTCATCGTGTAATTGTGT 57.452 30.769 0.00 0.00 0.00 3.72
1963 2123 6.944557 TTCTAGTCATCGTGTAATTGTGTG 57.055 37.500 0.00 0.00 0.00 3.82
1964 2124 6.020971 TCTAGTCATCGTGTAATTGTGTGT 57.979 37.500 0.00 0.00 0.00 3.72
1965 2125 7.148355 TCTAGTCATCGTGTAATTGTGTGTA 57.852 36.000 0.00 0.00 0.00 2.90
1966 2126 7.595604 TCTAGTCATCGTGTAATTGTGTGTAA 58.404 34.615 0.00 0.00 0.00 2.41
1967 2127 6.462073 AGTCATCGTGTAATTGTGTGTAAC 57.538 37.500 0.00 0.00 37.35 2.50
1968 2128 6.220930 AGTCATCGTGTAATTGTGTGTAACT 58.779 36.000 0.00 0.00 38.04 2.24
1969 2129 6.365247 AGTCATCGTGTAATTGTGTGTAACTC 59.635 38.462 0.00 0.00 38.04 3.01
1970 2130 6.365247 GTCATCGTGTAATTGTGTGTAACTCT 59.635 38.462 0.00 0.00 38.04 3.24
1971 2131 6.926826 TCATCGTGTAATTGTGTGTAACTCTT 59.073 34.615 0.00 0.00 38.04 2.85
1972 2132 7.439955 TCATCGTGTAATTGTGTGTAACTCTTT 59.560 33.333 0.00 0.00 38.04 2.52
1973 2133 8.705134 CATCGTGTAATTGTGTGTAACTCTTTA 58.295 33.333 0.00 0.00 38.04 1.85
1974 2134 8.821147 TCGTGTAATTGTGTGTAACTCTTTAT 57.179 30.769 0.00 0.00 38.04 1.40
1975 2135 9.911138 TCGTGTAATTGTGTGTAACTCTTTATA 57.089 29.630 0.00 0.00 38.04 0.98
1984 2144 9.713713 TGTGTGTAACTCTTTATATGTTTAGCA 57.286 29.630 0.00 0.00 38.04 3.49
2003 2163 3.964909 GCATTATTGCTTTAACCCCGAG 58.035 45.455 2.33 0.00 45.77 4.63
2004 2164 3.630312 GCATTATTGCTTTAACCCCGAGA 59.370 43.478 2.33 0.00 45.77 4.04
2005 2165 4.497507 GCATTATTGCTTTAACCCCGAGAC 60.498 45.833 2.33 0.00 45.77 3.36
2006 2166 4.563140 TTATTGCTTTAACCCCGAGACT 57.437 40.909 0.00 0.00 0.00 3.24
2007 2167 2.943036 TTGCTTTAACCCCGAGACTT 57.057 45.000 0.00 0.00 0.00 3.01
2008 2168 2.943036 TGCTTTAACCCCGAGACTTT 57.057 45.000 0.00 0.00 0.00 2.66
2009 2169 2.500229 TGCTTTAACCCCGAGACTTTG 58.500 47.619 0.00 0.00 0.00 2.77
2010 2170 1.199327 GCTTTAACCCCGAGACTTTGC 59.801 52.381 0.00 0.00 0.00 3.68
2011 2171 1.463444 CTTTAACCCCGAGACTTTGCG 59.537 52.381 0.00 0.00 0.00 4.85
2012 2172 0.680618 TTAACCCCGAGACTTTGCGA 59.319 50.000 0.00 0.00 0.00 5.10
2013 2173 0.680618 TAACCCCGAGACTTTGCGAA 59.319 50.000 0.00 0.00 0.00 4.70
2014 2174 0.179040 AACCCCGAGACTTTGCGAAA 60.179 50.000 0.00 0.00 0.00 3.46
2015 2175 0.036306 ACCCCGAGACTTTGCGAAAT 59.964 50.000 0.00 0.00 0.00 2.17
2016 2176 0.447801 CCCCGAGACTTTGCGAAATG 59.552 55.000 0.00 0.00 0.00 2.32
2017 2177 0.179189 CCCGAGACTTTGCGAAATGC 60.179 55.000 0.00 0.00 46.70 3.56
2018 2178 0.798776 CCGAGACTTTGCGAAATGCT 59.201 50.000 0.00 0.00 46.63 3.79
2019 2179 1.464687 CCGAGACTTTGCGAAATGCTG 60.465 52.381 0.00 0.00 46.63 4.41
2020 2180 1.195448 CGAGACTTTGCGAAATGCTGT 59.805 47.619 0.00 0.00 46.63 4.40
2021 2181 2.411748 CGAGACTTTGCGAAATGCTGTA 59.588 45.455 0.00 0.00 46.63 2.74
2022 2182 3.120683 CGAGACTTTGCGAAATGCTGTAA 60.121 43.478 0.00 0.00 46.63 2.41
2023 2183 4.610456 CGAGACTTTGCGAAATGCTGTAAA 60.610 41.667 0.00 0.00 46.63 2.01
2024 2184 5.181690 AGACTTTGCGAAATGCTGTAAAA 57.818 34.783 0.00 0.00 46.63 1.52
2025 2185 5.587289 AGACTTTGCGAAATGCTGTAAAAA 58.413 33.333 0.00 0.00 46.63 1.94
2026 2186 5.687285 AGACTTTGCGAAATGCTGTAAAAAG 59.313 36.000 0.00 0.00 46.63 2.27
2027 2187 4.209080 ACTTTGCGAAATGCTGTAAAAAGC 59.791 37.500 0.00 0.00 46.63 3.51
2146 2321 3.773630 CAAGCGTACGTGCGGTGG 61.774 66.667 30.06 24.04 42.56 4.61
2241 2437 0.679640 CGCAGTAAGCCCCAATGGAA 60.680 55.000 0.00 0.00 41.38 3.53
2316 2512 5.947228 TCCTTGTGCTGAATTTTCTGTAG 57.053 39.130 0.00 0.00 0.00 2.74
2318 2514 5.827797 TCCTTGTGCTGAATTTTCTGTAGTT 59.172 36.000 0.00 0.00 0.00 2.24
2448 2810 6.373779 CAATTACTCTTCAGTTTCAATGCGT 58.626 36.000 0.00 0.00 33.62 5.24
2454 2816 5.688823 TCTTCAGTTTCAATGCGTTATGTG 58.311 37.500 0.00 0.00 0.00 3.21
2455 2817 5.238432 TCTTCAGTTTCAATGCGTTATGTGT 59.762 36.000 0.00 0.00 0.00 3.72
2502 2864 6.022315 AGCTTCCTAGTGCAGAAGGATATAT 58.978 40.000 15.90 2.97 41.50 0.86
2525 2887 7.823745 ATACAAAGAATTGTCACCTTCAGTT 57.176 32.000 0.00 0.00 46.78 3.16
2526 2888 6.530019 ACAAAGAATTGTCACCTTCAGTTT 57.470 33.333 0.00 0.00 46.78 2.66
2527 2889 7.639113 ACAAAGAATTGTCACCTTCAGTTTA 57.361 32.000 0.00 0.00 46.78 2.01
2528 2890 8.062065 ACAAAGAATTGTCACCTTCAGTTTAA 57.938 30.769 0.00 0.00 46.78 1.52
2529 2891 8.527810 ACAAAGAATTGTCACCTTCAGTTTAAA 58.472 29.630 0.00 0.00 46.78 1.52
2530 2892 9.364989 CAAAGAATTGTCACCTTCAGTTTAAAA 57.635 29.630 0.00 0.00 0.00 1.52
2531 2893 9.936759 AAAGAATTGTCACCTTCAGTTTAAAAA 57.063 25.926 0.00 0.00 0.00 1.94
2532 2894 8.926715 AGAATTGTCACCTTCAGTTTAAAAAC 57.073 30.769 0.00 0.00 39.17 2.43
2533 2895 8.527810 AGAATTGTCACCTTCAGTTTAAAAACA 58.472 29.630 8.21 0.00 41.30 2.83
2534 2896 9.145865 GAATTGTCACCTTCAGTTTAAAAACAA 57.854 29.630 8.21 0.00 41.30 2.83
2535 2897 9.665719 AATTGTCACCTTCAGTTTAAAAACAAT 57.334 25.926 8.21 0.00 41.30 2.71
2536 2898 9.665719 ATTGTCACCTTCAGTTTAAAAACAATT 57.334 25.926 8.21 0.00 41.30 2.32
2537 2899 8.472683 TGTCACCTTCAGTTTAAAAACAATTG 57.527 30.769 3.24 3.24 41.30 2.32
2538 2900 8.091449 TGTCACCTTCAGTTTAAAAACAATTGT 58.909 29.630 4.92 4.92 41.30 2.71
2539 2901 8.931775 GTCACCTTCAGTTTAAAAACAATTGTT 58.068 29.630 18.13 18.13 41.30 2.83
2542 2904 9.373603 ACCTTCAGTTTAAAAACAATTGTTACC 57.626 29.630 23.53 8.53 41.30 2.85
2543 2905 9.594478 CCTTCAGTTTAAAAACAATTGTTACCT 57.406 29.630 23.53 13.24 41.30 3.08
2551 2913 9.660180 TTAAAAACAATTGTTACCTTCAAAGCT 57.340 25.926 23.53 1.19 37.25 3.74
2553 2915 8.642908 AAAACAATTGTTACCTTCAAAGCTAC 57.357 30.769 23.53 0.00 37.25 3.58
2554 2916 7.582667 AACAATTGTTACCTTCAAAGCTACT 57.417 32.000 22.10 0.00 36.32 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
392 449 1.658102 TTGTGTCACGTACGCCGAC 60.658 57.895 24.13 24.13 40.70 4.79
393 450 1.658102 GTTGTGTCACGTACGCCGA 60.658 57.895 16.72 9.69 40.70 5.54
522 598 1.489481 TCATGAATCCAGCTCCGTCT 58.511 50.000 0.00 0.00 0.00 4.18
528 604 1.764723 TCGTCCATCATGAATCCAGCT 59.235 47.619 0.00 0.00 0.00 4.24
535 621 3.181466 CCTACACCATCGTCCATCATGAA 60.181 47.826 0.00 0.00 0.00 2.57
536 622 2.365293 CCTACACCATCGTCCATCATGA 59.635 50.000 0.00 0.00 0.00 3.07
544 630 1.090052 GCAAGCCCTACACCATCGTC 61.090 60.000 0.00 0.00 0.00 4.20
545 631 1.078426 GCAAGCCCTACACCATCGT 60.078 57.895 0.00 0.00 0.00 3.73
546 632 2.173669 CGCAAGCCCTACACCATCG 61.174 63.158 0.00 0.00 0.00 3.84
721 825 2.128507 GCTAGCGGTGTAGGCCTCT 61.129 63.158 9.68 0.34 0.00 3.69
722 826 2.417936 GCTAGCGGTGTAGGCCTC 59.582 66.667 9.68 1.02 0.00 4.70
723 827 3.528370 CGCTAGCGGTGTAGGCCT 61.528 66.667 29.29 11.78 35.56 5.19
726 830 3.833645 TGGCGCTAGCGGTGTAGG 61.834 66.667 35.86 9.20 46.35 3.18
731 841 4.742201 CACAGTGGCGCTAGCGGT 62.742 66.667 35.86 22.68 46.35 5.68
793 908 0.752376 GACCCTCGCTGCCTACTACT 60.752 60.000 0.00 0.00 0.00 2.57
794 909 1.734748 GACCCTCGCTGCCTACTAC 59.265 63.158 0.00 0.00 0.00 2.73
795 910 1.455217 GGACCCTCGCTGCCTACTA 60.455 63.158 0.00 0.00 0.00 1.82
818 933 1.305633 TGGCTCTCCTCTCCCACAG 60.306 63.158 0.00 0.00 0.00 3.66
820 935 1.305718 ACTGGCTCTCCTCTCCCAC 60.306 63.158 0.00 0.00 0.00 4.61
821 936 1.305633 CACTGGCTCTCCTCTCCCA 60.306 63.158 0.00 0.00 0.00 4.37
822 937 1.000993 TCACTGGCTCTCCTCTCCC 59.999 63.158 0.00 0.00 0.00 4.30
823 938 0.033601 TCTCACTGGCTCTCCTCTCC 60.034 60.000 0.00 0.00 0.00 3.71
826 947 0.817013 CACTCTCACTGGCTCTCCTC 59.183 60.000 0.00 0.00 0.00 3.71
980 1111 1.756561 GCGCCTCTCCCTCTCTCTT 60.757 63.158 0.00 0.00 0.00 2.85
983 1114 3.387609 ATGGCGCCTCTCCCTCTCT 62.388 63.158 29.70 0.00 0.00 3.10
1534 1688 1.671054 ACGACCCAAACATGAGCGG 60.671 57.895 0.00 0.00 0.00 5.52
1583 1737 0.324943 TCCTACACTTGGAAGCTGGC 59.675 55.000 0.00 0.00 0.00 4.85
1729 1888 1.135373 TCAGCAAAAACGAACGCCAAA 60.135 42.857 0.00 0.00 0.00 3.28
1734 1893 3.795561 AGAGATCAGCAAAAACGAACG 57.204 42.857 0.00 0.00 0.00 3.95
1801 1961 4.683501 TGTACGTGTAGCATTACTCGAA 57.316 40.909 12.67 0.00 45.00 3.71
1802 1962 4.683501 TTGTACGTGTAGCATTACTCGA 57.316 40.909 12.67 0.00 45.00 4.04
1820 1980 9.940166 CTTTATAAAACCTTGTAACTCGTTTGT 57.060 29.630 0.00 0.00 0.00 2.83
1823 1983 9.768662 TCTCTTTATAAAACCTTGTAACTCGTT 57.231 29.630 0.00 0.00 0.00 3.85
1824 1984 9.939802 ATCTCTTTATAAAACCTTGTAACTCGT 57.060 29.630 0.00 0.00 0.00 4.18
1857 2017 5.324409 GCCTTCCCATATATTGACCAATCA 58.676 41.667 0.00 0.00 32.50 2.57
1858 2018 4.396166 CGCCTTCCCATATATTGACCAATC 59.604 45.833 0.00 0.00 32.50 2.67
1859 2019 4.335416 CGCCTTCCCATATATTGACCAAT 58.665 43.478 0.64 0.64 34.93 3.16
1860 2020 3.497763 CCGCCTTCCCATATATTGACCAA 60.498 47.826 0.00 0.00 0.00 3.67
1861 2021 2.039746 CCGCCTTCCCATATATTGACCA 59.960 50.000 0.00 0.00 0.00 4.02
1862 2022 2.711542 CCGCCTTCCCATATATTGACC 58.288 52.381 0.00 0.00 0.00 4.02
1863 2023 2.084546 GCCGCCTTCCCATATATTGAC 58.915 52.381 0.00 0.00 0.00 3.18
1864 2024 1.004277 GGCCGCCTTCCCATATATTGA 59.996 52.381 0.71 0.00 0.00 2.57
1865 2025 1.463674 GGCCGCCTTCCCATATATTG 58.536 55.000 0.71 0.00 0.00 1.90
1866 2026 0.331616 GGGCCGCCTTCCCATATATT 59.668 55.000 9.86 0.00 43.37 1.28
1867 2027 1.999346 GGGCCGCCTTCCCATATAT 59.001 57.895 9.86 0.00 43.37 0.86
1868 2028 3.490851 GGGCCGCCTTCCCATATA 58.509 61.111 9.86 0.00 43.37 0.86
1874 2034 4.570874 GAGGATGGGCCGCCTTCC 62.571 72.222 17.64 18.95 43.43 3.46
1875 2035 3.483869 AGAGGATGGGCCGCCTTC 61.484 66.667 17.64 8.80 43.43 3.46
1876 2036 3.801997 CAGAGGATGGGCCGCCTT 61.802 66.667 17.64 6.65 43.43 4.35
1877 2037 4.804420 TCAGAGGATGGGCCGCCT 62.804 66.667 16.73 16.73 43.43 5.52
1878 2038 2.837031 TTTTCAGAGGATGGGCCGCC 62.837 60.000 0.00 0.00 43.43 6.13
1879 2039 0.753111 ATTTTCAGAGGATGGGCCGC 60.753 55.000 0.00 0.00 43.43 6.53
1880 2040 1.312815 GATTTTCAGAGGATGGGCCG 58.687 55.000 0.00 0.00 43.43 6.13
1881 2041 2.442236 TGATTTTCAGAGGATGGGCC 57.558 50.000 0.00 0.00 0.00 5.80
1882 2042 2.626743 CCATGATTTTCAGAGGATGGGC 59.373 50.000 0.00 0.00 29.88 5.36
1883 2043 3.228453 CCCATGATTTTCAGAGGATGGG 58.772 50.000 0.00 0.00 35.92 4.00
1884 2044 3.228453 CCCCATGATTTTCAGAGGATGG 58.772 50.000 0.00 0.00 29.88 3.51
1885 2045 3.228453 CCCCCATGATTTTCAGAGGATG 58.772 50.000 0.00 0.00 29.88 3.51
1886 2046 3.607490 CCCCCATGATTTTCAGAGGAT 57.393 47.619 0.00 0.00 29.88 3.24
1903 2063 2.466846 ACCAATCATAAACTTGCCCCC 58.533 47.619 0.00 0.00 0.00 5.40
1904 2064 5.669164 TTAACCAATCATAAACTTGCCCC 57.331 39.130 0.00 0.00 0.00 5.80
1905 2065 8.232913 TCTATTAACCAATCATAAACTTGCCC 57.767 34.615 0.00 0.00 0.00 5.36
1906 2066 9.683069 CATCTATTAACCAATCATAAACTTGCC 57.317 33.333 0.00 0.00 0.00 4.52
1927 2087 9.521503 CACGATGACTAGAATTTCTTTCATCTA 57.478 33.333 27.60 6.11 39.83 1.98
1928 2088 8.037758 ACACGATGACTAGAATTTCTTTCATCT 58.962 33.333 27.60 19.61 39.83 2.90
1929 2089 8.190888 ACACGATGACTAGAATTTCTTTCATC 57.809 34.615 24.53 24.53 39.26 2.92
1930 2090 9.653287 TTACACGATGACTAGAATTTCTTTCAT 57.347 29.630 17.07 17.07 36.75 2.57
1931 2091 9.653287 ATTACACGATGACTAGAATTTCTTTCA 57.347 29.630 3.86 8.30 36.75 2.69
1934 2094 9.436957 ACAATTACACGATGACTAGAATTTCTT 57.563 29.630 3.86 0.00 0.00 2.52
1935 2095 8.873830 CACAATTACACGATGACTAGAATTTCT 58.126 33.333 4.03 4.03 0.00 2.52
1936 2096 8.656849 ACACAATTACACGATGACTAGAATTTC 58.343 33.333 0.00 0.00 0.00 2.17
1937 2097 8.443160 CACACAATTACACGATGACTAGAATTT 58.557 33.333 0.00 0.00 0.00 1.82
1938 2098 7.602644 ACACACAATTACACGATGACTAGAATT 59.397 33.333 0.00 0.00 0.00 2.17
1939 2099 7.097192 ACACACAATTACACGATGACTAGAAT 58.903 34.615 0.00 0.00 0.00 2.40
1940 2100 6.452242 ACACACAATTACACGATGACTAGAA 58.548 36.000 0.00 0.00 0.00 2.10
1941 2101 6.020971 ACACACAATTACACGATGACTAGA 57.979 37.500 0.00 0.00 0.00 2.43
1942 2102 7.541091 AGTTACACACAATTACACGATGACTAG 59.459 37.037 0.00 0.00 0.00 2.57
1943 2103 7.372714 AGTTACACACAATTACACGATGACTA 58.627 34.615 0.00 0.00 0.00 2.59
1944 2104 6.220930 AGTTACACACAATTACACGATGACT 58.779 36.000 0.00 0.00 0.00 3.41
1945 2105 6.365247 AGAGTTACACACAATTACACGATGAC 59.635 38.462 0.00 0.00 0.00 3.06
1946 2106 6.452242 AGAGTTACACACAATTACACGATGA 58.548 36.000 0.00 0.00 0.00 2.92
1947 2107 6.706055 AGAGTTACACACAATTACACGATG 57.294 37.500 0.00 0.00 0.00 3.84
1948 2108 7.724305 AAAGAGTTACACACAATTACACGAT 57.276 32.000 0.00 0.00 0.00 3.73
1949 2109 8.821147 ATAAAGAGTTACACACAATTACACGA 57.179 30.769 0.00 0.00 0.00 4.35
1958 2118 9.713713 TGCTAAACATATAAAGAGTTACACACA 57.286 29.630 0.00 0.00 0.00 3.72
1983 2143 4.881850 AGTCTCGGGGTTAAAGCAATAATG 59.118 41.667 0.00 0.00 0.00 1.90
1984 2144 5.112129 AGTCTCGGGGTTAAAGCAATAAT 57.888 39.130 0.00 0.00 0.00 1.28
1985 2145 4.563140 AGTCTCGGGGTTAAAGCAATAA 57.437 40.909 0.00 0.00 0.00 1.40
1986 2146 4.563140 AAGTCTCGGGGTTAAAGCAATA 57.437 40.909 0.00 0.00 0.00 1.90
1987 2147 3.434940 AAGTCTCGGGGTTAAAGCAAT 57.565 42.857 0.00 0.00 0.00 3.56
1988 2148 2.882137 CAAAGTCTCGGGGTTAAAGCAA 59.118 45.455 0.00 0.00 0.00 3.91
1989 2149 2.500229 CAAAGTCTCGGGGTTAAAGCA 58.500 47.619 0.00 0.00 0.00 3.91
1990 2150 1.199327 GCAAAGTCTCGGGGTTAAAGC 59.801 52.381 0.00 0.00 0.00 3.51
1991 2151 1.463444 CGCAAAGTCTCGGGGTTAAAG 59.537 52.381 0.00 0.00 0.00 1.85
1992 2152 1.070445 TCGCAAAGTCTCGGGGTTAAA 59.930 47.619 0.00 0.00 0.00 1.52
1993 2153 0.680618 TCGCAAAGTCTCGGGGTTAA 59.319 50.000 0.00 0.00 0.00 2.01
1994 2154 0.680618 TTCGCAAAGTCTCGGGGTTA 59.319 50.000 0.00 0.00 0.00 2.85
1995 2155 0.179040 TTTCGCAAAGTCTCGGGGTT 60.179 50.000 0.00 0.00 0.00 4.11
1996 2156 0.036306 ATTTCGCAAAGTCTCGGGGT 59.964 50.000 0.00 0.00 0.00 4.95
1997 2157 0.447801 CATTTCGCAAAGTCTCGGGG 59.552 55.000 0.00 0.00 0.00 5.73
1998 2158 0.179189 GCATTTCGCAAAGTCTCGGG 60.179 55.000 0.00 0.00 41.79 5.14
1999 2159 0.798776 AGCATTTCGCAAAGTCTCGG 59.201 50.000 0.00 0.00 46.13 4.63
2000 2160 1.195448 ACAGCATTTCGCAAAGTCTCG 59.805 47.619 0.00 0.00 46.13 4.04
2001 2161 2.977405 ACAGCATTTCGCAAAGTCTC 57.023 45.000 0.00 0.00 46.13 3.36
2002 2162 4.829064 TTTACAGCATTTCGCAAAGTCT 57.171 36.364 0.00 0.00 46.13 3.24
2003 2163 5.610338 GCTTTTTACAGCATTTCGCAAAGTC 60.610 40.000 0.00 0.00 46.13 3.01
2004 2164 4.209080 GCTTTTTACAGCATTTCGCAAAGT 59.791 37.500 0.00 0.00 46.13 2.66
2005 2165 4.661402 CGCTTTTTACAGCATTTCGCAAAG 60.661 41.667 0.00 0.00 46.13 2.77
2006 2166 3.181377 CGCTTTTTACAGCATTTCGCAAA 59.819 39.130 0.00 0.00 46.13 3.68
2007 2167 2.723658 CGCTTTTTACAGCATTTCGCAA 59.276 40.909 0.00 0.00 46.13 4.85
2008 2168 2.031595 TCGCTTTTTACAGCATTTCGCA 60.032 40.909 0.00 0.00 46.13 5.10
2009 2169 2.338520 GTCGCTTTTTACAGCATTTCGC 59.661 45.455 0.00 0.00 40.09 4.70
2010 2170 3.599514 CAGTCGCTTTTTACAGCATTTCG 59.400 43.478 0.00 0.00 40.09 3.46
2011 2171 3.914364 CCAGTCGCTTTTTACAGCATTTC 59.086 43.478 0.00 0.00 40.09 2.17
2012 2172 3.317993 ACCAGTCGCTTTTTACAGCATTT 59.682 39.130 0.00 0.00 40.09 2.32
2013 2173 2.884639 ACCAGTCGCTTTTTACAGCATT 59.115 40.909 0.00 0.00 40.09 3.56
2014 2174 2.504367 ACCAGTCGCTTTTTACAGCAT 58.496 42.857 0.00 0.00 40.09 3.79
2015 2175 1.961793 ACCAGTCGCTTTTTACAGCA 58.038 45.000 0.00 0.00 40.09 4.41
2016 2176 3.349488 AAACCAGTCGCTTTTTACAGC 57.651 42.857 0.00 0.00 36.33 4.40
2017 2177 4.668289 ACAAAACCAGTCGCTTTTTACAG 58.332 39.130 0.00 0.00 0.00 2.74
2018 2178 4.705337 ACAAAACCAGTCGCTTTTTACA 57.295 36.364 0.00 0.00 0.00 2.41
2019 2179 5.722863 GCAAACAAAACCAGTCGCTTTTTAC 60.723 40.000 0.00 0.00 0.00 2.01
2020 2180 4.327627 GCAAACAAAACCAGTCGCTTTTTA 59.672 37.500 0.00 0.00 0.00 1.52
2021 2181 3.124466 GCAAACAAAACCAGTCGCTTTTT 59.876 39.130 0.00 0.00 0.00 1.94
2022 2182 2.670905 GCAAACAAAACCAGTCGCTTTT 59.329 40.909 0.00 0.00 0.00 2.27
2023 2183 2.267426 GCAAACAAAACCAGTCGCTTT 58.733 42.857 0.00 0.00 0.00 3.51
2024 2184 1.470805 GGCAAACAAAACCAGTCGCTT 60.471 47.619 0.00 0.00 0.00 4.68
2025 2185 0.102300 GGCAAACAAAACCAGTCGCT 59.898 50.000 0.00 0.00 0.00 4.93
2026 2186 1.206115 CGGCAAACAAAACCAGTCGC 61.206 55.000 0.00 0.00 0.00 5.19
2027 2187 1.206115 GCGGCAAACAAAACCAGTCG 61.206 55.000 0.00 0.00 0.00 4.18
2059 2227 0.865111 TTCCATCGCACGAACACAAG 59.135 50.000 0.00 0.00 0.00 3.16
2061 2229 0.795698 CATTCCATCGCACGAACACA 59.204 50.000 0.00 0.00 0.00 3.72
2241 2437 6.575132 GCTTATAAATTTATACGTCGCGTGT 58.425 36.000 15.92 9.11 41.39 4.49
2316 2512 8.932945 TCTCAACATCACTTCTCACATATAAC 57.067 34.615 0.00 0.00 0.00 1.89
2373 2569 7.369803 ACTGCTAGACAACTGAATAACAATG 57.630 36.000 0.00 0.00 0.00 2.82
2384 2583 6.163135 AGTTTCTACAACTGCTAGACAACT 57.837 37.500 0.00 0.00 0.00 3.16
2448 2810 7.732025 TCTTTGGAGTAAGTTCTGACACATAA 58.268 34.615 0.00 0.00 0.00 1.90
2454 2816 8.231161 GCTTTATTCTTTGGAGTAAGTTCTGAC 58.769 37.037 0.00 0.00 0.00 3.51
2455 2817 8.157476 AGCTTTATTCTTTGGAGTAAGTTCTGA 58.843 33.333 0.00 0.00 0.00 3.27
2502 2864 7.639113 AAACTGAAGGTGACAATTCTTTGTA 57.361 32.000 2.25 0.00 46.01 2.41
2513 2875 8.474006 ACAATTGTTTTTAAACTGAAGGTGAC 57.526 30.769 4.92 0.00 39.59 3.67
2525 2887 9.660180 AGCTTTGAAGGTAACAATTGTTTTTAA 57.340 25.926 27.66 15.97 39.31 1.52
2527 2889 9.093970 GTAGCTTTGAAGGTAACAATTGTTTTT 57.906 29.630 27.66 18.85 40.31 1.94
2528 2890 8.474831 AGTAGCTTTGAAGGTAACAATTGTTTT 58.525 29.630 27.66 16.59 40.31 2.43
2529 2891 8.007405 AGTAGCTTTGAAGGTAACAATTGTTT 57.993 30.769 27.66 10.94 40.31 2.83
2530 2892 7.582667 AGTAGCTTTGAAGGTAACAATTGTT 57.417 32.000 25.99 25.99 40.31 2.83


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

AutoCloner maintained by Alex Coulton.