Multiple sequence alignment - TraesCS5A01G341400

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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 TraesCS5A01G341400 chr5A 100.000 2264 0 0 1 2264 547532923 547535186 0.000000e+00 4181
1 TraesCS5A01G341400 chr5A 98.223 1913 18 5 1 1908 671875946 671874045 0.000000e+00 3330
2 TraesCS5A01G341400 chr5A 89.858 917 80 8 489 1402 181455576 181456482 0.000000e+00 1166
3 TraesCS5A01G341400 chr5A 99.405 168 1 0 2097 2264 472578659 472578492 2.830000e-79 305
4 TraesCS5A01G341400 chr5A 82.540 189 29 4 1726 1912 316506806 316506620 1.800000e-36 163
5 TraesCS5A01G341400 chr5A 87.162 148 11 4 1955 2096 546210063 546209918 6.470000e-36 161
6 TraesCS5A01G341400 chr6A 98.769 1869 17 4 1 1863 83359972 83361840 0.000000e+00 3319
7 TraesCS5A01G341400 chr6A 95.722 187 8 0 1910 2096 480852549 480852363 3.650000e-78 302
8 TraesCS5A01G341400 chr6A 95.187 187 9 0 1910 2096 592696163 592695977 1.700000e-76 296
9 TraesCS5A01G341400 chr1A 97.858 1914 16 6 1 1908 75741293 75739399 0.000000e+00 3284
10 TraesCS5A01G341400 chr1A 95.676 185 7 1 1720 1904 20881140 20880957 1.700000e-76 296
11 TraesCS5A01G341400 chr1A 98.225 169 3 0 2096 2264 372232775 372232607 1.700000e-76 296
12 TraesCS5A01G341400 chr1A 82.632 190 29 4 1726 1913 446143997 446144184 5.000000e-37 165
13 TraesCS5A01G341400 chr4B 89.152 1899 175 24 1 1886 295124561 295122681 0.000000e+00 2337
14 TraesCS5A01G341400 chr4B 88.314 676 69 9 723 1394 510389129 510389798 0.000000e+00 802
15 TraesCS5A01G341400 chr2B 90.554 1408 119 8 1 1402 551156854 551158253 0.000000e+00 1851
16 TraesCS5A01G341400 chr2B 85.266 638 75 15 1287 1912 47064050 47063420 6.820000e-180 640
17 TraesCS5A01G341400 chr2B 86.139 202 12 8 1910 2096 103711811 103712011 1.060000e-48 204
18 TraesCS5A01G341400 chr5D 89.640 917 79 10 489 1402 177305676 177306579 0.000000e+00 1153
19 TraesCS5A01G341400 chr6B 92.643 734 50 2 1 732 129396301 129397032 0.000000e+00 1053
20 TraesCS5A01G341400 chr2D 92.507 734 53 1 1 732 52067256 52067989 0.000000e+00 1050
21 TraesCS5A01G341400 chr2D 87.603 121 9 4 1978 2096 164530197 164530081 3.920000e-28 135
22 TraesCS5A01G341400 chr4A 92.371 734 54 1 1 732 91227483 91226750 0.000000e+00 1044
23 TraesCS5A01G341400 chr4A 98.817 169 2 0 2096 2264 541675602 541675770 3.650000e-78 302
24 TraesCS5A01G341400 chr4A 96.629 178 5 1 2087 2264 42697326 42697502 6.120000e-76 294
25 TraesCS5A01G341400 chr2A 92.234 734 55 1 1 732 615517851 615517118 0.000000e+00 1038
26 TraesCS5A01G341400 chr2A 83.810 210 11 6 1910 2096 186404873 186405082 6.430000e-41 178
27 TraesCS5A01G341400 chr3A 87.587 717 71 14 1112 1818 671626027 671626735 0.000000e+00 815
28 TraesCS5A01G341400 chr3A 91.237 194 10 3 1910 2096 516683019 516682826 8.020000e-65 257
29 TraesCS5A01G341400 chr7B 88.148 675 71 8 723 1394 72302822 72302154 0.000000e+00 795
30 TraesCS5A01G341400 chr3B 98.830 171 2 0 2094 2264 127858511 127858681 2.830000e-79 305
31 TraesCS5A01G341400 chr3B 97.714 175 4 0 2090 2264 753746759 753746933 3.650000e-78 302
32 TraesCS5A01G341400 chr3B 96.133 181 5 2 2086 2264 663973906 663974086 6.120000e-76 294
33 TraesCS5A01G341400 chr3B 87.179 195 16 5 1910 2096 819035585 819035392 1.760000e-51 213
34 TraesCS5A01G341400 chr7A 97.159 176 5 0 2089 2264 99810356 99810531 4.730000e-77 298
35 TraesCS5A01G341400 chr5B 95.652 184 5 3 2083 2264 291075355 291075537 2.200000e-75 292
36 TraesCS5A01G341400 chr5B 89.103 156 11 2 1947 2096 482296805 482296650 2.970000e-44 189


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 TraesCS5A01G341400 chr5A 547532923 547535186 2263 False 4181 4181 100.000 1 2264 1 chr5A.!!$F2 2263
1 TraesCS5A01G341400 chr5A 671874045 671875946 1901 True 3330 3330 98.223 1 1908 1 chr5A.!!$R4 1907
2 TraesCS5A01G341400 chr5A 181455576 181456482 906 False 1166 1166 89.858 489 1402 1 chr5A.!!$F1 913
3 TraesCS5A01G341400 chr6A 83359972 83361840 1868 False 3319 3319 98.769 1 1863 1 chr6A.!!$F1 1862
4 TraesCS5A01G341400 chr1A 75739399 75741293 1894 True 3284 3284 97.858 1 1908 1 chr1A.!!$R2 1907
5 TraesCS5A01G341400 chr4B 295122681 295124561 1880 True 2337 2337 89.152 1 1886 1 chr4B.!!$R1 1885
6 TraesCS5A01G341400 chr4B 510389129 510389798 669 False 802 802 88.314 723 1394 1 chr4B.!!$F1 671
7 TraesCS5A01G341400 chr2B 551156854 551158253 1399 False 1851 1851 90.554 1 1402 1 chr2B.!!$F2 1401
8 TraesCS5A01G341400 chr2B 47063420 47064050 630 True 640 640 85.266 1287 1912 1 chr2B.!!$R1 625
9 TraesCS5A01G341400 chr5D 177305676 177306579 903 False 1153 1153 89.640 489 1402 1 chr5D.!!$F1 913
10 TraesCS5A01G341400 chr6B 129396301 129397032 731 False 1053 1053 92.643 1 732 1 chr6B.!!$F1 731
11 TraesCS5A01G341400 chr2D 52067256 52067989 733 False 1050 1050 92.507 1 732 1 chr2D.!!$F1 731
12 TraesCS5A01G341400 chr4A 91226750 91227483 733 True 1044 1044 92.371 1 732 1 chr4A.!!$R1 731
13 TraesCS5A01G341400 chr2A 615517118 615517851 733 True 1038 1038 92.234 1 732 1 chr2A.!!$R1 731
14 TraesCS5A01G341400 chr3A 671626027 671626735 708 False 815 815 87.587 1112 1818 1 chr3A.!!$F1 706
15 TraesCS5A01G341400 chr7B 72302154 72302822 668 True 795 795 88.148 723 1394 1 chr7B.!!$R1 671

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
860 867 3.788227 AGCACCATACAAAGGAGAACA 57.212 42.857 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1959 0.033781 GCTGTTGCCAATTCCTGCAA 59.966 50.0 3.17 3.17 44.64 4.08 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
629 634 5.243507 ACAAGTGTGTTATTCCATGCAATCA 59.756 36.000 0.00 0.00 32.58 2.57
860 867 3.788227 AGCACCATACAAAGGAGAACA 57.212 42.857 0.00 0.00 0.00 3.18
1109 1118 0.868406 CTCCACTTTCTTCGGTGTGC 59.132 55.000 0.00 0.00 0.00 4.57
1718 1749 8.966868 CCTTTTTATCTCTATAAAACCAGCCAA 58.033 33.333 3.44 0.00 43.76 4.52
1839 1873 1.570813 CTCGGCAAATCGCTATGTGA 58.429 50.000 0.00 0.00 41.91 3.58
1908 1942 1.494960 GAGAGGATCAGAACAGGCCT 58.505 55.000 0.00 0.00 37.82 5.19
1912 1946 3.454082 AGAGGATCAGAACAGGCCTTTAG 59.546 47.826 0.00 0.00 37.82 1.85
1913 1947 2.507471 AGGATCAGAACAGGCCTTTAGG 59.493 50.000 0.00 0.00 38.53 2.69
1914 1948 2.505819 GGATCAGAACAGGCCTTTAGGA 59.494 50.000 0.00 0.00 37.39 2.94
1915 1949 3.137360 GGATCAGAACAGGCCTTTAGGAT 59.863 47.826 0.00 2.56 37.39 3.24
1916 1950 4.385754 GGATCAGAACAGGCCTTTAGGATT 60.386 45.833 0.00 0.00 37.39 3.01
1917 1951 3.955471 TCAGAACAGGCCTTTAGGATTG 58.045 45.455 0.00 0.00 37.39 2.67
1918 1952 3.019564 CAGAACAGGCCTTTAGGATTGG 58.980 50.000 0.00 0.00 37.39 3.16
1919 1953 2.649816 AGAACAGGCCTTTAGGATTGGT 59.350 45.455 0.00 0.00 37.39 3.67
1920 1954 3.076032 AGAACAGGCCTTTAGGATTGGTT 59.924 43.478 0.00 0.00 37.39 3.67
1921 1955 3.542969 ACAGGCCTTTAGGATTGGTTT 57.457 42.857 0.00 0.00 37.39 3.27
1922 1956 3.856900 ACAGGCCTTTAGGATTGGTTTT 58.143 40.909 0.00 0.00 37.39 2.43
1923 1957 3.578282 ACAGGCCTTTAGGATTGGTTTTG 59.422 43.478 0.00 0.00 37.39 2.44
1924 1958 2.567169 AGGCCTTTAGGATTGGTTTTGC 59.433 45.455 0.00 0.00 37.39 3.68
1925 1959 2.567169 GGCCTTTAGGATTGGTTTTGCT 59.433 45.455 0.00 0.00 37.39 3.91
1926 1960 3.007940 GGCCTTTAGGATTGGTTTTGCTT 59.992 43.478 0.00 0.00 37.39 3.91
1927 1961 3.996363 GCCTTTAGGATTGGTTTTGCTTG 59.004 43.478 0.00 0.00 37.39 4.01
1928 1962 3.996363 CCTTTAGGATTGGTTTTGCTTGC 59.004 43.478 0.00 0.00 37.39 4.01
1929 1963 4.502950 CCTTTAGGATTGGTTTTGCTTGCA 60.503 41.667 0.00 0.00 37.39 4.08
1930 1964 2.825861 AGGATTGGTTTTGCTTGCAG 57.174 45.000 0.00 0.00 0.00 4.41
1931 1965 1.345415 AGGATTGGTTTTGCTTGCAGG 59.655 47.619 0.00 0.00 0.00 4.85
1932 1966 1.344114 GGATTGGTTTTGCTTGCAGGA 59.656 47.619 0.00 0.00 0.00 3.86
1933 1967 2.224257 GGATTGGTTTTGCTTGCAGGAA 60.224 45.455 0.00 0.00 0.00 3.36
1934 1968 3.557686 GGATTGGTTTTGCTTGCAGGAAT 60.558 43.478 0.00 0.00 0.00 3.01
1935 1969 3.557228 TTGGTTTTGCTTGCAGGAATT 57.443 38.095 0.00 0.00 0.00 2.17
1936 1970 2.836262 TGGTTTTGCTTGCAGGAATTG 58.164 42.857 0.00 0.00 0.00 2.32
1937 1971 2.145536 GGTTTTGCTTGCAGGAATTGG 58.854 47.619 0.00 0.00 0.00 3.16
1938 1972 1.532437 GTTTTGCTTGCAGGAATTGGC 59.468 47.619 0.00 0.00 0.00 4.52
1939 1973 0.757512 TTTGCTTGCAGGAATTGGCA 59.242 45.000 0.00 0.00 38.46 4.92
1940 1974 0.757512 TTGCTTGCAGGAATTGGCAA 59.242 45.000 0.68 0.68 46.84 4.52
1941 1975 0.033781 TGCTTGCAGGAATTGGCAAC 59.966 50.000 0.00 0.00 44.41 4.17
1958 1992 5.424121 GGCAACAGCCTATTACAGTAATG 57.576 43.478 15.12 3.08 45.21 1.90
1959 1993 4.261197 GGCAACAGCCTATTACAGTAATGC 60.261 45.833 15.12 10.92 45.21 3.56
1960 1994 4.576463 GCAACAGCCTATTACAGTAATGCT 59.424 41.667 15.12 12.81 30.32 3.79
1961 1995 5.066505 GCAACAGCCTATTACAGTAATGCTT 59.933 40.000 15.12 5.64 28.46 3.91
1962 1996 6.719365 CAACAGCCTATTACAGTAATGCTTC 58.281 40.000 15.12 3.19 28.46 3.86
1963 1997 5.368989 ACAGCCTATTACAGTAATGCTTCC 58.631 41.667 15.12 1.01 28.46 3.46
1964 1998 5.131142 ACAGCCTATTACAGTAATGCTTCCT 59.869 40.000 15.12 2.99 28.46 3.36
1965 1999 5.698545 CAGCCTATTACAGTAATGCTTCCTC 59.301 44.000 15.12 0.00 28.46 3.71
1966 2000 5.604650 AGCCTATTACAGTAATGCTTCCTCT 59.395 40.000 15.12 1.60 26.89 3.69
1967 2001 6.782988 AGCCTATTACAGTAATGCTTCCTCTA 59.217 38.462 15.12 0.00 26.89 2.43
1968 2002 6.869388 GCCTATTACAGTAATGCTTCCTCTAC 59.131 42.308 15.12 0.00 0.00 2.59
1969 2003 7.379750 CCTATTACAGTAATGCTTCCTCTACC 58.620 42.308 15.12 0.00 0.00 3.18
1970 2004 5.609533 TTACAGTAATGCTTCCTCTACCC 57.390 43.478 0.00 0.00 0.00 3.69
1971 2005 2.431057 ACAGTAATGCTTCCTCTACCCG 59.569 50.000 0.00 0.00 0.00 5.28
1972 2006 2.431057 CAGTAATGCTTCCTCTACCCGT 59.569 50.000 0.00 0.00 0.00 5.28
1973 2007 2.694109 AGTAATGCTTCCTCTACCCGTC 59.306 50.000 0.00 0.00 0.00 4.79
1974 2008 1.568504 AATGCTTCCTCTACCCGTCA 58.431 50.000 0.00 0.00 0.00 4.35
1975 2009 1.794714 ATGCTTCCTCTACCCGTCAT 58.205 50.000 0.00 0.00 0.00 3.06
1976 2010 1.568504 TGCTTCCTCTACCCGTCATT 58.431 50.000 0.00 0.00 0.00 2.57
1977 2011 1.480954 TGCTTCCTCTACCCGTCATTC 59.519 52.381 0.00 0.00 0.00 2.67
1978 2012 1.480954 GCTTCCTCTACCCGTCATTCA 59.519 52.381 0.00 0.00 0.00 2.57
1979 2013 2.738964 GCTTCCTCTACCCGTCATTCAC 60.739 54.545 0.00 0.00 0.00 3.18
1980 2014 2.526888 TCCTCTACCCGTCATTCACT 57.473 50.000 0.00 0.00 0.00 3.41
1981 2015 2.816411 TCCTCTACCCGTCATTCACTT 58.184 47.619 0.00 0.00 0.00 3.16
1982 2016 2.496070 TCCTCTACCCGTCATTCACTTG 59.504 50.000 0.00 0.00 0.00 3.16
1983 2017 2.496070 CCTCTACCCGTCATTCACTTGA 59.504 50.000 0.00 0.00 0.00 3.02
1984 2018 3.512680 CTCTACCCGTCATTCACTTGAC 58.487 50.000 0.00 0.00 42.10 3.18
1985 2019 2.232941 TCTACCCGTCATTCACTTGACC 59.767 50.000 0.00 0.00 42.46 4.02
1986 2020 1.056660 ACCCGTCATTCACTTGACCT 58.943 50.000 0.00 0.00 42.46 3.85
1987 2021 1.270839 ACCCGTCATTCACTTGACCTG 60.271 52.381 0.00 0.00 42.46 4.00
1988 2022 1.442769 CCGTCATTCACTTGACCTGG 58.557 55.000 0.00 0.00 42.46 4.45
1989 2023 1.001974 CCGTCATTCACTTGACCTGGA 59.998 52.381 0.00 0.00 42.46 3.86
1990 2024 2.341257 CGTCATTCACTTGACCTGGAG 58.659 52.381 0.00 0.00 42.46 3.86
1991 2025 2.029020 CGTCATTCACTTGACCTGGAGA 60.029 50.000 0.00 0.00 42.46 3.71
1992 2026 3.594134 GTCATTCACTTGACCTGGAGAG 58.406 50.000 0.00 0.00 40.11 3.20
1993 2027 3.259374 GTCATTCACTTGACCTGGAGAGA 59.741 47.826 0.00 0.00 40.11 3.10
1994 2028 3.513119 TCATTCACTTGACCTGGAGAGAG 59.487 47.826 0.00 0.00 0.00 3.20
1995 2029 1.930251 TCACTTGACCTGGAGAGAGG 58.070 55.000 0.00 0.00 39.28 3.69
2001 2035 2.854253 ACCTGGAGAGAGGTTTGCA 58.146 52.632 0.00 0.00 44.53 4.08
2002 2036 1.366319 ACCTGGAGAGAGGTTTGCAT 58.634 50.000 0.00 0.00 44.53 3.96
2003 2037 1.280421 ACCTGGAGAGAGGTTTGCATC 59.720 52.381 0.00 0.00 44.53 3.91
2004 2038 1.407989 CCTGGAGAGAGGTTTGCATCC 60.408 57.143 0.00 0.00 0.00 3.51
2005 2039 1.280133 CTGGAGAGAGGTTTGCATCCA 59.720 52.381 10.40 6.28 35.60 3.41
2006 2040 1.280133 TGGAGAGAGGTTTGCATCCAG 59.720 52.381 10.40 0.00 33.11 3.86
2007 2041 1.377536 GAGAGAGGTTTGCATCCAGC 58.622 55.000 10.40 3.20 45.96 4.85
2008 2042 0.990374 AGAGAGGTTTGCATCCAGCT 59.010 50.000 10.40 7.20 45.94 4.24
2009 2043 1.353694 AGAGAGGTTTGCATCCAGCTT 59.646 47.619 10.40 0.00 45.94 3.74
2010 2044 2.165998 GAGAGGTTTGCATCCAGCTTT 58.834 47.619 10.40 0.00 45.94 3.51
2011 2045 3.009473 AGAGAGGTTTGCATCCAGCTTTA 59.991 43.478 10.40 0.00 45.94 1.85
2012 2046 3.758554 GAGAGGTTTGCATCCAGCTTTAA 59.241 43.478 10.40 0.00 45.94 1.52
2013 2047 4.347607 AGAGGTTTGCATCCAGCTTTAAT 58.652 39.130 10.40 0.00 45.94 1.40
2014 2048 4.774200 AGAGGTTTGCATCCAGCTTTAATT 59.226 37.500 10.40 0.00 45.94 1.40
2015 2049 5.246883 AGAGGTTTGCATCCAGCTTTAATTT 59.753 36.000 10.40 0.00 45.94 1.82
2016 2050 5.482006 AGGTTTGCATCCAGCTTTAATTTC 58.518 37.500 10.40 0.00 45.94 2.17
2017 2051 5.246883 AGGTTTGCATCCAGCTTTAATTTCT 59.753 36.000 10.40 0.00 45.94 2.52
2018 2052 5.349543 GGTTTGCATCCAGCTTTAATTTCTG 59.650 40.000 0.00 0.00 45.94 3.02
2019 2053 5.981088 TTGCATCCAGCTTTAATTTCTGA 57.019 34.783 0.00 0.00 45.94 3.27
2020 2054 5.571784 TGCATCCAGCTTTAATTTCTGAG 57.428 39.130 0.00 0.00 45.94 3.35
2021 2055 4.400251 TGCATCCAGCTTTAATTTCTGAGG 59.600 41.667 0.00 0.00 45.94 3.86
2022 2056 4.202090 GCATCCAGCTTTAATTTCTGAGGG 60.202 45.833 0.00 0.00 41.15 4.30
2023 2057 4.657814 TCCAGCTTTAATTTCTGAGGGT 57.342 40.909 0.00 0.00 0.00 4.34
2024 2058 4.998051 TCCAGCTTTAATTTCTGAGGGTT 58.002 39.130 0.00 0.00 0.00 4.11
2025 2059 5.393866 TCCAGCTTTAATTTCTGAGGGTTT 58.606 37.500 0.00 0.00 0.00 3.27
2026 2060 5.838521 TCCAGCTTTAATTTCTGAGGGTTTT 59.161 36.000 0.00 0.00 0.00 2.43
2027 2061 7.007723 TCCAGCTTTAATTTCTGAGGGTTTTA 58.992 34.615 0.00 0.00 0.00 1.52
2028 2062 7.673926 TCCAGCTTTAATTTCTGAGGGTTTTAT 59.326 33.333 0.00 0.00 0.00 1.40
2029 2063 8.314021 CCAGCTTTAATTTCTGAGGGTTTTATT 58.686 33.333 0.00 0.00 0.00 1.40
2038 2072 8.950007 TTTCTGAGGGTTTTATTAATGAAGGT 57.050 30.769 0.00 0.00 0.00 3.50
2039 2073 8.575649 TTCTGAGGGTTTTATTAATGAAGGTC 57.424 34.615 0.00 0.00 0.00 3.85
2040 2074 7.116736 TCTGAGGGTTTTATTAATGAAGGTCC 58.883 38.462 0.00 1.18 0.00 4.46
2041 2075 6.795590 TGAGGGTTTTATTAATGAAGGTCCA 58.204 36.000 0.00 0.00 0.00 4.02
2042 2076 7.242359 TGAGGGTTTTATTAATGAAGGTCCAA 58.758 34.615 0.00 0.00 0.00 3.53
2043 2077 7.730784 TGAGGGTTTTATTAATGAAGGTCCAAA 59.269 33.333 0.00 0.00 0.00 3.28
2044 2078 7.903145 AGGGTTTTATTAATGAAGGTCCAAAC 58.097 34.615 0.00 0.00 0.00 2.93
2045 2079 7.511028 AGGGTTTTATTAATGAAGGTCCAAACA 59.489 33.333 0.00 0.00 0.00 2.83
2046 2080 8.318412 GGGTTTTATTAATGAAGGTCCAAACAT 58.682 33.333 0.00 0.00 0.00 2.71
2053 2087 8.815565 TTAATGAAGGTCCAAACATATTAGCA 57.184 30.769 0.00 0.00 0.00 3.49
2054 2088 7.902920 AATGAAGGTCCAAACATATTAGCAT 57.097 32.000 0.00 0.00 0.00 3.79
2055 2089 8.995027 AATGAAGGTCCAAACATATTAGCATA 57.005 30.769 0.00 0.00 0.00 3.14
2056 2090 9.592196 AATGAAGGTCCAAACATATTAGCATAT 57.408 29.630 0.00 0.00 0.00 1.78
2057 2091 8.621532 TGAAGGTCCAAACATATTAGCATATC 57.378 34.615 0.00 0.00 0.00 1.63
2058 2092 8.439971 TGAAGGTCCAAACATATTAGCATATCT 58.560 33.333 0.00 0.00 0.00 1.98
2059 2093 9.289782 GAAGGTCCAAACATATTAGCATATCTT 57.710 33.333 0.00 0.00 0.00 2.40
2060 2094 8.627208 AGGTCCAAACATATTAGCATATCTTG 57.373 34.615 0.00 0.00 0.00 3.02
2061 2095 8.439971 AGGTCCAAACATATTAGCATATCTTGA 58.560 33.333 0.00 0.00 0.00 3.02
2062 2096 9.236006 GGTCCAAACATATTAGCATATCTTGAT 57.764 33.333 0.00 0.00 0.00 2.57
2072 2106 8.774890 ATTAGCATATCTTGATGAGATGTCAC 57.225 34.615 0.00 0.00 44.80 3.67
2073 2107 6.422344 AGCATATCTTGATGAGATGTCACT 57.578 37.500 0.00 0.00 44.80 3.41
2074 2108 7.536159 AGCATATCTTGATGAGATGTCACTA 57.464 36.000 0.00 0.00 44.80 2.74
2075 2109 8.136563 AGCATATCTTGATGAGATGTCACTAT 57.863 34.615 0.00 0.00 44.80 2.12
2076 2110 8.035984 AGCATATCTTGATGAGATGTCACTATG 58.964 37.037 0.00 0.00 44.80 2.23
2077 2111 8.033626 GCATATCTTGATGAGATGTCACTATGA 58.966 37.037 0.00 0.00 44.80 2.15
2078 2112 9.924650 CATATCTTGATGAGATGTCACTATGAA 57.075 33.333 0.00 0.00 44.80 2.57
2090 2124 9.784531 AGATGTCACTATGAAATAATACCAAGG 57.215 33.333 0.00 0.00 0.00 3.61
2091 2125 7.801716 TGTCACTATGAAATAATACCAAGGC 57.198 36.000 0.00 0.00 0.00 4.35
2092 2126 7.342581 TGTCACTATGAAATAATACCAAGGCA 58.657 34.615 0.00 0.00 0.00 4.75
2093 2127 7.998383 TGTCACTATGAAATAATACCAAGGCAT 59.002 33.333 0.00 0.00 0.00 4.40
2094 2128 9.502091 GTCACTATGAAATAATACCAAGGCATA 57.498 33.333 0.00 0.00 0.00 3.14
2106 2140 8.904099 AATACCAAGGCATAATGTTAGAGTAC 57.096 34.615 0.00 0.00 0.00 2.73
2107 2141 5.357257 ACCAAGGCATAATGTTAGAGTACG 58.643 41.667 0.00 0.00 0.00 3.67
2108 2142 5.105064 ACCAAGGCATAATGTTAGAGTACGT 60.105 40.000 0.00 0.00 0.00 3.57
2109 2143 6.097270 ACCAAGGCATAATGTTAGAGTACGTA 59.903 38.462 0.00 0.00 0.00 3.57
2110 2144 6.982141 CCAAGGCATAATGTTAGAGTACGTAA 59.018 38.462 0.00 0.00 0.00 3.18
2111 2145 7.656137 CCAAGGCATAATGTTAGAGTACGTAAT 59.344 37.037 0.00 0.00 0.00 1.89
2112 2146 8.487970 CAAGGCATAATGTTAGAGTACGTAATG 58.512 37.037 0.00 0.00 0.00 1.90
2113 2147 7.152645 AGGCATAATGTTAGAGTACGTAATGG 58.847 38.462 0.00 0.00 0.00 3.16
2114 2148 6.367969 GGCATAATGTTAGAGTACGTAATGGG 59.632 42.308 0.00 0.00 0.00 4.00
2115 2149 6.128634 GCATAATGTTAGAGTACGTAATGGGC 60.129 42.308 0.00 0.00 0.00 5.36
2116 2150 3.806625 TGTTAGAGTACGTAATGGGCC 57.193 47.619 0.00 0.00 0.00 5.80
2117 2151 3.368248 TGTTAGAGTACGTAATGGGCCT 58.632 45.455 4.53 0.00 0.00 5.19
2118 2152 4.535781 TGTTAGAGTACGTAATGGGCCTA 58.464 43.478 4.53 0.00 0.00 3.93
2119 2153 4.955450 TGTTAGAGTACGTAATGGGCCTAA 59.045 41.667 4.53 0.00 0.00 2.69
2120 2154 5.599656 TGTTAGAGTACGTAATGGGCCTAAT 59.400 40.000 4.53 0.00 0.00 1.73
2121 2155 4.602340 AGAGTACGTAATGGGCCTAATG 57.398 45.455 4.53 0.00 0.00 1.90
2122 2156 3.323979 AGAGTACGTAATGGGCCTAATGG 59.676 47.826 4.53 0.00 0.00 3.16
2123 2157 2.370849 AGTACGTAATGGGCCTAATGGG 59.629 50.000 4.53 0.00 38.36 4.00
2135 2169 3.933861 CCTAATGGGCCTGTTAGTCTT 57.066 47.619 20.36 1.36 0.00 3.01
2137 2171 4.962155 CCTAATGGGCCTGTTAGTCTTAG 58.038 47.826 20.36 9.16 0.00 2.18
2138 2172 3.933861 AATGGGCCTGTTAGTCTTAGG 57.066 47.619 4.53 0.00 34.67 2.69
2139 2173 1.580059 TGGGCCTGTTAGTCTTAGGG 58.420 55.000 4.53 0.00 32.15 3.53
2140 2174 1.203389 TGGGCCTGTTAGTCTTAGGGT 60.203 52.381 4.53 0.00 32.15 4.34
2141 2175 1.914108 GGGCCTGTTAGTCTTAGGGTT 59.086 52.381 0.84 0.00 32.15 4.11
2142 2176 3.109928 GGGCCTGTTAGTCTTAGGGTTA 58.890 50.000 0.84 0.00 32.15 2.85
2143 2177 3.520721 GGGCCTGTTAGTCTTAGGGTTAA 59.479 47.826 0.84 0.00 32.15 2.01
2144 2178 4.165565 GGGCCTGTTAGTCTTAGGGTTAAT 59.834 45.833 0.84 0.00 32.15 1.40
2145 2179 5.339778 GGGCCTGTTAGTCTTAGGGTTAATT 60.340 44.000 0.84 0.00 32.15 1.40
2146 2180 6.126681 GGGCCTGTTAGTCTTAGGGTTAATTA 60.127 42.308 0.84 0.00 32.15 1.40
2147 2181 6.990939 GGCCTGTTAGTCTTAGGGTTAATTAG 59.009 42.308 0.00 0.00 32.15 1.73
2148 2182 7.147602 GGCCTGTTAGTCTTAGGGTTAATTAGA 60.148 40.741 0.00 0.00 32.15 2.10
2149 2183 7.927092 GCCTGTTAGTCTTAGGGTTAATTAGAG 59.073 40.741 0.00 0.00 32.15 2.43
2150 2184 9.198475 CCTGTTAGTCTTAGGGTTAATTAGAGA 57.802 37.037 0.00 0.00 0.00 3.10
2160 2194 6.983984 AGGGTTAATTAGAGATAAGAGTCGC 58.016 40.000 0.00 0.00 0.00 5.19
2161 2195 6.778559 AGGGTTAATTAGAGATAAGAGTCGCT 59.221 38.462 0.00 0.00 32.84 4.93
2162 2196 7.288158 AGGGTTAATTAGAGATAAGAGTCGCTT 59.712 37.037 0.00 0.00 40.68 4.68
2163 2197 7.382759 GGGTTAATTAGAGATAAGAGTCGCTTG 59.617 40.741 0.00 0.00 37.42 4.01
2164 2198 7.095982 GGTTAATTAGAGATAAGAGTCGCTTGC 60.096 40.741 0.00 0.00 37.42 4.01
2165 2199 5.782893 ATTAGAGATAAGAGTCGCTTGCT 57.217 39.130 0.00 0.00 37.42 3.91
2166 2200 5.584253 TTAGAGATAAGAGTCGCTTGCTT 57.416 39.130 0.00 0.00 37.42 3.91
2167 2201 6.694877 TTAGAGATAAGAGTCGCTTGCTTA 57.305 37.500 0.00 0.00 37.42 3.09
2168 2202 5.181690 AGAGATAAGAGTCGCTTGCTTAG 57.818 43.478 0.00 0.00 37.42 2.18
2169 2203 4.037446 AGAGATAAGAGTCGCTTGCTTAGG 59.963 45.833 0.00 0.00 37.42 2.69
2170 2204 2.961526 TAAGAGTCGCTTGCTTAGGG 57.038 50.000 0.00 0.00 37.42 3.53
2171 2205 0.250513 AAGAGTCGCTTGCTTAGGGG 59.749 55.000 0.00 0.00 37.41 4.79
2172 2206 0.905337 AGAGTCGCTTGCTTAGGGGT 60.905 55.000 4.21 0.00 37.41 4.95
2173 2207 0.460459 GAGTCGCTTGCTTAGGGGTC 60.460 60.000 4.21 0.00 37.41 4.46
2174 2208 1.192146 AGTCGCTTGCTTAGGGGTCA 61.192 55.000 4.21 0.00 37.41 4.02
2175 2209 0.321298 GTCGCTTGCTTAGGGGTCAA 60.321 55.000 4.21 0.00 37.41 3.18
2176 2210 0.036388 TCGCTTGCTTAGGGGTCAAG 60.036 55.000 0.00 0.00 39.95 3.02
2177 2211 0.321653 CGCTTGCTTAGGGGTCAAGT 60.322 55.000 0.00 0.00 39.36 3.16
2178 2212 1.066430 CGCTTGCTTAGGGGTCAAGTA 60.066 52.381 0.00 0.00 39.36 2.24
2179 2213 2.614481 CGCTTGCTTAGGGGTCAAGTAA 60.614 50.000 0.00 0.00 39.36 2.24
2180 2214 3.010420 GCTTGCTTAGGGGTCAAGTAAG 58.990 50.000 8.11 8.11 44.06 2.34
2181 2215 2.781681 TGCTTAGGGGTCAAGTAAGC 57.218 50.000 6.41 6.41 45.90 3.09
2182 2216 1.280998 TGCTTAGGGGTCAAGTAAGCC 59.719 52.381 10.06 0.00 45.37 4.35
2183 2217 1.560146 GCTTAGGGGTCAAGTAAGCCT 59.440 52.381 2.53 0.00 41.83 4.58
2184 2218 2.026169 GCTTAGGGGTCAAGTAAGCCTT 60.026 50.000 2.53 0.00 41.83 4.35
2197 2231 3.827505 AGCCTTGCTTGGAAGTCAA 57.172 47.368 1.52 0.00 33.89 3.18
2209 2243 5.859495 CTTGGAAGTCAAGTAAACCTCTCT 58.141 41.667 0.00 0.00 45.81 3.10
2210 2244 6.989155 TTGGAAGTCAAGTAAACCTCTCTA 57.011 37.500 0.00 0.00 0.00 2.43
2211 2245 7.554959 TTGGAAGTCAAGTAAACCTCTCTAT 57.445 36.000 0.00 0.00 0.00 1.98
2212 2246 8.660295 TTGGAAGTCAAGTAAACCTCTCTATA 57.340 34.615 0.00 0.00 0.00 1.31
2213 2247 8.840200 TGGAAGTCAAGTAAACCTCTCTATAT 57.160 34.615 0.00 0.00 0.00 0.86
2214 2248 9.931698 TGGAAGTCAAGTAAACCTCTCTATATA 57.068 33.333 0.00 0.00 0.00 0.86
2241 2275 9.599056 AAGAGAGGAGATGTATCAATCTAATCA 57.401 33.333 0.00 0.00 37.03 2.57
2242 2276 9.599056 AGAGAGGAGATGTATCAATCTAATCAA 57.401 33.333 0.00 0.00 37.03 2.57
2243 2277 9.859427 GAGAGGAGATGTATCAATCTAATCAAG 57.141 37.037 0.00 0.00 37.03 3.02
2244 2278 8.313292 AGAGGAGATGTATCAATCTAATCAAGC 58.687 37.037 0.00 0.00 37.03 4.01
2245 2279 7.971201 AGGAGATGTATCAATCTAATCAAGCA 58.029 34.615 0.00 0.00 37.03 3.91
2246 2280 8.435187 AGGAGATGTATCAATCTAATCAAGCAA 58.565 33.333 0.00 0.00 37.03 3.91
2247 2281 8.719648 GGAGATGTATCAATCTAATCAAGCAAG 58.280 37.037 0.00 0.00 37.03 4.01
2248 2282 9.486497 GAGATGTATCAATCTAATCAAGCAAGA 57.514 33.333 0.00 0.00 37.03 3.02
2249 2283 9.842775 AGATGTATCAATCTAATCAAGCAAGAA 57.157 29.630 0.00 0.00 35.09 2.52
2259 2293 9.911788 ATCTAATCAAGCAAGAATTAAGAAGGA 57.088 29.630 0.00 0.00 0.00 3.36
2260 2294 9.739276 TCTAATCAAGCAAGAATTAAGAAGGAA 57.261 29.630 0.00 0.00 0.00 3.36
2263 2297 9.866798 AATCAAGCAAGAATTAAGAAGGAAATC 57.133 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
629 634 3.244526 GGGAATGTGGCCTTGTCATTTTT 60.245 43.478 3.32 0.00 32.90 1.94
860 867 2.040178 GGAAGTCGGGGACATGATAGT 58.960 52.381 0.00 0.00 34.60 2.12
1109 1118 2.353803 GGAACATAATCCGGATCCCTCG 60.354 54.545 19.43 7.54 0.00 4.63
1908 1942 4.502950 CCTGCAAGCAAAACCAATCCTAAA 60.503 41.667 0.00 0.00 0.00 1.85
1912 1946 1.344114 TCCTGCAAGCAAAACCAATCC 59.656 47.619 0.00 0.00 0.00 3.01
1913 1947 2.818130 TCCTGCAAGCAAAACCAATC 57.182 45.000 0.00 0.00 0.00 2.67
1914 1948 3.775261 ATTCCTGCAAGCAAAACCAAT 57.225 38.095 0.00 0.00 0.00 3.16
1915 1949 3.204526 CAATTCCTGCAAGCAAAACCAA 58.795 40.909 0.00 0.00 0.00 3.67
1916 1950 2.485124 CCAATTCCTGCAAGCAAAACCA 60.485 45.455 0.00 0.00 0.00 3.67
1917 1951 2.145536 CCAATTCCTGCAAGCAAAACC 58.854 47.619 0.00 0.00 0.00 3.27
1918 1952 1.532437 GCCAATTCCTGCAAGCAAAAC 59.468 47.619 0.00 0.00 0.00 2.43
1919 1953 1.140452 TGCCAATTCCTGCAAGCAAAA 59.860 42.857 0.00 0.00 33.87 2.44
1920 1954 0.757512 TGCCAATTCCTGCAAGCAAA 59.242 45.000 0.00 0.00 33.87 3.68
1921 1955 0.757512 TTGCCAATTCCTGCAAGCAA 59.242 45.000 0.00 0.00 42.19 3.91
1922 1956 2.438730 TTGCCAATTCCTGCAAGCA 58.561 47.368 3.17 0.00 42.19 3.91
1925 1959 0.033781 GCTGTTGCCAATTCCTGCAA 59.966 50.000 3.17 3.17 44.64 4.08
1926 1960 1.667151 GCTGTTGCCAATTCCTGCA 59.333 52.632 0.00 0.00 35.27 4.41
1927 1961 4.584688 GCTGTTGCCAATTCCTGC 57.415 55.556 0.00 0.00 0.00 4.85
1937 1971 4.576463 AGCATTACTGTAATAGGCTGTTGC 59.424 41.667 18.90 14.27 38.76 4.17
1938 1972 6.238484 GGAAGCATTACTGTAATAGGCTGTTG 60.238 42.308 19.80 7.39 30.63 3.33
1939 1973 5.823045 GGAAGCATTACTGTAATAGGCTGTT 59.177 40.000 19.80 9.96 30.63 3.16
1940 1974 5.131142 AGGAAGCATTACTGTAATAGGCTGT 59.869 40.000 19.80 12.86 38.34 4.40
1941 1975 5.615289 AGGAAGCATTACTGTAATAGGCTG 58.385 41.667 19.80 9.11 38.34 4.85
1942 1976 5.604650 AGAGGAAGCATTACTGTAATAGGCT 59.395 40.000 15.65 15.65 41.39 4.58
1943 1977 5.859495 AGAGGAAGCATTACTGTAATAGGC 58.141 41.667 12.39 12.43 41.39 3.93
1944 1978 7.379750 GGTAGAGGAAGCATTACTGTAATAGG 58.620 42.308 12.39 3.54 41.39 2.57
1945 1979 7.379750 GGGTAGAGGAAGCATTACTGTAATAG 58.620 42.308 12.39 8.62 41.39 1.73
1946 1980 6.015688 CGGGTAGAGGAAGCATTACTGTAATA 60.016 42.308 12.39 0.00 41.39 0.98
1947 1981 5.221461 CGGGTAGAGGAAGCATTACTGTAAT 60.221 44.000 7.22 7.22 41.39 1.89
1948 1982 4.098960 CGGGTAGAGGAAGCATTACTGTAA 59.901 45.833 2.26 2.26 41.39 2.41
1949 1983 3.635373 CGGGTAGAGGAAGCATTACTGTA 59.365 47.826 0.00 0.00 41.39 2.74
1950 1984 2.431057 CGGGTAGAGGAAGCATTACTGT 59.569 50.000 0.00 0.00 41.39 3.55
1951 1985 2.431057 ACGGGTAGAGGAAGCATTACTG 59.569 50.000 0.00 0.00 41.39 2.74
1952 1986 2.694109 GACGGGTAGAGGAAGCATTACT 59.306 50.000 0.00 0.00 46.66 2.24
1953 1987 2.429610 TGACGGGTAGAGGAAGCATTAC 59.570 50.000 0.00 0.00 0.00 1.89
1954 1988 2.742348 TGACGGGTAGAGGAAGCATTA 58.258 47.619 0.00 0.00 0.00 1.90
1955 1989 1.568504 TGACGGGTAGAGGAAGCATT 58.431 50.000 0.00 0.00 0.00 3.56
1956 1990 1.794714 ATGACGGGTAGAGGAAGCAT 58.205 50.000 0.00 0.00 0.00 3.79
1957 1991 1.480954 GAATGACGGGTAGAGGAAGCA 59.519 52.381 0.00 0.00 0.00 3.91
1958 1992 1.480954 TGAATGACGGGTAGAGGAAGC 59.519 52.381 0.00 0.00 0.00 3.86
1959 1993 2.761208 AGTGAATGACGGGTAGAGGAAG 59.239 50.000 0.00 0.00 0.00 3.46
1960 1994 2.816411 AGTGAATGACGGGTAGAGGAA 58.184 47.619 0.00 0.00 0.00 3.36
1961 1995 2.496070 CAAGTGAATGACGGGTAGAGGA 59.504 50.000 0.00 0.00 0.00 3.71
1962 1996 2.496070 TCAAGTGAATGACGGGTAGAGG 59.504 50.000 0.00 0.00 0.00 3.69
1963 1997 3.512680 GTCAAGTGAATGACGGGTAGAG 58.487 50.000 0.00 0.00 40.23 2.43
1964 1998 3.587797 GTCAAGTGAATGACGGGTAGA 57.412 47.619 0.00 0.00 40.23 2.59
1972 2006 3.510459 TCTCTCCAGGTCAAGTGAATGA 58.490 45.455 0.00 0.00 0.00 2.57
1973 2007 3.369261 CCTCTCTCCAGGTCAAGTGAATG 60.369 52.174 0.00 0.00 0.00 2.67
1974 2008 2.836981 CCTCTCTCCAGGTCAAGTGAAT 59.163 50.000 0.00 0.00 0.00 2.57
1975 2009 2.251818 CCTCTCTCCAGGTCAAGTGAA 58.748 52.381 0.00 0.00 0.00 3.18
1976 2010 1.148027 ACCTCTCTCCAGGTCAAGTGA 59.852 52.381 0.00 0.00 44.08 3.41
1977 2011 1.638529 ACCTCTCTCCAGGTCAAGTG 58.361 55.000 0.00 0.00 44.08 3.16
1978 2012 2.370189 CAAACCTCTCTCCAGGTCAAGT 59.630 50.000 0.00 0.00 46.97 3.16
1979 2013 2.873649 GCAAACCTCTCTCCAGGTCAAG 60.874 54.545 0.00 0.00 46.97 3.02
1980 2014 1.072331 GCAAACCTCTCTCCAGGTCAA 59.928 52.381 0.00 0.00 46.97 3.18
1981 2015 0.687354 GCAAACCTCTCTCCAGGTCA 59.313 55.000 0.00 0.00 46.97 4.02
1982 2016 0.687354 TGCAAACCTCTCTCCAGGTC 59.313 55.000 0.00 0.00 46.97 3.85
1984 2018 1.407989 GGATGCAAACCTCTCTCCAGG 60.408 57.143 0.00 0.00 39.80 4.45
1985 2019 1.280133 TGGATGCAAACCTCTCTCCAG 59.720 52.381 13.16 0.00 0.00 3.86
1986 2020 1.280133 CTGGATGCAAACCTCTCTCCA 59.720 52.381 13.16 7.83 0.00 3.86
1987 2021 2.016096 GCTGGATGCAAACCTCTCTCC 61.016 57.143 13.16 3.64 42.31 3.71
1988 2022 1.065564 AGCTGGATGCAAACCTCTCTC 60.066 52.381 13.16 0.00 45.94 3.20
1989 2023 0.990374 AGCTGGATGCAAACCTCTCT 59.010 50.000 13.16 6.01 45.94 3.10
1990 2024 1.831580 AAGCTGGATGCAAACCTCTC 58.168 50.000 13.16 0.00 45.94 3.20
1991 2025 2.299326 AAAGCTGGATGCAAACCTCT 57.701 45.000 13.16 8.23 45.94 3.69
1992 2026 4.725790 ATTAAAGCTGGATGCAAACCTC 57.274 40.909 13.16 6.48 45.94 3.85
1993 2027 5.246883 AGAAATTAAAGCTGGATGCAAACCT 59.753 36.000 13.16 0.00 45.94 3.50
1994 2028 5.349543 CAGAAATTAAAGCTGGATGCAAACC 59.650 40.000 6.38 6.38 45.94 3.27
1995 2029 6.158598 TCAGAAATTAAAGCTGGATGCAAAC 58.841 36.000 0.00 0.00 45.94 2.93
1996 2030 6.343716 TCAGAAATTAAAGCTGGATGCAAA 57.656 33.333 0.00 0.00 45.94 3.68
1997 2031 5.105635 CCTCAGAAATTAAAGCTGGATGCAA 60.106 40.000 0.00 0.00 45.94 4.08
1998 2032 4.400251 CCTCAGAAATTAAAGCTGGATGCA 59.600 41.667 0.00 0.00 45.94 3.96
1999 2033 4.202090 CCCTCAGAAATTAAAGCTGGATGC 60.202 45.833 0.00 0.00 43.29 3.91
2000 2034 4.952335 ACCCTCAGAAATTAAAGCTGGATG 59.048 41.667 0.00 0.00 0.00 3.51
2001 2035 5.198602 ACCCTCAGAAATTAAAGCTGGAT 57.801 39.130 0.00 0.00 0.00 3.41
2002 2036 4.657814 ACCCTCAGAAATTAAAGCTGGA 57.342 40.909 0.00 0.00 0.00 3.86
2003 2037 5.728637 AAACCCTCAGAAATTAAAGCTGG 57.271 39.130 0.00 0.00 0.00 4.85
2012 2046 9.547279 ACCTTCATTAATAAAACCCTCAGAAAT 57.453 29.630 0.00 0.00 0.00 2.17
2013 2047 8.950007 ACCTTCATTAATAAAACCCTCAGAAA 57.050 30.769 0.00 0.00 0.00 2.52
2014 2048 7.614192 GGACCTTCATTAATAAAACCCTCAGAA 59.386 37.037 0.00 0.00 0.00 3.02
2015 2049 7.116736 GGACCTTCATTAATAAAACCCTCAGA 58.883 38.462 0.00 0.00 0.00 3.27
2016 2050 6.889722 TGGACCTTCATTAATAAAACCCTCAG 59.110 38.462 0.00 0.00 0.00 3.35
2017 2051 6.795590 TGGACCTTCATTAATAAAACCCTCA 58.204 36.000 0.00 0.00 0.00 3.86
2018 2052 7.712204 TTGGACCTTCATTAATAAAACCCTC 57.288 36.000 0.00 0.00 0.00 4.30
2019 2053 7.511028 TGTTTGGACCTTCATTAATAAAACCCT 59.489 33.333 0.00 0.00 0.00 4.34
2020 2054 7.672240 TGTTTGGACCTTCATTAATAAAACCC 58.328 34.615 0.00 0.00 0.00 4.11
2027 2061 9.420118 TGCTAATATGTTTGGACCTTCATTAAT 57.580 29.630 0.00 0.00 0.00 1.40
2028 2062 8.815565 TGCTAATATGTTTGGACCTTCATTAA 57.184 30.769 0.00 0.00 0.00 1.40
2029 2063 8.995027 ATGCTAATATGTTTGGACCTTCATTA 57.005 30.769 0.00 0.00 0.00 1.90
2030 2064 7.902920 ATGCTAATATGTTTGGACCTTCATT 57.097 32.000 0.00 0.00 0.00 2.57
2031 2065 9.236006 GATATGCTAATATGTTTGGACCTTCAT 57.764 33.333 0.00 0.00 0.00 2.57
2032 2066 8.439971 AGATATGCTAATATGTTTGGACCTTCA 58.560 33.333 0.00 0.00 0.00 3.02
2033 2067 8.854614 AGATATGCTAATATGTTTGGACCTTC 57.145 34.615 0.00 0.00 0.00 3.46
2034 2068 9.071276 CAAGATATGCTAATATGTTTGGACCTT 57.929 33.333 0.00 0.00 31.61 3.50
2035 2069 8.439971 TCAAGATATGCTAATATGTTTGGACCT 58.560 33.333 0.00 0.00 31.61 3.85
2036 2070 8.621532 TCAAGATATGCTAATATGTTTGGACC 57.378 34.615 0.00 0.00 31.61 4.46
2046 2080 9.866798 GTGACATCTCATCAAGATATGCTAATA 57.133 33.333 0.00 0.00 43.13 0.98
2047 2081 8.595421 AGTGACATCTCATCAAGATATGCTAAT 58.405 33.333 0.00 0.00 43.13 1.73
2048 2082 7.960262 AGTGACATCTCATCAAGATATGCTAA 58.040 34.615 0.00 0.00 43.13 3.09
2049 2083 7.536159 AGTGACATCTCATCAAGATATGCTA 57.464 36.000 0.00 0.00 43.13 3.49
2050 2084 6.422344 AGTGACATCTCATCAAGATATGCT 57.578 37.500 0.00 0.00 43.13 3.79
2051 2085 8.033626 TCATAGTGACATCTCATCAAGATATGC 58.966 37.037 0.00 0.00 43.13 3.14
2052 2086 9.924650 TTCATAGTGACATCTCATCAAGATATG 57.075 33.333 0.00 0.00 43.13 1.78
2064 2098 9.784531 CCTTGGTATTATTTCATAGTGACATCT 57.215 33.333 0.00 0.00 0.00 2.90
2065 2099 8.507249 GCCTTGGTATTATTTCATAGTGACATC 58.493 37.037 0.00 0.00 0.00 3.06
2066 2100 7.998383 TGCCTTGGTATTATTTCATAGTGACAT 59.002 33.333 0.00 0.00 0.00 3.06
2067 2101 7.342581 TGCCTTGGTATTATTTCATAGTGACA 58.657 34.615 0.00 0.00 0.00 3.58
2068 2102 7.801716 TGCCTTGGTATTATTTCATAGTGAC 57.198 36.000 0.00 0.00 0.00 3.67
2080 2114 9.991906 GTACTCTAACATTATGCCTTGGTATTA 57.008 33.333 0.00 0.00 0.00 0.98
2081 2115 7.656137 CGTACTCTAACATTATGCCTTGGTATT 59.344 37.037 0.00 0.00 0.00 1.89
2082 2116 7.152645 CGTACTCTAACATTATGCCTTGGTAT 58.847 38.462 0.00 0.00 0.00 2.73
2083 2117 6.097270 ACGTACTCTAACATTATGCCTTGGTA 59.903 38.462 0.00 0.00 0.00 3.25
2084 2118 5.105064 ACGTACTCTAACATTATGCCTTGGT 60.105 40.000 0.00 0.00 0.00 3.67
2085 2119 5.357257 ACGTACTCTAACATTATGCCTTGG 58.643 41.667 0.00 0.00 0.00 3.61
2086 2120 7.997107 TTACGTACTCTAACATTATGCCTTG 57.003 36.000 0.00 0.00 0.00 3.61
2087 2121 7.656137 CCATTACGTACTCTAACATTATGCCTT 59.344 37.037 0.00 0.00 0.00 4.35
2088 2122 7.152645 CCATTACGTACTCTAACATTATGCCT 58.847 38.462 0.00 0.00 0.00 4.75
2089 2123 6.367969 CCCATTACGTACTCTAACATTATGCC 59.632 42.308 0.00 0.00 0.00 4.40
2090 2124 6.128634 GCCCATTACGTACTCTAACATTATGC 60.129 42.308 0.00 0.00 0.00 3.14
2091 2125 6.367969 GGCCCATTACGTACTCTAACATTATG 59.632 42.308 0.00 0.00 0.00 1.90
2092 2126 6.269307 AGGCCCATTACGTACTCTAACATTAT 59.731 38.462 0.00 0.00 0.00 1.28
2093 2127 5.599656 AGGCCCATTACGTACTCTAACATTA 59.400 40.000 0.00 0.00 0.00 1.90
2094 2128 4.407945 AGGCCCATTACGTACTCTAACATT 59.592 41.667 0.00 0.00 0.00 2.71
2095 2129 3.965347 AGGCCCATTACGTACTCTAACAT 59.035 43.478 0.00 0.00 0.00 2.71
2096 2130 3.368248 AGGCCCATTACGTACTCTAACA 58.632 45.455 0.00 0.00 0.00 2.41
2097 2131 5.520376 TTAGGCCCATTACGTACTCTAAC 57.480 43.478 0.00 0.00 0.00 2.34
2098 2132 5.011329 CCATTAGGCCCATTACGTACTCTAA 59.989 44.000 0.00 0.00 0.00 2.10
2099 2133 4.525487 CCATTAGGCCCATTACGTACTCTA 59.475 45.833 0.00 0.00 0.00 2.43
2100 2134 3.323979 CCATTAGGCCCATTACGTACTCT 59.676 47.826 0.00 0.00 0.00 3.24
2101 2135 3.556423 CCCATTAGGCCCATTACGTACTC 60.556 52.174 0.00 0.00 0.00 2.59
2102 2136 2.370849 CCCATTAGGCCCATTACGTACT 59.629 50.000 0.00 0.00 0.00 2.73
2103 2137 2.774687 CCCATTAGGCCCATTACGTAC 58.225 52.381 0.00 0.00 0.00 3.67
2115 2149 3.933861 AAGACTAACAGGCCCATTAGG 57.066 47.619 21.77 8.97 33.47 2.69
2116 2150 4.202367 CCCTAAGACTAACAGGCCCATTAG 60.202 50.000 18.04 18.04 35.03 1.73
2117 2151 3.714798 CCCTAAGACTAACAGGCCCATTA 59.285 47.826 0.00 0.00 0.00 1.90
2118 2152 2.509964 CCCTAAGACTAACAGGCCCATT 59.490 50.000 0.00 0.00 0.00 3.16
2119 2153 2.127708 CCCTAAGACTAACAGGCCCAT 58.872 52.381 0.00 0.00 0.00 4.00
2120 2154 1.203389 ACCCTAAGACTAACAGGCCCA 60.203 52.381 0.00 0.00 0.00 5.36
2121 2155 1.581223 ACCCTAAGACTAACAGGCCC 58.419 55.000 0.00 0.00 0.00 5.80
2122 2156 4.831674 TTAACCCTAAGACTAACAGGCC 57.168 45.455 0.00 0.00 0.00 5.19
2123 2157 7.789026 TCTAATTAACCCTAAGACTAACAGGC 58.211 38.462 0.00 0.00 0.00 4.85
2124 2158 9.198475 TCTCTAATTAACCCTAAGACTAACAGG 57.802 37.037 0.00 0.00 0.00 4.00
2134 2168 8.574737 GCGACTCTTATCTCTAATTAACCCTAA 58.425 37.037 0.00 0.00 0.00 2.69
2135 2169 7.943447 AGCGACTCTTATCTCTAATTAACCCTA 59.057 37.037 0.00 0.00 0.00 3.53
2136 2170 6.778559 AGCGACTCTTATCTCTAATTAACCCT 59.221 38.462 0.00 0.00 0.00 4.34
2137 2171 6.983984 AGCGACTCTTATCTCTAATTAACCC 58.016 40.000 0.00 0.00 0.00 4.11
2138 2172 7.095982 GCAAGCGACTCTTATCTCTAATTAACC 60.096 40.741 0.00 0.00 32.74 2.85
2139 2173 7.650104 AGCAAGCGACTCTTATCTCTAATTAAC 59.350 37.037 0.00 0.00 32.74 2.01
2140 2174 7.717568 AGCAAGCGACTCTTATCTCTAATTAA 58.282 34.615 0.00 0.00 32.74 1.40
2141 2175 7.278461 AGCAAGCGACTCTTATCTCTAATTA 57.722 36.000 0.00 0.00 32.74 1.40
2142 2176 6.155475 AGCAAGCGACTCTTATCTCTAATT 57.845 37.500 0.00 0.00 32.74 1.40
2143 2177 5.782893 AGCAAGCGACTCTTATCTCTAAT 57.217 39.130 0.00 0.00 32.74 1.73
2144 2178 5.584253 AAGCAAGCGACTCTTATCTCTAA 57.416 39.130 0.00 0.00 32.74 2.10
2145 2179 5.239744 CCTAAGCAAGCGACTCTTATCTCTA 59.760 44.000 0.00 0.00 32.74 2.43
2146 2180 4.037446 CCTAAGCAAGCGACTCTTATCTCT 59.963 45.833 0.00 0.00 32.74 3.10
2147 2181 4.295051 CCTAAGCAAGCGACTCTTATCTC 58.705 47.826 0.00 0.00 32.74 2.75
2148 2182 3.068873 CCCTAAGCAAGCGACTCTTATCT 59.931 47.826 0.00 0.00 32.74 1.98
2149 2183 3.385577 CCCTAAGCAAGCGACTCTTATC 58.614 50.000 0.00 0.00 32.74 1.75
2150 2184 2.103263 CCCCTAAGCAAGCGACTCTTAT 59.897 50.000 0.00 0.00 32.74 1.73
2151 2185 1.480954 CCCCTAAGCAAGCGACTCTTA 59.519 52.381 0.00 0.00 32.74 2.10
2152 2186 0.250513 CCCCTAAGCAAGCGACTCTT 59.749 55.000 0.00 0.00 34.78 2.85
2153 2187 0.905337 ACCCCTAAGCAAGCGACTCT 60.905 55.000 0.00 0.00 0.00 3.24
2154 2188 0.460459 GACCCCTAAGCAAGCGACTC 60.460 60.000 0.00 0.00 0.00 3.36
2155 2189 1.192146 TGACCCCTAAGCAAGCGACT 61.192 55.000 0.00 0.00 0.00 4.18
2156 2190 0.321298 TTGACCCCTAAGCAAGCGAC 60.321 55.000 0.00 0.00 0.00 5.19
2157 2191 0.036388 CTTGACCCCTAAGCAAGCGA 60.036 55.000 0.00 0.00 33.48 4.93
2158 2192 0.321653 ACTTGACCCCTAAGCAAGCG 60.322 55.000 0.00 0.00 41.97 4.68
2159 2193 2.781681 TACTTGACCCCTAAGCAAGC 57.218 50.000 0.00 0.00 41.97 4.01
2160 2194 3.010420 GCTTACTTGACCCCTAAGCAAG 58.990 50.000 0.00 0.00 41.32 4.01
2161 2195 2.290705 GGCTTACTTGACCCCTAAGCAA 60.291 50.000 10.04 0.00 42.79 3.91
2162 2196 1.280998 GGCTTACTTGACCCCTAAGCA 59.719 52.381 10.04 0.00 42.79 3.91
2163 2197 1.560146 AGGCTTACTTGACCCCTAAGC 59.440 52.381 0.00 0.00 41.07 3.09
2179 2213 1.613836 CTTGACTTCCAAGCAAGGCT 58.386 50.000 12.19 0.00 44.90 4.58
2187 2221 5.888982 AGAGAGGTTTACTTGACTTCCAA 57.111 39.130 0.00 0.00 0.00 3.53
2188 2222 8.840200 ATATAGAGAGGTTTACTTGACTTCCA 57.160 34.615 0.00 0.00 0.00 3.53
2215 2249 9.599056 TGATTAGATTGATACATCTCCTCTCTT 57.401 33.333 0.00 0.00 0.00 2.85
2216 2250 9.599056 TTGATTAGATTGATACATCTCCTCTCT 57.401 33.333 0.00 0.00 0.00 3.10
2217 2251 9.859427 CTTGATTAGATTGATACATCTCCTCTC 57.141 37.037 0.00 0.00 0.00 3.20
2218 2252 8.313292 GCTTGATTAGATTGATACATCTCCTCT 58.687 37.037 0.00 0.00 0.00 3.69
2219 2253 8.093307 TGCTTGATTAGATTGATACATCTCCTC 58.907 37.037 0.00 0.00 0.00 3.71
2220 2254 7.971201 TGCTTGATTAGATTGATACATCTCCT 58.029 34.615 0.00 0.00 0.00 3.69
2221 2255 8.613060 TTGCTTGATTAGATTGATACATCTCC 57.387 34.615 0.00 0.00 0.00 3.71
2222 2256 9.486497 TCTTGCTTGATTAGATTGATACATCTC 57.514 33.333 0.00 0.00 0.00 2.75
2223 2257 9.842775 TTCTTGCTTGATTAGATTGATACATCT 57.157 29.630 0.00 0.00 0.00 2.90
2233 2267 9.911788 TCCTTCTTAATTCTTGCTTGATTAGAT 57.088 29.630 0.00 0.00 0.00 1.98
2234 2268 9.739276 TTCCTTCTTAATTCTTGCTTGATTAGA 57.261 29.630 0.00 0.00 0.00 2.10
2237 2271 9.866798 GATTTCCTTCTTAATTCTTGCTTGATT 57.133 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.