Multiple sequence alignment - TraesCS6D01G184800

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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 TraesCS6D01G184800 chr6D 100.000 2285 0 0 1 2285 235785365 235783081 0.000000e+00 4220
1 TraesCS6D01G184800 chr6D 89.174 351 28 8 1940 2285 202981665 202982010 1.620000e-116 429
2 TraesCS6D01G184800 chr2B 97.162 1938 51 2 1 1937 429178885 429176951 0.000000e+00 3271
3 TraesCS6D01G184800 chr1B 96.801 1938 60 2 1 1937 256213355 256211419 0.000000e+00 3234
4 TraesCS6D01G184800 chr4A 92.023 351 23 4 1939 2285 190831944 190831595 2.640000e-134 488
5 TraesCS6D01G184800 chr2A 89.859 355 26 8 1939 2285 46875371 46875019 4.480000e-122 448
6 TraesCS6D01G184800 chr2A 89.429 350 27 7 1940 2285 778455474 778455817 1.250000e-117 433
7 TraesCS6D01G184800 chr3D 89.773 352 27 8 1940 2285 464115583 464115235 2.080000e-120 442
8 TraesCS6D01G184800 chr3D 88.506 348 36 4 1940 2285 599058735 599058390 3.510000e-113 418
9 TraesCS6D01G184800 chrUn 88.636 352 31 8 1940 2285 197869719 197869371 9.760000e-114 420
10 TraesCS6D01G184800 chrUn 88.352 352 32 8 1940 2285 202524434 202524086 4.540000e-112 414
11 TraesCS6D01G184800 chr6A 88.286 350 35 5 1940 2285 36083610 36083263 4.540000e-112 414


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 TraesCS6D01G184800 chr6D 235783081 235785365 2284 True 4220 4220 100.000 1 2285 1 chr6D.!!$R1 2284
1 TraesCS6D01G184800 chr2B 429176951 429178885 1934 True 3271 3271 97.162 1 1937 1 chr2B.!!$R1 1936
2 TraesCS6D01G184800 chr1B 256211419 256213355 1936 True 3234 3234 96.801 1 1937 1 chr1B.!!$R1 1936

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
248 249 0.379669 GCCTGTTTCTCATGATGCGG 59.62 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2041 0.031917 TAGTCAAGCCCGGGGATGTA 60.032 55.0 25.28 0.0 0.0 2.29 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
78 79 0.970937 GATGACCGTGACCAGGAGGA 60.971 60.000 0.00 0.00 38.69 3.71
123 124 0.670546 CATGAAGGTGACCGACGCTT 60.671 55.000 0.00 0.00 0.00 4.68
146 147 1.455248 CTCTTCGAAGGACCGACTCT 58.545 55.000 24.37 0.00 38.39 3.24
202 203 2.664851 CAAGGGCACGAAGACGCA 60.665 61.111 0.00 0.00 43.96 5.24
248 249 0.379669 GCCTGTTTCTCATGATGCGG 59.620 55.000 0.00 0.00 0.00 5.69
315 316 2.107750 CTCTGCATCCGGTCGCAT 59.892 61.111 18.52 0.00 37.54 4.73
539 540 2.827423 CTCCTCCGCCTGCATCAT 59.173 61.111 0.00 0.00 0.00 2.45
553 554 2.553602 TGCATCATGTTGTCAGTTCCAC 59.446 45.455 5.69 0.00 0.00 4.02
579 580 2.679716 GGATGAGCCTGCAACCCT 59.320 61.111 0.00 0.00 0.00 4.34
585 586 0.610232 GAGCCTGCAACCCTTGTGAT 60.610 55.000 0.00 0.00 0.00 3.06
657 659 1.203994 ACGTCTACCCCGATCTTTGTG 59.796 52.381 0.00 0.00 0.00 3.33
721 723 2.038557 AGGAGAAAGGCGTCTTGCTTTA 59.961 45.455 12.59 0.00 42.86 1.85
809 811 1.372251 CTCAAGACGCAGCGACACT 60.372 57.895 24.65 14.43 0.00 3.55
837 839 1.452953 TATCGCCGGCTAGTGGTCAG 61.453 60.000 26.68 5.22 0.00 3.51
1152 1154 1.152984 CATCACCATTGCGGCCCTA 60.153 57.895 0.00 0.00 39.03 3.53
1244 1246 0.461693 GATGGTCCAGAGCTGCAGAC 60.462 60.000 20.43 10.66 0.00 3.51
1302 1307 0.250467 AGCGATGCTTGTGTTCCTGT 60.250 50.000 0.00 0.00 33.89 4.00
1381 1386 2.110835 TTCGCCTGCTTGCAGTCA 59.889 55.556 19.49 2.22 0.00 3.41
1442 1447 0.676466 TGATGCTAGTTTGTGCCCCG 60.676 55.000 0.00 0.00 0.00 5.73
1494 1499 6.325919 TGGTTTCCAATGAGTAATCACAAC 57.674 37.500 0.00 0.00 0.00 3.32
1937 1942 7.399765 TGGGGACTTCAATCAAATTTATCATGT 59.600 33.333 0.00 0.00 0.00 3.21
1938 1943 7.922811 GGGGACTTCAATCAAATTTATCATGTC 59.077 37.037 0.00 0.00 0.00 3.06
1939 1944 8.689972 GGGACTTCAATCAAATTTATCATGTCT 58.310 33.333 0.00 0.00 0.00 3.41
1940 1945 9.512435 GGACTTCAATCAAATTTATCATGTCTG 57.488 33.333 0.00 0.00 0.00 3.51
1956 1961 8.824159 ATCATGTCTGTTAGAATAAATCCGAG 57.176 34.615 0.00 0.00 0.00 4.63
1957 1962 7.210174 TCATGTCTGTTAGAATAAATCCGAGG 58.790 38.462 0.00 0.00 0.00 4.63
1958 1963 5.357257 TGTCTGTTAGAATAAATCCGAGGC 58.643 41.667 0.00 0.00 0.00 4.70
1959 1964 4.750598 GTCTGTTAGAATAAATCCGAGGCC 59.249 45.833 0.00 0.00 0.00 5.19
1960 1965 4.407621 TCTGTTAGAATAAATCCGAGGCCA 59.592 41.667 5.01 0.00 0.00 5.36
1961 1966 5.071788 TCTGTTAGAATAAATCCGAGGCCAT 59.928 40.000 5.01 0.00 0.00 4.40
1962 1967 5.305585 TGTTAGAATAAATCCGAGGCCATC 58.694 41.667 5.01 0.00 0.00 3.51
1972 1977 3.114558 GAGGCCATCGTCGATCATC 57.885 57.895 5.01 0.00 0.00 2.92
1973 1978 0.389166 GAGGCCATCGTCGATCATCC 60.389 60.000 5.01 6.78 0.00 3.51
1974 1979 1.734477 GGCCATCGTCGATCATCCG 60.734 63.158 4.34 0.00 0.00 4.18
1975 1980 1.285950 GCCATCGTCGATCATCCGA 59.714 57.895 4.34 0.00 36.06 4.55
1976 1981 0.730834 GCCATCGTCGATCATCCGAG 60.731 60.000 4.34 0.00 39.43 4.63
1977 1982 0.109551 CCATCGTCGATCATCCGAGG 60.110 60.000 4.34 0.00 43.32 4.63
1978 1983 4.870190 TCGTCGATCATCCGAGGA 57.130 55.556 0.00 0.00 46.68 3.71
1979 1984 2.318224 TCGTCGATCATCCGAGGAC 58.682 57.895 0.00 0.00 44.89 3.85
1980 1985 1.164662 TCGTCGATCATCCGAGGACC 61.165 60.000 0.00 0.00 44.89 4.46
1981 1986 1.444917 CGTCGATCATCCGAGGACCA 61.445 60.000 0.00 0.00 44.30 4.02
1982 1987 0.744874 GTCGATCATCCGAGGACCAA 59.255 55.000 0.00 0.00 39.43 3.67
1983 1988 1.032794 TCGATCATCCGAGGACCAAG 58.967 55.000 0.00 0.00 34.19 3.61
1984 1989 0.598680 CGATCATCCGAGGACCAAGC 60.599 60.000 0.00 0.00 0.00 4.01
1985 1990 0.465705 GATCATCCGAGGACCAAGCA 59.534 55.000 0.00 0.00 0.00 3.91
1986 1991 0.911769 ATCATCCGAGGACCAAGCAA 59.088 50.000 0.00 0.00 0.00 3.91
1987 1992 0.911769 TCATCCGAGGACCAAGCAAT 59.088 50.000 0.00 0.00 0.00 3.56
1988 1993 1.134401 TCATCCGAGGACCAAGCAATC 60.134 52.381 0.00 0.00 0.00 2.67
1989 1994 0.911769 ATCCGAGGACCAAGCAATCA 59.088 50.000 0.00 0.00 0.00 2.57
1990 1995 0.690192 TCCGAGGACCAAGCAATCAA 59.310 50.000 0.00 0.00 0.00 2.57
1991 1996 1.073125 TCCGAGGACCAAGCAATCAAA 59.927 47.619 0.00 0.00 0.00 2.69
1992 1997 1.200020 CCGAGGACCAAGCAATCAAAC 59.800 52.381 0.00 0.00 0.00 2.93
1993 1998 1.135972 CGAGGACCAAGCAATCAAACG 60.136 52.381 0.00 0.00 0.00 3.60
1994 1999 2.151202 GAGGACCAAGCAATCAAACGA 58.849 47.619 0.00 0.00 0.00 3.85
1995 2000 2.154462 AGGACCAAGCAATCAAACGAG 58.846 47.619 0.00 0.00 0.00 4.18
1996 2001 1.401539 GGACCAAGCAATCAAACGAGC 60.402 52.381 0.00 0.00 0.00 5.03
1997 2002 1.266718 GACCAAGCAATCAAACGAGCA 59.733 47.619 0.00 0.00 0.00 4.26
1998 2003 1.001378 ACCAAGCAATCAAACGAGCAC 60.001 47.619 0.00 0.00 0.00 4.40
1999 2004 1.321016 CAAGCAATCAAACGAGCACG 58.679 50.000 0.76 0.76 45.75 5.34
2000 2005 1.069973 CAAGCAATCAAACGAGCACGA 60.070 47.619 11.40 0.00 42.66 4.35
2001 2006 0.512952 AGCAATCAAACGAGCACGAC 59.487 50.000 11.40 0.00 42.66 4.34
2002 2007 0.234625 GCAATCAAACGAGCACGACA 59.765 50.000 11.40 0.00 42.66 4.35
2003 2008 1.937359 CAATCAAACGAGCACGACAC 58.063 50.000 11.40 0.00 42.66 3.67
2004 2009 0.865769 AATCAAACGAGCACGACACC 59.134 50.000 11.40 0.00 42.66 4.16
2005 2010 1.282248 ATCAAACGAGCACGACACCG 61.282 55.000 11.40 0.00 42.66 4.94
2006 2011 1.947146 CAAACGAGCACGACACCGA 60.947 57.895 11.40 0.00 42.66 4.69
2007 2012 1.660575 AAACGAGCACGACACCGAG 60.661 57.895 11.40 0.00 42.66 4.63
2008 2013 2.067091 AAACGAGCACGACACCGAGA 62.067 55.000 11.40 0.00 42.66 4.04
2009 2014 1.863662 AACGAGCACGACACCGAGAT 61.864 55.000 11.40 0.00 42.66 2.75
2010 2015 1.154016 CGAGCACGACACCGAGATT 60.154 57.895 0.00 0.00 42.66 2.40
2011 2016 0.732880 CGAGCACGACACCGAGATTT 60.733 55.000 0.00 0.00 42.66 2.17
2012 2017 0.716108 GAGCACGACACCGAGATTTG 59.284 55.000 0.00 0.00 39.50 2.32
2013 2018 0.033504 AGCACGACACCGAGATTTGT 59.966 50.000 0.00 0.00 39.50 2.83
2014 2019 0.865769 GCACGACACCGAGATTTGTT 59.134 50.000 0.00 0.00 39.50 2.83
2015 2020 2.063266 GCACGACACCGAGATTTGTTA 58.937 47.619 0.00 0.00 39.50 2.41
2016 2021 2.477375 GCACGACACCGAGATTTGTTAA 59.523 45.455 0.00 0.00 39.50 2.01
2017 2022 3.124636 GCACGACACCGAGATTTGTTAAT 59.875 43.478 0.00 0.00 39.50 1.40
2018 2023 4.637968 CACGACACCGAGATTTGTTAATG 58.362 43.478 0.00 0.00 39.50 1.90
2019 2024 4.387559 CACGACACCGAGATTTGTTAATGA 59.612 41.667 0.00 0.00 39.50 2.57
2020 2025 4.625742 ACGACACCGAGATTTGTTAATGAG 59.374 41.667 0.00 0.00 39.50 2.90
2021 2026 4.032900 CGACACCGAGATTTGTTAATGAGG 59.967 45.833 0.00 0.00 38.22 3.86
2022 2027 4.906618 ACACCGAGATTTGTTAATGAGGT 58.093 39.130 0.00 0.00 0.00 3.85
2023 2028 5.313712 ACACCGAGATTTGTTAATGAGGTT 58.686 37.500 0.00 0.00 0.00 3.50
2024 2029 5.411669 ACACCGAGATTTGTTAATGAGGTTC 59.588 40.000 0.00 0.00 0.00 3.62
2025 2030 5.411361 CACCGAGATTTGTTAATGAGGTTCA 59.589 40.000 0.00 0.00 0.00 3.18
2026 2031 5.411669 ACCGAGATTTGTTAATGAGGTTCAC 59.588 40.000 0.00 0.00 0.00 3.18
2027 2032 5.163754 CCGAGATTTGTTAATGAGGTTCACC 60.164 44.000 0.00 0.00 0.00 4.02
2028 2033 5.445939 CGAGATTTGTTAATGAGGTTCACCG 60.446 44.000 0.00 0.00 42.08 4.94
2029 2034 5.556915 AGATTTGTTAATGAGGTTCACCGA 58.443 37.500 0.00 0.00 42.08 4.69
2030 2035 6.180472 AGATTTGTTAATGAGGTTCACCGAT 58.820 36.000 0.00 0.00 42.08 4.18
2031 2036 7.335627 AGATTTGTTAATGAGGTTCACCGATA 58.664 34.615 0.00 0.00 42.08 2.92
2032 2037 7.993183 AGATTTGTTAATGAGGTTCACCGATAT 59.007 33.333 0.00 0.00 42.08 1.63
2033 2038 6.918892 TTGTTAATGAGGTTCACCGATATG 57.081 37.500 0.00 0.00 42.08 1.78
2034 2039 5.364778 TGTTAATGAGGTTCACCGATATGG 58.635 41.667 0.00 0.00 46.41 2.74
2035 2040 2.550830 ATGAGGTTCACCGATATGGC 57.449 50.000 0.00 0.00 43.94 4.40
2036 2041 1.496060 TGAGGTTCACCGATATGGCT 58.504 50.000 0.00 0.00 43.94 4.75
2037 2042 2.673258 TGAGGTTCACCGATATGGCTA 58.327 47.619 0.00 0.00 43.94 3.93
2038 2043 2.364324 TGAGGTTCACCGATATGGCTAC 59.636 50.000 0.00 0.00 43.94 3.58
2039 2044 2.364324 GAGGTTCACCGATATGGCTACA 59.636 50.000 0.00 0.00 43.94 2.74
2040 2045 2.972713 AGGTTCACCGATATGGCTACAT 59.027 45.455 0.00 0.00 43.94 2.29
2041 2046 3.006967 AGGTTCACCGATATGGCTACATC 59.993 47.826 0.00 0.00 43.94 3.06
2042 2047 3.326747 GTTCACCGATATGGCTACATCC 58.673 50.000 0.00 0.00 43.94 3.51
2043 2048 1.899814 TCACCGATATGGCTACATCCC 59.100 52.381 0.00 0.00 43.94 3.85
2044 2049 1.066143 CACCGATATGGCTACATCCCC 60.066 57.143 0.00 0.00 43.94 4.81
2045 2050 0.175760 CCGATATGGCTACATCCCCG 59.824 60.000 0.00 0.00 38.53 5.73
2046 2051 0.175760 CGATATGGCTACATCCCCGG 59.824 60.000 0.00 0.00 38.53 5.73
2047 2052 0.541863 GATATGGCTACATCCCCGGG 59.458 60.000 15.80 15.80 38.53 5.73
2048 2053 1.562672 ATATGGCTACATCCCCGGGC 61.563 60.000 17.73 0.37 38.53 6.13
2049 2054 2.689573 TATGGCTACATCCCCGGGCT 62.690 60.000 17.73 0.11 38.53 5.19
2050 2055 3.489513 GGCTACATCCCCGGGCTT 61.490 66.667 17.73 0.00 0.00 4.35
2051 2056 2.203209 GCTACATCCCCGGGCTTG 60.203 66.667 17.73 17.23 0.00 4.01
2052 2057 2.742116 GCTACATCCCCGGGCTTGA 61.742 63.158 23.39 13.45 0.00 3.02
2053 2058 1.146263 CTACATCCCCGGGCTTGAC 59.854 63.158 23.39 0.00 0.00 3.18
2054 2059 1.306654 TACATCCCCGGGCTTGACT 60.307 57.895 23.39 8.18 0.00 3.41
2055 2060 0.031917 TACATCCCCGGGCTTGACTA 60.032 55.000 23.39 7.33 0.00 2.59
2056 2061 0.694444 ACATCCCCGGGCTTGACTAT 60.694 55.000 23.39 2.58 0.00 2.12
2057 2062 0.250467 CATCCCCGGGCTTGACTATG 60.250 60.000 17.73 5.52 0.00 2.23
2058 2063 1.418908 ATCCCCGGGCTTGACTATGG 61.419 60.000 17.73 0.00 0.00 2.74
2059 2064 2.510906 CCCGGGCTTGACTATGGG 59.489 66.667 8.08 0.00 0.00 4.00
2060 2065 2.203209 CCGGGCTTGACTATGGGC 60.203 66.667 0.00 0.00 0.00 5.36
2061 2066 2.588877 CGGGCTTGACTATGGGCG 60.589 66.667 0.00 0.00 0.00 6.13
2062 2067 2.902343 GGGCTTGACTATGGGCGC 60.902 66.667 0.00 0.00 0.00 6.53
2063 2068 2.190578 GGCTTGACTATGGGCGCT 59.809 61.111 7.64 0.00 0.00 5.92
2064 2069 1.889573 GGCTTGACTATGGGCGCTC 60.890 63.158 7.64 2.47 0.00 5.03
2065 2070 1.889573 GCTTGACTATGGGCGCTCC 60.890 63.158 3.94 6.36 0.00 4.70
2066 2071 1.826024 CTTGACTATGGGCGCTCCT 59.174 57.895 3.94 0.00 36.20 3.69
2067 2072 0.249657 CTTGACTATGGGCGCTCCTC 60.250 60.000 3.94 0.00 36.20 3.71
2068 2073 0.687757 TTGACTATGGGCGCTCCTCT 60.688 55.000 3.94 0.46 36.20 3.69
2069 2074 1.109920 TGACTATGGGCGCTCCTCTC 61.110 60.000 3.94 0.00 36.20 3.20
2070 2075 2.136196 GACTATGGGCGCTCCTCTCG 62.136 65.000 3.94 0.00 36.20 4.04
2071 2076 2.123854 TATGGGCGCTCCTCTCGT 60.124 61.111 3.94 0.00 36.20 4.18
2072 2077 2.413437 CTATGGGCGCTCCTCTCGTG 62.413 65.000 3.94 0.00 36.20 4.35
2073 2078 2.904178 TATGGGCGCTCCTCTCGTGA 62.904 60.000 3.94 0.00 36.20 4.35
2074 2079 4.500116 GGGCGCTCCTCTCGTGAC 62.500 72.222 7.64 0.00 0.00 3.67
2075 2080 3.749064 GGCGCTCCTCTCGTGACA 61.749 66.667 7.64 0.00 0.00 3.58
2076 2081 2.505118 GCGCTCCTCTCGTGACAC 60.505 66.667 0.00 0.00 0.00 3.67
2077 2082 2.179517 CGCTCCTCTCGTGACACC 59.820 66.667 0.00 0.00 0.00 4.16
2078 2083 2.179517 GCTCCTCTCGTGACACCG 59.820 66.667 0.00 0.00 0.00 4.94
2079 2084 2.627737 GCTCCTCTCGTGACACCGT 61.628 63.158 0.00 0.00 0.00 4.83
2080 2085 1.502640 CTCCTCTCGTGACACCGTC 59.497 63.158 0.00 0.00 0.00 4.79
2081 2086 1.228033 TCCTCTCGTGACACCGTCA 60.228 57.895 0.00 0.00 40.50 4.35
2089 2094 3.500455 TGACACCGTCACAATACCG 57.500 52.632 0.00 0.00 37.67 4.02
2090 2095 0.668096 TGACACCGTCACAATACCGC 60.668 55.000 0.00 0.00 37.67 5.68
2091 2096 0.668096 GACACCGTCACAATACCGCA 60.668 55.000 0.00 0.00 32.09 5.69
2092 2097 0.947180 ACACCGTCACAATACCGCAC 60.947 55.000 0.00 0.00 0.00 5.34
2093 2098 0.946700 CACCGTCACAATACCGCACA 60.947 55.000 0.00 0.00 0.00 4.57
2094 2099 0.947180 ACCGTCACAATACCGCACAC 60.947 55.000 0.00 0.00 0.00 3.82
2095 2100 1.632046 CCGTCACAATACCGCACACC 61.632 60.000 0.00 0.00 0.00 4.16
2096 2101 1.785321 GTCACAATACCGCACACCG 59.215 57.895 0.00 0.00 0.00 4.94
2137 2142 4.402528 TGCCGGCGCCTGTGTTAT 62.403 61.111 26.68 0.00 0.00 1.89
2138 2143 3.131478 GCCGGCGCCTGTGTTATT 61.131 61.111 26.68 0.00 0.00 1.40
2139 2144 1.816259 GCCGGCGCCTGTGTTATTA 60.816 57.895 26.68 0.00 0.00 0.98
2140 2145 1.164041 GCCGGCGCCTGTGTTATTAT 61.164 55.000 26.68 0.00 0.00 1.28
2141 2146 0.586319 CCGGCGCCTGTGTTATTATG 59.414 55.000 26.68 3.45 0.00 1.90
2142 2147 1.295792 CGGCGCCTGTGTTATTATGT 58.704 50.000 26.68 0.00 0.00 2.29
2143 2148 1.668751 CGGCGCCTGTGTTATTATGTT 59.331 47.619 26.68 0.00 0.00 2.71
2144 2149 2.538737 CGGCGCCTGTGTTATTATGTTG 60.539 50.000 26.68 0.00 0.00 3.33
2145 2150 2.223479 GGCGCCTGTGTTATTATGTTGG 60.223 50.000 22.15 0.00 0.00 3.77
2146 2151 2.794631 GCGCCTGTGTTATTATGTTGGC 60.795 50.000 0.00 0.00 36.14 4.52
2147 2152 2.421775 CGCCTGTGTTATTATGTTGGCA 59.578 45.455 0.00 0.00 39.09 4.92
2148 2153 3.066621 CGCCTGTGTTATTATGTTGGCAT 59.933 43.478 0.00 0.00 39.09 4.40
2149 2154 4.362279 GCCTGTGTTATTATGTTGGCATG 58.638 43.478 0.00 0.00 38.99 4.06
2150 2155 4.737352 GCCTGTGTTATTATGTTGGCATGG 60.737 45.833 0.00 0.00 38.99 3.66
2151 2156 4.202141 CCTGTGTTATTATGTTGGCATGGG 60.202 45.833 0.00 0.00 36.58 4.00
2152 2157 4.348486 TGTGTTATTATGTTGGCATGGGT 58.652 39.130 0.00 0.00 36.58 4.51
2153 2158 4.774726 TGTGTTATTATGTTGGCATGGGTT 59.225 37.500 0.00 0.00 36.58 4.11
2154 2159 5.952347 TGTGTTATTATGTTGGCATGGGTTA 59.048 36.000 0.00 0.00 36.58 2.85
2155 2160 6.127591 TGTGTTATTATGTTGGCATGGGTTAC 60.128 38.462 0.00 0.00 36.58 2.50
2156 2161 5.952347 TGTTATTATGTTGGCATGGGTTACA 59.048 36.000 0.00 0.00 36.58 2.41
2157 2162 6.609212 TGTTATTATGTTGGCATGGGTTACAT 59.391 34.615 5.64 5.64 41.57 2.29
2158 2163 5.789643 ATTATGTTGGCATGGGTTACATC 57.210 39.130 3.66 0.00 37.84 3.06
2159 2164 1.458398 TGTTGGCATGGGTTACATCG 58.542 50.000 0.00 0.00 37.84 3.84
2160 2165 1.271652 TGTTGGCATGGGTTACATCGT 60.272 47.619 0.00 0.00 37.84 3.73
2161 2166 1.132262 GTTGGCATGGGTTACATCGTG 59.868 52.381 0.00 0.00 37.84 4.35
2162 2167 0.326595 TGGCATGGGTTACATCGTGT 59.673 50.000 0.00 0.00 37.84 4.49
2163 2168 0.732571 GGCATGGGTTACATCGTGTG 59.267 55.000 0.00 0.00 37.84 3.82
2164 2169 1.448985 GCATGGGTTACATCGTGTGT 58.551 50.000 0.00 1.87 44.95 3.72
2165 2170 1.396996 GCATGGGTTACATCGTGTGTC 59.603 52.381 0.00 0.00 42.29 3.67
2166 2171 2.935238 GCATGGGTTACATCGTGTGTCT 60.935 50.000 0.00 0.00 42.29 3.41
2167 2172 3.677700 GCATGGGTTACATCGTGTGTCTA 60.678 47.826 0.00 0.00 42.29 2.59
2168 2173 3.861276 TGGGTTACATCGTGTGTCTAG 57.139 47.619 0.00 0.00 42.29 2.43
2169 2174 2.094390 TGGGTTACATCGTGTGTCTAGC 60.094 50.000 0.00 1.15 42.29 3.42
2170 2175 2.537401 GGTTACATCGTGTGTCTAGCC 58.463 52.381 0.00 0.00 42.29 3.93
2171 2176 2.165845 GGTTACATCGTGTGTCTAGCCT 59.834 50.000 0.00 0.00 42.29 4.58
2172 2177 3.436496 GTTACATCGTGTGTCTAGCCTC 58.564 50.000 0.00 0.00 42.29 4.70
2173 2178 0.452184 ACATCGTGTGTCTAGCCTCG 59.548 55.000 0.00 0.00 35.77 4.63
2174 2179 0.867753 CATCGTGTGTCTAGCCTCGC 60.868 60.000 0.00 0.00 0.00 5.03
2175 2180 1.032657 ATCGTGTGTCTAGCCTCGCT 61.033 55.000 0.00 0.00 43.41 4.93
2176 2181 0.392060 TCGTGTGTCTAGCCTCGCTA 60.392 55.000 0.00 0.00 40.44 4.26
2177 2182 0.663688 CGTGTGTCTAGCCTCGCTAT 59.336 55.000 0.00 0.00 40.54 2.97
2178 2183 1.871676 CGTGTGTCTAGCCTCGCTATA 59.128 52.381 0.00 0.00 40.54 1.31
2179 2184 2.484651 CGTGTGTCTAGCCTCGCTATAT 59.515 50.000 0.00 0.00 40.54 0.86
2180 2185 3.683340 CGTGTGTCTAGCCTCGCTATATA 59.317 47.826 0.00 0.00 40.54 0.86
2181 2186 4.333095 CGTGTGTCTAGCCTCGCTATATAT 59.667 45.833 0.00 0.00 40.54 0.86
2182 2187 5.574082 GTGTGTCTAGCCTCGCTATATATG 58.426 45.833 0.00 0.00 40.54 1.78
2183 2188 5.354513 GTGTGTCTAGCCTCGCTATATATGA 59.645 44.000 0.00 0.00 40.54 2.15
2184 2189 5.586643 TGTGTCTAGCCTCGCTATATATGAG 59.413 44.000 0.00 5.54 40.54 2.90
2185 2190 5.818336 GTGTCTAGCCTCGCTATATATGAGA 59.182 44.000 11.74 1.37 40.54 3.27
2186 2191 6.018262 GTGTCTAGCCTCGCTATATATGAGAG 60.018 46.154 11.74 8.82 40.54 3.20
2193 2198 5.995282 CCTCGCTATATATGAGAGGTCTAGG 59.005 48.000 18.29 5.89 43.44 3.02
2194 2199 6.183361 CCTCGCTATATATGAGAGGTCTAGGA 60.183 46.154 18.29 0.00 43.44 2.94
2195 2200 7.381789 TCGCTATATATGAGAGGTCTAGGAT 57.618 40.000 0.00 0.00 0.00 3.24
2196 2201 8.493787 TCGCTATATATGAGAGGTCTAGGATA 57.506 38.462 0.00 0.00 0.00 2.59
2197 2202 9.106977 TCGCTATATATGAGAGGTCTAGGATAT 57.893 37.037 0.00 0.00 0.00 1.63
2204 2209 9.914834 ATATGAGAGGTCTAGGATATAAGTGTC 57.085 37.037 0.00 0.00 0.00 3.67
2205 2210 6.544650 TGAGAGGTCTAGGATATAAGTGTCC 58.455 44.000 0.00 0.00 35.96 4.02
2206 2211 6.333168 TGAGAGGTCTAGGATATAAGTGTCCT 59.667 42.308 0.00 0.00 46.48 3.85
2207 2212 7.516557 TGAGAGGTCTAGGATATAAGTGTCCTA 59.483 40.741 1.59 1.59 43.42 2.94
2208 2213 7.692172 AGAGGTCTAGGATATAAGTGTCCTAC 58.308 42.308 0.00 0.00 43.42 3.18
2209 2214 7.518303 AGAGGTCTAGGATATAAGTGTCCTACT 59.482 40.741 0.00 0.00 43.42 2.57
2223 2228 3.144657 TCCTACTTGGACACGACTACA 57.855 47.619 0.00 0.00 40.56 2.74
2224 2229 3.693807 TCCTACTTGGACACGACTACAT 58.306 45.455 0.00 0.00 40.56 2.29
2225 2230 4.847198 TCCTACTTGGACACGACTACATA 58.153 43.478 0.00 0.00 40.56 2.29
2226 2231 5.443283 TCCTACTTGGACACGACTACATAT 58.557 41.667 0.00 0.00 40.56 1.78
2227 2232 5.530171 TCCTACTTGGACACGACTACATATC 59.470 44.000 0.00 0.00 40.56 1.63
2228 2233 4.650754 ACTTGGACACGACTACATATCC 57.349 45.455 0.00 0.00 0.00 2.59
2229 2234 4.279145 ACTTGGACACGACTACATATCCT 58.721 43.478 0.00 0.00 0.00 3.24
2230 2235 5.443283 ACTTGGACACGACTACATATCCTA 58.557 41.667 0.00 0.00 0.00 2.94
2231 2236 6.069331 ACTTGGACACGACTACATATCCTAT 58.931 40.000 0.00 0.00 0.00 2.57
2232 2237 6.207025 ACTTGGACACGACTACATATCCTATC 59.793 42.308 0.00 0.00 0.00 2.08
2233 2238 5.877491 TGGACACGACTACATATCCTATCT 58.123 41.667 0.00 0.00 0.00 1.98
2234 2239 7.012661 TGGACACGACTACATATCCTATCTA 57.987 40.000 0.00 0.00 0.00 1.98
2235 2240 7.455891 TGGACACGACTACATATCCTATCTAA 58.544 38.462 0.00 0.00 0.00 2.10
2236 2241 7.940688 TGGACACGACTACATATCCTATCTAAA 59.059 37.037 0.00 0.00 0.00 1.85
2237 2242 8.235905 GGACACGACTACATATCCTATCTAAAC 58.764 40.741 0.00 0.00 0.00 2.01
2238 2243 8.687292 ACACGACTACATATCCTATCTAAACA 57.313 34.615 0.00 0.00 0.00 2.83
2239 2244 8.566260 ACACGACTACATATCCTATCTAAACAC 58.434 37.037 0.00 0.00 0.00 3.32
2240 2245 8.565416 CACGACTACATATCCTATCTAAACACA 58.435 37.037 0.00 0.00 0.00 3.72
2241 2246 9.128404 ACGACTACATATCCTATCTAAACACAA 57.872 33.333 0.00 0.00 0.00 3.33
2257 2262 9.031537 TCTAAACACAATATAACTCAGAGTCCA 57.968 33.333 2.72 0.00 0.00 4.02
2258 2263 9.653287 CTAAACACAATATAACTCAGAGTCCAA 57.347 33.333 2.72 0.00 0.00 3.53
2259 2264 7.907214 AACACAATATAACTCAGAGTCCAAC 57.093 36.000 2.72 0.00 0.00 3.77
2260 2265 7.246171 ACACAATATAACTCAGAGTCCAACT 57.754 36.000 2.72 0.00 0.00 3.16
2261 2266 7.099764 ACACAATATAACTCAGAGTCCAACTG 58.900 38.462 2.72 2.29 36.80 3.16
2262 2267 7.099764 CACAATATAACTCAGAGTCCAACTGT 58.900 38.462 2.72 2.91 36.81 3.55
2263 2268 8.251026 CACAATATAACTCAGAGTCCAACTGTA 58.749 37.037 2.72 0.00 36.81 2.74
2264 2269 8.812972 ACAATATAACTCAGAGTCCAACTGTAA 58.187 33.333 2.72 0.00 36.81 2.41
2265 2270 9.088512 CAATATAACTCAGAGTCCAACTGTAAC 57.911 37.037 2.72 0.00 36.81 2.50
2266 2271 4.338379 AACTCAGAGTCCAACTGTAACC 57.662 45.455 2.72 0.00 36.81 2.85
2267 2272 3.577919 ACTCAGAGTCCAACTGTAACCT 58.422 45.455 0.00 0.00 36.81 3.50
2268 2273 4.737578 ACTCAGAGTCCAACTGTAACCTA 58.262 43.478 0.00 0.00 36.81 3.08
2269 2274 4.523558 ACTCAGAGTCCAACTGTAACCTAC 59.476 45.833 0.00 0.00 36.81 3.18
2270 2275 3.830755 TCAGAGTCCAACTGTAACCTACC 59.169 47.826 0.00 0.00 36.81 3.18
2271 2276 3.833070 CAGAGTCCAACTGTAACCTACCT 59.167 47.826 0.00 0.00 0.00 3.08
2272 2277 4.283722 CAGAGTCCAACTGTAACCTACCTT 59.716 45.833 0.00 0.00 0.00 3.50
2273 2278 4.283722 AGAGTCCAACTGTAACCTACCTTG 59.716 45.833 0.00 0.00 0.00 3.61
2274 2279 3.971971 AGTCCAACTGTAACCTACCTTGT 59.028 43.478 0.00 0.00 0.00 3.16
2275 2280 5.149976 AGTCCAACTGTAACCTACCTTGTA 58.850 41.667 0.00 0.00 0.00 2.41
2276 2281 5.011431 AGTCCAACTGTAACCTACCTTGTAC 59.989 44.000 0.00 0.00 0.00 2.90
2277 2282 4.900652 TCCAACTGTAACCTACCTTGTACA 59.099 41.667 0.00 0.00 0.00 2.90
2278 2283 4.992951 CCAACTGTAACCTACCTTGTACAC 59.007 45.833 0.00 0.00 0.00 2.90
2279 2284 5.453621 CCAACTGTAACCTACCTTGTACACA 60.454 44.000 0.00 0.00 0.00 3.72
2280 2285 5.874897 ACTGTAACCTACCTTGTACACAA 57.125 39.130 0.00 0.00 0.00 3.33
2281 2286 6.429521 ACTGTAACCTACCTTGTACACAAT 57.570 37.500 0.00 0.00 35.02 2.71
2282 2287 7.543359 ACTGTAACCTACCTTGTACACAATA 57.457 36.000 0.00 0.00 35.02 1.90
2283 2288 8.142485 ACTGTAACCTACCTTGTACACAATAT 57.858 34.615 0.00 0.00 35.02 1.28
2284 2289 8.599792 ACTGTAACCTACCTTGTACACAATATT 58.400 33.333 0.00 0.00 35.02 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.495939 GCGTCGATGTTGAACATTGTC 58.504 47.619 21.45 16.27 39.27 3.18
105 106 0.389948 GAAGCGTCGGTCACCTTCAT 60.390 55.000 0.00 0.00 34.68 2.57
123 124 0.327259 TCGGTCCTTCGAAGAGGAGA 59.673 55.000 26.61 16.13 38.43 3.71
234 235 1.408683 CCTTCCCCGCATCATGAGAAA 60.409 52.381 0.09 0.00 0.00 2.52
248 249 0.250901 TGAGCAGAAGCAACCTTCCC 60.251 55.000 0.17 0.00 46.97 3.97
534 535 3.066380 TCGTGGAACTGACAACATGATG 58.934 45.455 0.00 0.00 31.75 3.07
539 540 2.971660 TCTTCGTGGAACTGACAACA 57.028 45.000 0.00 0.00 31.75 3.33
579 580 8.981659 TGATATCTCTAGTTGGAGAAATCACAA 58.018 33.333 3.98 0.00 44.21 3.33
585 586 7.502561 TCACGATGATATCTCTAGTTGGAGAAA 59.497 37.037 3.98 0.00 44.21 2.52
809 811 0.815213 AGCCGGCGATACGTACACTA 60.815 55.000 23.20 0.00 0.00 2.74
893 895 1.832167 GGGGTTGAGCTTGGTGCAA 60.832 57.895 0.00 0.00 45.94 4.08
1026 1028 0.597118 GACATAGCAGCCTCTCAGCG 60.597 60.000 0.00 0.00 38.01 5.18
1152 1154 2.164624 GTCTAGATGGAAGAGTGCACGT 59.835 50.000 12.01 0.00 0.00 4.49
1244 1246 0.798776 AGCGTCTTCATTTCCTTGCG 59.201 50.000 0.00 0.00 0.00 4.85
1273 1278 2.629050 AAGCATCGCTATGTCGCCGT 62.629 55.000 0.00 0.00 38.25 5.68
1274 1279 1.951130 AAGCATCGCTATGTCGCCG 60.951 57.895 0.00 0.00 38.25 6.46
1275 1280 1.154205 ACAAGCATCGCTATGTCGCC 61.154 55.000 0.00 0.00 38.25 5.54
1286 1291 1.949525 ACACACAGGAACACAAGCATC 59.050 47.619 0.00 0.00 0.00 3.91
1302 1307 2.303163 ACTACAGCAACGTGAACACA 57.697 45.000 5.80 0.00 0.00 3.72
1381 1386 8.584157 TCAAAATTAACAACAATACATCAGGCT 58.416 29.630 0.00 0.00 0.00 4.58
1442 1447 1.168714 CAGCAAAGTTACAGCCTCCC 58.831 55.000 0.00 0.00 0.00 4.30
1494 1499 3.634397 TTCCAGTTTAGGATGCTCAGG 57.366 47.619 0.00 0.00 37.56 3.86
1937 1942 4.407621 TGGCCTCGGATTTATTCTAACAGA 59.592 41.667 3.32 0.00 0.00 3.41
1938 1943 4.703897 TGGCCTCGGATTTATTCTAACAG 58.296 43.478 3.32 0.00 0.00 3.16
1939 1944 4.764050 TGGCCTCGGATTTATTCTAACA 57.236 40.909 3.32 0.00 0.00 2.41
1940 1945 4.389077 CGATGGCCTCGGATTTATTCTAAC 59.611 45.833 14.53 0.00 43.82 2.34
1941 1946 4.566004 CGATGGCCTCGGATTTATTCTAA 58.434 43.478 14.53 0.00 43.82 2.10
1942 1947 4.188247 CGATGGCCTCGGATTTATTCTA 57.812 45.455 14.53 0.00 43.82 2.10
1943 1948 3.045601 CGATGGCCTCGGATTTATTCT 57.954 47.619 14.53 0.00 43.82 2.40
1954 1959 0.389166 GGATGATCGACGATGGCCTC 60.389 60.000 16.49 1.34 0.00 4.70
1955 1960 1.668294 GGATGATCGACGATGGCCT 59.332 57.895 16.49 0.00 0.00 5.19
1956 1961 1.734477 CGGATGATCGACGATGGCC 60.734 63.158 16.49 11.96 0.00 5.36
1957 1962 0.730834 CTCGGATGATCGACGATGGC 60.731 60.000 16.49 2.04 35.93 4.40
1958 1963 0.109551 CCTCGGATGATCGACGATGG 60.110 60.000 16.49 4.35 35.93 3.51
1959 1964 0.875059 TCCTCGGATGATCGACGATG 59.125 55.000 16.49 0.00 35.93 3.84
1960 1965 0.875728 GTCCTCGGATGATCGACGAT 59.124 55.000 10.78 10.78 35.93 3.73
1961 1966 1.164662 GGTCCTCGGATGATCGACGA 61.165 60.000 0.00 0.00 35.18 4.20
1962 1967 1.283181 GGTCCTCGGATGATCGACG 59.717 63.158 0.00 0.00 35.18 5.12
1963 1968 0.744874 TTGGTCCTCGGATGATCGAC 59.255 55.000 0.00 0.00 35.18 4.20
1964 1969 1.032794 CTTGGTCCTCGGATGATCGA 58.967 55.000 0.00 0.00 37.60 3.59
1965 1970 0.598680 GCTTGGTCCTCGGATGATCG 60.599 60.000 0.00 0.00 0.00 3.69
1966 1971 0.465705 TGCTTGGTCCTCGGATGATC 59.534 55.000 0.00 0.00 0.00 2.92
1967 1972 0.911769 TTGCTTGGTCCTCGGATGAT 59.088 50.000 0.00 0.00 0.00 2.45
1968 1973 0.911769 ATTGCTTGGTCCTCGGATGA 59.088 50.000 0.00 0.00 0.00 2.92
1969 1974 1.303309 GATTGCTTGGTCCTCGGATG 58.697 55.000 0.00 0.00 0.00 3.51
1970 1975 0.911769 TGATTGCTTGGTCCTCGGAT 59.088 50.000 0.00 0.00 0.00 4.18
1971 1976 0.690192 TTGATTGCTTGGTCCTCGGA 59.310 50.000 0.00 0.00 0.00 4.55
1972 1977 1.200020 GTTTGATTGCTTGGTCCTCGG 59.800 52.381 0.00 0.00 0.00 4.63
1973 1978 1.135972 CGTTTGATTGCTTGGTCCTCG 60.136 52.381 0.00 0.00 0.00 4.63
1974 1979 2.151202 TCGTTTGATTGCTTGGTCCTC 58.849 47.619 0.00 0.00 0.00 3.71
1975 1980 2.154462 CTCGTTTGATTGCTTGGTCCT 58.846 47.619 0.00 0.00 0.00 3.85
1976 1981 1.401539 GCTCGTTTGATTGCTTGGTCC 60.402 52.381 0.00 0.00 0.00 4.46
1977 1982 1.266718 TGCTCGTTTGATTGCTTGGTC 59.733 47.619 0.00 0.00 0.00 4.02
1978 1983 1.001378 GTGCTCGTTTGATTGCTTGGT 60.001 47.619 0.00 0.00 0.00 3.67
1979 1984 1.689959 GTGCTCGTTTGATTGCTTGG 58.310 50.000 0.00 0.00 0.00 3.61
1980 1985 1.069973 TCGTGCTCGTTTGATTGCTTG 60.070 47.619 8.17 0.00 38.33 4.01
1981 1986 1.069906 GTCGTGCTCGTTTGATTGCTT 60.070 47.619 8.17 0.00 38.33 3.91
1982 1987 0.512952 GTCGTGCTCGTTTGATTGCT 59.487 50.000 8.17 0.00 38.33 3.91
1983 1988 0.234625 TGTCGTGCTCGTTTGATTGC 59.765 50.000 8.17 0.00 38.33 3.56
1984 1989 1.398451 GGTGTCGTGCTCGTTTGATTG 60.398 52.381 8.17 0.00 38.33 2.67
1985 1990 0.865769 GGTGTCGTGCTCGTTTGATT 59.134 50.000 8.17 0.00 38.33 2.57
1986 1991 1.282248 CGGTGTCGTGCTCGTTTGAT 61.282 55.000 8.17 0.00 38.33 2.57
1987 1992 1.947146 CGGTGTCGTGCTCGTTTGA 60.947 57.895 8.17 0.00 38.33 2.69
1988 1993 1.876453 CTCGGTGTCGTGCTCGTTTG 61.876 60.000 8.17 0.00 38.33 2.93
1989 1994 1.660575 CTCGGTGTCGTGCTCGTTT 60.661 57.895 8.17 0.00 38.33 3.60
1990 1995 1.863662 ATCTCGGTGTCGTGCTCGTT 61.864 55.000 8.17 0.00 38.33 3.85
1991 1996 1.863662 AATCTCGGTGTCGTGCTCGT 61.864 55.000 8.17 0.00 38.33 4.18
1992 1997 0.732880 AAATCTCGGTGTCGTGCTCG 60.733 55.000 0.81 0.81 37.69 5.03
1993 1998 0.716108 CAAATCTCGGTGTCGTGCTC 59.284 55.000 0.00 0.00 37.69 4.26
1994 1999 0.033504 ACAAATCTCGGTGTCGTGCT 59.966 50.000 0.00 0.00 37.69 4.40
1995 2000 0.865769 AACAAATCTCGGTGTCGTGC 59.134 50.000 0.00 0.00 37.69 5.34
1996 2001 4.387559 TCATTAACAAATCTCGGTGTCGTG 59.612 41.667 0.00 0.00 37.69 4.35
1997 2002 4.562082 TCATTAACAAATCTCGGTGTCGT 58.438 39.130 0.00 0.00 37.69 4.34
1998 2003 4.032900 CCTCATTAACAAATCTCGGTGTCG 59.967 45.833 0.00 0.00 37.82 4.35
1999 2004 4.935808 ACCTCATTAACAAATCTCGGTGTC 59.064 41.667 0.00 0.00 0.00 3.67
2000 2005 4.906618 ACCTCATTAACAAATCTCGGTGT 58.093 39.130 0.00 0.00 0.00 4.16
2001 2006 5.411361 TGAACCTCATTAACAAATCTCGGTG 59.589 40.000 0.00 0.00 0.00 4.94
2002 2007 5.411669 GTGAACCTCATTAACAAATCTCGGT 59.588 40.000 0.00 0.00 0.00 4.69
2003 2008 5.163754 GGTGAACCTCATTAACAAATCTCGG 60.164 44.000 0.00 0.00 0.00 4.63
2004 2009 5.445939 CGGTGAACCTCATTAACAAATCTCG 60.446 44.000 0.00 0.00 0.00 4.04
2005 2010 5.642063 TCGGTGAACCTCATTAACAAATCTC 59.358 40.000 0.00 0.00 0.00 2.75
2006 2011 5.556915 TCGGTGAACCTCATTAACAAATCT 58.443 37.500 0.00 0.00 0.00 2.40
2007 2012 5.873179 TCGGTGAACCTCATTAACAAATC 57.127 39.130 0.00 0.00 0.00 2.17
2008 2013 7.013274 CCATATCGGTGAACCTCATTAACAAAT 59.987 37.037 0.00 0.00 0.00 2.32
2009 2014 6.317642 CCATATCGGTGAACCTCATTAACAAA 59.682 38.462 0.00 0.00 0.00 2.83
2010 2015 5.820423 CCATATCGGTGAACCTCATTAACAA 59.180 40.000 0.00 0.00 0.00 2.83
2011 2016 5.364778 CCATATCGGTGAACCTCATTAACA 58.635 41.667 0.00 0.00 0.00 2.41
2012 2017 4.213482 GCCATATCGGTGAACCTCATTAAC 59.787 45.833 0.00 0.00 36.97 2.01
2013 2018 4.102524 AGCCATATCGGTGAACCTCATTAA 59.897 41.667 0.00 0.00 36.97 1.40
2014 2019 3.646162 AGCCATATCGGTGAACCTCATTA 59.354 43.478 0.00 0.00 36.97 1.90
2015 2020 2.439507 AGCCATATCGGTGAACCTCATT 59.560 45.455 0.00 0.00 36.97 2.57
2016 2021 2.050144 AGCCATATCGGTGAACCTCAT 58.950 47.619 0.00 0.00 36.97 2.90
2017 2022 1.496060 AGCCATATCGGTGAACCTCA 58.504 50.000 0.00 0.00 36.97 3.86
2018 2023 2.364324 TGTAGCCATATCGGTGAACCTC 59.636 50.000 0.00 0.00 36.97 3.85
2019 2024 2.394632 TGTAGCCATATCGGTGAACCT 58.605 47.619 0.00 0.00 36.97 3.50
2020 2025 2.902705 TGTAGCCATATCGGTGAACC 57.097 50.000 0.00 0.00 36.97 3.62
2021 2026 3.326747 GGATGTAGCCATATCGGTGAAC 58.673 50.000 0.00 0.00 36.97 3.18
2022 2027 2.301870 GGGATGTAGCCATATCGGTGAA 59.698 50.000 0.00 0.00 36.97 3.18
2023 2028 1.899814 GGGATGTAGCCATATCGGTGA 59.100 52.381 0.00 0.00 36.97 4.02
2024 2029 1.066143 GGGGATGTAGCCATATCGGTG 60.066 57.143 0.00 0.00 36.97 4.94
2025 2030 1.276622 GGGGATGTAGCCATATCGGT 58.723 55.000 0.00 0.00 36.97 4.69
2026 2031 0.175760 CGGGGATGTAGCCATATCGG 59.824 60.000 0.00 0.00 38.11 4.18
2027 2032 0.175760 CCGGGGATGTAGCCATATCG 59.824 60.000 0.00 0.00 0.00 2.92
2028 2033 0.541863 CCCGGGGATGTAGCCATATC 59.458 60.000 14.71 0.00 0.00 1.63
2029 2034 1.562672 GCCCGGGGATGTAGCCATAT 61.563 60.000 25.28 0.00 0.00 1.78
2030 2035 2.221299 GCCCGGGGATGTAGCCATA 61.221 63.158 25.28 0.00 0.00 2.74
2031 2036 3.570212 GCCCGGGGATGTAGCCAT 61.570 66.667 25.28 0.00 0.00 4.40
2032 2037 4.815973 AGCCCGGGGATGTAGCCA 62.816 66.667 25.28 0.00 0.00 4.75
2033 2038 3.489513 AAGCCCGGGGATGTAGCC 61.490 66.667 25.28 1.76 0.00 3.93
2034 2039 2.203209 CAAGCCCGGGGATGTAGC 60.203 66.667 25.28 5.39 0.00 3.58
2035 2040 1.146263 GTCAAGCCCGGGGATGTAG 59.854 63.158 25.28 4.66 0.00 2.74
2036 2041 0.031917 TAGTCAAGCCCGGGGATGTA 60.032 55.000 25.28 0.00 0.00 2.29
2037 2042 0.694444 ATAGTCAAGCCCGGGGATGT 60.694 55.000 25.28 5.51 0.00 3.06
2038 2043 0.250467 CATAGTCAAGCCCGGGGATG 60.250 60.000 25.28 15.02 0.00 3.51
2039 2044 1.418908 CCATAGTCAAGCCCGGGGAT 61.419 60.000 25.28 8.03 0.00 3.85
2040 2045 2.070039 CCATAGTCAAGCCCGGGGA 61.070 63.158 25.28 8.48 0.00 4.81
2041 2046 2.510906 CCATAGTCAAGCCCGGGG 59.489 66.667 25.28 9.31 0.00 5.73
2042 2047 2.510906 CCCATAGTCAAGCCCGGG 59.489 66.667 19.09 19.09 0.00 5.73
2043 2048 2.203209 GCCCATAGTCAAGCCCGG 60.203 66.667 0.00 0.00 0.00 5.73
2044 2049 2.588877 CGCCCATAGTCAAGCCCG 60.589 66.667 0.00 0.00 0.00 6.13
2045 2050 2.902343 GCGCCCATAGTCAAGCCC 60.902 66.667 0.00 0.00 0.00 5.19
2046 2051 1.889573 GAGCGCCCATAGTCAAGCC 60.890 63.158 2.29 0.00 0.00 4.35
2047 2052 1.889573 GGAGCGCCCATAGTCAAGC 60.890 63.158 2.29 0.00 34.14 4.01
2048 2053 0.249657 GAGGAGCGCCCATAGTCAAG 60.250 60.000 15.92 0.00 37.41 3.02
2049 2054 0.687757 AGAGGAGCGCCCATAGTCAA 60.688 55.000 15.92 0.00 37.41 3.18
2050 2055 1.075970 AGAGGAGCGCCCATAGTCA 60.076 57.895 15.92 0.00 37.41 3.41
2051 2056 1.663173 GAGAGGAGCGCCCATAGTC 59.337 63.158 15.92 5.90 37.41 2.59
2052 2057 2.196925 CGAGAGGAGCGCCCATAGT 61.197 63.158 15.92 0.00 37.41 2.12
2053 2058 2.196925 ACGAGAGGAGCGCCCATAG 61.197 63.158 15.92 7.81 37.41 2.23
2054 2059 2.123854 ACGAGAGGAGCGCCCATA 60.124 61.111 15.92 0.00 37.41 2.74
2055 2060 3.842923 CACGAGAGGAGCGCCCAT 61.843 66.667 15.92 0.00 37.41 4.00
2057 2062 4.500116 GTCACGAGAGGAGCGCCC 62.500 72.222 2.29 5.07 33.31 6.13
2058 2063 3.749064 TGTCACGAGAGGAGCGCC 61.749 66.667 2.29 0.00 0.00 6.53
2059 2064 2.505118 GTGTCACGAGAGGAGCGC 60.505 66.667 0.00 0.00 0.00 5.92
2060 2065 2.179517 GGTGTCACGAGAGGAGCG 59.820 66.667 0.00 0.00 0.00 5.03
2061 2066 2.179517 CGGTGTCACGAGAGGAGC 59.820 66.667 0.00 0.00 35.47 4.70
2062 2067 1.235281 TGACGGTGTCACGAGAGGAG 61.235 60.000 0.00 0.00 37.67 3.69
2063 2068 1.228033 TGACGGTGTCACGAGAGGA 60.228 57.895 0.00 0.00 37.67 3.71
2064 2069 3.351450 TGACGGTGTCACGAGAGG 58.649 61.111 0.00 0.00 37.67 3.69
2071 2076 0.668096 GCGGTATTGTGACGGTGTCA 60.668 55.000 0.00 0.00 40.50 3.58
2072 2077 0.668096 TGCGGTATTGTGACGGTGTC 60.668 55.000 0.00 0.00 0.00 3.67
2073 2078 0.947180 GTGCGGTATTGTGACGGTGT 60.947 55.000 0.00 0.00 0.00 4.16
2074 2079 0.946700 TGTGCGGTATTGTGACGGTG 60.947 55.000 0.00 0.00 0.00 4.94
2075 2080 0.947180 GTGTGCGGTATTGTGACGGT 60.947 55.000 0.00 0.00 0.00 4.83
2076 2081 1.632046 GGTGTGCGGTATTGTGACGG 61.632 60.000 0.00 0.00 0.00 4.79
2077 2082 1.785321 GGTGTGCGGTATTGTGACG 59.215 57.895 0.00 0.00 0.00 4.35
2078 2083 1.632046 CCGGTGTGCGGTATTGTGAC 61.632 60.000 0.00 0.00 0.00 3.67
2079 2084 1.374885 CCGGTGTGCGGTATTGTGA 60.375 57.895 0.00 0.00 0.00 3.58
2080 2085 3.034370 GCCGGTGTGCGGTATTGTG 62.034 63.158 1.90 0.00 0.00 3.33
2081 2086 2.744709 GCCGGTGTGCGGTATTGT 60.745 61.111 1.90 0.00 0.00 2.71
2082 2087 3.505184 GGCCGGTGTGCGGTATTG 61.505 66.667 1.90 0.00 0.00 1.90
2083 2088 4.023234 TGGCCGGTGTGCGGTATT 62.023 61.111 1.90 0.00 0.00 1.89
2084 2089 4.770874 GTGGCCGGTGTGCGGTAT 62.771 66.667 1.90 0.00 0.00 2.73
2120 2125 2.523453 TAATAACACAGGCGCCGGCA 62.523 55.000 28.98 9.80 42.47 5.69
2121 2126 1.164041 ATAATAACACAGGCGCCGGC 61.164 55.000 27.22 19.07 38.90 6.13
2122 2127 0.586319 CATAATAACACAGGCGCCGG 59.414 55.000 25.72 25.72 0.00 6.13
2123 2128 1.295792 ACATAATAACACAGGCGCCG 58.704 50.000 23.20 18.60 0.00 6.46
2124 2129 2.223479 CCAACATAATAACACAGGCGCC 60.223 50.000 21.89 21.89 0.00 6.53
2125 2130 2.794631 GCCAACATAATAACACAGGCGC 60.795 50.000 0.00 0.00 0.00 6.53
2126 2131 2.421775 TGCCAACATAATAACACAGGCG 59.578 45.455 0.00 0.00 43.59 5.52
2127 2132 4.362279 CATGCCAACATAATAACACAGGC 58.638 43.478 0.00 0.00 41.15 4.85
2128 2133 4.202141 CCCATGCCAACATAATAACACAGG 60.202 45.833 0.00 0.00 33.67 4.00
2129 2134 4.402155 ACCCATGCCAACATAATAACACAG 59.598 41.667 0.00 0.00 33.67 3.66
2130 2135 4.348486 ACCCATGCCAACATAATAACACA 58.652 39.130 0.00 0.00 33.67 3.72
2131 2136 5.337578 AACCCATGCCAACATAATAACAC 57.662 39.130 0.00 0.00 33.67 3.32
2132 2137 5.952347 TGTAACCCATGCCAACATAATAACA 59.048 36.000 0.00 0.00 33.67 2.41
2133 2138 6.458232 TGTAACCCATGCCAACATAATAAC 57.542 37.500 0.00 0.00 33.67 1.89
2134 2139 6.016693 CGATGTAACCCATGCCAACATAATAA 60.017 38.462 0.00 0.00 33.67 1.40
2135 2140 5.471797 CGATGTAACCCATGCCAACATAATA 59.528 40.000 0.00 0.00 33.67 0.98
2136 2141 4.278170 CGATGTAACCCATGCCAACATAAT 59.722 41.667 0.00 0.00 33.67 1.28
2137 2142 3.629855 CGATGTAACCCATGCCAACATAA 59.370 43.478 0.00 0.00 33.67 1.90
2138 2143 3.210227 CGATGTAACCCATGCCAACATA 58.790 45.455 0.00 0.00 33.67 2.29
2139 2144 2.023673 CGATGTAACCCATGCCAACAT 58.976 47.619 0.00 0.00 36.79 2.71
2140 2145 1.271652 ACGATGTAACCCATGCCAACA 60.272 47.619 0.00 0.00 32.56 3.33
2141 2146 1.132262 CACGATGTAACCCATGCCAAC 59.868 52.381 0.00 0.00 32.56 3.77
2142 2147 1.271652 ACACGATGTAACCCATGCCAA 60.272 47.619 0.00 0.00 32.56 4.52
2143 2148 0.326595 ACACGATGTAACCCATGCCA 59.673 50.000 0.00 0.00 32.56 4.92
2144 2149 0.732571 CACACGATGTAACCCATGCC 59.267 55.000 0.00 0.00 32.56 4.40
2145 2150 1.396996 GACACACGATGTAACCCATGC 59.603 52.381 0.00 0.00 43.56 4.06
2146 2151 2.972625 AGACACACGATGTAACCCATG 58.027 47.619 0.00 0.00 43.56 3.66
2147 2152 3.430374 GCTAGACACACGATGTAACCCAT 60.430 47.826 0.00 0.00 43.56 4.00
2148 2153 2.094390 GCTAGACACACGATGTAACCCA 60.094 50.000 0.00 0.00 43.56 4.51
2149 2154 2.537401 GCTAGACACACGATGTAACCC 58.463 52.381 0.00 0.00 43.56 4.11
2150 2155 2.165845 AGGCTAGACACACGATGTAACC 59.834 50.000 0.00 0.00 43.56 2.85
2151 2156 3.436496 GAGGCTAGACACACGATGTAAC 58.564 50.000 0.00 0.00 43.56 2.50
2152 2157 2.096980 CGAGGCTAGACACACGATGTAA 59.903 50.000 0.00 0.00 43.56 2.41
2153 2158 1.669265 CGAGGCTAGACACACGATGTA 59.331 52.381 0.00 0.00 43.56 2.29
2155 2160 0.867753 GCGAGGCTAGACACACGATG 60.868 60.000 12.64 0.00 0.00 3.84
2156 2161 1.032657 AGCGAGGCTAGACACACGAT 61.033 55.000 12.64 4.68 36.99 3.73
2157 2162 0.392060 TAGCGAGGCTAGACACACGA 60.392 55.000 12.64 0.00 40.44 4.35
2158 2163 0.663688 ATAGCGAGGCTAGACACACG 59.336 55.000 0.00 1.57 44.66 4.49
2159 2164 5.354513 TCATATATAGCGAGGCTAGACACAC 59.645 44.000 0.00 0.00 44.66 3.82
2160 2165 5.497474 TCATATATAGCGAGGCTAGACACA 58.503 41.667 0.00 0.00 44.66 3.72
2161 2166 5.818336 TCTCATATATAGCGAGGCTAGACAC 59.182 44.000 0.00 0.00 44.66 3.67
2162 2167 5.990668 TCTCATATATAGCGAGGCTAGACA 58.009 41.667 0.00 0.00 44.66 3.41
2163 2168 5.468746 CCTCTCATATATAGCGAGGCTAGAC 59.531 48.000 0.00 0.00 44.66 2.59
2164 2169 5.131308 ACCTCTCATATATAGCGAGGCTAGA 59.869 44.000 17.93 0.00 44.66 2.43
2165 2170 5.373222 ACCTCTCATATATAGCGAGGCTAG 58.627 45.833 17.93 0.00 44.66 3.42
2166 2171 5.131308 AGACCTCTCATATATAGCGAGGCTA 59.869 44.000 17.93 0.00 45.55 3.93
2167 2172 4.080015 AGACCTCTCATATATAGCGAGGCT 60.080 45.833 17.93 14.44 43.92 4.58
2168 2173 4.204012 AGACCTCTCATATATAGCGAGGC 58.796 47.826 17.93 13.14 43.92 4.70
2169 2174 5.995282 CCTAGACCTCTCATATATAGCGAGG 59.005 48.000 17.02 17.02 45.22 4.63
2170 2175 6.822442 TCCTAGACCTCTCATATATAGCGAG 58.178 44.000 0.00 5.85 0.00 5.03
2171 2176 6.809976 TCCTAGACCTCTCATATATAGCGA 57.190 41.667 0.00 0.00 0.00 4.93
2178 2183 9.914834 GACACTTATATCCTAGACCTCTCATAT 57.085 37.037 0.00 0.00 0.00 1.78
2179 2184 8.330247 GGACACTTATATCCTAGACCTCTCATA 58.670 40.741 0.00 0.00 31.75 2.15
2180 2185 7.019153 AGGACACTTATATCCTAGACCTCTCAT 59.981 40.741 0.00 0.00 43.85 2.90
2181 2186 6.333168 AGGACACTTATATCCTAGACCTCTCA 59.667 42.308 0.00 0.00 43.85 3.27
2182 2187 6.786122 AGGACACTTATATCCTAGACCTCTC 58.214 44.000 0.00 0.00 43.85 3.20
2183 2188 6.790177 AGGACACTTATATCCTAGACCTCT 57.210 41.667 0.00 0.00 43.85 3.69
2184 2189 7.692172 AGTAGGACACTTATATCCTAGACCTC 58.308 42.308 0.16 0.00 46.10 3.85
2185 2190 7.651229 AGTAGGACACTTATATCCTAGACCT 57.349 40.000 0.16 0.00 46.10 3.85
2186 2191 7.177041 CCAAGTAGGACACTTATATCCTAGACC 59.823 44.444 0.16 0.00 46.04 3.85
2187 2192 7.943447 TCCAAGTAGGACACTTATATCCTAGAC 59.057 40.741 0.16 0.00 46.04 2.59
2188 2193 8.053776 TCCAAGTAGGACACTTATATCCTAGA 57.946 38.462 0.16 0.00 46.04 2.43
2203 2208 3.144657 TGTAGTCGTGTCCAAGTAGGA 57.855 47.619 0.00 0.00 46.75 2.94
2204 2209 5.278364 GGATATGTAGTCGTGTCCAAGTAGG 60.278 48.000 0.00 0.00 39.60 3.18
2205 2210 5.531659 AGGATATGTAGTCGTGTCCAAGTAG 59.468 44.000 6.13 0.00 41.41 2.57
2206 2211 5.443283 AGGATATGTAGTCGTGTCCAAGTA 58.557 41.667 6.13 0.00 41.41 2.24
2207 2212 4.279145 AGGATATGTAGTCGTGTCCAAGT 58.721 43.478 6.13 0.00 41.41 3.16
2208 2213 4.920640 AGGATATGTAGTCGTGTCCAAG 57.079 45.455 6.13 0.00 41.41 3.61
2209 2214 6.304624 AGATAGGATATGTAGTCGTGTCCAA 58.695 40.000 6.13 0.00 41.41 3.53
2210 2215 5.877491 AGATAGGATATGTAGTCGTGTCCA 58.123 41.667 6.13 0.00 41.41 4.02
2211 2216 7.918536 TTAGATAGGATATGTAGTCGTGTCC 57.081 40.000 0.00 0.00 39.95 4.02
2212 2217 8.781196 TGTTTAGATAGGATATGTAGTCGTGTC 58.219 37.037 0.00 0.00 0.00 3.67
2213 2218 8.566260 GTGTTTAGATAGGATATGTAGTCGTGT 58.434 37.037 0.00 0.00 0.00 4.49
2214 2219 8.565416 TGTGTTTAGATAGGATATGTAGTCGTG 58.435 37.037 0.00 0.00 0.00 4.35
2215 2220 8.687292 TGTGTTTAGATAGGATATGTAGTCGT 57.313 34.615 0.00 0.00 0.00 4.34
2231 2236 9.031537 TGGACTCTGAGTTATATTGTGTTTAGA 57.968 33.333 12.27 0.00 0.00 2.10
2232 2237 9.653287 TTGGACTCTGAGTTATATTGTGTTTAG 57.347 33.333 12.27 0.00 0.00 1.85
2233 2238 9.431887 GTTGGACTCTGAGTTATATTGTGTTTA 57.568 33.333 12.27 0.00 0.00 2.01
2234 2239 8.157476 AGTTGGACTCTGAGTTATATTGTGTTT 58.843 33.333 12.27 0.00 0.00 2.83
2235 2240 7.604164 CAGTTGGACTCTGAGTTATATTGTGTT 59.396 37.037 12.27 0.00 35.20 3.32
2236 2241 7.099764 CAGTTGGACTCTGAGTTATATTGTGT 58.900 38.462 12.27 0.00 35.20 3.72
2237 2242 7.099764 ACAGTTGGACTCTGAGTTATATTGTG 58.900 38.462 12.27 6.83 36.81 3.33
2238 2243 7.246171 ACAGTTGGACTCTGAGTTATATTGT 57.754 36.000 12.27 11.11 36.81 2.71
2239 2244 9.088512 GTTACAGTTGGACTCTGAGTTATATTG 57.911 37.037 12.27 10.53 36.81 1.90
2240 2245 8.258708 GGTTACAGTTGGACTCTGAGTTATATT 58.741 37.037 12.27 0.00 36.81 1.28
2241 2246 7.620094 AGGTTACAGTTGGACTCTGAGTTATAT 59.380 37.037 12.27 0.00 36.81 0.86
2242 2247 6.952358 AGGTTACAGTTGGACTCTGAGTTATA 59.048 38.462 12.27 0.00 36.81 0.98
2243 2248 5.780793 AGGTTACAGTTGGACTCTGAGTTAT 59.219 40.000 12.27 0.00 36.81 1.89
2244 2249 5.145564 AGGTTACAGTTGGACTCTGAGTTA 58.854 41.667 12.27 1.72 36.81 2.24
2245 2250 3.967987 AGGTTACAGTTGGACTCTGAGTT 59.032 43.478 12.27 0.00 36.81 3.01
2246 2251 3.577919 AGGTTACAGTTGGACTCTGAGT 58.422 45.455 10.66 10.66 36.81 3.41
2247 2252 4.082136 GGTAGGTTACAGTTGGACTCTGAG 60.082 50.000 2.45 2.45 36.81 3.35
2248 2253 3.830755 GGTAGGTTACAGTTGGACTCTGA 59.169 47.826 0.00 0.00 36.81 3.27
2249 2254 3.833070 AGGTAGGTTACAGTTGGACTCTG 59.167 47.826 0.00 0.00 38.68 3.35
2250 2255 4.129317 AGGTAGGTTACAGTTGGACTCT 57.871 45.455 0.00 0.00 0.00 3.24
2251 2256 4.040095 ACAAGGTAGGTTACAGTTGGACTC 59.960 45.833 0.00 0.00 31.85 3.36
2252 2257 3.971971 ACAAGGTAGGTTACAGTTGGACT 59.028 43.478 0.00 0.00 31.85 3.85
2253 2258 4.347360 ACAAGGTAGGTTACAGTTGGAC 57.653 45.455 0.00 0.00 31.85 4.02
2254 2259 4.900652 TGTACAAGGTAGGTTACAGTTGGA 59.099 41.667 0.00 0.00 31.85 3.53
2255 2260 4.992951 GTGTACAAGGTAGGTTACAGTTGG 59.007 45.833 0.00 0.00 31.85 3.77
2256 2261 5.603596 TGTGTACAAGGTAGGTTACAGTTG 58.396 41.667 0.00 0.00 33.08 3.16
2257 2262 5.874897 TGTGTACAAGGTAGGTTACAGTT 57.125 39.130 0.00 0.00 0.00 3.16
2258 2263 5.874897 TTGTGTACAAGGTAGGTTACAGT 57.125 39.130 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.