Multiple sequence alignment - TraesCS6D01G044500

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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 TraesCS6D01G044500 chr6D 100.000 2735 0 0 1 2735 19320057 19322791 0.000000e+00 5051.0
1 TraesCS6D01G044500 chr6D 91.935 62 5 0 2030 2091 19322023 19322084 1.350000e-13 87.9
2 TraesCS6D01G044500 chr6D 84.000 75 11 1 2188 2261 472622707 472622633 1.360000e-08 71.3
3 TraesCS6D01G044500 chr6B 91.537 1926 119 16 1 1895 33323072 33324984 0.000000e+00 2614.0
4 TraesCS6D01G044500 chr6B 88.166 338 37 3 2037 2372 33324984 33325320 1.530000e-107 399.0
5 TraesCS6D01G044500 chr6B 79.245 212 20 7 223 415 33258436 33258642 2.860000e-25 126.0
6 TraesCS6D01G044500 chr6B 80.374 107 15 5 708 814 33259584 33259684 2.920000e-10 76.8
7 TraesCS6D01G044500 chr6A 89.943 1929 141 34 1 1901 19332059 19330156 0.000000e+00 2438.0
8 TraesCS6D01G044500 chr6A 90.718 571 44 8 2148 2713 19330139 19329573 0.000000e+00 752.0
9 TraesCS6D01G044500 chr6A 79.867 452 41 23 1 405 19526201 19526649 4.460000e-73 285.0
10 TraesCS6D01G044500 chr6A 83.036 112 12 6 704 814 19527517 19527622 8.060000e-16 95.3
11 TraesCS6D01G044500 chr2D 80.000 210 30 10 2061 2262 43950526 43950321 7.890000e-31 145.0
12 TraesCS6D01G044500 chrUn 86.842 76 9 1 2188 2262 211683526 211683601 1.750000e-12 84.2
13 TraesCS6D01G044500 chrUn 86.842 76 9 1 2188 2262 427876894 427876969 1.750000e-12 84.2
14 TraesCS6D01G044500 chr4B 84.000 75 12 0 2188 2262 603179908 603179982 3.780000e-09 73.1


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 TraesCS6D01G044500 chr6D 19320057 19322791 2734 False 2569.45 5051 95.9675 1 2735 2 chr6D.!!$F1 2734
1 TraesCS6D01G044500 chr6B 33323072 33325320 2248 False 1506.50 2614 89.8515 1 2372 2 chr6B.!!$F2 2371
2 TraesCS6D01G044500 chr6A 19329573 19332059 2486 True 1595.00 2438 90.3305 1 2713 2 chr6A.!!$R1 2712

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
431 450 0.615331 TTGAGCTGCCTTCACCTAGG 59.385 55.0 7.41 7.41 38.4 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1964 0.108585 CCCTCTCTCTCTCTCTCCGG 59.891 65.0 0.0 0.0 0.0 5.14 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
68 69 6.872628 ATACTGTGTTATCAGCATCCATTG 57.127 37.500 0.00 0.00 38.84 2.82
136 137 7.035004 GCCAAACATTATCTCTACATTTGCAA 58.965 34.615 0.00 0.00 0.00 4.08
160 161 4.384056 TGCTCTTCAAGGCTTGATATAGC 58.616 43.478 31.47 31.47 39.84 2.97
163 164 5.472820 GCTCTTCAAGGCTTGATATAGCATT 59.527 40.000 32.28 0.00 45.08 3.56
171 172 8.474710 AAGGCTTGATATAGCATTGAAGAAAT 57.525 30.769 0.00 0.00 42.86 2.17
188 189 3.336694 AGAAATTGGGGCCCTAGAAAAGA 59.663 43.478 25.93 0.00 0.00 2.52
209 210 1.488705 ATGGACAAACTCCGGCCTGA 61.489 55.000 0.00 0.00 43.03 3.86
217 218 1.194781 ACTCCGGCCTGACATGACTT 61.195 55.000 0.00 0.00 0.00 3.01
246 247 6.547510 AGATCCTCTTTTTATGGGCATGTAAC 59.452 38.462 0.00 0.00 0.00 2.50
314 315 9.372369 GAGTATAATGTTGTGAAGCTAAGAACT 57.628 33.333 9.77 0.00 0.00 3.01
327 328 5.376625 AGCTAAGAACTTGGTGACATTCAA 58.623 37.500 0.00 0.00 42.32 2.69
358 360 1.828832 CTCGAAGTGAGCATACGTCC 58.171 55.000 0.00 0.00 38.03 4.79
359 361 1.402259 CTCGAAGTGAGCATACGTCCT 59.598 52.381 0.00 0.00 38.03 3.85
403 422 1.074566 CCTCCTTTGGTGCCTCTCTTT 59.925 52.381 0.00 0.00 0.00 2.52
404 423 2.305927 CCTCCTTTGGTGCCTCTCTTTA 59.694 50.000 0.00 0.00 0.00 1.85
405 424 3.339141 CTCCTTTGGTGCCTCTCTTTAC 58.661 50.000 0.00 0.00 0.00 2.01
431 450 0.615331 TTGAGCTGCCTTCACCTAGG 59.385 55.000 7.41 7.41 38.40 3.02
478 497 1.604693 CGGTAGCCAATCGTACCCATC 60.605 57.143 0.00 0.00 36.12 3.51
479 498 1.414919 GGTAGCCAATCGTACCCATCA 59.585 52.381 0.00 0.00 33.74 3.07
503 522 1.927487 TCAAGGCAAGAACCATGCAT 58.073 45.000 0.00 0.00 45.60 3.96
507 526 1.027357 GGCAAGAACCATGCATCGAT 58.973 50.000 0.00 0.00 45.60 3.59
568 589 1.166531 GCGACCTCAAAGCAACAGGT 61.167 55.000 0.00 0.00 43.63 4.00
587 608 1.947146 CGCCAATCAATGCGCCATG 60.947 57.895 4.18 3.66 44.64 3.66
602 623 2.632377 GCCATGCTCTACTGCTACAAA 58.368 47.619 0.00 0.00 0.00 2.83
612 633 5.484715 TCTACTGCTACAAACCCATGTTAC 58.515 41.667 0.00 0.00 34.75 2.50
631 652 2.106566 ACACACCAAATGCACTTCCAA 58.893 42.857 0.00 0.00 0.00 3.53
747 771 7.732222 ACCCATAATTTAGCCAGAAAAATGA 57.268 32.000 0.00 0.00 0.00 2.57
757 782 4.400567 AGCCAGAAAAATGACTTCCATAGC 59.599 41.667 0.00 0.00 34.45 2.97
771 796 6.006449 ACTTCCATAGCAAAGAGTTTGTGAT 58.994 36.000 1.62 0.00 42.56 3.06
772 797 6.491403 ACTTCCATAGCAAAGAGTTTGTGATT 59.509 34.615 1.62 0.00 42.56 2.57
818 845 6.837471 TTTTAGTTTTGTAACACCACCAGT 57.163 33.333 0.00 0.00 36.70 4.00
821 848 2.679336 GTTTTGTAACACCACCAGTCGT 59.321 45.455 0.00 0.00 34.31 4.34
832 859 1.099295 ACCAGTCGTCAGTCGTCACA 61.099 55.000 0.00 0.00 40.80 3.58
833 860 0.660595 CCAGTCGTCAGTCGTCACAC 60.661 60.000 0.00 0.00 40.80 3.82
835 862 1.099295 AGTCGTCAGTCGTCACACCA 61.099 55.000 0.00 0.00 40.80 4.17
846 873 1.990563 CGTCACACCATACCGTTCTTC 59.009 52.381 0.00 0.00 0.00 2.87
1005 1032 2.282958 TCTCTCGCCCTTCACCGT 60.283 61.111 0.00 0.00 0.00 4.83
1476 1509 3.854669 CCAGGTAGCCGGCTCAGG 61.855 72.222 36.73 25.45 0.00 3.86
1608 1641 2.240921 GGAGGAAAAGGAGCTGGAGAAT 59.759 50.000 0.00 0.00 0.00 2.40
1922 1957 3.329386 TGCTCTTGTTAGATGTGTCTGC 58.671 45.455 0.00 0.00 35.87 4.26
1923 1958 3.007290 TGCTCTTGTTAGATGTGTCTGCT 59.993 43.478 0.00 0.00 35.87 4.24
1924 1959 3.999663 GCTCTTGTTAGATGTGTCTGCTT 59.000 43.478 0.00 0.00 35.87 3.91
1925 1960 4.453819 GCTCTTGTTAGATGTGTCTGCTTT 59.546 41.667 0.00 0.00 35.87 3.51
1926 1961 5.639506 GCTCTTGTTAGATGTGTCTGCTTTA 59.360 40.000 0.00 0.00 35.87 1.85
1927 1962 6.314896 GCTCTTGTTAGATGTGTCTGCTTTAT 59.685 38.462 0.00 0.00 35.87 1.40
1928 1963 7.601073 TCTTGTTAGATGTGTCTGCTTTATG 57.399 36.000 0.00 0.00 35.87 1.90
1929 1964 5.801350 TGTTAGATGTGTCTGCTTTATGC 57.199 39.130 0.00 0.00 43.25 3.14
1930 1965 4.635765 TGTTAGATGTGTCTGCTTTATGCC 59.364 41.667 0.00 0.00 42.00 4.40
1931 1966 2.283298 AGATGTGTCTGCTTTATGCCG 58.717 47.619 0.00 0.00 42.00 5.69
1932 1967 1.331756 GATGTGTCTGCTTTATGCCGG 59.668 52.381 0.00 0.00 42.00 6.13
1933 1968 0.323302 TGTGTCTGCTTTATGCCGGA 59.677 50.000 5.05 0.00 42.00 5.14
1934 1969 1.009829 GTGTCTGCTTTATGCCGGAG 58.990 55.000 5.05 0.00 42.00 4.63
1935 1970 0.901827 TGTCTGCTTTATGCCGGAGA 59.098 50.000 5.05 0.00 42.00 3.71
1936 1971 1.134699 TGTCTGCTTTATGCCGGAGAG 60.135 52.381 5.05 0.00 42.00 3.20
1937 1972 1.137086 GTCTGCTTTATGCCGGAGAGA 59.863 52.381 5.05 0.00 42.00 3.10
1938 1973 1.410517 TCTGCTTTATGCCGGAGAGAG 59.589 52.381 5.05 0.00 42.00 3.20
1939 1974 1.410517 CTGCTTTATGCCGGAGAGAGA 59.589 52.381 5.05 0.00 42.00 3.10
1940 1975 1.410517 TGCTTTATGCCGGAGAGAGAG 59.589 52.381 5.05 0.00 42.00 3.20
1941 1976 1.683917 GCTTTATGCCGGAGAGAGAGA 59.316 52.381 5.05 0.00 35.15 3.10
1942 1977 2.288152 GCTTTATGCCGGAGAGAGAGAG 60.288 54.545 5.05 0.00 35.15 3.20
1943 1978 3.218453 CTTTATGCCGGAGAGAGAGAGA 58.782 50.000 5.05 0.00 0.00 3.10
1944 1979 2.559698 TATGCCGGAGAGAGAGAGAG 57.440 55.000 5.05 0.00 0.00 3.20
1945 1980 0.843309 ATGCCGGAGAGAGAGAGAGA 59.157 55.000 5.05 0.00 0.00 3.10
1946 1981 0.180171 TGCCGGAGAGAGAGAGAGAG 59.820 60.000 5.05 0.00 0.00 3.20
1947 1982 0.535102 GCCGGAGAGAGAGAGAGAGG 60.535 65.000 5.05 0.00 0.00 3.69
1948 1983 0.108585 CCGGAGAGAGAGAGAGAGGG 59.891 65.000 0.00 0.00 0.00 4.30
1949 1984 0.108585 CGGAGAGAGAGAGAGAGGGG 59.891 65.000 0.00 0.00 0.00 4.79
1950 1985 0.478507 GGAGAGAGAGAGAGAGGGGG 59.521 65.000 0.00 0.00 0.00 5.40
1951 1986 1.518367 GAGAGAGAGAGAGAGGGGGA 58.482 60.000 0.00 0.00 0.00 4.81
1952 1987 1.421646 GAGAGAGAGAGAGAGGGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
1953 1988 1.010793 AGAGAGAGAGAGAGGGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
1954 1989 1.421646 GAGAGAGAGAGAGGGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
1955 1990 1.010793 AGAGAGAGAGAGGGGGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
1956 1991 1.421646 GAGAGAGAGAGGGGGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
1957 1992 0.478507 GAGAGAGAGGGGGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1958 1993 0.998945 AGAGAGAGGGGGAGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
1959 1994 0.996762 GAGAGAGGGGGAGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
1960 1995 0.998945 AGAGAGGGGGAGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
1961 1996 2.018086 AGAGGGGGAGAGAGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
1962 1997 3.039526 AGGGGGAGAGAGGGAGGG 61.040 72.222 0.00 0.00 0.00 4.30
1963 1998 3.036959 GGGGGAGAGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1964 1999 2.612251 GGGGAGAGAGGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
1965 2000 2.612251 GGGAGAGAGGGAGGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1966 2001 2.612251 GGAGAGAGGGAGGGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
1967 2002 2.015726 GGAGAGAGGGAGGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
1968 2003 1.541672 GAGAGAGGGAGGGAGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
1969 2004 2.018086 AGAGAGGGAGGGAGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
1970 2005 3.039526 AGAGGGAGGGAGGGAGGG 61.040 72.222 0.00 0.00 0.00 4.30
1971 2006 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1972 2007 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1973 2008 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1974 2009 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1975 2010 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1976 2011 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1977 2012 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1994 2029 2.408565 GAGGGAGAGAGAGAGAGAGGA 58.591 57.143 0.00 0.00 0.00 3.71
1997 2032 4.577096 AGGGAGAGAGAGAGAGAGGATTA 58.423 47.826 0.00 0.00 0.00 1.75
2032 2067 9.559732 TTTCTTGTGAGTTAATTCATTGAGAGA 57.440 29.630 3.79 1.87 0.00 3.10
2033 2068 8.768957 TCTTGTGAGTTAATTCATTGAGAGAG 57.231 34.615 3.79 0.00 0.00 3.20
2034 2069 8.588472 TCTTGTGAGTTAATTCATTGAGAGAGA 58.412 33.333 3.79 0.00 0.00 3.10
2035 2070 8.768957 TTGTGAGTTAATTCATTGAGAGAGAG 57.231 34.615 3.79 0.00 0.00 3.20
2036 2071 8.127150 TGTGAGTTAATTCATTGAGAGAGAGA 57.873 34.615 3.79 0.00 0.00 3.10
2037 2072 8.249638 TGTGAGTTAATTCATTGAGAGAGAGAG 58.750 37.037 3.79 0.00 0.00 3.20
2038 2073 8.465999 GTGAGTTAATTCATTGAGAGAGAGAGA 58.534 37.037 3.79 0.00 0.00 3.10
2039 2074 8.685427 TGAGTTAATTCATTGAGAGAGAGAGAG 58.315 37.037 0.00 0.00 0.00 3.20
2040 2075 8.821686 AGTTAATTCATTGAGAGAGAGAGAGA 57.178 34.615 0.00 0.00 0.00 3.10
2041 2076 8.906867 AGTTAATTCATTGAGAGAGAGAGAGAG 58.093 37.037 0.00 0.00 0.00 3.20
2042 2077 8.902806 GTTAATTCATTGAGAGAGAGAGAGAGA 58.097 37.037 0.00 0.00 0.00 3.10
2043 2078 7.578310 AATTCATTGAGAGAGAGAGAGAGAG 57.422 40.000 0.00 0.00 0.00 3.20
2044 2079 5.955961 TCATTGAGAGAGAGAGAGAGAGA 57.044 43.478 0.00 0.00 0.00 3.10
2045 2080 5.922053 TCATTGAGAGAGAGAGAGAGAGAG 58.078 45.833 0.00 0.00 0.00 3.20
2046 2081 5.662657 TCATTGAGAGAGAGAGAGAGAGAGA 59.337 44.000 0.00 0.00 0.00 3.10
2047 2082 5.604758 TTGAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.00 0.00 3.20
2048 2083 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
2049 2084 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
2050 2085 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2051 2086 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2052 2087 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2053 2088 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2054 2089 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2055 2090 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2056 2091 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2057 2092 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
2058 2093 6.142498 AGAGAGAGAGAGAGAGAGAGAGAAT 58.858 44.000 0.00 0.00 0.00 2.40
2059 2094 6.614906 AGAGAGAGAGAGAGAGAGAGAGAATT 59.385 42.308 0.00 0.00 0.00 2.17
2060 2095 6.825610 AGAGAGAGAGAGAGAGAGAGAATTC 58.174 44.000 0.00 0.00 0.00 2.17
2061 2096 6.385176 AGAGAGAGAGAGAGAGAGAGAATTCA 59.615 42.308 8.44 0.00 0.00 2.57
2062 2097 7.072202 AGAGAGAGAGAGAGAGAGAGAATTCAT 59.928 40.741 8.44 0.00 0.00 2.57
2063 2098 7.580910 AGAGAGAGAGAGAGAGAGAATTCATT 58.419 38.462 8.44 0.00 0.00 2.57
2064 2099 8.057623 AGAGAGAGAGAGAGAGAGAATTCATTT 58.942 37.037 8.44 0.00 0.00 2.32
2065 2100 8.599624 AGAGAGAGAGAGAGAGAATTCATTTT 57.400 34.615 8.44 0.00 0.00 1.82
2066 2101 9.699410 AGAGAGAGAGAGAGAGAATTCATTTTA 57.301 33.333 8.44 0.00 0.00 1.52
2099 2134 9.739276 TTGTGAGTTAATTCATTGGTATCTTCT 57.261 29.630 3.79 0.00 0.00 2.85
2104 2139 9.911788 AGTTAATTCATTGGTATCTTCTGACAT 57.088 29.630 0.00 0.00 0.00 3.06
2382 2420 9.515020 TTTCACTCAATTTAAAACACTGATGTC 57.485 29.630 0.00 0.00 38.45 3.06
2406 2444 2.317530 GCCTTAGCCTTCTGTACTGG 57.682 55.000 0.00 0.00 0.00 4.00
2407 2445 1.831736 GCCTTAGCCTTCTGTACTGGA 59.168 52.381 0.00 0.00 0.00 3.86
2408 2446 2.159028 GCCTTAGCCTTCTGTACTGGAG 60.159 54.545 1.03 1.03 0.00 3.86
2409 2447 2.432510 CCTTAGCCTTCTGTACTGGAGG 59.567 54.545 20.29 20.29 0.00 4.30
2410 2448 3.366396 CTTAGCCTTCTGTACTGGAGGA 58.634 50.000 26.97 7.70 0.00 3.71
2413 2451 1.938585 CCTTCTGTACTGGAGGACCA 58.061 55.000 20.00 0.00 44.76 4.02
2451 2489 6.010201 TGGTTATATCCCTTTTCTTCCCCTTT 60.010 38.462 0.00 0.00 0.00 3.11
2454 2492 3.254093 TCCCTTTTCTTCCCCTTTTCC 57.746 47.619 0.00 0.00 0.00 3.13
2473 2511 4.613265 TCCCTTATATATAGCCGGTCCA 57.387 45.455 1.90 0.00 0.00 4.02
2536 2575 9.689976 CATTTTTGTTTTGGTTTTTCCTTCTTT 57.310 25.926 0.00 0.00 37.07 2.52
2546 2585 9.554395 TTGGTTTTTCCTTCTTTCAATTAATCC 57.446 29.630 0.00 0.00 37.07 3.01
2659 2698 7.835822 ACATTCGGGAAATCATAAAATGTTCA 58.164 30.769 0.00 0.00 33.39 3.18
2662 2701 6.272318 TCGGGAAATCATAAAATGTTCATGC 58.728 36.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.244402 ACATGATCATCTTCTTTGTTGCCAA 59.756 36.000 4.86 0.00 0.00 4.52
123 124 5.946298 TGAAGAGCATTTGCAAATGTAGAG 58.054 37.500 38.75 22.62 45.77 2.43
124 125 5.963176 TGAAGAGCATTTGCAAATGTAGA 57.037 34.783 38.75 21.73 45.77 2.59
136 137 5.472820 GCTATATCAAGCCTTGAAGAGCATT 59.527 40.000 23.16 6.69 43.95 3.56
145 146 6.872628 TCTTCAATGCTATATCAAGCCTTG 57.127 37.500 0.00 0.00 44.60 3.61
160 161 2.190538 AGGGCCCCAATTTCTTCAATG 58.809 47.619 21.43 0.00 0.00 2.82
163 164 2.283834 TCTAGGGCCCCAATTTCTTCA 58.716 47.619 21.43 0.00 0.00 3.02
166 167 3.336694 TCTTTTCTAGGGCCCCAATTTCT 59.663 43.478 21.43 0.00 0.00 2.52
171 172 3.440127 CATTTCTTTTCTAGGGCCCCAA 58.560 45.455 21.43 6.13 0.00 4.12
246 247 0.597568 TGAATTTCCTTGCGGCACTG 59.402 50.000 0.05 0.00 0.00 3.66
252 253 6.609237 TCTTCATAGATGAATTTCCTTGCG 57.391 37.500 5.44 0.00 44.92 4.85
291 292 8.946085 CCAAGTTCTTAGCTTCACAACATTATA 58.054 33.333 0.00 0.00 0.00 0.98
314 315 6.567687 ATCACGTATTTTGAATGTCACCAA 57.432 33.333 0.00 0.00 0.00 3.67
327 328 5.035443 GCTCACTTCGAGTATCACGTATTT 58.965 41.667 0.00 0.00 44.33 1.40
353 355 0.544357 TCCCATGTGGAAGAGGACGT 60.544 55.000 0.00 0.00 41.40 4.34
377 396 1.213296 GGCACCAAAGGAGGGAGATA 58.787 55.000 0.00 0.00 0.00 1.98
403 422 4.158025 GTGAAGGCAGCTCAACTACTAGTA 59.842 45.833 1.89 1.89 0.00 1.82
404 423 3.056465 GTGAAGGCAGCTCAACTACTAGT 60.056 47.826 0.00 0.00 0.00 2.57
405 424 3.516615 GTGAAGGCAGCTCAACTACTAG 58.483 50.000 0.00 0.00 0.00 2.57
431 450 2.807676 TCTTCAGGGGCAAAGGAAATC 58.192 47.619 0.00 0.00 0.00 2.17
438 457 2.819608 CGATTTCTTCTTCAGGGGCAAA 59.180 45.455 0.00 0.00 0.00 3.68
478 497 3.799281 TGGTTCTTGCCTTGAAAACTG 57.201 42.857 0.00 0.00 0.00 3.16
479 498 3.493176 GCATGGTTCTTGCCTTGAAAACT 60.493 43.478 0.00 0.00 36.21 2.66
503 522 6.573434 GCACTATTGGACATATGGATATCGA 58.427 40.000 7.80 0.00 0.00 3.59
507 526 4.081142 CCCGCACTATTGGACATATGGATA 60.081 45.833 7.80 0.00 0.00 2.59
587 608 2.762535 TGGGTTTGTAGCAGTAGAGC 57.237 50.000 0.00 0.00 0.00 4.09
612 633 2.472816 GTTGGAAGTGCATTTGGTGTG 58.527 47.619 0.00 0.00 0.00 3.82
631 652 0.550914 ACCCATGCATATCAACCCGT 59.449 50.000 0.00 0.00 0.00 5.28
657 680 2.558554 ATCACAGGTAGCACGTCGCC 62.559 60.000 6.39 0.00 44.04 5.54
694 718 5.187381 TGAATTTGATTACATGGGTGCACAT 59.813 36.000 20.43 0.81 0.00 3.21
701 725 8.263640 TGGGTAATTTGAATTTGATTACATGGG 58.736 33.333 15.40 0.00 37.77 4.00
738 762 7.449704 ACTCTTTGCTATGGAAGTCATTTTTCT 59.550 33.333 0.00 0.00 37.30 2.52
739 763 7.597386 ACTCTTTGCTATGGAAGTCATTTTTC 58.403 34.615 0.00 0.00 37.30 2.29
747 771 5.376625 TCACAAACTCTTTGCTATGGAAGT 58.623 37.500 0.00 0.00 44.39 3.01
811 838 1.081376 GACGACTGACGACTGGTGG 60.081 63.158 6.52 0.00 45.77 4.61
812 839 0.660595 GTGACGACTGACGACTGGTG 60.661 60.000 6.52 0.00 45.77 4.17
813 840 1.099295 TGTGACGACTGACGACTGGT 61.099 55.000 6.52 0.00 45.77 4.00
814 841 0.660595 GTGTGACGACTGACGACTGG 60.661 60.000 6.52 0.00 45.77 4.00
816 843 1.099295 TGGTGTGACGACTGACGACT 61.099 55.000 6.52 0.00 45.77 4.18
817 844 0.039437 ATGGTGTGACGACTGACGAC 60.039 55.000 6.52 0.52 45.77 4.34
818 845 1.198408 GTATGGTGTGACGACTGACGA 59.802 52.381 6.52 0.00 45.77 4.20
821 848 0.524414 CGGTATGGTGTGACGACTGA 59.476 55.000 0.00 0.00 0.00 3.41
832 859 1.982958 ACCCAAGAAGAACGGTATGGT 59.017 47.619 0.00 0.00 0.00 3.55
833 860 2.236395 AGACCCAAGAAGAACGGTATGG 59.764 50.000 0.00 0.00 0.00 2.74
835 862 2.165845 CGAGACCCAAGAAGAACGGTAT 59.834 50.000 0.00 0.00 0.00 2.73
846 873 1.442769 CATGTCCAACGAGACCCAAG 58.557 55.000 0.00 0.00 35.83 3.61
1005 1032 3.007506 TCCTGAGAACAACAATTAGGCGA 59.992 43.478 0.00 0.00 0.00 5.54
1374 1407 4.154347 CACGGGAGGAGGCAGCTC 62.154 72.222 0.00 0.00 0.00 4.09
1460 1493 4.537433 GCCTGAGCCGGCTACCTG 62.537 72.222 32.97 21.13 46.63 4.00
1608 1641 1.070786 GAAACTCGCCCACACCTGA 59.929 57.895 0.00 0.00 0.00 3.86
1635 1668 2.364448 GAGGTCCTCCCGAAGCCT 60.364 66.667 7.78 0.00 38.74 4.58
1731 1764 6.349973 CGGTACATACTGAGTAACGTTAGA 57.650 41.667 8.60 0.00 45.02 2.10
1849 1882 3.685139 ATCGCATCCCTCGATAACAAT 57.315 42.857 0.00 0.00 43.88 2.71
1852 1885 3.570926 TGTATCGCATCCCTCGATAAC 57.429 47.619 6.67 3.49 46.37 1.89
1855 1888 3.131223 CCTTATGTATCGCATCCCTCGAT 59.869 47.826 3.40 3.40 46.79 3.59
1901 1936 3.007290 AGCAGACACATCTAACAAGAGCA 59.993 43.478 0.00 0.00 32.25 4.26
1902 1937 3.594134 AGCAGACACATCTAACAAGAGC 58.406 45.455 0.00 0.00 32.25 4.09
1903 1938 7.675870 GCATAAAGCAGACACATCTAACAAGAG 60.676 40.741 0.00 0.00 44.79 2.85
1904 1939 6.092670 GCATAAAGCAGACACATCTAACAAGA 59.907 38.462 0.00 0.00 44.79 3.02
1906 1941 6.182039 GCATAAAGCAGACACATCTAACAA 57.818 37.500 0.00 0.00 44.79 2.83
1921 1956 1.683917 TCTCTCTCTCCGGCATAAAGC 59.316 52.381 0.00 0.00 44.65 3.51
1922 1957 3.218453 TCTCTCTCTCTCCGGCATAAAG 58.782 50.000 0.00 0.00 0.00 1.85
1923 1958 3.117851 TCTCTCTCTCTCTCCGGCATAAA 60.118 47.826 0.00 0.00 0.00 1.40
1924 1959 2.439880 TCTCTCTCTCTCTCCGGCATAA 59.560 50.000 0.00 0.00 0.00 1.90
1925 1960 2.038426 CTCTCTCTCTCTCTCCGGCATA 59.962 54.545 0.00 0.00 0.00 3.14
1926 1961 0.843309 TCTCTCTCTCTCTCCGGCAT 59.157 55.000 0.00 0.00 0.00 4.40
1927 1962 0.180171 CTCTCTCTCTCTCTCCGGCA 59.820 60.000 0.00 0.00 0.00 5.69
1928 1963 0.535102 CCTCTCTCTCTCTCTCCGGC 60.535 65.000 0.00 0.00 0.00 6.13
1929 1964 0.108585 CCCTCTCTCTCTCTCTCCGG 59.891 65.000 0.00 0.00 0.00 5.14
1930 1965 0.108585 CCCCTCTCTCTCTCTCTCCG 59.891 65.000 0.00 0.00 0.00 4.63
1931 1966 0.478507 CCCCCTCTCTCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
1932 1967 1.421646 CTCCCCCTCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1933 1968 1.010793 TCTCCCCCTCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
1934 1969 1.421646 CTCTCCCCCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1935 1970 1.010793 TCTCTCCCCCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
1936 1971 1.421646 CTCTCTCCCCCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1937 1972 1.522900 CTCTCTCCCCCTCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
1938 1973 0.478507 CCTCTCTCCCCCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1939 1974 0.998945 CCCTCTCTCCCCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1940 1975 0.996762 TCCCTCTCTCCCCCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
1941 1976 0.998945 CTCCCTCTCTCCCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1942 1977 1.541672 CTCCCTCTCTCCCCCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
1943 1978 2.018086 CCTCCCTCTCTCCCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
1944 1979 2.612251 CCTCCCTCTCTCCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
1945 1980 3.039526 CCCTCCCTCTCTCCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
1946 1981 3.036959 TCCCTCCCTCTCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
1947 1982 2.612251 CTCCCTCCCTCTCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1948 1983 2.612251 CCTCCCTCCCTCTCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
1949 1984 2.015726 TCCCTCCCTCCCTCTCTCC 61.016 68.421 0.00 0.00 0.00 3.71
1950 1985 1.541672 CTCCCTCCCTCCCTCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
1951 1986 2.018086 CCTCCCTCCCTCCCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
1952 1987 2.612251 CCTCCCTCCCTCCCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
1953 1988 3.039526 CCCTCCCTCCCTCCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
1954 1989 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1955 1990 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1956 1991 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1957 1992 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1958 1993 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1959 1994 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1960 1995 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1961 1996 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1962 1997 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1963 1998 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1964 1999 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
1965 2000 2.015726 TCTCTCCCTCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
1966 2001 0.996762 TCTCTCTCCCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
1967 2002 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
1968 2003 0.996762 TCTCTCTCTCCCTCCCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
1969 2004 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
1970 2005 1.421646 CTCTCTCTCTCTCCCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
1971 2006 1.010793 TCTCTCTCTCTCTCCCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
1972 2007 1.421646 CTCTCTCTCTCTCTCCCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
1973 2008 1.421646 CCTCTCTCTCTCTCTCCCTCC 59.578 61.905 0.00 0.00 0.00 4.30
1974 2009 2.408565 TCCTCTCTCTCTCTCTCCCTC 58.591 57.143 0.00 0.00 0.00 4.30
1975 2010 2.587060 TCCTCTCTCTCTCTCTCCCT 57.413 55.000 0.00 0.00 0.00 4.20
1976 2011 3.884037 AATCCTCTCTCTCTCTCTCCC 57.116 52.381 0.00 0.00 0.00 4.30
1977 2012 7.839680 AAATTAATCCTCTCTCTCTCTCTCC 57.160 40.000 0.00 0.00 0.00 3.71
2008 2043 8.588472 TCTCTCTCAATGAATTAACTCACAAGA 58.412 33.333 0.00 0.00 0.00 3.02
2011 2046 8.127150 TCTCTCTCTCAATGAATTAACTCACA 57.873 34.615 0.00 0.00 0.00 3.58
2021 2056 6.156775 TCTCTCTCTCTCTCTCTCTCAATGAA 59.843 42.308 0.00 0.00 0.00 2.57
2022 2057 5.662657 TCTCTCTCTCTCTCTCTCTCAATGA 59.337 44.000 0.00 0.00 0.00 2.57
2023 2058 5.922053 TCTCTCTCTCTCTCTCTCTCAATG 58.078 45.833 0.00 0.00 0.00 2.82
2024 2059 5.901853 TCTCTCTCTCTCTCTCTCTCTCAAT 59.098 44.000 0.00 0.00 0.00 2.57
2025 2060 5.272402 TCTCTCTCTCTCTCTCTCTCTCAA 58.728 45.833 0.00 0.00 0.00 3.02
2026 2061 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
2027 2062 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2028 2063 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2029 2064 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2030 2065 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2031 2066 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2032 2067 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2033 2068 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2034 2069 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2035 2070 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2036 2071 6.385176 TGAATTCTCTCTCTCTCTCTCTCTCT 59.615 42.308 7.05 0.00 0.00 3.10
2037 2072 6.586344 TGAATTCTCTCTCTCTCTCTCTCTC 58.414 44.000 7.05 0.00 0.00 3.20
2038 2073 6.566079 TGAATTCTCTCTCTCTCTCTCTCT 57.434 41.667 7.05 0.00 0.00 3.10
2039 2074 7.814264 AATGAATTCTCTCTCTCTCTCTCTC 57.186 40.000 7.05 0.00 0.00 3.20
2040 2075 8.599624 AAAATGAATTCTCTCTCTCTCTCTCT 57.400 34.615 7.05 0.00 0.00 3.10
2070 2105 9.739276 AGATACCAATGAATTAACTCACAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
2071 2106 9.739276 AAGATACCAATGAATTAACTCACAAGA 57.261 29.630 0.00 0.00 0.00 3.02
2072 2107 9.994432 GAAGATACCAATGAATTAACTCACAAG 57.006 33.333 0.00 0.00 0.00 3.16
2073 2108 9.739276 AGAAGATACCAATGAATTAACTCACAA 57.261 29.630 0.00 0.00 0.00 3.33
2074 2109 9.166173 CAGAAGATACCAATGAATTAACTCACA 57.834 33.333 0.00 0.00 0.00 3.58
2075 2110 9.383519 TCAGAAGATACCAATGAATTAACTCAC 57.616 33.333 0.00 0.00 0.00 3.51
2076 2111 9.383519 GTCAGAAGATACCAATGAATTAACTCA 57.616 33.333 0.00 0.00 0.00 3.41
2077 2112 9.383519 TGTCAGAAGATACCAATGAATTAACTC 57.616 33.333 0.00 0.00 0.00 3.01
2078 2113 9.911788 ATGTCAGAAGATACCAATGAATTAACT 57.088 29.630 0.00 0.00 0.00 2.24
2121 2156 9.076781 TGTCAGGAATTCAAATATGTGAAGAAA 57.923 29.630 13.67 0.00 40.72 2.52
2122 2157 8.634335 TGTCAGGAATTCAAATATGTGAAGAA 57.366 30.769 13.67 0.00 40.72 2.52
2124 2159 8.900781 AGATGTCAGGAATTCAAATATGTGAAG 58.099 33.333 13.67 0.69 40.72 3.02
2405 2443 1.700186 GGGATCTAACCATGGTCCTCC 59.300 57.143 20.07 19.64 0.00 4.30
2406 2444 2.370189 CAGGGATCTAACCATGGTCCTC 59.630 54.545 20.07 12.05 37.96 3.71
2407 2445 2.412591 CAGGGATCTAACCATGGTCCT 58.587 52.381 20.07 16.24 37.96 3.85
2408 2446 2.938956 CAGGGATCTAACCATGGTCC 57.061 55.000 20.07 14.54 37.96 4.46
2413 2451 5.731678 GGGATATAACCAGGGATCTAACCAT 59.268 44.000 0.99 0.00 0.00 3.55
2432 2470 4.264668 GGGAAAAGGGGAAGAAAAGGGATA 60.265 45.833 0.00 0.00 0.00 2.59
2451 2489 4.713321 GTGGACCGGCTATATATAAGGGAA 59.287 45.833 0.00 0.00 0.00 3.97
2454 2492 4.710375 AGTGTGGACCGGCTATATATAAGG 59.290 45.833 0.00 6.90 0.00 2.69
2521 2560 7.870445 CGGATTAATTGAAAGAAGGAAAAACCA 59.130 33.333 0.00 0.00 42.04 3.67
2522 2561 7.330946 CCGGATTAATTGAAAGAAGGAAAAACC 59.669 37.037 0.00 0.00 39.35 3.27
2536 2575 6.859112 TTTTGGAAATCCCGGATTAATTGA 57.141 33.333 13.24 0.00 37.93 2.57
2546 2585 6.859420 AATTTTGACTTTTTGGAAATCCCG 57.141 33.333 0.00 0.00 37.93 5.14
2615 2654 7.008628 CCGAATGTTTTCTGAATTCATAAGCAC 59.991 37.037 8.96 9.23 31.88 4.40
2618 2657 7.761409 TCCCGAATGTTTTCTGAATTCATAAG 58.239 34.615 8.96 0.00 31.88 1.73
2621 2660 6.588719 TTCCCGAATGTTTTCTGAATTCAT 57.411 33.333 8.96 0.00 31.88 2.57
2630 2669 9.150348 ACATTTTATGATTTCCCGAATGTTTTC 57.850 29.630 0.00 0.00 33.81 2.29


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

AutoCloner maintained by Alex Coulton.