Multiple sequence alignment - TraesCS1D01G119700

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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 TraesCS1D01G119700 chr1D 100.000 4052 0 0 1 4052 116546500 116550551 0.000000e+00 7483.0
1 TraesCS1D01G119700 chr1D 97.682 647 9 3 3410 4052 58728785 58729429 0.000000e+00 1107.0
2 TraesCS1D01G119700 chr1D 97.531 648 10 3 3409 4052 416253514 416252869 0.000000e+00 1103.0
3 TraesCS1D01G119700 chr1D 97.231 650 13 2 3407 4052 155433397 155434045 0.000000e+00 1096.0
4 TraesCS1D01G119700 chr1A 95.364 1855 53 23 1 1842 127757775 127759609 0.000000e+00 2918.0
5 TraesCS1D01G119700 chr1A 98.327 1315 19 2 1954 3267 127759605 127760917 0.000000e+00 2303.0
6 TraesCS1D01G119700 chr1A 97.049 305 4 2 245 545 445845165 445845468 3.610000e-140 508.0
7 TraesCS1D01G119700 chr1A 95.385 130 5 1 1830 1958 168567504 168567633 5.310000e-49 206.0
8 TraesCS1D01G119700 chr1A 100.000 33 0 0 3377 3409 127761273 127761305 1.220000e-05 62.1
9 TraesCS1D01G119700 chr1B 95.880 1529 52 6 319 1842 178512151 178513673 0.000000e+00 2464.0
10 TraesCS1D01G119700 chr1B 96.224 768 16 6 1954 2713 178513669 178514431 0.000000e+00 1245.0
11 TraesCS1D01G119700 chr1B 96.484 512 14 3 2777 3287 178514425 178514933 0.000000e+00 843.0
12 TraesCS1D01G119700 chr1B 95.714 280 8 4 51 330 178511855 178512130 7.990000e-122 448.0
13 TraesCS1D01G119700 chr1B 94.667 75 1 1 3290 3364 178515040 178515111 3.310000e-21 113.0
14 TraesCS1D01G119700 chr1B 96.296 54 1 1 1 53 178511782 178511835 2.010000e-13 87.9
15 TraesCS1D01G119700 chr5D 97.385 650 12 2 3407 4052 491160509 491161157 0.000000e+00 1101.0
16 TraesCS1D01G119700 chr5D 97.372 647 12 2 3410 4052 148497797 148498442 0.000000e+00 1096.0
17 TraesCS1D01G119700 chr5D 97.372 647 11 3 3410 4052 245452839 245453483 0.000000e+00 1096.0
18 TraesCS1D01G119700 chr5D 97.231 650 11 5 3409 4052 565546043 565545395 0.000000e+00 1094.0
19 TraesCS1D01G119700 chr5D 97.218 647 12 3 3410 4052 350857275 350857919 0.000000e+00 1090.0
20 TraesCS1D01G119700 chr5D 97.500 120 3 0 1841 1960 118840568 118840449 5.310000e-49 206.0
21 TraesCS1D01G119700 chr5D 93.233 133 6 3 1827 1958 461071773 461071643 4.130000e-45 193.0
22 TraesCS1D01G119700 chr5D 89.362 94 6 2 2671 2761 215302077 215301985 9.200000e-22 115.0
23 TraesCS1D01G119700 chr5D 80.342 117 11 2 2641 2746 252615896 252615781 1.210000e-10 78.7
24 TraesCS1D01G119700 chr2D 97.372 647 12 2 3410 4052 204087324 204086679 0.000000e+00 1096.0
25 TraesCS1D01G119700 chr2D 86.290 124 16 1 2623 2746 484372633 484372755 2.540000e-27 134.0
26 TraesCS1D01G119700 chr2D 89.888 89 9 0 107 195 175825114 175825026 9.200000e-22 115.0
27 TraesCS1D01G119700 chr7D 97.358 492 12 1 54 545 595751991 595751501 0.000000e+00 835.0
28 TraesCS1D01G119700 chr7D 97.674 301 6 1 245 545 588776001 588776300 2.160000e-142 516.0
29 TraesCS1D01G119700 chr3D 98.339 301 4 1 245 545 220219356 220219057 9.980000e-146 527.0
30 TraesCS1D01G119700 chr3D 73.069 479 102 19 2144 2605 79630962 79630494 1.170000e-30 145.0
31 TraesCS1D01G119700 chr3D 87.059 85 11 0 111 195 400786169 400786253 3.330000e-16 97.1
32 TraesCS1D01G119700 chr6A 98.007 301 5 1 245 545 455873097 455872798 4.640000e-144 521.0
33 TraesCS1D01G119700 chr6A 96.667 120 4 0 1840 1959 147303659 147303778 2.470000e-47 200.0
34 TraesCS1D01G119700 chr6A 93.893 131 7 1 1841 1971 272995015 272994886 3.200000e-46 196.0
35 TraesCS1D01G119700 chr6A 92.473 93 7 0 110 202 209391426 209391334 2.540000e-27 134.0
36 TraesCS1D01G119700 chr6A 88.542 96 8 1 2671 2763 411770347 411770252 3.310000e-21 113.0
37 TraesCS1D01G119700 chr6A 86.207 87 9 2 111 197 299985126 299985043 1.550000e-14 91.6
38 TraesCS1D01G119700 chrUn 97.342 301 7 1 245 545 70734511 70734810 1.000000e-140 510.0
39 TraesCS1D01G119700 chrUn 91.358 81 7 0 2666 2746 126680531 126680611 1.190000e-20 111.0
40 TraesCS1D01G119700 chr5A 95.455 308 6 3 245 545 24003002 24002696 6.090000e-133 484.0
41 TraesCS1D01G119700 chr2A 97.479 119 3 0 1841 1959 78845689 78845571 1.910000e-48 204.0
42 TraesCS1D01G119700 chr2A 86.290 124 16 1 2623 2746 628670040 628670162 2.540000e-27 134.0
43 TraesCS1D01G119700 chr2A 94.521 73 4 0 111 183 67713361 67713289 3.310000e-21 113.0
44 TraesCS1D01G119700 chr4D 96.667 120 4 0 1839 1958 367720889 367720770 2.470000e-47 200.0
45 TraesCS1D01G119700 chr2B 95.276 127 5 1 1832 1958 643184743 643184618 2.470000e-47 200.0
46 TraesCS1D01G119700 chr2B 88.172 93 6 2 2671 2763 180422913 180422826 5.540000e-19 106.0
47 TraesCS1D01G119700 chr3A 93.130 131 7 2 1831 1961 12239987 12239859 1.490000e-44 191.0
48 TraesCS1D01G119700 chr3A 73.849 478 98 20 2144 2605 93895160 93894694 9.010000e-37 165.0
49 TraesCS1D01G119700 chr3A 94.203 69 4 0 110 178 482404555 482404487 5.540000e-19 106.0
50 TraesCS1D01G119700 chr3B 73.263 475 105 18 2144 2605 126001513 126001048 1.950000e-33 154.0
51 TraesCS1D01G119700 chr6B 91.398 93 8 0 110 202 278674698 278674606 1.180000e-25 128.0
52 TraesCS1D01G119700 chr4A 93.902 82 5 0 2671 2752 565304188 565304107 1.530000e-24 124.0
53 TraesCS1D01G119700 chr5B 88.298 94 7 2 2671 2761 230882863 230882771 4.280000e-20 110.0
54 TraesCS1D01G119700 chr7B 81.579 76 9 4 2630 2701 642470024 642469950 1.570000e-04 58.4


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 TraesCS1D01G119700 chr1D 116546500 116550551 4051 False 7483.000000 7483 100.0000 1 4052 1 chr1D.!!$F2 4051
1 TraesCS1D01G119700 chr1D 58728785 58729429 644 False 1107.000000 1107 97.6820 3410 4052 1 chr1D.!!$F1 642
2 TraesCS1D01G119700 chr1D 416252869 416253514 645 True 1103.000000 1103 97.5310 3409 4052 1 chr1D.!!$R1 643
3 TraesCS1D01G119700 chr1D 155433397 155434045 648 False 1096.000000 1096 97.2310 3407 4052 1 chr1D.!!$F3 645
4 TraesCS1D01G119700 chr1A 127757775 127761305 3530 False 1761.033333 2918 97.8970 1 3409 3 chr1A.!!$F3 3408
5 TraesCS1D01G119700 chr1B 178511782 178515111 3329 False 866.816667 2464 95.8775 1 3364 6 chr1B.!!$F1 3363
6 TraesCS1D01G119700 chr5D 491160509 491161157 648 False 1101.000000 1101 97.3850 3407 4052 1 chr5D.!!$F4 645
7 TraesCS1D01G119700 chr5D 148497797 148498442 645 False 1096.000000 1096 97.3720 3410 4052 1 chr5D.!!$F1 642
8 TraesCS1D01G119700 chr5D 245452839 245453483 644 False 1096.000000 1096 97.3720 3410 4052 1 chr5D.!!$F2 642
9 TraesCS1D01G119700 chr5D 565545395 565546043 648 True 1094.000000 1094 97.2310 3409 4052 1 chr5D.!!$R5 643
10 TraesCS1D01G119700 chr5D 350857275 350857919 644 False 1090.000000 1090 97.2180 3410 4052 1 chr5D.!!$F3 642
11 TraesCS1D01G119700 chr2D 204086679 204087324 645 True 1096.000000 1096 97.3720 3410 4052 1 chr2D.!!$R2 642

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
199 223 1.180029 GGAGCGTAGGGTGTAGTTCA 58.820 55.0 0.0 0.0 0.0 3.18 F
1857 1919 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1926 0.110486 TTGAGGGACAAGCTTGGGAC 59.890 55.000 29.18 18.9 34.20 4.46 R
3799 4134 1.697982 GGCTTAAGACCCGGATATGGT 59.302 52.381 0.73 0.0 39.32 3.55 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
185 209 5.276868 CCAAAACGTCTTATATTCAGGAGCG 60.277 44.000 0.00 0.00 0.00 5.03
199 223 1.180029 GGAGCGTAGGGTGTAGTTCA 58.820 55.000 0.00 0.00 0.00 3.18
469 525 2.694628 TCCCCATGTCAAATTATGCAGC 59.305 45.455 0.00 0.00 0.00 5.25
670 726 5.347620 TGGTGACTGTACACAACTTAACT 57.652 39.130 3.48 0.00 41.88 2.24
733 789 2.880268 TCAGTTGAATTGACCACAGCAG 59.120 45.455 0.00 0.00 0.00 4.24
853 910 3.668447 TCTTTCAGGTGCAGTGAATCTC 58.332 45.455 11.31 0.00 33.95 2.75
951 1012 5.221441 TGTCTGTCTTAAGTCAAAGCAGCTA 60.221 40.000 0.00 0.00 33.95 3.32
1628 1689 3.740115 ACAACGTGCTTACCAGAAATCT 58.260 40.909 0.00 0.00 0.00 2.40
1674 1735 5.300286 CCATGATTACTTCAGCCCCTTTTAG 59.700 44.000 0.00 0.00 37.89 1.85
1773 1835 7.759489 TTTGTCACCTTTCTGTGCTATTATT 57.241 32.000 0.00 0.00 36.17 1.40
1811 1873 7.176690 GGATAACATAAATGGGGTAATGTGGAG 59.823 40.741 0.00 0.00 33.04 3.86
1846 1908 8.958119 TGACAAAAATATACATGACTACTCCC 57.042 34.615 0.00 0.00 0.00 4.30
1847 1909 8.768397 TGACAAAAATATACATGACTACTCCCT 58.232 33.333 0.00 0.00 0.00 4.20
1848 1910 9.262358 GACAAAAATATACATGACTACTCCCTC 57.738 37.037 0.00 0.00 0.00 4.30
1849 1911 8.211629 ACAAAAATATACATGACTACTCCCTCC 58.788 37.037 0.00 0.00 0.00 4.30
1850 1912 6.591750 AAATATACATGACTACTCCCTCCG 57.408 41.667 0.00 0.00 0.00 4.63
1851 1913 3.596940 ATACATGACTACTCCCTCCGT 57.403 47.619 0.00 0.00 0.00 4.69
1852 1914 1.765230 ACATGACTACTCCCTCCGTC 58.235 55.000 0.00 0.00 0.00 4.79
1853 1915 1.033574 CATGACTACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
1854 1916 0.465824 ATGACTACTCCCTCCGTCCG 60.466 60.000 0.00 0.00 0.00 4.79
1855 1917 1.222936 GACTACTCCCTCCGTCCGA 59.777 63.158 0.00 0.00 0.00 4.55
1856 1918 0.393537 GACTACTCCCTCCGTCCGAA 60.394 60.000 0.00 0.00 0.00 4.30
1857 1919 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
1858 1920 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
1859 1921 1.547372 CTACTCCCTCCGTCCGAAAAA 59.453 52.381 0.00 0.00 0.00 1.94
1877 1939 3.801114 AAAACTTGTCCCAAGCTTGTC 57.199 42.857 24.35 14.49 0.00 3.18
1878 1940 1.692411 AACTTGTCCCAAGCTTGTCC 58.308 50.000 24.35 12.15 0.00 4.02
1879 1941 0.178990 ACTTGTCCCAAGCTTGTCCC 60.179 55.000 24.35 11.81 0.00 4.46
1880 1942 0.111253 CTTGTCCCAAGCTTGTCCCT 59.889 55.000 24.35 0.00 0.00 4.20
1881 1943 0.110486 TTGTCCCAAGCTTGTCCCTC 59.890 55.000 24.35 10.65 0.00 4.30
1882 1944 1.059584 TGTCCCAAGCTTGTCCCTCA 61.060 55.000 24.35 12.85 0.00 3.86
1883 1945 0.110486 GTCCCAAGCTTGTCCCTCAA 59.890 55.000 24.35 0.00 34.61 3.02
1884 1946 0.850100 TCCCAAGCTTGTCCCTCAAA 59.150 50.000 24.35 0.00 35.48 2.69
1885 1947 1.428912 TCCCAAGCTTGTCCCTCAAAT 59.571 47.619 24.35 0.00 35.48 2.32
1886 1948 1.547372 CCCAAGCTTGTCCCTCAAATG 59.453 52.381 24.35 5.47 35.48 2.32
1887 1949 1.547372 CCAAGCTTGTCCCTCAAATGG 59.453 52.381 24.35 1.81 35.48 3.16
1888 1950 2.517959 CAAGCTTGTCCCTCAAATGGA 58.482 47.619 18.65 0.00 35.48 3.41
1889 1951 3.094572 CAAGCTTGTCCCTCAAATGGAT 58.905 45.455 18.65 0.00 35.48 3.41
1890 1952 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
1891 1953 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
1892 1954 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
1893 1955 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
1894 1956 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
1895 1957 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
1896 1958 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
1897 1959 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
1898 1960 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
1899 1961 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
1900 1962 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
1901 1963 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
1902 1964 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
1903 1965 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
1904 1966 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
1905 1967 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
1906 1968 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
1907 1969 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
1908 1970 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
1909 1971 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
1910 1972 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
1922 1984 5.986135 CACTAACTTGGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
1923 1985 5.661312 ACTAACTTGGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
1924 1986 5.636903 AACTTGGTGCTAGATACATCCAT 57.363 39.130 0.00 0.00 0.00 3.41
1925 1987 5.636903 ACTTGGTGCTAGATACATCCATT 57.363 39.130 0.00 0.00 0.00 3.16
1926 1988 6.006275 ACTTGGTGCTAGATACATCCATTT 57.994 37.500 0.00 0.00 0.00 2.32
1927 1989 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
1928 1990 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
1929 1991 6.000246 TGGTGCTAGATACATCCATTTGAA 58.000 37.500 0.00 0.00 0.00 2.69
1930 1992 6.057533 TGGTGCTAGATACATCCATTTGAAG 58.942 40.000 0.00 0.00 0.00 3.02
1931 1993 5.471456 GGTGCTAGATACATCCATTTGAAGG 59.529 44.000 0.00 0.00 0.00 3.46
1932 1994 6.291377 GTGCTAGATACATCCATTTGAAGGA 58.709 40.000 0.00 0.00 39.97 3.36
1933 1995 6.203723 GTGCTAGATACATCCATTTGAAGGAC 59.796 42.308 0.00 0.00 38.13 3.85
1934 1996 6.126796 TGCTAGATACATCCATTTGAAGGACA 60.127 38.462 0.00 0.00 38.13 4.02
1935 1997 6.767902 GCTAGATACATCCATTTGAAGGACAA 59.232 38.462 0.00 0.00 38.13 3.18
1936 1998 7.041508 GCTAGATACATCCATTTGAAGGACAAG 60.042 40.741 0.00 0.00 39.77 3.16
1937 1999 5.591877 AGATACATCCATTTGAAGGACAAGC 59.408 40.000 0.00 0.00 39.77 4.01
1938 2000 3.771216 ACATCCATTTGAAGGACAAGCT 58.229 40.909 0.00 0.00 39.77 3.74
1939 2001 4.154942 ACATCCATTTGAAGGACAAGCTT 58.845 39.130 0.00 0.00 39.77 3.74
1940 2002 4.590222 ACATCCATTTGAAGGACAAGCTTT 59.410 37.500 0.00 0.00 39.77 3.51
1941 2003 5.070847 ACATCCATTTGAAGGACAAGCTTTT 59.929 36.000 0.00 0.00 39.77 2.27
1942 2004 5.612725 TCCATTTGAAGGACAAGCTTTTT 57.387 34.783 0.00 0.00 39.77 1.94
1970 2032 4.646572 GGAGGGAGTATTATTCTGCCAAG 58.353 47.826 11.43 0.00 44.15 3.61
2000 2062 7.829725 TGTTAAAGTAAAGCTATCGTCCTGTA 58.170 34.615 0.00 0.00 0.00 2.74
2038 2100 2.899900 TCTCAGCACTTCTTTGGCTAGA 59.100 45.455 0.00 0.00 35.82 2.43
2937 3006 3.603158 TGGCTCAAGATAAACGCACTA 57.397 42.857 0.00 0.00 0.00 2.74
3042 3111 4.408921 AGGGTAGGAAATGACATCGAATCA 59.591 41.667 5.31 5.31 0.00 2.57
3067 3136 5.178996 CAGCTGTAACTCTGCATTATCCATC 59.821 44.000 5.25 0.00 42.26 3.51
3287 3357 3.157087 CCTTTGTTGGTTACTGATGGCT 58.843 45.455 0.00 0.00 0.00 4.75
3288 3358 3.191371 CCTTTGTTGGTTACTGATGGCTC 59.809 47.826 0.00 0.00 0.00 4.70
3368 3542 8.980143 AGTACAATGTATTTTATGGTTGTTGC 57.020 30.769 0.00 0.00 32.64 4.17
3454 3783 3.648507 TCCTCGAGCTAGGACTTAGTT 57.351 47.619 6.99 0.00 40.86 2.24
3638 3973 4.748892 TCTCGATGAGATTGTTCTTGTCC 58.251 43.478 0.00 0.00 33.35 4.02
3799 4134 5.163281 TGATTGTAACTACGGGCCTTAAA 57.837 39.130 0.84 0.00 0.00 1.52
3991 4327 1.000506 CCTTCGACAGAAAACCTCCGA 59.999 52.381 0.00 0.00 35.71 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 160 4.819630 AGTTCGATCTAAACTGCCAAAACA 59.180 37.500 8.96 0.00 35.68 2.83
469 525 6.094603 CAGTTTCTGATGGGAATTCAACCTAG 59.905 42.308 7.93 0.25 32.44 3.02
641 697 6.403878 AGTTGTGTACAGTCACCATAATACC 58.596 40.000 0.00 0.00 37.51 2.73
670 726 7.828717 TCAATCTGCATTTATTTACTGTCTCCA 59.171 33.333 0.00 0.00 0.00 3.86
951 1012 4.615912 GCTCGTTGTGTTTGCCAGAAATAT 60.616 41.667 0.00 0.00 0.00 1.28
1628 1689 5.163248 TGGAACTGAAGACAATGTTACCTGA 60.163 40.000 0.00 0.00 0.00 3.86
1773 1835 9.283768 CCATTTATGTTATCCTACTGTGCAATA 57.716 33.333 0.00 0.00 0.00 1.90
1861 1923 5.893518 TTGAGGGACAAGCTTGGGACAAG 62.894 52.174 29.18 3.71 37.48 3.16
1862 1924 4.092026 TTGAGGGACAAGCTTGGGACAA 62.092 50.000 29.18 21.59 37.48 3.18
1863 1925 1.059584 TGAGGGACAAGCTTGGGACA 61.060 55.000 29.18 17.71 0.00 4.02
1864 1926 0.110486 TTGAGGGACAAGCTTGGGAC 59.890 55.000 29.18 18.90 34.20 4.46
1865 1927 0.850100 TTTGAGGGACAAGCTTGGGA 59.150 50.000 29.18 4.51 39.77 4.37
1866 1928 1.547372 CATTTGAGGGACAAGCTTGGG 59.453 52.381 29.18 6.83 39.77 4.12
1867 1929 1.547372 CCATTTGAGGGACAAGCTTGG 59.453 52.381 29.18 12.28 39.77 3.61
1868 1930 2.517959 TCCATTTGAGGGACAAGCTTG 58.482 47.619 24.84 24.84 39.77 4.01
1869 1931 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
1870 1932 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
1871 1933 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
1872 1934 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
1873 1935 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
1874 1936 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
1875 1937 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
1876 1938 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
1877 1939 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
1878 1940 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
1879 1941 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
1880 1942 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
1881 1943 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
1882 1944 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
1883 1945 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
1884 1946 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
1885 1947 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
1886 1948 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
1898 1960 5.986135 GGATGTATCTAGCACCAAGTTAGTG 59.014 44.000 0.00 0.00 38.30 2.74
1899 1961 5.661312 TGGATGTATCTAGCACCAAGTTAGT 59.339 40.000 0.00 0.00 33.25 2.24
1900 1962 6.161855 TGGATGTATCTAGCACCAAGTTAG 57.838 41.667 0.00 0.00 32.79 2.34
1901 1963 6.747414 ATGGATGTATCTAGCACCAAGTTA 57.253 37.500 0.00 0.00 0.00 2.24
1902 1964 5.636903 ATGGATGTATCTAGCACCAAGTT 57.363 39.130 0.00 0.00 0.00 2.66
1903 1965 5.636903 AATGGATGTATCTAGCACCAAGT 57.363 39.130 0.00 0.00 0.00 3.16
1904 1966 6.057533 TCAAATGGATGTATCTAGCACCAAG 58.942 40.000 0.00 0.00 0.00 3.61
1905 1967 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
1906 1968 5.628797 TCAAATGGATGTATCTAGCACCA 57.371 39.130 0.00 0.00 0.00 4.17
1907 1969 5.471456 CCTTCAAATGGATGTATCTAGCACC 59.529 44.000 0.00 0.00 0.00 5.01
1908 1970 6.203723 GTCCTTCAAATGGATGTATCTAGCAC 59.796 42.308 0.00 0.00 35.87 4.40
1909 1971 6.126796 TGTCCTTCAAATGGATGTATCTAGCA 60.127 38.462 0.00 0.00 35.87 3.49
1910 1972 6.291377 TGTCCTTCAAATGGATGTATCTAGC 58.709 40.000 0.00 0.00 35.87 3.42
1911 1973 7.041508 GCTTGTCCTTCAAATGGATGTATCTAG 60.042 40.741 0.00 0.00 35.87 2.43
1912 1974 6.767902 GCTTGTCCTTCAAATGGATGTATCTA 59.232 38.462 0.00 0.00 35.87 1.98
1913 1975 5.591877 GCTTGTCCTTCAAATGGATGTATCT 59.408 40.000 0.00 0.00 35.87 1.98
1914 1976 5.591877 AGCTTGTCCTTCAAATGGATGTATC 59.408 40.000 0.00 0.00 35.87 2.24
1915 1977 5.513233 AGCTTGTCCTTCAAATGGATGTAT 58.487 37.500 0.00 0.00 35.87 2.29
1916 1978 4.922206 AGCTTGTCCTTCAAATGGATGTA 58.078 39.130 0.00 0.00 35.87 2.29
1917 1979 3.771216 AGCTTGTCCTTCAAATGGATGT 58.229 40.909 0.00 0.00 35.87 3.06
1918 1980 4.796038 AAGCTTGTCCTTCAAATGGATG 57.204 40.909 0.00 0.00 35.87 3.51
1919 1981 5.813513 AAAAGCTTGTCCTTCAAATGGAT 57.186 34.783 0.00 0.00 35.87 3.41
1920 1982 5.612725 AAAAAGCTTGTCCTTCAAATGGA 57.387 34.783 0.00 0.00 35.48 3.41
1939 2001 5.703730 ATAATACTCCCTCCGTCCAAAAA 57.296 39.130 0.00 0.00 0.00 1.94
1940 2002 5.427481 AGAATAATACTCCCTCCGTCCAAAA 59.573 40.000 0.00 0.00 0.00 2.44
1941 2003 4.966805 AGAATAATACTCCCTCCGTCCAAA 59.033 41.667 0.00 0.00 0.00 3.28
1942 2004 4.344102 CAGAATAATACTCCCTCCGTCCAA 59.656 45.833 0.00 0.00 0.00 3.53
1943 2005 3.895656 CAGAATAATACTCCCTCCGTCCA 59.104 47.826 0.00 0.00 0.00 4.02
1944 2006 3.306156 GCAGAATAATACTCCCTCCGTCC 60.306 52.174 0.00 0.00 0.00 4.79
1945 2007 3.306156 GGCAGAATAATACTCCCTCCGTC 60.306 52.174 0.00 0.00 0.00 4.79
1946 2008 2.633481 GGCAGAATAATACTCCCTCCGT 59.367 50.000 0.00 0.00 0.00 4.69
1947 2009 2.632996 TGGCAGAATAATACTCCCTCCG 59.367 50.000 0.00 0.00 0.00 4.63
1948 2010 4.505742 CCTTGGCAGAATAATACTCCCTCC 60.506 50.000 0.00 0.00 0.00 4.30
1949 2011 4.103311 ACCTTGGCAGAATAATACTCCCTC 59.897 45.833 0.00 0.00 0.00 4.30
1950 2012 4.047883 ACCTTGGCAGAATAATACTCCCT 58.952 43.478 0.00 0.00 0.00 4.20
1951 2013 4.439253 ACCTTGGCAGAATAATACTCCC 57.561 45.455 0.00 0.00 0.00 4.30
1952 2014 6.152831 ACAAAACCTTGGCAGAATAATACTCC 59.847 38.462 0.00 0.00 36.82 3.85
1953 2015 7.158099 ACAAAACCTTGGCAGAATAATACTC 57.842 36.000 0.00 0.00 36.82 2.59
1954 2016 7.539034 AACAAAACCTTGGCAGAATAATACT 57.461 32.000 0.00 0.00 36.82 2.12
1955 2017 9.699703 TTTAACAAAACCTTGGCAGAATAATAC 57.300 29.630 0.00 0.00 36.82 1.89
1956 2018 9.921637 CTTTAACAAAACCTTGGCAGAATAATA 57.078 29.630 0.00 0.00 36.82 0.98
1957 2019 8.428852 ACTTTAACAAAACCTTGGCAGAATAAT 58.571 29.630 0.00 0.00 36.82 1.28
1970 2032 7.747799 GGACGATAGCTTTACTTTAACAAAACC 59.252 37.037 0.00 0.00 42.67 3.27
2000 2062 4.263243 GCTGAGAATACTAATGCCCTCCAT 60.263 45.833 0.00 0.00 35.06 3.41
2038 2100 4.019860 TCAGAGGCTGCACTCTAAAGAAAT 60.020 41.667 16.68 0.00 45.71 2.17
2937 3006 2.363406 GCTTTGCAGAGGGGGCAT 60.363 61.111 6.36 0.00 41.58 4.40
3042 3111 4.080919 TGGATAATGCAGAGTTACAGCTGT 60.081 41.667 25.12 25.12 34.66 4.40
3067 3136 2.040544 GGGACATGTTGCACCCTCG 61.041 63.158 12.15 0.00 35.41 4.63
3143 3212 3.175594 TCGATAATATAAGGGGCCCGTT 58.824 45.455 31.20 31.20 0.00 4.44
3287 3357 4.450976 TGCAAGAGTCAAAGTTAGCAAGA 58.549 39.130 0.00 0.00 0.00 3.02
3288 3358 4.512944 TCTGCAAGAGTCAAAGTTAGCAAG 59.487 41.667 0.00 0.00 38.67 4.01
3344 3518 8.980143 AGCAACAACCATAAAATACATTGTAC 57.020 30.769 0.00 0.00 30.40 2.90
3346 3520 8.580720 TGTAGCAACAACCATAAAATACATTGT 58.419 29.630 0.00 0.00 30.91 2.71
3350 3524 9.456147 ACTATGTAGCAACAACCATAAAATACA 57.544 29.630 0.00 0.00 39.58 2.29
3353 3527 9.456147 TGTACTATGTAGCAACAACCATAAAAT 57.544 29.630 0.00 0.00 39.58 1.82
3354 3528 8.850007 TGTACTATGTAGCAACAACCATAAAA 57.150 30.769 0.00 0.00 39.58 1.52
3355 3529 8.850007 TTGTACTATGTAGCAACAACCATAAA 57.150 30.769 0.00 0.00 39.58 1.40
3356 3530 8.888716 CATTGTACTATGTAGCAACAACCATAA 58.111 33.333 8.89 0.00 39.58 1.90
3357 3531 8.044309 ACATTGTACTATGTAGCAACAACCATA 58.956 33.333 19.39 0.00 39.58 2.74
3359 3533 6.234920 ACATTGTACTATGTAGCAACAACCA 58.765 36.000 19.39 0.00 39.58 3.67
3360 3534 6.737254 ACATTGTACTATGTAGCAACAACC 57.263 37.500 19.39 0.00 39.58 3.77
3374 3548 9.988815 TGCAAAAACCATAAAATACATTGTACT 57.011 25.926 0.00 0.00 0.00 2.73
3454 3783 2.302199 CTAGCTGCGATGGCTCCACA 62.302 60.000 0.00 0.00 40.74 4.17
3664 3999 2.943449 GCGTCAGCCTCCCTATATAC 57.057 55.000 0.00 0.00 37.42 1.47
3799 4134 1.697982 GGCTTAAGACCCGGATATGGT 59.302 52.381 0.73 0.00 39.32 3.55
3991 4327 3.561143 TGGCCTTCACACAATTGTAAGT 58.439 40.909 11.53 3.01 33.30 2.24


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

AutoCloner maintained by Alex Coulton.