Multiple sequence alignment - TraesCS2D01G377800

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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 TraesCS2D01G377800 chr2D 100.000 2468 0 0 1 2468 482329304 482326837 0.000000e+00 4558.0
1 TraesCS2D01G377800 chr2D 92.361 576 42 2 1894 2468 482280009 482280583 0.000000e+00 819.0
2 TraesCS2D01G377800 chr2A 92.182 1842 82 15 1 1821 624818485 624816685 0.000000e+00 2547.0
3 TraesCS2D01G377800 chr2B 88.332 1894 79 41 4 1793 566383874 566382019 0.000000e+00 2143.0
4 TraesCS2D01G377800 chr7D 93.357 557 25 4 1920 2468 596410616 596411168 0.000000e+00 813.0
5 TraesCS2D01G377800 chr7D 97.059 34 0 1 1843 1875 47327691 47327724 3.430000e-04 56.5
6 TraesCS2D01G377800 chr1B 91.050 581 41 5 1894 2468 594208045 594208620 0.000000e+00 774.0
7 TraesCS2D01G377800 chr6D 90.534 412 24 12 2060 2468 455944749 455945148 4.670000e-147 531.0
8 TraesCS2D01G377800 chr6D 96.124 129 5 0 1894 2022 455944617 455944745 6.910000e-51 211.0
9 TraesCS2D01G377800 chr3D 94.872 39 1 1 1838 1875 24198399 24198361 2.650000e-05 60.2
10 TraesCS2D01G377800 chr3D 96.970 33 1 0 1843 1875 481917638 481917670 3.430000e-04 56.5
11 TraesCS2D01G377800 chr5A 100.000 30 0 0 1846 1875 625731621 625731592 3.430000e-04 56.5
12 TraesCS2D01G377800 chr4A 100.000 30 0 0 1846 1875 614880696 614880667 3.430000e-04 56.5
13 TraesCS2D01G377800 chr4A 97.059 34 0 1 1846 1879 710821060 710821028 3.430000e-04 56.5
14 TraesCS2D01G377800 chr3A 100.000 30 0 0 1846 1875 7129314 7129343 3.430000e-04 56.5
15 TraesCS2D01G377800 chr1D 100.000 30 0 0 1846 1875 373114235 373114264 3.430000e-04 56.5
16 TraesCS2D01G377800 chr3B 100.000 29 0 0 1846 1874 765563602 765563574 1.000000e-03 54.7


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 TraesCS2D01G377800 chr2D 482326837 482329304 2467 True 4558 4558 100.000 1 2468 1 chr2D.!!$R1 2467
1 TraesCS2D01G377800 chr2D 482280009 482280583 574 False 819 819 92.361 1894 2468 1 chr2D.!!$F1 574
2 TraesCS2D01G377800 chr2A 624816685 624818485 1800 True 2547 2547 92.182 1 1821 1 chr2A.!!$R1 1820
3 TraesCS2D01G377800 chr2B 566382019 566383874 1855 True 2143 2143 88.332 4 1793 1 chr2B.!!$R1 1789
4 TraesCS2D01G377800 chr7D 596410616 596411168 552 False 813 813 93.357 1920 2468 1 chr7D.!!$F2 548
5 TraesCS2D01G377800 chr1B 594208045 594208620 575 False 774 774 91.050 1894 2468 1 chr1B.!!$F1 574
6 TraesCS2D01G377800 chr6D 455944617 455945148 531 False 371 531 93.329 1894 2468 2 chr6D.!!$F1 574

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
991 1086 0.251297 CCAATCCACAAGGCACAGGA 60.251 55.0 0.0 0.0 33.74 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2000 0.095935 CACATGCACAACGCTAGCTC 59.904 55.0 13.93 0.0 43.06 4.09 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 148 3.504863 CTTCCTTTCACCGCAATGAATG 58.495 45.455 0.76 3.78 38.37 2.67
261 276 4.393371 GTGTGCAAGAATCTAACTCCTTCC 59.607 45.833 0.00 0.00 0.00 3.46
518 553 3.595758 GCTGTGGCCTTTGCGTGT 61.596 61.111 3.32 0.00 38.85 4.49
540 575 1.439353 AACATGCGCCTGCCGATAAG 61.439 55.000 12.92 0.00 41.78 1.73
596 631 0.961019 GCAAGCCACTCATTTGACCA 59.039 50.000 0.00 0.00 0.00 4.02
647 692 4.931661 TGATCCATCCGTAGAAAGGTAC 57.068 45.455 0.00 0.00 0.00 3.34
648 693 3.317149 TGATCCATCCGTAGAAAGGTACG 59.683 47.826 0.00 0.00 44.42 3.67
649 694 2.726821 TCCATCCGTAGAAAGGTACGT 58.273 47.619 0.00 0.00 43.51 3.57
650 695 3.884895 TCCATCCGTAGAAAGGTACGTA 58.115 45.455 0.00 0.00 43.51 3.57
729 780 4.037446 TGCAGACACAGGTAATTTTCAACC 59.963 41.667 0.00 0.00 35.91 3.77
991 1086 0.251297 CCAATCCACAAGGCACAGGA 60.251 55.000 0.00 0.00 33.74 3.86
1037 1132 8.939201 ATATACAGAATATATGCAGCAGTGTC 57.061 34.615 0.00 0.00 0.00 3.67
1038 1133 5.027293 ACAGAATATATGCAGCAGTGTCA 57.973 39.130 0.00 0.00 0.00 3.58
1104 1199 3.470888 ATGAAGGGAGGACGGCGG 61.471 66.667 13.24 0.00 0.00 6.13
1128 1223 2.043450 AGGAGGCTCCTCAGGTCG 60.043 66.667 30.46 0.00 45.66 4.79
1472 1585 0.672711 GCACTCTGCAGCTGATCACA 60.673 55.000 20.43 4.56 44.26 3.58
1473 1586 1.360820 CACTCTGCAGCTGATCACAG 58.639 55.000 20.43 15.11 45.91 3.66
1474 1587 0.975135 ACTCTGCAGCTGATCACAGT 59.025 50.000 20.43 7.17 45.04 3.55
1476 1589 0.971386 TCTGCAGCTGATCACAGTGA 59.029 50.000 20.43 5.50 45.04 3.41
1543 1656 4.404715 TGTAGGATCCAAAGTACAGTAGCC 59.595 45.833 15.82 0.00 0.00 3.93
1544 1657 2.431057 AGGATCCAAAGTACAGTAGCCG 59.569 50.000 15.82 0.00 0.00 5.52
1545 1658 2.167900 GGATCCAAAGTACAGTAGCCGT 59.832 50.000 6.95 0.00 0.00 5.68
1546 1659 3.445857 GATCCAAAGTACAGTAGCCGTC 58.554 50.000 0.00 0.00 0.00 4.79
1547 1660 2.522185 TCCAAAGTACAGTAGCCGTCT 58.478 47.619 0.00 0.00 0.00 4.18
1574 1687 2.550978 CTGCGGGATAACGAGATTTGT 58.449 47.619 0.00 0.00 35.47 2.83
1605 1718 4.218852 GTCTCAGATGTATAGGTGTAGGCC 59.781 50.000 0.00 0.00 0.00 5.19
1666 1779 5.667172 TCTGTATTCCATTCTCCAAGGATGA 59.333 40.000 0.00 0.00 0.00 2.92
1682 1795 2.456989 GATGAGTCGCATGCAAAATGG 58.543 47.619 19.57 0.00 37.34 3.16
1697 1810 1.750193 AATGGCGTGGTACAGAATGG 58.250 50.000 0.00 0.00 43.62 3.16
1724 1841 5.992829 TCCATTCTTTCTACGTAACTTGCAA 59.007 36.000 0.00 0.00 0.00 4.08
1757 1874 4.368315 CTCATAATTCGTTCGGTCCATGA 58.632 43.478 0.00 0.00 0.00 3.07
1821 1938 8.015658 GTGTTAATTTGAAAGCTAGTAGTGGTG 58.984 37.037 0.00 0.00 0.00 4.17
1822 1939 7.934665 TGTTAATTTGAAAGCTAGTAGTGGTGA 59.065 33.333 0.00 0.00 0.00 4.02
1823 1940 8.780249 GTTAATTTGAAAGCTAGTAGTGGTGAA 58.220 33.333 0.00 0.00 0.00 3.18
1824 1941 6.803154 ATTTGAAAGCTAGTAGTGGTGAAC 57.197 37.500 0.00 0.00 0.00 3.18
1825 1942 5.546621 TTGAAAGCTAGTAGTGGTGAACT 57.453 39.130 0.00 0.00 43.40 3.01
1826 1943 6.659745 TTGAAAGCTAGTAGTGGTGAACTA 57.340 37.500 0.00 0.00 40.56 2.24
1827 1944 6.659745 TGAAAGCTAGTAGTGGTGAACTAA 57.340 37.500 0.00 0.00 43.08 2.24
1828 1945 7.241042 TGAAAGCTAGTAGTGGTGAACTAAT 57.759 36.000 0.00 0.00 43.08 1.73
1829 1946 7.676947 TGAAAGCTAGTAGTGGTGAACTAATT 58.323 34.615 0.00 0.00 43.08 1.40
1830 1947 7.602644 TGAAAGCTAGTAGTGGTGAACTAATTG 59.397 37.037 0.00 0.00 43.08 2.32
1831 1948 6.852420 AGCTAGTAGTGGTGAACTAATTGA 57.148 37.500 0.00 0.00 43.08 2.57
1832 1949 7.425224 AGCTAGTAGTGGTGAACTAATTGAT 57.575 36.000 0.00 0.00 43.08 2.57
1833 1950 8.534954 AGCTAGTAGTGGTGAACTAATTGATA 57.465 34.615 0.00 0.00 43.08 2.15
1834 1951 8.978472 AGCTAGTAGTGGTGAACTAATTGATAA 58.022 33.333 0.00 0.00 43.08 1.75
1835 1952 9.250624 GCTAGTAGTGGTGAACTAATTGATAAG 57.749 37.037 0.00 0.00 43.08 1.73
1836 1953 9.250624 CTAGTAGTGGTGAACTAATTGATAAGC 57.749 37.037 0.00 0.00 43.08 3.09
1837 1954 7.852263 AGTAGTGGTGAACTAATTGATAAGCT 58.148 34.615 0.00 0.00 43.08 3.74
1838 1955 6.992063 AGTGGTGAACTAATTGATAAGCTG 57.008 37.500 0.00 0.00 37.36 4.24
1839 1956 6.711277 AGTGGTGAACTAATTGATAAGCTGA 58.289 36.000 0.00 0.00 37.36 4.26
1840 1957 6.595716 AGTGGTGAACTAATTGATAAGCTGAC 59.404 38.462 0.00 0.00 37.36 3.51
1841 1958 6.595716 GTGGTGAACTAATTGATAAGCTGACT 59.404 38.462 0.00 0.00 0.00 3.41
1842 1959 6.818644 TGGTGAACTAATTGATAAGCTGACTC 59.181 38.462 0.00 0.00 0.00 3.36
1843 1960 6.258947 GGTGAACTAATTGATAAGCTGACTCC 59.741 42.308 0.00 0.00 0.00 3.85
1844 1961 6.818644 GTGAACTAATTGATAAGCTGACTCCA 59.181 38.462 0.00 0.00 0.00 3.86
1845 1962 7.497249 GTGAACTAATTGATAAGCTGACTCCAT 59.503 37.037 0.00 0.00 0.00 3.41
1846 1963 8.704668 TGAACTAATTGATAAGCTGACTCCATA 58.295 33.333 0.00 0.00 0.00 2.74
1847 1964 9.202273 GAACTAATTGATAAGCTGACTCCATAG 57.798 37.037 0.00 0.00 0.00 2.23
1848 1965 7.675062 ACTAATTGATAAGCTGACTCCATAGG 58.325 38.462 0.00 0.00 0.00 2.57
1849 1966 4.963318 TTGATAAGCTGACTCCATAGGG 57.037 45.455 0.00 0.00 0.00 3.53
1850 1967 2.634940 TGATAAGCTGACTCCATAGGGC 59.365 50.000 0.00 0.00 0.00 5.19
1851 1968 2.174685 TAAGCTGACTCCATAGGGCA 57.825 50.000 0.00 0.00 0.00 5.36
1852 1969 1.516110 AAGCTGACTCCATAGGGCAT 58.484 50.000 0.00 0.00 0.00 4.40
1853 1970 1.516110 AGCTGACTCCATAGGGCATT 58.484 50.000 0.00 0.00 0.00 3.56
1854 1971 1.849039 AGCTGACTCCATAGGGCATTT 59.151 47.619 0.00 0.00 0.00 2.32
1855 1972 2.158696 AGCTGACTCCATAGGGCATTTC 60.159 50.000 0.00 0.00 0.00 2.17
1856 1973 2.158696 GCTGACTCCATAGGGCATTTCT 60.159 50.000 0.00 0.00 0.00 2.52
1857 1974 3.071602 GCTGACTCCATAGGGCATTTCTA 59.928 47.826 0.00 0.00 0.00 2.10
1858 1975 4.444876 GCTGACTCCATAGGGCATTTCTAA 60.445 45.833 0.00 0.00 0.00 2.10
1859 1976 5.036117 TGACTCCATAGGGCATTTCTAAC 57.964 43.478 0.00 0.00 0.00 2.34
1860 1977 4.141482 TGACTCCATAGGGCATTTCTAACC 60.141 45.833 0.00 0.00 0.00 2.85
1861 1978 3.181454 ACTCCATAGGGCATTTCTAACCG 60.181 47.826 0.00 0.00 0.00 4.44
1862 1979 3.042682 TCCATAGGGCATTTCTAACCGA 58.957 45.455 0.00 0.00 0.00 4.69
1863 1980 3.650942 TCCATAGGGCATTTCTAACCGAT 59.349 43.478 0.00 0.00 0.00 4.18
1864 1981 4.003648 CCATAGGGCATTTCTAACCGATC 58.996 47.826 0.00 0.00 0.00 3.69
1865 1982 2.640316 AGGGCATTTCTAACCGATCC 57.360 50.000 0.00 0.00 0.00 3.36
1866 1983 1.143073 AGGGCATTTCTAACCGATCCC 59.857 52.381 0.00 0.00 0.00 3.85
1867 1984 1.143073 GGGCATTTCTAACCGATCCCT 59.857 52.381 0.00 0.00 0.00 4.20
1868 1985 2.422945 GGGCATTTCTAACCGATCCCTT 60.423 50.000 0.00 0.00 0.00 3.95
1869 1986 3.181448 GGGCATTTCTAACCGATCCCTTA 60.181 47.826 0.00 0.00 0.00 2.69
1870 1987 4.506802 GGGCATTTCTAACCGATCCCTTAT 60.507 45.833 0.00 0.00 0.00 1.73
1871 1988 5.280317 GGGCATTTCTAACCGATCCCTTATA 60.280 44.000 0.00 0.00 0.00 0.98
1872 1989 6.235664 GGCATTTCTAACCGATCCCTTATAA 58.764 40.000 0.00 0.00 0.00 0.98
1873 1990 6.148976 GGCATTTCTAACCGATCCCTTATAAC 59.851 42.308 0.00 0.00 0.00 1.89
1874 1991 6.148976 GCATTTCTAACCGATCCCTTATAACC 59.851 42.308 0.00 0.00 0.00 2.85
1875 1992 5.813513 TTCTAACCGATCCCTTATAACCC 57.186 43.478 0.00 0.00 0.00 4.11
1876 1993 4.818447 TCTAACCGATCCCTTATAACCCA 58.182 43.478 0.00 0.00 0.00 4.51
1877 1994 4.836736 TCTAACCGATCCCTTATAACCCAG 59.163 45.833 0.00 0.00 0.00 4.45
1878 1995 2.335933 ACCGATCCCTTATAACCCAGG 58.664 52.381 0.00 0.00 0.00 4.45
1882 1999 1.454539 CCCTTATAACCCAGGGGCG 59.545 63.158 11.37 0.00 45.75 6.13
1883 2000 1.454539 CCTTATAACCCAGGGGCGG 59.545 63.158 11.37 0.00 39.32 6.13
1884 2001 1.057851 CCTTATAACCCAGGGGCGGA 61.058 60.000 11.37 0.00 39.32 5.54
1885 2002 0.396811 CTTATAACCCAGGGGCGGAG 59.603 60.000 11.37 0.00 39.32 4.63
2058 2180 1.577328 CTCGGTGCGTGCCTCAAATT 61.577 55.000 0.00 0.00 0.00 1.82
2099 2225 3.127533 GCACCAGGATGCACGTCC 61.128 66.667 8.64 0.26 45.39 4.79
2205 2339 2.685017 ACCTGATCTCCAGCGGCA 60.685 61.111 1.45 0.00 41.57 5.69
2212 2359 2.527951 ATCTCCAGCGGCAACCAGAC 62.528 60.000 1.45 0.00 0.00 3.51
2381 2529 6.656902 ACTTTGATTGATCTAGGCTCATCAA 58.343 36.000 18.92 18.92 41.97 2.57
2430 2581 5.044624 AGGCACATATTGGATATAGGCATGT 60.045 40.000 0.00 0.00 31.65 3.21
2455 2606 4.093408 GCATCAGAATCTCGTTACTGCAAA 59.907 41.667 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.756294 TTCGAGGTCAAGGAACTGCA 59.244 50.000 0.00 0.00 40.86 4.41
23 24 1.801178 GCTTTCGAGGTCAAGGAACTG 59.199 52.381 0.00 0.00 40.86 3.16
161 175 3.728373 GGCCTCATTGGACGGGGT 61.728 66.667 0.00 0.00 38.35 4.95
195 209 1.807495 ATAAGCTAGGGCGCGAGGAC 61.807 60.000 12.10 0.00 44.37 3.85
261 276 2.886859 ACTGCGTCTCGAAGTTGTG 58.113 52.632 0.00 0.00 44.06 3.33
491 526 2.674380 GCCACAGCCCTTGACAGG 60.674 66.667 0.00 0.00 40.45 4.00
518 553 3.736100 CGGCAGGCGCATGTTGAA 61.736 61.111 24.27 0.00 41.24 2.69
540 575 0.161024 GCGTACAGCTTGACACGAAC 59.839 55.000 9.59 0.00 44.04 3.95
596 631 2.368875 AGGAATTCCGCCACGATATTCT 59.631 45.455 18.82 0.00 42.08 2.40
647 692 1.153369 CCATCACCACTGGCCTACG 60.153 63.158 3.32 0.00 0.00 3.51
648 693 0.392998 CACCATCACCACTGGCCTAC 60.393 60.000 3.32 0.00 37.27 3.18
649 694 0.840288 ACACCATCACCACTGGCCTA 60.840 55.000 3.32 0.00 37.27 3.93
650 695 0.840288 TACACCATCACCACTGGCCT 60.840 55.000 3.32 0.00 37.27 5.19
729 780 3.682315 GATGCCGTCGTCGCGATG 61.682 66.667 22.29 22.29 41.82 3.84
1036 1131 1.451207 GTGTGGCACTGTGTGGTGA 60.451 57.895 19.83 0.00 39.34 4.02
1037 1132 1.717791 CTGTGTGGCACTGTGTGGTG 61.718 60.000 19.83 0.00 39.91 4.17
1038 1133 1.451927 CTGTGTGGCACTGTGTGGT 60.452 57.895 19.83 0.00 35.11 4.16
1293 1406 2.675423 TGGTCGAGGGAGGACACG 60.675 66.667 0.00 0.00 36.12 4.49
1472 1585 1.075525 TTCGGGGGATCGGATCACT 60.076 57.895 19.04 0.00 31.86 3.41
1473 1586 1.069258 GTTCGGGGGATCGGATCAC 59.931 63.158 18.99 15.67 0.00 3.06
1474 1587 2.495409 CGTTCGGGGGATCGGATCA 61.495 63.158 18.99 0.00 0.00 2.92
1476 1589 3.925090 GCGTTCGGGGGATCGGAT 61.925 66.667 0.00 0.00 0.00 4.18
1500 1613 4.452733 GGAGAGGGGCCAACGACG 62.453 72.222 4.39 0.00 0.00 5.12
1501 1614 3.003763 AGGAGAGGGGCCAACGAC 61.004 66.667 4.39 0.00 0.00 4.34
1502 1615 3.003173 CAGGAGAGGGGCCAACGA 61.003 66.667 4.39 0.00 0.00 3.85
1528 1641 3.314541 AAGACGGCTACTGTACTTTGG 57.685 47.619 0.00 0.00 0.00 3.28
1543 1656 1.299541 ATCCCGCAGCAATTAAGACG 58.700 50.000 0.00 0.00 0.00 4.18
1544 1657 3.303132 CGTTATCCCGCAGCAATTAAGAC 60.303 47.826 0.00 0.00 0.00 3.01
1545 1658 2.869801 CGTTATCCCGCAGCAATTAAGA 59.130 45.455 0.00 0.00 0.00 2.10
1546 1659 2.869801 TCGTTATCCCGCAGCAATTAAG 59.130 45.455 0.00 0.00 0.00 1.85
1547 1660 2.869801 CTCGTTATCCCGCAGCAATTAA 59.130 45.455 0.00 0.00 0.00 1.40
1574 1687 5.899547 ACCTATACATCTGAGACCATGAACA 59.100 40.000 0.00 0.00 0.00 3.18
1605 1718 4.789012 ACTAAATTTCTGCACACATGGG 57.211 40.909 0.00 0.00 0.00 4.00
1666 1779 4.895854 GCCATTTTGCATGCGACT 57.104 50.000 14.09 0.00 0.00 4.18
1682 1795 0.657840 GATGCCATTCTGTACCACGC 59.342 55.000 0.00 0.00 0.00 5.34
1697 1810 6.478588 CAAGTTACGTAGAAAGAATGGATGC 58.521 40.000 0.00 0.00 0.00 3.91
1707 1820 7.221067 CCAAACAAATTGCAAGTTACGTAGAAA 59.779 33.333 12.36 0.00 37.73 2.52
1708 1821 6.693545 CCAAACAAATTGCAAGTTACGTAGAA 59.306 34.615 12.36 0.00 37.73 2.10
1709 1822 6.202937 CCAAACAAATTGCAAGTTACGTAGA 58.797 36.000 12.36 0.00 37.73 2.59
1710 1823 5.108027 GCCAAACAAATTGCAAGTTACGTAG 60.108 40.000 12.36 2.09 37.73 3.51
1724 1841 5.659440 ACGAATTATGAGGCCAAACAAAT 57.341 34.783 5.01 0.00 0.00 2.32
1757 1874 2.167075 GCAATTGCAAAGCCTGGATAGT 59.833 45.455 25.36 0.00 41.59 2.12
1815 1932 6.595716 GTCAGCTTATCAATTAGTTCACCACT 59.404 38.462 0.00 0.00 39.87 4.00
1821 1938 9.202273 CTATGGAGTCAGCTTATCAATTAGTTC 57.798 37.037 0.00 0.00 0.00 3.01
1822 1939 8.153550 CCTATGGAGTCAGCTTATCAATTAGTT 58.846 37.037 0.00 0.00 0.00 2.24
1823 1940 7.256475 CCCTATGGAGTCAGCTTATCAATTAGT 60.256 40.741 0.00 0.00 0.00 2.24
1824 1941 7.102346 CCCTATGGAGTCAGCTTATCAATTAG 58.898 42.308 0.00 0.00 0.00 1.73
1825 1942 6.520742 GCCCTATGGAGTCAGCTTATCAATTA 60.521 42.308 0.00 0.00 0.00 1.40
1826 1943 5.747248 GCCCTATGGAGTCAGCTTATCAATT 60.747 44.000 0.00 0.00 0.00 2.32
1827 1944 4.263243 GCCCTATGGAGTCAGCTTATCAAT 60.263 45.833 0.00 0.00 0.00 2.57
1828 1945 3.071602 GCCCTATGGAGTCAGCTTATCAA 59.928 47.826 0.00 0.00 0.00 2.57
1829 1946 2.634940 GCCCTATGGAGTCAGCTTATCA 59.365 50.000 0.00 0.00 0.00 2.15
1830 1947 2.634940 TGCCCTATGGAGTCAGCTTATC 59.365 50.000 0.00 0.00 0.00 1.75
1831 1948 2.694397 TGCCCTATGGAGTCAGCTTAT 58.306 47.619 0.00 0.00 0.00 1.73
1832 1949 2.174685 TGCCCTATGGAGTCAGCTTA 57.825 50.000 0.00 0.00 0.00 3.09
1833 1950 1.516110 ATGCCCTATGGAGTCAGCTT 58.484 50.000 0.00 0.00 0.00 3.74
1834 1951 1.516110 AATGCCCTATGGAGTCAGCT 58.484 50.000 0.00 0.00 0.00 4.24
1835 1952 2.158696 AGAAATGCCCTATGGAGTCAGC 60.159 50.000 0.00 0.00 0.00 4.26
1836 1953 3.853355 AGAAATGCCCTATGGAGTCAG 57.147 47.619 0.00 0.00 0.00 3.51
1837 1954 4.141482 GGTTAGAAATGCCCTATGGAGTCA 60.141 45.833 0.00 0.00 0.00 3.41
1838 1955 4.390264 GGTTAGAAATGCCCTATGGAGTC 58.610 47.826 0.00 0.00 0.00 3.36
1839 1956 3.181454 CGGTTAGAAATGCCCTATGGAGT 60.181 47.826 0.00 0.00 0.00 3.85
1840 1957 3.071023 TCGGTTAGAAATGCCCTATGGAG 59.929 47.826 0.00 0.00 0.00 3.86
1841 1958 3.042682 TCGGTTAGAAATGCCCTATGGA 58.957 45.455 0.00 0.00 0.00 3.41
1842 1959 3.485463 TCGGTTAGAAATGCCCTATGG 57.515 47.619 0.00 0.00 0.00 2.74
1843 1960 4.003648 GGATCGGTTAGAAATGCCCTATG 58.996 47.826 0.00 0.00 0.00 2.23
1844 1961 3.009143 GGGATCGGTTAGAAATGCCCTAT 59.991 47.826 0.00 0.00 31.49 2.57
1845 1962 2.370849 GGGATCGGTTAGAAATGCCCTA 59.629 50.000 0.00 0.00 31.49 3.53
1846 1963 1.143073 GGGATCGGTTAGAAATGCCCT 59.857 52.381 0.00 0.00 31.49 5.19
1847 1964 1.143073 AGGGATCGGTTAGAAATGCCC 59.857 52.381 0.00 0.00 31.74 5.36
1848 1965 2.640316 AGGGATCGGTTAGAAATGCC 57.360 50.000 0.00 0.00 0.00 4.40
1849 1966 6.148976 GGTTATAAGGGATCGGTTAGAAATGC 59.851 42.308 0.00 0.00 0.00 3.56
1850 1967 6.653740 GGGTTATAAGGGATCGGTTAGAAATG 59.346 42.308 0.00 0.00 0.00 2.32
1851 1968 6.330778 TGGGTTATAAGGGATCGGTTAGAAAT 59.669 38.462 0.00 0.00 0.00 2.17
1852 1969 5.666718 TGGGTTATAAGGGATCGGTTAGAAA 59.333 40.000 0.00 0.00 0.00 2.52
1853 1970 5.218179 TGGGTTATAAGGGATCGGTTAGAA 58.782 41.667 0.00 0.00 0.00 2.10
1854 1971 4.818447 TGGGTTATAAGGGATCGGTTAGA 58.182 43.478 0.00 0.00 0.00 2.10
1855 1972 4.020485 CCTGGGTTATAAGGGATCGGTTAG 60.020 50.000 0.00 0.00 0.00 2.34
1856 1973 3.905591 CCTGGGTTATAAGGGATCGGTTA 59.094 47.826 0.00 0.00 0.00 2.85
1857 1974 2.709397 CCTGGGTTATAAGGGATCGGTT 59.291 50.000 0.00 0.00 0.00 4.44
1858 1975 2.335933 CCTGGGTTATAAGGGATCGGT 58.664 52.381 0.00 0.00 0.00 4.69
1865 1982 1.057851 TCCGCCCCTGGGTTATAAGG 61.058 60.000 12.71 5.60 37.65 2.69
1866 1983 0.396811 CTCCGCCCCTGGGTTATAAG 59.603 60.000 12.71 0.00 37.65 1.73
1867 1984 1.702022 GCTCCGCCCCTGGGTTATAA 61.702 60.000 12.71 0.00 37.65 0.98
1868 1985 2.144738 GCTCCGCCCCTGGGTTATA 61.145 63.158 12.71 0.00 37.65 0.98
1869 1986 2.615191 TAGCTCCGCCCCTGGGTTAT 62.615 60.000 12.71 0.00 37.65 1.89
1870 1987 3.320411 TAGCTCCGCCCCTGGGTTA 62.320 63.158 12.71 0.00 37.65 2.85
1871 1988 4.733725 TAGCTCCGCCCCTGGGTT 62.734 66.667 12.71 0.00 37.65 4.11
1878 1995 4.452733 ACAACGCTAGCTCCGCCC 62.453 66.667 13.93 0.00 0.00 6.13
1879 1996 3.188786 CACAACGCTAGCTCCGCC 61.189 66.667 13.93 0.00 0.00 6.13
1880 1997 3.854459 GCACAACGCTAGCTCCGC 61.854 66.667 13.93 4.51 37.77 5.54
1881 1998 1.811266 ATGCACAACGCTAGCTCCG 60.811 57.895 13.93 0.00 43.06 4.63
1882 1999 1.021390 ACATGCACAACGCTAGCTCC 61.021 55.000 13.93 0.00 43.06 4.70
1883 2000 0.095935 CACATGCACAACGCTAGCTC 59.904 55.000 13.93 0.00 43.06 4.09
1884 2001 1.300971 CCACATGCACAACGCTAGCT 61.301 55.000 13.93 0.00 43.06 3.32
1885 2002 1.135315 CCACATGCACAACGCTAGC 59.865 57.895 4.06 4.06 43.06 3.42
1886 2003 0.955428 ACCCACATGCACAACGCTAG 60.955 55.000 0.00 0.00 43.06 3.42
1887 2004 0.321996 TACCCACATGCACAACGCTA 59.678 50.000 0.00 0.00 43.06 4.26
1888 2005 0.955428 CTACCCACATGCACAACGCT 60.955 55.000 0.00 0.00 43.06 5.07
1889 2006 1.234615 ACTACCCACATGCACAACGC 61.235 55.000 0.00 0.00 42.89 4.84
1890 2007 1.234821 AACTACCCACATGCACAACG 58.765 50.000 0.00 0.00 0.00 4.10
1891 2008 3.181480 ACAAAACTACCCACATGCACAAC 60.181 43.478 0.00 0.00 0.00 3.32
1892 2009 3.027412 ACAAAACTACCCACATGCACAA 58.973 40.909 0.00 0.00 0.00 3.33
2018 2135 5.220416 CGAGGCAGTAGTAGTTTAATTGTGC 60.220 44.000 0.00 0.00 0.00 4.57
2099 2225 2.093783 GGAAGCGACAGTCAATTAACGG 59.906 50.000 0.41 0.00 0.00 4.44
2355 2503 7.795047 TGATGAGCCTAGATCAATCAAAGTTA 58.205 34.615 0.00 0.00 29.85 2.24
2430 2581 3.618594 GCAGTAACGAGATTCTGATGCAA 59.381 43.478 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.