Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign28 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:21:01 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign28 assembly : NCBIM34 bias : 5prime chromosome : 17 id : 3 strand : 1 ------------- Design window length: 2138bp All jobs for probe design are successful - total: 23 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 446 putative probes to analyse Selection criteria to rank probes: Minimum score ratio : 10 (i.e. self-hit must score at least 10 times higher than the next best hit) Maximum percent repetitive bases: 5 Favour probes to the 5prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 446/446 Putative probes exceeding selection criteria: 200/446 PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW --------------------------------------------------------------
Image
Unique (yellow), passed (green) and failed putative probes in the design window
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
1838 | 1000 | 30.7 | 5000 | - | 0 | 30.7 |
1839 | 1000 | 30.7 | 5000 | - | 50 | 30.7 |
1840 | 1000 | 30.7 | 5000 | - | 100 | 30.7 |
1841 | 1000 | 30.7 | 5000 | - | 150 | 30.7 |
1842 | 1000 | 30.7 | 5000 | 0.4 | 200 | 29.9 |
1861 | 950 | 29.1 | 4750 | - | 0 | 29.1 |
1862 | 950 | 29.1 | 4750 | - | 47 | 29.1 |
1863 | 950 | 29.1 | 4750 | - | 94 | 29.1 |
1864 | 950 | 29.1 | 4750 | - | 141 | 29.1 |
1865 | 950 | 29.1 | 4750 | - | 188 | 29.1 |
1866 | 950 | 29.1 | 4750 | - | 235 | 29.1 |
1887 | 900 | 27.6 | 4500 | - | 0 | 27.6 |
1888 | 900 | 27.6 | 4500 | - | 45 | 27.6 |
1889 | 900 | 27.6 | 4500 | - | 90 | 27.6 |
1890 | 900 | 27.6 | 4500 | - | 135 | 27.6 |
1891 | 900 | 27.6 | 4500 | - | 180 | 27.6 |
1892 | 900 | 27.6 | 4500 | - | 225 | 27.6 |
1893 | 900 | 27.6 | 4500 | - | 270 | 27.6 |
1915 | 850 | 26.1 | 4250 | - | 0 | 26.1 |
1916 | 850 | 26.1 | 4250 | - | 42 | 26.1 |
1917 | 850 | 26.1 | 4250 | - | 84 | 26.1 |
1918 | 850 | 26.1 | 4250 | - | 126 | 26.1 |
1919 | 850 | 26.1 | 4250 | - | 168 | 26.1 |
1920 | 850 | 26.1 | 4250 | - | 210 | 26.1 |
1921 | 850 | 26.1 | 4250 | - | 252 | 26.1 |
1922 | 850 | 26.1 | 4250 | - | 294 | 26.1 |
1923 | 850 | 26.1 | 4250 | - | 336 | 26.1 |
1947 | 800 | 25.5 | 4000 | - | 40 | 25.5 |
1843 | 1000 | 28.2 | 5000 | 1.7 | 250 | 24.8 |
1844 | 1000 | 28.2 | 5000 | 1.7 | 300 | 24.8 |
1845 | 1000 | 28.2 | 5000 | 1.7 | 350 | 24.8 |
1846 | 1000 | 28.2 | 5000 | 1.7 | 400 | 24.8 |
1847 | 1000 | 28.2 | 5000 | 1.7 | 450 | 24.8 |
1948 | 800 | 24.5 | 4000 | - | 80 | 24.5 |
1949 | 800 | 24.5 | 4000 | - | 120 | 24.5 |
1950 | 800 | 24.5 | 4000 | - | 160 | 24.5 |
1951 | 800 | 24.5 | 4000 | - | 200 | 24.5 |
1952 | 800 | 24.5 | 4000 | - | 240 | 24.5 |
1953 | 800 | 24.5 | 4000 | - | 280 | 24.5 |
1954 | 800 | 24.5 | 4000 | - | 320 | 24.5 |
1955 | 800 | 24.5 | 4000 | - | 360 | 24.5 |
1872 | 950 | 26.8 | 4750 | 1.8 | 517 | 23.3 |
1983 | 750 | 23.0 | 3750 | - | 111 | 23.0 |
1984 | 750 | 23.0 | 3750 | - | 148 | 23.0 |
1985 | 750 | 23.0 | 3750 | - | 185 | 23.0 |
1986 | 750 | 23.0 | 3750 | - | 222 | 23.0 |
1987 | 750 | 23.0 | 3750 | - | 259 | 23.0 |
1988 | 750 | 23.0 | 3750 | - | 296 | 23.0 |
1989 | 750 | 23.0 | 3750 | - | 333 | 23.0 |
1990 | 750 | 23.0 | 3750 | - | 370 | 23.0 |
1991 | 750 | 23.0 | 3750 | - | 407 | 23.0 |
1992 | 750 | 23.0 | 3750 | - | 444 | 23.0 |
2022 | 700 | 22.3 | 3500 | - | 140 | 22.3 |
2023 | 700 | 21.5 | 3500 | - | 175 | 21.5 |
2024 | 700 | 21.5 | 3500 | - | 210 | 21.5 |
2025 | 700 | 21.5 | 3500 | - | 245 | 21.5 |
2026 | 700 | 21.5 | 3500 | - | 280 | 21.5 |
2027 | 700 | 21.5 | 3500 | - | 315 | 21.5 |
2028 | 700 | 21.5 | 3500 | - | 350 | 21.5 |
2029 | 700 | 21.5 | 3500 | - | 385 | 21.5 |
2030 | 700 | 21.5 | 3500 | - | 420 | 21.5 |
2031 | 700 | 21.5 | 3500 | - | 455 | 21.5 |
2032 | 700 | 21.5 | 3500 | - | 490 | 21.5 |
2066 | 650 | 20.1 | 3250 | - | 192 | 20.1 |
2067 | 650 | 19.9 | 3250 | - | 224 | 19.9 |
2068 | 650 | 19.9 | 3250 | - | 256 | 19.9 |
2069 | 650 | 19.9 | 3250 | - | 288 | 19.9 |
2070 | 650 | 19.9 | 3250 | - | 320 | 19.9 |
2071 | 650 | 19.9 | 3250 | - | 352 | 19.9 |
2072 | 650 | 19.9 | 3250 | - | 384 | 19.9 |
2073 | 650 | 19.9 | 3250 | - | 416 | 19.9 |
2074 | 650 | 19.9 | 3250 | - | 448 | 19.9 |
2075 | 650 | 19.9 | 3250 | - | 480 | 19.9 |
2076 | 650 | 19.9 | 3250 | - | 512 | 19.9 |
2077 | 650 | 19.9 | 3250 | - | 544 | 19.9 |
1848 | 1000 | 28.2 | 5000 | 4.5 | 500 | 19.2 |
2115 | 600 | 19.1 | 3000 | - | 240 | 19.1 |
1900 | 900 | 25.4 | 4500 | 3.3 | 585 | 18.8 |
2116 | 600 | 18.4 | 3000 | - | 270 | 18.4 |
2117 | 600 | 18.4 | 3000 | - | 300 | 18.4 |
2118 | 600 | 18.4 | 3000 | - | 330 | 18.4 |
2119 | 600 | 18.4 | 3000 | - | 360 | 18.4 |
2120 | 600 | 18.4 | 3000 | - | 390 | 18.4 |
2121 | 600 | 18.4 | 3000 | - | 420 | 18.4 |
2122 | 600 | 18.4 | 3000 | - | 450 | 18.4 |
2123 | 600 | 18.4 | 3000 | - | 480 | 18.4 |
2124 | 600 | 18.4 | 3000 | - | 510 | 18.4 |
2125 | 600 | 18.4 | 3000 | - | 540 | 18.4 |
2126 | 600 | 18.4 | 3000 | - | 570 | 18.4 |
1930 | 850 | 24.0 | 4250 | 2.9 | 630 | 18.1 |
2170 | 550 | 16.9 | 2750 | - | 297 | 16.9 |
2171 | 550 | 16.9 | 2750 | - | 324 | 16.9 |
2172 | 550 | 16.9 | 2750 | - | 351 | 16.9 |
2173 | 550 | 16.9 | 2750 | - | 378 | 16.9 |
2174 | 550 | 16.9 | 2750 | - | 405 | 16.9 |
2175 | 550 | 16.9 | 2750 | - | 432 | 16.9 |
2176 | 550 | 16.9 | 2750 | - | 459 | 16.9 |
2177 | 550 | 16.9 | 2750 | - | 486 | 16.9 |
2178 | 550 | 16.9 | 2750 | - | 513 | 16.9 |
2179 | 550 | 16.9 | 2750 | - | 540 | 16.9 |
2180 | 550 | 16.9 | 2750 | - | 567 | 16.9 |
2181 | 550 | 16.9 | 2750 | - | 594 | 16.9 |
2182 | 550 | 16.9 | 2750 | - | 621 | 16.9 |
1999 | 750 | 21.2 | 3750 | 2.3 | 703 | 16.7 |
1963 | 800 | 22.6 | 4000 | 3.1 | 680 | 16.3 |
2183 | 550 | 16.9 | 2750 | 0.4 | 648 | 16.1 |
2232 | 500 | 15.3 | 2500 | - | 350 | 15.3 |
2233 | 500 | 15.3 | 2500 | - | 375 | 15.3 |
2234 | 500 | 15.3 | 2500 | - | 400 | 15.3 |
2235 | 500 | 15.3 | 2500 | - | 425 | 15.3 |
2236 | 500 | 15.3 | 2500 | - | 450 | 15.3 |
2237 | 500 | 15.3 | 2500 | - | 475 | 15.3 |
2238 | 500 | 15.3 | 2500 | - | 500 | 15.3 |
2239 | 500 | 15.3 | 2500 | - | 525 | 15.3 |
2240 | 500 | 15.3 | 2500 | - | 550 | 15.3 |
2241 | 500 | 15.3 | 2500 | - | 575 | 15.3 |
2242 | 500 | 15.3 | 2500 | - | 600 | 15.3 |
2243 | 500 | 15.3 | 2500 | - | 625 | 15.3 |
2244 | 500 | 15.3 | 2500 | - | 650 | 15.3 |
2245 | 500 | 15.3 | 2500 | - | 675 | 15.3 |
2040 | 700 | 19.8 | 3500 | 2.4 | 770 | 14.9 |
2136 | 600 | 16.9 | 3000 | 2.8 | 870 | 11.3 |
2086 | 650 | 18.4 | 3250 | 4.2 | 832 | 10.1 |
2193 | 550 | 15.5 | 2750 | 3.1 | 918 | 9.4 |
2257 | 500 | 14.1 | 2500 | 4.0 | 975 | 6.1 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
1867 | 950 | 28.3 | 4750 | 1.8 | 282 | 24.7 |
1894 | 900 | 27.6 | 4500 | 1.9 | 315 | 23.8 |
1956 | 800 | 24.5 | 4000 | 0.5 | 400 | 23.5 |
1868 | 950 | 26.8 | 4750 | 1.8 | 329 | 23.3 |
1869 | 950 | 26.8 | 4750 | 1.8 | 376 | 23.3 |
1870 | 950 | 26.8 | 4750 | 1.8 | 423 | 23.3 |
1871 | 950 | 26.8 | 4750 | 1.8 | 470 | 23.3 |
1895 | 900 | 25.4 | 4500 | 1.9 | 360 | 21.6 |
1896 | 900 | 25.4 | 4500 | 1.9 | 405 | 21.6 |
1897 | 900 | 25.4 | 4500 | 1.9 | 450 | 21.6 |
1898 | 900 | 25.4 | 4500 | 1.9 | 495 | 21.6 |
1899 | 900 | 25.4 | 4500 | 1.9 | 540 | 21.6 |
1924 | 850 | 25.3 | 4250 | 2.0 | 378 | 21.3 |
1925 | 850 | 24.0 | 4250 | 2.0 | 420 | 20.0 |
1926 | 850 | 24.0 | 4250 | 2.0 | 462 | 20.0 |
1927 | 850 | 24.0 | 4250 | 2.0 | 504 | 20.0 |
1928 | 850 | 24.0 | 4250 | 2.0 | 546 | 20.0 |
1929 | 850 | 24.0 | 4250 | 2.0 | 588 | 20.0 |
1957 | 800 | 22.9 | 4000 | 2.1 | 440 | 18.6 |
1958 | 800 | 22.6 | 4000 | 2.1 | 480 | 18.3 |
1959 | 800 | 22.6 | 4000 | 2.1 | 520 | 18.3 |
1960 | 800 | 22.6 | 4000 | 2.1 | 560 | 18.3 |
1961 | 800 | 22.6 | 4000 | 2.1 | 600 | 18.3 |
1962 | 800 | 22.6 | 4000 | 2.1 | 640 | 18.3 |
1993 | 750 | 22.3 | 3750 | 2.3 | 481 | 17.8 |
2127 | 600 | 18.4 | 3000 | 0.7 | 600 | 17.1 |
1994 | 750 | 21.2 | 3750 | 2.3 | 518 | 16.7 |
1995 | 750 | 21.2 | 3750 | 2.3 | 555 | 16.7 |
1996 | 750 | 21.2 | 3750 | 2.3 | 592 | 16.7 |
1997 | 750 | 21.2 | 3750 | 2.3 | 629 | 16.7 |
1998 | 750 | 21.2 | 3750 | 2.3 | 666 | 16.7 |
2033 | 700 | 20.8 | 3500 | 2.4 | 525 | 16.0 |
2034 | 700 | 19.8 | 3500 | 2.4 | 560 | 14.9 |
2035 | 700 | 19.8 | 3500 | 2.4 | 595 | 14.9 |
2036 | 700 | 19.8 | 3500 | 2.4 | 630 | 14.9 |
2037 | 700 | 19.8 | 3500 | 2.4 | 665 | 14.9 |
2038 | 700 | 19.8 | 3500 | 2.4 | 700 | 14.9 |
2039 | 700 | 19.8 | 3500 | 2.4 | 735 | 14.9 |
2078 | 650 | 19.3 | 3250 | 2.6 | 576 | 14.1 |
2246 | 500 | 15.3 | 2500 | 0.8 | 700 | 13.7 |
2079 | 650 | 18.4 | 3250 | 2.6 | 608 | 13.1 |
2080 | 650 | 18.4 | 3250 | 2.6 | 640 | 13.1 |
2081 | 650 | 18.4 | 3250 | 2.6 | 672 | 13.1 |
2082 | 650 | 18.4 | 3250 | 2.6 | 704 | 13.1 |
2083 | 650 | 18.4 | 3250 | 2.6 | 736 | 13.1 |
2084 | 650 | 18.4 | 3250 | 2.6 | 768 | 13.1 |
2085 | 650 | 18.4 | 3250 | 2.6 | 800 | 13.1 |
2128 | 600 | 17.9 | 3000 | 2.8 | 630 | 12.2 |
2000 | 750 | 21.2 | 3750 | 4.7 | 740 | 11.9 |
2129 | 600 | 16.9 | 3000 | 2.8 | 660 | 11.3 |
2130 | 600 | 16.9 | 3000 | 2.8 | 690 | 11.3 |
2131 | 600 | 16.9 | 3000 | 2.8 | 720 | 11.3 |
2132 | 600 | 16.9 | 3000 | 2.8 | 750 | 11.3 |
2133 | 600 | 16.9 | 3000 | 2.8 | 780 | 11.3 |
2134 | 600 | 16.9 | 3000 | 2.8 | 810 | 11.3 |
2135 | 600 | 16.9 | 3000 | 2.8 | 840 | 11.3 |
2184 | 550 | 16.4 | 2750 | 3.1 | 675 | 10.2 |
2185 | 550 | 15.5 | 2750 | 3.1 | 702 | 9.4 |
2186 | 550 | 15.5 | 2750 | 3.1 | 729 | 9.4 |
2187 | 550 | 15.5 | 2750 | 3.1 | 756 | 9.4 |
2188 | 550 | 15.5 | 2750 | 3.1 | 783 | 9.4 |
2189 | 550 | 15.5 | 2750 | 3.1 | 810 | 9.4 |
2190 | 550 | 15.5 | 2750 | 3.1 | 837 | 9.4 |
2191 | 550 | 15.5 | 2750 | 3.1 | 864 | 9.4 |
2192 | 550 | 15.5 | 2750 | 3.1 | 891 | 9.4 |
2247 | 500 | 14.9 | 2500 | 3.4 | 725 | 8.1 |
2248 | 500 | 14.1 | 2500 | 3.4 | 750 | 7.3 |
2249 | 500 | 14.1 | 2500 | 3.4 | 775 | 7.3 |
2250 | 500 | 14.1 | 2500 | 3.4 | 800 | 7.3 |
2251 | 500 | 14.1 | 2500 | 3.4 | 825 | 7.3 |
2252 | 500 | 14.1 | 2500 | 3.4 | 850 | 7.3 |
2253 | 500 | 14.1 | 2500 | 3.4 | 875 | 7.3 |
2254 | 500 | 14.1 | 2500 | 3.4 | 900 | 7.3 |
2255 | 500 | 14.1 | 2500 | 3.4 | 925 | 7.3 |
2256 | 500 | 14.1 | 2500 | 3.4 | 950 | 7.3 |
Overall score = score_ratio - 2 * repetitive DNA content