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
Image
Unique putative probes (0)
Putative probes (125)
Redundant probes (75)

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