Automated design of genomic Southern blot probes

Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant

Design Case - ProbeDesign43 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (206)
Redundant probes (8)

Summary

`./analyse_probe_search_results : Tue Sep 13 14:38:24 2005`

Connected to host: host, as user: user
Database       : southern_blot_designs

Fetched probe design: ProbeDesign43
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 25
  strand        : 1
  -------------

Design window length: 3001bp

All jobs for probe design are successful - total: 46
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 907 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 3prime end of design window
  ------------------------

Putative probes without hits                : 0
Putative probes with single_self_hit        : 907/907
Putative probes exceeding selection criteria: 214/907

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
27287	1150	34.6	5750	1.0	1710	32.7
27358	1050	33.2	5250	0.3	1716	32.7
27321	1100	34.8	5500	1.5	1705	31.9
27398	1000	31.6	5000	-	1750	31.6
27322	1100	33.1	5500	0.9	1760	31.3
27225	1250	31.7	6250	0.8	1736	30.1
27441	950	30.1	4750	-	1739	30.1
27442	950	30.1	4750	-	1786	30.1
27359	1050	31.6	5250	1.0	1768	29.7
27399	1000	31.6	5000	1.0	1800	29.6
27397	1000	31.6	5000	1.1	1700	29.4
27255	1200	30.5	6000	0.8	1740	28.8
27256	1200	30.5	6000	0.8	1800	28.8
27487	900	28.5	4500	-	1755	28.5
27488	900	28.5	4500	-	1800	28.5
27489	900	28.5	4500	-	1845	28.5
27486	900	28.5	4500	0.1	1710	28.3
27196	1300	33.0	6500	2.4	1690	28.2
27400	1000	30.1	5000	1.0	1850	28.1
27443	950	30.1	4750	1.1	1833	28.0
27288	1150	29.2	5750	0.9	1767	27.4
27289	1150	29.2	5750	0.9	1824	27.4
27536	850	26.9	4250	-	1722	26.9
27537	850	26.9	4250	-	1764	26.9
27538	850	26.9	4250	-	1806	26.9
27539	850	26.9	4250	-	1848	26.9
27540	850	26.9	4250	-	1890	26.9
27444	950	28.6	4750	1.1	1880	26.5
27490	900	28.5	4500	1.1	1890	26.3
27323	1100	27.9	5500	0.9	1815	26.1
27324	1100	27.9	5500	0.9	1870	26.1
27440	950	30.1	4750	2.0	1692	26.1
27590	800	25.3	4000	-	1720	25.3
27591	800	25.3	4000	-	1760	25.3
27592	800	25.3	4000	-	1800	25.3
27593	800	25.3	4000	-	1840	25.3
27594	800	25.3	4000	-	1880	25.3
27595	800	25.3	4000	-	1920	25.3
27596	800	25.3	4000	-	1960	25.3
27491	900	27.1	4500	1.1	1935	24.9
27360	1050	26.6	5250	1.0	1820	24.7
27361	1050	26.6	5250	1.0	1872	24.7
27362	1050	26.6	5250	1.0	1924	24.7
27541	850	26.9	4250	1.2	1932	24.5
27357	1050	33.2	5250	4.5	1664	24.3
27224	1250	31.7	6250	3.8	1674	24.2
27650	750	23.7	3750	-	1739	23.7
27651	750	23.7	3750	-	1776	23.7
27652	750	23.7	3750	-	1813	23.7
27653	750	23.7	3750	-	1850	23.7
27654	750	23.7	3750	-	1887	23.7
27655	750	23.7	3750	-	1924	23.7
27656	750	23.7	3750	-	1961	23.7
27657	750	23.7	3750	-	1998	23.7
27254	1200	30.5	6000	3.4	1680	23.6
27401	1000	25.4	5000	1.0	1900	23.4
27402	1000	25.4	5000	1.0	1950	23.4
27542	850	25.6	4250	1.2	1974	23.2
27543	850	25.6	4250	1.2	2016	23.2
27597	800	25.3	4000	1.2	2000	22.8
27713	700	22.2	3500	-	1715	22.2
27714	700	22.2	3500	-	1750	22.2
27715	700	22.2	3500	-	1785	22.2
27716	700	22.2	3500	-	1820	22.2
27717	700	22.2	3500	-	1855	22.2
27718	700	22.2	3500	-	1890	22.2
27719	700	22.2	3500	-	1925	22.2
27720	700	22.2	3500	-	1960	22.2
27721	700	22.2	3500	-	1995	22.2
27722	700	22.2	3500	-	2030	22.2
27445	950	24.1	4750	1.1	1927	22.0
27446	950	24.1	4750	1.1	1974	22.0
27447	950	24.1	4750	1.1	2021	22.0
27598	800	24.1	4000	1.2	2040	21.6
27723	700	22.2	3500	0.3	2065	21.6
27649	750	23.7	3750	1.2	1702	21.3
27658	750	23.7	3750	1.3	2035	21.1
27492	900	22.8	4500	1.1	1980	20.6
27493	900	22.8	4500	1.1	2025	20.6
27494	900	22.8	4500	1.1	2070	20.6
27784	650	20.6	3250	-	1728	20.6
27785	650	20.6	3250	-	1760	20.6
27786	650	20.6	3250	-	1792	20.6
27787	650	20.6	3250	-	1824	20.6
27788	650	20.6	3250	-	1856	20.6
27789	650	20.6	3250	-	1888	20.6
27790	650	20.6	3250	-	1920	20.6
27791	650	20.6	3250	-	1952	20.6
27792	650	20.6	3250	-	1984	20.6
27793	650	20.6	3250	-	2016	20.6
27794	650	20.6	3250	-	2048	20.6
27795	650	20.6	3250	-	2080	20.6
27796	650	20.6	3250	-	2112	20.6
27659	750	22.6	3750	1.3	2072	19.9
27660	750	22.6	3750	1.3	2109	19.9
27535	850	26.9	4250	3.6	1680	19.6
27862	600	19.5	3000	-	1740	19.5
27724	700	22.2	3500	1.4	2100	19.3
27544	850	21.6	4250	1.2	2058	19.2
27545	850	21.6	4250	1.2	2100	19.2
27863	600	19.0	3000	-	1770	19.0
27864	600	19.0	3000	-	1800	19.0
27865	600	19.0	3000	-	1830	19.0
27866	600	19.0	3000	-	1860	19.0
27867	600	19.0	3000	-	1890	19.0
27868	600	19.0	3000	-	1920	19.0
27869	600	19.0	3000	-	1950	19.0
27870	600	19.0	3000	-	1980	19.0
27871	600	19.0	3000	-	2010	19.0
27872	600	19.0	3000	-	2040	19.0
27873	600	19.0	3000	-	2070	19.0
27874	600	19.0	3000	-	2100	19.0
27875	600	19.0	3000	-	2130	19.0
27876	600	19.0	3000	-	2160	19.0
27725	700	21.1	3500	1.4	2135	18.2
27599	800	20.3	4000	1.2	2080	17.8
27600	800	20.3	4000	1.2	2120	17.8
27601	800	20.3	4000	1.2	2160	17.8
27797	650	20.6	3250	1.5	2144	17.5
27952	550	17.4	2750	-	1809	17.4
27953	550	17.4	2750	-	1836	17.4
27954	550	17.4	2750	-	1863	17.4
27955	550	17.4	2750	-	1890	17.4
27956	550	17.4	2750	-	1917	17.4
27957	550	17.4	2750	-	1944	17.4
27958	550	17.4	2750	-	1971	17.4
27959	550	17.4	2750	-	1998	17.4
27960	550	17.4	2750	-	2025	17.4
27961	550	17.4	2750	-	2052	17.4
27962	550	17.4	2750	-	2079	17.4
27963	550	17.4	2750	-	2106	17.4
27964	550	17.4	2750	-	2133	17.4
27965	550	17.4	2750	-	2160	17.4
27966	550	17.4	2750	-	2187	17.4
27967	550	17.4	2750	0.2	2214	17.0
27798	650	19.6	3250	1.5	2176	16.5
27799	650	19.6	3250	1.5	2208	16.5
27661	750	19.0	3750	1.3	2146	16.4
27662	750	19.0	3750	1.3	2183	16.4
27663	750	19.0	3750	1.3	2220	16.4
27783	650	20.7	3250	2.3	1696	16.1
28050	500	15.8	2500	-	1850	15.8
28051	500	15.8	2500	-	1875	15.8
28052	500	15.8	2500	-	1900	15.8
28053	500	15.8	2500	-	1925	15.8
28054	500	15.8	2500	-	1950	15.8
28055	500	15.8	2500	-	1975	15.8
28056	500	15.8	2500	-	2000	15.8
28057	500	15.8	2500	-	2025	15.8
28058	500	15.8	2500	-	2050	15.8
28059	500	15.8	2500	-	2075	15.8
28060	500	15.8	2500	-	2100	15.8
28061	500	15.8	2500	-	2125	15.8
28062	500	15.8	2500	-	2150	15.8
28063	500	15.8	2500	-	2175	15.8
28064	500	15.8	2500	-	2200	15.8
28065	500	15.8	2500	-	2225	15.8
28066	500	15.8	2500	-	2250	15.8
27877	600	19.0	3000	1.7	2190	15.7
27726	700	17.8	3500	1.4	2170	14.9
27727	700	17.8	3500	1.4	2205	14.9
27728	700	17.8	3500	1.4	2240	14.9
27729	700	17.8	3500	1.4	2275	14.9
27878	600	18.1	3000	1.7	2220	14.7
27879	600	18.1	3000	1.7	2250	14.7
27837	600	17.5	3000	1.7	990	14.2
27838	600	17.5	3000	1.7	1020	14.2
27968	550	17.4	2750	1.8	2241	13.8
27800	650	16.5	3250	1.5	2240	13.4
27801	650	16.5	3250	1.5	2272	13.4
27802	650	16.5	3250	1.5	2304	13.4
27803	650	16.5	3250	1.5	2336	13.4
27969	550	16.6	2750	1.8	2268	12.9
27970	550	16.6	2750	1.8	2295	12.9
27922	550	16.1	2750	1.8	999	12.4
27923	550	16.1	2750	1.8	1026	12.4
27924	550	16.1	2750	1.8	1053	12.4
28068	500	16.2	2500	2.0	2300	12.2
27760	650	19.0	3250	3.5	960	11.9
27880	600	15.2	3000	1.7	2280	11.9
27881	600	15.2	3000	1.7	2310	11.9
27882	600	15.2	3000	1.7	2340	11.9
27883	600	15.2	3000	1.7	2370	11.9
28015	500	14.6	2500	1.4	975	11.8
28069	500	15.1	2500	2.0	2325	11.1
28070	500	15.1	2500	2.0	2350	11.1
28016	500	14.6	2500	2.0	1000	10.6
28017	500	14.6	2500	2.0	1025	10.6
28018	500	14.6	2500	2.0	1050	10.6
28019	500	14.6	2500	2.0	1075	10.6
28020	500	14.6	2500	2.0	1100	10.6
27971	550	14.0	2750	1.8	2322	10.3
27972	550	14.0	2750	1.8	2349	10.3
27973	550	14.0	2750	1.8	2376	10.3
27974	550	14.0	2750	1.8	2403	10.3
27975	550	14.0	2750	1.8	2430	10.3
27761	650	19.0	3250	4.6	992	9.8
27925	550	16.1	2750	3.3	1080	9.5
28021	500	14.6	2500	2.6	1125	9.4
27921	550	16.1	2750	3.5	972	9.2
28071	500	12.7	2500	2.0	2375	8.7
28072	500	12.7	2500	2.0	2400	8.7
28073	500	12.7	2500	2.0	2425	8.7
28074	500	12.7	2500	2.0	2450	8.7
28075	500	12.7	2500	2.0	2475	8.7
28014	500	14.6	2500	4.6	950	5.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
27403	1000	25.4	5000	1.0	2000	23.4
27546	850	21.6	4250	1.2	2142	19.2
27602	800	20.3	4000	1.2	2200	17.8
27589	800	25.3	4000	3.9	1680	17.6
27712	700	22.2	3500	4.4	1680	13.3
27884	600	15.2	3000	1.7	2400	11.9
27836	600	17.5	3000	3.8	960	9.9
28076	500	12.7	2500	2.0	2500	8.7

Overall score = score_ratio - 2 * repetitive DNA content