Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign47 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (131)
Redundant probes (79)

Summary

`./analyse_probe_search_results : Wed Sep 21 13:54:29 2005`

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

Fetched probe design: ProbeDesign47
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 8
  id            : 29
  strand        : 1
  -------------

Design window length: 4712bp

All jobs for probe design are successful - total: 81
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1611 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        : 1611/1611
Putative probes exceeding selection criteria: 210/1611

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
30780	1150	33.2	5750	3.1	1995	27.0
30845	1100	31.8	5500	2.5	2035	26.7
30913	1050	30.3	5250	2.7	2028	25.0
30914	1050	30.3	5250	2.7	2080	25.0
30986	1000	28.9	5000	2.8	2050	23.3
30987	1000	28.9	5000	2.8	2100	23.3
30988	1000	28.9	5000	2.8	2150	23.3
30985	1000	28.9	5000	3.1	2000	22.7
30844	1100	31.8	5500	4.6	1980	22.5
31151	900	26.0	4500	2.2	2250	21.6
31063	950	27.5	4750	2.9	2021	21.6
31064	950	27.5	4750	2.9	2068	21.6
31065	950	27.5	4750	2.9	2115	21.6
31066	950	27.5	4750	2.9	2162	21.6
31067	950	27.5	4750	2.9	2209	21.6
30915	1050	30.3	5250	4.5	2132	21.4
31328	800	23.8	4000	1.4	2000	21.1
30846	1100	30.9	5500	5.0	2090	20.9
31431	750	22.3	3750	1.1	2035	20.2
31240	850	24.6	4250	2.4	2268	19.9
31241	850	24.6	4250	2.4	2310	19.9
31146	900	26.0	4500	3.1	2025	19.8
31147	900	26.0	4500	3.1	2070	19.8
31148	900	26.0	4500	3.1	2115	19.8
31149	900	26.0	4500	3.1	2160	19.8
31150	900	26.0	4500	3.1	2205	19.8
31430	750	22.3	3750	1.7	1998	18.9
31100	950	26.7	4750	4.0	3760	18.7
31542	700	20.8	3500	1.1	2030	18.5
31543	700	20.8	3500	1.1	2065	18.5
31544	700	20.8	3500	1.1	2100	18.5
31432	750	22.3	3750	2.0	2072	18.3
31335	800	23.1	4000	2.5	2280	18.1
31336	800	23.1	4000	2.5	2320	18.1
31337	800	23.1	4000	2.5	2360	18.1
31662	650	19.3	3250	1.2	2016	16.9
31663	650	19.3	3250	1.2	2048	16.9
31664	650	19.3	3250	1.2	2080	16.9
31665	650	19.3	3250	1.2	2112	16.9
31666	650	19.3	3250	1.2	2144	16.9
31437	750	21.7	3750	2.7	2257	16.3
31438	750	21.7	3750	2.7	2294	16.3
31439	750	21.7	3750	2.7	2331	16.3
31440	750	21.7	3750	2.7	2368	16.3
31441	750	21.7	3750	2.7	2405	16.3
31541	700	20.8	3500	2.3	1995	16.3
31851	600	17.4	3000	1.0	3750	15.4
32003	550	16.4	2750	0.5	3753	15.3
31793	600	17.9	3000	1.3	2010	15.2
31794	600	17.9	3000	1.3	2040	15.2
31795	600	17.9	3000	1.3	2070	15.2
31796	600	17.9	3000	1.3	2100	15.2
31797	600	17.9	3000	1.3	2130	15.2
31798	600	17.9	3000	1.3	2160	15.2
31799	600	17.9	3000	1.3	2190	15.2
31549	700	20.2	3500	2.9	2275	14.5
31550	700	20.2	3500	2.9	2310	14.5
31551	700	20.2	3500	2.9	2345	14.5
31552	700	20.2	3500	2.9	2380	14.5
31553	700	20.2	3500	2.9	2415	14.5
31554	700	20.2	3500	2.9	2450	14.5
32072	500	15.8	2500	0.8	1325	14.2
31667	650	19.3	3250	2.9	2176	13.5
31939	550	16.4	2750	1.5	2025	13.5
31940	550	16.4	2750	1.5	2052	13.5
31941	550	16.4	2750	1.5	2079	13.5
31942	550	16.4	2750	1.5	2106	13.5
31943	550	16.4	2750	1.5	2133	13.5
31944	550	16.4	2750	1.5	2160	13.5
31945	550	16.4	2750	1.5	2187	13.5
31670	650	18.8	3250	3.1	2272	12.6
31671	650	18.8	3250	3.1	2304	12.6
31672	650	18.8	3250	3.1	2336	12.6
31673	650	18.8	3250	3.1	2368	12.6
31674	650	18.8	3250	3.1	2400	12.6
31675	650	18.8	3250	3.1	2432	12.6
31676	650	18.8	3250	3.1	2464	12.6
31677	650	18.8	3250	3.1	2496	12.6
32107	500	15.4	2500	1.6	2200	12.2
32169	500	14.5	2500	1.2	3750	12.1
31716	650	16.8	3250	2.5	3744	11.9
32073	500	15.8	2500	2.0	1350	11.8
32100	500	14.9	2500	1.6	2025	11.7
32101	500	14.9	2500	1.6	2050	11.7
32102	500	14.9	2500	1.6	2075	11.7
32103	500	14.9	2500	1.6	2100	11.7
32104	500	14.9	2500	1.6	2125	11.7
32105	500	14.9	2500	1.6	2150	11.7
32106	500	14.9	2500	1.6	2175	11.7
31938	550	16.4	2750	2.4	1998	11.6
31661	650	19.3	3250	4.2	1984	11.0
31811	600	17.3	3000	3.3	2550	10.7
31613	650	17.0	3250	3.2	448	10.6
31614	650	17.0	3250	3.2	480	10.6
32099	500	14.9	2500	2.2	2000	10.5
31742	600	15.7	3000	3.5	480	8.7
31743	600	15.7	3000	3.5	510	8.7
31744	600	14.0	3000	3.5	540	7.0
31881	550	14.4	2750	3.8	459	6.8
31882	550	14.4	2750	3.8	486	6.8
31883	550	14.4	2750	3.8	513	6.8
31884	550	14.4	2750	3.8	540	6.8
31885	550	14.4	2750	3.8	567	6.8
32125	500	14.5	2500	4.0	2650	6.5
31961	550	15.9	2750	4.7	2619	6.4
30584	1300	14.8	6500	4.2	455	6.3
30585	1300	14.8	6500	4.2	520	6.3
31497	700	12.1	3500	3.0	455	6.1
30889	1050	11.9	5250	3.2	780	5.5
32038	500	13.1	2500	4.2	475	4.7
32039	500	13.1	2500	4.2	500	4.7
32040	500	13.1	2500	4.2	525	4.7
32041	500	13.1	2500	4.2	550	4.7
32042	500	13.1	2500	4.2	575	4.7
32043	500	13.1	2500	4.2	600	4.7
32044	500	13.1	2500	4.2	625	4.7
30961	1000	11.4	5000	3.4	800	4.6
30960	1000	11.4	5000	3.6	750	4.2
31886	550	11.8	2750	3.8	594	4.1
31036	950	10.8	4750	3.6	752	3.6
31037	950	10.8	4750	3.6	799	3.6
31038	950	10.8	4750	3.6	846	3.6
31615	650	10.0	3250	3.2	512	3.6
30757	1150	13.1	5750	4.8	684	3.5
31039	950	10.8	4750	3.9	893	3.0
31118	900	10.2	4500	3.8	765	2.7
31119	900	10.2	4500	3.8	810	2.7
31120	900	10.2	4500	3.8	855	2.7
31121	900	10.2	4500	3.8	900	2.7
30962	1000	11.4	5000	4.4	850	2.6
31122	900	10.2	4500	4.3	945	1.6

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
31234	850	24.9	4250	3.3	2016	18.3
31235	850	24.6	4250	3.3	2058	18.0
31236	850	24.6	4250	3.3	2100	18.0
31237	850	24.6	4250	3.3	2142	18.0
31238	850	24.6	4250	3.3	2184	18.0
31239	850	24.6	4250	3.3	2226	18.0
31185	900	25.3	4500	4.2	3780	16.8
31329	800	23.8	4000	3.5	2040	16.8
31330	800	23.1	4000	3.5	2080	16.1
31331	800	23.1	4000	3.5	2120	16.1
31332	800	23.1	4000	3.5	2160	16.1
31333	800	23.1	4000	3.5	2200	16.1
31334	800	23.1	4000	3.5	2240	16.1
31276	850	23.9	4250	4.5	3780	14.9
31277	850	23.9	4250	4.5	3822	14.9
31433	750	21.9	3750	3.7	2109	14.5
31434	750	21.7	3750	3.7	2146	14.2
31435	750	21.7	3750	3.7	2183	14.2
31436	750	21.7	3750	3.7	2220	14.2
31372	800	22.5	4000	4.8	3760	13.0
31373	800	22.5	4000	4.8	3800	13.0
31374	800	22.5	4000	4.8	3840	13.0
31375	800	22.5	4000	4.8	3880	13.0
31545	700	20.8	3500	4.0	2135	12.8
31546	700	20.2	3500	4.0	2170	12.2
31547	700	20.2	3500	4.0	2205	12.2
31548	700	20.2	3500	4.0	2240	12.2
31801	600	17.9	3000	3.3	2250	11.2
31802	600	17.3	3000	3.3	2280	10.7
31803	600	17.3	3000	3.3	2310	10.7
31804	600	17.3	3000	3.3	2340	10.7
31805	600	17.3	3000	3.3	2370	10.7
31806	600	17.3	3000	3.3	2400	10.7
31807	600	17.3	3000	3.3	2430	10.7
31808	600	17.3	3000	3.3	2460	10.7
31809	600	17.3	3000	3.3	2490	10.7
31810	600	17.3	3000	3.3	2520	10.7
31668	650	19.0	3250	4.3	2208	10.4
31949	550	17.6	2750	3.6	2295	10.4
31669	650	18.8	3250	4.3	2240	10.2
31741	600	15.7	3000	3.5	450	8.7
31950	550	15.9	2750	3.6	2322	8.6
31951	550	15.9	2750	3.6	2349	8.6
31952	550	15.9	2750	3.6	2376	8.6
31953	550	15.9	2750	3.6	2403	8.6
31954	550	15.9	2750	3.6	2430	8.6
31955	550	15.9	2750	3.6	2457	8.6
31956	550	15.9	2750	3.6	2484	8.6
31957	550	15.9	2750	3.6	2511	8.6
31958	550	15.9	2750	3.6	2538	8.6
31959	550	15.9	2750	3.6	2565	8.6
31960	550	15.9	2750	3.6	2592	8.6
32113	500	14.9	2500	4.0	2350	6.9
32114	500	14.5	2500	4.0	2375	6.5
32115	500	14.5	2500	4.0	2400	6.5
32116	500	14.5	2500	4.0	2425	6.5
32117	500	14.5	2500	4.0	2450	6.5
32118	500	14.5	2500	4.0	2475	6.5
32119	500	14.5	2500	4.0	2500	6.5
32120	500	14.5	2500	4.0	2525	6.5
32121	500	14.5	2500	4.0	2550	6.5
32122	500	14.5	2500	4.0	2575	6.5
32123	500	14.5	2500	4.0	2600	6.5
32124	500	14.5	2500	4.0	2625	6.5
30638	1250	14.2	6250	4.4	496	5.4
30639	1250	14.2	6250	4.4	558	5.4
32037	500	13.1	2500	4.2	450	4.7
30694	1200	13.6	6000	4.6	480	4.5
30695	1200	13.6	6000	4.6	540	4.5
30696	1200	13.6	6000	4.6	600	4.5
30753	1150	13.1	5750	4.8	456	3.5
30754	1150	13.1	5750	4.8	513	3.5
30755	1150	13.1	5750	4.8	570	3.5
30756	1150	13.1	5750	4.8	627	3.5
30817	1100	12.5	5500	5.0	495	2.5
30818	1100	12.5	5500	5.0	550	2.5
30819	1100	12.5	5500	5.0	605	2.5
30820	1100	12.5	5500	5.0	660	2.5
30821	1100	12.5	5500	5.0	715	2.5

Overall score = score_ratio - 2 * repetitive DNA content