Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign56 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (29)
Redundant probes (241)

Summary

`./analyse_probe_search_results : Thu Sep 29 17:21:25 2005`

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

Fetched probe design: ProbeDesign56
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 11
  id            : 43
  strand        : 1
  -------------

Design window length: 3501bp

All jobs for probe design are successful - total: 56
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1114 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        : 1114/1114
Putative probes exceeding selection criteria: 270/1114

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
45034	1300	40.9	6500	0.7	1560	39.5
45035	1300	40.9	6500	0.7	1625	39.5
45036	1300	40.9	6500	0.7	1690	39.5
45070	1250	39.3	6250	0.7	1612	37.9
45111	1200	37.7	6000	0.8	1800	36.2
45037	1300	38.2	6500	1.7	1755	34.9
45038	1300	35.5	6500	1.7	1820	32.1
45039	1300	35.5	6500	1.7	1885	32.1
45040	1300	35.5	6500	2.5	1950	30.6
45041	1300	35.5	6500	2.5	2015	30.6
45042	1300	35.5	6500	2.5	2080	30.6
45043	1300	35.5	6500	2.5	2145	30.6
45294	1000	31.4	5000	0.9	2000	29.6
45080	1250	34.2	6250	2.6	2232	29.0
45156	1150	31.4	5750	1.9	2052	27.6
45200	1100	30.1	5500	2.0	2090	26.1
45161	1150	31.4	5750	2.8	2337	25.9
45407	900	28.3	4500	1.7	2115	25.0
45469	850	26.7	4250	1.1	2142	24.6
45298	1000	27.3	5000	2.2	2200	22.9
45537	800	25.2	4000	1.1	2200	22.9
45253	1050	28.7	5250	3.0	2444	22.6
45353	950	26.0	4750	2.3	2256	21.3
45611	750	23.6	3750	1.2	2257	21.2
45304	1000	27.3	5000	3.2	2500	20.9
45411	900	24.6	4500	2.4	2295	19.7
45691	700	22.0	3500	1.4	2310	19.2
45876	600	18.9	3000	1.5	2400	15.9
45984	550	17.3	2750	1.6	2457	14.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
45071	1250	39.3	6250	0.7	1674	37.9
45072	1250	39.3	6250	0.7	1736	37.9
45109	1200	37.7	6000	0.8	1680	36.2
45110	1200	37.7	6000	0.8	1740	36.2
45150	1150	36.2	5750	0.8	1710	34.6
45151	1150	36.2	5750	0.8	1767	34.6
45152	1150	36.2	5750	0.8	1824	34.6
45073	1250	36.8	6250	1.8	1798	33.2
45194	1100	34.6	5500	0.8	1760	33.0
45195	1100	34.6	5500	0.8	1815	33.0
45196	1100	34.6	5500	0.8	1870	33.0
45241	1050	33.0	5250	0.9	1820	31.3
45242	1050	33.0	5250	0.9	1872	31.3
45243	1050	33.0	5250	0.9	1924	31.3
45153	1150	34.8	5750	1.9	1881	31.0
45112	1200	34.7	6000	1.8	1860	31.0
45074	1250	34.2	6250	1.8	1860	30.6
45075	1250	34.2	6250	1.8	1922	30.6
45292	1000	31.4	5000	0.9	1900	29.6
45293	1000	31.4	5000	0.9	1950	29.6
45197	1100	33.3	5500	2.0	1925	29.3
45113	1200	32.8	6000	1.8	1920	29.1
45114	1200	32.8	6000	1.8	1980	29.1
45076	1250	34.2	6250	2.6	1984	29.0
45077	1250	34.2	6250	2.6	2046	29.0
45078	1250	34.2	6250	2.6	2108	29.0
45079	1250	34.2	6250	2.6	2170	29.0
45346	950	29.9	4750	0.9	1927	28.0
45347	950	29.9	4750	0.9	1974	28.0
45348	950	29.9	4750	0.9	2021	28.0
45244	1050	31.8	5250	2.1	1976	27.6
45154	1150	31.4	5750	1.9	1938	27.6
45155	1150	31.4	5750	1.9	1995	27.6
45115	1200	32.8	6000	2.7	2040	27.5
45116	1200	32.8	6000	2.7	2100	27.5
45117	1200	32.8	6000	2.7	2160	27.5
45118	1200	32.8	6000	2.7	2220	27.5
45119	1200	32.8	6000	2.7	2280	27.5
45404	900	28.3	4500	1.0	1980	26.3
45405	900	28.3	4500	1.0	2025	26.3
45406	900	28.3	4500	1.0	2070	26.3
45349	950	29.9	4750	1.9	2068	26.1
45198	1100	30.1	5500	2.0	1980	26.1
45199	1100	30.1	5500	2.0	2035	26.1
45157	1150	31.4	5750	2.8	2109	25.9
45158	1150	31.4	5750	2.8	2166	25.9
45159	1150	31.4	5750	2.8	2223	25.9
45160	1150	31.4	5750	2.8	2280	25.9
45295	1000	29.4	5000	2.2	2050	25.0
45466	850	26.7	4250	1.1	2016	24.6
45467	850	26.7	4250	1.1	2058	24.6
45468	850	26.7	4250	1.1	2100	24.6
45245	1050	28.7	5250	2.1	2028	24.5
45246	1050	28.7	5250	2.1	2080	24.5
45247	1050	28.7	5250	2.1	2132	24.5
45201	1100	30.1	5500	2.9	2145	24.2
45202	1100	30.1	5500	2.9	2200	24.2
45203	1100	30.1	5500	2.9	2255	24.2
45204	1100	30.1	5500	2.9	2310	24.2
45205	1100	30.1	5500	2.9	2365	24.2
45296	1000	27.3	5000	2.2	2100	22.9
45297	1000	27.3	5000	2.2	2150	22.9
45534	800	25.2	4000	1.1	2080	22.9
45535	800	25.2	4000	1.1	2120	22.9
45536	800	25.2	4000	1.1	2160	22.9
45248	1050	28.7	5250	3.0	2184	22.6
45249	1050	28.7	5250	3.0	2236	22.6
45250	1050	28.7	5250	3.0	2288	22.6
45251	1050	28.7	5250	3.0	2340	22.6
45252	1050	28.7	5250	3.0	2392	22.6
45350	950	26.0	4750	2.3	2115	21.3
45351	950	26.0	4750	2.3	2162	21.3
45352	950	26.0	4750	2.3	2209	21.3
45607	750	23.6	3750	1.2	2109	21.2
45608	750	23.6	3750	1.2	2146	21.2
45609	750	23.6	3750	1.2	2183	21.2
45610	750	23.6	3750	1.2	2220	21.2
45408	900	26.0	4500	2.4	2160	21.1
45299	1000	27.3	5000	3.2	2250	20.9
45300	1000	27.3	5000	3.2	2300	20.9
45301	1000	27.3	5000	3.2	2350	20.9
45302	1000	27.3	5000	3.2	2400	20.9
45303	1000	27.3	5000	3.2	2450	20.9
45470	850	25.8	4250	2.6	2184	20.6
45409	900	24.6	4500	2.4	2205	19.7
45410	900	24.6	4500	2.4	2250	19.7
45687	700	22.0	3500	1.3	2170	19.4
45688	700	22.0	3500	1.3	2205	19.4
45689	700	22.0	3500	1.3	2240	19.4
45690	700	22.0	3500	1.3	2275	19.4
45354	950	26.0	4750	3.4	2303	19.2
45355	950	26.0	4750	3.4	2350	19.2
45356	950	26.0	4750	3.4	2397	19.2
45357	950	26.0	4750	3.4	2444	19.2
45358	950	26.0	4750	3.4	2491	19.2
45359	950	26.0	4750	3.4	2538	19.2
45538	800	24.1	4000	2.8	2240	18.6
45471	850	23.2	4250	2.6	2226	18.0
45472	850	23.2	4250	2.6	2268	18.0
45473	850	23.2	4250	2.6	2310	18.0
45474	850	23.2	4250	2.6	2352	18.0
45775	650	20.4	3250	1.4	2208	17.7
45776	650	20.4	3250	1.4	2240	17.7
45777	650	20.4	3250	1.4	2272	17.7
45778	650	20.4	3250	1.4	2304	17.7
45779	650	20.4	3250	1.4	2336	17.7
45412	900	24.6	4500	3.6	2340	17.5
45413	900	24.6	4500	3.6	2385	17.5
45414	900	24.6	4500	3.6	2430	17.5
45415	900	24.6	4500	3.6	2475	17.5
45416	900	24.6	4500	3.6	2520	17.5
45417	900	24.6	4500	3.6	2565	17.5
45539	800	21.9	4000	2.8	2280	16.4
45540	800	21.9	4000	2.8	2320	16.4
45541	800	21.9	4000	2.8	2360	16.4
45542	800	21.9	4000	2.8	2400	16.4
45612	750	22.1	3750	2.9	2294	16.2
45549	800	21.9	4000	2.9	2680	16.1
45872	600	18.9	3000	1.5	2280	15.9
45873	600	18.9	3000	1.5	2310	15.9
45874	600	18.9	3000	1.5	2340	15.9
45875	600	18.9	3000	1.5	2370	15.9
45475	850	23.2	4250	3.8	2394	15.7
45476	850	23.2	4250	3.8	2436	15.7
45477	850	23.2	4250	3.8	2478	15.7
45478	850	23.2	4250	3.8	2520	15.7
45479	850	23.2	4250	3.8	2562	15.7
45480	850	23.2	4250	3.8	2604	15.7
45481	850	23.2	4250	3.8	2646	15.7
45780	650	20.4	3250	2.8	2368	14.9
45613	750	20.5	3750	2.9	2331	14.6
45614	750	20.5	3750	2.9	2368	14.6
45615	750	20.5	3750	2.9	2405	14.6
45616	750	20.5	3750	2.9	2442	14.6
45623	750	20.5	3750	3.1	2701	14.4
45624	750	20.5	3750	3.1	2738	14.4
45692	700	20.6	3500	3.1	2345	14.3
45979	550	17.3	2750	1.6	2322	14.0
45980	550	17.3	2750	1.6	2349	14.0
45981	550	17.3	2750	1.6	2376	14.0
45982	550	17.3	2750	1.6	2403	14.0
45983	550	17.3	2750	1.6	2430	14.0
45543	800	21.9	4000	4.0	2440	13.9
45544	800	21.9	4000	4.0	2480	13.9
45545	800	21.9	4000	4.0	2520	13.9
45546	800	21.9	4000	4.0	2560	13.9
45547	800	21.9	4000	4.0	2600	13.9
45548	800	21.9	4000	4.0	2640	13.9
45693	700	19.1	3500	3.1	2380	12.8
45694	700	19.1	3500	3.1	2415	12.8
45695	700	19.1	3500	3.1	2450	12.8
45696	700	19.1	3500	3.1	2485	12.8
45702	700	19.1	3500	3.3	2695	12.6
45703	700	19.1	3500	3.3	2730	12.6
45704	700	19.1	3500	3.3	2765	12.6
45705	700	19.1	3500	3.3	2800	12.6
45781	650	19.1	3250	3.4	2400	12.3
46098	500	15.7	2500	1.8	2375	12.1
46099	500	15.7	2500	1.8	2400	12.1
46100	500	15.7	2500	1.8	2425	12.1
46101	500	15.7	2500	1.8	2450	12.1
46102	500	15.7	2500	1.8	2475	12.1
46103	500	15.7	2500	1.8	2500	12.1
45697	700	19.1	3500	3.6	2520	12.0
45617	750	20.5	3750	4.3	2479	12.0
45618	750	20.5	3750	4.3	2516	12.0
45619	750	20.5	3750	4.3	2553	12.0
45620	750	20.5	3750	4.3	2590	12.0
45621	750	20.5	3750	4.3	2627	12.0
45622	750	20.5	3750	4.3	2664	12.0
45782	650	17.8	3250	3.4	2432	11.0
45783	650	17.8	3250	3.4	2464	11.0
45784	650	17.8	3250	3.4	2496	11.0
45785	650	17.8	3250	3.4	2528	11.0
45786	650	17.8	3250	3.4	2560	11.0
45877	600	18.2	3000	3.7	2430	10.8
45790	650	17.8	3250	3.5	2688	10.7
45791	650	17.8	3250	3.5	2720	10.7
45792	650	17.8	3250	3.5	2752	10.7
45793	650	17.8	3250	3.5	2784	10.7
45794	650	17.8	3250	3.5	2816	10.7
45795	650	17.8	3250	3.5	2848	10.7
45878	600	17.3	3000	3.7	2460	10.0
45698	700	19.1	3500	4.6	2555	10.0
45699	700	19.1	3500	4.6	2590	10.0
45700	700	19.1	3500	4.6	2625	10.0
45701	700	19.1	3500	4.6	2660	10.0
45879	600	16.4	3000	3.7	2490	9.1
45880	600	16.4	3000	3.7	2520	9.1
45881	600	16.4	3000	3.7	2550	9.1
45882	600	16.4	3000	3.7	2580	9.1
45883	600	16.4	3000	3.7	2610	9.1
45886	600	16.4	3000	3.8	2700	8.7
45887	600	16.4	3000	3.8	2730	8.7
45888	600	16.4	3000	3.8	2760	8.7
45889	600	16.4	3000	3.8	2790	8.7
45890	600	16.4	3000	3.8	2820	8.7
45891	600	16.4	3000	3.8	2850	8.7
45892	600	16.4	3000	3.8	2880	8.7
45985	550	16.7	2750	4.0	2484	8.7
46110	500	13.7	2500	2.6	2675	8.5
46111	500	13.7	2500	2.6	2700	8.5
45787	650	17.8	3250	4.9	2592	7.9
45788	650	17.8	3250	4.9	2624	7.9
45789	650	17.8	3250	4.9	2656	7.9
45986	550	15.4	2750	4.0	2511	7.4
45992	550	15.0	2750	3.8	2673	7.4
45885	600	16.4	3000	4.7	2670	7.1
45987	550	15.0	2750	4.0	2538	7.0
45988	550	15.0	2750	4.0	2565	7.0
45989	550	15.0	2750	4.0	2592	7.0
45990	550	15.0	2750	4.0	2619	7.0
45991	550	15.0	2750	4.0	2646	7.0
45993	550	15.0	2750	4.2	2700	6.7
45994	550	15.0	2750	4.2	2727	6.7
45995	550	15.0	2750	4.2	2754	6.7
45996	550	15.0	2750	4.2	2781	6.7
45997	550	15.0	2750	4.2	2808	6.7
45998	550	15.0	2750	4.2	2835	6.7
45999	550	15.0	2750	4.2	2862	6.7
46000	550	15.0	2750	4.2	2889	6.7
46001	550	15.0	2750	4.2	2916	6.7
46002	550	15.0	2750	4.2	2943	6.7
46123	500	15.6	2500	4.6	3000	6.4
46104	500	15.2	2500	4.4	2525	6.4
46105	500	14.7	2500	4.4	2550	5.9
46122	500	14.8	2500	4.6	2975	5.6
46112	500	13.7	2500	4.2	2725	5.3
46106	500	13.7	2500	4.4	2575	4.9
46107	500	13.7	2500	4.4	2600	4.9
46108	500	13.7	2500	4.4	2625	4.9
46109	500	13.7	2500	4.4	2650	4.9
46113	500	13.7	2500	4.6	2750	4.5
46114	500	13.7	2500	4.6	2775	4.5
46115	500	13.7	2500	4.6	2800	4.5
46116	500	13.7	2500	4.6	2825	4.5
46117	500	13.7	2500	4.6	2850	4.5
46118	500	13.7	2500	4.6	2875	4.5
46119	500	13.7	2500	4.6	2900	4.5
46120	500	13.7	2500	4.6	2925	4.5
46121	500	13.7	2500	4.6	2950	4.5

Overall score = score_ratio - 2 * repetitive DNA content