Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign42 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (295)
Redundant probes (8)

Summary

`./analyse_probe_search_results : Tue Sep 13 14:29:52 2005`

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

Fetched probe design: ProbeDesign42
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : X
  id            : 24
  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: 303/1114

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
26207	1150	35.7	5750	-	2337	35.7
26251	1100	34.2	5500	-	2365	34.2
26206	1150	35.1	5750	0.8	2280	33.5
26250	1100	34.2	5500	0.5	2310	33.3
26297	1050	32.6	5250	-	2340	32.6
26298	1050	32.6	5250	-	2392	32.6
26299	1050	32.6	5250	-	2444	32.6
26126	1250	34.0	6250	0.7	2232	32.5
26249	1100	33.5	5500	0.8	2255	31.9
26347	1000	31.1	5000	-	2350	31.1
26348	1000	31.1	5000	-	2400	31.1
26349	1000	31.1	5000	-	2450	31.1
26089	1300	33.5	6500	1.2	2145	31.0
26125	1250	32.2	6250	0.7	2170	30.8
26350	1000	31.1	5000	0.3	2500	30.5
26296	1050	32.0	5250	0.9	2288	30.3
26401	950	29.5	4750	-	2350	29.5
26402	950	29.5	4750	-	2397	29.5
26403	950	29.5	4750	-	2444	29.5
26404	950	29.5	4750	-	2491	29.5
26405	950	29.5	4750	-	2538	29.5
26163	1200	30.9	6000	0.8	2160	29.4
26164	1200	30.9	6000	0.8	2220	29.4
26346	1000	31.1	5000	0.9	2300	29.3
26345	1000	30.5	5000	0.9	2250	28.7
26204	1150	29.6	5750	0.8	2166	28.1
26205	1150	29.6	5750	0.8	2223	28.1
26458	900	28.0	4500	-	2340	28.0
26459	900	28.0	4500	-	2385	28.0
26460	900	28.0	4500	-	2430	28.0
26461	900	28.0	4500	-	2475	28.0
26462	900	28.0	4500	-	2520	28.0
26463	900	28.0	4500	-	2565	28.0
26295	1050	29.7	5250	0.9	2236	27.9
26400	950	29.5	4750	0.9	2303	27.6
26248	1100	28.4	5500	0.8	2200	26.7
26521	850	26.4	4250	-	2394	26.4
26522	850	26.4	4250	-	2436	26.4
26523	850	26.4	4250	-	2478	26.4
26524	850	26.4	4250	-	2520	26.4
26525	850	26.4	4250	-	2562	26.4
26526	850	26.4	4250	-	2604	26.4
26527	850	26.4	4250	-	2646	26.4
26519	850	27.4	4250	0.6	2310	26.2
26520	850	26.2	4250	-	2352	26.2
26586	800	26.0	4000	-	2320	26.0
26587	800	25.8	4000	-	2360	25.8
26588	800	25.8	4000	-	2400	25.8
26484	850	25.8	4250	-	840	25.8
26399	950	27.6	4750	0.9	2256	25.7
26247	1100	28.4	5500	1.5	2145	25.4
26456	900	27.4	4500	1.0	2250	25.4
26457	900	27.4	4500	1.0	2295	25.4
26294	1050	27.1	5250	0.9	2184	25.3
26485	850	25.8	4250	0.2	882	25.3
26589	800	24.8	4000	-	2440	24.8
26590	800	24.8	4000	-	2480	24.8
26591	800	24.8	4000	-	2520	24.8
26592	800	24.8	4000	-	2560	24.8
26593	800	24.8	4000	-	2600	24.8
26594	800	24.8	4000	-	2640	24.8
26595	800	24.8	4000	-	2680	24.8
26659	750	24.4	3750	-	2331	24.4
26660	750	24.4	3750	-	2368	24.4
26549	800	24.2	4000	-	840	24.2
26550	800	24.2	4000	-	880	24.2
26551	800	24.2	4000	-	920	24.2
26661	750	24.2	3750	-	2405	24.2
26662	750	24.2	3750	-	2442	24.2
26344	1000	25.8	5000	0.9	2200	24.0
26518	850	25.9	4250	1.1	2268	23.8
26124	1250	32.2	6250	4.2	2108	23.7
26343	1000	25.8	5000	1.1	2150	23.6
26663	750	23.3	3750	-	2479	23.3
26664	750	23.3	3750	-	2516	23.3
26665	750	23.3	3750	-	2553	23.3
26666	750	23.3	3750	-	2590	23.3
26667	750	23.3	3750	-	2627	23.3
26668	750	23.3	3750	-	2664	23.3
26669	750	23.3	3750	-	2701	23.3
26670	750	23.3	3750	-	2738	23.3
26739	700	23.2	3500	-	2380	23.2
26740	700	23.2	3500	-	2415	23.2
26741	700	23.2	3500	-	2450	23.2
26088	1300	32.7	6500	4.8	2080	23.0
26619	750	22.7	3750	-	851	22.7
26620	750	22.7	3750	-	888	22.7
26621	750	22.7	3750	-	925	22.7
26622	750	22.7	3750	-	962	22.7
26738	700	22.7	3500	-	2345	22.7
26397	950	24.5	4750	0.9	2162	22.6
26398	950	24.5	4750	0.9	2209	22.6
26742	700	22.6	3500	-	2485	22.6
26585	800	24.4	4000	1.1	2280	22.1
26743	700	21.7	3500	-	2520	21.7
26744	700	21.7	3500	-	2555	21.7
26745	700	21.7	3500	-	2590	21.7
26746	700	21.7	3500	-	2625	21.7
26747	700	21.7	3500	-	2660	21.7
26748	700	21.7	3500	-	2695	21.7
26749	700	21.7	3500	-	2730	21.7
26750	700	21.7	3500	-	2765	21.7
26425	900	27.3	4500	2.8	855	21.7
26293	1050	27.1	5250	2.8	2132	21.5
26827	650	21.5	3250	-	2400	21.5
26828	650	21.5	3250	-	2432	21.5
26829	650	21.5	3250	-	2464	21.5
26830	650	21.5	3250	-	2496	21.5
26737	700	22.7	3500	0.7	2310	21.3
26695	700	21.2	3500	-	840	21.2
26696	700	21.2	3500	-	875	21.2
26697	700	21.2	3500	-	910	21.2
26698	700	21.2	3500	-	945	21.2
26699	700	21.2	3500	-	980	21.2
26700	700	21.2	3500	-	1015	21.2
26454	900	23.2	4500	1.0	2160	21.2
26455	900	23.2	4500	1.0	2205	21.2
26825	650	21.1	3250	-	2336	21.1
26826	650	21.1	3250	-	2368	21.1
26584	800	23.3	4000	1.1	2240	21.0
26831	650	21.0	3250	-	2528	21.0
26203	1150	29.6	5750	4.5	2109	20.6
26657	750	22.9	3750	1.2	2257	20.5
26658	750	22.9	3750	1.2	2294	20.5
26833	650	20.2	3250	-	2592	20.2
26834	650	20.2	3250	-	2624	20.2
26835	650	20.2	3250	-	2656	20.2
26836	650	20.2	3250	-	2688	20.2
26837	650	20.2	3250	-	2720	20.2
26838	650	20.2	3250	-	2752	20.2
26839	650	20.2	3250	-	2784	20.2
26840	650	20.2	3250	-	2816	20.2
26841	650	20.2	3250	0.2	2848	19.9
26922	600	19.9	3000	-	2400	19.9
26923	600	19.9	3000	-	2430	19.9
26924	600	19.9	3000	-	2460	19.9
26925	600	19.9	3000	-	2490	19.9
26926	600	19.9	3000	-	2520	19.9
26927	600	19.9	3000	-	2550	19.9
26516	850	21.9	4250	1.1	2184	19.8
26517	850	21.9	4250	1.1	2226	19.8
26779	650	19.7	3250	-	864	19.7
26780	650	19.7	3250	-	896	19.7
26781	650	19.7	3250	-	928	19.7
26782	650	19.7	3250	-	960	19.7
26783	650	19.7	3250	-	992	19.7
26784	650	19.7	3250	-	1024	19.7
26785	650	19.7	3250	-	1056	19.7
26920	600	19.5	3000	-	2340	19.5
26921	600	19.5	3000	-	2370	19.5
26928	600	19.4	3000	-	2580	19.4
26736	700	21.3	3500	1.3	2275	18.8
26832	650	18.7	3250	-	2560	18.7
26930	600	18.6	3000	-	2640	18.6
26931	600	18.6	3000	-	2670	18.6
26932	600	18.6	3000	-	2700	18.6
26933	600	18.6	3000	-	2730	18.6
26934	600	18.6	3000	-	2760	18.6
26935	600	18.6	3000	-	2790	18.6
26936	600	18.6	3000	-	2820	18.6
26937	600	18.6	3000	-	2850	18.6
26938	600	18.6	3000	-	2880	18.6
26582	800	20.6	4000	1.1	2160	18.4
26583	800	20.6	4000	1.1	2200	18.4
26824	650	21.1	3250	1.4	2304	18.3
27027	550	18.2	2750	-	2376	18.2
27028	550	18.2	2750	-	2403	18.2
27029	550	18.2	2750	-	2430	18.2
27030	550	18.2	2750	-	2457	18.2
27031	550	18.2	2750	-	2484	18.2
27032	550	18.2	2750	-	2511	18.2
27033	550	18.2	2750	-	2538	18.2
27034	550	18.2	2750	-	2565	18.2
27035	550	18.2	2750	-	2592	18.2
26870	600	18.2	3000	-	840	18.2
26871	600	18.2	3000	-	870	18.2
26872	600	18.2	3000	-	900	18.2
26873	600	18.2	3000	-	930	18.2
26874	600	18.2	3000	-	960	18.2
26875	600	18.2	3000	-	990	18.2
26876	600	18.2	3000	-	1020	18.2
26877	600	18.2	3000	-	1050	18.2
26878	600	18.2	3000	-	1080	18.2
26879	600	18.2	3000	-	1110	18.2
27025	550	17.9	2750	-	2322	17.9
27026	550	17.9	2750	-	2349	17.9
26919	600	19.5	3000	0.8	2310	17.8
26735	700	20.3	3500	1.3	2240	17.8
27036	550	17.7	2750	-	2619	17.7
27037	550	17.7	2750	-	2646	17.7
26623	750	22.7	3750	2.5	999	17.7
26515	850	21.9	4250	2.2	2142	17.4
26929	600	17.2	3000	-	2610	17.2
26778	650	19.7	3250	1.2	832	17.2
26786	650	19.7	3250	1.2	1088	17.2
27038	550	17.1	2750	-	2673	17.1
27039	550	17.1	2750	-	2700	17.1
27040	550	17.1	2750	-	2727	17.1
27041	550	17.1	2750	-	2754	17.1
27042	550	17.1	2750	-	2781	17.1
27043	550	17.1	2750	-	2808	17.1
27044	550	17.1	2750	-	2835	17.1
27045	550	17.1	2750	-	2862	17.1
27046	550	17.1	2750	-	2889	17.1
27047	550	17.1	2750	-	2916	17.1
27048	550	17.1	2750	-	2943	17.1
26823	650	19.8	3250	1.4	2272	17.0
26655	750	19.3	3750	1.2	2183	16.9
26656	750	19.3	3750	1.2	2220	16.9
26552	800	24.2	4000	3.8	960	16.7
26971	550	16.7	2750	-	864	16.7
26972	550	16.7	2750	-	891	16.7
26973	550	16.7	2750	-	918	16.7
26974	550	16.7	2750	-	945	16.7
26975	550	16.7	2750	-	972	16.7
26976	550	16.7	2750	-	999	16.7
26977	550	16.7	2750	-	1026	16.7
26978	550	16.7	2750	-	1053	16.7
26979	550	16.7	2750	-	1080	16.7
26980	550	16.7	2750	-	1107	16.7
26981	550	16.7	2750	-	1134	16.7
26982	550	16.7	2750	-	1161	16.7
27144	500	16.6	2500	-	2375	16.6
27145	500	16.6	2500	-	2400	16.6
27146	500	16.6	2500	-	2425	16.6
27147	500	16.6	2500	-	2450	16.6
27148	500	16.6	2500	-	2475	16.6
27149	500	16.6	2500	-	2500	16.6
27150	500	16.6	2500	-	2525	16.6
27151	500	16.6	2500	-	2550	16.6
27152	500	16.6	2500	-	2575	16.6
27153	500	16.6	2500	-	2600	16.6
27154	500	16.6	2500	-	2625	16.6
27155	500	16.6	2500	-	2650	16.6
27142	500	16.2	2500	-	2325	16.2
27143	500	16.2	2500	-	2350	16.2
26424	900	22.4	4500	3.1	810	16.2
27156	500	16.1	2500	-	2675	16.1
27157	500	16.1	2500	-	2700	16.1
26822	650	18.9	3250	1.4	2240	16.1
26970	550	16.7	2750	0.5	837	15.6
27158	500	15.5	2500	-	2725	15.5
27159	500	15.5	2500	-	2750	15.5
27160	500	15.5	2500	-	2775	15.5
27161	500	15.5	2500	-	2800	15.5
27162	500	15.5	2500	-	2825	15.5
27163	500	15.5	2500	-	2850	15.5
27164	500	15.5	2500	-	2875	15.5
27165	500	15.5	2500	-	2900	15.5
27166	500	15.5	2500	-	2925	15.5
27167	500	15.5	2500	-	2950	15.5
27168	500	15.5	2500	-	2975	15.5
26733	700	18.0	3500	1.3	2170	15.5
26734	700	18.0	3500	1.3	2205	15.5
26654	750	19.3	3750	2.0	2146	15.3
26917	600	18.3	3000	1.5	2250	15.3
26918	600	18.3	3000	1.5	2280	15.3
27083	500	15.2	2500	-	850	15.2
27084	500	15.2	2500	-	875	15.2
27085	500	15.2	2500	-	900	15.2
27086	500	15.2	2500	-	925	15.2
27087	500	15.2	2500	-	950	15.2
27088	500	15.2	2500	-	975	15.2
27089	500	15.2	2500	-	1000	15.2
27090	500	15.2	2500	-	1025	15.2
27091	500	15.2	2500	-	1050	15.2
27092	500	15.2	2500	-	1075	15.2
27093	500	15.2	2500	-	1100	15.2
27094	500	15.2	2500	-	1125	15.2
27095	500	15.2	2500	-	1150	15.2
27096	500	15.2	2500	-	1175	15.2
26880	600	18.2	3000	1.7	1140	14.8
26396	950	24.5	4750	4.8	2115	14.8
26820	650	16.8	3250	1.4	2176	14.0
26821	650	16.8	3250	1.4	2208	14.0
27023	550	16.8	2750	1.6	2268	13.5
27024	550	16.8	2750	1.6	2295	13.5
27022	550	16.3	2750	1.6	2241	13.0
27141	500	16.2	2500	1.8	2300	12.6
26914	600	15.5	3000	1.5	2160	12.5
26915	600	15.5	3000	1.5	2190	12.5
26916	600	15.5	3000	1.5	2220	12.5
26483	850	21.1	4250	4.7	798	11.7
27139	500	15.2	2500	1.8	2250	11.6
27140	500	15.2	2500	1.8	2275	11.6
26819	650	16.8	3250	2.6	2144	11.5
27019	550	14.2	2750	1.6	2160	10.9
27020	550	14.2	2750	1.6	2187	10.9
27021	550	14.2	2750	1.6	2214	10.9
26732	700	18.0	3500	3.7	2135	10.6
27136	500	12.9	2500	1.8	2175	9.3
27137	500	12.9	2500	1.8	2200	9.3
27138	500	12.9	2500	1.8	2225	9.3
27082	500	15.2	2500	3.0	825	9.2
27135	500	12.9	2500	2.2	2150	8.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
26165	1200	36.6	6000	0.8	2280	35.1
26751	700	21.7	3500	0.4	2800	20.9
26701	700	21.2	3500	2.9	1050	15.5
27169	500	15.5	2500	0.6	3000	14.3
26618	750	18.7	3750	3.2	814	12.3
26548	800	19.9	4000	4.8	800	10.4
26694	700	17.4	3500	4.7	805	8.0
26869	600	14.9	3000	4.7	810	5.6

Overall score = score_ratio - 2 * repetitive DNA content