Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign71 - back to list

Summary
Image
Unique putative probes (1)
Putative probes (255)
Redundant probes (58)

Summary

`./analyse_probe_search_results : Thu Oct 20 11:04:42 2005`

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

Fetched probe design: ProbeDesign71
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 68
  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 3prime end of design window
  ------------------------

Putative probes without hits                    : 0
Putative probes with single_self_hit            : 1114/1114
Putative probes that are unique                 : 1/1114
Putative probes exceeding selection criteria    : 313/1114 (but not unique)
Putative probes with successfully-picked primers: 266/314

Identified 58 'redundant' probes exceeding selection criteria
(but wholly contained by other probes, and higher repetitive DNA content)

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Unique putative probes

Putative probe ID	Length	Actual	%rep DNA	Distance
66300	500	2500	8.4	575

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
65447	1100	34.0	5500	1.1	605	31.8
65492	1050	32.4	5250	0.9	624	30.7
65541	1000	30.9	5000	0.9	650	29.1
65542	1000	30.9	5000	0.9	700	29.1
65493	1050	32.4	5250	2.4	676	27.6
65540	1000	30.9	5000	1.7	600	27.5
65592	950	29.3	4750	0.9	611	27.4
65593	950	29.3	4750	0.9	658	27.4
65594	950	29.3	4750	0.9	705	27.4
65595	950	29.3	4750	0.9	752	27.4
65648	900	27.8	4500	1.0	630	25.8
65649	900	27.8	4500	1.0	675	25.8
65650	900	27.8	4500	1.0	720	25.8
65651	900	27.8	4500	1.0	765	25.8
65652	900	27.8	4500	1.0	810	25.8
65404	1150	35.5	5750	5.0	570	25.6
65479	1100	30.6	5500	3.2	2365	24.2
65707	850	26.2	4250	1.1	630	24.1
65708	850	26.2	4250	1.1	672	24.1
65709	850	26.2	4250	1.1	714	24.1
65710	850	26.2	4250	1.1	756	24.1
65711	850	26.2	4250	1.1	798	24.1
65712	850	26.2	4250	1.1	840	24.1
65491	1050	32.4	5250	4.3	572	23.8
65526	1050	29.2	5250	3.3	2392	22.5
65527	1050	29.2	5250	3.3	2444	22.5
65772	800	24.7	4000	1.1	640	22.4
65773	800	24.7	4000	1.1	680	22.4
65774	800	24.7	4000	1.1	720	22.4
65775	800	24.7	4000	1.1	760	22.4
65776	800	24.7	4000	1.1	800	22.4
65777	800	24.7	4000	1.1	840	22.4
65778	800	24.7	4000	1.1	880	22.4
65435	1150	31.9	5750	4.8	2337	22.4
65755	850	23.6	4250	1.1	2646	21.5
65576	1000	27.8	5000	3.5	2400	20.8
65577	1000	27.8	5000	3.5	2450	20.8
65578	1000	27.8	5000	3.5	2500	20.8
65841	750	23.1	3750	1.2	629	20.7
65842	750	23.1	3750	1.2	666	20.7
65843	750	23.1	3750	1.2	703	20.7
65844	750	23.1	3750	1.2	740	20.7
65845	750	23.1	3750	1.2	777	20.7
65846	750	23.1	3750	1.2	814	20.7
65847	750	23.1	3750	1.2	851	20.7
65848	750	23.1	3750	1.2	888	20.7
65849	750	23.1	3750	1.2	925	20.7
65647	900	27.8	4500	3.6	585	20.7
65771	800	24.7	4000	2.1	600	20.4
65294	1300	27.7	6500	3.6	650	20.4
65295	1300	27.7	6500	3.6	715	20.4
65917	700	22.9	3500	1.3	630	20.3
65850	750	23.1	3750	1.5	962	20.2
65928	700	21.6	3500	0.7	1015	20.2
66012	650	20.1	3250	-	1024	20.1
66013	650	20.1	3250	-	1056	20.1
65822	800	22.2	4000	1.1	2640	20.0
65823	800	22.2	4000	1.1	2680	20.0
65779	800	24.7	4000	2.4	920	19.9
65706	850	26.2	4250	3.4	588	19.4
65575	1000	27.8	5000	4.2	2350	19.4
65754	850	23.6	4250	2.1	2604	19.4
66011	650	20.1	3250	0.5	992	19.1
65328	1250	26.6	6250	3.8	620	19.1
65331	1250	26.6	6250	3.8	806	19.1
65918	700	21.6	3500	1.3	665	19.0
65919	700	21.6	3500	1.3	700	19.0
65920	700	21.6	3500	1.3	735	19.0
65921	700	21.6	3500	1.3	770	19.0
65922	700	21.6	3500	1.3	805	19.0
65923	700	21.6	3500	1.3	840	19.0
65924	700	21.6	3500	1.3	875	19.0
65925	700	21.6	3500	1.3	910	19.0
65926	700	21.6	3500	1.3	945	19.0
65927	700	21.6	3500	1.3	980	19.0
65630	950	26.4	4750	3.7	2397	19.0
65631	950	26.4	4750	3.7	2444	19.0
65632	950	26.4	4750	3.7	2491	19.0
66104	600	18.5	3000	-	1020	18.5
66105	600	18.5	3000	-	1050	18.5
66106	600	18.5	3000	-	1080	18.5
66107	600	18.5	3000	-	1110	18.5
65999	650	21.2	3250	1.4	608	18.5
66000	650	21.2	3250	1.4	640	18.5
66001	650	21.2	3250	1.4	672	18.5
65895	750	20.8	3750	1.2	2627	18.4
65896	750	20.8	3750	1.2	2664	18.4
65897	750	20.8	3750	1.2	2701	18.4
65898	750	20.8	3750	1.2	2738	18.4
65296	1300	27.7	6500	4.8	780	18.1
66069	650	18.1	3250	-	2848	18.1
65840	750	24.5	3750	3.3	592	17.8
65369	1200	25.5	6000	3.9	840	17.7
65629	950	26.4	4750	4.4	2350	17.5
66002	650	20.1	3250	1.4	704	17.3
66003	650	20.1	3250	1.4	736	17.3
66004	650	20.1	3250	1.4	768	17.3
66005	650	20.1	3250	1.4	800	17.3
66006	650	20.1	3250	1.4	832	17.3
66007	650	20.1	3250	1.4	864	17.3
66008	650	20.1	3250	1.4	896	17.3
66009	650	20.1	3250	1.4	928	17.3
66010	650	20.1	3250	1.4	960	17.3
65687	900	25.0	4500	3.9	2385	17.2
65688	900	25.0	4500	3.9	2430	17.2
65689	900	25.0	4500	3.9	2475	17.2
65690	900	25.0	4500	3.9	2520	17.2
65691	900	25.0	4500	3.9	2565	17.2
66204	550	17.0	2750	-	999	17.0
66205	550	17.0	2750	-	1026	17.0
66206	550	17.0	2750	-	1053	17.0
66207	550	17.0	2750	-	1080	17.0
66208	550	17.0	2750	-	1107	17.0
66209	550	17.0	2750	-	1134	17.0
65974	700	19.4	3500	1.3	2625	16.9
65975	700	19.4	3500	1.3	2660	16.9
65976	700	19.4	3500	1.3	2695	16.9
65977	700	19.4	3500	1.3	2730	16.9
65978	700	19.4	3500	1.3	2765	16.9
65979	700	19.4	3500	1.3	2800	16.9
66103	600	18.5	3000	0.8	990	16.9
65821	800	22.2	4000	2.8	2600	16.7
66165	600	16.7	3000	-	2850	16.7
66166	600	16.7	3000	-	2880	16.7
66210	550	17.0	2750	0.2	1161	16.6
66091	600	19.6	3000	1.5	630	16.6
66092	600	19.6	3000	1.5	660	16.6
66093	600	19.6	3000	1.5	690	16.6
66094	600	19.6	3000	1.5	720	16.6
65916	700	22.9	3500	3.1	595	16.6
65365	1200	25.5	6000	4.6	600	16.4
65410	1150	24.5	5750	4.1	912	16.3
66095	600	18.5	3000	1.5	750	15.5
66096	600	18.5	3000	1.5	780	15.5
66097	600	18.5	3000	1.5	810	15.5
66098	600	18.5	3000	1.5	840	15.5
66099	600	18.5	3000	1.5	870	15.5
66100	600	18.5	3000	1.5	900	15.5
66101	600	18.5	3000	1.5	930	15.5
66102	600	18.5	3000	1.5	960	15.5
66317	500	15.4	2500	-	1000	15.4
66318	500	15.4	2500	-	1025	15.4
66319	500	15.4	2500	-	1050	15.4
66320	500	15.4	2500	-	1075	15.4
66321	500	15.4	2500	-	1100	15.4
66322	500	15.4	2500	-	1125	15.4
66323	500	15.4	2500	-	1150	15.4
66324	500	15.4	2500	-	1175	15.4
66325	500	15.4	2500	-	1200	15.4
65749	850	23.6	4250	4.1	2394	15.4
65750	850	23.6	4250	4.1	2436	15.4
65751	850	23.6	4250	4.1	2478	15.4
65752	850	23.6	4250	4.1	2520	15.4
65753	850	23.6	4250	4.1	2562	15.4
66062	650	18.1	3250	1.4	2624	15.3
66063	650	18.1	3250	1.4	2656	15.3
66064	650	18.1	3250	1.4	2688	15.3
66065	650	18.1	3250	1.4	2720	15.3
66066	650	18.1	3250	1.4	2752	15.3
66067	650	18.1	3250	1.4	2784	15.3
66068	650	18.1	3250	1.4	2816	15.3
66273	550	15.3	2750	-	2862	15.3
66274	550	15.3	2750	-	2889	15.3
66275	550	15.3	2750	-	2916	15.3
66276	550	15.3	2750	-	2943	15.3
65453	1100	23.4	5500	4.3	935	14.9
66190	550	18.0	2750	1.6	621	14.7
66191	550	18.0	2750	1.6	648	14.7
66192	550	18.0	2750	1.6	675	14.7
66193	550	18.0	2750	1.6	702	14.7
66194	550	18.0	2750	1.6	729	14.7
66195	550	18.0	2750	1.6	756	14.7
66196	550	18.0	2750	1.6	783	14.7
65748	850	23.6	4250	4.7	2352	14.2
66090	600	19.6	3000	2.8	600	13.9
66391	500	13.9	2500	-	2850	13.9
66392	500	13.9	2500	-	2875	13.9
66393	500	13.9	2500	-	2900	13.9
66394	500	13.9	2500	-	2925	13.9
66395	500	13.9	2500	-	2950	13.9
66396	500	13.9	2500	-	2975	13.9
66397	500	13.9	2500	-	3000	13.9
66272	550	15.3	2750	0.7	2835	13.8
65499	1050	22.3	5250	4.3	988	13.8
66197	550	17.0	2750	1.6	810	13.7
66198	550	17.0	2750	1.6	837	13.7
66199	550	17.0	2750	1.6	864	13.7
66200	550	17.0	2750	1.6	891	13.7
66201	550	17.0	2750	1.6	918	13.7
66202	550	17.0	2750	1.6	945	13.7
66203	550	17.0	2750	1.6	972	13.7
65549	1000	21.3	5000	3.8	1050	13.7
66158	600	16.7	3000	1.5	2640	13.7
66159	600	16.7	3000	1.5	2670	13.7
66160	600	16.7	3000	1.5	2700	13.7
66161	600	16.7	3000	1.5	2730	13.7
66162	600	16.7	3000	1.5	2760	13.7
66163	600	16.7	3000	1.5	2790	13.7
66164	600	16.7	3000	1.5	2820	13.7
65815	800	22.2	4000	4.4	2360	13.5
65816	800	22.2	4000	4.4	2400	13.5
65817	800	22.2	4000	4.4	2440	13.5
65818	800	22.2	4000	4.4	2480	13.5
65819	800	22.2	4000	4.4	2520	13.5
65820	800	22.2	4000	4.4	2560	13.5
66302	500	16.3	2500	1.8	625	12.7
66303	500	16.3	2500	1.8	650	12.7
66304	500	16.3	2500	1.8	675	12.7
66305	500	16.3	2500	1.8	700	12.7
66306	500	16.3	2500	1.8	725	12.7
66307	500	16.3	2500	1.8	750	12.7
66308	500	16.3	2500	1.8	775	12.7
66309	500	16.3	2500	1.8	800	12.7
66310	500	16.3	2500	1.8	825	12.7
66157	600	16.7	3000	2.0	2610	12.7
65894	750	20.8	3750	4.3	2590	12.3
65602	950	20.2	4750	4.0	1081	12.2
66264	550	15.3	2750	1.6	2619	12.0
66265	550	15.3	2750	1.6	2646	12.0
66266	550	15.3	2750	1.6	2673	12.0
66267	550	15.3	2750	1.6	2700	12.0
66268	550	15.3	2750	1.6	2727	12.0
66269	550	15.3	2750	1.6	2754	12.0
66270	550	15.3	2750	1.6	2781	12.0
66271	550	15.3	2750	1.6	2808	12.0
66311	500	15.4	2500	1.8	850	11.8
66312	500	15.4	2500	1.8	875	11.8
66313	500	15.4	2500	1.8	900	11.8
66314	500	15.4	2500	1.8	925	11.8
66315	500	15.4	2500	1.8	950	11.8
66316	500	15.4	2500	1.8	975	11.8
65888	750	20.8	3750	4.7	2368	11.5
65889	750	20.8	3750	4.7	2405	11.5
65890	750	20.8	3750	4.7	2442	11.5
65891	750	20.8	3750	4.7	2479	11.5
65892	750	20.8	3750	4.7	2516	11.5
65893	750	20.8	3750	4.7	2553	11.5
65659	900	19.1	4500	4.2	1125	10.7
65973	700	19.4	3500	4.6	2590	10.3
66382	500	13.9	2500	1.8	2625	10.3
66383	500	13.9	2500	1.8	2650	10.3
66384	500	13.9	2500	1.8	2675	10.3
66385	500	13.9	2500	1.8	2700	10.3
66386	500	13.9	2500	1.8	2725	10.3
66387	500	13.9	2500	1.8	2750	10.3
66388	500	13.9	2500	1.8	2775	10.3
66389	500	13.9	2500	1.8	2800	10.3
66390	500	13.9	2500	1.8	2825	10.3
66189	550	18.0	2750	4.2	594	9.6
66301	500	16.3	2500	3.4	600	9.5
66326	500	15.4	2500	3.0	1225	9.4
65720	850	18.1	4250	4.5	1176	9.1
66061	650	18.1	3250	4.6	2592	8.8
65787	800	17.0	4000	4.8	1240	7.5
66381	500	13.9	2500	4.4	2600	5.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
65525	1050	29.2	5250	5.0	2340	19.3
65329	1250	26.6	6250	3.8	682	19.1
65330	1250	26.6	6250	3.8	744	19.1
65633	950	26.4	4750	3.7	2538	19.0
65366	1200	25.5	6000	3.9	660	17.7
65367	1200	25.5	6000	3.9	720	17.7
65368	1200	25.5	6000	3.9	780	17.7
65713	850	24.3	4250	3.6	882	17.0
65405	1150	24.5	5750	4.1	627	16.3
65406	1150	24.5	5750	4.1	684	16.3
65407	1150	24.5	5750	4.1	741	16.3
65408	1150	24.5	5750	4.1	798	16.3
65409	1150	24.5	5750	4.1	855	16.3
65448	1100	23.4	5500	4.3	660	14.9
65449	1100	23.4	5500	4.3	715	14.9
65450	1100	23.4	5500	4.3	770	14.9
65451	1100	23.4	5500	4.3	825	14.9
65452	1100	23.4	5500	4.3	880	14.9
65548	1000	21.3	5000	3.8	1000	13.7
65494	1050	22.3	5250	4.5	728	13.4
65495	1050	22.3	5250	4.5	780	13.4
65496	1050	22.3	5250	4.5	832	13.4
65497	1050	22.3	5250	4.5	884	13.4
65498	1050	22.3	5250	4.5	936	13.4
65601	950	20.2	4750	4.0	1034	12.2
65967	700	22.2	3500	5.0	2380	12.2
65543	1000	21.3	5000	4.7	750	11.9
65544	1000	21.3	5000	4.7	800	11.9
65545	1000	21.3	5000	4.7	850	11.9
65546	1000	21.3	5000	4.7	900	11.9
65547	1000	21.3	5000	4.7	950	11.9
65657	900	19.1	4500	4.2	1035	10.7
65658	900	19.1	4500	4.2	1080	10.7
65600	950	20.2	4750	4.8	987	10.5
65596	950	20.2	4750	4.9	799	10.3
65597	950	20.2	4750	4.9	846	10.3
65598	950	20.2	4750	4.9	893	10.3
65599	950	20.2	4750	4.9	940	10.3
65656	900	19.1	4500	4.8	990	9.6
65660	900	19.1	4500	4.8	1170	9.6
65968	700	19.4	3500	5.0	2415	9.4
65969	700	19.4	3500	5.0	2450	9.4
65970	700	19.4	3500	5.0	2485	9.4
65971	700	19.4	3500	5.0	2520	9.4
65972	700	19.4	3500	5.0	2555	9.4
65716	850	18.1	4250	4.5	1008	9.1
65717	850	18.1	4250	4.5	1050	9.1
65718	850	18.1	4250	4.5	1092	9.1
65719	850	18.1	4250	4.5	1134	9.1
66014	650	17.6	3250	4.3	1088	9.0
65721	850	18.1	4250	4.8	1218	8.4
65781	800	17.0	4000	4.8	1000	7.5
65782	800	17.0	4000	4.8	1040	7.5
65783	800	17.0	4000	4.8	1080	7.5
65784	800	17.0	4000	4.8	1120	7.5
65785	800	17.0	4000	4.8	1160	7.5
65786	800	17.0	4000	4.8	1200	7.5
66108	600	15.4	3000	5.0	1140	5.4

Overall score = score_ratio - 2 * repetitive DNA content