Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign79 - back to list

Summary
Image
Unique putative probes (69)
Putative probes (236)
Redundant probes (3)

Summary

`./analyse_probe_search_results : Thu Oct 20 11:07:44 2005`

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

Fetched probe design: ProbeDesign79
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 2
  id            : 70
  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 that are unique                 : 69/907
Putative probes exceeding selection criteria    : 239/907 (but not unique)
Putative probes with successfully-picked primers: 295/308

Identified 3 '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
67173	750	3750	-	1961
67213	700	3500	-	1120
67237	700	3500	-	1960
67238	700	3500	-	1995
67281	650	3250	-	1088
67282	650	3250	-	1120
67283	650	3250	-	1152
67284	650	3250	-	1184
67309	650	3250	-	1984
67310	650	3250	-	2016
67311	650	3250	-	2048
67358	600	3000	-	1110
67359	600	3000	-	1140
67360	600	3000	-	1170
67361	600	3000	-	1200
67362	600	3000	-	1230
67387	600	3000	-	1980
67388	600	3000	-	2010
67389	600	3000	-	2040
67390	600	3000	-	2070
67391	600	3000	-	2100
67443	550	2750	-	1107
67444	550	2750	-	1134
67445	550	2750	-	1161
67446	550	2750	-	1188
67447	550	2750	-	1215
67448	550	2750	-	1242
67449	550	2750	-	1269
67475	550	2750	-	1971
67476	550	2750	-	1998
67477	550	2750	-	2025
67478	550	2750	-	2052
67479	550	2750	-	2079
67480	550	2750	-	2106
67481	550	2750	-	2133
67482	550	2750	-	2160
67537	500	2500	-	1100
67538	500	2500	-	1125
67539	500	2500	-	1150
67540	500	2500	-	1175
67541	500	2500	-	1200
67542	500	2500	-	1225
67543	500	2500	-	1250
67544	500	2500	-	1275
67545	500	2500	-	1300
67546	500	2500	-	1325
67572	500	2500	-	1975
67573	500	2500	-	2000
67574	500	2500	-	2025
67575	500	2500	-	2050
67576	500	2500	-	2075
67577	500	2500	-	2100
67578	500	2500	-	2125
67579	500	2500	-	2150
67580	500	2500	-	2175
67581	500	2500	-	2200
67308	650	3250	0.5	1952
67450	550	2750	0.5	1296
67386	600	3000	0.8	1950
67571	500	2500	1.0	1950
67547	500	2500	1.4	1350
67214	700	3500	1.7	1155
67582	500	2500	1.8	2225
67474	550	2750	2.0	1944
67150	750	3750	2.3	1110
67363	600	3000	2.8	1260
67285	650	3250	3.5	1216
67236	700	3500	4.3	1925
67570	500	2500	6.0	1925

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
66694	1300	41.1	6500	-	455	41.1
66695	1300	41.1	6500	-	520	41.1
66722	1250	39.6	6250	-	496	39.6
66723	1250	39.6	6250	-	558	39.6
66751	1200	38.0	6000	-	480	38.0
66752	1200	38.0	6000	-	540	38.0
66753	1200	38.0	6000	-	600	38.0
66782	1150	36.4	5750	-	456	36.4
66783	1150	36.4	5750	-	513	36.4
66784	1150	36.4	5750	-	570	36.4
66785	1150	36.4	5750	-	627	36.4
66786	1150	36.4	5750	-	684	36.4
66721	1250	39.6	6250	1.6	434	36.4
66724	1250	39.6	6250	2.2	620	35.2
66754	1200	38.0	6000	1.4	660	35.1
66816	1100	34.8	5500	-	495	34.8
66817	1100	34.8	5500	-	550	34.8
66818	1100	34.8	5500	-	605	34.8
66819	1100	34.8	5500	-	660	34.8
66856	1050	34.5	5250	-	728	34.5
66857	1050	34.5	5250	-	780	34.5
66820	1100	34.2	5500	-	715	34.2
66851	1050	33.2	5250	-	468	33.2
66852	1050	33.2	5250	-	520	33.2
66853	1050	33.2	5250	-	572	33.2
66854	1050	33.2	5250	-	624	33.2
66855	1050	33.2	5250	-	676	33.2
66895	1000	32.9	5000	-	750	32.9
66896	1000	32.9	5000	-	800	32.9
66750	1200	38.0	6000	2.8	420	32.3
66815	1100	34.8	5500	1.3	440	32.3
66890	1000	31.6	5000	-	500	31.6
66891	1000	31.6	5000	-	550	31.6
66892	1000	31.6	5000	-	600	31.6
66893	1000	31.6	5000	-	650	31.6
66894	1000	31.6	5000	-	700	31.6
66897	1000	32.9	5000	0.7	850	31.5
66937	950	31.2	4750	-	752	31.2
66938	950	31.2	4750	-	799	31.2
66939	950	31.2	4750	-	846	31.2
66940	950	31.2	4750	-	893	31.2
66936	950	31.0	4750	-	705	31.0
66889	1000	31.6	5000	0.4	450	30.8
66821	1100	35.0	5500	2.5	770	30.1
66931	950	30.1	4750	-	470	30.1
66932	950	30.1	4750	-	517	30.1
66933	950	30.1	4750	-	564	30.1
66934	950	30.1	4750	-	611	30.1
66935	950	30.1	4750	-	658	30.1
66982	900	29.6	4500	-	765	29.6
66983	900	29.6	4500	-	810	29.6
66984	900	29.6	4500	-	855	29.6
66985	900	29.6	4500	-	900	29.6
66986	900	29.6	4500	0.2	945	29.2
66981	900	29.0	4500	-	720	29.0
66976	900	28.5	4500	-	495	28.5
66977	900	28.5	4500	-	540	28.5
66978	900	28.5	4500	-	585	28.5
66979	900	28.5	4500	-	630	28.5
66980	900	28.5	4500	-	675	28.5
67030	850	28.0	4250	-	756	28.0
67031	850	28.0	4250	-	798	28.0
67032	850	28.0	4250	-	840	28.0
67033	850	28.0	4250	-	882	28.0
67034	850	28.0	4250	-	924	28.0
67035	850	28.0	4250	-	966	28.0
66975	900	28.5	4500	0.4	450	27.6
67023	850	26.9	4250	-	462	26.9
67024	850	26.9	4250	-	504	26.9
67025	850	26.9	4250	-	546	26.9
67026	850	26.9	4250	-	588	26.9
67027	850	26.9	4250	-	630	26.9
67028	850	26.9	4250	-	672	26.9
67029	850	26.4	4250	-	714	26.4
67083	800	26.3	4000	-	760	26.3
67084	800	26.3	4000	-	800	26.3
67085	800	26.3	4000	-	840	26.3
67086	800	26.3	4000	-	880	26.3
67087	800	26.3	4000	-	920	26.3
67088	800	26.3	4000	-	960	26.3
67089	800	26.3	4000	-	1000	26.3
67090	800	26.3	4000	-	1040	26.3
66850	1050	33.2	5250	3.6	416	26.0
67082	800	25.8	4000	-	720	25.8
67076	800	25.3	4000	-	480	25.3
67077	800	25.3	4000	-	520	25.3
67078	800	25.3	4000	-	560	25.3
67079	800	25.3	4000	-	600	25.3
67080	800	25.3	4000	-	640	25.3
67081	800	25.3	4000	-	680	25.3
67140	750	24.7	3750	-	740	24.7
67141	750	24.7	3750	-	777	24.7
67142	750	24.7	3750	-	814	24.7
67143	750	24.7	3750	-	851	24.7
67144	750	24.7	3750	-	888	24.7
67145	750	24.7	3750	-	925	24.7
67146	750	24.7	3750	-	962	24.7
67147	750	24.7	3750	-	999	24.7
67148	750	24.7	3750	-	1036	24.7
67149	750	24.7	3750	-	1073	24.7
66696	1300	31.0	6500	3.2	585	24.5
67036	850	28.0	4250	1.8	1008	24.4
67133	750	23.7	3750	-	481	23.7
67134	750	23.7	3750	-	518	23.7
67135	750	23.7	3750	-	555	23.7
67136	750	23.7	3750	-	592	23.7
67137	750	23.7	3750	-	629	23.7
67138	750	23.7	3750	-	666	23.7
67139	750	23.7	3750	-	703	23.7
66930	950	30.1	4750	3.3	423	23.5
67202	700	23.0	3500	-	735	23.0
67203	700	23.0	3500	-	770	23.0
67204	700	23.0	3500	-	805	23.0
67205	700	23.0	3500	-	840	23.0
67206	700	23.0	3500	-	875	23.0
67207	700	23.0	3500	-	910	23.0
67208	700	23.0	3500	-	945	23.0
67209	700	23.0	3500	-	980	23.0
67210	700	23.0	3500	-	1015	23.0
67211	700	23.0	3500	-	1050	23.0
67212	700	23.0	3500	-	1085	23.0
67194	700	22.2	3500	-	455	22.2
67195	700	22.2	3500	-	490	22.2
67196	700	22.2	3500	-	525	22.2
67197	700	22.2	3500	-	560	22.2
67198	700	22.2	3500	-	595	22.2
67199	700	22.2	3500	-	630	22.2
67200	700	22.2	3500	-	665	22.2
67201	700	22.2	3500	-	700	22.2
67075	800	25.3	4000	1.8	440	21.8
67270	650	21.4	3250	-	736	21.4
67271	650	21.4	3250	-	768	21.4
67272	650	21.4	3250	-	800	21.4
67273	650	21.4	3250	-	832	21.4
67274	650	21.4	3250	-	864	21.4
67275	650	21.4	3250	-	896	21.4
67276	650	21.4	3250	-	928	21.4
67277	650	21.4	3250	-	960	21.4
67278	650	21.4	3250	-	992	21.4
67279	650	21.4	3250	-	1024	21.4
67280	650	21.4	3250	-	1056	21.4
67132	750	23.7	3750	1.3	444	21.1
67262	650	20.6	3250	-	480	20.6
67263	650	20.6	3250	-	512	20.6
67264	650	20.6	3250	-	544	20.6
67265	650	20.6	3250	-	576	20.6
67266	650	20.6	3250	-	608	20.6
67267	650	20.6	3250	-	640	20.6
67268	650	20.6	3250	-	672	20.6
67269	650	20.6	3250	-	704	20.6
67346	600	19.7	3000	-	750	19.7
67347	600	19.7	3000	-	780	19.7
67348	600	19.7	3000	-	810	19.7
67349	600	19.7	3000	-	840	19.7
67350	600	19.7	3000	-	870	19.7
67351	600	19.7	3000	-	900	19.7
67352	600	19.7	3000	-	930	19.7
67353	600	19.7	3000	-	960	19.7
67354	600	19.7	3000	-	990	19.7
67355	600	19.7	3000	-	1020	19.7
67356	600	19.7	3000	-	1050	19.7
67357	600	19.7	3000	-	1080	19.7
67345	600	19.4	3000	-	720	19.4
66787	1150	27.4	5750	4.2	741	19.0
67337	600	19.0	3000	-	480	19.0
67338	600	19.0	3000	-	510	19.0
67339	600	19.0	3000	-	540	19.0
67340	600	19.0	3000	-	570	19.0
67341	600	19.0	3000	-	600	19.0
67342	600	19.0	3000	-	630	19.0
67343	600	19.0	3000	-	660	19.0
67344	600	19.0	3000	-	690	19.0
67022	850	26.9	4250	4.0	420	18.9
67261	650	20.6	3250	0.9	448	18.7
66693	1300	28.0	6500	4.9	390	18.2
67429	550	18.1	2750	-	729	18.1
67430	550	18.1	2750	-	756	18.1
67431	550	18.1	2750	-	783	18.1
67432	550	18.1	2750	-	810	18.1
67433	550	18.1	2750	-	837	18.1
67434	550	18.1	2750	-	864	18.1
67435	550	18.1	2750	-	891	18.1
67436	550	18.1	2750	-	918	18.1
67437	550	18.1	2750	-	945	18.1
67438	550	18.1	2750	-	972	18.1
67439	550	18.1	2750	-	999	18.1
67440	550	18.1	2750	-	1026	18.1
67441	550	18.1	2750	-	1053	18.1
67442	550	18.1	2750	-	1080	18.1
67336	600	19.0	3000	0.7	450	17.7
67419	550	17.4	2750	-	459	17.4
67420	550	17.4	2750	-	486	17.4
67421	550	17.4	2750	-	513	17.4
67422	550	17.4	2750	-	540	17.4
67423	550	17.4	2750	-	567	17.4
67424	550	17.4	2750	-	594	17.4
67425	550	17.4	2750	-	621	17.4
67426	550	17.4	2750	-	648	17.4
67427	550	17.4	2750	-	675	17.4
67428	550	17.4	2750	-	702	17.4
67239	700	21.1	3500	2.0	2030	17.1
66781	1150	26.6	5750	4.8	399	17.1
67172	750	25.0	3750	4.1	1924	16.7
67522	500	16.4	2500	-	725	16.4
67523	500	16.4	2500	-	750	16.4
67524	500	16.4	2500	-	775	16.4
67525	500	16.4	2500	-	800	16.4
67526	500	16.4	2500	-	825	16.4
67527	500	16.4	2500	-	850	16.4
67528	500	16.4	2500	-	875	16.4
67529	500	16.4	2500	-	900	16.4
67530	500	16.4	2500	-	925	16.4
67531	500	16.4	2500	-	950	16.4
67532	500	16.4	2500	-	975	16.4
67533	500	16.4	2500	-	1000	16.4
67534	500	16.4	2500	-	1025	16.4
67535	500	16.4	2500	-	1050	16.4
67536	500	16.4	2500	-	1075	16.4
67512	500	15.8	2500	-	475	15.8
67513	500	15.8	2500	-	500	15.8
67514	500	15.8	2500	-	525	15.8
67515	500	15.8	2500	-	550	15.8
67516	500	15.8	2500	-	575	15.8
67517	500	15.8	2500	-	600	15.8
67518	500	15.8	2500	-	625	15.8
67519	500	15.8	2500	-	650	15.8
67520	500	15.8	2500	-	675	15.8
67521	500	15.8	2500	-	700	15.8
67312	650	19.6	3250	2.2	2080	15.3
67511	500	15.8	2500	0.8	450	14.2
67112	800	23.5	4000	4.9	1920	13.8
67392	600	18.1	3000	2.3	2130	13.4
67193	700	22.2	3500	4.9	420	12.4
67418	550	17.4	2750	4.0	432	9.4
67174	750	14.6	3750	4.3	1998	6.1
67483	550	13.7	2750	3.8	2187	6.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
66858	1050	26.2	5250	3.7	832	18.8
66941	950	22.6	4750	4.9	940	12.7
67091	800	20.1	4000	4.6	1080	10.9

Overall score = score_ratio - 2 * repetitive DNA content