Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign73 - back to list

Summary
Image
Unique putative probes (20)
Putative probes (311)
Redundant probes (9)

Summary

`./analyse_probe_search_results : Tue Oct 18 14:47:44 2005`

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

Fetched probe design: ProbeDesign73
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 8
  id            : 64
  strand        : 1
  -------------

Design window length: 5001bp

All jobs for probe design are successful - total: 87
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1729 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            : 1729/1729
Putative probes that are unique                 : 20/1729
Putative probes exceeding selection criteria    : 320/1729 (but not unique)
Putative probes with successfully-picked primers: 337/340

Identified 9 '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
63397	550	2750	-	621
63564	500	2500	-	625
63565	500	2500	-	650
63566	500	2500	-	675
63671	500	2500	2.0	3300
63672	500	2500	2.0	3325
63673	500	2500	2.0	3350
63496	550	2750	2.2	3294
63354	600	3000	16.2	3810
63355	600	3000	16.2	3840
63515	550	2750	17.6	3807
63516	550	2750	17.6	3834
63517	550	2750	17.6	3861
63518	550	2750	17.6	3888
63691	500	2500	19.4	3800
63692	500	2500	19.4	3825
63693	500	2500	19.4	3850
63694	500	2500	19.4	3875
63695	500	2500	19.4	3900
63696	500	2500	19.4	3925

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
62429	1000	25.5	5000	-	2050	25.5
62513	950	24.2	4750	-	2068	24.2
62514	950	24.2	4750	-	2115	24.2
62602	900	23.0	4500	-	2070	23.0
62603	900	23.0	4500	-	2115	23.0
62604	900	23.0	4500	-	2160	23.0
62697	850	21.7	4250	-	2058	21.7
62698	850	21.7	4250	-	2100	21.7
62699	850	21.7	4250	-	2142	21.7
62700	850	21.7	4250	-	2184	21.7
62351	1050	26.8	5250	2.6	2028	21.6
62701	850	21.7	4250	0.6	2226	20.5
62799	800	20.4	4000	-	2080	20.4
62800	800	20.4	4000	-	2120	20.4
62801	800	20.4	4000	-	2160	20.4
62802	800	20.4	4000	-	2200	20.4
62803	800	20.4	4000	-	2240	20.4
62943	750	23.1	3750	1.6	3330	19.9
62430	1000	25.5	5000	2.9	2100	19.7
62942	750	23.1	3750	1.7	3293	19.7
62909	750	19.1	3750	-	2072	19.1
62910	750	19.1	3750	-	2109	19.1
62911	750	19.1	3750	-	2146	19.1
62912	750	19.1	3750	-	2183	19.1
62913	750	19.1	3750	-	2220	19.1
62914	750	19.1	3750	-	2257	19.1
62915	750	19.1	3750	-	2294	19.1
63063	700	21.6	3500	1.4	3325	18.7
63064	700	21.6	3500	1.4	3360	18.7
62119	1200	18.7	6000	-	600	18.7
62120	1200	18.7	6000	-	660	18.7
62512	950	24.2	4750	2.8	2021	18.6
62798	800	20.4	4000	1.0	2040	18.4
62804	800	20.4	4000	1.1	2280	18.2
62184	1150	17.9	5750	-	627	17.9
62185	1150	17.9	5750	-	684	17.9
62058	1250	19.5	6250	0.8	620	17.9
63027	700	17.9	3500	-	2065	17.9
63028	700	17.9	3500	-	2100	17.9
63029	700	17.9	3500	-	2135	17.9
63030	700	17.9	3500	-	2170	17.9
63031	700	17.9	3500	-	2205	17.9
63032	700	17.9	3500	-	2240	17.9
63033	700	17.9	3500	-	2275	17.9
63034	700	17.9	3500	-	2310	17.9
63035	700	17.9	3500	-	2345	17.9
62601	900	23.0	4500	2.6	2025	17.8
63466	550	17.7	2750	-	2484	17.7
63467	550	17.7	2750	-	2511	17.7
62829	800	24.7	4000	3.5	3280	17.7
63267	600	17.3	3000	-	1200	17.3
63268	600	17.3	3000	-	1230	17.3
63269	600	17.3	3000	-	1260	17.3
63247	600	17.1	3000	-	600	17.1
62252	1100	17.1	5500	-	605	17.1
62253	1100	17.1	5500	-	660	17.1
62254	1100	17.1	5500	-	715	17.1
63062	700	21.6	3500	2.3	3290	17.0
63194	650	20.1	3250	1.5	3296	17.0
63195	650	20.1	3250	1.5	3328	17.0
63196	650	20.1	3250	1.5	3360	17.0
63197	650	20.1	3250	1.5	3392	17.0
63198	650	20.1	3250	1.5	3424	17.0
63504	550	17.0	2750	-	3510	17.0
63129	650	18.8	3250	0.9	1216	16.9
63396	550	18.3	2750	0.7	594	16.9
63563	500	16.7	2500	-	600	16.7
63155	650	16.6	3250	-	2048	16.6
63156	650	16.6	3250	-	2080	16.6
63157	650	16.6	3250	-	2112	16.6
63158	650	16.6	3250	-	2144	16.6
63159	650	16.6	3250	-	2176	16.6
63160	650	16.6	3250	-	2208	16.6
63161	650	16.6	3250	-	2240	16.6
63162	650	16.6	3250	-	2272	16.6
63163	650	16.6	3250	-	2304	16.6
63164	650	16.6	3250	-	2336	16.6
63165	650	16.6	3250	-	2368	16.6
63166	650	16.6	3250	-	2400	16.6
62916	750	19.1	3750	1.3	2331	16.5
62324	1050	16.4	5250	-	624	16.4
62325	1050	16.4	5250	-	676	16.4
62326	1050	16.4	5250	-	728	16.4
62327	1050	16.4	5250	-	780	16.4
63309	600	16.3	3000	-	2460	16.3
63398	550	16.3	2750	-	648	16.3
63638	500	16.1	2500	-	2475	16.1
63639	500	16.1	2500	-	2500	16.1
63640	500	16.1	2500	-	2525	16.1
63641	500	16.1	2500	-	2550	16.1
63419	550	15.9	2750	-	1215	15.9
63420	550	15.9	2750	-	1242	15.9
63421	550	15.9	2750	-	1269	15.9
63422	550	15.9	2750	-	1296	15.9
63503	550	17.0	2750	0.5	3483	15.9
63343	600	18.5	3000	1.3	3480	15.9
62908	750	19.1	3750	1.7	2035	15.7
62515	950	24.2	4750	4.3	2162	15.6
62400	1000	15.6	5000	-	600	15.6
62401	1000	15.6	5000	-	650	15.6
62402	1000	15.6	5000	-	700	15.6
62403	1000	15.6	5000	-	750	15.6
62404	1000	15.6	5000	-	800	15.6
62405	1000	15.6	5000	-	850	15.6
63679	500	15.4	2500	-	3500	15.4
63680	500	15.4	2500	-	3525	15.4
63681	500	15.4	2500	-	3550	15.4
63682	500	15.4	2500	-	3575	15.4
62605	900	23.0	4500	3.8	2205	15.4
63128	650	15.4	3250	-	1184	15.4
62255	1100	17.1	5500	0.9	770	15.3
63296	600	15.3	3000	-	2070	15.3
63297	600	15.3	3000	-	2100	15.3
63298	600	15.3	3000	-	2130	15.3
63299	600	15.3	3000	-	2160	15.3
63300	600	15.3	3000	-	2190	15.3
63301	600	15.3	3000	-	2220	15.3
63302	600	15.3	3000	-	2250	15.3
63303	600	15.3	3000	-	2280	15.3
63304	600	15.3	3000	-	2310	15.3
63305	600	15.3	3000	-	2340	15.3
63306	600	15.3	3000	-	2370	15.3
63307	600	15.3	3000	-	2400	15.3
63308	600	15.3	3000	-	2430	15.3
63036	700	17.9	3500	1.3	2380	15.3
63337	600	18.5	3000	1.7	3300	15.2
63338	600	18.5	3000	1.7	3330	15.2
63339	600	18.5	3000	1.7	3360	15.2
63340	600	18.5	3000	1.7	3390	15.2
63341	600	18.5	3000	1.7	3420	15.2
63342	600	18.5	3000	1.7	3450	15.2
62482	950	14.8	4750	-	611	14.8
62483	950	14.8	4750	-	658	14.8
62484	950	14.8	4750	-	705	14.8
62485	950	14.8	4750	-	752	14.8
62486	950	14.8	4750	-	799	14.8
62487	950	14.8	4750	-	846	14.8
62488	950	14.8	4750	-	893	14.8
63465	550	14.8	2750	-	2457	14.8
63642	500	16.1	2500	0.8	2575	14.5
63587	500	14.5	2500	-	1200	14.5
63588	500	14.5	2500	-	1225	14.5
63589	500	14.5	2500	-	1250	14.5
63590	500	14.5	2500	-	1275	14.5
63591	500	14.5	2500	-	1300	14.5
63592	500	14.5	2500	-	1325	14.5
63593	500	14.5	2500	-	1350	14.5
62000	1300	20.2	6500	2.9	585	14.4
63567	500	14.3	2500	-	700	14.3
62696	850	21.7	4250	3.8	2016	14.2
63450	550	14.0	2750	-	2052	14.0
63451	550	14.0	2750	-	2079	14.0
63452	550	14.0	2750	-	2106	14.0
63453	550	14.0	2750	-	2133	14.0
63454	550	14.0	2750	-	2160	14.0
63455	550	14.0	2750	-	2187	14.0
63456	550	14.0	2750	-	2214	14.0
63457	550	14.0	2750	-	2241	14.0
63458	550	14.0	2750	-	2268	14.0
63459	550	14.0	2750	-	2295	14.0
63460	550	14.0	2750	-	2322	14.0
63461	550	14.0	2750	-	2349	14.0
63462	550	14.0	2750	-	2376	14.0
63463	550	14.0	2750	-	2403	14.0
63464	550	14.0	2750	-	2430	14.0
62570	900	14.0	4500	-	630	14.0
62571	900	14.0	4500	-	675	14.0
62572	900	14.0	4500	-	720	14.0
62573	900	14.0	4500	-	765	14.0
62574	900	14.0	4500	-	810	14.0
62575	900	14.0	4500	-	855	14.0
62576	900	14.0	4500	-	900	14.0
62577	900	14.0	4500	-	945	14.0
63065	700	21.6	3500	3.9	3395	13.9
63505	550	17.0	2750	1.6	3537	13.7
63637	500	13.4	2500	-	2450	13.4
63497	550	17.0	2750	1.8	3321	13.3
63498	550	17.0	2750	1.8	3348	13.3
63499	550	17.0	2750	1.8	3375	13.3
63500	550	17.0	2750	1.8	3402	13.3
63501	550	17.0	2750	1.8	3429	13.3
63502	550	17.0	2750	1.8	3456	13.3
63248	600	13.3	3000	-	630	13.3
62663	850	13.2	4250	-	630	13.2
62664	850	13.2	4250	-	672	13.2
62665	850	13.2	4250	-	714	13.2
62666	850	13.2	4250	-	756	13.2
62667	850	13.2	4250	-	798	13.2
62668	850	13.2	4250	-	840	13.2
62669	850	13.2	4250	-	882	13.2
62670	850	13.2	4250	-	924	13.2
62671	850	13.2	4250	-	966	13.2
62672	850	13.2	4250	-	1008	13.2
63167	650	16.6	3250	1.7	2432	13.2
62057	1250	19.5	6250	3.2	558	13.1
62183	1150	17.9	5750	2.4	570	13.0
63418	550	13.0	2750	-	1188	13.0
63001	700	12.9	3500	-	1155	12.9
63399	550	12.9	2750	-	675	12.9
63621	500	12.8	2500	-	2050	12.8
63622	500	12.8	2500	-	2075	12.8
63623	500	12.8	2500	-	2100	12.8
63624	500	12.8	2500	-	2125	12.8
63625	500	12.8	2500	-	2150	12.8
63626	500	12.8	2500	-	2175	12.8
63627	500	12.8	2500	-	2200	12.8
63628	500	12.8	2500	-	2225	12.8
63629	500	12.8	2500	-	2250	12.8
63630	500	12.8	2500	-	2275	12.8
63631	500	12.8	2500	-	2300	12.8
63632	500	12.8	2500	-	2325	12.8
63633	500	12.8	2500	-	2350	12.8
63634	500	12.8	2500	-	2375	12.8
63635	500	12.8	2500	-	2400	12.8
63636	500	12.8	2500	-	2425	12.8
63026	700	17.9	3500	2.6	2030	12.7
63295	600	15.3	3000	1.3	2040	12.6
62186	1150	17.9	5750	2.7	741	12.5
62762	800	12.5	4000	-	600	12.5
62763	800	12.5	4000	-	640	12.5
62764	800	12.5	4000	-	680	12.5
62765	800	12.5	4000	-	720	12.5
62766	800	12.5	4000	-	760	12.5
62767	800	12.5	4000	-	800	12.5
62768	800	12.5	4000	-	840	12.5
62769	800	12.5	4000	-	880	12.5
62770	800	12.5	4000	-	920	12.5
62771	800	12.5	4000	-	960	12.5
62772	800	12.5	4000	-	1000	12.5
62773	800	12.5	4000	-	1040	12.5
63266	600	12.4	3000	-	1170	12.4
62328	1050	16.4	5250	2.1	832	12.2
63127	650	11.9	3250	-	1152	11.9
62428	1000	21.5	5000	4.8	2000	11.9
63110	650	11.7	3250	-	608	11.7
62870	750	11.7	3750	-	629	11.7
62871	750	11.7	3750	-	666	11.7
62872	750	11.7	3750	-	703	11.7
63568	500	11.7	2500	-	725	11.7
62873	750	11.7	3750	-	740	11.7
62874	750	11.7	3750	-	777	11.7
62875	750	11.7	3750	-	814	11.7
62876	750	11.7	3750	-	851	11.7
62877	750	11.7	3750	-	888	11.7
62878	750	11.7	3750	-	925	11.7
62879	750	11.7	3750	-	962	11.7
62880	750	11.7	3750	-	999	11.7
62881	750	11.7	3750	-	1036	11.7
62882	750	11.7	3750	-	1073	11.7
62883	750	11.7	3750	-	1110	11.7
63674	500	15.4	2500	2.0	3375	11.4
63675	500	15.4	2500	2.0	3400	11.4
63676	500	15.4	2500	2.0	3425	11.4
63677	500	15.4	2500	2.0	3450	11.4
63678	500	15.4	2500	2.0	3475	11.4
62323	1050	16.4	5250	2.5	572	11.4
63423	550	15.9	2750	2.4	1323	11.2
62569	900	14.0	4500	1.4	585	11.1
62626	900	20.7	4500	4.9	3150	11.0
62986	700	10.9	3500	-	630	10.9
62987	700	10.9	3500	-	665	10.9
62988	700	10.9	3500	-	700	10.9
62989	700	10.9	3500	-	735	10.9
62990	700	10.9	3500	-	770	10.9
62991	700	10.9	3500	-	805	10.9
62992	700	10.9	3500	-	840	10.9
62993	700	10.9	3500	-	875	10.9
62994	700	10.9	3500	-	910	10.9
62995	700	10.9	3500	-	945	10.9
62996	700	10.9	3500	-	980	10.9
62997	700	10.9	3500	-	1015	10.9
62998	700	10.9	3500	-	1050	10.9
62999	700	10.9	3500	-	1085	10.9
63000	700	10.9	3500	-	1120	10.9
62662	850	13.2	4250	1.2	588	10.9
63586	500	10.8	2500	-	1175	10.8
63417	550	10.5	2750	-	1161	10.5
63249	600	10.4	3000	-	660	10.4
63111	650	10.2	3250	-	640	10.2
63112	650	10.1	3250	-	672	10.1
63113	650	10.1	3250	-	704	10.1
63114	650	10.1	3250	-	736	10.1
63115	650	10.1	3250	-	768	10.1
63116	650	10.1	3250	-	800	10.1
63117	650	10.1	3250	-	832	10.1
63118	650	10.1	3250	-	864	10.1
63119	650	10.1	3250	-	896	10.1
63120	650	10.1	3250	-	928	10.1
63121	650	10.1	3250	-	960	10.1
63122	650	10.1	3250	-	992	10.1
63123	650	10.1	3250	-	1024	10.1
63124	650	10.1	3250	-	1056	10.1
63125	650	10.1	3250	-	1088	10.1
63126	650	10.1	3250	-	1120	10.1
62985	700	11.0	3500	0.4	595	10.1
62869	750	11.7	3750	0.8	592	10.1
62118	1200	18.7	6000	4.8	540	9.0
62121	1200	18.7	6000	5.0	720	8.7
62489	950	14.8	4750	3.2	940	8.5
62251	1100	17.1	5500	4.4	550	8.4
63002	700	16.6	3500	4.3	1190	8.0
62406	1000	15.6	5000	4.0	900	7.6
62774	800	12.5	4000	2.5	1080	7.5
62578	900	14.0	4500	3.3	990	7.4
63683	500	15.4	2500	4.4	3600	6.6
63270	600	16.0	3000	5.0	1290	6.0
62399	1000	15.6	5000	4.8	550	6.0
63449	550	14.0	2750	4.2	2025	5.7
62673	850	13.2	4250	4.7	1050	3.8
63620	500	12.8	2500	4.6	2025	3.6
62884	750	13.1	3750	4.9	1147	3.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
63310	600	19.4	3000	3.2	2490	13.0
63468	550	17.7	2750	3.1	2538	11.6
63246	600	20.0	3000	4.7	570	10.7
63594	500	14.5	2500	3.0	1375	8.5
63109	650	15.1	3250	3.4	576	8.3
62481	950	14.8	4750	3.6	564	7.6
63562	500	16.7	2500	4.6	575	7.5
63154	650	16.6	3250	4.9	2016	6.7
62761	800	12.5	4000	4.8	560	3.0

Overall score = score_ratio - 2 * repetitive DNA content