Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign103 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (132)
Redundant probes (19)

Summary

`./analyse_probe_search_results : Tue Jan 31 16:24:50 2006`

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

Fetched probe design: ProbeDesign103
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 11
  id            : 103
  strand        : 1
  -------------

Design window length: 5319bp

All jobs for probe design are successful - total: 93
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1860 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            : 1860/1860
Putative probes that are unique                 : 0/1860
Putative probes exceeding selection criteria    : 151/1860 (both unique and not unique)
Putative probes with successfully-picked primers: 150/151

Identified 19 '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

No probes

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
98043	850	25.9	4250	-	4452	25.9
97837	950	24.5	4750	-	4324	24.5
98155	800	24.4	4000	-	4440	24.4
98156	800	24.4	4000	-	4480	24.4
97936	900	24.3	4500	-	4410	24.3
98279	750	23.4	3750	-	4514	23.4
98280	750	23.4	3750	-	4551	23.4
97934	900	23.2	4500	-	4320	23.2
97935	900	23.2	4500	-	4365	23.2
98042	850	23.0	4250	-	4410	23.0
98277	750	22.9	3750	-	4440	22.9
98278	750	22.9	3750	-	4477	22.9
98154	800	22.3	4000	-	4400	22.3
97744	1000	25.8	5000	1.8	4300	22.2
98040	850	21.9	4250	-	4326	21.9
98041	850	21.9	4250	-	4368	21.9
98410	700	21.9	3500	-	4515	21.9
98411	700	21.9	3500	-	4550	21.9
98412	700	21.9	3500	-	4585	21.9
98408	700	21.3	3500	-	4445	21.3
98409	700	21.3	3500	-	4480	21.3
98152	800	20.6	4000	-	4320	20.6
98153	800	20.6	4000	-	4360	20.6
98276	750	20.6	3750	-	4403	20.6
98554	650	20.3	3250	-	4512	20.3
98555	650	20.3	3250	-	4544	20.3
98556	650	20.3	3250	-	4576	20.3
98557	650	20.3	3250	-	4608	20.3
98558	650	20.3	3250	-	4640	20.3
98552	650	19.8	3250	-	4448	19.8
98553	650	19.8	3250	-	4480	19.8
98274	750	19.3	3750	-	4329	19.3
98275	750	19.3	3750	-	4366	19.3
98407	700	18.9	3500	-	4410	18.9
98709	600	18.8	3000	-	4500	18.8
98710	600	18.8	3000	-	4530	18.8
98711	600	18.8	3000	-	4560	18.8
98712	600	18.8	3000	-	4590	18.8
98713	600	18.8	3000	-	4620	18.8
98714	600	18.8	3000	-	4650	18.8
98715	600	18.8	3000	-	4680	18.8
98716	600	18.8	3000	-	4710	18.8
98551	650	18.5	3250	-	4416	18.5
98707	600	18.3	3000	-	4440	18.3
98708	600	18.3	3000	-	4470	18.3
98405	700	18.0	3500	-	4340	18.0
98406	700	18.0	3500	-	4375	18.0
98550	650	17.6	3250	-	4384	17.6
98883	550	17.2	2750	-	4482	17.2
98884	550	17.2	2750	-	4509	17.2
98885	550	17.2	2750	-	4536	17.2
98886	550	17.2	2750	-	4563	17.2
98887	550	17.2	2750	-	4590	17.2
98888	550	17.2	2750	-	4617	17.2
98889	550	17.2	2750	-	4644	17.2
98890	550	17.2	2750	-	4671	17.2
98891	550	17.2	2750	-	4698	17.2
98892	550	17.2	2750	-	4725	17.2
98893	550	17.2	2750	-	4752	17.2
98881	550	16.8	2750	-	4428	16.8
98882	550	16.8	2750	-	4455	16.8
98548	650	16.8	3250	-	4320	16.8
98549	650	16.8	3250	-	4352	16.8
98096	800	25.3	4000	4.4	2080	16.6
97789	950	25.4	4750	4.4	2068	16.6
97885	900	24.1	4500	3.9	2115	16.3
98706	600	16.2	3000	-	4410	16.2
97836	950	24.5	4750	4.3	4277	15.9
99074	500	15.6	2500	-	4500	15.6
99075	500	15.6	2500	-	4525	15.6
99076	500	15.6	2500	-	4550	15.6
99077	500	15.6	2500	-	4575	15.6
99078	500	15.6	2500	-	4600	15.6
99079	500	15.6	2500	-	4625	15.6
99080	500	15.6	2500	-	4650	15.6
99081	500	15.6	2500	-	4675	15.6
99082	500	15.6	2500	-	4700	15.6
99083	500	15.6	2500	-	4725	15.6
99084	500	15.6	2500	-	4750	15.6
99085	500	15.6	2500	-	4775	15.6
99086	500	15.6	2500	-	4800	15.6
98703	600	15.5	3000	-	4320	15.5
98704	600	15.5	3000	-	4350	15.5
98705	600	15.5	3000	-	4380	15.5
99071	500	15.2	2500	-	4425	15.2
99072	500	15.2	2500	-	4450	15.2
99073	500	15.2	2500	-	4475	15.2
98880	550	15.1	2750	-	4401	15.1
97987	850	22.7	4250	4.1	2100	14.5
97988	850	22.7	4250	4.1	2142	14.5
98944	500	14.5	2500	-	1250	14.5
98877	550	14.2	2750	-	4320	14.2
98878	550	14.2	2750	-	4347	14.2
98879	550	14.2	2750	-	4374	14.2
99070	500	14.0	2500	-	4400	14.0
98039	850	21.9	4250	4.0	4284	13.9
97933	900	23.2	4500	4.8	4275	13.6
98486	650	17.4	3250	2.0	2336	13.4
98487	650	17.4	3250	2.0	2368	13.4
98995	500	13.4	2500	0.2	2525	13.0
99067	500	12.9	2500	-	4325	12.9
99068	500	12.9	2500	-	4350	12.9
99069	500	12.9	2500	-	4375	12.9
98097	800	21.4	4000	4.4	2120	12.6
98098	800	21.4	4000	4.4	2160	12.6
98099	800	21.4	4000	4.4	2200	12.6
98945	500	14.5	2500	1.0	1275	12.5
98273	750	19.3	3750	3.5	4292	12.4
98637	600	16.0	3000	2.2	2340	11.7
98638	600	16.0	3000	2.2	2370	11.7
98639	600	16.0	3000	2.2	2400	11.7
98943	500	11.5	2500	-	1225	11.5
98988	500	15.8	2500	2.6	2350	10.6
98989	500	15.8	2500	2.6	2375	10.6
98803	550	17.4	2750	3.5	2322	10.5
98762	550	10.3	2750	-	1215	10.3
98804	550	14.7	2750	2.4	2349	10.0
98805	550	14.7	2750	2.4	2376	10.0
98806	550	14.7	2750	2.4	2403	10.0
98807	550	14.7	2750	2.4	2430	10.0
98808	550	14.7	2750	2.4	2457	10.0
98640	600	16.0	3000	3.2	2430	9.7
98987	500	15.8	2500	3.2	2325	9.4
98348	700	18.7	3500	4.9	2345	9.0
98990	500	13.4	2500	2.6	2400	8.2
98991	500	13.4	2500	2.6	2425	8.2
98992	500	13.4	2500	2.6	2450	8.2
98993	500	13.4	2500	2.6	2475	8.2
98994	500	13.4	2500	2.6	2500	8.2
98763	550	15.9	2750	4.0	1242	7.9
98809	550	14.7	2750	4.2	2484	6.3
98599	600	10.1	3000	5.0	1200	0.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
97884	900	24.1	4500	4.4	2070	15.2
98214	750	23.7	3750	4.7	2109	14.4
98404	700	18.0	3500	1.9	4305	14.3
98341	700	22.2	3500	5.0	2100	12.2
98342	700	22.2	3500	5.0	2135	12.2
98343	700	22.2	3500	5.0	2170	12.2
98151	800	20.6	4000	4.8	4280	11.1
98215	750	20.1	3750	4.7	2146	10.7
98216	750	20.1	3750	4.7	2183	10.7
98217	750	20.1	3750	4.7	2220	10.7
98218	750	20.1	3750	4.7	2257	10.7
98347	700	18.7	3500	4.4	2310	9.9
98344	700	18.7	3500	5.0	2205	8.7
98345	700	18.7	3500	5.0	2240	8.7
98346	700	18.7	3500	5.0	2275	8.7
98547	650	16.8	3250	4.6	4288	7.5
98702	600	15.5	3000	4.7	4290	6.1
99066	500	12.9	2500	3.6	4300	5.7
98876	550	14.2	2750	4.5	4293	5.1

Overall score = score_ratio - 2 * repetitive DNA content