Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign66 - back to list

Summary
Image
Unique putative probes (17)
Putative probes (135)
Redundant probes (0)

Summary

`./analyse_probe_search_results : Fri Oct 7 10:50:47 2005`

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

Fetched probe design: ProbeDesign66
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 1
  id            : 57
  strand        : 1
  -------------

Design window length: 1501bp

All jobs for probe design are successful - total: 15
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 289 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            : 289/289
Putative probes that are unique                 : 17/289
Putative probes exceeding selection criteria    : 135/289 (but not unique)
Putative probes with successfully-picked primers: 152/152

Identified 0 '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
55358	600	3000	-	900
55373	550	2750	-	378
55392	550	2750	-	891
55393	550	2750	-	918
55394	550	2750	-	945
55410	500	2500	-	375
55411	500	2500	-	400
55412	500	2500	-	425
55413	500	2500	-	450
55431	500	2500	-	900
55432	500	2500	-	925
55433	500	2500	-	950
55434	500	2500	-	975
55435	500	2500	-	1000
55372	550	2750	0.4	351
55409	500	2500	0.6	350
55339	600	3000	3.8	330

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
55176	1100	36.4	5500	-	385	36.4
55168	1150	38.1	5750	1.0	342	36.2
55184	1050	34.8	5250	-	364	34.8
55185	1050	34.8	5250	-	416	34.8
55194	1000	33.1	5000	-	400	33.1
55195	1000	33.1	5000	-	450	33.1
55196	1000	33.1	5000	-	500	33.1
55193	1000	33.1	5000	0.3	350	32.5
55175	1100	36.4	5500	2.1	330	32.2
55205	950	31.5	4750	-	376	31.5
55206	950	31.5	4750	-	423	31.5
55207	950	31.5	4750	-	470	31.5
55208	950	31.5	4750	-	517	31.5
55217	900	29.8	4500	-	360	29.8
55218	900	29.8	4500	-	405	29.8
55219	900	29.8	4500	-	450	29.8
55220	900	29.8	4500	-	495	29.8
55221	900	29.8	4500	-	540	29.8
55222	900	29.8	4500	-	585	29.8
55232	850	28.1	4250	-	378	28.1
55233	850	28.1	4250	-	420	28.1
55234	850	28.1	4250	-	462	28.1
55235	850	28.1	4250	-	504	28.1
55236	850	28.1	4250	-	546	28.1
55237	850	28.1	4250	-	588	28.1
55238	850	28.1	4250	-	630	28.1
55248	800	26.5	4000	-	360	26.5
55249	800	26.5	4000	-	400	26.5
55250	800	26.5	4000	-	440	26.5
55251	800	26.5	4000	-	480	26.5
55252	800	26.5	4000	-	520	26.5
55253	800	26.5	4000	-	560	26.5
55254	800	26.5	4000	-	600	26.5
55255	800	26.5	4000	-	640	26.5
55256	800	26.5	4000	-	680	26.5
55204	950	31.5	4750	2.5	329	26.4
55267	750	24.8	3750	-	370	24.8
55268	750	24.8	3750	-	407	24.8
55269	750	24.8	3750	-	444	24.8
55270	750	24.8	3750	-	481	24.8
55271	750	24.8	3750	-	518	24.8
55272	750	24.8	3750	-	555	24.8
55273	750	24.8	3750	-	592	24.8
55274	750	24.8	3750	-	629	24.8
55275	750	24.8	3750	-	666	24.8
55276	750	24.8	3750	-	703	24.8
55277	750	24.8	3750	-	740	24.8
55231	850	28.1	4250	2.0	336	24.1
55289	700	23.2	3500	-	385	23.2
55290	700	23.2	3500	-	420	23.2
55291	700	23.2	3500	-	455	23.2
55292	700	23.2	3500	-	490	23.2
55293	700	23.2	3500	-	525	23.2
55294	700	23.2	3500	-	560	23.2
55295	700	23.2	3500	-	595	23.2
55296	700	23.2	3500	-	630	23.2
55297	700	23.2	3500	-	665	23.2
55298	700	23.2	3500	-	700	23.2
55299	700	23.2	3500	-	735	23.2
55300	700	23.2	3500	-	770	23.2
55288	700	23.2	3500	0.4	350	22.3
55313	650	21.5	3250	-	384	21.5
55314	650	21.5	3250	-	416	21.5
55315	650	21.5	3250	-	448	21.5
55316	650	21.5	3250	-	480	21.5
55317	650	21.5	3250	-	512	21.5
55318	650	21.5	3250	-	544	21.5
55319	650	21.5	3250	-	576	21.5
55320	650	21.5	3250	-	608	21.5
55321	650	21.5	3250	-	640	21.5
55322	650	21.5	3250	-	672	21.5
55323	650	21.5	3250	-	704	21.5
55324	650	21.5	3250	-	736	21.5
55325	650	21.5	3250	-	768	21.5
55326	650	21.5	3250	-	800	21.5
55327	650	21.5	3250	-	832	21.5
55312	650	21.5	3250	0.2	352	21.2
55340	600	19.9	3000	-	360	19.9
55341	600	19.9	3000	-	390	19.9
55342	600	19.9	3000	-	420	19.9
55343	600	19.9	3000	-	450	19.9
55344	600	19.9	3000	-	480	19.9
55345	600	19.9	3000	-	510	19.9
55346	600	19.9	3000	-	540	19.9
55347	600	19.9	3000	-	570	19.9
55348	600	19.9	3000	-	600	19.9
55349	600	19.9	3000	-	630	19.9
55350	600	19.9	3000	-	660	19.9
55351	600	19.9	3000	-	690	19.9
55352	600	19.9	3000	-	720	19.9
55353	600	19.9	3000	-	750	19.9
55354	600	19.9	3000	-	780	19.9
55355	600	19.9	3000	-	810	19.9
55356	600	19.9	3000	-	840	19.9
55357	600	19.9	3000	-	870	19.9
55266	750	24.8	3750	2.7	333	19.5
55374	550	18.2	2750	-	405	18.2
55375	550	18.2	2750	-	432	18.2
55376	550	18.2	2750	-	459	18.2
55377	550	18.2	2750	-	486	18.2
55378	550	18.2	2750	-	513	18.2
55379	550	18.2	2750	-	540	18.2
55380	550	18.2	2750	-	567	18.2
55381	550	18.2	2750	-	594	18.2
55382	550	18.2	2750	-	621	18.2
55383	550	18.2	2750	-	648	18.2
55384	550	18.2	2750	-	675	18.2
55385	550	18.2	2750	-	702	18.2
55386	550	18.2	2750	-	729	18.2
55387	550	18.2	2750	-	756	18.2
55388	550	18.2	2750	-	783	18.2
55389	550	18.2	2750	-	810	18.2
55390	550	18.2	2750	-	837	18.2
55391	550	18.2	2750	-	864	18.2
55414	500	16.6	2500	-	475	16.6
55415	500	16.6	2500	-	500	16.6
55416	500	16.6	2500	-	525	16.6
55417	500	16.6	2500	-	550	16.6
55418	500	16.6	2500	-	575	16.6
55419	500	16.6	2500	-	600	16.6
55420	500	16.6	2500	-	625	16.6
55421	500	16.6	2500	-	650	16.6
55422	500	16.6	2500	-	675	16.6
55423	500	16.6	2500	-	700	16.6
55424	500	16.6	2500	-	725	16.6
55425	500	16.6	2500	-	750	16.6
55426	500	16.6	2500	-	775	16.6
55427	500	16.6	2500	-	800	16.6
55428	500	16.6	2500	-	825	16.6
55429	500	16.6	2500	-	850	16.6
55430	500	16.6	2500	-	875	16.6
55183	1050	23.1	5250	3.9	312	15.3
55216	900	21.2	4500	4.2	315	12.8
55247	800	20.7	4000	4.1	320	12.5
55161	1200	20.9	6000	4.4	300	12.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

No probes

Overall score = score_ratio - 2 * repetitive DNA content