Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign123 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (120)
Redundant probes (46)

Summary

`./analyse_probe_search_results : Wed Jun 28 17:25:07 2006`

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

Fetched probe design: ProbeDesign123
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : 11
  id            : 117
  strand        : 1
  -------------

Design window length: 1501bp

All jobs for probe design are successful - total: 15
Fetched conf : Exonerate mouse_NCBIM36 (id: 2)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/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                 : 0/289

  No putative probes pass with the above criteria
  Now trying: score-ratio 2, and percent repetitive 40

Putative probes exceeding selection criteria    : 166/289 (both unique and not unique)
Putative probes with successfully-picked primers: 166/166

Identified 46 '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
109434	500	14.2	2500	13.8	0	-13.4
109435	500	14.2	2500	16.6	25	-19.0
109398	550	10.5	2750	19.6	0	-28.7
109460	500	14.5	2500	23.4	650	-32.3
109436	500	9.6	2500	21.6	50	-33.6
109216	1050	7.4	5250	21.1	0	-34.8
109459	500	10.0	2500	22.8	625	-35.6
109225	1000	7.1	5000	21.6	0	-36.1
109226	1000	7.1	5000	22.2	50	-37.3
109236	950	6.7	4750	22.7	0	-38.7
109237	950	6.7	4750	22.7	47	-38.7
109238	950	6.7	4750	22.7	94	-38.7
109458	500	6.8	2500	22.8	600	-38.8
109461	500	13.3	2500	26.2	675	-39.1
109457	500	5.1	2500	22.8	575	-40.5
109456	500	4.2	2500	22.8	550	-41.4
109248	900	6.4	4500	24.0	0	-41.6
109249	900	6.4	4500	24.0	45	-41.6
109250	900	6.4	4500	24.0	90	-41.6
109251	900	6.4	4500	24.0	135	-41.6
109208	1100	7.8	5500	24.7	0	-41.7
109399	550	7.1	2750	24.5	27	-42.0
109422	550	14.6	2750	28.4	648	-42.1
109217	1050	7.4	5250	26.1	52	-44.7
109262	850	6.0	4250	25.4	0	-44.8
109263	850	6.0	4250	25.4	42	-44.8
109264	850	6.0	4250	25.4	84	-44.8
109265	850	6.0	4250	25.4	126	-44.8
109266	850	6.0	4250	25.4	168	-44.8
109462	500	13.3	2500	29.4	700	-45.5
109437	500	6.6	2500	26.6	75	-46.6
109367	600	6.0	3000	26.3	0	-46.7
109227	1000	7.1	5000	27.2	100	-47.3
109201	1150	8.2	5750	28.0	0	-47.8
109423	550	14.6	2750	31.3	675	-47.9
109278	800	5.7	4000	27.0	0	-48.3
109279	800	5.7	4000	27.0	40	-48.3
109280	800	5.7	4000	27.0	80	-48.3
109281	800	5.7	4000	27.0	120	-48.3
109282	800	5.7	4000	27.0	160	-48.3
109283	800	5.7	4000	27.0	200	-48.3
109284	800	5.7	4000	27.0	240	-48.3
109267	850	6.0	4250	27.3	210	-48.6
109239	950	6.7	4750	27.7	141	-48.6
109421	550	10.2	2750	29.8	621	-49.4
109416	550	4.0	2750	26.7	486	-49.5
109455	500	3.6	2500	26.6	525	-49.6
109252	900	6.4	4500	28.0	180	-49.6
109209	1100	7.8	5500	29.7	55	-51.7
109195	1200	8.5	6000	30.2	0	-52.0
109296	750	5.3	3750	28.8	0	-52.3
109297	750	5.3	3750	28.8	37	-52.3
109298	750	5.3	3750	28.8	74	-52.3
109299	750	5.3	3750	28.8	111	-52.3
109300	750	5.3	3750	28.8	148	-52.3
109301	750	5.3	3750	28.8	185	-52.3
109302	750	5.3	3750	28.8	222	-52.3
109303	750	5.3	3750	28.8	259	-52.3
109420	550	7.0	2750	29.8	594	-52.7
109304	750	5.3	3750	29.1	296	-52.8
109400	550	5.3	2750	29.5	54	-53.6
109419	550	5.2	2750	29.8	567	-54.4
109218	1050	7.4	5250	31.0	104	-54.6
109389	600	14.6	3000	34.7	660	-54.8
109388	600	13.4	3000	34.2	630	-54.9
109382	600	4.3	3000	29.7	450	-55.1
109454	500	3.6	2500	29.4	500	-55.2
109418	550	4.4	2750	29.8	540	-55.3
109463	500	13.3	2500	34.4	725	-55.5
109417	550	4.0	2750	29.8	513	-55.6
109202	1150	8.2	5750	32.2	57	-56.2
109317	700	5.0	3500	30.9	0	-56.7
109318	700	5.0	3500	30.9	35	-56.7
109319	700	5.0	3500	30.9	70	-56.7
109320	700	5.0	3500	30.9	105	-56.7
109321	700	5.0	3500	30.9	140	-56.7
109322	700	5.0	3500	30.9	175	-56.7
109323	700	5.0	3500	30.9	210	-56.7
109324	700	5.0	3500	30.9	245	-56.7
109325	700	5.0	3500	30.9	280	-56.7
109326	700	5.0	3500	30.9	315	-56.7
109190	1250	8.9	6250	33.0	0	-57.2
109228	1000	7.1	5000	32.2	150	-57.3
109285	800	5.7	4000	31.5	280	-57.3
109368	600	4.8	3000	31.3	30	-57.9
109438	500	5.0	2500	31.6	100	-58.2
109268	850	6.0	4250	32.2	252	-58.4
109327	700	5.0	3500	31.7	350	-58.5
109340	650	4.6	3250	31.5	0	-58.5
109240	950	6.7	4750	32.6	188	-58.5
109415	550	3.9	2750	31.3	459	-58.6
109383	600	4.3	3000	31.5	480	-58.7
109253	900	6.4	4500	33.0	225	-59.6
109453	500	3.6	2500	31.6	475	-59.6
109210	1100	7.8	5500	33.9	110	-60.0
109387	600	8.2	3000	34.2	600	-60.1
109341	650	4.6	3250	33.2	32	-61.9
109342	650	4.6	3250	33.2	64	-61.9
109343	650	4.6	3250	33.2	96	-61.9
109344	650	4.6	3250	33.2	128	-61.9
109345	650	4.6	3250	33.2	160	-61.9
109346	650	4.6	3250	33.2	192	-61.9
109347	650	4.6	3250	33.2	224	-61.9
109348	650	4.6	3250	33.2	256	-61.9
109349	650	4.6	3250	33.2	288	-61.9
109350	650	4.6	3250	33.2	320	-61.9
109351	650	4.6	3250	33.2	352	-61.9
109352	650	4.6	3250	33.2	384	-61.9
109196	1200	8.5	6000	35.2	60	-62.0
109186	1300	9.2	6500	35.6	0	-62.0
109305	750	5.3	3750	34.0	333	-62.7
109219	1050	7.4	5250	35.1	156	-62.8
109381	600	4.3	3000	33.7	420	-63.1
109401	550	4.4	2750	34.4	81	-64.4
109414	550	3.9	2750	34.5	432	-65.2
109452	500	3.5	2500	34.4	450	-65.3
109353	650	4.6	3250	35.1	416	-65.5
109354	650	4.6	3250	35.1	448	-65.5
109384	600	4.4	3000	35.5	510	-66.6
109191	1250	8.9	6250	38.0	62	-67.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
109424	550	13.6	2750	36.2	702	-58.7
109360	650	15.6	3250	39.2	640	-62.8
109390	600	14.4	3000	39.5	690	-64.6
109229	1000	7.1	5000	36.3	200	-65.5
109386	600	5.8	3000	35.7	570	-65.5
109203	1150	8.2	5750	37.1	114	-66.1
109464	500	12.4	2500	39.4	750	-66.4
109241	950	6.7	4750	36.6	235	-66.5
109385	600	4.8	3000	35.7	540	-66.6
109286	800	5.7	4000	36.5	320	-67.3
109369	600	4.3	3000	35.8	60	-67.4
109370	600	4.3	3000	36.0	90	-67.7
109371	600	4.3	3000	36.0	120	-67.7
109372	600	4.3	3000	36.0	150	-67.7
109373	600	4.3	3000	36.0	180	-67.7
109374	600	4.3	3000	36.0	210	-67.7
109375	600	4.3	3000	36.0	240	-67.7
109376	600	4.3	3000	36.0	270	-67.7
109377	600	4.3	3000	36.0	300	-67.7
109378	600	4.3	3000	36.0	330	-67.7
109379	600	4.3	3000	36.0	360	-67.7
109380	600	4.3	3000	36.0	390	-67.7
109269	850	6.0	4250	37.2	294	-68.3
109359	650	10.0	3250	39.2	608	-68.5
109328	700	5.0	3500	36.7	385	-68.5
109355	650	4.6	3250	36.8	480	-68.9
109439	500	4.1	2500	36.6	125	-69.1
109254	900	6.4	4500	38.0	270	-69.6
109211	1100	7.8	5500	38.9	165	-70.0
109358	650	6.7	3250	39.2	576	-71.8
109306	750	5.3	3750	38.9	370	-72.5
109357	650	5.3	3250	39.2	544	-73.2
109402	550	3.9	2750	38.7	108	-73.6
109329	700	5.0	3500	39.7	420	-74.5
109403	550	3.9	2750	39.3	135	-74.6
109404	550	3.9	2750	39.3	162	-74.6
109405	550	3.9	2750	39.3	189	-74.6
109406	550	3.9	2750	39.3	216	-74.6
109407	550	3.9	2750	39.3	243	-74.6
109408	550	3.9	2750	39.3	270	-74.6
109409	550	3.9	2750	39.3	297	-74.6
109410	550	3.9	2750	39.3	324	-74.6
109411	550	3.9	2750	39.3	351	-74.6
109412	550	3.9	2750	39.3	378	-74.6
109413	550	3.9	2750	39.3	405	-74.6
109451	500	3.5	2500	39.4	425	-75.3

Overall score = score_ratio - 2 * repetitive DNA content