Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign24 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (251)
Redundant probes (1)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:45:28 2005`

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

Fetched probe design: ProbeDesign24
  assembly      : NCBIM33
  bias          : 5prime
  chromosome    : 12
  id            : 1
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 41
Fetched conf : Exonerate mouse_NCBI33 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM33/genome/masked_dusted
Fetched 405 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        : 405/405
Putative probes exceeding selection criteria: 252/405

PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW
--------------------------------------------------------------

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
15	1000	32.9	5000	-	700	32.9
16	1000	32.9	5000	-	750	32.9
17	1000	32.9	5000	-	800	32.9
18	1000	32.9	5000	-	850	32.9
19	1000	32.9	5000	-	900	32.9
20	1000	32.9	5000	-	950	32.9
21	1000	32.9	5000	-	1000	32.9
37	950	31.2	4750	-	705	31.2
38	950	31.2	4750	-	752	31.2
39	950	31.2	4750	-	799	31.2
40	950	31.2	4750	-	846	31.2
41	950	31.2	4750	-	893	31.2
42	950	31.2	4750	-	940	31.2
43	950	31.2	4750	-	987	31.2
44	950	31.2	4750	-	1034	31.2
9	1000	29.9	5000	-	400	29.9
10	1000	29.9	5000	-	450	29.9
11	1000	29.9	5000	-	500	29.9
12	1000	29.9	5000	-	550	29.9
13	1000	29.9	5000	-	600	29.9
14	1000	29.9	5000	-	650	29.9
60	900	29.6	4500	-	675	29.6
61	900	29.6	4500	-	720	29.6
62	900	29.6	4500	-	765	29.6
63	900	29.6	4500	-	810	29.6
64	900	29.6	4500	-	855	29.6
65	900	29.6	4500	-	900	29.6
66	900	29.6	4500	-	945	29.6
67	900	29.6	4500	-	990	29.6
68	900	29.6	4500	-	1035	29.6
69	900	29.6	4500	-	1080	29.6
31	950	28.4	4750	-	423	28.4
32	950	28.4	4750	-	470	28.4
33	950	28.4	4750	-	517	28.4
34	950	28.4	4750	-	564	28.4
35	950	28.4	4750	-	611	28.4
36	950	28.4	4750	-	658	28.4
86	850	28.0	4250	-	672	28.0
87	850	28.0	4250	-	714	28.0
88	850	28.0	4250	-	756	28.0
89	850	28.0	4250	-	798	28.0
90	850	28.0	4250	-	840	28.0
91	850	28.0	4250	-	882	28.0
92	850	28.0	4250	-	924	28.0
93	850	28.0	4250	-	966	28.0
94	850	28.0	4250	-	1008	28.0
95	850	28.0	4250	-	1050	28.0
96	850	28.0	4250	-	1092	28.0
97	850	28.0	4250	-	1134	28.0
54	900	26.9	4500	-	405	26.9
55	900	26.9	4500	-	450	26.9
56	900	26.9	4500	-	495	26.9
57	900	26.9	4500	-	540	26.9
58	900	26.9	4500	-	585	26.9
59	900	26.9	4500	-	630	26.9
115	800	26.3	4000	-	680	26.3
116	800	26.3	4000	-	720	26.3
117	800	26.3	4000	-	760	26.3
118	800	26.3	4000	-	800	26.3
119	800	26.3	4000	-	840	26.3
120	800	26.3	4000	-	880	26.3
121	800	26.3	4000	-	920	26.3
122	800	26.3	4000	-	960	26.3
123	800	26.3	4000	-	1000	26.3
124	800	26.3	4000	-	1040	26.3
125	800	26.3	4000	-	1080	26.3
126	800	26.3	4000	-	1120	26.3
127	800	26.3	4000	-	1160	26.3
128	800	26.3	4000	-	1200	26.3
30	950	28.4	4750	1.3	376	25.9
80	850	25.4	4250	-	420	25.4
81	850	25.4	4250	-	462	25.4
82	850	25.4	4250	-	504	25.4
83	850	25.4	4250	-	546	25.4
84	850	25.4	4250	-	588	25.4
85	850	25.4	4250	-	630	25.4
147	750	24.7	3750	-	666	24.7
148	750	24.7	3750	-	703	24.7
149	750	24.7	3750	-	740	24.7
150	750	24.7	3750	-	777	24.7
151	750	24.7	3750	-	814	24.7
152	750	24.7	3750	-	851	24.7
153	750	24.7	3750	-	888	24.7
154	750	24.7	3750	-	925	24.7
155	750	24.7	3750	-	962	24.7
156	750	24.7	3750	-	999	24.7
157	750	24.7	3750	-	1036	24.7
158	750	24.7	3750	-	1073	24.7
159	750	24.7	3750	-	1110	24.7
160	750	24.7	3750	-	1147	24.7
161	750	24.7	3750	-	1184	24.7
162	750	24.7	3750	-	1221	24.7
108	800	24.0	4000	-	400	24.0
109	800	24.0	4000	-	440	24.0
110	800	24.0	4000	-	480	24.0
111	800	24.0	4000	-	520	24.0
112	800	24.0	4000	-	560	24.0
113	800	24.0	4000	-	600	24.0
114	800	24.0	4000	-	640	24.0
79	850	25.4	4250	1.2	378	23.1
182	700	23.0	3500	-	665	23.0
183	700	23.0	3500	-	700	23.0
184	700	23.0	3500	-	735	23.0
185	700	23.0	3500	-	770	23.0
186	700	23.0	3500	-	805	23.0
187	700	23.0	3500	-	840	23.0
188	700	23.0	3500	-	875	23.0
189	700	23.0	3500	-	910	23.0
190	700	23.0	3500	-	945	23.0
191	700	23.0	3500	-	980	23.0
192	700	23.0	3500	-	1015	23.0
193	700	23.0	3500	-	1050	23.0
194	700	23.0	3500	-	1085	23.0
195	700	23.0	3500	-	1120	23.0
196	700	23.0	3500	-	1155	23.0
197	700	23.0	3500	-	1190	23.0
198	700	23.0	3500	-	1225	23.0
140	750	22.5	3750	-	407	22.5
141	750	22.5	3750	-	444	22.5
142	750	22.5	3750	-	481	22.5
143	750	22.5	3750	-	518	22.5
144	750	22.5	3750	-	555	22.5
145	750	22.5	3750	-	592	22.5
146	750	22.5	3750	-	629	22.5
222	650	21.4	3250	-	672	21.4
223	650	21.4	3250	-	704	21.4
224	650	21.4	3250	-	736	21.4
225	650	21.4	3250	-	768	21.4
226	650	21.4	3250	-	800	21.4
227	650	21.4	3250	-	832	21.4
228	650	21.4	3250	-	864	21.4
229	650	21.4	3250	-	896	21.4
230	650	21.4	3250	-	928	21.4
231	650	21.4	3250	-	960	21.4
232	650	21.4	3250	-	992	21.4
233	650	21.4	3250	-	1024	21.4
234	650	21.4	3250	-	1056	21.4
235	650	21.4	3250	-	1088	21.4
236	650	21.4	3250	-	1120	21.4
237	650	21.4	3250	-	1152	21.4
238	650	21.4	3250	-	1184	21.4
239	650	21.4	3250	-	1216	21.4
175	700	21.0	3500	-	420	21.0
176	700	21.0	3500	-	455	21.0
177	700	21.0	3500	-	490	21.0
178	700	21.0	3500	-	525	21.0
179	700	21.0	3500	-	560	21.0
180	700	21.0	3500	-	595	21.0
181	700	21.0	3500	-	630	21.0
53	900	26.9	4500	3.1	360	20.7
8	1000	27.8	5000	3.8	350	20.2
174	700	21.0	3500	0.4	385	20.1
268	600	19.7	3000	-	720	19.7
269	600	19.7	3000	-	750	19.7
270	600	19.7	3000	-	780	19.7
271	600	19.7	3000	-	810	19.7
272	600	19.7	3000	-	840	19.7
273	600	19.7	3000	-	870	19.7
274	600	19.7	3000	-	900	19.7
275	600	19.7	3000	-	930	19.7
276	600	19.7	3000	-	960	19.7
277	600	19.7	3000	-	990	19.7
278	600	19.7	3000	-	1020	19.7
279	600	19.7	3000	-	1050	19.7
280	600	19.7	3000	-	1080	19.7
281	600	19.7	3000	-	1110	19.7
282	600	19.7	3000	-	1140	19.7
283	600	19.7	3000	-	1170	19.7
284	600	19.7	3000	-	1200	19.7
285	600	19.7	3000	-	1230	19.7
214	650	19.5	3250	-	416	19.5
215	650	19.5	3250	-	448	19.5
216	650	19.5	3250	-	480	19.5
217	650	19.5	3250	-	512	19.5
218	650	19.5	3250	-	544	19.5
219	650	19.5	3250	-	576	19.5
220	650	19.5	3250	-	608	19.5
221	650	19.5	3250	-	640	19.5
213	650	19.5	3250	0.6	384	18.2
337	550	18.2	2750	-	1242	18.2
319	550	18.1	2750	-	756	18.1
320	550	18.1	2750	-	783	18.1
321	550	18.1	2750	-	810	18.1
322	550	18.1	2750	-	837	18.1
323	550	18.1	2750	-	864	18.1
324	550	18.1	2750	-	891	18.1
325	550	18.1	2750	-	918	18.1
326	550	18.1	2750	-	945	18.1
327	550	18.1	2750	-	972	18.1
328	550	18.1	2750	-	999	18.1
329	550	18.1	2750	-	1026	18.1
330	550	18.1	2750	-	1053	18.1
331	550	18.1	2750	-	1080	18.1
332	550	18.1	2750	-	1107	18.1
333	550	18.1	2750	-	1134	18.1
334	550	18.1	2750	-	1161	18.1
335	550	18.1	2750	-	1188	18.1
336	550	18.1	2750	-	1215	18.1
257	600	18.0	3000	-	390	18.0
258	600	18.0	3000	-	420	18.0
259	600	18.0	3000	-	450	18.0
260	600	18.0	3000	-	480	18.0
261	600	18.0	3000	-	510	18.0
262	600	18.0	3000	-	540	18.0
263	600	18.0	3000	-	570	18.0
264	600	18.0	3000	-	600	18.0
265	600	18.0	3000	-	630	18.0
266	600	18.0	3000	-	660	18.0
139	750	22.5	3750	2.4	370	17.7
107	800	24.0	4000	3.5	360	17.0
306	550	16.5	2750	-	405	16.5
307	550	16.5	2750	-	432	16.5
308	550	16.5	2750	-	459	16.5
309	550	16.5	2750	-	486	16.5
310	550	16.5	2750	-	513	16.5
311	550	16.5	2750	-	540	16.5
312	550	16.5	2750	-	567	16.5
313	550	16.5	2750	-	594	16.5
314	550	16.5	2750	-	621	16.5
315	550	16.5	2750	-	648	16.5
377	500	16.4	2500	-	800	16.4
378	500	16.4	2500	-	825	16.4
379	500	16.4	2500	-	850	16.4
380	500	16.4	2500	-	875	16.4
381	500	16.4	2500	-	900	16.4
382	500	16.4	2500	-	925	16.4
383	500	16.4	2500	-	950	16.4
384	500	16.4	2500	-	975	16.4
385	500	16.4	2500	-	1000	16.4
386	500	16.4	2500	-	1025	16.4
387	500	16.4	2500	-	1050	16.4
388	500	16.4	2500	-	1075	16.4
389	500	16.4	2500	-	1100	16.4
390	500	16.4	2500	-	1125	16.4
391	500	16.4	2500	-	1150	16.4
392	500	16.4	2500	-	1175	16.4
393	500	16.4	2500	-	1200	16.4
394	500	16.4	2500	-	1225	16.4
361	500	15.0	2500	-	400	15.0
362	500	15.0	2500	-	425	15.0
363	500	15.0	2500	-	450	15.0
364	500	15.0	2500	-	475	15.0
365	500	15.0	2500	-	500	15.0
366	500	15.0	2500	-	525	15.0
367	500	15.0	2500	-	550	15.0
368	500	15.0	2500	-	575	15.0
369	500	15.0	2500	-	600	15.0
370	500	15.0	2500	-	625	15.0
371	500	15.0	2500	-	650	15.0
305	550	16.5	2750	1.8	378	12.8
360	500	15.0	2500	2.6	375	9.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
256	600	18.0	3000	4.7	360	8.6

Overall score = score_ratio - 2 * repetitive DNA content