Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign57 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (196)
Redundant probes (0)

Summary

`./analyse_probe_search_results : Thu Sep 29 17:22:41 2005`

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

Fetched probe design: ProbeDesign57
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 11
  id            : 44
  strand        : 1
  -------------

Design window length: 1401bp

All jobs for probe design are successful - total: 13
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 247 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        : 247/247
Putative probes exceeding selection criteria: 196/247

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
46124	1300	28.0	6500	-	0	28.0
46125	1300	28.0	6500	-	65	28.0
46126	1250	26.9	6250	-	0	26.9
46127	1250	26.9	6250	-	62	26.9
46128	1250	26.9	6250	-	124	26.9
46129	1200	25.9	6000	-	0	25.9
46130	1200	25.9	6000	-	60	25.9
46131	1200	25.9	6000	-	120	25.9
46132	1200	25.9	6000	-	180	25.9
46182	850	25.3	4250	-	0	25.3
46133	1150	24.8	5750	-	0	24.8
46134	1150	24.8	5750	-	57	24.8
46135	1150	24.8	5750	-	114	24.8
46136	1150	24.8	5750	-	171	24.8
46137	1150	24.8	5750	-	228	24.8
46138	1100	23.7	5500	-	0	23.7
46139	1100	23.7	5500	-	55	23.7
46140	1100	23.7	5500	-	110	23.7
46141	1100	23.7	5500	-	165	23.7
46142	1100	23.7	5500	-	220	23.7
46143	1100	23.7	5500	-	275	23.7
46144	1050	22.6	5250	-	0	22.6
46145	1050	22.6	5250	-	52	22.6
46146	1050	22.6	5250	-	104	22.6
46147	1050	22.6	5250	-	156	22.6
46148	1050	22.6	5250	-	208	22.6
46149	1050	22.6	5250	-	260	22.6
46150	1050	22.6	5250	-	312	22.6
46151	1000	21.6	5000	-	0	21.6
46152	1000	21.6	5000	-	50	21.6
46153	1000	21.6	5000	-	100	21.6
46154	1000	21.6	5000	-	150	21.6
46155	1000	21.6	5000	-	200	21.6
46156	1000	21.6	5000	-	250	21.6
46157	1000	21.6	5000	-	300	21.6
46158	1000	21.6	5000	-	350	21.6
46159	1000	21.6	5000	-	400	21.6
46160	950	20.5	4750	-	0	20.5
46161	950	20.5	4750	-	47	20.5
46162	950	20.5	4750	-	94	20.5
46163	950	20.5	4750	-	141	20.5
46164	950	20.5	4750	-	188	20.5
46165	950	20.5	4750	-	235	20.5
46166	950	20.5	4750	-	282	20.5
46167	950	20.5	4750	-	329	20.5
46168	950	20.5	4750	-	376	20.5
46169	950	20.5	4750	-	423	20.5
46170	900	19.4	4500	-	0	19.4
46171	900	19.4	4500	-	45	19.4
46172	900	19.4	4500	-	90	19.4
46173	900	19.4	4500	-	135	19.4
46174	900	19.4	4500	-	180	19.4
46175	900	19.4	4500	-	225	19.4
46176	900	19.4	4500	-	270	19.4
46177	900	19.4	4500	-	315	19.4
46178	900	19.4	4500	-	360	19.4
46179	900	19.4	4500	-	405	19.4
46180	900	19.4	4500	-	450	19.4
46181	900	19.4	4500	-	495	19.4
46333	550	18.3	2750	-	837	18.3
46183	850	18.3	4250	-	42	18.3
46184	850	18.3	4250	-	84	18.3
46185	850	18.3	4250	-	126	18.3
46186	850	18.3	4250	-	168	18.3
46187	850	18.3	4250	-	210	18.3
46188	850	18.3	4250	-	252	18.3
46189	850	18.3	4250	-	294	18.3
46190	850	18.3	4250	-	336	18.3
46191	850	18.3	4250	-	378	18.3
46192	850	18.3	4250	-	420	18.3
46193	850	18.3	4250	-	462	18.3
46194	850	18.3	4250	-	504	18.3
46195	850	18.3	4250	-	546	18.3
46215	750	18.3	3750	-	111	18.3
46313	550	18.0	2750	-	297	18.0
46198	800	17.2	4000	-	80	17.2
46199	800	17.2	4000	-	120	17.2
46200	800	17.2	4000	-	160	17.2
46201	800	17.2	4000	-	200	17.2
46202	800	17.2	4000	-	240	17.2
46203	800	17.2	4000	-	280	17.2
46204	800	17.2	4000	-	320	17.2
46205	800	17.2	4000	-	360	17.2
46206	800	17.2	4000	-	400	17.2
46207	800	17.2	4000	-	440	17.2
46208	800	17.2	4000	-	480	17.2
46209	800	17.2	4000	-	520	17.2
46210	800	17.2	4000	-	560	17.2
46211	800	17.2	4000	-	600	17.2
46368	500	16.7	2500	-	850	16.7
46369	500	16.7	2500	-	875	16.7
46370	500	16.7	2500	-	900	16.7
46216	750	16.2	3750	-	148	16.2
46217	750	16.2	3750	-	185	16.2
46218	750	16.2	3750	-	222	16.2
46219	750	16.2	3750	-	259	16.2
46220	750	16.2	3750	-	296	16.2
46221	750	16.2	3750	-	333	16.2
46222	750	16.2	3750	-	370	16.2
46223	750	16.2	3750	-	407	16.2
46224	750	16.2	3750	-	444	16.2
46225	750	16.2	3750	-	481	16.2
46226	750	16.2	3750	-	518	16.2
46227	750	16.2	3750	-	555	16.2
46228	750	16.2	3750	-	592	16.2
46229	750	16.2	3750	-	629	16.2
46235	700	15.8	3500	-	175	15.8
46367	500	15.4	2500	-	825	15.4
46236	700	15.1	3500	-	210	15.1
46237	700	15.1	3500	-	245	15.1
46238	700	15.1	3500	-	280	15.1
46239	700	15.1	3500	-	315	15.1
46240	700	15.1	3500	-	350	15.1
46241	700	15.1	3500	-	385	15.1
46242	700	15.1	3500	-	420	15.1
46243	700	15.1	3500	-	455	15.1
46244	700	15.1	3500	-	490	15.1
46245	700	15.1	3500	-	525	15.1
46246	700	15.1	3500	-	560	15.1
46247	700	15.1	3500	-	595	15.1
46248	700	15.1	3500	-	630	15.1
46249	700	15.1	3500	-	665	15.1
46250	700	15.1	3500	-	700	15.1
46258	650	15.0	3250	-	224	15.0
46348	500	14.9	2500	-	350	14.9
46284	600	14.6	3000	-	270	14.6
46332	550	14.3	2750	-	810	14.3
46259	650	14.0	3250	-	256	14.0
46260	650	14.0	3250	-	288	14.0
46261	650	14.0	3250	-	320	14.0
46262	650	14.0	3250	-	352	14.0
46263	650	14.0	3250	-	384	14.0
46264	650	14.0	3250	-	416	14.0
46265	650	14.0	3250	-	448	14.0
46266	650	14.0	3250	-	480	14.0
46267	650	14.0	3250	-	512	14.0
46268	650	14.0	3250	-	544	14.0
46269	650	14.0	3250	-	576	14.0
46270	650	14.0	3250	-	608	14.0
46271	650	14.0	3250	-	640	14.0
46272	650	14.0	3250	-	672	14.0
46273	650	14.0	3250	-	704	14.0
46274	650	14.0	3250	-	736	14.0
46285	600	12.9	3000	-	300	12.9
46286	600	12.9	3000	-	330	12.9
46287	600	12.9	3000	-	360	12.9
46288	600	12.9	3000	-	390	12.9
46289	600	12.9	3000	-	420	12.9
46290	600	12.9	3000	-	450	12.9
46291	600	12.9	3000	-	480	12.9
46292	600	12.9	3000	-	510	12.9
46293	600	12.9	3000	-	540	12.9
46294	600	12.9	3000	-	570	12.9
46295	600	12.9	3000	-	600	12.9
46296	600	12.9	3000	-	630	12.9
46297	600	12.9	3000	-	660	12.9
46298	600	12.9	3000	-	690	12.9
46299	600	12.9	3000	-	720	12.9
46300	600	12.9	3000	-	750	12.9
46301	600	12.9	3000	-	780	12.9
46314	550	12.7	2750	-	324	12.7
46315	550	11.9	2750	-	351	11.9
46316	550	11.9	2750	-	378	11.9
46317	550	11.9	2750	-	405	11.9
46318	550	11.9	2750	-	432	11.9
46319	550	11.9	2750	-	459	11.9
46320	550	11.9	2750	-	486	11.9
46321	550	11.9	2750	-	513	11.9
46322	550	11.9	2750	-	540	11.9
46323	550	11.9	2750	-	567	11.9
46324	550	11.9	2750	-	594	11.9
46325	550	11.9	2750	-	621	11.9
46326	550	11.9	2750	-	648	11.9
46327	550	11.9	2750	-	675	11.9
46328	550	11.9	2750	-	702	11.9
46329	550	11.9	2750	-	729	11.9
46330	550	11.9	2750	-	756	11.9
46331	550	11.9	2750	-	783	11.9
46366	500	11.6	2500	-	800	11.6
46349	500	11.3	2500	-	375	11.3
46350	500	10.8	2500	-	400	10.8
46351	500	10.8	2500	-	425	10.8
46352	500	10.8	2500	-	450	10.8
46353	500	10.8	2500	-	475	10.8
46354	500	10.8	2500	-	500	10.8
46355	500	10.8	2500	-	525	10.8
46356	500	10.8	2500	-	550	10.8
46357	500	10.8	2500	-	575	10.8
46358	500	10.8	2500	-	600	10.8
46359	500	10.8	2500	-	625	10.8
46360	500	10.8	2500	-	650	10.8
46361	500	10.8	2500	-	675	10.8
46362	500	10.8	2500	-	700	10.8
46363	500	10.8	2500	-	725	10.8
46364	500	10.8	2500	-	750	10.8
46365	500	10.8	2500	-	775	10.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

No probes

Overall score = score_ratio - 2 * repetitive DNA content