Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign102 - back to list

Summary
Image
Unique putative probes (300)
Putative probes (35)
Redundant probes (177)

Summary

`./analyse_probe_search_results : Tue Jan 31 11:33:29 2006`

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

Fetched probe design: ProbeDesign102
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 11
  id            : 93
  strand        : 1
  -------------

Design window length: 2046bp

All jobs for probe design are successful - total: 26
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 512 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            : 512/512
Putative probes that are unique                 : 300/512
Putative probes exceeding selection criteria    : 512/512 (both unique and not unique)
Putative probes with successfully-picked primers: 512/512

Identified 177 '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
88218	1300	6500	-	0
88219	1300	6500	-	65
88220	1300	6500	-	130
88221	1300	6500	-	195
88230	1250	6250	-	0
88231	1250	6250	-	62
88232	1250	6250	-	124
88233	1250	6250	-	186
88234	1250	6250	-	248
88243	1200	6000	-	0
88244	1200	6000	-	60
88245	1200	6000	-	120
88246	1200	6000	-	180
88247	1200	6000	-	240
88248	1200	6000	-	300
88258	1150	5750	-	0
88259	1150	5750	-	57
88260	1150	5750	-	114
88261	1150	5750	-	171
88262	1150	5750	-	228
88263	1150	5750	-	285
88264	1150	5750	-	342
88274	1100	5500	-	0
88275	1100	5500	-	55
88276	1100	5500	-	110
88277	1100	5500	-	165
88278	1100	5500	-	220
88279	1100	5500	-	275
88280	1100	5500	-	330
88281	1100	5500	-	385
88292	1050	5250	-	0
88293	1050	5250	-	52
88294	1050	5250	-	104
88295	1050	5250	-	156
88296	1050	5250	-	208
88297	1050	5250	-	260
88298	1050	5250	-	312
88299	1050	5250	-	364
88300	1050	5250	-	416
88301	1050	5250	-	468
88312	1000	5000	-	0
88313	1000	5000	-	50
88314	1000	5000	-	100
88315	1000	5000	-	150
88316	1000	5000	-	200
88317	1000	5000	-	250
88318	1000	5000	-	300
88319	1000	5000	-	350
88320	1000	5000	-	400
88321	1000	5000	-	450
88322	1000	5000	-	500
88333	950	4750	-	0
88334	950	4750	-	47
88335	950	4750	-	94
88336	950	4750	-	141
88337	950	4750	-	188
88338	950	4750	-	235
88339	950	4750	-	282
88340	950	4750	-	329
88341	950	4750	-	376
88342	950	4750	-	423
88343	950	4750	-	470
88344	950	4750	-	517
88345	950	4750	-	564
88357	900	4500	-	0
88358	900	4500	-	45
88359	900	4500	-	90
88360	900	4500	-	135
88361	900	4500	-	180
88362	900	4500	-	225
88363	900	4500	-	270
88364	900	4500	-	315
88365	900	4500	-	360
88366	900	4500	-	405
88367	900	4500	-	450
88368	900	4500	-	495
88369	900	4500	-	540
88370	900	4500	-	585
88371	900	4500	-	630
88383	850	4250	-	0
88384	850	4250	-	42
88385	850	4250	-	84
88386	850	4250	-	126
88387	850	4250	-	168
88388	850	4250	-	210
88389	850	4250	-	252
88390	850	4250	-	294
88391	850	4250	-	336
88392	850	4250	-	378
88393	850	4250	-	420
88394	850	4250	-	462
88395	850	4250	-	504
88396	850	4250	-	546
88397	850	4250	-	588
88398	850	4250	-	630
88399	850	4250	-	672
88412	800	4000	-	0
88413	800	4000	-	40
88414	800	4000	-	80
88415	800	4000	-	120
88416	800	4000	-	160
88417	800	4000	-	200
88418	800	4000	-	240
88419	800	4000	-	280
88420	800	4000	-	320
88421	800	4000	-	360
88422	800	4000	-	400
88423	800	4000	-	440
88424	800	4000	-	480
88425	800	4000	-	520
88426	800	4000	-	560
88427	800	4000	-	600
88428	800	4000	-	640
88429	800	4000	-	680
88430	800	4000	-	720
88444	750	3750	-	0
88445	750	3750	-	37
88446	750	3750	-	74
88447	750	3750	-	111
88448	750	3750	-	148
88449	750	3750	-	185
88450	750	3750	-	222
88451	750	3750	-	259
88452	750	3750	-	296
88453	750	3750	-	333
88454	750	3750	-	370
88455	750	3750	-	407
88456	750	3750	-	444
88457	750	3750	-	481
88458	750	3750	-	518
88459	750	3750	-	555
88460	750	3750	-	592
88461	750	3750	-	629
88462	750	3750	-	666
88463	750	3750	-	703
88464	750	3750	-	740
88465	750	3750	-	777
88480	700	3500	-	0
88481	700	3500	-	35
88482	700	3500	-	70
88483	700	3500	-	105
88484	700	3500	-	140
88485	700	3500	-	175
88486	700	3500	-	210
88487	700	3500	-	245
88488	700	3500	-	280
88489	700	3500	-	315
88490	700	3500	-	350
88491	700	3500	-	385
88492	700	3500	-	420
88493	700	3500	-	455
88494	700	3500	-	490
88495	700	3500	-	525
88496	700	3500	-	560
88497	700	3500	-	595
88498	700	3500	-	630
88499	700	3500	-	665
88500	700	3500	-	700
88501	700	3500	-	735
88502	700	3500	-	770
88503	700	3500	-	805
88519	650	3250	-	0
88520	650	3250	-	32
88521	650	3250	-	64
88522	650	3250	-	96
88523	650	3250	-	128
88524	650	3250	-	160
88525	650	3250	-	192
88526	650	3250	-	224
88527	650	3250	-	256
88528	650	3250	-	288
88529	650	3250	-	320
88530	650	3250	-	352
88531	650	3250	-	384
88532	650	3250	-	416
88533	650	3250	-	448
88534	650	3250	-	480
88535	650	3250	-	512
88536	650	3250	-	544
88537	650	3250	-	576
88538	650	3250	-	608
88539	650	3250	-	640
88540	650	3250	-	672
88541	650	3250	-	704
88542	650	3250	-	736
88543	650	3250	-	768
88544	650	3250	-	800
88545	650	3250	-	832
88546	650	3250	-	864
88563	600	3000	-	0
88564	600	3000	-	30
88565	600	3000	-	60
88566	600	3000	-	90
88567	600	3000	-	120
88568	600	3000	-	150
88569	600	3000	-	180
88570	600	3000	-	210
88571	600	3000	-	240
88572	600	3000	-	270
88573	600	3000	-	300
88574	600	3000	-	330
88575	600	3000	-	360
88576	600	3000	-	390
88577	600	3000	-	420
88578	600	3000	-	450
88579	600	3000	-	480
88580	600	3000	-	510
88581	600	3000	-	540
88582	600	3000	-	570
88583	600	3000	-	600
88584	600	3000	-	630
88585	600	3000	-	660
88586	600	3000	-	690
88587	600	3000	-	720
88588	600	3000	-	750
88589	600	3000	-	780
88590	600	3000	-	810
88591	600	3000	-	840
88592	600	3000	-	870
88593	600	3000	-	900
88594	600	3000	-	930
88612	550	2750	-	0
88613	550	2750	-	27
88614	550	2750	-	54
88615	550	2750	-	81
88616	550	2750	-	108
88617	550	2750	-	135
88618	550	2750	-	162
88619	550	2750	-	189
88620	550	2750	-	216
88621	550	2750	-	243
88622	550	2750	-	270
88623	550	2750	-	297
88624	550	2750	-	324
88625	550	2750	-	351
88626	550	2750	-	378
88627	550	2750	-	405
88628	550	2750	-	432
88629	550	2750	-	459
88630	550	2750	-	486
88631	550	2750	-	513
88632	550	2750	-	540
88633	550	2750	-	567
88634	550	2750	-	594
88635	550	2750	-	621
88636	550	2750	-	648
88637	550	2750	-	675
88638	550	2750	-	702
88639	550	2750	-	729
88640	550	2750	-	756
88641	550	2750	-	783
88642	550	2750	-	810
88643	550	2750	-	837
88644	550	2750	-	864
88645	550	2750	-	891
88646	550	2750	-	918
88647	550	2750	-	945
88648	550	2750	-	972
88668	500	2500	-	0
88669	500	2500	-	25
88670	500	2500	-	50
88671	500	2500	-	75
88672	500	2500	-	100
88673	500	2500	-	125
88674	500	2500	-	150
88675	500	2500	-	175
88676	500	2500	-	200
88677	500	2500	-	225
88678	500	2500	-	250
88679	500	2500	-	275
88680	500	2500	-	300
88681	500	2500	-	325
88682	500	2500	-	350
88683	500	2500	-	375
88684	500	2500	-	400
88685	500	2500	-	425
88686	500	2500	-	450
88687	500	2500	-	475
88688	500	2500	-	500
88689	500	2500	-	525
88690	500	2500	-	550
88691	500	2500	-	575
88692	500	2500	-	600
88693	500	2500	-	625
88694	500	2500	-	650
88695	500	2500	-	675
88696	500	2500	-	700
88697	500	2500	-	725
88698	500	2500	-	750
88699	500	2500	-	775
88700	500	2500	-	800
88701	500	2500	-	825
88702	500	2500	-	850
88703	500	2500	-	875
88704	500	2500	-	900
88705	500	2500	-	925
88706	500	2500	-	950
88707	500	2500	-	975
88708	500	2500	-	1000
88709	500	2500	-	1025

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
88222	1300	43.0	6500	0.7	260	41.7
88265	1150	38.1	5750	0.6	399	36.9
88282	1100	36.4	5500	-	440	36.4
88266	1150	35.7	5750	0.8	456	34.1
88223	1300	37.6	6500	1.8	325	34.0
88250	1200	37.3	6000	1.7	420	33.9
88236	1250	37.2	6250	1.8	372	33.7
88224	1300	36.7	6500	1.8	390	33.2
88225	1300	36.7	6500	1.8	455	33.2
88226	1300	36.7	6500	1.8	520	33.2
88227	1300	36.7	6500	1.8	585	33.2
88228	1300	36.7	6500	1.8	650	33.2
88229	1300	36.7	6500	1.8	715	33.2
88302	1050	34.8	5250	0.9	520	33.1
88283	1100	34.6	5500	0.8	495	33.0
88257	1200	33.9	6000	1.9	840	30.1
88324	1000	31.4	5000	0.9	600	29.6
88346	950	31.5	4750	0.9	611	29.6
88372	900	29.8	4500	1.0	675	27.8
88347	950	29.5	4750	0.9	658	27.6
88400	850	28.1	4250	1.1	714	26.0
88401	850	26.4	4250	1.1	756	24.3
88504	700	23.2	3500	-	840	23.2
88432	800	25.2	4000	1.1	800	22.9
88466	750	24.8	3750	1.2	814	22.4
88467	750	23.6	3750	1.2	851	21.2
88505	700	23.2	3500	1.3	875	20.6
88547	650	21.5	3250	0.6	896	20.3
88506	700	21.7	3500	1.4	910	18.9
88548	650	21.5	3250	1.4	928	18.8
88549	650	20.2	3250	1.5	960	17.1
88596	600	19.9	3000	1.5	990	16.9
88479	750	21.2	3750	3.1	1295	15.1
88650	550	18.2	2750	1.6	1026	14.9
88651	550	17.3	2750	1.6	1053	14.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
88235	1250	41.4	6250	0.7	310	40.0
88249	1200	39.7	6000	0.8	360	38.2
88237	1250	35.3	6250	1.8	434	31.6
88238	1250	35.3	6250	1.8	496	31.6
88239	1250	35.3	6250	1.8	558	31.6
88240	1250	35.3	6250	1.8	620	31.6
88241	1250	35.3	6250	1.8	682	31.6
88242	1250	35.3	6250	1.8	744	31.6
88323	1000	33.1	5000	0.8	550	31.5
88251	1200	33.9	6000	1.9	480	30.1
88252	1200	33.9	6000	1.9	540	30.1
88253	1200	33.9	6000	1.9	600	30.1
88254	1200	33.9	6000	1.9	660	30.1
88255	1200	33.9	6000	1.9	720	30.1
88256	1200	33.9	6000	1.9	780	30.1
88267	1150	32.5	5750	2.0	513	28.5
88268	1150	32.5	5750	2.0	570	28.5
88269	1150	32.5	5750	2.0	627	28.5
88270	1150	32.5	5750	2.0	684	28.5
88271	1150	32.5	5750	2.0	741	28.5
88272	1150	32.5	5750	2.0	798	28.5
88273	1150	32.5	5750	2.0	855	28.5
88303	1050	31.2	5250	2.1	572	27.1
88284	1100	31.1	5500	2.1	550	26.9
88285	1100	31.1	5500	2.1	605	26.9
88286	1100	31.1	5500	2.1	660	26.9
88287	1100	31.1	5500	2.1	715	26.9
88288	1100	31.1	5500	2.1	770	26.9
88289	1100	31.1	5500	2.1	825	26.9
88290	1100	31.1	5500	2.1	880	26.9
88291	1100	31.1	5500	2.1	935	26.9
88304	1050	29.7	5250	2.2	624	25.3
88305	1050	29.7	5250	2.2	676	25.3
88306	1050	29.7	5250	2.2	728	25.3
88307	1050	29.7	5250	2.2	780	25.3
88308	1050	29.7	5250	2.2	832	25.3
88309	1050	29.7	5250	2.2	884	25.3
88310	1050	29.7	5250	2.2	936	25.3
88311	1050	29.7	5250	2.2	988	25.3
88431	800	26.5	4000	1.1	760	24.2
88325	1000	28.2	5000	2.3	650	23.6
88326	1000	28.2	5000	2.3	700	23.6
88327	1000	28.2	5000	2.3	750	23.6
88328	1000	28.2	5000	2.3	800	23.6
88329	1000	28.2	5000	2.3	850	23.6
88330	1000	28.2	5000	2.3	900	23.6
88331	1000	28.2	5000	2.3	950	23.6
88332	1000	28.2	5000	2.3	1000	23.6
88373	900	28.0	4500	2.2	720	23.5
88348	950	26.8	4750	2.4	705	22.0
88349	950	26.8	4750	2.4	752	22.0
88350	950	26.8	4750	2.4	799	22.0
88351	950	26.8	4750	2.4	846	22.0
88352	950	26.8	4750	2.4	893	22.0
88353	950	26.8	4750	2.4	940	22.0
88354	950	26.8	4750	2.4	987	22.0
88355	950	26.8	4750	2.4	1034	22.0
88356	950	26.8	4750	2.4	1081	22.0
88374	900	25.4	4500	2.6	765	20.3
88375	900	25.4	4500	2.6	810	20.3
88376	900	25.4	4500	2.6	855	20.3
88377	900	25.4	4500	2.6	900	20.3
88378	900	25.4	4500	2.6	945	20.3
88379	900	25.4	4500	2.6	990	20.3
88380	900	25.4	4500	2.6	1035	20.3
88381	900	25.4	4500	2.6	1080	20.3
88382	900	25.4	4500	2.6	1125	20.3
88402	850	24.0	4250	2.7	798	18.6
88403	850	24.0	4250	2.7	840	18.6
88404	850	24.0	4250	2.7	882	18.6
88405	850	24.0	4250	2.7	924	18.6
88406	850	24.0	4250	2.7	966	18.6
88407	850	24.0	4250	2.7	1008	18.6
88408	850	24.0	4250	2.7	1050	18.6
88409	850	24.0	4250	2.7	1092	18.6
88410	850	24.0	4250	2.7	1134	18.6
88411	850	24.0	4250	2.7	1176	18.6
88595	600	19.9	3000	1.5	960	16.9
88433	800	22.6	4000	2.9	840	16.8
88434	800	22.6	4000	2.9	880	16.8
88435	800	22.6	4000	2.9	920	16.8
88436	800	22.6	4000	2.9	960	16.8
88437	800	22.6	4000	2.9	1000	16.8
88438	800	22.6	4000	2.9	1040	16.8
88439	800	22.6	4000	2.9	1080	16.8
88440	800	22.6	4000	2.9	1120	16.8
88441	800	22.6	4000	2.9	1160	16.8
88442	800	22.6	4000	2.9	1200	16.8
88443	800	22.6	4000	2.9	1240	16.8
88649	550	18.2	2750	1.3	999	15.7
88468	750	21.2	3750	3.1	888	15.1
88469	750	21.2	3750	3.1	925	15.1
88470	750	21.2	3750	3.1	962	15.1
88471	750	21.2	3750	3.1	999	15.1
88472	750	21.2	3750	3.1	1036	15.1
88473	750	21.2	3750	3.1	1073	15.1
88474	750	21.2	3750	3.1	1110	15.1
88475	750	21.2	3750	3.1	1147	15.1
88476	750	21.2	3750	3.1	1184	15.1
88477	750	21.2	3750	3.1	1221	15.1
88478	750	21.2	3750	3.1	1258	15.1
88710	500	16.6	2500	1.6	1050	13.4
88507	700	19.8	3500	3.3	945	13.2
88508	700	19.8	3500	3.3	980	13.2
88509	700	19.8	3500	3.3	1015	13.2
88510	700	19.8	3500	3.3	1050	13.2
88511	700	19.8	3500	3.3	1085	13.2
88512	700	19.8	3500	3.3	1120	13.2
88513	700	19.8	3500	3.3	1155	13.2
88514	700	19.8	3500	3.3	1190	13.2
88515	700	19.8	3500	3.3	1225	13.2
88516	700	19.8	3500	3.3	1260	13.2
88517	700	19.8	3500	3.3	1295	13.2
88518	700	19.8	3500	3.3	1330	13.2
88711	500	16.6	2500	1.8	1075	13.0
88712	500	15.7	2500	1.8	1100	12.1
88597	600	18.6	3000	3.3	1020	12.0
88550	650	18.4	3250	3.5	992	11.3
88551	650	18.4	3250	3.5	1024	11.3
88552	650	18.4	3250	3.5	1056	11.3
88553	650	18.4	3250	3.5	1088	11.3
88554	650	18.4	3250	3.5	1120	11.3
88555	650	18.4	3250	3.5	1152	11.3
88556	650	18.4	3250	3.5	1184	11.3
88557	650	18.4	3250	3.5	1216	11.3
88558	650	18.4	3250	3.5	1248	11.3
88559	650	18.4	3250	3.5	1280	11.3
88560	650	18.4	3250	3.5	1312	11.3
88561	650	18.4	3250	3.5	1344	11.3
88562	650	18.4	3250	3.5	1376	11.3
88598	600	16.9	3000	3.8	1050	9.3
88599	600	16.9	3000	3.8	1080	9.3
88600	600	16.9	3000	3.8	1110	9.3
88601	600	16.9	3000	3.8	1140	9.3
88602	600	16.9	3000	3.8	1170	9.3
88603	600	16.9	3000	3.8	1200	9.3
88604	600	16.9	3000	3.8	1230	9.3
88605	600	16.9	3000	3.8	1260	9.3
88606	600	16.9	3000	3.8	1290	9.3
88607	600	16.9	3000	3.8	1320	9.3
88608	600	16.9	3000	3.8	1350	9.3
88609	600	16.9	3000	3.8	1380	9.3
88610	600	16.9	3000	3.8	1410	9.3
88611	600	16.9	3000	3.8	1440	9.3
88652	550	15.5	2750	4.2	1080	7.2
88653	550	15.5	2750	4.2	1107	7.2
88654	550	15.5	2750	4.2	1134	7.2
88655	550	15.5	2750	4.2	1161	7.2
88656	550	15.5	2750	4.2	1188	7.2
88657	550	15.5	2750	4.2	1215	7.2
88658	550	15.5	2750	4.2	1242	7.2
88659	550	15.5	2750	4.2	1269	7.2
88660	550	15.5	2750	4.2	1296	7.2
88661	550	15.5	2750	4.2	1323	7.2
88662	550	15.5	2750	4.2	1350	7.2
88663	550	15.5	2750	4.2	1377	7.2
88664	550	15.5	2750	4.2	1404	7.2
88665	550	15.5	2750	4.2	1431	7.2
88666	550	15.5	2750	4.2	1458	7.2
88667	550	15.5	2750	4.2	1485	7.2
88713	500	14.5	2500	4.6	1125	5.3
88714	500	14.1	2500	4.6	1150	4.9
88715	500	14.1	2500	4.6	1175	4.9
88716	500	14.1	2500	4.6	1200	4.9
88717	500	14.1	2500	4.6	1225	4.9
88718	500	14.1	2500	4.6	1250	4.9
88719	500	14.1	2500	4.6	1275	4.9
88720	500	14.1	2500	4.6	1300	4.9
88721	500	14.1	2500	4.6	1325	4.9
88722	500	14.1	2500	4.6	1350	4.9
88723	500	14.1	2500	4.6	1375	4.9
88724	500	14.1	2500	4.6	1400	4.9
88725	500	14.1	2500	4.6	1425	4.9
88726	500	14.1	2500	4.6	1450	4.9
88727	500	14.1	2500	4.6	1475	4.9
88728	500	14.1	2500	4.6	1500	4.9
88729	500	14.1	2500	4.6	1525	4.9

Overall score = score_ratio - 2 * repetitive DNA content