Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign82 - back to list

Summary
Image
Unique putative probes (273)
Putative probes (189)
Redundant probes (30)

Summary

`./analyse_probe_search_results : Wed Nov 9 09:32:47 2005`

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

Fetched probe design: ProbeDesign82
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 1
  id            : 73
  strand        : 1
  -------------

Design window length: 2501bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 699 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            : 699/699
Putative probes that are unique                 : 273/699
Putative probes exceeding selection criteria    : 492/699 (both unique and not unique)
Putative probes with successfully-picked primers: 490/492

Identified 30 '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
68842	850	4250	-	798
68883	800	4000	-	800
68884	800	4000	-	840
68927	750	3750	-	777
68928	750	3750	-	814
68929	750	3750	-	851
68930	750	3750	-	888
68977	700	3500	-	805
68978	700	3500	-	840
68979	700	3500	-	875
68980	700	3500	-	910
68981	700	3500	-	945
69031	650	3250	-	800
69032	650	3250	-	832
69033	650	3250	-	864
69034	650	3250	-	896
69035	650	3250	-	928
69036	650	3250	-	960
69037	650	3250	-	992
69090	600	3000	-	780
69091	600	3000	-	810
69092	600	3000	-	840
69093	600	3000	-	870
69094	600	3000	-	900
69095	600	3000	-	930
69096	600	3000	-	960
69097	600	3000	-	990
69098	600	3000	-	1020
69099	600	3000	-	1050
69157	550	2750	-	783
69158	550	2750	-	810
69159	550	2750	-	837
69160	550	2750	-	864
69161	550	2750	-	891
69162	550	2750	-	918
69163	550	2750	-	945
69164	550	2750	-	972
69165	550	2750	-	999
69166	550	2750	-	1026
69167	550	2750	-	1053
69168	550	2750	-	1080
69169	550	2750	-	1107
69209	500	2500	-	200
69232	500	2500	-	775
69233	500	2500	-	800
69234	500	2500	-	825
69235	500	2500	-	850
69236	500	2500	-	875
69237	500	2500	-	900
69238	500	2500	-	925
69239	500	2500	-	950
69240	500	2500	-	975
69241	500	2500	-	1000
69242	500	2500	-	1025
69243	500	2500	-	1050
69244	500	2500	-	1075
69245	500	2500	-	1100
69246	500	2500	-	1125
69247	500	2500	-	1150
68976	700	3500	0.6	770
69030	650	3250	0.9	768
68804	900	4500	1.0	765
69210	500	2500	1.6	225
68882	800	4000	1.8	760
68841	850	4250	2.1	756
69156	550	2750	3.3	756
69089	600	3000	4.0	750
69135	550	2750	4.0	189
68586	1300	6500	4.4	195
68587	1300	6500	4.4	260
68588	1300	6500	4.4	325
68926	750	3750	4.5	740
68605	1250	6250	4.6	186
68606	1250	6250	4.6	248
68607	1250	6250	4.6	310
68608	1250	6250	4.6	372
68626	1200	6000	4.8	180
68627	1200	6000	4.8	240
68628	1200	6000	4.8	300
68629	1200	6000	4.8	360
68630	1200	6000	4.8	420
69231	500	2500	4.8	750
68649	1150	5750	5.0	228
68650	1150	5750	5.0	285
68651	1150	5750	5.0	342
68652	1150	5750	5.0	399
68653	1150	5750	5.0	456
68654	1150	5750	5.0	513
68673	1100	5500	5.2	220
68674	1100	5500	5.2	275
68675	1100	5500	5.2	330
68676	1100	5500	5.2	385
68677	1100	5500	5.2	440
68678	1100	5500	5.2	495
68679	1100	5500	5.2	550
68699	1050	5250	5.4	208
68700	1050	5250	5.4	260
68701	1050	5250	5.4	312
68702	1050	5250	5.4	364
68703	1050	5250	5.4	416
68704	1050	5250	5.4	468
68705	1050	5250	5.4	520
68706	1050	5250	5.4	572
68975	700	3500	5.6	735
68727	1000	5000	5.7	200
68728	1000	5000	5.7	250
68729	1000	5000	5.7	300
68730	1000	5000	5.7	350
68731	1000	5000	5.7	400
68732	1000	5000	5.7	450
68733	1000	5000	5.7	500
68734	1000	5000	5.7	550
68735	1000	5000	5.7	600
68736	1000	5000	5.7	650
69029	650	3250	5.8	736
68758	950	4750	6.0	188
68759	950	4750	6.0	235
68760	950	4750	6.0	282
68761	950	4750	6.0	329
68762	950	4750	6.0	376
68763	950	4750	6.0	423
68764	950	4750	6.0	470
68765	950	4750	6.0	517
68766	950	4750	6.0	564
68767	950	4750	6.0	611
68768	950	4750	6.0	658
68769	950	4750	6.0	705
68803	900	4500	6.0	720
68791	900	4500	6.3	180
68792	900	4500	6.3	225
68793	900	4500	6.3	270
68794	900	4500	6.3	315
68795	900	4500	6.3	360
68796	900	4500	6.3	405
68797	900	4500	6.3	450
68798	900	4500	6.3	495
68799	900	4500	6.3	540
68800	900	4500	6.3	585
68801	900	4500	6.3	630
68802	900	4500	6.3	675
69211	500	2500	6.6	250
68828	850	4250	6.7	210
68829	850	4250	6.7	252
68830	850	4250	6.7	294
68831	850	4250	6.7	336
68832	850	4250	6.7	378
68833	850	4250	6.7	420
68834	850	4250	6.7	462
68835	850	4250	6.7	504
68836	850	4250	6.7	546
68837	850	4250	6.7	588
68838	850	4250	6.7	630
68839	850	4250	6.7	672
68840	850	4250	6.7	714
68881	800	4000	6.8	720
68868	800	4000	7.1	200
68869	800	4000	7.1	240
68870	800	4000	7.1	280
68871	800	4000	7.1	320
68872	800	4000	7.1	360
68873	800	4000	7.1	400
68874	800	4000	7.1	440
68875	800	4000	7.1	480
68876	800	4000	7.1	520
68877	800	4000	7.1	560
68878	800	4000	7.1	600
68879	800	4000	7.1	640
68880	800	4000	7.1	680
68911	750	3750	7.6	185
68912	750	3750	7.6	222
68913	750	3750	7.6	259
68914	750	3750	7.6	296
68915	750	3750	7.6	333
68916	750	3750	7.6	370
68917	750	3750	7.6	407
68918	750	3750	7.6	444
68919	750	3750	7.6	481
68920	750	3750	7.6	518
68921	750	3750	7.6	555
68922	750	3750	7.6	592
68923	750	3750	7.6	629
68924	750	3750	7.6	666
68925	750	3750	7.6	703
68960	700	3500	8.1	210
68961	700	3500	8.1	245
68962	700	3500	8.1	280
68963	700	3500	8.1	315
68964	700	3500	8.1	350
68965	700	3500	8.1	385
68966	700	3500	8.1	420
68967	700	3500	8.1	455
68968	700	3500	8.1	490
68969	700	3500	8.1	525
68970	700	3500	8.1	560
68971	700	3500	8.1	595
68972	700	3500	8.1	630
68973	700	3500	8.1	665
68974	700	3500	8.1	700
69155	550	2750	8.2	729
69012	650	3250	8.8	192
69013	650	3250	8.8	224
69014	650	3250	8.8	256
69015	650	3250	8.8	288
69016	650	3250	8.8	320
69017	650	3250	8.8	352
69018	650	3250	8.8	384
69019	650	3250	8.8	416
69020	650	3250	8.8	448
69021	650	3250	8.8	480
69022	650	3250	8.8	512
69023	650	3250	8.8	544
69024	650	3250	8.8	576
69025	650	3250	8.8	608
69026	650	3250	8.8	640
69027	650	3250	8.8	672
69028	650	3250	8.8	704
69136	550	2750	8.9	216
69088	600	3000	9.0	720
69070	600	3000	9.5	180
69071	600	3000	9.5	210
69072	600	3000	9.5	240
69073	600	3000	9.5	270
69074	600	3000	9.5	300
69075	600	3000	9.5	330
69076	600	3000	9.5	360
69077	600	3000	9.5	390
69078	600	3000	9.5	420
69079	600	3000	9.5	450
69080	600	3000	9.5	480
69081	600	3000	9.5	510
69082	600	3000	9.5	540
69083	600	3000	9.5	570
69084	600	3000	9.5	600
69085	600	3000	9.5	630
69086	600	3000	9.5	660
69087	600	3000	9.5	690
69230	500	2500	9.8	725
69137	550	2750	10.4	243
69138	550	2750	10.4	270
69139	550	2750	10.4	297
69140	550	2750	10.4	324
69141	550	2750	10.4	351
69142	550	2750	10.4	378
69143	550	2750	10.4	405
69144	550	2750	10.4	432
69145	550	2750	10.4	459
69146	550	2750	10.4	486
69147	550	2750	10.4	513
69148	550	2750	10.4	540
69149	550	2750	10.4	567
69150	550	2750	10.4	594
69151	550	2750	10.4	621
69152	550	2750	10.4	648
69153	550	2750	10.4	675
69154	550	2750	10.4	702
69212	500	2500	11.4	275
69213	500	2500	11.4	300
69214	500	2500	11.4	325
69215	500	2500	11.4	350
69216	500	2500	11.4	375
69217	500	2500	11.4	400
69218	500	2500	11.4	425
69219	500	2500	11.4	450
69220	500	2500	11.4	475
69221	500	2500	11.4	500
69222	500	2500	11.4	525
69223	500	2500	11.4	550
69224	500	2500	11.4	575
69225	500	2500	11.4	600
69226	500	2500	11.4	625
69227	500	2500	11.4	650
69228	500	2500	11.4	675
69229	500	2500	11.4	700

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
68595	1300	38.0	6500	0.7	780	36.6
68615	1250	36.5	6250	-	806	36.5
68636	1200	35.1	6000	-	780	35.1
68637	1200	35.1	6000	-	840	35.1
68583	1300	43.0	6500	4.4	0	34.3
68584	1300	43.0	6500	4.4	65	34.3
68585	1300	43.0	6500	4.4	130	34.3
68659	1150	33.6	5750	-	798	33.6
68660	1150	33.6	5750	-	855	33.6
68661	1150	33.6	5750	-	912	33.6
68603	1250	41.4	6250	4.6	62	32.3
68604	1250	41.4	6250	4.6	124	32.3
68684	1100	32.2	5500	-	825	32.2
68685	1100	32.2	5500	-	880	32.2
68686	1100	32.2	5500	-	935	32.2
68614	1250	36.5	6250	2.4	744	31.7
68683	1100	32.2	5500	0.4	770	31.4
68589	1300	40.1	6500	4.4	390	31.4
68710	1050	30.7	5250	-	780	30.7
68711	1050	30.7	5250	-	832	30.7
68712	1050	30.7	5250	-	884	30.7
68713	1050	30.7	5250	-	936	30.7
68714	1050	30.7	5250	-	988	30.7
68638	1200	35.1	6000	2.4	900	30.3
68590	1300	38.0	6500	4.4	455	29.2
68591	1300	38.0	6500	4.4	520	29.2
68592	1300	38.0	6500	4.4	585	29.2
68593	1300	38.0	6500	4.4	650	29.2
68594	1300	38.0	6500	4.4	715	29.2
68739	1000	29.2	5000	-	800	29.2
68740	1000	29.2	5000	-	850	29.2
68741	1000	29.2	5000	-	900	29.2
68742	1000	29.2	5000	-	950	29.2
68743	1000	29.2	5000	-	1000	29.2
68744	1000	29.2	5000	-	1050	29.2
68687	1100	32.2	5500	1.7	990	28.7
68658	1150	33.6	5750	2.9	741	27.9
68771	950	27.8	4750	-	799	27.8
68805	900	27.8	4500	-	810	27.8
68772	950	27.8	4750	-	846	27.8
68773	950	27.8	4750	-	893	27.8
68774	950	27.8	4750	-	940	27.8
68775	950	27.8	4750	-	987	27.8
68776	950	27.8	4750	-	1034	27.8
68777	950	27.8	4750	-	1081	27.8
68715	1050	30.7	5250	1.8	1040	27.1
68806	900	26.3	4500	-	855	26.3
68807	900	26.3	4500	-	900	26.3
68808	900	26.3	4500	-	945	26.3
68809	900	26.3	4500	-	990	26.3
68810	900	26.3	4500	-	1035	26.3
68811	900	26.3	4500	-	1080	26.3
68812	900	26.3	4500	-	1125	26.3
68813	900	26.3	4500	-	1170	26.3
68843	850	26.2	4250	-	840	26.2
68844	850	26.2	4250	-	882	26.2
68885	800	25.2	4000	-	880	25.2
68845	850	24.9	4250	-	924	24.9
68846	850	24.9	4250	-	966	24.9
68847	850	24.9	4250	-	1008	24.9
68848	850	24.9	4250	-	1050	24.9
68849	850	24.9	4250	-	1092	24.9
68850	850	24.9	4250	-	1134	24.9
68851	850	24.9	4250	-	1176	24.9
68852	850	24.9	4250	-	1218	24.9
68886	800	24.7	4000	-	920	24.7
68770	950	29.3	4750	2.3	752	24.7
68931	750	24.5	3750	-	925	24.5
68738	1000	29.2	5000	2.4	750	24.4
68745	1000	29.2	5000	2.9	1100	23.4
68887	800	23.4	4000	-	960	23.4
68888	800	23.4	4000	-	1000	23.4
68889	800	23.4	4000	-	1040	23.4
68890	800	23.4	4000	-	1080	23.4
68891	800	23.4	4000	-	1120	23.4
68892	800	23.4	4000	-	1160	23.4
68893	800	23.4	4000	-	1200	23.4
68894	800	23.4	4000	-	1240	23.4
68954	700	23.2	3500	-	0	23.2
68932	750	23.1	3750	-	962	23.1
68616	1250	30.0	6250	3.8	868	22.5
68982	700	22.0	3500	-	980	22.0
68709	1050	30.7	5250	4.4	728	21.9
68933	750	21.9	3750	-	999	21.9
68934	750	21.9	3750	-	1036	21.9
68935	750	21.9	3750	-	1073	21.9
68936	750	21.9	3750	-	1110	21.9
68937	750	21.9	3750	-	1147	21.9
68938	750	21.9	3750	-	1184	21.9
68939	750	21.9	3750	-	1221	21.9
68940	750	21.9	3750	-	1258	21.9
68941	750	21.9	3750	-	1295	21.9
69038	650	21.7	3250	-	1024	21.7
68983	700	21.6	3500	-	1015	21.6
69006	650	21.5	3250	-	0	21.5
69007	650	21.5	3250	-	32	21.5
69008	650	21.5	3250	-	64	21.5
68984	700	20.5	3500	-	1050	20.5
68985	700	20.5	3500	-	1085	20.5
68986	700	20.5	3500	-	1120	20.5
68987	700	20.5	3500	-	1155	20.5
68988	700	20.5	3500	-	1190	20.5
68989	700	20.5	3500	-	1225	20.5
68990	700	20.5	3500	-	1260	20.5
68991	700	20.5	3500	-	1295	20.5
68992	700	20.5	3500	-	1330	20.5
68993	700	20.5	3500	-	1365	20.5
69039	650	20.1	3250	-	1056	20.1
69064	600	19.9	3000	-	0	19.9
69065	600	19.9	3000	-	30	19.9
69066	600	19.9	3000	-	60	19.9
69067	600	19.9	3000	-	90	19.9
68662	1150	27.6	5750	4.2	969	19.3
69040	650	19.0	3250	-	1088	19.0
69041	650	19.0	3250	-	1120	19.0
69042	650	19.0	3250	-	1152	19.0
69043	650	19.0	3250	-	1184	19.0
69044	650	19.0	3250	-	1216	19.0
69045	650	19.0	3250	-	1248	19.0
69046	650	19.0	3250	-	1280	19.0
69047	650	19.0	3250	-	1312	19.0
69048	650	19.0	3250	-	1344	19.0
69049	650	19.0	3250	-	1376	19.0
69050	650	19.0	3250	-	1408	19.0
68942	750	21.9	3750	1.5	1332	19.0
69100	600	18.9	3000	-	1080	18.9
69068	600	19.9	3000	0.5	120	18.9
69101	600	18.5	3000	-	1110	18.5
69128	550	18.2	2750	-	0	18.2
69129	550	18.2	2750	-	27	18.2
69130	550	18.2	2750	-	54	18.2
69131	550	18.2	2750	-	81	18.2
69132	550	18.2	2750	-	108	18.2
69133	550	18.2	2750	-	135	18.2
69134	550	18.2	2750	-	162	18.2
68955	700	23.2	3500	2.6	35	18.0
69102	600	17.5	3000	-	1140	17.5
69103	600	17.5	3000	-	1170	17.5
69104	600	17.5	3000	-	1200	17.5
69105	600	17.5	3000	-	1230	17.5
69106	600	17.5	3000	-	1260	17.5
69107	600	17.5	3000	-	1290	17.5
69108	600	17.5	3000	-	1320	17.5
69109	600	17.5	3000	-	1350	17.5
69110	600	17.5	3000	-	1380	17.5
69111	600	17.5	3000	-	1410	17.5
69112	600	17.5	3000	-	1440	17.5
69113	600	17.5	3000	-	1470	17.5
69170	550	17.0	2750	-	1134	17.0
69171	550	17.0	2750	-	1161	17.0
69201	500	16.6	2500	-	0	16.6
69202	500	16.6	2500	-	25	16.6
69203	500	16.6	2500	-	50	16.6
69204	500	16.6	2500	-	75	16.6
69205	500	16.6	2500	-	100	16.6
69206	500	16.6	2500	-	125	16.6
69207	500	16.6	2500	-	150	16.6
69208	500	16.6	2500	-	175	16.6
69248	500	16.3	2500	-	1175	16.3
69172	550	16.1	2750	-	1188	16.1
69173	550	16.1	2750	-	1215	16.1
69174	550	16.1	2750	-	1242	16.1
69175	550	16.1	2750	-	1269	16.1
69176	550	16.1	2750	-	1296	16.1
69177	550	16.1	2750	-	1323	16.1
69178	550	16.1	2750	-	1350	16.1
69179	550	16.1	2750	-	1377	16.1
69180	550	16.1	2750	-	1404	16.1
69181	550	16.1	2750	-	1431	16.1
69182	550	16.1	2750	-	1458	16.1
69183	550	16.1	2750	-	1485	16.1
69184	550	16.1	2750	-	1512	16.1
69249	500	15.4	2500	-	1200	15.4
69250	500	15.4	2500	-	1225	15.4
69251	500	14.6	2500	-	1250	14.6
69252	500	14.6	2500	-	1275	14.6
69253	500	14.6	2500	-	1300	14.6
69254	500	14.6	2500	-	1325	14.6
69255	500	14.6	2500	-	1350	14.6
69256	500	14.6	2500	-	1375	14.6
69257	500	14.6	2500	-	1400	14.6
69258	500	14.6	2500	-	1425	14.6
69259	500	14.6	2500	-	1450	14.6
69260	500	14.6	2500	-	1475	14.6
69261	500	14.6	2500	-	1500	14.6
69262	500	14.6	2500	-	1525	14.6
69263	500	14.6	2500	-	1550	14.6
69051	650	19.0	3250	2.9	1440	13.2
69185	550	16.1	2750	3.3	1539	9.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
68602	1250	41.4	6250	4.6	0	32.3
68623	1200	39.7	6000	4.8	0	30.2
68624	1200	39.7	6000	4.8	60	30.2
68625	1200	39.7	6000	4.8	120	30.2
68609	1250	38.6	6250	4.6	434	29.5
68631	1200	37.7	6000	4.8	480	28.2
68645	1150	38.1	5750	5.0	0	28.2
68646	1150	38.1	5750	5.0	57	28.2
68647	1150	38.1	5750	5.0	114	28.2
68648	1150	38.1	5750	5.0	171	28.2
68610	1250	36.5	6250	4.6	496	27.4
68611	1250	36.5	6250	4.6	558	27.4
68612	1250	36.5	6250	4.6	620	27.4
68613	1250	36.5	6250	4.6	682	27.4
68778	950	27.8	4750	0.7	1128	26.3
68635	1200	35.1	6000	4.5	720	26.1
68632	1200	35.1	6000	4.8	540	25.6
68633	1200	35.1	6000	4.8	600	25.6
68634	1200	35.1	6000	4.8	660	25.6
68655	1150	35.5	5750	5.0	570	25.6
68656	1150	33.6	5750	5.0	627	23.7
68657	1150	33.6	5750	5.0	684	23.7
68895	800	23.4	4000	1.1	1280	21.1
68906	750	24.8	3750	4.4	0	16.0
69264	500	14.6	2500	0.8	1575	13.0
69009	650	21.5	3250	4.5	96	12.6
68814	900	22.2	4500	4.9	1215	12.4
68994	700	20.5	3500	4.1	1400	12.2
68853	850	21.1	4250	4.6	1260	12.0
69114	600	17.5	3000	4.8	1500	7.9

Overall score = score_ratio - 2 * repetitive DNA content