Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign65 - back to list

Summary
Image
Unique putative probes (108)
Putative probes (151)
Redundant probes (29)

Summary

`./analyse_probe_search_results : Fri Oct 7 10:40:22 2005`

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

Fetched probe design: ProbeDesign65
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 7
  id            : 60
  strand        : 1
  -------------

Design window length: 3001bp

All jobs for probe design are successful - total: 46
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 907 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            : 907/907
Putative probes that are unique                 : 108/907
Putative probes exceeding selection criteria    : 180/907 (but not unique)
Putative probes with successfully-picked primers: 280/288

Identified 29 '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
58645	900	4500	-	0
58692	850	4250	-	0
58693	850	4250	-	42
58694	850	4250	-	84
58744	800	4000	-	0
58745	800	4000	-	40
58746	800	4000	-	80
58747	800	4000	-	120
58800	750	3750	-	0
58801	750	3750	-	37
58802	750	3750	-	74
58803	750	3750	-	111
58804	750	3750	-	148
58805	750	3750	-	185
58861	700	3500	-	0
58862	700	3500	-	35
58863	700	3500	-	70
58864	700	3500	-	105
58865	700	3500	-	140
58866	700	3500	-	175
58867	700	3500	-	210
58892	700	3500	-	1085
58927	650	3250	-	0
58928	650	3250	-	32
58929	650	3250	-	64
58930	650	3250	-	96
58931	650	3250	-	128
58932	650	3250	-	160
58933	650	3250	-	192
58934	650	3250	-	224
58935	650	3250	-	256
58936	650	3250	-	288
58961	650	3250	-	1088
58962	650	3250	-	1120
58963	650	3250	-	1152
59001	600	3000	-	0
59002	600	3000	-	30
59003	600	3000	-	60
59004	600	3000	-	90
59005	600	3000	-	120
59006	600	3000	-	150
59007	600	3000	-	180
59008	600	3000	-	210
59009	600	3000	-	240
59010	600	3000	-	270
59011	600	3000	-	300
59012	600	3000	-	330
59037	600	3000	-	1080
59038	600	3000	-	1110
59039	600	3000	-	1140
59040	600	3000	-	1170
59041	600	3000	-	1200
59082	550	2750	-	0
59083	550	2750	-	27
59084	550	2750	-	54
59085	550	2750	-	81
59086	550	2750	-	108
59087	550	2750	-	135
59088	550	2750	-	162
59089	550	2750	-	189
59090	550	2750	-	216
59091	550	2750	-	243
59092	550	2750	-	270
59093	550	2750	-	297
59094	550	2750	-	324
59095	550	2750	-	351
59096	550	2750	-	378
59122	550	2750	-	1080
59123	550	2750	-	1107
59124	550	2750	-	1134
59125	550	2750	-	1161
59126	550	2750	-	1188
59127	550	2750	-	1215
59128	550	2750	-	1242
59173	500	2500	-	0
59174	500	2500	-	25
59175	500	2500	-	50
59176	500	2500	-	75
59177	500	2500	-	100
59178	500	2500	-	125
59179	500	2500	-	150
59180	500	2500	-	175
59181	500	2500	-	200
59182	500	2500	-	225
59183	500	2500	-	250
59184	500	2500	-	275
59185	500	2500	-	300
59186	500	2500	-	325
59187	500	2500	-	350
59188	500	2500	-	375
59189	500	2500	-	400
59190	500	2500	-	425
59216	500	2500	-	1075
59217	500	2500	-	1100
59218	500	2500	-	1125
59219	500	2500	-	1150
59220	500	2500	-	1175
59221	500	2500	-	1200
59222	500	2500	-	1225
59223	500	2500	-	1250
59224	500	2500	-	1275
59225	500	2500	-	1300
58960	650	3250	2.0	1056
58891	700	3500	2.7	1050
59121	550	2750	2.9	1053
59036	600	3000	3.2	1050
59215	500	2500	3.8	1050
58828	750	3750	4.4	1036

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
58367	1300	41.7	6500	4.5	0	32.7
58368	1300	41.7	6500	4.5	65	32.7
58369	1300	41.7	6500	4.5	130	32.7
58370	1300	41.7	6500	4.5	195	32.7
58371	1300	41.7	6500	4.5	260	32.7
58372	1300	41.7	6500	4.5	325	32.7
58373	1300	41.7	6500	4.5	390	32.7
58374	1300	41.7	6500	4.5	455	32.7
58375	1300	41.7	6500	4.5	520	32.7
58376	1300	41.7	6500	4.5	585	32.7
58377	1300	41.7	6500	4.5	650	32.7
58378	1300	41.7	6500	4.5	715	32.7
58379	1300	41.7	6500	4.5	780	32.7
58582	1000	32.5	5000	-	1100	32.5
58560	1000	32.1	5000	-	0	32.1
58543	1050	34.1	5250	1.4	1092	31.2
58624	950	30.8	4750	-	1081	30.8
58625	950	30.8	4750	-	1128	30.8
58626	950	30.8	4750	-	1175	30.8
58395	1250	40.1	6250	4.6	62	30.8
58396	1250	40.1	6250	4.6	124	30.8
58397	1250	40.1	6250	4.6	186	30.8
58398	1250	40.1	6250	4.6	248	30.8
58408	1250	40.1	6250	4.6	868	30.8
58601	950	30.4	4750	-	0	30.4
58602	950	30.4	4750	-	47	30.4
58669	900	29.2	4500	-	1080	29.2
58670	900	29.2	4500	-	1125	29.2
58671	900	29.2	4500	-	1170	29.2
58672	900	29.2	4500	-	1215	29.2
58646	900	29.0	4500	-	45	29.0
58647	900	28.8	4500	-	90	28.8
58581	1000	32.5	5000	1.9	1050	28.7
58542	1050	34.1	5250	2.8	1040	28.6
58506	1100	35.7	5500	3.8	1045	28.1
58583	1000	32.5	5000	2.3	1150	27.9
58718	850	27.6	4250	-	1092	27.6
58719	850	27.6	4250	-	1134	27.6
58720	850	27.6	4250	-	1176	27.6
58721	850	27.6	4250	-	1218	27.6
58722	850	27.6	4250	-	1260	27.6
58695	850	27.2	4250	-	126	27.2
58522	1050	33.7	5250	3.7	0	26.2
58771	800	26.0	4000	-	1080	26.0
58772	800	26.0	4000	-	1120	26.0
58773	800	26.0	4000	-	1160	26.0
58774	800	26.0	4000	-	1200	26.0
58775	800	26.0	4000	-	1240	26.0
58776	800	26.0	4000	-	1280	26.0
58777	800	26.0	4000	-	1320	26.0
58748	800	25.6	4000	-	160	25.6
58749	800	25.6	4000	-	200	25.6
58696	850	27.2	4250	0.8	168	25.6
58829	750	24.4	3750	-	1073	24.4
58830	750	24.4	3750	-	1110	24.4
58831	750	24.4	3750	-	1147	24.4
58832	750	24.4	3750	-	1184	24.4
58833	750	24.4	3750	-	1221	24.4
58834	750	24.4	3750	-	1258	24.4
58835	750	24.4	3750	-	1295	24.4
58836	750	24.4	3750	-	1332	24.4
58837	750	24.4	3750	-	1369	24.4
58561	1000	32.1	5000	3.9	50	24.3
58806	750	24.0	3750	-	222	24.0
58807	750	24.0	3750	-	259	24.0
58648	900	28.8	4500	2.7	135	23.5
58603	950	30.4	4750	3.5	94	23.5
58623	950	30.8	4750	3.7	1034	23.5
58717	850	27.6	4250	2.2	1050	23.1
58893	700	22.7	3500	-	1120	22.7
58894	700	22.7	3500	-	1155	22.7
58895	700	22.7	3500	-	1190	22.7
58896	700	22.7	3500	-	1225	22.7
58897	700	22.7	3500	-	1260	22.7
58898	700	22.7	3500	-	1295	22.7
58899	700	22.7	3500	-	1330	22.7
58900	700	22.7	3500	-	1365	22.7
58901	700	22.7	3500	-	1400	22.7
58868	700	22.6	3500	-	245	22.6
58869	700	22.4	3500	-	280	22.4
58673	900	29.2	4500	3.7	1260	21.9
58723	850	27.6	4250	2.9	1302	21.7
58668	900	29.2	4500	3.8	1035	21.7
58627	950	30.8	4750	4.7	1222	21.4
58870	700	22.4	3500	0.6	315	21.3
58964	650	21.1	3250	-	1184	21.1
58965	650	21.1	3250	-	1216	21.1
58966	650	21.1	3250	-	1248	21.1
58967	650	21.1	3250	-	1280	21.1
58968	650	21.1	3250	-	1312	21.1
58969	650	21.1	3250	-	1344	21.1
58970	650	21.1	3250	-	1376	21.1
58971	650	21.1	3250	-	1408	21.1
58972	650	21.1	3250	-	1440	21.1
58973	650	21.1	3250	-	1472	21.1
58937	650	20.8	3250	-	320	20.8
58938	650	20.8	3250	-	352	20.8
58902	700	22.7	3500	1.1	1435	20.4
59042	600	19.5	3000	-	1230	19.5
59043	600	19.5	3000	-	1260	19.5
59044	600	19.5	3000	-	1290	19.5
59045	600	19.5	3000	-	1320	19.5
59046	600	19.5	3000	-	1350	19.5
59047	600	19.5	3000	-	1380	19.5
59048	600	19.5	3000	-	1410	19.5
59049	600	19.5	3000	-	1440	19.5
59050	600	19.5	3000	-	1470	19.5
59051	600	19.5	3000	-	1500	19.5
59013	600	19.2	3000	-	360	19.2
59014	600	19.2	3000	-	390	19.2
58770	800	26.0	4000	3.6	1040	18.7
59052	600	19.5	3000	0.5	1530	18.5
58750	800	25.6	4000	3.6	240	18.4
59129	550	17.9	2750	-	1269	17.9
59130	550	17.9	2750	-	1296	17.9
59131	550	17.9	2750	-	1323	17.9
59132	550	17.9	2750	-	1350	17.9
59133	550	17.9	2750	-	1377	17.9
59134	550	17.9	2750	-	1404	17.9
59135	550	17.9	2750	-	1431	17.9
59136	550	17.9	2750	-	1458	17.9
59137	550	17.9	2750	-	1485	17.9
59138	550	17.9	2750	-	1512	17.9
59139	550	17.9	2750	-	1539	17.9
59140	550	17.9	2750	-	1566	17.9
58778	800	26.0	4000	4.1	1360	17.7
59097	550	17.6	2750	-	405	17.6
59098	550	17.6	2750	-	432	17.6
59099	550	17.6	2750	-	459	17.6
58838	750	24.4	3750	3.9	1406	16.6
59226	500	16.2	2500	-	1325	16.2
59227	500	16.2	2500	-	1350	16.2
59228	500	16.2	2500	-	1375	16.2
59229	500	16.2	2500	-	1400	16.2
59230	500	16.2	2500	-	1425	16.2
59231	500	16.2	2500	-	1450	16.2
59232	500	16.2	2500	-	1475	16.2
59233	500	16.2	2500	-	1500	16.2
59234	500	16.2	2500	-	1525	16.2
59235	500	16.2	2500	-	1550	16.2
59236	500	16.2	2500	-	1575	16.2
59237	500	16.2	2500	-	1600	16.2
59238	500	16.2	2500	-	1625	16.2
59015	600	19.2	3000	1.5	420	16.2
59191	500	16.0	2500	-	450	16.0
59192	500	16.0	2500	-	475	16.0
59193	500	16.0	2500	-	500	16.0
58939	650	20.8	3250	3.5	384	13.8
58974	650	21.1	3250	4.2	1504	12.8
59141	550	17.9	2750	2.9	1593	12.0
59194	500	16.0	2500	2.8	525	10.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
58394	1250	40.1	6250	4.6	0	30.8
58399	1250	40.1	6250	4.6	310	30.8
58400	1250	40.1	6250	4.6	372	30.8
58401	1250	40.1	6250	4.6	434	30.8
58402	1250	40.1	6250	4.6	496	30.8
58403	1250	40.1	6250	4.6	558	30.8
58404	1250	40.1	6250	4.6	620	30.8
58405	1250	40.1	6250	4.6	682	30.8
58406	1250	40.1	6250	4.6	744	30.8
58407	1250	40.1	6250	4.6	806	30.8
58423	1200	38.5	6000	4.8	0	28.8
58424	1200	38.5	6000	4.8	60	28.8
58425	1200	38.5	6000	4.8	120	28.8
58426	1200	38.5	6000	4.8	180	28.8
58427	1200	38.5	6000	4.8	240	28.8
58428	1200	38.5	6000	4.8	300	28.8
58429	1200	38.5	6000	4.8	360	28.8
58430	1200	38.5	6000	4.8	420	28.8
58431	1200	38.5	6000	4.8	480	28.8
58432	1200	38.5	6000	4.8	540	28.8
58433	1200	38.5	6000	4.8	600	28.8
58434	1200	38.5	6000	4.8	660	28.8
58435	1200	38.5	6000	4.8	720	28.8
58436	1200	38.5	6000	4.8	780	28.8
58437	1200	38.5	6000	4.8	840	28.8
58438	1200	38.5	6000	4.8	900	28.8
58808	750	24.0	3750	4.7	296	14.7
59100	550	17.6	2750	4.5	486	8.5
59239	500	16.2	2500	4.6	1650	7.0

Overall score = score_ratio - 2 * repetitive DNA content