Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign19 - back to list

Summary
Image
Unique putative probes (8)
Putative probes (285)
Redundant probes (8)

Summary

`./analyse_probe_search_results : Tue Feb 13 12:57:13 2007`

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

Fetched probe design: ProbeDesign19
  assembly      : NCBIM36
  bias          : 3prime
  chromosome    : 16
  id            : 5
  strand        : 1
  -------------

Design window length: 2461bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 684 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            : 684/684
Putative probes that are unique                 : 8/684
Putative probes exceeding selection criteria    : 301/684 (both unique and not unique)
Putative probes with successfully-picked primers: 296/301

Identified 8 '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
5367	550	2750	-	1512
5368	550	2750	-	1539
5369	550	2750	-	1566
5443	500	2500	-	1525
5444	500	2500	-	1550
5445	500	2500	-	1575
5446	500	2500	-	1600
5447	500	2500	-	1625

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
4836	1200	38.7	6000	-	1260	38.7
4859	1150	37.1	5750	-	1254	37.1
4860	1150	37.1	5750	-	1311	37.1
4884	1100	35.5	5500	-	1265	35.5
4885	1100	35.5	5500	-	1320	35.5
4835	1200	38.7	6000	1.8	1200	35.2
4910	1050	33.9	5250	-	1248	33.9
4911	1050	33.9	5250	-	1300	33.9
4912	1050	33.9	5250	-	1352	33.9
4913	1050	33.9	5250	-	1404	33.9
4883	1100	35.5	5500	1.0	1210	33.5
4858	1150	37.1	5750	2.1	1197	32.9
4939	1000	32.3	5000	-	1250	32.3
4940	1000	32.3	5000	-	1300	32.3
4941	1000	32.3	5000	-	1350	32.3
4942	1000	32.3	5000	-	1400	32.3
4943	1000	32.3	5000	-	1450	32.3
4976	950	31.5	4750	-	1504	31.5
4914	1000	30.9	5000	-	0	30.9
4970	950	30.6	4750	-	1222	30.6
4971	950	30.6	4750	-	1269	30.6
4972	950	30.6	4750	-	1316	30.6
4973	950	30.6	4750	-	1363	30.6
4974	950	30.6	4750	-	1410	30.6
4975	950	30.6	4750	-	1457	30.6
5011	900	29.8	4500	-	1530	29.8
4944	950	29.3	4750	-	0	29.3
4945	950	29.3	4750	-	47	29.3
4909	1050	33.9	5250	2.4	1196	29.1
5005	900	29.0	4500	-	1260	29.0
5006	900	29.0	4500	-	1305	29.0
5007	900	29.0	4500	-	1350	29.0
5008	900	29.0	4500	-	1395	29.0
5009	900	29.0	4500	-	1440	29.0
5010	900	29.0	4500	-	1485	29.0
4814	1250	35.7	6250	3.4	1178	28.8
5048	850	28.1	4250	-	1512	28.1
5049	850	28.1	4250	-	1554	28.1
5050	850	28.1	4250	-	1596	28.1
4938	1000	32.3	5000	2.1	1200	28.1
4977	900	27.8	4500	-	0	27.8
4978	900	27.8	4500	-	45	27.8
4979	900	27.8	4500	-	90	27.8
5004	900	29.0	4500	0.7	1215	27.7
5042	850	27.4	4250	-	1260	27.4
5043	850	27.4	4250	-	1302	27.4
5044	850	27.4	4250	-	1344	27.4
5045	850	27.4	4250	-	1386	27.4
5046	850	27.4	4250	-	1428	27.4
5047	850	27.4	4250	-	1470	27.4
5041	850	27.4	4250	0.4	1218	26.7
5089	800	26.5	4000	-	1520	26.5
5090	800	26.5	4000	-	1560	26.5
5091	800	26.5	4000	-	1600	26.5
5092	800	26.5	4000	-	1640	26.5
5012	850	26.2	4250	-	0	26.2
5013	850	26.2	4250	-	42	26.2
5014	850	26.2	4250	-	84	26.2
5015	850	26.2	4250	-	126	26.2
5016	850	26.2	4250	-	168	26.2
5082	800	25.8	4000	-	1240	25.8
5083	800	25.8	4000	-	1280	25.8
5084	800	25.8	4000	-	1320	25.8
5085	800	25.8	4000	-	1360	25.8
5086	800	25.8	4000	-	1400	25.8
5087	800	25.8	4000	-	1440	25.8
5088	800	25.8	4000	-	1480	25.8
5134	750	24.8	3750	-	1517	24.8
5135	750	24.8	3750	-	1554	24.8
5136	750	24.8	3750	-	1591	24.8
5137	750	24.8	3750	-	1628	24.8
5138	750	24.8	3750	-	1665	24.8
5139	750	24.8	3750	-	1702	24.8
5051	800	24.7	4000	-	0	24.7
5052	800	24.7	4000	-	40	24.7
5053	800	24.7	4000	-	80	24.7
5054	800	24.7	4000	-	120	24.7
5055	800	24.7	4000	-	160	24.7
5056	800	24.7	4000	-	200	24.7
5126	750	24.2	3750	-	1221	24.2
5127	750	24.2	3750	-	1258	24.2
5128	750	24.2	3750	-	1295	24.2
5129	750	24.2	3750	-	1332	24.2
5130	750	24.2	3750	-	1369	24.2
5131	750	24.2	3750	-	1406	24.2
5132	750	24.2	3750	-	1443	24.2
5133	750	24.2	3750	-	1480	24.2
4980	900	27.8	4500	1.9	135	24.0
5183	700	23.2	3500	-	1505	23.2
5184	700	23.2	3500	-	1540	23.2
5185	700	23.2	3500	-	1575	23.2
5186	700	23.2	3500	-	1610	23.2
5187	700	23.2	3500	-	1645	23.2
5188	700	23.2	3500	-	1680	23.2
5189	700	23.2	3500	-	1715	23.2
5190	700	23.2	3500	-	1750	23.2
5093	750	23.1	3750	-	0	23.1
5094	750	23.1	3750	-	37	23.1
5095	750	23.1	3750	-	74	23.1
5096	750	23.1	3750	-	111	23.1
5097	750	23.1	3750	-	148	23.1
5098	750	23.1	3750	-	185	23.1
5099	750	23.1	3750	-	222	23.1
5100	750	23.1	3750	-	259	23.1
4886	1050	29.0	5250	3.0	0	22.9
5175	700	22.6	3500	-	1225	22.6
5176	700	22.6	3500	-	1260	22.6
5177	700	22.6	3500	-	1295	22.6
5178	700	22.6	3500	-	1330	22.6
5179	700	22.6	3500	-	1365	22.6
5180	700	22.6	3500	-	1400	22.6
5181	700	22.6	3500	-	1435	22.6
5182	700	22.6	3500	-	1470	22.6
5140	700	21.6	3500	-	0	21.6
5141	700	21.6	3500	-	35	21.6
5142	700	21.6	3500	-	70	21.6
5143	700	21.6	3500	-	105	21.6
5144	700	21.6	3500	-	140	21.6
5145	700	21.6	3500	-	175	21.6
5146	700	21.6	3500	-	210	21.6
5147	700	21.6	3500	-	245	21.6
5148	700	21.6	3500	-	280	21.6
5149	700	21.6	3500	-	315	21.6
5238	650	21.5	3250	-	1504	21.5
5239	650	21.5	3250	-	1536	21.5
5240	650	21.5	3250	-	1568	21.5
5241	650	21.5	3250	-	1600	21.5
5242	650	21.5	3250	-	1632	21.5
5243	650	21.5	3250	-	1664	21.5
5244	650	21.5	3250	-	1696	21.5
5245	650	21.5	3250	-	1728	21.5
5246	650	21.5	3250	-	1760	21.5
5247	650	21.5	3250	-	1792	21.5
5230	650	21.0	3250	-	1248	21.0
5231	650	21.0	3250	-	1280	21.0
5232	650	21.0	3250	-	1312	21.0
5233	650	21.0	3250	-	1344	21.0
5234	650	21.0	3250	-	1376	21.0
5235	650	21.0	3250	-	1408	21.0
5236	650	21.0	3250	-	1440	21.0
5237	650	21.0	3250	-	1472	21.0
4946	950	26.2	4750	2.7	94	20.8
5081	800	25.8	4000	2.6	1200	20.6
5191	650	20.1	3250	-	0	20.1
5192	650	20.1	3250	-	32	20.1
5193	650	20.1	3250	-	64	20.1
5194	650	20.1	3250	-	96	20.1
5195	650	20.1	3250	-	128	20.1
5196	650	20.1	3250	-	160	20.1
5197	650	20.1	3250	-	192	20.1
5198	650	20.1	3250	-	224	20.1
5199	650	20.1	3250	-	256	20.1
5200	650	20.1	3250	-	288	20.1
5201	650	20.1	3250	-	320	20.1
5202	650	20.1	3250	-	352	20.1
5299	600	19.9	3000	-	1530	19.9
5300	600	19.9	3000	-	1560	19.9
5301	600	19.9	3000	-	1590	19.9
5302	600	19.9	3000	-	1620	19.9
5303	600	19.9	3000	-	1650	19.9
5304	600	19.9	3000	-	1680	19.9
5305	600	19.9	3000	-	1710	19.9
5306	600	19.9	3000	-	1740	19.9
5307	600	19.9	3000	-	1770	19.9
5308	600	19.9	3000	-	1800	19.9
5309	600	19.9	3000	-	1830	19.9
5310	600	19.9	3000	-	1860	19.9
5229	650	21.0	3250	0.8	1216	19.4
5289	600	19.4	3000	-	1230	19.4
5290	600	19.4	3000	-	1260	19.4
5291	600	19.4	3000	-	1290	19.4
5292	600	19.4	3000	-	1320	19.4
5293	600	19.4	3000	-	1350	19.4
5294	600	19.4	3000	-	1380	19.4
5295	600	19.4	3000	-	1410	19.4
5296	600	19.4	3000	-	1440	19.4
5297	600	19.4	3000	-	1470	19.4
5298	600	19.4	3000	-	1500	19.4
5262	600	19.5	3000	0.3	420	18.8
5248	600	18.5	3000	-	0	18.5
5249	600	18.5	3000	-	30	18.5
5250	600	18.5	3000	-	60	18.5
5251	600	18.5	3000	-	90	18.5
5252	600	18.5	3000	-	120	18.5
5253	600	18.5	3000	-	150	18.5
5254	600	18.5	3000	-	180	18.5
5255	600	18.5	3000	-	210	18.5
5256	600	18.5	3000	-	240	18.5
5257	600	18.5	3000	-	270	18.5
5258	600	18.5	3000	-	300	18.5
5259	600	18.5	3000	-	330	18.5
5260	600	18.5	3000	-	360	18.5
5261	600	18.5	3000	-	390	18.5
5370	550	18.2	2750	-	1593	18.2
5371	550	18.2	2750	-	1620	18.2
5372	550	18.2	2750	-	1647	18.2
5373	550	18.2	2750	-	1674	18.2
5374	550	18.2	2750	-	1701	18.2
5375	550	18.2	2750	-	1728	18.2
5376	550	18.2	2750	-	1755	18.2
5377	550	18.2	2750	-	1782	18.2
5378	550	18.2	2750	-	1809	18.2
5379	550	18.2	2750	-	1836	18.2
5380	550	18.2	2750	-	1863	18.2
5381	550	18.2	2750	-	1890	18.2
5326	550	17.9	2750	-	405	17.9
5327	550	17.9	2750	-	432	17.9
5328	550	17.9	2750	-	459	17.9
5357	550	17.7	2750	-	1242	17.7
5358	550	17.7	2750	-	1269	17.7
5359	550	17.7	2750	-	1296	17.7
5360	550	17.7	2750	-	1323	17.7
5361	550	17.7	2750	-	1350	17.7
5362	550	17.7	2750	-	1377	17.7
5363	550	17.7	2750	-	1404	17.7
5364	550	17.7	2750	-	1431	17.7
5365	550	17.7	2750	-	1458	17.7
5366	550	17.7	2750	-	1485	17.7
5057	800	23.0	4000	2.8	240	17.5
5311	550	17.0	2750	-	0	17.0
5312	550	17.0	2750	-	27	17.0
5313	550	17.0	2750	-	54	17.0
5314	550	17.0	2750	-	81	17.0
5315	550	17.0	2750	-	108	17.0
5316	550	17.0	2750	-	135	17.0
5317	550	17.0	2750	-	162	17.0
5318	550	17.0	2750	-	189	17.0
5319	550	17.0	2750	-	216	17.0
5320	550	17.0	2750	-	243	17.0
5321	550	17.0	2750	-	270	17.0
5322	550	17.0	2750	-	297	17.0
5323	550	17.0	2750	-	324	17.0
5324	550	17.0	2750	-	351	17.0
5325	550	17.0	2750	-	378	17.0
5448	500	16.6	2500	-	1650	16.6
5449	500	16.6	2500	-	1675	16.6
5450	500	16.6	2500	-	1700	16.6
5451	500	16.6	2500	-	1725	16.6
5452	500	16.6	2500	-	1750	16.6
5453	500	16.6	2500	-	1775	16.6
5454	500	16.6	2500	-	1800	16.6
5455	500	16.6	2500	-	1825	16.6
5456	500	16.6	2500	-	1850	16.6
5457	500	16.6	2500	-	1875	16.6
5458	500	16.6	2500	-	1900	16.6
5459	500	16.6	2500	-	1925	16.6
5460	500	16.6	2500	-	1950	16.6
5398	500	16.2	2500	-	400	16.2
5399	500	16.2	2500	-	425	16.2
5400	500	16.2	2500	-	450	16.2
5401	500	16.2	2500	-	475	16.2
5402	500	16.2	2500	-	500	16.2
5431	500	16.1	2500	-	1225	16.1
5432	500	16.1	2500	-	1250	16.1
5433	500	16.1	2500	-	1275	16.1
5434	500	16.1	2500	-	1300	16.1
5435	500	16.1	2500	-	1325	16.1
5436	500	16.1	2500	-	1350	16.1
5437	500	16.1	2500	-	1375	16.1
5438	500	16.1	2500	-	1400	16.1
5439	500	16.1	2500	-	1425	16.1
5440	500	16.1	2500	-	1450	16.1
5441	500	16.1	2500	-	1475	16.1
5442	500	16.1	2500	-	1500	16.1
4969	950	25.7	4750	4.8	1175	16.0
5356	550	17.7	2750	1.1	1215	15.6
5382	500	15.4	2500	-	0	15.4
5383	500	15.4	2500	-	25	15.4
5384	500	15.4	2500	-	50	15.4
5385	500	15.4	2500	-	75	15.4
5386	500	15.4	2500	-	100	15.4
5387	500	15.4	2500	-	125	15.4
5388	500	15.4	2500	-	150	15.4
5389	500	15.4	2500	-	175	15.4
5390	500	15.4	2500	-	200	15.4
5391	500	15.4	2500	-	225	15.4
5392	500	15.4	2500	-	250	15.4
5393	500	15.4	2500	-	275	15.4
5394	500	15.4	2500	-	300	15.4
5395	500	15.4	2500	-	325	15.4
5396	500	15.4	2500	-	350	15.4
5397	500	15.4	2500	-	375	15.4
5203	650	20.1	3250	2.5	384	15.1
5403	500	16.2	2500	1.4	525	13.4
5017	850	19.9	4250	4.9	210	10.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
4915	1000	27.6	5000	3.2	50	21.2
5174	700	22.6	3500	4.4	1190	13.7
5101	750	20.7	3750	3.7	296	13.3
5125	750	23.0	3750	4.9	1184	13.1
5288	600	19.4	3000	3.5	1200	12.4
5329	550	17.7	2750	3.3	486	11.2
5150	700	19.3	3500	4.6	350	10.2
5430	500	16.1	2500	4.2	1200	7.7

Overall score = score_ratio - 2 * repetitive DNA content