Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign59 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (256)
Redundant probes (34)

Summary

`./analyse_probe_search_results : Fri Sep 30 10:00:09 2005`

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

Fetched probe design: ProbeDesign59
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 10
  id            : 46
  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 700 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        : 700/700
Putative probes exceeding selection criteria: 290/700

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
47504	900	27.8	4500	-	945	27.8
47542	850	26.2	4250	-	966	26.2
47543	850	26.2	4250	-	1008	26.2
47583	800	24.7	4000	-	960	24.7
47584	800	24.7	4000	-	1000	24.7
47585	800	24.7	4000	-	1040	24.7
47628	750	23.1	3750	-	962	23.1
47629	750	23.1	3750	-	999	23.1
47630	750	23.1	3750	-	1036	23.1
47631	750	23.1	3750	-	1073	23.1
47632	750	23.1	3750	-	1110	23.1
47677	700	21.6	3500	-	945	21.6
47678	700	21.6	3500	-	980	21.6
47679	700	21.6	3500	-	1015	21.6
47680	700	21.6	3500	-	1050	21.6
47681	700	21.6	3500	-	1085	21.6
47682	700	21.6	3500	-	1120	21.6
47683	700	21.6	3500	-	1155	21.6
47541	850	25.8	4250	2.1	924	21.5
47469	950	20.9	4750	0.2	940	20.5
47732	650	20.1	3250	-	960	20.1
47733	650	20.1	3250	-	992	20.1
47734	650	20.1	3250	-	1024	20.1
47735	650	20.1	3250	-	1056	20.1
47736	650	20.1	3250	-	1088	20.1
47737	650	20.1	3250	-	1120	20.1
47738	650	20.1	3250	-	1152	20.1
47739	650	20.1	3250	-	1184	20.1
47293	1300	20.0	6500	-	975	20.0
47294	1300	20.0	6500	-	1040	20.0
47586	800	20.0	4000	-	1080	20.0
47295	1300	20.0	6500	-	1105	20.0
47296	1300	20.0	6500	-	1170	20.0
47505	900	19.8	4500	-	990	19.8
47313	1250	19.2	6250	-	992	19.2
47314	1250	19.2	6250	-	1054	19.2
47315	1250	19.2	6250	-	1116	19.2
47316	1250	19.2	6250	-	1178	19.2
47317	1250	19.2	6250	-	1240	19.2
47800	600	19.1	3000	-	1200	19.1
47627	750	23.1	3750	2.3	925	18.6
47792	600	18.5	3000	-	960	18.5
47793	600	18.5	3000	-	990	18.5
47794	600	18.5	3000	-	1020	18.5
47795	600	18.5	3000	-	1050	18.5
47796	600	18.5	3000	-	1080	18.5
47797	600	18.5	3000	-	1110	18.5
47798	600	18.5	3000	-	1140	18.5
47799	600	18.5	3000	-	1170	18.5
47334	1200	18.5	6000	-	960	18.5
47335	1200	18.5	6000	-	1020	18.5
47336	1200	18.5	6000	-	1080	18.5
47337	1200	18.5	6000	-	1140	18.5
47338	1200	18.5	6000	-	1200	18.5
47339	1200	18.5	6000	-	1260	18.5
47357	1150	17.7	5750	-	969	17.7
47358	1150	17.7	5750	-	1026	17.7
47359	1150	17.7	5750	-	1083	17.7
47360	1150	17.7	5750	-	1140	17.7
47361	1150	17.7	5750	-	1197	17.7
47362	1150	17.7	5750	-	1254	17.7
47363	1150	17.7	5750	-	1311	17.7
47759	650	17.7	3250	-	1824	17.7
47312	1250	19.2	6250	1.0	930	17.3
47859	550	17.0	2750	-	945	17.0
47860	550	17.0	2750	-	972	17.0
47861	550	17.0	2750	-	999	17.0
47862	550	17.0	2750	-	1026	17.0
47863	550	17.0	2750	-	1053	17.0
47864	550	17.0	2750	-	1080	17.0
47865	550	17.0	2750	-	1107	17.0
47866	550	17.0	2750	-	1134	17.0
47867	550	17.0	2750	-	1161	17.0
47868	550	17.0	2750	-	1188	17.0
47382	1100	16.9	5500	-	990	16.9
47383	1100	16.9	5500	-	1045	16.9
47384	1100	16.9	5500	-	1100	16.9
47385	1100	16.9	5500	-	1155	16.9
47386	1100	16.9	5500	-	1210	16.9
47387	1100	16.9	5500	-	1265	16.9
47388	1100	16.9	5500	-	1320	16.9
47389	1100	16.9	5500	-	1375	16.9
47821	600	16.3	3000	-	1830	16.3
47822	600	16.3	3000	-	1860	16.3
47823	600	16.3	3000	-	1890	16.3
47409	1050	16.2	5250	-	988	16.2
47410	1050	16.2	5250	-	1040	16.2
47411	1050	16.2	5250	-	1092	16.2
47412	1050	16.2	5250	-	1144	16.2
47413	1050	16.2	5250	-	1196	16.2
47414	1050	16.2	5250	-	1248	16.2
47415	1050	16.2	5250	-	1300	16.2
47416	1050	16.2	5250	-	1352	16.2
47417	1050	16.2	5250	-	1404	16.2
47582	800	21.6	4000	2.8	920	16.1
47945	500	15.9	2500	-	1200	15.9
47873	550	15.8	2750	-	1323	15.8
47731	650	20.1	3250	2.2	928	15.8
47381	1100	16.9	5500	0.6	935	15.7
47544	850	15.6	4250	-	1050	15.6
47935	500	15.4	2500	-	950	15.4
47936	500	15.4	2500	-	975	15.4
47937	500	15.4	2500	-	1000	15.4
47938	500	15.4	2500	-	1025	15.4
47939	500	15.4	2500	-	1050	15.4
47940	500	15.4	2500	-	1075	15.4
47941	500	15.4	2500	-	1100	15.4
47942	500	15.4	2500	-	1125	15.4
47943	500	15.4	2500	-	1150	15.4
47944	500	15.4	2500	-	1175	15.4
47684	700	15.4	3500	-	1190	15.4
47437	1000	15.4	5000	-	950	15.4
47438	1000	15.4	5000	-	1000	15.4
47439	1000	15.4	5000	-	1050	15.4
47440	1000	15.4	5000	-	1100	15.4
47441	1000	15.4	5000	-	1150	15.4
47442	1000	15.4	5000	-	1200	15.4
47443	1000	15.4	5000	-	1250	15.4
47444	1000	15.4	5000	-	1300	15.4
47445	1000	15.4	5000	-	1350	15.4
47446	1000	15.4	5000	-	1400	15.4
47447	1000	15.4	5000	-	1450	15.4
47448	1000	15.4	5000	-	1500	15.4
47292	1300	20.0	6500	2.5	910	15.1
47408	1050	16.2	5250	0.6	936	15.0
47892	550	14.9	2750	-	1836	14.9
47893	550	14.9	2750	-	1863	14.9
47894	550	14.9	2750	-	1890	14.9
47895	550	14.9	2750	-	1917	14.9
47470	950	14.6	4750	-	987	14.6
47471	950	14.6	4750	-	1034	14.6
47472	950	14.6	4750	-	1081	14.6
47473	950	14.6	4750	-	1128	14.6
47474	950	14.6	4750	-	1175	14.6
47475	950	14.6	4750	-	1222	14.6
47476	950	14.6	4750	-	1269	14.6
47477	950	14.6	4750	-	1316	14.6
47478	950	14.6	4750	-	1363	14.6
47479	950	14.6	4750	-	1410	14.6
47480	950	14.6	4750	-	1457	14.6
47481	950	14.6	4750	-	1504	14.6
47482	950	14.6	4750	-	1551	14.6
47896	550	14.6	2750	-	1944	14.6
47633	750	14.5	3750	-	1147	14.5
47791	600	18.5	3000	2.0	930	14.5
47952	500	14.0	2500	-	1375	14.0
47506	900	13.8	4500	-	1035	13.8
47507	900	13.8	4500	-	1080	13.8
47508	900	13.8	4500	-	1125	13.8
47509	900	13.8	4500	-	1170	13.8
47510	900	13.8	4500	-	1215	13.8
47511	900	13.8	4500	-	1260	13.8
47512	900	13.8	4500	-	1305	13.8
47513	900	13.8	4500	-	1350	13.8
47514	900	13.8	4500	-	1395	13.8
47515	900	13.8	4500	-	1440	13.8
47516	900	13.8	4500	-	1485	13.8
47517	900	13.8	4500	-	1530	13.8
47518	900	13.8	4500	-	1575	13.8
47970	500	13.6	2500	-	1825	13.6
47971	500	13.6	2500	-	1850	13.6
47972	500	13.6	2500	-	1875	13.6
47973	500	13.6	2500	-	1900	13.6
47974	500	13.6	2500	-	1925	13.6
47975	500	13.6	2500	-	1950	13.6
47976	500	13.6	2500	-	1975	13.6
47289	1300	20.0	6500	3.4	715	13.2
47290	1300	20.0	6500	3.4	780	13.2
47291	1300	20.0	6500	3.4	845	13.2
47803	600	13.2	3000	-	1290	13.2
47545	850	13.1	4250	-	1092	13.1
47546	850	13.1	4250	-	1134	13.1
47547	850	13.1	4250	-	1176	13.1
47548	850	13.1	4250	-	1218	13.1
47549	850	13.1	4250	-	1260	13.1
47550	850	13.1	4250	-	1302	13.1
47551	850	13.1	4250	-	1344	13.1
47552	850	13.1	4250	-	1386	13.1
47553	850	13.1	4250	-	1428	13.1
47554	850	13.1	4250	-	1470	13.1
47555	850	13.1	4250	-	1512	13.1
47556	850	13.1	4250	-	1554	13.1
47557	850	13.1	4250	-	1596	13.1
47558	850	13.1	4250	-	1638	13.1
47356	1150	17.7	5750	2.6	912	12.5
47587	800	12.4	4000	-	1120	12.4
47741	650	12.4	3250	-	1248	12.4
47588	800	12.3	4000	-	1160	12.3
47589	800	12.3	4000	-	1200	12.3
47590	800	12.3	4000	-	1240	12.3
47591	800	12.3	4000	-	1280	12.3
47592	800	12.3	4000	-	1320	12.3
47593	800	12.3	4000	-	1360	12.3
47594	800	12.3	4000	-	1400	12.3
47595	800	12.3	4000	-	1440	12.3
47596	800	12.3	4000	-	1480	12.3
47597	800	12.3	4000	-	1520	12.3
47598	800	12.3	4000	-	1560	12.3
47599	800	12.3	4000	-	1600	12.3
47600	800	12.3	4000	-	1640	12.3
47601	800	12.3	4000	-	1680	12.3
47977	500	12.0	2500	-	2000	12.0
47634	750	11.5	3750	-	1184	11.5
47635	750	11.5	3750	-	1221	11.5
47636	750	11.5	3750	-	1258	11.5
47637	750	11.5	3750	-	1295	11.5
47638	750	11.5	3750	-	1332	11.5
47639	750	11.5	3750	-	1369	11.5
47640	750	11.5	3750	-	1406	11.5
47641	750	11.5	3750	-	1443	11.5
47642	750	11.5	3750	-	1480	11.5
47643	750	11.5	3750	-	1517	11.5
47644	750	11.5	3750	-	1554	11.5
47645	750	11.5	3750	-	1591	11.5
47646	750	11.5	3750	-	1628	11.5
47647	750	11.5	3750	-	1665	11.5
47648	750	11.5	3750	-	1702	11.5
47649	750	11.5	3750	-	1739	11.5
47685	700	10.8	3500	-	1225	10.8
47686	700	10.8	3500	-	1260	10.8
47687	700	10.8	3500	-	1295	10.8
47688	700	10.8	3500	-	1330	10.8
47689	700	10.8	3500	-	1365	10.8
47690	700	10.8	3500	-	1400	10.8
47691	700	10.8	3500	-	1435	10.8
47692	700	10.8	3500	-	1470	10.8
47693	700	10.8	3500	-	1505	10.8
47694	700	10.8	3500	-	1540	10.8
47695	700	10.8	3500	-	1575	10.8
47696	700	10.8	3500	-	1610	10.8
47697	700	10.8	3500	-	1645	10.8
47698	700	10.8	3500	-	1680	10.8
47699	700	10.8	3500	-	1715	10.8
47700	700	10.8	3500	-	1750	10.8
47701	700	10.8	3500	-	1785	10.8
47874	550	10.1	2750	-	1350	10.1
47742	650	10.0	3250	-	1280	10.0
47743	650	10.0	3250	-	1312	10.0
47744	650	10.0	3250	-	1344	10.0
47745	650	10.0	3250	-	1376	10.0
47746	650	10.0	3250	-	1408	10.0
47747	650	10.0	3250	-	1440	10.0
47748	650	10.0	3250	-	1472	10.0
47749	650	10.0	3250	-	1504	10.0
47750	650	10.0	3250	-	1536	10.0
47751	650	10.0	3250	-	1568	10.0
47752	650	10.0	3250	-	1600	10.0
47753	650	10.0	3250	-	1632	10.0
47754	650	10.0	3250	-	1664	10.0
47755	650	10.0	3250	-	1696	10.0
47756	650	10.0	3250	-	1728	10.0
47757	650	10.0	3250	-	1760	10.0
47758	650	10.0	3250	-	1792	10.0
47308	1250	19.2	6250	4.8	682	9.6
47432	1000	17.2	5000	4.4	700	8.4
47464	950	16.3	4750	4.6	705	7.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
47309	1250	19.2	6250	3.5	744	12.2
47310	1250	19.2	6250	3.5	806	12.2
47311	1250	19.2	6250	3.5	868	12.2
47353	1150	19.8	5750	3.8	741	12.1
47333	1200	18.5	6000	3.5	900	11.5
47330	1200	18.6	6000	3.7	720	11.2
47331	1200	18.5	6000	3.7	780	11.1
47332	1200	18.5	6000	3.7	840	11.1
47377	1100	18.9	5500	4.0	715	10.9
47378	1100	18.9	5500	4.0	770	10.9
47354	1150	17.7	5750	3.8	798	10.0
47355	1150	17.7	5750	3.8	855	10.0
47436	1000	18.2	5000	4.2	900	9.8
47404	1050	18.0	5250	4.2	728	9.7
47405	1050	18.0	5250	4.2	780	9.7
47406	1050	18.0	5250	4.2	832	9.7
47379	1100	17.0	5500	4.0	825	9.0
47380	1100	16.9	5500	4.0	880	8.9
47934	500	15.4	2500	3.4	925	8.6
47433	1000	17.2	5000	4.4	750	8.4
47434	1000	17.2	5000	4.4	800	8.4
47435	1000	17.2	5000	4.4	850	8.4
47407	1050	16.2	5250	4.2	884	7.8
47468	950	16.6	4750	4.6	893	7.3
47465	950	16.3	4750	4.6	752	7.1
47466	950	16.3	4750	4.6	799	7.1
47467	950	16.3	4750	4.6	846	7.1
47503	900	16.4	4500	4.7	900	7.0
47676	700	14.9	3500	4.6	910	5.8
47499	900	15.5	4500	4.9	720	5.7
47500	900	15.5	4500	4.9	765	5.7
47501	900	15.5	4500	4.9	810	5.7
47502	900	15.5	4500	4.9	855	5.7
47858	550	14.1	2750	4.4	918	5.4

Overall score = score_ratio - 2 * repetitive DNA content