Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign51 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (222)
Redundant probes (119)

Summary

`./analyse_probe_search_results : Mon Sep 26 11:54:54 2005`

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

Fetched probe design: ProbeDesign51
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 6
  id            : 33
  strand        : 1
  -------------

Design window length: 4501bp

All jobs for probe design are successful - total: 77
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1526 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        : 1526/1526
Putative probes exceeding selection criteria: 341/1526

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
35297	850	25.9	4250	-	966	25.9
35385	800	24.4	4000	-	960	24.4
35386	800	24.4	4000	-	1000	24.4
35584	700	23.0	3500	-	980	23.0
35480	750	22.9	3750	-	962	22.9
35481	750	22.9	3750	-	999	22.9
35482	750	22.9	3750	-	1036	22.9
35483	750	22.9	3750	0.5	1073	21.8
35585	700	21.3	3500	-	1015	21.3
35586	700	21.3	3500	-	1050	21.3
35587	700	21.3	3500	-	1085	21.3
35588	700	21.3	3500	0.1	1120	21.1
34818	1200	27.5	6000	3.4	960	20.7
35583	700	20.6	3500	-	945	20.6
35698	650	19.8	3250	-	1056	19.8
35699	650	19.8	3250	-	1088	19.8
35700	650	19.8	3250	-	1120	19.8
35701	650	19.8	3250	-	1152	19.8
35822	600	19.7	3000	-	1080	19.7
36052	550	18.3	2750	-	3645	18.3
35823	600	18.3	3000	-	1110	18.3
35824	600	18.3	3000	-	1140	18.3
35825	600	18.3	3000	-	1170	18.3
35826	600	18.3	3000	-	1200	18.3
35959	550	18.1	2750	-	1134	18.1
35296	850	17.9	4250	-	924	17.9
34764	1250	27.5	6250	4.9	930	17.8
35384	800	16.8	4000	-	920	16.8
35960	550	16.8	2750	-	1161	16.8
35961	550	16.8	2750	-	1188	16.8
35962	550	16.8	2750	-	1215	16.8
35963	550	16.8	2750	-	1242	16.8
35964	550	16.8	2750	-	1269	16.8
35069	1000	22.9	5000	3.1	1150	16.7
34758	1250	16.7	6250	-	558	16.7
36102	500	16.2	2500	-	950	16.2
35213	900	16.2	4500	-	900	16.2
35952	550	16.2	2750	-	945	16.2
34857	1200	16.2	6000	-	3300	16.2
34856	1200	16.2	6000	0.1	3240	16.0
34811	1200	16.0	6000	-	540	16.0
34812	1200	16.0	6000	-	600	16.0
34707	1300	17.3	6500	0.7	520	15.9
35479	750	15.8	3750	-	925	15.8
34915	1150	15.5	5750	-	3249	15.5
34916	1150	15.5	5750	-	3306	15.5
34868	1150	15.3	5750	-	570	15.3
34869	1150	15.3	5750	-	627	15.3
36112	500	15.2	2500	-	1200	15.2
36113	500	15.2	2500	-	1225	15.2
36114	500	15.2	2500	-	1250	15.2
36115	500	15.2	2500	-	1275	15.2
36116	500	15.2	2500	-	1300	15.2
35779	650	14.8	3250	-	3648	14.8
34976	1100	14.8	5500	-	3245	14.8
34977	1100	14.8	5500	-	3300	14.8
34978	1100	14.8	5500	-	3355	14.8
34927	1100	14.7	5500	-	550	14.7
34928	1100	14.7	5500	-	605	14.7
34929	1100	14.7	5500	-	660	14.7
34930	1100	14.7	5500	-	715	14.7
35827	600	18.3	3000	1.8	1230	14.6
35907	600	14.4	3000	-	3630	14.4
35042	1050	14.2	5250	-	3276	14.2
35043	1050	14.2	5250	-	3328	14.2
35044	1050	14.2	5250	-	3380	14.2
35045	1050	14.2	5250	-	3432	14.2
34801	1250	16.8	6250	1.4	3224	14.1
35694	650	14.0	3250	-	928	14.0
34990	1050	14.0	5250	-	572	14.0
34991	1050	14.0	5250	-	624	14.0
34992	1050	14.0	5250	-	676	14.0
34993	1050	14.0	5250	-	728	14.0
35295	850	13.9	4250	-	882	13.9
35582	700	13.8	3500	-	910	13.8
35111	1000	13.5	5000	-	3250	13.5
35112	1000	13.5	5000	-	3300	13.5
35113	1000	13.5	5000	-	3350	13.5
35114	1000	13.5	5000	-	3400	13.5
35115	1000	13.5	5000	-	3450	13.5
35116	1000	13.5	5000	-	3500	13.5
35057	1000	13.3	5000	-	550	13.3
35058	1000	13.3	5000	-	600	13.3
35059	1000	13.3	5000	-	650	13.3
35060	1000	13.3	5000	-	700	13.3
35061	1000	13.3	5000	-	750	13.3
35062	1000	13.3	5000	-	800	13.3
35817	600	13.2	3000	-	930	13.2
34708	1300	17.3	6500	2.1	585	13.2
34709	1300	17.3	6500	2.1	650	13.2
34710	1300	17.3	6500	2.1	715	13.2
34711	1300	17.3	6500	2.1	780	13.2
34712	1300	17.3	6500	2.1	845	13.2
35273	900	13.2	4500	-	3600	13.2
35478	750	13.0	3750	-	888	13.0
36117	500	15.2	2500	1.2	1325	12.8
35186	950	12.8	4750	-	3243	12.8
35187	950	12.8	4750	-	3290	12.8
35188	950	12.8	4750	-	3337	12.8
35189	950	12.8	4750	-	3384	12.8
35190	950	12.8	4750	-	3431	12.8
35191	950	12.8	4750	-	3478	12.8
35192	950	12.8	4750	-	3525	12.8
34867	1150	15.3	5750	1.3	513	12.7
34870	1150	15.3	5750	1.3	684	12.7
35383	800	12.7	4000	-	880	12.7
35129	950	12.7	4750	-	564	12.7
35130	950	12.7	4750	-	611	12.7
35131	950	12.7	4750	-	658	12.7
35132	950	12.7	4750	-	705	12.7
35133	950	12.7	4750	-	752	12.7
35134	950	12.7	4750	-	799	12.7
35135	950	12.7	4750	-	846	12.7
35778	650	12.5	3250	-	3616	12.5
35360	850	12.4	4250	-	3612	12.4
36056	550	12.3	2750	-	3753	12.3
35266	900	12.1	4500	-	3285	12.1
35267	900	12.1	4500	-	3330	12.1
35268	900	12.1	4500	-	3375	12.1
35269	900	12.1	4500	-	3420	12.1
35270	900	12.1	4500	-	3465	12.1
35271	900	12.1	4500	-	3510	12.1
35272	900	12.1	4500	-	3555	12.1
35205	900	12.0	4500	-	540	12.0
35206	900	12.0	4500	-	585	12.0
35207	900	12.0	4500	-	630	12.0
35208	900	12.0	4500	-	675	12.0
35209	900	12.0	4500	-	720	12.0
35210	900	12.0	4500	-	765	12.0
35211	900	12.0	4500	-	810	12.0
35212	900	12.0	4500	-	855	12.0
35265	900	12.1	4500	0.1	3240	11.9
34994	1050	14.0	5250	1.0	780	11.9
35305	850	19.5	4250	3.9	1302	11.7
35451	800	11.7	4000	-	3600	11.7
35452	800	11.7	4000	-	3640	11.7
35453	800	11.7	4000	-	3680	11.7
35951	550	11.6	2750	-	918	11.6
34757	1250	16.7	6250	2.6	496	11.5
35221	900	20.6	4500	4.6	1260	11.5
35352	850	11.5	4250	-	3276	11.5
35353	850	11.5	4250	-	3318	11.5
35354	850	11.5	4250	-	3360	11.5
35355	850	11.5	4250	-	3402	11.5
35356	850	11.5	4250	-	3444	11.5
35357	850	11.5	4250	-	3486	11.5
35358	850	11.5	4250	-	3528	11.5
35359	850	11.5	4250	-	3570	11.5
35659	700	11.4	3500	-	3605	11.4
35287	850	11.3	4250	-	546	11.3
35288	850	11.3	4250	-	588	11.3
35289	850	11.3	4250	-	630	11.3
35290	850	11.3	4250	-	672	11.3
35291	850	11.3	4250	-	714	11.3
35292	850	11.3	4250	-	756	11.3
35293	850	11.3	4250	-	798	11.3
35294	850	11.3	4250	-	840	11.3
35693	650	11.2	3250	-	896	11.2
36209	500	11.2	2500	-	3625	11.2
36216	500	11.2	2500	-	3800	11.2
36051	550	11.0	2750	-	3618	11.0
35552	750	11.0	3750	-	3626	11.0
35553	750	11.0	3750	-	3663	11.0
35554	750	11.0	3750	-	3700	11.0
35555	750	11.0	3750	-	3737	11.0
35041	1050	14.2	5250	1.6	3224	10.9
35660	700	10.9	3500	-	3640	10.9
35816	600	10.8	3000	-	900	10.8
35443	800	10.8	4000	-	3280	10.8
35444	800	10.8	4000	-	3320	10.8
35445	800	10.8	4000	-	3360	10.8
35446	800	10.8	4000	-	3400	10.8
35447	800	10.8	4000	-	3440	10.8
35448	800	10.8	4000	-	3480	10.8
35449	800	10.8	4000	-	3520	10.8
35450	800	10.8	4000	-	3560	10.8
35375	800	10.7	4000	-	560	10.7
35376	800	10.7	4000	-	600	10.7
35377	800	10.7	4000	-	640	10.7
35378	800	10.7	4000	-	680	10.7
35379	800	10.7	4000	-	720	10.7
35380	800	10.7	4000	-	760	10.7
35381	800	10.7	4000	-	800	10.7
35382	800	10.7	4000	-	840	10.7
35910	600	10.6	3000	-	3720	10.6
35442	800	10.8	4000	0.1	3240	10.5
36101	500	10.5	2500	-	925	10.5
35551	750	10.5	3750	-	3589	10.5
35128	950	12.7	4750	1.2	517	10.4
35780	650	10.4	3250	-	3680	10.4
35581	700	10.3	3500	-	875	10.3
35661	700	10.2	3500	-	3675	10.2
35662	700	10.2	3500	-	3710	10.2
35663	700	10.2	3500	-	3745	10.2
35664	700	10.2	3500	-	3780	10.2
35542	750	10.1	3750	-	3256	10.1
35543	750	10.1	3750	-	3293	10.1
35544	750	10.1	3750	-	3330	10.1
35545	750	10.1	3750	-	3367	10.1
35546	750	10.1	3750	-	3404	10.1
35547	750	10.1	3750	-	3441	10.1
35548	750	10.1	3750	-	3478	10.1
35549	750	10.1	3750	-	3515	10.1
35550	750	10.1	3750	-	3552	10.1
35469	750	10.0	3750	-	555	10.0
35470	750	10.0	3750	-	592	10.0
35471	750	10.0	3750	-	629	10.0
35472	750	10.0	3750	-	666	10.0
35473	750	10.0	3750	-	703	10.0
35474	750	10.0	3750	-	740	10.0
35475	750	10.0	3750	-	777	10.0
35476	750	10.0	3750	-	814	10.0
35477	750	10.0	3750	-	851	10.0
35351	850	11.5	4250	0.8	3234	9.8
34748	1300	17.5	6500	4.3	3185	8.9
34926	1100	14.7	5500	3.0	495	8.7
34810	1200	16.0	6000	4.0	480	8.0
35468	750	10.0	3750	1.3	518	7.3
34914	1150	15.5	5750	4.3	3192	7.0
35110	1000	13.5	5000	4.1	3200	5.3
35204	900	12.0	4500	3.7	495	4.7
35541	750	10.1	3750	2.9	3219	4.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
34875	1150	26.4	5750	2.3	969	21.7
34934	1100	25.2	5500	2.5	935	20.3
34935	1100	25.2	5500	2.5	990	20.3
34936	1100	25.2	5500	2.5	1045	20.3
35387	800	24.4	4000	2.6	1040	19.1
34997	1050	24.1	5250	2.6	936	18.9
34998	1050	24.1	5250	2.6	988	18.9
34999	1050	24.1	5250	2.6	1040	18.9
35000	1050	24.1	5250	2.6	1092	18.9
34874	1150	22.6	5750	2.3	912	17.9
35065	1000	22.9	5000	2.7	950	17.5
35066	1000	22.9	5000	2.7	1000	17.5
35067	1000	22.9	5000	2.7	1050	17.5
35068	1000	22.9	5000	2.7	1100	17.5
34817	1200	21.6	6000	2.2	900	17.1
35214	900	22.6	4500	2.9	945	16.8
34876	1150	26.4	5750	5.0	1026	16.5
35137	950	21.8	4750	2.8	940	16.1
35138	950	21.8	4750	2.8	987	16.1
35139	950	21.8	4750	2.8	1034	16.1
35140	950	21.8	4750	2.8	1081	16.1
35141	950	21.8	4750	2.8	1128	16.1
35142	950	21.8	4750	2.8	1175	16.1
35702	650	19.8	3250	2.3	1184	15.2
35215	900	20.6	4500	3.0	990	14.6
35216	900	20.6	4500	3.0	1035	14.6
35217	900	20.6	4500	3.0	1080	14.6
35218	900	20.6	4500	3.0	1125	14.6
35219	900	20.6	4500	3.0	1170	14.6
35220	900	20.6	4500	3.0	1215	14.6
35298	850	20.2	4250	3.2	1008	13.9
34763	1250	17.6	6250	2.2	868	13.2
35299	850	19.5	4250	3.2	1050	13.1
35300	850	19.5	4250	3.2	1092	13.1
35301	850	19.5	4250	3.2	1134	13.1
35302	850	19.5	4250	3.2	1176	13.1
35303	850	19.5	4250	3.2	1218	13.1
35304	850	19.5	4250	3.2	1260	13.1
35064	1000	18.0	5000	2.7	900	12.6
34933	1100	17.5	5500	2.5	880	12.6
34989	1050	14.0	5250	0.8	520	12.5
34759	1250	16.7	6250	2.2	620	12.3
34760	1250	16.7	6250	2.2	682	12.3
34761	1250	16.7	6250	2.2	744	12.3
34762	1250	16.7	6250	2.2	806	12.3
35388	800	19.0	4000	3.4	1080	12.3
34996	1050	17.3	5250	2.6	884	12.1
35389	800	18.3	4000	3.4	1120	11.6
35390	800	18.3	4000	3.4	1160	11.6
35391	800	18.3	4000	3.4	1200	11.6
35392	800	18.3	4000	3.4	1240	11.6
35393	800	18.3	4000	3.4	1280	11.6
35394	800	18.3	4000	3.4	1320	11.6
34813	1200	16.0	6000	2.2	660	11.5
34814	1200	16.0	6000	2.2	720	11.5
34815	1200	16.0	6000	2.2	780	11.5
34816	1200	16.0	6000	2.2	840	11.5
35136	950	16.4	4750	2.5	893	11.4
35484	750	17.9	3750	3.6	1110	10.7
34871	1150	15.3	5750	2.3	741	10.6
34872	1150	15.3	5750	2.3	798	10.6
34873	1150	15.3	5750	2.3	855	10.6
35485	750	17.2	3750	3.6	1147	10.0
35486	750	17.2	3750	3.6	1184	10.0
35487	750	17.2	3750	3.6	1221	10.0
35488	750	17.2	3750	3.6	1258	10.0
35489	750	17.2	3750	3.6	1295	10.0
35490	750	17.2	3750	3.6	1332	10.0
35491	750	17.2	3750	3.6	1369	10.0
34931	1100	14.7	5500	2.5	770	9.8
34932	1100	14.7	5500	2.5	825	9.8
35589	700	16.7	3500	3.9	1155	9.0
34995	1050	14.0	5250	2.6	832	8.9
35374	800	10.7	4000	1.0	520	8.7
35590	700	16.1	3500	3.9	1190	8.3
35591	700	16.1	3500	3.9	1225	8.3
35592	700	16.1	3500	3.9	1260	8.3
35593	700	16.1	3500	3.9	1295	8.3
35594	700	16.1	3500	3.9	1330	8.3
35595	700	16.1	3500	3.9	1365	8.3
35596	700	16.1	3500	3.9	1400	8.3
35597	700	16.1	3500	3.9	1435	8.3
35063	1000	13.3	5000	2.7	850	7.9
35056	1000	13.3	5000	2.8	500	7.7
35492	750	17.2	3750	4.9	1406	7.3
35703	650	15.5	3250	4.2	1216	7.2
35704	650	14.9	3250	4.2	1248	6.6
35705	650	14.9	3250	4.2	1280	6.6
35706	650	14.9	3250	4.2	1312	6.6
35707	650	14.9	3250	4.2	1344	6.6
35708	650	14.9	3250	4.2	1376	6.6
35709	650	14.9	3250	4.2	1408	6.6
35710	650	14.9	3250	4.2	1440	6.6
35711	650	14.9	3250	4.2	1472	6.6
35286	850	11.3	4250	2.8	504	5.7
34975	1100	14.8	5500	4.6	3190	5.6
35828	600	14.3	3000	4.5	1260	5.3
35829	600	13.8	3000	4.5	1290	4.8
35830	600	13.8	3000	4.5	1320	4.8
35831	600	13.8	3000	4.5	1350	4.8
35832	600	13.8	3000	4.5	1380	4.8
35833	600	13.8	3000	4.5	1410	4.8
35834	600	13.8	3000	4.5	1440	4.8
35835	600	13.8	3000	4.5	1470	4.8
35836	600	13.8	3000	4.5	1500	4.8
35837	600	13.8	3000	4.5	1530	4.8
35965	550	13.5	2750	4.9	1296	3.7
35185	950	12.8	4750	4.7	3196	3.3
35966	550	13.1	2750	4.9	1323	3.3
35967	550	12.6	2750	4.9	1350	2.8
35968	550	12.6	2750	4.9	1377	2.8
35969	550	12.6	2750	4.9	1404	2.8
35970	550	12.6	2750	4.9	1431	2.8
35971	550	12.6	2750	4.9	1458	2.8
35972	550	12.6	2750	4.9	1485	2.8
35973	550	12.6	2750	4.9	1512	2.8
35974	550	12.6	2750	4.9	1539	2.8
35975	550	12.6	2750	4.9	1566	2.8
35976	550	12.6	2750	4.9	1593	2.8

Overall score = score_ratio - 2 * repetitive DNA content