Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign46 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (161)
Redundant probes (133)

Summary

`./analyse_probe_search_results : Wed Sep 21 13:53:25 2005`

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

Fetched probe design: ProbeDesign46
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 8
  id            : 28
  strand        : 1
  -------------

Design window length: 2473bp

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 686 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        : 686/686
Putative probes exceeding selection criteria: 294/686

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
29908	1300	38.7	6500	1.5	1105	35.6
29929	1250	37.2	6250	1.6	1178	34.0
29951	1200	35.7	6000	1.9	1260	31.9
29909	1300	36.9	6500	2.5	1170	31.9
29948	1200	35.7	6000	2.8	1080	30.2
29996	1100	33.7	5500	1.8	1100	30.1
29971	1150	35.3	5750	2.6	1083	30.1
29975	1150	34.2	5750	2.1	1311	30.1
30000	1100	32.7	5500	1.8	1320	29.1
30091	950	28.3	4750	-	1504	28.3
30022	1050	32.2	5250	2.0	1092	28.2
30028	1050	31.2	5250	1.9	1404	27.4
30126	900	26.8	4500	-	1530	26.8
30051	1000	30.7	5000	2.0	1100	26.7
30058	1000	29.8	5000	2.0	1450	25.8
30163	850	25.3	4250	-	1512	25.3
30164	850	25.3	4250	-	1554	25.3
30165	850	25.3	4250	-	1596	25.3
30090	950	28.3	4750	2.1	1457	24.1
30204	800	23.8	4000	-	1520	23.8
30205	800	23.8	4000	-	1560	23.8
30206	800	23.8	4000	-	1600	23.8
30207	800	23.8	4000	-	1640	23.8
30059	950	22.6	4750	-	0	22.6
30082	950	29.1	4750	3.4	1081	22.4
30249	750	22.3	3750	-	1517	22.3
30250	750	22.3	3750	-	1554	22.3
30251	750	22.3	3750	-	1591	22.3
30252	750	22.3	3750	-	1628	22.3
30253	750	22.3	3750	-	1665	22.3
30254	750	22.3	3750	-	1702	22.3
30092	900	21.4	4500	-	0	21.4
30093	900	21.4	4500	-	45	21.4
30153	850	26.1	4250	2.5	1092	21.1
30299	700	21.0	3500	-	1540	21.0
30300	700	20.8	3500	-	1575	20.8
30301	700	20.8	3500	-	1610	20.8
30302	700	20.8	3500	-	1645	20.8
30303	700	20.8	3500	-	1680	20.8
30304	700	20.8	3500	-	1715	20.8
30305	700	20.8	3500	-	1750	20.8
30116	900	27.6	4500	3.7	1080	20.3
30127	850	20.2	4250	-	0	20.2
30128	850	20.2	4250	-	42	20.2
30129	850	20.2	4250	-	84	20.2
30130	850	20.2	4250	-	126	20.2
30306	650	19.7	3250	-	0	19.7
30029	1000	23.8	5000	2.2	0	19.4
30356	650	19.3	3250	-	1600	19.3
30357	650	19.3	3250	-	1632	19.3
30358	650	19.3	3250	-	1664	19.3
30359	650	19.3	3250	-	1696	19.3
30360	650	19.3	3250	-	1728	19.3
30361	650	19.3	3250	-	1760	19.3
30362	650	19.3	3250	-	1792	19.3
30166	800	19.0	4000	-	0	19.0
30167	800	19.0	4000	-	40	19.0
30168	800	19.0	4000	-	80	19.0
30169	800	19.0	4000	-	120	19.0
30170	800	19.0	4000	-	160	19.0
29927	1250	28.4	6250	4.7	1054	19.0
30094	900	21.4	4500	1.3	90	18.8
30060	950	22.6	4750	2.0	47	18.6
30255	700	17.9	3500	-	0	17.9
30208	750	17.9	3750	-	0	17.9
30209	750	17.9	3750	-	37	17.9
30210	750	17.9	3750	-	74	17.9
30211	750	17.9	3750	-	111	17.9
30212	750	17.9	3750	-	148	17.9
30213	750	17.9	3750	-	185	17.9
30214	750	17.9	3750	-	222	17.9
30418	600	17.9	3000	-	1650	17.9
30419	600	17.9	3000	-	1680	17.9
30420	600	17.9	3000	-	1710	17.9
30421	600	17.9	3000	-	1740	17.9
30422	600	17.9	3000	-	1770	17.9
30423	600	17.9	3000	-	1800	17.9
30424	600	17.9	3000	-	1830	17.9
30307	650	16.9	3250	-	32	16.9
30425	600	17.9	3000	0.5	1860	16.9
30256	700	16.7	3500	-	35	16.7
30257	700	16.7	3500	-	70	16.7
30258	700	16.7	3500	-	105	16.7
30259	700	16.7	3500	-	140	16.7
30260	700	16.7	3500	-	175	16.7
30261	700	16.7	3500	-	210	16.7
30262	700	16.7	3500	-	245	16.7
30365	600	16.4	3000	-	60	16.4
30489	550	16.4	2750	-	1701	16.4
30490	550	16.4	2750	-	1728	16.4
30491	550	16.4	2750	-	1755	16.4
30492	550	16.4	2750	-	1782	16.4
30493	550	16.4	2750	-	1809	16.4
30494	550	16.4	2750	-	1836	16.4
30495	550	16.4	2750	-	1863	16.4
30496	550	16.4	2750	-	1890	16.4
30193	800	24.5	4000	4.1	1080	16.3
30263	700	16.7	3500	0.3	280	16.1
30366	600	15.5	3000	-	90	15.5
30308	650	15.5	3250	-	64	15.5
30309	650	15.5	3250	-	96	15.5
30310	650	15.5	3250	-	128	15.5
30311	650	15.5	3250	-	160	15.5
30312	650	15.5	3250	-	192	15.5
30313	650	15.5	3250	-	224	15.5
30314	650	15.5	3250	-	256	15.5
30315	650	15.5	3250	-	288	15.5
30316	650	15.5	3250	-	320	15.5
30504	500	15.2	2500	-	150	15.2
30430	550	15.0	2750	-	108	15.0
30568	500	14.9	2500	-	1750	14.9
30569	500	14.9	2500	-	1775	14.9
30570	500	14.9	2500	-	1800	14.9
30571	500	14.9	2500	-	1825	14.9
30572	500	14.9	2500	-	1850	14.9
30573	500	14.9	2500	-	1875	14.9
30574	500	14.9	2500	-	1900	14.9
30575	500	14.9	2500	-	1925	14.9
30576	500	14.9	2500	-	1950	14.9
30367	600	14.3	3000	-	120	14.3
30368	600	14.3	3000	-	150	14.3
30369	600	14.3	3000	-	180	14.3
30370	600	14.3	3000	-	210	14.3
30371	600	14.3	3000	-	240	14.3
30372	600	14.3	3000	-	270	14.3
30373	600	14.3	3000	-	300	14.3
30374	600	14.3	3000	-	330	14.3
30375	600	14.3	3000	-	360	14.3
30431	550	14.2	2750	-	135	14.2
30505	500	13.6	2500	-	175	13.6
30286	700	21.5	3500	4.0	1085	13.5
30432	550	13.1	2750	-	162	13.1
30433	550	13.1	2750	-	189	13.1
30434	550	13.1	2750	-	216	13.1
30435	550	13.1	2750	-	243	13.1
30436	550	13.1	2750	-	270	13.1
30437	550	13.1	2750	-	297	13.1
30438	550	13.1	2750	-	324	13.1
30439	550	13.1	2750	-	351	13.1
30440	550	13.1	2750	-	378	13.1
30441	550	13.1	2750	-	405	13.1
30506	500	12.8	2500	-	200	12.8
30497	550	16.4	2750	1.8	1917	12.7
30340	650	19.9	3250	3.8	1088	12.2
30507	500	11.9	2500	-	225	11.9
30508	500	11.9	2500	-	250	11.9
30509	500	11.9	2500	-	275	11.9
30510	500	11.9	2500	-	300	11.9
30511	500	11.9	2500	-	325	11.9
30512	500	11.9	2500	-	350	11.9
30513	500	11.9	2500	-	375	11.9
30514	500	11.9	2500	-	400	11.9
30515	500	11.9	2500	-	425	11.9
30516	500	11.9	2500	-	450	11.9
30517	500	11.9	2500	-	475	11.9
30442	550	13.1	2750	0.7	432	11.6
30376	600	14.3	3000	2.0	390	10.3
30131	850	19.1	4250	4.7	168	9.6
30215	750	17.9	3750	4.1	259	9.6
30317	650	15.5	3250	3.7	352	8.1
30542	500	15.3	2500	4.0	1100	7.3

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
29928	1250	37.2	6250	1.6	1116	34.0
29949	1200	35.7	6000	1.7	1140	32.4
29950	1200	35.7	6000	1.7	1200	32.4
29972	1150	34.2	5750	1.7	1140	30.7
29973	1150	34.2	5750	1.7	1197	30.7
29974	1150	34.2	5750	1.7	1254	30.7
29997	1100	32.7	5500	1.8	1155	29.1
29998	1100	32.7	5500	1.8	1210	29.1
29999	1100	32.7	5500	1.8	1265	29.1
30023	1050	32.2	5250	1.9	1144	28.4
30024	1050	31.2	5250	1.9	1196	27.4
30025	1050	31.2	5250	1.9	1248	27.4
30026	1050	31.2	5250	1.9	1300	27.4
30027	1050	31.2	5250	1.9	1352	27.4
30052	1000	30.7	5000	2.0	1150	26.7
30053	1000	30.7	5000	2.0	1200	26.7
30054	1000	29.8	5000	2.0	1250	25.8
30055	1000	29.8	5000	2.0	1300	25.8
30056	1000	29.8	5000	2.0	1350	25.8
30057	1000	29.8	5000	2.0	1400	25.8
30083	950	29.1	4750	2.1	1128	24.9
30084	950	29.1	4750	2.1	1175	24.9
30085	950	29.1	4750	2.1	1222	24.9
30086	950	29.1	4750	2.1	1269	24.9
30121	900	28.7	4500	2.2	1305	24.2
30087	950	28.3	4750	2.1	1316	24.1
30088	950	28.3	4750	2.1	1363	24.1
30089	950	28.3	4750	2.1	1410	24.1
30117	900	27.6	4500	2.2	1125	23.2
30118	900	27.6	4500	2.2	1170	23.2
30119	900	27.6	4500	2.2	1215	23.2
30120	900	27.6	4500	2.2	1260	23.2
30125	900	26.8	4500	2.0	1485	22.8
30158	850	27.1	4250	2.4	1302	22.4
30159	850	27.1	4250	2.4	1344	22.4
30122	900	26.8	4500	2.2	1350	22.3
30123	900	26.8	4500	2.2	1395	22.3
30124	900	26.8	4500	2.2	1440	22.3
30160	850	26.4	4250	2.4	1386	21.7
30154	850	26.1	4250	2.4	1134	21.4
30155	850	26.1	4250	2.4	1176	21.4
30156	850	26.1	4250	2.4	1218	21.4
30157	850	26.1	4250	2.4	1260	21.4
30161	850	25.3	4250	2.4	1428	20.6
30162	850	25.3	4250	2.4	1470	20.6
30199	800	25.5	4000	2.5	1320	20.5
30200	800	25.5	4000	2.5	1360	20.5
30201	800	25.5	4000	2.5	1400	20.5
30194	800	24.5	4000	2.5	1120	19.5
30195	800	24.5	4000	2.5	1160	19.5
30196	800	24.5	4000	2.5	1200	19.5
30197	800	24.5	4000	2.5	1240	19.5
30198	800	24.5	4000	2.5	1280	19.5
30202	800	24.0	4000	2.5	1440	19.0
30248	750	24.2	3750	2.7	1480	18.9
30203	800	23.8	4000	2.5	1480	18.8
30244	750	23.9	3750	2.7	1332	18.6
30245	750	23.9	3750	2.7	1369	18.6
30246	750	23.9	3750	2.7	1406	18.6
30247	750	23.9	3750	2.7	1443	18.6
30238	750	23.0	3750	2.7	1110	17.7
30239	750	23.0	3750	2.7	1147	17.7
30240	750	23.0	3750	2.7	1184	17.7
30241	750	23.0	3750	2.7	1221	17.7
30242	750	23.0	3750	2.7	1258	17.7
30243	750	23.0	3750	2.7	1295	17.7
30297	700	22.6	3500	2.9	1470	16.9
30293	700	22.3	3500	2.9	1330	16.6
30294	700	22.3	3500	2.9	1365	16.6
30295	700	22.3	3500	2.9	1400	16.6
30296	700	22.3	3500	2.9	1435	16.6
30287	700	21.5	3500	2.9	1120	15.8
30288	700	21.5	3500	2.9	1155	15.8
30289	700	21.5	3500	2.9	1190	15.8
30290	700	21.5	3500	2.9	1225	15.8
30291	700	21.5	3500	2.9	1260	15.8
30292	700	21.5	3500	2.9	1295	15.8
30352	650	21.0	3250	3.1	1472	14.8
30347	650	20.7	3250	3.1	1312	14.5
30348	650	20.7	3250	3.1	1344	14.5
30349	650	20.7	3250	3.1	1376	14.5
30350	650	20.7	3250	3.1	1408	14.5
30351	650	20.7	3250	3.1	1440	14.5
30341	650	19.9	3250	3.1	1120	13.8
30342	650	19.9	3250	3.1	1152	13.8
30343	650	19.9	3250	3.1	1184	13.8
30344	650	19.9	3250	3.1	1216	13.8
30345	650	19.9	3250	3.1	1248	13.8
30346	650	19.9	3250	3.1	1280	13.8
30171	800	19.0	4000	2.8	200	13.5
30412	600	19.4	3000	3.3	1470	12.7
30407	600	19.1	3000	3.3	1320	12.4
30408	600	19.1	3000	3.3	1350	12.4
30409	600	19.1	3000	3.3	1380	12.4
30410	600	19.1	3000	3.3	1410	12.4
30411	600	19.1	3000	3.3	1440	12.4
30400	600	18.4	3000	3.3	1110	11.7
30401	600	18.4	3000	3.3	1140	11.7
30402	600	18.4	3000	3.3	1170	11.7
30403	600	18.4	3000	3.3	1200	11.7
30404	600	18.4	3000	3.3	1230	11.7
30405	600	18.4	3000	3.3	1260	11.7
30406	600	18.4	3000	3.3	1290	11.7
30475	550	17.5	2750	3.6	1323	10.2
30476	550	17.5	2750	3.6	1350	10.2
30477	550	17.5	2750	3.6	1377	10.2
30478	550	17.5	2750	3.6	1404	10.2
30479	550	17.5	2750	3.6	1431	10.2
30480	550	17.5	2750	3.6	1458	10.2
30467	550	16.9	2750	3.6	1107	9.6
30468	550	16.9	2750	3.6	1134	9.6
30469	550	16.9	2750	3.6	1161	9.6
30470	550	16.9	2750	3.6	1188	9.6
30471	550	16.9	2750	3.6	1215	9.6
30472	550	16.9	2750	3.6	1242	9.6
30473	550	16.9	2750	3.6	1269	9.6
30474	550	16.9	2750	3.6	1296	9.6
30557	500	16.1	2500	4.0	1475	8.1
30550	500	15.9	2500	4.0	1300	7.9
30551	500	15.9	2500	4.0	1325	7.9
30552	500	15.9	2500	4.0	1350	7.9
30553	500	15.9	2500	4.0	1375	7.9
30554	500	15.9	2500	4.0	1400	7.9
30555	500	15.9	2500	4.0	1425	7.9
30556	500	15.9	2500	4.0	1450	7.9
30543	500	15.3	2500	4.0	1125	7.3
30544	500	15.3	2500	4.0	1150	7.3
30545	500	15.3	2500	4.0	1175	7.3
30546	500	15.3	2500	4.0	1200	7.3
30547	500	15.3	2500	4.0	1225	7.3
30548	500	15.3	2500	4.0	1250	7.3
30549	500	15.3	2500	4.0	1275	7.3
30518	500	11.9	2500	4.4	500	3.1

Overall score = score_ratio - 2 * repetitive DNA content