Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign45 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (105)
Redundant probes (250)

Summary

`./analyse_probe_search_results : Wed Sep 14 17:06:37 2005`

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

Fetched probe design: ProbeDesign45
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 17
  id            : 27
  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 exceeding selection criteria: 355/907

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
29161	1050	29.0	5250	0.3	1144	28.4
29200	1000	27.6	5000	-	1150	27.6
29201	1000	27.6	5000	0.2	1200	27.2
29391	800	26.5	4000	-	1200	26.5
29243	950	26.2	4750	-	1175	26.2
29244	950	26.2	4750	-	1222	26.2
29288	900	24.9	4500	-	1170	24.9
29289	900	24.9	4500	-	1215	24.9
29290	900	24.9	4500	-	1260	24.9
29450	750	24.8	3750	-	1221	24.8
29337	850	24.6	4250	-	1176	24.6
29392	800	23.7	4000	-	1240	23.7
29338	850	23.5	4250	-	1218	23.5
29339	850	23.5	4250	-	1260	23.5
29340	850	23.5	4250	-	1302	23.5
29341	850	23.5	4250	-	1344	23.5
29291	900	24.9	4500	0.8	1305	23.3
29390	800	23.1	4000	-	1160	23.1
29002	1300	26.5	6500	2.0	1170	22.5
29003	1300	26.5	6500	2.0	1235	22.5
29004	1300	26.5	6500	2.0	1300	22.5
29005	1300	26.5	6500	2.0	1365	22.5
29006	1300	26.5	6500	2.0	1430	22.5
29007	1300	26.5	6500	2.0	1495	22.5
29008	1300	26.5	6500	2.0	1560	22.5
29009	1300	26.5	6500	2.0	1625	22.5
29010	1300	26.5	6500	2.0	1690	22.5
29242	950	26.2	4750	2.0	1128	22.2
29452	750	22.2	3750	-	1295	22.2
29393	800	22.1	4000	-	1280	22.1
29394	800	22.1	4000	-	1320	22.1
29395	800	22.1	4000	-	1360	22.1
29512	700	21.7	3500	-	1190	21.7
29448	750	21.7	3750	-	1147	21.7
29449	750	21.7	3750	-	1184	21.7
29396	800	22.1	4000	0.2	1400	21.6
29582	650	21.5	3250	-	1216	21.5
29336	850	24.6	4250	1.5	1134	21.5
29124	1100	30.4	5500	4.5	1100	21.5
29033	1250	25.5	6250	2.1	1364	21.4
29034	1250	25.5	6250	2.1	1426	21.4
29035	1250	25.5	6250	2.1	1488	21.4
29036	1250	25.5	6250	2.1	1550	21.4
29037	1250	25.5	6250	2.1	1612	21.4
29287	900	26.0	4500	2.4	1125	21.1
29453	750	20.7	3750	-	1332	20.7
29454	750	20.7	3750	-	1369	20.7
29455	750	20.7	3750	-	1406	20.7
29456	750	20.7	3750	-	1443	20.7
29221	950	28.4	4750	3.9	141	20.7
29511	700	20.2	3500	-	1155	20.2
29070	1200	24.5	6000	2.2	1800	20.2
29658	600	19.9	3000	-	1200	19.9
29104	1100	27.9	5500	4.2	0	19.6
29517	700	19.3	3500	-	1365	19.3
29518	700	19.3	3500	-	1400	19.3
29519	700	19.3	3500	-	1435	19.3
29520	700	19.3	3500	-	1470	19.3
29125	1100	23.8	5500	2.4	1155	19.1
29059	1200	24.5	6000	2.8	1140	19.0
29580	650	18.8	3250	-	1152	18.8
29581	650	18.8	3250	-	1184	18.8
29744	550	18.2	2750	-	1215	18.2
29588	650	18.0	3250	-	1408	18.0
29589	650	18.0	3250	-	1440	18.0
29590	650	18.0	3250	-	1472	18.0
29591	650	18.0	3250	-	1504	18.0
29592	650	18.0	3250	-	1536	18.0
29666	600	17.8	3000	-	1440	17.8
29091	1150	23.5	5750	2.9	1140	17.7
29754	550	17.4	2750	-	1485	17.4
29657	600	17.3	3000	-	1170	17.3
29521	700	19.3	3500	1.0	1505	17.3
29743	550	16.9	2750	-	1188	16.9
29667	600	16.6	3000	-	1470	16.6
29668	600	16.6	3000	-	1500	16.6
29669	600	16.6	3000	-	1530	16.6
29670	600	16.6	3000	-	1560	16.6
29671	600	16.6	3000	-	1590	16.6
29838	500	16.6	2500	-	1200	16.6
29140	1050	25.6	5250	4.6	52	16.5
29029	1250	25.5	6250	4.6	1116	16.4
29389	800	23.1	4000	3.4	1120	16.4
29742	550	15.9	2750	-	1161	15.9
29755	550	15.2	2750	-	1512	15.2
29756	550	15.2	2750	-	1539	15.2
29757	550	15.2	2750	-	1566	15.2
29758	550	15.2	2750	-	1593	15.2
29759	550	15.2	2750	-	1620	15.2
29760	550	15.2	2750	-	1647	15.2
29656	600	17.3	3000	1.2	1140	15.0
29852	500	14.7	2500	-	1550	14.7
29836	500	14.5	2500	-	1150	14.5
29837	500	14.5	2500	-	1175	14.5
29853	500	13.8	2500	-	1575	13.8
29854	500	13.8	2500	-	1600	13.8
29855	500	13.8	2500	-	1625	13.8
29856	500	13.8	2500	-	1650	13.8
29857	500	13.8	2500	-	1675	13.8
29858	500	13.8	2500	0.4	1700	13.0
29510	700	20.2	3500	3.9	1120	12.5
29781	550	16.1	2750	1.8	2214	12.4
29741	550	15.9	2750	2.4	1134	11.2
29579	650	18.8	3250	4.2	1120	10.5
29835	500	14.5	2500	4.4	1125	5.7

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
29245	950	26.2	4750	2.2	1269	21.8
29030	1250	25.5	6250	2.1	1178	21.4
29031	1250	25.5	6250	2.1	1240	21.4
29032	1250	25.5	6250	2.1	1302	21.4
29038	1250	25.5	6250	2.1	1674	21.4
29039	1250	25.5	6250	2.1	1736	21.4
29162	1050	25.1	5250	2.5	1196	20.2
29060	1200	24.5	6000	2.2	1200	20.2
29061	1200	24.5	6000	2.2	1260	20.2
29062	1200	24.5	6000	2.2	1320	20.2
29063	1200	24.5	6000	2.2	1380	20.2
29064	1200	24.5	6000	2.2	1440	20.2
29065	1200	24.5	6000	2.2	1500	20.2
29066	1200	24.5	6000	2.2	1560	20.2
29067	1200	24.5	6000	2.2	1620	20.2
29068	1200	24.5	6000	2.2	1680	20.2
29069	1200	24.5	6000	2.2	1740	20.2
29092	1150	23.5	5750	2.3	1197	18.9
29093	1150	23.5	5750	2.3	1254	18.9
29094	1150	23.5	5750	2.3	1311	18.9
29095	1150	23.5	5750	2.3	1368	18.9
29096	1150	23.5	5750	2.3	1425	18.9
29097	1150	23.5	5750	2.3	1482	18.9
29098	1150	23.5	5750	2.3	1539	18.9
29099	1150	23.5	5750	2.3	1596	18.9
29100	1150	23.5	5750	2.3	1653	18.9
29101	1150	23.5	5750	2.3	1710	18.9
29102	1150	23.5	5750	2.3	1767	18.9
29103	1150	23.5	5750	2.3	1824	18.9
29199	1000	27.6	5000	4.7	1100	18.2
29202	1000	23.3	5000	2.6	1250	18.1
29126	1100	22.4	5500	2.4	1210	17.7
29127	1100	22.4	5500	2.4	1265	17.7
29128	1100	22.4	5500	2.4	1320	17.7
29129	1100	22.4	5500	2.4	1375	17.7
29130	1100	22.4	5500	2.4	1430	17.7
29131	1100	22.4	5500	2.4	1485	17.7
29132	1100	22.4	5500	2.4	1540	17.7
29133	1100	22.4	5500	2.4	1595	17.7
29134	1100	22.4	5500	2.4	1650	17.7
29135	1100	22.4	5500	2.4	1705	17.7
29136	1100	22.4	5500	2.4	1760	17.7
29137	1100	22.4	5500	2.4	1815	17.7
29138	1100	22.4	5500	2.4	1870	17.7
29163	1050	21.4	5250	2.5	1248	16.5
29164	1050	21.4	5250	2.5	1300	16.5
29165	1050	21.4	5250	2.5	1352	16.5
29166	1050	21.4	5250	2.5	1404	16.5
29167	1050	21.4	5250	2.5	1456	16.5
29168	1050	21.4	5250	2.5	1508	16.5
29169	1050	21.4	5250	2.5	1560	16.5
29170	1050	21.4	5250	2.5	1612	16.5
29171	1050	21.4	5250	2.5	1664	16.5
29172	1050	21.4	5250	2.5	1716	16.5
29173	1050	21.4	5250	2.5	1768	16.5
29174	1050	21.4	5250	2.5	1820	16.5
29175	1050	21.4	5250	2.5	1872	16.5
29176	1050	21.4	5250	2.5	1924	16.5
29179	1000	25.4	5000	4.6	100	16.2
29342	850	21.7	4250	3.1	1386	15.6
29203	1000	20.4	5000	2.6	1300	15.2
29204	1000	20.4	5000	2.6	1350	15.2
29205	1000	20.4	5000	2.6	1400	15.2
29206	1000	20.4	5000	2.6	1450	15.2
29207	1000	20.4	5000	2.6	1500	15.2
29208	1000	20.4	5000	2.6	1550	15.2
29209	1000	20.4	5000	2.6	1600	15.2
29210	1000	20.4	5000	2.6	1650	15.2
29211	1000	20.4	5000	2.6	1700	15.2
29212	1000	20.4	5000	2.6	1750	15.2
29213	1000	20.4	5000	2.6	1800	15.2
29214	1000	20.4	5000	2.6	1850	15.2
29215	1000	20.4	5000	2.6	1900	15.2
29216	1000	20.4	5000	2.6	1950	15.2
29217	1000	20.4	5000	2.6	2000	15.2
29292	900	20.9	4500	2.9	1350	15.2
29489	700	23.3	3500	4.4	385	14.5
29246	950	19.4	4750	2.7	1316	13.9
29247	950	19.4	4750	2.7	1363	13.9
29248	950	19.4	4750	2.7	1410	13.9
29249	950	19.4	4750	2.7	1457	13.9
29250	950	19.4	4750	2.7	1504	13.9
29251	950	19.4	4750	2.7	1551	13.9
29252	950	19.4	4750	2.7	1598	13.9
29253	950	19.4	4750	2.7	1645	13.9
29254	950	19.4	4750	2.7	1692	13.9
29255	950	19.4	4750	2.7	1739	13.9
29256	950	19.4	4750	2.7	1786	13.9
29257	950	19.4	4750	2.7	1833	13.9
29258	950	19.4	4750	2.7	1880	13.9
29259	950	19.4	4750	2.7	1927	13.9
29260	950	19.4	4750	2.7	1974	13.9
29261	950	19.4	4750	2.7	2021	13.9
29397	800	19.9	4000	3.2	1440	13.4
29457	750	19.5	3750	3.5	1480	12.6
29293	900	18.4	4500	2.9	1395	12.6
29294	900	18.4	4500	2.9	1440	12.6
29295	900	18.4	4500	2.9	1485	12.6
29296	900	18.4	4500	2.9	1530	12.6
29297	900	18.4	4500	2.9	1575	12.6
29298	900	18.4	4500	2.9	1620	12.6
29299	900	18.4	4500	2.9	1665	12.6
29300	900	18.4	4500	2.9	1710	12.6
29301	900	18.4	4500	2.9	1755	12.6
29302	900	18.4	4500	2.9	1800	12.6
29303	900	18.4	4500	2.9	1845	12.6
29304	900	18.4	4500	2.9	1890	12.6
29305	900	18.4	4500	2.9	1935	12.6
29306	900	18.4	4500	2.9	1980	12.6
29307	900	18.4	4500	2.9	2025	12.6
29308	900	18.4	4500	2.9	2070	12.6
29613	650	16.9	3250	2.5	2208	12.0
29447	750	21.7	3750	4.9	1110	11.8
29593	650	18.0	3250	3.1	1568	11.8
29541	700	16.9	3500	2.7	2205	11.5
29343	850	17.3	4250	3.1	1428	11.2
29344	850	17.3	4250	3.1	1470	11.2
29345	850	17.3	4250	3.1	1512	11.2
29346	850	17.3	4250	3.1	1554	11.2
29347	850	17.3	4250	3.1	1596	11.2
29348	850	17.3	4250	3.1	1638	11.2
29349	850	17.3	4250	3.1	1680	11.2
29350	850	17.3	4250	3.1	1722	11.2
29351	850	17.3	4250	3.1	1764	11.2
29352	850	17.3	4250	3.1	1806	11.2
29353	850	17.3	4250	3.1	1848	11.2
29354	850	17.3	4250	3.1	1890	11.2
29355	850	17.3	4250	3.1	1932	11.2
29356	850	17.3	4250	3.1	1974	11.2
29357	850	17.3	4250	3.1	2016	11.2
29358	850	17.3	4250	3.1	2058	11.2
29359	850	17.3	4250	3.1	2100	11.2
29360	850	17.3	4250	3.1	2142	11.2
29416	800	17.0	4000	3.0	2200	11.0
29522	700	17.4	3500	3.7	1540	10.0
29398	800	16.3	4000	3.2	1480	9.8
29399	800	16.3	4000	3.2	1520	9.8
29400	800	16.3	4000	3.2	1560	9.8
29401	800	16.3	4000	3.2	1600	9.8
29402	800	16.3	4000	3.2	1640	9.8
29403	800	16.3	4000	3.2	1680	9.8
29404	800	16.3	4000	3.2	1720	9.8
29405	800	16.3	4000	3.2	1760	9.8
29406	800	16.3	4000	3.2	1800	9.8
29407	800	16.3	4000	3.2	1840	9.8
29408	800	16.3	4000	3.2	1880	9.8
29409	800	16.3	4000	3.2	1920	9.8
29410	800	16.3	4000	3.2	1960	9.8
29411	800	16.3	4000	3.2	2000	9.8
29412	800	16.3	4000	3.2	2040	9.8
29413	800	16.3	4000	3.2	2080	9.8
29414	800	16.3	4000	3.2	2120	9.8
29415	800	16.3	4000	3.2	2160	9.8
29672	600	16.6	3000	3.7	1620	9.2
29458	750	15.3	3750	3.5	1517	8.4
29459	750	15.3	3750	3.5	1554	8.4
29460	750	15.3	3750	3.5	1591	8.4
29461	750	15.3	3750	3.5	1628	8.4
29462	750	15.3	3750	3.5	1665	8.4
29463	750	15.3	3750	3.5	1702	8.4
29464	750	15.3	3750	3.5	1739	8.4
29465	750	15.3	3750	3.5	1776	8.4
29466	750	15.3	3750	3.5	1813	8.4
29467	750	15.3	3750	3.5	1850	8.4
29468	750	15.3	3750	3.5	1887	8.4
29469	750	15.3	3750	3.5	1924	8.4
29470	750	15.3	3750	3.5	1961	8.4
29471	750	15.3	3750	3.5	1998	8.4
29472	750	15.3	3750	3.5	2035	8.4
29473	750	15.3	3750	3.5	2072	8.4
29474	750	15.3	3750	3.5	2109	8.4
29475	750	15.3	3750	3.5	2146	8.4
29476	750	15.3	3750	3.5	2183	8.4
29594	650	15.1	3250	4.0	1600	7.1
29523	700	14.3	3500	3.7	1575	6.9
29524	700	14.3	3500	3.7	1610	6.9
29525	700	14.3	3500	3.7	1645	6.9
29526	700	14.3	3500	3.7	1680	6.9
29527	700	14.3	3500	3.7	1715	6.9
29528	700	14.3	3500	3.7	1750	6.9
29529	700	14.3	3500	3.7	1785	6.9
29530	700	14.3	3500	3.7	1820	6.9
29531	700	14.3	3500	3.7	1855	6.9
29532	700	14.3	3500	3.7	1890	6.9
29533	700	14.3	3500	3.7	1925	6.9
29534	700	14.3	3500	3.7	1960	6.9
29535	700	14.3	3500	3.7	1995	6.9
29536	700	14.3	3500	3.7	2030	6.9
29537	700	14.3	3500	3.7	2065	6.9
29538	700	14.3	3500	3.7	2100	6.9
29539	700	14.3	3500	3.7	2135	6.9
29540	700	14.3	3500	3.7	2170	6.9
29673	600	14.0	3000	4.3	1650	5.3
29595	650	13.3	3250	4.0	1632	5.3
29596	650	13.3	3250	4.0	1664	5.3
29597	650	13.3	3250	4.0	1696	5.3
29598	650	13.3	3250	4.0	1728	5.3
29599	650	13.3	3250	4.0	1760	5.3
29600	650	13.3	3250	4.0	1792	5.3
29601	650	13.3	3250	4.0	1824	5.3
29602	650	13.3	3250	4.0	1856	5.3
29603	650	13.3	3250	4.0	1888	5.3
29604	650	13.3	3250	4.0	1920	5.3
29605	650	13.3	3250	4.0	1952	5.3
29606	650	13.3	3250	4.0	1984	5.3
29607	650	13.3	3250	4.0	2016	5.3
29608	650	13.3	3250	4.0	2048	5.3
29609	650	13.3	3250	4.0	2080	5.3
29610	650	13.3	3250	4.0	2112	5.3
29611	650	13.3	3250	4.0	2144	5.3
29612	650	13.3	3250	4.0	2176	5.3
29761	550	14.5	2750	4.7	1674	5.0
29674	600	12.2	3000	4.3	1680	3.6
29675	600	12.2	3000	4.3	1710	3.6
29676	600	12.2	3000	4.3	1740	3.6
29677	600	12.2	3000	4.3	1770	3.6
29678	600	12.2	3000	4.3	1800	3.6
29679	600	12.2	3000	4.3	1830	3.6
29680	600	12.2	3000	4.3	1860	3.6
29681	600	12.2	3000	4.3	1890	3.6
29682	600	12.2	3000	4.3	1920	3.6
29683	600	12.2	3000	4.3	1950	3.6
29684	600	12.2	3000	4.3	1980	3.6
29685	600	12.2	3000	4.3	2010	3.6
29686	600	12.2	3000	4.3	2040	3.6
29687	600	12.2	3000	4.3	2070	3.6
29688	600	12.2	3000	4.3	2100	3.6
29689	600	12.2	3000	4.3	2130	3.6
29690	600	12.2	3000	4.3	2160	3.6
29691	600	12.2	3000	4.3	2190	3.6
29762	550	12.5	2750	4.7	1701	3.0
29763	550	11.2	2750	4.7	1728	1.8
29764	550	11.2	2750	4.7	1755	1.8
29765	550	11.2	2750	4.7	1782	1.8
29766	550	11.2	2750	4.7	1809	1.8
29767	550	11.2	2750	4.7	1836	1.8
29768	550	11.2	2750	4.7	1863	1.8
29769	550	11.2	2750	4.7	1890	1.8
29770	550	11.2	2750	4.7	1917	1.8
29771	550	11.2	2750	4.7	1944	1.8
29772	550	11.2	2750	4.7	1971	1.8
29773	550	11.2	2750	4.7	1998	1.8
29774	550	11.2	2750	4.7	2025	1.8
29775	550	11.2	2750	4.7	2052	1.8
29776	550	11.2	2750	4.7	2079	1.8
29777	550	11.2	2750	4.7	2106	1.8
29778	550	11.2	2750	4.7	2133	1.8
29779	550	11.2	2750	4.7	2160	1.8
29780	550	11.2	2750	4.7	2187	1.8
29878	500	10.6	2500	4.8	2200	1.0

Overall score = score_ratio - 2 * repetitive DNA content