Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign27 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (169)
Redundant probes (5)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:56:23 2005`

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

Fetched probe design: ProbeDesign27
  assembly      : NCBIM33
  bias          : 3prime
  chromosome    : 3
  id            : 4
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 41
Fetched conf : Exonerate mouse_NCBI33 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM33/genome/masked_dusted
Fetched 405 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        : 405/405
Putative probes exceeding selection criteria: 174/405

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
1220	1000	31.4	5000	-	200	31.4
1221	1000	31.4	5000	-	250	31.4
1222	1000	31.4	5000	-	300	31.4
1223	1000	31.4	5000	-	350	31.4
1246	950	30.8	4750	-	423	30.8
1242	950	29.9	4750	-	235	29.9
1243	950	29.9	4750	-	282	29.9
1244	950	29.9	4750	-	329	29.9
1245	950	29.9	4750	-	376	29.9
1224	1000	32.5	5000	1.5	400	29.5
1269	900	29.2	4500	-	405	29.2
1270	900	29.2	4500	-	450	29.2
1265	900	28.3	4500	-	225	28.3
1266	900	28.3	4500	-	270	28.3
1267	900	28.3	4500	-	315	28.3
1268	900	28.3	4500	-	360	28.3
1295	850	27.6	4250	-	420	27.6
1296	850	27.6	4250	-	462	27.6
1297	850	27.6	4250	-	504	27.6
1241	950	29.9	4750	1.3	188	27.3
1271	900	29.2	4500	1.1	495	27.0
1290	850	26.7	4250	-	210	26.7
1291	850	26.7	4250	-	252	26.7
1292	850	26.7	4250	-	294	26.7
1293	850	26.7	4250	-	336	26.7
1294	850	26.7	4250	-	378	26.7
1323	800	26.3	4000	-	400	26.3
1324	800	26.0	4000	-	440	26.0
1325	800	26.0	4000	-	480	26.0
1326	800	26.0	4000	-	520	26.0
1327	800	26.0	4000	-	560	26.0
1318	800	25.2	4000	-	200	25.2
1319	800	25.2	4000	-	240	25.2
1320	800	25.2	4000	-	280	25.2
1321	800	25.2	4000	-	320	25.2
1322	800	25.2	4000	-	360	25.2
1298	850	27.6	4250	1.3	546	25.0
1355	750	24.7	3750	-	407	24.7
1356	750	24.7	3750	-	444	24.7
1357	750	24.7	3750	-	481	24.7
1358	750	24.4	3750	-	518	24.4
1359	750	24.4	3750	-	555	24.4
1360	750	24.4	3750	-	592	24.4
1361	750	24.4	3750	-	629	24.4
1264	900	28.3	4500	2.2	180	23.9
1350	750	23.6	3750	-	222	23.6
1351	750	23.6	3750	-	259	23.6
1352	750	23.6	3750	-	296	23.6
1353	750	23.6	3750	-	333	23.6
1354	750	23.6	3750	-	370	23.6
1390	700	23.0	3500	-	420	23.0
1391	700	23.0	3500	-	455	23.0
1392	700	23.0	3500	-	490	23.0
1393	700	23.0	3500	-	525	23.0
1394	700	22.7	3500	-	560	22.7
1395	700	22.7	3500	-	595	22.7
1396	700	22.7	3500	-	630	22.7
1397	700	22.7	3500	-	665	22.7
1384	700	22.0	3500	-	210	22.0
1385	700	22.0	3500	-	245	22.0
1386	700	22.0	3500	-	280	22.0
1387	700	22.0	3500	-	315	22.0
1388	700	22.0	3500	-	350	22.0
1389	700	22.0	3500	-	385	22.0
1429	650	21.4	3250	-	416	21.4
1430	650	21.4	3250	-	448	21.4
1431	650	21.4	3250	-	480	21.4
1432	650	21.4	3250	-	512	21.4
1433	650	21.4	3250	-	544	21.4
1434	650	21.4	3250	-	576	21.4
1435	650	21.1	3250	-	608	21.1
1436	650	21.1	3250	-	640	21.1
1437	650	21.1	3250	-	672	21.1
1438	650	21.1	3250	-	704	21.1
1439	650	21.1	3250	0.2	736	20.8
1423	650	20.4	3250	-	224	20.4
1424	650	20.4	3250	-	256	20.4
1425	650	20.4	3250	-	288	20.4
1426	650	20.4	3250	-	320	20.4
1427	650	20.4	3250	-	352	20.4
1428	650	20.4	3250	-	384	20.4
1473	600	19.7	3000	-	420	19.7
1474	600	19.7	3000	-	450	19.7
1475	600	19.7	3000	-	480	19.7
1476	600	19.7	3000	-	510	19.7
1477	600	19.7	3000	-	540	19.7
1478	600	19.7	3000	-	570	19.7
1479	600	19.7	3000	-	600	19.7
1480	600	19.7	3000	-	630	19.7
1349	750	23.6	3750	2.0	185	19.6
1481	600	19.5	3000	-	660	19.5
1482	600	19.5	3000	-	690	19.5
1483	600	19.5	3000	-	720	19.5
1484	600	19.5	3000	-	750	19.5
1485	600	19.5	3000	-	780	19.5
1289	850	26.7	4250	3.8	168	19.2
1219	1000	28.9	5000	5.0	150	18.9
1466	600	18.9	3000	-	210	18.9
1467	600	18.9	3000	-	240	18.9
1468	600	18.9	3000	-	270	18.9
1469	600	18.9	3000	-	300	18.9
1470	600	18.9	3000	-	330	18.9
1471	600	18.9	3000	-	360	18.9
1472	600	18.9	3000	-	390	18.9
1521	550	18.1	2750	-	405	18.1
1522	550	18.1	2750	-	432	18.1
1523	550	18.1	2750	-	459	18.1
1524	550	18.1	2750	-	486	18.1
1525	550	18.1	2750	-	513	18.1
1526	550	18.1	2750	-	540	18.1
1527	550	18.1	2750	-	567	18.1
1528	550	18.1	2750	-	594	18.1
1529	550	18.1	2750	-	621	18.1
1530	550	18.1	2750	-	648	18.1
1531	550	18.1	2750	-	675	18.1
1422	650	20.4	3250	1.2	192	18.0
1532	550	17.9	2750	-	702	17.9
1533	550	17.9	2750	-	729	17.9
1534	550	17.9	2750	-	756	17.9
1535	550	17.9	2750	-	783	17.9
1536	550	17.9	2750	-	810	17.9
1514	550	17.3	2750	-	216	17.3
1515	550	17.3	2750	-	243	17.3
1516	550	17.3	2750	-	270	17.3
1517	550	17.3	2750	-	297	17.3
1518	550	17.3	2750	-	324	17.3
1519	550	17.3	2750	-	351	17.3
1520	550	17.3	2750	-	378	17.3
1537	550	17.9	2750	0.4	837	17.1
1576	500	16.4	2500	-	400	16.4
1577	500	16.4	2500	-	425	16.4
1578	500	16.4	2500	-	450	16.4
1579	500	16.4	2500	-	475	16.4
1580	500	16.4	2500	-	500	16.4
1581	500	16.4	2500	-	525	16.4
1582	500	16.4	2500	-	550	16.4
1583	500	16.4	2500	-	575	16.4
1584	500	16.4	2500	-	600	16.4
1585	500	16.4	2500	-	625	16.4
1586	500	16.4	2500	-	650	16.4
1587	500	16.4	2500	-	675	16.4
1588	500	16.4	2500	-	700	16.4
1589	500	16.4	2500	-	725	16.4
1590	500	16.2	2500	-	750	16.2
1591	500	16.2	2500	-	775	16.2
1592	500	16.2	2500	-	800	16.2
1593	500	16.2	2500	-	825	16.2
1594	500	16.2	2500	-	850	16.2
1595	500	16.2	2500	-	875	16.2
1247	950	22.6	4750	3.3	470	16.1
1568	500	15.7	2500	-	200	15.7
1569	500	15.7	2500	-	225	15.7
1570	500	15.7	2500	-	250	15.7
1571	500	15.7	2500	-	275	15.7
1572	500	15.7	2500	-	300	15.7
1573	500	15.7	2500	-	325	15.7
1574	500	15.7	2500	-	350	15.7
1575	500	15.7	2500	-	375	15.7
1317	800	25.2	4000	5.0	160	15.2
1383	700	22.0	3500	3.6	175	14.9
1225	1000	23.3	5000	4.4	450	14.5
1272	900	21.4	4500	3.8	540	13.9
1513	550	17.3	2750	2.0	189	13.3
1299	850	20.2	4250	3.8	588	12.7
1465	600	18.9	3000	3.3	180	12.2
1362	750	18.8	3750	4.1	666	10.6
1329	800	19.0	4000	4.2	640	10.5
1486	600	17.8	3000	4.2	810	9.4
1567	500	15.7	2500	5.0	175	5.7

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
1328	800	26.0	4000	1.9	600	22.2
1398	700	22.7	3500	2.1	700	18.4
1596	500	16.2	2500	3.0	900	10.2
1399	700	16.7	3500	4.4	735	7.8
1440	650	15.6	3250	4.8	768	6.0

Overall score = score_ratio - 2 * repetitive DNA content