Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign95 - back to list

Summary
Image
Unique putative probes (45)
Putative probes (186)
Redundant probes (3)

Summary

`./analyse_probe_search_results : Wed Dec 21 12:02:17 2005`

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

Fetched probe design: ProbeDesign95
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 5
  id            : 86
  strand        : 1
  -------------

Design window length: 3296bp

All jobs for probe design are successful - total: 52
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1025 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            : 1025/1025
Putative probes that are unique                 : 45/1025
Putative probes exceeding selection criteria    : 234/1025 (both unique and not unique)
Putative probes with successfully-picked primers: 172/234

Identified 3 'redundant' probes exceeding selection criteria
(but wholly contained by other probes, and higher repetitive DNA content)

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Unique putative probes

Putative probe ID	Length	Actual	%rep DNA	Distance
80512	650	3250	-	544
80538	650	3250	-	1376
80539	650	3250	-	1408
80596	600	3000	-	540
80597	600	3000	-	570
80598	600	3000	-	600
80623	600	3000	-	1350
80624	600	3000	-	1380
80625	600	3000	-	1410
80626	600	3000	-	1440
80688	550	2750	-	540
80689	550	2750	-	567
80690	550	2750	-	594
80691	550	2750	-	621
80692	550	2750	-	648
80718	550	2750	-	1350
80719	550	2750	-	1377
80720	550	2750	-	1404
80721	550	2750	-	1431
80722	550	2750	-	1458
80723	550	2750	-	1485
80791	500	2500	-	525
80792	500	2500	-	550
80793	500	2500	-	575
80794	500	2500	-	600
80795	500	2500	-	625
80796	500	2500	-	650
80797	500	2500	-	675
80798	500	2500	-	700
80824	500	2500	-	1350
80825	500	2500	-	1375
80826	500	2500	-	1400
80827	500	2500	-	1425
80828	500	2500	-	1450
80829	500	2500	-	1475
80830	500	2500	-	1500
80831	500	2500	-	1525
80832	500	2500	-	1550
80537	650	3250	0.6	1344
80435	700	3500	1.6	525
80513	650	3250	1.8	576
80693	550	2750	2.0	675
80799	500	2500	2.2	725
80458	700	3500	2.6	1330
80599	600	3000	2.7	630

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
79922	1200	31.9	6000	-	0	31.9
79957	1150	30.6	5750	-	0	30.6
79958	1150	30.6	5750	-	57	30.6
79995	1100	29.3	5500	-	0	29.3
79996	1100	29.3	5500	-	55	29.3
79997	1100	29.3	5500	-	110	29.3
80035	1050	27.9	5250	-	0	27.9
80036	1050	27.9	5250	-	52	27.9
80037	1050	27.9	5250	-	104	27.9
80038	1050	27.9	5250	-	156	27.9
80079	1000	26.6	5000	-	0	26.6
80080	1000	26.6	5000	-	50	26.6
80081	1000	26.6	5000	-	100	26.6
80082	1000	26.6	5000	-	150	26.6
80083	1000	26.6	5000	-	200	26.6
80297	800	26.1	4000	-	360	26.1
80298	800	26.1	4000	-	400	26.1
79888	1250	31.1	6250	2.9	0	25.3
80125	950	25.3	4750	-	0	25.3
80126	950	25.3	4750	-	47	25.3
80127	950	25.3	4750	-	94	25.3
80128	950	25.3	4750	-	141	25.3
80129	950	25.3	4750	-	188	25.3
80130	950	25.3	4750	-	235	25.3
80361	750	24.5	3750	-	370	24.5
80362	750	24.5	3750	-	407	24.5
80363	750	24.5	3750	-	444	24.5
80238	850	27.8	4250	1.6	378	24.5
80175	900	23.9	4500	-	0	23.9
80176	900	23.9	4500	-	45	23.9
80177	900	23.9	4500	-	90	23.9
80178	900	23.9	4500	-	135	23.9
80179	900	23.9	4500	-	180	23.9
80180	900	23.9	4500	-	225	23.9
80181	900	23.9	4500	-	270	23.9
80182	900	23.9	4500	0.1	315	23.7
80237	850	23.1	4250	-	336	23.1
80430	700	22.9	3500	-	350	22.9
80431	700	22.9	3500	-	385	22.9
80432	700	22.9	3500	-	420	22.9
80433	700	22.9	3500	-	455	22.9
80434	700	22.9	3500	-	490	22.9
80229	850	22.6	4250	-	0	22.6
80230	850	22.6	4250	-	42	22.6
80231	850	22.6	4250	-	84	22.6
80232	850	22.6	4250	-	126	22.6
80233	850	22.6	4250	-	168	22.6
80234	850	22.6	4250	-	210	22.6
80235	850	22.6	4250	-	252	22.6
80236	850	22.6	4250	-	294	22.6
80131	950	25.3	4750	1.9	282	21.5
80288	800	21.3	4000	-	0	21.3
80289	800	21.3	4000	-	40	21.3
80290	800	21.3	4000	-	80	21.3
80291	800	21.3	4000	-	120	21.3
80292	800	21.3	4000	-	160	21.3
80293	800	21.3	4000	-	200	21.3
80294	800	21.3	4000	-	240	21.3
80295	800	21.3	4000	-	280	21.3
80296	800	21.3	4000	-	320	21.3
80506	650	21.2	3250	-	352	21.2
80507	650	21.2	3250	-	384	21.2
80508	650	21.2	3250	-	416	21.2
80509	650	21.2	3250	-	448	21.2
80510	650	21.2	3250	-	480	21.2
80511	650	21.2	3250	-	512	21.2
80459	700	21.9	3500	0.4	1365	21.0
80360	750	20.2	3750	-	333	20.2
80364	750	24.5	3750	2.3	481	20.0
80351	750	19.9	3750	-	0	19.9
80352	750	19.9	3750	-	37	19.9
80353	750	19.9	3750	-	74	19.9
80354	750	19.9	3750	-	111	19.9
80355	750	19.9	3750	-	148	19.9
80356	750	19.9	3750	-	185	19.9
80357	750	19.9	3750	-	222	19.9
80358	750	19.9	3750	-	259	19.9
80359	750	19.9	3750	-	296	19.9
80590	600	19.6	3000	-	360	19.6
80591	600	19.6	3000	-	390	19.6
80592	600	19.6	3000	-	420	19.6
80593	600	19.6	3000	-	450	19.6
80594	600	19.6	3000	-	480	19.6
80595	600	19.6	3000	-	510	19.6
80420	700	18.6	3500	-	0	18.6
80421	700	18.6	3500	-	35	18.6
80422	700	18.6	3500	-	70	18.6
80423	700	18.6	3500	-	105	18.6
80424	700	18.6	3500	-	140	18.6
80425	700	18.6	3500	-	175	18.6
80426	700	18.6	3500	-	210	18.6
80427	700	18.6	3500	-	245	18.6
80428	700	18.6	3500	-	280	18.6
80429	700	18.6	3500	-	315	18.6
80681	550	18.0	2750	-	351	18.0
80682	550	18.0	2750	-	378	18.0
80683	550	18.0	2750	-	405	18.0
80684	550	18.0	2750	-	432	18.0
80685	550	18.0	2750	-	459	18.0
80686	550	18.0	2750	-	486	18.0
80687	550	18.0	2750	-	513	18.0
80724	550	17.9	2750	-	1512	17.9
80495	650	17.3	3250	-	0	17.3
80496	650	17.3	3250	-	32	17.3
80497	650	17.3	3250	-	64	17.3
80498	650	17.3	3250	-	96	17.3
80499	650	17.3	3250	-	128	17.3
80500	650	17.3	3250	-	160	17.3
80501	650	17.3	3250	-	192	17.3
80502	650	17.3	3250	-	224	17.3
80503	650	17.3	3250	-	256	17.3
80504	650	17.3	3250	-	288	17.3
80505	650	17.3	3250	-	320	17.3
79923	1200	24.8	6000	3.8	60	17.1
80784	500	16.3	2500	-	350	16.3
80785	500	16.3	2500	-	375	16.3
80786	500	16.3	2500	-	400	16.3
80787	500	16.3	2500	-	425	16.3
80788	500	16.3	2500	-	450	16.3
80789	500	16.3	2500	-	475	16.3
80790	500	16.3	2500	-	500	16.3
80578	600	16.0	3000	-	0	16.0
80579	600	16.0	3000	-	30	16.0
80580	600	16.0	3000	-	60	16.0
80581	600	16.0	3000	-	90	16.0
80582	600	16.0	3000	-	120	16.0
80583	600	16.0	3000	-	150	16.0
80584	600	16.0	3000	-	180	16.0
80585	600	16.0	3000	-	210	16.0
80586	600	16.0	3000	-	240	16.0
80587	600	16.0	3000	-	270	16.0
80588	600	16.0	3000	-	300	16.0
80667	600	15.9	3000	-	2670	15.9
80589	600	15.5	3000	-	330	15.5
80768	550	14.8	2750	-	2700	14.8
80769	550	14.8	2750	-	2727	14.8
80767	550	14.7	2750	-	2673	14.7
80668	550	14.6	2750	-	0	14.6
80669	550	14.6	2750	-	27	14.6
80670	550	14.6	2750	-	54	14.6
80671	550	14.6	2750	-	81	14.6
80672	550	14.6	2750	-	108	14.6
80673	550	14.6	2750	-	135	14.6
80674	550	14.6	2750	-	162	14.6
80675	550	14.6	2750	-	189	14.6
80676	550	14.6	2750	-	216	14.6
80677	550	14.6	2750	-	243	14.6
80678	550	14.6	2750	-	270	14.6
80679	550	14.6	2750	-	297	14.6
80680	550	14.2	2750	-	324	14.2
79959	1150	22.4	5750	4.3	114	13.7
80877	500	13.4	2500	-	2675	13.4
80878	500	13.4	2500	-	2700	13.4
80879	500	13.4	2500	-	2725	13.4
80880	500	13.4	2500	-	2750	13.4
80881	500	13.4	2500	-	2775	13.4
80770	500	13.3	2500	-	0	13.3
80771	500	13.3	2500	-	25	13.3
80772	500	13.3	2500	-	50	13.3
80773	500	13.3	2500	-	75	13.3
80774	500	13.3	2500	-	100	13.3
80775	500	13.3	2500	-	125	13.3
80776	500	13.3	2500	-	150	13.3
80777	500	13.3	2500	-	175	13.3
80778	500	13.3	2500	-	200	13.3
80779	500	13.3	2500	-	225	13.3
80780	500	13.3	2500	-	250	13.3
80781	500	13.3	2500	-	275	13.3
80782	500	13.3	2500	-	300	13.3
80627	600	16.0	3000	1.3	1470	13.3
80783	500	13.0	2500	-	325	13.0
79998	1100	21.3	5500	4.6	165	12.0
80666	600	11.5	3000	-	2640	11.5
80766	550	10.5	2750	-	2646	10.5
80577	650	12.5	3250	1.7	2624	9.1
80387	750	17.6	3750	4.8	1332	8.0
80717	550	16.8	2750	4.5	1323	7.7
80388	750	17.5	3750	4.9	1369	7.7
80389	750	17.5	3750	4.9	1406	7.7
80622	600	16.8	3000	4.7	1320	7.4
80833	500	12.6	2500	2.6	1575	7.4
80823	500	16.2	2500	4.6	1325	7.0
80540	650	15.2	3250	4.3	1440	6.6
80765	550	10.5	2750	2.9	2619	4.7
80665	600	11.5	3000	4.2	2610	3.2
80725	550	12.9	2750	4.9	1539	3.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
80084	1000	24.9	5000	3.6	250	17.7
80299	800	23.0	4000	3.2	440	16.5
80039	1050	21.8	5250	4.2	208	13.4

Overall score = score_ratio - 2 * repetitive DNA content