Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign49 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (203)
Redundant probes (83)

Summary

`./analyse_probe_search_results : Wed Sep 21 14:08:09 2005`

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

Fetched probe design: ProbeDesign49
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 19
  id            : 31
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 25
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 494 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        : 494/494
Putative probes exceeding selection criteria: 286/494

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
33517	1250	39.3	6250	-	0	39.3
33530	1200	37.7	6000	-	0	37.7
33531	1200	37.7	6000	-	60	37.7
33506	1300	40.9	6500	1.9	0	37.0
33507	1300	40.9	6500	1.9	65	37.0
33508	1300	40.9	6500	1.9	130	37.0
33509	1300	40.9	6500	1.9	195	37.0
33544	1150	36.2	5750	-	0	36.2
33545	1150	36.2	5750	-	57	36.2
33546	1150	36.2	5750	-	114	36.2
33518	1250	39.3	6250	2.0	62	35.3
33519	1250	39.3	6250	2.0	124	35.3
33520	1250	39.3	6250	2.0	186	35.3
33521	1250	39.3	6250	2.0	248	35.3
33559	1100	34.6	5500	-	0	34.6
33560	1100	34.6	5500	-	55	34.6
33561	1100	34.6	5500	-	110	34.6
33562	1100	34.6	5500	-	165	34.6
33535	1200	37.7	6000	2.1	300	33.6
33576	1050	33.0	5250	-	0	33.0
33577	1050	33.0	5250	-	52	33.0
33578	1050	33.0	5250	-	104	33.0
33579	1050	33.0	5250	-	156	33.0
33580	1050	33.0	5250	-	208	33.0
33595	1000	31.4	5000	-	0	31.4
33596	1000	31.4	5000	-	50	31.4
33597	1000	31.4	5000	-	100	31.4
33598	1000	31.4	5000	-	150	31.4
33599	1000	31.4	5000	-	200	31.4
33600	1000	31.4	5000	-	250	31.4
33616	950	29.9	4750	-	0	29.9
33617	950	29.9	4750	-	47	29.9
33618	950	29.9	4750	-	94	29.9
33619	950	29.9	4750	-	141	29.9
33620	950	29.9	4750	-	188	29.9
33621	950	29.9	4750	-	235	29.9
33622	950	29.9	4750	-	282	29.9
33647	900	28.5	4500	-	360	28.5
33639	900	28.3	4500	-	0	28.3
33640	900	28.3	4500	-	45	28.3
33641	900	28.3	4500	-	90	28.3
33642	900	28.3	4500	-	135	28.3
33643	900	28.3	4500	-	180	28.3
33644	900	28.3	4500	-	225	28.3
33645	900	28.3	4500	-	270	28.3
33646	900	28.3	4500	-	315	28.3
33623	950	29.9	4750	0.8	329	28.2
33673	850	26.9	4250	-	378	26.9
33674	850	26.9	4250	-	420	26.9
33664	850	26.7	4250	-	0	26.7
33665	850	26.7	4250	-	42	26.7
33666	850	26.7	4250	-	84	26.7
33667	850	26.7	4250	-	126	26.7
33668	850	26.7	4250	-	168	26.7
33669	850	26.7	4250	-	210	26.7
33670	850	26.7	4250	-	252	26.7
33671	850	26.7	4250	-	294	26.7
33672	850	26.2	4250	-	336	26.2
33585	1050	33.2	5250	3.7	468	25.8
33701	800	25.3	4000	-	360	25.3
33702	800	25.3	4000	-	400	25.3
33703	800	25.3	4000	-	440	25.3
33692	800	25.2	4000	-	0	25.2
33693	800	25.2	4000	-	40	25.2
33694	800	25.2	4000	-	80	25.2
33695	800	25.2	4000	-	120	25.2
33696	800	25.2	4000	-	160	25.2
33697	800	25.2	4000	-	200	25.2
33698	800	25.2	4000	-	240	25.2
33699	800	25.2	4000	-	280	25.2
33700	800	25.2	4000	-	320	25.2
33732	750	23.7	3750	-	333	23.7
33733	750	23.7	3750	-	370	23.7
33734	750	23.7	3750	-	407	23.7
33735	750	23.7	3750	-	444	23.7
33736	750	23.7	3750	-	481	23.7
33737	750	23.7	3750	-	518	23.7
33723	750	23.6	3750	-	0	23.6
33724	750	23.6	3750	-	37	23.6
33725	750	23.6	3750	-	74	23.6
33726	750	23.6	3750	-	111	23.6
33727	750	23.6	3750	-	148	23.6
33728	750	23.6	3750	-	185	23.6
33729	750	23.6	3750	-	222	23.6
33730	750	23.6	3750	-	259	23.6
33731	750	23.6	3750	-	296	23.6
33704	800	25.3	4000	1.1	480	23.1
33628	950	30.1	4750	3.7	564	22.7
33768	700	22.2	3500	-	385	22.2
33769	700	22.2	3500	-	420	22.2
33770	700	22.2	3500	-	455	22.2
33771	700	22.2	3500	-	490	22.2
33772	700	22.2	3500	-	525	22.2
33773	700	22.2	3500	-	560	22.2
33757	700	22.0	3500	-	0	22.0
33758	700	22.0	3500	-	35	22.0
33759	700	22.0	3500	-	70	22.0
33760	700	22.0	3500	-	105	22.0
33761	700	22.0	3500	-	140	22.0
33762	700	22.0	3500	-	175	22.0
33763	700	22.0	3500	-	210	22.0
33764	700	22.0	3500	-	245	22.0
33765	700	22.0	3500	-	280	22.0
33766	700	22.0	3500	-	315	22.0
33767	700	21.6	3500	-	350	21.6
33807	650	20.6	3250	-	384	20.6
33808	650	20.6	3250	-	416	20.6
33809	650	20.6	3250	-	448	20.6
33810	650	20.6	3250	-	480	20.6
33811	650	20.6	3250	-	512	20.6
33812	650	20.6	3250	-	544	20.6
33813	650	20.6	3250	-	576	20.6
33814	650	20.6	3250	-	608	20.6
33795	650	20.4	3250	-	0	20.4
33796	650	20.4	3250	-	32	20.4
33797	650	20.4	3250	-	64	20.4
33798	650	20.4	3250	-	96	20.4
33799	650	20.4	3250	-	128	20.4
33800	650	20.4	3250	-	160	20.4
33801	650	20.4	3250	-	192	20.4
33802	650	20.4	3250	-	224	20.4
33803	650	20.4	3250	-	256	20.4
33804	650	20.4	3250	-	288	20.4
33805	650	20.4	3250	-	320	20.4
33806	650	20.1	3250	-	352	20.1
33850	600	19.9	3000	-	360	19.9
33851	600	19.0	3000	-	390	19.0
33852	600	19.0	3000	-	420	19.0
33853	600	19.0	3000	-	450	19.0
33854	600	19.0	3000	-	480	19.0
33855	600	19.0	3000	-	510	19.0
33856	600	19.0	3000	-	540	19.0
33857	600	19.0	3000	-	570	19.0
33858	600	19.0	3000	-	600	19.0
33859	600	19.0	3000	-	630	19.0
33860	600	19.0	3000	-	660	19.0
33838	600	18.9	3000	-	0	18.9
33839	600	18.9	3000	-	30	18.9
33840	600	18.9	3000	-	60	18.9
33841	600	18.9	3000	-	90	18.9
33842	600	18.9	3000	-	120	18.9
33843	600	18.9	3000	-	150	18.9
33844	600	18.9	3000	-	180	18.9
33845	600	18.9	3000	-	210	18.9
33846	600	18.9	3000	-	240	18.9
33847	600	18.9	3000	-	270	18.9
33848	600	18.9	3000	-	300	18.9
33849	600	18.9	3000	-	330	18.9
33901	550	17.4	2750	-	432	17.4
33902	550	17.4	2750	-	459	17.4
33903	550	17.4	2750	-	486	17.4
33904	550	17.4	2750	-	513	17.4
33905	550	17.4	2750	-	540	17.4
33906	550	17.4	2750	-	567	17.4
33907	550	17.4	2750	-	594	17.4
33908	550	17.4	2750	-	621	17.4
33909	550	17.4	2750	-	648	17.4
33910	550	17.4	2750	-	675	17.4
33911	550	17.4	2750	-	702	17.4
33885	550	17.3	2750	-	0	17.3
33886	550	17.3	2750	-	27	17.3
33887	550	17.3	2750	-	54	17.3
33888	550	17.3	2750	-	81	17.3
33889	550	17.3	2750	-	108	17.3
33890	550	17.3	2750	-	135	17.3
33891	550	17.3	2750	-	162	17.3
33892	550	17.3	2750	-	189	17.3
33893	550	17.3	2750	-	216	17.3
33894	550	17.3	2750	-	243	17.3
33895	550	17.3	2750	-	270	17.3
33896	550	17.3	2750	-	297	17.3
33897	550	17.3	2750	-	324	17.3
33898	550	17.0	2750	-	351	17.0
33958	500	15.8	2500	-	475	15.8
33959	500	15.8	2500	-	500	15.8
33960	500	15.8	2500	-	525	15.8
33961	500	15.8	2500	-	550	15.8
33962	500	15.8	2500	-	575	15.8
33963	500	15.8	2500	-	600	15.8
33964	500	15.8	2500	-	625	15.8
33965	500	15.8	2500	-	650	15.8
33966	500	15.8	2500	-	675	15.8
33967	500	15.8	2500	-	700	15.8
33968	500	15.8	2500	-	725	15.8
33969	500	15.8	2500	-	750	15.8
33939	500	15.7	2500	-	0	15.7
33940	500	15.7	2500	-	25	15.7
33941	500	15.7	2500	-	50	15.7
33942	500	15.7	2500	-	75	15.7
33943	500	15.7	2500	-	100	15.7
33944	500	15.7	2500	-	125	15.7
33945	500	15.7	2500	-	150	15.7
33946	500	15.7	2500	-	175	15.7
33947	500	15.7	2500	-	200	15.7
33948	500	15.7	2500	-	225	15.7
33949	500	15.7	2500	-	250	15.7
33950	500	15.7	2500	-	275	15.7
33951	500	15.7	2500	-	300	15.7
33952	500	15.7	2500	-	325	15.7
33953	500	15.4	2500	-	350	15.4
33780	700	22.2	3500	3.7	805	14.7
33912	550	17.4	2750	1.5	729	14.5
33970	500	15.8	2500	0.8	775	14.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
33532	1200	37.7	6000	2.1	120	33.6
33533	1200	37.7	6000	2.1	180	33.6
33534	1200	37.7	6000	2.1	240	33.6
33547	1150	36.2	5750	2.2	171	31.8
33548	1150	36.2	5750	2.2	228	31.8
33549	1150	36.2	5750	2.2	285	31.8
33550	1150	35.5	5750	2.2	342	31.1
33566	1100	34.8	5500	2.3	385	30.3
33563	1100	34.6	5500	2.3	220	30.0
33564	1100	34.6	5500	2.3	275	30.0
33565	1100	34.6	5500	2.3	330	30.0
33583	1050	33.2	5250	2.4	364	28.5
33584	1050	33.2	5250	2.4	416	28.5
33581	1050	33.0	5250	2.4	260	28.3
33582	1050	33.0	5250	2.4	312	28.3
33603	1000	31.6	5000	2.5	400	26.6
33604	1000	31.6	5000	2.5	450	26.6
33605	1000	31.6	5000	2.5	500	26.6
33601	1000	31.4	5000	2.5	300	26.4
33602	1000	30.9	5000	2.5	350	25.9
33624	950	30.1	4750	2.6	376	24.8
33625	950	30.1	4750	2.6	423	24.8
33626	950	30.1	4750	2.6	470	24.8
33627	950	30.1	4750	2.6	517	24.8
33648	900	28.5	4500	2.8	405	22.9
33649	900	28.5	4500	2.8	450	22.9
33650	900	28.5	4500	2.8	495	22.9
33651	900	28.5	4500	2.8	540	22.9
33652	900	28.5	4500	2.8	585	22.9
33675	850	26.9	4250	2.9	462	21.0
33676	850	26.9	4250	2.9	504	21.0
33677	850	26.9	4250	2.9	546	21.0
33678	850	26.9	4250	2.9	588	21.0
33679	850	26.9	4250	2.9	630	21.0
33705	800	25.3	4000	3.1	520	19.1
33706	800	25.3	4000	3.1	560	19.1
33707	800	25.3	4000	3.1	600	19.1
33708	800	25.3	4000	3.1	640	19.1
33709	800	25.3	4000	3.1	680	19.1
33738	750	23.7	3750	3.3	555	17.1
33739	750	23.7	3750	3.3	592	17.1
33740	750	23.7	3750	3.3	629	17.1
33741	750	23.7	3750	3.3	666	17.1
33742	750	23.7	3750	3.3	703	17.1
33743	750	23.7	3750	3.3	740	17.1
33774	700	22.2	3500	3.4	595	15.3
33775	700	22.2	3500	3.6	630	15.0
33776	700	22.2	3500	3.6	665	15.0
33777	700	22.2	3500	3.6	700	15.0
33778	700	22.2	3500	3.6	735	15.0
33779	700	22.2	3500	3.6	770	15.0
33815	650	20.6	3250	2.9	640	14.7
33816	650	20.6	3250	3.8	672	12.9
33817	650	20.6	3250	3.8	704	12.9
33818	650	20.6	3250	3.8	736	12.9
33819	650	20.6	3250	3.8	768	12.9
33820	650	20.6	3250	3.8	800	12.9
33821	650	20.6	3250	3.8	832	12.9
33861	600	19.0	3000	3.2	690	12.7
33862	600	19.0	3000	4.2	720	10.7
33863	600	19.0	3000	4.2	750	10.7
33864	600	19.0	3000	4.2	780	10.7
33865	600	19.0	3000	4.2	810	10.7
33866	600	19.0	3000	4.2	840	10.7
33867	600	19.0	3000	4.2	870	10.7
33868	600	19.0	3000	4.2	900	10.7
33919	550	17.9	2750	4.5	918	8.8
33920	550	17.9	2750	4.5	945	8.8
33913	550	17.4	2750	4.5	756	8.3
33914	550	17.4	2750	4.5	783	8.3
33915	550	17.4	2750	4.5	810	8.3
33916	550	17.4	2750	4.5	837	8.3
33917	550	17.4	2750	4.5	864	8.3
33918	550	17.4	2750	4.5	891	8.3
33979	500	16.4	2500	5.0	1000	6.4
33976	500	16.2	2500	5.0	925	6.2
33977	500	16.2	2500	5.0	950	6.2
33978	500	16.2	2500	5.0	975	6.2
33971	500	15.8	2500	5.0	800	5.8
33972	500	15.8	2500	5.0	825	5.8
33973	500	15.8	2500	5.0	850	5.8
33974	500	15.8	2500	5.0	875	5.8
33975	500	15.8	2500	5.0	900	5.8

Overall score = score_ratio - 2 * repetitive DNA content