Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign74 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (109)
Redundant probes (130)

Summary

`./analyse_probe_search_results : Thu Oct 20 15:11:42 2005`

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

Fetched probe design: ProbeDesign74
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 4
  id            : 65
  strand        : 1
  -------------

Design window length: 1501bp

All jobs for probe design are successful - total: 15
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 289 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            : 289/289
Putative probes that are unique                 : 0/289

  No putative probes pass with the above criteria
  Now trying: score-ratio 2, and percent repetitive 40


  No putative probes pass with the relaxed criteria
  Now trying: score-ratio 2, and percent repetitive 80

Putative probes exceeding selection criteria    : 239/289 (both unique and not unique)
Putative probes with successfully-picked primers: 234/239

Identified 130 '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

No probes

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
64002	500	9.1	2500	42.6	850	-76.1
64003	500	9.3	2500	43.0	875	-76.7
63964	550	10.0	2750	46.2	864	-82.4
63963	550	9.4	2750	46.2	837	-82.9
63962	550	9.4	2750	46.2	810	-83.0
64008	500	10.0	2500	48.0	1000	-86.0
64006	500	12.5	2500	49.4	950	-86.3
64004	500	9.6	2500	48.0	900	-86.4
64001	500	8.5	2500	47.6	825	-86.7
64005	500	11.0	2500	49.4	925	-87.8
64007	500	10.0	2500	49.4	975	-88.8
63929	600	10.6	3000	50.7	840	-90.7
63927	600	10.2	3000	50.7	780	-91.1
63928	600	10.2	3000	50.7	810	-91.1
63965	550	10.6	2750	51.1	891	-91.6
63930	600	11.1	3000	51.7	870	-92.3
63961	550	9.4	2750	50.9	783	-92.5
63926	600	10.2	3000	52.2	750	-94.1
63967	550	11.0	2750	53.6	945	-96.3
64000	500	8.5	2500	52.6	800	-96.7
63966	550	11.2	2750	54.0	918	-96.8
63898	650	11.1	3250	54.5	768	-97.9
63899	650	11.1	3250	54.5	800	-97.9
63900	650	11.1	3250	54.5	832	-97.9
63897	650	10.2	3250	54.5	736	-98.8
63931	600	11.5	3000	55.5	900	-99.5
63847	750	8.2	3750	54.4	629	-100.6
63896	650	8.4	3250	54.9	704	-101.5
63960	550	9.4	2750	55.8	756	-102.3
63846	750	8.2	3750	55.5	592	-102.7
63869	700	7.7	3500	55.4	630	-103.2
63826	800	8.8	4000	56.1	560	-103.5
63827	800	8.8	4000	56.1	600	-103.5
63873	700	11.9	3500	57.7	770	-103.5
63872	700	10.9	3500	57.7	735	-104.5
63870	700	7.7	3500	56.3	665	-104.9
63925	600	8.8	3000	57.2	720	-105.5
63871	700	9.0	3500	57.4	700	-105.9
63999	500	8.5	2500	57.6	775	-106.7
63809	850	9.3	4250	58.7	546	-108.1
63810	850	9.3	4250	58.7	588	-108.1
63739	1150	12.6	5750	60.5	228	-108.5
63828	800	8.8	4000	58.6	640	-108.5
63747	1100	12.0	5500	60.5	275	-108.9
63850	750	11.9	3750	60.5	740	-109.1
63808	850	9.3	4250	59.3	504	-109.3
63868	700	7.7	3500	59.0	595	-110.3
63848	750	8.2	3750	59.3	666	-110.5
63811	850	9.3	4250	59.9	630	-110.5
63849	750	9.6	3750	60.3	703	-110.9
63732	1200	13.1	6000	62.2	180	-111.2
63733	1200	13.1	6000	62.2	240	-111.2
63755	1050	11.5	5250	61.8	260	-112.1
63793	900	9.8	4500	61.0	495	-112.2
63794	900	9.8	4500	61.0	540	-112.2
63795	900	9.8	4500	61.0	585	-112.2
63894	650	7.1	3250	59.7	640	-112.3
63895	650	7.1	3250	59.7	672	-112.3
63746	1100	12.0	5500	62.3	220	-112.5
63845	750	8.2	3750	60.4	555	-112.6
63756	1050	11.5	5250	62.1	312	-112.7
63728	1250	13.7	6250	63.3	248	-112.9
63959	550	8.4	2750	60.7	729	-113.1
63726	1250	13.7	6250	63.4	124	-113.2
63825	800	8.8	4000	61.0	520	-113.2
63740	1150	12.6	5750	63.0	285	-113.5
63727	1250	13.7	6250	63.7	186	-113.7
63792	900	9.8	4500	62.0	450	-114.2
63738	1150	12.6	5750	63.8	171	-115.1
63721	1300	14.2	6500	64.8	65	-115.5
63722	1300	14.2	6500	64.9	130	-115.6
63723	1300	14.2	6500	64.9	195	-115.6
63779	950	10.4	4750	63.1	423	-115.7
63780	950	10.4	4750	63.1	470	-115.7
63781	950	10.4	4750	63.1	517	-115.7
63893	650	7.1	3250	61.5	608	-116.0
63829	800	9.5	4000	62.7	680	-116.0
63924	600	7.2	3000	61.8	690	-116.5
63998	500	8.5	2500	62.6	750	-116.7
63734	1200	13.1	6000	65.2	300	-117.4
63769	1000	10.9	5000	64.2	500	-117.5
63765	1000	10.9	5000	64.9	300	-118.9
63767	1000	10.9	5000	64.9	400	-118.9
63768	1000	10.9	5000	64.9	450	-118.9
63807	850	9.3	4250	64.2	462	-119.2
63764	1000	10.9	5000	65.5	250	-120.1
63867	700	7.7	3500	64.0	560	-120.3
63725	1250	13.7	6250	67.2	62	-120.7
63754	1050	11.5	5250	66.4	208	-121.3
63844	750	8.2	3750	65.3	518	-122.5
63745	1100	12.0	5500	67.3	165	-122.5
63922	600	6.6	3000	64.7	630	-122.8
63923	600	6.6	3000	64.7	660	-122.8
63824	800	8.8	4000	66.0	480	-123.2
63958	550	7.1	2750	65.3	702	-123.4
63737	1150	12.6	5750	68.5	114	-124.5
63720	1300	14.2	6500	69.4	0	-124.5
63892	650	7.1	3250	66.5	576	-125.8
63776	950	10.4	4750	68.3	282	-126.2
63777	950	10.4	4750	68.3	329	-126.2
63975	500	11.0	2500	68.8	175	-126.6
63997	500	7.4	2500	67.6	725	-127.8
63806	850	9.3	4250	69.2	420	-129.1
63921	600	6.6	3000	68.0	600	-129.4
63977	500	6.8	2500	68.4	225	-130.0
63978	500	6.8	2500	68.4	250	-130.0
63976	500	7.4	2500	68.8	200	-130.2
63866	700	7.7	3500	69.0	525	-130.3
63882	650	7.1	3250	69.2	256	-131.3

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
63731	1200	13.1	6000	65.2	120	-117.2
63766	1000	10.9	5000	64.9	350	-118.9
63748	1100	12.0	5500	65.5	330	-118.9
63757	1050	11.5	5250	66.6	364	-121.7
63758	1050	11.5	5250	66.6	416	-121.7
63778	950	10.4	4750	66.5	376	-122.7
63741	1150	12.6	5750	68.0	342	-123.4
63749	1100	12.0	5500	68.1	385	-124.1
63791	900	9.8	4500	67.0	405	-124.2
63730	1200	13.1	6000	70.2	60	-127.2
63763	1000	10.9	5000	70.5	200	-130.1
63724	1250	13.7	6250	72.2	0	-130.6
63775	950	10.4	4750	70.5	235	-130.7
63753	1050	11.5	5250	71.3	156	-131.2
63744	1100	12.0	5500	72.0	110	-132.0
63843	750	8.2	3750	70.3	481	-132.3
63937	550	10.5	2750	71.6	135	-132.8
63823	800	8.8	4000	71.0	440	-133.2
63790	900	9.8	4500	72.0	360	-134.2
63957	550	6.2	2750	70.2	675	-134.2
63736	1150	12.6	5750	73.5	57	-134.4
63788	900	9.8	4500	72.1	270	-134.4
63789	900	9.8	4500	72.1	315	-134.4
63857	700	7.7	3500	71.3	210	-134.9
63858	700	7.7	3500	71.3	245	-134.9
63938	550	7.6	2750	71.3	162	-135.0
63939	550	7.5	2750	71.3	189	-135.0
63955	550	6.0	2750	70.5	621	-135.1
63956	550	6.0	2750	70.5	648	-135.1
63940	550	7.1	2750	71.3	216	-135.5
63974	500	11.2	2500	73.4	150	-135.6
63891	650	7.1	3250	71.4	544	-135.7
63936	550	11.9	2750	73.8	108	-135.8
63941	550	6.5	2750	71.3	243	-136.1
63904	600	10.5	3000	73.5	90	-136.5
63729	1200	13.1	6000	75.2	0	-137.2
63996	500	6.4	2500	72.2	700	-138.0
63905	600	8.3	3000	73.2	120	-138.1
63835	750	8.2	3750	73.2	185	-138.2
63836	750	8.2	3750	73.2	222	-138.2
63979	500	5.9	2500	72.2	275	-138.5
63805	850	9.3	4250	74.1	378	-138.9
63837	750	8.2	3750	73.6	259	-139.0
63906	600	8.2	3000	73.7	150	-139.2
63920	600	6.6	3000	73.0	570	-139.4
63903	600	11.8	3000	75.7	60	-139.6
63875	650	11.1	3250	75.5	32	-140.0
63762	1000	10.9	5000	75.5	150	-140.1
63907	600	7.1	3000	73.7	180	-140.2
63815	800	8.8	4000	74.5	120	-140.2
63908	600	7.0	3000	73.7	210	-140.3
63909	600	7.0	3000	73.7	240	-140.3
63865	700	7.7	3500	74.0	490	-140.3
63752	1050	11.5	5250	76.0	104	-140.5
63774	950	10.4	4750	75.5	188	-140.6
63834	750	8.2	3750	74.4	148	-140.6
63883	650	7.1	3250	74.0	288	-140.9
63816	800	8.8	4000	74.9	160	-141.0
63817	800	8.8	4000	74.9	200	-141.0
63818	800	8.8	4000	74.9	240	-141.0
63881	650	7.2	3250	74.2	224	-141.1
63942	550	6.5	2750	73.8	270	-141.2
63787	900	9.8	4500	75.6	225	-141.3
63876	650	9.0	3250	75.2	64	-141.5
63877	650	8.9	3250	75.2	96	-141.6
63859	700	7.7	3500	74.7	280	-141.8
63743	1100	12.0	5500	77.0	55	-142.0
63842	750	8.2	3750	75.2	444	-142.2
63798	850	9.3	4250	76.0	84	-142.7
63799	850	9.3	4250	76.0	126	-142.7
63878	650	7.7	3250	75.2	128	-142.7
63822	800	8.8	4000	76.0	400	-143.2
63910	600	6.6	3000	75.0	270	-143.4
63800	850	9.3	4250	76.4	168	-143.4
63801	850	9.3	4250	76.4	210	-143.4
63802	850	9.3	4250	76.4	252	-143.4
63803	850	9.3	4250	76.4	294	-143.4
63804	850	9.3	4250	76.4	336	-143.4
63911	600	6.6	3000	75.0	300	-143.4
63879	650	7.6	3250	75.7	160	-143.8
63880	650	7.6	3250	75.7	192	-143.8
63856	700	7.7	3500	75.9	175	-144.0
63851	700	10.4	3500	77.3	0	-144.2
63735	1150	12.6	5750	78.4	0	-144.3
63852	700	9.6	3500	77.0	35	-144.4
63954	550	6.0	2750	75.3	594	-144.5
63783	900	9.8	4500	77.3	45	-144.8
63784	900	9.8	4500	77.3	90	-144.8
63973	500	10.8	2500	77.8	125	-144.8
63853	700	8.8	3500	77.0	70	-145.2
63785	900	9.8	4500	77.7	135	-145.5
63786	900	9.8	4500	77.7	180	-145.5
63890	650	7.1	3250	76.3	512	-145.5
63935	550	11.9	2750	78.7	81	-145.6
63854	700	8.2	3500	77.0	105	-145.8
63797	850	9.3	4250	77.8	42	-146.2
63782	900	9.8	4500	78.1	0	-146.4
63855	700	8.2	3500	77.4	140	-146.6
63770	950	10.4	4750	78.5	0	-146.7
63771	950	10.4	4750	78.5	47	-146.7
63772	950	10.4	4750	78.5	94	-146.7
63971	500	10.8	2500	78.8	75	-146.8
63972	500	10.8	2500	78.8	100	-146.8
63830	750	10.2	3750	78.5	0	-146.9
63814	800	8.8	4000	77.9	80	-147.0
63819	800	8.8	4000	77.9	280	-147.0
63874	650	11.1	3250	79.1	0	-147.1
63773	950	10.4	4750	78.8	141	-147.3
63831	750	8.9	3750	78.5	37	-148.2
63759	1000	10.9	5000	79.6	0	-148.3
63760	1000	10.9	5000	79.6	50	-148.3
63761	1000	10.9	5000	79.6	100	-148.3
63832	750	8.8	3750	78.5	74	-148.3
63980	500	5.9	2500	77.2	300	-148.5
63970	500	9.0	2500	78.8	50	-148.6
63833	750	8.4	3750	78.5	111	-148.6
63995	500	5.6	2500	77.2	675	-148.8
63838	750	8.2	3750	78.5	296	-148.9
63968	500	8.5	2500	78.8	0	-149.1
63969	500	8.5	2500	78.8	25	-149.1
63919	600	6.6	3000	78.0	540	-149.4
63993	500	5.5	2500	77.6	625	-149.7
63994	500	5.5	2500	77.6	650	-149.7
63864	700	7.7	3500	79.0	455	-150.3
63812	800	9.4	4000	79.9	0	-150.4
63813	800	9.4	4000	79.9	40	-150.4
63884	650	7.1	3250	78.9	320	-150.7
63943	550	6.5	2750	78.7	297	-151.0
63912	600	6.6	3000	78.8	330	-151.1
63860	700	7.7	3500	79.7	315	-151.8

Overall score = score_ratio - 2 * repetitive DNA content