Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign63 - back to list

Summary
Image
Unique putative probes (98)
Putative probes (212)
Redundant probes (57)

Summary

`./analyse_probe_search_results : Fri Oct 7 10:48:16 2005`

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

Fetched probe design: ProbeDesign63
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 1
  id            : 54
  strand        : 1
  -------------

Design window length: 2201bp

All jobs for probe design are successful - total: 29
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 577 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            : 577/577
Putative probes that are unique                 : 98/577
Putative probes exceeding selection criteria    : 269/577 (but not unique)
Putative probes with successfully-picked primers: 347/367

Identified 57 '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
53017	800	4000	-	1400
53056	750	3750	-	1406
53057	750	3750	-	1443
53098	700	3500	-	1400
53099	700	3500	-	1435
53100	700	3500	-	1470
53103	650	3250	-	64
53144	650	3250	-	1376
53145	650	3250	-	1408
53146	650	3250	-	1440
53147	650	3250	-	1472
53148	650	3250	-	1504
53149	650	3250	-	1536
53152	600	3000	-	60
53153	600	3000	-	90
53154	600	3000	-	120
53173	600	3000	-	690
53174	600	3000	-	720
53196	600	3000	-	1380
53197	600	3000	-	1410
53198	600	3000	-	1440
53199	600	3000	-	1470
53200	600	3000	-	1500
53201	600	3000	-	1530
53202	600	3000	-	1560
53203	600	3000	-	1590
53206	550	2750	-	54
53207	550	2750	-	81
53208	550	2750	-	108
53209	550	2750	-	135
53210	550	2750	-	162
53230	550	2750	-	702
53231	550	2750	-	729
53232	550	2750	-	756
53255	550	2750	-	1377
53256	550	2750	-	1404
53257	550	2750	-	1431
53258	550	2750	-	1458
53259	550	2750	-	1485
53260	550	2750	-	1512
53261	550	2750	-	1539
53262	550	2750	-	1566
53263	550	2750	-	1593
53264	550	2750	-	1620
53265	550	2750	-	1647
53269	500	2500	-	75
53270	500	2500	-	100
53271	500	2500	-	125
53272	500	2500	-	150
53273	500	2500	-	175
53274	500	2500	-	200
53275	500	2500	-	225
53294	500	2500	-	700
53295	500	2500	-	725
53296	500	2500	-	750
53297	500	2500	-	775
53298	500	2500	-	800
53322	500	2500	-	1400
53323	500	2500	-	1425
53324	500	2500	-	1450
53325	500	2500	-	1475
53326	500	2500	-	1500
53327	500	2500	-	1525
53328	500	2500	-	1550
53329	500	2500	-	1575
53330	500	2500	-	1600
53331	500	2500	-	1625
53332	500	2500	-	1650
53333	500	2500	-	1675
53334	500	2500	-	1700
53321	500	2500	0.2	1375
53299	500	2500	0.8	825
53055	750	3750	0.9	1369
53097	700	3500	1.6	1365
53016	800	4000	2.0	1360
53233	550	2750	2.2	783
52981	850	4250	3.8	1344
53195	600	3000	4.3	1350
53254	550	2750	4.7	1350
53175	600	3000	4.8	750
53143	650	3250	4.9	1344
53123	650	3250	5.1	704
53320	500	2500	5.2	1350
53300	500	2500	5.8	850
53054	750	3750	5.9	1332
52980	850	4250	6.5	1302
53096	700	3500	6.6	1330
53015	800	4000	6.9	1320
53234	550	2750	7.1	810
53124	650	3250	8.5	736
53142	650	3250	8.5	1312
53176	600	3000	9.2	780
53194	600	3000	9.2	1320
53253	550	2750	9.6	1323
53235	550	2750	10.0	837
53319	500	2500	10.2	1325
53301	500	2500	10.8	875
53318	500	2500	11.0	1300

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
52769	1300	42.8	6500	4.2	715	34.3
52770	1300	42.8	6500	4.2	780	34.3
52771	1300	42.8	6500	4.2	845	34.3
52758	1300	32.7	6500	-	0	32.7
52787	1250	41.1	6250	4.4	930	32.3
52772	1250	31.4	6250	-	0	31.4
52773	1250	31.4	6250	-	62	31.4
52788	1200	30.2	6000	-	0	30.2
52789	1200	30.2	6000	-	60	30.2
52790	1200	30.2	6000	-	120	30.2
52805	1150	28.9	5750	-	0	28.9
52806	1150	28.9	5750	-	57	28.9
52807	1150	28.9	5750	-	114	28.9
52808	1150	28.9	5750	-	171	28.9
52824	1100	27.6	5500	-	0	27.6
52825	1100	27.6	5500	-	55	27.6
52826	1100	27.6	5500	-	110	27.6
52827	1100	27.6	5500	-	165	27.6
52828	1100	27.6	5500	-	220	27.6
52845	1050	26.4	5250	-	0	26.4
52846	1050	26.4	5250	-	52	26.4
52847	1050	26.4	5250	-	104	26.4
52848	1050	26.4	5250	-	156	26.4
52849	1050	26.4	5250	-	208	26.4
52850	1050	26.4	5250	-	260	26.4
52844	1100	36.2	5500	5.0	1100	26.2
52759	1300	32.7	6500	3.4	65	25.9
52868	1000	25.1	5000	-	0	25.1
52869	1000	25.1	5000	-	50	25.1
52870	1000	25.1	5000	-	100	25.1
52871	1000	25.1	5000	-	150	25.1
52872	1000	25.1	5000	-	200	25.1
52873	1000	25.1	5000	-	250	25.1
52874	1000	25.1	5000	-	300	25.1
52760	1300	32.7	6500	4.2	130	24.2
52761	1300	32.7	6500	4.2	195	24.2
52762	1300	32.7	6500	4.2	260	24.2
52763	1300	32.7	6500	4.2	325	24.2
52764	1300	32.7	6500	4.2	390	24.2
52765	1300	32.7	6500	4.2	455	24.2
52766	1300	32.7	6500	4.2	520	24.2
52767	1300	32.7	6500	4.2	585	24.2
52768	1300	32.7	6500	4.2	650	24.2
52893	950	23.9	4750	-	0	23.9
52894	950	23.9	4750	-	47	23.9
52895	950	23.9	4750	-	94	23.9
52896	950	23.9	4750	-	141	23.9
52897	950	23.9	4750	-	188	23.9
52898	950	23.9	4750	-	235	23.9
52899	950	23.9	4750	-	282	23.9
52900	950	23.9	4750	-	329	23.9
52774	1250	31.4	6250	4.2	124	22.9
52901	950	23.9	4750	0.5	376	22.8
52920	900	22.6	4500	-	0	22.6
52921	900	22.6	4500	-	45	22.6
52922	900	22.6	4500	-	90	22.6
52923	900	22.6	4500	-	135	22.6
52924	900	22.6	4500	-	180	22.6
52925	900	22.6	4500	-	225	22.6
52926	900	22.6	4500	-	270	22.6
52927	900	22.6	4500	-	315	22.6
52928	900	22.6	4500	-	360	22.6
52929	900	22.6	4500	-	405	22.6
52775	1250	31.4	6250	4.4	186	22.6
52776	1250	31.4	6250	4.4	248	22.6
52949	850	21.4	4250	-	0	21.4
52950	850	21.4	4250	-	42	21.4
52951	850	21.4	4250	-	84	21.4
52952	850	21.4	4250	-	126	21.4
52953	850	21.4	4250	-	168	21.4
52954	850	21.4	4250	-	210	21.4
52955	850	21.4	4250	-	252	21.4
52956	850	21.4	4250	-	294	21.4
52957	850	21.4	4250	-	336	21.4
52958	850	21.4	4250	-	378	21.4
52959	850	21.4	4250	-	420	21.4
52960	850	21.4	4250	-	462	21.4
53058	700	21.3	3500	-	0	21.3
52982	800	20.1	4000	-	0	20.1
52983	800	20.1	4000	-	40	20.1
52984	800	20.1	4000	-	80	20.1
52985	800	20.1	4000	-	120	20.1
52986	800	20.1	4000	-	160	20.1
52987	800	20.1	4000	-	200	20.1
52988	800	20.1	4000	-	240	20.1
52989	800	20.1	4000	-	280	20.1
52990	800	20.1	4000	-	320	20.1
52991	800	20.1	4000	-	360	20.1
52992	800	20.1	4000	-	400	20.1
52993	800	20.1	4000	-	440	20.1
52994	800	20.1	4000	-	480	20.1
52995	800	20.1	4000	-	520	20.1
53101	650	19.8	3250	-	0	19.8
53102	650	19.8	3250	-	32	19.8
53059	700	19.4	3500	-	35	19.4
53018	750	19.4	3750	-	0	19.4
52875	1000	25.1	5000	2.9	350	19.3
53019	750	18.8	3750	-	37	18.8
53020	750	18.8	3750	-	74	18.8
53021	750	18.8	3750	-	111	18.8
53022	750	18.8	3750	-	148	18.8
53023	750	18.8	3750	-	185	18.8
53024	750	18.8	3750	-	222	18.8
53025	750	18.8	3750	-	259	18.8
53026	750	18.8	3750	-	296	18.8
53027	750	18.8	3750	-	333	18.8
53028	750	18.8	3750	-	370	18.8
53029	750	18.8	3750	-	407	18.8
53030	750	18.8	3750	-	444	18.8
53031	750	18.8	3750	-	481	18.8
53032	750	18.8	3750	-	518	18.8
53033	750	18.8	3750	-	555	18.8
53150	600	18.3	3000	-	0	18.3
53151	600	18.3	3000	-	30	18.3
53060	700	17.6	3500	-	70	17.6
53061	700	17.6	3500	-	105	17.6
53062	700	17.6	3500	-	140	17.6
53063	700	17.6	3500	-	175	17.6
53064	700	17.6	3500	-	210	17.6
53065	700	17.6	3500	-	245	17.6
53066	700	17.6	3500	-	280	17.6
53067	700	17.6	3500	-	315	17.6
53068	700	17.6	3500	-	350	17.6
53069	700	17.6	3500	-	385	17.6
53070	700	17.6	3500	-	420	17.6
53071	700	17.6	3500	-	455	17.6
53072	700	17.6	3500	-	490	17.6
53073	700	17.6	3500	-	525	17.6
53074	700	17.6	3500	-	560	17.6
53075	700	17.6	3500	-	595	17.6
53104	650	16.8	3250	-	96	16.8
53204	550	16.8	2750	-	0	16.8
53205	550	16.8	2750	-	27	16.8
53105	650	16.3	3250	-	128	16.3
53106	650	16.3	3250	-	160	16.3
53107	650	16.3	3250	-	192	16.3
53108	650	16.3	3250	-	224	16.3
53109	650	16.3	3250	-	256	16.3
53110	650	16.3	3250	-	288	16.3
53111	650	16.3	3250	-	320	16.3
53112	650	16.3	3250	-	352	16.3
53113	650	16.3	3250	-	384	16.3
53114	650	16.3	3250	-	416	16.3
53115	650	16.3	3250	-	448	16.3
53116	650	16.3	3250	-	480	16.3
53117	650	16.3	3250	-	512	16.3
53118	650	16.3	3250	-	544	16.3
53119	650	16.3	3250	-	576	16.3
53120	650	16.3	3250	-	608	16.3
53121	650	16.3	3250	-	640	16.3
53122	650	16.6	3250	0.2	672	16.3
52930	900	22.6	4500	3.2	450	16.2
53268	500	16.1	2500	-	50	16.1
53155	600	15.5	3000	-	150	15.5
53266	500	15.2	2500	-	0	15.2
53267	500	15.2	2500	-	25	15.2
53156	600	15.1	3000	-	180	15.1
53157	600	15.1	3000	-	210	15.1
53158	600	15.1	3000	-	240	15.1
53159	600	15.1	3000	-	270	15.1
53160	600	15.1	3000	-	300	15.1
53161	600	15.1	3000	-	330	15.1
53162	600	15.1	3000	-	360	15.1
53163	600	15.1	3000	-	390	15.1
53164	600	15.1	3000	-	420	15.1
53165	600	15.1	3000	-	450	15.1
53166	600	15.1	3000	-	480	15.1
53167	600	15.1	3000	-	510	15.1
53168	600	15.1	3000	-	540	15.1
53169	600	15.1	3000	-	570	15.1
53170	600	15.1	3000	-	600	15.1
53171	600	15.1	3000	-	630	15.1
53172	600	15.1	3000	-	660	15.1
53076	700	17.6	3500	1.3	630	15.0
53211	550	14.9	2750	-	189	14.9
53229	550	14.6	2750	-	675	14.6
53212	550	13.9	2750	-	216	13.9
53213	550	13.8	2750	-	243	13.8
53214	550	13.8	2750	-	270	13.8
53215	550	13.8	2750	-	297	13.8
53216	550	13.8	2750	-	324	13.8
53217	550	13.8	2750	-	351	13.8
53218	550	13.8	2750	-	378	13.8
53219	550	13.8	2750	-	405	13.8
53220	550	13.8	2750	-	432	13.8
53221	550	13.8	2750	-	459	13.8
53222	550	13.8	2750	-	486	13.8
53223	550	13.8	2750	-	513	13.8
53224	550	13.8	2750	-	540	13.8
53225	550	13.8	2750	-	567	13.8
53226	550	13.8	2750	-	594	13.8
53227	550	13.8	2750	-	621	13.8
53228	550	13.8	2750	-	648	13.8
53293	500	13.3	2500	-	675	13.3
53034	750	18.8	3750	2.8	592	13.2
53276	500	13.0	2500	-	250	13.0
53277	500	12.6	2500	-	275	12.6
53278	500	12.6	2500	-	300	12.6
53279	500	12.6	2500	-	325	12.6
53280	500	12.6	2500	-	350	12.6
53281	500	12.6	2500	-	375	12.6
53282	500	12.6	2500	-	400	12.6
53283	500	12.6	2500	-	425	12.6
53284	500	12.6	2500	-	450	12.6
53285	500	12.6	2500	-	475	12.6
53286	500	12.6	2500	-	500	12.6
53287	500	12.6	2500	-	525	12.6
53288	500	12.6	2500	-	550	12.6
53289	500	12.6	2500	-	575	12.6
53290	500	12.6	2500	-	600	12.6
53291	500	12.6	2500	-	625	12.6
53292	500	12.6	2500	-	650	12.6

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
52784	1250	41.1	6250	4.4	744	32.3
52785	1250	41.1	6250	4.4	806	32.3
52786	1250	41.1	6250	4.4	868	32.3
52800	1200	39.5	6000	4.6	720	30.3
52801	1200	39.5	6000	4.6	780	30.3
52802	1200	39.5	6000	4.6	840	30.3
52803	1200	39.5	6000	4.6	900	30.3
52804	1200	39.5	6000	4.6	960	30.3
52818	1150	37.8	5750	4.8	741	28.3
52819	1150	37.8	5750	4.8	798	28.3
52820	1150	37.8	5750	4.8	855	28.3
52821	1150	37.8	5750	4.8	912	28.3
52822	1150	37.8	5750	4.8	969	28.3
52823	1150	37.8	5750	4.8	1026	28.3
52783	1250	35.5	6250	4.4	682	26.7
52837	1100	36.2	5500	5.0	715	26.2
52838	1100	36.2	5500	5.0	770	26.2
52839	1100	36.2	5500	5.0	825	26.2
52840	1100	36.2	5500	5.0	880	26.2
52841	1100	36.2	5500	5.0	935	26.2
52842	1100	36.2	5500	5.0	990	26.2
52843	1100	36.2	5500	5.0	1045	26.2
52817	1150	34.6	5750	4.8	684	25.1
52777	1250	31.4	6250	4.4	310	22.6
52778	1250	31.4	6250	4.4	372	22.6
52779	1250	31.4	6250	4.4	434	22.6
52780	1250	31.4	6250	4.4	496	22.6
52781	1250	31.4	6250	4.4	558	22.6
52782	1250	31.4	6250	4.4	620	22.6
52791	1200	30.2	6000	4.6	180	21.0
52792	1200	30.2	6000	4.6	240	21.0
52793	1200	30.2	6000	4.6	300	21.0
52794	1200	30.2	6000	4.6	360	21.0
52795	1200	30.2	6000	4.6	420	21.0
52796	1200	30.2	6000	4.6	480	21.0
52797	1200	30.2	6000	4.6	540	21.0
52798	1200	30.2	6000	4.6	600	21.0
52799	1200	30.2	6000	4.6	660	21.0
52809	1150	28.9	5750	4.8	228	19.3
52810	1150	28.9	5750	4.8	285	19.3
52811	1150	28.9	5750	4.8	342	19.3
52812	1150	28.9	5750	4.8	399	19.3
52813	1150	28.9	5750	4.8	456	19.3
52814	1150	28.9	5750	4.8	513	19.3
52815	1150	28.9	5750	4.8	570	19.3
52816	1150	28.9	5750	4.8	627	19.3
52851	1050	26.4	5250	3.9	312	18.6
52829	1100	27.6	5500	4.9	275	17.8
52830	1100	27.6	5500	5.0	330	17.6
52831	1100	27.6	5500	5.0	385	17.6
52832	1100	27.6	5500	5.0	440	17.6
52833	1100	27.6	5500	5.0	495	17.6
52834	1100	27.6	5500	5.0	550	17.6
52835	1100	27.6	5500	5.0	605	17.6
52836	1100	27.6	5500	5.0	660	17.6
52961	850	21.4	4250	3.9	504	13.6
52996	800	20.1	4000	4.9	560	10.4

Overall score = score_ratio - 2 * repetitive DNA content