Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign85 - back to list

Summary
Image
Unique putative probes (299)
Putative probes (58)
Redundant probes (15)

Summary

`./analyse_probe_search_results : Thu Dec 1 17:07:05 2005`

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

Fetched probe design: ProbeDesign85
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 17
  id            : 76
  strand        : 1
  -------------

Design window length: 4001bp

All jobs for probe design are successful - total: 66
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1318 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            : 1318/1318
Putative probes that are unique                 : 299/1318
Putative probes exceeding selection criteria    : 372/1318 (both unique and not unique)
Putative probes with successfully-picked primers: 372/372

Identified 15 '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
71905	1300	6500	-	130
71947	1250	6250	-	124
71948	1250	6250	-	186
71992	1200	6000	-	120
71993	1200	6000	-	180
71994	1200	6000	-	240
72039	1150	5750	-	114
72040	1150	5750	-	171
72041	1150	5750	-	228
72042	1150	5750	-	285
72090	1100	5500	-	110
72091	1100	5500	-	165
72092	1100	5500	-	220
72093	1100	5500	-	275
72094	1100	5500	-	330
72143	1050	5250	-	104
72144	1050	5250	-	156
72145	1050	5250	-	208
72146	1050	5250	-	260
72147	1050	5250	-	312
72148	1050	5250	-	364
72200	1000	5000	-	100
72201	1000	5000	-	150
72202	1000	5000	-	200
72203	1000	5000	-	250
72204	1000	5000	-	300
72205	1000	5000	-	350
72206	1000	5000	-	400
72262	950	4750	-	141
72263	950	4750	-	188
72264	950	4750	-	235
72265	950	4750	-	282
72266	950	4750	-	329
72267	950	4750	-	376
72268	950	4750	-	423
72269	950	4750	-	470
72327	900	4500	-	135
72328	900	4500	-	180
72329	900	4500	-	225
72330	900	4500	-	270
72331	900	4500	-	315
72332	900	4500	-	360
72333	900	4500	-	405
72334	900	4500	-	450
72335	900	4500	-	495
72336	900	4500	-	540
72396	850	4250	-	126
72397	850	4250	-	168
72398	850	4250	-	210
72399	850	4250	-	252
72400	850	4250	-	294
72401	850	4250	-	336
72402	850	4250	-	378
72403	850	4250	-	420
72404	850	4250	-	462
72405	850	4250	-	504
72406	850	4250	-	546
72407	850	4250	-	588
72472	800	4000	-	120
72473	800	4000	-	160
72474	800	4000	-	200
72475	800	4000	-	240
72476	800	4000	-	280
72477	800	4000	-	320
72478	800	4000	-	360
72479	800	4000	-	400
72480	800	4000	-	440
72481	800	4000	-	480
72482	800	4000	-	520
72483	800	4000	-	560
72484	800	4000	-	600
72485	800	4000	-	640
72553	750	3750	-	111
72554	750	3750	-	148
72555	750	3750	-	185
72556	750	3750	-	222
72557	750	3750	-	259
72558	750	3750	-	296
72559	750	3750	-	333
72560	750	3750	-	370
72561	750	3750	-	407
72562	750	3750	-	444
72563	750	3750	-	481
72564	750	3750	-	518
72565	750	3750	-	555
72566	750	3750	-	592
72567	750	3750	-	629
72568	750	3750	-	666
72641	700	3500	-	105
72642	700	3500	-	140
72643	700	3500	-	175
72644	700	3500	-	210
72645	700	3500	-	245
72646	700	3500	-	280
72647	700	3500	-	315
72648	700	3500	-	350
72649	700	3500	-	385
72650	700	3500	-	420
72651	700	3500	-	455
72652	700	3500	-	490
72653	700	3500	-	525
72654	700	3500	-	560
72655	700	3500	-	595
72656	700	3500	-	630
72657	700	3500	-	665
72658	700	3500	-	700
72659	700	3500	-	735
72737	650	3250	-	128
72738	650	3250	-	160
72739	650	3250	-	192
72740	650	3250	-	224
72741	650	3250	-	256
72742	650	3250	-	288
72743	650	3250	-	320
72744	650	3250	-	352
72745	650	3250	-	384
72746	650	3250	-	416
72747	650	3250	-	448
72748	650	3250	-	480
72749	650	3250	-	512
72750	650	3250	-	544
72751	650	3250	-	576
72752	650	3250	-	608
72753	650	3250	-	640
72754	650	3250	-	672
72755	650	3250	-	704
72756	650	3250	-	736
72757	650	3250	-	768
72842	600	3000	-	120
72843	600	3000	-	150
72844	600	3000	-	180
72845	600	3000	-	210
72846	600	3000	-	240
72847	600	3000	-	270
72848	600	3000	-	300
72849	600	3000	-	330
72850	600	3000	-	360
72851	600	3000	-	390
72852	600	3000	-	420
72853	600	3000	-	450
72854	600	3000	-	480
72855	600	3000	-	510
72856	600	3000	-	540
72857	600	3000	-	570
72858	600	3000	-	600
72859	600	3000	-	630
72860	600	3000	-	660
72861	600	3000	-	690
72862	600	3000	-	720
72863	600	3000	-	750
72864	600	3000	-	780
72865	600	3000	-	810
72866	600	3000	-	840
72956	550	2750	-	108
72957	550	2750	-	135
72958	550	2750	-	162
72959	550	2750	-	189
72960	550	2750	-	216
72961	550	2750	-	243
72962	550	2750	-	270
72963	550	2750	-	297
72964	550	2750	-	324
72965	550	2750	-	351
72966	550	2750	-	378
72967	550	2750	-	405
72968	550	2750	-	432
72969	550	2750	-	459
72970	550	2750	-	486
72971	550	2750	-	513
72972	550	2750	-	540
72973	550	2750	-	567
72974	550	2750	-	594
72975	550	2750	-	621
72976	550	2750	-	648
72977	550	2750	-	675
72978	550	2750	-	702
72979	550	2750	-	729
72980	550	2750	-	756
72981	550	2750	-	783
72982	550	2750	-	810
72983	550	2750	-	837
72984	550	2750	-	864
72985	550	2750	-	891
73084	500	2500	-	100
73085	500	2500	-	125
73086	500	2500	-	150
73087	500	2500	-	175
73088	500	2500	-	200
73089	500	2500	-	225
73090	500	2500	-	250
73091	500	2500	-	275
73092	500	2500	-	300
73093	500	2500	-	325
73094	500	2500	-	350
73095	500	2500	-	375
73096	500	2500	-	400
73097	500	2500	-	425
73098	500	2500	-	450
73099	500	2500	-	475
73100	500	2500	-	500
73101	500	2500	-	525
73102	500	2500	-	550
73103	500	2500	-	575
73104	500	2500	-	600
73105	500	2500	-	625
73106	500	2500	-	650
73107	500	2500	-	675
73108	500	2500	-	700
73109	500	2500	-	725
73110	500	2500	-	750
73111	500	2500	-	775
73112	500	2500	-	800
73113	500	2500	-	825
73114	500	2500	-	850
73115	500	2500	-	875
73116	500	2500	-	900
73117	500	2500	-	925
72207	1000	5000	0.3	450
72758	650	3250	0.5	800
73118	500	2500	0.6	950
72736	650	3250	0.6	96
72261	950	4750	0.6	94
72569	750	3750	0.8	703
72326	900	4500	1.1	90
72510	800	4000	1.1	1640
72594	750	3750	1.2	1628
72595	750	3750	1.2	1665
72684	700	3500	1.3	1610
72685	700	3500	1.3	1645
72686	700	3500	1.3	1680
72687	700	3500	1.3	1715
72784	650	3250	1.4	1632
72785	650	3250	1.4	1664
72786	650	3250	1.4	1696
72787	650	3250	1.4	1728
72788	650	3250	1.4	1760
72789	650	3250	1.4	1792
72892	600	3000	1.5	1620
72893	600	3000	1.5	1650
72894	600	3000	1.5	1680
72895	600	3000	1.5	1710
72896	600	3000	1.5	1740
72897	600	3000	1.5	1770
72898	600	3000	1.5	1800
72899	600	3000	1.5	1830
73012	550	2750	1.6	1620
73013	550	2750	1.6	1647
73014	550	2750	1.6	1674
73015	550	2750	1.6	1701
73016	550	2750	1.6	1728
73017	550	2750	1.6	1755
73018	550	2750	1.6	1782
73019	550	2750	1.6	1809
73020	550	2750	1.6	1836
73021	550	2750	1.6	1863
73022	550	2750	1.6	1890
72841	600	3000	1.7	90
72688	700	3500	1.7	1750
73145	500	2500	1.8	1625
73146	500	2500	1.8	1650
73147	500	2500	1.8	1675
73148	500	2500	1.8	1700
73149	500	2500	1.8	1725
73150	500	2500	1.8	1750
73151	500	2500	1.8	1775
73152	500	2500	1.8	1800
73153	500	2500	1.8	1825
73154	500	2500	1.8	1850
73155	500	2500	1.8	1875
73156	500	2500	1.8	1900
73157	500	2500	1.8	1925
72149	1050	5250	1.8	416
72596	750	3750	1.9	1702
72395	850	4250	1.9	84
72270	950	4750	2.1	517
73158	500	2500	2.4	1950
72471	800	4000	2.5	80
72660	700	3500	3.3	770
72095	1100	5500	3.5	385
72955	550	2750	3.5	81
72900	600	3000	3.7	1860
71906	1300	6500	3.7	195
72986	550	2750	3.8	918
72867	600	3000	3.8	870
72408	850	4250	3.9	630
72043	1150	5750	3.9	342
71949	1250	6250	4.1	248
72486	800	4000	4.1	680
72337	900	4500	4.2	585
71995	1200	6000	4.4	300
73023	550	2750	5.3	1917
72208	1000	5000	5.3	500
72759	650	3250	5.4	832
73119	500	2500	5.6	975
72570	750	3750	5.7	740
72987	550	2750	8.7	945
72868	600	3000	8.8	900
73120	500	2500	10.6	1000
73207	500	2500	11.8	3175

Putative probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
71904	1300	37.6	6500	2.5	65	32.5
71946	1250	36.1	6250	2.6	62	30.8
71903	1300	37.6	6500	4.2	0	29.3
71991	1200	34.7	6000	2.8	60	29.2
72038	1150	33.2	5750	2.9	57	27.5
72089	1100	31.8	5500	3.0	55	25.8
72509	800	26.7	4000	1.1	1600	24.4
72142	1050	30.3	5250	3.1	52	24.1
72431	850	25.8	4250	1.1	1596	23.6
72199	1000	28.9	5000	3.3	50	22.3
72731	700	21.3	3500	-	3255	21.3
72260	950	27.5	4750	3.5	47	20.5
72593	750	22.7	3750	1.2	1591	20.3
72835	650	19.8	3250	-	3264	19.8
72836	650	19.8	3250	-	3296	19.8
72834	650	19.8	3250	0.3	3232	19.2
72783	650	21.7	3250	1.4	1600	18.9
72732	700	21.3	3500	1.3	3290	18.8
72325	900	26.0	4500	3.7	45	18.7
72946	600	18.3	3000	-	3240	18.3
72947	600	18.3	3000	-	3270	18.3
72948	600	18.3	3000	-	3300	18.3
72949	600	18.3	3000	-	3330	18.3
72950	600	18.3	3000	-	3360	18.3
72637	750	22.9	3750	2.4	3219	18.1
72430	850	25.8	4250	4.1	1554	17.5
72730	700	21.3	3500	2.0	3220	17.3
72683	700	21.2	3500	2.0	1575	17.2
72508	800	24.2	4000	3.6	1560	17.0
72394	850	24.6	4250	3.9	42	16.8
73072	550	16.8	2750	-	3240	16.8
73073	550	16.8	2750	-	3267	16.8
73074	550	16.8	2750	-	3294	16.8
73075	550	16.8	2750	-	3321	16.8
73076	550	16.8	2750	-	3348	16.8
73077	550	16.8	2750	-	3375	16.8
73078	550	16.8	2750	-	3402	16.8
72552	750	22.9	3750	3.5	74	15.9
72359	900	24.7	4500	4.7	1575	15.4
73210	500	15.2	2500	-	3250	15.2
73211	500	15.2	2500	-	3275	15.2
73212	500	15.2	2500	-	3300	15.2
73213	500	15.2	2500	-	3325	15.2
73214	500	15.2	2500	-	3350	15.2
73215	500	15.2	2500	-	3375	15.2
73216	500	15.2	2500	-	3400	15.2
73217	500	15.2	2500	-	3425	15.2
73218	500	15.2	2500	-	3450	15.2
72891	600	18.2	3000	1.5	1590	15.2
72470	800	23.1	4000	4.1	40	14.9
73011	550	16.7	2750	1.6	1593	13.4
72782	650	19.7	3250	3.2	1568	13.2
73144	500	16.7	2500	1.8	1600	13.1
73209	500	15.2	2500	1.8	3225	11.6
73220	500	15.2	2500	1.8	3500	11.6
72945	600	18.3	3000	4.0	3210	10.3
73143	500	15.2	2500	2.6	1575	10.0
73071	550	16.8	2750	3.8	3213	9.1

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
71945	1250	36.1	6250	4.3	0	27.5
71990	1200	34.7	6000	4.5	0	25.7
72037	1150	33.2	5750	4.7	0	23.8
72088	1100	31.8	5500	4.9	0	22.0
72837	650	19.8	3250	1.4	3328	17.0
72951	600	18.3	3000	1.5	3390	15.3
73079	550	16.8	2750	1.6	3429	13.5
72592	750	22.7	3750	4.7	1554	13.4
72551	750	21.7	3750	4.4	37	12.9
72640	700	21.3	3500	4.3	70	12.8
73219	500	15.2	2500	1.8	3475	11.6
72639	700	20.2	3500	4.7	35	10.8
72890	600	18.2	3000	4.8	1560	8.5
73010	550	16.7	2750	4.2	1566	8.3
73083	500	15.2	2500	5.0	75	5.2

Overall score = score_ratio - 2 * repetitive DNA content