Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign35 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (248)
Redundant probes (84)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:30:45 2005`

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

Fetched probe design: ProbeDesign35
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 11
  strand        : 1
  -------------

Design window length: 5232bp

All jobs for probe design are successful - total: 94
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1865 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        : 1865/1865
Putative probes exceeding selection criteria: 332/1865

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
9192	1000	29.8	5000	0.9	450	28.0
9191	1000	29.4	5000	1.2	400	27.0
9277	950	28.3	4750	0.9	423	26.4
9279	950	28.3	4750	1.2	517	26.0
9369	900	27.6	4500	1.0	405	25.6
9471	850	25.3	4250	0.2	588	24.8
9370	900	26.8	4500	1.0	450	24.8
9371	900	26.8	4500	1.0	495	24.8
9467	850	26.1	4250	1.1	420	24.0
9468	850	26.1	4250	1.1	462	24.0
9577	800	23.8	4000	-	600	23.8
9578	800	23.8	4000	-	640	23.8
9469	850	25.3	4250	1.1	504	23.2
9470	850	25.3	4250	1.1	546	23.2
9689	750	22.3	3750	-	592	22.3
9690	750	22.3	3750	-	629	22.3
9691	750	22.3	3750	-	666	22.3
9692	750	22.3	3750	-	703	22.3
9573	800	24.5	4000	1.1	440	22.3
9574	800	24.5	4000	1.1	480	22.3
9575	800	24.5	4000	1.1	520	22.3
9472	850	25.3	4250	1.8	630	21.8
9576	800	23.8	4000	1.1	560	21.6
9812	700	21.5	3500	-	595	21.5
9813	700	21.5	3500	-	630	21.5
9190	1000	28.2	5000	3.4	350	21.4
9183	1000	28.1	5000	3.4	0	21.3
9184	1000	28.1	5000	3.4	50	21.3
9185	1000	28.1	5000	3.4	100	21.3
9186	1000	28.1	5000	3.4	150	21.3
9187	1000	28.1	5000	3.4	200	21.3
9188	1000	28.1	5000	3.4	250	21.3
9189	1000	28.1	5000	3.4	300	21.3
9373	900	26.8	4500	2.8	585	21.2
9193	1000	29.8	5000	4.4	500	21.0
9814	700	20.8	3500	-	665	20.8
9815	700	20.8	3500	-	700	20.8
9816	700	20.8	3500	-	735	20.8
9684	750	23.0	3750	1.2	407	20.6
9685	750	23.0	3750	1.2	444	20.6
9686	750	23.0	3750	1.2	481	20.6
9687	750	23.0	3750	1.2	518	20.6
9688	750	23.0	3750	1.2	555	20.6
9572	800	23.5	4000	1.5	400	20.5
9579	800	23.8	4000	1.9	680	20.1
9944	650	19.9	3250	-	608	19.9
9945	650	19.9	3250	-	640	19.9
9946	650	19.9	3250	-	672	19.9
9817	700	20.8	3500	0.7	770	19.4
9947	650	19.3	3250	-	704	19.3
9948	650	19.3	3250	-	736	19.3
9949	650	19.3	3250	-	768	19.3
9950	650	19.3	3250	-	800	19.3
9807	700	21.5	3500	1.3	420	18.9
9808	700	21.5	3500	1.3	455	18.9
9809	700	21.5	3500	1.3	490	18.9
9810	700	21.5	3500	1.3	525	18.9
9811	700	21.5	3500	1.3	560	18.9
10033	650	18.9	3250	-	3456	18.9
10034	650	18.9	3250	-	3488	18.9
10089	600	18.4	3000	-	600	18.4
10090	600	18.4	3000	-	630	18.4
10091	600	18.4	3000	-	660	18.4
10092	600	18.4	3000	-	690	18.4
10093	600	18.4	3000	-	720	18.4
10094	600	17.9	3000	-	750	17.9
10095	600	17.9	3000	-	780	17.9
10096	600	17.9	3000	-	810	17.9
10097	600	17.9	3000	-	840	17.9
10184	600	17.4	3000	-	3450	17.4
10185	600	17.4	3000	-	3480	17.4
10186	600	17.4	3000	-	3510	17.4
10187	600	17.4	3000	-	3540	17.4
9938	650	19.9	3250	1.4	416	17.2
9939	650	19.9	3250	1.4	448	17.2
9940	650	19.9	3250	1.4	480	17.2
9941	650	19.9	3250	1.4	512	17.2
9942	650	19.9	3250	1.4	544	17.2
9943	650	19.9	3250	1.4	576	17.2
9893	700	20.3	3500	1.7	3430	16.9
10246	550	16.9	2750	-	594	16.9
10247	550	16.9	2750	-	621	16.9
10248	550	16.9	2750	-	648	16.9
10249	550	16.9	2750	-	675	16.9
10250	550	16.9	2750	-	702	16.9
10251	550	16.9	2750	-	729	16.9
10252	550	16.9	2750	-	756	16.9
10253	550	16.9	2750	-	783	16.9
10254	550	16.4	2750	-	810	16.4
10255	550	16.4	2750	-	837	16.4
10256	550	16.4	2750	-	864	16.4
10257	550	16.4	2750	-	891	16.4
10098	600	17.9	3000	0.8	870	16.2
10352	550	16.0	2750	-	3456	16.0
10353	550	16.0	2750	-	3483	16.0
10354	550	16.0	2750	-	3510	16.0
10355	550	16.0	2750	-	3537	16.0
10356	550	16.0	2750	-	3564	16.0
10357	550	16.0	2750	-	3591	16.0
9693	750	22.3	3750	3.3	740	15.7
10083	600	18.4	3000	1.5	420	15.4
10084	600	18.4	3000	1.5	450	15.4
10085	600	18.4	3000	1.5	480	15.4
10086	600	18.4	3000	1.5	510	15.4
10087	600	18.4	3000	1.5	540	15.4
10088	600	18.4	3000	1.5	570	15.4
10422	500	15.3	2500	-	600	15.3
10423	500	15.3	2500	-	625	15.3
10424	500	15.3	2500	-	650	15.3
10425	500	15.3	2500	-	675	15.3
10426	500	15.3	2500	-	700	15.3
10427	500	15.3	2500	-	725	15.3
10428	500	15.3	2500	-	750	15.3
10429	500	15.3	2500	-	775	15.3
10430	500	15.3	2500	-	800	15.3
10431	500	15.3	2500	-	825	15.3
10258	550	16.4	2750	0.5	918	15.3
10432	500	14.9	2500	-	850	14.9
10433	500	14.9	2500	-	875	14.9
10434	500	14.9	2500	-	900	14.9
10435	500	14.9	2500	-	925	14.9
10436	500	14.9	2500	-	950	14.9
10536	500	14.5	2500	-	3450	14.5
10537	500	14.5	2500	-	3475	14.5
10538	500	14.5	2500	-	3500	14.5
10539	500	14.5	2500	-	3525	14.5
10540	500	14.5	2500	-	3550	14.5
10541	500	14.5	2500	-	3575	14.5
10542	500	14.5	2500	-	3600	14.5
10543	500	14.5	2500	-	3625	14.5
10240	550	17.7	2750	1.6	432	14.5
10755	450	14.2	2250	-	3674	14.2
9951	650	19.3	3250	2.6	832	14.1
10615	450	13.8	2250	-	594	13.8
10616	450	13.8	2250	-	616	13.8
10617	450	13.8	2250	-	638	13.8
10618	450	13.8	2250	-	660	13.8
10619	450	13.8	2250	-	682	13.8
10620	450	13.8	2250	-	704	13.8
10621	450	13.8	2250	-	726	13.8
10622	450	13.8	2250	-	748	13.8
10623	450	13.8	2250	-	770	13.8
10624	450	13.8	2250	-	792	13.8
10625	450	13.8	2250	-	814	13.8
10626	450	13.8	2250	-	836	13.8
10627	450	13.8	2250	-	858	13.8
10628	450	13.8	2250	-	880	13.8
10239	550	16.9	2750	1.6	405	13.6
10241	550	16.9	2750	1.6	459	13.6
10242	550	16.9	2750	1.6	486	13.6
10243	550	16.9	2750	1.6	513	13.6
10244	550	16.9	2750	1.6	540	13.6
10245	550	16.9	2750	1.6	567	13.6
9894	700	20.3	3500	3.4	3465	13.5
10629	450	13.4	2250	-	902	13.4
10630	450	13.4	2250	-	924	13.4
10631	450	13.4	2250	-	946	13.4
10632	450	13.4	2250	-	968	13.4
10633	450	13.4	2250	-	990	13.4
10634	450	13.4	2250	-	1012	13.4
10032	650	18.9	3250	2.8	3424	13.4
10754	450	13.2	2250	-	3652	13.2
10745	450	13.1	2250	-	3454	13.1
10746	450	13.1	2250	-	3476	13.1
10747	450	13.1	2250	-	3498	13.1
10748	450	13.1	2250	-	3520	13.1
10749	450	13.1	2250	-	3542	13.1
10750	450	13.1	2250	-	3564	13.1
10751	450	13.1	2250	-	3586	13.1
10752	450	13.1	2250	-	3608	13.1
10753	450	13.1	2250	-	3630	13.1
10990	400	12.7	2000	-	3680	12.7
10991	400	12.7	2000	-	3700	12.7
10992	400	12.7	2000	-	3720	12.7
10993	400	12.7	2000	-	3740	12.7
10416	500	16.2	2500	1.8	450	12.6
10417	500	16.2	2500	1.8	475	12.6
10415	500	16.1	2500	1.8	425	12.5
10836	400	12.3	2000	-	600	12.3
10837	400	12.3	2000	-	620	12.3
10838	400	12.3	2000	-	640	12.3
10839	400	12.3	2000	-	660	12.3
10840	400	12.3	2000	-	680	12.3
10841	400	12.3	2000	-	700	12.3
10842	400	12.3	2000	-	720	12.3
10843	400	12.3	2000	-	740	12.3
10844	400	12.3	2000	-	760	12.3
10845	400	12.3	2000	-	780	12.3
10846	400	12.3	2000	-	800	12.3
10847	400	12.3	2000	-	820	12.3
10848	400	12.3	2000	-	840	12.3
10849	400	12.3	2000	-	860	12.3
10850	400	12.3	2000	-	880	12.3
10851	400	12.3	2000	-	900	12.3
10852	400	12.3	2000	-	920	12.3
10756	450	14.2	2250	1.1	3696	12.0
10853	400	11.9	2000	-	940	11.9
10854	400	11.9	2000	-	960	11.9
10855	400	11.9	2000	-	980	11.9
10856	400	11.9	2000	-	1000	11.9
10857	400	11.9	2000	-	1020	11.9
10858	400	11.9	2000	-	1040	11.9
10859	400	11.9	2000	-	1060	11.9
10989	400	11.8	2000	-	3660	11.8
10418	500	15.3	2500	1.8	500	11.7
10419	500	15.3	2500	1.8	525	11.7
10420	500	15.3	2500	1.8	550	11.7
10421	500	15.3	2500	1.8	575	11.7
10979	400	11.6	2000	-	3460	11.6
10980	400	11.6	2000	-	3480	11.6
10981	400	11.6	2000	-	3500	11.6
10982	400	11.6	2000	-	3520	11.6
10983	400	11.6	2000	-	3540	11.6
10984	400	11.6	2000	-	3560	11.6
10985	400	11.6	2000	-	3580	11.6
10986	400	11.6	2000	-	3600	11.6
10987	400	11.6	2000	-	3620	11.6
10988	400	11.6	2000	-	3640	11.6
10351	550	16.0	2750	2.4	3429	11.3
10544	500	14.6	2500	1.8	3650	11.0
10437	500	14.9	2500	2.0	975	10.9
10978	400	11.6	2000	0.5	3440	10.6
10608	450	14.6	2250	2.0	440	10.6
10609	450	14.6	2250	2.0	462	10.6
10610	450	14.6	2250	2.0	484	10.6
10611	450	14.6	2250	2.0	506	10.6
10612	450	14.6	2250	2.0	528	10.6
10183	600	17.4	3000	3.7	3420	10.1
10414	500	14.7	2500	2.4	400	9.9
10607	450	13.9	2250	2.0	418	9.9
10613	450	13.8	2250	2.0	550	9.8
10614	450	13.8	2250	2.0	572	9.8
10008	650	18.2	3250	4.5	2656	9.2
10009	650	18.2	3250	4.6	2688	8.9
10035	650	17.8	3250	4.5	3520	8.8
10828	400	13.0	2000	2.2	440	8.5
10829	400	13.0	2000	2.2	460	8.5
10830	400	13.0	2000	2.2	480	8.5
10831	400	13.0	2000	2.2	500	8.5
10832	400	13.0	2000	2.2	520	8.5
10833	400	13.0	2000	2.2	540	8.5
10834	400	13.0	2000	2.2	560	8.5
10835	400	13.0	2000	2.2	580	8.5
10827	400	12.4	2000	2.2	420	7.9
10160	600	16.8	3000	4.5	2730	7.8
10826	400	11.8	2000	3.0	400	5.8
10635	450	13.4	2250	4.2	1034	4.9
10860	400	11.9	2000	3.8	1080	4.4

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
9278	950	28.3	4750	0.9	470	26.4
9372	900	26.8	4500	1.0	540	24.8
9276	950	26.8	4750	3.6	376	19.7
9268	950	26.7	4750	3.6	0	19.5
9269	950	26.7	4750	3.6	47	19.5
9270	950	26.7	4750	3.6	94	19.5
9271	950	26.7	4750	3.6	141	19.5
9272	950	26.7	4750	3.6	188	19.5
9273	950	26.7	4750	3.6	235	19.5
9274	950	26.7	4750	3.6	282	19.5
9275	950	26.7	4750	3.6	329	19.5
9368	900	25.4	4500	3.8	360	17.9
9360	900	25.3	4500	3.8	0	17.7
9361	900	25.3	4500	3.8	45	17.7
9362	900	25.3	4500	3.8	90	17.7
9363	900	25.3	4500	3.8	135	17.7
9364	900	25.3	4500	3.8	180	17.7
9365	900	25.3	4500	3.8	225	17.7
9366	900	25.3	4500	3.8	270	17.7
9367	900	25.3	4500	3.8	315	17.7
9466	850	24.0	4250	4.0	378	16.0
9457	850	23.9	4250	4.0	0	15.9
9458	850	23.9	4250	4.0	42	15.9
9459	850	23.9	4250	4.0	84	15.9
9460	850	23.9	4250	4.0	126	15.9
9461	850	23.9	4250	4.0	168	15.9
9462	850	23.9	4250	4.0	210	15.9
9463	850	23.9	4250	4.0	252	15.9
9464	850	23.9	4250	4.0	294	15.9
9465	850	23.9	4250	4.0	336	15.9
9571	800	22.6	4000	4.2	360	14.1
9562	800	22.5	4000	4.2	0	14.0
9563	800	22.5	4000	4.2	40	14.0
9564	800	22.5	4000	4.2	80	14.0
9565	800	22.5	4000	4.2	120	14.0
9566	800	22.5	4000	4.2	160	14.0
9567	800	22.5	4000	4.2	200	14.0
9568	800	22.5	4000	4.2	240	14.0
9569	800	22.5	4000	4.2	280	14.0
9570	800	22.5	4000	4.2	320	14.0
9683	750	21.2	3750	4.5	370	12.1
9806	700	19.8	3500	3.9	385	12.1
9673	750	21.1	3750	4.5	0	12.0
9674	750	21.1	3750	4.5	37	12.0
9675	750	21.1	3750	4.5	74	12.0
9676	750	21.1	3750	4.5	111	12.0
9677	750	21.1	3750	4.5	148	12.0
9678	750	21.1	3750	4.5	185	12.0
9679	750	21.1	3750	4.5	222	12.0
9680	750	21.1	3750	4.5	259	12.0
9681	750	21.1	3750	4.5	296	12.0
9682	750	21.1	3750	4.5	333	12.0
9805	700	19.8	3500	4.9	350	10.1
9795	700	19.7	3500	4.9	0	9.9
9796	700	19.7	3500	4.9	35	9.9
9797	700	19.7	3500	4.9	70	9.9
9798	700	19.7	3500	4.9	105	9.9
9799	700	19.7	3500	4.9	140	9.9
9800	700	19.7	3500	4.9	175	9.9
9801	700	19.7	3500	4.9	210	9.9
9802	700	19.7	3500	4.9	245	9.9
9803	700	19.7	3500	4.9	280	9.9
9804	700	19.7	3500	4.9	315	9.9
9937	650	18.4	3250	4.3	384	9.7
10082	600	16.9	3000	3.7	390	9.6
10744	450	13.1	2250	2.2	3432	8.6
10158	600	16.8	3000	4.5	2670	7.8
10159	600	16.8	3000	4.5	2700	7.8
10535	500	14.5	2500	3.4	3425	7.7
10188	600	16.4	3000	4.8	3570	6.7
10224	550	15.4	2750	4.5	0	6.4
10225	550	15.4	2750	4.5	27	6.4
10358	550	15.9	2750	4.9	3618	6.1
10606	450	13.0	2250	3.6	396	5.9
10323	550	15.4	2750	4.9	2673	5.5
10324	550	15.4	2750	4.9	2700	5.5
10325	550	15.4	2750	4.9	2727	5.5
10326	550	15.4	2750	4.9	2754	5.5
10327	550	15.4	2750	4.9	2781	5.5
10398	500	14.0	2500	5.0	0	4.0
10399	500	14.0	2500	5.0	25	4.0
10400	500	14.0	2500	5.0	50	4.0
10401	500	14.0	2500	5.0	75	4.0
10994	400	12.7	2000	4.8	3760	3.2

Overall score = score_ratio - 2 * repetitive DNA content