Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign31 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (208)
Redundant probes (53)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:24:12 2005`

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

Fetched probe design: ProbeDesign31
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 5
  id            : 6
  strand        : 1
  -------------

Design window length: 4998bp

All jobs for probe design are successful - total: 67
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1329 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        : 1329/1329
Putative probes exceeding selection criteria: 261/1329

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
4782	1000	30.1	5000	-	1800	30.1
4783	1000	30.1	5000	-	1850	30.1
4784	1000	30.1	5000	-	1900	30.1
4864	950	28.6	4750	-	1786	28.6
4865	950	28.6	4750	-	1833	28.6
4866	950	28.6	4750	-	1880	28.6
4867	950	28.6	4750	-	1927	28.6
4868	950	28.6	4750	0.2	1974	28.2
4781	1000	30.1	5000	1.3	1750	27.5
4953	900	27.1	4500	-	1800	27.1
4954	900	27.1	4500	-	1845	27.1
4955	900	27.1	4500	-	1890	27.1
4956	900	27.1	4500	-	1935	27.1
4957	900	27.1	4500	-	1980	27.1
4958	900	27.1	4500	0.3	2025	26.4
5047	850	25.6	4250	-	1764	25.6
5048	850	25.6	4250	-	1806	25.6
5049	850	25.6	4250	-	1848	25.6
5050	850	25.6	4250	-	1890	25.6
5051	850	25.6	4250	-	1932	25.6
5052	850	25.6	4250	-	1974	25.6
5053	850	25.6	4250	-	2016	25.6
5054	850	25.6	4250	-	2058	25.6
4952	900	27.1	4500	0.9	1755	25.3
4863	950	27.3	4750	1.6	1739	24.1
5149	800	24.1	4000	-	1800	24.1
5150	800	24.1	4000	-	1840	24.1
5151	800	24.1	4000	-	1880	24.1
5152	800	24.1	4000	-	1920	24.1
5153	800	24.1	4000	-	1960	24.1
5154	800	24.1	4000	-	2000	24.1
5155	800	24.1	4000	-	2040	24.1
5156	800	24.1	4000	-	2080	24.1
5157	800	24.1	4000	-	2120	24.1
5148	800	24.1	4000	0.4	1760	23.3
5257	750	22.6	3750	-	1776	22.6
5258	750	22.6	3750	-	1813	22.6
5259	750	22.6	3750	-	1850	22.6
5260	750	22.6	3750	-	1887	22.6
5261	750	22.6	3750	-	1924	22.6
5262	750	22.6	3750	-	1961	22.6
5263	750	22.6	3750	-	1998	22.6
5264	750	22.6	3750	-	2035	22.6
5265	750	22.6	3750	-	2072	22.6
5266	750	22.6	3750	-	2109	22.6
5267	750	22.6	3750	-	2146	22.6
4785	1000	25.6	5000	1.8	1950	22.0
4786	1000	25.6	5000	1.8	2000	22.0
4787	1000	25.6	5000	1.8	2050	22.0
4788	1000	25.6	5000	1.8	2100	22.0
5375	700	21.1	3500	-	1785	21.1
5376	700	21.1	3500	-	1820	21.1
5377	700	21.1	3500	-	1855	21.1
5378	700	21.1	3500	-	1890	21.1
5379	700	21.1	3500	-	1925	21.1
5380	700	21.1	3500	-	1960	21.1
5381	700	21.1	3500	-	1995	21.1
5382	700	21.1	3500	-	2030	21.1
5383	700	21.1	3500	-	2065	21.1
5384	700	21.1	3500	-	2100	21.1
5385	700	21.1	3500	-	2135	21.1
5386	700	21.1	3500	-	2170	21.1
5387	700	21.1	3500	-	2205	21.1
4872	950	24.4	4750	1.9	2162	20.6
5518	650	19.9	3250	-	2272	19.9
5268	750	22.6	3750	1.5	2183	19.7
5503	650	19.6	3250	-	1792	19.6
5504	650	19.6	3250	-	1824	19.6
5505	650	19.6	3250	-	1856	19.6
5506	650	19.6	3250	-	1888	19.6
5507	650	19.6	3250	-	1920	19.6
5508	650	19.6	3250	-	1952	19.6
5509	650	19.6	3250	-	1984	19.6
5510	650	19.6	3250	-	2016	19.6
5511	650	19.6	3250	-	2048	19.6
5512	650	19.6	3250	-	2080	19.6
5513	650	19.6	3250	-	2112	19.6
5514	650	19.6	3250	-	2144	19.6
5515	650	19.6	3250	-	2176	19.6
5516	650	19.6	3250	-	2208	19.6
5517	650	19.6	3250	-	2240	19.6
5415	700	21.6	3500	1.1	3185	19.3
5502	650	19.6	3250	0.5	1760	18.7
5658	600	18.4	3000	-	2250	18.4
5659	600	18.4	3000	-	2280	18.4
5660	600	18.4	3000	-	2310	18.4
5046	850	24.0	4250	2.8	1722	18.4
5295	750	23.1	3750	2.4	3182	18.3
5547	650	20.7	3250	1.2	3200	18.2
5642	600	18.1	3000	-	1770	18.1
5643	600	18.1	3000	-	1800	18.1
5644	600	18.1	3000	-	1830	18.1
5645	600	18.1	3000	-	1860	18.1
5646	600	18.1	3000	-	1890	18.1
5647	600	18.1	3000	-	1920	18.1
5648	600	18.1	3000	-	1950	18.1
5649	600	18.1	3000	-	1980	18.1
5650	600	18.1	3000	-	2010	18.1
5651	600	18.1	3000	-	2040	18.1
5652	600	18.1	3000	-	2070	18.1
5653	600	18.1	3000	-	2100	18.1
5654	600	18.1	3000	-	2130	18.1
5655	600	18.1	3000	-	2160	18.1
5656	600	18.1	3000	-	2190	18.1
5657	600	18.1	3000	-	2220	18.1
5296	750	23.1	3750	2.7	3219	17.8
5548	650	20.1	3250	1.2	3232	17.6
5256	750	21.6	3750	2.0	1739	17.6
5374	700	21.1	3500	1.9	1750	17.4
5059	850	21.8	4250	2.4	2268	17.1
5814	550	16.9	2750	-	2268	16.9
5815	550	16.9	2750	-	2295	16.9
5816	550	16.9	2750	-	2322	16.9
5817	550	16.9	2750	-	2349	16.9
5796	550	16.6	2750	-	1782	16.6
5797	550	16.6	2750	-	1809	16.6
5798	550	16.6	2750	-	1836	16.6
5799	550	16.6	2750	-	1863	16.6
5800	550	16.6	2750	-	1890	16.6
5801	550	16.6	2750	-	1917	16.6
5802	550	16.6	2750	-	1944	16.6
5803	550	16.6	2750	-	1971	16.6
5804	550	16.6	2750	-	1998	16.6
5805	550	16.6	2750	-	2025	16.6
5806	550	16.6	2750	-	2052	16.6
5807	550	16.6	2750	-	2079	16.6
5808	550	16.6	2750	-	2106	16.6
5809	550	16.6	2750	-	2133	16.6
5810	550	16.6	2750	-	2160	16.6
5811	550	16.6	2750	-	2187	16.6
5812	550	16.6	2750	-	2214	16.6
5813	550	16.6	2750	-	2241	16.6
5416	700	21.6	3500	2.6	3220	16.5
5417	700	21.6	3500	2.6	3255	16.5
5689	600	19.1	3000	1.3	3180	16.4
5690	600	19.1	3000	1.3	3210	16.4
5691	600	19.1	3000	1.3	3240	16.4
5692	600	19.1	3000	1.3	3270	16.4
5183	800	24.7	4000	4.1	3160	16.4
4780	1000	25.6	5000	4.6	1700	16.4
4951	900	24.3	4500	4.0	1710	16.3
5147	800	22.6	4000	3.2	1720	16.1
5546	650	20.7	3250	2.3	3168	16.1
5693	600	18.5	3000	1.3	3300	15.9
5966	500	15.6	2500	-	1775	15.6
5967	500	15.6	2500	-	1800	15.6
5818	550	16.9	2750	0.7	2376	15.4
5985	500	15.3	2500	-	2250	15.3
5986	500	15.3	2500	-	2275	15.3
5987	500	15.3	2500	-	2300	15.3
5988	500	15.3	2500	-	2325	15.3
5989	500	15.3	2500	-	2350	15.3
5990	500	15.3	2500	-	2375	15.3
5991	500	15.3	2500	-	2400	15.3
5848	550	18.1	2750	1.5	3186	15.2
5849	550	18.1	2750	1.5	3213	15.2
5968	500	15.1	2500	-	1825	15.1
5969	500	15.1	2500	-	1850	15.1
5970	500	15.1	2500	-	1875	15.1
5971	500	15.1	2500	-	1900	15.1
5972	500	15.1	2500	-	1925	15.1
5973	500	15.1	2500	-	1950	15.1
5974	500	15.1	2500	-	1975	15.1
5975	500	15.1	2500	-	2000	15.1
5976	500	15.1	2500	-	2025	15.1
5977	500	15.1	2500	-	2050	15.1
5978	500	15.1	2500	-	2075	15.1
5979	500	15.1	2500	-	2100	15.1
5980	500	15.1	2500	-	2125	15.1
5981	500	15.1	2500	-	2150	15.1
5982	500	15.1	2500	-	2175	15.1
5983	500	15.1	2500	-	2200	15.1
5984	500	15.1	2500	-	2225	15.1
5162	800	20.5	4000	2.8	2320	15.0
5850	550	17.5	2750	1.5	3240	14.6
5851	550	17.5	2750	1.5	3267	14.6
5852	550	17.5	2750	1.5	3294	14.6
5853	550	17.5	2750	1.5	3321	14.6
5549	650	20.1	3250	2.8	3264	14.5
5550	650	20.1	3250	2.8	3296	14.5
5795	550	17.2	2750	1.5	1755	14.3
5992	500	15.3	2500	0.6	2425	14.1
5854	550	17.0	2750	1.5	3348	14.1
6022	500	16.6	2500	1.6	3175	13.4
6023	500	16.6	2500	1.6	3200	13.4
6024	500	16.6	2500	1.6	3225	13.4
6025	500	16.4	2500	1.6	3250	13.2
5501	650	18.7	3250	2.8	1728	13.1
5414	700	22.3	3500	4.7	3150	12.9
6026	500	15.9	2500	1.6	3275	12.7
6027	500	15.9	2500	1.6	3300	12.7
6028	500	15.9	2500	1.6	3325	12.7
6029	500	15.9	2500	1.6	3350	12.7
6030	500	15.9	2500	1.6	3375	12.7
5694	600	18.5	3000	3.0	3330	12.5
5695	600	18.5	3000	3.0	3360	12.5
5641	600	17.2	3000	2.5	1740	12.2
6031	500	15.4	2500	1.6	3400	12.2
5373	700	19.4	3500	4.4	1715	10.6
5855	550	17.0	2750	3.3	3375	10.4
5856	550	17.0	2750	3.3	3402	10.4
5551	650	19.2	3250	4.5	3328	10.3
5965	500	15.4	2500	2.6	1750	10.2
5847	550	18.2	2750	4.4	3159	9.5
5794	550	15.8	2750	3.3	1728	9.3
6032	500	15.4	2500	3.6	3425	8.2
6033	500	15.4	2500	3.6	3450	8.2
5964	500	14.3	2500	4.2	1725	5.9

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
4869	950	24.4	4750	1.9	2021	20.6
4870	950	24.4	4750	1.9	2068	20.6
4871	950	24.4	4750	1.9	2115	20.6
4959	900	23.1	4500	2.0	2070	19.1
4960	900	23.1	4500	2.0	2115	19.1
4961	900	23.1	4500	2.0	2160	19.1
4962	900	23.1	4500	2.0	2205	19.1
5055	850	21.8	4250	2.1	2100	17.6
5056	850	21.8	4250	2.1	2142	17.6
5057	850	21.8	4250	2.1	2184	17.6
5058	850	21.8	4250	2.1	2226	17.6
5158	800	20.5	4000	2.2	2160	16.0
5159	800	20.5	4000	2.2	2200	16.0
5160	800	20.5	4000	2.2	2240	16.0
5161	800	20.5	4000	2.2	2280	16.0
5269	750	19.2	3750	2.4	2220	14.4
5270	750	19.2	3750	2.4	2257	14.4
5271	750	19.2	3750	2.4	2294	14.4
5272	750	19.2	3750	2.4	2331	14.4
5273	750	19.2	3750	2.7	2368	13.9
5388	700	18.0	3500	2.6	2240	12.9
5389	700	17.9	3500	2.6	2275	12.8
5390	700	17.9	3500	2.6	2310	12.8
5391	700	17.9	3500	2.6	2345	12.8
5392	700	17.9	3500	2.6	2380	12.8
5393	700	17.9	3500	2.6	2415	12.8
5519	650	16.7	3250	2.8	2304	11.1
5520	650	16.7	3250	2.8	2336	11.1
5521	650	16.7	3250	2.8	2368	11.1
5522	650	16.7	3250	2.8	2400	11.1
5523	650	16.7	3250	2.8	2432	11.1
5524	650	16.7	3250	2.8	2464	11.1
5661	600	15.5	3000	3.0	2340	9.5
5662	600	15.4	3000	3.0	2370	9.4
5663	600	15.4	3000	3.0	2400	9.4
5664	600	15.4	3000	3.0	2430	9.4
5665	600	15.4	3000	3.0	2460	9.4
5666	600	15.4	3000	3.0	2490	9.4
5667	600	15.4	3000	3.7	2520	8.1
5819	550	14.1	2750	3.3	2403	7.6
5820	550	14.1	2750	3.3	2430	7.6
5821	550	14.1	2750	3.3	2457	7.6
5822	550	14.1	2750	3.3	2484	7.6
5823	550	14.1	2750	3.3	2511	7.6
5824	550	14.1	2750	3.3	2538	7.6
5825	550	14.1	2750	3.3	2565	7.6
5993	500	12.8	2500	3.6	2450	5.6
5994	500	12.8	2500	3.6	2475	5.6
5995	500	12.8	2500	3.6	2500	5.6
5996	500	12.8	2500	3.6	2525	5.6
5997	500	12.8	2500	3.6	2550	5.6
5998	500	12.8	2500	3.6	2575	5.6
5999	500	12.8	2500	3.6	2600	5.6

Overall score = score_ratio - 2 * repetitive DNA content