Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign39 - back to list

Summary
Image
Unique putative probes (0)
Putative probes (146)
Redundant probes (2)

Summary

`./analyse_probe_search_results : Mon Sep 5 11:39:14 2005`

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

Fetched probe design: ProbeDesign39
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 15
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 28
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 557 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        : 557/557
Putative probes exceeding selection criteria: 148/557

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
19112	950	29.1	4750	-	0	29.1
19135	900	27.6	4500	-	0	27.6
19136	900	27.6	4500	-	45	27.6
19160	850	26.1	4250	-	0	26.1
19161	850	26.1	4250	-	42	26.1
19162	850	26.1	4250	-	84	26.1
19188	800	24.5	4000	-	0	24.5
19189	800	24.5	4000	-	40	24.5
19190	800	24.5	4000	-	80	24.5
19191	800	24.5	4000	-	120	24.5
19192	800	24.5	4000	-	160	24.5
19091	1000	30.7	5000	3.2	0	24.3
19163	850	26.1	4250	0.9	126	24.2
19113	950	29.1	4750	3.1	47	23.0
19219	750	23.0	3750	-	0	23.0
19220	750	23.0	3750	-	37	23.0
19221	750	23.0	3750	-	74	23.0
19222	750	23.0	3750	-	111	23.0
19223	750	23.0	3750	-	148	23.0
19224	750	23.0	3750	-	185	23.0
19137	900	27.6	4500	2.4	90	22.7
19225	750	23.0	3750	0.5	222	21.9
19253	700	21.5	3500	-	0	21.5
19254	700	21.5	3500	-	35	21.5
19255	700	21.5	3500	-	70	21.5
19256	700	21.5	3500	-	105	21.5
19257	700	21.5	3500	-	140	21.5
19258	700	21.5	3500	-	175	21.5
19259	700	21.5	3500	-	210	21.5
19260	700	21.5	3500	-	245	21.5
19291	650	19.9	3250	-	0	19.9
19292	650	19.9	3250	-	32	19.9
19293	650	19.9	3250	-	64	19.9
19294	650	19.9	3250	-	96	19.9
19295	650	19.9	3250	-	128	19.9
19296	650	19.9	3250	-	160	19.9
19297	650	19.9	3250	-	192	19.9
19298	650	19.9	3250	-	224	19.9
19299	650	19.9	3250	-	256	19.9
19300	650	19.9	3250	-	288	19.9
19301	650	19.9	3250	0.3	320	19.3
19335	600	18.4	3000	-	30	18.4
19336	600	18.4	3000	-	60	18.4
19337	600	18.4	3000	-	90	18.4
19338	600	18.4	3000	-	120	18.4
19339	600	18.4	3000	-	150	18.4
19340	600	18.4	3000	-	180	18.4
19341	600	18.4	3000	-	210	18.4
19342	600	18.4	3000	-	240	18.4
19343	600	18.4	3000	-	270	18.4
19344	600	18.4	3000	-	300	18.4
19345	600	18.4	3000	-	330	18.4
19346	600	18.4	3000	-	360	18.4
19261	700	21.5	3500	1.7	280	18.0
19383	550	18.0	2750	-	54	18.0
19384	550	16.9	2750	-	81	16.9
19385	550	16.9	2750	-	108	16.9
19386	550	16.9	2750	-	135	16.9
19387	550	16.9	2750	-	162	16.9
19388	550	16.9	2750	-	189	16.9
19389	550	16.9	2750	-	216	16.9
19390	550	16.9	2750	-	243	16.9
19391	550	16.9	2750	-	270	16.9
19392	550	16.9	2750	-	297	16.9
19393	550	16.9	2750	-	324	16.9
19394	550	16.9	2750	-	351	16.9
19395	550	16.9	2750	-	378	16.9
19396	550	16.9	2750	-	405	16.9
19432	550	16.8	2750	-	1377	16.8
19440	500	15.3	2500	-	125	15.3
19441	500	15.3	2500	-	150	15.3
19442	500	15.3	2500	-	175	15.3
19443	500	15.3	2500	-	200	15.3
19444	500	15.3	2500	-	225	15.3
19445	500	15.3	2500	-	250	15.3
19446	500	15.3	2500	-	275	15.3
19447	500	15.3	2500	-	300	15.3
19448	500	15.3	2500	-	325	15.3
19449	500	15.3	2500	-	350	15.3
19450	500	15.3	2500	-	375	15.3
19451	500	15.3	2500	-	400	15.3
19452	500	15.3	2500	-	425	15.3
19453	500	15.3	2500	-	450	15.3
19490	500	15.2	2500	-	1375	15.2
19491	500	15.2	2500	-	1400	15.2
19492	500	15.2	2500	-	1425	15.2
19503	450	14.7	2250	-	154	14.7
19138	900	24.2	4500	5.0	135	14.2
19504	450	13.8	2250	-	176	13.8
19505	450	13.8	2250	-	198	13.8
19506	450	13.8	2250	-	220	13.8
19507	450	13.8	2250	-	242	13.8
19508	450	13.8	2250	-	264	13.8
19509	450	13.8	2250	-	286	13.8
19510	450	13.8	2250	-	308	13.8
19511	450	13.8	2250	-	330	13.8
19512	450	13.8	2250	-	352	13.8
19513	450	13.8	2250	-	374	13.8
19514	450	13.8	2250	-	396	13.8
19515	450	13.8	2250	-	418	13.8
19516	450	13.8	2250	-	440	13.8
19517	450	13.8	2250	-	462	13.8
19518	450	13.8	2250	-	484	13.8
19519	450	13.8	2250	-	506	13.8
19559	450	13.7	2250	-	1386	13.7
19560	450	13.7	2250	-	1408	13.7
19561	450	13.7	2250	-	1430	13.7
19562	450	13.7	2250	-	1452	13.7
19563	450	13.7	2250	-	1474	13.7
19433	550	16.8	2750	1.8	1404	13.1
19493	500	15.2	2500	1.2	1450	12.8
19564	450	13.7	2250	0.4	1496	12.8
19454	500	15.3	2500	1.4	475	12.5
19578	400	12.3	2000	-	220	12.3
19579	400	12.3	2000	-	240	12.3
19580	400	12.3	2000	-	260	12.3
19581	400	12.3	2000	-	280	12.3
19582	400	12.3	2000	-	300	12.3
19583	400	12.3	2000	-	320	12.3
19584	400	12.3	2000	-	340	12.3
19585	400	12.3	2000	-	360	12.3
19586	400	12.3	2000	-	380	12.3
19587	400	12.3	2000	-	400	12.3
19588	400	12.3	2000	-	420	12.3
19589	400	12.3	2000	-	440	12.3
19590	400	12.3	2000	-	460	12.3
19591	400	12.3	2000	-	480	12.3
19592	400	12.3	2000	-	500	12.3
19593	400	12.3	2000	-	520	12.3
19636	400	12.2	2000	-	1380	12.2
19637	400	12.2	2000	-	1400	12.2
19638	400	12.2	2000	-	1420	12.2
19639	400	12.2	2000	-	1440	12.2
19640	400	12.2	2000	-	1460	12.2
19641	400	12.2	2000	-	1480	12.2
19642	400	12.2	2000	-	1500	12.2
19643	400	12.2	2000	-	1520	12.2
19644	400	12.2	2000	-	1540	12.2
19397	550	16.9	2750	2.5	432	11.8
19558	450	13.7	2250	1.8	1364	10.2
19520	450	13.8	2250	2.2	528	9.4
19379	600	18.3	3000	4.7	1350	9.0
19431	550	16.8	2750	4.0	1350	8.8
19489	500	15.2	2500	4.4	1350	6.4
19635	400	12.2	2000	3.0	1360	6.2
19645	400	12.2	2000	4.0	1560	4.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe ID	Length	Score ratio	Actual	%rep DNA	Distance	Overall
19193	800	24.5	4000	4.0	200	16.5
19347	600	18.4	3000	3.7	390	11.1

Overall score = score_ratio - 2 * repetitive DNA content