Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign42 - back to list

Summary

./analyse_probe_search_results : Tue Sep 13 14:29:52 2005

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

Fetched probe design: ProbeDesign42
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : X
  id            : 24
  strand        : 1
  -------------

Design window length: 3501bp

All jobs for probe design are successful - total: 56
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1114 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 5prime end of design window
  ------------------------

Putative probes without hits                : 0
Putative probes with single_self_hit        : 1114/1114
Putative probes exceeding selection criteria: 303/1114

PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW
--------------------------------------------------------------

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Chart

Unique putative probes

No probes

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
26207115035.75750-233735.7
26251110034.25500-236534.2
26206115035.157500.8228033.5
26250110034.255000.5231033.3
26297105032.65250-234032.6
26298105032.65250-239232.6
26299105032.65250-244432.6
26126125034.062500.7223232.5
26249110033.555000.8225531.9
26347100031.15000-235031.1
26348100031.15000-240031.1
26349100031.15000-245031.1
26089130033.565001.2214531.0
26125125032.262500.7217030.8
26350100031.150000.3250030.5
26296105032.052500.9228830.3
2640195029.54750-235029.5
2640295029.54750-239729.5
2640395029.54750-244429.5
2640495029.54750-249129.5
2640595029.54750-253829.5
26163120030.960000.8216029.4
26164120030.960000.8222029.4
26346100031.150000.9230029.3
26345100030.550000.9225028.7
26204115029.657500.8216628.1
26205115029.657500.8222328.1
2645890028.04500-234028.0
2645990028.04500-238528.0
2646090028.04500-243028.0
2646190028.04500-247528.0
2646290028.04500-252028.0
2646390028.04500-256528.0
26295105029.752500.9223627.9
2640095029.547500.9230327.6
26248110028.455000.8220026.7
2652185026.44250-239426.4
2652285026.44250-243626.4
2652385026.44250-247826.4
2652485026.44250-252026.4
2652585026.44250-256226.4
2652685026.44250-260426.4
2652785026.44250-264626.4
2651985027.442500.6231026.2
2652085026.24250-235226.2
2658680026.04000-232026.0
2658780025.84000-236025.8
2658880025.84000-240025.8
2648485025.84250-84025.8
2639995027.647500.9225625.7
26247110028.455001.5214525.4
2645690027.445001.0225025.4
2645790027.445001.0229525.4
26294105027.152500.9218425.3
2648585025.842500.288225.3
2658980024.84000-244024.8
2659080024.84000-248024.8
2659180024.84000-252024.8
2659280024.84000-256024.8
2659380024.84000-260024.8
2659480024.84000-264024.8
2659580024.84000-268024.8
2665975024.43750-233124.4
2666075024.43750-236824.4
2654980024.24000-84024.2
2655080024.24000-88024.2
2655180024.24000-92024.2
2666175024.23750-240524.2
2666275024.23750-244224.2
26344100025.850000.9220024.0
2651885025.942501.1226823.8
26124125032.262504.2210823.7
26343100025.850001.1215023.6
2666375023.33750-247923.3
2666475023.33750-251623.3
2666575023.33750-255323.3
2666675023.33750-259023.3
2666775023.33750-262723.3
2666875023.33750-266423.3
2666975023.33750-270123.3
2667075023.33750-273823.3
2673970023.23500-238023.2
2674070023.23500-241523.2
2674170023.23500-245023.2
26088130032.765004.8208023.0
2661975022.73750-85122.7
2662075022.73750-88822.7
2662175022.73750-92522.7
2662275022.73750-96222.7
2673870022.73500-234522.7
2639795024.547500.9216222.6
2639895024.547500.9220922.6
2674270022.63500-248522.6
2658580024.440001.1228022.1
2674370021.73500-252021.7
2674470021.73500-255521.7
2674570021.73500-259021.7
2674670021.73500-262521.7
2674770021.73500-266021.7
2674870021.73500-269521.7
2674970021.73500-273021.7
2675070021.73500-276521.7
2642590027.345002.885521.7
26293105027.152502.8213221.5
2682765021.53250-240021.5
2682865021.53250-243221.5
2682965021.53250-246421.5
2683065021.53250-249621.5
2673770022.735000.7231021.3
2669570021.23500-84021.2
2669670021.23500-87521.2
2669770021.23500-91021.2
2669870021.23500-94521.2
2669970021.23500-98021.2
2670070021.23500-101521.2
2645490023.245001.0216021.2
2645590023.245001.0220521.2
2682565021.13250-233621.1
2682665021.13250-236821.1
2658480023.340001.1224021.0
2683165021.03250-252821.0
26203115029.657504.5210920.6
2665775022.937501.2225720.5
2665875022.937501.2229420.5
2683365020.23250-259220.2
2683465020.23250-262420.2
2683565020.23250-265620.2
2683665020.23250-268820.2
2683765020.23250-272020.2
2683865020.23250-275220.2
2683965020.23250-278420.2
2684065020.23250-281620.2
2684165020.232500.2284819.9
2692260019.93000-240019.9
2692360019.93000-243019.9
2692460019.93000-246019.9
2692560019.93000-249019.9
2692660019.93000-252019.9
2692760019.93000-255019.9
2651685021.942501.1218419.8
2651785021.942501.1222619.8
2677965019.73250-86419.7
2678065019.73250-89619.7
2678165019.73250-92819.7
2678265019.73250-96019.7
2678365019.73250-99219.7
2678465019.73250-102419.7
2678565019.73250-105619.7
2692060019.53000-234019.5
2692160019.53000-237019.5
2692860019.43000-258019.4
2673670021.335001.3227518.8
2683265018.73250-256018.7
2693060018.63000-264018.6
2693160018.63000-267018.6
2693260018.63000-270018.6
2693360018.63000-273018.6
2693460018.63000-276018.6
2693560018.63000-279018.6
2693660018.63000-282018.6
2693760018.63000-285018.6
2693860018.63000-288018.6
2658280020.640001.1216018.4
2658380020.640001.1220018.4
2682465021.132501.4230418.3
2702755018.22750-237618.2
2702855018.22750-240318.2
2702955018.22750-243018.2
2703055018.22750-245718.2
2703155018.22750-248418.2
2703255018.22750-251118.2
2703355018.22750-253818.2
2703455018.22750-256518.2
2703555018.22750-259218.2
2687060018.23000-84018.2
2687160018.23000-87018.2
2687260018.23000-90018.2
2687360018.23000-93018.2
2687460018.23000-96018.2
2687560018.23000-99018.2
2687660018.23000-102018.2
2687760018.23000-105018.2
2687860018.23000-108018.2
2687960018.23000-111018.2
2702555017.92750-232217.9
2702655017.92750-234917.9
2691960019.530000.8231017.8
2673570020.335001.3224017.8
2703655017.72750-261917.7
2703755017.72750-264617.7
2662375022.737502.599917.7
2651585021.942502.2214217.4
2692960017.23000-261017.2
2677865019.732501.283217.2
2678665019.732501.2108817.2
2703855017.12750-267317.1
2703955017.12750-270017.1
2704055017.12750-272717.1
2704155017.12750-275417.1
2704255017.12750-278117.1
2704355017.12750-280817.1
2704455017.12750-283517.1
2704555017.12750-286217.1
2704655017.12750-288917.1
2704755017.12750-291617.1
2704855017.12750-294317.1
2682365019.832501.4227217.0
2665575019.337501.2218316.9
2665675019.337501.2222016.9
2655280024.240003.896016.7
2697155016.72750-86416.7
2697255016.72750-89116.7
2697355016.72750-91816.7
2697455016.72750-94516.7
2697555016.72750-97216.7
2697655016.72750-99916.7
2697755016.72750-102616.7
2697855016.72750-105316.7
2697955016.72750-108016.7
2698055016.72750-110716.7
2698155016.72750-113416.7
2698255016.72750-116116.7
2714450016.62500-237516.6
2714550016.62500-240016.6
2714650016.62500-242516.6
2714750016.62500-245016.6
2714850016.62500-247516.6
2714950016.62500-250016.6
2715050016.62500-252516.6
2715150016.62500-255016.6
2715250016.62500-257516.6
2715350016.62500-260016.6
2715450016.62500-262516.6
2715550016.62500-265016.6
2714250016.22500-232516.2
2714350016.22500-235016.2
2642490022.445003.181016.2
2715650016.12500-267516.1
2715750016.12500-270016.1
2682265018.932501.4224016.1
2697055016.727500.583715.6
2715850015.52500-272515.5
2715950015.52500-275015.5
2716050015.52500-277515.5
2716150015.52500-280015.5
2716250015.52500-282515.5
2716350015.52500-285015.5
2716450015.52500-287515.5
2716550015.52500-290015.5
2716650015.52500-292515.5
2716750015.52500-295015.5
2716850015.52500-297515.5
2673370018.035001.3217015.5
2673470018.035001.3220515.5
2665475019.337502.0214615.3
2691760018.330001.5225015.3
2691860018.330001.5228015.3
2708350015.22500-85015.2
2708450015.22500-87515.2
2708550015.22500-90015.2
2708650015.22500-92515.2
2708750015.22500-95015.2
2708850015.22500-97515.2
2708950015.22500-100015.2
2709050015.22500-102515.2
2709150015.22500-105015.2
2709250015.22500-107515.2
2709350015.22500-110015.2
2709450015.22500-112515.2
2709550015.22500-115015.2
2709650015.22500-117515.2
2688060018.230001.7114014.8
2639695024.547504.8211514.8
2682065016.832501.4217614.0
2682165016.832501.4220814.0
2702355016.827501.6226813.5
2702455016.827501.6229513.5
2702255016.327501.6224113.0
2714150016.225001.8230012.6
2691460015.530001.5216012.5
2691560015.530001.5219012.5
2691660015.530001.5222012.5
2648385021.142504.779811.7
2713950015.225001.8225011.6
2714050015.225001.8227511.6
2681965016.832502.6214411.5
2701955014.227501.6216010.9
2702055014.227501.6218710.9
2702155014.227501.6221410.9
2673270018.035003.7213510.6
2713650012.925001.821759.3
2713750012.925001.822009.3
2713850012.925001.822259.3
2708250015.225003.08259.2
2713550012.925002.221508.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
26165120036.660000.8228035.1
2675170021.735000.4280020.9
2670170021.235002.9105015.5
2716950015.525000.6300014.3
2661875018.737503.281412.3
2654880019.940004.880010.4
2669470017.435004.78058.0
2686960014.930004.78105.6

Overall score = score_ratio - 2 * repetitive DNA content

© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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