Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign124 - back to list

Summary

./analyse_probe_search_results : Thu Jun 29 10:00:49 2006

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

Fetched probe design: ProbeDesign124
  assembly      : NCBIM36
  bias          : 3prime
  chromosome    : 11
  id            : 118
  strand        : 1
  -------------

Design window length: 5001bp

All jobs for probe design are successful - total: 87
Fetched conf : Exonerate mouse_NCBIM36 (id: 2)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 1729 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            : 1729/1729
Putative probes that are unique                 : 111/1729
Putative probes exceeding selection criteria    : 264/1729 (both unique and not unique)
Putative probes with successfully-picked primers: 263/264

Identified 119 '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

Chart

Unique putative probes

Putative probe IDLengthActual%rep DNADistance
1100979004500-2565
1101938504250-2562
1101948504250-2604
1102958004000-2560
1102968004000-2600
1102978004000-2640
1102988004000-2680
1104077503750-2590
1104087503750-2627
1104097503750-2664
1104107503750-2701
1104117503750-2738
1105267003500-2590
1105277003500-2625
1105287003500-2660
1105297003500-2695
1105307003500-2730
1105317003500-2765
1106556503250-2560
1106566503250-2592
1106576503250-2624
1106586503250-2656
1106596503250-2688
1106606503250-2720
1106616503250-2752
1106626503250-2784
1106636503250-2816
1107456003000-1020
1107466003000-1050
1107976003000-2580
1107986003000-2610
1107996003000-2640
1108006003000-2670
1108016003000-2700
1108026003000-2730
1108036003000-2760
1108046003000-2790
1108056003000-2820
1108066003000-2850
1108076003000-2880
1108955502750-999
1108965502750-1026
1108975502750-1053
1108985502750-1080
1108995502750-1107
1109535502750-2565
1109545502750-2592
1109555502750-2619
1109565502750-2646
1109575502750-2673
1109585502750-2700
1109595502750-2727
1109605502750-2754
1109615502750-2781
1109625502750-2808
1109635502750-2835
1109645502750-2862
1109655502750-2889
1109665502750-2916
1110405002500-425
1110635002500-1000
1110645002500-1025
1110655002500-1050
1110665002500-1075
1110675002500-1100
1110685002500-1125
1110695002500-1150
1111265002500-2575
1111275002500-2600
1111285002500-2625
1111295002500-2650
1111305002500-2675
1111315002500-2700
1111325002500-2725
1111335002500-2750
1111345002500-2775
1111355002500-2800
1111365002500-2825
1111375002500-2850
1111385002500-2875
1111395002500-2900
1111405002500-2925
1111415002500-2950
1111425002500-2975
11060765032500.21024
11060665032500.3992
11107050025000.41175
11074460030000.7990
11096755027500.92943
11019585042500.92646
11074760030001.21080
11066465032501.52848
11053270035001.72800
11090055027502.01134
11103950025002.0400
11114350025002.43000
11009890045002.42610
11080860030003.72910
110856600300012.34350
110857600300012.34380
111019550275013.54347
111020550275013.54374
111021550275013.54401
111022550275013.54428
111197500250014.84350
111198500250014.84375
111199500250014.84400
111200500250014.84425
111201500250014.84450
111202500250014.84475
111203500250014.84500

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
109514130041.165002.1253537.0
109515130041.165002.6260035.9
109574125039.662502.2260435.2
109637120038.060002.2264033.5
109705115036.457502.3273631.7
109575125039.662504.0266631.6
11000795031.04750-253831.0
109775110034.855002.5275029.9
109771110034.855002.8253029.2
109850105033.252502.6280828.1
109776110034.855003.5280527.7
109635120033.160003.4252026.3
11040675025.03750-255325.0
11052570023.33500-255523.3
11009690024.945001.6252021.8
11019285023.542501.6252020.2
11079660020.03000-255020.0
11065465021.232500.9252819.4
11029480022.140001.8252018.6
11095255018.02750-253818.0
11048070023.035003.098017.0
11112550016.72500-255016.7
109701115025.857504.6250816.6
11052470019.335002.0252015.3
11040575018.737502.4251613.9
11112450016.325001.8252512.7
11079560016.630002.3252011.9
109922100019.050004.625009.8
11104150015.825003.44509.0
11089455016.427504.09728.4
11106250015.625003.89758.0
11000695015.947504.524916.8
11087355015.027504.94055.2
11095155012.727504.225114.3

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
109573125039.662502.2254235.2
109636120038.060002.2258033.5
109638120038.060002.8270032.3
109702115036.457502.3256531.7
109703115036.457502.3262231.7
109704115036.457502.3267931.7
109772110034.855002.5258529.9
109773110034.855002.5264029.9
109774110034.855002.5269529.9
109845105033.252502.6254828.1
109846105033.252502.6260028.1
109847105033.252502.6265228.1
109848105033.252502.6270428.1
109849105033.252502.6275628.1
109923100031.650002.7255026.2
109924100031.650002.7260026.2
109925100031.650002.7265026.2
109926100031.650002.7270026.2
109927100031.650002.7275026.2
109928100031.650002.7280026.2
109929100031.650002.7285026.2
109851105033.252504.2286024.8
109930100031.650003.4290024.8
11000895030.147502.8258524.4
11000995030.147502.8263224.4
11001095030.147502.8267924.4
11001195030.147502.8272624.4
11001295030.147502.8277324.4
11001395030.147502.8282024.4
11001495030.147502.8286724.4
11001595030.147502.8291424.4
11009990028.545003.0265522.5
11010090028.545003.0270022.5
11010190028.545003.0274522.5
11010290028.545003.0279022.5
11010390028.545003.0283522.5
11010490028.545003.0288022.5
11010590028.545003.0292522.5
11010690028.545003.0297022.5
11001695030.147504.7296120.6
11019685026.942503.2268820.5
11019785026.942503.2273020.5
11019885026.942503.2277220.5
11019985026.942503.2281420.5
11020085026.942503.2285620.5
11020185026.942503.2289820.5
11020285026.942503.2294020.5
11020385026.942503.2298220.5
11020485026.942503.2302420.5
11029980025.340003.4272018.6
11030080025.340003.4276018.6
11030180025.340003.4280018.6
11030280025.340003.4284018.6
11030380025.340003.4288018.6
11030480025.340003.4292018.6
11030580025.340003.4296018.6
11030680025.340003.4300018.6
11030780025.340003.4304018.6
11030880025.340003.4308018.6
11041275023.737503.6277516.5
11041375023.737503.6281216.5
11041475023.737503.6284916.5
11041575023.737503.6288616.5
11041675023.737503.6292316.5
11041775023.737503.6296016.5
11041875023.737503.6299716.5
11041975023.737503.6303416.5
11042075023.737503.6307116.5
11042175023.737503.6310816.5
11042275023.737503.9314516.0
11053370022.235003.9283514.4
11053470022.235003.9287014.4
11053570022.235003.9290514.4
11053670022.235003.9294014.4
11053770022.235003.9297514.4
11053870022.235003.9301014.4
11053970022.235003.9304514.4
11054070022.235003.9308014.4
11054170022.235003.9311514.4
11054270022.235003.9315014.4
11054370022.235003.9318514.4
11066565020.632504.2288012.3
11066665020.632504.2291212.3
11066765020.632504.2294412.3
11066865020.632504.2297612.3
11066965020.632504.2300812.3
11067065020.632504.2304012.3
11067165020.632504.2307212.3
11067265020.632504.2310412.3
11067365020.632504.2313612.3
11067465020.632504.2316812.3
11067565020.632504.2320012.3
11067665020.632504.2323212.3
11080960019.030004.5294010.0
11081060019.030004.5297010.0
11081160019.030004.5300010.0
11081260019.030004.5303010.0
11081360019.030004.5306010.0
11081460019.030004.5309010.0
11081560019.030004.5312010.0
11081660019.030004.5315010.0
11081760019.030004.5318010.0
11081860019.030004.5321010.0
11081960019.030004.5324010.0
11082060019.030004.5327010.0
11096855017.427504.929707.6
11096955017.427504.929977.6
11097055017.427504.930247.6
11097155017.427504.930517.6
11097255017.427504.930787.6
11097355017.427504.931057.6
11097455017.427504.931327.6
11097555017.427504.931597.6
11097655017.427504.931867.6
11097755017.427504.932137.6
11097855017.427504.932407.6
11097955017.427504.932677.6
11098055017.427504.932947.6
11098155017.427504.933217.6

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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