Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign82 - back to list

Summary

./analyse_probe_search_results : Wed Nov 9 09:32:47 2005

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

Fetched probe design: ProbeDesign82
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 1
  id            : 73
  strand        : 1
  -------------

Design window length: 2501bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 699 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            : 699/699
Putative probes that are unique                 : 273/699
Putative probes exceeding selection criteria    : 492/699 (both unique and not unique)
Putative probes with successfully-picked primers: 490/492

Identified 30 '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
688428504250-798
688838004000-800
688848004000-840
689277503750-777
689287503750-814
689297503750-851
689307503750-888
689777003500-805
689787003500-840
689797003500-875
689807003500-910
689817003500-945
690316503250-800
690326503250-832
690336503250-864
690346503250-896
690356503250-928
690366503250-960
690376503250-992
690906003000-780
690916003000-810
690926003000-840
690936003000-870
690946003000-900
690956003000-930
690966003000-960
690976003000-990
690986003000-1020
690996003000-1050
691575502750-783
691585502750-810
691595502750-837
691605502750-864
691615502750-891
691625502750-918
691635502750-945
691645502750-972
691655502750-999
691665502750-1026
691675502750-1053
691685502750-1080
691695502750-1107
692095002500-200
692325002500-775
692335002500-800
692345002500-825
692355002500-850
692365002500-875
692375002500-900
692385002500-925
692395002500-950
692405002500-975
692415002500-1000
692425002500-1025
692435002500-1050
692445002500-1075
692455002500-1100
692465002500-1125
692475002500-1150
6897670035000.6770
6903065032500.9768
6880490045001.0765
6921050025001.6225
6888280040001.8760
6884185042502.1756
6915655027503.3756
6908960030004.0750
6913555027504.0189
68586130065004.4195
68587130065004.4260
68588130065004.4325
6892675037504.5740
68605125062504.6186
68606125062504.6248
68607125062504.6310
68608125062504.6372
68626120060004.8180
68627120060004.8240
68628120060004.8300
68629120060004.8360
68630120060004.8420
6923150025004.8750
68649115057505.0228
68650115057505.0285
68651115057505.0342
68652115057505.0399
68653115057505.0456
68654115057505.0513
68673110055005.2220
68674110055005.2275
68675110055005.2330
68676110055005.2385
68677110055005.2440
68678110055005.2495
68679110055005.2550
68699105052505.4208
68700105052505.4260
68701105052505.4312
68702105052505.4364
68703105052505.4416
68704105052505.4468
68705105052505.4520
68706105052505.4572
6897570035005.6735
68727100050005.7200
68728100050005.7250
68729100050005.7300
68730100050005.7350
68731100050005.7400
68732100050005.7450
68733100050005.7500
68734100050005.7550
68735100050005.7600
68736100050005.7650
6902965032505.8736
6875895047506.0188
6875995047506.0235
6876095047506.0282
6876195047506.0329
6876295047506.0376
6876395047506.0423
6876495047506.0470
6876595047506.0517
6876695047506.0564
6876795047506.0611
6876895047506.0658
6876995047506.0705
6880390045006.0720
6879190045006.3180
6879290045006.3225
6879390045006.3270
6879490045006.3315
6879590045006.3360
6879690045006.3405
6879790045006.3450
6879890045006.3495
6879990045006.3540
6880090045006.3585
6880190045006.3630
6880290045006.3675
6921150025006.6250
6882885042506.7210
6882985042506.7252
6883085042506.7294
6883185042506.7336
6883285042506.7378
6883385042506.7420
6883485042506.7462
6883585042506.7504
6883685042506.7546
6883785042506.7588
6883885042506.7630
6883985042506.7672
6884085042506.7714
6888180040006.8720
6886880040007.1200
6886980040007.1240
6887080040007.1280
6887180040007.1320
6887280040007.1360
6887380040007.1400
6887480040007.1440
6887580040007.1480
6887680040007.1520
6887780040007.1560
6887880040007.1600
6887980040007.1640
6888080040007.1680
6891175037507.6185
6891275037507.6222
6891375037507.6259
6891475037507.6296
6891575037507.6333
6891675037507.6370
6891775037507.6407
6891875037507.6444
6891975037507.6481
6892075037507.6518
6892175037507.6555
6892275037507.6592
6892375037507.6629
6892475037507.6666
6892575037507.6703
6896070035008.1210
6896170035008.1245
6896270035008.1280
6896370035008.1315
6896470035008.1350
6896570035008.1385
6896670035008.1420
6896770035008.1455
6896870035008.1490
6896970035008.1525
6897070035008.1560
6897170035008.1595
6897270035008.1630
6897370035008.1665
6897470035008.1700
6915555027508.2729
6901265032508.8192
6901365032508.8224
6901465032508.8256
6901565032508.8288
6901665032508.8320
6901765032508.8352
6901865032508.8384
6901965032508.8416
6902065032508.8448
6902165032508.8480
6902265032508.8512
6902365032508.8544
6902465032508.8576
6902565032508.8608
6902665032508.8640
6902765032508.8672
6902865032508.8704
6913655027508.9216
6908860030009.0720
6907060030009.5180
6907160030009.5210
6907260030009.5240
6907360030009.5270
6907460030009.5300
6907560030009.5330
6907660030009.5360
6907760030009.5390
6907860030009.5420
6907960030009.5450
6908060030009.5480
6908160030009.5510
6908260030009.5540
6908360030009.5570
6908460030009.5600
6908560030009.5630
6908660030009.5660
6908760030009.5690
6923050025009.8725
69137550275010.4243
69138550275010.4270
69139550275010.4297
69140550275010.4324
69141550275010.4351
69142550275010.4378
69143550275010.4405
69144550275010.4432
69145550275010.4459
69146550275010.4486
69147550275010.4513
69148550275010.4540
69149550275010.4567
69150550275010.4594
69151550275010.4621
69152550275010.4648
69153550275010.4675
69154550275010.4702
69212500250011.4275
69213500250011.4300
69214500250011.4325
69215500250011.4350
69216500250011.4375
69217500250011.4400
69218500250011.4425
69219500250011.4450
69220500250011.4475
69221500250011.4500
69222500250011.4525
69223500250011.4550
69224500250011.4575
69225500250011.4600
69226500250011.4625
69227500250011.4650
69228500250011.4675
69229500250011.4700

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
68595130038.065000.778036.6
68615125036.56250-80636.5
68636120035.16000-78035.1
68637120035.16000-84035.1
68583130043.065004.4034.3
68584130043.065004.46534.3
68585130043.065004.413034.3
68659115033.65750-79833.6
68660115033.65750-85533.6
68661115033.65750-91233.6
68603125041.462504.66232.3
68604125041.462504.612432.3
68684110032.25500-82532.2
68685110032.25500-88032.2
68686110032.25500-93532.2
68614125036.562502.474431.7
68683110032.255000.477031.4
68589130040.165004.439031.4
68710105030.75250-78030.7
68711105030.75250-83230.7
68712105030.75250-88430.7
68713105030.75250-93630.7
68714105030.75250-98830.7
68638120035.160002.490030.3
68590130038.065004.445529.2
68591130038.065004.452029.2
68592130038.065004.458529.2
68593130038.065004.465029.2
68594130038.065004.471529.2
68739100029.25000-80029.2
68740100029.25000-85029.2
68741100029.25000-90029.2
68742100029.25000-95029.2
68743100029.25000-100029.2
68744100029.25000-105029.2
68687110032.255001.799028.7
68658115033.657502.974127.9
6877195027.84750-79927.8
6880590027.84500-81027.8
6877295027.84750-84627.8
6877395027.84750-89327.8
6877495027.84750-94027.8
6877595027.84750-98727.8
6877695027.84750-103427.8
6877795027.84750-108127.8
68715105030.752501.8104027.1
6880690026.34500-85526.3
6880790026.34500-90026.3
6880890026.34500-94526.3
6880990026.34500-99026.3
6881090026.34500-103526.3
6881190026.34500-108026.3
6881290026.34500-112526.3
6881390026.34500-117026.3
6884385026.24250-84026.2
6884485026.24250-88226.2
6888580025.24000-88025.2
6884585024.94250-92424.9
6884685024.94250-96624.9
6884785024.94250-100824.9
6884885024.94250-105024.9
6884985024.94250-109224.9
6885085024.94250-113424.9
6885185024.94250-117624.9
6885285024.94250-121824.9
6888680024.74000-92024.7
6877095029.347502.375224.7
6893175024.53750-92524.5
68738100029.250002.475024.4
68745100029.250002.9110023.4
6888780023.44000-96023.4
6888880023.44000-100023.4
6888980023.44000-104023.4
6889080023.44000-108023.4
6889180023.44000-112023.4
6889280023.44000-116023.4
6889380023.44000-120023.4
6889480023.44000-124023.4
6895470023.23500-023.2
6893275023.13750-96223.1
68616125030.062503.886822.5
6898270022.03500-98022.0
68709105030.752504.472821.9
6893375021.93750-99921.9
6893475021.93750-103621.9
6893575021.93750-107321.9
6893675021.93750-111021.9
6893775021.93750-114721.9
6893875021.93750-118421.9
6893975021.93750-122121.9
6894075021.93750-125821.9
6894175021.93750-129521.9
6903865021.73250-102421.7
6898370021.63500-101521.6
6900665021.53250-021.5
6900765021.53250-3221.5
6900865021.53250-6421.5
6898470020.53500-105020.5
6898570020.53500-108520.5
6898670020.53500-112020.5
6898770020.53500-115520.5
6898870020.53500-119020.5
6898970020.53500-122520.5
6899070020.53500-126020.5
6899170020.53500-129520.5
6899270020.53500-133020.5
6899370020.53500-136520.5
6903965020.13250-105620.1
6906460019.93000-019.9
6906560019.93000-3019.9
6906660019.93000-6019.9
6906760019.93000-9019.9
68662115027.657504.296919.3
6904065019.03250-108819.0
6904165019.03250-112019.0
6904265019.03250-115219.0
6904365019.03250-118419.0
6904465019.03250-121619.0
6904565019.03250-124819.0
6904665019.03250-128019.0
6904765019.03250-131219.0
6904865019.03250-134419.0
6904965019.03250-137619.0
6905065019.03250-140819.0
6894275021.937501.5133219.0
6910060018.93000-108018.9
6906860019.930000.512018.9
6910160018.53000-111018.5
6912855018.22750-018.2
6912955018.22750-2718.2
6913055018.22750-5418.2
6913155018.22750-8118.2
6913255018.22750-10818.2
6913355018.22750-13518.2
6913455018.22750-16218.2
6895570023.235002.63518.0
6910260017.53000-114017.5
6910360017.53000-117017.5
6910460017.53000-120017.5
6910560017.53000-123017.5
6910660017.53000-126017.5
6910760017.53000-129017.5
6910860017.53000-132017.5
6910960017.53000-135017.5
6911060017.53000-138017.5
6911160017.53000-141017.5
6911260017.53000-144017.5
6911360017.53000-147017.5
6917055017.02750-113417.0
6917155017.02750-116117.0
6920150016.62500-016.6
6920250016.62500-2516.6
6920350016.62500-5016.6
6920450016.62500-7516.6
6920550016.62500-10016.6
6920650016.62500-12516.6
6920750016.62500-15016.6
6920850016.62500-17516.6
6924850016.32500-117516.3
6917255016.12750-118816.1
6917355016.12750-121516.1
6917455016.12750-124216.1
6917555016.12750-126916.1
6917655016.12750-129616.1
6917755016.12750-132316.1
6917855016.12750-135016.1
6917955016.12750-137716.1
6918055016.12750-140416.1
6918155016.12750-143116.1
6918255016.12750-145816.1
6918355016.12750-148516.1
6918455016.12750-151216.1
6924950015.42500-120015.4
6925050015.42500-122515.4
6925150014.62500-125014.6
6925250014.62500-127514.6
6925350014.62500-130014.6
6925450014.62500-132514.6
6925550014.62500-135014.6
6925650014.62500-137514.6
6925750014.62500-140014.6
6925850014.62500-142514.6
6925950014.62500-145014.6
6926050014.62500-147514.6
6926150014.62500-150014.6
6926250014.62500-152514.6
6926350014.62500-155014.6
6905165019.032502.9144013.2
6918555016.127503.315399.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
68602125041.462504.6032.3
68623120039.760004.8030.2
68624120039.760004.86030.2
68625120039.760004.812030.2
68609125038.662504.643429.5
68631120037.760004.848028.2
68645115038.157505.0028.2
68646115038.157505.05728.2
68647115038.157505.011428.2
68648115038.157505.017128.2
68610125036.562504.649627.4
68611125036.562504.655827.4
68612125036.562504.662027.4
68613125036.562504.668227.4
6877895027.847500.7112826.3
68635120035.160004.572026.1
68632120035.160004.854025.6
68633120035.160004.860025.6
68634120035.160004.866025.6
68655115035.557505.057025.6
68656115033.657505.062723.7
68657115033.657505.068423.7
6889580023.440001.1128021.1
6890675024.837504.4016.0
6926450014.625000.8157513.0
6900965021.532504.59612.6
6881490022.245004.9121512.4
6899470020.535004.1140012.2
6885385021.142504.6126012.0
6911460017.530004.815007.9

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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