Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign102 - back to list

Summary

./analyse_probe_search_results : Tue Jan 31 11:33:29 2006

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

Fetched probe design: ProbeDesign102
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 11
  id            : 93
  strand        : 1
  -------------

Design window length: 2046bp

All jobs for probe design are successful - total: 26
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 512 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            : 512/512
Putative probes that are unique                 : 300/512
Putative probes exceeding selection criteria    : 512/512 (both unique and not unique)
Putative probes with successfully-picked primers: 512/512

Identified 177 '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
8821813006500-0
8821913006500-65
8822013006500-130
8822113006500-195
8823012506250-0
8823112506250-62
8823212506250-124
8823312506250-186
8823412506250-248
8824312006000-0
8824412006000-60
8824512006000-120
8824612006000-180
8824712006000-240
8824812006000-300
8825811505750-0
8825911505750-57
8826011505750-114
8826111505750-171
8826211505750-228
8826311505750-285
8826411505750-342
8827411005500-0
8827511005500-55
8827611005500-110
8827711005500-165
8827811005500-220
8827911005500-275
8828011005500-330
8828111005500-385
8829210505250-0
8829310505250-52
8829410505250-104
8829510505250-156
8829610505250-208
8829710505250-260
8829810505250-312
8829910505250-364
8830010505250-416
8830110505250-468
8831210005000-0
8831310005000-50
8831410005000-100
8831510005000-150
8831610005000-200
8831710005000-250
8831810005000-300
8831910005000-350
8832010005000-400
8832110005000-450
8832210005000-500
883339504750-0
883349504750-47
883359504750-94
883369504750-141
883379504750-188
883389504750-235
883399504750-282
883409504750-329
883419504750-376
883429504750-423
883439504750-470
883449504750-517
883459504750-564
883579004500-0
883589004500-45
883599004500-90
883609004500-135
883619004500-180
883629004500-225
883639004500-270
883649004500-315
883659004500-360
883669004500-405
883679004500-450
883689004500-495
883699004500-540
883709004500-585
883719004500-630
883838504250-0
883848504250-42
883858504250-84
883868504250-126
883878504250-168
883888504250-210
883898504250-252
883908504250-294
883918504250-336
883928504250-378
883938504250-420
883948504250-462
883958504250-504
883968504250-546
883978504250-588
883988504250-630
883998504250-672
884128004000-0
884138004000-40
884148004000-80
884158004000-120
884168004000-160
884178004000-200
884188004000-240
884198004000-280
884208004000-320
884218004000-360
884228004000-400
884238004000-440
884248004000-480
884258004000-520
884268004000-560
884278004000-600
884288004000-640
884298004000-680
884308004000-720
884447503750-0
884457503750-37
884467503750-74
884477503750-111
884487503750-148
884497503750-185
884507503750-222
884517503750-259
884527503750-296
884537503750-333
884547503750-370
884557503750-407
884567503750-444
884577503750-481
884587503750-518
884597503750-555
884607503750-592
884617503750-629
884627503750-666
884637503750-703
884647503750-740
884657503750-777
884807003500-0
884817003500-35
884827003500-70
884837003500-105
884847003500-140
884857003500-175
884867003500-210
884877003500-245
884887003500-280
884897003500-315
884907003500-350
884917003500-385
884927003500-420
884937003500-455
884947003500-490
884957003500-525
884967003500-560
884977003500-595
884987003500-630
884997003500-665
885007003500-700
885017003500-735
885027003500-770
885037003500-805
885196503250-0
885206503250-32
885216503250-64
885226503250-96
885236503250-128
885246503250-160
885256503250-192
885266503250-224
885276503250-256
885286503250-288
885296503250-320
885306503250-352
885316503250-384
885326503250-416
885336503250-448
885346503250-480
885356503250-512
885366503250-544
885376503250-576
885386503250-608
885396503250-640
885406503250-672
885416503250-704
885426503250-736
885436503250-768
885446503250-800
885456503250-832
885466503250-864
885636003000-0
885646003000-30
885656003000-60
885666003000-90
885676003000-120
885686003000-150
885696003000-180
885706003000-210
885716003000-240
885726003000-270
885736003000-300
885746003000-330
885756003000-360
885766003000-390
885776003000-420
885786003000-450
885796003000-480
885806003000-510
885816003000-540
885826003000-570
885836003000-600
885846003000-630
885856003000-660
885866003000-690
885876003000-720
885886003000-750
885896003000-780
885906003000-810
885916003000-840
885926003000-870
885936003000-900
885946003000-930
886125502750-0
886135502750-27
886145502750-54
886155502750-81
886165502750-108
886175502750-135
886185502750-162
886195502750-189
886205502750-216
886215502750-243
886225502750-270
886235502750-297
886245502750-324
886255502750-351
886265502750-378
886275502750-405
886285502750-432
886295502750-459
886305502750-486
886315502750-513
886325502750-540
886335502750-567
886345502750-594
886355502750-621
886365502750-648
886375502750-675
886385502750-702
886395502750-729
886405502750-756
886415502750-783
886425502750-810
886435502750-837
886445502750-864
886455502750-891
886465502750-918
886475502750-945
886485502750-972
886685002500-0
886695002500-25
886705002500-50
886715002500-75
886725002500-100
886735002500-125
886745002500-150
886755002500-175
886765002500-200
886775002500-225
886785002500-250
886795002500-275
886805002500-300
886815002500-325
886825002500-350
886835002500-375
886845002500-400
886855002500-425
886865002500-450
886875002500-475
886885002500-500
886895002500-525
886905002500-550
886915002500-575
886925002500-600
886935002500-625
886945002500-650
886955002500-675
886965002500-700
886975002500-725
886985002500-750
886995002500-775
887005002500-800
887015002500-825
887025002500-850
887035002500-875
887045002500-900
887055002500-925
887065002500-950
887075002500-975
887085002500-1000
887095002500-1025

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
88222130043.065000.726041.7
88265115038.157500.639936.9
88282110036.45500-44036.4
88266115035.757500.845634.1
88223130037.665001.832534.0
88250120037.360001.742033.9
88236125037.262501.837233.7
88224130036.765001.839033.2
88225130036.765001.845533.2
88226130036.765001.852033.2
88227130036.765001.858533.2
88228130036.765001.865033.2
88229130036.765001.871533.2
88302105034.852500.952033.1
88283110034.655000.849533.0
88257120033.960001.984030.1
88324100031.450000.960029.6
8834695031.547500.961129.6
8837290029.845001.067527.8
8834795029.547500.965827.6
8840085028.142501.171426.0
8840185026.442501.175624.3
8850470023.23500-84023.2
8843280025.240001.180022.9
8846675024.837501.281422.4
8846775023.637501.285121.2
8850570023.235001.387520.6
8854765021.532500.689620.3
8850670021.735001.491018.9
8854865021.532501.492818.8
8854965020.232501.596017.1
8859660019.930001.599016.9
8847975021.237503.1129515.1
8865055018.227501.6102614.9
8865155017.327501.6105314.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
88235125041.462500.731040.0
88249120039.760000.836038.2
88237125035.362501.843431.6
88238125035.362501.849631.6
88239125035.362501.855831.6
88240125035.362501.862031.6
88241125035.362501.868231.6
88242125035.362501.874431.6
88323100033.150000.855031.5
88251120033.960001.948030.1
88252120033.960001.954030.1
88253120033.960001.960030.1
88254120033.960001.966030.1
88255120033.960001.972030.1
88256120033.960001.978030.1
88267115032.557502.051328.5
88268115032.557502.057028.5
88269115032.557502.062728.5
88270115032.557502.068428.5
88271115032.557502.074128.5
88272115032.557502.079828.5
88273115032.557502.085528.5
88303105031.252502.157227.1
88284110031.155002.155026.9
88285110031.155002.160526.9
88286110031.155002.166026.9
88287110031.155002.171526.9
88288110031.155002.177026.9
88289110031.155002.182526.9
88290110031.155002.188026.9
88291110031.155002.193526.9
88304105029.752502.262425.3
88305105029.752502.267625.3
88306105029.752502.272825.3
88307105029.752502.278025.3
88308105029.752502.283225.3
88309105029.752502.288425.3
88310105029.752502.293625.3
88311105029.752502.298825.3
8843180026.540001.176024.2
88325100028.250002.365023.6
88326100028.250002.370023.6
88327100028.250002.375023.6
88328100028.250002.380023.6
88329100028.250002.385023.6
88330100028.250002.390023.6
88331100028.250002.395023.6
88332100028.250002.3100023.6
8837390028.045002.272023.5
8834895026.847502.470522.0
8834995026.847502.475222.0
8835095026.847502.479922.0
8835195026.847502.484622.0
8835295026.847502.489322.0
8835395026.847502.494022.0
8835495026.847502.498722.0
8835595026.847502.4103422.0
8835695026.847502.4108122.0
8837490025.445002.676520.3
8837590025.445002.681020.3
8837690025.445002.685520.3
8837790025.445002.690020.3
8837890025.445002.694520.3
8837990025.445002.699020.3
8838090025.445002.6103520.3
8838190025.445002.6108020.3
8838290025.445002.6112520.3
8840285024.042502.779818.6
8840385024.042502.784018.6
8840485024.042502.788218.6
8840585024.042502.792418.6
8840685024.042502.796618.6
8840785024.042502.7100818.6
8840885024.042502.7105018.6
8840985024.042502.7109218.6
8841085024.042502.7113418.6
8841185024.042502.7117618.6
8859560019.930001.596016.9
8843380022.640002.984016.8
8843480022.640002.988016.8
8843580022.640002.992016.8
8843680022.640002.996016.8
8843780022.640002.9100016.8
8843880022.640002.9104016.8
8843980022.640002.9108016.8
8844080022.640002.9112016.8
8844180022.640002.9116016.8
8844280022.640002.9120016.8
8844380022.640002.9124016.8
8864955018.227501.399915.7
8846875021.237503.188815.1
8846975021.237503.192515.1
8847075021.237503.196215.1
8847175021.237503.199915.1
8847275021.237503.1103615.1
8847375021.237503.1107315.1
8847475021.237503.1111015.1
8847575021.237503.1114715.1
8847675021.237503.1118415.1
8847775021.237503.1122115.1
8847875021.237503.1125815.1
8871050016.625001.6105013.4
8850770019.835003.394513.2
8850870019.835003.398013.2
8850970019.835003.3101513.2
8851070019.835003.3105013.2
8851170019.835003.3108513.2
8851270019.835003.3112013.2
8851370019.835003.3115513.2
8851470019.835003.3119013.2
8851570019.835003.3122513.2
8851670019.835003.3126013.2
8851770019.835003.3129513.2
8851870019.835003.3133013.2
8871150016.625001.8107513.0
8871250015.725001.8110012.1
8859760018.630003.3102012.0
8855065018.432503.599211.3
8855165018.432503.5102411.3
8855265018.432503.5105611.3
8855365018.432503.5108811.3
8855465018.432503.5112011.3
8855565018.432503.5115211.3
8855665018.432503.5118411.3
8855765018.432503.5121611.3
8855865018.432503.5124811.3
8855965018.432503.5128011.3
8856065018.432503.5131211.3
8856165018.432503.5134411.3
8856265018.432503.5137611.3
8859860016.930003.810509.3
8859960016.930003.810809.3
8860060016.930003.811109.3
8860160016.930003.811409.3
8860260016.930003.811709.3
8860360016.930003.812009.3
8860460016.930003.812309.3
8860560016.930003.812609.3
8860660016.930003.812909.3
8860760016.930003.813209.3
8860860016.930003.813509.3
8860960016.930003.813809.3
8861060016.930003.814109.3
8861160016.930003.814409.3
8865255015.527504.210807.2
8865355015.527504.211077.2
8865455015.527504.211347.2
8865555015.527504.211617.2
8865655015.527504.211887.2
8865755015.527504.212157.2
8865855015.527504.212427.2
8865955015.527504.212697.2
8866055015.527504.212967.2
8866155015.527504.213237.2
8866255015.527504.213507.2
8866355015.527504.213777.2
8866455015.527504.214047.2
8866555015.527504.214317.2
8866655015.527504.214587.2
8866755015.527504.214857.2
8871350014.525004.611255.3
8871450014.125004.611504.9
8871550014.125004.611754.9
8871650014.125004.612004.9
8871750014.125004.612254.9
8871850014.125004.612504.9
8871950014.125004.612754.9
8872050014.125004.613004.9
8872150014.125004.613254.9
8872250014.125004.613504.9
8872350014.125004.613754.9
8872450014.125004.614004.9
8872550014.125004.614254.9
8872650014.125004.614504.9
8872750014.125004.614754.9
8872850014.125004.615004.9
8872950014.125004.615254.9

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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