Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign47 - back to list

Summary

./analyse_probe_search_results : Wed Sep 21 13:54:29 2005

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

Fetched probe design: ProbeDesign47
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 8
  id            : 29
  strand        : 1
  -------------

Design window length: 4712bp

All jobs for probe design are successful - total: 81
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 1611 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        : 1611/1611
Putative probes exceeding selection criteria: 210/1611

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
30780115033.257503.1199527.0
30845110031.855002.5203526.7
30913105030.352502.7202825.0
30914105030.352502.7208025.0
30986100028.950002.8205023.3
30987100028.950002.8210023.3
30988100028.950002.8215023.3
30985100028.950003.1200022.7
30844110031.855004.6198022.5
3115190026.045002.2225021.6
3106395027.547502.9202121.6
3106495027.547502.9206821.6
3106595027.547502.9211521.6
3106695027.547502.9216221.6
3106795027.547502.9220921.6
30915105030.352504.5213221.4
3132880023.840001.4200021.1
30846110030.955005.0209020.9
3143175022.337501.1203520.2
3124085024.642502.4226819.9
3124185024.642502.4231019.9
3114690026.045003.1202519.8
3114790026.045003.1207019.8
3114890026.045003.1211519.8
3114990026.045003.1216019.8
3115090026.045003.1220519.8
3143075022.337501.7199818.9
3110095026.747504.0376018.7
3154270020.835001.1203018.5
3154370020.835001.1206518.5
3154470020.835001.1210018.5
3143275022.337502.0207218.3
3133580023.140002.5228018.1
3133680023.140002.5232018.1
3133780023.140002.5236018.1
3166265019.332501.2201616.9
3166365019.332501.2204816.9
3166465019.332501.2208016.9
3166565019.332501.2211216.9
3166665019.332501.2214416.9
3143775021.737502.7225716.3
3143875021.737502.7229416.3
3143975021.737502.7233116.3
3144075021.737502.7236816.3
3144175021.737502.7240516.3
3154170020.835002.3199516.3
3185160017.430001.0375015.4
3200355016.427500.5375315.3
3179360017.930001.3201015.2
3179460017.930001.3204015.2
3179560017.930001.3207015.2
3179660017.930001.3210015.2
3179760017.930001.3213015.2
3179860017.930001.3216015.2
3179960017.930001.3219015.2
3154970020.235002.9227514.5
3155070020.235002.9231014.5
3155170020.235002.9234514.5
3155270020.235002.9238014.5
3155370020.235002.9241514.5
3155470020.235002.9245014.5
3207250015.825000.8132514.2
3166765019.332502.9217613.5
3193955016.427501.5202513.5
3194055016.427501.5205213.5
3194155016.427501.5207913.5
3194255016.427501.5210613.5
3194355016.427501.5213313.5
3194455016.427501.5216013.5
3194555016.427501.5218713.5
3167065018.832503.1227212.6
3167165018.832503.1230412.6
3167265018.832503.1233612.6
3167365018.832503.1236812.6
3167465018.832503.1240012.6
3167565018.832503.1243212.6
3167665018.832503.1246412.6
3167765018.832503.1249612.6
3210750015.425001.6220012.2
3216950014.525001.2375012.1
3171665016.832502.5374411.9
3207350015.825002.0135011.8
3210050014.925001.6202511.7
3210150014.925001.6205011.7
3210250014.925001.6207511.7
3210350014.925001.6210011.7
3210450014.925001.6212511.7
3210550014.925001.6215011.7
3210650014.925001.6217511.7
3193855016.427502.4199811.6
3166165019.332504.2198411.0
3181160017.330003.3255010.7
3161365017.032503.244810.6
3161465017.032503.248010.6
3209950014.925002.2200010.5
3174260015.730003.54808.7
3174360015.730003.55108.7
3174460014.030003.55407.0
3188155014.427503.84596.8
3188255014.427503.84866.8
3188355014.427503.85136.8
3188455014.427503.85406.8
3188555014.427503.85676.8
3212550014.525004.026506.5
3196155015.927504.726196.4
30584130014.865004.24556.3
30585130014.865004.25206.3
3149770012.135003.04556.1
30889105011.952503.27805.5
3203850013.125004.24754.7
3203950013.125004.25004.7
3204050013.125004.25254.7
3204150013.125004.25504.7
3204250013.125004.25754.7
3204350013.125004.26004.7
3204450013.125004.26254.7
30961100011.450003.48004.6
30960100011.450003.67504.2
3188655011.827503.85944.1
3103695010.847503.67523.6
3103795010.847503.67993.6
3103895010.847503.68463.6
3161565010.032503.25123.6
30757115013.157504.86843.5
3103995010.847503.98933.0
3111890010.245003.87652.7
3111990010.245003.88102.7
3112090010.245003.88552.7
3112190010.245003.89002.7
30962100011.450004.48502.6
3112290010.245004.39451.6

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
3123485024.942503.3201618.3
3123585024.642503.3205818.0
3123685024.642503.3210018.0
3123785024.642503.3214218.0
3123885024.642503.3218418.0
3123985024.642503.3222618.0
3118590025.345004.2378016.8
3132980023.840003.5204016.8
3133080023.140003.5208016.1
3133180023.140003.5212016.1
3133280023.140003.5216016.1
3133380023.140003.5220016.1
3133480023.140003.5224016.1
3127685023.942504.5378014.9
3127785023.942504.5382214.9
3143375021.937503.7210914.5
3143475021.737503.7214614.2
3143575021.737503.7218314.2
3143675021.737503.7222014.2
3137280022.540004.8376013.0
3137380022.540004.8380013.0
3137480022.540004.8384013.0
3137580022.540004.8388013.0
3154570020.835004.0213512.8
3154670020.235004.0217012.2
3154770020.235004.0220512.2
3154870020.235004.0224012.2
3180160017.930003.3225011.2
3180260017.330003.3228010.7
3180360017.330003.3231010.7
3180460017.330003.3234010.7
3180560017.330003.3237010.7
3180660017.330003.3240010.7
3180760017.330003.3243010.7
3180860017.330003.3246010.7
3180960017.330003.3249010.7
3181060017.330003.3252010.7
3166865019.032504.3220810.4
3194955017.627503.6229510.4
3166965018.832504.3224010.2
3174160015.730003.54508.7
3195055015.927503.623228.6
3195155015.927503.623498.6
3195255015.927503.623768.6
3195355015.927503.624038.6
3195455015.927503.624308.6
3195555015.927503.624578.6
3195655015.927503.624848.6
3195755015.927503.625118.6
3195855015.927503.625388.6
3195955015.927503.625658.6
3196055015.927503.625928.6
3211350014.925004.023506.9
3211450014.525004.023756.5
3211550014.525004.024006.5
3211650014.525004.024256.5
3211750014.525004.024506.5
3211850014.525004.024756.5
3211950014.525004.025006.5
3212050014.525004.025256.5
3212150014.525004.025506.5
3212250014.525004.025756.5
3212350014.525004.026006.5
3212450014.525004.026256.5
30638125014.262504.44965.4
30639125014.262504.45585.4
3203750013.125004.24504.7
30694120013.660004.64804.5
30695120013.660004.65404.5
30696120013.660004.66004.5
30753115013.157504.84563.5
30754115013.157504.85133.5
30755115013.157504.85703.5
30756115013.157504.86273.5
30817110012.555005.04952.5
30818110012.555005.05502.5
30819110012.555005.06052.5
30820110012.555005.06602.5
30821110012.555005.07152.5

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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